Multiple sequence alignment - TraesCS3A01G206600

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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 TraesCS3A01G206600 chr3A 100.000 6769 0 0 1 6769 363460800 363454032 0.000000e+00 12501.0
1 TraesCS3A01G206600 chr3A 89.167 120 11 2 6439 6558 210156761 210156878 1.520000e-31 148.0
2 TraesCS3A01G206600 chr3D 96.278 6099 138 27 1 6068 276536432 276542472 0.000000e+00 9923.0
3 TraesCS3A01G206600 chr3D 88.462 286 9 7 6064 6328 276542508 276542790 2.350000e-84 324.0
4 TraesCS3A01G206600 chr3D 89.806 206 12 8 6570 6769 276542920 276543122 8.710000e-64 255.0
5 TraesCS3A01G206600 chr3D 83.969 131 20 1 6436 6566 105707865 105707736 2.560000e-24 124.0
6 TraesCS3A01G206600 chr3D 93.750 48 3 0 6326 6373 276542819 276542866 9.420000e-09 73.1
7 TraesCS3A01G206600 chr3D 97.059 34 1 0 6405 6438 276542879 276542912 2.640000e-04 58.4
8 TraesCS3A01G206600 chr3B 95.475 5216 122 40 880 6028 373878364 373873196 0.000000e+00 8220.0
9 TraesCS3A01G206600 chr3B 85.056 629 61 16 163 787 373879072 373878473 1.610000e-170 610.0
10 TraesCS3A01G206600 chr3B 88.889 162 5 6 6611 6769 373847274 373847123 3.220000e-43 187.0
11 TraesCS3A01G206600 chr3B 90.714 140 6 3 6191 6330 373847579 373847447 5.390000e-41 180.0
12 TraesCS3A01G206600 chr3B 93.939 66 4 0 1 66 373879556 373879491 4.320000e-17 100.0
13 TraesCS3A01G206600 chr3B 95.238 63 2 1 6563 6625 373847351 373847290 1.550000e-16 99.0
14 TraesCS3A01G206600 chr3B 93.846 65 4 0 1 65 373879911 373879847 1.550000e-16 99.0
15 TraesCS3A01G206600 chr3B 85.047 107 3 2 6116 6209 373847706 373847600 5.590000e-16 97.1
16 TraesCS3A01G206600 chr3B 94.915 59 3 0 794 852 373878422 373878364 7.230000e-15 93.5
17 TraesCS3A01G206600 chr3B 95.918 49 2 0 6020 6068 373847776 373847728 5.630000e-11 80.5
18 TraesCS3A01G206600 chr3B 100.000 33 0 0 6406 6438 373847381 373847349 2.040000e-05 62.1
19 TraesCS3A01G206600 chr6A 87.786 131 15 1 6435 6565 106974144 106974015 1.180000e-32 152.0
20 TraesCS3A01G206600 chr7D 87.805 123 14 1 6436 6558 621819455 621819576 7.080000e-30 143.0
21 TraesCS3A01G206600 chr7D 84.058 138 19 3 6436 6571 92808395 92808531 5.510000e-26 130.0
22 TraesCS3A01G206600 chr2D 87.805 123 14 1 6443 6565 165471943 165471822 7.080000e-30 143.0
23 TraesCS3A01G206600 chr5A 87.705 122 14 1 6446 6567 521020293 521020173 2.550000e-29 141.0
24 TraesCS3A01G206600 chr7B 85.385 130 18 1 6436 6565 714437096 714437224 4.260000e-27 134.0
25 TraesCS3A01G206600 chr7B 95.122 41 2 0 71 111 480856416 480856456 1.580000e-06 65.8
26 TraesCS3A01G206600 chr4A 87.755 98 11 1 6445 6542 143704396 143704300 5.550000e-21 113.0
27 TraesCS3A01G206600 chr5B 85.714 63 7 2 66 127 508240112 508240051 1.580000e-06 65.8


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 TraesCS3A01G206600 chr3A 363454032 363460800 6768 True 12501.0 12501 100.0000 1 6769 1 chr3A.!!$R1 6768
1 TraesCS3A01G206600 chr3D 276536432 276543122 6690 False 2126.7 9923 93.0710 1 6769 5 chr3D.!!$F1 6768
2 TraesCS3A01G206600 chr3B 373873196 373879911 6715 True 1824.5 8220 92.6462 1 6028 5 chr3B.!!$R2 6027

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
241 981 0.107456 CTGCACTGGTGGTTGAGTCT 59.893 55.000 2.84 0.0 0.00 3.24 F
1038 1857 0.036875 CCTCCTCTTCACCACCAACC 59.963 60.000 0.00 0.0 0.00 3.77 F
1932 2754 0.325296 TGCTCGGGTGGAAGGAGTAT 60.325 55.000 0.00 0.0 0.00 2.12 F
2145 2967 1.133253 CTCCAATGTGCAGTTCGCG 59.867 57.895 0.00 0.0 46.97 5.87 F
2397 3219 1.894978 GCAACCTCCTTGGGGCAAATA 60.895 52.381 0.00 0.0 41.11 1.40 F
3919 4747 2.349817 GCCAGTGTTTCATCACGAGTTG 60.350 50.000 0.00 0.0 42.40 3.16 F
4719 5547 0.387622 CATGGACCACAAAGCTTGCG 60.388 55.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 2592 0.107654 GGACAATCAGGGGGAACTCG 60.108 60.000 0.00 0.00 34.16 4.18 R
2145 2967 1.453197 CCCATCCGCAGGGTTAACC 60.453 63.158 16.85 16.85 39.56 2.85 R
3524 4352 5.300752 TCTTTTGAGAGCTGGTCTAAGTTG 58.699 41.667 9.69 1.41 34.71 3.16 R
3878 4706 5.337788 TGGCCATAAAAAGTAAGGTGGAAT 58.662 37.500 0.00 0.00 0.00 3.01 R
4131 4959 6.237901 TCCATACTGCACAATTATACCATCC 58.762 40.000 0.00 0.00 0.00 3.51 R
5552 6380 0.383231 GGAAAAGGGCGAGCATGATG 59.617 55.000 0.00 0.00 0.00 3.07 R
6236 7169 0.305922 GCATGTGAATCCGCAGCTAC 59.694 55.000 0.00 0.00 36.09 3.58 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
