Multiple sequence alignment - TraesCS7A01G233400

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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 TraesCS7A01G233400 chr7A 100.000 5571 0 0 1 5571 205167433 205173003 0.000000e+00 10288.0
1 TraesCS7A01G233400 chr7B 94.499 4981 205 31 434 5383 159138234 159143176 0.000000e+00 7616.0
2 TraesCS7A01G233400 chr7B 89.919 248 10 3 1 247 159137347 159137580 7.010000e-79 305.0
3 TraesCS7A01G233400 chr7B 87.864 206 24 1 5367 5571 159145246 159145451 2.010000e-59 241.0
4 TraesCS7A01G233400 chr7B 95.238 105 5 0 325 429 425252176 425252072 3.450000e-37 167.0
5 TraesCS7A01G233400 chr7B 92.035 113 8 1 331 443 562993065 562993176 2.080000e-34 158.0
6 TraesCS7A01G233400 chr7D 96.247 2718 78 6 2105 4812 195310529 195313232 0.000000e+00 4433.0
7 TraesCS7A01G233400 chr7D 90.572 1697 120 16 434 2101 195308798 195310483 0.000000e+00 2211.0
8 TraesCS7A01G233400 chr7D 82.418 273 15 9 1 254 195308022 195308280 2.030000e-49 207.0
9 TraesCS7A01G233400 chr2A 96.190 105 3 1 332 435 68155824 68155928 2.670000e-38 171.0
10 TraesCS7A01G233400 chr2A 96.190 105 3 1 332 435 728602663 728602559 2.670000e-38 171.0
11 TraesCS7A01G233400 chr6B 97.000 100 3 0 330 429 710231644 710231545 9.600000e-38 169.0
12 TraesCS7A01G233400 chr2D 96.970 99 3 0 331 429 445894981 445894883 3.450000e-37 167.0
13 TraesCS7A01G233400 chr3D 93.636 110 6 1 332 441 292887841 292887733 4.470000e-36 163.0
14 TraesCS7A01G233400 chr3D 93.458 107 7 0 324 430 138076232 138076338 5.780000e-35 159.0
15 TraesCS7A01G233400 chr1A 95.146 103 5 0 329 431 58289819 58289717 4.470000e-36 163.0
16 TraesCS7A01G233400 chr4A 100.000 43 0 0 2491 2533 695036783 695036741 4.630000e-11 80.5


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 TraesCS7A01G233400 chr7A 205167433 205173003 5570 False 10288.000000 10288 100.000000 1 5571 1 chr7A.!!$F1 5570
1 TraesCS7A01G233400 chr7B 159137347 159145451 8104 False 2720.666667 7616 90.760667 1 5571 3 chr7B.!!$F2 5570
2 TraesCS7A01G233400 chr7D 195308022 195313232 5210 False 2283.666667 4433 89.745667 1 4812 3 chr7D.!!$F1 4811

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
345 960 0.324091 TGTTCTACTCCCTCCGTCCC 60.324 60.000 0.0 0.0 0.00 4.46 F
347 962 0.410663 TTCTACTCCCTCCGTCCCAA 59.589 55.000 0.0 0.0 0.00 4.12 F
863 1485 0.442699 GCACTTGCAGCTTACGTACC 59.557 55.000 0.0 0.0 41.59 3.34 F
903 1533 1.471287 TGCTGAAGATGCTGATTGTGC 59.529 47.619 0.0 0.0 0.00 4.57 F
2685 3382 1.536766 TGCAAAGAATGGAACTGCGAG 59.463 47.619 0.0 0.0 0.00 5.03 F
3872 4571 0.041839 GCGGCTGATTGTATCGCTTG 60.042 55.000 0.0 0.0 42.62 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1208 1848 1.305802 TACCGCAGATGTCCCCAGT 60.306 57.895 0.00 0.00 0.00 4.00 R
1910 2558 1.335324 GCCTGAAATGTGTGTGCTCAC 60.335 52.381 11.94 11.94 44.08 3.51 R
2634 3331 1.136336 GCTTGCTGTTCTTTCCGTACG 60.136 52.381 8.69 8.69 0.00 3.67 R
2730 3427 3.006110 CACACCTGGAATGCATTTTCTGT 59.994 43.478 14.33 8.13 0.00 3.41 R
4342 5041 0.773644 ACAGATCAACAAGGGCAGGT 59.226 50.000 0.00 0.00 0.00 4.00 R
5257 5957 0.034186 GTGCCATCCCATGAACCAGA 60.034 55.000 0.00 0.00 0.00 3.86 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
34 35 3.140325 TCTCTTGGTTTTAGCCCACAG 57.860 47.619 0.00 0.00 0.00 3.66
89 91 6.158598 TCATTGTTTTTGCTTAATCTCTGGC 58.841 36.000 0.00 0.00 0.00 4.85
90 92 4.519540 TGTTTTTGCTTAATCTCTGGCC 57.480 40.909 0.00 0.00 0.00 5.36
91 93 4.151883 TGTTTTTGCTTAATCTCTGGCCT 58.848 39.130 3.32 0.00 0.00 5.19
92 94 4.218417 TGTTTTTGCTTAATCTCTGGCCTC 59.782 41.667 3.32 0.00 0.00 4.70
93 95 4.307032 TTTTGCTTAATCTCTGGCCTCT 57.693 40.909 3.32 0.00 0.00 3.69
94 96 2.996249 TGCTTAATCTCTGGCCTCTG 57.004 50.000 3.32 0.00 0.00 3.35
95 97 1.487976 TGCTTAATCTCTGGCCTCTGG 59.512 52.381 3.32 0.00 0.00 3.86
140 142 1.569479 GCTGGTTGCTTGTCTCCGTC 61.569 60.000 0.00 0.00 38.95 4.79
160 162 5.107989 CCGTCTGATCCAACGAATTAATACG 60.108 44.000 16.06 0.00 41.29 3.06
249 269 7.684937 TTTGTACCTGAGTTCTCTACTACTC 57.315 40.000 0.00 0.00 40.89 2.59
