Multiple sequence alignment - TraesCS5D01G052200

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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 TraesCS5D01G052200 chr5D 100.000 6044 0 0 1 6044 50318337 50324380 0.000000e+00 11162.0
1 TraesCS5D01G052200 chr5D 95.652 46 2 0 4540 4585 50322797 50322842 2.340000e-09 75.0
2 TraesCS5D01G052200 chr5D 95.652 46 2 0 4461 4506 50322876 50322921 2.340000e-09 75.0
3 TraesCS5D01G052200 chr5A 91.348 2878 161 42 9 2856 39732286 39735105 0.000000e+00 3855.0
4 TraesCS5D01G052200 chr5A 91.410 2433 121 48 3249 5657 39735873 39738241 0.000000e+00 3254.0
5 TraesCS5D01G052200 chr5A 94.510 255 8 4 5787 6039 39738416 39738666 7.350000e-104 388.0
6 TraesCS5D01G052200 chr5A 97.129 209 6 0 3049 3257 39735480 39735688 2.680000e-93 353.0
7 TraesCS5D01G052200 chr5A 95.862 145 6 0 2873 3017 39735151 39735295 1.010000e-57 235.0
8 TraesCS5D01G052200 chr5A 85.870 92 10 3 2973 3062 39735200 39735110 1.790000e-15 95.3
9 TraesCS5D01G052200 chr5A 100.000 35 0 0 1319 1353 327089606 327089640 1.410000e-06 65.8
10 TraesCS5D01G052200 chr5B 95.874 1721 46 5 2873 4585 53021939 53023642 0.000000e+00 2761.0
11 TraesCS5D01G052200 chr5B 94.232 1335 55 10 1545 2872 53020585 53021904 0.000000e+00 2019.0
12 TraesCS5D01G052200 chr5B 94.399 1232 44 13 4462 5680 53023598 53024817 0.000000e+00 1869.0
13 TraesCS5D01G052200 chr5B 88.212 1544 93 46 1 1520 53019135 53020613 0.000000e+00 1760.0
14 TraesCS5D01G052200 chr5B 95.635 252 10 1 5787 6038 53024842 53025092 2.620000e-108 403.0
15 TraesCS5D01G052200 chr5B 95.652 46 2 0 4540 4585 53023516 53023561 2.340000e-09 75.0
16 TraesCS5D01G052200 chr5B 93.478 46 3 0 4461 4506 53023676 53023721 1.090000e-07 69.4
17 TraesCS5D01G052200 chr4A 85.314 892 91 19 1065 1955 590664661 590663809 0.000000e+00 885.0
18 TraesCS5D01G052200 chr4A 82.890 263 32 9 1076 1334 67175040 67175293 2.190000e-54 224.0
19 TraesCS5D01G052200 chr4D 85.111 900 95 19 1057 1955 11858481 11859342 0.000000e+00 883.0
20 TraesCS5D01G052200 chr4D 83.688 282 33 9 1057 1334 385739444 385739716 2.800000e-63 254.0
21 TraesCS5D01G052200 chr4B 86.957 598 61 7 1060 1649 21941082 21940494 0.000000e+00 656.0
22 TraesCS5D01G052200 chr4B 76.037 217 29 15 2872 3076 55703152 55702947 2.320000e-14 91.6
23 TraesCS5D01G052200 chr6B 83.156 564 57 21 1043 1598 382771903 382771370 1.180000e-131 481.0
24 TraesCS5D01G052200 chr6D 82.862 566 57 19 1043 1598 223941566 223942101 7.090000e-129 472.0
25 TraesCS5D01G052200 chr1D 81.979 283 36 12 1452 1733 222338340 222338072 6.100000e-55 226.0
26 TraesCS5D01G052200 chr1D 97.143 35 1 0 1319 1353 222339407 222339373 6.540000e-05 60.2
27 TraesCS5D01G052200 chr1A 83.884 242 29 8 1452 1693 288512020 288511789 7.880000e-54 222.0
28 TraesCS5D01G052200 chr1B 84.416 231 27 7 1452 1682 321876821 321876600 1.020000e-52 219.0
29 TraesCS5D01G052200 chr1B 81.429 210 29 7 2878 3079 635119113 635119320 4.850000e-36 163.0
30 TraesCS5D01G052200 chr1B 85.000 120 16 2 1078 1195 461306001 461305882 2.960000e-23 121.0
31 TraesCS5D01G052200 chr3A 78.351 97 20 1 5684 5780 1518864 1518959 1.820000e-05 62.1
32 TraesCS5D01G052200 chr2D 97.297 37 0 1 1582 1617 349004953 349004917 1.820000e-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 TraesCS5D01G052200 chr5D 50318337 50324380 6043 False 3770.666667 11162 97.101333 1 6044 3 chr5D.!!$F1 6043
1 TraesCS5D01G052200 chr5A 39732286 39738666 6380 False 1617.000000 3855 94.051800 9 6039 5 chr5A.!!$F2 6030
2 TraesCS5D01G052200 chr5B 53019135 53025092 5957 False 1279.485714 2761 93.926000 1 6038 7 chr5B.!!$F1 6037
3 TraesCS5D01G052200 chr4A 590663809 590664661 852 True 885.000000 885 85.314000 1065 1955 1 chr4A.!!$R1 890
4 TraesCS5D01G052200 chr4D 11858481 11859342 861 False 883.000000 883 85.111000 1057 1955 1 chr4D.!!$F1 898
5 TraesCS5D01G052200 chr4B 21940494 21941082 588 True 656.000000 656 86.957000 1060 1649 1 chr4B.!!$R1 589
6 TraesCS5D01G052200 chr6B 382771370 382771903 533 True 481.000000 481 83.156000 1043 1598 1 chr6B.!!$R1 555
7 TraesCS5D01G052200 chr6D 223941566 223942101 535 False 472.000000 472 82.862000 1043 1598 1 chr6D.!!$F1 555

