Multiple sequence alignment - TraesCS2B01G381200

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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 TraesCS2B01G381200 chr2B 100.000 5358 0 0 1 5358 545225305 545230662 0.000000e+00 9895.0
1 TraesCS2B01G381200 chr2B 90.580 414 34 3 365 774 706197147 706197559 1.310000e-150 544.0
2 TraesCS2B01G381200 chr2B 85.851 417 43 7 2304 2713 545159043 545159450 3.830000e-116 429.0
3 TraesCS2B01G381200 chr2B 84.530 362 26 13 1 343 706196618 706196968 1.110000e-86 331.0
4 TraesCS2B01G381200 chr2B 82.530 332 37 10 1723 2045 545158577 545158896 6.840000e-69 272.0
5 TraesCS2B01G381200 chr2B 82.955 264 39 6 3741 4000 545159893 545160154 3.230000e-57 233.0
6 TraesCS2B01G381200 chr2B 86.256 211 28 1 3306 3516 545159563 545159772 1.500000e-55 228.0
7 TraesCS2B01G381200 chr2B 94.186 86 5 0 1483 1568 545158487 545158572 1.210000e-26 132.0
8 TraesCS2B01G381200 chr2D 91.241 4133 243 61 901 4979 462783785 462787852 0.000000e+00 5517.0
9 TraesCS2B01G381200 chr2D 81.985 2176 273 73 1725 3836 462245770 462247890 0.000000e+00 1736.0
10 TraesCS2B01G381200 chr2D 93.132 597 31 6 4763 5358 462789231 462789818 0.000000e+00 867.0
11 TraesCS2B01G381200 chr2D 89.952 209 19 2 896 1103 462263832 462264039 8.850000e-68 268.0
12 TraesCS2B01G381200 chr2D 84.364 275 32 8 2834 3108 462247450 462247713 5.320000e-65 259.0
13 TraesCS2B01G381200 chr2D 87.047 193 22 3 1185 1376 462245424 462245614 1.170000e-51 215.0
14 TraesCS2B01G381200 chr2D 78.042 378 52 18 3288 3648 462246808 462247171 5.440000e-50 209.0
15 TraesCS2B01G381200 chr2D 94.118 85 5 0 1483 1567 462245678 462245762 4.360000e-26 130.0
16 TraesCS2B01G381200 chr2D 93.750 64 4 0 796 859 462259544 462259607 4.420000e-16 97.1
17 TraesCS2B01G381200 chr2A 88.788 2640 218 50 1105 3713 607597445 607600037 0.000000e+00 3164.0
18 TraesCS2B01G381200 chr2A 88.034 1170 81 32 3716 4869 607600122 607601248 0.000000e+00 1330.0
19 TraesCS2B01G381200 chr2A 85.440 989 97 34 2433 3392 607519159 607520129 0.000000e+00 985.0
20 TraesCS2B01G381200 chr2A 93.708 445 22 4 4915 5358 607601244 607601683 0.000000e+00 662.0
21 TraesCS2B01G381200 chr2A 84.953 638 70 20 2644 3266 610225940 610226566 1.640000e-174 623.0
22 TraesCS2B01G381200 chr2A 80.464 819 114 24 1723 2510 610210579 610211382 7.730000e-163 584.0
23 TraesCS2B01G381200 chr2A 82.900 462 53 14 3381 3836 607520249 607520690 5.030000e-105 392.0
24 TraesCS2B01G381200 chr2A 84.857 350 44 6 896 1237 607593849 607594197 1.430000e-90 344.0
25 TraesCS2B01G381200 chr2A 80.353 453 63 12 1719 2151 607518354 607518800 2.410000e-83 320.0
26 TraesCS2B01G381200 chr2A 82.946 387 32 18 1006 1376 607517834 607518202 8.660000e-83 318.0
27 TraesCS2B01G381200 chr2A 95.000 200 4 4 902 1096 607596915 607597113 5.210000e-80 309.0
28 TraesCS2B01G381200 chr2A 85.156 256 32 4 3306 3557 610226738 610226991 1.910000e-64 257.0
29 TraesCS2B01G381200 chr2A 84.980 253 28 5 2848 3100 607520262 607520504 1.150000e-61 248.0
30 TraesCS2B01G381200 chr2A 82.329 249 23 11 3589 3836 610227186 610227414 4.230000e-46 196.0
31 TraesCS2B01G381200 chr2A 84.772 197 23 5 2834 3030 610226811 610227000 1.970000e-44 191.0
32 TraesCS2B01G381200 chr3B 91.871 775 41 5 1 774 803568181 803567428 0.000000e+00 1062.0
33 TraesCS2B01G381200 chr3B 95.238 357 17 0 394 750 803568892 803568536 2.800000e-157 566.0
34 TraesCS2B01G381200 chr7B 92.494 413 28 1 365 774 593564934 593565346 5.980000e-164 588.0
35 TraesCS2B01G381200 chr7B 90.295 237 23 0 365 601 336602327 336602563 1.450000e-80 311.0
36 TraesCS2B01G381200 chr7B 83.473 357 28 11 7 343 593564410 593564755 2.420000e-78 303.0
37 TraesCS2B01G381200 chr7B 83.193 357 28 10 7 343 336601804 336602148 1.130000e-76 298.0
38 TraesCS2B01G381200 chr4A 90.338 414 35 2 365 775 673116451 673116040 6.110000e-149 538.0
39 TraesCS2B01G381200 chr4A 88.674 362 23 3 421 782 24157242 24156899 4.960000e-115 425.0
40 TraesCS2B01G381200 chr4A 82.913 357 30 7 7 343 673116975 673116630 5.250000e-75 292.0
41 TraesCS2B01G381200 chr1A 92.244 361 27 1 415 774 17075455 17075815 1.330000e-140 510.0
42 TraesCS2B01G381200 chr6D 92.705 329 24 0 365 693 8345398 8345070 4.860000e-130 475.0
43 TraesCS2B01G381200 chr6D 83.754 357 24 11 13 343 8345856 8345508 1.870000e-79 307.0
44 TraesCS2B01G381200 chr6D 91.304 69 5 1 1849 1917 292399063 292399130 5.710000e-15 93.5
45 TraesCS2B01G381200 chr6D 91.304 69 5 1 1849 1917 462703649 462703716 5.710000e-15 93.5
