Multiple sequence alignment - TraesCS2B01G385100

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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 TraesCS2B01G385100 chr2B 100.000 6348 0 0 1 6348 548675141 548681488 0.000000e+00 11723.0
1 TraesCS2B01G385100 chr2B 80.677 1832 262 63 660 2452 793705099 793703321 0.000000e+00 1338.0
2 TraesCS2B01G385100 chr2B 80.221 996 151 28 3071 4035 793702719 793701739 0.000000e+00 706.0
3 TraesCS2B01G385100 chr2B 87.133 443 46 9 2503 2938 793703243 793702805 5.720000e-135 492.0
4 TraesCS2B01G385100 chr2B 78.788 330 51 14 5199 5515 793701171 793700848 3.000000e-48 204.0
5 TraesCS2B01G385100 chr2B 82.500 80 14 0 6085 6164 383541832 383541911 3.180000e-08 71.3
6 TraesCS2B01G385100 chr2D 93.161 5805 309 40 570 6348 470069091 470074833 0.000000e+00 8440.0
7 TraesCS2B01G385100 chr2D 80.647 1886 279 61 655 2503 2142047 2140211 0.000000e+00 1382.0
8 TraesCS2B01G385100 chr2D 91.886 456 33 3 101 555 470068653 470069105 8.980000e-178 634.0
9 TraesCS2B01G385100 chr2D 79.623 903 135 27 3071 3939 2139219 2138332 2.530000e-168 603.0
10 TraesCS2B01G385100 chr2D 86.041 437 53 7 2508 2938 2140177 2139743 4.480000e-126 462.0
11 TraesCS2B01G385100 chr2D 86.667 105 14 0 1 105 471504495 471504391 4.020000e-22 117.0
12 TraesCS2B01G385100 chr2A 91.082 3465 272 24 569 4014 611351111 611354557 0.000000e+00 4652.0
13 TraesCS2B01G385100 chr2A 86.412 1413 120 29 4051 5411 611354828 611356220 0.000000e+00 1480.0
14 TraesCS2B01G385100 chr2A 83.159 671 80 9 5404 6071 611356252 611356892 3.300000e-162 582.0
15 TraesCS2B01G385100 chr2A 89.474 456 42 4 101 555 611350676 611351126 7.140000e-159 571.0
16 TraesCS2B01G385100 chrUn 81.718 1001 131 37 852 1826 124829438 124830412 0.000000e+00 787.0
17 TraesCS2B01G385100 chr6B 80.294 340 67 0 857 1196 681233819 681234158 2.270000e-64 257.0
18 TraesCS2B01G385100 chr6B 80.000 340 68 0 857 1196 681362875 681363214 1.060000e-62 252.0
19 TraesCS2B01G385100 chr6B 90.588 170 15 1 1337 1506 681363316 681363484 2.300000e-54 224.0
20 TraesCS2B01G385100 chr6B 76.602 359 50 20 2576 2931 681236115 681236442 3.940000e-37 167.0
21 TraesCS2B01G385100 chr6B 76.257 358 51 17 2576 2930 681365099 681365425 6.590000e-35 159.0
22 TraesCS2B01G385100 chr6B 83.193 119 20 0 6207 6325 510233090 510232972 6.730000e-20 110.0
23 TraesCS2B01G385100 chr6B 80.702 114 21 1 6093 6206 160897599 160897487 3.150000e-13 87.9
24 TraesCS2B01G385100 chr7D 80.896 335 47 13 2579 2907 72263732 72263409 1.370000e-61 248.0
25 TraesCS2B01G385100 chr7D 77.044 318 61 11 5630 5942 1751504 1751194 8.460000e-39 172.0
26 TraesCS2B01G385100 chr7D 85.926 135 19 0 3108 3242 72263275 72263141 1.840000e-30 145.0
27 TraesCS2B01G385100 chr7D 89.623 106 9 2 1 106 549094130 549094027 3.990000e-27 134.0
28 TraesCS2B01G385100 chr3D 78.914 313 58 7 5626 5935 239600580 239600273 8.340000e-49 206.0
29 TraesCS2B01G385100 chr3D 80.882 136 26 0 6206 6341 78083021 78082886 2.420000e-19 108.0
30 TraesCS2B01G385100 chr3D 78.351 97 21 0 6085 6181 165712441 165712345 5.310000e-06 63.9
31 TraesCS2B01G385100 chr3A 78.914 313 58 7 5626 5935 340277170 340276863 8.340000e-49 206.0
32 TraesCS2B01G385100 chr3A 78.502 307 54 10 5626 5929 451688372 451688669 2.340000e-44 191.0
33 TraesCS2B01G385100 chr3A 83.761 117 15 4 6186 6302 91293350 91293462 2.420000e-19 108.0
34 TraesCS2B01G385100 chr4B 78.571 308 55 11 5627 5929 178379280 178379581 6.490000e-45 193.0
35 TraesCS2B01G385100 chr4A 78.176 307 56 11 5626 5929 536786294 536786592 1.090000e-42 185.0
36 TraesCS2B01G385100 chr7B 77.389 314 60 10 5621 5929 644305072 644305379 6.540000e-40 176.0
37 TraesCS2B01G385100 chr6D 89.524 105 11 0 1 105 456792787 456792683 3.990000e-27 134.0
38 TraesCS2B01G385100 chr3B 88.571 105 10 2 1 105 421476462 421476360 6.680000e-25 126.0
