Multiple sequence alignment - TraesCS4B01G018400

Loading Multiple Alignment...

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 TraesCS4B01G018400 chr4B 100.000 4159 0 0 1 4159 13302974 13298816 0.000000e+00 7681.0
1 TraesCS4B01G018400 chr4D 87.806 2124 148 50 37 2087 7463407 7461322 0.000000e+00 2385.0
2 TraesCS4B01G018400 chr4D 87.865 890 49 31 2731 3596 7460566 7459712 0.000000e+00 990.0
3 TraesCS4B01G018400 chr4D 87.879 660 36 21 2083 2731 7461275 7460649 0.000000e+00 736.0
4 TraesCS4B01G018400 chr4D 90.424 543 25 14 3617 4159 7421932 7421417 0.000000e+00 689.0
5 TraesCS4B01G018400 chr4A 88.591 1604 102 32 501 2075 596158681 596160232 0.000000e+00 1873.0
6 TraesCS4B01G018400 chr4A 90.261 1109 51 27 2507 3596 596161262 596162332 0.000000e+00 1397.0
7 TraesCS4B01G018400 chr4A 87.368 570 25 20 3593 4159 596162356 596162881 9.880000e-171 610.0
8 TraesCS4B01G018400 chr4A 86.019 515 38 13 2083 2593 596160280 596160764 4.760000e-144 521.0
9 TraesCS4B01G018400 chr4A 77.853 736 110 29 1 714 596156312 596157016 1.390000e-109 407.0
10 TraesCS4B01G018400 chr4A 87.234 282 25 10 99 372 596158357 596158635 1.120000e-80 311.0
11 TraesCS4B01G018400 chr4A 87.500 112 13 1 1 112 596158200 596158310 1.210000e-25 128.0
12 TraesCS4B01G018400 chr4A 90.141 71 7 0 699 769 596157040 596157110 4.430000e-15 93.5
13 TraesCS4B01G018400 chr5B 89.600 375 23 9 2104 2470 395475439 395475805 2.930000e-126 462.0
14 TraesCS4B01G018400 chr5B 91.343 335 19 7 2103 2431 657063454 657063124 2.280000e-122 449.0
15 TraesCS4B01G018400 chr6B 91.343 335 19 6 2103 2431 473184737 473184407 2.280000e-122 449.0
16 TraesCS4B01G018400 chr6B 91.045 335 20 6 2103 2431 643477183 643476853 1.060000e-120 444.0
17 TraesCS4B01G018400 chr6B 90.149 335 23 6 2103 2431 616756659 616756329 1.070000e-115 427.0
18 TraesCS4B01G018400 chr6B 84.709 327 24 11 2508 2831 643476823 643476520 1.880000e-78 303.0
19 TraesCS4B01G018400 chr6B 90.686 204 14 4 2507 2707 643476255 643476054 2.460000e-67 267.0
20 TraesCS4B01G018400 chr6B 89.706 204 16 4 2507 2707 473184019 473183818 5.340000e-64 255.0
21 TraesCS4B01G018400 chr6B 91.146 192 12 4 2507 2695 616755941 616755752 5.340000e-64 255.0
22 TraesCS4B01G018400 chr6B 89.216 204 17 4 2507 2707 62202086 62201885 2.480000e-62 250.0
23 TraesCS4B01G018400 chr2B 91.045 335 20 6 2103 2431 764924993 764924663 1.060000e-120 444.0
24 TraesCS4B01G018400 chr3B 88.391 379 26 12 2104 2473 760026044 760025675 1.370000e-119 440.0
25 TraesCS4B01G018400 chr3B 85.276 163 15 8 2665 2827 760025561 760025408 4.300000e-35 159.0
26 TraesCS4B01G018400 chr7B 90.991 333 17 7 2105 2431 574880535 574880860 1.780000e-118 436.0
27 TraesCS4B01G018400 chr7B 90.196 204 14 5 2507 2707 135317333 135317533 1.150000e-65 261.0
28 TraesCS4B01G018400 chr7B 91.667 192 11 5 2507 2695 708808917 708808728 1.150000e-65 261.0
29 TraesCS4B01G018400 chr6A 88.235 221 17 5 2432 2649 613831846 613831632 5.340000e-64 255.0


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 TraesCS4B01G018400 chr4B 13298816 13302974 4158 True 7681.000000 7681 100.000000 1 4159 1 chr4B.!!$R1 4158
1 TraesCS4B01G018400 chr4D 7459712 7463407 3695 True 1370.333333 2385 87.850000 37 3596 3 chr4D.!!$R2 3559
2 TraesCS4B01G018400 chr4D 7421417 7421932 515 True 689.000000 689 90.424000 3617 4159 1 chr4D.!!$R1 542
3 TraesCS4B01G018400 chr4A 596156312 596162881 6569 False 667.562500 1873 86.870875 1 4159 8 chr4A.!!$F1 4158
4 TraesCS4B01G018400 chr6B 473183818 473184737 919 True 352.000000 449 90.524500 2103 2707 2 chr6B.!!$R2 604
5 TraesCS4B01G018400 chr6B 616755752 616756659 907 True 341.000000 427 90.647500 2103 2695 2 chr6B.!!$R3 592
6 TraesCS4B01G018400 chr6B 643476054 643477183 1129 True 338.000000 444 88.813333 2103 2831 3 chr6B.!!$R4 728
7 TraesCS4B01G018400 chr3B 760025408 760026044 636 True 299.500000 440 86.833500 2104 2827 2 chr3B.!!$R1 723

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
887 2874 0.107831 TGTAGTTGGAGCAGCGGTTT 59.892 50.0 0.0 0.0 0.0 3.27 F
1841 3876 0.179000 ACCTTCATCCATCGGTGAGC 59.821 55.0 0.0 0.0 0.0 4.26 F
2501 5822 0.676736 GGGGTTGTTTTGATTCCGCA 59.323 50.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2844 6249 0.391661 TTGAGCGCATCTCCAGGTTC 60.392 55.0 11.47 0.0 41.18 3.62 R
2930 6336 0.042794 CTTTGTGCAAAGCAAAGCGC 60.043 50.0 13.42 0.0 43.86 5.92 R