46 TraesCS2B01G381200 chr1D 97.110 173 5 0 602 774 9739773 9739945 5.250000e-75 292.0
47 TraesCS2B01G381200 chr1D 89.634 164 8 2 180 342 9739005 9739160 3.270000e-47 200.0
48 TraesCS2B01G381200 chr4D 92.632 95 7 0 2868 2962 432946377 432946471 2.600000e-28 137.0
49 TraesCS2B01G381200 chr1B 79.899 199 29 8 2438 2633 656674768 656674958 9.360000e-28 135.0
50 TraesCS2B01G381200 chr1B 95.522 67 3 0 274 340 664389086 664389020 2.040000e-19 108.0
51 TraesCS2B01G381200 chr6B 91.429 70 5 1 1849 1918 121782596 121782528 1.590000e-15 95.3
52 TraesCS2B01G381200 chr6B 97.674 43 1 0 801 843 226364971 226365013 2.070000e-09 75.0
53 TraesCS2B01G381200 chr6A 95.349 43 2 0 801 843 151463676 151463634 9.630000e-08 69.4


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 TraesCS2B01G381200 chr2B 545225305 545230662 5357 False 9895.00 9895 100.0000 1 5358 1 chr2B.!!$F1 5357
1 TraesCS2B01G381200 chr2B 706196618 706197559 941 False 437.50 544 87.5550 1 774 2 chr2B.!!$F3 773
2 TraesCS2B01G381200 chr2B 545158487 545160154 1667 False 258.80 429 86.3556 1483 4000 5 chr2B.!!$F2 2517
3 TraesCS2B01G381200 chr2D 462783785 462789818 6033 False 3192.00 5517 92.1865 901 5358 2 chr2D.!!$F4 4457
4 TraesCS2B01G381200 chr2D 462245424 462247890 2466 False 509.80 1736 85.1112 1185 3836 5 chr2D.!!$F3 2651
5 TraesCS2B01G381200 chr2A 607593849 607601683 7834 False 1161.80 3164 90.0774 896 5358 5 chr2A.!!$F3 4462
6 TraesCS2B01G381200 chr2A 610210579 610211382 803 False 584.00 584 80.4640 1723 2510 1 chr2A.!!$F1 787
7 TraesCS2B01G381200 chr2A 607517834 607520690 2856 False 452.60 985 83.3238 1006 3836 5 chr2A.!!$F2 2830
8 TraesCS2B01G381200 chr2A 610225940 610227414 1474 False 316.75 623 84.3025 2644 3836 4 chr2A.!!$F4 1192
9 TraesCS2B01G381200 chr3B 803567428 803568892 1464 True 814.00 1062 93.5545 1 774 2 chr3B.!!$R1 773
10 TraesCS2B01G381200 chr7B 593564410 593565346 936 False 445.50 588 87.9835 7 774 2 chr7B.!!$F2 767
11 TraesCS2B01G381200 chr7B 336601804 336602563 759 False 304.50 311 86.7440 7 601 2 chr7B.!!$F1 594
12 TraesCS2B01G381200 chr4A 673116040 673116975 935 True 415.00 538 86.6255 7 775 2 chr4A.!!$R2 768
13 TraesCS2B01G381200 chr6D 8345070 8345856 786 True 391.00 475 88.2295 13 693 2 chr6D.!!$R1 680
14 TraesCS2B01G381200 chr1D 9739005 9739945 940 False 246.00 292 93.3720 180 774 2 chr1D.!!$F1 594

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
803 1999 0.102300 GCCCTTGCACACGTTCTTTT 59.898 50.0 0.0 0.0 37.47 2.27 F
807 2003 0.179124 TTGCACACGTTCTTTTGGCC 60.179 50.0 0.0 0.0 0.00 5.36 F
896 2092 0.185901 GGGCATGGATGGTATGTGGT 59.814 55.0 0.0 0.0 0.00 4.16 F
1480 4004 0.243636 CCCCAAATCCAACAAGTCGC 59.756 55.0 0.0 0.0 0.00 5.19 F
3050 5755 0.609957 CCTGTGCTTTGGATGAGGCA 60.610 55.0 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 4911 0.034059 AAGAGGTGCAGTCAAGGTCG 59.966 55.000 0.00 0.0 0.00 4.79 R
2755 5445 2.426024 GCTCACATGGATTTGCTCACAT 59.574 45.455 0.00 0.0 0.00 3.21 R
2897 5597 2.489971 CACCAAAGCGGACACTAAGAA 58.510 47.619 0.00 0.0 38.63 2.52 R
3458 6474 2.570752 AGTCAATCAGCACAGATCCACT 59.429 45.455 0.00 0.0 0.00 4.00 R
4970 9838 0.968393 ACCTCTCTCGCAGAAGGACC 60.968 60.000 14.79 0.0 34.09 4.46 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
185 922 1.349688 TGGTTTCCTGGCAACTCGTAT 59.650 47.619 9.05 0.00 37.61 3.06
189 927 0.973632 TCCTGGCAACTCGTATGTGT 59.026 50.000 0.00 0.00 37.61 3.72
278 1019 2.604139 GAATTGGTTGGGAACTTGGGA 58.396 47.619 0.00 0.00 0.00 4.37
303 1044 7.936950 TCAAAATCGCATGACAAAAATTACA 57.063 28.000 0.00 0.00 0.00 2.41
430 1336 2.046313 CAAGATGCAACAAGACAACGC 58.954 47.619 0.00 0.00 0.00 4.84
445 1351 0.667487 AACGCCATGAGTGACGACAG 60.667 55.000 0.00 0.00 34.63 3.51
484 1491 2.224137 GCGAGATCATGATGGGACTTGA 60.224 50.000 14.30 0.00 0.00 3.02
507 1697 2.609459 GCATTGATCTGAACCTGTACGG 59.391 50.000 0.00 0.00 39.35 4.02
518 1708 2.598099 TGTACGGCGTGGTGGAGA 60.598 61.111 24.86 0.00 0.00 3.71
605 1801 6.561519 ATTGCCTAGTTAGTGATTACCAGT 57.438 37.500 0.00 0.00 0.00 4.00
651 1847 5.535753 AACCACCTTCAATTCTTTCCAAG 57.464 39.130 0.00 0.00 0.00 3.61
775 1971 8.390921 TGAGGGGAAAAAGTATACTTTCTTCAT 58.609 33.333 29.49 22.34 44.69 2.57
776 1972 8.581253 AGGGGAAAAAGTATACTTTCTTCATG 57.419 34.615 29.49 0.00 44.69 3.07
777 1973 8.390921 AGGGGAAAAAGTATACTTTCTTCATGA 58.609 33.333 29.49 0.00 44.69 3.07
778 1974 9.190317 GGGGAAAAAGTATACTTTCTTCATGAT 57.810 33.333 29.49 16.16 44.69 2.45
