Multiple sequence alignment - TraesCS6D01G172500

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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 TraesCS6D01G172500 chr6D 100.000 4810 0 0 1 4810 159351705 159346896 0.000000e+00 8883.0
1 TraesCS6D01G172500 chr6D 100.000 3814 0 0 5391 9204 159346315 159342502 0.000000e+00 7044.0
2 TraesCS6D01G172500 chr6D 96.066 1576 61 1 3236 4810 305355460 305357035 0.000000e+00 2566.0
3 TraesCS6D01G172500 chr6D 96.005 1577 59 3 3238 4810 411945578 411944002 0.000000e+00 2560.0
4 TraesCS6D01G172500 chr6D 95.256 1581 67 3 3237 4810 132053110 132051531 0.000000e+00 2497.0
5 TraesCS6D01G172500 chr6D 97.389 651 13 2 1 651 83000341 83000987 0.000000e+00 1105.0
6 TraesCS6D01G172500 chr6D 92.642 530 21 13 5558 6083 411943374 411942859 0.000000e+00 747.0
7 TraesCS6D01G172500 chr6D 92.717 508 23 11 5579 6083 132050788 132050292 0.000000e+00 721.0
8 TraesCS6D01G172500 chr6B 94.530 2212 71 26 7018 9202 289689455 289687267 0.000000e+00 3369.0
9 TraesCS6D01G172500 chr6B 94.358 2127 74 7 797 2879 289697192 289695068 0.000000e+00 3221.0
10 TraesCS6D01G172500 chr6B 96.970 495 13 2 6532 7025 289690134 289689641 0.000000e+00 830.0
11 TraesCS6D01G172500 chr6B 94.260 453 14 7 6084 6536 289694633 289694193 0.000000e+00 682.0
12 TraesCS6D01G172500 chr6B 97.514 362 4 2 2878 3237 289694987 289694629 1.700000e-171 614.0
13 TraesCS6D01G172500 chr6A 97.335 1726 35 6 7486 9202 217638857 217637134 0.000000e+00 2922.0
14 TraesCS6D01G172500 chr6A 97.503 1442 31 3 1800 3237 217641873 217640433 0.000000e+00 2459.0
15 TraesCS6D01G172500 chr6A 97.793 1133 25 0 6084 7216 217640437 217639305 0.000000e+00 1954.0
16 TraesCS6D01G172500 chr6A 93.267 802 18 8 972 1745 217642657 217641864 0.000000e+00 1149.0
17 TraesCS6D01G172500 chr6A 89.899 693 45 8 5393 6084 574740564 574741232 0.000000e+00 869.0
18 TraesCS6D01G172500 chr6A 98.049 205 4 0 7245 7449 217639062 217638858 3.160000e-94 357.0
19 TraesCS6D01G172500 chr6A 93.846 130 8 0 796 925 217645567 217645438 7.290000e-46 196.0
20 TraesCS6D01G172500 chr1D 96.125 1574 59 2 3238 4810 322387573 322389145 0.000000e+00 2567.0
21 TraesCS6D01G172500 chr1D 84.797 2289 231 65 1006 3241 41510951 41508727 0.000000e+00 2191.0
22 TraesCS6D01G172500 chr1D 82.770 1776 194 56 6563 8281 41508093 41506373 0.000000e+00 1482.0
23 TraesCS6D01G172500 chr1D 98.310 651 10 1 1 651 421848859 421848210 0.000000e+00 1140.0
24 TraesCS6D01G172500 chr1D 98.006 652 12 1 1 651 314332969 314333620 0.000000e+00 1131.0
25 TraesCS6D01G172500 chr1D 91.279 688 33 7 5397 6083 319645786 319645125 0.000000e+00 913.0
26 TraesCS6D01G172500 chr1D 92.182 550 29 12 5538 6083 322389843 322390382 0.000000e+00 765.0
27 TraesCS6D01G172500 chr1D 94.779 249 12 1 5391 5638 322389734 322389982 4.030000e-103 387.0
28 TraesCS6D01G172500 chr1D 83.375 397 49 10 6084 6474 41508734 41508349 1.470000e-92 351.0
29 TraesCS6D01G172500 chr1D 91.000 100 8 1 652 751 49428845 49428747 5.800000e-27 134.0
30 TraesCS6D01G172500 chr5D 95.807 1574 65 1 3238 4810 70158198 70159771 0.000000e+00 2540.0
31 TraesCS6D01G172500 chr5D 97.389 651 17 0 1 651 27015015 27014365 0.000000e+00 1109.0
32 TraesCS6D01G172500 chr5D 93.939 528 18 9 5558 6083 70160362 70160877 0.000000e+00 785.0
33 TraesCS6D01G172500 chr5D 94.937 237 11 1 5394 5630 67957984 67958219 4.060000e-98 370.0
34 TraesCS6D01G172500 chr3D 95.365 1575 70 3 3238 4810 1214602 1213029 0.000000e+00 2501.0
35 TraesCS6D01G172500 chr3D 95.041 1573 77 1 3238 4809 96684203 96682631 0.000000e+00 2471.0
36 TraesCS6D01G172500 chr3D 98.003 651 13 0 1 651 365793813 365793163 0.000000e+00 1131.0
37 TraesCS6D01G172500 chr3D 85.983 692 65 14 5395 6083 678907 679569 0.000000e+00 712.0
38 TraesCS6D01G172500 chr3D 94.850 233 12 0 5393 5625 489458962 489458730 1.890000e-96 364.0
39 TraesCS6D01G172500 chr7B 95.076 1584 66 6 3237 4810 366046523 366044942 0.000000e+00 2483.0
40 TraesCS6D01G172500 chr7B 83.696 92 13 2 661 751 544104522 544104432 1.650000e-12 86.1
41 TraesCS6D01G172500 chr7D 95.051 1576 74 4 3236 4810 206689520 206687948 0.000000e+00 2475.0
42 TraesCS6D01G172500 chr7D 97.849 651 14 0 1 651 546237639 546238289 0.000000e+00 1125.0
43 TraesCS6D01G172500 chr7D 97.699 652 15 0 1 652 15589100 15588449 0.000000e+00 1122.0
