Multiple sequence alignment - TraesCS5A01G223500

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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 TraesCS5A01G223500 chr5A 100.000 5202 0 0 1 5202 439373449 439378650 0.000000e+00 9607
1 TraesCS5A01G223500 chr5D 93.784 4279 170 39 40 4256 338385928 338390172 0.000000e+00 6340
2 TraesCS5A01G223500 chr5D 92.669 682 44 2 4524 5202 235209931 235209253 0.000000e+00 977
3 TraesCS5A01G223500 chr5D 91.935 682 39 3 4524 5202 502648783 502648115 0.000000e+00 941
4 TraesCS5A01G223500 chr5D 89.488 371 28 5 1 364 338382936 338383302 4.750000e-125 459
5 TraesCS5A01G223500 chr5B 95.858 2680 85 16 1578 4256 397514380 397517034 0.000000e+00 4311
6 TraesCS5A01G223500 chr5B 88.942 1474 99 34 1 1427 397512712 397514168 0.000000e+00 1760
7 TraesCS5A01G223500 chr5B 89.730 370 23 2 4519 4874 610351928 610352296 4.750000e-125 459
8 TraesCS5A01G223500 chr5B 85.632 348 38 6 4524 4869 676333531 676333194 6.410000e-94 355
9 TraesCS5A01G223500 chr5B 94.175 103 5 1 4334 4436 397517059 397517160 6.970000e-34 156
10 TraesCS5A01G223500 chr1D 93.139 685 38 2 4524 5202 69777387 69776706 0.000000e+00 996
11 TraesCS5A01G223500 chr1D 94.795 365 15 2 4841 5202 11316324 11315961 2.720000e-157 566
12 TraesCS5A01G223500 chr1D 94.247 365 17 2 4841 5202 261732396 261732033 5.890000e-154 555
13 TraesCS5A01G223500 chr1D 92.697 356 23 1 4524 4879 261732664 261732312 1.290000e-140 510
14 TraesCS5A01G223500 chr1D 71.512 853 175 52 2833 3650 112469587 112468768 3.220000e-37 167
15 TraesCS5A01G223500 chr2D 93.119 683 38 5 4524 5202 181291561 181290884 0.000000e+00 992
16 TraesCS5A01G223500 chr7D 92.522 682 45 2 4524 5202 105681291 105680613 0.000000e+00 972
17 TraesCS5A01G223500 chr7D 91.496 682 42 3 4524 5202 45633171 45632503 0.000000e+00 924
18 TraesCS5A01G223500 chr7D 91.349 682 42 7 4524 5202 94454545 94455212 0.000000e+00 917
19 TraesCS5A01G223500 chr3D 92.489 466 32 1 4524 4989 171319065 171319527 0.000000e+00 664
20 TraesCS5A01G223500 chr6B 87.143 350 29 12 4523 4870 90999829 90999494 2.940000e-102 383
21 TraesCS5A01G223500 chr1A 72.660 940 171 63 2734 3636 549359452 549358562 3.130000e-57 233
22 TraesCS5A01G223500 chr1A 71.378 842 174 52 2833 3639 119710745 119709936 1.940000e-34 158
23 TraesCS5A01G223500 chr1B 73.839 646 116 41 3022 3636 626154322 626154945 1.900000e-49 207
24 TraesCS5A01G223500 chr1B 71.037 839 182 47 2833 3639 172008267 172007458 4.200000e-31 147
25 TraesCS5A01G223500 chr1B 77.340 203 38 8 2734 2932 626154052 626154250 4.260000e-21 113
26 TraesCS5A01G223500 chr4B 84.848 99 13 2 2833 2930 660354172 660354269 1.190000e-16 99


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 TraesCS5A01G223500 chr5A 439373449 439378650 5201 False 9607.000000 9607 100.000000 1 5202 1 chr5A.!!$F1 5201
1 TraesCS5A01G223500 chr5D 338382936 338390172 7236 False 3399.500000 6340 91.636000 1 4256 2 chr5D.!!$F1 4255
2 TraesCS5A01G223500 chr5D 235209253 235209931 678 True 977.000000 977 92.669000 4524 5202 1 chr5D.!!$R1 678
3 TraesCS5A01G223500 chr5D 502648115 502648783 668 True 941.000000 941 91.935000 4524 5202 1 chr5D.!!$R2 678
4 TraesCS5A01G223500 chr5B 397512712 397517160 4448 False 2075.666667 4311 92.991667 1 4436 3 chr5B.!!$F2 4435
5 TraesCS5A01G223500 chr1D 69776706 69777387 681 True 996.000000 996 93.139000 4524 5202 1 chr1D.!!$R2 678
6 TraesCS5A01G223500 chr1D 261732033 261732664 631 True 532.500000 555 93.472000 4524 5202 2 chr1D.!!$R4 678
7 TraesCS5A01G223500 chr2D 181290884 181291561 677 True 992.000000 992 93.119000 4524 5202 1 chr2D.!!$R1 678
8 TraesCS5A01G223500 chr7D 105680613 105681291 678 True 972.000000 972 92.522000 4524 5202 1 chr7D.!!$R2 678
9 TraesCS5A01G223500 chr7D 45632503 45633171 668 True 924.000000 924 91.496000 4524 5202 1 chr7D.!!$R1 678
10 TraesCS5A01G223500 chr7D 94454545 94455212 667 False 917.000000 917 91.349000 4524 5202 1 chr7D.!!$F1 678
11 TraesCS5A01G223500 chr1A 549358562 549359452 890 True 233.000000 233 72.660000 2734 3636 1 chr1A.!!$R2 902

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
297 3262 0.332632 CCCTTCATGGTGGGTGACAT 59.667 55.000 13.63 0.0 38.65 3.06 F
912 3917 0.393808 AAGCCGGTGTGTGAACTTGT 60.394 50.000 1.90 0.0 0.00 3.16 F
1187 4219 1.867233 TCGCTTCACTTGTTCTTCTGC 59.133 47.619 0.00 0.0 0.00 4.26 F
