Multiple sequence alignment - TraesCS3A01G273300

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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 TraesCS3A01G273300 chr3A 100.000 7382 0 0 970 8351 502382761 502390142 0.000000e+00 13633.0
1 TraesCS3A01G273300 chr3A 100.000 621 0 0 1 621 502381792 502382412 0.000000e+00 1147.0
2 TraesCS3A01G273300 chr3A 93.976 166 10 0 2743 2908 83748187 83748022 1.390000e-62 252.0
3 TraesCS3A01G273300 chr3A 92.941 170 12 0 2743 2912 34532615 34532446 1.800000e-61 248.0
4 TraesCS3A01G273300 chr3A 99.138 116 1 0 2475 2590 502384151 502384266 8.490000e-50 209.0
5 TraesCS3A01G273300 chr3A 99.138 116 1 0 2360 2475 502384266 502384381 8.490000e-50 209.0
6 TraesCS3A01G273300 chr3A 74.825 286 67 4 7711 7995 514346257 514345976 3.160000e-24 124.0
7 TraesCS3A01G273300 chr3D 97.446 4111 65 15 2475 6568 378231339 378235426 0.000000e+00 6974.0
8 TraesCS3A01G273300 chr3D 91.782 1801 104 21 6569 8341 378235468 378237252 0.000000e+00 2466.0
9 TraesCS3A01G273300 chr3D 95.950 1506 44 5 970 2475 378229966 378231454 0.000000e+00 2427.0
10 TraesCS3A01G273300 chr3D 92.117 444 23 7 5 447 378229136 378229568 4.280000e-172 616.0
11 TraesCS3A01G273300 chr3D 90.270 185 16 2 2743 2925 71517844 71517660 3.010000e-59 241.0
12 TraesCS3A01G273300 chr3D 94.410 161 2 3 467 621 378229633 378229792 3.010000e-59 241.0
13 TraesCS3A01G273300 chr3D 84.783 92 13 1 7712 7802 267247080 267246989 3.210000e-14 91.6
14 TraesCS3A01G273300 chr3B 95.791 3065 94 19 2475 5515 493118582 493121635 0.000000e+00 4913.0
15 TraesCS3A01G273300 chr3B 91.355 1793 91 26 6569 8341 493122978 493124726 0.000000e+00 2394.0
16 TraesCS3A01G273300 chr3B 96.004 1076 31 6 5500 6568 493121866 493122936 0.000000e+00 1738.0
17 TraesCS3A01G273300 chr3B 95.392 868 27 6 970 1837 493117661 493118515 0.000000e+00 1369.0
18 TraesCS3A01G273300 chr3B 96.859 191 6 0 2285 2475 493118507 493118697 3.760000e-83 320.0
19 TraesCS3A01G273300 chr3B 92.941 170 12 0 2743 2912 42630984 42630815 1.800000e-61 248.0
20 TraesCS3A01G273300 chr3B 85.778 225 25 3 5 223 493116800 493117023 1.810000e-56 231.0
21 TraesCS3A01G273300 chr3B 94.079 152 4 2 470 621 493117342 493117488 8.430000e-55 226.0
22 TraesCS3A01G273300 chr3B 90.698 129 3 2 236 363 493117070 493117190 6.710000e-36 163.0
23 TraesCS3A01G273300 chr6D 92.398 171 13 0 2740 2910 304099283 304099453 2.330000e-60 244.0
24 TraesCS3A01G273300 chr1D 92.353 170 13 0 2742 2911 175820003 175819834 8.370000e-60 243.0
25 TraesCS3A01G273300 chr1D 80.435 92 15 3 3557 3646 376065750 376065660 5.410000e-07 67.6
26 TraesCS3A01G273300 chr1D 82.432 74 10 2 7692 7764 379880898 379880827 2.520000e-05 62.1
27 TraesCS3A01G273300 chr7B 91.716 169 14 0 2743 2911 152467773 152467605 1.400000e-57 235.0
28 TraesCS3A01G273300 chr6A 78.146 151 22 8 7638 7778 1016177 1016028 1.490000e-12 86.1
29 TraesCS3A01G273300 chr4B 78.182 110 15 7 7646 7746 60422683 60422792 2.520000e-05 62.1
30 TraesCS3A01G273300 chr5A 97.143 35 1 0 7716 7750 45742734 45742700 9.050000e-05 60.2
31 TraesCS3A01G273300 chr7A 100.000 31 0 0 188 218 218398066 218398036 3.260000e-04 58.4
32 TraesCS3A01G273300 chr5D 94.444 36 0 1 182 215 460680482 460680447 4.000000e-03 54.7
33 TraesCS3A01G273300 chr2D 100.000 29 0 0 182 210 131645882 131645910 4.000000e-03 54.7


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 TraesCS3A01G273300 chr3A 502381792 502390142 8350 False 7390.00 13633 100.0000 1 8351 2 chr3A.!!$F1 8350
1 TraesCS3A01G273300 chr3D 378229136 378237252 8116 False 2544.80 6974 94.3410 5 8341 5 chr3D.!!$F1 8336
2 TraesCS3A01G273300 chr3B 493116800 493124726 7926 False 1419.25 4913 93.2445 5 8341 8 chr3B.!!$F1 8336

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
169 175 0.103026 TTGGAGATGATGCCGACTCG 59.897 55.000 0.00 0.00 0.00 4.18 F
397 464 0.606401 CCATCGATTCCCATTCCCCG 60.606 60.000 0.00 0.00 0.00 5.73 F
1256 1376 1.745087 GATTTCTCCGCTTTCATGCCA 59.255 47.619 0.00 0.00 0.00 4.92 F
2158 2278 1.068472 ACTTGTCAAGTCGGACTAGCG 60.068 52.381 12.62 3.56 42.08 4.26 F
2466 2586 0.110486 TCTTCCCTTTGGTCCTGCAC 59.890 55.000 0.00 0.00 0.00 4.57 F
2467 2587 0.111253 CTTCCCTTTGGTCCTGCACT 59.889 55.000 0.00 0.00 0.00 4.40 F
2473 2593 0.178992 TTTGGTCCTGCACTCCCTTG 60.179 55.000 0.00 0.00 0.00 3.61 F
2487 2607 0.258484 CCCTTGCCCATCCACATGTA 59.742 55.000 0.00 0.00 0.00 2.29 F
3946 4082 0.750850 TCCACCCTCTAACGCTATGC 59.249 55.000 0.00 0.00 0.00 3.14 F
3962 4104 4.034394 CGCTATGCTTTCTTGATACTTGCA 59.966 41.667 0.00 0.00 0.00 4.08 F
4161 4303 4.706962 AGGCCATCTTATTTTGTTCACTCC 59.293 41.667 5.01 0.00 0.00 3.85 F
5438 5585 0.756294 TGTGAGTGGTGTGTGGGTAG 59.244 55.000 0.00 0.00 0.00 3.18 F
6562 6966 0.732571 AACACAACACTGCCAACTCG 59.267 50.000 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1423 0.107017 ATTGGGCACGGAAGATGAGG 60.107 55.000 0.00 0.00 0.00 3.86 R
1359 1479 0.524862 GCAGAATGGGCACTGACAAG 59.475 55.000 0.00 0.00 36.38 3.16 R
2447 2567 0.110486 GTGCAGGACCAAAGGGAAGA 59.890 55.000 0.00 0.00 38.05 2.87 R
3253 3386 0.824759 GTAGATCGAAGCACCCTGGT 59.175 55.000 0.00 0.00 0.00 4.00 R
3765 3898 2.817258 TGCACTGGCTAATGTTTACCAC 59.183 45.455 0.00 0.00 41.91 4.16 R
4161 4303 7.535258 GTCACAACAATGAGTATAAACAAGCAG 59.465 37.037 0.00 0.00 0.00 4.24 R
4481 4623 7.695055 TCCCTTGGAGTTCATTTAGTAAATCA 58.305 34.615 5.10 0.00 0.00 2.57 R
