Multiple sequence alignment - TraesCS4D01G344400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G344400 chr4D 100.000 3455 0 0 1 3455 499693461 499696915 0.000000e+00 6381.0
1 TraesCS4D01G344400 chr4D 88.083 2165 218 24 870 3008 499713058 499710908 0.000000e+00 2532.0
2 TraesCS4D01G344400 chr4D 86.350 1685 184 19 816 2478 499702052 499700392 0.000000e+00 1796.0
3 TraesCS4D01G344400 chr4D 93.666 521 32 1 1723 2243 499830833 499831352 0.000000e+00 778.0
4 TraesCS4D01G344400 chr4D 83.961 717 75 23 2222 2930 499833646 499834330 0.000000e+00 651.0
5 TraesCS4D01G344400 chr4D 87.154 397 48 3 1923 2318 499844655 499845049 6.800000e-122 448.0
6 TraesCS4D01G344400 chr4D 94.466 253 14 0 3203 3455 499835011 499835263 1.160000e-104 390.0
7 TraesCS4D01G344400 chr4D 87.347 245 27 4 3213 3455 499710529 499710287 9.440000e-71 278.0
8 TraesCS4D01G344400 chr4D 85.992 257 30 5 3203 3455 499676881 499677135 1.580000e-68 270.0
9 TraesCS4D01G344400 chr4D 85.878 262 20 3 1466 1727 499794184 499794428 2.640000e-66 263.0
10 TraesCS4D01G344400 chr4D 82.833 233 15 10 1 226 499703583 499703369 5.890000e-43 185.0
11 TraesCS4D01G344400 chr4D 89.286 112 6 3 262 372 499703364 499703258 6.010000e-28 135.0
12 TraesCS4D01G344400 chr5A 92.134 1767 131 4 864 2624 680748930 680750694 0.000000e+00 2486.0
13 TraesCS4D01G344400 chr5A 90.194 1754 161 6 870 2618 680696986 680695239 0.000000e+00 2276.0
14 TraesCS4D01G344400 chr5A 97.163 282 8 0 3174 3455 680661763 680661482 8.680000e-131 477.0
15 TraesCS4D01G344400 chr5A 87.879 396 43 4 2749 3144 680662154 680661764 8.740000e-126 460.0
16 TraesCS4D01G344400 chr5A 96.047 253 10 0 3203 3455 680752365 680752617 2.480000e-111 412.0
17 TraesCS4D01G344400 chr5A 86.856 388 22 15 1 371 680664335 680663960 1.150000e-109 407.0
18 TraesCS4D01G344400 chr5A 86.056 251 33 2 3206 3455 680694844 680694595 5.680000e-68 268.0
19 TraesCS4D01G344400 chr5A 88.106 227 12 5 816 1035 680663029 680662811 4.430000e-64 255.0
20 TraesCS4D01G344400 chr5A 78.788 231 25 9 59 278 680697936 680697719 2.160000e-27 134.0
21 TraesCS4D01G344400 chr5A 97.059 34 1 0 2628 2661 680750765 680750798 1.340000e-04 58.4
22 TraesCS4D01G344400 chr4B 89.062 1801 165 13 799 2590 642750922 642749145 0.000000e+00 2206.0
23 TraesCS4D01G344400 chr4B 87.408 1628 180 12 864 2475 642963633 642965251 0.000000e+00 1847.0
24 TraesCS4D01G344400 chr4B 92.832 837 51 3 870 1699 642780944 642780110 0.000000e+00 1205.0
25 TraesCS4D01G344400 chr4B 87.132 917 112 3 1685 2599 642779699 642778787 0.000000e+00 1035.0
26 TraesCS4D01G344400 chr4B 94.150 359 21 0 3097 3455 642748604 642748246 6.520000e-152 547.0
27 TraesCS4D01G344400 chr4B 94.094 254 12 3 2848 3101 642748900 642748650 1.950000e-102 383.0
28 TraesCS4D01G344400 chr4B 84.127 252 36 4 3206 3455 642777976 642777727 1.240000e-59 241.0
29 TraesCS4D01G344400 chr4B 84.916 179 25 1 3203 3379 642961143 642961321 2.740000e-41 180.0
30 TraesCS4D01G344400 chr4B 96.739 92 3 0 2485 2576 642965902 642965993 1.660000e-33 154.0
31 TraesCS4D01G344400 chr4B 82.486 177 21 4 775 947 486974453 486974623 2.780000e-31 147.0
32 TraesCS4D01G344400 chr4B 87.379 103 12 1 2606 2708 642965989 642966090 2.180000e-22 117.0
33 TraesCS4D01G344400 chr4B 92.982 57 4 0 571 627 603006384 603006440 2.210000e-12 84.2
34 TraesCS4D01G344400 chr7A 92.982 57 4 0 571 627 25224031 25223975 2.210000e-12 84.2
35 TraesCS4D01G344400 chr6B 92.982 57 4 0 571 627 693624586 693624642 2.210000e-12 84.2
36 TraesCS4D01G344400 chr3A 92.982 57 3 1 571 627 496386702 496386757 7.950000e-12 82.4
37 TraesCS4D01G344400 chr3D 94.231 52 3 0 571 622 578590035 578590086 2.860000e-11 80.5
38 TraesCS4D01G344400 chr6A 91.228 57 5 0 571 627 471274936 471274880 1.030000e-10 78.7
39 TraesCS4D01G344400 chr2D 89.474 57 5 1 571 627 92462926 92462981 1.720000e-08 71.3


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 TraesCS4D01G344400 chr4D 499693461 499696915 3454 False 6381.000000 6381 100.000000 1 3455 1 chr4D.!!$F2 3454
1 TraesCS4D01G344400 chr4D 499710287 499713058 2771 True 1405.000000 2532 87.715000 870 3455 2 chr4D.!!$R2 2585
2 TraesCS4D01G344400 chr4D 499700392 499703583 3191 True 705.333333 1796 86.156333 1 2478 3 chr4D.!!$R1 2477
3 TraesCS4D01G344400 chr4D 499830833 499835263 4430 False 606.333333 778 90.697667 1723 3455 3 chr4D.!!$F5 1732