2756 5872 1.728426 CGACGACGAGAACCACACC 60.728 63.158 0.00 0.0 42.66 4.16 F
3732 6871 0.528470 CTCTCACCTTGTCCGACTCC 59.472 60.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 4168 0.251341 AGCGAGGACCAGCCATTTTT 60.251 50.000 8.16 0.0 40.02 1.94 R
2603 5711 0.038251 CTATGCCGCCGATGAAGCTA 60.038 55.000 0.00 0.0 0.00 3.32 R
2987 6103 1.218316 GCTGTCGAAGGTGTAGGGG 59.782 63.158 0.00 0.0 0.00 4.79 R
3739 6878 0.037882 ACTCGTCATCCACTGCACAG 60.038 55.000 0.00 0.0 0.00 3.66 R
4829 7968 0.913205 GGAGGAGGGGGAAGAAGAAC 59.087 60.000 0.00 0.0 0.00 3.01 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
41 42 9.834628 ACTAACCGTAATCATGTTTTTATGTTG 57.165 29.630 0.00 0.00 0.00 3.33
43 44 8.964420 AACCGTAATCATGTTTTTATGTTGAG 57.036 30.769 0.00 0.00 0.00 3.02
71 72 8.856153 TGTGAGCCTTTCATAAGTTTGTTATA 57.144 30.769 0.00 0.00 38.29 0.98
72 73 8.726988 TGTGAGCCTTTCATAAGTTTGTTATAC 58.273 33.333 0.00 0.00 38.29 1.47
76 81 8.612619 AGCCTTTCATAAGTTTGTTATACATCG 58.387 33.333 0.00 0.00 0.00 3.84
108 116 1.202371 TGCTCTTTGAGACGTGTCGTT 60.202 47.619 8.31 0.00 41.37 3.85
109 117 1.190323 GCTCTTTGAGACGTGTCGTTG 59.810 52.381 8.31 0.63 41.37 4.10
110 118 2.460918 CTCTTTGAGACGTGTCGTTGT 58.539 47.619 8.31 0.00 41.37 3.32
164 172 9.757227 CTTAGGGTTGAAGAATCTATGTAGAAG 57.243 37.037 0.00 0.00 35.69 2.85
198 206 4.555906 CGGTTAGCGAGGTTTGTTCATTTT 60.556 41.667 0.00 0.00 0.00 1.82
199 207 4.679654 GGTTAGCGAGGTTTGTTCATTTTG 59.320 41.667 0.00 0.00 0.00 2.44
200 208 5.278604 GTTAGCGAGGTTTGTTCATTTTGT 58.721 37.500 0.00 0.00 0.00 2.83
201 209 3.964909 AGCGAGGTTTGTTCATTTTGTC 58.035 40.909 0.00 0.00 0.00 3.18
202 210 3.632145 AGCGAGGTTTGTTCATTTTGTCT 59.368 39.130 0.00 0.00 0.00 3.41
204 212 4.497340 GCGAGGTTTGTTCATTTTGTCTGA 60.497 41.667 0.00 0.00 0.00 3.27
261 3226 8.764287 GCTATTTGCTTGTGTTTCTTTTGTATT 58.236 29.630 0.00 0.00 38.95 1.89
265 3230 4.085107 GCTTGTGTTTCTTTTGTATTGGCG 60.085 41.667 0.00 0.00 0.00 5.69
287 3252 2.038659 GAGACTCTCCTCCCTTCATGG 58.961 57.143 0.00 0.00 0.00 3.66
291 3256 0.621571 TCTCCTCCCTTCATGGTGGG 60.622 60.000 15.15 15.15 44.66 4.61
297 3262 0.332632 CCCTTCATGGTGGGTGACAT 59.667 55.000 13.63 0.00 38.65 3.06
299 3264 1.372582 CTTCATGGTGGGTGACATCG 58.627 55.000 0.00 0.00 30.79 3.84
301 3266 1.451927 CATGGTGGGTGACATCGGG 60.452 63.158 0.00 0.00 30.79 5.14
334 3299 2.749076 TGATGCCACATGCTTCTTGTAC 59.251 45.455 0.00 0.00 42.91 2.90
384 3352 1.106285 CATTCCTTGGGCCAGCTAAC 58.894 55.000 6.23 0.00 0.00 2.34
389 3357 0.678048 CTTGGGCCAGCTAACTCCAC 60.678 60.000 6.23 0.00 0.00 4.02
397 3365 0.603569 AGCTAACTCCACACGTCCAG 59.396 55.000 0.00 0.00 0.00 3.86
471 3462 2.009042 GCAAGGATGTGGGAAGACGAG 61.009 57.143 0.00 0.00 0.00 4.18
486 3477 5.065346 GGAAGACGAGCTCGATGATCATATA 59.935 44.000 40.58 0.00 43.02 0.86
490 3481 6.804295 AGACGAGCTCGATGATCATATAAAAC 59.196 38.462 40.58 9.48 43.02 2.43
491 3482 6.682746 ACGAGCTCGATGATCATATAAAACT 58.317 36.000 40.58 10.63 43.02 2.66
493 3484 6.252441 CGAGCTCGATGATCATATAAAACTCC 59.748 42.308 32.06 0.00 43.02 3.85
494 3485 6.997655 AGCTCGATGATCATATAAAACTCCA 58.002 36.000 8.54 0.00 0.00 3.86
496 3487 6.091441 GCTCGATGATCATATAAAACTCCACC 59.909 42.308 8.54 0.00 0.00 4.61
497 3488 7.303182 TCGATGATCATATAAAACTCCACCT 57.697 36.000 8.54 0.00 0.00 4.00
498 3489 8.417273 TCGATGATCATATAAAACTCCACCTA 57.583 34.615 8.54 0.00 0.00 3.08
499 3490 8.523658 TCGATGATCATATAAAACTCCACCTAG 58.476 37.037 8.54 0.00 0.00 3.02
500 3491 8.523658 CGATGATCATATAAAACTCCACCTAGA 58.476 37.037 8.54 0.00 0.00 2.43
501 3492 9.646427 GATGATCATATAAAACTCCACCTAGAC 57.354 37.037 8.54 0.00 0.00 2.59
502 3493 8.547481 TGATCATATAAAACTCCACCTAGACA 57.453 34.615 0.00 0.00 0.00 3.41
503 3494 8.421784 TGATCATATAAAACTCCACCTAGACAC 58.578 37.037 0.00 0.00 0.00 3.67
504 3495 7.120923 TCATATAAAACTCCACCTAGACACC 57.879 40.000 0.00 0.00 0.00 4.16
511 3502 1.265454 CCACCTAGACACCCACCCTC 61.265 65.000 0.00 0.00 0.00 4.30
514 3505 1.305046 CTAGACACCCACCCTCGGT 60.305 63.158 0.00 0.00 35.62 4.69
527 3518 4.336280 CACCCTCGGTCTATAGATCATCA 58.664 47.826 13.42 0.00 31.02 3.07
648 3649 6.397272 TGAACTTTAAGCAATTAAGCATGGG 58.603 36.000 0.00 0.00 36.85 4.00
912 3917 0.393808 AAGCCGGTGTGTGAACTTGT 60.394 50.000 1.90 0.00 0.00 3.16
948 3954 3.318557 GGACTCCTGTATAAAGAGGTCCG 59.681 52.174 14.33 0.00 37.43 4.79
992 3998 3.426568 GGCAGCAGCAAGGACGAC 61.427 66.667 2.65 0.00 44.61 4.34
993 3999 3.782244 GCAGCAGCAAGGACGACG 61.782 66.667 0.00 0.00 41.58 5.12
