Multiple sequence alignment - TraesCS1B01G258700

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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 TraesCS1B01G258700 chr1B 100.000 5067 0 0 1 5067 456189206 456184140 0.000000e+00 9358.0
1 TraesCS1B01G258700 chr1B 78.673 211 19 19 4477 4686 572257824 572258009 3.210000e-22 117.0
2 TraesCS1B01G258700 chr1A 92.072 2157 110 22 2230 4368 440185840 440183727 0.000000e+00 2979.0
3 TraesCS1B01G258700 chr1A 91.602 1548 79 25 709 2240 440187461 440185949 0.000000e+00 2091.0
4 TraesCS1B01G258700 chr1A 92.149 484 31 6 4427 4907 440183632 440183153 0.000000e+00 676.0
5 TraesCS1B01G258700 chr1A 91.437 327 20 5 23 342 567626665 567626990 4.660000e-120 442.0
6 TraesCS1B01G258700 chr1A 90.741 108 9 1 4961 5067 8087744 8087637 5.290000e-30 143.0
7 TraesCS1B01G258700 chr1A 79.137 139 18 8 4496 4626 518951324 518951459 9.040000e-13 86.1
8 TraesCS1B01G258700 chr1D 95.852 1567 49 11 2805 4368 340559146 340557593 0.000000e+00 2519.0
9 TraesCS1B01G258700 chr1D 88.938 1139 54 35 637 1762 340562764 340561685 0.000000e+00 1339.0
10 TraesCS1B01G258700 chr1D 96.610 531 17 1 2232 2762 340559935 340559406 0.000000e+00 880.0
11 TraesCS1B01G258700 chr1D 95.745 470 13 6 1777 2240 340560511 340560043 0.000000e+00 750.0
12 TraesCS1B01G258700 chr1D 85.660 530 45 10 4391 4907 340557510 340556999 3.470000e-146 529.0
13 TraesCS1B01G258700 chr1D 90.741 108 9 1 4961 5067 416626126 416626019 5.290000e-30 143.0
14 TraesCS1B01G258700 chr2D 93.831 308 10 3 328 634 620007616 620007317 5.980000e-124 455.0
15 TraesCS1B01G258700 chr2D 92.405 316 17 6 35 344 620007951 620007637 1.290000e-120 444.0
16 TraesCS1B01G258700 chr2D 87.770 139 14 3 4546 4682 37911776 37911913 5.250000e-35 159.0
17 TraesCS1B01G258700 chr2D 87.143 140 14 4 4546 4682 37930121 37930259 6.790000e-34 156.0
18 TraesCS1B01G258700 chr2D 92.593 54 3 1 4906 4959 635208537 635208485 5.440000e-10 76.8
19 TraesCS1B01G258700 chr4D 93.485 307 17 3 41 344 3914337 3914031 2.150000e-123 453.0
20 TraesCS1B01G258700 chr4D 97.872 47 1 0 4913 4959 40801589 40801543 1.170000e-11 82.4
21 TraesCS1B01G258700 chr4D 89.474 57 6 0 4903 4959 502682068 502682012 7.040000e-09 73.1
22 TraesCS1B01G258700 chr6B 91.925 322 21 3 25 341 508615464 508615785 3.600000e-121 446.0
23 TraesCS1B01G258700 chr6B 90.769 325 23 5 24 341 55671853 55672177 1.300000e-115 427.0
24 TraesCS1B01G258700 chr6B 92.105 190 12 3 447 634 55674296 55674484 1.080000e-66 265.0
25 TraesCS1B01G258700 chr6B 85.096 208 19 9 4488 4687 115297730 115297933 8.600000e-48 202.0
26 TraesCS1B01G258700 chr6B 93.137 102 4 1 328 429 55672201 55672299 4.090000e-31 147.0
27 TraesCS1B01G258700 chr7D 92.405 316 17 6 35 344 362363289 362362975 1.290000e-120 444.0
28 TraesCS1B01G258700 chr7D 92.834 307 13 3 328 633 362362954 362362656 2.170000e-118 436.0
29 TraesCS1B01G258700 chr7D 96.000 50 2 0 4910 4959 73143783 73143734 1.170000e-11 82.4
30 TraesCS1B01G258700 chr7D 92.727 55 4 0 576 630 395975721 395975775 4.210000e-11 80.5
