Multiple sequence alignment - TraesCS7D01G296000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G296000 chr7D 100.000 4061 0 0 1 4061 371786908 371790968 0.000000e+00 7500.0
1 TraesCS7D01G296000 chr7D 93.424 806 50 3 2 805 94928923 94928119 0.000000e+00 1192.0
2 TraesCS7D01G296000 chr7D 100.000 595 0 0 4286 4880 371791193 371791787 0.000000e+00 1099.0
3 TraesCS7D01G296000 chr7D 98.450 129 2 0 3251 3379 463561918 463561790 1.370000e-55 228.0
4 TraesCS7D01G296000 chr7B 95.684 1761 47 16 841 2579 367015350 367017103 0.000000e+00 2804.0
5 TraesCS7D01G296000 chr7B 93.265 1366 67 17 2577 3935 367017206 367018553 0.000000e+00 1989.0
6 TraesCS7D01G296000 chr7B 93.390 590 39 0 4291 4880 368207443 368206854 0.000000e+00 874.0
7 TraesCS7D01G296000 chr7A 95.670 1755 57 12 841 2579 416423366 416425117 0.000000e+00 2802.0
8 TraesCS7D01G296000 chr7A 94.444 684 30 7 2579 3258 416425223 416425902 0.000000e+00 1046.0
9 TraesCS7D01G296000 chr7A 95.915 563 19 3 3377 3935 416425896 416426458 0.000000e+00 909.0
10 TraesCS7D01G296000 chr4D 94.219 813 44 3 2 813 88469407 88470217 0.000000e+00 1238.0
11 TraesCS7D01G296000 chr4D 92.881 590 42 0 4291 4880 65842826 65843415 0.000000e+00 857.0
12 TraesCS7D01G296000 chr4D 92.126 127 7 3 3936 4061 439253848 439253724 5.020000e-40 176.0
13 TraesCS7D01G296000 chr2A 92.574 808 59 1 2 808 693244275 693245082 0.000000e+00 1158.0
14 TraesCS7D01G296000 chr2B 91.615 811 50 4 1 810 777843068 777842275 0.000000e+00 1105.0
15 TraesCS7D01G296000 chr2B 93.051 590 41 0 4291 4880 689723026 689722437 0.000000e+00 863.0
16 TraesCS7D01G296000 chr6D 93.898 590 36 0 4291 4880 127182048 127181459 0.000000e+00 891.0
17 TraesCS7D01G296000 chr6D 92.749 593 43 0 4288 4880 239855129 239855721 0.000000e+00 857.0
18 TraesCS7D01G296000 chr6D 93.431 137 8 1 3243 3379 35938394 35938529 8.280000e-48 202.0
19 TraesCS7D01G296000 chr3D 93.592 593 37 1 4288 4880 156247969 156248560 0.000000e+00 883.0
20 TraesCS7D01G296000 chr3D 92.366 131 7 3 3932 4061 590827500 590827372 3.000000e-42 183.0
21 TraesCS7D01G296000 chr4B 93.051 590 41 0 4291 4880 64814805 64814216 0.000000e+00 863.0
22 TraesCS7D01G296000 chr4B 93.534 232 12 2 580 810 632397077 632396848 4.680000e-90 342.0
23 TraesCS7D01G296000 chr3A 92.917 593 42 0 4288 4880 649993872 649994464 0.000000e+00 863.0
24 TraesCS7D01G296000 chr3A 92.188 128 7 3 3935 4061 340894164 340894039 1.400000e-40 178.0
25 TraesCS7D01G296000 chr3A 88.462 52 5 1 3601 3651 652638656 652638707 1.470000e-05 62.1
26 TraesCS7D01G296000 chr3A 88.462 52 5 1 3601 3651 652686811 652686862 1.470000e-05 62.1
27 TraesCS7D01G296000 chr2D 92.917 593 42 0 4288 4880 600096029 600096621 0.000000e+00 863.0
28 TraesCS7D01G296000 chr2D 92.806 139 9 1 3247 3385 645613184 645613047 2.980000e-47 200.0
29 TraesCS7D01G296000 chr5B 93.985 399 24 0 414 812 539019315 539018917 5.400000e-169 604.0
30 TraesCS7D01G296000 chr5B 93.216 398 25 2 413 810 116845759 116845364 7.040000e-163 584.0
31 TraesCS7D01G296000 chr5B 92.079 202 15 1 177 377 116845964 116845763 2.880000e-72 283.0
32 TraesCS7D01G296000 chr5B 93.007 143 7 2 3239 3380 44454494 44454354 6.400000e-49 206.0
33 TraesCS7D01G296000 chr5B 93.651 126 6 2 3936 4061 653742259 653742136 2.320000e-43 187.0
34 TraesCS7D01G296000 chr5B 89.286 56 5 1 3593 3647 391148442 391148497 8.760000e-08 69.4
35 TraesCS7D01G296000 chr5D 96.923 130 4 0 3250 3379 215301528 215301657 8.220000e-53 219.0
36 TraesCS7D01G296000 chr1B 93.478 138 8 1 3244 3381 409879801 409879937 2.300000e-48 204.0
37 TraesCS7D01G296000 chr1B 87.692 65 8 0 111 175 204273311 204273375 5.240000e-10 76.8
38 TraesCS7D01G296000 chr1A 91.333 150 10 3 3242 3390 505092531 505092384 8.280000e-48 202.0
39 TraesCS7D01G296000 chr5A 93.382 136 8 1 3244 3379 389062757 389062623 2.980000e-47 200.0
40 TraesCS7D01G296000 chr5A 88.406 69 6 2 3593 3659 598666782 598666714 1.130000e-11 82.4
41 TraesCS7D01G296000 chr6A 93.651 126 6 2 3936 4061 99379342 99379219 2.320000e-43 187.0
42 TraesCS7D01G296000 chr6A 92.913 127 7 1 3935 4061 521993445 521993569 3.000000e-42 183.0
43 TraesCS7D01G296000 chr1D 93.077 130 6 2 3932 4061 34662087 34662213 2.320000e-43 187.0
