Multiple sequence alignment - TraesCS2B01G126300

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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 TraesCS2B01G126300 chr2B 100.000 3530 0 0 1 3530 94252741 94249212 0.000000e+00 6519.0
1 TraesCS2B01G126300 chr2B 93.277 1904 109 12 1642 3530 94089962 94088063 0.000000e+00 2789.0
2 TraesCS2B01G126300 chr2B 90.718 905 72 8 1639 2535 94099378 94098478 0.000000e+00 1195.0
3 TraesCS2B01G126300 chr2B 88.229 960 96 12 1649 2597 93408785 93409738 0.000000e+00 1131.0
4 TraesCS2B01G126300 chr2B 86.737 852 96 12 1756 2598 93109161 93110004 0.000000e+00 931.0
5 TraesCS2B01G126300 chr2B 94.898 294 15 0 932 1225 94090608 94090315 8.930000e-126 460.0
6 TraesCS2B01G126300 chr2B 86.441 354 34 7 875 1225 93407974 93408316 3.330000e-100 375.0
7 TraesCS2B01G126300 chr2B 85.387 349 39 8 878 1225 93108353 93108690 5.610000e-93 351.0
8 TraesCS2B01G126300 chr2B 90.071 282 11 5 1 278 94102620 94102352 2.020000e-92 350.0
9 TraesCS2B01G126300 chr2B 85.085 295 26 10 904 1192 94101842 94101560 5.770000e-73 285.0
10 TraesCS2B01G126300 chr2B 95.062 162 6 1 1241 1400 237581571 237581410 1.630000e-63 254.0
11 TraesCS2B01G126300 chr2B 84.848 264 23 8 467 723 94091142 94090889 2.100000e-62 250.0
12 TraesCS2B01G126300 chr2B 87.387 222 13 9 721 940 94090840 94090632 1.270000e-59 241.0
13 TraesCS2B01G126300 chr2B 90.419 167 6 5 33 195 94092651 94092491 9.930000e-51 211.0
14 TraesCS2B01G126300 chr2B 90.164 61 2 1 2602 2662 93409770 93409826 3.780000e-10 76.8
15 TraesCS2B01G126300 chr2B 87.692 65 4 1 2598 2662 93110023 93110083 4.890000e-09 73.1
16 TraesCS2B01G126300 chr2B 100.000 30 0 0 694 723 93108139 93108168 4.920000e-04 56.5
17 TraesCS2B01G126300 chr2D 95.011 1904 76 6 1636 3528 60167048 60165153 0.000000e+00 2972.0
18 TraesCS2B01G126300 chr2D 87.488 1015 97 16 1589 2591 59724528 59725524 0.000000e+00 1144.0
19 TraesCS2B01G126300 chr2D 91.935 496 21 9 732 1225 60167846 60167368 0.000000e+00 676.0
20 TraesCS2B01G126300 chr2D 88.740 373 35 5 2225 2591 59836618 59836989 1.930000e-122 449.0
21 TraesCS2B01G126300 chr2D 87.966 349 30 7 878 1225 59723801 59724138 5.490000e-108 401.0
22 TraesCS2B01G126300 chr2D 88.316 291 21 7 1636 1919 59836260 59836544 1.570000e-88 337.0
23 TraesCS2B01G126300 chr2D 84.082 245 21 6 487 723 60168140 60167906 1.650000e-53 220.0
24 TraesCS2B01G126300 chr2D 86.432 199 10 5 1 195 60168539 60168354 5.980000e-48 202.0
25 TraesCS2B01G126300 chr2D 93.651 63 4 0 878 940 59830739 59830801 1.040000e-15 95.3
26 TraesCS2B01G126300 chr2D 100.000 30 0 0 694 723 59723587 59723616 4.920000e-04 56.5
27 TraesCS2B01G126300 chr2D 100.000 30 0 0 694 723 59830524 59830553 4.920000e-04 56.5
28 TraesCS2B01G126300 chr2A 95.128 1170 50 3 1636 2800 60283558 60282391 0.000000e+00 1838.0
29 TraesCS2B01G126300 chr2A 94.580 1144 55 3 1636 2774 60760306 60759165 0.000000e+00 1762.0
30 TraesCS2B01G126300 chr2A 88.900 1018 93 13 1589 2597 59718100 59719106 0.000000e+00 1236.0
31 TraesCS2B01G126300 chr2A 94.264 645 35 2 2888 3530 60759177 60758533 0.000000e+00 985.0
32 TraesCS2B01G126300 chr2A 93.972 647 37 2 2885 3530 60281104 60280459 0.000000e+00 977.0
33 TraesCS2B01G126300 chr2A 91.165 498 25 9 730 1225 60761420 60760940 0.000000e+00 658.0
34 TraesCS2B01G126300 chr2A 90.202 347 28 4 879 1225 60284132 60283792 6.950000e-122 448.0
35 TraesCS2B01G126300 chr2A 88.539 349 28 6 878 1225 59717368 59717705 2.540000e-111 412.0
36 TraesCS2B01G126300 chr2A 85.824 261 20 6 467 723 60761725 60761478 9.720000e-66 261.0
37 TraesCS2B01G126300 chr2A 86.432 199 10 5 1 195 60762093 60761908 5.980000e-48 202.0
38 TraesCS2B01G126300 chr2A 85.075 134 11 2 290 414 60593919 60593786 1.030000e-25 128.0
39 TraesCS2B01G126300 chr2A 89.062 64 3 1 2598 2661 59719126 59719185 3.780000e-10 76.8
40 TraesCS2B01G126300 chr2A 80.189 106 13 7 3429 3530 115436448 115436549 4.890000e-09 73.1
41 TraesCS2B01G126300 chr2A 97.059 34 1 0 1181 1214 711510050 711510017 1.370000e-04 58.4
42 TraesCS2B01G126300 chr2A 100.000 30 0 0 694 723 59706445 59706474 4.920000e-04 56.5
43 TraesCS2B01G126300 chr2A 100.000 30 0 0 694 723 59835316 59835345 4.920000e-04 56.5
44 TraesCS2B01G126300 chr3B 93.939 165 9 1 1239 1402 719421241 719421077 7.570000e-62 248.0
45 TraesCS2B01G126300 chr3B 93.373 166 9 2 1241 1404 602591120 602591285 9.790000e-61 244.0
46 TraesCS2B01G126300 chr6B 93.902 164 8 1 1241 1402 699977610 699977447 2.720000e-61 246.0
47 TraesCS2B01G126300 chr5B 93.413 167 8 2 1236 1400 595395490 595395325 9.790000e-61 244.0
48 TraesCS2B01G126300 chr3D 92.442 172 11 1 1238 1407 571465531 571465360 9.790000e-61 244.0
49 TraesCS2B01G126300 chr3D 92.442 172 11 1 1238 1407 579494789 579494960 9.790000e-61 244.0
50 TraesCS2B01G126300 chr3D 83.732 209 27 4 3323 3530 333397369 333397571 1.290000e-44 191.0
