Multiple sequence alignment - TraesCS3A01G316600

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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 TraesCS3A01G316600 chr3A 100.000 6648 0 0 1 6648 557262844 557256197 0.000000e+00 12277.0
1 TraesCS3A01G316600 chr3D 94.750 5962 207 39 105 6034 428464773 428470660 0.000000e+00 9178.0
2 TraesCS3A01G316600 chr3D 89.175 582 39 8 1405 1984 548524732 548525291 0.000000e+00 704.0
3 TraesCS3A01G316600 chr3D 91.515 165 11 3 2 166 428464615 428464776 2.410000e-54 224.0
4 TraesCS3A01G316600 chr3D 87.565 193 15 2 6292 6484 428472904 428473087 1.450000e-51 215.0
5 TraesCS3A01G316600 chr3D 89.623 106 10 1 6040 6144 428470718 428470823 4.180000e-27 134.0
6 TraesCS3A01G316600 chr3B 94.305 3758 135 33 2290 6030 560117396 560121091 0.000000e+00 5681.0
7 TraesCS3A01G316600 chr3B 95.439 1732 53 8 573 2291 560115584 560117302 0.000000e+00 2737.0
8 TraesCS3A01G316600 chr3B 92.034 477 23 6 105 578 560114874 560115338 0.000000e+00 656.0
9 TraesCS3A01G316600 chr3B 84.492 374 30 12 6292 6646 560122686 560123050 1.770000e-90 344.0
10 TraesCS3A01G316600 chr3B 94.578 166 8 1 1 166 560114713 560114877 8.560000e-64 255.0
11 TraesCS3A01G316600 chr3B 87.179 117 12 2 6031 6144 560121145 560121261 5.410000e-26 130.0
12 TraesCS3A01G316600 chr5D 87.099 1558 160 23 749 2291 410559239 410560770 0.000000e+00 1725.0
13 TraesCS3A01G316600 chr5D 93.299 582 31 3 1405 1984 493821226 493820651 0.000000e+00 852.0
14 TraesCS3A01G316600 chr5D 88.603 544 35 13 2363 2901 410560964 410561485 2.610000e-178 636.0
15 TraesCS3A01G316600 chr5D 77.268 1025 175 31 1680 2679 30431110 30430119 3.500000e-152 549.0
16 TraesCS3A01G316600 chr5D 81.155 658 101 16 4419 5061 30428680 30428031 2.140000e-139 507.0
17 TraesCS3A01G316600 chr5D 82.601 592 48 19 166 752 410548093 410548634 7.800000e-129 472.0
18 TraesCS3A01G316600 chr5D 90.441 272 20 5 2885 3150 410561499 410561770 2.950000e-93 353.0
19 TraesCS3A01G316600 chr5D 84.404 218 21 5 6287 6503 410603629 410603834 1.130000e-47 202.0
20 TraesCS3A01G316600 chr5D 83.163 196 27 6 3673 3863 30429306 30429112 2.460000e-39 174.0
21 TraesCS3A01G316600 chr5D 80.328 183 31 4 4112 4291 255417288 255417108 4.180000e-27 134.0
22 TraesCS3A01G316600 chr6A 86.845 821 73 24 2801 3596 612117494 612116684 0.000000e+00 885.0
23 TraesCS3A01G316600 chr6A 86.974 760 65 17 4320 5074 612116220 612115490 0.000000e+00 824.0
24 TraesCS3A01G316600 chr6A 82.609 184 27 4 4111 4291 594219006 594218825 2.480000e-34 158.0
25 TraesCS3A01G316600 chr6B 86.807 758 68 18 4320 5074 710649542 710648814 0.000000e+00 817.0
26 TraesCS3A01G316600 chr6B 86.915 726 63 22 2801 3504 710650786 710650071 0.000000e+00 785.0
27 TraesCS3A01G316600 chr6D 85.821 670 66 12 4320 4988 465983675 465983034 0.000000e+00 684.0
28 TraesCS3A01G316600 chr6D 87.214 524 43 15 2801 3309 465984713 465984199 5.780000e-160 575.0
29 TraesCS3A01G316600 chr6D 87.781 311 32 5 3806 4114 465983979 465983673 6.340000e-95 359.0
30 TraesCS3A01G316600 chr5B 78.316 1033 166 32 1680 2681 22820146 22819141 1.230000e-171 614.0
31 TraesCS3A01G316600 chr5B 77.702 1027 171 35 1684 2679 22513258 22512259 5.780000e-160 575.0
32 TraesCS3A01G316600 chr5B 80.945 656 107 12 4419 5061 22817669 22817019 2.770000e-138 503.0
33 TraesCS3A01G316600 chr5B 80.368 652 116 11 4419 5061 22510825 22510177 1.000000e-132 484.0
34 TraesCS3A01G316600 chr5B 86.585 164 19 3 3702 3863 22511397 22511235 1.910000e-40 178.0
35 TraesCS3A01G316600 chr5B 86.897 145 17 2 3702 3845 22818303 22818160 1.920000e-35 161.0
36 TraesCS3A01G316600 chr5A 82.692 208 26 3 6288 6495 522107903 522108100 6.850000e-40 176.0
37 TraesCS3A01G316600 chr5A 82.967 182 26 4 4113 4291 404561128 404560949 6.900000e-35 159.0
38 TraesCS3A01G316600 chr4D 84.393 173 22 4 4113 4282 125689858 125690028 1.480000e-36 165.0
39 TraesCS3A01G316600 chr4D 83.237 173 24 4 4113 4282 125589251 125589421 3.210000e-33 154.0
40 TraesCS3A01G316600 chr4D 91.111 45 4 0 4288 4332 423984842 423984886 2.000000e-05 62.1
41 TraesCS3A01G316600 chr4B 83.815 173 23 4 4113 4282 329805707 329805877 6.900000e-35 159.0
42 TraesCS3A01G316600 chr7D 81.868 182 28 4 4113 4291 516422167 516421988 1.490000e-31 148.0
43 TraesCS3A01G316600 chr2D 97.436 39 1 0 4287 4325 144469830 144469792 4.300000e-07 67.6
44 TraesCS3A01G316600 chr2D 89.362 47 3 2 4287 4333 340301658 340301614 2.590000e-04 58.4
45 TraesCS3A01G316600 chr2B 91.667 48 2 2 4287 4333 570832700 570832654 1.550000e-06 65.8
46 TraesCS3A01G316600 chr2B 86.207 58 6 2 4287 4342 342299149 342299092 2.000000e-05 62.1
47 TraesCS3A01G316600 chr2B 86.792 53 5 2 4287 4337 157756209 157756261 2.590000e-04 58.4
48 TraesCS3A01G316600 chr1B 89.796 49 4 1 4287 4335 410815268 410815315 2.000000e-05 62.1


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 TraesCS3A01G316600 chr3A 557256197 557262844 6647 True 12277.000000 12277 100.000000 1 6648 1 chr3A.!!$R1 6647
1 TraesCS3A01G316600 chr3D 428464615 428473087 8472 False 2437.750000 9178 90.863250 2 6484 4 chr3D.!!$F2 6482
2 TraesCS3A01G316600 chr3D 548524732 548525291 559 False 704.000000 704 89.175000 1405 1984 1 chr3D.!!$F1 579
3 TraesCS3A01G316600 chr3B 560114713 560123050 8337 False 1633.833333 5681 91.337833 1 6646 6 chr3B.!!$F1 6645
