Multiple sequence alignment - TraesCS4B01G171900

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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 TraesCS4B01G171900 chr4B 100.000 3033 0 0 3185 6217 376142704 376139672 0.000000e+00 5602.0
1 TraesCS4B01G171900 chr4B 100.000 2339 0 0 583 2921 376145306 376142968 0.000000e+00 4320.0
2 TraesCS4B01G171900 chr4B 100.000 368 0 0 1 368 376145888 376145521 0.000000e+00 680.0
3 TraesCS4B01G171900 chr4B 93.706 143 9 0 1319 1461 561393536 561393678 1.360000e-51 215.0
4 TraesCS4B01G171900 chr4D 87.932 3157 162 95 3185 6217 301736113 301733052 0.000000e+00 3517.0
5 TraesCS4B01G171900 chr4D 91.026 1872 77 36 1078 2896 301738318 301736485 0.000000e+00 2442.0
6 TraesCS4B01G171900 chr4D 94.574 258 13 1 1 257 301745204 301744947 1.260000e-106 398.0
7 TraesCS4B01G171900 chr4D 92.857 98 4 2 249 343 301739363 301739266 8.400000e-29 139.0
8 TraesCS4B01G171900 chr4D 90.789 76 2 4 240 311 301745912 301745838 5.130000e-16 97.1
9 TraesCS4B01G171900 chr4A 90.321 2552 106 45 3422 5899 179139778 179142262 0.000000e+00 3214.0
10 TraesCS4B01G171900 chr4A 92.937 1430 54 13 1494 2896 179137974 179139383 0.000000e+00 2037.0
11 TraesCS4B01G171900 chr4A 81.753 833 87 28 671 1464 179137096 179137902 2.440000e-178 636.0
12 TraesCS4B01G171900 chr4A 93.548 341 22 0 1 341 179136601 179136941 5.560000e-140 508.0
13 TraesCS4B01G171900 chr4A 88.421 285 33 0 1028 1312 668710609 668710325 1.660000e-90 344.0
14 TraesCS4B01G171900 chr4A 88.211 246 11 2 3185 3419 179139495 179139733 1.710000e-70 278.0
15 TraesCS4B01G171900 chr4A 98.182 110 2 0 6108 6217 179142259 179142368 6.360000e-45 193.0
16 TraesCS4B01G171900 chr4A 90.000 80 3 4 236 311 179072820 179072898 1.430000e-16 99.0
17 TraesCS4B01G171900 chr1D 89.161 286 29 2 1028 1313 138269394 138269111 7.670000e-94 355.0
18 TraesCS4B01G171900 chr1D 94.161 137 8 0 1328 1464 294746569 294746433 6.320000e-50 209.0
19 TraesCS4B01G171900 chr5A 88.811 286 31 1 1037 1322 565442754 565443038 3.570000e-92 350.0
20 TraesCS4B01G171900 chr7A 88.028 284 32 2 1030 1313 12803729 12803448 9.990000e-88 335.0
21 TraesCS4B01G171900 chr2D 88.364 275 32 0 1039 1313 557881912 557881638 1.290000e-86 331.0
22 TraesCS4B01G171900 chr7D 88.364 275 30 2 1039 1313 94547217 94547489 4.650000e-86 329.0
23 TraesCS4B01G171900 chr6B 87.943 282 31 3 1029 1310 234663194 234663472 4.650000e-86 329.0
24 TraesCS4B01G171900 chr5D 83.039 283 23 12 1328 1586 447145089 447144808 3.750000e-57 233.0
25 TraesCS4B01G171900 chr5D 93.793 145 9 0 1319 1463 548985734 548985878 1.050000e-52 219.0
26 TraesCS4B01G171900 chr5D 91.096 146 12 1 1319 1464 283103519 283103663 4.920000e-46 196.0
27 TraesCS4B01G171900 chr5B 93.431 137 9 0 1328 1464 526191875 526191739 2.940000e-48 204.0
28 TraesCS4B01G171900 chr3D 89.933 149 14 1 1317 1464 593048419 593048271 2.290000e-44 191.0
29 TraesCS4B01G171900 chr3B 100.000 28 0 0 1559 1586 479918903 479918930 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 TraesCS4B01G171900 chr4B 376139672 376145888 6216 True 3534.000000 5602 100.000000 1 6217 3 chr4B.!!$R1 6216
1 TraesCS4B01G171900 chr4D 301733052 301739363 6311 True 2032.666667 3517 90.605000 249 6217 3 chr4D.!!$R1 5968
2 TraesCS4B01G171900 chr4D 301744947 301745912 965 True 247.550000 398 92.681500 1 311 2 chr4D.!!$R2 310
3 TraesCS4B01G171900 chr4A 179136601 179142368 5767 False 1144.333333 3214 90.825333 1 6217 6 chr4A.!!$F2 6216

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
639 1576 0.393077 ACCGGGTGTCAAGTCTGAAG 59.607 55.0 6.32 0.0 31.88 3.02 F
1501 2627 0.461135 CCATATTTTGCAGCGCCCTT 59.539 50.0 2.29 0.0 0.00 3.95 F
3299 4556 0.103937 GAGCTGAATGACGAGGAGGG 59.896 60.0 0.00 0.0 0.00 4.30 F
4567 5982 0.034670 AAGCCCCAGATGCTCTCAAC 60.035 55.0 0.00 0.0 38.34 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 3262 0.320247 GATCTAGGATGCAGCCACCG 60.320 60.0 25.38 10.81 0.00 4.94 R
3456 4766 0.682292 TGTGCTCCCGATACACAACA 59.318 50.0 0.00 0.00 41.11 3.33 R
4886 6321 0.109132 CCAGCTTGCAATCCGGAAAC 60.109 55.0 9.01 0.64 0.00 2.78 R
5634 7103 0.035317 TGCGATGCTTTGAGAGTGGT 59.965 50.0 0.00 0.00 0.00 4.16 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
52 761 2.431419 TCTTACATATTTGACCGGGCGA 59.569 45.455 6.32 0.00 0.00 5.54
86 795 2.197605 TCGGAGCGTTGACTGGTGA 61.198 57.895 0.00 0.00 0.00 4.02
89 798 1.367840 GAGCGTTGACTGGTGAGGT 59.632 57.895 0.00 0.00 0.00 3.85
126 835 1.001517 TTTGGCATAGAAGCGGGCA 60.002 52.632 0.00 0.00 34.64 5.36
228 938 1.819305 GCCTCCTCCTCTTTTGCACAA 60.819 52.381 0.00 0.00 0.00 3.33
230 940 2.157738 CTCCTCCTCTTTTGCACAAGG 58.842 52.381 12.50 4.81 0.00 3.61
600 1536 1.376037 GTAGGTGGAGCAGTGTGCC 60.376 63.158 0.00 0.00 46.52 5.01
601 1537 1.841103 TAGGTGGAGCAGTGTGCCA 60.841 57.895 2.44 2.44 46.52 4.92
616 1552 0.544833 TGCCATGCAGGGTTTTGGAT 60.545 50.000 20.22 0.00 38.09 3.41