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
505 540 0.242825 TAACTGACTGAACCCTCGCG 59.757 55.000 0.0 0.0 0.00 5.87 F
1141 1193 0.179056 CAGCCATTCGGGGATACGTT 60.179 55.000 0.0 0.0 37.04 3.99 F
2048 2126 0.177141 GGTAGGGCAGTGTGCGATTA 59.823 55.000 0.0 0.0 46.21 1.75 F
3322 3794 1.276138 TGTCAGCTCACCGATCACATT 59.724 47.619 0.0 0.0 0.00 2.71 F
3538 4016 0.041535 AATTCCCATGCCTTGCCTGA 59.958 50.000 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 1689 0.035317 ACCACGCTCAAGCAGATGAA 59.965 50.000 2.50 0.00 42.21 2.57 R
2456 2539 0.401738 CTTCCTGGTTCCCTTGAGCA 59.598 55.000 0.00 0.00 0.00 4.26 R
3533 4011 1.200948 GAGGCAACAATCTGTTCAGGC 59.799 52.381 0.00 0.00 38.77 4.85 R
4950 5514 0.521291 GTGCAACGCCATTCTGCTTA 59.479 50.000 0.00 0.00 37.00 3.09 R
5428 6004 0.255318 AAAGCTGCAGGCAGAGCTAT 59.745 50.000 24.46 5.23 46.30 2.97 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
45 47 2.617021 GGAAGGTTCGGTTCAATGGCTA 60.617 50.000 0.00 0.00 0.00 3.93
75 78 4.542075 GGAAGCTTCCATCCGTCC 57.458 61.111 35.71 10.84 46.76 4.79
76 79 1.602237 GGAAGCTTCCATCCGTCCA 59.398 57.895 35.71 0.00 46.76 4.02
82 85 0.541392 CTTCCATCCGTCCACATCCA 59.459 55.000 0.00 0.00 0.00 3.41
83 86 1.141657 CTTCCATCCGTCCACATCCAT 59.858 52.381 0.00 0.00 0.00 3.41
84 87 0.469494 TCCATCCGTCCACATCCATG 59.531 55.000 0.00 0.00 0.00 3.66
85 88 0.469494 CCATCCGTCCACATCCATGA 59.531 55.000 0.00 0.00 0.00 3.07
126 139 2.781681 ATACGAAAACACCCCTGAGG 57.218 50.000 0.00 0.00 43.78 3.86
157 170 2.668144 ACCCTCTTATCCTCTCTCCG 57.332 55.000 0.00 0.00 0.00 4.63
216 229 4.849329 CTCTCCGCCGTACACGCC 62.849 72.222 0.00 0.00 38.18 5.68
223 236 4.446413 CCGTACACGCCCACCCTC 62.446 72.222 0.00 0.00 38.18 4.30
224 237 4.446413 CGTACACGCCCACCCTCC 62.446 72.222 0.00 0.00 0.00 4.30
225 238 3.315949 GTACACGCCCACCCTCCA 61.316 66.667 0.00 0.00 0.00 3.86
226 239 3.315949 TACACGCCCACCCTCCAC 61.316 66.667 0.00 0.00 0.00 4.02
383 418 4.222847 GAACCCTAGCCCCGCTCG 62.223 72.222 0.00 0.00 40.44 5.03
458 493 0.384669 GCGGAGTACTGATTAGCGGT 59.615 55.000 0.00 0.00 39.97 5.68
469 504 2.297597 TGATTAGCGGTTTGTTTTGGGG 59.702 45.455 0.00 0.00 0.00 4.96
470 505 1.041437 TTAGCGGTTTGTTTTGGGGG 58.959 50.000 0.00 0.00 0.00 5.40
482 517 3.861247 TTGGGGGCAATTGGGGGTG 62.861 63.158 7.72 0.00 0.00 4.61
484 519 4.720680 GGGGCAATTGGGGGTGCT 62.721 66.667 7.72 0.00 40.70 4.40
485 520 2.607442 GGGCAATTGGGGGTGCTT 60.607 61.111 7.72 0.00 40.70 3.91
486 521 2.223443 GGGCAATTGGGGGTGCTTT 61.223 57.895 7.72 0.00 40.70 3.51
502 537 3.498777 GTGCTTTAACTGACTGAACCCTC 59.501 47.826 0.00 0.00 0.00 4.30
505 540 0.242825 TAACTGACTGAACCCTCGCG 59.757 55.000 0.00 0.00 0.00 5.87
506 541 2.811317 CTGACTGAACCCTCGCGC 60.811 66.667 0.00 0.00 0.00 6.86
507 542 3.288308 CTGACTGAACCCTCGCGCT 62.288 63.158 5.56 0.00 0.00 5.92
508 543 2.811317 GACTGAACCCTCGCGCTG 60.811 66.667 5.56 0.00 0.00 5.18
551 593 0.734889 CGGTGGATTGATTGTGCTCC 59.265 55.000 0.00 0.00 0.00 4.70
577 619 0.248377 GCTGCGGAATTCAGTCATGC 60.248 55.000 7.93 7.82 34.21 4.06
594 636 4.221422 CCGTGGGGCATCGATCGT 62.221 66.667 15.94 0.00 0.00 3.73
596 638 3.272334 GTGGGGCATCGATCGTGC 61.272 66.667 24.91 24.91 41.78 5.34
597 639 4.889856 TGGGGCATCGATCGTGCG 62.890 66.667 25.44 13.92 43.40 5.34
622 670 4.082354 CACGAGCCTTGTACTAGTACCTTT 60.082 45.833 26.41 10.50 35.26 3.11
624 672 4.182339 GAGCCTTGTACTAGTACCTTTGC 58.818 47.826 26.41 21.96 35.26 3.68
625 673 2.928116 GCCTTGTACTAGTACCTTTGCG 59.072 50.000 26.41 11.41 35.26 4.85
626 674 3.518590 CCTTGTACTAGTACCTTTGCGG 58.481 50.000 26.41 14.75 35.26 5.69
627 675 3.518590 CTTGTACTAGTACCTTTGCGGG 58.481 50.000 26.41 7.22 36.97 6.13
628 676 2.528564 TGTACTAGTACCTTTGCGGGT 58.471 47.619 26.41 1.65 42.86 5.28
629 677 3.696045 TGTACTAGTACCTTTGCGGGTA 58.304 45.455 26.41 4.67 40.48 3.69
630 678 4.085733 TGTACTAGTACCTTTGCGGGTAA 58.914 43.478 26.41 4.19 42.63 2.85
631 679 3.599730 ACTAGTACCTTTGCGGGTAAC 57.400 47.619 0.00 1.61 42.63 2.50
632 680 7.071131 TGTACTAGTACCTTTGCGGGTAACC 62.071 48.000 26.41 0.00 42.63 2.85
647 695 4.487714 GGTAACCAGTGGATGATTCTCA 57.512 45.455 18.40 0.00 0.00 3.27
