Multiple sequence alignment - TraesCS2D01G548800

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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 TraesCS2D01G548800 chr2D 100.000 4500 0 0 1 4500 624347982 624352481 0.000000e+00 8311.0
1 TraesCS2D01G548800 chr2D 78.086 1191 177 48 876 2022 626114768 626113618 0.000000e+00 676.0
2 TraesCS2D01G548800 chr2D 77.762 697 97 35 2232 2911 626113485 626112830 4.250000e-100 375.0
3 TraesCS2D01G548800 chr2D 86.667 165 18 3 3360 3523 626112346 626112185 3.580000e-41 180.0
4 TraesCS2D01G548800 chr2B 89.116 3565 232 74 90 3577 766526713 766530198 0.000000e+00 4290.0
5 TraesCS2D01G548800 chr2B 78.548 1198 172 45 872 2025 767695976 767694820 0.000000e+00 710.0
6 TraesCS2D01G548800 chr2B 83.022 536 25 25 4001 4500 766532202 766532707 4.160000e-115 425.0
7 TraesCS2D01G548800 chr2B 78.390 708 101 32 2223 2911 767694355 767693681 3.240000e-111 412.0
8 TraesCS2D01G548800 chr2B 83.827 439 31 23 3573 3994 766530265 766530680 9.130000e-102 381.0
9 TraesCS2D01G548800 chr2B 91.429 140 10 2 3360 3498 767693199 767693061 1.650000e-44 191.0
10 TraesCS2D01G548800 chr2B 85.294 68 5 4 345 410 767696710 767696646 1.040000e-06 65.8
11 TraesCS2D01G548800 chr2A 90.753 1460 82 20 907 2334 755740885 755742323 0.000000e+00 1899.0
12 TraesCS2D01G548800 chr2A 86.468 872 90 15 1 849 755739996 755740862 0.000000e+00 931.0
13 TraesCS2D01G548800 chr2A 86.447 819 86 13 2340 3151 755742457 755743257 0.000000e+00 874.0
14 TraesCS2D01G548800 chr2A 77.778 1188 171 52 876 2012 756484941 756486086 0.000000e+00 645.0
15 TraesCS2D01G548800 chr2A 79.900 602 89 22 2301 2882 756486306 756486895 3.240000e-111 412.0
16 TraesCS2D01G548800 chr2A 88.806 268 19 9 3308 3573 755747299 755747557 7.260000e-83 318.0
17 TraesCS2D01G548800 chr2A 79.003 381 31 25 3966 4330 755748066 755748413 9.800000e-52 215.0
18 TraesCS2D01G548800 chr2A 86.667 165 18 3 3360 3523 756487304 756487465 3.580000e-41 180.0
19 TraesCS2D01G548800 chr2A 82.787 122 8 5 3715 3836 755747940 755748048 3.710000e-16 97.1
20 TraesCS2D01G548800 chr2A 91.667 48 3 1 367 414 756484088 756484134 1.040000e-06 65.8
21 TraesCS2D01G548800 chr4D 89.820 167 16 1 2833 2999 234419995 234419830 3.530000e-51 213.0
22 TraesCS2D01G548800 chr4D 76.179 424 58 25 3020 3420 234416038 234415635 2.760000e-42 183.0


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 TraesCS2D01G548800 chr2D 624347982 624352481 4499 False 8311.000000 8311 100.000000 1 4500 1 chr2D.!!$F1 4499
1 TraesCS2D01G548800 chr2D 626112185 626114768 2583 True 410.333333 676 80.838333 876 3523 3 chr2D.!!$R1 2647
2 TraesCS2D01G548800 chr2B 766526713 766532707 5994 False 1698.666667 4290 85.321667 90 4500 3 chr2B.!!$F1 4410
3 TraesCS2D01G548800 chr2B 767693061 767696710 3649 True 344.700000 710 83.415250 345 3498 4 chr2B.!!$R1 3153
4 TraesCS2D01G548800 chr2A 755739996 755743257 3261 False 1234.666667 1899 87.889333 1 3151 3 chr2A.!!$F1 3150
5 TraesCS2D01G548800 chr2A 756484088 756487465 3377 False 325.700000 645 84.003000 367 3523 4 chr2A.!!$F3 3156
6 TraesCS2D01G548800 chr2A 755747299 755748413 1114 False 210.033333 318 83.532000 3308 4330 3 chr2A.!!$F2 1022

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
543 730 0.107459 GCATTCTCTGGTCCTCACCC 60.107 60.0 0.00 0.00 42.99 4.61 F
1015 1430 0.174162 AATCATGCGGGCAAAGCTTC 59.826 50.0 0.00 0.00 35.28 3.86 F
1761 2215 0.813610 TTCATCGGCGCCACCTTATG 60.814 55.0 28.98 19.63 35.61 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 1880 0.118346 AGGGACACCATCTACCACCA 59.882 55.0 0.0 0.0 40.13 4.17 R
2543 3475 0.878416 CCCGGTTCTTGCGAAAATGA 59.122 50.0 0.0 0.0 0.00 2.57 R
3606 4804 0.388659 GCCACACAAGCACATTTGGA 59.611 50.0 0.0 0.0 32.32 3.53 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
45 46 6.092122 TGAATTTCATATTCACACGGTCTCAC 59.908 38.462 0.00 0.00 33.55 3.51
54 55 7.772332 ATTCACACGGTCTCACTTTATATTC 57.228 36.000 0.00 0.00 0.00 1.75
59 60 7.330946 CACACGGTCTCACTTTATATTCTTTCA 59.669 37.037 0.00 0.00 0.00 2.69
62 63 7.435488 ACGGTCTCACTTTATATTCTTTCATCG 59.565 37.037 0.00 0.00 0.00 3.84
63 64 7.567771 CGGTCTCACTTTATATTCTTTCATCGC 60.568 40.741 0.00 0.00 0.00 4.58
64 65 7.307455 GGTCTCACTTTATATTCTTTCATCGCC 60.307 40.741 0.00 0.00 0.00 5.54
113 114 6.839124 ATATGACATCCAAACAACATGTGT 57.161 33.333 0.00 0.00 44.64 3.72
128 129 4.958509 ACATGTGTGAAATTTTCATGCCA 58.041 34.783 14.54 11.50 42.47 4.92
228 252 2.639751 CTTTTTGAGTTTCTGTCCGCG 58.360 47.619 0.00 0.00 0.00 6.46
247 272 2.874457 GCGTTCAAATCGGGGCCTATAT 60.874 50.000 0.84 0.00 0.00 0.86
251 276 5.470777 CGTTCAAATCGGGGCCTATATTTTA 59.529 40.000 0.84 0.00 0.00 1.52
