Multiple sequence alignment - TraesCS4A01G380600

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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 TraesCS4A01G380600 chr4A 100.000 4356 0 0 1 4356 658227015 658222660 0.000000e+00 8045
1 TraesCS4A01G380600 chr4A 92.237 1842 108 16 2102 3926 657889102 657890925 0.000000e+00 2577
2 TraesCS4A01G380600 chr4A 89.157 913 88 7 2 906 657886173 657887082 0.000000e+00 1127
3 TraesCS4A01G380600 chr4A 90.103 485 32 3 1560 2035 657888272 657888749 2.230000e-172 616
4 TraesCS4A01G380600 chr4A 82.705 451 32 20 897 1313 657887556 657887994 4.140000e-95 359
5 TraesCS4A01G380600 chr7D 94.314 2392 108 16 1560 3945 45656708 45654339 0.000000e+00 3639
6 TraesCS4A01G380600 chr7D 85.658 509 30 15 1015 1504 45569545 45570029 3.030000e-136 496
7 TraesCS4A01G380600 chr7D 84.292 452 18 22 1015 1433 45657286 45656855 4.080000e-105 392
8 TraesCS4A01G380600 chr7D 92.797 236 14 1 1774 2009 45570444 45570676 5.400000e-89 339
9 TraesCS4A01G380600 chr7D 84.906 265 32 5 3687 3947 45570685 45570945 1.200000e-65 261
10 TraesCS4A01G380600 chr7D 88.398 181 7 4 1560 1730 45570250 45570426 5.710000e-49 206
11 TraesCS4A01G380600 chr7A 90.834 2553 156 32 1560 4091 47695380 47697875 0.000000e+00 3347
12 TraesCS4A01G380600 chr7A 93.155 2206 125 11 1560 3758 47797361 47795175 0.000000e+00 3214
13 TraesCS4A01G380600 chr7A 80.277 578 36 30 945 1504 47694714 47695231 8.900000e-97 364
14 TraesCS4A01G380600 chr7A 79.151 518 30 28 945 1441 47797997 47797537 1.980000e-73 287
15 TraesCS4A01G380600 chr7A 83.957 187 24 4 4175 4355 47697907 47698093 1.610000e-39 174
16 TraesCS4A01G380600 chr5B 89.594 1749 148 18 2063 3804 305055635 305053914 0.000000e+00 2191
17 TraesCS4A01G380600 chr5B 86.420 486 43 9 1585 2061 305056246 305055775 1.080000e-140 510
18 TraesCS4A01G380600 chr5B 85.443 158 14 6 3870 4023 305053756 305053604 5.830000e-34 156
19 TraesCS4A01G380600 chr5B 81.457 151 15 6 1249 1398 305056566 305056428 1.280000e-20 111
20 TraesCS4A01G380600 chr5D 89.498 1533 134 13 2289 3816 269342205 269340695 0.000000e+00 1914
21 TraesCS4A01G380600 chr5D 87.449 486 38 5 1585 2061 269343128 269342657 4.960000e-149 538
22 TraesCS4A01G380600 chr5D 92.357 314 21 2 2063 2376 269342517 269342207 1.110000e-120 444
23 TraesCS4A01G380600 chr5D 95.062 81 4 0 1088 1168 269343689 269343609 1.270000e-25 128
24 TraesCS4A01G380600 chr5D 90.625 96 8 1 2063 2157 52727942 52727847 4.570000e-25 126
25 TraesCS4A01G380600 chr5A 89.498 1533 134 13 2289 3816 358049410 358047900 0.000000e+00 1914
26 TraesCS4A01G380600 chr5A 87.037 486 40 4 1585 2061 358050422 358049951 1.070000e-145 527
27 TraesCS4A01G380600 chr5A 92.357 314 21 2 2063 2376 358049811 358049501 1.110000e-120 444
28 TraesCS4A01G380600 chr5A 81.818 187 11 9 1088 1252 358051010 358050825 7.600000e-28 135
29 TraesCS4A01G380600 chr5A 80.263 152 13 9 1249 1398 358050738 358050602 9.970000e-17 99
30 TraesCS4A01G380600 chr2B 91.016 679 43 8 1497 2166 275457259 275456590 0.000000e+00 900
31 TraesCS4A01G380600 chr3D 87.578 161 15 3 3824 3983 566397710 566397866 9.620000e-42 182
32 TraesCS4A01G380600 chr3D 85.093 161 18 4 3824 3983 566391467 566391622 4.510000e-35 159
33 TraesCS4A01G380600 chr3D 86.087 115 10 4 3570 3681 566391197 566391308 7.650000e-23 119
34 TraesCS4A01G380600 chr3B 86.709 158 16 3 3827 3983 755607019 755606866 2.080000e-38 171
35 TraesCS4A01G380600 chr3B 85.802 162 17 5 3824 3983 754772779 754772622 2.690000e-37 167
36 TraesCS4A01G380600 chr3B 85.366 164 19 3 3827 3989 754723167 754723008 9.690000e-37 165
37 TraesCS4A01G380600 chr3A 86.709 158 16 4 3827 3983 700954937 700954784 2.080000e-38 171
38 TraesCS4A01G380600 chr3A 87.097 93 5 4 3599 3687 700962791 700962702 9.970000e-17 99


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 TraesCS4A01G380600 chr4A 658222660 658227015 4355 True 8045.00 8045 100.000000 1 4356 1 chr4A.!!$R1 4355
1 TraesCS4A01G380600 chr4A 657886173 657890925 4752 False 1169.75 2577 88.550500 2 3926 4 chr4A.!!$F1 3924
2 TraesCS4A01G380600 chr7D 45654339 45657286 2947 True 2015.50 3639 89.303000 1015 3945 2 chr7D.!!$R1 2930
3 TraesCS4A01G380600 chr7D 45569545 45570945 1400 False 325.50 496 87.939750 1015 3947 4 chr7D.!!$F1 2932
4 TraesCS4A01G380600 chr7A 47795175 47797997 2822 True 1750.50 3214 86.153000 945 3758 2 chr7A.!!$R1 2813
5 TraesCS4A01G380600 chr7A 47694714 47698093 3379 False 1295.00 3347 85.022667 945 4355 3 chr7A.!!$F1 3410
6 TraesCS4A01G380600 chr5B 305053604 305056566 2962 True 742.00 2191 85.728500 1249 4023 4 chr5B.!!$R1 2774