639 1576 0.393077 ACCGGGTGTCAAGTCTGAAG 59.607 55.000 6.32 0.00 31.88 3.02
648 1585 1.006102 AAGTCTGAAGTGGCGGACG 60.006 57.895 0.00 0.00 46.36 4.79
664 1601 3.141488 CGTCTGGACTCCCTCCCG 61.141 72.222 0.00 0.00 38.49 5.14
665 1602 2.760385 GTCTGGACTCCCTCCCGG 60.760 72.222 0.00 0.00 38.49 5.73
666 1603 2.944954 TCTGGACTCCCTCCCGGA 60.945 66.667 0.73 0.00 38.49 5.14
667 1604 2.283809 CTGGACTCCCTCCCGGAT 59.716 66.667 0.73 0.00 41.00 4.18
668 1605 1.383248 CTGGACTCCCTCCCGGATT 60.383 63.158 0.73 0.00 41.00 3.01
669 1606 0.983378 CTGGACTCCCTCCCGGATTT 60.983 60.000 0.73 0.00 41.00 2.17
678 1615 3.096357 CCCGGATTTGGGGTCCTT 58.904 61.111 0.73 0.00 46.17 3.36
700 1637 3.195002 CGTCGGGCGTCAATGCAT 61.195 61.111 0.00 0.00 36.28 3.96
738 1675 1.178534 CGTGCAGGGTTTTGGATGGT 61.179 55.000 0.00 0.00 0.00 3.55
741 1678 1.427368 TGCAGGGTTTTGGATGGTACT 59.573 47.619 0.00 0.00 0.00 2.73
742 1679 1.818674 GCAGGGTTTTGGATGGTACTG 59.181 52.381 0.00 0.00 0.00 2.74
743 1680 2.446435 CAGGGTTTTGGATGGTACTGG 58.554 52.381 0.00 0.00 0.00 4.00
756 1694 1.002087 GGTACTGGGGTGTCAAGTCTG 59.998 57.143 0.00 0.00 0.00 3.51
770 1708 1.888215 AGTCTGAAGTGACGGACGTA 58.112 50.000 0.00 0.00 46.85 3.57
781 1719 0.750911 ACGGACGTATGGACTCCCTC 60.751 60.000 0.00 0.00 0.00 4.30
783 1721 1.453762 GGACGTATGGACTCCCTCCG 61.454 65.000 0.00 0.00 43.03 4.63
792 1731 0.981277 GACTCCCTCCGGATTTGGGA 60.981 60.000 24.59 24.59 46.78 4.37
844 1784 2.294791 CCCAATTTGAACGGCTGTGTTA 59.705 45.455 0.00 0.00 30.75 2.41
867 1807 1.614850 GGCCTAAAAATGTCCGGACCA 60.615 52.381 31.19 19.32 0.00 4.02
882 1822 1.777272 GGACCATAGGAGATTTGGGCT 59.223 52.381 0.00 0.00 38.68 5.19
885 1825 2.158755 ACCATAGGAGATTTGGGCTTCG 60.159 50.000 0.00 0.00 34.72 3.79
894 1834 4.697756 TGGGCTTCGGCGTTGGAG 62.698 66.667 6.85 2.40 42.91 3.86
895 1835 4.388499 GGGCTTCGGCGTTGGAGA 62.388 66.667 6.85 0.00 42.91 3.71
896 1836 2.125106 GGCTTCGGCGTTGGAGAT 60.125 61.111 6.85 0.00 42.91 2.75
897 1837 2.464459 GGCTTCGGCGTTGGAGATG 61.464 63.158 6.85 0.00 42.91 2.90
898 1838 3.093278 CTTCGGCGTTGGAGATGC 58.907 61.111 6.85 0.00 39.65 3.91
905 1845 2.024176 GCGTTGGAGATGCCTTTAGA 57.976 50.000 0.00 0.00 37.63 2.10
906 1846 1.936547 GCGTTGGAGATGCCTTTAGAG 59.063 52.381 0.00 0.00 37.63 2.43
907 1847 1.936547 CGTTGGAGATGCCTTTAGAGC 59.063 52.381 0.00 0.00 37.63 4.09
908 1848 2.677902 CGTTGGAGATGCCTTTAGAGCA 60.678 50.000 0.00 0.00 45.94 4.26
922 1862 3.491208 GAGCATCTCCAACAGGCAT 57.509 52.632 0.00 0.00 0.00 4.40
924 1864 1.035932 AGCATCTCCAACAGGCATGC 61.036 55.000 9.90 9.90 38.08 4.06
982 1955 2.022623 GCAATAATCGCGTGCGCA 59.977 55.556 5.66 5.66 42.06 6.09
987 1960 2.349969 ATAATCGCGTGCGCAGAGGA 62.350 55.000 12.22 8.72 42.06 3.71
1000 1973 2.975799 GAGGAAAACGGCACCGCA 60.976 61.111 9.43 0.00 44.19 5.69
1001 1974 2.282180 AGGAAAACGGCACCGCAT 60.282 55.556 9.43 0.00 44.19 4.73
1019 1992 1.305219 ATGCGGTGTATTTGCTGCGT 61.305 50.000 0.00 0.00 39.68 5.24
1023 1996 1.017177 GGTGTATTTGCTGCGTCCGA 61.017 55.000 0.00 0.00 0.00 4.55
1064 2059 1.006998 ACAGCCAGATCTGAGACCTCT 59.993 52.381 24.62 7.81 37.51 3.69
1072 2167 0.749818 TCTGAGACCTCTAGGCGCTG 60.750 60.000 7.64 0.00 39.32 5.18
1075 2170 4.577246 GACCTCTAGGCGCTGGCG 62.577 72.222 7.64 10.80 41.24 5.69
1108 2203 0.744874 CTTCCTCATTCGCTCCGGTA 59.255 55.000 0.00 0.00 0.00 4.02
1171 2266 1.199615 CTTCCTCCACCTTCTCTCCC 58.800 60.000 0.00 0.00 0.00 4.30
1195 2290 2.669569 CACCCCTTGAGCACACCG 60.670 66.667 0.00 0.00 0.00 4.94
1254 2349 2.727544 CGCCCACAAGGTGTTTGG 59.272 61.111 0.00 0.00 41.64 3.28
1317 2412 6.968263 TTTGTGGATGAATTTGGTGAACTA 57.032 33.333 0.00 0.00 0.00 2.24
1318 2413 7.537596 TTTGTGGATGAATTTGGTGAACTAT 57.462 32.000 0.00 0.00 0.00 2.12
1319 2414 7.537596 TTGTGGATGAATTTGGTGAACTATT 57.462 32.000 0.00 0.00 0.00 1.73
1320 2415 6.923012 TGTGGATGAATTTGGTGAACTATTG 58.077 36.000 0.00 0.00 0.00 1.90
1321 2416 6.493115 TGTGGATGAATTTGGTGAACTATTGT 59.507 34.615 0.00 0.00 0.00 2.71
1322 2417 6.808212 GTGGATGAATTTGGTGAACTATTGTG 59.192 38.462 0.00 0.00 0.00 3.33
1323 2418 6.071447 TGGATGAATTTGGTGAACTATTGTGG 60.071 38.462 0.00 0.00 0.00 4.17
1324 2419 6.071391 GGATGAATTTGGTGAACTATTGTGGT 60.071 38.462 0.00 0.00 0.00 4.16
1325 2420 6.083098 TGAATTTGGTGAACTATTGTGGTG 57.917 37.500 0.00 0.00 0.00 4.17
1326 2421 5.010516 TGAATTTGGTGAACTATTGTGGTGG 59.989 40.000 0.00 0.00 0.00 4.61
1327 2422 3.586470 TTGGTGAACTATTGTGGTGGT 57.414 42.857 0.00 0.00 0.00 4.16
1328 2423 2.857483 TGGTGAACTATTGTGGTGGTG 58.143 47.619 0.00 0.00 0.00 4.17
1329 2424 2.439880 TGGTGAACTATTGTGGTGGTGA 59.560 45.455 0.00 0.00 0.00 4.02
1330 2425 3.117851 TGGTGAACTATTGTGGTGGTGAA 60.118 43.478 0.00 0.00 0.00 3.18
1331 2426 3.252458 GGTGAACTATTGTGGTGGTGAAC 59.748 47.826 0.00 0.00 0.00 3.18
1332 2427 4.134563 GTGAACTATTGTGGTGGTGAACT 58.865 43.478 0.00 0.00 0.00 3.01
1346 2441 3.317711 TGGTGAACTATTTGTTGTGCTGG 59.682 43.478 0.00 0.00 39.30 4.85