51 TraesCS2B01G126300 chr3A 93.373 166 9 1 1239 1402 581269290 581269125 9.790000e-61 244.0
52 TraesCS2B01G126300 chr7B 92.398 171 11 1 1232 1400 316400762 316400932 3.520000e-60 243.0
53 TraesCS2B01G126300 chr4A 79.532 171 34 1 1057 1227 191375793 191375962 1.720000e-23 121.0


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 TraesCS2B01G126300 chr2B 94249212 94252741 3529 True 6519.000000 6519 100.000000 1 3530 1 chr2B.!!$R1 3529
1 TraesCS2B01G126300 chr2B 94088063 94092651 4588 True 790.200000 2789 90.165800 33 3530 5 chr2B.!!$R3 3497
2 TraesCS2B01G126300 chr2B 94098478 94102620 4142 True 610.000000 1195 88.624667 1 2535 3 chr2B.!!$R4 2534
3 TraesCS2B01G126300 chr2B 93407974 93409826 1852 False 527.600000 1131 88.278000 875 2662 3 chr2B.!!$F2 1787
4 TraesCS2B01G126300 chr2B 93108139 93110083 1944 False 352.900000 931 89.954000 694 2662 4 chr2B.!!$F1 1968
5 TraesCS2B01G126300 chr2D 60165153 60168539 3386 True 1017.500000 2972 89.365000 1 3528 4 chr2D.!!$R1 3527
6 TraesCS2B01G126300 chr2D 59723587 59725524 1937 False 533.833333 1144 91.818000 694 2591 3 chr2D.!!$F1 1897
7 TraesCS2B01G126300 chr2D 59836260 59836989 729 False 393.000000 449 88.528000 1636 2591 2 chr2D.!!$F3 955
8 TraesCS2B01G126300 chr2A 60280459 60284132 3673 True 1087.666667 1838 93.100667 879 3530 3 chr2A.!!$R3 2651
9 TraesCS2B01G126300 chr2A 60758533 60762093 3560 True 773.600000 1762 90.453000 1 3530 5 chr2A.!!$R4 3529
10 TraesCS2B01G126300 chr2A 59717368 59719185 1817 False 574.933333 1236 88.833667 878 2661 3 chr2A.!!$F4 1783

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
646 1869 1.075542 CGCTCGGACACAATAAAGCA 58.924 50.0 0.0 0.0 0.0 3.91 F
1254 3941 0.257039 TGTACTACTCCCTCCGTCCC 59.743 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 5898 1.007154 TGCGTCCGTCGTTGATCAA 60.007 52.632 3.38 3.38 42.13 2.57 R
3034 8065 0.036732 GGTGACAAGAGATGTGGCCA 59.963 55.000 0.00 0.00 44.12 5.36 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
25 26 6.894654 TGTTTATGATTTAGGGCATCTTCCAA 59.105 34.615 0.00 0.00 0.00 3.53
26 27 7.068593 TGTTTATGATTTAGGGCATCTTCCAAG 59.931 37.037 0.00 0.00 0.00 3.61
27 28 4.591321 TGATTTAGGGCATCTTCCAAGT 57.409 40.909 0.00 0.00 0.00 3.16
28 29 4.934356 TGATTTAGGGCATCTTCCAAGTT 58.066 39.130 0.00 0.00 0.00 2.66
29 30 4.949856 TGATTTAGGGCATCTTCCAAGTTC 59.050 41.667 0.00 0.00 0.00 3.01
30 31 4.657814 TTTAGGGCATCTTCCAAGTTCT 57.342 40.909 0.00 0.00 0.00 3.01
31 32 2.503895 AGGGCATCTTCCAAGTTCTG 57.496 50.000 0.00 0.00 0.00 3.02
75 80 6.767902 CAGCTAATTGGCCATCTCTAACTTAA 59.232 38.462 6.09 0.00 0.00 1.85
129 134 3.066203 CCCCGTTTGAATACCATTAGCAC 59.934 47.826 0.00 0.00 0.00 4.40
208 213 3.303132 GGTTGTCAAGTGTTTAGCTGTCG 60.303 47.826 0.00 0.00 0.00 4.35
245 250 1.473278 CCGTCAGAGGTCTAGGAACAC 59.527 57.143 0.00 0.00 0.00 3.32
259 264 2.909006 AGGAACACAGTGACATCCATCT 59.091 45.455 19.88 4.39 32.47 2.90
278 283 2.714793 TCTCAGGATGCATGGATGGAAT 59.285 45.455 2.46 0.00 34.76 3.01
279 284 3.082548 CTCAGGATGCATGGATGGAATC 58.917 50.000 2.46 0.00 38.43 2.52
298 303 9.787435 ATGGAATCATGGAAAATTGGAAATATG 57.213 29.630 0.00 0.00 31.34 1.78
299 304 7.716123 TGGAATCATGGAAAATTGGAAATATGC 59.284 33.333 0.00 0.00 0.00 3.14
300 305 7.935210 GGAATCATGGAAAATTGGAAATATGCT 59.065 33.333 0.00 0.00 0.00 3.79
301 306 8.671384 AATCATGGAAAATTGGAAATATGCTG 57.329 30.769 0.00 0.00 0.00 4.41
302 307 6.050432 TCATGGAAAATTGGAAATATGCTGC 58.950 36.000 0.00 0.00 0.00 5.25
303 308 5.680594 TGGAAAATTGGAAATATGCTGCT 57.319 34.783 0.00 0.00 0.00 4.24
304 309 6.788598 TGGAAAATTGGAAATATGCTGCTA 57.211 33.333 0.00 0.00 0.00 3.49
305 310 6.572519 TGGAAAATTGGAAATATGCTGCTAC 58.427 36.000 0.00 0.00 0.00 3.58
306 311 6.380846 TGGAAAATTGGAAATATGCTGCTACT 59.619 34.615 0.00 0.00 0.00 2.57
307 312 7.559533 TGGAAAATTGGAAATATGCTGCTACTA 59.440 33.333 0.00 0.00 0.00 1.82
308 313 8.078596 GGAAAATTGGAAATATGCTGCTACTAG 58.921 37.037 0.00 0.00 0.00 2.57
309 314 8.525290 AAAATTGGAAATATGCTGCTACTAGT 57.475 30.769 0.00 0.00 0.00 2.57
310 315 7.502120 AATTGGAAATATGCTGCTACTAGTG 57.498 36.000 5.39 0.00 0.00 2.74
311 316 4.960938 TGGAAATATGCTGCTACTAGTGG 58.039 43.478 5.39 3.15 0.00 4.00
312 317 4.408921 TGGAAATATGCTGCTACTAGTGGT 59.591 41.667 5.39 0.00 0.00 4.16
313 318 4.752101 GGAAATATGCTGCTACTAGTGGTG 59.248 45.833 5.39 1.40 0.00 4.17
314 319 5.359194 AAATATGCTGCTACTAGTGGTGT 57.641 39.130 5.39 0.00 0.00 4.16
328 333 7.898014 ACTAGTGGTGTATCAGTGATCAATA 57.102 36.000 9.42 4.39 0.00 1.90
388 403 2.373540 TTGGACGATTAACTGACGGG 57.626 50.000 0.00 0.00 0.00 5.28
410 428 4.284829 TGGATACATGCAGTCAACAGAA 57.715 40.909 0.00 0.00 46.17 3.02
419 450 1.876156 CAGTCAACAGAAGAAGGTGGC 59.124 52.381 0.00 0.00 0.00 5.01
424 455 3.152341 CAACAGAAGAAGGTGGCATCTT 58.848 45.455 13.94 13.94 38.56 2.40
461 1665 8.694975 CATGGTATGTCTATGCAGATTAGTAC 57.305 38.462 0.00 0.00 32.09 2.73