4 TraesCS3A01G316600 chr5D 410559239 410561770 2531 False 904.666667 1725 88.714333 749 3150 3 chr5D.!!$F3 2401
5 TraesCS3A01G316600 chr5D 493820651 493821226 575 True 852.000000 852 93.299000 1405 1984 1 chr5D.!!$R2 579
6 TraesCS3A01G316600 chr5D 410548093 410548634 541 False 472.000000 472 82.601000 166 752 1 chr5D.!!$F1 586
7 TraesCS3A01G316600 chr5D 30428031 30431110 3079 True 410.000000 549 80.528667 1680 5061 3 chr5D.!!$R3 3381
8 TraesCS3A01G316600 chr6A 612115490 612117494 2004 True 854.500000 885 86.909500 2801 5074 2 chr6A.!!$R2 2273
9 TraesCS3A01G316600 chr6B 710648814 710650786 1972 True 801.000000 817 86.861000 2801 5074 2 chr6B.!!$R1 2273
10 TraesCS3A01G316600 chr6D 465983034 465984713 1679 True 539.333333 684 86.938667 2801 4988 3 chr6D.!!$R1 2187
11 TraesCS3A01G316600 chr5B 22817019 22820146 3127 True 426.000000 614 82.052667 1680 5061 3 chr5B.!!$R2 3381
12 TraesCS3A01G316600 chr5B 22510177 22513258 3081 True 412.333333 575 81.551667 1684 5061 3 chr5B.!!$R1 3377

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
164 216 2.012673 GCCTGATTAAGCACTGACCAG 58.987 52.381 0.00 0.00 0.00 4.00 F
1303 1625 1.184431 TAATGCTGGGCCACATTGTG 58.816 50.000 28.92 9.92 37.11 3.33 F
1588 1930 4.153117 ACGTCTGAAAAGATTGCTGATGAC 59.847 41.667 4.70 0.00 0.00 3.06 F
2388 2992 0.251742 TGGAACTTCCAATGCCCCTG 60.252 55.000 8.15 0.00 45.00 4.45 F
3582 4334 0.033781 TGCCACATTTTGCTCAAGGC 59.966 50.000 0.00 0.00 40.93 4.35 F
4678 5599 0.181350 CTCAATCTGGGCCAGGTACC 59.819 60.000 32.23 2.73 31.51 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 2095 1.607251 GGGAACACCTCTGTAACACGG 60.607 57.143 0.00 0.0 35.85 4.94 R
2373 2977 1.002134 CGTCAGGGGCATTGGAAGT 60.002 57.895 0.00 0.0 0.00 3.01 R
2958 3677 1.803453 ATTCCTTCCCAGGCCTTGCA 61.803 55.000 0.00 0.0 40.58 4.08 R
4149 4982 2.600470 TGCAAAGCTTGACTTTTGGG 57.400 45.000 0.00 0.0 46.73 4.12 R
5385 6318 1.264288 CGTGGAAAGACTTGAACAGGC 59.736 52.381 0.00 0.0 0.00 4.85 R
6454 9463 0.031178 AAAGGCTGCGACTTTTGCTG 59.969 50.000 3.91 0.0 37.67 4.41 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
91 92 5.303589 CCTCCAGTTATATCCTACGGTCAAA 59.696 44.000 0.00 0.00 0.00 2.69
97 98 8.192774 CAGTTATATCCTACGGTCAAAGTTGTA 58.807 37.037 0.00 0.00 0.00 2.41
99 100 3.665745 TCCTACGGTCAAAGTTGTACC 57.334 47.619 0.00 0.00 0.00 3.34
100 101 2.964464 TCCTACGGTCAAAGTTGTACCA 59.036 45.455 7.47 0.00 32.34 3.25
103 104 2.988570 ACGGTCAAAGTTGTACCAACA 58.011 42.857 9.53 0.00 32.34 3.33
164 216 2.012673 GCCTGATTAAGCACTGACCAG 58.987 52.381 0.00 0.00 0.00 4.00
264 316 8.834465 CATATGGCAGGTAGATTAATCATAAGC 58.166 37.037 17.56 13.08 0.00 3.09
776 1087 4.437239 AGACTGTTTCTGTGTCTTGACAG 58.563 43.478 3.45 0.00 44.14 3.51
780 1091 4.769688 TGTTTCTGTGTCTTGACAGTCAT 58.230 39.130 3.45 0.00 43.38 3.06
810 1124 2.415893 CCTCTGCGCCTTGTAAAAATGG 60.416 50.000 4.18 0.00 0.00 3.16
836 1150 6.767456 ACAAATATGTTGCCTTTTGATTGGA 58.233 32.000 0.00 0.00 35.91 3.53
873 1191 9.884465 CTATGCCTACTTCATTATAAGTTTTGC 57.116 33.333 0.00 0.00 40.20 3.68
874 1192 7.938140 TGCCTACTTCATTATAAGTTTTGCT 57.062 32.000 0.00 0.00 40.20 3.91
875 1193 7.761409 TGCCTACTTCATTATAAGTTTTGCTG 58.239 34.615 0.00 0.00 40.20 4.41
1132 1450 6.551227 GCTTTTGTTCCCCTGATTTATATCCT 59.449 38.462 0.00 0.00 0.00 3.24
1184 1502 6.308766 GCAAATGCTAATTGGACTAAACACTG 59.691 38.462 0.00 0.00 38.21 3.66
1187 1505 5.616270 TGCTAATTGGACTAAACACTGTGA 58.384 37.500 15.86 0.00 0.00 3.58
1188 1506 6.058833 TGCTAATTGGACTAAACACTGTGAA 58.941 36.000 15.86 0.00 0.00 3.18
1241 1563 9.074443 GTGAAGCTGTACTAAACTACTAATCAC 57.926 37.037 0.00 0.00 0.00 3.06
1261 1583 6.208988 TCACGTGAATCAAGTATTAGCTCT 57.791 37.500 17.62 0.00 0.00 4.09
1290 1612 2.827921 CCCCAAACAAGCTCTTAATGCT 59.172 45.455 0.00 0.00 43.32 3.79
1303 1625 1.184431 TAATGCTGGGCCACATTGTG 58.816 50.000 28.92 9.92 37.11 3.33
1442 1766 4.757149 GTCCTGTTGTAGCATGTTTCTCTT 59.243 41.667 0.00 0.00 0.00 2.85
1588 1930 4.153117 ACGTCTGAAAAGATTGCTGATGAC 59.847 41.667 4.70 0.00 0.00 3.06
1834 2179 8.954950 AAGGTTAGACATCTGAGACATTATTG 57.045 34.615 0.00 0.00 0.00 1.90
2197 2584 5.127194 TGAAAATGCTCTACGGAGTGTATCT 59.873 40.000 0.55 0.00 45.73 1.98
2253 2640 7.094162 TGCCTCGAACAAATTTGATATGGTAAA 60.094 33.333 24.64 7.34 0.00 2.01
2373 2977 0.610174 AGCTCGTGATGCTTCTGGAA 59.390 50.000 0.88 0.00 37.52 3.53
2388 2992 0.251742 TGGAACTTCCAATGCCCCTG 60.252 55.000 8.15 0.00 45.00 4.45
2427 3031 6.708054 TGATCTTCCTTTGAAGTCTTCAGAAC 59.292 38.462 14.75 7.69 46.66 3.01
2491 3095 8.314751 TCCTTTGGATCTCACTTTAAAGACTAG 58.685 37.037 21.92 14.15 0.00 2.57
2599 3205 4.279420 AGAAAGTGCATTCTTCCCAAAGAC 59.721 41.667 0.00 0.00 41.23 3.01
2940 3659 1.204941 ACTCAGAGTTATCGTGGTGGC 59.795 52.381 0.00 0.00 0.00 5.01
2958 3677 3.189287 GTGGCTCTCAAAATTCACGATGT 59.811 43.478 0.00 0.00 0.00 3.06
3142 3876 4.519213 CCTGTAATTCCCGTGGATGTAAA 58.481 43.478 0.00 0.00 0.00 2.01
3377 4123 1.696884 TGTCCTCATTGTACCTGCACA 59.303 47.619 0.00 0.00 0.00 4.57
3381 4127 3.820467 TCCTCATTGTACCTGCACAAAAG 59.180 43.478 0.00 0.00 41.50 2.27
3401 4147 9.125026 ACAAAAGATGGTATATCTTTGCTAAGG 57.875 33.333 13.73 5.05 44.77 2.69
3487 4233 6.737720 TCTATCTAGTGGAAGATGCATTGT 57.262 37.500 0.00 0.00 36.85 2.71
3558 4310 8.976986 AAAATATGAATGAGAACTTTGAGCAC 57.023 30.769 0.00 0.00 0.00 4.40
3582 4334 0.033781 TGCCACATTTTGCTCAAGGC 59.966 50.000 0.00 0.00 40.93 4.35