39 TraesCS2B01G385100 chr3B 81.739 115 20 1 6205 6319 801302441 801302328 1.880000e-15 95.3
40 TraesCS2B01G385100 chr4D 83.333 120 19 1 6200 6319 299446370 299446252 6.730000e-20 110.0
41 TraesCS2B01G385100 chr5B 80.282 142 27 1 6201 6341 590541600 590541459 8.700000e-19 106.0
42 TraesCS2B01G385100 chr5B 80.282 142 27 1 6201 6341 590553289 590553148 8.700000e-19 106.0
43 TraesCS2B01G385100 chr7A 79.688 128 24 2 6205 6332 679196636 679196511 2.440000e-14 91.6
44 TraesCS2B01G385100 chr1D 79.464 112 17 4 124 234 421030658 421030764 2.450000e-09 75.0
45 TraesCS2B01G385100 chr6A 79.381 97 20 0 6069 6165 328576648 328576744 1.140000e-07 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 TraesCS2B01G385100 chr2B 548675141 548681488 6347 False 11723.000000 11723 100.000000 1 6348 1 chr2B.!!$F2 6347
1 TraesCS2B01G385100 chr2B 793700848 793705099 4251 True 685.000000 1338 81.704750 660 5515 4 chr2B.!!$R1 4855
2 TraesCS2B01G385100 chr2D 470068653 470074833 6180 False 4537.000000 8440 92.523500 101 6348 2 chr2D.!!$F1 6247
3 TraesCS2B01G385100 chr2D 2138332 2142047 3715 True 815.666667 1382 82.103667 655 3939 3 chr2D.!!$R2 3284
4 TraesCS2B01G385100 chr2A 611350676 611356892 6216 False 1821.250000 4652 87.531750 101 6071 4 chr2A.!!$F1 5970
5 TraesCS2B01G385100 chrUn 124829438 124830412 974 False 787.000000 787 81.718000 852 1826 1 chrUn.!!$F1 974
6 TraesCS2B01G385100 chr6B 681233819 681236442 2623 False 212.000000 257 78.448000 857 2931 2 chr6B.!!$F1 2074
7 TraesCS2B01G385100 chr6B 681362875 681365425 2550 False 211.666667 252 82.281667 857 2930 3 chr6B.!!$F2 2073

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
87 88 0.545548 AGAGGCCGGGGGATAATCTC 60.546 60.000 2.18 0.0 0.00 2.75 F
90 91 0.545548 GGCCGGGGGATAATCTCTCT 60.546 60.000 2.18 0.0 0.00 3.10 F
445 447 0.926155 CATCAGTTCACCATCGAGCG 59.074 55.000 0.00 0.0 0.00 5.03 F
1645 1685 1.135402 GTCGGATGAATTGCACCCAAC 60.135 52.381 0.00 0.0 32.95 3.77 F
2011 3190 0.109412 CGGGCTTCGAAACTACGTCT 60.109 55.000 0.00 0.0 42.43 4.18 F
3046 4690 0.605319 CAAAAGGAGGGTAGCGTGCA 60.605 55.000 8.81 0.0 0.00 4.57 F
3806 5494 0.846427 TGGGTGGCTCCTCAAAGGAT 60.846 55.000 5.46 0.0 44.81 3.24 F
4350 6274 2.869078 CCCCCTCCCCACCCTTTT 60.869 66.667 0.00 0.0 0.00 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1138 1152 1.043816 GGATGATCGAGCCAGGAGAA 58.956 55.000 0.0 0.0 0.00 2.87 R
1465 1489 1.755179 ATGCTGTGCCAGGAATGTAC 58.245 50.000 0.0 0.0 35.08 2.90 R
2011 3190 2.429610 GAGTGTAGCAGTTATCCCCGAA 59.570 50.000 0.0 0.0 0.00 4.30 R
3043 4687 1.811778 ATCTATCCCTCCTGCTTGCA 58.188 50.000 0.0 0.0 0.00 4.08 R
3828 5516 0.312416 GCACCAACACATAACCGCAA 59.688 50.000 0.0 0.0 0.00 4.85 R
4321 6245 0.919289 GGAGGGGGTGAAGGGATTGA 60.919 60.000 0.0 0.0 0.00 2.57 R
5281 7258 1.280421 AGTCCAGGAGAAAGCACCATC 59.720 52.381 0.0 0.0 0.00 3.51 R
6295 8316 0.317854 GGGCAACTTTTGTCACTCGC 60.318 55.000 0.0 0.0 36.88 5.03 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
20 21 3.297134 TTGAGGCTTGGAGACTTTGTT 57.703 42.857 0.00 0.00 30.20 2.83
21 22 2.575532 TGAGGCTTGGAGACTTTGTTG 58.424 47.619 0.00 0.00 30.20 3.33
22 23 2.172505 TGAGGCTTGGAGACTTTGTTGA 59.827 45.455 0.00 0.00 30.20 3.18
23 24 3.214328 GAGGCTTGGAGACTTTGTTGAA 58.786 45.455 0.00 0.00 30.20 2.69
24 25 3.823304 GAGGCTTGGAGACTTTGTTGAAT 59.177 43.478 0.00 0.00 30.20 2.57
25 26 4.218312 AGGCTTGGAGACTTTGTTGAATT 58.782 39.130 0.00 0.00 17.74 2.17
26 27 4.038402 AGGCTTGGAGACTTTGTTGAATTG 59.962 41.667 0.00 0.00 17.74 2.32
27 28 4.202151 GGCTTGGAGACTTTGTTGAATTGT 60.202 41.667 0.00 0.00 0.00 2.71
28 29 5.351458 GCTTGGAGACTTTGTTGAATTGTT 58.649 37.500 0.00 0.00 0.00 2.83
29 30 5.812127 GCTTGGAGACTTTGTTGAATTGTTT 59.188 36.000 0.00 0.00 0.00 2.83
30 31 6.237915 GCTTGGAGACTTTGTTGAATTGTTTG 60.238 38.462 0.00 0.00 0.00 2.93
31 32 5.108517 TGGAGACTTTGTTGAATTGTTTGC 58.891 37.500 0.00 0.00 0.00 3.68
