Multiple sequence alignment - TraesCS7D01G394400

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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 TraesCS7D01G394400 chr7D 100.000 5618 0 0 1 5618 509615746 509610129 0.000000e+00 10375.0
1 TraesCS7D01G394400 chr7D 81.287 2501 436 25 983 3473 509559803 509557325 0.000000e+00 1997.0
2 TraesCS7D01G394400 chr7D 89.655 377 38 1 4419 4794 509556100 509555724 3.940000e-131 479.0
3 TraesCS7D01G394400 chr7D 80.206 389 49 17 3606 3990 509557182 509556818 3.340000e-67 267.0
4 TraesCS7D01G394400 chr7D 100.000 35 0 0 4854 4888 545268065 545268031 1.310000e-06 65.8
5 TraesCS7D01G394400 chr7A 88.018 3522 343 40 1 3485 580510490 580507011 0.000000e+00 4093.0
6 TraesCS7D01G394400 chr7A 81.360 2441 435 16 1039 3473 580474472 580472046 0.000000e+00 1969.0
7 TraesCS7D01G394400 chr7A 77.805 2433 481 38 997 3395 580693865 580696272 0.000000e+00 1447.0
8 TraesCS7D01G394400 chr7A 91.642 682 36 11 4292 4963 580506627 580505957 0.000000e+00 924.0
9 TraesCS7D01G394400 chr7A 90.716 377 34 1 4419 4794 580470855 580470479 8.400000e-138 501.0
10 TraesCS7D01G394400 chr7A 88.202 178 21 0 4615 4792 84496552 84496729 4.410000e-51 213.0
11 TraesCS7D01G394400 chr7A 95.349 43 1 1 4854 4895 580505900 580505858 3.630000e-07 67.6
12 TraesCS7D01G394400 chr7A 100.000 35 0 0 4854 4888 627046928 627046894 1.310000e-06 65.8
13 TraesCS7D01G394400 chr7B 86.514 3663 379 60 371 3972 537831845 537828237 0.000000e+00 3921.0
14 TraesCS7D01G394400 chr7B 89.496 2894 241 35 984 3849 537795894 537793036 0.000000e+00 3602.0
15 TraesCS7D01G394400 chr7B 81.575 2502 416 32 989 3473 537676900 537674427 0.000000e+00 2025.0
16 TraesCS7D01G394400 chr7B 77.503 2427 496 31 997 3395 538243223 538245627 0.000000e+00 1411.0
17 TraesCS7D01G394400 chr7B 92.405 474 29 6 4318 4786 537827530 537827059 0.000000e+00 669.0
18 TraesCS7D01G394400 chr7B 95.855 386 12 3 1 385 537834229 537833847 6.180000e-174 621.0
19 TraesCS7D01G394400 chr7B 91.512 377 31 1 4419 4794 537673207 537672831 8.340000e-143 518.0
20 TraesCS7D01G394400 chr7B 87.413 429 30 9 4248 4663 537792270 537791853 6.590000e-129 472.0
21 TraesCS7D01G394400 chr7B 89.697 165 16 1 3848 4012 537792922 537792759 5.700000e-50 209.0
22 TraesCS7D01G394400 chr7B 96.491 57 2 0 4683 4739 537791854 537791798 1.670000e-15 95.3
23 TraesCS7D01G394400 chr6A 85.801 662 70 13 4978 5618 298506195 298506853 0.000000e+00 680.0
24 TraesCS7D01G394400 chr6A 89.809 157 16 0 320 476 411770409 411770253 9.540000e-48 202.0
25 TraesCS7D01G394400 chr6A 94.949 99 3 2 4008 4104 616776282 616776380 2.710000e-33 154.0
26 TraesCS7D01G394400 chr5B 91.228 171 15 0 4615 4785 667412454 667412624 3.380000e-57 233.0
27 TraesCS7D01G394400 chr1A 90.395 177 16 1 4615 4791 531824263 531824438 1.220000e-56 231.0
28 TraesCS7D01G394400 chr1A 88.506 174 17 3 311 483 155857870 155857699 2.050000e-49 207.0
29 TraesCS7D01G394400 chr1A 96.774 93 3 0 4009 4101 486046164 486046072 7.540000e-34 156.0
30 TraesCS7D01G394400 chr2B 91.139 158 13 1 321 478 522201994 522202150 4.410000e-51 213.0
31 TraesCS7D01G394400 chr2B 100.000 35 0 0 4854 4888 182135294 182135260 1.310000e-06 65.8
32 TraesCS7D01G394400 chr2D 89.873 158 15 1 321 478 443243838 443243994 9.540000e-48 202.0
33 TraesCS7D01G394400 chr5D 77.391 345 70 6 5146 5486 53007185 53006845 1.230000e-46 198.0
34 TraesCS7D01G394400 chr5D 92.308 104 7 1 4009 4111 225253183 225253286 4.540000e-31 147.0
35 TraesCS7D01G394400 chr5D 100.000 35 0 0 4854 4888 289422555 289422521 1.310000e-06 65.8
36 TraesCS7D01G394400 chr5D 100.000 35 0 0 4854 4888 289728659 289728625 1.310000e-06 65.8
37 TraesCS7D01G394400 chr2A 89.308 159 16 1 322 479 141506316 141506474 1.230000e-46 198.0
38 TraesCS7D01G394400 chr4B 89.542 153 16 0 324 476 106227561 106227409 1.600000e-45 195.0
39 TraesCS7D01G394400 chr4B 93.069 101 5 2 4001 4099 538676161 538676061 4.540000e-31 147.0
40 TraesCS7D01G394400 chr1D 87.356 174 16 6 311 483 137418288 137418456 1.600000e-45 195.0
41 TraesCS7D01G394400 chr1D 95.833 96 4 0 4009 4104 437574219 437574314 7.540000e-34 156.0
42 TraesCS7D01G394400 chr3D 100.000 87 0 0 4010 4096 112210089 112210175 1.620000e-35 161.0
43 TraesCS7D01G394400 chr6D 96.774 93 3 0 4011 4103 452939100 452939008 7.540000e-34 156.0
44 TraesCS7D01G394400 chr4D 96.739 92 3 0 4010 4101 41339601 41339510 2.710000e-33 154.0
45 TraesCS7D01G394400 chr4D 95.833 96 3 1 4011 4106 84532158 84532252 2.710000e-33 154.0
46 TraesCS7D01G394400 chr1B 97.333 75 2 0 4891 4965 426498808 426498734 1.640000e-25 128.0
47 TraesCS7D01G394400 chr1B 100.000 35 0 0 4854 4888 133113077 133113043 1.310000e-06 65.8
48 TraesCS7D01G394400 chr1B 100.000 35 0 0 4854 4888 426498679 426498645 1.310000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G394400 chr7D 509610129 509615746 5617 True 10375.000000 10375 100.000000 1 5618 1 chr7D.!!$R1 5617
1 TraesCS7D01G394400 chr7D 509555724 509559803 4079 True 914.333333 1997 83.716000 983 4794 3 chr7D.!!$R3 3811
