Multiple sequence alignment - TraesCS7D01G249200

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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 TraesCS7D01G249200 chr7D 100.000 5168 0 0 1 5168 220508596 220513763 0.000000e+00 9544.0
1 TraesCS7D01G249200 chr7D 94.286 245 10 2 2262 2505 295315703 295315462 6.320000e-99 372.0
2 TraesCS7D01G249200 chr7A 95.506 1691 67 4 2505 4191 232746248 232747933 0.000000e+00 2693.0
3 TraesCS7D01G249200 chr7A 92.978 1182 64 10 204 1381 232744062 232745228 0.000000e+00 1705.0
4 TraesCS7D01G249200 chr7A 94.862 798 27 6 1461 2247 232745452 232746246 0.000000e+00 1234.0
5 TraesCS7D01G249200 chr7A 88.717 647 36 18 4527 5168 232748291 232748905 0.000000e+00 756.0
6 TraesCS7D01G249200 chr7A 85.205 365 20 13 4180 4517 232747952 232748309 1.380000e-90 344.0
7 TraesCS7D01G249200 chr7A 93.269 208 13 1 1 207 232743599 232743806 6.500000e-79 305.0
8 TraesCS7D01G249200 chr7A 77.692 130 24 4 4559 4683 427614541 427614670 2.000000e-09 75.0
9 TraesCS7D01G249200 chr7A 83.077 65 9 2 4599 4661 61800773 61800709 2.010000e-04 58.4
10 TraesCS7D01G249200 chr7B 91.210 1422 67 20 1 1381 178418781 178417377 0.000000e+00 1881.0
11 TraesCS7D01G249200 chr7B 94.440 1151 56 3 2505 3653 178416437 178415293 0.000000e+00 1764.0
12 TraesCS7D01G249200 chr7B 94.291 543 23 4 1706 2247 178416974 178416439 0.000000e+00 824.0
13 TraesCS7D01G249200 chr7B 95.374 281 12 1 1414 1693 178417311 178417031 3.670000e-121 446.0
14 TraesCS7D01G249200 chr7B 87.320 347 32 5 3851 4194 178415225 178414888 2.260000e-103 387.0
15 TraesCS7D01G249200 chr7B 82.850 379 21 24 4825 5168 178407795 178407426 3.020000e-77 300.0
16 TraesCS7D01G249200 chr7B 98.649 74 0 1 3768 3841 178415283 178415211 4.200000e-26 130.0
17 TraesCS7D01G249200 chr7B 83.333 78 11 2 4550 4626 228824875 228824799 2.580000e-08 71.3
18 TraesCS7D01G249200 chr6A 98.585 212 3 0 2262 2473 200000801 200000590 4.890000e-100 375.0
19 TraesCS7D01G249200 chr2A 96.889 225 4 3 2262 2484 231350036 231350259 1.760000e-99 374.0
20 TraesCS7D01G249200 chr2A 95.982 224 8 1 2262 2484 231352237 231352460 3.800000e-96 363.0
21 TraesCS7D01G249200 chr5A 93.548 248 11 4 2262 2505 239405863 239405617 1.060000e-96 364.0
22 TraesCS7D01G249200 chr5A 90.182 275 12 5 2262 2521 308178942 308178668 1.380000e-90 344.0
23 TraesCS7D01G249200 chr5A 89.818 275 11 6 2262 2521 308092403 308092131 2.310000e-88 337.0
24 TraesCS7D01G249200 chr3D 93.522 247 13 1 2262 2505 200426945 200427191 1.060000e-96 364.0
25 TraesCS7D01G249200 chr3D 81.579 114 19 2 4557 4669 543933903 543933791 5.510000e-15 93.5
26 TraesCS7D01G249200 chr5B 95.982 224 8 1 2262 2484 711721782 711721559 3.800000e-96 363.0
27 TraesCS7D01G249200 chr3A 94.492 236 7 6 2262 2496 358877310 358877080 4.920000e-95 359.0
28 TraesCS7D01G249200 chr3A 80.972 247 10 12 2275 2508 145256063 145256285 1.490000e-35 161.0
29 TraesCS7D01G249200 chr5D 91.051 257 17 4 2262 2512 526267557 526267301 4.960000e-90 342.0
30 TraesCS7D01G249200 chr5D 85.185 108 13 2 4654 4758 2593682 2593575 1.970000e-19 108.0
31 TraesCS7D01G249200 chr4D 80.687 233 35 7 4535 4761 31335714 31335486 6.880000e-39 172.0
32 TraesCS7D01G249200 chr1B 82.123 179 27 3 4531 4705 397451630 397451453 1.160000e-31 148.0
33 TraesCS7D01G249200 chr1D 82.051 156 24 2 4531 4682 295971242 295971087 4.200000e-26 130.0
34 TraesCS7D01G249200 chr1D 88.889 45 2 3 4555 4598 333332554 333332596 9.000000e-03 52.8
35 TraesCS7D01G249200 chr1A 82.166 157 23 3 4531 4682 368829449 368829293 4.200000e-26 130.0
36 TraesCS7D01G249200 chr1A 79.012 162 30 2 4603 4760 65791011 65790850 1.970000e-19 108.0
37 TraesCS7D01G249200 chr4B 79.769 173 26 3 4595 4758 104812452 104812624 3.270000e-22 117.0
38 TraesCS7D01G249200 chr6D 75.556 225 39 10 4541 4750 333593548 333593771 4.260000e-16 97.1


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 TraesCS7D01G249200 chr7D 220508596 220513763 5167 False 9544.000000 9544 100.000000 1 5168 1 chr7D.!!$F1 5167
1 TraesCS7D01G249200 chr7A 232743599 232748905 5306 False 1172.833333 2693 91.756167 1 5168 6 chr7A.!!$F2 5167
2 TraesCS7D01G249200 chr7B 178414888 178418781 3893 True 905.333333 1881 93.547333 1 4194 6 chr7B.!!$R3 4193
