Multiple sequence alignment - TraesCS1A01G227000

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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 TraesCS1A01G227000 chr1A 100.000 8211 0 0 1 8211 397744497 397736287 0.000000e+00 15163.0
1 TraesCS1A01G227000 chr1A 89.438 1458 108 17 3069 4511 12200265 12198839 0.000000e+00 1797.0
2 TraesCS1A01G227000 chr1A 86.395 294 30 7 7927 8211 508209591 508209883 6.190000e-81 313.0
3 TraesCS1A01G227000 chr1A 80.876 251 29 9 2663 2912 535892373 535892605 6.550000e-41 180.0
4 TraesCS1A01G227000 chr1A 90.566 106 10 0 6552 6657 106228075 106228180 3.090000e-29 141.0
5 TraesCS1A01G227000 chr1D 92.745 1916 91 18 4512 6419 316620897 316619022 0.000000e+00 2724.0
6 TraesCS1A01G227000 chr1D 95.863 1281 38 4 6460 7740 316619025 316617760 0.000000e+00 2058.0
7 TraesCS1A01G227000 chr1D 92.201 1295 72 6 1796 3070 316622173 316620888 0.000000e+00 1805.0
8 TraesCS1A01G227000 chr1D 93.843 877 22 11 930 1793 316623108 316622251 0.000000e+00 1291.0
9 TraesCS1A01G227000 chr1D 87.119 295 26 9 7927 8211 102156251 102156543 2.860000e-84 324.0
10 TraesCS1A01G227000 chr1D 86.869 297 26 8 7927 8211 18761096 18760801 3.700000e-83 320.0
11 TraesCS1A01G227000 chr1D 80.702 399 59 10 2635 3025 442682854 442682466 2.240000e-75 294.0
12 TraesCS1A01G227000 chr1D 95.098 102 3 2 754 853 316623536 316623435 8.530000e-35 159.0
13 TraesCS1A01G227000 chr1D 91.509 106 9 0 6552 6657 128529211 128529106 6.640000e-31 147.0
14 TraesCS1A01G227000 chr1D 93.023 43 2 1 678 720 316623663 316623622 2.470000e-05 62.1
15 TraesCS1A01G227000 chr1B 94.151 1761 64 12 6465 8211 428722646 428720911 0.000000e+00 2645.0
16 TraesCS1A01G227000 chr1B 93.125 1789 81 10 4512 6293 428724501 428722748 0.000000e+00 2584.0
17 TraesCS1A01G227000 chr1B 92.639 1277 81 5 1796 3070 428725757 428724492 0.000000e+00 1825.0
18 TraesCS1A01G227000 chr1B 93.511 1048 32 13 754 1793 428726853 428725834 0.000000e+00 1526.0
19 TraesCS1A01G227000 chr1B 93.137 102 7 0 6552 6653 465698736 465698837 5.130000e-32 150.0
20 TraesCS1A01G227000 chr1B 93.000 100 5 1 6321 6420 428722749 428722652 2.390000e-30 145.0
21 TraesCS1A01G227000 chr1B 89.189 111 12 0 6547 6657 301273391 301273501 1.110000e-28 139.0
22 TraesCS1A01G227000 chr1B 88.043 92 9 1 5683 5774 4516583 4516672 3.130000e-19 108.0
23 TraesCS1A01G227000 chr2A 95.274 1439 53 6 3071 4507 192608960 192607535 0.000000e+00 2266.0
24 TraesCS1A01G227000 chr2A 94.368 657 34 3 1 656 19351878 19352532 0.000000e+00 1005.0
25 TraesCS1A01G227000 chr2A 93.930 659 36 4 1 657 16571393 16572049 0.000000e+00 992.0
26 TraesCS1A01G227000 chr2A 93.825 664 33 6 1 661 16575632 16576290 0.000000e+00 992.0
27 TraesCS1A01G227000 chr2A 91.765 85 6 1 5690 5774 177658409 177658326 5.210000e-22 117.0
28 TraesCS1A01G227000 chr5A 95.015 662 29 4 1 661 572036093 572036751 0.000000e+00 1037.0
29 TraesCS1A01G227000 chr7D 90.339 797 58 8 3071 3860 136311840 136312624 0.000000e+00 1027.0
30 TraesCS1A01G227000 chr7D 93.750 320 20 0 4183 4502 136312760 136313079 1.600000e-131 481.0
31 TraesCS1A01G227000 chr7D 89.310 290 24 7 7927 8211 197873082 197873369 2.820000e-94 357.0
32 TraesCS1A01G227000 chr2B 94.512 656 30 6 1 655 461573207 461572557 0.000000e+00 1007.0
33 TraesCS1A01G227000 chr2B 91.509 106 9 0 6552 6657 216462808 216462913 6.640000e-31 147.0
34 TraesCS1A01G227000 chr2B 93.750 80 5 0 5694 5773 113263500 113263421 4.030000e-23 121.0
35 TraesCS1A01G227000 chr4A 94.207 656 32 6 1 655 719415459 719416109 0.000000e+00 996.0
36 TraesCS1A01G227000 chr4A 93.902 656 34 6 1 655 720554665 720554015 0.000000e+00 985.0
37 TraesCS1A01G227000 chrUn 93.930 659 36 4 1 657 282689767 282690423 0.000000e+00 992.0
38 TraesCS1A01G227000 chrUn 86.869 297 26 8 7927 8211 161362 161067 3.700000e-83 320.0
39 TraesCS1A01G227000 chrUn 85.915 71 8 2 5707 5777 134112339 134112271 3.180000e-09 75.0
40 TraesCS1A01G227000 chr2D 93.893 655 37 3 1 655 119842935 119842284 0.000000e+00 985.0
41 TraesCS1A01G227000 chr2D 86.780 295 28 8 7927 8211 617044652 617044945 1.330000e-82 318.0
42 TraesCS1A01G227000 chr2D 91.765 85 6 1 5690 5774 172409666 172409749 5.210000e-22 117.0
43 TraesCS1A01G227000 chr2D 86.905 84 6 2 5694 5773 74129646 74129564 1.140000e-13 89.8
44 TraesCS1A01G227000 chr5B 87.031 293 27 11 7927 8211 588793449 588793160 3.700000e-83 320.0
45 TraesCS1A01G227000 chr5B 86.486 296 28 9 7927 8211 586912591 586912885 1.720000e-81 315.0
46 TraesCS1A01G227000 chr5D 87.031 293 23 10 7929 8211 495365721 495366008 4.780000e-82 316.0
47 TraesCS1A01G227000 chr5D 90.566 106 10 0 6552 6657 52281054 52281159 3.090000e-29 141.0
48 TraesCS1A01G227000 chr7A 90.000 110 11 0 6552 6661 48103180 48103071 8.590000e-30 143.0
49 TraesCS1A01G227000 chr6D 82.759 87 11 4 5689 5774 159233475 159233558 3.180000e-09 75.0


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 TraesCS1A01G227000 chr1A 397736287 397744497 8210 True 15163.00 15163 100.0000 1 8211 1 chr1A.!!$R2 8210
1 TraesCS1A01G227000 chr1A 12198839 12200265 1426 True 1797.00 1797 89.4380 3069 4511 1 chr1A.!!$R1 1442
2 TraesCS1A01G227000 chr1D 316617760 316623663 5903 True 1349.85 2724 93.7955 678 7740 6 chr1D.!!$R4 7062
