Multiple sequence alignment - TraesCS5B01G100100

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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 TraesCS5B01G100100 chr5B 100.000 5978 0 0 1 5978 133015963 133009986 0.000000e+00 11040
1 TraesCS5B01G100100 chr5A 92.669 2046 87 19 580 2615 130141534 130139542 0.000000e+00 2889
2 TraesCS5B01G100100 chr5A 92.176 933 65 6 3531 4462 130138407 130137482 0.000000e+00 1312
3 TraesCS5B01G100100 chr5A 91.481 810 44 15 4472 5274 130137440 130136649 0.000000e+00 1090
4 TraesCS5B01G100100 chr5A 94.712 624 11 1 5377 5978 130134895 130134272 0.000000e+00 950
5 TraesCS5B01G100100 chr5A 94.840 562 22 5 2638 3196 130139549 130138992 0.000000e+00 870
6 TraesCS5B01G100100 chr5A 90.820 610 22 14 1 576 130142663 130142054 0.000000e+00 785
7 TraesCS5B01G100100 chr5A 95.906 342 11 3 3196 3536 130138927 130138588 8.760000e-153 551
8 TraesCS5B01G100100 chr5A 87.606 355 29 9 5036 5380 130136511 130136162 1.210000e-106 398
9 TraesCS5B01G100100 chr5D 92.484 2049 92 19 585 2613 119771944 119769938 0.000000e+00 2874
10 TraesCS5B01G100100 chr5D 93.756 1009 51 10 4974 5978 119767056 119766056 0.000000e+00 1504
11 TraesCS5B01G100100 chr5D 91.711 941 65 8 3531 4470 119768800 119767872 0.000000e+00 1293
12 TraesCS5B01G100100 chr5D 91.718 809 44 13 4472 5274 119767843 119767052 0.000000e+00 1101
13 TraesCS5B01G100100 chr5D 95.179 560 22 3 2640 3196 119769943 119769386 0.000000e+00 880
14 TraesCS5B01G100100 chr5D 91.935 496 21 9 1 483 119813912 119813423 0.000000e+00 676
15 TraesCS5B01G100100 chr5D 95.575 339 12 3 3199 3536 119769317 119768981 1.900000e-149 540


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 TraesCS5B01G100100 chr5B 133009986 133015963 5977 True 11040.000000 11040 100.000000 1 5978 1 chr5B.!!$R1 5977
1 TraesCS5B01G100100 chr5A 130134272 130142663 8391 True 1105.625000 2889 92.526250 1 5978 8 chr5A.!!$R1 5977
2 TraesCS5B01G100100 chr5D 119766056 119771944 5888 True 1365.333333 2874 93.403833 585 5978 6 chr5D.!!$R2 5393

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
142 143 0.108567 GGTTCAGAGTCGAAGCCTCC 60.109 60.0 12.76 2.69 37.41 4.30 F
872 1446 0.317479 AAGCTTCTGCCGACGTTAGT 59.683 50.0 0.00 0.00 40.80 2.24 F
2624 3213 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.0 0.00 0.00 0.00 3.82 F
3655 4500 0.460987 CTTCACCACAGGGATCGAGC 60.461 60.0 0.00 0.00 38.05 5.03 F
4504 5384 0.454957 AATGCAGCGTCGATTTGTGC 60.455 50.0 0.00 0.00 34.62 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2636 0.179048 TGGTGTGTCCTGCAAGTGAG 60.179 55.000 0.00 0.0 37.07 3.51 R
2627 3216 0.035458 TCCACACACACACACACACA 59.965 50.000 0.00 0.0 0.00 3.72 R
4489 5366 0.436913 TAACGCACAAATCGACGCTG 59.563 50.000 0.00 0.0 0.00 5.18 R
4727 5608 0.766131 TGAAAAAGGGCCACGGAGTA 59.234 50.000 6.18 0.0 41.61 2.59 R
5539 8073 4.209538 TGAATTCCAGGAGCAACATATGG 58.790 43.478 7.80 0.0 0.00 2.74 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
120 121 2.579201 CGTGGACCAGATCGCCTT 59.421 61.111 0.00 0.00 0.00 4.35
142 143 0.108567 GGTTCAGAGTCGAAGCCTCC 60.109 60.000 12.76 2.69 37.41 4.30
262 263 1.634973 TGGAGATTGTTCATGCTCCCA 59.365 47.619 11.03 0.00 44.95 4.37
274 275 0.597568 TGCTCCCAAAATGAGTTGCG 59.402 50.000 0.00 0.00 32.31 4.85
304 305 4.396166 ACAACTGGACAGACAAGTTTCTTG 59.604 41.667 6.29 7.78 0.00 3.02
324 325 7.647907 TCTTGATAGTGTTTTCGTAGGTTTC 57.352 36.000 0.00 0.00 0.00 2.78
418 425 3.840890 TGCCGTGTTGCCTAAATAAAG 57.159 42.857 0.00 0.00 0.00 1.85
426 433 4.941263 TGTTGCCTAAATAAAGATGAGCGT 59.059 37.500 0.00 0.00 0.00 5.07
427 434 5.064707 TGTTGCCTAAATAAAGATGAGCGTC 59.935 40.000 0.00 0.00 0.00 5.19
482 519 0.584396 TTGTGACGTGGCAAATCGAC 59.416 50.000 0.00 0.00 0.00 4.20
531 568 7.877612 TCATGCACAGAGATTGTAGTTAGAAAA 59.122 33.333 0.00 0.00 38.16 2.29
562 599 9.482627 TTGTTGTTCAGTTTACAAATTTGTCTT 57.517 25.926 26.46 6.06 42.35 3.01
627 1180 3.248029 GTGAGCTTCACTGCACGG 58.752 61.111 8.50 0.00 43.73 4.94
691 1244 0.953471 TCGCAATCAAACGGTCCCTG 60.953 55.000 0.00 0.00 0.00 4.45
692 1245 1.212751 GCAATCAAACGGTCCCTGC 59.787 57.895 0.00 0.00 0.00 4.85
693 1246 1.501741 CAATCAAACGGTCCCTGCG 59.498 57.895 0.00 0.00 0.00 5.18
694 1247 0.953471 CAATCAAACGGTCCCTGCGA 60.953 55.000 0.00 0.00 0.00 5.10
