Multiple sequence alignment - TraesCS1D01G279400

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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 TraesCS1D01G279400 chr1D 100.000 5190 0 0 1 5190 377186708 377191897 0.000000e+00 9585.0
1 TraesCS1D01G279400 chr1B 93.879 1944 83 21 1 1924 504087652 504089579 0.000000e+00 2898.0
2 TraesCS1D01G279400 chr1B 89.709 1924 120 36 2818 4683 504090846 504092749 0.000000e+00 2385.0
3 TraesCS1D01G279400 chr1B 92.675 587 25 7 1960 2543 504089569 504090140 0.000000e+00 830.0
4 TraesCS1D01G279400 chr1B 84.211 418 34 12 4725 5125 504092759 504093161 1.360000e-100 377.0
5 TraesCS1D01G279400 chr1B 91.373 255 16 3 2544 2793 504090533 504090786 1.380000e-90 344.0
6 TraesCS1D01G279400 chr1A 92.508 1535 61 26 1025 2541 477730922 477732420 0.000000e+00 2148.0
7 TraesCS1D01G279400 chr1A 84.513 1498 110 54 3192 4586 477733644 477735122 0.000000e+00 1369.0
8 TraesCS1D01G279400 chr1A 93.333 375 21 2 2818 3192 477733195 477733565 7.600000e-153 551.0
9 TraesCS1D01G279400 chr1A 91.743 218 15 3 2575 2791 477732919 477733134 3.040000e-77 300.0
10 TraesCS1D01G279400 chr1A 88.557 201 14 7 601 801 477730294 477730485 8.690000e-58 235.0
11 TraesCS1D01G279400 chr1A 93.976 83 0 1 787 864 477730503 477730585 2.540000e-23 121.0
12 TraesCS1D01G279400 chr1A 85.149 101 4 6 1820 1920 505525753 505525664 5.530000e-15 93.5
13 TraesCS1D01G279400 chr3D 82.710 428 52 9 1484 1909 471775891 471775484 1.370000e-95 361.0
14 TraesCS1D01G279400 chr3D 81.915 94 8 4 1820 1913 161403666 161403750 2.590000e-08 71.3
15 TraesCS1D01G279400 chr3D 80.851 94 9 4 1820 1913 161499700 161499784 1.210000e-06 65.8
16 TraesCS1D01G279400 chr3B 82.710 428 52 9 1484 1909 627213753 627213346 1.370000e-95 361.0
17 TraesCS1D01G279400 chr3A 82.135 431 55 9 1484 1909 614541161 614540748 2.970000e-92 350.0
18 TraesCS1D01G279400 chr4B 80.597 134 20 4 2137 2268 25484573 25484444 1.190000e-16 99.0
19 TraesCS1D01G279400 chr4A 86.139 101 3 6 1820 1920 16031336 16031425 1.190000e-16 99.0
20 TraesCS1D01G279400 chr4A 82.353 119 16 4 2137 2253 585663404 585663519 1.190000e-16 99.0
21 TraesCS1D01G279400 chr2A 82.353 119 15 4 2137 2253 195808063 195808177 1.190000e-16 99.0
22 TraesCS1D01G279400 chr6D 86.667 90 9 2 2135 2224 254167062 254167148 4.280000e-16 97.1
23 TraesCS1D01G279400 chr6A 90.141 71 6 1 2154 2224 364670036 364669967 1.990000e-14 91.6


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 TraesCS1D01G279400 chr1D 377186708 377191897 5189 False 9585.000000 9585 100.000000 1 5190 1 chr1D.!!$F1 5189
1 TraesCS1D01G279400 chr1B 504087652 504093161 5509 False 1366.800000 2898 90.369400 1 5125 5 chr1B.!!$F1 5124
2 TraesCS1D01G279400 chr1A 477730294 477735122 4828 False 787.333333 2148 90.771667 601 4586 6 chr1A.!!$F1 3985

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
907 961 0.537371 CAAACCCCTCCACAGTCCAC 60.537 60.0 0.00 0.0 0.00 4.02 F
1938 2179 0.319728 TCAGTCTGCTTGCTCTGTCC 59.680 55.0 0.00 0.0 0.00 4.02 F
1976 2217 0.450583 CTACTCTGTTAGTGCGCCGA 59.549 55.0 4.18 0.0 39.39 5.54 F
3621 4480 0.040058 TCCTTCTGGCATGCATGGTT 59.960 50.0 27.34 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 3322 0.179181 TACGACGAACGATCACCAGC 60.179 55.000 0.0 0.0 45.77 4.85 R
3480 4339 0.719465 GATCGCCTAACACAACCACG 59.281 55.000 0.0 0.0 0.00 4.94 R
3877 4746 1.470098 CTTCACTCAAATCTTGGGGCG 59.530 52.381 0.0 0.0 34.70 6.13 R
4717 5686 0.034616 ACACTGCTGCTTCTCAGGTC 59.965 55.000 0.0 0.0 43.06 3.85 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
117 122 9.959749 TCCAACTAAAATTACAATTCAGTTCAC 57.040 29.630 9.81 0.00 34.23 3.18
121 126 9.878599 ACTAAAATTACAATTCAGTTCACTTCG 57.121 29.630 0.00 0.00 0.00 3.79
151 156 9.487790 AAATCAACAAACCATTAAACATAGTGG 57.512 29.630 0.00 0.00 37.74 4.00
161 166 7.929245 ACCATTAAACATAGTGGTTTTGGAAAC 59.071 33.333 13.51 0.00 42.03 2.78
166 171 7.833285 AACATAGTGGTTTTGGAAACTACAT 57.167 32.000 18.07 9.50 34.58 2.29
175 180 9.132923 TGGTTTTGGAAACTACATAACATGTTA 57.867 29.630 20.14 20.14 41.63 2.41
197 202 0.620556 AGACTGCCACCCATGTTAGG 59.379 55.000 0.00 0.00 0.00 2.69
211 216 5.390613 CCATGTTAGGACACAAATTTCGTC 58.609 41.667 8.24 8.24 38.91 4.20
246 251 2.307392 TGCTTCCTTATACCTTGTGGCA 59.693 45.455 0.00 0.00 36.63 4.92
355 361 9.248291 CATTTTAATGTTCAAACAAGTGCTACT 57.752 29.630 0.00 0.00 43.03 2.57
366 372 3.384789 ACAAGTGCTACTGAGTTGTCTCA 59.615 43.478 0.00 0.00 46.85 3.27
382 388 4.592942 TGTCTCATCCCCATTTCAAGAAG 58.407 43.478 0.00 0.00 0.00 2.85
384 390 5.222109 TGTCTCATCCCCATTTCAAGAAGAA 60.222 40.000 0.00 0.00 0.00 2.52
385 391 5.124617 GTCTCATCCCCATTTCAAGAAGAAC 59.875 44.000 0.00 0.00 35.56 3.01
388 394 5.419788 TCATCCCCATTTCAAGAAGAACATG 59.580 40.000 0.00 0.00 35.56 3.21
389 395 4.996793 TCCCCATTTCAAGAAGAACATGA 58.003 39.130 0.00 0.00 35.56 3.07
390 396 5.582953 TCCCCATTTCAAGAAGAACATGAT 58.417 37.500 0.00 0.00 35.56 2.45
391 397 6.018469 TCCCCATTTCAAGAAGAACATGATT 58.982 36.000 0.00 0.00 35.56 2.57
393 399 7.673504 TCCCCATTTCAAGAAGAACATGATTTA 59.326 33.333 0.00 0.00 35.56 1.40
394 400 7.761249 CCCCATTTCAAGAAGAACATGATTTAC 59.239 37.037 0.00 0.00 35.56 2.01
395 401 8.526147 CCCATTTCAAGAAGAACATGATTTACT 58.474 33.333 0.00 0.00 35.56 2.24