2 TraesCS7D01G394400 chr7A 580505858 580510490 4632 True 1694.866667 4093 91.669667 1 4963 3 chr7A.!!$R3 4962
3 TraesCS7D01G394400 chr7A 580693865 580696272 2407 False 1447.000000 1447 77.805000 997 3395 1 chr7A.!!$F2 2398
4 TraesCS7D01G394400 chr7A 580470479 580474472 3993 True 1235.000000 1969 86.038000 1039 4794 2 chr7A.!!$R2 3755
5 TraesCS7D01G394400 chr7B 537827059 537834229 7170 True 1737.000000 3921 91.591333 1 4786 3 chr7B.!!$R3 4785
6 TraesCS7D01G394400 chr7B 538243223 538245627 2404 False 1411.000000 1411 77.503000 997 3395 1 chr7B.!!$F1 2398
7 TraesCS7D01G394400 chr7B 537672831 537676900 4069 True 1271.500000 2025 86.543500 989 4794 2 chr7B.!!$R1 3805
8 TraesCS7D01G394400 chr7B 537791798 537795894 4096 True 1094.575000 3602 90.774250 984 4739 4 chr7B.!!$R2 3755
9 TraesCS7D01G394400 chr6A 298506195 298506853 658 False 680.000000 680 85.801000 4978 5618 1 chr6A.!!$F1 640

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
689 2722 0.322456 TTTGCTGATGGAACCTCGGG 60.322 55.0 0.0 0.0 0.00 5.14 F
1454 3517 0.252103 AACCTCCAGTTCCTCGCCTA 60.252 55.0 0.0 0.0 30.99 3.93 F
1989 4083 0.036294 GCCCCAACTCCTACTGTGTC 60.036 60.0 0.0 0.0 0.00 3.67 F
2403 4503 0.108138 ATGCACTACTCGGTTGCTCC 60.108 55.0 0.0 0.0 0.00 4.70 F
3186 5289 0.249447 TCATGCTATTCGAGTGGGCG 60.249 55.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 3618 0.170561 CGAGAGAAATCCGTGTCCGT 59.829 55.0 0.00 0.0 0.00 4.69 R
2844 4947 0.038310 GCAAGTACTCCAGGCCCTTT 59.962 55.0 0.00 0.0 0.00 3.11 R
3146 5249 0.741326 CGAGTCGTCACCATCCTGAT 59.259 55.0 3.82 0.0 0.00 2.90 R
4215 6718 0.773644 ACCAAGGAAGCATGTGGACT 59.226 50.0 4.88 0.0 35.04 3.85 R
5093 8124 0.105778 GGAAGGGGAGATCAGCGAAG 59.894 60.0 0.00 0.0 0.00 3.79 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
305 307 7.905604 AAGAAATGAAACATGTATCTGTCGA 57.094 32.000 0.00 0.00 0.00 4.20
327 329 8.944927 GTCGAAAAAGAAATGAAACAAGTACTC 58.055 33.333 0.00 0.00 0.00 2.59
328 330 8.670135 TCGAAAAAGAAATGAAACAAGTACTCA 58.330 29.630 0.00 0.00 0.00 3.41
332 334 8.738645 AAAGAAATGAAACAAGTACTCACTCT 57.261 30.769 0.00 0.00 32.29 3.24
439 2457 8.638873 TGACTATATACATCCGACTCACAAAAT 58.361 33.333 0.00 0.00 0.00 1.82
471 2504 8.469309 AACATCTTATATTTGTGAATGGAGGG 57.531 34.615 0.00 0.00 0.00 4.30
472 2505 7.815383 ACATCTTATATTTGTGAATGGAGGGA 58.185 34.615 0.00 0.00 0.00 4.20
474 2507 7.451731 TCTTATATTTGTGAATGGAGGGAGT 57.548 36.000 0.00 0.00 0.00 3.85
475 2508 8.561536 TCTTATATTTGTGAATGGAGGGAGTA 57.438 34.615 0.00 0.00 0.00 2.59
476 2509 8.998814 TCTTATATTTGTGAATGGAGGGAGTAA 58.001 33.333 0.00 0.00 0.00 2.24
477 2510 8.974060 TTATATTTGTGAATGGAGGGAGTAAC 57.026 34.615 0.00 0.00 0.00 2.50
478 2511 4.715534 TTTGTGAATGGAGGGAGTAACA 57.284 40.909 0.00 0.00 0.00 2.41
479 2512 4.715534 TTGTGAATGGAGGGAGTAACAA 57.284 40.909 0.00 0.00 0.00 2.83
480 2513 4.715534 TGTGAATGGAGGGAGTAACAAA 57.284 40.909 0.00 0.00 0.00 2.83
481 2514 5.255397 TGTGAATGGAGGGAGTAACAAAT 57.745 39.130 0.00 0.00 0.00 2.32
482 2515 6.381498 TGTGAATGGAGGGAGTAACAAATA 57.619 37.500 0.00 0.00 0.00 1.40
483 2516 6.785076 TGTGAATGGAGGGAGTAACAAATAA 58.215 36.000 0.00 0.00 0.00 1.40
484 2517 7.235079 TGTGAATGGAGGGAGTAACAAATAAA 58.765 34.615 0.00 0.00 0.00 1.40
485 2518 7.393234 TGTGAATGGAGGGAGTAACAAATAAAG 59.607 37.037 0.00 0.00 0.00 1.85
486 2519 7.610305 GTGAATGGAGGGAGTAACAAATAAAGA 59.390 37.037 0.00 0.00 0.00 2.52
487 2520 8.336235 TGAATGGAGGGAGTAACAAATAAAGAT 58.664 33.333 0.00 0.00 0.00 2.40
488 2521 8.753497 AATGGAGGGAGTAACAAATAAAGATC 57.247 34.615 0.00 0.00 0.00 2.75
552 2585 2.584391 GGCCTTCACGTCACCTCCT 61.584 63.158 0.00 0.00 0.00 3.69
615 2648 2.330216 AGCTAGTGTCACCTCCTTTGT 58.670 47.619 0.00 0.00 0.00 2.83
664 2697 7.040478 GCACATGCCCATCTAACTTAATTATCA 60.040 37.037 0.00 0.00 34.31 2.15
688 2721 1.672881 GATTTGCTGATGGAACCTCGG 59.327 52.381 0.00 0.00 0.00 4.63
689 2722 0.322456 TTTGCTGATGGAACCTCGGG 60.322 55.000 0.00 0.00 0.00 5.14
696 2729 2.202892 GGAACCTCGGGCTTAGCG 60.203 66.667 0.00 0.00 0.00 4.26
763 2796 6.053650 GTGTAGTTTAAACAAGTCTGTCCCT 58.946 40.000 20.06 0.00 33.45 4.20
766 2799 6.694877 AGTTTAAACAAGTCTGTCCCTTTC 57.305 37.500 20.06 0.00 33.45 2.62
815 2848 5.301805 TCTCCTGCAAACGTATGAGATATGA 59.698 40.000 0.00 0.00 0.00 2.15
837 2870 4.890088 ACGCTTAACCTTGACATTGTCTA 58.110 39.130 17.26 9.34 33.15 2.59
888 2921 7.008357 GCTTCGTTTTGGCTATCAATTAACTTC 59.992 37.037 0.00 0.00 34.98 3.01
986 3019 9.588096 ACATAACATGAGTATATACTGACCAGA 57.412 33.333 20.13 2.33 36.50 3.86
1128 3182 3.062466 TCGACTCTCAGGCCACCG 61.062 66.667 5.01 0.00 0.00 4.94
1145 3199 1.623811 ACCGAACTACATCACCTGCTT 59.376 47.619 0.00 0.00 0.00 3.91
1231 3285 3.741388 CGTCTGGTTCAACTTCAACCTCT 60.741 47.826 0.00 0.00 43.43 3.69
1359 3422 2.962569 CTCTTCCTCGCCGACACA 59.037 61.111 0.00 0.00 0.00 3.72
1361 3424 0.319555 CTCTTCCTCGCCGACACAAA 60.320 55.000 0.00 0.00 0.00 2.83
1362 3425 0.320374 TCTTCCTCGCCGACACAAAT 59.680 50.000 0.00 0.00 0.00 2.32
1363 3426 1.546923 TCTTCCTCGCCGACACAAATA 59.453 47.619 0.00 0.00 0.00 1.40
