Multiple sequence alignment - TraesCS5D01G088000

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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 TraesCS5D01G088000 chr5D 100.000 4635 0 0 1 4635 94029702 94025068 0.000000e+00 8560.0
1 TraesCS5D01G088000 chr5D 100.000 222 0 0 4964 5185 94024739 94024518 1.340000e-110 411.0
2 TraesCS5D01G088000 chr5A 93.866 1989 84 16 2633 4610 87933451 87931490 0.000000e+00 2963.0
3 TraesCS5D01G088000 chr5A 92.882 857 43 4 801 1650 87935456 87934611 0.000000e+00 1229.0
4 TraesCS5D01G088000 chr5A 89.037 976 90 16 2004 2972 87934266 87933301 0.000000e+00 1194.0
5 TraesCS5D01G088000 chr5A 83.740 615 76 16 56 650 87939025 87938415 1.260000e-155 560.0
6 TraesCS5D01G088000 chr5A 95.000 220 10 1 1644 1863 87934483 87934265 1.380000e-90 344.0
7 TraesCS5D01G088000 chr5A 92.667 150 10 1 1858 2007 568062552 568062700 1.130000e-51 215.0
8 TraesCS5D01G088000 chr5A 93.382 136 6 3 672 806 87938423 87938290 1.140000e-46 198.0
9 TraesCS5D01G088000 chr5A 95.283 106 5 0 4964 5069 87931335 87931230 8.930000e-38 169.0
10 TraesCS5D01G088000 chr5B 93.438 1585 68 12 2634 4209 101323753 101322196 0.000000e+00 2318.0
11 TraesCS5D01G088000 chr5B 93.814 1164 54 12 712 1863 101325731 101324574 0.000000e+00 1735.0
12 TraesCS5D01G088000 chr5B 87.247 988 95 21 2002 2972 101324577 101323604 0.000000e+00 1098.0
13 TraesCS5D01G088000 chr5B 93.798 387 9 2 4263 4635 101322198 101321813 7.530000e-158 568.0
14 TraesCS5D01G088000 chr5B 92.793 222 15 1 4964 5185 101321786 101321566 2.330000e-83 320.0
15 TraesCS5D01G088000 chr5B 94.828 116 6 0 1887 2002 663632298 663632413 1.150000e-41 182.0
16 TraesCS5D01G088000 chr5B 75.806 248 43 15 2727 2967 101323939 101323702 5.490000e-20 110.0
17 TraesCS5D01G088000 chr4B 79.682 817 126 23 2179 2970 603169064 603168263 2.110000e-153 553.0
18 TraesCS5D01G088000 chr4B 78.893 488 81 15 2329 2814 603188232 603187765 1.400000e-80 311.0
19 TraesCS5D01G088000 chr4B 77.322 366 67 4 3828 4180 603186453 603186091 8.800000e-48 202.0
20 TraesCS5D01G088000 chr4B 81.347 193 30 4 1232 1418 603169882 603169690 8.990000e-33 152.0
21 TraesCS5D01G088000 chr4B 90.099 101 10 0 2178 2278 602784129 602784029 1.170000e-26 132.0
22 TraesCS5D01G088000 chr4A 79.294 821 133 23 2179 2971 684506687 684505876 1.640000e-149 540.0
23 TraesCS5D01G088000 chr4A 78.870 478 79 13 2339 2814 684516813 684516356 2.350000e-78 303.0
24 TraesCS5D01G088000 chr4A 75.692 506 70 30 3334 3831 684515799 684515339 2.450000e-48 204.0
25 TraesCS5D01G088000 chr4A 91.089 101 9 0 2178 2278 684434239 684434139 2.520000e-28 137.0
26 TraesCS5D01G088000 chr4A 84.444 135 20 1 1283 1416 684509323 684509189 1.170000e-26 132.0
27 TraesCS5D01G088000 chr4D 80.462 476 73 13 2340 2814 477628775 477628319 3.840000e-91 346.0
28 TraesCS5D01G088000 chr4D 76.776 366 69 4 3828 4180 477626917 477626555 1.910000e-44 191.0
29 TraesCS5D01G088000 chr4D 81.356 177 30 3 1232 1405 477585221 477585045 1.950000e-29 141.0
30 TraesCS5D01G088000 chr4D 77.091 275 40 13 2026 2280 477629147 477628876 2.520000e-28 137.0
31 TraesCS5D01G088000 chr2D 83.799 358 44 12 20 367 30493799 30494152 1.390000e-85 327.0
32 TraesCS5D01G088000 chr2D 83.509 285 40 6 22 305 617510255 617510533 5.150000e-65 259.0
33 TraesCS5D01G088000 chr2D 80.308 325 57 5 7 326 607682146 607682468 6.710000e-59 239.0
34 TraesCS5D01G088000 chr2D 94.286 105 6 0 1863 1967 89543147 89543043 1.490000e-35 161.0
35 TraesCS5D01G088000 chr1A 80.851 376 59 8 15 384 15349166 15348798 3.060000e-72 283.0
36 TraesCS5D01G088000 chr1A 86.275 51 5 2 1137 1186 254386331 254386282 3.000000e-03 54.7
37 TraesCS5D01G088000 chr2B 81.982 333 52 6 35 362 195622379 195622708 5.110000e-70 276.0
38 TraesCS5D01G088000 chr2B 81.525 341 50 11 43 376 722982807 722983141 8.560000e-68 268.0
39 TraesCS5D01G088000 chr2B 91.176 136 12 0 1868 2003 341941123 341941258 8.870000e-43 185.0
40 TraesCS5D01G088000 chr2B 94.495 109 6 0 1898 2006 564856889 564856997 8.930000e-38 169.0
41 TraesCS5D01G088000 chr2A 80.328 366 58 14 7 367 703677829 703677473 1.110000e-66 265.0
42 TraesCS5D01G088000 chr2A 86.755 151 11 2 1856 2006 440946925 440947066 5.370000e-35 159.0
43 TraesCS5D01G088000 chr7A 78.693 352 65 10 17 364 17804267 17804612 5.220000e-55 226.0
44 TraesCS5D01G088000 chr7A 91.971 137 10 1 1861 1997 172593770 172593635 1.910000e-44 191.0
45 TraesCS5D01G088000 chr3B 91.781 146 12 0 1860 2005 639108712 639108857 2.450000e-48 204.0
46 TraesCS5D01G088000 chr1B 91.935 124 8 2 1890 2012 447509706 447509584 6.900000e-39 172.0
47 TraesCS5D01G088000 chr1B 86.275 51 5 2 1137 1186 288811409 288811360 3.000000e-03 54.7
48 TraesCS5D01G088000 chr3A 83.432 169 26 2 2337 2504 609474833 609475000 6.950000e-34 156.0
49 TraesCS5D01G088000 chr3D 81.768 181 31 2 2328 2507 466281714 466281893 3.230000e-32 150.0
50 TraesCS5D01G088000 chr6D 89.831 59 4 2 424 481 19345724 19345667 2.000000e-09 75.0
51 TraesCS5D01G088000 chr6B 88.679 53 3 3 425 475 26771172 26771223 1.560000e-05 62.1
52 TraesCS5D01G088000 chr1D 86.275 51 5 2 1137 1186 200880080 200880031 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G088000 chr5D 94024518 94029702 5184 True 4485.500000 8560 100.000000 1 5185 2 chr5D.!!$R1 5184
1 TraesCS5D01G088000 chr5A 87931230 87939025 7795 True 951.000000 2963 91.884286 56 5069 7 chr5A.!!$R1 5013