4520 4662 3.281727 TTTACCTCCCATGAGTCATGC 57.718 47.619 25.08 0.00 40.20 4.06 R
5096 5240 1.750778 GAGTCTTGCTCTAGCTCTGCT 59.249 52.381 3.26 0.00 40.98 4.24 R
5438 5585 3.119137 ACAACCTGAAACTGAGCCAAAAC 60.119 43.478 0.00 0.00 0.00 2.43 R
6062 6465 0.036388 CTTTTGCTGGGCGACTAGGA 60.036 55.000 2.91 0.00 39.75 2.94 R
6566 6970 1.278985 TGCATTCCTCGAGGTGTCATT 59.721 47.619 30.17 5.45 36.34 2.57 R
8049 8506 0.030235 CGGCTATCGGATCGTTGTCA 59.970 55.000 0.00 0.00 34.75 3.58 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
169 175 0.103026 TTGGAGATGATGCCGACTCG 59.897 55.000 0.00 0.00 0.00 4.18
186 192 2.271800 CTCGGTATCTTGAAGGTGTGC 58.728 52.381 0.00 0.00 0.00 4.57
192 198 1.092921 TCTTGAAGGTGTGCGCGTTT 61.093 50.000 8.43 0.00 0.00 3.60
196 202 1.996898 TGAAGGTGTGCGCGTTTATAG 59.003 47.619 8.43 0.00 0.00 1.31
213 219 7.096436 GCGTTTATAGAGATGAGTGTATGTGTG 60.096 40.741 0.00 0.00 0.00 3.82
219 225 7.881775 AGAGATGAGTGTATGTGTGTGTATA 57.118 36.000 0.00 0.00 0.00 1.47
357 424 8.886719 CACAATGCATTCTCTCTAATTAGTCAA 58.113 33.333 9.53 2.34 0.00 3.18
380 447 8.112822 TCAATGGACTTTTAATATCTTCACCCA 58.887 33.333 0.00 0.00 0.00 4.51
383 450 6.765989 TGGACTTTTAATATCTTCACCCATCG 59.234 38.462 0.00 0.00 0.00 3.84
397 464 0.606401 CCATCGATTCCCATTCCCCG 60.606 60.000 0.00 0.00 0.00 5.73
441 509 2.227149 ACGTTCCCCTATTCGCAAAAAC 59.773 45.455 0.00 0.00 0.00 2.43
446 514 5.277857 TCCCCTATTCGCAAAAACAAAAA 57.722 34.783 0.00 0.00 0.00 1.94
1256 1376 1.745087 GATTTCTCCGCTTTCATGCCA 59.255 47.619 0.00 0.00 0.00 4.92
1260 1380 3.451894 CCGCTTTCATGCCACCCC 61.452 66.667 0.00 0.00 0.00 4.95
1303 1423 5.043248 CCATATCCCGCAAAGAATGTTTTC 58.957 41.667 0.00 0.00 0.00 2.29
1351 1471 3.483558 GCTCGTGCTTTTCTGTCTTTTTG 59.516 43.478 1.41 0.00 36.03 2.44
1356 1476 3.132111 TGCTTTTCTGTCTTTTTGTCCCC 59.868 43.478 0.00 0.00 0.00 4.81
1357 1477 3.384789 GCTTTTCTGTCTTTTTGTCCCCT 59.615 43.478 0.00 0.00 0.00 4.79
1359 1479 2.951229 TCTGTCTTTTTGTCCCCTCC 57.049 50.000 0.00 0.00 0.00 4.30
1360 1480 2.418669 TCTGTCTTTTTGTCCCCTCCT 58.581 47.619 0.00 0.00 0.00 3.69
1361 1481 2.783510 TCTGTCTTTTTGTCCCCTCCTT 59.216 45.455 0.00 0.00 0.00 3.36
1362 1482 2.887152 CTGTCTTTTTGTCCCCTCCTTG 59.113 50.000 0.00 0.00 0.00 3.61
1363 1483 2.243736 TGTCTTTTTGTCCCCTCCTTGT 59.756 45.455 0.00 0.00 0.00 3.16
1365 1485 2.512056 TCTTTTTGTCCCCTCCTTGTCA 59.488 45.455 0.00 0.00 0.00 3.58
1493 1613 5.287035 GCTAGTTTTCTTCATTGCGGATTTG 59.713 40.000 0.00 0.00 0.00 2.32
1596 1716 1.952367 GCTTTGGATCTGGAGTGGTGG 60.952 57.143 0.00 0.00 0.00 4.61
1739 1859 2.203584 ACCCTCTGATGCCTCATCTTT 58.796 47.619 8.11 0.00 41.06 2.52
1795 1915 7.229306 ACCGTGAGATATGAAATAATGTGCATT 59.771 33.333 0.00 2.83 29.06 3.56
1847 1967 5.147032 TCATGACAAGGGAGAAATTTTGGT 58.853 37.500 0.00 0.00 0.00 3.67
1877 1997 6.308766 CCAGTCACATATTTGTTAAAGCAAGC 59.691 38.462 0.00 0.00 32.34 4.01
2038 2158 1.068474 GATTCCTTGTGTCACGACCG 58.932 55.000 0.00 0.00 0.00 4.79
2061 2181 6.317140 CCGCATTTCATAGCATTATATGTCCT 59.683 38.462 0.00 0.00 35.16 3.85
2158 2278 1.068472 ACTTGTCAAGTCGGACTAGCG 60.068 52.381 12.62 3.56 42.08 4.26
2166 2286 2.641305 AGTCGGACTAGCGTATGACTT 58.359 47.619 9.33 0.00 35.41 3.01
2179 2299 4.163552 CGTATGACTTACGTTTCTCAGCA 58.836 43.478 11.62 0.00 46.81 4.41
2442 2562 6.317789 ACCACATAAAAGATGTGTGTCTTG 57.682 37.500 14.71 3.32 46.43 3.02
2443 2563 5.827797 ACCACATAAAAGATGTGTGTCTTGT 59.172 36.000 14.71 3.85 46.43 3.16
2444 2564 6.144854 CCACATAAAAGATGTGTGTCTTGTG 58.855 40.000 14.71 0.00 46.43 3.33
2445 2565 6.144854 CACATAAAAGATGTGTGTCTTGTGG 58.855 40.000 9.10 0.00 43.81 4.17
2446 2566 5.827797 ACATAAAAGATGTGTGTCTTGTGGT 59.172 36.000 0.00 0.00 38.41 4.16
2447 2567 6.321181 ACATAAAAGATGTGTGTCTTGTGGTT 59.679 34.615 0.00 0.00 38.41 3.67
2448 2568 4.900635 AAAGATGTGTGTCTTGTGGTTC 57.099 40.909 0.00 0.00 38.41 3.62
2449 2569 3.845781 AGATGTGTGTCTTGTGGTTCT 57.154 42.857 0.00 0.00 0.00 3.01
2450 2570 4.156455 AGATGTGTGTCTTGTGGTTCTT 57.844 40.909 0.00 0.00 0.00 2.52
2451 2571 4.130118 AGATGTGTGTCTTGTGGTTCTTC 58.870 43.478 0.00 0.00 0.00 2.87
2452 2572 2.639065 TGTGTGTCTTGTGGTTCTTCC 58.361 47.619 0.00 0.00 0.00 3.46
2453 2573 1.947456 GTGTGTCTTGTGGTTCTTCCC 59.053 52.381 0.00 0.00 34.77 3.97
2454 2574 1.843851 TGTGTCTTGTGGTTCTTCCCT 59.156 47.619 0.00 0.00 34.77 4.20
2455 2575 2.241176 TGTGTCTTGTGGTTCTTCCCTT 59.759 45.455 0.00 0.00 34.77 3.95
2456 2576 3.288092 GTGTCTTGTGGTTCTTCCCTTT 58.712 45.455 0.00 0.00 34.77 3.11
2457 2577 3.066760 GTGTCTTGTGGTTCTTCCCTTTG 59.933 47.826 0.00 0.00 34.77 2.77
2458 2578 2.623416 GTCTTGTGGTTCTTCCCTTTGG 59.377 50.000 0.00 0.00 34.77 3.28
2459 2579 2.243736 TCTTGTGGTTCTTCCCTTTGGT 59.756 45.455 0.00 0.00 34.77 3.67
2460 2580 2.358322 TGTGGTTCTTCCCTTTGGTC 57.642 50.000 0.00 0.00 34.77 4.02
2461 2581 1.133606 TGTGGTTCTTCCCTTTGGTCC 60.134 52.381 0.00 0.00 34.77 4.46
2462 2582 1.145119 GTGGTTCTTCCCTTTGGTCCT 59.855 52.381 0.00 0.00 34.77 3.85
2463 2583 1.144913 TGGTTCTTCCCTTTGGTCCTG 59.855 52.381 0.00 0.00 34.77 3.86
2464 2584 1.248486 GTTCTTCCCTTTGGTCCTGC 58.752 55.000 0.00 0.00 0.00 4.85
2465 2585 0.850100 TTCTTCCCTTTGGTCCTGCA 59.150 50.000 0.00 0.00 0.00 4.41
2466 2586 0.110486 TCTTCCCTTTGGTCCTGCAC 59.890 55.000 0.00 0.00 0.00 4.57
2467 2587 0.111253 CTTCCCTTTGGTCCTGCACT 59.889 55.000 0.00 0.00 0.00 4.40
