Multiple sequence alignment - TraesCS4A01G014800

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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 TraesCS4A01G014800 chr4A 100.000 4172 0 0 1 4172 9456222 9452051 0.000000e+00 7705.0
1 TraesCS4A01G014800 chr4A 92.000 50 1 3 3824 3871 9452365 9452317 2.690000e-07 67.6
2 TraesCS4A01G014800 chr4A 92.000 50 1 3 3858 3906 9452399 9452352 2.690000e-07 67.6
3 TraesCS4A01G014800 chr4D 94.776 3120 121 26 595 3704 459316063 459319150 0.000000e+00 4820.0
4 TraesCS4A01G014800 chr4D 88.142 253 11 4 3874 4126 459319314 459319547 2.460000e-72 283.0
5 TraesCS4A01G014800 chr4D 94.413 179 8 1 3695 3871 459319168 459319346 1.480000e-69 274.0
6 TraesCS4A01G014800 chr4B 94.098 2999 128 26 541 3535 574057713 574060666 0.000000e+00 4512.0
7 TraesCS4A01G014800 chr4B 95.517 290 12 1 3582 3871 574060667 574060955 2.940000e-126 462.0
8 TraesCS4A01G014800 chr4B 88.384 198 9 10 3925 4122 574063142 574063325 4.200000e-55 226.0
9 TraesCS4A01G014800 chr2A 100.000 31 0 0 4129 4159 11647210 11647240 1.620000e-04 58.4
10 TraesCS4A01G014800 chr2B 90.000 40 4 0 570 609 758529129 758529090 8.000000e-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 TraesCS4A01G014800 chr4A 9452051 9456222 4171 True 2613.400000 7705 94.666667 1 4172 3 chr4A.!!$R1 4171
1 TraesCS4A01G014800 chr4D 459316063 459319547 3484 False 1792.333333 4820 92.443667 595 4126 3 chr4D.!!$F1 3531
2 TraesCS4A01G014800 chr4B 574057713 574063325 5612 False 1733.333333 4512 92.666333 541 4122 3 chr4B.!!$F1 3581

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
37 38 0.172578 TGAGCCGTTCCACTACGATG 59.827 55.0 0.00 0.00 43.99 3.84 F
38 39 0.172803 GAGCCGTTCCACTACGATGT 59.827 55.0 0.00 0.00 43.99 3.06 F
39 40 0.172803 AGCCGTTCCACTACGATGTC 59.827 55.0 0.00 0.00 43.99 3.06 F
40 41 0.172803 GCCGTTCCACTACGATGTCT 59.827 55.0 0.00 0.00 43.99 3.41 F
1620 1626 0.107945 GAGCTGAGGTGTCCCACATC 60.108 60.0 0.00 2.32 44.10 3.06 F
1819 1825 1.651240 CTCCTGCAGCGATGGTTTGG 61.651 60.0 8.66 0.00 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1323 1.464429 CGCCGAAGATGAAGACGACG 61.464 60.000 0.00 0.0 0.00 5.12 R
1590 1596 2.527624 TCAGCTCTGGCACCAGGT 60.528 61.111 16.52 0.0 43.75 4.00 R
1593 1599 2.527624 ACCTCAGCTCTGGCACCA 60.528 61.111 1.65 0.0 41.70 4.17 R
1919 1925 2.807676 CCTTCCAGCCCATTACTTTGT 58.192 47.619 0.00 0.0 0.00 2.83 R
2964 2979 0.698238 CTGGTCTGGAAATCCCCACA 59.302 55.000 0.00 0.0 34.29 4.17 R
3342 3358 1.854126 CAAAGGCAGAAGCAAAACACG 59.146 47.619 0.00 0.0 44.61 4.49 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
17 18 3.797353 CCCACATCTCCCCCGGTG 61.797 72.222 0.00 0.00 0.00 4.94
18 19 3.009115 CCACATCTCCCCCGGTGT 61.009 66.667 0.00 0.00 0.00 4.16
19 20 2.268920 CACATCTCCCCCGGTGTG 59.731 66.667 0.00 3.10 36.40 3.82
20 21 2.121832 ACATCTCCCCCGGTGTGA 59.878 61.111 0.00 0.00 0.00 3.58
21 22 1.990060 ACATCTCCCCCGGTGTGAG 60.990 63.158 0.00 3.04 0.00 3.51
22 23 3.083997 ATCTCCCCCGGTGTGAGC 61.084 66.667 0.00 0.00 0.00 4.26
30 31 3.041940 CGGTGTGAGCCGTTCCAC 61.042 66.667 0.00 0.00 46.11 4.02
31 32 2.426023 GGTGTGAGCCGTTCCACT 59.574 61.111 0.00 0.00 34.57 4.00
32 33 1.669440 GGTGTGAGCCGTTCCACTA 59.331 57.895 0.00 0.00 34.57 2.74
33 34 0.669625 GGTGTGAGCCGTTCCACTAC 60.670 60.000 0.00 0.00 34.57 2.73
34 35 1.007336 GTGTGAGCCGTTCCACTACG 61.007 60.000 0.00 0.00 41.06 3.51
35 36 1.174078 TGTGAGCCGTTCCACTACGA 61.174 55.000 0.00 0.00 43.99 3.43
36 37 0.172803 GTGAGCCGTTCCACTACGAT 59.827 55.000 0.00 0.00 43.99 3.73
37 38 0.172578 TGAGCCGTTCCACTACGATG 59.827 55.000 0.00 0.00 43.99 3.84
38 39 0.172803 GAGCCGTTCCACTACGATGT 59.827 55.000 0.00 0.00 43.99 3.06
39 40 0.172803 AGCCGTTCCACTACGATGTC 59.827 55.000 0.00 0.00 43.99 3.06
40 41 0.172803 GCCGTTCCACTACGATGTCT 59.827 55.000 0.00 0.00 43.99 3.41
41 42 1.909376 CCGTTCCACTACGATGTCTG 58.091 55.000 0.00 0.00 43.99 3.51
42 43 1.471287 CCGTTCCACTACGATGTCTGA 59.529 52.381 0.00 0.00 43.99 3.27
43 44 2.516923 CGTTCCACTACGATGTCTGAC 58.483 52.381 0.00 0.00 43.99 3.51
44 45 2.516923 GTTCCACTACGATGTCTGACG 58.483 52.381 2.98 0.00 0.00 4.35
45 46 2.103537 TCCACTACGATGTCTGACGA 57.896 50.000 2.98 0.00 0.00 4.20
46 47 2.640184 TCCACTACGATGTCTGACGAT 58.360 47.619 2.98 0.00 0.00 3.73
47 48 3.800531 TCCACTACGATGTCTGACGATA 58.199 45.455 2.98 0.00 0.00 2.92
48 49 3.808174 TCCACTACGATGTCTGACGATAG 59.192 47.826 2.98 4.92 46.19 2.08
61 62 2.199152 CGATAGTCTGCTCGTTGCG 58.801 57.895 0.00 0.00 46.63 4.85
62 63 0.248094 CGATAGTCTGCTCGTTGCGA 60.248 55.000 0.00 0.00 46.63 5.10
79 80 2.288961 CGAGTAGCAACATACGGGTT 57.711 50.000 0.00 0.00 0.00 4.11
