Multiple sequence alignment - TraesCS6A01G033600

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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 TraesCS6A01G033600 chr6A 100.000 3068 0 0 1 3068 16454810 16451743 0.000000e+00 5666.0
1 TraesCS6A01G033600 chr6A 97.778 135 3 0 2934 3068 545563336 545563470 1.840000e-57 233.0
2 TraesCS6A01G033600 chr6A 95.804 143 3 3 2928 3068 36420564 36420705 8.560000e-56 228.0
3 TraesCS6A01G033600 chr2B 91.793 1986 141 11 406 2378 46592966 46590990 0.000000e+00 2745.0
4 TraesCS6A01G033600 chr2B 83.682 478 33 20 54 492 46593432 46592961 2.850000e-110 409.0
5 TraesCS6A01G033600 chr6D 92.656 1525 101 5 929 2444 16187927 16186405 0.000000e+00 2185.0
6 TraesCS6A01G033600 chr6D 83.240 358 38 13 1 343 16188437 16188087 2.970000e-80 309.0
7 TraesCS6A01G033600 chr6B 92.616 1097 63 10 1351 2444 27938043 27936962 0.000000e+00 1561.0
8 TraesCS6A01G033600 chr6B 91.717 833 63 4 639 1466 28012663 28013494 0.000000e+00 1151.0
9 TraesCS6A01G033600 chr6B 87.268 754 66 17 1 737 27939262 27938522 0.000000e+00 833.0
10 TraesCS6A01G033600 chr6B 91.115 619 47 6 1826 2438 28013496 28014112 0.000000e+00 832.0
11 TraesCS6A01G033600 chr6B 94.652 374 17 1 743 1113 27938425 27938052 7.380000e-161 577.0
12 TraesCS6A01G033600 chr6B 88.631 431 41 6 177 600 28012237 28012666 4.530000e-143 518.0
13 TraesCS6A01G033600 chr6B 84.488 303 33 10 2467 2766 28014436 28014727 1.390000e-73 287.0
14 TraesCS6A01G033600 chr6B 97.761 134 3 0 2935 3068 32999271 32999404 6.620000e-57 231.0
15 TraesCS6A01G033600 chr6B 79.817 327 27 11 2444 2766 27936817 27936526 5.190000e-48 202.0
16 TraesCS6A01G033600 chr6B 81.333 150 6 5 2791 2934 27936190 27936057 5.410000e-18 102.0
17 TraesCS6A01G033600 chr6B 93.333 60 4 0 2875 2934 28015315 28015374 4.210000e-14 89.8
18 TraesCS6A01G033600 chr1A 92.611 406 29 1 506 911 253307282 253306878 1.590000e-162 582.0
19 TraesCS6A01G033600 chr1A 96.403 139 5 0 2930 3068 378066951 378067089 2.380000e-56 230.0
20 TraesCS6A01G033600 chr7B 97.122 139 3 1 2931 3068 709813229 709813091 1.840000e-57 233.0
21 TraesCS6A01G033600 chr7B 95.804 143 4 2 2928 3068 122310586 122310444 2.380000e-56 230.0
22 TraesCS6A01G033600 chr5A 97.778 135 2 1 2935 3068 16752385 16752251 6.620000e-57 231.0
23 TraesCS6A01G033600 chr2A 91.975 162 10 2 2909 3068 691361381 691361221 1.110000e-54 224.0
24 TraesCS6A01G033600 chr3A 92.357 157 6 5 2917 3068 494329446 494329601 5.150000e-53 219.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G033600 chr6A 16451743 16454810 3067 True 5666.00 5666 100.0000 1 3068 1 chr6A.!!$R1 3067
1 TraesCS6A01G033600 chr2B 46590990 46593432 2442 True 1577.00 2745 87.7375 54 2378 2 chr2B.!!$R1 2324
2 TraesCS6A01G033600 chr6D 16186405 16188437 2032 True 1247.00 2185 87.9480 1 2444 2 chr6D.!!$R1 2443
3 TraesCS6A01G033600 chr6B 27936057 27939262 3205 True 655.00 1561 87.1372 1 2934 5 chr6B.!!$R1 2933
4 TraesCS6A01G033600 chr6B 28012237 28015374 3137 False 575.56 1151 89.8568 177 2934 5 chr6B.!!$F2 2757

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
153 160 0.465460 TATTGATTGGAGGGCCGCAC 60.465 55.0 10.15 0.0 36.79 5.34 F
404 551 0.688487 CCCCAGTTTTCCTACACGGA 59.312 55.0 0.00 0.0 41.06 4.69 F
1134 1396 0.179111 TCATCATTGCGTCGACCCTC 60.179 55.0 10.58 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1387 0.526662 ACAAGATCACGAGGGTCGAC 59.473 55.0 7.13 7.13 43.74 4.20 R
1871 2143 1.002857 AAAAGAGCCTAGCCACCCAT 58.997 50.0 0.00 0.00 0.00 4.00 R
3000 4347 0.040646 TCTCCTTCCCCTCGTTGCTA 59.959 55.0 0.00 0.00 0.00 3.49 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
25 26 2.098426 AATTTGTGGCGGCAACCTGG 62.098 55.000 15.50 0.00 0.00 4.45
88 95 0.794605 GAAATTTCGAGCTGTGCGGC 60.795 55.000 1.68 0.00 0.00 6.53
129 136 4.811557 GGTTGCTAGCTGAATTAGTTCGAT 59.188 41.667 17.23 0.00 37.15 3.59
134 141 6.763135 TGCTAGCTGAATTAGTTCGATTTCAT 59.237 34.615 17.23 0.00 37.15 2.57
149 156 4.082571 CGATTTCATATTGATTGGAGGGCC 60.083 45.833 0.00 0.00 0.00 5.80
153 160 0.465460 TATTGATTGGAGGGCCGCAC 60.465 55.000 10.15 0.00 36.79 5.34
154 161 4.776322 TGATTGGAGGGCCGCACG 62.776 66.667 10.15 0.00 36.79 5.34
155 162 4.778143 GATTGGAGGGCCGCACGT 62.778 66.667 10.15 0.00 36.79 4.49
156 163 3.379865 GATTGGAGGGCCGCACGTA 62.380 63.158 10.15 0.00 36.79 3.57
246 293 5.171339 AGGAACTGCATAAGAGTGTCAAT 57.829 39.130 0.00 0.00 37.18 2.57
264 311 6.375455 GTGTCAATCCATCTTACAACAGGAAT 59.625 38.462 0.00 0.00 31.17 3.01
