Multiple sequence alignment - TraesCS7A01G180600

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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 TraesCS7A01G180600 chr7A 100.000 3093 0 0 1 3093 134882033 134878941 0.000000e+00 5712.0
1 TraesCS7A01G180600 chr7A 85.451 543 32 18 878 1404 134728662 134728151 3.530000e-144 521.0
2 TraesCS7A01G180600 chr7A 93.605 172 11 0 2529 2700 134728116 134727945 1.100000e-64 257.0
3 TraesCS7A01G180600 chr7A 96.386 83 3 0 2727 2809 134727949 134727867 1.500000e-28 137.0
4 TraesCS7A01G180600 chr7D 94.467 1211 57 7 1001 2210 135777788 135776587 0.000000e+00 1857.0
5 TraesCS7A01G180600 chr7D 90.022 892 49 17 1 856 135787537 135786650 0.000000e+00 1118.0
6 TraesCS7A01G180600 chr7D 87.783 221 16 4 2434 2645 135776372 135776154 6.620000e-62 248.0
7 TraesCS7A01G180600 chr7D 96.970 132 3 1 878 1009 135785432 135785302 1.440000e-53 220.0
8 TraesCS7A01G180600 chr7D 84.685 111 13 3 1148 1254 135766515 135766405 1.170000e-19 108.0
9 TraesCS7A01G180600 chr7B 92.193 935 35 9 1279 2211 97680391 97679493 0.000000e+00 1288.0
10 TraesCS7A01G180600 chr7B 93.789 322 17 3 535 855 97687533 97687214 6.000000e-132 481.0
11 TraesCS7A01G180600 chr7B 91.343 335 15 2 878 1212 97680727 97680407 2.190000e-121 446.0
12 TraesCS7A01G180600 chr7B 92.742 124 5 2 2212 2332 97679452 97679330 3.170000e-40 176.0
13 TraesCS7A01G180600 chrUn 92.500 40 2 1 2998 3036 41678984 41678945 4.310000e-04 56.5
14 TraesCS7A01G180600 chr5B 100.000 30 0 0 3045 3074 704269267 704269296 4.310000e-04 56.5
15 TraesCS7A01G180600 chr6B 92.308 39 1 2 3038 3074 670894312 670894350 2.000000e-03 54.7


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 TraesCS7A01G180600 chr7A 134878941 134882033 3092 True 5712.000000 5712 100.000000 1 3093 1 chr7A.!!$R1 3092
1 TraesCS7A01G180600 chr7A 134727867 134728662 795 True 305.000000 521 91.814000 878 2809 3 chr7A.!!$R2 1931
2 TraesCS7A01G180600 chr7D 135776154 135777788 1634 True 1052.500000 1857 91.125000 1001 2645 2 chr7D.!!$R2 1644
3 TraesCS7A01G180600 chr7D 135785302 135787537 2235 True 669.000000 1118 93.496000 1 1009 2 chr7D.!!$R3 1008
4 TraesCS7A01G180600 chr7B 97679330 97680727 1397 True 636.666667 1288 92.092667 878 2332 3 chr7B.!!$R2 1454

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
607 641 0.036732 TACAGGCTGCTTCCCAGTTG 59.963 55.0 15.89 0.0 43.71 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 3704 0.464036 ACAGCGTCTTGAACCAGACA 59.536 50.0 6.8 0.0 43.11 3.41 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
29 30 4.370917 ACTTTGTATTTGGCAACTGCTTG 58.629 39.130 0.00 0.00 41.70 4.01
80 81 4.990543 TCAAACAGTAAGCACTTCATCG 57.009 40.909 0.00 0.00 30.46 3.84
92 93 3.309682 GCACTTCATCGCATTTGCTACTA 59.690 43.478 0.51 0.00 39.32 1.82
104 105 8.765219 TCGCATTTGCTACTAATAAATTCTCTC 58.235 33.333 0.51 0.00 39.32 3.20
106 107 8.012241 GCATTTGCTACTAATAAATTCTCTCGG 58.988 37.037 0.00 0.00 38.21 4.63
159 160 8.579682 AACTGAAAAATCAACTGCTAATGTTC 57.420 30.769 0.00 0.00 0.00 3.18
217 219 1.165270 GCTGGGTTGCAATACTTCGT 58.835 50.000 0.59 0.00 0.00 3.85
224 226 3.187637 GGTTGCAATACTTCGTAGTTGCA 59.812 43.478 15.07 15.07 43.08 4.08
236 238 5.128992 TCGTAGTTGCAATCTCTTACACA 57.871 39.130 0.59 0.00 0.00 3.72
247 249 6.488006 GCAATCTCTTACACATATGGGTCATT 59.512 38.462 15.42 3.88 31.69 2.57
277 279 6.565234 TCTCTTTTCCTAGATTTAGCTGTCG 58.435 40.000 0.00 0.00 0.00 4.35
278 280 6.153000 TCTCTTTTCCTAGATTTAGCTGTCGT 59.847 38.462 0.00 0.00 0.00 4.34
296 298 6.642683 TGTCGTTTCTACTTATTTGCTAGC 57.357 37.500 8.10 8.10 0.00 3.42
320 322 3.287222 TCTTGTGTAGCTTGCTTGGTTT 58.713 40.909 0.00 0.00 0.00 3.27
331 333 6.909909 AGCTTGCTTGGTTTTAGTAACATAC 58.090 36.000 0.00 0.00 0.00 2.39
396 405 6.166279 CACACTTACCTCAGAAATCAGCTAA 58.834 40.000 0.00 0.00 0.00 3.09
407 416 8.565896 TCAGAAATCAGCTAAGAAATGCTAAA 57.434 30.769 0.00 0.00 37.81 1.85
439 448 6.893020 ATCACTTATTTGTCCCCTCTAGTT 57.107 37.500 0.00 0.00 0.00 2.24
481 490 5.309543 TGATCCTACAAGAAAGAGGGAAACA 59.690 40.000 0.00 0.00 0.00 2.83
483 492 5.621193 TCCTACAAGAAAGAGGGAAACAAG 58.379 41.667 0.00 0.00 0.00 3.16
485 494 2.959030 ACAAGAAAGAGGGAAACAAGGC 59.041 45.455 0.00 0.00 0.00 4.35
514 548 3.553096 GGCGAGAGACGGTGAAATATGAT 60.553 47.826 0.00 0.00 42.83 2.45
551 585 1.194781 ACGTCATCAAGGGTGAGCCT 61.195 55.000 0.00 0.00 37.14 4.58
594 628 4.773323 AAAGACAAAATGAGCTACAGGC 57.227 40.909 0.00 0.00 42.19 4.85
604 638 1.451028 GCTACAGGCTGCTTCCCAG 60.451 63.158 15.89 3.62 44.67 4.45
607 641 0.036732 TACAGGCTGCTTCCCAGTTG 59.963 55.000 15.89 0.00 43.71 3.16