469 1673 3.912496 TGCAGATTAGTACACCATGCT 57.088 42.857 0.00 0.00 33.47 3.79
516 1738 5.387788 CCTCCATTATCACATCCCAATCAA 58.612 41.667 0.00 0.00 0.00 2.57
518 1740 6.495872 CCTCCATTATCACATCCCAATCAATT 59.504 38.462 0.00 0.00 0.00 2.32
523 1745 9.037737 CATTATCACATCCCAATCAATTGAAAC 57.962 33.333 13.09 0.00 40.14 2.78
526 1748 5.047164 TCACATCCCAATCAATTGAAACCAG 60.047 40.000 13.09 1.09 40.14 4.00
543 1765 7.230747 TGAAACCAGATATTGACCTTTCTTGA 58.769 34.615 0.00 0.00 0.00 3.02
554 1777 7.403312 TTGACCTTTCTTGAAAATCTGAACA 57.597 32.000 0.00 0.00 0.00 3.18
558 1781 5.068987 CCTTTCTTGAAAATCTGAACACCCA 59.931 40.000 0.00 0.00 0.00 4.51
606 1829 2.229792 CCTGCTAACAACCACATGTGT 58.770 47.619 23.79 9.81 32.81 3.72
607 1830 3.181449 ACCTGCTAACAACCACATGTGTA 60.181 43.478 23.79 8.79 32.81 2.90
621 1844 4.079253 ACATGTGTATTGGGTGGAAGAAC 58.921 43.478 0.00 0.00 0.00 3.01
639 1862 2.736144 ACTATTTCGCTCGGACACAA 57.264 45.000 0.00 0.00 0.00 3.33
640 1863 3.247006 ACTATTTCGCTCGGACACAAT 57.753 42.857 0.00 0.00 0.00 2.71
641 1864 4.380841 ACTATTTCGCTCGGACACAATA 57.619 40.909 0.00 0.00 0.00 1.90
642 1865 4.751060 ACTATTTCGCTCGGACACAATAA 58.249 39.130 0.00 0.00 0.00 1.40
643 1866 5.172934 ACTATTTCGCTCGGACACAATAAA 58.827 37.500 0.00 0.00 0.00 1.40
644 1867 4.600012 ATTTCGCTCGGACACAATAAAG 57.400 40.909 0.00 0.00 0.00 1.85
645 1868 1.355971 TCGCTCGGACACAATAAAGC 58.644 50.000 0.00 0.00 0.00 3.51
646 1869 1.075542 CGCTCGGACACAATAAAGCA 58.924 50.000 0.00 0.00 0.00 3.91
647 1870 1.201921 CGCTCGGACACAATAAAGCAC 60.202 52.381 0.00 0.00 0.00 4.40
679 1908 4.617959 CTTATGATTCAGGCAAATGCTGG 58.382 43.478 5.25 0.00 41.70 4.85
747 2031 6.848562 ACCCTATAGATTTCCCATTGTTCT 57.151 37.500 0.00 0.00 0.00 3.01
754 2038 6.484364 AGATTTCCCATTGTTCTTTGTTGT 57.516 33.333 0.00 0.00 0.00 3.32
768 2052 4.334203 TCTTTGTTGTGTTGCACTACGAAT 59.666 37.500 13.73 0.00 40.54 3.34
795 2079 7.147479 ACCATGCCAACCATACTATATATCTCC 60.147 40.741 0.00 0.00 31.47 3.71
796 2080 7.147497 CCATGCCAACCATACTATATATCTCCA 60.147 40.741 0.00 0.00 31.47 3.86
797 2081 7.806680 TGCCAACCATACTATATATCTCCAA 57.193 36.000 0.00 0.00 0.00 3.53
798 2082 8.213489 TGCCAACCATACTATATATCTCCAAA 57.787 34.615 0.00 0.00 0.00 3.28
799 2083 8.321353 TGCCAACCATACTATATATCTCCAAAG 58.679 37.037 0.00 0.00 0.00 2.77
805 2089 7.492669 CCATACTATATATCTCCAAAGCAACCG 59.507 40.741 0.00 0.00 0.00 4.44
809 2093 8.157476 ACTATATATCTCCAAAGCAACCGAAAT 58.843 33.333 0.00 0.00 0.00 2.17
823 2107 3.748083 ACCGAAATAGATGCAGCATCAT 58.252 40.909 32.41 21.50 42.72 2.45
825 2109 5.494724 ACCGAAATAGATGCAGCATCATAT 58.505 37.500 32.41 23.09 42.72 1.78
842 2126 9.407380 AGCATCATATCACACCACTAAAAATTA 57.593 29.630 0.00 0.00 0.00 1.40
873 2157 3.312973 TCGGTTGTCATGTTACACCAAAC 59.687 43.478 0.00 0.00 0.00 2.93
876 2175 2.222886 TGTCATGTTACACCAAACGGG 58.777 47.619 0.00 0.00 44.81 5.28
892 2191 1.085501 CGGGCAATGGCTTGAAATGC 61.086 55.000 6.78 0.00 40.87 3.56
1236 3923 4.287766 AGCAAGTCCCCTTTACTTACTG 57.712 45.455 0.00 0.00 35.44 2.74
1237 3924 3.651423 AGCAAGTCCCCTTTACTTACTGT 59.349 43.478 0.00 0.00 35.44 3.55
1238 3925 4.842380 AGCAAGTCCCCTTTACTTACTGTA 59.158 41.667 0.00 0.00 35.44 2.74
1239 3926 4.934001 GCAAGTCCCCTTTACTTACTGTAC 59.066 45.833 0.00 0.00 35.44 2.90
1243 3930 6.798766 AGTCCCCTTTACTTACTGTACTACT 58.201 40.000 0.00 0.00 0.00 2.57
1244 3931 6.889177 AGTCCCCTTTACTTACTGTACTACTC 59.111 42.308 0.00 0.00 0.00 2.59
1245 3932 6.096141 GTCCCCTTTACTTACTGTACTACTCC 59.904 46.154 0.00 0.00 0.00 3.85
1246 3933 5.362143 CCCCTTTACTTACTGTACTACTCCC 59.638 48.000 0.00 0.00 0.00 4.30
1247 3934 6.193504 CCCTTTACTTACTGTACTACTCCCT 58.806 44.000 0.00 0.00 0.00 4.20
1249 3936 6.320926 CCTTTACTTACTGTACTACTCCCTCC 59.679 46.154 0.00 0.00 0.00 4.30
1250 3937 3.883669 ACTTACTGTACTACTCCCTCCG 58.116 50.000 0.00 0.00 0.00 4.63
1252 3939 2.416680 ACTGTACTACTCCCTCCGTC 57.583 55.000 0.00 0.00 0.00 4.79
1253 3940 1.064832 ACTGTACTACTCCCTCCGTCC 60.065 57.143 0.00 0.00 0.00 4.79
1254 3941 0.257039 TGTACTACTCCCTCCGTCCC 59.743 60.000 0.00 0.00 0.00 4.46
1255 3942 0.550432 GTACTACTCCCTCCGTCCCT 59.450 60.000 0.00 0.00 0.00 4.20
1256 3943 1.771255 GTACTACTCCCTCCGTCCCTA 59.229 57.143 0.00 0.00 0.00 3.53
1257 3944 1.302907 ACTACTCCCTCCGTCCCTAA 58.697 55.000 0.00 0.00 0.00 2.69
1258 3945 1.642762 ACTACTCCCTCCGTCCCTAAA 59.357 52.381 0.00 0.00 0.00 1.85
1259 3946 2.246849 ACTACTCCCTCCGTCCCTAAAT 59.753 50.000 0.00 0.00 0.00 1.40
1260 3947 3.464833 ACTACTCCCTCCGTCCCTAAATA 59.535 47.826 0.00 0.00 0.00 1.40
1261 3948 3.409804 ACTCCCTCCGTCCCTAAATAA 57.590 47.619 0.00 0.00 0.00 1.40
1262 3949 3.306613 ACTCCCTCCGTCCCTAAATAAG 58.693 50.000 0.00 0.00 0.00 1.73
1263 3950 3.306613 CTCCCTCCGTCCCTAAATAAGT 58.693 50.000 0.00 0.00 0.00 2.24
1264 3951 3.303049 TCCCTCCGTCCCTAAATAAGTC 58.697 50.000 0.00 0.00 0.00 3.01
1265 3952 3.052338 TCCCTCCGTCCCTAAATAAGTCT 60.052 47.826 0.00 0.00 0.00 3.24
