Multiple sequence alignment - TraesCS2D01G262400

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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 TraesCS2D01G262400 chr2D 100.000 6832 0 0 1 6832 318568671 318561840 0.000000e+00 12617.0
1 TraesCS2D01G262400 chr2D 93.413 167 9 2 4774 4939 498472994 498473159 5.290000e-61 246.0
2 TraesCS2D01G262400 chr2A 92.383 4976 208 74 1718 6595 412471647 412476549 0.000000e+00 6931.0
3 TraesCS2D01G262400 chr2A 94.424 1345 29 20 388 1719 412470232 412471543 0.000000e+00 2026.0
4 TraesCS2D01G262400 chr2A 90.524 401 16 1 1 401 412469451 412469829 1.700000e-140 510.0
5 TraesCS2D01G262400 chr2A 88.095 84 10 0 2 85 771349013 771348930 4.360000e-17 100.0
6 TraesCS2D01G262400 chr2A 93.182 44 3 0 960 1003 377016221 377016178 1.590000e-06 65.8
7 TraesCS2D01G262400 chr2B 93.910 3366 132 47 496 3816 387109070 387105733 0.000000e+00 5012.0
8 TraesCS2D01G262400 chr2B 92.883 2178 85 32 3826 5967 387105602 387103459 0.000000e+00 3099.0
9 TraesCS2D01G262400 chr2B 93.506 616 28 8 6227 6832 387103446 387102833 0.000000e+00 905.0
10 TraesCS2D01G262400 chr2B 92.814 167 10 2 4774 4939 585712491 585712656 2.460000e-59 241.0
11 TraesCS2D01G262400 chr2B 88.947 190 17 4 4773 4959 708240684 708240496 1.480000e-56 231.0
12 TraesCS2D01G262400 chr2B 93.571 140 3 1 147 280 387109431 387109292 3.230000e-48 204.0
13 TraesCS2D01G262400 chr2B 89.796 147 15 0 1 147 387109618 387109472 9.050000e-44 189.0
14 TraesCS2D01G262400 chr2B 91.729 133 8 3 300 429 387109300 387109168 1.510000e-41 182.0
15 TraesCS2D01G262400 chr2B 77.596 183 32 7 5134 5312 775106366 775106543 1.210000e-17 102.0
16 TraesCS2D01G262400 chr2B 95.455 44 2 0 960 1003 130141978 130141935 3.420000e-08 71.3
17 TraesCS2D01G262400 chr7D 95.092 163 7 1 4778 4939 566026575 566026737 8.790000e-64 255.0
18 TraesCS2D01G262400 chr7D 86.486 185 23 2 6024 6208 31567186 31567004 1.160000e-47 202.0
19 TraesCS2D01G262400 chr7D 84.865 185 25 2 6022 6204 360337353 360337536 4.210000e-42 183.0
20 TraesCS2D01G262400 chr7D 94.118 85 5 0 1 85 388999054 388999138 5.560000e-26 130.0
21 TraesCS2D01G262400 chr7A 93.605 172 9 2 4769 4939 652302162 652302332 8.790000e-64 255.0
22 TraesCS2D01G262400 chr7A 85.635 181 24 2 6027 6206 650029761 650029940 9.050000e-44 189.0
23 TraesCS2D01G262400 chr7A 92.105 114 7 2 455 567 23555589 23555477 7.090000e-35 159.0
24 TraesCS2D01G262400 chr7A 90.090 111 4 4 460 568 688310193 688310298 3.320000e-28 137.0
25 TraesCS2D01G262400 chr7A 97.674 43 1 0 961 1003 23555475 23555433 2.640000e-09 75.0
26 TraesCS2D01G262400 chr5D 93.865 163 9 1 4778 4939 461072763 461072601 1.900000e-60 244.0
27 TraesCS2D01G262400 chr4D 93.373 166 9 2 4777 4940 378279919 378280084 1.900000e-60 244.0
28 TraesCS2D01G262400 chr3A 87.363 182 23 0 6028 6209 27037554 27037735 6.940000e-50 209.0
29 TraesCS2D01G262400 chr3A 84.456 193 24 6 6024 6214 56733263 56733451 1.170000e-42 185.0
30 TraesCS2D01G262400 chr3D 86.667 180 23 1 6028 6207 598246109 598246287 1.500000e-46 198.0
31 TraesCS2D01G262400 chr7B 85.714 189 22 5 6028 6214 556738924 556738739 1.940000e-45 195.0
32 TraesCS2D01G262400 chr7B 87.574 169 20 1 6045 6212 750437196 750437028 1.940000e-45 195.0
33 TraesCS2D01G262400 chr7B 90.588 85 8 0 1 85 384202741 384202825 5.600000e-21 113.0
34 TraesCS2D01G262400 chr6B 89.024 82 9 0 3 84 2612128 2612047 1.210000e-17 102.0
35 TraesCS2D01G262400 chr6A 80.137 146 18 5 1 135 444690195 444690050 1.570000e-16 99.0
36 TraesCS2D01G262400 chr3B 86.667 90 10 2 1 90 684295982 684296069 1.570000e-16 99.0
37 TraesCS2D01G262400 chr4A 97.727 44 1 0 960 1003 706702715 706702758 7.350000e-10 76.8
38 TraesCS2D01G262400 chr4A 93.182 44 3 0 960 1003 677473886 677473929 1.590000e-06 65.8
39 TraesCS2D01G262400 chr1B 95.455 44 2 0 960 1003 544766823 544766780 3.420000e-08 71.3
40 TraesCS2D01G262400 chr1B 75.352 142 25 8 8 140 599297447 599297307 7.400000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G262400 chr2D 318561840 318568671 6831 True 12617.000000 12617 100.000000 1 6832 1 chr2D.!!$R1 6831
1 TraesCS2D01G262400 chr2A 412469451 412476549 7098 False 3155.666667 6931 92.443667 1 6595 3 chr2A.!!$F1 6594
