Multiple sequence alignment - TraesCS4D01G237100

Loading Multiple Alignment...

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 TraesCS4D01G237100 chr4D 100.000 7392 0 0 1 7392 399187338 399179947 0.000000e+00 13651.0
1 TraesCS4D01G237100 chr4B 94.731 2809 99 23 3869 6653 492217279 492214496 0.000000e+00 4322.0
2 TraesCS4D01G237100 chr4B 92.604 1609 59 22 3 1601 492222108 492220550 0.000000e+00 2257.0
3 TraesCS4D01G237100 chr4B 89.170 1662 119 29 2059 3683 492219219 492217582 0.000000e+00 2015.0
4 TraesCS4D01G237100 chr4B 84.876 767 86 20 6639 7391 492214473 492213723 0.000000e+00 747.0
5 TraesCS4D01G237100 chr4B 91.746 315 11 9 1688 1994 492220507 492220200 2.470000e-114 424.0
6 TraesCS4D01G237100 chr4B 90.674 193 15 3 3681 3870 492217505 492217313 3.420000e-63 254.0
7 TraesCS4D01G237100 chr4B 92.000 75 2 1 1997 2071 492219312 492219242 1.310000e-17 102.0
8 TraesCS4D01G237100 chr4A 90.945 2297 120 46 3871 6132 56504450 56502207 0.000000e+00 3009.0
9 TraesCS4D01G237100 chr4A 88.217 1290 91 30 1 1275 56508281 56507038 0.000000e+00 1483.0
10 TraesCS4D01G237100 chr4A 89.464 1063 91 15 2629 3683 56505795 56504746 0.000000e+00 1323.0
11 TraesCS4D01G237100 chr4A 90.598 819 46 16 1402 2197 56507041 56506231 0.000000e+00 1057.0
12 TraesCS4D01G237100 chr4A 87.689 528 35 17 6133 6654 56502081 56501578 8.260000e-164 588.0
13 TraesCS4D01G237100 chr4A 85.504 407 12 20 2232 2631 56506232 56505866 1.500000e-101 381.0
14 TraesCS4D01G237100 chr4A 90.052 191 16 2 3681 3870 56504671 56504483 2.060000e-60 244.0
15 TraesCS4D01G237100 chr4A 88.889 72 5 2 1279 1348 362483745 362483815 1.320000e-12 86.1


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 TraesCS4D01G237100 chr4D 399179947 399187338 7391 True 13651.000000 13651 100.000000 1 7392 1 chr4D.!!$R1 7391
1 TraesCS4D01G237100 chr4B 492213723 492222108 8385 True 1445.857143 4322 90.828714 3 7391 7 chr4B.!!$R1 7388
2 TraesCS4D01G237100 chr4A 56501578 56508281 6703 True 1155.000000 3009 88.924143 1 6654 7 chr4A.!!$R1 6653

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
915 976 0.178876 TCATTGACCACAGGGGGAGA 60.179 55.0 0.00 0.0 42.91 3.71 F
1967 2053 0.250640 CTCCCCACATATCTGCTGGC 60.251 60.0 0.00 0.0 0.00 4.85 F
3619 4759 0.250338 GCGTTTGACTTCTCCCAGGT 60.250 55.0 0.00 0.0 0.00 4.00 F
4387 5655 0.108186 TATTGACTGCCAGCTCCACG 60.108 55.0 0.00 0.0 0.00 4.94 F
5278 6559 0.669932 GTGACCAGTCTCTGCAGCAG 60.670 60.0 17.10 17.1 0.00 4.24 F
5866 7166 0.962356 CAGGCTGACCATTTCGCCTT 60.962 55.0 9.42 0.0 46.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2092 0.109723 TTTGCGGCCACCTTTCTACT 59.890 50.000 2.24 0.00 0.00 2.57 R
3749 4969 0.578683 CGATCACCAGTATGCGCAAG 59.421 55.000 17.11 4.69 43.44 4.01 R
4911 6185 1.711375 TCAGTACCACCTGGAGAGAGT 59.289 52.381 0.00 0.00 38.94 3.24 R
5842 7142 0.034670 GAAATGGTCAGCCTGCCTCT 60.035 55.000 6.71 0.00 35.27 3.69 R
6091 7397 0.602638 GTGTTGGATGCGGACAGACA 60.603 55.000 0.00 0.00 0.00 3.41 R
6934 8409 0.819259 ATTCGCCATGGTTCGGGATG 60.819 55.000 14.67 0.00 0.00 3.51 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
40 41 6.874134 CACTAAGTGTACCTAATATCATGGCC 59.126 42.308 0.00 0.00 0.00 5.36
295 355 9.276590 CATGATTCTATCACCTGCAGTATTTTA 57.723 33.333 13.81 0.00 43.01 1.52
296 356 8.893219 TGATTCTATCACCTGCAGTATTTTAG 57.107 34.615 13.81 7.21 33.59 1.85
297 357 8.704668 TGATTCTATCACCTGCAGTATTTTAGA 58.295 33.333 13.81 9.32 33.59 2.10
298 358 9.547753 GATTCTATCACCTGCAGTATTTTAGAA 57.452 33.333 13.81 16.53 0.00 2.10
300 360 8.893219 TCTATCACCTGCAGTATTTTAGAATG 57.107 34.615 13.81 0.00 0.00 2.67
301 361 8.486210 TCTATCACCTGCAGTATTTTAGAATGT 58.514 33.333 13.81 0.00 0.00 2.71
302 362 7.944729 ATCACCTGCAGTATTTTAGAATGTT 57.055 32.000 13.81 0.00 0.00 2.71
303 363 7.144722 TCACCTGCAGTATTTTAGAATGTTG 57.855 36.000 13.81 0.00 0.00 3.33
304 364 6.150976 TCACCTGCAGTATTTTAGAATGTTGG 59.849 38.462 13.81 0.00 0.00 3.77
305 365 6.150976 CACCTGCAGTATTTTAGAATGTTGGA 59.849 38.462 13.81 0.00 0.00 3.53
306 366 6.375455 ACCTGCAGTATTTTAGAATGTTGGAG 59.625 38.462 13.81 6.28 32.91 3.86
307 367 6.194796 TGCAGTATTTTAGAATGTTGGAGC 57.805 37.500 0.00 0.00 0.00 4.70
308 368 5.945784 TGCAGTATTTTAGAATGTTGGAGCT 59.054 36.000 0.00 0.00 0.00 4.09
309 369 6.434028 TGCAGTATTTTAGAATGTTGGAGCTT 59.566 34.615 0.00 0.00 0.00 3.74
310 370 7.609918 TGCAGTATTTTAGAATGTTGGAGCTTA 59.390 33.333 0.00 0.00 0.00 3.09
311 371 8.458843 GCAGTATTTTAGAATGTTGGAGCTTAA 58.541 33.333 0.00 0.00 0.00 1.85
319 379 7.396540 AGAATGTTGGAGCTTAATAGTTTGG 57.603 36.000 0.00 0.00 0.00 3.28
326 386 6.721318 TGGAGCTTAATAGTTTGGAGAATGT 58.279 36.000 0.00 0.00 0.00 2.71
327 387 7.857456 TGGAGCTTAATAGTTTGGAGAATGTA 58.143 34.615 0.00 0.00 0.00 2.29
342 402 8.090788 TGGAGAATGTAGGAGCTTAATAGTTT 57.909 34.615 0.00 0.00 0.00 2.66
387 447 3.665745 TTTCCTTGAATTGCTTCTGGC 57.334 42.857 0.00 0.00 42.22 4.85
422 482 3.758755 TGAGCCAGCTAATCAGGTATG 57.241 47.619 0.00 0.00 0.00 2.39
424 484 1.770658 AGCCAGCTAATCAGGTATGCA 59.229 47.619 0.00 0.00 33.76 3.96
471 531 7.813627 AGAGTAGTTTAATTTCTTGAGGACGAC 59.186 37.037 0.00 0.00 0.00 4.34
683 743 1.467713 GCTCCACTCGTAGTCGAAAGG 60.468 57.143 0.00 0.00 45.61 3.11
