Multiple sequence alignment - TraesCS4A01G375200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G375200 chr4A 100.000 5314 0 0 1 5314 649903628 649898315 0.000000e+00 9814.0
1 TraesCS4A01G375200 chr4A 92.025 1442 48 20 3211 4648 650042799 650041421 0.000000e+00 1964.0
2 TraesCS4A01G375200 chr4A 88.802 1536 117 27 1676 3208 650044177 650042694 0.000000e+00 1832.0
3 TraesCS4A01G375200 chr4A 82.036 334 55 5 1342 1673 649906652 649906322 4.050000e-71 279.0
4 TraesCS4A01G375200 chr4A 100.000 105 0 0 3104 3208 649900418 649900314 1.510000e-45 195.0
5 TraesCS4A01G375200 chr4A 100.000 105 0 0 3211 3315 649900525 649900421 1.510000e-45 195.0
6 TraesCS4A01G375200 chr4A 84.884 172 23 2 1144 1315 650044802 650044634 2.540000e-38 171.0
7 TraesCS4A01G375200 chr4A 80.214 187 5 5 5153 5308 650040698 650040513 1.560000e-20 111.0
8 TraesCS4A01G375200 chr4A 85.047 107 12 2 3460 3564 649904985 649904881 7.280000e-19 106.0
9 TraesCS4A01G375200 chr4A 84.091 88 8 2 3714 3801 649904783 649904702 4.410000e-11 80.5
10 TraesCS4A01G375200 chr7D 94.095 1558 74 5 807 2361 42688886 42687344 0.000000e+00 2351.0
11 TraesCS4A01G375200 chr7D 91.172 725 26 6 3268 3985 42686446 42685753 0.000000e+00 950.0
12 TraesCS4A01G375200 chr7D 93.333 585 38 1 4064 4648 42685619 42685036 0.000000e+00 863.0
13 TraesCS4A01G375200 chr7D 94.706 510 18 5 2361 2869 42687277 42686776 0.000000e+00 784.0
14 TraesCS4A01G375200 chr7D 88.769 650 57 11 7 645 42689815 42689171 0.000000e+00 782.0
15 TraesCS4A01G375200 chr7D 89.826 403 29 2 4646 5036 42685083 42684681 1.710000e-139 507.0
16 TraesCS4A01G375200 chr7D 90.634 331 18 8 4984 5314 42684688 42684371 1.370000e-115 427.0
17 TraesCS4A01G375200 chr7D 95.531 179 7 1 2871 3049 42686730 42686553 8.710000e-73 285.0
18 TraesCS4A01G375200 chr7D 79.101 445 39 24 3460 3895 42691516 42691117 1.900000e-64 257.0
19 TraesCS4A01G375200 chr7D 90.184 163 15 1 4967 5128 397554916 397555078 1.500000e-50 211.0
20 TraesCS4A01G375200 chr7D 89.630 135 7 3 644 778 42689090 42688963 1.180000e-36 165.0
21 TraesCS4A01G375200 chr7D 97.500 80 2 0 4516 4595 42690675 42690596 2.580000e-28 137.0
22 TraesCS4A01G375200 chr7D 81.875 160 2 2 3076 3208 42686558 42686399 5.630000e-20 110.0
23 TraesCS4A01G375200 chr7D 93.750 64 4 0 3994 4057 42685765 42685702 4.380000e-16 97.1
24 TraesCS4A01G375200 chr7D 90.141 71 7 0 1 71 66539530 66539600 5.670000e-15 93.5
25 TraesCS4A01G375200 chr7A 86.441 354 40 2 2513 2865 42126853 42126507 1.080000e-101 381.0
26 TraesCS4A01G375200 chr3A 90.476 168 14 2 4962 5127 600921022 600920855 2.490000e-53 220.0
27 TraesCS4A01G375200 chr5D 90.854 164 14 1 4965 5127 461072600 461072763 8.960000e-53 219.0
28 TraesCS4A01G375200 chr5A 89.080 174 17 2 4964 5135 320214240 320214413 1.160000e-51 215.0
29 TraesCS4A01G375200 chr3B 90.244 164 15 1 4965 5127 552226570 552226407 4.170000e-51 213.0
30 TraesCS4A01G375200 chr3B 87.879 66 7 1 6 71 691368290 691368354 5.710000e-10 76.8
31 TraesCS4A01G375200 chr4D 89.697 165 16 1 4967 5130 75266909 75266745 5.390000e-50 209.0
32 TraesCS4A01G375200 chr2A 88.889 171 18 1 4966 5135 758586576 758586746 5.390000e-50 209.0
33 TraesCS4A01G375200 chr1D 89.697 165 16 1 4967 5130 225704946 225704782 5.390000e-50 209.0
34 TraesCS4A01G375200 chr2D 88.824 170 17 2 4963 5131 318563730 318563898 1.940000e-49 207.0
35 TraesCS4A01G375200 chr2B 100.000 32 0 0 4015 4046 184593002 184593033 5.750000e-05 60.2
36 TraesCS4A01G375200 chr3D 97.059 34 1 0 4017 4050 571358711 571358744 2.070000e-04 58.4


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 TraesCS4A01G375200 chr4A 649898315 649903628 5313 True 3401.333333 9814 100.000000 1 5314 3 chr4A.!!$R1 5313
1 TraesCS4A01G375200 chr4A 650040513 650044802 4289 True 1019.500000 1964 86.481250 1144 5308 4 chr4A.!!$R3 4164
2 TraesCS4A01G375200 chr7D 42684371 42691516 7145 True 593.469231 2351 90.763231 7 5314 13 chr7D.!!$R1 5307

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
779 2587 1.538419 GCGAGAAATAGTAGCGCCCTT 60.538 52.381 2.29 0.00 41.65 3.95 F
1437 3313 0.253044 ACACCTACCTAGTCCGCGTA 59.747 55.000 4.92 0.00 0.00 4.42 F
1743 3676 0.108138 AGCCACAGATAACGCACCTC 60.108 55.000 0.00 0.00 0.00 3.85 F
1792 3725 0.532115 GAAAAACGATGGGCATGCCT 59.468 50.000 34.70 17.99 36.10 4.75 F
3286 5361 1.480789 ACCTTTGTTGGTGGGTGTTC 58.519 50.000 0.00 0.00 39.17 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 3508 0.250338 GAACAGCGGGGAGAAGTTGT 60.250 55.000 0.00 0.0 33.29 3.32 R
3328 5403 1.051812 CTCTAGGGGGCACATACCAG 58.948 60.000 0.00 0.0 0.00 4.00 R
3546 5630 2.867109 AGTTCTGGCACTAGCAATGT 57.133 45.000 0.00 0.0 44.61 2.71 R
3766 5850 2.736192 GGTTACTTGCGCGGTAGTTTTA 59.264 45.455 8.83 0.0 0.00 1.52 R
4627 6790 0.109532 TGAAACATCCAACTGCCGGA 59.890 50.000 5.05 0.0 36.84 5.14 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