695 1248 0.673644 AATCAAACGGTCCCTGCGAG 60.674 55.000 0.00 0.00 0.00 5.03
696 1249 3.423154 CAAACGGTCCCTGCGAGC 61.423 66.667 0.00 0.00 35.53 5.03
697 1250 3.626924 AAACGGTCCCTGCGAGCT 61.627 61.111 0.00 0.00 36.81 4.09
698 1251 3.883744 AAACGGTCCCTGCGAGCTG 62.884 63.158 0.00 0.00 36.81 4.24
813 1387 3.003173 CCAGCGGTCCTCTTCCCA 61.003 66.667 0.00 0.00 0.00 4.37
814 1388 2.266055 CAGCGGTCCTCTTCCCAC 59.734 66.667 0.00 0.00 0.00 4.61
815 1389 2.120718 AGCGGTCCTCTTCCCACT 59.879 61.111 0.00 0.00 0.00 4.00
816 1390 1.985116 AGCGGTCCTCTTCCCACTC 60.985 63.158 0.00 0.00 0.00 3.51
817 1391 1.985116 GCGGTCCTCTTCCCACTCT 60.985 63.158 0.00 0.00 0.00 3.24
818 1392 1.950973 GCGGTCCTCTTCCCACTCTC 61.951 65.000 0.00 0.00 0.00 3.20
819 1393 1.324005 CGGTCCTCTTCCCACTCTCC 61.324 65.000 0.00 0.00 0.00 3.71
820 1394 1.324005 GGTCCTCTTCCCACTCTCCG 61.324 65.000 0.00 0.00 0.00 4.63
821 1395 1.682684 TCCTCTTCCCACTCTCCGC 60.683 63.158 0.00 0.00 0.00 5.54
872 1446 0.317479 AAGCTTCTGCCGACGTTAGT 59.683 50.000 0.00 0.00 40.80 2.24
876 1450 0.942410 TTCTGCCGACGTTAGTGTGC 60.942 55.000 0.00 0.00 0.00 4.57
981 1567 1.374252 CCACGGGACCTTCGACTTG 60.374 63.158 0.00 0.00 0.00 3.16
1020 1606 2.664851 CCGGTGAGTTGCTCGCAA 60.665 61.111 11.14 0.00 42.14 4.85
1022 1608 1.577328 CCGGTGAGTTGCTCGCAATT 61.577 55.000 7.67 3.30 42.14 2.32
1026 1612 2.420022 GGTGAGTTGCTCGCAATTGTAT 59.580 45.455 7.67 0.00 42.14 2.29
1027 1613 3.485877 GGTGAGTTGCTCGCAATTGTATC 60.486 47.826 7.67 3.04 42.14 2.24
1028 1614 3.125146 GTGAGTTGCTCGCAATTGTATCA 59.875 43.478 7.67 5.30 40.33 2.15
1029 1615 3.125146 TGAGTTGCTCGCAATTGTATCAC 59.875 43.478 7.67 0.00 38.28 3.06
1165 1751 2.675348 AGCGCTTGTGCTAATCTTCTTC 59.325 45.455 2.64 0.00 45.14 2.87
1166 1752 2.535732 GCGCTTGTGCTAATCTTCTTCG 60.536 50.000 0.00 0.00 36.97 3.79
1167 1753 2.923655 CGCTTGTGCTAATCTTCTTCGA 59.076 45.455 0.00 0.00 36.97 3.71
1168 1754 3.000277 CGCTTGTGCTAATCTTCTTCGAG 60.000 47.826 0.00 0.00 36.97 4.04
1169 1755 3.929610 GCTTGTGCTAATCTTCTTCGAGT 59.070 43.478 0.00 0.00 36.03 4.18
1170 1756 5.103000 GCTTGTGCTAATCTTCTTCGAGTA 58.897 41.667 0.00 0.00 36.03 2.59
1182 1768 7.776933 TCTTCTTCGAGTAAATTGATCATGG 57.223 36.000 0.00 0.00 0.00 3.66
1225 1811 5.166398 CCATGTTTTTCCTTCTCATCTTGC 58.834 41.667 0.00 0.00 0.00 4.01
1252 1838 4.281688 AGCATACAAGAACCACTGCATTTT 59.718 37.500 0.00 0.00 32.18 1.82
1259 1845 5.453567 AGAACCACTGCATTTTAAACCTC 57.546 39.130 0.00 0.00 0.00 3.85
1293 1879 2.467946 GTCGTGGCGGAGAACGAGAA 62.468 60.000 0.00 0.00 45.77 2.87
1396 1982 3.655810 CTCAGTCCCAGGACAGCGC 62.656 68.421 18.77 0.00 46.76 5.92
1427 2013 6.594159 ACCTCGATACAAGGTCTTTATTTGTG 59.406 38.462 0.00 0.00 43.85 3.33
1494 2080 4.925646 GGCAATTTTCACTTGATGGTTCTC 59.074 41.667 0.00 0.00 0.00 2.87
1499 2085 5.694231 TTTCACTTGATGGTTCTCACATG 57.306 39.130 0.00 0.00 0.00 3.21
1525 2111 3.243002 GCTCCAATTATCTTCTGCAGCAC 60.243 47.826 9.47 0.00 0.00 4.40
1549 2135 1.877443 GCTGCCGTAGTTCAGGAAAAA 59.123 47.619 0.00 0.00 0.00 1.94
1651 2237 1.900498 GGCTGCTTGTGCCTTCAGT 60.900 57.895 0.00 0.00 46.38 3.41
1694 2280 7.630242 TGTCATTGAATTTCTATGGAGGAAC 57.370 36.000 17.07 10.19 31.94 3.62
1884 2471 8.751666 GTTCAATCAGAATCAGCTGAACCAGC 62.752 46.154 22.50 10.69 46.94 4.85
1936 2524 8.035394 TCACTGGTAATCATCAAGTACTCTTTC 58.965 37.037 0.00 0.00 0.00 2.62
1960 2548 5.869753 AGTTATCAGTGATGTGAAACTGC 57.130 39.130 16.15 0.00 42.88 4.40
2048 2636 3.873910 TCCATCCGGAAACAAGATTCTC 58.126 45.455 9.01 0.00 38.83 2.87
2118 2706 8.770828 GTTAGCCTAATACATCGCTCATTTTTA 58.229 33.333 0.00 0.00 32.76 1.52
2380 2969 1.964933 TCACGTGGTGGTCAATCAGTA 59.035 47.619 17.00 0.00 33.87 2.74
2464 3053 2.224281 TGACCTGCACGTTCTTGATCTT 60.224 45.455 0.00 0.00 0.00 2.40
2526 3115 5.118990 TCTGAGGATTTGGTTTGATCGATC 58.881 41.667 18.72 18.72 0.00 3.69
2542 3131 6.115446 TGATCGATCTAAACAAAATGGAGCT 58.885 36.000 25.02 0.00 0.00 4.09
2545 3134 5.582269 TCGATCTAAACAAAATGGAGCTGAG 59.418 40.000 0.00 0.00 0.00 3.35
2616 3205 9.710900 ATTCTACCATATATATGTGTGTGTGTG 57.289 33.333 19.11 5.43 31.82 3.82
2617 3206 8.245195 TCTACCATATATATGTGTGTGTGTGT 57.755 34.615 19.11 10.16 31.82 3.72
2618 3207 8.141268 TCTACCATATATATGTGTGTGTGTGTG 58.859 37.037 19.11 4.39 31.82 3.82
2619 3208 6.649155 ACCATATATATGTGTGTGTGTGTGT 58.351 36.000 19.11 4.92 31.82 3.72