648 696 5.041191 GGTAACCAGTGGATGATTCTCAT 57.959 43.478 18.40 0.00 40.34 2.90
649 697 5.440610 GGTAACCAGTGGATGATTCTCATT 58.559 41.667 18.40 0.00 37.20 2.57
650 698 5.888161 GGTAACCAGTGGATGATTCTCATTT 59.112 40.000 18.40 0.00 37.20 2.32
651 699 7.054124 GGTAACCAGTGGATGATTCTCATTTA 58.946 38.462 18.40 0.00 37.20 1.40
678 726 7.596248 CAGTAGTGGTTTTCAAATCTCAATTGG 59.404 37.037 5.42 0.00 0.00 3.16
805 853 8.577296 GGGGGATAAATAAACAGAAATAAGCTC 58.423 37.037 0.00 0.00 0.00 4.09
841 889 7.986085 TGCTAGAAGCTCAGTTTTCTTTAAT 57.014 32.000 0.00 0.00 42.97 1.40
896 946 2.678324 CAGTTTGGTCTCGGAGAAGAC 58.322 52.381 9.72 6.29 34.09 3.01
902 952 0.248702 GTCTCGGAGAAGACATCGGC 60.249 60.000 9.72 0.00 35.70 5.54
913 963 1.970917 GACATCGGCGTGCTTTCCTG 61.971 60.000 6.85 0.00 0.00 3.86
965 1015 3.330267 GTGTCTTTTCTCCGAGCTTGAT 58.670 45.455 1.22 0.00 0.00 2.57
1141 1193 0.179056 CAGCCATTCGGGGATACGTT 60.179 55.000 0.00 0.00 37.04 3.99
1154 1206 8.985315 TCGGGGATACGTTGAGTATATATATT 57.015 34.615 0.00 0.00 45.47 1.28
1177 1229 7.736447 TTAAAAATTAAAACATGCCCTGTGG 57.264 32.000 0.00 0.00 38.39 4.17
1190 1242 3.780294 TGCCCTGTGGTATAGAGTGAAAT 59.220 43.478 0.00 0.00 0.00 2.17
1192 1244 5.070446 TGCCCTGTGGTATAGAGTGAAATAG 59.930 44.000 0.00 0.00 0.00 1.73
1218 1282 6.138263 AGGAGAGAAACAGAGATGAGATCAT 58.862 40.000 0.00 0.00 39.70 2.45
1230 1294 6.376864 AGAGATGAGATCATAATACTGTCCCG 59.623 42.308 0.00 0.00 36.57 5.14
1241 1305 0.958822 ACTGTCCCGTTTCCATTTGC 59.041 50.000 0.00 0.00 0.00 3.68
1324 1393 6.890558 GCAACTTGCAAAATACATCAAATGT 58.109 32.000 8.97 0.00 44.26 2.71
1366 1435 4.277476 AGTAGAGACTGGAGAAGACATGG 58.723 47.826 0.00 0.00 33.41 3.66
1469 1538 5.183713 TCCCTAACATCAAGCAACAATCAAG 59.816 40.000 0.00 0.00 0.00 3.02
1615 1689 2.686835 GAGGAGAGGCTGCTGGGT 60.687 66.667 0.00 0.00 30.82 4.51
1617 1691 2.250741 GAGGAGAGGCTGCTGGGTTC 62.251 65.000 0.00 0.00 30.82 3.62
1656 1734 3.507009 GTCGGGAGGTCGAGTCCG 61.507 72.222 7.51 8.14 43.42 4.79
1707 1785 2.622011 GGCGGTGATGGCGTTTTCA 61.622 57.895 0.00 0.00 0.00 2.69
1712 1790 2.606795 CGGTGATGGCGTTTTCAATTGT 60.607 45.455 5.13 0.00 0.00 2.71
1733 1811 2.342279 CAGCGTTCCTTCCGTGGA 59.658 61.111 0.00 0.00 0.00 4.02
1748 1826 2.125912 GGAGAGCGTGTGTGCGAT 60.126 61.111 0.00 0.00 40.67 4.58
1900 1978 2.728435 GGGACACGCTTATCCCGGT 61.728 63.158 0.00 0.00 45.26 5.28
1916 1994 1.885157 GGTGTGTCCGGTCGTATCA 59.115 57.895 0.00 0.00 0.00 2.15
2022 2100 6.930164 TCAATTTTGAACCGTAGCAGTAGTAA 59.070 34.615 0.00 0.00 33.55 2.24
2048 2126 0.177141 GGTAGGGCAGTGTGCGATTA 59.823 55.000 0.00 0.00 46.21 1.75
2115 2193 3.153919 GGAATTGGAGCTTTGGTGTACA 58.846 45.455 0.00 0.00 0.00 2.90
2235 2313 1.843368 ACTGGACATGCTGGGATTTG 58.157 50.000 0.00 0.00 0.00 2.32
2413 2493 9.195411 GTCTCATTTTTATGCAACAATTTCTCA 57.805 29.630 0.00 0.00 0.00 3.27
2809 2901 5.277683 CCGCATTATATTGATAGGCATCAGC 60.278 44.000 0.00 0.00 42.11 4.26
2992 3118 3.265791 CCAACTACACTTGCCATCTCTC 58.734 50.000 0.00 0.00 0.00 3.20
3063 3342 3.782046 CGAATGTTCGGGACTTATCAGT 58.218 45.455 7.24 0.00 46.30 3.41
3267 3739 7.123997 TGTTGATTATATCCAATGCCACAGTTT 59.876 33.333 0.00 0.00 0.00 2.66
3286 3758 5.290158 CAGTTTGCATATCACATTTCCTTGC 59.710 40.000 0.00 0.00 0.00 4.01
3322 3794 1.276138 TGTCAGCTCACCGATCACATT 59.724 47.619 0.00 0.00 0.00 2.71
3533 4011 1.551430 TGAGCAAATTCCCATGCCTTG 59.449 47.619 0.00 0.00 43.57 3.61
3538 4016 0.041535 AATTCCCATGCCTTGCCTGA 59.958 50.000 0.00 0.00 0.00 3.86
3620 4098 5.744171 TGCATGATACTGGAGTTATTGTGT 58.256 37.500 0.00 0.00 0.00 3.72
3886 4364 5.185828 TGCATGATCGTAGACCTTGCTATAT 59.814 40.000 0.00 0.00 42.51 0.86
4242 4724 9.420118 ACAATAGGGCAAATAATCAAGTGAATA 57.580 29.630 0.00 0.00 0.00 1.75
4325 4807 9.699410 ATCTTATTAGGGTGAACATCATTTCAA 57.301 29.630 0.00 0.00 37.24 2.69
4541 5105 5.823861 AAGGCAACCCATAAATTTCAGTT 57.176 34.783 0.00 0.00 37.17 3.16
4673 5237 7.016563 AGGACTTGCATGAACCATATACAGATA 59.983 37.037 6.60 0.00 0.00 1.98
4674 5238 7.826252 GGACTTGCATGAACCATATACAGATAT 59.174 37.037 6.60 0.00 0.00 1.63
4690 5254 4.641989 ACAGATATGTTTCCAGTGCCAATC 59.358 41.667 0.00 0.00 0.00 2.67
4757 5321 3.928727 ATGTTCATTCTTGTGGCTGTG 57.071 42.857 0.00 0.00 0.00 3.66
