Multiple sequence alignment - TraesCS1A01G372400

Loading Multiple Alignment...

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 TraesCS1A01G372400 chr1A 100.000 5518 0 0 1 5518 548945886 548940369 0.000000e+00 10190.0
1 TraesCS1A01G372400 chr1B 90.539 4672 332 49 182 4806 625572681 625568073 0.000000e+00 6078.0
2 TraesCS1A01G372400 chr1B 90.797 3336 196 41 1365 4659 625508626 625505361 0.000000e+00 4357.0
3 TraesCS1A01G372400 chr1D 91.958 4290 238 51 550 4806 455085521 455081306 0.000000e+00 5912.0
4 TraesCS1A01G372400 chr7A 96.503 715 24 1 4804 5518 729272376 729271663 0.000000e+00 1181.0
5 TraesCS1A01G372400 chr7A 96.084 715 26 2 4803 5516 735502541 735503254 0.000000e+00 1164.0
6 TraesCS1A01G372400 chr7A 95.938 714 27 2 4806 5518 27948976 27948264 0.000000e+00 1157.0
7 TraesCS1A01G372400 chr7A 95.798 714 30 0 4805 5518 527992946 527993659 0.000000e+00 1153.0
8 TraesCS1A01G372400 chr7A 89.600 125 13 0 1329 1453 643653589 643653465 5.720000e-35 159.0
9 TraesCS1A01G372400 chr3D 95.098 714 32 2 4805 5518 14531972 14532682 0.000000e+00 1122.0
10 TraesCS1A01G372400 chr3D 94.515 711 36 2 4806 5516 127297741 127298448 0.000000e+00 1094.0
11 TraesCS1A01G372400 chr3A 96.607 619 19 2 4804 5422 95016987 95017603 0.000000e+00 1026.0
12 TraesCS1A01G372400 chr3A 83.085 201 15 6 19 217 358269909 358269726 1.230000e-36 165.0
13 TraesCS1A01G372400 chr3A 83.085 201 14 8 19 217 630363948 630363766 1.230000e-36 165.0
14 TraesCS1A01G372400 chr3A 86.842 76 8 2 2652 2726 690908555 690908629 3.540000e-12 84.2
15 TraesCS1A01G372400 chr7D 92.113 710 54 2 4807 5516 519238085 519238792 0.000000e+00 1000.0
16 TraesCS1A01G372400 chr7B 91.049 715 59 4 4805 5516 34489167 34488455 0.000000e+00 961.0
17 TraesCS1A01G372400 chr7B 88.470 451 40 6 473 916 596287422 596286977 8.140000e-148 534.0
18 TraesCS1A01G372400 chr7B 97.297 37 1 0 3625 3661 111314090 111314126 4.610000e-06 63.9
19 TraesCS1A01G372400 chr4B 90.022 451 33 6 473 916 236135766 236136211 1.720000e-159 573.0
20 TraesCS1A01G372400 chr4B 88.692 451 39 7 473 916 294099411 294099856 1.750000e-149 540.0
21 TraesCS1A01G372400 chr4B 92.000 125 10 0 1329 1453 237985382 237985258 5.680000e-40 176.0
22 TraesCS1A01G372400 chr4B 80.476 210 22 10 10 217 236135070 236135262 5.760000e-30 143.0
23 TraesCS1A01G372400 chr2B 90.476 126 12 0 1328 1453 190180958 190180833 3.420000e-37 167.0
24 TraesCS1A01G372400 chr5D 95.122 41 2 0 3621 3661 102287142 102287182 1.280000e-06 65.8
25 TraesCS1A01G372400 chr5D 88.889 45 2 2 3629 3671 505994501 505994544 1.000000e-02 52.8
26 TraesCS1A01G372400 chr5A 97.368 38 1 0 3624 3661 97225789 97225752 1.280000e-06 65.8
27 TraesCS1A01G372400 chr5A 97.143 35 1 0 3627 3661 195628454 195628420 5.970000e-05 60.2
28 TraesCS1A01G372400 chr2A 100.000 35 0 0 3622 3656 87855943 87855977 1.280000e-06 65.8
29 TraesCS1A01G372400 chr2A 92.683 41 2 1 3622 3661 678966142 678966182 2.150000e-04 58.4
30 TraesCS1A01G372400 chr4D 94.737 38 2 0 3624 3661 498612885 498612922 5.970000e-05 60.2
31 TraesCS1A01G372400 chr6B 94.737 38 1 1 3624 3661 130944113 130944149 2.150000e-04 58.4


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 TraesCS1A01G372400 chr1A 548940369 548945886 5517 True 10190 10190 100.000 1 5518 1 chr1A.!!$R1 5517
1 TraesCS1A01G372400 chr1B 625568073 625572681 4608 True 6078 6078 90.539 182 4806 1 chr1B.!!$R2 4624
2 TraesCS1A01G372400 chr1B 625505361 625508626 3265 True 4357 4357 90.797 1365 4659 1 chr1B.!!$R1 3294
3 TraesCS1A01G372400 chr1D 455081306 455085521 4215 True 5912 5912 91.958 550 4806 1 chr1D.!!$R1 4256
4 TraesCS1A01G372400 chr7A 729271663 729272376 713 True 1181 1181 96.503 4804 5518 1 chr7A.!!$R3 714
5 TraesCS1A01G372400 chr7A 735502541 735503254 713 False 1164 1164 96.084 4803 5516 1 chr7A.!!$F2 713
6 TraesCS1A01G372400 chr7A 27948264 27948976 712 True 1157 1157 95.938 4806 5518 1 chr7A.!!$R1 712
7 TraesCS1A01G372400 chr7A 527992946 527993659 713 False 1153 1153 95.798 4805 5518 1 chr7A.!!$F1 713
8 TraesCS1A01G372400 chr3D 14531972 14532682 710 False 1122 1122 95.098 4805 5518 1 chr3D.!!$F1 713
