Multiple sequence alignment - TraesCS7D01G454700

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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 TraesCS7D01G454700 chr7D 100.000 7938 0 0 336 8273 573839870 573831933 0.000000e+00 14659.0
1 TraesCS7D01G454700 chr7D 88.690 2794 223 42 1071 3828 573915319 573912583 0.000000e+00 3323.0
2 TraesCS7D01G454700 chr7D 87.451 1028 96 9 990 1993 573916334 573915316 0.000000e+00 1153.0
3 TraesCS7D01G454700 chr7D 96.429 84 3 0 3876 3959 573912565 573912482 1.120000e-28 139.0
4 TraesCS7D01G454700 chr7D 100.000 36 0 0 1 36 573840205 573840170 5.360000e-07 67.6
5 TraesCS7D01G454700 chr7B 93.366 5231 199 53 336 5528 632670491 632665371 0.000000e+00 7601.0
6 TraesCS7D01G454700 chr7B 90.173 2595 153 55 5723 8273 632665266 632662730 0.000000e+00 3286.0
7 TraesCS7D01G454700 chr7B 89.029 2534 179 38 1444 3959 632939850 632942302 0.000000e+00 3048.0
8 TraesCS7D01G454700 chr7B 84.375 448 51 9 986 1417 632938789 632939233 9.930000e-114 422.0
9 TraesCS7D01G454700 chr7B 88.055 293 22 2 336 628 632938459 632938738 1.330000e-87 335.0
10 TraesCS7D01G454700 chr7B 92.727 110 7 1 5579 5688 632665372 632665264 3.090000e-34 158.0
11 TraesCS7D01G454700 chr7B 91.667 84 5 1 3876 3959 632710132 632710051 1.890000e-21 115.0
12 TraesCS7D01G454700 chr7B 97.222 36 0 1 1 36 632670630 632670596 8.970000e-05 60.2
13 TraesCS7D01G454700 chr7A 93.903 3543 140 41 1670 5199 663545227 663541748 0.000000e+00 5276.0
14 TraesCS7D01G454700 chr7A 93.357 1400 67 16 6352 7735 663540588 663539199 0.000000e+00 2047.0
15 TraesCS7D01G454700 chr7A 92.800 1125 62 10 5243 6352 663541747 663540627 0.000000e+00 1611.0
16 TraesCS7D01G454700 chr7A 90.496 968 53 23 336 1289 663546720 663545778 0.000000e+00 1242.0
17 TraesCS7D01G454700 chr7A 90.976 410 22 3 1254 1649 663545769 663545361 9.450000e-149 538.0
18 TraesCS7D01G454700 chr7A 81.053 570 48 22 7718 8273 663539020 663538497 4.650000e-107 399.0
19 TraesCS7D01G454700 chr7A 97.222 36 0 1 1 36 663546854 663546820 8.970000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G454700 chr7D 573831933 573840205 8272 True 7363.300000 14659 100.000000 1 8273 2 chr7D.!!$R1 8272
1 TraesCS7D01G454700 chr7D 573912482 573916334 3852 True 1538.333333 3323 90.856667 990 3959 3 chr7D.!!$R2 2969
2 TraesCS7D01G454700 chr7B 632662730 632670630 7900 True 2776.300000 7601 93.372000 1 8273 4 chr7B.!!$R2 8272
3 TraesCS7D01G454700 chr7B 632938459 632942302 3843 False 1268.333333 3048 87.153000 336 3959 3 chr7B.!!$F1 3623
4 TraesCS7D01G454700 chr7A 663538497 663546854 8357 True 1596.171429 5276 91.401000 1 8273 7 chr7A.!!$R1 8272

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
904 917 0.170339 GGTTGTGAATAACCTGGCGC 59.830 55.000 0.00 0.0 45.29 6.53 F
941 954 0.780002 GCTGCTGTTTTGTCGCATTG 59.220 50.000 0.00 0.0 32.62 2.82 F
1856 3588 0.251354 TCTGCAGCCTGATGGAGTTC 59.749 55.000 9.47 0.0 39.46 3.01 F
2364 4098 2.307392 TGGCTGCAAATACAGGGAAGTA 59.693 45.455 0.50 0.0 38.16 2.24 F
4217 5975 2.039084 TCTTCCTGCCAAGAGTTCCTTC 59.961 50.000 0.00 0.0 31.42 3.46 F
5176 6960 0.105246 TGCCCATGAAACCCACCTTT 60.105 50.000 0.00 0.0 0.00 3.11 F
6058 7859 0.391793 AGCGCTCTGTTTAGAAGGGC 60.392 55.000 2.64 2.8 38.77 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 3588 1.231958 TTTGCTTGGTACGCCTTCGG 61.232 55.000 0.00 0.0 40.69 4.30 R
2186 3919 3.370978 CGTTGCGATACATTGTTCCTTCT 59.629 43.478 0.00 0.0 0.00 2.85 R
3727 5485 3.254060 CAAGGATCAACTACAGGACGTG 58.746 50.000 0.00 0.0 0.00 4.49 R
4238 5996 2.210116 GCAGTCAGAAAACGACCTTCA 58.790 47.619 0.00 0.0 33.70 3.02 R
6065 7866 0.464036 AAGCCAAGACACACTGACGA 59.536 50.000 0.00 0.0 0.00 4.20 R
6547 8390 0.312416 GGTGCGCAACAAACCATACA 59.688 50.000 23.15 0.0 33.94 2.29 R
7967 10049 0.313672 GACAGCCGTTGCCAATCAAA 59.686 50.000 0.00 0.0 38.69 2.69 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
31 32 1.073098 TTTCTTCCTCCCCAAGACCC 58.927 55.000 0.00 0.00 29.30 4.46
32 33 0.196118 TTCTTCCTCCCCAAGACCCT 59.804 55.000 0.00 0.00 29.30 4.34
34 35 1.229853 TTCCTCCCCAAGACCCTCC 60.230 63.158 0.00 0.00 0.00 4.30
35 36 3.083997 CCTCCCCAAGACCCTCCG 61.084 72.222 0.00 0.00 0.00 4.63
