Multiple sequence alignment - TraesCS1D01G020000

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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 TraesCS1D01G020000 chr1D 100.000 3562 0 0 1 3562 8711804 8715365 0.000000e+00 6578
1 TraesCS1D01G020000 chr1D 85.299 619 91 0 1787 2405 252528696 252528078 1.080000e-179 640
2 TraesCS1D01G020000 chr1D 86.250 400 55 0 1145 1544 252529222 252528823 5.460000e-118 435
3 TraesCS1D01G020000 chr1D 95.312 64 3 0 999 1062 252529387 252529324 6.290000e-18 102
4 TraesCS1D01G020000 chr1A 89.182 3106 178 58 567 3554 10066742 10069807 0.000000e+00 3729
5 TraesCS1D01G020000 chr1A 84.814 619 94 0 1787 2405 323643083 323642465 1.090000e-174 623
6 TraesCS1D01G020000 chr1A 86.250 400 55 0 1145 1544 323643608 323643209 5.460000e-118 435
7 TraesCS1D01G020000 chr1A 82.231 242 15 11 15 232 10066079 10066316 2.180000e-42 183
8 TraesCS1D01G020000 chr1B 91.435 2405 121 38 651 3009 11857882 11860247 0.000000e+00 3221
9 TraesCS1D01G020000 chr1B 86.268 619 85 0 1787 2405 360808768 360809386 0.000000e+00 673
10 TraesCS1D01G020000 chr1B 85.851 417 56 3 1130 1544 360808226 360808641 1.170000e-119 440
11 TraesCS1D01G020000 chr5D 86.538 624 82 2 1782 2404 210375313 210374691 0.000000e+00 686
12 TraesCS1D01G020000 chr5D 80.866 554 86 16 999 1544 210375928 210375387 5.500000e-113 418
13 TraesCS1D01G020000 chr5B 86.378 624 83 2 1782 2404 223984469 223983847 0.000000e+00 680
14 TraesCS1D01G020000 chr5B 80.978 552 89 13 999 1544 223985083 223984542 1.180000e-114 424
15 TraesCS1D01G020000 chr5B 84.878 410 61 1 1145 1553 680360522 680360113 2.560000e-111 412
16 TraesCS1D01G020000 chr5B 89.308 159 17 0 3068 3226 502024144 502024302 2.170000e-47 200
17 TraesCS1D01G020000 chr5B 88.024 167 20 0 3070 3236 490757412 490757578 7.800000e-47 198
18 TraesCS1D01G020000 chr5A 86.378 624 83 2 1782 2404 272132572 272131950 0.000000e+00 680
19 TraesCS1D01G020000 chr5A 81.273 550 87 14 999 1544 272133183 272132646 7.060000e-117 431
20 TraesCS1D01G020000 chr4B 85.427 398 58 0 1146 1543 39120609 39121006 7.110000e-112 414
21 TraesCS1D01G020000 chr4A 85.427 398 58 0 1146 1543 576703435 576703038 7.110000e-112 414
22 TraesCS1D01G020000 chr4A 85.250 400 59 0 1145 1544 629859028 629859427 2.560000e-111 412
23 TraesCS1D01G020000 chr4A 89.634 164 15 2 3069 3231 137966978 137967140 1.300000e-49 207
24 TraesCS1D01G020000 chr4A 89.634 164 15 2 3069 3231 137972831 137972669 1.300000e-49 207
25 TraesCS1D01G020000 chr4A 88.272 162 19 0 3070 3231 614112477 614112316 1.010000e-45 195
26 TraesCS1D01G020000 chr4D 88.690 168 14 4 3065 3231 509826583 509826420 2.170000e-47 200
27 TraesCS1D01G020000 chr7B 87.059 170 20 2 3070 3238 102234478 102234310 1.310000e-44 191
28 TraesCS1D01G020000 chr2D 85.876 177 25 0 3066 3242 571078954 571079130 4.690000e-44 189


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 TraesCS1D01G020000 chr1D 8711804 8715365 3561 False 6578.000000 6578 100.000000 1 3562 1 chr1D.!!$F1 3561
1 TraesCS1D01G020000 chr1D 252528078 252529387 1309 True 392.333333 640 88.953667 999 2405 3 chr1D.!!$R1 1406
2 TraesCS1D01G020000 chr1A 10066079 10069807 3728 False 1956.000000 3729 85.706500 15 3554 2 chr1A.!!$F1 3539
3 TraesCS1D01G020000 chr1A 323642465 323643608 1143 True 529.000000 623 85.532000 1145 2405 2 chr1A.!!$R1 1260
4 TraesCS1D01G020000 chr1B 11857882 11860247 2365 False 3221.000000 3221 91.435000 651 3009 1 chr1B.!!$F1 2358
5 TraesCS1D01G020000 chr1B 360808226 360809386 1160 False 556.500000 673 86.059500 1130 2405 2 chr1B.!!$F2 1275
6 TraesCS1D01G020000 chr5D 210374691 210375928 1237 True 552.000000 686 83.702000 999 2404 2 chr5D.!!$R1 1405
7 TraesCS1D01G020000 chr5B 223983847 223985083 1236 True 552.000000 680 83.678000 999 2404 2 chr5B.!!$R2 1405
8 TraesCS1D01G020000 chr5A 272131950 272133183 1233 True 555.500000 680 83.825500 999 2404 2 chr5A.!!$R1 1405

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
388 459 0.179156 CAATCACTTGCGTGCCATCC 60.179 55.0 0.0 0.0 40.99 3.51 F