36 37 5.710099 GTGACATGAATTCCTAAGGTCCAAA 59.290 40.000 0.00 0.00 0.00 3.28
41 42 6.959639 TGAATTCCTAAGGTCCAAATATGC 57.040 37.500 2.27 0.00 0.00 3.14
66 801 4.227073 GGGATTGGGATTTGGGAATTTTGA 59.773 41.667 0.00 0.00 0.00 2.69
100 835 2.079288 GGGTGGAGGGAAGGGGATC 61.079 68.421 0.00 0.00 0.00 3.36
105 840 0.919289 GGAGGGAAGGGGATCACCAA 60.919 60.000 18.46 0.00 42.91 3.67
106 841 0.999712 GAGGGAAGGGGATCACCAAA 59.000 55.000 18.46 0.00 42.91 3.28
107 842 1.002857 AGGGAAGGGGATCACCAAAG 58.997 55.000 18.46 0.00 42.91 2.77
111 846 1.149133 AAGGGGATCACCAAAGCCCT 61.149 55.000 18.46 7.24 42.91 5.19
130 870 0.476771 TCCAACCCCTCAAACCTCAC 59.523 55.000 0.00 0.00 0.00 3.51
152 892 6.084326 ACATGTGTGAAAAAGACCAATACC 57.916 37.500 0.00 0.00 0.00 2.73
166 906 4.086457 ACCAATACCAAACAAGGCCTTAG 58.914 43.478 20.00 15.05 0.00 2.18
206 946 5.826643 TGGATGTGTAAAGGCCTTATTTCT 58.173 37.500 20.84 4.94 0.00 2.52
239 979 0.767375 ATCTGCACTGGTGGTTGAGT 59.233 50.000 2.84 0.00 0.00 3.41
241 981 0.107456 CTGCACTGGTGGTTGAGTCT 59.893 55.000 2.84 0.00 0.00 3.24
334 1075 2.807676 CTTGGCTAGGATTTTGTGGGT 58.192 47.619 0.00 0.00 0.00 4.51
335 1076 2.214376 TGGCTAGGATTTTGTGGGTG 57.786 50.000 0.00 0.00 0.00 4.61
336 1077 1.272425 TGGCTAGGATTTTGTGGGTGG 60.272 52.381 0.00 0.00 0.00 4.61
337 1078 0.817654 GCTAGGATTTTGTGGGTGGC 59.182 55.000 0.00 0.00 0.00 5.01
338 1079 1.890573 GCTAGGATTTTGTGGGTGGCA 60.891 52.381 0.00 0.00 0.00 4.92
339 1080 1.818674 CTAGGATTTTGTGGGTGGCAC 59.181 52.381 9.70 9.70 0.00 5.01
340 1081 1.178534 AGGATTTTGTGGGTGGCACG 61.179 55.000 12.17 0.00 0.00 5.34
341 1082 1.288752 GATTTTGTGGGTGGCACGG 59.711 57.895 12.17 0.00 0.00 4.94
342 1083 1.152652 ATTTTGTGGGTGGCACGGA 60.153 52.632 12.17 0.00 0.00 4.69
343 1084 0.757188 ATTTTGTGGGTGGCACGGAA 60.757 50.000 12.17 0.00 0.00 4.30
344 1085 1.388065 TTTTGTGGGTGGCACGGAAG 61.388 55.000 12.17 0.00 0.00 3.46
345 1086 3.783362 TTGTGGGTGGCACGGAAGG 62.783 63.158 12.17 0.00 0.00 3.46
362 1103 1.359168 AGGTAGGGTTTCGAAGGCTT 58.641 50.000 0.00 0.00 0.00 4.35
365 1106 2.347731 GTAGGGTTTCGAAGGCTTGAG 58.652 52.381 3.46 0.00 0.00 3.02
374 1115 2.368875 TCGAAGGCTTGAGGTCTCTTTT 59.631 45.455 3.46 0.00 0.00 2.27
378 1119 2.975489 AGGCTTGAGGTCTCTTTTCAGA 59.025 45.455 0.00 0.00 0.00 3.27
387 1128 6.099845 TGAGGTCTCTTTTCAGACTAGGTTTT 59.900 38.462 0.00 0.00 42.31 2.43
444 1185 3.311871 CAGCACTATCTGGAAGCAATGAC 59.688 47.826 0.00 0.00 0.00 3.06
478 1219 2.223688 CCACACTGAGGATGATCGAGAC 60.224 54.545 0.00 0.00 0.00 3.36
502 1246 4.394729 ACTCGTAATTTTGAGGAGGCAAA 58.605 39.130 10.34 0.00 36.53 3.68
522 1266 5.181245 GCAAAGTAGAAGGCTGAACAATGTA 59.819 40.000 0.00 0.00 0.00 2.29
569 1313 3.833732 ACGGATAGAGACTATGCCAAGA 58.166 45.455 0.00 0.00 0.00 3.02
602 1346 8.675504 TGTACAAGACAAGGTTTTAAATTTCGA 58.324 29.630 0.00 0.00 34.15 3.71
624 1368 5.570973 CGAACATCACCAAAATATGCGAAAA 59.429 36.000 0.00 0.00 0.00 2.29
629 1373 7.601886 ACATCACCAAAATATGCGAAAATTTGA 59.398 29.630 0.00 0.00 33.86 2.69
634 1378 9.824534 ACCAAAATATGCGAAAATTTGAAAATC 57.175 25.926 0.00 0.00 33.86 2.17
747 1492 4.833938 GGTTACAAGTATTTTGGACCCCAA 59.166 41.667 0.00 0.00 42.29 4.12
762 1508 5.066593 GGACCCCAACAAAATATGCAAAAA 58.933 37.500 0.00 0.00 0.00 1.94
804 1594 1.583054 GTACACGAATGAGATGGGCC 58.417 55.000 0.00 0.00 0.00 5.80
956 1746 3.100514 CCCCCGCCCCTTAATCCA 61.101 66.667 0.00 0.00 0.00 3.41
1038 1857 0.036875 CCTCCTCTTCACCACCAACC 59.963 60.000 0.00 0.00 0.00 3.77
1039 1858 1.059913 CTCCTCTTCACCACCAACCT 58.940 55.000 0.00 0.00 0.00 3.50
1040 1859 1.421646 CTCCTCTTCACCACCAACCTT 59.578 52.381 0.00 0.00 0.00 3.50
1041 1860 1.142870 TCCTCTTCACCACCAACCTTG 59.857 52.381 0.00 0.00 0.00 3.61
1791 2613 1.077716 GTTCCCCCTGATTGTCCGG 60.078 63.158 0.00 0.00 0.00 5.14
1794 2616 3.411517 CCCCTGATTGTCCGGCCT 61.412 66.667 0.00 0.00 0.00 5.19
1932 2754 0.325296 TGCTCGGGTGGAAGGAGTAT 60.325 55.000 0.00 0.00 0.00 2.12
1959 2781 2.400798 GTGATGCGTGACATGGCG 59.599 61.111 0.00 0.00 39.84 5.69
2145 2967 1.133253 CTCCAATGTGCAGTTCGCG 59.867 57.895 0.00 0.00 46.97 5.87
2360 3182 4.994852 TGACTATGTTGTCACAAAGGTAGC 59.005 41.667 0.00 0.00 41.43 3.58
2397 3219 1.894978 GCAACCTCCTTGGGGCAAATA 60.895 52.381 0.00 0.00 41.11 1.40
2797 3624 6.505044 TCAGAATCCAAACATCACAATCAG 57.495 37.500 0.00 0.00 0.00 2.90
3082 3910 4.875544 ATTGATTTGCTCATTTGCATGC 57.124 36.364 11.82 11.82 42.96 4.06