3814 7279 0.108520 CGGGCTGCTGCATTTCATTT 60.109 50.0 17.89 0.0 41.91 2.32 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
59 1948 3.746045 TGGTAAGAAGAGTGTTCGCTT 57.254 42.857 0.00 0.00 36.47 4.68
81 1970 2.666508 TGAATCGCTAGAAAACTGACGC 59.333 45.455 0.00 0.00 0.00 5.19
82 1971 1.641577 ATCGCTAGAAAACTGACGCC 58.358 50.000 0.00 0.00 0.00 5.68
84 1973 1.067142 TCGCTAGAAAACTGACGCCAT 60.067 47.619 0.00 0.00 0.00 4.40
85 1974 2.164827 TCGCTAGAAAACTGACGCCATA 59.835 45.455 0.00 0.00 0.00 2.74
97 1986 5.593010 ACTGACGCCATATCTTTAGTCTTC 58.407 41.667 0.00 0.00 0.00 2.87
103 2051 6.183361 ACGCCATATCTTTAGTCTTCAGGAAT 60.183 38.462 0.00 0.00 0.00 3.01
104 2052 6.708054 CGCCATATCTTTAGTCTTCAGGAATT 59.292 38.462 0.00 0.00 0.00 2.17
105 2053 7.095439 CGCCATATCTTTAGTCTTCAGGAATTC 60.095 40.741 0.00 0.00 0.00 2.17
191 2149 8.397575 AGAGAAACGCATATCTACTCTTATCA 57.602 34.615 0.00 0.00 30.61 2.15
220 2179 5.499139 TCAAACACTCCACACAAAAGATC 57.501 39.130 0.00 0.00 0.00 2.75
272 2231 6.494893 TCACTAGCATGACCACAATTAAAC 57.505 37.500 0.00 0.00 0.00 2.01
273 2232 5.121611 TCACTAGCATGACCACAATTAAACG 59.878 40.000 0.00 0.00 0.00 3.60
280 2239 5.578005 TGACCACAATTAAACGTTCCAAA 57.422 34.783 0.00 0.00 0.00 3.28
312 2271 7.568199 AAAGTGCAATTAACTCAACTGTAGT 57.432 32.000 0.00 0.00 0.00 2.73
313 2272 6.545504 AGTGCAATTAACTCAACTGTAGTG 57.454 37.500 0.00 0.00 0.00 2.74
314 2273 5.049405 AGTGCAATTAACTCAACTGTAGTGC 60.049 40.000 0.00 0.00 0.00 4.40
316 2275 5.179368 TGCAATTAACTCAACTGTAGTGCTC 59.821 40.000 0.00 0.00 0.00 4.26
330 2290 0.611714 GTGCTCCTCCCCGAGTTAAA 59.388 55.000 0.00 0.00 32.11 1.52
336 2296 3.509442 TCCTCCCCGAGTTAAAACACTA 58.491 45.455 0.00 0.00 0.00 2.74
341 2301 3.744426 CCCCGAGTTAAAACACTACACTG 59.256 47.826 0.00 0.00 0.00 3.66
344 2304 3.805422 CGAGTTAAAACACTACACTGCCA 59.195 43.478 0.00 0.00 0.00 4.92
363 2323 3.365064 GCCATCATCAAAGATCGCATCAG 60.365 47.826 0.00 0.00 33.16 2.90
373 2333 6.310467 TCAAAGATCGCATCAGTTACAGTTAC 59.690 38.462 0.00 0.00 0.00 2.50
379 2339 7.563888 TCGCATCAGTTACAGTTACTAGTAT 57.436 36.000 2.79 0.00 0.00 2.12
396 2356 9.642327 TTACTAGTATCACTCGTTGCAAATAAA 57.358 29.630 0.00 0.00 0.00 1.40
397 2357 8.542497 ACTAGTATCACTCGTTGCAAATAAAA 57.458 30.769 0.00 0.00 0.00 1.52
399 2359 9.988350 CTAGTATCACTCGTTGCAAATAAAAAT 57.012 29.630 0.00 0.00 0.00 1.82
401 2361 9.341899 AGTATCACTCGTTGCAAATAAAAATTC 57.658 29.630 0.00 0.00 0.00 2.17
408 2376 9.649024 CTCGTTGCAAATAAAAATTCAACAAAT 57.351 25.926 0.00 0.00 35.01 2.32
440 2408 7.342769 TCAATTATTGTTCTCCGAGCTAGTA 57.657 36.000 4.77 0.00 0.00 1.82
442 2410 7.867909 TCAATTATTGTTCTCCGAGCTAGTATG 59.132 37.037 4.77 0.00 0.00 2.39
471 2439 3.947132 CTCTCTGCCAGTGTGCCCG 62.947 68.421 0.00 0.00 0.00 6.13
472 2440 4.007644 CTCTGCCAGTGTGCCCGA 62.008 66.667 0.00 0.00 0.00 5.14
487 2455 9.180678 CAGTGTGCCCGATTTATTTATTTTATC 57.819 33.333 0.00 0.00 0.00 1.75
515 2483 1.341913 GGGCCTCCTCTTCTCTTCCC 61.342 65.000 0.84 0.00 0.00 3.97
516 2484 1.341913 GGCCTCCTCTTCTCTTCCCC 61.342 65.000 0.00 0.00 0.00 4.81
519 2487 0.820871 CTCCTCTTCTCTTCCCCGTG 59.179 60.000 0.00 0.00 0.00 4.94
716 2702 0.979665 TTTGTGCTCTCCTCTCCTGG 59.020 55.000 0.00 0.00 0.00 4.45
748 2734 0.328258 ACCTACCTCGGCAAGCATTT 59.672 50.000 0.00 0.00 0.00 2.32
762 2749 0.681175 GCATTTCCTTGCCCACAACT 59.319 50.000 0.00 0.00 36.60 3.16
822 2809 0.900647 AACGAGACTCTGGTCCCTGG 60.901 60.000 0.03 0.00 43.05 4.45
880 2867 0.676466 CGGCCATTGTAGTTGGAGCA 60.676 55.000 2.24 0.00 36.26 4.26
881 2868 1.098050 GGCCATTGTAGTTGGAGCAG 58.902 55.000 0.00 0.00 36.26 4.24
882 2869 0.453390 GCCATTGTAGTTGGAGCAGC 59.547 55.000 0.00 0.00 36.26 5.25
887 2874 0.107831 TGTAGTTGGAGCAGCGGTTT 59.892 50.000 0.00 0.00 0.00 3.27
922 2909 1.005394 TCCGAGGACGTTGCTTTCC 60.005 57.895 0.00 0.00 37.88 3.13
1010 3008 1.539827 CGTCTTTTCCATGGTTGGTCC 59.460 52.381 12.58 0.00 44.06 4.46
1012 3010 3.230976 GTCTTTTCCATGGTTGGTCCTT 58.769 45.455 12.58 0.00 44.06 3.36
1017 3015 3.743714 CATGGTTGGTCCTTGGTCA 57.256 52.632 0.00 0.00 37.61 4.02
1018 3016 2.220653 CATGGTTGGTCCTTGGTCAT 57.779 50.000 0.00 0.00 37.61 3.06
1019 3017 1.820519 CATGGTTGGTCCTTGGTCATG 59.179 52.381 0.00 0.00 37.61 3.07
1054 3065 4.773117 GTGCTCCGTCCGTCCGTC 62.773 72.222 0.00 0.00 0.00 4.79
1168 3179 4.749310 CCGCCGCTGCTCAGTCTT 62.749 66.667 0.00 0.00 34.43 3.01
1174 3185 1.474478 CCGCTGCTCAGTCTTCTTCTA 59.526 52.381 0.00 0.00 0.00 2.10