1581 1830 0.250901 AGTTCGGTGATGCTTTGCCT 60.251 50.0 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1847 0.698238 AGGGCAGCATAACAGAACCA 59.302 50.000 0.00 0.00 0.00 3.67 R
3331 3644 1.067364 CAAGGTGTCAGCAAATGCACA 59.933 47.619 8.28 1.31 45.16 4.57 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 4.172923 TCTCCTCTCCTCCGTCCT 57.827 61.111 0.00 0.00 0.00 3.85
19 20 1.152839 CTCCTCTCCTCCGTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
50 51 2.477176 CGTCTCAGCCTCCTCCGAG 61.477 68.421 0.00 0.00 35.72 4.63
52 53 2.441901 CTCAGCCTCCTCCGAGCT 60.442 66.667 0.00 0.00 34.49 4.09
53 54 2.441164 TCAGCCTCCTCCGAGCTC 60.441 66.667 2.73 2.73 34.49 4.09
54 55 3.898509 CAGCCTCCTCCGAGCTCG 61.899 72.222 29.06 29.06 34.49 5.03
57 58 3.591835 CCTCCTCCGAGCTCGCTC 61.592 72.222 30.49 8.82 39.55 5.03
101 122 3.333680 ACCAACCTCTCTCTCTCTCTCTT 59.666 47.826 0.00 0.00 0.00 2.85
119 144 3.999663 CTCTTTCTCTTGGTACCTTGCTG 59.000 47.826 14.36 0.00 0.00 4.41
129 154 2.012673 GTACCTTGCTGGATCTTGCTG 58.987 52.381 10.71 5.19 39.71 4.41
135 160 2.747460 TGGATCTTGCTGTGCGCC 60.747 61.111 4.18 0.00 38.05 6.53
222 247 3.119096 GAACTCGGGCGCTTCACC 61.119 66.667 7.64 0.00 0.00 4.02
232 257 1.901650 GCGCTTCACCGTCTTCTTGG 61.902 60.000 0.00 0.00 0.00 3.61
234 259 0.955919 GCTTCACCGTCTTCTTGGGG 60.956 60.000 0.00 0.00 0.00 4.96
237 262 3.647771 ACCGTCTTCTTGGGGCCC 61.648 66.667 18.17 18.17 0.00 5.80
243 268 4.360405 TTCTTGGGGCCCGCCTTC 62.360 66.667 19.83 0.88 36.10 3.46
246 271 4.676951 TTGGGGCCCGCCTTCTTG 62.677 66.667 19.83 0.00 36.10 3.02
249 274 4.803908 GGGCCCGCCTTCTTGGAG 62.804 72.222 5.69 0.00 38.35 3.86
250 275 4.035102 GGCCCGCCTTCTTGGAGT 62.035 66.667 0.00 0.00 38.35 3.85
266 337 2.192608 GAGTTGCTGCCGCTTCTTGG 62.193 60.000 0.70 0.00 36.97 3.61
276 347 1.377856 GCTTCTTGGCTGGACCTCC 60.378 63.158 0.00 0.00 40.22 4.30
280 351 3.612247 CTTGGCTGGACCTCCACCG 62.612 68.421 5.67 0.00 42.01 4.94
341 412 2.050714 CGTGTTGCTGCTTGCTGG 60.051 61.111 0.00 0.00 43.37 4.85
342 413 2.355481 GTGTTGCTGCTTGCTGGC 60.355 61.111 0.00 3.51 43.37 4.85
344 415 4.712425 GTTGCTGCTTGCTGGCCG 62.712 66.667 0.00 0.00 43.37 6.13
361 432 4.699522 GGCGACTGCTCCCGGTTT 62.700 66.667 0.00 0.00 42.25 3.27
365 436 4.699522 ACTGCTCCCGGTTTCCGC 62.700 66.667 0.00 0.00 46.86 5.54
367 438 4.697756 TGCTCCCGGTTTCCGCAG 62.698 66.667 0.00 2.41 46.86 5.18
387 458 3.317608 CAATCACTTGCGTGCCATC 57.682 52.632 0.00 0.00 40.99 3.51
388 459 0.179156 CAATCACTTGCGTGCCATCC 60.179 55.000 0.00 0.00 40.99 3.51
389 460 0.608856 AATCACTTGCGTGCCATCCA 60.609 50.000 0.00 0.00 40.99 3.41
392 463 4.170062 CTTGCGTGCCATCCAGCG 62.170 66.667 0.00 0.00 34.65 5.18
409 480 2.825836 GCGTCCATTCCCCTGCTG 60.826 66.667 0.00 0.00 0.00 4.41
410 481 2.671070 CGTCCATTCCCCTGCTGT 59.329 61.111 0.00 0.00 0.00 4.40
411 482 1.746615 CGTCCATTCCCCTGCTGTG 60.747 63.158 0.00 0.00 0.00 3.66
412 483 1.380302 GTCCATTCCCCTGCTGTGT 59.620 57.895 0.00 0.00 0.00 3.72
413 484 0.251341 GTCCATTCCCCTGCTGTGTT 60.251 55.000 0.00 0.00 0.00 3.32
414 485 0.482446 TCCATTCCCCTGCTGTGTTT 59.518 50.000 0.00 0.00 0.00 2.83
417 488 1.270550 CATTCCCCTGCTGTGTTTGTC 59.729 52.381 0.00 0.00 0.00 3.18
418 489 0.467290 TTCCCCTGCTGTGTTTGTCC 60.467 55.000 0.00 0.00 0.00 4.02
419 490 2.260869 CCCCTGCTGTGTTTGTCCG 61.261 63.158 0.00 0.00 0.00 4.79
420 491 2.260869 CCCTGCTGTGTTTGTCCGG 61.261 63.158 0.00 0.00 0.00 5.14
423 494 2.904866 GCTGTGTTTGTCCGGCCA 60.905 61.111 2.24 0.00 0.00 5.36
424 495 2.268076 GCTGTGTTTGTCCGGCCAT 61.268 57.895 2.24 0.00 0.00 4.40
427 498 1.372872 GTGTTTGTCCGGCCATTGC 60.373 57.895 2.24 0.00 0.00 3.56
428 499 2.126502 GTTTGTCCGGCCATTGCG 60.127 61.111 2.24 0.00 38.85 4.85
444 515 4.577246 CGCCTCCACGCTAGCTCC 62.577 72.222 13.93 0.00 0.00 4.70
446 517 1.828660 GCCTCCACGCTAGCTCCTA 60.829 63.158 13.93 0.00 0.00 2.94
447 518 1.801309 GCCTCCACGCTAGCTCCTAG 61.801 65.000 13.93 5.19 37.16 3.02
448 519 1.175983 CCTCCACGCTAGCTCCTAGG 61.176 65.000 13.93 0.82 34.88 3.02
449 520 1.801309 CTCCACGCTAGCTCCTAGGC 61.801 65.000 13.93 0.00 34.88 3.93
450 521 2.127869 CCACGCTAGCTCCTAGGCA 61.128 63.158 13.93 0.00 34.88 4.75
451 522 1.467678 CCACGCTAGCTCCTAGGCAT 61.468 60.000 13.93 0.00 34.88 4.40