1493 2614 1.138459 CGCCGCACCATATTTTGCA 59.862 52.632 6.21 0.00 38.76 4.08
1501 2627 0.461135 CCATATTTTGCAGCGCCCTT 59.539 50.000 2.29 0.00 0.00 3.95
1504 2630 0.810648 TATTTTGCAGCGCCCTTCTG 59.189 50.000 2.29 0.00 34.79 3.02
1552 2687 9.429600 GACACTATAAAAATAATTTAGCGCGTT 57.570 29.630 8.43 3.54 0.00 4.84
1585 2720 2.606725 CGCTTGTTGGAGATGCTCTTAG 59.393 50.000 0.00 0.00 0.00 2.18
1601 2736 3.585862 TCTTAGCAGATTCTTTCGCGTT 58.414 40.909 5.77 0.00 0.00 4.84
1609 2746 3.921021 AGATTCTTTCGCGTTCTACACAG 59.079 43.478 5.77 0.00 0.00 3.66
1641 2778 5.981915 GGATTAATTTCAGATTGCAGAAGGC 59.018 40.000 0.00 0.00 45.13 4.35
1770 2907 3.823304 GAGGCAAACTCCAGATTGTTTCT 59.177 43.478 0.00 0.00 40.49 2.52
1832 2969 3.578282 CAGGATTGGCAACCCTTTAAAGT 59.422 43.478 11.50 0.00 0.00 2.66
1854 2991 7.414814 AGTGCCCACGTAAAATAAAAATTTG 57.585 32.000 0.00 0.00 36.20 2.32
1895 3032 5.575157 TCAAAGATTTACAGGGCCATACAA 58.425 37.500 6.18 0.00 0.00 2.41
1896 3033 6.194235 TCAAAGATTTACAGGGCCATACAAT 58.806 36.000 6.18 0.00 0.00 2.71
1910 3051 5.163550 GGCCATACAATCTGGAAAAGTAACC 60.164 44.000 0.00 0.00 35.70 2.85
1913 3054 6.127730 CCATACAATCTGGAAAAGTAACCACC 60.128 42.308 0.00 0.00 35.70 4.61
2097 3262 4.260170 AGCAGAAGAATGATGACAAGGAC 58.740 43.478 0.00 0.00 0.00 3.85
2182 3347 5.240844 GGGAAGAGAAAAAGGAATGACGAAA 59.759 40.000 0.00 0.00 0.00 3.46
2238 3403 3.072476 TGTTTTCTCTCTCCCGGTTGATT 59.928 43.478 0.00 0.00 0.00 2.57
2265 3430 9.730705 TGTTCATTCATCTACATCTTTCTTTCT 57.269 29.630 0.00 0.00 0.00 2.52
2320 3485 3.020274 AGAGATCGATGCGGCATATACT 58.980 45.455 16.66 12.46 0.00 2.12
2347 3512 1.000145 GATCACCGCCTCGTTTTCTC 59.000 55.000 0.00 0.00 0.00 2.87
2355 3520 2.288666 GCCTCGTTTTCTCATGGCATA 58.711 47.619 0.00 0.00 40.04 3.14
2356 3521 2.880890 GCCTCGTTTTCTCATGGCATAT 59.119 45.455 0.00 0.00 40.04 1.78
2357 3522 3.304257 GCCTCGTTTTCTCATGGCATATG 60.304 47.826 0.00 0.00 40.04 1.78
2358 3523 3.304257 CCTCGTTTTCTCATGGCATATGC 60.304 47.826 19.79 19.79 41.14 3.14
2574 3740 3.029981 ATGGGGGAGGAAAGGGCC 61.030 66.667 0.00 0.00 0.00 5.80
2695 3861 9.961264 AAAGGAGGTTACTAGGATTTTAAGAAG 57.039 33.333 0.00 0.00 0.00 2.85
2696 3862 8.912614 AGGAGGTTACTAGGATTTTAAGAAGA 57.087 34.615 0.00 0.00 0.00 2.87
2749 3918 3.307242 CCTTTCGGTTTGAATAGAGCTCG 59.693 47.826 8.37 0.00 36.22 5.03
2767 3936 3.994392 GCTCGTGTGACTGGAATTTTCTA 59.006 43.478 0.00 0.00 0.00 2.10
2848 4017 0.959553 CGGCGCTAAGGAAGGAGATA 59.040 55.000 7.64 0.00 0.00 1.98
2858 4027 2.966516 AGGAAGGAGATAGCCGTAAAGG 59.033 50.000 0.00 0.00 44.97 3.11
2896 4065 2.660064 ATTGGCGCGGGAGAAGAGT 61.660 57.895 8.83 0.00 0.00 3.24
2911 4096 5.810074 GGAGAAGAGTTAGAGAGATGTTTGC 59.190 44.000 0.00 0.00 0.00 3.68
3263 4520 2.090719 TCGGATATTGGGAGAAGAGGGT 60.091 50.000 0.00 0.00 0.00 4.34
3266 4523 3.913163 GGATATTGGGAGAAGAGGGTGAT 59.087 47.826 0.00 0.00 0.00 3.06
3267 4524 5.094387 GGATATTGGGAGAAGAGGGTGATA 58.906 45.833 0.00 0.00 0.00 2.15
3299 4556 0.103937 GAGCTGAATGACGAGGAGGG 59.896 60.000 0.00 0.00 0.00 4.30
3312 4569 2.234908 CGAGGAGGGCAGGAAATATAGG 59.765 54.545 0.00 0.00 0.00 2.57
3420 4688 1.546029 GTGGCTTGGCTAAAGAAAGGG 59.454 52.381 4.17 0.00 38.24 3.95
3456 4766 2.958578 CTTGTTGGTCGGGCTGTGGT 62.959 60.000 0.00 0.00 0.00 4.16
3583 4893 2.684881 GACATCCAGGTAAACCATGCAG 59.315 50.000 1.26 0.00 38.89 4.41
3619 4943 4.562757 CCCCTCGCGATTTATAGATGGAAA 60.563 45.833 10.36 0.00 0.00 3.13
3620 4944 4.389077 CCCTCGCGATTTATAGATGGAAAC 59.611 45.833 10.36 0.00 0.00 2.78
3662 4986 1.352017 TCATCTTGACATGGTGGTGCT 59.648 47.619 0.00 0.00 0.00 4.40
3663 4987 1.471287 CATCTTGACATGGTGGTGCTG 59.529 52.381 0.00 0.00 0.00 4.41
3664 4988 0.250858 TCTTGACATGGTGGTGCTGG 60.251 55.000 0.00 0.00 0.00 4.85
3665 4989 0.538057 CTTGACATGGTGGTGCTGGT 60.538 55.000 0.00 0.00 0.00 4.00
3666 4990 0.822944 TTGACATGGTGGTGCTGGTG 60.823 55.000 0.00 0.00 0.00 4.17
3667 4991 2.598394 ACATGGTGGTGCTGGTGC 60.598 61.111 0.00 0.00 40.20 5.01
3668 4992 2.282674 CATGGTGGTGCTGGTGCT 60.283 61.111 0.00 0.00 40.48 4.40
3669 4993 2.282674 ATGGTGGTGCTGGTGCTG 60.283 61.111 0.00 0.00 40.48 4.41
3670 4994 3.873679 ATGGTGGTGCTGGTGCTGG 62.874 63.158 0.00 0.00 40.48 4.85
3671 4995 4.586235 GGTGGTGCTGGTGCTGGT 62.586 66.667 0.00 0.00 40.48 4.00
3672 4996 3.289834 GTGGTGCTGGTGCTGGTG 61.290 66.667 0.00 0.00 40.48 4.17
3674 4998 4.962836 GGTGCTGGTGCTGGTGCT 62.963 66.667 0.00 0.00 40.48 4.40
3675 4999 3.667282 GTGCTGGTGCTGGTGCTG 61.667 66.667 0.00 0.00 40.48 4.41
3676 5000 4.960866 TGCTGGTGCTGGTGCTGG 62.961 66.667 0.00 0.00 40.48 4.85
3677 5001 4.962836 GCTGGTGCTGGTGCTGGT 62.963 66.667 0.00 0.00 40.48 4.00
3678 5002 2.981909 CTGGTGCTGGTGCTGGTG 60.982 66.667 0.00 0.00 40.48 4.17
3714 5038 1.381463 GGAACGGGTAGAGAGGCCT 60.381 63.158 3.86 3.86 0.00 5.19
3804 5128 2.489329 CAGCCCGTCTCATTCATTGTTT 59.511 45.455 0.00 0.00 0.00 2.83
3807 5131 3.181506 GCCCGTCTCATTCATTGTTTCTC 60.182 47.826 0.00 0.00 0.00 2.87
