Multiple sequence alignment - TraesCS7A01G146700

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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 TraesCS7A01G146700 chr7A 100.000 5830 0 0 1 5830 98737084 98731255 0.000000e+00 10767.0
1 TraesCS7A01G146700 chr7A 83.165 1580 142 49 925 2472 98098143 98099630 0.000000e+00 1330.0
2 TraesCS7A01G146700 chr7A 83.103 1160 103 48 1462 2580 98545926 98547033 0.000000e+00 970.0
3 TraesCS7A01G146700 chr7A 84.499 858 90 28 3235 4067 98547661 98548500 0.000000e+00 808.0
4 TraesCS7A01G146700 chr7A 82.041 980 76 51 223 1184 98544613 98545510 0.000000e+00 743.0
5 TraesCS7A01G146700 chr7A 83.556 675 91 11 4104 4764 98548498 98549166 1.070000e-171 614.0
6 TraesCS7A01G146700 chr7A 83.968 499 52 19 3273 3748 98101606 98102099 2.480000e-123 453.0
7 TraesCS7A01G146700 chr7A 79.116 747 74 46 81 809 98097414 98098096 1.930000e-119 440.0
8 TraesCS7A01G146700 chr7A 96.791 187 5 1 5049 5235 702614057 702613872 1.580000e-80 311.0
9 TraesCS7A01G146700 chr7A 95.676 185 7 1 5050 5234 239034225 239034042 4.420000e-76 296.0
10 TraesCS7A01G146700 chr7A 95.161 186 8 1 5050 5234 119302404 119302589 5.710000e-75 292.0
11 TraesCS7A01G146700 chr7A 80.282 142 26 2 1572 1712 691468237 691468097 7.990000e-19 106.0
12 TraesCS7A01G146700 chr7B 87.965 2634 146 78 12 2588 49190222 49187703 0.000000e+00 2950.0
13 TraesCS7A01G146700 chr7B 91.621 1838 109 12 3220 5050 49186982 49185183 0.000000e+00 2499.0
14 TraesCS7A01G146700 chr7B 82.822 1304 125 48 1322 2582 49026866 49028113 0.000000e+00 1075.0
15 TraesCS7A01G146700 chr7B 94.852 641 29 2 2582 3219 49187680 49187041 0.000000e+00 998.0
16 TraesCS7A01G146700 chr7B 92.487 599 34 6 5233 5830 49185192 49184604 0.000000e+00 846.0
17 TraesCS7A01G146700 chr7B 90.940 596 54 0 3472 4067 49033787 49034382 0.000000e+00 802.0
18 TraesCS7A01G146700 chr7B 92.777 443 31 1 2673 3115 153181760 153182201 1.770000e-179 640.0
19 TraesCS7A01G146700 chr7B 90.359 446 43 0 2676 3121 42360435 42359990 2.340000e-163 586.0
20 TraesCS7A01G146700 chr7B 82.723 683 92 14 4104 4764 49034380 49035058 8.420000e-163 584.0
21 TraesCS7A01G146700 chr7B 84.683 457 36 20 732 1184 49026191 49026617 5.400000e-115 425.0
22 TraesCS7A01G146700 chr7B 81.701 541 54 27 81 607 49025602 49026111 5.440000e-110 409.0
23 TraesCS7A01G146700 chr7B 82.533 229 40 0 5596 5824 50680143 50680371 9.910000e-48 202.0
24 TraesCS7A01G146700 chr7B 98.214 56 1 0 2825 2880 49028247 49028302 1.340000e-16 99.0
25 TraesCS7A01G146700 chr7D 91.499 1835 102 12 3220 5050 95062428 95060644 0.000000e+00 2475.0
26 TraesCS7A01G146700 chr7D 90.944 1314 59 27 1305 2588 95064680 95063397 0.000000e+00 1712.0
27 TraesCS7A01G146700 chr7D 80.587 1669 172 79 964 2580 94936529 94938097 0.000000e+00 1147.0
28 TraesCS7A01G146700 chr7D 93.656 599 29 5 5233 5830 95060653 95060063 0.000000e+00 887.0
29 TraesCS7A01G146700 chr7D 85.619 904 55 29 1 854 95066032 95065154 0.000000e+00 880.0
30 TraesCS7A01G146700 chr7D 81.699 836 93 17 3223 4034 94938713 94939512 4.930000e-180 641.0
31 TraesCS7A01G146700 chr7D 84.604 669 78 17 4101 4764 94939510 94940158 4.930000e-180 641.0
32 TraesCS7A01G146700 chr7D 92.821 390 20 3 2837 3219 95062875 95062487 5.100000e-155 558.0
33 TraesCS7A01G146700 chr7D 88.836 421 47 0 3614 4034 94796895 94797315 8.660000e-143 518.0
34 TraesCS7A01G146700 chr7D 88.848 269 23 5 994 1255 95065080 95064812 2.030000e-84 324.0
35 TraesCS7A01G146700 chr7D 95.187 187 9 0 2666 2852 95063323 95063137 4.420000e-76 296.0
36 TraesCS7A01G146700 chr7D 81.728 301 23 24 81 371 94935855 94936133 7.600000e-54 222.0
37 TraesCS7A01G146700 chr7D 92.806 139 9 1 3431 3569 94796752 94796889 3.560000e-47 200.0
38 TraesCS7A01G146700 chr7D 92.593 108 8 0 2364 2471 94793243 94793350 7.820000e-34 156.0
39 TraesCS7A01G146700 chr7D 84.956 113 17 0 1596 1708 606302100 606302212 1.330000e-21 115.0
40 TraesCS7A01G146700 chr7D 95.522 67 2 1 2582 2648 95063373 95063308 7.990000e-19 106.0
41 TraesCS7A01G146700 chr4A 91.541 662 29 9 1940 2588 650174612 650173965 0.000000e+00 887.0
42 TraesCS7A01G146700 chr4A 91.537 449 38 0 2673 3121 670379069 670378621 2.310000e-173 619.0
43 TraesCS7A01G146700 chr4A 82.090 335 41 10 5499 5826 621741161 621740839 9.630000e-68 268.0
44 TraesCS7A01G146700 chr4A 96.377 138 4 1 2583 2719 650173943 650173806 5.880000e-55 226.0
45 TraesCS7A01G146700 chr4A 91.304 138 12 0 2978 3115 26836430 26836567 7.710000e-44 189.0
46 TraesCS7A01G146700 chr6B 92.325 443 34 0 2673 3115 672451864 672452306 1.070000e-176 630.0
47 TraesCS7A01G146700 chr6B 90.265 113 10 1 1056 1168 667074941 667074830 4.710000e-31 147.0
48 TraesCS7A01G146700 chr6A 89.394 462 36 4 2673 3121 437701810 437701349 2.360000e-158 569.0
49 TraesCS7A01G146700 chr6A 89.091 110 11 1 1056 1165 590079124 590079016 1.020000e-27 135.0
50 TraesCS7A01G146700 chr3A 96.237 186 5 1 5050 5233 713869072 713869257 2.640000e-78 303.0
51 TraesCS7A01G146700 chr3A 95.213 188 8 1 5048 5235 714166209 714166023 4.420000e-76 296.0
52 TraesCS7A01G146700 chr3A 100.000 31 0 0 3572 3602 714093567 714093597 2.270000e-04 58.4