2468 2588 0.110486 TTCCCTTTGGTCCTGCACTC 59.890 55.000 0.00 0.00 0.00 3.51
2469 2589 1.303643 CCCTTTGGTCCTGCACTCC 60.304 63.158 0.00 0.00 0.00 3.85
2470 2590 1.303643 CCTTTGGTCCTGCACTCCC 60.304 63.158 0.00 0.00 0.00 4.30
2471 2591 1.763770 CTTTGGTCCTGCACTCCCT 59.236 57.895 0.00 0.00 0.00 4.20
2472 2592 0.111253 CTTTGGTCCTGCACTCCCTT 59.889 55.000 0.00 0.00 0.00 3.95
2473 2593 0.178992 TTTGGTCCTGCACTCCCTTG 60.179 55.000 0.00 0.00 0.00 3.61
2474 2594 2.360475 GGTCCTGCACTCCCTTGC 60.360 66.667 0.00 0.00 43.31 4.01
2475 2595 2.360475 GTCCTGCACTCCCTTGCC 60.360 66.667 0.00 0.00 42.25 4.52
2476 2596 3.650950 TCCTGCACTCCCTTGCCC 61.651 66.667 0.00 0.00 42.25 5.36
2477 2597 3.970410 CCTGCACTCCCTTGCCCA 61.970 66.667 0.00 0.00 42.25 5.36
2478 2598 2.357836 CTGCACTCCCTTGCCCAT 59.642 61.111 0.00 0.00 42.25 4.00
2479 2599 1.751927 CTGCACTCCCTTGCCCATC 60.752 63.158 0.00 0.00 42.25 3.51
2480 2600 2.440980 GCACTCCCTTGCCCATCC 60.441 66.667 0.00 0.00 36.42 3.51
2481 2601 3.089838 CACTCCCTTGCCCATCCA 58.910 61.111 0.00 0.00 0.00 3.41
2482 2602 1.379044 CACTCCCTTGCCCATCCAC 60.379 63.158 0.00 0.00 0.00 4.02
2483 2603 1.852157 ACTCCCTTGCCCATCCACA 60.852 57.895 0.00 0.00 0.00 4.17
2484 2604 1.217057 ACTCCCTTGCCCATCCACAT 61.217 55.000 0.00 0.00 0.00 3.21
2485 2605 0.754217 CTCCCTTGCCCATCCACATG 60.754 60.000 0.00 0.00 0.00 3.21
2486 2606 1.000739 CCCTTGCCCATCCACATGT 59.999 57.895 0.00 0.00 0.00 3.21
2487 2607 0.258484 CCCTTGCCCATCCACATGTA 59.742 55.000 0.00 0.00 0.00 2.29
2488 2608 1.133388 CCCTTGCCCATCCACATGTAT 60.133 52.381 0.00 0.00 0.00 2.29
2489 2609 2.233271 CCTTGCCCATCCACATGTATC 58.767 52.381 0.00 0.00 0.00 2.24
2490 2610 2.233271 CTTGCCCATCCACATGTATCC 58.767 52.381 0.00 0.00 0.00 2.59
2491 2611 1.220703 TGCCCATCCACATGTATCCA 58.779 50.000 0.00 0.00 0.00 3.41
2492 2612 1.568123 TGCCCATCCACATGTATCCAA 59.432 47.619 0.00 0.00 0.00 3.53
2493 2613 2.177451 TGCCCATCCACATGTATCCAAT 59.823 45.455 0.00 0.00 0.00 3.16
2494 2614 2.559668 GCCCATCCACATGTATCCAATG 59.440 50.000 0.00 0.00 0.00 2.82
2495 2615 3.751569 GCCCATCCACATGTATCCAATGA 60.752 47.826 0.00 0.00 0.00 2.57
2496 2616 4.077108 CCCATCCACATGTATCCAATGAG 58.923 47.826 0.00 0.00 0.00 2.90
2497 2617 3.504906 CCATCCACATGTATCCAATGAGC 59.495 47.826 0.00 0.00 0.00 4.26
2498 2618 4.395625 CATCCACATGTATCCAATGAGCT 58.604 43.478 0.00 0.00 0.00 4.09
2499 2619 3.812262 TCCACATGTATCCAATGAGCTG 58.188 45.455 0.00 0.00 0.00 4.24
2500 2620 3.200605 TCCACATGTATCCAATGAGCTGT 59.799 43.478 0.00 0.00 0.00 4.40
2501 2621 3.949754 CCACATGTATCCAATGAGCTGTT 59.050 43.478 0.00 0.00 0.00 3.16
2502 2622 5.104569 TCCACATGTATCCAATGAGCTGTTA 60.105 40.000 0.00 0.00 0.00 2.41
2503 2623 5.589855 CCACATGTATCCAATGAGCTGTTAA 59.410 40.000 0.00 0.00 0.00 2.01
2504 2624 6.263842 CCACATGTATCCAATGAGCTGTTAAT 59.736 38.462 0.00 0.00 0.00 1.40
2505 2625 7.445096 CCACATGTATCCAATGAGCTGTTAATA 59.555 37.037 0.00 0.00 0.00 0.98
2506 2626 9.006839 CACATGTATCCAATGAGCTGTTAATAT 57.993 33.333 0.00 0.00 0.00 1.28
2507 2627 9.006839 ACATGTATCCAATGAGCTGTTAATATG 57.993 33.333 0.00 0.00 0.00 1.78
2508 2628 7.984422 TGTATCCAATGAGCTGTTAATATGG 57.016 36.000 0.00 0.00 0.00 2.74
2509 2629 7.517320 TGTATCCAATGAGCTGTTAATATGGT 58.483 34.615 0.00 0.00 0.00 3.55
2510 2630 6.889301 ATCCAATGAGCTGTTAATATGGTG 57.111 37.500 0.00 0.00 0.00 4.17
2511 2631 4.580167 TCCAATGAGCTGTTAATATGGTGC 59.420 41.667 0.00 0.00 0.00 5.01
2512 2632 4.338964 CCAATGAGCTGTTAATATGGTGCA 59.661 41.667 0.00 0.00 0.00 4.57
2513 2633 5.010314 CCAATGAGCTGTTAATATGGTGCAT 59.990 40.000 0.00 0.00 0.00 3.96
2514 2634 5.954296 ATGAGCTGTTAATATGGTGCATC 57.046 39.130 0.00 0.00 0.00 3.91
2515 2635 4.779696 TGAGCTGTTAATATGGTGCATCA 58.220 39.130 0.00 0.00 0.00 3.07
2516 2636 4.818005 TGAGCTGTTAATATGGTGCATCAG 59.182 41.667 5.59 0.00 0.00 2.90
2517 2637 4.785301 AGCTGTTAATATGGTGCATCAGT 58.215 39.130 5.59 0.00 0.00 3.41
2518 2638 5.195940 AGCTGTTAATATGGTGCATCAGTT 58.804 37.500 5.59 5.71 0.00 3.16
2519 2639 5.297776 AGCTGTTAATATGGTGCATCAGTTC 59.702 40.000 5.59 0.00 0.00 3.01
2520 2640 5.066375 GCTGTTAATATGGTGCATCAGTTCA 59.934 40.000 5.59 0.00 0.00 3.18
2521 2641 6.682423 TGTTAATATGGTGCATCAGTTCAG 57.318 37.500 5.59 0.00 0.00 3.02
2522 2642 6.179756 TGTTAATATGGTGCATCAGTTCAGT 58.820 36.000 5.59 0.00 0.00 3.41
2523 2643 6.658816 TGTTAATATGGTGCATCAGTTCAGTT 59.341 34.615 5.59 0.00 0.00 3.16
2524 2644 7.176515 TGTTAATATGGTGCATCAGTTCAGTTT 59.823 33.333 5.59 0.00 0.00 2.66
2525 2645 3.928727 ATGGTGCATCAGTTCAGTTTG 57.071 42.857 5.59 0.00 0.00 2.93
2526 2646 2.929641 TGGTGCATCAGTTCAGTTTGA 58.070 42.857 0.00 0.00 0.00 2.69
2527 2647 3.489355 TGGTGCATCAGTTCAGTTTGAT 58.511 40.909 0.00 0.00 34.48 2.57
2538 2658 8.492673 TCAGTTCAGTTTGATGATAATACCAC 57.507 34.615 0.00 0.00 0.00 4.16
2539 2659 8.100164 TCAGTTCAGTTTGATGATAATACCACA 58.900 33.333 0.00 0.00 0.00 4.17
2540 2660 8.896744 CAGTTCAGTTTGATGATAATACCACAT 58.103 33.333 0.00 0.00 0.00 3.21
2553 2673 9.679661 TGATAATACCACATAAAAGATGTGTGT 57.320 29.630 14.71 13.71 46.43 3.72
2555 2675 9.905713 ATAATACCACATAAAAGATGTGTGTCT 57.094 29.630 14.71 4.85 46.43 3.41
2556 2676 8.635765 AATACCACATAAAAGATGTGTGTCTT 57.364 30.769 14.71 9.22 46.43 3.01
2687 2807 7.824779 GTCCATCCAAATCAAGTACTTAGAAGT 59.175 37.037 8.04 0.00 42.91 3.01
2716 2836 4.211794 GTGAACAATTGCCTCCAACATTTG 59.788 41.667 5.05 0.00 35.53 2.32