4 TraesCS4D01G344400 chr5A 680748930 680752617 3687 False 985.466667 2486 95.080000 864 3455 3 chr5A.!!$F1 2591
5 TraesCS4D01G344400 chr5A 680694595 680697936 3341 True 892.666667 2276 85.012667 59 3455 3 chr5A.!!$R2 3396
6 TraesCS4D01G344400 chr5A 680661482 680664335 2853 True 399.750000 477 90.001000 1 3455 4 chr5A.!!$R1 3454
7 TraesCS4D01G344400 chr4B 642748246 642750922 2676 True 1045.333333 2206 92.435333 799 3455 3 chr4B.!!$R1 2656
8 TraesCS4D01G344400 chr4B 642777727 642780944 3217 True 827.000000 1205 88.030333 870 3455 3 chr4B.!!$R2 2585
9 TraesCS4D01G344400 chr4B 642961143 642966090 4947 False 574.500000 1847 89.110500 864 3379 4 chr4B.!!$F3 2515

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
407 1307 0.036388 TGCCCAAGAGTCGGTTCATC 60.036 55.0 0.0 0.0 0.0 2.92 F
1830 3927 0.179059 TGTGCTCTCTTTGCCGACAA 60.179 50.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 4257 0.396139 AAGTTCATGCGGATGCCCAT 60.396 50.000 12.67 0.00 41.78 4.0 R
2740 8042 1.068588 TCATAGGGTGCATCGTAGTGC 59.931 52.381 5.52 3.81 45.25 4.4 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 30 5.079643 ACCTCATTAGCTGAACAAATGGTT 58.920 37.500 0.00 0.00 44.10 3.67
36 39 3.648009 TGAACAAATGGTTTGCGGATTC 58.352 40.909 2.54 0.87 44.39 2.52
40 43 4.640364 ACAAATGGTTTGCGGATTCAATT 58.360 34.783 2.54 0.00 44.39 2.32
43 46 4.533919 ATGGTTTGCGGATTCAATTTGA 57.466 36.364 0.00 0.00 0.00 2.69
44 47 3.911868 TGGTTTGCGGATTCAATTTGAG 58.088 40.909 0.00 0.00 0.00 3.02
45 48 3.320541 TGGTTTGCGGATTCAATTTGAGT 59.679 39.130 0.00 0.00 0.00 3.41
68 75 6.490381 AGTTTTGAGGAATTCAAGTTAGGGTC 59.510 38.462 7.93 0.00 46.01 4.46
73 80 7.166167 TGAGGAATTCAAGTTAGGGTCTTAAC 58.834 38.462 7.93 0.00 34.48 2.01
96 107 2.354503 CCAATGTCAGCAGACTAGCAGT 60.355 50.000 10.83 0.00 45.20 4.40
169 195 6.924111 TCCAATTCCTTTCAACAGCTTTATC 58.076 36.000 0.00 0.00 0.00 1.75
325 354 5.733620 TTGTGGTCGTTTTCTCCTAGTAT 57.266 39.130 0.00 0.00 0.00 2.12
328 357 5.948162 TGTGGTCGTTTTCTCCTAGTATAGT 59.052 40.000 0.00 0.00 36.82 2.12
329 358 7.112122 TGTGGTCGTTTTCTCCTAGTATAGTA 58.888 38.462 0.00 0.00 36.82 1.82
385 415 7.291411 TCTGCTAATTTCACCTAGATACTCC 57.709 40.000 0.00 0.00 0.00 3.85
387 417 7.344612 TCTGCTAATTTCACCTAGATACTCCAA 59.655 37.037 0.00 0.00 0.00 3.53
388 418 8.034313 TGCTAATTTCACCTAGATACTCCAAT 57.966 34.615 0.00 0.00 0.00 3.16
389 419 7.933577 TGCTAATTTCACCTAGATACTCCAATG 59.066 37.037 0.00 0.00 0.00 2.82
390 420 7.095017 GCTAATTTCACCTAGATACTCCAATGC 60.095 40.741 0.00 0.00 0.00 3.56
405 1305 0.400213 AATGCCCAAGAGTCGGTTCA 59.600 50.000 0.00 0.00 0.00 3.18
406 1306 0.620556 ATGCCCAAGAGTCGGTTCAT 59.379 50.000 0.00 0.00 0.00 2.57
407 1307 0.036388 TGCCCAAGAGTCGGTTCATC 60.036 55.000 0.00 0.00 0.00 2.92
408 1308 0.036388 GCCCAAGAGTCGGTTCATCA 60.036 55.000 0.00 0.00 0.00 3.07
409 1309 1.610624 GCCCAAGAGTCGGTTCATCAA 60.611 52.381 0.00 0.00 0.00 2.57
413 1313 3.563808 CCAAGAGTCGGTTCATCAACAAA 59.436 43.478 0.00 0.00 33.70 2.83
416 1316 1.880027 AGTCGGTTCATCAACAAAGGC 59.120 47.619 0.00 0.00 33.70 4.35
418 1318 0.243636 CGGTTCATCAACAAAGGCCC 59.756 55.000 0.00 0.00 33.70 5.80
420 1320 1.691434 GGTTCATCAACAAAGGCCCAA 59.309 47.619 0.00 0.00 33.70 4.12
421 1321 2.289010 GGTTCATCAACAAAGGCCCAAG 60.289 50.000 0.00 0.00 33.70 3.61
425 1398 1.691196 TCAACAAAGGCCCAAGAGTG 58.309 50.000 0.00 0.00 0.00 3.51
427 1400 2.173782 TCAACAAAGGCCCAAGAGTGTA 59.826 45.455 0.00 0.00 0.00 2.90
428 1401 2.955660 CAACAAAGGCCCAAGAGTGTAA 59.044 45.455 0.00 0.00 0.00 2.41
455 1429 4.102524 ACAGAAAGAAGTATGTGGTGGTGA 59.897 41.667 0.00 0.00 0.00 4.02
465 1440 2.305928 TGTGGTGGTGATCAACAAAGG 58.694 47.619 16.70 0.00 45.83 3.11
466 1441 1.000274 GTGGTGGTGATCAACAAAGGC 60.000 52.381 16.70 2.39 45.83 4.35
475 1450 1.981256 TCAACAAAGGCCCAAGAGTC 58.019 50.000 0.00 0.00 0.00 3.36
483 1458 1.446272 GCCCAAGAGTCGGTTCTCG 60.446 63.158 0.00 0.00 39.21 4.04
491 1466 1.080705 GTCGGTTCTCGGTCAGGTG 60.081 63.158 0.00 0.00 39.77 4.00
492 1467 1.228337 TCGGTTCTCGGTCAGGTGA 60.228 57.895 0.00 0.00 39.77 4.02
493 1468 1.080705 CGGTTCTCGGTCAGGTGAC 60.081 63.158 1.17 1.17 44.04 3.67
495 1470 0.391597 GGTTCTCGGTCAGGTGACAA 59.608 55.000 12.09 0.00 46.47 3.18
496 1471 1.605712 GGTTCTCGGTCAGGTGACAAG 60.606 57.143 12.09 8.53 46.47 3.16