4801 5365 7.451731 TCCCCTTTCTGTATCTTGTAATGAT 57.548 36.000 0.00 0.00 34.76 2.45
4950 5514 4.581309 TTCTGATTCCAGCTCCAAAGAT 57.419 40.909 0.00 0.00 40.20 2.40
5010 5574 2.764314 CCAATCTCCCAAAGGCGCG 61.764 63.158 0.00 0.00 0.00 6.86
5293 5866 4.728110 GGGGTTAGCCGCGGGTTT 62.728 66.667 37.09 7.03 37.97 3.27
5394 5970 0.036105 TGTGCTGCATCCTCATTCGT 60.036 50.000 5.27 0.00 0.00 3.85
5409 5985 5.163622 CCTCATTCGTGGTGCAGAAAATAAT 60.164 40.000 0.00 0.00 0.00 1.28
5467 6043 2.527497 TCTTTGCCCTTGATTGCATCA 58.473 42.857 0.00 0.00 37.33 3.07
5507 6083 6.322456 TCTCATGTTTTGGTTGGATGTTGTTA 59.678 34.615 0.00 0.00 0.00 2.41
5511 6087 3.314307 TTGGTTGGATGTTGTTACCCA 57.686 42.857 0.00 0.00 0.00 4.51
5531 6107 1.958205 CATGATTCGGAGCCTCGCC 60.958 63.158 0.00 0.00 0.00 5.54
5535 6111 0.667792 GATTCGGAGCCTCGCCATAC 60.668 60.000 0.00 0.00 0.00 2.39
5551 6127 3.303593 GCCATACGATGTTTGCATCTCTG 60.304 47.826 6.11 1.70 46.96 3.35
5553 6129 4.333649 CCATACGATGTTTGCATCTCTGTT 59.666 41.667 6.11 0.00 46.96 3.16
5555 6131 6.037062 CCATACGATGTTTGCATCTCTGTTTA 59.963 38.462 6.11 0.00 46.96 2.01
5556 6132 7.254898 CCATACGATGTTTGCATCTCTGTTTAT 60.255 37.037 6.11 0.00 46.96 1.40
5557 6133 8.764287 CATACGATGTTTGCATCTCTGTTTATA 58.236 33.333 6.11 0.00 46.96 0.98
5558 6134 7.792374 ACGATGTTTGCATCTCTGTTTATAT 57.208 32.000 6.11 0.00 46.96 0.86
5559 6135 7.633621 ACGATGTTTGCATCTCTGTTTATATG 58.366 34.615 6.11 0.00 46.96 1.78
5560 6136 7.280876 ACGATGTTTGCATCTCTGTTTATATGT 59.719 33.333 6.11 0.00 46.96 2.29
5562 6138 9.443283 GATGTTTGCATCTCTGTTTATATGTTC 57.557 33.333 0.00 0.00 45.97 3.18
5565 6141 7.792374 TTGCATCTCTGTTTATATGTTCTCC 57.208 36.000 0.00 0.00 0.00 3.71
5567 6143 7.568349 TGCATCTCTGTTTATATGTTCTCCTT 58.432 34.615 0.00 0.00 0.00 3.36
5610 6189 5.211973 TGATTATCAGAGACTACTGCCCTT 58.788 41.667 0.00 0.00 37.75 3.95
5667 6246 5.191722 TCAGGCCTTCAGAATTAGTAACCAT 59.808 40.000 0.00 0.00 0.00 3.55
5684 6263 8.511604 AGTAACCATACTTTTGAATCTCATGG 57.488 34.615 0.00 0.00 39.36 3.66
5685 6264 5.841957 ACCATACTTTTGAATCTCATGGC 57.158 39.130 0.00 0.00 35.85 4.40
5687 6266 4.891756 CCATACTTTTGAATCTCATGGCCT 59.108 41.667 3.32 0.00 0.00 5.19
5688 6267 5.221185 CCATACTTTTGAATCTCATGGCCTG 60.221 44.000 3.32 0.00 0.00 4.85
5689 6268 3.771216 ACTTTTGAATCTCATGGCCTGT 58.229 40.909 3.32 0.00 0.00 4.00
5691 6270 4.219288 ACTTTTGAATCTCATGGCCTGTTC 59.781 41.667 3.32 1.20 0.00 3.18
5692 6271 3.726557 TTGAATCTCATGGCCTGTTCT 57.273 42.857 3.32 0.00 0.00 3.01
5694 6273 2.573009 TGAATCTCATGGCCTGTTCTGA 59.427 45.455 3.32 0.00 0.00 3.27
5695 6274 3.204526 GAATCTCATGGCCTGTTCTGAG 58.795 50.000 3.32 8.71 37.14 3.35
5696 6275 1.649321 TCTCATGGCCTGTTCTGAGT 58.351 50.000 3.32 0.00 37.12 3.41
5698 6277 0.615331 TCATGGCCTGTTCTGAGTCC 59.385 55.000 3.32 0.00 0.00 3.85
5699 6278 0.393537 CATGGCCTGTTCTGAGTCCC 60.394 60.000 3.32 0.00 0.00 4.46
5700 6279 0.548682 ATGGCCTGTTCTGAGTCCCT 60.549 55.000 3.32 0.00 0.00 4.20
5701 6280 1.194781 TGGCCTGTTCTGAGTCCCTC 61.195 60.000 3.32 0.00 0.00 4.30
5702 6281 1.599576 GCCTGTTCTGAGTCCCTCC 59.400 63.158 0.00 0.00 0.00 4.30
5704 6283 1.216710 CTGTTCTGAGTCCCTCCGC 59.783 63.158 0.00 0.00 0.00 5.54
5705 6284 1.228894 TGTTCTGAGTCCCTCCGCT 60.229 57.895 0.00 0.00 0.00 5.52
5706 6285 1.251527 TGTTCTGAGTCCCTCCGCTC 61.252 60.000 0.00 0.00 0.00 5.03
5707 6286 1.682684 TTCTGAGTCCCTCCGCTCC 60.683 63.158 0.00 0.00 0.00 4.70
5708 6287 2.363018 CTGAGTCCCTCCGCTCCA 60.363 66.667 0.00 0.00 0.00 3.86
5710 6289 3.827898 GAGTCCCTCCGCTCCACG 61.828 72.222 0.00 0.00 43.15 4.94
5721 6323 2.752238 CTCCACGACTCCGCTCCT 60.752 66.667 0.00 0.00 39.95 3.69
5737 6339 1.298014 CCTGGAGCAGGTGGAGTTC 59.702 63.158 0.00 0.00 45.82 3.01
5739 6341 1.461268 TGGAGCAGGTGGAGTTCCA 60.461 57.895 0.00 0.00 42.96 3.53
5750 6352 2.841215 TGGAGTTCCAGTTAAACACCG 58.159 47.619 0.00 0.00 42.01 4.94
5751 6353 1.534163 GGAGTTCCAGTTAAACACCGC 59.466 52.381 0.00 0.00 35.64 5.68
5752 6354 1.193874 GAGTTCCAGTTAAACACCGCG 59.806 52.381 0.00 0.00 0.00 6.46
5753 6355 0.236449 GTTCCAGTTAAACACCGCGG 59.764 55.000 26.86 26.86 0.00 6.46
5754 6356 0.106335 TTCCAGTTAAACACCGCGGA 59.894 50.000 35.90 5.52 0.00 5.54