7 TraesCS4A01G380600 chr5D 269340695 269343689 2994 True 756.00 1914 91.091500 1088 3816 4 chr5D.!!$R2 2728
8 TraesCS4A01G380600 chr5A 358047900 358051010 3110 True 623.80 1914 86.194600 1088 3816 5 chr5A.!!$R1 2728
9 TraesCS4A01G380600 chr2B 275456590 275457259 669 True 900.00 900 91.016000 1497 2166 1 chr2B.!!$R1 669

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
490 494 0.036875 GCCTCAGTGTAGCCACCTTT 59.963 55.000 0.00 0.0 42.88 3.11 F
807 813 0.248661 CCGACGTGGCAGACATCTAG 60.249 60.000 0.00 0.0 0.00 2.43 F
872 881 1.000163 TGAACGTCCAGAGCTTGACTC 60.000 52.381 9.42 0.0 46.66 3.36 F
2687 4066 0.670162 GAAGCACAAGCCAAAGAGCA 59.330 50.000 0.00 0.0 43.56 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2635 0.252761 CCCCCATTTTCATTGGTGGC 59.747 55.000 0.00 0.00 31.99 5.01 R
2083 3117 1.228276 GGATCCTGGCGAAATCCCC 60.228 63.158 3.84 0.00 34.14 4.81 R
2816 4195 2.162681 GTGAGGTAGCAGCAAACCATT 58.837 47.619 16.95 0.02 38.30 3.16 R
3989 5496 0.110238 CTAGCAACGCACGCAACAAT 60.110 50.000 0.00 0.00 0.00 2.71 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
65 66 1.338107 GCTTTTAACCAGCTTGGGGT 58.662 50.000 7.06 0.00 43.37 4.95
132 135 5.066634 CCATAGCACTCGTATATGGAGGTAG 59.933 48.000 12.02 2.40 45.91 3.18
134 137 3.155501 GCACTCGTATATGGAGGTAGGT 58.844 50.000 9.57 0.00 35.82 3.08
161 164 1.217001 CATGCCAATTAGCGTCGCTA 58.783 50.000 22.68 22.68 40.44 4.26
164 167 0.853419 GCCAATTAGCGTCGCTAGAC 59.147 55.000 24.76 11.49 42.34 2.59
197 200 2.671070 CGCCACACCCCAATCTCT 59.329 61.111 0.00 0.00 0.00 3.10
203 206 1.811266 CACCCCAATCTCTGACGCG 60.811 63.158 3.53 3.53 0.00 6.01
238 241 4.286808 TGACCATCTGAAACTCATCTCCAA 59.713 41.667 0.00 0.00 0.00 3.53
248 251 1.490910 CTCATCTCCAACCCTAACCCC 59.509 57.143 0.00 0.00 0.00 4.95
250 253 0.986550 ATCTCCAACCCTAACCCCGG 60.987 60.000 0.00 0.00 0.00 5.73
251 254 1.921857 CTCCAACCCTAACCCCGGT 60.922 63.158 0.00 0.00 0.00 5.28
255 258 3.198299 AACCCTAACCCCGGTCCCT 62.198 63.158 0.00 0.00 0.00 4.20
308 312 0.179084 TGGACCGCGAATGATCTTCC 60.179 55.000 8.23 0.33 0.00 3.46
311 315 2.598632 CCGCGAATGATCTTCCCGC 61.599 63.158 8.23 14.29 42.11 6.13
320 324 2.311688 GATCTTCCCGCCACGACCAT 62.312 60.000 0.00 0.00 0.00 3.55
323 327 3.599285 TTCCCGCCACGACCATGAC 62.599 63.158 0.00 0.00 0.00 3.06
330 334 1.153823 CACGACCATGACGAGGACC 60.154 63.158 16.44 0.00 34.70 4.46
345 349 4.697756 ACCGCCACACCATCCACG 62.698 66.667 0.00 0.00 0.00 4.94
349 353 2.034879 GCCACACCATCCACGACTG 61.035 63.158 0.00 0.00 0.00 3.51
381 385 1.305219 CCACCGATGCGACAACCATT 61.305 55.000 0.00 0.00 0.00 3.16
383 387 1.735018 CACCGATGCGACAACCATTTA 59.265 47.619 0.00 0.00 0.00 1.40
489 493 1.679898 GCCTCAGTGTAGCCACCTT 59.320 57.895 0.00 0.00 42.88 3.50
490 494 0.036875 GCCTCAGTGTAGCCACCTTT 59.963 55.000 0.00 0.00 42.88 3.11
515 519 0.693049 ACGATGAAAGGCCAAGGACT 59.307 50.000 5.01 0.00 32.88 3.85
592 596 4.511246 ATGGTGCCCGCCATGGAG 62.511 66.667 18.40 13.36 46.63 3.86
603 607 2.264480 CATGGAGGACGTCGGCAA 59.736 61.111 9.92 0.00 0.00 4.52
605 609 0.953471 CATGGAGGACGTCGGCAAAA 60.953 55.000 9.92 0.00 0.00 2.44
607 611 0.250553 TGGAGGACGTCGGCAAAAAT 60.251 50.000 9.92 0.00 0.00 1.82
618 622 1.067283 CGGCAAAAATATGTGGTGGCA 60.067 47.619 4.77 0.00 34.65 4.92
621 625 2.261345 CAAAAATATGTGGTGGCAGCG 58.739 47.619 12.58 0.00 0.00 5.18
622 626 0.817013 AAAATATGTGGTGGCAGCGG 59.183 50.000 12.58 0.00 0.00 5.52
623 627 1.666209 AAATATGTGGTGGCAGCGGC 61.666 55.000 12.58 0.00 40.13 6.53
664 668 0.457851 GGATGGAGTGACTGAGGTCG 59.542 60.000 0.00 0.00 44.83 4.79
667 671 1.606889 GGAGTGACTGAGGTCGGGT 60.607 63.158 0.00 0.00 44.83 5.28
676 680 4.369850 AGGTCGGGTAAGGCCTAC 57.630 61.111 5.16 4.61 45.84 3.18
680 684 1.754234 TCGGGTAAGGCCTACGGTC 60.754 63.158 5.16 0.00 37.43 4.79
684 688 0.685458 GGTAAGGCCTACGGTCTGGA 60.685 60.000 5.16 0.00 36.17 3.86
694 698 2.990479 GGTCTGGAGGATTGCGGT 59.010 61.111 0.00 0.00 0.00 5.68
702 706 2.895372 GGATTGCGGTGGTAGCGG 60.895 66.667 2.54 0.00 39.82 5.52
703 707 2.125269 GATTGCGGTGGTAGCGGT 60.125 61.111 2.54 0.00 39.82 5.68
709 713 2.577593 GGTGGTAGCGGTGGACTC 59.422 66.667 0.00 0.00 0.00 3.36
710 714 2.577593 GTGGTAGCGGTGGACTCC 59.422 66.667 0.00 0.00 0.00 3.85
728 732 3.535962 GAGAGCGGAGGAGGGCAG 61.536 72.222 0.00 0.00 0.00 4.85
733 737 3.847602 CGGAGGAGGGCAGCAGAG 61.848 72.222 0.00 0.00 0.00 3.35
734 738 2.686835 GGAGGAGGGCAGCAGAGT 60.687 66.667 0.00 0.00 0.00 3.24
735 739 1.381872 GGAGGAGGGCAGCAGAGTA 60.382 63.158 0.00 0.00 0.00 2.59
784 790 2.187958 TGGGTGGGTCTAGATTGTCAG 58.812 52.381 0.00 0.00 0.00 3.51
792 798 2.025155 TCTAGATTGTCAGAGCCCGAC 58.975 52.381 0.00 0.00 0.00 4.79
793 799 0.738975 TAGATTGTCAGAGCCCGACG 59.261 55.000 0.00 0.00 36.11 5.12