793 1989 6.409704 TCTTCATGATATATAGCCCTTGCAC 58.590 40.000 0.00 0.00 41.13 4.57
794 1990 5.760484 TCATGATATATAGCCCTTGCACA 57.240 39.130 0.00 0.00 41.13 4.57
795 1991 5.491070 TCATGATATATAGCCCTTGCACAC 58.509 41.667 0.00 0.00 41.13 3.82
796 1992 3.925379 TGATATATAGCCCTTGCACACG 58.075 45.455 0.00 0.00 41.13 4.49
797 1993 3.323691 TGATATATAGCCCTTGCACACGT 59.676 43.478 0.00 0.00 41.13 4.49
799 1995 2.018542 TATAGCCCTTGCACACGTTC 57.981 50.000 0.00 0.00 41.13 3.95
802 1998 0.751643 AGCCCTTGCACACGTTCTTT 60.752 50.000 0.00 0.00 41.13 2.52
803 1999 0.102300 GCCCTTGCACACGTTCTTTT 59.898 50.000 0.00 0.00 37.47 2.27
807 2003 0.179124 TTGCACACGTTCTTTTGGCC 60.179 50.000 0.00 0.00 0.00 5.36
808 2004 1.299850 GCACACGTTCTTTTGGCCC 60.300 57.895 0.00 0.00 0.00 5.80
810 2006 2.190841 ACACGTTCTTTTGGCCCGG 61.191 57.895 0.00 0.00 0.00 5.73
811 2007 3.292159 ACGTTCTTTTGGCCCGGC 61.292 61.111 0.00 0.00 0.00 6.13
832 2028 2.586079 CGTAGCACGGCCCAGATG 60.586 66.667 0.00 0.00 38.08 2.90
833 2029 2.203070 GTAGCACGGCCCAGATGG 60.203 66.667 0.00 0.00 37.09 3.51
852 2048 1.903404 CCAGGCCTGGTTCAACCAC 60.903 63.158 39.52 0.00 44.79 4.16
853 2049 1.903404 CAGGCCTGGTTCAACCACC 60.903 63.158 26.14 6.64 44.79 4.61
855 2051 1.903404 GGCCTGGTTCAACCACCTG 60.903 63.158 4.67 0.00 44.79 4.00
856 2052 2.564721 GCCTGGTTCAACCACCTGC 61.565 63.158 4.67 5.16 44.79 4.85
857 2053 2.260869 CCTGGTTCAACCACCTGCG 61.261 63.158 4.67 0.00 44.79 5.18
858 2054 1.227823 CTGGTTCAACCACCTGCGA 60.228 57.895 4.67 0.00 44.79 5.10
859 2055 0.817634 CTGGTTCAACCACCTGCGAA 60.818 55.000 4.67 0.00 44.79 4.70
860 2056 0.394488 TGGTTCAACCACCTGCGAAA 60.394 50.000 4.67 0.00 44.79 3.46
861 2057 0.958822 GGTTCAACCACCTGCGAAAT 59.041 50.000 0.01 0.00 38.42 2.17
863 2059 0.958091 TTCAACCACCTGCGAAATGG 59.042 50.000 0.00 0.00 39.57 3.16
864 2060 0.893270 TCAACCACCTGCGAAATGGG 60.893 55.000 0.00 0.00 37.86 4.00
865 2061 2.275380 AACCACCTGCGAAATGGGC 61.275 57.895 0.00 0.00 37.86 5.36
866 2062 3.814268 CCACCTGCGAAATGGGCG 61.814 66.667 0.00 0.00 0.00 6.13
867 2063 2.745884 CACCTGCGAAATGGGCGA 60.746 61.111 0.00 0.00 0.00 5.54
868 2064 2.436646 ACCTGCGAAATGGGCGAG 60.437 61.111 0.00 0.00 0.00 5.03
869 2065 3.204827 CCTGCGAAATGGGCGAGG 61.205 66.667 0.00 0.00 0.00 4.63
870 2066 2.436646 CTGCGAAATGGGCGAGGT 60.437 61.111 0.00 0.00 0.00 3.85
872 2068 1.429148 CTGCGAAATGGGCGAGGTAC 61.429 60.000 0.00 0.00 0.00 3.34
873 2069 2.178235 GCGAAATGGGCGAGGTACC 61.178 63.158 2.73 2.73 0.00 3.34
875 2071 1.523032 GAAATGGGCGAGGTACCGG 60.523 63.158 6.18 0.00 0.00 5.28
890 2086 3.562250 CGGAGGGCATGGATGGTA 58.438 61.111 0.00 0.00 0.00 3.25
891 2087 2.069776 CGGAGGGCATGGATGGTAT 58.930 57.895 0.00 0.00 0.00 2.73
893 2089 0.773644 GGAGGGCATGGATGGTATGT 59.226 55.000 0.00 0.00 0.00 2.29
894 2090 1.546323 GGAGGGCATGGATGGTATGTG 60.546 57.143 0.00 0.00 0.00 3.21
896 2092 0.185901 GGGCATGGATGGTATGTGGT 59.814 55.000 0.00 0.00 0.00 4.16
898 2094 2.158534 GGGCATGGATGGTATGTGGTTA 60.159 50.000 0.00 0.00 0.00 2.85
906 3072 4.142249 GGATGGTATGTGGTTAAAACTGCC 60.142 45.833 0.00 0.00 0.00 4.85
915 3081 5.830991 TGTGGTTAAAACTGCCATTCTTACT 59.169 36.000 0.00 0.00 34.52 2.24
1131 3649 2.172293 AGGTTAGATCTACCCGTCGTCT 59.828 50.000 10.43 0.00 36.27 4.18
1150 3668 4.493747 CTCGCGAGGGTTCCGTCC 62.494 72.222 28.40 0.00 0.00 4.79
1152 3670 4.065281 CGCGAGGGTTCCGTCCTT 62.065 66.667 0.00 0.00 34.21 3.36
1175 3693 8.042515 CCTTGATTTGGTTTGATTGATACCATT 58.957 33.333 0.00 0.00 41.31 3.16
1346 3868 1.811266 AGCACGGCTCTTGCATACG 60.811 57.895 7.34 0.00 42.83 3.06
1372 3894 7.549488 GTGCTACTGGTATTGATTTGTTCTAGT 59.451 37.037 0.00 0.00 0.00 2.57
1480 4004 0.243636 CCCCAAATCCAACAAGTCGC 59.756 55.000 0.00 0.00 0.00 5.19
1524 4063 3.691118 GCAGACCTGTAATGATTCTTGCA 59.309 43.478 0.00 0.00 0.00 4.08
1581 4120 2.223829 CCGAGTCGGCACATAGATTTCT 60.224 50.000 20.50 0.00 41.17 2.52
1593 4132 6.349611 GCACATAGATTTCTCAAGAGGCAAAA 60.350 38.462 0.00 0.00 0.00 2.44
1689 4228 2.945080 ATGGCCATCATAGACCTGTG 57.055 50.000 14.09 0.00 33.61 3.66
1699 4238 5.798125 TCATAGACCTGTGATGATTCCTC 57.202 43.478 0.00 0.00 0.00 3.71
1701 4240 6.614657 TCATAGACCTGTGATGATTCCTCTA 58.385 40.000 0.00 0.00 0.00 2.43
1716 4255 5.602291 TTCCTCTAGATAGGTTCCCCTAG 57.398 47.826 0.00 0.00 46.50 3.02
1728 4267 6.464530 AGGTTCCCCTAGTTTGAAGTAAAT 57.535 37.500 0.00 0.00 40.19 1.40
1767 4307 4.978099 AGGTGTCATCTGAATTCTGTTGT 58.022 39.130 17.75 3.66 0.00 3.32
1770 4310 5.413833 GGTGTCATCTGAATTCTGTTGTCAT 59.586 40.000 18.65 3.35 0.00 3.06
