Multiple sequence alignment - TraesCS7A01G175500

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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 TraesCS7A01G175500 chr7A 100.000 2363 0 0 1520 3882 128914835 128912473 0.000000e+00 4364.0
1 TraesCS7A01G175500 chr7A 100.000 1099 0 0 1 1099 128916354 128915256 0.000000e+00 2030.0
2 TraesCS7A01G175500 chr7B 97.401 1462 38 0 1549 3010 91212764 91211303 0.000000e+00 2490.0
3 TraesCS7A01G175500 chr7B 90.730 507 26 9 3216 3709 91210541 91210043 0.000000e+00 656.0
4 TraesCS7A01G175500 chr7B 85.825 388 25 17 2 371 91214561 91214186 6.080000e-103 385.0
5 TraesCS7A01G175500 chr7B 91.398 279 14 5 821 1099 91213467 91213199 1.320000e-99 374.0
6 TraesCS7A01G175500 chr7B 87.500 288 25 5 468 755 91213893 91213617 4.840000e-84 322.0
7 TraesCS7A01G175500 chr7B 97.122 139 4 0 2996 3134 91211290 91211152 6.480000e-58 235.0
8 TraesCS7A01G175500 chr7B 96.491 57 2 0 411 467 91214171 91214115 1.150000e-15 95.3
9 TraesCS7A01G175500 chr7D 97.334 1463 39 0 1548 3010 129799145 129797683 0.000000e+00 2486.0
10 TraesCS7A01G175500 chr7D 91.707 627 46 5 3192 3817 129797133 129796512 0.000000e+00 865.0
11 TraesCS7A01G175500 chr7D 87.055 618 35 21 468 1068 129800226 129799637 0.000000e+00 656.0
12 TraesCS7A01G175500 chr7D 97.778 90 1 1 3001 3089 129797667 129797578 1.870000e-33 154.0
13 TraesCS7A01G175500 chr7D 90.000 110 2 5 2 102 129800473 129800364 2.430000e-27 134.0
14 TraesCS7A01G175500 chr6D 86.503 163 20 2 267 428 454064142 454064303 1.110000e-40 178.0
15 TraesCS7A01G175500 chr3D 85.890 163 21 2 267 428 452487074 452487235 5.160000e-39 172.0
16 TraesCS7A01G175500 chr3A 85.890 163 21 2 267 428 163893467 163893628 5.160000e-39 172.0
17 TraesCS7A01G175500 chr5B 85.000 160 23 1 264 422 589664361 589664520 1.120000e-35 161.0
18 TraesCS7A01G175500 chr4D 84.663 163 23 2 267 428 449386834 449386673 1.120000e-35 161.0
19 TraesCS7A01G175500 chr4A 84.663 163 23 2 267 428 137523221 137523060 1.120000e-35 161.0
20 TraesCS7A01G175500 chr1D 85.000 160 22 2 267 425 466407123 466406965 1.120000e-35 161.0
21 TraesCS7A01G175500 chr1A 84.049 163 24 2 267 428 556086517 556086356 5.190000e-34 156.0
22 TraesCS7A01G175500 chr6B 82.822 163 26 2 267 428 114966763 114966924 1.120000e-30 145.0
23 TraesCS7A01G175500 chr5D 100.000 28 0 0 242 269 488893088 488893061 7.000000e-03 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 TraesCS7A01G175500 chr7A 128912473 128916354 3881 True 3197.000000 4364 100.000000 1 3882 2 chr7A.!!$R1 3881
1 TraesCS7A01G175500 chr7B 91210043 91214561 4518 True 651.042857 2490 92.352429 2 3709 7 chr7B.!!$R1 3707
2 TraesCS7A01G175500 chr7D 129796512 129800473 3961 True 859.000000 2486 92.774800 2 3817 5 chr7D.!!$R1 3815

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
66 75 0.036765 TGCCAAGTAGTAAGCCCACG 60.037 55.0 0.0 0.0 0.00 4.94 F
372 475 0.108945 AACCGCCTAGCAACGACTAC 60.109 55.0 0.0 0.0 0.00 2.73 F
374 477 0.108992 CCGCCTAGCAACGACTACAA 60.109 55.0 0.0 0.0 0.00 2.41 F
624 948 0.182299 CTCCATCTTCCCCTTCTGCC 59.818 60.0 0.0 0.0 0.00 4.85 F
2230 3019 0.400213 AGGCACGGACAATCTTTGGA 59.600 50.0 0.0 0.0 34.12 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2854 0.251341 GACAGAGCCCACCCAACAAT 60.251 55.0 0.0 0.0 0.00 2.71 R
2315 3104 0.874390 TCGAACACCAGCTTTGCATC 59.126 50.0 0.0 0.0 0.00 3.91 R
2412 3201 2.632028 AGATTGATCCCCTCATCGACAG 59.368 50.0 0.0 0.0 32.72 3.51 R
2524 3313 2.553904 CCCAAGCAAGTCCATCACTTCT 60.554 50.0 0.0 0.0 44.14 2.85 R
3848 5206 0.033504 AAGTAGGGAGTGCGTGTGTG 59.966 55.0 0.0 0.0 0.00 3.82 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
66 75 0.036765 TGCCAAGTAGTAAGCCCACG 60.037 55.000 0.00 0.00 0.00 4.94
90 100 4.084013 CCGGGTAATCTAAAATAGCAAGCG 60.084 45.833 0.00 0.00 0.00 4.68
96 106 9.252962 GGTAATCTAAAATAGCAAGCGTAGTTA 57.747 33.333 0.00 0.00 0.00 2.24
131 225 7.200455 ACTGATAACAACTAAAACTGTTTGCC 58.800 34.615 6.53 0.00 37.05 4.52
133 227 7.422399 TGATAACAACTAAAACTGTTTGCCTC 58.578 34.615 6.53 0.00 37.05 4.70
134 228 5.914898 AACAACTAAAACTGTTTGCCTCT 57.085 34.783 6.53 0.00 31.76 3.69
135 229 5.248870 ACAACTAAAACTGTTTGCCTCTG 57.751 39.130 6.53 4.24 0.00 3.35
136 230 4.705023 ACAACTAAAACTGTTTGCCTCTGT 59.295 37.500 6.53 4.81 0.00 3.41
137 231 5.185056 ACAACTAAAACTGTTTGCCTCTGTT 59.815 36.000 6.53 3.91 0.00 3.16
149 243 4.045636 TGCCTCTGTTTTGAAGAAAAGC 57.954 40.909 0.00 0.00 31.57 3.51
150 244 3.045688 GCCTCTGTTTTGAAGAAAAGCG 58.954 45.455 0.00 0.00 31.57 4.68
161 255 5.338614 TGAAGAAAAGCGTGCTTAGTTAC 57.661 39.130 7.64 1.52 34.84 2.50
171 265 3.246226 CGTGCTTAGTTACATCCAGATGC 59.754 47.826 7.56 0.00 42.39 3.91