3 TraesCS7D01G249200 chr2A 231350036 231352460 2424 False 368.500000 374 96.435500 2262 2484 2 chr2A.!!$F1 222

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
790 1063 1.202698 ACAAGTGTGGGAGTTCAGAGC 60.203 52.381 0.00 0.0 0.00 4.09 F
856 1136 1.407437 CGGCTTATCCAAGTGCCTTCT 60.407 52.381 0.00 0.0 42.90 2.85 F
1027 1307 1.715931 TCACCAACATCCCCCATCTTT 59.284 47.619 0.00 0.0 0.00 2.52 F
2496 2999 2.370445 GCCCTCCTTCTAGCAGCCA 61.370 63.158 0.00 0.0 0.00 4.75 F
2940 3445 1.428912 TCTGTGGAGGGCCTGAAATTT 59.571 47.619 12.95 0.0 34.31 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2527 0.825010 CCAGCTGCTTTCACCTTGGT 60.825 55.000 8.66 0.00 0.00 3.67 R
2334 2826 3.418047 GCTTACTTGACCCCTAAGCAAA 58.582 45.455 4.20 0.00 41.32 3.68 R
2940 3445 6.681729 ATCTAAACGGCCTAATCTTATGGA 57.318 37.500 0.00 0.00 0.00 3.41 R
3545 4915 0.109153 TCGGCATGCCAGCTTCATAT 59.891 50.000 34.93 0.00 35.37 1.78 R
4851 6369 0.109179 TTCGTACCGGTTCATGTCCG 60.109 55.000 15.04 19.44 46.49 4.79 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
190 192 5.116680 GGTAACGCTAGAAGTATTGTATGCG 59.883 44.000 0.00 0.00 42.45 4.73
247 508 1.656429 CGACTGTTGCGTTTGTGTAGC 60.656 52.381 0.00 0.00 0.00 3.58
406 676 5.592282 TGATAATTCATCGCCCTTTGCTTTA 59.408 36.000 0.00 0.00 36.33 1.85
407 677 4.799564 AATTCATCGCCCTTTGCTTTAA 57.200 36.364 0.00 0.00 38.05 1.52
408 678 3.569250 TTCATCGCCCTTTGCTTTAAC 57.431 42.857 0.00 0.00 38.05 2.01
424 694 7.667043 TGCTTTAACATAAGTTCACTACTGG 57.333 36.000 0.00 0.00 39.15 4.00
486 756 4.083431 CCATTGCTCTCTTGTTCTGTGAAG 60.083 45.833 0.00 0.00 0.00 3.02
551 822 2.163211 GAGAGATCTTGCCTTGGTTTGC 59.837 50.000 0.00 0.00 0.00 3.68
613 885 8.034215 TGGCATTTTCTCTATTTTGGTGTAATG 58.966 33.333 0.00 0.00 0.00 1.90
615 887 8.863049 GCATTTTCTCTATTTTGGTGTAATGTG 58.137 33.333 0.00 0.00 0.00 3.21
616 888 9.912634 CATTTTCTCTATTTTGGTGTAATGTGT 57.087 29.630 0.00 0.00 0.00 3.72
617 889 9.912634 ATTTTCTCTATTTTGGTGTAATGTGTG 57.087 29.630 0.00 0.00 0.00 3.82
618 890 8.684386 TTTCTCTATTTTGGTGTAATGTGTGA 57.316 30.769 0.00 0.00 0.00 3.58
619 891 7.667043 TCTCTATTTTGGTGTAATGTGTGAC 57.333 36.000 0.00 0.00 0.00 3.67
620 892 6.367695 TCTCTATTTTGGTGTAATGTGTGACG 59.632 38.462 0.00 0.00 0.00 4.35
621 893 5.992829 TCTATTTTGGTGTAATGTGTGACGT 59.007 36.000 0.00 0.00 0.00 4.34
622 894 4.966965 TTTTGGTGTAATGTGTGACGTT 57.033 36.364 0.00 0.00 0.00 3.99
623 895 6.621316 ATTTTGGTGTAATGTGTGACGTTA 57.379 33.333 0.00 0.00 0.00 3.18
624 896 6.432607 TTTTGGTGTAATGTGTGACGTTAA 57.567 33.333 0.00 0.00 32.02 2.01
699 971 2.848694 AGATATATGGGAGCATGGGTGG 59.151 50.000 0.00 0.00 0.00 4.61
765 1038 9.294030 CCTCAAAATCTATTGTGAATTTACAGC 57.706 33.333 3.07 0.00 33.86 4.40
790 1063 1.202698 ACAAGTGTGGGAGTTCAGAGC 60.203 52.381 0.00 0.00 0.00 4.09
856 1136 1.407437 CGGCTTATCCAAGTGCCTTCT 60.407 52.381 0.00 0.00 42.90 2.85
1027 1307 1.715931 TCACCAACATCCCCCATCTTT 59.284 47.619 0.00 0.00 0.00 2.52
1130 1429 3.517500 TGTGGATATTGTGGTGCTACAGA 59.482 43.478 0.00 0.00 0.00 3.41
1255 1560 2.823829 GCCTTTCAGGTATGGCGCG 61.824 63.158 0.00 0.00 37.80 6.86
1283 1588 7.319646 TCATGGCTAATTTTTCGCAGTAAATT 58.680 30.769 0.00 0.00 36.98 1.82
1408 1763 2.957680 TGAGCATTTTTCACTTGCCTCA 59.042 40.909 0.00 0.00 37.07 3.86
1409 1764 3.243501 TGAGCATTTTTCACTTGCCTCAC 60.244 43.478 0.00 0.00 37.07 3.51
1444 1810 6.374333 ACAATAACTTGTATTGCGATCCAACT 59.626 34.615 6.09 0.00 43.77 3.16
1456 1822 6.266168 TGCGATCCAACTATTTGACAAAAT 57.734 33.333 4.41 0.00 39.38 1.82
1489 1937 5.467063 AGCAAGAACTAAGAGTTTTCTTCCG 59.533 40.000 0.00 0.00 42.60 4.30
1575 2023 7.040409 GCAAATACCCAATGTTATAGAAGGAGG 60.040 40.741 0.00 0.00 0.00 4.30
1577 2025 3.722101 ACCCAATGTTATAGAAGGAGGGG 59.278 47.826 0.00 0.00 38.09 4.79
1617 2065 3.008049 TGCTCCCTTTTCTACTTCCTCAC 59.992 47.826 0.00 0.00 0.00 3.51
1712 2169 7.863901 ACCTAGTTCCTATCAATCTAATGCT 57.136 36.000 0.00 0.00 0.00 3.79
1713 2170 7.675062 ACCTAGTTCCTATCAATCTAATGCTG 58.325 38.462 0.00 0.00 0.00 4.41
1808 2299 9.678260 ATCAATTATAAGAAGTGGATCATAGGC 57.322 33.333 0.00 0.00 0.00 3.93
1941 2432 8.634335 TCTTGATCTTTAAACATCATCACCAA 57.366 30.769 6.94 0.00 0.00 3.67
1968 2459 9.183368 GATGATCTCAAAGAAGTTCCCTAATTT 57.817 33.333 0.00 0.00 0.00 1.82
2036 2527 4.345859 AACGGTGTGAGGAATGTCTTAA 57.654 40.909 0.00 0.00 0.00 1.85
