Multiple sequence alignment - TraesCS3D01G129500

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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 TraesCS3D01G129500 chr3D 100.000 6003 0 0 1 6003 89540498 89546500 0.000000e+00 11086.0
1 TraesCS3D01G129500 chr3D 87.850 214 11 6 5715 5913 89627441 89627654 2.800000e-58 237.0
2 TraesCS3D01G129500 chr3D 95.205 146 7 0 5768 5913 89638086 89638231 1.300000e-56 231.0
3 TraesCS3D01G129500 chr3A 95.355 5275 197 25 53 5295 106302666 106307924 0.000000e+00 8340.0
4 TraesCS3D01G129500 chr3A 96.396 333 9 1 5584 5913 106308770 106309102 4.090000e-151 545.0
5 TraesCS3D01G129500 chr3A 90.050 201 13 5 5378 5575 106308478 106308674 2.780000e-63 254.0
6 TraesCS3D01G129500 chr3A 93.151 146 10 0 5768 5913 106397206 106397351 1.310000e-51 215.0
7 TraesCS3D01G129500 chr3A 92.793 111 7 1 5893 6003 512874545 512874436 6.230000e-35 159.0
8 TraesCS3D01G129500 chr3A 91.304 69 2 4 2 67 106285316 106285383 2.300000e-14 91.6
9 TraesCS3D01G129500 chr3B 94.154 4499 184 33 1 4437 139031410 139035891 0.000000e+00 6778.0
10 TraesCS3D01G129500 chr3B 94.945 455 8 6 4831 5285 139036490 139036929 0.000000e+00 699.0
11 TraesCS3D01G129500 chr3B 95.185 270 13 0 4476 4745 139035888 139036157 1.550000e-115 427.0
12 TraesCS3D01G129500 chr3B 91.958 286 11 5 5631 5913 139037645 139037921 2.030000e-104 390.0
13 TraesCS3D01G129500 chr3B 91.573 178 10 2 5413 5589 139037459 139037632 2.160000e-59 241.0
14 TraesCS3D01G129500 chr3B 93.151 146 10 0 5768 5913 139195445 139195590 1.310000e-51 215.0
15 TraesCS3D01G129500 chr7D 98.936 94 1 0 5910 6003 320286022 320285929 1.030000e-37 169.0
16 TraesCS3D01G129500 chr5D 98.936 94 1 0 5910 6003 265671376 265671283 1.030000e-37 169.0
17 TraesCS3D01G129500 chr5D 98.936 94 1 0 5910 6003 342525685 342525778 1.030000e-37 169.0
18 TraesCS3D01G129500 chr4D 98.936 94 1 0 5910 6003 69396040 69396133 1.030000e-37 169.0
19 TraesCS3D01G129500 chr4D 97.959 98 1 1 5906 6003 481841714 481841810 1.030000e-37 169.0
20 TraesCS3D01G129500 chr4B 97.938 97 2 0 5907 6003 12866768 12866864 1.030000e-37 169.0
21 TraesCS3D01G129500 chr1D 96.970 99 3 0 5905 6003 92207204 92207106 3.720000e-37 167.0
22 TraesCS3D01G129500 chr6D 96.040 101 4 0 5903 6003 97586896 97586796 1.340000e-36 165.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G129500 chr3D 89540498 89546500 6002 False 11086.000000 11086 100.000000 1 6003 1 chr3D.!!$F1 6002
1 TraesCS3D01G129500 chr3A 106302666 106309102 6436 False 3046.333333 8340 93.933667 53 5913 3 chr3A.!!$F3 5860
2 TraesCS3D01G129500 chr3B 139031410 139037921 6511 False 1707.000000 6778 93.563000 1 5913 5 chr3B.!!$F2 5912

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
304 310 0.815615 GGCCTCCACGGATGTCATTC 60.816 60.000 0.00 0.0 33.16 2.67 F
1119 1174 1.593265 GAACCCCACCGTCGTATGT 59.407 57.895 0.00 0.0 0.00 2.29 F
1272 1330 0.327000 ACATGGAGGAGAAGGGGGAG 60.327 60.000 0.00 0.0 0.00 4.30 F
1710 1771 0.393537 CAGGAGGCTGATCCCACAAC 60.394 60.000 0.00 0.0 40.53 3.32 F
2077 2140 3.873952 GTCTGTGAATCCTGTTATCCTGC 59.126 47.826 0.00 0.0 0.00 4.85 F
3859 3931 1.264749 GGGCCATCCTGAAAAACCCC 61.265 60.000 4.39 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1258 1.056660 AGAAACCTCGCTTCTTCCCA 58.943 50.000 0.00 0.0 28.46 4.37 R
3014 3085 1.865595 TGGGGGCCCTGAAATGATATT 59.134 47.619 24.38 0.0 36.94 1.28 R
3342 3414 8.950210 TCTTCTCAGTATTTTGTGATTCCATTC 58.050 33.333 0.00 0.0 0.00 2.67 R
3859 3931 4.150627 CAGTTTACCTGAGTGTTGTCATCG 59.849 45.833 0.00 0.0 44.49 3.84 R
4066 4138 9.762381 AGAATATACAAGGAACATTAACCCAAA 57.238 29.630 0.00 0.0 0.00 3.28 R
5972 7093 0.036765 AAGGTCAGCCGCGTGAAATA 60.037 50.000 4.92 0.0 40.50 1.40 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
100 103 6.719370 TCCAATCTTTAGCACAAATACACCTT 59.281 34.615 0.00 0.00 0.00 3.50
229 235 2.948979 CTGTAGAGGTGTGTGCCAAAAA 59.051 45.455 0.00 0.00 0.00 1.94
254 260 4.942761 AATGAGTGCTCCAAAATGTGTT 57.057 36.364 0.00 0.00 0.00 3.32