2 TraesCS5D01G088000 chr5B 101321566 101325731 4165 True 1024.833333 2318 89.482667 712 5185 6 chr5B.!!$R1 4473
3 TraesCS5D01G088000 chr4B 603168263 603169882 1619 True 352.500000 553 80.514500 1232 2970 2 chr4B.!!$R2 1738
4 TraesCS5D01G088000 chr4B 603186091 603188232 2141 True 256.500000 311 78.107500 2329 4180 2 chr4B.!!$R3 1851
5 TraesCS5D01G088000 chr4A 684505876 684509323 3447 True 336.000000 540 81.869000 1283 2971 2 chr4A.!!$R2 1688
6 TraesCS5D01G088000 chr4A 684515339 684516813 1474 True 253.500000 303 77.281000 2339 3831 2 chr4A.!!$R3 1492
7 TraesCS5D01G088000 chr4D 477626555 477629147 2592 True 224.666667 346 78.109667 2026 4180 3 chr4D.!!$R2 2154

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
407 410 0.035739 TAGTGACGGTTTGAAGGCCC 59.964 55.0 0.00 0.00 0.00 5.80 F
731 750 0.248012 GGGGGCGGGTACAAAATTTG 59.752 55.0 3.89 3.89 0.00 2.32 F
1867 6985 0.313987 AGTTGTTTGCTTAAGGCCGC 59.686 50.0 4.29 0.00 40.92 6.53 F
1872 6990 0.318275 TTTGCTTAAGGCCGCGTTTG 60.318 50.0 4.92 0.00 40.92 2.93 F
1959 7077 0.377203 GCGGAGTTGATTAAAGCCCG 59.623 55.0 0.00 0.00 37.13 6.13 F
1964 7082 0.377203 GTTGATTAAAGCCCGCTCCG 59.623 55.0 0.00 0.00 0.00 4.63 F
3527 9403 0.255890 TGTAGCTTCATGGGGGCTTC 59.744 55.0 11.76 8.49 37.50 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 7110 0.179056 ATATGCACTTAGGCCGCGTT 60.179 50.000 4.92 0.0 0.00 4.84 R
2724 8131 0.038251 CTGACAGTTGGCGCTACAGA 60.038 55.000 7.64 0.0 0.00 3.41 R
3090 8764 0.606096 CCGACATACACTGTGGACCA 59.394 55.000 13.09 0.0 38.54 4.02 R
3378 9245 0.886043 TGACCTGCACACATCTGCAC 60.886 55.000 0.00 0.0 42.36 4.57 R
3447 9315 2.564947 CTCAGCCTCCTGAACAGTACTT 59.435 50.000 0.00 0.0 46.84 2.24 R
3894 9819 2.787994 CTGAACAGCTTCTCCAACCAT 58.212 47.619 0.00 0.0 0.00 3.55 R
5106 11171 0.179067 GACCGGACTTTGTGTGTGGA 60.179 55.000 9.46 0.0 0.00 4.02 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
27 28 8.887036 TGCACAAATATATCCGATATATGTCC 57.113 34.615 17.91 8.27 38.20 4.02
28 29 8.482128 TGCACAAATATATCCGATATATGTCCA 58.518 33.333 17.91 10.24 38.20 4.02
29 30 9.494271 GCACAAATATATCCGATATATGTCCAT 57.506 33.333 17.91 3.59 38.20 3.41
39 40 8.786826 TCCGATATATGTCCATTTTTATGTCC 57.213 34.615 0.00 0.00 0.00 4.02
40 41 8.379331 TCCGATATATGTCCATTTTTATGTCCA 58.621 33.333 0.00 0.00 0.00 4.02
41 42 8.668353 CCGATATATGTCCATTTTTATGTCCAG 58.332 37.037 0.00 0.00 0.00 3.86
42 43 9.435688 CGATATATGTCCATTTTTATGTCCAGA 57.564 33.333 0.00 0.00 0.00 3.86
44 45 5.818136 ATGTCCATTTTTATGTCCAGACG 57.182 39.130 0.00 0.00 0.00 4.18
45 46 4.647611 TGTCCATTTTTATGTCCAGACGT 58.352 39.130 0.00 0.00 0.00 4.34
46 47 4.454161 TGTCCATTTTTATGTCCAGACGTG 59.546 41.667 0.00 0.00 0.00 4.49
47 48 4.006989 TCCATTTTTATGTCCAGACGTGG 58.993 43.478 0.00 0.00 46.63 4.94
48 49 3.756434 CCATTTTTATGTCCAGACGTGGT 59.244 43.478 0.00 0.00 45.28 4.16
49 50 4.142687 CCATTTTTATGTCCAGACGTGGTC 60.143 45.833 0.00 0.00 45.28 4.02
50 51 2.754946 TTTATGTCCAGACGTGGTCC 57.245 50.000 0.00 0.00 45.28 4.46
51 52 1.634960 TTATGTCCAGACGTGGTCCA 58.365 50.000 0.00 0.00 45.28 4.02
52 53 0.892755 TATGTCCAGACGTGGTCCAC 59.107 55.000 12.40 12.40 45.28 4.02
64 65 1.018752 TGGTCCACGAACATGATGCG 61.019 55.000 0.00 2.16 0.00 4.73
98 99 8.507249 GCCATCCAATACTAATCACAAAGTATC 58.493 37.037 0.00 0.00 37.82 2.24
157 158 6.474427 GCATGTGGTGAGATATTTGTGATTTG 59.526 38.462 0.00 0.00 0.00 2.32
163 164 6.404734 GGTGAGATATTTGTGATTTGGTGTCC 60.405 42.308 0.00 0.00 0.00 4.02
168 169 1.313772 TGTGATTTGGTGTCCGGTTG 58.686 50.000 0.00 0.00 0.00 3.77
186 187 3.551846 GTTGGGAGTAGAGAGAGGAGAG 58.448 54.545 0.00 0.00 0.00 3.20
230 233 3.288092 GGAGAAGAGAGAAGAGGGAGAC 58.712 54.545 0.00 0.00 0.00 3.36
231 234 3.308832 GGAGAAGAGAGAAGAGGGAGACA 60.309 52.174 0.00 0.00 0.00 3.41
232 235 3.947834 GAGAAGAGAGAAGAGGGAGACAG 59.052 52.174 0.00 0.00 0.00 3.51
235 238 2.378547 AGAGAGAAGAGGGAGACAGTGT 59.621 50.000 0.00 0.00 0.00 3.55
238 241 4.941713 AGAGAAGAGGGAGACAGTGTATT 58.058 43.478 0.00 0.00 0.00 1.89
247 250 4.636206 GGGAGACAGTGTATTTGATTGGTC 59.364 45.833 0.00 0.00 0.00 4.02
275 278 2.217038 TCCGGACTCCAGCAAAGCT 61.217 57.895 0.00 0.00 40.77 3.74
276 279 1.743252 CCGGACTCCAGCAAAGCTC 60.743 63.158 0.00 0.00 36.40 4.09
282 285 3.058160 CCAGCAAAGCTCCCCACG 61.058 66.667 0.00 0.00 36.40 4.94
285 288 0.605319 CAGCAAAGCTCCCCACGTTA 60.605 55.000 0.00 0.00 36.40 3.18
300 303 3.488721 CCACGTTAGTCTCTTGGATACCG 60.489 52.174 0.00 0.00 0.00 4.02
313 316 1.338020 GGATACCGGAATCCGTACGTT 59.662 52.381 21.12 2.23 46.80 3.99
315 318 0.738389 TACCGGAATCCGTACGTTCC 59.262 55.000 21.12 21.69 46.80 3.62
316 319 1.250154 ACCGGAATCCGTACGTTCCA 61.250 55.000 27.42 7.08 46.80 3.53
327 330 1.730612 GTACGTTCCAACTGCTAAGCC 59.269 52.381 0.00 0.00 0.00 4.35
338 341 4.244425 ACTGCTAAGCCGACATATACAG 57.756 45.455 0.00 0.00 0.00 2.74
340 343 2.963101 TGCTAAGCCGACATATACAGGT 59.037 45.455 0.00 0.00 0.00 4.00
342 345 3.256136 GCTAAGCCGACATATACAGGTCT 59.744 47.826 0.00 0.00 33.27 3.85
346 349 1.540267 CCGACATATACAGGTCTCCGG 59.460 57.143 0.00 0.00 33.27 5.14
363 366 2.158740 TCCGGTTGGATGACAAAAGTGA 60.159 45.455 0.00 0.00 41.58 3.41
367 370 3.826157 GGTTGGATGACAAAAGTGATCCA 59.174 43.478 11.85 11.85 42.12 3.41
374 377 5.545063 TGACAAAAGTGATCCAGACACTA 57.455 39.130 0.00 0.00 46.01 2.74