122 1817 9.398170 CTAAAATCGTCATGAACAACTTTTCAT 57.602 29.630 0.00 0.00 45.32 2.57
220 1916 9.940166 ACATTTTCTCAAATTTTCATGAAAAGC 57.060 25.926 31.05 0.00 42.72 3.51
235 1931 1.851658 AAAGCTTTTCACGCGCAAAT 58.148 40.000 5.73 0.00 0.00 2.32
318 2015 6.636447 TGAACACTTTTTAATGTGCGATGAAG 59.364 34.615 8.03 0.00 37.52 3.02
321 2018 8.039603 ACACTTTTTAATGTGCGATGAAGATA 57.960 30.769 8.03 0.00 37.52 1.98
334 2031 8.269424 GTGCGATGAAGATATTTAACTACACTG 58.731 37.037 0.00 0.00 0.00 3.66
435 2132 8.960591 CCTAATATTCTGTGAACAGTTTCCAAT 58.039 33.333 10.14 5.25 44.12 3.16
443 2140 8.617809 TCTGTGAACAGTTTCCAATTAAACTAC 58.382 33.333 10.14 2.99 45.59 2.73
446 2143 9.575783 GTGAACAGTTTCCAATTAAACTACAAA 57.424 29.630 6.12 0.00 45.59 2.83
520 2224 9.545105 AAAAAGAAAACATGTCTAATGCATGAA 57.455 25.926 0.00 0.00 44.60 2.57
527 2231 7.199541 ACATGTCTAATGCATGAAGAATAGC 57.800 36.000 12.33 3.19 44.60 2.97
539 2243 9.565090 TGCATGAAGAATAGCTCTTAAATACAT 57.435 29.630 0.00 0.00 44.82 2.29
585 2289 4.523813 AGCACTTTGAAAATACGTTGTCG 58.476 39.130 0.00 0.00 43.34 4.35
676 2462 5.958987 TCCTTTTTGAGGGGTGTAAGAAAAA 59.041 36.000 0.00 0.00 46.31 1.94
681 2467 7.610580 TTTGAGGGGTGTAAGAAAAATCAAT 57.389 32.000 0.00 0.00 0.00 2.57
682 2468 6.834168 TGAGGGGTGTAAGAAAAATCAATC 57.166 37.500 0.00 0.00 0.00 2.67
683 2469 6.310941 TGAGGGGTGTAAGAAAAATCAATCA 58.689 36.000 0.00 0.00 0.00 2.57
684 2470 6.780031 TGAGGGGTGTAAGAAAAATCAATCAA 59.220 34.615 0.00 0.00 0.00 2.57
685 2471 6.993079 AGGGGTGTAAGAAAAATCAATCAAC 58.007 36.000 0.00 0.00 0.00 3.18
686 2472 6.782494 AGGGGTGTAAGAAAAATCAATCAACT 59.218 34.615 0.00 0.00 0.00 3.16
687 2473 7.947890 AGGGGTGTAAGAAAAATCAATCAACTA 59.052 33.333 0.00 0.00 0.00 2.24
688 2474 8.581578 GGGGTGTAAGAAAAATCAATCAACTAA 58.418 33.333 0.00 0.00 0.00 2.24
716 2502 6.408107 AAAATAAAGGAAAACCGTTGCCTA 57.592 33.333 6.41 0.00 42.75 3.93
734 2520 2.104281 CCTAAACGTCCCTCCTATTGGG 59.896 54.545 0.00 0.00 45.90 4.12
739 2525 2.078665 TCCCTCCTATTGGGCTGGC 61.079 63.158 0.00 0.00 44.23 4.85
779 2587 1.538419 GCGAGAAATAGTAGCGCCCTT 60.538 52.381 2.29 0.00 41.65 3.95
955 2789 4.864334 CATCCGCCCCACTGCTCC 62.864 72.222 0.00 0.00 0.00 4.70
1033 2867 4.840005 CTTTCCGCCTCCGCCTCC 62.840 72.222 0.00 0.00 0.00 4.30
1197 3031 1.094073 ACGGCATCATCAAGCAGAGC 61.094 55.000 0.00 0.00 0.00 4.09
1241 3075 4.819761 GGCGCTGCTCCATCGACA 62.820 66.667 7.64 0.00 30.87 4.35
1276 3110 3.474570 GGCGTGGGGAGCTCTCAT 61.475 66.667 17.22 0.00 34.52 2.90
1361 3237 0.954452 GTGAGCTCCTTTTGGTGGTG 59.046 55.000 12.15 0.00 42.94 4.17
1399 3275 2.598632 GCAGCTTGCGTCAACGTCT 61.599 57.895 4.29 0.00 42.22 4.18
1425 3301 4.595762 TTCAGTTGTCTACCACACCTAC 57.404 45.455 0.00 0.00 33.41 3.18
1437 3313 0.253044 ACACCTACCTAGTCCGCGTA 59.747 55.000 4.92 0.00 0.00 4.42
1496 3372 1.536496 CGTGCCGTATACCAATCGGAA 60.536 52.381 7.01 0.00 46.05 4.30
1497 3373 1.862827 GTGCCGTATACCAATCGGAAC 59.137 52.381 7.01 2.60 46.05 3.62
1500 3376 2.476821 CCGTATACCAATCGGAACCAC 58.523 52.381 0.00 0.00 46.05 4.16
1533 3409 3.885521 CCCCTAGACGACCGCGAC 61.886 72.222 8.23 0.00 41.64 5.19
1554 3430 0.678048 ATGGCGAGTCCTGCTTTTCC 60.678 55.000 0.00 0.00 35.26 3.13
1585 3461 1.276989 GGAACTACCCATCCACGTTCA 59.723 52.381 0.00 0.00 36.57 3.18
1632 3508 2.267426 CGTGTCAATCTTATCACGGCA 58.733 47.619 8.36 0.00 46.12 5.69
1707 3637 0.892814 AGAGCAAGAAACAGGGCAGC 60.893 55.000 0.00 0.00 0.00 5.25
1708 3638 1.152694 AGCAAGAAACAGGGCAGCA 60.153 52.632 0.00 0.00 0.00 4.41
1709 3639 1.177256 AGCAAGAAACAGGGCAGCAG 61.177 55.000 0.00 0.00 0.00 4.24
1743 3676 0.108138 AGCCACAGATAACGCACCTC 60.108 55.000 0.00 0.00 0.00 3.85
1746 3679 1.269166 CACAGATAACGCACCTCGAC 58.731 55.000 0.00 0.00 41.67 4.20
1792 3725 0.532115 GAAAAACGATGGGCATGCCT 59.468 50.000 34.70 17.99 36.10 4.75
1876 3809 1.797713 CGGATGCTGAAATTGCTGCTG 60.798 52.381 15.58 1.04 34.32 4.41
2111 4044 2.692709 TGTTGGTGGTGATTCCCATT 57.307 45.000 0.00 0.00 36.74 3.16
2164 4097 3.979101 TGGCATCCCCAAAGAAAATTC 57.021 42.857 0.00 0.00 41.82 2.17
2166 4099 3.261390 TGGCATCCCCAAAGAAAATTCAG 59.739 43.478 0.00 0.00 41.82 3.02
2196 4129 8.031864 ACATAGTAGTTCATATGCAGTGATAGC 58.968 37.037 5.52 0.00 33.53 2.97
2230 4164 6.430451 AGTTCATGTTAACTTTGAAAGCTCG 58.570 36.000 19.42 0.00 36.26 5.03
2252 4186 7.518052 GCTCGAAAATCATTCATCCAAGTCTAG 60.518 40.741 0.00 0.00 0.00 2.43
2364 4365 9.653287 TCAAGGATTTATATGATCGGTAATGTC 57.347 33.333 0.00 0.00 0.00 3.06
2463 4464 3.909662 CCGATGGGAACTTGCTGG 58.090 61.111 0.00 0.00 34.06 4.85
2488 4490 7.661847 GGTTAGCCAAACTCTATGTTATGCTAT 59.338 37.037 10.50 0.00 42.29 2.97
2489 4491 8.499162 GTTAGCCAAACTCTATGTTATGCTATG 58.501 37.037 10.50 0.00 42.29 2.23
2490 4492 5.471456 AGCCAAACTCTATGTTATGCTATGC 59.529 40.000 0.00 0.00 41.06 3.14
2491 4493 5.471456 GCCAAACTCTATGTTATGCTATGCT 59.529 40.000 0.00 0.00 38.03 3.79