53 TraesCS7A01G146700 chr1A 96.175 183 6 1 5050 5232 585625023 585625204 1.230000e-76 298.0
54 TraesCS7A01G146700 chr1A 94.118 187 9 2 5050 5235 61717408 61717223 3.440000e-72 283.0
55 TraesCS7A01G146700 chr1A 83.544 158 16 5 1496 1643 527184808 527184965 7.880000e-29 139.0
56 TraesCS7A01G146700 chr2A 91.848 184 9 2 5049 5232 753599267 753599444 9.700000e-63 252.0
57 TraesCS7A01G146700 chr3D 88.119 202 20 2 5040 5241 429728332 429728135 2.720000e-58 237.0
58 TraesCS7A01G146700 chr5B 90.278 144 14 0 2978 3121 668067228 668067085 7.710000e-44 189.0
59 TraesCS7A01G146700 chr2B 88.652 141 16 0 2981 3121 123454861 123454721 7.770000e-39 172.0
60 TraesCS7A01G146700 chr1D 84.000 175 17 8 1496 1659 429718781 429718955 2.170000e-34 158.0
61 TraesCS7A01G146700 chr1B 92.754 69 5 0 2673 2741 186142715 186142783 3.720000e-17 100.0


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 TraesCS7A01G146700 chr7A 98731255 98737084 5829 True 10767.000000 10767 100.000000 1 5830 1 chr7A.!!$R1 5829
1 TraesCS7A01G146700 chr7A 98544613 98549166 4553 False 783.750000 970 83.299750 223 4764 4 chr7A.!!$F3 4541
2 TraesCS7A01G146700 chr7A 98097414 98102099 4685 False 741.000000 1330 82.083000 81 3748 3 chr7A.!!$F2 3667
3 TraesCS7A01G146700 chr7B 49184604 49190222 5618 True 1823.250000 2950 91.731250 12 5830 4 chr7B.!!$R2 5818
4 TraesCS7A01G146700 chr7B 49033787 49035058 1271 False 693.000000 802 86.831500 3472 4764 2 chr7B.!!$F4 1292
5 TraesCS7A01G146700 chr7B 49025602 49028302 2700 False 502.000000 1075 86.855000 81 2880 4 chr7B.!!$F3 2799
6 TraesCS7A01G146700 chr7D 95060063 95066032 5969 True 904.750000 2475 91.762000 1 5830 8 chr7D.!!$R1 5829
7 TraesCS7A01G146700 chr7D 94935855 94940158 4303 False 662.750000 1147 82.154500 81 4764 4 chr7D.!!$F3 4683
8 TraesCS7A01G146700 chr7D 94793243 94797315 4072 False 291.333333 518 91.411667 2364 4034 3 chr7D.!!$F2 1670
9 TraesCS7A01G146700 chr4A 650173806 650174612 806 True 556.500000 887 93.959000 1940 2719 2 chr4A.!!$R3 779

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
771 848 0.105964 GGTTCTTGGTTGTTTGGGGC 59.894 55.0 0.00 0.0 0.00 5.80 F
1128 1242 0.390472 CCGTCTGCCTCAAGGTTCTC 60.390 60.0 0.00 0.0 37.57 2.87 F
1858 2346 0.248289 TGAACGGGGAGACGAAATCC 59.752 55.0 0.00 0.0 37.61 3.01 F
2438 2946 0.318441 GCGAGCCATCTGCAGGTATA 59.682 55.0 15.13 0.0 44.83 1.47 F
4175 8447 0.373716 GTTGCACATCCCGTTCGATC 59.626 55.0 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2340 0.035439 TCCCCTTGAGCACGGATTTC 60.035 55.000 0.00 0.0 0.00 2.17 R
2328 2833 0.514691 GCAGCAAGAGAAAGGACACG 59.485 55.000 0.00 0.0 0.00 4.49 R
2659 3423 1.068748 GTTCTGCTCTGCAACACCATG 60.069 52.381 0.00 0.0 38.41 3.66 R
4179 8451 0.248296 GTCAAGTTTTGTCGCGCCAA 60.248 50.000 0.00 0.0 0.00 4.52 R
5556 9870 0.175989 GCGGAGATTCTTCGTTCCCT 59.824 55.000 15.54 0.0 34.53 4.20 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
52 55 5.570205 TTATTTCAGTTCACCCCACAGTA 57.430 39.130 0.00 0.00 0.00 2.74
150 156 2.428925 CCCCAACTGCCATGCCATC 61.429 63.158 0.00 0.00 0.00 3.51
159 165 1.526917 CCATGCCATCGGAGGGTTC 60.527 63.158 10.76 0.00 0.00 3.62
300 326 2.356793 CCATCGCCATCTCGCTCC 60.357 66.667 0.00 0.00 0.00 4.70
338 365 1.533033 CCTCCCCAAACAACACCCC 60.533 63.158 0.00 0.00 0.00 4.95
339 366 1.541672 CTCCCCAAACAACACCCCT 59.458 57.895 0.00 0.00 0.00 4.79
356 386 4.329545 TCCCACCTCACCAAGCGC 62.330 66.667 0.00 0.00 0.00 5.92
410 440 1.992277 GCTGCTTCCTCCTCCTCCA 60.992 63.158 0.00 0.00 0.00 3.86
419 449 0.689412 CTCCTCCTCCACCTCTTCCC 60.689 65.000 0.00 0.00 0.00 3.97
443 476 1.723220 GTCGTCTTCTACCTTTGCCC 58.277 55.000 0.00 0.00 0.00 5.36
481 524 3.619767 TGTGGCTGAGCTGAGCGT 61.620 61.111 19.24 0.00 40.13 5.07
533 578 4.436998 CCCGGAGTGTCGCTGTCC 62.437 72.222 0.73 0.00 0.00 4.02
547 596 2.436824 GTCCGCCTCTGCCTTTCC 60.437 66.667 0.00 0.00 0.00 3.13
551 600 1.308783 CCGCCTCTGCCTTTCCTTTC 61.309 60.000 0.00 0.00 0.00 2.62
554 603 0.405585 CCTCTGCCTTTCCTTTCCCA 59.594 55.000 0.00 0.00 0.00 4.37
629 681 2.222027 CTTCCCGGCCTCAATAATGAC 58.778 52.381 0.00 0.00 0.00 3.06
758 835 2.568509 TCCCGGAGTAATTTCGGTTCTT 59.431 45.455 0.73 0.00 41.98 2.52
769 846 1.394618 TCGGTTCTTGGTTGTTTGGG 58.605 50.000 0.00 0.00 0.00 4.12
770 847 0.387565 CGGTTCTTGGTTGTTTGGGG 59.612 55.000 0.00 0.00 0.00 4.96
771 848 0.105964 GGTTCTTGGTTGTTTGGGGC 59.894 55.000 0.00 0.00 0.00 5.80
818 899 1.145377 AGGTGGTGTTGGTGTCGAC 59.855 57.895 9.11 9.11 0.00 4.20
825 906 4.351938 TTGGTGTCGACCGCTCGG 62.352 66.667 14.12 6.79 46.62 4.63
990 1080 1.536766 TCAAGTTGCTCTGAATTGGCG 59.463 47.619 0.00 0.00 0.00 5.69
1039 1129 3.287954 ATGGAGGCCAGGAAGGGGA 62.288 63.158 5.01 0.00 36.75 4.81
1053 1155 0.649992 AGGGGATGATGGAGAGGGAA 59.350 55.000 0.00 0.00 0.00 3.97
1128 1242 0.390472 CCGTCTGCCTCAAGGTTCTC 60.390 60.000 0.00 0.00 37.57 2.87
1155 1269 2.582498 CTACGCCGCTGCCAGTAC 60.582 66.667 0.00 0.00 0.00 2.73
1209 1340 8.682936 ATAAGAAACTTCATTCTGTTGTCACT 57.317 30.769 0.00 0.00 39.54 3.41
1210 1341 7.396540 AAGAAACTTCATTCTGTTGTCACTT 57.603 32.000 0.00 0.00 39.54 3.16
