Multiple sequence alignment - TraesCS3A01G526800

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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 TraesCS3A01G526800 chr3A 100.000 8553 0 0 1 8553 740357496 740348944 0.000000e+00 15795.0
1 TraesCS3A01G526800 chr3A 90.883 351 25 7 8204 8553 63069447 63069791 1.680000e-126 464.0
2 TraesCS3A01G526800 chr3A 89.320 103 7 2 1378 1480 740355669 740355571 9.010000e-25 126.0
3 TraesCS3A01G526800 chr3A 89.320 103 7 2 1828 1926 740356119 740356017 9.010000e-25 126.0
4 TraesCS3A01G526800 chr3B 95.254 5331 207 23 2928 8224 817826184 817820866 0.000000e+00 8401.0
5 TraesCS3A01G526800 chr3B 87.095 1511 77 48 401 1826 817828773 817827296 0.000000e+00 1602.0
6 TraesCS3A01G526800 chr3B 88.494 1069 49 27 401 1414 817836434 817835385 0.000000e+00 1225.0
7 TraesCS3A01G526800 chr3B 94.200 500 22 4 2371 2866 817826681 817826185 0.000000e+00 756.0
8 TraesCS3A01G526800 chr3B 92.286 350 22 4 8204 8553 817820843 817820499 7.710000e-135 492.0
9 TraesCS3A01G526800 chr3B 93.215 339 16 5 1956 2293 817827015 817826683 7.710000e-135 492.0
10 TraesCS3A01G526800 chr3B 93.281 253 17 0 7954 8206 370553799 370553547 2.920000e-99 374.0
11 TraesCS3A01G526800 chr3B 84.293 382 50 9 2 375 817829274 817828895 1.750000e-96 364.0
12 TraesCS3A01G526800 chr3B 83.770 382 52 9 2 375 817836935 817836556 3.800000e-93 353.0
13 TraesCS3A01G526800 chr3B 98.000 100 1 1 1828 1927 817827257 817827159 1.140000e-38 172.0
14 TraesCS3A01G526800 chr3B 90.291 103 6 2 1828 1926 817827772 817827670 1.940000e-26 132.0
15 TraesCS3A01G526800 chr3B 95.833 72 2 1 2305 2376 566185593 566185523 1.950000e-21 115.0
16 TraesCS3A01G526800 chr3B 96.970 66 2 0 2305 2370 312180504 312180569 2.520000e-20 111.0
17 TraesCS3A01G526800 chr3B 97.826 46 1 0 5665 5710 675295616 675295661 7.120000e-11 80.5
18 TraesCS3A01G526800 chr3D 98.164 3431 53 3 4783 8206 608068593 608065166 0.000000e+00 5978.0
19 TraesCS3A01G526800 chr3D 94.811 2428 88 11 2375 4776 608071168 608068753 0.000000e+00 3751.0
20 TraesCS3A01G526800 chr3D 88.112 1430 81 34 577 1955 608073009 608071618 0.000000e+00 1616.0
21 TraesCS3A01G526800 chr3D 97.450 353 6 2 8204 8553 608065125 608064773 4.420000e-167 599.0
22 TraesCS3A01G526800 chr3D 82.828 297 33 9 1996 2279 608071445 608071154 5.130000e-62 250.0
23 TraesCS3A01G526800 chr3D 89.362 141 12 1 1973 2113 608071527 608071390 3.170000e-39 174.0
24 TraesCS3A01G526800 chr3D 88.696 115 9 2 1366 1480 608071758 608071648 4.160000e-28 137.0
25 TraesCS3A01G526800 chr3D 98.462 65 1 0 2305 2369 564548039 564547975 1.950000e-21 115.0
26 TraesCS3A01G526800 chr3D 86.076 79 3 6 5669 5740 372629454 372629531 2.560000e-10 78.7
27 TraesCS3A01G526800 chr3D 84.615 78 4 4 5670 5740 372629531 372629455 4.280000e-08 71.3
28 TraesCS3A01G526800 chr2A 92.023 351 21 7 8204 8553 599426111 599425767 3.590000e-133 486.0
29 TraesCS3A01G526800 chr2A 92.157 255 20 0 7952 8206 599426406 599426152 2.270000e-95 361.0
30 TraesCS3A01G526800 chr7B 91.738 351 22 7 8204 8553 587653680 587654024 1.670000e-131 481.0
31 TraesCS3A01G526800 chr7B 91.168 351 24 6 8204 8553 241773971 241773627 3.610000e-128 470.0
32 TraesCS3A01G526800 chr7B 92.095 253 20 0 7954 8206 587653387 587653639 2.940000e-94 357.0
33 TraesCS3A01G526800 chr7B 95.714 70 3 0 2305 2374 623567294 623567363 7.020000e-21 113.0
34 TraesCS3A01G526800 chr5A 91.168 351 24 7 8204 8553 237958715 237959059 3.610000e-128 470.0
35 TraesCS3A01G526800 chr5A 92.095 253 19 1 7954 8206 8043608 8043859 1.060000e-93 355.0
36 TraesCS3A01G526800 chr5A 91.700 253 20 1 7954 8206 7959902 7960153 4.910000e-92 350.0
37 TraesCS3A01G526800 chr6A 90.598 351 26 7 8204 8553 123505919 123506263 7.820000e-125 459.0
38 TraesCS3A01G526800 chr6A 90.274 329 25 7 8226 8553 283034647 283034969 2.850000e-114 424.0
39 TraesCS3A01G526800 chr6A 90.805 261 23 1 7946 8206 123505619 123505878 1.770000e-91 348.0
40 TraesCS3A01G526800 chr7A 91.829 257 20 1 7950 8206 702619782 702619527 2.940000e-94 357.0
41 TraesCS3A01G526800 chr7A 95.652 69 3 0 2305 2373 459178926 459178994 2.520000e-20 111.0
42 TraesCS3A01G526800 chr1B 78.736 348 66 8 4394 4738 17355371 17355029 8.640000e-55 226.0
43 TraesCS3A01G526800 chr1B 79.217 332 61 8 4410 4738 16921231 16920905 3.110000e-54 224.0
44 TraesCS3A01G526800 chr1B 87.629 97 8 3 1174 1268 17358275 17358181 9.080000e-20 110.0
45 TraesCS3A01G526800 chr1A 79.118 340 56 11 4410 4738 13672905 13672570 4.020000e-53 220.0
46 TraesCS3A01G526800 chr1A 78.694 291 36 16 1000 1268 13676213 13675927 4.110000e-38 171.0
47 TraesCS3A01G526800 chr1D 78.371 356 62 11 4394 4738 11547151 11546800 5.200000e-52 217.0