3 TraesCS1A01G227000 chr1B 428720911 428726853 5942 True 1745.00 2645 93.2852 754 8211 5 chr1B.!!$R1 7457
4 TraesCS1A01G227000 chr2A 192607535 192608960 1425 True 2266.00 2266 95.2740 3071 4507 1 chr2A.!!$R2 1436
5 TraesCS1A01G227000 chr2A 19351878 19352532 654 False 1005.00 1005 94.3680 1 656 1 chr2A.!!$F1 655
6 TraesCS1A01G227000 chr2A 16571393 16576290 4897 False 992.00 992 93.8775 1 661 2 chr2A.!!$F2 660
7 TraesCS1A01G227000 chr5A 572036093 572036751 658 False 1037.00 1037 95.0150 1 661 1 chr5A.!!$F1 660
8 TraesCS1A01G227000 chr7D 136311840 136313079 1239 False 754.00 1027 92.0445 3071 4502 2 chr7D.!!$F2 1431
9 TraesCS1A01G227000 chr2B 461572557 461573207 650 True 1007.00 1007 94.5120 1 655 1 chr2B.!!$R2 654
10 TraesCS1A01G227000 chr4A 719415459 719416109 650 False 996.00 996 94.2070 1 655 1 chr4A.!!$F1 654
11 TraesCS1A01G227000 chr4A 720554015 720554665 650 True 985.00 985 93.9020 1 655 1 chr4A.!!$R1 654
12 TraesCS1A01G227000 chrUn 282689767 282690423 656 False 992.00 992 93.9300 1 657 1 chrUn.!!$F1 656
13 TraesCS1A01G227000 chr2D 119842284 119842935 651 True 985.00 985 93.8930 1 655 1 chr2D.!!$R2 654

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
878 5178 0.253327 AATCCCACGCTCTTTCTCCC 59.747 55.000 0.00 0.00 0.00 4.30 F
881 5181 0.391793 CCCACGCTCTTTCTCCCTTC 60.392 60.000 0.00 0.00 0.00 3.46 F
1743 6305 0.179048 TGTGGTGCTTGTCTGGTCTG 60.179 55.000 0.00 0.00 0.00 3.51 F
1934 6572 0.036671 CCTGCTGCTGACACTCATGA 60.037 55.000 8.20 0.00 0.00 3.07 F
2791 7450 0.039618 TGGAAAGACCAGGGGCAATC 59.960 55.000 0.00 0.00 44.64 2.67 F
3862 8538 0.530650 GTGGTCATCCGCACATCGAT 60.531 55.000 0.00 0.00 43.16 3.59 F
3985 8661 0.524862 CAGGCTGACTTGCAACATCC 59.475 55.000 9.42 0.00 34.04 3.51 F
5219 9912 1.068895 AGAATCCAGCGAGCTCATCAG 59.931 52.381 15.40 1.49 0.00 2.90 F
5981 10679 1.149101 TCAAGACAGGGGCCTTTCTT 58.851 50.000 0.84 6.25 41.93 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 6283 0.034574 ACCAGACAAGCACCACAACA 60.035 50.000 0.00 0.00 0.00 3.33 R
1766 6328 1.065709 GCAGAGACGTCCCCCAAAATA 60.066 52.381 13.01 0.00 0.00 1.40 R
3601 8277 0.393808 GCAGGCGGAATGAGGGTTTA 60.394 55.000 0.00 0.00 0.00 2.01 R
3914 8590 0.106819 TAGTCGGTCCCTGGCTAGTC 60.107 60.000 0.00 0.00 0.00 2.59 R
3954 8630 0.172578 TCAGCCTGTCCATAACGTCG 59.827 55.000 0.00 0.00 0.00 5.12 R
5378 10071 3.369546 AATGCGTTCCACAAGAAAAGG 57.630 42.857 0.00 0.00 35.85 3.11 R
5550 10248 3.603532 TCATCAAGCAGGAAAGCTACTG 58.396 45.455 8.24 8.24 45.89 2.74 R
6455 11160 0.037232 GCGCACAAGTCTTACTCCCT 60.037 55.000 0.30 0.00 0.00 4.20 R
7357 12062 1.131638 GGCTCACATGGACCATAGGA 58.868 55.000 6.67 6.85 0.00 2.94 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
34 36 2.307309 CGGCGCTTCGTCAACTTCA 61.307 57.895 7.64 0.00 0.00 3.02
59 4300 4.201679 CCGTCTACGCATGCCCGA 62.202 66.667 13.15 2.95 38.18 5.14
156 4397 2.897350 CATCTTCTTCCCGGCGCC 60.897 66.667 19.07 19.07 0.00 6.53
157 4398 3.083997 ATCTTCTTCCCGGCGCCT 61.084 61.111 26.68 0.00 0.00 5.52
174 4415 1.000506 GCCTCACTACTTCGACACCAA 59.999 52.381 0.00 0.00 0.00 3.67
177 4418 3.306088 CCTCACTACTTCGACACCAATGT 60.306 47.826 0.00 0.00 43.71 2.71
199 4440 1.153647 CATGACTAACTCGGCGCCA 60.154 57.895 28.98 12.94 0.00 5.69
378 4619 1.761174 ACCTCATCGGTTGCCACTT 59.239 52.632 0.00 0.00 46.37 3.16
398 4639 4.796231 GCCACGACTCCGCGATGT 62.796 66.667 8.23 5.50 39.95 3.06
437 4683 3.384532 GGGGTGTCCGTCGGCTTA 61.385 66.667 6.34 0.00 0.00 3.09
617 4863 3.220110 CCATGAGGCTCAAGCAATACAT 58.780 45.455 22.84 0.00 44.36 2.29
619 4865 3.632643 TGAGGCTCAAGCAATACATCA 57.367 42.857 16.28 0.00 44.36 3.07
635 4881 7.275560 GCAATACATCAAACTATTCCACCAAAC 59.724 37.037 0.00 0.00 0.00 2.93
637 4883 5.393866 ACATCAAACTATTCCACCAAACCT 58.606 37.500 0.00 0.00 0.00 3.50
658 4905 5.147032 CCTCTCTCTCCCTTCTAACATCAT 58.853 45.833 0.00 0.00 0.00 2.45
659 4906 5.010922 CCTCTCTCTCCCTTCTAACATCATG 59.989 48.000 0.00 0.00 0.00 3.07
660 4907 5.770919 TCTCTCTCCCTTCTAACATCATGA 58.229 41.667 0.00 0.00 0.00 3.07
662 4909 6.669591 TCTCTCTCCCTTCTAACATCATGAAA 59.330 38.462 0.00 0.00 0.00 2.69
663 4910 7.346698 TCTCTCTCCCTTCTAACATCATGAAAT 59.653 37.037 0.00 0.00 0.00 2.17
716 4963 2.616960 CGTCACGGATTGGATTTGAGA 58.383 47.619 0.00 0.00 0.00 3.27
717 4964 2.348666 CGTCACGGATTGGATTTGAGAC 59.651 50.000 0.00 0.00 0.00 3.36
751 5032 3.853330 CTGTCATTGCCGCCGACG 61.853 66.667 0.00 0.00 39.67 5.12
768 5067 2.800746 GGCACGTCACATTTGCGC 60.801 61.111 0.00 0.00 37.11 6.09
774 5073 1.396996 ACGTCACATTTGCGCCTATTC 59.603 47.619 4.18 0.00 0.00 1.75
878 5178 0.253327 AATCCCACGCTCTTTCTCCC 59.747 55.000 0.00 0.00 0.00 4.30
880 5180 0.836400 TCCCACGCTCTTTCTCCCTT 60.836 55.000 0.00 0.00 0.00 3.95
881 5181 0.391793 CCCACGCTCTTTCTCCCTTC 60.392 60.000 0.00 0.00 0.00 3.46
883 5183 0.391793 CACGCTCTTTCTCCCTTCCC 60.392 60.000 0.00 0.00 0.00 3.97
884 5184 1.222113 CGCTCTTTCTCCCTTCCCC 59.778 63.158 0.00 0.00 0.00 4.81
972 5521 1.529244 CCGCCATCAATCCCTTCCC 60.529 63.158 0.00 0.00 0.00 3.97
973 5522 1.227102 CGCCATCAATCCCTTCCCA 59.773 57.895 0.00 0.00 0.00 4.37
974 5523 0.395586 CGCCATCAATCCCTTCCCAA 60.396 55.000 0.00 0.00 0.00 4.12