3524 4352 6.503524 TGTTGAGCAGTTCCTTATTTCAAAC 58.496 36.000 0.00 0.00 0.00 2.93
3878 4706 7.913297 CGAGAGGTTTGTTTTTACTTCATTTGA 59.087 33.333 0.00 0.00 0.00 2.69
3913 4741 4.782019 TTTATGGCCAGTGTTTCATCAC 57.218 40.909 13.05 0.00 38.46 3.06
3919 4747 2.349817 GCCAGTGTTTCATCACGAGTTG 60.350 50.000 0.00 0.00 42.40 3.16
3943 4771 8.394971 TGAATAGGCAATTACATTCTGGTATG 57.605 34.615 0.00 0.00 0.00 2.39
4131 4959 1.064621 CATTGATTTGGAGCGCCCG 59.935 57.895 2.29 0.00 37.93 6.13
4152 4980 5.245531 CCGGATGGTATAATTGTGCAGTAT 58.754 41.667 0.00 0.00 0.00 2.12
4509 5337 2.826128 AGTGCAAGTAGATCCAGAACGA 59.174 45.455 0.00 0.00 0.00 3.85
4719 5547 0.387622 CATGGACCACAAAGCTTGCG 60.388 55.000 0.00 0.00 0.00 4.85
5229 6057 2.307098 AGTACTTCAGCTTGAGGGCATT 59.693 45.455 0.00 0.00 34.17 3.56
5230 6058 3.519510 AGTACTTCAGCTTGAGGGCATTA 59.480 43.478 0.00 0.00 34.17 1.90
5325 6153 3.521126 AGGTGATGGTGATAACAAGCTCT 59.479 43.478 0.00 0.00 0.00 4.09
5496 6324 2.943199 GCAAGACTATTTCCAGCCTGCT 60.943 50.000 0.00 0.00 0.00 4.24
5570 6398 1.332997 CTCATCATGCTCGCCCTTTTC 59.667 52.381 0.00 0.00 0.00 2.29
5588 6416 7.069950 GCCCTTTTCCCATCTAATGTCTTTATT 59.930 37.037 0.00 0.00 0.00 1.40
5589 6417 8.633561 CCCTTTTCCCATCTAATGTCTTTATTC 58.366 37.037 0.00 0.00 0.00 1.75
5617 6452 1.123077 ACTAGAATCCTGCGCCATGA 58.877 50.000 4.18 0.00 0.00 3.07
5923 6804 1.570857 CCCATGCTCCTGGTTACCCA 61.571 60.000 0.00 0.00 38.87 4.51
5924 6805 0.552848 CCATGCTCCTGGTTACCCAT 59.447 55.000 0.00 0.00 40.90 4.00
5930 6811 2.821625 GCTCCTGGTTACCCATGGTTTT 60.822 50.000 11.73 0.00 40.90 2.43
6034 6915 9.445786 CGTCTCAATGTTTGTTAGTTATGTTTT 57.554 29.630 0.00 0.00 0.00 2.43
6051 6932 3.067320 TGTTTTGTGTCGGCAAATGATCA 59.933 39.130 0.00 0.00 38.05 2.92
6062 6943 4.618927 CGGCAAATGATCATTCTGTTTGGT 60.619 41.667 20.95 0.28 33.05 3.67
6099 7020 4.036971 GCTAGGCAATCTCTCTTTCGTAGA 59.963 45.833 0.00 0.00 0.00 2.59
6120 7045 2.807967 ACACGTTGAGATGGTTGATGTG 59.192 45.455 0.00 0.00 34.34 3.21
6175 7108 3.002348 AGTTGTCAAACAAGCGAGCTAAC 59.998 43.478 0.00 0.00 39.00 2.34
6198 7131 0.905337 AGGGTGTAGGTGGAGTGAGC 60.905 60.000 0.00 0.00 0.00 4.26
6212 7145 0.514691 GTGAGCAGAAGTCTTTGCCG 59.485 55.000 13.00 0.00 41.17 5.69
6293 7235 3.507622 TCAATGGTCAAACACACACACAA 59.492 39.130 0.00 0.00 0.00 3.33
6303 7245 3.585862 ACACACACACAATCGGAGATAC 58.414 45.455 0.00 0.00 45.12 2.24
6306 7248 5.105513 ACACACACACAATCGGAGATACATA 60.106 40.000 0.00 0.00 45.12 2.29
6315 7257 6.428159 ACAATCGGAGATACATATTTGCCTTC 59.572 38.462 0.00 0.00 45.12 3.46
6328 7301 8.956426 ACATATTTGCCTTCGAAAATTAGAAGA 58.044 29.630 14.98 0.00 44.76 2.87
6361 7334 0.312416 ATGTCTCGCTATCGACTGGC 59.688 55.000 0.00 0.00 40.21 4.85
6365 7338 0.031314 CTCGCTATCGACTGGCATGT 59.969 55.000 0.00 0.00 40.21 3.21
6374 7347 1.914634 GACTGGCATGTCGACTACTG 58.085 55.000 17.92 12.34 0.00 2.74
6375 7348 0.108615 ACTGGCATGTCGACTACTGC 60.109 55.000 22.02 22.02 33.84 4.40
6377 7350 1.405463 CTGGCATGTCGACTACTGCTA 59.595 52.381 26.03 22.10 34.56 3.49
6378 7351 1.405463 TGGCATGTCGACTACTGCTAG 59.595 52.381 26.03 8.30 34.56 3.42
6379 7352 1.676529 GGCATGTCGACTACTGCTAGA 59.323 52.381 26.03 4.08 34.56 2.43
6380 7353 2.541999 GGCATGTCGACTACTGCTAGAC 60.542 54.545 26.03 13.51 34.56 2.59
6381 7354 2.097629 GCATGTCGACTACTGCTAGACA 59.902 50.000 22.51 0.00 44.46 3.41
6385 7358 5.386958 TGTCGACTACTGCTAGACATTTT 57.613 39.130 17.92 0.00 36.98 1.82
6386 7359 5.399858 TGTCGACTACTGCTAGACATTTTC 58.600 41.667 17.92 0.00 36.98 2.29
6387 7360 4.496183 GTCGACTACTGCTAGACATTTTCG 59.504 45.833 8.70 0.00 32.57 3.46
6388 7361 3.240861 CGACTACTGCTAGACATTTTCGC 59.759 47.826 0.00 0.00 0.00 4.70
6389 7362 3.522553 ACTACTGCTAGACATTTTCGCC 58.477 45.455 0.00 0.00 0.00 5.54
6390 7363 2.770164 ACTGCTAGACATTTTCGCCT 57.230 45.000 0.00 0.00 0.00 5.52
6391 7364 2.622436 ACTGCTAGACATTTTCGCCTC 58.378 47.619 0.00 0.00 0.00 4.70
6392 7365 1.590238 CTGCTAGACATTTTCGCCTCG 59.410 52.381 0.00 0.00 0.00 4.63
6393 7366 0.931005 GCTAGACATTTTCGCCTCGG 59.069 55.000 0.00 0.00 0.00 4.63
6394 7367 1.739371 GCTAGACATTTTCGCCTCGGT 60.739 52.381 0.00 0.00 0.00 4.69
6395 7368 2.480759 GCTAGACATTTTCGCCTCGGTA 60.481 50.000 0.00 0.00 0.00 4.02
6396 7369 2.754946 AGACATTTTCGCCTCGGTAA 57.245 45.000 0.00 0.00 0.00 2.85
6397 7370 2.618053 AGACATTTTCGCCTCGGTAAG 58.382 47.619 0.00 0.00 0.00 2.34