3808 5132 3.375299 CCCGTCTCATTCATTGTTTCTCC 59.625 47.826 0.00 0.00 0.00 3.71
3831 5172 9.295214 CTCCTGTTTCTTTTCTTTCTTTCTTTC 57.705 33.333 0.00 0.00 0.00 2.62
3906 5270 4.019792 TGTGCAGAAGGATGTGTACATT 57.980 40.909 0.00 0.00 39.81 2.71
4001 5368 8.621286 CATTCCTCAATTAACCAACCATACTAC 58.379 37.037 0.00 0.00 0.00 2.73
4002 5369 7.504926 TCCTCAATTAACCAACCATACTACT 57.495 36.000 0.00 0.00 0.00 2.57
4003 5370 8.612486 TCCTCAATTAACCAACCATACTACTA 57.388 34.615 0.00 0.00 0.00 1.82
4004 5371 9.220906 TCCTCAATTAACCAACCATACTACTAT 57.779 33.333 0.00 0.00 0.00 2.12
4093 5464 1.114722 CAAGCCAGGCAGGTTTTCCA 61.115 55.000 15.80 0.00 38.99 3.53
4097 5468 0.111253 CCAGGCAGGTTTTCCAGTCT 59.889 55.000 0.00 0.00 42.18 3.24
4100 5471 1.072965 AGGCAGGTTTTCCAGTCTCTG 59.927 52.381 0.00 0.00 36.72 3.35
4281 5667 2.612972 GGCGAGAAGAAACACCAGATCA 60.613 50.000 0.00 0.00 0.00 2.92
4282 5668 3.067106 GCGAGAAGAAACACCAGATCAA 58.933 45.455 0.00 0.00 0.00 2.57
4298 5699 3.747976 AAAAGCACGCCATCGCCC 61.748 61.111 0.00 0.00 39.84 6.13
4324 5725 7.095187 CGTAAAGAGAGCAAGAAAAGGTAATGT 60.095 37.037 0.00 0.00 0.00 2.71
4325 5726 6.566197 AAGAGAGCAAGAAAAGGTAATGTG 57.434 37.500 0.00 0.00 0.00 3.21
4326 5727 5.625150 AGAGAGCAAGAAAAGGTAATGTGT 58.375 37.500 0.00 0.00 0.00 3.72
4327 5728 5.703130 AGAGAGCAAGAAAAGGTAATGTGTC 59.297 40.000 0.00 0.00 0.00 3.67
4328 5729 5.625150 AGAGCAAGAAAAGGTAATGTGTCT 58.375 37.500 0.00 0.00 0.00 3.41
4329 5730 5.471456 AGAGCAAGAAAAGGTAATGTGTCTG 59.529 40.000 0.00 0.00 0.00 3.51
4349 5750 3.259592 TCGAGGAGACGACATCCAA 57.740 52.632 7.79 0.00 39.47 3.53
4350 5751 1.541379 TCGAGGAGACGACATCCAAA 58.459 50.000 7.79 0.00 39.47 3.28
4351 5752 1.472878 TCGAGGAGACGACATCCAAAG 59.527 52.381 7.79 0.43 39.47 2.77
4353 5754 2.478709 CGAGGAGACGACATCCAAAGAG 60.479 54.545 7.79 0.00 39.47 2.85
4354 5755 2.755655 GAGGAGACGACATCCAAAGAGA 59.244 50.000 7.79 0.00 39.47 3.10
4355 5756 3.165875 AGGAGACGACATCCAAAGAGAA 58.834 45.455 7.79 0.00 39.47 2.87
4357 5758 2.917971 GAGACGACATCCAAAGAGAACG 59.082 50.000 0.00 0.00 0.00 3.95
4358 5759 2.296471 AGACGACATCCAAAGAGAACGT 59.704 45.455 0.00 0.00 33.03 3.99
4436 5851 4.729918 GGTGGTGCCAGGGAGCTG 62.730 72.222 11.91 0.00 37.17 4.24
4439 5854 2.360475 GGTGCCAGGGAGCTGAAC 60.360 66.667 2.23 0.00 0.00 3.18
4444 5859 2.069776 CCAGGGAGCTGAACAGGAA 58.930 57.895 0.00 0.00 0.00 3.36
4450 5865 3.931768 AGCTGAACAGGAAGCTCAG 57.068 52.632 3.99 0.00 46.82 3.35
4557 5972 9.875708 ATGTATGTAAAATATAAAAGCCCCAGA 57.124 29.630 0.00 0.00 0.00 3.86
4558 5973 9.875708 TGTATGTAAAATATAAAAGCCCCAGAT 57.124 29.630 0.00 0.00 0.00 2.90
4560 5975 7.049799 TGTAAAATATAAAAGCCCCAGATGC 57.950 36.000 0.00 0.00 0.00 3.91
4562 5977 6.410942 AAAATATAAAAGCCCCAGATGCTC 57.589 37.500 0.00 0.00 38.34 4.26
4563 5978 5.330648 AATATAAAAGCCCCAGATGCTCT 57.669 39.130 0.00 0.00 38.34 4.09
4564 5979 2.717639 TAAAAGCCCCAGATGCTCTC 57.282 50.000 0.00 0.00 38.34 3.20
4565 5980 0.700564 AAAAGCCCCAGATGCTCTCA 59.299 50.000 0.00 0.00 38.34 3.27
4566 5981 0.700564 AAAGCCCCAGATGCTCTCAA 59.299 50.000 0.00 0.00 38.34 3.02
4567 5982 0.034670 AAGCCCCAGATGCTCTCAAC 60.035 55.000 0.00 0.00 38.34 3.18
4568 5983 0.913451 AGCCCCAGATGCTCTCAACT 60.913 55.000 0.00 0.00 32.41 3.16
4569 5984 0.833287 GCCCCAGATGCTCTCAACTA 59.167 55.000 0.00 0.00 0.00 2.24
4570 5985 1.474143 GCCCCAGATGCTCTCAACTAC 60.474 57.143 0.00 0.00 0.00 2.73
4571 5986 2.114616 CCCCAGATGCTCTCAACTACT 58.885 52.381 0.00 0.00 0.00 2.57
4572 5987 3.300388 CCCCAGATGCTCTCAACTACTA 58.700 50.000 0.00 0.00 0.00 1.82
4573 5988 3.068873 CCCCAGATGCTCTCAACTACTAC 59.931 52.174 0.00 0.00 0.00 2.73
4574 5989 3.957497 CCCAGATGCTCTCAACTACTACT 59.043 47.826 0.00 0.00 0.00 2.57
4575 5990 4.037446 CCCAGATGCTCTCAACTACTACTC 59.963 50.000 0.00 0.00 0.00 2.59
4576 5991 4.260990 CCAGATGCTCTCAACTACTACTCG 60.261 50.000 0.00 0.00 0.00 4.18
4577 5992 4.572795 CAGATGCTCTCAACTACTACTCGA 59.427 45.833 0.00 0.00 0.00 4.04
4578 5993 5.238432 CAGATGCTCTCAACTACTACTCGAT 59.762 44.000 0.00 0.00 0.00 3.59
4579 5994 5.468746 AGATGCTCTCAACTACTACTCGATC 59.531 44.000 0.00 0.00 0.00 3.69
4580 5995 3.878103 TGCTCTCAACTACTACTCGATCC 59.122 47.826 0.00 0.00 0.00 3.36
4581 5996 4.131596 GCTCTCAACTACTACTCGATCCT 58.868 47.826 0.00 0.00 0.00 3.24
4582 5997 5.163332 TGCTCTCAACTACTACTCGATCCTA 60.163 44.000 0.00 0.00 0.00 2.94
4583 5998 5.178067 GCTCTCAACTACTACTCGATCCTAC 59.822 48.000 0.00 0.00 0.00 3.18
4584 5999 6.482898 TCTCAACTACTACTCGATCCTACT 57.517 41.667 0.00 0.00 0.00 2.57
4585 6000 6.282167 TCTCAACTACTACTCGATCCTACTG 58.718 44.000 0.00 0.00 0.00 2.74
4590 6005 9.656040 CAACTACTACTCGATCCTACTGTATAT 57.344 37.037 0.00 0.00 0.00 0.86
4606 6021 9.645059 CTACTGTATATGAGTAACAATCATGGG 57.355 37.037 0.00 0.00 37.91 4.00
4676 6102 2.047560 GGGCACACGTACCAGGAC 60.048 66.667 0.00 0.00 0.00 3.85
4811 6237 2.203437 GGTTTCACCCCCAACGCT 60.203 61.111 0.00 0.00 30.04 5.07
4813 6239 2.909965 TTTCACCCCCAACGCTGC 60.910 61.111 0.00 0.00 0.00 5.25