376 379 5.934043 TGACAAAAGTGATCCAGACACTATG 59.066 40.000 0.00 0.00 46.01 2.23
378 381 5.221925 ACAAAAGTGATCCAGACACTATGGT 60.222 40.000 0.97 0.00 46.01 3.55
380 383 3.034635 AGTGATCCAGACACTATGGTCC 58.965 50.000 0.00 0.00 45.10 4.46
381 384 2.766263 GTGATCCAGACACTATGGTCCA 59.234 50.000 0.00 0.00 38.59 4.02
390 393 6.071672 CCAGACACTATGGTCCAGACATATAG 60.072 46.154 14.66 14.66 38.59 1.31
394 397 6.902771 ACTATGGTCCAGACATATAGTGAC 57.097 41.667 18.41 0.00 39.52 3.67
405 408 4.189231 ACATATAGTGACGGTTTGAAGGC 58.811 43.478 0.00 0.00 0.00 4.35
407 410 0.035739 TAGTGACGGTTTGAAGGCCC 59.964 55.000 0.00 0.00 0.00 5.80
430 433 3.028850 TCTTGGAGATACCCTAACCACG 58.971 50.000 0.00 0.00 38.00 4.94
432 435 2.381911 TGGAGATACCCTAACCACGTC 58.618 52.381 0.00 0.00 38.00 4.34
438 441 0.251341 ACCCTAACCACGTCTACGGT 60.251 55.000 7.50 0.00 44.95 4.83
439 442 0.453390 CCCTAACCACGTCTACGGTC 59.547 60.000 7.50 0.00 44.95 4.79
440 443 0.453390 CCTAACCACGTCTACGGTCC 59.547 60.000 7.50 0.00 44.95 4.46
441 444 0.453390 CTAACCACGTCTACGGTCCC 59.547 60.000 7.50 0.00 44.95 4.46
444 447 2.677524 CACGTCTACGGTCCCCCA 60.678 66.667 7.50 0.00 44.95 4.96
464 467 2.757868 CAGGTAAAAATGCCCCATTCGA 59.242 45.455 0.00 0.00 32.43 3.71
469 472 4.400529 AAAAATGCCCCATTCGATAACC 57.599 40.909 0.00 0.00 32.43 2.85
555 570 4.827284 AGCCCATTAATTATAGCTTGCGTT 59.173 37.500 0.00 0.00 0.00 4.84
564 579 5.652994 TTATAGCTTGCGTTGGGAAAAAT 57.347 34.783 0.00 0.00 0.00 1.82
568 583 5.652994 AGCTTGCGTTGGGAAAAATAATA 57.347 34.783 0.00 0.00 0.00 0.98
570 585 6.639563 AGCTTGCGTTGGGAAAAATAATAAT 58.360 32.000 0.00 0.00 0.00 1.28
571 586 7.777095 AGCTTGCGTTGGGAAAAATAATAATA 58.223 30.769 0.00 0.00 0.00 0.98
613 629 6.887376 TTTTCTCCTGATTCGTATTCTTCG 57.113 37.500 0.00 0.00 0.00 3.79
614 630 3.966154 TCTCCTGATTCGTATTCTTCGC 58.034 45.455 0.00 0.00 0.00 4.70
615 631 3.380320 TCTCCTGATTCGTATTCTTCGCA 59.620 43.478 0.00 0.00 0.00 5.10
616 632 3.706698 TCCTGATTCGTATTCTTCGCAG 58.293 45.455 0.00 0.00 0.00 5.18
617 633 2.797156 CCTGATTCGTATTCTTCGCAGG 59.203 50.000 0.00 0.00 36.14 4.85
618 634 2.201732 TGATTCGTATTCTTCGCAGGC 58.798 47.619 0.00 0.00 0.00 4.85
619 635 2.201732 GATTCGTATTCTTCGCAGGCA 58.798 47.619 0.00 0.00 0.00 4.75
620 636 1.640428 TTCGTATTCTTCGCAGGCAG 58.360 50.000 0.00 0.00 0.00 4.85
621 637 0.806102 TCGTATTCTTCGCAGGCAGC 60.806 55.000 0.00 0.00 40.87 5.25
623 639 0.375106 GTATTCTTCGCAGGCAGCAC 59.625 55.000 1.96 0.00 46.13 4.40
639 658 1.444119 GCACTTTTGGGTCGCTGACA 61.444 55.000 10.14 0.00 33.68 3.58
642 661 0.804989 CTTTTGGGTCGCTGACATCC 59.195 55.000 10.14 4.66 33.68 3.51
643 662 0.608035 TTTTGGGTCGCTGACATCCC 60.608 55.000 10.14 0.00 40.26 3.85
644 663 1.488705 TTTGGGTCGCTGACATCCCT 61.489 55.000 10.14 0.00 40.48 4.20
645 664 1.899437 TTGGGTCGCTGACATCCCTC 61.899 60.000 10.14 0.00 40.48 4.30
646 665 2.060980 GGGTCGCTGACATCCCTCT 61.061 63.158 10.14 0.00 37.18 3.69
647 666 1.617947 GGGTCGCTGACATCCCTCTT 61.618 60.000 10.14 0.00 37.18 2.85
648 667 0.250513 GGTCGCTGACATCCCTCTTT 59.749 55.000 10.14 0.00 33.68 2.52
649 668 1.339151 GGTCGCTGACATCCCTCTTTT 60.339 52.381 10.14 0.00 33.68 2.27
650 669 1.734465 GTCGCTGACATCCCTCTTTTG 59.266 52.381 4.20 0.00 32.09 2.44
651 670 1.347707 TCGCTGACATCCCTCTTTTGT 59.652 47.619 0.00 0.00 0.00 2.83
652 671 2.154462 CGCTGACATCCCTCTTTTGTT 58.846 47.619 0.00 0.00 0.00 2.83
653 672 2.554032 CGCTGACATCCCTCTTTTGTTT 59.446 45.455 0.00 0.00 0.00 2.83
654 673 3.004734 CGCTGACATCCCTCTTTTGTTTT 59.995 43.478 0.00 0.00 0.00 2.43
655 674 4.301628 GCTGACATCCCTCTTTTGTTTTG 58.698 43.478 0.00 0.00 0.00 2.44
656 675 4.037923 GCTGACATCCCTCTTTTGTTTTGA 59.962 41.667 0.00 0.00 0.00 2.69
657 676 5.451798 GCTGACATCCCTCTTTTGTTTTGAA 60.452 40.000 0.00 0.00 0.00 2.69
658 677 6.537453 TGACATCCCTCTTTTGTTTTGAAA 57.463 33.333 0.00 0.00 0.00 2.69
659 678 6.940739 TGACATCCCTCTTTTGTTTTGAAAA 58.059 32.000 0.00 0.00 0.00 2.29
660 679 7.390027 TGACATCCCTCTTTTGTTTTGAAAAA 58.610 30.769 0.00 0.00 0.00 1.94
692 711 2.966050 CTCCTTTTTGAGAGGACGAGG 58.034 52.381 0.00 0.00 38.37 4.63
702 721 3.056536 TGAGAGGACGAGGATCACAAAAG 60.057 47.826 0.00 0.00 33.17 2.27
708 727 2.076863 CGAGGATCACAAAAGTGGGAC 58.923 52.381 0.00 0.00 40.97 4.46
709 728 2.076863 GAGGATCACAAAAGTGGGACG 58.923 52.381 0.00 0.00 40.97 4.79
710 729 1.697432 AGGATCACAAAAGTGGGACGA 59.303 47.619 0.00 0.00 40.97 4.20
715 734 1.303317 CAAAAGTGGGACGAGGGGG 60.303 63.158 0.00 0.00 0.00 5.40
730 749 2.673685 GGGGGCGGGTACAAAATTT 58.326 52.632 0.00 0.00 0.00 1.82
731 750 0.248012 GGGGGCGGGTACAAAATTTG 59.752 55.000 3.89 3.89 0.00 2.32
928 3793 3.022401 GCCATTTCGACGCGCTCAA 62.022 57.895 5.73 0.00 0.00 3.02
953 3818 1.005867 GCCAACTTCACCGACGGTA 60.006 57.895 21.25 3.93 32.11 4.02
1080 3945 4.796231 CGTTCGGGCTCCTCGGTG 62.796 72.222 0.00 0.00 0.00 4.94
1223 4088 4.994744 AAGGAAATTGCCTTGCGC 57.005 50.000 17.63 0.00 46.25 6.09
1241 4106 1.128136 CGCTGATGCTGTGTTGAAGAG 59.872 52.381 0.00 0.00 36.97 2.85
1421 4313 7.966204 CCAGGTATTTTGTTTCTAACGTTATGG 59.034 37.037 8.76 4.57 0.00 2.74
1426 4318 4.517952 TGTTTCTAACGTTATGGTCCGA 57.482 40.909 8.76 0.00 0.00 4.55
1431 4323 2.396590 AACGTTATGGTCCGAAGCAT 57.603 45.000 0.00 0.00 37.70 3.79
1471 6373 4.318332 TGTGATTTCAGAATCGACTTGCT 58.682 39.130 0.00 0.00 43.75 3.91
1681 6735 2.332117 TCCTTAGACCACCGGACTTTT 58.668 47.619 9.46 0.00 0.00 2.27
