Multiple sequence alignment - TraesCS3A01G377600

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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 TraesCS3A01G377600 chr3A 100.000 4189 0 0 1 4189 627274635 627278823 0.000000e+00 7736.0
1 TraesCS3A01G377600 chr3A 87.407 405 46 3 2590 2991 627677024 627677426 1.060000e-125 460.0
2 TraesCS3A01G377600 chr3A 81.771 384 64 5 3023 3404 627677423 627677802 2.430000e-82 316.0
3 TraesCS3A01G377600 chr3D 86.412 3113 227 92 1 2991 484344590 484347628 0.000000e+00 3225.0
4 TraesCS3A01G377600 chr3D 93.480 1181 57 10 3023 4189 484347625 484348799 0.000000e+00 1736.0
5 TraesCS3A01G377600 chr3D 92.099 405 26 4 2590 2991 484452569 484452970 2.190000e-157 566.0
6 TraesCS3A01G377600 chr3D 83.547 468 41 18 3012 3474 484452960 484453396 5.040000e-109 405.0
7 TraesCS3A01G377600 chr3D 76.344 465 67 18 3753 4186 58371859 58372311 4.240000e-50 209.0
8 TraesCS3A01G377600 chr3B 86.171 1627 119 51 1425 2991 647178389 647179969 0.000000e+00 1661.0
9 TraesCS3A01G377600 chr3B 83.445 1190 91 53 293 1419 647177200 647178346 0.000000e+00 1009.0
10 TraesCS3A01G377600 chr3B 83.524 437 39 12 3056 3474 647179990 647180411 1.100000e-100 377.0
11 TraesCS3A01G377600 chr3B 82.041 245 19 7 1 235 647176972 647177201 7.150000e-43 185.0
12 TraesCS3A01G377600 chr3B 80.405 148 24 5 4006 4151 724921712 724921856 1.590000e-19 108.0
13 TraesCS3A01G377600 chr5D 80.212 753 89 32 999 1723 10495640 10494920 1.040000e-140 510.0
14 TraesCS3A01G377600 chr5D 78.496 758 90 35 999 1723 511490989 511490272 2.990000e-116 429.0
15 TraesCS3A01G377600 chr5D 77.224 742 119 16 3479 4187 429717821 429718545 5.080000e-104 388.0
16 TraesCS3A01G377600 chr5D 81.663 409 55 13 3602 4009 505177544 505177155 5.220000e-84 322.0
17 TraesCS3A01G377600 chr5B 79.840 749 96 28 999 1723 76158284 76159001 2.910000e-136 496.0
18 TraesCS3A01G377600 chr5B 75.890 730 142 16 3475 4187 130735160 130734448 4.010000e-90 342.0
19 TraesCS3A01G377600 chr2D 79.814 753 89 34 999 1723 33338451 33337734 1.350000e-134 490.0
20 TraesCS3A01G377600 chr7D 79.416 753 95 30 999 1723 2873014 2872294 1.050000e-130 477.0
21 TraesCS3A01G377600 chr7D 78.718 733 124 14 3479 4187 153947447 153946723 1.060000e-125 460.0
22 TraesCS3A01G377600 chr7D 77.868 741 116 23 3473 4186 572730392 572729673 2.330000e-112 416.0
23 TraesCS3A01G377600 chr7D 80.000 75 13 2 3567 3640 63458028 63458101 2.000000e-03 54.7
24 TraesCS3A01G377600 chr2B 77.120 743 118 27 3481 4189 202903797 202903073 2.360000e-102 383.0
25 TraesCS3A01G377600 chr2B 78.072 529 93 16 3479 4000 6272726 6272214 3.140000e-81 313.0
26 TraesCS3A01G377600 chr2B 74.699 747 125 23 3475 4189 233743759 233744473 1.480000e-69 274.0
27 TraesCS3A01G377600 chr2B 100.000 28 0 0 3612 3639 551477152 551477125 8.000000e-03 52.8
28 TraesCS3A01G377600 chr1D 92.857 224 15 1 991 1213 368322530 368322307 1.450000e-84 324.0
29 TraesCS3A01G377600 chr1D 92.857 224 15 1 991 1213 369903976 369903753 1.450000e-84 324.0
30 TraesCS3A01G377600 chr1D 76.937 555 90 19 3662 4187 182082149 182081604 8.870000e-72 281.0
31 TraesCS3A01G377600 chr1D 95.062 81 4 0 1308 1388 368322216 368322136 1.220000e-25 128.0
32 TraesCS3A01G377600 chr1D 91.358 81 7 0 1308 1388 369903670 369903590 1.230000e-20 111.0
33 TraesCS3A01G377600 chr1D 88.571 70 8 0 1654 1723 368321989 368321920 7.460000e-13 86.1
34 TraesCS3A01G377600 chr1D 88.571 70 8 0 1654 1723 369903428 369903359 7.460000e-13 86.1
35 TraesCS3A01G377600 chr1B 92.857 224 15 1 991 1213 492358043 492357820 1.450000e-84 324.0
36 TraesCS3A01G377600 chr1B 83.942 137 21 1 1895 2030 492357313 492357177 3.400000e-26 130.0
37 TraesCS3A01G377600 chr1B 95.062 81 4 0 1308 1388 492357733 492357653 1.220000e-25 128.0
38 TraesCS3A01G377600 chr1B 83.065 124 18 3 3532 3653 448144022 448144144 4.430000e-20 110.0
39 TraesCS3A01G377600 chr1B 88.732 71 8 0 1654 1724 492357501 492357431 2.070000e-13 87.9
40 TraesCS3A01G377600 chr1A 93.119 218 15 0 996 1213 467259932 467259715 1.880000e-83 320.0
41 TraesCS3A01G377600 chr1A 92.473 93 7 0 2661 2753 467258493 467258401 2.630000e-27 134.0
42 TraesCS3A01G377600 chr1A 95.062 81 4 0 1308 1388 467259638 467259558 1.220000e-25 128.0
43 TraesCS3A01G377600 chr4D 75.205 730 143 26 3479 4189 464565989 464565279 1.130000e-80 311.0
44 TraesCS3A01G377600 chr6D 78.394 523 72 19 1074 1574 443355408 443355911 6.810000e-78 302.0
45 TraesCS3A01G377600 chr6D 72.659 662 141 23 3481 4117 381544547 381543901 2.570000e-42 183.0
46 TraesCS3A01G377600 chr4B 77.719 377 60 12 3824 4189 580860069 580859706 4.240000e-50 209.0
47 TraesCS3A01G377600 chrUn 81.893 243 35 7 2056 2291 87129845 87129605 3.300000e-46 196.0
48 TraesCS3A01G377600 chr7B 80.357 168 31 2 3474 3640 573102806 573102972 4.400000e-25 126.0
49 TraesCS3A01G377600 chr5A 94.286 70 4 0 4007 4076 25087995 25087926 1.590000e-19 108.0


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 TraesCS3A01G377600 chr3A 627274635 627278823 4188 False 7736.0 7736 100.00000 1 4189 1 chr3A.!!$F1 4188
1 TraesCS3A01G377600 chr3A 627677024 627677802 778 False 388.0 460 84.58900 2590 3404 2 chr3A.!!$F2 814
2 TraesCS3A01G377600 chr3D 484344590 484348799 4209 False 2480.5 3225 89.94600 1 4189 2 chr3D.!!$F2 4188
3 TraesCS3A01G377600 chr3D 484452569 484453396 827 False 485.5 566 87.82300 2590 3474 2 chr3D.!!$F3 884
4 TraesCS3A01G377600 chr3B 647176972 647180411 3439 False 808.0 1661 83.79525 1 3474 4 chr3B.!!$F2 3473
