Multiple sequence alignment - TraesCS6A01G072100

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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 TraesCS6A01G072100 chr6A 100.000 3549 0 0 1 3549 39425523 39429071 0.000000e+00 6554.0
1 TraesCS6A01G072100 chr6A 100.000 34 0 0 817 850 39460496 39460463 2.960000e-06 63.9
2 TraesCS6A01G072100 chr6D 91.402 3338 143 72 5 3276 35455263 35458522 0.000000e+00 4442.0
3 TraesCS6A01G072100 chr6D 82.313 1193 194 11 1371 2561 35492234 35491057 0.000000e+00 1018.0
4 TraesCS6A01G072100 chr6D 86.125 800 79 21 2 795 35453126 35453899 0.000000e+00 833.0
5 TraesCS6A01G072100 chr6D 86.040 351 40 6 2 350 11926754 11926411 5.600000e-98 368.0
6 TraesCS6A01G072100 chr6D 88.364 275 19 7 3284 3549 35467030 35467300 5.720000e-83 318.0
7 TraesCS6A01G072100 chr6D 96.970 33 1 0 818 850 35504440 35504408 4.950000e-04 56.5
8 TraesCS6A01G072100 chr6B 91.724 2163 129 28 1273 3420 73073502 73075629 0.000000e+00 2957.0
9 TraesCS6A01G072100 chr6B 90.047 1266 77 28 2170 3420 73102894 73104125 0.000000e+00 1594.0
10 TraesCS6A01G072100 chr6B 82.334 1234 197 14 1371 2599 73164113 73162896 0.000000e+00 1051.0
11 TraesCS6A01G072100 chr6B 80.904 1173 206 10 1377 2549 74205926 74204772 0.000000e+00 909.0
12 TraesCS6A01G072100 chr6B 80.904 1173 206 10 1377 2549 74341827 74340673 0.000000e+00 909.0
13 TraesCS6A01G072100 chr6B 82.285 1033 174 7 1371 2400 37632822 37633848 0.000000e+00 885.0
14 TraesCS6A01G072100 chr6B 80.563 1173 207 12 1377 2549 74448694 74447543 0.000000e+00 883.0
15 TraesCS6A01G072100 chr6B 81.633 1029 187 2 1377 2405 74029549 74028523 0.000000e+00 852.0
16 TraesCS6A01G072100 chr6B 92.053 302 17 6 351 650 73063526 73063822 5.480000e-113 418.0
17 TraesCS6A01G072100 chr6B 85.323 402 49 4 2 401 429265313 429264920 1.190000e-109 407.0
18 TraesCS6A01G072100 chr6B 85.522 297 14 8 795 1072 73063930 73064216 2.090000e-72 283.0
19 TraesCS6A01G072100 chr6B 92.913 127 8 1 1071 1197 73073367 73073492 2.180000e-42 183.0
20 TraesCS6A01G072100 chr1B 86.420 405 44 9 42 441 162141769 162142167 1.960000e-117 433.0
21 TraesCS6A01G072100 chr1B 92.754 69 5 0 1195 1263 568524120 568524188 2.250000e-17 100.0
22 TraesCS6A01G072100 chr2A 83.871 465 62 12 2 460 693891358 693891815 7.040000e-117 431.0
23 TraesCS6A01G072100 chr2A 91.892 74 4 2 1191 1263 103374727 103374799 6.270000e-18 102.0
24 TraesCS6A01G072100 chr7B 83.059 425 61 9 6 421 45177992 45178414 3.340000e-100 375.0
25 TraesCS6A01G072100 chr4B 83.500 400 62 3 2 399 419647946 419647549 1.560000e-98 370.0
26 TraesCS6A01G072100 chr4B 80.778 437 70 11 6 437 167957751 167958178 2.640000e-86 329.0
27 TraesCS6A01G072100 chr3D 81.995 411 66 7 18 425 497857876 497858281 3.390000e-90 342.0
28 TraesCS6A01G072100 chr5B 91.358 81 6 1 1184 1263 580683567 580683487 3.750000e-20 110.0
29 TraesCS6A01G072100 chr5B 85.000 60 7 2 2493 2551 546094053 546093995 3.830000e-05 60.2
30 TraesCS6A01G072100 chr2B 90.123 81 8 0 1183 1263 46846070 46846150 4.850000e-19 106.0
31 TraesCS6A01G072100 chr2B 92.958 71 4 1 1193 1263 799979274 799979205 6.270000e-18 102.0
32 TraesCS6A01G072100 chr5A 89.744 78 6 2 1193 1269 479748999 479748923 8.110000e-17 99.0
33 TraesCS6A01G072100 chr3A 92.754 69 4 1 1195 1263 24048033 24048100 8.110000e-17 99.0
34 TraesCS6A01G072100 chr3A 88.608 79 9 0 1195 1273 168540415 168540337 2.920000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G072100 chr6A 39425523 39429071 3548 False 6554.0 6554 100.0000 1 3549 1 chr6A.!!$F1 3548
1 TraesCS6A01G072100 chr6D 35453126 35458522 5396 False 2637.5 4442 88.7635 2 3276 2 chr6D.!!$F2 3274
2 TraesCS6A01G072100 chr6D 35491057 35492234 1177 True 1018.0 1018 82.3130 1371 2561 1 chr6D.!!$R2 1190
3 TraesCS6A01G072100 chr6B 73102894 73104125 1231 False 1594.0 1594 90.0470 2170 3420 1 chr6B.!!$F2 1250
4 TraesCS6A01G072100 chr6B 73073367 73075629 2262 False 1570.0 2957 92.3185 1071 3420 2 chr6B.!!$F4 2349
5 TraesCS6A01G072100 chr6B 73162896 73164113 1217 True 1051.0 1051 82.3340 1371 2599 1 chr6B.!!$R1 1228
