Multiple sequence alignment - TraesCS3B01G423600

Loading Multiple Alignment...

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 TraesCS3B01G423600 chr3B 100.000 5670 0 0 1 5670 661196312 661201981 0.000000e+00 10471.0
1 TraesCS3B01G423600 chr3D 93.242 4765 209 49 305 4999 499984244 499988965 0.000000e+00 6911.0
2 TraesCS3B01G423600 chr3D 91.909 309 18 3 1 305 499978619 499978924 5.250000e-115 425.0
3 TraesCS3B01G423600 chr3D 78.981 314 42 19 5234 5530 499989105 499989411 5.800000e-45 193.0
4 TraesCS3B01G423600 chr3D 92.000 50 4 0 5543 5592 507534148 507534197 2.830000e-08 71.3
5 TraesCS3B01G423600 chr3A 92.810 4798 232 58 305 5049 639478618 639483355 0.000000e+00 6844.0
6 TraesCS3B01G423600 chr3A 88.947 570 28 11 5115 5670 639483360 639483908 0.000000e+00 671.0
7 TraesCS3B01G423600 chr3A 83.013 312 35 9 1 305 639478238 639478538 3.370000e-67 267.0
8 TraesCS3B01G423600 chr7A 95.652 46 2 0 5547 5592 651990042 651989997 2.190000e-09 75.0
9 TraesCS3B01G423600 chr2B 93.478 46 2 1 5546 5591 735930848 735930804 3.670000e-07 67.6
10 TraesCS3B01G423600 chr4A 95.122 41 2 0 5551 5591 474726360 474726400 1.320000e-06 65.8
11 TraesCS3B01G423600 chr6A 95.000 40 0 2 5024 5062 455937819 455937781 1.710000e-05 62.1
12 TraesCS3B01G423600 chr2D 100.000 32 0 0 5024 5055 320284887 320284856 6.130000e-05 60.2
13 TraesCS3B01G423600 chr2A 100.000 31 0 0 5024 5054 733514139 733514169 2.210000e-04 58.4
14 TraesCS3B01G423600 chr6B 94.444 36 2 0 5028 5063 149484489 149484524 7.940000e-04 56.5


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 TraesCS3B01G423600 chr3B 661196312 661201981 5669 False 10471 10471 100.000000 1 5670 1 chr3B.!!$F1 5669
1 TraesCS3B01G423600 chr3D 499984244 499989411 5167 False 3552 6911 86.111500 305 5530 2 chr3D.!!$F3 5225
2 TraesCS3B01G423600 chr3A 639478238 639483908 5670 False 2594 6844 88.256667 1 5670 3 chr3A.!!$F1 5669

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
456 545 0.179059 TGACACACTGCAACATCCGT 60.179 50.000 0.00 0.0 0.0 4.69 F
976 1082 1.002274 GGAGAGGAAGGAGGGCTGA 59.998 63.158 0.00 0.0 0.0 4.26 F
1748 1872 0.530744 ATTCAGAGCGCGTAGTTCCA 59.469 50.000 8.43 0.0 0.0 3.53 F
1751 1875 0.666274 CAGAGCGCGTAGTTCCAACA 60.666 55.000 8.43 0.0 0.0 3.33 F
3331 3506 0.038166 AATGAGTTCCCGCCATGTGT 59.962 50.000 0.00 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1325 1440 0.169672 TCGATCGACAAGGTCCGAAC 59.830 55.0 15.15 0.0 38.36 3.95 R
2327 2463 1.131638 ACAGAGTGGAGCAGTTTGGA 58.868 50.0 0.00 0.0 0.00 3.53 R
3305 3480 0.527565 GCGGGAACTCATTGCAACAT 59.472 50.0 0.00 0.0 0.00 2.71 R
3715 3893 0.841961 TCTCTGATGATGGCCCCTTG 59.158 55.0 0.00 0.0 0.00 3.61 R
5005 5185 0.042131 TTGTGGGACGGAGGGAGTAT 59.958 55.0 0.00 0.0 0.00 2.12 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
26 27 7.288810 TCAATCATGCCTCACTTAACTTTTT 57.711 32.000 0.00 0.00 0.00 1.94
46 47 3.706802 TTTTGTGTGTATGTGTGCTGG 57.293 42.857 0.00 0.00 0.00 4.85
47 48 2.629336 TTGTGTGTATGTGTGCTGGA 57.371 45.000 0.00 0.00 0.00 3.86
57 58 5.874810 TGTATGTGTGCTGGATTCTCTAAAC 59.125 40.000 0.00 0.00 0.00 2.01
58 59 3.325870 TGTGTGCTGGATTCTCTAAACG 58.674 45.455 0.00 0.00 0.00 3.60
61 62 3.244078 TGTGCTGGATTCTCTAAACGTGT 60.244 43.478 0.00 0.00 0.00 4.49
62 63 3.368236 GTGCTGGATTCTCTAAACGTGTC 59.632 47.826 0.00 0.00 0.00 3.67
76 77 5.392767 AAACGTGTCTCTGTCTATCACAT 57.607 39.130 0.00 0.00 33.23 3.21
84 85 9.291664 GTGTCTCTGTCTATCACATAGTTTTAC 57.708 37.037 0.00 0.00 33.23 2.01
142 143 2.459060 CCATGACATGGCAAAGCAAA 57.541 45.000 21.35 0.00 44.70 3.68
144 145 2.548280 CCATGACATGGCAAAGCAAACA 60.548 45.455 21.35 0.00 44.70 2.83
145 146 3.331150 CATGACATGGCAAAGCAAACAT 58.669 40.909 4.70 0.00 0.00 2.71
166 167 0.544223 CCCATGTTATCCGACACCCA 59.456 55.000 0.00 0.00 31.30 4.51
176 177 1.204467 TCCGACACCCATTACGTTACC 59.796 52.381 0.00 0.00 0.00 2.85
201 202 1.203125 TGGTTAAAGGGAGCTTTGGGG 60.203 52.381 0.00 0.00 0.00 4.96
207 208 2.015456 AGGGAGCTTTGGGGAAAAAG 57.985 50.000 0.00 0.00 39.66 2.27
211 212 3.230976 GGAGCTTTGGGGAAAAAGAAGA 58.769 45.455 0.99 0.00 39.12 2.87
227 228 7.468141 AAAAGAAGACAAGTTGAGGAAAACT 57.532 32.000 10.54 0.00 42.21 2.66
270 272 2.100879 GAGCCGGGCGAGATAATGGT 62.101 60.000 14.39 0.00 0.00 3.55
