Multiple sequence alignment - TraesCS2D01G511400

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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 TraesCS2D01G511400 chr2D 100.000 4093 0 0 1 4093 602784135 602780043 0.000000e+00 7559.0
1 TraesCS2D01G511400 chr2D 91.567 1174 95 4 765 1935 603129569 603128397 0.000000e+00 1616.0
2 TraesCS2D01G511400 chr2D 81.903 1072 174 9 1957 3027 603128403 603127351 0.000000e+00 887.0
3 TraesCS2D01G511400 chr2A 91.628 1708 140 2 1974 3680 735565486 735563781 0.000000e+00 2359.0
4 TraesCS2D01G511400 chr2A 90.929 1356 121 2 1982 3336 735401495 735400141 0.000000e+00 1821.0
5 TraesCS2D01G511400 chr2A 92.883 1110 79 0 826 1935 735566732 735565623 0.000000e+00 1613.0
6 TraesCS2D01G511400 chr2A 90.325 1168 110 3 759 1925 735446767 735445602 0.000000e+00 1528.0
7 TraesCS2D01G511400 chr2A 90.257 1088 104 2 839 1925 735402736 735401650 0.000000e+00 1421.0
8 TraesCS2D01G511400 chr2A 81.139 1124 198 11 1962 3077 735445344 735444227 0.000000e+00 889.0
9 TraesCS2D01G511400 chr2A 81.752 1107 142 34 382 1458 735413140 735412064 0.000000e+00 870.0
10 TraesCS2D01G511400 chr2A 86.429 280 30 4 452 729 735447111 735446838 2.390000e-77 300.0
11 TraesCS2D01G511400 chr2A 80.662 393 48 15 3351 3725 735582529 735582147 3.120000e-71 279.0
12 TraesCS2D01G511400 chr2A 86.905 252 11 8 3732 3980 735563696 735563464 3.140000e-66 263.0
13 TraesCS2D01G511400 chr2A 90.476 147 9 2 3733 3878 735582110 735581968 5.400000e-44 189.0
14 TraesCS2D01G511400 chr2A 81.643 207 23 9 3893 4093 735576490 735576293 1.520000e-34 158.0
15 TraesCS2D01G511400 chr2A 88.889 81 8 1 3219 3298 735405046 735404966 9.360000e-17 99.0
16 TraesCS2D01G511400 chr2B 91.108 1237 104 2 1982 3212 733643443 733642207 0.000000e+00 1670.0
17 TraesCS2D01G511400 chr2B 90.403 1167 97 5 759 1925 733645939 733644788 0.000000e+00 1520.0
18 TraesCS2D01G511400 chr2B 90.370 1163 102 7 771 1931 733733078 733731924 0.000000e+00 1519.0
19 TraesCS2D01G511400 chr2B 90.893 1109 96 3 820 1925 733472858 733471752 0.000000e+00 1483.0
20 TraesCS2D01G511400 chr2B 89.270 1165 123 2 762 1925 733458594 733457431 0.000000e+00 1458.0
21 TraesCS2D01G511400 chr2B 89.295 1149 120 3 762 1908 733715776 733714629 0.000000e+00 1437.0
22 TraesCS2D01G511400 chr2B 83.459 1058 153 15 1962 3012 733471554 733470512 0.000000e+00 965.0
23 TraesCS2D01G511400 chr2B 82.156 1104 172 14 1964 3065 733714478 733713398 0.000000e+00 924.0
24 TraesCS2D01G511400 chr2B 81.472 1128 187 14 1962 3073 733731670 733730549 0.000000e+00 905.0
25 TraesCS2D01G511400 chr2B 83.114 989 152 10 1971 2953 733644674 733643695 0.000000e+00 887.0
26 TraesCS2D01G511400 chr2B 80.251 1114 204 10 1962 3065 733744312 733743205 0.000000e+00 824.0
27 TraesCS2D01G511400 chr2B 80.095 1055 187 9 2018 3061 733843577 733842535 0.000000e+00 763.0
28 TraesCS2D01G511400 chr2B 84.695 771 55 32 3219 3978 733642241 733641523 0.000000e+00 712.0
29 TraesCS2D01G511400 chr2B 82.796 558 59 15 130 684 733716525 733716002 8.010000e-127 464.0
30 TraesCS2D01G511400 chr2B 87.129 404 43 7 177 578 733607806 733607410 2.240000e-122 449.0
31 TraesCS2D01G511400 chr2B 86.914 405 44 7 177 579 733617577 733617180 2.900000e-121 446.0
32 TraesCS2D01G511400 chr2B 79.439 535 85 19 3219 3736 733468600 733468074 5.030000e-94 355.0
33 TraesCS2D01G511400 chr2B 82.529 435 32 19 3481 3877 733841795 733841367 3.920000e-90 342.0
34 TraesCS2D01G511400 chr2B 82.025 395 41 15 3351 3725 733730412 733730028 3.970000e-80 309.0
35 TraesCS2D01G511400 chr2B 81.503 346 31 13 29 371 733646778 733646463 1.890000e-63 254.0
36 TraesCS2D01G511400 chr2B 86.345 249 11 9 3733 3980 733729991 733729765 2.440000e-62 250.0
37 TraesCS2D01G511400 chr2B 82.692 260 27 11 3481 3725 733748885 733748629 8.910000e-52 215.0
38 TraesCS2D01G511400 chr2B 80.000 310 44 3 3501 3806 733712666 733712371 3.200000e-51 213.0
39 TraesCS2D01G511400 chr2B 80.137 292 41 11 2746 3027 733456595 733456311 6.940000e-48 202.0
40 TraesCS2D01G511400 chr2B 79.518 249 22 21 3660 3882 733470141 733469896 2.550000e-32 150.0
