Multiple sequence alignment - TraesCS1B01G358400

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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 TraesCS1B01G358400 chr1B 100.000 6213 0 0 1 6213 587988174 587994386 0.000000e+00 11474.0
1 TraesCS1B01G358400 chr1B 83.680 2212 315 27 2925 5119 588005098 588007280 0.000000e+00 2043.0
2 TraesCS1B01G358400 chr1B 77.352 2190 427 44 2948 5111 588153115 588155261 0.000000e+00 1232.0
3 TraesCS1B01G358400 chr1B 79.854 412 74 8 3899 4307 622704780 622704375 6.090000e-75 292.0
4 TraesCS1B01G358400 chr1B 78.092 283 46 15 5811 6085 533951513 533951239 1.390000e-36 165.0
5 TraesCS1B01G358400 chr1B 93.443 61 3 1 2869 2929 415223381 415223440 8.580000e-14 89.8
6 TraesCS1B01G358400 chr1A 89.055 3746 299 42 2550 6213 532476639 532480355 0.000000e+00 4543.0
7 TraesCS1B01G358400 chr1A 76.998 2065 389 51 3022 5047 532487976 532489993 0.000000e+00 1103.0
8 TraesCS1B01G358400 chr1A 90.187 856 62 7 1052 1886 532457830 532458684 0.000000e+00 1096.0
9 TraesCS1B01G358400 chr1A 95.205 292 13 1 2012 2302 532458736 532459027 1.580000e-125 460.0
10 TraesCS1B01G358400 chr1A 89.811 265 17 7 532 796 532452275 532452529 1.290000e-86 331.0
11 TraesCS1B01G358400 chr1A 89.362 235 25 0 2299 2533 532471267 532471501 4.710000e-76 296.0
12 TraesCS1B01G358400 chr1A 93.333 165 9 1 889 1053 532456834 532456996 6.220000e-60 243.0
13 TraesCS1B01G358400 chr1A 79.688 320 65 0 1410 1729 532640035 532639716 1.350000e-56 231.0
14 TraesCS1B01G358400 chr1A 79.126 206 30 11 5784 5986 154392478 154392673 5.050000e-26 130.0
15 TraesCS1B01G358400 chr1D 92.333 2726 188 12 3499 6213 434284578 434287293 0.000000e+00 3856.0
16 TraesCS1B01G358400 chr1D 90.977 2527 164 25 61 2550 434280873 434283372 0.000000e+00 3345.0
17 TraesCS1B01G358400 chr1D 84.327 1710 219 30 2925 4616 434337419 434339097 0.000000e+00 1628.0
18 TraesCS1B01G358400 chr1D 94.524 913 49 1 2550 3461 434283410 434284322 0.000000e+00 1408.0
19 TraesCS1B01G358400 chr1D 77.856 2127 405 45 3022 5119 434369702 434371791 0.000000e+00 1258.0
20 TraesCS1B01G358400 chr1D 85.686 503 68 2 4621 5119 434339136 434339638 1.530000e-145 527.0
21 TraesCS1B01G358400 chr1D 82.609 552 80 13 1987 2535 434322404 434322942 2.030000e-129 473.0
22 TraesCS1B01G358400 chr1D 90.083 363 30 3 2925 3286 434528833 434529190 3.390000e-127 466.0
23 TraesCS1B01G358400 chr1D 78.624 407 70 9 3905 4308 452623563 452623171 2.870000e-63 254.0
24 TraesCS1B01G358400 chr1D 74.817 409 87 13 5678 6084 292428806 292428412 2.980000e-38 171.0
25 TraesCS1B01G358400 chr1D 79.828 233 39 6 5690 5921 292429642 292429417 4.980000e-36 163.0
26 TraesCS1B01G358400 chr7A 77.246 1169 238 23 3894 5043 77562568 77561409 0.000000e+00 660.0
27 TraesCS1B01G358400 chr7A 98.148 54 1 0 2876 2929 126042179 126042232 1.840000e-15 95.3
28 TraesCS1B01G358400 chr7A 92.063 63 5 0 2875 2937 663675268 663675330 8.580000e-14 89.8
29 TraesCS1B01G358400 chr7A 90.769 65 6 0 2875 2939 727460135 727460071 3.090000e-13 87.9
30 TraesCS1B01G358400 chr5D 78.484 488 89 13 5675 6158 377480409 377479934 7.820000e-79 305.0
31 TraesCS1B01G358400 chr3D 82.773 238 32 7 5676 5911 364273757 364273527 2.940000e-48 204.0
32 TraesCS1B01G358400 chr3D 75.904 249 50 9 9 251 359599757 359599513 1.090000e-22 119.0
33 TraesCS1B01G358400 chr7B 76.253 379 86 3 1434 1810 15775597 15775973 1.370000e-46 198.0
34 TraesCS1B01G358400 chr7B 85.507 69 2 6 1906 1966 662141851 662141783 1.450000e-06 65.8
35 TraesCS1B01G358400 chr6B 73.408 534 108 19 4 510 67675822 67676348 1.070000e-37 169.0
36 TraesCS1B01G358400 chr6B 74.886 219 47 8 18 232 219565779 219565993 6.630000e-15 93.5
37 TraesCS1B01G358400 chr6B 80.702 114 16 4 1868 1976 693099116 693099228 3.990000e-12 84.2
38 TraesCS1B01G358400 chr6B 87.302 63 2 4 1909 1966 270074625 270074686 4.020000e-07 67.6
39 TraesCS1B01G358400 chr6B 86.154 65 4 2 1914 1973 675100660 675100596 1.450000e-06 65.8
40 TraesCS1B01G358400 chr2D 76.610 295 60 9 5701 5995 508236227 508235942 3.000000e-33 154.0
41 TraesCS1B01G358400 chr2B 98.214 56 1 0 2875 2930 412747189 412747244 1.430000e-16 99.0
42 TraesCS1B01G358400 chr7D 98.182 55 1 0 2875 2929 474349092 474349146 5.130000e-16 97.1
43 TraesCS1B01G358400 chr7D 86.364 66 2 4 1907 1966 394968958 394969022 1.450000e-06 65.8
44 TraesCS1B01G358400 chr6D 98.182 55 1 0 2875 2929 84620341 84620395 5.130000e-16 97.1
45 TraesCS1B01G358400 chr6D 86.364 66 2 5 1907 1966 307041608 307041672 1.450000e-06 65.8
46 TraesCS1B01G358400 chr4B 81.416 113 21 0 1404 1516 5406465 5406577 6.630000e-15 93.5
47 TraesCS1B01G358400 chr5B 86.364 66 2 5 1907 1966 357720497 357720561 1.450000e-06 65.8
48 TraesCS1B01G358400 chr4A 79.121 91 13 5 1888 1973 447568905 447568994 2.420000e-04 58.4
49 TraesCS1B01G358400 chr4D 100.000 28 0 0 5703 5730 443157911 443157938 1.100000e-02 52.8


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 TraesCS1B01G358400 chr1B 587988174 587994386 6212 False 11474.000000 11474 100.000000 1 6213 1 chr1B.!!$F2 6212
1 TraesCS1B01G358400 chr1B 588005098 588007280 2182 False 2043.000000 2043 83.680000 2925 5119 1 chr1B.!!$F3 2194
2 TraesCS1B01G358400 chr1B 588153115 588155261 2146 False 1232.000000 1232 77.352000 2948 5111 1 chr1B.!!$F4 2163