700 760 5.048364 TCGAAAGGTGGATGGTTATTTTGTG 60.048 40.000 0.00 0.00 0.00 3.33
703 763 3.511146 AGGTGGATGGTTATTTTGTGCAG 59.489 43.478 0.00 0.00 0.00 4.41
741 801 1.748122 CTCTGATGCTGTGTGCCCC 60.748 63.158 0.00 0.00 42.00 5.80
915 976 0.178876 TCATTGACCACAGGGGGAGA 60.179 55.000 0.00 0.00 42.91 3.71
1280 1342 0.958091 CCAGGAGATCTCGGTGCTAG 59.042 60.000 16.46 0.00 0.00 3.42
1287 1349 0.820074 ATCTCGGTGCTAGTCCCTCG 60.820 60.000 0.00 0.00 0.00 4.63
1309 1373 7.501225 CCTCGGTCCCATAATATTAGTGTTTTT 59.499 37.037 1.02 0.00 0.00 1.94
1313 1377 8.962679 GGTCCCATAATATTAGTGTTTTTGACA 58.037 33.333 1.02 0.00 35.42 3.58
1376 1440 6.260870 TGCTGTTACTTTTTCTGTCAAACA 57.739 33.333 0.00 0.00 0.00 2.83
1416 1480 1.597663 GCGTGTTGGCTATGTGTATCC 59.402 52.381 0.00 0.00 0.00 2.59
1432 1496 2.634815 ATCCATGTCATGCAGAGTCC 57.365 50.000 7.35 0.00 0.00 3.85
1462 1526 0.608130 TCAGTGCGGTTGTATCAGCT 59.392 50.000 0.00 0.00 0.00 4.24
1473 1539 4.082733 GGTTGTATCAGCTTCCTTTTGTCC 60.083 45.833 0.00 0.00 0.00 4.02
1474 1540 4.365514 TGTATCAGCTTCCTTTTGTCCA 57.634 40.909 0.00 0.00 0.00 4.02
1475 1541 4.326826 TGTATCAGCTTCCTTTTGTCCAG 58.673 43.478 0.00 0.00 0.00 3.86
1481 1547 5.363580 TCAGCTTCCTTTTGTCCAGAAAAAT 59.636 36.000 0.00 0.00 0.00 1.82
1492 1558 9.528018 TTTTGTCCAGAAAAATGTCTTTCATAC 57.472 29.630 0.00 0.00 37.70 2.39
1499 1565 8.177663 CAGAAAAATGTCTTTCATACGCATAGT 58.822 33.333 0.00 0.00 37.70 2.12
1519 1589 7.013655 GCATAGTATTTGTGTGGGAATCAGAAT 59.986 37.037 0.00 0.00 0.00 2.40
1567 1637 6.484977 AGAAATTTGTCAGTCTCACTTCCTTC 59.515 38.462 0.00 0.00 0.00 3.46
1572 1642 1.341531 CAGTCTCACTTCCTTCCGTGT 59.658 52.381 0.00 0.00 33.07 4.49
1574 1644 2.820787 AGTCTCACTTCCTTCCGTGTAG 59.179 50.000 0.00 0.00 33.07 2.74
1586 1660 9.211485 CTTCCTTCCGTGTAGAAGTTAAATTTA 57.789 33.333 0.00 0.00 41.45 1.40
1594 1668 8.875803 CGTGTAGAAGTTAAATTTATGCCAGTA 58.124 33.333 0.00 0.00 0.00 2.74
1607 1681 8.919777 ATTTATGCCAGTACTAAATCTTACCC 57.080 34.615 0.00 0.00 0.00 3.69
1610 1684 5.985911 TGCCAGTACTAAATCTTACCCTTC 58.014 41.667 0.00 0.00 0.00 3.46
1612 1686 5.598769 CCAGTACTAAATCTTACCCTTCCG 58.401 45.833 0.00 0.00 0.00 4.30
1787 1867 0.322816 ATGAAAGCCGGATGTGTGCT 60.323 50.000 5.05 0.00 36.79 4.40
1958 2044 1.384502 CCAGCTCCCTCCCCACATA 60.385 63.158 0.00 0.00 0.00 2.29
1959 2045 0.769776 CCAGCTCCCTCCCCACATAT 60.770 60.000 0.00 0.00 0.00 1.78
1960 2046 0.689623 CAGCTCCCTCCCCACATATC 59.310 60.000 0.00 0.00 0.00 1.63
1962 2048 0.689623 GCTCCCTCCCCACATATCTG 59.310 60.000 0.00 0.00 0.00 2.90
1964 2050 0.268869 TCCCTCCCCACATATCTGCT 59.731 55.000 0.00 0.00 0.00 4.24
1965 2051 0.399454 CCCTCCCCACATATCTGCTG 59.601 60.000 0.00 0.00 0.00 4.41
1966 2052 0.399454 CCTCCCCACATATCTGCTGG 59.601 60.000 0.00 0.00 0.00 4.85
1967 2053 0.250640 CTCCCCACATATCTGCTGGC 60.251 60.000 0.00 0.00 0.00 4.85
1968 2054 0.695462 TCCCCACATATCTGCTGGCT 60.695 55.000 0.00 0.00 0.00 4.75
2006 2092 3.540617 TCAAACAACAGCAGCAGTAGAA 58.459 40.909 0.00 0.00 0.00 2.10
2169 3178 5.418524 ACCATTGTTGCATTCTACAGCATAA 59.581 36.000 0.00 0.00 40.94 1.90
2170 3179 5.745294 CCATTGTTGCATTCTACAGCATAAC 59.255 40.000 0.00 0.00 40.94 1.89
2171 3180 5.956068 TTGTTGCATTCTACAGCATAACA 57.044 34.783 0.00 0.00 40.94 2.41
2172 3181 5.550232 TGTTGCATTCTACAGCATAACAG 57.450 39.130 0.00 0.00 40.94 3.16
2173 3182 4.395854 TGTTGCATTCTACAGCATAACAGG 59.604 41.667 0.00 0.00 40.94 4.00
2174 3183 4.220693 TGCATTCTACAGCATAACAGGT 57.779 40.909 0.00 0.00 35.51 4.00
2175 3184 5.351948 TGCATTCTACAGCATAACAGGTA 57.648 39.130 0.00 0.00 35.51 3.08
2176 3185 5.928976 TGCATTCTACAGCATAACAGGTAT 58.071 37.500 0.00 0.00 35.51 2.73
2177 3186 7.061566 TGCATTCTACAGCATAACAGGTATA 57.938 36.000 0.00 0.00 35.51 1.47
2185 3194 4.024556 CAGCATAACAGGTATAGTGCTTGC 60.025 45.833 0.00 0.00 40.60 4.01
2228 3250 1.202452 GGGCTAACCAAATGCTGATGC 60.202 52.381 0.00 0.00 39.85 3.91
2230 3252 1.401552 GCTAACCAAATGCTGATGCGA 59.598 47.619 0.00 0.00 43.34 5.10
2287 3309 6.037786 ACTTCTACTATTGCTTGTACTGCA 57.962 37.500 9.44 9.44 38.80 4.41
2288 3310 6.102663 ACTTCTACTATTGCTTGTACTGCAG 58.897 40.000 13.48 13.48 41.71 4.41
2289 3311 4.433615 TCTACTATTGCTTGTACTGCAGC 58.566 43.478 15.27 0.00 41.71 5.25
2290 3312 2.002586 ACTATTGCTTGTACTGCAGCG 58.997 47.619 15.27 0.00 41.71 5.18
2291 3313 1.328680 CTATTGCTTGTACTGCAGCGG 59.671 52.381 15.27 0.00 41.71 5.52
2294 3316 2.436646 CTTGTACTGCAGCGGGGG 60.437 66.667 15.27 0.00 0.00 5.40
2356 3390 4.021925 GTGGTGGCGCCCTTCTCT 62.022 66.667 26.77 0.00 36.04 3.10
2366 3400 2.614520 GCGCCCTTCTCTCCTTTTATTC 59.385 50.000 0.00 0.00 0.00 1.75
2368 3402 4.443034 GCGCCCTTCTCTCCTTTTATTCTA 60.443 45.833 0.00 0.00 0.00 2.10
2369 3403 5.671493 CGCCCTTCTCTCCTTTTATTCTAA 58.329 41.667 0.00 0.00 0.00 2.10
2379 3413 5.610791 TCCTTTTATTCTAACCTCCCTCCT 58.389 41.667 0.00 0.00 0.00 3.69
2465 3499 2.238084 TAGGCTGGTGAGACTGTGAT 57.762 50.000 0.00 0.00 38.42 3.06
2470 3504 2.417924 GCTGGTGAGACTGTGATAGTGG 60.418 54.545 0.00 0.00 40.53 4.00
2493 3527 1.948138 CAGGCAGCGCTAGTGATCG 60.948 63.158 10.99 0.00 0.00 3.69
2495 3529 1.226974 GGCAGCGCTAGTGATCGAA 60.227 57.895 10.99 0.00 0.00 3.71
2519 3562 3.011517 GGAGGAGCAGGGGAAGCA 61.012 66.667 0.00 0.00 0.00 3.91