402 408 9.003658 CAAGAAGAACATGATTTACTACACCTT 57.996 33.333 0.00 0.00 0.00 3.50
428 434 8.997621 ATAGTTACTTTTCGCTAGATTGTCAA 57.002 30.769 0.00 0.00 0.00 3.18
436 442 6.662414 TTCGCTAGATTGTCAATGGTTAAG 57.338 37.500 1.88 0.00 0.00 1.85
495 501 1.143305 CACACGAGAGCTTGTTGGAG 58.857 55.000 0.00 0.00 0.00 3.86
498 504 2.266554 CACGAGAGCTTGTTGGAGATC 58.733 52.381 0.00 0.00 32.36 2.75
507 513 4.051922 GCTTGTTGGAGATCTATACACCG 58.948 47.826 0.00 0.00 0.00 4.94
513 519 6.604396 TGTTGGAGATCTATACACCGAACTAA 59.396 38.462 0.00 0.00 0.00 2.24
558 566 5.534654 TGTTTCCAAAAATGGAGTCTACCAG 59.465 40.000 0.00 0.00 43.49 4.00
595 603 7.634671 TTGATCTCACAAGCAATTATCATGT 57.365 32.000 0.00 0.00 0.00 3.21
612 620 5.698741 TCATGTCCCATTATATGCCCTAG 57.301 43.478 0.00 0.00 0.00 3.02
624 632 2.795165 GCCCTAGCAAAGCCTTACC 58.205 57.895 0.00 0.00 39.53 2.85
667 675 6.553953 TCACCAAGCAATATCCAACTACTA 57.446 37.500 0.00 0.00 0.00 1.82
668 676 6.346096 TCACCAAGCAATATCCAACTACTAC 58.654 40.000 0.00 0.00 0.00 2.73
670 678 7.343574 TCACCAAGCAATATCCAACTACTACTA 59.656 37.037 0.00 0.00 0.00 1.82
673 681 9.561069 CCAAGCAATATCCAACTACTACTATTT 57.439 33.333 0.00 0.00 0.00 1.40
704 717 3.969287 TGGAGATGCTATATGACAGGC 57.031 47.619 0.00 0.00 0.00 4.85
708 721 4.161942 GGAGATGCTATATGACAGGCTGAT 59.838 45.833 23.66 7.78 0.00 2.90
767 784 7.468922 AAAAGAAAATAAAACTGCTGCTGAC 57.531 32.000 13.69 0.00 0.00 3.51
877 931 1.217511 CACGGTGAGCTGAGCTGAT 59.782 57.895 13.71 0.00 39.88 2.90
905 959 1.074951 CCAAACCCCTCCACAGTCC 59.925 63.158 0.00 0.00 0.00 3.85
906 960 1.715019 CCAAACCCCTCCACAGTCCA 61.715 60.000 0.00 0.00 0.00 4.02
907 961 0.537371 CAAACCCCTCCACAGTCCAC 60.537 60.000 0.00 0.00 0.00 4.02
908 962 0.991355 AAACCCCTCCACAGTCCACA 60.991 55.000 0.00 0.00 0.00 4.17
909 963 1.705997 AACCCCTCCACAGTCCACAC 61.706 60.000 0.00 0.00 0.00 3.82
910 964 2.750350 CCCTCCACAGTCCACACC 59.250 66.667 0.00 0.00 0.00 4.16
911 965 2.750350 CCTCCACAGTCCACACCC 59.250 66.667 0.00 0.00 0.00 4.61
912 966 1.843376 CCTCCACAGTCCACACCCT 60.843 63.158 0.00 0.00 0.00 4.34
958 1012 2.303311 CTCGTCTTTTCCTTTCTCCCCT 59.697 50.000 0.00 0.00 0.00 4.79
1130 1360 2.475818 CCGTATGTTGCCGCATTAGTA 58.524 47.619 0.00 0.00 0.00 1.82
1204 1438 0.527600 TGATCTTCGACGCGGATTGG 60.528 55.000 12.47 0.00 0.00 3.16
1324 1562 2.238521 GATCTTGTGGGTGGCTGAAAA 58.761 47.619 0.00 0.00 0.00 2.29
1325 1563 2.380064 TCTTGTGGGTGGCTGAAAAT 57.620 45.000 0.00 0.00 0.00 1.82
1327 1565 1.001181 CTTGTGGGTGGCTGAAAATGG 59.999 52.381 0.00 0.00 0.00 3.16
1328 1566 1.293179 GTGGGTGGCTGAAAATGGC 59.707 57.895 0.00 0.00 0.00 4.40
1329 1567 1.155859 TGGGTGGCTGAAAATGGCT 59.844 52.632 0.00 0.00 0.00 4.75
1330 1568 0.899717 TGGGTGGCTGAAAATGGCTC 60.900 55.000 0.00 0.00 0.00 4.70
1331 1569 1.607801 GGGTGGCTGAAAATGGCTCC 61.608 60.000 0.00 0.00 41.12 4.70
1332 1570 1.508088 GTGGCTGAAAATGGCTCCG 59.492 57.895 0.00 0.00 0.00 4.63
1333 1571 2.342650 TGGCTGAAAATGGCTCCGC 61.343 57.895 0.00 0.00 0.00 5.54
1367 1605 3.898741 TGGGATTTTGTTTTGGGTAGGTC 59.101 43.478 0.00 0.00 0.00 3.85
1372 1610 0.688487 TGTTTTGGGTAGGTCGAGGG 59.312 55.000 0.00 0.00 0.00 4.30
1376 1614 0.410663 TTGGGTAGGTCGAGGGAGAA 59.589 55.000 0.00 0.00 0.00 2.87
1929 2170 0.321021 CCTGCTCTGTCAGTCTGCTT 59.679 55.000 0.00 0.00 32.32 3.91
1932 2173 0.320596 GCTCTGTCAGTCTGCTTGCT 60.321 55.000 0.00 0.00 0.00 3.91
1933 2174 1.712401 CTCTGTCAGTCTGCTTGCTC 58.288 55.000 0.00 0.00 0.00 4.26
1934 2175 1.273048 CTCTGTCAGTCTGCTTGCTCT 59.727 52.381 0.00 0.00 0.00 4.09
1935 2176 1.000618 TCTGTCAGTCTGCTTGCTCTG 59.999 52.381 0.00 1.30 0.00 3.35
1938 2179 0.319728 TCAGTCTGCTTGCTCTGTCC 59.680 55.000 0.00 0.00 0.00 4.02
1947 2188 2.094417 GCTTGCTCTGTCCGTAATTCAC 59.906 50.000 0.00 0.00 0.00 3.18
1957 2198 1.308998 CGTAATTCACTCCCCATGGC 58.691 55.000 6.09 0.00 0.00 4.40
1964 2205 0.467384 CACTCCCCATGGCTACTCTG 59.533 60.000 6.09 0.00 0.00 3.35
1966 2207 1.207791 CTCCCCATGGCTACTCTGTT 58.792 55.000 6.09 0.00 0.00 3.16
1976 2217 0.450583 CTACTCTGTTAGTGCGCCGA 59.549 55.000 4.18 0.00 39.39 5.54
1977 2218 0.450583 TACTCTGTTAGTGCGCCGAG 59.549 55.000 4.18 3.20 39.39 4.63
1978 2219 1.213013 CTCTGTTAGTGCGCCGAGT 59.787 57.895 4.18 0.00 0.00 4.18
1984 2225 2.264813 GTTAGTGCGCCGAGTCATTTA 58.735 47.619 4.18 0.00 0.00 1.40
1987 2228 1.475280 AGTGCGCCGAGTCATTTACTA 59.525 47.619 4.18 0.00 39.07 1.82
1989 2230 1.206523 GCGCCGAGTCATTTACTACC 58.793 55.000 0.00 0.00 39.07 3.18
1992 2233 2.547826 GCCGAGTCATTTACTACCCAC 58.452 52.381 0.00 0.00 39.07 4.61
2036 2277 7.422399 TGCCAATTCACTAAAGTTCAGTTAAC 58.578 34.615 0.00 0.00 38.46 2.01
2105 2346 4.133820 CAGGGATTTATGTATTCGGTGCA 58.866 43.478 0.00 0.00 0.00 4.57
2106 2347 4.578516 CAGGGATTTATGTATTCGGTGCAA 59.421 41.667 0.00 0.00 0.00 4.08
2107 2348 4.578928 AGGGATTTATGTATTCGGTGCAAC 59.421 41.667 0.00 0.00 0.00 4.17
2221 2462 9.419297 GGTGTTTTCTTTAGTTCTTTGTTTCTT 57.581 29.630 0.00 0.00 0.00 2.52
2302 2546 8.216423 GGATCGATTAGTAGGGGTATGTATAGA 58.784 40.741 0.00 0.00 0.00 1.98
2303 2547 9.275398 GATCGATTAGTAGGGGTATGTATAGAG 57.725 40.741 0.00 0.00 0.00 2.43
2314 2558 4.951094 GGTATGTATAGAGGGCTGTAGGAG 59.049 50.000 0.00 0.00 0.00 3.69
2404 2648 4.753610 CAGAAACTCATCTGTTTGCTCTCA 59.246 41.667 0.00 0.00 41.54 3.27