2492 4494 6.348050 GCCAAACTCTATGTTATGCTATGCTC 60.348 42.308 0.00 0.00 38.03 4.26
2493 4495 6.707608 CCAAACTCTATGTTATGCTATGCTCA 59.292 38.462 0.00 0.00 38.03 4.26
2494 4496 7.095313 CCAAACTCTATGTTATGCTATGCTCAG 60.095 40.741 0.00 0.00 38.03 3.35
2495 4497 6.662865 ACTCTATGTTATGCTATGCTCAGT 57.337 37.500 0.00 0.00 0.00 3.41
2496 4498 7.767250 ACTCTATGTTATGCTATGCTCAGTA 57.233 36.000 0.00 0.00 0.00 2.74
2497 4499 7.825681 ACTCTATGTTATGCTATGCTCAGTAG 58.174 38.462 0.00 0.00 0.00 2.57
2498 4500 7.667635 ACTCTATGTTATGCTATGCTCAGTAGA 59.332 37.037 0.00 0.00 0.00 2.59
2499 4501 7.821652 TCTATGTTATGCTATGCTCAGTAGAC 58.178 38.462 0.00 0.00 0.00 2.59
2500 4502 6.662865 ATGTTATGCTATGCTCAGTAGACT 57.337 37.500 0.00 0.00 0.00 3.24
2501 4503 7.767250 ATGTTATGCTATGCTCAGTAGACTA 57.233 36.000 0.00 0.00 0.00 2.59
2520 4535 5.807520 AGACTATGCTGAAGTTCAACGTATG 59.192 40.000 7.06 5.52 0.00 2.39
2625 4640 8.845413 AATATTTCATGATAGAAGTGCTCCTC 57.155 34.615 0.00 0.00 0.00 3.71
2626 4641 5.682234 TTTCATGATAGAAGTGCTCCTCA 57.318 39.130 0.00 0.00 0.00 3.86
2627 4642 5.682234 TTCATGATAGAAGTGCTCCTCAA 57.318 39.130 0.00 0.00 0.00 3.02
2628 4643 5.883685 TCATGATAGAAGTGCTCCTCAAT 57.116 39.130 0.00 0.00 0.00 2.57
2629 4644 5.851720 TCATGATAGAAGTGCTCCTCAATC 58.148 41.667 0.00 0.00 0.00 2.67
2630 4645 4.679373 TGATAGAAGTGCTCCTCAATCC 57.321 45.455 0.00 0.00 0.00 3.01
2631 4646 4.293494 TGATAGAAGTGCTCCTCAATCCT 58.707 43.478 0.00 0.00 0.00 3.24
2632 4647 4.343526 TGATAGAAGTGCTCCTCAATCCTC 59.656 45.833 0.00 0.00 0.00 3.71
2652 4667 4.999950 CCTCATGATGTTTCCTATGTAGGC 59.000 45.833 0.00 0.00 43.31 3.93
3188 5263 6.240549 TGTTGGTGGGTGTTCAAAATAAAT 57.759 33.333 0.00 0.00 0.00 1.40
3189 5264 6.653989 TGTTGGTGGGTGTTCAAAATAAATT 58.346 32.000 0.00 0.00 0.00 1.82
3190 5265 7.112779 TGTTGGTGGGTGTTCAAAATAAATTT 58.887 30.769 0.00 0.00 0.00 1.82
3191 5266 7.281100 TGTTGGTGGGTGTTCAAAATAAATTTC 59.719 33.333 0.00 0.00 0.00 2.17
3192 5267 6.292150 TGGTGGGTGTTCAAAATAAATTTCC 58.708 36.000 0.00 0.00 0.00 3.13
3193 5268 5.703592 GGTGGGTGTTCAAAATAAATTTCCC 59.296 40.000 0.00 0.00 30.88 3.97
3194 5269 6.465178 GGTGGGTGTTCAAAATAAATTTCCCT 60.465 38.462 0.00 0.00 31.29 4.20
3195 5270 6.426633 GTGGGTGTTCAAAATAAATTTCCCTG 59.573 38.462 0.00 0.00 31.29 4.45
3196 5271 6.100424 TGGGTGTTCAAAATAAATTTCCCTGT 59.900 34.615 0.00 0.00 31.29 4.00
3197 5272 6.426633 GGGTGTTCAAAATAAATTTCCCTGTG 59.573 38.462 0.00 0.00 0.00 3.66
3198 5273 6.073276 GGTGTTCAAAATAAATTTCCCTGTGC 60.073 38.462 0.00 0.00 0.00 4.57
3199 5274 6.481644 GTGTTCAAAATAAATTTCCCTGTGCA 59.518 34.615 0.00 0.00 0.00 4.57
3200 5275 7.173047 GTGTTCAAAATAAATTTCCCTGTGCAT 59.827 33.333 0.00 0.00 0.00 3.96
3201 5276 7.387397 TGTTCAAAATAAATTTCCCTGTGCATC 59.613 33.333 0.00 0.00 0.00 3.91
3202 5277 7.002250 TCAAAATAAATTTCCCTGTGCATCA 57.998 32.000 0.00 0.00 0.00 3.07
3203 5278 7.448420 TCAAAATAAATTTCCCTGTGCATCAA 58.552 30.769 0.00 0.00 0.00 2.57
3204 5279 7.603404 TCAAAATAAATTTCCCTGTGCATCAAG 59.397 33.333 0.00 0.00 0.00 3.02
3205 5280 3.323751 AAATTTCCCTGTGCATCAAGC 57.676 42.857 0.00 0.00 45.96 4.01
3206 5281 2.226962 ATTTCCCTGTGCATCAAGCT 57.773 45.000 0.00 0.00 45.94 3.74
3207 5282 2.877097 TTTCCCTGTGCATCAAGCTA 57.123 45.000 0.00 0.00 45.94 3.32
3208 5283 2.877097 TTCCCTGTGCATCAAGCTAA 57.123 45.000 0.00 0.00 45.94 3.09
3209 5284 2.408271 TCCCTGTGCATCAAGCTAAG 57.592 50.000 0.00 0.00 45.94 2.18
3210 5285 1.908619 TCCCTGTGCATCAAGCTAAGA 59.091 47.619 0.00 0.00 45.94 2.10
3211 5286 2.507058 TCCCTGTGCATCAAGCTAAGAT 59.493 45.455 0.00 0.00 45.94 2.40
3212 5287 2.877168 CCCTGTGCATCAAGCTAAGATC 59.123 50.000 0.00 0.00 45.94 2.75
3213 5288 3.433314 CCCTGTGCATCAAGCTAAGATCT 60.433 47.826 0.00 0.00 45.94 2.75
3214 5289 4.197750 CCTGTGCATCAAGCTAAGATCTT 58.802 43.478 13.56 13.56 45.94 2.40
3215 5290 4.639310 CCTGTGCATCAAGCTAAGATCTTT 59.361 41.667 14.36 0.00 45.94 2.52
3216 5291 5.448768 CCTGTGCATCAAGCTAAGATCTTTG 60.449 44.000 14.36 13.01 45.94 2.77
3217 5292 5.005740 TGTGCATCAAGCTAAGATCTTTGT 58.994 37.500 14.36 0.04 45.94 2.83
3218 5293 5.122869 TGTGCATCAAGCTAAGATCTTTGTC 59.877 40.000 14.36 8.07 45.94 3.18
3219 5294 5.122869 GTGCATCAAGCTAAGATCTTTGTCA 59.877 40.000 14.36 4.11 45.94 3.58
3220 5295 5.884232 TGCATCAAGCTAAGATCTTTGTCAT 59.116 36.000 14.36 0.00 45.94 3.06
3221 5296 7.011763 GTGCATCAAGCTAAGATCTTTGTCATA 59.988 37.037 14.36 0.51 45.94 2.15
3222 5297 7.011763 TGCATCAAGCTAAGATCTTTGTCATAC 59.988 37.037 14.36 0.00 45.94 2.39
3223 5298 7.226325 GCATCAAGCTAAGATCTTTGTCATACT 59.774 37.037 14.36 0.92 41.15 2.12
3224 5299 9.755804 CATCAAGCTAAGATCTTTGTCATACTA 57.244 33.333 14.36 0.00 0.00 1.82
3226 5301 9.809096 TCAAGCTAAGATCTTTGTCATACTAAG 57.191 33.333 14.36 1.75 33.31 2.18
3227 5302 9.809096 CAAGCTAAGATCTTTGTCATACTAAGA 57.191 33.333 14.36 6.44 42.33 2.10
3229 5304 9.979578 AGCTAAGATCTTTGTCATACTAAGATG 57.020 33.333 14.36 7.70 45.73 2.90