615 649 4.261801 GCTGCTTCCCAGTTGTTATCTAA 58.738 43.478 0.00 0.00 43.71 2.10
619 653 3.926058 TCCCAGTTGTTATCTAAGCCC 57.074 47.619 0.00 0.00 0.00 5.19
625 659 5.888161 CCAGTTGTTATCTAAGCCCATTTCT 59.112 40.000 0.00 0.00 0.00 2.52
640 674 6.944234 CCCATTTCTAGGGTTTAGATGAAC 57.056 41.667 0.00 0.00 41.61 3.18
657 691 9.701098 TTAGATGAACGAGTGTAAATTTGTACT 57.299 29.630 0.00 4.96 0.00 2.73
663 697 5.163513 CGAGTGTAAATTTGTACTACGGGT 58.836 41.667 0.00 0.00 0.00 5.28
674 708 0.689055 ACTACGGGTCCCCTTGTTTC 59.311 55.000 1.00 0.00 0.00 2.78
707 741 2.037641 TGTCGCAATGATCATAGGGAGG 59.962 50.000 9.04 0.00 0.00 4.30
819 854 4.768448 TCCATATATTTGCATTGGAGCAGG 59.232 41.667 0.00 0.00 46.54 4.85
856 891 2.661718 TGTGGATGTATGAGCGGAGTA 58.338 47.619 0.00 0.00 0.00 2.59
857 892 3.028130 TGTGGATGTATGAGCGGAGTAA 58.972 45.455 0.00 0.00 0.00 2.24
858 893 3.641436 TGTGGATGTATGAGCGGAGTAAT 59.359 43.478 0.00 0.00 0.00 1.89
860 895 2.996621 GGATGTATGAGCGGAGTAATGC 59.003 50.000 0.00 0.00 0.00 3.56
861 896 3.306364 GGATGTATGAGCGGAGTAATGCT 60.306 47.826 0.00 0.00 45.90 3.79
863 898 3.457234 TGTATGAGCGGAGTAATGCTTG 58.543 45.455 0.00 0.00 42.60 4.01
869 2100 1.747206 GCGGAGTAATGCTTGGGTCAT 60.747 52.381 0.00 0.00 0.00 3.06
870 2101 2.213499 CGGAGTAATGCTTGGGTCATC 58.787 52.381 0.00 0.00 0.00 2.92
871 2102 2.158900 CGGAGTAATGCTTGGGTCATCT 60.159 50.000 0.00 0.00 0.00 2.90
873 2104 3.135530 GGAGTAATGCTTGGGTCATCTCT 59.864 47.826 0.00 0.00 0.00 3.10
875 2106 5.510520 GGAGTAATGCTTGGGTCATCTCTAG 60.511 48.000 0.00 0.00 0.00 2.43
876 2107 4.965532 AGTAATGCTTGGGTCATCTCTAGT 59.034 41.667 0.00 0.00 0.00 2.57
1025 2256 0.462759 AGCCTACGAGATGCTTTGGC 60.463 55.000 0.00 0.00 39.19 4.52
1120 2351 4.597032 CCCAACTGAGGCAAACCA 57.403 55.556 0.00 0.00 39.06 3.67
1142 2373 4.783621 TCATGGCAGTGGGAGCGC 62.784 66.667 0.00 0.00 0.00 5.92
1161 2392 1.855360 GCACATTACTACTCGCTCTGC 59.145 52.381 0.00 0.00 0.00 4.26
1168 2399 0.743688 CTACTCGCTCTGCTGATGGT 59.256 55.000 0.00 0.00 0.00 3.55
1178 2409 0.323360 TGCTGATGGTAAAGTGGCCC 60.323 55.000 0.00 0.00 0.00 5.80
1194 2441 2.281208 CCCGAACTCAACCCGCAA 60.281 61.111 0.00 0.00 0.00 4.85
1234 2481 2.666862 TTTACTGCGCCACCACCG 60.667 61.111 4.18 0.00 0.00 4.94
1254 2501 2.398554 CGTTGGCCGGAGTGAATGG 61.399 63.158 5.05 0.00 0.00 3.16
1316 2565 0.107214 TGCTTAAAGCCATCCCCTCG 60.107 55.000 0.00 0.00 41.51 4.63
1669 2924 1.227674 GGAGATGACCATGGCCGAC 60.228 63.158 13.04 1.29 0.00 4.79
1903 3158 1.080705 GGTCCACCTCGTCGTCAAG 60.081 63.158 0.00 0.00 0.00 3.02
1920 3175 4.899239 GCTCGTGCATCCCCGGAG 62.899 72.222 0.73 0.00 39.41 4.63
1956 3211 1.516365 CGGATCAGGTACGGCGATCT 61.516 60.000 16.62 4.59 36.59 2.75
1958 3213 1.884579 GGATCAGGTACGGCGATCTTA 59.115 52.381 16.62 0.00 36.59 2.10
2093 3348 1.839424 GCCTCCACTTTGGCTGTTAT 58.161 50.000 0.00 0.00 45.26 1.89
2094 3349 2.171003 GCCTCCACTTTGGCTGTTATT 58.829 47.619 0.00 0.00 45.26 1.40
2095 3350 3.352648 GCCTCCACTTTGGCTGTTATTA 58.647 45.455 0.00 0.00 45.26 0.98
2096 3351 3.378427 GCCTCCACTTTGGCTGTTATTAG 59.622 47.826 0.00 0.00 45.26 1.73
2097 3352 4.843728 CCTCCACTTTGGCTGTTATTAGA 58.156 43.478 0.00 0.00 37.47 2.10
2189 3444 4.333913 AAAGTCTCCATGGATCTCGATG 57.666 45.455 16.63 1.19 32.75 3.84
2200 3455 3.146066 GGATCTCGATGACAGACTAGCT 58.854 50.000 0.00 0.00 0.00 3.32
2226 3521 4.787598 CTTGTGCCATGTTAGTTCTTCAC 58.212 43.478 0.00 0.00 0.00 3.18
2230 3525 5.001232 GTGCCATGTTAGTTCTTCACCTTA 58.999 41.667 0.00 0.00 0.00 2.69
2258 3555 2.162809 GTGGTGGTGTTCGTTCAAGTTT 59.837 45.455 0.00 0.00 0.00 2.66
2293 3590 2.014010 AGCATGTTTGGGTGATGGTT 57.986 45.000 0.00 0.00 0.00 3.67
2312 3612 5.373222 TGGTTAGTGTTTGTAGCTTGTCAT 58.627 37.500 0.00 0.00 0.00 3.06
2332 3632 7.771183 TGTCATGGGCTTAATTTGTAATCTTC 58.229 34.615 0.00 0.00 0.00 2.87
2338 3638 8.912988 TGGGCTTAATTTGTAATCTTCTTATGG 58.087 33.333 0.00 0.00 0.00 2.74
2339 3639 9.131791 GGGCTTAATTTGTAATCTTCTTATGGA 57.868 33.333 0.00 0.00 0.00 3.41
2356 3659 9.745880 TTCTTATGGATCGTTTAGTATGAACTC 57.254 33.333 0.00 0.00 37.15 3.01
2374 3677 5.306937 TGAACTCTGAAGTGAAATGGAGGTA 59.693 40.000 0.00 0.00 35.36 3.08
2381 3684 5.473162 TGAAGTGAAATGGAGGTATGTTGTG 59.527 40.000 0.00 0.00 0.00 3.33
2386 3689 6.808212 GTGAAATGGAGGTATGTTGTGAAATG 59.192 38.462 0.00 0.00 0.00 2.32
2393 3696 4.022068 AGGTATGTTGTGAAATGCTTGTGG 60.022 41.667 0.00 0.00 0.00 4.17
2395 3698 4.877378 ATGTTGTGAAATGCTTGTGGAT 57.123 36.364 0.00 0.00 0.00 3.41
2396 3699 3.979948 TGTTGTGAAATGCTTGTGGATG 58.020 40.909 0.00 0.00 0.00 3.51
2397 3700 3.384146 TGTTGTGAAATGCTTGTGGATGT 59.616 39.130 0.00 0.00 0.00 3.06
2398 3701 4.582240 TGTTGTGAAATGCTTGTGGATGTA 59.418 37.500 0.00 0.00 0.00 2.29