2405 2649 4.996122 AGAAACTCATCTGTTTGCTCTCAG 59.004 41.667 0.00 0.00 39.86 3.35
2440 2692 4.695217 TGAGTGTTGACCAAGTTTGTTC 57.305 40.909 0.00 0.00 0.00 3.18
2444 2696 4.526650 AGTGTTGACCAAGTTTGTTCCTTT 59.473 37.500 0.00 0.00 0.00 3.11
2446 2698 6.033966 GTGTTGACCAAGTTTGTTCCTTTAG 58.966 40.000 0.00 0.00 0.00 1.85
2447 2699 5.712917 TGTTGACCAAGTTTGTTCCTTTAGT 59.287 36.000 0.00 0.00 0.00 2.24
2465 2719 3.498774 AGTTTGACTTGGTCTGATGCT 57.501 42.857 0.00 0.00 33.15 3.79
2467 2721 4.573900 AGTTTGACTTGGTCTGATGCTAG 58.426 43.478 0.00 0.00 33.15 3.42
2488 2742 2.156504 GTCTGTGAGACATGCGTTTCTG 59.843 50.000 0.00 0.00 44.45 3.02
2489 2743 2.138320 CTGTGAGACATGCGTTTCTGT 58.862 47.619 0.00 0.00 0.00 3.41
2490 2744 2.545526 CTGTGAGACATGCGTTTCTGTT 59.454 45.455 0.00 0.00 0.00 3.16
2491 2745 2.942376 TGTGAGACATGCGTTTCTGTTT 59.058 40.909 0.00 0.00 0.00 2.83
2568 3232 3.388024 TCAAAGTGTAGAAGGCACTCAGT 59.612 43.478 0.00 0.00 45.36 3.41
2620 3339 2.158959 GGCTGGTGATCGTTCGTCG 61.159 63.158 0.00 0.00 41.41 5.12
2628 3347 3.486375 GGTGATCGTTCGTCGTAGAATCA 60.486 47.826 0.00 0.00 39.69 2.57
2631 3350 3.818961 TCGTTCGTCGTAGAATCAGTT 57.181 42.857 0.00 0.00 39.69 3.16
2642 3361 7.318439 CGTCGTAGAATCAGTTCGTATAAAGAG 59.682 40.741 0.00 0.00 39.69 2.85
2752 3473 7.092578 GCTAATAGGCTAATAGGGGTATTTCCA 60.093 40.741 16.37 0.00 38.11 3.53
2764 3485 3.057174 GGGTATTTCCACAAACGATGCAA 60.057 43.478 0.00 0.00 38.11 4.08
2793 3514 4.022242 GCTGTAGGAGTTCTCACTGTACAA 60.022 45.833 0.00 0.00 32.33 2.41
2794 3515 5.704888 CTGTAGGAGTTCTCACTGTACAAG 58.295 45.833 0.00 0.00 32.33 3.16
2795 3516 5.138276 TGTAGGAGTTCTCACTGTACAAGT 58.862 41.667 0.00 0.00 40.93 3.16
2888 3652 3.588569 ACAGGAGGAGTTTGAGTAACCT 58.411 45.455 0.00 0.00 37.46 3.50
2893 3657 4.081586 GGAGGAGTTTGAGTAACCTACTGG 60.082 50.000 0.00 0.00 39.59 4.00
2940 3704 2.025863 GCATAGCAGCACATTTCCCCT 61.026 52.381 0.00 0.00 0.00 4.79
2964 3728 2.800544 ACTCGTACAATGTTGCTGTCAC 59.199 45.455 0.00 0.00 0.00 3.67
3124 3888 5.746307 ATATAGCTGTGTGATTGCAACTG 57.254 39.130 0.00 0.00 0.00 3.16
3125 3889 0.956633 AGCTGTGTGATTGCAACTGG 59.043 50.000 0.00 0.00 0.00 4.00
3191 4037 8.354711 AGAACTTCAGATCATGTAGTGAACTA 57.645 34.615 0.00 0.00 38.47 2.24
3192 4038 8.465999 AGAACTTCAGATCATGTAGTGAACTAG 58.534 37.037 0.00 0.00 38.47 2.57
3193 4039 7.710676 ACTTCAGATCATGTAGTGAACTAGT 57.289 36.000 0.00 0.00 37.82 2.57
3243 4089 6.070767 TGTGTTAAGAGAATAAGAGGACCAGG 60.071 42.308 0.00 0.00 0.00 4.45
3247 4093 3.034635 GAGAATAAGAGGACCAGGCTCA 58.965 50.000 0.00 0.00 0.00 4.26
3284 4130 3.518705 TGCCTATGGTTTCCTACGGTTAA 59.481 43.478 0.00 0.00 0.00 2.01
3370 4229 7.120138 TGACCCTGTAGAATTATTTCGTTTTCC 59.880 37.037 0.00 0.00 36.93 3.13
3419 4278 7.395190 TTGAATGTGGATGATGAACCTAAAG 57.605 36.000 0.00 0.00 0.00 1.85
3421 4280 6.375174 TGAATGTGGATGATGAACCTAAAGTG 59.625 38.462 0.00 0.00 0.00 3.16
3426 4285 5.710099 TGGATGATGAACCTAAAGTGTTTCC 59.290 40.000 0.00 0.00 0.00 3.13
3429 4288 5.313712 TGATGAACCTAAAGTGTTTCCCTC 58.686 41.667 0.00 0.00 0.00 4.30
3438 4297 1.147191 AGTGTTTCCCTCCCCTTTTCC 59.853 52.381 0.00 0.00 0.00 3.13
3444 4303 1.776969 CCTCCCCTTTTCCTTGCCT 59.223 57.895 0.00 0.00 0.00 4.75
3480 4339 1.443194 CAGCTCAACCGCATGCAAC 60.443 57.895 19.57 0.00 0.00 4.17
3510 4369 1.721664 TAGGCGATCCGGAGTTCGTG 61.722 60.000 24.21 6.24 37.50 4.35
3621 4480 0.040058 TCCTTCTGGCATGCATGGTT 59.960 50.000 27.34 0.00 0.00 3.67
3792 4651 5.989777 GTGAAGTTAAGCTGTGAAGAGGTAA 59.010 40.000 0.00 0.00 0.00 2.85
3830 4689 1.153449 GGCGGCCTTAAATTTGCCC 60.153 57.895 12.87 5.56 42.29 5.36
3837 4696 2.799562 GCCTTAAATTTGCCCTGATCGC 60.800 50.000 0.00 0.00 0.00 4.58
3877 4746 1.825281 CTGATCAGGATCTCCCGCCC 61.825 65.000 15.38 0.00 40.87 6.13
3911 4787 1.066303 AGTGAAGATAGCGGCGAAGAG 59.934 52.381 12.98 0.00 0.00 2.85
3913 4789 2.033049 GTGAAGATAGCGGCGAAGAGTA 59.967 50.000 12.98 0.00 0.00 2.59
3938 4818 1.745232 TGTGTTGTTCGCTTGTTCCT 58.255 45.000 0.00 0.00 0.00 3.36
3971 4851 6.152661 TGTTGTCTTGGTTTGAAGAAGAACAT 59.847 34.615 0.00 0.00 34.59 2.71
4003 4883 3.755378 AGTGCTGTGATTTCCTAGCTTTG 59.245 43.478 0.00 0.00 37.10 2.77
4004 4884 3.753272 GTGCTGTGATTTCCTAGCTTTGA 59.247 43.478 0.00 0.00 37.10 2.69
4005 4885 4.397417 GTGCTGTGATTTCCTAGCTTTGAT 59.603 41.667 0.00 0.00 37.10 2.57
4063 4945 4.453819 GTCAGTGCAGATTTCTATATGCCC 59.546 45.833 2.71 0.00 46.03 5.36
4069 4951 4.583871 CAGATTTCTATATGCCCACCCTC 58.416 47.826 0.00 0.00 0.00 4.30
4085 4967 4.398319 CACCCTCTGTTCCAGTGTTTATT 58.602 43.478 0.00 0.00 32.61 1.40
4114 4996 3.699894 CAGGACGAGGTGGCAGCT 61.700 66.667 20.74 20.74 0.00 4.24
4116 4998 4.008933 GGACGAGGTGGCAGCTGT 62.009 66.667 25.83 20.77 0.00 4.40
4136 5022 6.072452 AGCTGTCTTTAGCAAGGAAAATGTAC 60.072 38.462 0.00 0.00 46.07 2.90
4150 5036 2.105006 ATGTACTGCCAGCTCAGTTG 57.895 50.000 12.80 0.00 44.26 3.16
4226 5141 6.169800 TCACATGGAAACGATGATAGAAACA 58.830 36.000 0.00 0.00 0.00 2.83
4321 5263 1.476488 AGTTGCAAGTGTTGGACCAAC 59.524 47.619 27.46 27.46 43.78 3.77
4332 5274 2.047655 GACCAACATGGGCGACGA 60.048 61.111 0.00 0.00 43.37 4.20
4333 5275 2.358247 ACCAACATGGGCGACGAC 60.358 61.111 0.00 0.00 43.37 4.34
4363 5305 1.665679 CATAATTTGGTCGCTGCGAGT 59.334 47.619 26.68 5.35 36.23 4.18
