Multiple sequence alignment - TraesCS7A01G072200

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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 TraesCS7A01G072200 chr7A 100.000 2586 0 0 1 2586 37839756 37842341 0.000000e+00 4776.0
1 TraesCS7A01G072200 chr7A 84.524 84 12 1 1813 1895 371769948 371770031 5.930000e-12 82.4
2 TraesCS7A01G072200 chr7D 92.385 1484 96 10 878 2354 24925693 24924220 0.000000e+00 2098.0
3 TraesCS7A01G072200 chr7D 84.088 685 85 17 1 665 24927130 24926450 7.800000e-180 640.0
4 TraesCS7A01G072200 chr7D 76.435 331 69 8 1 329 34300147 34300470 1.230000e-38 171.0
5 TraesCS7A01G072200 chr3B 94.694 245 11 2 2343 2586 679526029 679526272 1.880000e-101 379.0
6 TraesCS7A01G072200 chr3B 95.359 237 10 1 2351 2586 773751919 773752155 2.430000e-100 375.0
7 TraesCS7A01G072200 chr3B 76.860 242 51 4 4 243 439345297 439345059 5.810000e-27 132.0
8 TraesCS7A01G072200 chr1B 95.041 242 11 1 2346 2586 26839776 26840017 1.880000e-101 379.0
9 TraesCS7A01G072200 chr1B 94.979 239 10 2 2349 2586 629665878 629666115 8.740000e-100 374.0
10 TraesCS7A01G072200 chr1B 84.091 88 13 1 1813 1899 370729982 370729895 1.650000e-12 84.2
11 TraesCS7A01G072200 chr2B 95.000 240 10 2 2348 2586 31397387 31397149 2.430000e-100 375.0
12 TraesCS7A01G072200 chr2A 95.726 234 8 2 2354 2586 1517775 1517543 2.430000e-100 375.0
13 TraesCS7A01G072200 chr2A 93.952 248 12 3 2341 2586 413006441 413006687 3.140000e-99 372.0
14 TraesCS7A01G072200 chr6A 94.979 239 10 2 2349 2586 14487951 14488188 8.740000e-100 374.0
15 TraesCS7A01G072200 chr6A 77.143 175 38 2 70 243 600150835 600150662 1.640000e-17 100.0
16 TraesCS7A01G072200 chr6A 85.882 85 11 1 1812 1895 502244227 502244311 3.540000e-14 89.8
17 TraesCS7A01G072200 chr3A 94.286 245 12 2 2344 2586 649848531 649848775 8.740000e-100 374.0
18 TraesCS7A01G072200 chr3A 77.273 242 50 4 4 243 464249200 464249438 1.250000e-28 137.0
19 TraesCS7A01G072200 chr4D 79.478 268 51 4 4 269 297843291 297843026 1.220000e-43 187.0
20 TraesCS7A01G072200 chr4D 77.567 263 57 2 4 265 342551580 342551319 9.580000e-35 158.0
21 TraesCS7A01G072200 chr4A 78.571 266 55 2 1 265 123877808 123878072 9.510000e-40 174.0
22 TraesCS7A01G072200 chrUn 87.097 93 8 4 1813 1903 19227924 19227834 4.550000e-18 102.0
23 TraesCS7A01G072200 chr1A 86.957 92 10 2 1813 1903 104946058 104946148 4.550000e-18 102.0
24 TraesCS7A01G072200 chr5A 77.273 176 35 4 70 242 693294061 693293888 5.890000e-17 99.0
25 TraesCS7A01G072200 chr6D 87.838 74 7 2 1822 1895 178858019 178858090 4.580000e-13 86.1
26 TraesCS7A01G072200 chr6B 87.838 74 8 1 1822 1895 42775722 42775650 4.580000e-13 86.1
27 TraesCS7A01G072200 chr3D 84.524 84 12 1 1813 1895 513957278 513957361 5.930000e-12 82.4


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 TraesCS7A01G072200 chr7A 37839756 37842341 2585 False 4776 4776 100.0000 1 2586 1 chr7A.!!$F1 2585
1 TraesCS7A01G072200 chr7D 24924220 24927130 2910 True 1369 2098 88.2365 1 2354 2 chr7D.!!$R1 2353

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
500 517 0.031585 TATCCGCGTCAGCATACACC 59.968 55.0 4.92 0.0 45.49 4.16 F
550 567 0.037790 AGAGAGCAGGCACGAAGTTC 60.038 55.0 0.00 0.0 41.61 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 2088 0.164647 GTCACGTCAAGCAGCACATC 59.835 55.0 0.0 0.0 0.0 3.06 R
2549 3118 0.179029 ACTTTTCCCCTGTCGGTGTG 60.179 55.0 0.0 0.0 0.0 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
27 28 5.739959 TCTTGGATGGTGTAAAATCGATGA 58.260 37.500 0.00 0.00 0.00 2.92
33 34 6.292919 GGATGGTGTAAAATCGATGACTAAGC 60.293 42.308 0.00 0.00 0.00 3.09
49 50 5.926542 TGACTAAGCTACTTTGTCACATCAC 59.073 40.000 16.84 0.00 45.56 3.06
57 58 4.245660 ACTTTGTCACATCACCGTAGATG 58.754 43.478 11.47 11.47 33.15 2.90
87 89 3.330701 TGAGGTAGGGCTCAAATTCTTGT 59.669 43.478 0.00 0.00 33.94 3.16
97 99 2.807967 TCAAATTCTTGTGCTCACGGAG 59.192 45.455 0.00 0.00 33.94 4.63
123 125 6.127897 CCAAGAATCTATGTTGGACCAAAGAC 60.128 42.308 8.94 0.00 43.01 3.01
125 127 6.784031 AGAATCTATGTTGGACCAAAGACTT 58.216 36.000 8.94 5.39 0.00 3.01
127 129 7.824779 AGAATCTATGTTGGACCAAAGACTTAC 59.175 37.037 8.94 0.00 0.00 2.34
128 130 6.428083 TCTATGTTGGACCAAAGACTTACA 57.572 37.500 8.94 1.50 0.00 2.41
169 171 3.696711 GATCGAATCGATGCTAGTTGC 57.303 47.619 23.67 1.85 47.00 4.17
170 172 1.852942 TCGAATCGATGCTAGTTGCC 58.147 50.000 0.00 0.00 42.00 4.52
177 179 0.447801 GATGCTAGTTGCCAACCACG 59.552 55.000 3.45 0.00 42.00 4.94
193 195 2.287547 ACCACGCATCACACAACAATTC 60.288 45.455 0.00 0.00 0.00 2.17
194 196 1.971284 CACGCATCACACAACAATTCG 59.029 47.619 0.00 0.00 0.00 3.34
197 199 1.981254 CATCACACAACAATTCGCCC 58.019 50.000 0.00 0.00 0.00 6.13
214 216 1.328279 CCCTCCCTTGTGTTGAAACC 58.672 55.000 0.00 0.00 0.00 3.27
217 219 2.623416 CCTCCCTTGTGTTGAAACCTTC 59.377 50.000 0.00 0.00 0.00 3.46
230 232 2.553911 AACCTTCTCCTCTACCCCTC 57.446 55.000 0.00 0.00 0.00 4.30