1779 4319 9.453572 TCTGAATTCTGTTGTCATAGCTATTTT 57.546 29.630 2.64 0.00 0.00 1.82
1785 4325 8.044060 TCTGTTGTCATAGCTATTTTCTTTGG 57.956 34.615 2.64 0.00 0.00 3.28
2007 4559 8.092068 TGTCCTTTCTCTTGTTTGACGATTATA 58.908 33.333 0.00 0.00 0.00 0.98
2008 4560 9.099454 GTCCTTTCTCTTGTTTGACGATTATAT 57.901 33.333 0.00 0.00 0.00 0.86
2085 4647 7.228906 CAGTAATGATTCTTGCAGGAATGATCT 59.771 37.037 26.79 15.44 36.24 2.75
2101 4663 5.709011 ATGATCTCACGATTCAAAGAACG 57.291 39.130 0.00 0.00 0.00 3.95
2114 4676 3.640029 TCAAAGAACGTCTAAGGGACTGT 59.360 43.478 0.00 0.00 40.86 3.55
2209 4884 2.964209 TGTTGCCCCCTTATTTGAACA 58.036 42.857 0.00 0.00 0.00 3.18
2266 4941 3.072944 CTGCACCTCTTTTCTGGAGAAG 58.927 50.000 0.00 0.00 35.21 2.85
2273 4951 4.202409 CCTCTTTTCTGGAGAAGGAACACT 60.202 45.833 1.92 0.00 35.21 3.55
2320 5000 5.687166 AAATTGTCAGAATTGCCATGGAT 57.313 34.783 18.40 0.00 0.00 3.41
2346 5027 9.904198 TGATGTTAAGATTGATATTTGGTCTCA 57.096 29.630 0.00 0.00 0.00 3.27
2427 5111 4.220382 CACATTATCTTCTTGGTTTGCCCA 59.780 41.667 0.00 0.00 43.27 5.36
2431 5117 4.541973 ATCTTCTTGGTTTGCCCATTTC 57.458 40.909 0.00 0.00 44.74 2.17
2455 5141 4.551388 TGTTTGTTTGGCCGATGATTAAC 58.449 39.130 0.00 0.00 0.00 2.01
2493 5181 6.883217 ACAAGCATATGTCTCAACTCTTCATT 59.117 34.615 4.29 0.00 0.00 2.57
2495 5183 8.886719 CAAGCATATGTCTCAACTCTTCATTTA 58.113 33.333 4.29 0.00 0.00 1.40
2589 5279 6.919662 GGGTGATGATTACAAATGCATAGTTG 59.080 38.462 0.00 4.40 37.85 3.16
2606 5296 2.880890 AGTTGAGATGACCAAACTGTGC 59.119 45.455 0.00 0.00 0.00 4.57
2610 5300 4.318332 TGAGATGACCAAACTGTGCTTAG 58.682 43.478 0.00 0.00 0.00 2.18
2739 5429 9.487790 TTTTAATTTGATAAAGGAAACTGCAGG 57.512 29.630 19.93 0.00 42.68 4.85
2753 5443 1.658673 GCAGGGAGCATGCTATTGC 59.341 57.895 22.74 24.39 44.79 3.56
2778 5468 3.273434 GTGAGCAAATCCATGTGAGCTA 58.727 45.455 0.00 0.00 31.61 3.32
2897 5597 4.214310 TGATTTCATATTTGTCGCCCCAT 58.786 39.130 0.00 0.00 0.00 4.00
2935 5635 2.355513 GGTGGATCTGTGCTGATTGACT 60.356 50.000 0.00 0.00 0.00 3.41
3050 5755 0.609957 CCTGTGCTTTGGATGAGGCA 60.610 55.000 0.00 0.00 0.00 4.75
3111 5819 5.762179 TTACTCTGATGTTCAGGAACCAT 57.238 39.130 9.49 3.82 44.39 3.55
3270 5995 7.834068 TTGTTTAGATATCACTCTCTTGCAC 57.166 36.000 5.32 0.00 0.00 4.57
3285 6010 4.112634 TCTTGCACGTTGCTGATATCTAC 58.887 43.478 3.98 0.00 45.31 2.59
3300 6025 8.765219 GCTGATATCTACGTATGTGAACAAATT 58.235 33.333 3.98 0.00 0.00 1.82
3364 6244 4.006319 ACTGCCTTAAACTTCTGATGCTC 58.994 43.478 0.00 0.00 0.00 4.26
3458 6474 0.323178 AGTCTTAGGGTCCGCTTCGA 60.323 55.000 0.00 0.00 0.00 3.71
3496 6516 5.679734 TTGACTTCTGAATCTGACTTTGC 57.320 39.130 0.00 0.00 0.00 3.68
3503 6523 6.829229 TCTGAATCTGACTTTGCAAATGAT 57.171 33.333 13.23 10.98 0.00 2.45
3656 6842 2.582978 GAGTAACCACCGGGGAGC 59.417 66.667 4.41 0.00 41.15 4.70
3681 6867 9.065871 GCATTATTAACTGCTTTGTTTAGACAG 57.934 33.333 0.00 0.00 34.86 3.51
3703 6889 3.953612 GCATGTGTTTCCCTTGATATCCA 59.046 43.478 0.00 0.00 0.00 3.41
3713 6899 8.624776 GTTTCCCTTGATATCCATTAGTTTCTG 58.375 37.037 0.00 0.00 0.00 3.02
3714 6900 7.451731 TCCCTTGATATCCATTAGTTTCTGT 57.548 36.000 0.00 0.00 0.00 3.41
3725 6993 7.136119 TCCATTAGTTTCTGTTTTTACTTGCG 58.864 34.615 0.00 0.00 0.00 4.85
3813 7081 3.042682 TGTGAGGACCAACAGGACTTTA 58.957 45.455 0.00 0.00 0.00 1.85
3819 7087 3.326880 GGACCAACAGGACTTTAGAGGAA 59.673 47.826 0.00 0.00 0.00 3.36
4014 7284 9.645059 AAATGTGTCATATATCTTCATCCTACG 57.355 33.333 0.00 0.00 0.00 3.51
4015 7285 7.996098 TGTGTCATATATCTTCATCCTACGA 57.004 36.000 0.00 0.00 0.00 3.43
4017 7287 6.962116 GTGTCATATATCTTCATCCTACGACG 59.038 42.308 0.00 0.00 0.00 5.12
4037 7310 5.221891 ACGCTTGCAGTTTATGTATTGAG 57.778 39.130 0.00 0.00 0.00 3.02
4039 7312 5.163854 ACGCTTGCAGTTTATGTATTGAGTC 60.164 40.000 0.00 0.00 0.00 3.36
4040 7315 5.573146 GCTTGCAGTTTATGTATTGAGTCC 58.427 41.667 0.00 0.00 0.00 3.85
4187 7466 5.835113 AAAGCTGACAACTTTTGCTTCTA 57.165 34.783 0.00 0.00 42.23 2.10
4201 7480 9.323985 ACTTTTGCTTCTATATCTTCAGCTAAG 57.676 33.333 0.00 0.00 36.45 2.18
4250 7529 1.672854 TAAGGATGCTCGTGGACCCG 61.673 60.000 0.00 0.00 0.00 5.28
4286 7565 1.264826 CCAAACCTTTTACGTGGTCCG 59.735 52.381 0.00 0.00 44.03 4.79
4296 7575 3.277652 CGTGGTCCGTTGTTGTAGT 57.722 52.632 0.00 0.00 0.00 2.73
4314 7593 5.830912 TGTAGTTCTTGTTTGAAATGCCAG 58.169 37.500 0.00 0.00 0.00 4.85
4315 7594 5.359576 TGTAGTTCTTGTTTGAAATGCCAGT 59.640 36.000 0.00 0.00 0.00 4.00
4333 7614 5.774690 TGCCAGTGGACTGAATAAATCTTTT 59.225 36.000 15.20 0.00 46.59 2.27