3 TraesCS1B01G358400 chr1A 532476639 532480355 3716 False 4543.000000 4543 89.055000 2550 6213 1 chr1A.!!$F4 3663
4 TraesCS1B01G358400 chr1A 532487976 532489993 2017 False 1103.000000 1103 76.998000 3022 5047 1 chr1A.!!$F5 2025
5 TraesCS1B01G358400 chr1A 532456834 532459027 2193 False 599.666667 1096 92.908333 889 2302 3 chr1A.!!$F6 1413
6 TraesCS1B01G358400 chr1D 434280873 434287293 6420 False 2869.666667 3856 92.611333 61 6213 3 chr1D.!!$F4 6152
7 TraesCS1B01G358400 chr1D 434369702 434371791 2089 False 1258.000000 1258 77.856000 3022 5119 1 chr1D.!!$F2 2097
8 TraesCS1B01G358400 chr1D 434337419 434339638 2219 False 1077.500000 1628 85.006500 2925 5119 2 chr1D.!!$F5 2194
9 TraesCS1B01G358400 chr1D 434322404 434322942 538 False 473.000000 473 82.609000 1987 2535 1 chr1D.!!$F1 548
10 TraesCS1B01G358400 chr7A 77561409 77562568 1159 True 660.000000 660 77.246000 3894 5043 1 chr7A.!!$R1 1149

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
38 39 0.107945 ATCTTCTCTGTTGGCTCGGC 60.108 55.0 0.00 0.0 0.00 5.54 F
807 836 0.179001 GTGGGTACAAAGTGGTGGCT 60.179 55.0 0.00 0.0 0.00 4.75 F
2227 3117 0.033208 ACCCAACAATCCATCGCCAT 60.033 50.0 0.00 0.0 0.00 4.40 F
2336 3227 0.036765 TGGCACCCAGATAACGTCAC 60.037 55.0 0.00 0.0 0.00 3.67 F
3733 4935 0.549950 AGGCATAGGCAAGAGCACAT 59.450 50.0 0.15 0.0 44.61 3.21 F
4729 5997 0.396695 ATGTCGACCCCGAGTACCAT 60.397 55.0 14.12 0.0 46.52 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 2597 0.319040 CACCTGCGGGTAGATCATCG 60.319 60.0 19.20 0.00 45.41 3.84 R
2311 3202 0.106569 TTATCTGGGTGCCATGGCTG 60.107 55.0 35.53 19.89 42.51 4.85 R
3827 5034 0.530744 AGCTCGTCGTGGCTTCATTA 59.469 50.0 9.01 0.00 34.96 1.90 R
3954 5161 0.552615 AACCCTCCCTGGCCAAGTAT 60.553 55.0 7.01 0.00 0.00 2.12 R
4966 6234 0.713883 GTCGTTGCGGTGACACATAG 59.286 55.0 8.08 0.00 35.20 2.23 R
6142 7471 0.738389 ACTGAACGTTTGCCAAGTGG 59.262 50.0 0.46 0.00 38.53 4.00 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 3.215671 CCTCGGGGATCTTCTCTGT 57.784 57.895 0.00 0.00 33.58 3.41
30 31 1.490574 CCTCGGGGATCTTCTCTGTT 58.509 55.000 0.00 0.00 33.58 3.16
31 32 1.137872 CCTCGGGGATCTTCTCTGTTG 59.862 57.143 0.00 0.00 33.58 3.33
32 33 1.137872 CTCGGGGATCTTCTCTGTTGG 59.862 57.143 0.00 0.00 0.00 3.77
33 34 0.462759 CGGGGATCTTCTCTGTTGGC 60.463 60.000 0.00 0.00 0.00 4.52
34 35 0.915364 GGGGATCTTCTCTGTTGGCT 59.085 55.000 0.00 0.00 0.00 4.75
35 36 1.134250 GGGGATCTTCTCTGTTGGCTC 60.134 57.143 0.00 0.00 0.00 4.70
36 37 1.472376 GGGATCTTCTCTGTTGGCTCG 60.472 57.143 0.00 0.00 0.00 5.03
37 38 1.472376 GGATCTTCTCTGTTGGCTCGG 60.472 57.143 0.00 0.00 0.00 4.63
38 39 0.107945 ATCTTCTCTGTTGGCTCGGC 60.108 55.000 0.00 0.00 0.00 5.54
39 40 1.188219 TCTTCTCTGTTGGCTCGGCT 61.188 55.000 0.00 0.00 0.00 5.52
40 41 0.321122 CTTCTCTGTTGGCTCGGCTT 60.321 55.000 0.00 0.00 0.00 4.35
41 42 0.973632 TTCTCTGTTGGCTCGGCTTA 59.026 50.000 0.00 0.00 0.00 3.09
42 43 1.195115 TCTCTGTTGGCTCGGCTTAT 58.805 50.000 0.00 0.00 0.00 1.73
43 44 1.137086 TCTCTGTTGGCTCGGCTTATC 59.863 52.381 0.00 0.00 0.00 1.75
44 45 0.901827 TCTGTTGGCTCGGCTTATCA 59.098 50.000 0.00 0.00 0.00 2.15
45 46 1.486310 TCTGTTGGCTCGGCTTATCAT 59.514 47.619 0.00 0.00 0.00 2.45
46 47 1.600957 CTGTTGGCTCGGCTTATCATG 59.399 52.381 0.00 0.00 0.00 3.07
47 48 0.308993 GTTGGCTCGGCTTATCATGC 59.691 55.000 0.00 0.00 0.00 4.06
48 49 0.819259 TTGGCTCGGCTTATCATGCC 60.819 55.000 0.00 0.00 46.42 4.40
57 58 3.664107 GGCTTATCATGCCTTATGTCGA 58.336 45.455 0.00 0.00 46.38 4.20
58 59 3.433615 GGCTTATCATGCCTTATGTCGAC 59.566 47.826 9.11 9.11 46.38 4.20
59 60 3.121944 GCTTATCATGCCTTATGTCGACG 59.878 47.826 11.62 0.00 38.01 5.12
83 84 6.314648 CGGTCATCTCTTTCATGAATCTTTCA 59.685 38.462 9.40 0.00 45.01 2.69
110 111 4.164843 AGAAAACACCCTTGTAGCTGAA 57.835 40.909 0.00 0.00 33.55 3.02
142 143 3.383620 TTTGTTTGGCAACTGCTATGG 57.616 42.857 0.00 0.00 41.70 2.74
180 181 2.354704 GGATGGAGGTGATCAAACGACA 60.355 50.000 0.00 0.00 0.00 4.35
186 187 2.303022 AGGTGATCAAACGACATGACCT 59.697 45.455 0.00 0.00 0.00 3.85
219 220 5.336451 GGTTGTGTCCCATTTATGAAGTTCC 60.336 44.000 0.00 0.00 0.00 3.62
221 222 3.377172 GTGTCCCATTTATGAAGTTCCGG 59.623 47.826 0.00 0.00 0.00 5.14
225 226 4.412199 TCCCATTTATGAAGTTCCGGAGAT 59.588 41.667 3.34 0.00 0.00 2.75
252 253 3.249080 ACACGTATTTTTCTTGTCCACGG 59.751 43.478 0.00 0.00 0.00 4.94
295 317 0.394625 GACTCGGAGGCACTAGACCT 60.395 60.000 5.84 8.55 41.55 3.85
315 337 3.610911 CTGTCTGGGTTCCTACAAATCC 58.389 50.000 0.00 0.00 0.00 3.01
320 342 1.612199 GGGTTCCTACAAATCCGTGCA 60.612 52.381 0.00 0.00 0.00 4.57
329 351 1.336440 CAAATCCGTGCAAACCAGACA 59.664 47.619 0.00 0.00 0.00 3.41
330 352 1.909700 AATCCGTGCAAACCAGACAT 58.090 45.000 0.00 0.00 0.00 3.06
343 372 0.824109 CAGACATGGGACGCCTCTTA 59.176 55.000 0.00 0.00 0.00 2.10
361 390 5.829924 CCTCTTATGGCTTTATGTTCATGGT 59.170 40.000 0.00 0.00 0.00 3.55
370 399 5.296780 GCTTTATGTTCATGGTGCTAGCTTA 59.703 40.000 17.23 2.30 0.00 3.09
371 400 6.512415 GCTTTATGTTCATGGTGCTAGCTTAG 60.512 42.308 17.23 1.72 0.00 2.18
380 409 1.134670 GTGCTAGCTTAGACCCTGTGG 60.135 57.143 17.23 0.00 37.80 4.17
395 424 2.544277 CCTGTGGACAACATGCAACAAG 60.544 50.000 0.00 0.00 38.39 3.16
432 461 1.972872 ATTTCTTAGGCGGGCATCTG 58.027 50.000 3.78 0.00 0.00 2.90
433 462 0.748005 TTTCTTAGGCGGGCATCTGC 60.748 55.000 3.78 0.00 44.31 4.26