254 274 4.457466 CTGAGTTCTCTACTACTCCCTCC 58.543 52.174 0.00 0.00 40.00 4.30
255 275 3.850774 TGAGTTCTCTACTACTCCCTCCA 59.149 47.826 0.00 0.00 40.00 3.86
258 278 5.451354 AGTTCTCTACTACTCCCTCCATTC 58.549 45.833 0.00 0.00 34.56 2.67
259 279 5.044030 AGTTCTCTACTACTCCCTCCATTCA 60.044 44.000 0.00 0.00 34.56 2.57
260 280 4.794334 TCTCTACTACTCCCTCCATTCAC 58.206 47.826 0.00 0.00 0.00 3.18
264 284 4.559862 ACTACTCCCTCCATTCACAAAG 57.440 45.455 0.00 0.00 0.00 2.77
265 285 3.910627 ACTACTCCCTCCATTCACAAAGT 59.089 43.478 0.00 0.00 0.00 2.66
267 287 4.184649 ACTCCCTCCATTCACAAAGTTT 57.815 40.909 0.00 0.00 0.00 2.66
268 288 4.546674 ACTCCCTCCATTCACAAAGTTTT 58.453 39.130 0.00 0.00 0.00 2.43
269 289 5.701224 ACTCCCTCCATTCACAAAGTTTTA 58.299 37.500 0.00 0.00 0.00 1.52
270 290 5.535030 ACTCCCTCCATTCACAAAGTTTTAC 59.465 40.000 0.00 0.00 0.00 2.01
271 291 5.450453 TCCCTCCATTCACAAAGTTTTACA 58.550 37.500 0.00 0.00 0.00 2.41
272 292 5.894393 TCCCTCCATTCACAAAGTTTTACAA 59.106 36.000 0.00 0.00 0.00 2.41
273 293 6.040391 TCCCTCCATTCACAAAGTTTTACAAG 59.960 38.462 0.00 0.00 0.00 3.16
274 294 6.215845 CCTCCATTCACAAAGTTTTACAAGG 58.784 40.000 0.00 0.00 0.00 3.61
276 296 7.013846 CCTCCATTCACAAAGTTTTACAAGGTA 59.986 37.037 0.00 0.00 0.00 3.08
277 297 7.708998 TCCATTCACAAAGTTTTACAAGGTAC 58.291 34.615 0.00 0.00 0.00 3.34
278 298 7.339721 TCCATTCACAAAGTTTTACAAGGTACA 59.660 33.333 0.00 0.00 0.00 2.90
279 299 8.141268 CCATTCACAAAGTTTTACAAGGTACAT 58.859 33.333 0.00 0.00 0.00 2.29
337 952 6.980416 AGAAGGTACATATGTTCTACTCCC 57.020 41.667 14.77 3.51 0.00 4.30
338 953 6.684538 AGAAGGTACATATGTTCTACTCCCT 58.315 40.000 14.77 5.62 0.00 4.20
339 954 6.778559 AGAAGGTACATATGTTCTACTCCCTC 59.221 42.308 14.77 5.94 0.00 4.30
340 955 5.395611 AGGTACATATGTTCTACTCCCTCC 58.604 45.833 14.77 2.37 0.00 4.30
341 956 4.217983 GGTACATATGTTCTACTCCCTCCG 59.782 50.000 14.77 0.00 0.00 4.63
342 957 3.912248 ACATATGTTCTACTCCCTCCGT 58.088 45.455 1.41 0.00 0.00 4.69
343 958 3.890147 ACATATGTTCTACTCCCTCCGTC 59.110 47.826 1.41 0.00 0.00 4.79
344 959 1.777941 ATGTTCTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
345 960 0.324091 TGTTCTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
346 961 0.324091 GTTCTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
347 962 0.410663 TTCTACTCCCTCCGTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
348 963 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
349 964 1.203212 TCTACTCCCTCCGTCCCAAAA 60.203 52.381 0.00 0.00 0.00 2.44
350 965 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
351 966 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
352 967 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
353 968 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
354 969 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
355 970 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
356 971 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
357 972 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
358 973 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
359 974 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
360 975 5.484715 CTCCGTCCCAAAATAAGTGTCTTA 58.515 41.667 0.00 0.00 0.00 2.10
361 976 5.867330 TCCGTCCCAAAATAAGTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
362 977 5.702209 TCCGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
363 978 5.106436 CCGTCCCAAAATAAGTGTCTTAACC 60.106 44.000 0.00 0.00 0.00 2.85
364 979 5.704053 CGTCCCAAAATAAGTGTCTTAACCT 59.296 40.000 0.00 0.00 0.00 3.50
365 980 6.206048 CGTCCCAAAATAAGTGTCTTAACCTT 59.794 38.462 0.00 0.00 0.00 3.50
366 981 7.388500 CGTCCCAAAATAAGTGTCTTAACCTTA 59.612 37.037 0.00 0.00 0.00 2.69
367 982 8.727910 GTCCCAAAATAAGTGTCTTAACCTTAG 58.272 37.037 0.00 0.00 0.00 2.18
368 983 8.442374 TCCCAAAATAAGTGTCTTAACCTTAGT 58.558 33.333 0.00 0.00 0.00 2.24
369 984 9.729281 CCCAAAATAAGTGTCTTAACCTTAGTA 57.271 33.333 0.00 0.00 0.00 1.82