6398 7371 2.232941 AGACATTTTCGCCTCGGTAAGA 59.767 45.455 0.00 0.00 0.00 2.10
6399 7372 2.344025 ACATTTTCGCCTCGGTAAGAC 58.656 47.619 0.00 0.00 0.00 3.01
6400 7373 2.289195 ACATTTTCGCCTCGGTAAGACA 60.289 45.455 0.00 0.00 0.00 3.41
6401 7374 2.754946 TTTTCGCCTCGGTAAGACAT 57.245 45.000 0.00 0.00 0.00 3.06
6402 7375 2.004583 TTTCGCCTCGGTAAGACATG 57.995 50.000 0.00 0.00 0.00 3.21
6403 7376 0.459585 TTCGCCTCGGTAAGACATGC 60.460 55.000 0.00 0.00 0.00 4.06
6407 7380 0.537188 CCTCGGTAAGACATGCTGGT 59.463 55.000 0.00 0.00 0.00 4.00
6438 7411 1.439679 CCAAGCTCGTGTTTCCTACC 58.560 55.000 0.00 0.00 0.00 3.18
6439 7412 1.439679 CAAGCTCGTGTTTCCTACCC 58.560 55.000 0.00 0.00 0.00 3.69
6442 7415 0.252197 GCTCGTGTTTCCTACCCCAT 59.748 55.000 0.00 0.00 0.00 4.00
6443 7416 1.742750 GCTCGTGTTTCCTACCCCATC 60.743 57.143 0.00 0.00 0.00 3.51
6444 7417 0.906775 TCGTGTTTCCTACCCCATCC 59.093 55.000 0.00 0.00 0.00 3.51
6445 7418 0.461339 CGTGTTTCCTACCCCATCCG 60.461 60.000 0.00 0.00 0.00 4.18
6446 7419 0.616891 GTGTTTCCTACCCCATCCGT 59.383 55.000 0.00 0.00 0.00 4.69
6447 7420 1.003928 GTGTTTCCTACCCCATCCGTT 59.996 52.381 0.00 0.00 0.00 4.44
6448 7421 1.706305 TGTTTCCTACCCCATCCGTTT 59.294 47.619 0.00 0.00 0.00 3.60
6449 7422 2.290450 TGTTTCCTACCCCATCCGTTTC 60.290 50.000 0.00 0.00 0.00 2.78
6450 7423 1.659022 TTCCTACCCCATCCGTTTCA 58.341 50.000 0.00 0.00 0.00 2.69
6451 7424 0.906775 TCCTACCCCATCCGTTTCAC 59.093 55.000 0.00 0.00 0.00 3.18
6452 7425 0.616371 CCTACCCCATCCGTTTCACA 59.384 55.000 0.00 0.00 0.00 3.58
6453 7426 1.003812 CCTACCCCATCCGTTTCACAA 59.996 52.381 0.00 0.00 0.00 3.33
6454 7427 2.356741 CCTACCCCATCCGTTTCACAAT 60.357 50.000 0.00 0.00 0.00 2.71
6455 7428 3.118186 CCTACCCCATCCGTTTCACAATA 60.118 47.826 0.00 0.00 0.00 1.90
6456 7429 2.718563 ACCCCATCCGTTTCACAATAC 58.281 47.619 0.00 0.00 0.00 1.89
6457 7430 2.040545 ACCCCATCCGTTTCACAATACA 59.959 45.455 0.00 0.00 0.00 2.29
6458 7431 3.287222 CCCCATCCGTTTCACAATACAT 58.713 45.455 0.00 0.00 0.00 2.29
6459 7432 3.066621 CCCCATCCGTTTCACAATACATG 59.933 47.826 0.00 0.00 0.00 3.21
6460 7433 3.489059 CCCATCCGTTTCACAATACATGC 60.489 47.826 0.00 0.00 0.00 4.06
6461 7434 3.489059 CCATCCGTTTCACAATACATGCC 60.489 47.826 0.00 0.00 0.00 4.40
6462 7435 3.066291 TCCGTTTCACAATACATGCCT 57.934 42.857 0.00 0.00 0.00 4.75
6463 7436 3.417101 TCCGTTTCACAATACATGCCTT 58.583 40.909 0.00 0.00 0.00 4.35
6464 7437 3.823873 TCCGTTTCACAATACATGCCTTT 59.176 39.130 0.00 0.00 0.00 3.11
6465 7438 4.083003 TCCGTTTCACAATACATGCCTTTC 60.083 41.667 0.00 0.00 0.00 2.62
6466 7439 4.320861 CCGTTTCACAATACATGCCTTTCA 60.321 41.667 0.00 0.00 0.00 2.69
6467 7440 5.401550 CGTTTCACAATACATGCCTTTCAT 58.598 37.500 0.00 0.00 35.31 2.57
6468 7441 5.863397 CGTTTCACAATACATGCCTTTCATT 59.137 36.000 0.00 0.00 31.79 2.57
6469 7442 6.365789 CGTTTCACAATACATGCCTTTCATTT 59.634 34.615 0.00 0.00 31.79 2.32
6470 7443 7.540400 CGTTTCACAATACATGCCTTTCATTTA 59.460 33.333 0.00 0.00 31.79 1.40
6471 7444 9.369904 GTTTCACAATACATGCCTTTCATTTAT 57.630 29.630 0.00 0.00 31.28 1.40
6472 7445 9.585099 TTTCACAATACATGCCTTTCATTTATC 57.415 29.630 0.00 0.00 29.29 1.75
6473 7446 8.291191 TCACAATACATGCCTTTCATTTATCA 57.709 30.769 0.00 0.00 29.29 2.15
6474 7447 8.747471 TCACAATACATGCCTTTCATTTATCAA 58.253 29.630 0.00 0.00 29.29 2.57
6475 7448 9.368674 CACAATACATGCCTTTCATTTATCAAA 57.631 29.630 0.00 0.00 29.29 2.69
6476 7449 9.941325 ACAATACATGCCTTTCATTTATCAAAA 57.059 25.926 0.00 0.00 29.29 2.44
6555 7528 8.532977 AATGAAAGTCAAATATTTTGGAACGG 57.467 30.769 0.00 0.00 0.00 4.44
6556 7529 7.278461 TGAAAGTCAAATATTTTGGAACGGA 57.722 32.000 0.00 0.00 0.00 4.69
6557 7530 7.367285 TGAAAGTCAAATATTTTGGAACGGAG 58.633 34.615 0.00 0.00 0.00 4.63
6558 7531 7.229707 TGAAAGTCAAATATTTTGGAACGGAGA 59.770 33.333 0.00 0.00 0.00 3.71
6559 7532 7.519032 AAGTCAAATATTTTGGAACGGAGAA 57.481 32.000 0.00 0.00 0.00 2.87
6560 7533 7.519032 AGTCAAATATTTTGGAACGGAGAAA 57.481 32.000 0.00 0.00 0.00 2.52
6561 7534 7.593825 AGTCAAATATTTTGGAACGGAGAAAG 58.406 34.615 0.00 0.00 0.00 2.62
6562 7535 7.230712 AGTCAAATATTTTGGAACGGAGAAAGT 59.769 33.333 0.00 0.00 0.00 2.66
6563 7536 8.508875 GTCAAATATTTTGGAACGGAGAAAGTA 58.491 33.333 0.00 0.00 0.00 2.24
6564 7537 8.508875 TCAAATATTTTGGAACGGAGAAAGTAC 58.491 33.333 0.00 0.00 0.00 2.73
6565 7538 8.512138 CAAATATTTTGGAACGGAGAAAGTACT 58.488 33.333 0.00 0.00 0.00 2.73