2642 3758 6.206600 CAAGTAGTTTTGCATTTCAGCTTG 57.793 37.500 0.00 0.00 34.99 4.01
2703 3819 1.479709 GGAGGAGAGTGAGCTGCTTA 58.520 55.000 2.53 0.00 36.65 3.09
2712 3828 6.317391 GGAGAGTGAGCTGCTTACATATTTTT 59.683 38.462 23.96 3.87 0.00 1.94
2728 3844 7.872138 ACATATTTTTCCTCCTTCCATGAGTA 58.128 34.615 0.00 0.00 0.00 2.59
2834 3956 1.222936 CCCATGAGTGTCCTCTGCC 59.777 63.158 0.00 0.00 38.61 4.85
2838 3960 0.901124 ATGAGTGTCCTCTGCCTGTC 59.099 55.000 0.00 0.00 38.61 3.51
2932 4054 1.034292 GTGGCATCAGCTTTCTCCCC 61.034 60.000 0.00 0.00 41.70 4.81
2983 4105 5.732331 TTTTGACTCATGATATCCCCCTT 57.268 39.130 0.00 0.00 0.00 3.95
3000 4122 2.868583 CCCTTGATCTACACGCTCAATG 59.131 50.000 0.00 0.00 28.38 2.82
3027 4149 1.070445 TGGAACTTTTAACGCCTCCGA 59.930 47.619 0.00 0.00 38.29 4.55
3038 4161 3.077907 CCTCCGAGGCCCTTTTCA 58.922 61.111 0.18 0.00 0.00 2.69
3039 4162 1.609783 CCTCCGAGGCCCTTTTCAT 59.390 57.895 0.18 0.00 0.00 2.57
3040 4163 0.749454 CCTCCGAGGCCCTTTTCATG 60.749 60.000 0.18 0.00 0.00 3.07
3049 4172 1.341080 CCCTTTTCATGGCACCTTGT 58.659 50.000 0.00 0.00 0.00 3.16
3054 4177 2.885135 TTCATGGCACCTTGTCTGAT 57.115 45.000 0.00 0.00 0.00 2.90
3080 4203 2.234414 GGCTTCTCAATTTGGATTGCCA 59.766 45.455 17.25 0.00 41.94 4.92
3081 4204 3.118519 GGCTTCTCAATTTGGATTGCCAT 60.119 43.478 17.25 0.00 45.46 4.40
3083 4206 4.331717 GCTTCTCAATTTGGATTGCCATTG 59.668 41.667 0.00 0.00 45.46 2.82
3088 4211 7.098477 TCTCAATTTGGATTGCCATTGTTAAG 58.902 34.615 0.00 0.00 45.46 1.85
3103 4226 1.265905 GTTAAGGTTGTTCTGCACCGG 59.734 52.381 0.00 0.00 0.00 5.28
3104 4227 0.470766 TAAGGTTGTTCTGCACCGGT 59.529 50.000 0.00 0.00 0.00 5.28
3136 4266 1.265236 CTGAGTCTCAAGGCTCCTGT 58.735 55.000 9.05 0.00 0.00 4.00
3162 4292 5.448360 GCTTGTGTAAATTCAGCATCTCTCC 60.448 44.000 0.00 0.00 0.00 3.71
3163 4293 4.183865 TGTGTAAATTCAGCATCTCTCCG 58.816 43.478 0.00 0.00 0.00 4.63
3164 4294 4.184629 GTGTAAATTCAGCATCTCTCCGT 58.815 43.478 0.00 0.00 0.00 4.69
3165 4295 5.105513 TGTGTAAATTCAGCATCTCTCCGTA 60.106 40.000 0.00 0.00 0.00 4.02
3192 4325 4.892433 TCATTGTTCCGGCATCAAATTTT 58.108 34.783 0.00 0.00 0.00 1.82
3239 4372 3.511477 ACTCACTGTAAGGTGATGAGGT 58.489 45.455 4.71 0.00 43.94 3.85
3332 4465 6.563222 AATTTCTTCCATGGTTTGCATTTG 57.437 33.333 12.58 0.00 0.00 2.32
3401 4537 6.015603 TGGATCTGATTCTGTGATAGCTAGTG 60.016 42.308 0.00 0.00 0.00 2.74
3402 4538 5.781210 TCTGATTCTGTGATAGCTAGTGG 57.219 43.478 0.00 0.00 0.00 4.00
3403 4539 5.204292 TCTGATTCTGTGATAGCTAGTGGT 58.796 41.667 0.00 0.00 0.00 4.16
3438 4574 3.252458 ACATATACACTCGCATAGACGCA 59.748 43.478 0.00 0.00 0.00 5.24
3469 4605 1.671054 ACCCCATCGAACGCACTTG 60.671 57.895 0.00 0.00 0.00 3.16
3513 4650 7.141758 ACATGATTTGTGTATAGACCAGGAT 57.858 36.000 0.00 0.00 37.11 3.24
3564 4702 2.481441 TCAGTCTGGGCATCTTGGTAT 58.519 47.619 0.00 0.00 0.00 2.73
3595 4733 6.349611 CCAAGTGGTGAGGTAATTCTTGAATG 60.350 42.308 0.00 0.00 34.62 2.67
3603 4741 5.437060 AGGTAATTCTTGAATGTATGGCGT 58.563 37.500 0.00 0.00 0.00 5.68
3611 4751 4.678509 TGAATGTATGGCGTTTGACTTC 57.321 40.909 0.00 0.00 0.00 3.01
3616 4756 0.400213 ATGGCGTTTGACTTCTCCCA 59.600 50.000 0.00 0.00 0.00 4.37
3618 4758 0.955919 GGCGTTTGACTTCTCCCAGG 60.956 60.000 0.00 0.00 0.00 4.45
3619 4759 0.250338 GCGTTTGACTTCTCCCAGGT 60.250 55.000 0.00 0.00 0.00 4.00
3624 4764 1.056660 TGACTTCTCCCAGGTTCCAC 58.943 55.000 0.00 0.00 0.00 4.02
3664 4804 4.800471 GCTTTTCACTTGCAATATGCCTAC 59.200 41.667 0.00 0.00 44.23 3.18
3713 4933 3.579147 TTATTTCGCGAGGCAAATACG 57.421 42.857 9.59 0.00 29.10 3.06
3715 4935 1.647346 TTTCGCGAGGCAAATACGAT 58.353 45.000 9.59 0.00 32.13 3.73
3768 4988 0.578683 CTTGCGCATACTGGTGATCG 59.421 55.000 12.75 0.00 0.00 3.69
3786 5006 7.860373 TGGTGATCGAAGTTTTAAAACAATGAG 59.140 33.333 28.03 16.06 41.30 2.90
3820 5040 4.836125 AATGTGACTCATGTTTGTGGAC 57.164 40.909 0.00 0.00 36.81 4.02
4097 5356 2.515071 GGCATCTGATCCTCGGGCT 61.515 63.158 0.00 0.00 0.00 5.19
4136 5395 6.231211 CAGTACCACCAACTGTAAAATCTCT 58.769 40.000 0.00 0.00 39.61 3.10
4387 5655 0.108186 TATTGACTGCCAGCTCCACG 60.108 55.000 0.00 0.00 0.00 4.94
4475 5743 2.288186 GCAATTTAGAAGGCTAGGCGTC 59.712 50.000 21.93 21.93 0.00 5.19
4476 5744 2.872858 CAATTTAGAAGGCTAGGCGTCC 59.127 50.000 24.86 12.01 0.00 4.79
4477 5745 1.861982 TTTAGAAGGCTAGGCGTCCT 58.138 50.000 24.86 17.68 37.71 3.85
4478 5746 1.400737 TTAGAAGGCTAGGCGTCCTC 58.599 55.000 24.86 13.77 34.61 3.71
5007 6286 4.070552 GGCGAGGGCAGTTCGACT 62.071 66.667 9.06 0.00 42.69 4.18
5137 6418 1.552337 GGTGCCATGTCTCAGAGAGAA 59.448 52.381 0.00 0.00 40.59 2.87
5278 6559 0.669932 GTGACCAGTCTCTGCAGCAG 60.670 60.000 17.10 17.10 0.00 4.24
5297 6578 2.719739 AGCATAATTGACAGTGCTGCT 58.280 42.857 0.00 4.44 45.44 4.24
5298 6579 2.422479 AGCATAATTGACAGTGCTGCTG 59.578 45.455 0.00 7.20 45.44 4.41
5412 6711 2.270205 CTCGTCCCAGGCTGCAAT 59.730 61.111 9.56 0.00 0.00 3.56
5419 6718 1.211949 TCCCAGGCTGCAATAAGGTAC 59.788 52.381 9.56 0.00 0.00 3.34
5421 6720 2.438021 CCCAGGCTGCAATAAGGTACTA 59.562 50.000 9.56 0.00 38.49 1.82
5438 6737 6.286758 AGGTACTATCAACATCATCAGCAAG 58.713 40.000 0.00 0.00 36.02 4.01
5441 6740 4.880120 ACTATCAACATCATCAGCAAGTGG 59.120 41.667 0.00 0.00 0.00 4.00