5 TraesCS3A01G377600 chr5D 10494920 10495640 720 True 510.0 510 80.21200 999 1723 1 chr5D.!!$R1 724
6 TraesCS3A01G377600 chr5D 511490272 511490989 717 True 429.0 429 78.49600 999 1723 1 chr5D.!!$R3 724
7 TraesCS3A01G377600 chr5D 429717821 429718545 724 False 388.0 388 77.22400 3479 4187 1 chr5D.!!$F1 708
8 TraesCS3A01G377600 chr5B 76158284 76159001 717 False 496.0 496 79.84000 999 1723 1 chr5B.!!$F1 724
9 TraesCS3A01G377600 chr5B 130734448 130735160 712 True 342.0 342 75.89000 3475 4187 1 chr5B.!!$R1 712
10 TraesCS3A01G377600 chr2D 33337734 33338451 717 True 490.0 490 79.81400 999 1723 1 chr2D.!!$R1 724
11 TraesCS3A01G377600 chr7D 2872294 2873014 720 True 477.0 477 79.41600 999 1723 1 chr7D.!!$R1 724
12 TraesCS3A01G377600 chr7D 153946723 153947447 724 True 460.0 460 78.71800 3479 4187 1 chr7D.!!$R2 708
13 TraesCS3A01G377600 chr7D 572729673 572730392 719 True 416.0 416 77.86800 3473 4186 1 chr7D.!!$R3 713
14 TraesCS3A01G377600 chr2B 202903073 202903797 724 True 383.0 383 77.12000 3481 4189 1 chr2B.!!$R2 708
15 TraesCS3A01G377600 chr2B 6272214 6272726 512 True 313.0 313 78.07200 3479 4000 1 chr2B.!!$R1 521
16 TraesCS3A01G377600 chr2B 233743759 233744473 714 False 274.0 274 74.69900 3475 4189 1 chr2B.!!$F1 714
17 TraesCS3A01G377600 chr1D 182081604 182082149 545 True 281.0 281 76.93700 3662 4187 1 chr1D.!!$R1 525
18 TraesCS3A01G377600 chr4D 464565279 464565989 710 True 311.0 311 75.20500 3479 4189 1 chr4D.!!$R1 710
19 TraesCS3A01G377600 chr6D 443355408 443355911 503 False 302.0 302 78.39400 1074 1574 1 chr6D.!!$F1 500

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
400 422 0.318445 GGCGCTACGATATTCCACGT 60.318 55.0 7.64 0.0 44.72 4.49 F
1580 1748 0.174389 CATGCTCTGCTCACGTACCT 59.826 55.0 0.00 0.0 0.00 3.08 F
2377 2620 0.179056 ACGCCTACTGCAAAGTGTGT 60.179 50.0 0.00 0.0 41.33 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 2025 0.394192 TGAGCATATTCCCTGCGAGG 59.606 55.0 0.00 0.0 44.38 4.63 R
3003 3282 0.323302 TGCATACTGTCTTTCCCGCA 59.677 50.0 0.00 0.0 0.00 5.69 R
4104 4483 0.175760 TCTGAACCACGGCTATCAGC 59.824 55.0 8.51 0.0 39.27 4.26 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
45 46 3.676172 GTGTCAAATGGTCAACATGCATG 59.324 43.478 25.09 25.09 40.44 4.06
83 84 1.203287 GCCTTTGCTGATTTCCTGGAC 59.797 52.381 0.00 0.00 33.53 4.02
106 115 9.991388 GGACGCAACTTTTATTATTGTATGTAA 57.009 29.630 0.00 0.00 0.00 2.41
108 117 9.498307 ACGCAACTTTTATTATTGTATGTAAGC 57.502 29.630 0.00 0.00 0.00 3.09
134 143 5.464389 ACGTTATAAATGGCACGTTATCTCC 59.536 40.000 8.18 0.02 43.10 3.71
156 174 4.026804 CCGTTGACATAAGTTATCGACAGC 60.027 45.833 0.00 0.00 30.66 4.40
166 184 4.801891 AGTTATCGACAGCGTCAAGTTTA 58.198 39.130 8.91 0.00 38.98 2.01
178 196 3.064931 GTCAAGTTTACGCTAGTGGCTT 58.935 45.455 8.42 3.90 39.13 4.35
181 199 2.960819 AGTTTACGCTAGTGGCTTCTG 58.039 47.619 8.42 0.00 39.13 3.02
259 277 3.091545 CAAAAAGCAGCTATTCCCCTGA 58.908 45.455 0.00 0.00 0.00 3.86
316 335 3.225235 GGCTGAGCCTGGTAGGAG 58.775 66.667 17.96 0.00 46.69 3.69
317 336 1.687493 GGCTGAGCCTGGTAGGAGT 60.687 63.158 17.96 0.00 46.69 3.85
318 337 0.397254 GGCTGAGCCTGGTAGGAGTA 60.397 60.000 17.96 0.00 46.69 2.59
319 338 1.710816 GCTGAGCCTGGTAGGAGTAT 58.289 55.000 0.00 0.00 37.67 2.12
320 339 2.491086 GGCTGAGCCTGGTAGGAGTATA 60.491 54.545 17.96 0.00 46.69 1.47
321 340 3.436243 GCTGAGCCTGGTAGGAGTATAT 58.564 50.000 0.00 0.00 37.67 0.86
326 345 4.675038 AGCCTGGTAGGAGTATATACCAC 58.325 47.826 9.32 3.04 45.05 4.16
327 346 3.442977 GCCTGGTAGGAGTATATACCACG 59.557 52.174 9.32 0.00 45.05 4.94
328 347 4.660168 CCTGGTAGGAGTATATACCACGT 58.340 47.826 9.32 8.28 45.05 4.49
329 348 5.804446 GCCTGGTAGGAGTATATACCACGTA 60.804 48.000 9.32 7.42 45.05 3.57
363 382 7.476540 AAAAAGTTACCCCAGGATATTTCAC 57.523 36.000 0.00 0.00 0.00 3.18
388 410 7.271868 ACGTTTTTCAATATAAAAAGGCGCTAC 59.728 33.333 7.64 0.00 43.15 3.58
400 422 0.318445 GGCGCTACGATATTCCACGT 60.318 55.000 7.64 0.00 44.72 4.49
401 423 1.069022 GGCGCTACGATATTCCACGTA 60.069 52.381 7.64 0.00 42.61 3.57
402 424 1.974680 GCGCTACGATATTCCACGTAC 59.025 52.381 0.00 0.00 42.61 3.67
442 464 2.645838 TCAAGCAAAGCTCCTCTTGT 57.354 45.000 16.37 0.00 38.25 3.16
443 465 2.224606 TCAAGCAAAGCTCCTCTTGTG 58.775 47.619 16.37 2.38 38.25 3.33
445 467 1.602311 AGCAAAGCTCCTCTTGTGTG 58.398 50.000 0.00 0.00 30.62 3.82
446 468 0.595095 GCAAAGCTCCTCTTGTGTGG 59.405 55.000 0.00 0.00 34.67 4.17
455 477 4.083271 GCTCCTCTTGTGTGGTTATTGAAC 60.083 45.833 0.00 0.00 34.56 3.18
554 592 0.318955 ACGTCGGGGTTCAGTTTACG 60.319 55.000 0.00 0.00 35.17 3.18
562 600 2.158254 GGGTTCAGTTTACGGCTAAACG 59.842 50.000 11.34 0.00 44.53 3.60
575 613 1.694639 CTAAACGTCGTCACTGTCCC 58.305 55.000 0.00 0.00 0.00 4.46
932 988 3.980989 CTGCAAGCAAAGCCCGCA 61.981 61.111 0.00 3.43 35.48 5.69
933 989 3.502990 CTGCAAGCAAAGCCCGCAA 62.503 57.895 0.00 0.00 36.16 4.85
934 990 3.037833 GCAAGCAAAGCCCGCAAC 61.038 61.111 0.00 0.00 0.00 4.17
935 991 2.416678 CAAGCAAAGCCCGCAACA 59.583 55.556 0.00 0.00 0.00 3.33
939 995 2.899044 GCAAAGCCCGCAACACGTA 61.899 57.895 0.00 0.00 41.42 3.57
941 997 2.255881 AAAGCCCGCAACACGTACC 61.256 57.895 0.00 0.00 41.42 3.34
943 999 2.944409 AAGCCCGCAACACGTACCAA 62.944 55.000 0.00 0.00 41.42 3.67
946 1002 1.562575 CCCGCAACACGTACCAACTC 61.563 60.000 0.00 0.00 41.42 3.01
947 1003 0.599204 CCGCAACACGTACCAACTCT 60.599 55.000 0.00 0.00 41.42 3.24