32 33 5.105392 TGGAGACTTTGTTGAATTGTTTGCT 60.105 36.000 0.00 0.00 0.00 3.91
33 34 5.812127 GGAGACTTTGTTGAATTGTTTGCTT 59.188 36.000 0.00 0.00 0.00 3.91
34 35 6.978080 GGAGACTTTGTTGAATTGTTTGCTTA 59.022 34.615 0.00 0.00 0.00 3.09
35 36 7.653311 GGAGACTTTGTTGAATTGTTTGCTTAT 59.347 33.333 0.00 0.00 0.00 1.73
36 37 8.947055 AGACTTTGTTGAATTGTTTGCTTATT 57.053 26.923 0.00 0.00 0.00 1.40
51 52 9.494271 TGTTTGCTTATTAATAAAATGGTTGCA 57.506 25.926 9.15 9.84 0.00 4.08
54 55 8.140677 TGCTTATTAATAAAATGGTTGCATGC 57.859 30.769 11.82 11.82 0.00 4.06
55 56 7.767659 TGCTTATTAATAAAATGGTTGCATGCA 59.232 29.630 18.46 18.46 0.00 3.96
56 57 8.776470 GCTTATTAATAAAATGGTTGCATGCAT 58.224 29.630 23.37 7.12 0.00 3.96
76 77 2.266070 TTTTTGATGCAGAGGCCGG 58.734 52.632 0.00 0.00 40.13 6.13
77 78 1.250154 TTTTTGATGCAGAGGCCGGG 61.250 55.000 2.18 0.00 40.13 5.73
78 79 3.643595 TTTGATGCAGAGGCCGGGG 62.644 63.158 2.18 0.00 40.13 5.73
82 83 3.792325 ATGCAGAGGCCGGGGGATA 62.792 63.158 2.18 0.00 40.13 2.59
83 84 3.168528 GCAGAGGCCGGGGGATAA 61.169 66.667 2.18 0.00 0.00 1.75
84 85 2.529744 GCAGAGGCCGGGGGATAAT 61.530 63.158 2.18 0.00 0.00 1.28
85 86 1.679898 CAGAGGCCGGGGGATAATC 59.320 63.158 2.18 0.00 0.00 1.75
86 87 0.838122 CAGAGGCCGGGGGATAATCT 60.838 60.000 2.18 0.00 0.00 2.40
87 88 0.545548 AGAGGCCGGGGGATAATCTC 60.546 60.000 2.18 0.00 0.00 2.75
88 89 0.545548 GAGGCCGGGGGATAATCTCT 60.546 60.000 2.18 0.00 0.00 3.10
89 90 0.545548 AGGCCGGGGGATAATCTCTC 60.546 60.000 2.18 0.00 0.00 3.20
90 91 0.545548 GGCCGGGGGATAATCTCTCT 60.546 60.000 2.18 0.00 0.00 3.10
91 92 1.353091 GCCGGGGGATAATCTCTCTT 58.647 55.000 2.18 0.00 0.00 2.85
92 93 1.700186 GCCGGGGGATAATCTCTCTTT 59.300 52.381 2.18 0.00 0.00 2.52
93 94 2.289756 GCCGGGGGATAATCTCTCTTTC 60.290 54.545 2.18 0.00 0.00 2.62
94 95 2.972713 CCGGGGGATAATCTCTCTTTCA 59.027 50.000 0.00 0.00 0.00 2.69
95 96 3.391296 CCGGGGGATAATCTCTCTTTCAA 59.609 47.826 0.00 0.00 0.00 2.69
96 97 4.503991 CCGGGGGATAATCTCTCTTTCAAG 60.504 50.000 0.00 0.00 0.00 3.02
97 98 4.345257 CGGGGGATAATCTCTCTTTCAAGA 59.655 45.833 0.00 0.00 0.00 3.02
98 99 5.163301 CGGGGGATAATCTCTCTTTCAAGAA 60.163 44.000 0.00 0.00 34.03 2.52
99 100 6.632672 CGGGGGATAATCTCTCTTTCAAGAAA 60.633 42.308 0.00 0.00 34.03 2.52
246 248 4.320275 GCTTTTTAAACCGAGAAGGAGGTG 60.320 45.833 0.00 0.00 45.00 4.00
254 256 4.405548 ACCGAGAAGGAGGTGGTATATAC 58.594 47.826 4.14 4.14 45.00 1.47
304 306 4.704540 TGGAGCCGATGTGTTTATGAAAAT 59.295 37.500 0.00 0.00 0.00 1.82
331 333 3.545703 ACTAGCCCTTTATGATGTGCAC 58.454 45.455 10.75 10.75 0.00 4.57
361 363 4.221041 GGGAGGTGCTATAGGTTGATCTAC 59.779 50.000 1.04 0.00 0.00 2.59
445 447 0.926155 CATCAGTTCACCATCGAGCG 59.074 55.000 0.00 0.00 0.00 5.03
449 451 1.798223 CAGTTCACCATCGAGCGAAAA 59.202 47.619 0.00 0.00 0.00 2.29
513 515 9.909644 GGACATACTTACATATCATCGTAAAGT 57.090 33.333 0.00 0.00 0.00 2.66
550 552 4.927267 TGGTGACCACAGAGGATTAATT 57.073 40.909 0.00 0.00 41.22 1.40
552 554 5.741011 TGGTGACCACAGAGGATTAATTAC 58.259 41.667 0.00 0.00 41.22 1.89
553 555 5.487488 TGGTGACCACAGAGGATTAATTACT 59.513 40.000 0.00 0.00 41.22 2.24
554 556 6.012858 TGGTGACCACAGAGGATTAATTACTT 60.013 38.462 0.00 0.00 41.22 2.24
555 557 6.884836 GGTGACCACAGAGGATTAATTACTTT 59.115 38.462 0.00 0.00 41.22 2.66
556 558 7.393515 GGTGACCACAGAGGATTAATTACTTTT 59.606 37.037 0.00 0.00 41.22 2.27
557 559 8.793592 GTGACCACAGAGGATTAATTACTTTTT 58.206 33.333 0.00 0.00 41.22 1.94
605 607 7.275920 ACTTGATAACTAAAGCGGAGAATCAT 58.724 34.615 0.00 0.00 36.25 2.45
621 623 7.169308 CGGAGAATCATGTAACCAGTTATACAC 59.831 40.741 0.00 0.00 35.05 2.90
809 817 7.999679 TGTTGATCATTTTAGATGGATGAACC 58.000 34.615 0.00 0.00 34.39 3.62
906 915 5.556915 ACAAATTTGATCGGTGAAGACCTA 58.443 37.500 24.64 0.00 40.58 3.08
1101 1115 4.019321 CCAGAAAACCTCAGGATGGTTCTA 60.019 45.833 0.00 0.00 45.99 2.10