4549 5505 2.283145 CTGGGCCAGCTATAAATGCT 57.717 50.000 22.68 0.00 42.06 3.79
4556 5512 3.433615 GCCAGCTATAAATGCTAACGAGG 59.566 47.826 0.00 0.00 38.92 4.63
4618 5574 0.253044 TGAGAGGTACCCTTGCATGC 59.747 55.000 11.82 11.82 31.76 4.06
4619 5575 0.811616 GAGAGGTACCCTTGCATGCG 60.812 60.000 14.09 0.35 31.76 4.73
4621 5577 0.676782 GAGGTACCCTTGCATGCGTT 60.677 55.000 14.09 0.00 31.76 4.84
4622 5578 0.251165 AGGTACCCTTGCATGCGTTT 60.251 50.000 14.09 0.00 0.00 3.60
4625 5581 0.595588 TACCCTTGCATGCGTTTGTG 59.404 50.000 14.09 1.71 0.00 3.33
4626 5582 2.023223 CCCTTGCATGCGTTTGTGC 61.023 57.895 14.09 0.00 41.61 4.57
4637 5594 0.670546 CGTTTGTGCGTCCTCTCCAT 60.671 55.000 0.00 0.00 0.00 3.41
4683 5652 3.081804 CAGAAGCGAAAACCCTACCAAT 58.918 45.455 0.00 0.00 0.00 3.16
4684 5653 4.258543 CAGAAGCGAAAACCCTACCAATA 58.741 43.478 0.00 0.00 0.00 1.90
4685 5654 4.881850 CAGAAGCGAAAACCCTACCAATAT 59.118 41.667 0.00 0.00 0.00 1.28
4687 5656 6.710744 CAGAAGCGAAAACCCTACCAATATAT 59.289 38.462 0.00 0.00 0.00 0.86
4689 5658 7.876582 AGAAGCGAAAACCCTACCAATATATAC 59.123 37.037 0.00 0.00 0.00 1.47
4690 5659 7.069877 AGCGAAAACCCTACCAATATATACA 57.930 36.000 0.00 0.00 0.00 2.29
4691 5660 6.932960 AGCGAAAACCCTACCAATATATACAC 59.067 38.462 0.00 0.00 0.00 2.90
4692 5661 6.707161 GCGAAAACCCTACCAATATATACACA 59.293 38.462 0.00 0.00 0.00 3.72
4693 5662 7.307573 GCGAAAACCCTACCAATATATACACAC 60.308 40.741 0.00 0.00 0.00 3.82
4694 5663 7.711772 CGAAAACCCTACCAATATATACACACA 59.288 37.037 0.00 0.00 0.00 3.72
4695 5664 9.569122 GAAAACCCTACCAATATATACACACAT 57.431 33.333 0.00 0.00 0.00 3.21
4696 5665 9.569122 AAAACCCTACCAATATATACACACATC 57.431 33.333 0.00 0.00 0.00 3.06
4697 5666 6.931838 ACCCTACCAATATATACACACATCG 58.068 40.000 0.00 0.00 0.00 3.84
4698 5667 6.722590 ACCCTACCAATATATACACACATCGA 59.277 38.462 0.00 0.00 0.00 3.59
4699 5668 7.233962 ACCCTACCAATATATACACACATCGAA 59.766 37.037 0.00 0.00 0.00 3.71
4700 5669 8.092068 CCCTACCAATATATACACACATCGAAA 58.908 37.037 0.00 0.00 0.00 3.46
4701 5670 8.922676 CCTACCAATATATACACACATCGAAAC 58.077 37.037 0.00 0.00 0.00 2.78
4702 5671 9.471084 CTACCAATATATACACACATCGAAACA 57.529 33.333 0.00 0.00 0.00 2.83
4703 5672 8.365399 ACCAATATATACACACATCGAAACAG 57.635 34.615 0.00 0.00 0.00 3.16
4704 5673 8.201464 ACCAATATATACACACATCGAAACAGA 58.799 33.333 0.00 0.00 0.00 3.41
4705 5674 8.703336 CCAATATATACACACATCGAAACAGAG 58.297 37.037 0.00 0.00 0.00 3.35
4706 5675 7.875316 ATATATACACACATCGAAACAGAGC 57.125 36.000 0.00 0.00 0.00 4.09
4707 5676 2.533266 ACACACATCGAAACAGAGCT 57.467 45.000 0.00 0.00 0.00 4.09
4708 5677 2.138320 ACACACATCGAAACAGAGCTG 58.862 47.619 0.00 0.00 0.00 4.24
4709 5678 1.462283 CACACATCGAAACAGAGCTGG 59.538 52.381 0.00 0.00 34.19 4.85
4710 5679 1.070758 ACACATCGAAACAGAGCTGGT 59.929 47.619 0.00 0.00 34.19 4.00
4711 5680 2.146342 CACATCGAAACAGAGCTGGTT 58.854 47.619 0.00 0.00 44.30 3.67
4712 5681 2.096069 CACATCGAAACAGAGCTGGTTG 60.096 50.000 5.36 0.00 41.20 3.77
4713 5682 1.135859 CATCGAAACAGAGCTGGTTGC 60.136 52.381 5.36 0.00 41.20 4.17
4722 5691 3.978272 GCTGGTTGCTGAGACCTG 58.022 61.111 0.00 0.00 38.04 4.00
4723 5692 1.372683 GCTGGTTGCTGAGACCTGA 59.627 57.895 9.73 0.00 38.09 3.86
4729 5698 1.051008 TTGCTGAGACCTGAGAAGCA 58.949 50.000 0.00 0.00 41.87 3.91
4732 5701 0.607112 CTGAGACCTGAGAAGCAGCA 59.393 55.000 0.00 0.00 43.50 4.41
4734 5703 0.607620 GAGACCTGAGAAGCAGCAGT 59.392 55.000 0.00 0.00 43.50 4.40
4738 5707 1.575576 CCTGAGAAGCAGCAGTGTGC 61.576 60.000 8.97 8.97 43.50 4.57
4784 5753 3.340814 AGCACGAAATGGTGAATCTCT 57.659 42.857 0.00 0.00 40.38 3.10
4808 5778 2.204090 AAGGCGAGGGGAGGGAAA 60.204 61.111 0.00 0.00 0.00 3.13
4820 5790 1.068541 GGAGGGAAATCACACGCAAAC 60.069 52.381 0.00 0.00 0.00 2.93
4821 5791 1.880027 GAGGGAAATCACACGCAAACT 59.120 47.619 0.00 0.00 0.00 2.66
4829 5799 0.039256 CACACGCAAACTCCAATGGG 60.039 55.000 0.00 0.00 35.78 4.00
4831 5801 0.893270 CACGCAAACTCCAATGGGGA 60.893 55.000 5.97 0.00 45.89 4.81
4840 5810 2.042741 CAATGGGGAGCATGGGCA 60.043 61.111 0.00 0.00 44.61 5.36
4842 5812 4.534824 ATGGGGAGCATGGGCAGC 62.535 66.667 0.00 0.00 44.61 5.25
4904 5874 3.474007 CGGCCACACGCTACTATAG 57.526 57.895 2.24 0.00 37.74 1.31
5066 6041 3.422303 GCCACGCGACAAGCATGA 61.422 61.111 15.93 0.00 42.45 3.07
5068 6043 1.154413 CCACGCGACAAGCATGAAC 60.154 57.895 15.93 0.00 42.45 3.18
5069 6044 1.507713 CACGCGACAAGCATGAACG 60.508 57.895 15.93 2.50 42.45 3.95
5072 6047 2.096406 CGACAAGCATGAACGGCG 59.904 61.111 4.80 4.80 36.08 6.46
5073 6048 2.480555 GACAAGCATGAACGGCGG 59.519 61.111 13.24 0.00 36.08 6.13
5090 6076 0.458543 CGGCCGGAGAATCGATATGG 60.459 60.000 20.10 0.00 34.37 2.74
5103 6089 6.990939 AGAATCGATATGGATGCATCAATAGG 59.009 38.462 27.25 19.89 0.00 2.57
5108 6094 6.202379 CGATATGGATGCATCAATAGGTGATC 59.798 42.308 27.25 18.26 44.01 2.92
5125 6111 6.294473 AGGTGATCATAGAATTAAGCTGGTG 58.706 40.000 0.00 0.00 0.00 4.17
5126 6112 6.100279 AGGTGATCATAGAATTAAGCTGGTGA 59.900 38.462 0.00 0.00 0.00 4.02
5127 6113 6.939163 GGTGATCATAGAATTAAGCTGGTGAT 59.061 38.462 0.00 8.94 0.00 3.06
5128 6114 7.446625 GGTGATCATAGAATTAAGCTGGTGATT 59.553 37.037 0.00 0.00 0.00 2.57
5129 6115 8.502387 GTGATCATAGAATTAAGCTGGTGATTC 58.498 37.037 0.00 7.67 0.00 2.52
5130 6116 7.386025 TGATCATAGAATTAAGCTGGTGATTCG 59.614 37.037 0.00 0.00 34.54 3.34