948 1004 0.782384 CGCAACACGTACCAACTCTC 59.218 55.000 0.00 0.00 36.87 3.20
949 1005 1.145803 GCAACACGTACCAACTCTCC 58.854 55.000 0.00 0.00 0.00 3.71
950 1006 1.270147 GCAACACGTACCAACTCTCCT 60.270 52.381 0.00 0.00 0.00 3.69
951 1007 2.029649 GCAACACGTACCAACTCTCCTA 60.030 50.000 0.00 0.00 0.00 2.94
952 1008 3.572584 CAACACGTACCAACTCTCCTAC 58.427 50.000 0.00 0.00 0.00 3.18
953 1009 1.808945 ACACGTACCAACTCTCCTACG 59.191 52.381 0.00 0.00 38.33 3.51
954 1010 2.079158 CACGTACCAACTCTCCTACGA 58.921 52.381 3.27 0.00 36.36 3.43
955 1011 2.095532 CACGTACCAACTCTCCTACGAG 59.904 54.545 3.27 0.00 36.36 4.18
956 1012 1.063764 CGTACCAACTCTCCTACGAGC 59.936 57.143 0.00 0.00 35.12 5.03
957 1013 2.367486 GTACCAACTCTCCTACGAGCT 58.633 52.381 0.00 0.00 35.94 4.09
958 1014 1.178276 ACCAACTCTCCTACGAGCTG 58.822 55.000 0.00 0.00 35.94 4.24
959 1015 1.271982 ACCAACTCTCCTACGAGCTGA 60.272 52.381 0.00 0.00 35.94 4.26
960 1016 1.403679 CCAACTCTCCTACGAGCTGAG 59.596 57.143 0.00 0.00 35.94 3.35
961 1017 1.099689 AACTCTCCTACGAGCTGAGC 58.900 55.000 0.00 0.00 35.94 4.26
962 1018 1.092921 ACTCTCCTACGAGCTGAGCG 61.093 60.000 0.00 0.00 35.94 5.03
975 1031 3.812019 GAGCGAGCGAACGGGAGA 61.812 66.667 0.00 0.00 0.00 3.71
982 1038 3.066233 GCGAACGGGAGAGAGGGTC 62.066 68.421 0.00 0.00 0.00 4.46
988 1044 3.519930 GGAGAGAGGGTCGGCGTC 61.520 72.222 6.85 0.00 0.00 5.19
989 1045 3.878519 GAGAGAGGGTCGGCGTCG 61.879 72.222 1.15 1.15 37.82 5.12
1220 1308 1.600413 CGTCCAGGCAAGCTGTTTTTC 60.600 52.381 0.00 0.00 0.00 2.29
1221 1309 1.683385 GTCCAGGCAAGCTGTTTTTCT 59.317 47.619 0.00 0.00 0.00 2.52
1224 1312 3.197549 TCCAGGCAAGCTGTTTTTCTTTT 59.802 39.130 0.00 0.00 0.00 2.27
1229 1317 5.939883 AGGCAAGCTGTTTTTCTTTTTCTTT 59.060 32.000 0.00 0.00 0.00 2.52
1230 1318 6.430925 AGGCAAGCTGTTTTTCTTTTTCTTTT 59.569 30.769 0.00 0.00 0.00 2.27
1233 1321 7.271223 GCAAGCTGTTTTTCTTTTTCTTTTTCC 59.729 33.333 0.00 0.00 0.00 3.13
1234 1322 8.506437 CAAGCTGTTTTTCTTTTTCTTTTTCCT 58.494 29.630 0.00 0.00 0.00 3.36
1235 1323 8.621532 AGCTGTTTTTCTTTTTCTTTTTCCTT 57.378 26.923 0.00 0.00 0.00 3.36
1236 1324 9.066892 AGCTGTTTTTCTTTTTCTTTTTCCTTT 57.933 25.926 0.00 0.00 0.00 3.11
1237 1325 9.329913 GCTGTTTTTCTTTTTCTTTTTCCTTTC 57.670 29.630 0.00 0.00 0.00 2.62
1273 1361 9.740239 TCAAATTTTCTTCTGTGAGAATGAAAG 57.260 29.630 0.00 0.00 35.70 2.62
1394 1523 1.142314 GGCCGCACCGTATGAGTTA 59.858 57.895 0.00 0.00 0.00 2.24
1411 1540 4.099573 TGAGTTATCTCTCGTCCCATTTCC 59.900 45.833 2.61 0.00 40.98 3.13
1442 1608 2.718789 CGATTCGTTCTGCTTTGTGACG 60.719 50.000 0.00 0.00 0.00 4.35
1445 1611 0.304705 CGTTCTGCTTTGTGACGCTT 59.695 50.000 0.00 0.00 0.00 4.68
1469 1636 1.268692 TGTGCGAACGACCGGATATAC 60.269 52.381 9.46 0.00 31.48 1.47
1575 1743 1.521010 CCTCCATGCTCTGCTCACG 60.521 63.158 0.00 0.00 0.00 4.35
1580 1748 0.174389 CATGCTCTGCTCACGTACCT 59.826 55.000 0.00 0.00 0.00 3.08
1592 1763 2.365941 TCACGTACCTTTGATGTGGTCA 59.634 45.455 0.00 0.00 37.74 4.02
1595 1766 2.742053 CGTACCTTTGATGTGGTCAAGG 59.258 50.000 0.00 0.00 46.85 3.61
1596 1767 3.556213 CGTACCTTTGATGTGGTCAAGGA 60.556 47.826 3.80 0.00 46.85 3.36
1597 1768 3.146104 ACCTTTGATGTGGTCAAGGAG 57.854 47.619 3.80 0.00 46.85 3.69
1598 1769 1.815003 CCTTTGATGTGGTCAAGGAGC 59.185 52.381 2.01 0.00 46.85 4.70
1599 1770 2.507484 CTTTGATGTGGTCAAGGAGCA 58.493 47.619 0.00 0.00 46.85 4.26
1606 1777 4.320608 TGTGGTCAAGGAGCAAATTTTC 57.679 40.909 0.00 0.00 41.75 2.29
1609 1780 3.573967 TGGTCAAGGAGCAAATTTTCCTC 59.426 43.478 11.11 8.91 42.95 3.71
1611 1782 4.321527 GGTCAAGGAGCAAATTTTCCTCTG 60.322 45.833 11.11 11.18 42.95 3.35
1612 1783 4.279420 GTCAAGGAGCAAATTTTCCTCTGT 59.721 41.667 11.11 0.00 42.95 3.41
1630 1809 5.632347 CCTCTGTTTGTTTCTGATGAAATGC 59.368 40.000 0.00 0.00 43.14 3.56
1746 1925 4.590222 AGGGAAGCACACAAGAAATTTCAT 59.410 37.500 19.99 5.47 0.00 2.57
1747 1926 4.925646 GGGAAGCACACAAGAAATTTCATC 59.074 41.667 19.99 0.00 0.00 2.92
1749 1928 5.984926 GGAAGCACACAAGAAATTTCATCAA 59.015 36.000 19.99 0.00 0.00 2.57
1750 1929 6.479660 GGAAGCACACAAGAAATTTCATCAAA 59.520 34.615 19.99 0.00 0.00 2.69
1751 1930 6.833342 AGCACACAAGAAATTTCATCAAAC 57.167 33.333 19.99 4.30 0.00 2.93
1786 1965 2.088423 GGAACACGCACAATTATGGGA 58.912 47.619 7.89 0.00 36.43 4.37
1792 1971 2.747446 ACGCACAATTATGGGAAGTCAC 59.253 45.455 7.89 0.00 36.43 3.67
1794 1973 3.378112 CGCACAATTATGGGAAGTCACAT 59.622 43.478 0.98 0.98 43.47 3.21
1798 1977 7.319646 GCACAATTATGGGAAGTCACATTTTA 58.680 34.615 0.49 0.00 40.98 1.52
1813 1992 6.018262 GTCACATTTTACTTTCCTTTTTGCCC 60.018 38.462 0.00 0.00 0.00 5.36
1825 2022 4.099419 TCCTTTTTGCCCTTTCAAAGTCTC 59.901 41.667 0.00 0.00 37.27 3.36
1826 2023 4.141959 CCTTTTTGCCCTTTCAAAGTCTCA 60.142 41.667 0.00 0.00 37.27 3.27
1827 2024 4.654091 TTTTGCCCTTTCAAAGTCTCAG 57.346 40.909 0.00 0.00 37.27 3.35
1828 2025 1.609208 TGCCCTTTCAAAGTCTCAGC 58.391 50.000 0.00 0.00 0.00 4.26
1829 2026 0.884514 GCCCTTTCAAAGTCTCAGCC 59.115 55.000 0.00 0.00 0.00 4.85
1830 2027 1.546548 GCCCTTTCAAAGTCTCAGCCT 60.547 52.381 0.00 0.00 0.00 4.58
1831 2028 2.431454 CCCTTTCAAAGTCTCAGCCTC 58.569 52.381 0.00 0.00 0.00 4.70
1832 2029 2.072298 CCTTTCAAAGTCTCAGCCTCG 58.928 52.381 0.00 0.00 0.00 4.63
1850 2047 3.519579 CTCGCAGGGAATATGCTCATAG 58.480 50.000 0.00 0.00 41.61 2.23
1854 2051 4.153117 CGCAGGGAATATGCTCATAGAAAC 59.847 45.833 0.00 0.00 41.61 2.78
1860 2065 6.881065 GGGAATATGCTCATAGAAACATGCTA 59.119 38.462 0.00 0.00 0.00 3.49
1876 2081 7.466746 AACATGCTACATGGACAGTTTATTT 57.533 32.000 11.91 0.00 0.00 1.40