332 395 4.870426 CGTACCTTGTGATCAAGCATACTT 59.130 41.667 0.00 0.00 46.74 2.24
390 454 2.618794 AGAATCAGATAGAGGCCCCAG 58.381 52.381 0.00 0.00 0.00 4.45
404 551 0.688487 CCCCAGTTTTCCTACACGGA 59.312 55.000 0.00 0.00 41.06 4.69
438 589 3.146066 TCTTCTTCAAACCACATTCGGG 58.854 45.455 0.00 0.00 0.00 5.14
593 748 9.657419 AAGGAATAATCATGGAAAACACATTTC 57.343 29.630 0.00 0.00 45.55 2.17
608 763 4.240096 CACATTTCCCAAAAGTGAGATGC 58.760 43.478 0.00 0.00 31.08 3.91
649 804 9.885743 CTCGTGCATAAAATAAAAATAGTTTGC 57.114 29.630 0.00 0.00 0.00 3.68
696 852 6.000219 GCAATATACAGGTTGGATGTCTGAT 59.000 40.000 0.00 0.00 33.19 2.90
748 1000 7.851228 TGTCCAACTTCTCATCAACTATATGT 58.149 34.615 0.00 0.00 0.00 2.29
904 1160 8.956426 TCTCAGTTGATTTTGTAAAGTTGTCTT 58.044 29.630 0.00 0.00 35.14 3.01
918 1174 6.927294 AAGTTGTCTTCTAGTTTCCTTGTG 57.073 37.500 0.00 0.00 0.00 3.33
1113 1375 1.081892 GCATCGCCATCATCGCTATT 58.918 50.000 0.00 0.00 0.00 1.73
1122 1384 4.155462 GCCATCATCGCTATTGTCATCATT 59.845 41.667 0.00 0.00 0.00 2.57
1125 1387 3.184986 TCATCGCTATTGTCATCATTGCG 59.815 43.478 6.91 6.91 42.70 4.85
1132 1394 0.739462 TGTCATCATTGCGTCGACCC 60.739 55.000 10.58 0.53 0.00 4.46
1134 1396 0.179111 TCATCATTGCGTCGACCCTC 60.179 55.000 10.58 0.00 0.00 4.30
1135 1397 1.226974 ATCATTGCGTCGACCCTCG 60.227 57.895 10.58 0.00 42.10 4.63
1142 1404 1.801332 CGTCGACCCTCGTGATCTT 59.199 57.895 10.58 0.00 41.35 2.40
1143 1405 0.523546 CGTCGACCCTCGTGATCTTG 60.524 60.000 10.58 0.00 41.35 3.02
1156 1418 3.935203 CGTGATCTTGTGCATTAAGGTCT 59.065 43.478 20.69 6.37 36.48 3.85
1168 1430 2.103537 TAAGGTCTTTTGCCGTAGCC 57.896 50.000 0.00 0.00 38.69 3.93
1208 1471 2.956964 GTCGCCATTCTCTCGCCG 60.957 66.667 0.00 0.00 0.00 6.46
1253 1516 5.362143 CCTCATCATTAGGAGAGTCTGACAA 59.638 44.000 10.88 0.00 35.51 3.18
1259 1522 2.603021 AGGAGAGTCTGACAAGAAGCA 58.397 47.619 10.88 0.00 33.05 3.91
1263 1526 2.038164 AGAGTCTGACAAGAAGCATGCA 59.962 45.455 21.98 0.00 33.05 3.96
1466 1738 2.483538 GCATCTGTGCCCAAAACTTTGT 60.484 45.455 1.76 0.00 45.76 2.83
1472 1744 1.686052 TGCCCAAAACTTTGTGCCTAG 59.314 47.619 7.10 0.00 40.19 3.02
1486 1758 2.232452 GTGCCTAGCGATATGATCCTGT 59.768 50.000 0.00 0.00 0.00 4.00
1554 1826 1.750399 GATTCGTGGCCATGCACCT 60.750 57.895 20.86 4.14 0.00 4.00
1740 2012 0.814457 CTTCCCTGGACAGACTCTCG 59.186 60.000 0.00 0.00 0.00 4.04
1803 2075 3.986006 GTGCCGGTGTCCTCACGA 61.986 66.667 1.90 0.00 44.68 4.35
1863 2135 1.448013 GGACGTAGAGGCTGTTGGC 60.448 63.158 0.00 0.00 40.90 4.52
1871 2143 4.704833 GGCTGTTGGCGGCTCTCA 62.705 66.667 11.43 5.87 45.94 3.27
1881 2153 2.434843 CGGCTCTCATGGGTGGCTA 61.435 63.158 17.82 0.00 0.00 3.93
1882 2154 1.449353 GGCTCTCATGGGTGGCTAG 59.551 63.158 13.53 0.00 0.00 3.42
1883 2155 1.449353 GCTCTCATGGGTGGCTAGG 59.551 63.158 0.00 0.00 0.00 3.02
1889 2161 0.257039 CATGGGTGGCTAGGCTCTTT 59.743 55.000 18.18 0.69 0.00 2.52
1905 2177 3.306364 GCTCTTTTCTGGCTACACTCTCA 60.306 47.826 0.00 0.00 0.00 3.27
1934 2206 1.373497 GTGGACACTCAGACAGCCG 60.373 63.158 0.00 0.00 0.00 5.52
2014 2286 4.994471 TGAGTGGCTGCGGCAGTG 62.994 66.667 28.88 8.36 41.82 3.66
2160 2435 1.606668 TGTTTTGAAACCTGCTAGGCG 59.393 47.619 4.32 0.00 39.63 5.52
2188 2463 3.763360 CCCTTGTGCCAATTCAGTTATGA 59.237 43.478 0.00 0.00 0.00 2.15
2212 2487 6.445357 AAGACGTGTTTCCAGTTTTATGTT 57.555 33.333 0.00 0.00 0.00 2.71
2214 2489 6.492254 AGACGTGTTTCCAGTTTTATGTTTC 58.508 36.000 0.00 0.00 0.00 2.78
2424 2702 2.412870 TCTGTCAAACTGTATGCCGTG 58.587 47.619 0.00 0.00 0.00 4.94
2425 2703 2.143122 CTGTCAAACTGTATGCCGTGT 58.857 47.619 0.00 0.00 0.00 4.49
2438 2716 4.695217 ATGCCGTGTACGAAAAATCAAT 57.305 36.364 5.91 0.00 43.02 2.57
2441 2719 3.168193 CCGTGTACGAAAAATCAATGGC 58.832 45.455 5.91 0.00 43.02 4.40
2457 2885 3.988976 ATGGCATCAGTGAGTGTACTT 57.011 42.857 0.00 0.00 0.00 2.24
2460 2888 3.181455 TGGCATCAGTGAGTGTACTTTGT 60.181 43.478 0.00 0.00 0.00 2.83
2463 2891 5.120830 GGCATCAGTGAGTGTACTTTGTAAG 59.879 44.000 0.00 0.00 0.00 2.34
2489 3071 6.617782 AGTATATCTCATCCATCCTGTTGG 57.382 41.667 0.00 0.00 38.18 3.77
2509 3091 3.054655 TGGTAGCCATTACTTTCCTGGTC 60.055 47.826 0.00 0.00 32.61 4.02
2541 3123 3.792124 GCTTTGATATGGTAACTTGCGCC 60.792 47.826 4.18 0.00 37.61 6.53
2550 3132 2.419667 GTAACTTGCGCCCTTCTGTAA 58.580 47.619 4.18 0.00 0.00 2.41
2551 3133 2.200373 AACTTGCGCCCTTCTGTAAT 57.800 45.000 4.18 0.00 0.00 1.89
2552 3134 3.343941 AACTTGCGCCCTTCTGTAATA 57.656 42.857 4.18 0.00 0.00 0.98
2553 3135 2.629051 ACTTGCGCCCTTCTGTAATAC 58.371 47.619 4.18 0.00 0.00 1.89