9 TraesCS1A01G372400 chr3D 127297741 127298448 707 False 1094 1094 94.515 4806 5516 1 chr3D.!!$F2 710
10 TraesCS1A01G372400 chr3A 95016987 95017603 616 False 1026 1026 96.607 4804 5422 1 chr3A.!!$F1 618
11 TraesCS1A01G372400 chr7D 519238085 519238792 707 False 1000 1000 92.113 4807 5516 1 chr7D.!!$F1 709
12 TraesCS1A01G372400 chr7B 34488455 34489167 712 True 961 961 91.049 4805 5516 1 chr7B.!!$R1 711
13 TraesCS1A01G372400 chr4B 236135070 236136211 1141 False 358 573 85.249 10 916 2 chr4B.!!$F2 906

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
97 100 0.034896 TTGGCCTCACGTTTCTCTCC 59.965 55.000 3.32 0.00 0.00 3.71 F
99 102 0.108567 GGCCTCACGTTTCTCTCCTC 60.109 60.000 0.00 0.00 0.00 3.71 F
272 306 0.111001 GTACGTGCGTGCGACAAATT 60.111 50.000 7.55 0.00 35.59 1.82 F
273 307 0.111045 TACGTGCGTGCGACAAATTG 60.111 50.000 7.55 0.00 35.59 2.32 F
975 1366 0.721718 CTTCGCCCGTTGATTGAGTC 59.278 55.000 0.00 0.00 0.00 3.36 F
1221 1612 1.672030 CATGTTCTCCACTGCCGCA 60.672 57.895 0.00 0.00 0.00 5.69 F
1506 1899 1.909700 ACCAATTGACGCAGGTTGAT 58.090 45.000 7.12 0.00 0.00 2.57 F
3023 3437 0.613260 ATACGAAGGTGGCTTGCAGA 59.387 50.000 0.00 0.00 0.00 4.26 F
4091 4529 0.175760 ACTGTATACCGGCAGCACAG 59.824 55.000 19.05 19.05 41.83 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1715 0.176680 CCTCGTGGAACATCTGGGAG 59.823 60.000 0.00 0.0 44.52 4.30 R
1770 2170 0.535335 GCATCGTCTTCCCTGTACCA 59.465 55.000 0.00 0.0 0.00 3.25 R
2221 2632 4.489306 ACTTAGACAGTAAATGGAGCCC 57.511 45.455 0.00 0.0 31.97 5.19 R
2308 2720 5.877012 GGCATCTTCATCAGAACTTAGACAA 59.123 40.000 0.00 0.0 34.16 3.18 R
2460 2873 3.507411 TGGCCTGACAAGAAGTAGTACT 58.493 45.455 3.32 0.0 0.00 2.73 R
2755 3169 4.958509 TGTTCCGGATGTGTTAGTAAACA 58.041 39.130 4.15 0.0 43.32 2.83 R
3268 3683 2.632028 TCTCCAGCCTGCTCATAAGATC 59.368 50.000 0.00 0.0 0.00 2.75 R
4491 4939 0.102481 AGTACGACATCGCCACCATC 59.898 55.000 0.14 0.0 44.43 3.51 R
5199 5663 0.944386 CGCTACTCTCTGAGGCTCTC 59.056 60.000 16.72 0.0 33.35 3.20 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
26 27 1.140652 CTTCTTCCCCTGCTCCTCATC 59.859 57.143 0.00 0.00 0.00 2.92
31 32 2.506061 CCCTGCTCCTCATCTCCCG 61.506 68.421 0.00 0.00 0.00 5.14
32 33 2.420890 CTGCTCCTCATCTCCCGC 59.579 66.667 0.00 0.00 0.00 6.13
40 41 3.470888 CATCTCCCGCCCGGTCTT 61.471 66.667 0.00 0.00 0.00 3.01
54 57 1.376037 GTCTTTGCTGCGCCTACCT 60.376 57.895 4.18 0.00 0.00 3.08
70 73 2.174319 CCTCTTTTAGCGCGGCTCC 61.174 63.158 8.83 0.00 40.44 4.70
71 74 2.508439 TCTTTTAGCGCGGCTCCG 60.508 61.111 8.83 3.56 40.44 4.63
72 75 2.813908 CTTTTAGCGCGGCTCCGT 60.814 61.111 8.83 0.00 40.44 4.69
73 76 2.357760 TTTTAGCGCGGCTCCGTT 60.358 55.556 8.83 0.00 40.44 4.44
74 77 2.563086 CTTTTAGCGCGGCTCCGTTG 62.563 60.000 8.83 4.44 40.44 4.10
75 78 3.869473 TTTAGCGCGGCTCCGTTGT 62.869 57.895 8.83 0.00 40.44 3.32
76 79 4.789075 TAGCGCGGCTCCGTTGTC 62.789 66.667 8.83 0.90 40.44 3.18
87 90 2.604174 CCGTTGTCGTTGGCCTCAC 61.604 63.158 3.32 0.00 35.01 3.51
97 100 0.034896 TTGGCCTCACGTTTCTCTCC 59.965 55.000 3.32 0.00 0.00 3.71
98 101 0.832135 TGGCCTCACGTTTCTCTCCT 60.832 55.000 3.32 0.00 0.00 3.69
99 102 0.108567 GGCCTCACGTTTCTCTCCTC 60.109 60.000 0.00 0.00 0.00 3.71
100 103 0.892063 GCCTCACGTTTCTCTCCTCT 59.108 55.000 0.00 0.00 0.00 3.69
101 104 1.135228 GCCTCACGTTTCTCTCCTCTC 60.135 57.143 0.00 0.00 0.00 3.20
102 105 1.474879 CCTCACGTTTCTCTCCTCTCC 59.525 57.143 0.00 0.00 0.00 3.71
103 106 2.163509 CTCACGTTTCTCTCCTCTCCA 58.836 52.381 0.00 0.00 0.00 3.86
104 107 2.558795 CTCACGTTTCTCTCCTCTCCAA 59.441 50.000 0.00 0.00 0.00 3.53
109 112 3.181480 CGTTTCTCTCCTCTCCAATCTCC 60.181 52.174 0.00 0.00 0.00 3.71
114 117 1.045350 TCCTCTCCAATCTCCAGCGG 61.045 60.000 0.00 0.00 0.00 5.52
126 129 2.879907 CAGCGGTTGGATTGCCAG 59.120 61.111 0.00 0.00 46.91 4.85
163 166 3.009714 AGGAGGTCGGGGAAAGGC 61.010 66.667 0.00 0.00 0.00 4.35
172 175 4.344865 GGGAAAGGCAGCCACCGA 62.345 66.667 15.80 0.00 33.69 4.69
174 177 3.056328 GAAAGGCAGCCACCGACC 61.056 66.667 15.80 0.00 33.69 4.79
176 179 4.643387 AAGGCAGCCACCGACCAC 62.643 66.667 15.80 0.00 33.69 4.16