238 240 2.769095 CTCCTCTACCCCTCTTCTTTGG 59.231 54.545 0.00 0.00 0.00 3.28
243 245 1.952621 ACCCCTCTTCTTTGGATCGA 58.047 50.000 0.00 0.00 0.00 3.59
268 270 1.478288 CCAATCCTCTGGATCAAGGCC 60.478 57.143 0.00 0.00 42.27 5.19
269 271 1.493871 CAATCCTCTGGATCAAGGCCT 59.506 52.381 0.00 0.00 42.27 5.19
283 285 0.680280 AGGCCTGTCTCGTCGTACAT 60.680 55.000 3.11 0.00 0.00 2.29
292 294 1.129998 CTCGTCGTACATGTCCGTCTT 59.870 52.381 10.78 0.00 0.00 3.01
293 295 1.129251 TCGTCGTACATGTCCGTCTTC 59.871 52.381 10.78 0.48 0.00 2.87
314 316 2.401351 GGCTATCCGTTGTACGATTCC 58.599 52.381 0.05 0.00 46.05 3.01
320 322 2.691526 TCCGTTGTACGATTCCAGCTAT 59.308 45.455 0.05 0.00 46.05 2.97
338 340 0.748005 ATTGGGTGTATGTGCTCGGC 60.748 55.000 0.00 0.00 0.00 5.54
343 345 0.179111 GTGTATGTGCTCGGCTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
350 352 1.043116 TGCTCGGCTGCTAGGTGTAT 61.043 55.000 0.00 0.00 0.00 2.29
351 353 0.598680 GCTCGGCTGCTAGGTGTATG 60.599 60.000 0.00 0.00 0.00 2.39
352 354 0.747255 CTCGGCTGCTAGGTGTATGT 59.253 55.000 0.00 0.00 0.00 2.29
353 355 0.459899 TCGGCTGCTAGGTGTATGTG 59.540 55.000 0.00 0.00 0.00 3.21
355 357 0.179000 GGCTGCTAGGTGTATGTGCT 59.821 55.000 0.00 0.00 0.00 4.40
356 358 1.576356 GCTGCTAGGTGTATGTGCTC 58.424 55.000 0.00 0.00 0.00 4.26
362 364 1.079127 GGTGTATGTGCTCGGCTGT 60.079 57.895 0.00 0.00 0.00 4.40
363 365 0.673644 GGTGTATGTGCTCGGCTGTT 60.674 55.000 0.00 0.00 0.00 3.16
364 366 0.443869 GTGTATGTGCTCGGCTGTTG 59.556 55.000 0.00 0.00 0.00 3.33
365 367 1.298157 TGTATGTGCTCGGCTGTTGC 61.298 55.000 6.38 6.38 38.76 4.17
366 368 1.003959 TATGTGCTCGGCTGTTGCA 60.004 52.632 10.89 10.89 41.91 4.08
371 373 0.605050 TGCTCGGCTGTTGCATGTAA 60.605 50.000 10.89 0.00 41.91 2.41
374 376 1.129251 CTCGGCTGTTGCATGTAAGTG 59.871 52.381 0.00 0.00 41.91 3.16
377 379 0.109132 GCTGTTGCATGTAAGTGCCC 60.109 55.000 0.00 0.00 44.43 5.36
397 399 0.462759 GGCCACTGAGCATACACCTC 60.463 60.000 0.00 0.00 0.00 3.85
401 403 0.539051 ACTGAGCATACACCTCTGGC 59.461 55.000 0.00 0.00 33.96 4.85
404 406 1.630369 TGAGCATACACCTCTGGCTTT 59.370 47.619 0.00 0.00 34.44 3.51
416 418 1.003580 TCTGGCTTTGAGTCATCCACC 59.996 52.381 0.00 0.00 0.00 4.61
440 442 0.329261 CATCCTTGAAGCCACCTCCA 59.671 55.000 0.00 0.00 0.00 3.86
453 455 1.128188 ACCTCCACCACCCTCTTCAC 61.128 60.000 0.00 0.00 0.00 3.18
460 462 2.567169 CACCACCCTCTTCACATAGACA 59.433 50.000 0.00 0.00 0.00 3.41
461 463 3.198635 CACCACCCTCTTCACATAGACAT 59.801 47.826 0.00 0.00 0.00 3.06
463 465 3.432749 CCACCCTCTTCACATAGACATGG 60.433 52.174 0.00 0.00 36.39 3.66
464 466 3.452264 CACCCTCTTCACATAGACATGGA 59.548 47.826 0.00 0.00 36.39 3.41
470 478 6.239515 CCTCTTCACATAGACATGGATCATGA 60.240 42.308 13.96 0.00 43.81 3.07
480 488 6.239396 AGACATGGATCATGAATCATCTTCC 58.761 40.000 13.96 11.94 43.81 3.46
482 490 7.237055 AGACATGGATCATGAATCATCTTCCTA 59.763 37.037 17.10 8.18 43.81 2.94
483 491 7.929959 ACATGGATCATGAATCATCTTCCTAT 58.070 34.615 17.10 9.53 43.81 2.57
484 492 8.047911 ACATGGATCATGAATCATCTTCCTATC 58.952 37.037 17.10 5.25 43.81 2.08
486 494 6.047870 GGATCATGAATCATCTTCCTATCCG 58.952 44.000 0.00 0.00 35.96 4.18
492 509 1.609072 TCATCTTCCTATCCGCGTCAG 59.391 52.381 4.92 0.00 0.00 3.51
496 513 1.269723 CTTCCTATCCGCGTCAGCATA 59.730 52.381 4.92 0.00 45.49 3.14
499 516 1.409412 CTATCCGCGTCAGCATACAC 58.591 55.000 4.92 0.00 45.49 2.90
500 517 0.031585 TATCCGCGTCAGCATACACC 59.968 55.000 4.92 0.00 45.49 4.16
505 522 0.736325 GCGTCAGCATACACCGTCTT 60.736 55.000 0.00 0.00 44.35 3.01
530 547 2.257034 GGTTGAGACATACCGACGAAC 58.743 52.381 0.00 0.00 0.00 3.95
544 561 2.091112 CGAACAGAGAGCAGGCACG 61.091 63.158 0.00 0.00 0.00 5.34
550 567 0.037790 AGAGAGCAGGCACGAAGTTC 60.038 55.000 0.00 0.00 41.61 3.01
557 574 0.670546 AGGCACGAAGTTCATCCACG 60.671 55.000 3.32 0.00 41.61 4.94
560 577 1.375523 ACGAAGTTCATCCACGCCC 60.376 57.895 3.32 0.00 37.78 6.13
577 594 3.245315 CGGCGTTCACGATCGGAC 61.245 66.667 20.98 13.48 43.02 4.79
610 627 3.815856 TGCCAAGTCAGCAAAATGAAA 57.184 38.095 0.00 0.00 37.28 2.69
612 629 2.472488 GCCAAGTCAGCAAAATGAAACG 59.528 45.455 0.00 0.00 0.00 3.60
613 630 3.795150 GCCAAGTCAGCAAAATGAAACGA 60.795 43.478 0.00 0.00 0.00 3.85
617 634 3.627577 AGTCAGCAAAATGAAACGACACT 59.372 39.130 0.00 0.00 0.00 3.55
620 637 2.948979 AGCAAAATGAAACGACACTGGA 59.051 40.909 0.00 0.00 0.00 3.86
674 706 4.889427 GGAAACCGAATGCTTGGC 57.111 55.556 0.00 0.00 0.00 4.52
675 707 1.963679 GGAAACCGAATGCTTGGCA 59.036 52.632 0.00 0.00 44.86 4.92
684 716 2.483877 CGAATGCTTGGCAGTGTAGAAA 59.516 45.455 0.00 0.00 43.65 2.52
753 827 2.240667 CTGGACCATGAATCTTGTCCCT 59.759 50.000 12.34 0.00 45.36 4.20
774 848 2.510411 CCTGCACACAGTCCACCA 59.490 61.111 0.00 0.00 42.81 4.17
784 858 0.764890 CAGTCCACCACCCTCTTGAA 59.235 55.000 0.00 0.00 0.00 2.69
785 859 1.142870 CAGTCCACCACCCTCTTGAAA 59.857 52.381 0.00 0.00 0.00 2.69