2399 3702 5.068329 TGTTGTGAAATGCTTGTGGATGTAA 59.932 36.000 0.00 0.00 0.00 2.41
2400 3703 5.119931 TGTGAAATGCTTGTGGATGTAAC 57.880 39.130 0.00 0.00 0.00 2.50
2401 3704 4.826733 TGTGAAATGCTTGTGGATGTAACT 59.173 37.500 0.00 0.00 0.00 2.24
2402 3705 5.156355 GTGAAATGCTTGTGGATGTAACTG 58.844 41.667 0.00 0.00 0.00 3.16
2403 3706 4.826733 TGAAATGCTTGTGGATGTAACTGT 59.173 37.500 0.00 0.00 0.00 3.55
2404 3707 5.048782 TGAAATGCTTGTGGATGTAACTGTC 60.049 40.000 0.00 0.00 0.00 3.51
2405 3708 3.769739 TGCTTGTGGATGTAACTGTCT 57.230 42.857 0.00 0.00 0.00 3.41
2406 3709 3.402110 TGCTTGTGGATGTAACTGTCTG 58.598 45.455 0.00 0.00 0.00 3.51
2407 3710 2.744202 GCTTGTGGATGTAACTGTCTGG 59.256 50.000 0.00 0.00 0.00 3.86
2408 3711 3.807209 GCTTGTGGATGTAACTGTCTGGT 60.807 47.826 0.00 0.00 0.00 4.00
2409 3712 4.389374 CTTGTGGATGTAACTGTCTGGTT 58.611 43.478 0.00 0.00 0.00 3.67
2410 3713 4.002906 TGTGGATGTAACTGTCTGGTTC 57.997 45.455 0.00 0.00 0.00 3.62
2411 3714 3.389656 TGTGGATGTAACTGTCTGGTTCA 59.610 43.478 0.00 0.00 0.00 3.18
2412 3715 4.141597 TGTGGATGTAACTGTCTGGTTCAA 60.142 41.667 0.00 0.00 0.00 2.69
2413 3716 4.452455 GTGGATGTAACTGTCTGGTTCAAG 59.548 45.833 0.00 0.00 0.00 3.02
2414 3717 4.346709 TGGATGTAACTGTCTGGTTCAAGA 59.653 41.667 0.00 0.00 0.00 3.02
2415 3718 4.691216 GGATGTAACTGTCTGGTTCAAGAC 59.309 45.833 0.75 0.75 45.70 3.01
2420 3723 3.290776 GTCTGGTTCAAGACGCTGT 57.709 52.632 0.00 0.00 37.44 4.40
2421 3724 2.433868 GTCTGGTTCAAGACGCTGTA 57.566 50.000 0.00 0.00 37.44 2.74
2422 3725 2.059541 GTCTGGTTCAAGACGCTGTAC 58.940 52.381 0.00 0.00 37.44 2.90
2423 3726 1.000506 TCTGGTTCAAGACGCTGTACC 59.999 52.381 0.00 2.71 37.30 3.34
2424 3727 0.753867 TGGTTCAAGACGCTGTACCA 59.246 50.000 7.02 7.02 42.49 3.25
2425 3728 1.346395 TGGTTCAAGACGCTGTACCAT 59.654 47.619 7.02 0.00 40.59 3.55
2426 3729 1.732259 GGTTCAAGACGCTGTACCATG 59.268 52.381 4.36 0.00 36.89 3.66
2427 3730 2.413837 GTTCAAGACGCTGTACCATGT 58.586 47.619 0.00 0.00 0.00 3.21
2428 3731 2.806244 GTTCAAGACGCTGTACCATGTT 59.194 45.455 0.00 0.00 0.00 2.71
2429 3732 2.683968 TCAAGACGCTGTACCATGTTC 58.316 47.619 0.00 0.00 0.00 3.18
2430 3733 2.299013 TCAAGACGCTGTACCATGTTCT 59.701 45.455 0.00 0.00 0.00 3.01
2431 3734 2.370281 AGACGCTGTACCATGTTCTG 57.630 50.000 0.00 0.00 0.00 3.02
2432 3735 1.618837 AGACGCTGTACCATGTTCTGT 59.381 47.619 0.00 0.00 0.00 3.41
2438 3741 5.165676 CGCTGTACCATGTTCTGTAAGTAA 58.834 41.667 0.00 0.00 33.76 2.24
2485 3788 0.952497 CACTGCTGATGCGTGGAACT 60.952 55.000 0.00 0.00 43.34 3.01
2494 3797 1.355210 GCGTGGAACTGTGGTTGTG 59.645 57.895 0.00 0.00 35.58 3.33
2500 3811 0.465460 GAACTGTGGTTGTGGCAGGA 60.465 55.000 0.00 0.00 35.58 3.86
2522 3833 2.711711 GCCATTGATCGGCTCATGT 58.288 52.632 3.09 0.00 46.56 3.21
2525 3836 2.808202 GCCATTGATCGGCTCATGTACT 60.808 50.000 3.09 0.00 46.56 2.73
2526 3837 3.470709 CCATTGATCGGCTCATGTACTT 58.529 45.455 0.00 0.00 32.72 2.24
2527 3838 3.879295 CCATTGATCGGCTCATGTACTTT 59.121 43.478 0.00 0.00 32.72 2.66
2592 3904 4.444838 CAATCGGGCCCGTGTCGA 62.445 66.667 41.57 24.68 40.74 4.20
2651 3963 6.380846 AGAAGAGCTCTGAATCATAACTCAGT 59.619 38.462 19.06 0.00 40.06 3.41
2658 3970 6.867550 TCTGAATCATAACTCAGTCGTGATT 58.132 36.000 14.36 14.36 40.94 2.57
2694 4006 2.759973 CCTGCACGGGAGCTCCTA 60.760 66.667 31.36 12.37 35.95 2.94
2699 4011 3.227276 ACGGGAGCTCCTATGGCG 61.227 66.667 31.36 26.18 35.95 5.69
2700 4012 3.996124 CGGGAGCTCCTATGGCGG 61.996 72.222 31.36 9.10 35.95 6.13
2701 4013 4.321966 GGGAGCTCCTATGGCGGC 62.322 72.222 31.36 9.17 35.95 6.53
2702 4014 4.671569 GGAGCTCCTATGGCGGCG 62.672 72.222 26.25 0.51 34.52 6.46
2705 4017 4.918201 GCTCCTATGGCGGCGCTT 62.918 66.667 32.30 21.23 32.16 4.68
2706 4018 2.663188 CTCCTATGGCGGCGCTTC 60.663 66.667 32.30 16.79 0.00 3.86
2707 4019 3.445518 CTCCTATGGCGGCGCTTCA 62.446 63.158 32.30 22.30 0.00 3.02
2708 4020 2.969238 CCTATGGCGGCGCTTCAG 60.969 66.667 32.30 22.99 0.00 3.02
2709 4021 2.969238 CTATGGCGGCGCTTCAGG 60.969 66.667 32.30 14.36 0.00 3.86
2710 4022 4.545706 TATGGCGGCGCTTCAGGG 62.546 66.667 32.30 0.00 0.00 4.45
2723 4035 4.090588 CAGGGGCGGCGAAGGTTA 62.091 66.667 12.98 0.00 0.00 2.85
2724 4036 3.782443 AGGGGCGGCGAAGGTTAG 61.782 66.667 12.98 0.00 0.00 2.34
2726 4038 4.468689 GGGCGGCGAAGGTTAGCT 62.469 66.667 12.98 0.00 0.00 3.32
2727 4039 3.195698 GGCGGCGAAGGTTAGCTG 61.196 66.667 12.98 0.00 42.31 4.24
2728 4040 3.195698 GCGGCGAAGGTTAGCTGG 61.196 66.667 12.98 0.00 39.94 4.85
2729 4041 3.195698 CGGCGAAGGTTAGCTGGC 61.196 66.667 0.00 0.05 36.18 4.85
2795 4107 2.752358 CTGCAGTGAGCTTCCCCA 59.248 61.111 5.25 0.00 45.94 4.96
