Multiple sequence alignment - TraesCS4A01G136000

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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 TraesCS4A01G136000 chr4A 100.000 6388 0 0 1 6388 189601730 189608117 0.000000e+00 11797.0
1 TraesCS4A01G136000 chr4A 87.952 83 10 0 6208 6290 355668985 355669067 1.470000e-16 99.0
2 TraesCS4A01G136000 chr4A 94.737 57 0 2 6152 6205 189607821 189607877 1.140000e-12 86.1
3 TraesCS4A01G136000 chr4A 94.737 57 0 2 6092 6148 189607881 189607934 1.140000e-12 86.1
4 TraesCS4A01G136000 chr4A 95.455 44 1 1 6169 6211 250424737 250424780 1.150000e-07 69.4
5 TraesCS4A01G136000 chr4A 97.368 38 0 1 6112 6148 250424737 250424774 5.350000e-06 63.9
6 TraesCS4A01G136000 chr4D 95.914 4674 146 18 529 5171 297933718 297929059 0.000000e+00 7531.0
7 TraesCS4A01G136000 chr4D 88.727 825 50 22 5167 5957 297928978 297928163 0.000000e+00 968.0
8 TraesCS4A01G136000 chr4D 96.044 455 13 2 1 450 297934168 297933714 0.000000e+00 736.0
9 TraesCS4A01G136000 chr4D 94.545 55 3 0 6169 6223 37256930 37256984 1.140000e-12 86.1
10 TraesCS4A01G136000 chr4B 96.007 3256 85 16 650 3882 369283810 369280577 0.000000e+00 5251.0
11 TraesCS4A01G136000 chr4B 94.481 2265 80 27 3878 6105 369280423 369278167 0.000000e+00 3448.0
12 TraesCS4A01G136000 chr4B 95.354 452 18 3 1 450 369284347 369283897 0.000000e+00 715.0
13 TraesCS4A01G136000 chr4B 95.506 89 3 1 529 616 369283901 369283813 2.400000e-29 141.0
14 TraesCS4A01G136000 chr6A 97.802 91 2 0 444 534 581742876 581742966 2.380000e-34 158.0
15 TraesCS4A01G136000 chr6A 92.157 102 7 1 433 533 26975955 26976056 6.680000e-30 143.0
16 TraesCS4A01G136000 chr6A 78.571 126 24 2 3489 3614 99506082 99505960 5.310000e-11 80.5
17 TraesCS4A01G136000 chr1D 97.778 90 2 0 443 532 467803505 467803594 8.580000e-34 156.0
18 TraesCS4A01G136000 chr6B 97.753 89 2 0 446 534 390046993 390046905 3.080000e-33 154.0
19 TraesCS4A01G136000 chr6B 85.827 127 11 4 6169 6289 172023315 172023190 1.870000e-25 128.0
20 TraesCS4A01G136000 chr5D 94.000 100 4 2 444 542 228556523 228556425 3.990000e-32 150.0
21 TraesCS4A01G136000 chr5D 85.849 106 15 0 3530 3635 548522651 548522546 5.230000e-21 113.0
22 TraesCS4A01G136000 chr3D 93.814 97 6 0 443 539 331018052 331017956 5.160000e-31 147.0
23 TraesCS4A01G136000 chr3D 81.034 116 18 4 6169 6282 395732968 395733081 8.820000e-14 89.8
24 TraesCS4A01G136000 chr3D 85.246 61 5 4 6090 6148 395732947 395733005 6.920000e-05 60.2
25 TraesCS4A01G136000 chr2B 92.308 104 6 2 432 533 335192827 335192930 5.160000e-31 147.0
26 TraesCS4A01G136000 chr2B 88.462 78 9 0 3544 3621 39409873 39409950 1.900000e-15 95.3
27 TraesCS4A01G136000 chr6D 90.826 109 9 1 448 555 467187173 467187281 1.860000e-30 145.0
28 TraesCS4A01G136000 chr6D 85.567 97 14 0 3518 3614 82698385 82698289 1.130000e-17 102.0
29 TraesCS4A01G136000 chr5B 91.429 105 7 2 444 548 3917781 3917883 6.680000e-30 143.0
30 TraesCS4A01G136000 chr5B 83.810 105 8 7 6182 6282 426361411 426361510 2.450000e-14 91.6
31 TraesCS4A01G136000 chr5A 89.247 93 10 0 3518 3610 708620028 708620120 4.050000e-22 117.0
32 TraesCS4A01G136000 chr5A 100.000 29 0 0 6113 6141 359054884 359054856 3.000000e-03 54.7
33 TraesCS4A01G136000 chr7D 84.783 92 12 2 6170 6260 604590784 604590694 2.450000e-14 91.6
34 TraesCS4A01G136000 chr7D 84.091 88 10 3 6200 6286 95936794 95936878 1.480000e-11 82.4
35 TraesCS4A01G136000 chr3A 86.585 82 11 0 6208 6289 33272582 33272501 2.450000e-14 91.6
36 TraesCS4A01G136000 chr7A 81.034 116 16 3 6169 6282 136442051 136441940 3.170000e-13 87.9
37 TraesCS4A01G136000 chr2D 89.706 68 7 0 6178 6245 398418594 398418661 3.170000e-13 87.9


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 TraesCS4A01G136000 chr4A 189601730 189608117 6387 False 3989.733333 11797 96.491333 1 6388 3 chr4A.!!$F2 6387
1 TraesCS4A01G136000 chr4D 297928163 297934168 6005 True 3078.333333 7531 93.561667 1 5957 3 chr4D.!!$R1 5956
2 TraesCS4A01G136000 chr4B 369278167 369284347 6180 True 2388.750000 5251 95.337000 1 6105 4 chr4B.!!$R1 6104

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
699 706 2.104792 CACCACTCCTCTCAACTTCCAA 59.895 50.0 0.0 0.0 0.00 3.53 F
1143 1151 1.056700 CGGGGGAGGAGAATGGTGAT 61.057 60.0 0.0 0.0 0.00 3.06 F
2619 2632 0.038166 TTTCTTTGCTGGCGAGGGAT 59.962 50.0 0.0 0.0 0.00 3.85 F
3624 3656 1.279496 CAGGATGAGGACAACTGGGA 58.721 55.0 0.0 0.0 39.69 4.37 F
4001 4192 1.884235 AAGCGGGAAAGTCTGTTCAG 58.116 50.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2079 1.075374 AGCAACAGGGCCATTTAGACA 59.925 47.619 6.18 0.0 0.00 3.41 R
2974 2988 1.273327 CCTGAAAAACATCCACCCTGC 59.727 52.381 0.00 0.0 0.00 4.85 R
3831 3863 0.108585 ACTGAACACAGGAATGCCGT 59.891 50.000 0.00 0.0 39.96 5.68 R
4466 4669 0.607489 CCTCAACTTCAGGTGGCTGG 60.607 60.000 0.00 0.0 0.00 4.85 R
5958 6293 1.593196 TCAGCCAACGAAAGACTTGG 58.407 50.000 0.00 0.0 40.11 3.61 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
82 83 2.597455 CACACCTCCCACCAAAGAATT 58.403 47.619 0.00 0.00 0.00 2.17
412 419 2.722094 ACTCTGTCAAACCAGCAAACA 58.278 42.857 0.00 0.00 32.32 2.83
447 454 9.762381 TTTTGAATGGGAAGGTACATTATTAGT 57.238 29.630 0.00 0.00 37.43 2.24
449 456 9.841295 TTGAATGGGAAGGTACATTATTAGTAC 57.159 33.333 0.00 0.00 40.78 2.73