31 TraesCS1B01G258700 chr4B 91.615 322 22 3 25 341 560025302 560025623 1.670000e-119 440.0
32 TraesCS1B01G258700 chr4B 92.308 52 4 0 4908 4959 662142960 662143011 1.960000e-09 75.0
33 TraesCS1B01G258700 chr3B 92.857 308 14 3 328 634 739021792 739021492 1.670000e-119 440.0
34 TraesCS1B01G258700 chr5A 91.304 322 23 3 25 341 562855416 562855737 7.790000e-118 435.0
35 TraesCS1B01G258700 chr7B 91.250 320 21 4 31 344 720140617 720140299 3.620000e-116 429.0
36 TraesCS1B01G258700 chr7B 91.223 319 23 3 31 344 742144263 742143945 3.620000e-116 429.0
37 TraesCS1B01G258700 chr5D 83.254 209 22 11 4488 4687 68699381 68699177 4.030000e-41 180.0
38 TraesCS1B01G258700 chr5D 90.741 108 9 1 4961 5067 30114910 30114803 5.290000e-30 143.0
39 TraesCS1B01G258700 chr5D 90.741 108 8 2 4961 5067 329771208 329771102 5.290000e-30 143.0
40 TraesCS1B01G258700 chr5D 90.741 108 9 1 4961 5067 375170781 375170888 5.290000e-30 143.0
41 TraesCS1B01G258700 chr5D 90.741 108 9 1 4961 5067 497848855 497848962 5.290000e-30 143.0
42 TraesCS1B01G258700 chr2A 87.857 140 13 4 4546 4682 42785987 42786125 1.460000e-35 161.0
43 TraesCS1B01G258700 chr2A 87.143 140 14 4 4546 4682 42792342 42792480 6.790000e-34 156.0
44 TraesCS1B01G258700 chr2A 91.667 108 8 1 4961 5067 43048072 43047965 1.140000e-31 148.0
45 TraesCS1B01G258700 chr6A 80.583 206 31 7 4487 4687 60379857 60380058 3.160000e-32 150.0
46 TraesCS1B01G258700 chr6A 90.741 108 9 1 4961 5067 22626877 22626984 5.290000e-30 143.0
47 TraesCS1B01G258700 chr6A 90.741 108 9 1 4961 5067 599872548 599872655 5.290000e-30 143.0
48 TraesCS1B01G258700 chr6A 96.154 52 2 0 4909 4960 378200163 378200112 9.040000e-13 86.1
49 TraesCS1B01G258700 chr7A 94.231 52 3 0 4908 4959 706279886 706279937 4.210000e-11 80.5
50 TraesCS1B01G258700 chr3D 96.000 50 1 1 4910 4959 356633109 356633061 4.210000e-11 80.5
51 TraesCS1B01G258700 chr3D 94.340 53 2 1 4908 4960 549521211 549521160 4.210000e-11 80.5
52 TraesCS1B01G258700 chr3A 95.918 49 1 1 4908 4955 71579651 71579603 1.510000e-10 78.7
53 TraesCS1B01G258700 chr2B 94.118 51 3 0 4909 4959 776795446 776795496 1.510000e-10 78.7
54 TraesCS1B01G258700 chr5B 92.157 51 4 0 4909 4959 606884215 606884265 7.040000e-09 73.1
55 TraesCS1B01G258700 chr5B 93.478 46 3 0 589 634 596933120 596933165 9.100000e-08 69.4


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 TraesCS1B01G258700 chr1B 456184140 456189206 5066 True 9358.000000 9358 100.000000 1 5067 1 chr1B.!!$R1 5066
1 TraesCS1B01G258700 chr1A 440183153 440187461 4308 True 1915.333333 2979 91.941000 709 4907 3 chr1A.!!$R2 4198
2 TraesCS1B01G258700 chr1D 340556999 340562764 5765 True 1203.400000 2519 92.561000 637 4907 5 chr1D.!!$R2 4270
3 TraesCS1B01G258700 chr2D 620007317 620007951 634 True 449.500000 455 93.118000 35 634 2 chr2D.!!$R2 599
4 TraesCS1B01G258700 chr6B 55671853 55674484 2631 False 279.666667 427 92.003667 24 634 3 chr6B.!!$F3 610
5 TraesCS1B01G258700 chr7D 362362656 362363289 633 True 440.000000 444 92.619500 35 633 2 chr7D.!!$R2 598

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