975 5524 1.406903 GCCATCAATCCCTTCCCAAG 58.593 55.000 0.00 0.00 0.00 3.61
976 5525 1.342374 GCCATCAATCCCTTCCCAAGT 60.342 52.381 0.00 0.00 0.00 3.16
1584 6133 4.270325 GCCGAGGTAGCAATTGTAAACTAG 59.730 45.833 7.40 4.13 0.00 2.57
1585 6134 5.416947 CCGAGGTAGCAATTGTAAACTAGT 58.583 41.667 7.40 0.00 0.00 2.57
1586 6135 6.567050 CCGAGGTAGCAATTGTAAACTAGTA 58.433 40.000 7.40 0.00 0.00 1.82
1587 6136 7.208080 CCGAGGTAGCAATTGTAAACTAGTAT 58.792 38.462 7.40 0.00 0.00 2.12
1588 6137 8.355169 CCGAGGTAGCAATTGTAAACTAGTATA 58.645 37.037 7.40 0.00 0.00 1.47
1589 6138 9.395707 CGAGGTAGCAATTGTAAACTAGTATAG 57.604 37.037 7.40 0.00 46.50 1.31
1688 6244 2.840038 TGGTAGAACTGGATGCTGTGAT 59.160 45.455 0.00 0.00 0.00 3.06
1721 6283 6.886459 AGTATGTGATGCCTAGTTTGTTCATT 59.114 34.615 0.00 0.00 0.00 2.57
1734 6296 3.162202 TGTTCATTGTTGTGGTGCTTG 57.838 42.857 0.00 0.00 0.00 4.01
1735 6297 2.495270 TGTTCATTGTTGTGGTGCTTGT 59.505 40.909 0.00 0.00 0.00 3.16
1736 6298 3.115554 GTTCATTGTTGTGGTGCTTGTC 58.884 45.455 0.00 0.00 0.00 3.18
1737 6299 2.653726 TCATTGTTGTGGTGCTTGTCT 58.346 42.857 0.00 0.00 0.00 3.41
1738 6300 2.358582 TCATTGTTGTGGTGCTTGTCTG 59.641 45.455 0.00 0.00 0.00 3.51
1743 6305 0.179048 TGTGGTGCTTGTCTGGTCTG 60.179 55.000 0.00 0.00 0.00 3.51
1793 6355 1.435515 GGACGTCTCTGCTGCCTAG 59.564 63.158 16.46 0.00 0.00 3.02
1794 6356 1.316706 GGACGTCTCTGCTGCCTAGT 61.317 60.000 16.46 0.00 0.00 2.57
1798 6435 1.000771 TCTCTGCTGCCTAGTCCGT 60.001 57.895 0.00 0.00 0.00 4.69
1817 6454 2.484264 CGTTTCCTTGGACTGGATCAAC 59.516 50.000 0.00 0.00 33.09 3.18
1818 6455 2.472695 TTCCTTGGACTGGATCAACG 57.527 50.000 0.00 0.00 33.09 4.10
1836 6473 5.234752 TCAACGTGTTGTTCTAGCATATGT 58.765 37.500 12.10 0.00 39.29 2.29
1840 6477 6.395629 ACGTGTTGTTCTAGCATATGTACTT 58.604 36.000 4.29 0.00 0.00 2.24
1885 6523 1.270732 CCATCCTGTCAGCCTAGCATC 60.271 57.143 0.00 0.00 0.00 3.91
1896 6534 1.419387 GCCTAGCATCCCTTCATCAGT 59.581 52.381 0.00 0.00 0.00 3.41
1916 6554 5.522460 TCAGTATACTTTGCGAATACTTGCC 59.478 40.000 1.56 0.00 34.89 4.52
1934 6572 0.036671 CCTGCTGCTGACACTCATGA 60.037 55.000 8.20 0.00 0.00 3.07
1946 6584 2.949644 ACACTCATGACATGATGCATGG 59.050 45.455 18.28 8.36 45.16 3.66
1975 6614 3.565307 TCCTTCTGGTGCAAATGTTTCT 58.435 40.909 0.00 0.00 34.23 2.52
1983 6622 9.461312 TTCTGGTGCAAATGTTTCTACTATTAT 57.539 29.630 0.00 0.00 0.00 1.28
2049 6688 4.950050 AGTAGGATGCAACTATACTGTGC 58.050 43.478 10.17 0.00 0.00 4.57
2060 6699 3.583086 ACTATACTGTGCTGGACCTGTTT 59.417 43.478 0.00 0.00 0.00 2.83
2133 6772 6.963049 TCTTCCAGTAAGCGAAAATAAGAC 57.037 37.500 0.00 0.00 34.97 3.01
2156 6795 4.376008 CCGTTCAAGATAAAGTGACACGTG 60.376 45.833 15.48 15.48 31.92 4.49
2310 6949 5.529014 TTTGTTGTGCTTTTCTTTTCTGC 57.471 34.783 0.00 0.00 0.00 4.26
2314 6953 2.036933 GTGCTTTTCTTTTCTGCGTCG 58.963 47.619 0.00 0.00 0.00 5.12
2319 6958 2.358737 CTTTTCTGCGTCGGGCCT 60.359 61.111 0.84 0.00 42.61 5.19
2350 6989 3.126001 TGTACTCTTGCACCTTCTTGG 57.874 47.619 0.00 0.00 42.93 3.61
2420 7059 6.039270 TGACACATTTCCCTTTTTAGTCAGTG 59.961 38.462 0.00 0.00 0.00 3.66
2421 7060 6.126409 ACACATTTCCCTTTTTAGTCAGTGA 58.874 36.000 0.00 0.00 0.00 3.41
2509 7148 7.297936 TCCTATTTAAGACGGATGCAGATTA 57.702 36.000 0.00 0.00 0.00 1.75
2545 7203 5.588648 GCTTTGTTCCATAATGCTACACCTA 59.411 40.000 0.00 0.00 0.00 3.08
2549 7207 6.759272 TGTTCCATAATGCTACACCTATCTC 58.241 40.000 0.00 0.00 0.00 2.75
2613 7271 7.177568 ACGATGACTGATAATAGATGGCTAAGT 59.822 37.037 0.00 0.00 0.00 2.24
2648 7307 7.452880 TGTACGTATAAGGTTAACAGTCTGT 57.547 36.000 8.10 0.00 0.00 3.41
2704 7363 0.881159 TTGCATGCCACTGCTTTTGC 60.881 50.000 16.68 0.00 42.75 3.68
2761 7420 2.440980 GGCAAGGATCTGGGCCAC 60.441 66.667 0.00 0.00 45.70 5.01
2791 7450 0.039618 TGGAAAGACCAGGGGCAATC 59.960 55.000 0.00 0.00 44.64 2.67
3025 7684 7.038941 CCCCTAGTTGGTCTCATAAGGTAATAG 60.039 44.444 0.00 0.00 0.00 1.73
3055 7714 6.857956 TCTACTGTATTGAGTCTCTTGCTTC 58.142 40.000 0.65 0.00 0.00 3.86
3066 7725 6.703607 TGAGTCTCTTGCTTCTCTACTTTTTG 59.296 38.462 0.65 0.00 0.00 2.44
3067 7726 5.994668 AGTCTCTTGCTTCTCTACTTTTTGG 59.005 40.000 0.00 0.00 0.00 3.28
3769 8445 0.685097 TGTGGACACAAGGCTCTACC 59.315 55.000 2.08 0.00 38.56 3.18
3811 8487 1.468506 TACGCACCTCAGGACAGCAA 61.469 55.000 0.00 0.00 0.00 3.91
3862 8538 0.530650 GTGGTCATCCGCACATCGAT 60.531 55.000 0.00 0.00 43.16 3.59
3954 8630 1.321743 CGCTACTTGCAATGACTCGTC 59.678 52.381 0.00 0.00 43.06 4.20
3985 8661 0.524862 CAGGCTGACTTGCAACATCC 59.475 55.000 9.42 0.00 34.04 3.51
4076 8752 4.215742 TCGTTCATAGGGCCGGCG 62.216 66.667 22.54 6.07 0.00 6.46
4096 8772 4.153475 GGCGCGTTATACATATGAACCAAT 59.847 41.667 10.38 0.00 0.00 3.16
4124 8800 3.382121 GGACAAAGTCGTCGAGCTCGA 62.382 57.143 33.84 33.84 38.62 4.04
4224 8900 2.321263 ATAGCAGCTGGACGCATGCT 62.321 55.000 17.12 6.97 46.94 3.79
4270 8946 2.751806 GAGCTTCCATGCTTAAACTGCT 59.248 45.455 0.00 0.00 44.17 4.24
4511 9188 3.353557 GGGGTTATGTGGACTTCTTTCC 58.646 50.000 0.00 0.00 36.03 3.13
4512 9189 3.010250 GGGGTTATGTGGACTTCTTTCCT 59.990 47.826 0.00 0.00 36.51 3.36
4513 9190 4.508584 GGGGTTATGTGGACTTCTTTCCTT 60.509 45.833 0.00 0.00 36.51 3.36
