Multiple sequence alignment - TraesCS2A01G198200

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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 TraesCS2A01G198200 chr2A 100.000 4070 0 0 1 4070 169386989 169391058 0.000000e+00 7516.0
1 TraesCS2A01G198200 chr2A 93.496 861 35 10 678 1527 169356968 169357818 0.000000e+00 1260.0
2 TraesCS2A01G198200 chr2A 86.197 681 69 11 1987 2652 169360251 169360921 0.000000e+00 713.0
3 TraesCS2A01G198200 chr2A 85.591 465 53 10 2672 3132 169361038 169361492 3.680000e-130 475.0
4 TraesCS2A01G198200 chr2A 90.402 323 24 3 1635 1954 169359936 169360254 6.290000e-113 418.0
5 TraesCS2A01G198200 chr2B 90.159 2195 117 24 1635 3778 215951916 215954062 0.000000e+00 2765.0
6 TraesCS2A01G198200 chr2B 91.349 867 54 9 699 1561 215950731 215951580 0.000000e+00 1166.0
7 TraesCS2A01G198200 chr2B 94.297 263 11 2 3810 4068 215954063 215954325 2.280000e-107 399.0
8 TraesCS2A01G198200 chr2B 81.925 426 63 10 1 423 412666667 412666253 8.370000e-92 348.0
9 TraesCS2A01G198200 chr2B 80.986 426 67 10 1 423 412720350 412719936 3.920000e-85 326.0
10 TraesCS2A01G198200 chr2B 84.062 320 39 10 108 423 412720914 412720603 8.550000e-77 298.0
11 TraesCS2A01G198200 chr2B 95.714 70 3 0 629 698 215950029 215950098 3.320000e-21 113.0
12 TraesCS2A01G198200 chr2D 90.667 675 46 8 931 1600 158790959 158791621 0.000000e+00 881.0
13 TraesCS2A01G198200 chr2D 86.873 678 66 10 1988 2652 158792038 158792705 0.000000e+00 737.0
14 TraesCS2A01G198200 chr2D 95.033 302 15 0 629 930 158790499 158790800 3.680000e-130 475.0
15 TraesCS2A01G198200 chr2D 91.358 324 18 7 1635 1954 158791723 158792040 6.250000e-118 435.0
16 TraesCS2A01G198200 chr2D 84.000 450 56 11 2672 3117 158792826 158793263 6.290000e-113 418.0
17 TraesCS2A01G198200 chr2D 82.944 428 60 9 1 423 347445700 347445281 1.380000e-99 374.0
18 TraesCS2A01G198200 chr2D 81.472 394 61 10 34 423 347446759 347446374 3.050000e-81 313.0
19 TraesCS2A01G198200 chr2D 100.000 28 0 0 4027 4054 473702554 473702581 7.000000e-03 52.8
20 TraesCS2A01G198200 chr6D 84.127 567 74 13 1 559 424613298 424613856 5.990000e-148 534.0
21 TraesCS2A01G198200 chr6D 81.903 431 62 13 1 423 424612962 424613384 2.330000e-92 350.0
22 TraesCS2A01G198200 chr6D 88.095 84 10 0 435 518 8308264 8308181 2.590000e-17 100.0
23 TraesCS2A01G198200 chr7D 84.798 421 51 12 10 423 611436058 611436472 1.050000e-110 411.0
24 TraesCS2A01G198200 chr3D 82.388 335 52 5 91 423 185225993 185226322 6.660000e-73 285.0
25 TraesCS2A01G198200 chr3D 87.234 94 12 0 432 525 526996893 526996986 1.550000e-19 108.0
26 TraesCS2A01G198200 chr7A 82.119 151 23 4 3547 3695 5164616 5164764 4.270000e-25 126.0
27 TraesCS2A01G198200 chr5B 86.087 115 13 3 435 548 294125064 294124952 1.990000e-23 121.0
28 TraesCS2A01G198200 chr5B 87.692 65 5 3 3866 3928 243363824 243363887 5.640000e-09 73.1
29 TraesCS2A01G198200 chr6B 85.841 113 15 1 432 544 14104688 14104799 7.150000e-23 119.0
30 TraesCS2A01G198200 chr6B 89.286 84 9 0 436 519 674151654 674151737 5.560000e-19 106.0
31 TraesCS2A01G198200 chr4D 80.769 156 25 5 3542 3695 18476825 18476673 2.570000e-22 117.0
32 TraesCS2A01G198200 chr4D 89.552 67 5 2 3410 3475 62116710 62116775 2.610000e-12 84.2
33 TraesCS2A01G198200 chr3B 87.879 99 8 3 435 530 814450259 814450162 3.320000e-21 113.0
34 TraesCS2A01G198200 chr3B 73.913 299 60 12 3412 3696 703029915 703029621 2.000000e-18 104.0
35 TraesCS2A01G198200 chr3B 86.957 92 9 1 435 523 753521486 753521395 2.590000e-17 100.0
36 TraesCS2A01G198200 chr3B 85.135 74 9 1 3858 3929 97717574 97717501 1.570000e-09 75.0
37 TraesCS2A01G198200 chrUn 84.956 113 14 3 3397 3508 137886364 137886474 1.200000e-20 111.0
38 TraesCS2A01G198200 chrUn 93.443 61 2 1 3421 3479 56508188 56508128 5.600000e-14 89.8
39 TraesCS2A01G198200 chrUn 93.443 61 2 1 3421 3479 322676328 322676268 5.600000e-14 89.8
40 TraesCS2A01G198200 chr5D 77.033 209 37 11 3727 3928 220669757 220669961 4.300000e-20 110.0
41 TraesCS2A01G198200 chr4A 87.912 91 8 2 435 525 576917715 576917628 2.000000e-18 104.0
42 TraesCS2A01G198200 chr4A 80.672 119 21 2 3392 3509 144376032 144376149 1.560000e-14 91.6
43 TraesCS2A01G198200 chr7B 83.962 106 14 2 3403 3508 12963332 12963434 9.310000e-17 99.0
44 TraesCS2A01G198200 chr7B 78.519 135 22 7 11 142 373654937 373654807 9.380000e-12 82.4
45 TraesCS2A01G198200 chr7B 92.453 53 2 2 3876 3927 553170532 553170583 1.570000e-09 75.0
46 TraesCS2A01G198200 chr7B 93.333 45 3 0 3883 3927 142285888 142285932 2.630000e-07 67.6
47 TraesCS2A01G198200 chr5A 75.000 208 41 10 3727 3928 295055040 295055242 7.250000e-13 86.1
48 TraesCS2A01G198200 chr4B 84.211 76 11 1 3880 3955 571467459 571467385 5.640000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G198200 chr2A 169386989 169391058 4069 False 7516.00 7516 100.00000 1 4070 1 chr2A.!!$F1 4069