585 592 1.275657 GAATGGTAATGCGACGCCG 59.724 57.895 18.69 0.00 39.16 6.46
601 610 1.102222 GCCGTACCACTCCGAGAGAT 61.102 60.000 1.33 0.00 33.32 2.75
612 621 3.055747 ACTCCGAGAGATTCTTTGGTTCC 60.056 47.826 1.33 0.00 33.32 3.62
648 657 2.224892 GCAGGGGTTCCTTCTTCTTTCT 60.225 50.000 0.00 0.00 42.67 2.52
732 741 5.671329 GCTTAGTGAAATTTCAGTAGCACCG 60.671 44.000 29.11 20.36 42.29 4.94
758 767 9.685828 GTACATTTCTTATTGTTTTGGCTTGTA 57.314 29.630 0.00 0.00 0.00 2.41
759 768 8.816640 ACATTTCTTATTGTTTTGGCTTGTAG 57.183 30.769 0.00 0.00 0.00 2.74
760 769 8.421002 ACATTTCTTATTGTTTTGGCTTGTAGT 58.579 29.630 0.00 0.00 0.00 2.73
786 795 0.933796 GATAGTTCTGAAGCCTGCGC 59.066 55.000 0.00 0.00 0.00 6.09
852 863 2.288825 GGGTTTGTGGCCTAGAAAAAGC 60.289 50.000 3.32 0.64 0.00 3.51
868 881 6.848451 AGAAAAAGCGTTTCTCTGTTTTACA 58.152 32.000 11.37 0.00 33.86 2.41
897 910 3.851098 AGCTCTCTCGGTTGTGAATAAC 58.149 45.455 0.00 0.00 0.00 1.89
904 917 0.170339 GGTTGTGAATAACCTGGCGC 59.830 55.000 0.00 0.00 45.29 6.53
912 925 2.876368 ATAACCTGGCGCACCTGCTC 62.876 60.000 10.83 0.00 39.32 4.26
916 929 2.282391 TGGCGCACCTGCTCATTT 60.282 55.556 10.83 0.00 39.32 2.32
941 954 0.780002 GCTGCTGTTTTGTCGCATTG 59.220 50.000 0.00 0.00 32.62 2.82
942 955 1.600164 GCTGCTGTTTTGTCGCATTGA 60.600 47.619 0.00 0.00 32.62 2.57
943 956 2.730069 CTGCTGTTTTGTCGCATTGAA 58.270 42.857 0.00 0.00 32.62 2.69
965 978 2.226437 AGTGGTTTGCTAATGCTTCGTG 59.774 45.455 0.00 0.00 40.48 4.35
972 985 6.036735 GGTTTGCTAATGCTTCGTGATAACTA 59.963 38.462 0.00 0.00 40.48 2.24
988 1001 7.327275 CGTGATAACTAGATGTAGAATCCTTGC 59.673 40.741 3.49 0.00 0.00 4.01
1016 1029 3.413846 ACTGATGTGCTGTCATTCTGT 57.586 42.857 0.00 0.00 0.00 3.41
1032 1045 5.637810 TCATTCTGTGATAACAGTTCGTTCC 59.362 40.000 10.16 0.00 39.14 3.62
1206 1227 8.954950 TGTTTCCATTTGCTTTTCTTTTCATA 57.045 26.923 0.00 0.00 0.00 2.15
1245 1273 5.453567 AAGCAAGTAAGCTAAAAGGGTTG 57.546 39.130 0.00 0.00 45.89 3.77
1284 1354 4.510038 ACAATCAAGAATTCACAGCCAC 57.490 40.909 8.44 0.00 0.00 5.01
1297 1367 4.431809 TCACAGCCACAATTTGTTTTGAG 58.568 39.130 0.00 0.00 0.00 3.02
1322 1392 6.033513 GCGGTTTAATTAGCTCATTTGTGTTC 59.966 38.462 0.00 0.00 0.00 3.18
1331 1401 5.255687 AGCTCATTTGTGTTCCACATATCA 58.744 37.500 0.00 0.00 44.16 2.15
1338 1408 3.439825 TGTGTTCCACATATCATGCACAC 59.560 43.478 0.00 0.00 39.62 3.82
1360 1433 4.051922 CTGGAAGTATGTATCAACGAGCC 58.948 47.826 0.00 0.00 0.00 4.70
1371 1460 0.886490 CAACGAGCCTGCCTTCTTGT 60.886 55.000 0.00 0.00 0.00 3.16
1522 2206 8.040727 GCAAATGGTTAAGTATGATTTCCCTTT 58.959 33.333 0.00 0.00 0.00 3.11
1616 3234 7.651304 TGAGTTTTTATGTACAGCACATTTTGG 59.349 33.333 0.33 0.00 46.01 3.28
1682 3413 5.695816 GGCTATTTGTCATCTGATCTCTGTC 59.304 44.000 0.00 0.00 0.00 3.51
1767 3498 3.967987 AGGCTATACCCAGGTGAGTTTAG 59.032 47.826 0.00 0.00 40.58 1.85
1856 3588 0.251354 TCTGCAGCCTGATGGAGTTC 59.749 55.000 9.47 0.00 39.46 3.01
1883 3615 2.767505 CGTACCAAGCAAAGAAGGACT 58.232 47.619 0.00 0.00 0.00 3.85
2111 3844 3.196463 CTGGCAAAACTTTTGCACATGA 58.804 40.909 30.86 14.13 46.58 3.07
2186 3919 7.624360 AGAATGATATCGGCAAAAACACTTA 57.376 32.000 0.00 0.00 0.00 2.24
2275 4008 4.531732 ACTATGGAAAAACATGCATTGGGT 59.468 37.500 0.00 0.00 33.15 4.51
2304 4038 6.017934 ACACATATGGTATTTCGTTGCAGATC 60.018 38.462 7.80 0.00 0.00 2.75
2364 4098 2.307392 TGGCTGCAAATACAGGGAAGTA 59.693 45.455 0.50 0.00 38.16 2.24
2393 4127 8.614469 AAGAAATTTTCACAGGTTTGTTTTGA 57.386 26.923 11.53 0.00 34.62 2.69
2494 4236 5.398416 GGCGAACACAGAGAAAATTTTGTAC 59.602 40.000 8.47 0.00 0.00 2.90
2625 4369 9.555727 TGAGTTCACAAAGTATTTACTAGCTTT 57.444 29.630 0.00 0.00 35.03 3.51
2920 4665 5.188359 ACGTTCCCTGTAAAGCTAGGATAAA 59.812 40.000 1.53 0.00 36.11 1.40
3041 4786 9.787435 TTAGTTTTGGTGTACTGAATATGTTCT 57.213 29.630 3.72 0.00 35.33 3.01
3281 5028 3.554960 GGGTCAAATGGCCAAAGAAGAAC 60.555 47.826 10.96 6.52 42.93 3.01
3403 5151 6.432607 TCATGCTGAAAGATTTCTGATGTC 57.567 37.500 14.21 0.43 38.07 3.06
3409 5157 6.293845 GCTGAAAGATTTCTGATGTCACAAGT 60.294 38.462 14.21 0.00 38.07 3.16
3417 5165 5.385509 TCTGATGTCACAAGTACGATCAA 57.614 39.130 0.00 0.00 0.00 2.57
3418 5166 5.161358 TCTGATGTCACAAGTACGATCAAC 58.839 41.667 0.00 0.00 0.00 3.18