3001 3132 4.330944 TCGACTGAAAAAGCTTACTGGA 57.669 40.909 0.00 0.00 0.00 3.86
3036 3169 4.137543 ACAGAAAGGTTCTACAAGGCTTG 58.862 43.478 25.06 25.06 38.11 4.01
3070 3203 1.343069 GGATCGGCCTATCAGTTCCT 58.657 55.000 18.27 0.00 0.00 3.36
3253 3386 5.073428 CCCTGAGATCTGCACATAGTAGTA 58.927 45.833 0.00 0.00 0.00 1.82
3267 3400 1.180029 GTAGTACCAGGGTGCTTCGA 58.820 55.000 14.30 0.00 41.18 3.71
3468 3601 5.514500 AGAAAAAGGTACCTAATGAGCCA 57.486 39.130 16.67 0.00 0.00 4.75
3537 3670 1.681327 CAGGCCCTCAAATGCAGCT 60.681 57.895 0.00 0.00 0.00 4.24
3765 3898 6.870769 AGGATCAATTTAGTGAGGCAAATTG 58.129 36.000 11.62 11.62 46.38 2.32
3840 3976 3.974642 GGGGGATGAGAGGTTACATAAGT 59.025 47.826 0.00 0.00 0.00 2.24
3946 4082 0.750850 TCCACCCTCTAACGCTATGC 59.249 55.000 0.00 0.00 0.00 3.14
3961 4103 4.034510 ACGCTATGCTTTCTTGATACTTGC 59.965 41.667 0.00 0.00 0.00 4.01
3962 4104 4.034394 CGCTATGCTTTCTTGATACTTGCA 59.966 41.667 0.00 0.00 0.00 4.08
3963 4105 5.277683 CGCTATGCTTTCTTGATACTTGCAT 60.278 40.000 0.00 0.00 41.60 3.96
3964 4106 6.073602 CGCTATGCTTTCTTGATACTTGCATA 60.074 38.462 0.00 0.00 39.79 3.14
3965 4107 7.360691 CGCTATGCTTTCTTGATACTTGCATAT 60.361 37.037 0.00 0.00 39.90 1.78
3966 4108 7.749570 GCTATGCTTTCTTGATACTTGCATATG 59.250 37.037 0.00 0.00 39.90 1.78
4161 4303 4.706962 AGGCCATCTTATTTTGTTCACTCC 59.293 41.667 5.01 0.00 0.00 3.85
4185 4327 6.803320 CCTGCTTGTTTATACTCATTGTTGTG 59.197 38.462 0.00 0.00 0.00 3.33
4190 4332 9.599322 CTTGTTTATACTCATTGTTGTGACTTC 57.401 33.333 0.00 0.00 0.00 3.01
4481 4623 5.100751 GCGATTGCAAGCTAGATTGTATT 57.899 39.130 21.02 13.39 42.15 1.89
4811 4955 8.277197 TCAGATTCTGATGACCTGGATTTTATT 58.723 33.333 12.38 0.00 35.39 1.40
5096 5240 6.575244 ACTAATGGAGTGGACATTATGGAA 57.425 37.500 0.00 0.00 39.34 3.53
5328 5475 8.747538 TGAAGAATAAAGCCCTAATTTACTCC 57.252 34.615 0.00 0.00 0.00 3.85
5438 5585 0.756294 TGTGAGTGGTGTGTGGGTAG 59.244 55.000 0.00 0.00 0.00 3.18
5950 6353 9.877178 GTTAATCAGGTATAGCTAACTATGCAT 57.123 33.333 3.79 3.79 41.73 3.96
6062 6465 8.293699 AGGCATATTTCGAAAAAGAACCTTAT 57.706 30.769 15.66 2.75 27.57 1.73
6149 6552 3.499338 TGCCAGTTTGTCCTTTCATCAT 58.501 40.909 0.00 0.00 0.00 2.45
6294 6698 7.976826 AGTACTCGTCATTACTCAAGAGTTAG 58.023 38.462 8.17 0.00 42.54 2.34
6528 6932 2.103373 TGAGCAGACACTAGATGGGAC 58.897 52.381 0.00 0.00 0.00 4.46
6529 6933 2.291865 TGAGCAGACACTAGATGGGACT 60.292 50.000 0.00 0.00 0.00 3.85
6530 6934 2.360801 GAGCAGACACTAGATGGGACTC 59.639 54.545 0.00 0.00 0.00 3.36
6562 6966 0.732571 AACACAACACTGCCAACTCG 59.267 50.000 0.00 0.00 0.00 4.18
6565 6969 0.532862 ACAACACTGCCAACTCGAGG 60.533 55.000 18.41 0.23 0.00 4.63
6566 6970 0.249868 CAACACTGCCAACTCGAGGA 60.250 55.000 18.41 0.00 0.00 3.71
6676 7122 3.567797 GGCTCGAGCAATGTCGGC 61.568 66.667 36.27 14.56 44.36 5.54
6715 7161 1.468914 GGAGGAAACAAGCGCCTTAAG 59.531 52.381 2.29 0.00 30.70 1.85
6920 7366 6.147821 GCAAGTCAAGTTTTAGATGCTACTCA 59.852 38.462 0.00 0.00 0.00 3.41
6987 7433 0.877071 AGCTGAATTGTTGTGCCTCG 59.123 50.000 0.00 0.00 0.00 4.63
6989 7435 1.001378 GCTGAATTGTTGTGCCTCGTT 60.001 47.619 0.00 0.00 0.00 3.85
7050 7496 3.389656 GCCCTGTTTCTCTATAGAGCCTT 59.610 47.826 22.81 0.00 41.80 4.35
7156 7602 5.221087 GCCTGTAGACTCTAGTGGACATTAC 60.221 48.000 7.96 0.00 0.00 1.89
7219 7665 3.755378 GCCATGTTGAGAGAAACTGATGT 59.245 43.478 0.00 0.00 0.00 3.06
7232 7678 3.963383 ACTGATGTGAACCGTTGTTTC 57.037 42.857 0.00 0.00 33.97 2.78
7234 7680 2.542178 CTGATGTGAACCGTTGTTTCGA 59.458 45.455 0.00 0.00 33.97 3.71
7321 7767 5.998454 ATGAAACGAGATCAATGACATCC 57.002 39.130 0.00 0.00 0.00 3.51
7329 7775 5.047448 CGAGATCAATGACATCCTATCTGGT 60.047 44.000 10.32 0.00 37.07 4.00
7358 7804 6.245115 TGACATGCAATTTCACTTCACTAG 57.755 37.500 0.00 0.00 25.88 2.57
7504 7950 1.219393 GCTGTACACTCAGGGCTCC 59.781 63.158 0.00 0.00 36.12 4.70
7528 7975 2.283529 CGCCCCTATACATCCGGCT 61.284 63.158 0.00 0.00 37.47 5.52
7537 7988 3.087253 CATCCGGCTGGGTGGGTA 61.087 66.667 17.94 0.00 43.16 3.69
7544 7995 1.489560 GGCTGGGTGGGTAAGTGACT 61.490 60.000 0.00 0.00 0.00 3.41
7581 8036 2.649816 ACCTAGTTGGGCTCCTCAAATT 59.350 45.455 0.00 0.00 41.11 1.82
7586 8041 1.075601 TGGGCTCCTCAAATTGGACT 58.924 50.000 0.00 0.00 0.00 3.85
7592 8047 5.398012 GGGCTCCTCAAATTGGACTTATACT 60.398 44.000 0.00 0.00 0.00 2.12
7593 8048 6.183361 GGGCTCCTCAAATTGGACTTATACTA 60.183 42.308 0.00 0.00 0.00 1.82
7594 8049 6.706716 GGCTCCTCAAATTGGACTTATACTAC 59.293 42.308 0.00 0.00 0.00 2.73
7595 8050 7.272978 GCTCCTCAAATTGGACTTATACTACA 58.727 38.462 0.00 0.00 0.00 2.74
7596 8051 7.934120 GCTCCTCAAATTGGACTTATACTACAT 59.066 37.037 0.00 0.00 0.00 2.29
7597 8052 9.482627 CTCCTCAAATTGGACTTATACTACATC 57.517 37.037 0.00 0.00 0.00 3.06
7599 8054 9.784531 CCTCAAATTGGACTTATACTACATCAT 57.215 33.333 0.00 0.00 0.00 2.45
7601 8056 9.559732 TCAAATTGGACTTATACTACATCATGG 57.440 33.333 0.00 0.00 0.00 3.66
7602 8057 7.986085 AATTGGACTTATACTACATCATGGC 57.014 36.000 0.00 0.00 0.00 4.40
7603 8058 6.747414 TTGGACTTATACTACATCATGGCT 57.253 37.500 0.00 0.00 0.00 4.75
7604 8059 6.101650 TGGACTTATACTACATCATGGCTG 57.898 41.667 0.00 0.00 0.00 4.85
7605 8060 5.838521 TGGACTTATACTACATCATGGCTGA 59.161 40.000 0.00 0.00 35.41 4.26
7606 8061 6.159988 GGACTTATACTACATCATGGCTGAC 58.840 44.000 0.00 0.00 33.22 3.51
7607 8062 5.773575 ACTTATACTACATCATGGCTGACG 58.226 41.667 0.00 0.00 33.22 4.35