5451 6750 6.899393 TCATCAGCAAGTGGAAATTTACTT 57.101 33.333 1.27 1.26 37.61 2.24
5455 6754 6.205784 TCAGCAAGTGGAAATTTACTTTTCG 58.794 36.000 1.27 0.00 36.63 3.46
5456 6755 4.982295 AGCAAGTGGAAATTTACTTTTCGC 59.018 37.500 1.27 4.64 36.63 4.70
5457 6756 4.982295 GCAAGTGGAAATTTACTTTTCGCT 59.018 37.500 1.27 0.00 43.63 4.93
5458 6757 5.117135 GCAAGTGGAAATTTACTTTTCGCTC 59.883 40.000 1.27 0.00 41.42 5.03
5459 6758 5.030874 AGTGGAAATTTACTTTTCGCTCG 57.969 39.130 1.27 0.00 38.56 5.03
5460 6759 4.514066 AGTGGAAATTTACTTTTCGCTCGT 59.486 37.500 1.27 0.00 38.56 4.18
5462 6761 6.203338 AGTGGAAATTTACTTTTCGCTCGTAA 59.797 34.615 1.27 0.00 38.56 3.18
5463 6762 6.852345 GTGGAAATTTACTTTTCGCTCGTAAA 59.148 34.615 1.27 0.00 36.63 2.01
5464 6763 7.059147 GTGGAAATTTACTTTTCGCTCGTAAAG 59.941 37.037 16.16 16.16 36.79 1.85
5465 6764 7.073883 GGAAATTTACTTTTCGCTCGTAAAGT 58.926 34.615 23.19 23.19 44.12 2.66
5466 6765 7.267811 GGAAATTTACTTTTCGCTCGTAAAGTC 59.732 37.037 23.29 12.35 42.10 3.01
5484 6783 6.740411 AAAGTCTTCAGAGATTTGCTCATC 57.260 37.500 0.00 0.00 46.45 2.92
5489 6788 6.478344 GTCTTCAGAGATTTGCTCATCGTAAT 59.522 38.462 0.00 0.00 46.45 1.89
5493 6792 6.870439 TCAGAGATTTGCTCATCGTAATATGG 59.130 38.462 0.00 0.00 46.45 2.74
5507 6806 9.280174 CATCGTAATATGGTTATGGGTTTACTT 57.720 33.333 0.00 0.00 0.00 2.24
5521 6820 5.481473 TGGGTTTACTTACTCTAACCGATGT 59.519 40.000 0.00 0.00 40.71 3.06
5616 6915 3.003113 GCGGCAGGTCGAGGTAAGT 62.003 63.158 0.00 0.00 0.00 2.24
5639 6938 7.054124 AGTACACTGAAACAGATTCCTCAAAA 58.946 34.615 5.76 0.00 37.22 2.44
5652 6951 7.821359 CAGATTCCTCAAAAATCACTCACTCTA 59.179 37.037 0.00 0.00 35.92 2.43
5653 6952 8.040132 AGATTCCTCAAAAATCACTCACTCTAG 58.960 37.037 0.00 0.00 35.92 2.43
5654 6953 6.042638 TCCTCAAAAATCACTCACTCTAGG 57.957 41.667 0.00 0.00 0.00 3.02
5655 6954 5.046304 TCCTCAAAAATCACTCACTCTAGGG 60.046 44.000 0.00 0.00 0.00 3.53
5657 6956 5.794894 TCAAAAATCACTCACTCTAGGGTC 58.205 41.667 0.00 0.00 0.00 4.46
5658 6957 5.544176 TCAAAAATCACTCACTCTAGGGTCT 59.456 40.000 0.00 0.00 0.00 3.85
5659 6958 6.724441 TCAAAAATCACTCACTCTAGGGTCTA 59.276 38.462 0.00 0.00 0.00 2.59
5803 7103 5.296151 TGGAGACTCTGAACAACAAAGAT 57.704 39.130 1.74 0.00 0.00 2.40
5805 7105 4.693095 GGAGACTCTGAACAACAAAGATCC 59.307 45.833 1.74 0.00 0.00 3.36
5820 7120 8.514594 CAACAAAGATCCCGCATATGTTTATAT 58.485 33.333 4.29 0.00 0.00 0.86
5842 7142 6.811253 ATACTGTTAAAAACATTCCTCGCA 57.189 33.333 0.00 0.00 41.26 5.10
5843 7143 5.108385 ACTGTTAAAAACATTCCTCGCAG 57.892 39.130 0.00 0.00 41.26 5.18
5844 7144 4.819630 ACTGTTAAAAACATTCCTCGCAGA 59.180 37.500 0.00 0.00 41.26 4.26
5845 7145 5.356882 TGTTAAAAACATTCCTCGCAGAG 57.643 39.130 0.00 0.00 45.59 3.35
5866 7166 0.962356 CAGGCTGACCATTTCGCCTT 60.962 55.000 9.42 0.00 46.00 4.35
5874 7180 1.296056 CCATTTCGCCTTCGGTTCGT 61.296 55.000 0.00 0.00 36.13 3.85
6038 7344 2.310538 GGATCATCATCCCAAACCACC 58.689 52.381 0.00 0.00 42.91 4.61
6061 7367 1.331756 GCAAGTGTTCATATGGCGAGG 59.668 52.381 2.13 0.00 0.00 4.63
6091 7397 1.675641 GCTGTCTGCGTTTCCCCAT 60.676 57.895 0.00 0.00 0.00 4.00
6099 7405 1.305930 GCGTTTCCCCATGTCTGTCC 61.306 60.000 0.00 0.00 0.00 4.02
6223 7654 0.467290 ACTTGGCAATGTTGGTCCGT 60.467 50.000 0.00 0.00 0.00 4.69
6583 8020 0.909133 TGATGTGCCTGCCTGGACTA 60.909 55.000 0.00 0.00 38.35 2.59
6677 8151 4.241590 TCATCAAAACTTGCCATGTGTC 57.758 40.909 0.00 0.00 0.00 3.67
6684 8158 0.729116 CTTGCCATGTGTCGATGGAC 59.271 55.000 6.97 0.12 45.24 4.02
6708 8182 7.441836 ACAATTCCAAACCTTACCATCTTTTC 58.558 34.615 0.00 0.00 0.00 2.29
6716 8190 9.546428 CAAACCTTACCATCTTTTCAAAAGAAT 57.454 29.630 16.52 8.04 0.00 2.40
6737 8211 7.915930 AGAATACAATCCTTATCTCTCCCATG 58.084 38.462 0.00 0.00 0.00 3.66
6741 8215 3.051940 TCCTTATCTCTCCCATGTGCT 57.948 47.619 0.00 0.00 0.00 4.40
6744 8218 3.494048 CCTTATCTCTCCCATGTGCTCAC 60.494 52.174 0.00 0.00 0.00 3.51
6750 8224 2.234661 TCTCCCATGTGCTCACTACAAG 59.765 50.000 1.47 0.00 0.00 3.16
6788 8262 8.237811 AGTTTCCATGTGTTTTTAGAGAACAT 57.762 30.769 0.00 0.00 39.03 2.71
6789 8263 8.695456 AGTTTCCATGTGTTTTTAGAGAACATT 58.305 29.630 0.00 0.00 39.03 2.71
6816 8290 7.552050 TTCTTAAAATTTCCCATGTGTCCAT 57.448 32.000 0.00 0.00 0.00 3.41
6832 8306 8.723311 CATGTGTCCATTTGCAAATTCTTAAAT 58.277 29.630 21.95 9.56 0.00 1.40
6833 8307 9.941325 ATGTGTCCATTTGCAAATTCTTAAATA 57.059 25.926 21.95 5.72 0.00 1.40
6868 8343 7.095910 CACATTTGCCATGATTTACAAAGGTA 58.904 34.615 4.58 0.00 42.90 3.08
6879 8354 8.545229 TGATTTACAAAGGTATTTTTGCCATG 57.455 30.769 0.00 0.00 40.80 3.66
6880 8355 8.370940 TGATTTACAAAGGTATTTTTGCCATGA 58.629 29.630 0.00 0.00 40.80 3.07
6882 8357 9.737844 ATTTACAAAGGTATTTTTGCCATGATT 57.262 25.926 0.00 0.00 40.80 2.57
6913 8388 8.916628 AACCATGGCAAATTTATGTTTACTTT 57.083 26.923 13.04 0.00 0.00 2.66
6934 8409 7.836842 ACTTTATGGACCATGACAAATTTACC 58.163 34.615 17.73 0.00 0.00 2.85
6937 8412 5.913137 TGGACCATGACAAATTTACCATC 57.087 39.130 0.00 0.00 0.00 3.51
6938 8413 4.709397 TGGACCATGACAAATTTACCATCC 59.291 41.667 0.00 0.00 0.00 3.51
6973 8448 5.507315 CGAATTTACTTTATGGGACCATGGC 60.507 44.000 13.04 4.47 37.82 4.40
6980 8455 2.250921 ATGGGACCATGGCAATTTCA 57.749 45.000 13.04 2.43 35.03 2.69
6981 8456 2.021262 TGGGACCATGGCAATTTCAA 57.979 45.000 13.04 0.00 0.00 2.69