2620 3209 6.538381 ACCATATATATGTGTGTGTGTGTGTG 59.462 38.462 19.11 3.85 31.82 3.82
2621 3210 6.538381 CCATATATATGTGTGTGTGTGTGTGT 59.462 38.462 19.11 0.00 31.82 3.72
2622 3211 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
2623 3212 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
2624 3213 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2625 3214 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2626 3215 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2627 3216 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2628 3217 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2629 3218 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2630 3219 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2631 3220 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2632 3221 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2633 3222 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2634 3223 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2635 3224 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2636 3225 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2756 3345 6.747659 AAAACTTGCAGTAAACGCATTAAG 57.252 33.333 0.00 0.00 39.58 1.85
2786 3375 2.494870 GCTTTGAGGTGCAGGATTGATT 59.505 45.455 0.00 0.00 0.00 2.57
2817 3406 9.162764 GACAATTATTTCTTTACAGAGGCACTA 57.837 33.333 0.00 0.00 41.55 2.74
2948 3537 3.812053 ACATGCAAACAGTGAGACTTCTC 59.188 43.478 0.00 0.00 43.15 2.87
2958 3547 5.188948 ACAGTGAGACTTCTCTCTAGAGCTA 59.811 44.000 15.35 2.30 42.81 3.32
2961 3550 5.523916 GTGAGACTTCTCTCTAGAGCTAGTG 59.476 48.000 15.35 8.31 43.26 2.74
3012 3601 2.355756 CTGACCGTTAATTGCAGATGGG 59.644 50.000 0.00 0.00 0.00 4.00
3132 3721 8.883302 TGGTAATAGTAAGAAAGGTAAGGTTGT 58.117 33.333 0.00 0.00 0.00 3.32
3169 3761 2.415168 ACATTACTGCATCCGTTCGTTG 59.585 45.455 0.00 0.00 0.00 4.10
3301 3959 1.234821 CTAGTTTTGAAGGCCGTGCA 58.765 50.000 0.00 0.00 0.00 4.57
3330 3988 5.200368 ACAAGTGAGGTTAGCCATTTTTG 57.800 39.130 0.00 0.37 37.19 2.44
3341 3999 9.271828 AGGTTAGCCATTTTTGTTCTTATTTTG 57.728 29.630 0.00 0.00 37.19 2.44
3367 4025 8.547069 GCAATTTGTAAAGCAATGTGAACTTTA 58.453 29.630 0.00 0.00 36.89 1.85
3397 4055 6.954944 ACATAACAATGTATATGTTCCGCAC 58.045 36.000 12.23 0.00 39.14 5.34
3418 4076 5.360591 CACAGTTACTTGGAAACTCTCTGT 58.639 41.667 0.00 0.00 34.99 3.41
3420 4078 6.984474 CACAGTTACTTGGAAACTCTCTGTAA 59.016 38.462 0.00 0.00 34.99 2.41
3421 4079 7.169982 CACAGTTACTTGGAAACTCTCTGTAAG 59.830 40.741 0.00 0.00 34.99 2.34
3455 4113 3.989056 TGGAGAAAGGGTCTTTTGGTTT 58.011 40.909 0.00 0.00 36.41 3.27
3529 4188 5.958380 TGAGTCTAAGCCTTTAAGGATCTCA 59.042 40.000 16.18 13.91 37.67 3.27
3554 4399 2.949714 GTGAAGTTCACACGGTCATG 57.050 50.000 27.37 0.00 46.22 3.07
3566 4411 1.002366 CGGTCATGCTGCTAACTGTC 58.998 55.000 0.00 0.00 0.00 3.51
3570 4415 3.503748 GGTCATGCTGCTAACTGTCTTTT 59.496 43.478 0.00 0.00 0.00 2.27
3578 4423 9.793252 ATGCTGCTAACTGTCTTTTTAATATTG 57.207 29.630 0.00 0.00 0.00 1.90
3655 4500 0.460987 CTTCACCACAGGGATCGAGC 60.461 60.000 0.00 0.00 38.05 5.03
3685 4530 9.167311 GTACTTCACACAATTAATGGAGAAGAT 57.833 33.333 20.76 12.74 34.37 2.40
3738 4583 3.638484 GTTACAGCAACGAGGCATTTTT 58.362 40.909 5.91 0.00 35.83 1.94
3764 4609 6.368791 TCTCCGTCATCAGTTTAATTGTTCTG 59.631 38.462 0.00 0.00 0.00 3.02
3767 4612 7.390440 TCCGTCATCAGTTTAATTGTTCTGATT 59.610 33.333 14.13 3.45 43.07 2.57
3845 4690 2.388735 AGTCTCAGACCAAGTGTGTCA 58.611 47.619 0.00 0.00 35.15 3.58
3916 4761 4.225042 TGCAGAAGTAAATTCTAGCAGGGA 59.775 41.667 9.67 0.00 46.91 4.20
3968 4813 7.061210 CGAGATGACAAGGTAATATCTTAAGCG 59.939 40.741 0.00 0.00 0.00 4.68
3974 4819 5.609533 AGGTAATATCTTAAGCGTGTGGT 57.390 39.130 0.00 0.00 0.00 4.16
4071 4916 1.948508 TGGTGCAAGCAGTAAAGCG 59.051 52.632 0.00 0.00 40.88 4.68
4080 4925 3.386768 AGCAGTAAAGCGTGAGAAGAA 57.613 42.857 0.00 0.00 40.15 2.52
4095 4940 5.929415 GTGAGAAGAACCAGGTAGAAGAAAG 59.071 44.000 0.00 0.00 0.00 2.62
4150 4995 4.825422 TGAAGAAGGAACTAGCTGATGTG 58.175 43.478 0.00 0.00 38.49 3.21
4196 5041 7.507733 ACTAAGGTAAGATATACCACACTCG 57.492 40.000 7.35 0.00 39.99 4.18
4204 5049 6.564709 AGATATACCACACTCGCGTAATTA 57.435 37.500 5.77 0.00 0.00 1.40
4232 5077 5.007724 CAGGAAATTCCATAACTTCGCCTAC 59.992 44.000 15.21 0.00 39.61 3.18
4233 5078 5.104485 AGGAAATTCCATAACTTCGCCTACT 60.104 40.000 15.21 0.00 39.61 2.57