2554 3136 2.236395 ACTTGCGCCCTTCTGTAATACT 59.764 45.455 4.18 0.00 0.00 2.12
2555 3137 3.270877 CTTGCGCCCTTCTGTAATACTT 58.729 45.455 4.18 0.00 0.00 2.24
2556 3138 3.343941 TGCGCCCTTCTGTAATACTTT 57.656 42.857 4.18 0.00 0.00 2.66
2557 3139 3.267483 TGCGCCCTTCTGTAATACTTTC 58.733 45.455 4.18 0.00 0.00 2.62
2558 3140 2.612672 GCGCCCTTCTGTAATACTTTCC 59.387 50.000 0.00 0.00 0.00 3.13
2559 3141 3.681874 GCGCCCTTCTGTAATACTTTCCT 60.682 47.826 0.00 0.00 0.00 3.36
2560 3142 3.871594 CGCCCTTCTGTAATACTTTCCTG 59.128 47.826 0.00 0.00 0.00 3.86
2561 3143 3.628032 GCCCTTCTGTAATACTTTCCTGC 59.372 47.826 0.00 0.00 0.00 4.85
2562 3144 4.626529 GCCCTTCTGTAATACTTTCCTGCT 60.627 45.833 0.00 0.00 0.00 4.24
2563 3145 5.501156 CCCTTCTGTAATACTTTCCTGCTT 58.499 41.667 0.00 0.00 0.00 3.91
2564 3146 5.946377 CCCTTCTGTAATACTTTCCTGCTTT 59.054 40.000 0.00 0.00 0.00 3.51
2567 3149 6.374417 TCTGTAATACTTTCCTGCTTTCCT 57.626 37.500 0.00 0.00 0.00 3.36
2568 3150 6.173339 TCTGTAATACTTTCCTGCTTTCCTG 58.827 40.000 0.00 0.00 0.00 3.86
2571 3153 6.823689 TGTAATACTTTCCTGCTTTCCTGATC 59.176 38.462 0.00 0.00 0.00 2.92
2572 3154 2.704572 ACTTTCCTGCTTTCCTGATCG 58.295 47.619 0.00 0.00 0.00 3.69
2573 3155 2.303022 ACTTTCCTGCTTTCCTGATCGA 59.697 45.455 0.00 0.00 0.00 3.59
2574 3156 2.386661 TTCCTGCTTTCCTGATCGAC 57.613 50.000 0.00 0.00 0.00 4.20
2575 3157 0.173481 TCCTGCTTTCCTGATCGACG 59.827 55.000 0.00 0.00 0.00 5.12
2577 3159 1.424493 CTGCTTTCCTGATCGACGCC 61.424 60.000 0.00 0.00 0.00 5.68
2578 3160 1.447838 GCTTTCCTGATCGACGCCA 60.448 57.895 0.00 0.00 0.00 5.69
2579 3161 0.811616 GCTTTCCTGATCGACGCCAT 60.812 55.000 0.00 0.00 0.00 4.40
2580 3162 0.933097 CTTTCCTGATCGACGCCATG 59.067 55.000 0.00 0.00 0.00 3.66
2582 3164 2.923426 TTCCTGATCGACGCCATGGC 62.923 60.000 27.67 27.67 37.85 4.40
2583 3165 2.107750 CTGATCGACGCCATGGCT 59.892 61.111 33.07 20.54 39.32 4.75
2624 3207 6.990341 CTGTAAGTTCATGATGGATGACAA 57.010 37.500 0.00 0.00 41.02 3.18
2670 3253 0.871057 GCTTGGTCACACTTGCTCTC 59.129 55.000 0.00 0.00 0.00 3.20
2689 3272 4.293494 TCTCTGGATCTTGCCTATGTTCT 58.707 43.478 0.00 0.00 0.00 3.01
2692 3275 4.225942 TCTGGATCTTGCCTATGTTCTGTT 59.774 41.667 0.00 0.00 0.00 3.16
2693 3276 4.517285 TGGATCTTGCCTATGTTCTGTTC 58.483 43.478 0.00 0.00 0.00 3.18
2697 3280 2.851263 TGCCTATGTTCTGTTCGGTT 57.149 45.000 0.00 0.00 0.00 4.44
2698 3281 2.422597 TGCCTATGTTCTGTTCGGTTG 58.577 47.619 0.00 0.00 0.00 3.77
2711 3294 1.770294 TCGGTTGGAATTATTGGCCC 58.230 50.000 0.00 0.00 0.00 5.80
2727 3310 2.398252 GCCCGGAGCCTAATATAACC 57.602 55.000 0.73 0.00 34.35 2.85
2728 3311 1.907255 GCCCGGAGCCTAATATAACCT 59.093 52.381 0.73 0.00 34.35 3.50
2731 3314 3.056035 CCCGGAGCCTAATATAACCTGTC 60.056 52.174 0.73 0.00 0.00 3.51
2747 3330 1.952296 CTGTCTTGCTGGCTTCTGTTT 59.048 47.619 0.00 0.00 0.00 2.83
2781 3397 5.171339 ACTTGCTTCTTGTACTGATGGAT 57.829 39.130 0.00 0.00 0.00 3.41
2789 3682 3.026707 TGTACTGATGGATCCCTCGAA 57.973 47.619 9.90 0.00 0.00 3.71
2793 3686 2.205074 CTGATGGATCCCTCGAAAACG 58.795 52.381 9.90 0.00 0.00 3.60
2837 4180 9.344772 TGCAATTTATAGTTTATATCAACCCGT 57.655 29.630 0.00 0.00 0.00 5.28
2852 4195 1.758280 ACCCGTGTCTTCACTTGTACA 59.242 47.619 0.00 0.00 41.89 2.90
2858 4201 5.038683 CGTGTCTTCACTTGTACAGTTGTA 58.961 41.667 0.00 0.00 41.89 2.41
2859 4202 5.690409 CGTGTCTTCACTTGTACAGTTGTAT 59.310 40.000 0.00 0.00 41.89 2.29
2860 4203 6.859508 CGTGTCTTCACTTGTACAGTTGTATA 59.140 38.462 0.00 0.00 41.89 1.47
2861 4204 7.149015 CGTGTCTTCACTTGTACAGTTGTATAC 60.149 40.741 0.00 0.00 41.89 1.47
2862 4205 7.866393 GTGTCTTCACTTGTACAGTTGTATACT 59.134 37.037 4.17 0.00 40.98 2.12
2893 4236 5.659440 ACAACATAAGGCTGGGTTAATTG 57.341 39.130 0.00 0.00 0.00 2.32
2929 4276 4.046938 TCATCTTGATGCTTCTCCGTAC 57.953 45.455 5.78 0.00 0.00 3.67
2934 4281 0.824759 GATGCTTCTCCGTACCCTGT 59.175 55.000 0.00 0.00 0.00 4.00
2935 4282 0.537188 ATGCTTCTCCGTACCCTGTG 59.463 55.000 0.00 0.00 0.00 3.66
2936 4283 0.830444 TGCTTCTCCGTACCCTGTGT 60.830 55.000 0.00 0.00 0.00 3.72
2937 4284 0.320697 GCTTCTCCGTACCCTGTGTT 59.679 55.000 0.00 0.00 0.00 3.32
2938 4285 1.939838 GCTTCTCCGTACCCTGTGTTG 60.940 57.143 0.00 0.00 0.00 3.33
2939 4286 0.682852 TTCTCCGTACCCTGTGTTGG 59.317 55.000 0.00 0.00 0.00 3.77
2946 4293 2.513895 CCCTGTGTTGGGGAACGT 59.486 61.111 0.00 0.00 46.50 3.99
2947 4294 1.756024 CCCTGTGTTGGGGAACGTA 59.244 57.895 0.00 0.00 46.50 3.57
2948 4295 0.321298 CCCTGTGTTGGGGAACGTAG 60.321 60.000 0.00 0.00 46.50 3.51