451 480 5.698741 TCTGCCTCTATCTTCAAATTCCA 57.301 39.130 0.00 0.00 0.00 3.53
453 482 6.060136 TCTGCCTCTATCTTCAAATTCCATG 58.940 40.000 0.00 0.00 0.00 3.66
471 500 2.312722 TGCATTTTTGCAGCACTGTT 57.687 40.000 0.00 0.00 40.23 3.16
484 513 2.038033 AGCACTGTTACCCGCTTTCTAA 59.962 45.455 0.00 0.00 0.00 2.10
499 528 4.617959 CTTTCTAAATAGCGGGATCACGA 58.382 43.478 24.26 0.00 35.47 4.35
501 530 3.220110 TCTAAATAGCGGGATCACGACT 58.780 45.455 24.26 19.53 35.47 4.18
509 538 0.323629 GGGATCACGACTGGTTTGGA 59.676 55.000 0.00 0.00 0.00 3.53
527 556 2.823154 TGGATACATGATGGACGCGATA 59.177 45.455 15.93 0.00 46.17 2.92
544 573 0.394216 ATAATTGCTGCCTCACGCCA 60.394 50.000 0.00 0.00 36.24 5.69
550 579 1.376424 CTGCCTCACGCCATCTTGT 60.376 57.895 0.00 0.00 36.24 3.16
556 585 1.154225 CACGCCATCTTGTTTCGCC 60.154 57.895 0.00 0.00 0.00 5.54
563 592 2.182614 ATCTTGTTTCGCCGCCAACG 62.183 55.000 0.00 0.00 39.67 4.10
573 602 2.604174 CCGCCAACGACTTGTGGTC 61.604 63.158 0.00 0.00 43.93 4.02
626 655 1.028905 GTGTTTGTGCTGTTGCCCTA 58.971 50.000 0.00 0.00 38.71 3.53
735 764 2.266055 GTCAACTCTCCAGCCCCG 59.734 66.667 0.00 0.00 0.00 5.73
736 765 2.203788 TCAACTCTCCAGCCCCGT 60.204 61.111 0.00 0.00 0.00 5.28
737 766 2.266055 CAACTCTCCAGCCCCGTC 59.734 66.667 0.00 0.00 0.00 4.79
760 789 9.207042 CGTCTGTCAACTAAAGTTTAGTTTTTC 57.793 33.333 29.92 23.03 35.76 2.29
785 814 2.473760 CGATCGAGTCGTGGCCTCT 61.474 63.158 10.26 0.00 45.19 3.69
807 836 0.179001 GTGGGTACAAAGTGGTGGCT 60.179 55.000 0.00 0.00 0.00 4.75
824 853 2.968574 TGGCTAGAGAATTCAGGCTAGG 59.031 50.000 21.41 10.66 35.95 3.02
848 877 1.326951 GGCCCACTCCTGAGAGACTC 61.327 65.000 0.22 0.00 43.39 3.36
849 878 0.613292 GCCCACTCCTGAGAGACTCA 60.613 60.000 5.02 0.00 43.39 3.41
858 887 1.661617 CTGAGAGACTCACCGTAGACG 59.338 57.143 5.02 0.00 35.39 4.18
861 890 0.803740 GAGACTCACCGTAGACGCTT 59.196 55.000 0.00 0.00 38.18 4.68
864 893 1.233285 ACTCACCGTAGACGCTTCGT 61.233 55.000 0.00 0.00 45.10 3.85
870 899 1.334992 CGTAGACGCTTCGTGGTGTG 61.335 60.000 0.00 0.00 41.37 3.82
871 900 0.318445 GTAGACGCTTCGTGGTGTGT 60.318 55.000 0.00 1.30 41.37 3.72
878 909 2.332312 CTTCGTGGTGTGTTCCCCCA 62.332 60.000 0.00 0.00 0.00 4.96
881 912 1.534697 GTGGTGTGTTCCCCCAAGA 59.465 57.895 0.00 0.00 0.00 3.02
914 945 3.060363 GGTTATACGCACGTCACTGAAAG 59.940 47.826 0.00 0.00 42.29 2.62
945 976 7.275920 AGTATTGAGTCCTGTTGGATATGTTC 58.724 38.462 0.00 0.00 45.29 3.18
960 991 0.746204 TGTTCGGCATGTGTGTGTGT 60.746 50.000 0.00 0.00 0.00 3.72
961 992 0.316937 GTTCGGCATGTGTGTGTGTG 60.317 55.000 0.00 0.00 0.00 3.82
962 993 0.746204 TTCGGCATGTGTGTGTGTGT 60.746 50.000 0.00 0.00 0.00 3.72
992 1023 1.262950 CACAACGGAGAAATCAACGCA 59.737 47.619 0.00 0.00 0.00 5.24
994 1025 2.356382 ACAACGGAGAAATCAACGCAAA 59.644 40.909 0.00 0.00 0.00 3.68
1086 1952 2.999063 GCCCAGCCCAACAGCAAT 60.999 61.111 0.00 0.00 34.23 3.56
1098 1964 4.142403 CCCAACAGCAATGGTATGTACTTG 60.142 45.833 0.00 0.00 36.14 3.16
1194 2080 8.562892 CCTTTGTCCATACTGTATGATCAATTC 58.437 37.037 25.40 10.09 38.45 2.17
1226 2112 2.221552 GCGCGTGTTCGATCGATCA 61.222 57.895 24.40 21.77 39.71 2.92
1290 2176 2.958739 AGGGGGAGGAGGGCTACA 60.959 66.667 0.00 0.00 0.00 2.74
1292 2178 1.386057 GGGGGAGGAGGGCTACATT 60.386 63.158 0.00 0.00 0.00 2.71
1319 2205 1.409427 GCCACCAAGCTCTCGTACTAT 59.591 52.381 0.00 0.00 0.00 2.12
1322 2208 2.688446 CACCAAGCTCTCGTACTATCCA 59.312 50.000 0.00 0.00 0.00 3.41
1380 2266 3.093717 ACATTTCGGCCGACTACATAG 57.906 47.619 31.19 15.66 0.00 2.23
1381 2267 2.223971 ACATTTCGGCCGACTACATAGG 60.224 50.000 31.19 13.71 0.00 2.57
1426 2312 2.436646 CGTCCGCAGCTTCCCATT 60.437 61.111 0.00 0.00 0.00 3.16
1454 2340 1.080705 GAACTGCTACACGCTCCGT 60.081 57.895 0.00 0.00 42.36 4.69
1488 2374 1.112113 GCTCAAGTACCTCATCCGGA 58.888 55.000 6.61 6.61 0.00 5.14
1560 2446 1.374125 CTCCACATCGGCGTCAACA 60.374 57.895 6.85 0.00 33.14 3.33
1628 2514 3.443045 GCCATCCTTGTGGTGCCG 61.443 66.667 0.00 0.00 41.47 5.69
1667 2553 3.499737 CTGATCAACACCGGCGCC 61.500 66.667 19.07 19.07 0.00 6.53
1711 2597 1.968540 AGCTCAGGCCGCTCAAAAC 60.969 57.895 0.00 0.00 39.73 2.43
1714 2600 1.003839 TCAGGCCGCTCAAAACGAT 60.004 52.632 0.00 0.00 0.00 3.73
1793 2679 3.763360 TCGGCCAGATTGATGAAAACAAT 59.237 39.130 2.24 0.00 42.38 2.71
1828 2714 2.486128 CAAAGACGATCGCAAACTTCG 58.514 47.619 16.60 2.01 38.76 3.79
1865 2751 9.299465 TCTATGCATGCCATGAATCTTAATTAA 57.701 29.630 16.68 0.00 35.34 1.40
1891 2777 4.388577 ACCTTTGTTCCTAAATGCTCCT 57.611 40.909 0.00 0.00 0.00 3.69
1892 2778 4.740902 ACCTTTGTTCCTAAATGCTCCTT 58.259 39.130 0.00 0.00 0.00 3.36
1898 2784 5.010282 TGTTCCTAAATGCTCCTTCCTTTC 58.990 41.667 0.00 0.00 0.00 2.62
1924 2810 7.434013 CCAAAATAAGTGTGTCAACTTTGTACC 59.566 37.037 5.95 0.00 40.77 3.34
1932 2818 6.809196 GTGTGTCAACTTTGTACCAATTTTGA 59.191 34.615 0.00 0.00 0.00 2.69
1933 2819 7.329717 GTGTGTCAACTTTGTACCAATTTTGAA 59.670 33.333 5.79 0.00 0.00 2.69
1934 2820 7.543868 TGTGTCAACTTTGTACCAATTTTGAAG 59.456 33.333 5.79 0.00 0.00 3.02
1935 2821 7.544217 GTGTCAACTTTGTACCAATTTTGAAGT 59.456 33.333 5.79 0.00 0.00 3.01
1936 2822 8.091449 TGTCAACTTTGTACCAATTTTGAAGTT 58.909 29.630 5.79 0.00 36.59 2.66
1937 2823 8.379902 GTCAACTTTGTACCAATTTTGAAGTTG 58.620 33.333 18.81 18.81 46.74 3.16