805 811 2.573869 CCGACGTGGCAGACATCT 59.426 61.111 0.00 0.00 0.00 2.90
807 813 0.248661 CCGACGTGGCAGACATCTAG 60.249 60.000 0.00 0.00 0.00 2.43
852 858 4.829872 TGTGGTCGTACTATGGGATTTT 57.170 40.909 0.00 0.00 0.00 1.82
872 881 1.000163 TGAACGTCCAGAGCTTGACTC 60.000 52.381 9.42 0.00 46.66 3.36
909 918 9.838339 ATGTTATTTGGAGGTCTGTAAATAGAG 57.162 33.333 0.00 0.00 0.00 2.43
910 919 8.822805 TGTTATTTGGAGGTCTGTAAATAGAGT 58.177 33.333 0.00 0.00 0.00 3.24
911 920 9.315525 GTTATTTGGAGGTCTGTAAATAGAGTC 57.684 37.037 0.00 0.00 0.00 3.36
912 921 5.934402 TTGGAGGTCTGTAAATAGAGTCC 57.066 43.478 0.00 0.00 34.04 3.85
913 922 4.942944 TGGAGGTCTGTAAATAGAGTCCA 58.057 43.478 0.00 0.00 38.09 4.02
915 924 4.710375 GGAGGTCTGTAAATAGAGTCCACA 59.290 45.833 4.27 0.00 33.80 4.17
918 1407 5.958380 AGGTCTGTAAATAGAGTCCACATCA 59.042 40.000 4.27 0.00 29.46 3.07
980 1478 2.511452 AATCTCCCTCCCATCCGCG 61.511 63.158 0.00 0.00 0.00 6.46
1009 1514 1.538849 CGTCTGAATCCATGGATCGCA 60.539 52.381 27.45 24.24 33.08 5.10
1066 1577 4.796231 ACGGCAGCGACGGACATC 62.796 66.667 8.57 0.00 39.02 3.06
1067 1578 4.794439 CGGCAGCGACGGACATCA 62.794 66.667 0.00 0.00 0.00 3.07
1068 1579 3.188786 GGCAGCGACGGACATCAC 61.189 66.667 0.00 0.00 0.00 3.06
1167 1708 3.414700 CGCAAGGACCACGACAGC 61.415 66.667 0.00 0.00 0.00 4.40
1168 1709 2.280797 GCAAGGACCACGACAGCA 60.281 61.111 0.00 0.00 0.00 4.41
1169 1710 2.320587 GCAAGGACCACGACAGCAG 61.321 63.158 0.00 0.00 0.00 4.24
1170 1711 2.031163 AAGGACCACGACAGCAGC 59.969 61.111 0.00 0.00 0.00 5.25
1171 1712 3.865929 AAGGACCACGACAGCAGCG 62.866 63.158 0.00 0.00 0.00 5.18
1172 1713 4.357947 GGACCACGACAGCAGCGA 62.358 66.667 0.00 0.00 0.00 4.93
1173 1714 2.807045 GACCACGACAGCAGCGAG 60.807 66.667 0.00 0.00 0.00 5.03
1224 1829 1.760086 CTCAGTGGATCCGCCTCCT 60.760 63.158 21.82 0.00 36.20 3.69
1304 2006 1.140852 AGCGCCTAATGTAAGCATCCA 59.859 47.619 2.29 0.00 33.50 3.41
1396 2112 5.177142 CGAAGTGATTCCTGATATGCTTGAG 59.823 44.000 0.00 0.00 0.00 3.02
1397 2113 5.627182 AGTGATTCCTGATATGCTTGAGT 57.373 39.130 0.00 0.00 0.00 3.41
1398 2114 5.999044 AGTGATTCCTGATATGCTTGAGTT 58.001 37.500 0.00 0.00 0.00 3.01
1399 2115 6.421485 AGTGATTCCTGATATGCTTGAGTTT 58.579 36.000 0.00 0.00 0.00 2.66
1400 2116 6.318144 AGTGATTCCTGATATGCTTGAGTTTG 59.682 38.462 0.00 0.00 0.00 2.93
1401 2117 6.317140 GTGATTCCTGATATGCTTGAGTTTGA 59.683 38.462 0.00 0.00 0.00 2.69
1422 2138 8.915654 GTTTGAGTACCAATTTGATTTGATGAC 58.084 33.333 0.00 0.00 34.23 3.06
1423 2139 6.841119 TGAGTACCAATTTGATTTGATGACG 58.159 36.000 0.00 0.00 0.00 4.35
1424 2140 6.652900 TGAGTACCAATTTGATTTGATGACGA 59.347 34.615 0.00 0.00 0.00 4.20
1474 2191 5.855045 ACCTGTCCTACTACTTTCTGTTTG 58.145 41.667 0.00 0.00 0.00 2.93
1494 2211 6.209788 TGTTTGTAAAAACTGTGAGGAAAGGT 59.790 34.615 9.88 0.00 33.95 3.50
1501 2337 2.301346 CTGTGAGGAAAGGTTTGCTGT 58.699 47.619 0.69 0.00 39.04 4.40
1544 2380 6.741109 TGCTGGTGAATATGATGCTTATTTG 58.259 36.000 0.00 0.00 0.00 2.32
1573 2455 1.163554 ACGAGGGTCTACAGTTCGTC 58.836 55.000 0.00 0.00 40.06 4.20
1609 2494 2.337583 ACGTTCATGTCAGGTTCATCG 58.662 47.619 0.00 0.00 0.00 3.84
1641 2526 3.313249 TCCATTCATATGCTGACTTTGCG 59.687 43.478 0.00 0.00 32.17 4.85
1655 2540 8.673711 TGCTGACTTTGCGTCTTAATTATATTT 58.326 29.630 0.00 0.00 43.25 1.40
1692 2588 1.338973 CAATTCTGCACCTGCTGTTGT 59.661 47.619 0.00 0.00 42.66 3.32
1739 2635 7.210174 TCCTTCAAAGGTATATTCGATCACTG 58.790 38.462 8.60 0.00 46.54 3.66
1771 2667 6.906848 TGAAAATGGGGGAGTTAGTATTAGG 58.093 40.000 0.00 0.00 0.00 2.69
1800 2696 5.047802 ACGAAGTTACCGGAAAATCTAGTGA 60.048 40.000 9.46 0.00 37.78 3.41
1937 2833 6.254522 AGAGTACCTGTGGTAAGACAATACT 58.745 40.000 0.00 0.00 40.12 2.12
1940 2836 3.583086 ACCTGTGGTAAGACAATACTGCT 59.417 43.478 0.00 0.00 32.11 4.24
1941 2837 4.775780 ACCTGTGGTAAGACAATACTGCTA 59.224 41.667 0.00 0.00 32.11 3.49
1942 2838 5.425539 ACCTGTGGTAAGACAATACTGCTAT 59.574 40.000 0.00 0.00 32.11 2.97
2083 3117 6.756074 CCTTCACAAGAGATTGCTACTAAGAG 59.244 42.308 0.00 0.00 0.00 2.85
2614 3993 8.690840 GTTGCAGTCATGTTTTAGTTTATTGTC 58.309 33.333 0.00 0.00 0.00 3.18
2687 4066 0.670162 GAAGCACAAGCCAAAGAGCA 59.330 50.000 0.00 0.00 43.56 4.26
2697 4076 7.092716 CACAAGCCAAAGAGCATAAAGTAAAT 58.907 34.615 0.00 0.00 34.23 1.40
2805 4184 2.977772 AGCAGAAGGAAGAGATTCCG 57.022 50.000 1.53 0.00 45.64 4.30
2816 4195 4.262635 GGAAGAGATTCCGGATATTGAGCA 60.263 45.833 4.15 0.00 0.00 4.26
2856 4235 5.368145 TCACTCTGTTGATTGTTTGTAGCT 58.632 37.500 0.00 0.00 0.00 3.32
3067 4447 6.940298 AGCCACTTAAGCTTACTAACAATGAA 59.060 34.615 5.45 0.00 37.24 2.57
3072 4452 9.209175 ACTTAAGCTTACTAACAATGAACAGAG 57.791 33.333 5.45 0.00 0.00 3.35