1203 1217 4.876125 CGTCTAGTGTACGTCCTCCTATA 58.124 47.826 0.00 0.00 35.66 1.31
1417 1441 2.433604 CTCAAGCTCAGATGGGAAGCTA 59.566 50.000 0.00 0.00 35.15 3.32
1465 1489 4.744795 AGGACTACTAGCATTTCCACTG 57.255 45.455 0.00 0.00 0.00 3.66
1645 1685 1.135402 GTCGGATGAATTGCACCCAAC 60.135 52.381 0.00 0.00 32.95 3.77
1654 1694 2.969821 TTGCACCCAACACTATTCCT 57.030 45.000 0.00 0.00 0.00 3.36
1668 1709 9.743057 CAACACTATTCCTTCAAACAACAATTA 57.257 29.630 0.00 0.00 0.00 1.40
1684 1726 8.788325 ACAACAATTACATCCCTAGTAAGAAC 57.212 34.615 0.00 0.00 35.18 3.01
1692 2018 6.173339 ACATCCCTAGTAAGAACATTGTGTG 58.827 40.000 0.00 0.00 0.00 3.82
2011 3190 0.109412 CGGGCTTCGAAACTACGTCT 60.109 55.000 0.00 0.00 42.43 4.18
2014 3193 1.647702 GGCTTCGAAACTACGTCTTCG 59.352 52.381 16.80 16.80 44.48 3.79
2050 3229 3.493503 CACTCAAGTTTCTAACCGGTGAC 59.506 47.826 8.52 2.30 0.00 3.67
2099 3278 3.314693 AGTGTGGACAAAGGGAAGTAGA 58.685 45.455 0.00 0.00 0.00 2.59
2187 3369 6.746364 CCTTGAGACGTACACACTAGTATTTC 59.254 42.308 0.00 0.00 0.00 2.17
2243 3429 5.036737 GTGCATTCTATTACACACAATGCC 58.963 41.667 11.36 1.53 45.78 4.40
2517 3723 8.940397 TCCTTCCCATAATCCAAGAAAATATC 57.060 34.615 0.00 0.00 0.00 1.63
2518 3724 8.510283 TCCTTCCCATAATCCAAGAAAATATCA 58.490 33.333 0.00 0.00 0.00 2.15
2627 3864 2.360475 GGCCAACCCTGACTCTGC 60.360 66.667 0.00 0.00 0.00 4.26
3012 4656 5.168569 GTGCACATATAGTACAGTGTGTGT 58.831 41.667 13.17 6.20 42.85 3.72
3043 4687 3.262405 TGTAATCAAAAGGAGGGTAGCGT 59.738 43.478 0.00 0.00 0.00 5.07
3046 4690 0.605319 CAAAAGGAGGGTAGCGTGCA 60.605 55.000 8.81 0.00 0.00 4.57
3049 4693 2.804828 AAGGAGGGTAGCGTGCAAGC 62.805 60.000 17.43 17.43 37.41 4.01
3053 4697 2.047274 GGTAGCGTGCAAGCAGGA 60.047 61.111 26.30 8.52 40.15 3.86
3058 4702 2.270205 CGTGCAAGCAGGAGGGAT 59.730 61.111 8.95 0.00 34.13 3.85
3439 5094 7.810658 GTGCATCCACAATATATAGTTGGAAG 58.189 38.462 14.01 11.90 41.67 3.46
3503 5161 7.554118 CCAAGAAAGGAAAAGTAGCTCATGATA 59.446 37.037 0.00 0.00 0.00 2.15
3517 5176 7.573968 AGCTCATGATAATTACCTTCAAACC 57.426 36.000 0.00 0.00 0.00 3.27
3568 5229 7.814264 ATAATTGAGCATAAGGAGTTCTTGG 57.186 36.000 0.00 0.00 36.93 3.61
3572 5233 5.003804 TGAGCATAAGGAGTTCTTGGAAAC 58.996 41.667 0.00 0.00 36.93 2.78
3716 5402 9.196552 GAATATTTCAAACAAAGGAAAGGAGTG 57.803 33.333 0.00 0.00 36.55 3.51
3806 5494 0.846427 TGGGTGGCTCCTCAAAGGAT 60.846 55.000 5.46 0.00 44.81 3.24
3931 5619 9.387123 GTGATTTGCTCTTTCTTGTACTAAAAG 57.613 33.333 0.00 2.02 0.00 2.27
4097 6019 7.510675 TCTTACTATGTTTCTTGGGGAGAAT 57.489 36.000 0.00 0.00 43.65 2.40
4114 6036 9.689008 TGGGGAGAATATATATATGTAGCCATT 57.311 33.333 6.00 0.00 32.29 3.16
4238 6160 6.448207 AAACCAATGTTTCATTTTGGGTTG 57.552 33.333 12.87 0.00 46.09 3.77
4350 6274 2.869078 CCCCCTCCCCACCCTTTT 60.869 66.667 0.00 0.00 0.00 2.27
4370 6294 3.553828 TTCGGGTTTGTCTTCTCAACT 57.446 42.857 0.00 0.00 0.00 3.16
4394 6318 6.780198 TTATAAGGCCCATTCCTCTTACAT 57.220 37.500 0.00 0.00 34.82 2.29
4402 6326 6.299141 GCCCATTCCTCTTACATTTAGATCA 58.701 40.000 0.00 0.00 0.00 2.92
4462 6386 3.329386 CTCGATGTTCTTCAAGCCAGAA 58.671 45.455 0.00 0.00 0.00 3.02
4543 6467 4.292186 AGGTGTGCTAACATGATGAGTT 57.708 40.909 0.00 0.00 38.92 3.01
5094 7068 9.569122 ACAGTGTGTTAAGTACAAAGGAAATAT 57.431 29.630 0.00 0.00 38.80 1.28
5269 7246 5.488341 GCCTTCTACAGTTGGAAAGTCATA 58.512 41.667 0.00 0.00 0.00 2.15
5281 7258 5.570320 TGGAAAGTCATAAAGGGAGGAAAG 58.430 41.667 0.00 0.00 0.00 2.62
5349 7326 9.177608 CATACAACTTCTCCCAAAATCTTGATA 57.822 33.333 0.00 0.00 34.14 2.15
5400 7377 2.961536 TCTCTAAGACCATGGGGGAA 57.038 50.000 18.09 0.00 41.15 3.97
5414 7430 4.119556 TGGGGGAATCACAATGTTGTTA 57.880 40.909 0.00 0.00 39.91 2.41
5450 7466 9.627395 GTATCTAGTAATGTATCATGTGTGTCC 57.373 37.037 0.00 0.00 0.00 4.02
5485 7501 6.594788 AAATAGCATATAAGCATTGGTGGG 57.405 37.500 2.37 0.00 36.85 4.61