6566 7539 8.631480 AATATTTTGGAACGGAGAAAGTACTT 57.369 30.769 1.12 1.12 0.00 2.24
6567 7540 5.996669 TTTTGGAACGGAGAAAGTACTTC 57.003 39.130 8.95 2.91 0.00 3.01
6568 7541 4.675976 TTGGAACGGAGAAAGTACTTCA 57.324 40.909 8.95 0.00 36.40 3.02
6594 7567 2.492025 TGGATAAGGTCTGGGAGCAAT 58.508 47.619 0.00 0.00 31.89 3.56
6606 7579 1.453745 GAGCAATTCCGCCATCCCA 60.454 57.895 0.00 0.00 0.00 4.37
6628 7606 6.338146 CCAATCTACACGAATAGACTTGGAA 58.662 40.000 20.82 0.00 39.35 3.53
6662 7640 3.311966 GCAGCTGGAATTTGACTTTCAC 58.688 45.455 17.12 0.00 0.00 3.18
6673 7651 5.833406 TTTGACTTTCACACATGTCATGT 57.167 34.783 12.87 12.87 46.22 3.21
6674 7652 5.422666 TTGACTTTCACACATGTCATGTC 57.577 39.130 15.73 3.08 42.70 3.06
6675 7653 4.450053 TGACTTTCACACATGTCATGTCA 58.550 39.130 15.73 5.64 42.70 3.58
6676 7654 5.065235 TGACTTTCACACATGTCATGTCAT 58.935 37.500 15.73 4.54 42.70 3.06
6678 7656 3.835378 TTCACACATGTCATGTCATGC 57.165 42.857 26.29 4.35 46.15 4.06
6679 7657 3.062122 TCACACATGTCATGTCATGCT 57.938 42.857 26.29 14.50 46.15 3.79
6680 7658 3.004862 TCACACATGTCATGTCATGCTC 58.995 45.455 26.29 4.68 46.15 4.26
6687 7665 2.038820 TGTCATGTCATGCTCCAGTCAA 59.961 45.455 8.03 0.00 0.00 3.18
6719 7697 1.739562 CAGTCAAGCCAGCTCGTCC 60.740 63.158 0.00 0.00 0.00 4.79
6735 7713 1.071987 TCCTCTTGCCACTGTGCTG 59.928 57.895 1.29 0.00 0.00 4.41
6747 7725 0.042188 CTGTGCTGTTCCGTTCAACG 60.042 55.000 1.89 1.89 42.11 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.513517 CCAAATCCCAATCCCTGCATAT 58.486 45.455 0.00 0.00 0.00 1.78
41 42 2.548464 TTCCCAAATCCCAATCCCTG 57.452 50.000 0.00 0.00 0.00 4.45
66 801 1.092549 ACCCAATCCCATCAAACCCT 58.907 50.000 0.00 0.00 0.00 4.34
100 835 1.908299 GGGTTGGAGGGCTTTGGTG 60.908 63.158 0.00 0.00 0.00 4.17
105 840 1.368268 TTTGAGGGGTTGGAGGGCTT 61.368 55.000 0.00 0.00 0.00 4.35
106 841 1.778383 TTTGAGGGGTTGGAGGGCT 60.778 57.895 0.00 0.00 0.00 5.19
107 842 1.606601 GTTTGAGGGGTTGGAGGGC 60.607 63.158 0.00 0.00 0.00 5.19
111 846 0.476771 GTGAGGTTTGAGGGGTTGGA 59.523 55.000 0.00 0.00 0.00 3.53
130 870 6.083098 TGGTATTGGTCTTTTTCACACATG 57.917 37.500 0.00 0.00 0.00 3.21
152 892 1.535462 CGTCACCTAAGGCCTTGTTTG 59.465 52.381 28.77 19.80 0.00 2.93
166 906 5.804979 CACATCCAAATAAAAATCCGTCACC 59.195 40.000 0.00 0.00 0.00 4.02
206 946 1.879737 GCAGATTGCATGCACCCACA 61.880 55.000 22.58 5.51 44.26 4.17
239 979 2.284625 ACGGTGAGGGGATGCAGA 60.285 61.111 0.00 0.00 0.00 4.26
241 981 3.399181 GGACGGTGAGGGGATGCA 61.399 66.667 0.00 0.00 0.00 3.96
319 1060 1.818674 GTGCCACCCACAAAATCCTAG 59.181 52.381 0.00 0.00 44.06 3.02
320 1061 1.884497 CGTGCCACCCACAAAATCCTA 60.884 52.381 0.00 0.00 44.91 2.94
321 1062 1.178534 CGTGCCACCCACAAAATCCT 61.179 55.000 0.00 0.00 44.91 3.24
322 1063 1.288752 CGTGCCACCCACAAAATCC 59.711 57.895 0.00 0.00 44.91 3.01
323 1064 1.175983 TCCGTGCCACCCACAAAATC 61.176 55.000 0.00 0.00 44.91 2.17
324 1065 0.757188 TTCCGTGCCACCCACAAAAT 60.757 50.000 0.00 0.00 44.91 1.82
325 1066 1.379977 TTCCGTGCCACCCACAAAA 60.380 52.632 0.00 0.00 44.91 2.44
326 1067 1.826054 CTTCCGTGCCACCCACAAA 60.826 57.895 0.00 0.00 44.91 2.83
327 1068 2.203280 CTTCCGTGCCACCCACAA 60.203 61.111 0.00 0.00 44.91 3.33
328 1069 4.263572 CCTTCCGTGCCACCCACA 62.264 66.667 0.00 0.00 44.91 4.17
329 1070 2.798148 CTACCTTCCGTGCCACCCAC 62.798 65.000 0.00 0.00 41.15 4.61
330 1071 2.527123 TACCTTCCGTGCCACCCA 60.527 61.111 0.00 0.00 0.00 4.51
331 1072 2.267961 CTACCTTCCGTGCCACCC 59.732 66.667 0.00 0.00 0.00 4.61
332 1073 2.267961 CCTACCTTCCGTGCCACC 59.732 66.667 0.00 0.00 0.00 4.61
333 1074 2.120737 AACCCTACCTTCCGTGCCAC 62.121 60.000 0.00 0.00 0.00 5.01
334 1075 1.420532 AAACCCTACCTTCCGTGCCA 61.421 55.000 0.00 0.00 0.00 4.92
335 1076 0.675837 GAAACCCTACCTTCCGTGCC 60.676 60.000 0.00 0.00 0.00 5.01
336 1077 1.017701 CGAAACCCTACCTTCCGTGC 61.018 60.000 0.00 0.00 0.00 5.34
337 1078 0.604578 TCGAAACCCTACCTTCCGTG 59.395 55.000 0.00 0.00 0.00 4.94
338 1079 1.274447 CTTCGAAACCCTACCTTCCGT 59.726 52.381 0.00 0.00 0.00 4.69
339 1080 1.405121 CCTTCGAAACCCTACCTTCCG 60.405 57.143 0.00 0.00 0.00 4.30
340 1081 1.678123 GCCTTCGAAACCCTACCTTCC 60.678 57.143 0.00 0.00 0.00 3.46
341 1082 1.278413 AGCCTTCGAAACCCTACCTTC 59.722 52.381 0.00 0.00 0.00 3.46
342 1083 1.359168 AGCCTTCGAAACCCTACCTT 58.641 50.000 0.00 0.00 0.00 3.50
343 1084 1.003233 CAAGCCTTCGAAACCCTACCT 59.997 52.381 0.00 0.00 0.00 3.08
