Multiple sequence alignment - TraesCS1D01G276800

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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 TraesCS1D01G276800 chr1D 100.000 4310 0 0 1 4310 373417139 373421448 0.000000e+00 7960.0
1 TraesCS1D01G276800 chr1D 86.523 512 50 8 34 542 488614013 488613518 2.930000e-151 545.0
2 TraesCS1D01G276800 chr1D 84.081 446 36 15 503 917 488613493 488613052 8.680000e-107 398.0
3 TraesCS1D01G276800 chr1B 93.305 1912 89 21 960 2848 498683044 498684939 0.000000e+00 2785.0
4 TraesCS1D01G276800 chr1B 94.176 704 32 7 2690 3392 498684937 498685632 0.000000e+00 1064.0
5 TraesCS1D01G276800 chr1B 85.155 485 66 6 38 520 681050651 681051131 3.870000e-135 492.0
6 TraesCS1D01G276800 chr1B 86.323 446 37 9 3868 4310 498687362 498687786 8.440000e-127 464.0
7 TraesCS1D01G276800 chr1B 86.547 223 26 2 696 914 681052949 681053171 4.310000e-60 243.0
8 TraesCS1D01G276800 chr1B 82.609 276 37 8 3395 3669 578098797 578099062 2.590000e-57 233.0
9 TraesCS1D01G276800 chr1A 92.159 1760 75 23 920 2664 473032224 473033935 0.000000e+00 2427.0
10 TraesCS1D01G276800 chr1A 93.911 739 30 8 2660 3392 473034014 473034743 0.000000e+00 1101.0
11 TraesCS1D01G276800 chr1A 86.408 515 64 6 31 542 587862737 587862226 3.760000e-155 558.0
12 TraesCS1D01G276800 chr1A 81.629 626 39 20 3691 4310 473035049 473035604 2.360000e-122 449.0
13 TraesCS1D01G276800 chr1A 82.742 423 40 18 521 911 587862183 587861762 3.190000e-91 346.0
14 TraesCS1D01G276800 chr1A 85.348 273 28 6 3400 3669 434422677 434422940 5.490000e-69 272.0
15 TraesCS1D01G276800 chr1A 78.797 349 39 13 596 916 499767206 499767547 7.310000e-48 202.0
16 TraesCS1D01G276800 chr7D 85.048 943 80 23 42 923 625766989 625766047 0.000000e+00 904.0
17 TraesCS1D01G276800 chr7D 90.196 102 8 2 2476 2577 193409845 193409944 9.730000e-27 132.0
18 TraesCS1D01G276800 chr2B 87.550 498 56 5 42 538 207118394 207117902 4.840000e-159 571.0
19 TraesCS1D01G276800 chr2B 81.567 434 43 14 520 919 53906442 53906012 1.490000e-84 324.0
20 TraesCS1D01G276800 chr2B 78.235 170 20 14 48 208 744111095 744111256 4.590000e-15 93.5
21 TraesCS1D01G276800 chr6B 86.853 502 45 7 48 538 366739620 366739129 3.790000e-150 542.0
22 TraesCS1D01G276800 chr6B 84.499 529 45 13 42 538 660703474 660703997 5.010000e-134 488.0
23 TraesCS1D01G276800 chr6B 85.480 427 48 7 502 914 660704025 660704451 2.380000e-117 433.0
24 TraesCS1D01G276800 chr6B 79.123 479 47 18 502 928 366739133 366738656 9.130000e-72 281.0
25 TraesCS1D01G276800 chr6B 91.176 102 7 2 2476 2577 530560462 530560363 2.090000e-28 137.0
26 TraesCS1D01G276800 chr6B 79.137 139 23 4 566 701 449841882 449841747 1.650000e-14 91.6
27 TraesCS1D01G276800 chr6D 83.837 563 60 17 397 928 239809529 239808967 1.380000e-139 507.0
28 TraesCS1D01G276800 chr6D 87.055 309 30 6 48 350 240026133 240025829 1.480000e-89 340.0
29 TraesCS1D01G276800 chr6D 83.099 284 39 4 3398 3679 446549552 446549276 2.570000e-62 250.0
30 TraesCS1D01G276800 chr6D 89.216 102 9 2 2476 2577 349927674 349927773 4.520000e-25 126.0
31 TraesCS1D01G276800 chr4A 83.804 531 43 13 136 652 693523552 693523051 8.440000e-127 464.0
32 TraesCS1D01G276800 chr4D 84.988 433 47 10 502 916 52491536 52491968 1.430000e-114 424.0
33 TraesCS1D01G276800 chr4D 87.989 358 35 4 184 538 52491188 52491540 2.400000e-112 416.0
34 TraesCS1D01G276800 chr3B 85.455 275 25 7 3399 3670 457573980 457574242 5.490000e-69 272.0
35 TraesCS1D01G276800 chr3B 85.185 270 28 7 3400 3669 97755886 97756143 2.560000e-67 267.0
36 TraesCS1D01G276800 chr3B 80.702 228 35 9 42 265 757935794 757936016 7.410000e-38 169.0
37 TraesCS1D01G276800 chr3A 84.615 273 30 8 3399 3670 475281058 475281319 1.190000e-65 261.0
38 TraesCS1D01G276800 chr2D 83.453 278 37 7 3394 3670 28912772 28913041 2.570000e-62 250.0
39 TraesCS1D01G276800 chr2D 89.320 103 9 2 2476 2578 566989099 566988999 1.260000e-25 128.0
40 TraesCS1D01G276800 chr5D 83.212 274 32 6 3400 3669 351395552 351395815 5.570000e-59 239.0
41 TraesCS1D01G276800 chr3D 83.088 272 33 7 3397 3668 54393207 54393465 7.210000e-58 235.0
42 TraesCS1D01G276800 chr3D 90.196 102 8 2 2476 2576 352795499 352795399 9.730000e-27 132.0
43 TraesCS1D01G276800 chr7A 79.037 353 41 15 596 920 516480746 516480399 1.210000e-50 211.0
44 TraesCS1D01G276800 chr7A 90.816 98 8 1 2476 2573 202994981 202995077 3.500000e-26 130.0


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 TraesCS1D01G276800 chr1D 373417139 373421448 4309 False 7960.000000 7960 100.0000 1 4310 1 chr1D.!!$F1 4309