255 261 3.988379 TGAGTGCTCCAAAATGTGTTC 57.012 42.857 0.00 0.00 0.00 3.18
274 280 5.007626 GTGTTCTTTTGAGCCCCAATTTTTC 59.992 40.000 0.00 0.00 34.23 2.29
276 282 5.213891 TCTTTTGAGCCCCAATTTTTCTC 57.786 39.130 0.00 0.00 34.23 2.87
304 310 0.815615 GGCCTCCACGGATGTCATTC 60.816 60.000 0.00 0.00 33.16 2.67
309 315 3.181455 CCTCCACGGATGTCATTCCAATA 60.181 47.826 0.00 0.00 35.34 1.90
404 411 2.489938 TGTGGGTGTATTTGAGCTCC 57.510 50.000 12.15 0.00 0.00 4.70
499 506 5.416271 ACTACGGTTAGGAATGAACACAT 57.584 39.130 0.00 0.00 0.00 3.21
535 551 3.561143 ACCAACTGCTAAACATCCACAA 58.439 40.909 0.00 0.00 0.00 3.33
539 555 2.224426 ACTGCTAAACATCCACAACCGA 60.224 45.455 0.00 0.00 0.00 4.69
542 558 2.550606 GCTAAACATCCACAACCGAACA 59.449 45.455 0.00 0.00 0.00 3.18
612 628 7.060633 GCAGTGATATTTACAAAGAAACAACGG 59.939 37.037 0.00 0.00 0.00 4.44
614 630 6.858993 GTGATATTTACAAAGAAACAACGGCA 59.141 34.615 0.00 0.00 0.00 5.69
619 635 4.320608 ACAAAGAAACAACGGCAATCAT 57.679 36.364 0.00 0.00 0.00 2.45
683 699 3.559238 CCAGTTGTAAATCTGGTGCAC 57.441 47.619 8.80 8.80 44.19 4.57
709 725 9.411999 CCATGCTGGTTGAAATTCCTCAAGAAT 62.412 40.741 0.00 0.00 38.69 2.40
855 873 5.461078 ACACAAAATCTCTACGTACACACAC 59.539 40.000 0.00 0.00 0.00 3.82
1119 1174 1.593265 GAACCCCACCGTCGTATGT 59.407 57.895 0.00 0.00 0.00 2.29
1152 1207 1.930204 CCTCCCCTCCATTTACCCTTT 59.070 52.381 0.00 0.00 0.00 3.11
1200 1258 5.549742 ACTATCTAGTCGTGGCTAGTAGT 57.450 43.478 8.26 11.34 39.44 2.73
1218 1276 1.157585 GTGGGAAGAAGCGAGGTTTC 58.842 55.000 0.00 0.00 0.00 2.78
1234 1292 2.215196 GTTTCTGTTTGCCTCACGGTA 58.785 47.619 0.00 0.00 0.00 4.02
1272 1330 0.327000 ACATGGAGGAGAAGGGGGAG 60.327 60.000 0.00 0.00 0.00 4.30
1275 1333 1.383386 GGAGGAGAAGGGGGAGGAC 60.383 68.421 0.00 0.00 0.00 3.85
1331 1389 9.352163 CTGTTCGTTTTAAAATTTGAAATTCCG 57.648 29.630 3.32 5.51 0.00 4.30
1347 1405 0.818445 TCCGCTCGATCTAGTGGGTC 60.818 60.000 22.72 0.00 45.52 4.46
1366 1424 4.018688 GGGTCTAGGGGTTTGTCAGTTTAT 60.019 45.833 0.00 0.00 0.00 1.40
1395 1453 8.659925 ATTCTGCTTGTAAATCTGTATCTCAG 57.340 34.615 0.00 0.00 44.85 3.35
1410 1468 1.170442 CTCAGTTGCCATGTCATGCA 58.830 50.000 7.35 6.58 35.27 3.96
1537 1596 1.005394 GGTTTCGCGGAGAACCAGA 60.005 57.895 24.85 0.00 38.83 3.86
1546 1605 2.492484 GCGGAGAACCAGAGACTTCTAA 59.508 50.000 0.00 0.00 35.59 2.10
1558 1617 9.457436 ACCAGAGACTTCTAAACAAAGTTTTTA 57.543 29.630 0.03 0.00 37.10 1.52
1657 1718 5.678583 AGCTTTGTGTATAGATGCACTGAT 58.321 37.500 11.31 0.00 42.76 2.90
1660 1721 6.925718 GCTTTGTGTATAGATGCACTGATAGA 59.074 38.462 11.31 0.00 42.76 1.98
1686 1747 7.069331 AGTGAAAAATGTGGTCTACAATCCAAA 59.931 33.333 0.00 0.00 43.77 3.28
1690 1751 1.467342 GTGGTCTACAATCCAAACCGC 59.533 52.381 0.00 0.00 35.38 5.68
1710 1771 0.393537 CAGGAGGCTGATCCCACAAC 60.394 60.000 0.00 0.00 40.53 3.32
1827 1888 5.016831 TGATGCCTCTGTCAGTTACTTAGA 58.983 41.667 0.00 0.00 0.00 2.10
1848 1909 8.683550 TTAGAGTACATGAACTTATGTTGTCG 57.316 34.615 0.00 0.00 41.31 4.35
1958 2019 9.802039 TTTATGACCCTAATTTGACTACTTTGT 57.198 29.630 0.00 0.00 0.00 2.83
1969 2030 7.639113 TTTGACTACTTTGTCTTGTTCCAAT 57.361 32.000 0.00 0.00 37.79 3.16
2049 2110 6.070596 TGACATCCAGTGTGATGATCTTAACT 60.071 38.462 21.37 3.82 43.94 2.24
2050 2111 6.715280 ACATCCAGTGTGATGATCTTAACTT 58.285 36.000 21.37 1.30 43.94 2.66
2051 2112 6.820656 ACATCCAGTGTGATGATCTTAACTTC 59.179 38.462 21.37 0.00 43.94 3.01
2052 2113 6.358974 TCCAGTGTGATGATCTTAACTTCA 57.641 37.500 0.00 0.00 0.00 3.02
2053 2114 6.401394 TCCAGTGTGATGATCTTAACTTCAG 58.599 40.000 0.00 0.00 0.00 3.02
2077 2140 3.873952 GTCTGTGAATCCTGTTATCCTGC 59.126 47.826 0.00 0.00 0.00 4.85
2162 2225 4.685169 ATTCAGTTATTTCAGTGTGCGG 57.315 40.909 0.00 0.00 0.00 5.69
2307 2372 5.674525 TCAGAGCTATTCAGGTAATGGTTG 58.325 41.667 0.00 0.00 30.99 3.77
2414 2479 8.140628 ACTGTGTAGATTATCTTCTAGCATGTG 58.859 37.037 0.00 0.00 0.00 3.21
2657 2724 9.176460 TCATCTGTAATGTTCTCATATTTTGCA 57.824 29.630 0.00 0.00 33.49 4.08
2927 2998 8.845413 ATTAACCATAACGTAAACCACTGTTA 57.155 30.769 0.00 0.00 33.30 2.41