3419 5167 4.242475 TGATGTCACAAGTACGATCAACC 58.758 43.478 0.00 0.00 0.00 3.77
3420 5168 4.021456 TGATGTCACAAGTACGATCAACCT 60.021 41.667 0.00 0.00 0.00 3.50
3458 5206 2.906389 TGTCCTGCTCCTAATGTGACTT 59.094 45.455 0.00 0.00 0.00 3.01
3662 5419 2.549754 AGCCACATTTGAGTTCAGTTCG 59.450 45.455 0.00 0.00 0.00 3.95
3671 5429 9.088512 ACATTTGAGTTCAGTTCGTATTATCTC 57.911 33.333 0.00 0.00 0.00 2.75
3701 5459 9.869844 CTCTGTTTTTATGAAACTAGACAACTG 57.130 33.333 0.00 0.00 0.00 3.16
3727 5485 5.585820 TTTGGAACTTTGGGTGTTCTTAC 57.414 39.130 0.00 0.00 42.27 2.34
4082 5840 3.758554 AGAAGCTTGTTTTATGACCGCAT 59.241 39.130 2.10 0.00 38.54 4.73
4147 5905 7.807977 ATTTCAGTGAACTTCATACTGTGTT 57.192 32.000 4.68 0.00 41.82 3.32
4158 5916 9.719355 AACTTCATACTGTGTTGTCATGTATTA 57.281 29.630 0.00 0.00 30.21 0.98
4168 5926 7.334171 TGTGTTGTCATGTATTATGACTCCTTG 59.666 37.037 17.74 0.00 46.25 3.61
4217 5975 2.039084 TCTTCCTGCCAAGAGTTCCTTC 59.961 50.000 0.00 0.00 31.42 3.46
4237 5995 7.425606 TCCTTCTCTTTTCTTTATTTGCACAC 58.574 34.615 0.00 0.00 0.00 3.82
4238 5996 7.285401 TCCTTCTCTTTTCTTTATTTGCACACT 59.715 33.333 0.00 0.00 0.00 3.55
4246 6004 4.213270 TCTTTATTTGCACACTGAAGGTCG 59.787 41.667 0.00 0.00 0.00 4.79
4316 6074 1.000060 GCTGTTGACATGTGGCATGTT 60.000 47.619 14.80 1.11 30.06 2.71
4320 6078 0.873721 TGACATGTGGCATGTTGTCG 59.126 50.000 14.80 0.00 41.02 4.35
4344 6103 6.201044 CGTGTTTTCTGACTTGTTGATCTAGT 59.799 38.462 0.00 0.00 35.08 2.57
4433 6196 4.036027 CACATTGGAAGCTATAGTTGCAGG 59.964 45.833 0.84 5.56 0.00 4.85
4448 6211 1.752498 TGCAGGCTTCAATGCATTAGG 59.248 47.619 12.53 6.37 46.97 2.69
4591 6354 9.161629 CTGTGTAATATAAACAATCAGTGTGGA 57.838 33.333 0.00 0.00 40.60 4.02
4895 6678 7.177568 AGAGAGTAAGCTGTCAACAGAAGATTA 59.822 37.037 14.20 4.43 46.59 1.75
4939 6723 9.077885 TCTGAACTTTGGCTATTTATTCTTGTT 57.922 29.630 0.00 0.00 0.00 2.83
5134 6918 7.385752 TGTTTTAAATAGTGGTAAGACGTCAGG 59.614 37.037 19.50 0.00 0.00 3.86
5176 6960 0.105246 TGCCCATGAAACCCACCTTT 60.105 50.000 0.00 0.00 0.00 3.11
5177 6961 1.055849 GCCCATGAAACCCACCTTTT 58.944 50.000 0.00 0.00 0.00 2.27
5215 6999 0.454957 GCTGCTATTTGTGGTGCGTG 60.455 55.000 0.00 0.00 0.00 5.34
5252 7036 1.456287 GCACCACCCTTCCTTCTGT 59.544 57.895 0.00 0.00 0.00 3.41
5266 7050 1.161563 TTCTGTCGGTTTTGTCCCGC 61.162 55.000 0.00 0.00 45.09 6.13
5383 7167 7.865889 CCCTTGAAAGTGTTTTAACCAATACTC 59.134 37.037 0.00 0.00 28.63 2.59
5521 7318 0.682852 CGTTGGTAAGGGTCTGGTCA 59.317 55.000 0.00 0.00 0.00 4.02
5570 7367 5.163237 TGGTAGGAACTAAGCAACAAAGAGT 60.163 40.000 0.00 0.00 45.48 3.24
5573 7370 3.883489 GGAACTAAGCAACAAAGAGTGGT 59.117 43.478 0.00 0.00 0.00 4.16
5576 7373 2.435372 AAGCAACAAAGAGTGGTGGA 57.565 45.000 0.00 0.00 45.90 4.02
5583 7380 6.719370 AGCAACAAAGAGTGGTGGAATAAATA 59.281 34.615 0.00 0.00 45.90 1.40
5621 7418 9.236691 GCATGTAAACACTATAATCCAAATGTG 57.763 33.333 0.00 0.00 0.00 3.21
5640 7437 5.811399 TGTGTTATATTTGGAAAGGAGCG 57.189 39.130 0.00 0.00 0.00 5.03
5721 7518 3.011818 TGAGTTGCATGCTGTAATCTGG 58.988 45.455 20.33 0.00 0.00 3.86
5742 7539 7.098477 TCTGGCAATATGAACTTTGGAATTTG 58.902 34.615 0.00 0.00 0.00 2.32
5783 7580 8.296713 TGCAAATTTTCTACTTATCTCGCTTTT 58.703 29.630 0.00 0.00 0.00 2.27
5784 7581 9.129209 GCAAATTTTCTACTTATCTCGCTTTTT 57.871 29.630 0.00 0.00 0.00 1.94
5923 7723 3.944055 TGAAAGGTCTCTGTAGCACTC 57.056 47.619 0.00 0.00 0.00 3.51
5924 7724 3.501349 TGAAAGGTCTCTGTAGCACTCT 58.499 45.455 0.00 0.00 0.00 3.24
5971 7772 7.885922 ACCAATAACATATGGTCACAACACTTA 59.114 33.333 7.80 0.00 46.94 2.24
5980 7781 7.849804 ATGGTCACAACACTTATATCTTCAC 57.150 36.000 0.00 0.00 0.00 3.18
6047 7848 1.135170 TCAGTCATCAAGAGCGCTCTG 60.135 52.381 38.78 29.56 40.36 3.35
6056 7857 2.663826 AGAGCGCTCTGTTTAGAAGG 57.336 50.000 37.86 0.00 38.75 3.46
6058 7859 0.391793 AGCGCTCTGTTTAGAAGGGC 60.392 55.000 2.64 2.80 38.77 5.19
6065 7866 2.835764 TCTGTTTAGAAGGGCGTGGTAT 59.164 45.455 0.00 0.00 0.00 2.73
6067 7868 2.199236 GTTTAGAAGGGCGTGGTATCG 58.801 52.381 0.00 0.00 0.00 2.92
6164 7967 4.704540 TGCCTGTATTAAATGGTGGTTCAG 59.295 41.667 0.00 0.00 0.00 3.02
6256 8059 4.705023 TGGGTTCTTAATCTTGCTAAAGCC 59.295 41.667 0.00 0.00 41.18 4.35