5490 7506 8.875604 TAGCATATAAGCATTGGTGGGACCAC 62.876 46.154 13.03 13.03 42.23 4.16
5557 7575 1.930371 GCTTTCCAACCATGTTGCGAC 60.930 52.381 0.00 0.00 0.00 5.19
5602 7620 3.774766 ACCACACTACATTCTCAGGCATA 59.225 43.478 0.00 0.00 0.00 3.14
5617 7635 3.809832 CAGGCATATTACTCCCTCAAACG 59.190 47.826 0.00 0.00 0.00 3.60
5624 7642 5.733620 ATTACTCCCTCAAACGACAACTA 57.266 39.130 0.00 0.00 0.00 2.24
5735 7754 7.094592 TGCAATAGTTCCTAGATATGAGAGTCG 60.095 40.741 0.00 0.00 0.00 4.18
5749 7768 2.047560 GTCGGAGGAAACCCCACG 60.048 66.667 0.00 0.00 38.42 4.94
5844 7863 6.443527 TGATGATCCTATTTCCCCGATGATAA 59.556 38.462 0.00 0.00 0.00 1.75
5853 7872 4.085357 TCCCCGATGATAAGGAATTGTG 57.915 45.455 0.00 0.00 0.00 3.33
5876 7896 4.946784 AAGTAACAAGGATGTCGCAATC 57.053 40.909 0.00 0.00 39.40 2.67
5888 7908 1.812571 GTCGCAATCCTTGGAACACAT 59.187 47.619 0.00 0.00 39.29 3.21
5889 7909 2.083774 TCGCAATCCTTGGAACACATC 58.916 47.619 0.00 0.00 39.29 3.06
5894 7914 2.631160 TCCTTGGAACACATCGTTGT 57.369 45.000 0.00 0.00 39.29 3.32
5962 7982 1.039068 CAACCATCACCTTGTTGCCA 58.961 50.000 0.00 0.00 33.72 4.92
5967 7987 4.865905 ACCATCACCTTGTTGCCAATATA 58.134 39.130 0.00 0.00 0.00 0.86
6002 8022 8.324191 TCAAGTCCTTAGACCATGAGAATATT 57.676 34.615 0.00 0.00 44.72 1.28
6004 8024 7.921041 AGTCCTTAGACCATGAGAATATTCA 57.079 36.000 17.56 0.00 44.72 2.57
6008 8029 7.565029 TCCTTAGACCATGAGAATATTCAGACA 59.435 37.037 17.56 13.59 0.00 3.41
6043 8064 2.691011 GTTACTTCAGGGTTGCCAAACA 59.309 45.455 0.00 0.00 38.10 2.83
6049 8070 3.096092 TCAGGGTTGCCAAACATTATCC 58.904 45.455 0.00 0.00 38.10 2.59
6057 8078 5.242069 TGCCAAACATTATCCGTAACATG 57.758 39.130 0.00 0.00 0.00 3.21
6059 8080 5.416013 TGCCAAACATTATCCGTAACATGAA 59.584 36.000 0.00 0.00 0.00 2.57
6080 8101 9.578439 CATGAAGATTGTAGCGATGATTATAGA 57.422 33.333 0.00 0.00 0.00 1.98
6105 8126 4.633126 GGAACTTTCGGGTACATAGGAAAC 59.367 45.833 0.00 0.00 0.00 2.78
6169 8190 2.030363 CCAGCGATGGAGAGATACTCAC 60.030 54.545 16.48 0.00 46.54 3.51
6181 8202 0.252696 ATACTCACTGGGCCCACTCA 60.253 55.000 24.45 5.93 0.00 3.41
6212 8233 6.849085 AGTATCCATCATCATCTCACTACC 57.151 41.667 0.00 0.00 0.00 3.18
6213 8234 4.797800 ATCCATCATCATCTCACTACCG 57.202 45.455 0.00 0.00 0.00 4.02
6247 8268 1.282157 AGGTGAACCCTAATGAGTGGC 59.718 52.381 0.00 0.00 43.87 5.01
6251 8272 2.203209 CCCTAATGAGTGGCGGGC 60.203 66.667 0.00 0.00 0.00 6.13
6253 8274 2.186903 CTAATGAGTGGCGGGCGT 59.813 61.111 0.00 0.00 0.00 5.68
6254 8275 1.883084 CTAATGAGTGGCGGGCGTC 60.883 63.158 0.00 0.00 0.00 5.19
6273 8294 4.263572 TGGAACACCCGCCACAGG 62.264 66.667 0.00 0.00 37.93 4.00
6295 8316 7.228706 ACAGGTATTTTTGAGAACAAGTAGTGG 59.771 37.037 0.00 0.00 37.32 4.00
6298 8319 3.462483 TTTGAGAACAAGTAGTGGCGA 57.538 42.857 0.00 0.00 37.32 5.54
6316 8337 0.317854 GAGTGACAAAAGTTGCCCGC 60.318 55.000 0.00 0.00 0.00 6.13
6321 8342 1.142748 CAAAAGTTGCCCGCCACAA 59.857 52.632 0.00 0.00 0.00 3.33
6325 8346 3.996614 GTTGCCCGCCACAACTAT 58.003 55.556 6.27 0.00 43.23 2.12
6341 8362 0.538584 CTATGTGAGGAGCAGTGGCA 59.461 55.000 0.00 0.00 44.61 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.951642 CAACAAAGTCTCCAAGCCTCAA 59.048 45.455 0.00 0.00 0.00 3.02
1 2 2.172505 TCAACAAAGTCTCCAAGCCTCA 59.827 45.455 0.00 0.00 0.00 3.86
2 3 2.851195 TCAACAAAGTCTCCAAGCCTC 58.149 47.619 0.00 0.00 0.00 4.70
3 4 3.297134 TTCAACAAAGTCTCCAAGCCT 57.703 42.857 0.00 0.00 0.00 4.58
4 5 4.202151 ACAATTCAACAAAGTCTCCAAGCC 60.202 41.667 0.00 0.00 0.00 4.35
5 6 4.936891 ACAATTCAACAAAGTCTCCAAGC 58.063 39.130 0.00 0.00 0.00 4.01
6 7 6.237915 GCAAACAATTCAACAAAGTCTCCAAG 60.238 38.462 0.00 0.00 0.00 3.61
7 8 5.580297 GCAAACAATTCAACAAAGTCTCCAA 59.420 36.000 0.00 0.00 0.00 3.53
8 9 5.105392 AGCAAACAATTCAACAAAGTCTCCA 60.105 36.000 0.00 0.00 0.00 3.86
9 10 5.351458 AGCAAACAATTCAACAAAGTCTCC 58.649 37.500 0.00 0.00 0.00 3.71
10 11 6.892310 AAGCAAACAATTCAACAAAGTCTC 57.108 33.333 0.00 0.00 0.00 3.36