175 269 6.708054 GTGCTTAGTTACATCCAGATGCTAAT 59.292 38.462 7.56 0.00 42.39 1.73
194 288 5.921408 GCTAATAACCAATTCGATCGAGTCT 59.079 40.000 18.54 4.53 0.00 3.24
212 306 4.018490 AGTCTGTGCATAAAATCATGGCA 58.982 39.130 0.00 0.00 0.00 4.92
213 307 4.647853 AGTCTGTGCATAAAATCATGGCAT 59.352 37.500 0.00 0.00 0.00 4.40
215 309 6.016527 AGTCTGTGCATAAAATCATGGCATAG 60.017 38.462 0.00 7.84 0.00 2.23
216 310 5.829391 TCTGTGCATAAAATCATGGCATAGT 59.171 36.000 0.00 0.00 30.66 2.12
218 312 6.274579 TGTGCATAAAATCATGGCATAGTTG 58.725 36.000 0.00 0.00 0.00 3.16
219 313 5.693104 GTGCATAAAATCATGGCATAGTTGG 59.307 40.000 0.00 0.00 0.00 3.77
222 316 6.810182 GCATAAAATCATGGCATAGTTGGATC 59.190 38.462 0.00 0.00 0.00 3.36
223 317 7.309621 GCATAAAATCATGGCATAGTTGGATCT 60.310 37.037 0.00 0.00 0.00 2.75
224 318 6.401047 AAAATCATGGCATAGTTGGATCTG 57.599 37.500 0.00 0.00 0.00 2.90
230 332 3.323115 TGGCATAGTTGGATCTGCTAGAG 59.677 47.826 0.00 0.00 35.03 2.43
248 350 7.680730 TGCTAGAGGAGAATTAACAAAGTCTT 58.319 34.615 0.00 0.00 0.00 3.01
249 351 8.812972 TGCTAGAGGAGAATTAACAAAGTCTTA 58.187 33.333 0.00 0.00 0.00 2.10
265 367 9.750783 ACAAAGTCTTATCTAACTCCTACACTA 57.249 33.333 0.00 0.00 0.00 2.74
305 407 8.641498 AACTTTCAAACTATTCATCATCTGGT 57.359 30.769 0.00 0.00 0.00 4.00
310 413 5.894298 AACTATTCATCATCTGGTAGGCA 57.106 39.130 0.00 0.00 0.00 4.75
315 418 3.642141 TCATCATCTGGTAGGCAGTACA 58.358 45.455 0.00 0.00 32.62 2.90
318 421 4.471904 TCATCTGGTAGGCAGTACAAAG 57.528 45.455 0.00 0.00 32.62 2.77
321 424 4.267349 TCTGGTAGGCAGTACAAAGAAC 57.733 45.455 0.00 0.00 32.62 3.01
322 425 3.644265 TCTGGTAGGCAGTACAAAGAACA 59.356 43.478 0.00 0.00 32.62 3.18
353 456 8.851541 AGTAAAATTTACATTCAGGTCCGTAA 57.148 30.769 17.00 0.00 0.00 3.18
357 460 2.088950 ACATTCAGGTCCGTAAACCG 57.911 50.000 0.00 0.00 44.49 4.44
371 474 0.604578 AAACCGCCTAGCAACGACTA 59.395 50.000 0.00 0.00 0.00 2.59
372 475 0.108945 AACCGCCTAGCAACGACTAC 60.109 55.000 0.00 0.00 0.00 2.73
373 476 1.246056 ACCGCCTAGCAACGACTACA 61.246 55.000 0.00 0.00 0.00 2.74
374 477 0.108992 CCGCCTAGCAACGACTACAA 60.109 55.000 0.00 0.00 0.00 2.41
375 478 1.670674 CCGCCTAGCAACGACTACAAA 60.671 52.381 0.00 0.00 0.00 2.83
376 479 1.389106 CGCCTAGCAACGACTACAAAC 59.611 52.381 0.00 0.00 0.00 2.93
377 480 2.409975 GCCTAGCAACGACTACAAACA 58.590 47.619 0.00 0.00 0.00 2.83
378 481 2.157085 GCCTAGCAACGACTACAAACAC 59.843 50.000 0.00 0.00 0.00 3.32
379 482 3.650139 CCTAGCAACGACTACAAACACT 58.350 45.455 0.00 0.00 0.00 3.55
380 483 3.428870 CCTAGCAACGACTACAAACACTG 59.571 47.826 0.00 0.00 0.00 3.66
381 484 2.210116 AGCAACGACTACAAACACTGG 58.790 47.619 0.00 0.00 0.00 4.00
382 485 2.159014 AGCAACGACTACAAACACTGGA 60.159 45.455 0.00 0.00 0.00 3.86
383 486 2.221055 GCAACGACTACAAACACTGGAG 59.779 50.000 0.00 0.00 42.47 3.86
384 487 2.150397 ACGACTACAAACACTGGAGC 57.850 50.000 0.00 0.00 40.05 4.70
385 488 1.411246 ACGACTACAAACACTGGAGCA 59.589 47.619 0.00 0.00 40.05 4.26
386 489 2.159014 ACGACTACAAACACTGGAGCAA 60.159 45.455 0.00 0.00 40.05 3.91
387 490 2.476619 CGACTACAAACACTGGAGCAAG 59.523 50.000 0.00 0.00 40.05 4.01
388 491 2.222027 ACTACAAACACTGGAGCAAGC 58.778 47.619 0.00 0.00 40.05 4.01
389 492 1.537202 CTACAAACACTGGAGCAAGCC 59.463 52.381 0.00 0.00 0.00 4.35
390 493 1.283793 CAAACACTGGAGCAAGCCG 59.716 57.895 0.00 0.00 0.00 5.52
391 494 1.148273 AAACACTGGAGCAAGCCGA 59.852 52.632 0.00 0.00 0.00 5.54
392 495 0.465460 AAACACTGGAGCAAGCCGAA 60.465 50.000 0.00 0.00 0.00 4.30
393 496 0.886490 AACACTGGAGCAAGCCGAAG 60.886 55.000 0.00 0.00 0.00 3.79
407 510 2.188469 GAAGGTATTCCGCCGCCA 59.812 61.111 0.00 0.00 39.05 5.69
409 512 1.227853 AAGGTATTCCGCCGCCATC 60.228 57.895 0.00 0.00 39.05 3.51
423 526 2.111878 CATCGCCCCTCCATCACC 59.888 66.667 0.00 0.00 0.00 4.02
467 570 5.295787 TGTTTCTCAACCTGTGTATTGTCAC 59.704 40.000 0.00 0.00 34.19 3.67
469 572 3.389656 TCTCAACCTGTGTATTGTCACCA 59.610 43.478 0.00 0.00 37.51 4.17
470 573 4.133820 CTCAACCTGTGTATTGTCACCAA 58.866 43.478 0.00 0.00 37.51 3.67
475 799 4.892934 ACCTGTGTATTGTCACCAAACATT 59.107 37.500 0.00 0.00 37.51 2.71
488 812 2.095768 CCAAACATTGTCACCTAGCACG 60.096 50.000 0.00 0.00 0.00 5.34
520 844 4.900635 ACCTCCATATTCGCATTTTGTC 57.099 40.909 0.00 0.00 0.00 3.18
551 875 7.112779 TCTGATACCCTCTTCTTTTCAATTCC 58.887 38.462 0.00 0.00 0.00 3.01
610 934 8.041143 TGTATATAGGGTTGTAAAAGCTCCAT 57.959 34.615 0.00 0.00 0.00 3.41
624 948 0.182299 CTCCATCTTCCCCTTCTGCC 59.818 60.000 0.00 0.00 0.00 4.85
625 949 0.549902 TCCATCTTCCCCTTCTGCCA 60.550 55.000 0.00 0.00 0.00 4.92
627 951 0.914644 CATCTTCCCCTTCTGCCAGA 59.085 55.000 0.00 0.00 0.00 3.86
640 964 5.046950 CCTTCTGCCAGAGTAGTAAAAGAGT 60.047 44.000 0.00 0.00 0.00 3.24