1392 3455 2.122324 TGGAGGAACCCGAACCCA 60.122 61.111 0.00 0.00 38.00 4.51
1398 3461 1.658114 GAACCCGAACCCAAGCAAC 59.342 57.895 0.00 0.00 0.00 4.17
1399 3462 2.125202 GAACCCGAACCCAAGCAACG 62.125 60.000 0.00 0.00 0.00 4.10
1434 3497 2.985456 GTGCTCCAGGACTCAGGG 59.015 66.667 0.00 0.00 33.32 4.45
1454 3517 0.252103 AACCTCCAGTTCCTCGCCTA 60.252 55.000 0.00 0.00 30.99 3.93
1521 3584 4.787280 CTCCTCCCGGGGCAGTCT 62.787 72.222 23.50 0.00 35.33 3.24
1555 3618 2.032528 CCCTTCAGTCCAAGCGCA 59.967 61.111 11.47 0.00 0.00 6.09
1642 3726 1.915489 ACCTCATGAACCATGCTACCA 59.085 47.619 0.00 0.00 41.18 3.25
1677 3767 0.446222 CCAACGCTTATTGGGTGACG 59.554 55.000 3.87 0.00 44.74 4.35
1729 3819 2.612212 GGCAACACGACTCTTTTCTTCA 59.388 45.455 0.00 0.00 0.00 3.02
1769 3859 2.972713 ACTACCATATCAAGGACGGCAT 59.027 45.455 0.00 0.00 0.00 4.40
1815 3906 4.927267 TCCAAACTCCACCATCAGTTAT 57.073 40.909 0.00 0.00 32.36 1.89
1839 3930 0.884704 AACACGCAACGCTTGATCCT 60.885 50.000 0.00 0.00 32.11 3.24
1898 3989 4.778143 CGGGGGAAGGAGCAACGG 62.778 72.222 0.00 0.00 0.00 4.44
1949 4040 1.584380 GAAGGTTGCAGCAGGAGCAG 61.584 60.000 2.05 0.00 43.75 4.24
1989 4083 0.036294 GCCCCAACTCCTACTGTGTC 60.036 60.000 0.00 0.00 0.00 3.67
2035 4129 0.602638 CAAGTGTCCAAGCGGCTACA 60.603 55.000 1.35 0.60 0.00 2.74
2048 4142 2.699954 CGGCTACACTTTCCTTGATGT 58.300 47.619 0.00 0.00 0.00 3.06
2073 4167 2.797156 GCTCAAGTACATAGGATGCACG 59.203 50.000 0.00 0.00 31.80 5.34
2108 4202 2.030540 CACAAAGCTGTCATGGGAACAG 60.031 50.000 8.34 8.34 37.48 3.16
2156 4250 1.686052 GATGCCAAACACCACTTGGAA 59.314 47.619 1.14 0.00 45.31 3.53
2164 4258 2.021457 ACACCACTTGGAAAAACTCGG 58.979 47.619 1.14 0.00 38.94 4.63
2165 4259 2.021457 CACCACTTGGAAAAACTCGGT 58.979 47.619 1.14 0.00 38.94 4.69
2186 4286 4.203950 TGTACGAAAGACATTTGTGCAC 57.796 40.909 10.75 10.75 41.43 4.57
2193 4293 1.949525 AGACATTTGTGCACCACAGAC 59.050 47.619 15.69 2.76 45.39 3.51
2285 4385 0.317160 AAGATGGCGTCGTTGACAGA 59.683 50.000 0.13 0.00 32.09 3.41
2292 4392 2.100631 GTCGTTGACAGATGCCGGG 61.101 63.158 2.18 0.00 32.09 5.73
2339 4439 2.512896 AGGCATTGATCAAGGTGAGGAT 59.487 45.455 20.25 0.00 0.00 3.24
2381 4481 1.040646 TCGCCGAGAAGGATATTGCT 58.959 50.000 0.00 0.00 45.00 3.91
2383 4483 1.795286 CGCCGAGAAGGATATTGCTTC 59.205 52.381 0.99 0.99 43.95 3.86
2403 4503 0.108138 ATGCACTACTCGGTTGCTCC 60.108 55.000 0.00 0.00 0.00 4.70
2433 4536 3.583383 CTGTTGGCAGCAGGTAGC 58.417 61.111 22.05 0.00 46.19 3.58
2447 4550 3.544684 CAGGTAGCCTCATGTTGCATTA 58.455 45.455 10.90 0.00 0.00 1.90
2470 4573 3.679824 ACCTTAGGAAGAAGAACACCG 57.320 47.619 4.77 0.00 0.00 4.94
2538 4641 5.151297 CCACCAATGGCTTTCATAAGTTT 57.849 39.130 0.00 0.00 39.82 2.66
2598 4701 3.134985 TGTTGAAGTTGCTACACTACCCA 59.865 43.478 0.13 0.00 0.00 4.51
2862 4965 1.826385 CAAAGGGCCTGGAGTACTTG 58.174 55.000 6.92 1.41 0.00 3.16
3027 5130 3.339093 AGGGGCACAAGGGGCTAC 61.339 66.667 0.00 0.00 0.00 3.58
3102 5205 1.280746 CAGCTTCGGTGTTGTGCTG 59.719 57.895 0.00 0.00 43.71 4.41
3105 5208 2.024918 CTTCGGTGTTGTGCTGCTT 58.975 52.632 0.00 0.00 0.00 3.91
3186 5289 0.249447 TCATGCTATTCGAGTGGGCG 60.249 55.000 0.00 0.00 0.00 6.13
3232 5335 4.518970 GGACTGAGGTTTTGTTTCATAGCA 59.481 41.667 0.00 0.00 0.00 3.49
3290 5393 1.193426 GTTCTTGCGTGTTGCTCTCTC 59.807 52.381 0.00 0.00 46.63 3.20
3321 5424 3.083997 AATCCTTCGCTCCGCCCT 61.084 61.111 0.00 0.00 0.00 5.19
3402 5505 2.069273 CCTACAAGCTCCAACTGTTCG 58.931 52.381 0.00 0.00 0.00 3.95
3411 5514 1.639534 CAACTGTTCGTCGCCGTTT 59.360 52.632 0.00 0.00 35.01 3.60
3428 5534 0.944311 TTTGCCTCTTCAGTCGACGC 60.944 55.000 10.46 6.15 0.00 5.19
3466 5572 2.194271 GTGGTGCTACTCTTGCGATAC 58.806 52.381 0.00 0.00 0.00 2.24
3505 5687 9.968870 TGTACTTTTTACCAATGGTAATTGTTC 57.031 29.630 23.81 18.45 45.95 3.18
3507 5689 8.880878 ACTTTTTACCAATGGTAATTGTTCAC 57.119 30.769 23.81 0.00 45.95 3.18
3508 5690 8.700973 ACTTTTTACCAATGGTAATTGTTCACT 58.299 29.630 23.81 1.36 45.95 3.41
3513 5695 6.630071 ACCAATGGTAATTGTTCACTATTGC 58.370 36.000 1.52 0.00 40.38 3.56
3541 5733 6.015504 GCTACGTTTCTGTAAACATGACATG 58.984 40.000 14.02 14.02 44.37 3.21
3569 5766 6.647895 TCATGCATTCTAGCTACATACATGTG 59.352 38.462 9.11 0.00 41.89 3.21
3583 5948 9.534565 CTACATACATGTGTTCTAGTAAATGCT 57.465 33.333 9.11 0.00 41.89 3.79
3631 5996 3.505680 GTGGTCCAGTTATGCAACAATCA 59.494 43.478 0.00 0.00 37.10 2.57
3654 6019 7.092079 TCATTTGGTTTGAGCACTAATTCATG 58.908 34.615 0.00 0.00 0.00 3.07
3823 6205 3.869912 GCTCATTCAGTTCTACCTGCCAA 60.870 47.826 0.00 0.00 32.32 4.52
3838 6220 4.459337 ACCTGCCAAAGAGCAAAGTATTAC 59.541 41.667 0.00 0.00 43.52 1.89
3841 6223 6.037610 CCTGCCAAAGAGCAAAGTATTACTAG 59.962 42.308 0.00 0.00 43.52 2.57
3842 6224 5.354234 TGCCAAAGAGCAAAGTATTACTAGC 59.646 40.000 11.30 11.30 40.56 3.42
3843 6225 5.354234 GCCAAAGAGCAAAGTATTACTAGCA 59.646 40.000 18.03 0.00 33.47 3.49
3844 6226 6.128007 GCCAAAGAGCAAAGTATTACTAGCAA 60.128 38.462 18.03 0.00 33.47 3.91
3886 6380 7.175104 AGTTAGTTGGGCATTTCTCATAAGAA 58.825 34.615 0.00 0.00 39.78 2.52
3889 6383 5.954150 AGTTGGGCATTTCTCATAAGAACAT 59.046 36.000 0.00 0.00 41.23 2.71