44 TraesCS6D01G172500 chr1B 84.358 2327 232 73 1006 3241 61528659 61526374 0.000000e+00 2159.0
45 TraesCS6D01G172500 chr1B 82.748 1878 208 54 6469 8281 61525922 61524096 0.000000e+00 1567.0
46 TraesCS6D01G172500 chr1B 95.745 235 9 1 5396 5630 303227998 303227765 2.430000e-100 377.0
47 TraesCS6D01G172500 chr1B 87.126 334 38 5 6084 6415 61526381 61526051 3.140000e-99 374.0
48 TraesCS6D01G172500 chr4D 88.268 1270 133 7 3238 4493 403409879 403411146 0.000000e+00 1506.0
49 TraesCS6D01G172500 chr4D 97.699 652 14 1 1 651 365050180 365050831 0.000000e+00 1120.0
50 TraesCS6D01G172500 chr4D 95.472 508 19 2 5577 6083 55291444 55290940 0.000000e+00 808.0
51 TraesCS6D01G172500 chr4D 95.868 363 15 0 3237 3599 55291302 55290940 1.030000e-163 588.0
52 TraesCS6D01G172500 chr1A 89.430 1192 93 22 2078 3241 41361081 41359895 0.000000e+00 1472.0
53 TraesCS6D01G172500 chr1A 83.992 1012 129 21 7287 8280 41358317 41357321 0.000000e+00 941.0
54 TraesCS6D01G172500 chr1A 84.806 928 98 18 6353 7252 41359697 41358785 0.000000e+00 893.0
55 TraesCS6D01G172500 chr1A 79.825 1140 146 46 1006 2094 41362203 41361097 0.000000e+00 754.0
56 TraesCS6D01G172500 chr1A 89.268 205 19 3 6084 6288 41359902 41359701 4.270000e-63 254.0
57 TraesCS6D01G172500 chr2D 98.310 651 11 0 1 651 598860984 598861634 0.000000e+00 1142.0
58 TraesCS6D01G172500 chr2D 94.661 487 22 2 5598 6083 582523703 582524186 0.000000e+00 752.0
59 TraesCS6D01G172500 chr2D 86.869 693 64 8 5394 6083 587240372 587241040 0.000000e+00 750.0
60 TraesCS6D01G172500 chr2D 87.755 98 11 1 654 751 454493445 454493541 7.550000e-21 113.0
61 TraesCS6D01G172500 chr2B 91.775 693 29 7 5393 6081 757216749 757216081 0.000000e+00 939.0
62 TraesCS6D01G172500 chr2B 94.444 36 2 0 886 921 581434782 581434747 1.000000e-03 56.5
63 TraesCS6D01G172500 chr3B 96.154 104 4 0 5393 5496 245513496 245513599 4.420000e-38 171.0
64 TraesCS6D01G172500 chr3B 84.946 93 10 4 661 751 791649110 791649200 3.540000e-14 91.6


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 TraesCS6D01G172500 chr6D 159342502 159351705 9203 True 7963.500000 8883 100.000000 1 9204 2 chr6D.!!$R2 9203
1 TraesCS6D01G172500 chr6D 305355460 305357035 1575 False 2566.000000 2566 96.066000 3236 4810 1 chr6D.!!$F2 1574
2 TraesCS6D01G172500 chr6D 411942859 411945578 2719 True 1653.500000 2560 94.323500 3238 6083 2 chr6D.!!$R3 2845
3 TraesCS6D01G172500 chr6D 132050292 132053110 2818 True 1609.000000 2497 93.986500 3237 6083 2 chr6D.!!$R1 2846
4 TraesCS6D01G172500 chr6D 83000341 83000987 646 False 1105.000000 1105 97.389000 1 651 1 chr6D.!!$F1 650
5 TraesCS6D01G172500 chr6B 289687267 289690134 2867 True 2099.500000 3369 95.750000 6532 9202 2 chr6B.!!$R1 2670
6 TraesCS6D01G172500 chr6B 289694193 289697192 2999 True 1505.666667 3221 95.377333 797 6536 3 chr6B.!!$R2 5739
7 TraesCS6D01G172500 chr6A 217637134 217645567 8433 True 1506.166667 2922 96.298833 796 9202 6 chr6A.!!$R1 8406
8 TraesCS6D01G172500 chr6A 574740564 574741232 668 False 869.000000 869 89.899000 5393 6084 1 chr6A.!!$F1 691
9 TraesCS6D01G172500 chr1D 41506373 41510951 4578 True 1341.333333 2191 83.647333 1006 8281 3 chr1D.!!$R4 7275
10 TraesCS6D01G172500 chr1D 322387573 322390382 2809 False 1239.666667 2567 94.362000 3238 6083 3 chr1D.!!$F2 2845
11 TraesCS6D01G172500 chr1D 421848210 421848859 649 True 1140.000000 1140 98.310000 1 651 1 chr1D.!!$R3 650
12 TraesCS6D01G172500 chr1D 314332969 314333620 651 False 1131.000000 1131 98.006000 1 651 1 chr1D.!!$F1 650
13 TraesCS6D01G172500 chr1D 319645125 319645786 661 True 913.000000 913 91.279000 5397 6083 1 chr1D.!!$R2 686
14 TraesCS6D01G172500 chr5D 70158198 70160877 2679 False 1662.500000 2540 94.873000 3238 6083 2 chr5D.!!$F2 2845
15 TraesCS6D01G172500 chr5D 27014365 27015015 650 True 1109.000000 1109 97.389000 1 651 1 chr5D.!!$R1 650
16 TraesCS6D01G172500 chr3D 1213029 1214602 1573 True 2501.000000 2501 95.365000 3238 4810 1 chr3D.!!$R1 1572
17 TraesCS6D01G172500 chr3D 96682631 96684203 1572 True 2471.000000 2471 95.041000 3238 4809 1 chr3D.!!$R2 1571
18 TraesCS6D01G172500 chr3D 365793163 365793813 650 True 1131.000000 1131 98.003000 1 651 1 chr3D.!!$R3 650
19 TraesCS6D01G172500 chr3D 678907 679569 662 False 712.000000 712 85.983000 5395 6083 1 chr3D.!!$F1 688