4237 5082 2.159099 TCCATAACTTCGCCTACTGCAG 60.159 50.000 13.48 13.48 41.33 4.41
4296 5141 6.598503 TCTCCATACAGATTACTCGGAGTTA 58.401 40.000 16.95 7.74 39.65 2.24
4363 5208 9.950680 TTCAGAAAATCAAACTCAAATCACTAC 57.049 29.630 0.00 0.00 0.00 2.73
4371 5216 8.853077 TCAAACTCAAATCACTACATCTCAAT 57.147 30.769 0.00 0.00 0.00 2.57
4465 5315 2.093973 AGCCTCAGTGTATCAAACCTCG 60.094 50.000 0.00 0.00 0.00 4.63
4470 5320 3.508402 TCAGTGTATCAAACCTCGCAGTA 59.492 43.478 0.00 0.00 0.00 2.74
4475 5352 7.539022 CAGTGTATCAAACCTCGCAGTATATAG 59.461 40.741 0.00 0.00 0.00 1.31
4489 5366 5.335191 GCAGTATATAGCAAGGTGGAAATGC 60.335 44.000 0.00 0.00 40.34 3.56
4496 5376 1.577328 AAGGTGGAAATGCAGCGTCG 61.577 55.000 0.00 0.00 0.00 5.12
4497 5377 2.032634 GGTGGAAATGCAGCGTCGA 61.033 57.895 0.00 0.00 0.00 4.20
4504 5384 0.454957 AATGCAGCGTCGATTTGTGC 60.455 50.000 0.00 0.00 34.62 4.57
4512 5392 1.722464 CGTCGATTTGTGCGTTAGGAA 59.278 47.619 0.00 0.00 0.00 3.36
4517 5397 5.006358 GTCGATTTGTGCGTTAGGAATATGT 59.994 40.000 0.00 0.00 0.00 2.29
4534 5415 9.638176 AGGAATATGTTCTCTTATTTGCAAGAT 57.362 29.630 0.00 0.00 34.14 2.40
4565 5446 5.426689 TCCTAAGCTCAATGTGATCAAGT 57.573 39.130 0.00 0.00 0.00 3.16
4601 5482 0.668706 CTGTGCAGGAACTCCAGTCG 60.669 60.000 0.00 0.00 34.60 4.18
4607 5488 2.273912 GGAACTCCAGTCGGTCCGT 61.274 63.158 11.88 0.00 35.64 4.69
4619 5500 0.526211 CGGTCCGTGATCAACTCTCA 59.474 55.000 2.08 0.00 0.00 3.27
4654 5535 1.001633 GGCTTCCAAACTCGAGGTACA 59.998 52.381 18.41 0.00 0.00 2.90
4667 5548 5.479375 ACTCGAGGTACATAAAGGTTCTTCA 59.521 40.000 18.41 0.00 0.00 3.02
4671 5552 6.051179 AGGTACATAAAGGTTCTTCAGGAC 57.949 41.667 0.00 0.00 0.00 3.85
4707 5588 5.163683 CCATGCTCTAGGTTTTGATGAGTTG 60.164 44.000 0.00 0.00 0.00 3.16
4716 5597 5.643777 AGGTTTTGATGAGTTGGTCGAATAG 59.356 40.000 0.00 0.00 0.00 1.73
4720 5601 5.614324 TGATGAGTTGGTCGAATAGGAAT 57.386 39.130 0.00 0.00 0.00 3.01
4727 5608 7.724506 TGAGTTGGTCGAATAGGAATATAGAGT 59.275 37.037 0.00 0.00 0.00 3.24
4733 5614 7.011295 GGTCGAATAGGAATATAGAGTACTCCG 59.989 44.444 19.38 10.55 0.00 4.63
4735 5616 7.548427 TCGAATAGGAATATAGAGTACTCCGTG 59.452 40.741 19.38 0.00 0.00 4.94
4736 5617 7.201626 CGAATAGGAATATAGAGTACTCCGTGG 60.202 44.444 19.38 0.00 0.00 4.94
4738 5619 3.193056 GGAATATAGAGTACTCCGTGGCC 59.807 52.174 19.38 10.33 0.00 5.36
4739 5620 2.283145 TATAGAGTACTCCGTGGCCC 57.717 55.000 19.38 0.00 0.00 5.80
4740 5621 0.556747 ATAGAGTACTCCGTGGCCCT 59.443 55.000 19.38 0.74 0.00 5.19
4741 5622 0.333993 TAGAGTACTCCGTGGCCCTT 59.666 55.000 19.38 0.00 0.00 3.95
4742 5623 0.544595 AGAGTACTCCGTGGCCCTTT 60.545 55.000 19.38 0.00 0.00 3.11
4743 5624 0.323957 GAGTACTCCGTGGCCCTTTT 59.676 55.000 12.13 0.00 0.00 2.27
4744 5625 0.769247 AGTACTCCGTGGCCCTTTTT 59.231 50.000 0.00 0.00 0.00 1.94
4745 5626 1.162698 GTACTCCGTGGCCCTTTTTC 58.837 55.000 0.00 0.00 0.00 2.29
4746 5627 0.766131 TACTCCGTGGCCCTTTTTCA 59.234 50.000 0.00 0.00 0.00 2.69
4747 5628 0.822121 ACTCCGTGGCCCTTTTTCAC 60.822 55.000 0.00 0.00 0.00 3.18
4748 5629 0.821711 CTCCGTGGCCCTTTTTCACA 60.822 55.000 0.00 0.00 0.00 3.58
4749 5630 0.178975 TCCGTGGCCCTTTTTCACAT 60.179 50.000 0.00 0.00 0.00 3.21
4750 5631 0.678950 CCGTGGCCCTTTTTCACATT 59.321 50.000 0.00 0.00 0.00 2.71
4751 5632 1.605202 CCGTGGCCCTTTTTCACATTG 60.605 52.381 0.00 0.00 0.00 2.82
4752 5633 1.339610 CGTGGCCCTTTTTCACATTGA 59.660 47.619 0.00 0.00 0.00 2.57
4753 5634 2.029110 CGTGGCCCTTTTTCACATTGAT 60.029 45.455 0.00 0.00 0.00 2.57
4754 5635 3.588955 GTGGCCCTTTTTCACATTGATC 58.411 45.455 0.00 0.00 0.00 2.92
4762 5643 5.337009 CCTTTTTCACATTGATCTCTTGGGG 60.337 44.000 0.00 0.00 0.00 4.96
4764 5645 4.387026 TTCACATTGATCTCTTGGGGTT 57.613 40.909 0.00 0.00 0.00 4.11
4768 5649 3.075882 ACATTGATCTCTTGGGGTTGGAA 59.924 43.478 0.00 0.00 0.00 3.53
4778 5659 3.017048 TGGGGTTGGAATGATGATGAC 57.983 47.619 0.00 0.00 0.00 3.06
4796 5677 1.947456 GACACGAGTTTTCCCTTTGCT 59.053 47.619 0.00 0.00 0.00 3.91
4842 5723 1.098869 TTCAACAACGGCTGCAGAAA 58.901 45.000 20.43 0.00 0.00 2.52
4933 5814 2.598394 GCAGCAACAAGAGGCCCA 60.598 61.111 0.00 0.00 0.00 5.36
4998 5879 0.106619 GCGGGGACTCTTCTCTAGGA 60.107 60.000 0.00 0.00 0.00 2.94
5011 5892 4.230314 TCTCTAGGATCGCATTCTTTCG 57.770 45.455 0.00 0.00 0.00 3.46
5141 6024 5.902613 TTTACCAAGATCAAATGCCAGAG 57.097 39.130 0.00 0.00 0.00 3.35