3342 3414 4.746115 TGCAATTTGCTAGCTTGTTTTGAG 59.254 37.500 21.19 0.00 45.31 3.02
3859 3931 1.264749 GGGCCATCCTGAAAAACCCC 61.265 60.000 4.39 0.00 0.00 4.95
3901 3973 4.874970 ACTGTCATCACAATTTTGCTTCC 58.125 39.130 0.00 0.00 29.82 3.46
3947 4019 6.689554 TGATGCATATGCTTTTTGTTGAGAA 58.310 32.000 27.13 3.67 42.66 2.87
3948 4020 6.809689 TGATGCATATGCTTTTTGTTGAGAAG 59.190 34.615 27.13 0.00 42.66 2.85
3949 4021 6.088016 TGCATATGCTTTTTGTTGAGAAGT 57.912 33.333 27.13 0.00 42.66 3.01
4006 4078 3.071602 ACACTATGCCCTAATCAGCGATT 59.928 43.478 8.46 8.46 36.20 3.34
4066 4138 9.725019 TTCACAAACAACATCAGTATTCTATCT 57.275 29.630 0.00 0.00 0.00 1.98
4286 4363 6.095860 ACTGCTAAGCATGATATCTTTGCAAA 59.904 34.615 23.97 12.14 45.19 3.68
4340 4417 3.249189 TGACTGGAGGGGTGGTGC 61.249 66.667 0.00 0.00 0.00 5.01
4500 4577 5.488341 TGGTAGCTTGTTTGTTATCTCTCC 58.512 41.667 0.00 0.00 0.00 3.71
4574 4651 5.834460 TGTAACTGGATTACTAGGAGACCA 58.166 41.667 0.00 0.00 43.26 4.02
4683 4760 1.279840 GGCGAGGTAATGCGAATGC 59.720 57.895 0.00 0.00 43.20 3.56
4689 4766 4.151689 GCGAGGTAATGCGAATGCTATTTA 59.848 41.667 0.00 0.00 43.34 1.40
4745 4822 6.432162 ACAATCTTACAGTTCGGTAGTACTCA 59.568 38.462 0.00 0.00 0.00 3.41
4761 4960 3.463048 ACTCAAATTGGAGGAAGGCAT 57.537 42.857 14.48 0.00 39.27 4.40
4923 5248 1.468914 CCCTTTTAGCCGCTTCTTCAC 59.531 52.381 0.00 0.00 0.00 3.18
4951 5276 3.624326 TGATTTCTTTTGCAGGTCACG 57.376 42.857 0.00 0.00 0.00 4.35
5135 5460 3.261643 ACTCAGAACAGTATGGTGCATCA 59.738 43.478 0.00 0.00 33.00 3.07
5285 5840 6.961359 TGAATGAGGTAACAGTTTGATACG 57.039 37.500 0.00 0.00 41.41 3.06
5288 5843 5.717078 TGAGGTAACAGTTTGATACGAGT 57.283 39.130 0.00 0.00 41.41 4.18
5289 5844 6.822667 TGAGGTAACAGTTTGATACGAGTA 57.177 37.500 0.00 0.00 41.41 2.59
5290 5845 6.615088 TGAGGTAACAGTTTGATACGAGTAC 58.385 40.000 0.00 0.00 41.41 2.73
5292 5847 6.985117 AGGTAACAGTTTGATACGAGTACAA 58.015 36.000 0.00 0.00 41.41 2.41
5293 5848 7.088905 AGGTAACAGTTTGATACGAGTACAAG 58.911 38.462 0.00 0.00 41.41 3.16
5294 5849 5.840940 AACAGTTTGATACGAGTACAAGC 57.159 39.130 0.00 0.00 0.00 4.01
5295 5850 4.243270 ACAGTTTGATACGAGTACAAGCC 58.757 43.478 0.00 0.00 0.00 4.35
5296 5851 4.242475 CAGTTTGATACGAGTACAAGCCA 58.758 43.478 0.00 0.00 0.00 4.75
5315 6315 4.036852 AGCCAAGTTTACTGAAGAAGTTGC 59.963 41.667 0.00 0.00 40.56 4.17
5316 6316 4.527564 CCAAGTTTACTGAAGAAGTTGCG 58.472 43.478 0.00 0.00 40.56 4.85
5326 6326 5.239525 ACTGAAGAAGTTGCGCTTTTTAGAT 59.760 36.000 9.73 0.00 34.57 1.98
5329 6329 7.464358 TGAAGAAGTTGCGCTTTTTAGATATC 58.536 34.615 9.73 0.00 37.59 1.63
5350 6350 5.223449 TCGATTTGGACCTAAGAAACAGT 57.777 39.130 0.00 0.00 0.00 3.55
5351 6351 4.994852 TCGATTTGGACCTAAGAAACAGTG 59.005 41.667 0.00 0.00 0.00 3.66
5361 6361 2.922740 AGAAACAGTGGGCGACTTTA 57.077 45.000 0.00 0.00 29.75 1.85
5381 6381 8.293699 ACTTTAGATTAGCAAAACCATTAGGG 57.706 34.615 0.00 0.00 44.81 3.53
5387 6417 4.600692 AGCAAAACCATTAGGGAAACAC 57.399 40.909 0.00 0.00 41.15 3.32
5396 6426 4.202172 CCATTAGGGAAACACAACGGTTTT 60.202 41.667 0.00 0.00 40.85 2.43
5401 6431 2.737252 GGAAACACAACGGTTTTGCAAA 59.263 40.909 8.05 8.05 40.85 3.68
5446 6476 4.278170 TCACGGATTGTTTTGCAGAAGAAT 59.722 37.500 11.56 11.56 0.00 2.40
5447 6477 4.618489 CACGGATTGTTTTGCAGAAGAATC 59.382 41.667 23.85 23.85 38.11 2.52
5470 6501 4.331992 CGAGATTCAATCAGCAATGTCACT 59.668 41.667 0.00 0.00 0.00 3.41
5501 6532 6.591935 TCACAATACCCTCCATTACTGATTC 58.408 40.000 0.00 0.00 0.00 2.52
5504 6535 7.000472 ACAATACCCTCCATTACTGATTCATG 59.000 38.462 0.00 0.00 0.00 3.07
5540 6571 2.490328 ATGCAATGAAATTACGGCCG 57.510 45.000 26.86 26.86 32.46 6.13
5541 6572 0.453793 TGCAATGAAATTACGGCCGG 59.546 50.000 31.76 11.88 32.46 6.13
5542 6573 0.869880 GCAATGAAATTACGGCCGGC 60.870 55.000 31.76 21.18 32.46 6.13
5577 6608 8.767085 CAATTTTGAACATGACAAGCAAACTAT 58.233 29.630 0.00 0.00 0.00 2.12
5616 6734 6.891908 ACCCTTGCTGAAACAATATTAGACAT 59.108 34.615 0.00 0.00 0.00 3.06
5909 7030 1.202510 CGGAGAGCTGAGGAAATGGAG 60.203 57.143 0.00 0.00 0.00 3.86
5913 7034 0.700564 AGCTGAGGAAATGGAGGCAA 59.299 50.000 0.00 0.00 0.00 4.52