1211 1342 6.789262 AGAAACTTCATTCTGTTGTCACTTG 58.211 36.000 0.00 0.00 38.22 3.16
1212 1343 6.375455 AGAAACTTCATTCTGTTGTCACTTGT 59.625 34.615 0.00 0.00 38.22 3.16
1220 1351 6.603237 TTCTGTTGTCACTTGTTAGTCATG 57.397 37.500 0.00 0.00 30.26 3.07
1267 1532 7.010923 GTGGTTTCACTTATCAGTCATCTGATC 59.989 40.741 12.96 0.00 46.03 2.92
1277 1551 2.170187 AGTCATCTGATCCTGTTCCAGC 59.830 50.000 0.00 0.00 0.00 4.85
1320 1650 6.590292 TGCACTGTACTAATTACTCTTGCTTC 59.410 38.462 0.00 0.00 34.25 3.86
1361 1691 5.220710 AGAGTTTTCACATGCAGAGTAGT 57.779 39.130 0.00 0.00 0.00 2.73
1362 1692 6.346477 AGAGTTTTCACATGCAGAGTAGTA 57.654 37.500 0.00 0.00 0.00 1.82
1429 1775 5.964887 TTTTAACACTCTTGCAATGCAAC 57.035 34.783 17.55 0.00 43.99 4.17
1441 1797 4.605968 TGCAATGCAACGCGATATATTTT 58.394 34.783 15.93 0.00 34.76 1.82
1442 1798 5.039984 TGCAATGCAACGCGATATATTTTT 58.960 33.333 15.93 0.00 34.76 1.94
1539 2003 0.959372 CCCCTGCTTGCTGTCTCTTG 60.959 60.000 0.00 0.00 0.00 3.02
1781 2259 2.540361 GCTGCTTTCAGTCACTGTGTTG 60.540 50.000 4.28 8.02 42.29 3.33
1846 2334 2.094597 TGTAGTGTTATCGGTGAACGGG 60.095 50.000 0.00 0.00 44.45 5.28
1852 2340 1.378882 TATCGGTGAACGGGGAGACG 61.379 60.000 0.00 0.00 44.45 4.18
1858 2346 0.248289 TGAACGGGGAGACGAAATCC 59.752 55.000 0.00 0.00 37.61 3.01
1900 2388 1.592669 CGCCTGCGATTACCTCCTG 60.593 63.158 5.43 0.00 42.83 3.86
1969 2457 1.578206 GGAGGAAGTTCAGCAACCGC 61.578 60.000 5.01 0.00 38.99 5.68
1980 2468 3.777925 CAACCGCGAGCCGAACAG 61.778 66.667 8.23 0.00 40.02 3.16
2314 2819 1.271543 TGTTCTTGCAGGCTACAGCAT 60.272 47.619 3.24 0.00 44.36 3.79
2438 2946 0.318441 GCGAGCCATCTGCAGGTATA 59.682 55.000 15.13 0.00 44.83 1.47
2493 3028 4.315803 ACCTGTGTTATCTCTTTCGTTGG 58.684 43.478 0.00 0.00 0.00 3.77
2659 3423 6.204301 TGCAGAGCAGAGCTTAATTTGATATC 59.796 38.462 0.00 0.00 39.88 1.63
2749 4206 7.079475 TGAGTTAAGTAGTTTAATTTTGCGGC 58.921 34.615 0.00 0.00 33.99 6.53
2777 4234 5.774498 AGTTTCACCTTCACATTTCTTCC 57.226 39.130 0.00 0.00 0.00 3.46
2806 4263 8.450578 TTCTTGACAAGTTGAATATGTTCAGT 57.549 30.769 14.75 0.16 44.62 3.41
2911 4673 5.940617 TGATTATTCTCCCAACCATGTAGG 58.059 41.667 0.00 0.00 45.67 3.18
2923 4690 6.213600 CCCAACCATGTAGGCTAGTAGATTAT 59.786 42.308 0.00 0.00 43.14 1.28
3019 4786 9.028284 AGGTAATACTGCTGTACAAGTTTACTA 57.972 33.333 19.00 3.09 0.00 1.82
3020 4787 9.080915 GGTAATACTGCTGTACAAGTTTACTAC 57.919 37.037 19.00 11.59 0.00 2.73
3031 4798 8.776470 TGTACAAGTTTACTACAGTATTTTGGC 58.224 33.333 0.00 0.00 0.00 4.52
3115 4882 4.083484 GGTGTTTTGGTATGTACTGCTGAC 60.083 45.833 0.00 0.00 0.00 3.51
3120 4887 7.663905 TGTTTTGGTATGTACTGCTGACTTTAT 59.336 33.333 0.00 0.00 0.00 1.40
3200 5735 1.909302 ACCACCCTGTCCAGATTACAG 59.091 52.381 0.00 0.00 43.26 2.74
3201 5736 1.407437 CCACCCTGTCCAGATTACAGC 60.407 57.143 0.00 0.00 42.47 4.40
3219 5783 5.006153 ACAGCGCTACATATGTAAACTGA 57.994 39.130 28.68 9.15 33.07 3.41
3220 5784 5.416083 ACAGCGCTACATATGTAAACTGAA 58.584 37.500 28.68 8.58 33.07 3.02
3221 5785 5.872617 ACAGCGCTACATATGTAAACTGAAA 59.127 36.000 28.68 8.00 33.07 2.69
3263 5886 6.304126 CAAAAGCTTTGCATGTCAATGAATC 58.696 36.000 13.54 3.58 35.67 2.52
3264 5887 4.119442 AGCTTTGCATGTCAATGAATCC 57.881 40.909 15.15 3.34 35.67 3.01
3320 5943 9.875691 ATTAAAAGGTTAAGAAAATCCATCAGC 57.124 29.630 0.00 0.00 32.76 4.26
3321 5944 5.921962 AAGGTTAAGAAAATCCATCAGCC 57.078 39.130 0.00 0.00 0.00 4.85
3738 8010 1.605457 CCAGTGTTCTAGCAGCAACGA 60.605 52.381 0.00 0.00 0.00 3.85
3929 8201 0.391793 GGGTGCTCTGGCTAACACTC 60.392 60.000 0.00 0.00 39.59 3.51
3965 8237 5.376625 TCCAAAGAGTTACAAGCAGTTCAT 58.623 37.500 0.00 0.00 0.00 2.57
3988 8260 3.157087 GCCACCAGAAGATCTTTTGGAA 58.843 45.455 38.35 0.00 44.86 3.53
3995 8267 5.649395 CCAGAAGATCTTTTGGAATGCACTA 59.351 40.000 31.94 0.00 44.86 2.74
4110 8382 4.169508 CGGGATTCTTGTATATCTCAGCG 58.830 47.826 0.00 0.00 0.00 5.18
4175 8447 0.373716 GTTGCACATCCCGTTCGATC 59.626 55.000 0.00 0.00 0.00 3.69
4177 8449 1.226859 GCACATCCCGTTCGATCGA 60.227 57.895 15.15 15.15 0.00 3.59
4179 8451 0.100682 CACATCCCGTTCGATCGAGT 59.899 55.000 18.54 7.99 0.00 4.18
4198 8470 0.248296 TTGGCGCGACAAAACTTGAC 60.248 50.000 28.17 0.00 0.00 3.18
4222 8494 1.202976 AGCTTTGTGGCTGGAGAACAT 60.203 47.619 0.00 0.00 41.43 2.71
4260 8532 4.280929 GGGGATATTTTCGGAAAGAATGGG 59.719 45.833 3.09 0.00 38.86 4.00
4438 8716 3.524789 TGGATGGAATGAGACAAGACCAT 59.475 43.478 0.00 0.00 40.21 3.55
4452 8730 6.014242 AGACAAGACCATAGACTGAACAATGA 60.014 38.462 0.00 0.00 0.00 2.57
4453 8731 6.715280 ACAAGACCATAGACTGAACAATGAT 58.285 36.000 0.00 0.00 0.00 2.45
4576 8866 6.294397 GCAACTTTGATGGTCTTCTCAATTCT 60.294 38.462 0.00 0.00 31.83 2.40
4610 8900 5.122396 GTGGTAAGAACCTCAGTTATGCTTG 59.878 44.000 0.00 0.00 46.91 4.01
4612 8902 5.351740 GGTAAGAACCTCAGTTATGCTTGAC 59.648 44.000 0.00 0.00 43.08 3.18
4613 8903 4.899352 AGAACCTCAGTTATGCTTGACT 57.101 40.909 0.00 0.00 35.94 3.41
4616 8906 6.769512 AGAACCTCAGTTATGCTTGACTTTA 58.230 36.000 0.00 0.00 35.94 1.85
4617 8907 6.651225 AGAACCTCAGTTATGCTTGACTTTAC 59.349 38.462 0.00 0.00 35.94 2.01