450 457 9.220906 TGAATGGGAAGGTACATTATTAGTACT 57.779 33.333 0.00 0.00 41.16 2.73
451 458 9.708092 GAATGGGAAGGTACATTATTAGTACTC 57.292 37.037 0.00 0.00 41.16 2.59
452 459 7.607615 TGGGAAGGTACATTATTAGTACTCC 57.392 40.000 0.00 0.00 41.16 3.85
453 460 6.556116 TGGGAAGGTACATTATTAGTACTCCC 59.444 42.308 17.34 17.34 46.69 4.30
454 461 6.786461 GGGAAGGTACATTATTAGTACTCCCT 59.214 42.308 17.09 1.19 44.99 4.20
455 462 7.039152 GGGAAGGTACATTATTAGTACTCCCTC 60.039 44.444 17.09 0.00 44.99 4.30
456 463 7.039152 GGAAGGTACATTATTAGTACTCCCTCC 60.039 44.444 0.00 0.00 41.16 4.30
457 464 6.008960 AGGTACATTATTAGTACTCCCTCCG 58.991 44.000 0.00 0.00 41.16 4.63
458 465 5.772169 GGTACATTATTAGTACTCCCTCCGT 59.228 44.000 0.00 0.00 41.16 4.69
459 466 6.942576 GGTACATTATTAGTACTCCCTCCGTA 59.057 42.308 0.00 0.00 41.16 4.02
460 467 7.448469 GGTACATTATTAGTACTCCCTCCGTAA 59.552 40.741 0.00 0.00 41.16 3.18
461 468 7.902920 ACATTATTAGTACTCCCTCCGTAAA 57.097 36.000 0.00 0.00 0.00 2.01
462 469 7.720442 ACATTATTAGTACTCCCTCCGTAAAC 58.280 38.462 0.00 0.00 0.00 2.01
463 470 7.562821 ACATTATTAGTACTCCCTCCGTAAACT 59.437 37.037 0.00 0.00 0.00 2.66
464 471 9.071276 CATTATTAGTACTCCCTCCGTAAACTA 57.929 37.037 0.00 0.00 0.00 2.24
465 472 9.646522 ATTATTAGTACTCCCTCCGTAAACTAA 57.353 33.333 0.00 0.00 0.00 2.24
466 473 9.646522 TTATTAGTACTCCCTCCGTAAACTAAT 57.353 33.333 0.00 9.13 33.92 1.73
468 475 9.819754 ATTAGTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
471 478 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
472 479 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
473 480 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
474 481 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
475 482 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
476 483 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
477 484 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
478 485 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
510 517 8.900781 ACTAAAGTAGTGATCTAAACGCTATCA 58.099 33.333 0.00 0.00 37.69 2.15
511 518 9.900710 CTAAAGTAGTGATCTAAACGCTATCAT 57.099 33.333 0.00 0.00 33.86 2.45
526 533 9.477484 AAACGCTATCATATTAGTTTACAGAGG 57.523 33.333 0.00 0.00 31.14 3.69
527 534 7.603651 ACGCTATCATATTAGTTTACAGAGGG 58.396 38.462 0.00 0.00 0.00 4.30
557 564 7.918562 ACATGACAGTACACAATTGTTTTTACC 59.081 33.333 8.77 0.21 37.15 2.85
699 706 2.104792 CACCACTCCTCTCAACTTCCAA 59.895 50.000 0.00 0.00 0.00 3.53
894 902 4.605640 ATCATTTTTGTGGTTCTGTGGG 57.394 40.909 0.00 0.00 0.00 4.61
1002 1010 7.979444 TCTTCTTTATTTGACTGGTTAGGTG 57.021 36.000 0.00 0.00 0.00 4.00
1008 1016 4.974368 TTTGACTGGTTAGGTGTTTGTG 57.026 40.909 0.00 0.00 0.00 3.33
1035 1043 4.941873 GGTTCGGTTCCATTGAAGACTTAT 59.058 41.667 0.00 0.00 0.00 1.73
1143 1151 1.056700 CGGGGGAGGAGAATGGTGAT 61.057 60.000 0.00 0.00 0.00 3.06
1308 1316 7.766278 TGTCCTTAGCATACATTTCTTCTCTTC 59.234 37.037 0.00 0.00 0.00 2.87
1547 1555 3.149196 CCTTGAGCTGGTAATGTGTTGT 58.851 45.455 0.00 0.00 0.00 3.32
1827 1837 3.505386 CCTACTAGGAGCTCATCATGGT 58.495 50.000 17.19 8.66 37.67 3.55
1977 1987 9.846248 ATCTTTAGACAATGCAAAAACTGATAC 57.154 29.630 0.00 0.00 0.00 2.24
1978 1988 8.845227 TCTTTAGACAATGCAAAAACTGATACA 58.155 29.630 0.00 0.00 0.00 2.29
2067 2079 5.372343 TGACTGGGACAAATACTGCATAT 57.628 39.130 0.00 0.00 38.70 1.78
2218 2230 6.999272 TGCAGTTGAAGGTTTAAATGTACCTA 59.001 34.615 0.00 0.00 43.88 3.08
2303 2315 3.374988 CCAAGAAATTCTGATGCACGCTA 59.625 43.478 0.00 0.00 0.00 4.26
2502 2514 5.083533 TGTGATGTGCTGATGTGTACATA 57.916 39.130 0.00 0.00 41.89 2.29
2619 2632 0.038166 TTTCTTTGCTGGCGAGGGAT 59.962 50.000 0.00 0.00 0.00 3.85
3258 3290 1.328279 CTTCCAAAACCTGGTCCCAC 58.672 55.000 0.00 0.00 46.51 4.61
3264 3296 3.118075 CCAAAACCTGGTCCCACAAAAAT 60.118 43.478 0.00 0.00 40.78 1.82
3276 3308 6.995686 GGTCCCACAAAAATGGAAAAGTTAAT 59.004 34.615 0.00 0.00 43.02 1.40
3466 3498 5.221682 TGACGGTAAGGTTGACAAGGATTTA 60.222 40.000 0.00 0.00 0.00 1.40
3610 3642 3.759581 AGTTTCACAGCAATCACAGGAT 58.240 40.909 0.00 0.00 34.43 3.24
3624 3656 1.279496 CAGGATGAGGACAACTGGGA 58.721 55.000 0.00 0.00 39.69 4.37
3658 3690 4.885907 CAGTTGAATGCCTGTGGAATAGAT 59.114 41.667 0.00 0.00 0.00 1.98
3786 3818 7.115947 CGGATATATTCGTGAAAAGGTAGGAAC 59.884 40.741 5.16 0.00 0.00 3.62
3831 3863 5.508280 TGGATATCTCATGCATTGATCCA 57.492 39.130 15.68 15.68 37.42 3.41
4001 4192 1.884235 AAGCGGGAAAGTCTGTTCAG 58.116 50.000 0.00 0.00 0.00 3.02
4050 4241 6.982852 TCCTCTGAAATATATCTGTCCGTTC 58.017 40.000 0.00 0.00 0.00 3.95
4062 4253 5.621197 TCTGTCCGTTCATTGTTATTTGG 57.379 39.130 0.00 0.00 0.00 3.28
4115 4306 8.084684 TCTGTATTACAGCACATGACATCTATC 58.915 37.037 17.35 0.00 45.54 2.08
4246 4449 3.916989 AGTGGGACCAAGGAAATAAGTCT 59.083 43.478 0.00 0.00 0.00 3.24
4370 4573 2.639286 GAAGCAAGGCACACACGG 59.361 61.111 0.00 0.00 0.00 4.94
4437 4640 5.308014 AGCGAAATTATGATACTGGCATGA 58.692 37.500 0.00 0.00 0.00 3.07
4466 4669 4.708601 CACGACCAGTTAGTGCAAAATAC 58.291 43.478 0.00 0.00 0.00 1.89
4541 4744 2.443887 TGGCAAGAAATCAAAGCTGC 57.556 45.000 0.00 0.00 0.00 5.25
4542 4745 1.687660 TGGCAAGAAATCAAAGCTGCA 59.312 42.857 1.02 0.00 0.00 4.41
4675 4878 5.636903 AAGTATGATAATCACAGTGGGCT 57.363 39.130 0.00 0.00 0.00 5.19
4738 4941 2.414161 GCCAAGTTGCGACCATTCTAAC 60.414 50.000 0.00 0.00 0.00 2.34