275 277 3.782046 CCGGGCGAGATAATGGTAATAG 58.218 50.000 0.00 0.00 0.00 1.73
280 282 5.411781 GGCGAGATAATGGTAATAGACTGG 58.588 45.833 0.00 0.00 0.00 4.00
281 283 5.047235 GGCGAGATAATGGTAATAGACTGGT 60.047 44.000 0.00 0.00 0.00 4.00
282 284 6.456501 GCGAGATAATGGTAATAGACTGGTT 58.543 40.000 0.00 0.00 0.00 3.67
285 287 9.326413 CGAGATAATGGTAATAGACTGGTTTTT 57.674 33.333 0.00 0.00 0.00 1.94
337 425 8.084985 TGATTGTATAAACATACCTGGACTCA 57.915 34.615 0.00 0.00 34.97 3.41
338 426 8.544622 TGATTGTATAAACATACCTGGACTCAA 58.455 33.333 0.00 0.00 34.97 3.02
420 509 4.853924 AATCTCATCACAACAACAACCC 57.146 40.909 0.00 0.00 0.00 4.11
424 513 1.107114 ATCACAACAACAACCCGCAA 58.893 45.000 0.00 0.00 0.00 4.85
439 528 1.735018 CCGCAAACATACATCGGTTGA 59.265 47.619 0.00 0.00 35.75 3.18
446 535 3.325870 ACATACATCGGTTGACACACTG 58.674 45.455 0.00 0.00 0.00 3.66
456 545 0.179059 TGACACACTGCAACATCCGT 60.179 50.000 0.00 0.00 0.00 4.69
462 551 2.497675 ACACTGCAACATCCGTCTATCT 59.502 45.455 0.00 0.00 0.00 1.98
501 590 3.453717 TGCATCTACAGAATTCAGCCTCT 59.546 43.478 8.44 0.00 0.00 3.69
521 610 2.014010 ACATCCACCACCAAAGCATT 57.986 45.000 0.00 0.00 0.00 3.56
565 654 7.278868 GCACATTATACTCAGACAAACTTAGCT 59.721 37.037 0.00 0.00 0.00 3.32
615 704 4.783764 ACAACTTAACAAAGCCCTATGC 57.216 40.909 0.00 0.00 41.71 3.14
661 750 2.441001 ACATTCCCCAGCCATAGAGAAG 59.559 50.000 0.00 0.00 0.00 2.85
705 794 3.712907 GCCTCGCACCCCCACTTA 61.713 66.667 0.00 0.00 0.00 2.24
781 871 1.227999 TTGTTGGGCTCGCGAGAAAG 61.228 55.000 38.74 14.86 41.32 2.62
782 872 1.374252 GTTGGGCTCGCGAGAAAGA 60.374 57.895 38.74 18.28 41.32 2.52
783 873 1.079819 TTGGGCTCGCGAGAAAGAG 60.080 57.895 38.74 13.63 41.32 2.85
784 874 1.532604 TTGGGCTCGCGAGAAAGAGA 61.533 55.000 38.74 15.77 41.32 3.10
785 875 1.215647 GGGCTCGCGAGAAAGAGAA 59.784 57.895 38.74 0.00 41.32 2.87
911 1017 2.677875 CTTTGCCTCCCACTGCCC 60.678 66.667 0.00 0.00 0.00 5.36
973 1079 1.764454 GAGGGAGAGGAAGGAGGGC 60.764 68.421 0.00 0.00 0.00 5.19
974 1080 2.250635 GAGGGAGAGGAAGGAGGGCT 62.251 65.000 0.00 0.00 0.00 5.19
976 1082 1.002274 GGAGAGGAAGGAGGGCTGA 59.998 63.158 0.00 0.00 0.00 4.26
977 1083 1.048160 GGAGAGGAAGGAGGGCTGAG 61.048 65.000 0.00 0.00 0.00 3.35
978 1084 1.685355 GAGAGGAAGGAGGGCTGAGC 61.685 65.000 0.00 0.00 0.00 4.26
979 1085 3.080121 AGGAAGGAGGGCTGAGCG 61.080 66.667 0.00 0.00 0.00 5.03
1182 1288 3.127352 CTACGCTGTCGCCTCCTCC 62.127 68.421 0.00 0.00 39.84 4.30
1183 1289 3.640257 TACGCTGTCGCCTCCTCCT 62.640 63.158 0.00 0.00 39.84 3.69
1184 1290 4.200283 CGCTGTCGCCTCCTCCTC 62.200 72.222 0.00 0.00 0.00 3.71
1260 1366 8.145122 TGTTTAAATTACCCAGTGAAATTGGTC 58.855 33.333 0.00 0.00 43.16 4.02
1301 1414 1.604604 ATTACTGTGGGTGTGTGTGC 58.395 50.000 0.00 0.00 0.00 4.57
1325 1440 3.187227 CGTTCTGGAATTGAAGTGGACTG 59.813 47.826 0.00 0.00 0.00 3.51
1366 1481 2.286365 TTAGGCTGTTTGGGGAACTG 57.714 50.000 0.00 0.00 39.08 3.16
1384 1499 7.775561 GGGGAACTGTCTTTCATAGATTTGTAT 59.224 37.037 0.00 0.00 34.79 2.29
1385 1500 8.831550 GGGAACTGTCTTTCATAGATTTGTATC 58.168 37.037 0.00 0.00 34.79 2.24
1389 1504 9.553064 ACTGTCTTTCATAGATTTGTATCATCC 57.447 33.333 0.00 0.00 34.79 3.51
1445 1561 5.339177 TGTGTCTGTTTTTGCTTGTGTATG 58.661 37.500 0.00 0.00 0.00 2.39
1446 1562 5.105957 TGTGTCTGTTTTTGCTTGTGTATGT 60.106 36.000 0.00 0.00 0.00 2.29
1451 1567 7.113404 GTCTGTTTTTGCTTGTGTATGTATGTG 59.887 37.037 0.00 0.00 0.00 3.21
1494 1610 1.768684 GAGTGACTGGGTGGGAGCAA 61.769 60.000 0.00 0.00 0.00 3.91
1628 1746 2.235898 GGATGTCTTGCTTCTCCAGAGT 59.764 50.000 0.00 0.00 0.00 3.24
1632 1752 3.508012 TGTCTTGCTTCTCCAGAGTAGTC 59.492 47.826 3.64 0.00 0.00 2.59
1636 1756 1.133407 GCTTCTCCAGAGTAGTCGGTG 59.867 57.143 3.64 6.36 0.00 4.94
1642 1762 2.303890 TCCAGAGTAGTCGGTGTCACTA 59.696 50.000 2.35 0.00 0.00 2.74
1688 1808 2.408368 GGTGCTGCGTAATTTGCTTTTC 59.592 45.455 0.00 0.00 0.00 2.29
1739 1859 3.853671 CCACACATTAAAATTCAGAGCGC 59.146 43.478 0.00 0.00 0.00 5.92
1748 1872 0.530744 ATTCAGAGCGCGTAGTTCCA 59.469 50.000 8.43 0.00 0.00 3.53
1751 1875 0.666274 CAGAGCGCGTAGTTCCAACA 60.666 55.000 8.43 0.00 0.00 3.33
1807 1931 5.937540 TGTTATATTTCTGTGACACCAGTGG 59.062 40.000 7.91 7.91 34.02 4.00
1820 1944 3.249687 CAGTGGCTGGGGACTTTAC 57.750 57.895 0.00 0.00 0.00 2.01