1184 3195 3.090790 AGTCTTCTTCTACTTCCCCGAC 58.909 50.000 0.00 0.00 0.00 4.79
1281 3292 1.066858 TCCATTCTCGAGACCAAGCAC 60.067 52.381 16.36 0.00 0.00 4.40
1346 3357 1.153086 GGAAGGCGCACATGGAGAT 60.153 57.895 10.83 0.00 0.00 2.75
1350 3361 2.515523 GCGCACATGGAGATGGCT 60.516 61.111 0.30 0.00 33.39 4.75
1358 3369 3.157252 GGAGATGGCTGCTCCGGA 61.157 66.667 2.93 2.93 42.22 5.14
1359 3370 2.420890 GAGATGGCTGCTCCGGAG 59.579 66.667 27.83 27.83 37.80 4.63
1437 3457 4.025401 CGCAAGGTGGTGTTCGGC 62.025 66.667 0.00 0.00 0.00 5.54
1725 3745 2.508891 GGATGCGCTCGTCGACAAG 61.509 63.158 17.16 7.95 41.67 3.16
1726 3746 2.507102 ATGCGCTCGTCGACAAGG 60.507 61.111 17.16 5.73 41.67 3.61
1733 3753 2.805353 CGTCGACAAGGCGGACAG 60.805 66.667 17.16 0.00 45.57 3.51
1841 3876 0.179000 ACCTTCATCCATCGGTGAGC 59.821 55.000 0.00 0.00 0.00 4.26
1847 3882 2.159043 TCATCCATCGGTGAGCTTTCTC 60.159 50.000 0.00 0.00 39.78 2.87
1861 3896 4.615949 AGCTTTCTCTCTGTATGTATGCG 58.384 43.478 0.00 0.00 0.00 4.73
1870 3905 5.048434 TCTCTGTATGTATGCGGATCTCTTG 60.048 44.000 0.00 0.00 0.00 3.02
1938 3978 9.658799 ATGGTTTATAGACACTGCATATATGTC 57.341 33.333 14.14 10.84 42.54 3.06
1983 4023 2.169144 TCTGCTGCTTGCTCTGCTTATA 59.831 45.455 0.00 0.00 43.37 0.98
1984 4024 3.139850 CTGCTGCTTGCTCTGCTTATAT 58.860 45.455 0.00 0.00 43.37 0.86
1985 4025 4.039609 TCTGCTGCTTGCTCTGCTTATATA 59.960 41.667 0.00 0.00 43.37 0.86
1986 4026 4.707105 TGCTGCTTGCTCTGCTTATATAA 58.293 39.130 0.00 0.00 43.37 0.98
1987 4027 5.311265 TGCTGCTTGCTCTGCTTATATAAT 58.689 37.500 0.00 0.00 43.37 1.28
1988 4028 5.180680 TGCTGCTTGCTCTGCTTATATAATG 59.819 40.000 0.00 0.00 43.37 1.90
2054 4101 9.669887 AGATGATCTCAAAGCTTGGATATATTC 57.330 33.333 3.39 3.85 0.00 1.75
2070 4117 6.525628 GGATATATTCATTTTGACAGCATGCG 59.474 38.462 13.01 9.99 42.53 4.73
2172 4317 1.908619 TGCAGAGTAGATGGAAGGCAA 59.091 47.619 0.00 0.00 0.00 4.52
2187 4332 3.602205 AGGCAAGGGAGGGATAAAATC 57.398 47.619 0.00 0.00 0.00 2.17
2209 4354 4.093850 TCATGCACTGACATCAAATTCTCG 59.906 41.667 0.00 0.00 0.00 4.04
2214 4359 5.149273 CACTGACATCAAATTCTCGGTTTG 58.851 41.667 0.00 0.00 37.79 2.93
2217 4362 6.655003 ACTGACATCAAATTCTCGGTTTGTAT 59.345 34.615 0.00 0.00 37.70 2.29
2267 4420 7.541783 GTGCTTCATCATTGCAAGTTTTATGTA 59.458 33.333 4.94 0.00 38.50 2.29
2301 4455 8.723777 TCAACTCGACGATTGTTGATATATAC 57.276 34.615 21.84 0.00 43.15 1.47
2329 4483 7.172190 AGCAGTATCAACATAATACATCTGCAC 59.828 37.037 0.00 0.00 33.82 4.57
2470 5791 6.359545 GTGCGAACAAAATAAAATGTTTCCC 58.640 36.000 0.00 0.00 39.73 3.97
2474 5795 6.926272 CGAACAAAATAAAATGTTTCCCTCCA 59.074 34.615 0.00 0.00 39.73 3.86
2475 5796 7.439655 CGAACAAAATAAAATGTTTCCCTCCAA 59.560 33.333 0.00 0.00 39.73 3.53
2476 5797 9.283768 GAACAAAATAAAATGTTTCCCTCCAAT 57.716 29.630 0.00 0.00 39.73 3.16
2477 5798 8.846943 ACAAAATAAAATGTTTCCCTCCAATC 57.153 30.769 0.00 0.00 0.00 2.67
2478 5799 7.882791 ACAAAATAAAATGTTTCCCTCCAATCC 59.117 33.333 0.00 0.00 0.00 3.01
2486 5807 1.935931 CCCTCCAATCCAAGGGGGT 60.936 63.158 0.00 0.00 46.01 4.95
2498 5819 2.038426 CCAAGGGGGTTGTTTTGATTCC 59.962 50.000 0.00 0.00 33.87 3.01
2499 5820 1.627864 AGGGGGTTGTTTTGATTCCG 58.372 50.000 0.00 0.00 0.00 4.30
2501 5822 0.676736 GGGGTTGTTTTGATTCCGCA 59.323 50.000 0.00 0.00 0.00 5.69
2502 5823 1.275010 GGGGTTGTTTTGATTCCGCAT 59.725 47.619 0.00 0.00 0.00 4.73
2503 5824 2.606108 GGGTTGTTTTGATTCCGCATC 58.394 47.619 0.00 0.00 0.00 3.91
2504 5825 2.029470 GGGTTGTTTTGATTCCGCATCA 60.029 45.455 0.00 0.00 40.43 3.07
2505 5826 3.368323 GGGTTGTTTTGATTCCGCATCAT 60.368 43.478 0.00 0.00 41.82 2.45
2586 5910 5.105513 CCTGGGGGATTATGTTAACAACAAC 60.106 44.000 13.23 5.18 38.90 3.32
2682 6007 1.990060 CTCCTGACCATGACCCGGT 60.990 63.158 0.00 0.00 40.30 5.28
2700 6025 2.288457 CGGTCCAGCTATCATCGTCATT 60.288 50.000 0.00 0.00 0.00 2.57
2714 6039 7.332003 TCATCGTCATTGCAAATACAAAAAC 57.668 32.000 1.71 0.00 32.27 2.43
2716 6041 7.598118 TCATCGTCATTGCAAATACAAAAACAT 59.402 29.630 1.71 0.00 32.27 2.71
2719 6044 9.249457 TCGTCATTGCAAATACAAAAACATAAA 57.751 25.926 1.71 0.00 32.27 1.40
2720 6045 9.855361 CGTCATTGCAAATACAAAAACATAAAA 57.145 25.926 1.71 0.00 32.27 1.52
2725 6050 8.925788 TGCAAATACAAAAACATAAAAATCGC 57.074 26.923 0.00 0.00 0.00 4.58
2726 6051 8.551205 TGCAAATACAAAAACATAAAAATCGCA 58.449 25.926 0.00 0.00 0.00 5.10
2789 6194 9.574516 AAGATTATACTGAGTTGAGTTTGGTTT 57.425 29.630 0.00 0.00 0.00 3.27