416 1031 8.934023 ACAAAGTTGAGATACTTATTTTGGGA 57.066 30.769 0.00 0.00 37.37 4.37
417 1032 8.793592 ACAAAGTTGAGATACTTATTTTGGGAC 58.206 33.333 0.00 0.00 37.37 4.46
418 1033 7.611213 AAGTTGAGATACTTATTTTGGGACG 57.389 36.000 0.00 0.00 36.62 4.79
419 1034 6.113411 AGTTGAGATACTTATTTTGGGACGG 58.887 40.000 0.00 0.00 0.00 4.79
420 1035 5.943349 TGAGATACTTATTTTGGGACGGA 57.057 39.130 0.00 0.00 0.00 4.69
421 1036 5.914033 TGAGATACTTATTTTGGGACGGAG 58.086 41.667 0.00 0.00 0.00 4.63
422 1037 5.163343 TGAGATACTTATTTTGGGACGGAGG 60.163 44.000 0.00 0.00 0.00 4.30
423 1038 2.801077 ACTTATTTTGGGACGGAGGG 57.199 50.000 0.00 0.00 0.00 4.30
424 1039 2.271777 ACTTATTTTGGGACGGAGGGA 58.728 47.619 0.00 0.00 0.00 4.20
425 1040 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
426 1041 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
427 1042 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
428 1043 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
429 1044 1.492764 TTTGGGACGGAGGGAGTATC 58.507 55.000 0.00 0.00 0.00 2.24
430 1045 0.635009 TTGGGACGGAGGGAGTATCT 59.365 55.000 0.00 0.00 33.73 1.98
431 1046 1.526315 TGGGACGGAGGGAGTATCTA 58.474 55.000 0.00 0.00 33.73 1.98
432 1047 1.854939 TGGGACGGAGGGAGTATCTAA 59.145 52.381 0.00 0.00 33.73 2.10
443 1058 7.014422 CGGAGGGAGTATCTAATAAGACAACTT 59.986 40.741 0.00 0.00 33.52 2.66
481 1096 9.816354 ATTTTATTTCGGATATGGTCAAAAAGG 57.184 29.630 0.00 0.00 0.00 3.11
482 1097 5.852282 ATTTCGGATATGGTCAAAAAGGG 57.148 39.130 0.00 0.00 0.00 3.95
494 1110 6.310941 TGGTCAAAAAGGGATGTATTCAAGA 58.689 36.000 0.00 0.00 0.00 3.02
518 1134 7.965107 AGAATTTTTCTTACATGCGCTAGAAAG 59.035 33.333 9.73 7.84 37.75 2.62
628 1245 4.987408 TGGCATTTCACCATGTATGAAG 57.013 40.909 9.01 2.30 37.38 3.02
629 1246 4.598022 TGGCATTTCACCATGTATGAAGA 58.402 39.130 9.01 3.40 37.38 2.87
630 1247 4.641541 TGGCATTTCACCATGTATGAAGAG 59.358 41.667 9.01 7.58 37.38 2.85
631 1248 4.498682 GGCATTTCACCATGTATGAAGAGC 60.499 45.833 17.88 17.88 37.38 4.09
632 1249 4.096833 GCATTTCACCATGTATGAAGAGCA 59.903 41.667 19.55 6.32 37.38 4.26
636 1253 3.118629 TCACCATGTATGAAGAGCACTCC 60.119 47.826 0.00 0.00 0.00 3.85
667 1284 7.089770 TGCGGCATAACTAATTGTTTTCATA 57.910 32.000 0.00 0.00 39.89 2.15
683 1303 3.998913 TCATACTTGATTGGCCACTCA 57.001 42.857 21.03 21.03 0.00 3.41
708 1328 7.355332 TGCTAATGTTAGGTTACTTTCGAAC 57.645 36.000 0.00 0.00 0.00 3.95
795 1416 6.449956 TCCTTAGGGAAATACCTGACATACT 58.550 40.000 0.00 0.00 42.02 2.12
801 1422 7.509546 AGGGAAATACCTGACATACTAATGTG 58.490 38.462 0.00 0.00 41.27 3.21
863 1485 0.442699 GCACTTGCAGCTTACGTACC 59.557 55.000 0.00 0.00 41.59 3.34
893 1515 5.954296 TCTCCTTTCTTTTGCTGAAGATG 57.046 39.130 3.70 1.61 35.70 2.90
903 1533 1.471287 TGCTGAAGATGCTGATTGTGC 59.529 47.619 0.00 0.00 0.00 4.57
940 1570 4.021192 ACAATGAAAGTTTGCATGTAGGGG 60.021 41.667 0.00 0.00 0.00 4.79
984 1622 8.871629 TTAACTTGCCCTATTTTGACAATCTA 57.128 30.769 0.00 0.00 0.00 1.98
1013 1652 9.699410 ATGGTTTTGACAGATGGAGAATAATAA 57.301 29.630 0.00 0.00 0.00 1.40
1043 1682 3.937814 TGTTTGGTACACCTGAGCATAG 58.062 45.455 0.00 0.00 39.29 2.23
1105 1745 8.870160 TTTCCATTTGTTGACAACTATTTCTG 57.130 30.769 18.73 7.98 35.28 3.02
1155 1795 9.349713 TGTTGTAAGGTGAAGTTCATATTTTCT 57.650 29.630 9.18 0.00 0.00 2.52
1162 1802 6.148811 GGTGAAGTTCATATTTTCTTGTCCGA 59.851 38.462 9.18 0.00 0.00 4.55
1179 1819 6.063640 TGTCCGATCATTATTTGATTGCTG 57.936 37.500 0.00 0.00 45.29 4.41
1186 1826 9.467258 CGATCATTATTTGATTGCTGGTAATTT 57.533 29.630 0.00 0.00 45.29 1.82
1193 1833 4.746729 TGATTGCTGGTAATTTGTCATGC 58.253 39.130 0.00 0.00 0.00 4.06
1208 1848 7.523293 TTTGTCATGCCATTCTTTCTTAGAA 57.477 32.000 0.00 0.00 46.50 2.10
1216 1856 4.944317 CCATTCTTTCTTAGAACTGGGGAC 59.056 45.833 0.00 0.00 45.33 4.46
1350 1997 6.528537 ACAATGCTAAATGCTGTATCCAAA 57.471 33.333 0.00 0.00 43.37 3.28
1358 2005 9.918630 GCTAAATGCTGTATCCAAATATGATTT 57.081 29.630 0.00 0.00 38.95 2.17
1455 2102 2.299297 AGCTTTCGTACTAGTTGGCAGT 59.701 45.455 0.00 0.00 0.00 4.40