48 TraesCS3A01G526800 chr1D 79.433 282 41 13 1000 1268 11550514 11550237 5.270000e-42 183.0
49 TraesCS3A01G526800 chr7D 95.833 72 3 0 2305 2376 301326485 301326414 5.420000e-22 117.0
50 TraesCS3A01G526800 chr6B 96.970 66 2 0 2304 2369 27942462 27942397 2.520000e-20 111.0
51 TraesCS3A01G526800 chr6B 95.833 48 2 0 5666 5713 616933654 616933607 2.560000e-10 78.7
52 TraesCS3A01G526800 chr6B 91.304 46 4 0 5668 5713 668427352 668427397 7.170000e-06 63.9
53 TraesCS3A01G526800 chr2D 94.521 73 3 1 2305 2377 25046818 25046747 2.520000e-20 111.0
54 TraesCS3A01G526800 chr2D 94.000 50 2 1 5666 5715 530555143 530555095 3.310000e-09 75.0
55 TraesCS3A01G526800 chr2B 96.970 66 2 0 2305 2370 629019368 629019303 2.520000e-20 111.0
56 TraesCS3A01G526800 chr2B 83.951 81 9 2 5670 5749 745861459 745861382 3.310000e-09 75.0


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 TraesCS3A01G526800 chr3A 740348944 740357496 8552 True 5349.000000 15795 92.880000 1 8553 3 chr3A.!!$R1 8552
1 TraesCS3A01G526800 chr3B 817820499 817829274 8775 True 1551.375000 8401 91.829250 2 8553 8 chr3B.!!$R3 8551
2 TraesCS3A01G526800 chr3B 817835385 817836935 1550 True 789.000000 1225 86.132000 2 1414 2 chr3B.!!$R4 1412
3 TraesCS3A01G526800 chr3D 608064773 608073009 8236 True 1786.428571 5978 91.346143 577 8553 7 chr3D.!!$R3 7976
4 TraesCS3A01G526800 chr2A 599425767 599426406 639 True 423.500000 486 92.090000 7952 8553 2 chr2A.!!$R1 601
5 TraesCS3A01G526800 chr7B 587653387 587654024 637 False 419.000000 481 91.916500 7954 8553 2 chr7B.!!$F2 599
6 TraesCS3A01G526800 chr6A 123505619 123506263 644 False 403.500000 459 90.701500 7946 8553 2 chr6A.!!$F2 607

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
399 484 0.247185 TAACACGACCCTTTAGGCCG 59.753 55.000 0.00 7.09 40.58 6.13 F
2320 2783 0.685660 AAGAAGTGGTCGGACCCTTC 59.314 55.000 30.71 30.71 41.64 3.46 F
2360 2823 0.671781 GAGCTATATGCACCGGGCTG 60.672 60.000 6.32 0.00 45.94 4.85 F
2469 2932 0.681175 GGTGAAATGGTGGCTGCTTT 59.319 50.000 0.00 0.00 0.00 3.51 F
2908 3403 1.240641 TTATGCAAGCACGTGGGTGG 61.241 55.000 18.88 2.45 44.54 4.61 F
2919 3414 2.091541 ACGTGGGTGGCATAATCTTTG 58.908 47.619 0.00 0.00 0.00 2.77 F
3094 3589 2.103771 TCATGAGTCTGGAGCTATTGGC 59.896 50.000 0.00 0.00 42.19 4.52 F
3984 4479 2.575532 TGCTGGGAACTCTTTGACAAG 58.424 47.619 0.00 0.00 0.00 3.16 F
4462 4957 2.739609 GCAAAAGCTTGAAACTGCCAGT 60.740 45.455 0.00 0.00 34.14 4.00 F
4605 5100 3.434167 CCAGTGCTATAAACATCCTGGCT 60.434 47.826 0.00 0.00 32.42 4.75 F
5326 5975 3.822594 TGTGTACGTGATCAAAATGGC 57.177 42.857 0.00 0.00 0.00 4.40 F
7421 8098 6.260377 CAGATGTAATGGCATGTTGTTGTAG 58.740 40.000 0.00 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 2798 0.035458 GGTGCATATAGCTCCCGCTT 59.965 55.000 0.00 0.0 46.47 4.68 R
3991 4486 0.609131 CACCTGGCGAAGTGGGAAAT 60.609 55.000 0.00 0.0 0.00 2.17 R
4027 4522 2.541120 GCTGCGATCCACATGCCTC 61.541 63.158 0.00 0.0 0.00 4.70 R
4462 4957 7.330700 GTGAAAACCATGTCTTTTTCTTCAACA 59.669 33.333 18.11 0.0 40.76 3.33 R
4492 4987 2.211806 GTGAGAGCTTGAGGCATGATC 58.788 52.381 0.00 0.0 44.79 2.92 R
4583 5078 2.880890 GCCAGGATGTTTATAGCACTGG 59.119 50.000 0.00 0.0 45.11 4.00 R
4681 5176 3.240134 GAGTGCCAAGACTCGCCCA 62.240 63.158 0.00 0.0 33.39 5.36 R
5593 6242 2.886523 TGTAGCAAGCAAGCAAACAGAT 59.113 40.909 3.19 0.0 36.85 2.90 R
6449 7119 2.497792 ATCGCTCATGGGGTTTGCCA 62.498 55.000 0.00 0.0 36.17 4.92 R
6533 7203 7.040478 CCAAAGGATAAACACTTCTCAATGACA 60.040 37.037 0.00 0.0 0.00 3.58 R
6969 7639 0.035458 AAGCGTATAGGGCTCATGGC 59.965 55.000 0.00 0.0 40.53 4.40 R
8269 9003 0.244178 GACCTTCCTCACGGACTGTC 59.756 60.000 0.00 0.0 39.60 3.51 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
27 28 4.240096 CATCTGGCTTTACTGGCAAAAAG 58.760 43.478 14.53 14.53 41.92 2.27
37 38 7.537649 GCTTTACTGGCAAAAAGAGTATAACAC 59.462 37.037 20.36 2.22 35.19 3.32
39 40 9.781633 TTTACTGGCAAAAAGAGTATAACACTA 57.218 29.630 0.00 0.00 37.72 2.74
41 42 7.450903 ACTGGCAAAAAGAGTATAACACTAGT 58.549 34.615 0.00 0.00 37.72 2.57
46 47 8.879759 GCAAAAAGAGTATAACACTAGTATGCA 58.120 33.333 0.00 0.00 37.72 3.96
79 80 7.654022 AAAAGACCCTCATAAAGACAAAACA 57.346 32.000 0.00 0.00 0.00 2.83
87 88 7.260603 CCTCATAAAGACAAAACATTCATCCC 58.739 38.462 0.00 0.00 0.00 3.85
126 128 6.582636 TCGTCATCTTGGCTTTCTTACATAT 58.417 36.000 0.00 0.00 0.00 1.78
127 129 7.047891 TCGTCATCTTGGCTTTCTTACATATT 58.952 34.615 0.00 0.00 0.00 1.28
163 167 0.620030 GTTAAAACCCCCGCCCTCTA 59.380 55.000 0.00 0.00 0.00 2.43
169 173 2.511452 CCCCCGCCCTCTACATCAG 61.511 68.421 0.00 0.00 0.00 2.90
193 198 4.732784 GTGATGCACACGACCATTTTTAT 58.267 39.130 0.00 0.00 39.78 1.40
204 209 9.308318 ACACGACCATTTTTATTAATTATTGGC 57.692 29.630 0.00 0.00 0.00 4.52
205 210 9.307121 CACGACCATTTTTATTAATTATTGGCA 57.693 29.630 0.00 0.00 0.00 4.92
