Multiple sequence alignment - TraesCS2D01G017000

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 TraesCS2D01G017000 chr2D 100.000 3851 0 0 1 3851 8293716 8297566 0.000000e+00 7112.0
1 TraesCS2D01G017000 chr2D 83.797 1259 160 23 1303 2536 8294928 8296167 0.000000e+00 1155.0
2 TraesCS2D01G017000 chr2D 83.797 1259 160 23 1213 2452 8295018 8296251 0.000000e+00 1155.0
3 TraesCS2D01G017000 chr2D 100.000 347 0 0 4148 4494 8297863 8298209 3.790000e-180 641.0
4 TraesCS2D01G017000 chr2D 83.892 627 77 11 1763 2368 8295628 8296251 1.080000e-160 577.0
5 TraesCS2D01G017000 chr2D 82.112 587 79 9 1723 2287 8295672 8296254 3.140000e-131 479.0
6 TraesCS2D01G017000 chr2D 88.720 328 30 7 1401 1722 8294939 8295265 1.170000e-105 394.0
7 TraesCS2D01G017000 chr2D 88.720 328 30 7 1224 1550 8295116 8295437 1.170000e-105 394.0
8 TraesCS2D01G017000 chr2D 80.299 335 48 6 2206 2540 8295438 8295754 2.090000e-58 237.0
9 TraesCS2D01G017000 chr2D 80.299 335 48 6 1723 2039 8295921 8296255 2.090000e-58 237.0
10 TraesCS2D01G017000 chrUn 95.530 1991 77 5 1 1986 11734680 11732697 0.000000e+00 3173.0
11 TraesCS2D01G017000 chrUn 97.122 1216 31 4 1931 3143 11732433 11731219 0.000000e+00 2049.0
12 TraesCS2D01G017000 chrUn 92.083 720 32 6 3144 3851 11731070 11730364 0.000000e+00 990.0
13 TraesCS2D01G017000 chrUn 86.111 612 70 3 1856 2455 11732433 11731825 0.000000e+00 645.0
14 TraesCS2D01G017000 chrUn 81.170 786 112 20 1306 2070 11733467 11732697 2.310000e-167 599.0
15 TraesCS2D01G017000 chrUn 86.148 527 67 2 2016 2539 11732432 11731909 8.440000e-157 564.0
16 TraesCS2D01G017000 chrUn 81.081 703 104 16 1216 1911 11733377 11732697 6.620000e-148 534.0
17 TraesCS2D01G017000 chrUn 86.895 351 35 11 1224 1570 11733282 11732939 2.540000e-102 383.0
18 TraesCS2D01G017000 chrUn 87.500 328 34 7 1401 1722 11733459 11733133 5.490000e-99 372.0
19 TraesCS2D01G017000 chrUn 79.403 335 51 6 1723 2039 11732158 11731824 2.100000e-53 220.0
20 TraesCS2D01G017000 chrUn 85.043 234 14 6 1913 2143 11732920 11732705 7.570000e-53 219.0
21 TraesCS2D01G017000 chrUn 80.657 274 32 7 1957 2227 11732960 11732705 4.590000e-45 193.0
22 TraesCS2D01G017000 chrUn 89.189 74 8 0 1763 1836 11732770 11732697 4.790000e-15 93.5
23 TraesCS2D01G017000 chr2B 86.680 2455 211 46 39 2452 4661732 4664111 0.000000e+00 2615.0
24 TraesCS2D01G017000 chr2B 91.653 1857 113 20 1303 3143 4662890 4664720 0.000000e+00 2532.0
25 TraesCS2D01G017000 chr2B 84.914 1160 118 32 1401 2536 4662901 4664027 0.000000e+00 1120.0
26 TraesCS2D01G017000 chr2B 88.870 575 39 8 3153 3708 4664905 4665473 0.000000e+00 684.0
27 TraesCS2D01G017000 chr2B 79.727 587 78 21 1957 2539 4663313 4663862 1.960000e-103 387.0


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 TraesCS2D01G017000 chr2D 8293716 8298209 4493 False 1238.100000 7112 87.1636 1 4494 10 chr2D.!!$F1 4493
1 TraesCS2D01G017000 chrUn 11730364 11734680 4316 True 771.884615 3173 86.7640 1 3851 13 chrUn.!!$R1 3850
2 TraesCS2D01G017000 chr2B 4661732 4665473 3741 False 1467.600000 2615 86.3688 39 3708 5 chr2B.!!$F1 3669

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
276 285 0.324943 GTTGGAAGCAGGGTCTAGCA 59.675 55.0 0.00 0.0 0.0 3.49 F
278 287 0.615331 TGGAAGCAGGGTCTAGCAAG 59.385 55.0 0.00 0.0 0.0 4.01 F
1230 1248 0.106335 TACGGCGAAAGGTGGAAACA 59.894 50.0 16.62 0.0 38.7 2.83 F
2118 2464 1.367346 TGGCACCTATTCCTGAACCA 58.633 50.0 0.00 0.0 0.0 3.67 F
3374 3915 0.320421 AACTTACATCCTGCGTGCGT 60.320 50.0 0.00 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1161 0.530431 GTTTTGTGCCCACAGCCTTG 60.530 55.0 1.02 0.0 42.94 3.61 R
1469 1487 0.955919 CACTTTCCGTTCCTCCTGCC 60.956 60.0 0.00 0.0 0.00 4.85 R
2508 2854 2.320681 TAGTAGGTGCCACTTCTGGT 57.679 50.0 0.00 0.0 40.17 4.00 R
3383 3924 0.108138 AGCTCTTTACCTGCGCGATT 60.108 50.0 12.10 0.0 0.00 3.34 R
4195 4750 0.036577 CAGGCAGAACCAGGAGTCAG 60.037 60.0 0.00 0.0 43.14 3.51 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
41 42 5.243954 GCCATTTTACCTGTCCTCTTTTCTT 59.756 40.000 0.00 0.00 0.00 2.52
62 63 2.577772 AAGCGCTGGAGTGAGCTGA 61.578 57.895 12.58 0.00 40.17 4.26
78 79 4.344390 TGAGCTGAGCATCTATTCATGAGT 59.656 41.667 7.39 0.00 34.92 3.41