41 TraesCS2D01G511400 chr2B 88.430 121 14 0 3732 3852 733748592 733748472 3.300000e-31 147.0
42 TraesCS2D01G511400 chr2B 81.287 171 11 10 3822 3989 733199679 733199527 7.190000e-23 119.0
43 TraesCS2D01G511400 chr2B 86.420 81 10 1 3219 3298 733749696 733749616 2.030000e-13 87.9
44 TraesCS2D01G511400 chr2B 92.593 54 4 0 3008 3061 733281605 733281552 1.220000e-10 78.7
45 TraesCS2D01G511400 chrUn 86.709 158 20 1 759 915 479972640 479972483 1.510000e-39 174.0


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 TraesCS2D01G511400 chr2D 602780043 602784135 4092 True 7559.000000 7559 100.000000 1 4093 1 chr2D.!!$R1 4092
1 TraesCS2D01G511400 chr2D 603127351 603129569 2218 True 1251.500000 1616 86.735000 765 3027 2 chr2D.!!$R2 2262
2 TraesCS2D01G511400 chr2A 735563464 735566732 3268 True 1411.666667 2359 90.472000 826 3980 3 chr2A.!!$R5 3154
3 TraesCS2D01G511400 chr2A 735400141 735405046 4905 True 1113.666667 1821 90.025000 839 3336 3 chr2A.!!$R3 2497
4 TraesCS2D01G511400 chr2A 735444227 735447111 2884 True 905.666667 1528 85.964333 452 3077 3 chr2A.!!$R4 2625
5 TraesCS2D01G511400 chr2A 735412064 735413140 1076 True 870.000000 870 81.752000 382 1458 1 chr2A.!!$R1 1076
6 TraesCS2D01G511400 chr2A 735581968 735582529 561 True 234.000000 279 85.569000 3351 3878 2 chr2A.!!$R6 527
7 TraesCS2D01G511400 chr2B 733641523 733646778 5255 True 1008.600000 1670 86.164600 29 3978 5 chr2B.!!$R8 3949
8 TraesCS2D01G511400 chr2B 733456311 733458594 2283 True 830.000000 1458 84.703500 762 3027 2 chr2B.!!$R6 2265
9 TraesCS2D01G511400 chr2B 733743205 733744312 1107 True 824.000000 824 80.251000 1962 3065 1 chr2B.!!$R5 1103
10 TraesCS2D01G511400 chr2B 733712371 733716525 4154 True 759.500000 1437 83.561750 130 3806 4 chr2B.!!$R9 3676
11 TraesCS2D01G511400 chr2B 733729765 733733078 3313 True 745.750000 1519 85.053000 771 3980 4 chr2B.!!$R10 3209
12 TraesCS2D01G511400 chr2B 733468074 733472858 4784 True 738.250000 1483 83.327250 820 3882 4 chr2B.!!$R7 3062
13 TraesCS2D01G511400 chr2B 733841367 733843577 2210 True 552.500000 763 81.312000 2018 3877 2 chr2B.!!$R12 1859

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
25 26 0.249657 CGGCTGGAGATGCTCTTACC 60.250 60.0 0.0 0.0 0.0 2.85 F
1656 3132 0.032813 ATGGGGAGATTGGCTTGGTG 60.033 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 3826 0.032540 CTTGGCCTTTCACTGTTGGC 59.967 55.0 3.32 0.0 44.22 4.52 R
3622 7579 0.246635 GCAAGCGAGAGTACTGGGAA 59.753 55.0 0.00 0.0 0.00 3.97 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
22 23 0.392193 CAACGGCTGGAGATGCTCTT 60.392 55.000 0.00 0.00 0.00 2.85
23 24 1.134699 CAACGGCTGGAGATGCTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
24 25 0.461961 ACGGCTGGAGATGCTCTTAC 59.538 55.000 0.00 0.00 0.00 2.34
25 26 0.249657 CGGCTGGAGATGCTCTTACC 60.250 60.000 0.00 0.00 0.00 2.85
26 27 0.249657 GGCTGGAGATGCTCTTACCG 60.250 60.000 0.00 0.00 0.00 4.02
27 28 0.461961 GCTGGAGATGCTCTTACCGT 59.538 55.000 0.00 0.00 0.00 4.83
31 32 0.924090 GAGATGCTCTTACCGTTGCG 59.076 55.000 0.00 0.00 0.00 4.85
41 42 1.717194 TACCGTTGCGATCTTTGGAC 58.283 50.000 0.00 0.00 0.00 4.02
59 60 2.034812 GGACTGGGACGCTCTTACATAG 59.965 54.545 0.00 0.00 0.00 2.23
77 78 6.187125 ACATAGCTTGTTTGACATGATCAC 57.813 37.500 0.00 0.00 36.92 3.06
112 113 4.917385 TGGTACCAGTTGTCATTAAGCAT 58.083 39.130 11.60 0.00 0.00 3.79
113 114 4.941263 TGGTACCAGTTGTCATTAAGCATC 59.059 41.667 11.60 0.00 0.00 3.91
114 115 4.335594 GGTACCAGTTGTCATTAAGCATCC 59.664 45.833 7.15 0.00 0.00 3.51
115 116 3.356290 ACCAGTTGTCATTAAGCATCCC 58.644 45.455 0.00 0.00 0.00 3.85
116 117 3.245229 ACCAGTTGTCATTAAGCATCCCA 60.245 43.478 0.00 0.00 0.00 4.37
117 118 3.763360 CCAGTTGTCATTAAGCATCCCAA 59.237 43.478 0.00 0.00 0.00 4.12
118 119 4.380867 CCAGTTGTCATTAAGCATCCCAAC 60.381 45.833 0.00 0.00 0.00 3.77
119 120 3.763897 AGTTGTCATTAAGCATCCCAACC 59.236 43.478 0.00 0.00 33.08 3.77
120 121 3.448093 TGTCATTAAGCATCCCAACCA 57.552 42.857 0.00 0.00 0.00 3.67
121 122 3.088532 TGTCATTAAGCATCCCAACCAC 58.911 45.455 0.00 0.00 0.00 4.16