1955 2841 8.463930 TGAAGTTGAGACACTTATTTTGGAAT 57.536 30.769 0.00 0.00 37.11 3.01
1970 2856 6.652205 TTTTGGAATGGAGGGAGTATAAGT 57.348 37.500 0.00 0.00 0.00 2.24
1979 2865 5.491078 TGGAGGGAGTATAAGTCATTTTGGT 59.509 40.000 0.00 0.00 0.00 3.67
1980 2866 5.823045 GGAGGGAGTATAAGTCATTTTGGTG 59.177 44.000 0.00 0.00 0.00 4.17
1981 2867 6.388619 AGGGAGTATAAGTCATTTTGGTGT 57.611 37.500 0.00 0.00 0.00 4.16
1982 2868 7.365295 GGAGGGAGTATAAGTCATTTTGGTGTA 60.365 40.741 0.00 0.00 0.00 2.90
1983 2869 8.102484 AGGGAGTATAAGTCATTTTGGTGTAT 57.898 34.615 0.00 0.00 0.00 2.29
1985 2871 9.185680 GGGAGTATAAGTCATTTTGGTGTATTT 57.814 33.333 0.00 0.00 0.00 1.40
2034 2924 0.548031 TCAGGTACCCCGACGATACT 59.452 55.000 8.74 0.00 35.12 2.12
2079 2969 4.100189 GTGGTCAGCTCTGGAACATATACT 59.900 45.833 0.00 0.00 38.20 2.12
2227 3117 0.033208 ACCCAACAATCCATCGCCAT 60.033 50.000 0.00 0.00 0.00 4.40
2305 3196 2.663602 CGTGAGTTCTCAATCAACCTCG 59.336 50.000 3.99 0.00 0.00 4.63
2311 3202 3.040147 TCTCAATCAACCTCGACAACC 57.960 47.619 0.00 0.00 0.00 3.77
2328 3219 2.277737 CAGCCATGGCACCCAGAT 59.722 61.111 37.18 13.31 44.88 2.90
2336 3227 0.036765 TGGCACCCAGATAACGTCAC 60.037 55.000 0.00 0.00 0.00 3.67
2357 3248 4.099573 CACACCGAAATACCTCTATGGAGT 59.900 45.833 5.27 0.00 37.86 3.85
2375 3266 0.784778 GTCGCCATCTACAATAGCGC 59.215 55.000 0.00 0.00 46.04 5.92
2383 3274 2.113243 CTACAATAGCGCCCCCTCCC 62.113 65.000 2.29 0.00 0.00 4.30
2436 3327 0.670546 CCGTCAGATCAACGCAACCT 60.671 55.000 13.43 0.00 38.77 3.50
2448 3339 2.906354 ACGCAACCTCCTATCATCAAC 58.094 47.619 0.00 0.00 0.00 3.18
2459 3350 6.146837 CCTCCTATCATCAACGCTATTGAAAG 59.853 42.308 4.58 1.98 31.55 2.62
2477 3368 0.896940 AGGTACACCGTCGTCACCAT 60.897 55.000 0.00 0.00 42.08 3.55
2623 3557 3.063452 CACTAAACTGCACACGTTCAACT 59.937 43.478 0.00 0.00 0.00 3.16
2767 3715 4.679373 AGGTGAAGTATCAGGTGCATAG 57.321 45.455 0.00 0.00 35.88 2.23
2839 3787 1.927174 GTTGACATGTAGCTACGCCAG 59.073 52.381 18.74 10.56 0.00 4.85
2874 3822 6.365247 CGCAAGGATTATACGCTTGTAAGTAT 59.635 38.462 0.00 0.00 37.35 2.12
2919 3867 8.780846 TCCAAACGCTCTTATATTTCTTTACA 57.219 30.769 0.00 0.00 0.00 2.41
2940 3888 6.403866 ACAGAGGAAGTAGCTCATATCAAG 57.596 41.667 0.00 0.00 0.00 3.02
3010 3958 8.024145 ACTGGAGAATAGGGTTACATTTCTAG 57.976 38.462 0.00 0.00 0.00 2.43
3140 4088 4.821260 TCCAGTACTTGTACGTCTTGTGTA 59.179 41.667 0.00 0.00 0.00 2.90
3289 4240 6.851222 ACTTCATTGACAGTTCTGTAAGTG 57.149 37.500 13.67 10.38 41.13 3.16
3311 4262 4.397417 TGGGGCAACTTTTGTCAAAATTTG 59.603 37.500 25.49 25.49 41.32 2.32
3313 4264 4.202000 GGGCAACTTTTGTCAAAATTTGGG 60.202 41.667 28.27 14.43 39.79 4.12
3318 4269 7.680588 GCAACTTTTGTCAAAATTTGGGCATTA 60.681 33.333 28.27 0.00 39.79 1.90
3344 4295 8.489489 ACCATGAATTACTTCTGAGTCATGTAT 58.511 33.333 11.30 0.00 34.79 2.29
3345 4296 9.334947 CCATGAATTACTTCTGAGTCATGTATT 57.665 33.333 11.30 0.00 34.79 1.89
3382 4334 6.889301 TTCTTTTCTGCAGAGATTTGTCAT 57.111 33.333 17.43 0.00 0.00 3.06
3462 4416 4.791334 TCATTGAATCTAAGGTACCCCCAA 59.209 41.667 8.74 3.25 34.66 4.12
3463 4417 5.254267 TCATTGAATCTAAGGTACCCCCAAA 59.746 40.000 8.74 0.00 34.66 3.28
3467 4421 3.278987 TCTAAGGTACCCCCAAACTCA 57.721 47.619 8.74 0.00 34.66 3.41
3512 4684 8.995027 TTCTATCTAACATTATTGCCCACATT 57.005 30.769 0.00 0.00 0.00 2.71
3513 4685 8.995027 TCTATCTAACATTATTGCCCACATTT 57.005 30.769 0.00 0.00 0.00 2.32
3573 4751 1.531149 CAACAATCGAGACCTTTGCGT 59.469 47.619 0.00 0.00 0.00 5.24
3578 4756 3.520290 ATCGAGACCTTTGCGTCAATA 57.480 42.857 0.00 0.00 35.07 1.90
3625 4812 1.202687 CGGAAGAGCAATCTGGCCATA 60.203 52.381 5.51 0.00 0.00 2.74
3695 4897 4.942483 TGGTAGTACTCTTGTGCTCTCTAC 59.058 45.833 0.00 0.00 39.73 2.59
3708 4910 1.589320 CTCTCTACGACGGAAGAGACG 59.411 57.143 21.46 15.68 42.52 4.18
3733 4935 0.549950 AGGCATAGGCAAGAGCACAT 59.450 50.000 0.15 0.00 44.61 3.21
3770 4977 6.430000 TCTTTTTCCCAATCACACTACTAAGC 59.570 38.462 0.00 0.00 0.00 3.09
3774 4981 4.404715 TCCCAATCACACTACTAAGCCTAC 59.595 45.833 0.00 0.00 0.00 3.18
3941 5148 8.749026 ATGAAGAGCTCAAGATGATAACAAAT 57.251 30.769 17.77 0.00 37.67 2.32
3954 5161 9.226606 AGATGATAACAAATAACTTCCAACGAA 57.773 29.630 0.00 0.00 0.00 3.85
4087 5297 4.318332 CTTGCAGAGGTACATGTCTTTCA 58.682 43.478 0.00 0.00 0.00 2.69
4095 5305 6.600822 AGAGGTACATGTCTTTCATTGATTGG 59.399 38.462 0.00 0.00 34.09 3.16
4134 5354 4.276058 AGGGATTGTGCCAAGAAATTTG 57.724 40.909 0.00 0.00 0.00 2.32
4221 5443 5.712152 AAATCTTGTCACCTTGATTGGTC 57.288 39.130 0.00 0.00 38.45 4.02
4300 5522 1.475280 GCATGAGCATCTTGAAGGCAA 59.525 47.619 0.00 0.00 42.34 4.52
4324 5547 9.950680 CAAGTAAGTCATTCACATGTTAACTTT 57.049 29.630 7.22 0.00 0.00 2.66
4412 5637 6.492429 CACAATGGAGGATGTTTATCATGGAT 59.508 38.462 0.00 0.00 36.83 3.41
4474 5701 4.142491 TGCACTTCAATGTCGAGTTTGTTT 60.142 37.500 7.04 0.00 0.00 2.83
4687 5955 3.002862 GCAATGACTACGTGTCCACAAAA 59.997 43.478 13.24 0.00 44.75 2.44
4729 5997 0.396695 ATGTCGACCCCGAGTACCAT 60.397 55.000 14.12 0.00 46.52 3.55
4919 6187 4.504826 CACGTATGTGTGGCATTTACGATA 59.495 41.667 20.42 7.49 40.22 2.92
5112 6384 4.430908 GACAACCCGGACTTGAGTTATAG 58.569 47.826 16.30 0.00 0.00 1.31
5122 6394 8.737175 CCGGACTTGAGTTATAGTGCTTATATA 58.263 37.037 0.00 0.00 31.39 0.86
5147 6419 5.595885 CTGACCAATCCAGTGATAGTACTG 58.404 45.833 5.39 0.00 45.93 2.74