3937 6432 3.193267 TGGGTGCTTCACAGATATTTTGC 59.807 43.478 0.00 0.00 35.86 3.68
3939 6434 3.193267 GGTGCTTCACAGATATTTTGCCA 59.807 43.478 0.00 0.00 35.86 4.92
3944 6439 5.928264 GCTTCACAGATATTTTGCCAAAAGT 59.072 36.000 8.75 0.00 33.22 2.66
3962 6457 8.520351 GCCAAAAGTACAACCAATATAAGTTCT 58.480 33.333 0.00 0.00 0.00 3.01
4012 6507 7.840931 TCAGCTTCTCACTCATTTGTCTAATA 58.159 34.615 0.00 0.00 0.00 0.98
4013 6508 7.761704 TCAGCTTCTCACTCATTTGTCTAATAC 59.238 37.037 0.00 0.00 0.00 1.89
4014 6509 7.763528 CAGCTTCTCACTCATTTGTCTAATACT 59.236 37.037 0.00 0.00 0.00 2.12
4015 6510 7.978975 AGCTTCTCACTCATTTGTCTAATACTC 59.021 37.037 0.00 0.00 0.00 2.59
4016 6511 7.223777 GCTTCTCACTCATTTGTCTAATACTCC 59.776 40.741 0.00 0.00 0.00 3.85
4017 6512 7.113658 TCTCACTCATTTGTCTAATACTCCC 57.886 40.000 0.00 0.00 0.00 4.30
4018 6513 6.897966 TCTCACTCATTTGTCTAATACTCCCT 59.102 38.462 0.00 0.00 0.00 4.20
4019 6514 7.068839 TCTCACTCATTTGTCTAATACTCCCTC 59.931 40.741 0.00 0.00 0.00 4.30
4020 6515 6.098409 TCACTCATTTGTCTAATACTCCCTCC 59.902 42.308 0.00 0.00 0.00 4.30
4021 6516 5.069251 ACTCATTTGTCTAATACTCCCTCCG 59.931 44.000 0.00 0.00 0.00 4.63
4022 6517 4.960469 TCATTTGTCTAATACTCCCTCCGT 59.040 41.667 0.00 0.00 0.00 4.69
4023 6518 4.996788 TTTGTCTAATACTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
4024 6519 2.941480 TGTCTAATACTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
4025 6520 2.237643 GTCTAATACTCCCTCCGTCCC 58.762 57.143 0.00 0.00 0.00 4.46
4026 6521 1.854939 TCTAATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37
4027 6522 2.449730 TCTAATACTCCCTCCGTCCCAT 59.550 50.000 0.00 0.00 0.00 4.00
4028 6523 3.659195 TCTAATACTCCCTCCGTCCCATA 59.341 47.826 0.00 0.00 0.00 2.74
4029 6524 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
4030 6525 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
4031 6526 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
4032 6527 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4033 6528 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4034 6529 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4035 6530 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4036 6531 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4037 6532 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
4038 6533 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
4039 6534 5.247564 CCCTCCGTCCCATAATATAAGAACA 59.752 44.000 0.00 0.00 0.00 3.18
4040 6535 6.070194 CCCTCCGTCCCATAATATAAGAACAT 60.070 42.308 0.00 0.00 0.00 2.71
4041 6536 7.394816 CCTCCGTCCCATAATATAAGAACATT 58.605 38.462 0.00 0.00 0.00 2.71
4042 6537 7.883311 CCTCCGTCCCATAATATAAGAACATTT 59.117 37.037 0.00 0.00 0.00 2.32
4043 6538 9.284968 CTCCGTCCCATAATATAAGAACATTTT 57.715 33.333 0.00 0.00 0.00 1.82
4044 6539 9.635404 TCCGTCCCATAATATAAGAACATTTTT 57.365 29.630 0.00 0.00 0.00 1.94
4045 6540 9.677567 CCGTCCCATAATATAAGAACATTTTTG 57.322 33.333 0.00 0.00 0.00 2.44
4059 6554 9.950680 AAGAACATTTTTGACATTAGTGTAGTG 57.049 29.630 0.00 0.00 39.09 2.74
4060 6555 9.120538 AGAACATTTTTGACATTAGTGTAGTGT 57.879 29.630 0.00 0.00 39.09 3.55
4061 6556 9.730420 GAACATTTTTGACATTAGTGTAGTGTT 57.270 29.630 0.00 0.00 39.09 3.32
4068 6563 9.705471 TTTGACATTAGTGTAGTGTTAAAAACG 57.295 29.630 0.00 0.00 39.09 3.60
4069 6564 8.422973 TGACATTAGTGTAGTGTTAAAAACGT 57.577 30.769 0.00 0.00 39.09 3.99
4070 6565 8.881743 TGACATTAGTGTAGTGTTAAAAACGTT 58.118 29.630 0.00 0.00 39.09 3.99
4071 6566 9.361712 GACATTAGTGTAGTGTTAAAAACGTTC 57.638 33.333 0.00 0.00 39.09 3.95
4072 6567 9.101655 ACATTAGTGTAGTGTTAAAAACGTTCT 57.898 29.630 0.00 0.00 36.63 3.01
4073 6568 9.925268 CATTAGTGTAGTGTTAAAAACGTTCTT 57.075 29.630 0.00 0.00 0.00 2.52
4088 6583 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
4089 6584 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
4090 6585 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
4091 6586 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
4092 6587 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
4093 6588 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
4094 6589 5.970640 TCTTATATTTTGGGACAGAGGGAGT 59.029 40.000 0.00 0.00 42.39 3.85
4100 6595 4.834406 TTGGGACAGAGGGAGTAGATAT 57.166 45.455 0.00 0.00 42.39 1.63
4122 6618 3.753294 AACAGACCAACAGTAGGTGAG 57.247 47.619 0.00 0.00 40.09 3.51
4127 6623 3.069729 AGACCAACAGTAGGTGAGTGAAC 59.930 47.826 0.00 0.00 40.09 3.18
4192 6694 9.685276 AGAAAATTTTGAAGGGTGAAGAAAAAT 57.315 25.926 8.47 0.00 0.00 1.82
4205 6708 7.614192 GGGTGAAGAAAAATAGGGTTTCTATGA 59.386 37.037 0.17 0.00 43.00 2.15
4238 6741 1.614051 CCACATGCTTCCTTGGTGCTA 60.614 52.381 0.00 0.00 0.00 3.49
4240 6743 1.073763 ACATGCTTCCTTGGTGCTACA 59.926 47.619 0.00 0.00 0.00 2.74
4241 6744 2.161855 CATGCTTCCTTGGTGCTACAA 58.838 47.619 8.26 0.00 0.00 2.41
4242 6745 2.356665 TGCTTCCTTGGTGCTACAAA 57.643 45.000 8.26 0.00 0.00 2.83
4243 6746 2.660572 TGCTTCCTTGGTGCTACAAAA 58.339 42.857 8.26 0.00 0.00 2.44
4244 6747 2.622942 TGCTTCCTTGGTGCTACAAAAG 59.377 45.455 8.26 0.00 0.00 2.27