1728 6828 4.926238 GGATTCTGTATTGATAGTCAGCCG 59.074 45.833 0.00 0.00 0.00 5.52
1828 6944 6.945016 CCATTATGATGCGTGTTCAAGAGAAC 60.945 42.308 0.00 1.59 41.76 3.01
1857 6975 7.623268 AATTTGTTAGATCGAAGTTGTTTGC 57.377 32.000 0.00 0.00 0.00 3.68
1858 6976 6.371809 TTTGTTAGATCGAAGTTGTTTGCT 57.628 33.333 0.00 0.00 0.00 3.91
1861 6979 7.485418 TGTTAGATCGAAGTTGTTTGCTTAA 57.515 32.000 0.00 0.00 0.00 1.85
1862 6980 7.572759 TGTTAGATCGAAGTTGTTTGCTTAAG 58.427 34.615 0.00 0.00 0.00 1.85
1863 6981 5.613358 AGATCGAAGTTGTTTGCTTAAGG 57.387 39.130 4.29 0.00 0.00 2.69
1864 6982 3.619233 TCGAAGTTGTTTGCTTAAGGC 57.381 42.857 4.29 0.00 42.22 4.35
1865 6983 2.292292 TCGAAGTTGTTTGCTTAAGGCC 59.708 45.455 4.29 0.00 40.92 5.19
1866 6984 2.661594 GAAGTTGTTTGCTTAAGGCCG 58.338 47.619 4.29 0.00 40.92 6.13
1867 6985 0.313987 AGTTGTTTGCTTAAGGCCGC 59.686 50.000 4.29 0.00 40.92 6.53
1868 6986 1.001745 GTTGTTTGCTTAAGGCCGCG 61.002 55.000 4.29 0.00 40.92 6.46
1869 6987 1.448922 TTGTTTGCTTAAGGCCGCGT 61.449 50.000 4.92 0.00 40.92 6.01
1870 6988 1.284715 GTTTGCTTAAGGCCGCGTT 59.715 52.632 4.92 3.47 40.92 4.84
1871 6989 0.318360 GTTTGCTTAAGGCCGCGTTT 60.318 50.000 4.92 0.00 40.92 3.60
1872 6990 0.318275 TTTGCTTAAGGCCGCGTTTG 60.318 50.000 4.92 0.00 40.92 2.93
1873 6991 2.136196 TTGCTTAAGGCCGCGTTTGG 62.136 55.000 4.92 0.00 40.92 3.28
1874 6992 2.329614 GCTTAAGGCCGCGTTTGGA 61.330 57.895 4.92 0.00 34.27 3.53
1875 6993 1.654023 GCTTAAGGCCGCGTTTGGAT 61.654 55.000 4.92 0.00 34.27 3.41
1876 6994 0.808755 CTTAAGGCCGCGTTTGGATT 59.191 50.000 4.92 0.00 0.00 3.01
1877 6995 0.806241 TTAAGGCCGCGTTTGGATTC 59.194 50.000 4.92 0.00 0.00 2.52
1878 6996 1.027792 TAAGGCCGCGTTTGGATTCC 61.028 55.000 4.92 0.00 0.00 3.01
1879 6997 3.822192 GGCCGCGTTTGGATTCCC 61.822 66.667 4.92 0.00 0.00 3.97
1880 6998 2.750237 GCCGCGTTTGGATTCCCT 60.750 61.111 4.92 0.00 0.00 4.20
1881 6999 2.761195 GCCGCGTTTGGATTCCCTC 61.761 63.158 4.92 0.00 0.00 4.30
1882 7000 2.112815 CCGCGTTTGGATTCCCTCC 61.113 63.158 4.92 0.00 45.19 4.30
1889 7007 4.610714 GGATTCCCTCCGCTCCGC 62.611 72.222 0.00 0.00 33.29 5.54
1922 7040 3.434319 CGCAGCGGCAATCCAGTT 61.434 61.111 7.00 0.00 41.24 3.16
1923 7041 2.180017 GCAGCGGCAATCCAGTTG 59.820 61.111 3.18 0.00 40.72 3.16
1924 7042 2.334946 GCAGCGGCAATCCAGTTGA 61.335 57.895 3.18 0.00 40.37 3.18
1925 7043 1.660560 GCAGCGGCAATCCAGTTGAT 61.661 55.000 3.18 0.00 40.37 2.57
1926 7044 0.813184 CAGCGGCAATCCAGTTGATT 59.187 50.000 1.45 0.00 44.67 2.57
1927 7045 2.016318 CAGCGGCAATCCAGTTGATTA 58.984 47.619 1.45 0.00 41.85 1.75
1928 7046 2.423185 CAGCGGCAATCCAGTTGATTAA 59.577 45.455 1.45 0.00 41.85 1.40
1929 7047 2.684881 AGCGGCAATCCAGTTGATTAAG 59.315 45.455 1.45 0.00 41.85 1.85
1930 7048 2.223572 GCGGCAATCCAGTTGATTAAGG 60.224 50.000 0.00 0.00 41.85 2.69
1931 7049 2.223572 CGGCAATCCAGTTGATTAAGGC 60.224 50.000 0.00 0.00 41.85 4.35
1932 7050 2.101415 GGCAATCCAGTTGATTAAGGCC 59.899 50.000 0.00 0.00 41.85 5.19
1933 7051 2.760092 GCAATCCAGTTGATTAAGGCCA 59.240 45.455 5.01 0.00 41.85 5.36
1934 7052 3.385755 GCAATCCAGTTGATTAAGGCCAT 59.614 43.478 5.01 0.00 41.85 4.40
1935 7053 4.584325 GCAATCCAGTTGATTAAGGCCATA 59.416 41.667 5.01 0.00 41.85 2.74
1936 7054 5.068987 GCAATCCAGTTGATTAAGGCCATAA 59.931 40.000 5.01 3.51 41.85 1.90
1937 7055 6.239402 GCAATCCAGTTGATTAAGGCCATAAT 60.239 38.462 12.95 12.95 41.85 1.28
1938 7056 7.687592 GCAATCCAGTTGATTAAGGCCATAATT 60.688 37.037 14.17 0.00 41.85 1.40
1939 7057 7.919385 ATCCAGTTGATTAAGGCCATAATTT 57.081 32.000 14.17 0.00 0.00 1.82
1940 7058 7.111247 TCCAGTTGATTAAGGCCATAATTTG 57.889 36.000 14.17 10.28 0.00 2.32
1941 7059 5.754890 CCAGTTGATTAAGGCCATAATTTGC 59.245 40.000 14.17 7.68 0.00 3.68
1942 7060 5.459762 CAGTTGATTAAGGCCATAATTTGCG 59.540 40.000 14.17 0.41 0.00 4.85
1943 7061 4.582701 TGATTAAGGCCATAATTTGCGG 57.417 40.909 14.17 0.00 0.00 5.69
1944 7062 4.211125 TGATTAAGGCCATAATTTGCGGA 58.789 39.130 14.17 0.00 0.00 5.54
1945 7063 4.278170 TGATTAAGGCCATAATTTGCGGAG 59.722 41.667 14.17 0.00 0.00 4.63
1946 7064 2.143876 AAGGCCATAATTTGCGGAGT 57.856 45.000 5.01 0.00 0.00 3.85
1947 7065 2.143876 AGGCCATAATTTGCGGAGTT 57.856 45.000 5.01 0.00 0.00 3.01
1948 7066 1.750778 AGGCCATAATTTGCGGAGTTG 59.249 47.619 5.01 0.00 0.00 3.16
1949 7067 1.748493 GGCCATAATTTGCGGAGTTGA 59.252 47.619 0.00 0.00 0.00 3.18
1950 7068 2.362077 GGCCATAATTTGCGGAGTTGAT 59.638 45.455 0.00 0.00 0.00 2.57
1951 7069 3.181476 GGCCATAATTTGCGGAGTTGATT 60.181 43.478 0.00 0.00 0.00 2.57
1952 7070 4.037446 GGCCATAATTTGCGGAGTTGATTA 59.963 41.667 0.00 0.00 0.00 1.75
1953 7071 5.451242 GGCCATAATTTGCGGAGTTGATTAA 60.451 40.000 0.00 0.00 0.00 1.40
1954 7072 6.039616 GCCATAATTTGCGGAGTTGATTAAA 58.960 36.000 0.00 0.00 0.00 1.52
1955 7073 6.198966 GCCATAATTTGCGGAGTTGATTAAAG 59.801 38.462 0.00 0.00 0.00 1.85
1956 7074 6.198966 CCATAATTTGCGGAGTTGATTAAAGC 59.801 38.462 0.00 0.00 0.00 3.51
1957 7075 3.569250 TTTGCGGAGTTGATTAAAGCC 57.431 42.857 0.00 0.00 0.00 4.35
1958 7076 1.459450 TGCGGAGTTGATTAAAGCCC 58.541 50.000 0.00 0.00 0.00 5.19
1959 7077 0.377203 GCGGAGTTGATTAAAGCCCG 59.623 55.000 0.00 0.00 37.13 6.13
1960 7078 0.377203 CGGAGTTGATTAAAGCCCGC 59.623 55.000 0.00 0.00 30.29 6.13
1961 7079 1.751437 GGAGTTGATTAAAGCCCGCT 58.249 50.000 0.00 0.00 0.00 5.52
1962 7080 1.671328 GGAGTTGATTAAAGCCCGCTC 59.329 52.381 0.00 0.00 0.00 5.03