87 88 3.216800 TCTATTCATGAGTTGCCCATGC 58.783 45.455 0.00 0.00 40.74 4.06
154 155 2.711311 CAGCATTGCATCGACGGG 59.289 61.111 11.91 0.00 0.00 5.28
190 191 4.080863 GGACTGTCACCTGGTTGATAGAAT 60.081 45.833 20.93 7.48 36.99 2.40
208 209 2.831859 TGGCACAAGCAAATCCCAA 58.168 47.368 0.00 0.00 44.61 4.12
259 268 4.640201 GGTGCTACATGTATGGTCAATGTT 59.360 41.667 5.91 0.00 0.00 2.71
276 285 0.324943 GTTGGAAGCAGGGTCTAGCA 59.675 55.000 0.00 0.00 0.00 3.49
277 286 1.064003 TTGGAAGCAGGGTCTAGCAA 58.936 50.000 0.00 0.00 0.00 3.91
278 287 0.615331 TGGAAGCAGGGTCTAGCAAG 59.385 55.000 0.00 0.00 0.00 4.01
279 288 0.905357 GGAAGCAGGGTCTAGCAAGA 59.095 55.000 0.00 0.00 0.00 3.02
280 289 1.279271 GGAAGCAGGGTCTAGCAAGAA 59.721 52.381 0.00 0.00 32.16 2.52
281 290 2.290323 GGAAGCAGGGTCTAGCAAGAAA 60.290 50.000 0.00 0.00 32.16 2.52
282 291 2.481289 AGCAGGGTCTAGCAAGAAAC 57.519 50.000 0.00 0.00 32.16 2.78
355 366 4.546674 AGGGGATGGTATGAAAATTGGTC 58.453 43.478 0.00 0.00 0.00 4.02
359 370 4.881850 GGATGGTATGAAAATTGGTCGAGT 59.118 41.667 0.00 0.00 0.00 4.18
452 463 1.317613 ATGTGTTGCTCCTTTTCGCA 58.682 45.000 0.00 0.00 0.00 5.10
575 586 3.636300 TGACCTTGTCTGGAATTTGGTTG 59.364 43.478 0.00 0.00 33.15 3.77
789 806 2.069273 CCCGCAACAAACTAGAGACAG 58.931 52.381 0.00 0.00 0.00 3.51
950 968 5.301551 AGCATTTCATGTGTTACAGGTTTCA 59.698 36.000 0.00 0.00 30.95 2.69
1050 1068 0.877071 CGGTGAAAACAGCAGCATCT 59.123 50.000 0.00 0.00 33.59 2.90
1143 1161 2.695613 GTGCTGCTGAAGAACCTTTC 57.304 50.000 0.00 0.00 0.00 2.62
1230 1248 0.106335 TACGGCGAAAGGTGGAAACA 59.894 50.000 16.62 0.00 38.70 2.83
1236 1254 2.098443 GCGAAAGGTGGAAACAGAACAA 59.902 45.455 0.00 0.00 44.46 2.83
1271 1289 2.033550 CGTCTCCGGAGATGAAGGTTAG 59.966 54.545 39.62 18.10 45.06 2.34
1469 1487 1.953686 TGGAAGCGAGAAAACAAAGGG 59.046 47.619 0.00 0.00 0.00 3.95
1525 1543 4.779993 AAAGTGAACCCTTCTCAAGAGT 57.220 40.909 0.00 0.00 0.00 3.24
1563 1581 2.958355 TGAGAAAACAAAAGGGCAGGAG 59.042 45.455 0.00 0.00 0.00 3.69
1572 1590 3.922171 AAAGGGCAGGAGATACAGAAG 57.078 47.619 0.00 0.00 0.00 2.85
1618 1636 4.408921 TGAACCCTTCTCAAGAGTTGAAGA 59.591 41.667 0.00 0.00 39.58 2.87
1784 1802 1.625818 AGTCAGTAAGCCAGAAGTGGG 59.374 52.381 0.00 0.00 45.17 4.61
2118 2464 1.367346 TGGCACCTATTCCTGAACCA 58.633 50.000 0.00 0.00 0.00 3.67
2508 2854 7.171653 TGGTACAACATGATCAGGTCAATAAA 58.828 34.615 14.24 0.00 36.11 1.40
2680 3026 2.490217 CACCGGTCGCTCCTAGTG 59.510 66.667 2.59 0.00 33.84 2.74
2825 3172 5.977489 AGTAAGAAATTTGGGTAGCAACC 57.023 39.130 0.00 0.00 45.97 3.77
2838 3185 8.514330 TTGGGTAGCAACCTTAGTTATTTATG 57.486 34.615 0.00 0.00 45.95 1.90
2841 3188 9.181061 GGGTAGCAACCTTAGTTATTTATGAAA 57.819 33.333 0.00 0.00 45.95 2.69
3050 3398 6.280643 CCGTCATATTGGACTGTCTTATCAA 58.719 40.000 7.85 3.87 35.63 2.57
3051 3399 6.931281 CCGTCATATTGGACTGTCTTATCAAT 59.069 38.462 7.85 10.69 35.63 2.57
3326 3863 2.638330 ATCGGGCCGACATGTTACCG 62.638 60.000 33.71 19.08 39.18 4.02
3328 3865 1.078988 GGGCCGACATGTTACCGAA 60.079 57.895 0.00 0.00 0.00 4.30
3369 3910 6.236017 TGTTTTAAGAACTTACATCCTGCG 57.764 37.500 0.00 0.00 0.00 5.18
3373 3914 0.370273 GAACTTACATCCTGCGTGCG 59.630 55.000 0.00 0.00 0.00 5.34
3374 3915 0.320421 AACTTACATCCTGCGTGCGT 60.320 50.000 0.00 0.00 0.00 5.24
3382 3923 0.314618 TCCTGCGTGCGTTAACACTA 59.685 50.000 6.39 0.00 38.45 2.74
3383 3924 1.141645 CCTGCGTGCGTTAACACTAA 58.858 50.000 6.39 0.00 38.45 2.24
3387 3928 2.159947 TGCGTGCGTTAACACTAAATCG 60.160 45.455 6.39 1.92 38.45 3.34
3718 4273 3.572682 GCTTAATGGCCAGTTTATACCCC 59.427 47.826 12.70 0.00 0.00 4.95
3724 4279 1.139455 GCCAGTTTATACCCCTGCGTA 59.861 52.381 0.00 0.00 0.00 4.42
3739 4294 4.452455 CCCTGCGTACCATCTGATTTATTC 59.548 45.833 0.00 0.00 0.00 1.75
3744 4299 5.992217 GCGTACCATCTGATTTATTCTTCCT 59.008 40.000 0.00 0.00 0.00 3.36
3775 4330 9.927668 TGAGTTGGAATTTGATATTCTTTTTCC 57.072 29.630 0.00 0.00 33.40 3.13
3835 4390 2.995466 TGCTTGTGCAGATAGTTTGC 57.005 45.000 0.00 0.00 45.31 3.68
4204 4759 3.691049 TTTTTGCGAAACTGACTCCTG 57.309 42.857 0.00 0.00 0.00 3.86
4205 4760 1.593196 TTTGCGAAACTGACTCCTGG 58.407 50.000 0.00 0.00 0.00 4.45