2809 4121 4.019771 AGCTTCCCCACAAAACAAGAAAAA 60.020 37.500 0.00 0.00 0.00 1.94
2810 4122 4.094294 GCTTCCCCACAAAACAAGAAAAAC 59.906 41.667 0.00 0.00 0.00 2.43
2811 4123 5.487433 CTTCCCCACAAAACAAGAAAAACT 58.513 37.500 0.00 0.00 0.00 2.66
2812 4124 6.607004 TTCCCCACAAAACAAGAAAAACTA 57.393 33.333 0.00 0.00 0.00 2.24
2813 4125 5.968254 TCCCCACAAAACAAGAAAAACTAC 58.032 37.500 0.00 0.00 0.00 2.73
2814 4126 5.480772 TCCCCACAAAACAAGAAAAACTACA 59.519 36.000 0.00 0.00 0.00 2.74
2815 4127 5.810074 CCCCACAAAACAAGAAAAACTACAG 59.190 40.000 0.00 0.00 0.00 2.74
2816 4128 6.394809 CCCACAAAACAAGAAAAACTACAGT 58.605 36.000 0.00 0.00 0.00 3.55
2817 4129 7.363094 CCCCACAAAACAAGAAAAACTACAGTA 60.363 37.037 0.00 0.00 0.00 2.74
2818 4130 7.700656 CCCACAAAACAAGAAAAACTACAGTAG 59.299 37.037 6.00 6.00 0.00 2.57
2819 4131 8.241367 CCACAAAACAAGAAAAACTACAGTAGT 58.759 33.333 7.48 7.48 41.73 2.73
2862 4174 9.286946 CTACAGTACAACTTGTATACTACTTGC 57.713 37.037 4.93 0.00 35.05 4.01
2863 4175 7.095270 ACAGTACAACTTGTATACTACTTGCC 58.905 38.462 4.93 0.00 35.05 4.52
2864 4176 7.039223 ACAGTACAACTTGTATACTACTTGCCT 60.039 37.037 4.93 0.60 35.05 4.75
2865 4177 7.488471 CAGTACAACTTGTATACTACTTGCCTC 59.512 40.741 4.93 0.00 35.05 4.70
2866 4178 6.354794 ACAACTTGTATACTACTTGCCTCA 57.645 37.500 4.17 0.00 0.00 3.86
2867 4179 6.398918 ACAACTTGTATACTACTTGCCTCAG 58.601 40.000 4.17 0.00 0.00 3.35
2868 4180 6.210784 ACAACTTGTATACTACTTGCCTCAGA 59.789 38.462 4.17 0.00 0.00 3.27
2869 4181 7.093289 ACAACTTGTATACTACTTGCCTCAGAT 60.093 37.037 4.17 0.00 0.00 2.90
2870 4182 8.414003 CAACTTGTATACTACTTGCCTCAGATA 58.586 37.037 4.17 0.00 0.00 1.98
2871 4183 8.534954 ACTTGTATACTACTTGCCTCAGATAA 57.465 34.615 4.17 0.00 0.00 1.75
2872 4184 8.978472 ACTTGTATACTACTTGCCTCAGATAAA 58.022 33.333 4.17 0.00 0.00 1.40
2873 4185 9.817809 CTTGTATACTACTTGCCTCAGATAAAA 57.182 33.333 4.17 0.00 0.00 1.52
2900 4212 8.635765 AAACTACTATATTACATGGCCAATGG 57.364 34.615 10.96 4.99 40.94 3.16
2901 4213 7.329746 ACTACTATATTACATGGCCAATGGT 57.670 36.000 10.96 11.66 40.94 3.55
2902 4214 7.755618 ACTACTATATTACATGGCCAATGGTT 58.244 34.615 10.96 0.00 40.94 3.67
2903 4215 7.883311 ACTACTATATTACATGGCCAATGGTTC 59.117 37.037 10.96 0.00 40.94 3.62
2904 4216 6.852404 ACTATATTACATGGCCAATGGTTCT 58.148 36.000 10.96 2.44 40.94 3.01
2905 4217 6.942576 ACTATATTACATGGCCAATGGTTCTC 59.057 38.462 10.96 0.00 40.94 2.87
2906 4218 3.448093 TTACATGGCCAATGGTTCTCA 57.552 42.857 10.96 0.00 40.94 3.27
2907 4219 2.307496 ACATGGCCAATGGTTCTCAA 57.693 45.000 10.96 0.00 40.94 3.02
2908 4220 2.607499 ACATGGCCAATGGTTCTCAAA 58.393 42.857 10.96 0.00 40.94 2.69
2909 4221 2.564062 ACATGGCCAATGGTTCTCAAAG 59.436 45.455 10.96 0.00 40.94 2.77
2910 4222 2.380064 TGGCCAATGGTTCTCAAAGT 57.620 45.000 0.61 0.00 0.00 2.66
2911 4223 2.238521 TGGCCAATGGTTCTCAAAGTC 58.761 47.619 0.61 0.00 0.00 3.01
2912 4224 1.200020 GGCCAATGGTTCTCAAAGTCG 59.800 52.381 0.00 0.00 0.00 4.18
2913 4225 1.200020 GCCAATGGTTCTCAAAGTCGG 59.800 52.381 0.00 0.00 0.00 4.79
2914 4226 2.504367 CCAATGGTTCTCAAAGTCGGT 58.496 47.619 0.00 0.00 0.00 4.69
2915 4227 2.226437 CCAATGGTTCTCAAAGTCGGTG 59.774 50.000 0.00 0.00 0.00 4.94
2916 4228 3.138304 CAATGGTTCTCAAAGTCGGTGA 58.862 45.455 0.00 0.00 0.00 4.02
2917 4229 2.992124 TGGTTCTCAAAGTCGGTGAA 57.008 45.000 0.00 0.00 0.00 3.18
2918 4230 2.557317 TGGTTCTCAAAGTCGGTGAAC 58.443 47.619 0.00 0.00 37.78 3.18
2919 4231 2.169769 TGGTTCTCAAAGTCGGTGAACT 59.830 45.455 0.00 0.00 38.28 3.01
2920 4232 3.203716 GGTTCTCAAAGTCGGTGAACTT 58.796 45.455 0.00 0.00 41.20 2.66
2922 4234 4.095932 GGTTCTCAAAGTCGGTGAACTTTT 59.904 41.667 0.00 0.00 44.95 2.27
2923 4235 5.392703 GGTTCTCAAAGTCGGTGAACTTTTT 60.393 40.000 0.00 0.00 44.95 1.94
2986 4298 7.789273 AAATTCATGCATTTGAAAGTGTTCA 57.211 28.000 6.82 0.00 42.12 3.18
2987 4299 7.972832 AATTCATGCATTTGAAAGTGTTCAT 57.027 28.000 6.82 0.00 43.29 2.57
2988 4300 7.591006 ATTCATGCATTTGAAAGTGTTCATC 57.409 32.000 6.82 0.00 43.29 2.92
2989 4301 6.086785 TCATGCATTTGAAAGTGTTCATCA 57.913 33.333 0.00 0.00 43.29 3.07
2990 4302 6.514063 TCATGCATTTGAAAGTGTTCATCAA 58.486 32.000 0.00 0.00 43.29 2.57
2991 4303 6.421501 TCATGCATTTGAAAGTGTTCATCAAC 59.578 34.615 0.00 0.00 43.29 3.18
2992 4304 5.904941 TGCATTTGAAAGTGTTCATCAACT 58.095 33.333 0.00 0.00 43.29 3.16
2993 4305 6.339730 TGCATTTGAAAGTGTTCATCAACTT 58.660 32.000 0.00 0.00 43.29 2.66
2994 4306 6.817641 TGCATTTGAAAGTGTTCATCAACTTT 59.182 30.769 0.66 0.66 43.29 2.66
2995 4307 7.121272 GCATTTGAAAGTGTTCATCAACTTTG 58.879 34.615 5.58 0.00 43.29 2.77
2996 4308 6.645700 TTTGAAAGTGTTCATCAACTTTGC 57.354 33.333 5.58 0.00 43.29 3.68