1152 4168 7.471657 AAATAACGATCGTTACATGTATGCA 57.528 32.000 35.71 17.22 42.44 3.96
1187 4219 1.867233 TCGCTTCACTTGTTCTTCTGC 59.133 47.619 0.00 0.00 0.00 4.26
1215 4247 4.070552 ACGCTTCCTCCGTCCAGC 62.071 66.667 0.00 0.00 32.83 4.85
1286 4318 2.605097 GGTAGTAGAAGCTTCCGATCGC 60.605 54.545 22.81 9.06 0.00 4.58
1434 4474 3.561213 CTGCGCCGCTCATGTCAG 61.561 66.667 11.67 0.00 0.00 3.51
1439 4529 2.202987 CCGCTCATGTCAGGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
1462 4552 3.063045 GCGGCGTGCTTAATTACTTACTT 59.937 43.478 9.37 0.00 41.73 2.24
1542 4644 2.097954 TCAAGCAGACACAGCAAAAGTG 59.902 45.455 0.00 0.00 42.56 3.16
1552 4654 3.983344 CACAGCAAAAGTGTAGCATTTCC 59.017 43.478 0.00 0.00 32.44 3.13
1553 4655 3.005791 ACAGCAAAAGTGTAGCATTTCCC 59.994 43.478 0.00 0.00 0.00 3.97
1570 4673 2.639286 CTTCTTGGTGTGCACGCC 59.361 61.111 37.09 37.09 46.40 5.68
1704 4812 2.809601 GCAGCCTGTACGTGGACG 60.810 66.667 0.00 0.00 46.33 4.79
2690 5806 3.787634 CCTCAACGCATTTTGAATCATCG 59.212 43.478 0.00 0.00 35.07 3.84
2756 5872 1.728426 CGACGACGAGAACCACACC 60.728 63.158 0.00 0.00 42.66 4.16
3004 6120 0.531200 GACCCCTACACCTTCGACAG 59.469 60.000 0.00 0.00 0.00 3.51
3640 6774 2.584261 AAGCTCATGATCGGTGCGCT 62.584 55.000 9.73 8.96 39.14 5.92
3642 6776 2.278792 TCATGATCGGTGCGCTCG 60.279 61.111 9.73 13.28 0.00 5.03
3645 6779 3.723235 ATGATCGGTGCGCTCGCTT 62.723 57.895 9.73 3.97 42.51 4.68
3652 6786 4.357947 TGCGCTCGCTTCGACCTT 62.358 61.111 9.73 0.00 42.51 3.50
3653 6787 3.843240 GCGCTCGCTTCGACCTTG 61.843 66.667 0.00 0.00 38.26 3.61
3654 6788 2.126463 CGCTCGCTTCGACCTTGA 60.126 61.111 0.00 0.00 0.00 3.02
3655 6789 1.517257 CGCTCGCTTCGACCTTGAT 60.517 57.895 0.00 0.00 0.00 2.57
3730 6869 0.962489 CACTCTCACCTTGTCCGACT 59.038 55.000 0.00 0.00 0.00 4.18
3731 6870 1.068194 CACTCTCACCTTGTCCGACTC 60.068 57.143 0.00 0.00 0.00 3.36
3732 6871 0.528470 CTCTCACCTTGTCCGACTCC 59.472 60.000 0.00 0.00 0.00 3.85
3733 6872 1.213013 CTCACCTTGTCCGACTCCG 59.787 63.158 0.00 0.00 0.00 4.63
3734 6873 1.228337 TCACCTTGTCCGACTCCGA 60.228 57.895 0.00 0.00 38.22 4.55
3735 6874 1.080705 CACCTTGTCCGACTCCGAC 60.081 63.158 0.00 0.00 38.22 4.79
3739 6878 2.820767 CTTGTCCGACTCCGACCTGC 62.821 65.000 0.00 0.00 38.22 4.85
3936 7075 0.801251 GAGCACTTCATGAGCCACAC 59.199 55.000 0.00 0.00 32.56 3.82
4226 7365 2.667137 GTTCTTCTGTCACGTGAGGAG 58.333 52.381 20.73 17.56 0.00 3.69
4273 7412 9.387257 TCATATATTCATATGATTGACTGGCAC 57.613 33.333 6.17 0.00 45.24 5.01
4274 7413 9.392259 CATATATTCATATGATTGACTGGCACT 57.608 33.333 6.17 0.00 44.70 4.40
4276 7415 4.077300 TCATATGATTGACTGGCACTCC 57.923 45.455 0.00 0.00 0.00 3.85
4277 7416 3.144506 CATATGATTGACTGGCACTCCC 58.855 50.000 0.00 0.00 0.00 4.30
4279 7418 0.615331 TGATTGACTGGCACTCCCTC 59.385 55.000 0.00 0.00 0.00 4.30
4280 7419 0.107459 GATTGACTGGCACTCCCTCC 60.107 60.000 0.00 0.00 0.00 4.30
4281 7420 1.903877 ATTGACTGGCACTCCCTCCG 61.904 60.000 0.00 0.00 0.00 4.63
4282 7421 4.459089 GACTGGCACTCCCTCCGC 62.459 72.222 0.00 0.00 0.00 5.54
4284 7423 4.154347 CTGGCACTCCCTCCGCTC 62.154 72.222 0.00 0.00 0.00 5.03
4291 7430 4.667935 TCCCTCCGCTCCCCCAAA 62.668 66.667 0.00 0.00 0.00 3.28
4292 7431 3.657350 CCCTCCGCTCCCCCAAAA 61.657 66.667 0.00 0.00 0.00 2.44
4293 7432 2.438795 CCTCCGCTCCCCCAAAAA 59.561 61.111 0.00 0.00 0.00 1.94
4319 7458 9.844257 AATTGACAACTTTCATTTATTTTGGGA 57.156 25.926 0.00 0.00 0.00 4.37
4320 7459 8.655651 TTGACAACTTTCATTTATTTTGGGAC 57.344 30.769 0.00 0.00 0.00 4.46
4321 7460 6.920758 TGACAACTTTCATTTATTTTGGGACG 59.079 34.615 0.00 0.00 0.00 4.79
4322 7461 6.220201 ACAACTTTCATTTATTTTGGGACGG 58.780 36.000 0.00 0.00 0.00 4.79
4323 7462 6.041069 ACAACTTTCATTTATTTTGGGACGGA 59.959 34.615 0.00 0.00 0.00 4.69
4324 7463 6.658188 ACTTTCATTTATTTTGGGACGGAA 57.342 33.333 0.00 0.00 0.00 4.30
4325 7464 6.687604 ACTTTCATTTATTTTGGGACGGAAG 58.312 36.000 0.00 0.00 0.00 3.46
4326 7465 5.652994 TTCATTTATTTTGGGACGGAAGG 57.347 39.130 0.00 0.00 0.00 3.46
4327 7466 4.924625 TCATTTATTTTGGGACGGAAGGA 58.075 39.130 0.00 0.00 0.00 3.36
4328 7467 4.947388 TCATTTATTTTGGGACGGAAGGAG 59.053 41.667 0.00 0.00 0.00 3.69
4329 7468 4.376225 TTTATTTTGGGACGGAAGGAGT 57.624 40.909 0.00 0.00 0.00 3.85
4330 7469 2.491675 ATTTTGGGACGGAAGGAGTC 57.508 50.000 0.00 0.00 37.86 3.36
4331 7470 1.430992 TTTTGGGACGGAAGGAGTCT 58.569 50.000 0.00 0.00 38.58 3.24