1830 1954 1.474498 GGGGACTTTACGGGCTATGTG 60.474 57.143 0.00 0.00 0.00 3.21
1831 1955 1.296727 GGACTTTACGGGCTATGTGC 58.703 55.000 0.00 0.00 41.94 4.57
1849 1973 8.216453 GCTATGTGCAAAATTCAGTTTTAACAG 58.784 33.333 0.00 0.00 38.18 3.16
1870 1994 5.221461 ACAGACAGTACTTACCTGTCCTTTG 60.221 44.000 14.95 10.47 46.03 2.77
1872 1996 3.971971 ACAGTACTTACCTGTCCTTTGGT 59.028 43.478 0.00 0.00 40.12 3.67
1959 2089 5.695851 ATTAGCCTCTCTGTTTTGTGTTG 57.304 39.130 0.00 0.00 0.00 3.33
1992 2122 4.322650 GCAGAAACCATTTTTATGCCTCCA 60.323 41.667 5.27 0.00 34.19 3.86
1993 2123 5.170748 CAGAAACCATTTTTATGCCTCCAC 58.829 41.667 0.00 0.00 0.00 4.02
1994 2124 5.047092 CAGAAACCATTTTTATGCCTCCACT 60.047 40.000 0.00 0.00 0.00 4.00
1995 2125 5.185828 AGAAACCATTTTTATGCCTCCACTC 59.814 40.000 0.00 0.00 0.00 3.51
1996 2126 3.365472 ACCATTTTTATGCCTCCACTCC 58.635 45.455 0.00 0.00 0.00 3.85
2032 2165 2.421073 AGTCATGATGTTTGTGCGATGG 59.579 45.455 0.00 0.00 0.00 3.51
2088 2224 7.998580 ACTAAACTAGTTATCTACCTGCAGTC 58.001 38.462 13.81 0.00 34.86 3.51
2181 2317 2.430465 AGTGATGTCAACATGCCAGAC 58.570 47.619 0.00 0.00 36.57 3.51
2716 2852 5.570589 GCATCAGAAGTTTGTAAATGCTGTC 59.429 40.000 0.00 0.00 36.12 3.51
2758 2894 5.719173 AGTGAGTGCTCTCTGAAATCTAAC 58.281 41.667 16.23 3.65 40.98 2.34
2759 2895 5.244851 AGTGAGTGCTCTCTGAAATCTAACA 59.755 40.000 16.23 0.00 40.98 2.41
2760 2896 5.347364 GTGAGTGCTCTCTGAAATCTAACAC 59.653 44.000 16.23 0.00 40.98 3.32
2762 2898 5.858381 AGTGCTCTCTGAAATCTAACACAA 58.142 37.500 0.00 0.00 0.00 3.33
2858 3030 1.893137 GAAGTGGGGCCGAAGAAAATT 59.107 47.619 0.00 0.00 0.00 1.82
2926 3098 3.457380 AGCCATCTTCAGGTATGACATGT 59.543 43.478 0.00 0.00 34.35 3.21
2927 3099 4.655649 AGCCATCTTCAGGTATGACATGTA 59.344 41.667 0.00 0.00 34.35 2.29
3123 3295 7.194607 TGACAAATTTGTGCAACTTTGAAAA 57.805 28.000 27.85 12.46 40.92 2.29
3139 3311 3.899734 TGAAAATCACAAATCAGGCGTG 58.100 40.909 0.00 0.00 0.00 5.34
3144 3316 1.872952 TCACAAATCAGGCGTGTGAAG 59.127 47.619 6.26 0.00 46.43 3.02
3186 3359 9.461312 TTTATAATGTGATGCAGGTAGTTTCTT 57.539 29.630 0.00 0.00 0.00 2.52
3241 3416 5.297776 CACAAGATCACCTTTGTCAGAGTTT 59.702 40.000 0.00 0.00 31.42 2.66
3256 3431 4.466726 TCAGAGTTTCCCCTAGAAGTAAGC 59.533 45.833 0.00 0.00 35.40 3.09
3276 3451 2.420372 GCGAAAGGAGATTCTTGGTTCC 59.580 50.000 0.00 0.00 0.00 3.62
3290 3465 5.369833 TCTTGGTTCCGTAAATGACAGAAA 58.630 37.500 0.00 0.00 0.00 2.52
3331 3506 0.038166 AATGAGTTCCCGCCATGTGT 59.962 50.000 0.00 0.00 0.00 3.72
3339 3514 2.364632 TCCCGCCATGTGTATTCTTTG 58.635 47.619 0.00 0.00 0.00 2.77
3343 3518 2.223340 CGCCATGTGTATTCTTTGCCTC 60.223 50.000 0.00 0.00 0.00 4.70
3346 3521 4.264253 CCATGTGTATTCTTTGCCTCTGA 58.736 43.478 0.00 0.00 0.00 3.27
3372 3547 2.265367 TCATGGGTCAGGACAAAGCTA 58.735 47.619 1.41 0.00 0.00 3.32
3376 3551 3.244582 TGGGTCAGGACAAAGCTACTAA 58.755 45.455 1.41 0.00 0.00 2.24
3382 3557 6.599638 GGTCAGGACAAAGCTACTAATTGATT 59.400 38.462 2.16 0.00 0.00 2.57
3389 3564 9.722056 GACAAAGCTACTAATTGATTATTGGTG 57.278 33.333 2.16 0.00 38.28 4.17
3404 3579 2.145397 TGGTGGAGCTACTGTAGGAG 57.855 55.000 16.09 0.00 0.00 3.69
3409 3584 3.004944 GTGGAGCTACTGTAGGAGCATAC 59.995 52.174 17.81 9.58 41.36 2.39
3410 3585 3.117474 TGGAGCTACTGTAGGAGCATACT 60.117 47.826 17.81 3.15 41.36 2.12
3411 3586 3.892588 GGAGCTACTGTAGGAGCATACTT 59.107 47.826 17.81 0.00 41.36 2.24
3415 3590 6.109359 AGCTACTGTAGGAGCATACTTTTTG 58.891 40.000 17.81 0.00 41.36 2.44
3416 3591 6.070767 AGCTACTGTAGGAGCATACTTTTTGA 60.071 38.462 17.81 0.00 41.36 2.69
3418 3593 5.491982 ACTGTAGGAGCATACTTTTTGAGG 58.508 41.667 0.00 0.00 0.00 3.86
3420 3595 3.372440 AGGAGCATACTTTTTGAGGGG 57.628 47.619 0.00 0.00 0.00 4.79
3421 3596 1.751351 GGAGCATACTTTTTGAGGGGC 59.249 52.381 0.00 0.00 0.00 5.80
3422 3597 2.621668 GGAGCATACTTTTTGAGGGGCT 60.622 50.000 0.00 0.00 34.30 5.19
3424 3599 1.751351 GCATACTTTTTGAGGGGCTCC 59.249 52.381 0.00 0.00 0.00 4.70
3426 3601 3.701664 CATACTTTTTGAGGGGCTCCTT 58.298 45.455 6.58 0.00 45.05 3.36
3429 3604 2.224892 ACTTTTTGAGGGGCTCCTTCTC 60.225 50.000 6.58 0.00 45.05 2.87
3430 3605 1.444933 TTTTGAGGGGCTCCTTCTCA 58.555 50.000 6.58 0.00 45.05 3.27
3432 3607 1.207791 TTGAGGGGCTCCTTCTCATC 58.792 55.000 6.58 0.00 45.05 2.92