452 523 0.319383 CACGCTAGCTCCTAGGCATG 60.319 60.000 13.93 0.00 34.88 4.06
453 524 1.373999 CGCTAGCTCCTAGGCATGC 60.374 63.158 13.93 9.90 34.88 4.06
454 525 1.750930 GCTAGCTCCTAGGCATGCA 59.249 57.895 21.36 0.00 34.88 3.96
455 526 0.320596 GCTAGCTCCTAGGCATGCAG 60.321 60.000 21.36 9.17 34.88 4.41
456 527 1.047002 CTAGCTCCTAGGCATGCAGT 58.953 55.000 21.36 8.63 31.03 4.40
457 528 1.415659 CTAGCTCCTAGGCATGCAGTT 59.584 52.381 21.36 8.28 31.03 3.16
458 529 0.622665 AGCTCCTAGGCATGCAGTTT 59.377 50.000 21.36 4.24 34.17 2.66
461 603 2.440409 CTCCTAGGCATGCAGTTTGTT 58.560 47.619 21.36 0.00 0.00 2.83
467 609 4.192429 AGGCATGCAGTTTGTTATTTCC 57.808 40.909 21.36 0.00 0.00 3.13
475 617 4.261447 GCAGTTTGTTATTTCCTGTCGGTT 60.261 41.667 0.00 0.00 0.00 4.44
499 641 1.003580 TGAGGATCACTTCCCTTGTGC 59.996 52.381 0.00 0.00 46.81 4.57
520 666 3.181476 GCAAAAACCAGCAGAGAGGAAAA 60.181 43.478 0.00 0.00 0.00 2.29
521 667 4.363138 CAAAAACCAGCAGAGAGGAAAAC 58.637 43.478 0.00 0.00 0.00 2.43
522 668 3.584733 AAACCAGCAGAGAGGAAAACT 57.415 42.857 0.00 0.00 0.00 2.66
523 669 4.706842 AAACCAGCAGAGAGGAAAACTA 57.293 40.909 0.00 0.00 0.00 2.24
524 670 4.917906 AACCAGCAGAGAGGAAAACTAT 57.082 40.909 0.00 0.00 0.00 2.12
530 676 5.635417 GCAGAGAGGAAAACTATGCTTTT 57.365 39.130 0.00 0.00 45.32 2.27
531 677 6.743575 GCAGAGAGGAAAACTATGCTTTTA 57.256 37.500 0.00 0.00 45.32 1.52
567 721 9.226606 TCATTTCAATTTCGTAATAGTCCTTGT 57.773 29.630 0.00 0.00 0.00 3.16
571 725 8.251750 TCAATTTCGTAATAGTCCTTGTCAAG 57.748 34.615 5.53 5.53 0.00 3.02
572 726 6.663944 ATTTCGTAATAGTCCTTGTCAAGC 57.336 37.500 7.09 0.00 0.00 4.01
581 735 0.959372 CCTTGTCAAGCTGGCCTGAG 60.959 60.000 14.77 0.00 0.00 3.35
590 744 1.451567 CTGGCCTGAGCTGATGTGG 60.452 63.158 3.32 0.00 39.73 4.17
615 769 3.272334 GCCATGGCGTCGGTCATC 61.272 66.667 23.48 0.00 36.00 2.92
616 770 2.961721 CCATGGCGTCGGTCATCG 60.962 66.667 0.00 0.00 36.00 3.84
619 773 0.526739 CATGGCGTCGGTCATCGTTA 60.527 55.000 0.00 0.00 36.00 3.18
620 774 0.387929 ATGGCGTCGGTCATCGTTAT 59.612 50.000 0.00 0.00 31.35 1.89
621 775 0.526739 TGGCGTCGGTCATCGTTATG 60.527 55.000 0.00 0.00 40.32 1.90
622 776 0.526954 GGCGTCGGTCATCGTTATGT 60.527 55.000 0.00 0.00 40.32 2.29
623 777 1.268692 GGCGTCGGTCATCGTTATGTA 60.269 52.381 0.00 0.00 40.32 2.29
655 817 4.095782 TGAAATCCTAGTTTTACGCCATGC 59.904 41.667 0.00 0.00 0.00 4.06
683 845 0.823356 AGCACCACCAACCATCACAC 60.823 55.000 0.00 0.00 0.00 3.82
692 854 3.886505 ACCAACCATCACACGTTTATTGT 59.113 39.130 0.00 0.00 0.00 2.71
734 900 5.758784 GCCTACAAACTATAGCTTAACCCTG 59.241 44.000 0.00 0.00 0.00 4.45
739 905 2.104963 ACTATAGCTTAACCCTGCCTGC 59.895 50.000 0.00 0.00 0.00 4.85
813 981 6.630071 CCCTTGTTTATTTAACATCCAGTGG 58.370 40.000 1.40 1.40 45.72 4.00
823 992 0.675083 CATCCAGTGGTTGCTTTGCA 59.325 50.000 9.54 0.00 36.47 4.08
861 1030 3.491267 CGTCTTTCTGTCTTTCTTTCGCT 59.509 43.478 0.00 0.00 0.00 4.93
941 1111 5.869888 GTGTTTCTCTGTATTAGGGTGACAG 59.130 44.000 0.00 0.00 41.62 3.51
967 1137 5.029650 TGCTCGCCATTAATTATTTAGCG 57.970 39.130 12.19 12.19 43.20 4.26
1206 1452 0.753262 CTAGCATAGTTGGTCGCCCT 59.247 55.000 0.00 0.00 34.79 5.19
1567 1816 3.497262 GGACTGTTCCACCTTTTAGTTCG 59.503 47.826 0.00 0.00 42.30 3.95
1580 1829 1.448985 TAGTTCGGTGATGCTTTGCC 58.551 50.000 0.00 0.00 0.00 4.52
1581 1830 0.250901 AGTTCGGTGATGCTTTGCCT 60.251 50.000 0.00 0.00 0.00 4.75
1585 1834 1.003118 TCGGTGATGCTTTGCCTAGTT 59.997 47.619 0.00 0.00 0.00 2.24
1587 1836 3.006940 CGGTGATGCTTTGCCTAGTTAA 58.993 45.455 0.00 0.00 0.00 2.01
1588 1837 3.438781 CGGTGATGCTTTGCCTAGTTAAA 59.561 43.478 0.00 0.00 0.00 1.52
1589 1838 4.671766 CGGTGATGCTTTGCCTAGTTAAAC 60.672 45.833 0.00 0.00 0.00 2.01
1590 1839 4.459337 GGTGATGCTTTGCCTAGTTAAACT 59.541 41.667 0.00 0.00 0.00 2.66
1591 1840 5.646360 GGTGATGCTTTGCCTAGTTAAACTA 59.354 40.000 0.00 0.00 0.00 2.24
1593 1842 5.646360 TGATGCTTTGCCTAGTTAAACTACC 59.354 40.000 0.00 0.00 0.00 3.18
1596 1845 6.066032 TGCTTTGCCTAGTTAAACTACCTTT 58.934 36.000 0.00 0.00 0.00 3.11
1597 1846 7.225725 TGCTTTGCCTAGTTAAACTACCTTTA 58.774 34.615 0.00 0.00 0.00 1.85