2997 4309 5.321959 TGAAAGTGTTCATCAACTTTGCA 57.678 34.783 5.58 0.00 38.88 4.08
2998 4310 5.718146 TGAAAGTGTTCATCAACTTTGCAA 58.282 33.333 5.58 0.00 38.88 4.08
2999 4311 6.162079 TGAAAGTGTTCATCAACTTTGCAAA 58.838 32.000 12.14 12.14 38.88 3.68
3000 4312 6.648310 TGAAAGTGTTCATCAACTTTGCAAAA 59.352 30.769 13.84 0.00 38.88 2.44
3001 4313 7.172190 TGAAAGTGTTCATCAACTTTGCAAAAA 59.828 29.630 13.84 0.00 38.88 1.94
3079 4391 8.542132 ACAGTTCATCAATTTGAAAAATGTTCG 58.458 29.630 17.80 3.69 37.36 3.95
3080 4392 8.754096 CAGTTCATCAATTTGAAAAATGTTCGA 58.246 29.630 2.68 0.00 37.36 3.71
3081 4393 8.971321 AGTTCATCAATTTGAAAAATGTTCGAG 58.029 29.630 2.68 0.00 37.36 4.04
3082 4394 7.872163 TCATCAATTTGAAAAATGTTCGAGG 57.128 32.000 2.68 0.00 0.00 4.63
3083 4395 7.432869 TCATCAATTTGAAAAATGTTCGAGGT 58.567 30.769 2.68 0.00 0.00 3.85
3084 4396 7.381948 TCATCAATTTGAAAAATGTTCGAGGTG 59.618 33.333 2.68 0.00 0.00 4.00
3085 4397 6.800543 TCAATTTGAAAAATGTTCGAGGTGA 58.199 32.000 0.00 0.00 0.00 4.02
3086 4398 6.695278 TCAATTTGAAAAATGTTCGAGGTGAC 59.305 34.615 0.00 0.00 0.00 3.67
3088 4400 5.828299 TTGAAAAATGTTCGAGGTGACTT 57.172 34.783 0.00 0.00 44.43 3.01
3089 4401 5.168526 TGAAAAATGTTCGAGGTGACTTG 57.831 39.130 0.00 0.00 44.43 3.16
3090 4402 4.036262 TGAAAAATGTTCGAGGTGACTTGG 59.964 41.667 0.00 0.00 44.43 3.61
3091 4403 1.523758 AATGTTCGAGGTGACTTGGC 58.476 50.000 0.00 0.00 44.43 4.52
3092 4404 0.321653 ATGTTCGAGGTGACTTGGCC 60.322 55.000 0.00 0.00 44.43 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.121221 AGCAGTTGCCAAATACAAAGTAC 57.879 39.130 0.00 0.00 43.38 2.73
24 25 6.770785 AGTGACAAAAGTAGAAATACCAAGCA 59.229 34.615 0.00 0.00 0.00 3.91
29 30 9.654663 ACATAGAGTGACAAAAGTAGAAATACC 57.345 33.333 0.00 0.00 0.00 2.73
80 81 8.012241 CCGAGAGAATTTATTAGTAGCAAATGC 58.988 37.037 0.00 0.00 42.49 3.56
92 93 6.177610 TGTTACTTGCCCGAGAGAATTTATT 58.822 36.000 0.00 0.00 0.00 1.40
104 105 4.398044 ACCTGAAAATATGTTACTTGCCCG 59.602 41.667 0.00 0.00 0.00 6.13
106 107 6.092748 CACACCTGAAAATATGTTACTTGCC 58.907 40.000 0.00 0.00 0.00 4.52
173 174 0.817654 TGATTCGACGCATGAGGAGT 59.182 50.000 0.00 0.00 0.00 3.85
174 175 1.926561 TTGATTCGACGCATGAGGAG 58.073 50.000 0.00 0.00 0.00 3.69
175 176 2.602257 ATTGATTCGACGCATGAGGA 57.398 45.000 0.00 0.00 0.00 3.71
176 177 4.766007 CTTTATTGATTCGACGCATGAGG 58.234 43.478 0.00 0.00 0.00 3.86
177 178 4.025396 AGCTTTATTGATTCGACGCATGAG 60.025 41.667 0.00 0.00 0.00 2.90
178 179 3.871006 AGCTTTATTGATTCGACGCATGA 59.129 39.130 0.00 0.00 0.00 3.07
180 181 3.002656 CCAGCTTTATTGATTCGACGCAT 59.997 43.478 0.00 0.00 0.00 4.73
182 183 2.286418 CCCAGCTTTATTGATTCGACGC 60.286 50.000 0.00 0.00 0.00 5.19
183 184 2.936498 ACCCAGCTTTATTGATTCGACG 59.064 45.455 0.00 0.00 0.00 5.12
217 219 6.992123 CCCATATGTGTAAGAGATTGCAACTA 59.008 38.462 0.00 0.00 0.00 2.24
224 226 8.938883 ACTAATGACCCATATGTGTAAGAGATT 58.061 33.333 1.24 0.00 0.00 2.40
277 279 7.292129 AGAACGCTAGCAAATAAGTAGAAAC 57.708 36.000 16.45 0.00 0.00 2.78
278 280 7.386848 ACAAGAACGCTAGCAAATAAGTAGAAA 59.613 33.333 16.45 0.00 0.00 2.52
296 298 2.349817 CCAAGCAAGCTACACAAGAACG 60.350 50.000 0.00 0.00 0.00 3.95
366 375 7.685481 TGATTTCTGAGGTAAGTGTGGAATTA 58.315 34.615 0.00 0.00 0.00 1.40
374 383 6.634805 TCTTAGCTGATTTCTGAGGTAAGTG 58.365 40.000 14.37 0.00 44.85 3.16
407 416 9.492730 AGGGGACAAATAAGTGATTATGAATTT 57.507 29.630 0.00 0.00 0.00 1.82
426 435 2.225522 TGGATGTCAACTAGAGGGGACA 60.226 50.000 0.00 4.95 43.61 4.02
427 436 2.467880 TGGATGTCAACTAGAGGGGAC 58.532 52.381 0.00 0.00 0.00 4.46
439 448 3.438216 TCAAAGATGCCTTGGATGTCA 57.562 42.857 0.00 0.00 31.91 3.58
481 490 3.241530 TCTCGCCACACCTGCCTT 61.242 61.111 0.00 0.00 0.00 4.35
483 492 3.695606 TCTCTCGCCACACCTGCC 61.696 66.667 0.00 0.00 0.00 4.85
485 494 2.126307 CGTCTCTCGCCACACCTG 60.126 66.667 0.00 0.00 0.00 4.00
533 567 1.599047 AGGCTCACCCTTGATGACG 59.401 57.895 0.00 0.00 43.06 4.35
551 585 1.341482 TGACCTGAAACTTGGCCACAA 60.341 47.619 3.88 0.00 34.87 3.33
594 628 4.333926 GCTTAGATAACAACTGGGAAGCAG 59.666 45.833 0.00 0.00 38.31 4.24
604 638 6.486993 CCCTAGAAATGGGCTTAGATAACAAC 59.513 42.308 0.00 0.00 37.99 3.32
619 653 7.010552 CACTCGTTCATCTAAACCCTAGAAATG 59.989 40.741 0.00 0.00 0.00 2.32
625 659 6.839124 TTACACTCGTTCATCTAAACCCTA 57.161 37.500 0.00 0.00 0.00 3.53
640 674 5.163513 ACCCGTAGTACAAATTTACACTCG 58.836 41.667 7.03 9.87 0.00 4.18
663 697 2.151502 TTTGTGCAGAAACAAGGGGA 57.848 45.000 4.66 0.00 40.93 4.81
694 728 8.685257 AAATATCATGTACCTCCCTATGATCA 57.315 34.615 0.00 0.00 39.96 2.92
745 779 0.530431 GCCATAAATTGCAAGCCCCG 60.530 55.000 4.94 0.00 0.00 5.73
750 784 3.781079 TTCTCGGCCATAAATTGCAAG 57.219 42.857 4.94 0.00 0.00 4.01