11 12 8.947055 AATAAGCAAACAATTCAACAAAGTCT 57.053 26.923 0.00 0.00 0.00 3.24
25 26 9.494271 TGCAACCATTTTATTAATAAGCAAACA 57.506 25.926 11.48 2.64 0.00 2.83
28 29 8.610896 GCATGCAACCATTTTATTAATAAGCAA 58.389 29.630 14.21 7.25 0.00 3.91
29 30 7.767659 TGCATGCAACCATTTTATTAATAAGCA 59.232 29.630 20.30 14.61 0.00 3.91
30 31 8.140677 TGCATGCAACCATTTTATTAATAAGC 57.859 30.769 20.30 7.09 0.00 3.09
58 59 1.250154 CCCGGCCTCTGCATCAAAAA 61.250 55.000 0.00 0.00 40.13 1.94
59 60 1.678635 CCCGGCCTCTGCATCAAAA 60.679 57.895 0.00 0.00 40.13 2.44
60 61 2.045045 CCCGGCCTCTGCATCAAA 60.045 61.111 0.00 0.00 40.13 2.69
61 62 4.113815 CCCCGGCCTCTGCATCAA 62.114 66.667 0.00 0.00 40.13 2.57
64 65 3.792325 TATCCCCCGGCCTCTGCAT 62.792 63.158 0.00 0.00 40.13 3.96
65 66 4.490606 TATCCCCCGGCCTCTGCA 62.491 66.667 0.00 0.00 40.13 4.41
66 67 2.470938 GATTATCCCCCGGCCTCTGC 62.471 65.000 0.00 0.00 0.00 4.26
67 68 0.838122 AGATTATCCCCCGGCCTCTG 60.838 60.000 0.00 0.00 0.00 3.35
68 69 0.545548 GAGATTATCCCCCGGCCTCT 60.546 60.000 0.00 0.00 0.00 3.69
69 70 0.545548 AGAGATTATCCCCCGGCCTC 60.546 60.000 0.00 0.00 0.00 4.70
70 71 0.545548 GAGAGATTATCCCCCGGCCT 60.546 60.000 0.00 0.00 0.00 5.19
71 72 0.545548 AGAGAGATTATCCCCCGGCC 60.546 60.000 0.00 0.00 0.00 6.13
72 73 1.353091 AAGAGAGATTATCCCCCGGC 58.647 55.000 0.00 0.00 0.00 6.13
73 74 2.972713 TGAAAGAGAGATTATCCCCCGG 59.027 50.000 0.00 0.00 0.00 5.73
74 75 4.345257 TCTTGAAAGAGAGATTATCCCCCG 59.655 45.833 0.00 0.00 0.00 5.73
75 76 5.896073 TCTTGAAAGAGAGATTATCCCCC 57.104 43.478 0.00 0.00 0.00 5.40
76 77 8.581253 TTTTTCTTGAAAGAGAGATTATCCCC 57.419 34.615 0.00 0.00 36.22 4.81
156 157 9.881529 CGAGTTATATCTCTTAAAGTAGGTGTC 57.118 37.037 8.76 0.00 32.83 3.67
157 158 9.406113 ACGAGTTATATCTCTTAAAGTAGGTGT 57.594 33.333 8.76 0.00 32.83 4.16
158 159 9.666626 CACGAGTTATATCTCTTAAAGTAGGTG 57.333 37.037 8.76 3.44 32.83 4.00
164 166 9.737427 ACATCACACGAGTTATATCTCTTAAAG 57.263 33.333 8.76 0.00 32.83 1.85
168 170 6.980978 CCAACATCACACGAGTTATATCTCTT 59.019 38.462 8.76 0.00 32.83 2.85
181 183 3.963665 ACAATTTGACCAACATCACACG 58.036 40.909 2.79 0.00 0.00 4.49
254 256 8.441608 ACATTATAACTAGTAGCACGATACTCG 58.558 37.037 0.00 0.00 46.93 4.18
304 306 6.486657 GCACATCATAAAGGGCTAGTAAATCA 59.513 38.462 0.00 0.00 0.00 2.57
320 322 1.270785 CCCCGCTATGTGCACATCATA 60.271 52.381 34.54 17.47 43.06 2.15
323 325 0.882042 CTCCCCGCTATGTGCACATC 60.882 60.000 34.54 20.51 43.06 3.06
331 333 2.366469 ATAGCACCTCCCCGCTATG 58.634 57.895 3.24 0.00 46.93 2.23
338 340 3.243724 AGATCAACCTATAGCACCTCCC 58.756 50.000 0.00 0.00 0.00 4.30
400 402 1.206132 TGCATGAACCTACCCGTACAG 59.794 52.381 0.00 0.00 0.00 2.74
449 451 7.944729 ACATAATGTCTTCTTGCCATACTTT 57.055 32.000 0.00 0.00 0.00 2.66
513 515 7.693533 TGGTCACCACCCTGTAATATTATTA 57.306 36.000 0.00 0.00 42.99 0.98
637 639 1.837439 CTCCCCACACATGGTAAGCTA 59.163 52.381 0.00 0.00 45.66 3.32
770 777 3.767131 TGATCAACATCCGAGTAAGACCA 59.233 43.478 0.00 0.00 0.00 4.02
809 817 6.310956 TCGATTGTTATACAACGTTTAGGGTG 59.689 38.462 0.00 0.00 41.40 4.61
906 915 7.405292 TCAAATCTTGATCTAGGGACACAATT 58.595 34.615 4.29 0.00 34.08 2.32
1101 1115 3.306088 CCGTCTGTTGTACTTCATGGAGT 60.306 47.826 12.36 12.36 0.00 3.85
1138 1152 1.043816 GGATGATCGAGCCAGGAGAA 58.956 55.000 0.00 0.00 0.00 2.87
1203 1217 5.994416 ACACCATCAATATAGGGAAAGGT 57.006 39.130 0.00 0.00 0.00 3.50
1417 1441 5.741011 AGAAATGCATCAAATTGCTTCCAT 58.259 33.333 0.00 0.00 43.18 3.41
1465 1489 1.755179 ATGCTGTGCCAGGAATGTAC 58.245 50.000 0.00 0.00 35.08 2.90
1555 1579 6.258068 GCCAGAGTGGTCTTGTATGTATTAAC 59.742 42.308 0.00 0.00 40.46 2.01
1645 1685 9.912634 ATGTAATTGTTGTTTGAAGGAATAGTG 57.087 29.630 0.00 0.00 0.00 2.74
1654 1694 9.575868 TTACTAGGGATGTAATTGTTGTTTGAA 57.424 29.630 0.00 0.00 0.00 2.69
1668 1709 6.173339 CACACAATGTTCTTACTAGGGATGT 58.827 40.000 0.00 0.00 0.00 3.06