1992 2216 0.743097 GGAAGGACATGATTGCTGCC 59.257 55.000 0.00 0.00 0.00 4.85
2027 2255 0.672711 GGGAGTTCCTGCACGGTAAC 60.673 60.000 0.00 6.01 35.95 2.50
2033 2261 2.572191 TCCTGCACGGTAACTAATCG 57.428 50.000 2.68 0.00 0.00 3.34
2103 2341 4.513442 TGTATCTGAATTGGCCTGTGTAC 58.487 43.478 3.32 0.00 0.00 2.90
2166 2404 3.056328 GGCTTCACGCTTGACCCC 61.056 66.667 0.00 0.00 39.13 4.95
2172 2410 1.216710 CACGCTTGACCCCTCTCTC 59.783 63.158 0.00 0.00 0.00 3.20
2199 2437 6.239829 GGGAGTTCATAATGACTCATCCAGAT 60.240 42.308 11.02 0.00 31.05 2.90
2208 2446 7.862274 AATGACTCATCCAGATATCAAGGTA 57.138 36.000 5.32 0.00 0.00 3.08
2210 2448 7.862274 TGACTCATCCAGATATCAAGGTATT 57.138 36.000 5.32 0.00 0.00 1.89
2211 2449 7.674120 TGACTCATCCAGATATCAAGGTATTG 58.326 38.462 5.32 6.80 37.80 1.90
2214 2452 7.071698 ACTCATCCAGATATCAAGGTATTGTGT 59.928 37.037 5.32 9.65 37.68 3.72
2215 2453 7.219322 TCATCCAGATATCAAGGTATTGTGTG 58.781 38.462 5.32 0.00 37.68 3.82
2217 2455 6.582636 TCCAGATATCAAGGTATTGTGTGAC 58.417 40.000 5.32 0.00 37.68 3.67
2219 2457 6.258727 CCAGATATCAAGGTATTGTGTGACAC 59.741 42.308 9.14 9.14 37.68 3.67
2221 2459 7.010830 CAGATATCAAGGTATTGTGTGACACTG 59.989 40.741 17.47 4.96 37.68 3.66
2222 2460 3.138304 TCAAGGTATTGTGTGACACTGC 58.862 45.455 17.47 0.79 37.68 4.40
2223 2461 3.141398 CAAGGTATTGTGTGACACTGCT 58.859 45.455 17.47 4.08 35.11 4.24
2224 2462 4.039852 TCAAGGTATTGTGTGACACTGCTA 59.960 41.667 17.47 3.12 37.68 3.49
2225 2463 4.617253 AGGTATTGTGTGACACTGCTAA 57.383 40.909 17.47 2.89 35.11 3.09
2226 2464 5.165961 AGGTATTGTGTGACACTGCTAAT 57.834 39.130 17.47 10.32 35.11 1.73
2227 2465 6.294361 AGGTATTGTGTGACACTGCTAATA 57.706 37.500 17.47 9.35 35.11 0.98
2228 2466 6.341316 AGGTATTGTGTGACACTGCTAATAG 58.659 40.000 17.47 0.00 35.11 1.73
2229 2467 5.523916 GGTATTGTGTGACACTGCTAATAGG 59.476 44.000 17.47 0.00 35.11 2.57
2230 2468 4.882842 TTGTGTGACACTGCTAATAGGA 57.117 40.909 17.47 0.00 35.11 2.94
2232 2470 5.420725 TGTGTGACACTGCTAATAGGATT 57.579 39.130 17.47 0.00 35.11 3.01
2234 2472 5.046663 TGTGTGACACTGCTAATAGGATTCA 60.047 40.000 17.47 0.00 35.11 2.57
2235 2473 6.051717 GTGTGACACTGCTAATAGGATTCAT 58.948 40.000 8.76 0.00 0.00 2.57
2237 2475 7.066284 GTGTGACACTGCTAATAGGATTCATTT 59.934 37.037 8.76 0.00 0.00 2.32
2238 2476 8.264347 TGTGACACTGCTAATAGGATTCATTTA 58.736 33.333 7.20 0.00 0.00 1.40
2239 2477 8.552034 GTGACACTGCTAATAGGATTCATTTAC 58.448 37.037 0.00 0.00 0.00 2.01
2257 2500 8.519799 TCATTTACTTTTCTGAAAACTCACCT 57.480 30.769 11.33 0.00 0.00 4.00
2276 2519 5.955959 TCACCTAGAGGCATACTACTCAAAA 59.044 40.000 0.00 0.00 39.32 2.44
2277 2520 6.096987 TCACCTAGAGGCATACTACTCAAAAG 59.903 42.308 0.00 0.00 39.32 2.27
2278 2521 6.096987 CACCTAGAGGCATACTACTCAAAAGA 59.903 42.308 0.00 0.00 39.32 2.52
2279 2522 6.841755 ACCTAGAGGCATACTACTCAAAAGAT 59.158 38.462 0.00 0.00 39.32 2.40
2281 2524 7.232534 CCTAGAGGCATACTACTCAAAAGATCT 59.767 40.741 0.00 0.00 36.20 2.75
2282 2525 6.815089 AGAGGCATACTACTCAAAAGATCTG 58.185 40.000 0.00 0.00 36.20 2.90
2283 2526 6.382570 AGAGGCATACTACTCAAAAGATCTGT 59.617 38.462 0.00 0.00 36.20 3.41
2284 2527 7.561722 AGAGGCATACTACTCAAAAGATCTGTA 59.438 37.037 0.00 0.00 36.20 2.74
2286 2529 8.147058 AGGCATACTACTCAAAAGATCTGTATG 58.853 37.037 15.88 15.88 39.04 2.39
2289 2532 9.190858 CATACTACTCAAAAGATCTGTATGCTC 57.809 37.037 10.75 0.00 32.78 4.26
2290 2533 7.416964 ACTACTCAAAAGATCTGTATGCTCT 57.583 36.000 0.00 0.00 0.00 4.09
2291 2534 7.264221 ACTACTCAAAAGATCTGTATGCTCTG 58.736 38.462 0.00 0.00 0.00 3.35
2292 2535 6.047511 ACTCAAAAGATCTGTATGCTCTGT 57.952 37.500 0.00 0.00 0.00 3.41
2293 2536 6.471146 ACTCAAAAGATCTGTATGCTCTGTT 58.529 36.000 0.00 0.00 0.00 3.16
2294 2537 6.370994 ACTCAAAAGATCTGTATGCTCTGTTG 59.629 38.462 0.00 0.00 37.44 3.33
2295 2538 6.233434 TCAAAAGATCTGTATGCTCTGTTGT 58.767 36.000 0.00 0.00 37.40 3.32
2333 2576 8.366671 CGAAAGGAAAGATCTATTCGGTTAAT 57.633 34.615 14.55 0.00 38.62 1.40
2342 2585 7.217906 AGATCTATTCGGTTAATGAAGGGAAC 58.782 38.462 0.00 0.00 0.00 3.62
2360 2603 2.317609 CGCCAAGAACTGGGACACG 61.318 63.158 0.00 0.00 46.54 4.49
2374 2617 0.512952 GACACGCCTACTGCAAAGTG 59.487 55.000 0.00 0.00 41.33 3.16
2377 2620 0.179056 ACGCCTACTGCAAAGTGTGT 60.179 50.000 0.00 0.00 41.33 3.72
2384 2627 4.516698 CCTACTGCAAAGTGTGTGATCTTT 59.483 41.667 0.00 0.00 34.74 2.52
2386 2629 6.204688 CCTACTGCAAAGTGTGTGATCTTTTA 59.795 38.462 0.00 0.00 32.52 1.52
2387 2630 6.639632 ACTGCAAAGTGTGTGATCTTTTAT 57.360 33.333 0.00 0.00 32.52 1.40
2388 2631 6.441274 ACTGCAAAGTGTGTGATCTTTTATG 58.559 36.000 0.00 0.00 32.52 1.90
2393 2636 7.357532 GCAAAGTGTGTGATCTTTTATGTTTCG 60.358 37.037 0.00 0.00 32.52 3.46
2399 2642 7.658167 TGTGTGATCTTTTATGTTTCGGAGTAA 59.342 33.333 0.00 0.00 0.00 2.24
2401 2644 9.878667 TGTGATCTTTTATGTTTCGGAGTAATA 57.121 29.630 0.00 0.00 0.00 0.98
2412 2655 8.937634 TGTTTCGGAGTAATATTACTTCCTTC 57.062 34.615 25.25 14.22 43.64 3.46
2416 2659 8.707796 TCGGAGTAATATTACTTCCTTCAGAT 57.292 34.615 25.25 3.42 43.64 2.90
2417 2660 9.803507 TCGGAGTAATATTACTTCCTTCAGATA 57.196 33.333 25.25 8.05 43.64 1.98
2418 2661 9.843334 CGGAGTAATATTACTTCCTTCAGATAC 57.157 37.037 25.25 10.59 43.64 2.24
2442 2685 2.099141 GCTCCAGCTAACATGTCACA 57.901 50.000 0.00 0.00 38.21 3.58
2444 2687 2.813754 GCTCCAGCTAACATGTCACAAA 59.186 45.455 0.00 0.00 38.21 2.83
2449 2692 7.629222 GCTCCAGCTAACATGTCACAAAATATT 60.629 37.037 0.00 0.00 38.21 1.28