6 TraesCS6A01G072100 chr6B 74204772 74205926 1154 True 909.0 909 80.9040 1377 2549 1 chr6B.!!$R3 1172
7 TraesCS6A01G072100 chr6B 74340673 74341827 1154 True 909.0 909 80.9040 1377 2549 1 chr6B.!!$R4 1172
8 TraesCS6A01G072100 chr6B 37632822 37633848 1026 False 885.0 885 82.2850 1371 2400 1 chr6B.!!$F1 1029
9 TraesCS6A01G072100 chr6B 74447543 74448694 1151 True 883.0 883 80.5630 1377 2549 1 chr6B.!!$R5 1172
10 TraesCS6A01G072100 chr6B 74028523 74029549 1026 True 852.0 852 81.6330 1377 2405 1 chr6B.!!$R2 1028
11 TraesCS6A01G072100 chr6B 73063526 73064216 690 False 350.5 418 88.7875 351 1072 2 chr6B.!!$F3 721

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
52 53 0.298707 CATTGCACGATCGAGAACCG 59.701 55.0 24.34 1.92 40.25 4.44 F
605 611 0.526211 GTCAAATGGAACGGAAGGCC 59.474 55.0 0.00 0.00 0.00 5.19 F
775 2869 1.007336 CGCGTACGTTTCCAGAGCTT 61.007 55.0 17.90 0.00 33.53 3.74 F
942 3069 1.050204 AAAGCATGCAAAAGGGCTCA 58.950 45.0 21.98 0.00 35.11 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 3223 1.153549 GGCTCGTCTCATCACCCAC 60.154 63.158 0.0 0.0 0.00 4.61 R
2094 4239 2.226437 GTGTGCAAATACACTGGGTCTG 59.774 50.000 0.0 0.0 45.70 3.51 R
2524 4669 3.055819 ACCGCGGATATCTTGCAGATAAT 60.056 43.478 35.9 0.0 40.28 1.28 R
2690 4845 3.149196 GCTTCCAAAACAGACCATGAGA 58.851 45.455 0.0 0.0 0.00 3.27 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
27 28 6.208204 CCTAAATAGGATCCAGGCATTTCTTG 59.792 42.308 15.82 7.71 46.63 3.02
36 37 2.235402 CAGGCATTTCTTGAAGGGCATT 59.765 45.455 11.12 0.00 45.85 3.56
40 41 2.818130 TTTCTTGAAGGGCATTGCAC 57.182 45.000 11.39 6.93 0.00 4.57
52 53 0.298707 CATTGCACGATCGAGAACCG 59.701 55.000 24.34 1.92 40.25 4.44
113 116 5.368145 TCACTGACAACTTCATAGCACTTT 58.632 37.500 0.00 0.00 32.17 2.66
130 133 4.848757 CACTTTCTAGTTGTGCTTTGTCC 58.151 43.478 0.00 0.00 30.26 4.02
147 150 6.868339 GCTTTGTCCTGTTATTTGCTACATTT 59.132 34.615 0.00 0.00 0.00 2.32
148 151 7.148755 GCTTTGTCCTGTTATTTGCTACATTTG 60.149 37.037 0.00 0.00 0.00 2.32
151 154 8.121305 TGTCCTGTTATTTGCTACATTTGAAT 57.879 30.769 0.00 0.00 0.00 2.57
157 160 9.288124 TGTTATTTGCTACATTTGAATCATTCG 57.712 29.630 0.00 0.00 0.00 3.34
158 161 8.745837 GTTATTTGCTACATTTGAATCATTCGG 58.254 33.333 0.00 0.00 0.00 4.30
162 165 5.030295 GCTACATTTGAATCATTCGGTGTG 58.970 41.667 10.66 2.66 0.00 3.82
183 186 8.166066 GGTGTGTTTAAATTTGAATAATTCGGC 58.834 33.333 0.00 0.00 0.00 5.54
185 188 9.482627 TGTGTTTAAATTTGAATAATTCGGCTT 57.517 25.926 0.00 0.00 0.00 4.35
192 195 9.705290 AAATTTGAATAATTCGGCTTGTAAACT 57.295 25.926 0.00 0.00 0.00 2.66
193 196 9.705290 AATTTGAATAATTCGGCTTGTAAACTT 57.295 25.926 0.00 0.00 0.00 2.66
201 204 4.778904 TCGGCTTGTAAACTTTGAATTCG 58.221 39.130 0.04 0.00 0.00 3.34
211 214 9.074443 TGTAAACTTTGAATTCGGTTTGTAAAC 57.926 29.630 22.56 16.63 38.17 2.01
240 243 5.716094 TGATGATTTGCTTGAACCTTCATG 58.284 37.500 0.00 0.00 37.00 3.07
252 256 7.062255 GCTTGAACCTTCATGTTTATGTTTAGC 59.938 37.037 0.00 0.00 37.00 3.09
257 261 7.820648 ACCTTCATGTTTATGTTTAGCTTCTG 58.179 34.615 0.00 0.00 35.73 3.02
262 266 9.448438 TCATGTTTATGTTTAGCTTCTGTATGT 57.552 29.630 0.00 0.00 35.73 2.29
263 267 9.494479 CATGTTTATGTTTAGCTTCTGTATGTG 57.506 33.333 0.00 0.00 0.00 3.21
264 268 8.615878 TGTTTATGTTTAGCTTCTGTATGTGT 57.384 30.769 0.00 0.00 0.00 3.72
349 353 6.233434 TCCGTTATAGTTAGAAGATCGGCTA 58.767 40.000 0.00 0.00 36.16 3.93
366 370 4.351874 GGCTATGTCAGGCCAATACTTA 57.648 45.455 5.01 1.72 46.84 2.24
423 427 5.248705 GGACGGGATCCTCCTCTATTTTATT 59.751 44.000 12.58 0.00 45.22 1.40
425 429 5.607171 ACGGGATCCTCCTCTATTTTATTGT 59.393 40.000 12.58 0.00 36.57 2.71
605 611 0.526211 GTCAAATGGAACGGAAGGCC 59.474 55.000 0.00 0.00 0.00 5.19
650 657 4.166888 GGCATCTGGAGCGCTGGA 62.167 66.667 18.48 11.00 0.00 3.86
651 658 2.588314 GCATCTGGAGCGCTGGAG 60.588 66.667 18.48 10.71 0.00 3.86
760 2854 3.649986 GGTTTGCAGCAGACGCGT 61.650 61.111 13.85 13.85 45.49 6.01
773 2867 3.070060 CGCGTACGTTTCCAGAGC 58.930 61.111 17.90 0.00 33.53 4.09
774 2868 1.443872 CGCGTACGTTTCCAGAGCT 60.444 57.895 17.90 0.00 33.53 4.09