122 123 2.427095 GTCATTAAGCATCCCAACCACC 59.573 50.000 0.00 0.00 0.00 4.61
123 124 2.042297 TCATTAAGCATCCCAACCACCA 59.958 45.455 0.00 0.00 0.00 4.17
124 125 1.917872 TTAAGCATCCCAACCACCAC 58.082 50.000 0.00 0.00 0.00 4.16
125 126 0.774276 TAAGCATCCCAACCACCACA 59.226 50.000 0.00 0.00 0.00 4.17
140 141 1.153168 CACAGATAAGGCCACCCCG 60.153 63.158 5.01 0.00 39.21 5.73
166 168 2.029020 TGTTCTGAGAGTTGACCATCGG 60.029 50.000 0.00 0.00 0.00 4.18
196 198 7.884877 TGGCAATCCATGAATAGAGTAATAAGG 59.115 37.037 0.00 0.00 37.47 2.69
197 199 7.885399 GGCAATCCATGAATAGAGTAATAAGGT 59.115 37.037 0.00 0.00 0.00 3.50
299 301 4.574421 TCCATTGATTGTGCTATGTTACGG 59.426 41.667 0.00 0.00 0.00 4.02
301 303 2.285083 TGATTGTGCTATGTTACGGCC 58.715 47.619 0.00 0.00 0.00 6.13
313 315 2.007608 GTTACGGCCTCCATTCTCAAC 58.992 52.381 0.00 0.00 0.00 3.18
340 344 0.827368 TTTGGTTCAACCTTGCCCAC 59.173 50.000 8.40 0.00 39.58 4.61
345 349 2.672996 CAACCTTGCCCACCTCCG 60.673 66.667 0.00 0.00 0.00 4.63
373 377 6.931281 TCTTCACCACATTTCTTAGACTTCTG 59.069 38.462 0.00 0.00 0.00 3.02
388 393 2.091885 ACTTCTGTCTGGGCTTTTTCCA 60.092 45.455 0.00 0.00 0.00 3.53
399 404 5.694995 TGGGCTTTTTCCAGAGATATTAGG 58.305 41.667 0.00 0.00 0.00 2.69
440 445 5.763204 TCTTCACTTCTTTGTTTAGCCGATT 59.237 36.000 0.00 0.00 0.00 3.34
532 553 2.579207 TCGTACCATGAAGCTGCTAC 57.421 50.000 0.90 0.00 0.00 3.58
533 554 2.100197 TCGTACCATGAAGCTGCTACT 58.900 47.619 0.90 0.00 0.00 2.57
548 569 6.599445 AGCTGCTACTATTCAAAATCCAGAT 58.401 36.000 0.00 0.00 0.00 2.90
629 653 4.434198 CGATGTACTCCATGAACAAACACG 60.434 45.833 0.00 0.00 32.56 4.49
632 656 4.876679 TGTACTCCATGAACAAACACGAAA 59.123 37.500 0.00 0.00 0.00 3.46
633 657 4.287238 ACTCCATGAACAAACACGAAAC 57.713 40.909 0.00 0.00 0.00 2.78
638 662 5.236695 TCCATGAACAAACACGAAACGATTA 59.763 36.000 0.00 0.00 0.00 1.75
642 666 6.950545 TGAACAAACACGAAACGATTATCTT 58.049 32.000 0.00 0.00 0.00 2.40
706 865 0.325577 TGGGTATCTCTGGCAGCTCA 60.326 55.000 10.34 0.00 0.00 4.26
723 882 4.518211 CAGCTCAAGGAGATGTTTGTTTCT 59.482 41.667 3.46 0.00 40.64 2.52
724 883 5.702670 CAGCTCAAGGAGATGTTTGTTTCTA 59.297 40.000 3.46 0.00 40.64 2.10
725 884 6.205464 CAGCTCAAGGAGATGTTTGTTTCTAA 59.795 38.462 3.46 0.00 40.64 2.10
726 885 6.772716 AGCTCAAGGAGATGTTTGTTTCTAAA 59.227 34.615 0.00 0.00 0.00 1.85
727 886 7.449704 AGCTCAAGGAGATGTTTGTTTCTAAAT 59.550 33.333 0.00 0.00 0.00 1.40
728 887 7.540055 GCTCAAGGAGATGTTTGTTTCTAAATG 59.460 37.037 0.00 0.00 0.00 2.32
729 888 7.885297 TCAAGGAGATGTTTGTTTCTAAATGG 58.115 34.615 0.00 0.00 0.00 3.16
755 1033 0.975040 TGTATGTTGCCCATTGCCCC 60.975 55.000 0.00 0.00 40.16 5.80
756 1034 1.756172 TATGTTGCCCATTGCCCCG 60.756 57.895 0.00 0.00 40.16 5.73
791 1148 7.479980 TGATTAATCCAAGGAAATTAAGCACG 58.520 34.615 12.90 0.00 38.26 5.34
795 1152 5.116069 TCCAAGGAAATTAAGCACGTTTC 57.884 39.130 0.00 0.00 0.00 2.78
815 1172 8.765044 CGTTTCCGTACTTTGTTTATTTGTTA 57.235 30.769 0.00 0.00 0.00 2.41
1119 2594 5.416952 CCTTGAGGACAAAAGTATGATTGCT 59.583 40.000 0.00 0.00 37.39 3.91
1488 2963 7.721286 ATCAAGACTAGTCAACACTGAAAAG 57.279 36.000 24.44 1.17 33.62 2.27
1656 3132 0.032813 ATGGGGAGATTGGCTTGGTG 60.033 55.000 0.00 0.00 0.00 4.17
1704 3180 2.113777 AGAGTTTAGGAGGGTGAGGGAA 59.886 50.000 0.00 0.00 0.00 3.97
1717 3193 6.081356 AGGGTGAGGGAAATGTTTGATTTTA 58.919 36.000 0.00 0.00 0.00 1.52
1718 3194 6.014584 AGGGTGAGGGAAATGTTTGATTTTAC 60.015 38.462 0.00 0.00 0.00 2.01
1785 3261 2.558359 GTTGGCAGGTAAATGCTTGAGT 59.442 45.455 0.00 0.00 45.75 3.41
1794 3270 9.480433 GCAGGTAAATGCTTGAGTATGGAACAG 62.480 44.444 0.00 0.00 42.64 3.16
1818 3294 2.932614 CAAACGCCCTGAGATGTTAGAG 59.067 50.000 0.00 0.00 0.00 2.43
1829 3305 4.040339 TGAGATGTTAGAGGTTGCAGAACA 59.960 41.667 0.00 0.00 34.73 3.18
1897 3373 2.760650 GCACTATTTTCTTGGGGAAGGG 59.239 50.000 0.00 0.00 35.16 3.95
1900 3376 4.706962 CACTATTTTCTTGGGGAAGGGAAG 59.293 45.833 0.00 0.00 35.16 3.46
1912 3388 4.166337 GGGGAAGGGAAGATAAACTAGCTT 59.834 45.833 0.00 0.00 37.07 3.74
1925 3467 1.070134 ACTAGCTTCAGCCGAAACACA 59.930 47.619 0.00 0.00 43.38 3.72
