Multiple sequence alignment - TraesCS5A01G519300

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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 TraesCS5A01G519300 chr5A 100.000 5906 0 0 1 5906 680846093 680840188 0.000000e+00 10907.0
1 TraesCS5A01G519300 chr5A 94.737 38 2 0 2738 2775 502072220 502072257 6.390000e-05 60.2
2 TraesCS5A01G519300 chr4D 90.584 5172 215 106 226 5220 500026364 500021288 0.000000e+00 6602.0
3 TraesCS5A01G519300 chr4D 87.326 576 52 13 5350 5906 500007865 500007292 1.790000e-179 640.0
4 TraesCS5A01G519300 chr4D 91.228 228 6 3 5 218 500026630 500026403 1.240000e-76 298.0
5 TraesCS5A01G519300 chr4B 90.169 5157 240 106 226 5190 643313766 643308685 0.000000e+00 6468.0
6 TraesCS5A01G519300 chr4B 82.132 666 74 18 5237 5883 643293910 643293271 4.050000e-146 529.0
7 TraesCS5A01G519300 chr4B 90.083 242 11 3 5 234 643314031 643313791 9.620000e-78 302.0
8 TraesCS5A01G519300 chr1D 75.197 254 52 10 2528 2774 270231109 270231358 6.260000e-20 110.0
9 TraesCS5A01G519300 chr5B 83.333 102 17 0 2691 2792 535700244 535700345 1.750000e-15 95.3
10 TraesCS5A01G519300 chr5B 94.737 38 2 0 2738 2775 476170498 476170535 6.390000e-05 60.2
11 TraesCS5A01G519300 chr2B 81.522 92 15 2 2688 2778 794866936 794866846 2.280000e-09 75.0
12 TraesCS5A01G519300 chr2A 82.558 86 13 2 2694 2778 763313718 763313634 2.280000e-09 75.0
13 TraesCS5A01G519300 chr5D 94.737 38 2 0 2738 2775 396370474 396370511 6.390000e-05 60.2


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 TraesCS5A01G519300 chr5A 680840188 680846093 5905 True 10907 10907 100.000 1 5906 1 chr5A.!!$R1 5905
1 TraesCS5A01G519300 chr4D 500021288 500026630 5342 True 3450 6602 90.906 5 5220 2 chr4D.!!$R2 5215
2 TraesCS5A01G519300 chr4D 500007292 500007865 573 True 640 640 87.326 5350 5906 1 chr4D.!!$R1 556
3 TraesCS5A01G519300 chr4B 643308685 643314031 5346 True 3385 6468 90.126 5 5190 2 chr4B.!!$R2 5185
4 TraesCS5A01G519300 chr4B 643293271 643293910 639 True 529 529 82.132 5237 5883 1 chr4B.!!$R1 646

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
800 945 0.035317 ACGACTCATGTGTGTGCCAT 59.965 50.000 4.90 0.0 0.00 4.40 F
803 948 0.599558 ACTCATGTGTGTGCCATTGC 59.400 50.000 0.00 0.0 38.26 3.56 F
962 1125 0.883833 CAAGCGTCCATCCTTTTGCT 59.116 50.000 0.00 0.0 0.00 3.91 F
1170 1341 1.275291 CTTCCAGGTGCGTCCTTTCTA 59.725 52.381 0.00 0.0 45.67 2.10 F
2797 3068 1.543802 GAGAGGGAATGCGAGATCGAT 59.456 52.381 6.39 0.0 43.02 3.59 F
3917 4211 0.044855 AGAGGTAATGTCAGGCCCCT 59.955 55.000 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2650 2921 0.181587 TCACTTTGCGGTCTTTCCCA 59.818 50.000 0.00 0.0 0.00 4.37 R
2674 2945 0.602638 TACCAACTGCACGCTTCTGG 60.603 55.000 0.00 0.0 0.00 3.86 R
2874 3146 2.024414 GGGCAATATGTGGAACCTCAC 58.976 52.381 0.00 0.0 38.09 3.51 R
3169 3445 1.274703 ATCTGCATCCCGAACCCACT 61.275 55.000 0.00 0.0 0.00 4.00 R
4527 4853 0.669077 CCCTGCTACTGCTACTACCG 59.331 60.000 0.00 0.0 40.48 4.02 R
5414 5773 0.031515 TTAGGATTCCTCTCCCCGCA 60.032 55.000 8.94 0.0 35.79 5.69 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
218 241 1.136446 CGTAAACCGTGAAAGCGAAGG 60.136 52.381 0.00 0.00 0.00 3.46
219 242 2.137523 GTAAACCGTGAAAGCGAAGGA 58.862 47.619 0.00 0.00 0.00 3.36
222 245 1.292223 CCGTGAAAGCGAAGGAGGA 59.708 57.895 0.00 0.00 0.00 3.71
223 246 1.014564 CCGTGAAAGCGAAGGAGGAC 61.015 60.000 0.00 0.00 0.00 3.85
287 342 0.814457 CAACGAGAGCTGACTAGGCT 59.186 55.000 0.00 0.00 43.26 4.58
298 353 3.631250 CTGACTAGGCTTCTCCTTCTCT 58.369 50.000 0.00 0.00 44.75 3.10
339 406 1.424302 CCAATGGCATCTCATCTCCCT 59.576 52.381 0.00 0.00 0.00 4.20
368 435 2.586079 CCGCATGCACCTCCTACG 60.586 66.667 19.57 0.00 0.00 3.51
377 444 0.885879 CACCTCCTACGCTACACACA 59.114 55.000 0.00 0.00 0.00 3.72
382 449 0.885879 CCTACGCTACACACACAGGA 59.114 55.000 0.00 0.00 0.00 3.86
383 450 1.135373 CCTACGCTACACACACAGGAG 60.135 57.143 0.00 0.00 0.00 3.69
420 509 2.106338 TGGCTATAGGCATGCAGCTTTA 59.894 45.455 24.04 9.83 46.12 1.85
424 513 5.577351 GCTATAGGCATGCAGCTTTAGCTT 61.577 45.833 25.06 7.31 44.65 3.74