3230 5305 8.707839 GCTAAGATCTTTGTCATACTAAGATGC 58.292 37.037 14.36 12.17 45.73 3.91
3231 5306 9.979578 CTAAGATCTTTGTCATACTAAGATGCT 57.020 33.333 14.36 12.44 45.73 3.79
3232 5307 8.659925 AAGATCTTTGTCATACTAAGATGCTG 57.340 34.615 17.40 0.00 45.73 4.41
3233 5308 6.705381 AGATCTTTGTCATACTAAGATGCTGC 59.295 38.462 17.40 0.00 45.73 5.25
3234 5309 5.982356 TCTTTGTCATACTAAGATGCTGCT 58.018 37.500 0.00 0.00 35.61 4.24
3235 5310 6.409704 TCTTTGTCATACTAAGATGCTGCTT 58.590 36.000 0.00 0.00 35.61 3.91
3236 5311 6.881065 TCTTTGTCATACTAAGATGCTGCTTT 59.119 34.615 0.00 0.00 35.61 3.51
3237 5312 7.391554 TCTTTGTCATACTAAGATGCTGCTTTT 59.608 33.333 0.00 0.00 35.61 2.27
3238 5313 7.452880 TTGTCATACTAAGATGCTGCTTTTT 57.547 32.000 0.00 0.00 0.00 1.94
3239 5314 6.845302 TGTCATACTAAGATGCTGCTTTTTG 58.155 36.000 0.00 0.00 0.00 2.44
3240 5315 5.741040 GTCATACTAAGATGCTGCTTTTTGC 59.259 40.000 0.00 0.00 43.25 3.68
3252 5327 3.990318 GCTTTTTGCACTACAAGGACT 57.010 42.857 0.00 0.00 40.06 3.85
3253 5328 4.307443 GCTTTTTGCACTACAAGGACTT 57.693 40.909 0.00 0.00 40.06 3.01
3254 5329 4.682787 GCTTTTTGCACTACAAGGACTTT 58.317 39.130 0.00 0.00 40.06 2.66
3255 5330 4.504097 GCTTTTTGCACTACAAGGACTTTG 59.496 41.667 0.00 0.00 40.06 2.77
3256 5331 5.907213 GCTTTTTGCACTACAAGGACTTTGT 60.907 40.000 8.14 8.14 45.86 2.83
3257 5332 7.339048 GCTTTTTGCACTACAAGGACTTTGTT 61.339 38.462 8.37 0.00 43.63 2.83
3258 5333 9.245494 GCTTTTTGCACTACAAGGACTTTGTTG 62.245 40.741 8.37 9.11 43.63 3.33
3286 5361 1.480789 ACCTTTGTTGGTGGGTGTTC 58.519 50.000 0.00 0.00 39.17 3.18
3328 5403 6.172634 GCATCAAGCTATTACGCATGTATGC 61.173 44.000 6.77 6.77 44.68 3.14
3382 5464 1.933181 TCTAATCCTGCGCAAACATCG 59.067 47.619 13.05 0.00 0.00 3.84
3472 5554 7.523293 TTCACATTTCATTAGGCTTCTGAAA 57.477 32.000 19.82 19.82 41.57 2.69
3537 5619 7.377766 TCCTTCAATTGCTACAAGATAACAC 57.622 36.000 0.00 0.00 0.00 3.32
3735 5819 7.448469 AGGCAAATCTGTAGATGTTTTGTTACT 59.552 33.333 0.00 0.00 34.49 2.24
3766 5850 7.867921 TGGATTACACTTCATATAGGGTTTGT 58.132 34.615 0.00 0.00 32.95 2.83
3801 5885 2.188817 AGTAACCAGGAACTAGCAGGG 58.811 52.381 0.00 0.00 36.02 4.45
3816 5900 1.606531 AGGGAAGAGTCATGCCTGC 59.393 57.895 7.72 0.00 37.23 4.85
3817 5901 1.203441 AGGGAAGAGTCATGCCTGCA 61.203 55.000 7.72 0.00 37.23 4.41
3818 5902 0.106819 GGGAAGAGTCATGCCTGCAT 60.107 55.000 0.00 0.00 37.08 3.96
4050 6134 6.183360 CCATAGCCCGCTATTTAAAACTTTGA 60.183 38.462 6.48 0.00 37.16 2.69
4141 6301 8.763356 TCATGCAAAATTTATTCAGAAACACAC 58.237 29.630 0.00 0.00 0.00 3.82
4162 6322 3.053619 ACCCTTCCTTGTTCTGTTTCAGT 60.054 43.478 0.00 0.00 32.61 3.41
4183 6343 6.531240 TCAGTTCTGCAAATTGTCTTTGTTTC 59.469 34.615 0.00 0.00 0.00 2.78
4198 6358 7.658167 TGTCTTTGTTTCGATGTGTTAATCCTA 59.342 33.333 0.00 0.00 0.00 2.94
4217 6377 6.374417 TCCTATAGGCTTCAAGAAAACACT 57.626 37.500 14.50 0.00 34.44 3.55
4351 6511 2.327343 TGTGTGGCGAGCAAGCATC 61.327 57.895 5.80 0.00 39.27 3.91
4369 6529 3.994392 GCATCAAGAACGTTTGTCCTCTA 59.006 43.478 0.46 0.00 0.00 2.43
4387 6547 5.842722 CCTCTATGAGGTGCCTCCAATAGG 61.843 54.167 14.97 12.30 45.33 2.57
4448 6608 1.341531 CACATTTGGTTTGCCCGGTTA 59.658 47.619 0.00 0.00 35.15 2.85
4455 6615 3.228453 TGGTTTGCCCGGTTACAATTTA 58.772 40.909 0.00 0.00 35.15 1.40
4471 6631 5.387279 ACAATTTATTACCGTCTTGCAACG 58.613 37.500 3.92 3.92 42.24 4.10
4513 6676 2.430694 GCCCTTCCATGTTTTATCCCAC 59.569 50.000 0.00 0.00 0.00 4.61
4529 6692 3.101437 TCCCACTAAATCCTGTAGCGAA 58.899 45.455 0.00 0.00 0.00 4.70
4530 6693 3.132289 TCCCACTAAATCCTGTAGCGAAG 59.868 47.826 0.00 0.00 0.00 3.79
4584 6747 4.978580 GCTGTTGAGAAGTGAAATTGGTTC 59.021 41.667 0.00 0.00 36.70 3.62
4599 6762 1.973812 GTTCTTGAGCCCACCCAGC 60.974 63.158 0.00 0.00 0.00 4.85
4618 6781 3.976942 CAGCCACAAAATTTTCGTCTCTG 59.023 43.478 0.00 8.19 0.00 3.35
4619 6782 3.632145 AGCCACAAAATTTTCGTCTCTGT 59.368 39.130 0.00 0.00 0.00 3.41
4620 6783 4.819630 AGCCACAAAATTTTCGTCTCTGTA 59.180 37.500 0.00 0.00 0.00 2.74
4621 6784 4.909880 GCCACAAAATTTTCGTCTCTGTAC 59.090 41.667 0.00 0.00 0.00 2.90
4622 6785 5.449304 CCACAAAATTTTCGTCTCTGTACC 58.551 41.667 0.00 0.00 0.00 3.34
4623 6786 5.238650 CCACAAAATTTTCGTCTCTGTACCT 59.761 40.000 0.00 0.00 0.00 3.08
4624 6787 6.136071 CACAAAATTTTCGTCTCTGTACCTG 58.864 40.000 0.00 0.00 0.00 4.00
4625 6788 5.147162 CAAAATTTTCGTCTCTGTACCTGC 58.853 41.667 0.00 0.00 0.00 4.85
4626 6789 3.678056 ATTTTCGTCTCTGTACCTGCA 57.322 42.857 0.00 0.00 0.00 4.41
4627 6790 3.678056 TTTTCGTCTCTGTACCTGCAT 57.322 42.857 0.00 0.00 0.00 3.96
4628 6791 2.941453 TTCGTCTCTGTACCTGCATC 57.059 50.000 0.00 0.00 0.00 3.91
4629 6792 1.103803 TCGTCTCTGTACCTGCATCC 58.896 55.000 0.00 0.00 0.00 3.51
4630 6793 0.248661 CGTCTCTGTACCTGCATCCG 60.249 60.000 0.00 0.00 0.00 4.18
4631 6794 0.103208 GTCTCTGTACCTGCATCCGG 59.897 60.000 0.00 0.00 0.00 5.14