6304 8107 7.254455 CGTGGTCTTGTGATTGATCCTTATAAC 60.254 40.741 0.00 0.00 0.00 1.89
6437 8280 4.017499 ACCCAGCTACATATGTTTCCCTTT 60.017 41.667 14.77 0.00 0.00 3.11
6547 8390 5.394224 TTGCACAACATCATTCATGTCAT 57.606 34.783 0.00 0.00 45.77 3.06
6580 8423 1.045407 CGCACCCTAGGCAGGTAATA 58.955 55.000 2.05 0.00 40.79 0.98
6581 8424 1.414919 CGCACCCTAGGCAGGTAATAA 59.585 52.381 2.05 0.00 40.79 1.40
6592 8435 7.973944 CCTAGGCAGGTAATAAAAATTTCACAC 59.026 37.037 0.00 0.00 37.15 3.82
6597 8440 9.423061 GCAGGTAATAAAAATTTCACACAATCT 57.577 29.630 0.00 0.00 0.00 2.40
6613 8456 8.206189 TCACACAATCTCATATAGATCTTTGCA 58.794 33.333 0.00 0.00 44.56 4.08
6619 8462 8.604640 ATCTCATATAGATCTTTGCAACACAG 57.395 34.615 0.00 0.00 41.32 3.66
6653 8496 6.165577 GCAATCAGGTTTCATTTGGTGTTAT 58.834 36.000 0.00 0.00 0.00 1.89
6659 8502 7.493971 TCAGGTTTCATTTGGTGTTATTGTTTG 59.506 33.333 0.00 0.00 0.00 2.93
6861 8704 1.630369 TGCCAGTGCCTGACTCTTATT 59.370 47.619 4.00 0.00 36.33 1.40
6951 8794 4.591321 AATAGGGGATGCTTTCTTGACA 57.409 40.909 0.00 0.00 0.00 3.58
6954 8797 3.891049 AGGGGATGCTTTCTTGACATAC 58.109 45.455 0.00 0.00 0.00 2.39
6972 8815 0.385751 ACGACCGGTATGCTCATCAG 59.614 55.000 7.34 0.00 0.00 2.90
6980 8824 4.747108 CCGGTATGCTCATCAGAAAACTAG 59.253 45.833 0.00 0.00 0.00 2.57
7026 8870 6.070951 TGAGGTTTCTTGATGATCCTTCAT 57.929 37.500 0.00 0.00 45.39 2.57
7085 8930 6.267471 TGTTCCATAATTTCTGAAGTGCCTTT 59.733 34.615 0.00 0.00 0.00 3.11
7159 9019 9.467258 CATGGCTAACTTAATAACCAAATCATG 57.533 33.333 0.00 0.00 0.00 3.07
7322 9186 4.377021 TGACACGGTTGAGATATTATGGC 58.623 43.478 0.00 0.00 0.00 4.40
7324 9188 3.074412 CACGGTTGAGATATTATGGCCC 58.926 50.000 0.00 0.00 0.00 5.80
7340 9204 1.599047 CCCTCGCTTCTGTGGATGT 59.401 57.895 0.00 0.00 0.00 3.06
7342 9206 0.247460 CCTCGCTTCTGTGGATGTCA 59.753 55.000 0.00 0.00 0.00 3.58
7400 9265 4.521943 GCTAACTTGATCGTTCATGCATC 58.478 43.478 0.00 0.00 31.80 3.91
7550 9424 2.262915 GGAGGTCGTGTCAGCAGG 59.737 66.667 0.00 0.00 0.00 4.85
7617 9492 1.870580 CGACGGTTGTAGCAGTTGGAA 60.871 52.381 0.00 0.00 0.00 3.53
7629 9506 2.811873 GCAGTTGGAAGTCCATGACACT 60.812 50.000 0.00 0.00 46.97 3.55
7630 9507 3.070018 CAGTTGGAAGTCCATGACACTC 58.930 50.000 0.00 0.00 46.97 3.51
7631 9508 2.705658 AGTTGGAAGTCCATGACACTCA 59.294 45.455 0.00 0.00 46.97 3.41
7632 9509 2.808543 GTTGGAAGTCCATGACACTCAC 59.191 50.000 0.00 0.00 46.97 3.51
7634 9511 2.224281 TGGAAGTCCATGACACTCACAC 60.224 50.000 0.00 0.00 42.01 3.82
7635 9512 2.061773 GAAGTCCATGACACTCACACG 58.938 52.381 0.00 0.00 34.60 4.49
7636 9513 1.040646 AGTCCATGACACTCACACGT 58.959 50.000 0.00 0.00 34.60 4.49
7637 9514 2.235891 AGTCCATGACACTCACACGTA 58.764 47.619 0.00 0.00 34.60 3.57
7638 9515 2.826128 AGTCCATGACACTCACACGTAT 59.174 45.455 0.00 0.00 34.60 3.06
7639 9516 3.119459 AGTCCATGACACTCACACGTATC 60.119 47.826 0.00 0.00 34.60 2.24
7640 9517 2.159435 TCCATGACACTCACACGTATCG 60.159 50.000 0.00 0.00 0.00 2.92
7645 9522 0.713883 CACTCACACGTATCGTTGGC 59.286 55.000 0.00 0.00 38.32 4.52
7683 9561 0.822164 GCAGAAGCCCATGATTTGCT 59.178 50.000 0.00 0.00 36.79 3.91
7693 9571 1.266175 CATGATTTGCTCATCGGAGGC 59.734 52.381 0.00 0.00 42.91 4.70
7772 9847 5.901413 AATCTATTTGGATCTGAGCTGGA 57.099 39.130 0.00 0.00 0.00 3.86
7778 9853 0.532573 GGATCTGAGCTGGAACGACA 59.467 55.000 0.00 0.00 0.00 4.35
7861 9939 0.725784 GCACCGTTCATTCGTGCTTG 60.726 55.000 4.24 0.00 36.13 4.01
7895 9973 1.228737 GGCTGGCCCTTGGTTAACA 60.229 57.895 8.10 0.00 0.00 2.41
7898 9976 0.251341 CTGGCCCTTGGTTAACAGCT 60.251 55.000 8.10 0.00 0.00 4.24
7930 10012 3.327757 TGGTCTTGCTAGGTGTTTCTGAT 59.672 43.478 0.00 0.00 0.00 2.90
7952 10034 1.538687 GCAGCCAGCTGGACCAAAAT 61.539 55.000 37.21 9.04 43.77 1.82
7967 10049 2.629617 CCAAAATCAAGGCTGGTTCTGT 59.370 45.455 0.00 0.00 0.00 3.41
7983 10065 0.314935 CTGTTTGATTGGCAACGGCT 59.685 50.000 0.00 0.00 40.87 5.52
7984 10066 0.031857 TGTTTGATTGGCAACGGCTG 59.968 50.000 0.00 0.00 40.87 4.85
7985 10067 0.031994 GTTTGATTGGCAACGGCTGT 59.968 50.000 0.00 0.00 40.87 4.40
7986 10068 0.313672 TTTGATTGGCAACGGCTGTC 59.686 50.000 0.00 0.00 40.87 3.51
7987 10069 1.523154 TTGATTGGCAACGGCTGTCC 61.523 55.000 0.00 0.00 40.87 4.02