206 211 9.877178 ACGACCATTTTTATTAATTATTGGCAA 57.123 25.926 0.68 0.68 0.00 4.52
226 232 8.228035 TGGCAAAGTACATAACAAAGTAAACT 57.772 30.769 0.00 0.00 0.00 2.66
228 234 9.603298 GGCAAAGTACATAACAAAGTAAACTAC 57.397 33.333 0.00 0.00 0.00 2.73
233 239 6.695292 ACATAACAAAGTAAACTACGACCG 57.305 37.500 0.00 0.00 0.00 4.79
242 248 6.212888 AGTAAACTACGACCGAACCATTAT 57.787 37.500 0.00 0.00 0.00 1.28
252 258 7.663827 ACGACCGAACCATTATAAGATATGAA 58.336 34.615 0.00 0.00 0.00 2.57
279 285 7.539034 AAAACACCTAATGACTAAATTGGCT 57.461 32.000 0.00 0.00 0.00 4.75
282 288 7.539034 ACACCTAATGACTAAATTGGCTTTT 57.461 32.000 0.00 0.00 0.00 2.27
304 311 1.875963 GCAGCAGCGCCTTTAAGAA 59.124 52.632 2.29 0.00 0.00 2.52
349 356 1.067199 GCCACGTACGGTTGTAGACG 61.067 60.000 21.06 0.00 0.00 4.18
361 368 3.243002 GGTTGTAGACGACCGAGATAAGG 60.243 52.174 3.27 0.00 40.35 2.69
366 373 3.285484 AGACGACCGAGATAAGGCTTTA 58.715 45.455 4.45 0.00 0.00 1.85
367 374 3.890147 AGACGACCGAGATAAGGCTTTAT 59.110 43.478 4.45 0.00 32.19 1.40
374 459 7.384115 CGACCGAGATAAGGCTTTATTTTCATA 59.616 37.037 4.45 0.00 29.67 2.15
386 471 7.855904 GGCTTTATTTTCATATCCAGTAACACG 59.144 37.037 0.00 0.00 0.00 4.49
393 478 4.468510 TCATATCCAGTAACACGACCCTTT 59.531 41.667 0.00 0.00 0.00 3.11
394 479 5.657745 TCATATCCAGTAACACGACCCTTTA 59.342 40.000 0.00 0.00 0.00 1.85
396 481 2.564062 TCCAGTAACACGACCCTTTAGG 59.436 50.000 0.00 0.00 43.78 2.69
398 483 1.277273 AGTAACACGACCCTTTAGGCC 59.723 52.381 0.00 0.00 40.58 5.19
399 484 0.247185 TAACACGACCCTTTAGGCCG 59.753 55.000 0.00 7.09 40.58 6.13
408 511 0.800631 CCTTTAGGCCGTCGGTTTTC 59.199 55.000 13.94 0.69 0.00 2.29
429 532 3.254166 TCTGGCAGAAGCAATGTTCTTTC 59.746 43.478 16.28 0.00 44.61 2.62
430 533 3.225104 TGGCAGAAGCAATGTTCTTTCT 58.775 40.909 0.00 0.00 44.61 2.52
443 546 5.666969 TGTTCTTTCTCAAACACGGTATG 57.333 39.130 0.00 0.00 30.73 2.39
445 548 4.002906 TCTTTCTCAAACACGGTATGCT 57.997 40.909 0.00 0.00 0.00 3.79
446 549 4.385825 TCTTTCTCAAACACGGTATGCTT 58.614 39.130 0.00 0.00 0.00 3.91
453 556 3.969117 AACACGGTATGCTTGCATATG 57.031 42.857 16.86 13.65 0.00 1.78
454 557 2.221169 ACACGGTATGCTTGCATATGG 58.779 47.619 16.86 13.84 0.00 2.74
456 559 2.618241 CACGGTATGCTTGCATATGGTT 59.382 45.455 16.86 2.01 0.00 3.67
459 562 5.641636 CACGGTATGCTTGCATATGGTTATA 59.358 40.000 16.86 0.00 0.00 0.98
461 570 5.220397 CGGTATGCTTGCATATGGTTATACG 60.220 44.000 16.86 8.97 0.00 3.06
465 574 6.685527 TGCTTGCATATGGTTATACGAAAA 57.314 33.333 4.56 0.00 0.00 2.29
467 576 6.317642 TGCTTGCATATGGTTATACGAAAACT 59.682 34.615 4.56 0.00 0.00 2.66
505 615 6.975197 TCAAATTTCGCACACAATACAAAAGA 59.025 30.769 0.00 0.00 0.00 2.52
716 853 1.153568 GGCCGTCGTACTTAACCCC 60.154 63.158 0.00 0.00 0.00 4.95
743 880 2.182030 CCCGGACAGCGACTTCTC 59.818 66.667 0.73 0.00 0.00 2.87
744 881 2.344203 CCCGGACAGCGACTTCTCT 61.344 63.158 0.73 0.00 0.00 3.10
745 882 1.137825 CCGGACAGCGACTTCTCTC 59.862 63.158 0.00 0.00 0.00 3.20
746 883 1.226156 CGGACAGCGACTTCTCTCG 60.226 63.158 0.00 0.00 36.70 4.04
752 889 2.492090 CGACTTCTCTCGCCCCAG 59.508 66.667 0.00 0.00 0.00 4.45
909 1068 3.935828 GCTGAATCCTACCAAGTTCTGTC 59.064 47.826 0.00 0.00 0.00 3.51
917 1076 4.213482 CCTACCAAGTTCTGTCCTTTTTCG 59.787 45.833 0.00 0.00 0.00 3.46
918 1077 3.617284 ACCAAGTTCTGTCCTTTTTCGT 58.383 40.909 0.00 0.00 0.00 3.85
955 1114 2.828128 GCGGTGGCATAGCAGCTTC 61.828 63.158 0.00 0.00 39.62 3.86
959 1118 1.587547 GTGGCATAGCAGCTTCCTAC 58.412 55.000 0.00 0.00 34.17 3.18
984 1143 3.676605 CCGCCGGGTTTGGGTTTC 61.677 66.667 2.18 0.00 0.00 2.78
985 1144 2.596338 CGCCGGGTTTGGGTTTCT 60.596 61.111 2.18 0.00 0.00 2.52
1436 1625 7.453126 TCTCTTTCAGGTAGTTCTTCTGAAGAT 59.547 37.037 19.93 9.51 44.83 2.40
1440 1629 6.853720 TCAGGTAGTTCTTCTGAAGATTACG 58.146 40.000 19.93 13.02 37.38 3.18
1497 1686 5.064325 CACATGTCACAGTGTTCTGGATATG 59.936 44.000 13.24 13.24 45.14 1.78
1499 1688 3.261643 TGTCACAGTGTTCTGGATATGCT 59.738 43.478 0.00 0.00 45.14 3.79
1507 1707 6.370994 CAGTGTTCTGGATATGCTATTGGATC 59.629 42.308 0.00 0.00 37.97 3.36
1508 1708 5.349817 GTGTTCTGGATATGCTATTGGATCG 59.650 44.000 0.00 0.00 0.00 3.69
1515 1715 5.877012 GGATATGCTATTGGATCGTGTCAAT 59.123 40.000 1.38 1.38 37.38 2.57
1521 1721 1.441738 TGGATCGTGTCAATGCTGTG 58.558 50.000 0.00 0.00 0.00 3.66
1547 1747 6.864342 TGCTAATGTTCTGGTCTAGTAAGTC 58.136 40.000 0.00 0.00 0.00 3.01
1550 1750 7.489757 GCTAATGTTCTGGTCTAGTAAGTCTTG 59.510 40.741 0.00 0.00 0.00 3.02
1554 1754 6.151312 TGTTCTGGTCTAGTAAGTCTTGCTAG 59.849 42.308 24.32 24.32 44.33 3.42
1559 1759 5.449451 GGTCTAGTAAGTCTTGCTAGCTGTC 60.449 48.000 25.08 16.79 43.17 3.51
1642 1859 3.305676 CCAGAGTTCATGTTCGTCTGAGT 60.306 47.826 14.58 0.00 37.43 3.41