4206 4761 0.468226 TTGCGAAACTGACTCCTGGT 59.532 50.000 0.00 0.00 0.00 4.00
4207 4762 0.468226 TGCGAAACTGACTCCTGGTT 59.532 50.000 0.00 0.00 0.00 3.67
4208 4763 1.149148 GCGAAACTGACTCCTGGTTC 58.851 55.000 0.00 0.00 35.41 3.62
4209 4764 1.270358 GCGAAACTGACTCCTGGTTCT 60.270 52.381 0.00 0.00 36.26 3.01
4210 4765 2.408050 CGAAACTGACTCCTGGTTCTG 58.592 52.381 0.00 0.00 36.26 3.02
4211 4766 2.147150 GAAACTGACTCCTGGTTCTGC 58.853 52.381 0.00 0.00 35.74 4.26
4212 4767 0.398318 AACTGACTCCTGGTTCTGCC 59.602 55.000 0.00 0.00 37.90 4.85
4213 4768 0.472734 ACTGACTCCTGGTTCTGCCT 60.473 55.000 0.00 0.00 38.35 4.75
4214 4769 0.036577 CTGACTCCTGGTTCTGCCTG 60.037 60.000 0.00 0.00 38.35 4.85
4215 4770 0.764369 TGACTCCTGGTTCTGCCTGT 60.764 55.000 0.00 0.00 38.35 4.00
4216 4771 0.321122 GACTCCTGGTTCTGCCTGTG 60.321 60.000 0.00 0.00 38.35 3.66
4217 4772 1.673665 CTCCTGGTTCTGCCTGTGC 60.674 63.158 0.00 0.00 38.35 4.57
4272 4827 3.965379 AAAAACTTTTGAACCGGGTGT 57.035 38.095 6.32 0.00 0.00 4.16
4273 4828 3.965379 AAAACTTTTGAACCGGGTGTT 57.035 38.095 6.32 0.00 40.81 3.32
4285 4840 2.752903 ACCGGGTGTTCAAATTATGAGC 59.247 45.455 6.32 0.00 39.77 4.26
4286 4841 2.099098 CCGGGTGTTCAAATTATGAGCC 59.901 50.000 0.00 0.00 39.77 4.70
4287 4842 2.752354 CGGGTGTTCAAATTATGAGCCA 59.248 45.455 0.00 0.00 39.77 4.75
4288 4843 3.381272 CGGGTGTTCAAATTATGAGCCAT 59.619 43.478 0.00 0.00 39.77 4.40
4289 4844 4.578516 CGGGTGTTCAAATTATGAGCCATA 59.421 41.667 0.00 0.00 39.77 2.74
4290 4845 5.241506 CGGGTGTTCAAATTATGAGCCATAT 59.758 40.000 0.00 0.00 39.77 1.78
4291 4846 6.239008 CGGGTGTTCAAATTATGAGCCATATT 60.239 38.462 0.00 0.00 39.77 1.28
4292 4847 7.147976 GGGTGTTCAAATTATGAGCCATATTC 58.852 38.462 0.00 0.00 39.77 1.75
4293 4848 6.857964 GGTGTTCAAATTATGAGCCATATTCG 59.142 38.462 0.00 0.00 39.77 3.34
4294 4849 6.360681 GTGTTCAAATTATGAGCCATATTCGC 59.639 38.462 0.00 0.00 39.77 4.70
4295 4850 5.627499 TCAAATTATGAGCCATATTCGCC 57.373 39.130 0.00 0.00 33.04 5.54
4296 4851 5.069318 TCAAATTATGAGCCATATTCGCCA 58.931 37.500 0.00 0.00 33.04 5.69
4297 4852 5.711506 TCAAATTATGAGCCATATTCGCCAT 59.288 36.000 0.00 0.00 33.04 4.40
4298 4853 6.209192 TCAAATTATGAGCCATATTCGCCATT 59.791 34.615 0.00 0.00 33.04 3.16
4299 4854 5.571784 ATTATGAGCCATATTCGCCATTG 57.428 39.130 0.00 0.00 0.00 2.82
4300 4855 2.346766 TGAGCCATATTCGCCATTGT 57.653 45.000 0.00 0.00 0.00 2.71
4301 4856 1.948834 TGAGCCATATTCGCCATTGTG 59.051 47.619 0.00 0.00 0.00 3.33
4302 4857 1.949525 GAGCCATATTCGCCATTGTGT 59.050 47.619 0.00 0.00 0.00 3.72
4303 4858 2.358898 GAGCCATATTCGCCATTGTGTT 59.641 45.455 0.00 0.00 0.00 3.32
4304 4859 2.358898 AGCCATATTCGCCATTGTGTTC 59.641 45.455 0.00 0.00 0.00 3.18
4305 4860 2.543653 GCCATATTCGCCATTGTGTTCC 60.544 50.000 0.00 0.00 0.00 3.62
4306 4861 2.951642 CCATATTCGCCATTGTGTTCCT 59.048 45.455 0.00 0.00 0.00 3.36
4307 4862 3.381272 CCATATTCGCCATTGTGTTCCTT 59.619 43.478 0.00 0.00 0.00 3.36
4308 4863 4.353737 CATATTCGCCATTGTGTTCCTTG 58.646 43.478 0.00 0.00 0.00 3.61
4309 4864 1.686355 TTCGCCATTGTGTTCCTTGT 58.314 45.000 0.00 0.00 0.00 3.16
4310 4865 0.950836 TCGCCATTGTGTTCCTTGTG 59.049 50.000 0.00 0.00 0.00 3.33
4311 4866 0.664166 CGCCATTGTGTTCCTTGTGC 60.664 55.000 0.00 0.00 0.00 4.57
4312 4867 0.675633 GCCATTGTGTTCCTTGTGCT 59.324 50.000 0.00 0.00 0.00 4.40
4313 4868 1.603678 GCCATTGTGTTCCTTGTGCTG 60.604 52.381 0.00 0.00 0.00 4.41
4314 4869 1.682854 CCATTGTGTTCCTTGTGCTGT 59.317 47.619 0.00 0.00 0.00 4.40
4315 4870 2.101249 CCATTGTGTTCCTTGTGCTGTT 59.899 45.455 0.00 0.00 0.00 3.16
4316 4871 2.937469 TTGTGTTCCTTGTGCTGTTG 57.063 45.000 0.00 0.00 0.00 3.33
4317 4872 1.102154 TGTGTTCCTTGTGCTGTTGG 58.898 50.000 0.00 0.00 0.00 3.77
4318 4873 0.249031 GTGTTCCTTGTGCTGTTGGC 60.249 55.000 0.00 0.00 42.22 4.52
4319 4874 0.395586 TGTTCCTTGTGCTGTTGGCT 60.396 50.000 0.00 0.00 42.39 4.75
4320 4875 0.746659 GTTCCTTGTGCTGTTGGCTT 59.253 50.000 0.00 0.00 42.39 4.35
4321 4876 1.136891 GTTCCTTGTGCTGTTGGCTTT 59.863 47.619 0.00 0.00 42.39 3.51
4322 4877 0.746063 TCCTTGTGCTGTTGGCTTTG 59.254 50.000 0.00 0.00 42.39 2.77
4323 4878 0.746063 CCTTGTGCTGTTGGCTTTGA 59.254 50.000 0.00 0.00 42.39 2.69
4324 4879 1.136695 CCTTGTGCTGTTGGCTTTGAA 59.863 47.619 0.00 0.00 42.39 2.69