4830 6256 0.325296 TGCCACCTACTACCCCTCAG 60.325 60.000 0.00 0.00 0.00 3.35
4990 6425 1.335506 GCACATGTTTGGTTACACGGG 60.336 52.381 0.00 0.00 0.00 5.28
5002 6437 4.457496 CACGGGCGCTGAGGACAT 62.457 66.667 7.64 0.00 0.00 3.06
5049 6484 0.670546 CGATGCAAAGGTCACCGTCT 60.671 55.000 0.00 0.00 0.00 4.18
5072 6507 3.121030 GCGCCGCAGACAAGTGAT 61.121 61.111 3.15 0.00 0.00 3.06
5084 6519 0.745486 CAAGTGATGCAGGCGATCCA 60.745 55.000 0.00 0.00 33.74 3.41
5196 6634 4.020218 TCATGGTGAAGTCGAATTCTCCTT 60.020 41.667 33.48 27.84 41.39 3.36
5256 6694 2.095718 GCAAGTTCACTCCGTCCATTTC 60.096 50.000 0.00 0.00 0.00 2.17
5257 6695 3.138304 CAAGTTCACTCCGTCCATTTCA 58.862 45.455 0.00 0.00 0.00 2.69
5258 6696 2.767505 AGTTCACTCCGTCCATTTCAC 58.232 47.619 0.00 0.00 0.00 3.18
5259 6697 1.459592 GTTCACTCCGTCCATTTCACG 59.540 52.381 0.00 0.00 36.99 4.35
5260 6698 0.677288 TCACTCCGTCCATTTCACGT 59.323 50.000 0.00 0.00 35.39 4.49
5261 6699 1.068474 CACTCCGTCCATTTCACGTC 58.932 55.000 0.00 0.00 35.39 4.34
5262 6700 0.966920 ACTCCGTCCATTTCACGTCT 59.033 50.000 0.00 0.00 35.39 4.18
5263 6701 1.343465 ACTCCGTCCATTTCACGTCTT 59.657 47.619 0.00 0.00 35.39 3.01
5264 6702 1.993370 CTCCGTCCATTTCACGTCTTC 59.007 52.381 0.00 0.00 35.39 2.87
5265 6703 1.341852 TCCGTCCATTTCACGTCTTCA 59.658 47.619 0.00 0.00 35.39 3.02
5266 6704 1.459592 CCGTCCATTTCACGTCTTCAC 59.540 52.381 0.00 0.00 35.39 3.18
5292 6730 4.022242 CGTGTCCTCGACTCCCATTATATT 60.022 45.833 0.00 0.00 33.15 1.28
5366 6804 9.810545 ACAACTAGCATCTCTTTTCTATCTAAC 57.189 33.333 0.00 0.00 0.00 2.34
5459 6927 1.421268 ACAAGACATTCTGCCACAGGA 59.579 47.619 0.00 0.00 31.51 3.86
5543 7012 6.241207 ACAGTTGTTTTCTGATTGATACCG 57.759 37.500 0.00 0.00 36.81 4.02
5578 7047 5.361285 GCAGACTGGACTCCTTTCTCTTATA 59.639 44.000 4.26 0.00 0.00 0.98
5634 7103 6.421377 TCTTAACACGTATGTAGCTCGTTA 57.579 37.500 0.00 0.00 38.45 3.18
5875 7344 5.940470 AGAATCAAGGATACAGTCACCAAAC 59.060 40.000 0.00 0.00 41.41 2.93
5881 7350 2.676632 TACAGTCACCAAACGTGTGT 57.323 45.000 4.73 0.00 43.51 3.72
5922 7391 0.108472 TCTGAGATGGCGCAAGAGTG 60.108 55.000 10.83 0.00 43.02 3.51
5959 7428 2.373169 ACCAAAGAGACCAGATGAGCAA 59.627 45.455 0.00 0.00 0.00 3.91
6034 7503 6.409704 TGAAATTAAGAGACTCCTGATGTGG 58.590 40.000 0.00 0.00 0.00 4.17
6053 7522 6.182507 TGTGGTAGTTCTTATTTGTGAGGT 57.817 37.500 0.00 0.00 0.00 3.85
6078 7547 7.386848 GTGACAAGTTACTATCTAAAACTGGCA 59.613 37.037 0.00 0.00 33.85 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 761 4.694339 GCTCCGACCATAGTTATTGAAGT 58.306 43.478 0.00 0.00 0.00 3.01
86 795 2.270205 CCAAGATCGCTGCCACCT 59.730 61.111 0.00 0.00 0.00 4.00
89 798 1.746615 GAAGCCAAGATCGCTGCCA 60.747 57.895 0.00 0.00 36.47 4.92
126 835 1.078356 CAGGATGAGCAGCAGCAGT 60.078 57.895 3.17 0.00 45.49 4.40
347 1174 3.451402 AAACCCTAGTCCACCCATTTC 57.549 47.619 0.00 0.00 0.00 2.17
596 1532 1.004679 CCAAAACCCTGCATGGCAC 60.005 57.895 8.09 0.00 33.79 5.01
600 1536 1.269012 ACCATCCAAAACCCTGCATG 58.731 50.000 0.00 0.00 0.00 4.06
601 1537 2.456577 GTACCATCCAAAACCCTGCAT 58.543 47.619 0.00 0.00 0.00 3.96
616 1552 0.470456 AGACTTGACACCCGGTACCA 60.470 55.000 13.54 0.00 0.00 3.25
639 1576 3.628280 GAGTCCAGACGTCCGCCAC 62.628 68.421 13.01 4.18 36.20 5.01
664 1601 1.685765 GGCCAAGGACCCCAAATCC 60.686 63.158 0.00 0.00 36.38 3.01
665 1602 1.685765 GGGCCAAGGACCCCAAATC 60.686 63.158 4.39 0.00 42.01 2.17
666 1603 2.449777 GGGCCAAGGACCCCAAAT 59.550 61.111 4.39 0.00 42.01 2.32
667 1604 4.293671 CGGGCCAAGGACCCCAAA 62.294 66.667 4.39 0.00 45.37 3.28
689 1626 1.010797 CGCCTACATGCATTGACGC 60.011 57.895 0.00 0.00 0.00 5.19
691 1628 0.940126 CTCCGCCTACATGCATTGAC 59.060 55.000 0.00 0.00 0.00 3.18
700 1637 2.656646 CACACTGCTCCGCCTACA 59.343 61.111 0.00 0.00 0.00 2.74
738 1675 2.391926 TCAGACTTGACACCCCAGTA 57.608 50.000 0.00 0.00 0.00 2.74
741 1678 1.140852 CACTTCAGACTTGACACCCCA 59.859 52.381 0.00 0.00 31.71 4.96
742 1679 1.416401 TCACTTCAGACTTGACACCCC 59.584 52.381 0.00 0.00 31.71 4.95
743 1680 2.484889 GTCACTTCAGACTTGACACCC 58.515 52.381 5.90 0.00 39.60 4.61
756 1694 1.471684 AGTCCATACGTCCGTCACTTC 59.528 52.381 0.00 0.00 0.00 3.01
781 1719 1.457455 CCCCCAATCCCAAATCCGG 60.457 63.158 0.00 0.00 0.00 5.14
783 1721 2.494888 AATCCCCCAATCCCAAATCC 57.505 50.000 0.00 0.00 0.00 3.01
792 1731 0.975556 GGGCGTTGAAATCCCCCAAT 60.976 55.000 0.00 0.00 35.75 3.16
844 1784 1.353022 TCCGGACATTTTTAGGCCACT 59.647 47.619 5.01 0.00 0.00 4.00
867 1807 1.202818 GCCGAAGCCCAAATCTCCTAT 60.203 52.381 0.00 0.00 0.00 2.57
882 1822 2.435938 GGCATCTCCAACGCCGAA 60.436 61.111 0.00 0.00 35.79 4.30
885 1825 1.017387 CTAAAGGCATCTCCAACGCC 58.983 55.000 0.00 0.00 46.62 5.68
895 1835 7.898316 CCTGTTGGAGATGCTCTAAAGGCAT 62.898 48.000 0.63 0.63 43.45 4.40
896 1836 2.305635 TGTTGGAGATGCTCTAAAGGCA 59.694 45.455 0.00 0.00 44.05 4.75
897 1837 2.941720 CTGTTGGAGATGCTCTAAAGGC 59.058 50.000 0.00 0.00 33.06 4.35