1678 1895 1.494721 AGCTGGTATTGGGGTGTATGG 59.505 52.381 0.00 0.00 0.00 2.74
1708 1925 6.311200 GTCACTGCACTTTTTGTTTCTGAATT 59.689 34.615 0.00 0.00 0.00 2.17
1723 1940 1.268265 GAATTGAATTGTTCGGGCGC 58.732 50.000 0.00 0.00 0.00 6.53
1741 1958 5.562506 GGCGCTACTGATAGTGACATATA 57.437 43.478 7.64 0.00 45.12 0.86
1745 1962 6.404844 GCGCTACTGATAGTGACATATACCAT 60.405 42.308 0.00 0.00 40.79 3.55
1793 2010 3.966979 TGTCCGGGTGTTACTGATAGTA 58.033 45.455 0.00 0.00 0.00 1.82
1794 2011 3.696051 TGTCCGGGTGTTACTGATAGTAC 59.304 47.826 0.00 0.00 28.93 2.73
1943 2261 1.968493 TGTTAGAGAGGTTGCGGAGTT 59.032 47.619 0.00 0.00 0.00 3.01
1946 2264 1.048601 AGAGAGGTTGCGGAGTTTGA 58.951 50.000 0.00 0.00 0.00 2.69
1949 2267 2.154462 AGAGGTTGCGGAGTTTGATTG 58.846 47.619 0.00 0.00 0.00 2.67
1951 2269 0.958822 GGTTGCGGAGTTTGATTGGT 59.041 50.000 0.00 0.00 0.00 3.67
2027 2419 9.971744 CTTTTTGTTTCTGAATCGAATTGTTTT 57.028 25.926 0.00 0.00 0.00 2.43
2054 2446 8.721133 TGGGTGTTACTGATAGTGATATATGT 57.279 34.615 0.00 0.00 0.00 2.29
2078 2470 3.814283 AGCTGCTCTTTTTGTCTCTGAAG 59.186 43.478 0.00 0.00 0.00 3.02
2115 2507 6.965500 GGTGTTACCGATAGTGATATATGTCG 59.035 42.308 0.00 0.00 0.00 4.35
2179 2642 3.172339 AGATGGTTCAAGCTCTGACTCT 58.828 45.455 0.00 0.00 32.21 3.24
2286 2749 5.561725 GCAAGTTGTTGACCAATTCTCTCTC 60.562 44.000 4.48 0.00 35.46 3.20
2287 2750 5.559148 AGTTGTTGACCAATTCTCTCTCT 57.441 39.130 0.00 0.00 35.02 3.10
2288 2751 5.546526 AGTTGTTGACCAATTCTCTCTCTC 58.453 41.667 0.00 0.00 35.02 3.20
2289 2752 5.306678 AGTTGTTGACCAATTCTCTCTCTCT 59.693 40.000 0.00 0.00 35.02 3.10
2290 2753 5.398603 TGTTGACCAATTCTCTCTCTCTC 57.601 43.478 0.00 0.00 0.00 3.20
2291 2754 5.083122 TGTTGACCAATTCTCTCTCTCTCT 58.917 41.667 0.00 0.00 0.00 3.10
2292 2755 5.184864 TGTTGACCAATTCTCTCTCTCTCTC 59.815 44.000 0.00 0.00 0.00 3.20
2293 2756 5.191727 TGACCAATTCTCTCTCTCTCTCT 57.808 43.478 0.00 0.00 0.00 3.10
2294 2757 5.192927 TGACCAATTCTCTCTCTCTCTCTC 58.807 45.833 0.00 0.00 0.00 3.20
2295 2758 5.044919 TGACCAATTCTCTCTCTCTCTCTCT 60.045 44.000 0.00 0.00 0.00 3.10
2296 2759 5.440610 ACCAATTCTCTCTCTCTCTCTCTC 58.559 45.833 0.00 0.00 0.00 3.20
2297 2760 5.192522 ACCAATTCTCTCTCTCTCTCTCTCT 59.807 44.000 0.00 0.00 0.00 3.10
2298 2761 5.762218 CCAATTCTCTCTCTCTCTCTCTCTC 59.238 48.000 0.00 0.00 0.00 3.20
2299 2762 6.351711 CAATTCTCTCTCTCTCTCTCTCTCA 58.648 44.000 0.00 0.00 0.00 3.27
2300 2763 6.566079 ATTCTCTCTCTCTCTCTCTCTCAA 57.434 41.667 0.00 0.00 0.00 3.02
2301 2764 6.373005 TTCTCTCTCTCTCTCTCTCTCAAA 57.627 41.667 0.00 0.00 0.00 2.69
2302 2765 6.373005 TCTCTCTCTCTCTCTCTCTCAAAA 57.627 41.667 0.00 0.00 0.00 2.44
2303 2766 6.409704 TCTCTCTCTCTCTCTCTCTCAAAAG 58.590 44.000 0.00 0.00 0.00 2.27
2304 2767 6.213397 TCTCTCTCTCTCTCTCTCTCAAAAGA 59.787 42.308 0.00 0.00 0.00 2.52
2305 2768 6.778821 TCTCTCTCTCTCTCTCTCAAAAGAA 58.221 40.000 0.00 0.00 0.00 2.52
2306 2769 6.881065 TCTCTCTCTCTCTCTCTCAAAAGAAG 59.119 42.308 0.00 0.00 0.00 2.85
2307 2770 6.542821 TCTCTCTCTCTCTCTCAAAAGAAGT 58.457 40.000 0.00 0.00 0.00 3.01
2308 2771 6.430925 TCTCTCTCTCTCTCTCAAAAGAAGTG 59.569 42.308 0.00 0.00 0.00 3.16
2309 2772 5.476599 TCTCTCTCTCTCTCAAAAGAAGTGG 59.523 44.000 0.00 0.00 0.00 4.00
2310 2773 5.144100 TCTCTCTCTCTCAAAAGAAGTGGT 58.856 41.667 0.00 0.00 0.00 4.16
2311 2774 5.242838 TCTCTCTCTCTCAAAAGAAGTGGTC 59.757 44.000 0.00 0.00 0.00 4.02
2312 2775 4.022762 TCTCTCTCTCAAAAGAAGTGGTCG 60.023 45.833 0.00 0.00 0.00 4.79
2313 2776 3.005897 TCTCTCTCAAAAGAAGTGGTCGG 59.994 47.826 0.00 0.00 0.00 4.79
2314 2777 2.963101 TCTCTCAAAAGAAGTGGTCGGA 59.037 45.455 0.00 0.00 0.00 4.55
2315 2778 3.060602 CTCTCAAAAGAAGTGGTCGGAC 58.939 50.000 0.00 0.00 0.00 4.79
2316 2779 2.143925 CTCAAAAGAAGTGGTCGGACC 58.856 52.381 20.36 20.36 39.22 4.46
2317 2780 1.202722 TCAAAAGAAGTGGTCGGACCC 60.203 52.381 23.81 14.91 37.50 4.46
2318 2781 1.137697 AAAAGAAGTGGTCGGACCCT 58.862 50.000 23.81 16.82 37.50 4.34
2319 2782 1.137697 AAAGAAGTGGTCGGACCCTT 58.862 50.000 23.81 23.17 37.50 3.95
2320 2783 0.685660 AAGAAGTGGTCGGACCCTTC 59.314 55.000 30.71 30.71 41.64 3.46
2321 2784 1.192803 AGAAGTGGTCGGACCCTTCC 61.193 60.000 32.30 22.75 41.97 3.46
2322 2785 2.181445 GAAGTGGTCGGACCCTTCCC 62.181 65.000 29.24 17.13 38.50 3.97
2323 2786 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
2330 2793 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
2358 2821 1.376037 GGAGCTATATGCACCGGGC 60.376 63.158 6.32 7.25 42.21 6.13
2359 2822 1.674057 GAGCTATATGCACCGGGCT 59.326 57.895 6.32 0.81 45.94 5.19
2360 2823 0.671781 GAGCTATATGCACCGGGCTG 60.672 60.000 6.32 0.00 45.94 4.85
2361 2824 2.328099 GCTATATGCACCGGGCTGC 61.328 63.158 6.32 8.50 45.15 5.25
2362 2825 1.672356 CTATATGCACCGGGCTGCC 60.672 63.158 11.05 11.05 45.15 4.85