2248 2740 9.979578 ATCTAAAAATGATTGTTGCAAAGTACA 57.020 25.926 0.00 0.07 0.00 2.90
2249 2741 9.462174 TCTAAAAATGATTGTTGCAAAGTACAG 57.538 29.630 0.00 0.00 0.00 2.74
2250 2742 9.248291 CTAAAAATGATTGTTGCAAAGTACAGT 57.752 29.630 0.00 0.00 0.00 3.55
2252 2744 8.801715 AAAATGATTGTTGCAAAGTACAGTAG 57.198 30.769 0.00 0.00 0.00 2.57
2253 2745 7.744087 AATGATTGTTGCAAAGTACAGTAGA 57.256 32.000 0.00 0.00 0.00 2.59
2254 2746 7.744087 ATGATTGTTGCAAAGTACAGTAGAA 57.256 32.000 0.00 0.00 0.00 2.10
2255 2747 7.561021 TGATTGTTGCAAAGTACAGTAGAAA 57.439 32.000 0.00 0.00 0.00 2.52
2256 2748 7.990917 TGATTGTTGCAAAGTACAGTAGAAAA 58.009 30.769 0.00 0.00 0.00 2.29
2257 2749 7.913297 TGATTGTTGCAAAGTACAGTAGAAAAC 59.087 33.333 0.00 0.00 0.00 2.43
2258 2750 6.995511 TGTTGCAAAGTACAGTAGAAAACT 57.004 33.333 0.00 0.00 39.81 2.66
2290 2782 2.693871 CCTAATGGCCTGGGCTGGT 61.694 63.158 21.72 8.78 41.60 4.00
2334 2826 6.141790 AGGGTTAATTAGAGATAAGGGTCGT 58.858 40.000 0.00 0.00 0.00 4.34
2495 2998 2.508436 GCCCTCCTTCTAGCAGCC 59.492 66.667 0.00 0.00 0.00 4.85
2496 2999 2.370445 GCCCTCCTTCTAGCAGCCA 61.370 63.158 0.00 0.00 0.00 4.75
2521 3024 9.221775 CACATAACAAAAACACTAGAGAAACAC 57.778 33.333 0.00 0.00 0.00 3.32
2940 3445 1.428912 TCTGTGGAGGGCCTGAAATTT 59.571 47.619 12.95 0.00 34.31 1.82
3008 3513 9.255304 GCTTGTCATTTTACAAATTCCTTACAA 57.745 29.630 0.00 0.00 38.81 2.41
3046 3551 7.735326 TTTAGCTATTCTAGAGGTGTTCCTT 57.265 36.000 0.00 0.00 45.24 3.36
3068 3573 8.730680 TCCTTTTTAGTGCTTGTCATTATTCTC 58.269 33.333 0.00 0.00 0.00 2.87
3074 3579 5.879223 AGTGCTTGTCATTATTCTCCTGAAG 59.121 40.000 0.00 0.00 35.44 3.02
3154 3659 2.393764 GATGTTGTGGCCTTGAAAACG 58.606 47.619 3.32 0.00 0.00 3.60
3645 5015 0.536006 ACCAGACAGTCAGCTTTGCC 60.536 55.000 2.66 0.00 0.00 4.52
3684 5138 8.002459 TCCTTCTTAGGGTTAATTTGACAAAGT 58.998 33.333 6.77 6.44 42.26 2.66
3685 5139 8.638873 CCTTCTTAGGGTTAATTTGACAAAGTT 58.361 33.333 6.15 3.98 37.94 2.66
3729 5183 7.098477 CCAGATGATTTGGCTTGTTTCAAATA 58.902 34.615 0.00 0.00 41.80 1.40
3917 5371 6.292274 GCACCAATGAATTAACATATTTGCCG 60.292 38.462 0.00 0.00 0.00 5.69
3963 5418 0.461961 AAGCAGCCTAAGCGACCTAG 59.538 55.000 0.00 0.00 46.67 3.02
3968 5423 3.798202 CAGCCTAAGCGACCTAGAAAAT 58.202 45.455 0.00 0.00 46.67 1.82
3975 5430 5.547181 AAGCGACCTAGAAAATGTTAAGC 57.453 39.130 0.00 0.00 0.00 3.09
3994 5449 2.092646 AGCAACCTACGCCAAATGGATA 60.093 45.455 2.98 0.00 37.39 2.59
4021 5476 4.146443 GCGATTTTCCTTGCATATTTACGC 59.854 41.667 0.00 0.00 0.00 4.42
4048 5503 1.448540 CGGCCCACTGACATCAGAC 60.449 63.158 15.76 2.37 46.59 3.51
4049 5504 1.448540 GGCCCACTGACATCAGACG 60.449 63.158 15.76 6.08 46.59 4.18
4072 5529 0.957395 AACTGCTTGCAGGTGGATCG 60.957 55.000 23.98 0.68 0.00 3.69
4213 5701 1.580994 AATAAGGAGGTGCCACCCCC 61.581 60.000 11.06 8.65 39.75 5.40
4214 5702 2.508216 ATAAGGAGGTGCCACCCCCT 62.508 60.000 11.84 11.84 39.75 4.79
4218 5706 3.569200 GAGGTGCCACCCCCTGTTC 62.569 68.421 11.06 0.00 39.75 3.18
4246 5734 4.024218 GCCTCTGAATCTATTGATGCACAC 60.024 45.833 0.00 0.00 33.46 3.82
4248 5736 5.587443 CCTCTGAATCTATTGATGCACACAA 59.413 40.000 9.94 9.94 33.46 3.33
4272 5760 6.668323 ACAAGTGTAAGATTCGTGGAAATTG 58.332 36.000 0.00 0.00 0.00 2.32
4274 5762 6.481954 AGTGTAAGATTCGTGGAAATTGTC 57.518 37.500 0.00 0.00 0.00 3.18
4276 5764 6.147821 AGTGTAAGATTCGTGGAAATTGTCTG 59.852 38.462 0.00 0.00 0.00 3.51
4291 5779 1.421268 TGTCTGTGCTCATTCCCTGTT 59.579 47.619 0.00 0.00 0.00 3.16
4304 5805 0.593128 CCCTGTTTGTTTGGAGCTCG 59.407 55.000 7.83 0.00 0.00 5.03
4306 5807 0.593128 CTGTTTGTTTGGAGCTCGGG 59.407 55.000 7.83 0.00 0.00 5.14
4317 5818 1.664151 GGAGCTCGGGAAATTTGTACG 59.336 52.381 7.83 0.00 0.00 3.67
4323 5824 4.469552 CTCGGGAAATTTGTACGGAAAAC 58.530 43.478 0.00 0.00 0.00 2.43
4331 5832 7.916977 GGAAATTTGTACGGAAAACAAACTACT 59.083 33.333 0.00 0.00 46.40 2.57
4368 5869 1.008767 CGGATCGACCTAGCGTTCC 60.009 63.158 8.86 8.86 43.34 3.62
4380 5881 3.451894 CGTTCCATTGCTGGGGCC 61.452 66.667 0.00 0.00 43.34 5.80
4444 5958 2.566833 TCCAGACTGAACAATGTGGG 57.433 50.000 3.32 0.00 0.00 4.61
4445 5959 1.774254 TCCAGACTGAACAATGTGGGT 59.226 47.619 3.32 0.00 0.00 4.51
4447 5961 3.392947 TCCAGACTGAACAATGTGGGTAA 59.607 43.478 3.32 0.00 0.00 2.85
4451 5965 2.225017 ACTGAACAATGTGGGTAAGGGG 60.225 50.000 0.00 0.00 0.00 4.79