2 TraesCS2D01G262400 chr2B 387102833 387109618 6785 True 1598.500000 5012 92.565833 1 6832 6 chr2B.!!$R3 6831

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
667 1204 0.038526 AGATTTGTTGCTGCTGCTGC 60.039 50.0 22.51 22.51 40.48 5.25 F
668 1205 0.038526 GATTTGTTGCTGCTGCTGCT 60.039 50.0 27.67 10.25 40.48 4.24 F
1366 1919 0.106149 ACTTGTCCGTGTCCTTGTCC 59.894 55.0 0.00 0.00 0.00 4.02 F
1367 1920 0.602905 CTTGTCCGTGTCCTTGTCCC 60.603 60.0 0.00 0.00 0.00 4.46 F
2213 2917 1.032114 ACCCGCTTTATTCTGCTGCC 61.032 55.0 0.00 0.00 0.00 4.85 F
3477 4194 0.386478 GCCTTGCTGCTGTTCTTTCG 60.386 55.0 0.00 0.00 0.00 3.46 F
4062 4916 0.037160 ATGTGGTGTGATCTGCAGCA 59.963 50.0 9.47 15.21 41.29 4.41 F
4219 5073 0.386113 GTTAAAAACACCGCCCTGCA 59.614 50.0 0.00 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 2056 1.538075 GAATTTTGGGCGGACGAGAAA 59.462 47.619 0.00 0.0 0.00 2.52 R
1927 2621 1.584724 GAGGGAGGAAGGATGACCAA 58.415 55.000 0.00 0.0 38.94 3.67 R
2785 3502 1.250328 TTGCTTCACTCAGGCATTGG 58.750 50.000 0.00 0.0 35.84 3.16 R
3114 3831 2.872557 CCATTGTGGTCAGCGCAG 59.127 61.111 11.47 0.0 31.35 5.18 R
4043 4897 0.037160 TGCTGCAGATCACACCACAT 59.963 50.000 20.43 0.0 0.00 3.21 R
4965 5829 0.107508 ATGATGGGCCACTGTTCTCG 60.108 55.000 9.28 0.0 0.00 4.04 R
5330 6195 0.536460 GGTCTTTTGGGTCGGCTTCA 60.536 55.000 0.00 0.0 0.00 3.02 R
5902 6792 2.623416 GCTAAGCTCAAACAACAAGGGT 59.377 45.455 0.00 0.0 0.00 4.34 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
66 67 2.699321 GTTTAGGGGATCGGCTAGAACT 59.301 50.000 0.00 0.00 0.00 3.01
69 70 1.120530 GGGGATCGGCTAGAACTGAA 58.879 55.000 0.00 0.00 0.00 3.02
164 206 1.064017 AGCACAAGACAAAGGGGACAA 60.064 47.619 0.00 0.00 0.00 3.18
375 491 5.358160 CCATCCCTAGTTGGTTCTGAATTTC 59.642 44.000 0.00 0.00 0.00 2.17
376 492 4.575885 TCCCTAGTTGGTTCTGAATTTCG 58.424 43.478 0.00 0.00 0.00 3.46
454 988 4.929819 TTGCAATGCAATATGAGATGCT 57.070 36.364 17.55 0.00 43.99 3.79
560 1094 7.062255 GCTGAAACAATTTACTAGCACCATTTC 59.938 37.037 0.00 0.00 0.00 2.17
584 1118 5.394005 CGCATCTTTCCTATCCTATGGAGAG 60.394 48.000 1.57 1.57 40.40 3.20
623 1157 4.686972 ACGTGTGTGAAGATGGATAGATG 58.313 43.478 0.00 0.00 0.00 2.90
667 1204 0.038526 AGATTTGTTGCTGCTGCTGC 60.039 50.000 22.51 22.51 40.48 5.25
668 1205 0.038526 GATTTGTTGCTGCTGCTGCT 60.039 50.000 27.67 10.25 40.48 4.24
669 1206 0.319555 ATTTGTTGCTGCTGCTGCTG 60.320 50.000 27.67 16.73 40.48 4.41
809 1350 1.569548 TCCATCCCGAGTTCCTAGTCT 59.430 52.381 0.00 0.00 0.00 3.24
840 1381 1.955495 AATTTCGGGGGCGCAAATCC 61.955 55.000 10.83 0.00 0.00 3.01
1040 1587 2.117423 CCCCCACACCCACCTTTC 59.883 66.667 0.00 0.00 0.00 2.62
1211 1758 3.081554 TCCAGAAGGAGGGCAAGC 58.918 61.111 0.00 0.00 39.61 4.01
1339 1886 3.696548 GGAAACAGGATTGATTGGAGGTC 59.303 47.826 0.00 0.00 0.00 3.85
1355 1908 1.012486 GGTCGGTGCTTACTTGTCCG 61.012 60.000 0.00 0.00 42.12 4.79
1357 1910 0.319211 TCGGTGCTTACTTGTCCGTG 60.319 55.000 0.00 0.00 41.58 4.94
1358 1911 0.599204 CGGTGCTTACTTGTCCGTGT 60.599 55.000 0.00 0.00 36.99 4.49
1359 1912 1.145803 GGTGCTTACTTGTCCGTGTC 58.854 55.000 0.00 0.00 0.00 3.67
1360 1913 1.145803 GTGCTTACTTGTCCGTGTCC 58.854 55.000 0.00 0.00 0.00 4.02
1361 1914 1.045407 TGCTTACTTGTCCGTGTCCT 58.955 50.000 0.00 0.00 0.00 3.85
1362 1915 1.414919 TGCTTACTTGTCCGTGTCCTT 59.585 47.619 0.00 0.00 0.00 3.36
1363 1916 1.798813 GCTTACTTGTCCGTGTCCTTG 59.201 52.381 0.00 0.00 0.00 3.61
1364 1917 2.805657 GCTTACTTGTCCGTGTCCTTGT 60.806 50.000 0.00 0.00 0.00 3.16
1365 1918 2.806608 TACTTGTCCGTGTCCTTGTC 57.193 50.000 0.00 0.00 0.00 3.18
1366 1919 0.106149 ACTTGTCCGTGTCCTTGTCC 59.894 55.000 0.00 0.00 0.00 4.02
1367 1920 0.602905 CTTGTCCGTGTCCTTGTCCC 60.603 60.000 0.00 0.00 0.00 4.46
1404 1957 3.011517 TGCCAGGCTCCCTTCCTC 61.012 66.667 14.15 0.00 0.00 3.71
1501 2056 2.224354 CCCGGCGGTTTAGGTAACATAT 60.224 50.000 26.32 0.00 38.55 1.78
1520 2075 1.611519 TTTCTCGTCCGCCCAAAATT 58.388 45.000 0.00 0.00 0.00 1.82
1736 2404 7.173218 ACAGTACTATGTTCCATTGTTTCTGTG 59.827 37.037 17.93 6.42 0.00 3.66
1753 2421 8.186163 TGTTTCTGTGGTCTTACGTATATACTG 58.814 37.037 11.05 7.14 0.00 2.74