4363 7644 0.886563 GCTTCAAGCAGTGATGCCTT 59.113 50.000 3.89 0.00 46.68 4.35
4365 7646 2.434428 CTTCAAGCAGTGATGCCTTCT 58.566 47.619 0.00 0.00 35.70 2.85
4369 7650 2.877168 CAAGCAGTGATGCCTTCTATCC 59.123 50.000 0.00 0.00 34.90 2.59
4400 7683 1.140312 TCTGTTCTTGCCCTGGTTCT 58.860 50.000 0.00 0.00 0.00 3.01
4618 7901 4.795268 AGTAATATGTACCATCGCAGTCG 58.205 43.478 0.00 0.00 0.00 4.18
4637 7920 3.689649 GTCGATCTGTTGTTATGCCCTTT 59.310 43.478 0.00 0.00 0.00 3.11
4668 7951 4.768130 TCTATATAACTCTGGCTGCGTC 57.232 45.455 0.00 0.00 0.00 5.19
4805 8091 3.554934 TCCAGTGTTCAGTGAAAGCAAT 58.445 40.909 7.25 0.00 0.00 3.56
4818 9686 0.322456 AAGCAATGCGGAGTGCCTTA 60.322 50.000 25.60 0.00 44.45 2.69
4854 9722 8.606040 AAAAACTGGATTAACACAATGGAATG 57.394 30.769 0.00 0.00 0.00 2.67
4855 9723 5.329035 ACTGGATTAACACAATGGAATGC 57.671 39.130 0.00 0.00 0.00 3.56
4856 9724 4.160252 ACTGGATTAACACAATGGAATGCC 59.840 41.667 0.00 0.00 0.00 4.40
4911 9779 7.977853 ACAATGAGAATTTAACCATGAATGCTC 59.022 33.333 6.07 6.07 37.60 4.26
4912 9780 6.455360 TGAGAATTTAACCATGAATGCTCC 57.545 37.500 9.35 0.00 36.71 4.70
4925 9793 6.980397 CCATGAATGCTCCCTAAATTTGTTAC 59.020 38.462 0.00 0.00 0.00 2.50
4926 9794 7.363705 CCATGAATGCTCCCTAAATTTGTTACA 60.364 37.037 0.00 0.00 0.00 2.41
4950 9818 6.478512 TTTTTACTTGCAACTGGATTTCCT 57.521 33.333 0.00 0.00 36.82 3.36
4955 9823 6.478512 ACTTGCAACTGGATTTCCTTTTTA 57.521 33.333 0.00 0.00 36.82 1.52
4956 9824 7.066307 ACTTGCAACTGGATTTCCTTTTTAT 57.934 32.000 0.00 0.00 36.82 1.40
4970 9838 6.554334 TCCTTTTTATGTTGTTCTTCTCCG 57.446 37.500 0.00 0.00 0.00 4.63
4986 9854 2.046864 CCGGTCCTTCTGCGAGAGA 61.047 63.158 0.00 0.00 0.00 3.10
4987 9855 1.431440 CGGTCCTTCTGCGAGAGAG 59.569 63.158 0.00 0.00 30.18 3.20
4988 9856 1.813192 GGTCCTTCTGCGAGAGAGG 59.187 63.158 0.00 0.00 30.18 3.69
4989 9857 0.968393 GGTCCTTCTGCGAGAGAGGT 60.968 60.000 0.00 0.00 30.18 3.85
4991 9859 1.135228 GTCCTTCTGCGAGAGAGGTTC 60.135 57.143 0.00 0.00 30.18 3.62
4992 9860 0.174617 CCTTCTGCGAGAGAGGTTCC 59.825 60.000 0.00 0.00 30.18 3.62
4993 9861 0.174617 CTTCTGCGAGAGAGGTTCCC 59.825 60.000 0.00 0.00 30.18 3.97
5018 9886 6.036577 AGAAATTTGTGTATTTGGCCGAAT 57.963 33.333 22.05 22.05 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 904 2.159627 CACATACGAGTTGCCAGGAAAC 59.840 50.000 1.20 1.20 0.00 2.78
185 922 2.809307 TTCCTTTCCGCCCGACACA 61.809 57.895 0.00 0.00 0.00 3.72
189 927 2.652095 ATCGTTCCTTTCCGCCCGA 61.652 57.895 0.00 0.00 0.00 5.14
278 1019 8.531622 TGTAATTTTTGTCATGCGATTTTGAT 57.468 26.923 0.00 0.00 0.00 2.57
303 1044 2.388735 TGTGAGGCGTCTAGGATTCAT 58.611 47.619 8.06 0.00 0.00 2.57
383 1289 5.001232 CCGACAACCTCCTTGAAAATCTTA 58.999 41.667 0.00 0.00 33.59 2.10
430 1336 1.807165 CCGCTGTCGTCACTCATGG 60.807 63.158 0.00 0.00 0.00 3.66
445 1351 4.505217 CAATGCAGACGTCGCCGC 62.505 66.667 23.01 20.28 37.70 6.53
484 1491 3.935203 CGTACAGGTTCAGATCAATGCTT 59.065 43.478 0.00 0.00 0.00 3.91
507 1697 0.107703 TCCATCAATCTCCACCACGC 60.108 55.000 0.00 0.00 0.00 5.34
518 1708 3.294214 GGTCCTTGAGCAATCCATCAAT 58.706 45.455 0.00 0.00 35.04 2.57
605 1801 6.560003 TTCTTATTAAGGATGCTGACTGGA 57.440 37.500 3.66 0.00 0.00 3.86
651 1847 0.322546 AATTTCACCCCTGAGCGGTC 60.323 55.000 7.89 7.89 0.00 4.79
775 1971 3.323691 ACGTGTGCAAGGGCTATATATCA 59.676 43.478 0.00 0.00 41.91 2.15
776 1972 3.926616 ACGTGTGCAAGGGCTATATATC 58.073 45.455 0.00 0.00 41.91 1.63
777 1973 4.040461 AGAACGTGTGCAAGGGCTATATAT 59.960 41.667 0.00 0.00 41.91 0.86
778 1974 3.386726 AGAACGTGTGCAAGGGCTATATA 59.613 43.478 0.00 0.00 41.91 0.86
779 1975 2.170607 AGAACGTGTGCAAGGGCTATAT 59.829 45.455 0.00 0.00 41.91 0.86
780 1976 1.553248 AGAACGTGTGCAAGGGCTATA 59.447 47.619 0.00 0.00 41.91 1.31
781 1977 0.324943 AGAACGTGTGCAAGGGCTAT 59.675 50.000 0.00 0.00 41.91 2.97
782 1978 0.107831 AAGAACGTGTGCAAGGGCTA 59.892 50.000 0.00 0.00 41.91 3.93
783 1979 0.751643 AAAGAACGTGTGCAAGGGCT 60.752 50.000 0.00 0.00 41.91 5.19
785 1981 1.535860 CCAAAAGAACGTGTGCAAGGG 60.536 52.381 0.00 0.00 0.00 3.95
786 1982 1.838913 CCAAAAGAACGTGTGCAAGG 58.161 50.000 0.00 0.00 0.00 3.61
787 1983 1.199624 GCCAAAAGAACGTGTGCAAG 58.800 50.000 0.00 0.00 0.00 4.01
788 1984 0.179124 GGCCAAAAGAACGTGTGCAA 60.179 50.000 0.00 0.00 0.00 4.08
789 1985 1.435515 GGCCAAAAGAACGTGTGCA 59.564 52.632 0.00 0.00 0.00 4.57
790 1986 1.299850 GGGCCAAAAGAACGTGTGC 60.300 57.895 4.39 0.00 0.00 4.57
793 1989 2.642700 CCGGGCCAAAAGAACGTG 59.357 61.111 4.39 0.00 0.00 4.49