806 880 5.468540 AACTTTGCCTTCCTTTTGATACC 57.531 39.130 0.00 0.00 0.00 2.73
842 916 0.321653 ACCGAGTTGATCTTGTGGGC 60.322 55.000 0.00 0.00 0.00 5.36
843 917 0.321564 CCGAGTTGATCTTGTGGGCA 60.322 55.000 0.00 0.00 0.00 5.36
864 938 0.326264 CCACCTTCCCTCCACTTCTG 59.674 60.000 0.00 0.00 0.00 3.02
866 940 1.301293 CCTTCCCTCCACTTCTGCC 59.699 63.158 0.00 0.00 0.00 4.85
867 941 1.078848 CTTCCCTCCACTTCTGCCG 60.079 63.158 0.00 0.00 0.00 5.69
870 1432 3.710722 CCTCCACTTCTGCCGGCT 61.711 66.667 29.70 2.88 0.00 5.52
906 1468 6.017357 TGACGTATCGGTCCATATATGCTATC 60.017 42.308 7.24 0.00 36.07 2.08
913 1478 4.038162 GGTCCATATATGCTATCGGGACTC 59.962 50.000 7.24 0.00 42.22 3.36
973 1538 8.595533 CACGTAATATATAGCCATTGCAAGTAG 58.404 37.037 4.94 0.00 41.13 2.57
976 1541 9.319143 GTAATATATAGCCATTGCAAGTAGAGG 57.681 37.037 4.94 2.90 41.13 3.69
978 1543 4.778213 ATAGCCATTGCAAGTAGAGGAA 57.222 40.909 4.94 0.00 41.13 3.36
1061 1626 4.247380 CATCCTGGCGGCTCTCCC 62.247 72.222 11.43 0.00 0.00 4.30
1170 1738 3.385384 TCCGAGTGGGAGCTGCAG 61.385 66.667 10.11 10.11 40.94 4.41
1185 1753 3.086391 GCAGCTCATCCTCTCCGCA 62.086 63.158 0.00 0.00 0.00 5.69
1239 1807 2.534298 CACAGCTTCATCGTCTACCTG 58.466 52.381 0.00 0.00 0.00 4.00
1240 1808 1.478510 ACAGCTTCATCGTCTACCTGG 59.521 52.381 0.00 0.00 0.00 4.45
1241 1809 1.478510 CAGCTTCATCGTCTACCTGGT 59.521 52.381 4.05 4.05 0.00 4.00
1275 1843 1.445582 GACGGTCTACAAGGTGCCG 60.446 63.158 0.00 0.00 46.83 5.69
1281 1849 3.385749 CTACAAGGTGCCGGCGGAT 62.386 63.158 33.44 9.05 0.00 4.18
1354 1922 1.185315 GGCCAGCTTTGCCTTGAATA 58.815 50.000 15.37 0.00 45.70 1.75
1355 1923 1.550072 GGCCAGCTTTGCCTTGAATAA 59.450 47.619 15.37 0.00 45.70 1.40
1359 1927 4.240096 CCAGCTTTGCCTTGAATAACTTG 58.760 43.478 0.00 0.00 0.00 3.16
1361 1929 2.995939 GCTTTGCCTTGAATAACTTGCC 59.004 45.455 0.00 0.00 0.00 4.52
1427 1995 2.668550 GGCCGTGGTGAGGTTCAC 60.669 66.667 0.62 0.62 46.23 3.18
1428 1996 2.426023 GCCGTGGTGAGGTTCACT 59.574 61.111 8.89 0.00 46.19 3.41
1475 2043 4.662961 CGTCAGGGTGCTGTGCGA 62.663 66.667 0.00 0.00 0.00 5.10
1520 2088 6.183360 GCCAAGAATCTTAGCTTTCCTGTAAG 60.183 42.308 6.17 0.00 0.00 2.34
1526 2094 5.178797 TCTTAGCTTTCCTGTAAGATGTGC 58.821 41.667 0.00 0.00 34.07 4.57
1542 2110 1.143838 TGCTGCTTGACGTGACACT 59.856 52.632 3.68 0.00 0.00 3.55
1575 2143 8.360390 TCTTGAATTCATGATACGTAGCTACAT 58.640 33.333 23.21 11.43 0.00 2.29
1620 2188 5.162075 ACGTCTGCTTAGCTTTTACTACTG 58.838 41.667 5.60 0.00 0.00 2.74
1664 2232 4.188462 CCGGACTGCATTATTTCTGTACA 58.812 43.478 0.00 0.00 0.00 2.90
1665 2233 4.816385 CCGGACTGCATTATTTCTGTACAT 59.184 41.667 0.00 0.00 0.00 2.29
1691 2259 4.755123 ACACAGTTTCTTTTCTGGATACCG 59.245 41.667 0.00 0.00 36.17 4.02
1838 2407 5.765510 TGCCCCATCTCATATTAAGTGTTT 58.234 37.500 0.00 0.00 0.00 2.83
1839 2408 6.194235 TGCCCCATCTCATATTAAGTGTTTT 58.806 36.000 0.00 0.00 0.00 2.43
1882 2451 8.310382 AGACATATTTCAGTGCTAGATACATCC 58.690 37.037 0.00 0.00 0.00 3.51
1903 2472 3.106672 CGGTTGAGCGACACTTAGATAC 58.893 50.000 0.00 0.00 0.00 2.24
1920 2489 7.712639 ACTTAGATACATTCATTTGAGCGACAT 59.287 33.333 0.00 0.00 0.00 3.06
1924 2493 8.892723 AGATACATTCATTTGAGCGACATTTAA 58.107 29.630 0.00 0.00 0.00 1.52
1934 2503 3.399330 AGCGACATTTAATATGGGACGG 58.601 45.455 0.00 0.00 0.00 4.79
1935 2504 2.482721 GCGACATTTAATATGGGACGGG 59.517 50.000 0.00 0.00 0.00 5.28
1959 2528 4.514441 GGGACTACATGATTCTGATGCAAG 59.486 45.833 0.00 0.00 0.00 4.01
1964 2533 2.723322 TGATTCTGATGCAAGGAGGG 57.277 50.000 0.00 0.00 0.00 4.30
1966 2535 0.627451 ATTCTGATGCAAGGAGGGCA 59.373 50.000 0.00 0.00 46.66 5.36
1967 2536 0.405198 TTCTGATGCAAGGAGGGCAA 59.595 50.000 0.00 0.00 45.60 4.52
1987 2556 3.560636 ATGGCATAGTGGTTACTGGTC 57.439 47.619 0.00 0.00 37.78 4.02
2025 2594 1.024579 CAACATGGTCGTGGGCTACC 61.025 60.000 0.00 0.00 36.24 3.18
2039 2608 5.092259 GTGGGCTACCTTATTAGTCCCTAT 58.908 45.833 0.00 0.00 42.45 2.57
2077 2646 9.675464 AATCCAAATACTAACAGAAATTACGGA 57.325 29.630 0.00 0.00 0.00 4.69
2095 2664 1.226746 GACTGTATGCCCATTACCGC 58.773 55.000 0.00 0.00 0.00 5.68
2100 2669 0.249699 TATGCCCATTACCGCGACAG 60.250 55.000 8.23 0.00 0.00 3.51
2129 2698 8.575649 AGAAAAACTGATCACCGGTTAATTAT 57.424 30.769 2.97 0.00 43.27 1.28
2134 2703 6.419791 ACTGATCACCGGTTAATTATTGGAA 58.580 36.000 2.97 0.00 0.00 3.53
2144 2713 8.200792 CCGGTTAATTATTGGAATTTTCATCCA 58.799 33.333 0.00 0.00 45.09 3.41
2172 2741 5.529060 GGATTAAGAACCTTGCTCCTACATG 59.471 44.000 0.00 0.00 0.00 3.21
2173 2742 5.755409 TTAAGAACCTTGCTCCTACATGA 57.245 39.130 0.00 0.00 0.00 3.07
2176 2745 5.957771 AGAACCTTGCTCCTACATGAATA 57.042 39.130 0.00 0.00 0.00 1.75
2182 2751 7.118723 ACCTTGCTCCTACATGAATAAATCAA 58.881 34.615 0.00 0.00 42.54 2.57
2183 2752 7.284034 ACCTTGCTCCTACATGAATAAATCAAG 59.716 37.037 0.00 4.73 42.54 3.02
2235 2804 8.325477 AGAAATAGCTATTCCTTAGTCCAAGT 57.675 34.615 19.11 0.00 31.77 3.16