497 1472 1.068741 GTTCTCGGTCAGGTGACAAGT 59.931 52.381 12.09 0.00 46.47 3.16
499 1474 2.589720 TCTCGGTCAGGTGACAAGTTA 58.410 47.619 12.09 0.00 46.47 2.24
500 1475 2.557056 TCTCGGTCAGGTGACAAGTTAG 59.443 50.000 12.09 2.28 46.47 2.34
512 1487 7.965107 CAGGTGACAAGTTAGAAAAATCTATGC 59.035 37.037 0.00 0.00 0.00 3.14
521 1496 4.526970 AGAAAAATCTATGCCGTGATGGT 58.473 39.130 0.00 0.00 41.21 3.55
537 1513 5.506483 CGTGATGGTTTGTTAACAATGACCA 60.506 40.000 32.19 32.19 45.43 4.02
539 1515 6.420604 GTGATGGTTTGTTAACAATGACCAAG 59.579 38.462 33.05 0.00 44.88 3.61
541 1517 6.142818 TGGTTTGTTAACAATGACCAAGAG 57.857 37.500 29.90 0.00 41.30 2.85
542 1518 5.888724 TGGTTTGTTAACAATGACCAAGAGA 59.111 36.000 29.90 14.97 41.30 3.10
543 1519 6.183360 TGGTTTGTTAACAATGACCAAGAGAC 60.183 38.462 29.90 18.10 41.30 3.36
544 1520 6.183360 GGTTTGTTAACAATGACCAAGAGACA 60.183 38.462 26.70 6.82 36.95 3.41
545 1521 7.254852 GTTTGTTAACAATGACCAAGAGACAA 58.745 34.615 21.17 0.00 35.55 3.18
547 1523 6.119536 TGTTAACAATGACCAAGAGACAAGT 58.880 36.000 5.64 0.00 0.00 3.16
549 1525 2.880890 ACAATGACCAAGAGACAAGTGC 59.119 45.455 0.00 0.00 0.00 4.40
550 1526 3.144506 CAATGACCAAGAGACAAGTGCT 58.855 45.455 0.00 0.00 0.00 4.40
551 1527 2.245159 TGACCAAGAGACAAGTGCTG 57.755 50.000 0.00 0.00 0.00 4.41
561 1553 2.434336 AGACAAGTGCTGTACCAGTCAA 59.566 45.455 16.31 0.00 38.84 3.18
568 1560 5.262009 AGTGCTGTACCAGTCAAGTCTATA 58.738 41.667 0.00 0.00 33.43 1.31
595 1587 3.375782 AGCAAGAAAGAATGCAACCAC 57.624 42.857 0.00 0.00 44.95 4.16
607 1599 4.989279 ATGCAACCACATACAAAGGATC 57.011 40.909 0.00 0.00 0.00 3.36
608 1600 3.088532 TGCAACCACATACAAAGGATCC 58.911 45.455 2.48 2.48 0.00 3.36
611 1603 3.004752 ACCACATACAAAGGATCCTGC 57.995 47.619 17.02 0.00 0.00 4.85
639 1631 4.142160 GGAATGGGTCCAATTTTAGTGAGC 60.142 45.833 0.00 0.00 46.97 4.26
659 1652 2.159462 GCAGAGCACTGGCATTTTCTAC 60.159 50.000 13.26 0.00 44.61 2.59
660 1653 3.076621 CAGAGCACTGGCATTTTCTACA 58.923 45.455 2.82 0.00 44.61 2.74
667 1678 3.327757 ACTGGCATTTTCTACAGACCAGA 59.672 43.478 15.87 0.00 44.80 3.86
671 1682 4.379918 GGCATTTTCTACAGACCAGAAAGC 60.380 45.833 0.00 0.00 41.64 3.51
690 1701 2.623416 AGCTTGACTTTGTTAACCAGCC 59.377 45.455 2.48 0.00 0.00 4.85
691 1702 2.360801 GCTTGACTTTGTTAACCAGCCA 59.639 45.455 2.48 0.00 0.00 4.75
692 1703 3.005791 GCTTGACTTTGTTAACCAGCCAT 59.994 43.478 2.48 0.00 0.00 4.40
693 1704 4.501400 GCTTGACTTTGTTAACCAGCCATT 60.501 41.667 2.48 0.00 0.00 3.16
694 1705 5.278758 GCTTGACTTTGTTAACCAGCCATTA 60.279 40.000 2.48 0.00 0.00 1.90
695 1706 5.699097 TGACTTTGTTAACCAGCCATTAC 57.301 39.130 2.48 0.00 0.00 1.89
696 1707 4.521256 TGACTTTGTTAACCAGCCATTACC 59.479 41.667 2.48 0.00 0.00 2.85
697 1708 4.475345 ACTTTGTTAACCAGCCATTACCA 58.525 39.130 2.48 0.00 0.00 3.25
698 1709 4.522789 ACTTTGTTAACCAGCCATTACCAG 59.477 41.667 2.48 0.00 0.00 4.00
699 1710 4.374689 TTGTTAACCAGCCATTACCAGA 57.625 40.909 2.48 0.00 0.00 3.86
700 1711 3.950397 TGTTAACCAGCCATTACCAGAG 58.050 45.455 2.48 0.00 0.00 3.35
702 1713 4.192317 GTTAACCAGCCATTACCAGAGAG 58.808 47.826 0.00 0.00 0.00 3.20
703 1714 2.254152 ACCAGCCATTACCAGAGAGA 57.746 50.000 0.00 0.00 0.00 3.10
704 1715 2.114616 ACCAGCCATTACCAGAGAGAG 58.885 52.381 0.00 0.00 0.00 3.20
705 1716 2.292521 ACCAGCCATTACCAGAGAGAGA 60.293 50.000 0.00 0.00 0.00 3.10
706 1717 2.364970 CCAGCCATTACCAGAGAGAGAG 59.635 54.545 0.00 0.00 0.00 3.20
707 1718 3.295093 CAGCCATTACCAGAGAGAGAGA 58.705 50.000 0.00 0.00 0.00 3.10
708 1719 3.318839 CAGCCATTACCAGAGAGAGAGAG 59.681 52.174 0.00 0.00 0.00 3.20
710 1721 3.569701 GCCATTACCAGAGAGAGAGAGAG 59.430 52.174 0.00 0.00 0.00 3.20
712 1723 5.065914 CCATTACCAGAGAGAGAGAGAGAG 58.934 50.000 0.00 0.00 0.00 3.20
714 1725 5.614324 TTACCAGAGAGAGAGAGAGAGAG 57.386 47.826 0.00 0.00 0.00 3.20
717 1728 3.494048 CCAGAGAGAGAGAGAGAGAGAGC 60.494 56.522 0.00 0.00 0.00 4.09
718 1729 3.133542 CAGAGAGAGAGAGAGAGAGAGCA 59.866 52.174 0.00 0.00 0.00 4.26
719 1730 3.133721 AGAGAGAGAGAGAGAGAGAGCAC 59.866 52.174 0.00 0.00 0.00 4.40
721 1732 3.264193 AGAGAGAGAGAGAGAGAGCACAA 59.736 47.826 0.00 0.00 0.00 3.33
722 1733 3.614092 AGAGAGAGAGAGAGAGCACAAG 58.386 50.000 0.00 0.00 0.00 3.16
723 1734 3.264193 AGAGAGAGAGAGAGAGCACAAGA 59.736 47.826 0.00 0.00 0.00 3.02
725 1736 4.012374 AGAGAGAGAGAGAGCACAAGAAG 58.988 47.826 0.00 0.00 0.00 2.85