1266 3953 3.710165 CCCTCCGTCCCTAAATAAGTCTT 59.290 47.826 0.00 0.00 0.00 3.01
1267 3954 4.163649 CCCTCCGTCCCTAAATAAGTCTTT 59.836 45.833 0.00 0.00 0.00 2.52
1268 3955 5.116882 CCTCCGTCCCTAAATAAGTCTTTG 58.883 45.833 0.00 0.00 0.00 2.77
1269 3956 5.338137 CCTCCGTCCCTAAATAAGTCTTTGT 60.338 44.000 0.00 0.00 0.00 2.83
1270 3957 6.127253 CCTCCGTCCCTAAATAAGTCTTTGTA 60.127 42.308 0.00 0.00 0.00 2.41
1271 3958 6.870769 TCCGTCCCTAAATAAGTCTTTGTAG 58.129 40.000 0.00 0.00 0.00 2.74
1272 3959 6.664816 TCCGTCCCTAAATAAGTCTTTGTAGA 59.335 38.462 0.00 0.00 0.00 2.59
1273 3960 6.979238 CCGTCCCTAAATAAGTCTTTGTAGAG 59.021 42.308 0.00 0.00 0.00 2.43
1274 3961 7.147949 CCGTCCCTAAATAAGTCTTTGTAGAGA 60.148 40.741 0.00 0.00 0.00 3.10
1275 3962 8.414778 CGTCCCTAAATAAGTCTTTGTAGAGAT 58.585 37.037 0.00 0.00 0.00 2.75
1284 3971 7.721286 AAGTCTTTGTAGAGATTTCACTGTG 57.279 36.000 0.17 0.17 0.00 3.66
1285 3972 6.226787 AGTCTTTGTAGAGATTTCACTGTGG 58.773 40.000 8.11 0.00 0.00 4.17
1286 3973 6.042093 AGTCTTTGTAGAGATTTCACTGTGGA 59.958 38.462 8.11 0.00 0.00 4.02
1287 3974 6.146347 GTCTTTGTAGAGATTTCACTGTGGAC 59.854 42.308 8.11 0.00 0.00 4.02
1288 3975 5.808366 TTGTAGAGATTTCACTGTGGACT 57.192 39.130 8.11 0.00 0.00 3.85
1289 3976 6.911250 TTGTAGAGATTTCACTGTGGACTA 57.089 37.500 8.11 0.00 0.00 2.59
1290 3977 6.268825 TGTAGAGATTTCACTGTGGACTAC 57.731 41.667 8.11 7.65 0.00 2.73
1291 3978 5.773176 TGTAGAGATTTCACTGTGGACTACA 59.227 40.000 11.28 11.28 36.46 2.74
1292 3979 6.437477 TGTAGAGATTTCACTGTGGACTACAT 59.563 38.462 11.28 0.00 38.92 2.29
1293 3980 7.614192 TGTAGAGATTTCACTGTGGACTACATA 59.386 37.037 11.28 0.00 38.92 2.29
1294 3981 6.868622 AGAGATTTCACTGTGGACTACATAC 58.131 40.000 8.11 0.00 38.92 2.39
1295 3982 5.651530 AGATTTCACTGTGGACTACATACG 58.348 41.667 8.11 0.00 38.92 3.06
1296 3983 3.861276 TTCACTGTGGACTACATACGG 57.139 47.619 8.11 0.00 38.92 4.02
1297 3984 3.076079 TCACTGTGGACTACATACGGA 57.924 47.619 8.11 0.00 38.92 4.69
1298 3985 3.014623 TCACTGTGGACTACATACGGAG 58.985 50.000 8.11 0.00 38.92 4.63
1299 3986 1.749634 ACTGTGGACTACATACGGAGC 59.250 52.381 0.00 0.00 38.92 4.70
1300 3987 1.749063 CTGTGGACTACATACGGAGCA 59.251 52.381 0.00 0.00 38.92 4.26
1301 3988 2.165641 CTGTGGACTACATACGGAGCAA 59.834 50.000 0.00 0.00 38.92 3.91
1302 3989 2.563620 TGTGGACTACATACGGAGCAAA 59.436 45.455 0.00 0.00 33.42 3.68
1303 3990 3.007074 TGTGGACTACATACGGAGCAAAA 59.993 43.478 0.00 0.00 33.42 2.44
1304 3991 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
1305 3992 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
1306 3993 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
1307 3994 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
1308 3995 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1309 3996 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1310 3997 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1311 3998 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1312 3999 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1313 4000 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1314 4001 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1315 4002 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1316 4003 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1317 4004 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1318 4005 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1331 4018 8.430801 AGTGAATCTACACTCTAAAATGCATC 57.569 34.615 0.00 0.00 46.36 3.91
1332 4019 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
1333 4020 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
1334 4021 9.534565 TGAATCTACACTCTAAAATGCATCTAC 57.465 33.333 0.00 0.00 0.00 2.59
1335 4022 9.534565 GAATCTACACTCTAAAATGCATCTACA 57.465 33.333 0.00 0.00 0.00 2.74
1338 4025 9.967346 TCTACACTCTAAAATGCATCTACATAC 57.033 33.333 0.00 0.00 0.00 2.39
1339 4026 9.750125 CTACACTCTAAAATGCATCTACATACA 57.250 33.333 0.00 0.00 0.00 2.29
1341 4028 9.618890 ACACTCTAAAATGCATCTACATACATT 57.381 29.630 0.00 0.00 34.30 2.71
1343 4030 9.836864 ACTCTAAAATGCATCTACATACATTCA 57.163 29.630 0.00 0.00 31.75 2.57
1350 4037 9.729281 AATGCATCTACATACATTCATATGTGA 57.271 29.630 0.00 0.00 43.93 3.58
1351 4038 9.901172 ATGCATCTACATACATTCATATGTGAT 57.099 29.630 1.90 6.78 43.93 3.06
1352 4039 9.729281 TGCATCTACATACATTCATATGTGATT 57.271 29.630 1.90 0.00 43.93 2.57
1363 4050 9.803507 ACATTCATATGTGATTCATAGTGGAAT 57.196 29.630 1.90 0.00 43.29 3.01
1394 4081 9.331282 CCAAAGACTTATATTTAGGAACAGAGG 57.669 37.037 0.00 0.00 0.00 3.69
1395 4082 9.331282 CAAAGACTTATATTTAGGAACAGAGGG 57.669 37.037 0.00 0.00 0.00 4.30
1396 4083 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
1438 4125 6.893005 ACAGTTCTGCTACTTACTCCTAGATT 59.107 38.462 0.00 0.00 0.00 2.40
1439 4126 7.147983 ACAGTTCTGCTACTTACTCCTAGATTG 60.148 40.741 0.00 0.00 0.00 2.67