898 1838 3.539604 CCTGTTGGAGATGCTCTAAAGG 58.460 50.000 0.00 0.00 33.06 3.11
899 1839 2.941720 GCCTGTTGGAGATGCTCTAAAG 59.058 50.000 0.00 0.00 33.06 1.85
900 1840 2.305635 TGCCTGTTGGAGATGCTCTAAA 59.694 45.455 0.00 0.00 33.06 1.85
901 1841 1.908619 TGCCTGTTGGAGATGCTCTAA 59.091 47.619 0.00 0.00 34.57 2.10
902 1842 1.571955 TGCCTGTTGGAGATGCTCTA 58.428 50.000 0.00 0.00 34.57 2.43
903 1843 0.917533 ATGCCTGTTGGAGATGCTCT 59.082 50.000 0.00 0.00 34.57 4.09
904 1844 1.022735 CATGCCTGTTGGAGATGCTC 58.977 55.000 0.00 0.00 34.57 4.26
905 1845 1.035932 GCATGCCTGTTGGAGATGCT 61.036 55.000 6.36 0.00 42.60 3.79
906 1846 1.035932 AGCATGCCTGTTGGAGATGC 61.036 55.000 15.66 0.00 44.49 3.91
907 1847 2.336945 TAGCATGCCTGTTGGAGATG 57.663 50.000 15.66 0.00 34.57 2.90
908 1848 2.709934 AGATAGCATGCCTGTTGGAGAT 59.290 45.455 15.66 0.00 34.57 2.75
909 1849 2.121948 AGATAGCATGCCTGTTGGAGA 58.878 47.619 15.66 0.00 34.57 3.71
910 1850 2.634815 AGATAGCATGCCTGTTGGAG 57.365 50.000 15.66 0.00 34.57 3.86
911 1851 4.077300 CTAAGATAGCATGCCTGTTGGA 57.923 45.455 15.66 0.00 34.57 3.53
977 1950 3.353836 GCCGTTTTCCTCTGCGCA 61.354 61.111 10.98 10.98 0.00 6.09
982 1955 2.668550 GCGGTGCCGTTTTCCTCT 60.669 61.111 12.46 0.00 42.09 3.69
1000 1973 1.305219 ACGCAGCAAATACACCGCAT 61.305 50.000 0.00 0.00 0.00 4.73
1001 1974 1.906994 GACGCAGCAAATACACCGCA 61.907 55.000 0.00 0.00 0.00 5.69
1034 2007 0.403271 ATCTGGCTGTTGGTGAAGCT 59.597 50.000 0.00 0.00 39.46 3.74
1046 2041 2.158475 CCTAGAGGTCTCAGATCTGGCT 60.158 54.545 22.42 12.07 0.00 4.75
1094 2189 1.518774 GGGTTACCGGAGCGAATGA 59.481 57.895 9.46 0.00 0.00 2.57
1145 2240 4.021925 GGTGGAGGAAGCAGCGGT 62.022 66.667 0.00 0.00 0.00 5.68
1179 2274 2.676163 GAACGGTGTGCTCAAGGGGT 62.676 60.000 0.00 0.00 0.00 4.95
1185 2280 2.741092 GGAGGAACGGTGTGCTCA 59.259 61.111 11.56 0.00 37.69 4.26
1195 2290 2.087009 CGCTGTTCGTCGGAGGAAC 61.087 63.158 27.76 27.76 41.76 3.62
1254 2349 1.720852 CATACCTTGCAAGCGTTTTGC 59.279 47.619 21.43 16.57 45.11 3.68
1299 2394 6.071391 ACCACAATAGTTCACCAAATTCATCC 60.071 38.462 0.00 0.00 0.00 3.51
1317 2412 5.362430 ACAACAAATAGTTCACCACCACAAT 59.638 36.000 0.00 0.00 38.74 2.71
1318 2413 4.707448 ACAACAAATAGTTCACCACCACAA 59.293 37.500 0.00 0.00 38.74 3.33
1319 2414 4.097135 CACAACAAATAGTTCACCACCACA 59.903 41.667 0.00 0.00 38.74 4.17
1320 2415 4.606961 CACAACAAATAGTTCACCACCAC 58.393 43.478 0.00 0.00 38.74 4.16
1321 2416 3.067461 GCACAACAAATAGTTCACCACCA 59.933 43.478 0.00 0.00 38.74 4.17
1322 2417 3.317993 AGCACAACAAATAGTTCACCACC 59.682 43.478 0.00 0.00 38.74 4.61
1323 2418 4.290155 CAGCACAACAAATAGTTCACCAC 58.710 43.478 0.00 0.00 38.74 4.16
1324 2419 3.317711 CCAGCACAACAAATAGTTCACCA 59.682 43.478 0.00 0.00 38.74 4.17
1325 2420 3.568007 TCCAGCACAACAAATAGTTCACC 59.432 43.478 0.00 0.00 38.74 4.02
1326 2421 4.829064 TCCAGCACAACAAATAGTTCAC 57.171 40.909 0.00 0.00 38.74 3.18
1327 2422 5.129634 TCTTCCAGCACAACAAATAGTTCA 58.870 37.500 0.00 0.00 38.74 3.18
1328 2423 5.689383 TCTTCCAGCACAACAAATAGTTC 57.311 39.130 0.00 0.00 38.74 3.01
1329 2424 7.759489 TTATCTTCCAGCACAACAAATAGTT 57.241 32.000 0.00 0.00 42.42 2.24
1330 2425 7.448469 AGTTTATCTTCCAGCACAACAAATAGT 59.552 33.333 0.00 0.00 0.00 2.12
1331 2426 7.820648 AGTTTATCTTCCAGCACAACAAATAG 58.179 34.615 0.00 0.00 0.00 1.73
1332 2427 7.759489 AGTTTATCTTCCAGCACAACAAATA 57.241 32.000 0.00 0.00 0.00 1.40
1425 2520 7.370383 ACAACATTTCGCACTCAAAATAGAAT 58.630 30.769 0.00 0.00 0.00 2.40
1472 2593 0.866906 CAAAATATGGTGCGGCGCTG 60.867 55.000 33.26 13.18 0.00 5.18
1481 2602 0.684153 AGGGCGCTGCAAAATATGGT 60.684 50.000 7.64 0.00 0.00 3.55
1527 2662 9.217223 CAACGCGCTAAATTATTTTTATAGTGT 57.783 29.630 5.73 0.00 0.00 3.55
1585 2720 2.666508 TGTAGAACGCGAAAGAATCTGC 59.333 45.455 15.93 10.06 0.00 4.26
1596 2731 2.040714 TGTACACTGTGTAGAACGCG 57.959 50.000 20.24 3.53 32.84 6.01
1601 2736 9.431887 GAAATTAATCCTTGTACACTGTGTAGA 57.568 33.333 20.24 16.63 32.84 2.59
1609 2746 8.243426 TGCAATCTGAAATTAATCCTTGTACAC 58.757 33.333 0.00 0.00 0.00 2.90
1641 2778 3.758023 TGCTTCCCATATGTGAACACTTG 59.242 43.478 1.24 2.37 0.00 3.16
1832 2969 5.758296 TGCAAATTTTTATTTTACGTGGGCA 59.242 32.000 0.00 0.00 0.00 5.36
1854 2991 1.814394 TGAATGCTGTTCCTGACATGC 59.186 47.619 0.00 0.00 37.69 4.06
1895 3032 3.782656 ACGGTGGTTACTTTTCCAGAT 57.217 42.857 0.00 0.00 34.16 2.90
1896 3033 3.555586 GCTACGGTGGTTACTTTTCCAGA 60.556 47.826 0.00 0.00 34.16 3.86
1910 3051 4.439057 ACTTAATGTACCATGCTACGGTG 58.561 43.478 2.94 0.00 37.33 4.94
1913 3054 7.201325 CGCTATAACTTAATGTACCATGCTACG 60.201 40.741 0.00 0.00 0.00 3.51
1927 3068 4.039245 AGCCTGAGATGCGCTATAACTTAA 59.961 41.667 9.73 0.00 0.00 1.85
2097 3262 0.320247 GATCTAGGATGCAGCCACCG 60.320 60.000 25.38 10.81 0.00 4.94
2182 3347 7.038088 AGCTTTGATGGAAATTTTTACCTGGAT 60.038 33.333 0.00 0.00 0.00 3.41
2263 3428 4.503296 GCTTCTCCCTGTAACTTGTGAAGA 60.503 45.833 0.00 0.00 32.75 2.87