271 305 1.489824 GTACGTGCGTGCGACAAAT 59.510 52.632 7.55 0.00 35.59 2.32
272 306 0.111001 GTACGTGCGTGCGACAAATT 60.111 50.000 7.55 0.00 35.59 1.82
273 307 0.111045 TACGTGCGTGCGACAAATTG 60.111 50.000 7.55 0.00 35.59 2.32
278 312 1.852067 GCGTGCGACAAATTGTCCCT 61.852 55.000 19.16 0.00 44.20 4.20
288 322 5.562890 CGACAAATTGTCCCTCTTTTCTTCC 60.563 44.000 19.16 0.00 44.20 3.46
289 323 4.278419 ACAAATTGTCCCTCTTTTCTTCCG 59.722 41.667 0.00 0.00 0.00 4.30
341 386 2.149973 ATGTTGGGGCTCCAGATTTC 57.850 50.000 4.89 0.00 45.04 2.17
425 471 1.228245 TTTTTGCTGCTCCCTCGCT 60.228 52.632 0.00 0.00 0.00 4.93
442 488 3.808728 TCGCTTTTAATCCCCTGATGAG 58.191 45.455 0.00 0.00 0.00 2.90
505 888 5.835113 TCTTGCTGCATTAATTTCCTACC 57.165 39.130 1.84 0.00 0.00 3.18
509 892 4.398988 TGCTGCATTAATTTCCTACCACAG 59.601 41.667 0.00 0.00 0.00 3.66
512 895 6.458342 GCTGCATTAATTTCCTACCACAGTAC 60.458 42.308 0.00 0.00 0.00 2.73
515 898 7.120579 TGCATTAATTTCCTACCACAGTACTTG 59.879 37.037 0.00 0.00 0.00 3.16
557 940 6.208599 TGTTTCTGGTCAGTTTAATTGATCCC 59.791 38.462 0.00 0.00 0.00 3.85
563 948 8.096621 TGGTCAGTTTAATTGATCCCAGTATA 57.903 34.615 0.00 0.00 0.00 1.47
575 960 2.527057 TCCCAGTATATCCCTTGGACCT 59.473 50.000 0.00 0.00 32.98 3.85
579 964 5.013183 CCCAGTATATCCCTTGGACCTAAAG 59.987 48.000 0.00 0.00 32.98 1.85
659 1044 1.399714 TGACACGACACCTTGAGAGT 58.600 50.000 0.00 0.00 0.00 3.24
803 1189 2.133281 TCCAAATCACATGCTCCCAG 57.867 50.000 0.00 0.00 0.00 4.45
883 1273 3.751246 CCAACACATGGCCCAGCG 61.751 66.667 0.00 0.00 43.80 5.18
927 1317 7.276438 CCTATTTGTTTTCTAATGGCTTCTTGC 59.724 37.037 0.00 0.00 41.94 4.01
975 1366 0.721718 CTTCGCCCGTTGATTGAGTC 59.278 55.000 0.00 0.00 0.00 3.36
1221 1612 1.672030 CATGTTCTCCACTGCCGCA 60.672 57.895 0.00 0.00 0.00 5.69
1242 1633 5.030936 GCAGCTGATTCGATTAAAGGTTTC 58.969 41.667 20.43 0.00 0.00 2.78
1254 1645 8.508875 TCGATTAAAGGTTTCATTTCTGTTACC 58.491 33.333 0.00 0.00 0.00 2.85
1258 1650 9.810545 TTAAAGGTTTCATTTCTGTTACCTTTG 57.189 29.630 21.17 0.00 45.63 2.77
1259 1651 6.405278 AGGTTTCATTTCTGTTACCTTTGG 57.595 37.500 0.00 0.00 35.28 3.28
1264 1656 5.324409 TCATTTCTGTTACCTTTGGATGCT 58.676 37.500 0.00 0.00 0.00 3.79
1267 1659 2.301870 TCTGTTACCTTTGGATGCTCGT 59.698 45.455 0.00 0.00 0.00 4.18
1273 1665 2.280628 CCTTTGGATGCTCGTAACCTC 58.719 52.381 0.00 0.00 0.00 3.85
1278 1670 3.596214 TGGATGCTCGTAACCTCTTTTC 58.404 45.455 0.00 0.00 0.00 2.29
1279 1671 3.007506 TGGATGCTCGTAACCTCTTTTCA 59.992 43.478 0.00 0.00 0.00 2.69
1280 1672 4.192317 GGATGCTCGTAACCTCTTTTCAT 58.808 43.478 0.00 0.00 0.00 2.57
1281 1673 4.034510 GGATGCTCGTAACCTCTTTTCATG 59.965 45.833 0.00 0.00 0.00 3.07
1282 1674 4.002906 TGCTCGTAACCTCTTTTCATGT 57.997 40.909 0.00 0.00 0.00 3.21
1283 1675 4.385825 TGCTCGTAACCTCTTTTCATGTT 58.614 39.130 0.00 0.00 0.00 2.71
1284 1676 4.451096 TGCTCGTAACCTCTTTTCATGTTC 59.549 41.667 0.00 0.00 0.00 3.18
1285 1677 4.691216 GCTCGTAACCTCTTTTCATGTTCT 59.309 41.667 0.00 0.00 0.00 3.01
1286 1678 5.163943 GCTCGTAACCTCTTTTCATGTTCTC 60.164 44.000 0.00 0.00 0.00 2.87
1287 1679 5.849510 TCGTAACCTCTTTTCATGTTCTCA 58.150 37.500 0.00 0.00 0.00 3.27
1294 1686 7.000472 ACCTCTTTTCATGTTCTCATTTCTGA 59.000 34.615 0.00 0.00 31.15 3.27
1308 1700 4.400251 TCATTTCTGATGGAGGCATTTGAC 59.600 41.667 0.00 0.00 0.00 3.18
1323 1715 6.150140 AGGCATTTGACTCAACTTGATTACTC 59.850 38.462 5.46 0.00 0.00 2.59
1324 1716 6.150140 GGCATTTGACTCAACTTGATTACTCT 59.850 38.462 5.46 0.00 0.00 3.24
1326 1718 7.625185 GCATTTGACTCAACTTGATTACTCTCC 60.625 40.741 5.46 0.00 0.00 3.71
1391 1783 4.882427 AGAATTGCATCAGGAGATCTTGTG 59.118 41.667 0.00 0.00 30.20 3.33
1463 1856 6.441274 TCTTGCATGATTTCTTGAGTGTTTC 58.559 36.000 0.00 0.00 0.00 2.78
1464 1857 5.125100 TGCATGATTTCTTGAGTGTTTCC 57.875 39.130 0.00 0.00 0.00 3.13
1506 1899 1.909700 ACCAATTGACGCAGGTTGAT 58.090 45.000 7.12 0.00 0.00 2.57
1622 2015 2.477863 GGTAAGCGCGATTTGAAAGCAT 60.478 45.455 17.40 0.00 0.00 3.79
1648 2041 3.906720 TCACATAGTAAGCAAGGGACC 57.093 47.619 0.00 0.00 0.00 4.46
1770 2170 5.731678 GGGATTGTATCTATATGGAGGGGTT 59.268 44.000 0.00 0.00 0.00 4.11
1877 2277 7.093814 TGTGCTGCTTTAAGATAACCAAATCAT 60.094 33.333 0.00 0.00 0.00 2.45