5283 6547 3.110447 TGCCCTGCAGATTTTTCAAAC 57.890 42.857 17.39 0.00 33.32 2.93
5499 8033 0.249447 CGCCATACAGGATTGAGCGA 60.249 55.000 0.00 0.00 41.22 4.93
5574 8108 7.408756 TCCTGGAATTCAATAAAATCCACAG 57.591 36.000 7.93 0.82 0.00 3.66
5892 8448 1.918293 ACCCGTCAGCATCCTTCCA 60.918 57.895 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.771854 TGGACTTTCCTTGGTACAGCA 59.228 47.619 0.00 0.00 37.46 4.41
103 104 1.811266 CAAGGCGATCTGGTCCACG 60.811 63.158 0.00 0.00 0.00 4.94
118 119 2.333014 GCTTCGACTCTGAACCTCAAG 58.667 52.381 0.00 0.00 0.00 3.02
120 121 0.603569 GGCTTCGACTCTGAACCTCA 59.396 55.000 0.00 0.00 0.00 3.86
142 143 1.705337 GCACGATTCCATGGACCACG 61.705 60.000 15.91 21.02 0.00 4.94
192 193 1.523934 GCCGTTCGTCTTTCTTTTCGA 59.476 47.619 0.00 0.00 0.00 3.71
262 263 4.002906 TGTCCTCTACGCAACTCATTTT 57.997 40.909 0.00 0.00 0.00 1.82
274 275 2.891580 TGTCTGTCCAGTTGTCCTCTAC 59.108 50.000 0.00 0.00 0.00 2.59
304 305 8.771766 AGAAAAGAAACCTACGAAAACACTATC 58.228 33.333 0.00 0.00 0.00 2.08
324 325 6.527957 CAGCAACAACAACAAGAAAGAAAAG 58.472 36.000 0.00 0.00 0.00 2.27
373 380 3.154827 ACGGTTTCCAGTTTCCATCAT 57.845 42.857 0.00 0.00 0.00 2.45
454 461 0.250295 CCACGTCACAACTGACCCAT 60.250 55.000 0.00 0.00 43.64 4.00
589 1142 7.095102 GCTCACAATTTCTTGCCAACAATATTT 60.095 33.333 0.00 0.00 35.69 1.40
622 1175 2.997621 TTCAAATGCGTGCACCGTGC 62.998 55.000 16.93 16.93 45.29 5.34
623 1176 0.998226 CTTCAAATGCGTGCACCGTG 60.998 55.000 12.15 0.00 39.32 4.94
624 1177 1.282570 CTTCAAATGCGTGCACCGT 59.717 52.632 12.15 2.58 39.32 4.83
625 1178 0.998226 CACTTCAAATGCGTGCACCG 60.998 55.000 12.15 7.80 40.40 4.94
626 1179 0.310543 TCACTTCAAATGCGTGCACC 59.689 50.000 12.15 4.74 0.00 5.01
627 1180 1.398595 GTCACTTCAAATGCGTGCAC 58.601 50.000 6.82 6.82 0.00 4.57
692 1245 4.933064 GATCGGGGTCGCAGCTCG 62.933 72.222 1.87 1.87 40.15 5.03
693 1246 2.579684 AAAGATCGGGGTCGCAGCTC 62.580 60.000 0.00 0.00 36.13 4.09
694 1247 2.660064 AAAGATCGGGGTCGCAGCT 61.660 57.895 0.00 0.00 36.13 4.24
695 1248 2.125106 AAAGATCGGGGTCGCAGC 60.125 61.111 0.00 0.00 36.13 5.25
696 1249 0.179073 ATCAAAGATCGGGGTCGCAG 60.179 55.000 0.00 0.00 36.13 5.18
697 1250 0.179084 GATCAAAGATCGGGGTCGCA 60.179 55.000 0.00 0.00 36.13 5.10
698 1251 0.880718 GGATCAAAGATCGGGGTCGC 60.881 60.000 0.00 0.00 36.13 5.19
701 1254 2.105477 CAGATGGATCAAAGATCGGGGT 59.895 50.000 0.00 0.00 0.00 4.95
813 1387 4.467107 GGGGGAGAGGCGGAGAGT 62.467 72.222 0.00 0.00 0.00 3.24
872 1446 1.067565 GTTCGAGATCTGGACAGCACA 60.068 52.381 6.97 0.00 0.00 4.57
876 1450 2.757868 AGAAGGTTCGAGATCTGGACAG 59.242 50.000 6.97 0.00 0.00 3.51
1020 1606 6.782988 AGCCCATGTACTAGTAGTGATACAAT 59.217 38.462 13.29 0.00 31.65 2.71
1022 1608 5.702266 AGCCCATGTACTAGTAGTGATACA 58.298 41.667 13.29 9.70 32.38 2.29
1026 1612 4.207955 CTGAGCCCATGTACTAGTAGTGA 58.792 47.826 13.29 0.00 0.00 3.41
1027 1613 3.954904 ACTGAGCCCATGTACTAGTAGTG 59.045 47.826 13.29 5.61 0.00 2.74
1028 1614 3.954904 CACTGAGCCCATGTACTAGTAGT 59.045 47.826 8.14 8.14 0.00 2.73
1029 1615 4.207955 TCACTGAGCCCATGTACTAGTAG 58.792 47.826 1.87 0.00 0.00 2.57
1104 1690 4.500116 GGAGAGAGACGCCACGCC 62.500 72.222 0.00 0.00 38.35 5.68
1165 1751 5.936686 ATCAGCCATGATCAATTTACTCG 57.063 39.130 0.00 0.00 42.76 4.18
1166 1752 7.486647 ACAAATCAGCCATGATCAATTTACTC 58.513 34.615 0.00 0.00 45.67 2.59
1167 1753 7.414222 ACAAATCAGCCATGATCAATTTACT 57.586 32.000 0.00 0.00 45.67 2.24
1168 1754 9.754382 ATTACAAATCAGCCATGATCAATTTAC 57.246 29.630 0.00 0.00 45.67 2.01
1169 1755 9.752961 CATTACAAATCAGCCATGATCAATTTA 57.247 29.630 0.00 0.00 45.67 1.40
1170 1756 8.262227 ACATTACAAATCAGCCATGATCAATTT 58.738 29.630 0.00 0.00 45.67 1.82
1182 1768 5.627499 TGGTTGAGACATTACAAATCAGC 57.373 39.130 0.00 0.00 0.00 4.26
1225 1811 3.005554 CAGTGGTTCTTGTATGCTCTGG 58.994 50.000 0.00 0.00 0.00 3.86
1252 1838 6.349944 CGACTACTTTAGGCTCTTGAGGTTTA 60.350 42.308 0.00 0.00 0.00 2.01
1259 1845 3.512680 CCACGACTACTTTAGGCTCTTG 58.487 50.000 0.00 0.00 0.00 3.02
1293 1879 3.738982 TGAACATCAACCATCTTGTCGT 58.261 40.909 0.00 0.00 0.00 4.34
1294 1880 3.125829 CCTGAACATCAACCATCTTGTCG 59.874 47.826 0.00 0.00 0.00 4.35
1295 1881 4.154918 GTCCTGAACATCAACCATCTTGTC 59.845 45.833 0.00 0.00 0.00 3.18
1296 1882 4.074970 GTCCTGAACATCAACCATCTTGT 58.925 43.478 0.00 0.00 0.00 3.16