1440 4127 7.067615 CAGTTCTGCTACTTACTCCTAGATTGA 59.932 40.741 0.00 0.00 0.00 2.57
1441 4128 6.945938 TCTGCTACTTACTCCTAGATTGAC 57.054 41.667 0.00 0.00 0.00 3.18
1442 4129 5.828859 TCTGCTACTTACTCCTAGATTGACC 59.171 44.000 0.00 0.00 0.00 4.02
1443 4130 5.767670 TGCTACTTACTCCTAGATTGACCT 58.232 41.667 0.00 0.00 0.00 3.85
1481 4349 8.783093 TGGTCAAAGTCATTACACTATCAAAAG 58.217 33.333 0.00 0.00 0.00 2.27
1495 4363 9.975218 ACACTATCAAAAGGTTAATGGAATACT 57.025 29.630 0.00 0.00 0.00 2.12
1552 4439 3.701532 AGCTGACGCTCTTAGACATAC 57.298 47.619 0.00 0.00 45.15 2.39
1559 4574 7.324135 GCTGACGCTCTTAGACATACTAATAAC 59.676 40.741 0.00 0.00 39.86 1.89
1581 4596 7.409465 AACTAATCTGACGTTTCAACTCTTC 57.591 36.000 0.00 0.00 0.00 2.87
1587 4602 5.064707 TCTGACGTTTCAACTCTTCCTTTTG 59.935 40.000 0.00 0.00 0.00 2.44
1598 4963 4.191544 CTCTTCCTTTTGTGACAGTGACA 58.808 43.478 0.00 0.00 0.00 3.58
1610 4983 5.163764 TGTGACAGTGACATTTCAGTTCAAC 60.164 40.000 0.00 0.00 32.63 3.18
1614 4987 5.824624 ACAGTGACATTTCAGTTCAACTCAT 59.175 36.000 0.00 0.00 32.63 2.90
1617 4990 5.471456 GTGACATTTCAGTTCAACTCATCCT 59.529 40.000 0.00 0.00 30.10 3.24
1619 4992 6.547141 TGACATTTCAGTTCAACTCATCCTTT 59.453 34.615 0.00 0.00 0.00 3.11
1620 4993 7.068593 TGACATTTCAGTTCAACTCATCCTTTT 59.931 33.333 0.00 0.00 0.00 2.27
1732 5207 2.110213 GACACGGCCACCTTCACA 59.890 61.111 2.24 0.00 0.00 3.58
1786 5307 2.093306 TTCGAGGCATGAACGTCATT 57.907 45.000 0.00 0.00 34.28 2.57
2025 5555 2.282251 AGGGACTCGACGACTGCA 60.282 61.111 0.00 0.00 0.00 4.41
2340 5870 0.478072 ACAGCAACCTGATGTCCCAA 59.522 50.000 0.00 0.00 44.55 4.12
2368 5898 2.842462 TGCACTCCGACCAGGTGT 60.842 61.111 0.00 0.00 46.77 4.16
2448 5978 0.468226 TCAACAGGGACTTCGCAGTT 59.532 50.000 0.00 0.00 38.63 3.16
2724 6288 6.042143 CCAAGTGCACATAACTTTTGTTTCT 58.958 36.000 21.04 0.00 43.32 2.52
2960 7990 5.250774 TCCTAATAAGTTGGAGGTCTTGCTT 59.749 40.000 0.00 0.00 0.00 3.91
3033 8064 2.615227 CTAAAGCCAGCTCCCGCCAT 62.615 60.000 0.00 0.00 36.60 4.40
3034 8065 2.210144 TAAAGCCAGCTCCCGCCATT 62.210 55.000 0.00 0.00 36.60 3.16
3118 8149 1.151450 CCATTCCTAGCCCCGCAAT 59.849 57.895 0.00 0.00 0.00 3.56
3130 8161 0.758734 CCCGCAATCACCTATCTCCA 59.241 55.000 0.00 0.00 0.00 3.86
3137 8168 4.446371 CAATCACCTATCTCCACCTTCAC 58.554 47.826 0.00 0.00 0.00 3.18
3168 8199 0.690762 ACCGCCACCAACTCACTATT 59.309 50.000 0.00 0.00 0.00 1.73
3192 8223 4.452455 GGAATCAATCAGTTTGACGAGTGT 59.548 41.667 0.00 0.00 46.80 3.55
3242 8273 1.541670 GGCACTCGGTAAAGTCACCAA 60.542 52.381 0.00 0.00 38.61 3.67
3436 8468 3.523547 TCGTTCGTCTGTTCCAAGAAAA 58.476 40.909 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.181329 TCAGAACTTGGAAGATGCCCTA 58.819 45.455 0.00 0.00 0.00 3.53
15 16 4.067896 TGAACTCAGAACTTGGAAGATGC 58.932 43.478 0.00 0.00 0.00 3.91
25 26 2.407340 AGGGACCTGAACTCAGAACT 57.593 50.000 8.33 0.00 46.59 3.01
26 27 3.579151 AGTAAGGGACCTGAACTCAGAAC 59.421 47.826 8.33 2.15 46.59 3.01
27 28 3.578716 CAGTAAGGGACCTGAACTCAGAA 59.421 47.826 8.33 0.00 46.59 3.02
28 29 3.165875 CAGTAAGGGACCTGAACTCAGA 58.834 50.000 8.33 0.00 46.59 3.27
29 30 2.354203 GCAGTAAGGGACCTGAACTCAG 60.354 54.545 0.00 0.00 43.40 3.35
30 31 1.623811 GCAGTAAGGGACCTGAACTCA 59.376 52.381 4.18 0.00 0.00 3.41
31 32 1.623811 TGCAGTAAGGGACCTGAACTC 59.376 52.381 4.18 2.15 0.00 3.01
75 80 4.946157 CAGTCCCAGCATCTAAGATGTTTT 59.054 41.667 0.00 0.00 0.00 2.43
129 134 1.129326 GTCACACGTCGACTTCCAAG 58.871 55.000 14.70 0.00 0.00 3.61
157 162 2.177531 CCGTCTGCATGCAGTTGC 59.822 61.111 39.08 29.00 43.96 4.17
158 163 1.672030 TCCCGTCTGCATGCAGTTG 60.672 57.895 39.08 31.48 43.96 3.16
159 164 1.672356 GTCCCGTCTGCATGCAGTT 60.672 57.895 39.08 0.00 43.96 3.16
170 175 2.621526 ACAACCTGAATTTTGTCCCGTC 59.378 45.455 0.00 0.00 29.75 4.79
208 213 6.100004 TCTGACGGTAGAGATGAAATGTTTC 58.900 40.000 0.00 0.00 37.69 2.78
259 264 2.444010 TGATTCCATCCATGCATCCTGA 59.556 45.455 0.00 0.00 0.00 3.86
267 272 5.995282 CCAATTTTCCATGATTCCATCCATG 59.005 40.000 0.00 0.00 39.72 3.66
278 283 6.050432 GCAGCATATTTCCAATTTTCCATGA 58.950 36.000 0.00 0.00 0.00 3.07
279 284 6.053005 AGCAGCATATTTCCAATTTTCCATG 58.947 36.000 0.00 0.00 0.00 3.66
283 288 8.624776 ACTAGTAGCAGCATATTTCCAATTTTC 58.375 33.333 0.00 0.00 0.00 2.29
284 289 8.408601 CACTAGTAGCAGCATATTTCCAATTTT 58.591 33.333 0.00 0.00 0.00 1.82
285 290 7.013655 CCACTAGTAGCAGCATATTTCCAATTT 59.986 37.037 0.00 0.00 0.00 1.82
286 291 6.488006 CCACTAGTAGCAGCATATTTCCAATT 59.512 38.462 0.00 0.00 0.00 2.32
287 292 6.000219 CCACTAGTAGCAGCATATTTCCAAT 59.000 40.000 0.00 0.00 0.00 3.16
288 293 5.104527 ACCACTAGTAGCAGCATATTTCCAA 60.105 40.000 0.00 0.00 0.00 3.53
289 294 4.408921 ACCACTAGTAGCAGCATATTTCCA 59.591 41.667 0.00 0.00 0.00 3.53
290 295 4.752101 CACCACTAGTAGCAGCATATTTCC 59.248 45.833 0.00 0.00 0.00 3.13
291 296 5.360591 ACACCACTAGTAGCAGCATATTTC 58.639 41.667 0.00 0.00 0.00 2.17