4245 6748 2.623416 GCTTCCTTGGTGCTACAAAAGT 59.377 45.455 7.01 0.00 0.00 2.66
4246 6749 3.550842 GCTTCCTTGGTGCTACAAAAGTG 60.551 47.826 7.01 0.00 0.00 3.16
4252 7259 2.948979 TGGTGCTACAAAAGTGTCAAGG 59.051 45.455 0.00 0.00 39.30 3.61
4285 7292 3.476552 TCCAACAAGAGTGTAAAGGCTG 58.523 45.455 0.00 0.00 36.80 4.85
4289 7296 3.931578 ACAAGAGTGTAAAGGCTGCTAG 58.068 45.455 0.00 0.00 35.72 3.42
4290 7297 3.325135 ACAAGAGTGTAAAGGCTGCTAGT 59.675 43.478 0.00 0.00 35.72 2.57
4335 7353 8.924511 AAACCTCAAACTTTATTCAGATCAGA 57.075 30.769 0.00 0.00 0.00 3.27
4339 7357 9.784680 CCTCAAACTTTATTCAGATCAGATTTG 57.215 33.333 0.00 0.00 0.00 2.32
4411 7430 7.678947 AGATAAGACTGAAACATCAACCTTG 57.321 36.000 0.00 0.00 0.00 3.61
4441 7462 3.817647 AGACTGAAACATCAAGCCTTGAC 59.182 43.478 9.77 0.00 43.48 3.18
4442 7463 3.554934 ACTGAAACATCAAGCCTTGACA 58.445 40.909 9.77 1.93 43.48 3.58
4445 7466 5.069516 ACTGAAACATCAAGCCTTGACATTT 59.930 36.000 9.77 12.67 43.48 2.32
4478 7499 1.892338 CATGGGGAATTGCGCAACT 59.108 52.632 27.64 16.51 0.00 3.16
4524 7545 2.660572 TCCTGCTAGGATGTCTCTCAC 58.339 52.381 1.25 0.00 40.06 3.51
4576 7599 3.767131 TCATCGTCTTCACCAGGAATACA 59.233 43.478 0.00 0.00 33.47 2.29
4604 7627 3.464907 CAGATACAGAACCATGGCAGAG 58.535 50.000 13.04 2.16 0.00 3.35
4613 7636 1.753073 ACCATGGCAGAGCAAAATAGC 59.247 47.619 13.04 0.00 0.00 2.97
4667 7690 2.851195 CAAGTGAGGTACCAGCAAACT 58.149 47.619 15.94 6.89 0.00 2.66
4732 7763 3.432378 ACTTCCCAGTGAGTACAGTAGG 58.568 50.000 0.00 0.00 31.18 3.18
4740 7771 5.169295 CAGTGAGTACAGTAGGGCTTTAAC 58.831 45.833 0.00 0.00 0.00 2.01
4786 7817 3.127425 AGTAACCCTCTTGTGAACTGC 57.873 47.619 0.00 0.00 0.00 4.40
4803 7834 2.420022 ACTGCATAGCCAACGATTTCAC 59.580 45.455 0.00 0.00 0.00 3.18
4816 7847 2.688507 GATTTCACGTCTGGAGCTTGA 58.311 47.619 0.00 0.00 0.00 3.02
4819 7850 1.865865 TCACGTCTGGAGCTTGAAAC 58.134 50.000 0.00 0.00 0.00 2.78
4822 7853 1.000955 ACGTCTGGAGCTTGAAACGAT 59.999 47.619 16.23 2.42 34.46 3.73
4826 7857 0.690192 TGGAGCTTGAAACGATGGGA 59.310 50.000 0.00 0.00 0.00 4.37
4828 7859 0.729690 GAGCTTGAAACGATGGGAGC 59.270 55.000 0.00 0.00 0.00 4.70
4829 7860 0.326264 AGCTTGAAACGATGGGAGCT 59.674 50.000 0.00 0.00 35.78 4.09
4830 7861 0.449388 GCTTGAAACGATGGGAGCTG 59.551 55.000 0.00 0.00 0.00 4.24
4831 7862 1.813513 CTTGAAACGATGGGAGCTGT 58.186 50.000 0.00 0.00 0.00 4.40
4869 7900 1.133513 ACCAATGTTCTGGCTTGTCCA 60.134 47.619 0.00 0.00 44.18 4.02
4914 7945 9.162793 CGATTCCAAAAAGATAATCATTCTTCG 57.837 33.333 0.00 0.00 32.33 3.79
4925 7956 8.734386 AGATAATCATTCTTCGAACTTTTTGCT 58.266 29.630 0.00 0.00 0.00 3.91
4963 7994 3.063997 CCATTGCTAAACTGGTCTAAGCG 59.936 47.826 0.00 0.00 35.95 4.68
4965 7996 3.671008 TGCTAAACTGGTCTAAGCGAA 57.329 42.857 0.00 0.00 35.95 4.70
4966 7997 3.997762 TGCTAAACTGGTCTAAGCGAAA 58.002 40.909 0.00 0.00 35.95 3.46
4967 7998 4.382291 TGCTAAACTGGTCTAAGCGAAAA 58.618 39.130 0.00 0.00 35.95 2.29
5110 8141 0.827368 GTCTTCGCTGATCTCCCCTT 59.173 55.000 0.00 0.00 0.00 3.95
5114 8145 2.812619 CGCTGATCTCCCCTTCCCC 61.813 68.421 0.00 0.00 0.00 4.81
5115 8146 1.694169 GCTGATCTCCCCTTCCCCA 60.694 63.158 0.00 0.00 0.00 4.96
5125 8156 3.771160 CTTCCCCAGTCCCCGTCG 61.771 72.222 0.00 0.00 0.00 5.12
5167 8198 2.108566 CTCCGCTGGGCTGATCTG 59.891 66.667 0.00 0.00 0.00 2.90
5178 8209 1.370437 CTGATCTGGCCGAGGATGG 59.630 63.158 9.85 1.13 0.00 3.51
5205 8237 2.778717 CCCCCTCCCATTCCCTCC 60.779 72.222 0.00 0.00 0.00 4.30
5212 8244 4.918201 CCATTCCCTCCGCCGCTC 62.918 72.222 0.00 0.00 0.00 5.03
5284 8316 4.527583 GCAGCTCAGCCTCTCCCG 62.528 72.222 0.00 0.00 0.00 5.14
5298 8330 4.379243 CCCGTGCGAGGTTCTGCT 62.379 66.667 0.00 0.00 0.00 4.24
5301 8333 3.426568 GTGCGAGGTTCTGCTGCC 61.427 66.667 0.00 0.00 0.00 4.85
5534 8586 3.782443 CCCCCTTCCGTCCCTTCG 61.782 72.222 0.00 0.00 0.00 3.79
5536 8588 2.577593 CCCTTCCGTCCCTTCGTC 59.422 66.667 0.00 0.00 0.00 4.20
5551 8603 1.805539 CGTCGCAGCCTTCGAATCA 60.806 57.895 0.00 0.00 37.73 2.57
5555 8607 0.580578 CGCAGCCTTCGAATCATCTG 59.419 55.000 0.00 5.15 0.00 2.90
5567 8619 2.611225 ATCATCTGCTCTCCGTTTCC 57.389 50.000 0.00 0.00 0.00 3.13
5613 8665 4.767255 GCTGGTCCTGTCCCGCAG 62.767 72.222 0.00 0.00 44.63 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.140325 ACCACACCTTCTGGTTATGTG 57.860 47.619 0.00 0.00 46.05 3.21
219 221 7.907389 AGAAACACTAGTGGATGAAACTCATA 58.093 34.615 26.12 0.00 37.20 2.15
305 307 9.788960 GAGTGAGTACTTGTTTCATTTCTTTTT 57.211 29.630 0.00 0.00 37.25 1.94
418 2436 6.591935 ACCATTTTGTGAGTCGGATGTATAT 58.408 36.000 0.00 0.00 0.00 0.86
465 2498 6.346096 CGATCTTTATTTGTTACTCCCTCCA 58.654 40.000 0.00 0.00 0.00 3.86
466 2499 5.758784 CCGATCTTTATTTGTTACTCCCTCC 59.241 44.000 0.00 0.00 0.00 4.30
467 2500 5.758784 CCCGATCTTTATTTGTTACTCCCTC 59.241 44.000 0.00 0.00 0.00 4.30
469 2502 4.820173 CCCCGATCTTTATTTGTTACTCCC 59.180 45.833 0.00 0.00 0.00 4.30
471 2504 7.046033 TCTTCCCCGATCTTTATTTGTTACTC 58.954 38.462 0.00 0.00 0.00 2.59
472 2505 6.954232 TCTTCCCCGATCTTTATTTGTTACT 58.046 36.000 0.00 0.00 0.00 2.24
