Multiple sequence alignment - TraesCS2D01G270300

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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 TraesCS2D01G270300 chr2D 100.000 3922 0 0 1 3922 334044366 334040445 0.000000e+00 7243.0
1 TraesCS2D01G270300 chr2D 75.349 215 37 8 1 203 553760360 553760150 5.400000e-14 89.8
2 TraesCS2D01G270300 chr2B 94.451 2415 61 33 641 3004 402220505 402218113 0.000000e+00 3650.0
3 TraesCS2D01G270300 chr2B 90.259 657 44 12 3008 3652 402218031 402217383 0.000000e+00 841.0
4 TraesCS2D01G270300 chr2B 93.031 287 16 2 3637 3922 402214078 402213795 2.180000e-112 416.0
5 TraesCS2D01G270300 chr2B 88.724 337 28 8 1 331 402258177 402257845 1.700000e-108 403.0
6 TraesCS2D01G270300 chr2B 94.860 214 11 0 432 645 782101581 782101368 6.280000e-88 335.0
7 TraesCS2D01G270300 chr2B 93.363 226 14 1 426 650 682130566 682130791 2.260000e-87 333.0
8 TraesCS2D01G270300 chr2B 93.607 219 14 0 426 644 736773229 736773011 1.050000e-85 327.0
9 TraesCS2D01G270300 chr2A 95.002 2141 52 24 646 2752 444626276 444624157 0.000000e+00 3310.0
10 TraesCS2D01G270300 chr2A 92.670 573 24 12 3367 3922 444623193 444622622 0.000000e+00 809.0
11 TraesCS2D01G270300 chr2A 90.934 364 25 4 3008 3370 444623580 444623224 2.120000e-132 483.0
12 TraesCS2D01G270300 chr2A 95.708 233 10 0 2772 3004 444623972 444623740 3.700000e-100 375.0
13 TraesCS2D01G270300 chr2A 90.805 174 13 3 175 345 444626564 444626391 3.050000e-56 230.0
14 TraesCS2D01G270300 chr2A 96.875 96 3 0 331 426 444626374 444626279 1.130000e-35 161.0
15 TraesCS2D01G270300 chr2A 75.234 214 40 12 1 203 694150788 694150577 5.400000e-14 89.8
16 TraesCS2D01G270300 chr2A 74.757 206 40 8 7 202 510857582 510857379 9.030000e-12 82.4
17 TraesCS2D01G270300 chr6D 84.171 537 77 5 1465 1999 161382106 161381576 7.510000e-142 514.0
18 TraesCS2D01G270300 chr6D 84.058 69 11 0 1367 1435 161382177 161382109 2.530000e-07 67.6
19 TraesCS2D01G270300 chr6B 83.450 429 68 3 1465 1891 291184803 291184376 2.840000e-106 396.0
20 TraesCS2D01G270300 chr6B 86.957 69 9 0 1372 1440 291184869 291184801 1.170000e-10 78.7
21 TraesCS2D01G270300 chr3B 94.144 222 13 0 426 647 813188298 813188519 4.850000e-89 339.0
22 TraesCS2D01G270300 chr1B 92.672 232 15 2 420 650 676078306 676078536 2.260000e-87 333.0
23 TraesCS2D01G270300 chr6A 92.609 230 17 0 416 645 547732332 547732103 8.120000e-87 331.0
24 TraesCS2D01G270300 chr4B 92.208 231 16 2 422 651 189677792 189677563 3.780000e-85 326.0
25 TraesCS2D01G270300 chr7B 93.182 220 15 0 425 644 595527909 595527690 1.360000e-84 324.0
26 TraesCS2D01G270300 chr3D 91.213 239 19 2 408 645 108290825 108291062 1.360000e-84 324.0


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 TraesCS2D01G270300 chr2D 334040445 334044366 3921 True 7243.000000 7243 100.000000 1 3922 1 chr2D.!!$R1 3921
1 TraesCS2D01G270300 chr2B 402213795 402220505 6710 True 1635.666667 3650 92.580333 641 3922 3 chr2B.!!$R4 3281
2 TraesCS2D01G270300 chr2A 444622622 444626564 3942 True 894.666667 3310 93.665667 175 3922 6 chr2A.!!$R3 3747
3 TraesCS2D01G270300 chr6D 161381576 161382177 601 True 290.800000 514 84.114500 1367 1999 2 chr6D.!!$R1 632

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
164 165 0.182775 GCGACCCCACTTCCCATAAT 59.817 55.000 0.00 0.00 0.00 1.28 F
625 660 0.457166 AATACGCGCACGCTCTGTAA 60.457 50.000 13.70 0.00 45.53 2.41 F
631 666 0.710567 CGCACGCTCTGTAAACTGAG 59.289 55.000 11.45 11.45 42.56 3.35 F
930 966 1.206849 GAGAGCACCTGGAGAAAGAGG 59.793 57.143 0.00 0.00 35.26 3.69 F
2142 2195 0.391597 AGTTTCCGCTTCCAAGTCGA 59.608 50.000 5.17 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1098 0.540830 ACCTGTCAACGAGCTCCTCT 60.541 55.000 8.47 0.0 0.0 3.69 R
1666 1710 1.064946 CATGGACGAGACCGAGAGC 59.935 63.158 0.00 0.0 39.5 4.09 R
2115 2168 3.547746 TGGAAGCGGAAACTAAAAGTGT 58.452 40.909 0.00 0.0 0.0 3.55 R
2841 3085 1.407258 CTCCACCGTCTCCTTCATCTC 59.593 57.143 0.00 0.0 0.0 2.75 R
3134 3536 1.734477 CGTTGAGGTCCAGAGCACG 60.734 63.158 0.00 0.0 0.0 5.34 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
22 23 5.851047 CTTTGGTTTGCAGAAATGATTCC 57.149 39.130 0.00 0.00 36.12 3.01
23 24 5.544650 CTTTGGTTTGCAGAAATGATTCCT 58.455 37.500 0.00 0.00 36.12 3.36
24 25 6.662865 TTTGGTTTGCAGAAATGATTCCTA 57.337 33.333 0.00 0.00 36.12 2.94
25 26 6.855763 TTGGTTTGCAGAAATGATTCCTAT 57.144 33.333 0.00 0.00 36.12 2.57