3611 4363 4.620609 TCATTTGCCGTTCGATTTCATTTG 59.379 37.500 0.00 0.00 0.00 2.32
3945 4707 5.702670 ACTATGGCATATTTCCGTCATTGAG 59.297 40.000 7.81 0.00 0.00 3.02
4039 4802 2.595238 ACCGAGACTACTCCTTGTGTT 58.405 47.619 0.00 0.00 39.76 3.32
4070 4887 9.743057 TTTAACTTTTGAGAATGTATGGTGTTG 57.257 29.630 0.00 0.00 0.00 3.33
4133 4966 4.534500 TGTACTCCCTATGTTCCACAATGT 59.466 41.667 0.00 0.00 0.00 2.71
4149 4982 6.368791 TCCACAATGTAGCGCATATAGATTTC 59.631 38.462 11.47 0.00 36.67 2.17
4191 5028 4.513406 ACTTTGACCAACTTTGTAGGGA 57.487 40.909 0.00 0.00 0.00 4.20
4318 5157 2.301346 CTACATTGTGGAATGGAGGGC 58.699 52.381 0.00 0.00 44.23 5.19
4332 5171 4.974368 TGGAGGGCGTAATAATTGTTTG 57.026 40.909 0.00 0.00 0.00 2.93
4386 5225 8.028938 ACATTGCTTTGGTAGTTTATGTCAATC 58.971 33.333 0.00 0.00 0.00 2.67
4416 5334 5.247792 CCCTTATGTGGTACCCTTATAGGAC 59.752 48.000 10.07 0.00 37.67 3.85
4678 5599 0.181350 CTCAATCTGGGCCAGGTACC 59.819 60.000 32.23 2.73 31.51 3.34
4739 5662 3.466836 TGCAGTTACTGACAGTTTGAGG 58.533 45.455 17.40 1.81 32.44 3.86
4740 5663 2.224314 GCAGTTACTGACAGTTTGAGGC 59.776 50.000 17.40 8.14 32.44 4.70
4743 5666 5.297547 CAGTTACTGACAGTTTGAGGCTTA 58.702 41.667 14.50 0.00 32.44 3.09
4927 5851 6.097554 TGTTTCTTTTGACCTGCCAGAATTTA 59.902 34.615 0.00 0.00 0.00 1.40
5065 5998 6.173339 TCCAGAGGTGATTTCATTTCTGTAC 58.827 40.000 16.41 0.00 37.42 2.90
5066 5999 6.013379 TCCAGAGGTGATTTCATTTCTGTACT 60.013 38.462 16.41 0.00 37.42 2.73
5071 6004 9.606631 GAGGTGATTTCATTTCTGTACTCTATT 57.393 33.333 0.00 0.00 0.00 1.73
5084 6017 4.386652 TGTACTCTATTTTGTTTCCGCGAC 59.613 41.667 8.23 0.00 0.00 5.19
5093 6026 1.950909 TGTTTCCGCGACAGGATTTTT 59.049 42.857 8.23 0.00 40.48 1.94
5139 6072 6.500684 TTGCCTGACTTGAAAATCTGATAC 57.499 37.500 0.00 0.00 0.00 2.24
5145 6078 6.409704 TGACTTGAAAATCTGATACCCTGAG 58.590 40.000 0.00 0.00 0.00 3.35
5200 6133 1.065126 GGAAAGCTGATACTGGCCTGT 60.065 52.381 20.00 20.00 0.00 4.00
5211 6144 1.001760 TGGCCTGTCCTCCTCTACC 59.998 63.158 3.32 0.00 35.26 3.18
5222 6155 2.628657 CCTCCTCTACCGGTTTAGATGG 59.371 54.545 15.04 13.57 0.00 3.51
5237 6170 3.127791 AGATGGAGAACCTGGATCAGT 57.872 47.619 0.00 0.00 37.04 3.41
5241 6174 2.711009 TGGAGAACCTGGATCAGTGTTT 59.289 45.455 0.00 0.00 37.04 2.83
5250 6183 1.003580 GGATCAGTGTTTGCTCCTCCA 59.996 52.381 0.00 0.00 38.73 3.86
5352 6285 1.142778 GCTCAGACACGGATCGCTTC 61.143 60.000 0.00 0.00 0.00 3.86
5385 6318 2.158900 AGTATGATCTTCCCTTGCACCG 60.159 50.000 0.00 0.00 0.00 4.94
5414 6348 4.819630 TCAAGTCTTTCCACGTGCTAAAAT 59.180 37.500 10.91 0.00 0.00 1.82
5421 6355 2.238646 TCCACGTGCTAAAATGGGATCT 59.761 45.455 10.91 0.00 32.73 2.75
5440 6374 6.127786 GGGATCTCTTTTGTTCTTCCAGAATG 60.128 42.308 0.00 0.00 36.50 2.67
5473 6407 0.394352 CCTCCATGGGCTTAAACGCT 60.394 55.000 13.02 0.00 0.00 5.07
5536 6473 0.823460 CAGAGTCCTCTCCTGAAGGC 59.177 60.000 0.00 0.00 41.26 4.35
5563 6500 2.043652 ATTGGCATTCCCAGCGCT 60.044 55.556 2.64 2.64 46.39 5.92
5587 6524 2.435059 GTCCGCTCCTTGCACTCC 60.435 66.667 0.00 0.00 43.06 3.85
5629 6566 0.035739 ACAACCACGGCGAATACCTT 59.964 50.000 16.62 0.00 0.00 3.50
5660 6597 1.727467 GTGTGAGTTGCAACGCCTT 59.273 52.632 27.22 9.76 0.00 4.35
5669 6606 1.305219 TGCAACGCCTTGGAGCATAC 61.305 55.000 0.00 0.00 0.00 2.39
5670 6607 1.993369 GCAACGCCTTGGAGCATACC 61.993 60.000 0.00 0.00 0.00 2.73
5694 6631 2.985847 GCAAGGCCGGTGCTTCTT 60.986 61.111 22.89 0.00 39.00 2.52
5696 6633 1.241315 GCAAGGCCGGTGCTTCTTTA 61.241 55.000 22.89 0.00 39.00 1.85
5699 6636 2.396157 GGCCGGTGCTTCTTTACGG 61.396 63.158 1.90 0.00 46.78 4.02
5707 6644 2.034179 GTGCTTCTTTACGGCCACTTTT 59.966 45.455 2.24 0.00 0.00 2.27
5755 6692 3.546543 CCAGGAAGCCCGGCGATA 61.547 66.667 9.30 0.00 37.58 2.92
5765 6703 0.962489 CCCGGCGATACAGAGAGAAT 59.038 55.000 9.30 0.00 0.00 2.40
5781 6719 2.431057 GAGAATCCGGAAGAGCCTTGTA 59.569 50.000 9.01 0.00 0.00 2.41
5856 6796 3.146847 GTGGAGGGTTGTACCTTTTGAG 58.853 50.000 0.00 0.00 42.10 3.02
5955 6895 5.931724 AGGGAGAAAACAACAACAACAAAAG 59.068 36.000 0.00 0.00 0.00 2.27
6007 6947 2.859526 TGAATGCTGCGTTTGAACAA 57.140 40.000 8.72 0.00 0.00 2.83
6030 6970 2.776526 TGTTGGGCTGGAGTGGGT 60.777 61.111 0.00 0.00 0.00 4.51
6031 6971 2.282462 GTTGGGCTGGAGTGGGTG 60.282 66.667 0.00 0.00 0.00 4.61
6032 6972 2.776526 TTGGGCTGGAGTGGGTGT 60.777 61.111 0.00 0.00 0.00 4.16
6034 6974 1.063070 TTGGGCTGGAGTGGGTGTTA 61.063 55.000 0.00 0.00 0.00 2.41
6035 6975 1.002502 GGGCTGGAGTGGGTGTTAC 60.003 63.158 0.00 0.00 0.00 2.50
6036 6976 1.489560 GGGCTGGAGTGGGTGTTACT 61.490 60.000 0.00 0.00 0.00 2.24
6037 6977 1.272807 GGCTGGAGTGGGTGTTACTA 58.727 55.000 0.00 0.00 0.00 1.82
6060 7055 5.738909 ACTGTGATCCTTACCAGAAGATTG 58.261 41.667 0.00 0.00 0.00 2.67
6066 7061 3.263425 TCCTTACCAGAAGATTGGGTGTC 59.737 47.826 0.00 0.00 42.76 3.67
6099 7094 4.254492 GGTAGTGCTTAACCAAGAGGAAG 58.746 47.826 0.00 0.00 38.69 3.46
6100 7095 2.784347 AGTGCTTAACCAAGAGGAAGC 58.216 47.619 0.00 0.00 42.29 3.86
6101 7096 2.106511 AGTGCTTAACCAAGAGGAAGCA 59.893 45.455 4.13 4.13 46.56 3.91
6113 7108 6.041979 ACCAAGAGGAAGCACAAATACAAATT 59.958 34.615 0.00 0.00 38.69 1.82
6122 7117 9.118236 GAAGCACAAATACAAATTCTGTTACTC 57.882 33.333 0.00 0.00 39.64 2.59
6139 7135 3.998099 ACTCTTTCTCTTGCTTTTGGC 57.002 42.857 0.00 0.00 42.22 4.52
6144 7140 0.179004 TCTCTTGCTTTTGGCGGGAA 60.179 50.000 0.00 0.00 45.43 3.97