1903 2581 2.158957 AGGTCAAACTGAACAAGAGCGA 60.159 45.455 0.00 0.00 36.30 4.93
1908 2586 2.440539 ACTGAACAAGAGCGACGATT 57.559 45.000 0.00 0.00 0.00 3.34
1913 2591 5.013861 TGAACAAGAGCGACGATTAAAAC 57.986 39.130 0.00 0.00 0.00 2.43
1917 2595 4.929808 ACAAGAGCGACGATTAAAACATCT 59.070 37.500 0.00 0.00 0.00 2.90
1918 2596 5.062308 ACAAGAGCGACGATTAAAACATCTC 59.938 40.000 0.00 0.00 0.00 2.75
1920 2598 4.800993 AGAGCGACGATTAAAACATCTCAG 59.199 41.667 0.00 0.00 0.00 3.35
1921 2599 4.495422 AGCGACGATTAAAACATCTCAGT 58.505 39.130 0.00 0.00 0.00 3.41
1962 2656 1.909302 CCCTCCTCACACTGGTATTGT 59.091 52.381 0.00 0.00 0.00 2.71
1963 2657 3.104512 CCCTCCTCACACTGGTATTGTA 58.895 50.000 0.00 0.00 0.00 2.41
1964 2658 3.711704 CCCTCCTCACACTGGTATTGTAT 59.288 47.826 0.00 0.00 0.00 2.29
1965 2659 4.164221 CCCTCCTCACACTGGTATTGTATT 59.836 45.833 0.00 0.00 0.00 1.89
1966 2660 5.118990 CCTCCTCACACTGGTATTGTATTG 58.881 45.833 0.00 0.00 0.00 1.90
2079 2778 2.857744 CGAGAGGGACGGGGTATGC 61.858 68.421 0.00 0.00 0.00 3.14
2094 2793 4.464947 GGGTATGCTTATCCTTGAAAGCT 58.535 43.478 8.36 0.00 46.57 3.74
2103 2803 7.066284 TGCTTATCCTTGAAAGCTGTATCTTTC 59.934 37.037 8.36 8.77 46.57 2.62
2124 2824 7.668469 TCTTTCCCCCAAATTCTTACTTAAGAC 59.332 37.037 10.09 0.00 41.64 3.01
2127 2827 7.858498 TCCCCCAAATTCTTACTTAAGACTAG 58.142 38.462 10.09 3.42 41.64 2.57
2167 2871 6.660521 TGGTTGAGATGCATGTATCTTTCTTT 59.339 34.615 24.69 4.36 37.53 2.52
2213 2917 1.032114 ACCCGCTTTATTCTGCTGCC 61.032 55.000 0.00 0.00 0.00 4.85
2407 3122 9.689976 CTCATCAGAAATACTAGATGTAACCAG 57.310 37.037 0.00 0.00 36.50 4.00
2422 3137 6.645884 TGTAACCAGTTAGGGGATTACATT 57.354 37.500 0.00 0.00 43.89 2.71
2425 3140 7.951245 TGTAACCAGTTAGGGGATTACATTTTT 59.049 33.333 0.00 0.00 43.89 1.94
2517 3233 7.357429 ACACTAAAACCACTACTACTCTTGT 57.643 36.000 0.00 0.00 0.00 3.16
2528 3244 8.091449 CCACTACTACTCTTGTGAAGAAAGATT 58.909 37.037 0.00 0.00 37.02 2.40
2590 3306 9.766277 TGTAAAATTGTTTCTTTGATGTTTTGC 57.234 25.926 0.00 0.00 0.00 3.68
2970 3687 7.959651 GCTTATAGTTTTCATGTGACAAGTCTG 59.040 37.037 1.53 0.00 0.00 3.51
3091 3808 6.934083 TGCTGTGTTACACTGAAAGATAATCA 59.066 34.615 23.14 7.72 35.76 2.57
3271 3988 5.163499 TGGTGGGTACTTTGAAATGACAAAC 60.163 40.000 0.00 0.00 36.11 2.93
3274 3991 7.255660 GGTGGGTACTTTGAAATGACAAACATA 60.256 37.037 0.00 0.00 38.38 2.29
3422 4139 8.620416 TGTTACATAATTCATGTCCTATTGCAC 58.380 33.333 0.00 0.00 44.99 4.57
3424 4141 7.031226 ACATAATTCATGTCCTATTGCACAC 57.969 36.000 0.00 0.00 44.99 3.82
3425 4142 4.989279 AATTCATGTCCTATTGCACACC 57.011 40.909 0.00 0.00 0.00 4.16
3428 4145 3.760738 TCATGTCCTATTGCACACCAAA 58.239 40.909 0.00 0.00 36.92 3.28
3429 4146 4.148079 TCATGTCCTATTGCACACCAAAA 58.852 39.130 0.00 0.00 36.92 2.44
3430 4147 4.586421 TCATGTCCTATTGCACACCAAAAA 59.414 37.500 0.00 0.00 36.92 1.94
3467 4184 2.098770 CAGAATTTCCTAGCCTTGCTGC 59.901 50.000 0.00 0.00 40.10 5.25
3477 4194 0.386478 GCCTTGCTGCTGTTCTTTCG 60.386 55.000 0.00 0.00 0.00 3.46
3485 4202 3.106242 TGCTGTTCTTTCGTTAGCAGA 57.894 42.857 0.00 0.00 39.26 4.26
3526 4243 5.118990 ACAGTGTGCAATATGATCCACTAC 58.881 41.667 0.00 0.00 32.29 2.73
3528 4245 5.761726 CAGTGTGCAATATGATCCACTACAT 59.238 40.000 2.45 0.00 32.29 2.29
3538 4255 3.389002 TGATCCACTACATCCATCCTGTG 59.611 47.826 0.00 0.00 0.00 3.66
3553 4270 2.637872 TCCTGTGCTAGCTAGGTTGTTT 59.362 45.455 27.04 0.00 33.30 2.83
3566 4283 6.868339 AGCTAGGTTGTTTCAATTACATTTGC 59.132 34.615 0.00 0.00 0.00 3.68
3575 4292 4.558178 TCAATTACATTTGCTGCACCAAG 58.442 39.130 0.00 0.00 0.00 3.61
3606 4326 2.496899 AATGGAGTGCACTTAGTGGG 57.503 50.000 22.65 0.00 33.64 4.61
3623 4343 2.875087 GGGTACCGCAAAAACTGTTT 57.125 45.000 5.65 0.00 40.86 2.83
3641 4361 6.523840 ACTGTTTGGTAATGAACAATGCATT 58.476 32.000 5.99 5.99 39.20 3.56
3643 4363 7.041916 ACTGTTTGGTAATGAACAATGCATTTG 60.042 33.333 9.83 8.18 41.36 2.32
3684 4409 5.643348 CACCAGTCATGTTCATTTACAGCTA 59.357 40.000 0.00 0.00 0.00 3.32
3730 4455 5.396654 GCTTTGAAAGTTGAGATTGAACGTC 59.603 40.000 6.81 0.00 0.00 4.34
3764 4489 6.663093 ACAAGTCACATAAATAAGGATGGCAA 59.337 34.615 0.00 0.00 0.00 4.52
3768 4493 8.199449 AGTCACATAAATAAGGATGGCAATTTG 58.801 33.333 0.00 0.00 0.00 2.32
