Multiple sequence alignment - TraesCS4D01G071300

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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 TraesCS4D01G071300 chr4D 100.000 7682 0 0 1 7682 46432736 46425055 0.000000e+00 14187.0
1 TraesCS4D01G071300 chr4A 92.125 6349 272 86 705 6954 552500145 552506364 0.000000e+00 8745.0
2 TraesCS4D01G071300 chr4A 85.832 607 69 13 108 706 552499496 552500093 5.060000e-176 628.0
3 TraesCS4D01G071300 chr4A 83.000 100 13 4 11 109 619955808 619955712 3.820000e-13 87.9
4 TraesCS4D01G071300 chr4A 97.222 36 0 1 6867 6902 12522226 12522260 8.330000e-05 60.2
5 TraesCS4D01G071300 chr4B 95.702 1745 38 14 3159 4882 67855486 67853758 0.000000e+00 2772.0
6 TraesCS4D01G071300 chr4B 94.016 1337 53 9 4882 6198 67853708 67852379 0.000000e+00 2001.0
7 TraesCS4D01G071300 chr4B 95.861 1208 36 5 544 1747 67858482 67857285 0.000000e+00 1941.0
8 TraesCS4D01G071300 chr4B 97.407 810 12 3 6149 6954 67852359 67851555 0.000000e+00 1371.0
9 TraesCS4D01G071300 chr4B 98.000 550 11 0 1764 2313 67857302 67856753 0.000000e+00 955.0
10 TraesCS4D01G071300 chr4B 96.341 574 11 6 2312 2876 67856629 67856057 0.000000e+00 935.0
11 TraesCS4D01G071300 chr4B 96.460 113 4 0 2900 3012 67855593 67855481 3.660000e-43 187.0
12 TraesCS4D01G071300 chr5A 93.089 738 38 4 6957 7681 524124430 524125167 0.000000e+00 1068.0
13 TraesCS4D01G071300 chr5A 88.299 735 69 13 6957 7682 683944603 683943877 0.000000e+00 865.0
14 TraesCS4D01G071300 chr6D 92.818 738 41 1 6957 7682 471803783 471804520 0.000000e+00 1059.0
15 TraesCS4D01G071300 chr2B 92.673 737 39 4 6959 7682 18199666 18200400 0.000000e+00 1048.0
16 TraesCS4D01G071300 chr2B 92.225 746 37 5 6956 7682 232352678 232353421 0.000000e+00 1037.0
17 TraesCS4D01G071300 chr2B 91.069 739 42 9 6955 7682 254284886 254285611 0.000000e+00 977.0
18 TraesCS4D01G071300 chr3D 92.412 738 42 3 6957 7682 250500115 250500850 0.000000e+00 1040.0
19 TraesCS4D01G071300 chr3D 92.204 744 41 3 6956 7682 549484301 549483558 0.000000e+00 1037.0
20 TraesCS4D01G071300 chr1D 91.544 745 41 10 6957 7682 109809693 109810434 0.000000e+00 1007.0
21 TraesCS4D01G071300 chr1D 86.085 733 83 7 6957 7675 45393190 45393917 0.000000e+00 771.0
22 TraesCS4D01G071300 chr1D 79.615 260 38 12 226 476 60178807 60179060 1.020000e-38 172.0
23 TraesCS4D01G071300 chr5D 90.141 426 29 2 6943 7356 449503840 449504264 6.780000e-150 542.0
24 TraesCS4D01G071300 chr5D 79.085 306 48 13 212 506 98247401 98247701 6.080000e-46 196.0
25 TraesCS4D01G071300 chr5D 89.333 75 5 3 11 83 328246468 328246395 2.950000e-14 91.6
26 TraesCS4D01G071300 chr5D 100.000 30 0 0 6873 6902 547433508 547433537 1.000000e-03 56.5
27 TraesCS4D01G071300 chr6B 89.015 264 15 3 6958 7207 216694353 216694616 1.610000e-81 315.0
28 TraesCS4D01G071300 chr6B 93.878 196 11 1 6958 7152 689196031 689195836 2.100000e-75 294.0
29 TraesCS4D01G071300 chr3B 81.992 261 35 9 231 482 730780616 730780359 2.170000e-50 211.0
30 TraesCS4D01G071300 chr3B 76.862 376 62 19 143 502 138527035 138526669 1.020000e-43 189.0
31 TraesCS4D01G071300 chr3B 89.000 100 4 5 2 100 779129460 779129553 4.870000e-22 117.0
32 TraesCS4D01G071300 chr6A 80.586 273 41 9 228 492 155811947 155812215 4.700000e-47 200.0
33 TraesCS4D01G071300 chr2D 80.556 252 40 5 237 482 394042342 394042590 1.320000e-42 185.0
34 TraesCS4D01G071300 chr2D 95.833 72 3 0 1 72 103463084 103463155 4.870000e-22 117.0
35 TraesCS4D01G071300 chr2D 85.263 95 6 5 15 109 131303945 131303859 2.950000e-14 91.6
36 TraesCS4D01G071300 chr2D 100.000 29 0 0 6873 6901 626748572 626748544 4.000000e-03 54.7
37 TraesCS4D01G071300 chr7B 81.277 235 28 12 259 483 436830128 436829900 7.920000e-40 176.0
38 TraesCS4D01G071300 chr5B 81.385 231 29 9 261 482 700338148 700337923 7.920000e-40 176.0
39 TraesCS4D01G071300 chr7D 91.304 69 3 3 7 72 33270068 33270000 2.950000e-14 91.6
40 TraesCS4D01G071300 chr7D 91.304 69 3 3 7 72 33289785 33289717 2.950000e-14 91.6
41 TraesCS4D01G071300 chr3A 86.747 83 3 5 29 107 534186783 534186705 1.370000e-12 86.1
42 TraesCS4D01G071300 chr3A 84.615 91 6 8 1 86 44265936 44265849 4.940000e-12 84.2
43 TraesCS4D01G071300 chr1B 94.444 36 2 0 6866 6901 564902982 564903017 1.000000e-03 56.5