4325 4880 2.418471 CCTTGTGCTGTTGGCTTTGAAA 60.418 45.455 0.00 0.00 42.39 2.69
4326 4881 2.292103 TGTGCTGTTGGCTTTGAAAC 57.708 45.000 0.00 0.00 42.39 2.78
4327 4882 1.547820 TGTGCTGTTGGCTTTGAAACA 59.452 42.857 0.00 0.00 42.39 2.83
4328 4883 2.028658 TGTGCTGTTGGCTTTGAAACAA 60.029 40.909 0.00 0.00 42.39 2.83
4329 4884 2.604462 GTGCTGTTGGCTTTGAAACAAG 59.396 45.455 0.00 0.00 42.39 3.16
4330 4885 2.495270 TGCTGTTGGCTTTGAAACAAGA 59.505 40.909 0.00 0.00 42.39 3.02
4331 4886 3.132646 TGCTGTTGGCTTTGAAACAAGAT 59.867 39.130 0.00 0.00 42.39 2.40
4332 4887 3.737774 GCTGTTGGCTTTGAAACAAGATC 59.262 43.478 0.00 0.00 35.95 2.75
4333 4888 4.737352 GCTGTTGGCTTTGAAACAAGATCA 60.737 41.667 0.00 0.00 35.95 2.92
4334 4889 5.336150 TGTTGGCTTTGAAACAAGATCAA 57.664 34.783 0.00 0.00 33.50 2.57
4335 4890 5.108517 TGTTGGCTTTGAAACAAGATCAAC 58.891 37.500 0.00 0.00 36.57 3.18
4336 4891 4.998671 TGGCTTTGAAACAAGATCAACA 57.001 36.364 0.00 0.00 36.57 3.33
4337 4892 4.681744 TGGCTTTGAAACAAGATCAACAC 58.318 39.130 0.00 0.00 36.57 3.32
4338 4893 4.159321 TGGCTTTGAAACAAGATCAACACA 59.841 37.500 0.00 0.00 36.57 3.72
4339 4894 5.163426 TGGCTTTGAAACAAGATCAACACAT 60.163 36.000 0.00 0.00 36.57 3.21
4340 4895 5.754890 GGCTTTGAAACAAGATCAACACATT 59.245 36.000 0.00 0.00 36.57 2.71
4341 4896 6.292488 GGCTTTGAAACAAGATCAACACATTG 60.292 38.462 0.00 0.00 36.57 2.82
4353 4908 5.895636 TCAACACATTGACAAGTTTCTGT 57.104 34.783 0.00 0.00 40.01 3.41
4354 4909 6.266168 TCAACACATTGACAAGTTTCTGTT 57.734 33.333 0.00 0.00 40.01 3.16
4355 4910 6.321717 TCAACACATTGACAAGTTTCTGTTC 58.678 36.000 0.00 0.00 40.01 3.18
4356 4911 5.895636 ACACATTGACAAGTTTCTGTTCA 57.104 34.783 0.00 0.00 0.00 3.18
4357 4912 6.266168 ACACATTGACAAGTTTCTGTTCAA 57.734 33.333 0.00 0.00 0.00 2.69
4358 4913 6.686630 ACACATTGACAAGTTTCTGTTCAAA 58.313 32.000 0.00 0.00 0.00 2.69
4359 4914 7.322664 ACACATTGACAAGTTTCTGTTCAAAT 58.677 30.769 0.00 0.00 0.00 2.32
4360 4915 7.818930 ACACATTGACAAGTTTCTGTTCAAATT 59.181 29.630 0.00 0.00 0.00 1.82
4361 4916 9.299963 CACATTGACAAGTTTCTGTTCAAATTA 57.700 29.630 0.00 0.00 0.00 1.40
4365 4920 9.734620 TTGACAAGTTTCTGTTCAAATTATGAG 57.265 29.630 0.00 0.00 39.77 2.90
4366 4921 7.862372 TGACAAGTTTCTGTTCAAATTATGAGC 59.138 33.333 0.00 0.00 39.77 4.26
4367 4922 7.147976 ACAAGTTTCTGTTCAAATTATGAGCC 58.852 34.615 0.00 0.00 39.77 4.70
4368 4923 6.899393 AGTTTCTGTTCAAATTATGAGCCA 57.101 33.333 0.00 0.00 39.77 4.75
4369 4924 7.472334 AGTTTCTGTTCAAATTATGAGCCAT 57.528 32.000 0.00 0.00 39.77 4.40
4370 4925 8.579850 AGTTTCTGTTCAAATTATGAGCCATA 57.420 30.769 0.00 0.00 39.77 2.74
4371 4926 9.193806 AGTTTCTGTTCAAATTATGAGCCATAT 57.806 29.630 0.00 0.00 39.77 1.78
4372 4927 9.807649 GTTTCTGTTCAAATTATGAGCCATATT 57.192 29.630 0.00 0.00 39.77 1.28
4374 4929 8.750515 TCTGTTCAAATTATGAGCCATATTCA 57.249 30.769 0.00 0.00 39.77 2.57
4375 4930 8.623903 TCTGTTCAAATTATGAGCCATATTCAC 58.376 33.333 0.00 0.00 39.77 3.18
4376 4931 7.715657 TGTTCAAATTATGAGCCATATTCACC 58.284 34.615 0.00 0.00 39.77 4.02
4377 4932 6.558771 TCAAATTATGAGCCATATTCACCG 57.441 37.500 0.00 0.00 33.04 4.94
4378 4933 6.061441 TCAAATTATGAGCCATATTCACCGT 58.939 36.000 0.00 0.00 33.04 4.83
4379 4934 6.545666 TCAAATTATGAGCCATATTCACCGTT 59.454 34.615 0.00 0.00 33.04 4.44
4380 4935 5.947228 ATTATGAGCCATATTCACCGTTG 57.053 39.130 0.00 0.00 0.00 4.10
4381 4936 2.779755 TGAGCCATATTCACCGTTGT 57.220 45.000 0.00 0.00 0.00 3.32
4382 4937 2.355197 TGAGCCATATTCACCGTTGTG 58.645 47.619 0.00 0.00 44.18 3.33
4383 4938 2.290008 TGAGCCATATTCACCGTTGTGT 60.290 45.455 0.00 0.00 43.26 3.72
4384 4939 2.747446 GAGCCATATTCACCGTTGTGTT 59.253 45.455 0.00 0.00 43.26 3.32
4385 4940 2.747446 AGCCATATTCACCGTTGTGTTC 59.253 45.455 0.00 0.00 43.26 3.18
4386 4941 2.159435 GCCATATTCACCGTTGTGTTCC 60.159 50.000 0.00 0.00 43.26 3.62
4387 4942 2.422127 CCATATTCACCGTTGTGTTCCC 59.578 50.000 0.00 0.00 43.26 3.97
4388 4943 3.343617 CATATTCACCGTTGTGTTCCCT 58.656 45.455 0.00 0.00 43.26 4.20
4389 4944 1.604604 ATTCACCGTTGTGTTCCCTG 58.395 50.000 0.00 0.00 43.26 4.45
4390 4945 0.253610 TTCACCGTTGTGTTCCCTGT 59.746 50.000 0.00 0.00 43.26 4.00
4391 4946 0.462937 TCACCGTTGTGTTCCCTGTG 60.463 55.000 0.00 0.00 43.26 3.66