26 27 6.855763 TGGTTTGCAGAAATGATTCCTATT 57.144 33.333 0.00 0.00 36.12 1.73
27 28 7.243604 TGGTTTGCAGAAATGATTCCTATTT 57.756 32.000 0.00 0.00 36.12 1.40
28 29 7.322664 TGGTTTGCAGAAATGATTCCTATTTC 58.677 34.615 0.00 0.00 42.20 2.17
93 94 8.607441 AAAAAGACATTAGCCTGGAAAAATTC 57.393 30.769 0.00 0.00 0.00 2.17
115 116 9.671279 AATTCCTATTATATGCATCGAATGACA 57.329 29.630 0.19 0.00 0.00 3.58
116 117 9.842775 ATTCCTATTATATGCATCGAATGACAT 57.157 29.630 0.19 0.00 33.67 3.06
117 118 9.671279 TTCCTATTATATGCATCGAATGACATT 57.329 29.630 0.19 0.00 32.25 2.71
118 119 9.671279 TCCTATTATATGCATCGAATGACATTT 57.329 29.630 0.19 0.00 32.25 2.32
128 129 9.449550 TGCATCGAATGACATTTATTTTCATAC 57.550 29.630 1.39 0.00 29.64 2.39
129 130 9.449550 GCATCGAATGACATTTATTTTCATACA 57.550 29.630 1.39 0.00 29.64 2.29
149 150 3.687572 AAGAATTGAGATGCATGCGAC 57.312 42.857 14.09 9.49 0.00 5.19
150 151 1.945394 AGAATTGAGATGCATGCGACC 59.055 47.619 14.09 4.40 0.00 4.79
151 152 1.002033 GAATTGAGATGCATGCGACCC 60.002 52.381 14.09 3.12 0.00 4.46
152 153 0.820891 ATTGAGATGCATGCGACCCC 60.821 55.000 14.09 1.62 0.00 4.95
153 154 2.190313 GAGATGCATGCGACCCCA 59.810 61.111 14.09 0.00 0.00 4.96
154 155 2.124570 AGATGCATGCGACCCCAC 60.125 61.111 14.09 0.00 0.00 4.61
155 156 2.124570 GATGCATGCGACCCCACT 60.125 61.111 14.09 0.00 0.00 4.00
156 157 1.750399 GATGCATGCGACCCCACTT 60.750 57.895 14.09 0.00 0.00 3.16
157 158 1.718757 GATGCATGCGACCCCACTTC 61.719 60.000 14.09 0.00 0.00 3.01
158 159 3.134127 GCATGCGACCCCACTTCC 61.134 66.667 0.00 0.00 0.00 3.46
159 160 2.438434 CATGCGACCCCACTTCCC 60.438 66.667 0.00 0.00 0.00 3.97
160 161 2.933287 ATGCGACCCCACTTCCCA 60.933 61.111 0.00 0.00 0.00 4.37
161 162 2.308722 ATGCGACCCCACTTCCCAT 61.309 57.895 0.00 0.00 0.00 4.00
162 163 0.986019 ATGCGACCCCACTTCCCATA 60.986 55.000 0.00 0.00 0.00 2.74
163 164 1.202099 TGCGACCCCACTTCCCATAA 61.202 55.000 0.00 0.00 0.00 1.90
164 165 0.182775 GCGACCCCACTTCCCATAAT 59.817 55.000 0.00 0.00 0.00 1.28
165 166 1.409661 GCGACCCCACTTCCCATAATT 60.410 52.381 0.00 0.00 0.00 1.40
166 167 2.948600 GCGACCCCACTTCCCATAATTT 60.949 50.000 0.00 0.00 0.00 1.82
167 168 3.361786 CGACCCCACTTCCCATAATTTT 58.638 45.455 0.00 0.00 0.00 1.82
168 169 3.380320 CGACCCCACTTCCCATAATTTTC 59.620 47.826 0.00 0.00 0.00 2.29
169 170 4.610333 GACCCCACTTCCCATAATTTTCT 58.390 43.478 0.00 0.00 0.00 2.52
170 171 5.630539 CGACCCCACTTCCCATAATTTTCTA 60.631 44.000 0.00 0.00 0.00 2.10
171 172 6.355588 ACCCCACTTCCCATAATTTTCTAT 57.644 37.500 0.00 0.00 0.00 1.98
172 173 6.752091 ACCCCACTTCCCATAATTTTCTATT 58.248 36.000 0.00 0.00 0.00 1.73
173 174 7.196187 ACCCCACTTCCCATAATTTTCTATTT 58.804 34.615 0.00 0.00 0.00 1.40
205 206 9.901172 ATATTTCTACCTTACGAACCAAAGAAT 57.099 29.630 0.00 0.00 0.00 2.40
208 209 6.633856 TCTACCTTACGAACCAAAGAATACC 58.366 40.000 0.00 0.00 0.00 2.73
298 302 7.770366 TTAGTATGCGTAGGAATTAGGATCA 57.230 36.000 0.00 0.00 0.00 2.92
324 328 8.331730 TCTTTAGTTTTAGGTAATGTCCTTGC 57.668 34.615 0.00 0.00 38.86 4.01
325 329 6.730960 TTAGTTTTAGGTAATGTCCTTGCG 57.269 37.500 0.00 0.00 38.86 4.85
436 471 5.912892 GTAGACTACTACTACTTCCTCCGT 58.087 45.833 5.32 0.00 43.80 4.69
437 472 5.022282 AGACTACTACTACTTCCTCCGTC 57.978 47.826 0.00 0.00 0.00 4.79
438 473 4.716287 AGACTACTACTACTTCCTCCGTCT 59.284 45.833 0.00 0.00 0.00 4.18
439 474 5.022282 ACTACTACTACTTCCTCCGTCTC 57.978 47.826 0.00 0.00 0.00 3.36
440 475 3.996921 ACTACTACTTCCTCCGTCTCA 57.003 47.619 0.00 0.00 0.00 3.27
441 476 3.876341 ACTACTACTTCCTCCGTCTCAG 58.124 50.000 0.00 0.00 0.00 3.35
442 477 2.883122 ACTACTTCCTCCGTCTCAGT 57.117 50.000 0.00 0.00 0.00 3.41
443 478 3.157750 ACTACTTCCTCCGTCTCAGTT 57.842 47.619 0.00 0.00 0.00 3.16
444 479 3.498334 ACTACTTCCTCCGTCTCAGTTT 58.502 45.455 0.00 0.00 0.00 2.66
445 480 4.660168 ACTACTTCCTCCGTCTCAGTTTA 58.340 43.478 0.00 0.00 0.00 2.01
446 481 3.938289 ACTTCCTCCGTCTCAGTTTAC 57.062 47.619 0.00 0.00 0.00 2.01
447 482 3.228453 ACTTCCTCCGTCTCAGTTTACA 58.772 45.455 0.00 0.00 0.00 2.41
448 483 3.640029 ACTTCCTCCGTCTCAGTTTACAA 59.360 43.478 0.00 0.00 0.00 2.41
449 484 3.936372 TCCTCCGTCTCAGTTTACAAG 57.064 47.619 0.00 0.00 0.00 3.16
450 485 3.228453 TCCTCCGTCTCAGTTTACAAGT 58.772 45.455 0.00 0.00 0.00 3.16
451 486 3.255149 TCCTCCGTCTCAGTTTACAAGTC 59.745 47.826 0.00 0.00 0.00 3.01
452 487 3.576648 CTCCGTCTCAGTTTACAAGTCC 58.423 50.000 0.00 0.00 0.00 3.85
453 488 3.228453 TCCGTCTCAGTTTACAAGTCCT 58.772 45.455 0.00 0.00 0.00 3.85