6146 7142 0.602562 TCTTGCTTTTGGCGGGAATG 59.397 50.000 0.00 0.00 45.43 2.67
6148 7144 1.543802 CTTGCTTTTGGCGGGAATGTA 59.456 47.619 0.00 0.00 45.43 2.29
6149 7145 1.173043 TGCTTTTGGCGGGAATGTAG 58.827 50.000 0.00 0.00 45.43 2.74
6150 7146 0.179137 GCTTTTGGCGGGAATGTAGC 60.179 55.000 0.00 0.00 0.00 3.58
6151 7147 1.173043 CTTTTGGCGGGAATGTAGCA 58.827 50.000 0.00 0.00 0.00 3.49
6152 7148 0.885196 TTTTGGCGGGAATGTAGCAC 59.115 50.000 0.00 0.00 0.00 4.40
6153 7149 0.250945 TTTGGCGGGAATGTAGCACA 60.251 50.000 0.00 0.00 0.00 4.57
6154 7150 0.250945 TTGGCGGGAATGTAGCACAA 60.251 50.000 0.00 0.00 0.00 3.33
6155 7151 0.958382 TGGCGGGAATGTAGCACAAC 60.958 55.000 0.00 0.00 0.00 3.32
6156 7152 0.958382 GGCGGGAATGTAGCACAACA 60.958 55.000 0.00 0.00 0.00 3.33
6157 7153 0.168128 GCGGGAATGTAGCACAACAC 59.832 55.000 0.00 0.00 30.75 3.32
6158 7154 1.518325 CGGGAATGTAGCACAACACA 58.482 50.000 0.00 0.00 30.75 3.72
6159 7155 2.083774 CGGGAATGTAGCACAACACAT 58.916 47.619 0.00 0.00 36.96 3.21
6160 7156 2.159531 CGGGAATGTAGCACAACACATG 60.160 50.000 0.00 0.00 35.59 3.21
6161 7157 2.415893 GGGAATGTAGCACAACACATGC 60.416 50.000 0.00 0.00 43.74 4.06
6162 7158 2.415893 GGAATGTAGCACAACACATGCC 60.416 50.000 0.00 0.00 42.36 4.40
6164 7160 1.685148 TGTAGCACAACACATGCCAA 58.315 45.000 0.00 0.00 44.53 4.52
6165 7161 2.027385 TGTAGCACAACACATGCCAAA 58.973 42.857 0.00 0.00 44.53 3.28
6166 7162 2.223688 TGTAGCACAACACATGCCAAAC 60.224 45.455 0.00 0.00 44.53 2.93
6167 7163 0.822811 AGCACAACACATGCCAAACA 59.177 45.000 0.00 0.00 44.53 2.83
6169 7165 1.471327 GCACAACACATGCCAAACAGT 60.471 47.619 0.00 0.00 37.08 3.55
6170 7166 2.195096 CACAACACATGCCAAACAGTG 58.805 47.619 0.00 0.00 35.09 3.66
6171 7167 1.824230 ACAACACATGCCAAACAGTGT 59.176 42.857 0.00 0.00 40.24 3.55
6172 7168 3.020274 ACAACACATGCCAAACAGTGTA 58.980 40.909 0.00 0.00 38.71 2.90
6173 7169 3.066621 ACAACACATGCCAAACAGTGTAG 59.933 43.478 0.00 0.00 38.71 2.74
6174 7170 3.207265 ACACATGCCAAACAGTGTAGA 57.793 42.857 0.00 0.00 38.23 2.59
6175 7171 3.141398 ACACATGCCAAACAGTGTAGAG 58.859 45.455 0.00 0.00 38.23 2.43
6176 7172 3.141398 CACATGCCAAACAGTGTAGAGT 58.859 45.455 0.00 0.00 0.00 3.24
6177 7173 4.202315 ACACATGCCAAACAGTGTAGAGTA 60.202 41.667 0.00 0.00 38.23 2.59
6178 7174 4.389992 CACATGCCAAACAGTGTAGAGTAG 59.610 45.833 0.00 0.00 0.00 2.57
6179 7175 4.283467 ACATGCCAAACAGTGTAGAGTAGA 59.717 41.667 0.00 0.00 0.00 2.59
6180 7176 4.948341 TGCCAAACAGTGTAGAGTAGAA 57.052 40.909 0.00 0.00 0.00 2.10
6181 7177 4.628074 TGCCAAACAGTGTAGAGTAGAAC 58.372 43.478 0.00 0.00 0.00 3.01
6182 7178 3.673809 GCCAAACAGTGTAGAGTAGAACG 59.326 47.826 0.00 0.00 0.00 3.95
6183 7179 4.795308 GCCAAACAGTGTAGAGTAGAACGT 60.795 45.833 0.00 0.00 0.00 3.99
6184 7180 5.287226 CCAAACAGTGTAGAGTAGAACGTT 58.713 41.667 0.00 0.00 0.00 3.99
6185 7181 5.175126 CCAAACAGTGTAGAGTAGAACGTTG 59.825 44.000 5.00 0.00 0.00 4.10
6186 7182 5.762825 AACAGTGTAGAGTAGAACGTTGA 57.237 39.130 5.00 0.00 0.00 3.18
6187 7183 5.961396 ACAGTGTAGAGTAGAACGTTGAT 57.039 39.130 5.00 0.00 0.00 2.57
6188 7184 7.444629 AACAGTGTAGAGTAGAACGTTGATA 57.555 36.000 5.00 0.00 0.00 2.15
6189 7185 7.627298 ACAGTGTAGAGTAGAACGTTGATAT 57.373 36.000 5.00 0.00 0.00 1.63
6190 7186 8.728337 ACAGTGTAGAGTAGAACGTTGATATA 57.272 34.615 5.00 0.00 0.00 0.86
6191 7187 9.339850 ACAGTGTAGAGTAGAACGTTGATATAT 57.660 33.333 5.00 0.00 0.00 0.86
6192 7188 9.600646 CAGTGTAGAGTAGAACGTTGATATATG 57.399 37.037 5.00 0.00 0.00 1.78
6193 7189 8.291032 AGTGTAGAGTAGAACGTTGATATATGC 58.709 37.037 5.00 0.00 0.00 3.14
6194 7190 8.074370 GTGTAGAGTAGAACGTTGATATATGCA 58.926 37.037 5.00 0.00 0.00 3.96
6195 7191 8.074370 TGTAGAGTAGAACGTTGATATATGCAC 58.926 37.037 5.00 0.00 0.00 4.57
6196 7192 7.039313 AGAGTAGAACGTTGATATATGCACA 57.961 36.000 5.00 0.00 0.00 4.57
6197 7193 7.661968 AGAGTAGAACGTTGATATATGCACAT 58.338 34.615 5.00 0.00 0.00 3.21
6198 7194 7.596621 AGAGTAGAACGTTGATATATGCACATG 59.403 37.037 5.00 0.00 0.00 3.21
6199 7195 5.348418 AGAACGTTGATATATGCACATGC 57.652 39.130 5.00 0.00 42.50 4.06
6211 7207 2.953466 GCACATGCATGACTCCATTT 57.047 45.000 32.75 4.93 41.59 2.32
6212 7208 2.536365 GCACATGCATGACTCCATTTG 58.464 47.619 32.75 17.99 41.59 2.32
6213 7209 2.737359 GCACATGCATGACTCCATTTGG 60.737 50.000 32.75 1.99 41.59 3.28
6214 7210 2.756207 CACATGCATGACTCCATTTGGA 59.244 45.455 32.75 0.00 43.08 3.53
6215 7211 2.756760 ACATGCATGACTCCATTTGGAC 59.243 45.455 32.75 0.00 39.78 4.02
6216 7212 2.583024 TGCATGACTCCATTTGGACA 57.417 45.000 0.00 0.00 39.78 4.02
6217 7213 2.161855 TGCATGACTCCATTTGGACAC 58.838 47.619 0.00 0.00 39.78 3.67
6218 7214 2.161855 GCATGACTCCATTTGGACACA 58.838 47.619 0.00 0.00 39.78 3.72
6219 7215 2.557924 GCATGACTCCATTTGGACACAA 59.442 45.455 0.00 0.00 39.78 3.33
6220 7216 3.612479 GCATGACTCCATTTGGACACAAC 60.612 47.826 0.00 0.00 39.78 3.32
6221 7217 3.289407 TGACTCCATTTGGACACAACA 57.711 42.857 0.00 0.00 39.78 3.33
6222 7218 2.948979 TGACTCCATTTGGACACAACAC 59.051 45.455 0.00 0.00 39.78 3.32
6223 7219 2.293399 GACTCCATTTGGACACAACACC 59.707 50.000 0.00 0.00 39.78 4.16
6224 7220 2.091885 ACTCCATTTGGACACAACACCT 60.092 45.455 0.00 0.00 39.78 4.00
6225 7221 3.137544 ACTCCATTTGGACACAACACCTA 59.862 43.478 0.00 0.00 39.78 3.08
6231 7227 0.037605 GGACACAACACCTACCGGAG 60.038 60.000 9.46 0.28 0.00 4.63
6254 7250 8.194769 GGAGATCAAAGTTGTGGAGTTTTAAAA 58.805 33.333 0.00 0.00 0.00 1.52