3433 3608 0.341258 TGAGGGGCTCCTTCTCATCT 59.659 55.000 6.58 0.00 45.05 2.90
3434 3609 1.047801 GAGGGGCTCCTTCTCATCTC 58.952 60.000 6.58 0.00 45.05 2.75
3435 3610 0.758685 AGGGGCTCCTTCTCATCTCG 60.759 60.000 0.00 0.00 41.56 4.04
3436 3611 1.045911 GGGGCTCCTTCTCATCTCGT 61.046 60.000 0.00 0.00 0.00 4.18
3442 3617 4.568760 GGCTCCTTCTCATCTCGTAAAAAG 59.431 45.833 0.00 0.00 0.00 2.27
3446 3621 5.639506 TCCTTCTCATCTCGTAAAAAGCTTG 59.360 40.000 0.00 0.00 0.00 4.01
3453 3628 4.987832 TCTCGTAAAAAGCTTGTTTGCAA 58.012 34.783 7.30 0.00 34.99 4.08
3537 3713 6.938030 ACAAATCCATGTGAATTTTGAAGCAT 59.062 30.769 12.98 0.00 32.88 3.79
3538 3714 7.118680 ACAAATCCATGTGAATTTTGAAGCATC 59.881 33.333 12.98 0.00 32.88 3.91
3540 3716 6.349243 TCCATGTGAATTTTGAAGCATCTT 57.651 33.333 0.00 0.00 0.00 2.40
3541 3717 7.465353 TCCATGTGAATTTTGAAGCATCTTA 57.535 32.000 0.00 0.00 0.00 2.10
3550 3726 5.437289 TTTGAAGCATCTTACCAACACTG 57.563 39.130 0.00 0.00 0.00 3.66
3554 3730 4.207891 AGCATCTTACCAACACTGTAGG 57.792 45.455 0.00 0.00 0.00 3.18
3560 3736 6.428083 TCTTACCAACACTGTAGGATTCAA 57.572 37.500 0.00 0.00 0.00 2.69
3623 3800 9.443323 TTCTGGTATTCATACGAAGAAAATTCA 57.557 29.630 9.60 0.00 35.51 2.57
3646 3824 5.673337 TTGTTATGCAGAAATATCGCCTC 57.327 39.130 0.00 0.00 0.00 4.70
3655 3833 3.967987 AGAAATATCGCCTCTACTTGGGT 59.032 43.478 0.00 0.00 0.00 4.51
3683 3861 1.239347 AAAGCAGAACGAGGAAAGGC 58.761 50.000 0.00 0.00 0.00 4.35
3686 3864 1.066787 AGCAGAACGAGGAAAGGCTAC 60.067 52.381 0.00 0.00 0.00 3.58
3715 3893 1.403323 GCTAGGCAAGATTTCAGCACC 59.597 52.381 0.00 0.00 0.00 5.01
3721 3899 1.547372 CAAGATTTCAGCACCAAGGGG 59.453 52.381 0.00 0.00 41.29 4.79
3832 4010 2.721971 AAGGCCAGAGCAGTGTGTCG 62.722 60.000 5.01 0.00 42.56 4.35
3844 4022 2.733552 CAGTGTGTCGGATTCTCAGTTG 59.266 50.000 0.00 0.00 0.00 3.16
3861 4039 1.327303 TTGGAAGAAACCAAGCGCAT 58.673 45.000 11.47 0.00 43.79 4.73
4153 4331 3.252284 CACCCCACTGCTCCTGGT 61.252 66.667 0.00 0.00 0.00 4.00
4162 4340 2.227388 CACTGCTCCTGGTCATTTGTTC 59.773 50.000 0.00 0.00 0.00 3.18
4171 4349 2.306847 GGTCATTTGTTCACACCACCT 58.693 47.619 0.00 0.00 0.00 4.00
4177 4355 1.961277 GTTCACACCACCTCCGCTG 60.961 63.158 0.00 0.00 0.00 5.18
4241 4419 0.323178 AGATGTGAAGCCAGCCCTTG 60.323 55.000 0.00 0.00 0.00 3.61
4264 4442 2.266554 GACTGCATCAAGTCCTTCTCG 58.733 52.381 0.00 0.00 40.66 4.04
4374 4552 1.880027 CAGTGTGGAAGGTTTGCCTAC 59.120 52.381 0.00 0.00 46.33 3.18
4633 4811 0.529773 ACTTCAGCAGCGAAACGACA 60.530 50.000 0.00 0.00 0.00 4.35
4642 4820 0.243095 GCGAAACGACAGACTACCCT 59.757 55.000 0.00 0.00 0.00 4.34
4674 4852 1.679139 TGCCTCTTTGCATAATCCCG 58.321 50.000 0.00 0.00 36.04 5.14
4914 5093 5.705441 TGGAGACTGTCGAATATTTGCTTTT 59.295 36.000 1.52 0.00 0.00 2.27
4915 5094 6.024049 GGAGACTGTCGAATATTTGCTTTTG 58.976 40.000 1.52 0.00 0.00 2.44
5005 5185 5.335583 GCACATCACAGGCAAACATAACTTA 60.336 40.000 0.00 0.00 0.00 2.24
5037 5217 4.684703 CCGTCCCACAAACGATCTTATATC 59.315 45.833 0.00 0.00 42.62 1.63
5049 5229 2.511659 TCTTATATCGTGGGACGGAGG 58.488 52.381 0.00 0.00 42.81 4.30
5050 5230 1.544691 CTTATATCGTGGGACGGAGGG 59.455 57.143 0.00 0.00 42.81 4.30
5051 5231 0.773014 TATATCGTGGGACGGAGGGA 59.227 55.000 0.00 0.00 42.81 4.20
5052 5232 0.539901 ATATCGTGGGACGGAGGGAG 60.540 60.000 0.00 0.00 42.81 4.30
5053 5233 1.929860 TATCGTGGGACGGAGGGAGT 61.930 60.000 0.00 0.00 42.81 3.85
5054 5234 1.929860 ATCGTGGGACGGAGGGAGTA 61.930 60.000 0.00 0.00 42.81 2.59
5055 5235 1.679977 CGTGGGACGGAGGGAGTAA 60.680 63.158 0.00 0.00 38.08 2.24
5068 5248 3.053826 AGGGAGTAAGTTTCAGGTTGGT 58.946 45.455 0.00 0.00 0.00 3.67
5072 5252 4.202326 GGAGTAAGTTTCAGGTTGGTCAGA 60.202 45.833 0.00 0.00 0.00 3.27
5092 5272 1.705745 ACAGGTTTCTTCTTCTCCCCC 59.294 52.381 0.00 0.00 0.00 5.40
5110 5290 4.436998 CGAGGGCGCGGAGAAAGT 62.437 66.667 8.83 0.00 0.00 2.66
5111 5291 2.047179 GAGGGCGCGGAGAAAGTT 60.047 61.111 8.83 0.00 0.00 2.66
5112 5292 1.217244 GAGGGCGCGGAGAAAGTTA 59.783 57.895 8.83 0.00 0.00 2.24
5113 5293 1.079336 AGGGCGCGGAGAAAGTTAC 60.079 57.895 8.83 0.00 0.00 2.50
5182 5362 6.983307 GTCAGTAGACTTTGATGCAGTATGAT 59.017 38.462 0.00 0.00 41.64 2.45
5183 5363 8.138074 GTCAGTAGACTTTGATGCAGTATGATA 58.862 37.037 0.00 0.00 41.64 2.15