1947 2347 2.037902 TGGCGGTGTATCAGTTCAGAAA 59.962 45.455 0.00 0.00 0.00 2.52
2022 2422 5.699001 ACAGTTCACATTCGTATGCAACTAA 59.301 36.000 15.31 0.00 36.65 2.24
2039 2439 5.122711 GCAACTAAACAGGCCGAAGTTATTA 59.877 40.000 10.91 2.14 0.00 0.98
2046 2446 7.492352 AACAGGCCGAAGTTATTATATTCAC 57.508 36.000 9.14 0.00 0.00 3.18
2156 2567 9.516314 CATCAATTTAGTCGTACATACTGAAGA 57.484 33.333 7.88 2.64 0.00 2.87
2221 2632 1.945394 AGAAGCAGTTGACAAGCTGTG 59.055 47.619 14.90 0.00 38.86 3.66
2275 2687 3.751518 ACTGTTAGGAACCAATGGTGAC 58.248 45.455 5.34 1.57 35.34 3.67
2460 2873 6.840527 TCAATAATCCATTGCTATCCTGACA 58.159 36.000 0.00 0.00 43.28 3.58
2725 3139 8.908786 ATGAGTTTATGGTATGTGTATCCTTG 57.091 34.615 0.00 0.00 0.00 3.61
2748 3162 7.307493 TGCTGTGATAGTTGTATTAGCTTTG 57.693 36.000 0.00 0.00 0.00 2.77
2755 3169 9.177608 TGATAGTTGTATTAGCTTTGAATGCTT 57.822 29.630 10.92 0.00 41.46 3.91
2760 3174 9.405587 GTTGTATTAGCTTTGAATGCTTGTTTA 57.594 29.630 10.92 0.00 41.46 2.01
2773 3187 3.749088 TGCTTGTTTACTAACACATCCGG 59.251 43.478 0.00 0.00 43.66 5.14
2863 3277 1.724654 GCAAAGGCGTTGTATGTGACG 60.725 52.381 14.46 0.00 39.63 4.35
2873 3287 4.090786 CGTTGTATGTGACGACTGCATTTA 59.909 41.667 0.00 0.00 39.99 1.40
2874 3288 5.220397 CGTTGTATGTGACGACTGCATTTAT 60.220 40.000 0.00 0.00 39.99 1.40
2950 3364 9.005777 AGTATTTTGCATTGATTCTTTTGCATT 57.994 25.926 8.74 2.85 43.91 3.56
3023 3437 0.613260 ATACGAAGGTGGCTTGCAGA 59.387 50.000 0.00 0.00 0.00 4.26
3268 3683 5.182001 AGTTTTCCCTTTCATGACATCTTCG 59.818 40.000 0.00 0.00 0.00 3.79
3314 3729 9.338291 GAAGGTTTCTATTTTATTGGAAACGAC 57.662 33.333 0.00 0.00 44.61 4.34
3383 3798 3.974642 AGGAACCTACTCCTCAAACAGTT 59.025 43.478 0.00 0.00 42.53 3.16
3439 3854 7.496346 TGGAAGTTAGATATTCAGAGTTGGT 57.504 36.000 0.00 0.00 0.00 3.67
3441 3856 7.824289 TGGAAGTTAGATATTCAGAGTTGGTTG 59.176 37.037 0.00 0.00 0.00 3.77
3470 3885 6.000891 TGTTTCATGTAATCACTCTGCAAC 57.999 37.500 0.00 0.00 0.00 4.17
3512 3928 4.023137 CCACTGGGAGCAAATGGG 57.977 61.111 0.00 0.00 35.59 4.00
3634 4053 7.769044 TCAGTTAGGGATTACAAAATGCTACTC 59.231 37.037 0.00 0.00 34.12 2.59
3635 4054 7.012421 CAGTTAGGGATTACAAAATGCTACTCC 59.988 40.741 0.00 0.00 34.12 3.85
3636 4055 4.793201 AGGGATTACAAAATGCTACTCCC 58.207 43.478 0.00 0.00 34.12 4.30
3637 4056 4.478686 AGGGATTACAAAATGCTACTCCCT 59.521 41.667 0.92 0.92 39.03 4.20
3638 4057 4.822350 GGGATTACAAAATGCTACTCCCTC 59.178 45.833 0.00 0.00 34.12 4.30
3639 4058 4.822350 GGATTACAAAATGCTACTCCCTCC 59.178 45.833 0.00 0.00 31.18 4.30
3640 4059 2.403252 ACAAAATGCTACTCCCTCCG 57.597 50.000 0.00 0.00 0.00 4.63
3641 4060 1.628846 ACAAAATGCTACTCCCTCCGT 59.371 47.619 0.00 0.00 0.00 4.69
3642 4061 2.835764 ACAAAATGCTACTCCCTCCGTA 59.164 45.455 0.00 0.00 0.00 4.02
3643 4062 3.262405 ACAAAATGCTACTCCCTCCGTAA 59.738 43.478 0.00 0.00 0.00 3.18
3644 4063 4.258543 CAAAATGCTACTCCCTCCGTAAA 58.741 43.478 0.00 0.00 0.00 2.01
3645 4064 3.821421 AATGCTACTCCCTCCGTAAAG 57.179 47.619 0.00 0.00 0.00 1.85
3646 4065 2.519771 TGCTACTCCCTCCGTAAAGA 57.480 50.000 0.00 0.00 0.00 2.52
3647 4066 2.811410 TGCTACTCCCTCCGTAAAGAA 58.189 47.619 0.00 0.00 0.00 2.52
3648 4067 3.167485 TGCTACTCCCTCCGTAAAGAAA 58.833 45.455 0.00 0.00 0.00 2.52
3649 4068 3.773119 TGCTACTCCCTCCGTAAAGAAAT 59.227 43.478 0.00 0.00 0.00 2.17
3650 4069 4.957954 TGCTACTCCCTCCGTAAAGAAATA 59.042 41.667 0.00 0.00 0.00 1.40
3651 4070 5.601313 TGCTACTCCCTCCGTAAAGAAATAT 59.399 40.000 0.00 0.00 0.00 1.28
3652 4071 6.779049 TGCTACTCCCTCCGTAAAGAAATATA 59.221 38.462 0.00 0.00 0.00 0.86
3653 4072 7.288389 TGCTACTCCCTCCGTAAAGAAATATAA 59.712 37.037 0.00 0.00 0.00 0.98
3654 4073 7.813627 GCTACTCCCTCCGTAAAGAAATATAAG 59.186 40.741 0.00 0.00 0.00 1.73
3655 4074 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3656 4075 7.724287 ACTCCCTCCGTAAAGAAATATAAGAC 58.276 38.462 0.00 0.00 0.00 3.01
3657 4076 7.059202 TCCCTCCGTAAAGAAATATAAGACC 57.941 40.000 0.00 0.00 0.00 3.85
3661 4080 8.137437 CCTCCGTAAAGAAATATAAGACCGTTA 58.863 37.037 0.00 0.00 0.00 3.18
3672 4091 8.833231 AATATAAGACCGTTAATGTGATCTGG 57.167 34.615 0.00 0.00 0.00 3.86