6267 7263 9.255304 GTGGAGTTTTAAAATTAACATGAGCAA 57.745 29.630 3.52 0.00 0.00 3.91
6276 8751 8.504812 AAAATTAACATGAGCAACCAAAAGTT 57.495 26.923 0.00 0.00 40.16 2.66
6281 8756 9.606631 TTAACATGAGCAACCAAAAGTTATTTT 57.393 25.926 0.00 0.00 39.22 1.82
6283 8758 9.606631 AACATGAGCAACCAAAAGTTATTTTAA 57.393 25.926 0.00 0.00 36.47 1.52
6285 8760 7.707774 TGAGCAACCAAAAGTTATTTTAAGC 57.292 32.000 0.00 0.00 36.47 3.09
6289 8764 7.719193 AGCAACCAAAAGTTATTTTAAGCCATT 59.281 29.630 0.00 0.00 36.47 3.16
6290 8765 7.802720 GCAACCAAAAGTTATTTTAAGCCATTG 59.197 33.333 0.00 0.00 36.47 2.82
6427 9436 1.271379 TCATGCTCCGAGTACAAACGT 59.729 47.619 0.00 0.00 0.00 3.99
6430 9439 1.058404 GCTCCGAGTACAAACGTGAC 58.942 55.000 0.00 0.00 0.00 3.67
6433 9442 1.069703 TCCGAGTACAAACGTGACGAG 60.070 52.381 13.70 3.47 0.00 4.18
6437 9446 2.723143 GAGTACAAACGTGACGAGGAAC 59.277 50.000 13.70 3.08 0.00 3.62
6454 9463 3.703052 AGGAACATCAAAATGAGGATGCC 59.297 43.478 0.00 0.00 43.64 4.40
6471 9480 2.263741 CCAGCAAAAGTCGCAGCCT 61.264 57.895 0.00 0.00 0.00 4.58
6473 9482 0.031178 CAGCAAAAGTCGCAGCCTTT 59.969 50.000 0.00 0.00 0.00 3.11
6476 9485 2.162408 AGCAAAAGTCGCAGCCTTTATC 59.838 45.455 0.00 0.00 0.00 1.75
6484 9493 1.488527 GCAGCCTTTATCGTAGTCGG 58.511 55.000 0.00 0.00 37.69 4.79
6485 9494 1.202382 GCAGCCTTTATCGTAGTCGGT 60.202 52.381 0.00 0.00 37.69 4.69
6486 9495 2.728922 CAGCCTTTATCGTAGTCGGTC 58.271 52.381 0.00 0.00 37.69 4.79
6489 9498 2.026641 CCTTTATCGTAGTCGGTCCCA 58.973 52.381 0.00 0.00 37.69 4.37
6490 9499 2.626743 CCTTTATCGTAGTCGGTCCCAT 59.373 50.000 0.00 0.00 37.69 4.00
6492 9501 3.996150 TTATCGTAGTCGGTCCCATTC 57.004 47.619 0.00 0.00 37.69 2.67
6493 9502 1.038280 ATCGTAGTCGGTCCCATTCC 58.962 55.000 0.00 0.00 37.69 3.01
6494 9503 0.033796 TCGTAGTCGGTCCCATTCCT 60.034 55.000 0.00 0.00 37.69 3.36
6495 9504 1.212688 TCGTAGTCGGTCCCATTCCTA 59.787 52.381 0.00 0.00 37.69 2.94
6496 9505 1.607628 CGTAGTCGGTCCCATTCCTAG 59.392 57.143 0.00 0.00 0.00 3.02
6497 9506 2.747467 CGTAGTCGGTCCCATTCCTAGA 60.747 54.545 0.00 0.00 0.00 2.43
6498 9507 2.074729 AGTCGGTCCCATTCCTAGAG 57.925 55.000 0.00 0.00 0.00 2.43
6499 9508 1.569548 AGTCGGTCCCATTCCTAGAGA 59.430 52.381 0.00 0.00 0.00 3.10
6500 9509 1.682323 GTCGGTCCCATTCCTAGAGAC 59.318 57.143 0.00 0.00 0.00 3.36
6520 9534 3.167485 ACTAACCTATGTGAACACGGGA 58.833 45.455 14.38 0.00 0.00 5.14
6521 9535 2.467566 AACCTATGTGAACACGGGAC 57.532 50.000 14.38 0.00 0.00 4.46
6522 9536 1.640917 ACCTATGTGAACACGGGACT 58.359 50.000 14.38 0.00 0.00 3.85
6523 9537 2.811410 ACCTATGTGAACACGGGACTA 58.189 47.619 14.38 0.00 0.00 2.59
6524 9538 2.494870 ACCTATGTGAACACGGGACTAC 59.505 50.000 14.38 0.00 0.00 2.73
6525 9539 2.758979 CCTATGTGAACACGGGACTACT 59.241 50.000 0.00 0.00 0.00 2.57
6526 9540 2.743636 ATGTGAACACGGGACTACTG 57.256 50.000 0.00 0.00 0.00 2.74
6527 9541 1.405872 TGTGAACACGGGACTACTGT 58.594 50.000 0.00 0.00 40.00 3.55
6529 9543 2.132762 GTGAACACGGGACTACTGTTG 58.867 52.381 0.00 0.00 36.23 3.33
6530 9544 1.758280 TGAACACGGGACTACTGTTGT 59.242 47.619 0.00 0.00 36.23 3.32
6531 9545 2.132762 GAACACGGGACTACTGTTGTG 58.867 52.381 0.00 0.00 36.23 3.33
6533 9547 1.758280 ACACGGGACTACTGTTGTGAA 59.242 47.619 0.00 0.00 36.23 3.18
6536 9550 3.813166 CACGGGACTACTGTTGTGAAAAT 59.187 43.478 0.00 0.00 36.23 1.82
6538 9552 5.467399 CACGGGACTACTGTTGTGAAAATAA 59.533 40.000 0.00 0.00 36.23 1.40
6539 9553 6.148811 CACGGGACTACTGTTGTGAAAATAAT 59.851 38.462 0.00 0.00 36.23 1.28
6540 9554 6.713450 ACGGGACTACTGTTGTGAAAATAATT 59.287 34.615 0.00 0.00 34.09 1.40
6550 9569 8.549777 TGTTGTGAAAATAATTTGTACGTGAC 57.450 30.769 0.00 0.00 0.00 3.67
6556 9575 8.283992 TGAAAATAATTTGTACGTGACGAACAT 58.716 29.630 13.70 0.00 34.09 2.71
6561 9580 0.780002 GTACGTGACGAACATGCGTT 59.220 50.000 13.70 0.00 45.72 4.84
6575 9594 3.006537 ACATGCGTTCTACAACTGTAGGT 59.993 43.478 15.20 2.86 46.01 3.08
6577 9596 2.288579 TGCGTTCTACAACTGTAGGTGG 60.289 50.000 15.20 7.14 46.01 4.61
6599 9627 3.696548 GGGATTTGTGAATGTTCTCCCTC 59.303 47.826 8.86 0.00 35.13 4.30
6608 9636 5.882557 GTGAATGTTCTCCCTCACAATGTAT 59.117 40.000 0.00 0.00 38.43 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.144155 ACAAAAAGCAGTACTCTTTTACTCTC 57.856 34.615 22.30 0.00 41.37 3.20
97 98 7.558444 TCCTTGTTTTACATAAACTCTGTTGGT 59.442 33.333 0.00 0.00 0.00 3.67
99 100 9.796120 TTTCCTTGTTTTACATAAACTCTGTTG 57.204 29.630 0.00 0.00 0.00 3.33
128 129 8.995027 TTAATCAGGCATCATTTTGTAGGTAT 57.005 30.769 0.00 0.00 0.00 2.73
164 216 4.881273 TGGTTAATCATGCATACTGGTCAC 59.119 41.667 0.00 0.00 0.00 3.67
264 316 9.282247 GCTAAGAGAAATTATTCAACATGTGTG 57.718 33.333 0.00 0.09 38.06 3.82
428 480 9.547279 TTATATTAGGCATCATCTACTCCTGAA 57.453 33.333 0.00 0.00 0.00 3.02
476 528 6.440647 TGAGGTGGTGAGACTACTGATAATTT 59.559 38.462 0.00 0.00 29.70 1.82
776 1087 0.036022 GCAGAGGGGCTGGATATGAC 59.964 60.000 0.00 0.00 45.03 3.06
810 1124 7.816995 TCCAATCAAAAGGCAACATATTTGTAC 59.183 33.333 0.00 0.00 37.81 2.90
1005 1323 2.092538 AGCAGATTCAATAGCAGCCTGT 60.093 45.455 0.00 0.00 0.00 4.00
1132 1450 8.756486 ATGACAACAGAATAATCATGGATTGA 57.244 30.769 1.86 0.00 39.12 2.57
1261 1583 4.672899 AGAGCTTGTTTGGGGCTTATTTA 58.327 39.130 0.00 0.00 36.37 1.40
1290 1612 3.668141 ATTAGATCACAATGTGGCCCA 57.332 42.857 13.95 0.00 33.87 5.36
1303 1625 8.023050 AGCAACAACATATCGCTTATTAGATC 57.977 34.615 0.00 0.00 0.00 2.75