4766 4969 1.147817 ACAAAGGAGGTTGCCCTGAAT 59.852 47.619 0.00 0.00 42.86 2.57
4894 5097 0.834612 TCCGTCCCTGTCACAAAAGT 59.165 50.000 0.00 0.00 0.00 2.66
5095 5298 7.989741 CAGGTAACATCAAAGGATCTTACAGAT 59.010 37.037 0.00 0.00 36.91 2.90
5230 5522 7.736447 TTGTTTTTGTTCAATGGTCAACTTT 57.264 28.000 0.00 0.00 0.00 2.66
5403 5701 3.111838 CGCTGAGACTTACAGTAGCATG 58.888 50.000 0.00 0.00 37.64 4.06
5472 5772 6.698008 TGATGTTCACAAATATGACCATCC 57.302 37.500 9.82 0.00 43.98 3.51
5566 5866 6.022107 AGGTACCAAAGAAAGGTTTTAGGT 57.978 37.500 15.94 0.00 40.54 3.08
5689 5989 4.778213 ATTATGAGCCTTTCTGCTACCA 57.222 40.909 0.00 0.00 42.95 3.25
5785 6092 5.712152 AACAGAGATGAATGTTTCAACCC 57.288 39.130 0.00 0.00 43.95 4.11
5833 6148 2.956799 TTCATGTGCCACGCTGGTGT 62.957 55.000 6.02 0.00 42.80 4.16
5834 6149 2.203337 ATGTGCCACGCTGGTGTT 60.203 55.556 6.02 0.00 42.80 3.32
5835 6150 1.827789 ATGTGCCACGCTGGTGTTT 60.828 52.632 6.02 0.00 42.80 2.83
5837 6152 0.536233 TGTGCCACGCTGGTGTTTAT 60.536 50.000 6.02 0.00 42.80 1.40
5838 6153 0.109781 GTGCCACGCTGGTGTTTATG 60.110 55.000 6.02 0.00 42.80 1.90
5839 6154 0.250510 TGCCACGCTGGTGTTTATGA 60.251 50.000 6.02 0.00 42.80 2.15
5910 6243 8.752766 TTAGGTGAGATAACGTGTAAGAAAAG 57.247 34.615 0.00 0.00 0.00 2.27
5914 6247 8.553696 GGTGAGATAACGTGTAAGAAAAGAAAA 58.446 33.333 0.00 0.00 0.00 2.29
5940 6275 1.850377 TTTGCACGGCTTTTGATGTG 58.150 45.000 0.00 0.00 35.48 3.21
5968 6303 8.443953 AGCTCATGAATATAACCAAGTCTTTC 57.556 34.615 0.00 0.00 0.00 2.62
6099 6436 4.071961 TGTCTCAACTGTTGCTACACAT 57.928 40.909 15.52 0.00 0.00 3.21
6105 6442 6.015772 TCTCAACTGTTGCTACACATGTACTA 60.016 38.462 15.52 0.00 0.00 1.82
6106 6443 5.924254 TCAACTGTTGCTACACATGTACTAC 59.076 40.000 15.52 0.00 0.00 2.73
6107 6444 5.723672 ACTGTTGCTACACATGTACTACT 57.276 39.130 0.00 0.00 0.00 2.57
6108 6445 6.097915 ACTGTTGCTACACATGTACTACTT 57.902 37.500 0.00 0.00 0.00 2.24
6109 6446 7.223260 ACTGTTGCTACACATGTACTACTTA 57.777 36.000 0.00 0.00 0.00 2.24
6110 6447 7.663827 ACTGTTGCTACACATGTACTACTTAA 58.336 34.615 0.00 0.00 0.00 1.85
6111 6448 7.597743 ACTGTTGCTACACATGTACTACTTAAC 59.402 37.037 0.00 0.00 0.00 2.01
6112 6449 7.663827 TGTTGCTACACATGTACTACTTAACT 58.336 34.615 0.00 0.00 0.00 2.24
6113 6450 8.795513 TGTTGCTACACATGTACTACTTAACTA 58.204 33.333 0.00 0.00 0.00 2.24
6114 6451 9.798994 GTTGCTACACATGTACTACTTAACTAT 57.201 33.333 0.00 0.00 0.00 2.12
6115 6452 9.797556 TTGCTACACATGTACTACTTAACTATG 57.202 33.333 0.00 0.00 0.00 2.23
6116 6453 7.919091 TGCTACACATGTACTACTTAACTATGC 59.081 37.037 0.00 0.00 0.00 3.14
6117 6454 7.919091 GCTACACATGTACTACTTAACTATGCA 59.081 37.037 0.00 0.00 0.00 3.96
6118 6455 9.234384 CTACACATGTACTACTTAACTATGCAC 57.766 37.037 0.00 0.00 0.00 4.57
6119 6456 6.750501 ACACATGTACTACTTAACTATGCACG 59.249 38.462 0.00 0.00 0.00 5.34
6120 6457 6.970613 CACATGTACTACTTAACTATGCACGA 59.029 38.462 0.00 0.00 0.00 4.35
6121 6458 7.165977 CACATGTACTACTTAACTATGCACGAG 59.834 40.741 0.00 0.00 0.00 4.18
6122 6459 6.990341 TGTACTACTTAACTATGCACGAGA 57.010 37.500 4.49 0.00 0.00 4.04
6123 6460 7.012959 TGTACTACTTAACTATGCACGAGAG 57.987 40.000 4.49 0.00 0.00 3.20
6124 6461 4.922719 ACTACTTAACTATGCACGAGAGC 58.077 43.478 4.49 0.00 0.00 4.09
6133 6470 1.559831 TGCACGAGAGCAATACATCG 58.440 50.000 0.00 0.00 42.46 3.84
6136 6473 2.941453 ACGAGAGCAATACATCGTGT 57.059 45.000 0.00 0.00 45.83 4.49
6138 6475 4.365899 ACGAGAGCAATACATCGTGTAA 57.634 40.909 0.00 0.00 45.83 2.41
6139 6476 4.933330 ACGAGAGCAATACATCGTGTAAT 58.067 39.130 0.00 0.00 45.83 1.89
6140 6477 5.348986 ACGAGAGCAATACATCGTGTAATT 58.651 37.500 0.00 0.00 45.83 1.40
6141 6478 5.459107 ACGAGAGCAATACATCGTGTAATTC 59.541 40.000 0.00 0.54 45.83 2.17
6142 6479 5.458779 CGAGAGCAATACATCGTGTAATTCA 59.541 40.000 2.70 0.00 36.31 2.57
6143 6480 6.560433 CGAGAGCAATACATCGTGTAATTCAC 60.560 42.308 2.70 0.00 43.03 3.18
6144 6481 6.106003 AGAGCAATACATCGTGTAATTCACA 58.894 36.000 8.20 0.00 46.44 3.58
6145 6482 6.763135 AGAGCAATACATCGTGTAATTCACAT 59.237 34.615 8.20 0.83 46.44 3.21
6146 6483 7.926018 AGAGCAATACATCGTGTAATTCACATA 59.074 33.333 8.20 0.00 46.44 2.29
6147 6484 8.607441 AGCAATACATCGTGTAATTCACATAT 57.393 30.769 8.20 0.59 46.44 1.78
6148 6485 9.705290 AGCAATACATCGTGTAATTCACATATA 57.295 29.630 8.20 0.00 46.44 0.86
6157 6494 9.836076 TCGTGTAATTCACATATATAGCTACAC 57.164 33.333 0.00 0.00 46.44 2.90
6158 6495 9.620660 CGTGTAATTCACATATATAGCTACACA 57.379 33.333 0.00 0.00 46.44 3.72
6166 6503 9.515226 TCACATATATAGCTACACATGTACTCA 57.485 33.333 12.92 0.55 0.00 3.41
6173 6510 5.352284 AGCTACACATGTACTCAACTATGC 58.648 41.667 0.00 0.00 0.00 3.14
6174 6511 5.105351 AGCTACACATGTACTCAACTATGCA 60.105 40.000 0.00 0.00 0.00 3.96
6175 6512 5.005779 GCTACACATGTACTCAACTATGCAC 59.994 44.000 0.00 0.00 0.00 4.57
6176 6513 3.926527 ACACATGTACTCAACTATGCACG 59.073 43.478 0.00 0.00 0.00 5.34
6177 6514 4.173256 CACATGTACTCAACTATGCACGA 58.827 43.478 0.00 0.00 0.00 4.35
6178 6515 4.266265 CACATGTACTCAACTATGCACGAG 59.734 45.833 0.00 0.00 0.00 4.18
6179 6516 4.157840 ACATGTACTCAACTATGCACGAGA 59.842 41.667 0.00 0.00 0.00 4.04
6180 6517 4.357018 TGTACTCAACTATGCACGAGAG 57.643 45.455 4.49 7.28 0.00 3.20
6181 6518 2.285827 ACTCAACTATGCACGAGAGC 57.714 50.000 4.49 0.00 0.00 4.09
