Multiple sequence alignment - TraesCS6A01G032900

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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 TraesCS6A01G032900 chr6A 100.000 3530 0 0 1 3530 16377111 16373582 0.000000e+00 6519.0
1 TraesCS6A01G032900 chr6A 88.421 2064 196 26 820 2845 16388392 16386334 0.000000e+00 2447.0
2 TraesCS6A01G032900 chr6A 85.065 1761 232 23 984 2732 16410040 16408299 0.000000e+00 1766.0
3 TraesCS6A01G032900 chr6A 87.209 1548 193 5 983 2529 15953431 15951888 0.000000e+00 1757.0
4 TraesCS6A01G032900 chr6A 86.517 89 12 0 149 237 14158616 14158528 8.060000e-17 99.0
5 TraesCS6A01G032900 chr6D 92.731 2724 141 28 269 2955 15699341 15696638 0.000000e+00 3880.0
6 TraesCS6A01G032900 chr6D 86.788 2195 210 53 679 2812 15748326 15746151 0.000000e+00 2374.0
7 TraesCS6A01G032900 chr6D 88.453 1888 195 17 678 2555 15711889 15710015 0.000000e+00 2257.0
8 TraesCS6A01G032900 chr6D 87.307 1552 188 8 982 2530 15385177 15383632 0.000000e+00 1766.0
9 TraesCS6A01G032900 chr6D 87.045 1567 196 7 983 2546 15419630 15418068 0.000000e+00 1762.0
10 TraesCS6A01G032900 chr6D 81.746 504 46 17 3060 3530 15696579 15696089 2.570000e-101 379.0
11 TraesCS6A01G032900 chr6D 94.118 119 5 2 15 132 15699635 15699518 2.800000e-41 180.0
12 TraesCS6A01G032900 chr6D 89.888 89 7 1 163 251 437928635 437928549 2.880000e-21 113.0
13 TraesCS6A01G032900 chr6D 97.872 47 1 0 2959 3005 15696588 15696634 8.120000e-12 82.4
14 TraesCS6A01G032900 chr6D 88.235 68 7 1 189 255 380995759 380995826 2.920000e-11 80.5
15 TraesCS6A01G032900 chr6B 86.782 2141 221 32 820 2912 27779979 27777853 0.000000e+00 2329.0
16 TraesCS6A01G032900 chr6B 90.308 454 20 13 676 1107 27711999 27711548 1.100000e-159 573.0
17 TraesCS6A01G032900 chr6B 89.578 403 22 11 284 681 27712518 27712131 8.800000e-136 494.0
18 TraesCS6A01G032900 chrUn 93.458 1070 52 11 1899 2955 76448929 76447865 0.000000e+00 1572.0
19 TraesCS6A01G032900 chrUn 93.458 1070 52 11 1899 2955 356328126 356329190 0.000000e+00 1572.0
20 TraesCS6A01G032900 chrUn 79.388 490 65 14 3060 3530 356329249 356329721 2.650000e-81 313.0
21 TraesCS6A01G032900 chrUn 78.980 490 65 14 3060 3530 76447806 76447336 2.060000e-77 300.0
22 TraesCS6A01G032900 chrUn 85.149 101 15 0 164 264 321270800 321270900 1.730000e-18 104.0
23 TraesCS6A01G032900 chr7B 85.000 120 18 0 145 264 673996100 673996219 4.790000e-24 122.0
24 TraesCS6A01G032900 chr7A 85.149 101 15 0 164 264 596662001 596662101 1.730000e-18 104.0
25 TraesCS6A01G032900 chr4A 83.505 97 11 5 146 237 508007497 508007401 6.280000e-13 86.1
26 TraesCS6A01G032900 chr3A 83.333 72 11 1 166 237 745633366 745633296 8.180000e-07 65.8


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 TraesCS6A01G032900 chr6A 16373582 16377111 3529 True 6519.000000 6519 100.000000 1 3530 1 chr6A.!!$R3 3529
1 TraesCS6A01G032900 chr6A 16386334 16388392 2058 True 2447.000000 2447 88.421000 820 2845 1 chr6A.!!$R4 2025
2 TraesCS6A01G032900 chr6A 16408299 16410040 1741 True 1766.000000 1766 85.065000 984 2732 1 chr6A.!!$R5 1748
3 TraesCS6A01G032900 chr6A 15951888 15953431 1543 True 1757.000000 1757 87.209000 983 2529 1 chr6A.!!$R2 1546
4 TraesCS6A01G032900 chr6D 15746151 15748326 2175 True 2374.000000 2374 86.788000 679 2812 1 chr6D.!!$R4 2133
5 TraesCS6A01G032900 chr6D 15710015 15711889 1874 True 2257.000000 2257 88.453000 678 2555 1 chr6D.!!$R3 1877
6 TraesCS6A01G032900 chr6D 15383632 15385177 1545 True 1766.000000 1766 87.307000 982 2530 1 chr6D.!!$R1 1548
7 TraesCS6A01G032900 chr6D 15418068 15419630 1562 True 1762.000000 1762 87.045000 983 2546 1 chr6D.!!$R2 1563
8 TraesCS6A01G032900 chr6D 15696089 15699635 3546 True 1479.666667 3880 89.531667 15 3530 3 chr6D.!!$R6 3515
9 TraesCS6A01G032900 chr6B 27777853 27779979 2126 True 2329.000000 2329 86.782000 820 2912 1 chr6B.!!$R1 2092
10 TraesCS6A01G032900 chr6B 27711548 27712518 970 True 533.500000 573 89.943000 284 1107 2 chr6B.!!$R2 823
11 TraesCS6A01G032900 chrUn 356328126 356329721 1595 False 942.500000 1572 86.423000 1899 3530 2 chrUn.!!$F2 1631
12 TraesCS6A01G032900 chrUn 76447336 76448929 1593 True 936.000000 1572 86.219000 1899 3530 2 chrUn.!!$R1 1631

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
818 1144 1.217942 ACAAAGGAAACCCAGGAAGCT 59.782 47.619 0.00 0.0 0.0 3.74 F