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 TraesCS4D01G071300 chr4D 46425055 46432736 7681 True 14187.000000 14187 100.000000 1 7682 1 chr4D.!!$R1 7681
1 TraesCS4D01G071300 chr4A 552499496 552506364 6868 False 4686.500000 8745 88.978500 108 6954 2 chr4A.!!$F2 6846
2 TraesCS4D01G071300 chr4B 67851555 67858482 6927 True 1451.714286 2772 96.255286 544 6954 7 chr4B.!!$R1 6410
3 TraesCS4D01G071300 chr5A 524124430 524125167 737 False 1068.000000 1068 93.089000 6957 7681 1 chr5A.!!$F1 724
4 TraesCS4D01G071300 chr5A 683943877 683944603 726 True 865.000000 865 88.299000 6957 7682 1 chr5A.!!$R1 725
5 TraesCS4D01G071300 chr6D 471803783 471804520 737 False 1059.000000 1059 92.818000 6957 7682 1 chr6D.!!$F1 725
6 TraesCS4D01G071300 chr2B 18199666 18200400 734 False 1048.000000 1048 92.673000 6959 7682 1 chr2B.!!$F1 723
7 TraesCS4D01G071300 chr2B 232352678 232353421 743 False 1037.000000 1037 92.225000 6956 7682 1 chr2B.!!$F2 726
8 TraesCS4D01G071300 chr2B 254284886 254285611 725 False 977.000000 977 91.069000 6955 7682 1 chr2B.!!$F3 727
9 TraesCS4D01G071300 chr3D 250500115 250500850 735 False 1040.000000 1040 92.412000 6957 7682 1 chr3D.!!$F1 725
10 TraesCS4D01G071300 chr3D 549483558 549484301 743 True 1037.000000 1037 92.204000 6956 7682 1 chr3D.!!$R1 726
11 TraesCS4D01G071300 chr1D 109809693 109810434 741 False 1007.000000 1007 91.544000 6957 7682 1 chr1D.!!$F3 725
12 TraesCS4D01G071300 chr1D 45393190 45393917 727 False 771.000000 771 86.085000 6957 7675 1 chr1D.!!$F1 718

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
49 50 0.108945 CGTAACAGGGGAGACGGAAC 60.109 60.000 0.00 0.0 0.00 3.62 F
51 52 0.115745 TAACAGGGGAGACGGAACCT 59.884 55.000 0.00 0.0 0.00 3.50 F
1390 1460 0.456221 CGGCCATGAGAGTACGTTCT 59.544 55.000 2.24 0.0 0.00 3.01 F
1479 1550 1.225855 GCCAGTTGACAATCACACGA 58.774 50.000 0.00 0.0 0.00 4.35 F
1569 1640 2.360801 GTGCATGTGTTGTAGGGTTTGT 59.639 45.455 0.00 0.0 0.00 2.83 F
3032 3711 1.088306 AAAACGGCGTCACAGAAACA 58.912 45.000 15.17 0.0 0.00 2.83 F
3033 3712 1.305201 AAACGGCGTCACAGAAACAT 58.695 45.000 15.17 0.0 0.00 2.71 F
3995 4695 1.320507 GCGTGTTTTAGTTTGGGGGA 58.679 50.000 0.00 0.0 0.00 4.81 F
4556 5267 0.378962 CGCTAGCTAGTTCTCTGCGT 59.621 55.000 21.62 0.0 35.77 5.24 F
4916 5689 0.455410 GAGAGAGACGCTCATGCAGT 59.545 55.000 9.00 0.0 46.45 4.40 F
6115 6922 0.904865 TGCGTTCCCTGGAGACTCAT 60.905 55.000 4.53 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 1154 0.379669 GCAGAGATGGCCATTTCGTG 59.620 55.000 25.91 23.28 0.00 4.35 R
1913 2005 0.538287 AGCTGGTGAAAAGGACAGGC 60.538 55.000 0.00 0.00 0.00 4.85 R
3016 3695 2.157834 TAATGTTTCTGTGACGCCGT 57.842 45.000 0.00 0.00 0.00 5.68 R
3017 3696 2.930040 AGATAATGTTTCTGTGACGCCG 59.070 45.455 0.00 0.00 0.00 6.46 R
3533 4224 6.509418 ACTGAAAACTACTTCTTTGCACAA 57.491 33.333 0.00 0.00 0.00 3.33 R
4105 4805 0.108851 CCACAAAACATAAGCGGGGC 60.109 55.000 0.00 0.00 0.00 5.80 R
4106 4806 0.530288 CCCACAAAACATAAGCGGGG 59.470 55.000 0.00 0.00 0.00 5.73 R
5167 5955 0.532573 TTCTCAGCCGGTCAAGCTAG 59.467 55.000 1.90 0.00 38.95 3.42 R
5969 6769 0.621609 TGCCCTAATTACGCCACCTT 59.378 50.000 0.00 0.00 0.00 3.50 R
6342 7222 0.667792 GACGTTGTCCTCTGTCCTGC 60.668 60.000 0.00 0.00 0.00 4.85 R
7150 8054 1.139520 GTTTGGATGGCGGTCATGC 59.860 57.895 7.18 7.18 43.44 4.06 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
19 20 2.068834 GTAAGAGGAGGGATGGACGA 57.931 55.000 0.00 0.00 0.00 4.20
20 21 2.385803 GTAAGAGGAGGGATGGACGAA 58.614 52.381 0.00 0.00 0.00 3.85
21 22 1.490574 AAGAGGAGGGATGGACGAAG 58.509 55.000 0.00 0.00 0.00 3.79
22 23 1.045911 AGAGGAGGGATGGACGAAGC 61.046 60.000 0.00 0.00 0.00 3.86
23 24 2.107141 GGAGGGATGGACGAAGCG 59.893 66.667 0.00 0.00 0.00 4.68
24 25 2.107141 GAGGGATGGACGAAGCGG 59.893 66.667 0.00 0.00 0.00 5.52
25 26 3.447025 GAGGGATGGACGAAGCGGG 62.447 68.421 0.00 0.00 0.00 6.13
26 27 4.547367 GGGATGGACGAAGCGGGG 62.547 72.222 0.00 0.00 0.00 5.73
27 28 4.547367 GGATGGACGAAGCGGGGG 62.547 72.222 0.00 0.00 0.00 5.40
41 42 2.284847 GGGGGACGTAACAGGGGA 60.285 66.667 0.00 0.00 0.00 4.81
42 43 2.364780 GGGGGACGTAACAGGGGAG 61.365 68.421 0.00 0.00 0.00 4.30
43 44 1.305549 GGGGACGTAACAGGGGAGA 60.306 63.158 0.00 0.00 0.00 3.71