1 TraesCS1D01G276800 chr1D 488613052 488614013 961 True 471.500000 545 85.3020 34 917 2 chr1D.!!$R1 883
2 TraesCS1D01G276800 chr1B 498683044 498687786 4742 False 1437.666667 2785 91.2680 960 4310 3 chr1B.!!$F2 3350
3 TraesCS1D01G276800 chr1B 681050651 681053171 2520 False 367.500000 492 85.8510 38 914 2 chr1B.!!$F3 876
4 TraesCS1D01G276800 chr1A 473032224 473035604 3380 False 1325.666667 2427 89.2330 920 4310 3 chr1A.!!$F3 3390
5 TraesCS1D01G276800 chr1A 587861762 587862737 975 True 452.000000 558 84.5750 31 911 2 chr1A.!!$R1 880
6 TraesCS1D01G276800 chr7D 625766047 625766989 942 True 904.000000 904 85.0480 42 923 1 chr7D.!!$R1 881
7 TraesCS1D01G276800 chr6B 660703474 660704451 977 False 460.500000 488 84.9895 42 914 2 chr6B.!!$F1 872
8 TraesCS1D01G276800 chr6B 366738656 366739620 964 True 411.500000 542 82.9880 48 928 2 chr6B.!!$R3 880
9 TraesCS1D01G276800 chr6D 239808967 239809529 562 True 507.000000 507 83.8370 397 928 1 chr6D.!!$R1 531
10 TraesCS1D01G276800 chr4A 693523051 693523552 501 True 464.000000 464 83.8040 136 652 1 chr4A.!!$R1 516
11 TraesCS1D01G276800 chr4D 52491188 52491968 780 False 420.000000 424 86.4885 184 916 2 chr4D.!!$F1 732

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
652 1140 0.028110 CAGATCGCATCGTCTCGTCA 59.972 55.0 0.00 0.00 0.00 4.35 F
1014 2816 0.102120 TTGGACTTGCTGCAAAACGG 59.898 50.0 16.74 7.15 0.00 4.44 F
1185 3002 0.179012 CTCTCGTACCCCTCCCTCTC 60.179 65.0 0.00 0.00 0.00 3.20 F
2090 3929 0.764890 TGGCTGTTTCCTGCTACAGT 59.235 50.0 0.00 0.00 42.86 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 3953 0.457853 GTGTCGTTCTCGGCTGCATA 60.458 55.000 0.50 0.00 42.59 3.14 R
2365 4204 1.200948 GAGAAAAGCATCCACCACAGC 59.799 52.381 0.00 0.00 0.00 4.40 R
2442 4285 1.967319 TGGCTGAAGTTCAGGTGTTC 58.033 50.000 29.45 15.01 44.43 3.18 R
3907 7558 0.103208 CGGAAGCTCGAGGCAATAGT 59.897 55.000 15.58 0.00 44.79 2.12 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
129 130 8.773404 ATTTAACACAATCTAGTCGCTAAACT 57.227 30.769 0.00 0.00 0.00 2.66
130 131 7.576750 TTAACACAATCTAGTCGCTAAACTG 57.423 36.000 0.00 0.00 0.00 3.16
132 133 4.021368 ACACAATCTAGTCGCTAAACTGGT 60.021 41.667 0.00 0.00 0.00 4.00
134 135 4.929808 ACAATCTAGTCGCTAAACTGGTTG 59.070 41.667 0.00 0.00 31.56 3.77
139 140 3.131396 AGTCGCTAAACTGGTTGTTCTG 58.869 45.455 0.00 0.00 38.03 3.02
325 382 2.926838 TCTTTCTTTTTGCAACAACGGC 59.073 40.909 0.00 0.00 0.00 5.68
424 483 3.973516 TCGTTGCCTGCGTCGAGT 61.974 61.111 0.00 0.00 0.00 4.18
472 531 1.971695 GCACCACTACCCCTGTTGC 60.972 63.158 0.00 0.00 0.00 4.17
499 562 2.283966 ACGCAGCTACAGGGGAGT 60.284 61.111 0.00 0.00 0.00 3.85
514 925 2.969806 GAGTACACCACCGCGACGA 61.970 63.158 8.23 0.00 0.00 4.20
563 1039 0.818040 CCCTCCCTTAATTTCGCCCG 60.818 60.000 0.00 0.00 0.00 6.13
564 1040 0.818040 CCTCCCTTAATTTCGCCCGG 60.818 60.000 0.00 0.00 0.00 5.73
565 1041 0.179468 CTCCCTTAATTTCGCCCGGA 59.821 55.000 0.73 0.00 0.00 5.14
566 1042 0.619505 TCCCTTAATTTCGCCCGGAA 59.380 50.000 0.73 0.00 0.00 4.30
567 1043 1.213430 TCCCTTAATTTCGCCCGGAAT 59.787 47.619 0.73 0.00 33.85 3.01
652 1140 0.028110 CAGATCGCATCGTCTCGTCA 59.972 55.000 0.00 0.00 0.00 4.35
702 2500 4.263572 CCGTTGACCACCCAGCCA 62.264 66.667 0.00 0.00 0.00 4.75
710 2508 4.562425 CACCCAGCCACACCGTGT 62.562 66.667 0.00 0.00 0.00 4.49
726 2524 4.070552 GTTCCGCCTCTCCGCTGT 62.071 66.667 0.00 0.00 0.00 4.40
789 2590 2.796304 CAAGCGTTTCTGAAACAGCAA 58.204 42.857 31.31 3.72 41.44 3.91
980 2782 6.216569 GCATATTTGAAGATACCGACTCTGA 58.783 40.000 0.00 0.00 0.00 3.27
1011 2813 0.463620 GGGTTGGACTTGCTGCAAAA 59.536 50.000 16.74 4.84 30.97 2.44
1012 2814 1.570813 GGTTGGACTTGCTGCAAAAC 58.429 50.000 16.74 16.13 30.97 2.43
1014 2816 0.102120 TTGGACTTGCTGCAAAACGG 59.898 50.000 16.74 7.15 0.00 4.44
1021 2823 3.297620 CTGCAAAACGGCTGCCCT 61.298 61.111 14.12 0.00 39.13 5.19
1022 2824 3.273080 CTGCAAAACGGCTGCCCTC 62.273 63.158 14.12 0.00 39.13 4.30
1086 2888 2.190841 AACACAACTTTCCGCCCCG 61.191 57.895 0.00 0.00 0.00 5.73
1161 2963 1.065851 GGCAGCTCGAAGGTAGAGTAC 59.934 57.143 0.00 0.00 37.99 2.73
1171 2988 4.505191 CGAAGGTAGAGTACTCTTCTCTCG 59.495 50.000 29.57 26.28 41.66 4.04
1173 2990 6.543430 AAGGTAGAGTACTCTTCTCTCGTA 57.457 41.667 29.57 7.17 41.66 3.43
1174 2991 5.906073 AGGTAGAGTACTCTTCTCTCGTAC 58.094 45.833 29.57 18.10 41.66 3.67
1175 2992 5.049828 GGTAGAGTACTCTTCTCTCGTACC 58.950 50.000 29.57 22.56 41.66 3.34
1176 2993 4.141233 AGAGTACTCTTCTCTCGTACCC 57.859 50.000 20.00 0.00 37.70 3.69