1926 3468 1.728971 CTAGCTTCAGCCGAAACACAG 59.271 52.381 0.00 0.00 43.38 3.66
1928 3470 1.785041 GCTTCAGCCGAAACACAGCA 61.785 55.000 0.00 0.00 34.31 4.41
1929 3471 0.662619 CTTCAGCCGAAACACAGCAA 59.337 50.000 0.00 0.00 0.00 3.91
1930 3472 0.380378 TTCAGCCGAAACACAGCAAC 59.620 50.000 0.00 0.00 0.00 4.17
1931 3473 0.463654 TCAGCCGAAACACAGCAACT 60.464 50.000 0.00 0.00 0.00 3.16
1932 3474 1.202592 TCAGCCGAAACACAGCAACTA 60.203 47.619 0.00 0.00 0.00 2.24
1933 3475 1.195448 CAGCCGAAACACAGCAACTAG 59.805 52.381 0.00 0.00 0.00 2.57
1934 3476 1.070134 AGCCGAAACACAGCAACTAGA 59.930 47.619 0.00 0.00 0.00 2.43
1935 3477 1.194772 GCCGAAACACAGCAACTAGAC 59.805 52.381 0.00 0.00 0.00 2.59
1936 3478 2.479837 CCGAAACACAGCAACTAGACA 58.520 47.619 0.00 0.00 0.00 3.41
1937 3479 3.067106 CCGAAACACAGCAACTAGACAT 58.933 45.455 0.00 0.00 0.00 3.06
1938 3480 3.498397 CCGAAACACAGCAACTAGACATT 59.502 43.478 0.00 0.00 0.00 2.71
1939 3481 4.377431 CCGAAACACAGCAACTAGACATTC 60.377 45.833 0.00 0.00 0.00 2.67
1940 3482 4.211164 CGAAACACAGCAACTAGACATTCA 59.789 41.667 0.00 0.00 0.00 2.57
1941 3483 5.106948 CGAAACACAGCAACTAGACATTCAT 60.107 40.000 0.00 0.00 0.00 2.57
1942 3484 6.090763 CGAAACACAGCAACTAGACATTCATA 59.909 38.462 0.00 0.00 0.00 2.15
1943 3485 7.360017 CGAAACACAGCAACTAGACATTCATAA 60.360 37.037 0.00 0.00 0.00 1.90
1944 3486 7.744087 AACACAGCAACTAGACATTCATAAA 57.256 32.000 0.00 0.00 0.00 1.40
1945 3487 7.744087 ACACAGCAACTAGACATTCATAAAA 57.256 32.000 0.00 0.00 0.00 1.52
1946 3488 8.165239 ACACAGCAACTAGACATTCATAAAAA 57.835 30.769 0.00 0.00 0.00 1.94
2003 3824 8.491331 CCGAAATGTGGGAAATTTTATCATTT 57.509 30.769 16.56 16.56 36.95 2.32
2005 3826 8.389603 CGAAATGTGGGAAATTTTATCATTTGG 58.610 33.333 19.17 16.19 35.26 3.28
2006 3827 7.628769 AATGTGGGAAATTTTATCATTTGGC 57.371 32.000 0.00 0.00 0.00 4.52
2008 3829 5.013495 TGTGGGAAATTTTATCATTTGGCCA 59.987 36.000 0.00 0.00 0.00 5.36
2016 3837 5.798125 TTTATCATTTGGCCAACAGTGAA 57.202 34.783 20.35 7.45 31.96 3.18
2024 3845 0.032540 GCCAACAGTGAAAGGCCAAG 59.967 55.000 5.01 0.00 41.25 3.61
2026 3847 1.756538 CCAACAGTGAAAGGCCAAGTT 59.243 47.619 5.01 0.00 0.00 2.66
2041 3862 2.031682 CCAAGTTTTTGAGCTGGACGAG 60.032 50.000 0.00 0.00 36.36 4.18
2042 3863 2.614057 CAAGTTTTTGAGCTGGACGAGT 59.386 45.455 0.00 0.00 36.36 4.18
2047 3868 0.601046 TTGAGCTGGACGAGTTGCTG 60.601 55.000 0.00 0.00 35.76 4.41
2065 3886 1.236616 TGCGGGCATCAACTGAAGTG 61.237 55.000 0.00 0.00 0.00 3.16
2083 3904 0.838554 TGCTGGGCAAGGGTACAGTA 60.839 55.000 0.00 0.00 34.76 2.74
2087 3908 1.223763 GGCAAGGGTACAGTAGGGC 59.776 63.158 0.00 0.00 0.00 5.19
2088 3909 1.272554 GGCAAGGGTACAGTAGGGCT 61.273 60.000 0.00 0.00 0.00 5.19
2105 3926 2.943033 GGGCTAACATACAAAGCGACAT 59.057 45.455 0.00 0.00 37.11 3.06
2108 3929 5.399013 GGCTAACATACAAAGCGACATTTT 58.601 37.500 0.00 0.00 37.11 1.82
2155 3976 3.840666 AGAGGCTGAAAGATGTGGACTTA 59.159 43.478 0.00 0.00 34.07 2.24
2189 5230 2.959357 GAGCGGCTTGTCACACTGC 61.959 63.158 2.97 0.00 35.89 4.40
2197 5238 2.974698 GTCACACTGCTTGGCGCT 60.975 61.111 7.64 0.00 40.11 5.92
2260 5301 3.188048 GTGACAAGGATGAGAAGTTGCTG 59.812 47.826 0.00 0.00 0.00 4.41
2314 5355 2.094762 AAGTGCTCCACGGTAATGTC 57.905 50.000 0.00 0.00 39.64 3.06
2332 5402 9.197694 GGTAATGTCTATACTGAACAATGCTAG 57.802 37.037 0.00 0.00 0.00 3.42
2361 5434 7.598493 TGTGCTTTCCTTTACAATTTCTAATGC 59.402 33.333 0.00 0.00 0.00 3.56
2395 5469 8.782533 CATCACTAATTCATGATGTGTGAATG 57.217 34.615 17.78 14.49 44.75 2.67
2396 5470 8.617809 CATCACTAATTCATGATGTGTGAATGA 58.382 33.333 17.78 8.00 44.75 2.57
2705 5791 1.834856 CTGCTGGAGCTTCTCACCCA 61.835 60.000 0.00 0.00 42.66 4.51
2736 5822 4.934602 CCACTGGAGAAGAGATTTCAGAAC 59.065 45.833 0.00 0.00 0.00 3.01
2738 5824 4.180057 CTGGAGAAGAGATTTCAGAACGG 58.820 47.826 0.00 0.00 0.00 4.44
2949 6110 0.543277 TGCAGCGGATTGAGGAGATT 59.457 50.000 0.00 0.00 0.00 2.40
2961 6132 3.636679 TGAGGAGATTGGACAGTCCTAG 58.363 50.000 20.82 0.00 39.65 3.02
3006 6185 6.591448 CACATCATAGTGAGTGAAAGTTGCTA 59.409 38.462 0.00 0.00 42.05 3.49
3153 6347 7.096477 GCTTTCACTGCTAGTTTGTAAATTGTG 60.096 37.037 0.00 0.00 0.00 3.33