474 2507 8.638629 TTTTCTTCCCCGATCTTTATTTGTTA 57.361 30.769 0.00 0.00 0.00 2.41
475 2508 7.533289 TTTTCTTCCCCGATCTTTATTTGTT 57.467 32.000 0.00 0.00 0.00 2.83
476 2509 7.178451 ACATTTTCTTCCCCGATCTTTATTTGT 59.822 33.333 0.00 0.00 0.00 2.83
477 2510 7.547227 ACATTTTCTTCCCCGATCTTTATTTG 58.453 34.615 0.00 0.00 0.00 2.32
478 2511 7.396055 TGACATTTTCTTCCCCGATCTTTATTT 59.604 33.333 0.00 0.00 0.00 1.40
479 2512 6.889722 TGACATTTTCTTCCCCGATCTTTATT 59.110 34.615 0.00 0.00 0.00 1.40
480 2513 6.423182 TGACATTTTCTTCCCCGATCTTTAT 58.577 36.000 0.00 0.00 0.00 1.40
481 2514 5.811190 TGACATTTTCTTCCCCGATCTTTA 58.189 37.500 0.00 0.00 0.00 1.85
482 2515 4.662278 TGACATTTTCTTCCCCGATCTTT 58.338 39.130 0.00 0.00 0.00 2.52
483 2516 4.301072 TGACATTTTCTTCCCCGATCTT 57.699 40.909 0.00 0.00 0.00 2.40
484 2517 4.164988 AGATGACATTTTCTTCCCCGATCT 59.835 41.667 0.00 0.00 0.00 2.75
485 2518 4.455606 AGATGACATTTTCTTCCCCGATC 58.544 43.478 0.00 0.00 0.00 3.69
486 2519 4.510167 AGATGACATTTTCTTCCCCGAT 57.490 40.909 0.00 0.00 0.00 4.18
487 2520 4.301072 AAGATGACATTTTCTTCCCCGA 57.699 40.909 0.00 0.00 0.00 5.14
488 2521 4.702131 AGAAAGATGACATTTTCTTCCCCG 59.298 41.667 14.60 0.00 39.86 5.73
527 2560 2.847234 ACGTGAAGGCCAGGGTGA 60.847 61.111 5.01 0.00 35.10 4.02
552 2585 4.158394 GCCAAACCATCAAGCTTAGATCAA 59.842 41.667 0.00 0.00 0.00 2.57
615 2648 0.323302 TTGGCACGAACCATGAGCTA 59.677 50.000 0.00 0.00 40.13 3.32
664 2697 3.760684 GAGGTTCCATCAGCAAATCAGTT 59.239 43.478 0.00 0.00 0.00 3.16
688 2721 2.180159 TTGACCCAGACCGCTAAGCC 62.180 60.000 0.00 0.00 0.00 4.35
689 2722 0.741221 CTTGACCCAGACCGCTAAGC 60.741 60.000 0.00 0.00 0.00 3.09
696 2729 4.022849 CACTTTTGAATCTTGACCCAGACC 60.023 45.833 0.00 0.00 0.00 3.85
763 2796 4.748892 TGATTGCCGTTTTGTTTCTGAAA 58.251 34.783 0.00 0.00 0.00 2.69
766 2799 5.655893 ATTTGATTGCCGTTTTGTTTCTG 57.344 34.783 0.00 0.00 0.00 3.02
815 2848 3.740115 AGACAATGTCAAGGTTAAGCGT 58.260 40.909 16.38 0.00 34.60 5.07
854 2887 0.243636 CCAAAACGAAGCATCCCACC 59.756 55.000 0.00 0.00 0.00 4.61
859 2892 4.355543 TTGATAGCCAAAACGAAGCATC 57.644 40.909 0.00 0.00 0.00 3.91
866 2899 7.752695 AGAGAAGTTAATTGATAGCCAAAACG 58.247 34.615 0.00 0.00 38.43 3.60
976 3009 7.925043 TTTGTGTTTACTTTTCTGGTCAGTA 57.075 32.000 0.00 0.00 0.00 2.74
986 3019 7.271511 TGATGGCTTCATTTGTGTTTACTTTT 58.728 30.769 0.00 0.00 0.00 2.27
1017 3050 2.160417 GCTGGAAAAAGAGGACGACATG 59.840 50.000 0.00 0.00 0.00 3.21
1018 3051 2.427506 GCTGGAAAAAGAGGACGACAT 58.572 47.619 0.00 0.00 0.00 3.06
1019 3052 1.542547 GGCTGGAAAAAGAGGACGACA 60.543 52.381 0.00 0.00 0.00 4.35
1128 3182 3.003480 GGACAAGCAGGTGATGTAGTTC 58.997 50.000 0.00 0.00 0.00 3.01
1145 3199 1.306654 AAGGCATACTCCCCGGACA 60.307 57.895 0.73 0.00 0.00 4.02
1359 3422 2.573369 CTCCAGATGCTGCTGCTATTT 58.427 47.619 17.00 1.79 40.48 1.40
1361 3424 0.397187 CCTCCAGATGCTGCTGCTAT 59.603 55.000 17.00 8.47 40.48 2.97
1362 3425 0.688749 TCCTCCAGATGCTGCTGCTA 60.689 55.000 17.00 3.79 40.48 3.49
1363 3426 1.559965 TTCCTCCAGATGCTGCTGCT 61.560 55.000 17.00 2.26 40.48 4.24
1392 3455 4.573162 GAGCCGTACTCGTTGCTT 57.427 55.556 0.00 0.00 35.46 3.91
1399 3462 1.025647 ACGAGGTCAGAGCCGTACTC 61.026 60.000 12.60 0.00 46.66 2.59
1555 3618 0.170561 CGAGAGAAATCCGTGTCCGT 59.829 55.000 0.00 0.00 0.00 4.69
1658 3748 0.446222 CGTCACCCAATAAGCGTTGG 59.554 55.000 10.48 10.48 46.58 3.77
1673 3763 1.600107 GATTGGTAGGTGCCCGTCA 59.400 57.895 0.00 0.00 0.00 4.35
1677 3767 2.192175 CCGGATTGGTAGGTGCCC 59.808 66.667 0.00 0.00 0.00 5.36
1729 3819 4.162690 GAGATGCCCCGGCGAGTT 62.163 66.667 9.30 0.00 45.51 3.01
1815 3906 2.109739 AAGCGTTGCGTGTTGGTGA 61.110 52.632 0.00 0.00 0.00 4.02
1854 3945 3.366739 CTTCGGCCGGGTGTAGACC 62.367 68.421 27.83 0.00 42.27 3.85
1879 3970 4.426313 GTTGCTCCTTCCCCCGGG 62.426 72.222 15.80 15.80 0.00 5.73
1898 3989 2.357517 CAGTGACTGCCCACGACC 60.358 66.667 0.00 0.00 41.67 4.79
1949 4040 0.652071 GCACAAACCTTGCAAAGTGC 59.348 50.000 18.28 18.28 44.25 4.40
2035 4129 2.157738 GAGCTGCACATCAAGGAAAGT 58.842 47.619 1.02 0.00 0.00 2.66
2048 4142 3.742327 GCATCCTATGTACTTGAGCTGCA 60.742 47.826 1.02 0.00 0.00 4.41
2073 4167 2.287608 GCTTTGTGGTACAAACTCCTGC 60.288 50.000 3.20 2.32 42.55 4.85
2098 4192 1.746615 CGGAGTGGCTGTTCCCATG 60.747 63.158 0.00 0.00 37.20 3.66
2164 4258 3.966218 GTGCACAAATGTCTTTCGTACAC 59.034 43.478 13.17 0.00 0.00 2.90
2165 4259 3.002862 GGTGCACAAATGTCTTTCGTACA 59.997 43.478 20.43 0.00 0.00 2.90
2183 4277 1.956170 CACTGGTCGTCTGTGGTGC 60.956 63.158 9.35 0.00 40.32 5.01
2186 4286 1.300931 CCACACTGGTCGTCTGTGG 60.301 63.158 17.05 12.01 46.82 4.17
2193 4293 0.962489 AGAAGTCTCCACACTGGTCG 59.038 55.000 0.00 0.00 39.03 4.79
2292 4392 0.881118 TGACATTTTCTTCCTGCCGC 59.119 50.000 0.00 0.00 0.00 6.53
2339 4439 4.096003 GCACCGAGGGGCTGCTTA 62.096 66.667 9.48 0.00 37.37 3.09
2364 4464 2.838736 TGAAGCAATATCCTTCTCGGC 58.161 47.619 13.89 0.00 39.47 5.54
2381 4481 1.001974 AGCAACCGAGTAGTGCATGAA 59.998 47.619 0.00 0.00 0.00 2.57
2383 4483 1.002366 GAGCAACCGAGTAGTGCATG 58.998 55.000 0.00 0.00 0.00 4.06