539 640 1.687996 GGACCCAAGGGAGAGAGAGAG 60.688 61.905 13.15 0.00 38.96 3.20
540 641 1.286553 GACCCAAGGGAGAGAGAGAGA 59.713 57.143 13.15 0.00 38.96 3.10
541 642 1.287739 ACCCAAGGGAGAGAGAGAGAG 59.712 57.143 13.15 0.00 38.96 3.20
542 643 1.568597 CCCAAGGGAGAGAGAGAGAGA 59.431 57.143 0.00 0.00 37.50 3.10
543 644 2.423373 CCCAAGGGAGAGAGAGAGAGAG 60.423 59.091 0.00 0.00 37.50 3.20
544 645 2.509548 CCAAGGGAGAGAGAGAGAGAGA 59.490 54.545 0.00 0.00 0.00 3.10
545 646 3.434167 CCAAGGGAGAGAGAGAGAGAGAG 60.434 56.522 0.00 0.00 0.00 3.20
546 647 3.421394 AGGGAGAGAGAGAGAGAGAGA 57.579 52.381 0.00 0.00 0.00 3.10
550 651 3.706594 GGAGAGAGAGAGAGAGAGACAGA 59.293 52.174 0.00 0.00 0.00 3.41
592 693 0.098905 CGAGAAGAATCGTCCGAGCA 59.901 55.000 0.00 0.00 37.91 4.26
732 839 4.760047 CACCCAAGGTCGGCCTCG 62.760 72.222 10.20 0.00 46.33 4.63
735 842 4.452733 CCAAGGTCGGCCTCGTCC 62.453 72.222 10.20 0.00 46.33 4.79
744 876 2.043852 GCCTCGTCCTCCTCCTCA 60.044 66.667 0.00 0.00 0.00 3.86
751 883 2.778270 TCGTCCTCCTCCTCAATCTCTA 59.222 50.000 0.00 0.00 0.00 2.43
758 892 2.627699 CCTCCTCAATCTCTACTGCTCC 59.372 54.545 0.00 0.00 0.00 4.70
776 910 3.321968 GCTCCTCTGAATTGGTTGGTTTT 59.678 43.478 0.00 0.00 0.00 2.43
782 927 6.868339 CCTCTGAATTGGTTGGTTTTTATGAC 59.132 38.462 0.00 0.00 0.00 3.06
797 942 1.432514 ATGACGACTCATGTGTGTGC 58.567 50.000 4.90 0.00 35.65 4.57
798 943 0.599991 TGACGACTCATGTGTGTGCC 60.600 55.000 4.90 0.00 0.00 5.01
799 944 0.599991 GACGACTCATGTGTGTGCCA 60.600 55.000 4.90 0.00 0.00 4.92
800 945 0.035317 ACGACTCATGTGTGTGCCAT 59.965 50.000 4.90 0.00 0.00 4.40
803 948 0.599558 ACTCATGTGTGTGCCATTGC 59.400 50.000 0.00 0.00 38.26 3.56
835 984 4.582656 TGCAGGTTTTGTACATTTGTAGCT 59.417 37.500 0.00 0.00 0.00 3.32
863 1014 4.021104 ACGATTCATTGCTGGCTATAGCTA 60.021 41.667 23.53 17.35 44.01 3.32
925 1084 1.381851 CTTTGGAGAGCCCTGCCTT 59.618 57.895 0.00 0.00 35.38 4.35
962 1125 0.883833 CAAGCGTCCATCCTTTTGCT 59.116 50.000 0.00 0.00 0.00 3.91
981 1144 2.043852 TGGGAGCTCTCGGAGGAC 60.044 66.667 14.64 0.00 0.00 3.85
1143 1313 2.028112 TGATCTTTACAAGTGCGAGCCT 60.028 45.455 0.00 0.00 0.00 4.58
1152 1322 3.249189 TGCGAGCCTTGGGACCTT 61.249 61.111 0.00 0.00 0.00 3.50
1170 1341 1.275291 CTTCCAGGTGCGTCCTTTCTA 59.725 52.381 0.00 0.00 45.67 2.10
1171 1342 1.568504 TCCAGGTGCGTCCTTTCTAT 58.431 50.000 0.00 0.00 45.67 1.98
1205 1390 6.874134 AGAAATGTTTGTATCGACACTAGCTT 59.126 34.615 0.00 0.00 34.48 3.74
1241 1426 2.372504 TCAATCCAAAACCCTACGTCCA 59.627 45.455 0.00 0.00 0.00 4.02
1289 1474 3.082548 CAGAGAACAAGGTCCTCGTAGA 58.917 50.000 0.00 0.00 32.52 2.59
1298 1483 6.574350 ACAAGGTCCTCGTAGATAATTTCAG 58.426 40.000 0.00 0.00 33.89 3.02
1313 1498 9.606631 AGATAATTTCAGGATCAACTTCAGTAC 57.393 33.333 0.00 0.00 0.00 2.73
1436 1626 5.132144 AGTCTTCCGTGGATTAATTATGGGT 59.868 40.000 10.37 0.00 0.00 4.51
1463 1653 3.402110 CACTGCATACACCTTGTTCTCA 58.598 45.455 0.00 0.00 0.00 3.27
1497 1687 3.844577 ACACGTACACCACTCTGATAC 57.155 47.619 0.00 0.00 0.00 2.24
1717 1920 6.603237 CATGAATGCATGCATTTGAAGAAT 57.397 33.333 38.66 23.93 45.50 2.40
1718 1921 7.707774 CATGAATGCATGCATTTGAAGAATA 57.292 32.000 38.66 20.84 45.50 1.75
1736 1939 8.527810 TGAAGAATATATTTGGTTTTCACCCAC 58.472 33.333 0.00 0.00 43.49 4.61
1791 1996 2.328319 AGTTTAGTGTACCGTCCCCAA 58.672 47.619 0.00 0.00 0.00 4.12
2028 2238 2.695359 TCCTTTATCACAGCGACAACC 58.305 47.619 0.00 0.00 0.00 3.77
2121 2331 3.815856 TCCACTTGCAATTTGCTTTCA 57.184 38.095 21.19 0.00 45.31 2.69
2150 2360 3.223435 TCGTTTGCTAAAAATCACCCCA 58.777 40.909 0.00 0.00 0.00 4.96
2160 2370 2.307496 AATCACCCCACTGAATGCAA 57.693 45.000 0.00 0.00 0.00 4.08
2321 2581 4.675510 CAGATGAACAAAAGTTGCACAGT 58.324 39.130 0.00 0.00 0.00 3.55
2324 2584 6.091169 CAGATGAACAAAAGTTGCACAGTTTT 59.909 34.615 0.00 0.00 38.38 2.43
2470 2741 4.251268 ACACCTACTCATAAAAAGACGGC 58.749 43.478 0.00 0.00 0.00 5.68
2471 2742 4.020485 ACACCTACTCATAAAAAGACGGCT 60.020 41.667 0.00 0.00 0.00 5.52
2674 2945 3.565516 GAAAGACCGCAAAGTGAATTCC 58.434 45.455 2.27 0.00 0.00 3.01