1963 7081 1.671328 GAGTTGATTAAAGCCCGCTCC 59.329 52.381 0.00 0.00 0.00 4.70
1964 7082 0.377203 GTTGATTAAAGCCCGCTCCG 59.623 55.000 0.00 0.00 0.00 4.63
1965 7083 1.373590 TTGATTAAAGCCCGCTCCGC 61.374 55.000 0.00 0.00 0.00 5.54
1997 7115 3.554692 GGATGACTGCCGAACGCG 61.555 66.667 3.53 3.53 42.08 6.01
2152 7299 4.092529 CACTACTACTGTGAAGCTGCATTG 59.907 45.833 0.00 0.00 37.60 2.82
2460 7663 8.934023 TGATAAGGAAACTAAGTGGAAAACAT 57.066 30.769 0.00 0.00 42.68 2.71
2473 7676 2.319472 GAAAACATTGAGGCTTGCGTC 58.681 47.619 8.18 8.18 0.00 5.19
2519 7722 5.078949 TCTCATCCAGAAAAGGAAAATGCA 58.921 37.500 0.00 0.00 41.92 3.96
2591 7812 5.874093 AGTCCTCTTCAGAATGTTGTGAAT 58.126 37.500 5.88 0.00 39.34 2.57
2616 7837 7.946207 TCAAAACCAGCAAATACATACTTCAA 58.054 30.769 0.00 0.00 0.00 2.69
2724 8131 7.171678 GTGCTCACACTTCTCAAGTTACTTATT 59.828 37.037 0.00 0.00 43.85 1.40
3001 8675 3.756933 AACCGCTCAACTTACTTACCA 57.243 42.857 0.00 0.00 0.00 3.25
3090 8764 2.363680 CCAGAGGAATATGCGTCAGAGT 59.636 50.000 6.18 0.00 0.00 3.24
3253 8927 4.399004 TGAAAAATATGCCCCAAATCCG 57.601 40.909 0.00 0.00 0.00 4.18
3283 9146 2.656002 TGAATGGACCGTTTGTTTGGA 58.344 42.857 0.00 0.00 0.00 3.53
3527 9403 0.255890 TGTAGCTTCATGGGGGCTTC 59.744 55.000 11.76 8.49 37.50 3.86
3529 9405 0.548031 TAGCTTCATGGGGGCTTCTG 59.452 55.000 11.76 0.00 37.50 3.02
3530 9406 1.000396 GCTTCATGGGGGCTTCTGT 60.000 57.895 0.00 0.00 0.00 3.41
3531 9407 0.255890 GCTTCATGGGGGCTTCTGTA 59.744 55.000 0.00 0.00 0.00 2.74
3532 9408 1.748591 GCTTCATGGGGGCTTCTGTAG 60.749 57.143 0.00 0.00 0.00 2.74
3544 9420 3.770666 GCTTCTGTAGCTTCATACGTGA 58.229 45.455 0.00 0.00 46.77 4.35
3545 9421 3.794028 GCTTCTGTAGCTTCATACGTGAG 59.206 47.826 0.00 0.00 46.77 3.51
3546 9422 4.675671 GCTTCTGTAGCTTCATACGTGAGT 60.676 45.833 0.00 0.00 46.77 3.41
3597 9486 3.581332 TCGGTCCCTTCATTCTGTTAACT 59.419 43.478 7.22 0.00 0.00 2.24
3600 9489 5.561679 GGTCCCTTCATTCTGTTAACTCTT 58.438 41.667 7.22 0.00 0.00 2.85
3668 9557 8.794335 ACCAGAGTGATCTTTAAACTATTTCC 57.206 34.615 0.00 0.00 0.00 3.13
3771 9666 5.030936 GGCTTCGCTGATTAACTTTTCATC 58.969 41.667 0.00 0.00 0.00 2.92
3894 9819 1.069090 GTGGCAAGTGGACGACTCA 59.931 57.895 0.00 0.00 31.73 3.41
4068 9993 2.256117 AGCAGGTCAGTGTAACAACC 57.744 50.000 0.00 0.00 43.06 3.77
4241 10179 3.619419 TCCTCCGAAATGCATGAATTGA 58.381 40.909 0.00 0.00 0.00 2.57
4261 10199 5.845391 TGAAAACCACAGTTTAGGGAAAG 57.155 39.130 0.00 0.00 45.54 2.62
4319 10257 1.940613 AGGAAAGTGAACTGCGTGAAC 59.059 47.619 0.00 0.00 0.00 3.18
4325 10263 2.354821 AGTGAACTGCGTGAACTTTTCC 59.645 45.455 0.00 0.00 0.00 3.13
4401 10339 3.217626 AGAAGTGCCCAAGAGAAAACTG 58.782 45.455 0.00 0.00 0.00 3.16
4440 10400 6.487828 TCCAAAACTTCCATGAGATTGAGAT 58.512 36.000 0.00 0.00 0.00 2.75
4501 10461 2.164422 GCTTTTCCTCCATTTTCCCTCG 59.836 50.000 0.00 0.00 0.00 4.63
4610 10570 6.366630 CAAAAACTGAAAGAAACGCCAAAAA 58.633 32.000 0.00 0.00 37.43 1.94
4630 10695 8.394877 CCAAAAATATATCTTTGTCACGTGCTA 58.605 33.333 11.67 0.00 31.84 3.49
5035 11100 5.123820 TGCTATTTCTGGAAGATGGTTTTCG 59.876 40.000 0.00 0.00 46.36 3.46
5096 11161 3.584848 AGGACAGTCTCATGGCTTAAAGT 59.415 43.478 0.00 0.00 0.00 2.66
5106 11171 6.325028 TCTCATGGCTTAAAGTATCTACAGCT 59.675 38.462 0.00 0.00 0.00 4.24
5107 11172 6.516718 TCATGGCTTAAAGTATCTACAGCTC 58.483 40.000 0.00 0.00 0.00 4.09
5115 11180 3.431415 AGTATCTACAGCTCCACACACA 58.569 45.455 0.00 0.00 0.00 3.72
5118 11183 3.111853 TCTACAGCTCCACACACAAAG 57.888 47.619 0.00 0.00 0.00 2.77
5125 11190 0.179067 TCCACACACAAAGTCCGGTC 60.179 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.494271 GGACATATATCGGATATATTTGTGCAT 57.506 33.333 23.85 8.27 36.53 3.96
2 3 8.482128 TGGACATATATCGGATATATTTGTGCA 58.518 33.333 25.74 25.74 39.68 4.57
13 14 9.396022 GGACATAAAAATGGACATATATCGGAT 57.604 33.333 0.00 0.00 0.00 4.18
14 15 8.379331 TGGACATAAAAATGGACATATATCGGA 58.621 33.333 0.00 0.00 0.00 4.55
15 16 8.560355 TGGACATAAAAATGGACATATATCGG 57.440 34.615 0.00 0.00 0.00 4.18
16 17 9.435688 TCTGGACATAAAAATGGACATATATCG 57.564 33.333 0.00 0.00 0.00 2.92
18 19 9.219603 CGTCTGGACATAAAAATGGACATATAT 57.780 33.333 1.63 0.00 0.00 0.86
19 20 8.208224 ACGTCTGGACATAAAAATGGACATATA 58.792 33.333 1.63 0.00 0.00 0.86
20 21 7.012327 CACGTCTGGACATAAAAATGGACATAT 59.988 37.037 1.63 0.00 0.00 1.78
21 22 6.315144 CACGTCTGGACATAAAAATGGACATA 59.685 38.462 1.63 0.00 0.00 2.29
22 23 5.123820 CACGTCTGGACATAAAAATGGACAT 59.876 40.000 1.63 0.00 0.00 3.06
23 24 4.454161 CACGTCTGGACATAAAAATGGACA 59.546 41.667 1.63 0.00 0.00 4.02
24 25 4.142687 CCACGTCTGGACATAAAAATGGAC 60.143 45.833 1.63 0.00 40.55 4.02
25 26 4.006989 CCACGTCTGGACATAAAAATGGA 58.993 43.478 1.63 0.00 40.55 3.41
26 27 3.756434 ACCACGTCTGGACATAAAAATGG 59.244 43.478 0.00 0.00 40.55 3.16
27 28 4.142687 GGACCACGTCTGGACATAAAAATG 60.143 45.833 0.00 0.00 40.55 2.32
28 29 4.007659 GGACCACGTCTGGACATAAAAAT 58.992 43.478 0.00 0.00 40.55 1.82
29 30 3.181453 TGGACCACGTCTGGACATAAAAA 60.181 43.478 0.00 0.00 40.55 1.94
30 31 2.369203 TGGACCACGTCTGGACATAAAA 59.631 45.455 0.00 0.00 40.55 1.52
31 32 1.972075 TGGACCACGTCTGGACATAAA 59.028 47.619 0.00 0.00 40.55 1.40
32 33 1.274167 GTGGACCACGTCTGGACATAA 59.726 52.381 9.33 0.00 40.55 1.90
33 34 0.892755 GTGGACCACGTCTGGACATA 59.107 55.000 9.33 0.00 40.55 2.29
34 35 1.671742 GTGGACCACGTCTGGACAT 59.328 57.895 9.33 0.00 40.55 3.06