775 2869 1.007336 CGCGTACGTTTCCAGAGCTT 61.007 55.000 17.90 0.00 33.53 3.74
793 2887 3.508048 GGGTCACCATGGGAACCT 58.492 61.111 27.55 2.11 43.82 3.50
868 2995 2.156891 GTGACTCCGTGTACGTACGTAA 59.843 50.000 28.34 16.10 42.24 3.18
942 3069 1.050204 AAAGCATGCAAAAGGGCTCA 58.950 45.000 21.98 0.00 35.11 4.26
974 3107 2.163613 CCATTCATCGCATCCATCCATG 59.836 50.000 0.00 0.00 0.00 3.66
986 3119 1.701292 CCATCCATGCTCCATACTCCA 59.299 52.381 0.00 0.00 0.00 3.86
1207 3352 4.159135 TGTTAGATTGTACTCCCTTCGTCC 59.841 45.833 0.00 0.00 0.00 4.79
1284 3429 8.559536 CATTACGGCACATAGTATCAATTTCTT 58.440 33.333 0.00 0.00 0.00 2.52
1829 3974 7.121611 TGTTAGTCTACGAGTTCATATCCAACA 59.878 37.037 0.00 0.00 0.00 3.33
2041 4186 7.625185 GCAGACTTTGGAACTTCAAGATACATC 60.625 40.741 0.00 0.00 0.00 3.06
2094 4239 1.876156 GCAAGGCACACTAGGATATGC 59.124 52.381 0.00 0.00 37.35 3.14
2159 4304 5.355350 AGTGATGTTTATAGCTTTGGTGCTC 59.645 40.000 0.00 0.00 42.97 4.26
2405 4550 3.623060 GGAATTGAGATTGCAAGTCGCTA 59.377 43.478 4.94 2.71 42.09 4.26
2406 4551 4.260538 GGAATTGAGATTGCAAGTCGCTAG 60.261 45.833 4.94 0.00 42.09 3.42
2428 4573 6.770286 AGATCATCTAAGGGATTTAAGGCA 57.230 37.500 0.00 0.00 31.27 4.75
2609 4754 4.917385 AGATTATGTGCACTTGGTTACCA 58.083 39.130 19.41 0.00 0.00 3.25
2626 4771 6.043590 TGGTTACCATGATGAGAATATGCTCT 59.956 38.462 12.15 0.00 35.91 4.09
3038 5197 1.255667 TTCCAGTCTACTCACCGGCC 61.256 60.000 0.00 0.00 0.00 6.13
3041 5200 2.753043 GTCTACTCACCGGCCCGA 60.753 66.667 3.71 0.00 0.00 5.14
3103 5266 4.578516 TCCGATAACAAAGGGTGCATAATG 59.421 41.667 0.00 0.00 0.00 1.90
3134 5298 9.301153 GAACACTAAACATTCAACTTGTTCATT 57.699 29.630 0.00 0.00 40.72 2.57
3156 5320 4.274602 TCACGTTTGGTTGGAGCTAATA 57.725 40.909 0.00 0.00 0.00 0.98
3310 5487 3.430895 AGACTATGCAAAACGGTAACACG 59.569 43.478 0.00 0.00 40.31 4.49
3320 5497 6.237622 GCAAAACGGTAACACGAAAGAATTTT 60.238 34.615 0.00 0.00 39.27 1.82
3321 5498 7.668190 CAAAACGGTAACACGAAAGAATTTTT 58.332 30.769 0.00 0.00 39.27 1.94
3337 5514 7.111247 AGAATTTTTGTGTTGGAACAGATGA 57.889 32.000 0.00 0.00 42.39 2.92
3340 5517 5.850557 TTTTGTGTTGGAACAGATGACAT 57.149 34.783 0.00 0.00 42.39 3.06
3341 5518 5.437289 TTTGTGTTGGAACAGATGACATC 57.563 39.130 7.39 7.39 42.39 3.06
3342 5519 4.356405 TGTGTTGGAACAGATGACATCT 57.644 40.909 12.37 12.37 42.39 2.90
3343 5520 5.482163 TGTGTTGGAACAGATGACATCTA 57.518 39.130 17.54 0.00 42.39 1.98
3344 5521 6.053632 TGTGTTGGAACAGATGACATCTAT 57.946 37.500 17.54 3.70 42.39 1.98
3411 5588 8.525290 AAGTGAATAGTTAGAAAATCCCATGG 57.475 34.615 4.14 4.14 0.00 3.66
3420 5597 8.150296 AGTTAGAAAATCCCATGGAAAACAAAG 58.850 33.333 15.22 0.00 34.34 2.77
3421 5598 5.308014 AGAAAATCCCATGGAAAACAAAGC 58.692 37.500 15.22 0.00 34.34 3.51
3422 5599 3.701205 AATCCCATGGAAAACAAAGCC 57.299 42.857 15.22 0.00 34.34 4.35
3423 5600 2.397044 TCCCATGGAAAACAAAGCCT 57.603 45.000 15.22 0.00 0.00 4.58
3424 5601 2.688477 TCCCATGGAAAACAAAGCCTT 58.312 42.857 15.22 0.00 0.00 4.35
3425 5602 3.044894 TCCCATGGAAAACAAAGCCTTT 58.955 40.909 15.22 0.00 0.00 3.11
3426 5603 4.227197 TCCCATGGAAAACAAAGCCTTTA 58.773 39.130 15.22 0.00 0.00 1.85
3427 5604 4.656112 TCCCATGGAAAACAAAGCCTTTAA 59.344 37.500 15.22 0.00 0.00 1.52
3428 5605 5.131142 TCCCATGGAAAACAAAGCCTTTAAA 59.869 36.000 15.22 0.00 0.00 1.52
3429 5606 5.238432 CCCATGGAAAACAAAGCCTTTAAAC 59.762 40.000 15.22 0.00 0.00 2.01
3430 5607 6.054941 CCATGGAAAACAAAGCCTTTAAACT 58.945 36.000 5.56 0.00 0.00 2.66
3431 5608 6.542005 CCATGGAAAACAAAGCCTTTAAACTT 59.458 34.615 5.56 0.00 0.00 2.66
3432 5609 7.066887 CCATGGAAAACAAAGCCTTTAAACTTT 59.933 33.333 5.56 0.00 36.56 2.66
3433 5610 9.103861 CATGGAAAACAAAGCCTTTAAACTTTA 57.896 29.630 4.10 0.00 34.42 1.85
3434 5611 9.674068 ATGGAAAACAAAGCCTTTAAACTTTAA 57.326 25.926 4.10 0.00 34.42 1.52
3435 5612 8.937884 TGGAAAACAAAGCCTTTAAACTTTAAC 58.062 29.630 4.10 0.00 34.42 2.01
3436 5613 8.392612 GGAAAACAAAGCCTTTAAACTTTAACC 58.607 33.333 4.10 0.00 34.42 2.85
3437 5614 7.528481 AAACAAAGCCTTTAAACTTTAACCG 57.472 32.000 4.10 0.00 34.42 4.44
3438 5615 6.211587 ACAAAGCCTTTAAACTTTAACCGT 57.788 33.333 4.10 0.00 34.42 4.83