3796 4215 5.794945 GTCACATTGGTTGATGTATGTTTCG 59.205 40.000 0.00 0.00 38.15 3.46
3817 4236 4.158025 TCGTCTTTCCTTAGTCTGTCATCC 59.842 45.833 0.00 0.00 0.00 3.51
3831 4251 7.886338 AGTCTGTCATCCTTTTGTTTTAATCC 58.114 34.615 0.00 0.00 0.00 3.01
3841 4262 6.295292 CCTTTTGTTTTAATCCTGCCTTAGCT 60.295 38.462 0.00 0.00 40.80 3.32
3902 4330 3.885297 ACACCTTGAAGACCTGAAACATG 59.115 43.478 0.00 0.00 0.00 3.21
3905 4333 3.508793 CCTTGAAGACCTGAAACATGCAT 59.491 43.478 0.00 0.00 0.00 3.96
3929 4358 4.025647 GCTTGGCAGATATACACTTTCGTC 60.026 45.833 0.00 0.00 0.00 4.20
3934 4363 6.127563 TGGCAGATATACACTTTCGTCAGTAA 60.128 38.462 0.00 0.00 0.00 2.24
3998 4436 5.360144 TCCTGAAGCTAGTGTTGACCTATAC 59.640 44.000 0.00 0.00 0.00 1.47
4091 4529 0.175760 ACTGTATACCGGCAGCACAG 59.824 55.000 19.05 19.05 41.83 3.66
4113 4551 0.888619 AATCTTGTCTCTGACGGCGA 59.111 50.000 16.62 0.00 34.95 5.54
4153 4591 2.097038 CGAGAACAAGGCGAGGCTG 61.097 63.158 0.00 0.00 0.00 4.85
4195 4633 3.189702 AGCCGATAGAGCTATTCGAGAAC 59.810 47.826 12.50 2.06 40.13 3.01
4196 4634 3.058155 GCCGATAGAGCTATTCGAGAACA 60.058 47.826 12.50 0.00 39.76 3.18
4324 4762 4.906065 TCGTACGATTAGCAGGTAATGT 57.094 40.909 15.28 10.11 30.93 2.71
4328 4766 4.481368 ACGATTAGCAGGTAATGTGGAA 57.519 40.909 9.66 0.00 30.93 3.53
4329 4767 5.036117 ACGATTAGCAGGTAATGTGGAAT 57.964 39.130 9.66 0.00 30.93 3.01
4338 4776 5.640732 CAGGTAATGTGGAATGTGCTTTAC 58.359 41.667 0.00 0.00 0.00 2.01
4339 4777 4.705023 AGGTAATGTGGAATGTGCTTTACC 59.295 41.667 0.00 0.00 40.35 2.85
4365 4807 9.941325 CAGGTTATATCAGCTCTTATTCTGAAT 57.059 33.333 8.14 8.14 41.96 2.57
4491 4939 2.360350 AACAGCCCCTGCACGATG 60.360 61.111 0.00 0.00 41.13 3.84
4496 4944 2.591753 CCCCTGCACGATGATGGT 59.408 61.111 0.00 0.00 0.00 3.55
4527 4975 0.405585 ACTTGCATAAGTGGCAGGGT 59.594 50.000 0.00 0.00 45.17 4.34
4542 4990 2.028748 GCAGGGTTTCATGTGCAAAGAT 60.029 45.455 0.00 0.00 35.91 2.40
4577 5031 7.827729 AGTTTTGTTATATCTATTATCCCGCCC 59.172 37.037 0.00 0.00 0.00 6.13
4585 5042 0.907704 ATTATCCCGCCCGGCTATGA 60.908 55.000 8.05 1.25 0.00 2.15
4599 5056 3.244700 CGGCTATGAAGGAATGGGAGAAT 60.245 47.826 0.00 0.00 0.00 2.40
4606 5063 2.460669 AGGAATGGGAGAATTGTTGGC 58.539 47.619 0.00 0.00 0.00 4.52
4701 5158 7.649306 GCAAAAATGTCACACTTGTAGAGAATT 59.351 33.333 0.00 0.00 0.00 2.17
4708 5165 5.758296 TCACACTTGTAGAGAATTTGTGTCC 59.242 40.000 0.00 0.00 35.38 4.02
4722 5179 4.764050 TTGTGTCCTGTCTTACTGGAAA 57.236 40.909 7.18 0.00 45.80 3.13
4773 5230 3.355626 TCTTCAGATAGCGAACGATGG 57.644 47.619 0.00 0.00 0.00 3.51
4777 5234 2.029918 TCAGATAGCGAACGATGGGATG 60.030 50.000 0.00 0.00 0.00 3.51
4780 5237 2.693250 TAGCGAACGATGGGATGCCG 62.693 60.000 0.00 0.00 0.00 5.69
4800 5257 3.873952 CCGAGAATTCAGAGATTCCAACC 59.126 47.826 8.44 0.00 36.84 3.77
4893 5357 2.406596 ACAACACACACCCTTTACGT 57.593 45.000 0.00 0.00 0.00 3.57
4911 5375 3.674997 ACGTGACATGGCAATTACTCTT 58.325 40.909 0.58 0.00 0.00 2.85
5035 5499 4.389077 CCGAAATACTCTTGCGTTTCTCTT 59.611 41.667 0.00 0.00 0.00 2.85
5089 5553 2.282462 CGCCTTGGCCTTCCTGTT 60.282 61.111 3.32 0.00 0.00 3.16
5199 5663 3.533606 ATCTCTGAATGACCAACCTCG 57.466 47.619 0.00 0.00 0.00 4.63
5474 5938 2.348998 CCAGAGGCCGAGTGCTTT 59.651 61.111 0.00 0.00 40.92 3.51
5506 5970 4.993584 GTCATCATCGGTAAGCTCATCAAT 59.006 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.033699 GAGCAGGGGAAGAAGGCAAT 60.034 55.000 0.00 0.00 0.00 3.56
4 5 2.264120 GAGGAGCAGGGGAAGAAGGC 62.264 65.000 0.00 0.00 0.00 4.35
5 6 0.911525 TGAGGAGCAGGGGAAGAAGG 60.912 60.000 0.00 0.00 0.00 3.46
6 7 1.140652 GATGAGGAGCAGGGGAAGAAG 59.859 57.143 0.00 0.00 0.00 2.85
7 8 1.207791 GATGAGGAGCAGGGGAAGAA 58.792 55.000 0.00 0.00 0.00 2.52
8 9 0.341258 AGATGAGGAGCAGGGGAAGA 59.659 55.000 0.00 0.00 0.00 2.87
13 14 2.506061 CGGGAGATGAGGAGCAGGG 61.506 68.421 0.00 0.00 0.00 4.45
17 18 3.934962 GGGCGGGAGATGAGGAGC 61.935 72.222 0.00 0.00 0.00 4.70
43 46 1.291132 GCTAAAAGAGGTAGGCGCAG 58.709 55.000 10.83 0.00 0.00 5.18
47 50 1.152383 CCGCGCTAAAAGAGGTAGGC 61.152 60.000 5.56 0.00 0.00 3.93
54 57 2.508439 CGGAGCCGCGCTAAAAGA 60.508 61.111 5.56 0.00 39.88 2.52
70 73 2.935955 GTGAGGCCAACGACAACG 59.064 61.111 5.01 0.00 45.75 4.10