35 36 3.134879 GTGGACCACGTCTGGACA 58.865 61.111 9.33 0.00 40.55 4.02
44 45 0.447801 GCATCATGTTCGTGGACCAC 59.552 55.000 15.13 15.13 0.00 4.16
45 46 1.018752 CGCATCATGTTCGTGGACCA 61.019 55.000 0.00 0.00 0.00 4.02
46 47 1.705337 CCGCATCATGTTCGTGGACC 61.705 60.000 5.73 0.00 31.75 4.46
47 48 1.705337 CCCGCATCATGTTCGTGGAC 61.705 60.000 11.33 0.00 31.75 4.02
48 49 1.449423 CCCGCATCATGTTCGTGGA 60.449 57.895 11.33 0.00 31.75 4.02
49 50 1.431488 CTCCCGCATCATGTTCGTGG 61.431 60.000 0.00 0.00 0.00 4.94
50 51 1.431488 CCTCCCGCATCATGTTCGTG 61.431 60.000 0.00 0.00 0.00 4.35
51 52 1.153369 CCTCCCGCATCATGTTCGT 60.153 57.895 0.00 0.00 0.00 3.85
52 53 1.889105 CCCTCCCGCATCATGTTCG 60.889 63.158 0.00 0.00 0.00 3.95
53 54 0.533755 CTCCCTCCCGCATCATGTTC 60.534 60.000 0.00 0.00 0.00 3.18
54 55 1.528824 CTCCCTCCCGCATCATGTT 59.471 57.895 0.00 0.00 0.00 2.71
64 65 0.402121 GTATTGGATGGCTCCCTCCC 59.598 60.000 7.61 0.00 41.29 4.30
82 83 5.046159 TCCAACCGGATACTTTGTGATTAGT 60.046 40.000 9.46 0.00 35.91 2.24
90 91 2.026636 TCCCTTCCAACCGGATACTTTG 60.027 50.000 9.46 0.56 42.41 2.77
127 128 5.298527 ACAAATATCTCACCACATGCATGAG 59.701 40.000 32.75 24.31 41.06 2.90
157 158 0.901580 TCTACTCCCAACCGGACACC 60.902 60.000 9.46 0.00 34.86 4.16
163 164 1.064611 TCCTCTCTCTACTCCCAACCG 60.065 57.143 0.00 0.00 0.00 4.44
168 169 2.372172 CCTCTCTCCTCTCTCTACTCCC 59.628 59.091 0.00 0.00 0.00 4.30
186 187 3.518003 GCACATGCATGGTCCCTC 58.482 61.111 29.41 8.65 41.59 4.30
204 205 3.837731 CCCTCTTCTCTCTTCTCCAAACT 59.162 47.826 0.00 0.00 0.00 2.66
208 209 2.922955 TCTCCCTCTTCTCTCTTCTCCA 59.077 50.000 0.00 0.00 0.00 3.86
230 233 5.156355 GCACTTGACCAATCAAATACACTG 58.844 41.667 0.00 0.00 44.28 3.66
231 234 4.826733 TGCACTTGACCAATCAAATACACT 59.173 37.500 0.00 0.00 44.28 3.55
232 235 5.119931 TGCACTTGACCAATCAAATACAC 57.880 39.130 0.00 0.00 44.28 2.90
235 238 5.105797 GGACATGCACTTGACCAATCAAATA 60.106 40.000 4.25 0.00 44.28 1.40
238 241 2.557924 GGACATGCACTTGACCAATCAA 59.442 45.455 4.25 0.00 42.73 2.57
247 250 1.021390 GGAGTCCGGACATGCACTTG 61.021 60.000 35.00 0.00 0.00 3.16
275 278 1.203087 TCCAAGAGACTAACGTGGGGA 60.203 52.381 0.00 0.00 37.46 4.81
276 279 1.263356 TCCAAGAGACTAACGTGGGG 58.737 55.000 0.00 0.00 37.46 4.96
282 285 4.996788 TTCCGGTATCCAAGAGACTAAC 57.003 45.455 0.00 0.00 0.00 2.34
285 288 2.966516 GGATTCCGGTATCCAAGAGACT 59.033 50.000 29.59 0.00 43.04 3.24
300 303 1.997606 CAGTTGGAACGTACGGATTCC 59.002 52.381 23.73 23.73 44.08 3.01
313 316 0.613260 ATGTCGGCTTAGCAGTTGGA 59.387 50.000 6.53 0.00 0.00 3.53
315 318 4.368315 TGTATATGTCGGCTTAGCAGTTG 58.632 43.478 6.53 0.00 0.00 3.16
316 319 4.501571 CCTGTATATGTCGGCTTAGCAGTT 60.502 45.833 6.53 0.00 0.00 3.16
327 330 2.228059 ACCGGAGACCTGTATATGTCG 58.772 52.381 9.46 0.00 36.61 4.35
346 349 4.761739 TCTGGATCACTTTTGTCATCCAAC 59.238 41.667 3.59 0.00 43.39 3.77
363 366 3.034635 GTCTGGACCATAGTGTCTGGAT 58.965 50.000 0.00 0.00 37.22 3.41
367 370 6.491745 CACTATATGTCTGGACCATAGTGTCT 59.508 42.308 25.07 8.20 43.03 3.41
374 377 3.574396 CCGTCACTATATGTCTGGACCAT 59.426 47.826 0.00 0.00 0.00 3.55
376 379 2.957006 ACCGTCACTATATGTCTGGACC 59.043 50.000 0.00 0.00 0.00 4.46
378 381 4.707934 TCAAACCGTCACTATATGTCTGGA 59.292 41.667 0.00 0.00 0.00 3.86
380 383 5.520288 CCTTCAAACCGTCACTATATGTCTG 59.480 44.000 0.00 0.00 0.00 3.51
381 384 5.661458 CCTTCAAACCGTCACTATATGTCT 58.339 41.667 0.00 0.00 0.00 3.41
390 393 2.613506 CGGGCCTTCAAACCGTCAC 61.614 63.158 0.84 0.00 42.53 3.67
405 408 2.364647 GTTAGGGTATCTCCAAGACGGG 59.635 54.545 0.00 0.00 38.11 5.28
407 410 3.028850 TGGTTAGGGTATCTCCAAGACG 58.971 50.000 0.00 0.00 38.11 4.18
409 412 3.028850 CGTGGTTAGGGTATCTCCAAGA 58.971 50.000 0.00 0.00 38.11 3.02
410 413 2.764572 ACGTGGTTAGGGTATCTCCAAG 59.235 50.000 0.00 0.00 38.11 3.61
438 441 0.041982 GGGCATTTTTACCTGGGGGA 59.958 55.000 0.00 0.00 36.25 4.81
439 442 0.980754 GGGGCATTTTTACCTGGGGG 60.981 60.000 0.00 0.00 38.88 5.40
440 443 0.252467 TGGGGCATTTTTACCTGGGG 60.252 55.000 0.00 0.00 0.00 4.96
441 444 1.878211 ATGGGGCATTTTTACCTGGG 58.122 50.000 0.00 0.00 0.00 4.45
444 447 3.094484 TCGAATGGGGCATTTTTACCT 57.906 42.857 0.00 0.00 33.90 3.08
469 472 4.701651 TCATGCATCTCTACCAAGGTTTTG 59.298 41.667 0.00 0.00 0.00 2.44
510 513 8.157476 GGGCTTCATCAAGGAATAAATAGACTA 58.843 37.037 0.00 0.00 0.00 2.59
511 514 7.001073 GGGCTTCATCAAGGAATAAATAGACT 58.999 38.462 0.00 0.00 0.00 3.24
512 515 6.772716 TGGGCTTCATCAAGGAATAAATAGAC 59.227 38.462 0.00 0.00 0.00 2.59
514 517 7.771927 ATGGGCTTCATCAAGGAATAAATAG 57.228 36.000 0.00 0.00 0.00 1.73
515 518 9.653516 TTAATGGGCTTCATCAAGGAATAAATA 57.346 29.630 0.00 0.00 34.44 1.40
516 519 8.551682 TTAATGGGCTTCATCAAGGAATAAAT 57.448 30.769 0.00 0.00 34.44 1.40
517 520 7.969690 TTAATGGGCTTCATCAAGGAATAAA 57.030 32.000 0.00 0.00 34.44 1.40
519 522 9.827198 ATAATTAATGGGCTTCATCAAGGAATA 57.173 29.630 0.00 0.00 34.44 1.75
520 523 8.731591 ATAATTAATGGGCTTCATCAAGGAAT 57.268 30.769 0.00 0.00 34.44 3.01
527 542 7.031975 GCAAGCTATAATTAATGGGCTTCATC 58.968 38.462 11.74 4.79 36.50 2.92
594 610 3.706698 TGCGAAGAATACGAATCAGGAG 58.293 45.455 0.00 0.00 0.00 3.69
596 612 2.797156 CCTGCGAAGAATACGAATCAGG 59.203 50.000 0.00 0.00 34.39 3.86
597 613 2.219674 GCCTGCGAAGAATACGAATCAG 59.780 50.000 0.00 0.00 0.00 2.90
602 618 0.806102 GCTGCCTGCGAAGAATACGA 60.806 55.000 0.00 0.00 0.00 3.43
610 626 1.359833 CAAAAGTGCTGCCTGCGAA 59.640 52.632 0.00 0.00 46.63 4.70