3157 6353 7.443879 TCACTGCTAGTTTGTAAATTGTGATCA 59.556 33.333 0.00 0.00 0.00 2.92
3239 6437 6.486253 AAATTGGCATATATACTCTGCACG 57.514 37.500 8.63 0.00 37.64 5.34
3298 6496 6.171921 AGCTAAGCTGCAATCCTTAGATATG 58.828 40.000 22.64 6.51 41.81 1.78
3308 6506 6.763135 GCAATCCTTAGATATGTGTGAAGACA 59.237 38.462 0.00 0.00 30.42 3.41
3375 6826 8.633408 CGAAGAAAAACTAATGAAAAGATGCAG 58.367 33.333 0.00 0.00 0.00 4.41
3405 7306 7.174253 TGTTTGCTTTTAGACTCATATTTCCGT 59.826 33.333 0.00 0.00 0.00 4.69
3428 7329 4.982241 AAAGAGACTGTCCCATTCTTCA 57.018 40.909 3.76 0.00 0.00 3.02
3527 7460 7.464830 AAATTCTACAGATTACGGATGAACG 57.535 36.000 0.00 0.00 40.31 3.95
3535 7468 2.068837 TACGGATGAACGGAACACAC 57.931 50.000 0.00 0.00 38.39 3.82
3585 7542 4.426112 TCGAGCAGGAGCAGCGTG 62.426 66.667 0.00 0.00 45.49 5.34
3622 7579 3.036084 CGAAGTCCACGCACGCTT 61.036 61.111 0.00 0.00 0.00 4.68
3640 7597 2.611518 CTTTCCCAGTACTCTCGCTTG 58.388 52.381 0.00 0.00 0.00 4.01
3882 7967 2.263945 GGCTTCGAGCTCAAGAAGTAC 58.736 52.381 23.82 16.76 44.07 2.73
3883 7968 2.352814 GGCTTCGAGCTCAAGAAGTACA 60.353 50.000 23.82 0.00 44.07 2.90
3884 7969 3.318017 GCTTCGAGCTCAAGAAGTACAA 58.682 45.455 23.82 0.00 44.07 2.41
3885 7970 3.929610 GCTTCGAGCTCAAGAAGTACAAT 59.070 43.478 23.82 0.00 44.07 2.71
3886 7971 5.103000 GCTTCGAGCTCAAGAAGTACAATA 58.897 41.667 23.82 0.00 44.07 1.90
3887 7972 5.751028 GCTTCGAGCTCAAGAAGTACAATAT 59.249 40.000 23.82 0.00 44.07 1.28
3888 7973 6.074569 GCTTCGAGCTCAAGAAGTACAATATC 60.075 42.308 23.82 8.49 44.07 1.63
3889 7974 6.701145 TCGAGCTCAAGAAGTACAATATCT 57.299 37.500 15.40 0.00 0.00 1.98
3890 7975 6.499172 TCGAGCTCAAGAAGTACAATATCTG 58.501 40.000 15.40 0.00 0.00 2.90
3891 7976 5.689514 CGAGCTCAAGAAGTACAATATCTGG 59.310 44.000 15.40 0.00 0.00 3.86
3892 7977 5.363939 AGCTCAAGAAGTACAATATCTGGC 58.636 41.667 0.00 0.57 0.00 4.85
3893 7978 5.104776 AGCTCAAGAAGTACAATATCTGGCA 60.105 40.000 0.00 0.00 0.00 4.92
3944 8029 1.381599 GGGCAATGGGCTGGAATGA 60.382 57.895 0.00 0.00 44.01 2.57
3945 8030 0.977108 GGGCAATGGGCTGGAATGAA 60.977 55.000 0.00 0.00 44.01 2.57
3947 8032 1.202604 GGCAATGGGCTGGAATGAATG 60.203 52.381 0.00 0.00 44.01 2.67
3948 8033 1.483415 GCAATGGGCTGGAATGAATGT 59.517 47.619 0.00 0.00 40.25 2.71
3949 8034 2.482490 GCAATGGGCTGGAATGAATGTC 60.482 50.000 0.00 0.00 40.25 3.06
3950 8035 3.028850 CAATGGGCTGGAATGAATGTCT 58.971 45.455 0.00 0.00 0.00 3.41
3951 8036 2.133281 TGGGCTGGAATGAATGTCTG 57.867 50.000 0.00 0.00 0.00 3.51
3953 8038 1.396653 GGCTGGAATGAATGTCTGGG 58.603 55.000 0.00 0.00 0.00 4.45
3954 8039 0.743097 GCTGGAATGAATGTCTGGGC 59.257 55.000 0.00 0.00 0.00 5.36
3956 8041 2.731572 CTGGAATGAATGTCTGGGCTT 58.268 47.619 0.00 0.00 0.00 4.35
3994 8198 3.620427 TTTGCCTAGCTTATCCAACGA 57.380 42.857 0.00 0.00 0.00 3.85
3995 8199 2.890808 TGCCTAGCTTATCCAACGAG 57.109 50.000 0.00 0.00 0.00 4.18
3996 8200 2.384828 TGCCTAGCTTATCCAACGAGA 58.615 47.619 0.00 0.00 0.00 4.04
3997 8201 2.965831 TGCCTAGCTTATCCAACGAGAT 59.034 45.455 0.00 0.00 0.00 2.75
3999 8203 3.991121 GCCTAGCTTATCCAACGAGATTC 59.009 47.826 0.00 0.00 0.00 2.52
4000 8204 4.561105 CCTAGCTTATCCAACGAGATTCC 58.439 47.826 0.00 0.00 0.00 3.01
4001 8205 3.477210 AGCTTATCCAACGAGATTCCC 57.523 47.619 0.00 0.00 0.00 3.97
4003 8207 3.070302 AGCTTATCCAACGAGATTCCCTC 59.930 47.826 0.00 0.00 38.55 4.30
4008 8250 4.093472 TCCAACGAGATTCCCTCAAAAA 57.907 40.909 0.00 0.00 42.06 1.94
4042 8284 1.222115 AACTCGTTCAACGGAGCTGC 61.222 55.000 10.69 0.00 42.81 5.25
4051 8293 0.751643 AACGGAGCTGCAAGTTTGGT 60.752 50.000 5.91 0.00 35.30 3.67
4077 8319 5.692814 CAAAACAGCGAGATGAGAAAATCA 58.307 37.500 0.00 0.00 43.70 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
14 15 1.523095 GATCGCAACGGTAAGAGCATC 59.477 52.381 0.00 0.00 0.00 3.91
15 16 1.137086 AGATCGCAACGGTAAGAGCAT 59.863 47.619 0.00 0.00 0.00 3.79
19 20 2.028839 TCCAAAGATCGCAACGGTAAGA 60.029 45.455 0.00 0.00 0.00 2.10
22 23 1.274167 AGTCCAAAGATCGCAACGGTA 59.726 47.619 0.00 0.00 0.00 4.02
23 24 0.034896 AGTCCAAAGATCGCAACGGT 59.965 50.000 0.00 0.00 0.00 4.83