71 74 1.433837 AACGTGAGGCCAACGACAAC 61.434 55.000 30.60 7.76 0.00 3.32
72 75 0.745128 AAACGTGAGGCCAACGACAA 60.745 50.000 30.60 0.00 0.00 3.18
73 76 1.153329 AAACGTGAGGCCAACGACA 60.153 52.632 30.60 9.71 0.00 4.35
74 77 0.878961 AGAAACGTGAGGCCAACGAC 60.879 55.000 30.60 21.24 0.00 4.34
75 78 0.599204 GAGAAACGTGAGGCCAACGA 60.599 55.000 30.60 0.00 0.00 3.85
76 79 0.600255 AGAGAAACGTGAGGCCAACG 60.600 55.000 24.52 24.52 0.00 4.10
77 80 1.149148 GAGAGAAACGTGAGGCCAAC 58.851 55.000 5.01 1.14 0.00 3.77
87 90 3.181480 GGAGATTGGAGAGGAGAGAAACG 60.181 52.174 0.00 0.00 0.00 3.60
97 100 0.539051 AACCGCTGGAGATTGGAGAG 59.461 55.000 1.50 0.00 0.00 3.20
98 101 0.250234 CAACCGCTGGAGATTGGAGA 59.750 55.000 1.50 0.00 0.00 3.71
99 102 2.772739 CAACCGCTGGAGATTGGAG 58.227 57.895 1.50 0.00 0.00 3.86
109 112 2.703798 CCTGGCAATCCAACCGCTG 61.704 63.158 0.00 0.00 42.91 5.18
114 117 3.451894 CGGCCCTGGCAATCCAAC 61.452 66.667 10.86 0.00 42.91 3.77
171 174 4.368543 GTGGACGGACGGGTGGTC 62.369 72.222 0.00 0.00 45.31 4.02
217 220 4.436998 AGAAGCCGGCGTTCCTCG 62.437 66.667 23.20 0.00 43.12 4.63
246 280 3.034370 GCACGCACGTACCCAATGG 62.034 63.158 0.00 0.00 37.80 3.16
256 290 1.320382 GACAATTTGTCGCACGCACG 61.320 55.000 13.42 0.00 37.67 5.34
271 305 3.473625 GAACGGAAGAAAAGAGGGACAA 58.526 45.455 0.00 0.00 0.00 3.18
272 306 2.224450 GGAACGGAAGAAAAGAGGGACA 60.224 50.000 0.00 0.00 0.00 4.02
273 307 2.424557 GGAACGGAAGAAAAGAGGGAC 58.575 52.381 0.00 0.00 0.00 4.46
341 386 1.408822 GGGAGCAGTTACCAATCCAGG 60.409 57.143 0.00 0.00 0.00 4.45
349 394 1.079336 GTCGGTGGGAGCAGTTACC 60.079 63.158 0.00 0.00 0.00 2.85
414 459 1.408266 GGGATTAAAAGCGAGGGAGCA 60.408 52.381 0.00 0.00 40.15 4.26
415 460 1.309950 GGGATTAAAAGCGAGGGAGC 58.690 55.000 0.00 0.00 37.41 4.70
417 462 1.211949 CAGGGGATTAAAAGCGAGGGA 59.788 52.381 0.00 0.00 0.00 4.20
491 874 8.786826 TCAAGTACTGTGGTAGGAAATTAATG 57.213 34.615 0.00 0.00 0.00 1.90
505 888 3.928992 ACTCGCATCAATCAAGTACTGTG 59.071 43.478 0.00 0.00 0.00 3.66
509 892 4.091509 ACGAAACTCGCATCAATCAAGTAC 59.908 41.667 0.00 0.00 45.12 2.73
512 895 3.120546 ACACGAAACTCGCATCAATCAAG 60.121 43.478 0.00 0.00 45.12 3.02
515 898 3.455619 AACACGAAACTCGCATCAATC 57.544 42.857 0.00 0.00 45.12 2.67
557 940 5.513267 GCCTTTAGGTCCAAGGGATATACTG 60.513 48.000 9.50 0.00 41.23 2.74
563 948 1.566231 CTGCCTTTAGGTCCAAGGGAT 59.434 52.381 9.50 0.00 40.63 3.85
724 1110 0.034089 AGGGTGGCCAGTAATCAAGC 60.034 55.000 5.11 0.00 0.00 4.01
803 1189 9.561270 GAAAATCTCAAAAGTAAACTGATAGGC 57.439 33.333 0.00 0.00 0.00 3.93
927 1317 5.525378 GGAACCTGTAACAATCATAGCAGAG 59.475 44.000 0.00 0.00 0.00 3.35
975 1366 2.617308 TCTCGATGTACTTTCTAGGCCG 59.383 50.000 0.00 0.00 0.00 6.13
1116 1507 0.992802 GTGAACGAGATGCGGAACTC 59.007 55.000 4.02 4.02 46.49 3.01
1152 1543 5.518847 CACAAATCTGCCATGTTCATCATTC 59.481 40.000 0.00 0.00 34.09 2.67
1221 1612 7.396540 AATGAAACCTTTAATCGAATCAGCT 57.603 32.000 0.00 0.00 0.00 4.24
1242 1633 5.644644 GAGCATCCAAAGGTAACAGAAATG 58.355 41.667 0.00 0.00 41.41 2.32
1254 1645 3.252974 AGAGGTTACGAGCATCCAAAG 57.747 47.619 0.00 0.00 0.00 2.77
1258 1650 3.596214 TGAAAAGAGGTTACGAGCATCC 58.404 45.455 0.00 0.00 0.00 3.51
1259 1651 4.631813 ACATGAAAAGAGGTTACGAGCATC 59.368 41.667 0.00 0.00 0.00 3.91
1264 1656 5.849510 TGAGAACATGAAAAGAGGTTACGA 58.150 37.500 0.00 0.00 0.00 3.43
1267 1659 8.786898 CAGAAATGAGAACATGAAAAGAGGTTA 58.213 33.333 0.00 0.00 36.79 2.85
1273 1665 7.823665 TCCATCAGAAATGAGAACATGAAAAG 58.176 34.615 0.00 0.00 36.79 2.27
1278 1670 4.036498 GCCTCCATCAGAAATGAGAACATG 59.964 45.833 0.00 0.00 36.79 3.21
1279 1671 4.205587 GCCTCCATCAGAAATGAGAACAT 58.794 43.478 0.00 0.00 38.50 2.71
1280 1672 3.009363 TGCCTCCATCAGAAATGAGAACA 59.991 43.478 0.00 0.00 0.00 3.18
1281 1673 3.614092 TGCCTCCATCAGAAATGAGAAC 58.386 45.455 0.00 0.00 0.00 3.01
1282 1674 4.515028 ATGCCTCCATCAGAAATGAGAA 57.485 40.909 0.00 0.00 0.00 2.87
1283 1675 4.515028 AATGCCTCCATCAGAAATGAGA 57.485 40.909 0.00 0.00 0.00 3.27
1284 1676 4.643334 TCAAATGCCTCCATCAGAAATGAG 59.357 41.667 0.00 0.00 0.00 2.90
1285 1677 4.400251 GTCAAATGCCTCCATCAGAAATGA 59.600 41.667 0.00 0.00 0.00 2.57