454 489 4.401022 TCCGTCTCAGTTTACAAGTCCTA 58.599 43.478 0.00 0.00 0.00 2.94
455 490 5.014858 TCCGTCTCAGTTTACAAGTCCTAT 58.985 41.667 0.00 0.00 0.00 2.57
456 491 6.182627 TCCGTCTCAGTTTACAAGTCCTATA 58.817 40.000 0.00 0.00 0.00 1.31
457 492 6.094603 TCCGTCTCAGTTTACAAGTCCTATAC 59.905 42.308 0.00 0.00 0.00 1.47
458 493 5.964168 CGTCTCAGTTTACAAGTCCTATACG 59.036 44.000 0.00 0.00 0.00 3.06
459 494 6.402983 CGTCTCAGTTTACAAGTCCTATACGT 60.403 42.308 0.00 0.00 0.00 3.57
460 495 7.201556 CGTCTCAGTTTACAAGTCCTATACGTA 60.202 40.741 0.00 0.00 0.00 3.57
461 496 8.619546 GTCTCAGTTTACAAGTCCTATACGTAT 58.380 37.037 13.54 13.54 0.00 3.06
462 497 9.836864 TCTCAGTTTACAAGTCCTATACGTATA 57.163 33.333 14.39 14.39 0.00 1.47
463 498 9.875675 CTCAGTTTACAAGTCCTATACGTATAC 57.124 37.037 11.27 5.09 0.00 1.47
464 499 8.840321 TCAGTTTACAAGTCCTATACGTATACC 58.160 37.037 11.27 3.14 0.00 2.73
465 500 8.844244 CAGTTTACAAGTCCTATACGTATACCT 58.156 37.037 11.27 5.25 0.00 3.08
468 503 9.507329 TTTACAAGTCCTATACGTATACCTAGG 57.493 37.037 11.27 12.68 33.46 3.02
469 504 7.084268 ACAAGTCCTATACGTATACCTAGGT 57.916 40.000 20.57 20.57 33.81 3.08
470 505 7.521669 ACAAGTCCTATACGTATACCTAGGTT 58.478 38.462 22.11 10.62 33.81 3.50
471 506 7.446625 ACAAGTCCTATACGTATACCTAGGTTG 59.553 40.741 22.11 17.00 33.81 3.77
472 507 5.942826 AGTCCTATACGTATACCTAGGTTGC 59.057 44.000 22.11 10.53 33.81 4.17
473 508 5.124617 GTCCTATACGTATACCTAGGTTGCC 59.875 48.000 22.11 7.02 33.81 4.52
474 509 5.012239 CCTATACGTATACCTAGGTTGCCA 58.988 45.833 22.11 1.21 0.00 4.92
475 510 5.477984 CCTATACGTATACCTAGGTTGCCAA 59.522 44.000 22.11 0.75 0.00 4.52
476 511 6.154021 CCTATACGTATACCTAGGTTGCCAAT 59.846 42.308 22.11 9.64 0.00 3.16
477 512 4.765813 ACGTATACCTAGGTTGCCAATT 57.234 40.909 22.11 0.00 0.00 2.32
478 513 5.106876 ACGTATACCTAGGTTGCCAATTT 57.893 39.130 22.11 0.00 0.00 1.82
479 514 4.879545 ACGTATACCTAGGTTGCCAATTTG 59.120 41.667 22.11 5.60 0.00 2.32
480 515 5.120399 CGTATACCTAGGTTGCCAATTTGA 58.880 41.667 22.11 0.00 0.00 2.69
481 516 5.763204 CGTATACCTAGGTTGCCAATTTGAT 59.237 40.000 22.11 5.71 0.00 2.57
482 517 6.073222 CGTATACCTAGGTTGCCAATTTGATC 60.073 42.308 22.11 0.00 0.00 2.92
483 518 4.046286 ACCTAGGTTGCCAATTTGATCA 57.954 40.909 9.21 0.00 0.00 2.92
484 519 3.763897 ACCTAGGTTGCCAATTTGATCAC 59.236 43.478 9.21 0.00 0.00 3.06
485 520 3.131046 CCTAGGTTGCCAATTTGATCACC 59.869 47.826 0.00 0.85 0.00 4.02
486 521 1.901833 AGGTTGCCAATTTGATCACCC 59.098 47.619 0.00 0.00 0.00 4.61
487 522 1.901833 GGTTGCCAATTTGATCACCCT 59.098 47.619 0.00 0.00 0.00 4.34
488 523 3.096092 GGTTGCCAATTTGATCACCCTA 58.904 45.455 0.00 0.00 0.00 3.53
489 524 3.513515 GGTTGCCAATTTGATCACCCTAA 59.486 43.478 0.00 0.00 0.00 2.69
490 525 4.162131 GGTTGCCAATTTGATCACCCTAAT 59.838 41.667 0.00 0.00 0.00 1.73
491 526 5.362430 GGTTGCCAATTTGATCACCCTAATA 59.638 40.000 0.00 0.00 0.00 0.98
492 527 6.041979 GGTTGCCAATTTGATCACCCTAATAT 59.958 38.462 0.00 0.00 0.00 1.28
493 528 7.232534 GGTTGCCAATTTGATCACCCTAATATA 59.767 37.037 0.00 0.00 0.00 0.86
494 529 8.637986 GTTGCCAATTTGATCACCCTAATATAA 58.362 33.333 0.00 0.00 0.00 0.98
495 530 8.774546 TGCCAATTTGATCACCCTAATATAAA 57.225 30.769 0.00 0.00 0.00 1.40
496 531 8.637986 TGCCAATTTGATCACCCTAATATAAAC 58.362 33.333 0.00 0.00 0.00 2.01
497 532 8.860088 GCCAATTTGATCACCCTAATATAAACT 58.140 33.333 0.00 0.00 0.00 2.66
593 628 6.870971 TGACTTGTATTAGGTTGGTCAAAC 57.129 37.500 0.00 0.00 38.12 2.93
594 629 6.597562 TGACTTGTATTAGGTTGGTCAAACT 58.402 36.000 6.50 6.50 41.91 2.66
595 630 6.485313 TGACTTGTATTAGGTTGGTCAAACTG 59.515 38.462 11.16 0.00 39.03 3.16
596 631 6.597562 ACTTGTATTAGGTTGGTCAAACTGA 58.402 36.000 11.16 3.73 39.03 3.41
597 632 6.485648 ACTTGTATTAGGTTGGTCAAACTGAC 59.514 38.462 11.16 7.24 46.23 3.51
607 642 3.655276 GTCAAACTGACGACCTAGGAA 57.345 47.619 17.98 0.00 37.67 3.36
608 643 4.189639 GTCAAACTGACGACCTAGGAAT 57.810 45.455 17.98 0.00 37.67 3.01
609 644 5.320549 GTCAAACTGACGACCTAGGAATA 57.679 43.478 17.98 0.00 37.67 1.75
610 645 5.100943 GTCAAACTGACGACCTAGGAATAC 58.899 45.833 17.98 4.87 37.67 1.89
611 646 4.103357 CAAACTGACGACCTAGGAATACG 58.897 47.826 17.98 16.64 0.00 3.06
612 647 1.674962 ACTGACGACCTAGGAATACGC 59.325 52.381 17.98 11.35 0.00 4.42
613 648 0.659427 TGACGACCTAGGAATACGCG 59.341 55.000 17.98 3.53 0.00 6.01
614 649 0.659711 GACGACCTAGGAATACGCGC 60.660 60.000 17.98 0.00 0.00 6.86
615 650 1.357690 CGACCTAGGAATACGCGCA 59.642 57.895 17.98 0.00 0.00 6.09