4632 6795 1.227380 CTCTGTACCTGCATCCGGC 60.227 63.158 0.00 0.00 45.13 6.13
4644 6807 3.670105 ATCCGGCAGTTGGATGTTT 57.330 47.368 0.00 0.00 44.51 2.83
4645 6808 1.463674 ATCCGGCAGTTGGATGTTTC 58.536 50.000 0.00 0.00 44.51 2.78
4646 6809 0.109532 TCCGGCAGTTGGATGTTTCA 59.890 50.000 0.00 0.00 0.00 2.69
4647 6810 0.240945 CCGGCAGTTGGATGTTTCAC 59.759 55.000 0.00 0.00 0.00 3.18
4648 6811 0.950836 CGGCAGTTGGATGTTTCACA 59.049 50.000 0.00 0.00 0.00 3.58
4649 6812 1.336440 CGGCAGTTGGATGTTTCACAA 59.664 47.619 0.00 0.00 0.00 3.33
4650 6813 2.223688 CGGCAGTTGGATGTTTCACAAA 60.224 45.455 0.00 0.00 0.00 2.83
4651 6814 3.383761 GGCAGTTGGATGTTTCACAAAG 58.616 45.455 0.00 0.00 0.00 2.77
4652 6815 3.181476 GGCAGTTGGATGTTTCACAAAGT 60.181 43.478 0.00 0.00 0.00 2.66
4653 6816 4.037446 GGCAGTTGGATGTTTCACAAAGTA 59.963 41.667 0.00 0.00 0.00 2.24
4654 6817 5.278957 GGCAGTTGGATGTTTCACAAAGTAT 60.279 40.000 0.00 0.00 0.00 2.12
4655 6818 6.215845 GCAGTTGGATGTTTCACAAAGTATT 58.784 36.000 0.00 0.00 0.00 1.89
4656 6819 6.363357 GCAGTTGGATGTTTCACAAAGTATTC 59.637 38.462 0.00 0.00 0.00 1.75
4657 6820 7.424803 CAGTTGGATGTTTCACAAAGTATTCA 58.575 34.615 0.00 0.00 0.00 2.57
4658 6821 8.084073 CAGTTGGATGTTTCACAAAGTATTCAT 58.916 33.333 0.00 0.00 0.00 2.57
4659 6822 8.299570 AGTTGGATGTTTCACAAAGTATTCATC 58.700 33.333 0.00 0.00 0.00 2.92
4660 6823 7.757941 TGGATGTTTCACAAAGTATTCATCA 57.242 32.000 0.00 0.00 34.17 3.07
4674 6837 6.418101 AGTATTCATCACTGTACCTGCATTT 58.582 36.000 0.00 0.00 0.00 2.32
4693 6856 1.401761 TGGCAGTTGCATGTTTCACT 58.598 45.000 6.43 0.00 44.36 3.41
4700 6863 4.855388 CAGTTGCATGTTTCACTATTCAGC 59.145 41.667 0.00 0.00 0.00 4.26
4770 6933 2.135139 CGCTCTTATTATGGCGCAGAA 58.865 47.619 10.83 0.00 41.08 3.02
4777 6940 2.849880 TTATGGCGCAGAAATCTTGC 57.150 45.000 10.83 0.00 0.00 4.01
4821 6984 5.379732 ACGTATTGTGTTAATTTGGTGGG 57.620 39.130 0.00 0.00 0.00 4.61
4855 7018 5.753921 ACTTCTCTGTTCACGGTTTTAGAAG 59.246 40.000 11.02 11.02 42.67 2.85
4869 7032 5.410439 GGTTTTAGAAGCGGTTTCAGATGTA 59.590 40.000 0.00 0.00 38.31 2.29
4872 7035 4.537135 AGAAGCGGTTTCAGATGTAGAA 57.463 40.909 0.00 0.00 38.31 2.10
4977 7517 0.556747 ATGGCTACTACTCCCTCCGT 59.443 55.000 0.00 0.00 0.00 4.69
5019 7604 7.450124 TGTAGAGATTCCAATACGGACTATC 57.550 40.000 0.00 0.00 46.36 2.08
5057 7642 6.777213 AGTGAATCTACACTCTAAATCCGT 57.223 37.500 0.00 0.00 46.36 4.69
5058 7643 7.171630 AGTGAATCTACACTCTAAATCCGTT 57.828 36.000 0.00 0.00 46.36 4.44
5059 7644 7.612677 AGTGAATCTACACTCTAAATCCGTTT 58.387 34.615 0.00 0.00 46.36 3.60
5060 7645 8.746530 AGTGAATCTACACTCTAAATCCGTTTA 58.253 33.333 0.00 0.00 46.36 2.01
5061 7646 9.530633 GTGAATCTACACTCTAAATCCGTTTAT 57.469 33.333 0.00 0.00 37.73 1.40
5092 7677 9.914131 ATCCGTATGTAATCCATATTGATATCG 57.086 33.333 0.00 0.00 38.29 2.92
5093 7678 7.865889 TCCGTATGTAATCCATATTGATATCGC 59.134 37.037 0.00 0.00 38.29 4.58
5094 7679 7.867909 CCGTATGTAATCCATATTGATATCGCT 59.132 37.037 0.00 0.00 38.29 4.93
5095 7680 9.893305 CGTATGTAATCCATATTGATATCGCTA 57.107 33.333 0.00 0.00 38.29 4.26
5105 7692 9.817365 CCATATTGATATCGCTAAAAAGTCTTG 57.183 33.333 0.00 0.00 0.00 3.02
5125 7712 5.482878 TCTTGTATTTAGAAACGGAGGGAGT 59.517 40.000 0.00 0.00 0.00 3.85
5131 7718 6.705863 TTTAGAAACGGAGGGAGTATCTAC 57.294 41.667 0.00 0.00 33.73 2.59
5157 7744 2.549992 CGAGTGGAAATCCTGTTGGTGA 60.550 50.000 0.44 0.00 36.82 4.02
5229 7830 6.015772 CCAATGCTGATGACATTTATGATCCA 60.016 38.462 0.00 0.00 35.58 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.155393 TGTGGCTTTATTTATAAAAGGGGGTG 59.845 38.462 1.21 0.00 35.04 4.61
3 4 6.265304 TGTGGCTTTATTTATAAAAGGGGGT 58.735 36.000 1.21 0.00 35.04 4.95
4 5 6.800072 TGTGGCTTTATTTATAAAAGGGGG 57.200 37.500 1.21 0.00 35.04 5.40
6 7 7.276878 CCGTTTGTGGCTTTATTTATAAAAGGG 59.723 37.037 1.21 0.00 35.04 3.95
7 8 8.180317 CCGTTTGTGGCTTTATTTATAAAAGG 57.820 34.615 1.21 0.00 35.04 3.11
38 1733 4.369182 GTTTCCTCACCACTATGTATCGG 58.631 47.826 0.00 0.00 0.00 4.18
218 1914 2.919666 ATATTTGCGCGTGAAAAGCT 57.080 40.000 8.43 0.00 39.95 3.74
219 1915 3.970828 AAATATTTGCGCGTGAAAAGC 57.029 38.095 8.43 0.00 38.22 3.51
289 1986 4.385447 CGCACATTAAAAAGTGTTCATGGG 59.615 41.667 0.00 0.00 38.02 4.00
418 2115 8.402472 TGTAGTTTAATTGGAAACTGTTCACAG 58.598 33.333 14.09 5.36 46.59 3.66
461 2158 7.342769 TCATGCTGCATTCAGAAATAATTCT 57.657 32.000 13.38 0.00 46.91 2.40
462 2159 8.589335 AATCATGCTGCATTCAGAAATAATTC 57.411 30.769 13.38 0.00 42.95 2.17
499 2201 8.922058 ATTCTTCATGCATTAGACATGTTTTC 57.078 30.769 0.00 0.00 44.26 2.29
501 2203 8.133627 GCTATTCTTCATGCATTAGACATGTTT 58.866 33.333 0.00 0.00 44.26 2.83
507 2211 7.727331 AAGAGCTATTCTTCATGCATTAGAC 57.273 36.000 0.00 0.00 42.54 2.59
561 2265 5.454232 CGACAACGTATTTTCAAAGTGCTTT 59.546 36.000 0.00 0.00 34.56 3.51
566 2270 4.539509 TGCGACAACGTATTTTCAAAGT 57.460 36.364 0.00 0.00 41.98 2.66
697 2483 5.185668 GTTTAGGCAACGGTTTTCCTTTA 57.814 39.130 14.38 4.05 46.39 1.85