1177 2994 3.118298 AGAGTACTCTTCTCTCGTACCCC 60.118 52.174 20.00 0.00 37.70 4.95
1178 2995 2.845586 AGTACTCTTCTCTCGTACCCCT 59.154 50.000 0.00 0.00 35.33 4.79
1179 2996 2.423446 ACTCTTCTCTCGTACCCCTC 57.577 55.000 0.00 0.00 0.00 4.30
1180 2997 1.064537 ACTCTTCTCTCGTACCCCTCC 60.065 57.143 0.00 0.00 0.00 4.30
1181 2998 0.258194 TCTTCTCTCGTACCCCTCCC 59.742 60.000 0.00 0.00 0.00 4.30
1182 2999 0.259356 CTTCTCTCGTACCCCTCCCT 59.741 60.000 0.00 0.00 0.00 4.20
1183 3000 0.258194 TTCTCTCGTACCCCTCCCTC 59.742 60.000 0.00 0.00 0.00 4.30
1184 3001 0.623911 TCTCTCGTACCCCTCCCTCT 60.624 60.000 0.00 0.00 0.00 3.69
1185 3002 0.179012 CTCTCGTACCCCTCCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
1186 3003 1.152715 CTCGTACCCCTCCCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
1187 3004 1.932231 TCGTACCCCTCCCTCTCCA 60.932 63.158 0.00 0.00 0.00 3.86
1326 3143 3.491104 CGAGAAATTTCCTCTAGGACGGG 60.491 52.174 14.61 0.00 45.39 5.28
1340 3157 2.738521 CGGGTGCTCCAGTTCGTG 60.739 66.667 7.20 0.00 34.36 4.35
1425 3245 8.674607 AGTTTCGAAGAACAAAATTCTTACTGT 58.325 29.630 0.00 0.00 45.90 3.55
1542 3362 0.811281 GATAAGTGGCCAGGTGTTGC 59.189 55.000 5.11 0.00 0.00 4.17
1601 3421 7.756395 TTCGTCGGAGAAATTATCCTACTAT 57.244 36.000 9.18 0.00 39.69 2.12
1602 3422 8.853077 TTCGTCGGAGAAATTATCCTACTATA 57.147 34.615 9.18 0.00 39.69 1.31
1603 3423 9.458727 TTCGTCGGAGAAATTATCCTACTATAT 57.541 33.333 9.18 0.00 39.69 0.86
1712 3535 1.340017 GGCACTGTCATACATGGGTGT 60.340 52.381 0.00 0.00 42.39 4.16
1724 3547 9.424319 GTCATACATGGGTGTCTTGTATAATAG 57.576 37.037 0.00 0.00 41.73 1.73
1813 3644 4.846137 GCTATTTCTTTATTATGCACGGCG 59.154 41.667 4.80 4.80 0.00 6.46
1902 3741 5.706916 TCTCACAGGTTCGTGTTCTAATAC 58.293 41.667 0.00 0.00 38.12 1.89
2090 3929 0.764890 TGGCTGTTTCCTGCTACAGT 59.235 50.000 0.00 0.00 42.86 3.55
2104 3943 6.264744 TCCTGCTACAGTATGGTAGTAATGTC 59.735 42.308 0.00 0.00 43.62 3.06
2107 3946 8.700439 TGCTACAGTATGGTAGTAATGTCATA 57.300 34.615 0.00 0.00 43.62 2.15
2131 3970 1.355971 TTTATGCAGCCGAGAACGAC 58.644 50.000 0.00 0.00 42.66 4.34
2318 4157 2.487746 ATGGAAAAAGGTTGGTGGGT 57.512 45.000 0.00 0.00 0.00 4.51
2348 4187 9.787435 ATCATTTTAGGCATGCATTATTTTGAT 57.213 25.926 21.36 15.02 0.00 2.57
2354 4193 6.046593 AGGCATGCATTATTTTGATCTTGTG 58.953 36.000 21.36 0.00 0.00 3.33
2407 4246 3.278574 CAGTTTGTTGTCTCTTGGGACA 58.721 45.455 0.00 0.00 43.41 4.02
2442 4285 6.992063 ATGTTCCAGTTTTGCTAGAGTATG 57.008 37.500 0.00 0.00 0.00 2.39
2468 4311 2.290514 CCTGAACTTCAGCCATCCTCAA 60.291 50.000 12.69 0.00 42.98 3.02
2488 4333 6.014156 CCTCAAGAAATATACTCCCTCCGATT 60.014 42.308 0.00 0.00 0.00 3.34
2563 4408 7.553881 AACCTTTGACAAGTAATATGGATCG 57.446 36.000 0.00 0.00 0.00 3.69
2564 4409 6.650120 ACCTTTGACAAGTAATATGGATCGT 58.350 36.000 0.00 0.00 0.00 3.73
2734 4818 1.267806 CTGACCTGTGCAATTGGACAC 59.732 52.381 26.64 18.10 41.48 3.67
2804 4888 8.027771 AGTGTGCTGTTGTAACTACTAGTATTC 58.972 37.037 2.33 0.00 0.00 1.75
2814 4898 7.765819 TGTAACTACTAGTATTCGCTACAGACA 59.234 37.037 2.33 0.00 32.34 3.41
2888 4972 5.355910 TCACCAGAGTTTACCAAGTTTCAAC 59.644 40.000 0.00 0.00 0.00 3.18
2939 5023 9.211485 CTTCAATTGCCTTAATTCAACATTCTT 57.789 29.630 0.00 0.00 36.87 2.52
3096 5181 3.385577 GGAAGAGACGGTGATAGAATGC 58.614 50.000 0.00 0.00 0.00 3.56
3140 5225 1.741401 CCAGCGGCGATTGAAGTCA 60.741 57.895 12.98 0.00 0.00 3.41
3158 5243 4.957296 AGTCACCACTCGTTGTTAAGAAT 58.043 39.130 0.00 0.00 0.00 2.40
3159 5244 6.092955 AGTCACCACTCGTTGTTAAGAATA 57.907 37.500 0.00 0.00 0.00 1.75
3160 5245 6.518493 AGTCACCACTCGTTGTTAAGAATAA 58.482 36.000 0.00 0.00 0.00 1.40
3193 5278 3.515630 TGATTGTTCGAGATGCTCTGTC 58.484 45.455 0.00 0.00 0.00 3.51
3205 5294 1.133482 TGCTCTGTCCGATCCCTGATA 60.133 52.381 0.00 0.00 0.00 2.15
3239 5328 6.032956 AGTAACGTACAATCAGGTGATTCA 57.967 37.500 2.07 0.00 42.41 2.57
3268 5357 2.613730 TCACTGTAAACTCTCGAGCG 57.386 50.000 7.81 3.64 0.00 5.03
3331 5422 4.038282 TGGAAGTTGACTACTGTTTCGCTA 59.962 41.667 0.00 0.00 37.12 4.26
3398 5652 8.656849 CAGTAGTATTGTTGTGCCTTAACTTAG 58.343 37.037 0.00 0.00 0.00 2.18
3407 5661 4.222145 TGTGCCTTAACTTAGTACTCCCTG 59.778 45.833 0.00 0.00 0.00 4.45
3408 5662 4.222366 GTGCCTTAACTTAGTACTCCCTGT 59.778 45.833 0.00 0.00 0.00 4.00
3410 5664 4.222366 GCCTTAACTTAGTACTCCCTGTGT 59.778 45.833 0.00 0.00 0.00 3.72
3411 5665 5.279859 GCCTTAACTTAGTACTCCCTGTGTT 60.280 44.000 0.00 0.00 0.00 3.32
3414 5668 3.853207 ACTTAGTACTCCCTGTGTTCCA 58.147 45.455 0.00 0.00 0.00 3.53
3415 5669 4.426704 ACTTAGTACTCCCTGTGTTCCAT 58.573 43.478 0.00 0.00 0.00 3.41