344 1085 1.002773 TCAAGCCTTCGAAACCCTACC 59.997 52.381 0.00 0.00 0.00 3.18
345 1086 2.347731 CTCAAGCCTTCGAAACCCTAC 58.652 52.381 0.00 0.00 0.00 3.18
362 1103 4.742012 ACCTAGTCTGAAAAGAGACCTCA 58.258 43.478 0.00 0.00 43.04 3.86
365 1106 6.289064 TGAAAACCTAGTCTGAAAAGAGACC 58.711 40.000 0.00 0.00 43.04 3.85
374 1115 2.354704 CCGCCATGAAAACCTAGTCTGA 60.355 50.000 0.00 0.00 0.00 3.27
378 1119 0.037590 TGCCGCCATGAAAACCTAGT 59.962 50.000 0.00 0.00 0.00 2.57
387 1128 1.865788 GCTTGAAGTTGCCGCCATGA 61.866 55.000 0.00 0.00 0.00 3.07
428 1169 3.450817 TCCTTCGTCATTGCTTCCAGATA 59.549 43.478 0.00 0.00 0.00 1.98
444 1185 0.608640 AGTGTGGCCTAACTCCTTCG 59.391 55.000 3.32 0.00 0.00 3.79
478 1219 2.603560 GCCTCCTCAAAATTACGAGTCG 59.396 50.000 11.85 11.85 0.00 4.18
502 1246 5.352284 CGATACATTGTTCAGCCTTCTACT 58.648 41.667 0.00 0.00 0.00 2.57
522 1266 1.542030 CTCGAGCTATAGCCAACCGAT 59.458 52.381 21.17 0.11 43.38 4.18
569 1313 4.706842 ACCTTGTCTTGTACAACCAGAT 57.293 40.909 3.59 0.00 43.22 2.90
594 1338 7.201427 CGCATATTTTGGTGATGTTCGAAATTT 60.201 33.333 0.00 0.00 31.59 1.82
602 1346 7.903995 AATTTTCGCATATTTTGGTGATGTT 57.096 28.000 0.00 0.00 0.00 2.71
776 1522 6.931281 CCATCTCATTCGTGTACCATAAATCT 59.069 38.462 0.00 0.00 0.00 2.40
800 1590 2.607442 AATTTGGTGCCCAGGCCC 60.607 61.111 6.14 7.68 41.09 5.80
804 1594 0.240945 GACACGAATTTGGTGCCCAG 59.759 55.000 10.98 0.00 38.98 4.45
841 1631 2.304761 TCGGCATGTTTTACTCTCCCTT 59.695 45.455 0.00 0.00 0.00 3.95
947 1737 7.954666 TTTTTGTAGAGGGAATGGATTAAGG 57.045 36.000 0.00 0.00 0.00 2.69
985 1804 1.764854 GGGTGGAAGGGGAGCGATA 60.765 63.158 0.00 0.00 0.00 2.92
1275 2097 3.622060 GAGCTTGCCGCCCTTGGTA 62.622 63.158 0.00 0.00 40.39 3.25
1611 2433 4.457496 ATGAGGCGCACACCGAGG 62.457 66.667 10.83 0.00 40.02 4.63
1770 2592 0.107654 GGACAATCAGGGGGAACTCG 60.108 60.000 0.00 0.00 34.16 4.18
1791 2613 2.419057 ACCAAGTGTGAAAGCAGGC 58.581 52.632 0.00 0.00 0.00 4.85
1830 2652 3.195661 CTCAAACTCGGCCCTGTTATAC 58.804 50.000 8.23 0.00 0.00 1.47
1932 2754 2.285773 ACGCATCACCTCCAGCTCA 61.286 57.895 0.00 0.00 0.00 4.26
1959 2781 2.357009 GCAGATGATGACCACATTGTCC 59.643 50.000 0.00 0.00 36.82 4.02
2145 2967 1.453197 CCCATCCGCAGGGTTAACC 60.453 63.158 16.85 16.85 39.56 2.85
2196 3018 1.736681 GCAAGAGCTGATGACCTTGAC 59.263 52.381 13.21 3.13 38.52 3.18
2360 3182 5.544650 AGGTTGCAAAGAGATTCAAAATGG 58.455 37.500 0.00 0.00 0.00 3.16
3082 3910 7.912250 CCTCCGAATGATGAAAAACATAAAGAG 59.088 37.037 0.00 0.00 39.56 2.85
3524 4352 5.300752 TCTTTTGAGAGCTGGTCTAAGTTG 58.699 41.667 9.69 1.41 34.71 3.16
3878 4706 5.337788 TGGCCATAAAAAGTAAGGTGGAAT 58.662 37.500 0.00 0.00 0.00 3.01
3913 4741 7.128331 CAGAATGTAATTGCCTATTCAACTCG 58.872 38.462 8.58 0.00 36.07 4.18
3919 4747 7.094205 CCCATACCAGAATGTAATTGCCTATTC 60.094 40.741 0.00 0.00 36.07 1.75
3973 4801 7.866729 TGACAAAGAAATTTATTACGTCAGCA 58.133 30.769 19.12 5.69 0.00 4.41
4131 4959 6.237901 TCCATACTGCACAATTATACCATCC 58.762 40.000 0.00 0.00 0.00 3.51
4719 5547 1.728971 CCACAGACATTGAGACGCTTC 59.271 52.381 0.00 0.00 0.00 3.86
5229 6057 2.009681 TCAGAACTGGCTCCACTGTA 57.990 50.000 1.93 0.00 0.00 2.74
5230 6058 1.071385 CTTCAGAACTGGCTCCACTGT 59.929 52.381 1.93 0.00 0.00 3.55
5325 6153 1.215382 CGAGTCAAGGTCATCGCCA 59.785 57.895 0.00 0.00 0.00 5.69
5421 6249 0.392863 TCTTGATGGCGTCCATGGTG 60.393 55.000 12.58 7.02 45.26 4.17
5496 6324 2.936928 CAGCTTCTGTGGTGCATCA 58.063 52.632 0.00 0.00 0.00 3.07
5551 6379 1.382522 GAAAAGGGCGAGCATGATGA 58.617 50.000 0.00 0.00 0.00 2.92
5552 6380 0.383231 GGAAAAGGGCGAGCATGATG 59.617 55.000 0.00 0.00 0.00 3.07
5553 6381 0.753111 GGGAAAAGGGCGAGCATGAT 60.753 55.000 0.00 0.00 0.00 2.45
5588 6416 6.390721 GCGCAGGATTCTAGTTCATATTAGA 58.609 40.000 0.30 0.00 0.00 2.10
5589 6417 5.578727 GGCGCAGGATTCTAGTTCATATTAG 59.421 44.000 10.83 0.00 0.00 1.73
5617 6452 6.710744 CAGTAGGTGTGACTAACAAAATCCTT 59.289 38.462 0.00 0.00 41.57 3.36
5772 6647 1.475280 CACCATCAGATTGCAACTGGG 59.525 52.381 21.19 18.30 36.22 4.45
5904 6780 4.986467 GGTAACCAGGAGCATGGG 57.014 61.111 6.11 0.00 45.25 4.00
5923 6804 5.774690 TGCAAGAGAACCTGATAAAAACCAT 59.225 36.000 0.00 0.00 0.00 3.55
5924 6805 5.136828 TGCAAGAGAACCTGATAAAAACCA 58.863 37.500 0.00 0.00 0.00 3.67
5930 6811 5.376625 ACAAACTGCAAGAGAACCTGATAA 58.623 37.500 0.00 0.00 37.43 1.75
6034 6915 3.127376 CAGAATGATCATTTGCCGACACA 59.873 43.478 21.57 0.00 39.69 3.72