24 25 0.443869 CAGTCCAAAGATCGCAACGG 59.556 55.000 0.00 0.00 0.00 4.44
25 26 0.443869 CCAGTCCAAAGATCGCAACG 59.556 55.000 0.00 0.00 0.00 4.10
26 27 0.804989 CCCAGTCCAAAGATCGCAAC 59.195 55.000 0.00 0.00 0.00 4.17
27 28 0.690192 TCCCAGTCCAAAGATCGCAA 59.310 50.000 0.00 0.00 0.00 4.85
31 32 0.250513 AGCGTCCCAGTCCAAAGATC 59.749 55.000 0.00 0.00 0.00 2.75
41 42 1.683917 AGCTATGTAAGAGCGTCCCAG 59.316 52.381 0.00 0.00 44.98 4.45
59 60 4.510038 AAGGTGATCATGTCAAACAAGC 57.490 40.909 0.00 0.00 38.90 4.01
77 78 9.634163 GACAACTGGTACCAAATTAAATAAAGG 57.366 33.333 17.11 1.60 0.00 3.11
95 96 3.355378 TGGGATGCTTAATGACAACTGG 58.645 45.455 0.00 0.00 0.00 4.00
112 113 1.633432 CCTTATCTGTGGTGGTTGGGA 59.367 52.381 0.00 0.00 0.00 4.37
113 114 1.955208 GCCTTATCTGTGGTGGTTGGG 60.955 57.143 0.00 0.00 0.00 4.12
114 115 1.463674 GCCTTATCTGTGGTGGTTGG 58.536 55.000 0.00 0.00 0.00 3.77
115 116 1.271871 TGGCCTTATCTGTGGTGGTTG 60.272 52.381 3.32 0.00 0.00 3.77
116 117 1.072266 TGGCCTTATCTGTGGTGGTT 58.928 50.000 3.32 0.00 0.00 3.67
117 118 0.328258 GTGGCCTTATCTGTGGTGGT 59.672 55.000 3.32 0.00 0.00 4.16
118 119 0.394352 GGTGGCCTTATCTGTGGTGG 60.394 60.000 3.32 0.00 0.00 4.61
119 120 0.394352 GGGTGGCCTTATCTGTGGTG 60.394 60.000 3.32 0.00 0.00 4.17
120 121 1.571773 GGGGTGGCCTTATCTGTGGT 61.572 60.000 3.32 0.00 0.00 4.16
121 122 1.227383 GGGGTGGCCTTATCTGTGG 59.773 63.158 3.32 0.00 0.00 4.17
122 123 1.153168 CGGGGTGGCCTTATCTGTG 60.153 63.158 3.32 0.00 0.00 3.66
123 124 1.205460 AACGGGGTGGCCTTATCTGT 61.205 55.000 3.32 0.00 0.00 3.41
124 125 0.463833 GAACGGGGTGGCCTTATCTG 60.464 60.000 3.32 0.00 0.00 2.90
125 126 1.912971 GAACGGGGTGGCCTTATCT 59.087 57.895 3.32 0.00 0.00 1.98
140 141 2.795470 GGTCAACTCTCAGAACACGAAC 59.205 50.000 0.00 0.00 0.00 3.95
192 194 8.978472 AGATTGAGTGTAGCTAATGTAACCTTA 58.022 33.333 0.00 0.00 0.00 2.69
193 195 7.766278 CAGATTGAGTGTAGCTAATGTAACCTT 59.234 37.037 0.00 0.00 0.00 3.50
196 198 8.480643 AACAGATTGAGTGTAGCTAATGTAAC 57.519 34.615 0.00 0.00 0.00 2.50
197 199 8.531982 AGAACAGATTGAGTGTAGCTAATGTAA 58.468 33.333 0.00 0.00 0.00 2.41
200 202 7.840342 AAGAACAGATTGAGTGTAGCTAATG 57.160 36.000 0.00 0.00 0.00 1.90
202 204 7.671302 AGAAAGAACAGATTGAGTGTAGCTAA 58.329 34.615 0.00 0.00 0.00 3.09
204 206 6.107901 AGAAAGAACAGATTGAGTGTAGCT 57.892 37.500 0.00 0.00 0.00 3.32
209 211 9.086336 GATCTAGAAGAAAGAACAGATTGAGTG 57.914 37.037 0.00 0.00 0.00 3.51
212 214 8.138928 TGGATCTAGAAGAAAGAACAGATTGA 57.861 34.615 0.00 0.00 0.00 2.57
214 216 9.612066 GAATGGATCTAGAAGAAAGAACAGATT 57.388 33.333 0.00 0.00 0.00 2.40
252 254 2.228138 TCTTTTGTTAGTGGTCGCGT 57.772 45.000 5.77 0.00 0.00 6.01
253 255 2.096417 CCTTCTTTTGTTAGTGGTCGCG 60.096 50.000 0.00 0.00 0.00 5.87
299 301 3.209410 CATACCAGTTGAGAATGGAGGC 58.791 50.000 0.00 0.00 39.02 4.70
301 303 5.124457 CCAAACATACCAGTTGAGAATGGAG 59.876 44.000 0.00 0.00 39.02 3.86
313 315 4.795962 GCAAGGTTGAACCAAACATACCAG 60.796 45.833 17.83 0.00 41.95 4.00
340 344 0.321671 ATGTGGTGAAGACACGGAGG 59.678 55.000 0.00 0.00 46.77 4.30
345 349 5.992217 AGTCTAAGAAATGTGGTGAAGACAC 59.008 40.000 0.00 0.00 45.27 3.67
440 445 4.952957 TGAACATGAAGAAAACAGGTTGGA 59.047 37.500 0.00 0.00 41.18 3.53
477 490 4.536765 ACATAATTGCTTCCTTACAGGGG 58.463 43.478 0.00 0.00 35.59 4.79
532 553 8.728337 TCAGTTCTGATCTGGATTTTGAATAG 57.272 34.615 14.07 0.00 34.15 1.73
533 554 8.950210 GTTCAGTTCTGATCTGGATTTTGAATA 58.050 33.333 14.07 0.00 34.15 1.75
583 605 4.332268 GCTGAGTAAGTACTACTACGTGCT 59.668 45.833 0.00 0.00 41.17 4.40
585 607 4.564372 TCGCTGAGTAAGTACTACTACGTG 59.436 45.833 0.00 2.74 41.17 4.49
587 609 5.233902 ACATCGCTGAGTAAGTACTACTACG 59.766 44.000 0.00 5.93 41.17 3.51
589 611 7.495901 AGTACATCGCTGAGTAAGTACTACTA 58.504 38.462 0.00 0.00 41.17 1.82
629 653 6.792250 CACACAACACTGAAGATAATCGTTTC 59.208 38.462 0.00 0.00 0.00 2.78
632 656 5.538118 TCACACAACACTGAAGATAATCGT 58.462 37.500 0.00 0.00 0.00 3.73
633 657 6.466308 TTCACACAACACTGAAGATAATCG 57.534 37.500 0.00 0.00 0.00 3.34
638 662 9.725019 TTTAGATATTCACACAACACTGAAGAT 57.275 29.630 0.00 0.00 32.34 2.40