5184 5364 8.355913 TCAGTAGACTTTGATGCAGTATGATAG 58.644 37.037 0.00 0.00 39.69 2.08
5208 5388 8.095937 AGTACAAACCAAAACTAATCTAGCAC 57.904 34.615 0.00 0.00 0.00 4.40
5224 5404 1.822990 AGCACCTGCAAAGATGAATGG 59.177 47.619 0.00 0.00 45.16 3.16
5267 5447 1.722464 CCAGTTTGCATCACAATTGCG 59.278 47.619 5.05 0.00 43.10 4.85
5322 5502 4.496336 GCCTCCGGCCAATCTGCT 62.496 66.667 2.24 0.00 44.06 4.24
5331 5511 1.324740 GCCAATCTGCTGGGCATCAA 61.325 55.000 0.00 0.00 46.92 2.57
5361 5541 3.504906 CCATTTGACTCTGTTGTGATGCT 59.495 43.478 0.00 0.00 0.00 3.79
5362 5542 4.022589 CCATTTGACTCTGTTGTGATGCTT 60.023 41.667 0.00 0.00 0.00 3.91
5483 5710 2.018542 TATGTAAGGCGTCCACAAGC 57.981 50.000 0.00 0.00 0.00 4.01
5490 5717 1.166531 GGCGTCCACAAGCTTCAAGT 61.167 55.000 0.00 0.00 0.00 3.16
5513 5740 2.157834 ACGCATTGACCGACAACTAA 57.842 45.000 0.00 0.00 41.52 2.24
5514 5741 2.695359 ACGCATTGACCGACAACTAAT 58.305 42.857 0.00 0.00 41.52 1.73
5516 5743 2.030457 CGCATTGACCGACAACTAATCC 59.970 50.000 0.00 0.00 41.52 3.01
5517 5744 2.030457 GCATTGACCGACAACTAATCCG 59.970 50.000 0.00 0.00 41.52 4.18
5532 5759 9.583765 ACAACTAATCCGAGATTTTTACTACTC 57.416 33.333 4.76 0.00 0.00 2.59
5534 5761 8.302515 ACTAATCCGAGATTTTTACTACTCCA 57.697 34.615 4.76 0.00 0.00 3.86
5555 5782 6.533730 TCCATCTGTCTCAAAATGTTAGTGT 58.466 36.000 0.00 0.00 0.00 3.55
5556 5783 6.650807 TCCATCTGTCTCAAAATGTTAGTGTC 59.349 38.462 0.00 0.00 0.00 3.67
5557 5784 6.427853 CCATCTGTCTCAAAATGTTAGTGTCA 59.572 38.462 0.00 0.00 0.00 3.58
5607 5841 7.505923 AGAGGGAGTAAAAACAATTTTGCTACT 59.494 33.333 12.14 9.85 46.96 2.57
5608 5842 8.700439 AGGGAGTAAAAACAATTTTGCTACTA 57.300 30.769 12.14 0.00 46.96 1.82
5609 5843 8.573885 AGGGAGTAAAAACAATTTTGCTACTAC 58.426 33.333 12.14 6.04 46.96 2.73
5622 5856 9.439500 AATTTTGCTACTACCGTAGTGATTTTA 57.561 29.630 19.60 0.00 44.02 1.52
5623 5857 8.830201 TTTTGCTACTACCGTAGTGATTTTAA 57.170 30.769 19.60 5.89 44.02 1.52
5628 5862 9.573133 GCTACTACCGTAGTGATTTTAAAACTA 57.427 33.333 19.60 0.00 44.02 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.282885 TCCAGCACACATACACACAAAA 58.717 40.909 0.00 0.00 0.00 2.44
28 29 2.629336 TCCAGCACACATACACACAA 57.371 45.000 0.00 0.00 0.00 3.33
34 35 5.005779 CGTTTAGAGAATCCAGCACACATAC 59.994 44.000 0.00 0.00 33.66 2.39
35 36 5.109210 CGTTTAGAGAATCCAGCACACATA 58.891 41.667 0.00 0.00 33.66 2.29
36 37 3.935203 CGTTTAGAGAATCCAGCACACAT 59.065 43.478 0.00 0.00 33.66 3.21
37 38 3.244078 ACGTTTAGAGAATCCAGCACACA 60.244 43.478 0.00 0.00 33.66 3.72
38 39 3.123621 CACGTTTAGAGAATCCAGCACAC 59.876 47.826 0.00 0.00 33.66 3.82
39 40 3.244078 ACACGTTTAGAGAATCCAGCACA 60.244 43.478 0.00 0.00 33.66 4.57
40 41 3.326747 ACACGTTTAGAGAATCCAGCAC 58.673 45.455 0.00 0.00 33.66 4.40
41 42 3.258372 AGACACGTTTAGAGAATCCAGCA 59.742 43.478 0.00 0.00 33.66 4.41
42 43 3.851098 AGACACGTTTAGAGAATCCAGC 58.149 45.455 0.00 0.00 33.66 4.85
43 44 5.098893 CAGAGACACGTTTAGAGAATCCAG 58.901 45.833 0.00 0.00 33.66 3.86
44 45 4.523173 ACAGAGACACGTTTAGAGAATCCA 59.477 41.667 0.00 0.00 33.66 3.41
45 46 5.061920 ACAGAGACACGTTTAGAGAATCC 57.938 43.478 0.00 0.00 33.66 3.01
46 47 5.945155 AGACAGAGACACGTTTAGAGAATC 58.055 41.667 0.00 0.00 0.00 2.52
47 48 5.968528 AGACAGAGACACGTTTAGAGAAT 57.031 39.130 0.00 0.00 0.00 2.40
57 58 5.743026 ACTATGTGATAGACAGAGACACG 57.257 43.478 3.59 0.00 45.33 4.49
58 59 9.291664 GTAAAACTATGTGATAGACAGAGACAC 57.708 37.037 3.59 0.00 45.33 3.67
144 145 2.370849 GGGTGTCGGATAACATGGGTAT 59.629 50.000 0.00 0.00 0.00 2.73
145 146 1.764134 GGGTGTCGGATAACATGGGTA 59.236 52.381 0.00 0.00 0.00 3.69
154 155 3.068024 GGTAACGTAATGGGTGTCGGATA 59.932 47.826 0.00 0.00 0.00 2.59
155 156 2.159057 GGTAACGTAATGGGTGTCGGAT 60.159 50.000 0.00 0.00 0.00 4.18
156 157 1.204467 GGTAACGTAATGGGTGTCGGA 59.796 52.381 0.00 0.00 0.00 4.55
176 177 4.142469 CCAAAGCTCCCTTTAACCATTACG 60.142 45.833 0.00 0.00 39.20 3.18
191 192 3.636764 TGTCTTCTTTTTCCCCAAAGCTC 59.363 43.478 0.00 0.00 34.26 4.09
194 195 5.598416 ACTTGTCTTCTTTTTCCCCAAAG 57.402 39.130 0.00 0.00 35.39 2.77
201 202 8.029522 AGTTTTCCTCAACTTGTCTTCTTTTTC 58.970 33.333 0.00 0.00 32.81 2.29
238 239 2.035449 GCCCGGCTCTTTACTTGTTTTT 59.965 45.455 0.71 0.00 0.00 1.94
241 242 0.953960 CGCCCGGCTCTTTACTTGTT 60.954 55.000 8.05 0.00 0.00 2.83