6988 8463 4.983053 ACCATGGCAATTTCAATTTTGGA 58.017 34.783 13.04 0.00 0.00 3.53
6989 8464 4.761227 ACCATGGCAATTTCAATTTTGGAC 59.239 37.500 13.04 0.00 0.00 4.02
6991 8466 4.428294 TGGCAATTTCAATTTTGGACCA 57.572 36.364 0.00 0.00 0.00 4.02
6992 8467 4.133078 TGGCAATTTCAATTTTGGACCAC 58.867 39.130 0.00 0.00 0.00 4.16
6993 8468 4.133078 GGCAATTTCAATTTTGGACCACA 58.867 39.130 0.00 0.00 0.00 4.17
6995 8470 5.067023 GGCAATTTCAATTTTGGACCACAAA 59.933 36.000 0.00 0.00 46.82 2.83
7014 8489 9.620259 ACCACAAAACATATTTACCAAACAATT 57.380 25.926 0.00 0.00 0.00 2.32
7060 8535 9.868277 TGGACAATTTATATTTTGGAACATGTC 57.132 29.630 0.00 0.00 39.30 3.06
7094 8569 6.302269 ACCATGGCAAATTTTACATTTGGAA 58.698 32.000 13.04 0.00 38.91 3.53
7095 8570 6.206438 ACCATGGCAAATTTTACATTTGGAAC 59.794 34.615 13.04 0.00 38.91 3.62
7111 8586 9.328845 ACATTTGGAACATGGCAAATTTATATC 57.671 29.630 0.00 0.00 39.30 1.63
7146 8621 9.884636 GGCAAATTTACTTTTTAATCCTATGGT 57.115 29.630 0.00 0.00 0.00 3.55
7169 8644 6.315144 GGTAAATTTATTTGTTGGACCATGGC 59.685 38.462 13.04 4.47 0.00 4.40
7215 8692 9.730420 GCAATTTTATTAACTACACCATGGTAG 57.270 33.333 19.28 15.28 44.97 3.18
7238 8715 5.951747 AGTTTTATTGTAGGTCACATGGCAT 59.048 36.000 0.00 0.00 36.90 4.40
7247 8724 6.765989 TGTAGGTCACATGGCATTTCTATTAC 59.234 38.462 0.00 0.00 30.04 1.89
7248 8725 6.006275 AGGTCACATGGCATTTCTATTACT 57.994 37.500 0.00 0.00 0.00 2.24
7259 8736 9.502091 TGGCATTTCTATTACTTATACCATGAC 57.498 33.333 0.00 0.00 0.00 3.06
7305 8785 9.709495 TGGCAATTTTATTAATTAGATCATGGC 57.291 29.630 0.00 0.00 0.00 4.40
7325 8805 8.934825 TCATGGCAGTTTATTTTCTTAATTTGC 58.065 29.630 0.00 0.00 0.00 3.68
7330 8810 8.177013 GCAGTTTATTTTCTTAATTTGCCATGG 58.823 33.333 7.63 7.63 0.00 3.66
7334 8814 9.950496 TTTATTTTCTTAATTTGCCATGGCTAA 57.050 25.926 35.53 33.21 42.51 3.09
7391 8875 6.687604 AGTTTTTGCCATTTACCATAGTGAC 58.312 36.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.821546 TGTCGTGAACAACCTCTGAAG 58.178 47.619 0.00 0.00 34.03 3.02
295 355 7.175104 TCCAAACTATTAAGCTCCAACATTCT 58.825 34.615 0.00 0.00 0.00 2.40
296 356 7.336931 TCTCCAAACTATTAAGCTCCAACATTC 59.663 37.037 0.00 0.00 0.00 2.67
297 357 7.175104 TCTCCAAACTATTAAGCTCCAACATT 58.825 34.615 0.00 0.00 0.00 2.71
298 358 6.721318 TCTCCAAACTATTAAGCTCCAACAT 58.279 36.000 0.00 0.00 0.00 2.71
299 359 6.121776 TCTCCAAACTATTAAGCTCCAACA 57.878 37.500 0.00 0.00 0.00 3.33
300 360 7.121315 ACATTCTCCAAACTATTAAGCTCCAAC 59.879 37.037 0.00 0.00 0.00 3.77
301 361 7.175104 ACATTCTCCAAACTATTAAGCTCCAA 58.825 34.615 0.00 0.00 0.00 3.53
302 362 6.721318 ACATTCTCCAAACTATTAAGCTCCA 58.279 36.000 0.00 0.00 0.00 3.86
303 363 7.442666 CCTACATTCTCCAAACTATTAAGCTCC 59.557 40.741 0.00 0.00 0.00 4.70
304 364 8.204836 TCCTACATTCTCCAAACTATTAAGCTC 58.795 37.037 0.00 0.00 0.00 4.09
305 365 8.090788 TCCTACATTCTCCAAACTATTAAGCT 57.909 34.615 0.00 0.00 0.00 3.74
306 366 7.041712 GCTCCTACATTCTCCAAACTATTAAGC 60.042 40.741 0.00 0.00 0.00 3.09
307 367 8.207545 AGCTCCTACATTCTCCAAACTATTAAG 58.792 37.037 0.00 0.00 0.00 1.85
308 368 8.090788 AGCTCCTACATTCTCCAAACTATTAA 57.909 34.615 0.00 0.00 0.00 1.40
309 369 7.676683 AGCTCCTACATTCTCCAAACTATTA 57.323 36.000 0.00 0.00 0.00 0.98
310 370 6.567602 AGCTCCTACATTCTCCAAACTATT 57.432 37.500 0.00 0.00 0.00 1.73
311 371 6.567602 AAGCTCCTACATTCTCCAAACTAT 57.432 37.500 0.00 0.00 0.00 2.12
312 372 7.490657 TTAAGCTCCTACATTCTCCAAACTA 57.509 36.000 0.00 0.00 0.00 2.24
313 373 4.917906 AAGCTCCTACATTCTCCAAACT 57.082 40.909 0.00 0.00 0.00 2.66
314 374 7.988028 ACTATTAAGCTCCTACATTCTCCAAAC 59.012 37.037 0.00 0.00 0.00 2.93
315 375 8.090788 ACTATTAAGCTCCTACATTCTCCAAA 57.909 34.615 0.00 0.00 0.00 3.28
316 376 7.676683 ACTATTAAGCTCCTACATTCTCCAA 57.323 36.000 0.00 0.00 0.00 3.53
317 377 7.676683 AACTATTAAGCTCCTACATTCTCCA 57.323 36.000 0.00 0.00 0.00 3.86
318 378 7.442666 CCAAACTATTAAGCTCCTACATTCTCC 59.557 40.741 0.00 0.00 0.00 3.71
319 379 8.204836 TCCAAACTATTAAGCTCCTACATTCTC 58.795 37.037 0.00 0.00 0.00 2.87
326 386 8.060075 ACTCTAGTCCAAACTATTAAGCTCCTA 58.940 37.037 0.00 0.00 37.36 2.94
327 387 6.898521 ACTCTAGTCCAAACTATTAAGCTCCT 59.101 38.462 0.00 0.00 37.36 3.69
342 402 6.849151 TGGTATGATAGCTAACTCTAGTCCA 58.151 40.000 0.00 0.00 0.00 4.02
387 447 3.666274 TGGCTCATTTGGAAGCATTTTG 58.334 40.909 0.00 0.00 0.00 2.44
468 528 5.077134 TGCATATTCTCCTCCATATGTCG 57.923 43.478 1.24 0.00 36.23 4.35
471 531 7.443477 CCTCTATGCATATTCTCCTCCATATG 58.557 42.308 6.92 0.00 36.71 1.78
594 654 9.646427 GAGTAAGCTTATGGATACCAAGAATAG 57.354 37.037 9.88 0.00 36.95 1.73
672 732 3.329929 AACCATCCACCTTTCGACTAC 57.670 47.619 0.00 0.00 0.00 2.73
683 743 3.258123 ACCTGCACAAAATAACCATCCAC 59.742 43.478 0.00 0.00 0.00 4.02
700 760 5.126061 AGTTTCATGGTTTCATATGACCTGC 59.874 40.000 4.48 0.00 36.86 4.85
703 763 6.599244 TCAGAGTTTCATGGTTTCATATGACC 59.401 38.462 4.48 5.75 33.36 4.02
741 801 7.615582 TTTACAGGTCTAAGCAAATGATGAG 57.384 36.000 0.00 0.00 0.00 2.90
1280 1342 4.776308 ACTAATATTATGGGACCGAGGGAC 59.224 45.833 0.00 0.00 0.00 4.46
1287 1349 8.962679 TGTCAAAAACACTAATATTATGGGACC 58.037 33.333 0.00 0.00 31.20 4.46
1376 1440 3.066760 CGCCAGAAGAACCAGAAAACTTT 59.933 43.478 0.00 0.00 0.00 2.66