1286 1678 4.401519 AGTCAAATGCCTCCATCAGAAATG 59.598 41.667 0.00 0.00 0.00 2.32
1287 1679 4.607239 AGTCAAATGCCTCCATCAGAAAT 58.393 39.130 0.00 0.00 0.00 2.17
1294 1686 3.446442 AGTTGAGTCAAATGCCTCCAT 57.554 42.857 7.25 0.00 0.00 3.41
1308 1700 5.667539 TCTGGGAGAGTAATCAAGTTGAG 57.332 43.478 11.91 0.00 0.00 3.02
1323 1715 0.176680 CCTCGTGGAACATCTGGGAG 59.823 60.000 0.00 0.00 44.52 4.30
1324 1716 0.544357 ACCTCGTGGAACATCTGGGA 60.544 55.000 11.17 0.00 44.52 4.37
1326 1718 3.143675 CACCTCGTGGAACATCTGG 57.856 57.895 11.17 0.00 44.52 3.86
1349 1741 7.308469 GCAATTCTCTTCTCATATTCCACCATC 60.308 40.741 0.00 0.00 0.00 3.51
1391 1783 3.567478 ACCTGAAAGCTATCACCATCC 57.433 47.619 0.00 0.00 0.00 3.51
1463 1856 3.601443 AGTTCAGAAGAATCGTCAGGG 57.399 47.619 0.00 0.00 35.92 4.45
1464 1857 5.931441 AAAAGTTCAGAAGAATCGTCAGG 57.069 39.130 0.00 0.00 35.92 3.86
1506 1899 4.941263 AGCCTTTGTAATTGCTGAATCGTA 59.059 37.500 0.00 0.00 31.70 3.43
1622 2015 6.374333 GTCCCTTGCTTACTATGTGAATTCAA 59.626 38.462 10.35 1.23 0.00 2.69
1648 2041 9.388463 CCACTATGGTTAGGATCACTCTGATCG 62.388 48.148 6.22 0.00 42.29 3.69
1770 2170 0.535335 GCATCGTCTTCCCTGTACCA 59.465 55.000 0.00 0.00 0.00 3.25
1877 2277 5.820131 CACTAATGTGCACTTTCAAGTTCA 58.180 37.500 20.08 1.99 34.87 3.18
1988 2388 6.989437 ACGAATGTGAACTGTTATATGAACG 58.011 36.000 0.00 0.00 0.00 3.95
2022 2422 7.280356 AGTGAATATAATAACTTCGGCCTGTT 58.720 34.615 0.00 6.03 0.00 3.16
2039 2439 8.408043 TGTGAAGACCATTGAAAAGTGAATAT 57.592 30.769 0.00 0.00 0.00 1.28
2080 2481 6.544197 ACTTGTGTGTATTGGTTTCACATGTA 59.456 34.615 0.00 0.00 41.76 2.29
2090 2491 6.823497 ACTGTTACTACTTGTGTGTATTGGT 58.177 36.000 0.00 0.00 0.00 3.67
2133 2544 8.912787 AGTCTTCAGTATGTACGACTAAATTG 57.087 34.615 0.00 0.00 36.66 2.32
2156 2567 7.658525 ATGACTGTCTATGAAGAGATCAAGT 57.341 36.000 9.51 0.00 42.54 3.16
2221 2632 4.489306 ACTTAGACAGTAAATGGAGCCC 57.511 45.455 0.00 0.00 31.97 5.19
2308 2720 5.877012 GGCATCTTCATCAGAACTTAGACAA 59.123 40.000 0.00 0.00 34.16 3.18
2460 2873 3.507411 TGGCCTGACAAGAAGTAGTACT 58.493 45.455 3.32 0.00 0.00 2.73
2572 2986 8.821686 AGATCTAGACTGAAGAAGAAAGATGA 57.178 34.615 0.00 0.00 0.00 2.92
2725 3139 7.539712 TCAAAGCTAATACAACTATCACAGC 57.460 36.000 0.00 0.00 0.00 4.40
2748 3162 6.021596 CGGATGTGTTAGTAAACAAGCATTC 58.978 40.000 0.00 0.00 46.84 2.67
2755 3169 4.958509 TGTTCCGGATGTGTTAGTAAACA 58.041 39.130 4.15 0.00 43.32 2.83
2760 3174 5.416271 AAGTATGTTCCGGATGTGTTAGT 57.584 39.130 4.15 0.00 0.00 2.24
2773 3187 8.773404 ACATCAGTTACCTGTAAAGTATGTTC 57.227 34.615 0.00 0.00 39.82 3.18
2863 3277 9.185192 GTGCCATAAGAAAATATAAATGCAGTC 57.815 33.333 0.00 0.00 0.00 3.51
2873 3287 8.416329 GGTTGATTCAGTGCCATAAGAAAATAT 58.584 33.333 0.00 0.00 0.00 1.28
2874 3288 7.615365 AGGTTGATTCAGTGCCATAAGAAAATA 59.385 33.333 6.72 0.00 0.00 1.40
3023 3437 8.414003 GTCAATGAAAGGTAAGAAAAGGTTTCT 58.586 33.333 0.00 0.00 0.00 2.52
3268 3683 2.632028 TCTCCAGCCTGCTCATAAGATC 59.368 50.000 0.00 0.00 0.00 2.75
3314 3729 7.246674 TTTCTGTTTAAGAACTGTACTGCAG 57.753 36.000 13.48 13.48 44.77 4.41
3439 3854 8.196771 AGAGTGATTACATGAAACAAAAAGCAA 58.803 29.630 0.00 0.00 0.00 3.91
3441 3856 7.358683 GCAGAGTGATTACATGAAACAAAAAGC 60.359 37.037 0.00 0.00 0.00 3.51
3470 3885 3.201290 CTGCATAGCCAAGGTTCAGTAG 58.799 50.000 0.00 0.00 0.00 2.57
3512 3928 6.012658 TCTTCAAACTGGAAATATGCACAC 57.987 37.500 0.00 0.00 0.00 3.82
3600 4016 5.626142 TGTAATCCCTAACTGAAACTGCAA 58.374 37.500 0.00 0.00 0.00 4.08
3634 4053 5.924825 CGGTCTTATATTTCTTTACGGAGGG 59.075 44.000 0.00 0.00 0.00 4.30
3635 4054 6.510536 ACGGTCTTATATTTCTTTACGGAGG 58.489 40.000 0.00 0.00 0.00 4.30
3636 4055 7.998753 AACGGTCTTATATTTCTTTACGGAG 57.001 36.000 0.00 0.00 0.00 4.63
3646 4065 9.273016 CCAGATCACATTAACGGTCTTATATTT 57.727 33.333 0.00 0.00 0.00 1.40
3647 4066 7.387948 GCCAGATCACATTAACGGTCTTATATT 59.612 37.037 0.00 0.00 0.00 1.28
3648 4067 6.874134 GCCAGATCACATTAACGGTCTTATAT 59.126 38.462 0.00 0.00 0.00 0.86
3649 4068 6.041637 AGCCAGATCACATTAACGGTCTTATA 59.958 38.462 0.00 0.00 0.00 0.98
3650 4069 5.057149 GCCAGATCACATTAACGGTCTTAT 58.943 41.667 0.00 0.00 0.00 1.73