1 TraesCS2A01G198200 chr2A 169356968 169361492 4524 False 716.50 1260 88.92150 678 3132 4 chr2A.!!$F2 2454
2 TraesCS2A01G198200 chr2B 215950029 215954325 4296 False 1110.75 2765 92.87975 629 4068 4 chr2B.!!$F1 3439
3 TraesCS2A01G198200 chr2B 412719936 412720914 978 True 312.00 326 82.52400 1 423 2 chr2B.!!$R2 422
4 TraesCS2A01G198200 chr2D 158790499 158793263 2764 False 589.20 881 89.58620 629 3117 5 chr2D.!!$F2 2488
5 TraesCS2A01G198200 chr2D 347445281 347446759 1478 True 343.50 374 82.20800 1 423 2 chr2D.!!$R1 422
6 TraesCS2A01G198200 chr6D 424612962 424613856 894 False 442.00 534 83.01500 1 559 2 chr6D.!!$F1 558

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
584 1653 0.039764 AGGATGTCCGTCACCTGAGA 59.960 55.0 0.0 0.0 42.08 3.27 F
594 1663 0.396435 TCACCTGAGATGTTTGCGGT 59.604 50.0 0.0 0.0 0.00 5.68 F
2321 6547 0.381801 GTGACCACACCTTTGCTGTG 59.618 55.0 0.0 0.0 40.74 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 6483 0.686441 ACATGCCATCCAGCTTGCAT 60.686 50.000 0.0 0.0 44.79 3.96 R
2396 6622 1.949257 CACCGTCCAGAAAACCAGC 59.051 57.895 0.0 0.0 0.00 4.85 R
3792 8155 0.250295 TGTAATCCGCTATGGGCTGC 60.250 55.000 0.0 0.0 38.76 5.25 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 333 3.137533 GCCTTTTGCCATTTTAGTTGCA 58.862 40.909 0.00 0.00 0.00 4.08
62 369 1.469079 GCCGCGAAAATAGCAAACCAT 60.469 47.619 8.23 0.00 34.19 3.55
66 373 3.354397 GCGAAAATAGCAAACCATCTCG 58.646 45.455 0.00 0.00 34.19 4.04
72 379 7.273381 CGAAAATAGCAAACCATCTCGAAAAAT 59.727 33.333 0.00 0.00 0.00 1.82
75 382 5.200368 AGCAAACCATCTCGAAAAATTGT 57.800 34.783 0.00 0.00 0.00 2.71
78 385 7.378181 AGCAAACCATCTCGAAAAATTGTAAT 58.622 30.769 0.00 0.00 0.00 1.89
226 1293 3.556423 GGAAGAGTGTCCGGTTTGTACAT 60.556 47.826 0.00 0.00 0.00 2.29
254 1321 5.856455 GTCCATCAAGTTTTTGTCGTAATGG 59.144 40.000 0.00 0.00 36.08 3.16
280 1347 6.488683 TCTCAAATTTTTACCACACCCTACAG 59.511 38.462 0.00 0.00 0.00 2.74
318 1385 3.196254 ACCATGCAAAGTTTCATCCCATC 59.804 43.478 0.00 0.00 0.00 3.51
320 1387 1.818060 TGCAAAGTTTCATCCCATCCG 59.182 47.619 0.00 0.00 0.00 4.18
321 1388 1.818674 GCAAAGTTTCATCCCATCCGT 59.181 47.619 0.00 0.00 0.00 4.69
413 1482 7.516627 CGAAAATAGCAAACCAACTCAAAAAGG 60.517 37.037 0.00 0.00 0.00 3.11
423 1492 5.123661 ACCAACTCAAAAAGGTGCAAATTTG 59.876 36.000 14.03 14.03 41.76 2.32
425 1494 6.250089 CAACTCAAAAAGGTGCAAATTTGTC 58.750 36.000 19.03 11.87 35.47 3.18
427 1496 5.351189 ACTCAAAAAGGTGCAAATTTGTCAC 59.649 36.000 25.04 25.04 35.01 3.67
433 1502 1.851666 GTGCAAATTTGTCACACCGTG 59.148 47.619 26.68 0.00 36.18 4.94
437 1506 1.314730 AATTTGTCACACCGTGGTCC 58.685 50.000 3.03 0.00 33.87 4.46
445 1514 2.044555 CACCGTGGTCCTCGCTAGA 61.045 63.158 7.84 0.00 0.00 2.43
460 1529 5.392919 CCTCGCTAGATGGTCTATGAATCTG 60.393 48.000 0.00 0.00 32.92 2.90
468 1537 7.905265 AGATGGTCTATGAATCTGGATGTAAG 58.095 38.462 0.00 0.00 29.52 2.34
471 1540 7.861629 TGGTCTATGAATCTGGATGTAAGTTT 58.138 34.615 0.00 0.00 0.00 2.66
504 1573 6.751514 TGATGTTCGTTTTACTGCCATAAT 57.248 33.333 0.00 0.00 0.00 1.28
555 1624 2.877786 CAAGAAAAATGTTTGGGGTGGC 59.122 45.455 0.00 0.00 0.00 5.01
565 1634 3.884774 GGGGTGGCGGGCATCATA 61.885 66.667 17.13 0.00 0.00 2.15
566 1635 2.281761 GGGTGGCGGGCATCATAG 60.282 66.667 17.13 0.00 0.00 2.23
567 1636 2.281761 GGTGGCGGGCATCATAGG 60.282 66.667 10.27 0.00 0.00 2.57
568 1637 2.818169 GGTGGCGGGCATCATAGGA 61.818 63.158 10.27 0.00 0.00 2.94
569 1638 1.376466 GTGGCGGGCATCATAGGAT 59.624 57.895 7.75 0.00 0.00 3.24
579 1648 3.032017 CATCATAGGATGTCCGTCACC 57.968 52.381 9.22 0.00 44.79 4.02
580 1649 2.454336 TCATAGGATGTCCGTCACCT 57.546 50.000 0.00 0.00 42.08 4.00
581 1650 2.031870 TCATAGGATGTCCGTCACCTG 58.968 52.381 0.00 0.00 42.08 4.00
582 1651 2.031870 CATAGGATGTCCGTCACCTGA 58.968 52.381 0.00 0.00 42.08 3.86
583 1652 1.763968 TAGGATGTCCGTCACCTGAG 58.236 55.000 0.00 0.00 42.08 3.35
584 1653 0.039764 AGGATGTCCGTCACCTGAGA 59.960 55.000 0.00 0.00 42.08 3.27
585 1654 1.115467 GGATGTCCGTCACCTGAGAT 58.885 55.000 0.00 0.00 0.00 2.75
586 1655 1.202463 GGATGTCCGTCACCTGAGATG 60.202 57.143 0.00 0.00 0.00 2.90
587 1656 1.478510 GATGTCCGTCACCTGAGATGT 59.521 52.381 0.00 0.00 0.00 3.06
588 1657 1.338107 TGTCCGTCACCTGAGATGTT 58.662 50.000 0.00 0.00 0.00 2.71
589 1658 1.691976 TGTCCGTCACCTGAGATGTTT 59.308 47.619 0.00 0.00 0.00 2.83
590 1659 2.069273 GTCCGTCACCTGAGATGTTTG 58.931 52.381 0.00 0.00 0.00 2.93
591 1660 0.798776 CCGTCACCTGAGATGTTTGC 59.201 55.000 0.00 0.00 0.00 3.68
592 1661 0.439985 CGTCACCTGAGATGTTTGCG 59.560 55.000 0.00 0.00 0.00 4.85
593 1662 0.798776 GTCACCTGAGATGTTTGCGG 59.201 55.000 0.00 0.00 0.00 5.69