1384 1448 0.588252 CAACACGCCAGAAGAACCAG 59.412 55.000 0.00 0.00 0.00 4.00
1416 1480 0.812811 CCCGGACTCTGCATGACATG 60.813 60.000 11.27 11.27 0.00 3.21
1432 1496 2.173669 CGCACTGAGCCAATACCCG 61.174 63.158 0.00 0.00 41.38 5.28
1462 1526 6.790232 AGACATTTTTCTGGACAAAAGGAA 57.210 33.333 0.00 0.00 31.07 3.36
1473 1539 8.177663 ACTATGCGTATGAAAGACATTTTTCTG 58.822 33.333 0.00 0.00 40.07 3.02
1474 1540 8.268850 ACTATGCGTATGAAAGACATTTTTCT 57.731 30.769 0.00 0.00 40.07 2.52
1481 1547 7.547722 ACACAAATACTATGCGTATGAAAGACA 59.452 33.333 0.00 0.00 38.78 3.41
1492 1558 4.574421 TGATTCCCACACAAATACTATGCG 59.426 41.667 0.00 0.00 0.00 4.73
1546 1616 4.646572 GGAAGGAAGTGAGACTGACAAAT 58.353 43.478 0.00 0.00 0.00 2.32
1560 1630 7.668525 AATTTAACTTCTACACGGAAGGAAG 57.331 36.000 8.71 6.53 44.82 3.46
1567 1637 7.079182 TGGCATAAATTTAACTTCTACACGG 57.921 36.000 1.21 0.00 0.00 4.94
1586 1660 6.409349 GGAAGGGTAAGATTTAGTACTGGCAT 60.409 42.308 5.39 0.00 0.00 4.40
1594 1668 6.370186 AAGAACGGAAGGGTAAGATTTAGT 57.630 37.500 0.00 0.00 0.00 2.24
1623 1703 1.568612 ATGTCAGGTTCAGCAACGCG 61.569 55.000 3.53 3.53 32.68 6.01
2006 2092 0.109723 TTTGCGGCCACCTTTCTACT 59.890 50.000 2.24 0.00 0.00 2.57
2169 3178 1.210478 CCCAGCAAGCACTATACCTGT 59.790 52.381 0.00 0.00 0.00 4.00
2170 3179 1.475751 CCCCAGCAAGCACTATACCTG 60.476 57.143 0.00 0.00 0.00 4.00
2171 3180 0.839946 CCCCAGCAAGCACTATACCT 59.160 55.000 0.00 0.00 0.00 3.08
2172 3181 0.819666 GCCCCAGCAAGCACTATACC 60.820 60.000 0.00 0.00 39.53 2.73
2173 3182 2.707902 GCCCCAGCAAGCACTATAC 58.292 57.895 0.00 0.00 39.53 1.47
2185 3194 1.079073 ATTTTGGACCCTGCCCCAG 59.921 57.895 0.00 0.00 33.43 4.45
2196 3205 0.968393 GTTAGCCCGCCCATTTTGGA 60.968 55.000 0.00 0.00 40.96 3.53
2228 3250 1.066858 ACAGGACCAGTTGCATACTCG 60.067 52.381 0.00 0.00 33.85 4.18
2230 3252 2.903784 TGTACAGGACCAGTTGCATACT 59.096 45.455 0.00 0.00 37.68 2.12
2241 3263 0.971386 TCCCGTTTCTGTACAGGACC 59.029 55.000 22.48 5.77 0.00 4.46
2291 3313 1.191535 GCCCTTGTTTTATGACCCCC 58.808 55.000 0.00 0.00 0.00 5.40
2294 3316 1.135402 CAGCGCCCTTGTTTTATGACC 60.135 52.381 2.29 0.00 0.00 4.02
2356 3390 5.610791 AGGAGGGAGGTTAGAATAAAAGGA 58.389 41.667 0.00 0.00 0.00 3.36
2366 3400 1.710816 CTGGCTAGGAGGGAGGTTAG 58.289 60.000 0.00 0.00 0.00 2.34
2368 3402 1.690985 GCTGGCTAGGAGGGAGGTT 60.691 63.158 0.00 0.00 0.00 3.50
2369 3403 2.041405 GCTGGCTAGGAGGGAGGT 60.041 66.667 0.00 0.00 0.00 3.85
2465 3499 2.665000 GCTGCCTGCAGTCCACTA 59.335 61.111 19.45 0.00 45.24 2.74
2470 3504 2.889503 CTAGCGCTGCCTGCAGTC 60.890 66.667 22.90 12.01 45.24 3.51
2493 3527 1.209261 CCCTGCTCCTCCTCTTCTTTC 59.791 57.143 0.00 0.00 0.00 2.62
2495 3529 0.620121 CCCCTGCTCCTCCTCTTCTT 60.620 60.000 0.00 0.00 0.00 2.52
2557 3600 3.067742 GCATCAATGGAGGTGAGGAAATG 59.932 47.826 0.00 0.00 0.00 2.32
2560 3603 1.918262 AGCATCAATGGAGGTGAGGAA 59.082 47.619 0.00 0.00 0.00 3.36
2642 3758 1.663695 AATGTACTGCCGGTATGCAC 58.336 50.000 1.90 0.00 36.04 4.57
2834 3956 2.625737 CCCATGTTACTGCTGAGACAG 58.374 52.381 0.00 3.00 43.59 3.51
2838 3960 2.048444 ATGCCCATGTTACTGCTGAG 57.952 50.000 0.00 0.00 0.00 3.35
2932 4054 2.125269 AAGCCCCGAAATCGTCCG 60.125 61.111 1.79 0.00 37.74 4.79
2983 4105 4.183865 CCTTTCATTGAGCGTGTAGATCA 58.816 43.478 0.00 0.00 44.44 2.92
3000 4122 3.551454 GGCGTTAAAAGTTCCACCCTTTC 60.551 47.826 0.00 0.00 31.11 2.62
3035 4158 2.885135 ATCAGACAAGGTGCCATGAA 57.115 45.000 0.00 0.00 0.00 2.57
3038 4161 3.007182 CCAAAAATCAGACAAGGTGCCAT 59.993 43.478 0.00 0.00 0.00 4.40
3039 4162 2.364970 CCAAAAATCAGACAAGGTGCCA 59.635 45.455 0.00 0.00 0.00 4.92
3040 4163 2.867647 GCCAAAAATCAGACAAGGTGCC 60.868 50.000 0.00 0.00 0.00 5.01
3044 4167 4.279169 TGAGAAGCCAAAAATCAGACAAGG 59.721 41.667 0.00 0.00 0.00 3.61
3049 4172 6.041865 TCCAAATTGAGAAGCCAAAAATCAGA 59.958 34.615 0.00 0.00 0.00 3.27
3054 4177 5.239087 GCAATCCAAATTGAGAAGCCAAAAA 59.761 36.000 0.00 0.00 44.25 1.94
3080 4203 3.004315 CGGTGCAGAACAACCTTAACAAT 59.996 43.478 0.00 0.00 29.21 2.71
3081 4204 2.356382 CGGTGCAGAACAACCTTAACAA 59.644 45.455 0.00 0.00 29.21 2.83
3083 4206 1.265905 CCGGTGCAGAACAACCTTAAC 59.734 52.381 0.00 0.00 29.21 2.01
3088 4211 1.525077 TCACCGGTGCAGAACAACC 60.525 57.895 30.25 0.00 29.21 3.77
3136 4266 6.409704 AGAGATGCTGAATTTACACAAGCTA 58.590 36.000 0.00 0.00 0.00 3.32
3162 4292 2.611751 TGCCGGAACAATGAATGATACG 59.388 45.455 5.05 0.00 0.00 3.06
3163 4293 4.275689 TGATGCCGGAACAATGAATGATAC 59.724 41.667 5.05 0.00 0.00 2.24
3164 4294 4.459330 TGATGCCGGAACAATGAATGATA 58.541 39.130 5.05 0.00 0.00 2.15
3165 4295 3.289836 TGATGCCGGAACAATGAATGAT 58.710 40.909 5.05 0.00 0.00 2.45
3239 4372 3.878086 ACTAGTGAAAAAGGGGAGGGTA 58.122 45.455 0.00 0.00 0.00 3.69
3251 4384 3.756933 AGCCGGTTGTTACTAGTGAAA 57.243 42.857 5.39 0.00 0.00 2.69
3253 4386 3.828451 ACTTAGCCGGTTGTTACTAGTGA 59.172 43.478 5.39 0.00 0.00 3.41
3332 4465 1.264288 CTCCTGCGTGTTCTGGAAAAC 59.736 52.381 0.00 0.00 34.35 2.43
3418 4554 4.703645 ATGCGTCTATGCGAGTGTATAT 57.296 40.909 0.00 0.00 37.81 0.86
3438 4574 2.749466 CGATGGGGTGGATGCAAACTAT 60.749 50.000 0.00 0.00 0.00 2.12
3469 4605 0.992802 GTTCGACATGAGAACTCCGC 59.007 55.000 22.23 5.18 43.24 5.54