1684 1726 7.552458 TTAATCAGGCTATACACACACAATG 57.448 36.000 0.00 0.00 0.00 2.82
1692 2018 4.459337 GCCCCAATTAATCAGGCTATACAC 59.541 45.833 13.44 0.00 40.57 2.90
1785 2847 8.428186 GGAACCATACGTATAAGACAAATTGA 57.572 34.615 7.96 0.00 0.00 2.57
1936 3115 9.607285 GCAATTTTCTCGTTCATTAAAGTCTTA 57.393 29.630 0.00 0.00 0.00 2.10
2011 3190 2.429610 GAGTGTAGCAGTTATCCCCGAA 59.570 50.000 0.00 0.00 0.00 4.30
2014 3193 3.197983 ACTTGAGTGTAGCAGTTATCCCC 59.802 47.826 0.00 0.00 0.00 4.81
2050 3229 2.810488 ATTCTTGCAGGGCCTTGGGG 62.810 60.000 17.71 0.00 0.00 4.96
2153 3335 8.308931 AGTGTGTACGTCTCAAGGAAAATATTA 58.691 33.333 0.00 0.00 0.00 0.98
2187 3369 6.273825 GTGTATGTCTAATAGTGTGGGTGAG 58.726 44.000 0.00 0.00 0.00 3.51
2243 3429 6.730960 TGGAAGTGTTAACGCTAAATTAGG 57.269 37.500 21.40 0.00 35.32 2.69
2462 3668 5.473066 TGGGTGTTACTAGGTGTAGTTTC 57.527 43.478 0.00 0.00 40.23 2.78
2517 3723 6.150976 ACATGAGTTACCCAATTACACACATG 59.849 38.462 0.00 0.00 37.06 3.21
2518 3724 6.245408 ACATGAGTTACCCAATTACACACAT 58.755 36.000 0.00 0.00 0.00 3.21
2627 3864 5.195940 ACTTGTATTCCTCCCATGTGATTG 58.804 41.667 0.00 0.00 0.00 2.67
2676 3913 6.159988 ACAAAGACCGAAGAGAGATAAACTG 58.840 40.000 0.00 0.00 0.00 3.16
2682 3919 6.055588 TGAAAAACAAAGACCGAAGAGAGAT 58.944 36.000 0.00 0.00 0.00 2.75
2782 4022 6.682423 ACAATGACGCAGATGAAATAATGA 57.318 33.333 0.00 0.00 0.00 2.57
3012 4656 6.481643 CCTCCTTTTGATTACAAGGAAGGTA 58.518 40.000 6.58 0.00 41.27 3.08
3016 4660 5.333566 ACCCTCCTTTTGATTACAAGGAA 57.666 39.130 6.58 0.00 37.32 3.36
3043 4687 1.811778 ATCTATCCCTCCTGCTTGCA 58.188 50.000 0.00 0.00 0.00 4.08
3046 4690 4.202409 GCAAACTATCTATCCCTCCTGCTT 60.202 45.833 0.00 0.00 0.00 3.91
3049 4693 4.963318 TGCAAACTATCTATCCCTCCTG 57.037 45.455 0.00 0.00 0.00 3.86
3456 5111 6.459670 TGGAAAGGTTTTGACCTAGTTTTC 57.540 37.500 0.00 0.00 39.65 2.29
3459 5117 5.762279 TCTTGGAAAGGTTTTGACCTAGTT 58.238 37.500 0.00 0.00 46.24 2.24
3460 5118 5.382664 TCTTGGAAAGGTTTTGACCTAGT 57.617 39.130 0.00 0.00 46.24 2.57
3461 5119 6.239036 CCTTTCTTGGAAAGGTTTTGACCTAG 60.239 42.308 23.37 0.00 46.24 3.02
3550 5211 5.003804 TGTTTCCAAGAACTCCTTATGCTC 58.996 41.667 0.00 0.00 32.86 4.26
3563 5224 3.896888 ACCATGCTGAATTGTTTCCAAGA 59.103 39.130 0.00 0.00 33.17 3.02
3566 5227 5.999205 AATACCATGCTGAATTGTTTCCA 57.001 34.783 0.00 0.00 0.00 3.53
3572 5233 9.671279 TCCATACTATAATACCATGCTGAATTG 57.329 33.333 0.00 0.00 0.00 2.32
3828 5516 0.312416 GCACCAACACATAACCGCAA 59.688 50.000 0.00 0.00 0.00 4.85
4061 5983 8.790718 AGAAACATAGTAAGAACTGACGAAGTA 58.209 33.333 0.00 0.00 38.56 2.24
4065 5987 6.866770 CCAAGAAACATAGTAAGAACTGACGA 59.133 38.462 0.00 0.00 36.36 4.20
4119 6041 5.648092 GCACAGTAGGTCCAATTTGAGTAAT 59.352 40.000 0.00 0.00 0.00 1.89
4129 6051 2.321719 TGTGTAGCACAGTAGGTCCAA 58.678 47.619 0.00 0.00 39.62 3.53
4208 6130 9.662545 CCAAAATGAAACATTGGTTTTATGAAC 57.337 29.630 0.00 0.00 46.84 3.18
4226 6148 3.552875 TGTTACCGACAACCCAAAATGA 58.447 40.909 0.00 0.00 34.69 2.57
4321 6245 0.919289 GGAGGGGGTGAAGGGATTGA 60.919 60.000 0.00 0.00 0.00 2.57
4350 6274 3.553828 AGTTGAGAAGACAAACCCGAA 57.446 42.857 0.00 0.00 0.00 4.30
4358 6282 5.013704 TGGGCCTTATAAAGTTGAGAAGACA 59.986 40.000 4.53 0.00 0.00 3.41
4360 6284 5.772393 TGGGCCTTATAAAGTTGAGAAGA 57.228 39.130 4.53 0.00 0.00 2.87
4363 6287 5.193728 AGGAATGGGCCTTATAAAGTTGAGA 59.806 40.000 4.53 0.00 33.46 3.27
4370 6294 6.584471 TGTAAGAGGAATGGGCCTTATAAA 57.416 37.500 4.53 0.00 38.73 1.40
4394 6318 7.712639 GTGGAGACAAGCAATCTATGATCTAAA 59.287 37.037 0.00 0.00 46.06 1.85
4402 6326 4.785346 ATGGTGGAGACAAGCAATCTAT 57.215 40.909 0.00 0.00 46.06 1.98
4503 6427 1.850345 CTACCCCTTTCCCAGGCATTA 59.150 52.381 0.00 0.00 42.29 1.90
4543 6467 1.771854 TGAAGTTACAAGCACCCTCCA 59.228 47.619 0.00 0.00 0.00 3.86
4754 6691 5.291178 TGAAAGAAATTCAACTGCATGGTG 58.709 37.500 0.00 0.00 44.94 4.17