3774 4499 3.683365 AAGGATGGCAATTTGTTCCAC 57.317 42.857 5.44 3.95 31.94 4.02
3793 4518 4.567558 TCCACTGTACAAACGTTTACACTG 59.432 41.667 14.20 18.11 0.00 3.66
3808 4533 6.347402 CGTTTACACTGAAGTTTGGATGGTAG 60.347 42.308 0.00 0.00 0.00 3.18
3820 4666 4.568072 TGGATGGTAGCACATACAACTT 57.432 40.909 0.00 0.00 38.70 2.66
3822 4668 4.225042 TGGATGGTAGCACATACAACTTCT 59.775 41.667 0.00 0.00 38.70 2.85
3824 4670 5.395768 GGATGGTAGCACATACAACTTCTCT 60.396 44.000 0.00 0.00 35.96 3.10
3832 4678 8.261492 AGCACATACAACTTCTCTTAATCAAG 57.739 34.615 0.00 0.00 0.00 3.02
3844 4690 9.265901 CTTCTCTTAATCAAGTTGTTCTTCTGA 57.734 33.333 2.11 0.00 33.63 3.27
3923 4769 2.725221 ATGTTCCTGGGCAGATCTTC 57.275 50.000 0.00 0.00 0.00 2.87
3935 4781 3.060895 GGCAGATCTTCGTAAGTGAAACG 59.939 47.826 0.00 0.00 45.86 3.60
3973 4819 2.699496 TTTTTGGCTGGGTGGGGT 59.301 55.556 0.00 0.00 0.00 4.95
3975 4821 3.765257 TTTTGGCTGGGTGGGGTGG 62.765 63.158 0.00 0.00 0.00 4.61
4026 4880 8.109705 TGAAATTCTTGAAAATCGGAATCTCA 57.890 30.769 0.00 0.00 0.00 3.27
4043 4897 7.282224 CGGAATCTCATTTTCCCTGTTGTATTA 59.718 37.037 0.00 0.00 39.63 0.98
4048 4902 7.339212 TCTCATTTTCCCTGTTGTATTATGTGG 59.661 37.037 0.00 0.00 0.00 4.17
4056 4910 6.115446 CCTGTTGTATTATGTGGTGTGATCT 58.885 40.000 0.00 0.00 0.00 2.75
4060 4914 5.118286 TGTATTATGTGGTGTGATCTGCAG 58.882 41.667 7.63 7.63 0.00 4.41
4061 4915 2.028420 TATGTGGTGTGATCTGCAGC 57.972 50.000 9.47 11.33 35.19 5.25
4062 4916 0.037160 ATGTGGTGTGATCTGCAGCA 59.963 50.000 9.47 15.21 41.29 4.41
4065 4919 1.667724 GTGGTGTGATCTGCAGCATAC 59.332 52.381 19.74 10.55 44.49 2.39
4067 4921 2.765699 TGGTGTGATCTGCAGCATACTA 59.234 45.455 9.47 6.02 39.10 1.82
4068 4922 3.197549 TGGTGTGATCTGCAGCATACTAA 59.802 43.478 9.47 1.61 39.10 2.24
4072 4926 6.197276 GTGTGATCTGCAGCATACTAATTTG 58.803 40.000 9.47 0.00 0.00 2.32
4140 4994 7.695055 TCTGGTTCTTTAATTTACAGATGGGA 58.305 34.615 0.00 0.00 0.00 4.37
4217 5071 1.324383 AGGTTAAAAACACCGCCCTG 58.676 50.000 0.00 0.00 39.56 4.45
4219 5073 0.386113 GTTAAAAACACCGCCCTGCA 59.614 50.000 0.00 0.00 0.00 4.41
4220 5074 0.386113 TTAAAAACACCGCCCTGCAC 59.614 50.000 0.00 0.00 0.00 4.57
4228 5082 0.827507 ACCGCCCTGCACATTTCTTT 60.828 50.000 0.00 0.00 0.00 2.52
4234 5088 4.260784 CGCCCTGCACATTTCTTTCTATAC 60.261 45.833 0.00 0.00 0.00 1.47
4240 5094 4.318121 GCACATTTCTTTCTATACGCCTCG 60.318 45.833 0.00 0.00 0.00 4.63
4244 5098 3.795623 TCTTTCTATACGCCTCGCTTT 57.204 42.857 0.00 0.00 0.00 3.51
4269 5123 8.025243 TCCATATGAAAGAAAGTTAACGTGTC 57.975 34.615 3.65 0.00 0.00 3.67
4274 5128 5.353123 TGAAAGAAAGTTAACGTGTCAGCTT 59.647 36.000 0.00 0.00 0.00 3.74
4297 5151 7.609760 TTGTACTAACATGCTTCAAATCGAT 57.390 32.000 0.00 0.00 34.97 3.59
4433 5287 7.391554 AGCTCTAAACTGCATATTTTTGTCTGA 59.608 33.333 1.78 0.00 0.00 3.27
4494 5348 6.509358 GCAAATACGCCGAAATGCATATTTTT 60.509 34.615 0.00 0.00 37.47 1.94
4665 5519 3.634397 CTTCTGGAAGCCACTGGAATA 57.366 47.619 0.00 0.00 0.00 1.75
4891 5754 5.351465 CACTCATTTTGCTCCGTATGTAGTT 59.649 40.000 0.00 0.00 0.00 2.24
4965 5829 4.580167 TGAAGCATGATAAACTGGGCATAC 59.420 41.667 0.00 0.00 0.00 2.39
4992 5856 1.076024 AGTGGCCCATCATCAGTGTTT 59.924 47.619 0.00 0.00 0.00 2.83
5064 5929 3.160269 CTGATAAGAATGGGAATGGGCC 58.840 50.000 0.00 0.00 0.00 5.80
5066 5931 0.923358 TAAGAATGGGAATGGGCCGT 59.077 50.000 0.00 0.00 0.00 5.68
5102 5967 5.969423 TGGACTTGGTTTCTATTACTACCG 58.031 41.667 0.00 0.00 33.29 4.02
5107 5972 6.870439 ACTTGGTTTCTATTACTACCGTGAAC 59.130 38.462 0.00 0.00 33.29 3.18
5126 5991 3.492102 ACATGTTAGCACCACAAGTCT 57.508 42.857 0.00 0.00 0.00 3.24
5146 6011 7.921786 AGTCTACAACTTAGCATATTTGCAA 57.078 32.000 10.86 0.00 43.20 4.08
5330 6195 1.607467 GCTGGCCCTGTTTCCACAT 60.607 57.895 0.00 0.00 30.39 3.21
5416 6281 1.064463 GTCAGCCCATTCCCATCTTGA 60.064 52.381 0.00 0.00 0.00 3.02
5502 6371 2.661718 ACCAATCACCGTTTGTCCTTT 58.338 42.857 0.00 0.00 0.00 3.11
5503 6372 2.360801 ACCAATCACCGTTTGTCCTTTG 59.639 45.455 0.00 0.00 0.00 2.77
5504 6373 2.288152 CCAATCACCGTTTGTCCTTTGG 60.288 50.000 0.00 0.00 0.00 3.28
5505 6374 2.621055 CAATCACCGTTTGTCCTTTGGA 59.379 45.455 0.00 0.00 0.00 3.53
5507 6376 2.018515 TCACCGTTTGTCCTTTGGAAC 58.981 47.619 0.00 0.00 31.38 3.62