256 258 5.411781 CAGTCTATTACCATTATCTCGCCC 58.588 45.833 0.00 0.00 0.00 6.13
258 260 6.026947 ACCAGTCTATTACCATTATCTCGC 57.973 41.667 0.00 0.00 0.00 5.03
405 494 1.107114 TTGCGGGTTGTTGTTGTGAT 58.893 45.000 0.00 0.00 0.00 3.06
420 509 2.158645 TGTCAACCGATGTATGTTTGCG 59.841 45.455 0.00 0.00 0.00 4.85
424 513 3.745975 CAGTGTGTCAACCGATGTATGTT 59.254 43.478 0.00 0.00 0.00 2.71
439 528 0.106708 AGACGGATGTTGCAGTGTGT 59.893 50.000 0.00 0.00 0.00 3.72
446 535 5.505286 CATTTTCAGATAGACGGATGTTGC 58.495 41.667 0.00 0.00 0.00 4.17
456 545 6.037940 GCAGATGAAGTGCATTTTCAGATAGA 59.962 38.462 17.83 0.00 40.86 1.98
495 584 0.252696 TGGTGGTGGATGTAGAGGCT 60.253 55.000 0.00 0.00 0.00 4.58
501 590 2.897271 ATGCTTTGGTGGTGGATGTA 57.103 45.000 0.00 0.00 0.00 2.29
521 610 1.982226 TGCTTTTCTGGCTAGTGGGTA 59.018 47.619 0.00 0.00 0.00 3.69
565 654 5.148502 GGGTCTTGTGATAGGAGATAAGGA 58.851 45.833 0.00 0.00 0.00 3.36
615 704 8.774586 GTTATTGTTATTAGGCATACTGACTGG 58.225 37.037 0.00 0.00 35.73 4.00
645 734 1.055040 CTCCTTCTCTATGGCTGGGG 58.945 60.000 0.00 0.00 0.00 4.96
661 750 2.163211 GCTTTTCTGATGGTTCTGCTCC 59.837 50.000 0.00 0.00 0.00 4.70
871 965 2.675371 GAGGCGGGTAAAAGGGCT 59.325 61.111 0.00 0.00 39.50 5.19
911 1017 3.775654 GTGGAGTGGGAGGGAGCG 61.776 72.222 0.00 0.00 0.00 5.03
959 1065 1.685355 GCTCAGCCCTCCTTCCTCTC 61.685 65.000 0.00 0.00 0.00 3.20
960 1066 1.688884 GCTCAGCCCTCCTTCCTCT 60.689 63.158 0.00 0.00 0.00 3.69
1119 1225 2.103042 CGAAGAGGAAAGCAGGCGG 61.103 63.158 0.00 0.00 0.00 6.13
1170 1276 2.043852 GGAGAGGAGGAGGCGACA 60.044 66.667 0.00 0.00 0.00 4.35
1182 1288 1.406069 GCACATACACCCACAGGAGAG 60.406 57.143 0.00 0.00 36.73 3.20
1183 1289 0.613260 GCACATACACCCACAGGAGA 59.387 55.000 0.00 0.00 36.73 3.71
1184 1290 0.324614 TGCACATACACCCACAGGAG 59.675 55.000 0.00 0.00 36.73 3.69
1286 1399 3.952675 GCGCACACACACCCACAG 61.953 66.667 0.30 0.00 0.00 3.66
1301 1414 1.135972 CCACTTCAATTCCAGAACGCG 60.136 52.381 3.53 3.53 0.00 6.01
1325 1440 0.169672 TCGATCGACAAGGTCCGAAC 59.830 55.000 15.15 0.00 38.36 3.95
1366 1481 9.213799 GGAGGATGATACAAATCTATGAAAGAC 57.786 37.037 0.00 0.00 36.93 3.01
1384 1499 0.464373 GGCAAATCGCTGGAGGATGA 60.464 55.000 0.00 0.00 41.91 2.92
1385 1500 1.450531 GGGCAAATCGCTGGAGGATG 61.451 60.000 0.00 0.00 41.91 3.51
1445 1561 2.548057 CACCAACCAGTCACACACATAC 59.452 50.000 0.00 0.00 0.00 2.39
1446 1562 2.171659 ACACCAACCAGTCACACACATA 59.828 45.455 0.00 0.00 0.00 2.29
1451 1567 1.400494 GTTGACACCAACCAGTCACAC 59.600 52.381 0.00 0.00 45.19 3.82
1472 1588 1.074850 TCCCACCCAGTCACTCACA 60.075 57.895 0.00 0.00 0.00 3.58
1494 1610 2.290960 GGTAAATGGACAAGGCCTCTGT 60.291 50.000 17.19 17.19 0.00 3.41
1628 1746 1.900245 TGCAGTAGTGACACCGACTA 58.100 50.000 9.75 0.00 0.00 2.59
1632 1752 1.067565 ACTGATGCAGTAGTGACACCG 60.068 52.381 0.42 0.00 43.46 4.94
1636 1756 5.424121 AACAAAACTGATGCAGTAGTGAC 57.576 39.130 0.42 0.00 44.62 3.67
1739 1859 6.961554 GCAAAGAAGATATTGTTGGAACTACG 59.038 38.462 0.00 0.00 0.00 3.51
1748 1872 3.356290 AGGCCGCAAAGAAGATATTGTT 58.644 40.909 0.00 0.00 0.00 2.83
1751 1875 4.016444 TGAAAGGCCGCAAAGAAGATATT 58.984 39.130 0.00 0.00 0.00 1.28
1807 1931 1.619807 TAGCCCGTAAAGTCCCCAGC 61.620 60.000 0.00 0.00 0.00 4.85
1820 1944 2.164219 ACTGAATTTTGCACATAGCCCG 59.836 45.455 0.00 0.00 44.83 6.13
1830 1954 7.755582 ACTGTCTGTTAAAACTGAATTTTGC 57.244 32.000 4.28 0.00 40.80 3.68
1870 1994 6.998673 AGTGATAATTGGCAATAGGTCTAACC 59.001 38.462 14.05 0.00 38.99 2.85
1872 1996 8.934697 AGTAGTGATAATTGGCAATAGGTCTAA 58.065 33.333 14.05 0.00 0.00 2.10
1910 2040 9.993454 AGGTTGGTAGTTAAGTTAGTTAAGAAG 57.007 33.333 0.00 0.00 30.93 2.85
1934 2064 5.491982 ACACAAAACAGAGAGGCTAATAGG 58.508 41.667 0.00 0.00 0.00 2.57
2020 2150 3.313249 TCATCATCATCCATCGCACAAAC 59.687 43.478 0.00 0.00 0.00 2.93
2027 2157 6.396450 ACAGATAACTCATCATCATCCATCG 58.604 40.000 0.00 0.00 35.96 3.84
2088 2224 2.310327 TAGCTAGGCCGCATGTGGTG 62.310 60.000 25.68 14.45 0.00 4.17
2181 2317 2.376109 AGAAGCTTGAAGCCATCCATG 58.624 47.619 14.45 0.00 43.77 3.66
2327 2463 1.131638 ACAGAGTGGAGCAGTTTGGA 58.868 50.000 0.00 0.00 0.00 3.53
2716 2852 4.023279 TCACTGTCGAATCCAATTTGGTTG 60.023 41.667 14.98 1.51 39.03 3.77
2858 3030 1.234821 GCACGTTCATCAGGTCCAAA 58.765 50.000 0.00 0.00 0.00 3.28