20 TraesCS6D01G172500 chr7B 366044942 366046523 1581 True 2483.000000 2483 95.076000 3237 4810 1 chr7B.!!$R1 1573
21 TraesCS6D01G172500 chr7D 206687948 206689520 1572 True 2475.000000 2475 95.051000 3236 4810 1 chr7D.!!$R2 1574
22 TraesCS6D01G172500 chr7D 546237639 546238289 650 False 1125.000000 1125 97.849000 1 651 1 chr7D.!!$F1 650
23 TraesCS6D01G172500 chr7D 15588449 15589100 651 True 1122.000000 1122 97.699000 1 652 1 chr7D.!!$R1 651
24 TraesCS6D01G172500 chr1B 61524096 61528659 4563 True 1366.666667 2159 84.744000 1006 8281 3 chr1B.!!$R2 7275
25 TraesCS6D01G172500 chr4D 403409879 403411146 1267 False 1506.000000 1506 88.268000 3238 4493 1 chr4D.!!$F2 1255
26 TraesCS6D01G172500 chr4D 365050180 365050831 651 False 1120.000000 1120 97.699000 1 651 1 chr4D.!!$F1 650
27 TraesCS6D01G172500 chr4D 55290940 55291444 504 True 698.000000 808 95.670000 3237 6083 2 chr4D.!!$R1 2846
28 TraesCS6D01G172500 chr1A 41357321 41362203 4882 True 862.800000 1472 85.464200 1006 8280 5 chr1A.!!$R1 7274
29 TraesCS6D01G172500 chr2D 598860984 598861634 650 False 1142.000000 1142 98.310000 1 651 1 chr2D.!!$F4 650
30 TraesCS6D01G172500 chr2D 587240372 587241040 668 False 750.000000 750 86.869000 5394 6083 1 chr2D.!!$F3 689
31 TraesCS6D01G172500 chr2B 757216081 757216749 668 True 939.000000 939 91.775000 5393 6081 1 chr2B.!!$R2 688

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
377 379 0.033090 GTCCGGGTTCTTCACGTTCT 59.967 55.000 0.00 0.0 41.99 3.01 F
1096 3848 0.179089 CAAGATGCTACCGCTGCTCT 60.179 55.000 0.00 0.0 36.97 4.09 F
1269 4031 0.457853 TGCCTACTTGTCGCATCGTC 60.458 55.000 0.00 0.0 0.00 4.20 F
1650 4450 2.401568 TGCCCATGAAGCTCTCTATCA 58.598 47.619 8.82 0.0 0.00 2.15 F
3307 8735 1.522569 GGAGGGTTGACGGAGATGG 59.477 63.158 0.00 0.0 0.00 3.51 F
3767 9197 0.615331 CTGCAGCCTCCAGGTAGAAA 59.385 55.000 0.00 0.0 37.57 2.52 F
4662 10098 0.179100 CGATGATTCGGTCAGCCAGT 60.179 55.000 2.27 0.0 40.11 4.00 F
4707 10143 0.737219 GAAGCGCATTTGCTGGATCT 59.263 50.000 11.47 0.0 46.60 2.75 F
5835 13712 1.082756 GTGGCGCGTTGAAGAACAG 60.083 57.895 8.43 0.0 31.78 3.16 F
6599 14654 1.744639 ATCAGCCGATGATCTGCGT 59.255 52.632 3.20 0.0 46.01 5.24 F
6763 14819 3.213506 CTCTCACCATCTCGACTCAGAT 58.786 50.000 0.00 0.0 33.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 4336 1.589716 GAACAGGCTGGCTCGCAATT 61.590 55.000 20.34 0.43 0.00 2.32 R
2009 4819 3.592059 TCCGTATCAAAGGGAAAACTCG 58.408 45.455 0.00 0.00 39.21 4.18 R
3246 6222 3.401683 CCCTAGACCAGGTAGGATCCTAA 59.598 52.174 23.33 4.25 43.80 2.69 R
3342 8770 1.589716 GCTGCCGCCTGTTCTTCATT 61.590 55.000 0.00 0.00 0.00 2.57 R
4382 9818 0.249489 AGTGCGAGCAGTTCTTTCGT 60.249 50.000 0.00 0.00 36.74 3.85 R
4696 10132 0.613260 AGGCGTACAGATCCAGCAAA 59.387 50.000 0.00 0.00 0.00 3.68 R
6361 14244 0.320697 AACCCGGAGCTAACTGTGTC 59.679 55.000 0.73 0.00 0.00 3.67 R
6599 14654 1.623811 GGGTGAAGTCCACTCTAGCAA 59.376 52.381 0.00 0.00 43.00 3.91 R
7033 15287 3.012518 GACATTGCAGTAAGACCAGCAT 58.987 45.455 0.00 0.00 36.80 3.79 R
7903 16846 4.262121 CCTGGATGTTGCAATTCACAAAGA 60.262 41.667 0.59 0.00 0.00 2.52 R
8644 17607 5.690857 GCCTTAAGTAACCTCTAATAGCACG 59.309 44.000 0.97 0.00 0.00 5.34 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
377 379 0.033090 GTCCGGGTTCTTCACGTTCT 59.967 55.000 0.00 0.00 41.99 3.01
446 448 3.193479 CCTCTCTTTTTGGATTTTCGGGG 59.807 47.826 0.00 0.00 0.00 5.73
591 594 3.940852 TGTACGATACGAACTCTGCCTTA 59.059 43.478 0.00 0.00 0.00 2.69
652 655 5.646360 CGTGTGGTTTCCCTAATCTTACAAT 59.354 40.000 0.00 0.00 0.00 2.71
653 656 6.183360 CGTGTGGTTTCCCTAATCTTACAATC 60.183 42.308 0.00 0.00 0.00 2.67
654 657 6.884836 GTGTGGTTTCCCTAATCTTACAATCT 59.115 38.462 0.00 0.00 0.00 2.40
655 658 7.065923 GTGTGGTTTCCCTAATCTTACAATCTC 59.934 40.741 0.00 0.00 0.00 2.75
656 659 6.258068 GTGGTTTCCCTAATCTTACAATCTCG 59.742 42.308 0.00 0.00 0.00 4.04
657 660 6.155565 TGGTTTCCCTAATCTTACAATCTCGA 59.844 38.462 0.00 0.00 0.00 4.04
658 661 6.479331 GGTTTCCCTAATCTTACAATCTCGAC 59.521 42.308 0.00 0.00 0.00 4.20
659 662 6.785337 TTCCCTAATCTTACAATCTCGACA 57.215 37.500 0.00 0.00 0.00 4.35
660 663 6.145338 TCCCTAATCTTACAATCTCGACAC 57.855 41.667 0.00 0.00 0.00 3.67
661 664 4.976731 CCCTAATCTTACAATCTCGACACG 59.023 45.833 0.00 0.00 0.00 4.49
662 665 5.450137 CCCTAATCTTACAATCTCGACACGT 60.450 44.000 0.00 0.00 0.00 4.49