1302 1675 0.032316 TGGCCATGGGTGCAATATGT 60.032 50.000 15.13 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 2539 0.463295 CACCGCTCATGCCAGAGATT 60.463 55.0 6.68 0.0 37.87 2.40 R
2955 3378 0.107945 CCTCCTGTCACTAGCAAGGC 60.108 60.0 0.00 0.0 0.00 4.35 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
56 57 2.342279 CTCCTTCCACGGCGTTCA 59.658 61.111 11.19 0.00 0.00 3.18
69 70 2.285756 CGGCGTTCACTTTCACTAACAA 59.714 45.455 0.00 0.00 0.00 2.83
73 74 5.049954 GGCGTTCACTTTCACTAACAATGTA 60.050 40.000 0.00 0.00 0.00 2.29
96 97 7.558444 TGTACTCTAAACTTTGGTCAATTGGTT 59.442 33.333 5.42 0.00 0.00 3.67
122 123 3.791973 CCAAACTTGTTTGGCACTGTA 57.208 42.857 25.97 0.00 44.15 2.74
135 297 7.068348 TGTTTGGCACTGTATAAACCTTAAACA 59.932 33.333 0.00 0.00 33.33 2.83
158 320 8.983307 ACAAGTCTTAATTACTACTTTCTCCG 57.017 34.615 8.31 2.33 29.93 4.63
159 321 8.583296 ACAAGTCTTAATTACTACTTTCTCCGT 58.417 33.333 8.31 2.79 29.93 4.69
160 322 9.074443 CAAGTCTTAATTACTACTTTCTCCGTC 57.926 37.037 8.31 0.00 29.93 4.79
161 323 8.578448 AGTCTTAATTACTACTTTCTCCGTCT 57.422 34.615 0.00 0.00 0.00 4.18
162 324 9.678260 AGTCTTAATTACTACTTTCTCCGTCTA 57.322 33.333 0.00 0.00 0.00 2.59
239 401 8.230472 ACATTCATTTAAGAGATAAGCTTGGG 57.770 34.615 9.86 0.00 0.00 4.12
240 402 8.055181 ACATTCATTTAAGAGATAAGCTTGGGA 58.945 33.333 9.86 0.00 0.00 4.37
241 403 7.865706 TTCATTTAAGAGATAAGCTTGGGAC 57.134 36.000 9.86 0.00 0.00 4.46
242 404 6.957631 TCATTTAAGAGATAAGCTTGGGACA 58.042 36.000 9.86 0.00 0.00 4.02
267 429 3.439857 TTTTTGGACAGATGGAGGGAG 57.560 47.619 0.00 0.00 0.00 4.30
268 430 2.044793 TTTGGACAGATGGAGGGAGT 57.955 50.000 0.00 0.00 0.00 3.85
269 431 2.940514 TTGGACAGATGGAGGGAGTA 57.059 50.000 0.00 0.00 0.00 2.59
270 432 2.160721 TGGACAGATGGAGGGAGTAC 57.839 55.000 0.00 0.00 0.00 2.73
276 438 2.383442 GATGGAGGGAGTACCAGCTA 57.617 55.000 0.00 0.00 43.89 3.32
277 439 2.243810 GATGGAGGGAGTACCAGCTAG 58.756 57.143 0.00 0.00 43.89 3.42
305 467 9.071221 CGCAAGCTAGATCTTGATTAATACTAG 57.929 37.037 7.34 0.00 44.61 2.57
340 502 7.980099 ACAGAATATTACAACTACTGCTACCAC 59.020 37.037 0.00 0.00 0.00 4.16
373 538 2.423185 GCATGTGCAACTACAATAGGCA 59.577 45.455 0.00 0.00 41.59 4.75
402 567 2.814280 TTCTCCACCGTCAACTCTTC 57.186 50.000 0.00 0.00 0.00 2.87
403 568 1.699730 TCTCCACCGTCAACTCTTCA 58.300 50.000 0.00 0.00 0.00 3.02
436 601 5.389516 GCAGTAACACAACATGTACTGTAGC 60.390 44.000 20.01 12.79 42.31 3.58
632 798 3.741344 CACTGTCCTGTAAGTACTTGCAC 59.259 47.826 20.78 12.77 32.01 4.57
633 799 3.386726 ACTGTCCTGTAAGTACTTGCACA 59.613 43.478 20.78 16.16 32.01 4.57
634 800 3.724374 TGTCCTGTAAGTACTTGCACAC 58.276 45.455 20.78 18.89 32.01 3.82
635 801 3.386726 TGTCCTGTAAGTACTTGCACACT 59.613 43.478 20.78 0.00 32.01 3.55
636 802 3.741344 GTCCTGTAAGTACTTGCACACTG 59.259 47.826 20.78 11.90 32.01 3.66
637 803 2.480419 CCTGTAAGTACTTGCACACTGC 59.520 50.000 20.78 0.00 45.29 4.40
664 830 3.339253 TGCCCTGCACTGCATATATAG 57.661 47.619 3.64 0.00 38.13 1.31
674 840 7.495055 TGCACTGCATATATAGTATCTCCATG 58.505 38.462 0.00 0.00 31.71 3.66
697 1002 4.893424 AGTACAATCGTTGCAACAACTT 57.107 36.364 28.01 14.98 0.00 2.66
706 1011 6.281848 TCGTTGCAACAACTTCTTACTAAG 57.718 37.500 28.01 7.60 0.00 2.18
707 1012 5.813672 TCGTTGCAACAACTTCTTACTAAGT 59.186 36.000 28.01 0.00 41.46 2.24
750 1058 8.986477 AGCAGAAAAATGTCAAACATATAACC 57.014 30.769 0.00 0.00 37.97 2.85
818 1144 1.217942 ACAAAGGAAACCCAGGAAGCT 59.782 47.619 0.00 0.00 0.00 3.74
1014 1381 3.385115 AGAGGATATGGAAACGGAGGTT 58.615 45.455 0.00 0.00 38.22 3.50
1061 1428 1.220206 CCATCCACTTCTCGCTGCT 59.780 57.895 0.00 0.00 0.00 4.24
1119 1492 1.002134 CTCCTTCGGCAACCCACAT 60.002 57.895 0.00 0.00 0.00 3.21
1236 1609 1.002134 CCTCACCAAGGCCGACATT 60.002 57.895 0.00 0.00 38.67 2.71
1299 1672 1.757731 GCTGGCCATGGGTGCAATA 60.758 57.895 15.13 0.00 0.00 1.90
1302 1675 0.032316 TGGCCATGGGTGCAATATGT 60.032 50.000 15.13 0.00 0.00 2.29
1374 1747 0.311790 CAGCGGTGTTTTGCATGTCT 59.688 50.000 6.41 0.00 0.00 3.41
1392 1765 2.369257 CTGTCATCGATGGTCCCGGG 62.369 65.000 24.61 16.85 0.00 5.73
1758 2131 2.122099 ACCAAGGTTCTCCGGGGT 60.122 61.111 0.00 0.00 39.16 4.95
2205 2578 2.233605 CTGGTGGTAATGTCGGCGGA 62.234 60.000 7.21 0.00 0.00 5.54
2350 2723 1.383664 TCCATGCTCCTCCCTCCAG 60.384 63.158 0.00 0.00 0.00 3.86