1297 1883 4.074259 TGTCCTGAACATCAACCATCTTG 58.926 43.478 0.00 0.00 31.20 3.02
1298 1884 4.371624 TGTCCTGAACATCAACCATCTT 57.628 40.909 0.00 0.00 31.20 2.40
1396 1982 1.206371 ACCTTGTATCGAGGTTTCGGG 59.794 52.381 3.09 0.00 45.27 5.14
1445 2031 5.189736 AGCACAAGATCAGAGGGTATAACAA 59.810 40.000 0.00 0.00 0.00 2.83
1446 2032 4.716784 AGCACAAGATCAGAGGGTATAACA 59.283 41.667 0.00 0.00 0.00 2.41
1447 2033 5.053145 CAGCACAAGATCAGAGGGTATAAC 58.947 45.833 0.00 0.00 0.00 1.89
1448 2034 4.101585 CCAGCACAAGATCAGAGGGTATAA 59.898 45.833 0.00 0.00 0.00 0.98
1494 2080 3.220110 AGATAATTGGAGCCAGCATGTG 58.780 45.455 0.00 0.00 0.00 3.21
1499 2085 2.292845 GCAGAAGATAATTGGAGCCAGC 59.707 50.000 0.00 0.00 0.00 4.85
1549 2135 5.722021 GGTTTCCACCAAAGACATACATT 57.278 39.130 0.00 0.00 43.61 2.71
1694 2280 4.020128 AGGGCTCAACTAAAGGAGTAACAG 60.020 45.833 0.00 0.00 37.44 3.16
1859 2446 4.456911 TGGTTCAGCTGATTCTGATTGAAC 59.543 41.667 19.04 20.54 42.12 3.18
1884 2471 1.199327 CAGCACATGGAGCAACAGAAG 59.801 52.381 13.81 0.00 0.00 2.85
1936 2524 6.815641 AGCAGTTTCACATCACTGATAACTAG 59.184 38.462 3.48 0.00 42.74 2.57
2048 2636 0.179048 TGGTGTGTCCTGCAAGTGAG 60.179 55.000 0.00 0.00 37.07 3.51
2118 2706 6.099413 TCTGGCATGACAAGATAAGAAGAGAT 59.901 38.462 1.11 0.00 0.00 2.75
2268 2857 2.156098 GTGGAAACTTGCGACCCAATA 58.844 47.619 0.00 0.00 31.91 1.90
2507 3096 6.884295 TGTTTAGATCGATCAAACCAAATCCT 59.116 34.615 29.60 12.80 32.20 3.24
2526 3115 6.076981 ACAACTCAGCTCCATTTTGTTTAG 57.923 37.500 0.00 0.00 0.00 1.85
2542 3131 8.484641 TTCATTTGTGCAATTTTAACAACTCA 57.515 26.923 0.00 0.00 33.73 3.41
2595 3184 6.538381 CACACACACACACACATATATATGGT 59.462 38.462 23.44 16.11 38.00 3.55
2596 3185 6.538381 ACACACACACACACACATATATATGG 59.462 38.462 23.44 15.57 38.00 2.74
2606 3195 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2607 3196 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2608 3197 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2609 3198 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2610 3199 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2611 3200 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2612 3201 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2613 3202 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2614 3203 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2615 3204 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2616 3205 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2617 3206 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2618 3207 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2619 3208 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2620 3209 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2621 3210 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2622 3211 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2623 3212 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2624 3213 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2625 3214 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2626 3215 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
2627 3216 0.035458 TCCACACACACACACACACA 59.965 50.000 0.00 0.00 0.00 3.72
2628 3217 0.726827 CTCCACACACACACACACAC 59.273 55.000 0.00 0.00 0.00 3.82
2629 3218 0.610687 TCTCCACACACACACACACA 59.389 50.000 0.00 0.00 0.00 3.72
2630 3219 1.732941 TTCTCCACACACACACACAC 58.267 50.000 0.00 0.00 0.00 3.82
2631 3220 2.481289 TTTCTCCACACACACACACA 57.519 45.000 0.00 0.00 0.00 3.72
2632 3221 5.493133 TTTATTTCTCCACACACACACAC 57.507 39.130 0.00 0.00 0.00 3.82
2633 3222 6.707440 ATTTTATTTCTCCACACACACACA 57.293 33.333 0.00 0.00 0.00 3.72
2634 3223 7.199766 TGAATTTTATTTCTCCACACACACAC 58.800 34.615 0.00 0.00 0.00 3.82
2635 3224 7.340122 TGAATTTTATTTCTCCACACACACA 57.660 32.000 0.00 0.00 0.00 3.72
2636 3225 8.641499 TTTGAATTTTATTTCTCCACACACAC 57.359 30.769 0.00 0.00 0.00 3.82
2717 3306 8.519492 TGCAAGTTTTATTTCATGCTCTAAAC 57.481 30.769 0.00 0.00 34.97 2.01
2756 3345 3.130160 CCTCAAAGCAGAGCCGGC 61.130 66.667 21.89 21.89 34.26 6.13
2802 3391 4.464597 AGAAGGAGTAGTGCCTCTGTAAAG 59.535 45.833 0.00 0.00 33.76 1.85
2803 3392 4.417437 AGAAGGAGTAGTGCCTCTGTAAA 58.583 43.478 0.00 0.00 33.76 2.01
2858 3447 6.708054 CACCAAATATCAAGAGATACCAGTCC 59.292 42.308 0.00 0.00 39.43 3.85