4392 4947 1.822186 ACCGTTGTGTTCCCTGTGC 60.822 57.895 0.00 0.00 0.00 4.57
4393 4948 2.551912 CCGTTGTGTTCCCTGTGCC 61.552 63.158 0.00 0.00 0.00 5.01
4394 4949 1.821759 CGTTGTGTTCCCTGTGCCA 60.822 57.895 0.00 0.00 0.00 4.92
4395 4950 1.172180 CGTTGTGTTCCCTGTGCCAT 61.172 55.000 0.00 0.00 0.00 4.40
4396 4951 1.039856 GTTGTGTTCCCTGTGCCATT 58.960 50.000 0.00 0.00 0.00 3.16
4397 4952 1.412343 GTTGTGTTCCCTGTGCCATTT 59.588 47.619 0.00 0.00 0.00 2.32
4398 4953 1.039068 TGTGTTCCCTGTGCCATTTG 58.961 50.000 0.00 0.00 0.00 2.32
4399 4954 0.318120 GTGTTCCCTGTGCCATTTGG 59.682 55.000 0.00 0.00 38.53 3.28
4400 4955 0.831288 TGTTCCCTGTGCCATTTGGG 60.831 55.000 0.00 0.00 40.95 4.12
4422 4977 4.227134 CCCATCTCCGGGCGACTG 62.227 72.222 0.00 0.00 40.07 3.51
4423 4978 3.461773 CCATCTCCGGGCGACTGT 61.462 66.667 0.00 0.00 33.66 3.55
4424 4979 2.579201 CATCTCCGGGCGACTGTT 59.421 61.111 0.00 0.00 33.66 3.16
4425 4980 1.672854 CCATCTCCGGGCGACTGTTA 61.673 60.000 0.00 0.00 33.66 2.41
4426 4981 0.174845 CATCTCCGGGCGACTGTTAA 59.825 55.000 0.00 0.00 33.66 2.01
4427 4982 0.899720 ATCTCCGGGCGACTGTTAAA 59.100 50.000 0.00 0.00 33.66 1.52
4428 4983 0.899720 TCTCCGGGCGACTGTTAAAT 59.100 50.000 0.00 0.00 33.66 1.40
4429 4984 1.276989 TCTCCGGGCGACTGTTAAATT 59.723 47.619 0.00 0.00 33.66 1.82
4430 4985 2.081462 CTCCGGGCGACTGTTAAATTT 58.919 47.619 0.00 0.00 33.66 1.82
4431 4986 2.078392 TCCGGGCGACTGTTAAATTTC 58.922 47.619 0.00 0.00 33.66 2.17
4432 4987 1.201987 CCGGGCGACTGTTAAATTTCG 60.202 52.381 0.00 0.00 33.66 3.46
4433 4988 1.461897 CGGGCGACTGTTAAATTTCGT 59.538 47.619 0.00 0.00 33.95 3.85
4434 4989 2.473376 CGGGCGACTGTTAAATTTCGTC 60.473 50.000 0.00 0.00 35.36 4.20
4435 4990 2.740447 GGGCGACTGTTAAATTTCGTCT 59.260 45.455 0.00 0.00 36.36 4.18
4436 4991 3.187842 GGGCGACTGTTAAATTTCGTCTT 59.812 43.478 0.00 0.00 36.36 3.01
4437 4992 4.319984 GGGCGACTGTTAAATTTCGTCTTT 60.320 41.667 0.00 0.00 36.36 2.52
4438 4993 5.106987 GGGCGACTGTTAAATTTCGTCTTTA 60.107 40.000 0.00 0.00 36.36 1.85
4439 4994 6.365050 GGCGACTGTTAAATTTCGTCTTTAA 58.635 36.000 0.00 0.00 33.36 1.52
4440 4995 7.019418 GGCGACTGTTAAATTTCGTCTTTAAT 58.981 34.615 0.00 0.00 33.36 1.40
4441 4996 7.536281 GGCGACTGTTAAATTTCGTCTTTAATT 59.464 33.333 0.00 0.00 33.36 1.40
4442 4997 8.898792 GCGACTGTTAAATTTCGTCTTTAATTT 58.101 29.630 0.00 0.00 37.61 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.079819 GCTCACTCCAGCGCTTGTA 60.080 57.895 7.50 0.00 0.00 2.41
62 63 3.117776 TGGGCAACTCATGAATAGATGCT 60.118 43.478 13.09 0.00 41.15 3.79
154 155 0.966370 ACAGTCCACTAGGGAGTCGC 60.966 60.000 0.00 0.00 46.98 5.19
190 191 1.070445 CTTTGGGATTTGCTTGTGCCA 59.930 47.619 0.00 0.00 38.71 4.92
208 209 3.903467 AGTCAAACTCCTGGCTTTTCTT 58.097 40.909 0.00 0.00 0.00 2.52
259 268 0.615331 CTTGCTAGACCCTGCTTCCA 59.385 55.000 0.00 0.00 0.00 3.53
276 285 4.220602 ACAACCTGCTGTTTCTTGTTTCTT 59.779 37.500 0.00 0.00 34.00 2.52
277 286 3.763897 ACAACCTGCTGTTTCTTGTTTCT 59.236 39.130 0.00 0.00 34.00 2.52
278 287 4.110036 ACAACCTGCTGTTTCTTGTTTC 57.890 40.909 0.00 0.00 34.00 2.78
279 288 4.494484 GAACAACCTGCTGTTTCTTGTTT 58.506 39.130 0.00 0.00 39.63 2.83
280 289 3.119137 GGAACAACCTGCTGTTTCTTGTT 60.119 43.478 0.00 0.00 39.63 2.83
281 290 2.427095 GGAACAACCTGCTGTTTCTTGT 59.573 45.455 0.00 0.00 39.63 3.16
282 291 2.426738 TGGAACAACCTGCTGTTTCTTG 59.573 45.455 0.00 0.00 39.63 3.02
351 360 1.152631 TGTCTCCACCACTCGACCA 60.153 57.895 0.00 0.00 0.00 4.02
355 366 1.472662 AACCCTGTCTCCACCACTCG 61.473 60.000 0.00 0.00 0.00 4.18
359 370 0.104882 TGGTAACCCTGTCTCCACCA 60.105 55.000 0.00 0.00 33.78 4.17
452 463 1.301716 GTGACCACGGTGTCAGCAT 60.302 57.895 7.45 0.00 45.40 3.79
575 586 5.235305 ACATCAATCGCATGGTTTAGTTC 57.765 39.130 0.00 0.00 0.00 3.01
703 716 6.549433 AAAAATGTGATAATGCTGGATGGT 57.451 33.333 0.00 0.00 0.00 3.55
729 742 5.122239 GCACTTTGAATGGGGCTTTAATTTC 59.878 40.000 0.00 0.00 0.00 2.17
789 806 6.606768 GTTCATGGTTCAGAATTCAGACTTC 58.393 40.000 8.44 0.00 0.00 3.01
882 900 4.290985 TGGACCACAGAAGATAATTGGGAA 59.709 41.667 0.00 0.00 0.00 3.97
896 914 5.882000 TCAATAAGATGAACATGGACCACAG 59.118 40.000 0.00 0.00 0.00 3.66