1442 1766 3.973206 AATGTGGAGACATAACACGGA 57.027 42.857 0.00 0.00 42.30 4.69
1751 2095 1.607251 GGGAACACCTCTGTAACACGG 60.607 57.143 0.00 0.00 35.85 4.94
1834 2179 5.850614 AGCATCATTAAGCCCATCAAAATC 58.149 37.500 0.00 0.00 0.00 2.17
2197 2584 2.099405 TCATCACCGATGTGTAGCTCA 58.901 47.619 0.00 0.00 43.26 4.26
2253 2640 3.886505 GCAGTGCACTAGGTAGATACTCT 59.113 47.826 21.20 0.00 0.00 3.24
2373 2977 1.002134 CGTCAGGGGCATTGGAAGT 60.002 57.895 0.00 0.00 0.00 3.01
2388 2992 3.678548 GGAAGATCACCAACTTGTACGTC 59.321 47.826 0.00 0.00 0.00 4.34
2427 3031 7.122650 TGGAATTTTTATCTTAGAAGGGCACAG 59.877 37.037 0.00 0.00 0.00 3.66
2491 3095 3.681897 AGATGATGAAACGAACTGCAGAC 59.318 43.478 23.35 12.87 0.00 3.51
2599 3205 3.007290 TCAACCAAGAGACAGATGAGGTG 59.993 47.826 0.00 0.00 0.00 4.00
2940 3659 4.408993 TGCACATCGTGAATTTTGAGAG 57.591 40.909 0.00 0.00 35.23 3.20
2958 3677 1.803453 ATTCCTTCCCAGGCCTTGCA 61.803 55.000 0.00 0.00 40.58 4.08
3377 4123 9.920946 TTCCTTAGCAAAGATATACCATCTTTT 57.079 29.630 9.04 0.81 43.52 2.27
3381 4127 7.391554 TGCATTCCTTAGCAAAGATATACCATC 59.608 37.037 0.00 0.00 37.90 3.51
3401 4147 3.886549 GCTGTCATGAGCTAATGCATTC 58.113 45.455 16.86 2.18 42.74 2.67
3509 4260 5.959618 ATAACAAAGTGTAAGGCAGGAAC 57.040 39.130 0.00 0.00 0.00 3.62
3558 4310 3.214697 TGAGCAAAATGTGGCATTACG 57.785 42.857 0.00 0.00 0.00 3.18
3611 4363 9.232473 CTAGAACCTAAATAAATATTCCAGGGC 57.768 37.037 13.90 8.43 34.52 5.19
4059 4876 4.967084 AGAACCACTACAACACCATACA 57.033 40.909 0.00 0.00 0.00 2.29
4133 4966 6.296026 ACTTTTGGGAAATCTATATGCGCTA 58.704 36.000 9.73 0.00 0.00 4.26
4149 4982 2.600470 TGCAAAGCTTGACTTTTGGG 57.400 45.000 0.00 0.00 46.73 4.12
4318 5157 7.009174 GGCCAATCAGAACAAACAATTATTACG 59.991 37.037 0.00 0.00 0.00 3.18
4332 5171 2.997986 CAGCAAAATGGCCAATCAGAAC 59.002 45.455 10.96 0.00 0.00 3.01
4625 5545 6.914654 TTTGAAAATTCCATCAGGTCATCA 57.085 33.333 0.00 0.00 35.89 3.07
4678 5599 3.372060 GGAAAGGTTGAAGAAGCAAACG 58.628 45.455 0.00 0.00 40.35 3.60
4739 5662 7.222611 TGTCTGCAAGTTCAAGAAAAATTAAGC 59.777 33.333 0.00 0.00 33.76 3.09
4740 5663 8.534778 GTGTCTGCAAGTTCAAGAAAAATTAAG 58.465 33.333 0.00 0.00 33.76 1.85
4743 5666 6.633856 AGTGTCTGCAAGTTCAAGAAAAATT 58.366 32.000 0.00 0.00 33.76 1.82
4942 5866 8.923270 AGAAAGGACCTGAAAAATGACAAAATA 58.077 29.630 0.00 0.00 0.00 1.40
4990 5919 4.131649 CGGTGAATATAACACTGGGACA 57.868 45.455 11.62 0.00 39.91 4.02
5029 5958 2.855209 CCTCTGGAATATGGAGGCAG 57.145 55.000 0.00 0.00 39.87 4.85
5065 5998 3.181520 CCTGTCGCGGAAACAAAATAGAG 60.182 47.826 6.13 0.00 0.00 2.43
5066 5999 2.739913 CCTGTCGCGGAAACAAAATAGA 59.260 45.455 6.13 0.00 0.00 1.98
5071 6004 1.600023 AATCCTGTCGCGGAAACAAA 58.400 45.000 6.13 0.00 36.49 2.83
5093 6026 7.361713 GCAATTACGCATAGAAATAGGCCATAA 60.362 37.037 5.01 0.00 0.00 1.90
5099 6032 5.700832 TCAGGCAATTACGCATAGAAATAGG 59.299 40.000 0.00 0.00 0.00 2.57
5104 6037 4.137116 AGTCAGGCAATTACGCATAGAA 57.863 40.909 0.00 0.00 0.00 2.10
5111 6044 5.796935 CAGATTTTCAAGTCAGGCAATTACG 59.203 40.000 0.00 0.00 0.00 3.18
5139 6072 2.161855 TGCAAAAGCATGTACTCAGGG 58.838 47.619 0.00 0.00 0.00 4.45
5145 6078 3.855689 ATGACCTGCAAAAGCATGTAC 57.144 42.857 0.00 0.00 0.00 2.90
5200 6133 3.563223 CATCTAAACCGGTAGAGGAGGA 58.437 50.000 8.00 0.00 34.53 3.71
5211 6144 2.500098 TCCAGGTTCTCCATCTAAACCG 59.500 50.000 0.00 0.00 45.70 4.44
5222 6155 2.485814 GCAAACACTGATCCAGGTTCTC 59.514 50.000 0.00 0.00 35.51 2.87
5237 6170 1.455849 CCTGGTGGAGGAGCAAACA 59.544 57.895 0.00 0.00 46.33 2.83
5241 6174 2.853542 TTGCCTGGTGGAGGAGCA 60.854 61.111 0.00 0.00 46.33 4.26
5250 6183 2.229792 CTGTAACACATGTTGCCTGGT 58.770 47.619 7.53 0.00 39.42 4.00
5352 6285 7.866393 AGGGAAGATCATACTTACGTTAAATCG 59.134 37.037 0.00 0.00 32.00 3.34
5379 6312 1.891919 GACTTGAACAGGCGGTGCA 60.892 57.895 0.00 0.00 31.28 4.57
5385 6318 1.264288 CGTGGAAAGACTTGAACAGGC 59.736 52.381 0.00 0.00 0.00 4.85
5414 6348 4.350816 TCTGGAAGAACAAAAGAGATCCCA 59.649 41.667 0.00 0.00 42.31 4.37
5446 6380 3.335711 CCCATGGAGGAGGGTTCC 58.664 66.667 15.22 0.00 44.39 3.62
5473 6407 3.882131 GCCTATGGAGGTGAAAGCA 57.118 52.632 0.00 0.00 45.78 3.91
5493 6427 2.032528 CCTTTGACTGGCCGCTCA 59.967 61.111 0.00 0.00 0.00 4.26
5563 6500 1.371183 CAAGGAGCGGACCAAGACA 59.629 57.895 0.00 0.00 0.00 3.41
5674 6611 3.056313 GAAGCACCGGCCTTGCATC 62.056 63.158 23.84 18.74 42.83 3.91
5707 6644 0.904649 CACAGGATCCTAGCACCACA 59.095 55.000 15.67 0.00 0.00 4.17
5711 6648 3.669251 GGATACACAGGATCCTAGCAC 57.331 52.381 15.67 4.26 39.94 4.40
5751 6688 3.815962 TCTTCCGGATTCTCTCTGTATCG 59.184 47.826 4.15 0.00 0.00 2.92
5752 6689 4.320935 GCTCTTCCGGATTCTCTCTGTATC 60.321 50.000 4.15 0.00 0.00 2.24
5753 6690 3.572255 GCTCTTCCGGATTCTCTCTGTAT 59.428 47.826 4.15 0.00 0.00 2.29
5754 6691 2.952978 GCTCTTCCGGATTCTCTCTGTA 59.047 50.000 4.15 0.00 0.00 2.74
5755 6692 1.754226 GCTCTTCCGGATTCTCTCTGT 59.246 52.381 4.15 0.00 0.00 3.41
5765 6703 1.757118 CTCATACAAGGCTCTTCCGGA 59.243 52.381 0.00 0.00 40.77 5.14
5781 6719 3.966215 CGTTGGTTGACGCCTCAT 58.034 55.556 0.00 0.00 36.12 2.90
5792 6730 2.925170 AGAGGCTGAGGCGTTGGT 60.925 61.111 0.00 0.00 39.81 3.67
5830 6768 0.601841 GGTACAACCCTCCACACACG 60.602 60.000 0.00 0.00 30.04 4.49
5856 6796 3.305709 TGAACTACACAGCACAGGC 57.694 52.632 0.00 0.00 41.61 4.85
5955 6895 7.035612 CCAAGTAATAAGAAAGCAAATGTCCC 58.964 38.462 0.00 0.00 0.00 4.46