80 81 3.425577 CGAGTAGCAACATACGGGTTA 57.574 47.619 0.00 0.00 0.00 2.85
81 82 3.973657 CGAGTAGCAACATACGGGTTAT 58.026 45.455 0.00 0.00 0.00 1.89
82 83 4.365723 CGAGTAGCAACATACGGGTTATT 58.634 43.478 0.00 0.00 0.00 1.40
83 84 4.807304 CGAGTAGCAACATACGGGTTATTT 59.193 41.667 0.00 0.00 0.00 1.40
84 85 5.292589 CGAGTAGCAACATACGGGTTATTTT 59.707 40.000 0.00 0.00 0.00 1.82
85 86 6.183360 CGAGTAGCAACATACGGGTTATTTTT 60.183 38.462 0.00 0.00 0.00 1.94
163 164 9.809096 TTTACTAATTTGTGAAAAACATGCTCA 57.191 25.926 2.59 0.00 38.99 4.26
164 165 9.979578 TTACTAATTTGTGAAAAACATGCTCAT 57.020 25.926 2.59 0.00 38.99 2.90
165 166 8.301730 ACTAATTTGTGAAAAACATGCTCATG 57.698 30.769 8.21 8.21 44.15 3.07
166 167 6.548441 AATTTGTGAAAAACATGCTCATGG 57.452 33.333 13.69 0.00 42.91 3.66
167 168 4.669206 TTGTGAAAAACATGCTCATGGT 57.331 36.364 13.69 4.71 41.22 3.55
168 169 3.979948 TGTGAAAAACATGCTCATGGTG 58.020 40.909 13.69 0.00 37.86 4.17
169 170 3.384146 TGTGAAAAACATGCTCATGGTGT 59.616 39.130 13.69 0.00 37.86 4.16
170 171 4.582240 TGTGAAAAACATGCTCATGGTGTA 59.418 37.500 13.69 0.00 37.86 2.90
171 172 5.243507 TGTGAAAAACATGCTCATGGTGTAT 59.756 36.000 13.69 0.00 37.86 2.29
172 173 5.574055 GTGAAAAACATGCTCATGGTGTATG 59.426 40.000 13.69 13.02 37.86 2.39
173 174 5.243507 TGAAAAACATGCTCATGGTGTATGT 59.756 36.000 13.69 13.98 37.86 2.29
174 175 6.432472 TGAAAAACATGCTCATGGTGTATGTA 59.568 34.615 17.79 5.51 37.86 2.29
175 176 6.832520 AAAACATGCTCATGGTGTATGTAA 57.167 33.333 17.79 0.00 37.86 2.41
176 177 6.832520 AAACATGCTCATGGTGTATGTAAA 57.167 33.333 17.79 0.00 37.86 2.01
177 178 6.832520 AACATGCTCATGGTGTATGTAAAA 57.167 33.333 17.79 0.00 42.91 1.52
178 179 6.832520 ACATGCTCATGGTGTATGTAAAAA 57.167 33.333 16.66 0.00 42.91 1.94
201 202 6.699575 AAATCCTGGTGTATTGAACTATGC 57.300 37.500 0.00 0.00 0.00 3.14
202 203 5.636903 ATCCTGGTGTATTGAACTATGCT 57.363 39.130 0.00 0.00 0.00 3.79
203 204 5.023533 TCCTGGTGTATTGAACTATGCTC 57.976 43.478 0.00 0.00 0.00 4.26
204 205 4.469586 TCCTGGTGTATTGAACTATGCTCA 59.530 41.667 0.00 0.00 0.00 4.26
205 206 5.130975 TCCTGGTGTATTGAACTATGCTCAT 59.869 40.000 0.00 0.00 0.00 2.90
206 207 5.468072 CCTGGTGTATTGAACTATGCTCATC 59.532 44.000 0.00 0.00 0.00 2.92
207 208 5.988287 TGGTGTATTGAACTATGCTCATCA 58.012 37.500 0.00 0.00 0.00 3.07
208 209 6.594744 TGGTGTATTGAACTATGCTCATCAT 58.405 36.000 0.00 0.00 39.17 2.45
209 210 6.484308 TGGTGTATTGAACTATGCTCATCATG 59.516 38.462 0.00 0.00 36.63 3.07
210 211 6.707608 GGTGTATTGAACTATGCTCATCATGA 59.292 38.462 0.00 0.00 36.63 3.07
211 212 7.227314 GGTGTATTGAACTATGCTCATCATGAA 59.773 37.037 0.00 0.00 36.63 2.57
212 213 8.781196 GTGTATTGAACTATGCTCATCATGAAT 58.219 33.333 0.00 0.00 36.63 2.57
213 214 9.346005 TGTATTGAACTATGCTCATCATGAATT 57.654 29.630 0.00 0.00 36.63 2.17
224 225 9.661563 ATGCTCATCATGAATTTTAAACATGTT 57.338 25.926 4.92 4.92 41.14 2.71
225 226 9.142515 TGCTCATCATGAATTTTAAACATGTTC 57.857 29.630 12.39 0.00 41.14 3.18
226 227 9.142515 GCTCATCATGAATTTTAAACATGTTCA 57.857 29.630 12.39 3.94 41.14 3.18
245 246 9.797556 CATGTTCATCATGTATTGTCAAAAGAT 57.202 29.630 0.00 0.00 46.18 2.40
246 247 9.797556 ATGTTCATCATGTATTGTCAAAAGATG 57.202 29.630 0.00 0.00 35.19 2.90
247 248 8.795513 TGTTCATCATGTATTGTCAAAAGATGT 58.204 29.630 0.00 0.00 34.71 3.06
248 249 9.630098 GTTCATCATGTATTGTCAAAAGATGTT 57.370 29.630 0.00 0.61 34.71 2.71
299 300 9.420118 TGTGCATATTAAAAATATTGACCCTCT 57.580 29.630 0.00 0.00 0.00 3.69
375 376 4.188247 TCCTGTAGAGGAATGTTTGTCG 57.812 45.455 6.06 0.00 46.19 4.35
376 377 3.576982 TCCTGTAGAGGAATGTTTGTCGT 59.423 43.478 6.06 0.00 46.19 4.34
377 378 3.679980 CCTGTAGAGGAATGTTTGTCGTG 59.320 47.826 0.00 0.00 42.93 4.35
378 379 4.307432 CTGTAGAGGAATGTTTGTCGTGT 58.693 43.478 0.00 0.00 0.00 4.49
379 380 5.456548 TGTAGAGGAATGTTTGTCGTGTA 57.543 39.130 0.00 0.00 0.00 2.90
380 381 6.032956 TGTAGAGGAATGTTTGTCGTGTAT 57.967 37.500 0.00 0.00 0.00 2.29
381 382 6.460781 TGTAGAGGAATGTTTGTCGTGTATT 58.539 36.000 0.00 0.00 0.00 1.89
382 383 6.932400 TGTAGAGGAATGTTTGTCGTGTATTT 59.068 34.615 0.00 0.00 0.00 1.40
383 384 8.089597 TGTAGAGGAATGTTTGTCGTGTATTTA 58.910 33.333 0.00 0.00 0.00 1.40
384 385 7.972832 AGAGGAATGTTTGTCGTGTATTTAA 57.027 32.000 0.00 0.00 0.00 1.52
385 386 8.029642 AGAGGAATGTTTGTCGTGTATTTAAG 57.970 34.615 0.00 0.00 0.00 1.85
386 387 7.876068 AGAGGAATGTTTGTCGTGTATTTAAGA 59.124 33.333 0.00 0.00 0.00 2.10
387 388 8.385898 AGGAATGTTTGTCGTGTATTTAAGAA 57.614 30.769 0.00 0.00 0.00 2.52
388 389 8.842280 AGGAATGTTTGTCGTGTATTTAAGAAA 58.158 29.630 0.00 0.00 0.00 2.52
389 390 9.620660 GGAATGTTTGTCGTGTATTTAAGAAAT 57.379 29.630 0.00 0.00 34.90 2.17
409 410 9.941664 AAGAAATATTAATCGTGCATTCAGAAG 57.058 29.630 0.00 0.00 0.00 2.85