616 651 0.933509 CGACCTAGGAATACGCGCAC 60.934 60.000 17.98 0.00 0.00 5.34
618 653 2.300787 CCTAGGAATACGCGCACGC 61.301 63.158 5.73 4.64 45.53 5.34
619 654 1.299165 CTAGGAATACGCGCACGCT 60.299 57.895 13.70 3.04 45.53 5.07
620 655 1.269444 CTAGGAATACGCGCACGCTC 61.269 60.000 13.70 3.50 45.53 5.03
621 656 1.721664 TAGGAATACGCGCACGCTCT 61.722 55.000 13.70 0.00 45.53 4.09
622 657 2.615618 GAATACGCGCACGCTCTG 59.384 61.111 13.70 0.00 45.53 3.35
623 658 2.126071 AATACGCGCACGCTCTGT 60.126 55.556 13.70 6.38 45.53 3.41
624 659 0.864377 GAATACGCGCACGCTCTGTA 60.864 55.000 13.70 8.43 45.53 2.74
625 660 0.457166 AATACGCGCACGCTCTGTAA 60.457 50.000 13.70 0.00 45.53 2.41
626 661 0.457166 ATACGCGCACGCTCTGTAAA 60.457 50.000 13.70 0.00 45.53 2.01
627 662 1.339235 TACGCGCACGCTCTGTAAAC 61.339 55.000 13.70 0.00 45.53 2.01
628 663 2.372690 CGCGCACGCTCTGTAAACT 61.373 57.895 13.70 0.00 39.32 2.66
629 664 1.130613 GCGCACGCTCTGTAAACTG 59.869 57.895 7.96 0.00 38.26 3.16
630 665 1.282248 GCGCACGCTCTGTAAACTGA 61.282 55.000 7.96 0.00 38.26 3.41
631 666 0.710567 CGCACGCTCTGTAAACTGAG 59.289 55.000 11.45 11.45 42.56 3.35
632 667 1.666023 CGCACGCTCTGTAAACTGAGA 60.666 52.381 18.00 0.00 42.37 3.27
633 668 1.989165 GCACGCTCTGTAAACTGAGAG 59.011 52.381 18.00 16.75 42.37 3.20
635 670 3.290308 ACGCTCTGTAAACTGAGAGTG 57.710 47.619 19.96 14.30 46.72 3.51
636 671 2.885266 ACGCTCTGTAAACTGAGAGTGA 59.115 45.455 19.96 0.00 46.72 3.41
637 672 3.057876 ACGCTCTGTAAACTGAGAGTGAG 60.058 47.826 19.96 9.11 46.72 3.51
638 673 3.671971 CGCTCTGTAAACTGAGAGTGAGG 60.672 52.174 18.00 0.00 45.74 3.86
639 674 3.367910 GCTCTGTAAACTGAGAGTGAGGG 60.368 52.174 18.00 0.00 42.37 4.30
644 679 4.765856 TGTAAACTGAGAGTGAGGGAGTAC 59.234 45.833 0.00 0.00 0.00 2.73
680 715 2.021457 TCATCAATGCTCCATGTGCTG 58.979 47.619 8.95 1.53 0.00 4.41
930 966 1.206849 GAGAGCACCTGGAGAAAGAGG 59.793 57.143 0.00 0.00 35.26 3.69
959 995 3.801638 GCAACAGAACAGAGAAGAGCAGA 60.802 47.826 0.00 0.00 0.00 4.26
981 1017 1.513158 CAGCGACGAATCAGAGGGT 59.487 57.895 0.00 0.00 0.00 4.34
1062 1098 3.052620 GCAGCGCTACCTCGAGTCA 62.053 63.158 10.99 0.00 0.00 3.41
1356 1400 4.128643 GCAAGCTCAATGAGAAGCTCTAT 58.871 43.478 15.38 0.00 36.51 1.98
1401 1445 2.828868 ACCAAGGTGAGCGCAAGA 59.171 55.556 11.47 0.00 43.02 3.02
1666 1710 3.354499 GAAGAAGGTGAAGCGCGCG 62.354 63.158 28.44 28.44 0.00 6.86
1948 1994 2.019249 CGCCATCCACAATTCATGAGT 58.981 47.619 0.00 0.00 0.00 3.41
2014 2060 2.480419 CTGCTTCCGTTAGTTCACTTGG 59.520 50.000 0.00 0.00 0.00 3.61
2057 2110 3.702555 GCCGTGCTGACGTCACAC 61.703 66.667 27.18 27.18 44.54 3.82
2101 2154 6.126409 TGGTTGACTGGATTTGACTTTTACT 58.874 36.000 0.00 0.00 0.00 2.24
2102 2155 6.262273 TGGTTGACTGGATTTGACTTTTACTC 59.738 38.462 0.00 0.00 0.00 2.59
2103 2156 6.294010 GGTTGACTGGATTTGACTTTTACTCC 60.294 42.308 0.00 0.00 0.00 3.85
2104 2157 5.935945 TGACTGGATTTGACTTTTACTCCA 58.064 37.500 0.00 0.00 0.00 3.86
2105 2158 6.361433 TGACTGGATTTGACTTTTACTCCAA 58.639 36.000 0.00 0.00 32.70 3.53
2106 2159 6.831353 TGACTGGATTTGACTTTTACTCCAAA 59.169 34.615 0.00 0.00 32.70 3.28
2115 2168 6.761312 TGACTTTTACTCCAAAATCGGTAGA 58.239 36.000 0.00 0.00 35.59 2.59
2134 2187 5.107182 GGTAGACACTTTTAGTTTCCGCTTC 60.107 44.000 0.00 0.00 0.00 3.86
2139 2192 4.036380 CACTTTTAGTTTCCGCTTCCAAGT 59.964 41.667 0.00 0.00 0.00 3.16
2140 2193 4.275196 ACTTTTAGTTTCCGCTTCCAAGTC 59.725 41.667 0.00 0.00 0.00 3.01
2141 2194 2.074547 TAGTTTCCGCTTCCAAGTCG 57.925 50.000 0.00 0.00 0.00 4.18
2142 2195 0.391597 AGTTTCCGCTTCCAAGTCGA 59.608 50.000 5.17 0.00 0.00 4.20
2143 2196 0.511653 GTTTCCGCTTCCAAGTCGAC 59.488 55.000 7.70 7.70 0.00 4.20
2147 2200 0.600255 CCGCTTCCAAGTCGACAGTT 60.600 55.000 19.50 0.54 0.00 3.16
2148 2201 1.217882 CGCTTCCAAGTCGACAGTTT 58.782 50.000 19.50 0.00 0.00 2.66
2149 2202 1.070577 CGCTTCCAAGTCGACAGTTTG 60.071 52.381 19.50 13.27 0.00 2.93
2150 2203 1.940613 GCTTCCAAGTCGACAGTTTGT 59.059 47.619 19.50 0.00 0.00 2.83
2152 2205 3.746492 GCTTCCAAGTCGACAGTTTGTAT 59.254 43.478 19.50 0.00 0.00 2.29
2153 2206 4.927425 GCTTCCAAGTCGACAGTTTGTATA 59.073 41.667 19.50 0.00 0.00 1.47
2155 2208 6.755141 GCTTCCAAGTCGACAGTTTGTATATA 59.245 38.462 19.50 0.00 0.00 0.86
2156 2209 7.254017 GCTTCCAAGTCGACAGTTTGTATATAC 60.254 40.741 19.50 5.89 0.00 1.47
2157 2210 7.160547 TCCAAGTCGACAGTTTGTATATACA 57.839 36.000 19.50 11.62 0.00 2.29
2159 2212 7.919091 TCCAAGTCGACAGTTTGTATATACATC 59.081 37.037 19.50 12.13 35.89 3.06