663 666 6.238566 CCCTAATCTTACAATCTCGACACGTA 60.239 42.308 0.00 0.00 0.00 3.57
664 667 7.361127 CCTAATCTTACAATCTCGACACGTAT 58.639 38.462 0.00 0.00 0.00 3.06
665 668 8.501580 CCTAATCTTACAATCTCGACACGTATA 58.498 37.037 0.00 0.00 0.00 1.47
669 672 8.599055 TCTTACAATCTCGACACGTATATAGT 57.401 34.615 0.00 0.00 0.00 2.12
670 673 8.493547 TCTTACAATCTCGACACGTATATAGTG 58.506 37.037 9.03 9.03 44.57 2.74
671 674 6.856135 ACAATCTCGACACGTATATAGTGA 57.144 37.500 15.37 0.00 41.83 3.41
672 675 6.656945 ACAATCTCGACACGTATATAGTGAC 58.343 40.000 15.37 9.79 41.83 3.67
673 676 6.482641 ACAATCTCGACACGTATATAGTGACT 59.517 38.462 15.37 0.00 41.83 3.41
674 677 5.902051 TCTCGACACGTATATAGTGACTG 57.098 43.478 15.37 8.02 41.83 3.51
675 678 5.354767 TCTCGACACGTATATAGTGACTGT 58.645 41.667 15.37 0.00 41.83 3.55
676 679 6.507023 TCTCGACACGTATATAGTGACTGTA 58.493 40.000 15.37 0.00 41.83 2.74
677 680 7.150640 TCTCGACACGTATATAGTGACTGTAT 58.849 38.462 15.37 7.05 41.83 2.29
678 681 7.654923 TCTCGACACGTATATAGTGACTGTATT 59.345 37.037 7.17 0.00 41.83 1.89
679 682 7.570161 TCGACACGTATATAGTGACTGTATTG 58.430 38.462 7.17 3.11 41.83 1.90
680 683 7.439056 TCGACACGTATATAGTGACTGTATTGA 59.561 37.037 7.17 0.00 41.83 2.57
681 684 8.228464 CGACACGTATATAGTGACTGTATTGAT 58.772 37.037 7.17 0.00 41.83 2.57
682 685 9.894783 GACACGTATATAGTGACTGTATTGATT 57.105 33.333 7.17 0.00 41.83 2.57
683 686 9.678941 ACACGTATATAGTGACTGTATTGATTG 57.321 33.333 7.17 3.62 41.83 2.67
684 687 9.678941 CACGTATATAGTGACTGTATTGATTGT 57.321 33.333 7.17 0.00 41.83 2.71
693 696 9.376075 AGTGACTGTATTGATTGTATTCTTGAG 57.624 33.333 0.00 0.00 0.00 3.02
694 697 9.155975 GTGACTGTATTGATTGTATTCTTGAGT 57.844 33.333 0.00 0.00 0.00 3.41
703 706 8.492673 TGATTGTATTCTTGAGTACAATGACC 57.507 34.615 25.46 16.37 46.14 4.02
704 707 8.100164 TGATTGTATTCTTGAGTACAATGACCA 58.900 33.333 25.46 17.97 46.14 4.02
705 708 8.862325 ATTGTATTCTTGAGTACAATGACCAA 57.138 30.769 22.08 3.56 45.09 3.67
706 709 8.684386 TTGTATTCTTGAGTACAATGACCAAA 57.316 30.769 12.55 0.00 36.26 3.28
707 710 8.322906 TGTATTCTTGAGTACAATGACCAAAG 57.677 34.615 3.96 0.00 35.37 2.77
708 711 7.936847 TGTATTCTTGAGTACAATGACCAAAGT 59.063 33.333 3.96 0.00 35.37 2.66
709 712 6.618287 TTCTTGAGTACAATGACCAAAGTG 57.382 37.500 0.00 0.00 35.37 3.16
710 713 5.924356 TCTTGAGTACAATGACCAAAGTGA 58.076 37.500 0.00 0.00 35.37 3.41
711 714 5.991606 TCTTGAGTACAATGACCAAAGTGAG 59.008 40.000 0.00 0.00 35.37 3.51
712 715 4.065088 TGAGTACAATGACCAAAGTGAGC 58.935 43.478 0.00 0.00 0.00 4.26
713 716 4.202357 TGAGTACAATGACCAAAGTGAGCT 60.202 41.667 0.00 0.00 0.00 4.09
714 717 4.718961 AGTACAATGACCAAAGTGAGCTT 58.281 39.130 0.00 0.00 36.30 3.74
715 718 5.865085 AGTACAATGACCAAAGTGAGCTTA 58.135 37.500 0.00 0.00 33.95 3.09
716 719 6.476378 AGTACAATGACCAAAGTGAGCTTAT 58.524 36.000 0.00 0.00 33.95 1.73
717 720 7.620880 AGTACAATGACCAAAGTGAGCTTATA 58.379 34.615 0.00 0.00 33.95 0.98
718 721 6.743575 ACAATGACCAAAGTGAGCTTATAC 57.256 37.500 0.00 0.00 33.95 1.47
719 722 5.351465 ACAATGACCAAAGTGAGCTTATACG 59.649 40.000 0.00 0.00 33.95 3.06
720 723 4.794278 TGACCAAAGTGAGCTTATACGA 57.206 40.909 0.00 0.00 33.95 3.43
721 724 5.339008 TGACCAAAGTGAGCTTATACGAT 57.661 39.130 0.00 0.00 33.95 3.73
722 725 6.459670 TGACCAAAGTGAGCTTATACGATA 57.540 37.500 0.00 0.00 33.95 2.92
723 726 6.869695 TGACCAAAGTGAGCTTATACGATAA 58.130 36.000 0.00 0.00 33.95 1.75
724 727 6.978659 TGACCAAAGTGAGCTTATACGATAAG 59.021 38.462 0.00 0.00 33.95 1.73
725 728 6.875076 ACCAAAGTGAGCTTATACGATAAGT 58.125 36.000 12.90 4.30 33.95 2.24
726 729 7.328737 ACCAAAGTGAGCTTATACGATAAGTT 58.671 34.615 12.90 8.95 33.95 2.66
727 730 7.822822 ACCAAAGTGAGCTTATACGATAAGTTT 59.177 33.333 12.90 5.88 33.95 2.66
728 731 9.309516 CCAAAGTGAGCTTATACGATAAGTTTA 57.690 33.333 12.90 4.99 33.95 2.01
734 737 9.472361 TGAGCTTATACGATAAGTTTAATGACC 57.528 33.333 12.90 0.44 0.00 4.02
735 738 9.472361 GAGCTTATACGATAAGTTTAATGACCA 57.528 33.333 12.90 0.00 0.00 4.02
736 739 9.257651 AGCTTATACGATAAGTTTAATGACCAC 57.742 33.333 12.90 0.00 0.00 4.16
737 740 8.212495 GCTTATACGATAAGTTTAATGACCACG 58.788 37.037 12.90 0.00 0.00 4.94
738 741 9.454585 CTTATACGATAAGTTTAATGACCACGA 57.545 33.333 0.00 0.00 0.00 4.35
739 742 7.925703 ATACGATAAGTTTAATGACCACGAG 57.074 36.000 0.00 0.00 0.00 4.18
740 743 5.717119 ACGATAAGTTTAATGACCACGAGT 58.283 37.500 0.00 0.00 0.00 4.18