5996 6936 4.330313 CCAACACAAAATTGTTCAAACGC 58.670 39.130 0.00 0.00 39.91 4.84
6007 6947 1.688197 CACTCCAGCCCAACACAAAAT 59.312 47.619 0.00 0.00 0.00 1.82
6030 6970 6.250711 TCTGGTAAGGATCACAGTAGTAACA 58.749 40.000 0.00 0.00 32.92 2.41
6031 6971 6.770746 TCTGGTAAGGATCACAGTAGTAAC 57.229 41.667 0.00 0.00 32.92 2.50
6032 6972 7.179966 TCTTCTGGTAAGGATCACAGTAGTAA 58.820 38.462 0.00 0.00 32.40 2.24
6034 6974 5.580998 TCTTCTGGTAAGGATCACAGTAGT 58.419 41.667 0.00 0.00 32.40 2.73
6035 6975 6.723298 ATCTTCTGGTAAGGATCACAGTAG 57.277 41.667 0.00 0.00 31.97 2.57
6036 6976 6.127054 CCAATCTTCTGGTAAGGATCACAGTA 60.127 42.308 0.00 0.00 32.92 2.74
6037 6977 5.338708 CCAATCTTCTGGTAAGGATCACAGT 60.339 44.000 0.00 0.00 32.92 3.55
6060 7055 4.082245 CACTACCAATTCAAATGGACACCC 60.082 45.833 0.00 0.00 40.56 4.61
6066 7061 6.099341 GGTTAAGCACTACCAATTCAAATGG 58.901 40.000 0.00 0.00 43.84 3.16
6099 7094 9.463443 AAAGAGTAACAGAATTTGTATTTGTGC 57.537 29.630 0.00 0.00 39.73 4.57
6113 7108 6.260936 CCAAAAGCAAGAGAAAGAGTAACAGA 59.739 38.462 0.00 0.00 0.00 3.41
6122 7117 1.336240 CCCGCCAAAAGCAAGAGAAAG 60.336 52.381 0.00 0.00 44.04 2.62
6139 7135 1.518325 TGTGTTGTGCTACATTCCCG 58.482 50.000 0.00 0.00 0.00 5.14
6144 7140 1.908344 TGGCATGTGTTGTGCTACAT 58.092 45.000 0.00 0.00 42.16 2.29
6146 7142 2.223688 TGTTTGGCATGTGTTGTGCTAC 60.224 45.455 0.00 0.00 42.16 3.58
6148 7144 0.822811 TGTTTGGCATGTGTTGTGCT 59.177 45.000 0.00 0.00 42.16 4.40
6149 7145 1.210870 CTGTTTGGCATGTGTTGTGC 58.789 50.000 0.00 0.00 41.78 4.57
6150 7146 2.195096 CACTGTTTGGCATGTGTTGTG 58.805 47.619 0.00 0.00 0.00 3.33
6151 7147 1.824230 ACACTGTTTGGCATGTGTTGT 59.176 42.857 9.26 0.00 36.66 3.32
6152 7148 2.582728 ACACTGTTTGGCATGTGTTG 57.417 45.000 9.26 0.00 36.66 3.33
6153 7149 3.550820 TCTACACTGTTTGGCATGTGTT 58.449 40.909 16.73 6.27 38.94 3.32
6154 7150 3.141398 CTCTACACTGTTTGGCATGTGT 58.859 45.455 16.10 16.10 40.19 3.72
6155 7151 3.141398 ACTCTACACTGTTTGGCATGTG 58.859 45.455 1.08 5.21 34.59 3.21
6156 7152 3.492102 ACTCTACACTGTTTGGCATGT 57.508 42.857 0.00 0.00 0.00 3.21
6157 7153 4.820897 TCTACTCTACACTGTTTGGCATG 58.179 43.478 0.00 0.00 0.00 4.06
6158 7154 5.238583 GTTCTACTCTACACTGTTTGGCAT 58.761 41.667 0.00 0.00 0.00 4.40
6159 7155 4.628074 GTTCTACTCTACACTGTTTGGCA 58.372 43.478 0.00 0.00 0.00 4.92
6160 7156 3.673809 CGTTCTACTCTACACTGTTTGGC 59.326 47.826 0.00 0.00 0.00 4.52
6161 7157 4.868067 ACGTTCTACTCTACACTGTTTGG 58.132 43.478 0.00 0.00 0.00 3.28
6162 7158 5.975344 TCAACGTTCTACTCTACACTGTTTG 59.025 40.000 0.00 0.00 0.00 2.93
6164 7160 5.762825 TCAACGTTCTACTCTACACTGTT 57.237 39.130 0.00 0.00 0.00 3.16
6165 7161 5.961396 ATCAACGTTCTACTCTACACTGT 57.039 39.130 0.00 0.00 0.00 3.55
6166 7162 9.600646 CATATATCAACGTTCTACTCTACACTG 57.399 37.037 0.00 0.00 0.00 3.66
6167 7163 8.291032 GCATATATCAACGTTCTACTCTACACT 58.709 37.037 0.00 0.00 0.00 3.55
6169 7165 8.074370 GTGCATATATCAACGTTCTACTCTACA 58.926 37.037 0.00 0.00 0.00 2.74
6170 7166 8.074370 TGTGCATATATCAACGTTCTACTCTAC 58.926 37.037 0.00 0.00 0.00 2.59
6171 7167 8.161699 TGTGCATATATCAACGTTCTACTCTA 57.838 34.615 0.00 0.00 0.00 2.43
6172 7168 7.039313 TGTGCATATATCAACGTTCTACTCT 57.961 36.000 0.00 0.00 0.00 3.24
6173 7169 7.620188 GCATGTGCATATATCAACGTTCTACTC 60.620 40.741 0.00 0.00 41.59 2.59
6174 7170 6.146184 GCATGTGCATATATCAACGTTCTACT 59.854 38.462 0.00 0.00 41.59 2.57
6175 7171 6.299604 GCATGTGCATATATCAACGTTCTAC 58.700 40.000 0.00 0.00 41.59 2.59
6176 7172 6.466308 GCATGTGCATATATCAACGTTCTA 57.534 37.500 0.00 0.00 41.59 2.10
6177 7173 5.348418 GCATGTGCATATATCAACGTTCT 57.652 39.130 0.00 0.00 41.59 3.01
6192 7188 2.536365 CAAATGGAGTCATGCATGTGC 58.464 47.619 25.43 18.70 35.91 4.57
6193 7189 2.756207 TCCAAATGGAGTCATGCATGTG 59.244 45.455 25.43 13.66 41.06 3.21
6194 7190 2.756760 GTCCAAATGGAGTCATGCATGT 59.243 45.455 25.43 8.12 46.49 3.21
6195 7191 2.756207 TGTCCAAATGGAGTCATGCATG 59.244 45.455 21.07 21.07 46.49 4.06
6196 7192 2.756760 GTGTCCAAATGGAGTCATGCAT 59.243 45.455 1.47 0.00 46.49 3.96
6197 7193 2.161855 GTGTCCAAATGGAGTCATGCA 58.838 47.619 1.47 0.00 46.49 3.96
6198 7194 2.161855 TGTGTCCAAATGGAGTCATGC 58.838 47.619 1.47 0.00 46.49 4.06
6199 7195 3.569277 TGTTGTGTCCAAATGGAGTCATG 59.431 43.478 1.47 0.00 46.49 3.07
6200 7196 3.569701 GTGTTGTGTCCAAATGGAGTCAT 59.430 43.478 1.47 0.00 46.49 3.06
6201 7197 2.948979 GTGTTGTGTCCAAATGGAGTCA 59.051 45.455 1.47 2.64 46.49 3.41
6202 7198 2.293399 GGTGTTGTGTCCAAATGGAGTC 59.707 50.000 1.47 0.00 46.49 3.36
6203 7199 2.091885 AGGTGTTGTGTCCAAATGGAGT 60.092 45.455 1.47 0.00 46.49 3.85
6204 7200 2.586425 AGGTGTTGTGTCCAAATGGAG 58.414 47.619 1.47 0.00 46.49 3.86
6205 7201 2.746279 AGGTGTTGTGTCCAAATGGA 57.254 45.000 0.00 0.00 43.08 3.41
6206 7202 2.556622 GGTAGGTGTTGTGTCCAAATGG 59.443 50.000 0.00 0.00 30.94 3.16
6207 7203 2.225491 CGGTAGGTGTTGTGTCCAAATG 59.775 50.000 0.00 0.00 30.94 2.32
6208 7204 2.500229 CGGTAGGTGTTGTGTCCAAAT 58.500 47.619 0.00 0.00 30.94 2.32
6209 7205 1.475392 CCGGTAGGTGTTGTGTCCAAA 60.475 52.381 0.00 0.00 30.94 3.28
6210 7206 0.107081 CCGGTAGGTGTTGTGTCCAA 59.893 55.000 0.00 0.00 0.00 3.53
6211 7207 0.759812 TCCGGTAGGTGTTGTGTCCA 60.760 55.000 0.00 0.00 39.05 4.02
6212 7208 0.037605 CTCCGGTAGGTGTTGTGTCC 60.038 60.000 0.00 0.00 39.05 4.02
6213 7209 0.963962 TCTCCGGTAGGTGTTGTGTC 59.036 55.000 0.00 0.00 39.05 3.67