2797 3068 1.543802 GAGAGGGAATGCGAGATCGAT 59.456 52.381 6.39 0.00 43.02 3.59
2800 3071 3.766591 AGAGGGAATGCGAGATCGATAAT 59.233 43.478 6.39 0.00 43.02 1.28
2818 3090 6.321945 TCGATAATGGCTTACAGGTACTACAA 59.678 38.462 0.00 0.00 36.02 2.41
2828 3100 7.040548 GCTTACAGGTACTACAATACTCCCTAG 60.041 44.444 0.00 0.00 36.02 3.02
2830 3102 6.363882 ACAGGTACTACAATACTCCCTAGTC 58.636 44.000 0.00 0.00 36.02 2.59
2832 3104 5.076182 GGTACTACAATACTCCCTAGTCCC 58.924 50.000 0.00 0.00 37.15 4.46
2833 3105 5.163001 GGTACTACAATACTCCCTAGTCCCT 60.163 48.000 0.00 0.00 37.15 4.20
2834 3106 6.044871 GGTACTACAATACTCCCTAGTCCCTA 59.955 46.154 0.00 0.00 37.15 3.53
2835 3107 5.951204 ACTACAATACTCCCTAGTCCCTAC 58.049 45.833 0.00 0.00 37.15 3.18
2836 3108 5.675884 ACTACAATACTCCCTAGTCCCTACT 59.324 44.000 0.00 0.00 37.15 2.57
2837 3109 6.853983 ACTACAATACTCCCTAGTCCCTACTA 59.146 42.308 0.00 0.00 37.15 1.82
2838 3110 5.951204 ACAATACTCCCTAGTCCCTACTAC 58.049 45.833 0.00 0.00 37.15 2.73
2839 3111 5.434376 ACAATACTCCCTAGTCCCTACTACA 59.566 44.000 0.00 0.00 37.15 2.74
2840 3112 5.846528 ATACTCCCTAGTCCCTACTACAG 57.153 47.826 0.00 0.00 37.15 2.74
2841 3113 3.472892 ACTCCCTAGTCCCTACTACAGT 58.527 50.000 0.00 0.00 37.15 3.55
2842 3114 3.857420 ACTCCCTAGTCCCTACTACAGTT 59.143 47.826 0.00 0.00 37.15 3.16
2874 3146 6.396829 GGGGGAAATCTTGAAGTAATCATG 57.603 41.667 0.00 0.00 38.03 3.07
2909 3185 2.244486 TGCCCAGACTCTTGATCTCT 57.756 50.000 0.00 0.00 0.00 3.10
2910 3186 2.544721 TGCCCAGACTCTTGATCTCTT 58.455 47.619 0.00 0.00 0.00 2.85
2911 3187 2.235650 TGCCCAGACTCTTGATCTCTTG 59.764 50.000 0.00 0.00 0.00 3.02
2912 3188 2.235898 GCCCAGACTCTTGATCTCTTGT 59.764 50.000 0.00 0.00 0.00 3.16
2914 3190 4.441356 GCCCAGACTCTTGATCTCTTGTAG 60.441 50.000 0.00 0.00 0.00 2.74
2915 3191 4.952957 CCCAGACTCTTGATCTCTTGTAGA 59.047 45.833 0.00 0.00 39.02 2.59
2916 3192 5.420421 CCCAGACTCTTGATCTCTTGTAGAA 59.580 44.000 0.00 0.00 37.89 2.10
2917 3193 6.329496 CCAGACTCTTGATCTCTTGTAGAAC 58.671 44.000 0.00 0.00 37.89 3.01
2918 3194 6.071672 CCAGACTCTTGATCTCTTGTAGAACA 60.072 42.308 0.00 0.00 37.89 3.18
2919 3195 7.363705 CCAGACTCTTGATCTCTTGTAGAACAT 60.364 40.741 0.00 0.00 36.93 2.71
2920 3196 8.034215 CAGACTCTTGATCTCTTGTAGAACATT 58.966 37.037 0.00 0.00 36.93 2.71
2921 3197 9.249053 AGACTCTTGATCTCTTGTAGAACATTA 57.751 33.333 0.00 0.00 36.93 1.90
2922 3198 9.862371 GACTCTTGATCTCTTGTAGAACATTAA 57.138 33.333 0.00 0.00 36.93 1.40
2923 3199 9.646427 ACTCTTGATCTCTTGTAGAACATTAAC 57.354 33.333 0.00 0.00 36.93 2.01
2924 3200 9.645059 CTCTTGATCTCTTGTAGAACATTAACA 57.355 33.333 0.00 0.00 36.93 2.41
2925 3201 9.424319 TCTTGATCTCTTGTAGAACATTAACAC 57.576 33.333 0.00 0.00 36.93 3.32
2946 3222 6.245408 ACACACATGGTTTTGTATACAGGAT 58.755 36.000 5.56 0.00 0.00 3.24
3015 3291 3.770040 ATGGAGCACTACGGCGCA 61.770 61.111 10.83 0.00 39.27 6.09
3048 3324 2.125753 GAGCAGCCTCAGTGGACG 60.126 66.667 0.00 0.00 38.03 4.79
3165 3441 2.408271 TGACTTCAGGATCCATGCAC 57.592 50.000 15.82 1.33 0.00 4.57
3169 3445 2.124612 CAGGATCCATGCACGGCA 60.125 61.111 15.82 1.01 44.86 5.69
3196 3472 1.152138 GGGATGCAGATGATGGGCA 59.848 57.895 0.00 0.00 42.43 5.36
3360 3654 4.747108 CACTGTTTCAGACTTCAGGTAGTG 59.253 45.833 3.70 0.00 35.18 2.74
3391 3685 7.686438 TCAGCTCAAATGCAGTAAAATCTTA 57.314 32.000 0.00 0.00 34.99 2.10
3499 3793 2.670148 GGTGGAGGACTTCCCGCAT 61.670 63.158 0.38 0.00 46.19 4.73
3511 3805 2.434884 CCGCATGACGTCAGCCTT 60.435 61.111 24.41 3.69 41.42 4.35
3712 4006 1.209747 TCCTCTCTCGTTGATCTCGGA 59.790 52.381 9.99 6.51 0.00 4.55
3856 4150 2.047179 GAGAAGAAGCGGCCGGTT 60.047 61.111 40.18 40.18 38.65 4.44
3892 4186 2.618241 TGTCAAGCTGGTGAACAATGAC 59.382 45.455 4.38 4.38 37.57 3.06
3912 4206 3.550437 CCTTGGAGAGGTAATGTCAGG 57.450 52.381 0.00 0.00 40.95 3.86
3913 4207 2.420687 CCTTGGAGAGGTAATGTCAGGC 60.421 54.545 0.00 0.00 40.95 4.85
3914 4208 1.204146 TGGAGAGGTAATGTCAGGCC 58.796 55.000 0.00 0.00 0.00 5.19
3915 4209 0.470341 GGAGAGGTAATGTCAGGCCC 59.530 60.000 0.00 0.00 0.00 5.80