5508 6377 1.746220 CACCGTTTGTCCTTTGGAACA 59.254 47.619 0.00 0.00 31.38 3.18
5873 6754 4.402155 TGTTGGCTCCAATAATTGATCCAC 59.598 41.667 4.47 0.00 38.28 4.02
5902 6792 7.624360 AATAATTAAACACCGAGCTTGATCA 57.376 32.000 1.22 0.00 0.00 2.92
6042 6933 9.974980 AAAGTCAAACTTTTGTAGAGAAAAACA 57.025 25.926 0.00 0.00 45.38 2.83
6171 7063 6.701400 ACATGATCAAAGTTTGTAAGGTTTGC 59.299 34.615 15.08 0.00 31.29 3.68
6173 7065 4.394439 TCAAAGTTTGTAAGGTTTGCCC 57.606 40.909 15.08 0.00 34.57 5.36
6183 7075 2.470057 AGGTTTGCCCTTCCTGAAAA 57.530 45.000 0.00 0.00 42.73 2.29
6184 7076 2.976440 AGGTTTGCCCTTCCTGAAAAT 58.024 42.857 0.00 0.00 42.73 1.82
6185 7077 4.126520 AGGTTTGCCCTTCCTGAAAATA 57.873 40.909 0.00 0.00 42.73 1.40
6186 7078 4.687976 AGGTTTGCCCTTCCTGAAAATAT 58.312 39.130 0.00 0.00 42.73 1.28
6187 7079 5.837829 AGGTTTGCCCTTCCTGAAAATATA 58.162 37.500 0.00 0.00 42.73 0.86
6188 7080 6.443832 AGGTTTGCCCTTCCTGAAAATATAT 58.556 36.000 0.00 0.00 42.73 0.86
6189 7081 7.591821 AGGTTTGCCCTTCCTGAAAATATATA 58.408 34.615 0.00 0.00 42.73 0.86
6190 7082 8.234525 AGGTTTGCCCTTCCTGAAAATATATAT 58.765 33.333 0.00 0.00 42.73 0.86
6191 7083 8.306761 GGTTTGCCCTTCCTGAAAATATATATG 58.693 37.037 0.00 0.00 0.00 1.78
6192 7084 7.466746 TTGCCCTTCCTGAAAATATATATGC 57.533 36.000 0.00 0.00 0.00 3.14
6193 7085 6.551085 TGCCCTTCCTGAAAATATATATGCA 58.449 36.000 0.00 0.00 0.00 3.96
6194 7086 6.434028 TGCCCTTCCTGAAAATATATATGCAC 59.566 38.462 0.00 0.00 0.00 4.57
6195 7087 6.660949 GCCCTTCCTGAAAATATATATGCACT 59.339 38.462 0.00 0.00 0.00 4.40
6196 7088 7.829211 GCCCTTCCTGAAAATATATATGCACTA 59.171 37.037 0.00 0.00 0.00 2.74
6197 7089 9.167311 CCCTTCCTGAAAATATATATGCACTAC 57.833 37.037 0.00 0.00 0.00 2.73
6198 7090 9.725019 CCTTCCTGAAAATATATATGCACTACA 57.275 33.333 0.00 0.00 0.00 2.74
6212 7104 8.887036 ATATGCACTACATTATGAAACGAAGA 57.113 30.769 0.00 0.00 40.38 2.87
6254 7146 8.677148 ATACTGCCGTACTTATCAATCAATTT 57.323 30.769 0.00 0.00 0.00 1.82
6256 7148 6.374333 ACTGCCGTACTTATCAATCAATTTGT 59.626 34.615 0.00 0.00 36.65 2.83
6257 7149 7.094377 ACTGCCGTACTTATCAATCAATTTGTT 60.094 33.333 0.00 0.00 36.65 2.83
6319 7211 8.109705 TCTGACTTTGCTAGAAAAATATGCAA 57.890 30.769 0.00 0.00 41.10 4.08
6364 7257 1.414527 GCTGCTAACGCTCGTCCTTC 61.415 60.000 0.00 0.00 36.97 3.46
6402 7298 1.909986 AGGGCAGTCCTAAAGAAGACC 59.090 52.381 0.00 0.00 45.98 3.85
6403 7299 1.628846 GGGCAGTCCTAAAGAAGACCA 59.371 52.381 0.00 0.00 31.51 4.02
6409 7305 3.008485 AGTCCTAAAGAAGACCAGCAAGG 59.992 47.826 0.00 0.00 45.67 3.61
6434 7330 7.282450 GGAACGACTCCAAGGACAATTAATTAT 59.718 37.037 0.00 0.00 44.67 1.28
6435 7331 8.575649 AACGACTCCAAGGACAATTAATTATT 57.424 30.769 0.00 0.00 0.00 1.40
6586 7484 9.366216 GGCAAATTAAACTAAAATTGTAGGAGG 57.634 33.333 7.58 0.00 0.00 4.30
6587 7485 8.869897 GCAAATTAAACTAAAATTGTAGGAGGC 58.130 33.333 7.58 0.00 0.00 4.70
6631 7529 1.610038 TGCTCATTCACCAACTTGCAG 59.390 47.619 0.00 0.00 0.00 4.41
6668 7566 3.565905 ACGAGAAATCGTACCGACTTT 57.434 42.857 0.74 0.00 45.19 2.66
6677 7575 3.674997 TCGTACCGACTTTGTAGTACCT 58.325 45.455 0.00 0.00 33.84 3.08
6699 7597 5.853572 TTACCCAGGGTAAGTCAAAGAAT 57.146 39.130 25.46 0.00 42.44 2.40
6706 7604 9.421399 CCCAGGGTAAGTCAAAGAATAATATTT 57.579 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.871299 AAAACGTAAATTTGCATAAATTCAACC 57.129 25.926 7.07 0.00 43.74 3.77
122 123 3.523564 TGCTCTTAGGGCATTTCTAACCT 59.476 43.478 1.11 0.00 34.56 3.50
164 206 7.234577 ACAATATGGGTGAAACAAACAGGTTAT 59.765 33.333 0.00 0.00 39.98 1.89
350 398 2.196595 TCAGAACCAACTAGGGATGGG 58.803 52.381 13.89 2.16 43.89 4.00
375 491 1.860950 CTTTGTATCCGCATCCACTCG 59.139 52.381 0.00 0.00 0.00 4.18
376 492 3.126831 CTCTTTGTATCCGCATCCACTC 58.873 50.000 0.00 0.00 0.00 3.51
453 987 7.254932 GCAAATTCAGGCCAGATTTAGTAGTAG 60.255 40.741 5.01 0.00 0.00 2.57
454 988 6.542370 GCAAATTCAGGCCAGATTTAGTAGTA 59.458 38.462 5.01 0.00 0.00 1.82
455 989 5.358160 GCAAATTCAGGCCAGATTTAGTAGT 59.642 40.000 5.01 0.00 0.00 2.73
560 1094 4.464244 TCTCCATAGGATAGGAAAGATGCG 59.536 45.833 0.00 0.00 32.57 4.73
584 1118 0.166814 CGTAACTGGCTCTGCTTTGC 59.833 55.000 0.00 0.00 0.00 3.68
623 1157 4.163427 TCCTTGTCTCCATCTATCCATCC 58.837 47.826 0.00 0.00 0.00 3.51