2264 3429 3.748568 GCTTCTCCCTGTAACTTGTGAAG 59.251 47.826 0.00 0.00 33.64 3.02
2265 3430 3.391296 AGCTTCTCCCTGTAACTTGTGAA 59.609 43.478 0.00 0.00 0.00 3.18
2266 3431 2.972713 AGCTTCTCCCTGTAACTTGTGA 59.027 45.455 0.00 0.00 0.00 3.58
2320 3485 1.940883 GAGGCGGTGATCACGTACCA 61.941 60.000 24.14 0.00 36.76 3.25
2355 3520 2.114625 ACACACAGGCAGCAGCAT 59.885 55.556 2.65 0.00 44.61 3.79
2356 3521 2.903350 CACACACAGGCAGCAGCA 60.903 61.111 2.65 0.00 44.61 4.41
2357 3522 4.338539 GCACACACAGGCAGCAGC 62.339 66.667 0.00 0.00 41.10 5.25
2358 3523 2.265904 ATGCACACACAGGCAGCAG 61.266 57.895 0.00 0.00 44.24 4.24
2574 3740 0.869454 CTTCTAGCTCTCTTGCCGCG 60.869 60.000 0.00 0.00 0.00 6.46
2767 3936 8.267183 AGGAAGAAACAAGGTGATTTGAATTTT 58.733 29.630 0.00 0.00 0.00 1.82
2773 3942 4.829492 AGGAGGAAGAAACAAGGTGATTTG 59.171 41.667 0.00 0.00 0.00 2.32
2785 3954 2.660556 ACTAGAGGGGAGGAGGAAGAAA 59.339 50.000 0.00 0.00 0.00 2.52
2848 4017 2.285442 AGGCCTCCCTTTACGGCT 60.285 61.111 0.00 0.00 43.29 5.52
2896 4065 1.992667 CGCACGCAAACATCTCTCTAA 59.007 47.619 0.00 0.00 0.00 2.10
3231 4483 5.505780 TCCCAATATCCGATCACTTTTGTT 58.494 37.500 0.00 0.00 0.00 2.83
3263 4520 0.824109 CTCTCCGGTTGCCACTATCA 59.176 55.000 0.00 0.00 0.00 2.15
3266 4523 1.609501 AGCTCTCCGGTTGCCACTA 60.610 57.895 0.00 0.00 0.00 2.74
3267 4524 2.925170 AGCTCTCCGGTTGCCACT 60.925 61.111 0.00 0.00 0.00 4.00
3299 4556 6.602278 ACCCTTAACTTCCTATATTTCCTGC 58.398 40.000 0.00 0.00 0.00 4.85
3312 4569 4.875578 ATCCCCCTAAACCCTTAACTTC 57.124 45.455 0.00 0.00 0.00 3.01
3420 4688 5.334724 CCAACAAGAAAGAGATGCTTGAGTC 60.335 44.000 0.00 0.00 41.03 3.36
3456 4766 0.682292 TGTGCTCCCGATACACAACA 59.318 50.000 0.00 0.00 41.11 3.33
3497 4807 4.679654 GGGACAAAGAAAACGCATGTAAAG 59.320 41.667 0.00 0.00 0.00 1.85
3583 4893 1.383523 CGAGGGGAAATTTCAGAGCC 58.616 55.000 19.49 10.96 0.00 4.70
3619 4943 4.695217 ACAAGAAATGTGTCAACGTTGT 57.305 36.364 26.47 6.60 41.93 3.32
3620 4944 6.008364 GAAACAAGAAATGTGTCAACGTTG 57.992 37.500 22.35 22.35 44.48 4.10
3672 4996 3.574074 ATCACCCACCTGCACCAGC 62.574 63.158 0.00 0.00 42.57 4.85
3673 4997 1.075482 AATCACCCACCTGCACCAG 59.925 57.895 0.00 0.00 0.00 4.00
3674 4998 1.228521 CAATCACCCACCTGCACCA 60.229 57.895 0.00 0.00 0.00 4.17
3675 4999 2.639327 GCAATCACCCACCTGCACC 61.639 63.158 0.00 0.00 34.87 5.01
3676 5000 2.964978 GCAATCACCCACCTGCAC 59.035 61.111 0.00 0.00 34.87 4.57
3677 5001 2.672651 CGCAATCACCCACCTGCA 60.673 61.111 0.00 0.00 34.39 4.41
3678 5002 4.120331 GCGCAATCACCCACCTGC 62.120 66.667 0.30 0.00 0.00 4.85
3679 5003 3.803082 CGCGCAATCACCCACCTG 61.803 66.667 8.75 0.00 0.00 4.00
3714 5038 0.866427 TTAACGTCGCAAAATCGCCA 59.134 45.000 0.00 0.00 0.00 5.69
3804 5128 8.581253 AAGAAAGAAAGAAAAGAAACAGGAGA 57.419 30.769 0.00 0.00 0.00 3.71
3807 5131 9.645059 AAGAAAGAAAGAAAGAAAAGAAACAGG 57.355 29.630 0.00 0.00 0.00 4.00
3856 5220 5.486735 TCATGGAACCAAATGCTCATTTT 57.513 34.783 5.19 0.00 38.84 1.82
3863 5227 4.724074 TGAAGATCATGGAACCAAATGC 57.276 40.909 0.00 0.00 0.00 3.56
3906 5270 2.229792 GACATTGCCTTCTGGAACACA 58.770 47.619 0.00 0.00 34.57 3.72
4001 5368 5.010249 CATGCATGCAACGTACTGTATAG 57.990 43.478 26.68 0.00 0.00 1.31
4003 5370 3.950087 CATGCATGCAACGTACTGTAT 57.050 42.857 26.68 0.00 0.00 2.29
4081 5452 1.072331 TCAGAGACTGGAAAACCTGCC 59.928 52.381 0.00 0.00 31.51 4.85
4093 5464 2.877866 TCCGGTTCTTCTTCAGAGACT 58.122 47.619 0.00 0.00 31.12 3.24
4097 5468 4.087182 AGTACATCCGGTTCTTCTTCAGA 58.913 43.478 0.00 0.00 0.00 3.27
4100 5471 3.783191 GGAGTACATCCGGTTCTTCTTC 58.217 50.000 0.00 0.00 38.67 2.87
4175 5546 0.644331 CTTGTTGATCTCTCGCTGCG 59.356 55.000 17.25 17.25 0.00 5.18
4281 5667 3.747976 GGGCGATGGCGTGCTTTT 61.748 61.111 0.00 0.00 41.24 2.27
4298 5699 6.780706 TTACCTTTTCTTGCTCTCTTTACG 57.219 37.500 0.00 0.00 0.00 3.18
4324 5725 1.373812 TCGTCTCCTCGACCAGACA 59.626 57.895 15.90 4.38 39.29 3.41
4325 5726 4.298009 TCGTCTCCTCGACCAGAC 57.702 61.111 8.42 8.42 39.56 3.51
4347 5748 3.730715 GCATTCACCAAACGTTCTCTTTG 59.269 43.478 0.00 0.00 0.00 2.77
4349 5750 3.003689 CAGCATTCACCAAACGTTCTCTT 59.996 43.478 0.00 0.00 0.00 2.85
4350 5751 2.549754 CAGCATTCACCAAACGTTCTCT 59.450 45.455 0.00 0.00 0.00 3.10
4351 5752 2.548057 TCAGCATTCACCAAACGTTCTC 59.452 45.455 0.00 0.00 0.00 2.87
4353 5754 2.650608 GTCAGCATTCACCAAACGTTC 58.349 47.619 0.00 0.00 0.00 3.95
4354 5755 1.002900 CGTCAGCATTCACCAAACGTT 60.003 47.619 0.00 0.00 0.00 3.99
4355 5756 0.586319 CGTCAGCATTCACCAAACGT 59.414 50.000 0.00 0.00 0.00 3.99
4357 5758 1.601903 TCACGTCAGCATTCACCAAAC 59.398 47.619 0.00 0.00 0.00 2.93
4358 5759 1.960417 TCACGTCAGCATTCACCAAA 58.040 45.000 0.00 0.00 0.00 3.28
4424 5839 2.752358 CTGTTCAGCTCCCTGGCA 59.248 61.111 0.00 0.00 39.61 4.92
4436 5851 3.184581 CGTTGTAACTGAGCTTCCTGTTC 59.815 47.826 1.65 0.00 31.97 3.18
4439 5854 3.026630 TCGTTGTAACTGAGCTTCCTG 57.973 47.619 0.00 0.00 0.00 3.86
4444 5859 1.726853 GCCATCGTTGTAACTGAGCT 58.273 50.000 0.00 0.00 0.00 4.09