4514 9191 5.077564 GGGTTATGTGGACTTCTTTCCTTT 58.922 41.667 0.00 0.00 36.51 3.11
4515 9192 5.538813 GGGTTATGTGGACTTCTTTCCTTTT 59.461 40.000 0.00 0.00 36.51 2.27
4516 9193 6.041637 GGGTTATGTGGACTTCTTTCCTTTTT 59.958 38.462 0.00 0.00 36.51 1.94
4526 9203 5.891551 ACTTCTTTCCTTTTTGGTTAGAGCA 59.108 36.000 0.00 0.00 37.07 4.26
4541 9218 7.535139 TGGTTAGAGCAACATTGTATTTTAGC 58.465 34.615 0.00 0.00 39.04 3.09
4698 9375 8.737175 GGTGTTTCAGGTATATGACGATATCTA 58.263 37.037 0.34 0.00 0.00 1.98
4841 9518 6.320171 CACAATGAATCTCCACAAACTGATC 58.680 40.000 0.00 0.00 0.00 2.92
4913 9590 6.017605 GTGACCTTTCAATATAGTCATGCCAG 60.018 42.308 0.00 0.00 39.46 4.85
4938 9615 8.548721 AGTCTTGAACTGTTAGTTTAATTGACG 58.451 33.333 0.00 0.00 38.80 4.35
4979 9656 3.695830 AGGCAGATTCACTTCCGTTTA 57.304 42.857 0.00 0.00 37.02 2.01
4980 9657 4.222124 AGGCAGATTCACTTCCGTTTAT 57.778 40.909 0.00 0.00 37.02 1.40
4981 9658 5.353394 AGGCAGATTCACTTCCGTTTATA 57.647 39.130 0.00 0.00 37.02 0.98
4982 9659 5.116882 AGGCAGATTCACTTCCGTTTATAC 58.883 41.667 0.00 0.00 37.02 1.47
4983 9660 4.873827 GGCAGATTCACTTCCGTTTATACA 59.126 41.667 0.00 0.00 0.00 2.29
4984 9661 5.353123 GGCAGATTCACTTCCGTTTATACAA 59.647 40.000 0.00 0.00 0.00 2.41
4985 9662 6.128117 GGCAGATTCACTTCCGTTTATACAAA 60.128 38.462 0.00 0.00 0.00 2.83
4986 9663 7.302524 GCAGATTCACTTCCGTTTATACAAAA 58.697 34.615 0.00 0.00 0.00 2.44
4987 9664 7.806014 GCAGATTCACTTCCGTTTATACAAAAA 59.194 33.333 0.00 0.00 0.00 1.94
4988 9665 9.840427 CAGATTCACTTCCGTTTATACAAAAAT 57.160 29.630 0.00 0.00 0.00 1.82
4991 9668 9.783256 ATTCACTTCCGTTTATACAAAAATAGC 57.217 29.630 0.00 0.00 0.00 2.97
4992 9669 8.556213 TCACTTCCGTTTATACAAAAATAGCT 57.444 30.769 0.00 0.00 0.00 3.32
5030 9721 3.554129 GGCTTGTTGAAACAACATACCCC 60.554 47.826 16.12 10.95 43.45 4.95
5052 9745 9.690913 ACCCCATATCATTCTATGTTGAATATG 57.309 33.333 0.00 0.00 35.18 1.78
5053 9746 8.627403 CCCCATATCATTCTATGTTGAATATGC 58.373 37.037 0.00 0.00 35.18 3.14
5062 9755 7.946187 ATTCTATGTTGAATATGCAGTTGCTGC 60.946 37.037 13.56 13.56 44.09 5.25
5077 9770 4.874966 AGTTGCTGCAGATAGATTCACTTC 59.125 41.667 20.43 0.00 0.00 3.01
5098 9791 9.950680 CACTTCTGTTTGTACATAAATGACTTT 57.049 29.630 0.00 0.00 32.86 2.66
5174 9867 6.586868 TGCTTGTTGTTGCTTTCTAATTTG 57.413 33.333 0.00 0.00 0.00 2.32
5218 9911 1.117994 AGAATCCAGCGAGCTCATCA 58.882 50.000 15.40 0.00 0.00 3.07
5219 9912 1.068895 AGAATCCAGCGAGCTCATCAG 59.931 52.381 15.40 1.49 0.00 2.90
5234 9927 4.157289 GCTCATCAGCAAAAGAATTCTCCA 59.843 41.667 8.78 0.00 46.06 3.86
5272 9965 8.983702 TTTCCTGGTTGGTGTATAATAATACC 57.016 34.615 0.00 0.00 34.75 2.73
5302 9995 5.601583 TTTGCCATTCAATCTGCATATGT 57.398 34.783 4.29 0.00 34.12 2.29
5378 10071 7.520614 GCATTGCTAGTGACCTGGTATATTTTC 60.521 40.741 0.00 0.00 0.00 2.29
5394 10087 7.753580 GGTATATTTTCCTTTTCTTGTGGAACG 59.246 37.037 0.00 0.00 42.39 3.95
5524 10217 8.260270 TGCAATCCAATCTTGATATAAGATCG 57.740 34.615 2.93 0.00 36.07 3.69
5530 10223 7.978414 TCCAATCTTGATATAAGATCGAGATGC 59.022 37.037 14.59 0.00 44.42 3.91
5550 10248 5.801350 TGCTGTATCTGTATTTGACTTGC 57.199 39.130 0.00 0.00 0.00 4.01
5600 10298 6.162777 GGATTGTTAACTGCATTGGCTTTAA 58.837 36.000 7.22 0.00 41.91 1.52
5606 10304 4.376340 ACTGCATTGGCTTTAAGTATGC 57.624 40.909 16.11 16.11 41.39 3.14
5612 10310 6.040729 TGCATTGGCTTTAAGTATGCATATGT 59.959 34.615 19.38 3.58 44.59 2.29
5613 10311 6.925165 GCATTGGCTTTAAGTATGCATATGTT 59.075 34.615 10.16 9.31 40.86 2.71
5622 10320 5.907197 AGTATGCATATGTTTACGTGCTC 57.093 39.130 10.16 0.00 38.37 4.26
5674 10372 7.642669 TCATGCTATAGCTGTTCAAATTTAGC 58.357 34.615 24.61 2.97 42.66 3.09
5675 10373 7.282901 TCATGCTATAGCTGTTCAAATTTAGCA 59.717 33.333 24.61 9.65 43.27 3.49
5699 10397 8.202137 GCACAATCTATTTTACTACTACCTCCA 58.798 37.037 0.00 0.00 0.00 3.86
5716 10414 9.228949 ACTACCTCCATACACTAATATAAGACG 57.771 37.037 0.00 0.00 0.00 4.18
5717 10415 9.228949 CTACCTCCATACACTAATATAAGACGT 57.771 37.037 0.00 0.00 0.00 4.34
5718 10416 8.474710 ACCTCCATACACTAATATAAGACGTT 57.525 34.615 0.00 0.00 0.00 3.99
5736 10434 7.749539 AGACGTTTTTGTAGTTCAATTTTGG 57.250 32.000 0.00 0.00 35.84 3.28
5774 10472 8.312564 GTCTTACATTAGTTTACAGAGGGAGTT 58.687 37.037 0.00 0.00 0.00 3.01
5822 10520 8.221801 TGAAATTGTGAAATTACGTATTGTGC 57.778 30.769 0.00 0.00 0.00 4.57
5981 10679 1.149101 TCAAGACAGGGGCCTTTCTT 58.851 50.000 0.84 6.25 41.93 2.52
6107 10812 5.650266 ACACATTTGTACTTGTCAGTTCCAA 59.350 36.000 0.00 0.00 32.60 3.53
6259 10964 5.763204 ACGTTACATTGATGAACTTCCTGTT 59.237 36.000 0.00 0.00 42.38 3.16
6294 10999 8.596293 CCATTTTGCCCATGTATCCTTTATATT 58.404 33.333 0.00 0.00 0.00 1.28
6325 11030 6.706270 CACAATGGAATATACTGAGGTACACC 59.294 42.308 0.00 0.00 0.00 4.16
6420 11125 6.324254 ACAGTTGACCTGAGAAAACTAGTACT 59.676 38.462 0.00 0.00 44.49 2.73
6421 11126 7.147707 ACAGTTGACCTGAGAAAACTAGTACTT 60.148 37.037 0.00 0.00 44.49 2.24
6422 11127 7.711339 CAGTTGACCTGAGAAAACTAGTACTTT 59.289 37.037 0.00 0.00 44.49 2.66
6425 11130 8.474710 TGACCTGAGAAAACTAGTACTTTAGT 57.525 34.615 0.00 0.00 35.44 2.24
6426 11131 8.358148 TGACCTGAGAAAACTAGTACTTTAGTG 58.642 37.037 0.00 0.00 34.24 2.74
6427 11132 8.474710 ACCTGAGAAAACTAGTACTTTAGTGA 57.525 34.615 0.00 0.00 34.24 3.41