4332 7471 0.685097 TTTGGGACGGAAGGAGTCTG 59.315 55.000 0.00 0.00 38.58 3.51
4333 7472 0.178944 TTGGGACGGAAGGAGTCTGA 60.179 55.000 0.00 0.00 38.58 3.27
4334 7473 0.178944 TGGGACGGAAGGAGTCTGAA 60.179 55.000 0.00 0.00 38.58 3.02
4335 7474 0.533032 GGGACGGAAGGAGTCTGAAG 59.467 60.000 0.00 0.00 38.58 3.02
4336 7475 1.258676 GGACGGAAGGAGTCTGAAGT 58.741 55.000 0.00 0.00 38.58 3.01
4337 7476 2.444421 GGACGGAAGGAGTCTGAAGTA 58.556 52.381 0.00 0.00 38.58 2.24
4338 7477 2.424246 GGACGGAAGGAGTCTGAAGTAG 59.576 54.545 0.00 0.00 38.58 2.57
4339 7478 1.819903 ACGGAAGGAGTCTGAAGTAGC 59.180 52.381 0.00 0.00 36.37 3.58
4340 7479 1.819288 CGGAAGGAGTCTGAAGTAGCA 59.181 52.381 0.00 0.00 34.07 3.49
4341 7480 2.231478 CGGAAGGAGTCTGAAGTAGCAA 59.769 50.000 0.00 0.00 34.07 3.91
4342 7481 3.118956 CGGAAGGAGTCTGAAGTAGCAAT 60.119 47.826 0.00 0.00 34.07 3.56
4372 7511 7.386848 ACAAAAGAGAGTAAGCAAGCGTATAAA 59.613 33.333 0.00 0.00 0.00 1.40
4381 7520 2.419574 GCAAGCGTATAAAGGGACCTGA 60.420 50.000 0.00 0.00 0.00 3.86
4390 7529 2.856760 AAGGGACCTGATGAGCTCTA 57.143 50.000 16.19 1.49 0.00 2.43
4395 7534 5.219739 AGGGACCTGATGAGCTCTATAAAA 58.780 41.667 16.19 0.00 0.00 1.52
4436 7575 0.100325 TCCAAGCGCACTTTGTTGTG 59.900 50.000 11.47 0.00 40.62 3.33
4437 7576 0.179140 CCAAGCGCACTTTGTTGTGT 60.179 50.000 11.47 0.00 39.89 3.72
4438 7577 1.191096 CAAGCGCACTTTGTTGTGTC 58.809 50.000 11.47 0.00 39.89 3.67
4439 7578 0.248054 AAGCGCACTTTGTTGTGTCG 60.248 50.000 11.47 0.00 39.89 4.35
4440 7579 2.285857 GCGCACTTTGTTGTGTCGC 61.286 57.895 0.30 15.65 46.48 5.19
4441 7580 1.351707 CGCACTTTGTTGTGTCGCT 59.648 52.632 0.00 0.00 39.89 4.93
4442 7581 0.925267 CGCACTTTGTTGTGTCGCTG 60.925 55.000 0.00 0.00 39.89 5.18
4443 7582 0.376852 GCACTTTGTTGTGTCGCTGA 59.623 50.000 0.00 0.00 39.89 4.26
4444 7583 1.595489 GCACTTTGTTGTGTCGCTGAG 60.595 52.381 0.00 0.00 39.89 3.35
4445 7584 1.665679 CACTTTGTTGTGTCGCTGAGT 59.334 47.619 0.00 0.00 33.61 3.41
4446 7585 2.863740 CACTTTGTTGTGTCGCTGAGTA 59.136 45.455 0.00 0.00 33.61 2.59
4447 7586 3.060272 CACTTTGTTGTGTCGCTGAGTAG 60.060 47.826 0.00 0.00 33.61 2.57
4448 7587 3.181479 ACTTTGTTGTGTCGCTGAGTAGA 60.181 43.478 0.00 0.00 0.00 2.59
4449 7588 2.417339 TGTTGTGTCGCTGAGTAGAC 57.583 50.000 3.84 3.84 37.85 2.59
4450 7589 1.328439 GTTGTGTCGCTGAGTAGACG 58.672 55.000 5.93 0.00 40.05 4.18
4451 7590 0.386858 TTGTGTCGCTGAGTAGACGC 60.387 55.000 13.81 13.81 45.18 5.19
4452 7591 1.209383 GTGTCGCTGAGTAGACGCA 59.791 57.895 15.14 0.00 44.56 5.24
4453 7592 1.066114 GTGTCGCTGAGTAGACGCAC 61.066 60.000 15.14 4.72 44.56 5.34
4454 7593 1.235281 TGTCGCTGAGTAGACGCACT 61.235 55.000 5.93 0.00 40.05 4.40
4455 7594 0.725686 GTCGCTGAGTAGACGCACTA 59.274 55.000 0.00 0.00 0.00 2.74
4470 7609 4.789095 CGCACTACGTGGCTAAATTATT 57.211 40.909 0.00 0.00 36.87 1.40
4471 7610 4.514506 CGCACTACGTGGCTAAATTATTG 58.485 43.478 0.00 0.00 36.87 1.90
4472 7611 4.033587 CGCACTACGTGGCTAAATTATTGT 59.966 41.667 0.00 0.00 36.87 2.71
4473 7612 5.232626 CGCACTACGTGGCTAAATTATTGTA 59.767 40.000 0.00 0.00 36.87 2.41
4474 7613 6.416514 GCACTACGTGGCTAAATTATTGTAC 58.583 40.000 0.00 0.00 33.64 2.90
4475 7614 6.257193 GCACTACGTGGCTAAATTATTGTACT 59.743 38.462 0.00 0.00 33.64 2.73
4476 7615 7.436080 GCACTACGTGGCTAAATTATTGTACTA 59.564 37.037 0.00 0.00 33.64 1.82
4477 7616 8.749499 CACTACGTGGCTAAATTATTGTACTAC 58.251 37.037 0.00 0.00 0.00 2.73
4478 7617 7.922811 ACTACGTGGCTAAATTATTGTACTACC 59.077 37.037 0.00 0.00 0.00 3.18
4479 7618 6.642430 ACGTGGCTAAATTATTGTACTACCA 58.358 36.000 0.00 0.00 0.00 3.25
4480 7619 7.104939 ACGTGGCTAAATTATTGTACTACCAA 58.895 34.615 0.00 0.00 0.00 3.67
4481 7620 7.607223 ACGTGGCTAAATTATTGTACTACCAAA 59.393 33.333 0.00 0.00 0.00 3.28
4482 7621 8.452534 CGTGGCTAAATTATTGTACTACCAAAA 58.547 33.333 0.00 0.00 0.00 2.44
4503 7642 5.651387 AAAAGAGTCGTCTCATGAGATCA 57.349 39.130 27.51 14.66 42.66 2.92
4504 7643 5.850557 AAAGAGTCGTCTCATGAGATCAT 57.149 39.130 27.51 14.32 42.66 2.45
4505 7644 5.437289 AAGAGTCGTCTCATGAGATCATC 57.563 43.478 27.51 20.83 42.66 2.92
4506 7645 3.498018 AGAGTCGTCTCATGAGATCATCG 59.502 47.826 27.51 23.96 42.66 3.84
4507 7646 2.551887 AGTCGTCTCATGAGATCATCGG 59.448 50.000 27.51 12.96 39.97 4.18
4508 7647 1.882623 TCGTCTCATGAGATCATCGGG 59.117 52.381 27.51 11.42 39.97 5.14
4509 7648 1.611006 CGTCTCATGAGATCATCGGGT 59.389 52.381 27.51 0.00 39.97 5.28