2949 4296 0.953960 CCTGTGTTGGGGAACGTAGC 60.954 60.000 0.00 0.00 0.00 3.58
2950 4297 0.250124 CTGTGTTGGGGAACGTAGCA 60.250 55.000 0.00 0.00 0.00 3.49
2951 4298 0.180642 TGTGTTGGGGAACGTAGCAA 59.819 50.000 0.00 0.00 0.00 3.91
2952 4299 1.310904 GTGTTGGGGAACGTAGCAAA 58.689 50.000 0.00 0.00 0.00 3.68
2953 4300 1.677052 GTGTTGGGGAACGTAGCAAAA 59.323 47.619 0.00 0.00 0.00 2.44
2954 4301 2.099427 GTGTTGGGGAACGTAGCAAAAA 59.901 45.455 0.00 0.00 0.00 1.94
2955 4302 2.959707 TGTTGGGGAACGTAGCAAAAAT 59.040 40.909 0.00 0.00 0.00 1.82
2956 4303 3.385111 TGTTGGGGAACGTAGCAAAAATT 59.615 39.130 0.00 0.00 0.00 1.82
2957 4304 3.926821 TGGGGAACGTAGCAAAAATTC 57.073 42.857 0.00 0.00 0.00 2.17
2958 4305 3.223435 TGGGGAACGTAGCAAAAATTCA 58.777 40.909 0.00 0.00 0.00 2.57
2959 4306 3.637229 TGGGGAACGTAGCAAAAATTCAA 59.363 39.130 0.00 0.00 0.00 2.69
2960 4307 4.099573 TGGGGAACGTAGCAAAAATTCAAA 59.900 37.500 0.00 0.00 0.00 2.69
2961 4308 5.051153 GGGGAACGTAGCAAAAATTCAAAA 58.949 37.500 0.00 0.00 0.00 2.44
2962 4309 5.524281 GGGGAACGTAGCAAAAATTCAAAAA 59.476 36.000 0.00 0.00 0.00 1.94
2982 4329 6.687081 AAAAATTTCTACGTGTCACCAAGA 57.313 33.333 0.00 0.00 0.00 3.02
2983 4330 6.877611 AAAATTTCTACGTGTCACCAAGAT 57.122 33.333 0.00 0.00 0.00 2.40
2984 4331 6.481954 AAATTTCTACGTGTCACCAAGATC 57.518 37.500 0.00 0.00 0.00 2.75
2985 4332 4.866508 TTTCTACGTGTCACCAAGATCT 57.133 40.909 0.00 0.00 0.00 2.75
2986 4333 5.970317 TTTCTACGTGTCACCAAGATCTA 57.030 39.130 0.00 0.00 0.00 1.98
2987 4334 6.525578 TTTCTACGTGTCACCAAGATCTAT 57.474 37.500 0.00 0.00 0.00 1.98
2988 4335 5.752892 TCTACGTGTCACCAAGATCTATC 57.247 43.478 0.00 0.00 0.00 2.08
2989 4336 5.437946 TCTACGTGTCACCAAGATCTATCT 58.562 41.667 0.00 0.00 39.22 1.98
2990 4337 6.589135 TCTACGTGTCACCAAGATCTATCTA 58.411 40.000 0.00 0.00 35.76 1.98
2991 4338 7.225011 TCTACGTGTCACCAAGATCTATCTAT 58.775 38.462 0.00 0.00 35.76 1.98
2992 4339 6.078202 ACGTGTCACCAAGATCTATCTATG 57.922 41.667 0.00 0.00 35.76 2.23
2993 4340 5.010112 ACGTGTCACCAAGATCTATCTATGG 59.990 44.000 8.57 8.57 39.18 2.74
2994 4341 5.241728 CGTGTCACCAAGATCTATCTATGGA 59.758 44.000 15.80 0.00 37.92 3.41
2995 4342 6.569418 CGTGTCACCAAGATCTATCTATGGAG 60.569 46.154 15.80 8.98 37.92 3.86
2996 4343 6.491745 GTGTCACCAAGATCTATCTATGGAGA 59.508 42.308 15.80 10.97 37.92 3.71
2997 4344 6.718912 TGTCACCAAGATCTATCTATGGAGAG 59.281 42.308 15.80 6.64 36.48 3.20
2998 4345 6.945435 GTCACCAAGATCTATCTATGGAGAGA 59.055 42.308 15.80 5.84 42.87 3.10
2999 4346 6.945435 TCACCAAGATCTATCTATGGAGAGAC 59.055 42.308 15.80 1.08 41.74 3.36
3000 4347 6.947733 CACCAAGATCTATCTATGGAGAGACT 59.052 42.308 15.80 3.27 41.74 3.24
3001 4348 8.106462 CACCAAGATCTATCTATGGAGAGACTA 58.894 40.741 15.80 0.00 41.74 2.59
3002 4349 8.328758 ACCAAGATCTATCTATGGAGAGACTAG 58.671 40.741 15.80 4.41 41.74 2.57
3003 4350 7.283127 CCAAGATCTATCTATGGAGAGACTAGC 59.717 44.444 5.47 0.00 41.74 3.42
3004 4351 7.509236 AGATCTATCTATGGAGAGACTAGCA 57.491 40.000 5.47 0.00 41.74 3.49
3005 4352 7.927788 AGATCTATCTATGGAGAGACTAGCAA 58.072 38.462 5.47 0.00 41.74 3.91
3006 4353 7.829211 AGATCTATCTATGGAGAGACTAGCAAC 59.171 40.741 5.47 0.00 41.74 4.17
3007 4354 5.935206 TCTATCTATGGAGAGACTAGCAACG 59.065 44.000 0.00 0.00 35.23 4.10
3008 4355 4.152284 TCTATGGAGAGACTAGCAACGA 57.848 45.455 0.00 0.00 0.00 3.85
3009 4356 4.130857 TCTATGGAGAGACTAGCAACGAG 58.869 47.826 0.00 0.00 0.00 4.18
3010 4357 1.464734 TGGAGAGACTAGCAACGAGG 58.535 55.000 0.00 0.00 0.00 4.63
3011 4358 0.741915 GGAGAGACTAGCAACGAGGG 59.258 60.000 0.00 0.00 0.00 4.30
3012 4359 0.741915 GAGAGACTAGCAACGAGGGG 59.258 60.000 0.00 0.00 0.00 4.79
3013 4360 0.331954 AGAGACTAGCAACGAGGGGA 59.668 55.000 0.00 0.00 0.00 4.81
3014 4361 1.183549 GAGACTAGCAACGAGGGGAA 58.816 55.000 0.00 0.00 0.00 3.97
3015 4362 1.135333 GAGACTAGCAACGAGGGGAAG 59.865 57.143 0.00 0.00 0.00 3.46
3016 4363 0.175989 GACTAGCAACGAGGGGAAGG 59.824 60.000 0.00 0.00 0.00 3.46
3017 4364 0.252103 ACTAGCAACGAGGGGAAGGA 60.252 55.000 0.00 0.00 0.00 3.36
3018 4365 0.461961 CTAGCAACGAGGGGAAGGAG 59.538 60.000 0.00 0.00 0.00 3.69
3019 4366 0.040646 TAGCAACGAGGGGAAGGAGA 59.959 55.000 0.00 0.00 0.00 3.71
3020 4367 1.219393 GCAACGAGGGGAAGGAGAG 59.781 63.158 0.00 0.00 0.00 3.20
3021 4368 1.545706 GCAACGAGGGGAAGGAGAGT 61.546 60.000 0.00 0.00 0.00 3.24
3022 4369 0.247736 CAACGAGGGGAAGGAGAGTG 59.752 60.000 0.00 0.00 0.00 3.51
3023 4370 1.545706 AACGAGGGGAAGGAGAGTGC 61.546 60.000 0.00 0.00 0.00 4.40