5914 7035 1.076024 AGCTGAGGAAATGGAGGCAAA 59.924 47.619 0.00 0.00 0.00 3.68
5915 7036 1.895131 GCTGAGGAAATGGAGGCAAAA 59.105 47.619 0.00 0.00 0.00 2.44
5916 7037 2.498885 GCTGAGGAAATGGAGGCAAAAT 59.501 45.455 0.00 0.00 0.00 1.82
5917 7038 3.055602 GCTGAGGAAATGGAGGCAAAATT 60.056 43.478 0.00 0.00 0.00 1.82
5918 7039 4.501071 CTGAGGAAATGGAGGCAAAATTG 58.499 43.478 0.00 0.00 0.00 2.32
5919 7040 4.158786 TGAGGAAATGGAGGCAAAATTGA 58.841 39.130 0.00 0.00 0.00 2.57
5920 7041 4.021192 TGAGGAAATGGAGGCAAAATTGAC 60.021 41.667 0.00 0.00 36.08 3.18
5921 7042 3.903090 AGGAAATGGAGGCAAAATTGACA 59.097 39.130 1.22 0.00 39.18 3.58
5922 7043 4.347583 AGGAAATGGAGGCAAAATTGACAA 59.652 37.500 1.22 0.00 39.18 3.18
5923 7044 5.062528 GGAAATGGAGGCAAAATTGACAAA 58.937 37.500 1.22 0.00 39.18 2.83
5924 7045 5.706833 GGAAATGGAGGCAAAATTGACAAAT 59.293 36.000 1.22 0.00 39.18 2.32
5925 7046 6.207221 GGAAATGGAGGCAAAATTGACAAATT 59.793 34.615 1.22 0.00 39.18 1.82
5926 7047 7.255555 GGAAATGGAGGCAAAATTGACAAATTT 60.256 33.333 1.22 4.41 45.81 1.82
5927 7048 6.563222 ATGGAGGCAAAATTGACAAATTTG 57.437 33.333 19.89 19.89 43.63 2.32
5928 7049 5.678583 TGGAGGCAAAATTGACAAATTTGA 58.321 33.333 25.81 7.64 43.63 2.69
5929 7050 6.297582 TGGAGGCAAAATTGACAAATTTGAT 58.702 32.000 25.81 16.03 43.63 2.57
5930 7051 6.427547 TGGAGGCAAAATTGACAAATTTGATC 59.572 34.615 25.81 21.20 43.63 2.92
5931 7052 6.652062 GGAGGCAAAATTGACAAATTTGATCT 59.348 34.615 25.81 21.14 43.63 2.75
5932 7053 7.818930 GGAGGCAAAATTGACAAATTTGATCTA 59.181 33.333 25.81 14.22 43.63 1.98
5933 7054 9.374838 GAGGCAAAATTGACAAATTTGATCTAT 57.625 29.630 25.81 15.60 43.63 1.98
5934 7055 9.158233 AGGCAAAATTGACAAATTTGATCTATG 57.842 29.630 25.81 13.77 43.63 2.23
5935 7056 8.392612 GGCAAAATTGACAAATTTGATCTATGG 58.607 33.333 25.81 12.90 43.63 2.74
5936 7057 9.153721 GCAAAATTGACAAATTTGATCTATGGA 57.846 29.630 25.81 2.42 43.63 3.41
5938 7059 8.915871 AAATTGACAAATTTGATCTATGGACG 57.084 30.769 24.64 0.00 42.97 4.79
5939 7060 7.864108 ATTGACAAATTTGATCTATGGACGA 57.136 32.000 24.64 4.88 0.00 4.20
5940 7061 7.680442 TTGACAAATTTGATCTATGGACGAA 57.320 32.000 24.64 4.18 0.00 3.85
5941 7062 7.680442 TGACAAATTTGATCTATGGACGAAA 57.320 32.000 24.64 0.00 0.00 3.46
5942 7063 8.279970 TGACAAATTTGATCTATGGACGAAAT 57.720 30.769 24.64 0.00 0.00 2.17
5943 7064 8.397906 TGACAAATTTGATCTATGGACGAAATC 58.602 33.333 24.64 6.30 0.00 2.17
5944 7065 8.279970 ACAAATTTGATCTATGGACGAAATCA 57.720 30.769 24.64 0.00 0.00 2.57
5945 7066 8.739039 ACAAATTTGATCTATGGACGAAATCAA 58.261 29.630 24.64 0.00 35.24 2.57
5946 7067 9.571810 CAAATTTGATCTATGGACGAAATCAAA 57.428 29.630 13.08 10.24 45.28 2.69
5949 7070 8.504812 TTTGATCTATGGACGAAATCAAATCA 57.495 30.769 5.07 0.00 39.89 2.57
5950 7071 7.482654 TGATCTATGGACGAAATCAAATCAC 57.517 36.000 0.00 0.00 0.00 3.06
5951 7072 7.047271 TGATCTATGGACGAAATCAAATCACA 58.953 34.615 0.00 0.00 0.00 3.58
5952 7073 6.908870 TCTATGGACGAAATCAAATCACAG 57.091 37.500 0.00 0.00 0.00 3.66
5953 7074 6.639563 TCTATGGACGAAATCAAATCACAGA 58.360 36.000 0.00 0.00 0.00 3.41
5954 7075 7.102993 TCTATGGACGAAATCAAATCACAGAA 58.897 34.615 0.00 0.00 0.00 3.02
5955 7076 6.764308 ATGGACGAAATCAAATCACAGAAT 57.236 33.333 0.00 0.00 0.00 2.40
5956 7077 5.941733 TGGACGAAATCAAATCACAGAATG 58.058 37.500 0.00 0.00 46.00 2.67
5957 7078 5.704978 TGGACGAAATCAAATCACAGAATGA 59.295 36.000 0.00 0.00 43.13 2.57
5958 7079 6.206438 TGGACGAAATCAAATCACAGAATGAA 59.794 34.615 0.00 0.00 41.93 2.57
5959 7080 6.524586 GGACGAAATCAAATCACAGAATGAAC 59.475 38.462 0.00 0.00 41.93 3.18
5960 7081 7.206981 ACGAAATCAAATCACAGAATGAACT 57.793 32.000 0.00 0.00 41.93 3.01
5961 7082 7.080099 ACGAAATCAAATCACAGAATGAACTG 58.920 34.615 0.00 0.00 41.93 3.16
5962 7083 6.033196 CGAAATCAAATCACAGAATGAACTGC 59.967 38.462 0.00 0.00 41.93 4.40
5963 7084 4.771590 TCAAATCACAGAATGAACTGCC 57.228 40.909 0.00 0.00 41.93 4.85
5964 7085 3.507233 TCAAATCACAGAATGAACTGCCC 59.493 43.478 0.00 0.00 41.93 5.36
5965 7086 1.742761 ATCACAGAATGAACTGCCCG 58.257 50.000 0.00 0.00 41.93 6.13