284 309 4.765339 ACAATGGGTTTTAGCTTACCACTC 59.235 41.667 12.63 0.00 36.10 3.51
330 355 0.798776 AGCGACCAAATTCTCTTGCG 59.201 50.000 0.00 0.00 0.00 4.85
337 362 2.313234 CAAATTCTCTTGCGCACACAG 58.687 47.619 11.12 5.13 0.00 3.66
540 726 3.173151 TGTAAGCATTCTCTGGTCCTCA 58.827 45.455 0.00 0.00 33.48 3.86
543 730 0.107459 GCATTCTCTGGTCCTCACCC 60.107 60.000 0.00 0.00 42.99 4.61
556 743 1.363744 CTCACCCGCACTTGAATCTC 58.636 55.000 0.00 0.00 0.00 2.75
558 745 1.079127 ACCCGCACTTGAATCTCCG 60.079 57.895 0.00 0.00 0.00 4.63
565 752 2.096496 GCACTTGAATCTCCGAATGTGG 59.904 50.000 0.00 0.00 0.00 4.17
573 760 4.856801 CCGAATGTGGCCGGGGAG 62.857 72.222 2.18 0.00 41.89 4.30
589 776 0.813821 GGAGCTGTCATTTTGGGAGC 59.186 55.000 0.00 0.00 0.00 4.70
599 786 5.011943 TGTCATTTTGGGAGCTTTTTAGCAT 59.988 36.000 0.00 0.00 37.25 3.79
619 806 3.587797 TTTCGAGCACGGAGTCTAATT 57.412 42.857 3.11 0.00 41.61 1.40
621 808 3.965292 TCGAGCACGGAGTCTAATTAG 57.035 47.619 6.11 6.11 41.61 1.73
632 819 4.765856 GGAGTCTAATTAGAGCCGATGGTA 59.234 45.833 15.58 0.00 32.01 3.25
637 824 7.179338 AGTCTAATTAGAGCCGATGGTATGATT 59.821 37.037 15.58 0.00 32.01 2.57
671 859 6.634805 TCTAGAGTTCAGGATAGTTTTGCAG 58.365 40.000 0.00 0.00 0.00 4.41
844 1080 3.344515 TGTGCGTCACTACTCACTAGAT 58.655 45.455 0.00 0.00 41.06 1.98
868 1281 4.805140 TGGCTTGGGTCCAATATGAATA 57.195 40.909 2.59 0.00 35.20 1.75
870 1283 5.324409 TGGCTTGGGTCCAATATGAATATC 58.676 41.667 2.59 0.00 35.20 1.63
944 1357 5.878116 CAGAATTGGTTTACCTCACGGATTA 59.122 40.000 0.00 0.00 36.82 1.75
1015 1430 0.174162 AATCATGCGGGCAAAGCTTC 59.826 50.000 0.00 0.00 35.28 3.86
1046 1461 1.145738 TGCTCCCTTCCTTTCAAAGCT 59.854 47.619 0.00 0.00 0.00 3.74
1177 1592 5.305902 TCCACCAGACACAATGTAAGTTCTA 59.694 40.000 0.00 0.00 0.00 2.10
1226 1643 1.864082 GCTCGGCTTTATTCTCAGAGC 59.136 52.381 0.00 0.00 41.92 4.09
1355 1772 4.473196 TGAAGGTTTGGCTCCATCTGTATA 59.527 41.667 0.00 0.00 0.00 1.47
1356 1773 5.132648 TGAAGGTTTGGCTCCATCTGTATAT 59.867 40.000 0.00 0.00 0.00 0.86
1357 1774 5.234466 AGGTTTGGCTCCATCTGTATATC 57.766 43.478 0.00 0.00 0.00 1.63
1360 1777 3.567375 TGGCTCCATCTGTATATCCCT 57.433 47.619 0.00 0.00 0.00 4.20
1361 1778 3.445008 TGGCTCCATCTGTATATCCCTC 58.555 50.000 0.00 0.00 0.00 4.30
1362 1779 3.181407 TGGCTCCATCTGTATATCCCTCA 60.181 47.826 0.00 0.00 0.00 3.86
1363 1780 3.450457 GGCTCCATCTGTATATCCCTCAG 59.550 52.174 0.00 0.00 0.00 3.35
1588 2042 3.503891 TCATGCGATGCAGTTCATTTTG 58.496 40.909 0.00 0.00 43.65 2.44
1600 2054 3.319122 AGTTCATTTTGACTGGCTTGACC 59.681 43.478 0.00 0.00 39.84 4.02
1761 2215 0.813610 TTCATCGGCGCCACCTTATG 60.814 55.000 28.98 19.63 35.61 1.90
1763 2217 1.523711 ATCGGCGCCACCTTATGTG 60.524 57.895 28.98 6.54 45.01 3.21
1923 2386 7.442364 TCTGAAAGAGTTTTATTCCTGTGTCAG 59.558 37.037 0.00 0.00 38.67 3.51
2065 2529 7.801893 TCTAGTTTGTTGGTATTCCCTTAGA 57.198 36.000 0.00 0.00 0.00 2.10
2104 2568 7.392953 TCAGTGAACTGGTAATCATTATGCAAA 59.607 33.333 10.45 0.00 43.91 3.68
2208 2991 5.822519 TCATTGATAAAGCAGGTGTACCATC 59.177 40.000 3.56 0.00 38.89 3.51
2259 3045 3.559238 ATTCCTGAATGCACACGTTTC 57.441 42.857 0.00 0.00 0.00 2.78
2422 3352 9.598517 TTCTCCATCATTAAATTTGGTATTTGC 57.401 29.630 0.00 0.00 0.00 3.68
2456 3386 3.087031 ACCATTGGCACTCTGAAATCTG 58.913 45.455 1.54 0.00 0.00 2.90
2543 3475 6.805016 ATCAGGTTGAAGAGTGTGATCTAT 57.195 37.500 0.00 0.00 0.00 1.98
2582 3514 4.213482 CGGGAATTTGGTCGATTAAGGATC 59.787 45.833 0.00 0.00 0.00 3.36
2632 3564 9.142014 TCAGATTTTATTTTCCTTTTCTGGACA 57.858 29.630 0.00 0.00 35.58 4.02
2770 3708 8.736244 TCTTTATTGCTTTTACCATGTAGTTCC 58.264 33.333 0.00 0.00 0.00 3.62
2780 3718 5.897377 ACCATGTAGTTCCAGTTTAATGC 57.103 39.130 0.00 0.00 0.00 3.56
2781 3719 5.321102 ACCATGTAGTTCCAGTTTAATGCA 58.679 37.500 0.00 0.00 0.00 3.96
2863 3805 4.580580 ACTCCTTCATTTGTTCTGTGGTTC 59.419 41.667 0.00 0.00 0.00 3.62
2868 3810 3.573538 TCATTTGTTCTGTGGTTCCATGG 59.426 43.478 4.97 4.97 0.00 3.66
2883 3825 5.010012 GGTTCCATGGTCATGTCCATTAATC 59.990 44.000 20.18 14.17 44.75 1.75
2960 4007 6.824305 ATGATTCAGTTAAACCTTGGTGAG 57.176 37.500 0.00 0.00 0.00 3.51
2964 4011 6.844097 TTCAGTTAAACCTTGGTGAGTTTT 57.156 33.333 0.00 0.00 37.39 2.43
2970 4017 3.971245 ACCTTGGTGAGTTTTTGCAAA 57.029 38.095 8.05 8.05 0.00 3.68
3004 4051 5.556355 GTGGCAAACACCTTACTTATACC 57.444 43.478 0.00 0.00 44.49 2.73
3005 4052 4.093850 GTGGCAAACACCTTACTTATACCG 59.906 45.833 0.00 0.00 44.49 4.02
3006 4053 3.624410 GGCAAACACCTTACTTATACCGG 59.376 47.826 0.00 0.00 0.00 5.28
3007 4054 3.064408 GCAAACACCTTACTTATACCGGC 59.936 47.826 0.00 0.00 0.00 6.13
3008 4055 4.255301 CAAACACCTTACTTATACCGGCA 58.745 43.478 0.00 0.00 0.00 5.69