44 TraesCS7D01G296000 chr1D 92.188 128 7 3 3935 4061 19558285 19558160 1.400000e-40 178.0
45 TraesCS7D01G296000 chr4A 92.913 127 6 3 3936 4061 232898367 232898491 1.080000e-41 182.0
46 TraesCS7D01G296000 chr3B 90.000 50 5 0 3602 3651 744906515 744906564 1.130000e-06 65.8
47 TraesCS7D01G296000 chr3B 90.000 50 5 0 3602 3651 746342152 746342201 1.130000e-06 65.8
48 TraesCS7D01G296000 chr3B 89.796 49 4 1 3603 3651 78521007 78521054 1.470000e-05 62.1


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 TraesCS7D01G296000 chr7D 371786908 371791787 4879 False 4299.500000 7500 100.0000 1 4880 2 chr7D.!!$F1 4879
1 TraesCS7D01G296000 chr7D 94928119 94928923 804 True 1192.000000 1192 93.4240 2 805 1 chr7D.!!$R1 803
2 TraesCS7D01G296000 chr7B 367015350 367018553 3203 False 2396.500000 2804 94.4745 841 3935 2 chr7B.!!$F1 3094
3 TraesCS7D01G296000 chr7B 368206854 368207443 589 True 874.000000 874 93.3900 4291 4880 1 chr7B.!!$R1 589
4 TraesCS7D01G296000 chr7A 416423366 416426458 3092 False 1585.666667 2802 95.3430 841 3935 3 chr7A.!!$F1 3094
5 TraesCS7D01G296000 chr4D 88469407 88470217 810 False 1238.000000 1238 94.2190 2 813 1 chr4D.!!$F2 811
6 TraesCS7D01G296000 chr4D 65842826 65843415 589 False 857.000000 857 92.8810 4291 4880 1 chr4D.!!$F1 589
7 TraesCS7D01G296000 chr2A 693244275 693245082 807 False 1158.000000 1158 92.5740 2 808 1 chr2A.!!$F1 806
8 TraesCS7D01G296000 chr2B 777842275 777843068 793 True 1105.000000 1105 91.6150 1 810 1 chr2B.!!$R2 809
9 TraesCS7D01G296000 chr2B 689722437 689723026 589 True 863.000000 863 93.0510 4291 4880 1 chr2B.!!$R1 589
10 TraesCS7D01G296000 chr6D 127181459 127182048 589 True 891.000000 891 93.8980 4291 4880 1 chr6D.!!$R1 589
11 TraesCS7D01G296000 chr6D 239855129 239855721 592 False 857.000000 857 92.7490 4288 4880 1 chr6D.!!$F2 592
12 TraesCS7D01G296000 chr3D 156247969 156248560 591 False 883.000000 883 93.5920 4288 4880 1 chr3D.!!$F1 592
13 TraesCS7D01G296000 chr4B 64814216 64814805 589 True 863.000000 863 93.0510 4291 4880 1 chr4B.!!$R1 589
14 TraesCS7D01G296000 chr3A 649993872 649994464 592 False 863.000000 863 92.9170 4288 4880 1 chr3A.!!$F1 592
15 TraesCS7D01G296000 chr2D 600096029 600096621 592 False 863.000000 863 92.9170 4288 4880 1 chr2D.!!$F1 592
16 TraesCS7D01G296000 chr5B 116845364 116845964 600 True 433.500000 584 92.6475 177 810 2 chr5B.!!$R4 633

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
839 843 0.172578 GGCGTCAAATAGGGTTTGCC 59.827 55.0 0.00 0.0 0.00 4.52 F
1297 1315 0.397957 ACAAACCCCAAACCCTCCAC 60.398 55.0 0.00 0.0 0.00 4.02 F
2259 2297 0.407139 AATTCCAGCTGACAGCCCTT 59.593 50.0 23.74 2.5 43.77 3.95 F
3267 3420 1.100510 CATGTACTCCTTCCGTCCGA 58.899 55.0 0.00 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2739 2889 1.388547 TGCCGTTCTGAAATATGGGC 58.611 50.000 0.00 1.6 39.48 5.36 R
2906 3057 1.276421 AGAAATAGCAGACGCACCTGT 59.724 47.619 4.55 0.0 42.27 4.00 R
3789 3946 0.099613 GAGCTTCGATCTCAGCACGA 59.900 55.000 13.74 0.0 38.61 4.35 R
4487 4645 0.627451 TCTACCTCTCCGCTAACCCA 59.373 55.000 0.00 0.0 0.00 4.51 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
175 176 3.869065 TGAAGGTATTCTACAAAGCCCG 58.131 45.455 0.00 0.00 36.33 6.13
277 278 2.037251 AGTACGACATGCAACTTCAGGT 59.963 45.455 0.00 0.00 33.28 4.00
424 427 3.181465 TGAAGGCGTATTTCTGGGATCTC 60.181 47.826 0.00 0.00 0.00 2.75
471 474 4.020751 ACTGATGCAAGAGTCTTAGAAGCA 60.021 41.667 15.55 15.55 34.78 3.91
557 560 3.951680 AGTGATTCAAAGACGGTGGTTTT 59.048 39.130 0.00 0.00 0.00 2.43
652 655 8.908903 AGTTTGGTACATGTGACTTTATTTTCA 58.091 29.630 9.11 0.00 39.30 2.69
681 684 2.097825 GCACTCAATTGGGAAGCTCAT 58.902 47.619 13.56 0.00 0.00 2.90
822 826 4.859784 AAAAACTACGCATGCGGC 57.140 50.000 39.95 3.93 44.69 6.53
831 835 4.595629 GCATGCGGCGTCAAATAG 57.404 55.556 9.37 1.14 0.00 1.73
832 836 1.009675 GCATGCGGCGTCAAATAGG 60.010 57.895 9.37 0.00 0.00 2.57
833 837 1.648720 CATGCGGCGTCAAATAGGG 59.351 57.895 9.37 0.00 0.00 3.53
834 838 1.095228 CATGCGGCGTCAAATAGGGT 61.095 55.000 9.37 0.00 0.00 4.34
835 839 0.393808 ATGCGGCGTCAAATAGGGTT 60.394 50.000 9.37 0.00 0.00 4.11