5758 6360 0.963962 AGTTAAACACCGCGGAGAGA 59.036 50.000 35.90 11.98 0.00 3.10
5762 6364 0.894184 AAACACCGCGGAGAGAGAGA 60.894 55.000 35.90 0.00 0.00 3.10
5763 6365 0.894184 AACACCGCGGAGAGAGAGAA 60.894 55.000 35.90 0.00 0.00 2.87
5764 6366 1.137825 CACCGCGGAGAGAGAGAAC 59.862 63.158 35.90 0.00 0.00 3.01
5765 6367 1.303398 ACCGCGGAGAGAGAGAACA 60.303 57.895 35.90 0.00 0.00 3.18
5766 6368 1.309499 ACCGCGGAGAGAGAGAACAG 61.309 60.000 35.90 0.00 0.00 3.16
5768 6370 1.309499 CGCGGAGAGAGAGAACAGGT 61.309 60.000 0.00 0.00 0.00 4.00
5770 6372 1.402613 GCGGAGAGAGAGAACAGGTAC 59.597 57.143 0.00 0.00 0.00 3.34
5772 6374 2.940410 CGGAGAGAGAGAACAGGTACTC 59.060 54.545 0.00 0.00 34.60 2.59
5774 6376 2.940410 GAGAGAGAGAACAGGTACTCCG 59.060 54.545 0.00 0.00 34.60 4.63
5775 6377 1.402613 GAGAGAGAACAGGTACTCCGC 59.597 57.143 0.00 0.00 34.60 5.54
5777 6379 1.133407 GAGAGAACAGGTACTCCGCAG 59.867 57.143 0.00 0.00 34.60 5.18
5778 6380 1.174783 GAGAACAGGTACTCCGCAGA 58.825 55.000 0.00 0.00 34.60 4.26
5779 6381 1.751924 GAGAACAGGTACTCCGCAGAT 59.248 52.381 0.00 0.00 34.60 2.90
5780 6382 2.166664 GAGAACAGGTACTCCGCAGATT 59.833 50.000 0.00 0.00 34.60 2.40
5781 6383 2.166664 AGAACAGGTACTCCGCAGATTC 59.833 50.000 0.00 0.00 34.60 2.52
5782 6384 1.853963 ACAGGTACTCCGCAGATTCT 58.146 50.000 0.00 0.00 34.60 2.40
5783 6385 2.180276 ACAGGTACTCCGCAGATTCTT 58.820 47.619 0.00 0.00 34.60 2.52
5784 6386 3.362706 ACAGGTACTCCGCAGATTCTTA 58.637 45.455 0.00 0.00 34.60 2.10
5785 6387 3.767673 ACAGGTACTCCGCAGATTCTTAA 59.232 43.478 0.00 0.00 34.60 1.85
5861 6486 6.155565 TCCCTCGATAAGATGGAAGTTAACAA 59.844 38.462 8.61 0.00 40.11 2.83
5926 6551 6.694844 CACTGACTGAAGCATATACTACTGTG 59.305 42.308 0.00 0.00 0.00 3.66
5929 6554 4.962995 ACTGAAGCATATACTACTGTGGGT 59.037 41.667 0.00 0.00 0.00 4.51
6039 6664 2.033372 TCCAACGTCACTGTCTTGGTA 58.967 47.619 0.00 0.00 35.58 3.25
6040 6665 2.431419 TCCAACGTCACTGTCTTGGTAA 59.569 45.455 0.00 0.00 35.58 2.85
6041 6666 2.542595 CCAACGTCACTGTCTTGGTAAC 59.457 50.000 0.00 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 2.193536 GCTTCCGGGTGCTTGTTGT 61.194 57.895 0.00 0.00 0.00 3.32
68 71 1.349026 GGATCATGGATGTGGACGGAT 59.651 52.381 0.00 0.00 0.00 4.18
70 73 0.469494 TGGATCATGGATGTGGACGG 59.531 55.000 0.00 0.00 0.00 4.79
71 74 2.420642 GATGGATCATGGATGTGGACG 58.579 52.381 0.00 0.00 0.00 4.79
74 77 2.107726 AGTGGATGGATCATGGATGTGG 59.892 50.000 0.00 0.00 0.00 4.17
75 78 3.409570 GAGTGGATGGATCATGGATGTG 58.590 50.000 0.00 0.00 0.00 3.21
76 79 2.038164 CGAGTGGATGGATCATGGATGT 59.962 50.000 0.00 0.00 0.00 3.06
82 85 1.115326 TCGGCGAGTGGATGGATCAT 61.115 55.000 4.99 0.00 0.00 2.45
83 86 1.115326 ATCGGCGAGTGGATGGATCA 61.115 55.000 17.22 0.00 0.00 2.92
84 87 0.888619 TATCGGCGAGTGGATGGATC 59.111 55.000 17.22 0.00 0.00 3.36
85 88 0.603569 GTATCGGCGAGTGGATGGAT 59.396 55.000 17.22 0.00 0.00 3.41
126 139 7.177744 AGAGGATAAGAGGGTATTCTCGATTTC 59.822 40.741 0.00 0.00 40.00 2.17
157 170 4.423209 AGAGGGGAGTGGGGAGGC 62.423 72.222 0.00 0.00 0.00 4.70
216 229 3.330720 GTGGAGGGTGGAGGGTGG 61.331 72.222 0.00 0.00 0.00 4.61
217 230 3.330720 GGTGGAGGGTGGAGGGTG 61.331 72.222 0.00 0.00 0.00 4.61
218 231 4.677151 GGGTGGAGGGTGGAGGGT 62.677 72.222 0.00 0.00 0.00 4.34
219 232 4.354943 AGGGTGGAGGGTGGAGGG 62.355 72.222 0.00 0.00 0.00 4.30
220 233 2.689034 GAGGGTGGAGGGTGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
221 234 2.689034 GGAGGGTGGAGGGTGGAG 60.689 72.222 0.00 0.00 0.00 3.86
222 235 3.537506 TGGAGGGTGGAGGGTGGA 61.538 66.667 0.00 0.00 0.00 4.02
223 236 3.330720 GTGGAGGGTGGAGGGTGG 61.331 72.222 0.00 0.00 0.00 4.61
224 237 3.330720 GGTGGAGGGTGGAGGGTG 61.331 72.222 0.00 0.00 0.00 4.61
225 238 4.677151 GGGTGGAGGGTGGAGGGT 62.677 72.222 0.00 0.00 0.00 4.34
226 239 4.354943 AGGGTGGAGGGTGGAGGG 62.355 72.222 0.00 0.00 0.00 4.30
227 240 2.689034 GAGGGTGGAGGGTGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
228 241 2.689034 GGAGGGTGGAGGGTGGAG 60.689 72.222 0.00 0.00 0.00 3.86
229 242 3.537506 TGGAGGGTGGAGGGTGGA 61.538 66.667 0.00 0.00 0.00 4.02
383 418 1.156736 CGATGATATTTGGACGGCCC 58.843 55.000 3.83 0.00 0.00 5.80