3439 5616 7.332213 ACAAAGCCTTTAAACTTTAACCGTA 57.668 32.000 4.10 0.00 34.42 4.02
3440 5617 7.195646 ACAAAGCCTTTAAACTTTAACCGTAC 58.804 34.615 4.10 0.00 34.42 3.67
3441 5618 6.940831 AAGCCTTTAAACTTTAACCGTACA 57.059 33.333 0.00 0.00 0.00 2.90
3442 5619 7.514784 AAGCCTTTAAACTTTAACCGTACAT 57.485 32.000 0.00 0.00 0.00 2.29
3443 5620 8.620116 AAGCCTTTAAACTTTAACCGTACATA 57.380 30.769 0.00 0.00 0.00 2.29
3444 5621 8.260270 AGCCTTTAAACTTTAACCGTACATAG 57.740 34.615 0.00 0.00 0.00 2.23
3445 5622 7.879677 AGCCTTTAAACTTTAACCGTACATAGT 59.120 33.333 0.00 0.00 0.00 2.12
3446 5623 8.171196 GCCTTTAAACTTTAACCGTACATAGTC 58.829 37.037 0.00 0.00 0.00 2.59
3447 5624 9.206870 CCTTTAAACTTTAACCGTACATAGTCA 57.793 33.333 0.00 0.00 0.00 3.41
3451 5628 7.998753 AACTTTAACCGTACATAGTCATAGC 57.001 36.000 0.00 0.00 0.00 2.97
3452 5629 7.344095 ACTTTAACCGTACATAGTCATAGCT 57.656 36.000 0.00 0.00 0.00 3.32
3453 5630 7.779073 ACTTTAACCGTACATAGTCATAGCTT 58.221 34.615 0.00 0.00 0.00 3.74
3454 5631 8.255905 ACTTTAACCGTACATAGTCATAGCTTT 58.744 33.333 0.00 0.00 0.00 3.51
3455 5632 9.740239 CTTTAACCGTACATAGTCATAGCTTTA 57.260 33.333 0.00 0.00 0.00 1.85
3456 5633 9.740239 TTTAACCGTACATAGTCATAGCTTTAG 57.260 33.333 0.00 0.00 0.00 1.85
3457 5634 7.578310 AACCGTACATAGTCATAGCTTTAGA 57.422 36.000 0.00 0.00 0.00 2.10
3458 5635 6.968250 ACCGTACATAGTCATAGCTTTAGAC 58.032 40.000 0.00 0.00 0.00 2.59
3459 5636 6.016443 ACCGTACATAGTCATAGCTTTAGACC 60.016 42.308 0.00 0.00 32.82 3.85
3460 5637 6.016527 CCGTACATAGTCATAGCTTTAGACCA 60.017 42.308 0.00 0.00 32.82 4.02
3461 5638 7.309255 CCGTACATAGTCATAGCTTTAGACCAT 60.309 40.741 0.00 0.00 32.82 3.55
3462 5639 7.751348 CGTACATAGTCATAGCTTTAGACCATC 59.249 40.741 0.00 0.00 32.82 3.51
3463 5640 7.847711 ACATAGTCATAGCTTTAGACCATCT 57.152 36.000 0.00 0.00 32.82 2.90
3464 5641 7.665690 ACATAGTCATAGCTTTAGACCATCTG 58.334 38.462 0.00 0.00 32.82 2.90
3465 5642 5.543507 AGTCATAGCTTTAGACCATCTGG 57.456 43.478 0.00 0.00 42.17 3.86
3466 5643 5.211973 AGTCATAGCTTTAGACCATCTGGA 58.788 41.667 2.55 0.00 38.94 3.86
3467 5644 5.843421 AGTCATAGCTTTAGACCATCTGGAT 59.157 40.000 2.55 0.00 38.94 3.41
3468 5645 6.014669 AGTCATAGCTTTAGACCATCTGGATC 60.015 42.308 2.55 0.00 38.94 3.36
3469 5646 6.014669 GTCATAGCTTTAGACCATCTGGATCT 60.015 42.308 2.55 5.11 38.94 2.75
3470 5647 6.556495 TCATAGCTTTAGACCATCTGGATCTT 59.444 38.462 2.55 0.00 38.94 2.40
3471 5648 5.707066 AGCTTTAGACCATCTGGATCTTT 57.293 39.130 2.55 0.00 38.94 2.52
3472 5649 6.814954 AGCTTTAGACCATCTGGATCTTTA 57.185 37.500 2.55 0.00 38.94 1.85
3473 5650 6.587273 AGCTTTAGACCATCTGGATCTTTAC 58.413 40.000 2.55 0.00 38.94 2.01
3474 5651 6.385467 AGCTTTAGACCATCTGGATCTTTACT 59.615 38.462 2.55 0.00 38.94 2.24
3475 5652 7.051000 GCTTTAGACCATCTGGATCTTTACTT 58.949 38.462 2.55 0.00 38.94 2.24
3476 5653 7.554476 GCTTTAGACCATCTGGATCTTTACTTT 59.446 37.037 2.55 0.00 38.94 2.66
3480 5657 8.380742 AGACCATCTGGATCTTTACTTTAAGA 57.619 34.615 2.55 0.00 37.31 2.10
3481 5658 8.826765 AGACCATCTGGATCTTTACTTTAAGAA 58.173 33.333 2.55 0.00 36.87 2.52
3482 5659 9.449719 GACCATCTGGATCTTTACTTTAAGAAA 57.550 33.333 2.55 0.00 36.87 2.52
3483 5660 9.232473 ACCATCTGGATCTTTACTTTAAGAAAC 57.768 33.333 2.55 0.00 36.87 2.78
3484 5661 9.454859 CCATCTGGATCTTTACTTTAAGAAACT 57.545 33.333 0.00 0.00 37.66 2.66
3497 5674 8.732746 ACTTTAAGAAACTTACTGACATGTGT 57.267 30.769 1.15 0.00 0.00 3.72
3498 5675 8.612619 ACTTTAAGAAACTTACTGACATGTGTG 58.387 33.333 1.15 0.00 0.00 3.82
3499 5676 8.725405 TTTAAGAAACTTACTGACATGTGTGA 57.275 30.769 1.15 0.00 0.00 3.58
3500 5677 6.604735 AAGAAACTTACTGACATGTGTGAC 57.395 37.500 1.15 0.00 0.00 3.67
3501 5678 5.057149 AGAAACTTACTGACATGTGTGACC 58.943 41.667 1.15 0.00 0.00 4.02
3502 5679 4.415881 AACTTACTGACATGTGTGACCA 57.584 40.909 1.15 0.00 0.00 4.02
3503 5680 4.415881 ACTTACTGACATGTGTGACCAA 57.584 40.909 1.15 0.00 0.00 3.67
3504 5681 4.776349 ACTTACTGACATGTGTGACCAAA 58.224 39.130 1.15 0.00 0.00 3.28
3505 5682 4.816385 ACTTACTGACATGTGTGACCAAAG 59.184 41.667 1.15 0.00 0.00 2.77