3009 4056 3.814005 ACACCTTACTTATACCGGCAG 57.186 47.619 0.00 0.00 0.00 4.85
3010 4057 3.102204 ACACCTTACTTATACCGGCAGT 58.898 45.455 0.00 0.77 0.00 4.40
3011 4058 3.516700 ACACCTTACTTATACCGGCAGTT 59.483 43.478 0.00 0.00 0.00 3.16
3012 4059 4.019950 ACACCTTACTTATACCGGCAGTTT 60.020 41.667 0.00 0.00 0.00 2.66
3013 4060 4.939439 CACCTTACTTATACCGGCAGTTTT 59.061 41.667 0.00 0.00 0.00 2.43
3014 4061 6.108015 CACCTTACTTATACCGGCAGTTTTA 58.892 40.000 0.00 0.00 0.00 1.52
3015 4062 6.594937 CACCTTACTTATACCGGCAGTTTTAA 59.405 38.462 0.00 0.00 0.00 1.52
3016 4063 7.281549 CACCTTACTTATACCGGCAGTTTTAAT 59.718 37.037 0.00 0.00 0.00 1.40
3017 4064 7.496920 ACCTTACTTATACCGGCAGTTTTAATC 59.503 37.037 0.00 0.00 0.00 1.75
3018 4065 5.978934 ACTTATACCGGCAGTTTTAATCG 57.021 39.130 0.00 0.00 0.00 3.34
3019 4066 5.663456 ACTTATACCGGCAGTTTTAATCGA 58.337 37.500 0.00 0.00 0.00 3.59
3020 4067 5.751990 ACTTATACCGGCAGTTTTAATCGAG 59.248 40.000 0.00 0.00 0.00 4.04
3021 4068 2.467566 ACCGGCAGTTTTAATCGAGT 57.532 45.000 0.00 0.00 0.00 4.18
3048 4095 5.268544 CCATTTTATGACTGCATTCGTCTG 58.731 41.667 1.50 0.00 35.94 3.51
3056 4103 1.210155 GCATTCGTCTGTTGCCACC 59.790 57.895 0.00 0.00 0.00 4.61
3060 4107 1.686355 TTCGTCTGTTGCCACCATTT 58.314 45.000 0.00 0.00 0.00 2.32
3065 4112 3.004315 CGTCTGTTGCCACCATTTTTAGT 59.996 43.478 0.00 0.00 0.00 2.24
3068 4115 5.240844 GTCTGTTGCCACCATTTTTAGTACT 59.759 40.000 0.00 0.00 0.00 2.73
3075 4122 5.803470 GCCACCATTTTTAGTACTCCAGAGT 60.803 44.000 0.00 5.50 45.02 3.24
3079 4126 5.582665 CCATTTTTAGTACTCCAGAGTCAGC 59.417 44.000 3.00 0.00 42.54 4.26
3083 4130 5.584253 TTAGTACTCCAGAGTCAGCAATC 57.416 43.478 3.00 0.00 42.54 2.67
3084 4131 3.435275 AGTACTCCAGAGTCAGCAATCA 58.565 45.455 3.00 0.00 42.54 2.57
3093 4140 3.134442 AGAGTCAGCAATCAGAGGAATCC 59.866 47.826 0.00 0.00 0.00 3.01
3126 4175 8.885494 TCAGATGGTTTCCAAAACTTAAATTG 57.115 30.769 2.90 0.00 36.95 2.32
3127 4176 8.482128 TCAGATGGTTTCCAAAACTTAAATTGT 58.518 29.630 2.90 0.00 36.95 2.71
3132 4181 8.043710 TGGTTTCCAAAACTTAAATTGTGTGAT 58.956 29.630 2.90 0.00 0.00 3.06
3137 4186 7.920151 TCCAAAACTTAAATTGTGTGATCAGTG 59.080 33.333 0.00 0.00 0.00 3.66
3145 4194 7.984422 AAATTGTGTGATCAGTGTATTCTGA 57.016 32.000 0.00 0.00 46.39 3.27
3151 4200 6.309980 GTGTGATCAGTGTATTCTGAGACAAG 59.690 42.308 0.00 0.00 45.70 3.16
3153 4202 6.309980 GTGATCAGTGTATTCTGAGACAAGTG 59.690 42.308 0.00 0.00 45.70 3.16
3156 4205 6.997655 TCAGTGTATTCTGAGACAAGTGAAT 58.002 36.000 0.00 0.00 39.20 2.57
3192 4241 7.972832 TCATCTTCATATGATCGAACTAGATGC 59.027 37.037 24.17 0.00 30.92 3.91
3197 4246 8.055279 TCATATGATCGAACTAGATGCACATA 57.945 34.615 0.00 0.00 0.00 2.29
3199 4248 6.581171 ATGATCGAACTAGATGCACATAGA 57.419 37.500 12.71 0.00 0.00 1.98
3200 4249 5.763088 TGATCGAACTAGATGCACATAGAC 58.237 41.667 12.71 6.51 0.00 2.59
3201 4250 5.299279 TGATCGAACTAGATGCACATAGACA 59.701 40.000 12.71 2.70 0.00 3.41
3202 4251 5.774498 TCGAACTAGATGCACATAGACAT 57.226 39.130 12.71 0.90 0.00 3.06
3227 4276 7.458409 AGATATTGTGCTTCAAACTGAACAT 57.542 32.000 0.00 0.00 39.62 2.71
3249 4299 1.543802 GTCTGACTGACTGACTGGAGG 59.456 57.143 0.00 0.00 42.21 4.30
3250 4300 0.246086 CTGACTGACTGACTGGAGGC 59.754 60.000 0.00 0.00 0.00 4.70
3251 4301 1.214062 GACTGACTGACTGGAGGCG 59.786 63.158 0.00 0.00 0.00 5.52
3254 4304 1.810606 CTGACTGACTGGAGGCGTGT 61.811 60.000 0.00 0.00 0.00 4.49
3255 4305 1.367840 GACTGACTGGAGGCGTGTT 59.632 57.895 0.00 0.00 0.00 3.32
3259 4314 4.643387 ACTGGAGGCGTGTTGGGC 62.643 66.667 0.00 0.00 0.00 5.36
3273 4328 3.670377 GGGCGTTCCACACTTGGC 61.670 66.667 0.00 0.00 43.56 4.52
3282 4337 1.028905 CCACACTTGGCCGAAAGAAA 58.971 50.000 9.71 0.00 35.56 2.52
3286 4341 3.252215 CACACTTGGCCGAAAGAAACATA 59.748 43.478 9.71 0.00 0.00 2.29
3289 4344 3.502211 ACTTGGCCGAAAGAAACATACTG 59.498 43.478 9.71 0.00 0.00 2.74
3295 4350 6.431543 TGGCCGAAAGAAACATACTGAAATAA 59.568 34.615 0.00 0.00 0.00 1.40
3330 4409 1.498865 GCCGCATACATCAACCGGAG 61.499 60.000 9.46 0.00 41.34 4.63
3394 4482 0.455815 CGGCCATAAAAGAGGGTTGC 59.544 55.000 2.24 0.00 0.00 4.17
3502 4590 2.751259 ACATGACCAGCAGCTGTAATTG 59.249 45.455 21.26 14.63 0.00 2.32
3539 4627 1.393603 GCTTGGGCCTGGAGAAATAC 58.606 55.000 4.53 0.00 0.00 1.89
3544 4632 3.393687 TGGGCCTGGAGAAATACTGTAT 58.606 45.455 4.53 0.00 0.00 2.29
3545 4633 3.136443 TGGGCCTGGAGAAATACTGTATG 59.864 47.826 4.53 0.00 0.00 2.39
3546 4634 3.136626 GGGCCTGGAGAAATACTGTATGT 59.863 47.826 0.84 0.00 0.00 2.29
3547 4635 4.347000 GGGCCTGGAGAAATACTGTATGTA 59.653 45.833 0.84 0.00 35.37 2.29
3548 4636 5.013183 GGGCCTGGAGAAATACTGTATGTAT 59.987 44.000 0.84 0.00 43.19 2.29
3549 4637 5.934625 GGCCTGGAGAAATACTGTATGTATG 59.065 44.000 0.00 0.00 40.69 2.39