5131 6117 5.466728 TCATAGAATTAAGCTGGTGATTCGC 59.533 40.000 0.00 0.00 34.54 4.70
5132 6118 3.609853 AGAATTAAGCTGGTGATTCGCA 58.390 40.909 0.00 0.00 34.54 5.10
5133 6119 4.009675 AGAATTAAGCTGGTGATTCGCAA 58.990 39.130 0.00 0.00 34.54 4.85
5134 6120 4.458989 AGAATTAAGCTGGTGATTCGCAAA 59.541 37.500 0.00 0.00 34.54 3.68
5135 6121 4.782019 ATTAAGCTGGTGATTCGCAAAA 57.218 36.364 0.00 0.00 0.00 2.44
5136 6122 4.576216 TTAAGCTGGTGATTCGCAAAAA 57.424 36.364 0.00 0.00 0.00 1.94
5137 6123 2.712057 AGCTGGTGATTCGCAAAAAG 57.288 45.000 0.00 0.00 0.00 2.27
5138 6124 2.229792 AGCTGGTGATTCGCAAAAAGA 58.770 42.857 0.00 0.00 0.00 2.52
5139 6125 2.622942 AGCTGGTGATTCGCAAAAAGAA 59.377 40.909 0.00 0.00 0.00 2.52
5140 6126 3.068024 AGCTGGTGATTCGCAAAAAGAAA 59.932 39.130 0.00 0.00 0.00 2.52
5141 6127 3.801594 GCTGGTGATTCGCAAAAAGAAAA 59.198 39.130 0.00 0.00 0.00 2.29
5142 6128 4.448732 GCTGGTGATTCGCAAAAAGAAAAT 59.551 37.500 0.00 0.00 0.00 1.82
5143 6129 5.633182 GCTGGTGATTCGCAAAAAGAAAATA 59.367 36.000 0.00 0.00 0.00 1.40
5144 6130 6.183360 GCTGGTGATTCGCAAAAAGAAAATAG 60.183 38.462 0.00 0.00 0.00 1.73
5145 6131 6.976088 TGGTGATTCGCAAAAAGAAAATAGA 58.024 32.000 0.00 0.00 0.00 1.98
5146 6132 7.429633 TGGTGATTCGCAAAAAGAAAATAGAA 58.570 30.769 0.00 0.00 0.00 2.10
5147 6133 8.087750 TGGTGATTCGCAAAAAGAAAATAGAAT 58.912 29.630 0.00 0.00 0.00 2.40
5148 6134 9.567848 GGTGATTCGCAAAAAGAAAATAGAATA 57.432 29.630 0.00 0.00 0.00 1.75
5161 6147 9.628500 AAGAAAATAGAATAGAATTAAGCCGGT 57.372 29.630 1.90 0.00 0.00 5.28
5162 6148 9.274206 AGAAAATAGAATAGAATTAAGCCGGTC 57.726 33.333 1.90 0.00 0.00 4.79
5163 6149 7.653767 AAATAGAATAGAATTAAGCCGGTCG 57.346 36.000 1.90 0.00 0.00 4.79
5164 6150 3.991367 AGAATAGAATTAAGCCGGTCGG 58.009 45.455 1.90 4.85 38.57 4.79
5165 6151 3.387050 AGAATAGAATTAAGCCGGTCGGT 59.613 43.478 11.25 0.00 37.65 4.69
5166 6152 2.877043 TAGAATTAAGCCGGTCGGTC 57.123 50.000 11.25 3.76 37.65 4.79
5167 6153 0.179119 AGAATTAAGCCGGTCGGTCG 60.179 55.000 11.25 0.00 37.65 4.79
5181 6167 4.871993 GTCGGTCGGACGATATATACAT 57.128 45.455 1.43 0.00 45.47 2.29
5182 6168 4.585364 GTCGGTCGGACGATATATACATG 58.415 47.826 1.43 0.00 45.47 3.21
5183 6169 4.093998 GTCGGTCGGACGATATATACATGT 59.906 45.833 2.69 2.69 45.47 3.21
5184 6170 5.291858 GTCGGTCGGACGATATATACATGTA 59.708 44.000 8.27 8.27 45.47 2.29
5185 6171 5.291858 TCGGTCGGACGATATATACATGTAC 59.708 44.000 7.96 0.00 38.06 2.90
5186 6172 5.063817 CGGTCGGACGATATATACATGTACA 59.936 44.000 7.96 0.00 35.47 2.90
5187 6173 6.253746 GGTCGGACGATATATACATGTACAC 58.746 44.000 7.96 0.00 0.00 2.90
5188 6174 6.253746 GTCGGACGATATATACATGTACACC 58.746 44.000 7.96 2.74 0.00 4.16
5189 6175 5.355071 TCGGACGATATATACATGTACACCC 59.645 44.000 7.96 1.02 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.849357 AATATTTTATCGATGCCGCGTAA 57.151 34.783 8.54 0.00 35.37 3.18
42 43 5.003684 CGTAATATTTTATCGATGCCGCGTA 59.996 40.000 8.54 0.00 35.37 4.42
112 117 6.237728 GGTTTGTTGATTTTTCCGAAGTGAAC 60.238 38.462 0.00 0.00 0.00 3.18
114 119 5.105716 TGGTTTGTTGATTTTTCCGAAGTGA 60.106 36.000 0.00 0.00 0.00 3.41
115 120 5.105752 TGGTTTGTTGATTTTTCCGAAGTG 58.894 37.500 0.00 0.00 0.00 3.16
116 121 5.331876 TGGTTTGTTGATTTTTCCGAAGT 57.668 34.783 0.00 0.00 0.00 3.01
117 122 6.843069 AATGGTTTGTTGATTTTTCCGAAG 57.157 33.333 0.00 0.00 0.00 3.79
119 124 7.764443 TGTTTAATGGTTTGTTGATTTTTCCGA 59.236 29.630 0.00 0.00 0.00 4.55
120 125 7.910304 TGTTTAATGGTTTGTTGATTTTTCCG 58.090 30.769 0.00 0.00 0.00 4.30
161 166 7.435488 GTGGCAGTCTAGTAACATGTTATGTAG 59.565 40.741 20.72 21.09 44.07 2.74
166 171 4.081309 GGGTGGCAGTCTAGTAACATGTTA 60.081 45.833 14.35 14.35 0.00 2.41
175 180 1.362224 AACATGGGTGGCAGTCTAGT 58.638 50.000 0.00 0.00 0.00 2.57
197 202 3.181520 CCGGAGATGACGAAATTTGTGTC 60.182 47.826 0.00 11.46 0.00 3.67
246 251 2.236146 TGTTCCATGAGTGGCTCGTAAT 59.764 45.455 0.00 0.00 45.63 1.89
331 337 8.462811 TCAGTAGCACTTGTTTGAACATTAAAA 58.537 29.630 0.00 0.00 38.95 1.52
335 341 5.590259 ACTCAGTAGCACTTGTTTGAACATT 59.410 36.000 0.00 0.00 38.95 2.71
366 372 5.582953 TCATGTTCTTCTTGAAATGGGGAT 58.417 37.500 0.00 0.00 36.30 3.85
391 397 9.573133 GCGAAAAGTAACTATAAGGTGTAGTAA 57.427 33.333 0.00 0.00 32.34 2.24
393 399 7.834803 AGCGAAAAGTAACTATAAGGTGTAGT 58.165 34.615 0.00 0.00 33.98 2.73
394 400 9.448294 CTAGCGAAAAGTAACTATAAGGTGTAG 57.552 37.037 0.00 0.00 0.00 2.74
395 401 9.177608 TCTAGCGAAAAGTAACTATAAGGTGTA 57.822 33.333 0.00 0.00 0.00 2.90
396 402 8.059798 TCTAGCGAAAAGTAACTATAAGGTGT 57.940 34.615 0.00 0.00 0.00 4.16
397 403 9.530633 AATCTAGCGAAAAGTAACTATAAGGTG 57.469 33.333 0.00 0.00 0.00 4.00
403 409 8.997621 TTGACAATCTAGCGAAAAGTAACTAT 57.002 30.769 0.00 0.00 0.00 2.12
405 411 7.148407 CCATTGACAATCTAGCGAAAAGTAACT 60.148 37.037 0.00 0.00 0.00 2.24
409 415 5.003804 ACCATTGACAATCTAGCGAAAAGT 58.996 37.500 0.00 0.00 0.00 2.66
410 416 5.551760 ACCATTGACAATCTAGCGAAAAG 57.448 39.130 0.00 0.00 0.00 2.27
428 434 4.472108 TCGTTGAGGGGTTATCTTAACCAT 59.528 41.667 16.13 6.08 42.03 3.55
459 465 6.091849 TCTCGTGTGGTCTAGCGTAATATATC 59.908 42.308 0.00 0.00 0.00 1.63
495 501 8.540492 CAACAATGTTAGTTCGGTGTATAGATC 58.460 37.037 0.00 0.00 0.00 2.75
498 504 7.821595 TCAACAATGTTAGTTCGGTGTATAG 57.178 36.000 0.00 0.00 0.00 1.31