656 980 8.807118 AGTAAAAGAGTTGTATGATCAGACTCA 58.193 33.333 20.42 5.54 39.27 3.41
661 985 4.099266 AGTTGTATGATCAGACTCAGCCTC 59.901 45.833 20.42 4.59 0.00 4.70
799 1233 4.722700 GGCAGGGATGTGGTGCGT 62.723 66.667 0.00 0.00 38.13 5.24
800 1234 3.434319 GCAGGGATGTGGTGCGTG 61.434 66.667 0.00 0.00 37.14 5.34
801 1235 3.434319 CAGGGATGTGGTGCGTGC 61.434 66.667 0.00 0.00 0.00 5.34
867 1304 0.668535 GGCGCCTTCAGTTTCAGTTT 59.331 50.000 22.15 0.00 0.00 2.66
987 1424 4.760047 CGACAAGCACCCCCTCCG 62.760 72.222 0.00 0.00 0.00 4.63
1059 1499 3.227276 CTCCCGTGGATCTCCCCG 61.227 72.222 0.00 0.00 34.29 5.73
1546 1986 4.637489 CGCCTCATCGCCTCCTCG 62.637 72.222 0.00 0.00 0.00 4.63
2065 2854 1.933021 ACCTGGTCACCTATTCGACA 58.067 50.000 0.00 0.00 33.66 4.35
2113 2902 4.093556 GGTAAGATGAAGGAAGCGTTTGAG 59.906 45.833 0.00 0.00 0.00 3.02
2171 2960 2.205074 CGGACCAGCTGACATACAATC 58.795 52.381 17.39 0.00 0.00 2.67
2185 2974 4.278419 ACATACAATCTGATCATCGACGGA 59.722 41.667 0.00 0.00 0.00 4.69
2230 3019 0.400213 AGGCACGGACAATCTTTGGA 59.600 50.000 0.00 0.00 34.12 3.53
2284 3073 6.160684 TGCTTTCAACTACGCAACTCTTATA 58.839 36.000 0.00 0.00 0.00 0.98
2315 3104 1.888391 GCAAGAAAGGGGAAGTGGAGG 60.888 57.143 0.00 0.00 0.00 4.30
2412 3201 2.084546 GTGCCTTTGTAGACATGGGAC 58.915 52.381 0.00 9.73 35.47 4.46
2429 3218 1.403814 GACTGTCGATGAGGGGATCA 58.596 55.000 0.00 0.00 43.70 2.92
2524 3313 1.753848 CAAAGATGGGCGGATGGCA 60.754 57.895 0.00 0.00 46.16 4.92
2699 3488 3.568538 CACTATGCAGCCTCAAACAAAC 58.431 45.455 0.00 0.00 0.00 2.93
2701 3490 3.891366 ACTATGCAGCCTCAAACAAACTT 59.109 39.130 0.00 0.00 0.00 2.66
2707 3496 4.209911 GCAGCCTCAAACAAACTTTTGATC 59.790 41.667 8.69 0.00 43.03 2.92
2727 3516 2.741985 TCTGTGCGATGTTGGGCG 60.742 61.111 0.00 0.00 0.00 6.13
2746 3535 2.435586 GTGGCAGATGCGACAGCT 60.436 61.111 14.11 0.00 46.84 4.24
2861 3650 4.121317 GAGATCTGTTGAGCTTCTGGATG 58.879 47.826 0.00 0.00 39.28 3.51
3054 3870 2.957402 ACAAGATGCAGTCCAGGAAA 57.043 45.000 0.00 0.00 0.00 3.13
3098 3914 0.882927 GCAACAGGACCTTGCGTACA 60.883 55.000 2.41 0.00 35.04 2.90
3144 3960 2.620115 CCTGAGCCAATTTGCGATACAT 59.380 45.455 0.00 0.00 36.02 2.29
3145 3961 3.304257 CCTGAGCCAATTTGCGATACATC 60.304 47.826 0.00 0.00 36.02 3.06
3147 3963 2.618241 GAGCCAATTTGCGATACATCCA 59.382 45.455 0.00 0.00 36.02 3.41
3148 3964 2.358898 AGCCAATTTGCGATACATCCAC 59.641 45.455 0.00 0.00 36.02 4.02
3149 3965 2.098934 GCCAATTTGCGATACATCCACA 59.901 45.455 0.00 0.00 0.00 4.17
3151 3967 4.104776 CCAATTTGCGATACATCCACAAC 58.895 43.478 0.00 0.00 0.00 3.32
3153 3969 2.481289 TTGCGATACATCCACAACCA 57.519 45.000 0.00 0.00 0.00 3.67
3154 3970 2.708216 TGCGATACATCCACAACCAT 57.292 45.000 0.00 0.00 0.00 3.55
3155 3971 2.997980 TGCGATACATCCACAACCATT 58.002 42.857 0.00 0.00 0.00 3.16
3156 3972 2.942376 TGCGATACATCCACAACCATTC 59.058 45.455 0.00 0.00 0.00 2.67
3157 3973 2.942376 GCGATACATCCACAACCATTCA 59.058 45.455 0.00 0.00 0.00 2.57
3158 3974 3.565482 GCGATACATCCACAACCATTCAT 59.435 43.478 0.00 0.00 0.00 2.57
3159 3975 4.036734 GCGATACATCCACAACCATTCATT 59.963 41.667 0.00 0.00 0.00 2.57
3160 3976 5.751680 CGATACATCCACAACCATTCATTC 58.248 41.667 0.00 0.00 0.00 2.67
3161 3977 5.528690 CGATACATCCACAACCATTCATTCT 59.471 40.000 0.00 0.00 0.00 2.40
3162 3978 6.512253 CGATACATCCACAACCATTCATTCTG 60.512 42.308 0.00 0.00 0.00 3.02
3163 3979 4.665451 ACATCCACAACCATTCATTCTGA 58.335 39.130 0.00 0.00 0.00 3.27
3164 3980 5.266788 ACATCCACAACCATTCATTCTGAT 58.733 37.500 0.00 0.00 0.00 2.90
3165 3981 5.718130 ACATCCACAACCATTCATTCTGATT 59.282 36.000 0.00 0.00 0.00 2.57
3166 3982 6.211986 ACATCCACAACCATTCATTCTGATTT 59.788 34.615 0.00 0.00 0.00 2.17
3167 3983 6.028146 TCCACAACCATTCATTCTGATTTG 57.972 37.500 0.00 0.00 0.00 2.32
3168 3984 5.047164 TCCACAACCATTCATTCTGATTTGG 60.047 40.000 5.53 5.53 36.59 3.28
3169 3985 5.172934 CACAACCATTCATTCTGATTTGGG 58.827 41.667 9.90 0.00 35.52 4.12
3170 3986 4.223477 ACAACCATTCATTCTGATTTGGGG 59.777 41.667 9.90 0.00 35.52 4.96
3171 3987 4.335735 ACCATTCATTCTGATTTGGGGA 57.664 40.909 9.90 0.00 35.52 4.81
3172 3988 4.284178 ACCATTCATTCTGATTTGGGGAG 58.716 43.478 9.90 0.00 35.52 4.30
3173 3989 3.640029 CCATTCATTCTGATTTGGGGAGG 59.360 47.826 0.00 0.00 30.63 4.30
3174 3990 3.386932 TTCATTCTGATTTGGGGAGGG 57.613 47.619 0.00 0.00 0.00 4.30
3175 3991 1.570501 TCATTCTGATTTGGGGAGGGG 59.429 52.381 0.00 0.00 0.00 4.79
3176 3992 0.936691 ATTCTGATTTGGGGAGGGGG 59.063 55.000 0.00 0.00 0.00 5.40
3190 4006 2.364186 GGGGGCATTTGAGGGTGG 60.364 66.667 0.00 0.00 0.00 4.61
3199 4386 2.351924 TTTGAGGGTGGGCACAGGAC 62.352 60.000 0.00 0.00 0.00 3.85
3220 4564 7.805071 CAGGACATTGACTACTTTGATGTTTTC 59.195 37.037 0.00 0.00 31.59 2.29