4452 5966 1.783979 TGAACAATGTGGGTAAGGGGT 59.216 47.619 0.00 0.00 0.00 4.95
4453 5967 2.224917 TGAACAATGTGGGTAAGGGGTC 60.225 50.000 0.00 0.00 0.00 4.46
4454 5968 0.326927 ACAATGTGGGTAAGGGGTCG 59.673 55.000 0.00 0.00 0.00 4.79
4455 5969 0.616371 CAATGTGGGTAAGGGGTCGA 59.384 55.000 0.00 0.00 0.00 4.20
4456 5970 0.616891 AATGTGGGTAAGGGGTCGAC 59.383 55.000 7.13 7.13 0.00 4.20
4472 5986 3.063510 TCGACTACGAGAGGAAGGAAA 57.936 47.619 0.00 0.00 43.81 3.13
4486 6000 4.283467 AGGAAGGAAATGGTTAAAGTTGCC 59.717 41.667 0.00 0.00 0.00 4.52
4498 6012 6.598457 TGGTTAAAGTTGCCGTAATGCTATTA 59.402 34.615 0.00 0.00 0.00 0.98
4499 6013 7.120873 TGGTTAAAGTTGCCGTAATGCTATTAA 59.879 33.333 0.00 0.00 0.00 1.40
4500 6014 7.642586 GGTTAAAGTTGCCGTAATGCTATTAAG 59.357 37.037 0.00 0.00 0.00 1.85
4501 6015 6.995511 AAAGTTGCCGTAATGCTATTAAGA 57.004 33.333 0.00 0.00 0.00 2.10
4502 6016 7.568199 AAAGTTGCCGTAATGCTATTAAGAT 57.432 32.000 0.00 0.00 0.00 2.40
4503 6017 6.545504 AGTTGCCGTAATGCTATTAAGATG 57.454 37.500 0.00 0.00 0.00 2.90
4504 6018 6.288294 AGTTGCCGTAATGCTATTAAGATGA 58.712 36.000 0.00 0.00 0.00 2.92
4505 6019 6.936900 AGTTGCCGTAATGCTATTAAGATGAT 59.063 34.615 0.00 0.00 0.00 2.45
4506 6020 6.726258 TGCCGTAATGCTATTAAGATGATG 57.274 37.500 0.00 0.00 0.00 3.07
4507 6021 6.230472 TGCCGTAATGCTATTAAGATGATGT 58.770 36.000 0.00 0.00 0.00 3.06
4508 6022 6.710295 TGCCGTAATGCTATTAAGATGATGTT 59.290 34.615 0.00 0.00 0.00 2.71
4509 6023 7.095229 TGCCGTAATGCTATTAAGATGATGTTC 60.095 37.037 0.00 0.00 0.00 3.18
4510 6024 7.095229 GCCGTAATGCTATTAAGATGATGTTCA 60.095 37.037 0.00 0.00 0.00 3.18
4511 6025 8.939929 CCGTAATGCTATTAAGATGATGTTCAT 58.060 33.333 0.00 0.00 40.34 2.57
4515 6029 7.514784 TGCTATTAAGATGATGTTCATTGGG 57.485 36.000 0.00 0.00 37.20 4.12
4516 6030 6.016024 TGCTATTAAGATGATGTTCATTGGGC 60.016 38.462 0.00 0.00 37.20 5.36
4517 6031 5.796424 ATTAAGATGATGTTCATTGGGCC 57.204 39.130 0.00 0.00 37.20 5.80
4518 6032 2.077687 AGATGATGTTCATTGGGCCC 57.922 50.000 17.59 17.59 37.20 5.80
4519 6033 0.670162 GATGATGTTCATTGGGCCCG 59.330 55.000 19.37 2.31 37.20 6.13
4520 6034 1.394266 ATGATGTTCATTGGGCCCGC 61.394 55.000 19.37 3.26 32.13 6.13
4521 6035 2.037049 ATGTTCATTGGGCCCGCA 59.963 55.556 19.37 6.62 0.00 5.69
4522 6036 1.603236 GATGTTCATTGGGCCCGCAA 61.603 55.000 19.37 7.25 0.00 4.85
4523 6037 1.190833 ATGTTCATTGGGCCCGCAAA 61.191 50.000 19.37 6.36 0.00 3.68
4524 6038 1.369321 GTTCATTGGGCCCGCAAAA 59.631 52.632 19.37 5.91 0.00 2.44
4525 6039 0.250081 GTTCATTGGGCCCGCAAAAA 60.250 50.000 19.37 5.45 0.00 1.94
4601 6116 8.924511 ATTTATATTGTCGTGAGGATGGAAAT 57.075 30.769 0.00 0.00 0.00 2.17
4604 6119 9.839817 TTATATTGTCGTGAGGATGGAAATTTA 57.160 29.630 0.00 0.00 0.00 1.40
4605 6120 6.683974 ATTGTCGTGAGGATGGAAATTTAG 57.316 37.500 0.00 0.00 0.00 1.85
4606 6121 5.160607 TGTCGTGAGGATGGAAATTTAGT 57.839 39.130 0.00 0.00 0.00 2.24
4608 6123 6.703319 TGTCGTGAGGATGGAAATTTAGTTA 58.297 36.000 0.00 0.00 0.00 2.24
4647 6163 6.913170 TCCTGACAAATAACTGAATTGAAGC 58.087 36.000 0.00 0.00 0.00 3.86
4648 6164 5.796935 CCTGACAAATAACTGAATTGAAGCG 59.203 40.000 0.00 0.00 0.00 4.68
4652 6168 6.555315 ACAAATAACTGAATTGAAGCGGATC 58.445 36.000 0.00 0.00 0.00 3.36
4669 6185 3.282021 GGATCTGCCATGCTTGTCTAAA 58.718 45.455 0.00 0.00 36.34 1.85
4683 6199 6.542005 TGCTTGTCTAAACTTGTCATTCTCAA 59.458 34.615 0.00 0.00 0.00 3.02
4685 6201 7.254932 GCTTGTCTAAACTTGTCATTCTCAACT 60.255 37.037 0.00 0.00 0.00 3.16
4739 6257 3.567473 GCTTCCCAGCTGACGTTC 58.433 61.111 17.39 0.00 43.51 3.95
4741 6259 2.357034 TTCCCAGCTGACGTTCGC 60.357 61.111 17.39 0.00 0.00 4.70
4807 6325 2.673610 GCGGAATTGCAGTGCCAAAATA 60.674 45.455 13.72 0.00 34.15 1.40
4823 6341 6.039616 GCCAAAATACCGCTCAAATTTATCA 58.960 36.000 0.00 0.00 0.00 2.15
4885 6403 0.605083 ACGAAGATGACAGCAGAGCA 59.395 50.000 0.00 0.00 0.00 4.26
4886 6404 1.206610 ACGAAGATGACAGCAGAGCAT 59.793 47.619 0.00 0.00 0.00 3.79
4887 6405 1.593469 CGAAGATGACAGCAGAGCATG 59.407 52.381 0.00 0.00 0.00 4.06
4888 6406 2.630158 GAAGATGACAGCAGAGCATGT 58.370 47.619 0.00 0.00 0.00 3.21
4889 6407 2.025589 AGATGACAGCAGAGCATGTG 57.974 50.000 0.00 0.00 0.00 3.21
4952 6470 1.202188 CGAGTGATTAGCGCAGAGACA 60.202 52.381 11.47 0.00 0.00 3.41
5005 6523 3.958860 AGTGGCTGGCTCCGCTTT 61.959 61.111 2.00 0.00 44.01 3.51