594 1663 0.396435 TCACCTGAGATGTTTGCGGT 59.604 50.000 0.00 0.00 0.00 5.68
595 1664 0.518636 CACCTGAGATGTTTGCGGTG 59.481 55.000 0.00 0.00 36.36 4.94
596 1665 0.606401 ACCTGAGATGTTTGCGGTGG 60.606 55.000 0.00 0.00 0.00 4.61
597 1666 1.503542 CTGAGATGTTTGCGGTGGC 59.496 57.895 0.00 0.00 40.52 5.01
598 1667 2.244436 CTGAGATGTTTGCGGTGGCG 62.244 60.000 0.00 0.00 44.10 5.69
599 1668 3.039202 GAGATGTTTGCGGTGGCGG 62.039 63.158 0.00 0.00 44.10 6.13
600 1669 4.114997 GATGTTTGCGGTGGCGGG 62.115 66.667 0.00 0.00 44.10 6.13
611 1680 4.708386 TGGCGGGCGTCGGAATTT 62.708 61.111 0.00 0.00 39.69 1.82
612 1681 3.436924 GGCGGGCGTCGGAATTTT 61.437 61.111 0.00 0.00 39.69 1.82
613 1682 2.202427 GCGGGCGTCGGAATTTTG 60.202 61.111 0.00 0.00 39.69 2.44
614 1683 2.202427 CGGGCGTCGGAATTTTGC 60.202 61.111 0.00 0.00 34.75 3.68
615 1684 2.958576 GGGCGTCGGAATTTTGCA 59.041 55.556 0.00 0.00 0.00 4.08
616 1685 1.154035 GGGCGTCGGAATTTTGCAG 60.154 57.895 0.00 0.00 0.00 4.41
617 1686 1.801512 GGCGTCGGAATTTTGCAGC 60.802 57.895 0.00 0.00 0.00 5.25
618 1687 2.145905 GCGTCGGAATTTTGCAGCG 61.146 57.895 0.00 0.00 0.00 5.18
619 1688 1.511887 CGTCGGAATTTTGCAGCGG 60.512 57.895 0.00 0.00 0.00 5.52
620 1689 1.801512 GTCGGAATTTTGCAGCGGC 60.802 57.895 0.31 0.31 41.68 6.53
621 1690 2.875711 CGGAATTTTGCAGCGGCG 60.876 61.111 0.51 0.51 45.35 6.46
622 1691 2.506881 GGAATTTTGCAGCGGCGG 60.507 61.111 9.78 0.00 45.35 6.13
623 1692 2.506881 GAATTTTGCAGCGGCGGG 60.507 61.111 9.78 0.00 45.35 6.13
624 1693 4.740431 AATTTTGCAGCGGCGGGC 62.740 61.111 9.78 11.86 45.35 6.13
758 2459 1.607612 TTCCTTCCCGGAATCAGGC 59.392 57.895 0.73 0.00 46.80 4.85
762 2463 1.369091 CTTCCCGGAATCAGGCGTTG 61.369 60.000 0.73 0.00 0.00 4.10
836 2537 6.346919 CGCAATAAGAATAGGAAATCACCGAG 60.347 42.308 0.00 0.00 34.73 4.63
937 2798 7.234187 ACTTCGGCAATTATATATATGTGCG 57.766 36.000 16.25 13.11 32.77 5.34
939 2800 7.333423 ACTTCGGCAATTATATATATGTGCGTT 59.667 33.333 16.25 3.08 32.77 4.84
940 2801 7.603963 TCGGCAATTATATATATGTGCGTTT 57.396 32.000 16.25 0.00 32.77 3.60
942 2803 6.194508 CGGCAATTATATATATGTGCGTTTGC 59.805 38.462 16.25 14.13 43.20 3.68
989 2850 3.744660 AGGCGATCTTCAAACAAGAAGT 58.255 40.909 0.00 0.00 44.18 3.01
990 2851 4.137543 AGGCGATCTTCAAACAAGAAGTT 58.862 39.130 0.00 0.00 44.18 2.66
991 2852 5.305585 AGGCGATCTTCAAACAAGAAGTTA 58.694 37.500 0.00 0.00 44.18 2.24
993 2854 6.073003 AGGCGATCTTCAAACAAGAAGTTAAG 60.073 38.462 0.00 0.00 44.18 1.85
1341 3212 5.421056 CCTGAAGAACCACATACTACAGGTA 59.579 44.000 0.00 0.00 37.95 3.08
1343 3222 7.364762 CCTGAAGAACCACATACTACAGGTAAT 60.365 40.741 0.00 0.00 37.95 1.89
1463 3343 5.171476 AGTCATCGTTGTCAGATTTACAGG 58.829 41.667 0.00 0.00 0.00 4.00
1479 3359 1.556911 ACAGGTCTATCTGCCCTTGTG 59.443 52.381 0.00 0.00 38.26 3.33
1614 5752 5.209818 CCATGCATGGCTCTTGAAATAAT 57.790 39.130 31.95 0.00 41.75 1.28
1641 5837 4.787551 ACATGTTCTTCCCCGCAATAATA 58.212 39.130 0.00 0.00 0.00 0.98
1678 5875 3.926058 ACCCATCGCCTTGTAGTATTT 57.074 42.857 0.00 0.00 0.00 1.40
1679 5876 4.230745 ACCCATCGCCTTGTAGTATTTT 57.769 40.909 0.00 0.00 0.00 1.82
1680 5877 4.595986 ACCCATCGCCTTGTAGTATTTTT 58.404 39.130 0.00 0.00 0.00 1.94
1732 5937 6.855836 TCTTATTTTGCTTTGGTATGCTCAG 58.144 36.000 0.00 0.00 0.00 3.35
1734 5939 4.771590 TTTTGCTTTGGTATGCTCAGAG 57.228 40.909 0.00 0.00 0.00 3.35
1763 5968 6.933521 TGAGAGATTTTTCTGAGAAACCTCTG 59.066 38.462 25.18 0.00 33.05 3.35
1878 6085 9.651913 GAGAACTCTCAAAGAAGATCTTGTAAT 57.348 33.333 14.00 0.00 42.42 1.89
1951 6158 1.378531 GAATTGACGGGCAGCATGTA 58.621 50.000 0.00 0.00 39.31 2.29
2046 6261 4.202243 ACCATCATTGTTTGGGTTCACAAG 60.202 41.667 11.36 0.00 36.36 3.16
2060 6280 5.869888 GGGTTCACAAGACTACTACTCATTG 59.130 44.000 0.00 0.00 0.00 2.82
2089 6309 6.226787 AGAAACGAGATTGACATTCTCACTT 58.773 36.000 21.36 15.08 39.69 3.16
2127 6353 0.981183 TCGCCCAGGTGTTGTTAGAT 59.019 50.000 0.00 0.00 0.00 1.98
2160 6386 1.880340 GACATTCCAGAGCGCGAGG 60.880 63.158 12.10 5.52 0.00 4.63
2232 6458 1.681166 GCTCAGATGCTGGTTGTGGAT 60.681 52.381 0.00 0.00 31.51 3.41
2257 6483 1.225855 GTCAAGCAATGTCACCGTCA 58.774 50.000 0.00 0.00 0.00 4.35
2306 6532 2.880890 ACATTTGACAAGCTGAGGTGAC 59.119 45.455 6.79 0.00 0.00 3.67
2307 6533 1.967319 TTTGACAAGCTGAGGTGACC 58.033 50.000 0.00 0.00 0.00 4.02
2321 6547 0.381801 GTGACCACACCTTTGCTGTG 59.618 55.000 0.00 0.00 40.74 3.66
2347 6573 4.149598 TCTTCTGACACTAGCACCTGTTA 58.850 43.478 0.00 0.00 0.00 2.41
2466 6695 8.336806 TGGACTAAACTTTGTTTATGTTGTACG 58.663 33.333 3.77 0.00 0.00 3.67
2516 6751 6.048732 TGATACAGGCTGATGACTACAAAA 57.951 37.500 23.66 0.00 0.00 2.44
2602 6837 1.452108 GGCCCTTCCAAGTGGATCG 60.452 63.158 0.00 0.00 44.98 3.69
2681 7017 2.864343 ACAACTACGTCTTGACAAGTGC 59.136 45.455 14.75 8.41 0.00 4.40