2477 2722 2.150397 ACGTGGAGAAGTGCAAGTAC 57.850 50.000 0.00 0.00 35.03 2.73
2516 2761 8.816894 TCATCACCTAAATCCCTTAGATACATC 58.183 37.037 0.00 0.00 39.66 3.06
2524 2769 2.289072 CCCTTAGATACATCGGCAGGTG 60.289 54.545 0.00 0.00 0.00 4.00
2525 2770 2.628178 CCTTAGATACATCGGCAGGTGA 59.372 50.000 3.42 0.00 0.00 4.02
2538 2783 2.289945 GGCAGGTGAGTGAATCTTCAGT 60.290 50.000 0.00 0.00 43.22 3.41
2539 2784 3.406764 GCAGGTGAGTGAATCTTCAGTT 58.593 45.455 1.99 0.00 40.75 3.16
2545 2790 5.210715 GTGAGTGAATCTTCAGTTTGCTTG 58.789 41.667 1.99 0.00 40.75 4.01
2562 2815 2.472488 GCTTGCCTGACGAAACAATTTG 59.528 45.455 0.00 0.00 0.00 2.32
2567 2820 2.293122 CCTGACGAAACAATTTGCCTCA 59.707 45.455 0.00 0.00 0.00 3.86
2575 2828 6.205853 ACGAAACAATTTGCCTCACATACTTA 59.794 34.615 0.00 0.00 0.00 2.24
2578 2831 5.954335 ACAATTTGCCTCACATACTTAAGC 58.046 37.500 1.29 0.00 0.00 3.09
2579 2832 5.711976 ACAATTTGCCTCACATACTTAAGCT 59.288 36.000 1.29 0.00 0.00 3.74
2580 2833 6.209391 ACAATTTGCCTCACATACTTAAGCTT 59.791 34.615 3.48 3.48 0.00 3.74
2583 2836 4.759782 TGCCTCACATACTTAAGCTTCTC 58.240 43.478 0.00 0.00 0.00 2.87
2586 2839 4.407296 CCTCACATACTTAAGCTTCTCCCT 59.593 45.833 0.00 0.00 0.00 4.20
2587 2840 5.598830 CCTCACATACTTAAGCTTCTCCCTA 59.401 44.000 0.00 0.00 0.00 3.53
2588 2841 6.098409 CCTCACATACTTAAGCTTCTCCCTAA 59.902 42.308 0.00 0.00 0.00 2.69
2599 2876 6.313519 AGCTTCTCCCTAACAATGAATGTA 57.686 37.500 0.00 0.00 42.99 2.29
2600 2877 6.352516 AGCTTCTCCCTAACAATGAATGTAG 58.647 40.000 0.00 0.00 42.99 2.74
2601 2878 5.008118 GCTTCTCCCTAACAATGAATGTAGC 59.992 44.000 0.00 0.00 42.99 3.58
2602 2879 5.692115 TCTCCCTAACAATGAATGTAGCA 57.308 39.130 0.00 0.00 42.99 3.49
2604 2881 5.880332 TCTCCCTAACAATGAATGTAGCAAC 59.120 40.000 0.00 0.00 42.99 4.17
2605 2882 4.947388 TCCCTAACAATGAATGTAGCAACC 59.053 41.667 0.00 0.00 42.99 3.77
2613 2890 6.434028 ACAATGAATGTAGCAACCACTTGTAT 59.566 34.615 0.00 0.00 41.63 2.29
2617 2894 8.574251 TGAATGTAGCAACCACTTGTATAATT 57.426 30.769 0.00 0.00 0.00 1.40
2775 3052 0.521242 GCCTACGCGCACAATTCAAG 60.521 55.000 5.73 0.00 0.00 3.02
3020 3299 4.497473 TTTTTGCGGGAAAGACAGTATG 57.503 40.909 0.00 0.00 46.00 2.39
3021 3300 1.448985 TTGCGGGAAAGACAGTATGC 58.551 50.000 0.00 0.00 42.53 3.14
3022 3301 0.323302 TGCGGGAAAGACAGTATGCA 59.677 50.000 0.00 0.00 42.53 3.96
3023 3302 1.065491 TGCGGGAAAGACAGTATGCAT 60.065 47.619 3.79 3.79 42.53 3.96
3024 3303 1.331756 GCGGGAAAGACAGTATGCATG 59.668 52.381 10.16 0.00 42.53 4.06
3104 3383 0.040870 CCGACATCCACGAGAGATCG 60.041 60.000 0.00 0.00 36.19 3.69
3149 3428 0.904865 ACGTGGAGGAGATCAAGGCA 60.905 55.000 0.00 0.00 0.00 4.75
3390 3684 5.348724 CACTGATGATGGCACGTAATATACC 59.651 44.000 0.00 0.00 0.00 2.73
3755 4058 1.899814 TGTGAAATCTAGCCTCACCGT 59.100 47.619 13.05 0.00 38.97 4.83
3869 4208 3.499737 CGGAGGCGGCAACATCAC 61.500 66.667 13.08 0.00 0.00 3.06
3985 4329 0.320421 TTCGAAGCCGCTAAGCAACT 60.320 50.000 0.00 0.00 35.37 3.16
4078 4457 1.068127 CCTAGGTTATGGACGAACGGG 59.932 57.143 0.00 0.00 0.00 5.28
4084 4463 2.116827 TATGGACGAACGGGCAAAAT 57.883 45.000 0.00 0.00 0.00 1.82
4104 4483 5.418310 AATTGGTAGTTCAGACAACAACG 57.582 39.130 0.00 0.00 0.00 4.10
4113 4492 1.394917 CAGACAACAACGCTGATAGCC 59.605 52.381 0.00 0.00 38.18 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.045561 TGTTGACCATTTGACACGGT 57.954 45.000 0.00 0.00 35.12 4.83
45 46 0.439600 GCATTTGCATTTGACACGGC 59.560 50.000 0.00 0.00 41.59 5.68
83 84 9.497030 TGCTTACATACAATAATAAAAGTTGCG 57.503 29.630 0.00 0.00 0.00 4.85
106 115 2.745281 ACGTGCCATTTATAACGTTGCT 59.255 40.909 11.99 0.32 46.27 3.91
107 116 3.125698 ACGTGCCATTTATAACGTTGC 57.874 42.857 11.99 4.18 46.27 4.17
111 120 5.388061 CGGAGATAACGTGCCATTTATAACG 60.388 44.000 0.00 0.00 41.64 3.18
112 121 5.464389 ACGGAGATAACGTGCCATTTATAAC 59.536 40.000 0.00 0.00 43.78 1.89
113 122 5.603596 ACGGAGATAACGTGCCATTTATAA 58.396 37.500 0.00 0.00 43.78 0.98
114 123 5.204409 ACGGAGATAACGTGCCATTTATA 57.796 39.130 0.00 0.00 43.78 0.98
115 124 4.067972 ACGGAGATAACGTGCCATTTAT 57.932 40.909 0.00 0.00 43.78 1.40
116 125 3.530265 ACGGAGATAACGTGCCATTTA 57.470 42.857 0.00 0.00 43.78 1.40
117 126 2.396590 ACGGAGATAACGTGCCATTT 57.603 45.000 0.00 0.00 43.78 2.32
118 127 2.006888 CAACGGAGATAACGTGCCATT 58.993 47.619 0.00 0.00 44.83 3.16
119 128 1.206132 TCAACGGAGATAACGTGCCAT 59.794 47.619 0.00 0.00 44.83 4.40
120 129 0.604073 TCAACGGAGATAACGTGCCA 59.396 50.000 0.00 0.00 44.83 4.92
134 143 4.316446 CGCTGTCGATAACTTATGTCAACG 60.316 45.833 0.00 0.00 38.10 4.10
156 174 1.389106 GCCACTAGCGTAAACTTGACG 59.611 52.381 0.00 0.00 43.19 4.35
178 196 1.070758 GGTCCAGTCAAGACTTGCAGA 59.929 52.381 10.50 4.75 40.20 4.26
181 199 1.230324 GTGGTCCAGTCAAGACTTGC 58.770 55.000 10.50 5.98 40.20 4.01
259 277 2.982130 CCTCAACGCTAGCCTGGT 59.018 61.111 9.66 0.00 0.00 4.00
345 364 4.847990 AACGTGAAATATCCTGGGGTAA 57.152 40.909 0.00 0.00 0.00 2.85
349 368 5.637006 TGAAAAACGTGAAATATCCTGGG 57.363 39.130 0.00 0.00 0.00 4.45
360 379 6.088350 GCGCCTTTTTATATTGAAAAACGTGA 59.912 34.615 0.00 0.00 34.23 4.35
361 380 6.088883 AGCGCCTTTTTATATTGAAAAACGTG 59.911 34.615 2.29 9.22 34.23 4.49
362 381 6.153756 AGCGCCTTTTTATATTGAAAAACGT 58.846 32.000 2.29 0.00 34.23 3.99
363 382 6.626199 AGCGCCTTTTTATATTGAAAAACG 57.374 33.333 2.29 11.01 34.23 3.60
383 405 3.532892 AGTACGTGGAATATCGTAGCG 57.467 47.619 0.00 0.00 41.90 4.26
400 422 1.509463 CTGCCCTTCACGCGTAGTA 59.491 57.895 13.44 0.00 0.00 1.82
401 423 2.261671 CTGCCCTTCACGCGTAGT 59.738 61.111 13.44 0.00 0.00 2.73