3196 4576 5.242795 ACCTTATGAAAGTACTTGGTGCT 57.757 39.130 9.34 0.00 0.00 4.40
3352 4739 4.458295 AGCTTTTTGATGATCCTGACACAG 59.542 41.667 0.00 0.00 0.00 3.66
3382 4769 5.121611 TGTTTCACTGTTTGTGTGTACAGAG 59.878 40.000 9.03 1.80 46.27 3.35
3425 4818 0.584876 ACACGCTTTAAAGTGGACGC 59.415 50.000 27.62 8.90 42.25 5.19
3582 4978 2.365617 AGTTGGCGACGAGGATAATGAT 59.634 45.455 0.00 0.00 0.00 2.45
3718 5117 3.640967 TGCTGCCAAGGTGTTTTTAGATT 59.359 39.130 0.00 0.00 0.00 2.40
3792 5194 4.813161 TCTTGAGCTCAAACTTCTGTTGAG 59.187 41.667 28.16 13.11 36.39 3.02
3808 5210 2.420058 TGAGGACAGTGAGAGCGATA 57.580 50.000 0.00 0.00 0.00 2.92
3839 5307 7.985184 TGGATCACTATACTTTGTATTGTCACC 59.015 37.037 0.00 6.80 0.00 4.02
3846 5314 4.870363 ACTTTGTATTGTCACCAACATGC 58.130 39.130 0.00 0.00 37.82 4.06
3863 5332 5.138125 ACATGCCATTTTTAGACTGTTGG 57.862 39.130 0.00 0.00 0.00 3.77
3984 5486 9.794685 TTGAATATTTTTATGCTGCGAATTACA 57.205 25.926 0.00 0.00 0.00 2.41
3985 5487 9.449550 TGAATATTTTTATGCTGCGAATTACAG 57.550 29.630 4.01 4.01 38.22 2.74
3999 5506 5.615581 GCGAATTACAGTATATTGTTGCGTG 59.384 40.000 6.17 0.00 32.56 5.34
4002 5509 2.343101 ACAGTATATTGTTGCGTGCGT 58.657 42.857 0.00 0.00 0.00 5.24
4009 5516 2.111932 TTGTTGCGTGCGTTGCTAGG 62.112 55.000 0.00 0.00 0.00 3.02
4029 5536 2.286294 GGTCGATGAAGTTGCTATGCTG 59.714 50.000 0.00 0.00 0.00 4.41
4034 5541 4.790140 CGATGAAGTTGCTATGCTGTTTTC 59.210 41.667 0.00 0.00 0.00 2.29
4035 5542 5.617529 CGATGAAGTTGCTATGCTGTTTTCA 60.618 40.000 0.00 0.00 0.00 2.69
4037 5544 5.280945 TGAAGTTGCTATGCTGTTTTCAAC 58.719 37.500 0.00 0.00 35.39 3.18
4062 5569 4.776795 TGTTGCTGTGAACTACGATCTA 57.223 40.909 0.00 0.00 0.00 1.98
4072 5579 8.219436 TGTGAACTACGATCTAAACTTTTACG 57.781 34.615 0.00 0.00 0.00 3.18
4073 5580 7.862372 TGTGAACTACGATCTAAACTTTTACGT 59.138 33.333 0.00 0.00 36.52 3.57
4074 5581 8.361579 GTGAACTACGATCTAAACTTTTACGTC 58.638 37.037 0.00 0.00 34.52 4.34
4076 5583 6.325596 ACTACGATCTAAACTTTTACGTCCC 58.674 40.000 0.00 0.00 34.52 4.46
4077 5584 5.397142 ACGATCTAAACTTTTACGTCCCT 57.603 39.130 0.00 0.00 0.00 4.20
4078 5585 5.166398 ACGATCTAAACTTTTACGTCCCTG 58.834 41.667 0.00 0.00 0.00 4.45
4079 5586 4.565564 CGATCTAAACTTTTACGTCCCTGG 59.434 45.833 0.00 0.00 0.00 4.45
4080 5587 5.622914 CGATCTAAACTTTTACGTCCCTGGA 60.623 44.000 0.00 0.00 0.00 3.86
4082 5589 6.117975 TCTAAACTTTTACGTCCCTGGATT 57.882 37.500 0.00 0.00 0.00 3.01
4083 5590 7.243604 TCTAAACTTTTACGTCCCTGGATTA 57.756 36.000 0.00 0.00 0.00 1.75
4084 5591 7.854337 TCTAAACTTTTACGTCCCTGGATTAT 58.146 34.615 0.00 0.00 0.00 1.28
4085 5592 8.980596 TCTAAACTTTTACGTCCCTGGATTATA 58.019 33.333 0.00 0.00 0.00 0.98
4093 5600 8.757982 TTACGTCCCTGGATTATATATACTCC 57.242 38.462 18.07 18.07 33.91 3.85
4095 5602 7.363031 ACGTCCCTGGATTATATATACTCCAT 58.637 38.462 24.51 11.58 40.11 3.41
4096 5603 7.287927 ACGTCCCTGGATTATATATACTCCATG 59.712 40.741 24.51 21.72 40.11 3.66
4097 5604 7.505923 CGTCCCTGGATTATATATACTCCATGA 59.494 40.741 24.51 20.99 40.11 3.07
4098 5605 8.643324 GTCCCTGGATTATATATACTCCATGAC 58.357 40.741 25.90 25.90 40.11 3.06
4101 5608 9.206690 CCTGGATTATATATACTCCATGACAGT 57.793 37.037 24.51 0.00 40.11 3.55
4110 5617 3.779444 ACTCCATGACAGTAACCTCTGA 58.221 45.455 0.00 0.00 38.63 3.27
4111 5618 3.766591 ACTCCATGACAGTAACCTCTGAG 59.233 47.826 0.00 0.00 38.63 3.35
4112 5619 3.766591 CTCCATGACAGTAACCTCTGAGT 59.233 47.826 3.66 0.00 38.63 3.41
4116 5623 5.186021 CCATGACAGTAACCTCTGAGTAACT 59.814 44.000 3.66 1.38 38.63 2.24
4117 5624 6.295349 CCATGACAGTAACCTCTGAGTAACTT 60.295 42.308 3.66 0.00 38.63 2.66
4118 5625 6.726490 TGACAGTAACCTCTGAGTAACTTT 57.274 37.500 3.66 0.00 38.63 2.66
4119 5626 7.120923 TGACAGTAACCTCTGAGTAACTTTT 57.879 36.000 3.66 0.00 38.63 2.27
4120 5627 7.562135 TGACAGTAACCTCTGAGTAACTTTTT 58.438 34.615 3.66 0.00 38.63 1.94
4122 5629 9.708092 GACAGTAACCTCTGAGTAACTTTTTAT 57.292 33.333 3.66 0.00 38.63 1.40
4128 5635 7.545489 ACCTCTGAGTAACTTTTTATAGGACG 58.455 38.462 3.66 0.00 0.00 4.79
4129 5636 7.178097 ACCTCTGAGTAACTTTTTATAGGACGT 59.822 37.037 3.66 0.00 0.00 4.34
4130 5637 8.033626 CCTCTGAGTAACTTTTTATAGGACGTT 58.966 37.037 3.66 0.00 0.00 3.99
4131 5638 9.420551 CTCTGAGTAACTTTTTATAGGACGTTT 57.579 33.333 0.00 0.00 0.00 3.60
4132 5639 9.415544 TCTGAGTAACTTTTTATAGGACGTTTC 57.584 33.333 0.00 0.00 0.00 2.78
4133 5640 9.420551 CTGAGTAACTTTTTATAGGACGTTTCT 57.579 33.333 0.00 0.00 0.00 2.52
4134 5641 9.199982 TGAGTAACTTTTTATAGGACGTTTCTG 57.800 33.333 0.00 0.00 0.00 3.02
4135 5642 9.201127 GAGTAACTTTTTATAGGACGTTTCTGT 57.799 33.333 0.00 0.00 0.00 3.41
4140 5647 9.631452 ACTTTTTATAGGACGTTTCTGTAGTAC 57.369 33.333 0.00 0.00 0.00 2.73