2236 2805 8.773216 AGAAATAGCTATTCCTTAGTCCAAGTT 58.227 33.333 19.11 0.00 31.77 2.66
2239 2808 9.755122 AATAGCTATTCCTTAGTCCAAGTTTTT 57.245 29.630 13.37 0.00 31.77 1.94
2276 2845 8.594881 AGTTAATCCGTGATGATAGTCAAATC 57.405 34.615 0.00 0.00 0.00 2.17
2284 2853 8.084684 CCGTGATGATAGTCAAATCAAGATCTA 58.915 37.037 0.00 0.00 39.25 1.98
2313 2882 7.614124 AATAACAATTCCAATCAACCATTGC 57.386 32.000 0.00 0.00 40.75 3.56
2327 2896 6.862209 TCAACCATTGCATCCAGTAAATAAC 58.138 36.000 0.00 0.00 0.00 1.89
2331 2900 5.743398 CCATTGCATCCAGTAAATAACAACG 59.257 40.000 0.00 0.00 0.00 4.10
2351 2920 5.277857 ACGAAATCACTCCAGGGTATTAG 57.722 43.478 0.00 0.00 0.00 1.73
2354 2923 4.965200 AATCACTCCAGGGTATTAGAGC 57.035 45.455 0.00 0.00 0.00 4.09
2355 2924 3.398318 TCACTCCAGGGTATTAGAGCA 57.602 47.619 0.00 0.00 0.00 4.26
2356 2925 3.928754 TCACTCCAGGGTATTAGAGCAT 58.071 45.455 0.00 0.00 0.00 3.79
2357 2926 3.898123 TCACTCCAGGGTATTAGAGCATC 59.102 47.826 0.00 0.00 0.00 3.91
2398 2967 4.382541 CCCCCAGGCCACCTTTCC 62.383 72.222 5.01 0.00 0.00 3.13
2399 2968 4.740822 CCCCAGGCCACCTTTCCG 62.741 72.222 5.01 0.00 0.00 4.30
2400 2969 4.740822 CCCAGGCCACCTTTCCGG 62.741 72.222 5.01 0.00 39.35 5.14
2430 2999 4.111967 AAAAATGGCCCAGTCCCG 57.888 55.556 0.00 0.00 0.00 5.14
2431 3000 2.282783 AAAAATGGCCCAGTCCCGC 61.283 57.895 0.00 0.00 0.00 6.13
2432 3001 4.759205 AAATGGCCCAGTCCCGCC 62.759 66.667 0.00 0.00 45.92 6.13
2448 3017 4.338710 CCCCCAGGACGCCGAAAA 62.339 66.667 0.00 0.00 33.47 2.29
2449 3018 2.045340 CCCCAGGACGCCGAAAAT 60.045 61.111 0.00 0.00 0.00 1.82
2450 3019 2.112815 CCCCAGGACGCCGAAAATC 61.113 63.158 0.00 0.00 0.00 2.17
2451 3020 2.461110 CCCAGGACGCCGAAAATCG 61.461 63.158 0.00 0.00 40.07 3.34
2452 3021 2.399611 CAGGACGCCGAAAATCGC 59.600 61.111 0.00 0.00 38.82 4.58
2453 3022 2.818274 AGGACGCCGAAAATCGCC 60.818 61.111 0.00 0.00 38.82 5.54
2454 3023 4.218478 GGACGCCGAAAATCGCCG 62.218 66.667 1.44 1.44 46.50 6.46
2455 3024 4.218478 GACGCCGAAAATCGCCGG 62.218 66.667 7.99 0.00 45.33 6.13
2457 3026 3.795342 CGCCGAAAATCGCCGGTT 61.795 61.111 1.90 0.00 46.84 4.44
2458 3027 2.202427 GCCGAAAATCGCCGGTTG 60.202 61.111 1.90 0.00 46.84 3.77
2459 3028 2.483288 CCGAAAATCGCCGGTTGG 59.517 61.111 1.90 0.00 40.78 3.77
2460 3029 2.036006 CCGAAAATCGCCGGTTGGA 61.036 57.895 1.90 0.00 40.78 3.53
2461 3030 1.133869 CGAAAATCGCCGGTTGGAC 59.866 57.895 1.90 0.00 37.49 4.02
2462 3031 1.504900 GAAAATCGCCGGTTGGACC 59.495 57.895 1.90 0.00 37.49 4.46
2463 3032 0.958876 GAAAATCGCCGGTTGGACCT 60.959 55.000 1.90 0.00 35.66 3.85
2464 3033 0.538746 AAAATCGCCGGTTGGACCTT 60.539 50.000 1.90 0.00 35.66 3.50
2465 3034 0.538746 AAATCGCCGGTTGGACCTTT 60.539 50.000 1.90 0.00 35.66 3.11
2466 3035 0.538746 AATCGCCGGTTGGACCTTTT 60.539 50.000 1.90 0.00 35.66 2.27
2467 3036 0.538746 ATCGCCGGTTGGACCTTTTT 60.539 50.000 1.90 0.00 35.66 1.94
2516 3085 4.722700 CACTGGGGAGCGGTTGGG 62.723 72.222 0.00 0.00 0.00 4.12
2534 3103 3.470888 GGCTCCAGCGCTAGGGAA 61.471 66.667 10.99 0.00 43.26 3.97
2535 3104 2.584608 GCTCCAGCGCTAGGGAAA 59.415 61.111 10.99 0.00 31.58 3.13
2536 3105 1.078426 GCTCCAGCGCTAGGGAAAA 60.078 57.895 10.99 0.00 31.58 2.29
2537 3106 1.092345 GCTCCAGCGCTAGGGAAAAG 61.092 60.000 10.99 8.59 31.58 2.27
2538 3107 1.078426 TCCAGCGCTAGGGAAAAGC 60.078 57.895 10.99 0.00 36.60 3.51
2539 3108 1.377202 CCAGCGCTAGGGAAAAGCA 60.377 57.895 10.99 0.00 40.08 3.91
2540 3109 1.648467 CCAGCGCTAGGGAAAAGCAC 61.648 60.000 10.99 0.00 40.08 4.40
2541 3110 1.741770 AGCGCTAGGGAAAAGCACG 60.742 57.895 8.99 0.00 40.08 5.34
2542 3111 2.785258 CGCTAGGGAAAAGCACGC 59.215 61.111 0.00 0.00 40.08 5.34
2543 3112 2.750888 CGCTAGGGAAAAGCACGCC 61.751 63.158 0.00 0.00 40.08 5.68
2544 3113 1.377333 GCTAGGGAAAAGCACGCCT 60.377 57.895 0.00 0.00 39.83 5.52
2545 3114 1.648467 GCTAGGGAAAAGCACGCCTG 61.648 60.000 0.00 0.00 39.83 4.85
2546 3115 1.002624 TAGGGAAAAGCACGCCTGG 60.003 57.895 0.00 0.00 0.00 4.45
2547 3116 4.056125 GGGAAAAGCACGCCTGGC 62.056 66.667 9.11 9.11 0.00 4.85
2548 3117 4.056125 GGAAAAGCACGCCTGGCC 62.056 66.667 14.12 0.00 0.00 5.36
2549 3118 4.056125 GAAAAGCACGCCTGGCCC 62.056 66.667 14.12 1.57 0.00 5.80
2550 3119 4.912395 AAAAGCACGCCTGGCCCA 62.912 61.111 14.12 0.00 0.00 5.36
2559 3128 4.704833 CCTGGCCCACACCGACAG 62.705 72.222 0.00 0.00 0.00 3.51
2560 3129 4.704833 CTGGCCCACACCGACAGG 62.705 72.222 0.00 0.00 45.13 4.00
2564 3133 3.246112 CCCACACCGACAGGGGAA 61.246 66.667 0.00 0.00 46.39 3.97
2565 3134 2.824880 CCCACACCGACAGGGGAAA 61.825 63.158 0.00 0.00 46.39 3.13
2566 3135 1.149627 CCACACCGACAGGGGAAAA 59.850 57.895 0.00 0.00 46.39 2.29
2567 3136 0.889186 CCACACCGACAGGGGAAAAG 60.889 60.000 0.00 0.00 46.39 2.27
2568 3137 0.179029 CACACCGACAGGGGAAAAGT 60.179 55.000 0.00 0.00 46.39 2.66
2569 3138 0.108019 ACACCGACAGGGGAAAAGTC 59.892 55.000 0.00 0.00 46.39 3.01
2570 3139 0.107831 CACCGACAGGGGAAAAGTCA 59.892 55.000 0.00 0.00 46.39 3.41