2363 2826 3.190738 TATATGCACCGGGCTGCCC 62.191 63.158 28.17 28.17 45.15 5.36
2368 2831 4.351054 CACCGGGCTGCCCTTCTT 62.351 66.667 33.39 13.23 42.67 2.52
2369 2832 4.035102 ACCGGGCTGCCCTTCTTC 62.035 66.667 33.39 8.22 42.67 2.87
2428 2891 8.087750 CCAAAAGCATTATGTTCCTACTTTCAA 58.912 33.333 0.00 0.00 0.00 2.69
2451 2914 5.841810 ACTTGTTGGATGTTGTTACATTGG 58.158 37.500 0.00 0.00 44.90 3.16
2469 2932 0.681175 GGTGAAATGGTGGCTGCTTT 59.319 50.000 0.00 0.00 0.00 3.51
2477 2940 1.332195 GGTGGCTGCTTTCTTTCCTT 58.668 50.000 0.00 0.00 0.00 3.36
2613 3080 5.711976 GGTTCCACATAGGCTGCATAATATT 59.288 40.000 0.50 0.00 37.29 1.28
2614 3081 6.884295 GGTTCCACATAGGCTGCATAATATTA 59.116 38.462 0.50 0.00 37.29 0.98
2615 3082 7.557719 GGTTCCACATAGGCTGCATAATATTAT 59.442 37.037 0.50 1.91 37.29 1.28
2668 3136 6.011096 TGACTATTTGGGGATTTTTCCTACCT 60.011 38.462 0.00 0.00 0.00 3.08
2761 3253 6.428159 GGTATGATAAATGCCTTACCTCTGTG 59.572 42.308 0.00 0.00 33.07 3.66
2827 3319 3.079578 ACTTGCTTGGTCATGACTCATG 58.920 45.455 24.50 20.54 42.60 3.07
2900 3395 3.366374 GGTCAGGTTTCTTATGCAAGCAC 60.366 47.826 0.00 0.00 0.00 4.40
2908 3403 1.240641 TTATGCAAGCACGTGGGTGG 61.241 55.000 18.88 2.45 44.54 4.61
2919 3414 2.091541 ACGTGGGTGGCATAATCTTTG 58.908 47.619 0.00 0.00 0.00 2.77
3094 3589 2.103771 TCATGAGTCTGGAGCTATTGGC 59.896 50.000 0.00 0.00 42.19 4.52
3103 3598 4.049393 GCTATTGGCGGCCTACAG 57.951 61.111 21.46 12.77 0.00 2.74
3121 3616 3.545703 ACAGTATGATAGCAAAGCACCC 58.454 45.455 0.00 0.00 39.69 4.61
3292 3787 4.440112 GCTACCAATAACCAGAACAATGGC 60.440 45.833 0.00 0.00 44.80 4.40
3772 4267 2.637382 TCAGTTGCCTGTTGATCCACTA 59.363 45.455 0.00 0.00 39.82 2.74
3984 4479 2.575532 TGCTGGGAACTCTTTGACAAG 58.424 47.619 0.00 0.00 0.00 3.16
3991 4486 4.202326 GGGAACTCTTTGACAAGTCCTGTA 60.202 45.833 0.00 0.00 38.84 2.74
3994 4489 6.486993 GGAACTCTTTGACAAGTCCTGTATTT 59.513 38.462 0.00 0.00 38.84 1.40
4281 4776 6.825721 CCTACTAAACTGCAAATCCAAGATCT 59.174 38.462 0.00 0.00 0.00 2.75
4370 4865 4.329528 GCAATGATCTCTTGTCTCACAGAC 59.670 45.833 9.40 0.00 45.26 3.51
4462 4957 2.739609 GCAAAAGCTTGAAACTGCCAGT 60.740 45.455 0.00 0.00 34.14 4.00
4492 4987 6.799512 AGAAAAAGACATGGTTTTCACTGAG 58.200 36.000 22.72 0.00 43.24 3.35
4528 5023 4.270566 GCTCTCACATTGATGACTGATGTC 59.729 45.833 0.00 0.00 43.20 3.06
4605 5100 3.434167 CCAGTGCTATAAACATCCTGGCT 60.434 47.826 0.00 0.00 32.42 4.75
4769 5264 9.515226 AAATTAGAACCTGTTTATTAGCTGTGA 57.485 29.630 0.00 0.00 0.00 3.58
4781 5429 9.974750 GTTTATTAGCTGTGATTTAGTCAAGAC 57.025 33.333 0.00 0.00 38.90 3.01
4788 5436 6.593382 GCTGTGATTTAGTCAAGACTCAAGAT 59.407 38.462 5.91 0.00 42.54 2.40
4902 5550 6.305272 TCAGCTGGAACTATTCTTCTTGAT 57.695 37.500 15.13 0.00 0.00 2.57
4966 5614 8.837788 TTGCTTGAGTATGGAATATATGACAG 57.162 34.615 0.00 0.00 0.00 3.51
4973 5621 8.615360 AGTATGGAATATATGACAGCACCTAT 57.385 34.615 0.00 0.00 0.00 2.57
5037 5685 8.585018 TGTCTGATTATGTCAACAGAACTCTTA 58.415 33.333 0.00 0.00 40.30 2.10
5199 5848 7.933396 TGAAGGACATAAATATGCAGACAATG 58.067 34.615 0.00 0.00 37.19 2.82
5326 5975 3.822594 TGTGTACGTGATCAAAATGGC 57.177 42.857 0.00 0.00 0.00 4.40
7421 8098 6.260377 CAGATGTAATGGCATGTTGTTGTAG 58.740 40.000 0.00 0.00 0.00 2.74
7454 8131 2.127708 AGATGGGGATGGTGGTACTTC 58.872 52.381 0.00 0.00 0.00 3.01
7675 8352 7.754027 CAGATTCAAATTGTTCTCTGGCTTTAG 59.246 37.037 11.47 0.00 0.00 1.85
7941 8627 8.606040 TCTGAATTTTCCAAAATTAAGGCTTG 57.394 30.769 16.88 0.00 45.70 4.01
8261 8990 0.810648 TAGCCGCAAAATGAAGCCAG 59.189 50.000 0.00 0.00 0.00 4.85
8269 9003 3.374678 GCAAAATGAAGCCAGAGAGAGAG 59.625 47.826 0.00 0.00 0.00 3.20
8270 9004 4.829968 CAAAATGAAGCCAGAGAGAGAGA 58.170 43.478 0.00 0.00 0.00 3.10
8276 9010 1.102978 GCCAGAGAGAGAGACAGTCC 58.897 60.000 0.00 0.00 0.00 3.85
8327 9061 1.117142 ATTTGGCCACTTGTGCAGCT 61.117 50.000 3.88 0.00 0.00 4.24
8358 9092 1.338973 CAAAAGCTTCAGCCTGCAGAA 59.661 47.619 17.39 0.00 43.38 3.02
8479 9214 4.023291 TCCCTGCAATAAACCTGGATTTC 58.977 43.478 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.094675 CCAGTAAAGCCAGATGGTTGG 58.905 52.381 0.00 0.00 41.35 3.77
27 28 8.135529 TCACATGTGCATACTAGTGTTATACTC 58.864 37.037 21.38 0.00 40.89 2.59
101 102 4.637276 TGTAAGAAAGCCAAGATGACGAA 58.363 39.130 0.00 0.00 0.00 3.85
202 207 9.603298 GTAGTTTACTTTGTTATGTACTTTGCC 57.397 33.333 0.00 0.00 0.00 4.52
203 208 9.309796 CGTAGTTTACTTTGTTATGTACTTTGC 57.690 33.333 0.00 0.00 0.00 3.68
206 211 9.196552 GGTCGTAGTTTACTTTGTTATGTACTT 57.803 33.333 0.00 0.00 0.00 2.24
226 232 8.339344 TCATATCTTATAATGGTTCGGTCGTA 57.661 34.615 0.00 0.00 0.00 3.43
228 234 8.528917 TTTCATATCTTATAATGGTTCGGTCG 57.471 34.615 0.00 0.00 0.00 4.79
286 292 0.179179 CTTCTTAAAGGCGCTGCTGC 60.179 55.000 7.64 5.34 0.00 5.25