4141 5648 9.630098 CTTTTTATAGGACGTTTCTGTAGTACA 57.370 33.333 2.36 2.36 0.00 2.90
4143 5650 9.577110 TTTTATAGGACGTTTCTGTAGTACATG 57.423 33.333 2.82 0.00 0.00 3.21
4144 5651 8.510243 TTATAGGACGTTTCTGTAGTACATGA 57.490 34.615 2.82 1.18 0.00 3.07
4145 5652 5.056894 AGGACGTTTCTGTAGTACATGAC 57.943 43.478 2.82 2.57 0.00 3.06
4146 5653 4.521639 AGGACGTTTCTGTAGTACATGACA 59.478 41.667 2.82 0.00 0.00 3.58
4147 5654 4.857588 GGACGTTTCTGTAGTACATGACAG 59.142 45.833 2.82 13.57 43.70 3.51
4148 5655 5.449107 ACGTTTCTGTAGTACATGACAGT 57.551 39.130 17.21 0.00 43.01 3.55
4149 5656 5.220381 ACGTTTCTGTAGTACATGACAGTG 58.780 41.667 17.21 10.99 43.01 3.66
4150 5657 5.220381 CGTTTCTGTAGTACATGACAGTGT 58.780 41.667 17.21 0.00 43.01 3.55
4151 5658 6.016860 ACGTTTCTGTAGTACATGACAGTGTA 60.017 38.462 17.21 6.60 43.01 2.90
4152 5659 6.859508 CGTTTCTGTAGTACATGACAGTGTAA 59.140 38.462 17.21 0.00 43.01 2.41
4153 5660 7.380333 CGTTTCTGTAGTACATGACAGTGTAAA 59.620 37.037 17.21 10.77 43.01 2.01
4154 5661 9.037737 GTTTCTGTAGTACATGACAGTGTAAAA 57.962 33.333 17.21 10.52 43.01 1.52
4155 5662 9.602568 TTTCTGTAGTACATGACAGTGTAAAAA 57.397 29.630 17.21 10.27 43.01 1.94
4184 5691 0.175531 AGTTGTGTGGTTTTGCAGCC 59.824 50.000 0.00 0.00 0.00 4.85
4211 5723 5.118510 GGTTCCGCAAAATAACATGTTTGAG 59.881 40.000 17.78 10.32 36.96 3.02
4217 5729 7.042791 CCGCAAAATAACATGTTTGAGTTTTCT 60.043 33.333 17.78 0.00 36.96 2.52
4253 5765 8.730680 ACCATATGTTGTCTAATCTTTCACAAC 58.269 33.333 1.24 6.80 45.86 3.32
4256 5768 5.030874 GTTGTCTAATCTTTCACAACGGG 57.969 43.478 0.00 0.00 39.31 5.28
4285 5798 2.134789 ATCTAAGTGGCTTTGGCAGG 57.865 50.000 0.00 0.00 39.19 4.85
4286 5799 1.064003 TCTAAGTGGCTTTGGCAGGA 58.936 50.000 0.00 0.00 39.19 3.86
4291 5804 2.436109 GGCTTTGGCAGGAGGTGA 59.564 61.111 2.74 0.00 40.87 4.02
4307 5820 6.366877 CAGGAGGTGATTTTGTGCTAATTTTG 59.633 38.462 0.00 0.00 0.00 2.44
4315 5828 4.862902 TTGTGCTAATTTTGCCAAGCTA 57.137 36.364 0.43 0.00 35.95 3.32
4316 5829 4.173036 TGTGCTAATTTTGCCAAGCTAC 57.827 40.909 0.43 0.00 35.95 3.58
4323 5836 2.675658 TTTGCCAAGCTACTTTCCCT 57.324 45.000 0.00 0.00 0.00 4.20
4326 5839 2.957474 TGCCAAGCTACTTTCCCTTTT 58.043 42.857 0.00 0.00 0.00 2.27
4328 5841 4.475345 TGCCAAGCTACTTTCCCTTTTTA 58.525 39.130 0.00 0.00 0.00 1.52
4331 5844 5.077564 CCAAGCTACTTTCCCTTTTTACCT 58.922 41.667 0.00 0.00 0.00 3.08
4337 5850 7.125204 AGCTACTTTCCCTTTTTACCTTTGTTT 59.875 33.333 0.00 0.00 0.00 2.83
4338 5851 7.437267 GCTACTTTCCCTTTTTACCTTTGTTTC 59.563 37.037 0.00 0.00 0.00 2.78
4344 5857 5.163457 CCCTTTTTACCTTTGTTTCTGCTGA 60.163 40.000 0.00 0.00 0.00 4.26
4346 5859 4.911514 TTTACCTTTGTTTCTGCTGACC 57.088 40.909 0.00 0.00 0.00 4.02
4355 5868 3.754850 TGTTTCTGCTGACCATCTCATTG 59.245 43.478 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.675029 AGCAACCCGTCGAACCCG 62.675 66.667 0.00 0.00 37.07 5.28
33 34 1.228533 TAAAAGCAACCCGTCGAACC 58.771 50.000 0.00 0.00 0.00 3.62
39 40 0.671796 GCTGGTTAAAAGCAACCCGT 59.328 50.000 6.54 0.00 46.29 5.28
44 45 1.691434 CCCCAAGCTGGTTAAAAGCAA 59.309 47.619 12.56 0.00 43.37 3.91
56 57 0.185175 AGACGGAAAAACCCCAAGCT 59.815 50.000 0.00 0.00 34.64 3.74
86 87 4.322349 GGAGGCATGTAGGTAGATGATGAC 60.322 50.000 0.00 0.00 0.00 3.06
183 186 1.021390 GCGTCAGAGATTGGGGTGTG 61.021 60.000 0.00 0.00 0.00 3.82
186 189 1.827399 AACGCGTCAGAGATTGGGGT 61.827 55.000 14.44 0.00 0.00 4.95
197 200 2.434185 GATGGGAGCAACGCGTCA 60.434 61.111 14.44 5.13 43.81 4.35
203 206 1.211457 AGATGGTCAGATGGGAGCAAC 59.789 52.381 0.00 0.00 46.98 4.17
238 241 3.619030 AGGGACCGGGGTTAGGGT 61.619 66.667 6.32 0.00 39.83 4.34
255 258 1.002017 ATTTACGGTCCGAGGGGGA 59.998 57.895 20.51 0.00 44.68 4.81
297 301 0.179084 TCGTGGCGGGAAGATCATTC 60.179 55.000 0.00 0.00 0.00 2.67
308 312 4.429212 TCGTCATGGTCGTGGCGG 62.429 66.667 15.68 0.05 46.46 6.13
311 315 1.153823 GTCCTCGTCATGGTCGTGG 60.154 63.158 18.76 18.76 41.38 4.94
323 327 4.082523 ATGGTGTGGCGGTCCTCG 62.083 66.667 0.00 0.00 42.76 4.63
330 334 3.118454 GTCGTGGATGGTGTGGCG 61.118 66.667 0.00 0.00 0.00 5.69
377 381 0.370273 GCAGCGACTCACGTAAATGG 59.630 55.000 0.00 0.00 44.60 3.16
381 385 1.372499 GTGGCAGCGACTCACGTAA 60.372 57.895 0.00 0.00 44.60 3.18
383 387 4.664677 GGTGGCAGCGACTCACGT 62.665 66.667 7.56 0.00 44.60 4.49
397 401 1.990799 TTTCTATGACGACAGCGGTG 58.009 50.000 14.13 14.13 43.17 4.94
402 406 3.557595 GCCTTCCATTTCTATGACGACAG 59.442 47.826 0.00 0.00 33.37 3.51
405 409 2.158813 GGGCCTTCCATTTCTATGACGA 60.159 50.000 0.84 0.00 33.37 4.20
444 448 1.604915 GCTTCCTCCCTTCCTGGAC 59.395 63.158 0.00 0.00 38.35 4.02
489 493 1.073125 TGGCCTTTCATCGTTCCTCAA 59.927 47.619 3.32 0.00 0.00 3.02
490 494 0.690192 TGGCCTTTCATCGTTCCTCA 59.310 50.000 3.32 0.00 0.00 3.86