3511 4648 7.989741 TCCTCTTTTCTTCCATCACAATCTATC 59.010 37.037 0.00 0.00 0.00 2.08
3513 4650 7.038017 AGTCCTCTTTTCTTCCATCACAATCTA 60.038 37.037 0.00 0.00 0.00 1.98
3595 4733 2.007608 GGGAGAAGTCAAACGCCATAC 58.992 52.381 0.00 0.00 0.00 2.39
3603 4741 2.131854 TGGAACCTGGGAGAAGTCAAA 58.868 47.619 0.00 0.00 0.00 2.69
3611 4751 1.302832 GTGCAGTGGAACCTGGGAG 60.303 63.158 0.00 0.00 37.80 4.30
3616 4756 2.071778 AACATTGTGCAGTGGAACCT 57.928 45.000 0.00 0.00 37.80 3.50
3618 4758 1.860326 GCAAACATTGTGCAGTGGAAC 59.140 47.619 0.00 0.00 41.80 3.62
3619 4759 1.755959 AGCAAACATTGTGCAGTGGAA 59.244 42.857 0.00 0.00 44.74 3.53
3624 4764 3.293311 AAGCTAGCAAACATTGTGCAG 57.707 42.857 18.83 0.24 44.74 4.41
3680 4820 8.870879 GCCTCGCGAAATAATTCTAAGTTATAT 58.129 33.333 11.33 0.00 33.17 0.86
3681 4821 7.868922 TGCCTCGCGAAATAATTCTAAGTTATA 59.131 33.333 11.33 0.00 33.17 0.98
3682 4822 6.704493 TGCCTCGCGAAATAATTCTAAGTTAT 59.296 34.615 11.33 0.00 33.17 1.89
3684 4824 4.873827 TGCCTCGCGAAATAATTCTAAGTT 59.126 37.500 11.33 0.00 33.17 2.66
3685 4825 4.439057 TGCCTCGCGAAATAATTCTAAGT 58.561 39.130 11.33 0.00 33.17 2.24
3688 4828 6.346279 CGTATTTGCCTCGCGAAATAATTCTA 60.346 38.462 11.33 0.00 35.42 2.10
3689 4829 4.900635 ATTTGCCTCGCGAAATAATTCT 57.099 36.364 11.33 0.00 35.42 2.40
3690 4830 4.607235 CGTATTTGCCTCGCGAAATAATTC 59.393 41.667 11.33 5.09 35.42 2.17
3692 4832 3.805422 TCGTATTTGCCTCGCGAAATAAT 59.195 39.130 11.33 10.07 35.42 1.28
3693 4833 3.188492 TCGTATTTGCCTCGCGAAATAA 58.812 40.909 11.33 2.09 35.42 1.40
3699 4919 1.139989 ATCATCGTATTTGCCTCGCG 58.860 50.000 0.00 0.00 0.00 5.87
3736 4956 7.274468 CCAGTATGCGCAAGAGTATTAGATTAG 59.726 40.741 17.11 0.00 43.02 1.73
3749 4969 0.578683 CGATCACCAGTATGCGCAAG 59.421 55.000 17.11 4.69 43.44 4.01
3768 4988 7.518731 TGTGCACTCATTGTTTTAAAACTTC 57.481 32.000 26.76 6.39 39.59 3.01
3820 5040 2.040009 ATCATGTTACTCCGCCCCCG 62.040 60.000 0.00 0.00 0.00 5.73
3857 5077 5.520649 GTGCAGCTCTTTTGATAGTACTACC 59.479 44.000 4.31 0.00 0.00 3.18
3872 5129 1.279496 TTATGGACCTGTGCAGCTCT 58.721 50.000 0.00 0.00 33.50 4.09
4097 5356 2.614481 GGTACTGCGGAAATCAAGACCA 60.614 50.000 0.00 0.00 0.00 4.02
4136 5395 5.105023 AGTTCTGAATTCAGCAGATCAGCTA 60.105 40.000 27.45 6.35 44.54 3.32
4387 5655 4.959596 GCGGAGGAGCAGATCGGC 62.960 72.222 10.10 10.10 37.05 5.54
4475 5743 3.806507 GCTGCATCCATTCTAAGGAGAGG 60.807 52.174 0.00 0.00 38.83 3.69
4476 5744 3.181457 TGCTGCATCCATTCTAAGGAGAG 60.181 47.826 0.00 0.00 38.83 3.20
4477 5745 2.773661 TGCTGCATCCATTCTAAGGAGA 59.226 45.455 0.00 0.00 38.83 3.71
4478 5746 3.204306 TGCTGCATCCATTCTAAGGAG 57.796 47.619 0.00 0.00 38.83 3.69
4847 6117 9.480053 ACAGATGAATGAACAAAAACCTTATTG 57.520 29.630 0.00 0.00 0.00 1.90
4911 6185 1.711375 TCAGTACCACCTGGAGAGAGT 59.289 52.381 0.00 0.00 38.94 3.24
5007 6286 6.018262 GTAACTCCATTACTTGCGAATGCATA 60.018 38.462 0.00 0.00 42.22 3.14
5026 6305 6.937465 ACAGGGAAAGAAAGAATCTGTAACTC 59.063 38.462 0.00 0.00 38.79 3.01
5272 6553 2.793933 CACTGTCAATTATGCTGCTGC 58.206 47.619 8.89 8.89 40.20 5.25
5278 6559 2.793933 CAGCAGCACTGTCAATTATGC 58.206 47.619 0.00 0.00 41.86 3.14
5297 6578 4.114073 CAAGAAAATCACAAACTGCAGCA 58.886 39.130 15.27 0.00 0.00 4.41
5298 6579 3.060070 GCAAGAAAATCACAAACTGCAGC 60.060 43.478 15.27 0.00 0.00 5.25
5299 6580 4.365723 AGCAAGAAAATCACAAACTGCAG 58.634 39.130 13.48 13.48 0.00 4.41
5300 6581 4.389890 AGCAAGAAAATCACAAACTGCA 57.610 36.364 0.00 0.00 0.00 4.41
5301 6582 5.045872 AGAAGCAAGAAAATCACAAACTGC 58.954 37.500 0.00 0.00 0.00 4.40
5302 6583 8.807667 ATTAGAAGCAAGAAAATCACAAACTG 57.192 30.769 0.00 0.00 0.00 3.16
5304 6585 8.854312 GCTATTAGAAGCAAGAAAATCACAAAC 58.146 33.333 0.00 0.00 42.30 2.93
5305 6586 8.796475 AGCTATTAGAAGCAAGAAAATCACAAA 58.204 29.630 0.00 0.00 45.30 2.83
5306 6587 8.340618 AGCTATTAGAAGCAAGAAAATCACAA 57.659 30.769 0.00 0.00 45.30 3.33
5307 6588 7.928307 AGCTATTAGAAGCAAGAAAATCACA 57.072 32.000 0.00 0.00 45.30 3.58
5308 6589 8.239998 ACAAGCTATTAGAAGCAAGAAAATCAC 58.760 33.333 0.00 0.00 45.30 3.06
5309 6590 8.340618 ACAAGCTATTAGAAGCAAGAAAATCA 57.659 30.769 0.00 0.00 45.30 2.57
5310 6591 7.912773 GGACAAGCTATTAGAAGCAAGAAAATC 59.087 37.037 0.00 0.00 45.30 2.17
5412 6711 7.360113 TGCTGATGATGTTGATAGTACCTTA 57.640 36.000 0.00 0.00 0.00 2.69
5419 6718 5.121105 TCCACTTGCTGATGATGTTGATAG 58.879 41.667 0.00 0.00 0.00 2.08
5420 6719 5.101648 TCCACTTGCTGATGATGTTGATA 57.898 39.130 0.00 0.00 0.00 2.15
5421 6720 3.959293 TCCACTTGCTGATGATGTTGAT 58.041 40.909 0.00 0.00 0.00 2.57
5438 6737 4.779987 ACGAGCGAAAAGTAAATTTCCAC 58.220 39.130 0.00 0.00 36.21 4.02
5441 6740 8.008279 AGACTTTACGAGCGAAAAGTAAATTTC 58.992 33.333 0.00 7.14 43.97 2.17
5451 6750 4.023450 TCTCTGAAGACTTTACGAGCGAAA 60.023 41.667 0.00 0.00 0.00 3.46
5455 6754 5.445275 GCAAATCTCTGAAGACTTTACGAGC 60.445 44.000 0.00 0.00 33.32 5.03
5456 6755 5.866633 AGCAAATCTCTGAAGACTTTACGAG 59.133 40.000 0.00 0.00 33.32 4.18
5457 6756 5.784177 AGCAAATCTCTGAAGACTTTACGA 58.216 37.500 0.00 0.00 33.32 3.43
5458 6757 5.635280 TGAGCAAATCTCTGAAGACTTTACG 59.365 40.000 0.00 0.00 42.38 3.18
5459 6758 7.463913 CGATGAGCAAATCTCTGAAGACTTTAC 60.464 40.741 0.00 0.00 42.38 2.01
5460 6759 6.533012 CGATGAGCAAATCTCTGAAGACTTTA 59.467 38.462 0.00 0.00 42.38 1.85