402 424 2.509336 CCTGCCCTTCACGCGTAG 60.509 66.667 13.44 6.77 0.00 3.51
455 477 2.584791 GTGTTGGAAGCTGTTATTGCG 58.415 47.619 0.00 0.00 35.28 4.85
515 552 4.084888 CGGCGAGACGGTTTTGCC 62.085 66.667 17.79 17.79 40.99 4.52
554 592 1.058404 GACAGTGACGACGTTTAGCC 58.942 55.000 0.13 0.00 0.00 3.93
562 600 2.214181 ATCAGCGGGACAGTGACGAC 62.214 60.000 0.00 0.00 0.00 4.34
656 694 1.118838 GTGATGGGAGTGAGAGGAGG 58.881 60.000 0.00 0.00 0.00 4.30
875 924 2.032799 GCGATCTATCTATGCCCGAGAG 59.967 54.545 0.00 0.00 0.00 3.20
876 925 2.017782 GCGATCTATCTATGCCCGAGA 58.982 52.381 0.00 0.00 0.00 4.04
879 928 1.745653 TGAGCGATCTATCTATGCCCG 59.254 52.381 0.90 0.00 0.00 6.13
928 984 0.599204 AGAGTTGGTACGTGTTGCGG 60.599 55.000 0.00 0.00 46.52 5.69
932 988 2.227388 CGTAGGAGAGTTGGTACGTGTT 59.773 50.000 0.00 0.00 34.84 3.32
933 989 1.808945 CGTAGGAGAGTTGGTACGTGT 59.191 52.381 0.00 0.00 34.84 4.49
934 990 2.079158 TCGTAGGAGAGTTGGTACGTG 58.921 52.381 0.00 0.00 39.39 4.49
935 991 2.354259 CTCGTAGGAGAGTTGGTACGT 58.646 52.381 6.59 0.00 43.27 3.57
939 995 1.178276 CAGCTCGTAGGAGAGTTGGT 58.822 55.000 16.47 0.00 43.03 3.67
941 997 1.202245 GCTCAGCTCGTAGGAGAGTTG 60.202 57.143 16.47 10.31 46.45 3.16
943 999 1.092921 CGCTCAGCTCGTAGGAGAGT 61.093 60.000 16.47 0.00 43.27 3.24
946 1002 1.646540 CTCGCTCAGCTCGTAGGAG 59.353 63.158 8.10 8.10 43.46 3.69
947 1003 2.473760 GCTCGCTCAGCTCGTAGGA 61.474 63.158 0.00 0.00 45.83 2.94
948 1004 2.025441 GCTCGCTCAGCTCGTAGG 59.975 66.667 0.00 0.00 45.83 3.18
956 1012 4.116328 TCCCGTTCGCTCGCTCAG 62.116 66.667 0.00 0.00 0.00 3.35
957 1013 4.116328 CTCCCGTTCGCTCGCTCA 62.116 66.667 0.00 0.00 0.00 4.26
958 1014 3.743091 CTCTCCCGTTCGCTCGCTC 62.743 68.421 0.00 0.00 0.00 5.03
959 1015 3.816524 CTCTCCCGTTCGCTCGCT 61.817 66.667 0.00 0.00 0.00 4.93
960 1016 3.743091 CTCTCTCCCGTTCGCTCGC 62.743 68.421 0.00 0.00 0.00 5.03
961 1017 2.405594 CTCTCTCCCGTTCGCTCG 59.594 66.667 0.00 0.00 0.00 5.03
962 1018 2.776913 CCCTCTCTCCCGTTCGCTC 61.777 68.421 0.00 0.00 0.00 5.03
971 1027 3.519930 GACGCCGACCCTCTCTCC 61.520 72.222 0.00 0.00 0.00 3.71
982 1038 2.005960 ATCTTCCTTCTCCGACGCCG 62.006 60.000 0.00 0.00 0.00 6.46
985 1041 1.103803 TCCATCTTCCTTCTCCGACG 58.896 55.000 0.00 0.00 0.00 5.12
986 1042 2.695666 TGATCCATCTTCCTTCTCCGAC 59.304 50.000 0.00 0.00 0.00 4.79
987 1043 2.695666 GTGATCCATCTTCCTTCTCCGA 59.304 50.000 0.00 0.00 0.00 4.55
988 1044 2.544694 CGTGATCCATCTTCCTTCTCCG 60.545 54.545 0.00 0.00 0.00 4.63
989 1045 2.804933 GCGTGATCCATCTTCCTTCTCC 60.805 54.545 0.00 0.00 0.00 3.71
990 1046 2.478831 GCGTGATCCATCTTCCTTCTC 58.521 52.381 0.00 0.00 0.00 2.87
991 1047 1.202463 CGCGTGATCCATCTTCCTTCT 60.202 52.381 0.00 0.00 0.00 2.85
992 1048 1.212616 CGCGTGATCCATCTTCCTTC 58.787 55.000 0.00 0.00 0.00 3.46
993 1049 0.179073 CCGCGTGATCCATCTTCCTT 60.179 55.000 4.92 0.00 0.00 3.36
994 1050 1.443407 CCGCGTGATCCATCTTCCT 59.557 57.895 4.92 0.00 0.00 3.36
1240 1328 8.310382 TCTCACAGAAGAAAATTTGAACCAAAA 58.690 29.630 0.00 0.00 36.90 2.44
1241 1329 7.835822 TCTCACAGAAGAAAATTTGAACCAAA 58.164 30.769 0.00 0.00 37.75 3.28
1242 1330 7.403312 TCTCACAGAAGAAAATTTGAACCAA 57.597 32.000 0.00 0.00 0.00 3.67
1243 1331 7.403312 TTCTCACAGAAGAAAATTTGAACCA 57.597 32.000 0.00 0.00 32.42 3.67
1244 1332 8.137437 TCATTCTCACAGAAGAAAATTTGAACC 58.863 33.333 0.00 0.00 37.69 3.62
1245 1333 9.520204 TTCATTCTCACAGAAGAAAATTTGAAC 57.480 29.630 0.00 0.00 37.69 3.18
1247 1335 9.740239 CTTTCATTCTCACAGAAGAAAATTTGA 57.260 29.630 0.00 0.00 37.69 2.69
1248 1336 9.525409 ACTTTCATTCTCACAGAAGAAAATTTG 57.475 29.630 0.00 0.00 37.69 2.32
1252 1340 9.559732 TCATACTTTCATTCTCACAGAAGAAAA 57.440 29.630 9.87 5.00 37.69 2.29
1253 1341 9.730705 ATCATACTTTCATTCTCACAGAAGAAA 57.269 29.630 0.00 0.00 37.69 2.52
1273 1361 5.633830 CCAATAGGCAACCATCATCATAC 57.366 43.478 0.00 0.00 37.17 2.39
1391 1520 4.674281 AGGAAATGGGACGAGAGATAAC 57.326 45.455 0.00 0.00 0.00 1.89
1394 1523 4.576330 AAAAGGAAATGGGACGAGAGAT 57.424 40.909 0.00 0.00 0.00 2.75
1442 1608 1.722507 GTCGTTCGCACAGCAAAGC 60.723 57.895 0.00 0.00 0.00 3.51
1445 1611 3.334751 CGGTCGTTCGCACAGCAA 61.335 61.111 0.00 0.00 0.00 3.91
1554 1721 0.616964 TGAGCAGAGCATGGAGGAGT 60.617 55.000 0.00 0.00 0.00 3.85
1575 1743 4.003648 CTCCTTGACCACATCAAAGGTAC 58.996 47.826 0.00 0.00 46.80 3.34
1580 1748 2.655090 TGCTCCTTGACCACATCAAA 57.345 45.000 0.00 0.00 46.80 2.69
1596 1767 6.536224 CAGAAACAAACAGAGGAAAATTTGCT 59.464 34.615 0.00 0.00 35.83 3.91
1597 1768 6.534793 TCAGAAACAAACAGAGGAAAATTTGC 59.465 34.615 0.00 0.00 35.83 3.68
1598 1769 8.545420 CATCAGAAACAAACAGAGGAAAATTTG 58.455 33.333 0.00 0.00 37.91 2.32
1599 1770 8.477256 TCATCAGAAACAAACAGAGGAAAATTT 58.523 29.630 0.00 0.00 0.00 1.82
1606 1777 5.632347 GCATTTCATCAGAAACAAACAGAGG 59.368 40.000 0.00 0.00 45.79 3.69
1609 1780 4.143473 GCGCATTTCATCAGAAACAAACAG 60.143 41.667 0.30 0.00 45.79 3.16
1611 1782 3.181550 CGCGCATTTCATCAGAAACAAAC 60.182 43.478 8.75 0.00 45.79 2.93
1612 1783 2.979151 CGCGCATTTCATCAGAAACAAA 59.021 40.909 8.75 0.00 45.79 2.83
1630 1809 2.613595 TGATGGAAAATGAAGATCCGCG 59.386 45.455 0.00 0.00 35.96 6.46
1731 1910 6.232581 TGGGTTTGATGAAATTTCTTGTGT 57.767 33.333 18.64 0.83 0.00 3.72
1746 1925 3.510360 TCCGAACAACTTTTTGGGTTTGA 59.490 39.130 0.00 0.00 37.00 2.69
1747 1926 3.851098 TCCGAACAACTTTTTGGGTTTG 58.149 40.909 0.00 0.00 37.00 2.93
1749 1928 3.258622 TGTTCCGAACAACTTTTTGGGTT 59.741 39.130 11.63 0.00 38.72 4.11