836 840 0.606944 TGCGGCGTCAAATAGGGTTT 60.607 50.000 9.37 0.00 0.00 3.27
837 841 0.179174 GCGGCGTCAAATAGGGTTTG 60.179 55.000 9.37 0.00 0.00 2.93
838 842 0.179174 CGGCGTCAAATAGGGTTTGC 60.179 55.000 0.00 0.00 0.00 3.68
839 843 0.172578 GGCGTCAAATAGGGTTTGCC 59.827 55.000 0.00 0.00 0.00 4.52
1109 1127 1.202154 GGTCTGTCATACGTCACTCCG 60.202 57.143 0.00 0.00 0.00 4.63
1221 1239 0.960364 GGTGCTCAATTTCCTCGCCA 60.960 55.000 0.00 0.00 0.00 5.69
1251 1269 2.812619 CCCTCTTCTCCGGCCATCC 61.813 68.421 2.24 0.00 0.00 3.51
1297 1315 0.397957 ACAAACCCCAAACCCTCCAC 60.398 55.000 0.00 0.00 0.00 4.02
1300 1323 1.726192 AACCCCAAACCCTCCACCTC 61.726 60.000 0.00 0.00 0.00 3.85
1346 1369 4.233632 TGGCTGTTTCATCCATGTGATA 57.766 40.909 0.00 0.00 30.56 2.15
1451 1474 2.094894 GCTGAGTGATGTTTCATCGGTG 59.905 50.000 0.00 0.00 33.56 4.94
1524 1550 1.079503 GGCATTCGTCAGAGGTTGTC 58.920 55.000 0.00 0.00 0.00 3.18
1532 1558 2.277084 GTCAGAGGTTGTCGTTGTTGT 58.723 47.619 0.00 0.00 0.00 3.32
1533 1559 2.676342 GTCAGAGGTTGTCGTTGTTGTT 59.324 45.455 0.00 0.00 0.00 2.83
1534 1560 2.675844 TCAGAGGTTGTCGTTGTTGTTG 59.324 45.455 0.00 0.00 0.00 3.33
1772 1800 5.789643 TCCAAGGTCTTCAAAATCCAAAG 57.210 39.130 0.00 0.00 0.00 2.77
1773 1801 4.588528 TCCAAGGTCTTCAAAATCCAAAGG 59.411 41.667 0.00 0.00 0.00 3.11
1832 1863 5.345609 TCGATAGTCGCTTACTCAGATTC 57.654 43.478 0.00 0.00 40.21 2.52
2040 2078 2.227388 CCTCCTCATGAAACTGCAACAC 59.773 50.000 0.00 0.00 0.00 3.32
2226 2264 3.514645 CCCTTTACAATGCATTGCTGTC 58.485 45.455 33.94 0.00 41.38 3.51
2237 2275 2.351157 GCATTGCTGTCTTCCACTTGAC 60.351 50.000 0.16 0.00 0.00 3.18
2259 2297 0.407139 AATTCCAGCTGACAGCCCTT 59.593 50.000 23.74 2.50 43.77 3.95
2270 2308 4.326826 CTGACAGCCCTTCTATTTGAACA 58.673 43.478 0.00 0.00 0.00 3.18
2366 2404 2.690497 AGGATATCCTGATATCGCCACG 59.310 50.000 23.95 0.00 46.61 4.94
2392 2430 1.137086 CTGTACCTCCAATCCACTCCG 59.863 57.143 0.00 0.00 0.00 4.63
2402 2440 5.607477 TCCAATCCACTCCGTTATATTGTC 58.393 41.667 0.00 0.00 0.00 3.18
2403 2441 5.129650 TCCAATCCACTCCGTTATATTGTCA 59.870 40.000 0.00 0.00 0.00 3.58
2533 2575 1.777878 TGGACTGGTTAAGCCCTTTCA 59.222 47.619 1.51 0.00 36.04 2.69
2606 2756 8.137437 ACTATTCTGGTTGTTTGTTTTCTGATG 58.863 33.333 0.00 0.00 0.00 3.07
2751 2902 4.523173 AGCATGATCAAGCCCATATTTCAG 59.477 41.667 18.76 0.00 0.00 3.02
2756 2907 3.278574 TCAAGCCCATATTTCAGAACGG 58.721 45.455 0.00 0.00 0.00 4.44
2766 2917 7.424803 CCATATTTCAGAACGGCATTAATGAA 58.575 34.615 19.73 0.00 0.00 2.57
2804 2955 2.697654 TGCAATGTAAAATGGCTTGGC 58.302 42.857 0.00 0.00 0.00 4.52
2906 3057 6.042638 AGCTTGCTGTCATCTAAGTTTCTA 57.957 37.500 0.00 0.00 0.00 2.10
2913 3064 5.479306 TGTCATCTAAGTTTCTACAGGTGC 58.521 41.667 0.00 0.00 0.00 5.01
2940 3091 7.815068 GTCTGCTATTTCTCAACTTTCAGAGTA 59.185 37.037 0.00 0.00 37.72 2.59
2961 3112 9.162764 AGAGTATGTGGTGTGTTGAAAATATAC 57.837 33.333 0.00 0.00 0.00 1.47
2989 3140 9.040939 AGTCCAATTTTAATACAACAAACAAGC 57.959 29.630 0.00 0.00 0.00 4.01
3018 3169 3.617263 AGCAATTCTTTACGTAGCCTTCG 59.383 43.478 0.00 0.00 0.00 3.79
3027 3178 1.404391 ACGTAGCCTTCGGAGTGTATG 59.596 52.381 0.00 0.00 0.00 2.39
3105 3258 1.492720 GCTCTACTAAGATGCCGTGC 58.507 55.000 0.00 0.00 0.00 5.34
3202 3355 3.077617 GCACTGAGCATCTTCCCTC 57.922 57.895 0.00 0.00 44.79 4.30
3258 3411 3.600388 GCAGTGTTAAGCATGTACTCCT 58.400 45.455 0.00 0.00 0.00 3.69
3267 3420 1.100510 CATGTACTCCTTCCGTCCGA 58.899 55.000 0.00 0.00 0.00 4.55
3271 3424 2.364970 TGTACTCCTTCCGTCCGAAAAA 59.635 45.455 0.00 0.00 0.00 1.94
3299 3452 6.945218 TGTCATCAAAATGGATAAAAAGGGG 58.055 36.000 0.00 0.00 33.42 4.79
3308 3461 8.996651 AAATGGATAAAAAGGGGTGTATCTAG 57.003 34.615 0.00 0.00 0.00 2.43
3320 3473 8.849543 AGGGGTGTATCTAGAACTAAAATACA 57.150 34.615 0.00 0.00 32.07 2.29
3570 3723 1.364721 TTCATGTGCGTTATGGACCG 58.635 50.000 0.00 0.00 38.31 4.79
3698 3855 2.332514 CGCCTAATGCATTGCCCG 59.667 61.111 22.27 15.82 41.33 6.13
3699 3856 2.028043 GCCTAATGCATTGCCCGC 59.972 61.111 22.27 13.06 40.77 6.13
3777 3934 2.100631 GGAGTTGACGCGGATGGTG 61.101 63.158 12.47 0.00 0.00 4.17
3783 3940 2.994995 ACGCGGATGGTGGAGACA 60.995 61.111 12.47 0.00 38.70 3.41
3789 3946 1.557269 GGATGGTGGAGACAGGCACT 61.557 60.000 0.00 0.00 44.46 4.40