5167 6439 4.145876 TGCATTTCAGATTGAACACGAC 57.854 40.909 0.00 0.00 35.89 4.34
5236 6508 8.160765 TGACAACTCCTATATTGGTTTGAGAAA 58.839 33.333 19.23 6.31 0.00 2.52
5262 6535 7.468922 TCGTATGAAGCAACAATAGATTCTG 57.531 36.000 0.00 0.00 0.00 3.02
5267 6540 7.628769 TGAAGCAACAATAGATTCTGCATAA 57.371 32.000 0.00 0.00 35.44 1.90
5326 6607 2.248280 TGCTTTTGCCGAAGTGAGTA 57.752 45.000 0.00 0.00 46.87 2.59
5345 6629 6.265649 GTGAGTACACATGGACTGATATACCT 59.734 42.308 0.18 0.00 45.32 3.08
5351 6635 6.839134 ACACATGGACTGATATACCTGAACTA 59.161 38.462 0.00 0.00 0.00 2.24
5448 6744 7.518211 GCCATTCTTGGTTGTTTGTTGTTAATC 60.518 37.037 0.00 0.00 45.57 1.75
5588 6908 1.595466 ACAACCACGATAACCGCAAA 58.405 45.000 0.00 0.00 43.32 3.68
5589 6909 2.156098 ACAACCACGATAACCGCAAAT 58.844 42.857 0.00 0.00 43.32 2.32
5632 6952 9.632807 GTAATCTATACATCGAAGCAGAAAGAT 57.367 33.333 0.00 0.00 0.00 2.40
5698 7018 1.289160 AGTGCATCTTGCCCCTTAGA 58.711 50.000 0.00 0.00 44.23 2.10
5781 7101 1.104577 GGAAAGTTCGTTGGGGTGCA 61.105 55.000 0.00 0.00 0.00 4.57
5782 7102 0.741915 GAAAGTTCGTTGGGGTGCAA 59.258 50.000 0.00 0.00 0.00 4.08
5783 7103 1.135333 GAAAGTTCGTTGGGGTGCAAA 59.865 47.619 0.00 0.00 0.00 3.68
5832 7152 6.015519 CCCCACAAATTTACATGAAGACAAGA 60.016 38.462 0.00 0.00 0.00 3.02
5866 7192 7.559486 AGCCCAAGGATTCTTCATTTTTATTC 58.441 34.615 0.00 0.00 0.00 1.75
5867 7193 7.401204 AGCCCAAGGATTCTTCATTTTTATTCT 59.599 33.333 0.00 0.00 0.00 2.40
5903 7229 1.884579 CATTGAGTCCATAGGCATGCC 59.115 52.381 30.12 30.12 0.00 4.40
5912 7238 3.195610 TCCATAGGCATGCCGATACTAAG 59.804 47.826 29.04 17.33 41.95 2.18
5936 7262 0.681243 GGGGACAAGGAAGCCATGAC 60.681 60.000 0.00 0.00 0.00 3.06
5945 7271 2.003301 GGAAGCCATGACGAGTCTTTC 58.997 52.381 4.78 2.00 0.00 2.62
5948 7274 2.966050 AGCCATGACGAGTCTTTCTTC 58.034 47.619 4.78 0.00 0.00 2.87
5949 7275 2.564947 AGCCATGACGAGTCTTTCTTCT 59.435 45.455 4.78 0.00 0.00 2.85
5950 7276 2.926838 GCCATGACGAGTCTTTCTTCTC 59.073 50.000 4.78 0.00 0.00 2.87
5951 7277 3.367910 GCCATGACGAGTCTTTCTTCTCT 60.368 47.826 4.78 0.00 0.00 3.10
5952 7278 4.142359 GCCATGACGAGTCTTTCTTCTCTA 60.142 45.833 4.78 0.00 0.00 2.43
5954 7280 6.568869 CCATGACGAGTCTTTCTTCTCTAAT 58.431 40.000 4.78 0.00 0.00 1.73
5963 7290 9.646427 GAGTCTTTCTTCTCTAATTGCTTAAGA 57.354 33.333 6.67 0.00 0.00 2.10
6011 7339 7.814264 AGCCTTCAAAATTCCTCACTATATG 57.186 36.000 0.00 0.00 0.00 1.78
6067 7395 2.183300 CCGGTCGGAATCAGCGAA 59.817 61.111 2.83 0.00 36.89 4.70
6069 7397 0.810031 CCGGTCGGAATCAGCGAATT 60.810 55.000 2.83 0.00 36.89 2.17
6091 7419 3.449377 TGTTCACCAGATATAGCCGTTGA 59.551 43.478 0.00 0.00 0.00 3.18
6108 7436 5.049680 GCCGTTGAAAAAGTCTAGTCATTCA 60.050 40.000 0.00 0.00 0.00 2.57
6116 7444 5.736951 AAGTCTAGTCATTCAGAGTTGCT 57.263 39.130 0.00 0.00 34.03 3.91
6118 7446 6.449635 AGTCTAGTCATTCAGAGTTGCTAG 57.550 41.667 0.00 0.00 0.00 3.42
6130 7459 6.643388 TCAGAGTTGCTAGCTATTTCATTCA 58.357 36.000 17.23 0.00 0.00 2.57
6155 7486 0.594796 GCTGAACCACTTGGCAAACG 60.595 55.000 0.00 0.00 39.32 3.60
6162 7493 1.944024 CCACTTGGCAAACGTTCAGTA 59.056 47.619 0.00 0.00 0.00 2.74
6166 7497 1.873863 GGCAAACGTTCAGTAGCCC 59.126 57.895 0.00 0.00 43.97 5.19
6170 7501 2.767505 CAAACGTTCAGTAGCCCTCTT 58.232 47.619 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.397816 ACAGAGAAGATCCCCGAGGG 60.398 60.000 0.00 0.00 46.11 4.30
11 12 1.137872 CAACAGAGAAGATCCCCGAGG 59.862 57.143 0.00 0.00 0.00 4.63
12 13 1.137872 CCAACAGAGAAGATCCCCGAG 59.862 57.143 0.00 0.00 0.00 4.63
13 14 1.195115 CCAACAGAGAAGATCCCCGA 58.805 55.000 0.00 0.00 0.00 5.14
14 15 0.462759 GCCAACAGAGAAGATCCCCG 60.463 60.000 0.00 0.00 0.00 5.73
15 16 0.915364 AGCCAACAGAGAAGATCCCC 59.085 55.000 0.00 0.00 0.00 4.81
16 17 1.472376 CGAGCCAACAGAGAAGATCCC 60.472 57.143 0.00 0.00 0.00 3.85
17 18 1.472376 CCGAGCCAACAGAGAAGATCC 60.472 57.143 0.00 0.00 0.00 3.36
18 19 1.933247 CCGAGCCAACAGAGAAGATC 58.067 55.000 0.00 0.00 0.00 2.75
19 20 0.107945 GCCGAGCCAACAGAGAAGAT 60.108 55.000 0.00 0.00 0.00 2.40
20 21 1.188219 AGCCGAGCCAACAGAGAAGA 61.188 55.000 0.00 0.00 0.00 2.87
21 22 0.321122 AAGCCGAGCCAACAGAGAAG 60.321 55.000 0.00 0.00 0.00 2.85
22 23 0.973632 TAAGCCGAGCCAACAGAGAA 59.026 50.000 0.00 0.00 0.00 2.87
23 24 1.137086 GATAAGCCGAGCCAACAGAGA 59.863 52.381 0.00 0.00 0.00 3.10
24 25 1.134699 TGATAAGCCGAGCCAACAGAG 60.135 52.381 0.00 0.00 0.00 3.35
25 26 0.901827 TGATAAGCCGAGCCAACAGA 59.098 50.000 0.00 0.00 0.00 3.41
26 27 1.600957 CATGATAAGCCGAGCCAACAG 59.399 52.381 0.00 0.00 0.00 3.16
27 28 1.667236 CATGATAAGCCGAGCCAACA 58.333 50.000 0.00 0.00 0.00 3.33
28 29 0.308993 GCATGATAAGCCGAGCCAAC 59.691 55.000 0.00 0.00 0.00 3.77
29 30 0.819259 GGCATGATAAGCCGAGCCAA 60.819 55.000 0.00 0.00 43.15 4.52
30 31 1.227943 GGCATGATAAGCCGAGCCA 60.228 57.895 0.00 0.00 43.15 4.75
31 32 3.660621 GGCATGATAAGCCGAGCC 58.339 61.111 0.00 0.00 43.15 4.70
37 38 3.121944 CGTCGACATAAGGCATGATAAGC 59.878 47.826 17.16 0.00 38.10 3.09
38 39 3.675225 CCGTCGACATAAGGCATGATAAG 59.325 47.826 17.16 0.00 38.10 1.73
39 40 3.069016 ACCGTCGACATAAGGCATGATAA 59.931 43.478 17.16 0.00 38.10 1.75
40 41 2.626266 ACCGTCGACATAAGGCATGATA 59.374 45.455 17.16 0.00 38.10 2.15
41 42 1.412710 ACCGTCGACATAAGGCATGAT 59.587 47.619 17.16 0.00 38.10 2.45
42 43 0.821517 ACCGTCGACATAAGGCATGA 59.178 50.000 17.16 0.00 38.10 3.07