3916 4210 0.470341 GAGAGGTAATGTCAGGCCCC 59.530 60.000 0.00 0.00 0.00 5.80
3917 4211 0.044855 AGAGGTAATGTCAGGCCCCT 59.955 55.000 0.00 0.00 0.00 4.79
3918 4212 1.294068 AGAGGTAATGTCAGGCCCCTA 59.706 52.381 0.00 0.00 0.00 3.53
3919 4213 2.089925 AGAGGTAATGTCAGGCCCCTAT 60.090 50.000 0.00 0.00 0.00 2.57
3920 4214 2.303311 GAGGTAATGTCAGGCCCCTATC 59.697 54.545 0.00 0.00 0.00 2.08
3921 4215 2.089925 AGGTAATGTCAGGCCCCTATCT 60.090 50.000 0.00 0.00 0.00 1.98
3922 4216 2.039084 GGTAATGTCAGGCCCCTATCTG 59.961 54.545 0.00 0.00 0.00 2.90
3923 4217 2.196742 AATGTCAGGCCCCTATCTGA 57.803 50.000 0.00 0.00 37.65 3.27
3924 4218 2.196742 ATGTCAGGCCCCTATCTGAA 57.803 50.000 0.00 0.00 41.07 3.02
3925 4219 2.196742 TGTCAGGCCCCTATCTGAAT 57.803 50.000 0.00 0.00 41.07 2.57
3926 4220 3.344535 TGTCAGGCCCCTATCTGAATA 57.655 47.619 0.00 0.00 41.07 1.75
3927 4221 3.664320 TGTCAGGCCCCTATCTGAATAA 58.336 45.455 0.00 0.00 41.07 1.40
3928 4222 4.242811 TGTCAGGCCCCTATCTGAATAAT 58.757 43.478 0.00 0.00 41.07 1.28
3937 4231 6.071896 GCCCCTATCTGAATAATTAACTTGCC 60.072 42.308 0.00 0.00 0.00 4.52
3947 4241 9.249053 TGAATAATTAACTTGCCTCCACAATAA 57.751 29.630 0.00 0.00 0.00 1.40
3956 4254 7.122715 ACTTGCCTCCACAATAATTTGGTATA 58.877 34.615 0.00 0.00 37.15 1.47
3959 4257 7.293828 TGCCTCCACAATAATTTGGTATATGA 58.706 34.615 0.00 0.00 37.15 2.15
3961 4259 8.806146 GCCTCCACAATAATTTGGTATATGATT 58.194 33.333 0.00 0.00 37.15 2.57
4074 4372 6.940867 TCACGCACTATCCTATACAAGATACT 59.059 38.462 0.00 0.00 0.00 2.12
4113 4411 9.483916 GGTACTTAAATTTTTGGCTGTAACATT 57.516 29.630 0.00 0.00 0.00 2.71
4129 4447 4.460948 AACATTTGCTCCATTGGCTTAG 57.539 40.909 0.00 0.00 0.00 2.18
4284 4604 1.515304 GCCTGACGACTTCGCTCTC 60.515 63.158 0.00 0.00 44.43 3.20
4338 4658 2.593436 AACCCCAACGCGTCCTTG 60.593 61.111 14.44 7.45 0.00 3.61
4527 4853 2.735134 CACGTCCAAAGTTAGTGGTAGC 59.265 50.000 0.00 0.00 37.43 3.58
4699 5025 1.302993 GCACCCAAGGAAGCCGTAA 60.303 57.895 0.00 0.00 0.00 3.18
4815 5153 3.984732 GGCAAGGGGAGCAAGGGT 61.985 66.667 0.00 0.00 0.00 4.34
4917 5255 1.222115 ACTTCTGAAAGGTCGCACGC 61.222 55.000 0.00 0.00 36.78 5.34
4931 5269 2.737376 ACGCCTTTCGCTTCGACC 60.737 61.111 0.00 0.00 43.23 4.79
5180 5533 5.601662 TCTATTCAGCGTATTTCTTCCTGG 58.398 41.667 0.00 0.00 0.00 4.45
5191 5544 8.644619 GCGTATTTCTTCCTGGAAAATTTTAAC 58.355 33.333 10.86 0.87 38.46 2.01
5201 5554 6.979238 CCTGGAAAATTTTAACGGTGTGTTTA 59.021 34.615 2.75 0.00 42.09 2.01
5209 5562 6.680874 TTTAACGGTGTGTTTACTTCACAT 57.319 33.333 2.23 0.00 45.43 3.21
5213 5566 4.034742 ACGGTGTGTTTACTTCACATGAAC 59.965 41.667 0.00 0.00 45.43 3.18
5220 5573 7.172532 TGTGTTTACTTCACATGAACTCCATAC 59.827 37.037 0.00 0.00 40.26 2.39
5221 5574 7.172532 GTGTTTACTTCACATGAACTCCATACA 59.827 37.037 0.00 0.00 36.05 2.29
5222 5575 7.882791 TGTTTACTTCACATGAACTCCATACAT 59.117 33.333 0.00 0.00 33.31 2.29
5223 5576 9.378551 GTTTACTTCACATGAACTCCATACATA 57.621 33.333 0.00 0.00 33.31 2.29
5235 5588 9.778741 TGAACTCCATACATATATTTCACTTCC 57.221 33.333 0.00 0.00 0.00 3.46
5253 5606 6.772716 TCACTTCCTAGAAAGTTTCTGCATTT 59.227 34.615 25.27 3.46 40.94 2.32
5257 5610 7.823745 TCCTAGAAAGTTTCTGCATTTTTCT 57.176 32.000 25.27 12.51 40.94 2.52
5262 5615 6.536224 AGAAAGTTTCTGCATTTTTCTTGGTG 59.464 34.615 17.35 0.00 38.91 4.17
5315 5671 6.376581 AGGGTCTCTTTGATTCACATGATTTC 59.623 38.462 0.00 0.00 0.00 2.17
5326 5682 9.713713 TGATTCACATGATTTCAAAAACATGAT 57.286 25.926 23.99 12.49 46.11 2.45
5406 5765 4.432712 ACAGGAATTTGCAAAGTTGTGTC 58.567 39.130 18.19 2.43 0.00 3.67
5419 5778 3.009723 AGTTGTGTCTTTGATATGCGGG 58.990 45.455 0.00 0.00 0.00 6.13
5420 5779 2.036958 TGTGTCTTTGATATGCGGGG 57.963 50.000 0.00 0.00 0.00 5.73
5437 5796 2.485657 CGGGGAGAGGAATCCTAAAAGC 60.486 54.545 0.00 0.00 39.50 3.51
5438 5797 2.780592 GGGGAGAGGAATCCTAAAAGCT 59.219 50.000 0.00 0.00 39.50 3.74
5443 5802 5.029807 AGAGGAATCCTAAAAGCTGTAGC 57.970 43.478 0.00 0.00 35.91 3.58
5454 5813 7.120726 TCCTAAAAGCTGTAGCCAAATTAAGAC 59.879 37.037 0.00 0.00 43.38 3.01
5472 5831 2.229784 AGACTAAAGCACATGCAAAGGC 59.770 45.455 6.64 2.44 45.16 4.35