4618 8908 6.115448 ACCTCAGTTATGCTTGACTTTACT 57.885 37.500 0.00 0.00 0.00 2.24
4622 8919 7.064016 CCTCAGTTATGCTTGACTTTACTCTTC 59.936 40.741 0.00 0.00 0.00 2.87
4623 8920 6.874134 TCAGTTATGCTTGACTTTACTCTTCC 59.126 38.462 0.00 0.00 0.00 3.46
4626 8923 2.039879 TGCTTGACTTTACTCTTCCCCC 59.960 50.000 0.00 0.00 0.00 5.40
4652 8949 8.345565 CCTCAAAATTTCACTATTTCGGATAGG 58.654 37.037 10.23 0.00 0.00 2.57
4682 8980 4.278170 TCCTTTCAAATCGTTTGCACTGAT 59.722 37.500 0.00 0.00 40.43 2.90
4684 8982 3.454042 TCAAATCGTTTGCACTGATCG 57.546 42.857 0.00 0.00 40.43 3.69
4689 8991 0.792640 CGTTTGCACTGATCGAAGCT 59.207 50.000 0.00 0.00 0.00 3.74
4690 8992 1.992667 CGTTTGCACTGATCGAAGCTA 59.007 47.619 0.00 0.00 0.00 3.32
4696 8998 4.816392 TGCACTGATCGAAGCTAAGTAAA 58.184 39.130 0.00 0.00 0.00 2.01
4697 8999 4.625742 TGCACTGATCGAAGCTAAGTAAAC 59.374 41.667 0.00 0.00 0.00 2.01
4712 9021 7.790314 AGCTAAGTAAACCCTATGTTCCTAGAT 59.210 37.037 0.00 0.00 35.67 1.98
4724 9033 7.557719 CCTATGTTCCTAGATTTTCAATGGTGT 59.442 37.037 0.00 0.00 0.00 4.16
4727 9036 7.657336 TGTTCCTAGATTTTCAATGGTGTTTC 58.343 34.615 0.00 0.00 0.00 2.78
4738 9047 3.884037 ATGGTGTTTCTTCTGAACCCT 57.116 42.857 0.00 0.00 31.02 4.34
4820 9129 0.744281 AACTTTTCCCACTTGGTGCG 59.256 50.000 0.00 0.00 34.77 5.34
4833 9142 0.823460 TGGTGCGTGCATATGAGAGA 59.177 50.000 6.97 0.00 0.00 3.10
4839 9151 4.854291 GTGCGTGCATATGAGAGATAGTAC 59.146 45.833 6.97 0.00 0.00 2.73
4842 9154 6.092807 TGCGTGCATATGAGAGATAGTACTAG 59.907 42.308 6.97 0.00 0.00 2.57
4861 9173 5.978814 ACTAGTATTTAGGCAAGTCCACTG 58.021 41.667 0.00 0.00 37.29 3.66
4877 9189 1.748493 CACTGCAGACCTAGAGGAGAC 59.252 57.143 23.35 0.00 38.94 3.36
4936 9248 8.741603 TGCTTGTGTACACTACTAGATATACA 57.258 34.615 25.60 8.62 0.00 2.29
4937 9249 9.181061 TGCTTGTGTACACTACTAGATATACAA 57.819 33.333 25.60 6.99 0.00 2.41
4948 9260 8.048514 ACTACTAGATATACAAGGTAGCTAGCC 58.951 40.741 19.06 11.24 40.20 3.93
4960 9272 3.583086 GGTAGCTAGCCAGGGATTTCATA 59.417 47.826 12.13 0.00 0.00 2.15
4990 9302 6.688073 AGGAATCTGTACTTTCTTTCTCCA 57.312 37.500 0.00 0.00 0.00 3.86
4992 9304 6.498651 AGGAATCTGTACTTTCTTTCTCCAGA 59.501 38.462 0.00 0.00 32.60 3.86
5050 9362 4.157472 TCACATGCTCTGAAAACACAAACA 59.843 37.500 0.00 0.00 0.00 2.83
5051 9363 4.501559 CACATGCTCTGAAAACACAAACAG 59.498 41.667 0.00 0.00 0.00 3.16
5053 9365 4.782019 TGCTCTGAAAACACAAACAGTT 57.218 36.364 0.00 0.00 0.00 3.16
5054 9366 5.132897 TGCTCTGAAAACACAAACAGTTT 57.867 34.783 0.00 0.00 40.66 2.66
5071 9383 9.817365 CAAACAGTTTGTCTAATTCACATCTAG 57.183 33.333 16.77 0.00 35.94 2.43
5072 9384 9.778741 AAACAGTTTGTCTAATTCACATCTAGA 57.221 29.630 0.00 0.00 0.00 2.43
5073 9385 9.950496 AACAGTTTGTCTAATTCACATCTAGAT 57.050 29.630 0.00 0.00 0.00 1.98
5074 9386 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
5107 9419 8.547967 GTGATGTCACATCTAACCTTCTAAAA 57.452 34.615 18.72 0.00 45.75 1.52
5108 9420 8.999431 GTGATGTCACATCTAACCTTCTAAAAA 58.001 33.333 18.72 0.00 45.75 1.94
5109 9421 9.739276 TGATGTCACATCTAACCTTCTAAAAAT 57.261 29.630 18.72 0.00 0.00 1.82
5121 9433 8.685838 AACCTTCTAAAAATAACTACACAGCA 57.314 30.769 0.00 0.00 0.00 4.41
5122 9434 8.685838 ACCTTCTAAAAATAACTACACAGCAA 57.314 30.769 0.00 0.00 0.00 3.91
5123 9435 8.565416 ACCTTCTAAAAATAACTACACAGCAAC 58.435 33.333 0.00 0.00 0.00 4.17
5124 9436 8.564574 CCTTCTAAAAATAACTACACAGCAACA 58.435 33.333 0.00 0.00 0.00 3.33
5125 9437 9.944663 CTTCTAAAAATAACTACACAGCAACAA 57.055 29.630 0.00 0.00 0.00 2.83
5126 9438 9.944663 TTCTAAAAATAACTACACAGCAACAAG 57.055 29.630 0.00 0.00 0.00 3.16
5127 9439 9.332502 TCTAAAAATAACTACACAGCAACAAGA 57.667 29.630 0.00 0.00 0.00 3.02
5128 9440 9.944663 CTAAAAATAACTACACAGCAACAAGAA 57.055 29.630 0.00 0.00 0.00 2.52
5130 9442 9.816354 AAAAATAACTACACAGCAACAAGAAAT 57.184 25.926 0.00 0.00 0.00 2.17
5175 9487 7.524717 AAAAATAGACCACAAACATAGTGCT 57.475 32.000 0.00 0.00 35.69 4.40
5176 9488 7.524717 AAAATAGACCACAAACATAGTGCTT 57.475 32.000 0.00 0.00 35.69 3.91
5177 9489 8.630054 AAAATAGACCACAAACATAGTGCTTA 57.370 30.769 0.00 0.00 35.69 3.09
5178 9490 8.807948 AAATAGACCACAAACATAGTGCTTAT 57.192 30.769 0.00 0.00 35.69 1.73
5179 9491 8.438676 AATAGACCACAAACATAGTGCTTATC 57.561 34.615 0.00 0.00 35.69 1.75
5180 9492 5.804639 AGACCACAAACATAGTGCTTATCA 58.195 37.500 0.00 0.00 35.69 2.15
5181 9493 5.877012 AGACCACAAACATAGTGCTTATCAG 59.123 40.000 0.00 0.00 35.69 2.90
5182 9494 4.943705 ACCACAAACATAGTGCTTATCAGG 59.056 41.667 0.00 0.00 35.69 3.86
5183 9495 4.943705 CCACAAACATAGTGCTTATCAGGT 59.056 41.667 0.00 0.00 35.69 4.00
5184 9496 5.415701 CCACAAACATAGTGCTTATCAGGTT 59.584 40.000 0.00 0.00 35.69 3.50
5185 9497 6.597672 CCACAAACATAGTGCTTATCAGGTTA 59.402 38.462 0.00 0.00 35.69 2.85
5186 9498 7.201644 CCACAAACATAGTGCTTATCAGGTTAG 60.202 40.741 0.00 0.00 35.69 2.34
5187 9499 7.549134 CACAAACATAGTGCTTATCAGGTTAGA 59.451 37.037 0.00 0.00 0.00 2.10
5188 9500 8.267894 ACAAACATAGTGCTTATCAGGTTAGAT 58.732 33.333 0.00 0.00 0.00 1.98
5189 9501 8.554528 CAAACATAGTGCTTATCAGGTTAGATG 58.445 37.037 0.00 0.00 0.00 2.90
5190 9502 7.366847 ACATAGTGCTTATCAGGTTAGATGT 57.633 36.000 0.00 0.00 0.00 3.06