3247 4591 6.975772 TGCCCGTAGTAAAAATAATTTGCATC 59.024 34.615 0.00 0.00 0.00 3.91
3263 4607 0.317799 CATCATCTCTGGCCGAGGAG 59.682 60.000 19.88 16.19 40.30 3.69
3266 4610 1.456705 ATCTCTGGCCGAGGAGACC 60.457 63.158 20.18 0.00 40.71 3.85
3308 4652 1.450312 GACTGGTGCTCATTCCCCG 60.450 63.158 0.00 0.00 0.00 5.73
3393 4737 3.501828 TGTTCAGATCACCGAAACCAATG 59.498 43.478 0.00 0.00 0.00 2.82
3423 4767 2.099756 TGCATCCACTGTATCTCACTCG 59.900 50.000 0.00 0.00 0.00 4.18
3424 4768 2.099921 GCATCCACTGTATCTCACTCGT 59.900 50.000 0.00 0.00 0.00 4.18
3425 4769 3.700154 CATCCACTGTATCTCACTCGTG 58.300 50.000 0.00 0.00 32.50 4.35
3426 4770 1.472878 TCCACTGTATCTCACTCGTGC 59.527 52.381 0.00 0.00 31.82 5.34
3429 4773 3.128764 CCACTGTATCTCACTCGTGCTAA 59.871 47.826 0.00 0.00 31.82 3.09
3430 4774 4.380550 CCACTGTATCTCACTCGTGCTAAA 60.381 45.833 0.00 0.00 31.82 1.85
3431 4775 5.344066 CACTGTATCTCACTCGTGCTAAAT 58.656 41.667 0.00 0.00 0.00 1.40
3437 4781 4.883083 TCTCACTCGTGCTAAATGTTCTT 58.117 39.130 0.00 0.00 0.00 2.52
3451 4795 7.854916 GCTAAATGTTCTTGTGCTATCATTCTC 59.145 37.037 0.00 0.00 0.00 2.87
3487 4831 9.234827 CAGCCAAAATGTTCTCATCCATATATA 57.765 33.333 0.00 0.00 32.56 0.86
3586 4943 8.749354 GTGTAAGATGGATAAATTTTCCTTGGT 58.251 33.333 15.75 6.69 34.17 3.67
3597 4954 2.380064 TTCCTTGGTTGGCTTCATGT 57.620 45.000 0.00 0.00 0.00 3.21
3599 4956 3.517296 TCCTTGGTTGGCTTCATGTTA 57.483 42.857 0.00 0.00 0.00 2.41
3600 4957 3.153919 TCCTTGGTTGGCTTCATGTTAC 58.846 45.455 0.00 0.00 0.00 2.50
3618 4975 9.087424 TCATGTTACTATTCATTTCAGAACTCG 57.913 33.333 0.00 0.00 0.00 4.18
3629 4986 5.453567 TTTCAGAACTCGAACTCTCATGA 57.546 39.130 0.00 0.00 0.00 3.07
3661 5018 5.796424 AGCCAAATGTTCTCTTTTGACAT 57.204 34.783 7.73 0.00 39.49 3.06
3668 5025 9.734620 CAAATGTTCTCTTTTGACATCACTTTA 57.265 29.630 0.00 0.00 39.49 1.85
3672 5029 9.734620 TGTTCTCTTTTGACATCACTTTATTTG 57.265 29.630 0.00 0.00 0.00 2.32
3709 5066 6.096141 TCAAGCCAAATGTTCAGTTGAAACTA 59.904 34.615 13.33 0.00 37.08 2.24
3713 5070 6.417930 GCCAAATGTTCAGTTGAAACTAGAAC 59.582 38.462 20.04 20.04 41.72 3.01
3730 5087 2.986728 AGAACAGAGGGCCTTTTTAGGA 59.013 45.455 7.89 0.00 0.00 2.94
3738 5095 5.492887 AGAGGGCCTTTTTAGGAGTAGAAAT 59.507 40.000 7.89 0.00 0.00 2.17
3746 5103 9.898152 CCTTTTTAGGAGTAGAAATGAGAGATT 57.102 33.333 0.00 0.00 0.00 2.40
3753 5110 6.533367 GGAGTAGAAATGAGAGATTGACACAC 59.467 42.308 0.00 0.00 0.00 3.82
3755 5112 4.248859 AGAAATGAGAGATTGACACACCG 58.751 43.478 0.00 0.00 0.00 4.94
3762 5119 1.204941 AGATTGACACACCGGCTACTC 59.795 52.381 0.00 0.00 0.00 2.59
3763 5120 0.249398 ATTGACACACCGGCTACTCC 59.751 55.000 0.00 0.00 0.00 3.85
3775 5132 1.137282 GGCTACTCCTGGACTAACAGC 59.863 57.143 0.00 0.00 37.16 4.40
3789 5147 3.525199 ACTAACAGCCCCTCATTCTCATT 59.475 43.478 0.00 0.00 0.00 2.57
3795 5153 3.073650 AGCCCCTCATTCTCATTACATCC 59.926 47.826 0.00 0.00 0.00 3.51
3797 5155 4.805609 GCCCCTCATTCTCATTACATCCTC 60.806 50.000 0.00 0.00 0.00 3.71
3800 5158 5.303971 CCTCATTCTCATTACATCCTCCAC 58.696 45.833 0.00 0.00 0.00 4.02
3805 5163 8.717717 TCATTCTCATTACATCCTCCACTAATT 58.282 33.333 0.00 0.00 0.00 1.40
3807 5165 8.737168 TTCTCATTACATCCTCCACTAATTTG 57.263 34.615 0.00 0.00 0.00 2.32
3817 5175 4.759693 CCTCCACTAATTTGTAGCAACACA 59.240 41.667 0.00 0.00 34.61 3.72
3818 5176 5.334879 CCTCCACTAATTTGTAGCAACACAC 60.335 44.000 0.00 0.00 34.61 3.82
3819 5177 4.212425 TCCACTAATTTGTAGCAACACACG 59.788 41.667 0.00 0.00 34.61 4.49
3820 5178 3.906008 CACTAATTTGTAGCAACACACGC 59.094 43.478 0.00 0.00 34.61 5.34
3821 5179 2.415697 AATTTGTAGCAACACACGCC 57.584 45.000 0.00 0.00 34.61 5.68
3822 5180 1.313772 ATTTGTAGCAACACACGCCA 58.686 45.000 0.00 0.00 34.61 5.69
3823 5181 0.378962 TTTGTAGCAACACACGCCAC 59.621 50.000 0.00 0.00 34.61 5.01
3824 5182 0.744771 TTGTAGCAACACACGCCACA 60.745 50.000 0.00 0.00 34.61 4.17
3825 5183 1.157257 TGTAGCAACACACGCCACAG 61.157 55.000 0.00 0.00 0.00 3.66
3826 5184 1.145156 TAGCAACACACGCCACAGT 59.855 52.632 0.00 0.00 0.00 3.55
3827 5185 0.462937 TAGCAACACACGCCACAGTT 60.463 50.000 0.00 0.00 0.00 3.16
3828 5186 1.298339 GCAACACACGCCACAGTTC 60.298 57.895 0.00 0.00 0.00 3.01
3829 5187 1.987704 GCAACACACGCCACAGTTCA 61.988 55.000 0.00 0.00 0.00 3.18
3830 5188 0.248054 CAACACACGCCACAGTTCAC 60.248 55.000 0.00 0.00 0.00 3.18
3831 5189 0.675208 AACACACGCCACAGTTCACA 60.675 50.000 0.00 0.00 0.00 3.58
3832 5190 1.351707 CACACGCCACAGTTCACAC 59.648 57.895 0.00 0.00 0.00 3.82
3833 5191 1.078778 ACACGCCACAGTTCACACA 60.079 52.632 0.00 0.00 0.00 3.72
3834 5192 1.351707 CACGCCACAGTTCACACAC 59.648 57.895 0.00 0.00 0.00 3.82
3835 5193 1.078778 ACGCCACAGTTCACACACA 60.079 52.632 0.00 0.00 0.00 3.72
3836 5194 1.351707 CGCCACAGTTCACACACAC 59.648 57.895 0.00 0.00 0.00 3.82