3123 3295 2.183478 TCACACGCCTGATTTGTGAT 57.817 45.000 0.00 0.00 43.63 3.06
3139 3311 8.992835 ATAAATTCCAATTTTCTGCTCTTCAC 57.007 30.769 2.68 0.00 39.24 3.18
3168 3341 3.365364 GCACAAGAAACTACCTGCATCAC 60.365 47.826 0.00 0.00 0.00 3.06
3209 3382 8.783093 TGACAAAGGTGATCTTGTGTAATTTAG 58.217 33.333 3.04 0.00 35.55 1.85
3215 3390 5.070446 ACTCTGACAAAGGTGATCTTGTGTA 59.930 40.000 3.04 0.00 35.55 2.90
3241 3416 2.764572 CCTTTCGCTTACTTCTAGGGGA 59.235 50.000 0.00 0.00 0.00 4.81
3256 3431 2.673368 CGGAACCAAGAATCTCCTTTCG 59.327 50.000 0.00 0.00 0.00 3.46
3290 3465 5.999205 TGCAACATCATAACATCCCTTTT 57.001 34.783 0.00 0.00 0.00 2.27
3305 3480 0.527565 GCGGGAACTCATTGCAACAT 59.472 50.000 0.00 0.00 0.00 2.71
3331 3506 5.559770 TGAACATGTCAGAGGCAAAGAATA 58.440 37.500 0.00 0.00 0.00 1.75
3339 3514 1.340405 ACCCATGAACATGTCAGAGGC 60.340 52.381 12.74 0.00 40.43 4.70
3343 3518 2.026915 TCCTGACCCATGAACATGTCAG 60.027 50.000 19.43 19.43 40.43 3.51
3346 3521 1.704628 TGTCCTGACCCATGAACATGT 59.295 47.619 12.74 0.00 37.11 3.21
3362 3537 8.903820 ACCAATAATCAATTAGTAGCTTTGTCC 58.096 33.333 0.00 0.00 0.00 4.02
3372 3547 7.716998 CAGTAGCTCCACCAATAATCAATTAGT 59.283 37.037 0.00 0.00 0.00 2.24
3376 3551 6.006275 ACAGTAGCTCCACCAATAATCAAT 57.994 37.500 0.00 0.00 0.00 2.57
3382 3557 4.215908 CTCCTACAGTAGCTCCACCAATA 58.784 47.826 1.50 0.00 0.00 1.90
3389 3564 3.492337 AGTATGCTCCTACAGTAGCTCC 58.508 50.000 1.50 0.00 39.53 4.70
3404 3579 1.751351 GGAGCCCCTCAAAAAGTATGC 59.249 52.381 0.00 0.00 31.08 3.14
3409 3584 2.224867 TGAGAAGGAGCCCCTCAAAAAG 60.225 50.000 0.00 0.00 43.48 2.27
3410 3585 1.780309 TGAGAAGGAGCCCCTCAAAAA 59.220 47.619 0.00 0.00 43.48 1.94
3411 3586 1.444933 TGAGAAGGAGCCCCTCAAAA 58.555 50.000 0.00 0.00 43.48 2.44
3415 3590 1.047801 GAGATGAGAAGGAGCCCCTC 58.952 60.000 0.00 0.00 43.48 4.30
3418 3593 1.693627 TACGAGATGAGAAGGAGCCC 58.306 55.000 0.00 0.00 0.00 5.19
3420 3595 4.033472 GCTTTTTACGAGATGAGAAGGAGC 59.967 45.833 0.00 0.00 0.00 4.70
3421 3596 5.415221 AGCTTTTTACGAGATGAGAAGGAG 58.585 41.667 0.00 0.00 0.00 3.69
3422 3597 5.407407 AGCTTTTTACGAGATGAGAAGGA 57.593 39.130 0.00 0.00 0.00 3.36
3424 3599 6.473397 ACAAGCTTTTTACGAGATGAGAAG 57.527 37.500 0.00 0.00 0.00 2.85
3425 3600 6.861065 AACAAGCTTTTTACGAGATGAGAA 57.139 33.333 0.00 0.00 0.00 2.87
3426 3601 6.658831 CAAACAAGCTTTTTACGAGATGAGA 58.341 36.000 0.00 0.00 0.00 3.27
3429 3604 4.975502 TGCAAACAAGCTTTTTACGAGATG 59.024 37.500 0.00 0.00 34.99 2.90
3430 3605 5.181690 TGCAAACAAGCTTTTTACGAGAT 57.818 34.783 0.00 0.00 34.99 2.75
3432 3607 5.888412 ATTGCAAACAAGCTTTTTACGAG 57.112 34.783 1.71 0.00 39.69 4.18
3433 3608 6.654793 AAATTGCAAACAAGCTTTTTACGA 57.345 29.167 1.71 0.00 39.69 3.43
3500 3675 9.993454 TTCACATGGATTTGTATGAAAATTGAA 57.007 25.926 0.00 0.00 29.89 2.69
3508 3684 9.642327 CTTCAAAATTCACATGGATTTGTATGA 57.358 29.630 0.00 0.00 33.76 2.15
3518 3694 6.532657 GGTAAGATGCTTCAAAATTCACATGG 59.467 38.462 0.00 0.00 0.00 3.66
3529 3705 4.460263 ACAGTGTTGGTAAGATGCTTCAA 58.540 39.130 2.07 0.00 0.00 2.69
3537 3713 6.042781 ACTTGAATCCTACAGTGTTGGTAAGA 59.957 38.462 21.00 4.68 30.86 2.10
3538 3714 6.231211 ACTTGAATCCTACAGTGTTGGTAAG 58.769 40.000 21.00 20.08 30.86 2.34
3540 3716 5.818678 ACTTGAATCCTACAGTGTTGGTA 57.181 39.130 21.00 10.16 30.86 3.25
3541 3717 4.706842 ACTTGAATCCTACAGTGTTGGT 57.293 40.909 21.00 5.21 30.86 3.67
3593 3770 9.667107 TTTTCTTCGTATGAATACCAGAAGATT 57.333 29.630 15.53 0.00 38.41 2.40
3594 3771 9.838339 ATTTTCTTCGTATGAATACCAGAAGAT 57.162 29.630 15.53 11.20 38.41 2.40
3596 3773 9.922305 GAATTTTCTTCGTATGAATACCAGAAG 57.078 33.333 0.00 9.86 33.81 2.85
3610 3787 7.592938 TCTGCATAACAATGAATTTTCTTCGT 58.407 30.769 0.00 0.00 0.00 3.85
3611 3788 8.451687 TTCTGCATAACAATGAATTTTCTTCG 57.548 30.769 0.00 0.00 0.00 3.79
3623 3800 6.000219 AGAGGCGATATTTCTGCATAACAAT 59.000 36.000 0.00 0.00 0.00 2.71
3646 3824 2.489938 TTTGCAGCCTACCCAAGTAG 57.510 50.000 0.00 0.00 44.85 2.57
3683 3861 1.045350 TGCCTAGCAGAGCCCAGTAG 61.045 60.000 0.00 0.00 33.32 2.57
3686 3864 1.153208 CTTGCCTAGCAGAGCCCAG 60.153 63.158 0.00 0.00 40.61 4.45
3715 3893 0.841961 TCTCTGATGATGGCCCCTTG 59.158 55.000 0.00 0.00 0.00 3.61
3721 3899 3.879892 GGTTAAGGTTCTCTGATGATGGC 59.120 47.826 0.00 0.00 0.00 4.40