3552 4640 7.880195 GCCTGGAGAAATACTGTATGTATGATT 59.120 37.037 0.00 0.00 40.69 2.57
3553 4641 9.784531 CCTGGAGAAATACTGTATGTATGATTT 57.215 33.333 0.22 0.00 40.69 2.17
3555 4643 9.056005 TGGAGAAATACTGTATGTATGATTTGC 57.944 33.333 0.22 0.00 40.69 3.68
3594 4792 4.693095 GCCTGTTTTCTCCTAGAGTTCTTG 59.307 45.833 0.00 0.00 0.00 3.02
3603 4801 1.208293 CTAGAGTTCTTGACAGGCCCC 59.792 57.143 0.00 0.00 0.00 5.80
3605 4803 0.329596 GAGTTCTTGACAGGCCCCAT 59.670 55.000 0.00 0.00 0.00 4.00
3606 4804 0.779997 AGTTCTTGACAGGCCCCATT 59.220 50.000 0.00 0.00 0.00 3.16
3619 4916 1.676615 GCCCCATTCCAAATGTGCTTG 60.677 52.381 0.00 0.00 0.00 4.01
3702 5004 3.321111 GTCCCTATCTCCTGTCGCAAATA 59.679 47.826 0.00 0.00 0.00 1.40
3739 5072 1.917568 TCGGCCCCCTTTTACTACAAT 59.082 47.619 0.00 0.00 0.00 2.71
3773 5106 2.186076 GTAGGAAACGCAGATCACTCG 58.814 52.381 0.00 0.00 0.00 4.18
3778 5111 2.159819 AACGCAGATCACTCGCAGGT 62.160 55.000 0.00 0.00 0.00 4.00
3779 5112 2.163390 CGCAGATCACTCGCAGGTG 61.163 63.158 0.00 0.23 38.44 4.00
3780 5113 2.459442 GCAGATCACTCGCAGGTGC 61.459 63.158 0.00 0.00 37.16 5.01
3781 5114 1.812922 CAGATCACTCGCAGGTGCC 60.813 63.158 0.00 0.00 37.16 5.01
3782 5115 2.265739 GATCACTCGCAGGTGCCA 59.734 61.111 0.00 0.00 37.16 4.92
3783 5116 1.153289 GATCACTCGCAGGTGCCAT 60.153 57.895 0.00 0.00 37.16 4.40
3784 5117 0.745845 GATCACTCGCAGGTGCCATT 60.746 55.000 0.00 0.00 37.16 3.16
3785 5118 0.745845 ATCACTCGCAGGTGCCATTC 60.746 55.000 0.00 0.00 37.16 2.67
3786 5119 1.672030 CACTCGCAGGTGCCATTCA 60.672 57.895 0.00 0.00 37.91 2.57
3787 5120 1.073025 ACTCGCAGGTGCCATTCAA 59.927 52.632 0.00 0.00 37.91 2.69
3788 5121 0.537143 ACTCGCAGGTGCCATTCAAA 60.537 50.000 0.00 0.00 37.91 2.69
3789 5122 0.597568 CTCGCAGGTGCCATTCAAAA 59.402 50.000 0.00 0.00 37.91 2.44
3790 5123 0.313672 TCGCAGGTGCCATTCAAAAC 59.686 50.000 0.00 0.00 37.91 2.43
3791 5124 1.003262 CGCAGGTGCCATTCAAAACG 61.003 55.000 0.00 0.00 37.91 3.60
3792 5125 1.284297 GCAGGTGCCATTCAAAACGC 61.284 55.000 0.00 0.00 34.31 4.84
3793 5126 0.031857 CAGGTGCCATTCAAAACGCA 59.968 50.000 0.00 0.00 0.00 5.24
3794 5127 0.314935 AGGTGCCATTCAAAACGCAG 59.685 50.000 0.00 0.00 0.00 5.18
3799 5132 1.247567 CCATTCAAAACGCAGACCCT 58.752 50.000 0.00 0.00 0.00 4.34
3826 5159 1.067354 GGCATGAAAAAGGCAGACCAG 60.067 52.381 0.00 0.00 37.29 4.00
3827 5160 1.670967 GCATGAAAAAGGCAGACCAGC 60.671 52.381 0.00 0.00 39.06 4.85
3836 5169 0.940126 GGCAGACCAGCAATATGTCG 59.060 55.000 0.00 0.00 35.83 4.35
3837 5170 0.940126 GCAGACCAGCAATATGTCGG 59.060 55.000 0.00 0.00 34.24 4.79
3838 5171 0.940126 CAGACCAGCAATATGTCGGC 59.060 55.000 0.00 0.00 34.24 5.54
3839 5172 0.833287 AGACCAGCAATATGTCGGCT 59.167 50.000 0.00 0.00 38.70 5.52
3840 5173 1.210478 AGACCAGCAATATGTCGGCTT 59.790 47.619 0.00 0.00 35.27 4.35
3841 5174 2.434336 AGACCAGCAATATGTCGGCTTA 59.566 45.455 0.00 0.00 35.27 3.09
3842 5175 2.802816 GACCAGCAATATGTCGGCTTAG 59.197 50.000 0.00 0.00 35.27 2.18
3844 5177 2.545526 CCAGCAATATGTCGGCTTAGTG 59.454 50.000 6.06 6.06 35.27 2.74
3845 5178 2.032549 CAGCAATATGTCGGCTTAGTGC 60.033 50.000 22.81 22.81 42.66 4.40
3887 5221 8.543774 TCCTATGATCTTATAAAGAATCCCAGC 58.456 37.037 0.00 0.00 41.63 4.85
3904 5242 0.037447 AGCCCAAAGAAGTCTCCAGC 59.963 55.000 0.00 0.00 0.00 4.85
3905 5243 0.037447 GCCCAAAGAAGTCTCCAGCT 59.963 55.000 0.00 0.00 0.00 4.24
3906 5244 1.818642 CCCAAAGAAGTCTCCAGCTG 58.181 55.000 6.78 6.78 0.00 4.24
3907 5245 1.349026 CCCAAAGAAGTCTCCAGCTGA 59.651 52.381 17.39 0.00 0.00 4.26
3908 5246 2.614987 CCCAAAGAAGTCTCCAGCTGAG 60.615 54.545 17.39 10.96 42.90 3.35
3918 5256 1.153005 CCAGCTGAGAAGGATGGGC 60.153 63.158 17.39 0.00 36.69 5.36
3919 5257 1.605992 CAGCTGAGAAGGATGGGCA 59.394 57.895 8.42 0.00 0.00 5.36
3938 5284 2.036346 GCAGATGTGTTTTCCCTTTGCT 59.964 45.455 0.00 0.00 0.00 3.91
3939 5285 3.645884 CAGATGTGTTTTCCCTTTGCTG 58.354 45.455 0.00 0.00 0.00 4.41
3941 5287 4.278170 CAGATGTGTTTTCCCTTTGCTGTA 59.722 41.667 0.00 0.00 0.00 2.74
3942 5288 4.278419 AGATGTGTTTTCCCTTTGCTGTAC 59.722 41.667 0.00 0.00 0.00 2.90
3943 5289 2.356382 TGTGTTTTCCCTTTGCTGTACG 59.644 45.455 0.00 0.00 0.00 3.67
3944 5290 2.356695 GTGTTTTCCCTTTGCTGTACGT 59.643 45.455 0.00 0.00 0.00 3.57
3945 5291 2.356382 TGTTTTCCCTTTGCTGTACGTG 59.644 45.455 0.00 0.00 0.00 4.49
3946 5292 2.335316 TTTCCCTTTGCTGTACGTGT 57.665 45.000 0.00 0.00 0.00 4.49
3950 5296 1.540363 CCCTTTGCTGTACGTGTGAGT 60.540 52.381 0.00 0.00 0.00 3.41
3959 5305 1.475280 GTACGTGTGAGTATGGGAGCA 59.525 52.381 0.00 0.00 0.00 4.26
3963 5309 2.609459 CGTGTGAGTATGGGAGCAATTC 59.391 50.000 0.00 0.00 0.00 2.17
3977 5323 6.471976 GGAGCAATTCCATTCAAAGTTTTC 57.528 37.500 0.00 0.00 46.01 2.29