3417 5671 6.021030 ACTTAGTACTCCCTGTGTTCCATAA 58.979 40.000 0.00 0.00 0.00 1.90
3419 5673 5.359194 AGTACTCCCTGTGTTCCATAATG 57.641 43.478 0.00 0.00 0.00 1.90
3421 5675 5.962031 AGTACTCCCTGTGTTCCATAATGTA 59.038 40.000 0.00 0.00 0.00 2.29
3422 5676 5.359194 ACTCCCTGTGTTCCATAATGTAG 57.641 43.478 0.00 0.00 0.00 2.74
3423 5677 4.783227 ACTCCCTGTGTTCCATAATGTAGT 59.217 41.667 0.00 0.00 0.00 2.73
3424 5678 5.097742 TCCCTGTGTTCCATAATGTAGTG 57.902 43.478 0.00 0.00 0.00 2.74
3426 5680 4.260985 CCTGTGTTCCATAATGTAGTGCA 58.739 43.478 0.00 0.00 0.00 4.57
3429 5683 6.712095 CCTGTGTTCCATAATGTAGTGCATAT 59.288 38.462 0.00 0.00 36.67 1.78
3431 5685 8.831715 TGTGTTCCATAATGTAGTGCATATAG 57.168 34.615 0.00 0.00 36.67 1.31
3432 5686 8.646900 TGTGTTCCATAATGTAGTGCATATAGA 58.353 33.333 0.00 0.00 36.67 1.98
3433 5687 9.658799 GTGTTCCATAATGTAGTGCATATAGAT 57.341 33.333 0.00 0.00 36.67 1.98
3447 5701 8.946085 AGTGCATATAGATTTTTCGAAAAGTCA 58.054 29.630 33.78 24.23 37.17 3.41
3459 5713 9.659830 TTTTTCGAAAAGTCATAGCTTAGAAAC 57.340 29.630 21.53 0.00 32.20 2.78
3460 5714 8.603242 TTTCGAAAAGTCATAGCTTAGAAACT 57.397 30.769 8.44 0.00 29.97 2.66
3465 5719 9.600646 GAAAAGTCATAGCTTAGAAACTTTGAC 57.399 33.333 0.00 7.69 42.00 3.18
3466 5720 7.674471 AAGTCATAGCTTAGAAACTTTGACC 57.326 36.000 10.66 0.00 42.39 4.02
3467 5721 6.769512 AGTCATAGCTTAGAAACTTTGACCA 58.230 36.000 10.66 0.00 42.39 4.02
3469 5723 7.389053 AGTCATAGCTTAGAAACTTTGACCAAG 59.611 37.037 10.66 0.00 42.39 3.61
3506 5760 9.558396 AAAAACATTTTCATCTAGAATGCCAAA 57.442 25.926 0.00 0.45 35.83 3.28
3507 5761 8.538409 AAACATTTTCATCTAGAATGCCAAAC 57.462 30.769 0.00 0.00 35.83 2.93
3508 5762 7.230849 ACATTTTCATCTAGAATGCCAAACA 57.769 32.000 0.00 0.00 35.83 2.83
3509 5763 7.844009 ACATTTTCATCTAGAATGCCAAACAT 58.156 30.769 0.00 0.00 42.30 2.71
3510 5764 8.970020 ACATTTTCATCTAGAATGCCAAACATA 58.030 29.630 0.00 0.00 38.34 2.29
3511 5765 9.976511 CATTTTCATCTAGAATGCCAAACATAT 57.023 29.630 0.00 0.00 38.34 1.78
3605 5859 9.512588 AGTTTTCTCTATGAACTTGATCAATGT 57.487 29.630 8.96 6.66 33.88 2.71
3609 5863 8.599055 TCTCTATGAACTTGATCAATGTATGC 57.401 34.615 8.96 4.24 32.06 3.14
3610 5864 8.206189 TCTCTATGAACTTGATCAATGTATGCA 58.794 33.333 8.96 8.87 32.06 3.96
3611 5865 8.735692 TCTATGAACTTGATCAATGTATGCAA 57.264 30.769 8.96 0.00 32.06 4.08
3612 5866 9.176460 TCTATGAACTTGATCAATGTATGCAAA 57.824 29.630 8.96 0.00 32.06 3.68
3613 5867 9.447040 CTATGAACTTGATCAATGTATGCAAAG 57.553 33.333 8.96 0.00 32.06 2.77
3614 5868 7.218228 TGAACTTGATCAATGTATGCAAAGT 57.782 32.000 8.96 0.00 31.29 2.66
3615 5869 7.660112 TGAACTTGATCAATGTATGCAAAGTT 58.340 30.769 8.96 5.23 37.86 2.66
3616 5870 8.143193 TGAACTTGATCAATGTATGCAAAGTTT 58.857 29.630 8.96 0.00 36.57 2.66
3617 5871 7.878477 ACTTGATCAATGTATGCAAAGTTTG 57.122 32.000 8.96 11.41 0.00 2.93
3618 5872 7.660112 ACTTGATCAATGTATGCAAAGTTTGA 58.340 30.769 19.82 5.11 0.00 2.69
3619 5873 7.596248 ACTTGATCAATGTATGCAAAGTTTGAC 59.404 33.333 19.82 9.14 0.00 3.18
3620 5874 7.218228 TGATCAATGTATGCAAAGTTTGACT 57.782 32.000 19.82 7.59 0.00 3.41
3621 5875 7.660112 TGATCAATGTATGCAAAGTTTGACTT 58.340 30.769 19.82 10.69 40.80 3.01
3623 5877 8.891671 ATCAATGTATGCAAAGTTTGACTTTT 57.108 26.923 19.82 4.79 45.38 2.27
3624 5878 8.351495 TCAATGTATGCAAAGTTTGACTTTTC 57.649 30.769 19.82 0.92 45.38 2.29
3625 5879 7.978414 TCAATGTATGCAAAGTTTGACTTTTCA 59.022 29.630 19.82 6.78 45.38 2.69
3626 5880 8.602328 CAATGTATGCAAAGTTTGACTTTTCAA 58.398 29.630 19.82 0.00 45.38 2.69
3627 5881 8.715191 ATGTATGCAAAGTTTGACTTTTCAAA 57.285 26.923 19.82 0.00 45.38 2.69
3671 5925 3.614568 ATGGAACGGAGGGAGTATACT 57.385 47.619 4.68 4.68 0.00 2.12
3679 5933 3.952323 CGGAGGGAGTATACTTCAAGACA 59.048 47.826 13.33 0.00 0.00 3.41
3731 5991 6.211184 TGATTTTAAGTTACGGAGGGAGTACA 59.789 38.462 0.00 0.00 0.00 2.90
3732 5992 5.649782 TTTAAGTTACGGAGGGAGTACAG 57.350 43.478 0.00 0.00 0.00 2.74
3733 5993 2.895242 AGTTACGGAGGGAGTACAGT 57.105 50.000 0.00 0.00 0.00 3.55
3734 5994 4.307032 AAGTTACGGAGGGAGTACAGTA 57.693 45.455 0.00 0.00 0.00 2.74
3735 5995 3.615155 AGTTACGGAGGGAGTACAGTAC 58.385 50.000 2.05 2.05 0.00 2.73
3754 6014 7.339732 CAGTACTACTGTAGAAGCACTTTTG 57.660 40.000 21.01 5.00 41.19 2.44
3755 6015 7.145985 CAGTACTACTGTAGAAGCACTTTTGA 58.854 38.462 21.01 0.00 41.19 2.69
3756 6016 7.652105 CAGTACTACTGTAGAAGCACTTTTGAA 59.348 37.037 21.01 0.00 41.19 2.69
3757 6017 8.368668 AGTACTACTGTAGAAGCACTTTTGAAT 58.631 33.333 21.01 0.00 0.00 2.57
3785 6045 1.476891 ACTGGTGTAGTATCAGGTGCG 59.523 52.381 0.00 0.00 42.07 5.34
3799 6059 0.457681 GGTGCGTGTTTTGCTGTGTT 60.458 50.000 0.00 0.00 0.00 3.32