447 482 3.574614 CCCAAAACAAACCGCTAATCAG 58.425 45.455 0.00 0.00 0.00 2.90
450 485 1.621317 CCCCCAAAACAAACCGCTAAT 59.379 47.619 0.00 0.00 0.00 1.73
458 493 1.133668 CCCAATTGCCCCCAAAACAAA 60.134 47.619 0.00 0.00 34.05 2.83
469 504 0.980423 TTAAAGCACCCCCAATTGCC 59.020 50.000 0.00 0.00 39.75 4.52
470 505 1.623311 AGTTAAAGCACCCCCAATTGC 59.377 47.619 0.00 0.00 39.16 3.56
482 517 2.737252 CGAGGGTTCAGTCAGTTAAAGC 59.263 50.000 0.00 0.00 0.00 3.51
484 519 2.762745 GCGAGGGTTCAGTCAGTTAAA 58.237 47.619 0.00 0.00 0.00 1.52
485 520 1.336517 CGCGAGGGTTCAGTCAGTTAA 60.337 52.381 0.00 0.00 0.00 2.01
486 521 0.242825 CGCGAGGGTTCAGTCAGTTA 59.757 55.000 0.00 0.00 0.00 2.24
551 593 1.138247 GAATTCCGCAGCCAGCAAG 59.862 57.895 0.00 0.00 46.13 4.01
577 619 4.221422 ACGATCGATGCCCCACGG 62.221 66.667 24.34 0.00 0.00 4.94
597 639 2.479219 GTACTAGTACAAGGCTCGTGCC 60.479 54.545 25.02 20.71 45.86 5.01
598 640 2.479219 GGTACTAGTACAAGGCTCGTGC 60.479 54.545 29.38 8.68 37.78 5.34
600 642 3.362870 AGGTACTAGTACAAGGCTCGT 57.637 47.619 29.38 4.85 36.02 4.18
612 654 2.234414 TGGTTACCCGCAAAGGTACTAG 59.766 50.000 0.00 0.00 42.16 2.57
622 670 1.195442 TCATCCACTGGTTACCCGCA 61.195 55.000 0.00 0.00 0.00 5.69
624 672 2.170607 AGAATCATCCACTGGTTACCCG 59.829 50.000 0.00 0.00 0.00 5.28
625 673 3.199946 TGAGAATCATCCACTGGTTACCC 59.800 47.826 0.00 0.00 42.56 3.69
626 674 4.487714 TGAGAATCATCCACTGGTTACC 57.512 45.455 0.00 0.00 42.56 2.85
640 688 8.999431 TGAAAACCACTACTGTAAATGAGAATC 58.001 33.333 1.37 0.00 0.00 2.52
641 689 8.918202 TGAAAACCACTACTGTAAATGAGAAT 57.082 30.769 1.37 0.00 0.00 2.40
642 690 8.740123 TTGAAAACCACTACTGTAAATGAGAA 57.260 30.769 1.37 0.00 0.00 2.87
643 691 8.740123 TTTGAAAACCACTACTGTAAATGAGA 57.260 30.769 1.37 0.00 0.00 3.27
644 692 9.612620 GATTTGAAAACCACTACTGTAAATGAG 57.387 33.333 0.00 0.00 0.00 2.90
645 693 9.349713 AGATTTGAAAACCACTACTGTAAATGA 57.650 29.630 0.00 0.00 0.00 2.57
646 694 9.612620 GAGATTTGAAAACCACTACTGTAAATG 57.387 33.333 0.00 0.00 0.00 2.32
647 695 9.349713 TGAGATTTGAAAACCACTACTGTAAAT 57.650 29.630 0.00 0.00 0.00 1.40
648 696 8.740123 TGAGATTTGAAAACCACTACTGTAAA 57.260 30.769 0.00 0.00 0.00 2.01
649 697 8.740123 TTGAGATTTGAAAACCACTACTGTAA 57.260 30.769 0.00 0.00 0.00 2.41
650 698 8.918202 ATTGAGATTTGAAAACCACTACTGTA 57.082 30.769 0.00 0.00 0.00 2.74
651 699 7.823745 ATTGAGATTTGAAAACCACTACTGT 57.176 32.000 0.00 0.00 0.00 3.55
678 726 4.564116 GTGCGCCATGGCATCAGC 62.564 66.667 34.93 28.47 45.99 4.26
686 734 1.079681 AAGCCAATTGTGCGCCATG 60.080 52.632 4.18 0.00 0.00 3.66
687 735 1.216178 GAAGCCAATTGTGCGCCAT 59.784 52.632 4.18 0.00 0.00 4.40
690 738 1.444895 CAGGAAGCCAATTGTGCGC 60.445 57.895 0.00 0.00 0.00 6.09
805 853 2.159028 GCTTCTAGCAAGACCCCACTAG 60.159 54.545 6.23 0.00 41.89 2.57
896 946 2.787249 CAGGAAAGCACGCCGATG 59.213 61.111 0.00 0.00 0.00 3.84
902 952 4.093952 CCGCAGCAGGAAAGCACG 62.094 66.667 0.00 0.00 36.85 5.34
913 963 2.719979 CTCATTCCATGCCGCAGC 59.280 61.111 0.00 0.00 40.48 5.25
982 1032 6.144078 AGTCATGGTTTGTTACTTTCCAAC 57.856 37.500 0.00 0.00 0.00 3.77
984 1034 6.039270 CAGAAGTCATGGTTTGTTACTTTCCA 59.961 38.462 0.00 0.00 30.83 3.53
1012 1062 0.971386 ATACCTGAAACACCGTCGGT 59.029 50.000 12.23 12.23 35.62 4.69
1110 1161 2.476241 CGAATGGCTGCTTTTGGAAAAC 59.524 45.455 0.00 0.00 0.00 2.43
1154 1206 6.831976 ACCACAGGGCATGTTTTAATTTTTA 58.168 32.000 0.14 0.00 41.41 1.52
1176 1228 8.927675 TCTCTCCTTCTATTTCACTCTATACC 57.072 38.462 0.00 0.00 0.00 2.73
1190 1242 6.726379 TCTCATCTCTGTTTCTCTCCTTCTA 58.274 40.000 0.00 0.00 0.00 2.10
1192 1244 5.913137 TCTCATCTCTGTTTCTCTCCTTC 57.087 43.478 0.00 0.00 0.00 3.46
1218 1282 4.396790 GCAAATGGAAACGGGACAGTATTA 59.603 41.667 0.00 0.00 0.00 0.98
1230 1294 4.590850 AAAGGAGACAGCAAATGGAAAC 57.409 40.909 0.00 0.00 0.00 2.78
1241 1305 3.879295 TGAGCACTTGAAAAAGGAGACAG 59.121 43.478 0.00 0.00 0.00 3.51
1469 1538 3.360340 GTGCCTGGTGCTGCTGTC 61.360 66.667 0.00 0.00 42.00 3.51
1615 1689 0.035317 ACCACGCTCAAGCAGATGAA 59.965 50.000 2.50 0.00 42.21 2.57
1617 1691 0.167470 CAACCACGCTCAAGCAGATG 59.833 55.000 2.50 0.00 42.21 2.90
1669 1747 2.285368 TGCCCCCTGGATTCGACT 60.285 61.111 0.00 0.00 0.00 4.18