651 1185 1.066752 CAGCAGCAGCAGCAACAAA 59.933 52.632 12.92 0.00 45.49 2.83
684 1221 2.935481 CCCCTTGGCACCTGGAGA 60.935 66.667 0.00 0.00 0.00 3.71
809 1350 2.243810 CCCGAAATTGAGTGGGGAAAA 58.756 47.619 0.00 0.00 40.51 2.29
830 1371 1.356624 CGAGAATGGGATTTGCGCC 59.643 57.895 4.18 0.00 0.00 6.53
840 1381 0.516877 TTTCTTGCGCACGAGAATGG 59.483 50.000 21.71 1.88 44.19 3.16
1211 1758 1.927174 GACGTTGGTGAAGATGATCCG 59.073 52.381 0.00 0.00 0.00 4.18
1355 1908 3.050275 GCGCAGGGACAAGGACAC 61.050 66.667 0.30 0.00 0.00 3.67
1357 1910 2.743928 CTGCGCAGGGACAAGGAC 60.744 66.667 29.88 0.00 0.00 3.85
1358 1911 4.020617 CCTGCGCAGGGACAAGGA 62.021 66.667 42.81 2.06 44.87 3.36
1404 1957 0.595053 CGACGTTGGGATCATCGAGG 60.595 60.000 0.00 0.00 38.87 4.63
1501 2056 1.538075 GAATTTTGGGCGGACGAGAAA 59.462 47.619 0.00 0.00 0.00 2.52
1520 2075 6.503944 AGGAGTAGTAGAAAAGAAGGGATGA 58.496 40.000 0.00 0.00 0.00 2.92
1736 2404 8.607459 ACGCATATACAGTATATACGTAAGACC 58.393 37.037 27.04 5.03 44.74 3.85
1753 2421 4.387559 TCAGTCAAACACACACGCATATAC 59.612 41.667 0.00 0.00 0.00 1.47
1888 2566 2.440539 ATCGTCGCTCTTGTTCAGTT 57.559 45.000 0.00 0.00 0.00 3.16
1927 2621 1.584724 GAGGGAGGAAGGATGACCAA 58.415 55.000 0.00 0.00 38.94 3.67
1962 2656 8.700973 TCACTGCAATAAGTAGACCATACAATA 58.299 33.333 0.00 0.00 33.69 1.90
1963 2657 7.564793 TCACTGCAATAAGTAGACCATACAAT 58.435 34.615 0.00 0.00 33.69 2.71
1964 2658 6.941857 TCACTGCAATAAGTAGACCATACAA 58.058 36.000 0.00 0.00 33.69 2.41
1965 2659 6.538945 TCACTGCAATAAGTAGACCATACA 57.461 37.500 0.00 0.00 33.69 2.29
1966 2660 6.647067 GGATCACTGCAATAAGTAGACCATAC 59.353 42.308 0.00 0.00 33.69 2.39
2094 2793 7.039722 AGTAAGAATTTGGGGGAAAGATACA 57.960 36.000 0.00 0.00 0.00 2.29
2103 2803 7.054751 CCTAGTCTTAAGTAAGAATTTGGGGG 58.945 42.308 6.37 0.34 43.30 5.40
2124 2824 5.943416 TCAACCACATTGGATTTACACCTAG 59.057 40.000 0.00 0.00 40.96 3.02
2127 2827 4.764823 TCTCAACCACATTGGATTTACACC 59.235 41.667 0.00 0.00 40.96 4.16
2135 2839 2.583024 TGCATCTCAACCACATTGGA 57.417 45.000 0.00 0.00 40.96 3.53
2167 2871 2.238521 GAACAGGGACCAAAATCTGCA 58.761 47.619 0.00 0.00 0.00 4.41
2213 2917 3.500343 AGAACCACCAAAGAGGGAAATG 58.500 45.455 0.00 0.00 43.89 2.32
2434 3149 8.792830 AGAAAACAAGCATAGCATTCTAGTTA 57.207 30.769 0.00 0.00 0.00 2.24
2577 3293 4.027458 CACTGTCAACGCAAAACATCAAAG 60.027 41.667 0.00 0.00 0.00 2.77
2580 3296 2.421775 ACACTGTCAACGCAAAACATCA 59.578 40.909 0.00 0.00 0.00 3.07
2590 3306 5.454232 GGTGAAACAAATTACACTGTCAACG 59.546 40.000 0.00 0.00 39.98 4.10
2729 3446 1.289830 TCGAACCTAGATTGGAGGGGA 59.710 52.381 0.00 0.00 38.52 4.81
2730 3447 1.689273 CTCGAACCTAGATTGGAGGGG 59.311 57.143 0.89 0.00 38.52 4.79
2785 3502 1.250328 TTGCTTCACTCAGGCATTGG 58.750 50.000 0.00 0.00 35.84 3.16
2794 3511 7.631717 AAGTTCCCTAATATTTGCTTCACTC 57.368 36.000 0.00 0.00 0.00 3.51
2893 3610 3.916761 TCTTGCACTTATAAACGGACGT 58.083 40.909 0.00 0.00 0.00 4.34
2970 3687 6.474102 GCAACTTAGAGTGCTCACTAGATTAC 59.526 42.308 2.07 0.00 42.66 1.89
3040 3757 8.135382 TGAGCCTAATCTCTTGTAGTAGTTTT 57.865 34.615 0.00 0.00 34.29 2.43
3114 3831 2.872557 CCATTGTGGTCAGCGCAG 59.127 61.111 11.47 0.00 31.35 5.18
3433 4150 9.224267 GCTAGGAAATTCTGATGCAGATTTATA 57.776 33.333 0.00 0.00 40.39 0.98
3434 4151 7.176340 GGCTAGGAAATTCTGATGCAGATTTAT 59.824 37.037 0.00 0.00 40.39 1.40
3435 4152 6.488006 GGCTAGGAAATTCTGATGCAGATTTA 59.512 38.462 0.00 0.00 40.39 1.40
3477 4194 8.084590 AGTATAAACACAACTGTTCTGCTAAC 57.915 34.615 0.00 0.00 39.88 2.34
3485 4202 7.254658 GCACACTGTAGTATAAACACAACTGTT 60.255 37.037 0.00 0.00 42.81 3.16
3496 4213 8.646900 TGGATCATATTGCACACTGTAGTATAA 58.353 33.333 0.00 0.00 0.00 0.98
3506 4223 5.180117 GGATGTAGTGGATCATATTGCACAC 59.820 44.000 2.42 0.00 40.09 3.82
3526 4243 2.028294 CCTAGCTAGCACAGGATGGATG 60.028 54.545 24.27 1.99 43.62 3.51
3528 4245 1.062886 ACCTAGCTAGCACAGGATGGA 60.063 52.381 31.39 2.33 43.62 3.41
3538 4255 6.737254 TGTAATTGAAACAACCTAGCTAGC 57.263 37.500 15.74 6.62 0.00 3.42
3553 4270 4.280425 TCTTGGTGCAGCAAATGTAATTGA 59.720 37.500 29.29 18.27 36.10 2.57
3566 4283 9.288576 TCCATTAATAAGAATATCTTGGTGCAG 57.711 33.333 2.94 0.00 37.29 4.41