4450 5865 1.296056 ACCAGCGCCATCGTTGTAAC 61.296 55.000 2.29 0.00 43.92 2.50
4556 5971 5.334569 GGATCGAGTAGTAGTTGAGAGCATC 60.335 48.000 1.46 0.00 0.00 3.91
4557 5972 4.517453 GGATCGAGTAGTAGTTGAGAGCAT 59.483 45.833 1.46 0.00 0.00 3.79
4558 5973 3.878103 GGATCGAGTAGTAGTTGAGAGCA 59.122 47.826 1.46 0.00 0.00 4.26
4559 5974 4.131596 AGGATCGAGTAGTAGTTGAGAGC 58.868 47.826 1.46 0.00 0.00 4.09
4560 5975 6.422701 CAGTAGGATCGAGTAGTAGTTGAGAG 59.577 46.154 1.46 0.00 0.00 3.20
4562 5977 6.050432 ACAGTAGGATCGAGTAGTAGTTGAG 58.950 44.000 1.46 0.00 0.00 3.02
4563 5978 5.987098 ACAGTAGGATCGAGTAGTAGTTGA 58.013 41.667 0.00 0.00 0.00 3.18
4564 5979 7.966246 ATACAGTAGGATCGAGTAGTAGTTG 57.034 40.000 0.00 0.00 0.00 3.16
4565 5980 9.656040 CATATACAGTAGGATCGAGTAGTAGTT 57.344 37.037 0.00 0.00 0.00 2.24
4566 5981 9.033711 TCATATACAGTAGGATCGAGTAGTAGT 57.966 37.037 0.00 0.00 0.00 2.73
4567 5982 9.524106 CTCATATACAGTAGGATCGAGTAGTAG 57.476 40.741 0.00 0.00 0.00 2.57
4568 5983 9.033711 ACTCATATACAGTAGGATCGAGTAGTA 57.966 37.037 0.00 0.00 29.82 1.82
4569 5984 7.909518 ACTCATATACAGTAGGATCGAGTAGT 58.090 38.462 0.00 0.00 29.82 2.73
4570 5985 9.872721 TTACTCATATACAGTAGGATCGAGTAG 57.127 37.037 0.00 0.00 35.53 2.57
4571 5986 9.650539 GTTACTCATATACAGTAGGATCGAGTA 57.349 37.037 0.00 0.00 33.52 2.59
4572 5987 8.155510 TGTTACTCATATACAGTAGGATCGAGT 58.844 37.037 0.00 0.00 35.51 4.18
4573 5988 8.549338 TGTTACTCATATACAGTAGGATCGAG 57.451 38.462 0.00 0.00 0.00 4.04
4574 5989 8.913487 TTGTTACTCATATACAGTAGGATCGA 57.087 34.615 0.00 0.00 0.00 3.59
4575 5990 9.776158 GATTGTTACTCATATACAGTAGGATCG 57.224 37.037 0.00 0.00 0.00 3.69
4579 5994 9.645059 CCATGATTGTTACTCATATACAGTAGG 57.355 37.037 0.00 0.00 32.18 3.18
4580 5995 9.645059 CCCATGATTGTTACTCATATACAGTAG 57.355 37.037 0.00 0.00 32.18 2.57
4581 5996 9.154632 ACCCATGATTGTTACTCATATACAGTA 57.845 33.333 0.00 0.00 32.18 2.74
4582 5997 7.933577 CACCCATGATTGTTACTCATATACAGT 59.066 37.037 0.00 0.00 32.18 3.55
4583 5998 7.095060 GCACCCATGATTGTTACTCATATACAG 60.095 40.741 0.00 0.00 32.18 2.74
4584 5999 6.710295 GCACCCATGATTGTTACTCATATACA 59.290 38.462 0.00 0.00 32.18 2.29
4585 6000 6.128553 CGCACCCATGATTGTTACTCATATAC 60.129 42.308 0.00 0.00 32.18 1.47
4590 6005 2.290008 ACGCACCCATGATTGTTACTCA 60.290 45.455 0.00 0.00 0.00 3.41
4606 6021 1.444119 TTGCTTCAGTTCCCACGCAC 61.444 55.000 0.00 0.00 0.00 5.34
4698 6124 2.467946 CTTGCTTTGAGCCCTGCGTG 62.468 60.000 0.00 0.00 41.51 5.34
4745 6171 2.047844 CTGCCCCGAGTGTCACAG 60.048 66.667 5.62 0.00 0.00 3.66
4811 6237 0.325296 CTGAGGGGTAGTAGGTGGCA 60.325 60.000 0.00 0.00 0.00 4.92
4813 6239 3.225608 CCTGAGGGGTAGTAGGTGG 57.774 63.158 0.00 0.00 0.00 4.61
4886 6321 0.109132 CCAGCTTGCAATCCGGAAAC 60.109 55.000 9.01 0.64 0.00 2.78
4990 6425 0.809241 CTTGGAGATGTCCTCAGCGC 60.809 60.000 10.72 0.00 44.30 5.92
5002 6437 1.536073 CGCTCTGGTCACCTTGGAGA 61.536 60.000 13.67 0.00 0.00 3.71
5031 6466 1.079503 GAGACGGTGACCTTTGCATC 58.920 55.000 0.00 0.00 0.00 3.91
5032 6467 0.396435 TGAGACGGTGACCTTTGCAT 59.604 50.000 0.00 0.00 0.00 3.96
5033 6468 0.249868 CTGAGACGGTGACCTTTGCA 60.250 55.000 0.00 0.00 0.00 4.08
5049 6484 3.513768 TTGTCTGCGGCGCTTCTGA 62.514 57.895 33.26 21.02 0.00 3.27
5084 6519 4.699522 GGTCCGAAAGTGGCCGCT 62.700 66.667 14.67 14.67 0.00 5.52
5196 6634 3.087370 TCATTCTCGTCTCTTCTCCCA 57.913 47.619 0.00 0.00 0.00 4.37
5259 6697 0.725118 CGAGGACACGACGTGAAGAC 60.725 60.000 33.12 18.57 36.96 3.01
5260 6698 0.881600 TCGAGGACACGACGTGAAGA 60.882 55.000 33.12 19.53 37.37 2.87
5261 6699 1.572941 TCGAGGACACGACGTGAAG 59.427 57.895 33.12 17.80 37.37 3.02
5262 6700 3.735143 TCGAGGACACGACGTGAA 58.265 55.556 33.12 9.02 37.37 3.18
5292 6730 4.680237 CCCCGCTGACGTTGAGCA 62.680 66.667 17.64 0.00 36.12 4.26
5340 6778 9.810545 GTTAGATAGAAAAGAGATGCTAGTTGT 57.189 33.333 0.00 0.00 0.00 3.32
5366 6804 2.530701 ACCTCAGGTGTCTGACTAAGG 58.469 52.381 9.51 10.23 44.39 2.69
5496 6965 4.638421 TGTGGCATGTTAATTACTACTGGC 59.362 41.667 0.00 0.00 0.00 4.85
5543 7012 4.954875 AGTCCAGTCTGCTAATATGCTTC 58.045 43.478 0.00 0.00 0.00 3.86
5578 7047 6.883744 TGCCAGTGTTTCCTTTAAGAAAAAT 58.116 32.000 0.00 0.00 37.49 1.82
5634 7103 0.035317 TGCGATGCTTTGAGAGTGGT 59.965 50.000 0.00 0.00 0.00 4.16
5875 7344 3.061028 TCTTGTAACACAAACGACACACG 59.939 43.478 0.00 0.00 37.69 4.49
5881 7350 5.640357 AGACAGTTTCTTGTAACACAAACGA 59.360 36.000 0.00 0.00 37.69 3.85
5959 7428 6.625081 CGTTTCTTTTCTTCCTCACCAGTTTT 60.625 38.462 0.00 0.00 0.00 2.43
6034 7503 7.441458 ACTTGTCACCTCACAAATAAGAACTAC 59.559 37.037 0.00 0.00 35.83 2.73
6053 7522 7.386848 GTGCCAGTTTTAGATAGTAACTTGTCA 59.613 37.037 0.00 0.00 30.08 3.58
6078 7547 8.234136 TGATACCATCTTCTGTAATTCGTAGT 57.766 34.615 0.00 0.00 0.00 2.73
6114 7583 0.246635 AGCACACCCGCTAGTTACTG 59.753 55.000 0.00 0.00 41.55 2.74


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

AutoCloner maintained by Alex Coulton.