794 1990 3.292159 GCCGGGCCAAAAGAACGT 61.292 61.111 8.12 0.00 0.00 3.99
814 2010 4.530857 ATCTGGGCCGTGCTACGC 62.531 66.667 0.00 0.58 40.91 4.42
815 2011 2.586079 CATCTGGGCCGTGCTACG 60.586 66.667 0.00 2.27 42.11 3.51
816 2012 2.203070 CCATCTGGGCCGTGCTAC 60.203 66.667 0.00 0.00 0.00 3.58
842 2038 0.958822 ATTTCGCAGGTGGTTGAACC 59.041 50.000 7.57 7.57 40.85 3.62
843 2039 1.335872 CCATTTCGCAGGTGGTTGAAC 60.336 52.381 0.00 0.00 0.00 3.18
844 2040 0.958091 CCATTTCGCAGGTGGTTGAA 59.042 50.000 0.00 0.00 0.00 2.69
845 2041 0.893270 CCCATTTCGCAGGTGGTTGA 60.893 55.000 0.00 0.00 0.00 3.18
846 2042 1.586028 CCCATTTCGCAGGTGGTTG 59.414 57.895 0.00 0.00 0.00 3.77
847 2043 2.275380 GCCCATTTCGCAGGTGGTT 61.275 57.895 0.00 0.00 0.00 3.67
848 2044 2.676471 GCCCATTTCGCAGGTGGT 60.676 61.111 0.00 0.00 0.00 4.16
849 2045 3.814268 CGCCCATTTCGCAGGTGG 61.814 66.667 0.00 0.00 0.00 4.61
850 2046 2.745884 TCGCCCATTTCGCAGGTG 60.746 61.111 0.00 0.00 0.00 4.00
851 2047 2.436646 CTCGCCCATTTCGCAGGT 60.437 61.111 0.00 0.00 0.00 4.00
852 2048 2.587322 TACCTCGCCCATTTCGCAGG 62.587 60.000 0.00 0.00 33.56 4.85
853 2049 1.153449 TACCTCGCCCATTTCGCAG 60.153 57.895 0.00 0.00 0.00 5.18
855 2051 2.178235 GGTACCTCGCCCATTTCGC 61.178 63.158 4.06 0.00 0.00 4.70
856 2052 1.881252 CGGTACCTCGCCCATTTCG 60.881 63.158 10.90 0.00 0.00 3.46
857 2053 1.523032 CCGGTACCTCGCCCATTTC 60.523 63.158 10.90 0.00 0.00 2.17
858 2054 1.968050 CTCCGGTACCTCGCCCATTT 61.968 60.000 10.90 0.00 0.00 2.32
859 2055 2.364579 TCCGGTACCTCGCCCATT 60.365 61.111 10.90 0.00 0.00 3.16
860 2056 2.838225 CTCCGGTACCTCGCCCAT 60.838 66.667 10.90 0.00 0.00 4.00
865 2061 2.838225 ATGCCCTCCGGTACCTCG 60.838 66.667 10.90 0.00 0.00 4.63
866 2062 2.808206 CCATGCCCTCCGGTACCTC 61.808 68.421 10.90 0.00 0.00 3.85
867 2063 2.621672 ATCCATGCCCTCCGGTACCT 62.622 60.000 10.90 0.00 0.00 3.08
868 2064 2.147387 ATCCATGCCCTCCGGTACC 61.147 63.158 0.16 0.16 0.00 3.34
869 2065 1.071471 CATCCATGCCCTCCGGTAC 59.929 63.158 0.00 0.00 0.00 3.34
870 2066 2.146724 CCATCCATGCCCTCCGGTA 61.147 63.158 0.00 0.00 0.00 4.02
872 2068 1.492133 ATACCATCCATGCCCTCCGG 61.492 60.000 0.00 0.00 0.00 5.14
873 2069 0.321919 CATACCATCCATGCCCTCCG 60.322 60.000 0.00 0.00 0.00 4.63
875 2071 1.546323 CCACATACCATCCATGCCCTC 60.546 57.143 0.00 0.00 0.00 4.30
878 2074 2.071778 AACCACATACCATCCATGCC 57.928 50.000 0.00 0.00 0.00 4.40
879 2075 5.127031 AGTTTTAACCACATACCATCCATGC 59.873 40.000 0.00 0.00 0.00 4.06
883 2079 4.142249 GGCAGTTTTAACCACATACCATCC 60.142 45.833 0.00 0.00 0.00 3.51
884 2080 4.461081 TGGCAGTTTTAACCACATACCATC 59.539 41.667 0.00 0.00 0.00 3.51
885 2081 4.411927 TGGCAGTTTTAACCACATACCAT 58.588 39.130 0.00 0.00 0.00 3.55
886 2082 3.833732 TGGCAGTTTTAACCACATACCA 58.166 40.909 0.00 0.00 0.00 3.25
887 2083 5.185056 AGAATGGCAGTTTTAACCACATACC 59.815 40.000 0.00 0.00 35.99 2.73
888 2084 6.267496 AGAATGGCAGTTTTAACCACATAC 57.733 37.500 0.00 0.00 35.99 2.39
889 2085 6.909550 AAGAATGGCAGTTTTAACCACATA 57.090 33.333 0.00 0.00 35.99 2.29
890 2086 5.806654 AAGAATGGCAGTTTTAACCACAT 57.193 34.783 0.00 0.00 35.99 3.21
891 2087 5.830991 AGTAAGAATGGCAGTTTTAACCACA 59.169 36.000 0.00 0.00 35.99 4.17
893 2089 7.174253 CACTAGTAAGAATGGCAGTTTTAACCA 59.826 37.037 0.00 0.00 37.99 3.67
894 2090 7.174426 ACACTAGTAAGAATGGCAGTTTTAACC 59.826 37.037 0.00 0.00 0.00 2.85
896 2092 7.117236 CGACACTAGTAAGAATGGCAGTTTTAA 59.883 37.037 0.00 0.00 0.00 1.52
898 2094 5.408604 CGACACTAGTAAGAATGGCAGTTTT 59.591 40.000 0.00 0.00 0.00 2.43
906 3072 5.102313 TGTGATGCGACACTAGTAAGAATG 58.898 41.667 12.83 0.00 40.87 2.67
915 3081 1.011968 GGCGTTGTGATGCGACACTA 61.012 55.000 12.83 4.37 40.87 2.74
1102 3620 4.891756 CGGGTAGATCTAACCTAAGTTCCA 59.108 45.833 29.90 0.00 40.76 3.53
1103 3621 4.892345 ACGGGTAGATCTAACCTAAGTTCC 59.108 45.833 29.90 12.37 40.76 3.62
1131 3649 2.986306 GACGGAACCCTCGCGAGAA 61.986 63.158 36.59 0.69 41.32 2.87
1150 3668 9.090692 GAATGGTATCAATCAAACCAAATCAAG 57.909 33.333 0.00 0.00 45.91 3.02
1152 3670 7.257003 CGAATGGTATCAATCAAACCAAATCA 58.743 34.615 0.00 0.00 45.91 2.57
1175 3693 1.226859 CGAAGCGCTACCAATCCGA 60.227 57.895 12.05 0.00 0.00 4.55
1240 3759 2.821810 GGCTTCAAGGGAGCGAGC 60.822 66.667 0.00 0.00 0.00 5.03
1245 3764 2.092538 AGATGATGTGGCTTCAAGGGAG 60.093 50.000 0.00 0.00 0.00 4.30
1346 3868 6.743575 AGAACAAATCAATACCAGTAGCAC 57.256 37.500 0.00 0.00 0.00 4.40
1372 3894 0.601576 ACAAACAGACCGCACGCATA 60.602 50.000 0.00 0.00 0.00 3.14