3024 4371 1.984570 CGAGGGGAAGGAGAGTGCA 60.985 63.158 0.00 0.00 0.00 4.57
3025 4372 1.333636 CGAGGGGAAGGAGAGTGCAT 61.334 60.000 0.00 0.00 0.00 3.96
3026 4373 0.467804 GAGGGGAAGGAGAGTGCATC 59.532 60.000 0.00 0.00 0.00 3.91
3027 4374 0.043940 AGGGGAAGGAGAGTGCATCT 59.956 55.000 0.00 0.00 42.61 2.90
3028 4375 1.292242 AGGGGAAGGAGAGTGCATCTA 59.708 52.381 0.00 0.00 38.84 1.98
3029 4376 1.414550 GGGGAAGGAGAGTGCATCTAC 59.585 57.143 0.00 0.00 38.84 2.59
3030 4377 2.111384 GGGAAGGAGAGTGCATCTACA 58.889 52.381 9.98 0.00 42.01 2.74
3031 4378 2.703007 GGGAAGGAGAGTGCATCTACAT 59.297 50.000 9.98 0.00 42.01 2.29
3032 4379 3.898123 GGGAAGGAGAGTGCATCTACATA 59.102 47.826 9.98 0.00 42.01 2.29
3033 4380 4.262249 GGGAAGGAGAGTGCATCTACATAC 60.262 50.000 9.98 0.82 42.01 2.39
3034 4381 4.262249 GGAAGGAGAGTGCATCTACATACC 60.262 50.000 9.98 6.83 42.01 2.73
3035 4382 3.235200 AGGAGAGTGCATCTACATACCC 58.765 50.000 9.98 2.71 42.01 3.69
3036 4383 3.116939 AGGAGAGTGCATCTACATACCCT 60.117 47.826 9.98 4.47 42.01 4.34
3037 4384 3.643792 GGAGAGTGCATCTACATACCCTT 59.356 47.826 0.00 0.00 38.94 3.95
3038 4385 4.502259 GGAGAGTGCATCTACATACCCTTG 60.502 50.000 0.00 0.00 38.94 3.61
3039 4386 4.033709 AGAGTGCATCTACATACCCTTGT 58.966 43.478 0.00 0.00 36.10 3.16
3040 4387 5.208890 AGAGTGCATCTACATACCCTTGTA 58.791 41.667 0.00 0.00 36.10 2.41
3041 4388 5.303078 AGAGTGCATCTACATACCCTTGTAG 59.697 44.000 5.47 5.47 46.85 2.74
3050 4397 5.455056 ACATACCCTTGTAGATCGCTAAG 57.545 43.478 0.00 0.00 0.00 2.18
3051 4398 2.892784 ACCCTTGTAGATCGCTAAGC 57.107 50.000 0.00 0.00 0.00 3.09
3064 4411 2.882742 GCTAAGCGGAAGTGTTCAAG 57.117 50.000 0.00 0.00 0.00 3.02
3065 4412 2.143925 GCTAAGCGGAAGTGTTCAAGT 58.856 47.619 0.00 0.00 0.00 3.16
3066 4413 2.096218 GCTAAGCGGAAGTGTTCAAGTG 60.096 50.000 0.00 0.00 0.00 3.16
3067 4414 2.325583 AAGCGGAAGTGTTCAAGTGA 57.674 45.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.262448 TTAGGACCAGGTTGCCGCC 62.262 63.158 0.00 0.00 0.00 6.13
25 26 5.125739 AGCACAGACAGTATACACTTAGGAC 59.874 44.000 5.50 0.00 30.46 3.85
29 30 7.170828 CACAAAAGCACAGACAGTATACACTTA 59.829 37.037 5.50 0.00 30.46 2.24
88 95 0.392998 CCTGTGAATCCCCCACTTCG 60.393 60.000 0.00 0.00 35.66 3.79
123 130 6.672147 CCCTCCAATCAATATGAAATCGAAC 58.328 40.000 0.00 0.00 0.00 3.95
124 131 5.241506 GCCCTCCAATCAATATGAAATCGAA 59.758 40.000 0.00 0.00 0.00 3.71
129 136 3.221771 CGGCCCTCCAATCAATATGAAA 58.778 45.455 0.00 0.00 0.00 2.69
134 141 0.465460 GTGCGGCCCTCCAATCAATA 60.465 55.000 0.00 0.00 0.00 1.90
153 160 3.537793 TGCTATACATCTCGCAGTACG 57.462 47.619 0.00 0.00 45.62 3.67
154 161 3.670991 GCTTGCTATACATCTCGCAGTAC 59.329 47.826 0.00 0.00 33.48 2.73
155 162 3.317993 TGCTTGCTATACATCTCGCAGTA 59.682 43.478 0.00 0.00 33.48 2.74
156 163 2.101415 TGCTTGCTATACATCTCGCAGT 59.899 45.455 0.00 0.00 33.48 4.40
246 293 6.767902 GCTGAATATTCCTGTTGTAAGATGGA 59.232 38.462 12.90 0.00 0.00 3.41
299 355 1.136085 CACAAGGTACGGTTCATTGCG 60.136 52.381 11.24 0.00 31.12 4.85
332 395 1.885887 GTTGCTGGTGTGCCAAATAGA 59.114 47.619 0.00 0.00 45.51 1.98
429 580 2.093306 TAACTCTGCACCCGAATGTG 57.907 50.000 0.00 0.00 39.29 3.21
430 581 2.851263 TTAACTCTGCACCCGAATGT 57.149 45.000 0.00 0.00 0.00 2.71
434 585 5.553123 TCTAATTTTTAACTCTGCACCCGA 58.447 37.500 0.00 0.00 0.00 5.14
438 589 7.809806 ACATTGCTCTAATTTTTAACTCTGCAC 59.190 33.333 0.00 0.00 0.00 4.57
469 620 7.095695 ACTTCTAGAGATGTCTTACTTCTGC 57.904 40.000 0.00 0.00 33.42 4.26
593 748 2.233271 ACACAGCATCTCACTTTTGGG 58.767 47.619 0.00 0.00 0.00 4.12
608 763 3.805422 TGCACGAGTACCTTTTTACACAG 59.195 43.478 0.00 0.00 0.00 3.66
649 804 7.199766 TGCCATTTGTTAGTTTTCTTGTAGTG 58.800 34.615 0.00 0.00 0.00 2.74
664 819 5.719085 TCCAACCTGTATATTGCCATTTGTT 59.281 36.000 0.00 0.00 0.00 2.83
709 870 2.746362 GTTGGACAGAGAGGCAAAGATG 59.254 50.000 0.00 0.00 0.00 2.90
724 885 8.723942 AACATATAGTTGATGAGAAGTTGGAC 57.276 34.615 0.00 0.00 39.49 4.02
762 1017 3.814842 TCTGTGTTATGGTGCAACTTCAG 59.185 43.478 2.04 0.33 36.74 3.02
855 1110 5.611374 ACTGTAGCTGCTGAAAAGAAAGTA 58.389 37.500 13.43 0.00 0.00 2.24
904 1160 4.973168 AGCATGTTCACAAGGAAACTAGA 58.027 39.130 0.00 0.00 42.68 2.43
918 1174 6.384224 TGATGACAAAAAGATGAGCATGTTC 58.616 36.000 2.05 2.05 0.00 3.18
1113 1375 0.739462 GGGTCGACGCAATGATGACA 60.739 55.000 25.93 0.00 0.00 3.58
1122 1384 3.047718 GATCACGAGGGTCGACGCA 62.048 63.158 31.03 13.15 43.74 5.24
1125 1387 0.526662 ACAAGATCACGAGGGTCGAC 59.473 55.000 7.13 7.13 43.74 4.20
1132 1394 3.935203 ACCTTAATGCACAAGATCACGAG 59.065 43.478 10.71 0.00 0.00 4.18