3894 4051 2.232756 TTTGACAGAGTGCAGCGTTA 57.767 45.000 0.00 0.00 0.00 3.18
3935 4093 1.822613 CTCGGCTGCATGGCTCATT 60.823 57.895 0.50 0.00 39.32 2.57
3936 4094 2.060004 CTCGGCTGCATGGCTCATTG 62.060 60.000 0.50 0.00 39.32 2.82
3937 4095 2.412323 CGGCTGCATGGCTCATTGT 61.412 57.895 0.50 0.00 39.32 2.71
3938 4096 1.096967 CGGCTGCATGGCTCATTGTA 61.097 55.000 0.50 0.00 39.32 2.41
3939 4097 1.325355 GGCTGCATGGCTCATTGTAT 58.675 50.000 0.50 0.00 38.32 2.29
3940 4098 1.000607 GGCTGCATGGCTCATTGTATG 60.001 52.381 0.50 0.00 38.32 2.39
3941 4099 1.951602 GCTGCATGGCTCATTGTATGA 59.048 47.619 0.00 0.00 37.76 2.15
3957 4115 9.509956 TCATTGTATGAGATTATGATTGCATGA 57.490 29.630 0.00 0.00 33.48 3.07
3970 4128 6.657836 TGATTGCATGATATATTGCTCTCG 57.342 37.500 10.07 0.00 39.60 4.04
3971 4129 6.168389 TGATTGCATGATATATTGCTCTCGT 58.832 36.000 10.07 0.00 39.60 4.18
3972 4130 5.851047 TTGCATGATATATTGCTCTCGTG 57.149 39.130 10.07 0.02 39.60 4.35
3973 4131 3.681417 TGCATGATATATTGCTCTCGTGC 59.319 43.478 10.07 9.21 46.12 5.34
3974 4132 3.681417 GCATGATATATTGCTCTCGTGCA 59.319 43.478 9.91 0.00 45.54 4.57
3975 4133 4.331992 GCATGATATATTGCTCTCGTGCAT 59.668 41.667 9.91 0.00 45.54 3.96
3976 4134 5.521372 GCATGATATATTGCTCTCGTGCATA 59.479 40.000 9.91 0.00 45.54 3.14
3977 4135 6.292221 GCATGATATATTGCTCTCGTGCATAG 60.292 42.308 9.91 0.00 45.54 2.23
3978 4136 5.654497 TGATATATTGCTCTCGTGCATAGG 58.346 41.667 0.00 0.00 42.96 2.57
3979 4137 2.154854 TATTGCTCTCGTGCATAGGC 57.845 50.000 0.00 0.00 42.96 3.93
3996 4154 7.624706 GCATAGGCACGTATATATGATGTAC 57.375 40.000 8.98 0.00 40.72 2.90
3997 4155 7.200455 GCATAGGCACGTATATATGATGTACA 58.800 38.462 8.98 0.00 40.72 2.90
3998 4156 7.704899 GCATAGGCACGTATATATGATGTACAA 59.295 37.037 8.98 0.00 40.72 2.41
3999 4157 9.020813 CATAGGCACGTATATATGATGTACAAC 57.979 37.037 8.98 0.00 0.00 3.32
4000 4158 6.090783 AGGCACGTATATATGATGTACAACG 58.909 40.000 8.98 5.22 34.98 4.10
4001 4159 6.072342 AGGCACGTATATATGATGTACAACGA 60.072 38.462 16.74 0.44 33.65 3.85
4002 4160 6.750501 GGCACGTATATATGATGTACAACGAT 59.249 38.462 16.74 7.33 33.65 3.73
4003 4161 7.253651 GGCACGTATATATGATGTACAACGATG 60.254 40.741 16.74 12.28 33.65 3.84
4004 4162 7.253651 GCACGTATATATGATGTACAACGATGG 60.254 40.741 16.74 8.49 33.65 3.51
4005 4163 7.220108 CACGTATATATGATGTACAACGATGGG 59.780 40.741 16.74 3.01 33.65 4.00
4006 4164 6.198403 CGTATATATGATGTACAACGATGGGC 59.802 42.308 0.00 0.00 31.88 5.36
4007 4165 1.967319 ATGATGTACAACGATGGGCC 58.033 50.000 0.00 0.00 0.00 5.80
4008 4166 0.615850 TGATGTACAACGATGGGCCA 59.384 50.000 9.61 9.61 0.00 5.36
4009 4167 1.014352 GATGTACAACGATGGGCCAC 58.986 55.000 9.28 1.58 0.00 5.01
4010 4168 0.742990 ATGTACAACGATGGGCCACG 60.743 55.000 21.45 21.45 0.00 4.94
4011 4169 2.104253 GTACAACGATGGGCCACGG 61.104 63.158 24.92 16.29 0.00 4.94
4012 4170 2.284276 TACAACGATGGGCCACGGA 61.284 57.895 24.92 10.33 0.00 4.69
4013 4171 1.618876 TACAACGATGGGCCACGGAT 61.619 55.000 24.92 14.71 0.00 4.18
4014 4172 2.180204 CAACGATGGGCCACGGATC 61.180 63.158 24.92 12.81 0.00 3.36
4015 4173 2.367202 AACGATGGGCCACGGATCT 61.367 57.895 24.92 4.23 0.00 2.75
4016 4174 2.029666 CGATGGGCCACGGATCTC 59.970 66.667 9.28 0.00 0.00 2.75
4017 4175 2.502492 CGATGGGCCACGGATCTCT 61.502 63.158 9.28 0.00 0.00 3.10
4018 4176 1.369321 GATGGGCCACGGATCTCTC 59.631 63.158 9.28 0.00 0.00 3.20
4019 4177 1.383109 ATGGGCCACGGATCTCTCA 60.383 57.895 9.28 0.00 0.00 3.27
4020 4178 0.982852 ATGGGCCACGGATCTCTCAA 60.983 55.000 9.28 0.00 0.00 3.02
4021 4179 0.982852 TGGGCCACGGATCTCTCAAT 60.983 55.000 0.00 0.00 0.00 2.57
4022 4180 0.181350 GGGCCACGGATCTCTCAATT 59.819 55.000 4.39 0.00 0.00 2.32
4023 4181 1.416401 GGGCCACGGATCTCTCAATTA 59.584 52.381 4.39 0.00 0.00 1.40
4024 4182 2.039084 GGGCCACGGATCTCTCAATTAT 59.961 50.000 4.39 0.00 0.00 1.28
4025 4183 3.260884 GGGCCACGGATCTCTCAATTATA 59.739 47.826 4.39 0.00 0.00 0.98
4026 4184 4.246458 GGCCACGGATCTCTCAATTATAC 58.754 47.826 0.00 0.00 0.00 1.47
4027 4185 4.262463 GGCCACGGATCTCTCAATTATACA 60.262 45.833 0.00 0.00 0.00 2.29
4028 4186 5.297547 GCCACGGATCTCTCAATTATACAA 58.702 41.667 0.00 0.00 0.00 2.41
4029 4187 5.406780 GCCACGGATCTCTCAATTATACAAG 59.593 44.000 0.00 0.00 0.00 3.16