5191 9503 7.212976 ACATAGTGCTTATCAGGTTAGATGTG 58.787 38.462 0.00 0.00 0.00 3.21
5192 9504 5.939764 AGTGCTTATCAGGTTAGATGTGA 57.060 39.130 0.00 0.00 0.00 3.58
5193 9505 5.665459 AGTGCTTATCAGGTTAGATGTGAC 58.335 41.667 0.00 0.00 0.00 3.67
5194 9506 5.187772 AGTGCTTATCAGGTTAGATGTGACA 59.812 40.000 0.00 0.00 0.00 3.58
5195 9507 6.051717 GTGCTTATCAGGTTAGATGTGACAT 58.948 40.000 0.00 0.00 0.00 3.06
5196 9508 7.069950 AGTGCTTATCAGGTTAGATGTGACATA 59.930 37.037 0.00 0.00 0.00 2.29
5197 9509 7.710907 GTGCTTATCAGGTTAGATGTGACATAA 59.289 37.037 0.00 0.00 0.00 1.90
5198 9510 7.710907 TGCTTATCAGGTTAGATGTGACATAAC 59.289 37.037 0.00 0.00 0.00 1.89
5199 9511 7.928706 GCTTATCAGGTTAGATGTGACATAACT 59.071 37.037 10.13 2.33 31.53 2.24
5228 9540 5.764487 CATCTAGATGTGTGCTAGACAGA 57.236 43.478 22.42 0.00 44.98 3.41
5229 9541 5.518812 CATCTAGATGTGTGCTAGACAGAC 58.481 45.833 22.42 0.55 44.98 3.51
5230 9542 3.948473 TCTAGATGTGTGCTAGACAGACC 59.052 47.826 10.44 0.00 41.82 3.85
5231 9543 1.827969 AGATGTGTGCTAGACAGACCC 59.172 52.381 10.44 4.81 41.82 4.46
5232 9544 1.550524 GATGTGTGCTAGACAGACCCA 59.449 52.381 10.44 1.09 41.82 4.51
5233 9545 1.419381 TGTGTGCTAGACAGACCCAA 58.581 50.000 10.44 0.00 41.82 4.12
5234 9546 1.765904 TGTGTGCTAGACAGACCCAAA 59.234 47.619 10.44 0.00 41.82 3.28
5235 9547 2.143925 GTGTGCTAGACAGACCCAAAC 58.856 52.381 0.00 0.00 36.56 2.93
5236 9548 1.765904 TGTGCTAGACAGACCCAAACA 59.234 47.619 0.00 0.00 0.00 2.83
5237 9549 2.143925 GTGCTAGACAGACCCAAACAC 58.856 52.381 0.00 0.00 0.00 3.32
5238 9550 1.765904 TGCTAGACAGACCCAAACACA 59.234 47.619 0.00 0.00 0.00 3.72
5239 9551 2.171659 TGCTAGACAGACCCAAACACAA 59.828 45.455 0.00 0.00 0.00 3.33
5240 9552 3.211045 GCTAGACAGACCCAAACACAAA 58.789 45.455 0.00 0.00 0.00 2.83
5241 9553 3.003378 GCTAGACAGACCCAAACACAAAC 59.997 47.826 0.00 0.00 0.00 2.93
5242 9554 3.366052 AGACAGACCCAAACACAAACT 57.634 42.857 0.00 0.00 0.00 2.66
5243 9555 3.279434 AGACAGACCCAAACACAAACTC 58.721 45.455 0.00 0.00 0.00 3.01
5244 9556 2.357952 GACAGACCCAAACACAAACTCC 59.642 50.000 0.00 0.00 0.00 3.85
5245 9557 1.333619 CAGACCCAAACACAAACTCCG 59.666 52.381 0.00 0.00 0.00 4.63
5246 9558 0.666374 GACCCAAACACAAACTCCGG 59.334 55.000 0.00 0.00 0.00 5.14
5247 9559 0.256464 ACCCAAACACAAACTCCGGA 59.744 50.000 2.93 2.93 0.00 5.14
5248 9560 1.341187 ACCCAAACACAAACTCCGGAA 60.341 47.619 5.23 0.00 0.00 4.30
5368 9681 5.745227 TCTGGAAATAAACCTGACCTGATC 58.255 41.667 0.00 0.00 32.09 2.92
5429 9742 3.926058 ACAAACTACGATAATGCCCCT 57.074 42.857 0.00 0.00 0.00 4.79
5442 9755 2.910360 CCCCTGGTCGCATGATCA 59.090 61.111 0.00 0.00 33.18 2.92
5482 9796 4.254492 GGGTTTTCAGTGACTAGGATGAC 58.746 47.826 0.00 0.00 0.00 3.06
5496 9810 1.202110 GGATGACAACTGCATTCGCTG 60.202 52.381 0.00 0.00 42.42 5.18
5526 9840 7.504926 AAAACCACCTACACCTATCTTGATA 57.495 36.000 0.00 0.00 0.00 2.15
5541 9855 8.944029 CCTATCTTGATATTTGATCATGTGACC 58.056 37.037 0.00 0.00 0.00 4.02
5549 9863 0.251916 GATCATGTGACCGGGGAACA 59.748 55.000 6.32 7.57 0.00 3.18
5550 9864 0.253044 ATCATGTGACCGGGGAACAG 59.747 55.000 6.32 2.00 0.00 3.16
5573 9887 3.263261 GAACAGGGAACGAAGAATCTCC 58.737 50.000 0.00 0.00 0.00 3.71
5594 9908 3.303132 CCGCGATCAGTTATTAACTTGGC 60.303 47.826 8.23 5.90 40.46 4.52
5605 9919 1.055849 TAACTTGGCTGCAGAGGTCA 58.944 50.000 20.43 6.65 0.00 4.02
5638 9952 1.663695 CGATTGTCGGCTTGGGTATT 58.336 50.000 0.00 0.00 36.00 1.89
5704 10018 3.154473 CCCTCCTCCGCGGAATGA 61.154 66.667 30.53 25.41 42.53 2.57
5779 10093 3.527186 CGCCTCGTCGCATCATAC 58.473 61.111 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.534475 AAAATGCAGAATGGTGATGTATGT 57.466 33.333 0.00 0.00 35.86 2.29
34 37 3.935818 TTTACTGTGGGGTGAACTGAA 57.064 42.857 0.00 0.00 0.00 3.02
43 46 8.894768 TTTTATTTTCACATTTTACTGTGGGG 57.105 30.769 4.54 0.00 45.29 4.96
150 156 3.322466 ACCTGCCAGAACCCTCCG 61.322 66.667 0.00 0.00 0.00 4.63
210 216 3.482783 GGAGTGCTCGCTGCGTTC 61.483 66.667 22.48 14.66 46.63 3.95
303 329 3.706373 GTGGAAGGGGCGAGCAGA 61.706 66.667 0.00 0.00 0.00 4.26
338 365 2.046892 CGCTTGGTGAGGTGGGAG 60.047 66.667 0.00 0.00 0.00 4.30
339 366 4.329545 GCGCTTGGTGAGGTGGGA 62.330 66.667 0.00 0.00 0.00 4.37
410 440 2.362632 CGACGAGGGGGAAGAGGT 60.363 66.667 0.00 0.00 0.00 3.85
419 449 1.461559 AAGGTAGAAGACGACGAGGG 58.538 55.000 0.00 0.00 0.00 4.30
443 476 4.724697 CAGCAAGCAACCGACGCG 62.725 66.667 3.53 3.53 0.00 6.01
533 578 1.308783 GGAAAGGAAAGGCAGAGGCG 61.309 60.000 0.00 0.00 42.47 5.52
547 596 3.947834 ACACAAAACAGAGAGTGGGAAAG 59.052 43.478 0.00 0.00 36.35 2.62
551 600 2.158755 AGGACACAAAACAGAGAGTGGG 60.159 50.000 0.00 0.00 36.35 4.61
554 603 2.945668 GCAAGGACACAAAACAGAGAGT 59.054 45.455 0.00 0.00 0.00 3.24
694 757 1.133025 GTGGATTTGGATTCTGGCACG 59.867 52.381 0.00 0.00 0.00 5.34
700 763 2.042162 ACTGCAGGTGGATTTGGATTCT 59.958 45.455 19.93 0.00 0.00 2.40
758 835 4.531426 AGCCGCCCCAAACAACCA 62.531 61.111 0.00 0.00 0.00 3.67
769 846 2.203084 GGGAAAGCTAGAGCCGCC 60.203 66.667 0.00 0.00 43.38 6.13
770 847 0.812014 GAAGGGAAAGCTAGAGCCGC 60.812 60.000 0.00 0.00 43.38 6.53
771 848 0.827368 AGAAGGGAAAGCTAGAGCCG 59.173 55.000 0.00 0.00 43.38 5.52