6428 11133 9.091220 ACCTGAGAAAACTAGTACTTTAGTGAT 57.909 33.333 0.00 0.00 34.24 3.06
6429 11134 9.575783 CCTGAGAAAACTAGTACTTTAGTGATC 57.424 37.037 0.00 2.21 34.24 2.92
6436 11141 9.754382 AAACTAGTACTTTAGTGATCAAAACGA 57.246 29.630 0.00 0.00 34.24 3.85
6437 11142 9.924650 AACTAGTACTTTAGTGATCAAAACGAT 57.075 29.630 0.00 0.00 34.24 3.73
6454 11159 9.663904 TCAAAACGATCTTGAATTTCTTTACAG 57.336 29.630 0.00 0.00 29.93 2.74
6455 11160 9.663904 CAAAACGATCTTGAATTTCTTTACAGA 57.336 29.630 0.00 0.00 0.00 3.41
6456 11161 9.884465 AAAACGATCTTGAATTTCTTTACAGAG 57.116 29.630 0.00 0.00 0.00 3.35
6457 11162 7.602517 ACGATCTTGAATTTCTTTACAGAGG 57.397 36.000 0.00 0.00 0.00 3.69
6458 11163 6.595716 ACGATCTTGAATTTCTTTACAGAGGG 59.404 38.462 0.00 0.00 0.00 4.30
6459 11164 6.818644 CGATCTTGAATTTCTTTACAGAGGGA 59.181 38.462 0.00 0.00 0.00 4.20
6460 11165 7.010923 CGATCTTGAATTTCTTTACAGAGGGAG 59.989 40.741 0.00 0.00 0.00 4.30
6461 11166 7.079451 TCTTGAATTTCTTTACAGAGGGAGT 57.921 36.000 0.00 0.00 0.00 3.85
6462 11167 8.202461 TCTTGAATTTCTTTACAGAGGGAGTA 57.798 34.615 0.00 0.00 0.00 2.59
6473 11178 1.546476 AGAGGGAGTAAGACTTGTGCG 59.454 52.381 0.00 0.00 0.00 5.34
6489 11194 4.550577 TGTGCGCAATTCATTCGATAAT 57.449 36.364 14.00 0.00 0.00 1.28
6495 11200 6.086222 GCGCAATTCATTCGATAATAATGGT 58.914 36.000 0.30 0.00 35.48 3.55
6600 11305 4.565166 CGCTCAAACGGATGTATCTAAACA 59.435 41.667 0.00 0.00 0.00 2.83
6662 11367 0.390472 CAGACGGAGGGAGTGCTTTC 60.390 60.000 0.00 0.00 0.00 2.62
6705 11410 5.957771 TTTAGCAGTCATCCAGATAACCT 57.042 39.130 0.00 0.00 0.00 3.50
6770 11475 7.657761 AGCATCTAGTATCCATTTTAACTTCGG 59.342 37.037 0.00 0.00 0.00 4.30
6872 11577 7.064016 GTGTACTATCCTTCTGAGCAAGAAAAG 59.936 40.741 3.77 0.00 44.38 2.27
6958 11663 5.356190 TCATCTTTCTTGTTGATCCATCAGC 59.644 40.000 0.00 0.00 38.19 4.26
6969 11674 4.863548 TGATCCATCAGCCTTTGAAATCT 58.136 39.130 0.00 0.00 39.77 2.40
6975 11680 5.993441 CCATCAGCCTTTGAAATCTTTTGTT 59.007 36.000 0.00 0.00 39.77 2.83
7311 12016 3.682377 TGTTGTGGTACAGCGAATATGTG 59.318 43.478 0.00 0.00 41.80 3.21
7352 12057 2.239907 GGGCTTTCATACACCTCTTCCT 59.760 50.000 0.00 0.00 0.00 3.36
7353 12058 3.454812 GGGCTTTCATACACCTCTTCCTA 59.545 47.826 0.00 0.00 0.00 2.94
7354 12059 4.080526 GGGCTTTCATACACCTCTTCCTAA 60.081 45.833 0.00 0.00 0.00 2.69
7355 12060 5.119694 GGCTTTCATACACCTCTTCCTAAG 58.880 45.833 0.00 0.00 0.00 2.18
7356 12061 5.338463 GGCTTTCATACACCTCTTCCTAAGT 60.338 44.000 0.00 0.00 0.00 2.24
7357 12062 6.174049 GCTTTCATACACCTCTTCCTAAGTT 58.826 40.000 0.00 0.00 0.00 2.66
7358 12063 6.314152 GCTTTCATACACCTCTTCCTAAGTTC 59.686 42.308 0.00 0.00 0.00 3.01
7359 12064 5.934402 TCATACACCTCTTCCTAAGTTCC 57.066 43.478 0.00 0.00 0.00 3.62
7559 12264 2.572104 AGGACCCTTTGTAGATGACCAC 59.428 50.000 0.00 0.00 0.00 4.16
7604 12309 3.567164 AGAATCAGGCAGGCATTTAATCG 59.433 43.478 0.00 0.00 0.00 3.34
7674 12379 6.092748 GGTAAAATTTGTGTGCTCTATGGTG 58.907 40.000 0.00 0.00 0.00 4.17
7805 12510 2.383368 AGCTCATCTGCTCACTTCAC 57.617 50.000 0.00 0.00 39.34 3.18
7816 12521 2.156504 GCTCACTTCACACTCAACATCG 59.843 50.000 0.00 0.00 0.00 3.84
7827 12532 6.145534 TCACACTCAACATCGAGAATTACAAC 59.854 38.462 0.00 0.00 36.47 3.32
7872 12577 6.199937 ACATCTTCATGACCAAAGCATAAC 57.800 37.500 0.00 0.00 33.72 1.89
7914 12619 3.164268 AGCATAATTGGCCACAAAGTGA 58.836 40.909 3.88 0.00 40.55 3.41
7915 12620 3.056607 AGCATAATTGGCCACAAAGTGAC 60.057 43.478 3.88 0.00 40.55 3.67
7925 12630 4.322801 GGCCACAAAGTGACTAGTAGACAT 60.323 45.833 3.59 0.00 35.23 3.06
7927 12632 5.566826 GCCACAAAGTGACTAGTAGACATGA 60.567 44.000 3.59 0.00 35.23 3.07
7959 12670 3.891977 TCTACACCTGAGCTCATATGTCC 59.108 47.826 27.40 0.00 0.00 4.02
7960 12671 1.410517 ACACCTGAGCTCATATGTCCG 59.589 52.381 18.63 3.16 0.00 4.79
7961 12672 0.390860 ACCTGAGCTCATATGTCCGC 59.609 55.000 18.63 4.63 0.00 5.54
8056 12769 7.675962 AGAAATATTTGTTGTGCATGCAAAT 57.324 28.000 24.58 19.63 42.92 2.32
8108 12821 5.520649 GGCGTGGTAAAGAAAACAAAATTGA 59.479 36.000 0.00 0.00 0.00 2.57
8109 12822 6.407623 GCGTGGTAAAGAAAACAAAATTGAC 58.592 36.000 0.00 0.00 0.00 3.18
8110 12823 6.623633 CGTGGTAAAGAAAACAAAATTGACG 58.376 36.000 0.00 0.00 0.00 4.35
8111 12824 6.251801 CGTGGTAAAGAAAACAAAATTGACGT 59.748 34.615 0.00 0.00 0.00 4.34
8112 12825 7.201367 CGTGGTAAAGAAAACAAAATTGACGTT 60.201 33.333 0.00 0.00 0.00 3.99
8113 12826 9.074443 GTGGTAAAGAAAACAAAATTGACGTTA 57.926 29.630 0.00 0.00 0.00 3.18
8114 12827 9.804758 TGGTAAAGAAAACAAAATTGACGTTAT 57.195 25.926 0.00 0.00 0.00 1.89
8134 12847 9.372541 ACGTTATGTAAATGTTACTTTCAAACG 57.627 29.630 13.40 13.40 39.29 3.60
8140 12853 8.535592 TGTAAATGTTACTTTCAAACGCATTTG 58.464 29.630 0.00 0.00 45.67 2.32
8144 12857 1.147473 CTTTCAAACGCATTTGGGGC 58.853 50.000 5.29 0.00 44.61 5.80
8145 12858 0.755686 TTTCAAACGCATTTGGGGCT 59.244 45.000 5.29 0.00 44.61 5.19
8148 12861 0.867086 CAAACGCATTTGGGGCTTTG 59.133 50.000 0.00 0.00 41.39 2.77
8149 12862 0.755686 AAACGCATTTGGGGCTTTGA 59.244 45.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 1.022735 ATGCGTAGACGGACGAAGAT 58.977 50.000 10.44 0.00 45.82 2.40
59 4300 2.567497 GCACCAGTGTTGCCAGCAT 61.567 57.895 0.25 0.00 0.00 3.79