7608 8063 5.302059 ACTTATACTACATCATGGCTGACGT 59.698 40.000 0.00 0.00 33.22 4.34
7609 8064 6.489022 ACTTATACTACATCATGGCTGACGTA 59.511 38.462 0.00 0.07 33.22 3.57
7610 8065 5.984695 ATACTACATCATGGCTGACGTAT 57.015 39.130 0.00 2.18 30.35 3.06
7611 8066 8.570068 TTATACTACATCATGGCTGACGTATA 57.430 34.615 0.00 5.83 30.35 1.47
7612 8067 5.122512 ACTACATCATGGCTGACGTATAC 57.877 43.478 0.00 0.00 30.35 1.47
7613 8068 4.827835 ACTACATCATGGCTGACGTATACT 59.172 41.667 0.56 0.00 30.35 2.12
7614 8069 4.244425 ACATCATGGCTGACGTATACTC 57.756 45.455 0.56 0.00 33.22 2.59
7615 8070 3.005897 ACATCATGGCTGACGTATACTCC 59.994 47.826 0.56 0.00 33.22 3.85
7620 8075 2.158430 TGGCTGACGTATACTCCCCATA 60.158 50.000 0.56 0.00 0.00 2.74
7636 8092 4.230733 TCCCCATATCAGACTAGATCGGAT 59.769 45.833 0.00 5.12 43.68 4.18
7680 8136 3.181435 TGACAAGTCCACCAAATCCATCA 60.181 43.478 0.00 0.00 0.00 3.07
7683 8139 4.264083 ACAAGTCCACCAAATCCATCATCT 60.264 41.667 0.00 0.00 0.00 2.90
7692 8148 1.135094 ATCCATCATCTTCCCACGCT 58.865 50.000 0.00 0.00 0.00 5.07
7708 8164 1.644786 CGCTTCCGTTTCCCACATCC 61.645 60.000 0.00 0.00 0.00 3.51
7792 8249 2.023015 AGATGTCATCTCTGGTACCCCA 60.023 50.000 10.07 0.00 34.37 4.96
7795 8252 1.341531 GTCATCTCTGGTACCCCATCG 59.658 57.143 10.07 0.00 40.90 3.84
7816 8273 0.597637 CCACCGACGGCATAGATGTC 60.598 60.000 15.39 0.00 0.00 3.06
7823 8280 1.373497 GGCATAGATGTCGCCTCGG 60.373 63.158 0.00 0.00 42.78 4.63
7847 8304 1.086634 GTCATGGAGCTCTTGACCGC 61.087 60.000 26.59 12.04 41.79 5.68
7865 8322 4.090057 GGCGACGAGTTGCAAGGC 62.090 66.667 16.33 0.00 41.74 4.35
7866 8323 3.345808 GCGACGAGTTGCAAGGCA 61.346 61.111 10.37 0.00 39.74 4.75
7881 8338 0.965866 AGGCAGAGAACGTCATCCGA 60.966 55.000 0.00 0.00 40.70 4.55
7884 8341 1.135373 GCAGAGAACGTCATCCGAAGA 60.135 52.381 0.00 0.00 40.70 2.87
7906 8363 1.007387 CGGCAAAGGAAGCAACACC 60.007 57.895 0.00 0.00 0.00 4.16
7912 8369 0.183492 AAGGAAGCAACACCAGCAGA 59.817 50.000 0.00 0.00 0.00 4.26
7927 8384 0.110644 GCAGAAAGCGACAACGAAGG 60.111 55.000 0.00 0.00 42.66 3.46
7945 8402 2.332117 AGGAAGTTTCGACCAAGGGTA 58.668 47.619 0.00 0.00 35.25 3.69
8028 8485 0.320374 TACCACTGACAAGGAAGCCG 59.680 55.000 0.83 0.00 0.00 5.52
8029 8486 1.371183 CCACTGACAAGGAAGCCGA 59.629 57.895 0.00 0.00 0.00 5.54
8033 8490 0.600255 CTGACAAGGAAGCCGACGTT 60.600 55.000 0.00 0.00 0.00 3.99
8087 8545 1.405105 CGAATGGGCATTTTCGGATGT 59.595 47.619 7.54 0.00 40.67 3.06
8095 8553 3.972502 GGCATTTTCGGATGTATTTACGC 59.027 43.478 0.00 0.00 0.00 4.42
8126 8605 1.345415 CTTGCTGCAATTCCAAAGGGT 59.655 47.619 16.38 0.00 34.93 4.34
8168 8648 4.404098 CGCCCGGTTTGCCTAGGT 62.404 66.667 11.31 0.00 0.00 3.08
8179 8659 2.550277 TGCCTAGGTCCTGATCAAGA 57.450 50.000 11.31 0.00 0.00 3.02
8235 8715 6.871492 TGCTCTATTTTGTATCACTTCGTTCA 59.129 34.615 0.00 0.00 0.00 3.18
8341 8823 5.936686 ATCGAACATGATCAATGATGGTC 57.063 39.130 0.00 0.10 38.72 4.02
8349 8831 5.688814 TGATCAATGATGGTCAAGAGTCT 57.311 39.130 0.00 0.00 43.64 3.24
8350 8832 6.796785 TGATCAATGATGGTCAAGAGTCTA 57.203 37.500 0.00 0.00 43.64 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.592637 CATCCACGTCTTTGCAGCAA 59.407 50.000 2.83 2.83 0.00 3.91
1 2 0.534877 ACATCCACGTCTTTGCAGCA 60.535 50.000 0.00 0.00 0.00 4.41
2 3 0.593128 AACATCCACGTCTTTGCAGC 59.407 50.000 0.00 0.00 0.00 5.25
3 4 1.872952 TCAACATCCACGTCTTTGCAG 59.127 47.619 0.00 0.00 0.00 4.41
169 175 0.727398 GCGCACACCTTCAAGATACC 59.273 55.000 0.30 0.00 0.00 2.73
177 183 2.264813 TCTATAAACGCGCACACCTTC 58.735 47.619 5.73 0.00 0.00 3.46
178 184 2.094390 TCTCTATAAACGCGCACACCTT 60.094 45.455 5.73 0.00 0.00 3.50
186 192 6.086896 CACATACACTCATCTCTATAAACGCG 59.913 42.308 3.53 3.53 0.00 6.01
192 198 7.881775 ACACACACATACACTCATCTCTATA 57.118 36.000 0.00 0.00 0.00 1.31
196 202 7.596621 CCATATACACACACATACACTCATCTC 59.403 40.741 0.00 0.00 0.00 2.75
213 219 1.808411 CCACGGATGCCCATATACAC 58.192 55.000 0.00 0.00 0.00 2.90
219 225 0.033601 TTTAAGCCACGGATGCCCAT 60.034 50.000 0.00 0.00 0.00 4.00
299 340 1.135046 CACATTATGCTCTCCGCTCG 58.865 55.000 0.00 0.00 40.11 5.03
357 424 7.445402 CGATGGGTGAAGATATTAAAAGTCCAT 59.555 37.037 0.00 0.00 33.42 3.41
380 447 0.843984 AACGGGGAATGGGAATCGAT 59.156 50.000 0.00 0.00 0.00 3.59
383 450 2.437085 AGAAACGGGGAATGGGAATC 57.563 50.000 0.00 0.00 0.00 2.52
417 485 2.178235 GCGAATAGGGGAACGTGGC 61.178 63.158 0.00 0.00 0.00 5.01
418 486 0.391927 TTGCGAATAGGGGAACGTGG 60.392 55.000 0.00 0.00 0.00 4.94
456 524 3.897141 ATGGGGAACGTTTGTGTTTTT 57.103 38.095 0.46 0.00 30.75 1.94
457 525 3.897141 AATGGGGAACGTTTGTGTTTT 57.103 38.095 0.46 0.00 30.75 2.43
458 526 3.897141 AAATGGGGAACGTTTGTGTTT 57.103 38.095 0.46 0.00 36.94 2.83
459 527 3.449377 AGAAAATGGGGAACGTTTGTGTT 59.551 39.130 0.46 0.00 38.29 3.32
460 528 3.028130 AGAAAATGGGGAACGTTTGTGT 58.972 40.909 0.46 0.00 38.29 3.72
461 529 3.726291 AGAAAATGGGGAACGTTTGTG 57.274 42.857 0.46 0.00 38.29 3.33
524 638 2.125512 ATGGTTCGTCAGAGCGGC 60.126 61.111 0.00 0.00 0.00 6.53
532 646 1.221021 GGGAGGGTGATGGTTCGTC 59.779 63.158 0.00 0.00 0.00 4.20
1108 1228 0.721718 GATTGCGGAGGAAACAGTCG 59.278 55.000 0.00 0.00 44.10 4.18
1238 1358 0.881118 GTGGCATGAAAGCGGAGAAA 59.119 50.000 0.00 0.00 34.64 2.52
1256 1376 3.971702 GAGGCCTGCTTGTGGGGT 61.972 66.667 12.00 0.00 0.00 4.95
1260 1380 2.749044 ATGCGAGGCCTGCTTGTG 60.749 61.111 12.00 0.00 0.00 3.33
1303 1423 0.107017 ATTGGGCACGGAAGATGAGG 60.107 55.000 0.00 0.00 0.00 3.86