3506 5683 1.949525 ACTGACATGTGTGACCAAAGC 59.050 47.619 1.15 0.00 0.00 3.51
3507 5684 2.224606 CTGACATGTGTGACCAAAGCT 58.775 47.619 1.15 0.00 0.00 3.74
3508 5685 2.620115 CTGACATGTGTGACCAAAGCTT 59.380 45.455 1.15 0.00 0.00 3.74
3509 5686 2.618241 TGACATGTGTGACCAAAGCTTC 59.382 45.455 1.15 0.00 0.00 3.86
3510 5687 2.880890 GACATGTGTGACCAAAGCTTCT 59.119 45.455 1.15 0.00 0.00 2.85
3511 5688 2.880890 ACATGTGTGACCAAAGCTTCTC 59.119 45.455 0.00 0.00 0.00 2.87
3512 5689 2.708216 TGTGTGACCAAAGCTTCTCA 57.292 45.000 0.00 0.00 0.00 3.27
3513 5690 2.288666 TGTGTGACCAAAGCTTCTCAC 58.711 47.619 18.44 18.44 36.97 3.51
3514 5691 2.288666 GTGTGACCAAAGCTTCTCACA 58.711 47.619 21.80 21.80 40.51 3.58
3515 5692 2.880890 GTGTGACCAAAGCTTCTCACAT 59.119 45.455 25.53 0.00 43.61 3.21
3516 5693 2.880268 TGTGACCAAAGCTTCTCACATG 59.120 45.455 21.80 8.13 38.45 3.21
3517 5694 3.141398 GTGACCAAAGCTTCTCACATGA 58.859 45.455 19.58 0.00 34.38 3.07
3518 5695 3.188048 GTGACCAAAGCTTCTCACATGAG 59.812 47.826 19.58 2.24 43.36 2.90
3532 5709 4.998788 TCACATGAGAATTGTCCTACTCG 58.001 43.478 0.00 0.00 32.81 4.18
3533 5710 4.462834 TCACATGAGAATTGTCCTACTCGT 59.537 41.667 0.00 0.00 32.81 4.18
3534 5711 4.800993 CACATGAGAATTGTCCTACTCGTC 59.199 45.833 0.00 0.00 32.81 4.20
3535 5712 4.142138 ACATGAGAATTGTCCTACTCGTCC 60.142 45.833 0.00 0.00 32.81 4.79
3536 5713 3.427573 TGAGAATTGTCCTACTCGTCCA 58.572 45.455 0.00 0.00 32.81 4.02
3537 5714 4.023980 TGAGAATTGTCCTACTCGTCCAT 58.976 43.478 0.00 0.00 32.81 3.41
3538 5715 4.098044 TGAGAATTGTCCTACTCGTCCATC 59.902 45.833 0.00 0.00 32.81 3.51
3539 5716 4.023980 AGAATTGTCCTACTCGTCCATCA 58.976 43.478 0.00 0.00 0.00 3.07
3540 5717 4.651503 AGAATTGTCCTACTCGTCCATCAT 59.348 41.667 0.00 0.00 0.00 2.45
3541 5718 5.129485 AGAATTGTCCTACTCGTCCATCATT 59.871 40.000 0.00 0.00 0.00 2.57
3542 5719 3.801114 TGTCCTACTCGTCCATCATTG 57.199 47.619 0.00 0.00 0.00 2.82
3543 5720 3.361786 TGTCCTACTCGTCCATCATTGA 58.638 45.455 0.00 0.00 0.00 2.57
3544 5721 3.767131 TGTCCTACTCGTCCATCATTGAA 59.233 43.478 0.00 0.00 0.00 2.69
3545 5722 4.113354 GTCCTACTCGTCCATCATTGAAC 58.887 47.826 0.00 0.00 0.00 3.18
3546 5723 3.767131 TCCTACTCGTCCATCATTGAACA 59.233 43.478 0.00 0.00 0.00 3.18
3547 5724 4.221924 TCCTACTCGTCCATCATTGAACAA 59.778 41.667 0.00 0.00 0.00 2.83
3548 5725 4.935205 CCTACTCGTCCATCATTGAACAAA 59.065 41.667 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.000472 TCAAGAAATGCCTGGATCCTATTTAG 59.000 38.462 14.23 0.71 0.00 1.85
4 5 6.910191 TCAAGAAATGCCTGGATCCTATTTA 58.090 36.000 14.23 0.00 0.00 1.40
5 6 5.769835 TCAAGAAATGCCTGGATCCTATTT 58.230 37.500 14.23 13.53 0.00 1.40
6 7 5.393068 TCAAGAAATGCCTGGATCCTATT 57.607 39.130 14.23 5.87 0.00 1.73
27 28 1.089481 TCGATCGTGCAATGCCCTTC 61.089 55.000 15.94 0.00 0.00 3.46
36 37 3.270000 TCGGTTCTCGATCGTGCA 58.730 55.556 15.94 0.00 43.74 4.57
52 53 8.553459 TCTTCTTGGAATTGAGTATGAACTTC 57.447 34.615 0.00 0.00 35.56 3.01
66 69 7.997223 TGATGCTCAATAAGATCTTCTTGGAAT 59.003 33.333 25.08 18.07 37.29 3.01
69 72 6.766944 AGTGATGCTCAATAAGATCTTCTTGG 59.233 38.462 25.08 18.73 37.29 3.61
83 86 3.807553 TGAAGTTGTCAGTGATGCTCAA 58.192 40.909 0.00 0.00 0.00 3.02
113 116 3.838244 ACAGGACAAAGCACAACTAGA 57.162 42.857 0.00 0.00 0.00 2.43
123 126 8.081633 TCAAATGTAGCAAATAACAGGACAAAG 58.918 33.333 0.00 0.00 0.00 2.77
127 130 8.243426 TGATTCAAATGTAGCAAATAACAGGAC 58.757 33.333 0.00 0.00 0.00 3.85
147 150 8.138074 TCAAATTTAAACACACCGAATGATTCA 58.862 29.630 5.95 0.00 0.00 2.57
148 151 8.514136 TCAAATTTAAACACACCGAATGATTC 57.486 30.769 0.00 0.00 0.00 2.52
151 154 9.967346 TTATTCAAATTTAAACACACCGAATGA 57.033 25.926 0.00 0.00 0.00 2.57
156 159 8.369588 CCGAATTATTCAAATTTAAACACACCG 58.630 33.333 5.76 0.00 0.00 4.94
157 160 8.166066 GCCGAATTATTCAAATTTAAACACACC 58.834 33.333 5.76 0.00 0.00 4.16
158 161 8.921670 AGCCGAATTATTCAAATTTAAACACAC 58.078 29.630 5.76 0.00 0.00 3.82
183 186 7.749539 ACAAACCGAATTCAAAGTTTACAAG 57.250 32.000 14.41 7.89 31.50 3.16
185 188 9.074443 GTTTACAAACCGAATTCAAAGTTTACA 57.926 29.630 14.41 6.30 31.50 2.41
211 214 9.674824 GAAGGTTCAAGCAAATCATCAATATAG 57.325 33.333 0.00 0.00 0.00 1.31