2691 7027 3.817084 TCTTGACAAGTGCTCCTGAAATG 59.183 43.478 14.75 0.00 0.00 2.32
2702 7041 7.655490 AGTGCTCCTGAAATGCAATTATTATC 58.345 34.615 0.00 0.00 33.67 1.75
2723 7062 4.013728 TCATGTTGTTTACAGTATGGCCC 58.986 43.478 0.00 0.00 43.62 5.80
2740 7079 2.285024 CCGACCGGGAACAGGGTAA 61.285 63.158 6.32 0.00 36.82 2.85
2744 7083 2.799017 GACCGGGAACAGGGTAATTTT 58.201 47.619 6.32 0.00 36.82 1.82
2745 7084 2.751259 GACCGGGAACAGGGTAATTTTC 59.249 50.000 6.32 0.00 36.82 2.29
2920 7259 4.404654 GCGCCGCCAAGTTCAAGG 62.405 66.667 0.00 0.00 0.00 3.61
2926 7265 0.958876 CGCCAAGTTCAAGGGGGTAC 60.959 60.000 0.00 0.00 34.49 3.34
2954 7293 1.463056 CGGCTGCACGAACTTCAAATA 59.537 47.619 0.50 0.00 35.47 1.40
3100 7439 9.045223 CAGAACTCCTTTTCCCTTTAATTTTTG 57.955 33.333 0.00 0.00 0.00 2.44
3172 7511 2.030363 TGAGCGGAAAAACGATTGCAAT 60.030 40.909 12.83 12.83 35.47 3.56
3184 7523 9.786105 AAAAACGATTGCAATTCAATTCTTTTT 57.214 22.222 14.33 9.65 44.95 1.94
3204 7543 1.029681 GGCGCCCACCCTTAAAATAG 58.970 55.000 18.11 0.00 0.00 1.73
3205 7544 1.409101 GGCGCCCACCCTTAAAATAGA 60.409 52.381 18.11 0.00 0.00 1.98
3206 7545 1.674441 GCGCCCACCCTTAAAATAGAC 59.326 52.381 0.00 0.00 0.00 2.59
3211 7550 2.606272 CCACCCTTAAAATAGACGACGC 59.394 50.000 0.00 0.00 0.00 5.19
3226 7565 3.266636 ACGACGCAATGTTTATCCATGA 58.733 40.909 0.00 0.00 0.00 3.07
3240 7579 2.376109 TCCATGAACTAGTCCGGACTC 58.624 52.381 39.49 25.34 42.54 3.36
3242 7581 1.409427 CATGAACTAGTCCGGACTCCC 59.591 57.143 39.49 24.88 42.54 4.30
3245 7584 1.807771 AACTAGTCCGGACTCCCCCA 61.808 60.000 39.49 21.37 42.54 4.96
3253 7592 1.923395 GGACTCCCCCATGGACACA 60.923 63.158 15.22 0.00 38.61 3.72
3258 7597 2.342659 CTCCCCCATGGACACAGATAT 58.657 52.381 15.22 0.00 38.61 1.63
3260 7599 2.057140 CCCCCATGGACACAGATATGA 58.943 52.381 15.22 0.00 35.39 2.15
3281 7620 0.899717 AGCCGCCATCCAAACATGTT 60.900 50.000 4.92 4.92 0.00 2.71
3284 7623 2.874849 CCGCCATCCAAACATGTTTAC 58.125 47.619 22.87 8.17 0.00 2.01
3287 7626 4.201910 CCGCCATCCAAACATGTTTACTAG 60.202 45.833 22.87 10.96 0.00 2.57
3288 7627 4.394920 CGCCATCCAAACATGTTTACTAGT 59.605 41.667 22.87 0.00 0.00 2.57
3290 7629 5.163652 GCCATCCAAACATGTTTACTAGTCC 60.164 44.000 22.87 6.39 0.00 3.85
3291 7630 5.943416 CCATCCAAACATGTTTACTAGTCCA 59.057 40.000 22.87 0.00 0.00 4.02
3292 7631 6.128007 CCATCCAAACATGTTTACTAGTCCAC 60.128 42.308 22.87 0.00 0.00 4.02
3293 7632 5.931294 TCCAAACATGTTTACTAGTCCACA 58.069 37.500 22.87 3.88 0.00 4.17
3294 7633 6.539173 TCCAAACATGTTTACTAGTCCACAT 58.461 36.000 22.87 12.19 0.00 3.21
3295 7634 6.653320 TCCAAACATGTTTACTAGTCCACATC 59.347 38.462 22.87 0.00 0.00 3.06
3296 7635 6.655003 CCAAACATGTTTACTAGTCCACATCT 59.345 38.462 22.87 3.87 0.00 2.90
3297 7636 7.174946 CCAAACATGTTTACTAGTCCACATCTT 59.825 37.037 22.87 8.66 0.00 2.40
3298 7637 7.907214 AACATGTTTACTAGTCCACATCTTC 57.093 36.000 14.26 0.00 0.00 2.87
3299 7638 7.004555 ACATGTTTACTAGTCCACATCTTCA 57.995 36.000 14.26 0.00 0.00 3.02
3300 7639 7.450074 ACATGTTTACTAGTCCACATCTTCAA 58.550 34.615 14.26 0.00 0.00 2.69
3301 7640 7.387948 ACATGTTTACTAGTCCACATCTTCAAC 59.612 37.037 14.26 0.00 0.00 3.18
3302 7641 5.924254 TGTTTACTAGTCCACATCTTCAACG 59.076 40.000 0.00 0.00 0.00 4.10
3303 7642 2.960819 ACTAGTCCACATCTTCAACGC 58.039 47.619 0.00 0.00 0.00 4.84
3304 7643 2.271800 CTAGTCCACATCTTCAACGCC 58.728 52.381 0.00 0.00 0.00 5.68
3305 7644 0.670546 AGTCCACATCTTCAACGCCG 60.671 55.000 0.00 0.00 0.00 6.46
3306 7645 0.669318 GTCCACATCTTCAACGCCGA 60.669 55.000 0.00 0.00 0.00 5.54
3307 7646 0.669318 TCCACATCTTCAACGCCGAC 60.669 55.000 0.00 0.00 0.00 4.79
3308 7647 1.635663 CCACATCTTCAACGCCGACC 61.636 60.000 0.00 0.00 0.00 4.79
3309 7648 1.375523 ACATCTTCAACGCCGACCC 60.376 57.895 0.00 0.00 0.00 4.46
3310 7649 1.079127 CATCTTCAACGCCGACCCT 60.079 57.895 0.00 0.00 0.00 4.34
3311 7650 0.673644 CATCTTCAACGCCGACCCTT 60.674 55.000 0.00 0.00 0.00 3.95
3329 7668 7.201582 CCGACCCTTAAATAGACACAATTACAC 60.202 40.741 0.00 0.00 0.00 2.90
3360 7701 0.396435 TTTGGACTCATGCGGACACT 59.604 50.000 0.00 0.00 0.00 3.55
3361 7702 0.396435 TTGGACTCATGCGGACACTT 59.604 50.000 0.00 0.00 0.00 3.16
3373 7714 2.004733 CGGACACTTTTACCGGATTCC 58.995 52.381 9.46 0.34 42.48 3.01
3563 7926 2.307098 ACTATGCCCTTTGAGCTTCACT 59.693 45.455 0.00 0.00 0.00 3.41
3569 7932 3.317993 GCCCTTTGAGCTTCACTTAACAA 59.682 43.478 0.00 0.00 0.00 2.83
3592 7955 8.335356 ACAATGTATGAACGTAAATAGCATGTC 58.665 33.333 0.00 0.00 0.00 3.06
3647 8010 5.130643 TCCGGGTTATACAACATGGTGATTA 59.869 40.000 19.90 5.52 36.29 1.75
3711 8074 3.936203 GTGTCGGTGTCCTGGCCA 61.936 66.667 4.71 4.71 0.00 5.36
3778 8141 0.618981 CCCCTAGGTTGGTTCTGTCC 59.381 60.000 8.29 0.00 0.00 4.02
3780 8143 0.249398 CCTAGGTTGGTTCTGTCCCG 59.751 60.000 0.00 0.00 0.00 5.14