4510 7649 2.606551 CGTCTCATGAGATCATCGGGTG 60.607 54.545 27.51 6.60 39.97 4.61
4511 7650 2.363680 GTCTCATGAGATCATCGGGTGT 59.636 50.000 27.51 0.00 39.97 4.16
4512 7651 2.363359 TCTCATGAGATCATCGGGTGTG 59.637 50.000 21.67 0.00 33.61 3.82
4513 7652 2.363359 CTCATGAGATCATCGGGTGTGA 59.637 50.000 18.34 0.00 33.61 3.58
4514 7653 2.765699 TCATGAGATCATCGGGTGTGAA 59.234 45.455 0.00 0.00 33.61 3.18
4515 7654 3.389002 TCATGAGATCATCGGGTGTGAAT 59.611 43.478 0.00 0.00 33.61 2.57
4516 7655 3.912496 TGAGATCATCGGGTGTGAATT 57.088 42.857 0.00 0.00 0.00 2.17
4517 7656 4.220693 TGAGATCATCGGGTGTGAATTT 57.779 40.909 0.00 0.00 0.00 1.82
4518 7657 5.351948 TGAGATCATCGGGTGTGAATTTA 57.648 39.130 0.00 0.00 0.00 1.40
4519 7658 5.928976 TGAGATCATCGGGTGTGAATTTAT 58.071 37.500 0.00 0.00 0.00 1.40
4520 7659 6.356556 TGAGATCATCGGGTGTGAATTTATT 58.643 36.000 0.00 0.00 0.00 1.40
4521 7660 6.260714 TGAGATCATCGGGTGTGAATTTATTG 59.739 38.462 0.00 0.00 0.00 1.90
4522 7661 6.122277 AGATCATCGGGTGTGAATTTATTGT 58.878 36.000 0.00 0.00 0.00 2.71
4546 7685 8.530311 TGTGAGTAAATTGCATAAAACCATCAT 58.470 29.630 0.00 0.00 0.00 2.45
4547 7686 8.810427 GTGAGTAAATTGCATAAAACCATCATG 58.190 33.333 0.00 0.00 0.00 3.07
4565 7704 3.010027 TCATGTTGAGGGATAGGTTTGCA 59.990 43.478 0.00 0.00 0.00 4.08
4611 7750 1.605712 GCAGAAAGCACCACGTCTAGT 60.606 52.381 0.00 0.00 44.79 2.57
4628 7767 6.689669 ACGTCTAGTGTAATTGTTTTGCAAAC 59.310 34.615 12.39 8.01 40.91 2.93
4639 7778 3.194329 TGTTTTGCAAACACCACTGATCA 59.806 39.130 12.39 0.00 0.00 2.92
4801 7940 0.913205 GTCTCTTTTCCCCCTCCTCC 59.087 60.000 0.00 0.00 0.00 4.30
4802 7941 0.800239 TCTCTTTTCCCCCTCCTCCT 59.200 55.000 0.00 0.00 0.00 3.69
4803 7942 1.208706 CTCTTTTCCCCCTCCTCCTC 58.791 60.000 0.00 0.00 0.00 3.71
4927 8113 2.656069 CGTCGTCCTCCCCCATTGT 61.656 63.158 0.00 0.00 0.00 2.71
4930 8116 1.131303 TCGTCCTCCCCCATTGTTGT 61.131 55.000 0.00 0.00 0.00 3.32
4971 8157 4.819761 GAGATGCGCAGTCCGGCA 62.820 66.667 18.32 0.00 44.29 5.69
5045 8231 1.000107 GTAGTGGAGGAGGACCCGT 60.000 63.158 0.00 0.00 40.87 5.28
5178 8370 1.002624 GGTGAAGGCCAATCCGACA 60.003 57.895 5.01 0.00 40.77 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.749923 AACTTATGAAAGGCTCACATTCTC 57.250 37.500 10.67 0.00 36.69 2.87
43 44 6.681777 ACAAACTTATGAAAGGCTCACATTC 58.318 36.000 10.67 1.31 36.69 2.67
71 72 8.797438 TCAAAGAGCATAGACTATTATCGATGT 58.203 33.333 8.54 0.00 35.01 3.06
72 73 9.288124 CTCAAAGAGCATAGACTATTATCGATG 57.712 37.037 8.54 0.00 35.48 3.84
76 81 8.293867 ACGTCTCAAAGAGCATAGACTATTATC 58.706 37.037 0.00 0.00 36.94 1.75
108 116 2.435234 GTAACGGCGCCATCCACA 60.435 61.111 28.98 1.13 0.00 4.17
109 117 3.560278 CGTAACGGCGCCATCCAC 61.560 66.667 28.98 16.61 0.00 4.02
110 118 3.761140 TCGTAACGGCGCCATCCA 61.761 61.111 28.98 4.90 0.00 3.41
198 206 3.019964 GGGTGCAACACATCAGACA 57.980 52.632 3.06 0.00 42.56 3.41
261 3226 1.679305 GGAGGAGAGTCTCACGCCA 60.679 63.158 21.53 0.00 35.58 5.69
265 3230 2.223803 TGAAGGGAGGAGAGTCTCAC 57.776 55.000 21.53 13.93 37.45 3.51
287 3252 2.536997 CTTCCCCCGATGTCACCCAC 62.537 65.000 0.00 0.00 0.00 4.61
291 3256 1.486726 AGATTCTTCCCCCGATGTCAC 59.513 52.381 0.00 0.00 0.00 3.67
297 3262 2.303022 GCATCATAGATTCTTCCCCCGA 59.697 50.000 0.00 0.00 0.00 5.14
299 3264 2.376518 TGGCATCATAGATTCTTCCCCC 59.623 50.000 0.00 0.00 0.00 5.40
301 3266 4.090761 TGTGGCATCATAGATTCTTCCC 57.909 45.455 0.00 0.00 0.00 3.97
334 3299 0.033228 CAAGCCTAGAGGATGGAGCG 59.967 60.000 0.00 0.00 37.39 5.03
384 3352 2.386661 AATTAGCTGGACGTGTGGAG 57.613 50.000 0.00 0.00 0.00 3.86
389 3357 4.929808 ACTGAACTTAATTAGCTGGACGTG 59.070 41.667 0.00 0.00 0.00 4.49
421 3396 4.814234 TCACGGTATGGCATTGTAAATCTC 59.186 41.667 4.78 0.00 0.00 2.75
471 3462 6.091441 GGTGGAGTTTTATATGATCATCGAGC 59.909 42.308 12.53 0.00 0.00 5.03
486 3477 2.105993 GTGGGTGTCTAGGTGGAGTTTT 59.894 50.000 0.00 0.00 0.00 2.43
490 3481 1.265454 GGGTGGGTGTCTAGGTGGAG 61.265 65.000 0.00 0.00 0.00 3.86
491 3482 1.229400 GGGTGGGTGTCTAGGTGGA 60.229 63.158 0.00 0.00 0.00 4.02
493 3484 1.605058 CGAGGGTGGGTGTCTAGGTG 61.605 65.000 0.00 0.00 0.00 4.00
494 3485 1.305046 CGAGGGTGGGTGTCTAGGT 60.305 63.158 0.00 0.00 0.00 3.08
496 3487 1.305046 ACCGAGGGTGGGTGTCTAG 60.305 63.158 0.00 0.00 36.14 2.43
497 3488 1.304713 GACCGAGGGTGGGTGTCTA 60.305 63.158 0.00 0.00 38.07 2.59
498 3489 1.797018 TAGACCGAGGGTGGGTGTCT 61.797 60.000 0.00 0.00 38.07 3.41
499 3490 0.686769 ATAGACCGAGGGTGGGTGTC 60.687 60.000 0.00 0.00 38.07 3.67