531 537 6.208599 GGTAGACTCCATTTTTGGAAACATGA 59.791 38.462 0.00 0.00 42.32 3.07
535 541 5.768164 TCTGGTAGACTCCATTTTTGGAAAC 59.232 40.000 0.00 0.00 37.55 2.78
567 575 8.114331 TGATAATTGCTTGTGAGATCAAACTT 57.886 30.769 0.00 0.00 0.00 2.66
612 620 4.981806 TCATTACATGGTAAGGCTTTGC 57.018 40.909 4.45 0.00 0.00 3.68
624 632 7.770201 TGGTGATGTGGTTTTATCATTACATG 58.230 34.615 0.00 0.00 35.91 3.21
682 695 4.081031 AGCCTGTCATATAGCATCTCCATG 60.081 45.833 0.00 0.00 0.00 3.66
704 717 3.576550 GAGAAACCCTAGGCCTCTATCAG 59.423 52.174 9.68 0.00 0.00 2.90
708 721 1.938069 AGGAGAAACCCTAGGCCTCTA 59.062 52.381 9.68 0.00 40.05 2.43
747 760 4.870363 TGGTCAGCAGCAGTTTTATTTTC 58.130 39.130 0.00 0.00 0.00 2.29
748 761 4.584325 TCTGGTCAGCAGCAGTTTTATTTT 59.416 37.500 0.00 0.00 46.58 1.82
756 769 1.070445 GTGTCTGGTCAGCAGCAGT 59.930 57.895 0.00 0.00 46.58 4.40
758 771 2.427320 GGTGTCTGGTCAGCAGCA 59.573 61.111 0.00 0.00 35.03 4.41
765 782 1.045407 TGGTGTACTGGTGTCTGGTC 58.955 55.000 0.00 0.00 0.00 4.02
767 784 0.756294 TGTGGTGTACTGGTGTCTGG 59.244 55.000 0.00 0.00 0.00 3.86
877 931 1.228737 GGGGTTTGGCTTGGCACTA 60.229 57.895 0.00 0.00 0.00 2.74
905 959 1.687493 GGGAGGAGGAGAGGGTGTG 60.687 68.421 0.00 0.00 0.00 3.82
906 960 2.781406 GGGAGGAGGAGAGGGTGT 59.219 66.667 0.00 0.00 0.00 4.16
907 961 2.443016 CGGGAGGAGGAGAGGGTG 60.443 72.222 0.00 0.00 0.00 4.61
908 962 2.617538 TCGGGAGGAGGAGAGGGT 60.618 66.667 0.00 0.00 0.00 4.34
909 963 2.123640 GTCGGGAGGAGGAGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
910 964 1.000486 TTGTCGGGAGGAGGAGAGG 60.000 63.158 0.00 0.00 0.00 3.69
911 965 1.671901 GCTTGTCGGGAGGAGGAGAG 61.672 65.000 0.00 0.00 0.00 3.20
912 966 1.682684 GCTTGTCGGGAGGAGGAGA 60.683 63.158 0.00 0.00 0.00 3.71
958 1012 0.196118 AGGTGAGGGGAAAAGAGGGA 59.804 55.000 0.00 0.00 0.00 4.20
1204 1438 1.314581 CAACGCGACGGAAATGAAAC 58.685 50.000 15.93 0.00 0.00 2.78
1334 1572 1.275010 CAAAATCCCAAGAAACGGGGG 59.725 52.381 0.00 0.00 44.62 5.40
1367 1605 1.137872 CATTGTCCCTCTTCTCCCTCG 59.862 57.143 0.00 0.00 0.00 4.63
1372 1610 1.134670 CCGACCATTGTCCCTCTTCTC 60.135 57.143 0.00 0.00 38.32 2.87
1376 1614 2.990479 GCCGACCATTGTCCCTCT 59.010 61.111 0.00 0.00 38.32 3.69
1929 2170 2.094182 GGAGTGAATTACGGACAGAGCA 60.094 50.000 0.00 0.00 0.00 4.26
1932 2173 1.829222 GGGGAGTGAATTACGGACAGA 59.171 52.381 0.00 0.00 0.00 3.41
1933 2174 1.553248 TGGGGAGTGAATTACGGACAG 59.447 52.381 0.00 0.00 0.00 3.51
1934 2175 1.646912 TGGGGAGTGAATTACGGACA 58.353 50.000 0.00 0.00 0.00 4.02
1935 2176 2.561569 CATGGGGAGTGAATTACGGAC 58.438 52.381 0.00 0.00 0.00 4.79
1938 2179 1.134098 AGCCATGGGGAGTGAATTACG 60.134 52.381 15.13 0.00 35.59 3.18
1947 2188 1.207791 AACAGAGTAGCCATGGGGAG 58.792 55.000 15.13 0.00 35.59 4.30
1957 2198 0.450583 TCGGCGCACTAACAGAGTAG 59.549 55.000 10.83 0.00 35.64 2.57
1964 2205 1.076332 AAATGACTCGGCGCACTAAC 58.924 50.000 10.83 0.00 0.00 2.34
1966 2207 1.475280 AGTAAATGACTCGGCGCACTA 59.525 47.619 10.83 0.00 29.95 2.74
1987 2228 9.869757 GCAATTTATTCAAGTTAATTAGTGGGT 57.130 29.630 0.00 0.00 0.00 4.51
1989 2230 9.868277 TGGCAATTTATTCAAGTTAATTAGTGG 57.132 29.630 0.00 0.00 0.00 4.00
2010 2251 6.463995 AACTGAACTTTAGTGAATTGGCAA 57.536 33.333 0.68 0.68 0.00 4.52
2148 2389 0.964860 TCATCCACCCAAATGCACCG 60.965 55.000 0.00 0.00 0.00 4.94
2221 2462 7.840210 CCCCCTTTACCTTTACCAATGTAATAA 59.160 37.037 0.00 0.00 36.84 1.40
2222 2463 7.355890 CCCCCTTTACCTTTACCAATGTAATA 58.644 38.462 0.00 0.00 36.84 0.98
2223 2464 6.199376 CCCCCTTTACCTTTACCAATGTAAT 58.801 40.000 0.00 0.00 36.84 1.89
2314 2558 5.824624 TCCAATGATCTCAACATTTCCTAGC 59.175 40.000 0.00 0.00 36.07 3.42
2398 2642 4.035558 TCAACACAACAATTCACTGAGAGC 59.964 41.667 0.00 0.00 0.00 4.09
2404 2648 5.182950 TCAACACTCAACACAACAATTCACT 59.817 36.000 0.00 0.00 0.00 3.41
2405 2649 5.286082 GTCAACACTCAACACAACAATTCAC 59.714 40.000 0.00 0.00 0.00 3.18
2440 2692 5.335191 GCATCAGACCAAGTCAAACTAAAGG 60.335 44.000 0.00 0.00 34.60 3.11
2444 2696 4.623932 AGCATCAGACCAAGTCAAACTA 57.376 40.909 0.00 0.00 34.60 2.24
2446 2698 4.319177 ACTAGCATCAGACCAAGTCAAAC 58.681 43.478 0.00 0.00 34.60 2.93
2447 2699 4.284490 AGACTAGCATCAGACCAAGTCAAA 59.716 41.667 0.00 0.00 36.63 2.69
2465 2719 3.255888 AGAAACGCATGTCTCACAGACTA 59.744 43.478 5.31 0.00 45.27 2.59
2467 2721 2.156504 CAGAAACGCATGTCTCACAGAC 59.843 50.000 0.00 0.00 45.26 3.51
2481 2735 2.920490 CACCACCAAACAAACAGAAACG 59.080 45.455 0.00 0.00 0.00 3.60
2488 2742 3.018149 TGACCTACACCACCAAACAAAC 58.982 45.455 0.00 0.00 0.00 2.93
2489 2743 3.283751 CTGACCTACACCACCAAACAAA 58.716 45.455 0.00 0.00 0.00 2.83
2490 2744 2.422235 CCTGACCTACACCACCAAACAA 60.422 50.000 0.00 0.00 0.00 2.83
2491 2745 1.142060 CCTGACCTACACCACCAAACA 59.858 52.381 0.00 0.00 0.00 2.83
2568 3232 8.450578 AATTTCATTTTCCATGATAGCTCGTA 57.549 30.769 0.00 0.00 0.00 3.43
2603 3322 0.179181 TACGACGAACGATCACCAGC 60.179 55.000 0.00 0.00 45.77 4.85
2666 3387 6.438259 TGTCACACCGAAGTAAAATTTTGA 57.562 33.333 13.76 0.00 0.00 2.69
2764 3485 6.070538 ACAGTGAGAACTCCTACAGCATAAAT 60.071 38.462 0.00 0.00 0.00 1.40
2793 3514 6.040842 TGTCCTCTTTTAAGGTAACGTACACT 59.959 38.462 0.00 0.00 46.39 3.55
2794 3515 6.215845 TGTCCTCTTTTAAGGTAACGTACAC 58.784 40.000 0.00 0.00 46.39 2.90