1598 1847 7.886446 TGCTTTGCCTAGTTAAACTACCTTTAT 59.114 33.333 0.00 0.00 0.00 1.40
1599 1848 8.182227 GCTTTGCCTAGTTAAACTACCTTTATG 58.818 37.037 0.00 0.00 0.00 1.90
1615 1868 4.202050 CCTTTATGGTTCTGTTATGCTGCC 60.202 45.833 0.00 0.00 0.00 4.85
1629 1903 0.962855 GCTGCCCTCTTCAACCTTCC 60.963 60.000 0.00 0.00 0.00 3.46
1636 1910 3.245052 CCCTCTTCAACCTTCCATTGTCT 60.245 47.826 0.00 0.00 0.00 3.41
1654 1931 9.440773 CCATTGTCTAGCTATGATTATGCTTAA 57.559 33.333 0.00 0.00 38.15 1.85
1665 1942 5.893687 TGATTATGCTTAATGTGGCTTGTG 58.106 37.500 9.42 0.00 0.00 3.33
1672 1949 5.925397 TGCTTAATGTGGCTTGTGTAATTTG 59.075 36.000 0.00 0.00 0.00 2.32
1676 1953 4.517952 TGTGGCTTGTGTAATTTGGATG 57.482 40.909 0.00 0.00 0.00 3.51
1712 1989 4.701956 TTGCTGCTTATTTCTTACTGCC 57.298 40.909 0.00 0.00 0.00 4.85
1723 2000 5.581126 TTTCTTACTGCCCTATTGCATTG 57.419 39.130 0.00 0.00 41.16 2.82
1740 2017 3.304592 GCATTGGGGAAAACAATTGCAAC 60.305 43.478 0.00 0.00 36.47 4.17
1743 2020 5.359194 TTGGGGAAAACAATTGCAACTAA 57.641 34.783 0.00 0.00 0.00 2.24
1885 2181 0.881118 TTCGTTTGGATCTTGCTGGC 59.119 50.000 0.00 0.00 0.00 4.85
1888 2184 1.074775 TTTGGATCTTGCTGGCCGT 59.925 52.632 0.00 0.00 0.00 5.68
1984 2280 5.576563 TTGTAAGGGACATCAAGGAGAAA 57.423 39.130 0.00 0.00 38.07 2.52
2170 2466 4.099633 AGTCTTCTGGAATCCATGAGACA 58.900 43.478 29.98 8.02 42.53 3.41
2375 2671 0.470833 CTGGATCGGAGGGTCCATCT 60.471 60.000 3.08 0.00 40.66 2.90
2406 2702 2.171659 TCAGCACTTTCCAACAGGTACA 59.828 45.455 0.00 0.00 0.00 2.90
2407 2703 2.290641 CAGCACTTTCCAACAGGTACAC 59.709 50.000 0.00 0.00 0.00 2.90
2420 2716 2.037772 CAGGTACACCTCTTGTTCAGCT 59.962 50.000 0.00 0.00 46.65 4.24
2421 2717 2.706190 AGGTACACCTCTTGTTCAGCTT 59.294 45.455 0.00 0.00 44.77 3.74
2430 2728 4.453819 CCTCTTGTTCAGCTTTACCTTCTG 59.546 45.833 0.00 0.00 0.00 3.02
2435 2733 5.925509 TGTTCAGCTTTACCTTCTGTAACT 58.074 37.500 0.00 0.00 39.13 2.24
2441 2739 6.876257 CAGCTTTACCTTCTGTAACTCATCTT 59.124 38.462 0.00 0.00 39.13 2.40
2446 2744 5.342866 ACCTTCTGTAACTCATCTTACCCT 58.657 41.667 0.00 0.00 0.00 4.34
2447 2745 5.785940 ACCTTCTGTAACTCATCTTACCCTT 59.214 40.000 0.00 0.00 0.00 3.95
2448 2746 6.070710 ACCTTCTGTAACTCATCTTACCCTTC 60.071 42.308 0.00 0.00 0.00 3.46
2449 2747 6.070767 CCTTCTGTAACTCATCTTACCCTTCA 60.071 42.308 0.00 0.00 0.00 3.02
2450 2748 7.365117 CCTTCTGTAACTCATCTTACCCTTCAT 60.365 40.741 0.00 0.00 0.00 2.57
2451 2749 7.496346 TCTGTAACTCATCTTACCCTTCATT 57.504 36.000 0.00 0.00 0.00 2.57
2452 2750 7.556844 TCTGTAACTCATCTTACCCTTCATTC 58.443 38.462 0.00 0.00 0.00 2.67
2456 2754 9.178758 GTAACTCATCTTACCCTTCATTCAAAT 57.821 33.333 0.00 0.00 0.00 2.32
2468 2766 7.179694 ACCCTTCATTCAAATCAACATCTGAAT 59.820 33.333 0.00 0.00 38.69 2.57
2469 2767 7.705325 CCCTTCATTCAAATCAACATCTGAATC 59.295 37.037 0.00 0.00 36.59 2.52
2482 2780 9.835389 TCAACATCTGAATCATATTATGTGTGA 57.165 29.630 3.67 0.00 32.16 3.58
2485 2783 9.269453 ACATCTGAATCATATTATGTGTGACTG 57.731 33.333 3.67 0.00 30.22 3.51
2486 2784 8.718734 CATCTGAATCATATTATGTGTGACTGG 58.281 37.037 3.67 0.00 30.22 4.00
2855 3162 9.364989 GCTCATGGTTTTTGCTATGTATTTTTA 57.635 29.630 0.00 0.00 0.00 1.52
2966 3278 7.147846 GGACCATTTTCCATGTGATTATCAACT 60.148 37.037 0.00 0.00 35.49 3.16
3043 3355 2.073232 AGGTTCAGCTGCCTGATGT 58.927 52.632 9.47 0.00 46.84 3.06
3046 3358 1.740025 GGTTCAGCTGCCTGATGTTAC 59.260 52.381 9.47 0.00 46.84 2.50
3081 3393 7.669722 TGAAAAGCAAATATTACTCCCTCTGTT 59.330 33.333 0.00 0.00 0.00 3.16
3092 3404 7.989947 TTACTCCCTCTGTTCCTAAATATGT 57.010 36.000 0.00 0.00 0.00 2.29
3093 3405 6.487299 ACTCCCTCTGTTCCTAAATATGTC 57.513 41.667 0.00 0.00 0.00 3.06
3125 3438 9.982651 TTAGAGATTTCAATACAGGCTACATAC 57.017 33.333 0.00 0.00 0.00 2.39
3134 3447 9.528489 TCAATACAGGCTACATACAGATGTATA 57.472 33.333 5.21 0.00 45.42 1.47
3142 3455 7.708322 GGCTACATACAGATGTATATGGACATG 59.292 40.741 5.21 0.00 45.42 3.21
3152 3465 8.801299 AGATGTATATGGACATGTTCTAGAGTG 58.199 37.037 5.55 0.00 40.18 3.51
3161 3474 6.531948 GGACATGTTCTAGAGTGTACATTCAC 59.468 42.308 19.24 9.72 38.46 3.18
3178 3491 6.112734 ACATTCACTCATTTTGCTCCGTATA 58.887 36.000 0.00 0.00 0.00 1.47