3781 8144 0.249398 CTAGGTTGGTTCTGTCCCGG 59.751 60.000 0.00 0.00 0.00 5.73
3783 8146 2.671963 GTTGGTTCTGTCCCGGGC 60.672 66.667 18.49 12.24 0.00 6.13
3784 8147 3.961414 TTGGTTCTGTCCCGGGCC 61.961 66.667 18.49 4.39 0.00 5.80
3786 8149 4.717313 GGTTCTGTCCCGGGCCAC 62.717 72.222 18.49 11.07 0.00 5.01
3787 8150 3.637273 GTTCTGTCCCGGGCCACT 61.637 66.667 18.49 0.00 0.00 4.00
3789 8152 2.457323 TTCTGTCCCGGGCCACTTT 61.457 57.895 18.49 0.00 0.00 2.66
3790 8153 2.672996 CTGTCCCGGGCCACTTTG 60.673 66.667 18.49 0.00 0.00 2.77
3791 8154 4.278513 TGTCCCGGGCCACTTTGG 62.279 66.667 18.49 0.00 41.55 3.28
3814 8177 2.543777 GCCCATAGCGGATTACAAGA 57.456 50.000 0.00 0.00 36.56 3.02
3815 8178 2.846193 GCCCATAGCGGATTACAAGAA 58.154 47.619 0.00 0.00 36.56 2.52
3816 8179 2.808543 GCCCATAGCGGATTACAAGAAG 59.191 50.000 0.00 0.00 36.56 2.85
3817 8180 3.494398 GCCCATAGCGGATTACAAGAAGA 60.494 47.826 0.00 0.00 36.56 2.87
3833 8196 5.129485 ACAAGAAGACTCAAAGACTTGGAGA 59.871 40.000 23.87 5.94 38.93 3.71
3868 8231 2.110188 ACTGGAGTTGTGGAGGACTCTA 59.890 50.000 0.00 0.00 41.52 2.43
3874 8237 3.166679 GTTGTGGAGGACTCTACCTTCT 58.833 50.000 12.41 0.00 39.91 2.85
3901 8266 2.071540 GCCGACCTAGTTGTGTAAACC 58.928 52.381 0.00 0.00 0.00 3.27
3912 8277 0.900421 GTGTAAACCCTAGGACCGCT 59.100 55.000 11.48 0.00 0.00 5.52
3914 8279 0.177373 GTAAACCCTAGGACCGCTGG 59.823 60.000 11.48 0.00 0.00 4.85
3946 8311 0.811915 GCTAGAGGTTGAGCTCGTCA 59.188 55.000 9.64 0.00 35.73 4.35
4012 8377 5.984926 CACTCCAATGCAATAAAACACAAGT 59.015 36.000 0.00 0.00 0.00 3.16
4014 8379 7.326789 CACTCCAATGCAATAAAACACAAGTAG 59.673 37.037 0.00 0.00 0.00 2.57
4037 8402 2.555757 ACGTACGGTATTAGGGCATCTC 59.444 50.000 21.06 0.00 0.00 2.75
4061 8426 3.961729 GGAACCTCAAACCGACCG 58.038 61.111 0.00 0.00 0.00 4.79
4068 8433 3.039588 CAAACCGACCGGACCGTG 61.040 66.667 16.07 6.98 38.96 4.94
4069 8434 3.539791 AAACCGACCGGACCGTGT 61.540 61.111 16.07 10.43 38.96 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.181456 TGCAACTAAAATGGCAAAAGGCT 60.181 39.130 0.00 0.00 44.01 4.58
6 7 3.137533 TGCAACTAAAATGGCAAAAGGC 58.862 40.909 0.00 0.00 43.74 4.35
7 8 5.055812 TCTTGCAACTAAAATGGCAAAAGG 58.944 37.500 0.00 0.00 44.65 3.11
8 9 6.601741 TTCTTGCAACTAAAATGGCAAAAG 57.398 33.333 0.00 0.00 44.65 2.27
12 318 6.286758 TGAATTTCTTGCAACTAAAATGGCA 58.713 32.000 0.00 0.00 0.00 4.92
13 319 6.783892 TGAATTTCTTGCAACTAAAATGGC 57.216 33.333 0.00 0.45 0.00 4.40
27 333 4.630894 TCGCGGCATTAATGAATTTCTT 57.369 36.364 19.73 0.00 0.00 2.52
87 394 2.511600 CGCTACCGGAAGCCCAAG 60.512 66.667 9.46 0.00 39.43 3.61
98 405 5.449107 TTCCATGAGTAATAGACGCTACC 57.551 43.478 0.00 0.00 0.00 3.18
99 406 7.491696 ACTTTTTCCATGAGTAATAGACGCTAC 59.508 37.037 0.00 0.00 0.00 3.58
148 873 6.485313 CCACCTCACACACTCAAAACTAAATA 59.515 38.462 0.00 0.00 0.00 1.40
150 875 4.638421 CCACCTCACACACTCAAAACTAAA 59.362 41.667 0.00 0.00 0.00 1.85
160 885 2.507407 AAACAACCACCTCACACACT 57.493 45.000 0.00 0.00 0.00 3.55
226 1293 4.578516 ACGACAAAAACTTGATGGACATCA 59.421 37.500 10.75 10.75 45.30 3.07
254 1321 5.784578 AGGGTGTGGTAAAAATTTGAGAC 57.215 39.130 0.00 0.00 0.00 3.36
289 1356 5.389859 TGAAACTTTGCATGGTATCTTGG 57.610 39.130 0.00 0.00 0.00 3.61
290 1357 6.038356 GGATGAAACTTTGCATGGTATCTTG 58.962 40.000 0.00 0.00 0.00 3.02
320 1387 0.177141 TTGGGCATGCTACGAGGTAC 59.823 55.000 18.92 0.00 0.00 3.34
321 1388 0.906066 TTTGGGCATGCTACGAGGTA 59.094 50.000 18.92 0.00 0.00 3.08
349 1418 3.786809 GGCAACTAAAAAGCCGGAC 57.213 52.632 5.05 0.00 38.86 4.79
413 1482 1.851666 CACGGTGTGACAAATTTGCAC 59.148 47.619 25.72 25.72 35.23 4.57
423 1492 2.049433 CGAGGACCACGGTGTGAC 60.049 66.667 7.45 0.00 35.23 3.67
425 1494 2.543687 CTAGCGAGGACCACGGTGTG 62.544 65.000 23.58 13.39 41.38 3.82
427 1496 1.384989 ATCTAGCGAGGACCACGGTG 61.385 60.000 23.58 14.25 41.38 4.94
430 1499 1.360551 CCATCTAGCGAGGACCACG 59.639 63.158 6.99 6.99 0.00 4.94
433 1502 2.273538 TAGACCATCTAGCGAGGACC 57.726 55.000 0.00 0.00 0.00 4.46
437 1506 5.392919 CCAGATTCATAGACCATCTAGCGAG 60.393 48.000 0.00 0.00 31.67 5.03
445 1514 7.623999 ACTTACATCCAGATTCATAGACCAT 57.376 36.000 0.00 0.00 0.00 3.55
480 1549 6.561737 TTATGGCAGTAAAACGAACATCAA 57.438 33.333 0.00 0.00 0.00 2.57
483 1552 7.151999 TCAATTATGGCAGTAAAACGAACAT 57.848 32.000 0.00 0.00 0.00 2.71
492 1561 8.659527 TCTATCCATCTTCAATTATGGCAGTAA 58.340 33.333 0.00 0.00 42.08 2.24
526 1595 6.318396 CCCCAAACATTTTTCTTGTGTCAAAT 59.682 34.615 0.00 0.00 0.00 2.32
533 1602 3.684130 GCCACCCCAAACATTTTTCTTGT 60.684 43.478 0.00 0.00 0.00 3.16
534 1603 2.877786 GCCACCCCAAACATTTTTCTTG 59.122 45.455 0.00 0.00 0.00 3.02
537 1606 1.507562 CGCCACCCCAAACATTTTTC 58.492 50.000 0.00 0.00 0.00 2.29
541 1610 2.603171 CCCGCCACCCCAAACATT 60.603 61.111 0.00 0.00 0.00 2.71