5013 6531 4.416738 GCTCCGCTTTGCCCCTCT 62.417 66.667 0.00 0.00 0.00 3.69
5014 6532 2.124942 CTCCGCTTTGCCCCTCTC 60.125 66.667 0.00 0.00 0.00 3.20
5015 6533 4.082523 TCCGCTTTGCCCCTCTCG 62.083 66.667 0.00 0.00 0.00 4.04
5017 6535 4.767255 CGCTTTGCCCCTCTCGCT 62.767 66.667 0.00 0.00 0.00 4.93
5018 6536 2.821810 GCTTTGCCCCTCTCGCTC 60.822 66.667 0.00 0.00 0.00 5.03
5019 6537 2.985456 CTTTGCCCCTCTCGCTCT 59.015 61.111 0.00 0.00 0.00 4.09
5020 6538 1.153469 CTTTGCCCCTCTCGCTCTC 60.153 63.158 0.00 0.00 0.00 3.20
5021 6539 1.610673 TTTGCCCCTCTCGCTCTCT 60.611 57.895 0.00 0.00 0.00 3.10
5022 6540 1.608717 TTTGCCCCTCTCGCTCTCTC 61.609 60.000 0.00 0.00 0.00 3.20
5023 6541 2.123897 GCCCCTCTCGCTCTCTCT 60.124 66.667 0.00 0.00 0.00 3.10
5024 6542 2.193536 GCCCCTCTCGCTCTCTCTC 61.194 68.421 0.00 0.00 0.00 3.20
5025 6543 1.531748 CCCCTCTCGCTCTCTCTCT 59.468 63.158 0.00 0.00 0.00 3.10
5026 6544 0.535102 CCCCTCTCGCTCTCTCTCTC 60.535 65.000 0.00 0.00 0.00 3.20
5027 6545 0.469917 CCCTCTCGCTCTCTCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
5028 6546 1.541233 CCCTCTCGCTCTCTCTCTCTC 60.541 61.905 0.00 0.00 0.00 3.20
5029 6547 1.414181 CCTCTCGCTCTCTCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
5030 6548 2.158900 CCTCTCGCTCTCTCTCTCTCTT 60.159 54.545 0.00 0.00 0.00 2.85
5031 6549 3.126831 CTCTCGCTCTCTCTCTCTCTTC 58.873 54.545 0.00 0.00 0.00 2.87
5054 6572 1.188219 TGAGCCCTCTGTCACTCCAC 61.188 60.000 0.00 0.00 0.00 4.02
5061 6579 1.210413 CTGTCACTCCACGAGTCCG 59.790 63.158 0.00 0.00 41.37 4.79
5085 6606 1.671054 GACAGGTAAAGCCGCTGCA 60.671 57.895 2.05 0.00 43.70 4.41
5093 6614 0.471617 AAAGCCGCTGCATCCTAGAT 59.528 50.000 2.05 0.00 41.13 1.98
5138 6659 3.300765 GCAGCAGCAACCAAGCCT 61.301 61.111 0.00 0.00 41.58 4.58
5154 6675 2.496817 CTTCCTTCCTCCTCGCCG 59.503 66.667 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 0.323999 TGGATCTGGCATGCAGCTTT 60.324 50.000 21.36 0.00 44.79 3.51
247 508 5.699458 CGGGCTTACATAAATAGGTTACAGG 59.301 44.000 0.00 0.00 0.00 4.00
391 661 5.185056 AACTTATGTTAAAGCAAAGGGCGAT 59.815 36.000 0.00 0.00 40.41 4.58
406 676 6.062095 AGCAAACCAGTAGTGAACTTATGTT 58.938 36.000 0.00 0.00 35.76 2.71
407 677 5.621193 AGCAAACCAGTAGTGAACTTATGT 58.379 37.500 0.00 0.00 35.76 2.29
408 678 5.122396 GGAGCAAACCAGTAGTGAACTTATG 59.878 44.000 0.00 0.00 35.76 1.90
424 694 2.440409 ACATCCATGACAGGAGCAAAC 58.560 47.619 0.00 0.00 41.90 2.93
529 800 3.683802 CAAACCAAGGCAAGATCTCTCT 58.316 45.455 0.00 0.00 0.00 3.10
551 822 3.134458 GTGGTCCACAGAACTCAGAAAG 58.866 50.000 17.59 0.00 34.08 2.62
613 885 7.270579 GCCTCTGAAAATTAATTAACGTCACAC 59.729 37.037 0.01 0.00 0.00 3.82
615 887 7.302524 TGCCTCTGAAAATTAATTAACGTCAC 58.697 34.615 0.01 0.00 0.00 3.67
616 888 7.389330 TCTGCCTCTGAAAATTAATTAACGTCA 59.611 33.333 0.01 3.97 0.00 4.35
617 889 7.748847 TCTGCCTCTGAAAATTAATTAACGTC 58.251 34.615 0.01 0.00 0.00 4.34
618 890 7.681939 TCTGCCTCTGAAAATTAATTAACGT 57.318 32.000 0.01 0.00 0.00 3.99
619 891 8.850452 GTTTCTGCCTCTGAAAATTAATTAACG 58.150 33.333 0.01 0.00 34.21 3.18
620 892 9.691362 TGTTTCTGCCTCTGAAAATTAATTAAC 57.309 29.630 0.01 0.00 34.21 2.01
623 895 9.211485 CAATGTTTCTGCCTCTGAAAATTAATT 57.789 29.630 0.00 0.00 34.21 1.40
624 896 8.587608 TCAATGTTTCTGCCTCTGAAAATTAAT 58.412 29.630 1.43 0.00 34.21 1.40
670 942 8.443176 CCCATGCTCCCATATATCTGTTTATAT 58.557 37.037 0.00 0.00 0.00 0.86
681 953 2.431687 TCCACCCATGCTCCCATATA 57.568 50.000 0.00 0.00 0.00 0.86
706 978 4.678509 TTTTATGTTCGCTGTGATGTCC 57.321 40.909 0.00 0.00 0.00 4.02
715 988 6.348213 GGTGTTGACTGTATTTTATGTTCGCT 60.348 38.462 0.00 0.00 0.00 4.93
765 1038 3.659786 TGAACTCCCACACTTGTTATCG 58.340 45.455 0.00 0.00 0.00 2.92
790 1063 6.648310 CCATCTGTAGTGCTGTAAGAATATGG 59.352 42.308 0.00 0.00 34.07 2.74
856 1136 2.429930 CAGCTGACGGTCCCCAAA 59.570 61.111 8.42 0.00 0.00 3.28
915 1195 4.816925 GGAAAAAGACACAGCTCACTAGTT 59.183 41.667 0.00 0.00 0.00 2.24
964 1244 4.142491 CGCCTTGTTTGAATGCCAGTAATA 60.142 41.667 0.00 0.00 0.00 0.98
1027 1307 0.415429 AAGAAGCTGGAGGAGGAGGA 59.585 55.000 0.00 0.00 0.00 3.71
1101 1400 5.532406 AGCACCACAATATCCACATGTTATC 59.468 40.000 0.00 0.00 0.00 1.75
1130 1429 4.263112 GCCTTCCCAGTTCTTCTTCTACTT 60.263 45.833 0.00 0.00 0.00 2.24
1255 1560 4.923281 ACTGCGAAAAATTAGCCATGAAAC 59.077 37.500 0.00 0.00 0.00 2.78