129 4370 2.484264 GGGAAGAAGATGTTGTTGACGG 59.516 50.000 0.00 0.00 0.00 4.79
156 4397 3.675225 CACATTGGTGTCGAAGTAGTGAG 59.325 47.826 0.00 0.00 40.24 3.51
157 4398 3.649073 CACATTGGTGTCGAAGTAGTGA 58.351 45.455 0.00 0.00 40.24 3.41
174 4415 1.134401 CCGAGTTAGTCATGGGCACAT 60.134 52.381 0.00 0.00 37.99 3.21
177 4418 1.220749 GCCGAGTTAGTCATGGGCA 59.779 57.895 0.00 0.00 40.24 5.36
365 4606 1.675641 GGCTGAAGTGGCAACCGAT 60.676 57.895 0.00 0.00 0.00 4.18
617 4863 5.073144 AGAGAGGTTTGGTGGAATAGTTTGA 59.927 40.000 0.00 0.00 0.00 2.69
619 4865 5.310857 AGAGAGAGGTTTGGTGGAATAGTTT 59.689 40.000 0.00 0.00 0.00 2.66
635 4881 4.541705 TGATGTTAGAAGGGAGAGAGAGG 58.458 47.826 0.00 0.00 0.00 3.69
637 4883 5.770919 TCATGATGTTAGAAGGGAGAGAGA 58.229 41.667 0.00 0.00 0.00 3.10
676 4923 3.566742 ACGGCGAACCAACTTCTATTTTT 59.433 39.130 16.62 0.00 34.57 1.94
683 4930 1.568025 GTGACGGCGAACCAACTTC 59.432 57.895 16.62 0.00 34.57 3.01
728 5009 0.248215 GGCGGCAATGACAGAATTCG 60.248 55.000 3.07 0.00 0.00 3.34
731 5012 1.078497 TCGGCGGCAATGACAGAAT 60.078 52.632 10.53 0.00 0.00 2.40
733 5014 2.434185 GTCGGCGGCAATGACAGA 60.434 61.111 6.63 0.00 32.91 3.41
751 5032 2.800746 GCGCAAATGTGACGTGCC 60.801 61.111 0.30 0.00 34.73 5.01
768 5067 1.211457 AGCCAGGCTCAACAGAATAGG 59.789 52.381 8.70 0.00 30.62 2.57
774 5073 1.731720 GAACTAGCCAGGCTCAACAG 58.268 55.000 20.38 12.74 40.44 3.16
972 5521 1.065126 GGAGGTGGAGATGGGAACTTG 60.065 57.143 0.00 0.00 0.00 3.16
973 5522 1.290134 GGAGGTGGAGATGGGAACTT 58.710 55.000 0.00 0.00 0.00 2.66
974 5523 0.621862 GGGAGGTGGAGATGGGAACT 60.622 60.000 0.00 0.00 0.00 3.01
975 5524 1.636769 GGGGAGGTGGAGATGGGAAC 61.637 65.000 0.00 0.00 0.00 3.62
976 5525 1.307866 GGGGAGGTGGAGATGGGAA 60.308 63.158 0.00 0.00 0.00 3.97
1054 5603 2.930682 GAGAAGCTTAAACCTAGCGGTG 59.069 50.000 0.00 0.00 44.73 4.94
1589 6138 9.392021 GCCGTATACAGAAGTAGAAAATAGTAC 57.608 37.037 3.32 0.00 32.86 2.73
1592 6141 7.137426 ACGCCGTATACAGAAGTAGAAAATAG 58.863 38.462 3.32 0.00 32.86 1.73
1688 6244 1.616865 GGCATCACATACTACGGGCTA 59.383 52.381 0.00 0.00 0.00 3.93
1692 6254 4.585955 AACTAGGCATCACATACTACGG 57.414 45.455 0.00 0.00 0.00 4.02
1693 6255 5.348986 ACAAACTAGGCATCACATACTACG 58.651 41.667 0.00 0.00 0.00 3.51
1721 6283 0.034574 ACCAGACAAGCACCACAACA 60.035 50.000 0.00 0.00 0.00 3.33
1734 6296 1.469308 CTACGTCAGACCAGACCAGAC 59.531 57.143 0.00 0.00 35.07 3.51
1735 6297 1.073444 ACTACGTCAGACCAGACCAGA 59.927 52.381 0.00 0.00 35.07 3.86
1736 6298 1.535833 ACTACGTCAGACCAGACCAG 58.464 55.000 0.00 0.00 35.07 4.00
1737 6299 1.611977 CAACTACGTCAGACCAGACCA 59.388 52.381 0.00 0.00 35.07 4.02
1738 6300 1.067776 CCAACTACGTCAGACCAGACC 60.068 57.143 0.00 0.00 35.07 3.85
1743 6305 2.735762 GCATCTCCAACTACGTCAGACC 60.736 54.545 0.00 0.00 0.00 3.85
1766 6328 1.065709 GCAGAGACGTCCCCCAAAATA 60.066 52.381 13.01 0.00 0.00 1.40
1794 6356 1.278127 GATCCAGTCCAAGGAAACGGA 59.722 52.381 5.24 5.24 38.93 4.69
1798 6435 2.105821 ACGTTGATCCAGTCCAAGGAAA 59.894 45.455 0.00 0.00 38.93 3.13
1817 6454 6.696198 CAAGTACATATGCTAGAACAACACG 58.304 40.000 1.58 0.00 0.00 4.49
1818 6455 6.478588 GCAAGTACATATGCTAGAACAACAC 58.521 40.000 1.58 0.00 39.46 3.32
1836 6473 4.830046 TGCCTGACCAAATTTAAGCAAGTA 59.170 37.500 0.00 0.00 0.00 2.24
1840 6477 5.681954 GCATATGCCTGACCAAATTTAAGCA 60.682 40.000 17.26 0.00 34.31 3.91
1885 6523 4.693283 TCGCAAAGTATACTGATGAAGGG 58.307 43.478 18.42 9.06 0.00 3.95
1896 6534 4.272504 GCAGGCAAGTATTCGCAAAGTATA 59.727 41.667 0.00 0.00 0.00 1.47
1916 6554 1.077123 GTCATGAGTGTCAGCAGCAG 58.923 55.000 0.00 0.00 0.00 4.24
1934 6572 2.992847 ATGATCCCCATGCATCATGT 57.007 45.000 0.00 0.00 39.94 3.21
1991 6630 2.322355 TTAACCCCGTGACGAACAAA 57.678 45.000 6.54 0.00 0.00 2.83
2049 6688 6.824305 AATTCAGATAACAAACAGGTCCAG 57.176 37.500 0.00 0.00 0.00 3.86
2133 6772 3.739300 ACGTGTCACTTTATCTTGAACGG 59.261 43.478 0.65 0.00 33.96 4.44
2156 6795 5.594725 TGGAGATACAGTGAGATACAGGAAC 59.405 44.000 0.00 0.00 0.00 3.62
2276 6915 7.614124 AAAGCACAACAAATCAAAACAAGAT 57.386 28.000 0.00 0.00 0.00 2.40
2278 6917 7.520686 AGAAAAGCACAACAAATCAAAACAAG 58.479 30.769 0.00 0.00 0.00 3.16
2319 6958 3.263170 TGCAAGAGTACATAAGGCCAAGA 59.737 43.478 5.01 0.00 0.00 3.02
2405 7044 7.979444 TTCATAGTTCACTGACTAAAAAGGG 57.021 36.000 0.00 0.00 35.86 3.95
2432 7071 9.168451 TCAGAACAAACACTAAACATTAGTTCA 57.832 29.630 0.00 0.00 36.84 3.18
2497 7136 4.473199 CAAGCATTCATAATCTGCATCCG 58.527 43.478 0.00 0.00 38.37 4.18
2509 7148 2.027837 GGAACAAAGCCCAAGCATTCAT 60.028 45.455 0.00 0.00 43.56 2.57
2588 7246 7.542890 ACTTAGCCATCTATTATCAGTCATCG 58.457 38.462 0.00 0.00 0.00 3.84
2648 7307 9.683870 TTAAAGAAGGTTAGGTAAACTGTTGAA 57.316 29.630 0.00 0.00 38.23 2.69
2679 7338 1.097232 GCAGTGGCATGCAATACTCA 58.903 50.000 21.36 3.75 45.77 3.41
2704 7363 5.874895 TCCAGTTGGATATACGATAGACG 57.125 43.478 0.00 0.00 43.01 4.18
2761 7420 5.591877 CCCTGGTCTTTCCAATAATTCAGAG 59.408 44.000 0.00 0.00 46.59 3.35
2953 7612 8.058667 TCAAGAATGATAGTCATGTGCAAAAT 57.941 30.769 0.00 0.00 37.15 1.82
3025 7684 7.038154 AGAGACTCAATACAGTAGAGAATGC 57.962 40.000 5.02 0.00 33.69 3.56
3055 7714 6.972901 GGACTTGTTTCAACCAAAAAGTAGAG 59.027 38.462 0.00 0.00 31.23 2.43