1750 1929 2.826725 TGTTCCGAACAACTTTTTGGGT 59.173 40.909 11.63 0.00 38.72 4.51
1751 1930 3.183754 GTGTTCCGAACAACTTTTTGGG 58.816 45.455 15.52 0.00 44.16 4.12
1786 1965 7.279981 GGCAAAAAGGAAAGTAAAATGTGACTT 59.720 33.333 0.00 0.00 37.50 3.01
1792 1971 7.281999 TGAAAGGGCAAAAAGGAAAGTAAAATG 59.718 33.333 0.00 0.00 0.00 2.32
1794 1973 6.712276 TGAAAGGGCAAAAAGGAAAGTAAAA 58.288 32.000 0.00 0.00 0.00 1.52
1798 1977 4.835284 TTGAAAGGGCAAAAAGGAAAGT 57.165 36.364 0.00 0.00 0.00 2.66
1813 1992 1.462670 GCGAGGCTGAGACTTTGAAAG 59.537 52.381 2.89 2.89 0.00 2.62
1825 2022 1.233285 GCATATTCCCTGCGAGGCTG 61.233 60.000 0.00 0.00 32.73 4.85
1826 2023 1.072159 GCATATTCCCTGCGAGGCT 59.928 57.895 0.00 0.00 32.73 4.58
1827 2024 0.952984 GAGCATATTCCCTGCGAGGC 60.953 60.000 0.00 0.00 44.38 4.70
1828 2025 0.394192 TGAGCATATTCCCTGCGAGG 59.606 55.000 0.00 0.00 44.38 4.63
1829 2026 2.469274 ATGAGCATATTCCCTGCGAG 57.531 50.000 0.00 0.00 44.38 5.03
1830 2027 3.165071 TCTATGAGCATATTCCCTGCGA 58.835 45.455 0.00 0.00 44.38 5.10
1831 2028 3.599730 TCTATGAGCATATTCCCTGCG 57.400 47.619 0.00 0.00 44.38 5.18
1832 2029 5.065914 TGTTTCTATGAGCATATTCCCTGC 58.934 41.667 0.00 0.00 39.97 4.85
1850 2047 5.376854 AAACTGTCCATGTAGCATGTTTC 57.623 39.130 8.11 0.00 0.00 2.78
1854 2051 7.325660 AGAAATAAACTGTCCATGTAGCATG 57.674 36.000 2.38 2.38 0.00 4.06
1876 2081 9.466497 AGCAAGAAAATCCATGTAAGAATAAGA 57.534 29.630 0.00 0.00 0.00 2.10
1891 2096 7.414984 CCCAAAGATCTGTAGAGCAAGAAAATC 60.415 40.741 0.00 0.00 31.88 2.17
1892 2097 6.376581 CCCAAAGATCTGTAGAGCAAGAAAAT 59.623 38.462 0.00 0.00 31.88 1.82
1897 2102 4.478206 TCCCAAAGATCTGTAGAGCAAG 57.522 45.455 0.00 0.00 31.88 4.01
1899 2104 4.679373 GATCCCAAAGATCTGTAGAGCA 57.321 45.455 0.00 0.00 46.85 4.26
1992 2216 2.300152 ACTCCCATACATGCAGTATCCG 59.700 50.000 0.00 0.00 41.47 4.18
2027 2255 4.048241 GAGGTCAGGGAACTTCGATTAG 57.952 50.000 0.00 0.00 40.21 1.73
2033 2261 0.680061 ACACGAGGTCAGGGAACTTC 59.320 55.000 0.00 0.00 40.21 3.01
2103 2341 1.466167 ACAAGCTGCAGACAATTAGCG 59.534 47.619 20.43 0.00 40.92 4.26
2166 2404 3.891977 TCATTATGAACTCCCCGAGAGAG 59.108 47.826 9.13 2.56 46.50 3.20
2172 2410 3.819564 TGAGTCATTATGAACTCCCCG 57.180 47.619 16.29 0.00 0.00 5.73
2199 2437 4.935205 GCAGTGTCACACAATACCTTGATA 59.065 41.667 11.40 0.00 36.74 2.15
2208 2446 5.420725 TCCTATTAGCAGTGTCACACAAT 57.579 39.130 11.40 3.58 36.74 2.71
2210 2448 5.046663 TGAATCCTATTAGCAGTGTCACACA 60.047 40.000 11.40 0.00 36.74 3.72
2211 2449 5.419542 TGAATCCTATTAGCAGTGTCACAC 58.580 41.667 0.00 0.00 34.10 3.82
2214 2452 8.486210 AGTAAATGAATCCTATTAGCAGTGTCA 58.514 33.333 0.00 0.00 0.00 3.58
2215 2453 8.894768 AGTAAATGAATCCTATTAGCAGTGTC 57.105 34.615 0.00 0.00 0.00 3.67
2228 2466 9.965824 TGAGTTTTCAGAAAAGTAAATGAATCC 57.034 29.630 14.81 2.08 34.32 3.01
2230 2468 9.750125 GGTGAGTTTTCAGAAAAGTAAATGAAT 57.250 29.630 14.81 0.00 34.32 2.57
2232 2470 8.519799 AGGTGAGTTTTCAGAAAAGTAAATGA 57.480 30.769 14.81 0.00 34.32 2.57
2234 2472 9.847224 TCTAGGTGAGTTTTCAGAAAAGTAAAT 57.153 29.630 14.81 4.54 34.32 1.40
2235 2473 9.326413 CTCTAGGTGAGTTTTCAGAAAAGTAAA 57.674 33.333 14.81 5.36 37.99 2.01
2237 2475 7.442656 CCTCTAGGTGAGTTTTCAGAAAAGTA 58.557 38.462 14.81 0.35 41.11 2.24
2238 2476 6.292150 CCTCTAGGTGAGTTTTCAGAAAAGT 58.708 40.000 14.76 14.76 41.11 2.66
2239 2477 5.180304 GCCTCTAGGTGAGTTTTCAGAAAAG 59.820 44.000 8.67 0.00 41.11 2.27
2251 2494 4.720046 TGAGTAGTATGCCTCTAGGTGAG 58.280 47.826 0.00 0.00 42.30 3.51
2257 2500 7.561722 ACAGATCTTTTGAGTAGTATGCCTCTA 59.438 37.037 0.00 0.00 0.00 2.43
2276 2519 5.798132 TGAAACAACAGAGCATACAGATCT 58.202 37.500 0.00 0.00 45.65 2.75
2277 2520 5.871524 TCTGAAACAACAGAGCATACAGATC 59.128 40.000 0.00 0.00 41.21 2.75
2278 2521 5.798132 TCTGAAACAACAGAGCATACAGAT 58.202 37.500 0.00 0.00 41.21 2.90
2279 2522 5.213891 TCTGAAACAACAGAGCATACAGA 57.786 39.130 0.00 0.00 41.21 3.41
2289 2532 1.393539 CGGCGGTATCTGAAACAACAG 59.606 52.381 0.00 0.00 39.02 3.16
2290 2533 1.001068 TCGGCGGTATCTGAAACAACA 59.999 47.619 7.21 0.00 0.00 3.33
2291 2534 1.717194 TCGGCGGTATCTGAAACAAC 58.283 50.000 7.21 0.00 0.00 3.32
2292 2535 2.459060 TTCGGCGGTATCTGAAACAA 57.541 45.000 7.21 0.00 0.00 2.83
2293 2536 2.343101 CTTTCGGCGGTATCTGAAACA 58.657 47.619 7.21 0.00 36.66 2.83
2294 2537 1.664151 CCTTTCGGCGGTATCTGAAAC 59.336 52.381 7.21 0.00 36.66 2.78
2295 2538 1.551430 TCCTTTCGGCGGTATCTGAAA 59.449 47.619 7.21 0.00 38.58 2.69
2333 2576 0.472471 AGTTCTTGGCGTTCCCTTCA 59.528 50.000 0.00 0.00 0.00 3.02
2342 2585 2.317609 CGTGTCCCAGTTCTTGGCG 61.318 63.158 0.00 0.00 46.32 5.69
2360 2603 1.593196 TCACACACTTTGCAGTAGGC 58.407 50.000 3.37 0.00 45.13 3.93
2374 2617 6.481954 ACTCCGAAACATAAAAGATCACAC 57.518 37.500 0.00 0.00 0.00 3.82
2386 2629 9.543783 GAAGGAAGTAATATTACTCCGAAACAT 57.456 33.333 24.80 9.68 42.86 2.71
2387 2630 8.533657 TGAAGGAAGTAATATTACTCCGAAACA 58.466 33.333 24.80 20.00 42.86 2.83
2388 2631 8.937634 TGAAGGAAGTAATATTACTCCGAAAC 57.062 34.615 24.80 18.50 42.86 2.78
2401 2644 8.425703 GGAGCTTAAGTATCTGAAGGAAGTAAT 58.574 37.037 4.02 0.00 0.00 1.89
2424 2667 5.633830 ATTTTGTGACATGTTAGCTGGAG 57.366 39.130 0.00 0.00 0.00 3.86
2434 2677 9.272901 CGTACCTGTTAAATATTTTGTGACATG 57.727 33.333 5.91 6.69 0.00 3.21
2437 2680 7.747357 CCACGTACCTGTTAAATATTTTGTGAC 59.253 37.037 5.91 2.07 0.00 3.67
2439 2682 7.808672 TCCACGTACCTGTTAAATATTTTGTG 58.191 34.615 5.91 2.70 0.00 3.33
2442 2685 8.851541 TTCTCCACGTACCTGTTAAATATTTT 57.148 30.769 5.91 0.00 0.00 1.82