2636 3028 2.943036 AGGACGGTGTGGTATGTTTT 57.057 45.000 0.00 0.00 0.00 2.43
2659 3051 2.031120 ACCCACACCACATGACTTTTG 58.969 47.619 0.00 0.00 0.00 2.44
2694 3088 1.511613 TCCCAATAGAGGAGGCCTTG 58.488 55.000 6.77 0.00 31.76 3.61
2769 3173 5.056480 TGTATTGTTCTGACTCCTTGTGTG 58.944 41.667 0.00 0.00 0.00 3.82
2833 3251 8.135529 AGTTTTGCAACTTGTACTCCTATTTTC 58.864 33.333 0.00 0.00 40.66 2.29
2845 3264 4.141688 ACTCCTATTTTCCCTTGTCCGATC 60.142 45.833 0.00 0.00 0.00 3.69
2849 3271 1.263356 TTTCCCTTGTCCGATCGAGT 58.737 50.000 18.66 0.00 0.00 4.18
2852 3274 1.067142 TCCCTTGTCCGATCGAGTTTG 60.067 52.381 18.66 0.00 0.00 2.93
2854 3276 0.721718 CTTGTCCGATCGAGTTTGGC 59.278 55.000 18.66 0.63 0.00 4.52
2867 3289 0.531974 GTTTGGCTGACAGACGGTGA 60.532 55.000 6.65 0.00 0.00 4.02
2868 3290 0.396435 TTTGGCTGACAGACGGTGAT 59.604 50.000 6.65 0.00 0.00 3.06
2869 3291 0.037326 TTGGCTGACAGACGGTGATC 60.037 55.000 6.65 0.00 0.00 2.92
2928 3350 4.821589 GCCGGAGCGCTGCTACTT 62.822 66.667 26.78 0.00 39.88 2.24
2930 3352 3.558411 CGGAGCGCTGCTACTTGC 61.558 66.667 26.78 3.43 39.88 4.01
2943 3365 5.220491 GCTGCTACTTGCTAACTAACACATC 60.220 44.000 0.00 0.00 43.37 3.06
2955 3378 1.800805 AACACATCGGTCAAGAGCTG 58.199 50.000 0.00 0.00 0.00 4.24
2956 3379 0.671781 ACACATCGGTCAAGAGCTGC 60.672 55.000 0.00 0.00 0.00 5.25
2957 3380 1.078848 ACATCGGTCAAGAGCTGCC 60.079 57.895 0.00 0.00 0.00 4.85
2959 3382 0.392193 CATCGGTCAAGAGCTGCCTT 60.392 55.000 0.00 0.00 0.00 4.35
2961 3384 2.684843 CGGTCAAGAGCTGCCTTGC 61.685 63.158 19.53 15.56 42.34 4.01
2964 3387 1.367659 GTCAAGAGCTGCCTTGCTAG 58.632 55.000 19.53 0.00 44.17 3.42
2965 3388 0.979665 TCAAGAGCTGCCTTGCTAGT 59.020 50.000 19.53 0.00 44.17 2.57
2966 3389 1.085091 CAAGAGCTGCCTTGCTAGTG 58.915 55.000 14.78 0.00 44.17 2.74
2967 3390 0.979665 AAGAGCTGCCTTGCTAGTGA 59.020 50.000 0.00 0.00 44.17 3.41
2968 3391 0.248843 AGAGCTGCCTTGCTAGTGAC 59.751 55.000 0.00 0.00 44.17 3.67
2969 3392 0.036952 GAGCTGCCTTGCTAGTGACA 60.037 55.000 0.00 0.00 44.17 3.58
2970 3393 0.036577 AGCTGCCTTGCTAGTGACAG 60.037 55.000 0.00 5.96 42.10 3.51
2971 3394 1.023513 GCTGCCTTGCTAGTGACAGG 61.024 60.000 10.45 0.00 0.00 4.00
2972 3395 0.610174 CTGCCTTGCTAGTGACAGGA 59.390 55.000 0.00 0.00 0.00 3.86
2973 3396 0.610174 TGCCTTGCTAGTGACAGGAG 59.390 55.000 0.00 0.00 0.00 3.69
2974 3397 0.107945 GCCTTGCTAGTGACAGGAGG 60.108 60.000 0.00 0.00 0.00 4.30
2975 3398 1.270907 CCTTGCTAGTGACAGGAGGT 58.729 55.000 0.00 0.00 0.00 3.85
2976 3399 1.066573 CCTTGCTAGTGACAGGAGGTG 60.067 57.143 0.00 0.00 0.00 4.00
2977 3400 1.620819 CTTGCTAGTGACAGGAGGTGT 59.379 52.381 0.00 0.00 44.49 4.16
2980 3403 3.441101 TGCTAGTGACAGGAGGTGTATT 58.559 45.455 0.00 0.00 40.56 1.89
2981 3404 3.838317 TGCTAGTGACAGGAGGTGTATTT 59.162 43.478 0.00 0.00 40.56 1.40
2982 3405 4.286032 TGCTAGTGACAGGAGGTGTATTTT 59.714 41.667 0.00 0.00 40.56 1.82
2985 3408 7.048512 GCTAGTGACAGGAGGTGTATTTTATT 58.951 38.462 0.00 0.00 40.56 1.40
2986 3409 7.553044 GCTAGTGACAGGAGGTGTATTTTATTT 59.447 37.037 0.00 0.00 40.56 1.40
2987 3410 7.923414 AGTGACAGGAGGTGTATTTTATTTC 57.077 36.000 0.00 0.00 40.56 2.17
2988 3411 6.594159 AGTGACAGGAGGTGTATTTTATTTCG 59.406 38.462 0.00 0.00 40.56 3.46
2989 3412 5.878116 TGACAGGAGGTGTATTTTATTTCGG 59.122 40.000 0.00 0.00 40.56 4.30
2990 3413 4.638865 ACAGGAGGTGTATTTTATTTCGGC 59.361 41.667 0.00 0.00 37.75 5.54
2991 3414 4.638421 CAGGAGGTGTATTTTATTTCGGCA 59.362 41.667 0.00 0.00 0.00 5.69
2992 3415 4.881850 AGGAGGTGTATTTTATTTCGGCAG 59.118 41.667 0.00 0.00 0.00 4.85
2993 3416 4.036380 GGAGGTGTATTTTATTTCGGCAGG 59.964 45.833 0.00 0.00 0.00 4.85
2994 3417 4.595986 AGGTGTATTTTATTTCGGCAGGT 58.404 39.130 0.00 0.00 0.00 4.00
2995 3418 5.747342 AGGTGTATTTTATTTCGGCAGGTA 58.253 37.500 0.00 0.00 0.00 3.08
2996 3419 5.820947 AGGTGTATTTTATTTCGGCAGGTAG 59.179 40.000 0.00 0.00 0.00 3.18
2997 3420 5.505159 GGTGTATTTTATTTCGGCAGGTAGC 60.505 44.000 0.00 0.00 44.65 3.58
2998 3421 5.296035 GTGTATTTTATTTCGGCAGGTAGCT 59.704 40.000 0.00 0.00 44.79 3.32
3000 3423 5.914898 ATTTTATTTCGGCAGGTAGCTTT 57.085 34.783 0.00 0.00 44.79 3.51
3001 3424 7.553402 TGTATTTTATTTCGGCAGGTAGCTTTA 59.447 33.333 0.00 0.00 44.79 1.85
3003 3426 3.629142 ATTTCGGCAGGTAGCTTTACT 57.371 42.857 0.00 0.00 44.79 2.24
3005 3428 3.795623 TTCGGCAGGTAGCTTTACTAG 57.204 47.619 0.00 0.00 44.79 2.57