5475 5834 0.604578 AAAGCACATGCAAAGGCGAT 59.395 45.000 6.64 0.00 45.35 4.58
5480 5839 3.631686 AGCACATGCAAAGGCGATATTAA 59.368 39.130 6.64 0.00 45.35 1.40
5482 5841 3.976942 CACATGCAAAGGCGATATTAAGC 59.023 43.478 0.00 0.00 45.35 3.09
5487 5846 7.390440 ACATGCAAAGGCGATATTAAGCTATAA 59.610 33.333 0.00 0.00 45.35 0.98
5490 5849 8.879759 TGCAAAGGCGATATTAAGCTATAATAC 58.120 33.333 9.23 5.28 45.35 1.89
5510 5874 6.694445 ATACTATGCTTCTTATGGGCTCTT 57.306 37.500 0.00 0.00 0.00 2.85
5515 5880 3.780294 TGCTTCTTATGGGCTCTTCCTTA 59.220 43.478 0.00 0.00 34.39 2.69
5522 5887 3.543680 TGGGCTCTTCCTTATTCTTCG 57.456 47.619 0.00 0.00 34.39 3.79
5525 5890 2.609916 GGCTCTTCCTTATTCTTCGTGC 59.390 50.000 0.00 0.00 0.00 5.34
5544 5909 9.809096 CTTCGTGCATAGGAATGTAATATAGAT 57.191 33.333 0.00 0.00 35.38 1.98
5584 5949 6.558771 AAATTCCTTTTGTTTTGCCTATGC 57.441 33.333 0.00 0.00 38.26 3.14
5629 5994 3.954258 CCTCCATTTTCCCTATGGTTCAC 59.046 47.826 0.00 0.00 42.58 3.18
5636 6001 6.457159 TTTTCCCTATGGTTCACTCCTTTA 57.543 37.500 0.00 0.00 0.00 1.85
5670 6035 7.678947 GATGACTATCACATCCCAAATTAGG 57.321 40.000 0.00 0.00 38.40 2.69
5671 6036 6.823286 TGACTATCACATCCCAAATTAGGA 57.177 37.500 0.00 0.00 37.93 2.94
5672 6037 7.392766 TGACTATCACATCCCAAATTAGGAT 57.607 36.000 4.45 4.45 45.28 3.24
5713 6090 9.159254 AGAGGGAATTAATAATTTCCCAAATCC 57.841 33.333 21.43 6.61 46.13 3.01
5806 6184 5.086727 GCACGCCTCTTTAAATTTCAGTAC 58.913 41.667 0.00 0.00 0.00 2.73
5897 6275 9.611284 TTTCAAGCTTATATTTATGCTTATGCG 57.389 29.630 13.43 4.98 43.28 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 231 2.101233 GCCGTCCTCCTTCGCTTTC 61.101 63.158 0.00 0.00 0.00 2.62
219 242 4.798682 ATTCCCTCCCGCCGTCCT 62.799 66.667 0.00 0.00 0.00 3.85
223 246 4.286320 CTCGATTCCCTCCCGCCG 62.286 72.222 0.00 0.00 0.00 6.46
287 342 1.840737 CCCGTGAGAGAGAAGGAGAA 58.159 55.000 0.00 0.00 0.00 2.87
368 435 1.376037 GGCCTCCTGTGTGTGTAGC 60.376 63.158 0.00 0.00 0.00 3.58
392 473 5.512749 GCTGCATGCCTATAGCCATATCTAT 60.513 44.000 16.68 0.00 42.71 1.98
396 477 2.508716 AGCTGCATGCCTATAGCCATAT 59.491 45.455 20.57 3.32 44.23 1.78
399 480 0.475475 AAGCTGCATGCCTATAGCCA 59.525 50.000 20.57 0.00 44.23 4.75
400 481 1.613836 AAAGCTGCATGCCTATAGCC 58.386 50.000 20.57 6.60 44.23 3.93
401 482 2.161211 GCTAAAGCTGCATGCCTATAGC 59.839 50.000 16.68 17.18 44.23 2.97
424 513 1.531365 CCCTTGTCTTTGCTGGCCA 60.531 57.895 4.71 4.71 0.00 5.36
474 569 1.358046 GCTCGGATGCATGGCTTTC 59.642 57.895 2.46 0.00 0.00 2.62
539 640 2.238646 TCTCCCTGTCTCTGTCTCTCTC 59.761 54.545 0.00 0.00 0.00 3.20
540 641 2.239654 CTCTCCCTGTCTCTGTCTCTCT 59.760 54.545 0.00 0.00 0.00 3.10
541 642 2.643551 CTCTCCCTGTCTCTGTCTCTC 58.356 57.143 0.00 0.00 0.00 3.20
542 643 1.340991 GCTCTCCCTGTCTCTGTCTCT 60.341 57.143 0.00 0.00 0.00 3.10
543 644 1.102978 GCTCTCCCTGTCTCTGTCTC 58.897 60.000 0.00 0.00 0.00 3.36
544 645 0.704076 AGCTCTCCCTGTCTCTGTCT 59.296 55.000 0.00 0.00 0.00 3.41
545 646 1.204467 CAAGCTCTCCCTGTCTCTGTC 59.796 57.143 0.00 0.00 0.00 3.51
546 647 1.265236 CAAGCTCTCCCTGTCTCTGT 58.735 55.000 0.00 0.00 0.00 3.41
550 651 1.722034 TTCACAAGCTCTCCCTGTCT 58.278 50.000 0.00 0.00 0.00 3.41
592 693 6.204495 GTGGGATTATTTTGTGTGCAAACAAT 59.796 34.615 22.83 11.83 43.47 2.71
641 742 2.614013 GGAAAGGGGCAGAGGGGA 60.614 66.667 0.00 0.00 0.00 4.81
712 818 3.712907 GGCCGACCTTGGGTGCTA 61.713 66.667 0.00 0.00 35.25 3.49
732 839 3.888930 CAGTAGAGATTGAGGAGGAGGAC 59.111 52.174 0.00 0.00 0.00 3.85
735 842 3.565307 AGCAGTAGAGATTGAGGAGGAG 58.435 50.000 0.00 0.00 0.00 3.69
736 843 3.561143 GAGCAGTAGAGATTGAGGAGGA 58.439 50.000 0.00 0.00 0.00 3.71
738 845 3.565307 AGGAGCAGTAGAGATTGAGGAG 58.435 50.000 0.00 0.00 0.00 3.69
739 846 3.204158 AGAGGAGCAGTAGAGATTGAGGA 59.796 47.826 0.00 0.00 0.00 3.71
744 876 5.163322 CCAATTCAGAGGAGCAGTAGAGATT 60.163 44.000 0.00 0.00 0.00 2.40
751 883 2.553904 CCAACCAATTCAGAGGAGCAGT 60.554 50.000 0.00 0.00 0.00 4.40
758 892 6.582295 CGTCATAAAAACCAACCAATTCAGAG 59.418 38.462 0.00 0.00 0.00 3.35
776 910 2.993220 GCACACACATGAGTCGTCATAA 59.007 45.455 0.00 0.00 41.85 1.90