5114 7088 1.956477 GTAATGCACCCCCATCATGTC 59.044 52.381 0.00 0.00 0.00 3.06
5125 7099 6.908825 TGTGTTTTTGATAGAGTAATGCACC 58.091 36.000 0.00 0.00 0.00 5.01
5269 7246 1.713078 AGCACCATCTTTCCTCCCTTT 59.287 47.619 0.00 0.00 0.00 3.11
5281 7258 1.280421 AGTCCAGGAGAAAGCACCATC 59.720 52.381 0.00 0.00 0.00 3.51
5349 7326 6.183360 CCGTATTGAAGCAGTAACAATCATGT 60.183 38.462 0.00 0.00 43.14 3.21
5400 7377 7.895759 ACTTAGCCAAATAACAACATTGTGAT 58.104 30.769 0.00 0.00 41.31 3.06
5485 7501 7.545615 AGAACAAGAATTTGAACAAAAGTGGTC 59.454 33.333 4.12 7.94 42.31 4.02
5490 7506 9.086336 TGCTAAGAACAAGAATTTGAACAAAAG 57.914 29.630 4.12 0.00 37.73 2.27
5557 7575 4.245660 TGCTTGTGAGGAAGATAAACTCG 58.754 43.478 0.00 0.00 34.03 4.18
5602 7620 4.618920 AGTTGTCGTTTGAGGGAGTAAT 57.381 40.909 0.00 0.00 0.00 1.89
5617 7635 9.482627 CTCTAGGTCATATTTCCAATAGTTGTC 57.517 37.037 0.00 0.00 0.00 3.18
5624 7642 5.912149 TGCCTCTAGGTCATATTTCCAAT 57.088 39.130 0.00 0.00 37.57 3.16
5715 7733 5.514136 CCTCCGACTCTCATATCTAGGAACT 60.514 48.000 0.00 0.00 46.37 3.01
5718 7736 4.168883 TCCTCCGACTCTCATATCTAGGA 58.831 47.826 0.00 0.00 0.00 2.94
5722 7741 3.892588 GGTTTCCTCCGACTCTCATATCT 59.107 47.826 0.00 0.00 0.00 1.98
5735 7754 2.671963 GCACGTGGGGTTTCCTCC 60.672 66.667 18.88 0.00 36.20 4.30
5749 7768 5.752955 AGTGTTTAAATTTCCACACATGCAC 59.247 36.000 24.32 10.83 41.73 4.57
5793 7812 5.763088 CAATACATGCGCTAGTCTTAGAGA 58.237 41.667 9.73 0.00 0.00 3.10
5833 7852 3.820557 ACACAATTCCTTATCATCGGGG 58.179 45.455 0.00 0.00 0.00 5.73
5844 7863 7.231467 ACATCCTTGTTACTTACACAATTCCT 58.769 34.615 0.00 0.00 36.21 3.36
5853 7872 5.220605 GGATTGCGACATCCTTGTTACTTAC 60.221 44.000 6.13 0.00 35.79 2.34
5876 7896 1.535462 GGACAACGATGTGTTCCAAGG 59.465 52.381 1.86 0.00 40.74 3.61
5894 7914 6.270509 GGTCTATCCAACACCATTGTTTGGA 61.271 44.000 11.82 11.82 43.89 3.53
5930 7950 5.940470 AGGTGATGGTTGAATCTTGAAGTAC 59.060 40.000 0.00 0.00 0.00 2.73
5967 7987 8.375493 TGGTCTAAGGACTTGAGTATACATTT 57.625 34.615 5.50 0.00 41.82 2.32
6002 8022 3.038280 ACCATCCGGTATGAATGTCTGA 58.962 45.455 13.47 0.00 46.71 3.27
6030 8051 2.099405 CGGATAATGTTTGGCAACCCT 58.901 47.619 0.00 0.00 31.02 4.34
6043 8064 7.116376 CGCTACAATCTTCATGTTACGGATAAT 59.884 37.037 0.00 0.00 32.27 1.28
6049 8070 5.458779 TCATCGCTACAATCTTCATGTTACG 59.541 40.000 0.00 0.00 32.27 3.18
6057 8078 7.704472 CCCTCTATAATCATCGCTACAATCTTC 59.296 40.741 0.00 0.00 0.00 2.87
6059 8080 6.892456 TCCCTCTATAATCATCGCTACAATCT 59.108 38.462 0.00 0.00 0.00 2.40
6080 8101 2.770232 CCTATGTACCCGAAAGTTCCCT 59.230 50.000 0.00 0.00 0.00 4.20
6120 8141 7.716998 GGAGCAAATCCTAGTCTTGAATTATCA 59.283 37.037 0.00 0.00 45.64 2.15
6169 8190 5.505181 ACTATAATATTGAGTGGGCCCAG 57.495 43.478 29.55 11.39 0.00 4.45
6200 8221 2.108168 CCTTTCCCGGTAGTGAGATGA 58.892 52.381 0.00 0.00 0.00 2.92
6202 8223 1.497161 CCCTTTCCCGGTAGTGAGAT 58.503 55.000 0.00 0.00 0.00 2.75
6212 8233 1.766496 TCACCTATAAGCCCTTTCCCG 59.234 52.381 0.00 0.00 0.00 5.14
6213 8234 3.552875 GTTCACCTATAAGCCCTTTCCC 58.447 50.000 0.00 0.00 0.00 3.97
6253 8274 4.612412 GTGGCGGGTGTTCCACGA 62.612 66.667 0.00 0.00 42.67 4.35
6256 8277 4.263572 CCTGTGGCGGGTGTTCCA 62.264 66.667 0.00 0.00 34.36 3.53
6265 8286 3.252215 TGTTCTCAAAAATACCTGTGGCG 59.748 43.478 0.00 0.00 0.00 5.69
6273 8294 6.073440 TCGCCACTACTTGTTCTCAAAAATAC 60.073 38.462 0.00 0.00 32.87 1.89
6295 8316 0.317854 GGGCAACTTTTGTCACTCGC 60.318 55.000 0.00 0.00 36.88 5.03
6298 8319 1.733526 GCGGGCAACTTTTGTCACT 59.266 52.632 0.00 0.00 36.88 3.41
6321 8342 0.539051 GCCACTGCTCCTCACATAGT 59.461 55.000 0.00 0.00 33.53 2.12
6325 8346 1.071987 CTTGCCACTGCTCCTCACA 59.928 57.895 0.00 0.00 38.71 3.58
6329 8350 2.033757 CTGCTTGCCACTGCTCCT 59.966 61.111 0.00 0.00 38.71 3.69


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

AutoCloner maintained by Alex Coulton.