410 411 9.330063 AGAAATATTAATCGTGCATTCAGAAGA 57.670 29.630 0.00 0.00 0.00 2.87
411 412 9.935682 GAAATATTAATCGTGCATTCAGAAGAA 57.064 29.630 0.00 0.00 38.31 2.52
419 420 8.893219 ATCGTGCATTCAGAAGAATAAATAGA 57.107 30.769 0.00 0.00 42.46 1.98
420 421 8.893219 TCGTGCATTCAGAAGAATAAATAGAT 57.107 30.769 0.00 0.00 42.46 1.98
421 422 8.982685 TCGTGCATTCAGAAGAATAAATAGATC 58.017 33.333 0.00 0.00 42.46 2.75
422 423 8.768019 CGTGCATTCAGAAGAATAAATAGATCA 58.232 33.333 0.00 0.00 42.46 2.92
523 524 9.634163 AATCAATAAAATACAGAAAACCGAACC 57.366 29.630 0.00 0.00 0.00 3.62
524 525 8.167605 TCAATAAAATACAGAAAACCGAACCA 57.832 30.769 0.00 0.00 0.00 3.67
525 526 8.798402 TCAATAAAATACAGAAAACCGAACCAT 58.202 29.630 0.00 0.00 0.00 3.55
528 529 7.989416 AAAATACAGAAAACCGAACCATAGA 57.011 32.000 0.00 0.00 0.00 1.98
529 530 7.989416 AAATACAGAAAACCGAACCATAGAA 57.011 32.000 0.00 0.00 0.00 2.10
530 531 7.989416 AATACAGAAAACCGAACCATAGAAA 57.011 32.000 0.00 0.00 0.00 2.52
531 532 8.575649 AATACAGAAAACCGAACCATAGAAAT 57.424 30.769 0.00 0.00 0.00 2.17
532 533 6.496338 ACAGAAAACCGAACCATAGAAATC 57.504 37.500 0.00 0.00 0.00 2.17
533 534 5.414765 ACAGAAAACCGAACCATAGAAATCC 59.585 40.000 0.00 0.00 0.00 3.01
534 535 5.414454 CAGAAAACCGAACCATAGAAATCCA 59.586 40.000 0.00 0.00 0.00 3.41
535 536 6.095440 CAGAAAACCGAACCATAGAAATCCAT 59.905 38.462 0.00 0.00 0.00 3.41
536 537 7.282224 CAGAAAACCGAACCATAGAAATCCATA 59.718 37.037 0.00 0.00 0.00 2.74
537 538 6.937436 AAACCGAACCATAGAAATCCATAC 57.063 37.500 0.00 0.00 0.00 2.39
538 539 5.623956 ACCGAACCATAGAAATCCATACA 57.376 39.130 0.00 0.00 0.00 2.29
539 540 5.611374 ACCGAACCATAGAAATCCATACAG 58.389 41.667 0.00 0.00 0.00 2.74
545 546 6.055588 ACCATAGAAATCCATACAGAAACGG 58.944 40.000 0.00 0.00 0.00 4.44
548 549 5.160607 AGAAATCCATACAGAAACGGACA 57.839 39.130 0.00 0.00 0.00 4.02
549 550 5.745227 AGAAATCCATACAGAAACGGACAT 58.255 37.500 0.00 0.00 0.00 3.06
553 554 7.931578 AATCCATACAGAAACGGACATAAAA 57.068 32.000 0.00 0.00 0.00 1.52
557 558 7.392113 TCCATACAGAAACGGACATAAAACAAT 59.608 33.333 0.00 0.00 0.00 2.71
592 593 0.804989 CGAACCAGAGAAACCCATGC 59.195 55.000 0.00 0.00 0.00 4.06
609 610 4.142315 CCCATGCAGAAGAACATCGAAAAT 60.142 41.667 0.00 0.00 0.00 1.82
624 625 2.699954 GAAAATCCTGCCTCGAACTGA 58.300 47.619 0.00 0.00 0.00 3.41
628 629 2.507992 CTGCCTCGAACTGAGCCG 60.508 66.667 0.00 0.00 43.82 5.52
660 661 2.498481 CCTGGGACATCAACATGCAAAT 59.502 45.455 0.00 0.00 38.20 2.32
727 729 4.215109 CAGTTTTCTCCCTTCCCTTTGAA 58.785 43.478 0.00 0.00 0.00 2.69
829 831 2.438254 TGCAGCCGCGATTCCAAT 60.438 55.556 8.23 0.00 42.97 3.16
831 833 3.025619 CAGCCGCGATTCCAATCC 58.974 61.111 8.23 0.00 31.68 3.01
832 834 1.819208 CAGCCGCGATTCCAATCCA 60.819 57.895 8.23 0.00 31.68 3.41
833 835 1.077787 AGCCGCGATTCCAATCCAA 60.078 52.632 8.23 0.00 31.68 3.53
834 836 0.679640 AGCCGCGATTCCAATCCAAA 60.680 50.000 8.23 0.00 31.68 3.28
835 837 0.385390 GCCGCGATTCCAATCCAAAT 59.615 50.000 8.23 0.00 31.68 2.32
842 844 3.638160 CGATTCCAATCCAAATCCACCAT 59.362 43.478 0.00 0.00 31.68 3.55
888 890 2.621526 ACCAGAAAACCCACAATTCGAC 59.378 45.455 0.00 0.00 0.00 4.20
930 936 2.200337 AAACCGACCAAAGCCCTGC 61.200 57.895 0.00 0.00 0.00 4.85
931 937 4.660938 ACCGACCAAAGCCCTGCC 62.661 66.667 0.00 0.00 0.00 4.85
932 938 4.351054 CCGACCAAAGCCCTGCCT 62.351 66.667 0.00 0.00 0.00 4.75
933 939 3.058160 CGACCAAAGCCCTGCCTG 61.058 66.667 0.00 0.00 0.00 4.85
934 940 3.376918 GACCAAAGCCCTGCCTGC 61.377 66.667 0.00 0.00 0.00 4.85
935 941 3.875510 GACCAAAGCCCTGCCTGCT 62.876 63.158 0.00 0.00 41.89 4.24
936 942 3.379445 CCAAAGCCCTGCCTGCTG 61.379 66.667 0.00 0.00 39.48 4.41
937 943 4.065281 CAAAGCCCTGCCTGCTGC 62.065 66.667 0.00 0.00 39.48 5.25
1119 1125 3.452786 TTCCTCCTCGAGCCGCTG 61.453 66.667 6.99 0.00 0.00 5.18
1140 1146 4.501714 TACATCGCCGACCACGCC 62.502 66.667 0.00 0.00 38.29 5.68
1317 1323 4.246053 GACCTCCTCGTCCTCTCC 57.754 66.667 0.00 0.00 0.00 3.71
1590 1596 2.920912 GTGGAGGGGGACGTGTCA 60.921 66.667 0.00 0.00 0.00 3.58
1602 1608 2.828868 GTGTCACCTGGTGCCAGA 59.171 61.111 22.02 1.53 46.30 3.86
1620 1626 0.107945 GAGCTGAGGTGTCCCACATC 60.108 60.000 0.00 2.32 44.10 3.06
1819 1825 1.651240 CTCCTGCAGCGATGGTTTGG 61.651 60.000 8.66 0.00 0.00 3.28
1872 1878 2.940158 CATGATCCTGATGAAAGGCCA 58.060 47.619 5.01 0.00 37.24 5.36
1887 1893 2.292267 AGGCCATTCGATGACATTGAC 58.708 47.619 5.01 0.00 0.00 3.18
2041 2047 4.343526 ACCAACCAATGCATTCAGTGTTAA 59.656 37.500 9.53 0.00 36.63 2.01
2220 2226 8.360390 GTTGACCTGAAAAAGAAGATATTGGTT 58.640 33.333 0.00 0.00 0.00 3.67
2296 2302 7.156000 TGAACTGTCCAATTATCTGAACGTAA 58.844 34.615 0.00 0.00 0.00 3.18