2433 4536 5.760253 CCTAAGGTAGTAATGCAACATGAGG 59.240 44.000 0.00 0.00 0.00 3.86
2442 4545 7.278203 GTGTTCTTCTTCCTAAGGTAGTAATGC 59.722 40.741 0.00 0.00 0.00 3.56
2447 4550 4.220163 CGGTGTTCTTCTTCCTAAGGTAGT 59.780 45.833 0.00 0.00 0.00 2.73
2470 4573 1.168714 GCCCTCACAAAGTCATGGTC 58.831 55.000 0.00 0.00 0.00 4.02
2538 4641 1.198713 CAAAGCCTCCTCTGCCTAGA 58.801 55.000 0.00 0.00 0.00 2.43
2585 4688 3.223435 GCTATCTCTGGGTAGTGTAGCA 58.777 50.000 0.00 0.00 32.98 3.49
2598 4701 4.022603 TGAGCTTCTTCACTGCTATCTCT 58.977 43.478 0.00 0.00 37.16 3.10
2844 4947 0.038310 GCAAGTACTCCAGGCCCTTT 59.962 55.000 0.00 0.00 0.00 3.11
2884 4987 2.417933 GCTTGATGTCACAGTGGATGAC 59.582 50.000 0.00 6.88 45.58 3.06
3027 5130 2.035626 AACCACTCGGGGGCAATG 59.964 61.111 0.00 0.00 42.91 2.82
3102 5205 1.463831 CGGCAGCATATCATCTCAAGC 59.536 52.381 0.00 0.00 0.00 4.01
3105 5208 3.181462 ACTTTCGGCAGCATATCATCTCA 60.181 43.478 0.00 0.00 0.00 3.27
3146 5249 0.741326 CGAGTCGTCACCATCCTGAT 59.259 55.000 3.82 0.00 0.00 2.90
3186 5289 1.247567 CATCACCAACCAACTGACCC 58.752 55.000 0.00 0.00 0.00 4.46
3232 5335 2.127271 TCCACAATGGCGTCATCATT 57.873 45.000 1.37 0.00 37.47 2.57
3248 5351 2.568956 CTCTCCACTCTGACCAAATCCA 59.431 50.000 0.00 0.00 0.00 3.41
3402 5505 1.901650 CTGAAGAGGCAAACGGCGAC 61.902 60.000 16.62 0.00 46.16 5.19
3411 5514 2.258591 GCGTCGACTGAAGAGGCA 59.741 61.111 14.70 0.00 45.51 4.75
3428 5534 1.079543 CCTGACAACAGAGGGCTCG 60.080 63.158 0.00 0.00 46.03 5.03
3541 5733 6.450545 TGTATGTAGCTAGAATGCATGACTC 58.549 40.000 0.00 0.00 34.99 3.36
3631 5996 7.230849 TCATGAATTAGTGCTCAAACCAAAT 57.769 32.000 0.00 0.00 0.00 2.32
3793 6168 6.155221 AGGTAGAACTGAATGAGCTATTGACA 59.845 38.462 0.00 0.00 0.00 3.58
3823 6205 9.892130 ATAGTTTGCTAGTAATACTTTGCTCTT 57.108 29.630 15.26 5.57 31.15 2.85
3859 6353 5.649782 ATGAGAAATGCCCAACTAACTTG 57.350 39.130 0.00 0.00 0.00 3.16
3865 6359 5.324409 TGTTCTTATGAGAAATGCCCAACT 58.676 37.500 0.82 0.00 43.21 3.16
3903 6398 3.245371 TGAAGCACCCAGATTCATTTCCT 60.245 43.478 0.00 0.00 46.84 3.36
3932 6427 9.482627 CTTATATTGGTTGTACTTTTGGCAAAA 57.517 29.630 22.87 22.87 0.00 2.44
3972 6467 7.065085 GTGAGAAGCTGATAAGCATTTCTAACA 59.935 37.037 13.46 4.78 34.58 2.41
4012 6507 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4013 6508 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4014 6509 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
4015 6510 5.247564 TGTTCTTATATTATGGGACGGAGGG 59.752 44.000 0.00 0.00 0.00 4.30
4016 6511 6.354794 TGTTCTTATATTATGGGACGGAGG 57.645 41.667 0.00 0.00 0.00 4.30
4017 6512 8.848474 AAATGTTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
4018 6513 9.635404 AAAAATGTTCTTATATTATGGGACGGA 57.365 29.630 0.00 0.00 0.00 4.69
4019 6514 9.677567 CAAAAATGTTCTTATATTATGGGACGG 57.322 33.333 0.00 0.00 0.00 4.79
4033 6528 9.950680 CACTACACTAATGTCAAAAATGTTCTT 57.049 29.630 0.00 0.00 40.48 2.52
4034 6529 9.120538 ACACTACACTAATGTCAAAAATGTTCT 57.879 29.630 0.00 0.00 40.48 3.01
4035 6530 9.730420 AACACTACACTAATGTCAAAAATGTTC 57.270 29.630 0.00 0.00 40.48 3.18
4042 6537 9.705471 CGTTTTTAACACTACACTAATGTCAAA 57.295 29.630 0.00 0.00 40.48 2.69
4043 6538 8.881743 ACGTTTTTAACACTACACTAATGTCAA 58.118 29.630 0.00 0.00 40.48 3.18
4044 6539 8.422973 ACGTTTTTAACACTACACTAATGTCA 57.577 30.769 0.00 0.00 40.48 3.58
4045 6540 9.361712 GAACGTTTTTAACACTACACTAATGTC 57.638 33.333 0.46 0.00 40.48 3.06
4046 6541 9.101655 AGAACGTTTTTAACACTACACTAATGT 57.898 29.630 0.46 0.00 43.30 2.71
4047 6542 9.925268 AAGAACGTTTTTAACACTACACTAATG 57.075 29.630 0.46 0.00 0.00 1.90
4062 6557 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
4063 6558 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
4064 6559 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
4065 6560 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
4066 6561 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
4067 6562 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
4068 6563 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
4069 6564 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
4070 6565 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
4071 6566 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
4072 6567 7.136885 TCTACTCCCTCTGTCCCAAAATATAA 58.863 38.462 0.00 0.00 0.00 0.98
4073 6568 6.689561 TCTACTCCCTCTGTCCCAAAATATA 58.310 40.000 0.00 0.00 0.00 0.86
4074 6569 5.538877 TCTACTCCCTCTGTCCCAAAATAT 58.461 41.667 0.00 0.00 0.00 1.28
4075 6570 4.955335 TCTACTCCCTCTGTCCCAAAATA 58.045 43.478 0.00 0.00 0.00 1.40
4076 6571 3.803340 TCTACTCCCTCTGTCCCAAAAT 58.197 45.455 0.00 0.00 0.00 1.82
4077 6572 3.269592 TCTACTCCCTCTGTCCCAAAA 57.730 47.619 0.00 0.00 0.00 2.44
4078 6573 3.491766 ATCTACTCCCTCTGTCCCAAA 57.508 47.619 0.00 0.00 0.00 3.28
4079 6574 4.834406 ATATCTACTCCCTCTGTCCCAA 57.166 45.455 0.00 0.00 0.00 4.12
4080 6575 4.834406 AATATCTACTCCCTCTGTCCCA 57.166 45.455 0.00 0.00 0.00 4.37
4081 6576 6.075984 TGTTAATATCTACTCCCTCTGTCCC 58.924 44.000 0.00 0.00 0.00 4.46