794 829 6.239373 CCTGCTCCAATGCAAATATATGGAAA 60.239 38.462 0.00 0.00 42.83 3.13
819 854 7.322664 ACATCCACATTCCACAAAAATATGTC 58.677 34.615 0.00 0.00 0.00 3.06
856 891 5.426833 AGTTACTAGAGATGACCCAAGCATT 59.573 40.000 0.00 0.00 0.00 3.56
857 892 4.965532 AGTTACTAGAGATGACCCAAGCAT 59.034 41.667 0.00 0.00 0.00 3.79
858 893 4.353777 AGTTACTAGAGATGACCCAAGCA 58.646 43.478 0.00 0.00 0.00 3.91
860 895 6.377429 TGTGTAGTTACTAGAGATGACCCAAG 59.623 42.308 0.00 0.00 0.00 3.61
861 896 6.250711 TGTGTAGTTACTAGAGATGACCCAA 58.749 40.000 0.00 0.00 0.00 4.12
863 898 6.963083 ATGTGTAGTTACTAGAGATGACCC 57.037 41.667 0.00 0.00 0.00 4.46
1120 2351 0.617413 CTCCCACTGCCATGAGAACT 59.383 55.000 0.00 0.00 0.00 3.01
1142 2373 3.111838 CAGCAGAGCGAGTAGTAATGTG 58.888 50.000 0.00 0.00 0.00 3.21
1143 2374 3.017442 TCAGCAGAGCGAGTAGTAATGT 58.983 45.455 0.00 0.00 0.00 2.71
1161 2392 0.748005 CGGGGCCACTTTACCATCAG 60.748 60.000 1.96 0.00 0.00 2.90
1168 2399 0.766131 TTGAGTTCGGGGCCACTTTA 59.234 50.000 1.96 0.00 0.00 1.85
1178 2409 2.966309 GCTTGCGGGTTGAGTTCGG 61.966 63.158 0.00 0.00 0.00 4.30
1194 2441 2.032681 GGTTGGACTGAAGCGGCT 59.967 61.111 0.00 0.00 0.00 5.52
1316 2565 1.916181 TGGGGAGGAAGAAATGGAGTC 59.084 52.381 0.00 0.00 0.00 3.36
1480 2735 3.998672 TTGTCCCACTCCGACGCC 61.999 66.667 0.00 0.00 32.68 5.68
1481 2736 2.737376 GTTGTCCCACTCCGACGC 60.737 66.667 0.00 0.00 32.68 5.19
1639 2894 2.704198 ATCTCCGGGAGAGGGGGA 60.704 66.667 29.03 8.30 42.26 4.81
1699 2954 1.946156 CGGGTGCGTGATGATCTCG 60.946 63.158 12.06 12.06 36.57 4.04
1768 3023 1.153549 CTTGGGGTAGTCGAGCAGC 60.154 63.158 0.00 0.00 0.00 5.25
1903 3158 4.899239 CTCCGGGGATGCACGAGC 62.899 72.222 11.72 0.00 42.57 5.03
1939 3194 2.095161 CCTAAGATCGCCGTACCTGATC 60.095 54.545 8.02 8.02 39.00 2.92
1956 3211 0.940519 CACGACGTTGCGGAACCTAA 60.941 55.000 14.56 0.00 35.12 2.69
1958 3213 2.660552 CACGACGTTGCGGAACCT 60.661 61.111 14.56 2.19 35.12 3.50
2038 3293 2.280186 GCGGCCTCGAACATAGGG 60.280 66.667 0.00 0.00 39.00 3.53
2095 3350 8.834733 AGACCGGGATTAATACTAGTACTATCT 58.165 37.037 6.32 0.00 0.00 1.98
2096 3351 8.891720 CAGACCGGGATTAATACTAGTACTATC 58.108 40.741 6.32 8.19 0.00 2.08
2097 3352 7.833183 CCAGACCGGGATTAATACTAGTACTAT 59.167 40.741 6.32 0.00 0.00 2.12
2189 3444 2.926838 GCACAAGCTAAGCTAGTCTGTC 59.073 50.000 0.00 0.00 38.25 3.51
2226 3521 0.744414 CACCACCACATCGGCTAAGG 60.744 60.000 0.00 0.00 39.03 2.69
2230 3525 1.302511 GAACACCACCACATCGGCT 60.303 57.895 0.00 0.00 39.03 5.52
2293 3590 4.323417 CCCATGACAAGCTACAAACACTA 58.677 43.478 0.00 0.00 0.00 2.74
2312 3612 8.912988 CCATAAGAAGATTACAAATTAAGCCCA 58.087 33.333 0.00 0.00 0.00 5.36
2332 3632 9.186323 CAGAGTTCATACTAAACGATCCATAAG 57.814 37.037 0.00 0.00 33.84 1.73
2337 3637 7.221067 CACTTCAGAGTTCATACTAAACGATCC 59.779 40.741 0.00 0.00 33.84 3.36
2338 3638 7.968956 TCACTTCAGAGTTCATACTAAACGATC 59.031 37.037 0.00 0.00 33.84 3.69
2339 3639 7.827701 TCACTTCAGAGTTCATACTAAACGAT 58.172 34.615 0.00 0.00 33.84 3.73
2340 3640 7.210718 TCACTTCAGAGTTCATACTAAACGA 57.789 36.000 0.00 0.00 33.84 3.85
2341 3641 7.869016 TTCACTTCAGAGTTCATACTAAACG 57.131 36.000 0.00 0.00 33.84 3.60
2344 3644 8.593679 TCCATTTCACTTCAGAGTTCATACTAA 58.406 33.333 0.00 0.00 33.84 2.24
2356 3659 5.707298 ACAACATACCTCCATTTCACTTCAG 59.293 40.000 0.00 0.00 0.00 3.02
2374 3677 4.039488 ACATCCACAAGCATTTCACAACAT 59.961 37.500 0.00 0.00 0.00 2.71
2381 3684 5.182001 AGACAGTTACATCCACAAGCATTTC 59.818 40.000 0.00 0.00 0.00 2.17
2386 3689 2.744202 CCAGACAGTTACATCCACAAGC 59.256 50.000 0.00 0.00 0.00 4.01
2393 3696 4.386049 CGTCTTGAACCAGACAGTTACATC 59.614 45.833 6.80 0.00 43.11 3.06
2395 3698 3.713288 CGTCTTGAACCAGACAGTTACA 58.287 45.455 6.80 0.00 43.11 2.41
2396 3699 2.475487 GCGTCTTGAACCAGACAGTTAC 59.525 50.000 6.80 0.00 43.11 2.50
2397 3700 2.364324 AGCGTCTTGAACCAGACAGTTA 59.636 45.455 6.80 0.00 43.11 2.24
2398 3701 1.139058 AGCGTCTTGAACCAGACAGTT 59.861 47.619 6.80 0.00 43.11 3.16
2399 3702 0.753262 AGCGTCTTGAACCAGACAGT 59.247 50.000 6.80 0.00 43.11 3.55
2400 3703 1.143305 CAGCGTCTTGAACCAGACAG 58.857 55.000 6.80 1.97 43.11 3.51
2401 3704 0.464036 ACAGCGTCTTGAACCAGACA 59.536 50.000 6.80 0.00 43.11 3.41
2402 3705 2.059541 GTACAGCGTCTTGAACCAGAC 58.940 52.381 0.00 0.00 40.02 3.51
2403 3706 1.000506 GGTACAGCGTCTTGAACCAGA 59.999 52.381 0.00 0.00 0.00 3.86
2404 3707 1.270094 TGGTACAGCGTCTTGAACCAG 60.270 52.381 0.00 0.00 33.28 4.00
2405 3708 0.753867 TGGTACAGCGTCTTGAACCA 59.246 50.000 0.00 0.00 34.73 3.67
2406 3709 3.599412 TGGTACAGCGTCTTGAACC 57.401 52.632 0.00 0.00 0.00 3.62
2419 3722 5.346822 CCACGTTACTTACAGAACATGGTAC 59.653 44.000 0.00 0.00 34.87 3.34