3184 3497 7.652105 TCACTCATTTTGCTCCGTATATAGTTC 59.348 37.037 0.00 0.00 0.00 3.01
3188 3501 9.990360 TCATTTTGCTCCGTATATAGTTCATAA 57.010 29.630 0.00 0.00 0.00 1.90
3303 3616 7.604545 TCATCAAAGAATTACATGTTACGGACA 59.395 33.333 2.30 0.00 43.71 4.02
3339 3652 8.584157 TGTCTTTATTAGGAACATTGTGCATTT 58.416 29.630 0.00 0.00 0.00 2.32
3345 3658 2.733026 GGAACATTGTGCATTTGCTGAC 59.267 45.455 3.94 0.00 42.66 3.51
3346 3659 3.382855 GAACATTGTGCATTTGCTGACA 58.617 40.909 3.94 0.00 42.66 3.58
3348 3661 2.063266 CATTGTGCATTTGCTGACACC 58.937 47.619 3.94 0.00 42.66 4.16
3356 3669 4.280425 TGCATTTGCTGACACCTTGAAATA 59.720 37.500 3.94 0.00 42.66 1.40
3368 3681 8.567948 TGACACCTTGAAATAATTTGAGTTCTC 58.432 33.333 0.00 0.00 0.00 2.87
3440 3753 1.064003 AACCCTCCACTATGTGTGCA 58.936 50.000 0.00 0.00 44.92 4.57
3446 3780 0.800631 CCACTATGTGTGCACTGCTG 59.199 55.000 19.41 7.10 44.92 4.41
3461 3795 1.153005 GCTGGGGGCTCATCTTCAG 60.153 63.158 0.00 0.00 38.06 3.02
3462 3796 1.530771 CTGGGGGCTCATCTTCAGG 59.469 63.158 0.00 0.00 0.00 3.86
3464 3798 2.381941 GGGGGCTCATCTTCAGGCT 61.382 63.158 0.00 0.00 36.67 4.58
3496 3830 7.392953 TGAATATGAGCACCAAATACTTGTTCA 59.607 33.333 0.00 0.00 0.00 3.18
3535 3869 0.815095 TTTCATCGACGCTGCCTAGA 59.185 50.000 0.00 0.00 0.00 2.43
3536 3870 0.100682 TTCATCGACGCTGCCTAGAC 59.899 55.000 0.00 0.00 0.00 2.59
3554 3888 2.109304 AGACCCCGGAAAGGAAAATTCA 59.891 45.455 0.73 0.00 45.00 2.57
3555 3889 2.894765 GACCCCGGAAAGGAAAATTCAA 59.105 45.455 0.73 0.00 45.00 2.69
3556 3890 2.631062 ACCCCGGAAAGGAAAATTCAAC 59.369 45.455 0.73 0.00 45.00 3.18
3557 3891 2.897326 CCCCGGAAAGGAAAATTCAACT 59.103 45.455 0.73 0.00 45.00 3.16
3558 3892 3.323691 CCCCGGAAAGGAAAATTCAACTT 59.676 43.478 0.73 0.00 45.00 2.66
3559 3893 4.525100 CCCCGGAAAGGAAAATTCAACTTA 59.475 41.667 0.73 0.00 45.00 2.24
3560 3894 5.186992 CCCCGGAAAGGAAAATTCAACTTAT 59.813 40.000 0.73 0.00 45.00 1.73
3561 3895 6.295632 CCCCGGAAAGGAAAATTCAACTTATT 60.296 38.462 0.73 0.00 45.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.152839 GGAGGACGGAGGAGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
2 3 2.691779 GGGAGGACGGAGGAGAGGA 61.692 68.421 0.00 0.00 0.00 3.71
3 4 2.123640 GGGAGGACGGAGGAGAGG 60.124 72.222 0.00 0.00 0.00 3.69
4 5 2.123640 GGGGAGGACGGAGGAGAG 60.124 72.222 0.00 0.00 0.00 3.20
5 6 2.617538 AGGGGAGGACGGAGGAGA 60.618 66.667 0.00 0.00 0.00 3.71
6 7 2.123640 GAGGGGAGGACGGAGGAG 60.124 72.222 0.00 0.00 0.00 3.69
7 8 3.752167 GGAGGGGAGGACGGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
8 9 4.862823 GGGAGGGGAGGACGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
34 35 2.441164 GCTCGGAGGAGGCTGAGA 60.441 66.667 7.20 0.00 42.63 3.27
78 79 3.333680 AGAGAGAGAGAGAGAGGTTGGTT 59.666 47.826 0.00 0.00 0.00 3.67
92 93 5.263872 AGGTACCAAGAGAAAGAGAGAGA 57.736 43.478 15.94 0.00 0.00 3.10
101 122 2.334977 TCCAGCAAGGTACCAAGAGAA 58.665 47.619 15.94 0.00 39.02 2.87
205 230 3.119096 GGTGAAGCGCCCGAGTTC 61.119 66.667 2.29 0.71 0.00 3.01
214 239 1.291877 CCCAAGAAGACGGTGAAGCG 61.292 60.000 0.00 0.00 0.00 4.68
215 240 0.955919 CCCCAAGAAGACGGTGAAGC 60.956 60.000 0.00 0.00 0.00 3.86
232 257 4.803908 CTCCAAGAAGGCGGGCCC 62.804 72.222 13.57 13.57 37.29 5.80
234 259 2.034221 AACTCCAAGAAGGCGGGC 59.966 61.111 0.00 0.00 37.29 6.13
237 262 1.871772 CAGCAACTCCAAGAAGGCG 59.128 57.895 0.00 0.00 37.29 5.52
239 264 1.580845 CGGCAGCAACTCCAAGAAGG 61.581 60.000 0.00 0.00 39.47 3.46
240 265 1.871772 CGGCAGCAACTCCAAGAAG 59.128 57.895 0.00 0.00 0.00 2.85
241 266 2.260869 GCGGCAGCAACTCCAAGAA 61.261 57.895 3.18 0.00 44.35 2.52
293 364 4.301027 GATCTACGCGGGGGCCAG 62.301 72.222 12.47 0.00 0.00 4.85
319 390 3.289834 AAGCAGCAACACGCCCAG 61.290 61.111 0.00 0.00 44.04 4.45
344 415 4.699522 AAACCGGGAGCAGTCGCC 62.700 66.667 6.32 0.00 39.83 5.54
361 432 2.334946 GCAAGTGATTGCCTGCGGA 61.335 57.895 0.00 0.00 41.85 5.54
383 454 2.514592 AATGGACGCGCTGGATGG 60.515 61.111 5.73 0.00 0.00 3.51
384 455 2.537560 GGAATGGACGCGCTGGATG 61.538 63.158 5.73 0.00 0.00 3.51
385 456 2.203070 GGAATGGACGCGCTGGAT 60.203 61.111 5.73 0.00 0.00 3.41