500 3491 0.632835 TATAGACCGAGGGTGGGTGT 59.367 55.000 0.00 0.00 38.07 4.16
501 3492 1.133575 TCTATAGACCGAGGGTGGGTG 60.134 57.143 0.00 0.00 38.07 4.61
502 3493 1.229131 TCTATAGACCGAGGGTGGGT 58.771 55.000 0.00 0.00 41.48 4.51
503 3494 2.225041 TGATCTATAGACCGAGGGTGGG 60.225 54.545 4.10 0.00 35.25 4.61
504 3495 3.156288 TGATCTATAGACCGAGGGTGG 57.844 52.381 4.10 0.00 35.25 4.61
511 3502 4.486090 CCCGTTTGATGATCTATAGACCG 58.514 47.826 4.10 0.00 0.00 4.79
514 3505 5.144832 TCACCCCGTTTGATGATCTATAGA 58.855 41.667 4.57 4.57 0.00 1.98
648 3649 0.459489 TTGCTGTTGGTGTGGAAAGC 59.541 50.000 0.00 0.00 0.00 3.51
657 3658 0.698238 TCCTAGGCATTGCTGTTGGT 59.302 50.000 2.96 0.00 0.00 3.67
716 3717 3.313526 TCGCCTAATCTCTAACCGTACAC 59.686 47.826 0.00 0.00 0.00 2.90
898 3903 1.935933 AGACGACAAGTTCACACACC 58.064 50.000 0.00 0.00 0.00 4.16
992 3998 3.405093 TTAGAGCCCATGCCTGCCG 62.405 63.158 0.00 0.00 38.69 5.69
993 3999 1.527844 CTTAGAGCCCATGCCTGCC 60.528 63.158 0.00 0.00 38.69 4.85
1152 4168 0.251341 AGCGAGGACCAGCCATTTTT 60.251 50.000 8.16 0.00 40.02 1.94
1187 4219 2.383527 GGAAGCGTGGCGAGAACAG 61.384 63.158 0.00 0.00 0.00 3.16
1265 4297 2.605097 GCGATCGGAAGCTTCTACTACC 60.605 54.545 25.05 7.94 0.00 3.18
1286 4318 2.125106 GCCACTAGCTGGTTCGGG 60.125 66.667 0.00 0.00 42.99 5.14
1462 4552 6.841443 TTTACGTTCATTTTTACCTCGACA 57.159 33.333 0.00 0.00 0.00 4.35
1490 4580 5.236655 TCTCATCGCCATATATCGTCTTC 57.763 43.478 0.00 0.00 0.00 2.87
1542 4644 3.191371 CACACCAAGAAGGGAAATGCTAC 59.809 47.826 0.00 0.00 43.89 3.58
1544 4646 2.242043 CACACCAAGAAGGGAAATGCT 58.758 47.619 0.00 0.00 43.89 3.79
1545 4647 1.337167 GCACACCAAGAAGGGAAATGC 60.337 52.381 0.00 0.00 43.89 3.56
1546 4648 1.962807 TGCACACCAAGAAGGGAAATG 59.037 47.619 0.00 0.00 43.89 2.32
1547 4649 1.963515 GTGCACACCAAGAAGGGAAAT 59.036 47.619 13.17 0.00 43.89 2.17
1550 4652 1.227823 CGTGCACACCAAGAAGGGA 60.228 57.895 18.64 0.00 43.89 4.20
1551 4653 2.908073 GCGTGCACACCAAGAAGGG 61.908 63.158 18.64 0.00 43.89 3.95
1552 4654 2.639286 GCGTGCACACCAAGAAGG 59.361 61.111 18.64 0.00 45.67 3.46
1553 4655 1.518056 ATGGCGTGCACACCAAGAAG 61.518 55.000 29.08 5.20 39.96 2.85
1570 4673 0.802222 CACCGCACGAGTACTCCATG 60.802 60.000 17.23 15.79 0.00 3.66
2399 5507 1.138036 CGTCTTCATCACGCCGGTA 59.862 57.895 1.90 0.00 0.00 4.02
2603 5711 0.038251 CTATGCCGCCGATGAAGCTA 60.038 55.000 0.00 0.00 0.00 3.32
2690 5806 6.989437 TCGTCAGATAAAAATCGTTGATGAC 58.011 36.000 0.00 0.00 33.05 3.06
2756 5872 3.068691 TCGAGCTCCCGGAACAGG 61.069 66.667 8.47 0.00 0.00 4.00
2987 6103 1.218316 GCTGTCGAAGGTGTAGGGG 59.782 63.158 0.00 0.00 0.00 4.79
3548 6682 3.775654 CCCTTCTCCGGCTTCGCT 61.776 66.667 0.00 0.00 0.00 4.93
3602 6736 2.420568 GGCGTGGACGTAGATGGGA 61.421 63.158 0.52 0.00 42.22 4.37
3640 6774 4.932799 TGAAATTAATCAAGGTCGAAGCGA 59.067 37.500 0.00 0.00 0.00 4.93
3642 6776 9.173939 CATTATGAAATTAATCAAGGTCGAAGC 57.826 33.333 0.00 0.00 32.06 3.86
3645 6779 7.011950 ACGCATTATGAAATTAATCAAGGTCGA 59.988 33.333 0.00 0.00 32.06 4.20
3648 6782 7.915397 GTGACGCATTATGAAATTAATCAAGGT 59.085 33.333 0.00 0.00 32.06 3.50
3649 6783 7.112009 CGTGACGCATTATGAAATTAATCAAGG 59.888 37.037 0.00 0.00 32.06 3.61
3650 6784 7.974837 CGTGACGCATTATGAAATTAATCAAG 58.025 34.615 0.00 0.00 32.06 3.02
3651 6785 7.890879 CGTGACGCATTATGAAATTAATCAA 57.109 32.000 0.00 0.00 32.06 2.57
3739 6878 0.037882 ACTCGTCATCCACTGCACAG 60.038 55.000 0.00 0.00 0.00 3.66
3763 6902 4.137872 TTCGCCGACCCCACGATC 62.138 66.667 0.00 0.00 35.48 3.69
4253 7392 5.068636 GGAGTGCCAGTCAATCATATGAAT 58.931 41.667 9.99 0.00 41.27 2.57
4254 7393 4.454678 GGAGTGCCAGTCAATCATATGAA 58.545 43.478 9.99 0.00 41.27 2.57
4256 7395 3.144506 GGGAGTGCCAGTCAATCATATG 58.855 50.000 1.31 0.00 41.27 1.78
4257 7396 3.051581 AGGGAGTGCCAGTCAATCATAT 58.948 45.455 2.50 0.00 41.27 1.78
4258 7397 2.435805 GAGGGAGTGCCAGTCAATCATA 59.564 50.000 2.50 0.00 41.27 2.15
4259 7398 1.211457 GAGGGAGTGCCAGTCAATCAT 59.789 52.381 2.50 0.00 41.27 2.45
4262 7401 1.903877 CGGAGGGAGTGCCAGTCAAT 61.904 60.000 2.50 0.00 35.15 2.57
4263 7402 2.583441 CGGAGGGAGTGCCAGTCAA 61.583 63.158 2.50 0.00 35.15 3.18
4267 7406 4.154347 GAGCGGAGGGAGTGCCAG 62.154 72.222 2.50 0.00 35.15 4.85
4274 7413 4.667935 TTTGGGGGAGCGGAGGGA 62.668 66.667 0.00 0.00 0.00 4.20
4276 7415 2.438795 TTTTTGGGGGAGCGGAGG 59.561 61.111 0.00 0.00 0.00 4.30