612 628 2.049802 CCAAAAGTGCTGCCTGCG 60.050 61.111 0.00 0.00 46.63 5.18
613 629 2.341176 CCCAAAAGTGCTGCCTGC 59.659 61.111 0.00 0.00 43.25 4.85
614 630 1.662044 GACCCAAAAGTGCTGCCTG 59.338 57.895 0.00 0.00 0.00 4.85
615 631 1.898574 CGACCCAAAAGTGCTGCCT 60.899 57.895 0.00 0.00 0.00 4.75
616 632 2.644992 CGACCCAAAAGTGCTGCC 59.355 61.111 0.00 0.00 0.00 4.85
617 633 2.050077 GCGACCCAAAAGTGCTGC 60.050 61.111 0.00 0.00 0.00 5.25
618 634 1.283793 CAGCGACCCAAAAGTGCTG 59.716 57.895 0.00 0.00 45.88 4.41
619 635 1.148273 TCAGCGACCCAAAAGTGCT 59.852 52.632 0.00 0.00 36.05 4.40
620 636 1.282875 GTCAGCGACCCAAAAGTGC 59.717 57.895 0.00 0.00 0.00 4.40
621 637 1.197721 GATGTCAGCGACCCAAAAGTG 59.802 52.381 6.30 0.00 0.00 3.16
623 639 0.804989 GGATGTCAGCGACCCAAAAG 59.195 55.000 6.30 0.00 0.00 2.27
660 679 7.301868 TCTCAAAAAGGAGGTATGCATTTTT 57.698 32.000 3.54 1.20 35.58 1.94
661 680 6.071165 CCTCTCAAAAAGGAGGTATGCATTTT 60.071 38.462 3.54 0.00 42.86 1.82
662 681 5.420104 CCTCTCAAAAAGGAGGTATGCATTT 59.580 40.000 3.54 0.00 42.86 2.32
663 682 4.952335 CCTCTCAAAAAGGAGGTATGCATT 59.048 41.667 3.54 0.00 42.86 3.56
664 683 4.228210 TCCTCTCAAAAAGGAGGTATGCAT 59.772 41.667 3.79 3.79 46.56 3.96
665 684 3.587061 TCCTCTCAAAAAGGAGGTATGCA 59.413 43.478 8.56 0.00 46.56 3.96
666 685 3.942115 GTCCTCTCAAAAAGGAGGTATGC 59.058 47.826 8.56 0.00 46.56 3.14
667 686 4.081642 TCGTCCTCTCAAAAAGGAGGTATG 60.082 45.833 10.62 2.91 46.56 2.39
668 687 4.094476 TCGTCCTCTCAAAAAGGAGGTAT 58.906 43.478 10.62 0.00 46.56 2.73
669 688 3.503365 TCGTCCTCTCAAAAAGGAGGTA 58.497 45.455 10.62 0.00 46.56 3.08
670 689 2.300437 CTCGTCCTCTCAAAAAGGAGGT 59.700 50.000 10.62 0.00 46.56 3.85
715 734 4.991687 TGAAATTCAAATTTTGTACCCGCC 59.008 37.500 8.89 0.00 38.64 6.13
730 749 4.504689 GCCCCTTCCAACATTTGAAATTCA 60.505 41.667 0.00 0.00 0.00 2.57
731 750 4.002982 GCCCCTTCCAACATTTGAAATTC 58.997 43.478 0.00 0.00 0.00 2.17
878 3737 2.799540 CTCGACGGCTTTTAGCGCC 61.800 63.158 2.29 0.00 43.62 6.53
928 3793 2.746277 GTGAAGTTGGCGGCCGAT 60.746 61.111 33.48 6.51 0.00 4.18
953 3818 3.297620 CTGGCGGCAGTGGCTTTT 61.298 61.111 29.42 0.00 40.87 2.27
1040 3905 1.202313 GCCACAGTATCTGGAGACGTC 60.202 57.143 7.70 7.70 35.51 4.34
1044 3909 1.781786 GAGGCCACAGTATCTGGAGA 58.218 55.000 5.01 0.00 35.51 3.71
1049 3914 0.456221 CGAACGAGGCCACAGTATCT 59.544 55.000 5.01 0.00 0.00 1.98
1223 4088 2.082231 CCCTCTTCAACACAGCATCAG 58.918 52.381 0.00 0.00 0.00 2.90
1361 4229 3.027412 ACTATCTGCAGTTCATCGGAGT 58.973 45.455 14.67 1.73 0.00 3.85
1426 4318 8.498358 CACATACACATGATAAATACGATGCTT 58.502 33.333 0.00 0.00 35.96 3.91
1471 6373 8.862325 TGCTCTTTTCTATTTGAATCACCTTA 57.138 30.769 0.00 0.00 34.24 2.69
1681 6735 9.838339 TCCAAATAAAAGGAAAAATAAACAGCA 57.162 25.926 0.00 0.00 0.00 4.41
1706 6790 5.533482 ACGGCTGACTATCAATACAGAATC 58.467 41.667 0.00 0.00 32.90 2.52
1728 6828 0.808755 CCCGCAATCAAGTTGGGTAC 59.191 55.000 2.34 0.00 46.21 3.34
1828 6944 9.450807 AACAACTTCGATCTAACAAATTTTCTG 57.549 29.630 0.00 0.00 0.00 3.02
1835 6953 6.371809 AGCAAACAACTTCGATCTAACAAA 57.628 33.333 0.00 0.00 0.00 2.83
1856 6974 1.654023 ATCCAAACGCGGCCTTAAGC 61.654 55.000 12.47 0.00 42.60 3.09
1857 6975 0.808755 AATCCAAACGCGGCCTTAAG 59.191 50.000 12.47 0.00 0.00 1.85
1858 6976 0.806241 GAATCCAAACGCGGCCTTAA 59.194 50.000 12.47 0.00 0.00 1.85
1861 6979 2.750237 GGAATCCAAACGCGGCCT 60.750 61.111 12.47 0.00 0.00 5.19
1862 6980 3.822192 GGGAATCCAAACGCGGCC 61.822 66.667 12.47 0.00 0.00 6.13
1863 6981 2.750237 AGGGAATCCAAACGCGGC 60.750 61.111 12.47 0.00 34.83 6.53
1864 6982 3.497879 GAGGGAATCCAAACGCGG 58.502 61.111 12.47 0.00 34.83 6.46
1905 7023 3.434319 AACTGGATTGCCGCTGCG 61.434 61.111 16.34 16.34 41.78 5.18
1906 7024 1.660560 ATCAACTGGATTGCCGCTGC 61.661 55.000 0.00 0.00 38.29 5.25
1907 7025 0.813184 AATCAACTGGATTGCCGCTG 59.187 50.000 0.00 0.00 44.51 5.18
1908 7026 2.418368 TAATCAACTGGATTGCCGCT 57.582 45.000 0.00 0.00 45.70 5.52
1909 7027 2.223572 CCTTAATCAACTGGATTGCCGC 60.224 50.000 0.00 0.00 45.70 6.53
1910 7028 2.223572 GCCTTAATCAACTGGATTGCCG 60.224 50.000 0.00 0.00 45.70 5.69
1911 7029 2.101415 GGCCTTAATCAACTGGATTGCC 59.899 50.000 0.00 0.00 45.70 4.52
1912 7030 2.760092 TGGCCTTAATCAACTGGATTGC 59.240 45.455 3.32 0.00 45.70 3.56
1913 7031 6.713762 TTATGGCCTTAATCAACTGGATTG 57.286 37.500 3.32 0.00 45.70 2.67
1915 7033 7.687592 GCAAATTATGGCCTTAATCAACTGGAT 60.688 37.037 20.82 3.83 38.05 3.41
1916 7034 6.406849 GCAAATTATGGCCTTAATCAACTGGA 60.407 38.462 20.82 0.00 0.00 3.86
1917 7035 5.754890 GCAAATTATGGCCTTAATCAACTGG 59.245 40.000 20.82 7.37 0.00 4.00
1918 7036 5.459762 CGCAAATTATGGCCTTAATCAACTG 59.540 40.000 20.82 16.30 0.00 3.16
1919 7037 5.451798 CCGCAAATTATGGCCTTAATCAACT 60.452 40.000 20.82 6.03 0.00 3.16
1920 7038 4.744631 CCGCAAATTATGGCCTTAATCAAC 59.255 41.667 20.82 13.14 0.00 3.18
1921 7039 4.646945 TCCGCAAATTATGGCCTTAATCAA 59.353 37.500 20.82 0.00 0.00 2.57
1922 7040 4.211125 TCCGCAAATTATGGCCTTAATCA 58.789 39.130 20.82 0.00 0.00 2.57
1923 7041 4.278419 ACTCCGCAAATTATGGCCTTAATC 59.722 41.667 20.82 10.27 0.00 1.75
1924 7042 4.215109 ACTCCGCAAATTATGGCCTTAAT 58.785 39.130 16.25 16.25 0.00 1.40
1925 7043 3.626930 ACTCCGCAAATTATGGCCTTAA 58.373 40.909 13.07 13.07 0.00 1.85
1926 7044 3.290948 ACTCCGCAAATTATGGCCTTA 57.709 42.857 3.32 0.00 0.00 2.69