5966 7087 0.396435 TCACAGAATGAACTGCCCGT 59.604 50.000 0.00 0.00 39.69 5.28
5967 7088 0.518636 CACAGAATGAACTGCCCGTG 59.481 55.000 0.00 0.00 39.69 4.94
5968 7089 0.396435 ACAGAATGAACTGCCCGTGA 59.604 50.000 0.00 0.00 39.69 4.35
5969 7090 1.202758 ACAGAATGAACTGCCCGTGAA 60.203 47.619 0.00 0.00 39.69 3.18
5970 7091 1.879380 CAGAATGAACTGCCCGTGAAA 59.121 47.619 0.00 0.00 39.69 2.69
5971 7092 1.880027 AGAATGAACTGCCCGTGAAAC 59.120 47.619 0.00 0.00 0.00 2.78
5972 7093 1.880027 GAATGAACTGCCCGTGAAACT 59.120 47.619 0.00 0.00 31.75 2.66
5973 7094 2.851263 ATGAACTGCCCGTGAAACTA 57.149 45.000 0.00 0.00 31.75 2.24
5974 7095 2.851263 TGAACTGCCCGTGAAACTAT 57.149 45.000 0.00 0.00 31.75 2.12
5975 7096 3.134574 TGAACTGCCCGTGAAACTATT 57.865 42.857 0.00 0.00 31.75 1.73
5976 7097 3.482436 TGAACTGCCCGTGAAACTATTT 58.518 40.909 0.00 0.00 31.75 1.40
5977 7098 3.500680 TGAACTGCCCGTGAAACTATTTC 59.499 43.478 0.00 0.00 40.08 2.17
5978 7099 3.134574 ACTGCCCGTGAAACTATTTCA 57.865 42.857 0.00 0.00 46.68 2.69
5985 7106 1.803334 TGAAACTATTTCACGCGGCT 58.197 45.000 12.47 0.00 44.21 5.52
5986 7107 1.463056 TGAAACTATTTCACGCGGCTG 59.537 47.619 12.47 0.00 44.21 4.85
5987 7108 1.730064 GAAACTATTTCACGCGGCTGA 59.270 47.619 12.47 2.44 39.45 4.26
5988 7109 1.076332 AACTATTTCACGCGGCTGAC 58.924 50.000 12.47 0.00 0.00 3.51
5989 7110 0.739813 ACTATTTCACGCGGCTGACC 60.740 55.000 12.47 0.00 0.00 4.02
5990 7111 0.460284 CTATTTCACGCGGCTGACCT 60.460 55.000 12.47 0.00 0.00 3.85
5991 7112 0.036765 TATTTCACGCGGCTGACCTT 60.037 50.000 12.47 0.00 0.00 3.50
5992 7113 0.889186 ATTTCACGCGGCTGACCTTT 60.889 50.000 12.47 0.00 0.00 3.11
5993 7114 1.098712 TTTCACGCGGCTGACCTTTT 61.099 50.000 12.47 0.00 0.00 2.27
5994 7115 1.098712 TTCACGCGGCTGACCTTTTT 61.099 50.000 12.47 0.00 0.00 1.94
5995 7116 1.370414 CACGCGGCTGACCTTTTTG 60.370 57.895 12.47 0.00 0.00 2.44
5996 7117 1.822186 ACGCGGCTGACCTTTTTGT 60.822 52.632 12.47 0.00 0.00 2.83
5997 7118 1.370414 CGCGGCTGACCTTTTTGTG 60.370 57.895 0.00 0.00 0.00 3.33
5998 7119 1.733526 GCGGCTGACCTTTTTGTGT 59.266 52.632 0.00 0.00 0.00 3.72
5999 7120 0.594796 GCGGCTGACCTTTTTGTGTG 60.595 55.000 0.00 0.00 0.00 3.82
6000 7121 1.021202 CGGCTGACCTTTTTGTGTGA 58.979 50.000 0.00 0.00 0.00 3.58
6001 7122 1.268539 CGGCTGACCTTTTTGTGTGAC 60.269 52.381 0.00 0.00 0.00 3.67
6002 7123 1.268539 GGCTGACCTTTTTGTGTGACG 60.269 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 34 8.514594 TGAGTGAATTGCTTTAGGTTATCTTTG 58.485 33.333 0.00 0.00 0.00 2.77
84 87 4.941263 GTCCATGAAGGTGTATTTGTGCTA 59.059 41.667 0.00 0.00 39.02 3.49
100 103 8.690203 TTCTTTTCAGAATTTACTGTCCATGA 57.310 30.769 0.00 0.00 38.79 3.07
229 235 5.069516 ACACATTTTGGAGCACTCATTTCTT 59.930 36.000 0.00 0.00 0.00 2.52
230 236 4.586001 ACACATTTTGGAGCACTCATTTCT 59.414 37.500 0.00 0.00 0.00 2.52
231 237 4.874970 ACACATTTTGGAGCACTCATTTC 58.125 39.130 0.00 0.00 0.00 2.17
254 260 4.901250 AGAGAAAAATTGGGGCTCAAAAGA 59.099 37.500 2.76 0.00 39.05 2.52
255 261 5.219343 AGAGAAAAATTGGGGCTCAAAAG 57.781 39.130 2.76 0.00 39.05 2.27
274 280 2.076863 CGTGGAGGCCTGTAAAAAGAG 58.923 52.381 12.00 0.00 0.00 2.85
276 282 1.165270 CCGTGGAGGCCTGTAAAAAG 58.835 55.000 12.00 0.00 0.00 2.27
304 310 9.398170 CGAACATCCTGCTAATTTTTATATTGG 57.602 33.333 0.00 0.00 0.00 3.16
309 315 7.624360 TGTCGAACATCCTGCTAATTTTTAT 57.376 32.000 0.00 0.00 0.00 1.40
318 324 3.149196 ACAAATTGTCGAACATCCTGCT 58.851 40.909 0.00 0.00 0.00 4.24
369 375 5.241506 ACACCCACATGAACAGTAAATTCTG 59.758 40.000 0.00 0.00 40.80 3.02
387 394 1.271856 TCGGAGCTCAAATACACCCA 58.728 50.000 17.19 0.00 0.00 4.51
404 411 2.213499 GGACATGGATAACCTGCTTCG 58.787 52.381 0.00 0.00 37.04 3.79
412 419 3.871594 CGTCTTTGAGGGACATGGATAAC 59.128 47.826 0.00 0.00 33.73 1.89
453 460 1.583495 CGTGACTGACGGCCTACTCA 61.583 60.000 0.00 0.00 44.85 3.41
472 479 6.035758 GTGTTCATTCCTAACCGTAGTTCATC 59.964 42.308 0.00 0.00 37.42 2.92
499 506 5.304101 AGCAGTTGGTTATGGTGAAATTTCA 59.696 36.000 16.91 16.91 34.20 2.69
535 551 1.485032 GCGTCACTTCGTTGTTCGGT 61.485 55.000 0.00 0.00 40.32 4.69