681 705 3.262915 GCTGCCAGAGATACCCAATCTAT 59.737 47.826 0.00 0.00 45.35 1.98
690 849 1.759445 TCCTTGAGCTGCCAGAGATAC 59.241 52.381 0.00 0.00 0.00 2.24
697 856 0.694771 AACATCTCCTTGAGCTGCCA 59.305 50.000 0.00 0.00 30.01 4.92
706 865 7.839680 ACCATTTAGAAACAAACATCTCCTT 57.160 32.000 0.00 0.00 0.00 3.36
723 882 6.892456 TGGGCAACATACAAAGATACCATTTA 59.108 34.615 0.00 0.00 39.74 1.40
724 883 5.719085 TGGGCAACATACAAAGATACCATTT 59.281 36.000 0.00 0.00 39.74 2.32
725 884 5.268387 TGGGCAACATACAAAGATACCATT 58.732 37.500 0.00 0.00 39.74 3.16
726 885 4.865905 TGGGCAACATACAAAGATACCAT 58.134 39.130 0.00 0.00 39.74 3.55
727 886 4.308526 TGGGCAACATACAAAGATACCA 57.691 40.909 0.00 0.00 39.74 3.25
728 887 5.591099 CAATGGGCAACATACAAAGATACC 58.409 41.667 0.00 0.00 39.40 2.73
729 888 5.043248 GCAATGGGCAACATACAAAGATAC 58.957 41.667 0.00 0.00 43.97 2.24
755 1033 6.016860 TCCTTGGATTAATCATCAATGAAGCG 60.017 38.462 17.07 1.36 40.69 4.68
756 1034 7.281040 TCCTTGGATTAATCATCAATGAAGC 57.719 36.000 17.07 0.00 40.69 3.86
791 1148 8.957028 GGTAACAAATAAACAAAGTACGGAAAC 58.043 33.333 0.00 0.00 0.00 2.78
795 1152 7.863666 TGAGGTAACAAATAAACAAAGTACGG 58.136 34.615 0.00 0.00 41.41 4.02
1119 2594 9.653287 CTTACATTGTAGATAAACCTCTTGACA 57.347 33.333 0.00 0.00 0.00 3.58
1344 2819 1.882912 TATAGGCCAATGCTTCAGCG 58.117 50.000 5.01 0.00 45.83 5.18
1656 3132 9.893305 TTTGAAAGAGATCGAATAAAACTTTCC 57.107 29.630 18.37 8.90 40.12 3.13
1685 3161 2.735259 TTCCCTCACCCTCCTAAACT 57.265 50.000 0.00 0.00 0.00 2.66
1704 3180 9.881529 GATGTTGCAATTGTAAAATCAAACATT 57.118 25.926 25.87 0.61 35.35 2.71
1785 3261 1.612199 GGGCGTTTGTCCTGTTCCATA 60.612 52.381 0.00 0.00 36.72 2.74
1794 3270 0.321653 ACATCTCAGGGCGTTTGTCC 60.322 55.000 0.00 0.00 41.57 4.02
1818 3294 0.874390 TGCGAAGATGTTCTGCAACC 59.126 50.000 15.82 0.00 38.43 3.77
1829 3305 5.106515 GGAGCTTTTCTAAGTTTGCGAAGAT 60.107 40.000 0.00 0.00 33.74 2.40
1897 3373 4.683832 TCGGCTGAAGCTAGTTTATCTTC 58.316 43.478 1.74 0.00 41.70 2.87
1900 3376 4.630069 TGTTTCGGCTGAAGCTAGTTTATC 59.370 41.667 20.95 0.00 41.70 1.75
1945 3487 6.040391 TGCTGCTTTCTAGTGGTTGTATTTTT 59.960 34.615 0.00 0.00 0.00 1.94
1946 3488 5.534654 TGCTGCTTTCTAGTGGTTGTATTTT 59.465 36.000 0.00 0.00 0.00 1.82
1947 3489 5.070001 TGCTGCTTTCTAGTGGTTGTATTT 58.930 37.500 0.00 0.00 0.00 1.40
1948 3490 4.651778 TGCTGCTTTCTAGTGGTTGTATT 58.348 39.130 0.00 0.00 0.00 1.89
1949 3491 4.256920 CTGCTGCTTTCTAGTGGTTGTAT 58.743 43.478 0.00 0.00 0.00 2.29
1950 3492 3.664107 CTGCTGCTTTCTAGTGGTTGTA 58.336 45.455 0.00 0.00 0.00 2.41
1951 3493 2.498167 CTGCTGCTTTCTAGTGGTTGT 58.502 47.619 0.00 0.00 0.00 3.32
1952 3494 1.198637 GCTGCTGCTTTCTAGTGGTTG 59.801 52.381 8.53 0.00 36.03 3.77
1953 3495 1.202806 TGCTGCTGCTTTCTAGTGGTT 60.203 47.619 17.00 0.00 40.48 3.67
1954 3496 0.397941 TGCTGCTGCTTTCTAGTGGT 59.602 50.000 17.00 0.00 40.48 4.16
1955 3497 1.085091 CTGCTGCTGCTTTCTAGTGG 58.915 55.000 17.00 0.00 40.48 4.00
1992 3783 6.357579 TCACTGTTGGCCAAATGATAAAAT 57.642 33.333 22.47 0.00 0.00 1.82
2003 3824 3.854856 GCCTTTCACTGTTGGCCA 58.145 55.556 0.00 0.00 39.49 5.36
2005 3826 0.032540 CTTGGCCTTTCACTGTTGGC 59.967 55.000 3.32 0.00 44.22 4.52
2006 3827 1.402787 ACTTGGCCTTTCACTGTTGG 58.597 50.000 3.32 0.00 0.00 3.77
2008 3829 4.020662 TCAAAAACTTGGCCTTTCACTGTT 60.021 37.500 3.32 0.00 0.00 3.16
2016 3837 1.413812 CCAGCTCAAAAACTTGGCCTT 59.586 47.619 3.32 0.00 0.00 4.35
2024 3845 2.854805 GCAACTCGTCCAGCTCAAAAAC 60.855 50.000 0.00 0.00 0.00 2.43
2026 3847 0.944386 GCAACTCGTCCAGCTCAAAA 59.056 50.000 0.00 0.00 0.00 2.44
2047 3868 1.503542 CACTTCAGTTGATGCCCGC 59.496 57.895 0.00 0.00 0.00 6.13
2065 3886 0.107654 CTACTGTACCCTTGCCCAGC 60.108 60.000 0.00 0.00 0.00 4.85
2083 3904 2.027561 TGTCGCTTTGTATGTTAGCCCT 60.028 45.455 0.00 0.00 0.00 5.19
2105 3926 6.101150 ACCACCAGCTCATATCCACTATAAAA 59.899 38.462 0.00 0.00 0.00 1.52
2108 3929 4.752063 ACCACCAGCTCATATCCACTATA 58.248 43.478 0.00 0.00 0.00 1.31
2155 3976 1.977293 GCTCAAAGATCGCCTCCCCT 61.977 60.000 0.00 0.00 0.00 4.79
2189 5230 1.737838 TTGTTCTGGATAGCGCCAAG 58.262 50.000 2.29 0.00 37.52 3.61