1283 1588 4.022676 TGTTCTCGACATTACAGTGCTACA 60.023 41.667 0.00 0.00 32.00 2.74
1341 1646 3.741344 AGCAACGTTCTCATTGTACAGAC 59.259 43.478 0.00 0.00 0.00 3.51
1390 1745 3.375782 AGTGAGGCAAGTGAAAAATGC 57.624 42.857 0.00 0.00 39.33 3.56
1464 1830 6.645415 CGGAAGAAAACTCTTAGTTCTTGCTA 59.355 38.462 12.84 0.00 43.52 3.49
1479 1927 7.964604 ATATATTAGCAGACCGGAAGAAAAC 57.035 36.000 9.46 0.00 0.00 2.43
1489 1937 5.070001 TGGCCAACAATATATTAGCAGACC 58.930 41.667 0.61 0.00 0.00 3.85
1575 2023 0.598419 GAGCAACAGCAGCAAAACCC 60.598 55.000 0.00 0.00 0.00 4.11
1577 2025 1.484356 CAGAGCAACAGCAGCAAAAC 58.516 50.000 0.00 0.00 0.00 2.43
1617 2065 1.145759 ACGCACTCGCCATATCAACG 61.146 55.000 0.00 0.00 39.84 4.10
1712 2169 7.987750 TGCTCACATAAATGTAGGTTTAACA 57.012 32.000 0.00 0.00 39.39 2.41
1713 2170 9.855021 AAATGCTCACATAAATGTAGGTTTAAC 57.145 29.630 0.00 0.00 39.39 2.01
1787 2278 7.387265 TTGGCCTATGATCCACTTCTTATAA 57.613 36.000 3.32 0.00 30.97 0.98
1808 2299 8.183104 TCTAGGTCATACTCATACTTGATTGG 57.817 38.462 0.00 0.00 0.00 3.16
1898 2389 8.429641 AGATCAAGAAACAACTACCTCAAAGTA 58.570 33.333 0.00 0.00 0.00 2.24
1941 2432 7.502060 TTAGGGAACTTCTTTGAGATCATCT 57.498 36.000 0.00 0.00 43.67 2.90
1968 2459 2.642311 TCAGCCCTACAAAGTCAATCCA 59.358 45.455 0.00 0.00 0.00 3.41
2036 2527 0.825010 CCAGCTGCTTTCACCTTGGT 60.825 55.000 8.66 0.00 0.00 3.67
2157 2648 7.712639 TCATTAGCCTTTTAAACACATGCAAAA 59.287 29.630 0.00 0.00 0.00 2.44
2248 2740 5.640783 GCCCATTACGTAACAGTTTTCTACT 59.359 40.000 10.81 0.00 37.68 2.57
2249 2741 5.163824 GGCCCATTACGTAACAGTTTTCTAC 60.164 44.000 10.81 0.00 0.00 2.59
2250 2742 4.937015 GGCCCATTACGTAACAGTTTTCTA 59.063 41.667 10.81 0.00 0.00 2.10
2251 2743 3.754850 GGCCCATTACGTAACAGTTTTCT 59.245 43.478 10.81 0.00 0.00 2.52
2252 2744 3.754850 AGGCCCATTACGTAACAGTTTTC 59.245 43.478 10.81 0.00 0.00 2.29
2253 2745 3.758425 AGGCCCATTACGTAACAGTTTT 58.242 40.909 10.81 0.00 0.00 2.43
2254 2746 3.428413 AGGCCCATTACGTAACAGTTT 57.572 42.857 10.81 0.00 0.00 2.66
2255 2747 4.556592 TTAGGCCCATTACGTAACAGTT 57.443 40.909 10.81 0.00 0.00 3.16
2256 2748 4.448210 CATTAGGCCCATTACGTAACAGT 58.552 43.478 10.81 0.00 0.00 3.55
2257 2749 3.813166 CCATTAGGCCCATTACGTAACAG 59.187 47.826 10.81 6.39 0.00 3.16
2258 2750 3.811083 CCATTAGGCCCATTACGTAACA 58.189 45.455 10.81 0.00 0.00 2.41
2290 2782 4.147321 CCTAAGACTAACGGGCTATACCA 58.853 47.826 0.00 0.00 42.05 3.25
2334 2826 3.418047 GCTTACTTGACCCCTAAGCAAA 58.582 45.455 4.20 0.00 41.32 3.68
2393 2885 8.435187 TGCTTGATTAGATTGATACATCTCCTT 58.565 33.333 0.00 0.00 0.00 3.36
2495 2998 9.221775 GTGTTTCTCTAGTGTTTTTGTTATGTG 57.778 33.333 0.00 0.00 0.00 3.21
2496 2999 9.174166 AGTGTTTCTCTAGTGTTTTTGTTATGT 57.826 29.630 0.00 0.00 0.00 2.29
2521 3024 7.871853 TGCAAGATATTGTCATCAATCATCAG 58.128 34.615 1.46 0.70 42.45 2.90
2940 3445 6.681729 ATCTAAACGGCCTAATCTTATGGA 57.318 37.500 0.00 0.00 0.00 3.41
3033 3538 5.562298 AGCACTAAAAAGGAACACCTCTA 57.438 39.130 0.00 0.00 32.98 2.43
3046 3551 7.882791 TCAGGAGAATAATGACAAGCACTAAAA 59.117 33.333 0.00 0.00 0.00 1.52
3068 3573 4.393062 ACATGAGAAATGCGTTACTTCAGG 59.607 41.667 0.00 8.95 0.00 3.86
3074 3579 4.330074 AGTGCTACATGAGAAATGCGTTAC 59.670 41.667 0.00 0.00 0.00 2.50
3154 3659 2.549064 AGCCCTTTTTGCCAAATGAC 57.451 45.000 0.00 0.00 0.00 3.06
3544 4914 0.240145 CGGCATGCCAGCTTCATATG 59.760 55.000 34.93 11.86 35.37 1.78
3545 4915 0.109153 TCGGCATGCCAGCTTCATAT 59.891 50.000 34.93 0.00 35.37 1.78
3547 4917 0.109153 TATCGGCATGCCAGCTTCAT 59.891 50.000 34.93 17.90 35.37 2.57
3684 5138 7.855784 TCTGGCTCTAAGATGGTCATAATAA 57.144 36.000 0.00 0.00 0.00 1.40
3685 5139 7.845037 CATCTGGCTCTAAGATGGTCATAATA 58.155 38.462 5.67 0.00 44.83 0.98
3686 5140 6.709281 CATCTGGCTCTAAGATGGTCATAAT 58.291 40.000 5.67 0.00 44.83 1.28
3721 5175 9.632638 AAGCCATCTTATCTAGCTTATTTGAAA 57.367 29.630 0.00 0.00 41.76 2.69
3756 5210 7.679025 ACCCCTAGAACTATTCTGAGTTTTACT 59.321 37.037 1.26 0.00 39.79 2.24
3917 5371 3.938963 TGTCACCAAAAGTTCAGTCAGAC 59.061 43.478 0.00 0.00 0.00 3.51
3963 5418 4.163552 GGCGTAGGTTGCTTAACATTTTC 58.836 43.478 0.00 0.00 0.00 2.29
3968 5423 2.257691 TTGGCGTAGGTTGCTTAACA 57.742 45.000 0.00 0.00 0.00 2.41
3975 5430 5.334879 GCTAATATCCATTTGGCGTAGGTTG 60.335 44.000 0.00 0.00 34.44 3.77