4030 4188 5.928839 CCACGGATCTCTCAATTATACAAGG 59.071 44.000 0.00 0.00 0.00 3.61
4031 4189 6.239317 CCACGGATCTCTCAATTATACAAGGA 60.239 42.308 0.00 0.00 0.00 3.36
4032 4190 7.210174 CACGGATCTCTCAATTATACAAGGAA 58.790 38.462 0.00 0.00 0.00 3.36
4033 4191 7.169982 CACGGATCTCTCAATTATACAAGGAAC 59.830 40.741 0.00 0.00 0.00 3.62
4035 4193 8.577296 CGGATCTCTCAATTATACAAGGAACTA 58.423 37.037 0.00 0.00 38.49 2.24
4036 4194 9.921637 GGATCTCTCAATTATACAAGGAACTAG 57.078 37.037 0.00 0.00 38.49 2.57
4037 4195 9.921637 GATCTCTCAATTATACAAGGAACTAGG 57.078 37.037 0.00 0.00 38.49 3.02
4038 4196 9.661954 ATCTCTCAATTATACAAGGAACTAGGA 57.338 33.333 0.00 0.00 38.49 2.94
4039 4197 9.137459 TCTCTCAATTATACAAGGAACTAGGAG 57.863 37.037 0.00 0.00 38.49 3.69
4040 4198 8.251383 TCTCAATTATACAAGGAACTAGGAGG 57.749 38.462 0.00 0.00 38.49 4.30
4041 4199 6.827727 TCAATTATACAAGGAACTAGGAGGC 58.172 40.000 0.00 0.00 38.49 4.70
4042 4200 4.931661 TTATACAAGGAACTAGGAGGCG 57.068 45.455 0.00 0.00 38.49 5.52
4043 4201 1.481871 TACAAGGAACTAGGAGGCGG 58.518 55.000 0.00 0.00 38.49 6.13
4044 4202 1.265454 ACAAGGAACTAGGAGGCGGG 61.265 60.000 0.00 0.00 38.49 6.13
4045 4203 2.368011 AAGGAACTAGGAGGCGGGC 61.368 63.158 0.00 0.00 38.49 6.13
4046 4204 3.862991 GGAACTAGGAGGCGGGCC 61.863 72.222 0.18 0.18 0.00 5.80
4055 4213 4.060065 AGGCGGGCCTAATACACA 57.940 55.556 11.22 0.00 46.14 3.72
4056 4214 2.303043 AGGCGGGCCTAATACACAA 58.697 52.632 11.22 0.00 46.14 3.33
4057 4215 0.843984 AGGCGGGCCTAATACACAAT 59.156 50.000 11.22 0.00 46.14 2.71
4058 4216 2.051692 AGGCGGGCCTAATACACAATA 58.948 47.619 11.22 0.00 46.14 1.90
4059 4217 2.642807 AGGCGGGCCTAATACACAATAT 59.357 45.455 11.22 0.00 46.14 1.28
4060 4218 2.747446 GGCGGGCCTAATACACAATATG 59.253 50.000 0.84 0.00 0.00 1.78
4305 4463 2.816958 CTGCAGTCGAAGCGGCAT 60.817 61.111 5.25 0.00 38.72 4.40
4343 4501 0.395312 TGGACCGGAACTCCTCAAAC 59.605 55.000 9.46 0.00 0.00 2.93
4392 4550 6.602410 TGATATCTGCAAATTGTTGGGAAA 57.398 33.333 3.98 0.00 35.10 3.13
4459 4617 5.127031 CCCGGACAAAATGAATATCCAACTT 59.873 40.000 0.73 0.00 0.00 2.66
4478 4636 2.519377 TAATATGCTTGGTCCGTCGG 57.481 50.000 4.39 4.39 0.00 4.79
4487 4645 2.261671 GTCCGTCGGTGATGCACT 59.738 61.111 11.88 0.00 34.40 4.40
4542 4700 2.987125 GGTAGACCACCGTGGCAT 59.013 61.111 17.99 8.81 42.67 4.40
4623 4781 3.961838 TTGGCCACCGCACGATACC 62.962 63.158 3.88 0.00 36.38 2.73
4681 4839 2.350964 GCTTGAACGGCCACGAAATAAA 60.351 45.455 2.24 0.00 44.60 1.40
4690 4848 3.279434 GCCACGAAATAAATGAGGGTCT 58.721 45.455 0.00 0.00 0.00 3.85
4729 4887 2.143594 GAGGTGGAGCGACGAGTGTT 62.144 60.000 0.00 0.00 0.00 3.32
4828 4987 2.158914 CCATAGTGCCACAGACATAGCA 60.159 50.000 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.426829 GCTCTAAGCTATCGATCATCGCA 60.427 47.826 0.00 0.00 37.81 5.10
175 176 3.618594 TCACGAAAGAATGAGTAGCATGC 59.381 43.478 10.51 10.51 37.28 4.06
277 278 0.034896 GAGAAACTGAACCTCGGCCA 59.965 55.000 2.24 0.00 0.00 5.36
358 361 1.144936 CACCTCGCTCTCCATTCCC 59.855 63.158 0.00 0.00 0.00 3.97
424 427 1.656652 CCTTCGACAACCATAGCAGG 58.343 55.000 0.00 0.00 0.00 4.85
458 461 2.863137 CTCGCCAATGCTTCTAAGACTC 59.137 50.000 0.00 0.00 34.43 3.36
471 474 0.179124 GAGCTTCTCGACTCGCCAAT 60.179 55.000 0.00 0.00 0.00 3.16
478 481 1.445238 GCGCTTGAGCTTCTCGACT 60.445 57.895 0.00 0.00 39.32 4.18
557 560 7.773690 GCCCTTCTGTACCTTTTTCAATATCTA 59.226 37.037 0.00 0.00 0.00 1.98
652 655 1.611673 CCAATTGAGTGCTCGACCCTT 60.612 52.381 7.12 0.00 0.00 3.95
697 700 5.169295 GCGACCAACATCTAAAGAACTAGT 58.831 41.667 0.00 0.00 0.00 2.57
780 784 4.809673 AGCAGTAAACCAAGCTTTATTGC 58.190 39.130 12.85 12.85 44.03 3.56
814 818 1.009675 CCTATTTGACGCCGCATGC 60.010 57.895 7.91 7.91 0.00 4.06
815 819 1.095228 ACCCTATTTGACGCCGCATG 61.095 55.000 0.00 0.00 0.00 4.06
816 820 0.393808 AACCCTATTTGACGCCGCAT 60.394 50.000 0.00 0.00 0.00 4.73
817 821 0.606944 AAACCCTATTTGACGCCGCA 60.607 50.000 0.00 0.00 0.00 5.69
818 822 0.179174 CAAACCCTATTTGACGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
819 823 0.179174 GCAAACCCTATTTGACGCCG 60.179 55.000 3.62 0.00 0.00 6.46
820 824 0.172578 GGCAAACCCTATTTGACGCC 59.827 55.000 3.62 0.00 0.00 5.68