941 959 7.448161 TCAGTTATCAATGTTGATGAAACCTGT 59.552 33.333 16.40 0.00 46.68 4.00
995 1013 1.482182 TGTCGCTAGATGGCATGACTT 59.518 47.619 3.81 0.00 0.00 3.01
1050 1068 2.143122 CCTTTGTTTAGCAGCTCACGA 58.857 47.619 0.00 0.00 0.00 4.35
1143 1161 0.530431 GTTTTGTGCCCACAGCCTTG 60.530 55.000 1.02 0.00 42.94 3.61
1230 1248 7.041984 GGAGACGAGTTCACTTTATTTTGTTCT 60.042 37.037 0.00 0.00 0.00 3.01
1271 1289 1.933181 GCTTTGTTTTGTCCTTGCCAC 59.067 47.619 0.00 0.00 0.00 5.01
1469 1487 0.955919 CACTTTCCGTTCCTCCTGCC 60.956 60.000 0.00 0.00 0.00 4.85
1525 1543 3.583228 TCTCACTTCCACTACCCTTCAA 58.417 45.455 0.00 0.00 0.00 2.69
1563 1581 7.856145 ATGTTCAGTTTCCATCTTCTGTATC 57.144 36.000 0.00 0.00 0.00 2.24
1572 1590 7.548097 TCACTCTACTATGTTCAGTTTCCATC 58.452 38.462 0.00 0.00 0.00 3.51
1618 1636 3.746045 TGTTTTCTCGCTTCCACTACT 57.254 42.857 0.00 0.00 0.00 2.57
1784 1802 3.389329 TCCAGATTCAGCAATAGGAGGTC 59.611 47.826 0.00 0.00 0.00 3.85
2118 2464 6.139679 TGTTCATCCTGACCTTTTATTCCT 57.860 37.500 0.00 0.00 0.00 3.36
2508 2854 2.320681 TAGTAGGTGCCACTTCTGGT 57.679 50.000 0.00 0.00 40.17 4.00
2838 3185 8.956426 TCAATACCCTGTGACAGAAATAATTTC 58.044 33.333 15.33 0.00 39.96 2.17
2841 3188 7.633789 AGTCAATACCCTGTGACAGAAATAAT 58.366 34.615 15.33 0.00 45.40 1.28
2843 3190 6.620877 AGTCAATACCCTGTGACAGAAATA 57.379 37.500 15.33 3.61 45.40 1.40
2848 3195 4.543590 AGAAGTCAATACCCTGTGACAG 57.456 45.455 5.42 5.42 45.40 3.51
2850 3197 4.020128 AGGAAGAAGTCAATACCCTGTGAC 60.020 45.833 0.00 0.00 43.70 3.67
3198 3722 4.515191 AGCGTTGAGATTGCAGAAAACTAA 59.485 37.500 0.00 0.00 0.00 2.24
3258 3782 4.020928 TGAAAAGATGGCAAATGCATGACT 60.021 37.500 0.00 0.00 44.36 3.41
3369 3910 2.414985 CGCGATTTAGTGTTAACGCAC 58.585 47.619 20.62 5.06 44.96 5.34
3373 3914 2.414138 ACCTGCGCGATTTAGTGTTAAC 59.586 45.455 12.10 0.00 0.00 2.01
3374 3915 2.690786 ACCTGCGCGATTTAGTGTTAA 58.309 42.857 12.10 0.00 0.00 2.01
3382 3923 0.727398 GCTCTTTACCTGCGCGATTT 59.273 50.000 12.10 0.00 0.00 2.17
3383 3924 0.108138 AGCTCTTTACCTGCGCGATT 60.108 50.000 12.10 0.00 0.00 3.34
3387 3928 2.787915 GCAGCTCTTTACCTGCGC 59.212 61.111 0.00 0.00 44.12 6.09
3568 4110 6.961359 AAAAACCCGAAAAGAAAAGTTCTG 57.039 33.333 0.00 0.00 40.59 3.02
3613 4155 2.745821 CACAGCGCCGAGTATATAGGTA 59.254 50.000 2.29 0.00 0.00 3.08
3614 4156 1.540267 CACAGCGCCGAGTATATAGGT 59.460 52.381 2.29 0.00 0.00 3.08
3616 4158 1.200252 AGCACAGCGCCGAGTATATAG 59.800 52.381 2.29 0.00 44.04 1.31
3617 4159 1.068541 CAGCACAGCGCCGAGTATATA 60.069 52.381 2.29 0.00 44.04 0.86
3618 4160 0.319040 CAGCACAGCGCCGAGTATAT 60.319 55.000 2.29 0.00 44.04 0.86
3718 4273 6.073548 GGAAGAATAAATCAGATGGTACGCAG 60.074 42.308 0.00 0.00 0.00 5.18
3724 4279 8.964772 CAAAGAAGGAAGAATAAATCAGATGGT 58.035 33.333 0.00 0.00 0.00 3.55
3739 4294 7.042797 TCAAATTCCAACTCAAAGAAGGAAG 57.957 36.000 0.00 0.00 41.24 3.46
4184 4739 2.357637 CCAGGAGTCAGTTTCGCAAAAA 59.642 45.455 0.00 0.00 0.00 1.94
4185 4740 1.946768 CCAGGAGTCAGTTTCGCAAAA 59.053 47.619 0.00 0.00 0.00 2.44
4186 4741 1.134220 ACCAGGAGTCAGTTTCGCAAA 60.134 47.619 0.00 0.00 0.00 3.68
4187 4742 0.468226 ACCAGGAGTCAGTTTCGCAA 59.532 50.000 0.00 0.00 0.00 4.85
4188 4743 0.468226 AACCAGGAGTCAGTTTCGCA 59.532 50.000 0.00 0.00 0.00 5.10
4189 4744 1.149148 GAACCAGGAGTCAGTTTCGC 58.851 55.000 0.00 0.00 0.00 4.70
4190 4745 2.408050 CAGAACCAGGAGTCAGTTTCG 58.592 52.381 0.00 0.00 0.00 3.46
4191 4746 2.147150 GCAGAACCAGGAGTCAGTTTC 58.853 52.381 0.00 0.00 0.00 2.78
4192 4747 1.202818 GGCAGAACCAGGAGTCAGTTT 60.203 52.381 0.00 0.00 38.86 2.66
4193 4748 0.398318 GGCAGAACCAGGAGTCAGTT 59.602 55.000 0.00 0.00 38.86 3.16
4194 4749 0.472734 AGGCAGAACCAGGAGTCAGT 60.473 55.000 0.00 0.00 43.14 3.41
4195 4750 0.036577 CAGGCAGAACCAGGAGTCAG 60.037 60.000 0.00 0.00 43.14 3.51
4196 4751 0.764369 ACAGGCAGAACCAGGAGTCA 60.764 55.000 0.00 0.00 43.14 3.41
4197 4752 0.321122 CACAGGCAGAACCAGGAGTC 60.321 60.000 0.00 0.00 43.14 3.36
4198 4753 1.757306 CACAGGCAGAACCAGGAGT 59.243 57.895 0.00 0.00 43.14 3.85
4199 4754 1.673665 GCACAGGCAGAACCAGGAG 60.674 63.158 0.00 0.00 43.14 3.69
4200 4755 2.431683 GCACAGGCAGAACCAGGA 59.568 61.111 0.00 0.00 43.14 3.86
4252 4807 3.965379 ACACCCGGTTCAAAAGTTTTT 57.035 38.095 0.00 0.00 0.00 1.94