2390 2396 8.627487 TTATGTTCTTTTGTTAAGCAAGTGTG 57.373 30.769 0.00 0.00 38.47 3.82
2490 2496 4.221530 TGAGTAGCTCATGTCCTGATGAT 58.778 43.478 0.00 0.00 35.39 2.45
2557 2564 8.739039 TGCTAAGCAATTGACTAACACATATTT 58.261 29.630 10.34 0.00 34.76 1.40
2596 2603 4.922206 TCTAAAGACCACCTTGCATTCAT 58.078 39.130 0.00 0.00 34.79 2.57
2611 2618 8.357402 CCTTGCATTCATGATATTGATTCTGAA 58.643 33.333 0.00 0.00 0.00 3.02
2724 2731 8.691661 ACATGTATCAGGATTAAAATGTACCC 57.308 34.615 0.00 0.00 0.00 3.69
2791 2798 6.536582 AGTTGACAAACTCATTCGATCATAGG 59.463 38.462 0.00 0.00 43.34 2.57
2864 2879 4.223700 AGATGTCACTGCCAAATCTGTAGA 59.776 41.667 0.00 0.00 0.00 2.59
2865 2880 3.664107 TGTCACTGCCAAATCTGTAGAC 58.336 45.455 0.00 0.00 0.00 2.59
2868 2883 4.093998 GTCACTGCCAAATCTGTAGACATG 59.906 45.833 0.00 0.00 0.00 3.21
2886 2901 5.070446 AGACATGTAGAAACTTCTGACCACA 59.930 40.000 0.00 0.00 38.19 4.17
2890 2905 6.114187 TGTAGAAACTTCTGACCACATCAT 57.886 37.500 2.12 0.00 38.19 2.45
2946 2961 8.402798 TGCCTTTTATGACTGAACTTCAATTA 57.597 30.769 0.00 0.00 0.00 1.40
3249 3265 0.768221 ACCAACTCAAGCCTCCCTGA 60.768 55.000 0.00 0.00 0.00 3.86
3335 3351 4.402474 GCTGCTCCCATTTTATTTACTGGT 59.598 41.667 0.00 0.00 0.00 4.00
3342 3358 7.523415 TCCCATTTTATTTACTGGTCTATCCC 58.477 38.462 0.00 0.00 34.77 3.85
3353 3369 2.224670 TGGTCTATCCCGTGTTTTGCTT 60.225 45.455 0.00 0.00 34.77 3.91
3356 3372 3.125316 GTCTATCCCGTGTTTTGCTTCTG 59.875 47.826 0.00 0.00 0.00 3.02
3387 3403 7.115805 TGAGTGGCTATCGTTTTATAATTAGCG 59.884 37.037 0.00 0.00 0.00 4.26
3423 3439 6.259167 TGTTAGTTGAATGGTGTACACTGTTC 59.741 38.462 24.55 24.46 0.00 3.18
3488 3506 7.895429 TCTCTCAAATCCTGGTAATGGAAAAAT 59.105 33.333 0.00 0.00 37.13 1.82
3501 3519 8.145122 GGTAATGGAAAAATTTACTGTTGGTCA 58.855 33.333 0.00 0.00 0.00 4.02
3631 3649 4.397417 GTGCATTTGTCTCTCTTATGGCTT 59.603 41.667 0.00 0.00 0.00 4.35
3656 3674 5.989168 GTGGAAAAATGTCGAAAAGGGAATT 59.011 36.000 0.00 0.00 0.00 2.17
3863 3910 9.675464 AATGATGGCAGACAAAATATGATTTTT 57.325 25.926 0.00 0.00 0.00 1.94
3865 3912 9.585099 TGATGGCAGACAAAATATGATTTTTAC 57.415 29.630 0.00 0.00 0.00 2.01
3866 3913 9.585099 GATGGCAGACAAAATATGATTTTTACA 57.415 29.630 0.00 0.00 0.00 2.41
3881 3928 8.164058 TGATTTTTACATATCGAATGATGGCA 57.836 30.769 12.53 0.00 35.99 4.92
3882 3929 8.291740 TGATTTTTACATATCGAATGATGGCAG 58.708 33.333 12.53 0.00 35.99 4.85
3883 3930 7.800155 TTTTTACATATCGAATGATGGCAGA 57.200 32.000 12.53 0.00 35.99 4.26
3884 3931 6.785488 TTTACATATCGAATGATGGCAGAC 57.215 37.500 12.53 0.00 35.99 3.51
3885 3932 4.341366 ACATATCGAATGATGGCAGACA 57.659 40.909 12.53 0.00 35.99 3.41
3886 3933 4.707105 ACATATCGAATGATGGCAGACAA 58.293 39.130 12.53 0.00 35.99 3.18
3887 3934 5.125356 ACATATCGAATGATGGCAGACAAA 58.875 37.500 12.53 0.00 35.99 2.83
3888 3935 5.589855 ACATATCGAATGATGGCAGACAAAA 59.410 36.000 12.53 0.00 35.99 2.44
3889 3936 6.263842 ACATATCGAATGATGGCAGACAAAAT 59.736 34.615 12.53 0.00 35.99 1.82
3890 3937 7.445096 ACATATCGAATGATGGCAGACAAAATA 59.555 33.333 12.53 0.00 35.99 1.40
3891 3938 6.889301 ATCGAATGATGGCAGACAAAATAT 57.111 33.333 0.00 0.00 32.21 1.28
3892 3939 6.063640 TCGAATGATGGCAGACAAAATATG 57.936 37.500 0.00 0.00 0.00 1.78
3893 3940 5.821995 TCGAATGATGGCAGACAAAATATGA 59.178 36.000 0.00 0.00 0.00 2.15
3894 3941 6.487668 TCGAATGATGGCAGACAAAATATGAT 59.512 34.615 0.00 0.00 0.00 2.45
3895 3942 7.013559 TCGAATGATGGCAGACAAAATATGATT 59.986 33.333 0.00 0.00 0.00 2.57
3896 3943 7.650504 CGAATGATGGCAGACAAAATATGATTT 59.349 33.333 0.00 0.00 0.00 2.17
3897 3944 9.321562 GAATGATGGCAGACAAAATATGATTTT 57.678 29.630 0.00 0.00 0.00 1.82
3898 3945 9.675464 AATGATGGCAGACAAAATATGATTTTT 57.325 25.926 0.00 0.00 0.00 1.94
3978 6192 2.355513 GGTGCTGACTCCATCAATCTGT 60.356 50.000 0.00 0.00 36.69 3.41
3979 6193 2.676839 GTGCTGACTCCATCAATCTGTG 59.323 50.000 0.00 0.00 36.69 3.66
4026 6240 1.366111 CTCGTACCCCAATGCCAACG 61.366 60.000 0.00 0.00 0.00 4.10
4057 6271 1.241990 CCGACGACAACAGAGGAGGA 61.242 60.000 0.00 0.00 0.00 3.71
4058 6272 0.596577 CGACGACAACAGAGGAGGAA 59.403 55.000 0.00 0.00 0.00 3.36
4059 6273 1.401670 CGACGACAACAGAGGAGGAAG 60.402 57.143 0.00 0.00 0.00 3.46
4060 6274 1.887198 GACGACAACAGAGGAGGAAGA 59.113 52.381 0.00 0.00 0.00 2.87
4061 6275 1.889829 ACGACAACAGAGGAGGAAGAG 59.110 52.381 0.00 0.00 0.00 2.85
4062 6276 1.203523 CGACAACAGAGGAGGAAGAGG 59.796 57.143 0.00 0.00 0.00 3.69
4063 6277 1.552792 GACAACAGAGGAGGAAGAGGG 59.447 57.143 0.00 0.00 0.00 4.30
4064 6278 1.132689 ACAACAGAGGAGGAAGAGGGT 60.133 52.381 0.00 0.00 0.00 4.34
4065 6279 1.277557 CAACAGAGGAGGAAGAGGGTG 59.722 57.143 0.00 0.00 0.00 4.61
4066 6280 0.252467 ACAGAGGAGGAAGAGGGTGG 60.252 60.000 0.00 0.00 0.00 4.61