726 1737 4.009675 GAGAGAGAGAGAGCACAAGAAGA 58.990 47.826 0.00 0.00 0.00 2.87
727 1738 4.012374 AGAGAGAGAGAGCACAAGAAGAG 58.988 47.826 0.00 0.00 0.00 2.85
730 1741 4.588528 AGAGAGAGAGCACAAGAAGAGTTT 59.411 41.667 0.00 0.00 0.00 2.66
731 1742 4.630111 AGAGAGAGCACAAGAAGAGTTTG 58.370 43.478 0.00 0.00 0.00 2.93
733 1744 2.874701 GAGAGCACAAGAAGAGTTTGCA 59.125 45.455 0.00 0.00 35.57 4.08
734 1745 2.877168 AGAGCACAAGAAGAGTTTGCAG 59.123 45.455 0.00 0.00 35.57 4.41
735 1746 2.874701 GAGCACAAGAAGAGTTTGCAGA 59.125 45.455 0.00 0.00 35.57 4.26
740 1751 3.873952 ACAAGAAGAGTTTGCAGACAGAC 59.126 43.478 10.36 1.06 0.00 3.51
754 1765 3.496130 CAGACAGACACATCAACTTCCAC 59.504 47.826 0.00 0.00 0.00 4.02
755 1766 3.389329 AGACAGACACATCAACTTCCACT 59.611 43.478 0.00 0.00 0.00 4.00
758 1769 2.975489 AGACACATCAACTTCCACTCCT 59.025 45.455 0.00 0.00 0.00 3.69
760 1771 2.705658 ACACATCAACTTCCACTCCTGA 59.294 45.455 0.00 0.00 0.00 3.86
761 1772 3.244353 ACACATCAACTTCCACTCCTGAG 60.244 47.826 0.00 0.00 0.00 3.35
762 1773 3.007290 CACATCAACTTCCACTCCTGAGA 59.993 47.826 0.22 0.00 0.00 3.27
763 1774 3.648067 ACATCAACTTCCACTCCTGAGAA 59.352 43.478 0.22 0.00 0.00 2.87
764 1775 4.252073 CATCAACTTCCACTCCTGAGAAG 58.748 47.826 0.22 0.00 42.19 2.85
768 1779 3.515562 ACTTCCACTCCTGAGAAGTCAT 58.484 45.455 0.22 0.00 45.37 3.06
769 1780 4.678256 ACTTCCACTCCTGAGAAGTCATA 58.322 43.478 0.22 0.00 45.37 2.15
770 1781 5.087323 ACTTCCACTCCTGAGAAGTCATAA 58.913 41.667 0.22 0.00 45.37 1.90
771 1782 5.186797 ACTTCCACTCCTGAGAAGTCATAAG 59.813 44.000 0.22 0.00 45.37 1.73
773 1784 5.333581 TCCACTCCTGAGAAGTCATAAGAA 58.666 41.667 0.22 0.00 30.18 2.52
774 1785 5.186021 TCCACTCCTGAGAAGTCATAAGAAC 59.814 44.000 0.22 0.00 30.18 3.01
775 1786 5.186797 CCACTCCTGAGAAGTCATAAGAACT 59.813 44.000 0.22 0.00 30.18 3.01
776 1787 6.098679 CACTCCTGAGAAGTCATAAGAACTG 58.901 44.000 0.22 0.00 30.18 3.16
777 1788 5.777732 ACTCCTGAGAAGTCATAAGAACTGT 59.222 40.000 0.22 0.00 30.18 3.55
778 1789 6.030548 TCCTGAGAAGTCATAAGAACTGTG 57.969 41.667 0.00 0.00 30.18 3.66
779 1790 5.047021 TCCTGAGAAGTCATAAGAACTGTGG 60.047 44.000 0.00 0.00 30.18 4.17
780 1791 5.047021 CCTGAGAAGTCATAAGAACTGTGGA 60.047 44.000 0.00 0.00 30.18 4.02
782 1793 7.147828 CCTGAGAAGTCATAAGAACTGTGGATA 60.148 40.741 0.00 0.00 30.18 2.59
796 1807 2.293877 GGATACAAGTCCCCGTGGT 58.706 57.895 0.00 0.00 31.82 4.16
797 1808 1.488390 GGATACAAGTCCCCGTGGTA 58.512 55.000 0.00 0.00 31.82 3.25
806 1833 2.049767 CCCCGTGGTACCAAATGGC 61.050 63.158 18.31 2.33 39.32 4.40
856 1883 4.082571 AGCATGACTTTGATAACCAGCAAC 60.083 41.667 0.00 0.00 27.60 4.17
868 1895 0.236711 CCAGCAACAACTGAGAAGCG 59.763 55.000 0.00 0.00 40.25 4.68
875 2395 2.906354 ACAACTGAGAAGCGTGACTTT 58.094 42.857 0.00 0.00 39.29 2.66
876 2396 2.609459 ACAACTGAGAAGCGTGACTTTG 59.391 45.455 0.00 0.00 39.29 2.77
877 2397 2.866156 CAACTGAGAAGCGTGACTTTGA 59.134 45.455 0.00 0.00 39.29 2.69
878 2398 3.393089 ACTGAGAAGCGTGACTTTGAT 57.607 42.857 0.00 0.00 39.29 2.57
879 2399 4.521130 ACTGAGAAGCGTGACTTTGATA 57.479 40.909 0.00 0.00 39.29 2.15
880 2400 4.883083 ACTGAGAAGCGTGACTTTGATAA 58.117 39.130 0.00 0.00 39.29 1.75
881 2401 4.686554 ACTGAGAAGCGTGACTTTGATAAC 59.313 41.667 0.00 0.00 39.29 1.89
889 2409 5.063944 AGCGTGACTTTGATAACTAGCAATG 59.936 40.000 0.00 0.58 34.28 2.82
916 2549 2.112718 GGCAGGGGCAGAGCATAG 59.887 66.667 0.00 0.00 43.71 2.23
947 2580 9.950496 AGTTTGTAGAGACATCAACTATTCAAT 57.050 29.630 0.00 0.00 35.70 2.57
965 2598 3.250762 TCAATTTCCAAGCTCAGTGTTCG 59.749 43.478 0.00 0.00 0.00 3.95
1065 2719 6.009908 AGATCCATGAGTTCCATCATCAAA 57.990 37.500 0.00 0.00 37.84 2.69
1102 2756 3.458163 CGGAGGCCGTGGAAGCTA 61.458 66.667 0.00 0.00 42.73 3.32
1104 2758 2.501610 GAGGCCGTGGAAGCTAGG 59.498 66.667 0.00 0.00 0.00 3.02
1149 2803 1.037579 AGGTCATCATCGACGAGGCA 61.038 55.000 4.29 0.00 36.73 4.75
1313 2967 1.062886 TGGGGTGGTGTCCAAATTTCA 60.063 47.619 0.00 0.00 34.18 2.69
1316 2970 3.306710 GGGGTGGTGTCCAAATTTCATTC 60.307 47.826 0.00 0.00 34.18 2.67
1376 3030 2.664402 ACATCACAAGGGCTTGAAGT 57.336 45.000 0.00 0.00 42.93 3.01
1386 3040 1.302511 GCTTGAAGTGGCCCTCGAA 60.303 57.895 0.00 0.00 0.00 3.71
1446 3100 3.199946 TCAGGTTCCTGACAACATATCCC 59.800 47.826 16.47 0.00 38.06 3.85
1530 3184 5.010933 CAGAGGGAGACAGAAGTAGTTACA 58.989 45.833 0.00 0.00 0.00 2.41