821 825 3.713936 GGCAAACCCTATTTGACGC 57.286 52.632 3.62 0.00 0.00 5.19
833 837 7.177396 TTTTGCATGTAGTAGTTTGGGCAAAC 61.177 38.462 7.83 0.00 45.97 2.93
834 838 3.491342 TGCATGTAGTAGTTTGGGCAAA 58.509 40.909 0.00 0.00 0.00 3.68
835 839 3.147553 TGCATGTAGTAGTTTGGGCAA 57.852 42.857 0.00 0.00 0.00 4.52
836 840 2.869101 TGCATGTAGTAGTTTGGGCA 57.131 45.000 0.00 0.00 0.00 5.36
837 841 4.234574 GTTTTGCATGTAGTAGTTTGGGC 58.765 43.478 0.00 0.00 0.00 5.36
838 842 5.446143 TGTTTTGCATGTAGTAGTTTGGG 57.554 39.130 0.00 0.00 0.00 4.12
895 899 1.340991 GGGCCCTAGTGAAGCATTTGA 60.341 52.381 17.04 0.00 0.00 2.69
955 960 2.355115 GGGGGACGAAATGGCAGT 59.645 61.111 0.00 0.00 0.00 4.40
1083 1101 1.331138 GACGTATGACAGACCTCGAGG 59.669 57.143 30.11 30.11 42.17 4.63
1085 1103 1.736126 GTGACGTATGACAGACCTCGA 59.264 52.381 0.00 0.00 0.00 4.04
1109 1127 2.054453 GGGAAGTTGGGGCATGAGC 61.054 63.158 0.00 0.00 41.10 4.26
1251 1269 1.689582 GTACCAGGGGGAGGACAGG 60.690 68.421 0.00 0.00 38.05 4.00
1297 1315 5.557866 TGCATTTATGAGATGAGATGGAGG 58.442 41.667 0.00 0.00 0.00 4.30
1300 1323 5.995897 TGACTGCATTTATGAGATGAGATGG 59.004 40.000 0.00 0.00 0.00 3.51
1436 1459 5.084818 ACAGATACACCGATGAAACATCA 57.915 39.130 11.39 0.00 0.00 3.07
1451 1474 2.608090 GCAAAAGGCGTAGGACAGATAC 59.392 50.000 0.00 0.00 0.00 2.24
1524 1550 3.694734 ACTGCAGAAATCAACAACAACG 58.305 40.909 23.35 0.00 0.00 4.10
1532 1558 5.682234 TCCTGAGATACTGCAGAAATCAA 57.318 39.130 23.35 13.18 34.06 2.57
1533 1559 5.682234 TTCCTGAGATACTGCAGAAATCA 57.318 39.130 23.35 16.47 34.06 2.57
1534 1560 5.049543 GCATTCCTGAGATACTGCAGAAATC 60.050 44.000 23.35 20.98 34.06 2.17
1812 1840 4.915085 GCAGAATCTGAGTAAGCGACTATC 59.085 45.833 15.38 0.00 39.06 2.08
1832 1863 3.466836 TCTACACAAGACCAAAGTGCAG 58.533 45.455 0.00 0.00 36.76 4.41
2040 2078 3.710209 AGATGAAGACAAGGTTGAGGG 57.290 47.619 0.00 0.00 0.00 4.30
2226 2264 5.006386 AGCTGGAATTAAGTCAAGTGGAAG 58.994 41.667 8.99 0.00 0.00 3.46
2237 2275 2.019984 GGGCTGTCAGCTGGAATTAAG 58.980 52.381 23.68 4.09 41.99 1.85
2259 2297 8.537728 AATATGGCATCCTTTGTTCAAATAGA 57.462 30.769 1.65 0.68 0.00 1.98
2270 2308 3.893813 GCCTCTGAAATATGGCATCCTTT 59.106 43.478 1.65 5.41 44.34 3.11
2333 2371 5.371526 TCAGGATATCCTTTTGCAGTGATC 58.628 41.667 22.29 0.00 46.09 2.92
2385 2423 8.358148 AGTATAGTTGACAATATAACGGAGTGG 58.642 37.037 0.00 0.00 45.00 4.00
2579 2622 8.740123 TCAGAAAACAAACAACCAGAATAGTA 57.260 30.769 0.00 0.00 0.00 1.82
2580 2623 7.639113 TCAGAAAACAAACAACCAGAATAGT 57.361 32.000 0.00 0.00 0.00 2.12
2731 2881 5.240183 CGTTCTGAAATATGGGCTTGATCAT 59.760 40.000 0.00 0.00 0.00 2.45
2739 2889 1.388547 TGCCGTTCTGAAATATGGGC 58.611 50.000 0.00 1.60 39.48 5.36
2751 2902 7.810766 TTGAAGAATTTCATTAATGCCGTTC 57.189 32.000 10.76 12.71 42.60 3.95
2756 2907 8.333186 GCTGGAATTGAAGAATTTCATTAATGC 58.667 33.333 10.76 0.00 42.60 3.56
2766 2917 4.877378 TGCAAGCTGGAATTGAAGAATT 57.123 36.364 0.00 0.00 34.29 2.17
2804 2955 4.344679 AGTTGCAGATCATCTCCTCTTAGG 59.655 45.833 0.00 0.00 36.46 2.69
2906 3057 1.276421 AGAAATAGCAGACGCACCTGT 59.724 47.619 4.55 0.00 42.27 4.00
2913 3064 5.635280 TCTGAAAGTTGAGAAATAGCAGACG 59.365 40.000 0.00 0.00 33.76 4.18
2940 3091 8.177119 ACTTGTATATTTTCAACACACCACAT 57.823 30.769 0.00 0.00 0.00 3.21
2985 3136 5.509272 CGTAAAGAATTGCTGTGTATGCTTG 59.491 40.000 0.00 0.00 0.00 4.01
2989 3140 6.185399 GCTACGTAAAGAATTGCTGTGTATG 58.815 40.000 0.00 0.00 0.00 2.39
3027 3178 5.634439 TGAAAATGTTATCTGTTGCACATGC 59.366 36.000 0.00 0.00 42.50 4.06
3077 3229 4.446371 CATCTTAGTAGAGCCAACAAGGG 58.554 47.826 0.00 0.00 32.63 3.95
3105 3258 4.676546 TCGTTAGTCATGCATCTCTCAAG 58.323 43.478 0.00 0.00 0.00 3.02
3147 3300 3.663995 TTTTGTGAGCCAATGTCATGG 57.336 42.857 0.00 0.00 43.70 3.66
3202 3355 1.340248 ACTCAGCCGTGGAATATACCG 59.660 52.381 0.00 0.00 0.00 4.02
3271 3424 9.492973 CCTTTTTATCCATTTTGATGACAAGTT 57.507 29.630 0.00 0.00 37.32 2.66
3273 3426 7.550196 CCCCTTTTTATCCATTTTGATGACAAG 59.450 37.037 0.00 0.00 37.32 3.16
3279 3432 6.950860 ACACCCCTTTTTATCCATTTTGAT 57.049 33.333 0.00 0.00 0.00 2.57
3281 3434 8.078060 AGATACACCCCTTTTTATCCATTTTG 57.922 34.615 0.00 0.00 0.00 2.44