1134 1396 3.935203 AGACCTTAATGCACAAGATCACG 59.065 43.478 10.71 0.00 0.00 4.35
1135 1397 5.886960 AAGACCTTAATGCACAAGATCAC 57.113 39.130 10.71 1.43 0.00 3.06
1142 1404 2.030363 CGGCAAAAGACCTTAATGCACA 60.030 45.455 16.81 0.00 37.30 4.57
1143 1405 2.030274 ACGGCAAAAGACCTTAATGCAC 60.030 45.455 16.81 9.15 37.30 4.57
1185 1448 0.755686 GAGAGAATGGCGACCAGGAT 59.244 55.000 0.00 0.00 36.75 3.24
1208 1471 4.166888 TCCGGGAGATGCTGCTGC 62.167 66.667 8.89 8.89 40.20 5.25
1253 1516 2.124819 CCTCCGCTGCATGCTTCT 60.125 61.111 20.33 0.00 40.11 2.85
1263 1526 2.964310 ATGAACAGCTGCCTCCGCT 61.964 57.895 15.27 0.00 38.49 5.52
1459 1731 4.137116 TCATATCGCTAGGCACAAAGTT 57.863 40.909 0.00 0.00 0.00 2.66
1466 1738 2.493675 GACAGGATCATATCGCTAGGCA 59.506 50.000 0.00 0.00 0.00 4.75
1472 1744 2.354203 GGAAGGGACAGGATCATATCGC 60.354 54.545 0.00 0.00 0.00 4.58
1554 1826 1.067364 TCGCAGAACGGACAACAGTAA 59.933 47.619 0.00 0.00 43.89 2.24
1725 1997 2.716017 GCCCGAGAGTCTGTCCAGG 61.716 68.421 0.00 0.00 0.00 4.45
1740 2012 4.201122 CATCCCCTCCAGCTGCCC 62.201 72.222 8.66 0.00 0.00 5.36
1803 2075 3.379445 CAGCTCCCCGTGGTACGT 61.379 66.667 0.00 0.00 40.58 3.57
1863 2135 2.374830 CTAGCCACCCATGAGAGCCG 62.375 65.000 0.00 0.00 0.00 5.52
1871 2143 1.002857 AAAAGAGCCTAGCCACCCAT 58.997 50.000 0.00 0.00 0.00 4.00
1881 2153 1.981495 AGTGTAGCCAGAAAAGAGCCT 59.019 47.619 0.00 0.00 0.00 4.58
1882 2154 2.027653 AGAGTGTAGCCAGAAAAGAGCC 60.028 50.000 0.00 0.00 0.00 4.70
1883 2155 3.258228 GAGAGTGTAGCCAGAAAAGAGC 58.742 50.000 0.00 0.00 0.00 4.09
1889 2161 1.970640 TGCTTGAGAGTGTAGCCAGAA 59.029 47.619 0.00 0.00 34.03 3.02
1905 2177 1.056700 AGTGTCCACTCCAGGTGCTT 61.057 55.000 0.00 0.00 44.08 3.91
1922 2194 1.115930 AGTGGAACGGCTGTCTGAGT 61.116 55.000 0.00 0.00 45.86 3.41
1929 2201 1.086696 CCATTGTAGTGGAACGGCTG 58.913 55.000 0.00 0.00 45.86 4.85
1934 2206 3.370978 CGATGACACCATTGTAGTGGAAC 59.629 47.826 0.00 0.00 42.02 3.62
2014 2286 1.517242 CTCCTGGAACACAAGTCAGC 58.483 55.000 0.00 0.00 0.00 4.26
2088 2360 5.362430 TCAGAACAAACTTGCCTGGTTATTT 59.638 36.000 10.60 0.00 34.77 1.40
2090 2362 4.469657 TCAGAACAAACTTGCCTGGTTAT 58.530 39.130 10.60 0.00 34.77 1.89
2091 2363 3.892284 TCAGAACAAACTTGCCTGGTTA 58.108 40.909 10.60 0.00 34.77 2.85
2136 2411 4.610945 CCTAGCAGGTTTCAAAACAAGTG 58.389 43.478 7.82 3.51 40.63 3.16
2188 2463 6.445357 ACATAAAACTGGAAACACGTCTTT 57.555 33.333 0.00 0.00 35.60 2.52
2212 2487 6.422100 CAGAACTTGAAATGAGAAGAGACGAA 59.578 38.462 0.00 0.00 0.00 3.85
2214 2489 5.923114 TCAGAACTTGAAATGAGAAGAGACG 59.077 40.000 0.00 0.00 31.34 4.18
2412 2690 2.728690 TTTCGTACACGGCATACAGT 57.271 45.000 1.39 0.00 40.29 3.55
2424 2702 5.512788 CACTGATGCCATTGATTTTTCGTAC 59.487 40.000 0.00 0.00 0.00 3.67
2425 2703 5.414144 TCACTGATGCCATTGATTTTTCGTA 59.586 36.000 0.00 0.00 28.62 3.43
2438 2716 3.181455 ACAAAGTACACTCACTGATGCCA 60.181 43.478 0.00 0.00 0.00 4.92
2441 2719 5.696270 TGCTTACAAAGTACACTCACTGATG 59.304 40.000 0.00 0.00 0.00 3.07
2457 2885 8.097038 GGATGGATGAGATATACTTGCTTACAA 58.903 37.037 0.00 0.00 0.00 2.41
2460 2888 7.455953 ACAGGATGGATGAGATATACTTGCTTA 59.544 37.037 0.00 0.00 43.62 3.09
2463 2891 6.047511 ACAGGATGGATGAGATATACTTGC 57.952 41.667 0.00 0.00 43.62 4.01
2489 3071 3.118884 TCGACCAGGAAAGTAATGGCTAC 60.119 47.826 0.00 0.00 37.64 3.58
2509 3091 2.413112 CCATATCAAAGCCATAGCGTCG 59.587 50.000 0.00 0.00 46.67 5.12
2541 3123 6.094186 GGAAAGCAGGAAAGTATTACAGAAGG 59.906 42.308 0.00 0.00 0.00 3.46
2550 3132 4.162320 TCGATCAGGAAAGCAGGAAAGTAT 59.838 41.667 0.00 0.00 0.00 2.12
2551 3133 3.513912 TCGATCAGGAAAGCAGGAAAGTA 59.486 43.478 0.00 0.00 0.00 2.24
2552 3134 2.303022 TCGATCAGGAAAGCAGGAAAGT 59.697 45.455 0.00 0.00 0.00 2.66
2553 3135 2.675348 GTCGATCAGGAAAGCAGGAAAG 59.325 50.000 0.00 0.00 0.00 2.62
2554 3136 2.699954 GTCGATCAGGAAAGCAGGAAA 58.300 47.619 0.00 0.00 0.00 3.13
2555 3137 1.404181 CGTCGATCAGGAAAGCAGGAA 60.404 52.381 0.00 0.00 0.00 3.36
2556 3138 0.173481 CGTCGATCAGGAAAGCAGGA 59.827 55.000 0.00 0.00 0.00 3.86
2557 3139 1.424493 GCGTCGATCAGGAAAGCAGG 61.424 60.000 0.00 0.00 0.00 4.85
2558 3140 1.424493 GGCGTCGATCAGGAAAGCAG 61.424 60.000 0.00 0.00 0.00 4.24
2559 3141 1.447838 GGCGTCGATCAGGAAAGCA 60.448 57.895 0.00 0.00 0.00 3.91
2560 3142 0.811616 ATGGCGTCGATCAGGAAAGC 60.812 55.000 0.00 0.00 0.00 3.51
2561 3143 0.933097 CATGGCGTCGATCAGGAAAG 59.067 55.000 0.00 0.00 0.00 2.62
2562 3144 0.461870 CCATGGCGTCGATCAGGAAA 60.462 55.000 0.00 0.00 0.00 3.13