1351 1471 1.003233 GCACTGACAAGGAGGGGAC 60.003 63.158 0.00 0.00 0.00 4.46
1356 1476 1.004044 AGAATGGGCACTGACAAGGAG 59.996 52.381 0.00 0.00 0.00 3.69
1357 1477 1.067295 AGAATGGGCACTGACAAGGA 58.933 50.000 0.00 0.00 0.00 3.36
1359 1479 0.524862 GCAGAATGGGCACTGACAAG 59.475 55.000 0.00 0.00 36.38 3.16
1360 1480 1.236616 CGCAGAATGGGCACTGACAA 61.237 55.000 0.00 0.00 43.90 3.18
1361 1481 1.672030 CGCAGAATGGGCACTGACA 60.672 57.895 0.00 0.00 43.90 3.58
1362 1482 3.181367 CGCAGAATGGGCACTGAC 58.819 61.111 0.00 0.00 43.90 3.51
1596 1716 2.424684 ATTCCCCTACCTCTCCATCC 57.575 55.000 0.00 0.00 0.00 3.51
1739 1859 5.542635 ACCAGATTCAGGAGTTACTGTACAA 59.457 40.000 1.57 0.00 39.48 2.41
1789 1909 6.914757 GCTATTATTTGGTTCTCTCAATGCAC 59.085 38.462 0.00 0.00 0.00 4.57
1795 1915 6.816136 TCATCGCTATTATTTGGTTCTCTCA 58.184 36.000 0.00 0.00 0.00 3.27
1847 1967 7.517614 TTTAACAAATATGTGACTGGCTTCA 57.482 32.000 0.00 0.00 40.46 3.02
1855 1975 5.576774 GGGCTTGCTTTAACAAATATGTGAC 59.423 40.000 0.00 0.00 40.46 3.67
1856 1976 5.480073 AGGGCTTGCTTTAACAAATATGTGA 59.520 36.000 0.00 0.00 40.46 3.58
2038 2158 7.337689 TGGAGGACATATAATGCTATGAAATGC 59.662 37.037 0.00 0.00 34.01 3.56
2061 2181 0.676466 GATGGCGTGTGGATTGTGGA 60.676 55.000 0.00 0.00 0.00 4.02
2141 2261 1.812235 TACGCTAGTCCGACTTGACA 58.188 50.000 13.37 0.00 37.73 3.58
2166 2286 2.891580 AGAGGAAGTGCTGAGAAACGTA 59.108 45.455 0.00 0.00 0.00 3.57
2193 2313 9.650714 ACCTTTTAGACCTAATTTTGTAACCTT 57.349 29.630 0.00 0.00 0.00 3.50
2226 2346 6.531948 TGTACAAACATTTGCAAACTTACCAC 59.468 34.615 15.41 8.11 41.79 4.16
2442 2562 1.145119 AGGACCAAAGGGAAGAACCAC 59.855 52.381 0.00 0.00 41.20 4.16
2443 2563 1.144913 CAGGACCAAAGGGAAGAACCA 59.855 52.381 0.00 0.00 41.20 3.67
2444 2564 1.911057 CAGGACCAAAGGGAAGAACC 58.089 55.000 0.00 0.00 38.05 3.62
2445 2565 1.248486 GCAGGACCAAAGGGAAGAAC 58.752 55.000 0.00 0.00 38.05 3.01
2446 2566 0.850100 TGCAGGACCAAAGGGAAGAA 59.150 50.000 0.00 0.00 38.05 2.52
2447 2567 0.110486 GTGCAGGACCAAAGGGAAGA 59.890 55.000 0.00 0.00 38.05 2.87
2448 2568 0.111253 AGTGCAGGACCAAAGGGAAG 59.889 55.000 0.00 0.00 38.05 3.46
2449 2569 0.110486 GAGTGCAGGACCAAAGGGAA 59.890 55.000 0.00 0.00 38.05 3.97
2450 2570 1.761174 GAGTGCAGGACCAAAGGGA 59.239 57.895 0.00 0.00 38.05 4.20
2451 2571 1.303643 GGAGTGCAGGACCAAAGGG 60.304 63.158 0.00 0.00 41.29 3.95
2452 2572 1.303643 GGGAGTGCAGGACCAAAGG 60.304 63.158 0.00 0.00 0.00 3.11
2453 2573 0.111253 AAGGGAGTGCAGGACCAAAG 59.889 55.000 0.00 0.00 0.00 2.77
2454 2574 0.178992 CAAGGGAGTGCAGGACCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2455 2575 1.455849 CAAGGGAGTGCAGGACCAA 59.544 57.895 0.00 0.00 0.00 3.67
2456 2576 3.160585 CAAGGGAGTGCAGGACCA 58.839 61.111 0.00 0.00 0.00 4.02
2457 2577 2.360475 GCAAGGGAGTGCAGGACC 60.360 66.667 0.00 0.00 44.29 4.46
2458 2578 2.360475 GGCAAGGGAGTGCAGGAC 60.360 66.667 0.00 0.00 46.81 3.85
2459 2579 3.650950 GGGCAAGGGAGTGCAGGA 61.651 66.667 0.00 0.00 46.81 3.86
2460 2580 3.292481 ATGGGCAAGGGAGTGCAGG 62.292 63.158 0.00 0.00 46.81 4.85
2461 2581 1.751927 GATGGGCAAGGGAGTGCAG 60.752 63.158 0.00 0.00 46.81 4.41
2462 2582 2.356278 GATGGGCAAGGGAGTGCA 59.644 61.111 0.00 0.00 46.81 4.57
2463 2583 2.440980 GGATGGGCAAGGGAGTGC 60.441 66.667 0.00 0.00 44.14 4.40
2464 2584 1.379044 GTGGATGGGCAAGGGAGTG 60.379 63.158 0.00 0.00 0.00 3.51
2465 2585 1.217057 ATGTGGATGGGCAAGGGAGT 61.217 55.000 0.00 0.00 0.00 3.85
2466 2586 0.754217 CATGTGGATGGGCAAGGGAG 60.754 60.000 0.00 0.00 0.00 4.30
2467 2587 1.307309 CATGTGGATGGGCAAGGGA 59.693 57.895 0.00 0.00 0.00 4.20
2468 2588 0.258484 TACATGTGGATGGGCAAGGG 59.742 55.000 9.11 0.00 33.39 3.95
2469 2589 2.233271 GATACATGTGGATGGGCAAGG 58.767 52.381 9.11 0.00 33.39 3.61
2470 2590 2.233271 GGATACATGTGGATGGGCAAG 58.767 52.381 9.11 0.00 33.39 4.01
2471 2591 1.568123 TGGATACATGTGGATGGGCAA 59.432 47.619 9.11 0.00 46.17 4.52
2472 2592 1.220703 TGGATACATGTGGATGGGCA 58.779 50.000 9.11 0.00 46.17 5.36
2485 2605 7.573843 GCACCATATTAACAGCTCATTGGATAC 60.574 40.741 0.00 0.00 0.00 2.24
2486 2606 6.430925 GCACCATATTAACAGCTCATTGGATA 59.569 38.462 0.00 0.00 0.00 2.59
2487 2607 5.242393 GCACCATATTAACAGCTCATTGGAT 59.758 40.000 0.00 0.00 0.00 3.41
2488 2608 4.580167 GCACCATATTAACAGCTCATTGGA 59.420 41.667 0.00 0.00 0.00 3.53
2489 2609 4.338964 TGCACCATATTAACAGCTCATTGG 59.661 41.667 0.00 0.00 0.00 3.16
2490 2610 5.503662 TGCACCATATTAACAGCTCATTG 57.496 39.130 0.00 0.00 0.00 2.82
2491 2611 5.829391 TGATGCACCATATTAACAGCTCATT 59.171 36.000 0.00 0.00 0.00 2.57
2492 2612 5.379187 TGATGCACCATATTAACAGCTCAT 58.621 37.500 0.00 0.00 0.00 2.90
2493 2613 4.779696 TGATGCACCATATTAACAGCTCA 58.220 39.130 0.00 0.00 0.00 4.26
2494 2614 4.818546 ACTGATGCACCATATTAACAGCTC 59.181 41.667 0.00 0.00 0.00 4.09
2495 2615 4.785301 ACTGATGCACCATATTAACAGCT 58.215 39.130 0.00 0.00 0.00 4.24
2496 2616 5.066375 TGAACTGATGCACCATATTAACAGC 59.934 40.000 0.00 0.00 0.00 4.40
2497 2617 6.317140 ACTGAACTGATGCACCATATTAACAG 59.683 38.462 0.00 0.00 0.00 3.16
2498 2618 6.179756 ACTGAACTGATGCACCATATTAACA 58.820 36.000 0.00 0.00 0.00 2.41
2499 2619 6.683974 ACTGAACTGATGCACCATATTAAC 57.316 37.500 0.00 0.00 0.00 2.01
2500 2620 7.392953 TCAAACTGAACTGATGCACCATATTAA 59.607 33.333 0.00 0.00 0.00 1.40
2501 2621 6.883756 TCAAACTGAACTGATGCACCATATTA 59.116 34.615 0.00 0.00 0.00 0.98