3018 3441 4.364860 GCTTTACTAGCTCCTGAGTAAGC 58.635 47.826 6.86 8.80 46.77 3.09
3019 3442 4.142138 GCTTTACTAGCTCCTGAGTAAGCA 60.142 45.833 15.86 2.96 46.77 3.91
3020 3443 5.624738 GCTTTACTAGCTCCTGAGTAAGCAA 60.625 44.000 15.86 2.47 46.77 3.91
3021 3444 5.584253 TTACTAGCTCCTGAGTAAGCAAG 57.416 43.478 3.21 0.00 41.06 4.01
3022 3445 3.436243 ACTAGCTCCTGAGTAAGCAAGT 58.564 45.455 6.81 0.00 41.06 3.16
3023 3446 3.835395 ACTAGCTCCTGAGTAAGCAAGTT 59.165 43.478 6.81 0.00 41.06 2.66
3024 3447 3.778954 AGCTCCTGAGTAAGCAAGTTT 57.221 42.857 6.81 0.00 41.06 2.66
3025 3448 4.891992 AGCTCCTGAGTAAGCAAGTTTA 57.108 40.909 6.81 0.00 41.06 2.01
3026 3449 4.826556 AGCTCCTGAGTAAGCAAGTTTAG 58.173 43.478 6.81 0.00 41.06 1.85
3027 3450 3.935828 GCTCCTGAGTAAGCAAGTTTAGG 59.064 47.826 0.00 0.00 38.42 2.69
3028 3451 4.322801 GCTCCTGAGTAAGCAAGTTTAGGA 60.323 45.833 0.00 0.00 38.42 2.94
3029 3452 5.407407 TCCTGAGTAAGCAAGTTTAGGAG 57.593 43.478 0.00 0.00 0.00 3.69
3030 3453 5.084519 TCCTGAGTAAGCAAGTTTAGGAGA 58.915 41.667 0.00 0.00 0.00 3.71
3031 3454 5.047235 TCCTGAGTAAGCAAGTTTAGGAGAC 60.047 44.000 0.00 0.00 0.00 3.36
3032 3455 5.148651 TGAGTAAGCAAGTTTAGGAGACC 57.851 43.478 0.00 0.00 0.00 3.85
3033 3456 4.591498 TGAGTAAGCAAGTTTAGGAGACCA 59.409 41.667 0.00 0.00 0.00 4.02
3034 3457 4.895961 AGTAAGCAAGTTTAGGAGACCAC 58.104 43.478 0.00 0.00 0.00 4.16
3035 3458 3.857157 AAGCAAGTTTAGGAGACCACA 57.143 42.857 0.00 0.00 0.00 4.17
3036 3459 4.373156 AAGCAAGTTTAGGAGACCACAT 57.627 40.909 0.00 0.00 0.00 3.21
3037 3460 3.679389 AGCAAGTTTAGGAGACCACATG 58.321 45.455 0.00 0.00 0.00 3.21
3038 3461 2.162408 GCAAGTTTAGGAGACCACATGC 59.838 50.000 0.00 0.00 0.00 4.06
3039 3462 3.679389 CAAGTTTAGGAGACCACATGCT 58.321 45.455 0.00 0.00 0.00 3.79
3040 3463 3.618690 AGTTTAGGAGACCACATGCTC 57.381 47.619 0.00 0.00 0.00 4.26
3041 3464 3.177228 AGTTTAGGAGACCACATGCTCT 58.823 45.455 0.00 0.00 0.00 4.09
3042 3465 3.584848 AGTTTAGGAGACCACATGCTCTT 59.415 43.478 0.00 0.00 0.00 2.85
3043 3466 3.616956 TTAGGAGACCACATGCTCTTG 57.383 47.619 0.00 0.00 0.00 3.02
3044 3467 1.649321 AGGAGACCACATGCTCTTGA 58.351 50.000 0.00 0.00 0.00 3.02
3045 3468 2.194859 AGGAGACCACATGCTCTTGAT 58.805 47.619 0.00 0.00 0.00 2.57
3046 3469 3.378512 AGGAGACCACATGCTCTTGATA 58.621 45.455 0.00 0.00 0.00 2.15
3047 3470 3.133721 AGGAGACCACATGCTCTTGATAC 59.866 47.826 0.00 0.00 0.00 2.24
3048 3471 3.133721 GGAGACCACATGCTCTTGATACT 59.866 47.826 0.00 0.00 0.00 2.12
3049 3472 4.342378 GGAGACCACATGCTCTTGATACTA 59.658 45.833 0.00 0.00 0.00 1.82
3050 3473 5.011533 GGAGACCACATGCTCTTGATACTAT 59.988 44.000 0.00 0.00 0.00 2.12
3051 3474 6.209589 GGAGACCACATGCTCTTGATACTATA 59.790 42.308 0.00 0.00 0.00 1.31
3052 3475 7.093552 GGAGACCACATGCTCTTGATACTATAT 60.094 40.741 0.00 0.00 0.00 0.86
3053 3476 7.609960 AGACCACATGCTCTTGATACTATATG 58.390 38.462 0.00 0.00 0.00 1.78
3054 3477 6.705302 ACCACATGCTCTTGATACTATATGG 58.295 40.000 0.00 0.00 0.00 2.74
3055 3478 6.498303 ACCACATGCTCTTGATACTATATGGA 59.502 38.462 0.00 0.00 0.00 3.41
3056 3479 7.040494 CCACATGCTCTTGATACTATATGGAG 58.960 42.308 0.00 0.00 0.00 3.86
3057 3480 6.534436 CACATGCTCTTGATACTATATGGAGC 59.466 42.308 0.00 0.00 43.14 4.70
3086 3510 5.880332 TGAGACTTTAGGTTACATGGCAATC 59.120 40.000 0.00 0.00 0.00 2.67
3097 3521 2.068915 TGGCAATCCAGCTCTGACA 58.931 52.632 0.00 0.00 37.47 3.58
3123 3547 6.166982 GCTGCTATTAGAAATAAGGATCCGT 58.833 40.000 5.98 5.61 0.00 4.69
3146 3581 3.628032 CGCGGAGAGATCCATATAAGCTA 59.372 47.826 0.00 0.00 0.00 3.32
3155 3590 9.040259 AGAGATCCATATAAGCTATGCAAACTA 57.960 33.333 0.00 0.00 0.00 2.24
3179 3614 7.466746 AGCTCATTTACTTAATTTTCTGGCA 57.533 32.000 0.00 0.00 0.00 4.92
3182 3617 7.274250 GCTCATTTACTTAATTTTCTGGCACTG 59.726 37.037 0.00 0.00 0.00 3.66
3199 3634 4.485163 GCACTGCCAAACTGGTTATTTAG 58.515 43.478 0.00 0.00 40.46 1.85
3202 3637 4.765339 ACTGCCAAACTGGTTATTTAGTCC 59.235 41.667 0.00 0.00 40.46 3.85
3214 3649 9.490379 CTGGTTATTTAGTCCGATATAAGCTTT 57.510 33.333 3.20 0.00 34.04 3.51
3221 3656 9.826574 TTTAGTCCGATATAAGCTTTACATTGT 57.173 29.630 3.20 0.00 0.00 2.71
3237 3672 2.107950 TTGTATGTTTGAGCCCTCGG 57.892 50.000 0.00 0.00 0.00 4.63
3244 3679 2.304761 TGTTTGAGCCCTCGGATTAGTT 59.695 45.455 0.00 0.00 0.00 2.24
3247 3682 1.906574 TGAGCCCTCGGATTAGTTTGT 59.093 47.619 0.00 0.00 0.00 2.83