386 457 4.467084 GGGAATGGACGCGCTGGA 62.467 66.667 5.73 0.00 0.00 3.86
388 459 4.473520 AGGGGAATGGACGCGCTG 62.474 66.667 5.73 1.02 0.00 5.18
389 460 4.473520 CAGGGGAATGGACGCGCT 62.474 66.667 5.73 0.00 0.00 5.92
392 463 2.825836 CAGCAGGGGAATGGACGC 60.826 66.667 0.00 0.00 0.00 5.19
407 478 0.039256 CAATGGCCGGACAAACACAG 60.039 55.000 17.77 0.00 0.00 3.66
409 480 1.372872 GCAATGGCCGGACAAACAC 60.373 57.895 17.77 0.00 0.00 3.32
410 481 2.913765 CGCAATGGCCGGACAAACA 61.914 57.895 17.77 0.00 36.38 2.83
411 482 2.126502 CGCAATGGCCGGACAAAC 60.127 61.111 17.77 5.63 36.38 2.93
412 483 4.049640 GCGCAATGGCCGGACAAA 62.050 61.111 17.77 0.00 36.38 2.83
427 498 4.577246 GGAGCTAGCGTGGAGGCG 62.577 72.222 9.55 0.00 38.18 5.52
428 499 1.801309 CTAGGAGCTAGCGTGGAGGC 61.801 65.000 9.55 0.00 0.00 4.70
430 501 1.801309 GCCTAGGAGCTAGCGTGGAG 61.801 65.000 14.75 5.96 33.12 3.86
431 502 1.828660 GCCTAGGAGCTAGCGTGGA 60.829 63.158 14.75 0.00 33.12 4.02
432 503 1.467678 ATGCCTAGGAGCTAGCGTGG 61.468 60.000 14.75 9.30 33.12 4.94
434 505 2.045280 CATGCCTAGGAGCTAGCGT 58.955 57.895 14.75 0.45 33.12 5.07
435 506 1.373999 GCATGCCTAGGAGCTAGCG 60.374 63.158 14.75 0.00 33.12 4.26
436 507 0.320596 CTGCATGCCTAGGAGCTAGC 60.321 60.000 14.75 6.62 33.12 3.42
437 508 1.047002 ACTGCATGCCTAGGAGCTAG 58.953 55.000 14.75 14.00 34.16 3.42
438 509 1.500474 AACTGCATGCCTAGGAGCTA 58.500 50.000 14.75 3.54 0.00 3.32
440 511 0.737219 CAAACTGCATGCCTAGGAGC 59.263 55.000 14.75 13.51 0.00 4.70
441 512 2.119801 ACAAACTGCATGCCTAGGAG 57.880 50.000 14.75 7.90 0.00 3.69
442 513 2.584835 AACAAACTGCATGCCTAGGA 57.415 45.000 14.75 0.00 0.00 2.94
444 515 5.126061 AGGAAATAACAAACTGCATGCCTAG 59.874 40.000 16.68 9.52 0.00 3.02
446 517 3.834231 AGGAAATAACAAACTGCATGCCT 59.166 39.130 16.68 0.00 0.00 4.75
447 518 3.928375 CAGGAAATAACAAACTGCATGCC 59.072 43.478 16.68 0.00 0.00 4.40
448 519 4.559153 ACAGGAAATAACAAACTGCATGC 58.441 39.130 11.82 11.82 32.60 4.06
449 520 4.853196 CGACAGGAAATAACAAACTGCATG 59.147 41.667 0.00 0.00 32.60 4.06
450 521 4.082787 CCGACAGGAAATAACAAACTGCAT 60.083 41.667 0.00 0.00 41.02 3.96
451 522 3.252215 CCGACAGGAAATAACAAACTGCA 59.748 43.478 0.00 0.00 41.02 4.41
452 523 3.252458 ACCGACAGGAAATAACAAACTGC 59.748 43.478 0.00 0.00 41.02 4.40
453 524 5.008217 TGAACCGACAGGAAATAACAAACTG 59.992 40.000 0.00 0.00 41.02 3.16
454 525 5.127491 TGAACCGACAGGAAATAACAAACT 58.873 37.500 0.00 0.00 41.02 2.66
455 526 5.427036 TGAACCGACAGGAAATAACAAAC 57.573 39.130 0.00 0.00 41.02 2.93
456 527 6.263392 TCAATGAACCGACAGGAAATAACAAA 59.737 34.615 0.00 0.00 41.02 2.83
457 528 5.765677 TCAATGAACCGACAGGAAATAACAA 59.234 36.000 0.00 0.00 41.02 2.83
458 529 5.309638 TCAATGAACCGACAGGAAATAACA 58.690 37.500 0.00 0.00 41.02 2.41
461 603 4.224147 TCCTCAATGAACCGACAGGAAATA 59.776 41.667 0.00 0.00 41.02 1.40
467 609 2.932614 GTGATCCTCAATGAACCGACAG 59.067 50.000 0.00 0.00 0.00 3.51
487 629 2.168313 CTGGTTTTTGCACAAGGGAAGT 59.832 45.455 0.00 0.00 0.00 3.01
489 631 1.134551 GCTGGTTTTTGCACAAGGGAA 60.135 47.619 0.00 0.00 0.00 3.97
491 633 0.177604 TGCTGGTTTTTGCACAAGGG 59.822 50.000 0.00 0.00 33.94 3.95
492 634 1.136695 TCTGCTGGTTTTTGCACAAGG 59.863 47.619 0.00 0.00 35.20 3.61
493 635 2.099592 TCTCTGCTGGTTTTTGCACAAG 59.900 45.455 0.00 0.00 35.20 3.16
494 636 2.098614 TCTCTGCTGGTTTTTGCACAA 58.901 42.857 0.00 0.00 35.20 3.33
495 637 1.677576 CTCTCTGCTGGTTTTTGCACA 59.322 47.619 0.00 0.00 35.20 4.57
497 639 1.133823 TCCTCTCTGCTGGTTTTTGCA 60.134 47.619 0.00 0.00 37.63 4.08
498 640 1.609208 TCCTCTCTGCTGGTTTTTGC 58.391 50.000 0.00 0.00 0.00 3.68
499 641 4.098501 AGTTTTCCTCTCTGCTGGTTTTTG 59.901 41.667 0.00 0.00 0.00 2.44
550 704 5.637810 CAGCTTGACAAGGACTATTACGAAA 59.362 40.000 16.80 0.00 0.00 3.46
556 710 2.619074 GGCCAGCTTGACAAGGACTATT 60.619 50.000 16.80 0.00 0.00 1.73
557 711 1.065126 GGCCAGCTTGACAAGGACTAT 60.065 52.381 16.80 0.00 0.00 2.12
558 712 0.324943 GGCCAGCTTGACAAGGACTA 59.675 55.000 16.80 0.00 0.00 2.59
559 713 1.073897 GGCCAGCTTGACAAGGACT 59.926 57.895 16.80 3.57 0.00 3.85
560 714 1.073897 AGGCCAGCTTGACAAGGAC 59.926 57.895 16.80 3.49 0.00 3.85