818 899 4.840005 GGAGCTTTCCCCGAGCGG 62.840 72.222 1.06 1.06 44.71 5.52
883 973 1.086634 CAGCAAGAACGAGGCCTAGC 61.087 60.000 13.48 5.41 0.00 3.42
990 1080 0.383231 CCAAGAGCATCCCAATTCGC 59.617 55.000 0.00 0.00 33.66 4.70
1039 1129 2.021639 TCTCCCTTTCCCTCTCCATCAT 60.022 50.000 0.00 0.00 0.00 2.45
1053 1155 0.547954 GGAACTGGTCCCTCTCCCTT 60.548 60.000 0.00 0.00 41.10 3.95
1113 1227 3.432517 CTCGAGAACCTTGAGGCAG 57.567 57.895 6.58 0.00 38.11 4.85
1128 1242 3.584052 CGGCGTAGGAGGACCTCG 61.584 72.222 15.46 5.69 46.43 4.63
1206 1337 3.187227 GCAGGTGACATGACTAACAAGTG 59.813 47.826 0.00 0.00 30.32 3.16
1207 1338 3.181455 TGCAGGTGACATGACTAACAAGT 60.181 43.478 0.00 0.00 32.95 3.16
1208 1339 3.402110 TGCAGGTGACATGACTAACAAG 58.598 45.455 0.00 0.00 0.00 3.16
1209 1340 3.402110 CTGCAGGTGACATGACTAACAA 58.598 45.455 5.57 0.00 0.00 2.83
1210 1341 2.871637 GCTGCAGGTGACATGACTAACA 60.872 50.000 17.12 0.00 0.00 2.41
1211 1342 1.734465 GCTGCAGGTGACATGACTAAC 59.266 52.381 17.12 0.00 0.00 2.34
1212 1343 1.625315 AGCTGCAGGTGACATGACTAA 59.375 47.619 19.45 0.00 0.00 2.24
1220 1351 2.393271 ATTGACTAGCTGCAGGTGAC 57.607 50.000 28.10 17.85 0.00 3.67
1267 1532 2.799085 GAGCAAACTCGCTGGAACAGG 61.799 57.143 0.00 0.00 45.03 4.00
1361 1691 7.936496 TCAGAACATGGCAGATTGTTTTATA 57.064 32.000 6.43 0.00 36.25 0.98
1362 1692 6.839124 TCAGAACATGGCAGATTGTTTTAT 57.161 33.333 6.43 0.00 36.25 1.40
1450 1806 9.371136 GGATGCATAATAACTATCATTCTCGAA 57.629 33.333 0.00 0.00 0.00 3.71
1451 1807 8.753133 AGGATGCATAATAACTATCATTCTCGA 58.247 33.333 0.00 0.00 0.00 4.04
1452 1808 8.939201 AGGATGCATAATAACTATCATTCTCG 57.061 34.615 0.00 0.00 0.00 4.04
1480 1941 6.744112 ACAGTTGTTGTTGAAACTTGAAAGA 58.256 32.000 0.00 0.00 36.31 2.52
1539 2003 3.018149 TGGTTGGTGGTTGTTACTGTTC 58.982 45.455 0.00 0.00 0.00 3.18
1733 2201 4.285292 GAGCATGACTCAACAACAAAGTG 58.715 43.478 0.00 0.00 45.49 3.16
1766 2234 6.295249 TCCATATTTCAACACAGTGACTGAA 58.705 36.000 20.97 12.42 35.18 3.02
1803 2290 6.228258 ACACGAATTGAATGGTAAGTACAGT 58.772 36.000 0.00 0.00 0.00 3.55
1804 2291 6.721571 ACACGAATTGAATGGTAAGTACAG 57.278 37.500 0.00 0.00 0.00 2.74
1805 2292 7.329962 CACTACACGAATTGAATGGTAAGTACA 59.670 37.037 0.00 0.00 0.00 2.90
1806 2293 7.330208 ACACTACACGAATTGAATGGTAAGTAC 59.670 37.037 0.00 0.00 0.00 2.73
1807 2294 7.380536 ACACTACACGAATTGAATGGTAAGTA 58.619 34.615 0.00 0.00 0.00 2.24
1808 2295 6.228258 ACACTACACGAATTGAATGGTAAGT 58.772 36.000 0.00 0.00 0.00 2.24
1809 2296 6.721571 ACACTACACGAATTGAATGGTAAG 57.278 37.500 0.00 0.00 0.00 2.34
1810 2297 8.780846 ATAACACTACACGAATTGAATGGTAA 57.219 30.769 0.00 0.00 0.00 2.85
1811 2298 7.221259 CGATAACACTACACGAATTGAATGGTA 59.779 37.037 0.00 0.00 0.00 3.25
1821 2308 4.229096 GTTCACCGATAACACTACACGAA 58.771 43.478 0.00 0.00 0.00 3.85
1852 2340 0.035439 TCCCCTTGAGCACGGATTTC 60.035 55.000 0.00 0.00 0.00 2.17
1858 2346 3.080647 GGTTATCCCCTTGAGCACG 57.919 57.895 0.00 0.00 0.00 5.34
1891 2379 1.262640 GGACCGGCTTCAGGAGGTAA 61.263 60.000 0.00 0.00 37.07 2.85
1969 2457 1.068474 CAAGGTTACTGTTCGGCTCG 58.932 55.000 0.00 0.00 0.00 5.03
2314 2819 2.769663 AGGACACGAGCATAAATGGGTA 59.230 45.455 0.00 0.00 0.00 3.69
2328 2833 0.514691 GCAGCAAGAGAAAGGACACG 59.485 55.000 0.00 0.00 0.00 4.49
2438 2946 2.017049 GGAAGTAAATGCCATGTCGCT 58.983 47.619 0.00 0.00 0.00 4.93
2493 3028 7.758495 TCTGTAAAAGTTTTTCTTCCTGTGAC 58.242 34.615 6.10 0.00 35.02 3.67
2659 3423 1.068748 GTTCTGCTCTGCAACACCATG 60.069 52.381 0.00 0.00 38.41 3.66
2685 3515 8.141268 ACCAGGAACATGTTAACTTATTTGTTG 58.859 33.333 11.95 0.15 0.00 3.33
2749 4206 8.553459 AGAAATGTGAAGGTGAAACTATGTAG 57.447 34.615 0.00 0.00 36.74 2.74
2806 4263 7.382110 TGAATGTTTCTTTGTTTTCAGACCAA 58.618 30.769 0.00 0.00 0.00 3.67
2897 4659 2.263895 ACTAGCCTACATGGTTGGGA 57.736 50.000 0.00 0.00 38.35 4.37
3019 4786 3.581024 CAGTGCATGCCAAAATACTGT 57.419 42.857 19.98 0.00 32.92 3.55
3031 4798 4.747540 TTAACTTGTACAGCAGTGCATG 57.252 40.909 19.20 14.64 40.12 4.06
3200 5735 9.878599 AAATATTTCAGTTTACATATGTAGCGC 57.121 29.630 14.96 0.00 0.00 5.92
3313 5936 5.013495 TCCAGGATATAGAAAAGGCTGATGG 59.987 44.000 0.00 0.00 0.00 3.51
3320 5943 5.559148 AGCACTCCAGGATATAGAAAAGG 57.441 43.478 0.00 0.00 0.00 3.11
3321 5944 7.872113 AAAAGCACTCCAGGATATAGAAAAG 57.128 36.000 0.00 0.00 0.00 2.27
3440 7695 4.762289 ACCTGATTAGACATGGAGGAAC 57.238 45.455 0.00 0.00 0.00 3.62
3766 8038 3.935203 AGCTCACAATGTGGAACTTATCG 59.065 43.478 13.95 0.00 38.04 2.92
3830 8102 2.125552 CTGCCCAAGCGACGATGA 60.126 61.111 0.00 0.00 44.31 2.92
3929 8201 1.202687 TCTTTGGAGTGTGCCAGACAG 60.203 52.381 0.00 0.00 39.52 3.51
3965 8237 2.892852 CCAAAAGATCTTCTGGTGGCAA 59.107 45.455 18.29 0.00 28.39 4.52
3988 8260 4.022935 CCAACTTTGATGTGTGTAGTGCAT 60.023 41.667 0.00 0.00 0.00 3.96
3995 8267 1.956477 GGCTCCAACTTTGATGTGTGT 59.044 47.619 0.00 0.00 0.00 3.72
4087 8359 4.499183 GCTGAGATATACAAGAATCCCGG 58.501 47.826 0.00 0.00 0.00 5.73
4110 8382 4.193826 TCACTGATTAGAAGAGCACACC 57.806 45.455 0.00 0.00 0.00 4.16
4122 8394 6.206634 GTCAACAGAAAACCCATCACTGATTA 59.793 38.462 0.00 0.00 33.53 1.75