2420 3723 5.472148 CCACGTTACTTACAGAACATGGTA 58.528 41.667 0.00 0.00 34.87 3.25
2421 3724 4.312443 CCACGTTACTTACAGAACATGGT 58.688 43.478 0.00 0.00 34.87 3.55
2422 3725 3.124636 GCCACGTTACTTACAGAACATGG 59.875 47.826 0.00 0.00 40.90 3.66
2423 3726 3.743911 TGCCACGTTACTTACAGAACATG 59.256 43.478 0.00 0.00 0.00 3.21
2424 3727 3.994392 CTGCCACGTTACTTACAGAACAT 59.006 43.478 0.00 0.00 0.00 2.71
2425 3728 3.068448 TCTGCCACGTTACTTACAGAACA 59.932 43.478 0.00 0.00 31.60 3.18
2426 3729 3.645884 TCTGCCACGTTACTTACAGAAC 58.354 45.455 0.00 0.00 31.60 3.01
2427 3730 3.859627 GCTCTGCCACGTTACTTACAGAA 60.860 47.826 0.00 0.00 34.05 3.02
2428 3731 2.352421 GCTCTGCCACGTTACTTACAGA 60.352 50.000 0.00 0.00 33.42 3.41
2429 3732 1.993370 GCTCTGCCACGTTACTTACAG 59.007 52.381 0.00 0.00 0.00 2.74
2430 3733 1.341852 TGCTCTGCCACGTTACTTACA 59.658 47.619 0.00 0.00 0.00 2.41
2431 3734 2.074547 TGCTCTGCCACGTTACTTAC 57.925 50.000 0.00 0.00 0.00 2.34
2432 3735 2.616960 CATGCTCTGCCACGTTACTTA 58.383 47.619 0.00 0.00 0.00 2.24
2465 3768 2.327343 TTCCACGCATCAGCAGTGC 61.327 57.895 7.13 7.13 41.01 4.40
2471 3774 0.603707 ACCACAGTTCCACGCATCAG 60.604 55.000 0.00 0.00 0.00 2.90
2485 3788 2.203337 GCTCCTGCCACAACCACA 60.203 61.111 0.00 0.00 0.00 4.17
2522 3833 4.565166 CGGTCGACATGCAGATAAAAAGTA 59.435 41.667 18.91 0.00 0.00 2.24
2525 3836 2.675844 CCGGTCGACATGCAGATAAAAA 59.324 45.455 18.91 0.00 0.00 1.94
2526 3837 2.276201 CCGGTCGACATGCAGATAAAA 58.724 47.619 18.91 0.00 0.00 1.52
2527 3838 1.206132 ACCGGTCGACATGCAGATAAA 59.794 47.619 18.91 0.00 0.00 1.40
2592 3904 2.278857 GACCGACGATGCGCTCAT 60.279 61.111 9.73 0.00 35.17 2.90
2614 3926 3.055891 AGAGCTCTTCTTCTGCTTCCTTC 60.056 47.826 11.45 0.00 37.16 3.46
2615 3927 2.905736 AGAGCTCTTCTTCTGCTTCCTT 59.094 45.455 11.45 0.00 37.16 3.36
2651 3963 2.743664 CCTCATCAGTGCAAAATCACGA 59.256 45.455 0.00 0.00 41.61 4.35
2658 3970 1.466856 GGCATCCTCATCAGTGCAAA 58.533 50.000 0.00 0.00 39.27 3.68
2706 4018 4.090588 TAACCTTCGCCGCCCCTG 62.091 66.667 0.00 0.00 0.00 4.45
2707 4019 3.782443 CTAACCTTCGCCGCCCCT 61.782 66.667 0.00 0.00 0.00 4.79
2709 4021 4.468689 AGCTAACCTTCGCCGCCC 62.469 66.667 0.00 0.00 0.00 6.13
2710 4022 3.195698 CAGCTAACCTTCGCCGCC 61.196 66.667 0.00 0.00 0.00 6.13
2711 4023 3.195698 CCAGCTAACCTTCGCCGC 61.196 66.667 0.00 0.00 0.00 6.53
2712 4024 3.195698 GCCAGCTAACCTTCGCCG 61.196 66.667 0.00 0.00 0.00 6.46
2713 4025 3.195698 CGCCAGCTAACCTTCGCC 61.196 66.667 0.00 0.00 0.00 5.54
2714 4026 3.865830 GCGCCAGCTAACCTTCGC 61.866 66.667 0.00 0.00 41.01 4.70
2760 4072 2.035576 GCAGGTTATAGGAGGTGGTACG 59.964 54.545 0.00 0.00 0.00 3.67
2836 4148 9.286946 GCAAGTAGTATACAAGTTGTACTGTAG 57.713 37.037 17.79 7.97 46.26 2.74
2837 4149 8.246180 GGCAAGTAGTATACAAGTTGTACTGTA 58.754 37.037 17.79 4.46 46.26 2.74
2838 4150 7.039223 AGGCAAGTAGTATACAAGTTGTACTGT 60.039 37.037 17.79 5.44 46.26 3.55
2839 4151 7.321153 AGGCAAGTAGTATACAAGTTGTACTG 58.679 38.462 17.79 8.73 46.26 2.74
2840 4152 7.177921 TGAGGCAAGTAGTATACAAGTTGTACT 59.822 37.037 17.79 15.82 46.26 2.73
2841 4153 7.318141 TGAGGCAAGTAGTATACAAGTTGTAC 58.682 38.462 17.79 9.21 46.26 2.90
2842 4154 7.395206 TCTGAGGCAAGTAGTATACAAGTTGTA 59.605 37.037 17.74 17.74 46.26 2.41
2843 4155 6.210784 TCTGAGGCAAGTAGTATACAAGTTGT 59.789 38.462 14.05 14.05 46.26 3.32
2844 4156 6.631016 TCTGAGGCAAGTAGTATACAAGTTG 58.369 40.000 5.50 0.00 46.26 3.16
2845 4157 6.852420 TCTGAGGCAAGTAGTATACAAGTT 57.148 37.500 5.50 0.00 46.26 2.66
2846 4158 8.534954 TTATCTGAGGCAAGTAGTATACAAGT 57.465 34.615 5.50 0.00 46.26 3.16
2847 4159 9.817809 TTTTATCTGAGGCAAGTAGTATACAAG 57.182 33.333 5.50 0.00 46.26 3.16
2874 4186 9.077885 CCATTGGCCATGTAATATAGTAGTTTT 57.922 33.333 6.09 0.00 0.00 2.43
2875 4187 8.224720 ACCATTGGCCATGTAATATAGTAGTTT 58.775 33.333 6.09 0.00 0.00 2.66
2876 4188 7.755618 ACCATTGGCCATGTAATATAGTAGTT 58.244 34.615 6.09 0.00 0.00 2.24
2877 4189 7.329746 ACCATTGGCCATGTAATATAGTAGT 57.670 36.000 6.09 0.00 0.00 2.73
2878 4190 8.103305 AGAACCATTGGCCATGTAATATAGTAG 58.897 37.037 6.09 0.00 0.00 2.57
2879 4191 7.984475 AGAACCATTGGCCATGTAATATAGTA 58.016 34.615 6.09 0.00 0.00 1.82
2880 4192 6.852404 AGAACCATTGGCCATGTAATATAGT 58.148 36.000 6.09 0.00 0.00 2.12
2881 4193 6.942005 TGAGAACCATTGGCCATGTAATATAG 59.058 38.462 6.09 0.00 0.00 1.31
2882 4194 6.846988 TGAGAACCATTGGCCATGTAATATA 58.153 36.000 6.09 0.00 0.00 0.86
2883 4195 5.704354 TGAGAACCATTGGCCATGTAATAT 58.296 37.500 6.09 0.00 0.00 1.28
2884 4196 5.122707 TGAGAACCATTGGCCATGTAATA 57.877 39.130 6.09 0.00 0.00 0.98
2885 4197 3.979911 TGAGAACCATTGGCCATGTAAT 58.020 40.909 6.09 0.00 0.00 1.89