1453 3977 3.976015 TGTTGGATTTGGGGGATTCTAC 58.024 45.455 0.00 0.00 0.00 2.59
1456 3980 3.173151 ACTTGTTGGATTTGGGGGATTC 58.827 45.455 0.00 0.00 0.00 2.52
1491 4030 0.809385 CAGGTCTGCAAAGGCTCATG 59.191 55.000 0.00 0.00 41.91 3.07
1581 4120 6.237901 AGTGTATGTATGTTTTGCCTCTTGA 58.762 36.000 0.00 0.00 0.00 3.02
1593 4132 8.067751 ACTTGTGATACAGAGTGTATGTATGT 57.932 34.615 4.31 0.00 43.08 2.29
1647 4186 8.178964 CCATTCCATATGAAGCAAACAAATTTG 58.821 33.333 16.67 16.67 40.48 2.32
1716 4255 5.239963 TCGACCCCTTTGATTTACTTCAAAC 59.760 40.000 0.00 0.00 39.91 2.93
1728 4267 0.685097 CCTCAACTCGACCCCTTTGA 59.315 55.000 0.00 0.00 0.00 2.69
1767 4307 6.900194 AGCCTACCAAAGAAAATAGCTATGA 58.100 36.000 7.09 0.00 0.00 2.15
1770 4310 5.105064 ACGAGCCTACCAAAGAAAATAGCTA 60.105 40.000 0.00 0.00 0.00 3.32
1779 4319 3.202829 ACAAAACGAGCCTACCAAAGA 57.797 42.857 0.00 0.00 0.00 2.52
1785 4325 3.252458 ACCATCAAACAAAACGAGCCTAC 59.748 43.478 0.00 0.00 0.00 3.18
2007 4559 9.374838 GAAAAATCAAATTGATTACCAGCTCAT 57.625 29.630 20.05 0.36 45.57 2.90
2008 4560 8.366401 TGAAAAATCAAATTGATTACCAGCTCA 58.634 29.630 20.05 13.19 45.57 4.26
2045 4597 7.561722 AGAATCATTACTGGTCTGCTAGAACTA 59.438 37.037 0.00 0.00 31.84 2.24
2085 4647 4.921515 CCTTAGACGTTCTTTGAATCGTGA 59.078 41.667 10.66 0.00 36.67 4.35
2101 4663 4.495422 CATGTACACACAGTCCCTTAGAC 58.505 47.826 0.00 0.00 46.71 2.59
2114 4676 2.228582 GTGCAAATGCTCCATGTACACA 59.771 45.455 0.00 0.00 42.66 3.72
2168 4843 7.431084 GCAACAAAACCATAAATATACGTCAGG 59.569 37.037 0.00 0.00 0.00 3.86
2236 4911 0.034059 AAGAGGTGCAGTCAAGGTCG 59.966 55.000 0.00 0.00 0.00 4.79
2292 4972 5.299148 TGGCAATTCTGACAATTTTCTTGG 58.701 37.500 0.00 0.00 37.77 3.61
2320 5000 9.904198 TGAGACCAAATATCAATCTTAACATCA 57.096 29.630 0.00 0.00 0.00 3.07
2346 5027 6.073112 GCAAACAAATGCCACTTATGACAAAT 60.073 34.615 0.00 0.00 40.49 2.32
2377 5058 4.019231 GGAGGACTCAGAATTTGGGTAGTT 60.019 45.833 1.32 0.00 41.81 2.24
2427 5111 3.810310 TCGGCCAAACAAACAAGAAAT 57.190 38.095 2.24 0.00 0.00 2.17
2431 5117 2.791383 TCATCGGCCAAACAAACAAG 57.209 45.000 2.24 0.00 0.00 3.16
2495 5183 7.933577 TCGACCTCATTGATAATTATGCTTTCT 59.066 33.333 1.78 0.00 0.00 2.52
2589 5279 4.319177 ACTAAGCACAGTTTGGTCATCTC 58.681 43.478 0.00 0.00 33.68 2.75
2606 5296 8.283291 AGCGAAAGACTATTTTGTTCAACTAAG 58.717 33.333 0.00 0.00 0.00 2.18
2610 5300 5.851703 GGAGCGAAAGACTATTTTGTTCAAC 59.148 40.000 6.72 0.00 0.00 3.18
2725 5415 3.042481 GCTCCCTGCAGTTTCCTTT 57.958 52.632 13.81 0.00 42.31 3.11
2753 5443 4.261072 GCTCACATGGATTTGCTCACATAG 60.261 45.833 0.00 0.00 0.00 2.23
2754 5444 3.628942 GCTCACATGGATTTGCTCACATA 59.371 43.478 0.00 0.00 0.00 2.29
2755 5445 2.426024 GCTCACATGGATTTGCTCACAT 59.574 45.455 0.00 0.00 0.00 3.21
2897 5597 2.489971 CACCAAAGCGGACACTAAGAA 58.510 47.619 0.00 0.00 38.63 2.52
2935 5635 9.645059 CATTTACAGAGTCAGATTCAGAAGTAA 57.355 33.333 0.00 0.00 0.00 2.24
3050 5755 5.644644 CACAAGAAAAACTCAACAAGCTCT 58.355 37.500 0.00 0.00 0.00 4.09
3111 5819 7.466746 AATATTTCAAAAGGCTGCAAGAGTA 57.533 32.000 0.50 0.00 34.07 2.59
3151 5871 4.081322 ACAACGGAAACTGTGGTATCTT 57.919 40.909 0.00 0.00 0.00 2.40
3257 5982 2.605094 GCAACGTGCAAGAGAGTGA 58.395 52.632 6.65 0.00 44.26 3.41
3270 5995 5.449304 TCACATACGTAGATATCAGCAACG 58.551 41.667 5.32 11.10 39.37 4.10
3285 6010 4.646960 TCGCATGAATTTGTTCACATACG 58.353 39.130 0.00 0.00 33.23 3.06
3300 6025 2.736579 AAGTGCCACAGCTCGCATGA 62.737 55.000 0.00 0.00 40.80 3.07
3340 6220 4.829492 AGCATCAGAAGTTTAAGGCAGTTT 59.171 37.500 0.00 0.00 0.00 2.66
3364 6244 7.807977 AGGCATGTTTAGTAGAATGGTTATG 57.192 36.000 0.00 0.00 0.00 1.90
3458 6474 2.570752 AGTCAATCAGCACAGATCCACT 59.429 45.455 0.00 0.00 0.00 4.00
3527 6547 4.572389 GCTCATCGACATAAATCAACCACT 59.428 41.667 0.00 0.00 0.00 4.00
3531 6551 4.572389 ACCAGCTCATCGACATAAATCAAC 59.428 41.667 0.00 0.00 0.00 3.18
3544 6564 4.764172 ACAAACTCAGATACCAGCTCATC 58.236 43.478 0.00 0.00 0.00 2.92
3545 6565 4.833478 ACAAACTCAGATACCAGCTCAT 57.167 40.909 0.00 0.00 0.00 2.90
3597 6782 5.810525 ACAAGATGACACAAGAAAAACTCG 58.189 37.500 0.00 0.00 0.00 4.18
3630 6816 1.469251 CGGTGGTTACTCGACATCAGG 60.469 57.143 0.00 0.00 0.00 3.86
3656 6842 9.065871 GCTGTCTAAACAAAGCAGTTAATAATG 57.934 33.333 0.00 0.00 34.24 1.90
3681 6867 3.953612 TGGATATCAAGGGAAACACATGC 59.046 43.478 4.83 0.00 0.00 4.06
3686 6872 8.336235 AGAAACTAATGGATATCAAGGGAAACA 58.664 33.333 4.83 0.00 0.00 2.83
3725 6993 2.796032 GCTCAGAACAAACAGCACCAAC 60.796 50.000 0.00 0.00 0.00 3.77