2502 2622 5.711506 TCAAACTGAACTGATGCACCATATT 59.288 36.000 0.00 0.00 0.00 1.28
2503 2623 5.255687 TCAAACTGAACTGATGCACCATAT 58.744 37.500 0.00 0.00 0.00 1.78
2504 2624 4.650734 TCAAACTGAACTGATGCACCATA 58.349 39.130 0.00 0.00 0.00 2.74
2505 2625 3.489355 TCAAACTGAACTGATGCACCAT 58.511 40.909 0.00 0.00 0.00 3.55
2506 2626 2.929641 TCAAACTGAACTGATGCACCA 58.070 42.857 0.00 0.00 0.00 4.17
2507 2627 3.503363 TCATCAAACTGAACTGATGCACC 59.497 43.478 7.09 0.00 45.64 5.01
2508 2628 4.754372 TCATCAAACTGAACTGATGCAC 57.246 40.909 7.09 0.00 45.64 4.57
2509 2629 7.634671 ATTATCATCAAACTGAACTGATGCA 57.365 32.000 7.09 0.00 45.64 3.96
2510 2630 8.072567 GGTATTATCATCAAACTGAACTGATGC 58.927 37.037 7.09 0.00 45.64 3.91
2511 2631 9.112725 TGGTATTATCATCAAACTGAACTGATG 57.887 33.333 5.83 5.83 46.83 3.07
2512 2632 9.113838 GTGGTATTATCATCAAACTGAACTGAT 57.886 33.333 0.00 0.00 32.64 2.90
2513 2633 8.100164 TGTGGTATTATCATCAAACTGAACTGA 58.900 33.333 0.00 0.00 0.00 3.41
2514 2634 8.267620 TGTGGTATTATCATCAAACTGAACTG 57.732 34.615 0.00 0.00 0.00 3.16
2537 2657 5.827797 ACCACAAGACACACATCTTTTATGT 59.172 36.000 0.00 0.00 36.78 2.29
2538 2658 6.317789 ACCACAAGACACACATCTTTTATG 57.682 37.500 0.00 0.00 36.78 1.90
2539 2659 6.772716 AGAACCACAAGACACACATCTTTTAT 59.227 34.615 0.00 0.00 36.78 1.40
2540 2660 6.119536 AGAACCACAAGACACACATCTTTTA 58.880 36.000 0.00 0.00 36.78 1.52
2541 2661 4.949856 AGAACCACAAGACACACATCTTTT 59.050 37.500 0.00 0.00 36.78 2.27
2542 2662 4.526970 AGAACCACAAGACACACATCTTT 58.473 39.130 0.00 0.00 36.78 2.52
2543 2663 4.156455 AGAACCACAAGACACACATCTT 57.844 40.909 0.00 0.00 39.60 2.40
2544 2664 3.845781 AGAACCACAAGACACACATCT 57.154 42.857 0.00 0.00 0.00 2.90
2545 2665 3.251004 GGAAGAACCACAAGACACACATC 59.749 47.826 0.00 0.00 38.79 3.06
2546 2666 3.214328 GGAAGAACCACAAGACACACAT 58.786 45.455 0.00 0.00 38.79 3.21
2547 2667 2.639065 GGAAGAACCACAAGACACACA 58.361 47.619 0.00 0.00 38.79 3.72
2548 2668 1.947456 GGGAAGAACCACAAGACACAC 59.053 52.381 0.00 0.00 41.20 3.82
2549 2669 1.843851 AGGGAAGAACCACAAGACACA 59.156 47.619 0.00 0.00 41.20 3.72
2550 2670 2.640316 AGGGAAGAACCACAAGACAC 57.360 50.000 0.00 0.00 41.20 3.67
2551 2671 3.287222 CAAAGGGAAGAACCACAAGACA 58.713 45.455 0.00 0.00 41.20 3.41
2552 2672 2.623416 CCAAAGGGAAGAACCACAAGAC 59.377 50.000 0.00 0.00 41.20 3.01
2553 2673 2.243736 ACCAAAGGGAAGAACCACAAGA 59.756 45.455 0.00 0.00 41.20 3.02
2554 2674 2.623416 GACCAAAGGGAAGAACCACAAG 59.377 50.000 0.00 0.00 41.20 3.16
2555 2675 2.661718 GACCAAAGGGAAGAACCACAA 58.338 47.619 0.00 0.00 41.20 3.33
2556 2676 1.133606 GGACCAAAGGGAAGAACCACA 60.134 52.381 0.00 0.00 41.20 4.17
2687 2807 0.743688 AGGCAATTGTTCACGTGCAA 59.256 45.000 11.67 10.92 38.78 4.08
3001 3132 4.375313 ACCTTTCTGTAGGGGAAGATGAT 58.625 43.478 0.00 0.00 39.76 2.45
3036 3169 1.002544 CGATCCTGGGAGATTTAGGGC 59.997 57.143 0.00 0.00 32.39 5.19
3070 3203 0.827925 ACAGACCGACCTTCTCTGCA 60.828 55.000 0.00 0.00 35.75 4.41
3253 3386 0.824759 GTAGATCGAAGCACCCTGGT 59.175 55.000 0.00 0.00 0.00 4.00
3267 3400 9.699703 GTCTTACTCTTGTCTTTTGAAGTAGAT 57.300 33.333 0.00 0.00 0.00 1.98
3537 3670 3.519107 TGATGCACTCATTCTTGGGACTA 59.481 43.478 0.00 0.00 31.96 2.59
3765 3898 2.817258 TGCACTGGCTAATGTTTACCAC 59.183 45.455 0.00 0.00 41.91 4.16
3840 3976 8.758829 AGGACACATTACATGACTAATGACTTA 58.241 33.333 18.16 0.00 38.72 2.24
4161 4303 7.535258 GTCACAACAATGAGTATAAACAAGCAG 59.465 37.037 0.00 0.00 0.00 4.24
4481 4623 7.695055 TCCCTTGGAGTTCATTTAGTAAATCA 58.305 34.615 5.10 0.00 0.00 2.57
4520 4662 3.281727 TTTACCTCCCATGAGTCATGC 57.718 47.619 25.08 0.00 40.20 4.06
4587 4731 3.889517 TATATCGAGGGGACGCTGGCA 62.890 57.143 0.00 0.00 0.00 4.92
5096 5240 1.750778 GAGTCTTGCTCTAGCTCTGCT 59.249 52.381 3.26 0.00 40.98 4.24
5252 5396 5.551760 ATGCTTTCACGTAGGAATTTGAG 57.448 39.130 0.00 0.00 0.00 3.02
5265 5409 7.171337 TGCCAAATAAAGAGAAAATGCTTTCAC 59.829 33.333 0.00 0.00 42.99 3.18
5328 5475 6.391227 AATACTGAATGGCCTTTATTTCCG 57.609 37.500 3.32 0.00 0.00 4.30
5438 5585 3.119137 ACAACCTGAAACTGAGCCAAAAC 60.119 43.478 0.00 0.00 0.00 2.43
5595 5993 6.306199 AGTAAGGTCCATGCATGCATTATTA 58.694 36.000 30.32 19.30 33.90 0.98
5909 6307 8.102484 ACCTGATTAACAATAGGACCATAACT 57.898 34.615 0.00 0.00 34.42 2.24
5950 6353 7.418337 TTCAGCACCAATATAACTGTAGAGA 57.582 36.000 0.00 0.00 0.00 3.10
6062 6465 0.036388 CTTTTGCTGGGCGACTAGGA 60.036 55.000 2.91 0.00 39.75 2.94
6149 6552 2.230992 GTGTGGCCAGAAATGCATGTTA 59.769 45.455 5.11 0.00 0.00 2.41
6318 6722 7.541091 CGTTGTTCTCAGCAGTATAGTTTTCTA 59.459 37.037 0.00 0.00 36.78 2.10
6474 6878 6.634805 TGTTGTCTGAATGGAGTATCTTCTC 58.365 40.000 0.00 0.00 33.73 2.87
6528 6932 3.126001 TGTGTTTGTTAGCAGGAGGAG 57.874 47.619 0.00 0.00 0.00 3.69
6529 6933 3.211045 GTTGTGTTTGTTAGCAGGAGGA 58.789 45.455 0.00 0.00 0.00 3.71
6530 6934 2.948979 TGTTGTGTTTGTTAGCAGGAGG 59.051 45.455 0.00 0.00 0.00 4.30
6562 6966 1.475403 TCCTCGAGGTGTCATTCCTC 58.525 55.000 30.17 2.27 45.56 3.71
6565 6969 1.936547 GCATTCCTCGAGGTGTCATTC 59.063 52.381 30.17 9.89 36.34 2.67
6566 6970 1.278985 TGCATTCCTCGAGGTGTCATT 59.721 47.619 30.17 5.45 36.34 2.57
6690 7136 3.267974 GCTTGTTTCCTCCAGGCG 58.732 61.111 0.00 0.00 34.44 5.52
6715 7161 2.368875 TCCAACACTCCTTGGAGAGTTC 59.631 50.000 23.09 0.00 44.83 3.01
6853 7299 3.643237 TCAAACGATACCTCTCTGGGAT 58.357 45.455 0.00 0.00 43.67 3.85