3841 6102 2.284995 AGGAGCCCCTGGTGACTC 60.285 66.667 0.00 0.00 42.42 3.36
3842 6103 2.284995 GGAGCCCCTGGTGACTCT 60.285 66.667 7.51 0.00 0.00 3.24
3843 6104 1.001760 GGAGCCCCTGGTGACTCTA 59.998 63.158 7.51 0.00 0.00 2.43
3845 6106 1.306226 AGCCCCTGGTGACTCTACC 60.306 63.158 0.00 0.00 41.24 3.18
3848 6109 0.688087 CCCCTGGTGACTCTACCTCC 60.688 65.000 0.00 0.00 41.43 4.30
3849 6110 1.038130 CCCTGGTGACTCTACCTCCG 61.038 65.000 0.00 0.00 41.43 4.63
3850 6111 0.034380 CCTGGTGACTCTACCTCCGA 60.034 60.000 0.00 0.00 41.43 4.55
3851 6112 1.384525 CTGGTGACTCTACCTCCGAG 58.615 60.000 0.00 0.00 41.43 4.63
3938 7589 3.107017 GCTTCCGTTTTGTGGATGC 57.893 52.632 4.44 4.44 45.63 3.91
3959 7611 2.557056 CCGAGTGAGTTGACCTTGACTA 59.443 50.000 0.00 0.00 0.00 2.59
3960 7612 3.366476 CCGAGTGAGTTGACCTTGACTAG 60.366 52.174 0.00 0.00 0.00 2.57
3980 7632 0.382515 GAACTGGGACTCTCGATCCG 59.617 60.000 0.00 0.00 37.08 4.18
3982 7634 2.044352 TGGGACTCTCGATCCGCA 60.044 61.111 0.00 0.00 37.08 5.69
3989 7641 1.546476 ACTCTCGATCCGCAGAAAACT 59.454 47.619 0.00 0.00 0.00 2.66
3995 7647 0.736325 ATCCGCAGAAAACTCGTCCG 60.736 55.000 0.00 0.00 0.00 4.79
4139 7821 3.244105 GTGCGGCACACTGTACTG 58.756 61.111 27.10 0.00 46.41 2.74
4140 7822 2.664851 TGCGGCACACTGTACTGC 60.665 61.111 6.29 6.29 32.30 4.40
4143 7825 2.030562 GGCACACTGTACTGCCGT 59.969 61.111 7.99 0.00 43.56 5.68
4144 7826 1.290955 GGCACACTGTACTGCCGTA 59.709 57.895 7.99 0.00 43.56 4.02
4145 7827 1.012486 GGCACACTGTACTGCCGTAC 61.012 60.000 11.15 11.15 43.56 3.67
4177 7859 3.128068 GTGTAAATTCCCGGGCTTGTAAG 59.872 47.826 18.49 0.00 0.00 2.34
4203 7885 2.572149 TACGCAGGTACGGTGCCAA 61.572 57.895 17.72 0.00 37.60 4.52
4204 7886 2.768503 TACGCAGGTACGGTGCCAAC 62.769 60.000 17.72 7.65 37.60 3.77
4251 7933 3.285215 GCATGGCTGCCTGGATCG 61.285 66.667 21.03 2.95 42.88 3.69
4284 7966 2.919494 CGGGCTGAAGCACCAAACC 61.919 63.158 4.43 0.00 42.67 3.27
4286 7968 1.662044 GGCTGAAGCACCAAACCTG 59.338 57.895 4.43 0.00 44.36 4.00
4302 7984 1.290955 CTGGGGTAGCGAACGAACA 59.709 57.895 0.00 0.00 0.00 3.18
4305 7987 1.291272 GGGTAGCGAACGAACAGGT 59.709 57.895 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.149987 CGTAGCAGCACCCGTAAAAA 58.850 50.000 0.00 0.00 0.00 1.94
35 36 0.033781 ACGTAGCAGCACCCGTAAAA 59.966 50.000 0.00 0.00 0.00 1.52
36 37 0.668096 CACGTAGCAGCACCCGTAAA 60.668 55.000 0.00 0.00 31.42 2.01
37 38 1.080366 CACGTAGCAGCACCCGTAA 60.080 57.895 0.00 0.00 31.42 3.18
38 39 2.203972 GACACGTAGCAGCACCCGTA 62.204 60.000 0.00 0.00 31.42 4.02
39 40 3.569049 GACACGTAGCAGCACCCGT 62.569 63.158 0.00 0.00 0.00 5.28
40 41 2.809601 GACACGTAGCAGCACCCG 60.810 66.667 0.00 0.00 0.00 5.28
41 42 2.809601 CGACACGTAGCAGCACCC 60.810 66.667 0.00 0.00 0.00 4.61
44 45 4.735132 GGCCGACACGTAGCAGCA 62.735 66.667 0.00 0.00 0.00 4.41
139 140 4.257267 ACAAGGTCTTTATTGCAAAGGC 57.743 40.909 1.71 0.00 41.68 4.35
325 382 4.797868 TGCAAAACTTCTTTCACAACATCG 59.202 37.500 0.00 0.00 0.00 3.84
450 509 1.497161 ACAGGGGTAGTGGTGCTATC 58.503 55.000 0.00 0.00 31.50 2.08
451 510 1.559682 CAACAGGGGTAGTGGTGCTAT 59.440 52.381 0.00 0.00 31.50 2.97
462 521 1.228367 CTTCTGCAGCAACAGGGGT 60.228 57.895 9.47 0.00 38.26 4.95
486 549 0.412244 TGGTGTACTCCCCTGTAGCT 59.588 55.000 11.36 0.00 0.00 3.32
499 562 3.740397 CCTCGTCGCGGTGGTGTA 61.740 66.667 6.13 0.00 0.00 2.90
563 1039 2.110578 CCACAGATTTTCCCCCATTCC 58.889 52.381 0.00 0.00 0.00 3.01
564 1040 3.100207 TCCACAGATTTTCCCCCATTC 57.900 47.619 0.00 0.00 0.00 2.67
565 1041 3.273084 AGATCCACAGATTTTCCCCCATT 59.727 43.478 0.00 0.00 30.90 3.16
566 1042 2.861317 AGATCCACAGATTTTCCCCCAT 59.139 45.455 0.00 0.00 30.90 4.00
567 1043 2.287584 AGATCCACAGATTTTCCCCCA 58.712 47.619 0.00 0.00 30.90 4.96
702 2500 3.222354 GAGAGGCGGAACACGGTGT 62.222 63.158 8.21 8.21 44.51 4.16
710 2508 3.311110 AACAGCGGAGAGGCGGAA 61.311 61.111 0.00 0.00 38.18 4.30
726 2524 2.027192 GCTCTGTGGTGGTTAGATCCAA 60.027 50.000 0.00 0.00 39.34 3.53
789 2590 1.370437 CACAGGTCTGCAGCTCAGT 59.630 57.895 9.47 3.61 43.32 3.41
879 2680 4.933064 GCCGGCCGATCTCTCGTG 62.933 72.222 30.73 7.40 43.49 4.35
883 2684 3.222855 CTCTGCCGGCCGATCTCT 61.223 66.667 30.73 0.00 0.00 3.10
980 2782 1.625818 GTCCAACCCAGTCAGTCATCT 59.374 52.381 0.00 0.00 0.00 2.90
1161 2963 1.682740 GGAGGGGTACGAGAGAAGAG 58.317 60.000 0.00 0.00 0.00 2.85
1171 2988 1.382833 GGTGGAGAGGGAGGGGTAC 60.383 68.421 0.00 0.00 0.00 3.34
1173 2990 2.876858 AGGTGGAGAGGGAGGGGT 60.877 66.667 0.00 0.00 0.00 4.95
1174 2991 2.041405 GAGGTGGAGAGGGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