3813 7081 5.596772 GCTACCTTTAGATGAGAGTTCCTCT 59.403 44.000 0.00 0.00 44.28 3.69
3819 7087 4.096682 GTGACGCTACCTTTAGATGAGAGT 59.903 45.833 0.00 0.00 0.00 3.24
3901 7170 9.958180 TCAGACAAGATATTCTCAAACCAATAA 57.042 29.630 0.00 0.00 0.00 1.40
3981 7251 8.088365 TGAAGATATATGACACATTTCCTACCG 58.912 37.037 0.00 0.00 0.00 4.02
4009 7279 1.705256 TAAACTGCAAGCGTCGTAGG 58.295 50.000 0.00 0.00 37.60 3.18
4010 7280 2.666508 ACATAAACTGCAAGCGTCGTAG 59.333 45.455 0.00 0.00 37.60 3.51
4014 7284 5.163854 ACTCAATACATAAACTGCAAGCGTC 60.164 40.000 0.00 0.00 37.60 5.19
4015 7285 4.695455 ACTCAATACATAAACTGCAAGCGT 59.305 37.500 0.00 0.00 37.60 5.07
4017 7287 5.123820 TGGACTCAATACATAAACTGCAAGC 59.876 40.000 0.00 0.00 37.60 4.01
4037 7310 8.561738 TCTTCATAACAGGAAATAAACTGGAC 57.438 34.615 0.00 0.00 39.00 4.02
4039 7312 7.917505 GCATCTTCATAACAGGAAATAAACTGG 59.082 37.037 0.00 0.00 39.00 4.00
4040 7315 8.680903 AGCATCTTCATAACAGGAAATAAACTG 58.319 33.333 0.00 0.00 40.48 3.16
4083 7362 5.046529 TGAAACACAAATGCGCATAAAAGT 58.953 33.333 25.61 17.03 0.00 2.66
4084 7363 5.573296 TGAAACACAAATGCGCATAAAAG 57.427 34.783 25.61 16.37 0.00 2.27
4147 7426 5.695816 CAGCTTTTTAGCACAAATAAGGCAA 59.304 36.000 0.00 0.00 37.25 4.52
4201 7480 0.972883 ATATCTCCTCCCTCGCTTGC 59.027 55.000 0.00 0.00 0.00 4.01
4250 7529 6.575162 AGGTTTGGTTTAACTCACATCATC 57.425 37.500 0.00 0.00 0.00 2.92
4286 7565 7.391016 GCATTTCAAACAAGAACTACAACAAC 58.609 34.615 0.00 0.00 0.00 3.32
4296 7575 3.703556 TCCACTGGCATTTCAAACAAGAA 59.296 39.130 0.00 0.00 0.00 2.52
4314 7593 6.524586 CAGCGAAAAAGATTTATTCAGTCCAC 59.475 38.462 0.00 0.00 0.00 4.02
4315 7594 6.611381 CAGCGAAAAAGATTTATTCAGTCCA 58.389 36.000 0.00 0.00 0.00 4.02
4593 7876 9.165287 TCGACTGCGATGGTACATATTACTACC 62.165 44.444 0.00 0.00 42.51 3.18
4618 7901 3.774066 GCAAAGGGCATAACAACAGATC 58.226 45.455 0.00 0.00 43.97 2.75
4637 7920 6.233434 CCAGAGTTATATAGATTTGCCAGCA 58.767 40.000 0.00 0.00 0.00 4.41
4668 7951 4.672409 GGCAAAATCTTTCCAGGTTATCG 58.328 43.478 0.00 0.00 0.00 2.92
4805 8091 2.772077 TTTATGTAAGGCACTCCGCA 57.228 45.000 0.00 0.00 45.17 5.69
4834 9702 4.160065 TGGCATTCCATTGTGTTAATCCAG 59.840 41.667 0.00 0.00 37.47 3.86
4836 9704 4.402155 TCTGGCATTCCATTGTGTTAATCC 59.598 41.667 0.00 0.00 42.51 3.01
4837 9705 5.581126 TCTGGCATTCCATTGTGTTAATC 57.419 39.130 0.00 0.00 42.51 1.75
4839 9707 4.320861 CGTTCTGGCATTCCATTGTGTTAA 60.321 41.667 0.00 0.00 42.51 2.01
4841 9709 2.030007 CGTTCTGGCATTCCATTGTGTT 60.030 45.455 0.00 0.00 42.51 3.32
4842 9710 1.541147 CGTTCTGGCATTCCATTGTGT 59.459 47.619 0.00 0.00 42.51 3.72
4845 9713 4.129380 TCTATCGTTCTGGCATTCCATTG 58.871 43.478 0.00 0.00 42.51 2.82
4846 9714 4.422073 TCTATCGTTCTGGCATTCCATT 57.578 40.909 0.00 0.00 42.51 3.16
4847 9715 4.564406 GGATCTATCGTTCTGGCATTCCAT 60.564 45.833 0.00 0.00 42.51 3.41
4848 9716 3.244215 GGATCTATCGTTCTGGCATTCCA 60.244 47.826 0.00 0.00 40.85 3.53
4850 9718 3.995199 TGGATCTATCGTTCTGGCATTC 58.005 45.455 0.00 0.00 0.00 2.67
4852 9720 4.130118 GTTTGGATCTATCGTTCTGGCAT 58.870 43.478 0.00 0.00 0.00 4.40
4853 9721 3.531538 GTTTGGATCTATCGTTCTGGCA 58.468 45.455 0.00 0.00 0.00 4.92
4854 9722 2.540101 CGTTTGGATCTATCGTTCTGGC 59.460 50.000 0.00 0.00 0.00 4.85
4855 9723 3.551890 CACGTTTGGATCTATCGTTCTGG 59.448 47.826 6.99 0.00 32.47 3.86
4856 9724 4.421058 TCACGTTTGGATCTATCGTTCTG 58.579 43.478 6.99 0.00 32.47 3.02
4902 9770 7.716799 TGTAACAAATTTAGGGAGCATTCAT 57.283 32.000 0.00 0.00 0.00 2.57
4925 9793 6.930722 AGGAAATCCAGTTGCAAGTAAAAATG 59.069 34.615 6.43 0.00 38.89 2.32
4926 9794 7.066307 AGGAAATCCAGTTGCAAGTAAAAAT 57.934 32.000 6.43 0.00 38.89 1.82
4950 9818 5.239963 GGACCGGAGAAGAACAACATAAAAA 59.760 40.000 9.46 0.00 0.00 1.94
4955 9823 1.978580 AGGACCGGAGAAGAACAACAT 59.021 47.619 9.46 0.00 0.00 2.71
4956 9824 1.420430 AGGACCGGAGAAGAACAACA 58.580 50.000 9.46 0.00 0.00 3.33
4970 9838 0.968393 ACCTCTCTCGCAGAAGGACC 60.968 60.000 14.79 0.00 34.09 4.46
4988 9856 6.073276 GCCAAATACACAAATTTCTTGGGAAC 60.073 38.462 0.00 0.00 0.00 3.62
4989 9857 5.994668 GCCAAATACACAAATTTCTTGGGAA 59.005 36.000 0.00 0.00 0.00 3.97
4991 9859 4.694982 GGCCAAATACACAAATTTCTTGGG 59.305 41.667 0.00 0.00 0.00 4.12
4992 9860 4.388469 CGGCCAAATACACAAATTTCTTGG 59.612 41.667 2.24 0.00 0.00 3.61
4993 9861 5.226396 TCGGCCAAATACACAAATTTCTTG 58.774 37.500 2.24 0.00 0.00 3.02
5267 10135 3.749064 GGCGAGAGACGAGTGGCA 61.749 66.667 0.00 0.00 45.77 4.92


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

AutoCloner maintained by Alex Coulton.