515 519 8.418662 AGATACTTACATTAAGCATTGTCCGTA 58.581 33.333 0.00 0.00 39.39 4.02
592 596 2.477189 CCACATATTTTTGCCGACGTCC 60.477 50.000 10.58 0.00 0.00 4.79
603 607 0.817013 CCGCTGCCACCACATATTTT 59.183 50.000 0.00 0.00 0.00 1.82
605 609 2.120909 GCCGCTGCCACCACATATT 61.121 57.895 0.00 0.00 0.00 1.28
607 611 3.974835 CTGCCGCTGCCACCACATA 62.975 63.158 0.00 0.00 36.33 2.29
618 622 2.203337 TTTGTCAAGGCTGCCGCT 60.203 55.556 13.96 1.18 36.09 5.52
621 625 2.261215 CCTCTTTGTCAAGGCTGCC 58.739 57.895 11.65 11.65 0.00 4.85
641 645 0.900421 CTCAGTCACTCCATCCAGCA 59.100 55.000 0.00 0.00 0.00 4.41
675 679 2.579201 CGCAATCCTCCAGACCGT 59.421 61.111 0.00 0.00 0.00 4.83
676 680 2.202932 CCGCAATCCTCCAGACCG 60.203 66.667 0.00 0.00 0.00 4.79
680 684 0.179073 CTACCACCGCAATCCTCCAG 60.179 60.000 0.00 0.00 0.00 3.86
684 688 2.186903 CGCTACCACCGCAATCCT 59.813 61.111 0.00 0.00 0.00 3.24
694 698 3.066190 CGGAGTCCACCGCTACCA 61.066 66.667 10.49 0.00 46.20 3.25
753 759 0.038599 ACCCACCCAAACCGTTATCC 59.961 55.000 0.00 0.00 0.00 2.59
757 763 0.399075 CTAGACCCACCCAAACCGTT 59.601 55.000 0.00 0.00 0.00 4.44
759 765 0.909623 ATCTAGACCCACCCAAACCG 59.090 55.000 0.00 0.00 0.00 4.44
792 798 1.227380 GGCCTAGATGTCTGCCACG 60.227 63.158 0.00 0.00 43.46 4.94
793 799 1.147153 GGGCCTAGATGTCTGCCAC 59.853 63.158 0.84 0.93 45.83 5.01
826 832 5.936187 TCCCATAGTACGACCACAAATTA 57.064 39.130 0.00 0.00 0.00 1.40
827 833 4.829872 TCCCATAGTACGACCACAAATT 57.170 40.909 0.00 0.00 0.00 1.82
828 834 5.367945 AATCCCATAGTACGACCACAAAT 57.632 39.130 0.00 0.00 0.00 2.32
852 858 1.000163 GAGTCAAGCTCTGGACGTTCA 60.000 52.381 0.00 0.00 40.98 3.18
883 892 9.838339 CTCTATTTACAGACCTCCAAATAACAT 57.162 33.333 0.00 0.00 0.00 2.71
886 895 8.483758 GGACTCTATTTACAGACCTCCAAATAA 58.516 37.037 0.00 0.00 0.00 1.40
887 896 7.622081 TGGACTCTATTTACAGACCTCCAAATA 59.378 37.037 0.00 0.00 29.19 1.40
899 908 5.071788 GGGGATGATGTGGACTCTATTTACA 59.928 44.000 0.00 0.00 0.00 2.41
901 910 4.597507 GGGGGATGATGTGGACTCTATTTA 59.402 45.833 0.00 0.00 0.00 1.40
906 915 0.044702 TGGGGGATGATGTGGACTCT 59.955 55.000 0.00 0.00 0.00 3.24
907 916 0.181350 GTGGGGGATGATGTGGACTC 59.819 60.000 0.00 0.00 0.00 3.36
908 917 1.626356 CGTGGGGGATGATGTGGACT 61.626 60.000 0.00 0.00 0.00 3.85
909 918 1.153168 CGTGGGGGATGATGTGGAC 60.153 63.158 0.00 0.00 0.00 4.02
910 919 3.042733 GCGTGGGGGATGATGTGGA 62.043 63.158 0.00 0.00 0.00 4.02
911 920 2.516930 GCGTGGGGGATGATGTGG 60.517 66.667 0.00 0.00 0.00 4.17
912 921 0.964860 TTTGCGTGGGGGATGATGTG 60.965 55.000 0.00 0.00 0.00 3.21
913 922 0.965363 GTTTGCGTGGGGGATGATGT 60.965 55.000 0.00 0.00 0.00 3.06
915 924 1.748879 CGTTTGCGTGGGGGATGAT 60.749 57.895 0.00 0.00 0.00 2.45
980 1478 1.301009 GATTCAGACGGGCGGATCC 60.301 63.158 0.00 0.00 0.00 3.36
1022 1533 3.771160 GTCGGTGGCGGTCCTCAT 61.771 66.667 0.00 0.00 0.00 2.90
1052 1563 3.188786 GGTGATGTCCGTCGCTGC 61.189 66.667 0.00 0.00 0.00 5.25
1066 1577 1.827789 CCTTGTGGTGGTGGTGGTG 60.828 63.158 0.00 0.00 0.00 4.17
1067 1578 2.600731 CCTTGTGGTGGTGGTGGT 59.399 61.111 0.00 0.00 0.00 4.16
1068 1579 2.912025 GCCTTGTGGTGGTGGTGG 60.912 66.667 0.00 0.00 35.27 4.61
1152 1693 2.320587 GCTGCTGTCGTGGTCCTTG 61.321 63.158 0.00 0.00 0.00 3.61
1197 1802 0.399233 GATCCACTGAGGCCCTAGGT 60.399 60.000 8.29 0.00 37.29 3.08
1224 1829 1.537889 TGGCCTTTCCTCCTTCCGA 60.538 57.895 3.32 0.00 35.26 4.55
1327 2029 7.105588 TCACATCACTATAAAGCATGAACAGT 58.894 34.615 0.00 0.00 0.00 3.55
1328 2030 7.543947 TCACATCACTATAAAGCATGAACAG 57.456 36.000 0.00 0.00 0.00 3.16
1396 2112 8.915654 GTCATCAAATCAAATTGGTACTCAAAC 58.084 33.333 0.00 0.00 39.05 2.93
1397 2113 7.807433 CGTCATCAAATCAAATTGGTACTCAAA 59.193 33.333 0.00 0.00 39.05 2.69
1398 2114 7.174080 TCGTCATCAAATCAAATTGGTACTCAA 59.826 33.333 0.00 0.00 40.01 3.02
1399 2115 6.652900 TCGTCATCAAATCAAATTGGTACTCA 59.347 34.615 0.00 0.00 0.00 3.41
1400 2116 7.072177 TCGTCATCAAATCAAATTGGTACTC 57.928 36.000 0.00 0.00 0.00 2.59
1401 2117 7.174946 AGTTCGTCATCAAATCAAATTGGTACT 59.825 33.333 0.00 0.00 0.00 2.73
1474 2191 5.518847 GCAAACCTTTCCTCACAGTTTTTAC 59.481 40.000 0.00 0.00 0.00 2.01
1501 2337 8.407832 CACCAGCAATGTAAATATCATCTTCAA 58.592 33.333 0.00 0.00 0.00 2.69
1544 2380 5.301298 ACTGTAGACCCTCGTATATTTCACC 59.699 44.000 0.00 0.00 0.00 4.02
1555 2392 1.451067 AGACGAACTGTAGACCCTCG 58.549 55.000 0.00 0.00 35.68 4.63
1609 2494 9.403110 GTCAGCATATGAATGGAATCAATTAAC 57.597 33.333 6.97 0.00 40.43 2.01
1641 2526 7.920682 CACCACCCTGCAAAATATAATTAAGAC 59.079 37.037 0.00 0.00 0.00 3.01
1655 2540 1.993701 TTGAGAGCACCACCCTGCAA 61.994 55.000 0.00 0.00 39.86 4.08