6099 7020 2.807967 CACATCAACCATCTCAACGTGT 59.192 45.455 0.00 0.00 0.00 4.49
6120 7045 1.961180 CTGTCCCCCGTCCTCACATC 61.961 65.000 0.00 0.00 0.00 3.06
6175 7108 1.064825 ACTCCACCTACACCCTTTGG 58.935 55.000 0.00 0.00 37.80 3.28
6198 7131 1.291877 CCCGTCGGCAAAGACTTCTG 61.292 60.000 5.50 0.00 38.90 3.02
6235 7168 1.945387 CATGTGAATCCGCAGCTACT 58.055 50.000 0.00 0.00 36.09 2.57
6236 7169 0.305922 GCATGTGAATCCGCAGCTAC 59.694 55.000 0.00 0.00 36.09 3.58
6237 7170 1.153597 CGCATGTGAATCCGCAGCTA 61.154 55.000 0.00 0.00 36.09 3.32
6238 7171 2.466982 CGCATGTGAATCCGCAGCT 61.467 57.895 0.00 0.00 36.09 4.24
6293 7235 5.047306 TCGAAGGCAAATATGTATCTCCGAT 60.047 40.000 0.00 0.00 0.00 4.18
6303 7245 9.787532 TTCTTCTAATTTTCGAAGGCAAATATG 57.212 29.630 0.00 0.00 37.73 1.78
6306 7248 8.141268 TGTTTCTTCTAATTTTCGAAGGCAAAT 58.859 29.630 0.00 0.00 37.73 2.32
6328 7301 4.943705 AGCGAGACATCCATAAACATGTTT 59.056 37.500 25.99 25.99 33.22 2.83
6361 7334 4.560136 ATGTCTAGCAGTAGTCGACATG 57.440 45.455 19.50 14.06 42.03 3.21
6365 7338 4.659088 CGAAAATGTCTAGCAGTAGTCGA 58.341 43.478 11.49 0.00 35.94 4.20
6373 7346 1.640428 CGAGGCGAAAATGTCTAGCA 58.360 50.000 0.00 0.00 0.00 3.49
6374 7347 0.931005 CCGAGGCGAAAATGTCTAGC 59.069 55.000 0.00 0.00 0.00 3.42
6375 7348 2.295253 ACCGAGGCGAAAATGTCTAG 57.705 50.000 0.00 0.00 0.00 2.43
6377 7350 2.232941 TCTTACCGAGGCGAAAATGTCT 59.767 45.455 0.00 0.00 0.00 3.41
6378 7351 2.347755 GTCTTACCGAGGCGAAAATGTC 59.652 50.000 0.00 0.00 0.00 3.06
6379 7352 2.289195 TGTCTTACCGAGGCGAAAATGT 60.289 45.455 0.00 0.00 30.55 2.71
6380 7353 2.343101 TGTCTTACCGAGGCGAAAATG 58.657 47.619 0.00 0.00 30.55 2.32
6381 7354 2.754946 TGTCTTACCGAGGCGAAAAT 57.245 45.000 0.00 0.00 30.55 1.82
6385 7358 1.141019 GCATGTCTTACCGAGGCGA 59.859 57.895 0.00 0.00 30.55 5.54
6386 7359 1.141881 AGCATGTCTTACCGAGGCG 59.858 57.895 0.00 0.00 30.55 5.52
6387 7360 0.811616 CCAGCATGTCTTACCGAGGC 60.812 60.000 0.00 0.00 0.00 4.70
6388 7361 0.537188 ACCAGCATGTCTTACCGAGG 59.463 55.000 0.00 0.00 0.00 4.63
6389 7362 2.427453 AGTACCAGCATGTCTTACCGAG 59.573 50.000 0.00 0.00 0.00 4.63
6390 7363 2.165641 CAGTACCAGCATGTCTTACCGA 59.834 50.000 0.00 0.00 0.00 4.69
6391 7364 2.540515 CAGTACCAGCATGTCTTACCG 58.459 52.381 0.00 0.00 0.00 4.02
6392 7365 2.500098 TCCAGTACCAGCATGTCTTACC 59.500 50.000 0.00 0.00 0.00 2.85
6393 7366 3.887621 TCCAGTACCAGCATGTCTTAC 57.112 47.619 0.00 0.00 0.00 2.34
6394 7367 3.838317 ACTTCCAGTACCAGCATGTCTTA 59.162 43.478 0.00 0.00 0.00 2.10
6395 7368 2.639839 ACTTCCAGTACCAGCATGTCTT 59.360 45.455 0.00 0.00 0.00 3.01
6396 7369 2.260822 ACTTCCAGTACCAGCATGTCT 58.739 47.619 0.00 0.00 0.00 3.41
6397 7370 2.770164 ACTTCCAGTACCAGCATGTC 57.230 50.000 0.00 0.00 0.00 3.06
6398 7371 2.093447 GCTACTTCCAGTACCAGCATGT 60.093 50.000 0.00 0.00 29.97 3.21
6399 7372 2.555199 GCTACTTCCAGTACCAGCATG 58.445 52.381 0.00 0.00 29.97 4.06
6400 7373 1.486726 GGCTACTTCCAGTACCAGCAT 59.513 52.381 0.00 0.00 30.86 3.79
6401 7374 0.902531 GGCTACTTCCAGTACCAGCA 59.097 55.000 0.00 0.00 30.86 4.41
6402 7375 0.902531 TGGCTACTTCCAGTACCAGC 59.097 55.000 0.00 0.00 31.58 4.85
6403 7376 2.678190 GCTTGGCTACTTCCAGTACCAG 60.678 54.545 0.00 0.00 35.17 4.00
6407 7380 1.476891 CGAGCTTGGCTACTTCCAGTA 59.523 52.381 0.00 0.00 39.88 2.74
6438 7411 3.489059 GCATGTATTGTGAAACGGATGGG 60.489 47.826 0.00 0.00 42.39 4.00
6439 7412 3.489059 GGCATGTATTGTGAAACGGATGG 60.489 47.826 0.00 0.00 42.39 3.51
6442 7415 3.066291 AGGCATGTATTGTGAAACGGA 57.934 42.857 0.00 0.00 42.39 4.69
6443 7416 3.848272 AAGGCATGTATTGTGAAACGG 57.152 42.857 0.00 0.00 42.39 4.44
6444 7417 4.793071 TGAAAGGCATGTATTGTGAAACG 58.207 39.130 0.00 0.00 42.39 3.60
6445 7418 7.656707 AAATGAAAGGCATGTATTGTGAAAC 57.343 32.000 0.00 0.00 37.28 2.78
6446 7419 9.585099 GATAAATGAAAGGCATGTATTGTGAAA 57.415 29.630 0.00 0.00 37.50 2.69
6447 7420 8.747471 TGATAAATGAAAGGCATGTATTGTGAA 58.253 29.630 0.00 0.00 37.50 3.18
6448 7421 8.291191 TGATAAATGAAAGGCATGTATTGTGA 57.709 30.769 0.00 0.00 37.50 3.58
6449 7422 8.929827 TTGATAAATGAAAGGCATGTATTGTG 57.070 30.769 0.00 0.00 37.50 3.33
6450 7423 9.941325 TTTTGATAAATGAAAGGCATGTATTGT 57.059 25.926 0.00 0.00 37.50 2.71
6529 7502 8.987890 CCGTTCCAAAATATTTGACTTTCATTT 58.012 29.630 0.39 0.00 0.00 2.32
6530 7503 8.364142 TCCGTTCCAAAATATTTGACTTTCATT 58.636 29.630 0.39 0.00 0.00 2.57