1712 3806 5.876651 TTCAGAGCTCAAGATATAGCCAA 57.123 39.130 17.77 0.00 39.64 4.52
1718 3812 6.709846 AGAGCTCAAGATATAGCCAATTTGAC 59.290 38.462 17.77 0.00 39.64 3.18
1742 3836 0.321919 AGATGTGCGGCAAGACATGT 60.322 50.000 3.23 0.00 32.85 3.21
1759 3856 9.106070 CAAGACATGTGAATAATGAGAGATTGA 57.894 33.333 1.15 0.00 0.00 2.57
1830 3927 0.179059 TGTGCTCTCTTTGCCGACAA 60.179 50.000 0.00 0.00 0.00 3.18
1926 4023 4.334203 ACTCTAGTACTGAAGCATCTGTCG 59.666 45.833 5.39 0.00 38.51 4.35
1992 4090 1.614711 GGATCCCAAGATGCACCCA 59.385 57.895 0.00 0.00 40.40 4.51
2052 4153 7.101700 TGATGAATTATAATCTCGCTGATGCT 58.898 34.615 0.00 0.00 35.21 3.79
2093 4194 8.461222 TGTATTGAGAGCCAATTTTAACATCAG 58.539 33.333 0.00 0.00 42.55 2.90
2114 4215 0.843309 TTCTGGTGCAAGGTTCTGGA 59.157 50.000 0.00 0.00 0.00 3.86
2118 4219 3.073798 TCTGGTGCAAGGTTCTGGAATTA 59.926 43.478 0.00 0.00 0.00 1.40
2127 4228 4.094476 AGGTTCTGGAATTACGAAGAGGA 58.906 43.478 0.00 0.00 0.00 3.71
2202 4303 7.548097 TCAGTGAGAATAGACCTGTGTATTTC 58.452 38.462 1.77 3.22 30.42 2.17
2314 6730 3.128242 CGTAGATGTTCTGTACGGAACCT 59.872 47.826 34.09 27.91 41.90 3.50
2322 6738 0.040058 TGTACGGAACCTCTAGGCCA 59.960 55.000 5.01 0.00 39.32 5.36
2385 6801 1.346395 CCGCCCTACCATTGCTACATA 59.654 52.381 0.00 0.00 0.00 2.29
2400 6816 7.751047 TTGCTACATACAAACTTACGAGATC 57.249 36.000 0.00 0.00 0.00 2.75
2455 6879 2.784347 GCCCTCTGGAATGGTATTAGC 58.216 52.381 0.00 0.00 0.00 3.09
2478 6903 7.312899 AGCCATGTTTAGTTTTGCTAATGTAC 58.687 34.615 0.00 0.00 39.23 2.90
2480 6905 6.250527 CCATGTTTAGTTTTGCTAATGTACGC 59.749 38.462 0.00 0.00 39.23 4.42
2503 7569 4.213482 CCTTGTAAACTCTTGTGCCACTAC 59.787 45.833 0.00 0.00 0.00 2.73
2604 7678 2.418368 TGTCCAGAGTGCAAGTTGTT 57.582 45.000 4.48 0.00 0.00 2.83
2615 7689 4.464597 AGTGCAAGTTGTTCCCTTTTGTTA 59.535 37.500 4.48 0.00 0.00 2.41
2669 7934 5.705441 TGTTTTGATCAGTCATTAGTGGTCC 59.295 40.000 0.00 0.00 35.59 4.46
2768 8165 3.507622 CGATGCACCCTATGACTCTCATA 59.492 47.826 0.00 0.00 38.26 2.15
2826 8762 4.160439 CACCACATAGTTCTGAGCCTCTAA 59.840 45.833 0.00 0.00 0.00 2.10
2838 8774 6.864342 TCTGAGCCTCTAATGTAACTACAAC 58.136 40.000 0.00 0.00 39.99 3.32
2845 8783 7.764443 GCCTCTAATGTAACTACAACATCAGAA 59.236 37.037 0.00 0.00 39.99 3.02
2856 8794 7.450074 ACTACAACATCAGAATGTGGTCTTTA 58.550 34.615 1.93 0.00 45.22 1.85
3074 9582 2.143876 AGTTACCAATGACATGGCCC 57.856 50.000 0.00 0.00 44.75 5.80
3125 9681 4.659111 ATGGTTGTGTGCATCATAATGG 57.341 40.909 0.00 0.00 33.19 3.16
3147 9816 4.445019 GGTTCTCAAGTCTCAACCTCCTTT 60.445 45.833 0.00 0.00 36.19 3.11
3149 9818 5.373812 TCTCAAGTCTCAACCTCCTTTTT 57.626 39.130 0.00 0.00 0.00 1.94
3150 9819 5.126067 TCTCAAGTCTCAACCTCCTTTTTG 58.874 41.667 0.00 0.00 0.00 2.44
3443 10415 1.822114 TTCTCCACCGATGGCGAACA 61.822 55.000 0.00 0.00 43.36 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.649782 AACCATTTGTTCAGCTAATGAGG 57.350 39.130 7.58 0.00 40.91 3.86
27 30 5.595885 TCAAAACTCAAATTGAATCCGCAA 58.404 33.333 0.00 0.00 32.89 4.85
36 39 8.652810 ACTTGAATTCCTCAAAACTCAAATTG 57.347 30.769 2.27 0.00 43.54 2.32
40 43 7.014230 CCCTAACTTGAATTCCTCAAAACTCAA 59.986 37.037 2.27 0.00 43.54 3.02
43 46 6.373759 ACCCTAACTTGAATTCCTCAAAACT 58.626 36.000 2.27 0.00 43.54 2.66
44 47 6.490381 AGACCCTAACTTGAATTCCTCAAAAC 59.510 38.462 2.27 0.00 43.54 2.43
45 48 6.610830 AGACCCTAACTTGAATTCCTCAAAA 58.389 36.000 2.27 0.00 43.54 2.44
68 75 2.076100 TCTGCTGACATTGGCGTTAAG 58.924 47.619 0.00 0.00 0.00 1.85
73 80 1.284657 CTAGTCTGCTGACATTGGCG 58.715 55.000 23.61 3.71 45.20 5.69
202 228 6.488344 ACCACAAAACAAAACAAAACCAATCT 59.512 30.769 0.00 0.00 0.00 2.40
372 402 2.705658 TGGGCATTGGAGTATCTAGGTG 59.294 50.000 0.00 0.00 33.73 4.00
373 403 3.060479 TGGGCATTGGAGTATCTAGGT 57.940 47.619 0.00 0.00 33.73 3.08
375 405 4.346418 ACTCTTGGGCATTGGAGTATCTAG 59.654 45.833 0.00 0.00 37.29 2.43
377 407 3.118531 ACTCTTGGGCATTGGAGTATCT 58.881 45.455 0.00 0.00 37.29 1.98
381 411 0.036010 CGACTCTTGGGCATTGGAGT 60.036 55.000 0.00 0.00 41.05 3.85
385 415 0.804989 GAACCGACTCTTGGGCATTG 59.195 55.000 0.00 0.00 0.00 2.82
387 417 0.620556 ATGAACCGACTCTTGGGCAT 59.379 50.000 0.00 0.00 0.00 4.40
388 418 0.036388 GATGAACCGACTCTTGGGCA 60.036 55.000 0.00 0.00 0.00 5.36
389 419 0.036388 TGATGAACCGACTCTTGGGC 60.036 55.000 0.00 0.00 0.00 5.36