6214 7210 1.549170 GATCTCCGGTAGGTGTTGTGT 59.451 52.381 0.00 0.00 39.05 3.72
6215 7211 1.548719 TGATCTCCGGTAGGTGTTGTG 59.451 52.381 0.00 0.00 39.05 3.33
6216 7212 1.933021 TGATCTCCGGTAGGTGTTGT 58.067 50.000 0.00 0.00 39.05 3.32
6217 7213 3.262420 CTTTGATCTCCGGTAGGTGTTG 58.738 50.000 0.00 0.00 39.05 3.33
6218 7214 2.904434 ACTTTGATCTCCGGTAGGTGTT 59.096 45.455 0.00 0.00 39.05 3.32
6219 7215 2.537143 ACTTTGATCTCCGGTAGGTGT 58.463 47.619 0.00 0.00 39.05 4.16
6220 7216 3.262420 CAACTTTGATCTCCGGTAGGTG 58.738 50.000 0.00 0.00 39.05 4.00
6221 7217 2.904434 ACAACTTTGATCTCCGGTAGGT 59.096 45.455 0.00 0.00 39.05 3.08
6222 7218 3.262420 CACAACTTTGATCTCCGGTAGG 58.738 50.000 0.00 0.00 39.46 3.18
6223 7219 3.056107 TCCACAACTTTGATCTCCGGTAG 60.056 47.826 0.00 0.00 0.00 3.18
6224 7220 2.901192 TCCACAACTTTGATCTCCGGTA 59.099 45.455 0.00 0.00 0.00 4.02
6225 7221 1.697432 TCCACAACTTTGATCTCCGGT 59.303 47.619 0.00 0.00 0.00 5.28
6254 7250 9.777297 AAATAACTTTTGGTTGCTCATGTTAAT 57.223 25.926 0.00 0.00 38.75 1.40
6261 7257 6.704050 GGCTTAAAATAACTTTTGGTTGCTCA 59.296 34.615 0.00 0.00 38.75 4.26
6262 7258 6.704050 TGGCTTAAAATAACTTTTGGTTGCTC 59.296 34.615 0.00 0.00 38.75 4.26
6263 7259 6.587273 TGGCTTAAAATAACTTTTGGTTGCT 58.413 32.000 0.00 0.00 38.75 3.91
6264 7260 6.852858 TGGCTTAAAATAACTTTTGGTTGC 57.147 33.333 0.00 0.00 38.75 4.17
6267 7263 6.429692 GGCAATGGCTTAAAATAACTTTTGGT 59.570 34.615 0.00 0.00 40.87 3.67
6276 8751 3.304829 GAGGGGGCAATGGCTTAAAATA 58.695 45.455 6.78 0.00 40.87 1.40
6281 8756 2.700185 GGGAGGGGGCAATGGCTTA 61.700 63.158 6.78 0.00 40.87 3.09
6289 8764 2.789920 AAAAAGGGGGAGGGGGCA 60.790 61.111 0.00 0.00 0.00 5.36
6370 9379 9.107177 CAGCTCTTCACTTTTAGATGTGATTAT 57.893 33.333 3.25 0.00 41.93 1.28
6375 9384 4.694509 AGCAGCTCTTCACTTTTAGATGTG 59.305 41.667 0.00 0.00 35.68 3.21
6427 9436 4.002982 CCTCATTTTGATGTTCCTCGTCA 58.997 43.478 0.00 0.00 39.93 4.35
6430 9439 4.497006 GCATCCTCATTTTGATGTTCCTCG 60.497 45.833 0.00 0.00 40.37 4.63
6433 9442 3.448301 TGGCATCCTCATTTTGATGTTCC 59.552 43.478 0.00 0.00 40.37 3.62
6437 9446 2.429250 TGCTGGCATCCTCATTTTGATG 59.571 45.455 0.00 0.00 41.02 3.07
6454 9463 0.031178 AAAGGCTGCGACTTTTGCTG 59.969 50.000 3.91 0.00 37.67 4.41
6471 9480 3.068590 GGAATGGGACCGACTACGATAAA 59.931 47.826 0.00 0.00 42.66 1.40
6473 9482 2.158564 AGGAATGGGACCGACTACGATA 60.159 50.000 0.00 0.00 42.66 2.92
6476 9485 1.607628 CTAGGAATGGGACCGACTACG 59.392 57.143 0.00 0.00 39.43 3.51
6484 9493 4.548669 AGGTTAGTCTCTAGGAATGGGAC 58.451 47.826 0.00 0.00 0.00 4.46
6485 9494 4.901785 AGGTTAGTCTCTAGGAATGGGA 57.098 45.455 0.00 0.00 0.00 4.37
6486 9495 6.015010 CACATAGGTTAGTCTCTAGGAATGGG 60.015 46.154 0.00 0.00 0.00 4.00
6489 9498 7.839705 TGTTCACATAGGTTAGTCTCTAGGAAT 59.160 37.037 0.00 0.00 0.00 3.01
6490 9499 7.122353 GTGTTCACATAGGTTAGTCTCTAGGAA 59.878 40.741 0.00 0.00 0.00 3.36
6492 9501 6.458478 CGTGTTCACATAGGTTAGTCTCTAGG 60.458 46.154 3.87 0.00 0.00 3.02
6493 9502 6.458478 CCGTGTTCACATAGGTTAGTCTCTAG 60.458 46.154 3.87 0.00 0.00 2.43
6494 9503 5.356190 CCGTGTTCACATAGGTTAGTCTCTA 59.644 44.000 3.87 0.00 0.00 2.43
6495 9504 4.158025 CCGTGTTCACATAGGTTAGTCTCT 59.842 45.833 3.87 0.00 0.00 3.10
6496 9505 4.421948 CCGTGTTCACATAGGTTAGTCTC 58.578 47.826 3.87 0.00 0.00 3.36
6497 9506 3.194968 CCCGTGTTCACATAGGTTAGTCT 59.805 47.826 3.87 0.00 0.00 3.24
6498 9507 3.194116 TCCCGTGTTCACATAGGTTAGTC 59.806 47.826 3.87 0.00 0.00 2.59
6499 9508 3.056322 GTCCCGTGTTCACATAGGTTAGT 60.056 47.826 3.87 0.00 0.00 2.24
6500 9509 3.194968 AGTCCCGTGTTCACATAGGTTAG 59.805 47.826 3.87 0.00 0.00 2.34
6520 9534 9.872757 CGTACAAATTATTTTCACAACAGTAGT 57.127 29.630 0.00 0.00 0.00 2.73
6521 9535 9.872757 ACGTACAAATTATTTTCACAACAGTAG 57.127 29.630 0.00 0.00 0.00 2.57
6522 9536 9.653067 CACGTACAAATTATTTTCACAACAGTA 57.347 29.630 0.00 0.00 0.00 2.74
6523 9537 8.399425 TCACGTACAAATTATTTTCACAACAGT 58.601 29.630 0.00 0.00 0.00 3.55
6524 9538 8.678510 GTCACGTACAAATTATTTTCACAACAG 58.321 33.333 0.00 0.00 0.00 3.16
6525 9539 7.373703 CGTCACGTACAAATTATTTTCACAACA 59.626 33.333 0.00 0.00 0.00 3.33
6526 9540 7.583401 TCGTCACGTACAAATTATTTTCACAAC 59.417 33.333 0.00 0.00 0.00 3.32
6527 9541 7.628235 TCGTCACGTACAAATTATTTTCACAA 58.372 30.769 0.00 0.00 0.00 3.33
6529 9543 7.583401 TGTTCGTCACGTACAAATTATTTTCAC 59.417 33.333 7.24 0.00 34.57 3.18
6530 9544 7.628235 TGTTCGTCACGTACAAATTATTTTCA 58.372 30.769 7.24 0.00 34.57 2.69
6531 9545 8.563949 CATGTTCGTCACGTACAAATTATTTTC 58.436 33.333 13.96 0.00 40.11 2.29
6533 9547 6.521821 GCATGTTCGTCACGTACAAATTATTT 59.478 34.615 13.96 0.00 40.11 1.40
6536 9550 4.433152 CGCATGTTCGTCACGTACAAATTA 60.433 41.667 13.96 0.00 40.11 1.40
6538 9552 2.159894 CGCATGTTCGTCACGTACAAAT 60.160 45.455 13.96 0.00 40.11 2.32
6539 9553 1.190543 CGCATGTTCGTCACGTACAAA 59.809 47.619 13.96 0.00 40.11 2.83
6540 9554 0.779408 CGCATGTTCGTCACGTACAA 59.221 50.000 13.96 0.00 40.11 2.41
6565 9584 2.819608 CACAAATCCCCACCTACAGTTG 59.180 50.000 0.00 0.00 0.00 3.16
6575 9594 3.430453 GGAGAACATTCACAAATCCCCA 58.570 45.455 0.00 0.00 0.00 4.96
6577 9596 3.696548 GAGGGAGAACATTCACAAATCCC 59.303 47.826 7.50 7.50 35.24 3.85
6599 9627 7.764443 CCCGTCCCTATATAAAGATACATTGTG 59.236 40.741 0.00 0.00 0.00 3.33
6608 9636 2.565834 GCAGCCCGTCCCTATATAAAGA 59.434 50.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.