4082 6577 7.005296 TCTGTTAATATCTACTCCCTCTGTCC 58.995 42.308 0.00 0.00 0.00 4.02
4083 6578 7.040271 GGTCTGTTAATATCTACTCCCTCTGTC 60.040 44.444 0.00 0.00 0.00 3.51
4084 6579 6.778559 GGTCTGTTAATATCTACTCCCTCTGT 59.221 42.308 0.00 0.00 0.00 3.41
4085 6580 6.778069 TGGTCTGTTAATATCTACTCCCTCTG 59.222 42.308 0.00 0.00 0.00 3.35
4086 6581 6.923670 TGGTCTGTTAATATCTACTCCCTCT 58.076 40.000 0.00 0.00 0.00 3.69
4087 6582 7.069578 TGTTGGTCTGTTAATATCTACTCCCTC 59.930 40.741 0.00 0.00 0.00 4.30
4088 6583 6.901300 TGTTGGTCTGTTAATATCTACTCCCT 59.099 38.462 0.00 0.00 0.00 4.20
4089 6584 7.120923 TGTTGGTCTGTTAATATCTACTCCC 57.879 40.000 0.00 0.00 0.00 4.30
4090 6585 7.783042 ACTGTTGGTCTGTTAATATCTACTCC 58.217 38.462 0.00 0.00 0.00 3.85
4091 6586 9.953697 CTACTGTTGGTCTGTTAATATCTACTC 57.046 37.037 0.00 0.00 0.00 2.59
4092 6587 8.915036 CCTACTGTTGGTCTGTTAATATCTACT 58.085 37.037 0.00 0.00 0.00 2.57
4093 6588 8.693625 ACCTACTGTTGGTCTGTTAATATCTAC 58.306 37.037 8.14 0.00 31.03 2.59
4094 6589 8.692710 CACCTACTGTTGGTCTGTTAATATCTA 58.307 37.037 11.02 0.00 35.28 1.98
4100 6595 4.652421 ACTCACCTACTGTTGGTCTGTTAA 59.348 41.667 11.02 0.00 35.28 2.01
4205 6708 4.942761 AGCATGTGGACTGTGAAATTTT 57.057 36.364 0.00 0.00 0.00 1.82
4215 6718 0.773644 ACCAAGGAAGCATGTGGACT 59.226 50.000 4.88 0.00 35.04 3.85
4238 6741 5.659079 TGGGTAAATTCCTTGACACTTTTGT 59.341 36.000 0.00 0.00 39.32 2.83
4240 6743 5.897250 AGTGGGTAAATTCCTTGACACTTTT 59.103 36.000 0.00 0.00 34.59 2.27
4241 6744 5.454966 AGTGGGTAAATTCCTTGACACTTT 58.545 37.500 0.00 0.00 34.59 2.66
4242 6745 5.061721 AGTGGGTAAATTCCTTGACACTT 57.938 39.130 0.00 0.00 34.59 3.16
4243 6746 4.506802 GGAGTGGGTAAATTCCTTGACACT 60.507 45.833 0.00 0.00 40.28 3.55
4244 6747 3.756963 GGAGTGGGTAAATTCCTTGACAC 59.243 47.826 0.00 0.00 0.00 3.67
4245 6748 3.396276 TGGAGTGGGTAAATTCCTTGACA 59.604 43.478 0.00 0.00 0.00 3.58
4246 6749 4.028993 TGGAGTGGGTAAATTCCTTGAC 57.971 45.455 0.00 0.00 0.00 3.18
4252 7259 5.070685 ACTCTTGTTGGAGTGGGTAAATTC 58.929 41.667 0.00 0.00 43.89 2.17
4278 7285 7.168905 ACTAATGAACTTTACTAGCAGCCTTT 58.831 34.615 0.00 0.00 0.00 3.11
4441 7462 4.441079 CCATGCTTTTCTGGCTAGGAAATG 60.441 45.833 3.71 0.24 31.10 2.32
4442 7463 3.703052 CCATGCTTTTCTGGCTAGGAAAT 59.297 43.478 3.71 0.00 31.10 2.17
4445 7466 1.064463 CCCATGCTTTTCTGGCTAGGA 60.064 52.381 0.00 0.00 0.00 2.94
4478 7499 5.394224 CCACTACTTTCTTCTATTCCTCGCA 60.394 44.000 0.00 0.00 0.00 5.10
4524 7545 1.081892 CAAGGTGCATCGAGGACTTG 58.918 55.000 0.00 8.15 38.81 3.16
4576 7599 1.977854 TGGTTCTGTATCTGCACTGGT 59.022 47.619 0.00 0.00 0.00 4.00
4604 7627 3.879295 TGGAGCTACTCATGCTATTTTGC 59.121 43.478 0.00 0.00 41.30 3.68
4613 7636 3.391965 GCATCTTCTGGAGCTACTCATG 58.608 50.000 0.00 0.00 31.08 3.07
4644 7667 0.764890 TGCTGGTACCTCACTTGCTT 59.235 50.000 14.36 0.00 0.00 3.91
4645 7668 0.764890 TTGCTGGTACCTCACTTGCT 59.235 50.000 14.36 0.00 0.00 3.91
4667 7690 1.270785 CGTGGCATATGCTGGGTATGA 60.271 52.381 26.12 0.00 41.70 2.15
4732 7763 2.096013 GCAAGTCATCCTCGTTAAAGCC 59.904 50.000 0.00 0.00 0.00 4.35
4740 7771 3.270027 TGGTTTATGCAAGTCATCCTCG 58.730 45.455 0.00 0.00 36.63 4.63
4786 7817 2.930040 AGACGTGAAATCGTTGGCTATG 59.070 45.455 0.00 0.00 44.21 2.23
4803 7834 1.391485 CATCGTTTCAAGCTCCAGACG 59.609 52.381 6.38 6.38 0.00 4.18
4816 7847 1.675641 GGCACAGCTCCCATCGTTT 60.676 57.895 0.00 0.00 0.00 3.60
4828 7859 3.190118 GTCTTGAAGAAAGATGGGCACAG 59.810 47.826 0.00 0.00 46.53 3.66
4829 7860 3.149196 GTCTTGAAGAAAGATGGGCACA 58.851 45.455 0.00 0.00 46.53 4.57
4830 7861 2.489722 GGTCTTGAAGAAAGATGGGCAC 59.510 50.000 0.00 0.00 46.53 5.01
4831 7862 2.108075 TGGTCTTGAAGAAAGATGGGCA 59.892 45.455 0.00 0.00 46.53 5.36
4869 7900 2.167693 TCGTGTGGTTTCAAGTCTCTGT 59.832 45.455 0.00 0.00 0.00 3.41
4914 7945 6.183360 CCTTTTGTTCTGTCAGCAAAAAGTTC 60.183 38.462 20.86 0.00 40.23 3.01
4925 7956 2.364970 CAATGGCCCTTTTGTTCTGTCA 59.635 45.455 0.00 0.00 0.00 3.58
4965 7996 2.102578 CAAGCCATCGATCCCCTTTTT 58.897 47.619 0.00 0.00 0.00 1.94
4966 7997 1.767759 CAAGCCATCGATCCCCTTTT 58.232 50.000 0.00 0.00 0.00 2.27
4967 7998 0.753111 GCAAGCCATCGATCCCCTTT 60.753 55.000 0.00 0.00 0.00 3.11
5087 8118 1.590259 GAGATCAGCGAAGACGGGC 60.590 63.158 0.00 0.00 40.15 6.13
5093 8124 0.105778 GGAAGGGGAGATCAGCGAAG 59.894 60.000 0.00 0.00 0.00 3.79
5099 8130 0.326618 GACTGGGGAAGGGGAGATCA 60.327 60.000 0.00 0.00 0.00 2.92
5160 8191 1.370437 CCATCCTCGGCCAGATCAG 59.630 63.158 2.24 0.00 0.00 2.90
5267 8299 4.527583 CGGGAGAGGCTGAGCTGC 62.528 72.222 3.72 0.00 0.00 5.25
5280 8312 4.373116 GCAGAACCTCGCACGGGA 62.373 66.667 0.00 0.00 0.00 5.14
5284 8316 3.426568 GGCAGCAGAACCTCGCAC 61.427 66.667 0.00 0.00 0.00 5.34
5527 8579 3.296709 GAAGGCTGCGACGAAGGGA 62.297 63.158 4.68 0.00 0.00 4.20
5534 8586 0.579156 GATGATTCGAAGGCTGCGAC 59.421 55.000 19.16 7.91 37.52 5.19
5536 8588 0.580578 CAGATGATTCGAAGGCTGCG 59.419 55.000 9.11 9.11 0.00 5.18
5593 8645 4.087892 CGGGACAGGACCAGCCAG 62.088 72.222 0.00 0.00 40.02 4.85


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

AutoCloner maintained by Alex Coulton.