1101 2935 3.536917 TAGTGGCGCCGATGGAGG 61.537 66.667 23.90 0.00 0.00 4.30
1104 2938 2.890474 GTGTAGTGGCGCCGATGG 60.890 66.667 23.90 0.00 0.00 3.51
1241 3075 2.780924 ATGGGGTGGTGTGGTGGT 60.781 61.111 0.00 0.00 0.00 4.16
1270 3104 1.639635 CCCTGGGTTGGGGATGAGAG 61.640 65.000 3.97 0.00 46.50 3.20
1298 3132 3.437795 GCTTGATGCTGCTGCGGT 61.438 61.111 10.62 1.94 43.34 5.68
1304 3138 2.079158 TGAAGTAGTGCTTGATGCTGC 58.921 47.619 0.00 0.00 43.37 5.25
1349 3225 0.104671 CTTGCACCACCACCAAAAGG 59.895 55.000 0.00 0.00 0.00 3.11
1399 3275 5.302360 GGTGTGGTAGACAACTGAATACAA 58.698 41.667 0.00 0.00 39.45 2.41
1425 3301 1.002033 GTGTATGGTACGCGGACTAGG 60.002 57.143 22.94 0.00 0.00 3.02
1437 3313 0.321298 GGGTGCGACTTGTGTATGGT 60.321 55.000 0.00 0.00 0.00 3.55
1496 3372 2.101582 GGAGAGCGAATGACATAGTGGT 59.898 50.000 0.00 0.00 0.00 4.16
1497 3373 2.546795 GGGAGAGCGAATGACATAGTGG 60.547 54.545 0.00 0.00 0.00 4.00
1500 3376 1.967066 AGGGGAGAGCGAATGACATAG 59.033 52.381 0.00 0.00 0.00 2.23
1533 3409 1.936547 GAAAAGCAGGACTCGCCATAG 59.063 52.381 0.00 0.00 40.02 2.23
1545 3421 3.822735 TCCTCTTGAACATGGAAAAGCAG 59.177 43.478 0.00 0.00 0.00 4.24
1569 3445 3.131396 GCTAATGAACGTGGATGGGTAG 58.869 50.000 0.00 0.00 0.00 3.18
1585 3461 2.690881 TGGGTGGAGCGGGCTAAT 60.691 61.111 0.00 0.00 0.00 1.73
1632 3508 0.250338 GAACAGCGGGGAGAAGTTGT 60.250 55.000 0.00 0.00 33.29 3.32
1792 3725 2.108157 GGACCACGACACTGCACA 59.892 61.111 0.00 0.00 0.00 4.57
1876 3809 1.009829 CCTACCTCATGCGCAAGAAC 58.990 55.000 17.11 0.00 43.02 3.01
1955 3888 2.242043 ACAGAAAGGAGGCAACAATGG 58.758 47.619 0.00 0.00 41.41 3.16
2012 3945 6.440647 AGGACACCACTTCTTGTAGATGATTA 59.559 38.462 0.00 0.00 0.00 1.75
2095 4028 0.614415 GCCAATGGGAATCACCACCA 60.614 55.000 0.00 0.00 44.72 4.17
2097 4030 0.819582 CTGCCAATGGGAATCACCAC 59.180 55.000 0.00 0.00 44.72 4.16
2111 4044 0.840288 ACCCCACACTACATCTGCCA 60.840 55.000 0.00 0.00 0.00 4.92
2164 4097 7.708322 ACTGCATATGAACTACTATGTCAACTG 59.292 37.037 6.97 0.00 0.00 3.16
2166 4099 7.706607 TCACTGCATATGAACTACTATGTCAAC 59.293 37.037 6.97 0.00 0.00 3.18
2196 4129 9.463443 CAAAGTTAACATGAACTTCTTTAAGGG 57.537 33.333 11.68 0.00 46.52 3.95
2226 4160 5.065731 AGACTTGGATGAATGATTTTCGAGC 59.934 40.000 0.00 0.00 0.00 5.03
2364 4365 2.930682 GGTCGCTACTTGCCTTAGAAAG 59.069 50.000 0.00 0.00 38.78 2.62
2463 4464 6.927294 AGCATAACATAGAGTTTGGCTAAC 57.073 37.500 3.52 3.52 42.71 2.34
2488 4490 4.019858 ACTTCAGCATAGTCTACTGAGCA 58.980 43.478 10.07 0.00 41.21 4.26
2489 4491 4.647424 ACTTCAGCATAGTCTACTGAGC 57.353 45.455 0.00 0.00 41.21 4.26
2490 4492 6.201226 TGAACTTCAGCATAGTCTACTGAG 57.799 41.667 0.00 0.00 41.21 3.35
2491 4493 6.390721 GTTGAACTTCAGCATAGTCTACTGA 58.609 40.000 1.00 0.00 38.62 3.41
2492 4494 5.287274 CGTTGAACTTCAGCATAGTCTACTG 59.713 44.000 6.45 0.00 0.00 2.74
2493 4495 5.047943 ACGTTGAACTTCAGCATAGTCTACT 60.048 40.000 6.45 0.00 0.00 2.57
2494 4496 5.162075 ACGTTGAACTTCAGCATAGTCTAC 58.838 41.667 6.45 0.00 0.00 2.59
2495 4497 5.386958 ACGTTGAACTTCAGCATAGTCTA 57.613 39.130 6.45 0.00 0.00 2.59
2496 4498 4.258702 ACGTTGAACTTCAGCATAGTCT 57.741 40.909 6.45 0.00 0.00 3.24
2497 4499 5.500931 GCATACGTTGAACTTCAGCATAGTC 60.501 44.000 0.00 0.00 0.00 2.59
2498 4500 4.330074 GCATACGTTGAACTTCAGCATAGT 59.670 41.667 0.00 0.00 0.00 2.12
2499 4501 4.260375 GGCATACGTTGAACTTCAGCATAG 60.260 45.833 0.00 0.00 0.00 2.23
2500 4502 3.621268 GGCATACGTTGAACTTCAGCATA 59.379 43.478 0.00 0.00 0.00 3.14
2501 4503 2.420022 GGCATACGTTGAACTTCAGCAT 59.580 45.455 0.00 0.00 0.00 3.79
2572 4587 8.746530 ACATAGAAGAGATAACGTAAAACAGGA 58.253 33.333 0.00 0.00 0.00 3.86
2625 4640 7.389884 CCTACATAGGAAACATCATGAGGATTG 59.610 40.741 15.42 3.19 46.63 2.67
2626 4641 7.456725 CCTACATAGGAAACATCATGAGGATT 58.543 38.462 15.42 8.67 46.63 3.01
2627 4642 6.521427 GCCTACATAGGAAACATCATGAGGAT 60.521 42.308 15.42 0.00 46.63 3.24
2628 4643 5.221722 GCCTACATAGGAAACATCATGAGGA 60.222 44.000 15.42 0.00 46.63 3.71
2629 4644 4.999950 GCCTACATAGGAAACATCATGAGG 59.000 45.833 5.68 5.68 46.63 3.86
2630 4645 5.699915 CAGCCTACATAGGAAACATCATGAG 59.300 44.000 9.25 0.00 46.63 2.90
2631 4646 5.455183 CCAGCCTACATAGGAAACATCATGA 60.455 44.000 9.25 0.00 46.63 3.07
2632 4647 4.758674 CCAGCCTACATAGGAAACATCATG 59.241 45.833 9.25 0.00 46.63 3.07
2652 4667 1.202114 GCGATCTGCCTCTATCTCCAG 59.798 57.143 0.00 0.00 37.76 3.86
2893 4952 5.278561 GGAATCAGGGTCTATTCGTACTCAG 60.279 48.000 0.00 0.00 33.72 3.35
3188 5263 2.877097 TAGCTTGATGCACAGGGAAA 57.123 45.000 0.00 0.00 45.94 3.13
3189 5264 2.305635 TCTTAGCTTGATGCACAGGGAA 59.694 45.455 0.00 0.00 45.94 3.97
3190 5265 1.908619 TCTTAGCTTGATGCACAGGGA 59.091 47.619 0.00 0.00 45.94 4.20
3191 5266 2.408271 TCTTAGCTTGATGCACAGGG 57.592 50.000 0.00 0.00 45.94 4.45
3192 5267 3.806380 AGATCTTAGCTTGATGCACAGG 58.194 45.455 6.63 0.00 45.94 4.00