292 297 5.359194 ACACCACTAGTAGCAGCATATTT 57.641 39.130 0.00 0.00 0.00 1.40
293 298 6.267699 TGATACACCACTAGTAGCAGCATATT 59.732 38.462 0.00 0.00 33.42 1.28
294 299 5.775195 TGATACACCACTAGTAGCAGCATAT 59.225 40.000 0.00 0.00 33.42 1.78
295 300 5.137551 TGATACACCACTAGTAGCAGCATA 58.862 41.667 0.00 0.00 33.42 3.14
296 301 3.960755 TGATACACCACTAGTAGCAGCAT 59.039 43.478 0.00 0.00 33.42 3.79
297 302 3.361786 TGATACACCACTAGTAGCAGCA 58.638 45.455 0.00 0.00 33.42 4.41
298 303 3.971150 CTGATACACCACTAGTAGCAGC 58.029 50.000 5.79 0.00 45.35 5.25
300 305 4.595986 TCACTGATACACCACTAGTAGCA 58.404 43.478 0.00 0.00 35.71 3.49
301 306 5.299531 TGATCACTGATACACCACTAGTAGC 59.700 44.000 0.00 0.00 0.00 3.58
302 307 6.944234 TGATCACTGATACACCACTAGTAG 57.056 41.667 0.00 0.00 0.00 2.57
303 308 7.898014 ATTGATCACTGATACACCACTAGTA 57.102 36.000 0.00 0.00 0.00 1.82
304 309 6.798427 ATTGATCACTGATACACCACTAGT 57.202 37.500 0.00 0.00 0.00 2.57
305 310 6.865726 GCTATTGATCACTGATACACCACTAG 59.134 42.308 0.00 0.00 0.00 2.57
306 311 6.323739 TGCTATTGATCACTGATACACCACTA 59.676 38.462 0.00 0.00 0.00 2.74
307 312 5.129320 TGCTATTGATCACTGATACACCACT 59.871 40.000 0.00 0.00 0.00 4.00
308 313 5.359756 TGCTATTGATCACTGATACACCAC 58.640 41.667 0.00 0.00 0.00 4.16
309 314 5.129320 ACTGCTATTGATCACTGATACACCA 59.871 40.000 0.00 0.00 0.00 4.17
310 315 5.605534 ACTGCTATTGATCACTGATACACC 58.394 41.667 0.00 0.00 0.00 4.16
311 316 6.276091 TGACTGCTATTGATCACTGATACAC 58.724 40.000 0.00 0.00 0.00 2.90
312 317 6.322201 TCTGACTGCTATTGATCACTGATACA 59.678 38.462 0.00 0.00 0.00 2.29
313 318 6.640499 GTCTGACTGCTATTGATCACTGATAC 59.360 42.308 0.00 0.00 0.00 2.24
314 319 6.548993 AGTCTGACTGCTATTGATCACTGATA 59.451 38.462 10.00 0.00 0.00 2.15
388 403 3.599343 TCTGTTGACTGCATGTATCCAC 58.401 45.455 0.00 0.00 0.00 4.02
448 1652 4.132336 CAGCATGGTGTACTAATCTGCAT 58.868 43.478 16.80 0.00 0.00 3.96
493 1712 4.989277 TGATTGGGATGTGATAATGGAGG 58.011 43.478 0.00 0.00 0.00 4.30
501 1723 5.484644 TGGTTTCAATTGATTGGGATGTGAT 59.515 36.000 9.40 0.00 38.30 3.06
502 1724 4.837298 TGGTTTCAATTGATTGGGATGTGA 59.163 37.500 9.40 0.00 38.30 3.58
516 1738 8.526147 CAAGAAAGGTCAATATCTGGTTTCAAT 58.474 33.333 0.00 0.00 0.00 2.57
518 1740 7.230747 TCAAGAAAGGTCAATATCTGGTTTCA 58.769 34.615 0.00 0.00 0.00 2.69
523 1745 8.964772 AGATTTTCAAGAAAGGTCAATATCTGG 58.035 33.333 10.53 0.00 0.00 3.86
543 1765 6.484364 AATTTGTCTGGGTGTTCAGATTTT 57.516 33.333 0.00 0.00 44.43 1.82
554 1777 2.550639 GCCATGCAAAATTTGTCTGGGT 60.551 45.455 21.46 0.00 35.91 4.51
558 1781 2.872842 GCCAGCCATGCAAAATTTGTCT 60.873 45.455 7.60 0.00 0.00 3.41
590 1813 4.764823 ACCCAATACACATGTGGTTGTTAG 59.235 41.667 28.89 22.72 32.26 2.34
606 1829 4.879545 GCGAAATAGTTCTTCCACCCAATA 59.120 41.667 0.96 0.00 0.00 1.90
607 1830 3.694566 GCGAAATAGTTCTTCCACCCAAT 59.305 43.478 0.96 0.00 0.00 3.16
621 1844 5.712217 TTTATTGTGTCCGAGCGAAATAG 57.288 39.130 0.00 0.00 0.00 1.73
645 1868 6.128336 GCCTGAATCATAAGCTAGCATTAGTG 60.128 42.308 18.83 8.24 0.00 2.74
646 1869 5.936956 GCCTGAATCATAAGCTAGCATTAGT 59.063 40.000 18.83 0.00 0.00 2.24
647 1870 5.936372 TGCCTGAATCATAAGCTAGCATTAG 59.064 40.000 18.83 4.17 0.00 1.73
679 1908 2.149973 AGTTGGAGATGGGAAATGGC 57.850 50.000 0.00 0.00 0.00 4.40
723 1956 7.226059 AGAACAATGGGAAATCTATAGGGTT 57.774 36.000 0.00 0.00 0.00 4.11
747 2031 4.624336 ATTCGTAGTGCAACACAACAAA 57.376 36.364 0.00 0.00 41.43 2.83
754 2038 2.675844 GCATGGTATTCGTAGTGCAACA 59.324 45.455 0.00 0.00 41.43 3.33
768 2052 8.854237 AGATATATAGTATGGTTGGCATGGTA 57.146 34.615 0.00 0.00 0.00 3.25
791 2075 4.280436 TCTATTTCGGTTGCTTTGGAGA 57.720 40.909 0.00 0.00 0.00 3.71
792 2076 4.731773 GCATCTATTTCGGTTGCTTTGGAG 60.732 45.833 0.00 0.00 0.00 3.86
795 2079 4.095410 TGCATCTATTTCGGTTGCTTTG 57.905 40.909 0.00 0.00 34.47 2.77
796 2080 3.428045 GCTGCATCTATTTCGGTTGCTTT 60.428 43.478 0.00 0.00 34.47 3.51
797 2081 2.098117 GCTGCATCTATTTCGGTTGCTT 59.902 45.455 0.00 0.00 34.47 3.91
798 2082 1.672881 GCTGCATCTATTTCGGTTGCT 59.327 47.619 0.00 0.00 34.47 3.91
799 2083 1.401552 TGCTGCATCTATTTCGGTTGC 59.598 47.619 0.00 0.00 0.00 4.17
805 2089 7.242079 GTGTGATATGATGCTGCATCTATTTC 58.758 38.462 34.64 27.40 41.06 2.17
809 2093 4.040706 TGGTGTGATATGATGCTGCATCTA 59.959 41.667 34.64 25.51 41.06 1.98
825 2109 8.524487 ACACTGTTTTAATTTTTAGTGGTGTGA 58.476 29.630 0.00 0.00 39.71 3.58
842 2126 3.013921 ACATGACAACCGACACTGTTTT 58.986 40.909 0.00 0.00 0.00 2.43
873 2157 1.085501 GCATTTCAAGCCATTGCCCG 61.086 55.000 0.00 0.00 38.69 6.13
876 2175 0.994263 GACGCATTTCAAGCCATTGC 59.006 50.000 0.00 0.00 36.30 3.56
892 2191 7.145985 ACATACACCTGTTTATATAGCTGACG 58.854 38.462 0.00 0.00 0.00 4.35
1236 3923 0.550432 AGGGACGGAGGGAGTAGTAC 59.450 60.000 0.00 0.00 0.00 2.73
1237 3924 2.196742 TAGGGACGGAGGGAGTAGTA 57.803 55.000 0.00 0.00 0.00 1.82
1238 3925 1.302907 TTAGGGACGGAGGGAGTAGT 58.697 55.000 0.00 0.00 0.00 2.73