3257 3692 5.475719 TCGGATTAGTTTGTGAGTAGGTTG 58.524 41.667 0.00 0.00 0.00 3.77
3264 3699 3.746045 TTGTGAGTAGGTTGTCTGTCC 57.254 47.619 0.00 0.00 0.00 4.02
3274 3709 3.330701 AGGTTGTCTGTCCATATGTTGGT 59.669 43.478 1.24 0.00 46.52 3.67
3294 3729 4.573201 TGGTGTTGCTAAGTAAGTGTTGTC 59.427 41.667 0.00 0.00 0.00 3.18
3295 3730 4.573201 GGTGTTGCTAAGTAAGTGTTGTCA 59.427 41.667 0.00 0.00 0.00 3.58
3296 3731 5.238650 GGTGTTGCTAAGTAAGTGTTGTCAT 59.761 40.000 0.00 0.00 0.00 3.06
3297 3732 6.363473 GTGTTGCTAAGTAAGTGTTGTCATC 58.637 40.000 0.00 0.00 0.00 2.92
3327 3762 5.515797 AGCGTTGCTACTTATCTGATACA 57.484 39.130 0.00 0.00 36.99 2.29
3328 3763 5.282510 AGCGTTGCTACTTATCTGATACAC 58.717 41.667 0.00 0.00 36.99 2.90
3340 3800 9.295825 ACTTATCTGATACACTAAGAGAGATGG 57.704 37.037 0.00 0.00 0.00 3.51
3362 3822 2.777832 GTGAAACTCCTCTCTGCCAT 57.222 50.000 0.00 0.00 0.00 4.40
3363 3823 3.895232 GTGAAACTCCTCTCTGCCATA 57.105 47.619 0.00 0.00 0.00 2.74
3364 3824 3.791245 GTGAAACTCCTCTCTGCCATAG 58.209 50.000 0.00 0.00 0.00 2.23
3365 3825 3.196685 GTGAAACTCCTCTCTGCCATAGT 59.803 47.826 0.00 0.00 0.00 2.12
3366 3826 3.196469 TGAAACTCCTCTCTGCCATAGTG 59.804 47.826 0.00 0.00 0.00 2.74
3367 3827 1.118838 ACTCCTCTCTGCCATAGTGC 58.881 55.000 0.00 0.00 0.00 4.40
3368 3828 0.392336 CTCCTCTCTGCCATAGTGCC 59.608 60.000 0.00 0.00 0.00 5.01
3369 3829 0.325577 TCCTCTCTGCCATAGTGCCA 60.326 55.000 0.00 0.00 0.00 4.92
3370 3830 0.763652 CCTCTCTGCCATAGTGCCAT 59.236 55.000 0.00 0.00 0.00 4.40
3371 3831 1.973515 CCTCTCTGCCATAGTGCCATA 59.026 52.381 0.00 0.00 0.00 2.74
3372 3832 2.289320 CCTCTCTGCCATAGTGCCATAC 60.289 54.545 0.00 0.00 0.00 2.39
3388 3848 1.135689 CATACGTTGCACTTTCCAGGC 60.136 52.381 0.00 0.00 0.00 4.85
3395 3855 1.142870 TGCACTTTCCAGGCACTTACT 59.857 47.619 0.00 0.00 34.60 2.24
3401 3861 0.320374 TCCAGGCACTTACTTCACCG 59.680 55.000 0.00 0.00 34.60 4.94
3418 3878 3.005472 TCACCGAAGTCCAAAGTGTAGAG 59.995 47.826 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 7.724061 ACCAATTGACCAAAGTTTAGAGTACAT 59.276 33.333 7.12 0.00 0.00 2.29
73 74 6.833933 AGAACCAATTGACCAAAGTTTAGAGT 59.166 34.615 7.12 0.00 0.00 3.24
82 83 3.117322 TGGGAGAGAACCAATTGACCAAA 60.117 43.478 7.12 0.00 34.44 3.28
135 297 9.022884 AGACGGAGAAAGTAGTAATTAAGACTT 57.977 33.333 7.23 7.23 33.60 3.01
213 375 9.342308 CCCAAGCTTATCTCTTAAATGAATGTA 57.658 33.333 0.00 0.00 0.00 2.29
214 376 8.055181 TCCCAAGCTTATCTCTTAAATGAATGT 58.945 33.333 0.00 0.00 0.00 2.71
215 377 8.348507 GTCCCAAGCTTATCTCTTAAATGAATG 58.651 37.037 0.00 0.00 0.00 2.67
216 378 8.055181 TGTCCCAAGCTTATCTCTTAAATGAAT 58.945 33.333 0.00 0.00 0.00 2.57
217 379 7.402054 TGTCCCAAGCTTATCTCTTAAATGAA 58.598 34.615 0.00 0.00 0.00 2.57
218 380 6.957631 TGTCCCAAGCTTATCTCTTAAATGA 58.042 36.000 0.00 0.00 0.00 2.57
219 381 7.630242 TTGTCCCAAGCTTATCTCTTAAATG 57.370 36.000 0.00 0.00 0.00 2.32
220 382 7.890655 AGTTTGTCCCAAGCTTATCTCTTAAAT 59.109 33.333 0.00 0.00 0.00 1.40
221 383 7.231467 AGTTTGTCCCAAGCTTATCTCTTAAA 58.769 34.615 0.00 0.00 0.00 1.52
222 384 6.779860 AGTTTGTCCCAAGCTTATCTCTTAA 58.220 36.000 0.00 0.00 0.00 1.85
223 385 6.374417 AGTTTGTCCCAAGCTTATCTCTTA 57.626 37.500 0.00 0.00 0.00 2.10
224 386 5.248380 AGTTTGTCCCAAGCTTATCTCTT 57.752 39.130 0.00 0.00 0.00 2.85
225 387 4.917906 AGTTTGTCCCAAGCTTATCTCT 57.082 40.909 0.00 0.00 0.00 3.10
226 388 5.966742 AAAGTTTGTCCCAAGCTTATCTC 57.033 39.130 0.00 0.00 0.00 2.75
227 389 6.731292 AAAAAGTTTGTCCCAAGCTTATCT 57.269 33.333 0.00 0.00 0.00 1.98
247 409 2.716424 ACTCCCTCCATCTGTCCAAAAA 59.284 45.455 0.00 0.00 0.00 1.94
248 410 2.348472 ACTCCCTCCATCTGTCCAAAA 58.652 47.619 0.00 0.00 0.00 2.44
249 411 2.044793 ACTCCCTCCATCTGTCCAAA 57.955 50.000 0.00 0.00 0.00 3.28
250 412 2.467880 GTACTCCCTCCATCTGTCCAA 58.532 52.381 0.00 0.00 0.00 3.53
251 413 1.343075 GGTACTCCCTCCATCTGTCCA 60.343 57.143 0.00 0.00 0.00 4.02
252 414 1.343075 TGGTACTCCCTCCATCTGTCC 60.343 57.143 0.00 0.00 0.00 4.02
253 415 2.035632 CTGGTACTCCCTCCATCTGTC 58.964 57.143 0.00 0.00 33.01 3.51
254 416 1.967274 GCTGGTACTCCCTCCATCTGT 60.967 57.143 0.00 0.00 33.01 3.41
255 417 0.755686 GCTGGTACTCCCTCCATCTG 59.244 60.000 0.00 0.00 33.01 2.90
256 418 0.639392 AGCTGGTACTCCCTCCATCT 59.361 55.000 0.00 0.00 33.01 2.90
257 419 2.243810 CTAGCTGGTACTCCCTCCATC 58.756 57.143 0.00 0.00 33.01 3.51
258 420 1.759562 GCTAGCTGGTACTCCCTCCAT 60.760 57.143 7.70 0.00 33.01 3.41