1175 2992 2.041405 GGAGGTGGAGAGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
1176 2993 1.075600 GAGGAGGTGGAGAGGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
1177 2994 1.075600 GGAGGAGGTGGAGAGGGAG 60.076 68.421 0.00 0.00 0.00 4.30
1178 2995 2.637640 GGGAGGAGGTGGAGAGGGA 61.638 68.421 0.00 0.00 0.00 4.20
1179 2996 2.041405 GGGAGGAGGTGGAGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
1180 2997 2.041405 GGGGAGGAGGTGGAGAGG 60.041 72.222 0.00 0.00 0.00 3.69
1181 2998 2.041405 GGGGGAGGAGGTGGAGAG 60.041 72.222 0.00 0.00 0.00 3.20
1182 2999 2.540910 AGGGGGAGGAGGTGGAGA 60.541 66.667 0.00 0.00 0.00 3.71
1183 3000 2.041405 GAGGGGGAGGAGGTGGAG 60.041 72.222 0.00 0.00 0.00 3.86
1184 3001 2.540910 AGAGGGGGAGGAGGTGGA 60.541 66.667 0.00 0.00 0.00 4.02
1185 3002 1.297409 TAGAGAGGGGGAGGAGGTGG 61.297 65.000 0.00 0.00 0.00 4.61
1186 3003 0.105913 GTAGAGAGGGGGAGGAGGTG 60.106 65.000 0.00 0.00 0.00 4.00
1187 3004 0.254395 AGTAGAGAGGGGGAGGAGGT 60.254 60.000 0.00 0.00 0.00 3.85
1326 3143 3.248029 CTGCACGAACTGGAGCAC 58.752 61.111 0.00 0.00 30.59 4.40
1340 3157 4.622701 AATCGAATCCTTAACAAGCTGC 57.377 40.909 0.00 0.00 0.00 5.25
1425 3245 1.774217 AGCCAGGAAGTCCCCAACA 60.774 57.895 0.00 0.00 36.42 3.33
1455 3275 4.402155 TGCTTAATTAACAAGGGGCATCAG 59.598 41.667 4.06 0.00 0.00 2.90
1456 3276 4.348486 TGCTTAATTAACAAGGGGCATCA 58.652 39.130 4.06 0.00 0.00 3.07
1526 3346 1.829533 CAGCAACACCTGGCCACTT 60.830 57.895 0.00 0.00 0.00 3.16
1535 3355 1.879380 TCTAATGTGCACAGCAACACC 59.121 47.619 25.84 0.00 41.47 4.16
1542 3362 6.095580 TCCTTACTACTCTCTAATGTGCACAG 59.904 42.308 25.84 11.98 0.00 3.66
1601 3421 4.570079 GCACTAGGGACCTATCAGCCTATA 60.570 50.000 0.00 0.00 0.00 1.31
1602 3422 3.819754 GCACTAGGGACCTATCAGCCTAT 60.820 52.174 0.00 0.00 0.00 2.57
1603 3423 2.491086 GCACTAGGGACCTATCAGCCTA 60.491 54.545 0.00 0.00 0.00 3.93
1604 3424 1.759562 GCACTAGGGACCTATCAGCCT 60.760 57.143 0.00 0.00 0.00 4.58
1724 3547 7.285401 ACAACACAAGACATATTGGAATATCCC 59.715 37.037 0.00 0.00 35.03 3.85
1774 3605 2.469465 TAGCAGAGCAACCCTGTGGC 62.469 60.000 0.00 0.00 35.47 5.01
1902 3741 1.303309 CTGCCTCAAGGGAATAAGCG 58.697 55.000 0.00 0.00 34.22 4.68
2072 3911 2.762535 TACTGTAGCAGGAAACAGCC 57.237 50.000 2.52 0.00 45.65 4.85
2114 3953 0.457853 GTGTCGTTCTCGGCTGCATA 60.458 55.000 0.50 0.00 42.59 3.14
2131 3970 3.276857 CTTCCTCTTCCCATCATGTGTG 58.723 50.000 0.00 0.00 0.00 3.82
2318 4157 9.616156 AAATAATGCATGCCTAAAATGATCAAA 57.384 25.926 16.68 0.00 0.00 2.69
2348 4187 4.262036 CCACAGCTAGTACTTGACACAAGA 60.262 45.833 16.65 0.38 0.00 3.02
2354 4193 2.561419 TCCACCACAGCTAGTACTTGAC 59.439 50.000 8.60 0.10 0.00 3.18
2365 4204 1.200948 GAGAAAAGCATCCACCACAGC 59.799 52.381 0.00 0.00 0.00 4.40
2407 4246 9.807649 GCAAAACTGGAACATAATTAATCAGAT 57.192 29.630 5.38 0.00 38.20 2.90
2438 4281 3.437049 GGCTGAAGTTCAGGTGTTCATAC 59.563 47.826 29.45 12.49 44.43 2.39
2442 4285 1.967319 TGGCTGAAGTTCAGGTGTTC 58.033 50.000 29.45 15.01 44.43 3.18
2468 4311 7.560796 AATGAATCGGAGGGAGTATATTTCT 57.439 36.000 0.00 0.00 0.00 2.52
2488 4333 8.208718 ACTAAAGCTGCGACAATTAATAATGA 57.791 30.769 0.00 0.00 0.00 2.57
2497 4342 4.315803 AGTTGTACTAAAGCTGCGACAAT 58.684 39.130 0.00 0.00 0.00 2.71
2541 4386 7.385205 CCTACGATCCATATTACTTGTCAAAGG 59.615 40.741 0.00 0.00 37.76 3.11
2544 4389 6.551975 TCCCTACGATCCATATTACTTGTCAA 59.448 38.462 0.00 0.00 0.00 3.18
2545 4390 6.072649 TCCCTACGATCCATATTACTTGTCA 58.927 40.000 0.00 0.00 0.00 3.58
2562 4407 7.713750 TGAACTGATCTTAATTACTCCCTACG 58.286 38.462 0.00 0.00 0.00 3.51
2734 4818 4.520492 GGGGTACTTGATATTCAGGCAATG 59.480 45.833 0.00 0.00 0.00 2.82
2771 4855 5.909477 AGTTACAACAGCACACTAGTAACA 58.091 37.500 13.59 0.00 38.72 2.41
2814 4898 7.568349 ACTGAACATGATCCAACATACTGTAT 58.432 34.615 0.00 0.00 0.00 2.29
2888 4972 3.370061 GCTGTTACAAGGTAACCTTAGCG 59.630 47.826 14.63 0.00 42.67 4.26
2939 5023 3.469008 AATAGTTAGCAGTGCGCCATA 57.531 42.857 10.00 2.59 44.04 2.74
3140 5225 9.886132 AGATTATTATTCTTAACAACGAGTGGT 57.114 29.630 0.00 0.00 0.00 4.16
3158 5243 9.869757 TCTCGAACAATCAGTTTCAGATTATTA 57.130 29.630 0.00 0.00 41.51 0.98
3159 5244 8.777865 TCTCGAACAATCAGTTTCAGATTATT 57.222 30.769 0.00 0.00 41.51 1.40
3160 5245 8.824781 CATCTCGAACAATCAGTTTCAGATTAT 58.175 33.333 0.00 0.00 41.51 1.28
3193 5278 6.095440 ACTTGTTTTCATTTATCAGGGATCGG 59.905 38.462 0.00 0.00 0.00 4.18
3205 5294 9.445786 CTGATTGTACGTTACTTGTTTTCATTT 57.554 29.630 0.00 0.00 0.00 2.32
3239 5328 9.078990 TCGAGAGTTTACAGTGAATATATGGAT 57.921 33.333 0.00 0.00 0.00 3.41