43 44 1.209128 GACCGTCGACATAAGGCATG 58.791 55.000 17.16 0.00 40.78 4.06
44 45 0.821517 TGACCGTCGACATAAGGCAT 59.178 50.000 17.16 0.00 0.00 4.40
45 46 0.821517 ATGACCGTCGACATAAGGCA 59.178 50.000 17.16 9.56 0.00 4.75
46 47 1.067212 AGATGACCGTCGACATAAGGC 59.933 52.381 17.16 3.50 0.00 4.35
47 48 2.619177 AGAGATGACCGTCGACATAAGG 59.381 50.000 17.16 10.97 0.00 2.69
48 49 3.972950 AGAGATGACCGTCGACATAAG 57.027 47.619 17.16 3.34 0.00 1.73
49 50 4.157105 TGAAAGAGATGACCGTCGACATAA 59.843 41.667 17.16 0.00 0.00 1.90
50 51 3.692593 TGAAAGAGATGACCGTCGACATA 59.307 43.478 17.16 0.00 0.00 2.29
51 52 2.492088 TGAAAGAGATGACCGTCGACAT 59.508 45.455 17.16 2.13 0.00 3.06
52 53 1.883926 TGAAAGAGATGACCGTCGACA 59.116 47.619 17.16 0.00 0.00 4.35
53 54 2.631418 TGAAAGAGATGACCGTCGAC 57.369 50.000 5.18 5.18 0.00 4.20
54 55 2.752903 TCATGAAAGAGATGACCGTCGA 59.247 45.455 0.00 0.00 0.00 4.20
55 56 3.150848 TCATGAAAGAGATGACCGTCG 57.849 47.619 0.00 0.00 0.00 5.12
56 57 5.355596 AGATTCATGAAAGAGATGACCGTC 58.644 41.667 13.09 0.72 29.39 4.79
57 58 5.350504 AGATTCATGAAAGAGATGACCGT 57.649 39.130 13.09 0.00 29.39 4.83
58 59 6.314648 TGAAAGATTCATGAAAGAGATGACCG 59.685 38.462 13.09 0.00 34.08 4.79
59 60 7.336427 ACTGAAAGATTCATGAAAGAGATGACC 59.664 37.037 13.09 0.00 39.30 4.02
83 84 6.879458 CAGCTACAAGGGTGTTTTCTATAACT 59.121 38.462 0.00 0.00 39.30 2.24
88 89 4.967084 TCAGCTACAAGGGTGTTTTCTA 57.033 40.909 0.00 0.00 39.30 2.10
89 90 3.857157 TCAGCTACAAGGGTGTTTTCT 57.143 42.857 0.00 0.00 39.30 2.52
142 143 4.787871 CCAGATGGGAGGCGATTC 57.212 61.111 0.00 0.00 40.01 2.52
180 181 1.432807 ACAACCCATTCCCAAGGTCAT 59.567 47.619 0.00 0.00 32.00 3.06
186 187 0.178947 GGGACACAACCCATTCCCAA 60.179 55.000 0.37 0.00 46.35 4.12
219 220 0.750850 AATACGTGTCCCCATCTCCG 59.249 55.000 0.00 0.00 0.00 4.63
221 222 4.514401 AGAAAAATACGTGTCCCCATCTC 58.486 43.478 0.00 0.00 0.00 2.75
225 226 3.816523 GACAAGAAAAATACGTGTCCCCA 59.183 43.478 0.00 0.00 39.49 4.96
234 235 5.584442 ACAAACCGTGGACAAGAAAAATAC 58.416 37.500 0.00 0.00 0.00 1.89
252 253 0.951040 CCAGAGCCTCACGGACAAAC 60.951 60.000 0.00 0.00 0.00 2.93
273 294 0.394488 TCTAGTGCCTCCGAGTCAGG 60.394 60.000 0.00 0.00 0.00 3.86
275 296 0.680280 GGTCTAGTGCCTCCGAGTCA 60.680 60.000 0.00 0.00 0.00 3.41
280 302 0.681564 AGACAGGTCTAGTGCCTCCG 60.682 60.000 0.00 0.54 38.35 4.63
295 317 2.027561 CGGATTTGTAGGAACCCAGACA 60.028 50.000 0.00 0.00 0.00 3.41
315 337 0.888736 TCCCATGTCTGGTTTGCACG 60.889 55.000 0.00 0.00 41.37 5.34
320 342 1.303317 GGCGTCCCATGTCTGGTTT 60.303 57.895 0.00 0.00 41.37 3.27
329 351 1.451936 GCCATAAGAGGCGTCCCAT 59.548 57.895 2.06 0.00 46.12 4.00
330 352 2.908015 GCCATAAGAGGCGTCCCA 59.092 61.111 2.06 0.00 46.12 4.37
338 367 6.732154 CACCATGAACATAAAGCCATAAGAG 58.268 40.000 0.00 0.00 0.00 2.85
343 372 3.368248 AGCACCATGAACATAAAGCCAT 58.632 40.909 0.00 0.00 0.00 4.40
351 380 4.446371 GTCTAAGCTAGCACCATGAACAT 58.554 43.478 18.83 0.00 0.00 2.71
357 386 1.765314 CAGGGTCTAAGCTAGCACCAT 59.235 52.381 18.83 10.50 31.66 3.55
358 387 1.195115 CAGGGTCTAAGCTAGCACCA 58.805 55.000 18.83 0.00 31.66 4.17
361 390 1.195115 CCACAGGGTCTAAGCTAGCA 58.805 55.000 18.83 0.00 0.00 3.49
370 399 0.250901 GCATGTTGTCCACAGGGTCT 60.251 55.000 0.00 0.00 39.40 3.85
371 400 0.537143 TGCATGTTGTCCACAGGGTC 60.537 55.000 0.00 0.00 39.40 4.46
406 435 2.224548 GCCCGCCTAAGAAATATCCACT 60.225 50.000 0.00 0.00 0.00 4.00
413 442 1.972872 CAGATGCCCGCCTAAGAAAT 58.027 50.000 0.00 0.00 0.00 2.17
432 461 4.581824 TGCATGGAATTTGAAGATAGAGGC 59.418 41.667 0.00 0.00 0.00 4.70
433 462 6.896021 ATGCATGGAATTTGAAGATAGAGG 57.104 37.500 0.00 0.00 0.00 3.69
451 480 2.536761 ACAGTGCTGCAAAAATGCAT 57.463 40.000 2.77 0.00 44.47 3.96
453 482 2.476241 GGTAACAGTGCTGCAAAAATGC 59.524 45.455 2.77 0.00 0.00 3.56
465 494 5.220605 GCTATTTAGAAAGCGGGTAACAGTG 60.221 44.000 0.00 0.00 39.74 3.66
484 513 0.389391 CCAGTCGTGATCCCGCTATT 59.611 55.000 0.00 0.00 0.00 1.73
495 524 3.595173 TCATGTATCCAAACCAGTCGTG 58.405 45.455 0.00 0.00 0.00 4.35
499 528 4.526970 GTCCATCATGTATCCAAACCAGT 58.473 43.478 0.00 0.00 0.00 4.00
501 530 3.540617 CGTCCATCATGTATCCAAACCA 58.459 45.455 0.00 0.00 0.00 3.67
509 538 4.093408 GCAATTATCGCGTCCATCATGTAT 59.907 41.667 5.77 0.00 0.00 2.29
519 548 0.233332 GAGGCAGCAATTATCGCGTC 59.767 55.000 5.77 0.00 32.86 5.19
523 552 0.041839 GCGTGAGGCAGCAATTATCG 60.042 55.000 0.00 0.00 42.87 2.92
544 573 1.579429 GTTGGCGGCGAAACAAGAT 59.421 52.632 12.98 0.00 0.00 2.40
556 585 2.935955 GACCACAAGTCGTTGGCG 59.064 61.111 0.00 0.00 38.07 5.69
563 592 6.540551 AGAAAGAGAAGAAAAGACCACAAGTC 59.459 38.462 0.00 0.00 46.71 3.01
651 680 8.645730 TCACGTTCATACAACAAAGTTAAGTA 57.354 30.769 0.00 0.00 0.00 2.24
658 687 6.032775 GCAATCATCACGTTCATACAACAAAG 59.967 38.462 0.00 0.00 0.00 2.77
735 764 9.207042 CGAAAAACTAAACTTTAGTTGACAGAC 57.793 33.333 22.17 12.41 37.77 3.51
736 765 8.938906 ACGAAAAACTAAACTTTAGTTGACAGA 58.061 29.630 22.17 0.00 37.77 3.41
737 766 8.995906 CACGAAAAACTAAACTTTAGTTGACAG 58.004 33.333 22.17 17.03 37.77 3.51
785 814 1.475392 CCACCACTTTGTACCCACGAA 60.475 52.381 0.00 0.00 0.00 3.85
807 836 2.968574 CTGCCCTAGCCTGAATTCTCTA 59.031 50.000 7.05 5.03 38.69 2.43
838 867 1.661617 CGTCTACGGTGAGTCTCTCAG 59.338 57.143 0.65 0.94 41.46 3.35
858 887 2.258726 GGGGAACACACCACGAAGC 61.259 63.158 0.00 0.00 0.00 3.86