539 555 2.241880 CCCGCGTCACTTCGTTGTT 61.242 57.895 4.92 0.00 0.00 2.83
542 558 2.355481 GTCCCGCGTCACTTCGTT 60.355 61.111 4.92 0.00 0.00 3.85
567 583 2.095969 TGCAAGGCGATCGTTTTAACTG 60.096 45.455 17.81 6.11 0.00 3.16
568 584 2.147958 TGCAAGGCGATCGTTTTAACT 58.852 42.857 17.81 3.13 0.00 2.24
570 586 2.095969 CACTGCAAGGCGATCGTTTTAA 60.096 45.455 17.81 3.20 39.30 1.52
612 628 6.033341 TGCACGAGGTATTAAAAATGATTGC 58.967 36.000 0.00 0.00 0.00 3.56
644 660 2.900546 TGGTTGTGGAGTTTTGTGGTTT 59.099 40.909 0.00 0.00 0.00 3.27
645 661 2.495669 CTGGTTGTGGAGTTTTGTGGTT 59.504 45.455 0.00 0.00 0.00 3.67
715 731 6.542370 GCCTAGATTATGCACTGGTTTTTCTA 59.458 38.462 0.00 0.00 0.00 2.10
716 732 5.358160 GCCTAGATTATGCACTGGTTTTTCT 59.642 40.000 0.00 0.00 0.00 2.52
717 733 5.450550 GGCCTAGATTATGCACTGGTTTTTC 60.451 44.000 0.00 0.00 0.00 2.29
719 735 3.954258 GGCCTAGATTATGCACTGGTTTT 59.046 43.478 0.00 0.00 0.00 2.43
777 794 5.839517 TGTGGAATGGAAAAATGGGAAAT 57.160 34.783 0.00 0.00 0.00 2.17
855 873 0.532862 GTGGTGACTGGTGACCTGTG 60.533 60.000 19.21 3.66 37.75 3.66
1084 1139 1.159285 TTCGACGAGGCGTAGAAGAA 58.841 50.000 10.59 4.22 43.81 2.52
1174 1229 8.250332 ACTACTAGCCACGACTAGATAGTATAC 58.750 40.741 15.40 0.00 41.92 1.47
1200 1258 1.056660 AGAAACCTCGCTTCTTCCCA 58.943 50.000 0.00 0.00 28.46 4.37
1234 1292 2.764314 GCGCCTGCAATCATTCGGT 61.764 57.895 0.00 0.00 42.15 4.69
1275 1333 4.705519 CCAACTTTGGCAGCGGCG 62.706 66.667 0.51 0.51 42.21 6.46
1347 1405 4.331968 TGCATAAACTGACAAACCCCTAG 58.668 43.478 0.00 0.00 0.00 3.02
1537 1596 9.457436 TGACCTAAAAACTTTGTTTAGAAGTCT 57.543 29.630 5.67 0.00 39.79 3.24
1546 1605 4.953579 TGCTCCTGACCTAAAAACTTTGTT 59.046 37.500 0.00 0.00 0.00 2.83
1558 1617 2.114616 CTCTACCAATGCTCCTGACCT 58.885 52.381 0.00 0.00 0.00 3.85
1620 1679 4.737054 CACAAAGCTCTTGTGTTTTGTCT 58.263 39.130 22.81 0.00 43.40 3.41
1657 1718 7.606456 GGATTGTAGACCACATTTTTCACTCTA 59.394 37.037 0.00 0.00 36.90 2.43
1660 1721 6.068010 TGGATTGTAGACCACATTTTTCACT 58.932 36.000 0.00 0.00 36.90 3.41
1664 1725 6.521162 GGTTTGGATTGTAGACCACATTTTT 58.479 36.000 0.00 0.00 36.90 1.94
1690 1751 1.565390 TTGTGGGATCAGCCTCCTGG 61.565 60.000 0.00 0.00 39.61 4.45
1710 1771 5.151389 GCGTTTAGGGTTTAATCTTGTGTG 58.849 41.667 0.00 0.00 0.00 3.82
1827 1888 6.032956 TCCGACAACATAAGTTCATGTACT 57.967 37.500 0.00 0.00 38.19 2.73
1848 1909 4.502604 CCAAAATCCAGCATTCCATCATCC 60.503 45.833 0.00 0.00 0.00 3.51
2049 2110 4.963318 AACAGGATTCACAGACTCTGAA 57.037 40.909 13.25 0.00 35.18 3.02
2050 2111 5.127845 GGATAACAGGATTCACAGACTCTGA 59.872 44.000 13.25 0.00 35.18 3.27
2051 2112 5.128499 AGGATAACAGGATTCACAGACTCTG 59.872 44.000 4.36 4.36 37.52 3.35
2052 2113 5.128499 CAGGATAACAGGATTCACAGACTCT 59.872 44.000 0.00 0.00 0.00 3.24
2053 2114 5.355596 CAGGATAACAGGATTCACAGACTC 58.644 45.833 0.00 0.00 0.00 3.36
2077 2140 5.333875 GCAACCTAAAACTAGAGTTTGGACG 60.334 44.000 15.03 8.50 46.47 4.79
2162 2225 4.600012 AAGCACAACTGATACGTATTGC 57.400 40.909 16.30 16.30 0.00 3.56
2307 2372 4.927425 TCATCACAAAAGTAGAACTACGGC 59.073 41.667 6.37 0.00 40.80 5.68
2355 2420 4.643334 TCTGCCTATACTGTCACGTAACAT 59.357 41.667 0.00 0.00 0.00 2.71
2414 2479 9.878599 GTATAAGCATTGTATTGGAACATACAC 57.121 33.333 0.00 0.00 39.30 2.90
2657 2724 6.183360 GCCAGGTAAAATCACTTGCATAAGAT 60.183 38.462 0.00 0.00 37.36 2.40
3011 3082 3.716353 GGGGGCCCTGAAATGATATTTTT 59.284 43.478 24.38 0.00 0.00 1.94
3014 3085 1.865595 TGGGGGCCCTGAAATGATATT 59.134 47.619 24.38 0.00 36.94 1.28
3342 3414 8.950210 TCTTCTCAGTATTTTGTGATTCCATTC 58.050 33.333 0.00 0.00 0.00 2.67
3859 3931 4.150627 CAGTTTACCTGAGTGTTGTCATCG 59.849 45.833 0.00 0.00 44.49 3.84
4066 4138 9.762381 AGAATATACAAGGAACATTAACCCAAA 57.238 29.630 0.00 0.00 0.00 3.28
4340 4417 4.758674 CCATGTCCTTTGATATGTAGCCAG 59.241 45.833 0.00 0.00 38.15 4.85
4547 4624 8.921205 GGTCTCCTAGTAATCCAGTTACAATAA 58.079 37.037 1.38 0.00 44.18 1.40
4556 4633 6.889198 TGAAAATGGTCTCCTAGTAATCCAG 58.111 40.000 0.00 0.00 0.00 3.86
4564 4641 4.122776 CCACGATGAAAATGGTCTCCTAG 58.877 47.826 0.00 0.00 0.00 3.02