3651 4070 4.161565 AGCCAGATCACATTAACGGTCTTA 59.838 41.667 0.00 0.00 0.00 2.10
3652 4071 3.055094 AGCCAGATCACATTAACGGTCTT 60.055 43.478 0.00 0.00 0.00 3.01
3653 4072 2.501723 AGCCAGATCACATTAACGGTCT 59.498 45.455 0.00 0.00 0.00 3.85
3654 4073 2.609459 CAGCCAGATCACATTAACGGTC 59.391 50.000 0.00 0.00 0.00 4.79
3655 4074 2.236146 TCAGCCAGATCACATTAACGGT 59.764 45.455 0.00 0.00 0.00 4.83
3656 4075 2.609459 GTCAGCCAGATCACATTAACGG 59.391 50.000 0.00 0.00 0.00 4.44
3657 4076 3.062639 GTGTCAGCCAGATCACATTAACG 59.937 47.826 0.00 0.00 32.25 3.18
3661 4080 1.352017 TGGTGTCAGCCAGATCACATT 59.648 47.619 0.00 0.00 33.97 2.71
3672 4091 4.150451 GCACATTAACATTTTGGTGTCAGC 59.850 41.667 0.00 0.00 0.00 4.26
3796 4215 5.669164 AGGATGACAGACTAAGGAAAGAC 57.331 43.478 0.00 0.00 0.00 3.01
3817 4236 6.691508 AGCTAAGGCAGGATTAAAACAAAAG 58.308 36.000 0.00 0.00 41.70 2.27
3831 4251 4.515191 TGTCTAAACACAAAGCTAAGGCAG 59.485 41.667 0.00 0.00 41.70 4.85
3841 4262 4.710324 ACGGAAGGATGTCTAAACACAAA 58.290 39.130 0.00 0.00 38.48 2.83
3902 4330 3.144506 AGTGTATATCTGCCAAGCATGC 58.855 45.455 10.51 10.51 38.13 4.06
3905 4333 3.871006 CGAAAGTGTATATCTGCCAAGCA 59.129 43.478 0.00 0.00 36.92 3.91
3929 4358 5.431765 ACATGAGAAAGGGCACTATTACTG 58.568 41.667 0.00 0.00 0.00 2.74
3934 4363 4.080356 TGCTAACATGAGAAAGGGCACTAT 60.080 41.667 0.00 0.00 0.00 2.12
4091 4529 2.535331 GCCGTCAGAGACAAGATTCTC 58.465 52.381 0.00 0.00 42.22 2.87
4113 4551 7.985184 TCTCGTACATTACCTGAAAAGCATTAT 59.015 33.333 0.00 0.00 0.00 1.28
4171 4609 2.744741 CTCGAATAGCTCTATCGGCTCA 59.255 50.000 13.60 0.00 40.74 4.26
4195 4633 1.136141 GCTTCAGCAACTGTCACGATG 60.136 52.381 0.00 0.00 41.59 3.84
4196 4634 1.151668 GCTTCAGCAACTGTCACGAT 58.848 50.000 0.00 0.00 41.59 3.73
4324 4762 2.969821 ACCTGGTAAAGCACATTCCA 57.030 45.000 0.00 0.00 0.00 3.53
4328 4766 5.765182 GCTGATATAACCTGGTAAAGCACAT 59.235 40.000 0.00 0.00 0.00 3.21
4329 4767 5.104527 AGCTGATATAACCTGGTAAAGCACA 60.105 40.000 0.00 0.00 0.00 4.57
4338 4776 7.901029 TCAGAATAAGAGCTGATATAACCTGG 58.099 38.462 0.00 0.00 36.31 4.45
4339 4777 9.941325 ATTCAGAATAAGAGCTGATATAACCTG 57.059 33.333 0.00 0.00 40.51 4.00
4365 4807 9.959749 CAAAACAGGCTTAAGACAAAACTATAA 57.040 29.630 11.83 0.00 0.00 0.98
4367 4809 6.923508 GCAAAACAGGCTTAAGACAAAACTAT 59.076 34.615 11.83 0.00 0.00 2.12
4368 4810 6.270064 GCAAAACAGGCTTAAGACAAAACTA 58.730 36.000 11.83 0.00 0.00 2.24
4374 4816 1.960689 GGGCAAAACAGGCTTAAGACA 59.039 47.619 11.83 0.00 0.00 3.41
4382 4824 1.194121 ATGAAGGGGGCAAAACAGGC 61.194 55.000 0.00 0.00 0.00 4.85
4478 4920 2.903855 CCATCATCGTGCAGGGGC 60.904 66.667 6.56 0.00 41.68 5.80
4491 4939 0.102481 AGTACGACATCGCCACCATC 59.898 55.000 0.14 0.00 44.43 3.51
4496 4944 0.108377 ATGCAAGTACGACATCGCCA 60.108 50.000 0.14 0.00 44.43 5.69
4527 4975 3.853831 ATGCGATCTTTGCACATGAAA 57.146 38.095 0.00 0.00 46.57 2.69
4577 5031 1.694150 TCTCCCATTCCTTCATAGCCG 59.306 52.381 0.00 0.00 0.00 5.52
4585 5042 2.833943 GCCAACAATTCTCCCATTCCTT 59.166 45.455 0.00 0.00 0.00 3.36
4599 5056 2.023673 CACTGACAGGAAAGCCAACAA 58.976 47.619 7.51 0.00 36.29 2.83
4606 5063 3.079578 ACATGCATCACTGACAGGAAAG 58.920 45.455 7.51 0.98 0.00 2.62
4701 5158 4.764050 TTTCCAGTAAGACAGGACACAA 57.236 40.909 0.00 0.00 33.23 3.33
4708 5165 8.527810 GGATAGGATAGATTTCCAGTAAGACAG 58.472 40.741 0.00 0.00 38.32 3.51
4749 5206 5.235186 CCATCGTTCGCTATCTGAAGATTTT 59.765 40.000 0.00 0.00 36.05 1.82
4763 5220 3.640000 CGGCATCCCATCGTTCGC 61.640 66.667 0.00 0.00 0.00 4.70
4773 5230 2.898729 TCTCTGAATTCTCGGCATCC 57.101 50.000 7.05 0.00 0.00 3.51
4777 5234 3.185246 TGGAATCTCTGAATTCTCGGC 57.815 47.619 7.05 0.00 36.19 5.54
4780 5237 7.401955 AATTGGTTGGAATCTCTGAATTCTC 57.598 36.000 7.05 0.00 36.19 2.87
4911 5375 7.833285 AGAAGTTAGGGTCTTTTATTTTGCA 57.167 32.000 0.00 0.00 0.00 4.08
5035 5499 4.707934 TCGTGTCATGGGTAATCTAGAACA 59.292 41.667 0.00 0.00 0.00 3.18
5089 5553 2.429571 GCGACGTCGGCACTACAA 60.430 61.111 36.13 0.00 40.23 2.41
5199 5663 0.944386 CGCTACTCTCTGAGGCTCTC 59.056 60.000 16.72 0.00 33.35 3.20


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

AutoCloner maintained by Alex Coulton.