6190 6527 1.559831 TGCACGAGAGCAATACATCG 58.440 50.000 0.00 0.00 42.46 3.84
6193 6530 2.941453 ACGAGAGCAATACATCGTGT 57.059 45.000 0.00 0.00 45.83 4.49
6195 6532 4.365899 ACGAGAGCAATACATCGTGTAA 57.634 40.909 0.00 0.00 45.83 2.41
6196 6533 4.933330 ACGAGAGCAATACATCGTGTAAT 58.067 39.130 0.00 0.00 45.83 1.89
6197 6534 5.348986 ACGAGAGCAATACATCGTGTAATT 58.651 37.500 0.00 0.00 45.83 1.40
6198 6535 5.459107 ACGAGAGCAATACATCGTGTAATTC 59.541 40.000 0.00 0.54 45.83 2.17
6199 6536 5.458779 CGAGAGCAATACATCGTGTAATTCA 59.541 40.000 2.70 0.00 36.31 2.57
6200 6537 6.560433 CGAGAGCAATACATCGTGTAATTCAC 60.560 42.308 2.70 0.00 43.03 3.18
6201 6538 6.106003 AGAGCAATACATCGTGTAATTCACA 58.894 36.000 8.20 0.00 46.44 3.58
6202 6539 6.763135 AGAGCAATACATCGTGTAATTCACAT 59.237 34.615 8.20 0.83 46.44 3.21
6203 6540 7.926018 AGAGCAATACATCGTGTAATTCACATA 59.074 33.333 8.20 0.00 46.44 2.29
6204 6541 8.607441 AGCAATACATCGTGTAATTCACATAT 57.393 30.769 8.20 0.59 46.44 1.78
6205 6542 9.056005 AGCAATACATCGTGTAATTCACATATT 57.944 29.630 8.20 0.00 46.44 1.28
6206 6543 9.663904 GCAATACATCGTGTAATTCACATATTT 57.336 29.630 8.20 0.00 46.44 1.40
6214 6551 9.168451 TCGTGTAATTCACATATTTTACATGGT 57.832 29.630 11.73 0.00 46.44 3.55
6240 6577 8.965986 ATCAGTTTTTAGGTTTTAATTCTCGC 57.034 30.769 0.00 0.00 0.00 5.03
6241 6578 7.364970 TCAGTTTTTAGGTTTTAATTCTCGCC 58.635 34.615 0.00 0.00 0.00 5.54
6242 6579 7.229907 TCAGTTTTTAGGTTTTAATTCTCGCCT 59.770 33.333 0.00 0.00 0.00 5.52
6243 6580 7.865889 CAGTTTTTAGGTTTTAATTCTCGCCTT 59.134 33.333 0.00 0.00 0.00 4.35
6244 6581 8.080417 AGTTTTTAGGTTTTAATTCTCGCCTTC 58.920 33.333 0.00 0.00 0.00 3.46
6245 6582 7.754851 TTTTAGGTTTTAATTCTCGCCTTCT 57.245 32.000 0.00 0.00 0.00 2.85
6246 6583 6.737254 TTAGGTTTTAATTCTCGCCTTCTG 57.263 37.500 0.00 0.00 0.00 3.02
6247 6584 4.652822 AGGTTTTAATTCTCGCCTTCTGT 58.347 39.130 0.00 0.00 0.00 3.41
6248 6585 5.070685 AGGTTTTAATTCTCGCCTTCTGTT 58.929 37.500 0.00 0.00 0.00 3.16
6249 6586 5.048713 AGGTTTTAATTCTCGCCTTCTGTTG 60.049 40.000 0.00 0.00 0.00 3.33
6250 6587 4.419522 TTTAATTCTCGCCTTCTGTTGC 57.580 40.909 0.00 0.00 0.00 4.17
6251 6588 1.168714 AATTCTCGCCTTCTGTTGCC 58.831 50.000 0.00 0.00 0.00 4.52
6252 6589 1.021390 ATTCTCGCCTTCTGTTGCCG 61.021 55.000 0.00 0.00 0.00 5.69
6253 6590 3.793144 CTCGCCTTCTGTTGCCGC 61.793 66.667 0.00 0.00 0.00 6.53
6271 6608 3.499737 CGCCGCGCTTTTCCTCAT 61.500 61.111 5.56 0.00 0.00 2.90
6272 6609 2.100991 GCCGCGCTTTTCCTCATG 59.899 61.111 5.56 0.00 0.00 3.07
6273 6610 2.690778 GCCGCGCTTTTCCTCATGT 61.691 57.895 5.56 0.00 0.00 3.21
6274 6611 1.135315 CCGCGCTTTTCCTCATGTG 59.865 57.895 5.56 0.00 0.00 3.21
6275 6612 1.512734 CGCGCTTTTCCTCATGTGC 60.513 57.895 5.56 0.00 0.00 4.57
6276 6613 1.153958 GCGCTTTTCCTCATGTGCC 60.154 57.895 0.00 0.00 0.00 5.01
6277 6614 1.135315 CGCTTTTCCTCATGTGCCG 59.865 57.895 0.00 0.00 0.00 5.69
6278 6615 1.153958 GCTTTTCCTCATGTGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
6279 6616 1.508088 CTTTTCCTCATGTGCCGCC 59.492 57.895 0.00 0.00 0.00 6.13
6280 6617 2.257286 CTTTTCCTCATGTGCCGCCG 62.257 60.000 0.00 0.00 0.00 6.46
6298 6635 3.055719 CTGCCGCCCGTGTGATTT 61.056 61.111 0.00 0.00 0.00 2.17
6299 6636 3.039202 CTGCCGCCCGTGTGATTTC 62.039 63.158 0.00 0.00 0.00 2.17
6300 6637 3.810896 GCCGCCCGTGTGATTTCC 61.811 66.667 0.00 0.00 0.00 3.13
6301 6638 3.131478 CCGCCCGTGTGATTTCCC 61.131 66.667 0.00 0.00 0.00 3.97
6302 6639 3.496131 CGCCCGTGTGATTTCCCG 61.496 66.667 0.00 0.00 0.00 5.14
6303 6640 3.810896 GCCCGTGTGATTTCCCGC 61.811 66.667 0.00 0.00 0.00 6.13
6304 6641 3.496131 CCCGTGTGATTTCCCGCG 61.496 66.667 0.00 0.00 0.00 6.46
6305 6642 4.160635 CCGTGTGATTTCCCGCGC 62.161 66.667 0.00 0.00 33.49 6.86
6306 6643 4.160635 CGTGTGATTTCCCGCGCC 62.161 66.667 0.00 0.00 0.00 6.53
6307 6644 4.160635 GTGTGATTTCCCGCGCCG 62.161 66.667 0.00 0.00 0.00 6.46
6310 6647 4.708386 TGATTTCCCGCGCCGGTT 62.708 61.111 14.57 1.36 46.80 4.44
6311 6648 4.174129 GATTTCCCGCGCCGGTTG 62.174 66.667 14.57 0.00 46.80 3.77
6312 6649 4.708386 ATTTCCCGCGCCGGTTGA 62.708 61.111 14.57 4.22 46.80 3.18
6318 6655 4.796231 CGCGCCGGTTGAGCTACT 62.796 66.667 1.90 0.00 0.00 2.57
6319 6656 2.434359 GCGCCGGTTGAGCTACTT 60.434 61.111 1.90 0.00 0.00 2.24
6320 6657 2.453638 GCGCCGGTTGAGCTACTTC 61.454 63.158 1.90 0.00 0.00 3.01
6321 6658 1.215647 CGCCGGTTGAGCTACTTCT 59.784 57.895 1.90 0.00 0.00 2.85
6322 6659 0.802607 CGCCGGTTGAGCTACTTCTC 60.803 60.000 1.90 0.00 0.00 2.87
6323 6660 0.533032 GCCGGTTGAGCTACTTCTCT 59.467 55.000 1.90 0.00 34.29 3.10
6324 6661 1.737363 GCCGGTTGAGCTACTTCTCTG 60.737 57.143 1.90 0.00 34.29 3.35
6325 6662 1.634702 CGGTTGAGCTACTTCTCTGC 58.365 55.000 0.00 0.00 34.29 4.26
6326 6663 1.203523 CGGTTGAGCTACTTCTCTGCT 59.796 52.381 0.00 0.00 40.02 4.24
6327 6664 2.423892 CGGTTGAGCTACTTCTCTGCTA 59.576 50.000 0.00 0.00 37.16 3.49
6328 6665 3.488384 CGGTTGAGCTACTTCTCTGCTAG 60.488 52.174 0.00 0.00 37.16 3.42
6329 6666 3.443976 GTTGAGCTACTTCTCTGCTAGC 58.556 50.000 8.10 8.10 37.16 3.42
6330 6667 2.028130 TGAGCTACTTCTCTGCTAGCC 58.972 52.381 13.29 0.00 37.16 3.93
6331 6668 1.001815 GAGCTACTTCTCTGCTAGCCG 60.002 57.143 13.29 5.93 37.16 5.52
6332 6669 0.596341 GCTACTTCTCTGCTAGCCGC 60.596 60.000 13.29 0.00 39.77 6.53
6333 6670 0.031449 CTACTTCTCTGCTAGCCGCC 59.969 60.000 13.29 0.00 38.05 6.13