3978 5324 5.990996 GGAGCAATTCCATTCAAAGTTTTCA 59.009 36.000 0.00 0.00 46.01 2.69
3980 5326 7.250445 AGCAATTCCATTCAAAGTTTTCAAC 57.750 32.000 0.00 0.00 0.00 3.18
3986 6850 6.572519 TCCATTCAAAGTTTTCAACAAGGAG 58.427 36.000 0.00 0.00 0.00 3.69
4011 6875 0.034059 CACACTGGACTGGACTGGAC 59.966 60.000 0.00 0.00 0.00 4.02
4012 6876 0.105453 ACACTGGACTGGACTGGACT 60.105 55.000 0.00 0.00 0.00 3.85
4013 6877 0.319728 CACTGGACTGGACTGGACTG 59.680 60.000 0.00 0.00 0.00 3.51
4015 6879 0.542938 CTGGACTGGACTGGACTGGA 60.543 60.000 0.00 0.00 0.00 3.86
4017 6881 1.594310 GACTGGACTGGACTGGAGC 59.406 63.158 0.00 0.00 0.00 4.70
4018 6882 1.152247 ACTGGACTGGACTGGAGCA 60.152 57.895 0.00 0.00 0.00 4.26
4019 6883 1.190833 ACTGGACTGGACTGGAGCAG 61.191 60.000 0.00 0.00 37.52 4.24
4020 6884 2.267324 GGACTGGACTGGAGCAGC 59.733 66.667 0.00 0.00 34.37 5.25
4024 6888 3.243816 TGGACTGGAGCAGCAGCA 61.244 61.111 3.17 0.00 45.49 4.41
4050 6921 3.376078 GCCTGTGGTGTGGGCATG 61.376 66.667 0.00 0.00 44.69 4.06
4102 6982 2.822561 TCATCTCCAGTGAGTCACAGAC 59.177 50.000 24.73 0.00 39.75 3.51
4103 6983 1.621992 TCTCCAGTGAGTCACAGACC 58.378 55.000 24.73 0.00 39.75 3.85
4104 6984 1.133482 TCTCCAGTGAGTCACAGACCA 60.133 52.381 24.73 6.17 39.75 4.02
4106 6986 2.301296 CTCCAGTGAGTCACAGACCAAT 59.699 50.000 24.73 0.00 36.74 3.16
4107 6987 3.506398 TCCAGTGAGTCACAGACCAATA 58.494 45.455 24.73 0.00 36.74 1.90
4108 6988 3.258372 TCCAGTGAGTCACAGACCAATAC 59.742 47.826 24.73 0.00 36.74 1.89
4109 6989 3.259374 CCAGTGAGTCACAGACCAATACT 59.741 47.826 24.73 0.00 36.74 2.12
4110 6990 4.462834 CCAGTGAGTCACAGACCAATACTA 59.537 45.833 24.73 0.00 36.74 1.82
4111 6991 5.403246 CAGTGAGTCACAGACCAATACTAC 58.597 45.833 24.73 0.00 36.74 2.73
4128 7008 1.978455 TACCATGATGACCACCCGGC 61.978 60.000 0.00 0.00 34.57 6.13
4147 7027 4.069232 CTCGCAAGGGGCAGACGA 62.069 66.667 0.00 0.00 45.17 4.20
4148 7028 3.376935 CTCGCAAGGGGCAGACGAT 62.377 63.158 0.00 0.00 45.17 3.73
4229 7135 4.514577 CGCTGCCGGTGTCCCTAG 62.515 72.222 1.90 0.00 0.00 3.02
4426 7335 1.001393 TCCCGGAATCCAAAGCCAC 60.001 57.895 0.73 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 6.201044 AGACACGGCGATGAAAGAATATAAAG 59.799 38.462 16.62 0.00 0.00 1.85
54 55 1.278238 GGTAGACACGGCGATGAAAG 58.722 55.000 16.62 0.00 0.00 2.62
59 60 0.535335 ACAATGGTAGACACGGCGAT 59.465 50.000 16.62 0.00 0.00 4.58
62 63 0.796312 CACACAATGGTAGACACGGC 59.204 55.000 0.00 0.00 0.00 5.68
63 64 2.066262 GACACACAATGGTAGACACGG 58.934 52.381 0.00 0.00 0.00 4.94
64 65 2.987149 GAGACACACAATGGTAGACACG 59.013 50.000 0.00 0.00 0.00 4.49
206 208 2.033424 GCGGACAGAAACTCAAAAAGCT 59.967 45.455 0.00 0.00 0.00 3.74
208 210 2.031683 ACGCGGACAGAAACTCAAAAAG 59.968 45.455 12.47 0.00 0.00 2.27
228 252 5.784578 AAAATATAGGCCCCGATTTGAAC 57.215 39.130 0.00 0.00 0.00 3.18
271 296 4.274147 CTCCAGAGAGAGTGGTAAGCTAA 58.726 47.826 0.00 0.00 43.39 3.09
284 309 2.296365 TGCTTGGGCCTCCAGAGAG 61.296 63.158 4.53 0.00 45.04 3.20
313 338 0.516877 TGCGCAAGAGAATTTGGTCG 59.483 50.000 8.16 0.00 43.02 4.79
428 467 0.036010 CACCTGGTCTTGATCCGCTT 60.036 55.000 0.00 0.00 0.00 4.68
540 726 1.079127 CGGAGATTCAAGTGCGGGT 60.079 57.895 0.00 0.00 0.00 5.28
543 730 2.002586 ACATTCGGAGATTCAAGTGCG 58.997 47.619 0.00 0.00 35.04 5.34
556 743 4.856801 CTCCCCGGCCACATTCGG 62.857 72.222 2.24 0.00 45.29 4.30
558 745 4.115199 AGCTCCCCGGCCACATTC 62.115 66.667 2.24 0.00 0.00 2.67
565 752 1.678970 AAAATGACAGCTCCCCGGC 60.679 57.895 0.00 0.00 0.00 6.13
572 759 2.299326 AAGCTCCCAAAATGACAGCT 57.701 45.000 0.00 0.00 42.34 4.24
573 760 3.391506 AAAAGCTCCCAAAATGACAGC 57.608 42.857 0.00 0.00 0.00 4.40
577 764 5.743636 ATGCTAAAAAGCTCCCAAAATGA 57.256 34.783 0.00 0.00 35.49 2.57
589 776 3.120338 TCCGTGCTCGAAATGCTAAAAAG 60.120 43.478 10.21 0.00 39.71 2.27
599 786 3.587797 AATTAGACTCCGTGCTCGAAA 57.412 42.857 10.21 0.00 39.71 3.46
613 800 7.178451 TCAATCATACCATCGGCTCTAATTAGA 59.822 37.037 14.42 14.42 0.00 2.10
619 806 5.245977 TGATTCAATCATACCATCGGCTCTA 59.754 40.000 0.00 0.00 33.59 2.43
621 808 4.318332 TGATTCAATCATACCATCGGCTC 58.682 43.478 0.00 0.00 33.59 4.70
637 824 7.852550 ATCCTGAACTCTAGATCATGATTCA 57.147 36.000 10.14 7.50 31.73 2.57
671 859 0.822532 CCTCATCCCAATGCCTGAGC 60.823 60.000 0.00 0.00 35.00 4.26
744 948 4.829064 AGAAAGCACTTTTACAATCGCA 57.171 36.364 0.00 0.00 32.11 5.10
865 1278 4.666512 AGAGGCCAAAACACACAGATATT 58.333 39.130 5.01 0.00 0.00 1.28
868 1281 2.624838 CAAGAGGCCAAAACACACAGAT 59.375 45.455 5.01 0.00 0.00 2.90
870 1283 1.750778 ACAAGAGGCCAAAACACACAG 59.249 47.619 5.01 0.00 0.00 3.66
944 1357 4.961438 AGTGCAAAACCTGATGGAAAAT 57.039 36.364 0.00 0.00 37.04 1.82