561 715 1.073722 CAGGCCAGCTTGACAAGGA 59.926 57.895 16.80 0.00 0.00 3.36
562 716 0.959372 CTCAGGCCAGCTTGACAAGG 60.959 60.000 16.80 2.52 0.00 3.61
563 717 1.584380 GCTCAGGCCAGCTTGACAAG 61.584 60.000 11.02 11.02 36.38 3.16
564 718 1.601759 GCTCAGGCCAGCTTGACAA 60.602 57.895 5.01 0.00 36.38 3.18
565 719 2.033141 GCTCAGGCCAGCTTGACA 59.967 61.111 5.01 0.00 36.38 3.58
571 725 2.113433 CACATCAGCTCAGGCCAGC 61.113 63.158 5.01 6.16 39.73 4.85
572 726 1.451567 CCACATCAGCTCAGGCCAG 60.452 63.158 5.01 0.00 39.73 4.85
581 735 3.171987 CGTGAGCACCACATCAGC 58.828 61.111 9.43 0.00 45.98 4.26
605 759 2.032550 AGGTACATAACGATGACCGACG 59.967 50.000 0.00 0.00 41.76 5.12
606 760 3.705043 AGGTACATAACGATGACCGAC 57.295 47.619 0.00 0.00 41.76 4.79
609 763 4.933400 ACACAAAGGTACATAACGATGACC 59.067 41.667 0.00 0.00 36.48 4.02
612 766 6.474819 TTCACACAAAGGTACATAACGATG 57.525 37.500 0.00 0.00 39.16 3.84
613 767 7.148306 GGATTTCACACAAAGGTACATAACGAT 60.148 37.037 0.00 0.00 0.00 3.73
615 769 6.148811 AGGATTTCACACAAAGGTACATAACG 59.851 38.462 0.00 0.00 0.00 3.18
616 770 7.448748 AGGATTTCACACAAAGGTACATAAC 57.551 36.000 0.00 0.00 0.00 1.89
619 773 6.779860 ACTAGGATTTCACACAAAGGTACAT 58.220 36.000 0.00 0.00 0.00 2.29
620 774 6.182507 ACTAGGATTTCACACAAAGGTACA 57.817 37.500 0.00 0.00 0.00 2.90
621 775 7.506328 AAACTAGGATTTCACACAAAGGTAC 57.494 36.000 0.00 0.00 0.00 3.34
622 776 9.059260 GTAAAACTAGGATTTCACACAAAGGTA 57.941 33.333 0.00 0.00 0.00 3.08
623 777 7.255001 CGTAAAACTAGGATTTCACACAAAGGT 60.255 37.037 0.00 0.00 0.00 3.50
655 817 1.334869 GTTGGTGGTGCTGACTTGAAG 59.665 52.381 0.00 0.00 0.00 3.02
714 879 4.227527 AGGCAGGGTTAAGCTATAGTTTGT 59.772 41.667 11.72 0.00 0.00 2.83
734 900 1.330655 TACCTACTCCAGCAGCAGGC 61.331 60.000 0.00 0.00 45.30 4.85
739 905 2.093500 TGTGCATTACCTACTCCAGCAG 60.093 50.000 0.00 0.00 0.00 4.24
823 992 5.359576 AGAAAGACGATCATACTGAGAGCTT 59.640 40.000 0.00 0.00 0.00 3.74
833 1002 7.273598 CGAAAGAAAGACAGAAAGACGATCATA 59.726 37.037 0.00 0.00 0.00 2.15
861 1030 2.567169 AGCTACAGATGTGCCAAGTGTA 59.433 45.455 0.00 0.00 0.00 2.90
905 1074 2.035066 AGAGAAACACATGGCTTGTTGC 59.965 45.455 2.88 0.00 37.26 4.17
941 1111 7.216317 CGCTAAATAATTAATGGCGAGCAATAC 59.784 37.037 20.36 0.00 43.05 1.89
987 1157 3.310774 CGTCAGCCATTTCCTACAGAATG 59.689 47.826 0.00 0.00 46.00 2.67
1206 1452 1.301637 CATGACACCAGTGTGCCGA 60.302 57.895 8.43 0.00 46.86 5.54
1567 1816 4.459337 AGTTTAACTAGGCAAAGCATCACC 59.541 41.667 0.00 0.00 0.00 4.02
1593 1842 4.202050 GGGCAGCATAACAGAACCATAAAG 60.202 45.833 0.00 0.00 0.00 1.85
1596 1845 2.509548 AGGGCAGCATAACAGAACCATA 59.490 45.455 0.00 0.00 0.00 2.74
1597 1846 1.285962 AGGGCAGCATAACAGAACCAT 59.714 47.619 0.00 0.00 0.00 3.55
1598 1847 0.698238 AGGGCAGCATAACAGAACCA 59.302 50.000 0.00 0.00 0.00 3.67
1599 1848 1.065126 AGAGGGCAGCATAACAGAACC 60.065 52.381 0.00 0.00 0.00 3.62
1603 1856 2.408271 TGAAGAGGGCAGCATAACAG 57.592 50.000 0.00 0.00 0.00 3.16
1615 1868 4.026356 AGACAATGGAAGGTTGAAGAGG 57.974 45.455 0.00 0.00 0.00 3.69
1636 1910 7.397221 AGCCACATTAAGCATAATCATAGCTA 58.603 34.615 0.00 0.00 37.70 3.32
1654 1931 4.527816 ACATCCAAATTACACAAGCCACAT 59.472 37.500 0.00 0.00 0.00 3.21
1665 1942 6.816640 TCACTACTGCAGTACATCCAAATTAC 59.183 38.462 22.67 0.00 34.98 1.89
1672 1949 3.557595 GCAATCACTACTGCAGTACATCC 59.442 47.826 22.67 4.26 38.48 3.51
1712 1989 4.550076 TTGTTTTCCCCAATGCAATAGG 57.450 40.909 0.00 0.00 0.00 2.57
1723 2000 9.476202 GATATATTAGTTGCAATTGTTTTCCCC 57.524 33.333 0.59 0.00 0.00 4.81
1740 2017 8.612619 AGCCACAACAACTTTTCGATATATTAG 58.387 33.333 0.00 0.00 0.00 1.73
1743 2020 6.597672 TCAGCCACAACAACTTTTCGATATAT 59.402 34.615 0.00 0.00 0.00 0.86
1752 2029 6.654582 AGAAAATTTTCAGCCACAACAACTTT 59.345 30.769 28.00 3.53 39.61 2.66
1888 2184 2.820728 TAAGGGAGTCCGTGAGATCA 57.179 50.000 4.85 0.00 38.33 2.92
2170 2466 5.221925 ACACTTCATGATGGAGTTGTAGGTT 60.222 40.000 2.98 0.00 0.00 3.50
2375 2671 2.289694 GGAAAGTGCTGAGTGAGGCTAA 60.290 50.000 0.00 0.00 0.00 3.09
2406 2702 4.103311 AGAAGGTAAAGCTGAACAAGAGGT 59.897 41.667 0.00 0.00 0.00 3.85
2407 2703 4.453819 CAGAAGGTAAAGCTGAACAAGAGG 59.546 45.833 0.00 0.00 0.00 3.69