6334 6671 1.725557 TACTTCTCTGCTAGCCGCCG 61.726 60.000 13.29 0.62 38.05 6.46
6335 6672 4.514577 TTCTCTGCTAGCCGCCGC 62.515 66.667 13.29 0.00 38.05 6.53
6337 6674 4.940593 CTCTGCTAGCCGCCGCTC 62.941 72.222 13.29 0.00 43.95 5.03
6342 6679 4.271816 CTAGCCGCCGCTCGACAT 62.272 66.667 1.83 0.00 43.95 3.06
6343 6680 4.266070 TAGCCGCCGCTCGACATC 62.266 66.667 1.83 0.00 43.95 3.06
6345 6682 4.266070 GCCGCCGCTCGACATCTA 62.266 66.667 0.00 0.00 41.67 1.98
6346 6683 2.353607 CCGCCGCTCGACATCTAC 60.354 66.667 0.00 0.00 41.67 2.59
6347 6684 2.353607 CGCCGCTCGACATCTACC 60.354 66.667 0.00 0.00 41.67 3.18
6348 6685 2.027751 GCCGCTCGACATCTACCC 59.972 66.667 0.00 0.00 0.00 3.69
6349 6686 2.782222 GCCGCTCGACATCTACCCA 61.782 63.158 0.00 0.00 0.00 4.51
6350 6687 1.360551 CCGCTCGACATCTACCCAG 59.639 63.158 0.00 0.00 0.00 4.45
6351 6688 1.299468 CGCTCGACATCTACCCAGC 60.299 63.158 0.00 0.00 0.00 4.85
6352 6689 1.068250 GCTCGACATCTACCCAGCC 59.932 63.158 0.00 0.00 0.00 4.85
6353 6690 1.676678 GCTCGACATCTACCCAGCCA 61.677 60.000 0.00 0.00 0.00 4.75
6354 6691 0.387202 CTCGACATCTACCCAGCCAG 59.613 60.000 0.00 0.00 0.00 4.85
6355 6692 0.324368 TCGACATCTACCCAGCCAGT 60.324 55.000 0.00 0.00 0.00 4.00
6356 6693 0.179100 CGACATCTACCCAGCCAGTG 60.179 60.000 0.00 0.00 0.00 3.66
6357 6694 0.462759 GACATCTACCCAGCCAGTGC 60.463 60.000 0.00 0.00 37.95 4.40
6358 6695 1.522355 CATCTACCCAGCCAGTGCG 60.522 63.158 0.00 0.00 44.33 5.34
6359 6696 3.391665 ATCTACCCAGCCAGTGCGC 62.392 63.158 0.00 0.00 44.33 6.09
6360 6697 4.087892 CTACCCAGCCAGTGCGCT 62.088 66.667 9.73 0.00 44.33 5.92
6361 6698 4.082523 TACCCAGCCAGTGCGCTC 62.083 66.667 9.73 4.74 44.33 5.03
6368 6705 3.184683 CCAGTGCGCTCGCTTCTC 61.185 66.667 9.73 4.01 42.51 2.87
6369 6706 3.184683 CAGTGCGCTCGCTTCTCC 61.185 66.667 9.73 0.00 42.51 3.71
6370 6707 4.443266 AGTGCGCTCGCTTCTCCC 62.443 66.667 9.73 0.00 42.51 4.30
6373 6710 4.577246 GCGCTCGCTTCTCCCGAT 62.577 66.667 0.00 0.00 38.26 4.18
6374 6711 2.354072 CGCTCGCTTCTCCCGATC 60.354 66.667 0.00 0.00 33.83 3.69
6375 6712 2.354072 GCTCGCTTCTCCCGATCG 60.354 66.667 8.51 8.51 33.83 3.69
6376 6713 2.354072 CTCGCTTCTCCCGATCGC 60.354 66.667 10.32 0.00 33.83 4.58
6377 6714 2.829003 TCGCTTCTCCCGATCGCT 60.829 61.111 10.32 0.00 0.00 4.93
6378 6715 2.105128 CGCTTCTCCCGATCGCTT 59.895 61.111 10.32 0.00 0.00 4.68
6379 6716 1.946650 CGCTTCTCCCGATCGCTTC 60.947 63.158 10.32 0.00 0.00 3.86
6380 6717 1.592939 GCTTCTCCCGATCGCTTCC 60.593 63.158 10.32 0.00 0.00 3.46
6381 6718 1.068250 CTTCTCCCGATCGCTTCCC 59.932 63.158 10.32 0.00 0.00 3.97
6382 6719 2.685387 CTTCTCCCGATCGCTTCCCG 62.685 65.000 10.32 0.00 38.61 5.14
6383 6720 3.528370 CTCCCGATCGCTTCCCGT 61.528 66.667 10.32 0.00 38.35 5.28
6384 6721 3.774959 CTCCCGATCGCTTCCCGTG 62.775 68.421 10.32 0.00 38.35 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.223971 GGTATCTTCGGCTCGGATTTGA 60.224 50.000 0.00 0.00 0.00 2.69
412 419 6.314917 ACCTTCCCATTCAAAATAGACAGTT 58.685 36.000 0.00 0.00 0.00 3.16
445 452 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
446 453 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
447 454 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
448 455 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
449 456 7.039923 TGCTCTTATATTAGTTTACGGAGGGAG 60.040 40.741 0.00 0.00 0.00 4.30
450 457 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
451 458 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
452 459 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
484 491 8.900781 TGATAGCGTTTAGATCACTACTTTAGT 58.099 33.333 0.00 0.00 40.28 2.24
485 492 9.900710 ATGATAGCGTTTAGATCACTACTTTAG 57.099 33.333 0.00 0.00 32.62 1.85
500 507 9.477484 CCTCTGTAAACTAATATGATAGCGTTT 57.523 33.333 0.00 0.00 0.00 3.60
501 508 8.088981 CCCTCTGTAAACTAATATGATAGCGTT 58.911 37.037 0.00 0.00 0.00 4.84
502 509 7.450634 TCCCTCTGTAAACTAATATGATAGCGT 59.549 37.037 0.00 0.00 0.00 5.07
503 510 7.827701 TCCCTCTGTAAACTAATATGATAGCG 58.172 38.462 0.00 0.00 0.00 4.26
504 511 8.808092 ACTCCCTCTGTAAACTAATATGATAGC 58.192 37.037 0.00 0.00 0.00 2.97
507 514 9.656323 TGTACTCCCTCTGTAAACTAATATGAT 57.344 33.333 0.00 0.00 0.00 2.45
508 515 9.656323 ATGTACTCCCTCTGTAAACTAATATGA 57.344 33.333 0.00 0.00 0.00 2.15
509 516 9.698309 CATGTACTCCCTCTGTAAACTAATATG 57.302 37.037 0.00 0.00 0.00 1.78
510 517 9.656323 TCATGTACTCCCTCTGTAAACTAATAT 57.344 33.333 0.00 0.00 0.00 1.28
511 518 8.910944 GTCATGTACTCCCTCTGTAAACTAATA 58.089 37.037 0.00 0.00 0.00 0.98
512 519 7.399191 TGTCATGTACTCCCTCTGTAAACTAAT 59.601 37.037 0.00 0.00 0.00 1.73
513 520 6.722590 TGTCATGTACTCCCTCTGTAAACTAA 59.277 38.462 0.00 0.00 0.00 2.24
514 521 6.250711 TGTCATGTACTCCCTCTGTAAACTA 58.749 40.000 0.00 0.00 0.00 2.24
515 522 5.084519 TGTCATGTACTCCCTCTGTAAACT 58.915 41.667 0.00 0.00 0.00 2.66
516 523 5.047235 ACTGTCATGTACTCCCTCTGTAAAC 60.047 44.000 0.00 0.00 0.00 2.01
517 524 5.084519 ACTGTCATGTACTCCCTCTGTAAA 58.915 41.667 0.00 0.00 0.00 2.01
518 525 4.673968 ACTGTCATGTACTCCCTCTGTAA 58.326 43.478 0.00 0.00 0.00 2.41
519 526 4.317530 ACTGTCATGTACTCCCTCTGTA 57.682 45.455 0.00 0.00 0.00 2.74
520 527 3.176924 ACTGTCATGTACTCCCTCTGT 57.823 47.619 0.00 0.00 0.00 3.41
521 528 4.017126 TGTACTGTCATGTACTCCCTCTG 58.983 47.826 11.43 0.00 42.22 3.35