1046 1461 0.251916 CCGGCAGGTGGAGATGTAAA 59.748 55.000 0.00 0.00 0.00 2.01
1177 1592 8.010733 TGAATTCCAAACAAAAGATGAGAAGT 57.989 30.769 2.27 0.00 0.00 3.01
1226 1643 3.420839 AGGCGAAACAACACAAAAGAG 57.579 42.857 0.00 0.00 0.00 2.85
1355 1772 7.664731 CAGAATATGCATTACTTTCTGAGGGAT 59.335 37.037 23.31 0.80 43.72 3.85
1356 1773 6.994496 CAGAATATGCATTACTTTCTGAGGGA 59.006 38.462 23.31 0.00 43.72 4.20
1357 1774 6.769822 ACAGAATATGCATTACTTTCTGAGGG 59.230 38.462 28.86 15.05 43.72 4.30
1361 1778 9.844790 TGAAAACAGAATATGCATTACTTTCTG 57.155 29.630 24.62 24.62 45.49 3.02
1432 1880 0.118346 AGGGACACCATCTACCACCA 59.882 55.000 0.00 0.00 40.13 4.17
1557 2011 6.375945 ACTGCATCGCATGAAAAATGTATA 57.624 33.333 0.00 0.00 38.13 1.47
1588 2042 1.228657 GGTTCACGGTCAAGCCAGTC 61.229 60.000 0.00 0.00 36.97 3.51
1600 2054 3.982213 CATGCTGTCATGGTTCACG 57.018 52.632 0.00 0.00 44.84 4.35
1761 2215 6.566197 AAAACAGAGAAATCAGATCACCAC 57.434 37.500 0.00 0.00 0.00 4.16
2104 2568 7.613022 TGGCAATCTCTGTTTCTCAAAGATAAT 59.387 33.333 0.00 0.00 33.25 1.28
2259 3045 5.579511 GGTGGCATGATGAAATGAAAAGAAG 59.420 40.000 0.00 0.00 0.00 2.85
2344 3264 8.733458 TCATGTTTGGAAGATGATTTTCAGTAG 58.267 33.333 0.00 0.00 36.39 2.57
2422 3352 1.875514 CCAATGGTCTGCATCCATACG 59.124 52.381 19.38 14.57 43.85 3.06
2456 3386 3.062763 CCTCATCTGACAGAACACACAC 58.937 50.000 9.70 0.00 0.00 3.82
2543 3475 0.878416 CCCGGTTCTTGCGAAAATGA 59.122 50.000 0.00 0.00 0.00 2.57
2582 3514 1.531149 CTGCTGTTGTCAAACCTACCG 59.469 52.381 0.00 0.00 35.25 4.02
2780 3718 9.559958 AAGACACGATAATAAAAAGAAGCATTG 57.440 29.630 0.00 0.00 0.00 2.82
2842 3784 3.888930 GGAACCACAGAACAAATGAAGGA 59.111 43.478 0.00 0.00 0.00 3.36
2868 3810 5.698545 GTCCTAGCAGATTAATGGACATGAC 59.301 44.000 13.02 0.00 42.32 3.06
2883 3825 2.388735 TGGTCATACCTGTCCTAGCAG 58.611 52.381 0.00 0.00 39.58 4.24
2937 3906 6.306987 ACTCACCAAGGTTTAACTGAATCAT 58.693 36.000 0.00 0.00 0.00 2.45
2940 3909 7.418337 AAAACTCACCAAGGTTTAACTGAAT 57.582 32.000 0.00 0.00 43.23 2.57
2982 4029 4.093850 CGGTATAAGTAAGGTGTTTGCCAC 59.906 45.833 0.00 0.00 43.74 5.01
2995 4042 6.804677 TCGATTAAAACTGCCGGTATAAGTA 58.195 36.000 1.90 0.00 0.00 2.24
3001 4048 3.598019 ACTCGATTAAAACTGCCGGTA 57.402 42.857 1.90 0.00 0.00 4.02
3004 4051 2.284417 GGCTACTCGATTAAAACTGCCG 59.716 50.000 0.00 0.00 0.00 5.69
3005 4052 2.612672 GGGCTACTCGATTAAAACTGCC 59.387 50.000 0.00 0.00 37.34 4.85
3006 4053 3.267483 TGGGCTACTCGATTAAAACTGC 58.733 45.455 0.00 0.00 0.00 4.40
3007 4054 6.436843 AAATGGGCTACTCGATTAAAACTG 57.563 37.500 0.00 0.00 0.00 3.16
3008 4055 8.621286 CATAAAATGGGCTACTCGATTAAAACT 58.379 33.333 0.00 0.00 0.00 2.66
3009 4056 8.617809 TCATAAAATGGGCTACTCGATTAAAAC 58.382 33.333 0.00 0.00 0.00 2.43
3010 4057 8.617809 GTCATAAAATGGGCTACTCGATTAAAA 58.382 33.333 0.00 0.00 0.00 1.52
3011 4058 7.990886 AGTCATAAAATGGGCTACTCGATTAAA 59.009 33.333 0.00 0.00 0.00 1.52
3012 4059 7.441157 CAGTCATAAAATGGGCTACTCGATTAA 59.559 37.037 0.00 0.00 0.00 1.40
3013 4060 6.929049 CAGTCATAAAATGGGCTACTCGATTA 59.071 38.462 0.00 0.00 0.00 1.75
3014 4061 5.760253 CAGTCATAAAATGGGCTACTCGATT 59.240 40.000 0.00 0.00 0.00 3.34
3015 4062 5.300752 CAGTCATAAAATGGGCTACTCGAT 58.699 41.667 0.00 0.00 0.00 3.59
3016 4063 4.693283 CAGTCATAAAATGGGCTACTCGA 58.307 43.478 0.00 0.00 0.00 4.04
3017 4064 3.248602 GCAGTCATAAAATGGGCTACTCG 59.751 47.826 0.00 0.00 0.00 4.18
3018 4065 4.199310 TGCAGTCATAAAATGGGCTACTC 58.801 43.478 0.00 0.00 0.00 2.59
3019 4066 4.235079 TGCAGTCATAAAATGGGCTACT 57.765 40.909 0.00 0.00 0.00 2.57
3020 4067 5.520376 AATGCAGTCATAAAATGGGCTAC 57.480 39.130 0.00 0.00 31.46 3.58
3021 4068 4.275689 CGAATGCAGTCATAAAATGGGCTA 59.724 41.667 15.31 0.00 31.46 3.93
3048 4095 4.521256 TGGAGTACTAAAAATGGTGGCAAC 59.479 41.667 0.00 0.00 0.00 4.17
3056 4103 6.166279 TGCTGACTCTGGAGTACTAAAAATG 58.834 40.000 3.03 0.00 42.66 2.32
3060 4107 5.480422 TGATTGCTGACTCTGGAGTACTAAA 59.520 40.000 3.03 0.00 42.66 1.85
3065 4112 3.698539 CTCTGATTGCTGACTCTGGAGTA 59.301 47.826 3.03 0.00 42.66 2.59
3068 4115 1.829849 CCTCTGATTGCTGACTCTGGA 59.170 52.381 0.00 0.00 0.00 3.86
3075 4122 3.834489 GAGGATTCCTCTGATTGCTGA 57.166 47.619 23.09 0.00 46.41 4.26
3093 4140 3.599343 TGGAAACCATCTGAATGTCGAG 58.401 45.455 0.00 0.00 0.00 4.04
3095 4142 4.764679 TTTGGAAACCATCTGAATGTCG 57.235 40.909 0.00 0.00 31.53 4.35
3096 4143 6.089249 AGTTTTGGAAACCATCTGAATGTC 57.911 37.500 0.00 0.00 31.53 3.06
3097 4144 6.484364 AAGTTTTGGAAACCATCTGAATGT 57.516 33.333 0.00 0.00 31.53 2.71
3102 4151 8.550376 CACAATTTAAGTTTTGGAAACCATCTG 58.450 33.333 0.00 0.00 31.53 2.90
3126 4175 5.714047 TGTCTCAGAATACACTGATCACAC 58.286 41.667 0.00 0.00 44.32 3.82