3193 5268 5.123502 ACAAAGATCTTAGCTTGATGCACAG 59.876 40.000 8.75 0.00 45.94 3.66
3194 5269 5.005740 ACAAAGATCTTAGCTTGATGCACA 58.994 37.500 8.75 0.00 45.94 4.57
3195 5270 5.122869 TGACAAAGATCTTAGCTTGATGCAC 59.877 40.000 8.75 1.05 45.94 4.57
3196 5271 5.247862 TGACAAAGATCTTAGCTTGATGCA 58.752 37.500 8.75 0.00 45.94 3.96
3197 5272 5.808042 TGACAAAGATCTTAGCTTGATGC 57.192 39.130 8.75 0.00 43.29 3.91
3198 5273 8.659925 AGTATGACAAAGATCTTAGCTTGATG 57.340 34.615 8.75 3.95 0.00 3.07
3200 5275 9.809096 CTTAGTATGACAAAGATCTTAGCTTGA 57.191 33.333 8.75 0.00 0.00 3.02
3201 5276 9.809096 TCTTAGTATGACAAAGATCTTAGCTTG 57.191 33.333 8.75 5.85 0.00 4.01
3203 5278 9.979578 CATCTTAGTATGACAAAGATCTTAGCT 57.020 33.333 8.75 0.00 37.76 3.32
3204 5279 8.707839 GCATCTTAGTATGACAAAGATCTTAGC 58.292 37.037 8.75 1.92 37.76 3.09
3205 5280 9.979578 AGCATCTTAGTATGACAAAGATCTTAG 57.020 33.333 8.75 0.00 37.76 2.18
3206 5281 9.755804 CAGCATCTTAGTATGACAAAGATCTTA 57.244 33.333 8.75 0.00 37.76 2.10
3207 5282 7.226325 GCAGCATCTTAGTATGACAAAGATCTT 59.774 37.037 0.88 0.88 37.76 2.40
3208 5283 6.705381 GCAGCATCTTAGTATGACAAAGATCT 59.295 38.462 0.00 0.00 37.76 2.75
3209 5284 6.705381 AGCAGCATCTTAGTATGACAAAGATC 59.295 38.462 0.00 0.00 37.76 2.75
3210 5285 6.590068 AGCAGCATCTTAGTATGACAAAGAT 58.410 36.000 0.00 0.00 39.87 2.40
3211 5286 5.982356 AGCAGCATCTTAGTATGACAAAGA 58.018 37.500 0.00 0.00 34.00 2.52
3212 5287 6.674694 AAGCAGCATCTTAGTATGACAAAG 57.325 37.500 0.00 0.00 0.00 2.77
3213 5288 7.452880 AAAAGCAGCATCTTAGTATGACAAA 57.547 32.000 0.00 0.00 0.00 2.83
3214 5289 7.307694 CAAAAAGCAGCATCTTAGTATGACAA 58.692 34.615 0.00 0.00 0.00 3.18
3215 5290 6.623549 GCAAAAAGCAGCATCTTAGTATGACA 60.624 38.462 0.00 0.00 44.79 3.58
3216 5291 5.741040 GCAAAAAGCAGCATCTTAGTATGAC 59.259 40.000 0.00 0.00 44.79 3.06
3217 5292 5.883661 GCAAAAAGCAGCATCTTAGTATGA 58.116 37.500 0.00 0.00 44.79 2.15
3232 5307 3.990318 AGTCCTTGTAGTGCAAAAAGC 57.010 42.857 0.00 0.00 45.96 3.51
3233 5308 5.650543 ACAAAGTCCTTGTAGTGCAAAAAG 58.349 37.500 0.00 0.00 46.75 2.27
3234 5309 5.652994 ACAAAGTCCTTGTAGTGCAAAAA 57.347 34.783 0.00 0.00 46.75 1.94
3244 5319 8.019515 AGGTAAACTAACCAACAAAGTCCTTGT 61.020 37.037 0.00 0.00 42.66 3.16
3245 5320 6.320418 AGGTAAACTAACCAACAAAGTCCTTG 59.680 38.462 0.00 0.00 42.40 3.61
3246 5321 6.429151 AGGTAAACTAACCAACAAAGTCCTT 58.571 36.000 0.00 0.00 42.40 3.36
3247 5322 6.009908 AGGTAAACTAACCAACAAAGTCCT 57.990 37.500 0.00 0.00 42.40 3.85
3248 5323 6.704289 AAGGTAAACTAACCAACAAAGTCC 57.296 37.500 0.00 0.00 42.40 3.85
3249 5324 7.541162 ACAAAGGTAAACTAACCAACAAAGTC 58.459 34.615 0.00 0.00 42.40 3.01
3250 5325 7.470935 ACAAAGGTAAACTAACCAACAAAGT 57.529 32.000 0.00 0.00 42.40 2.66
3251 5326 7.276878 CCAACAAAGGTAAACTAACCAACAAAG 59.723 37.037 0.00 0.00 42.40 2.77
3252 5327 7.097834 CCAACAAAGGTAAACTAACCAACAAA 58.902 34.615 0.00 0.00 42.40 2.83
3253 5328 6.210984 ACCAACAAAGGTAAACTAACCAACAA 59.789 34.615 0.00 0.00 42.40 2.83
3254 5329 5.715753 ACCAACAAAGGTAAACTAACCAACA 59.284 36.000 0.00 0.00 42.40 3.33
3255 5330 6.037726 CACCAACAAAGGTAAACTAACCAAC 58.962 40.000 0.00 0.00 40.77 3.77
3256 5331 5.127356 CCACCAACAAAGGTAAACTAACCAA 59.873 40.000 0.00 0.00 40.77 3.67
3257 5332 4.645588 CCACCAACAAAGGTAAACTAACCA 59.354 41.667 0.00 0.00 40.77 3.67
3258 5333 4.038282 CCCACCAACAAAGGTAAACTAACC 59.962 45.833 0.00 0.00 40.77 2.85
3259 5334 4.646040 ACCCACCAACAAAGGTAAACTAAC 59.354 41.667 0.00 0.00 40.77 2.34
3260 5335 4.645588 CACCCACCAACAAAGGTAAACTAA 59.354 41.667 0.00 0.00 40.77 2.24
3261 5336 4.208746 CACCCACCAACAAAGGTAAACTA 58.791 43.478 0.00 0.00 40.77 2.24
3262 5337 3.028130 CACCCACCAACAAAGGTAAACT 58.972 45.455 0.00 0.00 40.77 2.66
3263 5338 2.761767 ACACCCACCAACAAAGGTAAAC 59.238 45.455 0.00 0.00 40.77 2.01
3264 5339 3.103080 ACACCCACCAACAAAGGTAAA 57.897 42.857 0.00 0.00 40.77 2.01
3265 5340 2.830651 ACACCCACCAACAAAGGTAA 57.169 45.000 0.00 0.00 40.77 2.85
3266 5341 2.025226 TGAACACCCACCAACAAAGGTA 60.025 45.455 0.00 0.00 40.77 3.08
3286 5361 7.624764 GCTTGATGCACAGGGAAATTTATTTTG 60.625 37.037 0.00 0.00 42.31 2.44
3328 5403 1.051812 CTCTAGGGGGCACATACCAG 58.948 60.000 0.00 0.00 0.00 4.00
3382 5464 8.026607 TCGAAAGGATGATAAACAAATGGAAAC 58.973 33.333 0.00 0.00 0.00 2.78
3537 5619 7.761409 TCTGGCACTAGCAATGTAAAATAAAG 58.239 34.615 0.00 0.00 44.61 1.85
3544 5628 4.286297 AGTTCTGGCACTAGCAATGTAA 57.714 40.909 0.00 0.00 44.61 2.41
3545 5629 3.981071 AGTTCTGGCACTAGCAATGTA 57.019 42.857 0.00 0.00 44.61 2.29
3546 5630 2.867109 AGTTCTGGCACTAGCAATGT 57.133 45.000 0.00 0.00 44.61 2.71
3735 5819 7.389232 CCTATATGAAGTGTAATCCAGCATCA 58.611 38.462 0.00 0.00 0.00 3.07
3766 5850 2.736192 GGTTACTTGCGCGGTAGTTTTA 59.264 45.455 8.83 0.00 0.00 1.52
3816 5900 1.476477 TGGACATCCCAACATGCATG 58.524 50.000 25.09 25.09 43.29 4.06
3906 5990 3.002348 GCCGAGATAGCGCACTAATTTTT 59.998 43.478 11.47 0.00 30.45 1.94