1480 2127 8.726870 TTGTAGTAACAACTTAAAAGAGCAGT 57.273 30.769 0.00 0.00 40.69 4.40
1486 2133 9.946165 GTAACAACTTAAAAGAGCAGTATGTTT 57.054 29.630 0.00 0.00 39.31 2.83
1558 2205 2.297701 CACCAGGTACTTGTGCAAACT 58.702 47.619 4.10 0.00 44.92 2.66
1568 2215 5.536554 ACTTGTGCAAACTCTCATATTCG 57.463 39.130 0.00 0.00 0.00 3.34
1586 2233 8.826710 TCATATTCGGCTAGTTTTCAGTTATTG 58.173 33.333 0.00 0.00 0.00 1.90
1605 2252 9.606631 AGTTATTGTGATTATTCTTCTCTGACC 57.393 33.333 0.00 0.00 0.00 4.02
1615 2262 3.214328 TCTTCTCTGACCCTGTTTTTGC 58.786 45.455 0.00 0.00 0.00 3.68
1713 2360 2.619074 GGCTCAACCAGGATGTAAAGCT 60.619 50.000 8.32 0.00 38.86 3.74
1884 2532 9.913310 TTTTTCTTGATAAAATGGGTTTCCTTT 57.087 25.926 0.00 0.00 32.49 3.11
1888 2536 7.453126 TCTTGATAAAATGGGTTTCCTTTGCTA 59.547 33.333 0.00 0.00 31.67 3.49
1910 2558 9.317936 TGCTACTCATGTATTGTCTTTTGATAG 57.682 33.333 0.00 0.00 0.00 2.08
2021 2669 3.967326 TGATTCAGAATATGGTCCCGTCT 59.033 43.478 0.00 0.00 0.00 4.18
2198 2888 4.880164 AGTAGCCTGAGTATGGGAAACTA 58.120 43.478 0.00 0.00 0.00 2.24
2246 2939 8.435931 AGGTGTATCCAGTATTTGCATATAGA 57.564 34.615 0.00 0.00 39.02 1.98
2464 3161 2.002586 CTTCGACATTCGGATGCAACT 58.997 47.619 2.75 0.00 40.88 3.16
2685 3382 1.536766 TGCAAAGAATGGAACTGCGAG 59.463 47.619 0.00 0.00 0.00 5.03
2730 3427 1.110518 TCTAGTGACACCGGTGCACA 61.111 55.000 38.96 32.79 38.85 4.57
2764 3461 0.758734 CAGGTGTGAACTCTGGGACA 59.241 55.000 0.00 0.00 0.00 4.02
3647 4344 8.681806 GTCCGTAAGAAGTAGTAATAAGACCTT 58.318 37.037 0.00 0.00 43.02 3.50
3657 4354 9.449719 AGTAGTAATAAGACCTTGTTTTGGATG 57.550 33.333 0.00 0.00 0.00 3.51
3660 4357 8.960591 AGTAATAAGACCTTGTTTTGGATGATG 58.039 33.333 0.00 0.00 0.00 3.07
3661 4358 8.956426 GTAATAAGACCTTGTTTTGGATGATGA 58.044 33.333 0.00 0.00 0.00 2.92
3662 4359 5.712152 AAGACCTTGTTTTGGATGATGAC 57.288 39.130 0.00 0.00 0.00 3.06
3752 4451 4.488879 CTTTTGCACAAAGGCCTAAGATC 58.511 43.478 5.16 0.00 0.00 2.75
3872 4571 0.041839 GCGGCTGATTGTATCGCTTG 60.042 55.000 0.00 0.00 42.62 4.01
3984 4683 1.421268 TGTGGCTCCTTCTGTGATTGT 59.579 47.619 0.00 0.00 0.00 2.71
4075 4774 8.316214 TCCAGTAATGACGTAAAATCCTTACTT 58.684 33.333 0.00 0.00 36.17 2.24
4151 4850 4.404394 TGACCGAGTATTGCCTGAAGATTA 59.596 41.667 0.00 0.00 0.00 1.75
4219 4918 6.209391 TCAGATCAGAGCATTATATCGGTTCA 59.791 38.462 0.00 0.00 0.00 3.18
4342 5041 5.248248 TCTTGTGATGAAGGAAGGTGTCATA 59.752 40.000 0.00 0.00 32.18 2.15
4438 5137 1.768077 GGGCTCAGGGGTAGCTCAT 60.768 63.158 0.00 0.00 40.36 2.90
4439 5138 1.449353 GGCTCAGGGGTAGCTCATG 59.551 63.158 0.00 0.00 39.97 3.07
4440 5139 1.227793 GCTCAGGGGTAGCTCATGC 60.228 63.158 0.00 0.00 37.01 4.06
4452 5151 1.773054 GCTCATGCTGCTGTCGATGG 61.773 60.000 0.00 0.00 36.03 3.51
4507 5206 3.316308 GCAAACAGCCGATATCCAAATCT 59.684 43.478 0.00 0.00 37.23 2.40
4561 5260 0.955905 CAAAACCCCGGTCACGAAAT 59.044 50.000 0.00 0.00 44.60 2.17
4658 5358 1.095807 GCAAATGGGAGCGGGTAGTC 61.096 60.000 0.00 0.00 0.00 2.59
4686 5386 5.483231 TCCAAATGAAATGCTTAATGTGGGA 59.517 36.000 0.00 0.00 0.00 4.37
4736 5436 7.584987 ACTAGAGTTTGTATTTGCACATGTTC 58.415 34.615 0.00 0.00 0.00 3.18
4767 5467 3.732048 TTGCTAGGGTAAGAAAAGGGG 57.268 47.619 0.00 0.00 0.00 4.79
4823 5523 1.400846 CACTCTGATGCATGCTGTTCC 59.599 52.381 20.33 4.00 0.00 3.62
4824 5524 0.656259 CTCTGATGCATGCTGTTCCG 59.344 55.000 20.33 9.64 0.00 4.30
4843 5543 3.194116 TCCGTGTAACAGATACCTGGAAC 59.806 47.826 0.00 0.00 44.60 3.62
4889 5589 5.726980 TGGGAGATTTTTCATTGGAACTG 57.273 39.130 0.00 0.00 31.35 3.16
4917 5617 2.445427 CATGGGTTATGTGAACAGCCA 58.555 47.619 0.00 0.00 42.16 4.75
4957 5657 1.065854 GTGAGATTGGGACCTGGTCAG 60.066 57.143 26.94 0.00 33.68 3.51
4964 5664 1.302832 GGACCTGGTCAGTGCAAGG 60.303 63.158 26.94 6.48 33.68 3.61
4971 5671 3.305608 CCTGGTCAGTGCAAGGATTTTTC 60.306 47.826 2.67 0.00 30.92 2.29
4972 5672 3.565307 TGGTCAGTGCAAGGATTTTTCT 58.435 40.909 0.00 0.00 0.00 2.52
4977 5677 5.689068 GTCAGTGCAAGGATTTTTCTTCTTG 59.311 40.000 0.00 0.00 39.46 3.02
4980 5680 5.127682 AGTGCAAGGATTTTTCTTCTTGTGT 59.872 36.000 0.00 0.00 38.90 3.72