3837 5195 1.365368 CGCCACAGTTCACACACACA 61.365 55.000 0.00 0.00 0.00 3.72
3838 5196 0.098728 GCCACAGTTCACACACACAC 59.901 55.000 0.00 0.00 0.00 3.82
3839 5197 1.447945 CCACAGTTCACACACACACA 58.552 50.000 0.00 0.00 0.00 3.72
3840 5198 1.130373 CCACAGTTCACACACACACAC 59.870 52.381 0.00 0.00 0.00 3.82
3841 5199 1.803555 CACAGTTCACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
3842 5200 1.804151 ACAGTTCACACACACACACAC 59.196 47.619 0.00 0.00 0.00 3.82
3843 5201 1.803555 CAGTTCACACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
3844 5202 1.804151 AGTTCACACACACACACACAC 59.196 47.619 0.00 0.00 0.00 3.82
3845 5203 1.533299 GTTCACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
3846 5204 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
3847 5205 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3848 5206 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3849 5207 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3850 5208 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3851 5209 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3852 5210 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3853 5211 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3854 5212 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3855 5213 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
3856 5214 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
3857 5215 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
3858 5216 1.225991 CACACACACACACACGCAC 60.226 57.895 0.00 0.00 0.00 5.34
3859 5217 1.375396 ACACACACACACACGCACT 60.375 52.632 0.00 0.00 0.00 4.40
3860 5218 1.348250 CACACACACACACGCACTC 59.652 57.895 0.00 0.00 0.00 3.51
3861 5219 1.813753 ACACACACACACGCACTCC 60.814 57.895 0.00 0.00 0.00 3.85
3862 5220 2.203015 ACACACACACGCACTCCC 60.203 61.111 0.00 0.00 0.00 4.30
3863 5221 2.108976 CACACACACGCACTCCCT 59.891 61.111 0.00 0.00 0.00 4.20
3864 5222 1.365999 CACACACACGCACTCCCTA 59.634 57.895 0.00 0.00 0.00 3.53
3865 5223 0.944311 CACACACACGCACTCCCTAC 60.944 60.000 0.00 0.00 0.00 3.18
3866 5224 1.113517 ACACACACGCACTCCCTACT 61.114 55.000 0.00 0.00 0.00 2.57
3867 5225 0.033504 CACACACGCACTCCCTACTT 59.966 55.000 0.00 0.00 0.00 2.24
3868 5226 0.756903 ACACACGCACTCCCTACTTT 59.243 50.000 0.00 0.00 0.00 2.66
3869 5227 1.965643 ACACACGCACTCCCTACTTTA 59.034 47.619 0.00 0.00 0.00 1.85
3870 5228 2.565834 ACACACGCACTCCCTACTTTAT 59.434 45.455 0.00 0.00 0.00 1.40
3871 5229 3.007614 ACACACGCACTCCCTACTTTATT 59.992 43.478 0.00 0.00 0.00 1.40
3872 5230 3.617263 CACACGCACTCCCTACTTTATTC 59.383 47.826 0.00 0.00 0.00 1.75
3873 5231 3.259876 ACACGCACTCCCTACTTTATTCA 59.740 43.478 0.00 0.00 0.00 2.57
3874 5232 4.250464 CACGCACTCCCTACTTTATTCAA 58.750 43.478 0.00 0.00 0.00 2.69
3875 5233 4.330074 CACGCACTCCCTACTTTATTCAAG 59.670 45.833 0.00 0.00 38.64 3.02
3876 5234 3.309954 CGCACTCCCTACTTTATTCAAGC 59.690 47.826 0.00 0.00 35.65 4.01
3877 5235 4.261801 GCACTCCCTACTTTATTCAAGCA 58.738 43.478 0.00 0.00 35.65 3.91
3878 5236 4.095036 GCACTCCCTACTTTATTCAAGCAC 59.905 45.833 0.00 0.00 35.65 4.40
3879 5237 4.636206 CACTCCCTACTTTATTCAAGCACC 59.364 45.833 0.00 0.00 35.65 5.01
3880 5238 3.869065 TCCCTACTTTATTCAAGCACCG 58.131 45.455 0.00 0.00 35.65 4.94
3881 5239 3.516300 TCCCTACTTTATTCAAGCACCGA 59.484 43.478 0.00 0.00 35.65 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.292186 ACCATGCAAAGCTCTTAGAGAA 57.708 40.909 14.14 0.00 0.00 2.87
66 75 4.320275 GCTTGCTATTTTAGATTACCCGGC 60.320 45.833 0.00 0.00 0.00 6.13
125 219 5.220472 GCTTTTCTTCAAAACAGAGGCAAAC 60.220 40.000 0.00 0.00 0.00 2.93
128 222 3.489059 CGCTTTTCTTCAAAACAGAGGCA 60.489 43.478 0.00 0.00 0.00 4.75
129 223 3.045688 CGCTTTTCTTCAAAACAGAGGC 58.954 45.455 0.00 0.00 0.00 4.70
131 225 3.483558 GCACGCTTTTCTTCAAAACAGAG 59.516 43.478 0.00 0.00 0.00 3.35
133 227 3.438360 AGCACGCTTTTCTTCAAAACAG 58.562 40.909 0.00 0.00 0.00 3.16
134 228 3.502191 AGCACGCTTTTCTTCAAAACA 57.498 38.095 0.00 0.00 0.00 2.83
135 229 5.034797 ACTAAGCACGCTTTTCTTCAAAAC 58.965 37.500 9.96 0.00 37.47 2.43
136 230 5.243426 ACTAAGCACGCTTTTCTTCAAAA 57.757 34.783 9.96 0.00 37.47 2.44
137 231 4.893424 ACTAAGCACGCTTTTCTTCAAA 57.107 36.364 9.96 0.00 37.47 2.69
149 243 3.246226 GCATCTGGATGTAACTAAGCACG 59.754 47.826 11.52 0.00 40.80 5.34
150 244 4.446371 AGCATCTGGATGTAACTAAGCAC 58.554 43.478 11.52 0.00 40.80 4.40
161 255 6.427853 TCGAATTGGTTATTAGCATCTGGATG 59.572 38.462 6.24 6.24 41.60 3.51
171 265 6.918569 ACAGACTCGATCGAATTGGTTATTAG 59.081 38.462 19.92 5.19 0.00 1.73
175 269 4.421058 CACAGACTCGATCGAATTGGTTA 58.579 43.478 19.92 0.00 0.00 2.85
194 288 6.274579 CAACTATGCCATGATTTTATGCACA 58.725 36.000 0.00 0.00 0.00 4.57