522 529 4.017808 GTGTACTGTCATGTACTCCCTCT 58.982 47.826 11.43 0.00 42.22 3.69
523 530 3.762288 TGTGTACTGTCATGTACTCCCTC 59.238 47.826 11.43 0.00 42.22 4.30
524 531 3.774734 TGTGTACTGTCATGTACTCCCT 58.225 45.455 11.43 0.00 42.22 4.20
525 532 4.530710 TTGTGTACTGTCATGTACTCCC 57.469 45.455 11.43 4.04 42.22 4.30
526 533 5.932303 ACAATTGTGTACTGTCATGTACTCC 59.068 40.000 11.07 5.65 42.22 3.85
527 534 7.421530 AACAATTGTGTACTGTCATGTACTC 57.578 36.000 12.82 9.30 42.22 2.59
557 564 1.079127 CTGGCTGGTTAGTGTCCCG 60.079 63.158 0.00 0.00 0.00 5.14
620 627 1.902508 GAGAATGCATATCGGGGAGGA 59.097 52.381 0.00 0.00 0.00 3.71
627 634 2.069273 GGAACCGGAGAATGCATATCG 58.931 52.381 9.46 1.74 0.00 2.92
649 656 4.148825 ATGCGTGTCGGGAGGAGC 62.149 66.667 0.00 0.00 0.00 4.70
949 957 6.245115 TGTCACATTAGAAAACTGCATCTG 57.755 37.500 0.00 0.00 0.00 2.90
1002 1010 2.094649 TGGAACCGAACCAAACACAAAC 60.095 45.455 0.00 0.00 34.25 2.93
1008 1016 3.316868 TCTTCAATGGAACCGAACCAAAC 59.683 43.478 0.00 0.00 40.93 2.93
1143 1151 4.464008 AGTCCTTCACTTCAAATTCAGCA 58.536 39.130 0.00 0.00 26.56 4.41
1229 1237 2.568956 TCCCAGACTTCTGTCCAGAATG 59.431 50.000 9.99 6.24 45.40 2.67
1296 1304 9.018582 CCAAGGATTTGTTAGAAGAGAAGAAAT 57.981 33.333 0.00 0.00 33.75 2.17
1308 1316 5.943416 TCCATGTGTACCAAGGATTTGTTAG 59.057 40.000 4.74 0.00 36.04 2.34
1827 1837 9.494271 GTCTCCAATGCATAAGTTGATATAAGA 57.506 33.333 0.00 0.00 0.00 2.10
1881 1891 4.982241 GGGACCATGGAGAGATTTATGA 57.018 45.455 21.47 0.00 0.00 2.15
1920 1930 7.012138 CCAAATGTCTGAGATAAGTCATTCCTG 59.988 40.741 0.00 0.00 35.69 3.86
2067 2079 1.075374 AGCAACAGGGCCATTTAGACA 59.925 47.619 6.18 0.00 0.00 3.41
2218 2230 1.532868 GTCAAACAGCAAGTCATCGCT 59.467 47.619 0.00 0.00 39.66 4.93
2303 2315 5.243730 AGACATTTCACACGGAATTTGGAAT 59.756 36.000 0.00 0.00 34.91 3.01
2478 2490 3.747529 TGTACACATCAGCACATCACAAG 59.252 43.478 0.00 0.00 0.00 3.16
2479 2491 3.737850 TGTACACATCAGCACATCACAA 58.262 40.909 0.00 0.00 0.00 3.33
2502 2514 6.320494 TGTTACGGATTTATGCACAACTTT 57.680 33.333 0.00 0.00 0.00 2.66
2619 2632 4.734398 AATGTCAAACAAGACTTGGCAA 57.266 36.364 19.16 0.00 41.41 4.52
2818 2832 1.927487 AGGGCTGACAATGAAATGCA 58.073 45.000 0.00 0.00 0.00 3.96
2974 2988 1.273327 CCTGAAAAACATCCACCCTGC 59.727 52.381 0.00 0.00 0.00 4.85
3264 3296 7.201875 GGAGTGAAGTTCCAATTAACTTTTCCA 60.202 37.037 17.47 7.96 46.92 3.53
3466 3498 5.895636 TGCCACGATTTAGAATGTCAAAT 57.104 34.783 0.00 0.00 0.00 2.32
3610 3642 1.490490 GGCATATCCCAGTTGTCCTCA 59.510 52.381 0.00 0.00 0.00 3.86
3624 3656 3.385755 GGCATTCAACTGAAAGGGCATAT 59.614 43.478 12.93 0.00 39.30 1.78
3831 3863 0.108585 ACTGAACACAGGAATGCCGT 59.891 50.000 0.00 0.00 39.96 5.68
3954 4145 8.909923 CCGAAACAATAAACTATATTCCCCTTT 58.090 33.333 0.00 0.00 0.00 3.11
4115 4306 2.102252 CAGGATCTTCCCTTTCTCTCCG 59.898 54.545 0.00 0.00 37.19 4.63
4246 4449 1.750206 CATCGCCAATTCCCAATGACA 59.250 47.619 0.00 0.00 0.00 3.58
4437 4640 1.138266 ACTAACTGGTCGTGCACACTT 59.862 47.619 18.64 7.46 0.00 3.16
4466 4669 0.607489 CCTCAACTTCAGGTGGCTGG 60.607 60.000 0.00 0.00 0.00 4.85
4541 4744 3.521937 TCCCATACCCTTTAGGAGTGTTG 59.478 47.826 0.00 0.00 39.89 3.33
4542 4745 3.522343 GTCCCATACCCTTTAGGAGTGTT 59.478 47.826 0.00 0.00 39.89 3.32
4675 4878 8.089625 TGTATCTCTCACAAAAGAATATGGGA 57.910 34.615 0.00 0.00 0.00 4.37
4738 4941 1.873591 CAACCTCCTTTGTCGAACCAG 59.126 52.381 0.00 0.00 0.00 4.00
4766 4969 7.123355 AGTTCCATTTTCAACCAATTCTTCA 57.877 32.000 0.00 0.00 0.00 3.02
4894 5097 5.846164 TCCAAGGCTCCAGATTGAGAATATA 59.154 40.000 0.00 0.00 34.11 0.86
5107 5310 8.071177 AGCATATTTCAAGGCAAAAGATTACT 57.929 30.769 0.00 0.00 0.00 2.24
5111 5314 7.014038 CCTCTAGCATATTTCAAGGCAAAAGAT 59.986 37.037 0.00 0.00 0.00 2.40
5114 5317 5.951747 ACCTCTAGCATATTTCAAGGCAAAA 59.048 36.000 0.00 0.00 0.00 2.44
5117 5321 4.164030 TGACCTCTAGCATATTTCAAGGCA 59.836 41.667 0.00 0.00 0.00 4.75
5196 5488 7.010091 CCATTGAACAAAAACAAACCTAGTGTC 59.990 37.037 0.00 0.00 0.00 3.67
5230 5522 5.357596 TGCAGTGAAGATAAATAAGCATGCA 59.642 36.000 21.98 0.00 36.52 3.96
5428 5727 8.793592 ACATCAACTGGGTTAACTATTCTTTTC 58.206 33.333 5.42 0.00 0.00 2.29
5436 5735 5.931294 TGTGAACATCAACTGGGTTAACTA 58.069 37.500 5.42 0.00 29.10 2.24
5444 5743 6.072008 TGGTCATATTTGTGAACATCAACTGG 60.072 38.462 0.00 0.00 40.70 4.00
5566 5866 6.354794 ACAACTGTATAGTTAGTCCTTGCA 57.645 37.500 4.38 0.00 45.12 4.08
5664 5964 6.437162 TGGTAGCAGAAAGGCTCATAATTTTT 59.563 34.615 0.00 0.00 44.54 1.94
5759 6066 7.756722 GGGTTGAAACATTCATCTCTGTTTATG 59.243 37.037 1.05 0.00 43.61 1.90
5801 6116 3.119245 GGCACATGAATGTCATTTCAGCT 60.119 43.478 0.00 0.00 39.39 4.24
5845 6174 2.249139 GACTGAGTCCTAACCACACCT 58.751 52.381 0.00 0.00 0.00 4.00
5910 6243 3.123050 AGCCGTGCAAAAGAACATTTTC 58.877 40.909 0.00 0.00 0.00 2.29
5914 6247 2.865551 CAAAAGCCGTGCAAAAGAACAT 59.134 40.909 0.00 0.00 0.00 2.71
5916 6249 2.535331 TCAAAAGCCGTGCAAAAGAAC 58.465 42.857 0.00 0.00 0.00 3.01
5918 6251 2.100584 ACATCAAAAGCCGTGCAAAAGA 59.899 40.909 0.00 0.00 0.00 2.52
5919 6252 2.219216 CACATCAAAAGCCGTGCAAAAG 59.781 45.455 0.00 0.00 0.00 2.27
5940 6275 8.443953 AGACTTGGTTATATTCATGAGCTTTC 57.556 34.615 0.00 0.00 0.00 2.62
5958 6293 1.593196 TCAGCCAACGAAAGACTTGG 58.407 50.000 0.00 0.00 40.11 3.61
5968 6303 4.159377 TCTTGCTAAATTTCAGCCAACG 57.841 40.909 13.55 0.00 38.29 4.10