2160 2213 7.704899 CCAAGTCGACAGTTTGTATATACATCA 59.295 37.037 19.50 4.00 35.89 3.07
2705 2777 2.420022 CGCCACATGCTTTAAGCTAACT 59.580 45.455 18.20 0.00 42.97 2.24
2768 2998 7.922278 TGAGATTTTGGATAATATTTGCTGTGC 59.078 33.333 0.00 0.00 0.00 4.57
2841 3085 0.387202 AGATGAGATGGACCGCTTCG 59.613 55.000 0.00 0.00 0.00 3.79
2882 3126 1.080230 TGCTCTCTCGCAGCTTGAC 60.080 57.895 0.00 0.00 37.79 3.18
3004 3248 8.511321 TCTTTTGCAAGGCCAATATTATATACG 58.489 33.333 5.01 0.00 0.00 3.06
3005 3249 7.753309 TTTGCAAGGCCAATATTATATACGT 57.247 32.000 5.01 0.00 0.00 3.57
3006 3250 8.850007 TTTGCAAGGCCAATATTATATACGTA 57.150 30.769 5.01 0.00 0.00 3.57
3039 3439 5.659463 TGTAATGTATGCCAGAATTTTGCC 58.341 37.500 0.00 0.00 0.00 4.52
3042 3442 1.138859 GTATGCCAGAATTTTGCCCCC 59.861 52.381 0.00 0.00 0.00 5.40
3073 3474 3.602483 ACACCCGTTTATATGTGTGGAC 58.398 45.455 0.00 0.00 40.24 4.02
3134 3536 6.384305 TCAAGGGATAGATAAATAGGCTAGGC 59.616 42.308 8.55 8.55 0.00 3.93
3150 3552 2.343758 GCGTGCTCTGGACCTCAA 59.656 61.111 0.00 0.00 0.00 3.02
3151 3553 2.029844 GCGTGCTCTGGACCTCAAC 61.030 63.158 0.00 0.00 0.00 3.18
3204 3606 8.819845 TGATATGCTTCTGGACTATGACATATT 58.180 33.333 0.00 0.00 31.48 1.28
3247 3649 6.761714 AGGTGATTACTTTATAGGAGCGTTTG 59.238 38.462 0.00 0.00 0.00 2.93
3275 3678 3.281341 TGTAGTGGCAATTTTCTTGCG 57.719 42.857 0.00 0.00 45.78 4.85
3282 3685 2.029918 GGCAATTTTCTTGCGGTTCTCT 60.030 45.455 4.07 0.00 45.78 3.10
3284 3687 4.159120 GCAATTTTCTTGCGGTTCTCTAC 58.841 43.478 0.00 0.00 35.58 2.59
3352 3756 2.498167 GATCGCATGGTAGCAGGAAAT 58.502 47.619 11.30 2.32 0.00 2.17
3358 3762 5.046663 TCGCATGGTAGCAGGAAATATCATA 60.047 40.000 11.30 0.00 0.00 2.15
3370 3774 7.524202 GCAGGAAATATCATATGCCAAATGTGA 60.524 37.037 0.00 0.00 0.00 3.58
3371 3775 8.528643 CAGGAAATATCATATGCCAAATGTGAT 58.471 33.333 0.00 3.56 34.84 3.06
3372 3776 9.758021 AGGAAATATCATATGCCAAATGTGATA 57.242 29.630 0.00 7.09 36.84 2.15
3500 3951 1.454201 TTTGTTGTTGACGTGGAGCA 58.546 45.000 0.00 0.00 0.00 4.26
3503 3954 2.139917 TGTTGTTGACGTGGAGCATAC 58.860 47.619 0.00 0.00 0.00 2.39
3649 4102 3.876914 GTGATTCCCATGCTATTTCGTCA 59.123 43.478 0.00 0.00 0.00 4.35
3655 7428 4.455533 TCCCATGCTATTTCGTCATTATGC 59.544 41.667 0.00 0.00 0.00 3.14
3687 7460 5.531659 TCTCTTCGATGGTACTACCTTCATC 59.468 44.000 17.26 7.60 41.14 2.92
3702 7475 5.699839 ACCTTCATCGAACAAAATAGTTGC 58.300 37.500 0.00 0.00 0.00 4.17
3772 7546 3.181483 GCTAGGATTCCCAAATGTTGCTG 60.181 47.826 0.00 0.00 33.88 4.41
3848 7622 9.388506 AGGAACTAACATGATCTTCAAAGTATG 57.611 33.333 0.00 0.00 36.02 2.39
3849 7623 8.616076 GGAACTAACATGATCTTCAAAGTATGG 58.384 37.037 0.00 0.00 0.00 2.74
3850 7624 9.167311 GAACTAACATGATCTTCAAAGTATGGT 57.833 33.333 0.00 0.00 0.00 3.55
3899 7674 8.261522 AGTTTATTTGTGAAACCTTAAAAGCCA 58.738 29.630 0.00 0.00 37.48 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.544650 AGGAATCATTTCTGCAAACCAAAG 58.455 37.500 0.00 0.00 32.16 2.77
1 2 5.549742 AGGAATCATTTCTGCAAACCAAA 57.450 34.783 0.00 0.00 32.16 3.28
2 3 6.855763 ATAGGAATCATTTCTGCAAACCAA 57.144 33.333 0.00 0.00 32.16 3.67
3 4 6.855763 AATAGGAATCATTTCTGCAAACCA 57.144 33.333 0.00 0.00 32.16 3.67
4 5 7.550712 AGAAATAGGAATCATTTCTGCAAACC 58.449 34.615 9.00 0.00 46.15 3.27
7 8 9.412460 ACATAGAAATAGGAATCATTTCTGCAA 57.588 29.630 16.67 2.24 46.87 4.08
8 9 8.985315 ACATAGAAATAGGAATCATTTCTGCA 57.015 30.769 16.67 0.00 46.87 4.41
68 69 8.607441 GAATTTTTCCAGGCTAATGTCTTTTT 57.393 30.769 0.00 0.00 0.00 1.94
89 90 9.671279 TGTCATTCGATGCATATAATAGGAATT 57.329 29.630 0.00 0.00 0.00 2.17
90 91 9.842775 ATGTCATTCGATGCATATAATAGGAAT 57.157 29.630 0.00 0.00 0.00 3.01
91 92 9.671279 AATGTCATTCGATGCATATAATAGGAA 57.329 29.630 0.00 0.00 0.00 3.36
92 93 9.671279 AAATGTCATTCGATGCATATAATAGGA 57.329 29.630 0.00 0.00 0.00 2.94
102 103 9.449550 GTATGAAAATAAATGTCATTCGATGCA 57.550 29.630 0.00 0.00 34.01 3.96
103 104 9.449550 TGTATGAAAATAAATGTCATTCGATGC 57.550 29.630 0.00 0.00 34.01 3.91
119 120 9.529325 CATGCATCTCAATTCTTGTATGAAAAT 57.471 29.630 0.00 0.00 35.13 1.82
120 121 7.490079 GCATGCATCTCAATTCTTGTATGAAAA 59.510 33.333 14.21 0.00 35.13 2.29
121 122 6.976349 GCATGCATCTCAATTCTTGTATGAAA 59.024 34.615 14.21 0.00 35.13 2.69
122 123 6.500910 GCATGCATCTCAATTCTTGTATGAA 58.499 36.000 14.21 0.00 35.13 2.57
123 124 5.277634 CGCATGCATCTCAATTCTTGTATGA 60.278 40.000 19.57 0.00 35.13 2.15