3832 4010 4.398319 TGGTTTCTTCCAACTGAGAATCC 58.602 43.478 6.35 6.35 34.24 3.01
3844 4022 0.109132 CCATGCGCTTGGTTTCTTCC 60.109 55.000 29.15 0.00 31.74 3.46
4153 4331 2.582052 GGAGGTGGTGTGAACAAATGA 58.418 47.619 0.00 0.00 0.00 2.57
4171 4349 2.897436 CAACTCATTGAGATCAGCGGA 58.103 47.619 20.33 0.00 38.15 5.54
4177 4355 3.553511 CCGTACTGCAACTCATTGAGATC 59.446 47.826 20.33 8.71 38.15 2.75
4241 4419 3.406764 AGAAGGACTTGATGCAGTCAAC 58.593 45.455 6.21 0.43 44.53 3.18
4264 4442 1.966493 CTGTACATGTCAACGCCGGC 61.966 60.000 19.07 19.07 0.00 6.13
4330 4508 1.220206 CTTCCGGTCAGCAGCATCT 59.780 57.895 0.00 0.00 0.00 2.90
4374 4552 4.094442 GGCCGAAGTAACAATCTTTAGTGG 59.906 45.833 0.00 0.00 0.00 4.00
4633 4811 3.736094 TCCATCCATCAAAGGGTAGTCT 58.264 45.455 0.00 0.00 0.00 3.24
4642 4820 3.675348 AAGAGGCATCCATCCATCAAA 57.325 42.857 0.00 0.00 0.00 2.69
4869 5048 9.355916 TCTCCATATATATACTTTGAGGGATCG 57.644 37.037 0.00 0.00 0.00 3.69
4915 5094 4.082523 TACAGCAGTGCCGGCTCC 62.083 66.667 29.70 18.26 40.23 4.70
5005 5185 0.042131 TTGTGGGACGGAGGGAGTAT 59.958 55.000 0.00 0.00 0.00 2.12
5037 5217 1.664321 CTTACTCCCTCCGTCCCACG 61.664 65.000 0.00 0.00 42.11 4.94
5049 5229 4.065789 CTGACCAACCTGAAACTTACTCC 58.934 47.826 0.00 0.00 0.00 3.85
5050 5230 4.750598 GTCTGACCAACCTGAAACTTACTC 59.249 45.833 0.00 0.00 0.00 2.59
5051 5231 4.163458 TGTCTGACCAACCTGAAACTTACT 59.837 41.667 5.17 0.00 0.00 2.24
5052 5232 4.448210 TGTCTGACCAACCTGAAACTTAC 58.552 43.478 5.17 0.00 0.00 2.34
5053 5233 4.444306 CCTGTCTGACCAACCTGAAACTTA 60.444 45.833 5.17 0.00 0.00 2.24
5054 5234 3.545703 CTGTCTGACCAACCTGAAACTT 58.454 45.455 5.17 0.00 0.00 2.66
5055 5235 2.158755 CCTGTCTGACCAACCTGAAACT 60.159 50.000 5.17 0.00 0.00 2.66
5068 5248 3.325135 GGGAGAAGAAGAAACCTGTCTGA 59.675 47.826 0.00 0.00 0.00 3.27
5072 5252 1.705745 GGGGGAGAAGAAGAAACCTGT 59.294 52.381 0.00 0.00 0.00 4.00
5096 5276 0.174162 TAGTAACTTTCTCCGCGCCC 59.826 55.000 0.00 0.00 0.00 6.13
5097 5277 1.135170 AGTAGTAACTTTCTCCGCGCC 60.135 52.381 0.00 0.00 29.00 6.53
5099 5279 4.093998 TCAGTAGTAGTAACTTTCTCCGCG 59.906 45.833 0.00 0.00 37.15 6.46
5100 5280 5.557891 TCAGTAGTAGTAACTTTCTCCGC 57.442 43.478 0.00 0.00 37.15 5.54
5101 5281 7.556733 AGATCAGTAGTAGTAACTTTCTCCG 57.443 40.000 0.00 0.00 37.15 4.63
5150 5330 2.161012 TCAAAGTCTACTGACCGCTACG 59.839 50.000 0.00 0.00 43.91 3.51
5182 5362 9.211485 GTGCTAGATTAGTTTTGGTTTGTACTA 57.789 33.333 0.00 0.00 0.00 1.82
5183 5363 7.174426 GGTGCTAGATTAGTTTTGGTTTGTACT 59.826 37.037 0.00 0.00 0.00 2.73
5184 5364 7.174426 AGGTGCTAGATTAGTTTTGGTTTGTAC 59.826 37.037 0.00 0.00 0.00 2.90
5208 5388 3.508793 ACTGTTCCATTCATCTTTGCAGG 59.491 43.478 0.00 0.00 0.00 4.85
5224 5404 6.371548 TGGTTATGATTGCAACTCTACTGTTC 59.628 38.462 0.00 0.00 0.00 3.18
5267 5447 0.888285 AGCAGCAAGTGAGTTCCAGC 60.888 55.000 0.00 0.00 0.00 4.85
5325 5505 3.615496 GTCAAATGGAAGCACATTGATGC 59.385 43.478 2.66 0.00 46.50 3.91
5331 5511 3.759581 ACAGAGTCAAATGGAAGCACAT 58.240 40.909 0.00 0.00 0.00 3.21
5424 5651 8.463607 ACGGGGTGTTTAACAAATAATAATCAG 58.536 33.333 0.00 0.00 0.00 2.90
5483 5710 3.906008 CGGTCAATGCGTAAAACTTGAAG 59.094 43.478 0.00 0.00 30.06 3.02
5490 5717 2.873472 AGTTGTCGGTCAATGCGTAAAA 59.127 40.909 0.00 0.00 38.38 1.52
5513 5740 7.070074 ACAGATGGAGTAGTAAAAATCTCGGAT 59.930 37.037 0.00 0.00 0.00 4.18
5514 5741 6.380274 ACAGATGGAGTAGTAAAAATCTCGGA 59.620 38.462 0.00 0.00 0.00 4.55
5516 5743 7.484975 AGACAGATGGAGTAGTAAAAATCTCG 58.515 38.462 0.00 0.00 0.00 4.04
5517 5744 8.470805 TGAGACAGATGGAGTAGTAAAAATCTC 58.529 37.037 0.00 0.00 0.00 2.75
5532 5759 6.427853 TGACACTAACATTTTGAGACAGATGG 59.572 38.462 0.00 0.00 0.00 3.51
5534 5761 8.450578 TTTGACACTAACATTTTGAGACAGAT 57.549 30.769 0.00 0.00 0.00 2.90
5563 5790 8.414778 ACTCCCTCTATCTTAAAATGTAAGACG 58.585 37.037 0.00 0.00 36.51 4.18
5580 5807 7.833285 AGCAAAATTGTTTTTACTCCCTCTA 57.167 32.000 0.00 0.00 33.29 2.43
5622 5856 2.967887 ACTACACCCTGTCCGTAGTTTT 59.032 45.455 0.00 0.00 42.37 2.43
5623 5857 2.601905 ACTACACCCTGTCCGTAGTTT 58.398 47.619 0.00 0.00 42.37 2.66
5628 5862 3.700538 TGTAATACTACACCCTGTCCGT 58.299 45.455 0.00 0.00 32.93 4.69


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

AutoCloner maintained by Alex Coulton.