1239 3926 2.449137 TTTAGGGACGGAGGGAGTAG 57.551 55.000 0.00 0.00 0.00 2.57
1243 3930 3.052338 AGACTTATTTAGGGACGGAGGGA 60.052 47.826 0.00 0.00 0.00 4.20
1244 3931 3.306613 AGACTTATTTAGGGACGGAGGG 58.693 50.000 0.00 0.00 0.00 4.30
1245 3932 5.116882 CAAAGACTTATTTAGGGACGGAGG 58.883 45.833 0.00 0.00 0.00 4.30
1246 3933 5.731591 ACAAAGACTTATTTAGGGACGGAG 58.268 41.667 0.00 0.00 0.00 4.63
1247 3934 5.750352 ACAAAGACTTATTTAGGGACGGA 57.250 39.130 0.00 0.00 0.00 4.69
1249 3936 7.769220 TCTCTACAAAGACTTATTTAGGGACG 58.231 38.462 0.00 0.00 0.00 4.79
1258 3945 9.429359 CACAGTGAAATCTCTACAAAGACTTAT 57.571 33.333 0.00 0.00 0.00 1.73
1259 3946 7.872993 CCACAGTGAAATCTCTACAAAGACTTA 59.127 37.037 0.62 0.00 0.00 2.24
1260 3947 6.708054 CCACAGTGAAATCTCTACAAAGACTT 59.292 38.462 0.62 0.00 0.00 3.01
1261 3948 6.042093 TCCACAGTGAAATCTCTACAAAGACT 59.958 38.462 0.62 0.00 0.00 3.24
1262 3949 6.146347 GTCCACAGTGAAATCTCTACAAAGAC 59.854 42.308 0.62 0.00 0.00 3.01
1263 3950 6.042093 AGTCCACAGTGAAATCTCTACAAAGA 59.958 38.462 0.62 0.00 0.00 2.52
1264 3951 6.226787 AGTCCACAGTGAAATCTCTACAAAG 58.773 40.000 0.62 0.00 0.00 2.77
1265 3952 6.174720 AGTCCACAGTGAAATCTCTACAAA 57.825 37.500 0.62 0.00 0.00 2.83
1266 3953 5.808366 AGTCCACAGTGAAATCTCTACAA 57.192 39.130 0.62 0.00 0.00 2.41
1267 3954 5.773176 TGTAGTCCACAGTGAAATCTCTACA 59.227 40.000 0.62 8.30 34.82 2.74
1268 3955 6.268825 TGTAGTCCACAGTGAAATCTCTAC 57.731 41.667 0.62 6.10 31.89 2.59
1269 3956 7.201705 CGTATGTAGTCCACAGTGAAATCTCTA 60.202 40.741 0.62 0.00 41.51 2.43
1270 3957 6.404844 CGTATGTAGTCCACAGTGAAATCTCT 60.405 42.308 0.62 0.00 41.51 3.10
1271 3958 5.744345 CGTATGTAGTCCACAGTGAAATCTC 59.256 44.000 0.62 0.00 41.51 2.75
1272 3959 5.394224 CCGTATGTAGTCCACAGTGAAATCT 60.394 44.000 0.62 0.00 41.51 2.40
1273 3960 4.804139 CCGTATGTAGTCCACAGTGAAATC 59.196 45.833 0.62 0.00 41.51 2.17
1274 3961 4.464951 TCCGTATGTAGTCCACAGTGAAAT 59.535 41.667 0.62 0.00 41.51 2.17
1275 3962 3.827876 TCCGTATGTAGTCCACAGTGAAA 59.172 43.478 0.62 0.00 41.51 2.69
1276 3963 3.423749 TCCGTATGTAGTCCACAGTGAA 58.576 45.455 0.62 0.00 41.51 3.18
1277 3964 3.014623 CTCCGTATGTAGTCCACAGTGA 58.985 50.000 0.62 0.00 41.51 3.41
1278 3965 2.479730 GCTCCGTATGTAGTCCACAGTG 60.480 54.545 0.00 0.00 41.51 3.66
1279 3966 1.749634 GCTCCGTATGTAGTCCACAGT 59.250 52.381 0.00 0.00 41.51 3.55
1280 3967 1.749063 TGCTCCGTATGTAGTCCACAG 59.251 52.381 0.00 0.00 41.51 3.66
1281 3968 1.842052 TGCTCCGTATGTAGTCCACA 58.158 50.000 0.00 0.00 42.69 4.17
1282 3969 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
1283 3970 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
1284 3971 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
1285 3972 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1286 3973 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1287 3974 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1288 3975 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1289 3976 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1290 3977 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1291 3978 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1292 3979 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1293 3980 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1294 3981 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1295 3982 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1296 3983 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1307 3994 8.430801 AGATGCATTTTAGAGTGTAGATTCAC 57.569 34.615 0.00 0.00 38.46 3.18
1308 3995 9.534565 GTAGATGCATTTTAGAGTGTAGATTCA 57.465 33.333 0.00 0.00 0.00 2.57
1309 3996 9.534565 TGTAGATGCATTTTAGAGTGTAGATTC 57.465 33.333 0.00 0.00 0.00 2.52
1312 3999 9.967346 GTATGTAGATGCATTTTAGAGTGTAGA 57.033 33.333 0.00 0.00 0.00 2.59
1313 4000 9.750125 TGTATGTAGATGCATTTTAGAGTGTAG 57.250 33.333 0.00 0.00 0.00 2.74
1315 4002 9.618890 AATGTATGTAGATGCATTTTAGAGTGT 57.381 29.630 9.89 0.00 40.77 3.55
1317 4004 9.836864 TGAATGTATGTAGATGCATTTTAGAGT 57.163 29.630 15.62 0.00 42.85 3.24
1324 4011 9.729281 TCACATATGAATGTATGTAGATGCATT 57.271 29.630 14.65 14.65 44.70 3.56
1325 4012 9.901172 ATCACATATGAATGTATGTAGATGCAT 57.099 29.630 10.38 0.00 44.70 3.96
1326 4013 9.729281 AATCACATATGAATGTATGTAGATGCA 57.271 29.630 10.38 0.00 44.70 3.96
1368 4055 9.331282 CCTCTGTTCCTAAATATAAGTCTTTGG 57.669 37.037 0.00 0.00 0.00 3.28
1369 4056 9.331282 CCCTCTGTTCCTAAATATAAGTCTTTG 57.669 37.037 0.00 0.00 0.00 2.77
1370 4057 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
1371 4058 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
1372 4059 8.068733 ACTCCCTCTGTTCCTAAATATAAGTCT 58.931 37.037 0.00 0.00 0.00 3.24
1373 4060 8.252624 ACTCCCTCTGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
1374 4061 9.369672 CTACTCCCTCTGTTCCTAAATATAAGT 57.630 37.037 0.00 0.00 0.00 2.24