2862 3451 5.163099 CCCCACCAAATATCAAGAGATACCA 60.163 44.000 0.00 0.00 39.43 3.25
2948 3537 6.254589 GCAAATGTACAACACTAGCTCTAGAG 59.745 42.308 15.85 15.85 36.97 2.43
2958 3547 5.528043 TGGAATTGCAAATGTACAACACT 57.472 34.783 1.71 0.00 0.00 3.55
2961 3550 5.525378 TGGTTTGGAATTGCAAATGTACAAC 59.475 36.000 25.14 12.84 0.00 3.32
3012 3601 2.011046 GCTGCTCTGGTCTTGACCATC 61.011 57.143 21.09 13.97 39.34 3.51
3073 3662 0.107361 CCCAGTTATCCCCAACCGTC 60.107 60.000 0.00 0.00 0.00 4.79
3169 3761 4.131596 TCATTAGGTTACCAAATAGCGGC 58.868 43.478 3.51 0.00 0.00 6.53
3301 3959 2.547990 CTAACCTCACTTGTAGGGGGT 58.452 52.381 0.00 0.00 38.54 4.95
3330 3988 9.928236 TTGCTTTACAAATTGCAAAATAAGAAC 57.072 25.926 1.71 0.00 41.58 3.01
3341 3999 6.529463 AGTTCACATTGCTTTACAAATTGC 57.471 33.333 0.00 0.00 42.86 3.56
3373 4031 6.540551 TGTGCGGAACATATACATTGTTATGT 59.459 34.615 13.92 13.92 40.09 2.29
3381 4039 5.914033 AGTAACTGTGCGGAACATATACAT 58.086 37.500 11.74 0.00 38.39 2.29
3382 4040 5.333299 AGTAACTGTGCGGAACATATACA 57.667 39.130 11.74 0.00 38.39 2.29
3397 4055 7.434492 TCTTACAGAGAGTTTCCAAGTAACTG 58.566 38.462 0.00 0.00 36.04 3.16
3418 4076 7.834181 CCCTTTCTCCATTTATCCAAACTCTTA 59.166 37.037 0.00 0.00 0.00 2.10
3420 4078 6.190587 CCCTTTCTCCATTTATCCAAACTCT 58.809 40.000 0.00 0.00 0.00 3.24
3421 4079 5.952347 ACCCTTTCTCCATTTATCCAAACTC 59.048 40.000 0.00 0.00 0.00 3.01
3543 4388 0.443869 GTTAGCAGCATGACCGTGTG 59.556 55.000 0.00 0.00 39.69 3.82
3547 4392 1.002366 GACAGTTAGCAGCATGACCG 58.998 55.000 0.00 0.00 39.69 4.79
3552 4397 9.793252 CAATATTAAAAAGACAGTTAGCAGCAT 57.207 29.630 0.00 0.00 0.00 3.79
3554 4399 8.244113 ACCAATATTAAAAAGACAGTTAGCAGC 58.756 33.333 0.00 0.00 0.00 5.25
3578 4423 9.950680 CATAACACCATAGAATCACAATTAACC 57.049 33.333 0.00 0.00 0.00 2.85
3627 4472 4.111577 TCCCTGTGGTGAAGGAGATTATT 58.888 43.478 0.00 0.00 36.91 1.40
3628 4473 3.736094 TCCCTGTGGTGAAGGAGATTAT 58.264 45.455 0.00 0.00 36.91 1.28
3655 4500 9.653287 TCTCCATTAATTGTGTGAAGTACTAAG 57.347 33.333 0.00 0.00 0.00 2.18
3685 4530 6.775142 TGTATCCTCCAAATGACAACAGAAAA 59.225 34.615 0.00 0.00 0.00 2.29
3735 4580 7.936584 ACAATTAAACTGATGACGGAGAAAAA 58.063 30.769 0.00 0.00 0.00 1.94
3738 4583 6.934645 AGAACAATTAAACTGATGACGGAGAA 59.065 34.615 0.00 0.00 0.00 2.87
3739 4584 6.368791 CAGAACAATTAAACTGATGACGGAGA 59.631 38.462 0.00 0.00 32.90 3.71
3740 4585 6.368791 TCAGAACAATTAAACTGATGACGGAG 59.631 38.462 0.00 0.00 35.01 4.63
3741 4586 6.227522 TCAGAACAATTAAACTGATGACGGA 58.772 36.000 0.00 0.00 35.01 4.69
3742 4587 6.480524 TCAGAACAATTAAACTGATGACGG 57.519 37.500 0.00 0.00 35.01 4.79
3743 4588 8.955061 AAATCAGAACAATTAAACTGATGACG 57.045 30.769 15.90 0.00 45.40 4.35
3799 4644 8.306313 TGTCTTCAGAGCATAAACCTAGATAA 57.694 34.615 0.00 0.00 0.00 1.75
3803 4648 6.402222 ACTTGTCTTCAGAGCATAAACCTAG 58.598 40.000 0.00 0.00 0.00 3.02
3845 4690 6.322456 TCTCCAGTTCATCTATTCGTGAAGAT 59.678 38.462 0.00 0.00 35.22 2.40
3866 4711 1.106285 GGGTCATGCCATTTGTCTCC 58.894 55.000 8.20 0.00 39.65 3.71
3968 4813 1.470805 GGTTCCAACAAGCAACCACAC 60.471 52.381 0.00 0.00 38.01 3.82
3974 4819 0.681564 ACCGTGGTTCCAACAAGCAA 60.682 50.000 0.00 0.00 0.00 3.91
4027 4872 4.696479 TTTGCTGATATCTCCTCCCTTC 57.304 45.455 3.98 0.00 0.00 3.46
4071 4916 5.470047 TTCTTCTACCTGGTTCTTCTCAC 57.530 43.478 3.84 0.00 0.00 3.51
4080 4925 5.130477 TGTTCAAGTCTTTCTTCTACCTGGT 59.870 40.000 4.05 4.05 33.63 4.00
4095 4940 2.358898 TGCAGCTTTTCCTGTTCAAGTC 59.641 45.455 0.00 0.00 35.28 3.01
4124 4969 3.904339 TCAGCTAGTTCCTTCTTCAGGTT 59.096 43.478 0.00 0.00 44.37 3.50
4150 4995 1.541588 AGCTCCGCATTTTTGTTCTCC 59.458 47.619 0.00 0.00 0.00 3.71
4196 5041 9.959749 TTATGGAATTTCCTGAAATAATTACGC 57.040 29.630 16.25 0.00 39.88 4.42
4204 5049 6.405842 GGCGAAGTTATGGAATTTCCTGAAAT 60.406 38.462 16.25 6.95 42.35 2.17
4232 5077 2.733552 CAGCACACAAGTAGTACTGCAG 59.266 50.000 13.48 13.48 36.17 4.41
4233 5078 2.364002 TCAGCACACAAGTAGTACTGCA 59.636 45.455 13.75 0.00 36.17 4.41
4237 5082 7.062371 CAGATAACTTCAGCACACAAGTAGTAC 59.938 40.741 0.00 0.00 32.36 2.73
4312 5157 7.297614 AGCTCAGGGCCTTAAATATTTGAATA 58.702 34.615 1.32 0.00 43.05 1.75
4323 5168 1.656587 TCTGAAGCTCAGGGCCTTAA 58.343 50.000 1.32 0.00 44.39 1.85
4371 5216 9.725019 CTGCTACAATGATAACCTATAATTCCA 57.275 33.333 0.00 0.00 0.00 3.53