2795 3516 6.403866 TGTCCTCTTTTAAGGTAACGTACA 57.596 37.500 0.00 0.00 46.39 2.90
2796 3517 6.925718 AGTTGTCCTCTTTTAAGGTAACGTAC 59.074 38.462 0.00 0.00 46.39 3.67
2797 3518 6.925165 CAGTTGTCCTCTTTTAAGGTAACGTA 59.075 38.462 0.00 0.00 46.39 3.57
2798 3519 5.756833 CAGTTGTCCTCTTTTAAGGTAACGT 59.243 40.000 0.00 0.00 46.39 3.99
2799 3520 5.178809 CCAGTTGTCCTCTTTTAAGGTAACG 59.821 44.000 0.00 0.00 46.39 3.18
2800 3521 5.048921 GCCAGTTGTCCTCTTTTAAGGTAAC 60.049 44.000 0.00 0.00 37.69 2.50
2907 3671 6.659242 TGTGCTGCTATGCTGTACTCTATATA 59.341 38.462 15.41 0.00 41.68 0.86
2914 3678 2.996249 ATGTGCTGCTATGCTGTACT 57.004 45.000 15.41 3.04 41.68 2.73
2940 3704 5.803461 GTGACAGCAACATTGTACGAGTATA 59.197 40.000 0.00 0.00 0.00 1.47
2964 3728 5.578005 ATTGAGTGCAATGATTCCTTGAG 57.422 39.130 0.00 0.00 42.91 3.02
3094 3858 7.666804 TGCAATCACACAGCTATATAATTCCAT 59.333 33.333 0.00 0.00 0.00 3.41
3097 3861 8.562892 AGTTGCAATCACACAGCTATATAATTC 58.437 33.333 0.59 0.00 0.00 2.17
3108 3872 2.815503 TGATCCAGTTGCAATCACACAG 59.184 45.455 0.59 0.00 0.00 3.66
3124 3888 6.590234 AATCAACCCAGTAAGTTTTGATCC 57.410 37.500 0.00 0.00 36.18 3.36
3125 3889 8.887036 AAAAATCAACCCAGTAAGTTTTGATC 57.113 30.769 0.00 0.00 36.18 2.92
3153 3917 7.336176 TGATCTGAAGTTCTCAAGATTGGAATG 59.664 37.037 4.17 0.00 32.17 2.67
3243 4089 3.122297 GCAGATAGACACATCACTGAGC 58.878 50.000 0.00 0.00 0.00 4.26
3247 4093 4.282957 CCATAGGCAGATAGACACATCACT 59.717 45.833 0.00 0.00 0.00 3.41
3284 4130 3.808728 ACCGTGCAATAGAACATGCTAT 58.191 40.909 0.00 0.00 42.97 2.97
3370 4229 3.940852 TGCACATAGGTATCTTTGCACTG 59.059 43.478 3.21 0.00 35.13 3.66
3419 4278 1.147191 AGGAAAAGGGGAGGGAAACAC 59.853 52.381 0.00 0.00 0.00 3.32
3421 4280 2.248248 CAAGGAAAAGGGGAGGGAAAC 58.752 52.381 0.00 0.00 0.00 2.78
3426 4285 0.999712 TAGGCAAGGAAAAGGGGAGG 59.000 55.000 0.00 0.00 0.00 4.30
3438 4297 1.561643 TCTCACAGGTCCTAGGCAAG 58.438 55.000 2.96 0.00 0.00 4.01
3444 4303 2.382882 CTGCAGATCTCACAGGTCCTA 58.617 52.381 8.42 0.00 0.00 2.94
3480 4339 0.719465 GATCGCCTAACACAACCACG 59.281 55.000 0.00 0.00 0.00 4.94
3621 4480 2.270923 CATGAGATGACGAAGGCGAAA 58.729 47.619 0.00 0.00 41.64 3.46
3792 4651 1.529438 CGCGCCGACCATATATTTGTT 59.471 47.619 0.00 0.00 0.00 2.83
3837 4696 2.064014 GGTTCCTTTCGTACTGAACCG 58.936 52.381 11.70 0.00 45.05 4.44
3874 4736 2.362375 TCAAATCTTGGGGCGGGC 60.362 61.111 0.00 0.00 0.00 6.13
3877 4746 1.470098 CTTCACTCAAATCTTGGGGCG 59.530 52.381 0.00 0.00 34.70 6.13
3911 4787 4.211374 ACAAGCGAACAACACATCTTCTAC 59.789 41.667 0.00 0.00 0.00 2.59
3913 4789 3.206150 ACAAGCGAACAACACATCTTCT 58.794 40.909 0.00 0.00 0.00 2.85
3938 4818 6.869315 TCAAACCAAGACAACAATAATCGA 57.131 33.333 0.00 0.00 0.00 3.59
3971 4851 7.112122 AGGAAATCACAGCACTAACATAATCA 58.888 34.615 0.00 0.00 0.00 2.57
3985 4865 6.506500 AACATCAAAGCTAGGAAATCACAG 57.493 37.500 0.00 0.00 0.00 3.66
3989 4869 5.578336 GGCAAAACATCAAAGCTAGGAAATC 59.422 40.000 0.00 0.00 0.00 2.17
4003 4883 3.181476 ACCAACTCACAAGGCAAAACATC 60.181 43.478 0.00 0.00 0.00 3.06
4004 4884 2.765699 ACCAACTCACAAGGCAAAACAT 59.234 40.909 0.00 0.00 0.00 2.71
4005 4885 2.094286 CACCAACTCACAAGGCAAAACA 60.094 45.455 0.00 0.00 0.00 2.83
4056 4938 0.846693 GGAACAGAGGGTGGGCATAT 59.153 55.000 0.00 0.00 0.00 1.78
4102 4984 0.037326 TAAAGACAGCTGCCACCTCG 60.037 55.000 15.27 0.00 0.00 4.63
4114 4996 6.293955 GCAGTACATTTTCCTTGCTAAAGACA 60.294 38.462 0.00 0.00 35.19 3.41
4116 4998 5.183140 GGCAGTACATTTTCCTTGCTAAAGA 59.817 40.000 0.00 0.00 35.19 2.52
4136 5022 1.962822 TTCGCAACTGAGCTGGCAG 60.963 57.895 10.94 10.94 41.63 4.85
4150 5036 1.482278 TTTTCGGCAACATTGTTCGC 58.518 45.000 0.00 7.16 0.00 4.70
4298 5225 3.357203 TGGTCCAACACTTGCAACTAAA 58.643 40.909 0.00 0.00 0.00 1.85
4331 5273 2.166254 CCAAATTATGGCAGTGTGGGTC 59.834 50.000 0.00 0.00 43.80 4.46
4332 5274 2.178580 CCAAATTATGGCAGTGTGGGT 58.821 47.619 0.00 0.00 43.80 4.51
4333 5275 2.965572 CCAAATTATGGCAGTGTGGG 57.034 50.000 0.00 0.00 43.80 4.61
4363 5305 3.714001 CAGAGCCTCTGCCCTGCA 61.714 66.667 9.13 0.00 36.48 4.41
4549 5505 5.701750 TCAAAATTTTCACCGATCCTCGTTA 59.298 36.000 0.00 0.00 38.40 3.18
4556 5512 4.679654 AGCGTTTCAAAATTTTCACCGATC 59.320 37.500 0.00 0.00 0.00 3.69
4618 5574 0.670546 ATGGAGAGGACGCACAAACG 60.671 55.000 0.00 0.00 39.50 3.60
4619 5575 0.798776 CATGGAGAGGACGCACAAAC 59.201 55.000 0.00 0.00 0.00 2.93
4621 5577 1.296392 CCATGGAGAGGACGCACAA 59.704 57.895 5.56 0.00 0.00 3.33
4622 5578 2.981302 CCATGGAGAGGACGCACA 59.019 61.111 5.56 0.00 0.00 4.57
4683 5652 6.918022 CAGCTCTGTTTCGATGTGTGTATATA 59.082 38.462 0.00 0.00 0.00 0.86
4684 5653 5.750547 CAGCTCTGTTTCGATGTGTGTATAT 59.249 40.000 0.00 0.00 0.00 0.86
4685 5654 5.102313 CAGCTCTGTTTCGATGTGTGTATA 58.898 41.667 0.00 0.00 0.00 1.47
4687 5656 3.317150 CAGCTCTGTTTCGATGTGTGTA 58.683 45.455 0.00 0.00 0.00 2.90
4689 5658 1.462283 CCAGCTCTGTTTCGATGTGTG 59.538 52.381 0.00 0.00 0.00 3.82
4690 5659 1.070758 ACCAGCTCTGTTTCGATGTGT 59.929 47.619 0.00 0.00 0.00 3.72
4691 5660 1.800805 ACCAGCTCTGTTTCGATGTG 58.199 50.000 0.00 0.00 0.00 3.21
4692 5661 2.146342 CAACCAGCTCTGTTTCGATGT 58.854 47.619 0.00 0.00 0.00 3.06
4693 5662 1.135859 GCAACCAGCTCTGTTTCGATG 60.136 52.381 0.00 0.00 41.15 3.84
4694 5663 1.160137 GCAACCAGCTCTGTTTCGAT 58.840 50.000 0.00 0.00 41.15 3.59