3287 3440 7.803131 AGTTCTAGATACACCCCTTTTTATCC 58.197 38.462 0.00 0.00 0.00 2.59
3295 3448 8.849543 TGTATTTTAGTTCTAGATACACCCCT 57.150 34.615 0.00 0.00 30.60 4.79
3296 3449 9.708092 GATGTATTTTAGTTCTAGATACACCCC 57.292 37.037 14.34 8.08 36.40 4.95
3340 3493 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
3341 3494 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
3342 3495 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
3348 3501 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3351 3504 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3363 3516 1.222936 GAGTACTCCCTCCGTCCGA 59.777 63.158 12.13 0.00 0.00 4.55
3570 3723 9.209175 AGTAATTGACTCTTAACATTGTCAGAC 57.791 33.333 0.00 0.00 40.00 3.51
3599 3756 7.582667 AATTGAAGCTGGTTTAGTACAAAGT 57.417 32.000 0.00 0.00 0.00 2.66
3698 3855 2.178235 GCCGGTATCGAAGTTGGGC 61.178 63.158 1.90 0.00 39.00 5.36
3699 3856 0.391927 TTGCCGGTATCGAAGTTGGG 60.392 55.000 1.90 0.00 39.00 4.12
3789 3946 0.099613 GAGCTTCGATCTCAGCACGA 59.900 55.000 13.74 0.00 38.61 4.35
3944 4102 8.823818 CGAGAGCAATATATCATGCAATCATAA 58.176 33.333 11.11 0.00 44.95 1.90
3945 4103 7.983484 ACGAGAGCAATATATCATGCAATCATA 59.017 33.333 11.11 0.00 44.95 2.15
3946 4104 6.822170 ACGAGAGCAATATATCATGCAATCAT 59.178 34.615 11.11 0.00 44.95 2.45
3947 4105 6.091713 CACGAGAGCAATATATCATGCAATCA 59.908 38.462 11.11 0.00 44.95 2.57
3948 4106 6.476051 CACGAGAGCAATATATCATGCAATC 58.524 40.000 11.11 7.59 44.95 2.67
3949 4107 5.163784 GCACGAGAGCAATATATCATGCAAT 60.164 40.000 11.11 0.48 44.95 3.56
3950 4108 4.152938 GCACGAGAGCAATATATCATGCAA 59.847 41.667 11.11 0.00 44.95 4.08
3951 4109 3.681417 GCACGAGAGCAATATATCATGCA 59.319 43.478 11.11 0.00 44.95 3.96
3952 4110 3.681417 TGCACGAGAGCAATATATCATGC 59.319 43.478 1.74 1.74 42.46 4.06
3972 4130 7.200455 TGTACATCATATATACGTGCCTATGC 58.800 38.462 0.00 0.00 38.26 3.14
3973 4131 9.020813 GTTGTACATCATATATACGTGCCTATG 57.979 37.037 0.00 2.62 0.00 2.23
3974 4132 7.913821 CGTTGTACATCATATATACGTGCCTAT 59.086 37.037 0.00 0.00 0.00 2.57
3975 4133 7.119553 TCGTTGTACATCATATATACGTGCCTA 59.880 37.037 11.04 0.00 0.00 3.93
3976 4134 6.072342 TCGTTGTACATCATATATACGTGCCT 60.072 38.462 11.04 0.00 0.00 4.75
3977 4135 6.088173 TCGTTGTACATCATATATACGTGCC 58.912 40.000 11.04 0.00 0.00 5.01
3978 4136 7.253651 CCATCGTTGTACATCATATATACGTGC 60.254 40.741 11.04 0.00 0.00 5.34
3979 4137 7.220108 CCCATCGTTGTACATCATATATACGTG 59.780 40.741 11.04 9.01 0.00 4.49
3980 4138 7.255569 CCCATCGTTGTACATCATATATACGT 58.744 38.462 11.04 0.00 0.00 3.57
3981 4139 6.198403 GCCCATCGTTGTACATCATATATACG 59.802 42.308 0.00 0.80 0.00 3.06
3982 4140 6.479001 GGCCCATCGTTGTACATCATATATAC 59.521 42.308 0.00 0.00 0.00 1.47
3983 4141 6.155393 TGGCCCATCGTTGTACATCATATATA 59.845 38.462 0.00 0.00 0.00 0.86
3984 4142 5.045942 TGGCCCATCGTTGTACATCATATAT 60.046 40.000 0.00 0.00 0.00 0.86
3985 4143 4.284746 TGGCCCATCGTTGTACATCATATA 59.715 41.667 0.00 0.00 0.00 0.86
3986 4144 3.072330 TGGCCCATCGTTGTACATCATAT 59.928 43.478 0.00 0.00 0.00 1.78
3987 4145 2.436173 TGGCCCATCGTTGTACATCATA 59.564 45.455 0.00 0.00 0.00 2.15
3988 4146 1.211703 TGGCCCATCGTTGTACATCAT 59.788 47.619 0.00 0.00 0.00 2.45
3989 4147 0.615850 TGGCCCATCGTTGTACATCA 59.384 50.000 0.00 0.00 0.00 3.07
3990 4148 1.014352 GTGGCCCATCGTTGTACATC 58.986 55.000 0.00 0.00 0.00 3.06
3991 4149 0.742990 CGTGGCCCATCGTTGTACAT 60.743 55.000 0.00 0.00 0.00 2.29
3992 4150 1.374885 CGTGGCCCATCGTTGTACA 60.375 57.895 0.00 0.00 0.00 2.90
3993 4151 2.104253 CCGTGGCCCATCGTTGTAC 61.104 63.158 0.00 0.00 0.00 2.90
3994 4152 1.618876 ATCCGTGGCCCATCGTTGTA 61.619 55.000 0.00 0.00 0.00 2.41
3995 4153 2.869503 GATCCGTGGCCCATCGTTGT 62.870 60.000 0.00 0.00 0.00 3.32
3996 4154 2.124736 ATCCGTGGCCCATCGTTG 60.125 61.111 0.00 0.00 0.00 4.10
3997 4155 2.189521 GATCCGTGGCCCATCGTT 59.810 61.111 0.00 0.00 0.00 3.85
3998 4156 2.764128 AGATCCGTGGCCCATCGT 60.764 61.111 0.00 0.00 0.00 3.73
3999 4157 2.029666 GAGATCCGTGGCCCATCG 59.970 66.667 0.00 2.28 0.00 3.84
4000 4158 1.369321 GAGAGATCCGTGGCCCATC 59.631 63.158 0.00 0.00 0.00 3.51
4001 4159 0.982852 TTGAGAGATCCGTGGCCCAT 60.983 55.000 0.00 0.00 0.00 4.00
4002 4160 0.982852 ATTGAGAGATCCGTGGCCCA 60.983 55.000 0.00 0.00 0.00 5.36