4067 6281 1.306568 AGAGGAGGAAGAGGGTGGC 60.307 63.158 0.00 0.00 0.00 5.01
4071 6288 3.334054 AGGAAGAGGGTGGCAGGC 61.334 66.667 0.00 0.00 0.00 4.85
4146 6363 7.591006 TTTTAAGGACAATGCTAGACTTACG 57.409 36.000 0.00 0.00 0.00 3.18
4147 6364 4.803098 AAGGACAATGCTAGACTTACGT 57.197 40.909 0.00 0.00 0.00 3.57
4148 6365 5.909621 AAGGACAATGCTAGACTTACGTA 57.090 39.130 0.00 0.00 0.00 3.57
4149 6366 5.909621 AGGACAATGCTAGACTTACGTAA 57.090 39.130 7.94 7.94 0.00 3.18
4150 6367 6.276832 AGGACAATGCTAGACTTACGTAAA 57.723 37.500 9.68 0.00 0.00 2.01
4151 6368 6.694447 AGGACAATGCTAGACTTACGTAAAA 58.306 36.000 9.68 0.00 0.00 1.52
4152 6369 7.328737 AGGACAATGCTAGACTTACGTAAAAT 58.671 34.615 9.68 0.22 0.00 1.82
4153 6370 7.491696 AGGACAATGCTAGACTTACGTAAAATC 59.508 37.037 9.68 9.89 0.00 2.17
4154 6371 7.491696 GGACAATGCTAGACTTACGTAAAATCT 59.508 37.037 19.96 19.96 0.00 2.40
4155 6372 9.512435 GACAATGCTAGACTTACGTAAAATCTA 57.488 33.333 20.03 20.03 0.00 1.98
4170 6387 9.793252 ACGTAAAATCTATTATGTGTTCTACGT 57.207 29.630 0.00 0.00 34.53 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.797353 CACCGGGGGAGATGTGGG 61.797 72.222 6.32 0.00 0.00 4.61
1 2 3.009115 ACACCGGGGGAGATGTGG 61.009 66.667 9.50 0.00 33.07 4.17
2 3 2.244117 CTCACACCGGGGGAGATGTG 62.244 65.000 9.50 11.72 43.08 3.21
3 4 1.990060 CTCACACCGGGGGAGATGT 60.990 63.158 9.50 0.00 0.00 3.06
4 5 2.903357 CTCACACCGGGGGAGATG 59.097 66.667 9.50 0.00 0.00 2.90
5 6 3.083997 GCTCACACCGGGGGAGAT 61.084 66.667 22.05 0.00 0.00 2.75
14 15 0.669625 GTAGTGGAACGGCTCACACC 60.670 60.000 6.96 0.00 45.86 4.16
15 16 1.007336 CGTAGTGGAACGGCTCACAC 61.007 60.000 6.96 0.00 45.86 3.82
16 17 1.174078 TCGTAGTGGAACGGCTCACA 61.174 55.000 6.96 0.00 45.86 3.58
17 18 0.172803 ATCGTAGTGGAACGGCTCAC 59.827 55.000 0.00 0.00 45.86 3.51
18 19 0.172578 CATCGTAGTGGAACGGCTCA 59.827 55.000 0.00 0.00 45.86 4.26
19 20 0.172803 ACATCGTAGTGGAACGGCTC 59.827 55.000 0.00 0.00 45.86 4.70
20 21 0.172803 GACATCGTAGTGGAACGGCT 59.827 55.000 0.00 0.00 45.86 5.52
21 22 0.172803 AGACATCGTAGTGGAACGGC 59.827 55.000 0.00 0.00 45.86 5.68
22 23 1.471287 TCAGACATCGTAGTGGAACGG 59.529 52.381 0.00 0.00 45.86 4.44
23 24 2.516923 GTCAGACATCGTAGTGGAACG 58.483 52.381 0.00 0.00 45.86 3.95
24 25 2.161012 TCGTCAGACATCGTAGTGGAAC 59.839 50.000 0.41 0.00 0.00 3.62
25 26 2.429478 TCGTCAGACATCGTAGTGGAA 58.571 47.619 0.41 0.00 0.00 3.53
26 27 2.103537 TCGTCAGACATCGTAGTGGA 57.896 50.000 0.41 0.00 0.00 4.02
27 28 3.560481 ACTATCGTCAGACATCGTAGTGG 59.440 47.826 0.41 0.00 0.00 4.00
28 29 4.508492 AGACTATCGTCAGACATCGTAGTG 59.492 45.833 0.41 0.00 42.73 2.74
29 30 4.508492 CAGACTATCGTCAGACATCGTAGT 59.492 45.833 0.41 3.05 42.73 2.73
30 31 4.609559 GCAGACTATCGTCAGACATCGTAG 60.610 50.000 0.41 0.00 42.73 3.51
31 32 3.247886 GCAGACTATCGTCAGACATCGTA 59.752 47.826 0.41 0.00 42.73 3.43
32 33 2.032302 GCAGACTATCGTCAGACATCGT 59.968 50.000 0.41 0.00 42.73 3.73
33 34 2.289274 AGCAGACTATCGTCAGACATCG 59.711 50.000 0.41 0.00 42.73 3.84
34 35 3.605922 CGAGCAGACTATCGTCAGACATC 60.606 52.174 0.41 0.00 42.73 3.06
35 36 2.289274 CGAGCAGACTATCGTCAGACAT 59.711 50.000 0.41 0.00 42.73 3.06
36 37 1.666189 CGAGCAGACTATCGTCAGACA 59.334 52.381 0.41 0.00 42.73 3.41
37 38 2.376915 CGAGCAGACTATCGTCAGAC 57.623 55.000 0.00 0.00 42.73 3.51
43 44 0.248094 TCGCAACGAGCAGACTATCG 60.248 55.000 7.51 7.51 46.13 2.92
44 45 1.471964 CTCGCAACGAGCAGACTATC 58.528 55.000 3.83 0.00 46.75 2.08
45 46 3.631714 CTCGCAACGAGCAGACTAT 57.368 52.632 3.83 0.00 46.75 2.12
59 60 0.179119 ACCCGTATGTTGCTACTCGC 60.179 55.000 0.00 0.00 39.77 5.03
60 61 2.288961 AACCCGTATGTTGCTACTCG 57.711 50.000 0.00 2.58 0.00 4.18
61 62 6.673154 AAAATAACCCGTATGTTGCTACTC 57.327 37.500 0.00 0.00 0.00 2.59
137 138 9.809096 TGAGCATGTTTTTCACAAATTAGTAAA 57.191 25.926 0.00 0.00 39.50 2.01
138 139 9.979578 ATGAGCATGTTTTTCACAAATTAGTAA 57.020 25.926 0.00 0.00 39.50 2.24
139 140 9.409312 CATGAGCATGTTTTTCACAAATTAGTA 57.591 29.630 2.34 0.00 39.50 1.82
140 141 7.385752 CCATGAGCATGTTTTTCACAAATTAGT 59.614 33.333 9.39 0.00 39.50 2.24
141 142 7.385752 ACCATGAGCATGTTTTTCACAAATTAG 59.614 33.333 9.39 0.00 39.50 1.73
142 143 7.171167 CACCATGAGCATGTTTTTCACAAATTA 59.829 33.333 9.39 0.00 39.50 1.40
143 144 6.017770 CACCATGAGCATGTTTTTCACAAATT 60.018 34.615 9.39 0.00 39.50 1.82
144 145 5.467399 CACCATGAGCATGTTTTTCACAAAT 59.533 36.000 9.39 0.00 39.50 2.32
145 146 4.809958 CACCATGAGCATGTTTTTCACAAA 59.190 37.500 9.39 0.00 39.50 2.83
146 147 4.141981 ACACCATGAGCATGTTTTTCACAA 60.142 37.500 9.39 0.00 39.50 3.33
147 148 3.384146 ACACCATGAGCATGTTTTTCACA 59.616 39.130 9.39 0.00 40.71 3.58
148 149 3.981211 ACACCATGAGCATGTTTTTCAC 58.019 40.909 9.39 0.00 37.11 3.18