1375 4062 9.369672 ACTACTCCCTCTGTTCCTAAATATAAG 57.630 37.037 0.00 0.00 0.00 1.73
1376 4063 9.725206 AACTACTCCCTCTGTTCCTAAATATAA 57.275 33.333 0.00 0.00 0.00 0.98
1377 4064 9.725206 AAACTACTCCCTCTGTTCCTAAATATA 57.275 33.333 0.00 0.00 0.00 0.86
1378 4065 8.625467 AAACTACTCCCTCTGTTCCTAAATAT 57.375 34.615 0.00 0.00 0.00 1.28
1379 4066 7.899709 AGAAACTACTCCCTCTGTTCCTAAATA 59.100 37.037 0.00 0.00 0.00 1.40
1380 4067 6.731448 AGAAACTACTCCCTCTGTTCCTAAAT 59.269 38.462 0.00 0.00 0.00 1.40
1381 4068 6.082707 AGAAACTACTCCCTCTGTTCCTAAA 58.917 40.000 0.00 0.00 0.00 1.85
1382 4069 5.652324 AGAAACTACTCCCTCTGTTCCTAA 58.348 41.667 0.00 0.00 0.00 2.69
1383 4070 5.272405 AGAAACTACTCCCTCTGTTCCTA 57.728 43.478 0.00 0.00 0.00 2.94
1384 4071 4.134933 AGAAACTACTCCCTCTGTTCCT 57.865 45.455 0.00 0.00 0.00 3.36
1385 4072 5.018149 AGTAGAAACTACTCCCTCTGTTCC 58.982 45.833 5.73 0.00 32.84 3.62
1386 4073 5.622687 GCAGTAGAAACTACTCCCTCTGTTC 60.623 48.000 8.25 0.00 33.48 3.18
1387 4074 4.221041 GCAGTAGAAACTACTCCCTCTGTT 59.779 45.833 8.25 0.00 33.48 3.16
1388 4075 3.764972 GCAGTAGAAACTACTCCCTCTGT 59.235 47.826 8.25 0.00 33.48 3.41
1389 4076 3.764434 TGCAGTAGAAACTACTCCCTCTG 59.236 47.826 8.25 0.37 33.48 3.35
1390 4077 4.048970 TGCAGTAGAAACTACTCCCTCT 57.951 45.455 8.25 0.00 33.48 3.69
1391 4078 5.360144 TGTATGCAGTAGAAACTACTCCCTC 59.640 44.000 8.25 1.16 33.48 4.30
1392 4079 5.269991 TGTATGCAGTAGAAACTACTCCCT 58.730 41.667 8.25 0.00 33.48 4.20
1393 4080 5.593010 CTGTATGCAGTAGAAACTACTCCC 58.407 45.833 8.25 4.49 37.92 4.30
1416 4103 7.197703 GTCAATCTAGGAGTAAGTAGCAGAAC 58.802 42.308 0.00 0.00 0.00 3.01
1427 4114 8.060075 AGCTTAAACTAGGTCAATCTAGGAGTA 58.940 37.037 2.54 0.00 40.63 2.59
1428 4115 6.898521 AGCTTAAACTAGGTCAATCTAGGAGT 59.101 38.462 2.54 0.00 40.63 3.85
1438 4125 6.614694 TTGACCATAGCTTAAACTAGGTCA 57.385 37.500 21.11 21.11 42.37 4.02
1439 4126 7.104290 ACTTTGACCATAGCTTAAACTAGGTC 58.896 38.462 18.22 18.22 38.98 3.85
1440 4127 7.017319 ACTTTGACCATAGCTTAAACTAGGT 57.983 36.000 0.00 6.70 0.00 3.08
1441 4128 7.103641 TGACTTTGACCATAGCTTAAACTAGG 58.896 38.462 0.00 0.00 0.00 3.02
1442 4129 8.723942 ATGACTTTGACCATAGCTTAAACTAG 57.276 34.615 0.00 0.00 0.00 2.57
1451 4289 7.710907 TGATAGTGTAATGACTTTGACCATAGC 59.289 37.037 0.00 0.00 0.00 2.97
1500 4368 8.465201 GCAGTTAGGTATACAAGTAGTAGTGTT 58.535 37.037 5.01 0.00 35.85 3.32
1501 4369 7.833183 AGCAGTTAGGTATACAAGTAGTAGTGT 59.167 37.037 5.01 0.00 35.85 3.55
1502 4370 8.129840 CAGCAGTTAGGTATACAAGTAGTAGTG 58.870 40.741 5.01 0.00 35.85 2.74
1504 4372 8.344098 GTCAGCAGTTAGGTATACAAGTAGTAG 58.656 40.741 5.01 0.00 35.85 2.57
1505 4373 7.830697 TGTCAGCAGTTAGGTATACAAGTAGTA 59.169 37.037 5.01 0.00 37.06 1.82
1534 4421 8.561212 AGTTATTAGTATGTCTAAGAGCGTCAG 58.439 37.037 0.00 0.00 41.22 3.51
1551 4438 9.924650 AGTTGAAACGTCAGATTAGTTATTAGT 57.075 29.630 0.00 0.00 34.49 2.24
1559 4574 6.159988 AGGAAGAGTTGAAACGTCAGATTAG 58.840 40.000 0.00 0.00 34.49 1.73
1569 4584 5.949735 TGTCACAAAAGGAAGAGTTGAAAC 58.050 37.500 0.00 0.00 0.00 2.78
1581 4596 5.163622 ACTGAAATGTCACTGTCACAAAAGG 60.164 40.000 0.00 0.00 0.00 3.11
1587 4602 5.065218 AGTTGAACTGAAATGTCACTGTCAC 59.935 40.000 0.00 0.00 0.00 3.67
1660 5124 3.486708 GCATCGTCACACACACAAGAAAA 60.487 43.478 0.00 0.00 0.00 2.29
1667 5131 1.127397 CTGATGCATCGTCACACACAC 59.873 52.381 21.34 0.00 0.00 3.82
1786 5307 1.133823 ACCTGTGCCTTGATGTTGTCA 60.134 47.619 0.00 0.00 34.25 3.58
2223 5753 2.549332 GCAGTTGGCCTTGAGAGAC 58.451 57.895 3.32 0.00 36.11 3.36
2340 5870 2.759795 GAGTGCAGGAGCCCCTTT 59.240 61.111 0.00 0.00 42.02 3.11
2368 5898 1.007154 TGCGTCCGTCGTTGATCAA 60.007 52.632 3.38 3.38 42.13 2.57
2448 5978 2.692824 CCCCATCCTCACCATGGCA 61.693 63.158 13.04 0.00 39.78 4.92
2799 6363 3.531538 TCTTAGGCGTGGAAATGATGTC 58.468 45.455 0.00 0.00 0.00 3.06
2960 7990 3.437213 TCAGAATTAGGAACGGTGAGGA 58.563 45.455 0.00 0.00 0.00 3.71
2965 7995 8.575649 AAATTGTATTCAGAATTAGGAACGGT 57.424 30.769 0.00 0.00 28.15 4.83
3033 8064 1.545428 GGTGACAAGAGATGTGGCCAA 60.545 52.381 7.24 0.00 44.12 4.52
3034 8065 0.036732 GGTGACAAGAGATGTGGCCA 59.963 55.000 0.00 0.00 44.12 5.36
3118 8149 3.099905 CTGTGAAGGTGGAGATAGGTGA 58.900 50.000 0.00 0.00 0.00 4.02
3130 8161 0.842030 TGGGAGGATGCTGTGAAGGT 60.842 55.000 0.00 0.00 0.00 3.50
3137 8168 4.864334 GGCGGTGGGAGGATGCTG 62.864 72.222 0.00 0.00 0.00 4.41
3192 8223 9.369904 CAAAAATTCTCTTGGAAAACTTTCTGA 57.630 29.630 2.41 0.00 37.49 3.27
3194 8225 9.371136 GACAAAAATTCTCTTGGAAAACTTTCT 57.629 29.630 2.41 0.00 37.49 2.52
3199 8230 5.462068 CCCGACAAAAATTCTCTTGGAAAAC 59.538 40.000 0.00 0.00 37.49 2.43
3242 8273 0.258774 ACCTGGCACTCAGTTTTGGT 59.741 50.000 0.00 0.00 41.83 3.67
3436 8468 3.519510 TCTTCGGATCATTCCTTCTTGGT 59.480 43.478 0.00 0.00 40.17 3.67


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

AutoCloner maintained by Alex Coulton.