4003 4161 0.181350 AATTGAGAGATCCGTGGCCC 59.819 55.000 0.00 0.00 0.00 5.80
4004 4162 2.910688 TAATTGAGAGATCCGTGGCC 57.089 50.000 0.00 0.00 0.00 5.36
4005 4163 4.883083 TGTATAATTGAGAGATCCGTGGC 58.117 43.478 0.00 0.00 0.00 5.01
4006 4164 5.928839 CCTTGTATAATTGAGAGATCCGTGG 59.071 44.000 0.00 0.00 0.00 4.94
4007 4165 6.749139 TCCTTGTATAATTGAGAGATCCGTG 58.251 40.000 0.00 0.00 0.00 4.94
4008 4166 6.978674 TCCTTGTATAATTGAGAGATCCGT 57.021 37.500 0.00 0.00 0.00 4.69
4009 4167 7.437748 AGTTCCTTGTATAATTGAGAGATCCG 58.562 38.462 0.00 0.00 0.00 4.18
4010 4168 9.921637 CTAGTTCCTTGTATAATTGAGAGATCC 57.078 37.037 0.00 0.00 0.00 3.36
4011 4169 9.921637 CCTAGTTCCTTGTATAATTGAGAGATC 57.078 37.037 0.00 0.00 0.00 2.75
4012 4170 9.661954 TCCTAGTTCCTTGTATAATTGAGAGAT 57.338 33.333 0.00 0.00 0.00 2.75
4013 4171 9.137459 CTCCTAGTTCCTTGTATAATTGAGAGA 57.863 37.037 0.00 0.00 0.00 3.10
4014 4172 8.364142 CCTCCTAGTTCCTTGTATAATTGAGAG 58.636 40.741 0.00 0.00 0.00 3.20
4015 4173 7.202011 GCCTCCTAGTTCCTTGTATAATTGAGA 60.202 40.741 0.00 0.00 0.00 3.27
4016 4174 6.931840 GCCTCCTAGTTCCTTGTATAATTGAG 59.068 42.308 0.00 0.00 0.00 3.02
4017 4175 6.462487 CGCCTCCTAGTTCCTTGTATAATTGA 60.462 42.308 0.00 0.00 0.00 2.57
4018 4176 5.696724 CGCCTCCTAGTTCCTTGTATAATTG 59.303 44.000 0.00 0.00 0.00 2.32
4019 4177 5.221661 CCGCCTCCTAGTTCCTTGTATAATT 60.222 44.000 0.00 0.00 0.00 1.40
4020 4178 4.283722 CCGCCTCCTAGTTCCTTGTATAAT 59.716 45.833 0.00 0.00 0.00 1.28
4021 4179 3.640029 CCGCCTCCTAGTTCCTTGTATAA 59.360 47.826 0.00 0.00 0.00 0.98
4022 4180 3.228453 CCGCCTCCTAGTTCCTTGTATA 58.772 50.000 0.00 0.00 0.00 1.47
4023 4181 2.040178 CCGCCTCCTAGTTCCTTGTAT 58.960 52.381 0.00 0.00 0.00 2.29
4024 4182 1.481871 CCGCCTCCTAGTTCCTTGTA 58.518 55.000 0.00 0.00 0.00 2.41
4025 4183 1.265454 CCCGCCTCCTAGTTCCTTGT 61.265 60.000 0.00 0.00 0.00 3.16
4026 4184 1.522569 CCCGCCTCCTAGTTCCTTG 59.477 63.158 0.00 0.00 0.00 3.61
4027 4185 2.368011 GCCCGCCTCCTAGTTCCTT 61.368 63.158 0.00 0.00 0.00 3.36
4028 4186 2.764547 GCCCGCCTCCTAGTTCCT 60.765 66.667 0.00 0.00 0.00 3.36
4029 4187 2.941563 TAGGCCCGCCTCCTAGTTCC 62.942 65.000 12.53 0.00 44.43 3.62
4030 4188 1.047034 TTAGGCCCGCCTCCTAGTTC 61.047 60.000 12.53 0.00 44.43 3.01
4031 4189 0.400093 ATTAGGCCCGCCTCCTAGTT 60.400 55.000 12.53 0.00 44.43 2.24
4032 4190 0.485988 TATTAGGCCCGCCTCCTAGT 59.514 55.000 12.53 0.00 44.43 2.57
4033 4191 0.896226 GTATTAGGCCCGCCTCCTAG 59.104 60.000 12.53 0.00 44.43 3.02
4034 4192 0.189080 TGTATTAGGCCCGCCTCCTA 59.811 55.000 12.53 2.32 44.43 2.94
4035 4193 1.074775 TGTATTAGGCCCGCCTCCT 60.075 57.895 12.53 3.34 44.43 3.69
4036 4194 1.070957 GTGTATTAGGCCCGCCTCC 59.929 63.158 12.53 0.00 44.43 4.30
4037 4195 0.179468 TTGTGTATTAGGCCCGCCTC 59.821 55.000 12.53 0.00 44.43 4.70
4039 4197 2.554370 TATTGTGTATTAGGCCCGCC 57.446 50.000 0.00 0.00 0.00 6.13
4285 4443 2.507992 CCGCTTCGACTGCAGGAG 60.508 66.667 19.93 11.53 0.00 3.69
4286 4444 4.742201 GCCGCTTCGACTGCAGGA 62.742 66.667 19.93 3.27 0.00 3.86
4288 4446 2.806856 GATGCCGCTTCGACTGCAG 61.807 63.158 13.48 13.48 37.12 4.41
4289 4447 2.815211 GATGCCGCTTCGACTGCA 60.815 61.111 9.77 5.32 38.23 4.41
4361 4519 7.172868 ACAATTTGCAGATATCATGACCAAA 57.827 32.000 5.32 7.02 0.00 3.28
4459 4617 1.758280 ACCGACGGACCAAGCATATTA 59.242 47.619 23.38 0.00 0.00 0.98
4478 4636 1.369091 CCGCTAACCCAGTGCATCAC 61.369 60.000 0.00 0.00 33.09 3.06
4487 4645 0.627451 TCTACCTCTCCGCTAACCCA 59.373 55.000 0.00 0.00 0.00 4.51
4525 4683 1.449601 CATGCCACGGTGGTCTACC 60.450 63.158 26.86 11.43 46.56 3.18
4542 4700 1.461268 TCTCCTGCCCTGTTGACCA 60.461 57.895 0.00 0.00 0.00 4.02
4578 4736 1.300620 CCGAGTGTTCGTGGCTTCA 60.301 57.895 0.00 0.00 45.28 3.02
4665 4823 2.422127 CCTCATTTATTTCGTGGCCGTT 59.578 45.455 0.00 0.00 35.01 4.44
4690 4848 2.025981 TCGGGCTAGTGTGTCTACCTTA 60.026 50.000 0.00 0.00 0.00 2.69
4703 4861 3.905678 CGCTCCACCTCGGGCTAG 61.906 72.222 0.00 0.00 34.36 3.42
4729 4887 4.715130 ACTGGGCGGGCTGTCCTA 62.715 66.667 19.46 5.62 45.26 2.94
4805 4964 2.698855 ATGTCTGTGGCACTATGGAC 57.301 50.000 19.83 19.13 0.00 4.02


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

AutoCloner maintained by Alex Coulton.