149 150 5.243507 ACATACACCATGAGCATGTTTTTCA 59.756 36.000 9.39 0.00 38.10 2.69
150 151 5.713025 ACATACACCATGAGCATGTTTTTC 58.287 37.500 9.39 0.00 38.10 2.29
151 152 5.726980 ACATACACCATGAGCATGTTTTT 57.273 34.783 9.39 0.00 38.10 1.94
152 153 6.832520 TTACATACACCATGAGCATGTTTT 57.167 33.333 9.39 0.00 38.10 2.43
153 154 6.832520 TTTACATACACCATGAGCATGTTT 57.167 33.333 9.39 0.00 38.10 2.83
154 155 6.832520 TTTTACATACACCATGAGCATGTT 57.167 33.333 9.39 0.00 38.10 2.71
155 156 6.832520 TTTTTACATACACCATGAGCATGT 57.167 33.333 9.39 1.82 38.10 3.21
176 177 7.397192 AGCATAGTTCAATACACCAGGATTTTT 59.603 33.333 0.00 0.00 0.00 1.94
177 178 6.891908 AGCATAGTTCAATACACCAGGATTTT 59.108 34.615 0.00 0.00 0.00 1.82
178 179 6.426587 AGCATAGTTCAATACACCAGGATTT 58.573 36.000 0.00 0.00 0.00 2.17
179 180 6.006275 AGCATAGTTCAATACACCAGGATT 57.994 37.500 0.00 0.00 0.00 3.01
180 181 5.130975 TGAGCATAGTTCAATACACCAGGAT 59.869 40.000 0.00 0.00 0.00 3.24
181 182 4.469586 TGAGCATAGTTCAATACACCAGGA 59.530 41.667 0.00 0.00 0.00 3.86
182 183 4.769688 TGAGCATAGTTCAATACACCAGG 58.230 43.478 0.00 0.00 0.00 4.45
183 184 6.051074 TGATGAGCATAGTTCAATACACCAG 58.949 40.000 0.00 0.00 0.00 4.00
184 185 5.988287 TGATGAGCATAGTTCAATACACCA 58.012 37.500 0.00 0.00 0.00 4.17
185 186 6.707608 TCATGATGAGCATAGTTCAATACACC 59.292 38.462 0.00 0.00 34.82 4.16
186 187 7.719778 TCATGATGAGCATAGTTCAATACAC 57.280 36.000 0.00 0.00 34.82 2.90
187 188 8.913487 ATTCATGATGAGCATAGTTCAATACA 57.087 30.769 0.00 0.00 34.82 2.29
198 199 9.661563 AACATGTTTAAAATTCATGATGAGCAT 57.338 25.926 18.86 0.31 40.64 3.79
199 200 9.142515 GAACATGTTTAAAATTCATGATGAGCA 57.857 29.630 13.36 0.00 40.64 4.26
200 201 9.142515 TGAACATGTTTAAAATTCATGATGAGC 57.857 29.630 13.36 7.75 40.64 4.26
220 221 9.797556 CATCTTTTGACAATACATGATGAACAT 57.202 29.630 0.00 0.00 40.17 2.71
221 222 8.795513 ACATCTTTTGACAATACATGATGAACA 58.204 29.630 15.71 0.08 35.45 3.18
222 223 9.630098 AACATCTTTTGACAATACATGATGAAC 57.370 29.630 15.71 0.00 35.45 3.18
273 274 9.420118 AGAGGGTCAATATTTTTAATATGCACA 57.580 29.630 0.00 0.00 0.00 4.57
355 356 3.679980 CACGACAAACATTCCTCTACAGG 59.320 47.826 0.00 0.00 42.01 4.00
356 357 4.307432 ACACGACAAACATTCCTCTACAG 58.693 43.478 0.00 0.00 0.00 2.74
357 358 4.330944 ACACGACAAACATTCCTCTACA 57.669 40.909 0.00 0.00 0.00 2.74
358 359 6.963049 AATACACGACAAACATTCCTCTAC 57.037 37.500 0.00 0.00 0.00 2.59
359 360 9.146984 CTTAAATACACGACAAACATTCCTCTA 57.853 33.333 0.00 0.00 0.00 2.43
360 361 7.876068 TCTTAAATACACGACAAACATTCCTCT 59.124 33.333 0.00 0.00 0.00 3.69
361 362 8.025243 TCTTAAATACACGACAAACATTCCTC 57.975 34.615 0.00 0.00 0.00 3.71
362 363 7.972832 TCTTAAATACACGACAAACATTCCT 57.027 32.000 0.00 0.00 0.00 3.36
363 364 9.620660 ATTTCTTAAATACACGACAAACATTCC 57.379 29.630 0.00 0.00 0.00 3.01
383 384 9.941664 CTTCTGAATGCACGATTAATATTTCTT 57.058 29.630 0.00 0.00 0.00 2.52
384 385 9.330063 TCTTCTGAATGCACGATTAATATTTCT 57.670 29.630 0.00 0.00 0.00 2.52
385 386 9.935682 TTCTTCTGAATGCACGATTAATATTTC 57.064 29.630 0.00 0.00 0.00 2.17
393 394 9.330063 TCTATTTATTCTTCTGAATGCACGATT 57.670 29.630 0.00 0.00 42.34 3.34
394 395 8.893219 TCTATTTATTCTTCTGAATGCACGAT 57.107 30.769 0.00 0.00 42.34 3.73
395 396 8.893219 ATCTATTTATTCTTCTGAATGCACGA 57.107 30.769 0.00 0.00 42.34 4.35
396 397 8.768019 TGATCTATTTATTCTTCTGAATGCACG 58.232 33.333 0.00 0.00 42.34 5.34
497 498 9.634163 GGTTCGGTTTTCTGTATTTTATTGATT 57.366 29.630 0.00 0.00 0.00 2.57
498 499 8.798402 TGGTTCGGTTTTCTGTATTTTATTGAT 58.202 29.630 0.00 0.00 0.00 2.57
499 500 8.167605 TGGTTCGGTTTTCTGTATTTTATTGA 57.832 30.769 0.00 0.00 0.00 2.57
500 501 8.980143 ATGGTTCGGTTTTCTGTATTTTATTG 57.020 30.769 0.00 0.00 0.00 1.90
502 503 9.675464 TCTATGGTTCGGTTTTCTGTATTTTAT 57.325 29.630 0.00 0.00 0.00 1.40
503 504 9.504708 TTCTATGGTTCGGTTTTCTGTATTTTA 57.495 29.630 0.00 0.00 0.00 1.52
504 505 7.989416 TCTATGGTTCGGTTTTCTGTATTTT 57.011 32.000 0.00 0.00 0.00 1.82
505 506 7.989416 TTCTATGGTTCGGTTTTCTGTATTT 57.011 32.000 0.00 0.00 0.00 1.40
506 507 7.989416 TTTCTATGGTTCGGTTTTCTGTATT 57.011 32.000 0.00 0.00 0.00 1.89
507 508 7.282450 GGATTTCTATGGTTCGGTTTTCTGTAT 59.718 37.037 0.00 0.00 0.00 2.29
508 509 6.596497 GGATTTCTATGGTTCGGTTTTCTGTA 59.404 38.462 0.00 0.00 0.00 2.74
509 510 5.414765 GGATTTCTATGGTTCGGTTTTCTGT 59.585 40.000 0.00 0.00 0.00 3.41
510 511 5.414454 TGGATTTCTATGGTTCGGTTTTCTG 59.586 40.000 0.00 0.00 0.00 3.02
511 512 5.566469 TGGATTTCTATGGTTCGGTTTTCT 58.434 37.500 0.00 0.00 0.00 2.52
512 513 5.890424 TGGATTTCTATGGTTCGGTTTTC 57.110 39.130 0.00 0.00 0.00 2.29
513 514 6.887545 TGTATGGATTTCTATGGTTCGGTTTT 59.112 34.615 0.00 0.00 0.00 2.43