3994 5449 7.803189 CGTAAATATGCAAGGAAAATCGCTAAT 59.197 33.333 0.00 0.00 0.00 1.73
4021 5476 3.402681 AGTGGGCCGATCACCTGG 61.403 66.667 6.97 0.00 35.87 4.45
4048 5503 0.110056 CACCTGCAAGCAGTTTAGCG 60.110 55.000 19.60 6.74 42.15 4.26
4049 5504 0.242017 CCACCTGCAAGCAGTTTAGC 59.758 55.000 19.60 0.00 42.15 3.09
4072 5529 1.394227 CTCGTCCTCCGCGTAGATATC 59.606 57.143 4.92 0.00 36.19 1.63
4090 5547 4.877323 AGTCGGCGAAAAATTTATCCTC 57.123 40.909 12.92 0.00 0.00 3.71
4213 5701 1.915078 ATTCAGAGGCCGGGGAACAG 61.915 60.000 2.18 0.00 0.00 3.16
4214 5702 1.910580 GATTCAGAGGCCGGGGAACA 61.911 60.000 2.18 0.00 0.00 3.18
4218 5706 1.059913 AATAGATTCAGAGGCCGGGG 58.940 55.000 2.18 0.00 0.00 5.73
4246 5734 5.666969 TTCCACGAATCTTACACTTGTTG 57.333 39.130 0.00 0.00 0.00 3.33
4248 5736 6.262273 ACAATTTCCACGAATCTTACACTTGT 59.738 34.615 0.00 0.00 0.00 3.16
4272 5760 2.191128 AACAGGGAATGAGCACAGAC 57.809 50.000 0.00 0.00 0.00 3.51
4274 5762 2.233271 ACAAACAGGGAATGAGCACAG 58.767 47.619 0.00 0.00 0.00 3.66
4276 5764 3.383761 CAAACAAACAGGGAATGAGCAC 58.616 45.455 0.00 0.00 0.00 4.40
4291 5779 2.286365 ATTTCCCGAGCTCCAAACAA 57.714 45.000 8.47 0.00 0.00 2.83
4304 5805 6.044046 AGTTTGTTTTCCGTACAAATTTCCC 58.956 36.000 0.00 0.00 44.52 3.97
4306 5807 8.739461 CAGTAGTTTGTTTTCCGTACAAATTTC 58.261 33.333 0.00 0.00 44.52 2.17
4331 5832 0.953727 GTGCATGAGCCAGACAAACA 59.046 50.000 0.00 0.00 41.13 2.83
4342 5843 0.668535 TAGGTCGATCCGTGCATGAG 59.331 55.000 7.72 0.00 41.99 2.90
4380 5881 2.325666 AAAACGGACCAACAACGGCG 62.326 55.000 4.80 4.80 0.00 6.46
4382 5883 0.452585 ACAAAACGGACCAACAACGG 59.547 50.000 0.00 0.00 0.00 4.44
4383 5884 1.914700 CAACAAAACGGACCAACAACG 59.085 47.619 0.00 0.00 0.00 4.10
4384 5885 2.918600 GTCAACAAAACGGACCAACAAC 59.081 45.455 0.00 0.00 0.00 3.32
4385 5886 2.557056 TGTCAACAAAACGGACCAACAA 59.443 40.909 0.00 0.00 0.00 2.83
4386 5887 2.160205 TGTCAACAAAACGGACCAACA 58.840 42.857 0.00 0.00 0.00 3.33
4387 5888 2.923605 TGTCAACAAAACGGACCAAC 57.076 45.000 0.00 0.00 0.00 3.77
4444 5958 1.939255 CTCTCGTAGTCGACCCCTTAC 59.061 57.143 13.01 7.27 41.35 2.34
4445 5959 1.134280 CCTCTCGTAGTCGACCCCTTA 60.134 57.143 13.01 0.00 41.35 2.69
4447 5961 1.224039 CCTCTCGTAGTCGACCCCT 59.776 63.158 13.01 0.00 41.35 4.79
4451 5965 2.021355 TCCTTCCTCTCGTAGTCGAC 57.979 55.000 7.70 7.70 41.35 4.20
4452 5966 2.775911 TTCCTTCCTCTCGTAGTCGA 57.224 50.000 0.00 0.00 44.12 4.20
4453 5967 3.489398 CCATTTCCTTCCTCTCGTAGTCG 60.489 52.174 0.00 0.00 38.55 4.18
4454 5968 3.447944 ACCATTTCCTTCCTCTCGTAGTC 59.552 47.826 0.00 0.00 0.00 2.59
4455 5969 3.442076 ACCATTTCCTTCCTCTCGTAGT 58.558 45.455 0.00 0.00 0.00 2.73
4456 5970 4.473477 AACCATTTCCTTCCTCTCGTAG 57.527 45.455 0.00 0.00 0.00 3.51
4472 5986 3.761752 AGCATTACGGCAACTTTAACCAT 59.238 39.130 0.00 0.00 35.83 3.55
4498 6012 2.391678 GGGCCCAATGAACATCATCTT 58.608 47.619 19.95 0.00 35.76 2.40
4499 6013 1.751733 CGGGCCCAATGAACATCATCT 60.752 52.381 24.92 0.00 35.76 2.90
4500 6014 0.670162 CGGGCCCAATGAACATCATC 59.330 55.000 24.92 0.00 35.76 2.92
4501 6015 1.394266 GCGGGCCCAATGAACATCAT 61.394 55.000 24.92 0.00 39.09 2.45
4502 6016 2.051518 GCGGGCCCAATGAACATCA 61.052 57.895 24.92 0.00 0.00 3.07
4503 6017 1.603236 TTGCGGGCCCAATGAACATC 61.603 55.000 24.92 0.00 0.00 3.06
4504 6018 1.190833 TTTGCGGGCCCAATGAACAT 61.191 50.000 24.92 0.00 0.00 2.71
4505 6019 1.402896 TTTTGCGGGCCCAATGAACA 61.403 50.000 24.92 6.55 0.00 3.18
4506 6020 0.250081 TTTTTGCGGGCCCAATGAAC 60.250 50.000 24.92 3.64 0.00 3.18
4507 6021 2.136791 TTTTTGCGGGCCCAATGAA 58.863 47.368 24.92 8.14 0.00 2.57
4508 6022 3.876873 TTTTTGCGGGCCCAATGA 58.123 50.000 24.92 0.89 0.00 2.57
4525 6039 4.566070 CCCTGCCCAATGAACATCATTTTT 60.566 41.667 2.93 0.00 44.03 1.94
4538 6052 2.292389 TGATTTGTCATCCCTGCCCAAT 60.292 45.455 0.00 0.00 0.00 3.16
4541 6055 1.851304 TTGATTTGTCATCCCTGCCC 58.149 50.000 0.00 0.00 0.00 5.36
4576 6091 8.924511 ATTTCCATCCTCACGACAATATAAAT 57.075 30.769 0.00 0.00 0.00 1.40
4589 6104 6.095440 GCTTGCTAACTAAATTTCCATCCTCA 59.905 38.462 0.00 0.00 0.00 3.86
4591 6106 5.951747 TGCTTGCTAACTAAATTTCCATCCT 59.048 36.000 0.00 0.00 0.00 3.24
4601 6116 1.885560 TGCCGTGCTTGCTAACTAAA 58.114 45.000 0.00 0.00 0.00 1.85
4604 6119 1.200020 GATTTGCCGTGCTTGCTAACT 59.800 47.619 0.00 0.00 0.00 2.24