5003 5703 3.135530 AGGAAATGTGTAGCTCCCTCATC 59.864 47.826 0.00 0.00 0.00 2.92
5011 5711 1.377202 GCTCCCTCATCGGCACAAA 60.377 57.895 0.00 0.00 0.00 2.83
5032 5732 7.167468 CACAAAGGTAGTGTTGAATAAACTTGC 59.833 37.037 0.00 0.00 39.70 4.01
5093 5793 1.891150 CCATGGCAGCTCTTTTCAGTT 59.109 47.619 0.00 0.00 0.00 3.16
5105 5805 4.597079 TCTTTTCAGTTCAACAATCGTGC 58.403 39.130 0.00 0.00 0.00 5.34
5141 5841 1.798813 CGTATCGACTGCTCATGTGCA 60.799 52.381 20.38 20.38 41.05 4.57
5164 5864 6.308766 GCATTGTTAGTTGATTAGGTGCTTTG 59.691 38.462 0.00 0.00 0.00 2.77
5177 5877 0.316841 TGCTTTGCCCGTTGATTTCC 59.683 50.000 0.00 0.00 0.00 3.13
5220 5920 0.108329 GCGGCAGAAGTGGTTAGCTA 60.108 55.000 0.00 0.00 0.00 3.32
5250 5950 0.847373 TTGGGCTTAGTCCACAACCA 59.153 50.000 4.48 0.00 36.87 3.67
5255 5955 2.162681 GCTTAGTCCACAACCAGCAAT 58.837 47.619 0.00 0.00 35.59 3.56
5256 5956 3.343617 GCTTAGTCCACAACCAGCAATA 58.656 45.455 0.00 0.00 35.59 1.90
5257 5957 3.947834 GCTTAGTCCACAACCAGCAATAT 59.052 43.478 0.00 0.00 35.59 1.28
5280 5980 0.451783 GTTCATGGGATGGCACGAAC 59.548 55.000 0.00 0.00 0.00 3.95
5300 6000 4.284860 CGAGGATCATCGCGGGCA 62.285 66.667 17.54 0.00 35.66 5.36
5303 6003 0.886490 GAGGATCATCGCGGGCATTT 60.886 55.000 6.13 0.00 33.17 2.32
5308 6008 1.102154 TCATCGCGGGCATTTCATTT 58.898 45.000 6.13 0.00 0.00 2.32
5334 6035 4.443063 GCCGTTAAGGTCATTTTGTTTGTC 59.557 41.667 0.00 0.00 43.70 3.18
5430 8217 2.121786 CTGTGTTCATTGTGTGCAAGC 58.878 47.619 0.00 0.00 38.10 4.01
5433 8220 1.067364 TGTTCATTGTGTGCAAGCTGG 59.933 47.619 0.00 0.00 38.10 4.85
5434 8221 1.337703 GTTCATTGTGTGCAAGCTGGA 59.662 47.619 0.00 0.00 38.10 3.86
5442 8229 0.740737 GTGCAAGCTGGAAGTTGTGT 59.259 50.000 0.00 0.00 35.30 3.72
5444 8231 1.134753 TGCAAGCTGGAAGTTGTGTTG 59.865 47.619 0.00 0.00 35.30 3.33
5462 8249 0.397564 TGACAAGTGGCATCAGAGCA 59.602 50.000 0.00 0.00 35.83 4.26
5466 8253 1.400846 CAAGTGGCATCAGAGCATGTC 59.599 52.381 0.00 0.00 35.83 3.06
5476 8263 2.836372 TCAGAGCATGTCTTGTGATCCT 59.164 45.455 0.00 0.00 32.65 3.24
5510 8297 1.002087 GAGGAAGGCGTTGGAGAAGAA 59.998 52.381 0.00 0.00 0.00 2.52
5514 8301 2.033194 GGCGTTGGAGAAGAACGGG 61.033 63.158 0.00 0.00 45.01 5.28
5542 8329 4.421479 CCAGCTCGAAGACGCCGT 62.421 66.667 0.00 0.00 39.58 5.68
5546 8333 2.254350 CTCGAAGACGCCGTCACA 59.746 61.111 20.65 0.00 39.58 3.58
5551 8338 1.004277 GAAGACGCCGTCACAGTGAG 61.004 60.000 20.65 0.00 34.60 3.51
5557 8345 1.214062 CCGTCACAGTGAGAGGCTC 59.786 63.158 6.34 6.34 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.162681 CCTGTGGGCTAAAACCAAGAG 58.837 52.381 0.00 0.00 40.24 2.85
34 35 3.078097 GGAGCTTCTCCTTTTCTGAACC 58.922 50.000 5.65 0.00 46.41 3.62
64 66 6.309737 GCCAGAGATTAAGCAAAAACAATGAG 59.690 38.462 0.00 0.00 0.00 2.90
96 98 2.224257 GGAGAGAAATGCTAGCCAGAGG 60.224 54.545 13.29 0.00 0.00 3.69
97 99 2.433604 TGGAGAGAAATGCTAGCCAGAG 59.566 50.000 13.29 0.00 0.00 3.35
98 100 2.470990 TGGAGAGAAATGCTAGCCAGA 58.529 47.619 13.29 0.00 0.00 3.86
99 101 2.941720 GTTGGAGAGAAATGCTAGCCAG 59.058 50.000 13.29 0.00 33.16 4.85
100 102 2.677902 CGTTGGAGAGAAATGCTAGCCA 60.678 50.000 13.29 0.24 0.00 4.75
101 103 1.936547 CGTTGGAGAGAAATGCTAGCC 59.063 52.381 13.29 0.00 0.00 3.93
102 104 1.328986 GCGTTGGAGAGAAATGCTAGC 59.671 52.381 8.10 8.10 36.75 3.42
103 105 2.606725 CAGCGTTGGAGAGAAATGCTAG 59.393 50.000 2.78 0.00 45.76 3.42
140 142 5.054477 ACCCGTATTAATTCGTTGGATCAG 58.946 41.667 12.61 0.00 0.00 2.90
160 162 0.621082 CCTCCCCTTGAAGAGAACCC 59.379 60.000 0.00 0.00 31.43 4.11
249 269 5.782893 TGTAAAACTTTGTGAATGGAGGG 57.217 39.130 0.00 0.00 0.00 4.30
333 948 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
334 949 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
335 950 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
336 951 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
337 952 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
338 953 4.360951 AAGACACTTATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