1707 1785 1.537202 GAAGGAACGCTGCTCACAATT 59.463 47.619 0.00 0.00 0.00 2.32
1712 1790 2.048222 CGGAAGGAACGCTGCTCA 60.048 61.111 0.00 0.00 0.00 4.26
1733 1811 2.125912 GGATCGCACACACGCTCT 60.126 61.111 0.00 0.00 0.00 4.09
1900 1978 1.885157 GGTGATACGACCGGACACA 59.115 57.895 9.46 0.00 33.82 3.72
1978 2056 2.107378 TGACATGGCAAAGAACTGGGTA 59.893 45.455 0.00 0.00 0.00 3.69
2022 2100 2.736347 CACACTGCCCTACCTAGTAGT 58.264 52.381 0.00 0.00 34.62 2.73
2048 2126 7.844009 AGCATCACAATTATGGTCAAAATTCT 58.156 30.769 0.00 0.00 29.32 2.40
2115 2193 9.312904 CTACAAATACAATATCCCAATTCCCAT 57.687 33.333 0.00 0.00 0.00 4.00
2376 2456 7.555914 TGCATAAAAATGAGACAGGCATAGTTA 59.444 33.333 0.00 0.00 0.00 2.24
2413 2493 2.970640 TCAGCTCTATGATCACCTGCAT 59.029 45.455 0.00 0.00 0.00 3.96
2456 2539 0.401738 CTTCCTGGTTCCCTTGAGCA 59.598 55.000 0.00 0.00 0.00 4.26
2581 2664 5.243954 AGAAGAAAAATGGGAAGTTACAGGC 59.756 40.000 0.00 0.00 0.00 4.85
2619 2702 1.132817 AGAAGTGTACAGGGGTGGTCT 60.133 52.381 0.00 0.00 0.00 3.85
2739 2831 3.343617 CATACTGAACGACCAACCCATT 58.656 45.455 0.00 0.00 0.00 3.16
2893 3019 2.434185 GCCATCCTCGCGTCAACA 60.434 61.111 5.77 0.00 0.00 3.33
2992 3118 6.798207 TTTTTGTGGCAATTTATATACGCG 57.202 33.333 3.53 3.53 0.00 6.01
3033 3159 3.622459 CGAACATTCGGGATTTGCC 57.378 52.632 6.11 0.00 46.30 4.52
3046 3172 2.232941 GGACACTGATAAGTCCCGAACA 59.767 50.000 0.00 0.00 46.79 3.18
3237 3516 7.287235 TGTGGCATTGGATATAATCAACATTGA 59.713 33.333 0.00 0.00 42.14 2.57
3267 3739 3.363627 TGGCAAGGAAATGTGATATGCA 58.636 40.909 0.00 0.00 34.14 3.96
3286 3758 2.882761 CTGACATGGGCAATCAGTATGG 59.117 50.000 0.00 0.00 36.02 2.74
3533 4011 1.200948 GAGGCAACAATCTGTTCAGGC 59.799 52.381 0.00 0.00 38.77 4.85
3538 4016 3.515602 AGGAAGAGGCAACAATCTGTT 57.484 42.857 0.00 0.00 42.08 3.16
3605 4083 7.346751 ACAAATTTCACACAATAACTCCAGT 57.653 32.000 0.00 0.00 0.00 4.00
3620 4098 5.146010 GTGGGATTAGCCAACAAATTTCA 57.854 39.130 0.00 0.00 40.65 2.69
4242 4724 5.395611 GAGGTAGGGTATGTAGAATGGAGT 58.604 45.833 0.00 0.00 0.00 3.85
4541 5105 1.271379 GCTTAGCAACTTCCCAGGTGA 60.271 52.381 0.00 0.00 40.69 4.02
4673 5237 1.547372 GCAGATTGGCACTGGAAACAT 59.453 47.619 7.17 0.00 41.51 2.71
4674 5238 0.961019 GCAGATTGGCACTGGAAACA 59.039 50.000 7.17 0.00 36.09 2.83
4690 5254 5.107133 CCCAAGAATAAGAATTGCAAGCAG 58.893 41.667 4.94 0.00 0.00 4.24
4757 5321 4.546570 GGATACCAACAAGCACAAACTTC 58.453 43.478 0.00 0.00 0.00 3.01
4801 5365 8.404765 CACAATGTAGGCACATGTCAATTATTA 58.595 33.333 0.00 0.00 44.83 0.98
4950 5514 0.521291 GTGCAACGCCATTCTGCTTA 59.479 50.000 0.00 0.00 37.00 3.09
5019 5583 5.945191 TCATTCATGGTTTGCTGACTTATCA 59.055 36.000 0.00 0.00 0.00 2.15
5028 5592 3.362706 AGCATCTCATTCATGGTTTGCT 58.637 40.909 0.00 0.00 0.00 3.91
5030 5594 6.238676 CCTTCTAGCATCTCATTCATGGTTTG 60.239 42.308 0.00 0.00 33.96 2.93
5293 5866 1.271379 GCTACAAAAGCCTCCTGACCA 60.271 52.381 0.00 0.00 46.25 4.02
5348 5924 3.138283 AGAGACCAAATCCACACCAAAGA 59.862 43.478 0.00 0.00 0.00 2.52
5394 5970 5.765510 ACCCAGATATTATTTTCTGCACCA 58.234 37.500 0.00 0.00 38.41 4.17
5428 6004 0.255318 AAAGCTGCAGGCAGAGCTAT 59.745 50.000 24.46 5.23 46.30 2.97
5429 6005 0.392193 GAAAGCTGCAGGCAGAGCTA 60.392 55.000 24.46 0.00 46.30 3.32
5430 6006 1.674980 GAAAGCTGCAGGCAGAGCT 60.675 57.895 24.46 13.35 46.30 4.09
5431 6007 1.242665 AAGAAAGCTGCAGGCAGAGC 61.243 55.000 24.46 11.20 46.30 4.09
5433 6009 0.956633 CAAAGAAAGCTGCAGGCAGA 59.043 50.000 24.46 0.00 46.30 4.26
5434 6010 0.666577 GCAAAGAAAGCTGCAGGCAG 60.667 55.000 17.12 16.68 46.15 4.85
5435 6011 1.364901 GCAAAGAAAGCTGCAGGCA 59.635 52.632 17.12 0.00 44.79 4.75
5507 6083 1.153086 GCTCCGAATCATGCTGGGT 60.153 57.895 0.00 0.00 0.00 4.51
5511 6087 1.068753 CGAGGCTCCGAATCATGCT 59.931 57.895 9.32 0.00 0.00 3.79
5556 6132 8.349983 GCAACTGAACTTAAAAAGGAGAACATA 58.650 33.333 0.00 0.00 0.00 2.29
5557 6133 7.203218 GCAACTGAACTTAAAAAGGAGAACAT 58.797 34.615 0.00 0.00 0.00 2.71
5558 6134 6.405397 GGCAACTGAACTTAAAAAGGAGAACA 60.405 38.462 0.00 0.00 0.00 3.18
5559 6135 5.977725 GGCAACTGAACTTAAAAAGGAGAAC 59.022 40.000 0.00 0.00 0.00 3.01
5560 6136 6.144078 GGCAACTGAACTTAAAAAGGAGAA 57.856 37.500 0.00 0.00 0.00 2.87