4253 4808 3.965379 AACACCCGGTTCAAAAGTTTT 57.035 38.095 0.00 0.00 33.35 2.43
4263 4818 3.192633 GCTCATAATTTGAACACCCGGTT 59.807 43.478 0.00 0.00 44.10 4.44
4264 4819 2.752903 GCTCATAATTTGAACACCCGGT 59.247 45.455 0.00 0.00 32.78 5.28
4265 4820 2.099098 GGCTCATAATTTGAACACCCGG 59.901 50.000 0.00 0.00 32.78 5.73
4266 4821 2.752354 TGGCTCATAATTTGAACACCCG 59.248 45.455 0.00 0.00 32.78 5.28
4267 4822 6.655078 ATATGGCTCATAATTTGAACACCC 57.345 37.500 0.00 0.00 32.78 4.61
4268 4823 6.857964 CGAATATGGCTCATAATTTGAACACC 59.142 38.462 0.00 0.00 32.78 4.16
4269 4824 6.360681 GCGAATATGGCTCATAATTTGAACAC 59.639 38.462 0.00 0.00 32.78 3.32
4270 4825 6.437928 GCGAATATGGCTCATAATTTGAACA 58.562 36.000 0.00 0.00 32.78 3.18
4271 4826 5.858581 GGCGAATATGGCTCATAATTTGAAC 59.141 40.000 0.00 0.00 32.78 3.18
4272 4827 5.534278 TGGCGAATATGGCTCATAATTTGAA 59.466 36.000 0.00 0.00 32.78 2.69
4273 4828 5.069318 TGGCGAATATGGCTCATAATTTGA 58.931 37.500 0.00 0.00 35.06 2.69
4274 4829 5.375417 TGGCGAATATGGCTCATAATTTG 57.625 39.130 0.00 0.00 35.06 2.32
4275 4830 6.015180 ACAATGGCGAATATGGCTCATAATTT 60.015 34.615 0.00 0.00 35.06 1.82
4276 4831 5.477984 ACAATGGCGAATATGGCTCATAATT 59.522 36.000 0.00 0.00 35.06 1.40
4277 4832 5.012239 ACAATGGCGAATATGGCTCATAAT 58.988 37.500 0.00 0.00 35.06 1.28
4278 4833 4.216042 CACAATGGCGAATATGGCTCATAA 59.784 41.667 0.00 0.00 35.06 1.90
4279 4834 3.752747 CACAATGGCGAATATGGCTCATA 59.247 43.478 0.00 0.00 35.06 2.15
4280 4835 2.555325 CACAATGGCGAATATGGCTCAT 59.445 45.455 0.00 0.00 35.06 2.90
4281 4836 1.948834 CACAATGGCGAATATGGCTCA 59.051 47.619 0.00 0.00 35.06 4.26
4282 4837 1.949525 ACACAATGGCGAATATGGCTC 59.050 47.619 0.00 0.00 35.06 4.70
4283 4838 2.057137 ACACAATGGCGAATATGGCT 57.943 45.000 0.00 0.00 35.06 4.75
4284 4839 2.543653 GGAACACAATGGCGAATATGGC 60.544 50.000 0.00 0.00 0.00 4.40
4285 4840 2.951642 AGGAACACAATGGCGAATATGG 59.048 45.455 0.00 0.00 0.00 2.74
4286 4841 4.142403 ACAAGGAACACAATGGCGAATATG 60.142 41.667 0.00 0.00 0.00 1.78
4287 4842 4.016444 ACAAGGAACACAATGGCGAATAT 58.984 39.130 0.00 0.00 0.00 1.28
4288 4843 3.190327 CACAAGGAACACAATGGCGAATA 59.810 43.478 0.00 0.00 0.00 1.75
4289 4844 2.030007 CACAAGGAACACAATGGCGAAT 60.030 45.455 0.00 0.00 0.00 3.34
4290 4845 1.336440 CACAAGGAACACAATGGCGAA 59.664 47.619 0.00 0.00 0.00 4.70
4291 4846 0.950836 CACAAGGAACACAATGGCGA 59.049 50.000 0.00 0.00 0.00 5.54
4292 4847 0.664166 GCACAAGGAACACAATGGCG 60.664 55.000 0.00 0.00 0.00 5.69
4293 4848 0.675633 AGCACAAGGAACACAATGGC 59.324 50.000 0.00 0.00 0.00 4.40
4294 4849 1.682854 ACAGCACAAGGAACACAATGG 59.317 47.619 0.00 0.00 0.00 3.16
4295 4850 3.117794 CAACAGCACAAGGAACACAATG 58.882 45.455 0.00 0.00 0.00 2.82
4296 4851 2.101249 CCAACAGCACAAGGAACACAAT 59.899 45.455 0.00 0.00 0.00 2.71
4297 4852 1.476085 CCAACAGCACAAGGAACACAA 59.524 47.619 0.00 0.00 0.00 3.33
4298 4853 1.102154 CCAACAGCACAAGGAACACA 58.898 50.000 0.00 0.00 0.00 3.72
4299 4854 0.249031 GCCAACAGCACAAGGAACAC 60.249 55.000 0.00 0.00 42.97 3.32
4300 4855 2.114638 GCCAACAGCACAAGGAACA 58.885 52.632 0.00 0.00 42.97 3.18
4310 4865 3.163630 TCTTGTTTCAAAGCCAACAGC 57.836 42.857 0.00 0.00 44.25 4.40
4311 4866 4.935702 TGATCTTGTTTCAAAGCCAACAG 58.064 39.130 0.00 0.00 34.43 3.16
4312 4867 4.998671 TGATCTTGTTTCAAAGCCAACA 57.001 36.364 0.00 0.00 0.00 3.33
4313 4868 5.005682 GTGTTGATCTTGTTTCAAAGCCAAC 59.994 40.000 0.00 0.00 38.92 3.77
4314 4869 5.108517 GTGTTGATCTTGTTTCAAAGCCAA 58.891 37.500 0.00 0.00 35.03 4.52
4315 4870 4.159321 TGTGTTGATCTTGTTTCAAAGCCA 59.841 37.500 0.00 0.00 35.03 4.75
4316 4871 4.681744 TGTGTTGATCTTGTTTCAAAGCC 58.318 39.130 0.00 0.00 35.03 4.35
4317 4872 6.476380 TCAATGTGTTGATCTTGTTTCAAAGC 59.524 34.615 0.00 0.00 39.36 3.51
4318 4873 7.488792 TGTCAATGTGTTGATCTTGTTTCAAAG 59.511 33.333 0.00 0.00 45.46 2.77
4319 4874 7.318893 TGTCAATGTGTTGATCTTGTTTCAAA 58.681 30.769 0.00 0.00 45.46 2.69
4320 4875 6.861144 TGTCAATGTGTTGATCTTGTTTCAA 58.139 32.000 0.00 0.00 45.46 2.69
4321 4876 6.448207 TGTCAATGTGTTGATCTTGTTTCA 57.552 33.333 0.00 0.00 45.46 2.69
4322 4877 6.974622 ACTTGTCAATGTGTTGATCTTGTTTC 59.025 34.615 0.00 0.00 45.46 2.78