2886 4198 3.448093 TGAGAACCATTGGCCATGTAA 57.552 42.857 6.09 0.00 0.00 2.41
2887 4199 3.448093 TTGAGAACCATTGGCCATGTA 57.552 42.857 6.09 0.00 0.00 2.29
2888 4200 2.307496 TTGAGAACCATTGGCCATGT 57.693 45.000 6.09 0.87 0.00 3.21
2889 4201 2.564062 ACTTTGAGAACCATTGGCCATG 59.436 45.455 6.09 7.26 0.00 3.66
2890 4202 2.827921 GACTTTGAGAACCATTGGCCAT 59.172 45.455 6.09 0.00 0.00 4.40
2891 4203 2.238521 GACTTTGAGAACCATTGGCCA 58.761 47.619 0.00 0.00 0.00 5.36
2892 4204 1.200020 CGACTTTGAGAACCATTGGCC 59.800 52.381 1.54 0.00 0.00 5.36
2893 4205 1.200020 CCGACTTTGAGAACCATTGGC 59.800 52.381 1.54 0.00 0.00 4.52
2894 4206 2.226437 CACCGACTTTGAGAACCATTGG 59.774 50.000 0.00 0.00 0.00 3.16
2895 4207 3.138304 TCACCGACTTTGAGAACCATTG 58.862 45.455 0.00 0.00 0.00 2.82
2896 4208 3.485463 TCACCGACTTTGAGAACCATT 57.515 42.857 0.00 0.00 0.00 3.16
2897 4209 3.139077 GTTCACCGACTTTGAGAACCAT 58.861 45.455 0.00 0.00 34.13 3.55
2898 4210 2.169769 AGTTCACCGACTTTGAGAACCA 59.830 45.455 0.00 0.00 39.39 3.67
2899 4211 2.835027 AGTTCACCGACTTTGAGAACC 58.165 47.619 0.00 0.00 39.39 3.62
2900 4212 4.877323 AAAGTTCACCGACTTTGAGAAC 57.123 40.909 2.51 0.00 45.46 3.01
2901 4213 5.890424 AAAAAGTTCACCGACTTTGAGAA 57.110 34.783 4.01 0.00 46.23 2.87
2960 4272 8.675504 TGAACACTTTCAAATGCATGAATTTTT 58.324 25.926 9.08 0.00 38.87 1.94
2961 4273 8.211116 TGAACACTTTCAAATGCATGAATTTT 57.789 26.923 9.08 0.00 38.87 1.82
2962 4274 7.789273 TGAACACTTTCAAATGCATGAATTT 57.211 28.000 5.77 5.77 38.87 1.82
2963 4275 7.658167 TGATGAACACTTTCAAATGCATGAATT 59.342 29.630 0.00 0.00 45.01 2.17
2964 4276 7.156000 TGATGAACACTTTCAAATGCATGAAT 58.844 30.769 0.00 0.00 45.01 2.57
2965 4277 6.514063 TGATGAACACTTTCAAATGCATGAA 58.486 32.000 0.00 0.00 45.01 2.57
2966 4278 6.086785 TGATGAACACTTTCAAATGCATGA 57.913 33.333 0.00 0.00 45.01 3.07
2967 4279 6.422701 AGTTGATGAACACTTTCAAATGCATG 59.577 34.615 0.00 0.00 45.01 4.06
2968 4280 6.518493 AGTTGATGAACACTTTCAAATGCAT 58.482 32.000 0.00 0.00 45.01 3.96
2969 4281 5.904941 AGTTGATGAACACTTTCAAATGCA 58.095 33.333 0.00 0.00 45.01 3.96
2970 4282 6.833342 AAGTTGATGAACACTTTCAAATGC 57.167 33.333 0.00 0.00 45.01 3.56
2971 4283 7.121272 GCAAAGTTGATGAACACTTTCAAATG 58.879 34.615 0.00 0.00 45.01 2.32
2972 4284 6.817641 TGCAAAGTTGATGAACACTTTCAAAT 59.182 30.769 0.00 0.00 45.01 2.32
2973 4285 6.162079 TGCAAAGTTGATGAACACTTTCAAA 58.838 32.000 0.00 0.00 45.01 2.69
2974 4286 5.718146 TGCAAAGTTGATGAACACTTTCAA 58.282 33.333 0.00 0.00 45.01 2.69
2975 4287 5.321959 TGCAAAGTTGATGAACACTTTCA 57.678 34.783 0.00 0.00 45.93 2.69
2976 4288 6.645700 TTTGCAAAGTTGATGAACACTTTC 57.354 33.333 8.05 0.00 34.17 2.62
2977 4289 7.432350 TTTTTGCAAAGTTGATGAACACTTT 57.568 28.000 12.41 0.00 34.17 2.66
3053 4365 8.542132 CGAACATTTTTCAAATTGATGAACTGT 58.458 29.630 0.00 3.63 38.95 3.55
3054 4366 8.754096 TCGAACATTTTTCAAATTGATGAACTG 58.246 29.630 0.00 3.05 38.95 3.16
3055 4367 8.870160 TCGAACATTTTTCAAATTGATGAACT 57.130 26.923 0.00 0.00 38.95 3.01
3056 4368 8.216453 CCTCGAACATTTTTCAAATTGATGAAC 58.784 33.333 0.00 0.00 38.95 3.18
3057 4369 7.925483 ACCTCGAACATTTTTCAAATTGATGAA 59.075 29.630 0.00 0.00 37.53 2.57
3058 4370 7.381948 CACCTCGAACATTTTTCAAATTGATGA 59.618 33.333 0.00 0.00 0.00 2.92
3059 4371 7.381948 TCACCTCGAACATTTTTCAAATTGATG 59.618 33.333 0.00 0.00 0.00 3.07
3060 4372 7.382218 GTCACCTCGAACATTTTTCAAATTGAT 59.618 33.333 0.00 0.00 0.00 2.57
3061 4373 6.695278 GTCACCTCGAACATTTTTCAAATTGA 59.305 34.615 0.00 0.00 0.00 2.57
3062 4374 6.697019 AGTCACCTCGAACATTTTTCAAATTG 59.303 34.615 0.00 0.00 0.00 2.32
3063 4375 6.805713 AGTCACCTCGAACATTTTTCAAATT 58.194 32.000 0.00 0.00 0.00 1.82
3064 4376 6.391227 AGTCACCTCGAACATTTTTCAAAT 57.609 33.333 0.00 0.00 0.00 2.32
3065 4377 5.828299 AGTCACCTCGAACATTTTTCAAA 57.172 34.783 0.00 0.00 0.00 2.69
3066 4378 5.449862 CCAAGTCACCTCGAACATTTTTCAA 60.450 40.000 0.00 0.00 0.00 2.69
3067 4379 4.036262 CCAAGTCACCTCGAACATTTTTCA 59.964 41.667 0.00 0.00 0.00 2.69
3068 4380 4.537015 CCAAGTCACCTCGAACATTTTTC 58.463 43.478 0.00 0.00 0.00 2.29
3069 4381 3.243401 GCCAAGTCACCTCGAACATTTTT 60.243 43.478 0.00 0.00 0.00 1.94
3070 4382 2.293399 GCCAAGTCACCTCGAACATTTT 59.707 45.455 0.00 0.00 0.00 1.82
3071 4383 1.880027 GCCAAGTCACCTCGAACATTT 59.120 47.619 0.00 0.00 0.00 2.32
3072 4384 1.523758 GCCAAGTCACCTCGAACATT 58.476 50.000 0.00 0.00 0.00 2.71
3073 4385 0.321653 GGCCAAGTCACCTCGAACAT 60.322 55.000 0.00 0.00 0.00 2.71
3074 4386 1.070786 GGCCAAGTCACCTCGAACA 59.929 57.895 0.00 0.00 0.00 3.18
3075 4387 3.967715 GGCCAAGTCACCTCGAAC 58.032 61.111 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.