4574 4651 7.928706 TGACCAAATAAAAACCACGATGAAAAT 59.071 29.630 0.00 0.00 0.00 1.82
4689 4766 8.109705 TGCAATCAAATGTACTGTTAATGACT 57.890 30.769 0.00 0.00 0.00 3.41
4731 4808 4.868734 CCTCCAATTTGAGTACTACCGAAC 59.131 45.833 0.00 0.00 0.00 3.95
4745 4822 4.017130 AGTCCTAATGCCTTCCTCCAATTT 60.017 41.667 0.00 0.00 0.00 1.82
4900 5224 0.253327 AGAAGCGGCTAAAAGGGGAG 59.747 55.000 1.35 0.00 0.00 4.30
4923 5248 5.993441 ACCTGCAAAAGAAATCAAATTGGAG 59.007 36.000 0.00 0.00 38.63 3.86
4951 5276 4.236527 TCCTAAATCTTTGAGAAGGCCC 57.763 45.455 0.00 0.00 33.56 5.80
5021 5346 4.129148 GGGCATGTCAGGGTCCCC 62.129 72.222 3.51 0.00 0.00 4.81
5135 5460 6.321848 ACCGAACCGAAATTCTTACAAAAT 57.678 33.333 0.00 0.00 0.00 1.82
5285 5840 5.989777 TCTTCAGTAAACTTGGCTTGTACTC 59.010 40.000 0.00 0.00 0.00 2.59
5288 5843 6.354130 ACTTCTTCAGTAAACTTGGCTTGTA 58.646 36.000 0.00 0.00 31.97 2.41
5289 5844 5.193679 ACTTCTTCAGTAAACTTGGCTTGT 58.806 37.500 0.00 0.00 31.97 3.16
5290 5845 5.757850 ACTTCTTCAGTAAACTTGGCTTG 57.242 39.130 0.00 0.00 31.97 4.01
5292 5847 4.036852 GCAACTTCTTCAGTAAACTTGGCT 59.963 41.667 0.00 0.00 32.94 4.75
5293 5848 4.290969 GCAACTTCTTCAGTAAACTTGGC 58.709 43.478 0.00 0.00 32.94 4.52
5294 5849 4.527564 CGCAACTTCTTCAGTAAACTTGG 58.472 43.478 0.00 0.00 32.94 3.61
5295 5850 3.968724 GCGCAACTTCTTCAGTAAACTTG 59.031 43.478 0.30 0.00 32.94 3.16
5296 5851 3.877508 AGCGCAACTTCTTCAGTAAACTT 59.122 39.130 11.47 0.00 32.94 2.66
5315 6315 6.202954 AGGTCCAAATCGATATCTAAAAAGCG 59.797 38.462 0.00 0.00 0.00 4.68
5316 6316 7.497925 AGGTCCAAATCGATATCTAAAAAGC 57.502 36.000 0.00 0.00 0.00 3.51
5326 6326 6.816640 CACTGTTTCTTAGGTCCAAATCGATA 59.183 38.462 0.00 0.00 0.00 2.92
5329 6329 4.154195 CCACTGTTTCTTAGGTCCAAATCG 59.846 45.833 0.00 0.00 0.00 3.34
5350 6350 3.620427 TTGCTAATCTAAAGTCGCCCA 57.380 42.857 0.00 0.00 0.00 5.36
5351 6351 4.438336 GGTTTTGCTAATCTAAAGTCGCCC 60.438 45.833 0.00 0.00 0.00 6.13
5361 6361 6.723977 TGTTTCCCTAATGGTTTTGCTAATCT 59.276 34.615 0.00 0.00 34.77 2.40
5381 6381 4.150804 TCTTTTGCAAAACCGTTGTGTTTC 59.849 37.500 20.46 0.00 37.46 2.78
5418 6448 3.443037 TGCAAAACAATCCGTGAAACAG 58.557 40.909 0.00 0.00 35.74 3.16
5446 6476 4.330894 GTGACATTGCTGATTGAATCTCGA 59.669 41.667 6.73 0.00 0.00 4.04
5447 6477 4.331992 AGTGACATTGCTGATTGAATCTCG 59.668 41.667 6.73 0.00 0.00 4.04
5539 6570 1.400142 TCAAAATTGCTACATCCGCCG 59.600 47.619 0.00 0.00 0.00 6.46
5540 6571 3.179048 GTTCAAAATTGCTACATCCGCC 58.821 45.455 0.00 0.00 0.00 6.13
5541 6572 3.832276 TGTTCAAAATTGCTACATCCGC 58.168 40.909 0.00 0.00 0.00 5.54
5542 6573 5.512788 GTCATGTTCAAAATTGCTACATCCG 59.487 40.000 9.37 3.38 33.75 4.18
5552 6583 8.891671 ATAGTTTGCTTGTCATGTTCAAAATT 57.108 26.923 0.00 0.00 0.00 1.82
5577 6608 3.010138 AGCAAGGGTACTCTGGCATTTAA 59.990 43.478 24.29 0.00 0.00 1.52
5616 6734 7.997223 TGGTAAGCATACTAGCTAGTTCTCTTA 59.003 37.037 30.40 25.80 45.89 2.10
5623 6741 9.756571 ACTAATATGGTAAGCATACTAGCTAGT 57.243 33.333 28.50 28.50 45.89 2.57
5632 6750 8.859236 ACGTCTCTACTAATATGGTAAGCATA 57.141 34.615 0.00 0.00 0.00 3.14
5813 6934 2.977808 TCCCTTCTCTTGTCAAGGAGT 58.022 47.619 12.66 0.00 41.74 3.85
5909 7030 8.392612 CCATAGATCAAATTTGTCAATTTTGCC 58.607 33.333 20.61 16.08 40.09 4.52
5913 7034 8.739039 TCGTCCATAGATCAAATTTGTCAATTT 58.261 29.630 17.47 2.86 42.37 1.82
5914 7035 8.279970 TCGTCCATAGATCAAATTTGTCAATT 57.720 30.769 17.47 3.94 33.72 2.32
5915 7036 7.864108 TCGTCCATAGATCAAATTTGTCAAT 57.136 32.000 17.47 4.40 0.00 2.57
5916 7037 7.680442 TTCGTCCATAGATCAAATTTGTCAA 57.320 32.000 17.47 0.00 0.00 3.18
5917 7038 7.680442 TTTCGTCCATAGATCAAATTTGTCA 57.320 32.000 17.47 0.00 0.00 3.58
5918 7039 8.397906 TGATTTCGTCCATAGATCAAATTTGTC 58.602 33.333 17.47 13.64 0.00 3.18
5919 7040 8.279970 TGATTTCGTCCATAGATCAAATTTGT 57.720 30.769 17.47 5.61 0.00 2.83
5920 7041 9.571810 TTTGATTTCGTCCATAGATCAAATTTG 57.428 29.630 12.15 12.15 40.07 2.32
5924 7045 8.397906 GTGATTTGATTTCGTCCATAGATCAAA 58.602 33.333 10.93 10.93 45.34 2.69
5925 7046 7.552330 TGTGATTTGATTTCGTCCATAGATCAA 59.448 33.333 0.00 0.00 35.57 2.57