259 421 0.397254 GCTAGCTGGTACTCCCTCCA 60.397 60.000 7.70 0.00 0.00 3.86
260 422 1.116536 GGCTAGCTGGTACTCCCTCC 61.117 65.000 15.72 0.00 0.00 4.30
261 423 1.457009 CGGCTAGCTGGTACTCCCTC 61.457 65.000 16.30 0.00 0.00 4.30
262 424 1.455959 CGGCTAGCTGGTACTCCCT 60.456 63.158 16.30 0.00 0.00 4.20
263 425 3.130227 CGGCTAGCTGGTACTCCC 58.870 66.667 16.30 0.00 0.00 4.30
264 426 2.417936 GCGGCTAGCTGGTACTCC 59.582 66.667 24.73 3.25 44.04 3.85
277 439 1.876322 ATCAAGATCTAGCTTGCGGC 58.124 50.000 0.00 0.00 43.78 6.53
309 471 8.967918 AGCAGTAGTTGTAATATTCTGTGAGTA 58.032 33.333 0.00 0.00 0.00 2.59
310 472 7.841956 AGCAGTAGTTGTAATATTCTGTGAGT 58.158 34.615 0.00 0.00 0.00 3.41
311 473 9.239002 GTAGCAGTAGTTGTAATATTCTGTGAG 57.761 37.037 0.00 0.00 0.00 3.51
312 474 8.195436 GGTAGCAGTAGTTGTAATATTCTGTGA 58.805 37.037 0.00 0.00 0.00 3.58
313 475 7.979537 TGGTAGCAGTAGTTGTAATATTCTGTG 59.020 37.037 0.00 0.00 0.00 3.66
314 476 7.980099 GTGGTAGCAGTAGTTGTAATATTCTGT 59.020 37.037 0.00 0.00 0.00 3.41
315 477 7.979537 TGTGGTAGCAGTAGTTGTAATATTCTG 59.020 37.037 0.00 0.00 0.00 3.02
316 478 8.074613 TGTGGTAGCAGTAGTTGTAATATTCT 57.925 34.615 0.00 0.00 0.00 2.40
317 479 8.354011 CTGTGGTAGCAGTAGTTGTAATATTC 57.646 38.462 0.00 0.00 0.00 1.75
340 502 0.308068 GCACATGCATGAGCTAGCTG 59.692 55.000 33.28 20.55 40.51 4.24
364 529 8.034804 GTGGAGAAATGTTAATTTGCCTATTGT 58.965 33.333 0.00 0.00 36.10 2.71
373 538 6.264518 AGTTGACGGTGGAGAAATGTTAATTT 59.735 34.615 0.00 0.00 38.74 1.82
402 567 1.398739 TGTGTTACTGCAAACCGTGTG 59.601 47.619 0.00 0.00 0.00 3.82
403 568 1.740297 TGTGTTACTGCAAACCGTGT 58.260 45.000 0.00 0.00 0.00 4.49
636 802 3.654027 TGCAGTGCAGGGCATTATATGC 61.654 50.000 15.37 3.09 43.94 3.14
637 803 2.232399 TGCAGTGCAGGGCATTATATG 58.768 47.619 15.37 0.00 41.91 1.78
638 804 2.662535 TGCAGTGCAGGGCATTATAT 57.337 45.000 15.37 0.00 41.91 0.86
664 830 6.144080 GCAACGATTGTACTACATGGAGATAC 59.856 42.308 13.29 10.87 0.00 2.24
674 840 5.338614 AGTTGTTGCAACGATTGTACTAC 57.661 39.130 22.15 7.19 0.00 2.73
735 1043 7.040132 TGCACATCTTTGGTTATATGTTTGACA 60.040 33.333 0.00 0.00 30.32 3.58
750 1058 6.954616 TGCTCAAATTAATGCACATCTTTG 57.045 33.333 0.00 0.00 0.00 2.77
818 1144 0.525761 GCAGCTTCGGTTTGGCATAA 59.474 50.000 0.00 0.00 0.00 1.90
1048 1415 2.031516 CCACCAGCAGCGAGAAGTG 61.032 63.158 0.00 0.00 0.00 3.16
1061 1428 0.394192 CTTGTGCTCAGAGTCCACCA 59.606 55.000 0.00 0.00 0.00 4.17
1119 1492 3.733344 GAGGTGGAAGGCGCGCATA 62.733 63.158 34.42 8.31 0.00 3.14
1296 1669 1.215423 GGGCCAAGGAGGTCACATATT 59.785 52.381 4.39 0.00 46.80 1.28
1299 1672 2.971598 CGGGCCAAGGAGGTCACAT 61.972 63.158 4.39 0.00 46.80 3.21
1320 1693 1.012486 CGAGGAAGGCACAACCGTAC 61.012 60.000 0.00 0.00 46.52 3.67
1374 1747 2.431454 CCCGGGACCATCGATGACA 61.431 63.158 26.86 0.00 0.00 3.58
1392 1765 3.368531 GGAAGCGGATAGTGATGTATCCC 60.369 52.174 4.65 0.00 44.06 3.85
1758 2131 4.902308 CGATAGTTGGTGACGGCA 57.098 55.556 0.00 0.00 0.00 5.69
2166 2539 0.463295 CACCGCTCATGCCAGAGATT 60.463 55.000 6.68 0.00 37.87 2.40
2205 2578 1.366319 AGAGGAATTGTGTGAGCCCT 58.634 50.000 0.00 0.00 0.00 5.19
2636 3028 1.059584 AGTCATGTGGTGTGGGTGGA 61.060 55.000 0.00 0.00 0.00 4.02
2659 3051 1.191535 GGGATTTTGGTAAGTGCCCC 58.808 55.000 0.00 0.00 0.00 5.80
2694 3088 1.839424 ACAAGCCCTTATTGCAGACC 58.161 50.000 0.00 0.00 0.00 3.85
2748 3151 5.290493 ACACACAAGGAGTCAGAACAATA 57.710 39.130 0.00 0.00 0.00 1.90
2760 3163 5.701224 AGGAAATTTAAGGACACACAAGGA 58.299 37.500 0.00 0.00 0.00 3.36
2769 3173 6.280643 AGTGCACAAAAGGAAATTTAAGGAC 58.719 36.000 21.04 0.00 0.00 3.85
2833 3251 1.359848 CAAACTCGATCGGACAAGGG 58.640 55.000 16.41 0.18 0.00 3.95
2845 3264 1.284982 CCGTCTGTCAGCCAAACTCG 61.285 60.000 0.00 0.00 0.00 4.18
2849 3271 0.396435 ATCACCGTCTGTCAGCCAAA 59.604 50.000 0.00 0.00 0.00 3.28
2852 3274 0.737715 GTGATCACCGTCTGTCAGCC 60.738 60.000 15.31 0.00 0.00 4.85
2854 3276 2.732412 AAGTGATCACCGTCTGTCAG 57.268 50.000 22.21 0.00 0.00 3.51
2867 3289 7.956328 TCATGTAGTACTACTCCAAAGTGAT 57.044 36.000 28.56 11.55 36.92 3.06
2868 3290 7.450634 AGTTCATGTAGTACTACTCCAAAGTGA 59.549 37.037 28.56 18.18 36.92 3.41
2869 3291 7.542477 CAGTTCATGTAGTACTACTCCAAAGTG 59.458 40.741 28.56 23.09 36.92 3.16
2928 3350 3.945981 TGACCGATGTGTTAGTTAGCA 57.054 42.857 0.00 0.00 0.00 3.49