339 954 5.106436 GGTTAAGACACTTATTTTGGGACGG 60.106 44.000 0.00 0.00 0.00 4.79
340 955 5.704053 AGGTTAAGACACTTATTTTGGGACG 59.296 40.000 0.00 0.00 0.00 4.79
341 956 7.520451 AAGGTTAAGACACTTATTTTGGGAC 57.480 36.000 0.00 0.00 0.00 4.46
342 957 8.442374 ACTAAGGTTAAGACACTTATTTTGGGA 58.558 33.333 0.00 0.00 0.00 4.37
343 958 8.631480 ACTAAGGTTAAGACACTTATTTTGGG 57.369 34.615 0.00 0.00 0.00 4.12
391 1006 8.793592 GTCCCAAAATAAGTATCTCAACTTTGT 58.206 33.333 0.00 0.00 40.20 2.83
392 1007 7.962918 CGTCCCAAAATAAGTATCTCAACTTTG 59.037 37.037 0.00 0.00 40.20 2.77
393 1008 7.120726 CCGTCCCAAAATAAGTATCTCAACTTT 59.879 37.037 0.00 0.00 40.20 2.66
394 1009 6.598064 CCGTCCCAAAATAAGTATCTCAACTT 59.402 38.462 0.00 0.00 42.31 2.66
395 1010 6.070424 TCCGTCCCAAAATAAGTATCTCAACT 60.070 38.462 0.00 0.00 0.00 3.16
396 1011 6.110707 TCCGTCCCAAAATAAGTATCTCAAC 58.889 40.000 0.00 0.00 0.00 3.18
397 1012 6.302535 TCCGTCCCAAAATAAGTATCTCAA 57.697 37.500 0.00 0.00 0.00 3.02
398 1013 5.163343 CCTCCGTCCCAAAATAAGTATCTCA 60.163 44.000 0.00 0.00 0.00 3.27
399 1014 5.298347 CCTCCGTCCCAAAATAAGTATCTC 58.702 45.833 0.00 0.00 0.00 2.75
400 1015 4.102681 CCCTCCGTCCCAAAATAAGTATCT 59.897 45.833 0.00 0.00 0.00 1.98
401 1016 4.102054 TCCCTCCGTCCCAAAATAAGTATC 59.898 45.833 0.00 0.00 0.00 2.24
402 1017 4.042174 TCCCTCCGTCCCAAAATAAGTAT 58.958 43.478 0.00 0.00 0.00 2.12
403 1018 3.452878 TCCCTCCGTCCCAAAATAAGTA 58.547 45.455 0.00 0.00 0.00 2.24
404 1019 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
405 1020 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
406 1021 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
407 1022 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
408 1023 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
409 1024 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
410 1025 1.007963 AGATACTCCCTCCGTCCCAAA 59.992 52.381 0.00 0.00 0.00 3.28
411 1026 0.635009 AGATACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
412 1027 1.526315 TAGATACTCCCTCCGTCCCA 58.474 55.000 0.00 0.00 0.00 4.37
413 1028 2.671896 TTAGATACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
414 1029 5.415389 GTCTTATTAGATACTCCCTCCGTCC 59.585 48.000 0.00 0.00 31.86 4.79
415 1030 6.002704 TGTCTTATTAGATACTCCCTCCGTC 58.997 44.000 0.00 0.00 31.86 4.79
416 1031 5.950023 TGTCTTATTAGATACTCCCTCCGT 58.050 41.667 0.00 0.00 31.86 4.69
417 1032 6.490721 AGTTGTCTTATTAGATACTCCCTCCG 59.509 42.308 0.00 0.00 31.86 4.63
418 1033 7.842887 AGTTGTCTTATTAGATACTCCCTCC 57.157 40.000 0.00 0.00 31.86 4.30
494 1110 6.528072 GCTTTCTAGCGCATGTAAGAAAAATT 59.472 34.615 11.47 0.00 37.47 1.82
587 1204 1.821216 ATAGTTTGGCCAACCGACTG 58.179 50.000 25.18 0.00 39.70 3.51
628 1245 2.375766 CGCAACTCGTGGAGTGCTC 61.376 63.158 13.93 0.00 42.59 4.26
629 1246 2.356313 CGCAACTCGTGGAGTGCT 60.356 61.111 13.93 0.00 42.59 4.40
636 1253 1.635844 TAGTTATGCCGCAACTCGTG 58.364 50.000 0.00 0.00 37.42 4.35
667 1284 1.180029 GCATGAGTGGCCAATCAAGT 58.820 50.000 36.74 20.94 38.97 3.16
683 1303 7.822822 AGTTCGAAAGTAACCTAACATTAGCAT 59.177 33.333 0.00 0.00 0.00 3.79
725 1345 3.201290 GCATATTCCTGGTCACTGTCTG 58.799 50.000 0.00 0.00 0.00 3.51
754 1374 8.901841 TCCCTAAGGAATATGTCAGATAGACTA 58.098 37.037 0.00 0.00 43.13 2.59
772 1392 6.749036 AGTATGTCAGGTATTTCCCTAAGG 57.251 41.667 0.00 0.00 36.75 2.69
773 1393 9.712305 CATTAGTATGTCAGGTATTTCCCTAAG 57.288 37.037 0.00 0.00 36.75 2.18
835 1457 7.010080 ACGTAAGCTGCAAGTGCATAATTTTT 61.010 34.615 6.41 0.00 46.66 1.94
836 1458 5.564651 ACGTAAGCTGCAAGTGCATAATTTT 60.565 36.000 6.41 0.75 46.66 1.82
838 1460 3.440173 ACGTAAGCTGCAAGTGCATAATT 59.560 39.130 6.41 4.95 46.66 1.40
859 1481 4.657436 AGAAAGGAGATGATGACGGTAC 57.343 45.455 0.00 0.00 0.00 3.34
863 1485 4.394300 AGCAAAAGAAAGGAGATGATGACG 59.606 41.667 0.00 0.00 0.00 4.35
893 1515 7.168972 TGTTTTGTTATTTGTAGCACAATCAGC 59.831 33.333 3.15 0.00 38.00 4.26
984 1622 5.183530 TCTCCATCTGTCAAAACCATGAT 57.816 39.130 0.00 0.00 0.00 2.45