218 221 5.717119 ACATGAAGGTTCAAGCAAATCATC 58.283 37.500 0.00 0.00 41.13 2.92
233 236 7.820648 ACAGAAGCTAAACATAAACATGAAGG 58.179 34.615 0.00 0.00 0.00 3.46
240 243 7.481798 GCACACATACAGAAGCTAAACATAAAC 59.518 37.037 0.00 0.00 0.00 2.01
252 256 9.534565 AACTACATATTAGCACACATACAGAAG 57.465 33.333 0.00 0.00 0.00 2.85
260 264 8.560355 ACATTTCAACTACATATTAGCACACA 57.440 30.769 0.00 0.00 0.00 3.72
324 328 5.181622 AGCCGATCTTCTAACTATAACGGAG 59.818 44.000 0.00 0.00 40.16 4.63
327 331 7.528307 ACATAGCCGATCTTCTAACTATAACG 58.472 38.462 0.00 0.00 0.00 3.18
328 332 8.512956 TGACATAGCCGATCTTCTAACTATAAC 58.487 37.037 0.00 0.00 0.00 1.89
333 337 4.279671 CCTGACATAGCCGATCTTCTAACT 59.720 45.833 0.00 0.00 0.00 2.24
334 338 4.551388 CCTGACATAGCCGATCTTCTAAC 58.449 47.826 0.00 0.00 0.00 2.34
339 343 0.394565 GGCCTGACATAGCCGATCTT 59.605 55.000 0.00 0.00 39.87 2.40
349 353 5.900123 ACTCTACTAAGTATTGGCCTGACAT 59.100 40.000 3.32 0.00 0.00 3.06
390 394 1.109609 GGATCCCGTCCGAGTAAAGT 58.890 55.000 0.00 0.00 37.23 2.66
423 427 0.175760 GCCAAGTCTAGCCGATCACA 59.824 55.000 0.00 0.00 0.00 3.58
425 429 1.823295 GGCCAAGTCTAGCCGATCA 59.177 57.895 0.00 0.00 39.87 2.92
525 530 2.733593 GTCGTCTTCAGCGCCGTT 60.734 61.111 2.29 0.00 0.00 4.44
605 611 2.158959 CGCCTCGAAGGTACAAGCG 61.159 63.158 0.00 0.00 37.80 4.68
630 637 3.079478 AGCGCTCCAGATGCCAGA 61.079 61.111 2.64 0.00 0.00 3.86
657 664 1.826921 TATCTCCAGTCCGGCCGTC 60.827 63.158 26.12 16.74 33.14 4.79
658 665 2.125961 GTATCTCCAGTCCGGCCGT 61.126 63.158 26.12 1.61 33.14 5.68
659 666 2.728817 GTATCTCCAGTCCGGCCG 59.271 66.667 21.04 21.04 33.14 6.13
660 667 1.457831 AGGTATCTCCAGTCCGGCC 60.458 63.158 0.00 0.00 39.02 6.13
661 668 1.797211 CGAGGTATCTCCAGTCCGGC 61.797 65.000 0.00 0.00 39.02 6.13
664 671 2.223745 GAGACGAGGTATCTCCAGTCC 58.776 57.143 7.25 0.00 42.68 3.85
686 693 1.592939 GATTCTCTCTTCCCCGCGC 60.593 63.158 0.00 0.00 0.00 6.86
687 694 1.299468 CGATTCTCTCTTCCCCGCG 60.299 63.158 0.00 0.00 0.00 6.46
745 2839 2.653967 CGTACGCGTCTGCTGCAAA 61.654 57.895 18.63 0.00 39.65 3.68
768 2862 0.679002 CCATGGTGACCCAAGCTCTG 60.679 60.000 2.57 0.00 46.04 3.35
769 2863 1.687612 CCATGGTGACCCAAGCTCT 59.312 57.895 2.57 0.00 46.04 4.09
770 2864 1.379044 CCCATGGTGACCCAAGCTC 60.379 63.158 11.73 0.00 46.04 4.09
771 2865 1.434513 TTCCCATGGTGACCCAAGCT 61.435 55.000 11.73 0.00 46.04 3.74
772 2866 1.076549 TTCCCATGGTGACCCAAGC 59.923 57.895 11.73 0.00 46.04 4.01
773 2867 0.611896 GGTTCCCATGGTGACCCAAG 60.612 60.000 18.61 0.00 46.04 3.61
774 2868 1.071314 AGGTTCCCATGGTGACCCAA 61.071 55.000 23.32 0.54 46.04 4.12
778 2872 1.678970 GCCAGGTTCCCATGGTGAC 60.679 63.158 11.73 8.56 38.91 3.67
779 2873 2.159490 TGCCAGGTTCCCATGGTGA 61.159 57.895 11.73 4.83 38.91 4.02
780 2874 1.978617 GTGCCAGGTTCCCATGGTG 60.979 63.158 11.73 1.22 38.91 4.17
781 2875 2.440599 GTGCCAGGTTCCCATGGT 59.559 61.111 11.73 0.00 38.91 3.55
792 2886 3.561213 CAGCTCGATGCGTGCCAG 61.561 66.667 9.80 0.96 45.54 4.85
942 3069 2.679837 GCGATGAATGGTGAATGTGAGT 59.320 45.455 0.00 0.00 0.00 3.41
974 3107 4.899352 ATGGTCTTATGGAGTATGGAGC 57.101 45.455 0.00 0.00 0.00 4.70
1078 3223 1.153549 GGCTCGTCTCATCACCCAC 60.154 63.158 0.00 0.00 0.00 4.61
1194 3339 7.395489 GTCTTATATTATGGGACGAAGGGAGTA 59.605 40.741 0.00 0.00 0.00 2.59
1769 3914 5.540337 TGGTTTCAAGGCAACAACCATATAA 59.460 36.000 6.52 0.00 43.04 0.98
1793 3938 5.245526 ACTCGTAGACTAACAATGGGACTTT 59.754 40.000 0.00 0.00 0.00 2.66
1829 3974 5.651387 TGAAGATGATCACGAAGAGTTCT 57.349 39.130 0.00 0.00 0.00 3.01
2041 4186 2.834638 ACCCTGATTTCTCCAATGGG 57.165 50.000 0.00 0.00 39.06 4.00
2094 4239 2.226437 GTGTGCAAATACACTGGGTCTG 59.774 50.000 0.00 0.00 45.70 3.51
2159 4304 9.462174 CTTTCTAGTCATCAGTTCTATAAGCAG 57.538 37.037 0.00 0.00 0.00 4.24
2405 4550 6.770286 TGCCTTAAATCCCTTAGATGATCT 57.230 37.500 0.00 0.00 34.56 2.75
2406 4551 7.823745 TTTGCCTTAAATCCCTTAGATGATC 57.176 36.000 0.00 0.00 34.56 2.92
2524 4669 3.055819 ACCGCGGATATCTTGCAGATAAT 60.056 43.478 35.90 0.00 40.28 1.28
2690 4845 3.149196 GCTTCCAAAACAGACCATGAGA 58.851 45.455 0.00 0.00 0.00 3.27