7988 10070 1.675641 GATTGGCAACGGCTGTCCT 60.676 57.895 0.00 0.00 40.87 3.85
7989 10071 1.926511 GATTGGCAACGGCTGTCCTG 61.927 60.000 0.00 0.00 40.87 3.86
7990 10072 2.697147 ATTGGCAACGGCTGTCCTGT 62.697 55.000 0.00 0.00 40.87 4.00
7991 10073 3.357079 GGCAACGGCTGTCCTGTG 61.357 66.667 0.00 0.00 40.87 3.66
7992 10074 2.591715 GCAACGGCTGTCCTGTGT 60.592 61.111 0.00 0.00 36.96 3.72
7993 10075 2.607892 GCAACGGCTGTCCTGTGTC 61.608 63.158 0.00 0.00 36.96 3.67
8004 10086 2.224843 TGTCCTGTGTCTGATTGGCAAT 60.225 45.455 13.54 13.54 28.98 3.56
8046 10128 1.864862 CTCAACAGTCGGCTGCTTG 59.135 57.895 18.84 19.36 46.30 4.01
8048 10130 1.893808 CAACAGTCGGCTGCTTGGT 60.894 57.895 18.84 0.00 46.30 3.67
8050 10132 1.447317 AACAGTCGGCTGCTTGGTTG 61.447 55.000 18.84 0.00 46.30 3.77
8055 10137 2.848858 CGGCTGCTTGGTTGTGCTT 61.849 57.895 0.00 0.00 0.00 3.91
8063 10145 3.563808 TGCTTGGTTGTGCTTTACTGTAG 59.436 43.478 0.00 0.00 0.00 2.74
8167 10257 1.529865 GCGTACTTGTTCCTTCACCAC 59.470 52.381 0.00 0.00 0.00 4.16
8169 10259 3.199677 CGTACTTGTTCCTTCACCACAA 58.800 45.455 0.00 0.00 0.00 3.33
8174 10264 6.783708 ACTTGTTCCTTCACCACAAATAAA 57.216 33.333 0.00 0.00 30.15 1.40
8242 10336 6.403866 TTCTTTTATTTCTCCAGCTTGCAA 57.596 33.333 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
585 592 4.425520 CAAAGAATCTCTCGGAGTGGTAC 58.574 47.826 4.69 0.00 0.00 3.34
594 603 1.661112 GCGGAACCAAAGAATCTCTCG 59.339 52.381 0.00 0.00 0.00 4.04
601 610 1.407258 CCACAAAGCGGAACCAAAGAA 59.593 47.619 0.00 0.00 0.00 2.52
732 741 8.587952 ACAAGCCAAAACAATAAGAAATGTAC 57.412 30.769 0.00 0.00 0.00 2.90
758 767 7.255801 GCAGGCTTCAGAACTATCTATCTTACT 60.256 40.741 0.00 0.00 33.50 2.24
759 768 6.866248 GCAGGCTTCAGAACTATCTATCTTAC 59.134 42.308 0.00 0.00 33.50 2.34
760 769 6.294231 CGCAGGCTTCAGAACTATCTATCTTA 60.294 42.308 0.00 0.00 33.50 2.10
831 842 2.288825 GCTTTTTCTAGGCCACAAACCC 60.289 50.000 5.01 0.00 0.00 4.11
836 847 1.975660 AACGCTTTTTCTAGGCCACA 58.024 45.000 5.01 0.00 0.00 4.17
868 881 3.007398 ACAACCGAGAGAGCTCAAATTCT 59.993 43.478 17.77 9.85 41.36 2.40
941 954 3.914364 CGAAGCATTAGCAAACCACTTTC 59.086 43.478 0.00 0.00 45.49 2.62
942 955 3.317993 ACGAAGCATTAGCAAACCACTTT 59.682 39.130 0.00 0.00 45.49 2.66
943 956 2.884639 ACGAAGCATTAGCAAACCACTT 59.115 40.909 0.00 0.00 45.49 3.16
965 978 8.364142 ACAGCAAGGATTCTACATCTAGTTATC 58.636 37.037 0.00 0.00 0.00 1.75
972 985 7.885399 AGTAAAAACAGCAAGGATTCTACATCT 59.115 33.333 0.00 0.00 0.00 2.90
988 1001 5.422666 TGACAGCACATCAGTAAAAACAG 57.577 39.130 0.00 0.00 0.00 3.16
1016 1029 4.503910 CTCCATGGAACGAACTGTTATCA 58.496 43.478 17.00 0.00 42.09 2.15
1032 1045 1.134159 CAAGCCCTTCTCTCCTCCATG 60.134 57.143 0.00 0.00 0.00 3.66
1206 1227 9.523168 TTACTTGCTTACCCAACTAAATACATT 57.477 29.630 0.00 0.00 0.00 2.71
1284 1354 7.739911 GCTAATTAAACCGCTCAAAACAAATTG 59.260 33.333 0.00 0.00 0.00 2.32
1297 1367 5.399013 ACACAAATGAGCTAATTAAACCGC 58.601 37.500 0.00 0.00 0.00 5.68
1322 1392 2.921821 TCCAGTGTGCATGATATGTGG 58.078 47.619 0.00 0.00 0.00 4.17
1331 1401 5.357742 TGATACATACTTCCAGTGTGCAT 57.642 39.130 0.00 0.00 40.45 3.96
1338 1408 4.051922 GGCTCGTTGATACATACTTCCAG 58.948 47.826 0.00 0.00 0.00 3.86
1352 1425 0.886490 ACAAGAAGGCAGGCTCGTTG 60.886 55.000 13.88 13.88 0.00 4.10
1360 1433 3.993081 CACTTCACTCTACAAGAAGGCAG 59.007 47.826 0.00 0.00 42.24 4.85
1371 1460 1.047801 TGTGCAGCCACTTCACTCTA 58.952 50.000 0.00 0.00 42.54 2.43
1522 2206 2.289819 CCCCCTTCGCACTAGTTAACAA 60.290 50.000 8.61 0.00 0.00 2.83
1611 3229 3.637769 ACTCCAACTAACAAGCCCAAAA 58.362 40.909 0.00 0.00 0.00 2.44
1616 3234 4.338400 AGAAACAACTCCAACTAACAAGCC 59.662 41.667 0.00 0.00 0.00 4.35
1664 3282 5.221402 GCATAGGACAGAGATCAGATGACAA 60.221 44.000 0.00 0.00 0.00 3.18
1682 3413 5.237815 TGTGTACTGAAGAAACAGCATAGG 58.762 41.667 0.00 0.00 41.06 2.57
1767 3498 8.239681 ACTTTCAGTTTTCTTTAAGTTGTTGC 57.760 30.769 0.00 0.00 31.25 4.17
1794 3526 8.584157 AGTGGTATCAAGATTCAAGAGCTATAG 58.416 37.037 0.00 0.00 0.00 1.31
1801 3533 9.383519 GAACAATAGTGGTATCAAGATTCAAGA 57.616 33.333 0.00 0.00 0.00 3.02
1802 3534 9.388506 AGAACAATAGTGGTATCAAGATTCAAG 57.611 33.333 0.00 0.00 0.00 3.02