2844 6249 6.908870 TCATGGATTGAAGTGATAAACTCG 57.091 37.500 0.00 0.00 38.56 4.18
2929 6335 3.255642 TCAGAGCAGTTTTATTTGTGCCC 59.744 43.478 0.00 0.00 36.54 5.36
2930 6336 2.228822 AGAGCAGTTTTATTTGTGCCCG 59.771 45.455 0.00 0.00 36.54 6.13
2931 6337 1.067693 GCAGTTTTATTTGTGCCCGC 58.932 50.000 0.00 0.00 0.00 6.13
2932 6338 1.335935 CAGTTTTATTTGTGCCCGCG 58.664 50.000 0.00 0.00 0.00 6.46
2933 6339 0.388006 AGTTTTATTTGTGCCCGCGC 60.388 50.000 0.00 0.00 0.00 6.86
2934 6340 0.388006 GTTTTATTTGTGCCCGCGCT 60.388 50.000 5.56 0.00 35.36 5.92
2935 6341 0.315568 TTTTATTTGTGCCCGCGCTT 59.684 45.000 5.56 0.00 35.36 4.68
2969 6375 7.595875 CACAAAGAGCATAACATGAACATCAAA 59.404 33.333 0.00 0.00 0.00 2.69
2984 6390 2.317371 TCAAATGCCCCCAAAAGCTA 57.683 45.000 0.00 0.00 0.00 3.32
2987 6393 2.236893 CAAATGCCCCCAAAAGCTATGT 59.763 45.455 0.00 0.00 0.00 2.29
2988 6394 1.488390 ATGCCCCCAAAAGCTATGTG 58.512 50.000 0.00 0.00 0.00 3.21
2989 6395 1.257055 TGCCCCCAAAAGCTATGTGC 61.257 55.000 0.00 0.00 43.29 4.57
3047 6454 7.686438 ATTGGCACATTTCTGCGATATAATA 57.314 32.000 0.00 0.00 39.30 0.98
3049 6456 8.785329 TTGGCACATTTCTGCGATATAATATA 57.215 30.769 0.00 0.00 39.30 0.86
3050 6457 8.785329 TGGCACATTTCTGCGATATAATATAA 57.215 30.769 0.00 0.00 38.12 0.98
3051 6458 9.394767 TGGCACATTTCTGCGATATAATATAAT 57.605 29.630 0.00 0.00 38.12 1.28
3088 6495 0.401738 TCTTTCTTCAGGGGTGGCAG 59.598 55.000 0.00 0.00 0.00 4.85
3137 6544 2.120232 CGGGAAATGATCTTCGACGAG 58.880 52.381 0.00 0.00 31.81 4.18
3198 6605 2.933906 GACGGTGTGTTTCACAAGAGAA 59.066 45.455 4.13 0.00 46.28 2.87
3199 6606 3.541632 ACGGTGTGTTTCACAAGAGAAT 58.458 40.909 4.13 0.00 46.28 2.40
3200 6607 3.945285 ACGGTGTGTTTCACAAGAGAATT 59.055 39.130 4.13 0.00 46.28 2.17
3201 6608 4.398044 ACGGTGTGTTTCACAAGAGAATTT 59.602 37.500 4.13 0.00 46.28 1.82
3202 6609 4.970003 CGGTGTGTTTCACAAGAGAATTTC 59.030 41.667 4.13 0.00 46.28 2.17
3252 6659 1.543429 GGCCCTGAATAACCGAGATGG 60.543 57.143 0.00 0.00 46.41 3.51
3255 6662 2.438021 CCCTGAATAACCGAGATGGGAA 59.562 50.000 0.00 0.00 44.64 3.97
3261 6668 8.100791 CCTGAATAACCGAGATGGGAATTATTA 58.899 37.037 0.00 0.00 44.64 0.98
3297 6704 4.271291 AGTTTCTTCTCGACTTTGCAAGAC 59.729 41.667 0.00 0.00 0.00 3.01
3298 6705 2.394708 TCTTCTCGACTTTGCAAGACG 58.605 47.619 0.00 7.40 45.56 4.18
3299 6706 2.128035 CTTCTCGACTTTGCAAGACGT 58.872 47.619 16.78 9.09 44.73 4.34
3300 6707 1.487482 TCTCGACTTTGCAAGACGTG 58.513 50.000 16.78 15.11 44.73 4.49
3311 6718 2.014335 CAAGACGTGCTGGATGATGA 57.986 50.000 0.00 0.00 0.00 2.92
3375 6782 3.089284 CGGATTAAAAGACCTTTGCCCT 58.911 45.455 0.00 0.00 32.36 5.19
3412 6839 6.924629 AGATGTTCGACGTTCTAGTTAAAC 57.075 37.500 0.00 0.00 0.00 2.01
3440 6870 5.185454 TGAAATTCGATGCCAGTGTTCTAT 58.815 37.500 0.00 0.00 0.00 1.98
3444 6874 3.562182 TCGATGCCAGTGTTCTATCCTA 58.438 45.455 0.00 0.00 0.00 2.94
3458 6890 0.698238 ATCCTACCCTGTGCTGCAAA 59.302 50.000 2.77 0.00 0.00 3.68
3460 6892 1.098050 CCTACCCTGTGCTGCAAATC 58.902 55.000 2.77 0.00 0.00 2.17
3473 6905 5.122711 GTGCTGCAAATCAAATTTTGGCTAT 59.877 36.000 2.77 0.00 37.13 2.97
3474 6906 5.706369 TGCTGCAAATCAAATTTTGGCTATT 59.294 32.000 0.00 0.00 37.13 1.73
3475 6907 6.877855 TGCTGCAAATCAAATTTTGGCTATTA 59.122 30.769 0.00 0.00 37.13 0.98
3476 6908 7.064847 TGCTGCAAATCAAATTTTGGCTATTAG 59.935 33.333 0.00 3.90 37.13 1.73
3496 6928 6.485830 TTAGATTTAGAGGTGACATGGAGG 57.514 41.667 0.00 0.00 0.00 4.30
3527 6959 4.461781 CCCAGAATGCACTCTGAAAGAAAT 59.538 41.667 25.97 0.00 44.82 2.17
3536 6968 5.456822 GCACTCTGAAAGAAATTGTGTTCAC 59.543 40.000 0.00 0.00 46.34 3.18
3564 6996 3.591196 TTGGGAAAGCAAAATCATCCG 57.409 42.857 0.00 0.00 0.00 4.18
3571 7006 0.877213 GCAAAATCATCCGCATGGCC 60.877 55.000 0.00 0.00 34.14 5.36
3581 7017 1.606885 CCGCATGGCCCTTTTGACAT 61.607 55.000 0.00 0.00 0.00 3.06
3589 7025 2.689983 GGCCCTTTTGACATATCCACTG 59.310 50.000 0.00 0.00 0.00 3.66
3590 7026 2.689983 GCCCTTTTGACATATCCACTGG 59.310 50.000 0.00 0.00 0.00 4.00
3591 7027 3.624707 GCCCTTTTGACATATCCACTGGA 60.625 47.826 0.00 0.00 35.55 3.86
3612 7076 6.880484 TGGATCAATCATCAAATTTTCTGGG 58.120 36.000 0.00 0.00 32.33 4.45
3614 7078 6.982724 GGATCAATCATCAAATTTTCTGGGTC 59.017 38.462 0.00 0.00 32.33 4.46
3649 7114 2.545106 CCATCAAACACTTTGCTTTGCC 59.455 45.455 0.00 0.00 40.43 4.52
3650 7115 3.460103 CATCAAACACTTTGCTTTGCCT 58.540 40.909 0.00 0.00 40.43 4.75