5926 7047 7.047271 TGTGATTTGATTTCGTCCATAGATCA 58.953 34.615 0.00 0.00 0.00 2.92
5927 7048 7.439356 TCTGTGATTTGATTTCGTCCATAGATC 59.561 37.037 0.00 0.00 0.00 2.75
5928 7049 7.275183 TCTGTGATTTGATTTCGTCCATAGAT 58.725 34.615 0.00 0.00 0.00 1.98
5929 7050 6.639563 TCTGTGATTTGATTTCGTCCATAGA 58.360 36.000 0.00 0.00 0.00 1.98
5930 7051 6.908870 TCTGTGATTTGATTTCGTCCATAG 57.091 37.500 0.00 0.00 0.00 2.23
5931 7052 7.552330 TCATTCTGTGATTTGATTTCGTCCATA 59.448 33.333 0.00 0.00 0.00 2.74
5932 7053 6.375174 TCATTCTGTGATTTGATTTCGTCCAT 59.625 34.615 0.00 0.00 0.00 3.41
5933 7054 5.704978 TCATTCTGTGATTTGATTTCGTCCA 59.295 36.000 0.00 0.00 0.00 4.02
5934 7055 6.182039 TCATTCTGTGATTTGATTTCGTCC 57.818 37.500 0.00 0.00 0.00 4.79
5935 7056 7.269937 CAGTTCATTCTGTGATTTGATTTCGTC 59.730 37.037 0.00 0.00 36.54 4.20
5936 7057 7.080099 CAGTTCATTCTGTGATTTGATTTCGT 58.920 34.615 0.00 0.00 36.54 3.85
5937 7058 6.033196 GCAGTTCATTCTGTGATTTGATTTCG 59.967 38.462 0.00 0.00 36.54 3.46
5938 7059 6.309737 GGCAGTTCATTCTGTGATTTGATTTC 59.690 38.462 0.00 0.00 36.54 2.17
5939 7060 6.161381 GGCAGTTCATTCTGTGATTTGATTT 58.839 36.000 0.00 0.00 36.54 2.17
5940 7061 5.337009 GGGCAGTTCATTCTGTGATTTGATT 60.337 40.000 0.00 0.00 36.54 2.57
5941 7062 4.159135 GGGCAGTTCATTCTGTGATTTGAT 59.841 41.667 0.00 0.00 36.54 2.57
5942 7063 3.507233 GGGCAGTTCATTCTGTGATTTGA 59.493 43.478 0.00 0.00 36.54 2.69
5943 7064 3.671433 CGGGCAGTTCATTCTGTGATTTG 60.671 47.826 0.00 0.00 36.54 2.32
5944 7065 2.489329 CGGGCAGTTCATTCTGTGATTT 59.511 45.455 0.00 0.00 36.54 2.17
5945 7066 2.086869 CGGGCAGTTCATTCTGTGATT 58.913 47.619 0.00 0.00 36.54 2.57
5946 7067 1.003580 ACGGGCAGTTCATTCTGTGAT 59.996 47.619 0.00 0.00 36.54 3.06
5947 7068 0.396435 ACGGGCAGTTCATTCTGTGA 59.604 50.000 0.00 0.00 37.70 3.58
5948 7069 0.518636 CACGGGCAGTTCATTCTGTG 59.481 55.000 0.00 0.00 37.70 3.66
5949 7070 0.396435 TCACGGGCAGTTCATTCTGT 59.604 50.000 0.00 0.00 37.70 3.41
5950 7071 1.522668 TTCACGGGCAGTTCATTCTG 58.477 50.000 0.00 0.00 38.35 3.02
5951 7072 1.880027 GTTTCACGGGCAGTTCATTCT 59.120 47.619 0.00 0.00 0.00 2.40
5952 7073 1.880027 AGTTTCACGGGCAGTTCATTC 59.120 47.619 0.00 0.00 0.00 2.67
5953 7074 1.981256 AGTTTCACGGGCAGTTCATT 58.019 45.000 0.00 0.00 0.00 2.57
5954 7075 2.851263 TAGTTTCACGGGCAGTTCAT 57.149 45.000 0.00 0.00 0.00 2.57
5955 7076 2.851263 ATAGTTTCACGGGCAGTTCA 57.149 45.000 0.00 0.00 0.00 3.18
5956 7077 3.500680 TGAAATAGTTTCACGGGCAGTTC 59.499 43.478 1.24 0.00 44.21 3.01
5957 7078 3.482436 TGAAATAGTTTCACGGGCAGTT 58.518 40.909 1.24 0.00 44.21 3.16
5958 7079 3.134574 TGAAATAGTTTCACGGGCAGT 57.865 42.857 1.24 0.00 44.21 4.40
5966 7087 1.463056 CAGCCGCGTGAAATAGTTTCA 59.537 47.619 4.92 1.24 46.68 2.69
5967 7088 1.730064 TCAGCCGCGTGAAATAGTTTC 59.270 47.619 4.92 0.00 40.08 2.78
5968 7089 1.463444 GTCAGCCGCGTGAAATAGTTT 59.537 47.619 4.92 0.00 0.00 2.66
5969 7090 1.076332 GTCAGCCGCGTGAAATAGTT 58.924 50.000 4.92 0.00 0.00 2.24
5970 7091 0.739813 GGTCAGCCGCGTGAAATAGT 60.740 55.000 4.92 0.00 0.00 2.12
5971 7092 0.460284 AGGTCAGCCGCGTGAAATAG 60.460 55.000 4.92 0.00 40.50 1.73
5972 7093 0.036765 AAGGTCAGCCGCGTGAAATA 60.037 50.000 4.92 0.00 40.50 1.40
5973 7094 0.889186 AAAGGTCAGCCGCGTGAAAT 60.889 50.000 4.92 0.00 40.50 2.17
5974 7095 1.098712 AAAAGGTCAGCCGCGTGAAA 61.099 50.000 4.92 0.00 40.50 2.69
5975 7096 1.098712 AAAAAGGTCAGCCGCGTGAA 61.099 50.000 4.92 0.00 40.50 3.18
5976 7097 1.525077 AAAAAGGTCAGCCGCGTGA 60.525 52.632 4.92 0.00 40.50 4.35
5977 7098 1.370414 CAAAAAGGTCAGCCGCGTG 60.370 57.895 4.92 0.00 40.50 5.34
5978 7099 1.822186 ACAAAAAGGTCAGCCGCGT 60.822 52.632 4.92 0.00 40.50 6.01
5979 7100 1.370414 CACAAAAAGGTCAGCCGCG 60.370 57.895 0.00 0.00 40.50 6.46
5980 7101 0.594796 CACACAAAAAGGTCAGCCGC 60.595 55.000 0.00 0.00 40.50 6.53
5981 7102 1.021202 TCACACAAAAAGGTCAGCCG 58.979 50.000 0.00 0.00 40.50 5.52
5982 7103 1.268539 CGTCACACAAAAAGGTCAGCC 60.269 52.381 0.00 0.00 0.00 4.85
5983 7104 2.105323 CGTCACACAAAAAGGTCAGC 57.895 50.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.