2571 3140 0.841289 ACCGACAGGGGAAAAGTCAA 59.159 50.000 0.00 0.00 43.47 3.18
2572 3141 1.202770 ACCGACAGGGGAAAAGTCAAG 60.203 52.381 0.00 0.00 43.47 3.02
2573 3142 1.523758 CGACAGGGGAAAAGTCAAGG 58.476 55.000 0.00 0.00 32.68 3.61
2574 3143 1.202770 CGACAGGGGAAAAGTCAAGGT 60.203 52.381 0.00 0.00 32.68 3.50
2575 3144 2.748465 CGACAGGGGAAAAGTCAAGGTT 60.748 50.000 0.00 0.00 32.68 3.50
2576 3145 3.296854 GACAGGGGAAAAGTCAAGGTTT 58.703 45.455 0.00 0.00 32.68 3.27
2577 3146 3.704566 GACAGGGGAAAAGTCAAGGTTTT 59.295 43.478 0.00 0.00 32.68 2.43
2578 3147 3.704566 ACAGGGGAAAAGTCAAGGTTTTC 59.295 43.478 0.00 0.00 41.33 2.29
2579 3148 3.960755 CAGGGGAAAAGTCAAGGTTTTCT 59.039 43.478 7.92 0.00 41.63 2.52
2580 3149 4.405680 CAGGGGAAAAGTCAAGGTTTTCTT 59.594 41.667 7.92 0.00 41.63 2.52
2581 3150 4.649674 AGGGGAAAAGTCAAGGTTTTCTTC 59.350 41.667 7.92 2.57 41.63 2.87
2582 3151 4.202223 GGGGAAAAGTCAAGGTTTTCTTCC 60.202 45.833 7.92 6.79 41.63 3.46
2583 3152 4.202223 GGGAAAAGTCAAGGTTTTCTTCCC 60.202 45.833 7.92 1.01 41.63 3.97
2584 3153 4.202223 GGAAAAGTCAAGGTTTTCTTCCCC 60.202 45.833 7.92 0.00 41.63 4.81
2585 3154 2.677542 AGTCAAGGTTTTCTTCCCCC 57.322 50.000 0.00 0.00 32.41 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.817296 TCATCGATTTTACACCATCCAAGAG 59.183 40.000 0.00 0.00 0.00 2.85
14 15 8.869897 CAAAGTAGCTTAGTCATCGATTTTACA 58.130 33.333 0.00 0.00 0.00 2.41
18 19 7.063544 GTGACAAAGTAGCTTAGTCATCGATTT 59.936 37.037 0.00 0.00 40.80 2.17
19 20 6.531948 GTGACAAAGTAGCTTAGTCATCGATT 59.468 38.462 0.00 0.00 40.80 3.34
27 28 5.238583 GGTGATGTGACAAAGTAGCTTAGT 58.761 41.667 0.00 0.00 0.00 2.24
33 34 5.055642 TCTACGGTGATGTGACAAAGTAG 57.944 43.478 0.00 0.03 35.45 2.57
43 44 2.753452 ACGAAGTCATCTACGGTGATGT 59.247 45.455 15.95 1.93 43.03 3.06
47 48 3.172050 CTCAACGAAGTCATCTACGGTG 58.828 50.000 0.00 0.00 45.00 4.94
49 50 2.163815 ACCTCAACGAAGTCATCTACGG 59.836 50.000 0.00 0.00 45.00 4.02
57 58 0.896226 AGCCCTACCTCAACGAAGTC 59.104 55.000 0.00 0.00 45.00 3.01
97 99 3.620488 TGGTCCAACATAGATTCTTGGC 58.380 45.455 0.00 0.00 35.36 4.52
105 107 6.042781 AGTGTAAGTCTTTGGTCCAACATAGA 59.957 38.462 2.98 1.82 0.00 1.98
106 108 6.231211 AGTGTAAGTCTTTGGTCCAACATAG 58.769 40.000 2.98 0.00 0.00 2.23
123 125 4.338118 TGGAACAAAGCAAAGGAGTGTAAG 59.662 41.667 0.00 0.00 31.92 2.34
125 127 3.892284 TGGAACAAAGCAAAGGAGTGTA 58.108 40.909 0.00 0.00 31.92 2.90
167 169 2.203266 TGTGATGCGTGGTTGGCA 60.203 55.556 0.00 0.00 45.71 4.92
169 171 0.317770 GTTGTGTGATGCGTGGTTGG 60.318 55.000 0.00 0.00 0.00 3.77
170 172 0.380024 TGTTGTGTGATGCGTGGTTG 59.620 50.000 0.00 0.00 0.00 3.77
177 179 1.339711 GGCGAATTGTTGTGTGATGC 58.660 50.000 0.00 0.00 0.00 3.91
193 195 0.821711 TTTCAACACAAGGGAGGGCG 60.822 55.000 0.00 0.00 0.00 6.13
194 196 0.673985 GTTTCAACACAAGGGAGGGC 59.326 55.000 0.00 0.00 0.00 5.19
197 199 3.555966 AGAAGGTTTCAACACAAGGGAG 58.444 45.455 0.00 0.00 0.00 4.30
214 216 3.680777 AGAAGAGGGGTAGAGGAGAAG 57.319 52.381 0.00 0.00 0.00 2.85
217 219 2.769095 CCAAAGAAGAGGGGTAGAGGAG 59.231 54.545 0.00 0.00 0.00 3.69
230 232 1.339055 TGGCCAGTCGATCCAAAGAAG 60.339 52.381 0.00 0.00 0.00 2.85
238 240 0.755686 AGAGGATTGGCCAGTCGATC 59.244 55.000 20.77 19.64 40.02 3.69
243 245 0.842635 GATCCAGAGGATTGGCCAGT 59.157 55.000 5.11 1.42 43.27 4.00
268 270 1.529214 CGGACATGTACGACGAGACAG 60.529 57.143 26.59 0.00 39.85 3.51
269 271 0.445043 CGGACATGTACGACGAGACA 59.555 55.000 26.59 5.80 39.85 3.41
299 301 0.892755 AGCTGGAATCGTACAACGGA 59.107 50.000 0.00 0.00 42.81 4.69
314 316 2.874701 GAGCACATACACCCAATAGCTG 59.125 50.000 0.00 0.00 0.00 4.24
320 322 1.376683 GCCGAGCACATACACCCAA 60.377 57.895 0.00 0.00 0.00 4.12
328 330 2.362369 ACCTAGCAGCCGAGCACAT 61.362 57.895 0.00 0.00 36.85 3.21
331 333 1.043116 ATACACCTAGCAGCCGAGCA 61.043 55.000 0.00 0.00 36.85 4.26
332 334 0.598680 CATACACCTAGCAGCCGAGC 60.599 60.000 0.00 0.00 0.00 5.03
338 340 1.536922 CCGAGCACATACACCTAGCAG 60.537 57.143 0.00 0.00 0.00 4.24
343 345 1.219124 CAGCCGAGCACATACACCT 59.781 57.895 0.00 0.00 0.00 4.00
350 352 2.281692 ATGCAACAGCCGAGCACA 60.282 55.556 0.00 0.00 41.60 4.57
351 353 1.298157 TACATGCAACAGCCGAGCAC 61.298 55.000 0.00 0.00 41.60 4.40
352 354 0.605050 TTACATGCAACAGCCGAGCA 60.605 50.000 0.00 0.00 43.14 4.26
353 355 0.097674 CTTACATGCAACAGCCGAGC 59.902 55.000 0.00 0.00 0.00 5.03
355 357 1.155889 CACTTACATGCAACAGCCGA 58.844 50.000 0.00 0.00 0.00 5.54
356 358 0.454957 GCACTTACATGCAACAGCCG 60.455 55.000 0.00 0.00 45.39 5.52
364 366 3.518068 GGCCGGGCACTTACATGC 61.518 66.667 25.33 0.00 45.34 4.06
365 367 2.045438 TGGCCGGGCACTTACATG 60.045 61.111 29.27 0.00 0.00 3.21
366 368 2.045340 GTGGCCGGGCACTTACAT 60.045 61.111 44.03 0.00 0.00 2.29
374 376 4.175337 TATGCTCAGTGGCCGGGC 62.175 66.667 23.42 23.42 0.00 6.13
377 379 1.815421 GGTGTATGCTCAGTGGCCG 60.815 63.158 0.00 0.00 0.00 6.13
384 386 1.279496 AAGCCAGAGGTGTATGCTCA 58.721 50.000 0.00 0.00 0.00 4.26