287 293 0.449388 CCTTCTTAAAGGCGCTGCTG 59.551 55.000 7.64 0.00 45.50 4.41
288 294 2.859992 CCTTCTTAAAGGCGCTGCT 58.140 52.632 7.64 0.00 45.50 4.24
299 306 3.057736 CGTGAGGACGTCTTTCCTTCTTA 60.058 47.826 16.46 0.00 46.80 2.10
302 309 1.699343 CGTGAGGACGTCTTTCCTTC 58.301 55.000 16.46 4.91 46.80 3.46
331 338 0.516877 TCGTCTACAACCGTACGTGG 59.483 55.000 15.21 5.54 0.00 4.94
334 341 3.296516 GGTCGTCTACAACCGTACG 57.703 57.895 8.69 8.69 0.00 3.67
349 356 6.920569 TGAAAATAAAGCCTTATCTCGGTC 57.079 37.500 0.00 0.00 0.00 4.79
361 368 8.609176 TCGTGTTACTGGATATGAAAATAAAGC 58.391 33.333 0.00 0.00 0.00 3.51
366 373 5.820947 GGGTCGTGTTACTGGATATGAAAAT 59.179 40.000 0.00 0.00 0.00 1.82
367 374 5.046159 AGGGTCGTGTTACTGGATATGAAAA 60.046 40.000 0.00 0.00 0.00 2.29
374 459 3.197116 CCTAAAGGGTCGTGTTACTGGAT 59.803 47.826 0.00 0.00 0.00 3.41
386 471 2.176314 AACCGACGGCCTAAAGGGTC 62.176 60.000 15.39 0.00 37.43 4.46
393 478 1.294138 CCAGAAAACCGACGGCCTA 59.706 57.895 15.39 0.00 0.00 3.93
394 479 2.032071 CCAGAAAACCGACGGCCT 59.968 61.111 15.39 3.22 0.00 5.19
396 481 2.966309 CTGCCAGAAAACCGACGGC 61.966 63.158 15.39 0.00 43.28 5.68
398 483 0.512952 CTTCTGCCAGAAAACCGACG 59.487 55.000 8.74 0.00 33.19 5.12
399 484 0.238553 GCTTCTGCCAGAAAACCGAC 59.761 55.000 8.74 0.00 33.19 4.79
408 511 3.255149 AGAAAGAACATTGCTTCTGCCAG 59.745 43.478 0.00 0.00 38.71 4.85
443 546 6.725246 AGTTTTCGTATAACCATATGCAAGC 58.275 36.000 0.00 0.00 0.00 4.01
480 589 6.975197 TCTTTTGTATTGTGTGCGAAATTTGA 59.025 30.769 0.00 0.00 0.00 2.69
481 590 7.159437 TCTTTTGTATTGTGTGCGAAATTTG 57.841 32.000 0.00 0.00 0.00 2.32
484 593 5.460646 CCTCTTTTGTATTGTGTGCGAAAT 58.539 37.500 0.00 0.00 0.00 2.17
487 596 2.225491 GCCTCTTTTGTATTGTGTGCGA 59.775 45.455 0.00 0.00 0.00 5.10
488 597 2.584791 GCCTCTTTTGTATTGTGTGCG 58.415 47.619 0.00 0.00 0.00 5.34
489 598 2.668279 CGGCCTCTTTTGTATTGTGTGC 60.668 50.000 0.00 0.00 0.00 4.57
490 599 2.095263 CCGGCCTCTTTTGTATTGTGTG 60.095 50.000 0.00 0.00 0.00 3.82
491 600 2.159382 CCGGCCTCTTTTGTATTGTGT 58.841 47.619 0.00 0.00 0.00 3.72
492 601 2.159382 ACCGGCCTCTTTTGTATTGTG 58.841 47.619 0.00 0.00 0.00 3.33
493 602 2.224670 TGACCGGCCTCTTTTGTATTGT 60.225 45.455 0.00 0.00 0.00 2.71
494 603 2.432444 TGACCGGCCTCTTTTGTATTG 58.568 47.619 0.00 0.00 0.00 1.90
496 605 2.433436 GTTGACCGGCCTCTTTTGTAT 58.567 47.619 0.00 0.00 0.00 2.29
497 606 1.543871 GGTTGACCGGCCTCTTTTGTA 60.544 52.381 0.00 0.00 0.00 2.41
498 607 0.822121 GGTTGACCGGCCTCTTTTGT 60.822 55.000 0.00 0.00 0.00 2.83
499 608 0.537371 AGGTTGACCGGCCTCTTTTG 60.537 55.000 0.00 0.00 42.08 2.44
505 615 0.106419 TTTTTCAGGTTGACCGGCCT 60.106 50.000 0.00 0.00 42.08 5.19
743 880 4.154347 GGAGTGAGCTGGGGCGAG 62.154 72.222 0.00 0.00 44.37 5.03
746 883 3.334054 AAGGGAGTGAGCTGGGGC 61.334 66.667 0.00 0.00 39.06 5.80
747 884 2.674220 GGAAGGGAGTGAGCTGGGG 61.674 68.421 0.00 0.00 0.00 4.96
748 885 2.674220 GGGAAGGGAGTGAGCTGGG 61.674 68.421 0.00 0.00 0.00 4.45
749 886 1.614824 AGGGAAGGGAGTGAGCTGG 60.615 63.158 0.00 0.00 0.00 4.85
750 887 1.197430 ACAGGGAAGGGAGTGAGCTG 61.197 60.000 0.00 0.00 0.00 4.24
751 888 0.474660 AACAGGGAAGGGAGTGAGCT 60.475 55.000 0.00 0.00 0.00 4.09
752 889 0.402121 AAACAGGGAAGGGAGTGAGC 59.598 55.000 0.00 0.00 0.00 4.26
781 933 3.360340 GCAGAGCAAAGCCGCTGT 61.360 61.111 0.00 0.00 44.01 4.40
909 1068 1.270094 GCCCCCAAGAAACGAAAAAGG 60.270 52.381 0.00 0.00 0.00 3.11
917 1076 3.062466 GGAGCGCCCCCAAGAAAC 61.062 66.667 2.29 0.00 0.00 2.78
918 1077 4.715523 CGGAGCGCCCCCAAGAAA 62.716 66.667 15.53 0.00 0.00 2.52
973 1132 1.328279 CCTCCACAGAAACCCAAACC 58.672 55.000 0.00 0.00 0.00 3.27
974 1133 1.133606 TCCCTCCACAGAAACCCAAAC 60.134 52.381 0.00 0.00 0.00 2.93
975 1134 1.227249 TCCCTCCACAGAAACCCAAA 58.773 50.000 0.00 0.00 0.00 3.28
976 1135 1.455822 ATCCCTCCACAGAAACCCAA 58.544 50.000 0.00 0.00 0.00 4.12
977 1136 2.196595 CTATCCCTCCACAGAAACCCA 58.803 52.381 0.00 0.00 0.00 4.51
980 1139 2.478292 TCCCTATCCCTCCACAGAAAC 58.522 52.381 0.00 0.00 0.00 2.78
984 1143 1.356124 CCATCCCTATCCCTCCACAG 58.644 60.000 0.00 0.00 0.00 3.66
985 1144 0.647738 ACCATCCCTATCCCTCCACA 59.352 55.000 0.00 0.00 0.00 4.17
1436 1625 4.597004 AGTTCAGACAGGGAGATACGTAA 58.403 43.478 0.00 0.00 0.00 3.18
1440 1629 3.383185 CAGGAGTTCAGACAGGGAGATAC 59.617 52.174 0.00 0.00 0.00 2.24
1497 1686 2.874701 AGCATTGACACGATCCAATAGC 59.125 45.455 0.00 2.79 32.31 2.97
1499 1688 3.622612 CACAGCATTGACACGATCCAATA 59.377 43.478 0.00 0.00 32.31 1.90
1507 1707 0.800631 AGCATCACAGCATTGACACG 59.199 50.000 0.00 0.00 36.85 4.49
1508 1708 4.142534 ACATTAGCATCACAGCATTGACAC 60.143 41.667 0.00 0.00 36.85 3.67
1515 1715 3.011818 CCAGAACATTAGCATCACAGCA 58.988 45.455 0.00 0.00 36.85 4.41
1521 1721 7.493367 ACTTACTAGACCAGAACATTAGCATC 58.507 38.462 0.00 0.00 0.00 3.91