1739 2635 0.252761 CCCCCATTTTCATTGGTGGC 59.747 55.000 0.00 0.00 31.99 5.01
1771 2667 2.712057 TTCCGGTAACTTCGTCAGAC 57.288 50.000 0.00 0.00 0.00 3.51
1786 2682 6.036517 CAGTTCCATCTTCACTAGATTTTCCG 59.963 42.308 0.00 0.00 41.78 4.30
1800 2696 5.623824 GCAGATGAATTTGCAGTTCCATCTT 60.624 40.000 16.12 5.06 40.02 2.40
1916 2812 4.868734 GCAGTATTGTCTTACCACAGGTAC 59.131 45.833 0.00 0.00 37.97 3.34
1937 2833 6.706270 GCAAAGGACTAGCAGTAATAATAGCA 59.294 38.462 0.00 0.00 0.00 3.49
1940 2836 8.482943 TGAAGCAAAGGACTAGCAGTAATAATA 58.517 33.333 0.00 0.00 0.00 0.98
1941 2837 7.338710 TGAAGCAAAGGACTAGCAGTAATAAT 58.661 34.615 0.00 0.00 0.00 1.28
1942 2838 6.707290 TGAAGCAAAGGACTAGCAGTAATAA 58.293 36.000 0.00 0.00 0.00 1.40
2083 3117 1.228276 GGATCCTGGCGAAATCCCC 60.228 63.158 3.84 0.00 34.14 4.81
2588 3967 8.574196 ACAATAAACTAAAACATGACTGCAAC 57.426 30.769 0.00 0.00 0.00 4.17
2724 4103 3.552890 GCTTTGGGTTCATGTCAACTTCC 60.553 47.826 0.00 0.00 0.00 3.46
2778 4157 3.002102 CTCTTCCTTCTGCTTCTGCTTC 58.998 50.000 0.00 0.00 40.48 3.86
2816 4195 2.162681 GTGAGGTAGCAGCAAACCATT 58.837 47.619 16.95 0.02 38.30 3.16
2856 4235 8.998277 AAGTAGCTGTATACTGATAAAGGAGA 57.002 34.615 13.44 0.00 36.14 3.71
3067 4447 5.654650 CCTCTGTGTTCTATACTTCCTCTGT 59.345 44.000 0.00 0.00 0.00 3.41
3072 4452 3.707793 CGCCTCTGTGTTCTATACTTCC 58.292 50.000 0.00 0.00 0.00 3.46
3142 4522 1.228675 CTTGGGCTTTGGTGGCTCT 60.229 57.895 0.00 0.00 0.00 4.09
3196 4576 0.963962 GTCGGGTCCTGTGTACTTGA 59.036 55.000 0.00 0.00 0.00 3.02
3382 4769 2.430546 CTGTGTGACAGGTCTCTGAC 57.569 55.000 0.65 0.00 42.35 3.51
3425 4818 2.452813 CGGTTGTCTCGGGCATTCG 61.453 63.158 0.00 0.00 0.00 3.34
3537 4930 1.340017 GCAGCCCAGTCAATCCTGTTA 60.340 52.381 0.00 0.00 0.00 2.41
3582 4978 2.599281 TCTGGTTCCTCGTCGGCA 60.599 61.111 0.00 0.00 0.00 5.69
3718 5117 3.644265 TCCCAGTAGTGTGCAACTTTAGA 59.356 43.478 6.82 0.00 40.56 2.10
3792 5194 1.028905 AGCTATCGCTCTCACTGTCC 58.971 55.000 0.00 0.00 45.15 4.02
3808 5210 5.683876 ACAAAGTATAGTGATCCACAGCT 57.316 39.130 0.00 0.00 36.74 4.24
3839 5307 5.406175 CCAACAGTCTAAAAATGGCATGTTG 59.594 40.000 14.60 14.60 43.54 3.33
3846 5314 7.432869 TCAATTCACCAACAGTCTAAAAATGG 58.567 34.615 0.00 0.00 0.00 3.16
3863 5332 3.244976 CCCTTTCATGCGTTCAATTCAC 58.755 45.455 0.00 0.00 0.00 3.18
3918 5418 9.878737 TTAAACTGATAAGGCCTACTAGTAGAT 57.121 33.333 28.07 14.70 35.21 1.98
3919 5419 9.352191 CTTAAACTGATAAGGCCTACTAGTAGA 57.648 37.037 28.07 10.65 31.51 2.59
3920 5420 9.352191 TCTTAAACTGATAAGGCCTACTAGTAG 57.648 37.037 21.11 21.11 34.36 2.57
3921 5421 9.878737 ATCTTAAACTGATAAGGCCTACTAGTA 57.121 33.333 5.16 1.89 34.36 1.82
3922 5422 8.785184 ATCTTAAACTGATAAGGCCTACTAGT 57.215 34.615 5.16 5.82 34.36 2.57
3929 5429 5.125417 TGCACAATCTTAAACTGATAAGGCC 59.875 40.000 0.00 0.00 34.36 5.19
3984 5486 2.475519 GCAACGCACGCAACAATATACT 60.476 45.455 0.00 0.00 0.00 2.12
3985 5487 1.837747 GCAACGCACGCAACAATATAC 59.162 47.619 0.00 0.00 0.00 1.47
3989 5496 0.110238 CTAGCAACGCACGCAACAAT 60.110 50.000 0.00 0.00 0.00 2.71
3990 5497 1.278337 CTAGCAACGCACGCAACAA 59.722 52.632 0.00 0.00 0.00 2.83
3999 5506 0.924090 CTTCATCGACCTAGCAACGC 59.076 55.000 0.00 0.00 0.00 4.84
4002 5509 2.028112 AGCAACTTCATCGACCTAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
4009 5516 2.932614 ACAGCATAGCAACTTCATCGAC 59.067 45.455 0.00 0.00 0.00 4.20
4035 5542 1.967319 AGTTCACAGCAACATCCGTT 58.033 45.000 0.00 0.00 35.01 4.44
4037 5544 1.390123 CGTAGTTCACAGCAACATCCG 59.610 52.381 0.00 0.00 0.00 4.18
4046 5553 8.363755 CGTAAAAGTTTAGATCGTAGTTCACAG 58.636 37.037 0.00 0.00 0.00 3.66
4047 5554 7.862372 ACGTAAAAGTTTAGATCGTAGTTCACA 59.138 33.333 0.00 0.00 0.00 3.58
4048 5555 8.220618 ACGTAAAAGTTTAGATCGTAGTTCAC 57.779 34.615 0.00 0.00 0.00 3.18
4049 5556 7.538678 GGACGTAAAAGTTTAGATCGTAGTTCA 59.461 37.037 0.00 0.00 0.00 3.18
4050 5557 7.008719 GGGACGTAAAAGTTTAGATCGTAGTTC 59.991 40.741 0.00 0.00 0.00 3.01
4051 5558 6.808704 GGGACGTAAAAGTTTAGATCGTAGTT 59.191 38.462 0.00 0.00 0.00 2.24
4052 5559 6.151817 AGGGACGTAAAAGTTTAGATCGTAGT 59.848 38.462 0.00 0.00 0.00 2.73
4053 5560 6.471519 CAGGGACGTAAAAGTTTAGATCGTAG 59.528 42.308 0.00 0.00 0.00 3.51
4083 5590 9.249053 CAGAGGTTACTGTCATGGAGTATATAT 57.751 37.037 6.41 0.00 33.73 0.86
4084 5591 8.445588 TCAGAGGTTACTGTCATGGAGTATATA 58.554 37.037 6.41 0.00 38.79 0.86
4085 5592 7.298374 TCAGAGGTTACTGTCATGGAGTATAT 58.702 38.462 6.41 0.00 38.79 0.86
4091 5598 3.779444 ACTCAGAGGTTACTGTCATGGA 58.221 45.455 1.53 0.00 38.79 3.41
4092 5599 5.186021 AGTTACTCAGAGGTTACTGTCATGG 59.814 44.000 1.53 0.00 38.79 3.66
4093 5600 6.274157 AGTTACTCAGAGGTTACTGTCATG 57.726 41.667 1.53 0.00 38.79 3.07