4605 6120 1.617740 GATTTGCCGTGCTTGCTAAC 58.382 50.000 0.00 0.00 0.00 2.34
4606 6121 0.525761 GGATTTGCCGTGCTTGCTAA 59.474 50.000 0.00 0.00 0.00 3.09
4608 6123 1.604593 AGGATTTGCCGTGCTTGCT 60.605 52.632 0.00 0.00 43.43 3.91
4647 6163 0.463295 AGACAAGCATGGCAGATCCG 60.463 55.000 0.00 0.00 36.86 4.18
4648 6164 2.627515 TAGACAAGCATGGCAGATCC 57.372 50.000 0.00 0.00 36.86 3.36
4652 6168 3.254166 ACAAGTTTAGACAAGCATGGCAG 59.746 43.478 0.00 0.00 36.86 4.85
4705 6221 3.679502 GGAAGCATGGCAATTACAAACAC 59.320 43.478 0.00 0.00 0.00 3.32
4707 6223 3.261580 GGGAAGCATGGCAATTACAAAC 58.738 45.455 0.00 0.00 0.00 2.93
4711 6227 1.202452 GCTGGGAAGCATGGCAATTAC 60.202 52.381 0.00 0.00 34.41 1.89
4712 6228 1.113788 GCTGGGAAGCATGGCAATTA 58.886 50.000 0.00 0.00 34.41 1.40
4741 6259 2.027469 ACTTTAGGACCGGCTTAACCAG 60.027 50.000 0.00 0.12 39.03 4.00
4786 6304 0.599728 TTTTGGCACTGCAATTCCGC 60.600 50.000 2.82 0.00 0.00 5.54
4807 6325 5.975693 TTTTCCTGATAAATTTGAGCGGT 57.024 34.783 0.00 0.00 0.00 5.68
4848 6366 3.021473 TACCGGTTCATGTCCGCCC 62.021 63.158 15.04 3.57 45.71 6.13
4849 6367 1.812507 GTACCGGTTCATGTCCGCC 60.813 63.158 15.04 10.62 45.71 6.13
4850 6368 2.162754 CGTACCGGTTCATGTCCGC 61.163 63.158 15.04 10.47 45.71 5.54
4851 6369 0.109179 TTCGTACCGGTTCATGTCCG 60.109 55.000 15.04 19.44 46.49 4.79
4860 6378 0.172803 GCTGTCATCTTCGTACCGGT 59.827 55.000 13.98 13.98 0.00 5.28
4872 6390 2.289565 CATCACATGCTCTGCTGTCAT 58.710 47.619 0.00 0.00 0.00 3.06
5005 6523 2.441164 GAGAGAGCGAGAGGGGCA 60.441 66.667 0.00 0.00 0.00 5.36
5007 6525 0.535102 GAGAGAGAGAGCGAGAGGGG 60.535 65.000 0.00 0.00 0.00 4.79
5008 6526 0.469917 AGAGAGAGAGAGCGAGAGGG 59.530 60.000 0.00 0.00 0.00 4.30
5009 6527 1.414181 AGAGAGAGAGAGAGCGAGAGG 59.586 57.143 0.00 0.00 0.00 3.69
5010 6528 2.898729 AGAGAGAGAGAGAGCGAGAG 57.101 55.000 0.00 0.00 0.00 3.20
5011 6529 2.158957 GGAAGAGAGAGAGAGAGCGAGA 60.159 54.545 0.00 0.00 0.00 4.04
5012 6530 2.213499 GGAAGAGAGAGAGAGAGCGAG 58.787 57.143 0.00 0.00 0.00 5.03
5013 6531 1.134220 GGGAAGAGAGAGAGAGAGCGA 60.134 57.143 0.00 0.00 0.00 4.93
5014 6532 1.308998 GGGAAGAGAGAGAGAGAGCG 58.691 60.000 0.00 0.00 0.00 5.03
5015 6533 1.215423 AGGGGAAGAGAGAGAGAGAGC 59.785 57.143 0.00 0.00 0.00 4.09
5016 6534 2.509548 TCAGGGGAAGAGAGAGAGAGAG 59.490 54.545 0.00 0.00 0.00 3.20
5017 6535 2.509548 CTCAGGGGAAGAGAGAGAGAGA 59.490 54.545 0.00 0.00 35.09 3.10
5018 6536 2.936202 CTCAGGGGAAGAGAGAGAGAG 58.064 57.143 0.00 0.00 35.09 3.20
5019 6537 1.064017 GCTCAGGGGAAGAGAGAGAGA 60.064 57.143 0.00 0.00 35.09 3.10
5020 6538 1.402787 GCTCAGGGGAAGAGAGAGAG 58.597 60.000 0.00 0.00 35.09 3.20
5021 6539 0.032615 GGCTCAGGGGAAGAGAGAGA 60.033 60.000 0.00 0.00 35.09 3.10
5022 6540 1.048160 GGGCTCAGGGGAAGAGAGAG 61.048 65.000 0.00 0.00 35.09 3.20
5023 6541 1.002274 GGGCTCAGGGGAAGAGAGA 59.998 63.158 0.00 0.00 35.09 3.10
5024 6542 1.002792 AGGGCTCAGGGGAAGAGAG 59.997 63.158 0.00 0.00 35.09 3.20
5025 6543 1.002274 GAGGGCTCAGGGGAAGAGA 59.998 63.158 0.00 0.00 35.09 3.10
5026 6544 1.002792 AGAGGGCTCAGGGGAAGAG 59.997 63.158 0.00 0.00 36.21 2.85
5027 6545 1.306482 CAGAGGGCTCAGGGGAAGA 60.306 63.158 0.00 0.00 0.00 2.87
5028 6546 1.614824 ACAGAGGGCTCAGGGGAAG 60.615 63.158 0.00 0.00 0.00 3.46
5029 6547 1.613630 GACAGAGGGCTCAGGGGAA 60.614 63.158 0.00 0.00 0.00 3.97
5030 6548 2.039624 GACAGAGGGCTCAGGGGA 59.960 66.667 0.00 0.00 0.00 4.81
5031 6549 2.284921 TGACAGAGGGCTCAGGGG 60.285 66.667 0.00 0.00 0.00 4.79
5054 6572 1.139734 CCTGTCATGGACGGACTCG 59.860 63.158 6.77 0.00 41.05 4.18
5061 6579 1.369625 CGGCTTTACCTGTCATGGAC 58.630 55.000 0.00 0.00 35.61 4.02
5063 6581 0.392998 AGCGGCTTTACCTGTCATGG 60.393 55.000 0.00 0.00 35.61 3.66
5064 6582 0.729116 CAGCGGCTTTACCTGTCATG 59.271 55.000 0.00 0.00 35.61 3.07
5065 6583 1.026718 GCAGCGGCTTTACCTGTCAT 61.027 55.000 0.00 0.00 36.96 3.06
5066 6584 1.671054 GCAGCGGCTTTACCTGTCA 60.671 57.895 0.00 0.00 36.96 3.58
5067 6585 1.026718 ATGCAGCGGCTTTACCTGTC 61.027 55.000 10.92 0.00 41.91 3.51
5085 6606 2.612285 TCGCCTGGATCATCTAGGAT 57.388 50.000 21.09 0.00 46.88 3.24
5130 6651 0.476611 AGGAGGAAGGAAGGCTTGGT 60.477 55.000 3.46 0.00 0.00 3.67
5138 6659 3.075005 CCGGCGAGGAGGAAGGAA 61.075 66.667 9.30 0.00 45.00 3.36


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

AutoCloner maintained by Alex Coulton.