1013 1652 4.706476 CAGGTGTACCAAACATTCCATCAT 59.294 41.667 3.56 0.00 41.10 2.45
1043 1682 1.208052 TCTGCACCTTAGGATGTGAGC 59.792 52.381 4.77 0.00 34.37 4.26
1122 1762 8.282455 TGAACTTCACCTTACAACAAAATACA 57.718 30.769 0.00 0.00 0.00 2.29
1179 1819 6.633856 AGAAAGAATGGCATGACAAATTACC 58.366 36.000 4.70 0.00 0.00 2.85
1186 1826 6.149973 CAGTTCTAAGAAAGAATGGCATGACA 59.850 38.462 2.18 2.18 45.84 3.58
1193 1833 4.944317 GTCCCCAGTTCTAAGAAAGAATGG 59.056 45.833 0.00 0.00 45.84 3.16
1208 1848 1.305802 TACCGCAGATGTCCCCAGT 60.306 57.895 0.00 0.00 0.00 4.00
1315 1958 8.401046 GCATTTAGCATTGTACGGAATTTTTA 57.599 30.769 0.00 0.00 44.79 1.52
1366 2013 9.109393 GGCTTAATCATTTGAGACACTGTTATA 57.891 33.333 0.00 0.00 0.00 0.98
1373 2020 6.500684 TTCAGGCTTAATCATTTGAGACAC 57.499 37.500 0.00 0.00 28.84 3.67
1455 2102 8.726870 ACTGCTCTTTTAAGTTGTTACTACAA 57.273 30.769 0.00 0.00 41.82 2.41
1475 2122 8.630054 TGAAATGGTAGTTAAAACATACTGCT 57.370 30.769 0.00 0.00 0.00 4.24
1532 2179 3.957497 TGCACAAGTACCTGGTGAAAATT 59.043 39.130 10.23 0.00 37.60 1.82
1558 2205 6.222038 ACTGAAAACTAGCCGAATATGAGA 57.778 37.500 0.00 0.00 0.00 3.27
1586 2233 5.983540 ACAGGGTCAGAGAAGAATAATCAC 58.016 41.667 0.00 0.00 0.00 3.06
1737 2384 5.435686 TCCCTTTGTCAACTATGCTGTAT 57.564 39.130 0.00 0.00 0.00 2.29
1856 2504 8.933653 AGGAAACCCATTTTATCAAGAAAAAGA 58.066 29.630 0.00 0.00 32.29 2.52
1876 2524 7.119846 AGACAATACATGAGTAGCAAAGGAAAC 59.880 37.037 0.00 0.00 32.86 2.78
1884 2532 9.317936 CTATCAAAAGACAATACATGAGTAGCA 57.682 33.333 0.00 0.00 32.86 3.49
1888 2536 9.376075 CTCACTATCAAAAGACAATACATGAGT 57.624 33.333 0.00 0.00 0.00 3.41
1910 2558 1.335324 GCCTGAAATGTGTGTGCTCAC 60.335 52.381 11.94 11.94 44.08 3.51
2021 2669 3.041211 ACTAGCCTGATCAGCCAACATA 58.959 45.455 17.76 2.58 0.00 2.29
2167 2857 5.525378 CCATACTCAGGCTACTTTGATTGAC 59.475 44.000 0.00 0.00 0.00 3.18
2198 2888 7.397192 ACCTCCAACTAAAAATATGTGAATGCT 59.603 33.333 0.00 0.00 0.00 3.79
2246 2939 7.225427 AGAAATTTCTGCAGACAACGCATGT 62.225 40.000 19.86 0.00 39.79 3.21
2296 2989 5.539048 ACCTGATCAATATTGGCGTAGTAC 58.461 41.667 15.36 0.00 0.00 2.73
2425 3122 2.508526 AGCATCTTCAAGACCGCTTTT 58.491 42.857 7.26 0.00 33.89 2.27
2464 3161 7.177216 AGGAATGTATGCATTTCAAGTTCTTCA 59.823 33.333 16.17 0.00 44.61 3.02
2634 3331 1.136336 GCTTGCTGTTCTTTCCGTACG 60.136 52.381 8.69 8.69 0.00 3.67
2685 3382 8.519492 AATTACATTTGTGCATGTAGTTTCAC 57.481 30.769 0.00 0.00 40.08 3.18
2730 3427 3.006110 CACACCTGGAATGCATTTTCTGT 59.994 43.478 14.33 8.13 0.00 3.41
3193 3890 6.239204 GGGTAAAACTAGTTTTTGGCACATCT 60.239 38.462 32.37 11.92 42.22 2.90
3335 4032 5.527582 GGACAGCTTTTAAGTCTTTGACAGA 59.472 40.000 1.65 0.00 34.60 3.41
3353 4050 5.065731 CCTCATTTTCACTATTCAGGACAGC 59.934 44.000 0.00 0.00 0.00 4.40
3599 4296 4.331168 ACTTGCGATTTACTGCTGAGAATC 59.669 41.667 0.00 5.75 0.00 2.52
3647 4344 3.002791 GAGAGCGTCATCATCCAAAACA 58.997 45.455 0.00 0.00 0.00 2.83
3657 4354 4.241681 AGAAAAACAGAGAGAGCGTCATC 58.758 43.478 0.00 0.00 0.00 2.92
3659 4356 3.735237 AGAAAAACAGAGAGAGCGTCA 57.265 42.857 0.00 0.00 0.00 4.35
3660 4357 5.864474 TGAATAGAAAAACAGAGAGAGCGTC 59.136 40.000 0.00 0.00 0.00 5.19
3661 4358 5.784177 TGAATAGAAAAACAGAGAGAGCGT 58.216 37.500 0.00 0.00 0.00 5.07
3662 4359 6.712241 TTGAATAGAAAAACAGAGAGAGCG 57.288 37.500 0.00 0.00 0.00 5.03
3872 4571 6.560253 TTCCAGCTTTAACTCAGAATCAAC 57.440 37.500 0.00 0.00 0.00 3.18
3984 4683 5.425217 TCATTGTCTCCAGTATCCAAAGCTA 59.575 40.000 0.00 0.00 0.00 3.32
4060 4759 8.827677 CCTGGAGAAATAAGTAAGGATTTTACG 58.172 37.037 0.00 0.00 0.00 3.18
4104 4803 5.551233 AGCTTACTTCACTGAGCAATGTAA 58.449 37.500 0.00 0.00 37.59 2.41
4151 4850 1.665679 CACTTCGCATAAGTTCCGCAT 59.334 47.619 0.00 0.00 0.00 4.73
4209 4908 9.650539 CTAGATGATCTGAAATTGAACCGATAT 57.349 33.333 4.96 0.00 0.00 1.63
4210 4909 8.860088 TCTAGATGATCTGAAATTGAACCGATA 58.140 33.333 4.96 0.00 0.00 2.92
4219 4918 7.429374 TCCTGTGTCTAGATGATCTGAAATT 57.571 36.000 4.96 0.00 0.00 1.82
4342 5041 0.773644 ACAGATCAACAAGGGCAGGT 59.226 50.000 0.00 0.00 0.00 4.00