4175 8447 1.721133 GTTTTGTCGCGCCAACTCG 60.721 57.895 0.25 0.00 0.00 4.18
4177 8449 0.248458 CAAGTTTTGTCGCGCCAACT 60.248 50.000 0.25 4.17 0.00 3.16
4179 8451 0.248296 GTCAAGTTTTGTCGCGCCAA 60.248 50.000 0.00 0.00 0.00 4.52
4198 8470 1.364626 CTCCAGCCACAAAGCTAGCG 61.365 60.000 9.55 0.00 42.61 4.26
4222 8494 1.753903 TCCCCTTTTGGTCCATCTCA 58.246 50.000 0.00 0.00 38.10 3.27
4260 8532 5.357257 TCTCAGAAGGACAAACACTAACAC 58.643 41.667 0.00 0.00 0.00 3.32
4438 8716 7.168219 AGCTAAAACCATCATTGTTCAGTCTA 58.832 34.615 0.00 0.00 0.00 2.59
4452 8730 4.889409 CACCACCATCATAGCTAAAACCAT 59.111 41.667 0.00 0.00 0.00 3.55
4453 8731 4.269183 CACCACCATCATAGCTAAAACCA 58.731 43.478 0.00 0.00 0.00 3.67
4483 8761 2.073252 ACATATCGGTCTGCTCAGGA 57.927 50.000 0.00 0.00 0.00 3.86
4623 8920 5.394115 CCGAAATAGTGAAATTTTGAGGGGG 60.394 44.000 0.00 0.00 33.68 5.40
4626 8923 8.345565 CCTATCCGAAATAGTGAAATTTTGAGG 58.654 37.037 0.00 0.00 33.68 3.86
4652 8949 6.090628 TGCAAACGATTTGAAAGGAAATATGC 59.909 34.615 12.62 0.00 43.26 3.14
4682 8980 5.927281 ACATAGGGTTTACTTAGCTTCGA 57.073 39.130 0.00 0.00 0.00 3.71
4684 8982 6.651086 AGGAACATAGGGTTTACTTAGCTTC 58.349 40.000 0.00 0.00 40.63 3.86
4690 8992 9.682465 GAAAATCTAGGAACATAGGGTTTACTT 57.318 33.333 0.00 0.00 40.63 2.24
4696 8998 7.062957 CCATTGAAAATCTAGGAACATAGGGT 58.937 38.462 0.00 0.00 0.00 4.34
4697 8999 7.013655 CACCATTGAAAATCTAGGAACATAGGG 59.986 40.741 0.00 0.00 0.00 3.53
4712 9021 6.337356 GGTTCAGAAGAAACACCATTGAAAA 58.663 36.000 0.00 0.00 41.22 2.29
4724 9033 7.660030 AATCAGAAAAAGGGTTCAGAAGAAA 57.340 32.000 0.00 0.00 35.08 2.52
4727 9036 7.042797 TGAAATCAGAAAAAGGGTTCAGAAG 57.957 36.000 0.00 0.00 0.00 2.85
4738 9047 4.578516 TCTCCTGCGTTGAAATCAGAAAAA 59.421 37.500 0.00 0.00 0.00 1.94
4775 9084 4.158394 CACCCGAGGTCATTTTCATTGAAT 59.842 41.667 0.00 0.00 31.02 2.57
4780 9089 2.039746 TCACACCCGAGGTCATTTTCAT 59.960 45.455 0.00 0.00 31.02 2.57
4781 9090 1.418264 TCACACCCGAGGTCATTTTCA 59.582 47.619 0.00 0.00 31.02 2.69
4833 9142 8.858094 GTGGACTTGCCTAAATACTAGTACTAT 58.142 37.037 4.31 0.00 37.63 2.12
4839 9151 4.811557 GCAGTGGACTTGCCTAAATACTAG 59.188 45.833 0.00 0.00 37.63 2.57
4842 9154 3.343617 TGCAGTGGACTTGCCTAAATAC 58.656 45.455 0.00 0.00 37.63 1.89
4852 9164 2.175202 CTCTAGGTCTGCAGTGGACTT 58.825 52.381 14.67 3.95 34.47 3.01
4861 9173 2.137810 ACAGTCTCCTCTAGGTCTGC 57.862 55.000 13.85 0.00 35.13 4.26
4934 9246 0.042731 TCCCTGGCTAGCTACCTTGT 59.957 55.000 15.72 0.00 0.00 3.16
4935 9247 1.428869 ATCCCTGGCTAGCTACCTTG 58.571 55.000 15.72 0.00 0.00 3.61
4936 9248 2.198334 AATCCCTGGCTAGCTACCTT 57.802 50.000 15.72 0.00 0.00 3.50
4937 9249 2.050918 GAAATCCCTGGCTAGCTACCT 58.949 52.381 15.72 0.00 0.00 3.08
4948 9260 5.296151 TCCTACAAGCTATGAAATCCCTG 57.704 43.478 0.00 0.00 0.00 4.45
4960 9272 6.613153 AGAAAGTACAGATTCCTACAAGCT 57.387 37.500 0.00 0.00 0.00 3.74
4990 9302 1.006281 TGCTTCCATTGCCCATTCTCT 59.994 47.619 0.00 0.00 0.00 3.10
4992 9304 1.941377 TTGCTTCCATTGCCCATTCT 58.059 45.000 0.00 0.00 0.00 2.40
5076 9388 8.918202 AAGGTTAGATGTGACATCACTAAAAA 57.082 30.769 25.68 8.41 46.55 1.94
5077 9389 8.375506 AGAAGGTTAGATGTGACATCACTAAAA 58.624 33.333 25.68 9.96 46.55 1.52
5078 9390 7.907389 AGAAGGTTAGATGTGACATCACTAAA 58.093 34.615 25.68 12.15 46.55 1.85
5079 9391 7.482169 AGAAGGTTAGATGTGACATCACTAA 57.518 36.000 25.68 14.23 46.55 2.24
5080 9392 8.589701 TTAGAAGGTTAGATGTGACATCACTA 57.410 34.615 25.68 9.13 46.55 2.74
5081 9393 7.482169 TTAGAAGGTTAGATGTGACATCACT 57.518 36.000 25.68 15.15 46.55 3.41
5082 9394 8.547967 TTTTAGAAGGTTAGATGTGACATCAC 57.452 34.615 25.68 16.16 46.59 3.06
5083 9395 9.739276 ATTTTTAGAAGGTTAGATGTGACATCA 57.261 29.630 25.68 10.40 0.00 3.07
5095 9407 9.781633 TGCTGTGTAGTTATTTTTAGAAGGTTA 57.218 29.630 0.00 0.00 0.00 2.85
5096 9408 8.685838 TGCTGTGTAGTTATTTTTAGAAGGTT 57.314 30.769 0.00 0.00 0.00 3.50
5097 9409 8.565416 GTTGCTGTGTAGTTATTTTTAGAAGGT 58.435 33.333 0.00 0.00 0.00 3.50
5098 9410 8.564574 TGTTGCTGTGTAGTTATTTTTAGAAGG 58.435 33.333 0.00 0.00 0.00 3.46
5099 9411 9.944663 TTGTTGCTGTGTAGTTATTTTTAGAAG 57.055 29.630 0.00 0.00 0.00 2.85
5100 9412 9.944663 CTTGTTGCTGTGTAGTTATTTTTAGAA 57.055 29.630 0.00 0.00 0.00 2.10
5101 9413 9.332502 TCTTGTTGCTGTGTAGTTATTTTTAGA 57.667 29.630 0.00 0.00 0.00 2.10
5102 9414 9.944663 TTCTTGTTGCTGTGTAGTTATTTTTAG 57.055 29.630 0.00 0.00 0.00 1.85
5104 9416 9.816354 ATTTCTTGTTGCTGTGTAGTTATTTTT 57.184 25.926 0.00 0.00 0.00 1.94
5151 9463 7.524717 AGCACTATGTTTGTGGTCTATTTTT 57.475 32.000 0.00 0.00 41.52 1.94
5152 9464 7.524717 AAGCACTATGTTTGTGGTCTATTTT 57.475 32.000 0.00 0.00 44.03 1.82
5153 9465 8.807948 ATAAGCACTATGTTTGTGGTCTATTT 57.192 30.769 0.00 0.00 44.03 1.40
5154 9466 8.046708 TGATAAGCACTATGTTTGTGGTCTATT 58.953 33.333 0.00 0.00 44.03 1.73
5155 9467 7.564793 TGATAAGCACTATGTTTGTGGTCTAT 58.435 34.615 0.00 0.00 44.03 1.98
5156 9468 6.941857 TGATAAGCACTATGTTTGTGGTCTA 58.058 36.000 0.00 0.00 44.03 2.59
5157 9469 5.804639 TGATAAGCACTATGTTTGTGGTCT 58.195 37.500 0.00 0.00 44.03 3.85
5158 9470 5.065218 CCTGATAAGCACTATGTTTGTGGTC 59.935 44.000 0.00 0.00 44.03 4.02