390 420 2.076863 GTTGATGAACCGACTCTTGGG 58.923 52.381 0.00 0.00 0.00 4.12
405 1305 2.242043 CACTCTTGGGCCTTTGTTGAT 58.758 47.619 4.53 0.00 0.00 2.57
406 1306 1.064017 ACACTCTTGGGCCTTTGTTGA 60.064 47.619 4.53 0.00 0.00 3.18
407 1307 1.402787 ACACTCTTGGGCCTTTGTTG 58.597 50.000 4.53 0.00 0.00 3.33
408 1308 2.956333 GTTACACTCTTGGGCCTTTGTT 59.044 45.455 4.53 0.00 0.00 2.83
409 1309 2.174854 AGTTACACTCTTGGGCCTTTGT 59.825 45.455 4.53 3.26 0.00 2.83
413 1313 1.348036 GTCAGTTACACTCTTGGGCCT 59.652 52.381 4.53 0.00 0.00 5.19
416 1316 4.336889 TTCTGTCAGTTACACTCTTGGG 57.663 45.455 0.00 0.00 33.45 4.12
418 1318 6.758886 ACTTCTTTCTGTCAGTTACACTCTTG 59.241 38.462 0.00 0.00 33.45 3.02
420 1320 6.472686 ACTTCTTTCTGTCAGTTACACTCT 57.527 37.500 0.00 0.00 33.45 3.24
421 1321 7.868415 ACATACTTCTTTCTGTCAGTTACACTC 59.132 37.037 0.00 0.00 33.45 3.51
425 1398 6.929606 ACCACATACTTCTTTCTGTCAGTTAC 59.070 38.462 0.00 0.00 0.00 2.50
427 1400 5.760253 CACCACATACTTCTTTCTGTCAGTT 59.240 40.000 0.00 0.00 0.00 3.16
428 1401 5.300752 CACCACATACTTCTTTCTGTCAGT 58.699 41.667 0.00 0.00 0.00 3.41
433 1406 4.641396 TCACCACCACATACTTCTTTCTG 58.359 43.478 0.00 0.00 0.00 3.02
455 1429 2.519013 GACTCTTGGGCCTTTGTTGAT 58.481 47.619 4.53 0.00 0.00 2.57
465 1440 1.446272 CGAGAACCGACTCTTGGGC 60.446 63.158 0.00 0.00 41.76 5.36
466 1441 1.215647 CCGAGAACCGACTCTTGGG 59.784 63.158 10.69 2.65 41.68 4.12
475 1450 1.080705 GTCACCTGACCGAGAACCG 60.081 63.158 0.00 0.00 39.07 4.44
483 1458 6.486993 AGATTTTTCTAACTTGTCACCTGACC 59.513 38.462 2.98 0.00 44.15 4.02
491 1466 6.961554 CACGGCATAGATTTTTCTAACTTGTC 59.038 38.462 0.00 0.00 0.00 3.18
492 1467 6.653320 TCACGGCATAGATTTTTCTAACTTGT 59.347 34.615 0.00 0.00 0.00 3.16
493 1468 7.072177 TCACGGCATAGATTTTTCTAACTTG 57.928 36.000 0.00 0.00 0.00 3.16
495 1470 6.260936 CCATCACGGCATAGATTTTTCTAACT 59.739 38.462 0.00 0.00 0.00 2.24
496 1471 6.038271 ACCATCACGGCATAGATTTTTCTAAC 59.962 38.462 0.00 0.00 39.03 2.34
497 1472 6.119536 ACCATCACGGCATAGATTTTTCTAA 58.880 36.000 0.00 0.00 39.03 2.10
499 1474 4.526970 ACCATCACGGCATAGATTTTTCT 58.473 39.130 0.00 0.00 39.03 2.52
500 1475 4.900635 ACCATCACGGCATAGATTTTTC 57.099 40.909 0.00 0.00 39.03 2.29
512 1487 4.915085 GTCATTGTTAACAAACCATCACGG 59.085 41.667 23.97 6.57 39.55 4.94
521 1496 7.122055 ACTTGTCTCTTGGTCATTGTTAACAAA 59.878 33.333 23.97 6.87 39.55 2.83
550 1526 8.510243 TTTATCGTATAGACTTGACTGGTACA 57.490 34.615 0.00 0.00 0.00 2.90
551 1527 7.590689 GCTTTATCGTATAGACTTGACTGGTAC 59.409 40.741 0.00 0.00 0.00 3.34
568 1560 5.627499 TGCATTCTTTCTTGCTTTATCGT 57.373 34.783 0.00 0.00 39.60 3.73
595 1587 1.667236 TGCGCAGGATCCTTTGTATG 58.333 50.000 13.00 1.15 0.00 2.39
607 1599 2.440796 ACCCATTCCATGCGCAGG 60.441 61.111 18.32 17.38 0.00 4.85
608 1600 2.484062 GGACCCATTCCATGCGCAG 61.484 63.158 18.32 8.11 45.10 5.18
623 1615 3.753272 TGCTCTGCTCACTAAAATTGGAC 59.247 43.478 0.00 0.00 0.00 4.02
639 1631 3.076621 TGTAGAAAATGCCAGTGCTCTG 58.923 45.455 8.84 8.84 41.01 3.35
659 1652 3.629398 ACAAAGTCAAGCTTTCTGGTCTG 59.371 43.478 0.00 0.00 44.95 3.51
660 1653 3.891049 ACAAAGTCAAGCTTTCTGGTCT 58.109 40.909 0.00 0.00 44.95 3.85
671 1682 4.853924 ATGGCTGGTTAACAAAGTCAAG 57.146 40.909 16.01 0.89 0.00 3.02
686 1697 3.295093 TCTCTCTCTCTGGTAATGGCTG 58.705 50.000 0.00 0.00 0.00 4.85
687 1698 3.204158 TCTCTCTCTCTCTGGTAATGGCT 59.796 47.826 0.00 0.00 0.00 4.75
688 1699 3.561143 TCTCTCTCTCTCTGGTAATGGC 58.439 50.000 0.00 0.00 0.00 4.40
690 1701 5.928976 TCTCTCTCTCTCTCTCTGGTAATG 58.071 45.833 0.00 0.00 0.00 1.90
691 1702 5.905331 TCTCTCTCTCTCTCTCTCTGGTAAT 59.095 44.000 0.00 0.00 0.00 1.89
692 1703 5.277250 TCTCTCTCTCTCTCTCTCTGGTAA 58.723 45.833 0.00 0.00 0.00 2.85
693 1704 4.878968 TCTCTCTCTCTCTCTCTCTGGTA 58.121 47.826 0.00 0.00 0.00 3.25
694 1705 3.708631 CTCTCTCTCTCTCTCTCTCTGGT 59.291 52.174 0.00 0.00 0.00 4.00
695 1706 3.494048 GCTCTCTCTCTCTCTCTCTCTGG 60.494 56.522 0.00 0.00 0.00 3.86
696 1707 3.133542 TGCTCTCTCTCTCTCTCTCTCTG 59.866 52.174 0.00 0.00 0.00 3.35
697 1708 3.133721 GTGCTCTCTCTCTCTCTCTCTCT 59.866 52.174 0.00 0.00 0.00 3.10
698 1709 3.118629 TGTGCTCTCTCTCTCTCTCTCTC 60.119 52.174 0.00 0.00 0.00 3.20
699 1710 2.840038 TGTGCTCTCTCTCTCTCTCTCT 59.160 50.000 0.00 0.00 0.00 3.10
700 1711 3.266510 TGTGCTCTCTCTCTCTCTCTC 57.733 52.381 0.00 0.00 0.00 3.20