3651 7116 3.608316 TCAAACACTTTGCTTTGCCTT 57.392 38.095 0.00 0.00 40.43 4.35
3652 7117 3.260740 TCAAACACTTTGCTTTGCCTTG 58.739 40.909 0.00 0.00 40.43 3.61
3653 7118 1.655484 AACACTTTGCTTTGCCTTGC 58.345 45.000 0.00 0.00 0.00 4.01
3671 7136 5.409214 GCCTTGCTTGCTTATTCATCAAAAA 59.591 36.000 0.00 0.00 0.00 1.94
3676 7141 6.165577 GCTTGCTTATTCATCAAAAAGGGAA 58.834 36.000 0.00 0.00 0.00 3.97
3751 7216 7.150783 AGTAGCCATCTTGAAAAAGATTCAC 57.849 36.000 0.00 0.00 37.41 3.18
3781 7246 3.312285 TTTTGCCATGGCCCATGCG 62.312 57.895 33.44 12.39 40.20 4.73
3793 7258 4.648626 CATGCGATGGGGGCCGAT 62.649 66.667 0.00 0.00 0.00 4.18
3794 7259 4.335647 ATGCGATGGGGGCCGATC 62.336 66.667 0.00 0.25 0.00 3.69
3801 7266 1.355718 ATGGGGGCCGATCATCACTT 61.356 55.000 0.00 0.00 0.00 3.16
3808 7273 3.553096 GGGCCGATCATCACTTGTACTAG 60.553 52.174 2.56 2.56 0.00 2.57
3812 7277 6.448006 GCCGATCATCACTTGTACTAGTAAT 58.552 40.000 9.68 0.00 0.00 1.89
3814 7279 8.080417 GCCGATCATCACTTGTACTAGTAATAA 58.920 37.037 9.68 2.66 0.00 1.40
3857 7322 2.554142 CGGCATAATGAGAGCTCAACA 58.446 47.619 17.77 15.69 43.58 3.33
3858 7323 3.136763 CGGCATAATGAGAGCTCAACAT 58.863 45.455 17.77 17.24 43.58 2.71
3859 7324 4.309933 CGGCATAATGAGAGCTCAACATA 58.690 43.478 17.77 4.17 43.58 2.29
3860 7325 4.151335 CGGCATAATGAGAGCTCAACATAC 59.849 45.833 17.77 10.72 43.58 2.39
3861 7326 5.059161 GGCATAATGAGAGCTCAACATACA 58.941 41.667 17.77 12.12 43.58 2.29
3884 7349 5.413833 CAGCTCCTAATCATCACACTGTTTT 59.586 40.000 0.00 0.00 0.00 2.43
3991 7456 2.103094 TGAGTTCTGCTTGTACTGCTGT 59.897 45.455 0.66 0.66 0.00 4.40
3992 7457 3.134458 GAGTTCTGCTTGTACTGCTGTT 58.866 45.455 0.09 3.99 0.00 3.16
3993 7458 2.874701 AGTTCTGCTTGTACTGCTGTTG 59.125 45.455 0.09 0.00 0.00 3.33
3994 7459 2.614057 GTTCTGCTTGTACTGCTGTTGT 59.386 45.455 0.09 0.00 0.00 3.32
4006 7471 2.228822 CTGCTGTTGTTGTTGGGTATCC 59.771 50.000 0.00 0.00 0.00 2.59
4034 7499 4.799564 TCTTTGTCTTTTGGTTGCTGTT 57.200 36.364 0.00 0.00 0.00 3.16
4035 7500 5.906113 TCTTTGTCTTTTGGTTGCTGTTA 57.094 34.783 0.00 0.00 0.00 2.41
4036 7501 5.646606 TCTTTGTCTTTTGGTTGCTGTTAC 58.353 37.500 0.00 0.00 0.00 2.50
4056 7521 2.684881 ACTACTGCATTATTGGTGCTGC 59.315 45.455 0.00 0.00 42.91 5.25
4057 7522 1.843368 ACTGCATTATTGGTGCTGCT 58.157 45.000 0.00 0.00 42.91 4.24
4058 7523 1.475280 ACTGCATTATTGGTGCTGCTG 59.525 47.619 0.00 0.00 42.91 4.41
4076 7541 0.111639 TGGTACTGCTTTTGACCCCC 59.888 55.000 0.00 0.00 0.00 5.40
4091 7556 2.455565 CCCCGAGGAATCATGGGCT 61.456 63.158 0.00 0.00 40.50 5.19
4105 7570 3.394606 TCATGGGCTAAGGGGTTAATCTC 59.605 47.826 0.00 0.00 0.00 2.75
4126 7593 2.025887 CAGCTTTTGACCCCTGATAGGT 60.026 50.000 0.00 0.00 41.50 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 1948 3.122948 GCGTCAGTTTTCTAGCGATTCAA 59.877 43.478 0.00 0.00 0.00 2.69
81 1970 9.844257 AAGAATTCCTGAAGACTAAAGATATGG 57.156 33.333 0.65 0.00 0.00 2.74
85 1974 9.237187 GGAAAAGAATTCCTGAAGACTAAAGAT 57.763 33.333 0.65 0.00 35.73 2.40
97 1986 5.438761 AACTTGTCGGAAAAGAATTCCTG 57.561 39.130 14.75 0.00 36.45 3.86
103 2051 4.081322 AGCCTAACTTGTCGGAAAAGAA 57.919 40.909 14.75 1.86 0.00 2.52
104 2052 3.764237 AGCCTAACTTGTCGGAAAAGA 57.236 42.857 14.75 0.00 0.00 2.52
105 2053 5.934935 TTTAGCCTAACTTGTCGGAAAAG 57.065 39.130 6.37 6.37 0.00 2.27
141 2092 5.886609 TGGTCCCACTTTTGATCTAATTCA 58.113 37.500 0.00 0.00 0.00 2.57
149 2100 5.779241 TTCTCTATGGTCCCACTTTTGAT 57.221 39.130 0.00 0.00 0.00 2.57
152 2103 4.324267 CGTTTCTCTATGGTCCCACTTTT 58.676 43.478 0.00 0.00 0.00 2.27
191 2149 6.707440 TTGTGTGGAGTGTTTGATTTGTAT 57.293 33.333 0.00 0.00 0.00 2.29
220 2179 4.151689 ACCGTGTTATCTTCGTTTGACATG 59.848 41.667 0.00 0.00 0.00 3.21
287 2246 8.556194 CACTACAGTTGAGTTAATTGCACTTTA 58.444 33.333 0.00 0.00 29.74 1.85
288 2247 7.417612 CACTACAGTTGAGTTAATTGCACTTT 58.582 34.615 0.00 0.00 29.74 2.66
290 2249 5.049405 GCACTACAGTTGAGTTAATTGCACT 60.049 40.000 0.00 0.00 29.74 4.40
312 2271 1.002773 GTTTTAACTCGGGGAGGAGCA 59.997 52.381 0.00 0.00 37.57 4.26
313 2272 1.002773 TGTTTTAACTCGGGGAGGAGC 59.997 52.381 0.00 0.00 37.57 4.70
314 2273 2.302157 AGTGTTTTAACTCGGGGAGGAG 59.698 50.000 0.00 0.00 39.97 3.69
316 2275 2.853235 AGTGTTTTAACTCGGGGAGG 57.147 50.000 0.00 0.00 33.35 4.30
330 2290 3.701205 TGATGATGGCAGTGTAGTGTT 57.299 42.857 0.00 0.00 0.00 3.32
336 2296 2.941064 CGATCTTTGATGATGGCAGTGT 59.059 45.455 0.00 0.00 0.00 3.55
341 2301 2.551032 TGATGCGATCTTTGATGATGGC 59.449 45.455 4.89 4.89 44.66 4.40