1803 3535 9.166173 CAGAACAATAGTGGTATCAAGATTCAA 57.834 33.333 0.00 0.00 0.00 2.69
1804 3536 8.321353 ACAGAACAATAGTGGTATCAAGATTCA 58.679 33.333 0.00 0.00 0.00 2.57
1805 3537 8.723942 ACAGAACAATAGTGGTATCAAGATTC 57.276 34.615 0.00 0.00 0.00 2.52
1806 3538 8.543774 AGACAGAACAATAGTGGTATCAAGATT 58.456 33.333 0.00 0.00 0.00 2.40
1856 3588 1.231958 TTTGCTTGGTACGCCTTCGG 61.232 55.000 0.00 0.00 40.69 4.30
1883 3615 5.278758 GGTCACTTTCATTTTCATTTCCCGA 60.279 40.000 0.00 0.00 0.00 5.14
2186 3919 3.370978 CGTTGCGATACATTGTTCCTTCT 59.629 43.478 0.00 0.00 0.00 2.85
2275 4008 6.371825 TGCAACGAAATACCATATGTGTGTAA 59.628 34.615 1.24 0.00 0.00 2.41
2304 4038 5.747197 ACGTCTATAGGTGAAAGCAATAACG 59.253 40.000 0.00 0.40 36.26 3.18
2390 4124 5.860941 TGCAACCTAAAAAGGAACATCAA 57.139 34.783 0.00 0.00 0.00 2.57
2393 4127 4.284234 AGCATGCAACCTAAAAAGGAACAT 59.716 37.500 21.98 0.00 0.00 2.71
2445 4179 7.931948 CCTCCTGTTAAGAAGAAAAAGTGAGTA 59.068 37.037 0.00 0.00 0.00 2.59
2446 4180 6.768381 CCTCCTGTTAAGAAGAAAAAGTGAGT 59.232 38.462 0.00 0.00 0.00 3.41
2447 4181 6.293680 GCCTCCTGTTAAGAAGAAAAAGTGAG 60.294 42.308 0.00 0.00 0.00 3.51
2448 4182 5.531287 GCCTCCTGTTAAGAAGAAAAAGTGA 59.469 40.000 0.00 0.00 0.00 3.41
2494 4236 4.153117 GCTTGCTTTATATCATCCAGACCG 59.847 45.833 0.00 0.00 0.00 4.79
2920 4665 7.112122 TGCAGTTCCACAGATATGAATACTTT 58.888 34.615 0.00 0.00 0.00 2.66
3015 4760 9.787435 AGAACATATTCAGTACACCAAAACTAA 57.213 29.630 0.00 0.00 37.29 2.24
3016 4761 9.214957 CAGAACATATTCAGTACACCAAAACTA 57.785 33.333 0.00 0.00 37.29 2.24
3041 4786 7.362234 TCCTAGATGCCTAATACCATATAGCA 58.638 38.462 0.00 0.00 33.90 3.49
3210 4957 5.643379 ATGTGGCAAACGAGTTAAATGAT 57.357 34.783 0.00 0.00 0.00 2.45
3281 5028 5.987264 CATCTTTGCAAAATTCTGTCTCG 57.013 39.130 13.84 0.00 0.00 4.04
3356 5103 8.077991 TGAAAGACAAGCAAAAGAATGATAGTG 58.922 33.333 0.00 0.00 0.00 2.74
3357 5104 8.169977 TGAAAGACAAGCAAAAGAATGATAGT 57.830 30.769 0.00 0.00 0.00 2.12
3403 5151 5.950883 TCTTAGAGGTTGATCGTACTTGTG 58.049 41.667 0.00 0.00 0.00 3.33
3419 5167 6.092807 GCAGGACATTTTTACACCTCTTAGAG 59.907 42.308 1.56 1.56 0.00 2.43
3420 5168 5.938125 GCAGGACATTTTTACACCTCTTAGA 59.062 40.000 0.00 0.00 0.00 2.10
3476 5224 8.958506 ACATTTAGACTCTCGATACAAGTTAGT 58.041 33.333 0.00 0.00 0.00 2.24
3569 5326 8.563123 AAACCTTACAGGCTCTAATTAAGAAC 57.437 34.615 0.00 0.00 39.63 3.01
3570 5327 9.010029 CAAAACCTTACAGGCTCTAATTAAGAA 57.990 33.333 0.00 0.00 39.63 2.52
3571 5328 8.161425 ACAAAACCTTACAGGCTCTAATTAAGA 58.839 33.333 0.00 0.00 39.63 2.10
3580 5337 4.379499 GCATACACAAAACCTTACAGGCTC 60.379 45.833 0.00 0.00 39.63 4.70
3671 5429 9.424319 TGTCTAGTTTCATAAAAACAGAGCTAG 57.576 33.333 3.75 0.00 32.81 3.42
3701 5459 3.603158 ACACCCAAAGTTCCAAAACAC 57.397 42.857 0.00 0.00 37.88 3.32
3727 5485 3.254060 CAAGGATCAACTACAGGACGTG 58.746 50.000 0.00 0.00 0.00 4.49
3974 5732 8.365210 CGATCAAAATAGGACGAAAAACAAATG 58.635 33.333 0.00 0.00 0.00 2.32
4158 5916 7.502226 TGTTTTCAACAAGTATCAAGGAGTCAT 59.498 33.333 0.00 0.00 38.72 3.06
4217 5975 7.380602 CCTTCAGTGTGCAAATAAAGAAAAGAG 59.619 37.037 0.00 0.00 0.00 2.85
4237 5995 2.221981 GCAGTCAGAAAACGACCTTCAG 59.778 50.000 0.00 0.00 33.70 3.02
4238 5996 2.210116 GCAGTCAGAAAACGACCTTCA 58.790 47.619 0.00 0.00 33.70 3.02
4246 6004 4.504097 GGTTTCATGTTGCAGTCAGAAAAC 59.496 41.667 16.40 16.40 0.00 2.43
4316 6074 3.997681 TCAACAAGTCAGAAAACACGACA 59.002 39.130 0.00 0.00 31.92 4.35
4320 6078 7.484035 ACTAGATCAACAAGTCAGAAAACAC 57.516 36.000 0.00 0.00 0.00 3.32
4344 6103 8.241497 AGCTGGAATCATATAATTGCTTTCAA 57.759 30.769 0.00 0.00 36.51 2.69
4448 6211 4.802039 CACATGAGAAATTGTGGCTAATGC 59.198 41.667 0.00 0.00 39.61 3.56
4454 6217 5.697633 ACAAAATCACATGAGAAATTGTGGC 59.302 36.000 18.97 0.00 42.72 5.01
4591 6354 6.205464 CCATCGAGCATAGTACAAATTTCCAT 59.795 38.462 0.00 0.00 0.00 3.41
4687 6450 6.303054 TCTGACCTAAACACCAAAATCATCA 58.697 36.000 0.00 0.00 0.00 3.07
4939 6723 8.641499 GATGTAATCACAAAACCTTCAAAACA 57.359 30.769 0.00 0.00 44.70 2.83
5029 6813 7.729116 TCTTTGCCTTCTTCAAATTCATCTTT 58.271 30.769 0.00 0.00 33.54 2.52
5127 6911 2.943033 CTGTCTTTGAAAACCCTGACGT 59.057 45.455 0.00 0.00 0.00 4.34