702 1713 3.609853 TCTTGTGCTCTCTCTCTCTCTC 58.390 50.000 0.00 0.00 0.00 3.20
703 1714 3.719268 TCTTGTGCTCTCTCTCTCTCT 57.281 47.619 0.00 0.00 0.00 3.10
704 1715 4.009675 TCTTCTTGTGCTCTCTCTCTCTC 58.990 47.826 0.00 0.00 0.00 3.20
705 1716 4.012374 CTCTTCTTGTGCTCTCTCTCTCT 58.988 47.826 0.00 0.00 0.00 3.10
706 1717 3.758554 ACTCTTCTTGTGCTCTCTCTCTC 59.241 47.826 0.00 0.00 0.00 3.20
707 1718 3.766545 ACTCTTCTTGTGCTCTCTCTCT 58.233 45.455 0.00 0.00 0.00 3.10
708 1719 4.519540 AACTCTTCTTGTGCTCTCTCTC 57.480 45.455 0.00 0.00 0.00 3.20
710 1721 3.186205 GCAAACTCTTCTTGTGCTCTCTC 59.814 47.826 0.00 0.00 32.43 3.20
712 1723 2.874701 TGCAAACTCTTCTTGTGCTCTC 59.125 45.455 0.00 0.00 36.18 3.20
714 1725 2.874701 TCTGCAAACTCTTCTTGTGCTC 59.125 45.455 0.00 0.00 36.18 4.26
717 1728 3.873361 TCTGTCTGCAAACTCTTCTTGTG 59.127 43.478 0.00 0.00 0.00 3.33
718 1729 3.873952 GTCTGTCTGCAAACTCTTCTTGT 59.126 43.478 0.00 0.00 0.00 3.16
719 1730 3.873361 TGTCTGTCTGCAAACTCTTCTTG 59.127 43.478 0.00 0.00 0.00 3.02
721 1732 3.118629 TGTGTCTGTCTGCAAACTCTTCT 60.119 43.478 0.00 0.00 0.00 2.85
722 1733 3.198068 TGTGTCTGTCTGCAAACTCTTC 58.802 45.455 0.00 0.00 0.00 2.87
723 1734 3.266510 TGTGTCTGTCTGCAAACTCTT 57.733 42.857 0.00 0.00 0.00 2.85
725 1736 3.133691 TGATGTGTCTGTCTGCAAACTC 58.866 45.455 0.00 0.00 0.00 3.01
726 1737 3.198409 TGATGTGTCTGTCTGCAAACT 57.802 42.857 0.00 0.00 0.00 2.66
727 1738 3.313526 AGTTGATGTGTCTGTCTGCAAAC 59.686 43.478 0.00 0.00 0.00 2.93
730 1741 2.916702 AGTTGATGTGTCTGTCTGCA 57.083 45.000 0.00 0.00 0.00 4.41
731 1742 2.481952 GGAAGTTGATGTGTCTGTCTGC 59.518 50.000 0.00 0.00 0.00 4.26
733 1744 3.389329 AGTGGAAGTTGATGTGTCTGTCT 59.611 43.478 0.00 0.00 0.00 3.41
734 1745 3.733337 AGTGGAAGTTGATGTGTCTGTC 58.267 45.455 0.00 0.00 0.00 3.51
735 1746 3.495100 GGAGTGGAAGTTGATGTGTCTGT 60.495 47.826 0.00 0.00 0.00 3.41
740 1751 3.007290 TCTCAGGAGTGGAAGTTGATGTG 59.993 47.826 0.00 0.00 0.00 3.21
754 1765 6.098679 CACAGTTCTTATGACTTCTCAGGAG 58.901 44.000 0.00 0.00 0.00 3.69
755 1766 5.047021 CCACAGTTCTTATGACTTCTCAGGA 60.047 44.000 0.00 0.00 0.00 3.86
758 1769 6.611613 ATCCACAGTTCTTATGACTTCTCA 57.388 37.500 0.00 0.00 0.00 3.27
760 1771 7.482169 TGTATCCACAGTTCTTATGACTTCT 57.518 36.000 0.00 0.00 0.00 2.85
761 1772 7.819900 ACTTGTATCCACAGTTCTTATGACTTC 59.180 37.037 0.00 0.00 35.67 3.01
762 1773 7.680730 ACTTGTATCCACAGTTCTTATGACTT 58.319 34.615 0.00 0.00 35.67 3.01
763 1774 7.246171 ACTTGTATCCACAGTTCTTATGACT 57.754 36.000 0.00 0.00 35.67 3.41
764 1775 6.535508 GGACTTGTATCCACAGTTCTTATGAC 59.464 42.308 0.00 0.00 38.77 3.06
766 1777 5.817816 GGGACTTGTATCCACAGTTCTTATG 59.182 44.000 0.00 0.00 40.96 1.90
768 1779 4.224370 GGGGACTTGTATCCACAGTTCTTA 59.776 45.833 0.00 0.00 42.35 2.10
769 1780 3.009143 GGGGACTTGTATCCACAGTTCTT 59.991 47.826 0.00 0.00 42.35 2.52
770 1781 2.572104 GGGGACTTGTATCCACAGTTCT 59.428 50.000 0.00 0.00 42.35 3.01
771 1782 2.677037 CGGGGACTTGTATCCACAGTTC 60.677 54.545 0.00 0.00 43.02 3.01
773 1784 0.902531 CGGGGACTTGTATCCACAGT 59.097 55.000 0.00 0.00 43.02 3.55
774 1785 0.902531 ACGGGGACTTGTATCCACAG 59.097 55.000 0.00 0.00 43.02 3.66
775 1786 0.611200 CACGGGGACTTGTATCCACA 59.389 55.000 0.00 0.00 43.02 4.17
776 1787 0.107848 CCACGGGGACTTGTATCCAC 60.108 60.000 0.00 0.00 40.96 4.02
777 1788 0.545787 ACCACGGGGACTTGTATCCA 60.546 55.000 12.96 0.00 40.96 3.41
778 1789 1.137675 GTACCACGGGGACTTGTATCC 59.862 57.143 12.96 0.00 38.05 2.59
779 1790 1.137675 GGTACCACGGGGACTTGTATC 59.862 57.143 12.96 0.00 38.05 2.24
780 1791 1.197812 GGTACCACGGGGACTTGTAT 58.802 55.000 12.96 0.00 38.05 2.29
782 1793 1.055551 TTGGTACCACGGGGACTTGT 61.056 55.000 16.04 0.00 38.05 3.16
784 1795 1.069775 ATTTGGTACCACGGGGACTT 58.930 50.000 16.04 0.00 38.05 3.01
785 1796 0.326927 CATTTGGTACCACGGGGACT 59.673 55.000 16.04 0.00 38.05 3.85
786 1797 0.678684 CCATTTGGTACCACGGGGAC 60.679 60.000 16.04 3.14 38.05 4.46
791 1802 1.029947 GGGAGCCATTTGGTACCACG 61.030 60.000 16.04 6.12 45.58 4.94
817 1844 3.760151 TCATGCTTCCTGGTCAATCAAAG 59.240 43.478 0.00 0.00 0.00 2.77
820 1847 2.306805 AGTCATGCTTCCTGGTCAATCA 59.693 45.455 0.00 0.00 0.00 2.57
821 1848 2.996631 AGTCATGCTTCCTGGTCAATC 58.003 47.619 0.00 0.00 0.00 2.67
822 1849 3.446442 AAGTCATGCTTCCTGGTCAAT 57.554 42.857 0.00 0.00 30.06 2.57