3601 4321 1.314730 CAGTTTTTGCGGTACCCACT 58.685 50.000 6.25 0.00 0.00 4.00
3606 4326 3.153676 ACCAAACAGTTTTTGCGGTAC 57.846 42.857 4.33 0.00 0.00 3.34
3611 4331 6.654793 TGTTCATTACCAAACAGTTTTTGC 57.345 33.333 0.00 0.00 31.97 3.68
3623 4343 4.529769 TCCCAAATGCATTGTTCATTACCA 59.470 37.500 13.82 0.00 37.32 3.25
3641 4361 6.385759 ACTGGTGACATACATATAACTCCCAA 59.614 38.462 0.00 0.00 41.51 4.12
3643 4363 6.041637 TGACTGGTGACATACATATAACTCCC 59.958 42.308 0.00 0.00 41.51 4.30
3684 4409 4.573900 CTTTGAGATTGGACACAGCTAGT 58.426 43.478 0.00 0.00 0.00 2.57
3699 4424 6.949352 ATCTCAACTTTCAAAGCTTTGAGA 57.051 33.333 33.76 29.69 46.07 3.27
3764 4489 5.570234 AACGTTTGTACAGTGGAACAAAT 57.430 34.783 21.64 9.96 44.73 2.32
3768 4493 5.063817 AGTGTAAACGTTTGTACAGTGGAAC 59.936 40.000 23.46 9.71 33.58 3.62
3774 4499 6.340537 ACTTCAGTGTAAACGTTTGTACAG 57.659 37.500 23.46 16.88 31.04 2.74
3793 4518 4.941263 TGTATGTGCTACCATCCAAACTTC 59.059 41.667 0.00 0.00 0.00 3.01
3808 4533 8.034058 ACTTGATTAAGAGAAGTTGTATGTGC 57.966 34.615 3.94 0.00 37.36 4.57
3818 4664 9.265901 TCAGAAGAACAACTTGATTAAGAGAAG 57.734 33.333 3.94 0.00 39.13 2.85
3820 4666 9.784531 AATCAGAAGAACAACTTGATTAAGAGA 57.215 29.630 3.94 0.00 39.13 3.10
3832 4678 6.785191 TGTCAGAACAAATCAGAAGAACAAC 58.215 36.000 0.00 0.00 30.70 3.32
3836 4682 6.481313 CAGTCTGTCAGAACAAATCAGAAGAA 59.519 38.462 3.51 0.00 37.00 2.52
3957 4803 2.123077 CACCCCACCCAGCCAAAA 60.123 61.111 0.00 0.00 0.00 2.44
3961 4807 4.366684 CTTCCACCCCACCCAGCC 62.367 72.222 0.00 0.00 0.00 4.85
3962 4808 4.366684 CCTTCCACCCCACCCAGC 62.367 72.222 0.00 0.00 0.00 4.85
3963 4809 2.531685 TCCTTCCACCCCACCCAG 60.532 66.667 0.00 0.00 0.00 4.45
3964 4810 2.531685 CTCCTTCCACCCCACCCA 60.532 66.667 0.00 0.00 0.00 4.51
3965 4811 3.339093 CCTCCTTCCACCCCACCC 61.339 72.222 0.00 0.00 0.00 4.61
3966 4812 4.048470 GCCTCCTTCCACCCCACC 62.048 72.222 0.00 0.00 0.00 4.61
3968 4814 1.856873 ATTGCCTCCTTCCACCCCA 60.857 57.895 0.00 0.00 0.00 4.96
3970 4816 1.076705 GGATTGCCTCCTTCCACCC 60.077 63.158 0.00 0.00 41.29 4.61
3973 4819 1.297968 TCATGGATTGCCTCCTTCCA 58.702 50.000 4.25 0.00 45.21 3.53
3975 4821 3.010200 AGTTCATGGATTGCCTCCTTC 57.990 47.619 4.25 0.00 45.21 3.46
3976 4822 3.525199 AGTAGTTCATGGATTGCCTCCTT 59.475 43.478 4.25 0.00 45.21 3.36
4018 4872 7.410120 AATACAACAGGGAAAATGAGATTCC 57.590 36.000 0.00 0.00 44.61 3.01
4022 4876 7.339212 CCACATAATACAACAGGGAAAATGAGA 59.661 37.037 0.00 0.00 0.00 3.27
4026 4880 6.723977 ACACCACATAATACAACAGGGAAAAT 59.276 34.615 0.00 0.00 0.00 1.82
4043 4897 0.037160 TGCTGCAGATCACACCACAT 59.963 50.000 20.43 0.00 0.00 3.21
4048 4902 5.998454 AATTAGTATGCTGCAGATCACAC 57.002 39.130 20.43 6.24 0.00 3.82
4056 4910 5.131594 TGCAAACAAATTAGTATGCTGCA 57.868 34.783 4.13 4.13 36.75 4.41
4060 4914 9.573133 AAGATAACTGCAAACAAATTAGTATGC 57.427 29.630 0.00 0.00 0.00 3.14
4062 4916 9.573133 GCAAGATAACTGCAAACAAATTAGTAT 57.427 29.630 0.00 0.00 0.00 2.12
4065 4919 8.524870 AAGCAAGATAACTGCAAACAAATTAG 57.475 30.769 0.00 0.00 0.00 1.73
4067 4921 7.790823 AAAGCAAGATAACTGCAAACAAATT 57.209 28.000 0.00 0.00 0.00 1.82
4068 4922 9.492973 AATAAAGCAAGATAACTGCAAACAAAT 57.507 25.926 0.00 0.00 0.00 2.32
4131 4985 3.054361 GGTTCACCATAAGTCCCATCTGT 60.054 47.826 0.00 0.00 35.64 3.41
4140 4994 4.018688 GGTTTAGGAGGGTTCACCATAAGT 60.019 45.833 0.00 0.00 43.89 2.24
4217 5071 4.318121 CGAGGCGTATAGAAAGAAATGTGC 60.318 45.833 0.00 0.00 0.00 4.57
4219 5073 3.802685 GCGAGGCGTATAGAAAGAAATGT 59.197 43.478 0.00 0.00 0.00 2.71
4220 5074 4.051922 AGCGAGGCGTATAGAAAGAAATG 58.948 43.478 0.00 0.00 0.00 2.32
4228 5082 1.395635 TGGAAAGCGAGGCGTATAGA 58.604 50.000 0.00 0.00 0.00 1.98
4234 5088 1.581934 TTCATATGGAAAGCGAGGCG 58.418 50.000 2.13 0.00 30.98 5.52
4244 5098 7.658167 TGACACGTTAACTTTCTTTCATATGGA 59.342 33.333 2.13 0.00 0.00 3.41
4258 5112 4.317671 AGTACAAGCTGACACGTTAACT 57.682 40.909 3.71 0.00 0.00 2.24
4259 5113 5.459762 TGTTAGTACAAGCTGACACGTTAAC 59.540 40.000 0.00 0.00 31.39 2.01
4263 5117 3.720949 TGTTAGTACAAGCTGACACGT 57.279 42.857 0.00 0.00 31.39 4.49
4274 5128 6.593770 ACATCGATTTGAAGCATGTTAGTACA 59.406 34.615 0.00 0.00 38.95 2.90
4293 5147 4.645136 AGGATAGACTTACTGCAACATCGA 59.355 41.667 0.00 0.00 0.00 3.59