3127 4176 5.982890 TGTCTCAGAATACACTGATCACA 57.017 39.130 0.00 0.00 44.32 3.58
3132 4181 6.405278 TTCACTTGTCTCAGAATACACTGA 57.595 37.500 0.00 0.00 43.39 3.41
3137 4186 8.999431 TGGTTAAATTCACTTGTCTCAGAATAC 58.001 33.333 0.00 0.00 31.01 1.89
3145 4194 9.911788 AGATGATATGGTTAAATTCACTTGTCT 57.088 29.630 0.00 0.00 0.00 3.41
3173 4222 8.186821 TCTATGTGCATCTAGTTCGATCATATG 58.813 37.037 0.00 0.00 0.00 1.78
3174 4223 8.187480 GTCTATGTGCATCTAGTTCGATCATAT 58.813 37.037 0.00 0.00 0.00 1.78
3179 4228 5.774498 TGTCTATGTGCATCTAGTTCGAT 57.226 39.130 0.00 0.00 0.00 3.59
3181 4230 6.903419 TCTATGTCTATGTGCATCTAGTTCG 58.097 40.000 0.00 0.00 0.00 3.95
3191 4240 7.386025 TGAAGCACAATATCTATGTCTATGTGC 59.614 37.037 17.47 17.47 46.99 4.57
3192 4241 8.822652 TGAAGCACAATATCTATGTCTATGTG 57.177 34.615 0.00 0.00 0.00 3.21
3197 4246 8.043113 TCAGTTTGAAGCACAATATCTATGTCT 58.957 33.333 0.00 0.00 38.36 3.41
3199 4248 8.454106 GTTCAGTTTGAAGCACAATATCTATGT 58.546 33.333 0.00 0.00 37.00 2.29
3200 4249 8.453320 TGTTCAGTTTGAAGCACAATATCTATG 58.547 33.333 0.00 0.00 37.00 2.23
3201 4250 8.565896 TGTTCAGTTTGAAGCACAATATCTAT 57.434 30.769 0.00 0.00 37.00 1.98
3202 4251 7.977789 TGTTCAGTTTGAAGCACAATATCTA 57.022 32.000 0.00 0.00 37.00 1.98
3273 4328 7.752695 AGCTTATTTCAGTATGTTTCTTTCGG 58.247 34.615 0.00 0.00 37.40 4.30
3289 4344 7.905493 GCGGCACTCAATATATAAGCTTATTTC 59.095 37.037 23.47 2.53 0.00 2.17
3295 4350 4.271696 TGCGGCACTCAATATATAAGCT 57.728 40.909 0.00 0.00 0.00 3.74
3330 4409 4.982295 GGAAGACACAAAACACAATAAGCC 59.018 41.667 0.00 0.00 0.00 4.35
3394 4482 2.674852 CACCACCATCTTCAGAATGTCG 59.325 50.000 0.00 0.00 37.40 4.35
3502 4590 2.084546 AGCGGTTTGTAGCCATCTTTC 58.915 47.619 0.00 0.00 0.00 2.62
3539 4627 7.440556 AGAGCTTACAGCAAATCATACATACAG 59.559 37.037 0.00 0.00 45.56 2.74
3544 4632 5.733676 TCAGAGCTTACAGCAAATCATACA 58.266 37.500 0.00 0.00 45.56 2.29
3545 4633 6.259608 ACATCAGAGCTTACAGCAAATCATAC 59.740 38.462 0.00 0.00 45.56 2.39
3546 4634 6.259387 CACATCAGAGCTTACAGCAAATCATA 59.741 38.462 0.00 0.00 45.56 2.15
3547 4635 5.066117 CACATCAGAGCTTACAGCAAATCAT 59.934 40.000 0.00 0.00 45.56 2.45
3548 4636 4.393990 CACATCAGAGCTTACAGCAAATCA 59.606 41.667 0.00 0.00 45.56 2.57
3549 4637 4.730035 GCACATCAGAGCTTACAGCAAATC 60.730 45.833 0.00 0.00 45.56 2.17
3552 4640 2.079158 GCACATCAGAGCTTACAGCAA 58.921 47.619 0.00 0.00 45.56 3.91
3553 4641 1.676916 GGCACATCAGAGCTTACAGCA 60.677 52.381 0.00 0.00 45.56 4.41
3554 4642 1.012841 GGCACATCAGAGCTTACAGC 58.987 55.000 0.00 0.00 42.84 4.40
3555 4643 2.277969 CAGGCACATCAGAGCTTACAG 58.722 52.381 0.00 0.00 0.00 2.74
3568 4658 2.972713 ACTCTAGGAGAAAACAGGCACA 59.027 45.455 1.31 0.00 33.32 4.57
3594 4792 0.826062 CATTTGGAATGGGGCCTGTC 59.174 55.000 0.84 0.00 0.00 3.51
3603 4801 3.061322 CCACACAAGCACATTTGGAATG 58.939 45.455 0.00 0.00 32.32 2.67
3605 4803 1.202510 GCCACACAAGCACATTTGGAA 60.203 47.619 0.00 0.00 32.32 3.53
3606 4804 0.388659 GCCACACAAGCACATTTGGA 59.611 50.000 0.00 0.00 32.32 3.53
3619 4916 1.470098 CATGCCTAAGTCTTGCCACAC 59.530 52.381 0.00 0.00 0.00 3.82
3677 4974 1.676746 CGACAGGAGATAGGGACGAA 58.323 55.000 0.00 0.00 0.00 3.85
3680 4977 1.112113 TTGCGACAGGAGATAGGGAC 58.888 55.000 0.00 0.00 0.00 4.46
3683 4980 5.817816 AGTTTTATTTGCGACAGGAGATAGG 59.182 40.000 0.00 0.00 0.00 2.57
3702 5004 1.676006 CCGACACTTCTGCCAAGTTTT 59.324 47.619 0.00 0.00 0.00 2.43
3724 5026 7.130681 AGAGATCAGATTGTAGTAAAAGGGG 57.869 40.000 0.00 0.00 0.00 4.79
3773 5106 1.284297 GCGTTTTGAATGGCACCTGC 61.284 55.000 0.00 0.00 41.14 4.85
3778 5111 0.313672 GGTCTGCGTTTTGAATGGCA 59.686 50.000 0.00 0.00 0.00 4.92
3779 5112 0.388520 GGGTCTGCGTTTTGAATGGC 60.389 55.000 0.00 0.00 0.00 4.40
3780 5113 1.247567 AGGGTCTGCGTTTTGAATGG 58.752 50.000 0.00 0.00 0.00 3.16
3781 5114 3.334691 TCTAGGGTCTGCGTTTTGAATG 58.665 45.455 0.00 0.00 0.00 2.67
3782 5115 3.695830 TCTAGGGTCTGCGTTTTGAAT 57.304 42.857 0.00 0.00 0.00 2.57
3783 5116 3.478857 TTCTAGGGTCTGCGTTTTGAA 57.521 42.857 0.00 0.00 0.00 2.69
3784 5117 3.478857 TTTCTAGGGTCTGCGTTTTGA 57.521 42.857 0.00 0.00 0.00 2.69
3785 5118 3.119849 CCATTTCTAGGGTCTGCGTTTTG 60.120 47.826 0.00 0.00 0.00 2.44
3786 5119 3.081804 CCATTTCTAGGGTCTGCGTTTT 58.918 45.455 0.00 0.00 0.00 2.43
3787 5120 2.711542 CCATTTCTAGGGTCTGCGTTT 58.288 47.619 0.00 0.00 0.00 3.60
3788 5121 1.679032 GCCATTTCTAGGGTCTGCGTT 60.679 52.381 0.00 0.00 0.00 4.84
3789 5122 0.107654 GCCATTTCTAGGGTCTGCGT 60.108 55.000 0.00 0.00 0.00 5.24
3790 5123 0.107703 TGCCATTTCTAGGGTCTGCG 60.108 55.000 0.00 0.00 0.00 5.18
3791 5124 1.952296 CATGCCATTTCTAGGGTCTGC 59.048 52.381 0.00 0.00 0.00 4.26