44 45 1.611474 GGGGACGTAACAGGGGAGAC 61.611 65.000 0.00 0.00 0.00 3.36
45 46 1.509923 GGACGTAACAGGGGAGACG 59.490 63.158 0.00 0.00 41.02 4.18
46 47 1.509923 GACGTAACAGGGGAGACGG 59.490 63.158 0.00 0.00 39.57 4.79
47 48 0.962356 GACGTAACAGGGGAGACGGA 60.962 60.000 0.00 0.00 39.57 4.69
48 49 0.540365 ACGTAACAGGGGAGACGGAA 60.540 55.000 0.00 0.00 39.57 4.30
49 50 0.108945 CGTAACAGGGGAGACGGAAC 60.109 60.000 0.00 0.00 0.00 3.62
50 51 0.248565 GTAACAGGGGAGACGGAACC 59.751 60.000 0.00 0.00 0.00 3.62
51 52 0.115745 TAACAGGGGAGACGGAACCT 59.884 55.000 0.00 0.00 0.00 3.50
52 53 0.767060 AACAGGGGAGACGGAACCTT 60.767 55.000 0.00 0.00 0.00 3.50
53 54 0.115745 ACAGGGGAGACGGAACCTTA 59.884 55.000 0.00 0.00 0.00 2.69
54 55 0.535797 CAGGGGAGACGGAACCTTAC 59.464 60.000 0.00 0.00 0.00 2.34
55 56 0.969409 AGGGGAGACGGAACCTTACG 60.969 60.000 0.00 0.00 41.22 3.18
56 57 1.514553 GGGAGACGGAACCTTACGG 59.485 63.158 0.00 0.00 39.29 4.02
72 73 7.724490 ACCTTACGGTTCTTTTAGGTAGTAT 57.276 36.000 0.00 0.00 42.13 2.12
73 74 8.823220 ACCTTACGGTTCTTTTAGGTAGTATA 57.177 34.615 0.00 0.00 42.13 1.47
74 75 9.255029 ACCTTACGGTTCTTTTAGGTAGTATAA 57.745 33.333 0.00 0.00 42.13 0.98
75 76 9.741647 CCTTACGGTTCTTTTAGGTAGTATAAG 57.258 37.037 0.00 0.00 0.00 1.73
78 79 8.814038 ACGGTTCTTTTAGGTAGTATAAGAGA 57.186 34.615 0.00 0.00 32.32 3.10
79 80 9.418839 ACGGTTCTTTTAGGTAGTATAAGAGAT 57.581 33.333 0.00 0.00 32.32 2.75
124 125 0.911525 AGATGTGGGAGGTGAGGTGG 60.912 60.000 0.00 0.00 0.00 4.61
196 209 9.829507 TGTATTTGGAAAGTTTTGATTGTCAAT 57.170 25.926 0.00 0.00 36.11 2.57
217 230 8.973378 GTCAATTAATAGTAGAGATCAGTGTGC 58.027 37.037 0.00 0.00 0.00 4.57
218 231 8.695456 TCAATTAATAGTAGAGATCAGTGTGCA 58.305 33.333 0.00 0.00 0.00 4.57
223 236 4.029520 AGTAGAGATCAGTGTGCAGGATT 58.970 43.478 0.00 0.00 0.00 3.01
224 237 5.204292 AGTAGAGATCAGTGTGCAGGATTA 58.796 41.667 0.00 0.00 0.00 1.75
229 242 4.346127 AGATCAGTGTGCAGGATTATAGCA 59.654 41.667 0.00 0.00 35.63 3.49
238 251 7.432252 GTGTGCAGGATTATAGCAATTTGTTAC 59.568 37.037 0.00 0.00 40.35 2.50
239 252 7.339212 TGTGCAGGATTATAGCAATTTGTTACT 59.661 33.333 0.00 0.00 40.35 2.24
253 266 7.522073 GCAATTTGTTACTGAGGAATGTCTGAA 60.522 37.037 0.00 0.00 0.00 3.02
283 296 6.417191 TTGGAAGGTTATCGAGAAAAATCG 57.583 37.500 0.00 0.00 44.07 3.34
288 301 4.868734 AGGTTATCGAGAAAAATCGTGTCC 59.131 41.667 0.00 0.00 43.20 4.02
289 302 4.259690 GGTTATCGAGAAAAATCGTGTCCG 60.260 45.833 0.00 0.00 43.20 4.79
296 309 5.332808 CGAGAAAAATCGTGTCCGTTTTAGT 60.333 40.000 0.00 0.00 35.53 2.24
446 459 7.977789 TTTTTAATGGCAAGGAGAAAAATCC 57.022 32.000 0.00 0.00 39.89 3.01
455 468 5.072741 CAAGGAGAAAAATCCAGTGGAAGA 58.927 41.667 17.71 0.00 42.26 2.87
456 469 4.916183 AGGAGAAAAATCCAGTGGAAGAG 58.084 43.478 17.71 0.00 42.26 2.85
461 474 0.995024 AATCCAGTGGAAGAGGGTGG 59.005 55.000 17.71 0.00 34.34 4.61
463 476 1.127567 TCCAGTGGAAGAGGGTGGTG 61.128 60.000 10.20 0.00 0.00 4.17
482 495 5.411669 GTGGTGAGGTGAGACGAAAATAAAT 59.588 40.000 0.00 0.00 0.00 1.40
483 496 6.001460 TGGTGAGGTGAGACGAAAATAAATT 58.999 36.000 0.00 0.00 0.00 1.82
488 501 7.274904 TGAGGTGAGACGAAAATAAATTAGACG 59.725 37.037 0.00 0.00 0.00 4.18
505 518 4.342862 AGACGAAATAGATGGTGATGGG 57.657 45.455 0.00 0.00 0.00 4.00
506 519 3.711704 AGACGAAATAGATGGTGATGGGT 59.288 43.478 0.00 0.00 0.00 4.51
507 520 3.808728 ACGAAATAGATGGTGATGGGTG 58.191 45.455 0.00 0.00 0.00 4.61
508 521 3.141398 CGAAATAGATGGTGATGGGTGG 58.859 50.000 0.00 0.00 0.00 4.61
512 525 0.620556 AGATGGTGATGGGTGGTGAC 59.379 55.000 0.00 0.00 0.00 3.67
514 527 2.746277 GGTGATGGGTGGTGACGC 60.746 66.667 0.00 0.00 41.20 5.19
516 529 3.307108 TGATGGGTGGTGACGCGA 61.307 61.111 15.93 0.00 43.50 5.87
571 584 9.506042 AAAATAAACCATGGAAGGGAATCTATT 57.494 29.630 21.47 4.80 43.46 1.73
630 643 0.893727 GTCACGGCCCTCCAAAATGT 60.894 55.000 0.00 0.00 0.00 2.71
665 678 4.154347 GCCTGCTCCACCTCTCCG 62.154 72.222 0.00 0.00 0.00 4.63
676 689 2.356125 CCACCTCTCCGACCATTTCATT 60.356 50.000 0.00 0.00 0.00 2.57
771 835 2.567169 TCACTATCCACCAACCTCACTG 59.433 50.000 0.00 0.00 0.00 3.66
880 946 4.908601 ACCACTCATGACCTAATCACAA 57.091 40.909 0.00 0.00 41.24 3.33
902 968 4.751767 ACAGATCCTTCTCACTCCATTC 57.248 45.455 0.00 0.00 0.00 2.67