2563 3145 1.143838 CCATGGCGTCGATCAGGAA 59.856 57.895 0.00 0.00 0.00 3.36
2564 3146 2.814604 CCATGGCGTCGATCAGGA 59.185 61.111 0.00 0.00 0.00 3.86
2582 3164 3.994392 ACAGTAAACACACCATAGCGAAG 59.006 43.478 0.00 0.00 0.00 3.79
2583 3165 3.997762 ACAGTAAACACACCATAGCGAA 58.002 40.909 0.00 0.00 0.00 4.70
2622 3205 5.163457 ACCCTTCAGTAAACACACCAAATTG 60.163 40.000 0.00 0.00 0.00 2.32
2624 3207 4.340950 CACCCTTCAGTAAACACACCAAAT 59.659 41.667 0.00 0.00 0.00 2.32
2670 3253 4.148128 ACAGAACATAGGCAAGATCCAG 57.852 45.455 0.00 0.00 0.00 3.86
2689 3272 2.494073 GGCCAATAATTCCAACCGAACA 59.506 45.455 0.00 0.00 31.79 3.18
2692 3275 1.770294 GGGCCAATAATTCCAACCGA 58.230 50.000 4.39 0.00 0.00 4.69
2693 3276 0.383949 CGGGCCAATAATTCCAACCG 59.616 55.000 4.39 0.00 0.00 4.44
2697 3280 0.467290 GCTCCGGGCCAATAATTCCA 60.467 55.000 4.39 0.00 34.27 3.53
2698 3281 2.341452 GCTCCGGGCCAATAATTCC 58.659 57.895 4.39 0.00 34.27 3.01
2711 3294 5.230942 CAAGACAGGTTATATTAGGCTCCG 58.769 45.833 0.00 0.00 0.00 4.63
2718 3301 5.630415 AGCCAGCAAGACAGGTTATATTA 57.370 39.130 0.00 0.00 0.00 0.98
2722 3305 2.307098 AGAAGCCAGCAAGACAGGTTAT 59.693 45.455 0.00 0.00 0.00 1.89
2723 3306 1.699634 AGAAGCCAGCAAGACAGGTTA 59.300 47.619 0.00 0.00 0.00 2.85
2724 3307 0.475906 AGAAGCCAGCAAGACAGGTT 59.524 50.000 0.00 0.00 0.00 3.50
2725 3308 0.250640 CAGAAGCCAGCAAGACAGGT 60.251 55.000 0.00 0.00 0.00 4.00
2726 3309 0.250640 ACAGAAGCCAGCAAGACAGG 60.251 55.000 0.00 0.00 0.00 4.00
2727 3310 1.602311 AACAGAAGCCAGCAAGACAG 58.398 50.000 0.00 0.00 0.00 3.51
2728 3311 2.057137 AAACAGAAGCCAGCAAGACA 57.943 45.000 0.00 0.00 0.00 3.41
2731 3314 2.360165 ACAGAAAACAGAAGCCAGCAAG 59.640 45.455 0.00 0.00 0.00 4.01
2747 3330 3.531538 AGAAGCAAGTTCGTCAACAGAA 58.468 40.909 0.00 0.00 40.49 3.02
2789 3682 5.221087 GCAGACTAGCTCTACTTATCCGTTT 60.221 44.000 0.00 0.00 0.00 3.60
2793 3686 5.776173 TTGCAGACTAGCTCTACTTATCC 57.224 43.478 0.00 0.00 34.99 2.59
2835 4178 5.690409 ATACAACTGTACAAGTGAAGACACG 59.310 40.000 11.42 0.00 41.30 4.49
2837 4180 7.948357 AGTATACAACTGTACAAGTGAAGACA 58.052 34.615 5.50 0.00 39.81 3.41
2864 4207 4.287585 ACCCAGCCTTATGTTGTACTACAA 59.712 41.667 14.03 0.00 35.42 2.41
2865 4208 3.841845 ACCCAGCCTTATGTTGTACTACA 59.158 43.478 12.50 12.50 0.00 2.74
2866 4209 4.482952 ACCCAGCCTTATGTTGTACTAC 57.517 45.455 0.05 0.05 0.00 2.73
2867 4210 6.623979 TTAACCCAGCCTTATGTTGTACTA 57.376 37.500 0.00 0.00 0.00 1.82
2868 4211 5.508280 TTAACCCAGCCTTATGTTGTACT 57.492 39.130 0.00 0.00 0.00 2.73
2869 4212 6.152154 ACAATTAACCCAGCCTTATGTTGTAC 59.848 38.462 0.00 0.00 0.00 2.90
2870 4213 6.249951 ACAATTAACCCAGCCTTATGTTGTA 58.750 36.000 0.00 0.00 0.00 2.41
2871 4214 5.083821 ACAATTAACCCAGCCTTATGTTGT 58.916 37.500 0.00 0.00 0.00 3.32
2872 4215 5.659440 ACAATTAACCCAGCCTTATGTTG 57.341 39.130 0.00 0.00 0.00 3.33
2873 4216 7.839200 AGATTACAATTAACCCAGCCTTATGTT 59.161 33.333 0.00 0.00 0.00 2.71
2893 4236 6.801539 TCAAGATGAACAACACCAGATTAC 57.198 37.500 0.00 0.00 0.00 1.89
2934 4281 2.054232 TTTTGCTACGTTCCCCAACA 57.946 45.000 0.00 0.00 32.14 3.33
2935 4282 3.653539 ATTTTTGCTACGTTCCCCAAC 57.346 42.857 0.00 0.00 0.00 3.77
2936 4283 3.637229 TGAATTTTTGCTACGTTCCCCAA 59.363 39.130 0.00 0.00 0.00 4.12
2937 4284 3.223435 TGAATTTTTGCTACGTTCCCCA 58.777 40.909 0.00 0.00 0.00 4.96
2938 4285 3.926821 TGAATTTTTGCTACGTTCCCC 57.073 42.857 0.00 0.00 0.00 4.81
2939 4286 6.591313 TTTTTGAATTTTTGCTACGTTCCC 57.409 33.333 0.00 0.00 0.00 3.97
2959 4306 6.687081 TCTTGGTGACACGTAGAAATTTTT 57.313 33.333 0.00 0.00 42.67 1.94
2960 4307 6.710744 AGATCTTGGTGACACGTAGAAATTTT 59.289 34.615 11.01 0.00 42.67 1.82
2961 4308 6.231211 AGATCTTGGTGACACGTAGAAATTT 58.769 36.000 11.01 0.00 42.67 1.82
2962 4309 5.794894 AGATCTTGGTGACACGTAGAAATT 58.205 37.500 11.01 0.00 42.67 1.82
2963 4310 5.407407 AGATCTTGGTGACACGTAGAAAT 57.593 39.130 11.01 2.71 42.67 2.17
2964 4311 4.866508 AGATCTTGGTGACACGTAGAAA 57.133 40.909 11.01 0.00 42.67 2.52
2965 4312 5.886474 AGATAGATCTTGGTGACACGTAGAA 59.114 40.000 0.00 0.00 42.67 2.10
2966 4313 5.437946 AGATAGATCTTGGTGACACGTAGA 58.562 41.667 0.00 9.78 42.67 2.59
2967 4314 5.759506 AGATAGATCTTGGTGACACGTAG 57.240 43.478 0.00 0.00 42.67 3.51
2968 4315 6.206829 CCATAGATAGATCTTGGTGACACGTA 59.793 42.308 0.00 0.00 42.67 3.57
2969 4316 5.010112 CCATAGATAGATCTTGGTGACACGT 59.990 44.000 0.00 0.00 42.67 4.49
2970 4317 5.241728 TCCATAGATAGATCTTGGTGACACG 59.758 44.000 0.00 0.00 42.67 4.49
2971 4318 6.491745 TCTCCATAGATAGATCTTGGTGACAC 59.508 42.308 0.00 0.00 42.67 3.67