3907 5991 2.544267 GCCGAGATAGCGCACTAATTTT 59.456 45.455 11.47 0.00 30.45 1.82
3908 5992 2.135933 GCCGAGATAGCGCACTAATTT 58.864 47.619 11.47 0.00 30.45 1.82
4050 6134 2.705658 TGCTTGTATGCCAGCCTACTAT 59.294 45.455 4.42 0.00 0.00 2.12
4141 6301 3.555966 ACTGAAACAGAACAAGGAAGGG 58.444 45.455 5.76 0.00 35.18 3.95
4162 6322 5.645624 TCGAAACAAAGACAATTTGCAGAA 58.354 33.333 0.00 0.00 32.93 3.02
4183 6343 6.455647 TGAAGCCTATAGGATTAACACATCG 58.544 40.000 21.96 0.00 44.94 3.84
4198 6358 8.914011 ACTTTTAAGTGTTTTCTTGAAGCCTAT 58.086 29.630 0.00 0.00 37.98 2.57
4217 6377 9.901172 AAACTCTAGTCTCTTCCAAACTTTTAA 57.099 29.630 0.00 0.00 0.00 1.52
4351 6511 5.769967 CTCATAGAGGACAAACGTTCTTG 57.230 43.478 0.00 0.00 0.00 3.02
4448 6608 5.387279 CGTTGCAAGACGGTAATAAATTGT 58.613 37.500 0.00 0.00 39.27 2.71
4455 6615 1.231221 TTGCGTTGCAAGACGGTAAT 58.769 45.000 12.51 0.00 43.99 1.89
4471 6631 0.370273 CGTGTTCTATCGCACCTTGC 59.630 55.000 0.00 0.00 40.69 4.01
4482 6642 0.981183 ATGGAAGGGCACGTGTTCTA 59.019 50.000 18.38 11.37 0.00 2.10
4513 6676 3.804873 GCCTTCTTCGCTACAGGATTTAG 59.195 47.826 0.00 0.00 0.00 1.85
4584 6747 3.970410 TGGCTGGGTGGGCTCAAG 61.970 66.667 0.00 0.00 0.00 3.02
4599 6762 5.238650 AGGTACAGAGACGAAAATTTTGTGG 59.761 40.000 8.47 0.08 0.00 4.17
4626 6789 1.271871 TGAAACATCCAACTGCCGGAT 60.272 47.619 5.05 0.00 44.35 4.18
4627 6790 0.109532 TGAAACATCCAACTGCCGGA 59.890 50.000 5.05 0.00 36.84 5.14
4628 6791 0.240945 GTGAAACATCCAACTGCCGG 59.759 55.000 0.00 0.00 36.32 6.13
4629 6792 0.950836 TGTGAAACATCCAACTGCCG 59.049 50.000 0.00 0.00 45.67 5.69
4641 6804 8.015658 GGTACAGTGATGAATACTTTGTGAAAC 58.984 37.037 0.00 0.00 37.35 2.78
4642 6805 7.936847 AGGTACAGTGATGAATACTTTGTGAAA 59.063 33.333 0.00 0.00 0.00 2.69
4643 6806 7.387673 CAGGTACAGTGATGAATACTTTGTGAA 59.612 37.037 0.00 0.00 0.00 3.18
4644 6807 6.873605 CAGGTACAGTGATGAATACTTTGTGA 59.126 38.462 0.00 0.00 0.00 3.58
4645 6808 6.402550 GCAGGTACAGTGATGAATACTTTGTG 60.403 42.308 0.00 0.00 0.00 3.33
4646 6809 5.643777 GCAGGTACAGTGATGAATACTTTGT 59.356 40.000 0.00 0.00 0.00 2.83
4647 6810 5.643348 TGCAGGTACAGTGATGAATACTTTG 59.357 40.000 0.00 0.00 0.00 2.77
4648 6811 5.804639 TGCAGGTACAGTGATGAATACTTT 58.195 37.500 0.00 0.00 0.00 2.66
4649 6812 5.420725 TGCAGGTACAGTGATGAATACTT 57.579 39.130 0.00 0.00 0.00 2.24
4650 6813 5.620738 ATGCAGGTACAGTGATGAATACT 57.379 39.130 0.00 0.00 0.00 2.12
4651 6814 6.458751 CCAAATGCAGGTACAGTGATGAATAC 60.459 42.308 0.00 0.00 0.00 1.89
4652 6815 5.589855 CCAAATGCAGGTACAGTGATGAATA 59.410 40.000 0.00 0.00 0.00 1.75
4653 6816 4.400251 CCAAATGCAGGTACAGTGATGAAT 59.600 41.667 0.00 0.00 0.00 2.57
4654 6817 3.758023 CCAAATGCAGGTACAGTGATGAA 59.242 43.478 0.00 0.00 0.00 2.57
4655 6818 3.346315 CCAAATGCAGGTACAGTGATGA 58.654 45.455 0.00 0.00 0.00 2.92
4656 6819 2.159338 GCCAAATGCAGGTACAGTGATG 60.159 50.000 0.00 0.00 40.77 3.07
4657 6820 2.094675 GCCAAATGCAGGTACAGTGAT 58.905 47.619 0.00 0.00 40.77 3.06
4658 6821 1.533625 GCCAAATGCAGGTACAGTGA 58.466 50.000 0.00 0.00 40.77 3.41
4674 6837 1.401761 AGTGAAACATGCAACTGCCA 58.598 45.000 0.00 0.00 41.43 4.92
4693 6856 8.318412 TCTAGTTTGTAACCAGAATGCTGAATA 58.682 33.333 0.74 0.00 45.17 1.75
4700 6863 6.710744 ACAGGTTCTAGTTTGTAACCAGAATG 59.289 38.462 11.65 4.97 44.21 2.67
4744 6907 2.329379 GCCATAATAAGAGCGAGACCG 58.671 52.381 0.00 0.00 39.16 4.79
4777 6940 1.284297 TGTCAACTCGTGCGCATCTG 61.284 55.000 15.91 9.25 0.00 2.90
4821 6984 5.502606 GTGAACAGAGAAGTAAACAACAGC 58.497 41.667 0.00 0.00 0.00 4.40
4855 7018 3.426292 GGCTTTTCTACATCTGAAACCGC 60.426 47.826 0.00 0.00 33.77 5.68
4858 7021 9.914131 ATAAAAAGGCTTTTCTACATCTGAAAC 57.086 29.630 24.28 0.00 36.20 2.78
4869 7032 9.542462 GGTACAAGAAAATAAAAAGGCTTTTCT 57.458 29.630 24.28 13.78 41.91 2.52
5011 7551 3.431922 TTTTGCTCCGTAGATAGTCCG 57.568 47.619 0.00 0.00 0.00 4.79
5019 7604 4.872691 AGATTCACTCATTTTGCTCCGTAG 59.127 41.667 0.00 0.00 0.00 3.51
5054 7639 9.241317 GGATTACATACGGATGTATATAAACGG 57.759 37.037 20.99 0.00 45.77 4.44
5055 7640 9.791820 TGGATTACATACGGATGTATATAAACG 57.208 33.333 20.99 0.00 45.77 3.60
5091 7676 9.037417 CGTTTCTAAATACAAGACTTTTTAGCG 57.963 33.333 10.91 7.17 33.63 4.26
5092 7677 9.326339 CCGTTTCTAAATACAAGACTTTTTAGC 57.674 33.333 10.91 1.26 33.63 3.09
5095 7680 8.565416 CCTCCGTTTCTAAATACAAGACTTTTT 58.435 33.333 0.00 0.00 0.00 1.94
5099 7686 5.482878 TCCCTCCGTTTCTAAATACAAGACT 59.517 40.000 0.00 0.00 0.00 3.24
5105 7692 7.287512 AGATACTCCCTCCGTTTCTAAATAC 57.712 40.000 0.00 0.00 0.00 1.89
5125 7712 4.202223 GGATTTCCACTCGCTTGGTAGATA 60.202 45.833 2.45 0.00 37.93 1.98
5131 7718 1.089920 CAGGATTTCCACTCGCTTGG 58.910 55.000 0.00 0.00 38.89 3.61
5157 7744 4.168101 TCCCAACTCTTGAGAACCTACAT 58.832 43.478 4.49 0.00 0.00 2.29
5229 7830 6.239217 TGTAGAAGCATGAACATAGACCAT 57.761 37.500 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.