5601 6180 2.890311 CCAAATGTGTTCAAGGGCAGTA 59.110 45.455 0.00 0.00 0.00 2.74
5610 6189 1.216678 ACCAGGGTCCAAATGTGTTCA 59.783 47.619 0.00 0.00 0.00 3.18
5667 6246 4.922206 ACAGGCCATGAGATTCAAAAGTA 58.078 39.130 5.01 0.00 0.00 2.24
5680 6259 0.393537 GGGACTCAGAACAGGCCATG 60.394 60.000 5.01 2.64 44.74 3.66
5681 6260 0.548682 AGGGACTCAGAACAGGCCAT 60.549 55.000 5.01 0.00 44.74 4.40
5682 6261 1.152030 AGGGACTCAGAACAGGCCA 60.152 57.895 5.01 0.00 44.74 5.36
5683 6262 3.813150 AGGGACTCAGAACAGGCC 58.187 61.111 0.00 0.00 41.65 5.19
5694 6273 4.361971 TCGTGGAGCGGAGGGACT 62.362 66.667 0.00 0.00 40.32 3.85
5695 6274 4.131088 GTCGTGGAGCGGAGGGAC 62.131 72.222 0.00 0.00 41.72 4.46
5696 6275 4.361971 AGTCGTGGAGCGGAGGGA 62.362 66.667 0.00 0.00 41.72 4.20
5698 6277 3.827898 GGAGTCGTGGAGCGGAGG 61.828 72.222 0.00 0.00 41.72 4.30
5699 6278 4.180946 CGGAGTCGTGGAGCGGAG 62.181 72.222 0.00 0.00 41.72 4.63
5702 6281 4.838486 GAGCGGAGTCGTGGAGCG 62.838 72.222 0.00 0.00 43.01 5.03
5704 6283 2.752238 AGGAGCGGAGTCGTGGAG 60.752 66.667 0.00 0.00 38.89 3.86
5705 6284 3.062466 CAGGAGCGGAGTCGTGGA 61.062 66.667 0.00 0.00 38.89 4.02
5706 6285 4.135153 CCAGGAGCGGAGTCGTGG 62.135 72.222 5.48 5.48 43.96 4.94
5707 6286 3.057547 CTCCAGGAGCGGAGTCGTG 62.058 68.421 2.60 0.00 46.48 4.35
5708 6287 2.752238 CTCCAGGAGCGGAGTCGT 60.752 66.667 2.60 0.00 46.48 4.34
5721 6323 1.461268 TGGAACTCCACCTGCTCCA 60.461 57.895 0.00 0.00 42.01 3.86
5737 6339 0.320073 TCTCCGCGGTGTTTAACTGG 60.320 55.000 27.15 3.89 35.49 4.00
5739 6341 0.963962 TCTCTCCGCGGTGTTTAACT 59.036 50.000 27.15 0.00 0.00 2.24
5740 6342 1.068055 TCTCTCTCCGCGGTGTTTAAC 60.068 52.381 27.15 0.00 0.00 2.01
5742 6344 0.809385 CTCTCTCTCCGCGGTGTTTA 59.191 55.000 27.15 11.38 0.00 2.01
5744 6346 0.894184 TTCTCTCTCTCCGCGGTGTT 60.894 55.000 27.15 0.00 0.00 3.32
5745 6347 1.303398 TTCTCTCTCTCCGCGGTGT 60.303 57.895 27.15 0.00 0.00 4.16
5747 6349 1.303398 TGTTCTCTCTCTCCGCGGT 60.303 57.895 27.15 0.00 0.00 5.68
5748 6350 1.431440 CTGTTCTCTCTCTCCGCGG 59.569 63.158 22.12 22.12 0.00 6.46
5749 6351 1.309499 ACCTGTTCTCTCTCTCCGCG 61.309 60.000 0.00 0.00 0.00 6.46
5750 6352 1.402613 GTACCTGTTCTCTCTCTCCGC 59.597 57.143 0.00 0.00 0.00 5.54
5751 6353 2.940410 GAGTACCTGTTCTCTCTCTCCG 59.060 54.545 0.00 0.00 0.00 4.63
5752 6354 3.284617 GGAGTACCTGTTCTCTCTCTCC 58.715 54.545 4.30 0.00 34.48 3.71
5753 6355 2.940410 CGGAGTACCTGTTCTCTCTCTC 59.060 54.545 4.30 0.00 0.00 3.20
5754 6356 2.942306 GCGGAGTACCTGTTCTCTCTCT 60.942 54.545 4.30 0.00 0.00 3.10
5758 6360 1.178276 CTGCGGAGTACCTGTTCTCT 58.822 55.000 0.00 0.00 0.00 3.10
5762 6364 2.180276 AGAATCTGCGGAGTACCTGTT 58.820 47.619 3.10 0.00 0.00 3.16
5763 6365 1.853963 AGAATCTGCGGAGTACCTGT 58.146 50.000 3.10 0.00 0.00 4.00
5764 6366 2.969628 AAGAATCTGCGGAGTACCTG 57.030 50.000 3.10 0.00 0.00 4.00
5765 6367 4.222145 TGTTTAAGAATCTGCGGAGTACCT 59.778 41.667 3.10 0.00 0.00 3.08
5766 6368 4.501071 TGTTTAAGAATCTGCGGAGTACC 58.499 43.478 3.10 0.00 0.00 3.34
5768 6370 5.584649 CCAATGTTTAAGAATCTGCGGAGTA 59.415 40.000 3.10 0.00 0.00 2.59
5770 6372 4.635765 TCCAATGTTTAAGAATCTGCGGAG 59.364 41.667 0.00 0.00 0.00 4.63
5772 6374 4.963276 TCCAATGTTTAAGAATCTGCGG 57.037 40.909 0.00 0.00 0.00 5.69
5774 6376 9.455847 GTATGATTCCAATGTTTAAGAATCTGC 57.544 33.333 11.58 0.00 43.19 4.26
5779 6381 9.513906 TGACAGTATGATTCCAATGTTTAAGAA 57.486 29.630 0.00 0.00 39.69 2.52
5780 6382 9.685276 ATGACAGTATGATTCCAATGTTTAAGA 57.315 29.630 0.00 0.00 39.69 2.10
5781 6383 9.941664 GATGACAGTATGATTCCAATGTTTAAG 57.058 33.333 0.00 0.00 39.69 1.85
5782 6384 9.460019 TGATGACAGTATGATTCCAATGTTTAA 57.540 29.630 0.00 0.00 39.69 1.52
5783 6385 8.892723 GTGATGACAGTATGATTCCAATGTTTA 58.107 33.333 0.00 0.00 39.69 2.01
5784 6386 7.394077 TGTGATGACAGTATGATTCCAATGTTT 59.606 33.333 0.00 0.00 39.69 2.83
5785 6387 6.885918 TGTGATGACAGTATGATTCCAATGTT 59.114 34.615 0.00 0.00 39.69 2.71
5867 6492 9.267084 GAAAGCCTCTATATTCTTCTTGGTAAG 57.733 37.037 0.00 0.00 0.00 2.34
5926 6551 2.488153 GTGCAAGAAAGGATGTACACCC 59.512 50.000 0.00 0.00 0.00 4.61
5929 6554 3.325870 CTCGTGCAAGAAAGGATGTACA 58.674 45.455 3.39 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.