741 744 5.575606 ACGATAAGTTTAATGACCACGAGTG 59.424 40.000 0.00 0.00 0.00 3.51
742 745 5.500290 CGATAAGTTTAATGACCACGAGTGC 60.500 44.000 0.00 0.00 0.00 4.40
743 746 3.120321 AGTTTAATGACCACGAGTGCA 57.880 42.857 0.00 0.00 0.00 4.57
744 747 3.674997 AGTTTAATGACCACGAGTGCAT 58.325 40.909 0.00 0.00 0.00 3.96
745 748 4.072131 AGTTTAATGACCACGAGTGCATT 58.928 39.130 11.68 11.68 33.57 3.56
746 749 4.518970 AGTTTAATGACCACGAGTGCATTT 59.481 37.500 12.04 0.00 32.26 2.32
747 750 5.009610 AGTTTAATGACCACGAGTGCATTTT 59.990 36.000 12.04 1.60 32.26 1.82
748 751 6.205853 AGTTTAATGACCACGAGTGCATTTTA 59.794 34.615 12.04 2.71 32.26 1.52
749 752 4.419522 AATGACCACGAGTGCATTTTAC 57.580 40.909 0.00 0.00 0.00 2.01
750 753 3.120321 TGACCACGAGTGCATTTTACT 57.880 42.857 0.00 0.00 0.00 2.24
751 754 2.805671 TGACCACGAGTGCATTTTACTG 59.194 45.455 0.00 0.00 0.00 2.74
752 755 1.535462 ACCACGAGTGCATTTTACTGC 59.465 47.619 0.00 0.00 42.62 4.40
762 765 3.989167 TGCATTTTACTGCATTGAAGTGC 59.011 39.130 17.74 17.74 46.76 4.40
763 766 3.368843 GCATTTTACTGCATTGAAGTGCC 59.631 43.478 14.96 1.95 44.43 5.01
764 767 2.987413 TTTACTGCATTGAAGTGCCG 57.013 45.000 7.61 0.00 44.43 5.69
765 768 0.521291 TTACTGCATTGAAGTGCCGC 59.479 50.000 7.61 0.00 44.43 6.53
766 769 1.305219 TACTGCATTGAAGTGCCGCC 61.305 55.000 7.61 0.00 44.43 6.13
767 770 3.346631 CTGCATTGAAGTGCCGCCC 62.347 63.158 0.00 0.00 44.43 6.13
768 771 4.481112 GCATTGAAGTGCCGCCCG 62.481 66.667 0.00 0.00 39.18 6.13
769 772 4.481112 CATTGAAGTGCCGCCCGC 62.481 66.667 0.00 0.00 38.31 6.13
782 785 4.708386 CCCGCCAGGCACCGTAAA 62.708 66.667 13.30 0.00 35.76 2.01
783 786 2.437716 CCGCCAGGCACCGTAAAT 60.438 61.111 13.30 0.00 0.00 1.40
784 787 2.760159 CCGCCAGGCACCGTAAATG 61.760 63.158 13.30 0.00 0.00 2.32
785 788 2.489751 GCCAGGCACCGTAAATGC 59.510 61.111 6.55 0.00 42.62 3.56
786 789 2.046285 GCCAGGCACCGTAAATGCT 61.046 57.895 6.55 0.00 42.93 3.79
787 790 1.802636 CCAGGCACCGTAAATGCTG 59.197 57.895 0.00 0.00 42.93 4.41
788 791 1.137404 CAGGCACCGTAAATGCTGC 59.863 57.895 0.00 0.00 42.93 5.25
789 792 2.100216 GGCACCGTAAATGCTGCG 59.900 61.111 0.00 0.00 42.93 5.18
790 793 2.576847 GCACCGTAAATGCTGCGC 60.577 61.111 0.00 0.00 40.08 6.09
791 794 2.276617 CACCGTAAATGCTGCGCG 60.277 61.111 0.00 0.00 0.00 6.86
792 795 3.496131 ACCGTAAATGCTGCGCGG 61.496 61.111 13.18 13.18 46.83 6.46
793 796 4.886925 CCGTAAATGCTGCGCGGC 62.887 66.667 34.00 34.00 35.90 6.53
794 797 4.159295 CGTAAATGCTGCGCGGCA 62.159 61.111 42.86 42.86 46.63 5.69
828 831 1.029408 TGTGTGGTGTGTTGGCTGAC 61.029 55.000 0.00 0.00 0.00 3.51
917 920 1.134098 AGGATGATTTGTAGCACCCGG 60.134 52.381 0.00 0.00 0.00 5.73
974 1516 1.153939 CCGTGAGACGAGCCTCTTG 60.154 63.158 0.00 0.00 46.05 3.02
1096 3848 0.179089 CAAGATGCTACCGCTGCTCT 60.179 55.000 0.00 0.00 36.97 4.09
1119 3871 1.684049 CCTCACCTTCTCCTCCGCT 60.684 63.158 0.00 0.00 0.00 5.52
1267 4029 1.756375 GCTGCCTACTTGTCGCATCG 61.756 60.000 0.00 0.00 0.00 3.84
1268 4030 0.458543 CTGCCTACTTGTCGCATCGT 60.459 55.000 0.00 0.00 0.00 3.73
1269 4031 0.457853 TGCCTACTTGTCGCATCGTC 60.458 55.000 0.00 0.00 0.00 4.20
1394 4163 4.032445 TGAAAAGTACGCACGATTGATAGC 59.968 41.667 0.00 0.00 0.00 2.97
1650 4450 2.401568 TGCCCATGAAGCTCTCTATCA 58.598 47.619 8.82 0.00 0.00 2.15
1742 4544 3.117738 AGGGGTGACTCCATCATTGATTC 60.118 47.826 3.40 0.00 40.28 2.52
1914 4722 4.545610 ACATTTTGGTATGAACACTTGCG 58.454 39.130 0.00 0.00 0.00 4.85
2460 5317 6.431234 ACAATGTTGAGGTGAATCTCTTTACC 59.569 38.462 0.00 0.00 40.47 2.85
2570 5428 5.428496 TCATTGATACTAACGAGGTACCG 57.572 43.478 6.18 0.00 0.00 4.02
2629 5487 5.789574 ACCCATTGTAAATGACCCTCTAA 57.210 39.130 1.54 0.00 0.00 2.10
2921 5891 7.534239 CGCTGATTACTCTTTTGGTTTTCTAAC 59.466 37.037 0.00 0.00 0.00 2.34
3216 6189 2.430694 GTGCCTCTTTGTTTCTGGGTTT 59.569 45.455 0.00 0.00 0.00 3.27
3232 6208 3.054287 TGGGTTTGTGTACTGACCTTTCA 60.054 43.478 0.00 0.00 32.73 2.69
3233 6209 3.314357 GGGTTTGTGTACTGACCTTTCAC 59.686 47.826 0.00 0.00 32.73 3.18
3234 6210 3.314357 GGTTTGTGTACTGACCTTTCACC 59.686 47.826 0.00 0.00 0.00 4.02
3280 6256 1.680207 GGTCTAGGGCGTAGGTTGTAG 59.320 57.143 13.77 0.00 0.00 2.74
3307 8735 1.522569 GGAGGGTTGACGGAGATGG 59.477 63.158 0.00 0.00 0.00 3.51
3351 8779 1.154225 CCGTGGCGCAATGAAGAAC 60.154 57.895 10.83 0.00 0.00 3.01