4380 5079 1.952990 TGATTGAAGACGCTTTTGCCA 59.047 42.857 0.00 0.00 43.93 4.92
4438 5137 2.046988 CCACCATCGACAGCAGCA 60.047 61.111 0.00 0.00 0.00 4.41
4439 5138 1.812922 CTCCACCATCGACAGCAGC 60.813 63.158 0.00 0.00 0.00 5.25
4440 5139 0.817654 TACTCCACCATCGACAGCAG 59.182 55.000 0.00 0.00 0.00 4.24
4452 5151 1.107945 GGGTGAGCTCTCTACTCCAC 58.892 60.000 16.19 2.13 32.98 4.02
4507 5206 4.342378 AGCTTTCTTGAGATATACCGAGCA 59.658 41.667 0.00 0.00 0.00 4.26
4561 5260 6.672266 AAATCACTAAGTTCTCAGAGGACA 57.328 37.500 11.75 0.00 0.00 4.02
4658 5358 5.863397 ACATTAAGCATTTCATTTGGACACG 59.137 36.000 0.00 0.00 0.00 4.49
4736 5436 6.231211 TCTTACCCTAGCAAAGAAAGACAAG 58.769 40.000 0.00 0.00 0.00 3.16
4767 5467 4.192317 CACAAGACCTATGAGCTAAACCC 58.808 47.826 0.00 0.00 0.00 4.11
4823 5523 3.176708 CGTTCCAGGTATCTGTTACACG 58.823 50.000 1.52 1.08 39.31 4.49
4824 5524 3.924686 CACGTTCCAGGTATCTGTTACAC 59.075 47.826 1.52 0.00 39.31 2.90
4889 5589 3.804036 TCACATAACCCATGTTCGATCC 58.196 45.455 0.00 0.00 46.01 3.36
4917 5617 7.615403 TCTCACAGAAATCAACTAAGCAGTAT 58.385 34.615 0.00 0.00 33.48 2.12
4957 5657 5.351458 ACACAAGAAGAAAAATCCTTGCAC 58.649 37.500 0.00 0.00 39.51 4.57
4964 5664 9.185192 CACATTTCCTACACAAGAAGAAAAATC 57.815 33.333 0.00 0.00 30.86 2.17
4971 5671 5.934625 AGCTACACATTTCCTACACAAGAAG 59.065 40.000 0.00 0.00 0.00 2.85
4972 5672 5.865085 AGCTACACATTTCCTACACAAGAA 58.135 37.500 0.00 0.00 0.00 2.52
4977 5677 3.197983 AGGGAGCTACACATTTCCTACAC 59.802 47.826 0.00 0.00 0.00 2.90
4980 5680 3.719871 TGAGGGAGCTACACATTTCCTA 58.280 45.455 0.00 0.00 0.00 2.94
5003 5703 1.588674 TCAACACTACCTTTGTGCCG 58.411 50.000 0.00 0.00 38.86 5.69
5011 5711 5.607119 CGCAAGTTTATTCAACACTACCT 57.393 39.130 0.00 0.00 37.93 3.08
5032 5732 5.408356 ACATAGCACCTAAACTAGACAACG 58.592 41.667 0.00 0.00 0.00 4.10
5093 5793 1.882311 GCCATGGCACGATTGTTGA 59.118 52.632 32.08 0.00 41.49 3.18
5141 5841 6.389906 GCAAAGCACCTAATCAACTAACAAT 58.610 36.000 0.00 0.00 0.00 2.71
5177 5877 0.742505 TCCTATGACCGTGCTAACCG 59.257 55.000 0.00 0.00 0.00 4.44
5193 5893 4.845580 CTTCTGCCGCGCCATCCT 62.846 66.667 0.00 0.00 0.00 3.24
5220 5920 3.190439 ACTAAGCCCAACCCACTTATCT 58.810 45.455 0.00 0.00 0.00 1.98
5250 5950 4.404640 CATCCCATGAACCAGATATTGCT 58.595 43.478 0.00 0.00 0.00 3.91
5255 5955 2.134354 TGCCATCCCATGAACCAGATA 58.866 47.619 0.00 0.00 0.00 1.98
5256 5956 0.928505 TGCCATCCCATGAACCAGAT 59.071 50.000 0.00 0.00 0.00 2.90
5257 5957 0.034186 GTGCCATCCCATGAACCAGA 60.034 55.000 0.00 0.00 0.00 3.86
5300 6000 3.169908 ACCTTAACGGCCCAAATGAAAT 58.830 40.909 0.00 0.00 35.61 2.17
5303 6003 1.074084 TGACCTTAACGGCCCAAATGA 59.926 47.619 0.00 0.00 35.61 2.57
5308 6008 1.889829 CAAAATGACCTTAACGGCCCA 59.110 47.619 0.00 0.00 35.61 5.36
5334 6035 7.535258 CGTTTGTCATTCTCCTTTTATTCTGTG 59.465 37.037 0.00 0.00 0.00 3.66
5398 8185 5.177511 ACAATGAACACAGTGACACGAATAG 59.822 40.000 7.81 0.00 34.39 1.73
5401 8188 3.063316 CACAATGAACACAGTGACACGAA 59.937 43.478 7.81 0.00 34.39 3.85
5430 8217 3.181497 CCACTTGTCAACACAACTTCCAG 60.181 47.826 0.00 0.00 37.61 3.86
5433 8220 2.163412 TGCCACTTGTCAACACAACTTC 59.837 45.455 0.00 0.00 37.61 3.01
5434 8221 2.166829 TGCCACTTGTCAACACAACTT 58.833 42.857 0.00 0.00 37.61 2.66
5442 8229 1.202794 TGCTCTGATGCCACTTGTCAA 60.203 47.619 0.00 0.00 0.00 3.18
5444 8231 1.400846 CATGCTCTGATGCCACTTGTC 59.599 52.381 0.00 0.00 0.00 3.18
5493 8280 0.790814 CGTTCTTCTCCAACGCCTTC 59.209 55.000 0.00 0.00 40.14 3.46
5501 8288 2.221299 CCACCCCCGTTCTTCTCCA 61.221 63.158 0.00 0.00 0.00 3.86
5514 8301 3.791586 GAGCTGGAGCCTCCACCC 61.792 72.222 10.05 3.85 42.67 4.61
5527 8314 3.362797 TGACGGCGTCTTCGAGCT 61.363 61.111 36.17 0.28 39.71 4.09
5532 8319 1.004277 CTCACTGTGACGGCGTCTTC 61.004 60.000 36.17 28.09 33.15 2.87
5542 8329 2.640302 GGCGAGCCTCTCACTGTGA 61.640 63.158 10.50 10.50 0.00 3.58
5546 8333 2.757917 GAGGGCGAGCCTCTCACT 60.758 66.667 20.26 8.21 35.16 3.41


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

AutoCloner maintained by Alex Coulton.