4293 7432 9.844257 TCCCAAAATAAATGAAAGTTGTCAATT 57.156 25.926 0.00 0.00 0.00 2.32
4294 7433 9.271828 GTCCCAAAATAAATGAAAGTTGTCAAT 57.728 29.630 0.00 0.00 0.00 2.57
4295 7434 7.436673 CGTCCCAAAATAAATGAAAGTTGTCAA 59.563 33.333 0.00 0.00 0.00 3.18
4296 7435 6.920758 CGTCCCAAAATAAATGAAAGTTGTCA 59.079 34.615 0.00 0.00 0.00 3.58
4297 7436 6.364976 CCGTCCCAAAATAAATGAAAGTTGTC 59.635 38.462 0.00 0.00 0.00 3.18
4298 7437 6.041069 TCCGTCCCAAAATAAATGAAAGTTGT 59.959 34.615 0.00 0.00 0.00 3.32
4299 7438 6.451393 TCCGTCCCAAAATAAATGAAAGTTG 58.549 36.000 0.00 0.00 0.00 3.16
4300 7439 6.658188 TCCGTCCCAAAATAAATGAAAGTT 57.342 33.333 0.00 0.00 0.00 2.66
4301 7440 6.295067 CCTTCCGTCCCAAAATAAATGAAAGT 60.295 38.462 0.00 0.00 0.00 2.66
4302 7441 6.071616 TCCTTCCGTCCCAAAATAAATGAAAG 60.072 38.462 0.00 0.00 0.00 2.62
4303 7442 5.775701 TCCTTCCGTCCCAAAATAAATGAAA 59.224 36.000 0.00 0.00 0.00 2.69
4304 7443 5.326069 TCCTTCCGTCCCAAAATAAATGAA 58.674 37.500 0.00 0.00 0.00 2.57
4305 7444 4.924625 TCCTTCCGTCCCAAAATAAATGA 58.075 39.130 0.00 0.00 0.00 2.57
4306 7445 4.705023 ACTCCTTCCGTCCCAAAATAAATG 59.295 41.667 0.00 0.00 0.00 2.32
4307 7446 4.930696 ACTCCTTCCGTCCCAAAATAAAT 58.069 39.130 0.00 0.00 0.00 1.40
4308 7447 4.042435 AGACTCCTTCCGTCCCAAAATAAA 59.958 41.667 0.00 0.00 31.83 1.40
4309 7448 3.585732 AGACTCCTTCCGTCCCAAAATAA 59.414 43.478 0.00 0.00 31.83 1.40
4310 7449 3.055385 CAGACTCCTTCCGTCCCAAAATA 60.055 47.826 0.00 0.00 31.83 1.40
4311 7450 1.985895 AGACTCCTTCCGTCCCAAAAT 59.014 47.619 0.00 0.00 31.83 1.82
4312 7451 1.071699 CAGACTCCTTCCGTCCCAAAA 59.928 52.381 0.00 0.00 31.83 2.44
4313 7452 0.685097 CAGACTCCTTCCGTCCCAAA 59.315 55.000 0.00 0.00 31.83 3.28
4314 7453 0.178944 TCAGACTCCTTCCGTCCCAA 60.179 55.000 0.00 0.00 31.83 4.12
4315 7454 0.178944 TTCAGACTCCTTCCGTCCCA 60.179 55.000 0.00 0.00 31.83 4.37
4316 7455 0.533032 CTTCAGACTCCTTCCGTCCC 59.467 60.000 0.00 0.00 31.83 4.46
4317 7456 1.258676 ACTTCAGACTCCTTCCGTCC 58.741 55.000 0.00 0.00 31.83 4.79
4318 7457 2.159352 GCTACTTCAGACTCCTTCCGTC 60.159 54.545 0.00 0.00 0.00 4.79
4319 7458 1.819903 GCTACTTCAGACTCCTTCCGT 59.180 52.381 0.00 0.00 0.00 4.69
4320 7459 1.819288 TGCTACTTCAGACTCCTTCCG 59.181 52.381 0.00 0.00 0.00 4.30
4321 7460 3.963428 TTGCTACTTCAGACTCCTTCC 57.037 47.619 0.00 0.00 0.00 3.46
4322 7461 3.620821 GCATTGCTACTTCAGACTCCTTC 59.379 47.826 0.16 0.00 0.00 3.46
4323 7462 3.604582 GCATTGCTACTTCAGACTCCTT 58.395 45.455 0.16 0.00 0.00 3.36
4324 7463 2.093235 GGCATTGCTACTTCAGACTCCT 60.093 50.000 8.82 0.00 0.00 3.69
4325 7464 2.284190 GGCATTGCTACTTCAGACTCC 58.716 52.381 8.82 0.00 0.00 3.85
4326 7465 2.675348 GTGGCATTGCTACTTCAGACTC 59.325 50.000 16.94 0.00 37.08 3.36
4327 7466 2.038952 TGTGGCATTGCTACTTCAGACT 59.961 45.455 23.22 0.00 40.66 3.24
4328 7467 2.426522 TGTGGCATTGCTACTTCAGAC 58.573 47.619 23.22 0.00 40.66 3.51
4329 7468 2.857186 TGTGGCATTGCTACTTCAGA 57.143 45.000 23.22 2.66 40.66 3.27
4330 7469 3.921119 TTTGTGGCATTGCTACTTCAG 57.079 42.857 23.22 0.00 40.66 3.02
4331 7470 3.888323 TCTTTTGTGGCATTGCTACTTCA 59.112 39.130 23.22 7.29 40.66 3.02
4332 7471 4.216257 TCTCTTTTGTGGCATTGCTACTTC 59.784 41.667 23.22 0.80 40.66 3.01
4333 7472 4.144297 TCTCTTTTGTGGCATTGCTACTT 58.856 39.130 23.22 0.00 40.66 2.24
4334 7473 3.754965 TCTCTTTTGTGGCATTGCTACT 58.245 40.909 23.22 0.00 40.66 2.57
4335 7474 3.503748 ACTCTCTTTTGTGGCATTGCTAC 59.496 43.478 17.31 17.31 40.44 3.58
4336 7475 3.754965 ACTCTCTTTTGTGGCATTGCTA 58.245 40.909 8.82 0.00 0.00 3.49
4337 7476 2.590821 ACTCTCTTTTGTGGCATTGCT 58.409 42.857 8.82 0.00 0.00 3.91
4338 7477 4.479619 CTTACTCTCTTTTGTGGCATTGC 58.520 43.478 0.00 0.00 0.00 3.56
4339 7478 4.022935 TGCTTACTCTCTTTTGTGGCATTG 60.023 41.667 0.00 0.00 0.00 2.82
4340 7479 4.144297 TGCTTACTCTCTTTTGTGGCATT 58.856 39.130 0.00 0.00 0.00 3.56
4341 7480 3.754965 TGCTTACTCTCTTTTGTGGCAT 58.245 40.909 0.00 0.00 0.00 4.40
4342 7481 3.207265 TGCTTACTCTCTTTTGTGGCA 57.793 42.857 0.00 0.00 0.00 4.92
4372 7511 4.477536 TTATAGAGCTCATCAGGTCCCT 57.522 45.455 17.77 0.00 46.80 4.20
4381 7520 9.118300 CTGGATTTCACTTTTTATAGAGCTCAT 57.882 33.333 17.77 9.95 0.00 2.90
4395 7534 7.563906 TGGAAAATTCAAACTGGATTTCACTT 58.436 30.769 0.00 0.00 0.00 3.16
4436 7575 0.725686 TAGTGCGTCTACTCAGCGAC 59.274 55.000 0.00 0.00 32.19 5.19
4437 7576 0.725686 GTAGTGCGTCTACTCAGCGA 59.274 55.000 10.38 0.00 43.93 4.93