397 399 1.004044 AGGTGGATGACTCAAAGCCAG 59.996 52.381 0.00 0.00 0.00 4.85
401 403 2.038952 TGGACAGGTGGATGACTCAAAG 59.961 50.000 0.00 0.00 0.00 2.77
404 406 1.833630 GATGGACAGGTGGATGACTCA 59.166 52.381 0.00 0.00 0.00 3.41
416 418 1.457346 GTGGCTTCAAGGATGGACAG 58.543 55.000 0.00 0.00 0.00 3.51
440 442 2.902608 TGTCTATGTGAAGAGGGTGGT 58.097 47.619 0.00 0.00 0.00 4.16
453 455 8.794335 AAGATGATTCATGATCCATGTCTATG 57.206 34.615 13.14 0.00 41.98 2.23
460 462 7.575505 GGATAGGAAGATGATTCATGATCCAT 58.424 38.462 21.03 10.15 31.51 3.41
461 463 6.351626 CGGATAGGAAGATGATTCATGATCCA 60.352 42.308 21.03 6.11 31.51 3.41
463 465 5.523188 GCGGATAGGAAGATGATTCATGATC 59.477 44.000 3.32 2.14 35.21 2.92
464 466 5.426504 GCGGATAGGAAGATGATTCATGAT 58.573 41.667 3.32 0.00 0.00 2.45
470 478 2.628178 TGACGCGGATAGGAAGATGATT 59.372 45.455 12.47 0.00 0.00 2.57
480 488 1.409412 GTGTATGCTGACGCGGATAG 58.591 55.000 12.47 6.61 39.65 2.08
482 490 1.227263 GGTGTATGCTGACGCGGAT 60.227 57.895 12.47 0.00 39.65 4.18
483 491 2.183300 GGTGTATGCTGACGCGGA 59.817 61.111 12.47 0.00 39.65 5.54
484 492 3.254654 CGGTGTATGCTGACGCGG 61.255 66.667 12.47 0.00 39.65 6.46
486 494 0.736325 AAGACGGTGTATGCTGACGC 60.736 55.000 0.00 0.00 0.00 5.19
492 509 1.421410 CCGAGCAAGACGGTGTATGC 61.421 60.000 0.00 0.00 44.57 3.14
500 517 0.318699 TGTCTCAACCGAGCAAGACG 60.319 55.000 0.00 0.00 40.79 4.18
527 544 0.319900 TTCGTGCCTGCTCTCTGTTC 60.320 55.000 0.00 0.00 0.00 3.18
530 547 0.320247 AACTTCGTGCCTGCTCTCTG 60.320 55.000 0.00 0.00 0.00 3.35
544 561 2.106683 CCGGGCGTGGATGAACTTC 61.107 63.158 0.00 0.00 0.00 3.01
560 577 3.245315 GTCCGATCGTGAACGCCG 61.245 66.667 15.09 4.46 39.60 6.46
564 581 0.716108 CAGCTTGTCCGATCGTGAAC 59.284 55.000 15.09 9.71 0.00 3.18
594 611 4.096382 AGTGTCGTTTCATTTTGCTGACTT 59.904 37.500 0.00 0.00 0.00 3.01
599 616 2.948979 TCCAGTGTCGTTTCATTTTGCT 59.051 40.909 0.00 0.00 0.00 3.91
601 618 5.399301 GTGAATCCAGTGTCGTTTCATTTTG 59.601 40.000 0.00 0.00 0.00 2.44
602 619 5.067153 TGTGAATCCAGTGTCGTTTCATTTT 59.933 36.000 0.00 0.00 0.00 1.82
610 627 1.544246 TCGATGTGAATCCAGTGTCGT 59.456 47.619 0.00 0.00 0.00 4.34
612 629 1.920574 CGTCGATGTGAATCCAGTGTC 59.079 52.381 0.00 0.00 0.00 3.67
613 630 1.996292 CGTCGATGTGAATCCAGTGT 58.004 50.000 0.00 0.00 0.00 3.55
617 634 2.022764 ATTGCGTCGATGTGAATCCA 57.977 45.000 6.48 0.00 0.00 3.41
620 637 2.224079 GCCATATTGCGTCGATGTGAAT 59.776 45.455 6.48 7.71 0.00 2.57
656 673 1.861542 TGCCAAGCATTCGGTTTCCG 61.862 55.000 1.45 1.45 40.41 4.30
657 674 0.109132 CTGCCAAGCATTCGGTTTCC 60.109 55.000 0.00 0.00 38.13 3.13
658 675 0.598065 ACTGCCAAGCATTCGGTTTC 59.402 50.000 0.00 0.00 38.13 2.78
659 676 0.314935 CACTGCCAAGCATTCGGTTT 59.685 50.000 0.00 0.00 38.13 3.27
664 696 4.708726 ATTTCTACACTGCCAAGCATTC 57.291 40.909 0.00 0.00 38.13 2.67
665 697 4.641989 CCTATTTCTACACTGCCAAGCATT 59.358 41.667 0.00 0.00 38.13 3.56
669 701 2.945668 GCCCTATTTCTACACTGCCAAG 59.054 50.000 0.00 0.00 0.00 3.61
674 706 1.583054 GCCGCCCTATTTCTACACTG 58.417 55.000 0.00 0.00 0.00 3.66
675 707 0.104304 CGCCGCCCTATTTCTACACT 59.896 55.000 0.00 0.00 0.00 3.55
684 716 4.175337 ATGCACACGCCGCCCTAT 62.175 61.111 0.00 0.00 37.32 2.57
727 790 2.124151 ATTCATGGTCCAGGCGGC 60.124 61.111 0.00 0.00 0.00 6.53
730 793 2.019984 GACAAGATTCATGGTCCAGGC 58.980 52.381 0.00 0.00 0.00 4.85
735 798 2.019984 GCAGGGACAAGATTCATGGTC 58.980 52.381 0.00 0.00 0.00 4.02
736 799 1.341383 GGCAGGGACAAGATTCATGGT 60.341 52.381 0.00 0.00 0.00 3.55
739 802 0.259938 GGGGCAGGGACAAGATTCAT 59.740 55.000 0.00 0.00 0.00 2.57
742 805 1.693640 CAGGGGCAGGGACAAGATT 59.306 57.895 0.00 0.00 0.00 2.40
764 838 0.399949 TCAAGAGGGTGGTGGACTGT 60.400 55.000 0.00 0.00 0.00 3.55
774 848 2.755952 AGGCAAAGTTTCAAGAGGGT 57.244 45.000 0.00 0.00 0.00 4.34
784 858 4.022329 CGGTATCAAAAGGAAGGCAAAGTT 60.022 41.667 0.00 0.00 0.00 2.66
785 859 3.506067 CGGTATCAAAAGGAAGGCAAAGT 59.494 43.478 0.00 0.00 0.00 2.66
817 891 0.732880 AAGATCAACTCGGTCACGCG 60.733 55.000 3.53 3.53 40.69 6.01
820 894 2.069273 CCACAAGATCAACTCGGTCAC 58.931 52.381 0.00 0.00 0.00 3.67
822 896 1.726853 CCCACAAGATCAACTCGGTC 58.273 55.000 0.00 0.00 0.00 4.79
842 916 1.783250 AAGTGGAGGGAAGGTGGCTG 61.783 60.000 0.00 0.00 0.00 4.85
843 917 1.464198 AAGTGGAGGGAAGGTGGCT 60.464 57.895 0.00 0.00 0.00 4.75
866 940 0.870307 CGTCAGATTAACCGGAGCCG 60.870 60.000 9.46 1.06 39.44 5.52
867 941 0.175073 ACGTCAGATTAACCGGAGCC 59.825 55.000 9.46 0.00 0.00 4.70
870 1432 2.291465 CCGATACGTCAGATTAACCGGA 59.709 50.000 9.46 0.00 36.86 5.14
874 1436 4.297299 TGGACCGATACGTCAGATTAAC 57.703 45.455 0.00 0.00 34.24 2.01
876 1438 7.468220 GCATATATGGACCGATACGTCAGATTA 60.468 40.741 14.51 0.00 34.24 1.75
913 1478 4.087892 CCTGACTGGCCACTCCCG 62.088 72.222 0.00 0.00 0.00 5.14
925 1490 1.410882 GAGCCTATGACCTGACCTGAC 59.589 57.143 0.00 0.00 0.00 3.51
973 1538 1.682323 CTAACTACCTCGGCCTTCCTC 59.318 57.143 0.00 0.00 0.00 3.71