4695 5664 2.616969 GCAACCAGCTCTGTTTCGA 58.383 52.632 0.00 0.00 41.15 3.71
4705 5674 0.673022 CTCAGGTCTCAGCAACCAGC 60.673 60.000 0.00 0.00 46.19 4.85
4706 5675 0.972134 TCTCAGGTCTCAGCAACCAG 59.028 55.000 0.00 0.00 39.39 4.00
4707 5676 1.345741 CTTCTCAGGTCTCAGCAACCA 59.654 52.381 0.00 0.00 39.39 3.67
4708 5677 1.943507 GCTTCTCAGGTCTCAGCAACC 60.944 57.143 0.00 0.00 37.03 3.77
4709 5678 1.270518 TGCTTCTCAGGTCTCAGCAAC 60.271 52.381 0.00 0.00 37.54 4.17
4710 5679 1.001746 CTGCTTCTCAGGTCTCAGCAA 59.998 52.381 0.00 0.00 39.92 3.91
4711 5680 0.607112 CTGCTTCTCAGGTCTCAGCA 59.393 55.000 0.00 0.00 39.15 4.41
4712 5681 0.740516 GCTGCTTCTCAGGTCTCAGC 60.741 60.000 0.00 0.00 43.06 4.26
4713 5682 0.607112 TGCTGCTTCTCAGGTCTCAG 59.393 55.000 0.00 0.00 43.06 3.35
4714 5683 0.607112 CTGCTGCTTCTCAGGTCTCA 59.393 55.000 0.00 0.00 43.06 3.27
4715 5684 0.607620 ACTGCTGCTTCTCAGGTCTC 59.392 55.000 0.00 0.00 43.06 3.36
4716 5685 0.321021 CACTGCTGCTTCTCAGGTCT 59.679 55.000 0.00 0.00 43.06 3.85
4717 5686 0.034616 ACACTGCTGCTTCTCAGGTC 59.965 55.000 0.00 0.00 43.06 3.85
4718 5687 0.250209 CACACTGCTGCTTCTCAGGT 60.250 55.000 0.00 0.00 43.06 4.00
4719 5688 1.575576 GCACACTGCTGCTTCTCAGG 61.576 60.000 0.00 0.00 43.06 3.86
4720 5689 0.883370 TGCACACTGCTGCTTCTCAG 60.883 55.000 0.00 0.00 45.31 3.35
4721 5690 0.883370 CTGCACACTGCTGCTTCTCA 60.883 55.000 0.00 0.00 45.31 3.27
4722 5691 1.867615 CTGCACACTGCTGCTTCTC 59.132 57.895 0.00 0.00 45.31 2.87
4723 5692 4.060372 CTGCACACTGCTGCTTCT 57.940 55.556 0.00 0.00 45.31 2.85
4729 5698 4.552365 ACCACGCTGCACACTGCT 62.552 61.111 0.00 0.00 45.31 4.24
4753 5722 2.124507 TTTCGTGCTGGGGAGAAGGG 62.125 60.000 0.00 0.00 0.00 3.95
4796 5765 0.107654 CGTGTGATTTCCCTCCCCTC 60.108 60.000 0.00 0.00 0.00 4.30
4798 5767 1.749258 GCGTGTGATTTCCCTCCCC 60.749 63.158 0.00 0.00 0.00 4.81
4808 5778 1.541147 CCATTGGAGTTTGCGTGTGAT 59.459 47.619 0.00 0.00 0.00 3.06
4821 5791 3.018019 CCCATGCTCCCCATTGGA 58.982 61.111 3.62 0.00 38.68 3.53
4876 5846 4.595538 TGTGGCCGCGAAAGACGT 62.596 61.111 8.23 0.00 44.60 4.34
4902 5872 2.117156 GTGGCGCTCCTACGGACTA 61.117 63.158 7.64 0.00 0.00 2.59
4903 5873 3.450115 GTGGCGCTCCTACGGACT 61.450 66.667 7.64 0.00 0.00 3.85
4904 5874 4.509737 GGTGGCGCTCCTACGGAC 62.510 72.222 7.64 0.00 0.00 4.79
5024 5994 2.739132 GGTGGGTCTCGTTCCGTT 59.261 61.111 0.00 0.00 0.00 4.44
5026 5996 2.874664 TTGGGTGGGTCTCGTTCCG 61.875 63.158 0.00 0.00 0.00 4.30
5027 5997 1.302271 GTTGGGTGGGTCTCGTTCC 60.302 63.158 0.00 0.00 0.00 3.62
5066 6041 4.832608 GATTCTCCGGCCGCCGTT 62.833 66.667 29.21 9.36 46.80 4.44
5069 6044 2.227089 ATATCGATTCTCCGGCCGCC 62.227 60.000 22.85 0.00 0.00 6.13
5071 6046 0.458543 CCATATCGATTCTCCGGCCG 60.459 60.000 21.04 21.04 0.00 6.13
5072 6047 0.895530 TCCATATCGATTCTCCGGCC 59.104 55.000 1.71 0.00 0.00 6.13
5073 6048 2.544685 CATCCATATCGATTCTCCGGC 58.455 52.381 1.71 0.00 0.00 6.13
5090 6076 8.734218 ATTCTATGATCACCTATTGATGCATC 57.266 34.615 20.14 20.14 45.67 3.91
5103 6089 7.976135 ATCACCAGCTTAATTCTATGATCAC 57.024 36.000 0.00 0.00 0.00 3.06
5108 6094 5.237127 TGCGAATCACCAGCTTAATTCTATG 59.763 40.000 0.00 0.00 0.00 2.23
5135 6121 9.628500 ACCGGCTTAATTCTATTCTATTTTCTT 57.372 29.630 0.00 0.00 0.00 2.52
5136 6122 9.274206 GACCGGCTTAATTCTATTCTATTTTCT 57.726 33.333 0.00 0.00 0.00 2.52
5137 6123 8.221766 CGACCGGCTTAATTCTATTCTATTTTC 58.778 37.037 0.00 0.00 0.00 2.29
5138 6124 7.172703 CCGACCGGCTTAATTCTATTCTATTTT 59.827 37.037 0.00 0.00 0.00 1.82
5139 6125 6.649557 CCGACCGGCTTAATTCTATTCTATTT 59.350 38.462 0.00 0.00 0.00 1.40
5140 6126 6.164176 CCGACCGGCTTAATTCTATTCTATT 58.836 40.000 0.00 0.00 0.00 1.73
5141 6127 5.245526 ACCGACCGGCTTAATTCTATTCTAT 59.754 40.000 8.55 0.00 39.32 1.98
5142 6128 4.586001 ACCGACCGGCTTAATTCTATTCTA 59.414 41.667 8.55 0.00 39.32 2.10
5143 6129 3.387050 ACCGACCGGCTTAATTCTATTCT 59.613 43.478 8.55 0.00 39.32 2.40
5144 6130 3.725490 ACCGACCGGCTTAATTCTATTC 58.275 45.455 8.55 0.00 39.32 1.75
5145 6131 3.725490 GACCGACCGGCTTAATTCTATT 58.275 45.455 8.55 0.00 39.32 1.73
5146 6132 2.288030 CGACCGACCGGCTTAATTCTAT 60.288 50.000 8.55 0.00 39.32 1.98
5147 6133 1.066002 CGACCGACCGGCTTAATTCTA 59.934 52.381 8.55 0.00 39.32 2.10
5148 6134 0.179119 CGACCGACCGGCTTAATTCT 60.179 55.000 8.55 0.00 39.32 2.40
5149 6135 1.149964 CCGACCGACCGGCTTAATTC 61.150 60.000 8.55 0.00 43.25 2.17
5150 6136 1.153509 CCGACCGACCGGCTTAATT 60.154 57.895 8.55 0.00 43.25 1.40
5151 6137 2.497770 CCGACCGACCGGCTTAAT 59.502 61.111 8.55 0.00 43.25 1.40
5158 6144 1.081892 ATATATCGTCCGACCGACCG 58.918 55.000 0.00 0.00 40.08 4.79
5159 6145 3.002791 TGTATATATCGTCCGACCGACC 58.997 50.000 0.00 0.00 40.08 4.79
5160 6146 4.093998 ACATGTATATATCGTCCGACCGAC 59.906 45.833 0.00 0.00 40.08 4.79
5161 6147 4.256110 ACATGTATATATCGTCCGACCGA 58.744 43.478 0.00 0.00 41.73 4.69
5162 6148 4.611310 ACATGTATATATCGTCCGACCG 57.389 45.455 0.00 0.00 0.00 4.79
5163 6149 6.253746 GTGTACATGTATATATCGTCCGACC 58.746 44.000 9.18 0.00 0.00 4.79
5164 6150 6.253746 GGTGTACATGTATATATCGTCCGAC 58.746 44.000 9.18 0.00 0.00 4.79
5165 6151 5.355071 GGGTGTACATGTATATATCGTCCGA 59.645 44.000 9.18 0.00 0.00 4.55
5166 6152 5.575957 GGGTGTACATGTATATATCGTCCG 58.424 45.833 9.18 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.