3066 7725 4.261867 GGGTTATGTGGACTTGTTTCAACC 60.262 45.833 0.00 0.00 33.69 3.77
3067 7726 4.261867 GGGGTTATGTGGACTTGTTTCAAC 60.262 45.833 0.00 0.00 0.00 3.18
3245 7907 1.823041 GCTCCAGGAGAAGCATGCC 60.823 63.158 21.89 0.00 0.00 4.40
3601 8277 0.393808 GCAGGCGGAATGAGGGTTTA 60.394 55.000 0.00 0.00 0.00 2.01
3914 8590 0.106819 TAGTCGGTCCCTGGCTAGTC 60.107 60.000 0.00 0.00 0.00 2.59
3954 8630 0.172578 TCAGCCTGTCCATAACGTCG 59.827 55.000 0.00 0.00 0.00 5.12
4035 8711 1.445942 CACCACACCTGAAGTCCGT 59.554 57.895 0.00 0.00 0.00 4.69
4076 8752 5.106317 CCCCATTGGTTCATATGTATAACGC 60.106 44.000 1.90 0.00 0.00 4.84
4096 8772 1.228124 CGACTTTGTCCTTGCCCCA 60.228 57.895 0.00 0.00 0.00 4.96
4270 8946 2.882137 CGGAAACAGTTTAAGCCTGGAA 59.118 45.455 0.00 0.00 34.16 3.53
4511 9188 8.816640 AATACAATGTTGCTCTAACCAAAAAG 57.183 30.769 0.00 0.00 38.55 2.27
4512 9189 9.606631 AAAATACAATGTTGCTCTAACCAAAAA 57.393 25.926 0.00 0.00 38.55 1.94
4514 9191 9.906660 CTAAAATACAATGTTGCTCTAACCAAA 57.093 29.630 0.00 0.00 38.55 3.28
4515 9192 8.026607 GCTAAAATACAATGTTGCTCTAACCAA 58.973 33.333 0.00 0.00 38.55 3.67
4516 9193 7.535139 GCTAAAATACAATGTTGCTCTAACCA 58.465 34.615 0.00 0.00 38.55 3.67
4541 9218 6.556212 CAACTGTCTAGCCATATACTATCCG 58.444 44.000 0.00 0.00 0.00 4.18
4720 9397 5.809001 TCCATAACTGAAGCATGAGAAACT 58.191 37.500 0.00 0.00 0.00 2.66
4725 9402 6.939132 AGAAATCCATAACTGAAGCATGAG 57.061 37.500 0.00 0.00 0.00 2.90
4816 9493 4.022935 TCAGTTTGTGGAGATTCATTGTGC 60.023 41.667 0.00 0.00 0.00 4.57
4913 9590 8.333186 ACGTCAATTAAACTAACAGTTCAAGAC 58.667 33.333 0.00 0.00 37.47 3.01
4938 9615 8.314143 TGCCTACAGTAACTGTATAAACAAAC 57.686 34.615 0.00 0.00 44.49 2.93
5053 9746 4.190001 AGTGAATCTATCTGCAGCAACTG 58.810 43.478 9.47 0.00 34.12 3.16
5058 9751 4.440880 ACAGAAGTGAATCTATCTGCAGC 58.559 43.478 9.47 0.00 42.34 5.25
5062 9755 8.763049 TGTACAAACAGAAGTGAATCTATCTG 57.237 34.615 0.00 8.28 43.79 2.90
5129 9822 5.065474 GCAAAATAGAATGGCGTAAGGTACA 59.935 40.000 0.00 0.00 38.28 2.90
5139 9832 5.615325 GCAACAACAAGCAAAATAGAATGGC 60.615 40.000 0.00 0.00 0.00 4.40
5218 9911 6.600882 ACATCATTGGAGAATTCTTTTGCT 57.399 33.333 9.87 0.00 0.00 3.91
5219 9912 6.401796 GCAACATCATTGGAGAATTCTTTTGC 60.402 38.462 9.87 9.35 0.00 3.68
5234 9927 3.771216 ACCAGGAAAGAGCAACATCATT 58.229 40.909 0.00 0.00 0.00 2.57
5270 9963 5.541484 AGATTGAATGGCAAAAGAAAGAGGT 59.459 36.000 0.00 0.00 40.48 3.85
5272 9965 5.347907 GCAGATTGAATGGCAAAAGAAAGAG 59.652 40.000 0.00 0.00 40.48 2.85
5378 10071 3.369546 AATGCGTTCCACAAGAAAAGG 57.630 42.857 0.00 0.00 35.85 3.11
5479 10172 4.074259 GCAATCCCAGCAAAAAGGAAAAT 58.926 39.130 0.00 0.00 32.26 1.82
5524 10217 7.518052 GCAAGTCAAATACAGATACAGCATCTC 60.518 40.741 0.00 0.00 42.40 2.75
5550 10248 3.603532 TCATCAAGCAGGAAAGCTACTG 58.396 45.455 8.24 8.24 45.89 2.74
5600 10298 4.750098 GGAGCACGTAAACATATGCATACT 59.250 41.667 8.99 0.00 40.63 2.12
5659 10357 8.693542 AATAGATTGTGCTAAATTTGAACAGC 57.306 30.769 0.00 2.20 34.56 4.40
5710 10408 9.291664 CCAAAATTGAACTACAAAAACGTCTTA 57.708 29.630 0.00 0.00 42.03 2.10
5711 10409 8.030106 TCCAAAATTGAACTACAAAAACGTCTT 58.970 29.630 0.00 0.00 42.03 3.01
5712 10410 7.486870 GTCCAAAATTGAACTACAAAAACGTCT 59.513 33.333 0.00 0.00 42.03 4.18
5713 10411 7.486870 AGTCCAAAATTGAACTACAAAAACGTC 59.513 33.333 0.00 0.00 42.03 4.34
5714 10412 7.274686 CAGTCCAAAATTGAACTACAAAAACGT 59.725 33.333 0.00 0.00 42.03 3.99
5715 10413 7.608755 CAGTCCAAAATTGAACTACAAAAACG 58.391 34.615 0.00 0.00 42.03 3.60
5716 10414 7.064016 TGCAGTCCAAAATTGAACTACAAAAAC 59.936 33.333 0.00 0.00 42.03 2.43
5717 10415 7.099764 TGCAGTCCAAAATTGAACTACAAAAA 58.900 30.769 0.00 0.00 42.03 1.94
5718 10416 6.634805 TGCAGTCCAAAATTGAACTACAAAA 58.365 32.000 0.00 0.00 42.03 2.44
5736 10434 6.656003 ACTAATGTAAGACGTTTTTGCAGTC 58.344 36.000 7.73 0.00 35.30 3.51
5798 10496 8.447787 AGCACAATACGTAATTTCACAATTTC 57.552 30.769 0.00 0.00 34.29 2.17
5881 10579 8.511321 CCAAGTGTAAGTAAGATGCATAAAACA 58.489 33.333 0.00 0.00 0.00 2.83
5883 10581 8.630054 ACCAAGTGTAAGTAAGATGCATAAAA 57.370 30.769 0.00 0.00 0.00 1.52
5996 10694 7.027874 AGGGTATCTTAAAATGACAGGTTGA 57.972 36.000 0.00 0.00 0.00 3.18
6094 10799 6.757897 TTATAGGCATTTGGAACTGACAAG 57.242 37.500 0.00 0.00 0.00 3.16
6107 10812 7.460910 TCATACATGTGGTCATTATAGGCATT 58.539 34.615 9.11 0.00 31.15 3.56
6193 10898 8.464770 AATGAAACCAACACAAAATGATATCG 57.535 30.769 0.00 0.00 0.00 2.92
6259 10964 5.454062 ACATGGGCAAAATGGTAGCTAATA 58.546 37.500 0.00 0.00 0.00 0.98
6299 11004 7.418597 GGTGTACCTCAGTATATTCCATTGTGA 60.419 40.741 0.00 0.00 0.00 3.58
6428 11133 9.663904 CTGTAAAGAAATTCAAGATCGTTTTGA 57.336 29.630 0.00 0.00 33.00 2.69
6429 11134 9.663904 TCTGTAAAGAAATTCAAGATCGTTTTG 57.336 29.630 0.00 0.00 0.00 2.44
6430 11135 9.884465 CTCTGTAAAGAAATTCAAGATCGTTTT 57.116 29.630 0.00 0.00 0.00 2.43
6431 11136 8.507249 CCTCTGTAAAGAAATTCAAGATCGTTT 58.493 33.333 0.00 0.00 0.00 3.60
6432 11137 7.119846 CCCTCTGTAAAGAAATTCAAGATCGTT 59.880 37.037 0.00 0.00 0.00 3.85
6433 11138 6.595716 CCCTCTGTAAAGAAATTCAAGATCGT 59.404 38.462 0.00 0.00 0.00 3.73
6434 11139 6.818644 TCCCTCTGTAAAGAAATTCAAGATCG 59.181 38.462 0.00 0.00 0.00 3.69
6435 11140 7.826744 ACTCCCTCTGTAAAGAAATTCAAGATC 59.173 37.037 0.00 0.00 0.00 2.75