976 1541 1.112950 AGCTAACTACCTCGGCCTTC 58.887 55.000 0.00 0.00 0.00 3.46
978 1543 1.984066 CTAGCTAACTACCTCGGCCT 58.016 55.000 0.00 0.00 0.00 5.19
1042 1607 2.586792 GAGAGCCGCCAGGATGTT 59.413 61.111 0.00 0.00 41.02 2.71
1068 1633 4.657824 ACGACGCCGGTGACAAGG 62.658 66.667 24.59 5.63 40.78 3.61
1095 1660 4.131088 GTGAGGACCGCCGAGACC 62.131 72.222 0.00 0.00 39.96 3.85
1170 1738 1.424493 CGTTTGCGGAGAGGATGAGC 61.424 60.000 0.00 0.00 0.00 4.26
1175 1743 1.006571 GTGTCGTTTGCGGAGAGGA 60.007 57.895 0.00 0.00 38.89 3.71
1185 1753 2.660552 CGGTGGCTCGTGTCGTTT 60.661 61.111 0.00 0.00 0.00 3.60
1212 1780 2.535984 GACGATGAAGCTGTGGTAATCG 59.464 50.000 1.95 1.95 41.87 3.34
1215 1783 3.119245 GGTAGACGATGAAGCTGTGGTAA 60.119 47.826 0.00 0.00 0.00 2.85
1239 1807 2.359478 CCCTTGGCCGTGTACACC 60.359 66.667 20.11 7.23 0.00 4.16
1240 1808 2.359478 CCCCTTGGCCGTGTACAC 60.359 66.667 16.32 16.32 0.00 2.90
1241 1809 2.527123 TCCCCTTGGCCGTGTACA 60.527 61.111 0.00 0.00 0.00 2.90
1318 1886 2.391821 CGACACGCTCATGTTCGC 59.608 61.111 8.75 2.62 31.24 4.70
1351 1919 2.466867 CGGCTGTCGGCAAGTTATT 58.533 52.632 5.89 0.00 44.01 1.40
1361 1929 4.760047 CACCTTCCCCGGCTGTCG 62.760 72.222 0.00 0.00 38.88 4.35
1427 1995 4.077184 TGTAAGCCGGCCCGACAG 62.077 66.667 26.15 0.00 0.00 3.51
1428 1996 4.382320 GTGTAAGCCGGCCCGACA 62.382 66.667 26.15 21.74 0.00 4.35
1475 2043 1.969862 CCAAAGTAGTCGACGGGGT 59.030 57.895 10.46 0.00 0.00 4.95
1480 2048 0.947180 TTGGCGCCAAAGTAGTCGAC 60.947 55.000 38.61 7.70 32.44 4.20
1520 2088 0.164647 GTCACGTCAAGCAGCACATC 59.835 55.000 0.00 0.00 0.00 3.06
1526 2094 0.855349 GTGAGTGTCACGTCAAGCAG 59.145 55.000 0.00 0.00 37.67 4.24
1583 2151 8.499162 GCTAAGCAGACGTATCATGATTTATTT 58.501 33.333 14.65 1.68 0.00 1.40
1584 2152 7.875041 AGCTAAGCAGACGTATCATGATTTATT 59.125 33.333 14.65 0.00 0.00 1.40
1585 2153 7.382110 AGCTAAGCAGACGTATCATGATTTAT 58.618 34.615 14.65 0.00 0.00 1.40
1586 2154 6.749139 AGCTAAGCAGACGTATCATGATTTA 58.251 36.000 14.65 3.00 0.00 1.40
1620 2188 5.401376 CGGTATATGCATATACATACACGGC 59.599 44.000 38.71 25.46 44.29 5.68
1664 2232 7.824779 GGTATCCAGAAAAGAAACTGTGTAGAT 59.175 37.037 0.00 0.00 32.93 1.98
1665 2233 7.159372 GGTATCCAGAAAAGAAACTGTGTAGA 58.841 38.462 0.00 0.00 32.93 2.59
1751 2319 7.718753 TCAAAATGCATTCAAATAGTTTTGGGT 59.281 29.630 13.38 0.00 42.10 4.51
1816 2384 6.715347 AAAACACTTAATATGAGATGGGGC 57.285 37.500 0.00 0.00 0.00 5.80
1873 2442 1.067212 GTCGCTCAACCGGATGTATCT 59.933 52.381 9.46 0.00 0.00 1.98
1882 2451 2.279582 ATCTAAGTGTCGCTCAACCG 57.720 50.000 0.00 0.00 0.00 4.44
1903 2472 8.908678 CCATATTAAATGTCGCTCAAATGAATG 58.091 33.333 0.00 0.00 0.00 2.67
1934 2503 3.808618 GCATCAGAATCATGTAGTCCCCC 60.809 52.174 0.00 0.00 0.00 5.40
1935 2504 3.181451 TGCATCAGAATCATGTAGTCCCC 60.181 47.826 0.00 0.00 0.00 4.81
1939 2508 5.363562 TCCTTGCATCAGAATCATGTAGT 57.636 39.130 0.00 0.00 0.00 2.73
1954 2523 2.681064 GCCATTGCCCTCCTTGCA 60.681 61.111 0.00 0.00 36.84 4.08
1959 2528 0.825010 CCACTATGCCATTGCCCTCC 60.825 60.000 0.00 0.00 36.33 4.30
1964 2533 2.358898 CCAGTAACCACTATGCCATTGC 59.641 50.000 0.00 0.00 32.21 3.56
1966 2535 3.265737 TGACCAGTAACCACTATGCCATT 59.734 43.478 0.00 0.00 32.21 3.16
1967 2536 2.843730 TGACCAGTAACCACTATGCCAT 59.156 45.455 0.00 0.00 32.21 4.40
1987 2556 4.336433 TGTTGAAGGAAAAGAAGAGCACTG 59.664 41.667 0.00 0.00 0.00 3.66
2025 2594 8.964476 TGAAAGCTTCAATAGGGACTAATAAG 57.036 34.615 0.00 0.00 38.65 1.73
2060 2629 6.534079 GCATACAGTCCGTAATTTCTGTTAGT 59.466 38.462 0.00 0.00 40.77 2.24
2077 2646 0.531974 CGCGGTAATGGGCATACAGT 60.532 55.000 0.00 0.00 0.00 3.55
2095 2664 3.742882 TGATCAGTTTTTCTGCTCTGTCG 59.257 43.478 0.00 0.00 43.32 4.35
2100 2669 2.160417 CCGGTGATCAGTTTTTCTGCTC 59.840 50.000 0.00 0.00 43.32 4.26
2116 2685 8.940768 ATGAAAATTCCAATAATTAACCGGTG 57.059 30.769 8.52 0.00 0.00 4.94
2144 2713 5.645201 AGGAGCAAGGTTCTTAATCCTTTT 58.355 37.500 6.89 0.00 41.44 2.27
2148 2717 5.099042 TGTAGGAGCAAGGTTCTTAATCC 57.901 43.478 0.00 0.00 0.00 3.01
2151 2720 5.755409 TCATGTAGGAGCAAGGTTCTTAA 57.245 39.130 0.00 0.00 0.00 1.85
2152 2721 5.755409 TTCATGTAGGAGCAAGGTTCTTA 57.245 39.130 0.00 0.00 0.00 2.10
2172 2741 6.272822 AGTCTGGCCAAACTTGATTTATTC 57.727 37.500 5.69 0.00 0.00 1.75
2173 2742 7.775053 TTAGTCTGGCCAAACTTGATTTATT 57.225 32.000 18.83 0.00 0.00 1.40
2176 2745 6.670695 AATTAGTCTGGCCAAACTTGATTT 57.329 33.333 18.83 3.56 0.00 2.17
2182 2751 4.280929 GGACAAAATTAGTCTGGCCAAACT 59.719 41.667 17.60 17.60 38.23 2.66
2183 2752 4.038642 TGGACAAAATTAGTCTGGCCAAAC 59.961 41.667 7.01 3.00 45.47 2.93
2246 2815 7.016361 ACTATCATCACGGATTAACTTTTGC 57.984 36.000 0.00 0.00 0.00 3.68
2258 2827 6.927936 AGATCTTGATTTGACTATCATCACGG 59.072 38.462 0.00 0.00 34.67 4.94
2276 2845 9.806203 TTGGAATTGTTATTTGCATAGATCTTG 57.194 29.630 0.00 0.32 0.00 3.02
2284 2853 7.166851 TGGTTGATTGGAATTGTTATTTGCAT 58.833 30.769 0.00 0.00 0.00 3.96