4323 4878 6.866480 ACTTGTCAATGTGTTGATCTTGTTT 58.134 32.000 0.00 0.00 45.46 2.83
4324 4879 6.455360 ACTTGTCAATGTGTTGATCTTGTT 57.545 33.333 0.00 0.00 45.46 2.83
4325 4880 6.455360 AACTTGTCAATGTGTTGATCTTGT 57.545 33.333 0.00 0.00 45.46 3.16
4326 4881 7.166970 CAGAAACTTGTCAATGTGTTGATCTTG 59.833 37.037 0.00 0.00 45.46 3.02
4327 4882 7.148018 ACAGAAACTTGTCAATGTGTTGATCTT 60.148 33.333 0.00 0.00 45.46 2.40
4328 4883 6.319658 ACAGAAACTTGTCAATGTGTTGATCT 59.680 34.615 0.00 0.00 45.46 2.75
4329 4884 6.498304 ACAGAAACTTGTCAATGTGTTGATC 58.502 36.000 0.00 0.00 45.46 2.92
4330 4885 6.455360 ACAGAAACTTGTCAATGTGTTGAT 57.545 33.333 0.00 0.00 45.46 2.57
4331 4886 5.895636 ACAGAAACTTGTCAATGTGTTGA 57.104 34.783 0.00 0.00 41.89 3.18
4332 4887 6.092092 TGAACAGAAACTTGTCAATGTGTTG 58.908 36.000 5.25 0.00 36.65 3.33
4333 4888 6.266168 TGAACAGAAACTTGTCAATGTGTT 57.734 33.333 1.07 1.07 0.00 3.32
4334 4889 5.895636 TGAACAGAAACTTGTCAATGTGT 57.104 34.783 0.00 0.00 0.00 3.72
4335 4890 7.760131 ATTTGAACAGAAACTTGTCAATGTG 57.240 32.000 0.00 0.00 0.00 3.21
4339 4894 9.734620 CTCATAATTTGAACAGAAACTTGTCAA 57.265 29.630 0.00 0.00 32.78 3.18
4340 4895 7.862372 GCTCATAATTTGAACAGAAACTTGTCA 59.138 33.333 0.00 0.00 32.78 3.58
4341 4896 7.327032 GGCTCATAATTTGAACAGAAACTTGTC 59.673 37.037 0.00 0.00 32.78 3.18
4342 4897 7.147976 GGCTCATAATTTGAACAGAAACTTGT 58.852 34.615 0.00 0.00 32.78 3.16
4343 4898 7.147312 TGGCTCATAATTTGAACAGAAACTTG 58.853 34.615 0.00 0.00 32.78 3.16
4344 4899 7.288810 TGGCTCATAATTTGAACAGAAACTT 57.711 32.000 0.00 0.00 32.78 2.66
4345 4900 6.899393 TGGCTCATAATTTGAACAGAAACT 57.101 33.333 0.00 0.00 32.78 2.66
4346 4901 9.807649 AATATGGCTCATAATTTGAACAGAAAC 57.192 29.630 0.00 0.00 32.78 2.78
4348 4903 9.187996 TGAATATGGCTCATAATTTGAACAGAA 57.812 29.630 0.00 0.00 32.78 3.02
4349 4904 8.623903 GTGAATATGGCTCATAATTTGAACAGA 58.376 33.333 0.00 0.00 32.78 3.41
4350 4905 7.864379 GGTGAATATGGCTCATAATTTGAACAG 59.136 37.037 0.00 0.00 32.78 3.16
4351 4906 7.468494 CGGTGAATATGGCTCATAATTTGAACA 60.468 37.037 0.00 0.00 32.78 3.18
4352 4907 6.857964 CGGTGAATATGGCTCATAATTTGAAC 59.142 38.462 0.00 0.00 32.78 3.18
4353 4908 6.545666 ACGGTGAATATGGCTCATAATTTGAA 59.454 34.615 0.00 0.00 32.78 2.69
4354 4909 6.061441 ACGGTGAATATGGCTCATAATTTGA 58.939 36.000 0.00 0.00 29.74 2.69
4355 4910 6.317789 ACGGTGAATATGGCTCATAATTTG 57.682 37.500 0.00 0.00 29.74 2.32
4356 4911 6.321181 ACAACGGTGAATATGGCTCATAATTT 59.679 34.615 7.88 0.00 29.74 1.82
4357 4912 5.827797 ACAACGGTGAATATGGCTCATAATT 59.172 36.000 7.88 0.00 29.74 1.40
4358 4913 5.376625 ACAACGGTGAATATGGCTCATAAT 58.623 37.500 7.88 0.00 29.74 1.28
4359 4914 4.776349 ACAACGGTGAATATGGCTCATAA 58.224 39.130 7.88 0.00 29.74 1.90
4360 4915 4.415881 ACAACGGTGAATATGGCTCATA 57.584 40.909 7.88 0.00 0.00 2.15
4361 4916 3.281727 ACAACGGTGAATATGGCTCAT 57.718 42.857 7.88 0.00 0.00 2.90
4362 4917 2.779755 ACAACGGTGAATATGGCTCA 57.220 45.000 7.88 0.00 0.00 4.26
4374 4929 1.822186 GCACAGGGAACACAACGGT 60.822 57.895 0.00 0.00 0.00 4.83
4375 4930 2.551912 GGCACAGGGAACACAACGG 61.552 63.158 0.00 0.00 0.00 4.44
4376 4931 1.821759 TGGCACAGGGAACACAACG 60.822 57.895 0.00 0.00 0.00 4.10
4377 4932 4.251246 TGGCACAGGGAACACAAC 57.749 55.556 0.00 0.00 0.00 3.32
4406 4961 1.672854 TAACAGTCGCCCGGAGATGG 61.673 60.000 0.73 1.21 0.00 3.51
4407 4962 0.174845 TTAACAGTCGCCCGGAGATG 59.825 55.000 0.73 5.54 0.00 2.90
4408 4963 0.899720 TTTAACAGTCGCCCGGAGAT 59.100 50.000 0.73 0.00 0.00 2.75
4409 4964 0.899720 ATTTAACAGTCGCCCGGAGA 59.100 50.000 0.73 0.00 0.00 3.71
4410 4965 1.734163 AATTTAACAGTCGCCCGGAG 58.266 50.000 0.73 0.00 0.00 4.63
4411 4966 2.078392 GAAATTTAACAGTCGCCCGGA 58.922 47.619 0.73 0.00 0.00 5.14
4412 4967 1.201987 CGAAATTTAACAGTCGCCCGG 60.202 52.381 0.00 0.00 0.00 5.73
4413 4968 1.461897 ACGAAATTTAACAGTCGCCCG 59.538 47.619 0.00 0.00 36.99 6.13
4414 4969 2.740447 AGACGAAATTTAACAGTCGCCC 59.260 45.455 0.00 0.00 36.99 6.13
4415 4970 4.400036 AAGACGAAATTTAACAGTCGCC 57.600 40.909 0.00 0.00 36.99 5.54
4416 4971 8.431020 AATTAAAGACGAAATTTAACAGTCGC 57.569 30.769 0.00 0.00 35.54 5.19


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

AutoCloner maintained by Alex Coulton.