2815 4971 9.368674 CAATGACCATGCAAATTTTACATTCTA 57.631 29.630 0.00 0.00 0.00 2.10
2901 5057 7.898636 TCTCATGTTTTAAATGGGGTTTCCTAT 59.101 33.333 0.00 0.00 35.60 2.57
2909 5066 6.543430 TGGAATCTCATGTTTTAAATGGGG 57.457 37.500 0.00 0.00 0.00 4.96
2947 5105 4.161377 TGCCCTTAAAGCAAGTGTTTTTCT 59.839 37.500 0.00 0.00 37.28 2.52
3038 5197 2.099141 TCAAGGTGAGCTGATTTCGG 57.901 50.000 0.00 0.00 0.00 4.30
3041 5200 4.464008 TGAACTTCAAGGTGAGCTGATTT 58.536 39.130 0.00 0.00 0.00 2.17
3103 5266 5.689819 AGTTGAATGTTTAGTGTTCGCATC 58.310 37.500 0.00 0.00 0.00 3.91
3134 5298 2.623878 TAGCTCCAACCAAACGTGAA 57.376 45.000 0.00 0.00 0.00 3.18
3187 5351 0.112995 ACCACCACCATGCACAGATT 59.887 50.000 0.00 0.00 0.00 2.40
3280 5457 6.842163 ACCGTTTTGCATAGTCTATTTTCAG 58.158 36.000 0.00 0.00 0.00 3.02
3293 5470 3.312973 TCTTTCGTGTTACCGTTTTGCAT 59.687 39.130 0.00 0.00 0.00 3.96
3310 5487 7.826260 TCTGTTCCAACACAAAAATTCTTTC 57.174 32.000 0.00 0.00 34.70 2.62
3320 5497 4.717877 AGATGTCATCTGTTCCAACACAA 58.282 39.130 14.73 0.00 38.44 3.33
3321 5498 4.356405 AGATGTCATCTGTTCCAACACA 57.644 40.909 14.73 0.00 38.44 3.72
3324 5501 8.584157 AGATAGATAGATGTCATCTGTTCCAAC 58.416 37.037 23.17 9.42 40.51 3.77
3343 5520 9.772973 TGTTACCGTTTTGCATAATAGATAGAT 57.227 29.630 0.00 0.00 0.00 1.98
3344 5521 9.037737 GTGTTACCGTTTTGCATAATAGATAGA 57.962 33.333 0.00 0.00 0.00 1.98
3359 5536 5.184711 TCTGGTTAACTTGTGTTACCGTTT 58.815 37.500 5.42 0.00 38.26 3.60
3389 5566 9.540538 TTTTCCATGGGATTTTCTAACTATTCA 57.459 29.630 13.02 0.00 0.00 2.57
3409 5586 8.937884 GTTAAAGTTTAAAGGCTTTGTTTTCCA 58.062 29.630 22.32 0.00 36.47 3.53
3410 5587 8.392612 GGTTAAAGTTTAAAGGCTTTGTTTTCC 58.607 33.333 22.32 15.26 36.47 3.13
3411 5588 8.111836 CGGTTAAAGTTTAAAGGCTTTGTTTTC 58.888 33.333 22.32 8.22 36.47 2.29
3420 5597 8.032952 ACTATGTACGGTTAAAGTTTAAAGGC 57.967 34.615 9.62 0.00 0.00 4.35
3421 5598 9.206870 TGACTATGTACGGTTAAAGTTTAAAGG 57.793 33.333 9.62 7.35 0.00 3.11
3425 5602 9.520204 GCTATGACTATGTACGGTTAAAGTTTA 57.480 33.333 0.00 0.00 0.00 2.01
3426 5603 8.255905 AGCTATGACTATGTACGGTTAAAGTTT 58.744 33.333 0.00 0.00 0.00 2.66
3427 5604 7.779073 AGCTATGACTATGTACGGTTAAAGTT 58.221 34.615 0.00 0.00 0.00 2.66
3428 5605 7.344095 AGCTATGACTATGTACGGTTAAAGT 57.656 36.000 0.00 0.00 0.00 2.66
3429 5606 8.644318 AAAGCTATGACTATGTACGGTTAAAG 57.356 34.615 0.00 0.00 0.00 1.85
3430 5607 9.740239 CTAAAGCTATGACTATGTACGGTTAAA 57.260 33.333 0.00 0.00 0.00 1.52
3431 5608 9.123902 TCTAAAGCTATGACTATGTACGGTTAA 57.876 33.333 0.00 0.00 0.00 2.01
3432 5609 8.562892 GTCTAAAGCTATGACTATGTACGGTTA 58.437 37.037 0.00 0.00 0.00 2.85
3433 5610 7.424001 GTCTAAAGCTATGACTATGTACGGTT 58.576 38.462 0.00 0.00 0.00 4.44
3434 5611 6.016443 GGTCTAAAGCTATGACTATGTACGGT 60.016 42.308 11.64 0.00 0.00 4.83
3435 5612 6.016527 TGGTCTAAAGCTATGACTATGTACGG 60.017 42.308 11.64 0.00 0.00 4.02
3436 5613 6.967135 TGGTCTAAAGCTATGACTATGTACG 58.033 40.000 11.64 0.00 0.00 3.67
3437 5614 8.798402 AGATGGTCTAAAGCTATGACTATGTAC 58.202 37.037 14.06 0.00 33.24 2.90
3438 5615 8.797438 CAGATGGTCTAAAGCTATGACTATGTA 58.203 37.037 14.06 0.51 33.24 2.29
3439 5616 7.256119 CCAGATGGTCTAAAGCTATGACTATGT 60.256 40.741 14.06 9.36 33.24 2.29
3440 5617 7.039434 TCCAGATGGTCTAAAGCTATGACTATG 60.039 40.741 14.06 5.83 33.24 2.23
3441 5618 7.013220 TCCAGATGGTCTAAAGCTATGACTAT 58.987 38.462 10.63 10.63 35.22 2.12
3442 5619 6.373759 TCCAGATGGTCTAAAGCTATGACTA 58.626 40.000 11.64 7.58 36.34 2.59
3443 5620 5.211973 TCCAGATGGTCTAAAGCTATGACT 58.788 41.667 11.64 0.00 36.34 3.41
3444 5621 5.537300 TCCAGATGGTCTAAAGCTATGAC 57.463 43.478 0.00 0.00 36.34 3.06
3445 5622 6.080682 AGATCCAGATGGTCTAAAGCTATGA 58.919 40.000 0.00 0.00 36.34 2.15
3446 5623 6.357579 AGATCCAGATGGTCTAAAGCTATG 57.642 41.667 0.00 0.00 36.34 2.23
3447 5624 7.385894 AAAGATCCAGATGGTCTAAAGCTAT 57.614 36.000 0.00 0.00 36.34 2.97
3448 5625 6.814954 AAAGATCCAGATGGTCTAAAGCTA 57.185 37.500 0.00 0.00 36.34 3.32
3449 5626 5.707066 AAAGATCCAGATGGTCTAAAGCT 57.293 39.130 0.00 0.00 36.34 3.74