2298 2867 2.761767 CTGGATGCAATGGTTGATTGGA 59.238 45.455 0.00 0.00 45.44 3.53
2313 2882 8.450964 AGTGATTTCGTTGTTATTTACTGGATG 58.549 33.333 0.00 0.00 0.00 3.51
2327 2896 2.185004 ACCCTGGAGTGATTTCGTTG 57.815 50.000 0.00 0.00 0.00 4.10
2331 2900 5.163301 TGCTCTAATACCCTGGAGTGATTTC 60.163 44.000 0.00 0.00 0.00 2.17
2381 2950 4.382541 GGAAAGGTGGCCTGGGGG 62.383 72.222 3.32 0.00 32.13 5.40
2382 2951 4.740822 CGGAAAGGTGGCCTGGGG 62.741 72.222 3.32 0.00 32.13 4.96
2383 2952 4.740822 CCGGAAAGGTGGCCTGGG 62.741 72.222 3.32 0.00 32.13 4.45
2413 2982 2.282783 GCGGGACTGGGCCATTTTT 61.283 57.895 6.72 0.00 0.00 1.94
2414 2983 2.679996 GCGGGACTGGGCCATTTT 60.680 61.111 6.72 0.00 0.00 1.82
2431 3000 3.638592 ATTTTCGGCGTCCTGGGGG 62.639 63.158 6.85 0.00 0.00 5.40
2432 3001 2.045340 ATTTTCGGCGTCCTGGGG 60.045 61.111 6.85 0.00 0.00 4.96
2433 3002 2.461110 CGATTTTCGGCGTCCTGGG 61.461 63.158 6.85 0.00 36.00 4.45
2434 3003 3.089784 CGATTTTCGGCGTCCTGG 58.910 61.111 6.85 0.00 36.00 4.45
2435 3004 2.399611 GCGATTTTCGGCGTCCTG 59.600 61.111 6.85 0.00 40.84 3.86
2443 3012 1.133869 GTCCAACCGGCGATTTTCG 59.866 57.895 9.30 0.00 43.89 3.46
2444 3013 0.958876 AGGTCCAACCGGCGATTTTC 60.959 55.000 9.30 0.00 44.90 2.29
2445 3014 0.538746 AAGGTCCAACCGGCGATTTT 60.539 50.000 9.30 0.00 44.90 1.82
2446 3015 0.538746 AAAGGTCCAACCGGCGATTT 60.539 50.000 9.30 0.00 44.90 2.17
2447 3016 0.538746 AAAAGGTCCAACCGGCGATT 60.539 50.000 9.30 0.00 44.90 3.34
2448 3017 0.538746 AAAAAGGTCCAACCGGCGAT 60.539 50.000 9.30 0.00 44.90 4.58
2449 3018 1.152922 AAAAAGGTCCAACCGGCGA 60.153 52.632 9.30 0.00 44.90 5.54
2450 3019 3.439008 AAAAAGGTCCAACCGGCG 58.561 55.556 0.00 0.00 44.90 6.46
2499 3068 4.722700 CCCAACCGCTCCCCAGTG 62.723 72.222 0.00 0.00 0.00 3.66
2517 3086 2.536997 TTTTCCCTAGCGCTGGAGCC 62.537 60.000 23.73 0.00 37.91 4.70
2518 3087 1.078426 TTTTCCCTAGCGCTGGAGC 60.078 57.895 23.73 0.00 37.78 4.70
2519 3088 1.092345 GCTTTTCCCTAGCGCTGGAG 61.092 60.000 23.73 9.63 30.91 3.86
2520 3089 1.078426 GCTTTTCCCTAGCGCTGGA 60.078 57.895 23.73 17.66 0.00 3.86
2521 3090 1.377202 TGCTTTTCCCTAGCGCTGG 60.377 57.895 22.90 18.68 41.54 4.85
2522 3091 1.796796 GTGCTTTTCCCTAGCGCTG 59.203 57.895 22.90 10.13 43.84 5.18
2523 3092 1.741770 CGTGCTTTTCCCTAGCGCT 60.742 57.895 17.26 17.26 44.75 5.92
2524 3093 2.785258 CGTGCTTTTCCCTAGCGC 59.215 61.111 0.00 0.00 43.78 5.92
2525 3094 2.750888 GGCGTGCTTTTCCCTAGCG 61.751 63.158 0.00 0.00 41.54 4.26
2526 3095 1.377333 AGGCGTGCTTTTCCCTAGC 60.377 57.895 0.00 0.00 39.10 3.42
2527 3096 1.026718 CCAGGCGTGCTTTTCCCTAG 61.027 60.000 0.00 0.00 0.00 3.02
2528 3097 1.002624 CCAGGCGTGCTTTTCCCTA 60.003 57.895 0.00 0.00 0.00 3.53
2529 3098 2.282462 CCAGGCGTGCTTTTCCCT 60.282 61.111 0.00 0.00 0.00 4.20
2530 3099 4.056125 GCCAGGCGTGCTTTTCCC 62.056 66.667 0.00 0.00 0.00 3.97
2531 3100 4.056125 GGCCAGGCGTGCTTTTCC 62.056 66.667 5.00 0.00 0.00 3.13
2532 3101 4.056125 GGGCCAGGCGTGCTTTTC 62.056 66.667 4.39 0.00 0.00 2.29
2533 3102 4.912395 TGGGCCAGGCGTGCTTTT 62.912 61.111 0.00 0.00 0.00 2.27
2542 3111 4.704833 CTGTCGGTGTGGGCCAGG 62.705 72.222 6.40 0.00 0.00 4.45
2543 3112 4.704833 CCTGTCGGTGTGGGCCAG 62.705 72.222 6.40 0.00 0.00 4.85
2547 3116 2.346284 TTTTCCCCTGTCGGTGTGGG 62.346 60.000 0.00 0.00 40.59 4.61
2548 3117 0.889186 CTTTTCCCCTGTCGGTGTGG 60.889 60.000 0.00 0.00 0.00 4.17
2549 3118 0.179029 ACTTTTCCCCTGTCGGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2550 3119 0.108019 GACTTTTCCCCTGTCGGTGT 59.892 55.000 0.00 0.00 0.00 4.16
2551 3120 0.107831 TGACTTTTCCCCTGTCGGTG 59.892 55.000 0.00 0.00 33.81 4.94
2552 3121 0.841289 TTGACTTTTCCCCTGTCGGT 59.159 50.000 0.00 0.00 33.81 4.69
2553 3122 1.523758 CTTGACTTTTCCCCTGTCGG 58.476 55.000 0.00 0.00 33.81 4.79
2554 3123 1.202770 ACCTTGACTTTTCCCCTGTCG 60.203 52.381 0.00 0.00 33.81 4.35
2555 3124 2.658807 ACCTTGACTTTTCCCCTGTC 57.341 50.000 0.00 0.00 0.00 3.51
2556 3125 3.398318 AAACCTTGACTTTTCCCCTGT 57.602 42.857 0.00 0.00 0.00 4.00
2557 3126 3.960755 AGAAAACCTTGACTTTTCCCCTG 59.039 43.478 0.00 0.00 38.05 4.45
2558 3127 4.265856 AGAAAACCTTGACTTTTCCCCT 57.734 40.909 0.00 0.00 38.05 4.79
2559 3128 4.202223 GGAAGAAAACCTTGACTTTTCCCC 60.202 45.833 0.00 0.00 38.05 4.81
2560 3129 4.202223 GGGAAGAAAACCTTGACTTTTCCC 60.202 45.833 3.46 3.46 43.91 3.97
2561 3130 4.202223 GGGGAAGAAAACCTTGACTTTTCC 60.202 45.833 0.00 0.00 38.05 3.13
2562 3131 4.202223 GGGGGAAGAAAACCTTGACTTTTC 60.202 45.833 0.00 0.00 37.73 2.29
2563 3132 3.709653 GGGGGAAGAAAACCTTGACTTTT 59.290 43.478 0.00 0.00 34.68 2.27
2564 3133 3.305720 GGGGGAAGAAAACCTTGACTTT 58.694 45.455 0.00 0.00 34.68 2.66
2565 3134 2.958818 GGGGGAAGAAAACCTTGACTT 58.041 47.619 0.00 0.00 34.68 3.01
2566 3135 2.677542 GGGGGAAGAAAACCTTGACT 57.322 50.000 0.00 0.00 34.68 3.41


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

AutoCloner maintained by Alex Coulton.