344 2304 6.051074 TGTAACTGATGCGATCTTTGATGAT 58.949 36.000 0.00 0.00 0.00 2.45
363 2323 7.217825 GCAACGAGTGATACTAGTAACTGTAAC 59.782 40.741 11.20 2.02 32.85 2.50
373 2333 9.988350 ATTTTTATTTGCAACGAGTGATACTAG 57.012 29.630 0.00 0.00 0.00 2.57
379 2339 7.489435 TGTTGAATTTTTATTTGCAACGAGTGA 59.511 29.630 0.00 0.00 38.65 3.41
408 2376 9.481340 CTCGGAGAACAATAATTGATCATCTTA 57.519 33.333 0.00 0.00 35.19 2.10
440 2408 1.081833 AGAGAGGGACCTGTGGCAT 59.918 57.895 0.00 0.00 0.00 4.40
442 2410 2.985456 CAGAGAGGGACCTGTGGC 59.015 66.667 0.00 0.00 0.00 5.01
487 2455 3.457749 AGAAGAGGAGGCCCTTATTTGAG 59.542 47.826 0.00 0.00 44.53 3.02
590 2565 6.183360 TGGTAGTGGGTCTGTGTATTTATACG 60.183 42.308 0.00 0.00 36.06 3.06
664 2650 2.202797 CCCACGGATGAGCACTCG 60.203 66.667 0.00 0.00 0.00 4.18
666 2652 4.457496 CGCCCACGGATGAGCACT 62.457 66.667 0.00 0.00 34.97 4.40
696 2682 1.349026 CCAGGAGAGGAGAGCACAAAA 59.651 52.381 0.00 0.00 0.00 2.44
716 2702 1.516423 GTAGGTGGCCGAGGAGAAC 59.484 63.158 0.00 0.00 0.00 3.01
748 2734 2.203480 GGCAGTTGTGGGCAAGGA 60.203 61.111 0.00 0.00 34.94 3.36
762 2749 2.922503 TGGAAGACGAGCAGGGCA 60.923 61.111 0.00 0.00 0.00 5.36
797 2784 3.119424 GGGACCAGAGTCTCGTTCTTAAG 60.119 52.174 0.00 0.00 43.05 1.85
800 2787 1.258676 GGGACCAGAGTCTCGTTCTT 58.741 55.000 0.00 0.00 43.05 2.52
822 2809 2.420890 CCTCGATCCAGGCTCTGC 59.579 66.667 0.00 0.00 0.00 4.26
880 2867 2.202756 GATCGAGCCGAAACCGCT 60.203 61.111 1.44 0.00 39.99 5.52
881 2868 3.262686 GGATCGAGCCGAAACCGC 61.263 66.667 2.80 0.00 39.99 5.68
922 2909 3.737172 CGGGCCAAAAGCTCACCG 61.737 66.667 4.39 0.00 45.13 4.94
1010 3008 2.050350 CAGGCAGGCCATGACCAAG 61.050 63.158 13.63 0.00 37.86 3.61
1012 3010 4.746309 GCAGGCAGGCCATGACCA 62.746 66.667 13.63 0.00 37.86 4.02
1014 3012 2.827642 GAGCAGGCAGGCCATGAC 60.828 66.667 13.63 2.05 38.92 3.06
1015 3013 4.119363 GGAGCAGGCAGGCCATGA 62.119 66.667 13.63 0.00 38.92 3.07
1016 3014 4.435970 TGGAGCAGGCAGGCCATG 62.436 66.667 13.63 8.97 38.92 3.66
1017 3015 4.437587 GTGGAGCAGGCAGGCCAT 62.438 66.667 13.63 0.00 38.92 4.40
1074 3085 0.248825 CCGCTCTCCTCGATCTGTTG 60.249 60.000 0.00 0.00 0.00 3.33
1119 3130 0.617413 CAGGTTGAGGCATCAGACCT 59.383 55.000 21.64 21.64 42.61 3.85
1120 3131 0.615331 TCAGGTTGAGGCATCAGACC 59.385 55.000 18.80 18.80 36.61 3.85
1121 3132 2.011046 GCTCAGGTTGAGGCATCAGAC 61.011 57.143 0.00 3.29 44.43 3.51
1122 3133 0.251354 GCTCAGGTTGAGGCATCAGA 59.749 55.000 0.00 0.00 44.43 3.27
1123 3134 2.777969 GCTCAGGTTGAGGCATCAG 58.222 57.895 0.00 0.00 44.43 2.90
1166 3177 1.469423 GCGTCGGGGAAGTAGAAGAAG 60.469 57.143 0.00 0.00 0.00 2.85
1167 3178 0.529378 GCGTCGGGGAAGTAGAAGAA 59.471 55.000 0.00 0.00 0.00 2.52
1168 3179 1.318158 GGCGTCGGGGAAGTAGAAGA 61.318 60.000 0.00 0.00 0.00 2.87
1174 3185 3.752339 GTACGGCGTCGGGGAAGT 61.752 66.667 19.21 0.00 41.39 3.01
1437 3457 1.067749 CTGGATCCTGAGCTGCGAG 59.932 63.158 14.23 0.00 0.00 5.03
1613 3633 2.125326 TAGTCCTCCGACATGGCCG 61.125 63.158 0.00 0.00 41.87 6.13
1769 3804 0.963856 TGCATGGCAAGAGCTCAAGG 60.964 55.000 17.77 5.69 41.70 3.61
1841 3876 5.188327 TCCGCATACATACAGAGAGAAAG 57.812 43.478 0.00 0.00 0.00 2.62
1847 3882 5.048434 TCAAGAGATCCGCATACATACAGAG 60.048 44.000 0.00 0.00 0.00 3.35
1861 3896 6.128007 TGGCGAGTAAATTTTTCAAGAGATCC 60.128 38.462 0.00 0.00 0.00 3.36
1938 3978 3.314357 ACAGCCACATCAATCAATCATCG 59.686 43.478 0.00 0.00 0.00 3.84
1983 4023 9.399797 ACCATTCGCACATATCATTATCATTAT 57.600 29.630 0.00 0.00 0.00 1.28
1984 4024 8.791327 ACCATTCGCACATATCATTATCATTA 57.209 30.769 0.00 0.00 0.00 1.90
1985 4025 7.609146 AGACCATTCGCACATATCATTATCATT 59.391 33.333 0.00 0.00 0.00 2.57
1986 4026 7.065443 CAGACCATTCGCACATATCATTATCAT 59.935 37.037 0.00 0.00 0.00 2.45
1987 4027 6.369615 CAGACCATTCGCACATATCATTATCA 59.630 38.462 0.00 0.00 0.00 2.15
1988 4028 6.369890 ACAGACCATTCGCACATATCATTATC 59.630 38.462 0.00 0.00 0.00 1.75
2048 4095 6.038050 TCACGCATGCTGTCAAAATGAATATA 59.962 34.615 17.13 0.00 0.00 0.86
2050 4097 4.155644 TCACGCATGCTGTCAAAATGAATA 59.844 37.500 17.13 0.00 0.00 1.75
2053 4100 1.878734 TCACGCATGCTGTCAAAATGA 59.121 42.857 17.13 5.34 0.00 2.57
2054 4101 2.334971 TCACGCATGCTGTCAAAATG 57.665 45.000 17.13 0.00 0.00 2.32
2064 4111 1.459975 CATCTAGCAGATCACGCATGC 59.540 52.381 7.91 7.91 40.29 4.06
2070 4117 4.025061 GTGAATGCACATCTAGCAGATCAC 60.025 45.833 15.92 15.92 46.12 3.06