6531 7504 7.891561 TCCGTTCCAAAATATTTGACTTTCAT 58.108 30.769 0.39 0.00 0.00 2.57
6532 7505 7.229707 TCTCCGTTCCAAAATATTTGACTTTCA 59.770 33.333 0.39 0.00 0.00 2.69
6533 7506 7.590279 TCTCCGTTCCAAAATATTTGACTTTC 58.410 34.615 0.39 0.00 0.00 2.62
6534 7507 7.519032 TCTCCGTTCCAAAATATTTGACTTT 57.481 32.000 0.39 0.00 0.00 2.66
6535 7508 7.519032 TTCTCCGTTCCAAAATATTTGACTT 57.481 32.000 0.39 0.00 0.00 3.01
6536 7509 7.230712 ACTTTCTCCGTTCCAAAATATTTGACT 59.769 33.333 0.39 0.00 0.00 3.41
6537 7510 7.368059 ACTTTCTCCGTTCCAAAATATTTGAC 58.632 34.615 0.39 0.00 0.00 3.18
6538 7511 7.519032 ACTTTCTCCGTTCCAAAATATTTGA 57.481 32.000 0.39 0.00 0.00 2.69
6539 7512 8.512138 AGTACTTTCTCCGTTCCAAAATATTTG 58.488 33.333 0.39 0.00 0.00 2.32
6540 7513 8.631480 AGTACTTTCTCCGTTCCAAAATATTT 57.369 30.769 0.00 0.00 0.00 1.40
6541 7514 8.631480 AAGTACTTTCTCCGTTCCAAAATATT 57.369 30.769 1.12 0.00 0.00 1.28
6542 7515 7.881232 TGAAGTACTTTCTCCGTTCCAAAATAT 59.119 33.333 10.02 0.00 36.71 1.28
6543 7516 7.218614 TGAAGTACTTTCTCCGTTCCAAAATA 58.781 34.615 10.02 0.00 36.71 1.40
6544 7517 6.059484 TGAAGTACTTTCTCCGTTCCAAAAT 58.941 36.000 10.02 0.00 36.71 1.82
6545 7518 5.430007 TGAAGTACTTTCTCCGTTCCAAAA 58.570 37.500 10.02 0.00 36.71 2.44
6546 7519 5.026038 TGAAGTACTTTCTCCGTTCCAAA 57.974 39.130 10.02 0.00 36.71 3.28
6547 7520 4.675976 TGAAGTACTTTCTCCGTTCCAA 57.324 40.909 10.02 0.00 36.71 3.53
6548 7521 4.675976 TTGAAGTACTTTCTCCGTTCCA 57.324 40.909 10.02 0.00 36.71 3.53
6549 7522 4.451435 CCTTTGAAGTACTTTCTCCGTTCC 59.549 45.833 10.02 0.00 36.71 3.62
6550 7523 5.295152 TCCTTTGAAGTACTTTCTCCGTTC 58.705 41.667 10.02 0.00 36.71 3.95
6551 7524 5.286267 TCCTTTGAAGTACTTTCTCCGTT 57.714 39.130 10.02 0.00 36.71 4.44
6552 7525 4.950205 TCCTTTGAAGTACTTTCTCCGT 57.050 40.909 10.02 0.00 36.71 4.69
6553 7526 4.631813 CCATCCTTTGAAGTACTTTCTCCG 59.368 45.833 10.02 0.00 36.71 4.63
6554 7527 5.805728 TCCATCCTTTGAAGTACTTTCTCC 58.194 41.667 10.02 0.00 36.71 3.71
6555 7528 9.103861 CTTATCCATCCTTTGAAGTACTTTCTC 57.896 37.037 10.02 0.00 36.71 2.87
6556 7529 8.049721 CCTTATCCATCCTTTGAAGTACTTTCT 58.950 37.037 10.02 0.00 36.71 2.52
6557 7530 7.829706 ACCTTATCCATCCTTTGAAGTACTTTC 59.170 37.037 10.02 4.01 36.29 2.62
6558 7531 7.699878 ACCTTATCCATCCTTTGAAGTACTTT 58.300 34.615 10.02 0.00 0.00 2.66
6559 7532 7.182930 AGACCTTATCCATCCTTTGAAGTACTT 59.817 37.037 8.13 8.13 0.00 2.24
6560 7533 6.674419 AGACCTTATCCATCCTTTGAAGTACT 59.326 38.462 0.00 0.00 0.00 2.73
6561 7534 6.763610 CAGACCTTATCCATCCTTTGAAGTAC 59.236 42.308 0.00 0.00 0.00 2.73
6562 7535 6.126768 CCAGACCTTATCCATCCTTTGAAGTA 60.127 42.308 0.00 0.00 0.00 2.24
6563 7536 5.339530 CCAGACCTTATCCATCCTTTGAAGT 60.340 44.000 0.00 0.00 0.00 3.01
6564 7537 5.128919 CCAGACCTTATCCATCCTTTGAAG 58.871 45.833 0.00 0.00 0.00 3.02
6565 7538 4.079787 CCCAGACCTTATCCATCCTTTGAA 60.080 45.833 0.00 0.00 0.00 2.69
6566 7539 3.459598 CCCAGACCTTATCCATCCTTTGA 59.540 47.826 0.00 0.00 0.00 2.69
6567 7540 3.459598 TCCCAGACCTTATCCATCCTTTG 59.540 47.826 0.00 0.00 0.00 2.77
6568 7541 3.718956 CTCCCAGACCTTATCCATCCTTT 59.281 47.826 0.00 0.00 0.00 3.11
6594 7567 1.134220 GTGTAGATTGGGATGGCGGAA 60.134 52.381 0.00 0.00 0.00 4.30
6601 7574 6.463049 CCAAGTCTATTCGTGTAGATTGGGAT 60.463 42.308 18.83 0.00 34.85 3.85
6602 7575 5.163447 CCAAGTCTATTCGTGTAGATTGGGA 60.163 44.000 18.83 0.00 34.85 4.37
6606 7579 7.782049 TCATTCCAAGTCTATTCGTGTAGATT 58.218 34.615 3.56 0.00 33.58 2.40
6662 7640 2.354821 CTGGAGCATGACATGACATGTG 59.645 50.000 29.81 12.39 46.25 3.21
6673 7651 3.819368 TGAACTTTTGACTGGAGCATGA 58.181 40.909 0.00 0.00 0.00 3.07
6674 7652 4.572985 TTGAACTTTTGACTGGAGCATG 57.427 40.909 0.00 0.00 0.00 4.06
6675 7653 5.596836 TTTTGAACTTTTGACTGGAGCAT 57.403 34.783 0.00 0.00 0.00 3.79
6676 7654 5.596836 ATTTTGAACTTTTGACTGGAGCA 57.403 34.783 0.00 0.00 0.00 4.26
6677 7655 5.631096 GCTATTTTGAACTTTTGACTGGAGC 59.369 40.000 0.00 0.00 0.00 4.70
6678 7656 6.738114 TGCTATTTTGAACTTTTGACTGGAG 58.262 36.000 0.00 0.00 0.00 3.86
6679 7657 6.321181 ACTGCTATTTTGAACTTTTGACTGGA 59.679 34.615 0.00 0.00 0.00 3.86
6680 7658 6.507023 ACTGCTATTTTGAACTTTTGACTGG 58.493 36.000 0.00 0.00 0.00 4.00
6687 7665 5.068987 TGGCTTGACTGCTATTTTGAACTTT 59.931 36.000 0.00 0.00 0.00 2.66
6719 7697 0.590195 GAACAGCACAGTGGCAAGAG 59.410 55.000 1.84 0.00 35.83 2.85


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

AutoCloner maintained by Alex Coulton.