1547 1747 4.114073 CAATCTCTCTGACAGCTAGCAAG 58.886 47.826 18.83 11.61 0.00 4.01
1550 1750 2.472816 GCAATCTCTCTGACAGCTAGC 58.527 52.381 6.62 6.62 0.00 3.42
1554 1754 1.276415 GTCGCAATCTCTCTGACAGC 58.724 55.000 0.00 0.00 0.00 4.40
1559 1759 2.159503 ACTACACGTCGCAATCTCTCTG 60.160 50.000 0.00 0.00 0.00 3.35
1642 1859 3.181445 ACCAGCTCAAACAGTGACCATAA 60.181 43.478 0.00 0.00 31.13 1.90
1678 1895 4.096732 ACAAAAAGTGCAGTGACAGAAC 57.903 40.909 0.00 0.00 0.00 3.01
1708 1925 0.036765 AGTAGCGCCCGAACAATTCA 60.037 50.000 2.29 0.00 0.00 2.57
1723 1940 8.187480 GCAGATGGTATATGTCACTATCAGTAG 58.813 40.741 4.02 0.00 36.61 2.57
1741 1958 3.567164 CAGAAACAACAAGAGCAGATGGT 59.433 43.478 0.00 0.00 0.00 3.55
1745 1962 4.212004 CGATTCAGAAACAACAAGAGCAGA 59.788 41.667 0.00 0.00 0.00 4.26
1822 2041 1.069823 CCTGCCAATCTCGAGCACTAT 59.930 52.381 7.81 0.00 32.06 2.12
1823 2042 0.461548 CCTGCCAATCTCGAGCACTA 59.538 55.000 7.81 0.00 32.06 2.74
1824 2043 1.220206 CCTGCCAATCTCGAGCACT 59.780 57.895 7.81 0.00 32.06 4.40
1825 2044 2.467826 GCCTGCCAATCTCGAGCAC 61.468 63.158 7.81 0.00 32.06 4.40
1826 2045 2.124983 GCCTGCCAATCTCGAGCA 60.125 61.111 7.81 1.23 34.79 4.26
1943 2261 7.438757 CAGATGAACATGAACAAAACCAATCAA 59.561 33.333 0.00 0.00 0.00 2.57
1946 2264 7.053316 TCAGATGAACATGAACAAAACCAAT 57.947 32.000 0.00 0.00 0.00 3.16
1949 2267 5.010012 ACCTCAGATGAACATGAACAAAACC 59.990 40.000 0.00 0.00 0.00 3.27
1951 2269 8.298854 CAATACCTCAGATGAACATGAACAAAA 58.701 33.333 0.00 0.00 0.00 2.44
2027 2419 9.996554 CATATATCACTATCAGTAACACCCAAA 57.003 33.333 0.00 0.00 0.00 3.28
2028 2420 9.154632 ACATATATCACTATCAGTAACACCCAA 57.845 33.333 0.00 0.00 0.00 4.12
2029 2421 8.721133 ACATATATCACTATCAGTAACACCCA 57.279 34.615 0.00 0.00 0.00 4.51
2030 2422 8.803235 TGACATATATCACTATCAGTAACACCC 58.197 37.037 0.00 0.00 0.00 4.61
2031 2423 9.847706 CTGACATATATCACTATCAGTAACACC 57.152 37.037 0.00 0.00 31.06 4.16
2032 2424 9.347934 GCTGACATATATCACTATCAGTAACAC 57.652 37.037 0.00 0.00 36.71 3.32
2054 2446 3.136763 CAGAGACAAAAAGAGCAGCTGA 58.863 45.455 20.43 0.00 0.00 4.26
2078 2470 0.445043 GTAACACCCGAACAATCCGC 59.555 55.000 0.00 0.00 0.00 5.54
2124 2586 3.743911 CGCTAAACAGTCCACACACATAA 59.256 43.478 0.00 0.00 0.00 1.90
2129 2591 0.753867 TCCGCTAAACAGTCCACACA 59.246 50.000 0.00 0.00 0.00 3.72
2130 2592 1.732259 CATCCGCTAAACAGTCCACAC 59.268 52.381 0.00 0.00 0.00 3.82
2286 2749 5.243730 ACCACTTCTTTTGAGAGAGAGAGAG 59.756 44.000 0.00 0.00 0.00 3.20
2287 2750 5.144100 ACCACTTCTTTTGAGAGAGAGAGA 58.856 41.667 0.00 0.00 0.00 3.10
2288 2751 5.467035 ACCACTTCTTTTGAGAGAGAGAG 57.533 43.478 0.00 0.00 0.00 3.20
2289 2752 4.022762 CGACCACTTCTTTTGAGAGAGAGA 60.023 45.833 0.00 0.00 0.00 3.10
2290 2753 4.233789 CGACCACTTCTTTTGAGAGAGAG 58.766 47.826 0.00 0.00 0.00 3.20
2291 2754 3.005897 CCGACCACTTCTTTTGAGAGAGA 59.994 47.826 0.00 0.00 0.00 3.10
2292 2755 3.005897 TCCGACCACTTCTTTTGAGAGAG 59.994 47.826 0.00 0.00 0.00 3.20
2293 2756 2.963101 TCCGACCACTTCTTTTGAGAGA 59.037 45.455 0.00 0.00 0.00 3.10
2294 2757 3.060602 GTCCGACCACTTCTTTTGAGAG 58.939 50.000 0.00 0.00 0.00 3.20
2295 2758 2.224209 GGTCCGACCACTTCTTTTGAGA 60.224 50.000 13.05 0.00 38.42 3.27
2296 2759 2.143925 GGTCCGACCACTTCTTTTGAG 58.856 52.381 13.05 0.00 38.42 3.02
2297 2760 1.202722 GGGTCCGACCACTTCTTTTGA 60.203 52.381 19.43 0.00 41.02 2.69
2298 2761 1.202770 AGGGTCCGACCACTTCTTTTG 60.203 52.381 19.43 0.00 41.02 2.44
2299 2762 1.137697 AGGGTCCGACCACTTCTTTT 58.862 50.000 19.43 0.00 41.02 2.27
2300 2763 1.071857 GAAGGGTCCGACCACTTCTTT 59.928 52.381 26.17 11.40 41.02 2.52
2301 2764 0.685660 GAAGGGTCCGACCACTTCTT 59.314 55.000 26.17 18.16 41.02 2.52
2302 2765 1.192803 GGAAGGGTCCGACCACTTCT 61.193 60.000 29.04 14.80 41.36 2.85
2303 2766 1.295746 GGAAGGGTCCGACCACTTC 59.704 63.158 25.81 25.81 41.02 3.01
2304 2767 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2305 2768 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2306 2769 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2313 2776 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
2329 2792 2.699576 TATAGCTCCCGCTTGCGCAG 62.700 60.000 11.31 6.32 46.47 5.18
2330 2793 2.099652 ATATAGCTCCCGCTTGCGCA 62.100 55.000 5.66 5.66 46.47 6.09
2331 2794 1.374758 ATATAGCTCCCGCTTGCGC 60.375 57.895 9.71 0.00 46.47 6.09
2332 2795 1.630244 GCATATAGCTCCCGCTTGCG 61.630 60.000 8.14 8.14 46.47 4.85
2333 2796 0.603707 TGCATATAGCTCCCGCTTGC 60.604 55.000 0.00 3.30 46.47 4.01
2334 2797 1.151668 GTGCATATAGCTCCCGCTTG 58.848 55.000 0.00 0.00 46.47 4.01
2335 2798 0.035458 GGTGCATATAGCTCCCGCTT 59.965 55.000 0.00 0.00 46.47 4.68
2341 2804 0.671781 CAGCCCGGTGCATATAGCTC 60.672 60.000 15.92 0.00 45.94 4.09