514 515 6.419791 TGTATGGATTTCTATGGTTCGGTTT 58.580 36.000 0.00 0.00 0.00 3.27
515 516 5.996644 TGTATGGATTTCTATGGTTCGGTT 58.003 37.500 0.00 0.00 0.00 4.44
516 517 5.365605 TCTGTATGGATTTCTATGGTTCGGT 59.634 40.000 0.00 0.00 0.00 4.69
517 518 5.853936 TCTGTATGGATTTCTATGGTTCGG 58.146 41.667 0.00 0.00 0.00 4.30
518 519 7.516785 CGTTTCTGTATGGATTTCTATGGTTCG 60.517 40.741 0.00 0.00 0.00 3.95
519 520 7.254795 CCGTTTCTGTATGGATTTCTATGGTTC 60.255 40.741 0.00 0.00 0.00 3.62
520 521 6.542370 CCGTTTCTGTATGGATTTCTATGGTT 59.458 38.462 0.00 0.00 0.00 3.67
521 522 6.055588 CCGTTTCTGTATGGATTTCTATGGT 58.944 40.000 0.00 0.00 0.00 3.55
522 523 6.202954 GTCCGTTTCTGTATGGATTTCTATGG 59.797 42.308 0.00 0.00 35.72 2.74
523 524 6.761242 TGTCCGTTTCTGTATGGATTTCTATG 59.239 38.462 0.00 0.00 35.72 2.23
524 525 6.884832 TGTCCGTTTCTGTATGGATTTCTAT 58.115 36.000 0.00 0.00 35.72 1.98
525 526 6.288941 TGTCCGTTTCTGTATGGATTTCTA 57.711 37.500 0.00 0.00 35.72 2.10
526 527 5.160607 TGTCCGTTTCTGTATGGATTTCT 57.839 39.130 0.00 0.00 35.72 2.52
527 528 7.548196 TTATGTCCGTTTCTGTATGGATTTC 57.452 36.000 0.00 0.00 35.72 2.17
528 529 7.931578 TTTATGTCCGTTTCTGTATGGATTT 57.068 32.000 0.00 0.00 35.72 2.17
529 530 7.392113 TGTTTTATGTCCGTTTCTGTATGGATT 59.608 33.333 0.00 0.00 35.72 3.01
530 531 6.882140 TGTTTTATGTCCGTTTCTGTATGGAT 59.118 34.615 0.00 0.00 35.72 3.41
531 532 6.231951 TGTTTTATGTCCGTTTCTGTATGGA 58.768 36.000 0.00 0.00 0.00 3.41
532 533 6.489127 TGTTTTATGTCCGTTTCTGTATGG 57.511 37.500 0.00 0.00 0.00 2.74
553 554 7.013464 TGGTTCGGTTTTCTGTGTATTTATTGT 59.987 33.333 0.00 0.00 0.00 2.71
557 558 6.289834 TCTGGTTCGGTTTTCTGTGTATTTA 58.710 36.000 0.00 0.00 0.00 1.40
561 562 3.385433 TCTCTGGTTCGGTTTTCTGTGTA 59.615 43.478 0.00 0.00 0.00 2.90
566 567 3.211865 GGTTTCTCTGGTTCGGTTTTCT 58.788 45.455 0.00 0.00 0.00 2.52
592 593 4.437930 GGCAGGATTTTCGATGTTCTTCTG 60.438 45.833 0.00 0.00 0.00 3.02
609 610 2.973899 GCTCAGTTCGAGGCAGGA 59.026 61.111 0.00 0.00 42.55 3.86
643 644 5.927689 TCTTTTCATTTGCATGTTGATGTCC 59.072 36.000 0.00 0.00 31.50 4.02
645 646 7.211573 TCTTCTTTTCATTTGCATGTTGATGT 58.788 30.769 0.00 0.00 31.50 3.06
660 661 2.316108 GTTGGGCCCTTCTTCTTTTCA 58.684 47.619 25.70 0.00 0.00 2.69
740 742 0.813821 GAACTGCTGAAAGGATGCCC 59.186 55.000 0.00 0.00 29.63 5.36
741 743 0.813821 GGAACTGCTGAAAGGATGCC 59.186 55.000 0.00 0.00 29.63 4.40
742 744 0.813821 GGGAACTGCTGAAAGGATGC 59.186 55.000 0.00 0.00 29.63 3.91
743 745 1.272092 TGGGGAACTGCTGAAAGGATG 60.272 52.381 0.00 0.00 29.63 3.51
744 746 1.075601 TGGGGAACTGCTGAAAGGAT 58.924 50.000 0.00 0.00 29.63 3.24
745 747 0.850100 TTGGGGAACTGCTGAAAGGA 59.150 50.000 0.00 0.00 0.00 3.36
746 748 1.703411 TTTGGGGAACTGCTGAAAGG 58.297 50.000 0.00 0.00 0.00 3.11
747 749 2.232208 GGATTTGGGGAACTGCTGAAAG 59.768 50.000 0.00 0.00 0.00 2.62
748 750 2.247358 GGATTTGGGGAACTGCTGAAA 58.753 47.619 0.00 0.00 0.00 2.69
749 751 1.549950 GGGATTTGGGGAACTGCTGAA 60.550 52.381 0.00 0.00 0.00 3.02
750 752 0.039618 GGGATTTGGGGAACTGCTGA 59.960 55.000 0.00 0.00 0.00 4.26
809 811 3.567797 GGAATCGCGGCTGCACTC 61.568 66.667 19.50 10.02 42.97 3.51
813 815 2.329339 GATTGGAATCGCGGCTGC 59.671 61.111 7.70 7.70 37.91 5.25
829 831 1.005805 CAGGTGGATGGTGGATTTGGA 59.994 52.381 0.00 0.00 0.00 3.53
831 833 2.094675 GTCAGGTGGATGGTGGATTTG 58.905 52.381 0.00 0.00 0.00 2.32
832 834 1.005924 GGTCAGGTGGATGGTGGATTT 59.994 52.381 0.00 0.00 0.00 2.17
833 835 0.625849 GGTCAGGTGGATGGTGGATT 59.374 55.000 0.00 0.00 0.00 3.01
834 836 1.626356 CGGTCAGGTGGATGGTGGAT 61.626 60.000 0.00 0.00 0.00 3.41
835 837 2.290287 CGGTCAGGTGGATGGTGGA 61.290 63.158 0.00 0.00 0.00 4.02
842 844 1.679641 TATGACGCGGTCAGGTGGA 60.680 57.895 12.47 0.00 46.04 4.02
874 876 1.302993 CGGGGTCGAATTGTGGGTT 60.303 57.895 0.00 0.00 39.00 4.11
905 907 1.852067 CTTTGGTCGGTTTGGCCTCG 61.852 60.000 3.32 2.99 34.25 4.63
909 911 2.338620 GGCTTTGGTCGGTTTGGC 59.661 61.111 0.00 0.00 0.00 4.52
911 913 1.659794 CAGGGCTTTGGTCGGTTTG 59.340 57.895 0.00 0.00 0.00 2.93
1119 1125 3.463585 TGGTCGGCGATGTACCCC 61.464 66.667 14.79 9.15 31.97 4.95
1256 1262 4.493747 GGTCGGAGAAGTCGGCGG 62.494 72.222 7.21 0.00 39.69 6.13
1317 1323 1.464429 CGCCGAAGATGAAGACGACG 61.464 60.000 0.00 0.00 0.00 5.12
1590 1596 2.527624 TCAGCTCTGGCACCAGGT 60.528 61.111 16.52 0.00 43.75 4.00
1593 1599 2.527624 ACCTCAGCTCTGGCACCA 60.528 61.111 1.65 0.00 41.70 4.17
1620 1626 3.314635 GCAGAATCACCTTGGAAGCTATG 59.685 47.826 0.00 0.00 0.00 2.23
1819 1825 7.473366 TGTTTCTCTATCTCGACATACTTGAC 58.527 38.462 0.00 0.00 0.00 3.18
1872 1878 4.825422 AGAGTGTGTCAATGTCATCGAAT 58.175 39.130 0.00 0.00 0.00 3.34