2930 3352 4.563184 GCTCTTGACCGATGTGTTAGTTAG 59.437 45.833 0.00 0.00 0.00 2.34
2943 3365 2.684843 GCAAGGCAGCTCTTGACCG 61.685 63.158 21.34 2.47 44.98 4.79
2955 3378 0.107945 CCTCCTGTCACTAGCAAGGC 60.108 60.000 0.00 0.00 0.00 4.35
2956 3379 1.066573 CACCTCCTGTCACTAGCAAGG 60.067 57.143 0.00 0.00 0.00 3.61
2957 3380 1.620819 ACACCTCCTGTCACTAGCAAG 59.379 52.381 0.00 0.00 0.00 4.01
2959 3382 2.597578 TACACCTCCTGTCACTAGCA 57.402 50.000 0.00 0.00 33.91 3.49
2961 3384 9.099454 GAAATAAAATACACCTCCTGTCACTAG 57.901 37.037 0.00 0.00 33.91 2.57
2962 3385 7.762615 CGAAATAAAATACACCTCCTGTCACTA 59.237 37.037 0.00 0.00 33.91 2.74
2964 3387 6.183360 CCGAAATAAAATACACCTCCTGTCAC 60.183 42.308 0.00 0.00 33.91 3.67
2965 3388 5.878116 CCGAAATAAAATACACCTCCTGTCA 59.122 40.000 0.00 0.00 33.91 3.58
2966 3389 5.220796 GCCGAAATAAAATACACCTCCTGTC 60.221 44.000 0.00 0.00 33.91 3.51
2967 3390 4.638865 GCCGAAATAAAATACACCTCCTGT 59.361 41.667 0.00 0.00 36.82 4.00
2968 3391 4.638421 TGCCGAAATAAAATACACCTCCTG 59.362 41.667 0.00 0.00 0.00 3.86
2969 3392 4.850680 TGCCGAAATAAAATACACCTCCT 58.149 39.130 0.00 0.00 0.00 3.69
2970 3393 4.036380 CCTGCCGAAATAAAATACACCTCC 59.964 45.833 0.00 0.00 0.00 4.30
2971 3394 4.638865 ACCTGCCGAAATAAAATACACCTC 59.361 41.667 0.00 0.00 0.00 3.85
2972 3395 4.595986 ACCTGCCGAAATAAAATACACCT 58.404 39.130 0.00 0.00 0.00 4.00
2973 3396 4.976224 ACCTGCCGAAATAAAATACACC 57.024 40.909 0.00 0.00 0.00 4.16
2974 3397 5.296035 AGCTACCTGCCGAAATAAAATACAC 59.704 40.000 0.00 0.00 44.23 2.90
2975 3398 5.433526 AGCTACCTGCCGAAATAAAATACA 58.566 37.500 0.00 0.00 44.23 2.29
2976 3399 6.373186 AAGCTACCTGCCGAAATAAAATAC 57.627 37.500 0.00 0.00 44.23 1.89
2977 3400 7.771826 AGTAAAGCTACCTGCCGAAATAAAATA 59.228 33.333 0.00 0.00 44.23 1.40
2980 3403 5.493809 AGTAAAGCTACCTGCCGAAATAAA 58.506 37.500 0.00 0.00 44.23 1.40
2981 3404 5.093849 AGTAAAGCTACCTGCCGAAATAA 57.906 39.130 0.00 0.00 44.23 1.40
2982 3405 4.748277 AGTAAAGCTACCTGCCGAAATA 57.252 40.909 0.00 0.00 44.23 1.40
2985 3408 3.795623 CTAGTAAAGCTACCTGCCGAA 57.204 47.619 0.00 0.00 44.23 4.30
2997 3420 5.584253 TGCTTACTCAGGAGCTAGTAAAG 57.416 43.478 7.93 4.62 37.65 1.85
2998 3421 5.967088 CTTGCTTACTCAGGAGCTAGTAAA 58.033 41.667 7.93 0.00 37.65 2.01
3001 3424 3.436243 ACTTGCTTACTCAGGAGCTAGT 58.564 45.455 11.68 11.68 45.52 2.57
3003 3426 4.891992 AAACTTGCTTACTCAGGAGCTA 57.108 40.909 4.21 0.00 39.60 3.32
3005 3428 3.935828 CCTAAACTTGCTTACTCAGGAGC 59.064 47.826 0.00 0.00 39.33 4.70
3006 3429 5.186021 TCTCCTAAACTTGCTTACTCAGGAG 59.814 44.000 12.81 12.81 46.11 3.69
3008 3431 5.172205 GTCTCCTAAACTTGCTTACTCAGG 58.828 45.833 0.00 0.00 0.00 3.86
3010 3433 4.591498 TGGTCTCCTAAACTTGCTTACTCA 59.409 41.667 0.00 0.00 0.00 3.41
3012 3435 4.347000 TGTGGTCTCCTAAACTTGCTTACT 59.653 41.667 0.00 0.00 0.00 2.24
3013 3436 4.638304 TGTGGTCTCCTAAACTTGCTTAC 58.362 43.478 0.00 0.00 0.00 2.34
3014 3437 4.967084 TGTGGTCTCCTAAACTTGCTTA 57.033 40.909 0.00 0.00 0.00 3.09
3015 3438 3.857157 TGTGGTCTCCTAAACTTGCTT 57.143 42.857 0.00 0.00 0.00 3.91
3016 3439 3.679389 CATGTGGTCTCCTAAACTTGCT 58.321 45.455 0.00 0.00 0.00 3.91
3017 3440 2.162408 GCATGTGGTCTCCTAAACTTGC 59.838 50.000 0.00 0.00 36.80 4.01
3018 3441 3.679389 AGCATGTGGTCTCCTAAACTTG 58.321 45.455 0.00 0.00 0.00 3.16
3019 3442 3.944087 GAGCATGTGGTCTCCTAAACTT 58.056 45.455 5.03 0.00 39.31 2.66
3020 3443 3.618690 GAGCATGTGGTCTCCTAAACT 57.381 47.619 5.03 0.00 39.31 2.66
3029 3452 6.815641 CCATATAGTATCAAGAGCATGTGGTC 59.184 42.308 4.11 4.11 42.47 4.02
3030 3453 6.498303 TCCATATAGTATCAAGAGCATGTGGT 59.502 38.462 0.00 0.00 0.00 4.16
3031 3454 6.939622 TCCATATAGTATCAAGAGCATGTGG 58.060 40.000 0.00 0.00 0.00 4.17
3032 3455 6.534436 GCTCCATATAGTATCAAGAGCATGTG 59.466 42.308 17.17 0.00 43.62 3.21
3033 3456 6.638610 GCTCCATATAGTATCAAGAGCATGT 58.361 40.000 17.17 0.00 43.62 3.21
3037 3460 5.415221 GGTGCTCCATATAGTATCAAGAGC 58.585 45.833 15.99 15.99 44.25 4.09
3038 3461 5.184096 ACGGTGCTCCATATAGTATCAAGAG 59.816 44.000 5.52 0.00 0.00 2.85
3039 3462 5.048013 CACGGTGCTCCATATAGTATCAAGA 60.048 44.000 5.52 0.00 0.00 3.02
3040 3463 5.048013 TCACGGTGCTCCATATAGTATCAAG 60.048 44.000 2.51 0.00 0.00 3.02
3041 3464 4.830600 TCACGGTGCTCCATATAGTATCAA 59.169 41.667 2.51 0.00 0.00 2.57
3042 3465 4.403734 TCACGGTGCTCCATATAGTATCA 58.596 43.478 2.51 0.00 0.00 2.15