2972 4319 6.614657 TCTCCATAGATAGATCTTGGTGACA 58.385 40.000 0.00 0.00 38.32 3.58
2973 4320 6.945435 TCTCTCCATAGATAGATCTTGGTGAC 59.055 42.308 0.00 0.00 38.32 3.67
2974 4321 6.945435 GTCTCTCCATAGATAGATCTTGGTGA 59.055 42.308 0.00 7.70 38.32 4.02
2975 4322 6.947733 AGTCTCTCCATAGATAGATCTTGGTG 59.052 42.308 0.00 3.27 38.32 4.17
2976 4323 7.102518 AGTCTCTCCATAGATAGATCTTGGT 57.897 40.000 0.00 0.00 38.32 3.67
2977 4324 7.283127 GCTAGTCTCTCCATAGATAGATCTTGG 59.717 44.444 0.00 1.69 38.32 3.61
2978 4325 7.828717 TGCTAGTCTCTCCATAGATAGATCTTG 59.171 40.741 0.00 0.00 38.32 3.02
2979 4326 7.927788 TGCTAGTCTCTCCATAGATAGATCTT 58.072 38.462 0.00 0.00 38.32 2.40
2980 4327 7.509236 TGCTAGTCTCTCCATAGATAGATCT 57.491 40.000 0.00 0.00 40.86 2.75
2981 4328 7.201609 CGTTGCTAGTCTCTCCATAGATAGATC 60.202 44.444 0.00 0.00 28.96 2.75
2982 4329 6.597672 CGTTGCTAGTCTCTCCATAGATAGAT 59.402 42.308 0.00 0.00 28.96 1.98
2983 4330 5.935206 CGTTGCTAGTCTCTCCATAGATAGA 59.065 44.000 0.00 0.00 0.00 1.98
2984 4331 5.935206 TCGTTGCTAGTCTCTCCATAGATAG 59.065 44.000 0.00 0.00 0.00 2.08
2985 4332 5.866207 TCGTTGCTAGTCTCTCCATAGATA 58.134 41.667 0.00 0.00 0.00 1.98
2986 4333 4.720046 TCGTTGCTAGTCTCTCCATAGAT 58.280 43.478 0.00 0.00 0.00 1.98
2987 4334 4.130857 CTCGTTGCTAGTCTCTCCATAGA 58.869 47.826 0.00 0.00 0.00 1.98
2988 4335 3.252215 CCTCGTTGCTAGTCTCTCCATAG 59.748 52.174 0.00 0.00 0.00 2.23
2989 4336 3.215151 CCTCGTTGCTAGTCTCTCCATA 58.785 50.000 0.00 0.00 0.00 2.74
2990 4337 2.028130 CCTCGTTGCTAGTCTCTCCAT 58.972 52.381 0.00 0.00 0.00 3.41
2991 4338 1.464734 CCTCGTTGCTAGTCTCTCCA 58.535 55.000 0.00 0.00 0.00 3.86
2992 4339 0.741915 CCCTCGTTGCTAGTCTCTCC 59.258 60.000 0.00 0.00 0.00 3.71
2993 4340 0.741915 CCCCTCGTTGCTAGTCTCTC 59.258 60.000 0.00 0.00 0.00 3.20
2994 4341 0.331954 TCCCCTCGTTGCTAGTCTCT 59.668 55.000 0.00 0.00 0.00 3.10
2995 4342 1.135333 CTTCCCCTCGTTGCTAGTCTC 59.865 57.143 0.00 0.00 0.00 3.36
2996 4343 1.187087 CTTCCCCTCGTTGCTAGTCT 58.813 55.000 0.00 0.00 0.00 3.24
2997 4344 0.175989 CCTTCCCCTCGTTGCTAGTC 59.824 60.000 0.00 0.00 0.00 2.59
2998 4345 0.252103 TCCTTCCCCTCGTTGCTAGT 60.252 55.000 0.00 0.00 0.00 2.57
2999 4346 0.461961 CTCCTTCCCCTCGTTGCTAG 59.538 60.000 0.00 0.00 0.00 3.42
3000 4347 0.040646 TCTCCTTCCCCTCGTTGCTA 59.959 55.000 0.00 0.00 0.00 3.49
3001 4348 1.229209 TCTCCTTCCCCTCGTTGCT 60.229 57.895 0.00 0.00 0.00 3.91
3002 4349 1.219393 CTCTCCTTCCCCTCGTTGC 59.781 63.158 0.00 0.00 0.00 4.17
3003 4350 0.247736 CACTCTCCTTCCCCTCGTTG 59.752 60.000 0.00 0.00 0.00 4.10
3004 4351 1.545706 GCACTCTCCTTCCCCTCGTT 61.546 60.000 0.00 0.00 0.00 3.85
3005 4352 1.985116 GCACTCTCCTTCCCCTCGT 60.985 63.158 0.00 0.00 0.00 4.18
3006 4353 1.333636 ATGCACTCTCCTTCCCCTCG 61.334 60.000 0.00 0.00 0.00 4.63
3007 4354 0.467804 GATGCACTCTCCTTCCCCTC 59.532 60.000 0.00 0.00 0.00 4.30
3008 4355 0.043940 AGATGCACTCTCCTTCCCCT 59.956 55.000 0.00 0.00 0.00 4.79
3009 4356 1.414550 GTAGATGCACTCTCCTTCCCC 59.585 57.143 0.00 0.00 35.28 4.81
3010 4357 2.111384 TGTAGATGCACTCTCCTTCCC 58.889 52.381 0.00 0.00 35.28 3.97
3011 4358 4.262249 GGTATGTAGATGCACTCTCCTTCC 60.262 50.000 0.00 0.00 35.28 3.46
3012 4359 4.262249 GGGTATGTAGATGCACTCTCCTTC 60.262 50.000 0.00 0.00 35.28 3.46
3013 4360 3.643792 GGGTATGTAGATGCACTCTCCTT 59.356 47.826 0.00 0.00 35.28 3.36
3014 4361 3.116939 AGGGTATGTAGATGCACTCTCCT 60.117 47.826 0.00 0.00 35.28 3.69
3015 4362 3.235200 AGGGTATGTAGATGCACTCTCC 58.765 50.000 0.00 0.00 35.28 3.71
3016 4363 4.100189 ACAAGGGTATGTAGATGCACTCTC 59.900 45.833 0.00 0.00 35.28 3.20
3017 4364 4.033709 ACAAGGGTATGTAGATGCACTCT 58.966 43.478 0.00 0.00 38.06 3.24
3018 4365 4.408182 ACAAGGGTATGTAGATGCACTC 57.592 45.455 0.00 0.00 25.83 3.51
3027 4374 5.048224 GCTTAGCGATCTACAAGGGTATGTA 60.048 44.000 0.00 0.00 34.75 2.29
3028 4375 4.262079 GCTTAGCGATCTACAAGGGTATGT 60.262 45.833 0.00 0.00 37.32 2.29
3029 4376 4.238514 GCTTAGCGATCTACAAGGGTATG 58.761 47.826 0.00 0.00 0.00 2.39
3030 4377 4.522722 GCTTAGCGATCTACAAGGGTAT 57.477 45.455 0.00 0.00 0.00 2.73
3032 4379 2.892784 GCTTAGCGATCTACAAGGGT 57.107 50.000 0.00 0.00 0.00 4.34
3045 4392 2.096218 CACTTGAACACTTCCGCTTAGC 60.096 50.000 0.00 0.00 0.00 3.09
3046 4393 3.390135 TCACTTGAACACTTCCGCTTAG 58.610 45.455 0.00 0.00 0.00 2.18
3047 4394 3.462483 TCACTTGAACACTTCCGCTTA 57.538 42.857 0.00 0.00 0.00 3.09
3048 4395 2.325583 TCACTTGAACACTTCCGCTT 57.674 45.000 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.