782 927 4.359475 TGGCACACACATGAGTCG 57.641 55.556 0.00 0.00 0.00 4.18
803 948 3.354089 ACAAAACCTGCAAGAACGATG 57.646 42.857 0.00 0.00 34.07 3.84
804 949 3.880490 TGTACAAAACCTGCAAGAACGAT 59.120 39.130 0.00 0.00 34.07 3.73
807 952 5.810074 ACAAATGTACAAAACCTGCAAGAAC 59.190 36.000 0.00 0.00 34.07 3.01
835 984 1.358877 CCAGCAATGAATCGTCGTCA 58.641 50.000 0.00 0.00 0.00 4.35
962 1125 2.363018 CCTCCGAGAGCTCCCACA 60.363 66.667 10.93 0.00 0.00 4.17
981 1144 3.806521 CCATGAATCTGCTAACTTCCTCG 59.193 47.826 0.00 0.00 0.00 4.63
1183 1354 6.311445 CAGAAGCTAGTGTCGATACAAACATT 59.689 38.462 15.08 2.70 37.36 2.71
1194 1365 5.493133 ACTCTAATCAGAAGCTAGTGTCG 57.507 43.478 0.00 0.00 0.00 4.35
1241 1426 5.300286 GGGAATTAACTGCTGATGCTTACAT 59.700 40.000 0.00 0.00 39.98 2.29
1289 1474 9.739276 TTGTACTGAAGTTGATCCTGAAATTAT 57.261 29.630 0.00 0.00 0.00 1.28
1298 1483 6.868339 CCCAAAATTTGTACTGAAGTTGATCC 59.132 38.462 4.92 0.00 0.00 3.36
1313 1498 9.317936 GCTTTTATCTCCTTATCCCAAAATTTG 57.682 33.333 0.00 0.00 0.00 2.32
1335 1521 0.385390 CTGCCAGTTTGGAACGCTTT 59.615 50.000 0.00 0.00 40.96 3.51
1370 1560 7.807977 AACAGCTATCTTCTGTCAAAAAGAA 57.192 32.000 0.00 0.00 43.36 2.52
1436 1626 3.131933 ACAAGGTGTATGCAGTGCAAAAA 59.868 39.130 23.90 8.03 43.62 1.94
1463 1653 2.632987 ACGTGTAGGTGCTTTCCTTT 57.367 45.000 0.00 0.00 38.86 3.11
1497 1687 2.102925 ACAACAGGGCATCCAAAACAAG 59.897 45.455 0.00 0.00 34.83 3.16
1701 1904 8.597662 ACCAAATATATTCTTCAAATGCATGC 57.402 30.769 11.82 11.82 0.00 4.06
1712 1915 8.429237 TGTGGGTGAAAACCAAATATATTCTT 57.571 30.769 0.00 0.00 40.24 2.52
1717 1920 7.389053 GCATTTTGTGGGTGAAAACCAAATATA 59.611 33.333 0.00 0.00 40.24 0.86
1718 1921 6.206438 GCATTTTGTGGGTGAAAACCAAATAT 59.794 34.615 0.00 0.00 40.24 1.28
1729 1932 3.640498 TCATGAAAGCATTTTGTGGGTGA 59.360 39.130 0.00 0.00 39.27 4.02
1736 1939 8.339714 ACATGTTTCTTTCATGAAAGCATTTTG 58.660 29.630 33.93 27.95 45.48 2.44
1763 1966 7.394359 GGGGACGGTACACTAAACTATATATGA 59.606 40.741 0.00 0.00 0.00 2.15
1791 1996 0.539051 AAACAGAGCGCTAGGATGCT 59.461 50.000 11.50 0.00 45.90 3.79
1885 2095 5.652014 TCTTTCAACAAAAAGGAGCAAGAGA 59.348 36.000 0.00 0.00 36.97 3.10
1886 2096 5.894807 TCTTTCAACAAAAAGGAGCAAGAG 58.105 37.500 0.00 0.00 36.97 2.85
2098 2308 6.090358 CTTGAAAGCAAATTGCAAGTGGATAG 59.910 38.462 20.82 3.31 46.03 2.08
2121 2331 6.363357 GTGATTTTTAGCAAACGATCAAGCTT 59.637 34.615 0.00 0.00 38.47 3.74
2150 2360 2.294233 AGTTTCACGCATTGCATTCAGT 59.706 40.909 9.69 0.00 0.00 3.41
2160 2370 2.543777 ACAGTACCAGTTTCACGCAT 57.456 45.000 0.00 0.00 0.00 4.73
2211 2421 4.399303 ACTCACCAAAGAAGAACAAACCAG 59.601 41.667 0.00 0.00 0.00 4.00
2213 2423 4.398044 TCACTCACCAAAGAAGAACAAACC 59.602 41.667 0.00 0.00 0.00 3.27
2297 2557 3.119209 TGTGCAACTTTTGTTCATCTGCA 60.119 39.130 0.00 0.00 41.35 4.41
2412 2678 9.905713 ATGATTAGAGCTAATTGTAGAAACCAA 57.094 29.630 4.40 0.00 36.02 3.67
2413 2679 9.330063 CATGATTAGAGCTAATTGTAGAAACCA 57.670 33.333 4.40 0.00 36.02 3.67
2414 2680 8.778358 CCATGATTAGAGCTAATTGTAGAAACC 58.222 37.037 4.40 0.00 36.02 3.27
2489 2760 5.394663 GGAGAAGTCATGCATACAGTACAGT 60.395 44.000 0.00 0.00 0.00 3.55
2635 2906 1.668826 TCCCAGTTGCCTTCCAGTAT 58.331 50.000 0.00 0.00 0.00 2.12
2650 2921 0.181587 TCACTTTGCGGTCTTTCCCA 59.818 50.000 0.00 0.00 0.00 4.37
2674 2945 0.602638 TACCAACTGCACGCTTCTGG 60.603 55.000 0.00 0.00 0.00 3.86
2797 3068 8.543293 AGTATTGTAGTACCTGTAAGCCATTA 57.457 34.615 0.00 0.00 0.00 1.90
2800 3071 5.361857 GGAGTATTGTAGTACCTGTAAGCCA 59.638 44.000 0.00 0.00 0.00 4.75
2818 3090 5.233939 ACTGTAGTAGGGACTAGGGAGTAT 58.766 45.833 0.00 0.00 44.14 2.12
2855 3127 8.273780 ACCTCACATGATTACTTCAAGATTTC 57.726 34.615 0.00 0.00 38.03 2.17
2861 3133 5.705441 GTGGAACCTCACATGATTACTTCAA 59.295 40.000 0.00 0.00 38.03 2.69
2865 3137 4.908601 TGTGGAACCTCACATGATTACT 57.091 40.909 0.00 0.00 42.05 2.24
2874 3146 2.024414 GGGCAATATGTGGAACCTCAC 58.976 52.381 0.00 0.00 38.09 3.51
2909 3185 7.575414 AACCATGTGTGTTAATGTTCTACAA 57.425 32.000 0.00 0.00 0.00 2.41