3792 5125 3.565764 TCATGCCATTTCTAGGGTCTG 57.434 47.619 0.00 0.00 0.00 3.51
3793 5126 4.591321 TTTCATGCCATTTCTAGGGTCT 57.409 40.909 0.00 0.00 0.00 3.85
3794 5127 5.394553 CCTTTTTCATGCCATTTCTAGGGTC 60.395 44.000 0.00 0.00 0.00 4.46
3799 5132 4.771577 TCTGCCTTTTTCATGCCATTTCTA 59.228 37.500 0.00 0.00 0.00 2.10
3826 5159 2.670401 GCACTAAGCCGACATATTGC 57.330 50.000 0.00 0.00 37.23 3.56
3837 5170 6.783892 TTTGAATTTTGAATGGCACTAAGC 57.216 33.333 0.00 0.00 44.65 3.09
3838 5171 7.820872 AGGATTTGAATTTTGAATGGCACTAAG 59.179 33.333 0.00 0.00 0.00 2.18
3839 5172 7.678837 AGGATTTGAATTTTGAATGGCACTAA 58.321 30.769 0.00 0.00 0.00 2.24
3840 5173 7.243604 AGGATTTGAATTTTGAATGGCACTA 57.756 32.000 0.00 0.00 0.00 2.74
3841 5174 6.117975 AGGATTTGAATTTTGAATGGCACT 57.882 33.333 0.00 0.00 0.00 4.40
3842 5175 7.765360 TCATAGGATTTGAATTTTGAATGGCAC 59.235 33.333 0.00 0.00 0.00 5.01
3844 5177 8.897872 ATCATAGGATTTGAATTTTGAATGGC 57.102 30.769 0.00 0.00 0.00 4.40
3873 5207 4.608170 TCTTTGGGCTGGGATTCTTTAT 57.392 40.909 0.00 0.00 0.00 1.40
3887 5221 1.349026 TCAGCTGGAGACTTCTTTGGG 59.651 52.381 15.13 0.00 0.00 4.12
3904 5242 1.489649 ACATCTGCCCATCCTTCTCAG 59.510 52.381 0.00 0.00 0.00 3.35
3905 5243 1.211212 CACATCTGCCCATCCTTCTCA 59.789 52.381 0.00 0.00 0.00 3.27
3906 5244 1.211457 ACACATCTGCCCATCCTTCTC 59.789 52.381 0.00 0.00 0.00 2.87
3907 5245 1.293062 ACACATCTGCCCATCCTTCT 58.707 50.000 0.00 0.00 0.00 2.85
3908 5246 2.134789 AACACATCTGCCCATCCTTC 57.865 50.000 0.00 0.00 0.00 3.46
3910 5248 2.450476 GAAAACACATCTGCCCATCCT 58.550 47.619 0.00 0.00 0.00 3.24
3911 5249 1.478105 GGAAAACACATCTGCCCATCC 59.522 52.381 0.00 0.00 0.00 3.51
3913 5251 1.077663 AGGGAAAACACATCTGCCCAT 59.922 47.619 0.00 0.00 38.04 4.00
3914 5252 0.482446 AGGGAAAACACATCTGCCCA 59.518 50.000 0.00 0.00 38.04 5.36
3915 5253 1.632589 AAGGGAAAACACATCTGCCC 58.367 50.000 0.00 0.00 35.79 5.36
3918 5256 3.068590 ACAGCAAAGGGAAAACACATCTG 59.931 43.478 0.00 0.00 0.00 2.90
3919 5257 3.299503 ACAGCAAAGGGAAAACACATCT 58.700 40.909 0.00 0.00 0.00 2.90
3938 5284 1.475280 GCTCCCATACTCACACGTACA 59.525 52.381 0.00 0.00 0.00 2.90
3939 5285 1.475280 TGCTCCCATACTCACACGTAC 59.525 52.381 0.00 0.00 0.00 3.67
3941 5287 0.973632 TTGCTCCCATACTCACACGT 59.026 50.000 0.00 0.00 0.00 4.49
3942 5288 2.315925 ATTGCTCCCATACTCACACG 57.684 50.000 0.00 0.00 0.00 4.49
3943 5289 2.945668 GGAATTGCTCCCATACTCACAC 59.054 50.000 0.00 0.00 38.44 3.82
3944 5290 2.575735 TGGAATTGCTCCCATACTCACA 59.424 45.455 0.00 0.00 44.69 3.58
3945 5291 3.281727 TGGAATTGCTCCCATACTCAC 57.718 47.619 0.00 0.00 44.69 3.51
3946 5292 4.079844 TGAATGGAATTGCTCCCATACTCA 60.080 41.667 0.00 0.00 44.69 3.41
3950 5296 5.271598 ACTTTGAATGGAATTGCTCCCATA 58.728 37.500 0.00 0.00 44.69 2.74
3976 5322 0.843309 TGTGCTTCCCTCCTTGTTGA 59.157 50.000 0.00 0.00 0.00 3.18
3977 5323 0.954452 GTGTGCTTCCCTCCTTGTTG 59.046 55.000 0.00 0.00 0.00 3.33
3978 5324 0.846693 AGTGTGCTTCCCTCCTTGTT 59.153 50.000 0.00 0.00 0.00 2.83
3980 5326 0.607489 CCAGTGTGCTTCCCTCCTTG 60.607 60.000 0.00 0.00 0.00 3.61
3986 6850 1.302832 CCAGTCCAGTGTGCTTCCC 60.303 63.158 0.00 0.00 0.00 3.97
4011 6875 3.128188 CTGCTGCTGCTGCTCCAG 61.128 66.667 27.67 16.84 40.48 3.86
4017 6881 4.406173 GCACTGCTGCTGCTGCTG 62.406 66.667 27.75 27.75 40.63 4.41
4102 6982 4.389374 GGTGGTCATCATGGTAGTATTGG 58.611 47.826 0.00 0.00 0.00 3.16
4103 6983 4.389374 GGGTGGTCATCATGGTAGTATTG 58.611 47.826 0.00 0.00 0.00 1.90
4104 6984 3.071023 CGGGTGGTCATCATGGTAGTATT 59.929 47.826 0.00 0.00 0.00 1.89
4106 6986 2.036387 CGGGTGGTCATCATGGTAGTA 58.964 52.381 0.00 0.00 0.00 1.82
4107 6987 0.830648 CGGGTGGTCATCATGGTAGT 59.169 55.000 0.00 0.00 0.00 2.73
4108 6988 0.106708 CCGGGTGGTCATCATGGTAG 59.893 60.000 0.00 0.00 0.00 3.18
4109 6989 1.978455 GCCGGGTGGTCATCATGGTA 61.978 60.000 2.18 0.00 37.67 3.25
4110 6990 2.998097 CCGGGTGGTCATCATGGT 59.002 61.111 0.00 0.00 0.00 3.55
4111 6991 2.516930 GCCGGGTGGTCATCATGG 60.517 66.667 2.18 0.00 37.67 3.66
4128 7008 2.743928 GTCTGCCCCTTGCGAGTG 60.744 66.667 0.00 0.00 45.60 3.51
4145 7025 4.151335 GTGATCTTTTCCATCCATCGATCG 59.849 45.833 9.36 9.36 31.04 3.69
4146 7026 4.151335 CGTGATCTTTTCCATCCATCGATC 59.849 45.833 0.00 0.00 0.00 3.69
4147 7027 4.060900 CGTGATCTTTTCCATCCATCGAT 58.939 43.478 0.00 0.00 0.00 3.59
4148 7028 3.457234 CGTGATCTTTTCCATCCATCGA 58.543 45.455 0.00 0.00 0.00 3.59
4220 7126 2.202810 GCAGCGAGCTAGGGACAC 60.203 66.667 0.00 0.00 41.15 3.67
4308 7214 2.283101 GGAGCATTGGTGTGGGCA 60.283 61.111 0.00 0.00 0.00 5.36
4309 7215 3.443045 CGGAGCATTGGTGTGGGC 61.443 66.667 0.00 0.00 0.00 5.36
4310 7216 2.034066 ACGGAGCATTGGTGTGGG 59.966 61.111 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.