2172 4317 3.464833 AGTGCATGATTTTATCCCTCCCT 59.535 43.478 0.00 0.00 0.00 4.20
2187 4332 4.340263 CGAGAATTTGATGTCAGTGCATG 58.660 43.478 5.01 0.00 0.00 4.06
2209 4354 9.983804 GTCAAATACTAGCAGTAAATACAAACC 57.016 33.333 0.00 0.00 33.89 3.27
2214 4359 9.542462 TCCATGTCAAATACTAGCAGTAAATAC 57.458 33.333 0.00 0.00 33.89 1.89
2217 4362 7.549134 CACTCCATGTCAAATACTAGCAGTAAA 59.451 37.037 0.00 0.00 33.89 2.01
2238 4387 2.490903 ACTTGCAATGATGAAGCACTCC 59.509 45.455 0.00 0.00 38.11 3.85
2301 4455 8.867935 GCAGATGTATTATGTTGATACTGCTAG 58.132 37.037 0.00 0.00 31.40 3.42
2329 4483 7.040494 ACTGTCATGATCTTGATGAAGTACAG 58.960 38.462 13.82 15.35 31.65 2.74
2470 5791 0.409484 ACAACCCCCTTGGATTGGAG 59.591 55.000 0.00 0.00 38.00 3.86
2474 5795 3.053359 TCAAAACAACCCCCTTGGATT 57.947 42.857 0.00 0.00 38.00 3.01
2475 5796 2.785357 TCAAAACAACCCCCTTGGAT 57.215 45.000 0.00 0.00 38.00 3.41
2476 5797 2.785357 ATCAAAACAACCCCCTTGGA 57.215 45.000 0.00 0.00 38.00 3.53
2477 5798 2.038426 GGAATCAAAACAACCCCCTTGG 59.962 50.000 0.00 0.00 41.37 3.61
2478 5799 2.288763 CGGAATCAAAACAACCCCCTTG 60.289 50.000 0.00 0.00 35.77 3.61
2484 5805 3.296322 TGATGCGGAATCAAAACAACC 57.704 42.857 0.00 0.00 42.49 3.77
2498 5819 1.522676 ACGTGAAAGCGATATGATGCG 59.477 47.619 0.00 0.00 35.87 4.73
2499 5820 3.981416 TCTACGTGAAAGCGATATGATGC 59.019 43.478 0.00 0.00 35.59 3.91
2501 5822 6.757010 AGTTTTCTACGTGAAAGCGATATGAT 59.243 34.615 15.71 2.01 46.16 2.45
2502 5823 6.097356 AGTTTTCTACGTGAAAGCGATATGA 58.903 36.000 15.71 0.41 46.16 2.15
2503 5824 6.332504 AGTTTTCTACGTGAAAGCGATATG 57.667 37.500 15.71 0.00 46.16 1.78
2504 5825 7.306632 GCATAGTTTTCTACGTGAAAGCGATAT 60.307 37.037 15.68 10.15 46.16 1.63
2505 5826 6.020121 GCATAGTTTTCTACGTGAAAGCGATA 60.020 38.462 15.68 8.96 46.16 2.92
2586 5910 7.060421 TGCCAAATAGTTTAATCCCTAGGAAG 58.940 38.462 11.48 0.00 34.34 3.46
2682 6007 2.102925 TGCAATGACGATGATAGCTGGA 59.897 45.455 0.00 0.00 0.00 3.86
2683 6008 2.486918 TGCAATGACGATGATAGCTGG 58.513 47.619 0.00 0.00 0.00 4.85
2700 6025 8.551205 TGCGATTTTTATGTTTTTGTATTTGCA 58.449 25.926 0.00 0.00 0.00 4.08
2724 6049 7.171508 TGTCAAACTAGCAAGCATATAGTATGC 59.828 37.037 12.74 12.74 44.85 3.14
2725 6050 8.593492 TGTCAAACTAGCAAGCATATAGTATG 57.407 34.615 0.00 0.00 0.00 2.39
2726 6051 7.386299 GCTGTCAAACTAGCAAGCATATAGTAT 59.614 37.037 0.00 0.00 39.67 2.12
2729 6134 5.049818 GGCTGTCAAACTAGCAAGCATATAG 60.050 44.000 0.00 0.00 41.63 1.31
2789 6194 2.439507 GGCACAGATCCCTTTCCTATCA 59.560 50.000 0.00 0.00 0.00 2.15
2844 6249 0.391661 TTGAGCGCATCTCCAGGTTC 60.392 55.000 11.47 0.00 41.18 3.62
2930 6336 0.042794 CTTTGTGCAAAGCAAAGCGC 60.043 50.000 13.42 0.00 43.86 5.92
2934 6340 2.669300 TGCTCTTTGTGCAAAGCAAA 57.331 40.000 17.16 4.18 45.48 3.68
2935 6341 2.894763 ATGCTCTTTGTGCAAAGCAA 57.105 40.000 17.16 7.66 45.48 3.91
2969 6375 1.488390 CACATAGCTTTTGGGGGCAT 58.512 50.000 0.00 0.00 0.00 4.40
2998 6404 4.910195 TGCCAACTGATGAGTGAGTTATT 58.090 39.130 0.00 0.00 29.59 1.40
2999 6405 4.558226 TGCCAACTGATGAGTGAGTTAT 57.442 40.909 0.00 0.00 29.59 1.89
3003 6409 5.220989 CCAATAATGCCAACTGATGAGTGAG 60.221 44.000 0.00 0.00 30.61 3.51
3005 6411 4.735578 GCCAATAATGCCAACTGATGAGTG 60.736 45.833 0.00 0.00 30.61 3.51
3049 6456 8.762645 AGAAAGAAAGAAAGAAAAGGACCAATT 58.237 29.630 0.00 0.00 0.00 2.32
3050 6457 8.311395 AGAAAGAAAGAAAGAAAAGGACCAAT 57.689 30.769 0.00 0.00 0.00 3.16
3051 6458 7.718334 AGAAAGAAAGAAAGAAAAGGACCAA 57.282 32.000 0.00 0.00 0.00 3.67
3052 6459 7.396055 TGAAGAAAGAAAGAAAGAAAAGGACCA 59.604 33.333 0.00 0.00 0.00 4.02
3053 6460 7.772166 TGAAGAAAGAAAGAAAGAAAAGGACC 58.228 34.615 0.00 0.00 0.00 4.46
3073 6480 2.596851 GCTCTGCCACCCCTGAAGA 61.597 63.158 0.00 0.00 0.00 2.87
3126 6533 2.490217 CACCGCCTCGTCGAAGAT 59.510 61.111 0.35 0.00 40.67 2.40
3184 6591 8.469200 ACTGAAATGAAATTCTCTTGTGAAACA 58.531 29.630 0.00 0.00 40.54 2.83
3198 6605 5.259632 CCTTCTCCTCCACTGAAATGAAAT 58.740 41.667 0.00 0.00 0.00 2.17
3199 6606 4.655963 CCTTCTCCTCCACTGAAATGAAA 58.344 43.478 0.00 0.00 0.00 2.69
3200 6607 3.560025 GCCTTCTCCTCCACTGAAATGAA 60.560 47.826 0.00 0.00 0.00 2.57
3201 6608 2.026822 GCCTTCTCCTCCACTGAAATGA 60.027 50.000 0.00 0.00 0.00 2.57
3202 6609 2.290514 TGCCTTCTCCTCCACTGAAATG 60.291 50.000 0.00 0.00 0.00 2.32
3261 6668 9.678941 GTCGAGAAGAAACTAAAAATGGAAAAT 57.321 29.630 0.00 0.00 0.00 1.82
3266 6673 7.113544 GCAAAGTCGAGAAGAAACTAAAAATGG 59.886 37.037 0.00 0.00 0.00 3.16