1390 1460 0.456221 CGGCCATGAGAGTACGTTCT 59.544 55.000 2.24 0.00 0.00 3.01
1433 1503 4.024725 TGTTCGGTTGGTTGTTTCGATTAG 60.025 41.667 0.00 0.00 0.00 1.73
1442 1513 2.083774 TGTTTCGATTAGCAAGCCTGG 58.916 47.619 0.00 0.00 0.00 4.45
1463 1534 2.181521 GTTGGTCGAAACGGTGCCA 61.182 57.895 0.00 0.00 0.00 4.92
1479 1550 1.225855 GCCAGTTGACAATCACACGA 58.774 50.000 0.00 0.00 0.00 4.35
1546 1617 5.333645 GCCTCGTTATCTGAATGTTAGCATG 60.334 44.000 0.00 0.00 35.15 4.06
1569 1640 2.360801 GTGCATGTGTTGTAGGGTTTGT 59.639 45.455 0.00 0.00 0.00 2.83
1570 1641 3.566322 GTGCATGTGTTGTAGGGTTTGTA 59.434 43.478 0.00 0.00 0.00 2.41
1571 1642 3.566322 TGCATGTGTTGTAGGGTTTGTAC 59.434 43.478 0.00 0.00 0.00 2.90
1572 1643 3.818773 GCATGTGTTGTAGGGTTTGTACT 59.181 43.478 0.00 0.00 0.00 2.73
1573 1644 4.277423 GCATGTGTTGTAGGGTTTGTACTT 59.723 41.667 0.00 0.00 0.00 2.24
1574 1645 5.221165 GCATGTGTTGTAGGGTTTGTACTTT 60.221 40.000 0.00 0.00 0.00 2.66
1575 1646 5.821516 TGTGTTGTAGGGTTTGTACTTTG 57.178 39.130 0.00 0.00 0.00 2.77
1576 1647 5.254901 TGTGTTGTAGGGTTTGTACTTTGT 58.745 37.500 0.00 0.00 0.00 2.83
1602 1673 3.761897 TCATTTGGATTTCGGGTCTGTT 58.238 40.909 0.00 0.00 0.00 3.16
1832 1921 5.689819 CATTCGAAAACGGAACAAGAAGAT 58.310 37.500 0.00 0.00 0.00 2.40
1957 2049 6.525628 TGCTAATCACTTTCGTCTAGTTTACG 59.474 38.462 0.00 0.00 41.64 3.18
2356 2573 4.603131 ACATACTGAATTGTCCATGCCTT 58.397 39.130 0.00 0.00 0.00 4.35
2863 3092 8.045720 TGATATATCCCTTGTTAGAAAAGGCT 57.954 34.615 10.25 0.00 42.52 4.58
2865 3094 8.926092 ATATATCCCTTGTTAGAAAAGGCTTC 57.074 34.615 0.00 0.00 42.52 3.86
2866 3095 3.763057 TCCCTTGTTAGAAAAGGCTTCC 58.237 45.455 0.00 0.00 42.52 3.46
2867 3096 3.397955 TCCCTTGTTAGAAAAGGCTTCCT 59.602 43.478 0.00 3.71 42.52 3.36
2868 3097 3.759086 CCCTTGTTAGAAAAGGCTTCCTC 59.241 47.826 0.00 0.24 42.52 3.71
2869 3098 4.507512 CCCTTGTTAGAAAAGGCTTCCTCT 60.508 45.833 14.20 14.20 42.52 3.69
2870 3099 4.697828 CCTTGTTAGAAAAGGCTTCCTCTC 59.302 45.833 13.40 3.49 37.96 3.20
2871 3100 4.974645 TGTTAGAAAAGGCTTCCTCTCA 57.025 40.909 13.40 6.03 30.89 3.27
2872 3101 4.642429 TGTTAGAAAAGGCTTCCTCTCAC 58.358 43.478 13.40 13.19 30.89 3.51
2884 3113 4.141711 GCTTCCTCTCACTCTCTCTCTCTA 60.142 50.000 0.00 0.00 0.00 2.43
2885 3114 5.455326 GCTTCCTCTCACTCTCTCTCTCTAT 60.455 48.000 0.00 0.00 0.00 1.98
2888 3117 8.966155 TTCCTCTCACTCTCTCTCTCTATATA 57.034 38.462 0.00 0.00 0.00 0.86
3025 3704 6.536688 ACTAAATACATAAAAACGGCGTCAC 58.463 36.000 15.17 0.00 0.00 3.67
3029 3708 2.873472 ACATAAAAACGGCGTCACAGAA 59.127 40.909 15.17 0.00 0.00 3.02
3032 3711 1.088306 AAAACGGCGTCACAGAAACA 58.912 45.000 15.17 0.00 0.00 2.83
3033 3712 1.305201 AAACGGCGTCACAGAAACAT 58.695 45.000 15.17 0.00 0.00 2.71
3034 3713 1.305201 AACGGCGTCACAGAAACATT 58.695 45.000 15.17 0.00 0.00 2.71
3035 3714 2.157834 ACGGCGTCACAGAAACATTA 57.842 45.000 6.77 0.00 0.00 1.90
3036 3715 2.695359 ACGGCGTCACAGAAACATTAT 58.305 42.857 6.77 0.00 0.00 1.28
3037 3716 2.671396 ACGGCGTCACAGAAACATTATC 59.329 45.455 6.77 0.00 0.00 1.75
3038 3717 2.930040 CGGCGTCACAGAAACATTATCT 59.070 45.455 0.00 0.00 0.00 1.98
3039 3718 4.109766 CGGCGTCACAGAAACATTATCTA 58.890 43.478 0.00 0.00 0.00 1.98
3040 3719 4.745125 CGGCGTCACAGAAACATTATCTAT 59.255 41.667 0.00 0.00 0.00 1.98
3041 3720 5.332581 CGGCGTCACAGAAACATTATCTATG 60.333 44.000 0.00 0.00 40.26 2.23
3042 3721 5.435557 GCGTCACAGAAACATTATCTATGC 58.564 41.667 0.00 0.00 37.81 3.14
3043 3722 5.559035 GCGTCACAGAAACATTATCTATGCC 60.559 44.000 0.00 0.00 37.81 4.40
3044 3723 5.523552 CGTCACAGAAACATTATCTATGCCA 59.476 40.000 0.00 0.00 37.81 4.92
3045 3724 6.203530 CGTCACAGAAACATTATCTATGCCAT 59.796 38.462 0.00 0.00 37.81 4.40
3046 3725 7.384932 CGTCACAGAAACATTATCTATGCCATA 59.615 37.037 0.00 0.00 37.81 2.74
3047 3726 9.224267 GTCACAGAAACATTATCTATGCCATAT 57.776 33.333 0.00 0.00 37.81 1.78
3266 3951 9.773328 CCACACATAACTTGTATTTGAGTATTG 57.227 33.333 0.00 0.00 36.57 1.90
3533 4224 9.093458 ACAATTTTCTCTTAATTTCCATGGAGT 57.907 29.630 15.53 5.16 0.00 3.85
3559 4250 8.046294 TGTGCAAAGAAGTAGTTTTCAGTAAA 57.954 30.769 0.00 0.00 0.00 2.01
3606 4299 7.425577 TTGGCATAGAAATTACATCAGATCG 57.574 36.000 0.00 0.00 0.00 3.69
3621 4314 4.639135 CAGATCGTCTCTGGTATTCACA 57.361 45.455 9.11 0.00 46.52 3.58