3359 8787 1.865788 GCAATGAAGAACAGGCGGCA 61.866 55.000 13.08 0.00 0.00 5.69
3608 9038 1.553248 CGGTCATAACACTTCTCCCCA 59.447 52.381 0.00 0.00 0.00 4.96
3678 9108 1.486726 GAACTCCCCGAGGTGATCAAT 59.513 52.381 0.00 0.00 33.35 2.57
3689 9119 4.633126 CGAGGTGATCAATCAGTGTCAAAT 59.367 41.667 0.00 0.00 37.51 2.32
3708 9138 4.069232 CCTTCGCGACAGCTGGGA 62.069 66.667 19.93 6.80 42.32 4.37
3767 9197 0.615331 CTGCAGCCTCCAGGTAGAAA 59.385 55.000 0.00 0.00 37.57 2.52
4662 10098 0.179100 CGATGATTCGGTCAGCCAGT 60.179 55.000 2.27 0.00 40.11 4.00
4707 10143 0.737219 GAAGCGCATTTGCTGGATCT 59.263 50.000 11.47 0.00 46.60 2.75
4790 10232 2.284112 GGTACAGACCCGGGTGGA 60.284 66.667 36.01 12.56 40.23 4.02
5599 13476 4.504916 CGCGGTGGAGAGAGGCAG 62.505 72.222 0.00 0.00 0.00 4.85
5600 13477 4.828925 GCGGTGGAGAGAGGCAGC 62.829 72.222 0.00 0.00 0.00 5.25
5601 13478 4.504916 CGGTGGAGAGAGGCAGCG 62.505 72.222 0.00 0.00 0.00 5.18
5602 13479 4.154347 GGTGGAGAGAGGCAGCGG 62.154 72.222 0.00 0.00 0.00 5.52
5603 13480 4.828925 GTGGAGAGAGGCAGCGGC 62.829 72.222 0.00 0.00 40.13 6.53
5833 13710 2.127758 CGTGGCGCGTTGAAGAAC 60.128 61.111 13.13 0.00 35.54 3.01
5835 13712 1.082756 GTGGCGCGTTGAAGAACAG 60.083 57.895 8.43 0.00 31.78 3.16
5836 13713 2.250939 TGGCGCGTTGAAGAACAGG 61.251 57.895 8.43 0.00 31.78 4.00
5837 13714 2.127232 GCGCGTTGAAGAACAGGC 60.127 61.111 8.43 0.00 31.78 4.85
6034 13911 9.771534 GCTAAGCCCCTAATAATGATAAGATAG 57.228 37.037 0.00 0.00 0.00 2.08
6187 14065 5.329493 GTTTCAAGTTGCTACAAGTTCGTT 58.671 37.500 0.13 0.00 0.00 3.85
6599 14654 1.744639 ATCAGCCGATGATCTGCGT 59.255 52.632 3.20 0.00 46.01 5.24
6763 14819 3.213506 CTCTCACCATCTCGACTCAGAT 58.786 50.000 0.00 0.00 33.00 2.90
7064 15334 6.037610 GTCTTACTGCAATGTCTAATTCCTGG 59.962 42.308 0.00 0.00 0.00 4.45
7073 15343 9.120538 GCAATGTCTAATTCCTGGAAAATAGTA 57.879 33.333 22.01 16.25 0.00 1.82
7665 16604 4.511786 AGCCTTCTTTTCCTTCTATCCC 57.488 45.455 0.00 0.00 0.00 3.85
8192 17140 4.562963 GGAGGTCAACGTTCTGTATTTCCT 60.563 45.833 0.00 0.00 0.00 3.36
8266 17218 1.117150 TTCGCATGGTACCCTCTACC 58.883 55.000 10.07 0.00 38.07 3.18
8468 17430 8.603242 TGAGTGTTCTTTTAGTCCAAGATAAC 57.397 34.615 0.00 0.00 30.26 1.89
8643 17606 4.662278 ACTTTTGCCTTGATGCCTACTTA 58.338 39.130 0.00 0.00 0.00 2.24
8644 17607 4.459337 ACTTTTGCCTTGATGCCTACTTAC 59.541 41.667 0.00 0.00 0.00 2.34
8775 17740 6.021596 GTGTCGCTATTGTTTTCATTACTGG 58.978 40.000 0.00 0.00 0.00 4.00
8993 17958 1.135527 CCACTAGTTGGCATGCCATTG 59.864 52.381 38.78 26.63 46.64 2.82
9036 18001 8.203485 TGTGAAAATGTTTGATAGGCTTCTTTT 58.797 29.630 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
446 448 1.060698 GTCGGCGAATGTTAAGACTGC 59.939 52.381 12.92 0.00 0.00 4.40
652 655 5.354767 ACAGTCACTATATACGTGTCGAGA 58.645 41.667 0.00 0.00 34.14 4.04
653 656 5.654317 ACAGTCACTATATACGTGTCGAG 57.346 43.478 0.00 0.00 34.14 4.04
654 657 7.439056 TCAATACAGTCACTATATACGTGTCGA 59.561 37.037 0.00 0.00 34.14 4.20
655 658 7.570161 TCAATACAGTCACTATATACGTGTCG 58.430 38.462 0.00 0.00 34.14 4.35
656 659 9.894783 AATCAATACAGTCACTATATACGTGTC 57.105 33.333 0.00 6.76 34.14 3.67
657 660 9.678941 CAATCAATACAGTCACTATATACGTGT 57.321 33.333 0.00 0.00 34.14 4.49
658 661 9.678941 ACAATCAATACAGTCACTATATACGTG 57.321 33.333 0.00 6.17 0.00 4.49
667 670 9.376075 CTCAAGAATACAATCAATACAGTCACT 57.624 33.333 0.00 0.00 0.00 3.41
668 671 9.155975 ACTCAAGAATACAATCAATACAGTCAC 57.844 33.333 0.00 0.00 0.00 3.67
677 680 8.946085 GGTCATTGTACTCAAGAATACAATCAA 58.054 33.333 12.42 3.86 44.81 2.57
678 681 8.100164 TGGTCATTGTACTCAAGAATACAATCA 58.900 33.333 12.42 6.94 44.81 2.57
679 682 8.492673 TGGTCATTGTACTCAAGAATACAATC 57.507 34.615 12.42 4.85 44.81 2.67
681 684 8.684386 TTTGGTCATTGTACTCAAGAATACAA 57.316 30.769 6.58 6.58 43.49 2.41
682 685 7.936847 ACTTTGGTCATTGTACTCAAGAATACA 59.063 33.333 0.00 0.00 36.97 2.29
683 686 8.230486 CACTTTGGTCATTGTACTCAAGAATAC 58.770 37.037 0.00 0.00 36.97 1.89
684 687 8.154203 TCACTTTGGTCATTGTACTCAAGAATA 58.846 33.333 0.00 0.00 36.97 1.75
685 688 6.998074 TCACTTTGGTCATTGTACTCAAGAAT 59.002 34.615 0.00 0.00 36.97 2.40
686 689 6.353323 TCACTTTGGTCATTGTACTCAAGAA 58.647 36.000 0.00 0.00 36.97 2.52
687 690 5.924356 TCACTTTGGTCATTGTACTCAAGA 58.076 37.500 0.00 0.00 36.97 3.02
688 691 5.334414 GCTCACTTTGGTCATTGTACTCAAG 60.334 44.000 0.00 0.00 36.97 3.02