124 125 4.909880 CGCATGCATCTCAATTCTTGTATG 59.090 41.667 19.57 0.00 35.92 2.39
125 126 4.818005 TCGCATGCATCTCAATTCTTGTAT 59.182 37.500 19.57 0.00 0.00 2.29
126 127 4.034394 GTCGCATGCATCTCAATTCTTGTA 59.966 41.667 19.57 0.00 0.00 2.41
127 128 3.011818 TCGCATGCATCTCAATTCTTGT 58.988 40.909 19.57 0.00 0.00 3.16
128 129 3.360533 GTCGCATGCATCTCAATTCTTG 58.639 45.455 19.57 0.00 0.00 3.02
129 130 2.357009 GGTCGCATGCATCTCAATTCTT 59.643 45.455 19.57 0.00 0.00 2.52
130 131 1.945394 GGTCGCATGCATCTCAATTCT 59.055 47.619 19.57 0.00 0.00 2.40
131 132 1.002033 GGGTCGCATGCATCTCAATTC 60.002 52.381 19.57 0.00 0.00 2.17
132 133 1.027357 GGGTCGCATGCATCTCAATT 58.973 50.000 19.57 0.00 0.00 2.32
133 134 0.820891 GGGGTCGCATGCATCTCAAT 60.821 55.000 19.57 0.00 0.00 2.57
134 135 1.451927 GGGGTCGCATGCATCTCAA 60.452 57.895 19.57 0.00 0.00 3.02
135 136 2.190313 GGGGTCGCATGCATCTCA 59.810 61.111 19.57 0.00 0.00 3.27
136 137 2.182842 GTGGGGTCGCATGCATCTC 61.183 63.158 19.57 9.46 0.00 2.75
137 138 2.124570 GTGGGGTCGCATGCATCT 60.125 61.111 19.57 0.00 0.00 2.90
138 139 1.718757 GAAGTGGGGTCGCATGCATC 61.719 60.000 19.57 9.50 0.00 3.91
139 140 1.750399 GAAGTGGGGTCGCATGCAT 60.750 57.895 19.57 0.00 0.00 3.96
140 141 2.359850 GAAGTGGGGTCGCATGCA 60.360 61.111 19.57 1.73 0.00 3.96
141 142 3.134127 GGAAGTGGGGTCGCATGC 61.134 66.667 7.91 7.91 0.00 4.06
142 143 2.438434 GGGAAGTGGGGTCGCATG 60.438 66.667 0.00 0.00 0.00 4.06
143 144 0.986019 TATGGGAAGTGGGGTCGCAT 60.986 55.000 8.70 8.70 46.70 4.73
144 145 1.202099 TTATGGGAAGTGGGGTCGCA 61.202 55.000 0.00 0.00 41.53 5.10
145 146 0.182775 ATTATGGGAAGTGGGGTCGC 59.817 55.000 0.00 0.00 0.00 5.19
146 147 2.729028 AATTATGGGAAGTGGGGTCG 57.271 50.000 0.00 0.00 0.00 4.79
147 148 4.610333 AGAAAATTATGGGAAGTGGGGTC 58.390 43.478 0.00 0.00 0.00 4.46
148 149 4.692523 AGAAAATTATGGGAAGTGGGGT 57.307 40.909 0.00 0.00 0.00 4.95
149 150 7.675161 AAATAGAAAATTATGGGAAGTGGGG 57.325 36.000 0.00 0.00 0.00 4.96
188 189 7.910441 TTAAGGTATTCTTTGGTTCGTAAGG 57.090 36.000 0.00 0.00 36.93 2.69
208 209 8.898761 TGGTGCTACCATGTGTTATAATTTAAG 58.101 33.333 4.16 0.00 44.79 1.85
271 275 9.485206 GATCCTAATTCCTACGCATACTAAAAA 57.515 33.333 0.00 0.00 0.00 1.94
282 286 9.765795 AAACTAAAGATGATCCTAATTCCTACG 57.234 33.333 0.00 0.00 0.00 3.51
298 302 8.957466 GCAAGGACATTACCTAAAACTAAAGAT 58.043 33.333 0.00 0.00 39.62 2.40
384 419 1.953686 GTGCCTTGTTAGCTCAAACCA 59.046 47.619 0.00 0.00 0.00 3.67
426 461 3.228453 TGTAAACTGAGACGGAGGAAGT 58.772 45.455 0.00 0.00 0.00 3.01
427 462 3.936372 TGTAAACTGAGACGGAGGAAG 57.064 47.619 0.00 0.00 0.00 3.46
428 463 3.640029 ACTTGTAAACTGAGACGGAGGAA 59.360 43.478 0.00 0.00 0.00 3.36
429 464 3.228453 ACTTGTAAACTGAGACGGAGGA 58.772 45.455 0.00 0.00 0.00 3.71
430 465 3.576648 GACTTGTAAACTGAGACGGAGG 58.423 50.000 0.00 0.00 0.00 4.30
431 466 3.256136 AGGACTTGTAAACTGAGACGGAG 59.744 47.826 0.00 0.00 0.00 4.63
432 467 3.228453 AGGACTTGTAAACTGAGACGGA 58.772 45.455 0.00 0.00 0.00 4.69
433 468 3.662247 AGGACTTGTAAACTGAGACGG 57.338 47.619 0.00 0.00 0.00 4.79
434 469 5.964168 CGTATAGGACTTGTAAACTGAGACG 59.036 44.000 0.00 0.00 0.00 4.18
435 470 6.850555 ACGTATAGGACTTGTAAACTGAGAC 58.149 40.000 0.00 0.00 0.00 3.36
436 471 8.743085 ATACGTATAGGACTTGTAAACTGAGA 57.257 34.615 6.21 0.00 0.00 3.27
437 472 9.875675 GTATACGTATAGGACTTGTAAACTGAG 57.124 37.037 15.52 0.00 0.00 3.35
438 473 8.840321 GGTATACGTATAGGACTTGTAAACTGA 58.160 37.037 15.52 0.00 0.00 3.41
439 474 8.844244 AGGTATACGTATAGGACTTGTAAACTG 58.156 37.037 15.52 0.00 0.00 3.16
440 475 8.986929 AGGTATACGTATAGGACTTGTAAACT 57.013 34.615 15.52 0.00 0.00 2.66
442 477 9.507329 CCTAGGTATACGTATAGGACTTGTAAA 57.493 37.037 15.52 0.00 37.57 2.01
443 478 8.660435 ACCTAGGTATACGTATAGGACTTGTAA 58.340 37.037 23.07 5.83 38.53 2.41
444 479 8.207350 ACCTAGGTATACGTATAGGACTTGTA 57.793 38.462 23.07 6.10 38.53 2.41
445 480 7.084268 ACCTAGGTATACGTATAGGACTTGT 57.916 40.000 23.07 14.96 38.53 3.16
446 481 7.574592 GCAACCTAGGTATACGTATAGGACTTG 60.575 44.444 23.07 18.56 38.53 3.16
447 482 6.432472 GCAACCTAGGTATACGTATAGGACTT 59.568 42.308 23.07 11.56 38.53 3.01
448 483 5.942826 GCAACCTAGGTATACGTATAGGACT 59.057 44.000 23.07 18.69 38.53 3.85
449 484 5.124617 GGCAACCTAGGTATACGTATAGGAC 59.875 48.000 23.07 12.37 38.53 3.85
450 485 5.222109 TGGCAACCTAGGTATACGTATAGGA 60.222 44.000 23.07 9.16 38.53 2.94
451 486 5.012239 TGGCAACCTAGGTATACGTATAGG 58.988 45.833 16.67 16.41 40.58 2.57