212 306 5.332106 TCTCCTCTAGCAGATCCAACTAT 57.668 43.478 0.00 0.00 0.00 2.12
213 307 4.797912 TCTCCTCTAGCAGATCCAACTA 57.202 45.455 0.00 0.00 0.00 2.24
215 309 4.953940 ATTCTCCTCTAGCAGATCCAAC 57.046 45.455 0.00 0.00 0.00 3.77
216 310 6.384015 TGTTAATTCTCCTCTAGCAGATCCAA 59.616 38.462 0.00 0.00 0.00 3.53
218 312 6.412362 TGTTAATTCTCCTCTAGCAGATCC 57.588 41.667 0.00 0.00 0.00 3.36
219 313 7.984617 ACTTTGTTAATTCTCCTCTAGCAGATC 59.015 37.037 0.00 0.00 0.00 2.75
222 316 7.327214 AGACTTTGTTAATTCTCCTCTAGCAG 58.673 38.462 0.00 0.00 0.00 4.24
223 317 7.246171 AGACTTTGTTAATTCTCCTCTAGCA 57.754 36.000 0.00 0.00 0.00 3.49
224 318 9.825109 ATAAGACTTTGTTAATTCTCCTCTAGC 57.175 33.333 0.00 0.00 0.00 3.42
268 370 4.998033 AGTTTGAAAGTTTTTCCCGCAAAA 59.002 33.333 0.00 0.00 31.73 2.44
269 371 4.570930 AGTTTGAAAGTTTTTCCCGCAAA 58.429 34.783 0.00 0.00 0.00 3.68
270 372 4.195225 AGTTTGAAAGTTTTTCCCGCAA 57.805 36.364 0.00 0.00 0.00 4.85
271 373 3.878160 AGTTTGAAAGTTTTTCCCGCA 57.122 38.095 0.00 0.00 0.00 5.69
272 374 5.980715 TGAATAGTTTGAAAGTTTTTCCCGC 59.019 36.000 0.00 0.00 0.00 6.13
273 375 7.865385 TGATGAATAGTTTGAAAGTTTTTCCCG 59.135 33.333 0.00 0.00 0.00 5.14
305 407 6.267014 ACTTCTAGTGTTCTTTGTACTGCCTA 59.733 38.462 0.00 0.00 0.00 3.93
335 438 3.995705 CGGTTTACGGACCTGAATGTAAA 59.004 43.478 3.85 0.00 37.56 2.01
353 456 0.108945 GTAGTCGTTGCTAGGCGGTT 60.109 55.000 0.00 0.00 0.00 4.44
357 460 2.157085 GTGTTTGTAGTCGTTGCTAGGC 59.843 50.000 0.00 0.00 0.00 3.93
371 474 1.447317 CGGCTTGCTCCAGTGTTTGT 61.447 55.000 0.00 0.00 0.00 2.83
372 475 1.165907 TCGGCTTGCTCCAGTGTTTG 61.166 55.000 0.00 0.00 0.00 2.93
373 476 0.465460 TTCGGCTTGCTCCAGTGTTT 60.465 50.000 0.00 0.00 0.00 2.83
374 477 0.886490 CTTCGGCTTGCTCCAGTGTT 60.886 55.000 0.00 0.00 0.00 3.32
375 478 1.302033 CTTCGGCTTGCTCCAGTGT 60.302 57.895 0.00 0.00 0.00 3.55
376 479 2.037136 CCTTCGGCTTGCTCCAGTG 61.037 63.158 0.00 0.00 0.00 3.66
377 480 1.192146 TACCTTCGGCTTGCTCCAGT 61.192 55.000 0.00 0.00 0.00 4.00
378 481 0.179000 ATACCTTCGGCTTGCTCCAG 59.821 55.000 0.00 0.00 0.00 3.86
379 482 0.618458 AATACCTTCGGCTTGCTCCA 59.382 50.000 0.00 0.00 0.00 3.86
380 483 1.300481 GAATACCTTCGGCTTGCTCC 58.700 55.000 0.00 0.00 0.00 4.70
381 484 1.300481 GGAATACCTTCGGCTTGCTC 58.700 55.000 0.00 0.00 31.75 4.26
382 485 0.462047 CGGAATACCTTCGGCTTGCT 60.462 55.000 0.00 0.00 31.75 3.91
383 486 2.014594 CGGAATACCTTCGGCTTGC 58.985 57.895 0.00 0.00 31.75 4.01
388 491 2.965462 GCGGCGGAATACCTTCGG 60.965 66.667 9.78 0.00 35.44 4.30
389 492 2.965462 GGCGGCGGAATACCTTCG 60.965 66.667 9.78 0.00 31.75 3.79
390 493 1.227853 ATGGCGGCGGAATACCTTC 60.228 57.895 9.78 0.00 0.00 3.46
391 494 1.227853 GATGGCGGCGGAATACCTT 60.228 57.895 9.78 0.00 0.00 3.50
392 495 2.426023 GATGGCGGCGGAATACCT 59.574 61.111 9.78 0.00 0.00 3.08
393 496 3.041940 CGATGGCGGCGGAATACC 61.042 66.667 9.78 0.35 0.00 2.73
394 497 3.712881 GCGATGGCGGCGGAATAC 61.713 66.667 9.78 0.00 38.16 1.89
405 508 2.111878 GTGATGGAGGGGCGATGG 59.888 66.667 0.00 0.00 0.00 3.51
407 510 3.550431 CGGTGATGGAGGGGCGAT 61.550 66.667 0.00 0.00 0.00 4.58
419 522 3.992641 TCTCCTGCCCTCCGGTGA 61.993 66.667 4.76 0.00 0.00 4.02
423 526 0.757188 AGTATGTCTCCTGCCCTCCG 60.757 60.000 0.00 0.00 0.00 4.63
467 570 2.095768 CGTGCTAGGTGACAATGTTTGG 60.096 50.000 0.00 0.00 34.12 3.28
469 572 1.535462 GCGTGCTAGGTGACAATGTTT 59.465 47.619 0.00 0.00 0.00 2.83
470 573 1.156736 GCGTGCTAGGTGACAATGTT 58.843 50.000 0.00 0.00 0.00 2.71
475 799 2.049526 CGTGCGTGCTAGGTGACA 60.050 61.111 0.00 0.00 0.00 3.58
520 844 3.226777 AGAAGAGGGTATCAGATGACCG 58.773 50.000 0.00 0.00 36.51 4.79
551 875 3.525268 AACAGTTTGGTTGCTGAAAGG 57.475 42.857 0.00 0.00 36.62 3.11
592 916 4.336280 GAAGATGGAGCTTTTACAACCCT 58.664 43.478 0.00 0.00 0.00 4.34
595 919 3.444034 GGGGAAGATGGAGCTTTTACAAC 59.556 47.826 0.00 0.00 0.00 3.32
596 920 3.333680 AGGGGAAGATGGAGCTTTTACAA 59.666 43.478 0.00 0.00 0.00 2.41
597 921 2.919602 AGGGGAAGATGGAGCTTTTACA 59.080 45.455 0.00 0.00 0.00 2.41
610 934 0.178891 ACTCTGGCAGAAGGGGAAGA 60.179 55.000 19.29 0.00 0.00 2.87
640 964 4.026052 TGAGGCTGAGTCTGATCATACAA 58.974 43.478 13.15 1.14 0.00 2.41
656 980 4.953940 TTTGGTAATTTTGCTTGAGGCT 57.046 36.364 0.00 0.00 42.39 4.58
756 1176 3.782244 GTCGCAGGTCGCAGCTTG 61.782 66.667 0.00 0.00 42.60 4.01
784 1218 3.434319 GCACGCACCACATCCCTG 61.434 66.667 0.00 0.00 0.00 4.45
853 1290 1.334869 AGGCGCAAACTGAAACTGAAG 59.665 47.619 10.83 0.00 0.00 3.02
1846 2635 2.752238 CAGCGGGAGGAGACGAGT 60.752 66.667 0.00 0.00 0.00 4.18
2065 2854 0.251341 GACAGAGCCCACCCAACAAT 60.251 55.000 0.00 0.00 0.00 2.71
2113 2902 1.819288 TCGATCATCCCCTCGAATAGC 59.181 52.381 0.00 0.00 40.64 2.97