2444 2687 7.548075 CACTTCTCCACGTACCTGTTAAATATT 59.452 37.037 0.00 0.00 0.00 1.28
2449 2692 3.553508 GCACTTCTCCACGTACCTGTTAA 60.554 47.826 0.00 0.00 0.00 2.01
2498 2743 5.046591 CCTGCCGATGTATCTAAGGGATTTA 60.047 44.000 0.00 0.00 35.98 1.40
2505 2750 3.319405 ACTCACCTGCCGATGTATCTAAG 59.681 47.826 0.00 0.00 0.00 2.18
2507 2752 2.623416 CACTCACCTGCCGATGTATCTA 59.377 50.000 0.00 0.00 0.00 1.98
2516 2761 1.338105 TGAAGATTCACTCACCTGCCG 60.338 52.381 0.00 0.00 31.01 5.69
2524 2769 4.225208 GCAAGCAAACTGAAGATTCACTC 58.775 43.478 0.00 0.00 32.90 3.51
2525 2770 3.005155 GGCAAGCAAACTGAAGATTCACT 59.995 43.478 0.00 0.00 32.90 3.41
2538 2783 1.098869 TGTTTCGTCAGGCAAGCAAA 58.901 45.000 0.00 0.00 0.00 3.68
2539 2784 1.098869 TTGTTTCGTCAGGCAAGCAA 58.901 45.000 0.00 0.00 0.00 3.91
2545 2790 1.000274 AGGCAAATTGTTTCGTCAGGC 60.000 47.619 0.00 0.00 0.00 4.85
2562 2815 4.123506 GGAGAAGCTTAAGTATGTGAGGC 58.876 47.826 0.00 0.00 0.00 4.70
2567 2820 6.869206 TGTTAGGGAGAAGCTTAAGTATGT 57.131 37.500 0.00 0.00 0.00 2.29
2575 2828 5.574188 ACATTCATTGTTAGGGAGAAGCTT 58.426 37.500 0.00 0.00 33.74 3.74
2578 2831 6.115446 TGCTACATTCATTGTTAGGGAGAAG 58.885 40.000 0.00 0.00 39.87 2.85
2579 2832 6.061022 TGCTACATTCATTGTTAGGGAGAA 57.939 37.500 0.00 0.00 39.87 2.87
2580 2833 5.692115 TGCTACATTCATTGTTAGGGAGA 57.308 39.130 0.00 0.00 39.87 3.71
2583 2836 4.704540 TGGTTGCTACATTCATTGTTAGGG 59.295 41.667 0.00 0.00 39.87 3.53
2586 2839 6.264292 ACAAGTGGTTGCTACATTCATTGTTA 59.736 34.615 0.00 0.00 37.16 2.41
2587 2840 5.068987 ACAAGTGGTTGCTACATTCATTGTT 59.931 36.000 0.00 0.00 37.16 2.83
2588 2841 4.584325 ACAAGTGGTTGCTACATTCATTGT 59.416 37.500 0.00 1.49 38.60 2.71
2599 2876 6.714810 TGACAAGAATTATACAAGTGGTTGCT 59.285 34.615 0.00 0.00 37.14 3.91
2600 2877 6.801862 GTGACAAGAATTATACAAGTGGTTGC 59.198 38.462 0.00 0.00 37.14 4.17
2601 2878 7.870826 TGTGACAAGAATTATACAAGTGGTTG 58.129 34.615 0.00 0.00 39.82 3.77
2602 2879 8.349983 GTTGTGACAAGAATTATACAAGTGGTT 58.650 33.333 0.00 0.00 29.30 3.67
2604 2881 7.870826 TGTTGTGACAAGAATTATACAAGTGG 58.129 34.615 0.00 0.00 31.49 4.00
2617 2894 5.994668 TGCAGTGTTATATGTTGTGACAAGA 59.005 36.000 0.00 0.00 39.66 3.02
2775 3052 1.730547 GTGCAATTGGACGTGCTGC 60.731 57.895 14.63 10.72 41.48 5.25
2953 3232 1.135721 GGACATGAAATTCTGGCCAGC 59.864 52.381 28.91 14.10 40.55 4.85
2954 3233 1.402968 CGGACATGAAATTCTGGCCAG 59.597 52.381 27.87 27.87 40.92 4.85
2999 3278 3.305064 GCATACTGTCTTTCCCGCAAAAA 60.305 43.478 0.00 0.00 0.00 1.94
3000 3279 2.227865 GCATACTGTCTTTCCCGCAAAA 59.772 45.455 0.00 0.00 0.00 2.44
3001 3280 1.810151 GCATACTGTCTTTCCCGCAAA 59.190 47.619 0.00 0.00 0.00 3.68
3002 3281 1.271108 TGCATACTGTCTTTCCCGCAA 60.271 47.619 0.00 0.00 0.00 4.85
3003 3282 0.323302 TGCATACTGTCTTTCCCGCA 59.677 50.000 0.00 0.00 0.00 5.69
3004 3283 1.331756 CATGCATACTGTCTTTCCCGC 59.668 52.381 0.00 0.00 0.00 6.13
3005 3284 2.632377 ACATGCATACTGTCTTTCCCG 58.368 47.619 0.00 0.00 0.00 5.14
3006 3285 4.009675 TCAACATGCATACTGTCTTTCCC 58.990 43.478 0.00 0.00 0.00 3.97
3007 3286 4.455533 TGTCAACATGCATACTGTCTTTCC 59.544 41.667 0.00 0.00 0.00 3.13
3008 3287 5.180117 AGTGTCAACATGCATACTGTCTTTC 59.820 40.000 0.00 0.00 0.00 2.62
3009 3288 5.065914 AGTGTCAACATGCATACTGTCTTT 58.934 37.500 0.00 0.00 0.00 2.52
3010 3289 4.645535 AGTGTCAACATGCATACTGTCTT 58.354 39.130 0.00 0.00 0.00 3.01
3011 3290 4.277515 AGTGTCAACATGCATACTGTCT 57.722 40.909 0.00 0.00 0.00 3.41
3012 3291 4.378770 CCAAGTGTCAACATGCATACTGTC 60.379 45.833 0.00 0.00 0.00 3.51
3013 3292 3.503363 CCAAGTGTCAACATGCATACTGT 59.497 43.478 0.00 0.00 0.00 3.55
3014 3293 3.503363 ACCAAGTGTCAACATGCATACTG 59.497 43.478 0.00 0.00 0.00 2.74
3015 3294 3.754965 ACCAAGTGTCAACATGCATACT 58.245 40.909 0.00 0.00 0.00 2.12
3016 3295 4.503741 AACCAAGTGTCAACATGCATAC 57.496 40.909 0.00 0.00 0.00 2.39
3017 3296 5.301551 AGAAAACCAAGTGTCAACATGCATA 59.698 36.000 0.00 0.00 0.00 3.14
3018 3297 4.099881 AGAAAACCAAGTGTCAACATGCAT 59.900 37.500 0.00 0.00 0.00 3.96
3019 3298 3.446873 AGAAAACCAAGTGTCAACATGCA 59.553 39.130 0.00 0.00 0.00 3.96
3020 3299 3.798337 CAGAAAACCAAGTGTCAACATGC 59.202 43.478 0.00 0.00 0.00 4.06
3021 3300 3.798337 GCAGAAAACCAAGTGTCAACATG 59.202 43.478 0.00 0.00 0.00 3.21
3022 3301 3.489059 CGCAGAAAACCAAGTGTCAACAT 60.489 43.478 0.00 0.00 0.00 2.71
3023 3302 2.159448 CGCAGAAAACCAAGTGTCAACA 60.159 45.455 0.00 0.00 0.00 3.33
3024 3303 2.159435 ACGCAGAAAACCAAGTGTCAAC 60.159 45.455 0.00 0.00 0.00 3.18
3149 3428 3.450115 GCCTCCTCCGCGTACAGT 61.450 66.667 4.92 0.00 0.00 3.55
3179 3458 1.563435 CCGCCGATCATCATGCAGAC 61.563 60.000 0.00 0.00 0.00 3.51
3390 3684 5.295292 CAGCTGGAAACATGTAGTTATGGAG 59.705 44.000 5.57 0.00 40.26 3.86
3477 3771 4.751060 AGATAATGCATGCAACCAAACAG 58.249 39.130 26.68 0.00 0.00 3.16
3530 3826 2.609244 CCACCCTATTTGCAACCAAACG 60.609 50.000 0.00 0.00 43.20 3.60
3755 4058 1.605453 GGTGGCCGAGTAAATGGGA 59.395 57.895 0.00 0.00 0.00 4.37
3774 4090 2.104170 AGTGCTTGTCCTAGAGCTACC 58.896 52.381 3.15 0.00 39.60 3.18
3869 4208 4.834453 CTGCTGCCGGCTGGAGAG 62.834 72.222 39.70 24.91 42.39 3.20
4078 4457 5.587289 TGTTGTCTGAACTACCAATTTTGC 58.413 37.500 0.00 0.00 31.13 3.68
4084 4463 2.610374 GCGTTGTTGTCTGAACTACCAA 59.390 45.455 0.00 0.00 31.13 3.67
4104 4483 0.175760 TCTGAACCACGGCTATCAGC 59.824 55.000 8.51 0.00 39.27 4.26
4113 4492 0.320683 TGAGGCATGTCTGAACCACG 60.321 55.000 3.48 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.