2910 3186 7.575414 AAACCATGTGTGTTAATGTTCTACA 57.425 32.000 0.00 0.00 0.00 2.74
2911 3187 7.918562 ACAAAACCATGTGTGTTAATGTTCTAC 59.081 33.333 0.00 0.00 30.82 2.59
2912 3188 8.001881 ACAAAACCATGTGTGTTAATGTTCTA 57.998 30.769 0.00 0.00 30.82 2.10
2914 3190 8.810652 ATACAAAACCATGTGTGTTAATGTTC 57.189 30.769 8.75 0.00 34.75 3.18
2915 3191 9.685828 GTATACAAAACCATGTGTGTTAATGTT 57.314 29.630 0.00 0.00 34.75 2.71
2916 3192 8.851145 TGTATACAAAACCATGTGTGTTAATGT 58.149 29.630 2.20 1.78 34.75 2.71
2917 3193 9.340695 CTGTATACAAAACCATGTGTGTTAATG 57.659 33.333 7.06 0.00 34.75 1.90
2918 3194 8.519526 CCTGTATACAAAACCATGTGTGTTAAT 58.480 33.333 7.06 0.00 34.75 1.40
2919 3195 7.720074 TCCTGTATACAAAACCATGTGTGTTAA 59.280 33.333 7.06 0.00 34.75 2.01
2920 3196 7.225011 TCCTGTATACAAAACCATGTGTGTTA 58.775 34.615 7.06 0.00 34.75 2.41
2921 3197 6.065374 TCCTGTATACAAAACCATGTGTGTT 58.935 36.000 7.06 0.00 34.75 3.32
2922 3198 5.626142 TCCTGTATACAAAACCATGTGTGT 58.374 37.500 7.06 0.00 34.75 3.72
2923 3199 6.554419 CATCCTGTATACAAAACCATGTGTG 58.446 40.000 7.06 0.00 34.75 3.82
2924 3200 5.125417 GCATCCTGTATACAAAACCATGTGT 59.875 40.000 7.06 0.00 34.75 3.72
2925 3201 5.581605 GCATCCTGTATACAAAACCATGTG 58.418 41.667 7.06 0.00 34.75 3.21
2991 3267 2.743183 GCCGTAGTGCTCCATGATCTTT 60.743 50.000 0.00 0.00 0.00 2.52
3078 3354 1.283029 CCACCACCTCTTCCATCACAT 59.717 52.381 0.00 0.00 0.00 3.21
3165 3441 4.096003 ATCCCGAACCCACTGCCG 62.096 66.667 0.00 0.00 0.00 5.69
3169 3445 1.274703 ATCTGCATCCCGAACCCACT 61.275 55.000 0.00 0.00 0.00 4.00
3207 3483 3.461773 ATCCACCTGCCGTCCTCG 61.462 66.667 0.00 0.00 0.00 4.63
3334 3628 2.564771 CTGAAGTCTGAAACAGTGGCA 58.435 47.619 0.00 0.00 32.61 4.92
3511 3805 0.108992 GTATGCCGGTCTTCGTGTCA 60.109 55.000 1.90 0.00 37.11 3.58
3626 3920 3.904339 CCTAACCACATATCAGGGTAGCT 59.096 47.826 8.84 0.00 42.62 3.32
3627 3921 3.646637 ACCTAACCACATATCAGGGTAGC 59.353 47.826 8.84 0.00 42.62 3.58
3628 3922 4.503296 GCACCTAACCACATATCAGGGTAG 60.503 50.000 7.72 7.72 43.40 3.18
3905 4199 2.196742 TTCAGATAGGGGCCTGACAT 57.803 50.000 0.84 0.00 38.95 3.06
3906 4200 2.196742 ATTCAGATAGGGGCCTGACA 57.803 50.000 0.84 0.00 38.95 3.58
3907 4201 4.917906 ATTATTCAGATAGGGGCCTGAC 57.082 45.455 0.84 0.00 38.95 3.51
3908 4202 6.562608 AGTTAATTATTCAGATAGGGGCCTGA 59.437 38.462 0.84 0.00 37.61 3.86
3909 4203 6.784031 AGTTAATTATTCAGATAGGGGCCTG 58.216 40.000 0.84 0.00 0.00 4.85
3910 4204 7.234355 CAAGTTAATTATTCAGATAGGGGCCT 58.766 38.462 0.84 0.00 0.00 5.19
3911 4205 6.071896 GCAAGTTAATTATTCAGATAGGGGCC 60.072 42.308 0.00 0.00 0.00 5.80
3912 4206 6.071896 GGCAAGTTAATTATTCAGATAGGGGC 60.072 42.308 0.00 0.00 0.00 5.80
3913 4207 7.234355 AGGCAAGTTAATTATTCAGATAGGGG 58.766 38.462 0.00 0.00 0.00 4.79
3914 4208 7.391833 GGAGGCAAGTTAATTATTCAGATAGGG 59.608 40.741 0.00 0.00 0.00 3.53
3915 4209 7.939039 TGGAGGCAAGTTAATTATTCAGATAGG 59.061 37.037 0.00 0.00 0.00 2.57
3916 4210 8.778358 GTGGAGGCAAGTTAATTATTCAGATAG 58.222 37.037 0.00 0.00 0.00 2.08
3917 4211 8.271458 TGTGGAGGCAAGTTAATTATTCAGATA 58.729 33.333 0.00 0.00 0.00 1.98
3918 4212 7.118723 TGTGGAGGCAAGTTAATTATTCAGAT 58.881 34.615 0.00 0.00 0.00 2.90
3919 4213 6.480763 TGTGGAGGCAAGTTAATTATTCAGA 58.519 36.000 0.00 0.00 0.00 3.27
3920 4214 6.757897 TGTGGAGGCAAGTTAATTATTCAG 57.242 37.500 0.00 0.00 0.00 3.02
3921 4215 7.716799 ATTGTGGAGGCAAGTTAATTATTCA 57.283 32.000 0.00 0.00 0.00 2.57
3925 4219 9.868277 CAAATTATTGTGGAGGCAAGTTAATTA 57.132 29.630 0.00 0.00 30.11 1.40
3926 4220 7.823799 CCAAATTATTGTGGAGGCAAGTTAATT 59.176 33.333 0.00 0.00 37.03 1.40
3927 4221 7.038373 ACCAAATTATTGTGGAGGCAAGTTAAT 60.038 33.333 11.23 0.00 38.36 1.40
3928 4222 6.268847 ACCAAATTATTGTGGAGGCAAGTTAA 59.731 34.615 11.23 0.00 38.36 2.01
3982 4280 4.524316 TCAGGAAAATTGATGCTTGTGG 57.476 40.909 0.00 0.00 0.00 4.17
3991 4289 4.154737 CACGATCTGCTTCAGGAAAATTGA 59.845 41.667 0.00 0.00 31.51 2.57
4074 4372 8.635765 AAATTTAAGTACCTGAATTCTCTGCA 57.364 30.769 7.05 0.00 0.00 4.41
4113 4411 2.923121 CTAGCTAAGCCAATGGAGCAA 58.077 47.619 13.01 0.00 37.40 3.91