1927 7045 2.143876 ACTCCGCAAATTATGGCCTT 57.856 45.000 3.32 0.00 0.00 4.35
1928 7046 1.750778 CAACTCCGCAAATTATGGCCT 59.249 47.619 3.32 0.00 0.00 5.19
1929 7047 1.748493 TCAACTCCGCAAATTATGGCC 59.252 47.619 0.00 0.00 0.00 5.36
1930 7048 3.715628 ATCAACTCCGCAAATTATGGC 57.284 42.857 0.00 0.00 0.00 4.40
1931 7049 6.198966 GCTTTAATCAACTCCGCAAATTATGG 59.801 38.462 0.00 0.00 0.00 2.74
1932 7050 6.198966 GGCTTTAATCAACTCCGCAAATTATG 59.801 38.462 0.00 0.00 0.00 1.90
1933 7051 6.273071 GGCTTTAATCAACTCCGCAAATTAT 58.727 36.000 0.00 0.00 0.00 1.28
1934 7052 5.393678 GGGCTTTAATCAACTCCGCAAATTA 60.394 40.000 0.00 0.00 0.00 1.40
1935 7053 4.494484 GGCTTTAATCAACTCCGCAAATT 58.506 39.130 0.00 0.00 0.00 1.82
1936 7054 3.119137 GGGCTTTAATCAACTCCGCAAAT 60.119 43.478 0.00 0.00 0.00 2.32
1937 7055 2.230266 GGGCTTTAATCAACTCCGCAAA 59.770 45.455 0.00 0.00 0.00 3.68
1938 7056 1.816224 GGGCTTTAATCAACTCCGCAA 59.184 47.619 0.00 0.00 0.00 4.85
1939 7057 1.459450 GGGCTTTAATCAACTCCGCA 58.541 50.000 0.00 0.00 0.00 5.69
1940 7058 0.377203 CGGGCTTTAATCAACTCCGC 59.623 55.000 0.00 0.00 0.00 5.54
1941 7059 0.377203 GCGGGCTTTAATCAACTCCG 59.623 55.000 0.00 0.00 39.07 4.63
1942 7060 1.671328 GAGCGGGCTTTAATCAACTCC 59.329 52.381 0.00 0.00 0.00 3.85
1943 7061 1.671328 GGAGCGGGCTTTAATCAACTC 59.329 52.381 0.00 0.00 0.00 3.01
1944 7062 1.751437 GGAGCGGGCTTTAATCAACT 58.249 50.000 0.00 0.00 0.00 3.16
1945 7063 0.377203 CGGAGCGGGCTTTAATCAAC 59.623 55.000 0.00 0.00 0.00 3.18
1946 7064 2.775351 CGGAGCGGGCTTTAATCAA 58.225 52.632 0.00 0.00 0.00 2.57
1947 7065 4.532490 CGGAGCGGGCTTTAATCA 57.468 55.556 0.00 0.00 0.00 2.57
1976 7094 4.812476 TTCGGCAGTCATCCGCGG 62.812 66.667 22.12 22.12 46.05 6.46
1977 7095 3.554692 GTTCGGCAGTCATCCGCG 61.555 66.667 0.00 0.00 46.05 6.46
1978 7096 3.554692 CGTTCGGCAGTCATCCGC 61.555 66.667 0.00 0.00 46.05 5.54
1980 7098 3.554692 CGCGTTCGGCAGTCATCC 61.555 66.667 0.00 0.00 43.84 3.51
1990 7108 3.849953 GCACTTAGGCCGCGTTCG 61.850 66.667 4.92 0.00 0.00 3.95
1991 7109 0.808453 TATGCACTTAGGCCGCGTTC 60.808 55.000 4.92 0.00 0.00 3.95
1992 7110 0.179056 ATATGCACTTAGGCCGCGTT 60.179 50.000 4.92 0.00 0.00 4.84
1993 7111 0.677288 TATATGCACTTAGGCCGCGT 59.323 50.000 4.92 0.00 0.00 6.01
1994 7112 1.660607 CATATATGCACTTAGGCCGCG 59.339 52.381 0.00 0.00 0.00 6.46
1995 7113 2.972625 TCATATATGCACTTAGGCCGC 58.027 47.619 7.92 0.00 0.00 6.53
1996 7114 6.106003 TGTATTCATATATGCACTTAGGCCG 58.894 40.000 7.92 0.00 0.00 6.13
1997 7115 8.511604 AATGTATTCATATATGCACTTAGGCC 57.488 34.615 7.92 0.00 33.49 5.19
2094 7233 8.630037 TCCTAGAAACTCCAAAAACTCAAATTC 58.370 33.333 0.00 0.00 0.00 2.17
2152 7299 5.065988 ACACATCCAGTAACGAATTAATGCC 59.934 40.000 0.00 0.00 35.50 4.40
2335 7538 2.825205 AGCACTGCATTTGGAAAACAC 58.175 42.857 3.30 0.00 0.00 3.32
2460 7663 1.148273 ACTTGGACGCAAGCCTCAA 59.852 52.632 3.05 0.00 45.62 3.02
2473 7676 1.114722 TGGAAGCCCTTTGCACTTGG 61.115 55.000 0.00 0.00 44.83 3.61
2519 7722 1.377202 CGCCATTGCTGGGTACACT 60.377 57.895 0.00 0.00 43.36 3.55
2551 7772 2.275318 GACTCCGATTGCCAAGAGAAG 58.725 52.381 0.00 0.00 0.00 2.85
2591 7812 7.517614 TGAAGTATGTATTTGCTGGTTTTGA 57.482 32.000 0.00 0.00 0.00 2.69
2616 7837 3.871594 GCTACATTCAGTGCGGTTCTAAT 59.128 43.478 0.00 0.00 0.00 1.73
2724 8131 0.038251 CTGACAGTTGGCGCTACAGA 60.038 55.000 7.64 0.00 0.00 3.41
2866 8354 5.677852 GCGTTGTTTAAACCTCTTCCAGTTT 60.678 40.000 15.59 0.00 39.44 2.66
3090 8764 0.606096 CCGACATACACTGTGGACCA 59.394 55.000 13.09 0.00 38.54 4.02
3253 8927 1.376609 GGTCCATTCATGCCGGTGAC 61.377 60.000 1.90 0.00 0.00 3.67
3283 9146 5.779529 AACAGTGCTGATGAAACAGATTT 57.220 34.783 6.17 0.00 39.94 2.17
3378 9245 0.886043 TGACCTGCACACATCTGCAC 60.886 55.000 0.00 0.00 42.36 4.57
3447 9315 2.564947 CTCAGCCTCCTGAACAGTACTT 59.435 50.000 0.00 0.00 46.84 2.24
3600 9489 9.474313 ACCCATGAATCAAATAAGCTAGTAAAA 57.526 29.630 0.00 0.00 0.00 1.52
3614 9503 5.191727 ACTTCATACCACCCATGAATCAA 57.808 39.130 0.00 0.00 40.60 2.57
3660 9549 8.603304 TCTAAAAGCTACCAGAAAGGAAATAGT 58.397 33.333 0.00 0.00 41.22 2.12
3668 9557 8.233190 CAGACATTTCTAAAAGCTACCAGAAAG 58.767 37.037 16.80 12.72 39.60 2.62
3771 9666 5.111989 CCATATATCGCCTGTAATGTCCAG 58.888 45.833 0.00 0.00 0.00 3.86
3894 9819 2.787994 CTGAACAGCTTCTCCAACCAT 58.212 47.619 0.00 0.00 0.00 3.55
4068 9993 1.938861 CTGACACCGAAACCAACCG 59.061 57.895 0.00 0.00 0.00 4.44
4079 10005 2.289945 ACCAGATTTCTGAGCTGACACC 60.290 50.000 9.15 0.00 46.59 4.16
4241 10179 6.189133 TGTACTTTCCCTAAACTGTGGTTTT 58.811 36.000 0.00 0.00 42.28 2.43
4261 10199 3.927142 GCATGTCACTGTAGTTCCTGTAC 59.073 47.826 0.00 0.00 0.00 2.90
4297 10235 0.040958 CACGCAGTTCACTTTCCTGC 60.041 55.000 0.00 0.00 41.61 4.85
4440 10400 6.092670 CCTCTGAATTTCTTTTACATCTGCGA 59.907 38.462 0.00 0.00 0.00 5.10
4501 10461 7.626452 GCCAGATATGAAAACAGTTTGAGTACC 60.626 40.741 0.00 0.00 0.00 3.34
5035 11100 3.895041 TGTTCCTTGAAAATTGAGGGGTC 59.105 43.478 0.00 0.00 0.00 4.46
5096 11161 4.283467 ACTTTGTGTGTGGAGCTGTAGATA 59.717 41.667 0.00 0.00 0.00 1.98
5106 11171 0.179067 GACCGGACTTTGTGTGTGGA 60.179 55.000 9.46 0.00 0.00 4.02
5107 11172 1.164041 GGACCGGACTTTGTGTGTGG 61.164 60.000 9.46 0.00 0.00 4.17
5115 11180 0.250166 CGTTTGAGGGACCGGACTTT 60.250 55.000 9.46 0.00 0.00 2.66
5118 11183 2.741211 GCGTTTGAGGGACCGGAC 60.741 66.667 9.46 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.