3268 5357 3.527533 TCTCACGCAAATACATACCACC 58.472 45.455 0.00 0.00 0.00 4.61
3331 5422 6.887545 TGGAAGATCGGGTTAACATAACATTT 59.112 34.615 8.10 0.00 0.00 2.32
3407 5661 9.658799 ATCTATATGCACTACATTATGGAACAC 57.341 33.333 0.00 0.00 40.39 3.32
3421 5675 8.946085 TGACTTTTCGAAAAATCTATATGCACT 58.054 29.630 26.62 0.10 0.00 4.40
3422 5676 9.722056 ATGACTTTTCGAAAAATCTATATGCAC 57.278 29.630 26.62 11.20 0.00 4.57
3433 5687 9.659830 GTTTCTAAGCTATGACTTTTCGAAAAA 57.340 29.630 22.67 10.06 0.00 1.94
3434 5688 9.052759 AGTTTCTAAGCTATGACTTTTCGAAAA 57.947 29.630 21.35 21.35 0.00 2.29
3435 5689 8.603242 AGTTTCTAAGCTATGACTTTTCGAAA 57.397 30.769 6.47 6.47 0.00 3.46
3437 5691 8.495949 CAAAGTTTCTAAGCTATGACTTTTCGA 58.504 33.333 9.51 0.00 35.75 3.71
3438 5692 8.495949 TCAAAGTTTCTAAGCTATGACTTTTCG 58.504 33.333 9.51 3.33 35.75 3.46
3439 5693 9.600646 GTCAAAGTTTCTAAGCTATGACTTTTC 57.399 33.333 9.51 5.08 35.75 2.29
3440 5694 8.568794 GGTCAAAGTTTCTAAGCTATGACTTTT 58.431 33.333 9.51 0.99 35.75 2.27
3441 5695 7.719633 TGGTCAAAGTTTCTAAGCTATGACTTT 59.280 33.333 0.00 0.00 37.70 2.66
3442 5696 7.224297 TGGTCAAAGTTTCTAAGCTATGACTT 58.776 34.615 0.00 0.00 36.91 3.01
3445 5699 7.672983 CTTGGTCAAAGTTTCTAAGCTATGA 57.327 36.000 0.00 0.00 0.00 2.15
3485 5739 9.976511 ATATGTTTGGCATTCTAGATGAAAATG 57.023 29.630 0.00 0.00 38.29 2.32
3579 5833 9.512588 ACATTGATCAAGTTCATAGAGAAAACT 57.487 29.630 14.54 0.00 38.13 2.66
3583 5837 9.049523 GCATACATTGATCAAGTTCATAGAGAA 57.950 33.333 14.54 0.00 0.00 2.87
3584 5838 8.206189 TGCATACATTGATCAAGTTCATAGAGA 58.794 33.333 14.54 0.00 0.00 3.10
3585 5839 8.374327 TGCATACATTGATCAAGTTCATAGAG 57.626 34.615 14.54 0.00 0.00 2.43
3586 5840 8.735692 TTGCATACATTGATCAAGTTCATAGA 57.264 30.769 14.54 0.00 0.00 1.98
3587 5841 9.447040 CTTTGCATACATTGATCAAGTTCATAG 57.553 33.333 14.54 10.39 0.00 2.23
3588 5842 8.959548 ACTTTGCATACATTGATCAAGTTCATA 58.040 29.630 14.54 2.36 0.00 2.15
3589 5843 7.833786 ACTTTGCATACATTGATCAAGTTCAT 58.166 30.769 14.54 1.96 0.00 2.57
3590 5844 7.218228 ACTTTGCATACATTGATCAAGTTCA 57.782 32.000 14.54 8.17 0.00 3.18
3591 5845 8.430063 CAAACTTTGCATACATTGATCAAGTTC 58.570 33.333 14.54 6.16 33.06 3.01
3592 5846 8.143193 TCAAACTTTGCATACATTGATCAAGTT 58.857 29.630 14.54 5.37 34.44 2.66
3593 5847 7.596248 GTCAAACTTTGCATACATTGATCAAGT 59.404 33.333 14.54 13.57 0.00 3.16
3594 5848 7.811236 AGTCAAACTTTGCATACATTGATCAAG 59.189 33.333 14.54 8.57 0.00 3.02
3595 5849 7.660112 AGTCAAACTTTGCATACATTGATCAA 58.340 30.769 11.26 11.26 0.00 2.57
3596 5850 7.218228 AGTCAAACTTTGCATACATTGATCA 57.782 32.000 8.23 0.00 0.00 2.92
3597 5851 8.524870 AAAGTCAAACTTTGCATACATTGATC 57.475 30.769 4.36 0.00 45.83 2.92
3598 5852 8.891671 AAAAGTCAAACTTTGCATACATTGAT 57.108 26.923 5.88 0.00 46.78 2.57
3599 5853 7.978414 TGAAAAGTCAAACTTTGCATACATTGA 59.022 29.630 8.80 0.00 46.06 2.57
3600 5854 8.129161 TGAAAAGTCAAACTTTGCATACATTG 57.871 30.769 8.80 0.00 46.06 2.82
3632 5886 9.961265 CGTTCCATAATAGTGTCTACAGATTTA 57.039 33.333 0.00 0.00 0.00 1.40
3633 5887 7.926555 CCGTTCCATAATAGTGTCTACAGATTT 59.073 37.037 0.00 0.00 0.00 2.17
3634 5888 7.287005 TCCGTTCCATAATAGTGTCTACAGATT 59.713 37.037 0.00 0.00 0.00 2.40
3635 5889 6.776116 TCCGTTCCATAATAGTGTCTACAGAT 59.224 38.462 0.00 0.00 0.00 2.90
3636 5890 6.124340 TCCGTTCCATAATAGTGTCTACAGA 58.876 40.000 0.00 0.00 0.00 3.41
3637 5891 6.387041 TCCGTTCCATAATAGTGTCTACAG 57.613 41.667 0.00 0.00 0.00 2.74
3638 5892 5.301045 CCTCCGTTCCATAATAGTGTCTACA 59.699 44.000 0.00 0.00 0.00 2.74
3639 5893 5.278858 CCCTCCGTTCCATAATAGTGTCTAC 60.279 48.000 0.00 0.00 0.00 2.59
3640 5894 4.831155 CCCTCCGTTCCATAATAGTGTCTA 59.169 45.833 0.00 0.00 0.00 2.59
3641 5895 3.641906 CCCTCCGTTCCATAATAGTGTCT 59.358 47.826 0.00 0.00 0.00 3.41
3642 5896 3.640029 TCCCTCCGTTCCATAATAGTGTC 59.360 47.826 0.00 0.00 0.00 3.67
3643 5897 3.641906 CTCCCTCCGTTCCATAATAGTGT 59.358 47.826 0.00 0.00 0.00 3.55
3644 5898 3.641906 ACTCCCTCCGTTCCATAATAGTG 59.358 47.826 0.00 0.00 0.00 2.74
3646 5900 6.890814 AGTATACTCCCTCCGTTCCATAATAG 59.109 42.308 0.00 0.00 0.00 1.73
3649 5903 5.070823 AGTATACTCCCTCCGTTCCATAA 57.929 43.478 0.00 0.00 0.00 1.90
3651 5905 3.614568 AGTATACTCCCTCCGTTCCAT 57.385 47.619 0.00 0.00 0.00 3.41
3655 5909 4.401837 GTCTTGAAGTATACTCCCTCCGTT 59.598 45.833 5.70 0.00 0.00 4.44
3686 5941 5.001237 TCAGACGTTTTTAGACACTGTCA 57.999 39.130 11.80 0.00 34.60 3.58
3687 5942 6.526566 AATCAGACGTTTTTAGACACTGTC 57.473 37.500 0.38 0.38 0.00 3.51
3688 5943 6.920569 AAATCAGACGTTTTTAGACACTGT 57.079 33.333 0.00 0.00 0.00 3.55