689 692 4.515191 GCTCACTTTGGTCATTGTACTCAA 59.485 41.667 0.00 0.00 37.98 3.02
690 693 4.065088 GCTCACTTTGGTCATTGTACTCA 58.935 43.478 0.00 0.00 0.00 3.41
691 694 4.319177 AGCTCACTTTGGTCATTGTACTC 58.681 43.478 0.00 0.00 0.00 2.59
692 695 4.357918 AGCTCACTTTGGTCATTGTACT 57.642 40.909 0.00 0.00 0.00 2.73
693 696 6.743575 ATAAGCTCACTTTGGTCATTGTAC 57.256 37.500 0.00 0.00 37.33 2.90
694 697 6.533723 CGTATAAGCTCACTTTGGTCATTGTA 59.466 38.462 0.00 0.00 37.33 2.41
695 698 5.351465 CGTATAAGCTCACTTTGGTCATTGT 59.649 40.000 0.00 0.00 37.33 2.71
696 699 5.580691 TCGTATAAGCTCACTTTGGTCATTG 59.419 40.000 0.00 0.00 37.33 2.82
697 700 5.730550 TCGTATAAGCTCACTTTGGTCATT 58.269 37.500 0.00 0.00 37.33 2.57
698 701 5.339008 TCGTATAAGCTCACTTTGGTCAT 57.661 39.130 0.00 0.00 37.33 3.06
699 702 4.794278 TCGTATAAGCTCACTTTGGTCA 57.206 40.909 0.00 0.00 37.33 4.02
700 703 6.979238 ACTTATCGTATAAGCTCACTTTGGTC 59.021 38.462 11.94 0.00 37.33 4.02
701 704 6.875076 ACTTATCGTATAAGCTCACTTTGGT 58.125 36.000 11.94 0.00 37.33 3.67
702 705 7.772332 AACTTATCGTATAAGCTCACTTTGG 57.228 36.000 11.94 0.00 37.33 3.28
708 711 9.472361 GGTCATTAAACTTATCGTATAAGCTCA 57.528 33.333 11.94 0.00 0.00 4.26
709 712 9.472361 TGGTCATTAAACTTATCGTATAAGCTC 57.528 33.333 11.94 0.00 0.00 4.09
710 713 9.257651 GTGGTCATTAAACTTATCGTATAAGCT 57.742 33.333 11.94 0.00 0.00 3.74
711 714 8.212495 CGTGGTCATTAAACTTATCGTATAAGC 58.788 37.037 11.94 0.00 0.00 3.09
712 715 9.454585 TCGTGGTCATTAAACTTATCGTATAAG 57.545 33.333 10.96 10.96 0.00 1.73
713 716 9.454585 CTCGTGGTCATTAAACTTATCGTATAA 57.545 33.333 0.00 0.00 0.00 0.98
714 717 8.623903 ACTCGTGGTCATTAAACTTATCGTATA 58.376 33.333 0.00 0.00 0.00 1.47
715 718 7.434307 CACTCGTGGTCATTAAACTTATCGTAT 59.566 37.037 0.00 0.00 0.00 3.06
716 719 6.748658 CACTCGTGGTCATTAAACTTATCGTA 59.251 38.462 0.00 0.00 0.00 3.43
717 720 5.575606 CACTCGTGGTCATTAAACTTATCGT 59.424 40.000 0.00 0.00 0.00 3.73
718 721 5.500290 GCACTCGTGGTCATTAAACTTATCG 60.500 44.000 0.00 0.00 0.00 2.92
719 722 5.350365 TGCACTCGTGGTCATTAAACTTATC 59.650 40.000 0.00 0.00 0.00 1.75
720 723 5.242434 TGCACTCGTGGTCATTAAACTTAT 58.758 37.500 0.00 0.00 0.00 1.73
721 724 4.633175 TGCACTCGTGGTCATTAAACTTA 58.367 39.130 0.00 0.00 0.00 2.24
722 725 3.472652 TGCACTCGTGGTCATTAAACTT 58.527 40.909 0.00 0.00 0.00 2.66
723 726 3.120321 TGCACTCGTGGTCATTAAACT 57.880 42.857 0.00 0.00 0.00 2.66
724 727 4.419522 AATGCACTCGTGGTCATTAAAC 57.580 40.909 0.00 0.00 30.15 2.01
725 728 5.446143 AAAATGCACTCGTGGTCATTAAA 57.554 34.783 0.00 0.00 31.00 1.52
726 729 5.703592 AGTAAAATGCACTCGTGGTCATTAA 59.296 36.000 0.00 0.00 31.00 1.40
727 730 5.121611 CAGTAAAATGCACTCGTGGTCATTA 59.878 40.000 0.00 0.00 31.00 1.90
728 731 4.072131 AGTAAAATGCACTCGTGGTCATT 58.928 39.130 0.00 0.00 31.81 2.57
729 732 3.436704 CAGTAAAATGCACTCGTGGTCAT 59.563 43.478 0.00 0.00 0.00 3.06
730 733 2.805671 CAGTAAAATGCACTCGTGGTCA 59.194 45.455 0.00 0.00 0.00 4.02
731 734 2.412847 GCAGTAAAATGCACTCGTGGTC 60.413 50.000 0.00 0.00 45.77 4.02
732 735 1.535462 GCAGTAAAATGCACTCGTGGT 59.465 47.619 0.00 0.00 45.77 4.16
733 736 2.247311 GCAGTAAAATGCACTCGTGG 57.753 50.000 0.00 0.00 45.77 4.94
741 744 4.572950 GCACTTCAATGCAGTAAAATGC 57.427 40.909 0.00 0.00 45.39 3.56
751 754 4.481112 CGGGCGGCACTTCAATGC 62.481 66.667 12.47 0.00 45.34 3.56
752 755 4.481112 GCGGGCGGCACTTCAATG 62.481 66.667 12.47 0.00 42.87 2.82
765 768 3.987954 ATTTACGGTGCCTGGCGGG 62.988 63.158 14.98 8.39 38.36 6.13
766 769 2.437716 ATTTACGGTGCCTGGCGG 60.438 61.111 14.98 8.40 0.00 6.13
767 770 2.791256 CATTTACGGTGCCTGGCG 59.209 61.111 14.98 1.99 0.00 5.69
768 771 2.046285 AGCATTTACGGTGCCTGGC 61.046 57.895 12.87 12.87 43.50 4.85
769 772 1.802636 CAGCATTTACGGTGCCTGG 59.197 57.895 0.00 0.00 43.50 4.45
792 795 2.360852 AGCAGTCCATGGCAGTGC 60.361 61.111 24.87 24.87 0.00 4.40
793 796 1.303074 ACAGCAGTCCATGGCAGTG 60.303 57.895 6.96 10.42 0.00 3.66
794 797 1.303074 CACAGCAGTCCATGGCAGT 60.303 57.895 6.96 0.00 0.00 4.40
897 900 1.134098 CCGGGTGCTACAAATCATCCT 60.134 52.381 0.00 0.00 31.36 3.24
917 920 2.916716 CACGCAATGGTGTTTCTTATGC 59.083 45.455 0.00 0.00 35.01 3.14
974 1516 2.826128 GTTGGGAATCTGGGGAAGAAAC 59.174 50.000 0.00 0.00 38.79 2.78
1096 3848 1.270907 GAGGAGAAGGTGAGGAGCAA 58.729 55.000 0.00 0.00 0.00 3.91
1267 4029 5.512788 CGTTGATCCACAGCAAATTTATGAC 59.487 40.000 9.02 0.00 27.13 3.06