5159 9471 4.943705 CCTGATAAGCACTATGTTTGTGGT 59.056 41.667 0.00 0.00 46.30 4.16
5160 9472 4.943705 ACCTGATAAGCACTATGTTTGTGG 59.056 41.667 0.00 0.00 36.08 4.17
5161 9473 6.500684 AACCTGATAAGCACTATGTTTGTG 57.499 37.500 0.00 0.00 38.36 3.33
5162 9474 7.620880 TCTAACCTGATAAGCACTATGTTTGT 58.379 34.615 0.00 0.00 0.00 2.83
5163 9475 8.554528 CATCTAACCTGATAAGCACTATGTTTG 58.445 37.037 0.00 0.00 0.00 2.93
5164 9476 8.267894 ACATCTAACCTGATAAGCACTATGTTT 58.732 33.333 0.00 0.00 0.00 2.83
5165 9477 7.712639 CACATCTAACCTGATAAGCACTATGTT 59.287 37.037 0.00 0.00 0.00 2.71
5166 9478 7.069950 TCACATCTAACCTGATAAGCACTATGT 59.930 37.037 0.00 0.00 0.00 2.29
5167 9479 7.383572 GTCACATCTAACCTGATAAGCACTATG 59.616 40.741 0.00 0.00 0.00 2.23
5168 9480 7.069950 TGTCACATCTAACCTGATAAGCACTAT 59.930 37.037 0.00 0.00 0.00 2.12
5169 9481 6.379988 TGTCACATCTAACCTGATAAGCACTA 59.620 38.462 0.00 0.00 0.00 2.74
5170 9482 5.187772 TGTCACATCTAACCTGATAAGCACT 59.812 40.000 0.00 0.00 0.00 4.40
5171 9483 5.419542 TGTCACATCTAACCTGATAAGCAC 58.580 41.667 0.00 0.00 0.00 4.40
5172 9484 5.675684 TGTCACATCTAACCTGATAAGCA 57.324 39.130 0.00 0.00 0.00 3.91
5173 9485 7.928706 AGTTATGTCACATCTAACCTGATAAGC 59.071 37.037 0.00 0.00 0.00 3.09
5177 9489 8.928448 ACATAGTTATGTCACATCTAACCTGAT 58.072 33.333 0.00 0.00 42.96 2.90
5178 9490 8.306313 ACATAGTTATGTCACATCTAACCTGA 57.694 34.615 0.00 0.00 42.96 3.86
5206 9518 5.507149 GGTCTGTCTAGCACACATCTAGATG 60.507 48.000 27.63 27.63 42.90 2.90
5207 9519 4.582656 GGTCTGTCTAGCACACATCTAGAT 59.417 45.833 0.00 0.00 42.90 1.98
5208 9520 3.948473 GGTCTGTCTAGCACACATCTAGA 59.052 47.826 0.00 0.00 39.94 2.43
5209 9521 3.067461 GGGTCTGTCTAGCACACATCTAG 59.933 52.174 0.00 0.00 35.90 2.43
5210 9522 3.024547 GGGTCTGTCTAGCACACATCTA 58.975 50.000 0.00 0.00 0.00 1.98
5211 9523 1.827969 GGGTCTGTCTAGCACACATCT 59.172 52.381 0.00 0.00 0.00 2.90
5212 9524 1.550524 TGGGTCTGTCTAGCACACATC 59.449 52.381 0.00 0.00 0.00 3.06
5213 9525 1.644509 TGGGTCTGTCTAGCACACAT 58.355 50.000 0.00 0.00 0.00 3.21
5214 9526 1.419381 TTGGGTCTGTCTAGCACACA 58.581 50.000 0.00 0.00 0.00 3.72
5215 9527 2.143925 GTTTGGGTCTGTCTAGCACAC 58.856 52.381 0.00 0.00 0.00 3.82
5216 9528 1.765904 TGTTTGGGTCTGTCTAGCACA 59.234 47.619 0.00 0.00 0.00 4.57
5217 9529 2.143925 GTGTTTGGGTCTGTCTAGCAC 58.856 52.381 0.00 0.00 0.00 4.40
5218 9530 1.765904 TGTGTTTGGGTCTGTCTAGCA 59.234 47.619 0.00 0.00 0.00 3.49
5219 9531 2.543777 TGTGTTTGGGTCTGTCTAGC 57.456 50.000 0.00 0.00 0.00 3.42
5220 9532 4.451900 AGTTTGTGTTTGGGTCTGTCTAG 58.548 43.478 0.00 0.00 0.00 2.43
5221 9533 4.448210 GAGTTTGTGTTTGGGTCTGTCTA 58.552 43.478 0.00 0.00 0.00 2.59
5222 9534 3.279434 GAGTTTGTGTTTGGGTCTGTCT 58.721 45.455 0.00 0.00 0.00 3.41
5223 9535 2.357952 GGAGTTTGTGTTTGGGTCTGTC 59.642 50.000 0.00 0.00 0.00 3.51
5224 9536 2.375146 GGAGTTTGTGTTTGGGTCTGT 58.625 47.619 0.00 0.00 0.00 3.41
5225 9537 1.333619 CGGAGTTTGTGTTTGGGTCTG 59.666 52.381 0.00 0.00 0.00 3.51
5226 9538 1.675552 CGGAGTTTGTGTTTGGGTCT 58.324 50.000 0.00 0.00 0.00 3.85
5227 9539 0.666374 CCGGAGTTTGTGTTTGGGTC 59.334 55.000 0.00 0.00 0.00 4.46
5228 9540 0.256464 TCCGGAGTTTGTGTTTGGGT 59.744 50.000 0.00 0.00 0.00 4.51
5229 9541 1.394618 TTCCGGAGTTTGTGTTTGGG 58.605 50.000 3.34 0.00 0.00 4.12
5230 9542 3.512033 TTTTCCGGAGTTTGTGTTTGG 57.488 42.857 3.34 0.00 0.00 3.28
5270 9582 6.094881 TGGTTAAGTTTTGAGTTCCAGAGTTG 59.905 38.462 0.00 0.00 0.00 3.16
5368 9681 6.415867 CAGCTGAACTTTGTTGTTGTATCAAG 59.584 38.462 8.42 0.00 0.00 3.02
5429 9742 1.731709 CGAGTTTTGATCATGCGACCA 59.268 47.619 0.00 0.00 0.00 4.02
5442 9755 2.904434 ACCCACCTACATCTCGAGTTTT 59.096 45.455 13.13 0.00 0.00 2.43
5482 9796 1.154093 CAGCCAGCGAATGCAGTTG 60.154 57.895 0.00 0.00 46.23 3.16
5496 9810 1.611977 GGTGTAGGTGGTTTTTCAGCC 59.388 52.381 0.00 0.00 35.93 4.85
5526 9840 1.563879 TCCCCGGTCACATGATCAAAT 59.436 47.619 0.00 0.00 0.00 2.32
5537 9851 2.122324 TTCCCTGTTCCCCGGTCA 60.122 61.111 0.00 0.00 0.00 4.02
5541 9855 2.351276 CCTGTTCCCTGTTCCCCG 59.649 66.667 0.00 0.00 0.00 5.73
5549 9863 1.430992 TTCTTCGTTCCCTGTTCCCT 58.569 50.000 0.00 0.00 0.00 4.20
5550 9864 2.027100 AGATTCTTCGTTCCCTGTTCCC 60.027 50.000 0.00 0.00 0.00 3.97
5551 9865 3.263261 GAGATTCTTCGTTCCCTGTTCC 58.737 50.000 0.00 0.00 0.00 3.62
5552 9866 3.263261 GGAGATTCTTCGTTCCCTGTTC 58.737 50.000 0.00 0.00 0.00 3.18
5553 9867 2.353803 CGGAGATTCTTCGTTCCCTGTT 60.354 50.000 6.18 0.00 0.00 3.16
5554 9868 1.204941 CGGAGATTCTTCGTTCCCTGT 59.795 52.381 6.18 0.00 0.00 4.00
5555 9869 1.927895 CGGAGATTCTTCGTTCCCTG 58.072 55.000 6.18 0.00 0.00 4.45
5556 9870 0.175989 GCGGAGATTCTTCGTTCCCT 59.824 55.000 15.54 0.00 34.53 4.20
5573 9887 3.555956 AGCCAAGTTAATAACTGATCGCG 59.444 43.478 6.41 0.00 41.91 5.87
5594 9908 3.436015 CAGATTGTTCTTGACCTCTGCAG 59.564 47.826 7.63 7.63 33.21 4.41
5638 9952 1.003580 GATCTTCACCTGACCAAGCCA 59.996 52.381 0.00 0.00 0.00 4.75
5710 10024 4.286320 ACCCCGATCATCGCGCTC 62.286 66.667 5.56 0.00 38.82 5.03
5779 10093 1.954382 CAGATGCCAGTGATGAATGGG 59.046 52.381 0.00 0.00 37.05 4.00


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

AutoCloner maintained by Alex Coulton.