3297 6704 3.119388 ACCAAAAATCATCATCCAGCACG 60.119 43.478 0.00 0.00 0.00 5.34
3298 6705 4.082081 TGACCAAAAATCATCATCCAGCAC 60.082 41.667 0.00 0.00 0.00 4.40
3299 6706 4.087907 TGACCAAAAATCATCATCCAGCA 58.912 39.130 0.00 0.00 0.00 4.41
3300 6707 4.724074 TGACCAAAAATCATCATCCAGC 57.276 40.909 0.00 0.00 0.00 4.85
3311 6718 6.494491 TCATTCTGTTCTCCATGACCAAAAAT 59.506 34.615 0.00 0.00 0.00 1.82
3375 6782 5.635280 GTCGAACATCTTTCAGTGATTCAGA 59.365 40.000 0.00 0.00 0.00 3.27
3424 6851 2.898729 AGGATAGAACACTGGCATCG 57.101 50.000 0.00 0.00 0.00 3.84
3440 6870 0.698238 ATTTGCAGCACAGGGTAGGA 59.302 50.000 0.00 0.00 0.00 2.94
3444 6874 1.412079 TTTGATTTGCAGCACAGGGT 58.588 45.000 0.00 0.00 0.00 4.34
3473 6905 5.163301 GCCTCCATGTCACCTCTAAATCTAA 60.163 44.000 0.00 0.00 0.00 2.10
3474 6906 4.345257 GCCTCCATGTCACCTCTAAATCTA 59.655 45.833 0.00 0.00 0.00 1.98
3475 6907 3.135530 GCCTCCATGTCACCTCTAAATCT 59.864 47.826 0.00 0.00 0.00 2.40
3476 6908 3.118261 TGCCTCCATGTCACCTCTAAATC 60.118 47.826 0.00 0.00 0.00 2.17
3527 6959 7.469456 GCTTTCCCAATAGTTTAGTGAACACAA 60.469 37.037 7.68 0.00 40.84 3.33
3536 6968 9.305925 GATGATTTTGCTTTCCCAATAGTTTAG 57.694 33.333 0.00 0.00 0.00 1.85
3544 6976 2.353605 GCGGATGATTTTGCTTTCCCAA 60.354 45.455 0.00 0.00 0.00 4.12
3564 6996 2.036346 GGATATGTCAAAAGGGCCATGC 59.964 50.000 6.18 0.00 0.00 4.06
3571 7006 5.439721 TGATCCAGTGGATATGTCAAAAGG 58.560 41.667 24.89 0.00 43.27 3.11
3581 7017 8.771521 AAATTTGATGATTGATCCAGTGGATA 57.228 30.769 24.89 10.94 43.27 2.59
3589 7025 6.881570 ACCCAGAAAATTTGATGATTGATCC 58.118 36.000 0.00 0.00 0.00 3.36
3590 7026 7.779073 AGACCCAGAAAATTTGATGATTGATC 58.221 34.615 0.00 0.00 0.00 2.92
3591 7027 7.729124 AGACCCAGAAAATTTGATGATTGAT 57.271 32.000 0.00 0.00 0.00 2.57
3649 7114 6.091713 CCCTTTTTGATGAATAAGCAAGCAAG 59.908 38.462 0.00 0.00 0.00 4.01
3650 7115 5.933463 CCCTTTTTGATGAATAAGCAAGCAA 59.067 36.000 0.00 0.00 0.00 3.91
3651 7116 5.245751 TCCCTTTTTGATGAATAAGCAAGCA 59.754 36.000 0.00 0.00 0.00 3.91
3652 7117 5.723295 TCCCTTTTTGATGAATAAGCAAGC 58.277 37.500 0.00 0.00 0.00 4.01
3653 7118 7.605449 TCTTCCCTTTTTGATGAATAAGCAAG 58.395 34.615 0.00 0.00 0.00 4.01
3671 7136 2.716424 TGGTTTCAGTTCCATCTTCCCT 59.284 45.455 0.00 0.00 0.00 4.20
3676 7141 2.887152 GCAGTTGGTTTCAGTTCCATCT 59.113 45.455 0.00 0.00 35.08 2.90
3751 7216 2.376808 TGGCAAAACACACAAACCTG 57.623 45.000 0.00 0.00 0.00 4.00
3763 7228 2.669849 GCATGGGCCATGGCAAAA 59.330 55.556 39.54 21.89 41.64 2.44
3781 7246 1.302832 GTGATGATCGGCCCCCATC 60.303 63.158 15.79 15.79 37.71 3.51
3808 7273 5.234972 GGGCTGCTGCATTTCATTTTATTAC 59.765 40.000 17.89 0.00 41.91 1.89
3812 7277 2.417107 CGGGCTGCTGCATTTCATTTTA 60.417 45.455 17.89 0.00 41.91 1.52
3814 7279 0.108520 CGGGCTGCTGCATTTCATTT 60.109 50.000 17.89 0.00 41.91 2.32
3816 7281 2.420568 CCGGGCTGCTGCATTTCAT 61.421 57.895 17.89 0.00 41.91 2.57
3817 7282 3.063704 CCGGGCTGCTGCATTTCA 61.064 61.111 17.89 0.00 41.91 2.69
3818 7283 2.751436 TCCGGGCTGCTGCATTTC 60.751 61.111 17.89 0.00 41.91 2.17
3857 7322 5.365025 ACAGTGTGATGATTAGGAGCTGTAT 59.635 40.000 0.00 0.00 33.60 2.29
3858 7323 4.711846 ACAGTGTGATGATTAGGAGCTGTA 59.288 41.667 0.00 0.00 33.60 2.74
3859 7324 3.517100 ACAGTGTGATGATTAGGAGCTGT 59.483 43.478 0.00 0.00 0.00 4.40
3860 7325 4.134379 ACAGTGTGATGATTAGGAGCTG 57.866 45.455 0.00 0.00 0.00 4.24
3861 7326 4.833478 AACAGTGTGATGATTAGGAGCT 57.167 40.909 0.00 0.00 0.00 4.09
3956 7421 4.623886 GCAGAACTCACTCACCCATGAATA 60.624 45.833 0.00 0.00 33.30 1.75
4006 7471 6.536224 AGCAACCAAAAGACAAAGAAAAGATG 59.464 34.615 0.00 0.00 0.00 2.90
4034 7499 3.876914 GCAGCACCAATAATGCAGTAGTA 59.123 43.478 0.00 0.00 45.92 1.82
4035 7500 2.684881 GCAGCACCAATAATGCAGTAGT 59.315 45.455 0.00 0.00 45.92 2.73
4036 7501 2.947652 AGCAGCACCAATAATGCAGTAG 59.052 45.455 0.00 0.00 45.92 2.57
4056 7521 1.534729 GGGGTCAAAAGCAGTACCAG 58.465 55.000 0.00 0.00 33.46 4.00
4057 7522 0.111639 GGGGGTCAAAAGCAGTACCA 59.888 55.000 0.00 0.00 33.46 3.25
4058 7523 0.958876 CGGGGGTCAAAAGCAGTACC 60.959 60.000 0.00 0.00 0.00 3.34
4076 7541 1.271054 CCCTTAGCCCATGATTCCTCG 60.271 57.143 0.00 0.00 0.00 4.63
4091 7556 5.944007 GTCAAAAGCTGAGATTAACCCCTTA 59.056 40.000 0.00 0.00 33.60 2.69
4105 7570 2.025887 ACCTATCAGGGGTCAAAAGCTG 60.026 50.000 0.00 0.00 40.58 4.24


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

AutoCloner maintained by Alex Coulton.