3450 5627 6.587273 AGTAAAGATCCAGATGGTCTAAAGC 58.413 40.000 0.00 0.00 36.34 3.51
3454 5631 9.488762 TCTTAAAGTAAAGATCCAGATGGTCTA 57.511 33.333 0.00 0.00 31.87 2.59
3455 5632 8.380742 TCTTAAAGTAAAGATCCAGATGGTCT 57.619 34.615 0.00 0.00 31.87 3.85
3456 5633 9.449719 TTTCTTAAAGTAAAGATCCAGATGGTC 57.550 33.333 0.00 0.00 35.48 4.02
3457 5634 9.232473 GTTTCTTAAAGTAAAGATCCAGATGGT 57.768 33.333 0.00 0.00 35.48 3.55
3458 5635 9.454859 AGTTTCTTAAAGTAAAGATCCAGATGG 57.545 33.333 0.00 0.00 35.48 3.51
3471 5648 9.826574 ACACATGTCAGTAAGTTTCTTAAAGTA 57.173 29.630 0.00 0.00 0.00 2.24
3472 5649 8.612619 CACACATGTCAGTAAGTTTCTTAAAGT 58.387 33.333 0.00 0.00 0.00 2.66
3473 5650 8.826710 TCACACATGTCAGTAAGTTTCTTAAAG 58.173 33.333 0.00 0.00 0.00 1.85
3474 5651 8.609176 GTCACACATGTCAGTAAGTTTCTTAAA 58.391 33.333 0.00 0.00 0.00 1.52
3475 5652 7.225931 GGTCACACATGTCAGTAAGTTTCTTAA 59.774 37.037 0.00 0.00 0.00 1.85
3476 5653 6.704493 GGTCACACATGTCAGTAAGTTTCTTA 59.296 38.462 0.00 0.00 0.00 2.10
3477 5654 5.527582 GGTCACACATGTCAGTAAGTTTCTT 59.472 40.000 0.00 0.00 0.00 2.52
3478 5655 5.057149 GGTCACACATGTCAGTAAGTTTCT 58.943 41.667 0.00 0.00 0.00 2.52
3479 5656 4.814234 TGGTCACACATGTCAGTAAGTTTC 59.186 41.667 0.00 0.00 0.00 2.78
3480 5657 4.776349 TGGTCACACATGTCAGTAAGTTT 58.224 39.130 0.00 0.00 0.00 2.66
3481 5658 4.415881 TGGTCACACATGTCAGTAAGTT 57.584 40.909 0.00 0.00 0.00 2.66
3482 5659 4.415881 TTGGTCACACATGTCAGTAAGT 57.584 40.909 0.00 0.00 0.00 2.24
3483 5660 4.319766 GCTTTGGTCACACATGTCAGTAAG 60.320 45.833 0.00 0.00 0.00 2.34
3484 5661 3.563808 GCTTTGGTCACACATGTCAGTAA 59.436 43.478 0.00 0.00 0.00 2.24
3485 5662 3.138304 GCTTTGGTCACACATGTCAGTA 58.862 45.455 0.00 0.00 0.00 2.74
3486 5663 1.949525 GCTTTGGTCACACATGTCAGT 59.050 47.619 0.00 0.00 0.00 3.41
3487 5664 2.224606 AGCTTTGGTCACACATGTCAG 58.775 47.619 0.00 0.00 0.00 3.51
3488 5665 2.346766 AGCTTTGGTCACACATGTCA 57.653 45.000 0.00 0.00 0.00 3.58
3489 5666 2.880890 AGAAGCTTTGGTCACACATGTC 59.119 45.455 0.00 0.00 0.00 3.06
3490 5667 2.880890 GAGAAGCTTTGGTCACACATGT 59.119 45.455 0.00 0.00 0.00 3.21
3491 5668 2.880268 TGAGAAGCTTTGGTCACACATG 59.120 45.455 0.00 0.00 0.00 3.21
3492 5669 2.880890 GTGAGAAGCTTTGGTCACACAT 59.119 45.455 22.81 0.00 39.33 3.21
3493 5670 2.288666 GTGAGAAGCTTTGGTCACACA 58.711 47.619 22.81 5.08 39.33 3.72
3494 5671 2.288666 TGTGAGAAGCTTTGGTCACAC 58.711 47.619 24.97 16.91 43.33 3.82
3495 5672 2.708216 TGTGAGAAGCTTTGGTCACA 57.292 45.000 24.97 24.97 45.39 3.58
3496 5673 3.141398 TCATGTGAGAAGCTTTGGTCAC 58.859 45.455 21.73 21.73 39.85 3.67
3497 5674 3.405831 CTCATGTGAGAAGCTTTGGTCA 58.594 45.455 0.00 1.46 44.74 4.02
3509 5686 5.039984 CGAGTAGGACAATTCTCATGTGAG 58.960 45.833 3.61 3.61 43.36 3.51
3510 5687 4.462834 ACGAGTAGGACAATTCTCATGTGA 59.537 41.667 0.00 0.00 0.00 3.58
3511 5688 4.748892 ACGAGTAGGACAATTCTCATGTG 58.251 43.478 0.00 0.00 0.00 3.21
3512 5689 4.142138 GGACGAGTAGGACAATTCTCATGT 60.142 45.833 0.00 0.00 0.00 3.21
3513 5690 4.142160 TGGACGAGTAGGACAATTCTCATG 60.142 45.833 0.00 0.00 0.00 3.07
3514 5691 4.023980 TGGACGAGTAGGACAATTCTCAT 58.976 43.478 0.00 0.00 0.00 2.90
3515 5692 3.427573 TGGACGAGTAGGACAATTCTCA 58.572 45.455 0.00 0.00 0.00 3.27
3516 5693 4.098044 TGATGGACGAGTAGGACAATTCTC 59.902 45.833 0.00 0.00 0.00 2.87
3517 5694 4.023980 TGATGGACGAGTAGGACAATTCT 58.976 43.478 0.00 0.00 0.00 2.40
3518 5695 4.386867 TGATGGACGAGTAGGACAATTC 57.613 45.455 0.00 0.00 0.00 2.17
3519 5696 5.104941 TCAATGATGGACGAGTAGGACAATT 60.105 40.000 0.00 0.00 0.00 2.32
3520 5697 4.405680 TCAATGATGGACGAGTAGGACAAT 59.594 41.667 0.00 0.00 0.00 2.71
3521 5698 3.767131 TCAATGATGGACGAGTAGGACAA 59.233 43.478 0.00 0.00 0.00 3.18
3522 5699 3.361786 TCAATGATGGACGAGTAGGACA 58.638 45.455 0.00 0.00 0.00 4.02
3523 5700 4.113354 GTTCAATGATGGACGAGTAGGAC 58.887 47.826 0.00 0.00 0.00 3.85
3524 5701 3.767131 TGTTCAATGATGGACGAGTAGGA 59.233 43.478 0.00 0.00 37.94 2.94
3525 5702 4.123497 TGTTCAATGATGGACGAGTAGG 57.877 45.455 0.00 0.00 37.94 3.18


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

AutoCloner maintained by Alex Coulton.