452 487 6.579666 TTGGCAACCTAGGTATACGTATAG 57.420 41.667 16.67 5.86 0.00 1.31
453 488 7.543359 AATTGGCAACCTAGGTATACGTATA 57.457 36.000 16.67 11.27 0.00 1.47
454 489 6.429521 AATTGGCAACCTAGGTATACGTAT 57.570 37.500 16.67 13.54 0.00 3.06
455 490 5.874897 AATTGGCAACCTAGGTATACGTA 57.125 39.130 16.67 0.00 0.00 3.57
456 491 4.765813 AATTGGCAACCTAGGTATACGT 57.234 40.909 16.67 3.23 0.00 3.57
457 492 5.120399 TCAAATTGGCAACCTAGGTATACG 58.880 41.667 16.67 5.52 0.00 3.06
458 493 6.770785 TGATCAAATTGGCAACCTAGGTATAC 59.229 38.462 16.67 8.74 0.00 1.47
459 494 6.770785 GTGATCAAATTGGCAACCTAGGTATA 59.229 38.462 16.67 0.00 0.00 1.47
460 495 5.594317 GTGATCAAATTGGCAACCTAGGTAT 59.406 40.000 16.67 0.83 0.00 2.73
461 496 4.947388 GTGATCAAATTGGCAACCTAGGTA 59.053 41.667 16.67 0.00 0.00 3.08
462 497 3.763897 GTGATCAAATTGGCAACCTAGGT 59.236 43.478 9.21 9.21 0.00 3.08
463 498 3.131046 GGTGATCAAATTGGCAACCTAGG 59.869 47.826 7.41 7.41 0.00 3.02
464 499 3.131046 GGGTGATCAAATTGGCAACCTAG 59.869 47.826 13.81 0.00 35.26 3.02
465 500 3.096092 GGGTGATCAAATTGGCAACCTA 58.904 45.455 13.81 0.00 35.26 3.08
466 501 1.901833 GGGTGATCAAATTGGCAACCT 59.098 47.619 13.81 0.00 35.26 3.50
467 502 1.901833 AGGGTGATCAAATTGGCAACC 59.098 47.619 13.40 13.40 38.39 3.77
468 503 4.799564 TTAGGGTGATCAAATTGGCAAC 57.200 40.909 0.00 0.00 0.00 4.17
469 504 8.774546 TTATATTAGGGTGATCAAATTGGCAA 57.225 30.769 0.68 0.68 0.00 4.52
470 505 8.637986 GTTTATATTAGGGTGATCAAATTGGCA 58.362 33.333 0.00 0.00 0.00 4.92
471 506 8.860088 AGTTTATATTAGGGTGATCAAATTGGC 58.140 33.333 0.00 0.00 0.00 4.52
567 602 9.174166 GTTTGACCAACCTAATACAAGTCATAT 57.826 33.333 0.00 0.00 33.21 1.78
568 603 8.380099 AGTTTGACCAACCTAATACAAGTCATA 58.620 33.333 0.00 0.00 35.77 2.15
569 604 7.174946 CAGTTTGACCAACCTAATACAAGTCAT 59.825 37.037 0.00 0.00 35.77 3.06
570 605 6.485313 CAGTTTGACCAACCTAATACAAGTCA 59.515 38.462 0.00 0.00 35.77 3.41
571 606 6.708949 TCAGTTTGACCAACCTAATACAAGTC 59.291 38.462 0.00 0.00 35.77 3.01
572 607 6.485648 GTCAGTTTGACCAACCTAATACAAGT 59.514 38.462 0.00 0.00 41.37 3.16
573 608 6.347402 CGTCAGTTTGACCAACCTAATACAAG 60.347 42.308 3.81 0.00 44.20 3.16
574 609 5.467399 CGTCAGTTTGACCAACCTAATACAA 59.533 40.000 3.81 0.00 44.20 2.41
575 610 4.992319 CGTCAGTTTGACCAACCTAATACA 59.008 41.667 3.81 0.00 44.20 2.29
576 611 5.119743 GTCGTCAGTTTGACCAACCTAATAC 59.880 44.000 3.81 0.00 44.20 1.89
577 612 5.232463 GTCGTCAGTTTGACCAACCTAATA 58.768 41.667 3.81 0.00 44.20 0.98
578 613 4.062991 GTCGTCAGTTTGACCAACCTAAT 58.937 43.478 3.81 0.00 44.20 1.73
579 614 3.460103 GTCGTCAGTTTGACCAACCTAA 58.540 45.455 3.81 0.00 44.20 2.69
580 615 3.102052 GTCGTCAGTTTGACCAACCTA 57.898 47.619 3.81 0.00 44.20 3.08
581 616 1.949465 GTCGTCAGTTTGACCAACCT 58.051 50.000 3.81 0.00 44.20 3.50
587 622 3.655276 TTCCTAGGTCGTCAGTTTGAC 57.345 47.619 9.08 0.00 43.65 3.18
588 623 4.142534 CGTATTCCTAGGTCGTCAGTTTGA 60.143 45.833 9.08 0.00 0.00 2.69
589 624 4.103357 CGTATTCCTAGGTCGTCAGTTTG 58.897 47.826 9.08 0.00 0.00 2.93
590 625 3.428589 GCGTATTCCTAGGTCGTCAGTTT 60.429 47.826 9.08 0.00 0.00 2.66
591 626 2.098770 GCGTATTCCTAGGTCGTCAGTT 59.901 50.000 9.08 0.00 0.00 3.16
592 627 1.674962 GCGTATTCCTAGGTCGTCAGT 59.325 52.381 9.08 0.00 0.00 3.41
593 628 1.333881 CGCGTATTCCTAGGTCGTCAG 60.334 57.143 9.08 0.00 0.00 3.51
594 629 0.659427 CGCGTATTCCTAGGTCGTCA 59.341 55.000 9.08 0.00 0.00 4.35
595 630 0.659711 GCGCGTATTCCTAGGTCGTC 60.660 60.000 8.43 5.93 0.00 4.20
596 631 1.358046 GCGCGTATTCCTAGGTCGT 59.642 57.895 8.43 0.00 0.00 4.34
597 632 0.933509 GTGCGCGTATTCCTAGGTCG 60.934 60.000 8.43 10.72 0.00 4.79
598 633 0.933509 CGTGCGCGTATTCCTAGGTC 60.934 60.000 12.43 0.00 0.00 3.85
599 634 1.065273 CGTGCGCGTATTCCTAGGT 59.935 57.895 12.43 0.00 0.00 3.08
600 635 2.300787 GCGTGCGCGTATTCCTAGG 61.301 63.158 22.18 0.82 40.81 3.02
601 636 3.221956 GCGTGCGCGTATTCCTAG 58.778 61.111 22.18 0.00 40.81 3.02
611 646 1.130613 CAGTTTACAGAGCGTGCGC 59.869 57.895 8.67 8.67 42.33 6.09
612 647 0.710567 CTCAGTTTACAGAGCGTGCG 59.289 55.000 0.00 0.00 0.00 5.34
613 648 1.989165 CTCTCAGTTTACAGAGCGTGC 59.011 52.381 0.00 0.00 30.08 5.34
614 649 2.983136 CACTCTCAGTTTACAGAGCGTG 59.017 50.000 9.85 9.85 40.00 5.34
615 650 2.885266 TCACTCTCAGTTTACAGAGCGT 59.115 45.455 0.00 0.00 40.00 5.07
616 651 3.497118 CTCACTCTCAGTTTACAGAGCG 58.503 50.000 0.00 0.00 40.00 5.03
617 652 3.367910 CCCTCACTCTCAGTTTACAGAGC 60.368 52.174 0.00 0.00 40.00 4.09