3043 3466 4.700692 TCTCACGGTGCTCCATATAGTATC 59.299 45.833 2.51 0.00 0.00 2.24
3044 3467 4.459685 GTCTCACGGTGCTCCATATAGTAT 59.540 45.833 2.51 0.00 0.00 2.12
3045 3468 3.819337 GTCTCACGGTGCTCCATATAGTA 59.181 47.826 2.51 0.00 0.00 1.82
3046 3469 2.623889 GTCTCACGGTGCTCCATATAGT 59.376 50.000 2.51 0.00 0.00 2.12
3047 3470 2.887783 AGTCTCACGGTGCTCCATATAG 59.112 50.000 2.51 0.00 0.00 1.31
3048 3471 2.945456 AGTCTCACGGTGCTCCATATA 58.055 47.619 2.51 0.00 0.00 0.86
3049 3472 1.781786 AGTCTCACGGTGCTCCATAT 58.218 50.000 2.51 0.00 0.00 1.78
3050 3473 1.557099 AAGTCTCACGGTGCTCCATA 58.443 50.000 2.51 0.00 0.00 2.74
3051 3474 0.687354 AAAGTCTCACGGTGCTCCAT 59.313 50.000 2.51 0.00 0.00 3.41
3052 3475 1.272490 CTAAAGTCTCACGGTGCTCCA 59.728 52.381 2.51 0.00 0.00 3.86
3053 3476 1.404315 CCTAAAGTCTCACGGTGCTCC 60.404 57.143 2.51 0.00 0.00 4.70
3054 3477 1.272769 ACCTAAAGTCTCACGGTGCTC 59.727 52.381 2.51 0.00 0.00 4.26
3055 3478 1.339097 ACCTAAAGTCTCACGGTGCT 58.661 50.000 2.51 0.00 0.00 4.40
3056 3479 2.165319 AACCTAAAGTCTCACGGTGC 57.835 50.000 2.51 0.00 0.00 5.01
3057 3480 4.247267 TGTAACCTAAAGTCTCACGGTG 57.753 45.455 0.56 0.56 0.00 4.94
3058 3481 4.322499 CCATGTAACCTAAAGTCTCACGGT 60.322 45.833 0.00 0.00 0.00 4.83
3096 3520 6.091441 GGATCCTTATTTCTAATAGCAGCGTG 59.909 42.308 3.84 0.00 0.00 5.34
3097 3521 6.166982 GGATCCTTATTTCTAATAGCAGCGT 58.833 40.000 3.84 0.00 0.00 5.07
3123 3547 2.423892 GCTTATATGGATCTCTCCGCGA 59.576 50.000 8.23 0.00 45.37 5.87
3155 3590 7.177392 AGTGCCAGAAAATTAAGTAAATGAGCT 59.823 33.333 0.00 0.00 0.00 4.09
3159 3594 7.281991 GCAGTGCCAGAAAATTAAGTAAATG 57.718 36.000 2.85 0.00 0.00 2.32
3179 3614 4.765339 GGACTAAATAACCAGTTTGGCAGT 59.235 41.667 0.00 0.00 42.67 4.40
3182 3617 4.004982 TCGGACTAAATAACCAGTTTGGC 58.995 43.478 0.00 0.00 42.67 4.52
3188 3623 9.490379 AAAGCTTATATCGGACTAAATAACCAG 57.510 33.333 0.00 0.00 0.00 4.00
3199 3634 9.204570 ACATACAATGTAAAGCTTATATCGGAC 57.795 33.333 0.00 0.00 42.78 4.79
3210 3645 5.102313 GGGCTCAAACATACAATGTAAAGC 58.898 41.667 0.00 10.42 44.07 3.51
3214 3649 4.188462 CGAGGGCTCAAACATACAATGTA 58.812 43.478 0.00 0.00 44.07 2.29
3217 3652 2.238646 TCCGAGGGCTCAAACATACAAT 59.761 45.455 0.00 0.00 0.00 2.71
3221 3656 3.709653 ACTAATCCGAGGGCTCAAACATA 59.290 43.478 0.00 0.00 0.00 2.29
3237 3672 6.929606 ACAGACAACCTACTCACAAACTAATC 59.070 38.462 0.00 0.00 0.00 1.75
3244 3679 3.035363 TGGACAGACAACCTACTCACAA 58.965 45.455 0.00 0.00 0.00 3.33
3247 3682 5.023452 ACATATGGACAGACAACCTACTCA 58.977 41.667 7.80 0.00 0.00 3.41
3264 3699 7.094805 ACACTTACTTAGCAACACCAACATATG 60.095 37.037 0.00 0.00 0.00 1.78
3274 3709 6.288294 AGATGACAACACTTACTTAGCAACA 58.712 36.000 0.00 0.00 0.00 3.33
3294 3729 6.648725 AAGTAGCAACGCTTTTAGTAGATG 57.351 37.500 0.00 0.00 40.44 2.90
3295 3730 8.414778 AGATAAGTAGCAACGCTTTTAGTAGAT 58.585 33.333 0.00 0.00 40.44 1.98
3296 3731 7.701078 CAGATAAGTAGCAACGCTTTTAGTAGA 59.299 37.037 0.00 0.00 40.44 2.59
3297 3732 7.701078 TCAGATAAGTAGCAACGCTTTTAGTAG 59.299 37.037 0.00 0.00 40.44 2.57
3306 3741 5.282510 AGTGTATCAGATAAGTAGCAACGC 58.717 41.667 0.00 0.00 0.00 4.84
3327 3762 6.071051 GGAGTTTCACTTCCATCTCTCTTAGT 60.071 42.308 0.00 0.00 0.00 2.24
3328 3763 6.154363 AGGAGTTTCACTTCCATCTCTCTTAG 59.846 42.308 0.00 0.00 0.00 2.18
3340 3800 2.037772 TGGCAGAGAGGAGTTTCACTTC 59.962 50.000 0.00 0.00 0.00 3.01
3365 3825 0.878416 GGAAAGTGCAACGTATGGCA 59.122 50.000 5.48 5.48 45.86 4.92
3366 3826 0.878416 TGGAAAGTGCAACGTATGGC 59.122 50.000 0.00 0.00 45.86 4.40
3367 3827 1.468520 CCTGGAAAGTGCAACGTATGG 59.531 52.381 0.00 0.00 45.86 2.74
3368 3828 1.135689 GCCTGGAAAGTGCAACGTATG 60.136 52.381 0.00 0.00 45.86 2.39
3369 3829 1.165270 GCCTGGAAAGTGCAACGTAT 58.835 50.000 0.00 0.00 45.86 3.06
3370 3830 0.179043 TGCCTGGAAAGTGCAACGTA 60.179 50.000 0.00 0.00 45.86 3.57
3371 3831 1.453015 TGCCTGGAAAGTGCAACGT 60.453 52.632 0.00 0.00 45.86 3.99
3372 3832 1.008538 GTGCCTGGAAAGTGCAACG 60.009 57.895 0.00 0.00 45.86 4.10
3395 3855 2.702592 ACACTTTGGACTTCGGTGAA 57.297 45.000 0.00 0.00 0.00 3.18
3401 3861 3.402628 TGGCTCTACACTTTGGACTTC 57.597 47.619 0.00 0.00 0.00 3.01
3418 3878 2.519013 AGGGTCAACTCTTTGAATGGC 58.481 47.619 0.00 0.00 43.52 4.40
3505 3965 4.042187 GGCTATAGATCACCCACCTTTCAT 59.958 45.833 3.21 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.