548 1617 3.850098 CTATGATGCCCGCCACCCC 62.850 68.421 0.00 0.00 0.00 4.95
560 1629 2.630098 CAGGTGACGGACATCCTATGAT 59.370 50.000 0.00 0.00 32.03 2.45
561 1630 2.031870 CAGGTGACGGACATCCTATGA 58.968 52.381 0.00 0.00 32.03 2.15
562 1631 2.031870 TCAGGTGACGGACATCCTATG 58.968 52.381 0.00 0.00 32.03 2.23
563 1632 2.091830 TCTCAGGTGACGGACATCCTAT 60.092 50.000 0.00 0.00 32.03 2.57
564 1633 1.283905 TCTCAGGTGACGGACATCCTA 59.716 52.381 0.00 0.00 32.03 2.94
565 1634 0.039764 TCTCAGGTGACGGACATCCT 59.960 55.000 0.00 0.00 32.92 3.24
566 1635 1.115467 ATCTCAGGTGACGGACATCC 58.885 55.000 0.00 0.00 0.00 3.51
567 1636 1.478510 ACATCTCAGGTGACGGACATC 59.521 52.381 0.00 0.00 0.00 3.06
568 1637 1.561643 ACATCTCAGGTGACGGACAT 58.438 50.000 0.00 0.00 0.00 3.06
569 1638 1.338107 AACATCTCAGGTGACGGACA 58.662 50.000 0.00 0.00 0.00 4.02
570 1639 2.069273 CAAACATCTCAGGTGACGGAC 58.931 52.381 0.00 0.00 0.00 4.79
571 1640 1.608025 GCAAACATCTCAGGTGACGGA 60.608 52.381 0.00 0.00 0.00 4.69
572 1641 0.798776 GCAAACATCTCAGGTGACGG 59.201 55.000 0.00 0.00 0.00 4.79
573 1642 0.439985 CGCAAACATCTCAGGTGACG 59.560 55.000 0.00 0.00 0.00 4.35
574 1643 0.798776 CCGCAAACATCTCAGGTGAC 59.201 55.000 0.00 0.00 0.00 3.67
575 1644 0.396435 ACCGCAAACATCTCAGGTGA 59.604 50.000 0.00 0.00 0.00 4.02
576 1645 0.518636 CACCGCAAACATCTCAGGTG 59.481 55.000 0.00 0.00 42.31 4.00
577 1646 0.606401 CCACCGCAAACATCTCAGGT 60.606 55.000 0.00 0.00 0.00 4.00
578 1647 1.926511 GCCACCGCAAACATCTCAGG 61.927 60.000 0.00 0.00 34.03 3.86
579 1648 1.503542 GCCACCGCAAACATCTCAG 59.496 57.895 0.00 0.00 34.03 3.35
580 1649 2.324330 CGCCACCGCAAACATCTCA 61.324 57.895 0.00 0.00 34.03 3.27
581 1650 2.480555 CGCCACCGCAAACATCTC 59.519 61.111 0.00 0.00 34.03 2.75
582 1651 3.055719 CCGCCACCGCAAACATCT 61.056 61.111 0.00 0.00 34.03 2.90
583 1652 4.114997 CCCGCCACCGCAAACATC 62.115 66.667 0.00 0.00 34.03 3.06
594 1663 4.708386 AAATTCCGACGCCCGCCA 62.708 61.111 0.00 0.00 36.84 5.69
595 1664 3.436924 AAAATTCCGACGCCCGCC 61.437 61.111 0.00 0.00 36.84 6.13
596 1665 2.202427 CAAAATTCCGACGCCCGC 60.202 61.111 0.00 0.00 36.84 6.13
597 1666 2.202427 GCAAAATTCCGACGCCCG 60.202 61.111 0.00 0.00 38.18 6.13
598 1667 1.154035 CTGCAAAATTCCGACGCCC 60.154 57.895 0.00 0.00 0.00 6.13
599 1668 1.801512 GCTGCAAAATTCCGACGCC 60.802 57.895 0.00 0.00 0.00 5.68
600 1669 2.145905 CGCTGCAAAATTCCGACGC 61.146 57.895 0.00 0.00 0.00 5.19
601 1670 1.511887 CCGCTGCAAAATTCCGACG 60.512 57.895 0.00 0.00 0.00 5.12
602 1671 1.801512 GCCGCTGCAAAATTCCGAC 60.802 57.895 0.00 0.00 37.47 4.79
603 1672 2.566010 GCCGCTGCAAAATTCCGA 59.434 55.556 0.00 0.00 37.47 4.55
604 1673 2.875711 CGCCGCTGCAAAATTCCG 60.876 61.111 0.00 0.00 37.32 4.30
605 1674 2.506881 CCGCCGCTGCAAAATTCC 60.507 61.111 0.00 0.00 37.32 3.01
606 1675 2.506881 CCCGCCGCTGCAAAATTC 60.507 61.111 0.00 0.00 37.32 2.17
607 1676 4.740431 GCCCGCCGCTGCAAAATT 62.740 61.111 0.00 0.00 37.32 1.82
624 1693 0.313043 ATATGACCGGGCGACTTACG 59.687 55.000 6.32 0.00 45.66 3.18
625 1694 1.336609 GGATATGACCGGGCGACTTAC 60.337 57.143 6.32 0.00 0.00 2.34
626 1695 0.963962 GGATATGACCGGGCGACTTA 59.036 55.000 6.32 0.00 0.00 2.24
627 1696 1.046472 TGGATATGACCGGGCGACTT 61.046 55.000 6.32 0.00 0.00 3.01
636 1705 9.423061 GTTTAATTTGGCAATATGGATATGACC 57.577 33.333 0.00 0.00 0.00 4.02
708 2409 9.265901 CATATACTAGCATTAGATGGCAATACC 57.734 37.037 0.00 0.00 39.84 2.73
758 2459 3.435327 TCCTTTGATGGACGAATTCAACG 59.565 43.478 6.22 0.00 0.00 4.10
762 2463 5.818136 TCATTCCTTTGATGGACGAATTC 57.182 39.130 0.00 0.00 35.58 2.17
796 2497 6.370593 TCTTATTGCGTTGATTCTGTTGTTC 58.629 36.000 0.00 0.00 0.00 3.18
836 2537 9.750882 GTAATTACGGAGAAACAACAAGATAAC 57.249 33.333 0.00 0.00 0.00 1.89
931 2792 1.767127 TTCGTGACGCAAACGCACAT 61.767 50.000 0.00 0.00 45.53 3.21
934 2795 2.623718 CTTCGTGACGCAAACGCA 59.376 55.556 0.00 0.00 45.53 5.24
943 2804 3.524648 TTGGGCCGTCCTTCGTGAC 62.525 63.158 0.00 0.00 37.94 3.67
944 2805 3.234630 CTTGGGCCGTCCTTCGTGA 62.235 63.158 0.00 0.00 37.94 4.35
945 2806 2.742372 CTTGGGCCGTCCTTCGTG 60.742 66.667 0.00 0.00 37.94 4.35
989 2850 6.931281 CGGATGCCTCTTCATCTTAATCTTAA 59.069 38.462 4.10 0.00 41.83 1.85
990 2851 6.042093 ACGGATGCCTCTTCATCTTAATCTTA 59.958 38.462 4.10 0.00 41.83 2.10
991 2852 5.163258 ACGGATGCCTCTTCATCTTAATCTT 60.163 40.000 4.10 0.00 41.83 2.40
993 2854 4.636249 ACGGATGCCTCTTCATCTTAATC 58.364 43.478 4.10 0.00 41.83 1.75
1354 3233 9.125026 ACAAATTTTTGACAGTAGAGACAGAAT 57.875 29.630 9.88 0.00 40.55 2.40
1359 3238 8.603242 TCCTACAAATTTTTGACAGTAGAGAC 57.397 34.615 9.88 0.00 40.55 3.36
1463 3343 4.160626 AGTCTAACACAAGGGCAGATAGAC 59.839 45.833 0.00 0.00 38.55 2.59
1479 3359 5.140747 ACAAGGACATGTCAGAGTCTAAC 57.859 43.478 26.47 6.52 35.18 2.34