6042 6379 3.610911 TCGAGCTCACTCTGTCTTGATA 58.389 45.455 15.40 0.00 41.09 2.15
6069 6406 5.698545 AGCAACAGTTGAGACATAGAGTTTC 59.301 40.000 17.99 0.00 32.22 2.78
6077 6414 4.071961 TGTGTAGCAACAGTTGAGACAT 57.928 40.909 17.99 0.00 35.91 3.06
6099 6436 6.457934 GCTCTCGTGCATAGTTAAGTAGTACA 60.458 42.308 2.52 0.00 0.00 2.90
6105 6442 3.868757 TGCTCTCGTGCATAGTTAAGT 57.131 42.857 0.00 0.00 38.12 2.24
6106 6443 5.748630 TGTATTGCTCTCGTGCATAGTTAAG 59.251 40.000 0.00 0.00 42.96 1.85
6107 6444 5.656480 TGTATTGCTCTCGTGCATAGTTAA 58.344 37.500 0.00 0.00 42.96 2.01
6108 6445 5.257082 TGTATTGCTCTCGTGCATAGTTA 57.743 39.130 0.00 0.00 42.96 2.24
6109 6446 4.123497 TGTATTGCTCTCGTGCATAGTT 57.877 40.909 0.00 0.00 42.96 2.24
6110 6447 3.801114 TGTATTGCTCTCGTGCATAGT 57.199 42.857 0.00 0.00 42.96 2.12
6111 6448 3.363128 CGATGTATTGCTCTCGTGCATAG 59.637 47.826 0.00 0.00 42.96 2.23
6112 6449 3.243401 ACGATGTATTGCTCTCGTGCATA 60.243 43.478 0.00 0.00 42.26 3.14
6113 6450 2.130395 CGATGTATTGCTCTCGTGCAT 58.870 47.619 0.00 0.00 42.96 3.96
6114 6451 1.135112 ACGATGTATTGCTCTCGTGCA 60.135 47.619 0.00 0.00 42.26 4.57
6115 6452 1.560923 ACGATGTATTGCTCTCGTGC 58.439 50.000 0.00 0.00 42.26 5.34
6117 6454 2.941453 ACACGATGTATTGCTCTCGT 57.059 45.000 0.00 0.00 44.48 4.18
6118 6455 5.458779 TGAATTACACGATGTATTGCTCTCG 59.541 40.000 0.00 0.00 32.20 4.04
6119 6456 6.641062 GTGAATTACACGATGTATTGCTCTC 58.359 40.000 0.00 0.00 39.78 3.20
6120 6457 6.589830 GTGAATTACACGATGTATTGCTCT 57.410 37.500 0.00 0.00 39.78 4.09
6140 6477 9.515226 TGAGTACATGTGTAGCTATATATGTGA 57.485 33.333 30.21 17.68 31.84 3.58
6147 6484 8.297426 GCATAGTTGAGTACATGTGTAGCTATA 58.703 37.037 9.11 0.00 0.00 1.31
6148 6485 7.148641 GCATAGTTGAGTACATGTGTAGCTAT 58.851 38.462 9.11 6.36 0.00 2.97
6149 6486 6.096282 TGCATAGTTGAGTACATGTGTAGCTA 59.904 38.462 9.11 4.35 0.00 3.32
6150 6487 5.105351 TGCATAGTTGAGTACATGTGTAGCT 60.105 40.000 9.11 1.09 0.00 3.32
6151 6488 5.005779 GTGCATAGTTGAGTACATGTGTAGC 59.994 44.000 9.11 0.00 0.00 3.58
6152 6489 5.230097 CGTGCATAGTTGAGTACATGTGTAG 59.770 44.000 9.11 0.00 0.00 2.74
6153 6490 5.099575 CGTGCATAGTTGAGTACATGTGTA 58.900 41.667 9.11 0.00 0.00 2.90
6154 6491 3.926527 CGTGCATAGTTGAGTACATGTGT 59.073 43.478 9.11 0.00 0.00 3.72
6155 6492 4.173256 TCGTGCATAGTTGAGTACATGTG 58.827 43.478 9.11 0.00 0.00 3.21
6156 6493 4.157840 TCTCGTGCATAGTTGAGTACATGT 59.842 41.667 2.69 2.69 0.00 3.21
6157 6494 4.672409 TCTCGTGCATAGTTGAGTACATG 58.328 43.478 0.00 0.00 0.00 3.21
6158 6495 4.734989 GCTCTCGTGCATAGTTGAGTACAT 60.735 45.833 0.00 0.00 0.00 2.29
6159 6496 3.427638 GCTCTCGTGCATAGTTGAGTACA 60.428 47.826 0.00 0.00 0.00 2.90
6160 6497 3.109619 GCTCTCGTGCATAGTTGAGTAC 58.890 50.000 0.00 0.00 0.00 2.73
6161 6498 2.752903 TGCTCTCGTGCATAGTTGAGTA 59.247 45.455 0.00 0.00 38.12 2.59
6162 6499 1.546029 TGCTCTCGTGCATAGTTGAGT 59.454 47.619 0.00 0.00 38.12 3.41
6163 6500 2.284263 TGCTCTCGTGCATAGTTGAG 57.716 50.000 0.00 2.10 38.12 3.02
6164 6501 2.741759 TTGCTCTCGTGCATAGTTGA 57.258 45.000 0.00 0.00 42.96 3.18
6165 6502 3.865164 TGTATTGCTCTCGTGCATAGTTG 59.135 43.478 0.00 0.00 42.96 3.16
6166 6503 4.123497 TGTATTGCTCTCGTGCATAGTT 57.877 40.909 0.00 0.00 42.96 2.24
6167 6504 3.801114 TGTATTGCTCTCGTGCATAGT 57.199 42.857 0.00 0.00 42.96 2.12
6168 6505 3.363128 CGATGTATTGCTCTCGTGCATAG 59.637 47.826 0.00 0.00 42.96 2.23
6169 6506 3.243401 ACGATGTATTGCTCTCGTGCATA 60.243 43.478 0.00 0.00 42.26 3.14
6170 6507 2.130395 CGATGTATTGCTCTCGTGCAT 58.870 47.619 0.00 0.00 42.96 3.96
6171 6508 1.135112 ACGATGTATTGCTCTCGTGCA 60.135 47.619 0.00 0.00 42.26 4.57
6172 6509 1.560923 ACGATGTATTGCTCTCGTGC 58.439 50.000 0.00 0.00 42.26 5.34
6174 6511 2.941453 ACACGATGTATTGCTCTCGT 57.059 45.000 0.00 0.00 44.48 4.18
6175 6512 5.458779 TGAATTACACGATGTATTGCTCTCG 59.541 40.000 0.00 0.00 32.20 4.04
6176 6513 6.641062 GTGAATTACACGATGTATTGCTCTC 58.359 40.000 0.00 0.00 39.78 3.20
6177 6514 6.589830 GTGAATTACACGATGTATTGCTCT 57.410 37.500 0.00 0.00 39.78 4.09
6215 6552 8.027189 GGCGAGAATTAAAACCTAAAAACTGAT 58.973 33.333 0.00 0.00 0.00 2.90
6216 6553 7.229907 AGGCGAGAATTAAAACCTAAAAACTGA 59.770 33.333 0.00 0.00 0.00 3.41
6217 6554 7.368059 AGGCGAGAATTAAAACCTAAAAACTG 58.632 34.615 0.00 0.00 0.00 3.16
6218 6555 7.520451 AGGCGAGAATTAAAACCTAAAAACT 57.480 32.000 0.00 0.00 0.00 2.66
6219 6556 8.080417 AGAAGGCGAGAATTAAAACCTAAAAAC 58.920 33.333 0.00 0.00 0.00 2.43
6220 6557 8.079809 CAGAAGGCGAGAATTAAAACCTAAAAA 58.920 33.333 0.00 0.00 0.00 1.94
6221 6558 7.229907 ACAGAAGGCGAGAATTAAAACCTAAAA 59.770 33.333 0.00 0.00 0.00 1.52
6222 6559 6.713450 ACAGAAGGCGAGAATTAAAACCTAAA 59.287 34.615 0.00 0.00 0.00 1.85
6223 6560 6.235664 ACAGAAGGCGAGAATTAAAACCTAA 58.764 36.000 0.00 0.00 0.00 2.69
6224 6561 5.801380 ACAGAAGGCGAGAATTAAAACCTA 58.199 37.500 0.00 0.00 0.00 3.08
6225 6562 4.652822 ACAGAAGGCGAGAATTAAAACCT 58.347 39.130 0.00 0.00 0.00 3.50
6226 6563 5.154222 CAACAGAAGGCGAGAATTAAAACC 58.846 41.667 0.00 0.00 0.00 3.27
6227 6564 4.617223 GCAACAGAAGGCGAGAATTAAAAC 59.383 41.667 0.00 0.00 0.00 2.43
6228 6565 4.320935 GGCAACAGAAGGCGAGAATTAAAA 60.321 41.667 0.00 0.00 0.00 1.52
6229 6566 3.190535 GGCAACAGAAGGCGAGAATTAAA 59.809 43.478 0.00 0.00 0.00 1.52
6230 6567 2.747446 GGCAACAGAAGGCGAGAATTAA 59.253 45.455 0.00 0.00 0.00 1.40