3622 4315 5.193663 CAGATCGTCTCTGGTATTCACAT 57.806 43.478 9.11 0.00 46.52 3.21
3623 4316 6.319141 CAGATCGTCTCTGGTATTCACATA 57.681 41.667 9.11 0.00 46.52 2.29
3624 4317 6.918626 CAGATCGTCTCTGGTATTCACATAT 58.081 40.000 9.11 0.00 46.52 1.78
3842 4539 8.589335 TTTGAGTTGACACAGAAACTAGATAC 57.411 34.615 0.00 0.00 36.77 2.24
3980 4680 2.938451 AGGTCACATACATTGATGCGTG 59.062 45.455 0.00 0.00 0.00 5.34
3995 4695 1.320507 GCGTGTTTTAGTTTGGGGGA 58.679 50.000 0.00 0.00 0.00 4.81
4195 4900 5.923733 AGAGGAGAAGAAAAATCTAGCGA 57.076 39.130 0.00 0.00 0.00 4.93
4349 5059 6.575162 ACATGAAAATGACTTGAAGGTACC 57.425 37.500 2.73 2.73 0.00 3.34
4556 5267 0.378962 CGCTAGCTAGTTCTCTGCGT 59.621 55.000 21.62 0.00 35.77 5.24
4693 5408 2.635899 GCGCCATGCATGTAGCTC 59.364 61.111 26.47 16.11 45.94 4.09
4695 5410 1.524393 CGCCATGCATGTAGCTCCA 60.524 57.895 24.58 0.00 45.94 3.86
4696 5411 1.504647 CGCCATGCATGTAGCTCCAG 61.505 60.000 24.58 8.31 45.94 3.86
4697 5412 1.170919 GCCATGCATGTAGCTCCAGG 61.171 60.000 24.58 7.70 45.94 4.45
4905 5678 2.505819 AGAGAGGGTGAGAGAGAGAGAC 59.494 54.545 0.00 0.00 0.00 3.36
4916 5689 0.455410 GAGAGAGACGCTCATGCAGT 59.545 55.000 9.00 0.00 46.45 4.40
4922 5695 3.634448 AGAGACGCTCATGCAGTAGTATT 59.366 43.478 9.09 0.00 39.64 1.89
4923 5696 4.822350 AGAGACGCTCATGCAGTAGTATTA 59.178 41.667 9.09 0.00 39.64 0.98
4924 5697 4.861210 AGACGCTCATGCAGTAGTATTAC 58.139 43.478 0.00 0.00 39.64 1.89
5159 5935 2.359107 CCGGCCATCCATCCATCG 60.359 66.667 2.24 0.00 0.00 3.84
5167 5955 2.430465 CATCCATCCATCGATTGTCCC 58.570 52.381 0.00 0.00 0.00 4.46
5290 6078 3.982241 AAGCCAACTTGCCAGCGC 61.982 61.111 0.00 0.00 33.84 5.92
5312 6100 1.193665 CGTCGCGCATTGCATTAACC 61.194 55.000 8.75 0.00 46.97 2.85
5554 6347 6.717540 TGGTTTTAACTATTTTGCTGGCTCTA 59.282 34.615 0.00 0.00 0.00 2.43
5604 6401 1.906824 TGTCTGTCACGGGACTCCC 60.907 63.158 20.37 3.63 44.61 4.30
5615 6412 1.205055 GGGACTCCCTCCGATTTTCT 58.795 55.000 6.90 0.00 41.34 2.52
5627 6424 7.054751 CCCTCCGATTTTCTCTTTAATTACCT 58.945 38.462 0.00 0.00 0.00 3.08
5718 6516 5.894015 TTCGTTACGAGTTGCAGAAGGCA 62.894 47.826 7.69 0.00 44.10 4.75
5886 6684 5.126545 TGAGCTCCATTACACACTACGTATT 59.873 40.000 12.15 0.00 0.00 1.89
5969 6769 2.085320 GTCGTCTGTAGAGGCTCTGAA 58.915 52.381 26.95 13.41 0.00 3.02
5977 6777 1.743252 GAGGCTCTGAAAGGTGGCG 60.743 63.158 7.40 0.00 38.10 5.69
6030 6830 4.171005 GGACAAACTGCACATCATCAATG 58.829 43.478 0.00 0.00 41.48 2.82
6093 6900 2.295909 AGTAATGCATGCCACGTTGTTT 59.704 40.909 16.68 0.00 0.00 2.83
6106 6913 1.555477 GTTGTTTGTTGCGTTCCCTG 58.445 50.000 0.00 0.00 0.00 4.45
6115 6922 0.904865 TGCGTTCCCTGGAGACTCAT 60.905 55.000 4.53 0.00 0.00 2.90
6233 7113 1.541147 GGTTGAGCTGCATTGCAACTA 59.459 47.619 14.21 0.00 34.98 2.24
6342 7222 1.180029 CTTCACTCAATTGCCCAGGG 58.820 55.000 0.00 0.00 0.00 4.45
6994 7874 3.801997 CTCCCCGGCCTCTGCATT 61.802 66.667 0.00 0.00 40.13 3.56
7064 7945 5.522824 ACAAAGGTCTTAAAGTCTCAACGAC 59.477 40.000 0.00 0.00 43.17 4.34
7258 8162 0.393944 TCGGAGTGAGTAGCGACCAT 60.394 55.000 0.00 0.00 0.00 3.55
7379 8283 5.810587 CACAATAAAGCACATACTCCTACGT 59.189 40.000 0.00 0.00 0.00 3.57
7425 8329 1.262640 ATCCCGTTAAGCCACGTCCT 61.263 55.000 0.00 0.00 38.57 3.85
7544 8448 4.645863 TTGATGGATTCATCCCGATCAT 57.354 40.909 11.63 0.00 46.92 2.45
7577 8481 2.097110 TGTAGGTCCTGTCCAGTTGT 57.903 50.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.068834 TCGTCCATCCCTCCTCTTAC 57.931 55.000 0.00 0.00 0.00 2.34
1 2 2.667470 CTTCGTCCATCCCTCCTCTTA 58.333 52.381 0.00 0.00 0.00 2.10
2 3 1.490574 CTTCGTCCATCCCTCCTCTT 58.509 55.000 0.00 0.00 0.00 2.85
3 4 1.045911 GCTTCGTCCATCCCTCCTCT 61.046 60.000 0.00 0.00 0.00 3.69
4 5 1.443828 GCTTCGTCCATCCCTCCTC 59.556 63.158 0.00 0.00 0.00 3.71
5 6 2.427245 CGCTTCGTCCATCCCTCCT 61.427 63.158 0.00 0.00 0.00 3.69
6 7 2.107141 CGCTTCGTCCATCCCTCC 59.893 66.667 0.00 0.00 0.00 4.30
7 8 2.107141 CCGCTTCGTCCATCCCTC 59.893 66.667 0.00 0.00 0.00 4.30
8 9 3.470888 CCCGCTTCGTCCATCCCT 61.471 66.667 0.00 0.00 0.00 4.20
9 10 4.547367 CCCCGCTTCGTCCATCCC 62.547 72.222 0.00 0.00 0.00 3.85
10 11 4.547367 CCCCCGCTTCGTCCATCC 62.547 72.222 0.00 0.00 0.00 3.51
24 25 2.284847 TCCCCTGTTACGTCCCCC 60.285 66.667 0.00 0.00 0.00 5.40