861 890 2.768769 TGGGGGAACACACCACGA 60.769 61.111 0.00 0.00 40.38 4.35
870 899 2.556144 AGTTAACGTCTTGGGGGAAC 57.444 50.000 0.00 0.00 0.00 3.62
871 900 3.008266 CCTTAGTTAACGTCTTGGGGGAA 59.992 47.826 0.00 0.00 0.00 3.97
878 909 6.528072 GTGCGTATAACCTTAGTTAACGTCTT 59.472 38.462 0.00 0.00 41.68 3.01
881 912 4.793216 CGTGCGTATAACCTTAGTTAACGT 59.207 41.667 0.00 0.00 41.68 3.99
914 945 7.739498 TCCAACAGGACTCAATACTAAAAAC 57.261 36.000 0.00 0.00 0.00 2.43
945 976 1.009788 CACACACACACACATGCCG 60.010 57.895 0.00 0.00 0.00 5.69
960 991 2.899838 GTTGTGGTCAGGCGCACA 60.900 61.111 10.83 0.00 0.00 4.57
961 992 4.012895 CGTTGTGGTCAGGCGCAC 62.013 66.667 10.83 0.00 0.00 5.34
992 1023 1.665442 GTGGCCGCCATTGTTCTTT 59.335 52.632 16.96 0.00 35.28 2.52
994 1025 3.055719 CGTGGCCGCCATTGTTCT 61.056 61.111 16.96 0.00 35.28 3.01
1077 1943 5.627499 ACAAGTACATACCATTGCTGTTG 57.373 39.130 0.00 0.00 0.00 3.33
1078 1944 6.183360 GCATACAAGTACATACCATTGCTGTT 60.183 38.462 0.00 0.00 0.00 3.16
1086 1952 5.105675 TGAGAACGCATACAAGTACATACCA 60.106 40.000 0.00 0.00 0.00 3.25
1123 1989 4.085357 TGTGTCAACTTGCAGTAATCCT 57.915 40.909 0.00 0.00 0.00 3.24
1124 1990 4.829064 TTGTGTCAACTTGCAGTAATCC 57.171 40.909 0.00 0.00 0.00 3.01
1194 2080 3.505836 ACACGCGCAGATATATGAGATG 58.494 45.455 5.73 4.99 0.00 2.90
1290 2176 2.268076 GCTTGGTGGCCGTGTCAAT 61.268 57.895 0.00 0.00 0.00 2.57
1292 2178 3.825160 GAGCTTGGTGGCCGTGTCA 62.825 63.158 0.00 0.00 0.00 3.58
1319 2205 2.741092 GTGAAGCCGGTGTCTGGA 59.259 61.111 1.90 0.00 0.00 3.86
1380 2266 3.365265 CTTGCACAAGGACGGCCC 61.365 66.667 1.76 0.00 34.87 5.80
1381 2267 2.594592 ACTTGCACAAGGACGGCC 60.595 61.111 14.51 0.00 42.53 6.13
1488 2374 1.877443 GTTGCCGTACATGAACTTGGT 59.123 47.619 0.00 0.00 0.00 3.67
1560 2446 0.465460 ATGTTCACGGTGTGCCAGTT 60.465 50.000 8.17 0.00 32.98 3.16
1640 2526 2.362077 GGTGTTGATCAGGCAAACTTGT 59.638 45.455 0.00 0.00 0.00 3.16
1711 2597 0.319040 CACCTGCGGGTAGATCATCG 60.319 60.000 19.20 0.00 45.41 3.84
1714 2600 0.324368 AGTCACCTGCGGGTAGATCA 60.324 55.000 19.20 0.00 45.41 2.92
1765 2651 1.098050 ATCAATCTGGCCGAAGTTGC 58.902 50.000 0.00 0.00 0.00 4.17
1793 2679 1.699083 TCTTTGGCTCACCTGATGACA 59.301 47.619 0.00 0.00 36.63 3.58
1828 2714 4.202040 TGGCATGCATAGAAACAACATAGC 60.202 41.667 21.36 0.00 0.00 2.97
1865 2751 7.054751 GGAGCATTTAGGAACAAAGGTAGTAT 58.945 38.462 0.00 0.00 0.00 2.12
1886 2772 5.243954 ACACTTATTTTGGAAAGGAAGGAGC 59.756 40.000 0.00 0.00 0.00 4.70
1891 2777 7.123547 AGTTGACACACTTATTTTGGAAAGGAA 59.876 33.333 0.00 0.00 0.00 3.36
1892 2778 6.605594 AGTTGACACACTTATTTTGGAAAGGA 59.394 34.615 0.00 0.00 0.00 3.36
1898 2784 7.434013 GGTACAAAGTTGACACACTTATTTTGG 59.566 37.037 0.00 0.00 35.87 3.28
1932 2818 7.505585 TCCATTCCAAAATAAGTGTCTCAACTT 59.494 33.333 0.00 0.00 42.89 2.66
1933 2819 7.004086 TCCATTCCAAAATAAGTGTCTCAACT 58.996 34.615 0.00 0.00 0.00 3.16
1934 2820 7.214467 TCCATTCCAAAATAAGTGTCTCAAC 57.786 36.000 0.00 0.00 0.00 3.18
1935 2821 6.434028 CCTCCATTCCAAAATAAGTGTCTCAA 59.566 38.462 0.00 0.00 0.00 3.02
1936 2822 5.945784 CCTCCATTCCAAAATAAGTGTCTCA 59.054 40.000 0.00 0.00 0.00 3.27
1937 2823 5.358160 CCCTCCATTCCAAAATAAGTGTCTC 59.642 44.000 0.00 0.00 0.00 3.36
1938 2824 5.015178 TCCCTCCATTCCAAAATAAGTGTCT 59.985 40.000 0.00 0.00 0.00 3.41
1955 2841 5.491078 ACCAAAATGACTTATACTCCCTCCA 59.509 40.000 0.00 0.00 0.00 3.86
1985 2871 4.411993 TCGAATGCGTTCATGCTTAAAA 57.588 36.364 18.44 0.00 38.98 1.52
1991 2881 2.456942 TTGATCGAATGCGTTCATGC 57.543 45.000 18.44 7.01 43.39 4.06
2022 2912 2.882761 TCTGTCATAAGTATCGTCGGGG 59.117 50.000 0.00 0.00 0.00 5.73
2034 2924 4.100963 ACAGGCGTCCATATTCTGTCATAA 59.899 41.667 0.00 0.00 34.00 1.90
2079 2969 0.741927 TGCTCGTCGTCGATACCTCA 60.742 55.000 5.00 0.00 45.21 3.86
2161 3051 2.119801 ATGCCGCTTGAGACATTTCT 57.880 45.000 0.00 0.00 33.37 2.52
2227 3117 4.492494 AGTGCATGATGAAGATGTACCA 57.508 40.909 0.00 0.00 37.19 3.25
2236 3126 3.055312 AGCTCAGAGAAGTGCATGATGAA 60.055 43.478 0.00 0.00 0.00 2.57
2305 3196 2.639327 GGTGCCATGGCTGGTTGTC 61.639 63.158 35.53 16.54 45.10 3.18
2311 3202 0.106569 TTATCTGGGTGCCATGGCTG 60.107 55.000 35.53 19.89 42.51 4.85
2328 3219 3.507233 AGAGGTATTTCGGTGTGACGTTA 59.493 43.478 0.00 0.00 34.94 3.18
2336 3227 4.556898 CGACTCCATAGAGGTATTTCGGTG 60.557 50.000 0.00 0.00 45.11 4.94
2436 3327 5.991606 CCTTTCAATAGCGTTGATGATAGGA 59.008 40.000 15.11 0.00 41.01 2.94
2448 3339 2.601763 GACGGTGTACCTTTCAATAGCG 59.398 50.000 0.00 0.00 35.46 4.26
2459 3350 0.457337 GATGGTGACGACGGTGTACC 60.457 60.000 0.00 2.57 33.00 3.34
2646 3580 6.997655 TCAGATCTTCAGATTTGTGTAGTGT 58.002 36.000 7.11 0.00 37.74 3.55
2649 3583 6.592994 TGCTTCAGATCTTCAGATTTGTGTAG 59.407 38.462 7.11 5.43 37.74 2.74
2767 3715 1.658114 GGGTCGCCAAACCAGTTTC 59.342 57.895 0.00 0.00 41.40 2.78
2795 3743 2.567615 GTCCCACACCATAACAGTCTCT 59.432 50.000 0.00 0.00 0.00 3.10
2850 3798 5.986004 ACTTACAAGCGTATAATCCTTGC 57.014 39.130 7.72 0.00 39.55 4.01
2919 3867 5.467035 GCTTGATATGAGCTACTTCCTCT 57.533 43.478 0.00 0.00 37.18 3.69
2930 3878 9.368674 CATAAGATCCTAACAGCTTGATATGAG 57.631 37.037 0.00 0.00 0.00 2.90
2940 3888 8.718102 TTTCACTAACATAAGATCCTAACAGC 57.282 34.615 0.00 0.00 0.00 4.40
2986 3934 8.024145 ACTAGAAATGTAACCCTATTCTCCAG 57.976 38.462 0.00 0.00 32.87 3.86