4244 4564 2.036475 TGAGATTGCGAGAAGATAGGGC 59.964 50.000 0.00 0.00 0.00 5.19
4248 4568 2.961741 AGGCTGAGATTGCGAGAAGATA 59.038 45.455 0.00 0.00 0.00 1.98
4284 4604 1.722464 TCGTTGTCGAAACCAATAGCG 59.278 47.619 0.00 0.00 43.34 4.26
4321 4641 2.593436 CAAGGACGCGTTGGGGTT 60.593 61.111 15.53 0.00 39.74 4.11
4338 4658 4.125239 ACCTTCCCGTACAGGTCC 57.875 61.111 0.00 0.00 39.37 4.46
4527 4853 0.669077 CCCTGCTACTGCTACTACCG 59.331 60.000 0.00 0.00 40.48 4.02
4617 4943 2.362120 GGCCTCTGGTGCTGCAAT 60.362 61.111 2.77 0.00 0.00 3.56
4699 5025 1.403679 CATCTCTTCTTCTCGCTCGGT 59.596 52.381 0.00 0.00 0.00 4.69
4815 5153 5.279406 CCCACTCAAAAACATGCTGGAAATA 60.279 40.000 0.00 0.00 0.00 1.40
4917 5255 1.134965 AGAGATGGTCGAAGCGAAAGG 60.135 52.381 0.00 0.00 37.72 3.11
5158 5511 5.601662 TCCAGGAAGAAATACGCTGAATAG 58.398 41.667 0.00 0.00 0.00 1.73
5180 5533 9.074443 TGAAGTAAACACACCGTTAAAATTTTC 57.926 29.630 6.72 0.00 36.59 2.29
5209 5562 9.778741 GGAAGTGAAATATATGTATGGAGTTCA 57.221 33.333 0.00 0.00 0.00 3.18
5223 5576 8.951243 GCAGAAACTTTCTAGGAAGTGAAATAT 58.049 33.333 17.40 0.00 39.68 1.28
5224 5577 7.936847 TGCAGAAACTTTCTAGGAAGTGAAATA 59.063 33.333 17.40 0.65 39.68 1.40
5225 5578 6.772716 TGCAGAAACTTTCTAGGAAGTGAAAT 59.227 34.615 17.40 4.52 39.68 2.17
5226 5579 6.119536 TGCAGAAACTTTCTAGGAAGTGAAA 58.880 36.000 17.40 0.00 39.68 2.69
5227 5580 5.680619 TGCAGAAACTTTCTAGGAAGTGAA 58.319 37.500 17.40 0.00 39.68 3.18
5228 5581 5.290493 TGCAGAAACTTTCTAGGAAGTGA 57.710 39.130 17.40 0.00 39.68 3.41
5229 5582 6.566197 AATGCAGAAACTTTCTAGGAAGTG 57.434 37.500 17.40 6.00 39.68 3.16
5230 5583 7.588497 AAAATGCAGAAACTTTCTAGGAAGT 57.412 32.000 10.89 10.89 41.44 3.01
5231 5584 8.355913 AGAAAAATGCAGAAACTTTCTAGGAAG 58.644 33.333 9.40 9.40 38.11 3.46
5232 5585 8.237811 AGAAAAATGCAGAAACTTTCTAGGAA 57.762 30.769 3.64 0.00 38.11 3.36
5233 5586 7.823745 AGAAAAATGCAGAAACTTTCTAGGA 57.176 32.000 3.64 1.62 38.11 2.94
5234 5587 7.383300 CCAAGAAAAATGCAGAAACTTTCTAGG 59.617 37.037 3.64 0.00 38.11 3.02
5235 5588 7.922811 ACCAAGAAAAATGCAGAAACTTTCTAG 59.077 33.333 3.64 1.19 38.11 2.43
5332 5688 9.566432 GAATCATATCCTATTCCAGTGTTTTCT 57.434 33.333 0.00 0.00 0.00 2.52
5406 5765 1.694150 TCCTCTCCCCGCATATCAAAG 59.306 52.381 0.00 0.00 0.00 2.77
5414 5773 0.031515 TTAGGATTCCTCTCCCCGCA 60.032 55.000 8.94 0.00 35.79 5.69
5419 5778 4.495690 ACAGCTTTTAGGATTCCTCTCC 57.504 45.455 8.94 0.00 34.61 3.71
5420 5779 5.053811 GCTACAGCTTTTAGGATTCCTCTC 58.946 45.833 8.94 0.00 38.21 3.20
5437 5796 7.094805 TGTGCTTTAGTCTTAATTTGGCTACAG 60.095 37.037 0.00 0.00 0.00 2.74
5438 5797 6.712998 TGTGCTTTAGTCTTAATTTGGCTACA 59.287 34.615 0.00 0.00 0.00 2.74
5443 5802 6.389091 TGCATGTGCTTTAGTCTTAATTTGG 58.611 36.000 6.55 0.00 42.66 3.28
5454 5813 1.199789 TCGCCTTTGCATGTGCTTTAG 59.800 47.619 6.55 1.40 42.66 1.85
5480 5839 8.207545 GCCCATAAGAAGCATAGTATTATAGCT 58.792 37.037 0.00 0.00 37.08 3.32
5482 5841 9.757227 GAGCCCATAAGAAGCATAGTATTATAG 57.243 37.037 0.00 0.00 0.00 1.31
5487 5846 6.296145 GGAAGAGCCCATAAGAAGCATAGTAT 60.296 42.308 0.00 0.00 0.00 2.12
5490 5849 4.041444 AGGAAGAGCCCATAAGAAGCATAG 59.959 45.833 0.00 0.00 37.37 2.23
5510 5874 5.607939 TTCCTATGCACGAAGAATAAGGA 57.392 39.130 0.00 0.00 0.00 3.36
5544 5909 8.477419 AAGGAATTTTACAATCCTTTCAGACA 57.523 30.769 0.54 0.00 37.51 3.41
5552 5917 8.620416 GCAAAACAAAAGGAATTTTACAATCCT 58.380 29.630 0.00 0.00 0.00 3.24
5617 5982 6.423182 TGATTTAAAGGAGTGAACCATAGGG 58.577 40.000 0.00 0.00 41.29 3.53
5668 6033 9.782900 TTCCCTCTAATTTATTTTTCCAATCCT 57.217 29.630 0.00 0.00 0.00 3.24
5699 6076 8.288812 AGATGAACCATAGGATTTGGGAAATTA 58.711 33.333 0.00 0.00 38.64 1.40
5713 6090 6.036517 CCGAGTTTCTTGAAGATGAACCATAG 59.963 42.308 6.23 0.00 0.00 2.23
5774 6152 3.508744 AAAGAGGCGTGCATAAAATGG 57.491 42.857 0.00 0.00 0.00 3.16
5786 6164 7.126398 GCATAGTACTGAAATTTAAAGAGGCG 58.874 38.462 5.39 0.00 0.00 5.52
5851 6229 7.208064 TGAAACCTAGGGATTTAACTAGCAT 57.792 36.000 14.81 0.00 36.27 3.79


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

AutoCloner maintained by Alex Coulton.