4453 5298 6.387465 TGCTATATACTGCGAGGTTTGATAC 58.613 40.000 0.00 0.00 0.00 2.24
4465 5315 5.335191 GCATTTCCACCTTGCTATATACTGC 60.335 44.000 0.00 0.00 33.61 4.40
4470 5320 3.571401 GCTGCATTTCCACCTTGCTATAT 59.429 43.478 0.00 0.00 37.28 0.86
4475 5352 1.444895 CGCTGCATTTCCACCTTGC 60.445 57.895 0.00 0.00 36.91 4.01
4489 5366 0.436913 TAACGCACAAATCGACGCTG 59.563 50.000 0.00 0.00 0.00 5.18
4496 5376 7.011482 AGAGAACATATTCCTAACGCACAAATC 59.989 37.037 0.00 0.00 35.18 2.17
4497 5377 6.823689 AGAGAACATATTCCTAACGCACAAAT 59.176 34.615 0.00 0.00 35.18 2.32
4504 5384 8.826710 TGCAAATAAGAGAACATATTCCTAACG 58.173 33.333 0.00 0.00 35.18 3.18
4534 5415 7.950512 TCACATTGAGCTTAGGAAAAATTTCA 58.049 30.769 8.06 0.00 38.92 2.69
4539 5420 7.231317 ACTTGATCACATTGAGCTTAGGAAAAA 59.769 33.333 0.00 0.00 33.24 1.94
4543 5424 5.426689 ACTTGATCACATTGAGCTTAGGA 57.573 39.130 0.00 0.00 33.24 2.94
4601 5482 1.819288 TCTGAGAGTTGATCACGGACC 59.181 52.381 0.00 0.00 29.94 4.46
4607 5488 2.558359 TGCTTCGTCTGAGAGTTGATCA 59.442 45.455 0.00 0.00 0.00 2.92
4619 5500 4.443266 GCCCTCGCTGCTTCGTCT 62.443 66.667 0.00 0.00 0.00 4.18
4654 5535 3.916989 ACCCTGTCCTGAAGAACCTTTAT 59.083 43.478 0.00 0.00 0.00 1.40
4707 5588 7.011295 CGGAGTACTCTATATTCCTATTCGACC 59.989 44.444 21.88 0.00 0.00 4.79
4716 5597 3.193056 GGCCACGGAGTACTCTATATTCC 59.807 52.174 21.88 12.39 41.61 3.01
4720 5601 1.779092 AGGGCCACGGAGTACTCTATA 59.221 52.381 21.88 0.00 41.61 1.31
4727 5608 0.766131 TGAAAAAGGGCCACGGAGTA 59.234 50.000 6.18 0.00 41.61 2.59
4733 5614 3.259123 AGATCAATGTGAAAAAGGGCCAC 59.741 43.478 6.18 0.00 0.00 5.01
4735 5616 3.766051 AGAGATCAATGTGAAAAAGGGCC 59.234 43.478 0.00 0.00 0.00 5.80
4736 5617 5.166398 CAAGAGATCAATGTGAAAAAGGGC 58.834 41.667 0.00 0.00 0.00 5.19
4738 5619 5.337009 CCCCAAGAGATCAATGTGAAAAAGG 60.337 44.000 0.00 0.00 0.00 3.11
4739 5620 5.244626 ACCCCAAGAGATCAATGTGAAAAAG 59.755 40.000 0.00 0.00 0.00 2.27
4740 5621 5.147032 ACCCCAAGAGATCAATGTGAAAAA 58.853 37.500 0.00 0.00 0.00 1.94
4741 5622 4.739793 ACCCCAAGAGATCAATGTGAAAA 58.260 39.130 0.00 0.00 0.00 2.29
4742 5623 4.387026 ACCCCAAGAGATCAATGTGAAA 57.613 40.909 0.00 0.00 0.00 2.69
4743 5624 4.081406 CAACCCCAAGAGATCAATGTGAA 58.919 43.478 0.00 0.00 0.00 3.18
4744 5625 3.561960 CCAACCCCAAGAGATCAATGTGA 60.562 47.826 0.00 0.00 0.00 3.58
4745 5626 2.756760 CCAACCCCAAGAGATCAATGTG 59.243 50.000 0.00 0.00 0.00 3.21
4746 5627 2.649312 TCCAACCCCAAGAGATCAATGT 59.351 45.455 0.00 0.00 0.00 2.71
4747 5628 3.370840 TCCAACCCCAAGAGATCAATG 57.629 47.619 0.00 0.00 0.00 2.82
4748 5629 4.017222 TCATTCCAACCCCAAGAGATCAAT 60.017 41.667 0.00 0.00 0.00 2.57
4749 5630 3.333381 TCATTCCAACCCCAAGAGATCAA 59.667 43.478 0.00 0.00 0.00 2.57
4750 5631 2.918934 TCATTCCAACCCCAAGAGATCA 59.081 45.455 0.00 0.00 0.00 2.92
4751 5632 3.652057 TCATTCCAACCCCAAGAGATC 57.348 47.619 0.00 0.00 0.00 2.75
4752 5633 3.528905 TCATCATTCCAACCCCAAGAGAT 59.471 43.478 0.00 0.00 0.00 2.75
4753 5634 2.918934 TCATCATTCCAACCCCAAGAGA 59.081 45.455 0.00 0.00 0.00 3.10
4754 5635 3.370840 TCATCATTCCAACCCCAAGAG 57.629 47.619 0.00 0.00 0.00 2.85
4762 5643 3.935203 ACTCGTGTCATCATCATTCCAAC 59.065 43.478 0.00 0.00 0.00 3.77
4764 5645 3.893326 ACTCGTGTCATCATCATTCCA 57.107 42.857 0.00 0.00 0.00 3.53
4768 5649 3.941483 GGGAAAACTCGTGTCATCATCAT 59.059 43.478 0.00 0.00 0.00 2.45
4778 5659 1.946768 TCAGCAAAGGGAAAACTCGTG 59.053 47.619 0.00 0.00 0.00 4.35
4796 5677 4.151121 TGAAACTTCATCCTGCCAATTCA 58.849 39.130 0.00 0.00 31.01 2.57
4903 5784 1.200948 GTTGCTGCCTGAACCTGATTC 59.799 52.381 0.00 0.00 37.88 2.52
4998 5879 4.226761 GACCAAAAACGAAAGAATGCGAT 58.773 39.130 0.00 0.00 0.00 4.58
5011 5892 4.561735 TGATCAGAAACCGACCAAAAAC 57.438 40.909 0.00 0.00 0.00 2.43
5124 6006 2.358267 GAGGCTCTGGCATTTGATCTTG 59.642 50.000 7.40 0.00 40.87 3.02
5141 6024 4.639135 AACACTTTCAAGTTTCTGAGGC 57.361 40.909 0.00 0.00 37.08 4.70
5283 6547 9.017669 GTTATGTCAGTACTACCAAAATACGAG 57.982 37.037 0.00 0.00 0.00 4.18
5499 8033 8.161425 AGTTGTAACTATTAATGTGAACCTGGT 58.839 33.333 0.00 0.00 37.52 4.00
5539 8073 4.209538 TGAATTCCAGGAGCAACATATGG 58.790 43.478 7.80 0.00 0.00 2.74
5574 8108 4.262617 GTGGGAAGTTCATACCCTTTCTC 58.737 47.826 5.01 0.00 43.59 2.87
5892 8448 4.345257 ACTCAATATCAGGCGTACAAGGAT 59.655 41.667 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.