1614 5752 2.026729 TGCGGGGAAGAACATGTAATCA 60.027 45.455 0.00 0.00 0.00 2.57
1641 5837 6.572519 CGATGGGTTCCACAATGAAATAAAT 58.427 36.000 0.00 0.00 35.80 1.40
1732 5937 7.721286 TTCTCAGAAAAATCTCTCAACACTC 57.279 36.000 0.00 0.00 0.00 3.51
1734 5939 7.012799 AGGTTTCTCAGAAAAATCTCTCAACAC 59.987 37.037 0.00 0.00 0.00 3.32
1763 5968 1.230324 GGCGGCATCTAATTCCAGAC 58.770 55.000 3.07 0.00 0.00 3.51
1864 6071 4.759782 CACGTCCCATTACAAGATCTTCT 58.240 43.478 4.57 0.00 0.00 2.85
1951 6158 1.305201 AACGTTGACGATGGCAACTT 58.695 45.000 13.18 1.34 42.53 2.66
2013 6220 6.374894 CCCAAACAATGATGGTTTAATGCAAT 59.625 34.615 0.00 0.00 32.99 3.56
2014 6221 5.704515 CCCAAACAATGATGGTTTAATGCAA 59.295 36.000 0.00 0.00 32.99 4.08
2022 6229 3.708631 TGTGAACCCAAACAATGATGGTT 59.291 39.130 8.50 0.00 41.81 3.67
2026 6233 4.895297 AGTCTTGTGAACCCAAACAATGAT 59.105 37.500 0.00 0.00 35.82 2.45
2060 6280 5.866633 AGAATGTCAATCTCGTTTCTCAGAC 59.133 40.000 0.00 0.00 0.00 3.51
2089 6309 2.355716 CGAACTAGGGGAAGGCATGAAA 60.356 50.000 0.00 0.00 0.00 2.69
2127 6353 1.896220 ATGTCTTGCCTTTCTCGCAA 58.104 45.000 0.00 0.00 43.71 4.85
2160 6386 2.604046 AATACACCTCGATCACAGCC 57.396 50.000 0.00 0.00 0.00 4.85
2164 6390 4.767928 AGGGAGATAATACACCTCGATCAC 59.232 45.833 0.00 0.00 0.00 3.06
2165 6391 4.999310 AGGGAGATAATACACCTCGATCA 58.001 43.478 0.00 0.00 0.00 2.92
2232 6458 2.221169 GTGACATTGCTTGACCTGTCA 58.779 47.619 0.00 0.00 44.10 3.58
2257 6483 0.686441 ACATGCCATCCAGCTTGCAT 60.686 50.000 0.00 0.00 44.79 3.96
2313 6539 2.170397 TGTCAGAAGAGACCACAGCAAA 59.830 45.455 0.00 0.00 37.73 3.68
2317 6543 3.366883 GCTAGTGTCAGAAGAGACCACAG 60.367 52.174 0.00 0.00 38.74 3.66
2321 6547 2.094442 GGTGCTAGTGTCAGAAGAGACC 60.094 54.545 0.00 0.00 38.74 3.85
2347 6573 3.161067 CCAGGATCGATCTGGTAGATGT 58.839 50.000 23.96 0.00 44.97 3.06
2396 6622 1.949257 CACCGTCCAGAAAACCAGC 59.051 57.895 0.00 0.00 0.00 4.85
2516 6751 2.032681 GTTCAGGCAGCCCGTCTT 59.967 61.111 8.22 0.00 35.76 3.01
2595 6830 4.335315 TGGCTAAATCAATTGACGATCCAC 59.665 41.667 11.07 0.00 0.00 4.02
2602 6837 5.252969 TGCTGATGGCTAAATCAATTGAC 57.747 39.130 11.07 0.00 42.39 3.18
2681 7017 9.976511 AACATGATAATAATTGCATTTCAGGAG 57.023 29.630 0.00 0.00 0.00 3.69
2702 7041 3.181501 CGGGCCATACTGTAAACAACATG 60.182 47.826 4.39 0.00 37.50 3.21
2723 7062 0.251073 AATTACCCTGTTCCCGGTCG 59.749 55.000 0.00 0.00 33.36 4.79
2734 7073 3.405823 TCCGTTGACGAAAATTACCCT 57.594 42.857 4.91 0.00 43.02 4.34
2737 7076 4.849383 CACCATTCCGTTGACGAAAATTAC 59.151 41.667 4.91 0.00 43.02 1.89
2740 7079 2.227865 CCACCATTCCGTTGACGAAAAT 59.772 45.455 4.91 2.18 43.02 1.82
2744 7083 0.320073 GACCACCATTCCGTTGACGA 60.320 55.000 4.91 0.00 43.02 4.20
2745 7084 1.623081 CGACCACCATTCCGTTGACG 61.623 60.000 0.00 0.00 39.44 4.35
2850 7189 3.001358 GCCCATGGGAGGCCTCTTT 62.001 63.158 36.00 14.13 45.16 2.52
2954 7293 1.673808 GACGTCCTTGGTCGCCCTAT 61.674 60.000 3.51 0.00 0.00 2.57
3100 7439 3.433615 AGATGACACGTCTGCTAAAAAGC 59.566 43.478 0.00 0.00 0.00 3.51
3172 7511 1.414181 TGGGCGCCAAAAAGAATTGAA 59.586 42.857 30.85 0.00 31.84 2.69
3184 7523 0.331954 TATTTTAAGGGTGGGCGCCA 59.668 50.000 30.85 12.04 0.00 5.69
3204 7543 3.308595 TCATGGATAAACATTGCGTCGTC 59.691 43.478 0.00 0.00 0.00 4.20
3205 7544 3.266636 TCATGGATAAACATTGCGTCGT 58.733 40.909 0.00 0.00 0.00 4.34
3206 7545 3.942539 TCATGGATAAACATTGCGTCG 57.057 42.857 0.00 0.00 0.00 5.12
3211 7550 6.017934 CCGGACTAGTTCATGGATAAACATTG 60.018 42.308 0.00 0.00 0.00 2.82
3226 7565 1.001376 GGGGGAGTCCGGACTAGTT 59.999 63.158 36.38 16.04 42.66 2.24
3240 7579 2.057140 TCATATCTGTGTCCATGGGGG 58.943 52.381 13.02 0.00 38.37 5.40
3242 7581 4.511527 GCTATCATATCTGTGTCCATGGG 58.488 47.826 13.02 0.00 0.00 4.00
3245 7584 3.368843 GCGGCTATCATATCTGTGTCCAT 60.369 47.826 0.00 0.00 0.00 3.41
3253 7592 2.470990 TGGATGGCGGCTATCATATCT 58.529 47.619 24.77 0.00 0.00 1.98
3258 7597 0.254462 TGTTTGGATGGCGGCTATCA 59.746 50.000 24.77 10.63 0.00 2.15
3260 7599 1.321474 CATGTTTGGATGGCGGCTAT 58.679 50.000 11.43 0.00 0.00 2.97
3281 7620 4.491676 GCGTTGAAGATGTGGACTAGTAA 58.508 43.478 0.00 0.00 0.00 2.24
3284 7623 2.271800 GGCGTTGAAGATGTGGACTAG 58.728 52.381 0.00 0.00 0.00 2.57
3287 7626 0.669318 TCGGCGTTGAAGATGTGGAC 60.669 55.000 6.85 0.00 0.00 4.02
3288 7627 0.669318 GTCGGCGTTGAAGATGTGGA 60.669 55.000 6.85 0.00 0.00 4.02
3290 7629 1.635663 GGGTCGGCGTTGAAGATGTG 61.636 60.000 6.85 0.00 0.00 3.21
3291 7630 1.375523 GGGTCGGCGTTGAAGATGT 60.376 57.895 6.85 0.00 0.00 3.06
3292 7631 0.673644 AAGGGTCGGCGTTGAAGATG 60.674 55.000 6.85 0.00 0.00 2.90
3293 7632 0.899720 TAAGGGTCGGCGTTGAAGAT 59.100 50.000 6.85 0.00 0.00 2.40
3294 7633 0.680618 TTAAGGGTCGGCGTTGAAGA 59.319 50.000 6.85 0.00 0.00 2.87
3295 7634 1.515081 TTTAAGGGTCGGCGTTGAAG 58.485 50.000 6.85 0.00 0.00 3.02