6436 11141 7.694093 ACTCCCTCTGTAAAGAAATTCAAGAT 58.306 34.615 0.00 0.00 0.00 2.40
6437 11142 7.079451 ACTCCCTCTGTAAAGAAATTCAAGA 57.921 36.000 0.00 0.00 0.00 3.02
6438 11143 8.848474 TTACTCCCTCTGTAAAGAAATTCAAG 57.152 34.615 0.00 0.00 0.00 3.02
6439 11144 8.656806 TCTTACTCCCTCTGTAAAGAAATTCAA 58.343 33.333 0.00 0.00 30.72 2.69
6440 11145 8.095169 GTCTTACTCCCTCTGTAAAGAAATTCA 58.905 37.037 0.00 0.00 30.72 2.57
6441 11146 8.315482 AGTCTTACTCCCTCTGTAAAGAAATTC 58.685 37.037 0.00 0.00 30.72 2.17
6442 11147 8.208575 AGTCTTACTCCCTCTGTAAAGAAATT 57.791 34.615 0.00 0.00 30.72 1.82
6443 11148 7.800300 AGTCTTACTCCCTCTGTAAAGAAAT 57.200 36.000 0.00 0.00 30.72 2.17
6444 11149 7.070821 ACAAGTCTTACTCCCTCTGTAAAGAAA 59.929 37.037 0.00 0.00 30.72 2.52
6445 11150 6.553852 ACAAGTCTTACTCCCTCTGTAAAGAA 59.446 38.462 0.00 0.00 30.72 2.52
6446 11151 6.015350 CACAAGTCTTACTCCCTCTGTAAAGA 60.015 42.308 0.00 0.00 30.72 2.52
6447 11152 6.159988 CACAAGTCTTACTCCCTCTGTAAAG 58.840 44.000 0.00 0.00 30.72 1.85
6448 11153 5.510861 GCACAAGTCTTACTCCCTCTGTAAA 60.511 44.000 0.00 0.00 30.72 2.01
6449 11154 4.021368 GCACAAGTCTTACTCCCTCTGTAA 60.021 45.833 0.00 0.00 0.00 2.41
6450 11155 3.510360 GCACAAGTCTTACTCCCTCTGTA 59.490 47.826 0.00 0.00 0.00 2.74
6451 11156 2.300437 GCACAAGTCTTACTCCCTCTGT 59.700 50.000 0.00 0.00 0.00 3.41
6452 11157 2.672478 CGCACAAGTCTTACTCCCTCTG 60.672 54.545 0.00 0.00 0.00 3.35
6453 11158 1.546476 CGCACAAGTCTTACTCCCTCT 59.454 52.381 0.00 0.00 0.00 3.69
6454 11159 1.997669 CGCACAAGTCTTACTCCCTC 58.002 55.000 0.00 0.00 0.00 4.30
6455 11160 0.037232 GCGCACAAGTCTTACTCCCT 60.037 55.000 0.30 0.00 0.00 4.20
6456 11161 0.320421 TGCGCACAAGTCTTACTCCC 60.320 55.000 5.66 0.00 0.00 4.30
6457 11162 1.508632 TTGCGCACAAGTCTTACTCC 58.491 50.000 11.12 0.00 0.00 3.85
6458 11163 3.737305 GAATTGCGCACAAGTCTTACTC 58.263 45.455 11.12 0.00 45.20 2.59
6459 11164 3.813529 GAATTGCGCACAAGTCTTACT 57.186 42.857 11.12 0.00 45.20 2.24
6509 11214 5.895636 TGGATGCACCTTACAAACATTAG 57.104 39.130 0.00 0.00 39.86 1.73
6600 11305 7.233389 ACGGATGTATCTAGCACTGAAATAT 57.767 36.000 0.00 0.00 0.00 1.28
6762 11467 3.562557 GCCTGAAAGTTTCACCGAAGTTA 59.437 43.478 14.35 0.00 35.46 2.24
6770 11475 0.317854 GGCGTGCCTGAAAGTTTCAC 60.318 55.000 14.35 6.73 35.46 3.18
6872 11577 1.667467 GCGTAGAGCTTCGGATCATCC 60.667 57.143 0.00 0.00 44.04 3.51
7311 12016 4.658071 CCCGTTGTGTACATTTATTGCTC 58.342 43.478 0.00 0.00 0.00 4.26
7352 12057 4.141711 GCTCACATGGACCATAGGAACTTA 60.142 45.833 6.67 0.00 41.75 2.24
7353 12058 3.370953 GCTCACATGGACCATAGGAACTT 60.371 47.826 6.67 0.00 41.75 2.66
7354 12059 2.171448 GCTCACATGGACCATAGGAACT 59.829 50.000 6.67 0.00 46.37 3.01
7355 12060 2.565841 GCTCACATGGACCATAGGAAC 58.434 52.381 6.67 0.00 0.00 3.62
7356 12061 1.490490 GGCTCACATGGACCATAGGAA 59.510 52.381 6.67 0.00 0.00 3.36
7357 12062 1.131638 GGCTCACATGGACCATAGGA 58.868 55.000 6.67 6.85 0.00 2.94
7358 12063 1.135094 AGGCTCACATGGACCATAGG 58.865 55.000 6.67 2.32 0.00 2.57
7359 12064 3.287867 AAAGGCTCACATGGACCATAG 57.712 47.619 6.67 2.29 0.00 2.23
7604 12309 3.561528 CCCTAAAGTTTCACCTCCTTCCC 60.562 52.174 0.00 0.00 0.00 3.97
7650 12355 6.092748 CACCATAGAGCACACAAATTTTACC 58.907 40.000 0.00 0.00 0.00 2.85
7674 12379 8.795341 GTTGTTCAGTTAAAACTTGAGCTAAAC 58.205 33.333 0.00 0.00 37.08 2.01
7758 12463 2.290260 CCAAATCGCTGCTCCCCATATA 60.290 50.000 0.00 0.00 0.00 0.86
7803 12508 6.299604 GTTGTAATTCTCGATGTTGAGTGTG 58.700 40.000 0.00 0.00 37.28 3.82
7805 12510 5.408299 TGGTTGTAATTCTCGATGTTGAGTG 59.592 40.000 0.00 0.00 37.28 3.51
7827 12532 2.234661 TGACAGACTTCTACCATGCTGG 59.765 50.000 0.00 1.16 45.02 4.85
7872 12577 2.255172 TGCTTGTACGGCGGTTTGG 61.255 57.895 13.24 0.00 0.00 3.28
7914 12619 3.952931 ACTCCACGTCATGTCTACTAGT 58.047 45.455 0.00 0.00 0.00 2.57
7915 12620 4.966965 AACTCCACGTCATGTCTACTAG 57.033 45.455 0.00 0.00 0.00 2.57
7925 12630 2.035449 CAGGTGTAGAAACTCCACGTCA 59.965 50.000 0.00 0.00 40.97 4.35
7927 12632 2.296471 CTCAGGTGTAGAAACTCCACGT 59.704 50.000 0.07 0.00 40.97 4.49
7959 12670 7.996465 TTATTTATTTTACTGTTCACACGCG 57.004 32.000 3.53 3.53 0.00 6.01
8108 12821 9.372541 CGTTTGAAAGTAACATTTACATAACGT 57.627 29.630 0.00 0.00 0.00 3.99
8109 12822 8.352936 GCGTTTGAAAGTAACATTTACATAACG 58.647 33.333 0.00 0.00 36.27 3.18
8110 12823 9.171701 TGCGTTTGAAAGTAACATTTACATAAC 57.828 29.630 0.00 0.00 0.00 1.89
8111 12824 9.900710 ATGCGTTTGAAAGTAACATTTACATAA 57.099 25.926 0.00 0.00 0.00 1.90
8112 12825 9.900710 AATGCGTTTGAAAGTAACATTTACATA 57.099 25.926 0.00 0.00 0.00 2.29
8113 12826 8.810652 AATGCGTTTGAAAGTAACATTTACAT 57.189 26.923 0.00 0.00 0.00 2.29
8114 12827 8.535592 CAAATGCGTTTGAAAGTAACATTTACA 58.464 29.630 24.19 0.00 46.03 2.41
8115 12828 8.001549 CCAAATGCGTTTGAAAGTAACATTTAC 58.998 33.333 28.87 0.00 46.03 2.01
8116 12829 7.169982 CCCAAATGCGTTTGAAAGTAACATTTA 59.830 33.333 28.87 0.00 46.03 1.40
8117 12830 6.018343 CCCAAATGCGTTTGAAAGTAACATTT 60.018 34.615 28.87 0.00 46.03 2.32
8118 12831 5.465056 CCCAAATGCGTTTGAAAGTAACATT 59.535 36.000 28.87 0.00 46.03 2.71


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

AutoCloner maintained by Alex Coulton.