1268 4030 5.639757 CGTTGATCCACAGCAAATTTATGA 58.360 37.500 9.02 0.00 27.13 2.15
1269 4031 4.266029 GCGTTGATCCACAGCAAATTTATG 59.734 41.667 8.24 0.00 27.13 1.90
1565 4336 1.589716 GAACAGGCTGGCTCGCAATT 61.590 55.000 20.34 0.43 0.00 2.32
1650 4450 4.790790 AGTCATAACAGGGAAGGAGGATTT 59.209 41.667 0.00 0.00 0.00 2.17
1806 4608 9.161629 CATTATTATTATCACATACCAGCCGAA 57.838 33.333 0.00 0.00 0.00 4.30
1914 4722 8.699749 GTGTATTCAAGGAAAAACTACAATTGC 58.300 33.333 5.05 0.00 0.00 3.56
2009 4819 3.592059 TCCGTATCAAAGGGAAAACTCG 58.408 45.455 0.00 0.00 39.21 4.18
2460 5317 5.898174 TGATTCAGCAGCAATATTTTCAGG 58.102 37.500 0.00 0.00 0.00 3.86
2558 5416 3.792401 TCGTAGATTCGGTACCTCGTTA 58.208 45.455 10.90 0.00 0.00 3.18
2629 5487 9.628500 ACTTGTTGTAAAAGAGGTTAAGAATCT 57.372 29.630 0.00 0.00 0.00 2.40
2892 5860 6.870971 AAACCAAAAGAGTAATCAGCGTAA 57.129 33.333 0.00 0.00 0.00 3.18
3216 6189 4.196193 CAAAGGTGAAAGGTCAGTACACA 58.804 43.478 0.00 0.00 33.27 3.72
3232 6208 4.038633 GGATCCTAACTCCTACCAAAGGT 58.961 47.826 3.84 0.00 46.62 3.50
3246 6222 3.401683 CCCTAGACCAGGTAGGATCCTAA 59.598 52.174 23.33 4.25 43.80 2.69
3280 6256 3.347590 CAACCCTCCCCCTTCCCC 61.348 72.222 0.00 0.00 0.00 4.81
3342 8770 1.589716 GCTGCCGCCTGTTCTTCATT 61.590 55.000 0.00 0.00 0.00 2.57
3538 8968 4.780815 TGTGGCCCAAGTTATCTTATCAG 58.219 43.478 0.00 0.00 32.07 2.90
3665 9095 2.094026 TGACACTGATTGATCACCTCGG 60.094 50.000 10.45 10.45 32.50 4.63
3678 9108 2.029739 TCGCGAAGGTATTTGACACTGA 60.030 45.455 6.20 0.00 0.00 3.41
3689 9119 2.571757 CCAGCTGTCGCGAAGGTA 59.428 61.111 12.06 0.00 42.32 3.08
3962 9398 3.014085 GCAGGAATCACCGTCCCGA 62.014 63.158 0.00 0.00 44.74 5.14
4167 9603 1.764571 TTCACCTCCACGGTTCAGGG 61.765 60.000 6.99 0.00 46.37 4.45
4220 9656 3.198953 TTTTGGGCCACCGATCCGT 62.199 57.895 5.23 0.00 40.75 4.69
4296 9732 2.487532 CCTGGTACTACGCCCTCGG 61.488 68.421 0.00 0.00 40.69 4.63
4382 9818 0.249489 AGTGCGAGCAGTTCTTTCGT 60.249 50.000 0.00 0.00 36.74 3.85
4451 9887 2.910345 GCCGCGGTTTGCCAAACTA 61.910 57.895 28.70 0.00 42.08 2.24
4662 10098 2.039299 ACCGTCCCCAATACCGGA 59.961 61.111 9.46 0.00 43.01 5.14
4696 10132 0.613260 AGGCGTACAGATCCAGCAAA 59.387 50.000 0.00 0.00 0.00 3.68
5582 13459 4.504916 CTGCCTCTCTCCACCGCG 62.505 72.222 0.00 0.00 0.00 6.46
5583 13460 4.828925 GCTGCCTCTCTCCACCGC 62.829 72.222 0.00 0.00 0.00 5.68
5584 13461 4.504916 CGCTGCCTCTCTCCACCG 62.505 72.222 0.00 0.00 0.00 4.94
5585 13462 4.154347 CCGCTGCCTCTCTCCACC 62.154 72.222 0.00 0.00 0.00 4.61
5586 13463 4.828925 GCCGCTGCCTCTCTCCAC 62.829 72.222 0.00 0.00 0.00 4.02
5825 13702 2.668212 CCGCCGCCTGTTCTTCAA 60.668 61.111 0.00 0.00 0.00 2.69
6070 13948 1.884928 GCCAAGGTTGTTATGACCGGT 60.885 52.381 6.92 6.92 42.11 5.28
6361 14244 0.320697 AACCCGGAGCTAACTGTGTC 59.679 55.000 0.73 0.00 0.00 3.67
6362 14245 0.320697 GAACCCGGAGCTAACTGTGT 59.679 55.000 0.73 0.00 0.00 3.72
6428 14312 2.964123 CAGCAACAACGAACGTTACATG 59.036 45.455 12.07 11.77 36.46 3.21
6436 14320 3.247648 AGTGATGTACAGCAACAACGAAC 59.752 43.478 16.64 0.40 31.60 3.95
6599 14654 1.623811 GGGTGAAGTCCACTCTAGCAA 59.376 52.381 0.00 0.00 43.00 3.91
6683 14739 3.788227 AACACCAGGTGATTGAAGCTA 57.212 42.857 27.39 0.00 36.96 3.32
6763 14819 3.774766 ACTGTATAGGGCATGTTCTCACA 59.225 43.478 0.00 0.69 37.31 3.58
7033 15287 3.012518 GACATTGCAGTAAGACCAGCAT 58.987 45.455 0.00 0.00 36.80 3.79
7324 16254 8.345565 GTGAACACAGAAAACAGTCTGAATTAT 58.654 33.333 6.91 0.00 46.76 1.28
7903 16846 4.262121 CCTGGATGTTGCAATTCACAAAGA 60.262 41.667 0.59 0.00 0.00 2.52
8266 17218 6.150318 ACATATCGAGCTACGTATCCAAAAG 58.850 40.000 0.00 0.00 43.13 2.27
8643 17606 6.682362 GCCTTAAGTAACCTCTAATAGCACGT 60.682 42.308 0.97 0.00 0.00 4.49
8644 17607 5.690857 GCCTTAAGTAACCTCTAATAGCACG 59.309 44.000 0.97 0.00 0.00 5.34
8775 17740 4.438200 CCACACCTTTCGGTTGTATTATGC 60.438 45.833 0.00 0.00 42.13 3.14
8798 17763 6.487689 AGTTCTGTACTTGAGCATAAAAGC 57.512 37.500 0.00 0.00 31.29 3.51
8993 17958 5.934935 TTCACAAAGGACGGTAATTTCTC 57.065 39.130 0.00 0.00 0.00 2.87
9101 18066 9.806203 CAAGAGATACATGATTTTGGCATTAAA 57.194 29.630 0.00 0.00 0.00 1.52
9111 18076 7.246311 CGCTCAAAACAAGAGATACATGATTT 58.754 34.615 0.00 0.00 35.09 2.17


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

AutoCloner maintained by Alex Coulton.