3296 7635 2.188062 ATTTAAGGGTCGGCGTTGAA 57.812 45.000 6.85 0.00 0.00 2.69
3297 7636 2.496871 TCTATTTAAGGGTCGGCGTTGA 59.503 45.455 6.85 0.00 0.00 3.18
3298 7637 2.606272 GTCTATTTAAGGGTCGGCGTTG 59.394 50.000 6.85 0.00 0.00 4.10
3299 7638 2.234414 TGTCTATTTAAGGGTCGGCGTT 59.766 45.455 6.85 0.00 0.00 4.84
3300 7639 1.826720 TGTCTATTTAAGGGTCGGCGT 59.173 47.619 6.85 0.00 0.00 5.68
3301 7640 2.199236 GTGTCTATTTAAGGGTCGGCG 58.801 52.381 0.00 0.00 0.00 6.46
3302 7641 3.255969 TGTGTCTATTTAAGGGTCGGC 57.744 47.619 0.00 0.00 0.00 5.54
3303 7642 6.819649 TGTAATTGTGTCTATTTAAGGGTCGG 59.180 38.462 0.00 0.00 0.00 4.79
3304 7643 7.201582 GGTGTAATTGTGTCTATTTAAGGGTCG 60.202 40.741 0.00 0.00 0.00 4.79
3305 7644 7.066645 GGGTGTAATTGTGTCTATTTAAGGGTC 59.933 40.741 0.00 0.00 0.00 4.46
3306 7645 6.888088 GGGTGTAATTGTGTCTATTTAAGGGT 59.112 38.462 0.00 0.00 0.00 4.34
3307 7646 6.887545 TGGGTGTAATTGTGTCTATTTAAGGG 59.112 38.462 0.00 0.00 0.00 3.95
3308 7647 7.931578 TGGGTGTAATTGTGTCTATTTAAGG 57.068 36.000 0.00 0.00 0.00 2.69
3309 7648 9.840427 CTTTGGGTGTAATTGTGTCTATTTAAG 57.160 33.333 0.00 0.00 0.00 1.85
3310 7649 9.575868 TCTTTGGGTGTAATTGTGTCTATTTAA 57.424 29.630 0.00 0.00 0.00 1.52
3311 7650 9.005777 GTCTTTGGGTGTAATTGTGTCTATTTA 57.994 33.333 0.00 0.00 0.00 1.40
3373 7714 1.458398 TTGTACATGGTTGGATGGCG 58.542 50.000 0.00 0.00 0.00 5.69
3409 7770 9.887629 TTTGCATGTTATAAATGGATGAATTGT 57.112 25.926 0.00 0.00 0.00 2.71
3569 7932 7.217200 AGGACATGCTATTTACGTTCATACAT 58.783 34.615 0.00 0.00 0.00 2.29
3592 7955 3.606687 GTGTTGTACCATAGGACCAAGG 58.393 50.000 0.00 0.00 0.00 3.61
3647 8010 3.402110 TCACTCAATGCGACAACTTGAT 58.598 40.909 0.00 0.00 0.00 2.57
3790 8153 2.124507 TAATCCGCTATGGGCTGCCC 62.125 60.000 30.97 30.97 45.71 5.36
3791 8154 0.955919 GTAATCCGCTATGGGCTGCC 60.956 60.000 11.05 11.05 38.76 4.85
3792 8155 0.250295 TGTAATCCGCTATGGGCTGC 60.250 55.000 0.00 0.00 38.76 5.25
3793 8156 2.146342 CTTGTAATCCGCTATGGGCTG 58.854 52.381 0.00 0.00 38.76 4.85
3794 8157 2.047061 TCTTGTAATCCGCTATGGGCT 58.953 47.619 0.00 0.00 38.76 5.19
3795 8158 2.543777 TCTTGTAATCCGCTATGGGC 57.456 50.000 0.00 0.00 38.76 5.36
3796 8159 4.058817 GTCTTCTTGTAATCCGCTATGGG 58.941 47.826 0.00 0.00 38.76 4.00
3797 8160 4.950050 AGTCTTCTTGTAATCCGCTATGG 58.050 43.478 0.00 0.00 40.09 2.74
3798 8161 5.592054 TGAGTCTTCTTGTAATCCGCTATG 58.408 41.667 0.00 0.00 0.00 2.23
3799 8162 5.854010 TGAGTCTTCTTGTAATCCGCTAT 57.146 39.130 0.00 0.00 0.00 2.97
3800 8163 5.654603 TTGAGTCTTCTTGTAATCCGCTA 57.345 39.130 0.00 0.00 0.00 4.26
3801 8164 4.537135 TTGAGTCTTCTTGTAATCCGCT 57.463 40.909 0.00 0.00 0.00 5.52
3802 8165 4.929808 TCTTTGAGTCTTCTTGTAATCCGC 59.070 41.667 0.00 0.00 0.00 5.54
3803 8166 6.159988 AGTCTTTGAGTCTTCTTGTAATCCG 58.840 40.000 0.00 0.00 0.00 4.18
3804 8167 7.095017 CCAAGTCTTTGAGTCTTCTTGTAATCC 60.095 40.741 0.00 0.00 36.36 3.01
3805 8168 7.657761 TCCAAGTCTTTGAGTCTTCTTGTAATC 59.342 37.037 0.00 0.00 36.36 1.75
3806 8169 7.509546 TCCAAGTCTTTGAGTCTTCTTGTAAT 58.490 34.615 0.00 0.00 36.36 1.89
3807 8170 6.884832 TCCAAGTCTTTGAGTCTTCTTGTAA 58.115 36.000 0.00 0.00 36.36 2.41
3808 8171 6.323996 TCTCCAAGTCTTTGAGTCTTCTTGTA 59.676 38.462 12.19 0.00 36.36 2.41
3809 8172 5.129485 TCTCCAAGTCTTTGAGTCTTCTTGT 59.871 40.000 12.19 0.00 36.36 3.16
3810 8173 5.605534 TCTCCAAGTCTTTGAGTCTTCTTG 58.394 41.667 12.19 0.00 36.36 3.02
3811 8174 5.878406 TCTCCAAGTCTTTGAGTCTTCTT 57.122 39.130 12.19 0.00 36.36 2.52
3812 8175 5.129485 TGTTCTCCAAGTCTTTGAGTCTTCT 59.871 40.000 12.19 0.00 36.36 2.85
3813 8176 5.360591 TGTTCTCCAAGTCTTTGAGTCTTC 58.639 41.667 12.19 4.40 36.36 2.87
3814 8177 5.359194 TGTTCTCCAAGTCTTTGAGTCTT 57.641 39.130 12.19 0.00 36.36 3.01
3815 8178 5.359194 TTGTTCTCCAAGTCTTTGAGTCT 57.641 39.130 12.19 0.00 36.36 3.24
3816 8179 5.994668 AGATTGTTCTCCAAGTCTTTGAGTC 59.005 40.000 12.19 8.36 36.25 3.36
3817 8180 5.762218 CAGATTGTTCTCCAAGTCTTTGAGT 59.238 40.000 12.19 0.00 36.25 3.41
3833 8196 5.171476 CAACTCCAGTATCGTCAGATTGTT 58.829 41.667 0.00 0.00 38.26 2.83
3868 8231 0.824759 GGTCGGCTACATCAGAAGGT 59.175 55.000 0.00 0.00 0.00 3.50
3874 8237 2.165641 CACAACTAGGTCGGCTACATCA 59.834 50.000 0.00 0.00 0.00 3.07
3901 8266 1.120530 AACATACCAGCGGTCCTAGG 58.879 55.000 0.82 0.82 37.09 3.02
3912 8277 9.596308 TCAACCTCTAGCTTATATAACATACCA 57.404 33.333 0.00 0.00 0.00 3.25
3914 8279 9.575783 GCTCAACCTCTAGCTTATATAACATAC 57.424 37.037 0.00 0.00 35.80 2.39
4012 8377 2.158682 TGCCCTAATACCGTACGTCCTA 60.159 50.000 15.21 0.78 0.00 2.94
4014 8379 1.032014 TGCCCTAATACCGTACGTCC 58.968 55.000 15.21 0.00 0.00 4.79
4037 8402 1.281656 GTTTGAGGTTCCGCGTTGG 59.718 57.895 4.92 0.00 40.09 3.77


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

AutoCloner maintained by Alex Coulton.