2420 2716 7.456902 AGGGTAAGATGAGTTACAGAAGGTAAA 59.543 37.037 0.00 0.00 43.30 2.01
2421 2717 6.958192 AGGGTAAGATGAGTTACAGAAGGTAA 59.042 38.462 0.00 0.00 39.62 2.85
2430 2728 8.561738 TTTGAATGAAGGGTAAGATGAGTTAC 57.438 34.615 0.00 0.00 32.90 2.50
2435 2733 7.669304 TGTTGATTTGAATGAAGGGTAAGATGA 59.331 33.333 0.00 0.00 0.00 2.92
2441 2739 7.174413 TCAGATGTTGATTTGAATGAAGGGTA 58.826 34.615 0.00 0.00 0.00 3.69
2456 2754 9.835389 TCACACATAATATGATTCAGATGTTGA 57.165 29.630 7.33 10.01 0.00 3.18
2468 2766 7.045416 GGTACAACCAGTCACACATAATATGA 58.955 38.462 7.33 0.00 38.42 2.15
2469 2767 6.821160 TGGTACAACCAGTCACACATAATATG 59.179 38.462 0.00 0.00 44.79 1.78
2472 2770 5.235850 TGGTACAACCAGTCACACATAAT 57.764 39.130 0.00 0.00 44.79 1.28
2485 2783 4.102524 TGGATATCCACATCTGGTACAACC 59.897 45.833 20.98 0.00 42.01 3.77
2486 2784 5.290493 TGGATATCCACATCTGGTACAAC 57.710 43.478 20.98 0.00 42.01 3.32
2855 3162 9.790297 TCTCCCCTTAGAGCAATAATAAGATAT 57.210 33.333 0.00 0.00 33.66 1.63
2868 3175 2.708325 ACCATGATTCTCCCCTTAGAGC 59.292 50.000 0.00 0.00 33.66 4.09
2871 3182 9.236006 CATAATTTACCATGATTCTCCCCTTAG 57.764 37.037 0.00 0.00 0.00 2.18
2910 3221 4.495422 ACCACTGTATAACGCTTTGAGAG 58.505 43.478 0.00 0.00 0.00 3.20
2966 3278 4.009675 GCCTTATGAACCAGTGATGAACA 58.990 43.478 0.00 0.00 0.00 3.18
3010 3322 5.239525 AGCTGAACCTGAACATCAAAGTAAC 59.760 40.000 0.00 0.00 0.00 2.50
3043 3355 4.966965 TTGCTTTTCACTTTGTCCGTAA 57.033 36.364 0.00 0.00 0.00 3.18
3046 3358 7.807907 AGTAATATTTGCTTTTCACTTTGTCCG 59.192 33.333 0.00 0.00 0.00 4.79
3125 3438 8.801299 ACTCTAGAACATGTCCATATACATCTG 58.199 37.037 0.00 0.00 38.01 2.90
3134 3447 6.798427 ATGTACACTCTAGAACATGTCCAT 57.202 37.500 0.00 5.63 31.56 3.41
3136 3449 6.531948 GTGAATGTACACTCTAGAACATGTCC 59.468 42.308 5.83 0.00 37.73 4.02
3152 3465 4.154195 ACGGAGCAAAATGAGTGAATGTAC 59.846 41.667 0.00 0.00 0.00 2.90
3161 3474 7.946655 TGAACTATATACGGAGCAAAATGAG 57.053 36.000 0.00 0.00 0.00 2.90
3162 3475 9.990360 TTATGAACTATATACGGAGCAAAATGA 57.010 29.630 0.00 0.00 0.00 2.57
3165 3478 9.214957 CCATTATGAACTATATACGGAGCAAAA 57.785 33.333 0.00 0.00 0.00 2.44
3209 3522 8.483758 TCAAATACTCCCTCTGTTCCTAAATAC 58.516 37.037 0.00 0.00 0.00 1.89
3218 3531 7.988028 GCTTACTATTCAAATACTCCCTCTGTT 59.012 37.037 0.00 0.00 0.00 3.16
3220 3533 6.931840 GGCTTACTATTCAAATACTCCCTCTG 59.068 42.308 0.00 0.00 0.00 3.35
3221 3534 6.615726 TGGCTTACTATTCAAATACTCCCTCT 59.384 38.462 0.00 0.00 0.00 3.69
3224 3537 7.875327 TTTGGCTTACTATTCAAATACTCCC 57.125 36.000 0.00 0.00 0.00 4.30
3275 3588 9.004717 TCCGTAACATGTAATTCTTTGATGAAA 57.995 29.630 0.00 0.00 0.00 2.69
3310 3623 8.584157 TGCACAATGTTCCTAATAAAGACAATT 58.416 29.630 0.00 0.00 0.00 2.32
3315 3628 7.545265 GCAAATGCACAATGTTCCTAATAAAGA 59.455 33.333 0.00 0.00 41.59 2.52
3331 3644 1.067364 CAAGGTGTCAGCAAATGCACA 59.933 47.619 8.28 1.31 45.16 4.57
3332 3645 1.337703 TCAAGGTGTCAGCAAATGCAC 59.662 47.619 8.28 0.00 45.16 4.57
3339 3652 6.265196 ACTCAAATTATTTCAAGGTGTCAGCA 59.735 34.615 4.59 0.00 0.00 4.41
3345 3658 7.584987 ACGAGAACTCAAATTATTTCAAGGTG 58.415 34.615 0.00 0.00 0.00 4.00
3346 3659 7.745620 ACGAGAACTCAAATTATTTCAAGGT 57.254 32.000 0.00 0.00 0.00 3.50
3348 3661 9.663904 TTGAACGAGAACTCAAATTATTTCAAG 57.336 29.630 0.00 0.00 0.00 3.02
3356 3669 8.702163 ACAAATTTTGAACGAGAACTCAAATT 57.298 26.923 15.81 4.04 40.31 1.82
3400 3713 5.529800 GGTTTGTTGCTTTGAACTAGTAGGA 59.470 40.000 0.00 0.00 0.00 2.94
3402 3715 5.531287 AGGGTTTGTTGCTTTGAACTAGTAG 59.469 40.000 0.00 0.00 0.00 2.57
3403 3716 5.442391 AGGGTTTGTTGCTTTGAACTAGTA 58.558 37.500 0.00 0.00 0.00 1.82
3404 3717 4.278310 AGGGTTTGTTGCTTTGAACTAGT 58.722 39.130 0.00 0.00 0.00 2.57
3446 3780 2.194326 GCCTGAAGATGAGCCCCC 59.806 66.667 0.00 0.00 0.00 5.40
3464 3798 4.776435 TTGGTGCTCATATTCATCAGGA 57.224 40.909 0.00 0.00 0.00 3.86
3475 3809 5.072741 ACTGAACAAGTATTTGGTGCTCAT 58.927 37.500 2.81 0.00 37.36 2.90
3535 3869 2.631062 GTTGAATTTTCCTTTCCGGGGT 59.369 45.455 0.00 0.00 0.00 4.95
3536 3870 2.897326 AGTTGAATTTTCCTTTCCGGGG 59.103 45.455 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.