2171 2960 2.057316 GCAGAATCCGTCGATGATCAG 58.943 52.381 6.11 0.16 0.00 2.90
2194 2983 1.920325 CTTCTCCACCTGCCCCAGA 60.920 63.158 0.00 0.00 32.44 3.86
2230 3019 6.541641 GCTCACACTCATTCTTCCTCATAAAT 59.458 38.462 0.00 0.00 0.00 1.40
2272 3061 5.727791 GCAGTGTCCATTTATAAGAGTTGCG 60.728 44.000 0.00 0.00 0.00 4.85
2284 3073 2.629617 CCCTTTCTTGCAGTGTCCATTT 59.370 45.455 0.00 0.00 0.00 2.32
2315 3104 0.874390 TCGAACACCAGCTTTGCATC 59.126 50.000 0.00 0.00 0.00 3.91
2412 3201 2.632028 AGATTGATCCCCTCATCGACAG 59.368 50.000 0.00 0.00 32.72 3.51
2429 3218 4.564799 TCCCTCATCTCCATCAGAAGATT 58.435 43.478 0.00 0.00 33.62 2.40
2524 3313 2.553904 CCCAAGCAAGTCCATCACTTCT 60.554 50.000 0.00 0.00 44.14 2.85
2699 3488 1.428448 TCGCACAGACCGATCAAAAG 58.572 50.000 0.00 0.00 0.00 2.27
2701 3490 1.337728 ACATCGCACAGACCGATCAAA 60.338 47.619 0.00 0.00 42.93 2.69
2707 3496 2.390599 CCCAACATCGCACAGACCG 61.391 63.158 0.00 0.00 0.00 4.79
2727 3516 2.459442 GCTGTCGCATCTGCCACTC 61.459 63.158 1.77 0.00 37.91 3.51
2746 3535 2.156102 TGGCCAATCCATACAATGCA 57.844 45.000 0.61 0.00 40.72 3.96
2861 3650 4.186926 GTTCACCCTCCCGTAATTAAGAC 58.813 47.826 0.00 0.00 0.00 3.01
3054 3870 6.149474 CAGATCAAACGACCCTTTTGAGTTAT 59.851 38.462 0.00 0.00 44.17 1.89
3098 3914 2.884639 CCGTCCTTGTCCAAGTTTGATT 59.115 45.455 6.31 0.00 36.72 2.57
3156 3972 1.412074 CCCCCTCCCCAAATCAGAATG 60.412 57.143 0.00 0.00 37.54 2.67
3157 3973 0.936691 CCCCCTCCCCAAATCAGAAT 59.063 55.000 0.00 0.00 0.00 2.40
3158 3974 2.408920 CCCCCTCCCCAAATCAGAA 58.591 57.895 0.00 0.00 0.00 3.02
3159 3975 4.186911 CCCCCTCCCCAAATCAGA 57.813 61.111 0.00 0.00 0.00 3.27
3173 3989 2.364186 CCACCCTCAAATGCCCCC 60.364 66.667 0.00 0.00 0.00 5.40
3174 3990 2.364186 CCCACCCTCAAATGCCCC 60.364 66.667 0.00 0.00 0.00 5.80
3175 3991 3.076916 GCCCACCCTCAAATGCCC 61.077 66.667 0.00 0.00 0.00 5.36
3176 3992 2.283821 TGCCCACCCTCAAATGCC 60.284 61.111 0.00 0.00 0.00 4.40
3177 3993 1.880819 CTGTGCCCACCCTCAAATGC 61.881 60.000 0.00 0.00 0.00 3.56
3178 3994 1.252904 CCTGTGCCCACCCTCAAATG 61.253 60.000 0.00 0.00 0.00 2.32
3179 3995 1.077265 CCTGTGCCCACCCTCAAAT 59.923 57.895 0.00 0.00 0.00 2.32
3180 3996 2.081787 TCCTGTGCCCACCCTCAAA 61.082 57.895 0.00 0.00 0.00 2.69
3181 3997 2.449518 TCCTGTGCCCACCCTCAA 60.450 61.111 0.00 0.00 0.00 3.02
3182 3998 3.249189 GTCCTGTGCCCACCCTCA 61.249 66.667 0.00 0.00 0.00 3.86
3183 3999 2.142292 AATGTCCTGTGCCCACCCTC 62.142 60.000 0.00 0.00 0.00 4.30
3184 4000 2.162906 AATGTCCTGTGCCCACCCT 61.163 57.895 0.00 0.00 0.00 4.34
3185 4001 1.978617 CAATGTCCTGTGCCCACCC 60.979 63.158 0.00 0.00 0.00 4.61
3186 4002 1.074775 TCAATGTCCTGTGCCCACC 59.925 57.895 0.00 0.00 0.00 4.61
3187 4003 0.250901 AGTCAATGTCCTGTGCCCAC 60.251 55.000 0.00 0.00 0.00 4.61
3188 4004 1.003118 GTAGTCAATGTCCTGTGCCCA 59.997 52.381 0.00 0.00 0.00 5.36
3189 4005 1.279271 AGTAGTCAATGTCCTGTGCCC 59.721 52.381 0.00 0.00 0.00 5.36
3190 4006 2.770164 AGTAGTCAATGTCCTGTGCC 57.230 50.000 0.00 0.00 0.00 5.01
3199 4386 6.086765 GCACGAAAACATCAAAGTAGTCAATG 59.913 38.462 0.00 0.00 0.00 2.82
3263 4607 3.244976 CATGGTTTTTGCATCTTCGGTC 58.755 45.455 0.00 0.00 0.00 4.79
3266 4610 2.988493 CCACATGGTTTTTGCATCTTCG 59.012 45.455 0.00 0.00 0.00 3.79
3334 4678 7.574592 GCAAGTCAGCTAAATGTCTTCAAGAAT 60.575 37.037 0.00 0.00 0.00 2.40
3393 4737 7.227314 TGAGATACAGTGGATGCAATTCATAAC 59.773 37.037 0.00 0.00 31.90 1.89
3423 4767 6.182039 TGATAGCACAAGAACATTTAGCAC 57.818 37.500 0.00 0.00 0.00 4.40
3424 4768 7.337689 AGAATGATAGCACAAGAACATTTAGCA 59.662 33.333 0.00 0.00 0.00 3.49
3425 4769 7.701445 AGAATGATAGCACAAGAACATTTAGC 58.299 34.615 0.00 0.00 0.00 3.09
3426 4770 9.107177 AGAGAATGATAGCACAAGAACATTTAG 57.893 33.333 0.00 0.00 0.00 1.85
3429 4773 6.183360 GCAGAGAATGATAGCACAAGAACATT 60.183 38.462 0.00 0.00 0.00 2.71
3430 4774 5.296283 GCAGAGAATGATAGCACAAGAACAT 59.704 40.000 0.00 0.00 0.00 2.71
3431 4775 4.633126 GCAGAGAATGATAGCACAAGAACA 59.367 41.667 0.00 0.00 0.00 3.18
3451 4795 2.295349 ACATTTTGGCTGAAGAGTGCAG 59.705 45.455 0.00 0.00 36.47 4.41
3574 4931 4.102996 ACATGAAGCCAACCAAGGAAAATT 59.897 37.500 0.00 0.00 0.00 1.82
3586 4943 8.347004 TGAAATGAATAGTAACATGAAGCCAA 57.653 30.769 0.00 0.00 0.00 4.52
3597 4954 9.355215 GAGTTCGAGTTCTGAAATGAATAGTAA 57.645 33.333 0.00 0.00 0.00 2.24
3599 4956 7.607250 AGAGTTCGAGTTCTGAAATGAATAGT 58.393 34.615 0.00 0.00 0.00 2.12
3600 4957 7.757173 TGAGAGTTCGAGTTCTGAAATGAATAG 59.243 37.037 5.60 0.00 0.00 1.73
3618 4975 4.379290 GCTTGAAGCCTTTCATGAGAGTTC 60.379 45.833 5.74 10.16 42.60 3.01
3661 5018 7.990917 TGAAGTTGCTGTAACAAATAAAGTGA 58.009 30.769 11.16 0.00 41.88 3.41
3668 5025 4.099266 TGGCTTGAAGTTGCTGTAACAAAT 59.901 37.500 11.16 0.00 41.88 2.32