25 26 1.305549 TCTCCCCTGTTACGTCCCC 60.306 63.158 0.00 0.00 0.00 4.81
26 27 1.895966 GTCTCCCCTGTTACGTCCC 59.104 63.158 0.00 0.00 0.00 4.46
27 28 1.509923 CGTCTCCCCTGTTACGTCC 59.490 63.158 0.00 0.00 0.00 4.79
28 29 0.962356 TCCGTCTCCCCTGTTACGTC 60.962 60.000 0.00 0.00 33.63 4.34
29 30 0.540365 TTCCGTCTCCCCTGTTACGT 60.540 55.000 0.00 0.00 33.63 3.57
30 31 0.108945 GTTCCGTCTCCCCTGTTACG 60.109 60.000 0.00 0.00 35.20 3.18
31 32 0.248565 GGTTCCGTCTCCCCTGTTAC 59.751 60.000 0.00 0.00 0.00 2.50
32 33 0.115745 AGGTTCCGTCTCCCCTGTTA 59.884 55.000 0.00 0.00 0.00 2.41
33 34 0.767060 AAGGTTCCGTCTCCCCTGTT 60.767 55.000 0.00 0.00 0.00 3.16
34 35 0.115745 TAAGGTTCCGTCTCCCCTGT 59.884 55.000 0.00 0.00 0.00 4.00
35 36 0.535797 GTAAGGTTCCGTCTCCCCTG 59.464 60.000 0.00 0.00 0.00 4.45
36 37 0.969409 CGTAAGGTTCCGTCTCCCCT 60.969 60.000 0.00 0.00 0.00 4.79
37 38 1.514553 CGTAAGGTTCCGTCTCCCC 59.485 63.158 0.00 0.00 0.00 4.81
52 53 9.905713 TCTCTTATACTACCTAAAAGAACCGTA 57.094 33.333 0.00 0.00 0.00 4.02
53 54 8.814038 TCTCTTATACTACCTAAAAGAACCGT 57.186 34.615 0.00 0.00 0.00 4.83
87 88 8.328758 CCCACATCTCTATCTCTACTATCTCTT 58.671 40.741 0.00 0.00 0.00 2.85
88 89 7.682459 TCCCACATCTCTATCTCTACTATCTCT 59.318 40.741 0.00 0.00 0.00 3.10
89 90 7.857456 TCCCACATCTCTATCTCTACTATCTC 58.143 42.308 0.00 0.00 0.00 2.75
90 91 7.092444 CCTCCCACATCTCTATCTCTACTATCT 60.092 44.444 0.00 0.00 0.00 1.98
91 92 7.054124 CCTCCCACATCTCTATCTCTACTATC 58.946 46.154 0.00 0.00 0.00 2.08
92 93 6.507485 ACCTCCCACATCTCTATCTCTACTAT 59.493 42.308 0.00 0.00 0.00 2.12
93 94 5.852807 ACCTCCCACATCTCTATCTCTACTA 59.147 44.000 0.00 0.00 0.00 1.82
94 95 4.667858 ACCTCCCACATCTCTATCTCTACT 59.332 45.833 0.00 0.00 0.00 2.57
95 96 4.764823 CACCTCCCACATCTCTATCTCTAC 59.235 50.000 0.00 0.00 0.00 2.59
96 97 4.665483 TCACCTCCCACATCTCTATCTCTA 59.335 45.833 0.00 0.00 0.00 2.43
97 98 3.465210 TCACCTCCCACATCTCTATCTCT 59.535 47.826 0.00 0.00 0.00 3.10
98 99 3.826157 CTCACCTCCCACATCTCTATCTC 59.174 52.174 0.00 0.00 0.00 2.75
99 100 3.437784 CCTCACCTCCCACATCTCTATCT 60.438 52.174 0.00 0.00 0.00 1.98
100 101 2.896685 CCTCACCTCCCACATCTCTATC 59.103 54.545 0.00 0.00 0.00 2.08
101 102 2.248686 ACCTCACCTCCCACATCTCTAT 59.751 50.000 0.00 0.00 0.00 1.98
102 103 1.646447 ACCTCACCTCCCACATCTCTA 59.354 52.381 0.00 0.00 0.00 2.43
103 104 0.415429 ACCTCACCTCCCACATCTCT 59.585 55.000 0.00 0.00 0.00 3.10
104 105 0.539051 CACCTCACCTCCCACATCTC 59.461 60.000 0.00 0.00 0.00 2.75
105 106 0.911525 CCACCTCACCTCCCACATCT 60.912 60.000 0.00 0.00 0.00 2.90
106 107 0.909610 TCCACCTCACCTCCCACATC 60.910 60.000 0.00 0.00 0.00 3.06
166 179 9.883142 ACAATCAAAACTTTCCAAATACAGAAA 57.117 25.926 0.00 0.00 0.00 2.52
167 180 9.528018 GACAATCAAAACTTTCCAAATACAGAA 57.472 29.630 0.00 0.00 0.00 3.02
168 181 8.690884 TGACAATCAAAACTTTCCAAATACAGA 58.309 29.630 0.00 0.00 0.00 3.41
169 182 8.870160 TGACAATCAAAACTTTCCAAATACAG 57.130 30.769 0.00 0.00 0.00 2.74
196 209 6.833933 TCCTGCACACTGATCTCTACTATTAA 59.166 38.462 0.00 0.00 0.00 1.40
204 217 5.279406 GCTATAATCCTGCACACTGATCTCT 60.279 44.000 0.00 0.00 0.00 3.10
210 223 5.762825 AATTGCTATAATCCTGCACACTG 57.237 39.130 0.00 0.00 36.37 3.66
217 230 8.562892 CCTCAGTAACAAATTGCTATAATCCTG 58.437 37.037 0.00 0.00 0.00 3.86
218 231 8.494433 TCCTCAGTAACAAATTGCTATAATCCT 58.506 33.333 0.00 0.00 0.00 3.24
223 236 9.109393 GACATTCCTCAGTAACAAATTGCTATA 57.891 33.333 0.00 0.00 0.00 1.31
224 237 7.831193 AGACATTCCTCAGTAACAAATTGCTAT 59.169 33.333 0.00 0.00 0.00 2.97
229 242 8.641498 ATTCAGACATTCCTCAGTAACAAATT 57.359 30.769 0.00 0.00 0.00 1.82
238 251 8.742777 TCCAAAATAAATTCAGACATTCCTCAG 58.257 33.333 0.00 0.00 0.00 3.35
239 252 8.648698 TCCAAAATAAATTCAGACATTCCTCA 57.351 30.769 0.00 0.00 0.00 3.86
247 260 9.503427 CGATAACCTTCCAAAATAAATTCAGAC 57.497 33.333 0.00 0.00 0.00 3.51
283 296 7.009357 GTGAGATCATCTTACTAAAACGGACAC 59.991 40.741 2.26 0.00 31.15 3.67
356 369 4.712829 TGGCAGGTGATGATTCAATTCAAT 59.287 37.500 0.00 0.00 32.48 2.57
419 432 9.440773 GATTTTTCTCCTTGCCATTAAAAATCT 57.559 29.630 17.42 0.00 43.38 2.40
420 433 8.668353 GGATTTTTCTCCTTGCCATTAAAAATC 58.332 33.333 16.83 16.83 44.62 2.17
421 434 8.162746 TGGATTTTTCTCCTTGCCATTAAAAAT 58.837 29.630 0.00 0.00 38.52 1.82