5134 6918 5.979517 CAGATCCAAACTGTCTTTGAAAACC 59.020 40.000 0.00 0.00 0.00 3.27
5176 6960 5.531634 CAGCTCCAGTTCTAAAATTTGCAA 58.468 37.500 0.00 0.00 0.00 4.08
5177 6961 4.559300 GCAGCTCCAGTTCTAAAATTTGCA 60.559 41.667 0.00 0.00 0.00 4.08
5215 6999 4.527564 GTGCGTTCAATCTGGTTATATGC 58.472 43.478 0.00 0.00 0.00 3.14
5266 7050 2.017049 GGATTGGGATCAACCGACAAG 58.983 52.381 0.00 0.00 40.11 3.16
5279 7063 0.613260 TGTTCAGTCTCGGGATTGGG 59.387 55.000 8.06 0.00 31.31 4.12
5548 7345 5.179555 CCACTCTTTGTTGCTTAGTTCCTAC 59.820 44.000 0.00 0.00 0.00 3.18
5549 7346 5.163237 ACCACTCTTTGTTGCTTAGTTCCTA 60.163 40.000 0.00 0.00 0.00 2.94
5570 7367 7.602265 GCTTCTTTTTGCTTATTTATTCCACCA 59.398 33.333 0.00 0.00 0.00 4.17
5573 7370 9.153721 CATGCTTCTTTTTGCTTATTTATTCCA 57.846 29.630 0.00 0.00 0.00 3.53
5583 7380 6.340522 AGTGTTTACATGCTTCTTTTTGCTT 58.659 32.000 0.00 0.00 0.00 3.91
5621 7418 5.353123 TGTGTCGCTCCTTTCCAAATATAAC 59.647 40.000 0.00 0.00 0.00 1.89
5622 7419 5.492895 TGTGTCGCTCCTTTCCAAATATAA 58.507 37.500 0.00 0.00 0.00 0.98
5628 7425 1.879380 CAATGTGTCGCTCCTTTCCAA 59.121 47.619 0.00 0.00 0.00 3.53
5640 7437 8.492673 TTGGAGAATGATAACTACAATGTGTC 57.507 34.615 0.00 0.00 32.83 3.67
5690 7487 2.928757 GCATGCAACTCAGACAGACTAG 59.071 50.000 14.21 0.00 0.00 2.57
5692 7489 1.347050 AGCATGCAACTCAGACAGACT 59.653 47.619 21.98 0.00 0.00 3.24
5695 7492 1.520494 ACAGCATGCAACTCAGACAG 58.480 50.000 21.98 0.00 42.53 3.51
5758 7555 8.675040 AAAAGCGAGATAAGTAGAAAATTTGC 57.325 30.769 0.00 0.00 0.00 3.68
5783 7580 9.469807 TGAAAGCGAGATAAATTTTGCTAAAAA 57.530 25.926 0.00 0.00 39.53 1.94
5784 7581 9.638239 ATGAAAGCGAGATAAATTTTGCTAAAA 57.362 25.926 0.00 0.00 32.93 1.52
5785 7582 9.638239 AATGAAAGCGAGATAAATTTTGCTAAA 57.362 25.926 0.00 0.00 32.93 1.85
5923 7723 2.409948 AGCAGTTTAGCAGGCCTTAG 57.590 50.000 0.00 0.00 36.85 2.18
5924 7724 3.992943 TTAGCAGTTTAGCAGGCCTTA 57.007 42.857 0.00 0.00 36.85 2.69
5971 7772 5.077564 TGTAGCCGTAGATGGTGAAGATAT 58.922 41.667 0.00 0.00 0.00 1.63
5980 7781 2.910688 ACCAATGTAGCCGTAGATGG 57.089 50.000 0.00 0.00 0.00 3.51
6040 7841 1.696832 CGCCCTTCTAAACAGAGCGC 61.697 60.000 0.00 0.00 35.33 5.92
6047 7848 2.199236 CGATACCACGCCCTTCTAAAC 58.801 52.381 0.00 0.00 0.00 2.01
6056 7857 1.076533 CACACTGACGATACCACGCC 61.077 60.000 0.00 0.00 36.70 5.68
6058 7859 1.199327 AGACACACTGACGATACCACG 59.801 52.381 0.00 0.00 39.31 4.94
6065 7866 0.464036 AAGCCAAGACACACTGACGA 59.536 50.000 0.00 0.00 0.00 4.20
6067 7868 2.139118 GAGAAGCCAAGACACACTGAC 58.861 52.381 0.00 0.00 0.00 3.51
6164 7967 7.803189 ACACATATTCAACGTCAACTTGAAATC 59.197 33.333 3.90 0.00 40.22 2.17
6256 8059 3.238108 ACTCCATGTCTTAGAACTGCG 57.762 47.619 0.00 0.00 0.00 5.18
6304 8107 2.806856 GCGCTGATGGTCAAGCTCG 61.807 63.158 0.00 0.00 30.65 5.03
6458 8301 8.500753 TCGGTTCTGTTAATAACATAGCAAAT 57.499 30.769 6.27 0.00 41.26 2.32
6529 8372 6.604396 ACCATACATGACATGAATGATGTTGT 59.396 34.615 22.19 10.04 45.90 3.32
6547 8390 0.312416 GGTGCGCAACAAACCATACA 59.688 50.000 23.15 0.00 33.94 2.29
6592 8435 8.833493 TGTGTTGCAAAGATCTATATGAGATTG 58.167 33.333 0.00 0.00 45.48 2.67
6597 8440 7.414429 GCAACTGTGTTGCAAAGATCTATATGA 60.414 37.037 24.70 0.00 44.34 2.15
6603 8446 3.360249 GCAACTGTGTTGCAAAGATCT 57.640 42.857 24.70 0.00 44.34 2.75
6625 8468 6.070653 ACACCAAATGAAACCTGATTGCATAT 60.071 34.615 0.00 0.00 0.00 1.78
6629 8472 3.993920 ACACCAAATGAAACCTGATTGC 58.006 40.909 0.00 0.00 0.00 3.56
6633 8476 6.723298 ACAATAACACCAAATGAAACCTGA 57.277 33.333 0.00 0.00 0.00 3.86
6634 8477 7.279758 ACAAACAATAACACCAAATGAAACCTG 59.720 33.333 0.00 0.00 0.00 4.00
6635 8478 7.334858 ACAAACAATAACACCAAATGAAACCT 58.665 30.769 0.00 0.00 0.00 3.50
6653 8496 6.367422 CCAGTTGTGAAGCTTTTTACAAACAA 59.633 34.615 19.67 11.27 35.12 2.83
6659 8502 5.273944 CAGTCCAGTTGTGAAGCTTTTTAC 58.726 41.667 0.00 1.33 0.00 2.01
6861 8704 1.415659 CCATCCAACCAGGCAAAACAA 59.584 47.619 0.00 0.00 37.29 2.83
6951 8794 2.229062 CTGATGAGCATACCGGTCGTAT 59.771 50.000 12.40 0.00 45.52 3.06
6954 8797 0.668535 TCTGATGAGCATACCGGTCG 59.331 55.000 12.40 4.61 45.52 4.79
6980 8824 9.185192 CTCAGTTTAGAAAATGATGGAAACAAC 57.815 33.333 5.68 0.00 41.43 3.32
7085 8930 8.887264 ACATAAACCATAATTGACCCTTTACA 57.113 30.769 0.00 0.00 0.00 2.41