1919 1925 2.807676 CCTTCCAGCCCATTACTTTGT 58.192 47.619 0.00 0.00 0.00 2.83
2041 2047 1.145598 CATCCGTCAGCTCAGGCAT 59.854 57.895 0.00 0.00 41.70 4.40
2220 2226 3.091545 GAGAGGAAATGGTGCCAATTCA 58.908 45.455 17.66 0.00 37.52 2.57
2296 2302 4.413520 AGCATTGGTATATTCACCTGGAGT 59.586 41.667 0.00 0.00 39.50 3.85
2342 2348 7.726033 AATCAGAGTACTATGTCTCCAAGTT 57.274 36.000 16.69 0.00 0.00 2.66
2343 2349 8.855110 CATAATCAGAGTACTATGTCTCCAAGT 58.145 37.037 16.69 0.00 0.00 3.16
2557 2564 8.098912 GGTCTTTAGATGAACAAACTAAGGGTA 58.901 37.037 0.00 0.00 0.00 3.69
2633 2640 9.941664 CAGGATTTAATGCTAAACTCAGTAATG 57.058 33.333 0.00 0.00 29.82 1.90
2637 2644 8.635765 TTTCAGGATTTAATGCTAAACTCAGT 57.364 30.769 0.00 0.00 29.82 3.41
2656 2663 5.297776 CCCAGACAGTATAATTGCTTTCAGG 59.702 44.000 0.00 0.00 0.00 3.86
2719 2726 2.047560 GACCACACCTGCGGGTAC 60.048 66.667 19.20 3.16 45.41 3.34
2791 2798 2.661594 GGCCGACTGAATTGTGTTTTC 58.338 47.619 0.00 0.00 0.00 2.29
2864 2879 5.290493 TGTGGTCAGAAGTTTCTACATGT 57.710 39.130 2.69 2.69 35.34 3.21
2865 2880 5.934043 TGATGTGGTCAGAAGTTTCTACATG 59.066 40.000 10.96 0.00 34.58 3.21
2868 2883 7.440523 AAATGATGTGGTCAGAAGTTTCTAC 57.559 36.000 0.00 0.00 40.92 2.59
2946 2961 4.889409 CCCACAATTGTCAGGTATATTGCT 59.111 41.667 8.48 0.00 32.58 3.91
2964 2979 0.698238 CTGGTCTGGAAATCCCCACA 59.302 55.000 0.00 0.00 34.29 4.17
3037 3053 7.148804 CGTCACAACACTATAAATAGCGCATAT 60.149 37.037 11.47 5.23 33.68 1.78
3050 3066 4.330944 TTCTTCCACGTCACAACACTAT 57.669 40.909 0.00 0.00 0.00 2.12
3105 3121 2.240414 AGTGTGAGATGAATGCCCATCA 59.760 45.455 11.67 0.59 43.99 3.07
3221 3237 2.297701 GCTTGAGTTGGTTTCTGGACA 58.702 47.619 0.00 0.00 0.00 4.02
3249 3265 4.853924 AAAATCTCCATGTTTGCGTTCT 57.146 36.364 0.00 0.00 0.00 3.01
3335 3351 3.334691 CAGAAGCAAAACACGGGATAGA 58.665 45.455 0.00 0.00 0.00 1.98
3342 3358 1.854126 CAAAGGCAGAAGCAAAACACG 59.146 47.619 0.00 0.00 44.61 4.49
3387 3403 6.204882 ACCATTCAACTAACACAGAAAGCTAC 59.795 38.462 0.00 0.00 0.00 3.58
3423 3439 7.829378 GTCTATACAAAGACCAGTTAACCAG 57.171 40.000 0.88 0.00 40.06 4.00
3488 3506 8.684386 TCAACATATCTTTGACCAACAGTAAA 57.316 30.769 0.00 0.00 0.00 2.01
3501 3519 4.922206 TCCTGCCACTTCAACATATCTTT 58.078 39.130 0.00 0.00 0.00 2.52
3559 3577 5.772672 TGCTTGGACAAGGCTTTATAAGAAA 59.227 36.000 13.41 0.00 38.80 2.52
3631 3649 3.954904 TCCCTTTTCGACATTTTTCCACA 59.045 39.130 0.00 0.00 0.00 4.17
3863 3910 5.467035 TGTCTGCCATCATTCGATATGTA 57.533 39.130 0.00 0.00 0.00 2.29
3864 3911 4.341366 TGTCTGCCATCATTCGATATGT 57.659 40.909 0.00 0.00 0.00 2.29
3865 3912 5.678132 TTTGTCTGCCATCATTCGATATG 57.322 39.130 0.00 0.00 0.00 1.78
3866 3913 6.889301 ATTTTGTCTGCCATCATTCGATAT 57.111 33.333 0.00 0.00 0.00 1.63
3867 3914 7.661027 TCATATTTTGTCTGCCATCATTCGATA 59.339 33.333 0.00 0.00 0.00 2.92
3868 3915 6.487668 TCATATTTTGTCTGCCATCATTCGAT 59.512 34.615 0.00 0.00 0.00 3.59
3869 3916 5.821995 TCATATTTTGTCTGCCATCATTCGA 59.178 36.000 0.00 0.00 0.00 3.71
3870 3917 6.063640 TCATATTTTGTCTGCCATCATTCG 57.936 37.500 0.00 0.00 0.00 3.34
3871 3918 8.882415 AAATCATATTTTGTCTGCCATCATTC 57.118 30.769 0.00 0.00 0.00 2.67
3872 3919 9.675464 AAAAATCATATTTTGTCTGCCATCATT 57.325 25.926 0.00 0.00 31.55 2.57
3874 3921 9.585099 GTAAAAATCATATTTTGTCTGCCATCA 57.415 29.630 0.00 0.00 34.51 3.07
3875 3922 9.585099 TGTAAAAATCATATTTTGTCTGCCATC 57.415 29.630 0.00 0.00 34.51 3.51
3887 3934 9.706691 ACGACGAGGATATGTAAAAATCATATT 57.293 29.630 0.00 0.00 38.22 1.28
3888 3935 9.140286 CACGACGAGGATATGTAAAAATCATAT 57.860 33.333 0.00 0.00 40.00 1.78
3889 3936 7.597369 CCACGACGAGGATATGTAAAAATCATA 59.403 37.037 5.25 0.00 33.26 2.15
3890 3937 6.423905 CCACGACGAGGATATGTAAAAATCAT 59.576 38.462 5.25 0.00 0.00 2.45
3891 3938 5.751509 CCACGACGAGGATATGTAAAAATCA 59.248 40.000 5.25 0.00 0.00 2.57
3892 3939 5.333111 GCCACGACGAGGATATGTAAAAATC 60.333 44.000 15.98 0.00 0.00 2.17
3893 3940 4.510340 GCCACGACGAGGATATGTAAAAAT 59.490 41.667 15.98 0.00 0.00 1.82
3894 3941 3.866910 GCCACGACGAGGATATGTAAAAA 59.133 43.478 15.98 0.00 0.00 1.94
3895 3942 3.450578 GCCACGACGAGGATATGTAAAA 58.549 45.455 15.98 0.00 0.00 1.52
3896 3943 2.542205 CGCCACGACGAGGATATGTAAA 60.542 50.000 15.98 0.00 34.06 2.01
3897 3944 1.002142 CGCCACGACGAGGATATGTAA 60.002 52.381 15.98 0.00 34.06 2.41
3898 3945 0.589708 CGCCACGACGAGGATATGTA 59.410 55.000 15.98 0.00 34.06 2.29
4036 6250 2.142357 CTCCTCTGTTGTCGTCGGCA 62.142 60.000 0.00 0.00 0.00 5.69
4057 6271 3.655211 CCAGCCTGCCACCCTCTT 61.655 66.667 0.00 0.00 0.00 2.85
4144 6361 9.793252 ACGTAGAACACATAATAGATTTTACGT 57.207 29.630 0.00 0.00 37.83 3.57


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

AutoCloner maintained by Alex Coulton.