4297 5151 5.738619 TCAAGGATAGACTTACTGCAACA 57.261 39.130 0.00 0.00 0.00 3.33
4494 5348 6.204301 CAGAGAGAAGCTTCTTTGTCATTGAA 59.796 38.462 29.02 0.00 37.73 2.69
4755 5610 3.964031 AGCTAGGATCTCTTACACCTTGG 59.036 47.826 0.00 0.00 34.42 3.61
4891 5754 8.650143 AAGCCTTTTTAGAGATTCCAATACAA 57.350 30.769 0.00 0.00 0.00 2.41
4921 5784 4.225942 TCACTTCTACTCCTCCGTACCTAA 59.774 45.833 0.00 0.00 0.00 2.69
4926 5789 3.015327 GCTTCACTTCTACTCCTCCGTA 58.985 50.000 0.00 0.00 0.00 4.02
4965 5829 0.107508 ATGATGGGCCACTGTTCTCG 60.108 55.000 9.28 0.00 0.00 4.04
4992 5856 5.469760 CAGTGACAGTTTCCATGTGTATCAA 59.530 40.000 0.00 0.00 0.00 2.57
5064 5929 4.463879 CCAGGCTGGAGCAGGACG 62.464 72.222 29.96 0.00 40.96 4.79
5102 5967 3.315191 ACTTGTGGTGCTAACATGTTCAC 59.685 43.478 15.85 17.05 33.52 3.18
5107 5972 4.314961 TGTAGACTTGTGGTGCTAACATG 58.685 43.478 0.00 0.00 0.00 3.21
5146 6011 5.511888 CCCAAGATTGCTTTTGTTCCAGAAT 60.512 40.000 0.00 0.00 30.14 2.40
5226 6091 6.746364 GCTGTAGTATGCCGTTATGATAGTAC 59.254 42.308 0.00 0.00 32.51 2.73
5330 6195 0.536460 GGTCTTTTGGGTCGGCTTCA 60.536 55.000 0.00 0.00 0.00 3.02
5416 6281 5.393866 ACTGGTTTCCTACAATGGTTCAAT 58.606 37.500 0.00 0.00 0.00 2.57
5502 6371 6.907853 TGTTCCATATCACAAATTGTTCCA 57.092 33.333 0.00 0.00 0.00 3.53
5503 6372 8.776376 AATTGTTCCATATCACAAATTGTTCC 57.224 30.769 0.00 0.00 36.50 3.62
5505 6374 8.505625 GCAAATTGTTCCATATCACAAATTGTT 58.494 29.630 15.05 0.00 42.23 2.83
5507 6376 8.030744 TGCAAATTGTTCCATATCACAAATTG 57.969 30.769 11.88 11.88 42.74 2.32
5508 6377 7.334921 CCTGCAAATTGTTCCATATCACAAATT 59.665 33.333 0.00 0.00 36.50 1.82
5838 6719 5.748670 TGGAGCCAACAATTACAGTAGTA 57.251 39.130 0.00 0.00 0.00 1.82
5839 6720 4.634012 TGGAGCCAACAATTACAGTAGT 57.366 40.909 0.00 0.00 0.00 2.73
5840 6721 7.624360 TTATTGGAGCCAACAATTACAGTAG 57.376 36.000 3.70 0.00 39.18 2.57
5873 6754 9.781834 TCAAGCTCGGTGTTTAATTATTTATTG 57.218 29.630 0.00 0.00 0.00 1.90
5902 6792 2.623416 GCTAAGCTCAAACAACAAGGGT 59.377 45.455 0.00 0.00 0.00 4.34
5974 6865 3.617531 GCACTATATTGTGGATCGGAGGG 60.618 52.174 17.22 0.00 38.31 4.30
6011 6902 8.343168 TCTCTACAAAAGTTTGACTTTCCAAA 57.657 30.769 10.66 0.00 46.78 3.28
6012 6903 7.931578 TCTCTACAAAAGTTTGACTTTCCAA 57.068 32.000 10.66 0.00 46.78 3.53
6013 6904 7.931578 TTCTCTACAAAAGTTTGACTTTCCA 57.068 32.000 10.66 0.00 46.78 3.53
6167 7059 7.508636 TGCATATATATTTTCAGGAAGGGCAAA 59.491 33.333 0.00 0.00 0.00 3.68
6171 7063 9.167311 GTAGTGCATATATATTTTCAGGAAGGG 57.833 37.037 0.00 0.00 0.00 3.95
6186 7078 9.974980 TCTTCGTTTCATAATGTAGTGCATATA 57.025 29.630 0.00 0.00 36.67 0.86
6187 7079 8.887036 TCTTCGTTTCATAATGTAGTGCATAT 57.113 30.769 0.00 0.00 36.67 1.78
6188 7080 8.710835 TTCTTCGTTTCATAATGTAGTGCATA 57.289 30.769 0.00 0.00 36.67 3.14
6189 7081 7.609760 TTCTTCGTTTCATAATGTAGTGCAT 57.390 32.000 0.00 0.00 40.03 3.96
6190 7082 7.428282 TTTCTTCGTTTCATAATGTAGTGCA 57.572 32.000 0.00 0.00 0.00 4.57
6191 7083 6.466097 GCTTTCTTCGTTTCATAATGTAGTGC 59.534 38.462 0.00 0.00 0.00 4.40
6192 7084 7.518161 TGCTTTCTTCGTTTCATAATGTAGTG 58.482 34.615 0.00 0.00 0.00 2.74
6193 7085 7.667043 TGCTTTCTTCGTTTCATAATGTAGT 57.333 32.000 0.00 0.00 0.00 2.73
6212 7104 9.186837 ACGGCAGTATATACTAGTATATGCTTT 57.813 33.333 33.56 22.03 43.89 3.51
6257 7149 8.637986 AGGTATTGCTGTTTTGTATCAGAAAAA 58.362 29.630 0.00 0.00 33.61 1.94
6319 7211 3.767673 GCATATGCCATTCAATCAGGGAT 59.232 43.478 17.26 0.00 37.28 3.85
6402 7298 1.151668 CTTGGAGTCGTTCCTTGCTG 58.848 55.000 9.52 0.00 46.92 4.41
6403 7299 0.035458 CCTTGGAGTCGTTCCTTGCT 59.965 55.000 9.52 0.00 46.92 3.91
6409 7305 6.496338 AATTAATTGTCCTTGGAGTCGTTC 57.504 37.500 0.00 0.00 0.00 3.95
6472 7370 4.378046 CGTATGGCTATTATTTTCGCCCAC 60.378 45.833 0.00 0.00 41.80 4.61
6668 7566 4.690767 TTACCCTGGGTAAGGTACTACA 57.309 45.455 30.03 8.94 45.78 2.74
6677 7575 5.853572 ATTCTTTGACTTACCCTGGGTAA 57.146 39.130 31.07 31.07 44.72 2.85
6699 7597 8.248253 TGTGAACGTCTAGAAGCAGAAATATTA 58.752 33.333 5.51 0.00 0.00 0.98
6706 7604 3.318275 ACTTGTGAACGTCTAGAAGCAGA 59.682 43.478 5.51 0.00 0.00 4.26
6718 7616 1.226746 GGGACTGGAACTTGTGAACG 58.773 55.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.