3689 5944 9.370126 CTTAAAATCAGACGTTTTTAGACACTG 57.630 33.333 0.00 0.00 30.74 3.66
3731 5991 7.286215 TCAAAAGTGCTTCTACAGTAGTACT 57.714 36.000 7.50 0.00 39.29 2.73
3732 5992 7.941795 TTCAAAAGTGCTTCTACAGTAGTAC 57.058 36.000 7.50 0.00 0.00 2.73
3733 5993 9.204570 GAATTCAAAAGTGCTTCTACAGTAGTA 57.795 33.333 7.50 0.00 0.00 1.82
3734 5994 7.934120 AGAATTCAAAAGTGCTTCTACAGTAGT 59.066 33.333 8.44 0.00 29.68 2.73
3735 5995 8.316640 AGAATTCAAAAGTGCTTCTACAGTAG 57.683 34.615 8.44 0.47 29.68 2.57
3745 6005 6.998673 ACCAGTAGTAAGAATTCAAAAGTGCT 59.001 34.615 8.44 1.79 0.00 4.40
3785 6045 1.061421 TCGACGAACACAGCAAAACAC 59.939 47.619 0.00 0.00 0.00 3.32
3799 6059 0.865111 CAAGGTTTGCATGTCGACGA 59.135 50.000 11.62 0.00 0.00 4.20
3849 6110 4.767255 CTGCTGGGCCACCGTCTC 62.767 72.222 0.00 0.00 40.75 3.36
3858 6119 1.247567 TTTCTTTGTAGCTGCTGGGC 58.752 50.000 13.43 3.13 0.00 5.36
3906 7557 1.337071 CGGAAGCTCGAGGCAATAGTA 59.663 52.381 15.58 0.00 44.79 1.82
3907 7558 0.103208 CGGAAGCTCGAGGCAATAGT 59.897 55.000 15.58 0.00 44.79 2.12
3938 7589 1.341531 AGTCAAGGTCAACTCACTCGG 59.658 52.381 0.00 0.00 0.00 4.63
3959 7611 1.686741 GGATCGAGAGTCCCAGTTCCT 60.687 57.143 0.00 0.00 0.00 3.36
3960 7612 0.747852 GGATCGAGAGTCCCAGTTCC 59.252 60.000 0.00 0.00 0.00 3.62
3961 7613 0.382515 CGGATCGAGAGTCCCAGTTC 59.617 60.000 0.00 0.00 31.87 3.01
3962 7614 1.668101 GCGGATCGAGAGTCCCAGTT 61.668 60.000 0.00 0.00 31.87 3.16
3980 7632 1.070776 GTGAACGGACGAGTTTTCTGC 60.071 52.381 0.00 0.00 34.00 4.26
3982 7634 1.202336 ACGTGAACGGACGAGTTTTCT 60.202 47.619 7.86 0.00 42.10 2.52
3989 7641 0.381445 TTCAAGACGTGAACGGACGA 59.619 50.000 7.86 0.00 41.47 4.20
3995 7647 3.246699 TGAATCCGTTTCAAGACGTGAAC 59.753 43.478 3.11 0.00 46.09 3.18
4139 7821 0.108329 ACACCATACTGCTGTACGGC 60.108 55.000 20.17 20.17 35.59 5.68
4140 7822 3.513680 TTACACCATACTGCTGTACGG 57.486 47.619 13.56 13.56 37.94 4.02
4141 7823 5.006358 GGAATTTACACCATACTGCTGTACG 59.994 44.000 5.50 0.00 0.00 3.67
4142 7824 5.296035 GGGAATTTACACCATACTGCTGTAC 59.704 44.000 5.50 0.00 0.00 2.90
4143 7825 5.433526 GGGAATTTACACCATACTGCTGTA 58.566 41.667 5.87 5.87 0.00 2.74
4144 7826 4.270008 GGGAATTTACACCATACTGCTGT 58.730 43.478 0.66 0.66 0.00 4.40
4145 7827 3.312421 CGGGAATTTACACCATACTGCTG 59.688 47.826 0.00 0.00 0.00 4.41
4146 7828 3.541632 CGGGAATTTACACCATACTGCT 58.458 45.455 0.00 0.00 0.00 4.24
4147 7829 2.616842 CCGGGAATTTACACCATACTGC 59.383 50.000 0.00 0.00 0.00 4.40
4148 7830 3.211045 CCCGGGAATTTACACCATACTG 58.789 50.000 18.48 0.00 0.00 2.74
4149 7831 2.422377 GCCCGGGAATTTACACCATACT 60.422 50.000 29.31 0.00 0.00 2.12
4150 7832 1.951602 GCCCGGGAATTTACACCATAC 59.048 52.381 29.31 0.00 0.00 2.39
4151 7833 1.847737 AGCCCGGGAATTTACACCATA 59.152 47.619 29.31 0.00 0.00 2.74
4152 7834 0.629058 AGCCCGGGAATTTACACCAT 59.371 50.000 29.31 0.00 0.00 3.55
4153 7835 0.406361 AAGCCCGGGAATTTACACCA 59.594 50.000 29.31 0.00 0.00 4.17
4154 7836 0.815095 CAAGCCCGGGAATTTACACC 59.185 55.000 29.31 1.92 0.00 4.16
4155 7837 1.541379 ACAAGCCCGGGAATTTACAC 58.459 50.000 29.31 2.84 0.00 2.90
4156 7838 3.349022 CTTACAAGCCCGGGAATTTACA 58.651 45.455 29.31 0.00 0.00 2.41
4157 7839 2.686405 CCTTACAAGCCCGGGAATTTAC 59.314 50.000 29.31 4.69 0.00 2.01
4158 7840 2.946791 GCCTTACAAGCCCGGGAATTTA 60.947 50.000 29.31 6.16 0.00 1.40
4159 7841 1.847328 CCTTACAAGCCCGGGAATTT 58.153 50.000 29.31 12.49 0.00 1.82
4160 7842 0.683179 GCCTTACAAGCCCGGGAATT 60.683 55.000 29.31 15.96 0.00 2.17
4161 7843 1.076995 GCCTTACAAGCCCGGGAAT 60.077 57.895 29.31 9.24 0.00 3.01
4162 7844 2.353573 GCCTTACAAGCCCGGGAA 59.646 61.111 29.31 8.26 0.00 3.97
4163 7845 2.931105 TGCCTTACAAGCCCGGGA 60.931 61.111 29.31 0.00 0.00 5.14
4164 7846 2.750237 GTGCCTTACAAGCCCGGG 60.750 66.667 19.09 19.09 0.00 5.73
4177 7859 4.781959 TACCTGCGTACGCGTGCC 62.782 66.667 32.65 15.03 45.51 5.01
4203 7885 3.118454 CGGAAGCGTTGATGGCGT 61.118 61.111 0.00 0.00 35.00 5.68
4204 7886 3.864686 CCGGAAGCGTTGATGGCG 61.865 66.667 0.00 0.00 35.00 5.69
4235 7917 2.593725 CCGATCCAGGCAGCCATG 60.594 66.667 15.80 9.03 0.00 3.66
4236 7918 2.769621 TCCGATCCAGGCAGCCAT 60.770 61.111 15.80 0.00 0.00 4.40
4237 7919 3.473647 CTCCGATCCAGGCAGCCA 61.474 66.667 15.80 0.00 0.00 4.75
4238 7920 4.247380 CCTCCGATCCAGGCAGCC 62.247 72.222 1.84 1.84 0.00 4.85
4251 7933 2.440817 CCCGTATGTCACCCCCTCC 61.441 68.421 0.00 0.00 0.00 4.30
4284 7966 0.736325 CTGTTCGTTCGCTACCCCAG 60.736 60.000 0.00 0.00 0.00 4.45
4286 7968 1.447314 CCTGTTCGTTCGCTACCCC 60.447 63.158 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.