7130 8990 6.842437 TTGGTTATTAAGTTAGCCATGCAA 57.158 33.333 0.00 0.00 33.19 4.08
7159 9019 1.369625 CTGTGGCAGGAAATACGACC 58.630 55.000 0.00 0.00 0.00 4.79
7180 9040 5.193679 GGCTTCCTTGTATTCACCAGTAAT 58.806 41.667 0.00 0.00 0.00 1.89
7322 9186 0.460987 GACATCCACAGAAGCGAGGG 60.461 60.000 0.00 0.00 0.00 4.30
7324 9188 1.354040 GTGACATCCACAGAAGCGAG 58.646 55.000 0.00 0.00 45.03 5.03
7340 9204 1.013596 CGGCAAACTGTCAACTGTGA 58.986 50.000 0.00 0.00 0.00 3.58
7342 9206 0.732571 CACGGCAAACTGTCAACTGT 59.267 50.000 0.00 0.00 31.05 3.55
7400 9265 1.088340 CGCACCAGGAATCAGCTCAG 61.088 60.000 0.00 0.00 0.00 3.35
7550 9424 0.729690 GCGGTTGAGATGAGCTTTCC 59.270 55.000 0.00 0.00 0.00 3.13
7585 9460 1.546589 AACCGTCGGAAGGGCATACA 61.547 55.000 20.51 0.00 33.52 2.29
7617 9492 1.040646 ACGTGTGAGTGTCATGGACT 58.959 50.000 0.00 0.00 33.15 3.85
7629 9506 1.067495 TGATGCCAACGATACGTGTGA 60.067 47.619 0.00 0.00 39.99 3.58
7630 9507 1.324435 CTGATGCCAACGATACGTGTG 59.676 52.381 0.00 0.00 39.99 3.82
7631 9508 1.067142 ACTGATGCCAACGATACGTGT 60.067 47.619 0.00 0.00 39.99 4.49
7632 9509 1.640428 ACTGATGCCAACGATACGTG 58.360 50.000 0.00 0.00 39.99 4.49
7634 9511 2.787723 GCAAACTGATGCCAACGATACG 60.788 50.000 0.00 0.00 40.49 3.06
7635 9512 2.161410 TGCAAACTGATGCCAACGATAC 59.839 45.455 0.00 0.00 45.83 2.24
7636 9513 2.431454 TGCAAACTGATGCCAACGATA 58.569 42.857 0.00 0.00 45.83 2.92
7637 9514 1.246649 TGCAAACTGATGCCAACGAT 58.753 45.000 0.00 0.00 45.83 3.73
7638 9515 1.068402 CATGCAAACTGATGCCAACGA 60.068 47.619 0.00 0.00 45.83 3.85
7639 9516 1.342555 CATGCAAACTGATGCCAACG 58.657 50.000 0.00 0.00 45.83 4.10
7640 9517 1.073177 GCATGCAAACTGATGCCAAC 58.927 50.000 14.21 0.00 45.83 3.77
7645 9522 2.193447 GCTGATGCATGCAAACTGATG 58.807 47.619 26.68 11.50 39.41 3.07
7693 9571 4.402474 GGTAGGAAGATTCAAAACATGGGG 59.598 45.833 0.00 0.00 0.00 4.96
7772 9847 5.200368 AGATTTTGGAAGCATTTGTCGTT 57.800 34.783 0.00 0.00 0.00 3.85
7820 9898 4.806775 GCAAAGTTAAGCGGGAAAGAAAAA 59.193 37.500 0.00 0.00 0.00 1.94
7888 9966 1.657822 GCTCCAGCTAGCTGTTAACC 58.342 55.000 36.14 19.24 42.15 2.85
7905 9983 1.059913 AACACCTAGCAAGACCAGCT 58.940 50.000 0.00 0.00 45.77 4.24
7952 10034 2.727123 TCAAACAGAACCAGCCTTGA 57.273 45.000 0.00 0.00 0.00 3.02
7967 10049 0.313672 GACAGCCGTTGCCAATCAAA 59.686 50.000 0.00 0.00 38.69 2.69
7983 10065 0.764271 TGCCAATCAGACACAGGACA 59.236 50.000 0.00 0.00 0.00 4.02
7984 10066 1.896220 TTGCCAATCAGACACAGGAC 58.104 50.000 0.00 0.00 0.00 3.85
7985 10067 2.439409 CATTGCCAATCAGACACAGGA 58.561 47.619 0.00 0.00 0.00 3.86
7986 10068 1.475280 CCATTGCCAATCAGACACAGG 59.525 52.381 0.00 0.00 0.00 4.00
7987 10069 1.135199 GCCATTGCCAATCAGACACAG 60.135 52.381 0.00 0.00 0.00 3.66
7988 10070 0.889994 GCCATTGCCAATCAGACACA 59.110 50.000 0.00 0.00 0.00 3.72
7989 10071 0.889994 TGCCATTGCCAATCAGACAC 59.110 50.000 0.00 0.00 36.33 3.67
7990 10072 1.630223 TTGCCATTGCCAATCAGACA 58.370 45.000 0.00 0.00 36.33 3.41
7991 10073 2.546778 CATTGCCATTGCCAATCAGAC 58.453 47.619 0.00 0.00 36.33 3.51
7992 10074 1.483004 CCATTGCCATTGCCAATCAGA 59.517 47.619 0.00 0.00 36.33 3.27
7993 10075 1.948104 CCATTGCCATTGCCAATCAG 58.052 50.000 0.00 0.00 36.33 2.90
8004 10086 2.203669 AACAGCCAGCCATTGCCA 60.204 55.556 0.00 0.00 38.69 4.92
8046 10128 4.689345 CCTGTACTACAGTAAAGCACAACC 59.311 45.833 14.00 0.00 44.50 3.77
8048 10130 4.345837 ACCCTGTACTACAGTAAAGCACAA 59.654 41.667 14.00 0.00 44.50 3.33
8050 10132 4.532314 ACCCTGTACTACAGTAAAGCAC 57.468 45.455 14.00 0.00 44.50 4.40
8055 10137 4.019174 GGCTGTACCCTGTACTACAGTAA 58.981 47.826 16.83 0.00 44.50 2.24
8104 10188 1.153469 GCAGCAGCTCCAGTAGGTC 60.153 63.158 0.00 0.00 37.91 3.85
8105 10189 2.985456 GCAGCAGCTCCAGTAGGT 59.015 61.111 0.00 0.00 37.91 3.08
8185 10279 2.677003 CCGACCAACCGATGCACAC 61.677 63.158 0.00 0.00 0.00 3.82
8190 10284 2.303163 TTGATACCGACCAACCGATG 57.697 50.000 0.00 0.00 0.00 3.84
8191 10285 3.004862 GTTTTGATACCGACCAACCGAT 58.995 45.455 0.00 0.00 0.00 4.18
8194 10288 2.227149 GTGGTTTTGATACCGACCAACC 59.773 50.000 0.00 0.00 43.25 3.77


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

AutoCloner maintained by Alex Coulton.