6920 7366 4.646492 AGCAATCCAGAGTTCAAACTTGTT 59.354 37.500 0.00 0.00 39.88 2.83
6971 7417 2.425312 ACAAACGAGGCACAACAATTCA 59.575 40.909 0.00 0.00 0.00 2.57
6987 7433 6.806249 TGTCAACTGATGAACTTGAAACAAAC 59.194 34.615 0.00 0.00 40.50 2.93
6989 7435 6.507958 TGTCAACTGATGAACTTGAAACAA 57.492 33.333 0.00 0.00 40.50 2.83
7050 7496 5.009631 CAGGTGTACCCAATCAGAAATTCA 58.990 41.667 0.00 0.00 36.42 2.57
7156 7602 3.784338 AGAACATGGCAAACAACAGTTG 58.216 40.909 12.03 12.03 0.00 3.16
7219 7665 4.992319 AGATACAATCGAAACAACGGTTCA 59.008 37.500 0.00 0.00 35.82 3.18
7321 7767 5.205759 TGCATGTCACAGATACCAGATAG 57.794 43.478 0.00 0.00 0.00 2.08
7329 7775 6.430616 TGAAGTGAAATTGCATGTCACAGATA 59.569 34.615 20.59 7.12 43.34 1.98
7353 7799 3.310227 AGCACGATCGTACTCTTCTAGTG 59.690 47.826 22.26 4.98 39.39 2.74
7420 7866 6.503217 TCCTGGGCTAGAATATGATCTCATTT 59.497 38.462 0.00 0.00 37.76 2.32
7504 7950 2.767505 GGATGTATAGGGGCGTTTGAG 58.232 52.381 0.00 0.00 0.00 3.02
7528 7975 0.109723 GCAAGTCACTTACCCACCCA 59.890 55.000 0.00 0.00 0.00 4.51
7537 7988 4.759693 TCACGATTTTATGGCAAGTCACTT 59.240 37.500 0.00 0.00 0.00 3.16
7544 7995 4.839121 ACTAGGTCACGATTTTATGGCAA 58.161 39.130 0.00 0.00 0.00 4.52
7581 8036 5.838521 TCAGCCATGATGTAGTATAAGTCCA 59.161 40.000 0.00 0.00 0.00 4.02
7594 8049 3.579709 GGAGTATACGTCAGCCATGATG 58.420 50.000 0.00 0.00 46.22 3.07
7595 8050 2.563179 GGGAGTATACGTCAGCCATGAT 59.437 50.000 0.00 0.00 37.87 2.45
7596 8051 1.961394 GGGAGTATACGTCAGCCATGA 59.039 52.381 0.00 0.00 0.00 3.07
7597 8052 1.000955 GGGGAGTATACGTCAGCCATG 59.999 57.143 0.00 0.00 0.00 3.66
7599 8054 0.032912 TGGGGAGTATACGTCAGCCA 60.033 55.000 0.00 0.00 0.00 4.75
7600 8055 1.339097 ATGGGGAGTATACGTCAGCC 58.661 55.000 0.00 0.00 0.00 4.85
7601 8056 3.762288 TGATATGGGGAGTATACGTCAGC 59.238 47.826 0.00 0.00 0.00 4.26
7602 8057 5.124138 GTCTGATATGGGGAGTATACGTCAG 59.876 48.000 0.00 0.00 33.65 3.51
7603 8058 5.008331 GTCTGATATGGGGAGTATACGTCA 58.992 45.833 0.00 0.00 0.00 4.35
7604 8059 5.254901 AGTCTGATATGGGGAGTATACGTC 58.745 45.833 0.00 0.00 0.00 4.34
7605 8060 5.258216 AGTCTGATATGGGGAGTATACGT 57.742 43.478 0.00 0.00 0.00 3.57
7606 8061 6.651086 TCTAGTCTGATATGGGGAGTATACG 58.349 44.000 0.00 0.00 0.00 3.06
7607 8062 7.442969 CGATCTAGTCTGATATGGGGAGTATAC 59.557 44.444 0.00 0.00 0.00 1.47
7608 8063 7.420330 CCGATCTAGTCTGATATGGGGAGTATA 60.420 44.444 0.00 0.00 0.00 1.47
7609 8064 6.361433 CGATCTAGTCTGATATGGGGAGTAT 58.639 44.000 0.00 0.00 0.00 2.12
7610 8065 5.339282 CCGATCTAGTCTGATATGGGGAGTA 60.339 48.000 0.00 0.00 0.00 2.59
7611 8066 4.568804 CCGATCTAGTCTGATATGGGGAGT 60.569 50.000 0.00 0.00 0.00 3.85
7612 8067 3.951037 CCGATCTAGTCTGATATGGGGAG 59.049 52.174 0.00 0.00 0.00 4.30
7613 8068 3.591977 TCCGATCTAGTCTGATATGGGGA 59.408 47.826 0.00 0.00 0.00 4.81
7614 8069 3.969553 TCCGATCTAGTCTGATATGGGG 58.030 50.000 0.00 0.00 0.00 4.96
7615 8070 4.582656 GGATCCGATCTAGTCTGATATGGG 59.417 50.000 8.29 0.00 31.80 4.00
7620 8075 3.075283 AGGTGGATCCGATCTAGTCTGAT 59.925 47.826 7.39 0.00 41.99 2.90
7636 8092 5.951148 TCAATTTGATGCAATTAGAGGTGGA 59.049 36.000 0.00 0.00 0.00 4.02
7680 8136 0.036306 AAACGGAAGCGTGGGAAGAT 59.964 50.000 0.00 0.00 0.00 2.40
7683 8139 1.598685 GGAAACGGAAGCGTGGGAA 60.599 57.895 0.00 0.00 0.00 3.97
7692 8148 0.037590 CTGGGATGTGGGAAACGGAA 59.962 55.000 0.00 0.00 0.00 4.30
7759 8216 1.359475 GACATCTAGGGCGACGGAC 59.641 63.158 0.00 0.00 0.00 4.79
7823 8280 0.445436 CAAGAGCTCCATGACAACGC 59.555 55.000 10.93 0.00 0.00 4.84
7847 8304 3.777925 CCTTGCAACTCGTCGCCG 61.778 66.667 0.00 0.00 0.00 6.46
7865 8322 2.420372 TCTCTTCGGATGACGTTCTCTG 59.580 50.000 0.00 0.00 44.69 3.35
7866 8323 2.680841 CTCTCTTCGGATGACGTTCTCT 59.319 50.000 0.00 0.00 44.69 3.10
7881 8338 0.957888 GCTTCCTTTGCCGCTCTCTT 60.958 55.000 0.00 0.00 0.00 2.85
7884 8341 1.228245 TTGCTTCCTTTGCCGCTCT 60.228 52.632 0.00 0.00 0.00 4.09
7906 8363 0.581529 TTCGTTGTCGCTTTCTGCTG 59.418 50.000 0.00 0.00 40.11 4.41
7912 8369 1.949465 ACTTCCTTCGTTGTCGCTTT 58.051 45.000 0.00 0.00 36.96 3.51
7924 8381 1.493446 ACCCTTGGTCGAAACTTCCTT 59.507 47.619 0.00 0.00 0.00 3.36
7927 8384 4.070009 ACAATACCCTTGGTCGAAACTTC 58.930 43.478 0.00 0.00 37.09 3.01
7936 8393 2.355716 CGACATCCACAATACCCTTGGT 60.356 50.000 0.00 0.00 40.16 3.67
7945 8402 1.866015 TCCTCCTCGACATCCACAAT 58.134 50.000 0.00 0.00 0.00 2.71
8001 8458 2.774234 CCTTGTCAGTGGTAGGATGGAT 59.226 50.000 0.00 0.00 0.00 3.41
8048 8505 1.535226 CGGCTATCGGATCGTTGTCAA 60.535 52.381 0.00 0.00 34.75 3.18
8049 8506 0.030235 CGGCTATCGGATCGTTGTCA 59.970 55.000 0.00 0.00 34.75 3.58
8076 8534 6.128117 ACACTTGCGTAAATACATCCGAAAAT 60.128 34.615 0.00 0.00 0.00 1.82
8077 8535 5.179742 ACACTTGCGTAAATACATCCGAAAA 59.820 36.000 0.00 0.00 0.00 2.29
8080 8538 3.615056 CACACTTGCGTAAATACATCCGA 59.385 43.478 0.00 0.00 0.00 4.55
8111 8590 0.825425 TCGCACCCTTTGGAATTGCA 60.825 50.000 0.00 0.00 34.81 4.08
8126 8605 2.775856 TTGCCCGTGCTTTTTCGCA 61.776 52.632 0.00 0.00 38.71 5.10
8165 8645 5.222870 AGGACATTATCTTGATCAGGACCT 58.777 41.667 10.05 8.03 0.00 3.85
8168 8648 5.840693 TGCTAGGACATTATCTTGATCAGGA 59.159 40.000 10.27 10.27 0.00 3.86
8179 8659 4.497516 ACCATCTCCTGCTAGGACATTAT 58.502 43.478 1.25 0.00 40.06 1.28
8235 8715 8.603898 ATGATCCAATGGCACAATGATATAAT 57.396 30.769 0.00 0.00 42.85 1.28
8283 8765 9.402320 TCCTAAAATGACCATGATTCGAAATAA 57.598 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.