426 439 5.185635 CACTGGATTTTTCTCCTTGCCATTA 59.814 40.000 0.00 0.00 36.20 1.90
434 447 4.263683 CCTCTTCCACTGGATTTTTCTCCT 60.264 45.833 0.00 0.00 36.20 3.69
436 449 4.013050 CCCTCTTCCACTGGATTTTTCTC 58.987 47.826 0.00 0.00 0.00 2.87
446 459 0.322975 CTCACCACCCTCTTCCACTG 59.677 60.000 0.00 0.00 0.00 3.66
455 468 1.908793 CGTCTCACCTCACCACCCT 60.909 63.158 0.00 0.00 0.00 4.34
456 469 1.469335 TTCGTCTCACCTCACCACCC 61.469 60.000 0.00 0.00 0.00 4.61
461 474 8.381387 GTCTAATTTATTTTCGTCTCACCTCAC 58.619 37.037 0.00 0.00 0.00 3.51
463 476 7.487189 TCGTCTAATTTATTTTCGTCTCACCTC 59.513 37.037 0.00 0.00 0.00 3.85
482 495 5.365605 ACCCATCACCATCTATTTCGTCTAA 59.634 40.000 0.00 0.00 0.00 2.10
483 496 4.899457 ACCCATCACCATCTATTTCGTCTA 59.101 41.667 0.00 0.00 0.00 2.59
488 501 3.885297 CACCACCCATCACCATCTATTTC 59.115 47.826 0.00 0.00 0.00 2.17
494 507 0.744414 CGTCACCACCCATCACCATC 60.744 60.000 0.00 0.00 0.00 3.51
498 511 3.118454 CGCGTCACCACCCATCAC 61.118 66.667 0.00 0.00 0.00 3.06
522 535 5.353938 TCGTCTAATTAATTTCCGTCTGGG 58.646 41.667 5.91 0.00 35.24 4.45
539 552 5.883673 CCCTTCCATGGTTTATTTTCGTCTA 59.116 40.000 12.58 0.00 0.00 2.59
583 596 6.461577 AGATATGGTCTCATCTCTACTCCA 57.538 41.667 0.00 0.00 35.78 3.86
630 643 5.480073 AGCAGGCACCAAAAACTTTATATGA 59.520 36.000 0.00 0.00 0.00 2.15
665 678 5.712152 ACTTCCTGTTCAATGAAATGGTC 57.288 39.130 12.83 0.00 0.00 4.02
676 689 4.894114 GGAGGTATAGCTACTTCCTGTTCA 59.106 45.833 15.11 0.00 45.93 3.18
771 835 1.060163 TAGGGATGGGGGCTAGCAAC 61.060 60.000 18.24 8.65 0.00 4.17
880 946 4.080638 GGAATGGAGTGAGAAGGATCTGTT 60.081 45.833 0.00 0.00 35.54 3.16
902 968 3.172229 CTTCTTCTTCGAAGCTAGGGG 57.828 52.381 20.56 11.37 34.59 4.79
962 1032 2.566833 ACAACAAGGATGCTGCTACA 57.433 45.000 0.00 0.00 0.00 2.74
1084 1154 0.379669 GCAGAGATGGCCATTTCGTG 59.620 55.000 25.91 23.28 0.00 4.35
1390 1460 7.010923 CCGAACAAAAATTGAATCCAGTTTCAA 59.989 33.333 6.40 6.40 46.46 2.69
1433 1503 2.594592 ACCAACGACCAGGCTTGC 60.595 61.111 0.00 0.00 0.00 4.01
1463 1534 1.140052 TGGGTCGTGTGATTGTCAACT 59.860 47.619 0.00 0.00 0.00 3.16
1479 1550 7.123355 TCTTCAAAATTCAGACAAATTGGGT 57.877 32.000 0.00 0.00 0.00 4.51
1546 1617 2.185004 ACCCTACAACACATGCACTC 57.815 50.000 0.00 0.00 0.00 3.51
1570 1641 8.413229 CCCGAAATCCAAATGATATTACAAAGT 58.587 33.333 0.00 0.00 31.83 2.66
1571 1642 8.413229 ACCCGAAATCCAAATGATATTACAAAG 58.587 33.333 0.00 0.00 31.83 2.77
1572 1643 8.299990 ACCCGAAATCCAAATGATATTACAAA 57.700 30.769 0.00 0.00 31.83 2.83
1573 1644 7.777910 AGACCCGAAATCCAAATGATATTACAA 59.222 33.333 0.00 0.00 31.83 2.41
1574 1645 7.228507 CAGACCCGAAATCCAAATGATATTACA 59.771 37.037 0.00 0.00 31.83 2.41
1575 1646 7.228706 ACAGACCCGAAATCCAAATGATATTAC 59.771 37.037 0.00 0.00 31.83 1.89
1576 1647 7.287061 ACAGACCCGAAATCCAAATGATATTA 58.713 34.615 0.00 0.00 31.83 0.98
1832 1921 6.808829 TCAAGGAAACGTACAAGAAAGACTA 58.191 36.000 0.00 0.00 0.00 2.59
1913 2005 0.538287 AGCTGGTGAAAAGGACAGGC 60.538 55.000 0.00 0.00 0.00 4.85
2322 2539 9.260002 GACAATTCAGTATGTTTTTCCACAAAT 57.740 29.630 0.00 0.00 37.40 2.32
2356 2573 5.292345 CGTTGGAATATATGTTTGTCCGTGA 59.708 40.000 0.00 0.00 0.00 4.35
2863 3092 7.872061 ATATAGAGAGAGAGAGTGAGAGGAA 57.128 40.000 0.00 0.00 0.00 3.36
2924 3601 3.496884 TCAAGACCGAGCACATTGTAAAC 59.503 43.478 0.00 0.00 0.00 2.01
2998 3677 7.095313 TGACGCCGTTTTTATGTATTTAGTCAA 60.095 33.333 0.00 0.00 30.80 3.18
2999 3678 6.368243 TGACGCCGTTTTTATGTATTTAGTCA 59.632 34.615 0.00 0.00 0.00 3.41
3008 3687 2.485903 TCTGTGACGCCGTTTTTATGT 58.514 42.857 0.00 0.00 0.00 2.29
3016 3695 2.157834 TAATGTTTCTGTGACGCCGT 57.842 45.000 0.00 0.00 0.00 5.68
3017 3696 2.930040 AGATAATGTTTCTGTGACGCCG 59.070 45.455 0.00 0.00 0.00 6.46
3035 3714 9.516546 CCATCAGCAATAATATATGGCATAGAT 57.483 33.333 13.39 11.05 0.00 1.98
3036 3715 8.716779 TCCATCAGCAATAATATATGGCATAGA 58.283 33.333 13.39 8.94 35.02 1.98
3037 3716 8.913487 TCCATCAGCAATAATATATGGCATAG 57.087 34.615 13.39 0.00 35.02 2.23
3038 3717 9.871175 ATTCCATCAGCAATAATATATGGCATA 57.129 29.630 10.07 10.07 35.02 3.14
3039 3718 8.777578 ATTCCATCAGCAATAATATATGGCAT 57.222 30.769 4.88 4.88 35.02 4.40
3040 3719 9.697990 TTATTCCATCAGCAATAATATATGGCA 57.302 29.630 0.00 0.00 35.02 4.92