4438 7577 0.586748 CGTAGTGCGTCTACTCAGCG 60.587 60.000 14.08 6.25 44.80 5.18
4439 7578 3.221834 CGTAGTGCGTCTACTCAGC 57.778 57.895 14.08 0.00 44.80 4.26
4453 7592 7.922278 TGGTAGTACAATAATTTAGCCACGTAG 59.078 37.037 2.06 0.00 0.00 3.51
4454 7593 7.780064 TGGTAGTACAATAATTTAGCCACGTA 58.220 34.615 2.06 0.00 0.00 3.57
4455 7594 6.642430 TGGTAGTACAATAATTTAGCCACGT 58.358 36.000 2.06 0.00 0.00 4.49
4456 7595 7.542534 TTGGTAGTACAATAATTTAGCCACG 57.457 36.000 2.06 0.00 0.00 4.94
4480 7619 6.030548 TGATCTCATGAGACGACTCTTTTT 57.969 37.500 27.37 7.70 42.99 1.94
4481 7620 5.651387 TGATCTCATGAGACGACTCTTTT 57.349 39.130 27.37 8.48 42.99 2.27
4482 7621 5.505489 CGATGATCTCATGAGACGACTCTTT 60.505 44.000 27.37 9.24 42.99 2.52
4483 7622 4.024133 CGATGATCTCATGAGACGACTCTT 60.024 45.833 27.37 17.65 42.99 2.85
4484 7623 3.498018 CGATGATCTCATGAGACGACTCT 59.502 47.826 27.37 10.80 42.99 3.24
4485 7624 3.364864 CCGATGATCTCATGAGACGACTC 60.365 52.174 27.37 20.10 40.75 3.36
4486 7625 2.551887 CCGATGATCTCATGAGACGACT 59.448 50.000 27.37 11.98 40.75 4.18
4487 7626 2.351253 CCCGATGATCTCATGAGACGAC 60.351 54.545 27.37 20.10 40.75 4.34
4488 7627 1.882623 CCCGATGATCTCATGAGACGA 59.117 52.381 27.37 16.71 40.75 4.20
4489 7628 1.611006 ACCCGATGATCTCATGAGACG 59.389 52.381 27.37 23.46 40.75 4.18
4490 7629 2.363680 ACACCCGATGATCTCATGAGAC 59.636 50.000 27.37 19.87 40.75 3.36
4491 7630 2.363359 CACACCCGATGATCTCATGAGA 59.637 50.000 27.03 27.03 42.37 3.27
4492 7631 2.363359 TCACACCCGATGATCTCATGAG 59.637 50.000 17.07 17.07 36.57 2.90
4493 7632 2.387757 TCACACCCGATGATCTCATGA 58.612 47.619 0.00 0.00 36.57 3.07
4494 7633 2.896745 TCACACCCGATGATCTCATG 57.103 50.000 0.00 0.00 36.57 3.07
4495 7634 4.428294 AATTCACACCCGATGATCTCAT 57.572 40.909 0.00 0.00 39.70 2.90
4496 7635 3.912496 AATTCACACCCGATGATCTCA 57.088 42.857 0.00 0.00 0.00 3.27
4497 7636 6.260936 ACAATAAATTCACACCCGATGATCTC 59.739 38.462 0.00 0.00 0.00 2.75
4498 7637 6.038603 CACAATAAATTCACACCCGATGATCT 59.961 38.462 0.00 0.00 0.00 2.75
4499 7638 6.038161 TCACAATAAATTCACACCCGATGATC 59.962 38.462 0.00 0.00 0.00 2.92
4500 7639 5.885352 TCACAATAAATTCACACCCGATGAT 59.115 36.000 0.00 0.00 0.00 2.45
4501 7640 5.249420 TCACAATAAATTCACACCCGATGA 58.751 37.500 0.00 0.00 0.00 2.92
4502 7641 5.123820 ACTCACAATAAATTCACACCCGATG 59.876 40.000 0.00 0.00 0.00 3.84
4503 7642 5.253330 ACTCACAATAAATTCACACCCGAT 58.747 37.500 0.00 0.00 0.00 4.18
4504 7643 4.647611 ACTCACAATAAATTCACACCCGA 58.352 39.130 0.00 0.00 0.00 5.14
4505 7644 6.489127 TTACTCACAATAAATTCACACCCG 57.511 37.500 0.00 0.00 0.00 5.28
4506 7645 9.139174 CAATTTACTCACAATAAATTCACACCC 57.861 33.333 0.82 0.00 39.22 4.61
4507 7646 8.647226 GCAATTTACTCACAATAAATTCACACC 58.353 33.333 0.82 0.00 39.22 4.16
4508 7647 9.190858 TGCAATTTACTCACAATAAATTCACAC 57.809 29.630 0.00 0.00 39.22 3.82
4509 7648 9.926158 ATGCAATTTACTCACAATAAATTCACA 57.074 25.926 0.00 3.55 39.22 3.58
4518 7657 9.369904 GATGGTTTTATGCAATTTACTCACAAT 57.630 29.630 0.00 0.00 0.00 2.71
4519 7658 8.363390 TGATGGTTTTATGCAATTTACTCACAA 58.637 29.630 0.00 0.00 0.00 3.33
4520 7659 7.890515 TGATGGTTTTATGCAATTTACTCACA 58.109 30.769 0.00 0.00 0.00 3.58
4521 7660 8.810427 CATGATGGTTTTATGCAATTTACTCAC 58.190 33.333 0.00 0.00 0.00 3.51
4522 7661 8.530311 ACATGATGGTTTTATGCAATTTACTCA 58.470 29.630 0.00 0.00 0.00 3.41
4543 7682 3.010027 TGCAAACCTATCCCTCAACATGA 59.990 43.478 0.00 0.00 0.00 3.07
4546 7685 3.517296 TTGCAAACCTATCCCTCAACA 57.483 42.857 0.00 0.00 0.00 3.33
4547 7686 4.864704 TTTTGCAAACCTATCCCTCAAC 57.135 40.909 12.39 0.00 0.00 3.18
4611 7750 5.349817 CAGTGGTGTTTGCAAAACAATTACA 59.650 36.000 14.67 3.36 38.31 2.41
4829 7968 0.913205 GGAGGAGGGGGAAGAAGAAC 59.087 60.000 0.00 0.00 0.00 3.01
4914 8100 1.131303 ACGACAACAATGGGGGAGGA 61.131 55.000 0.00 0.00 0.00 3.71
4927 8113 1.478916 TCTATGGAATGGCGACGACAA 59.521 47.619 7.85 0.00 0.00 3.18
4930 8116 2.093921 TGTTTCTATGGAATGGCGACGA 60.094 45.455 0.00 0.00 0.00 4.20
4971 8157 1.548582 CCACCAGCATCTCCACCTTTT 60.549 52.381 0.00 0.00 0.00 2.27
5021 8207 2.015587 GTCCTCCTCCACTACGTACTG 58.984 57.143 0.00 0.00 0.00 2.74
5022 8208 1.064832 GGTCCTCCTCCACTACGTACT 60.065 57.143 0.00 0.00 0.00 2.73
5045 8231 1.133761 ACAGCTCGCCTAGATCCACTA 60.134 52.381 0.00 0.00 0.00 2.74
5178 8370 2.437359 GCGATGTGCTGGCTTCCT 60.437 61.111 0.00 0.00 41.73 3.36


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

AutoCloner maintained by Alex Coulton.