4095 5602 6.726490 AAAGTTACTCAGAGGTTACTGTCA 57.274 37.500 1.53 0.00 38.79 3.58
4096 5603 9.708092 ATAAAAAGTTACTCAGAGGTTACTGTC 57.292 33.333 1.53 0.00 38.79 3.51
4102 5609 8.033626 CGTCCTATAAAAAGTTACTCAGAGGTT 58.966 37.037 1.53 0.00 0.00 3.50
4103 5610 7.178097 ACGTCCTATAAAAAGTTACTCAGAGGT 59.822 37.037 1.53 0.00 0.00 3.85
4104 5611 7.545489 ACGTCCTATAAAAAGTTACTCAGAGG 58.455 38.462 1.53 0.00 0.00 3.69
4105 5612 8.983307 AACGTCCTATAAAAAGTTACTCAGAG 57.017 34.615 0.00 0.00 0.00 3.35
4106 5613 9.415544 GAAACGTCCTATAAAAAGTTACTCAGA 57.584 33.333 0.00 0.00 0.00 3.27
4107 5614 9.420551 AGAAACGTCCTATAAAAAGTTACTCAG 57.579 33.333 0.00 0.00 0.00 3.35
4108 5615 9.199982 CAGAAACGTCCTATAAAAAGTTACTCA 57.800 33.333 0.00 0.00 0.00 3.41
4117 5624 9.577110 CATGTACTACAGAAACGTCCTATAAAA 57.423 33.333 0.00 0.00 0.00 1.52
4118 5625 8.959548 TCATGTACTACAGAAACGTCCTATAAA 58.040 33.333 0.00 0.00 0.00 1.40
4119 5626 8.400947 GTCATGTACTACAGAAACGTCCTATAA 58.599 37.037 0.00 0.00 0.00 0.98
4120 5627 7.553760 TGTCATGTACTACAGAAACGTCCTATA 59.446 37.037 0.00 0.00 0.00 1.31
4122 5629 5.706833 TGTCATGTACTACAGAAACGTCCTA 59.293 40.000 0.00 0.00 0.00 2.94
4123 5630 4.521639 TGTCATGTACTACAGAAACGTCCT 59.478 41.667 0.00 0.00 0.00 3.85
4124 5631 4.801891 TGTCATGTACTACAGAAACGTCC 58.198 43.478 0.00 0.00 0.00 4.79
4125 5632 5.342525 CACTGTCATGTACTACAGAAACGTC 59.657 44.000 22.20 0.00 44.79 4.34
4126 5633 5.220381 CACTGTCATGTACTACAGAAACGT 58.780 41.667 22.20 0.00 44.79 3.99
4127 5634 5.220381 ACACTGTCATGTACTACAGAAACG 58.780 41.667 22.20 13.30 44.79 3.60
4128 5635 8.583810 TTTACACTGTCATGTACTACAGAAAC 57.416 34.615 22.20 0.00 44.79 2.78
4129 5636 9.602568 TTTTTACACTGTCATGTACTACAGAAA 57.397 29.630 22.20 13.43 44.79 2.52
4153 5660 9.581099 CAAAACCACACAACTATAAGACTTTTT 57.419 29.630 0.00 0.00 0.00 1.94
4154 5661 7.704899 GCAAAACCACACAACTATAAGACTTTT 59.295 33.333 0.00 0.00 0.00 2.27
4155 5662 7.147983 TGCAAAACCACACAACTATAAGACTTT 60.148 33.333 0.00 0.00 0.00 2.66
4156 5663 6.320164 TGCAAAACCACACAACTATAAGACTT 59.680 34.615 0.00 0.00 0.00 3.01
4157 5664 5.825679 TGCAAAACCACACAACTATAAGACT 59.174 36.000 0.00 0.00 0.00 3.24
4158 5665 6.067263 TGCAAAACCACACAACTATAAGAC 57.933 37.500 0.00 0.00 0.00 3.01
4159 5666 5.278266 GCTGCAAAACCACACAACTATAAGA 60.278 40.000 0.00 0.00 0.00 2.10
4160 5667 4.917415 GCTGCAAAACCACACAACTATAAG 59.083 41.667 0.00 0.00 0.00 1.73
4161 5668 4.261825 GGCTGCAAAACCACACAACTATAA 60.262 41.667 0.50 0.00 0.00 0.98
4162 5669 3.254657 GGCTGCAAAACCACACAACTATA 59.745 43.478 0.50 0.00 0.00 1.31
4163 5670 2.035832 GGCTGCAAAACCACACAACTAT 59.964 45.455 0.50 0.00 0.00 2.12
4164 5671 1.407258 GGCTGCAAAACCACACAACTA 59.593 47.619 0.50 0.00 0.00 2.24
4165 5672 0.175531 GGCTGCAAAACCACACAACT 59.824 50.000 0.50 0.00 0.00 3.16
4166 5673 0.809636 GGGCTGCAAAACCACACAAC 60.810 55.000 0.50 0.00 0.00 3.32
4167 5674 1.519719 GGGCTGCAAAACCACACAA 59.480 52.632 0.50 0.00 0.00 3.33
4168 5675 2.780094 CGGGCTGCAAAACCACACA 61.780 57.895 0.50 0.00 0.00 3.72
4169 5676 2.027460 CGGGCTGCAAAACCACAC 59.973 61.111 0.50 0.00 0.00 3.82
4170 5677 3.222855 CCGGGCTGCAAAACCACA 61.223 61.111 0.50 0.00 0.00 4.17
4171 5678 3.989787 CCCGGGCTGCAAAACCAC 61.990 66.667 8.08 0.00 0.00 4.16
4172 5679 4.531426 ACCCGGGCTGCAAAACCA 62.531 61.111 24.08 0.00 0.00 3.67
4173 5680 3.220999 GAACCCGGGCTGCAAAACC 62.221 63.158 24.08 0.00 0.00 3.27
4193 5700 9.986833 AAAGAAAACTCAAACATGTTATTTTGC 57.013 25.926 12.39 7.59 33.50 3.68
4226 5738 8.862325 TGTGAAAGATTAGACAACATATGGTT 57.138 30.769 7.80 0.00 41.47 3.67
4234 5746 4.612939 GCCCGTTGTGAAAGATTAGACAAC 60.613 45.833 0.00 0.00 43.05 3.32
4243 5755 1.475403 TTTTGGCCCGTTGTGAAAGA 58.525 45.000 0.00 0.00 0.00 2.52
4253 5765 3.181487 CCACTTAGATTGATTTTGGCCCG 60.181 47.826 0.00 0.00 0.00 6.13
4256 5768 4.725790 AGCCACTTAGATTGATTTTGGC 57.274 40.909 1.33 1.33 46.95 4.52
4285 5798 5.120674 GGCAAAATTAGCACAAAATCACCTC 59.879 40.000 5.33 0.00 0.00 3.85
4286 5799 4.996758 GGCAAAATTAGCACAAAATCACCT 59.003 37.500 5.33 0.00 0.00 4.00
4291 5804 5.065235 AGCTTGGCAAAATTAGCACAAAAT 58.935 33.333 10.46 0.00 36.11 1.82
4307 5820 4.321750 GGTAAAAAGGGAAAGTAGCTTGGC 60.322 45.833 0.00 0.00 0.00 4.52
4315 5828 7.327975 CAGAAACAAAGGTAAAAAGGGAAAGT 58.672 34.615 0.00 0.00 0.00 2.66
4316 5829 6.257849 GCAGAAACAAAGGTAAAAAGGGAAAG 59.742 38.462 0.00 0.00 0.00 2.62
4323 5836 5.186021 TGGTCAGCAGAAACAAAGGTAAAAA 59.814 36.000 0.00 0.00 0.00 1.94
4326 5839 3.892284 TGGTCAGCAGAAACAAAGGTAA 58.108 40.909 0.00 0.00 0.00 2.85
4328 5841 2.435372 TGGTCAGCAGAAACAAAGGT 57.565 45.000 0.00 0.00 0.00 3.50
4331 5844 3.819368 TGAGATGGTCAGCAGAAACAAA 58.181 40.909 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.