3010 3958 8.607459 CAGTGGATCAGTTTCAGTTAATGATAC 58.393 37.037 0.00 0.00 39.42 2.24
3204 4155 9.193806 AGTTATTGTTTGATAGATTCCTGCAAT 57.806 29.630 0.00 0.00 0.00 3.56
3289 4240 4.919206 CAAATTTTGACAAAAGTTGCCCC 58.081 39.130 29.79 0.00 45.45 5.80
3311 4262 5.827797 TCAGAAGTAATTCATGGTAATGCCC 59.172 40.000 5.62 0.00 36.04 5.36
3313 4264 7.280876 TGACTCAGAAGTAATTCATGGTAATGC 59.719 37.037 5.62 0.00 35.28 3.56
3318 4269 6.715280 ACATGACTCAGAAGTAATTCATGGT 58.285 36.000 5.62 0.51 37.89 3.55
3355 4306 7.230108 TGACAAATCTCTGCAGAAAAGAAATCT 59.770 33.333 18.85 0.00 30.24 2.40
3462 4416 6.074648 TGGGAATTAAAATGTGGAGTGAGTT 58.925 36.000 0.00 0.00 0.00 3.01
3463 4417 5.640147 TGGGAATTAAAATGTGGAGTGAGT 58.360 37.500 0.00 0.00 0.00 3.41
3467 4421 9.136323 GATAGAATGGGAATTAAAATGTGGAGT 57.864 33.333 0.00 0.00 0.00 3.85
3573 4751 6.345298 TCTAGCCGACATGAATTGTTATTGA 58.655 36.000 0.00 0.00 39.18 2.57
3578 4756 3.689649 GGTTCTAGCCGACATGAATTGTT 59.310 43.478 0.00 0.00 39.18 2.83
3625 4812 1.906574 ACCACAGGGACGACAATGTAT 59.093 47.619 0.00 0.00 38.05 2.29
3695 4897 1.134901 CACCTCGTCTCTTCCGTCG 59.865 63.158 0.00 0.00 0.00 5.12
3708 4910 0.833287 TCTTGCCTATGCCTCACCTC 59.167 55.000 0.00 0.00 36.33 3.85
3733 4935 4.996793 TGGGAAAAAGATCAGATGGTGAA 58.003 39.130 0.00 0.00 39.19 3.18
3770 4977 8.561738 AATAGGTGACAAACAATACAAGTAGG 57.438 34.615 0.00 0.00 0.00 3.18
3774 4981 9.226606 TCCTTAATAGGTGACAAACAATACAAG 57.773 33.333 0.00 0.00 42.60 3.16
3827 5034 0.530744 AGCTCGTCGTGGCTTCATTA 59.469 50.000 9.01 0.00 34.96 1.90
3941 5148 4.004982 GGCCAAGTATTCGTTGGAAGTTA 58.995 43.478 0.00 0.00 46.53 2.24
3954 5161 0.552615 AACCCTCCCTGGCCAAGTAT 60.553 55.000 7.01 0.00 0.00 2.12
4087 5297 5.186409 CCTTGGAACATCAAGTCCAATCAAT 59.814 40.000 5.63 0.00 41.72 2.57
4095 5305 3.263425 TCCCTACCTTGGAACATCAAGTC 59.737 47.826 0.00 0.00 41.72 3.01
4134 5354 9.550811 CGTTCACAACTTATAAATTTTACCCTC 57.449 33.333 0.00 0.00 0.00 4.30
4221 5443 0.911769 TACTCCCCATCCTTGCAGTG 59.088 55.000 0.00 0.00 0.00 3.66
4412 5637 2.230508 AGTGCGATTCGGAGTCTTTGTA 59.769 45.455 8.34 0.00 0.00 2.41
4474 5701 7.672983 TTGGAAACACAAAACATTAAGCAAA 57.327 28.000 0.00 0.00 42.67 3.68
4687 5955 1.662438 CGGGTGTGCCAACAAGTGTT 61.662 55.000 0.00 0.00 38.27 3.32
4919 6187 2.951642 CCACTTTCCACACACTGTTGAT 59.048 45.455 0.00 0.00 0.00 2.57
4966 6234 0.713883 GTCGTTGCGGTGACACATAG 59.286 55.000 8.08 0.00 35.20 2.23
5076 6348 1.453015 TTGTCGCTGCCACCACTTT 60.453 52.632 0.00 0.00 0.00 2.66
5077 6349 2.186826 GTTGTCGCTGCCACCACTT 61.187 57.895 0.00 0.00 0.00 3.16
5122 6394 3.110705 ACTATCACTGGATTGGTCAGCT 58.889 45.455 0.00 0.00 35.78 4.24
5147 6419 3.155998 CGTCGTGTTCAATCTGAAATGC 58.844 45.455 0.00 0.00 38.22 3.56
5167 6439 1.522668 TTGAATGCACCCTCTTGACG 58.477 50.000 0.00 0.00 0.00 4.35
5236 6508 8.554528 CAGAATCTATTGTTGCTTCATACGAAT 58.445 33.333 0.00 0.00 0.00 3.34
5326 6607 5.663106 AGTTCAGGTATATCAGTCCATGTGT 59.337 40.000 0.00 0.00 0.00 3.72
5343 6627 5.724328 TGCTACACTCTTGATTAGTTCAGG 58.276 41.667 0.00 0.00 35.27 3.86
5345 6629 9.890629 ATTAATGCTACACTCTTGATTAGTTCA 57.109 29.630 0.00 0.00 0.00 3.18
5512 6810 6.403049 TGTTTTCTACTCTAATCATTCGCCA 58.597 36.000 0.00 0.00 0.00 5.69
5656 6976 3.366396 TCACCTGGAGTATGAGTTCCTC 58.634 50.000 0.00 0.00 34.48 3.71
5810 7130 8.961092 CAACTCTTGTCTTCATGTAAATTTGTG 58.039 33.333 0.00 0.00 0.00 3.33
5832 7152 1.972588 ATCCTTGGGCTAGACCAACT 58.027 50.000 27.00 11.07 45.19 3.16
5866 7192 6.580788 ACTCAATGTGATCTTGGATCACTAG 58.419 40.000 28.84 23.26 46.25 2.57
5867 7193 6.407412 GGACTCAATGTGATCTTGGATCACTA 60.407 42.308 28.84 20.13 46.25 2.74
5903 7229 5.773680 TCCTTGTCCCCTATTCTTAGTATCG 59.226 44.000 0.00 0.00 0.00 2.92
5912 7238 1.564348 TGGCTTCCTTGTCCCCTATTC 59.436 52.381 0.00 0.00 0.00 1.75
5936 7262 6.959671 AAGCAATTAGAGAAGAAAGACTCG 57.040 37.500 0.00 0.00 38.08 4.18
5954 7280 9.320352 GGTTTTTGGAGTTTAATTCTTAAGCAA 57.680 29.630 0.00 0.00 0.00 3.91
5963 7290 7.282224 GCTTTTGAGGGTTTTTGGAGTTTAATT 59.718 33.333 0.00 0.00 0.00 1.40
5966 7293 5.395879 GGCTTTTGAGGGTTTTTGGAGTTTA 60.396 40.000 0.00 0.00 0.00 2.01
5979 7306 4.040829 AGGAATTTTGAAGGCTTTTGAGGG 59.959 41.667 0.00 0.00 0.00 4.30
6011 7339 6.624423 TCCGAAGTGTATGAAAGTTAGGTAC 58.376 40.000 0.00 0.00 0.00 3.34
6061 7389 5.333645 GCTATATCTGGTGAACAATTCGCTG 60.334 44.000 2.44 0.00 40.00 5.18
6062 7390 4.752101 GCTATATCTGGTGAACAATTCGCT 59.248 41.667 2.44 0.00 40.00 4.93
6067 7395 4.689612 ACGGCTATATCTGGTGAACAAT 57.310 40.909 0.00 0.00 0.00 2.71
6069 7397 3.449377 TCAACGGCTATATCTGGTGAACA 59.551 43.478 0.54 0.00 36.21 3.18
6091 7419 6.995091 AGCAACTCTGAATGACTAGACTTTTT 59.005 34.615 0.00 0.00 0.00 1.94
6108 7436 6.882656 TCTGAATGAAATAGCTAGCAACTCT 58.117 36.000 18.83 0.00 0.00 3.24
6116 7444 6.915544 CAGCAGTTCTGAATGAAATAGCTA 57.084 37.500 0.00 0.00 45.72 3.32
6130 7459 1.972872 CCAAGTGGTTCAGCAGTTCT 58.027 50.000 0.00 0.00 0.00 3.01
6142 7471 0.738389 ACTGAACGTTTGCCAAGTGG 59.262 50.000 0.46 0.00 38.53 4.00
6155 7486 5.818336 GGAAATTCTAAGAGGGCTACTGAAC 59.182 44.000 0.00 0.00 0.00 3.18
6162 7493 5.253096 TGGTTTAGGAAATTCTAAGAGGGCT 59.747 40.000 0.00 0.00 31.73 5.19
6166 7497 7.920738 CCGAATGGTTTAGGAAATTCTAAGAG 58.079 38.462 0.00 0.00 31.73 2.85


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

AutoCloner maintained by Alex Coulton.