2197 5238 4.941263 GGCACTATGTGTTTGTTCTGGATA 59.059 41.667 0.00 0.00 35.75 2.59
2240 5281 2.746362 CCAGCAACTTCTCATCCTTGTC 59.254 50.000 0.00 0.00 0.00 3.18
2260 5301 4.335416 CCATGGGGATGACATTATACACC 58.665 47.826 2.85 0.00 35.59 4.16
2314 5355 6.565435 GCACATGCTAGCATTGTTCAGTATAG 60.565 42.308 27.59 13.71 38.21 1.31
2332 5402 5.928264 AGAAATTGTAAAGGAAAGCACATGC 59.072 36.000 0.00 0.00 42.49 4.06
2342 5415 9.912634 CTCAAAAGCATTAGAAATTGTAAAGGA 57.087 29.630 0.00 0.00 0.00 3.36
2361 5434 7.092137 TCATGAATTAGTGATGCCTCAAAAG 57.908 36.000 0.00 0.00 31.85 2.27
2395 5469 0.037232 CCAGAACCTCGGTCACCTTC 60.037 60.000 0.00 0.00 0.00 3.46
2396 5470 2.058675 CCAGAACCTCGGTCACCTT 58.941 57.895 0.00 0.00 0.00 3.50
2529 5606 1.479323 GTACCGGTGAGCAGGATGTTA 59.521 52.381 19.93 0.00 39.31 2.41
2736 5822 1.227556 CAAATCTACTCCCCCGCCG 60.228 63.158 0.00 0.00 0.00 6.46
2738 5824 1.526225 GGCAAATCTACTCCCCCGC 60.526 63.158 0.00 0.00 0.00 6.13
2949 6110 1.618837 GTCAGCAACTAGGACTGTCCA 59.381 52.381 27.48 13.11 39.61 4.02
2961 6132 2.682856 TGTGAGGTTCTTTGTCAGCAAC 59.317 45.455 0.00 0.00 33.82 4.17
3006 6185 3.638160 ACATTTGAATGCAACTGTGACCT 59.362 39.130 8.56 0.00 40.04 3.85
3041 6231 4.079385 GGATAACCAGTTGAAAGGGGGTAT 60.079 45.833 0.00 0.00 36.04 2.73
3153 6347 6.992063 AACATGTAGGACAAGTGATTGATC 57.008 37.500 0.00 0.00 29.71 2.92
3157 6353 6.095440 GCCAATAACATGTAGGACAAGTGATT 59.905 38.462 0.00 0.00 32.67 2.57
3230 6428 5.278604 GTTTAATTTGGAAACGTGCAGAGT 58.721 37.500 0.00 0.00 0.00 3.24
3239 6437 5.811100 TGAACCCAACGTTTAATTTGGAAAC 59.189 36.000 0.00 0.00 44.51 2.78
3375 6826 9.846248 AAATATGAGTCTAAAAGCAAACATGAC 57.154 29.630 0.00 0.00 0.00 3.06
3527 7460 1.398692 TTCTTGGCTTGGTGTGTTCC 58.601 50.000 0.00 0.00 0.00 3.62
3535 7468 4.278170 TGAACACTGTAATTCTTGGCTTGG 59.722 41.667 5.79 0.00 0.00 3.61
3585 7542 1.530013 TTCGGAGAGGTGGTCGGTTC 61.530 60.000 0.00 0.00 38.43 3.62
3622 7579 0.246635 GCAAGCGAGAGTACTGGGAA 59.753 55.000 0.00 0.00 0.00 3.97
3874 7942 6.116126 GTCCTTGCCAGATATTGTACTTCTT 58.884 40.000 0.00 0.00 0.00 2.52
3882 7967 2.158900 AGGTCGTCCTTGCCAGATATTG 60.159 50.000 0.00 0.00 42.12 1.90
3883 7968 2.119495 AGGTCGTCCTTGCCAGATATT 58.881 47.619 0.00 0.00 42.12 1.28
3884 7969 1.414181 CAGGTCGTCCTTGCCAGATAT 59.586 52.381 0.00 0.00 43.07 1.63
3885 7970 0.824109 CAGGTCGTCCTTGCCAGATA 59.176 55.000 0.00 0.00 43.07 1.98
3886 7971 1.599047 CAGGTCGTCCTTGCCAGAT 59.401 57.895 0.00 0.00 43.07 2.90
3887 7972 2.583441 CCAGGTCGTCCTTGCCAGA 61.583 63.158 0.00 0.00 43.07 3.86
3888 7973 2.046892 CCAGGTCGTCCTTGCCAG 60.047 66.667 0.00 0.00 43.07 4.85
3889 7974 2.525629 TCCAGGTCGTCCTTGCCA 60.526 61.111 0.00 0.00 43.07 4.92
3890 7975 2.047179 GTCCAGGTCGTCCTTGCC 60.047 66.667 0.00 0.00 43.07 4.52
3891 7976 2.432628 CGTCCAGGTCGTCCTTGC 60.433 66.667 0.00 0.00 43.07 4.01
3892 7977 1.080705 GTCGTCCAGGTCGTCCTTG 60.081 63.158 5.97 0.00 43.07 3.61
3893 7978 2.623915 CGTCGTCCAGGTCGTCCTT 61.624 63.158 5.97 0.00 43.07 3.36
3944 8029 5.367937 ACTCATGACTATAAGCCCAGACATT 59.632 40.000 0.00 0.00 0.00 2.71
3945 8030 4.904251 ACTCATGACTATAAGCCCAGACAT 59.096 41.667 0.00 0.00 0.00 3.06
3947 8032 4.502259 CCACTCATGACTATAAGCCCAGAC 60.502 50.000 0.00 0.00 0.00 3.51
3948 8033 3.643320 CCACTCATGACTATAAGCCCAGA 59.357 47.826 0.00 0.00 0.00 3.86
3949 8034 3.244353 CCCACTCATGACTATAAGCCCAG 60.244 52.174 0.00 0.00 0.00 4.45
3950 8035 2.705658 CCCACTCATGACTATAAGCCCA 59.294 50.000 0.00 0.00 0.00 5.36
3951 8036 2.551071 GCCCACTCATGACTATAAGCCC 60.551 54.545 0.00 0.00 0.00 5.19
3953 8038 3.760580 AGCCCACTCATGACTATAAGC 57.239 47.619 0.00 0.00 0.00 3.09
3954 8039 5.220931 GCAAAAGCCCACTCATGACTATAAG 60.221 44.000 0.00 0.00 0.00 1.73
3956 8041 4.199310 GCAAAAGCCCACTCATGACTATA 58.801 43.478 0.00 0.00 0.00 1.31
4020 8262 2.031683 CAGCTCCGTTGAACGAGTTTTT 59.968 45.455 20.47 0.00 46.05 1.94
4030 8272 0.662619 CAAACTTGCAGCTCCGTTGA 59.337 50.000 0.00 0.00 0.00 3.18
4042 8284 1.587946 GCTGTTTTGCGACCAAACTTG 59.412 47.619 0.00 0.00 40.45 3.16


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

AutoCloner maintained by Alex Coulton.