6231 6568 2.356135 GGCAACAGAAGGCGAGAATTA 58.644 47.619 0.00 0.00 0.00 1.40
6232 6569 1.168714 GGCAACAGAAGGCGAGAATT 58.831 50.000 0.00 0.00 0.00 2.17
6233 6570 2.859992 GGCAACAGAAGGCGAGAAT 58.140 52.632 0.00 0.00 0.00 2.40
6234 6571 4.379174 GGCAACAGAAGGCGAGAA 57.621 55.556 0.00 0.00 0.00 2.87
6254 6591 3.499737 ATGAGGAAAAGCGCGGCG 61.500 61.111 19.62 19.62 0.00 6.46
6255 6592 2.100991 CATGAGGAAAAGCGCGGC 59.899 61.111 8.83 0.00 0.00 6.53
6256 6593 1.135315 CACATGAGGAAAAGCGCGG 59.865 57.895 8.83 0.00 0.00 6.46
6257 6594 1.512734 GCACATGAGGAAAAGCGCG 60.513 57.895 0.00 0.00 0.00 6.86
6258 6595 1.153958 GGCACATGAGGAAAAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
6259 6596 1.135315 CGGCACATGAGGAAAAGCG 59.865 57.895 0.00 0.00 0.00 4.68
6260 6597 1.153958 GCGGCACATGAGGAAAAGC 60.154 57.895 0.00 0.00 0.00 3.51
6261 6598 1.508088 GGCGGCACATGAGGAAAAG 59.492 57.895 3.07 0.00 0.00 2.27
6262 6599 2.331893 CGGCGGCACATGAGGAAAA 61.332 57.895 10.53 0.00 0.00 2.29
6263 6600 2.745884 CGGCGGCACATGAGGAAA 60.746 61.111 10.53 0.00 0.00 3.13
6281 6618 3.039202 GAAATCACACGGGCGGCAG 62.039 63.158 12.47 10.04 0.00 4.85
6282 6619 3.053291 GAAATCACACGGGCGGCA 61.053 61.111 12.47 0.00 0.00 5.69
6283 6620 3.810896 GGAAATCACACGGGCGGC 61.811 66.667 0.00 0.00 0.00 6.53
6284 6621 3.131478 GGGAAATCACACGGGCGG 61.131 66.667 0.00 0.00 0.00 6.13
6285 6622 3.496131 CGGGAAATCACACGGGCG 61.496 66.667 0.00 0.00 32.69 6.13
6286 6623 3.810896 GCGGGAAATCACACGGGC 61.811 66.667 0.00 0.00 37.15 6.13
6287 6624 3.496131 CGCGGGAAATCACACGGG 61.496 66.667 0.00 0.00 42.40 5.28
6288 6625 4.160635 GCGCGGGAAATCACACGG 62.161 66.667 8.83 0.00 37.15 4.94
6289 6626 4.160635 GGCGCGGGAAATCACACG 62.161 66.667 8.83 0.00 39.86 4.49
6290 6627 4.160635 CGGCGCGGGAAATCACAC 62.161 66.667 8.83 0.00 0.00 3.82
6301 6638 4.796231 AGTAGCTCAACCGGCGCG 62.796 66.667 0.00 0.00 34.52 6.86
6302 6639 2.434359 AAGTAGCTCAACCGGCGC 60.434 61.111 0.00 0.00 34.52 6.53
6303 6640 0.802607 GAGAAGTAGCTCAACCGGCG 60.803 60.000 0.00 0.00 35.01 6.46
6304 6641 0.533032 AGAGAAGTAGCTCAACCGGC 59.467 55.000 0.00 0.00 37.37 6.13
6305 6642 1.737363 GCAGAGAAGTAGCTCAACCGG 60.737 57.143 0.00 0.00 37.37 5.28
6306 6643 1.203523 AGCAGAGAAGTAGCTCAACCG 59.796 52.381 0.00 0.00 37.37 4.44
6307 6644 3.736740 GCTAGCAGAGAAGTAGCTCAACC 60.737 52.174 10.63 0.00 39.68 3.77
6308 6645 3.443976 GCTAGCAGAGAAGTAGCTCAAC 58.556 50.000 10.63 0.00 39.68 3.18
6309 6646 2.428890 GGCTAGCAGAGAAGTAGCTCAA 59.571 50.000 18.24 0.00 39.36 3.02
6310 6647 2.028130 GGCTAGCAGAGAAGTAGCTCA 58.972 52.381 18.24 0.00 39.36 4.26
6311 6648 1.001815 CGGCTAGCAGAGAAGTAGCTC 60.002 57.143 18.24 0.00 39.36 4.09
6312 6649 1.028905 CGGCTAGCAGAGAAGTAGCT 58.971 55.000 18.24 0.00 39.36 3.32
6313 6650 3.560826 CGGCTAGCAGAGAAGTAGC 57.439 57.895 18.24 0.00 38.79 3.58
6328 6665 4.266070 TAGATGTCGAGCGGCGGC 62.266 66.667 9.78 8.43 46.88 6.53
6329 6666 2.353607 GTAGATGTCGAGCGGCGG 60.354 66.667 9.78 0.00 41.33 6.13
6330 6667 2.353607 GGTAGATGTCGAGCGGCG 60.354 66.667 0.51 0.51 42.69 6.46
6331 6668 2.027751 GGGTAGATGTCGAGCGGC 59.972 66.667 0.00 0.00 0.00 6.53
6332 6669 1.360551 CTGGGTAGATGTCGAGCGG 59.639 63.158 0.00 0.00 0.00 5.52
6333 6670 1.299468 GCTGGGTAGATGTCGAGCG 60.299 63.158 0.00 0.00 0.00 5.03
6334 6671 1.068250 GGCTGGGTAGATGTCGAGC 59.932 63.158 0.00 0.00 34.65 5.03
6335 6672 0.387202 CTGGCTGGGTAGATGTCGAG 59.613 60.000 0.00 0.00 0.00 4.04
6336 6673 0.324368 ACTGGCTGGGTAGATGTCGA 60.324 55.000 0.00 0.00 0.00 4.20
6337 6674 0.179100 CACTGGCTGGGTAGATGTCG 60.179 60.000 0.00 0.00 0.00 4.35
6338 6675 0.462759 GCACTGGCTGGGTAGATGTC 60.463 60.000 0.00 0.00 36.96 3.06
6339 6676 1.604378 GCACTGGCTGGGTAGATGT 59.396 57.895 0.00 0.00 36.96 3.06
6340 6677 1.522355 CGCACTGGCTGGGTAGATG 60.522 63.158 0.00 0.00 38.10 2.90
6341 6678 2.903357 CGCACTGGCTGGGTAGAT 59.097 61.111 0.00 0.00 38.10 1.98
6342 6679 4.082523 GCGCACTGGCTGGGTAGA 62.083 66.667 0.30 0.00 38.10 2.59
6343 6680 4.087892 AGCGCACTGGCTGGGTAG 62.088 66.667 11.47 0.00 42.86 3.18
6344 6681 4.082523 GAGCGCACTGGCTGGGTA 62.083 66.667 11.47 0.00 44.93 3.69
6351 6688 3.184683 GAGAAGCGAGCGCACTGG 61.185 66.667 17.68 0.00 44.88 4.00
6352 6689 3.184683 GGAGAAGCGAGCGCACTG 61.185 66.667 17.68 0.00 44.88 3.66
6353 6690 4.443266 GGGAGAAGCGAGCGCACT 62.443 66.667 17.68 14.79 44.88 4.40
6356 6693 4.577246 ATCGGGAGAAGCGAGCGC 62.577 66.667 6.78 6.78 45.37 5.92
6357 6694 2.354072 GATCGGGAGAAGCGAGCG 60.354 66.667 0.00 0.00 45.37 5.03
6358 6695 2.354072 CGATCGGGAGAAGCGAGC 60.354 66.667 7.38 0.00 45.37 5.03
6359 6696 2.343163 AAGCGATCGGGAGAAGCGAG 62.343 60.000 18.30 0.00 46.49 5.03
6360 6697 2.337749 GAAGCGATCGGGAGAAGCGA 62.338 60.000 18.30 0.00 46.49 4.93
6361 6698 1.946650 GAAGCGATCGGGAGAAGCG 60.947 63.158 18.30 0.00 46.49 4.68
6362 6699 1.592939 GGAAGCGATCGGGAGAAGC 60.593 63.158 18.30 0.00 45.37 3.86
6363 6700 1.068250 GGGAAGCGATCGGGAGAAG 59.932 63.158 18.30 0.00 45.37 2.85
6364 6701 2.782222 CGGGAAGCGATCGGGAGAA 61.782 63.158 18.30 0.00 45.37 2.87
6365 6702 3.217017 CGGGAAGCGATCGGGAGA 61.217 66.667 18.30 0.00 46.90 3.71
6366 6703 3.528370 ACGGGAAGCGATCGGGAG 61.528 66.667 18.30 0.00 0.00 4.30
6367 6704 3.833645 CACGGGAAGCGATCGGGA 61.834 66.667 18.30 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.