3672 5029 3.708563 TTGGCTTGAAGTTGCTGTAAC 57.291 42.857 0.00 0.00 39.65 2.50
3709 5066 2.986728 TCCTAAAAAGGCCCTCTGTTCT 59.013 45.455 0.00 0.00 0.00 3.01
3713 5070 3.775316 TCTACTCCTAAAAAGGCCCTCTG 59.225 47.826 0.00 0.00 0.00 3.35
3730 5087 6.402222 GGTGTGTCAATCTCTCATTTCTACT 58.598 40.000 0.00 0.00 0.00 2.57
3738 5095 0.037326 GCCGGTGTGTCAATCTCTCA 60.037 55.000 1.90 0.00 0.00 3.27
3746 5103 1.228769 AGGAGTAGCCGGTGTGTCA 60.229 57.895 1.90 0.00 43.43 3.58
3753 5110 0.745468 GTTAGTCCAGGAGTAGCCGG 59.255 60.000 6.87 0.00 43.43 6.13
3755 5112 1.137282 GCTGTTAGTCCAGGAGTAGCC 59.863 57.143 14.07 6.05 32.92 3.93
3762 5119 0.909610 TGAGGGGCTGTTAGTCCAGG 60.910 60.000 1.50 0.00 43.30 4.45
3763 5120 1.207791 ATGAGGGGCTGTTAGTCCAG 58.792 55.000 1.50 0.00 43.30 3.86
3775 5132 4.263243 GGAGGATGTAATGAGAATGAGGGG 60.263 50.000 0.00 0.00 0.00 4.79
3789 5147 6.553953 TGCTACAAATTAGTGGAGGATGTA 57.446 37.500 0.00 0.00 29.23 2.29
3795 5153 5.614668 CGTGTGTTGCTACAAATTAGTGGAG 60.615 44.000 1.60 0.00 35.69 3.86
3797 5155 4.463209 CGTGTGTTGCTACAAATTAGTGG 58.537 43.478 1.60 0.00 35.69 4.00
3800 5158 3.058570 TGGCGTGTGTTGCTACAAATTAG 60.059 43.478 1.60 0.00 35.69 1.73
3805 5163 2.018544 GTGGCGTGTGTTGCTACAA 58.981 52.632 1.60 0.00 42.63 2.41
3807 5165 1.157870 ACTGTGGCGTGTGTTGCTAC 61.158 55.000 0.00 0.00 43.29 3.58
3817 5175 1.078778 TGTGTGTGAACTGTGGCGT 60.079 52.632 0.00 0.00 0.00 5.68
3818 5176 1.351707 GTGTGTGTGAACTGTGGCG 59.648 57.895 0.00 0.00 0.00 5.69
3819 5177 0.098728 GTGTGTGTGTGAACTGTGGC 59.901 55.000 0.00 0.00 0.00 5.01
3820 5178 1.130373 GTGTGTGTGTGTGAACTGTGG 59.870 52.381 0.00 0.00 0.00 4.17
3821 5179 1.803555 TGTGTGTGTGTGTGAACTGTG 59.196 47.619 0.00 0.00 0.00 3.66
3822 5180 1.804151 GTGTGTGTGTGTGTGAACTGT 59.196 47.619 0.00 0.00 0.00 3.55
3823 5181 1.803555 TGTGTGTGTGTGTGTGAACTG 59.196 47.619 0.00 0.00 0.00 3.16
3824 5182 1.804151 GTGTGTGTGTGTGTGTGAACT 59.196 47.619 0.00 0.00 0.00 3.01
3825 5183 1.533299 TGTGTGTGTGTGTGTGTGAAC 59.467 47.619 0.00 0.00 0.00 3.18
3826 5184 1.533299 GTGTGTGTGTGTGTGTGTGAA 59.467 47.619 0.00 0.00 0.00 3.18
3827 5185 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
3828 5186 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3829 5187 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3830 5188 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3831 5189 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3832 5190 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3833 5191 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3834 5192 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3835 5193 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3836 5194 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
3837 5195 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
3838 5196 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
3839 5197 1.669437 TGCGTGTGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
3840 5198 1.225991 GTGCGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
3841 5199 1.358725 GAGTGCGTGTGTGTGTGTGT 61.359 55.000 0.00 0.00 0.00 3.72
3842 5200 1.348250 GAGTGCGTGTGTGTGTGTG 59.652 57.895 0.00 0.00 0.00 3.82
3843 5201 1.813753 GGAGTGCGTGTGTGTGTGT 60.814 57.895 0.00 0.00 0.00 3.72
3844 5202 2.534019 GGGAGTGCGTGTGTGTGTG 61.534 63.158 0.00 0.00 0.00 3.82
3845 5203 1.396607 TAGGGAGTGCGTGTGTGTGT 61.397 55.000 0.00 0.00 0.00 3.72
3846 5204 0.944311 GTAGGGAGTGCGTGTGTGTG 60.944 60.000 0.00 0.00 0.00 3.82
3847 5205 1.113517 AGTAGGGAGTGCGTGTGTGT 61.114 55.000 0.00 0.00 0.00 3.72
3848 5206 0.033504 AAGTAGGGAGTGCGTGTGTG 59.966 55.000 0.00 0.00 0.00 3.82
3849 5207 0.756903 AAAGTAGGGAGTGCGTGTGT 59.243 50.000 0.00 0.00 0.00 3.72
3850 5208 2.736144 TAAAGTAGGGAGTGCGTGTG 57.264 50.000 0.00 0.00 0.00 3.82
3851 5209 3.259876 TGAATAAAGTAGGGAGTGCGTGT 59.740 43.478 0.00 0.00 0.00 4.49
3852 5210 3.857052 TGAATAAAGTAGGGAGTGCGTG 58.143 45.455 0.00 0.00 0.00 5.34
3853 5211 4.504858 CTTGAATAAAGTAGGGAGTGCGT 58.495 43.478 0.00 0.00 0.00 5.24
3854 5212 3.309954 GCTTGAATAAAGTAGGGAGTGCG 59.690 47.826 0.00 0.00 38.25 5.34
3855 5213 4.095036 GTGCTTGAATAAAGTAGGGAGTGC 59.905 45.833 0.00 0.00 38.25 4.40
3856 5214 4.636206 GGTGCTTGAATAAAGTAGGGAGTG 59.364 45.833 0.00 0.00 38.25 3.51
3857 5215 4.623171 CGGTGCTTGAATAAAGTAGGGAGT 60.623 45.833 0.00 0.00 38.25 3.85
3858 5216 3.871594 CGGTGCTTGAATAAAGTAGGGAG 59.128 47.826 0.00 0.00 38.25 4.30
3859 5217 3.516300 TCGGTGCTTGAATAAAGTAGGGA 59.484 43.478 0.00 0.00 38.25 4.20
3860 5218 3.869065 TCGGTGCTTGAATAAAGTAGGG 58.131 45.455 0.00 0.00 38.25 3.53


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

AutoCloner maintained by Alex Coulton.