823 1850 2.886523 CAAAGTCATGCTTCCTGGTCAA 59.113 45.455 3.38 0.00 36.17 3.18
824 1851 2.106338 TCAAAGTCATGCTTCCTGGTCA 59.894 45.455 3.38 0.00 36.17 4.02
856 1883 2.866156 TCAAAGTCACGCTTCTCAGTTG 59.134 45.455 0.00 0.00 36.17 3.16
868 1895 5.449177 GGCCATTGCTAGTTATCAAAGTCAC 60.449 44.000 0.00 0.00 37.74 3.67
875 2395 1.202758 CCCGGCCATTGCTAGTTATCA 60.203 52.381 2.24 0.00 37.74 2.15
876 2396 1.523758 CCCGGCCATTGCTAGTTATC 58.476 55.000 2.24 0.00 37.74 1.75
877 2397 0.110486 CCCCGGCCATTGCTAGTTAT 59.890 55.000 2.24 0.00 37.74 1.89
878 2398 1.529796 CCCCGGCCATTGCTAGTTA 59.470 57.895 2.24 0.00 37.74 2.24
879 2399 2.275418 CCCCGGCCATTGCTAGTT 59.725 61.111 2.24 0.00 37.74 2.24
880 2400 3.809013 CCCCCGGCCATTGCTAGT 61.809 66.667 2.24 0.00 37.74 2.57
881 2401 3.482232 CTCCCCCGGCCATTGCTAG 62.482 68.421 2.24 0.00 37.74 3.42
916 2549 7.954788 AGTTGATGTCTCTACAAACTCTTTC 57.045 36.000 0.00 0.00 39.58 2.62
947 2580 2.325583 ACGAACACTGAGCTTGGAAA 57.674 45.000 0.00 0.00 0.00 3.13
965 2598 2.419713 GGGAACTTGTATCCTCGGGAAC 60.420 54.545 0.00 0.00 37.14 3.62
1065 2719 1.834188 CCGGTGGCTTGGAGTATTTT 58.166 50.000 0.00 0.00 0.00 1.82
1098 2752 6.102027 TGAGTAGAATCCTCTCTAACCTAGCT 59.898 42.308 0.00 0.00 32.70 3.32
1102 2756 5.399727 CCCTGAGTAGAATCCTCTCTAACCT 60.400 48.000 4.51 0.00 32.70 3.50
1104 2758 4.830600 CCCCTGAGTAGAATCCTCTCTAAC 59.169 50.000 4.51 0.00 32.70 2.34
1149 2803 2.755469 GTGATGTGCCGCCCCATT 60.755 61.111 0.00 0.00 0.00 3.16
1193 2847 1.244816 CATGGCATACCTCAGCATGG 58.755 55.000 0.00 0.00 36.16 3.66
1376 3030 1.125093 TCTCAAACCTTCGAGGGCCA 61.125 55.000 14.47 0.00 40.58 5.36
1386 3040 6.070951 TCAAGAATCATGGATCTCAAACCT 57.929 37.500 0.00 0.00 0.00 3.50
1446 3100 2.279517 GGCTGACGATGTAGGCGG 60.280 66.667 0.00 0.00 0.00 6.13
1530 3184 2.722094 TGTGTGCACAGAAGGAAGTTT 58.278 42.857 22.40 0.00 36.21 2.66
1683 3352 8.806634 GCTATATCTTGAGCTCTGAAATTATCG 58.193 37.037 16.19 6.09 35.73 2.92
1712 3806 0.806868 CGCACATCTGCCTGTCAAAT 59.193 50.000 0.00 0.00 40.73 2.32
1718 3812 3.047718 CTTGCCGCACATCTGCCTG 62.048 63.158 0.00 0.00 40.73 4.85
1731 3825 5.819379 TCTCTCATTATTCACATGTCTTGCC 59.181 40.000 0.00 0.00 0.00 4.52
1742 3836 9.367444 CGATGATCATCAATCTCTCATTATTCA 57.633 33.333 30.13 0.00 37.69 2.57
1759 3856 4.550422 CCAACTATGTCGACGATGATCAT 58.450 43.478 8.25 8.25 0.00 2.45
1830 3927 8.685838 TGATTTTACTACCACTTTTAGTGCTT 57.314 30.769 1.31 0.00 44.63 3.91
1926 4023 3.887716 AGAAATACCAGAATGCCTCATGC 59.112 43.478 0.00 0.00 41.77 4.06
1992 4090 4.832266 TCCATTGCCAAATACACAAGTCTT 59.168 37.500 0.00 0.00 0.00 3.01
2052 4153 2.531522 ATACACATGCAGCGATGCTA 57.468 45.000 27.55 13.60 36.40 3.49
2093 4194 1.338020 CCAGAACCTTGCACCAGAAAC 59.662 52.381 0.00 0.00 0.00 2.78
2118 4219 8.424918 AGATGATTTTGTATGTATCCTCTTCGT 58.575 33.333 0.00 0.00 0.00 3.85
2156 4257 0.396139 AAGTTCATGCGGATGCCCAT 60.396 50.000 12.67 0.00 41.78 4.00
2314 6730 1.162329 TTCCCCCTTGTGGCCTAGA 59.838 57.895 3.32 0.00 0.00 2.43
2322 6738 3.501568 GGACCTTAAATGTTCCCCCTTGT 60.502 47.826 0.00 0.00 0.00 3.16
2385 6801 3.427773 GCTCTCGGATCTCGTAAGTTTGT 60.428 47.826 0.00 0.00 40.32 2.83
2422 6838 3.732938 AGGGCGCTTCCTCTTCAT 58.267 55.556 7.64 0.00 29.56 2.57
2455 6879 6.250527 GCGTACATTAGCAAAACTAAACATGG 59.749 38.462 0.00 0.00 43.99 3.66
2478 6903 1.069227 GGCACAAGAGTTTACAAGGCG 60.069 52.381 0.00 0.00 0.00 5.52
2480 6905 3.214328 AGTGGCACAAGAGTTTACAAGG 58.786 45.455 21.41 0.00 44.16 3.61
2604 7678 9.662947 GTATAGCTAGTTTTCTAACAAAAGGGA 57.337 33.333 0.00 0.00 36.70 4.20
2740 8042 1.068588 TCATAGGGTGCATCGTAGTGC 59.931 52.381 5.52 3.81 45.25 4.40
2794 8690 7.928706 GCTCAGAACTATGTGGTGAACTATTAT 59.071 37.037 0.00 0.00 0.00 1.28
2816 8752 6.599356 TGTTGTAGTTACATTAGAGGCTCA 57.401 37.500 18.26 0.00 35.89 4.26
2826 8762 7.168219 ACCACATTCTGATGTTGTAGTTACAT 58.832 34.615 0.00 0.00 43.92 2.29
2838 8774 7.466455 CGGAAGAATAAAGACCACATTCTGATG 60.466 40.741 0.00 0.00 38.65 3.07
2845 8783 4.222124 AGCGGAAGAATAAAGACCACAT 57.778 40.909 0.00 0.00 0.00 3.21
3108 9664 5.008980 TGAGAACCATTATGATGCACACAA 58.991 37.500 0.00 0.00 31.67 3.33
3125 9681 4.344359 AAGGAGGTTGAGACTTGAGAAC 57.656 45.455 0.00 0.00 0.00 3.01
3195 9912 2.612095 TTTACCCCCGCGGCCTTATG 62.612 60.000 22.85 4.41 33.26 1.90


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

AutoCloner maintained by Alex Coulton.