5462 6761 4.869297 CGATGAGCAAATCTCTGAAGACTT 59.131 41.667 0.00 0.00 42.38 3.01
5463 6762 4.081752 ACGATGAGCAAATCTCTGAAGACT 60.082 41.667 0.00 0.00 42.38 3.24
5464 6763 4.180057 ACGATGAGCAAATCTCTGAAGAC 58.820 43.478 0.00 0.00 42.38 3.01
5465 6764 4.462508 ACGATGAGCAAATCTCTGAAGA 57.537 40.909 0.00 0.00 42.38 2.87
5466 6765 6.841443 ATTACGATGAGCAAATCTCTGAAG 57.159 37.500 0.00 0.00 42.38 3.02
5484 6783 9.768662 AGTAAGTAAACCCATAACCATATTACG 57.231 33.333 0.00 0.00 0.00 3.18
5493 6792 7.547227 TCGGTTAGAGTAAGTAAACCCATAAC 58.453 38.462 0.00 0.00 38.52 1.89
5527 6826 5.046376 TGCCTGTGATCTTCTTTGTCATAGA 60.046 40.000 0.00 0.00 34.29 1.98
5530 6829 4.025040 TGCCTGTGATCTTCTTTGTCAT 57.975 40.909 0.00 0.00 0.00 3.06
5616 6915 7.873719 TTTTTGAGGAATCTGTTTCAGTGTA 57.126 32.000 1.34 0.00 35.94 2.90
5639 6938 4.798882 CCTAGACCCTAGAGTGAGTGATT 58.201 47.826 2.77 0.00 0.00 2.57
5652 6951 0.625849 CCATTGTTGGCCTAGACCCT 59.374 55.000 3.32 0.00 35.85 4.34
5653 6952 3.191182 CCATTGTTGGCCTAGACCC 57.809 57.895 3.32 0.00 35.85 4.46
5678 6977 2.503356 ACCAAAATGGGCAACACAGAAA 59.497 40.909 0.87 0.00 43.37 2.52
5680 6979 1.786937 ACCAAAATGGGCAACACAGA 58.213 45.000 0.87 0.00 43.37 3.41
5803 7103 9.999660 TTTAACAGTATATAAACATATGCGGGA 57.000 29.630 1.58 0.00 0.00 5.14
5820 7120 5.992829 TCTGCGAGGAATGTTTTTAACAGTA 59.007 36.000 0.00 0.00 45.95 2.74
5838 7138 4.074526 GTCAGCCTGCCTCTGCGA 62.075 66.667 0.00 0.00 41.78 5.10
5840 7140 2.833604 AATGGTCAGCCTGCCTCTGC 62.834 60.000 6.71 0.00 35.27 4.26
5842 7142 0.034670 GAAATGGTCAGCCTGCCTCT 60.035 55.000 6.71 0.00 35.27 3.69
5843 7143 1.372087 CGAAATGGTCAGCCTGCCTC 61.372 60.000 6.71 0.00 35.27 4.70
5844 7144 1.377725 CGAAATGGTCAGCCTGCCT 60.378 57.895 6.71 0.00 35.27 4.75
5845 7145 3.056313 GCGAAATGGTCAGCCTGCC 62.056 63.158 0.00 0.00 35.27 4.85
5850 7150 1.425428 CGAAGGCGAAATGGTCAGC 59.575 57.895 0.00 0.00 40.82 4.26
6036 7342 2.726821 CCATATGAACACTTGCTGGGT 58.273 47.619 3.65 0.00 0.00 4.51
6037 7343 1.406539 GCCATATGAACACTTGCTGGG 59.593 52.381 3.65 0.00 0.00 4.45
6038 7344 1.064505 CGCCATATGAACACTTGCTGG 59.935 52.381 3.65 0.00 0.00 4.85
6091 7397 0.602638 GTGTTGGATGCGGACAGACA 60.603 55.000 0.00 0.00 0.00 3.41
6099 7405 1.375396 TTCGAGGGTGTTGGATGCG 60.375 57.895 0.00 0.00 0.00 4.73
6223 7654 2.654877 GTCCGACGGGAAAGCAGA 59.345 61.111 15.25 0.00 46.08 4.26
6684 8158 7.441017 TGAAAAGATGGTAAGGTTTGGAATTG 58.559 34.615 0.00 0.00 0.00 2.32
6698 8172 9.093458 AGGATTGTATTCTTTTGAAAAGATGGT 57.907 29.630 19.81 12.02 42.31 3.55
6708 8182 9.061435 GGGAGAGATAAGGATTGTATTCTTTTG 57.939 37.037 0.00 0.00 0.00 2.44
6716 8190 5.221722 GCACATGGGAGAGATAAGGATTGTA 60.222 44.000 0.00 0.00 0.00 2.41
6732 8206 2.479566 ACTTGTAGTGAGCACATGGG 57.520 50.000 3.19 0.00 0.00 4.00
6737 8211 6.554334 TTTTGGATAACTTGTAGTGAGCAC 57.446 37.500 0.00 0.00 0.00 4.40
6764 8238 8.871686 AATGTTCTCTAAAAACACATGGAAAC 57.128 30.769 0.00 0.00 39.29 2.78
6765 8239 9.883142 AAAATGTTCTCTAAAAACACATGGAAA 57.117 25.926 0.00 0.00 39.29 3.13
6766 8240 9.883142 AAAAATGTTCTCTAAAAACACATGGAA 57.117 25.926 0.00 0.00 39.29 3.53
6789 8263 8.267894 TGGACACATGGGAAATTTTAAGAAAAA 58.732 29.630 0.00 0.00 38.87 1.94
6804 8278 2.835580 TTTGCAAATGGACACATGGG 57.164 45.000 8.05 0.00 37.40 4.00
6805 8279 4.571919 AGAATTTGCAAATGGACACATGG 58.428 39.130 24.74 0.00 37.40 3.66
6806 8280 7.655236 TTAAGAATTTGCAAATGGACACATG 57.345 32.000 24.74 0.00 37.40 3.21
6850 8325 7.413988 GGCAAAAATACCTTTGTAAATCATGGC 60.414 37.037 0.00 0.00 38.35 4.40
6851 8326 7.605691 TGGCAAAAATACCTTTGTAAATCATGG 59.394 33.333 0.00 0.00 38.35 3.66
6858 8333 9.566432 AAAATCATGGCAAAAATACCTTTGTAA 57.434 25.926 0.00 0.00 38.35 2.41
6882 8357 7.814264 ACATAAATTTGCCATGGTTCAAAAA 57.186 28.000 17.94 10.14 36.02 1.94
6887 8362 8.546597 AAGTAAACATAAATTTGCCATGGTTC 57.453 30.769 14.67 0.00 32.13 3.62
6895 8370 9.646427 TGGTCCATAAAGTAAACATAAATTTGC 57.354 29.630 0.00 0.00 0.00 3.68
6913 8388 6.549364 GGATGGTAAATTTGTCATGGTCCATA 59.451 38.462 3.38 0.00 34.02 2.74
6924 8399 3.768878 TGGTTCGGGATGGTAAATTTGT 58.231 40.909 0.00 0.00 0.00 2.83
6934 8409 0.819259 ATTCGCCATGGTTCGGGATG 60.819 55.000 14.67 0.00 0.00 3.51
6937 8412 1.064952 GTAAATTCGCCATGGTTCGGG 59.935 52.381 14.67 0.00 0.00 5.14
6938 8413 2.014128 AGTAAATTCGCCATGGTTCGG 58.986 47.619 14.67 0.62 0.00 4.30
6988 8463 9.620259 AATTGTTTGGTAAATATGTTTTGTGGT 57.380 25.926 0.00 0.00 0.00 4.16
7067 8542 7.939039 TCCAAATGTAAAATTTGCCATGGTAAA 59.061 29.630 27.23 27.23 37.60 2.01
7071 8546 6.206243 TGTTCCAAATGTAAAATTTGCCATGG 59.794 34.615 7.63 7.63 37.60 3.66
7146 8621 6.013379 TGGCCATGGTCCAACAAATAAATTTA 60.013 34.615 21.27 0.00 0.00 1.40
7185 8662 9.033481 CATGGTGTAGTTAATAAAATTGCCATG 57.967 33.333 0.00 0.00 41.27 3.66
7202 8679 8.044908 ACCTACAATAAAACTACCATGGTGTAG 58.955 37.037 28.17 22.66 43.13 2.74
7215 8692 5.637006 TGCCATGTGACCTACAATAAAAC 57.363 39.130 0.00 0.00 43.77 2.43
7301 8781 7.882271 TGGCAAATTAAGAAAATAAACTGCCAT 59.118 29.630 15.69 0.00 43.90 4.40
7305 8785 8.177013 GCCATGGCAAATTAAGAAAATAAACTG 58.823 33.333 32.08 0.00 41.49 3.16
7362 8846 9.914834 ACTATGGTAAATGGCAAAAACTATCTA 57.085 29.630 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.