3512 4203 7.523709 GCACAACTCCATGGAAATTAAGAGAAA 60.524 37.037 17.00 0.00 0.00 2.52
3533 4224 6.509418 ACTGAAAACTACTTCTTTGCACAA 57.491 33.333 0.00 0.00 0.00 3.33
3674 4367 8.536175 TCCACGTATAGAAATTATGGCATATCA 58.464 33.333 8.24 0.00 0.00 2.15
3956 4655 5.064579 CACGCATCAATGTATGTGACCTTTA 59.935 40.000 11.24 0.00 39.26 1.85
3980 4680 8.464404 GTTATAATCTGTCCCCCAAACTAAAAC 58.536 37.037 0.00 0.00 0.00 2.43
4104 4804 0.600557 CACAAAACATAAGCGGGGCA 59.399 50.000 0.00 0.00 0.00 5.36
4105 4805 0.108851 CCACAAAACATAAGCGGGGC 60.109 55.000 0.00 0.00 0.00 5.80
4106 4806 0.530288 CCCACAAAACATAAGCGGGG 59.470 55.000 0.00 0.00 0.00 5.73
4110 4810 7.158099 AGAATTAGACCCACAAAACATAAGC 57.842 36.000 0.00 0.00 0.00 3.09
4157 4862 2.040178 CCTCTACCATTCTTACGGCCT 58.960 52.381 0.00 0.00 0.00 5.19
4327 5037 6.824305 AGGTACCTTCAAGTCATTTTCATG 57.176 37.500 9.21 0.00 0.00 3.07
4349 5059 8.856490 ACTTTGTTAGTTTGCACTCAATTAAG 57.144 30.769 0.00 0.00 31.29 1.85
4589 5300 3.441163 CATGCATGGAAGTTTGGAATCG 58.559 45.455 19.40 0.00 0.00 3.34
5159 5935 1.473434 CCGGTCAAGCTAGGGACAATC 60.473 57.143 13.17 0.00 35.74 2.67
5167 5955 0.532573 TTCTCAGCCGGTCAAGCTAG 59.467 55.000 1.90 0.00 38.95 3.42
5194 5982 1.689582 GCTAGGCTAGGGTGGGTGT 60.690 63.158 22.40 0.00 0.00 4.16
5312 6100 1.979155 TCCCTGCGACTGAGTGAGG 60.979 63.158 0.00 0.00 0.00 3.86
5337 6125 4.508128 GCCGGCGTAGTGCTAGCA 62.508 66.667 14.93 14.93 45.43 3.49
5544 6337 3.099905 ACAATGAGTACTAGAGCCAGCA 58.900 45.455 0.00 0.00 0.00 4.41
5554 6347 3.429547 GGCAGATCGACACAATGAGTACT 60.430 47.826 0.00 0.00 0.00 2.73
5597 6390 2.112190 AGAGAAAATCGGAGGGAGTCC 58.888 52.381 0.00 0.00 42.85 3.85
5657 6455 9.950496 CAGCCTAAGGTAATCTATTATCACAAT 57.050 33.333 0.00 0.00 0.00 2.71
5663 6461 8.917414 TCCATCAGCCTAAGGTAATCTATTAT 57.083 34.615 0.00 0.00 0.00 1.28
5674 6472 4.019174 ACAATGTTTCCATCAGCCTAAGG 58.981 43.478 0.00 0.00 0.00 2.69
5675 6473 5.644644 GAACAATGTTTCCATCAGCCTAAG 58.355 41.667 0.00 0.00 0.00 2.18
5676 6474 4.155826 CGAACAATGTTTCCATCAGCCTAA 59.844 41.667 0.00 0.00 0.00 2.69
5677 6475 3.689161 CGAACAATGTTTCCATCAGCCTA 59.311 43.478 0.00 0.00 0.00 3.93
5678 6476 2.489329 CGAACAATGTTTCCATCAGCCT 59.511 45.455 0.00 0.00 0.00 4.58
5679 6477 2.228822 ACGAACAATGTTTCCATCAGCC 59.771 45.455 0.00 0.00 0.00 4.85
5680 6478 3.559238 ACGAACAATGTTTCCATCAGC 57.441 42.857 0.00 0.00 0.00 4.26
5797 6595 2.092968 GTGAATGGACATGAGGTAGGCA 60.093 50.000 0.00 0.00 0.00 4.75
5886 6684 6.208599 GGATCCAGGTAACAAAGAAATGTTGA 59.791 38.462 6.95 0.00 43.13 3.18
5923 6723 5.353400 ACAGAGCATCATTGTATGTTCAGTG 59.647 40.000 12.06 0.00 38.97 3.66
5924 6724 5.494724 ACAGAGCATCATTGTATGTTCAGT 58.505 37.500 12.06 8.91 38.97 3.41
5969 6769 0.621609 TGCCCTAATTACGCCACCTT 59.378 50.000 0.00 0.00 0.00 3.50
5977 6777 6.263168 ACTGCAAATATCACTGCCCTAATTAC 59.737 38.462 0.00 0.00 37.79 1.89
6030 6830 2.146342 CTGTCAGGGACACATTCACAC 58.854 52.381 0.00 0.00 37.67 3.82
6093 6900 1.070786 GTCTCCAGGGAACGCAACA 59.929 57.895 0.00 0.00 0.00 3.33
6106 6913 7.868415 GTGTGTAGACCATTATAATGAGTCTCC 59.132 40.741 31.42 25.93 41.59 3.71
6115 6922 8.991783 ACTAGCTAGTGTGTAGACCATTATAA 57.008 34.615 25.52 0.00 34.72 0.98
6195 7071 7.001073 GCTCAACCCCTAGATGAAAGATTATT 58.999 38.462 0.00 0.00 0.00 1.40
6233 7113 6.036083 CAGTGCGTTTGCTATGATTTACTAGT 59.964 38.462 0.00 0.00 43.34 2.57
6342 7222 0.667792 GACGTTGTCCTCTGTCCTGC 60.668 60.000 0.00 0.00 0.00 4.85
6777 7657 6.761731 ATTCTAATTTTGCTCTCTCGATCG 57.238 37.500 9.36 9.36 0.00 3.69
6778 7658 9.469807 TCTTATTCTAATTTTGCTCTCTCGATC 57.530 33.333 0.00 0.00 0.00 3.69
6779 7659 9.823647 TTCTTATTCTAATTTTGCTCTCTCGAT 57.176 29.630 0.00 0.00 0.00 3.59
6780 7660 9.653287 TTTCTTATTCTAATTTTGCTCTCTCGA 57.347 29.630 0.00 0.00 0.00 4.04
7150 8054 1.139520 GTTTGGATGGCGGTCATGC 59.860 57.895 7.18 7.18 43.44 4.06
7258 8162 2.368548 AGCCACTGCGTTGATCCATATA 59.631 45.455 0.00 0.00 44.33 0.86
7379 8283 1.792367 CGAAACAGCGAGACACATTCA 59.208 47.619 0.00 0.00 0.00 2.57
7425 8329 5.062934 CCGAATTCTGTCAGCACGTTATTTA 59.937 40.000 3.52 0.00 0.00 1.40
7544 8448 7.970102 ACAGGACCTACAAGATGTAGTTTTTA 58.030 34.615 14.51 0.00 46.68 1.52
7577 8481 1.999648 AAGGACAATCTGGCAAAGCA 58.000 45.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.