618 653 4.082845 TCCCTCACTCTCAGTTTACAGAG 58.917 47.826 0.00 0.00 41.81 3.35
619 654 4.082845 CTCCCTCACTCTCAGTTTACAGA 58.917 47.826 0.00 0.00 0.00 3.41
620 655 3.829601 ACTCCCTCACTCTCAGTTTACAG 59.170 47.826 0.00 0.00 0.00 2.74
621 656 3.845860 ACTCCCTCACTCTCAGTTTACA 58.154 45.455 0.00 0.00 0.00 2.41
622 657 5.011586 AGTACTCCCTCACTCTCAGTTTAC 58.988 45.833 0.00 0.00 0.00 2.01
623 658 5.258216 AGTACTCCCTCACTCTCAGTTTA 57.742 43.478 0.00 0.00 0.00 2.01
624 659 4.120946 AGTACTCCCTCACTCTCAGTTT 57.879 45.455 0.00 0.00 0.00 2.66
625 660 3.818295 AGTACTCCCTCACTCTCAGTT 57.182 47.619 0.00 0.00 0.00 3.16
626 661 3.847780 ACTAGTACTCCCTCACTCTCAGT 59.152 47.826 0.00 0.00 0.00 3.41
627 662 4.497291 ACTAGTACTCCCTCACTCTCAG 57.503 50.000 0.00 0.00 0.00 3.35
628 663 6.384342 TTTACTAGTACTCCCTCACTCTCA 57.616 41.667 0.91 0.00 0.00 3.27
629 664 6.203338 CGATTTACTAGTACTCCCTCACTCTC 59.797 46.154 0.91 0.00 0.00 3.20
630 665 6.056884 CGATTTACTAGTACTCCCTCACTCT 58.943 44.000 0.91 0.00 0.00 3.24
631 666 6.054295 TCGATTTACTAGTACTCCCTCACTC 58.946 44.000 0.91 0.00 0.00 3.51
632 667 5.999044 TCGATTTACTAGTACTCCCTCACT 58.001 41.667 0.91 0.00 0.00 3.41
633 668 5.821995 ACTCGATTTACTAGTACTCCCTCAC 59.178 44.000 0.91 0.00 0.00 3.51
634 669 5.999044 ACTCGATTTACTAGTACTCCCTCA 58.001 41.667 0.91 0.00 0.00 3.86
635 670 6.940831 AACTCGATTTACTAGTACTCCCTC 57.059 41.667 0.91 0.00 0.00 4.30
636 671 8.216423 TGATAACTCGATTTACTAGTACTCCCT 58.784 37.037 0.91 0.00 0.00 4.20
637 672 8.388484 TGATAACTCGATTTACTAGTACTCCC 57.612 38.462 0.91 0.00 0.00 4.30
644 679 9.416794 AGCATTGATGATAACTCGATTTACTAG 57.583 33.333 0.00 0.00 0.00 2.57
930 966 2.036475 TCTCTGTTCTGTTGCTCTGTCC 59.964 50.000 0.00 0.00 0.00 4.02
959 995 0.459237 CTCTGATTCGTCGCTGGCTT 60.459 55.000 0.00 0.00 0.00 4.35
981 1017 7.162082 GGTCCATGTCTTCTTTCTTTCTTCTA 58.838 38.462 0.00 0.00 0.00 2.10
1062 1098 0.540830 ACCTGTCAACGAGCTCCTCT 60.541 55.000 8.47 0.00 0.00 3.69
1401 1445 2.123428 GGCAATGCCGGCTGAGATT 61.123 57.895 29.70 16.16 39.62 2.40
1666 1710 1.064946 CATGGACGAGACCGAGAGC 59.935 63.158 0.00 0.00 39.50 4.09
1932 1976 7.170965 AGAACTGTTACTCATGAATTGTGGAT 58.829 34.615 0.00 0.00 0.00 3.41
1948 1994 5.223449 AGAATCGTGGGAAAGAACTGTTA 57.777 39.130 0.00 0.00 0.00 2.41
2014 2060 7.128331 CCACGTCATCTTATCATCAATTCAAC 58.872 38.462 0.00 0.00 0.00 3.18
2057 2110 5.382616 ACCAACTAGTAAAAAGAAGGGGTG 58.617 41.667 0.00 0.00 0.00 4.61
2101 2154 6.527423 ACTAAAAGTGTCTACCGATTTTGGA 58.473 36.000 0.00 0.00 0.00 3.53
2102 2155 6.796705 ACTAAAAGTGTCTACCGATTTTGG 57.203 37.500 0.00 0.00 0.00 3.28
2103 2156 7.801783 GGAAACTAAAAGTGTCTACCGATTTTG 59.198 37.037 0.00 0.00 32.96 2.44
2104 2157 7.307573 CGGAAACTAAAAGTGTCTACCGATTTT 60.308 37.037 0.00 0.00 39.11 1.82
2105 2158 6.146673 CGGAAACTAAAAGTGTCTACCGATTT 59.853 38.462 0.00 0.00 39.11 2.17
2106 2159 5.636543 CGGAAACTAAAAGTGTCTACCGATT 59.363 40.000 0.00 0.00 39.11 3.34
2115 2168 3.547746 TGGAAGCGGAAACTAAAAGTGT 58.452 40.909 0.00 0.00 0.00 3.55
2134 2187 7.704899 TGATGTATATACAAACTGTCGACTTGG 59.295 37.037 19.11 9.41 39.99 3.61
2705 2777 3.216800 AGTACCGATAATACAGCACGGA 58.783 45.455 0.00 0.00 45.31 4.69
2768 2998 4.060900 ACGGCTGCTAATATTGTCTCATG 58.939 43.478 0.00 0.00 0.00 3.07
2841 3085 1.407258 CTCCACCGTCTCCTTCATCTC 59.593 57.143 0.00 0.00 0.00 2.75
3011 3411 9.467258 CAAAATTCTGGCATACATTACATAAGG 57.533 33.333 0.00 0.00 0.00 2.69
3093 3494 3.118738 CCCTTGAGTTATTGCCTCGTACT 60.119 47.826 0.00 0.00 0.00 2.73
3134 3536 1.734477 CGTTGAGGTCCAGAGCACG 60.734 63.158 0.00 0.00 0.00 5.34
3150 3552 3.244078 TGCTCATGAAGACCTTTACACGT 60.244 43.478 0.00 0.00 0.00 4.49
3151 3553 3.325870 TGCTCATGAAGACCTTTACACG 58.674 45.455 0.00 0.00 0.00 4.49
3238 3640 5.390567 CCACTACATTTCTTACAAACGCTCC 60.391 44.000 0.00 0.00 0.00 4.70
3247 3649 8.915654 CAAGAAAATTGCCACTACATTTCTTAC 58.084 33.333 10.03 0.00 42.19 2.34
3649 4102 5.282055 TCGAAGAGATTGGTCTGCATAAT 57.718 39.130 0.00 0.00 33.97 1.28
3655 7428 3.533606 ACCATCGAAGAGATTGGTCTG 57.466 47.619 0.19 0.00 43.63 3.51
3722 7495 4.221041 TCAATGACATCATGCAATTGGTGT 59.779 37.500 5.90 5.90 43.53 4.16
3723 7496 4.749976 TCAATGACATCATGCAATTGGTG 58.250 39.130 7.72 0.00 36.56 4.17
3724 7497 4.679639 GCTCAATGACATCATGCAATTGGT 60.680 41.667 7.72 0.00 36.56 3.67
3725 7498 3.802139 GCTCAATGACATCATGCAATTGG 59.198 43.478 7.72 5.55 36.56 3.16
3772 7546 4.695928 GGAGTAGGTGTCAAAATCAGTTCC 59.304 45.833 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.