2342 2805 1.372683 CAGCCCGGTGCATATAGCT 59.627 57.895 15.92 4.82 45.94 3.32
2343 2806 2.328099 GCAGCCCGGTGCATATAGC 61.328 63.158 13.70 0.00 43.41 2.97
2344 2807 1.672356 GGCAGCCCGGTGCATATAG 60.672 63.158 19.47 3.93 45.93 1.31
2345 2808 2.429930 GGCAGCCCGGTGCATATA 59.570 61.111 19.47 0.00 45.93 0.86
2346 2809 4.586235 GGGCAGCCCGGTGCATAT 62.586 66.667 17.05 0.00 45.93 1.78
2355 2818 1.047801 TTTTTGAAGAAGGGCAGCCC 58.952 50.000 24.90 24.90 45.90 5.19
2382 2845 5.036117 TGGCTCTAAATAGTCCATTGGTC 57.964 43.478 1.86 0.00 0.00 4.02
2428 2891 5.362430 ACCAATGTAACAACATCCAACAAGT 59.638 36.000 0.00 0.00 0.00 3.16
2451 2914 1.615392 AGAAAGCAGCCACCATTTCAC 59.385 47.619 6.79 0.00 34.77 3.18
2469 2932 8.934023 ATTTAAGACCAACATACAAGGAAAGA 57.066 30.769 0.00 0.00 0.00 2.52
2586 3049 0.749454 GCAGCCTATGTGGAACCAGG 60.749 60.000 0.00 0.00 40.11 4.45
2794 3286 6.000840 TGACCAAGCAAGTATTACAATGACA 58.999 36.000 0.00 0.00 0.00 3.58
2827 3319 6.497437 TGTGTAAATGCAATGTCATATGCTC 58.503 36.000 16.03 0.00 42.97 4.26
2862 3356 8.528044 AAACCTGACCTAAATGTTCAGTTTAA 57.472 30.769 0.00 0.00 0.00 1.52
2864 3358 6.833933 AGAAACCTGACCTAAATGTTCAGTTT 59.166 34.615 0.00 0.00 0.00 2.66
2867 3361 6.884280 AAGAAACCTGACCTAAATGTTCAG 57.116 37.500 0.00 0.00 0.00 3.02
2900 3395 2.091541 ACAAAGATTATGCCACCCACG 58.908 47.619 0.00 0.00 0.00 4.94
2908 3403 8.125448 GGATTGAACTCTACACAAAGATTATGC 58.875 37.037 0.00 0.00 0.00 3.14
2919 3414 4.626172 GGAAAGACGGATTGAACTCTACAC 59.374 45.833 0.00 0.00 0.00 2.90
3094 3589 3.660501 TTGCTATCATACTGTAGGCCG 57.339 47.619 0.00 0.00 0.00 6.13
3103 3598 2.618709 GTGGGGTGCTTTGCTATCATAC 59.381 50.000 0.00 0.00 0.00 2.39
3121 3616 2.036098 TGATTGCCTGGCAGGTGG 59.964 61.111 32.80 11.30 40.61 4.61
3772 4267 3.554934 TGCCCGAAGAAATTGAGCATAT 58.445 40.909 0.00 0.00 0.00 1.78
3928 4423 3.641906 ACCCAAGATTCCCATAGTAGTCG 59.358 47.826 0.00 0.00 0.00 4.18
3984 4479 2.007608 GCGAAGTGGGAAATACAGGAC 58.992 52.381 0.00 0.00 0.00 3.85
3991 4486 0.609131 CACCTGGCGAAGTGGGAAAT 60.609 55.000 0.00 0.00 0.00 2.17
4027 4522 2.541120 GCTGCGATCCACATGCCTC 61.541 63.158 0.00 0.00 0.00 4.70
4462 4957 7.330700 GTGAAAACCATGTCTTTTTCTTCAACA 59.669 33.333 18.11 0.00 40.76 3.33
4492 4987 2.211806 GTGAGAGCTTGAGGCATGATC 58.788 52.381 0.00 0.00 44.79 2.92
4528 5023 8.143835 ACCTTCTGAACAACATAATTTCCAAAG 58.856 33.333 0.00 0.00 0.00 2.77
4570 5065 8.682710 GTTTATAGCACTGGGACAAATAATTGA 58.317 33.333 0.00 0.00 38.70 2.57
4583 5078 2.880890 GCCAGGATGTTTATAGCACTGG 59.119 50.000 0.00 0.00 45.11 4.00
4605 5100 6.783708 ACTGGTTCAAAAGTTTATGGTCAA 57.216 33.333 0.00 0.00 0.00 3.18
4681 5176 3.240134 GAGTGCCAAGACTCGCCCA 62.240 63.158 0.00 0.00 33.39 5.36
4732 5227 8.721133 AACAGGTTCTAATTTTCCATACCTTT 57.279 30.769 0.00 0.00 32.45 3.11
4763 5258 5.928839 TCTTGAGTCTTGACTAAATCACAGC 59.071 40.000 3.00 0.00 36.92 4.40
4879 5527 5.745312 TCAAGAAGAATAGTTCCAGCTGA 57.255 39.130 17.39 0.00 0.00 4.26
4902 5550 6.015603 TGTTTGAATATCATGGTGCAGTTTCA 60.016 34.615 0.00 0.00 0.00 2.69
4966 5614 7.813627 GGTAGCTTCTAACTGTATTATAGGTGC 59.186 40.741 0.00 0.00 0.00 5.01
4984 5632 3.378427 CCTGCCAAACATAAGGTAGCTTC 59.622 47.826 11.11 0.00 36.44 3.86
5199 5848 6.322491 GCCCATCACATAAGTTAAAGAACAC 58.678 40.000 0.00 0.00 38.10 3.32
5305 5954 3.565902 TGCCATTTTGATCACGTACACAA 59.434 39.130 0.00 0.00 0.00 3.33
5326 5975 5.289917 TGCATTTCTGTATAACGTGGTTG 57.710 39.130 0.00 0.00 0.00 3.77
5593 6242 2.886523 TGTAGCAAGCAAGCAAACAGAT 59.113 40.909 3.19 0.00 36.85 2.90
6082 6749 5.557891 AAATCATACTCACTTTGCTGAGC 57.442 39.130 0.00 0.00 41.38 4.26
6267 6934 3.254411 TCACTTGTGCAACTGTCAAAACA 59.746 39.130 0.00 0.00 38.04 2.83
6449 7119 2.497792 ATCGCTCATGGGGTTTGCCA 62.498 55.000 0.00 0.00 36.17 4.92
6533 7203 7.040478 CCAAAGGATAAACACTTCTCAATGACA 60.040 37.037 0.00 0.00 0.00 3.58
6969 7639 0.035458 AAGCGTATAGGGCTCATGGC 59.965 55.000 0.00 0.00 40.53 4.40
7421 8098 5.824624 CCATCCCCATCTGTATATGTTATGC 59.175 44.000 0.00 0.00 0.00 3.14
7454 8131 3.795101 CAGCTTTGCAGAGAAAACAGTTG 59.205 43.478 8.73 0.00 0.00 3.16
7973 8659 0.388659 AAAGTTTGGCGCTTCATGCA 59.611 45.000 7.64 0.00 43.06 3.96
8189 8875 4.031611 GGACTATCAACCTAGGGTGTTCT 58.968 47.826 26.17 14.39 35.34 3.01
8261 8990 2.006888 CTCACGGACTGTCTCTCTCTC 58.993 57.143 7.85 0.00 0.00 3.20
8269 9003 0.244178 GACCTTCCTCACGGACTGTC 59.756 60.000 0.00 0.00 39.60 3.51
8270 9004 0.469331 TGACCTTCCTCACGGACTGT 60.469 55.000 0.00 0.00 39.60 3.55
8276 9010 1.079543 CCAGCTGACCTTCCTCACG 60.080 63.158 17.39 0.00 0.00 4.35
8358 9092 4.439057 CACCGCCATTACAAGTATACACT 58.561 43.478 5.50 0.00 36.19 3.55
8479 9214 5.234757 TGATGCAGCTTTTAAGTGCAAAAAG 59.765 36.000 14.92 14.92 42.13 2.27


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

AutoCloner maintained by Alex Coulton.