638 2666 0.104487 TGCGAACGTTTCCCTGTACA 59.896 50.0 0.46 0.0 0.00 2.90 F
1388 3429 0.601558 TAGGAGCGCGATATGTTCCC 59.398 55.0 12.10 0.0 0.00 3.97 F
1774 4988 0.179048 TGCAGCCGATTAGTGATGGG 60.179 55.0 0.00 0.0 36.75 4.00 F
2173 5394 0.179124 CTGCGTTCTAGTCCTCCTGC 60.179 60.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 3512 0.252239 GCCACTCCATCCCCCTTTTT 60.252 55.0 0.00 0.0 0.00 1.94 R
2921 6481 0.460987 CAACTCTAGCAGGGCCTTCG 60.461 60.0 1.32 0.0 0.00 3.79 R
3748 7310 0.973632 TAAGAAGAGCAAGCGGGTCA 59.026 50.0 12.10 0.0 46.51 4.02 R
4162 7724 0.027194 CGCAATGAGTGGATTCAGCG 59.973 55.0 0.00 0.0 36.10 5.18 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
24 25 2.351706 AAAAAGGACGGTGGTAGCAA 57.648 45.000 0.00 0.00 0.00 3.91
25 26 2.351706 AAAAGGACGGTGGTAGCAAA 57.648 45.000 0.00 0.00 0.00 3.68
26 27 2.351706 AAAGGACGGTGGTAGCAAAA 57.648 45.000 0.00 0.00 0.00 2.44
27 28 2.351706 AAGGACGGTGGTAGCAAAAA 57.648 45.000 0.00 0.00 0.00 1.94
69 70 3.584834 ACGATGGTAGCAAAAATTTGGC 58.415 40.909 0.00 0.00 38.57 4.52
146 148 2.212652 GCTCCCAGCAAAAACAAAAGG 58.787 47.619 0.00 0.00 41.89 3.11
155 157 3.371285 GCAAAAACAAAAGGCGGTTGTAA 59.629 39.130 8.88 0.00 38.24 2.41
320 324 0.687757 ATAGAGCGGGGCAAGTGAGA 60.688 55.000 0.00 0.00 0.00 3.27
429 470 1.467734 GAGCAGCCTGATCTGTGTTTG 59.532 52.381 1.98 0.00 36.49 2.93
430 471 0.524862 GCAGCCTGATCTGTGTTTGG 59.475 55.000 0.00 0.00 36.49 3.28
431 472 1.901591 CAGCCTGATCTGTGTTTGGT 58.098 50.000 0.00 0.00 0.00 3.67
432 473 2.233271 CAGCCTGATCTGTGTTTGGTT 58.767 47.619 0.00 0.00 0.00 3.67
433 474 2.624838 CAGCCTGATCTGTGTTTGGTTT 59.375 45.455 0.00 0.00 0.00 3.27
434 475 2.624838 AGCCTGATCTGTGTTTGGTTTG 59.375 45.455 0.00 0.00 0.00 2.93
435 476 2.362077 GCCTGATCTGTGTTTGGTTTGT 59.638 45.455 0.00 0.00 0.00 2.83
446 487 4.026744 TGTTTGGTTTGTGATTTGGAGGA 58.973 39.130 0.00 0.00 0.00 3.71
451 2477 4.959210 TGGTTTGTGATTTGGAGGAAAAGA 59.041 37.500 0.00 0.00 0.00 2.52
496 2522 8.414778 GGAAGAAAGAGATAAAGGAGATACGAA 58.585 37.037 0.00 0.00 0.00 3.85
506 2532 2.028385 AGGAGATACGAAAGCGGTTTGT 60.028 45.455 18.67 16.80 43.17 2.83
547 2574 1.219393 GAGAGAAAGGTGCGAGGGG 59.781 63.158 0.00 0.00 0.00 4.79
581 2608 3.195002 CGTACGCAGGCCATGTGG 61.195 66.667 5.01 0.00 44.07 4.17
634 2662 2.556287 GCTGCGAACGTTTCCCTG 59.444 61.111 0.46 0.00 0.00 4.45
635 2663 2.251642 GCTGCGAACGTTTCCCTGT 61.252 57.895 0.46 0.00 0.00 4.00
636 2664 0.947180 GCTGCGAACGTTTCCCTGTA 60.947 55.000 0.46 0.00 0.00 2.74
637 2665 0.788391 CTGCGAACGTTTCCCTGTAC 59.212 55.000 0.46 0.00 0.00 2.90
638 2666 0.104487 TGCGAACGTTTCCCTGTACA 59.896 50.000 0.46 0.00 0.00 2.90
639 2667 1.219646 GCGAACGTTTCCCTGTACAA 58.780 50.000 0.46 0.00 0.00 2.41
640 2668 1.802365 GCGAACGTTTCCCTGTACAAT 59.198 47.619 0.46 0.00 0.00 2.71
646 2674 6.292168 CGAACGTTTCCCTGTACAATATGATC 60.292 42.308 0.46 0.00 0.00 2.92
720 2748 4.095610 CCGTTAAAGCATCAATCGAAACC 58.904 43.478 0.00 0.00 0.00 3.27
806 2836 1.059369 CGAGGCGAAACATTGCTCG 59.941 57.895 0.00 0.00 38.11 5.03
812 2842 1.156736 CGAAACATTGCTCGGGAGTT 58.843 50.000 0.00 0.00 0.00 3.01
860 2894 3.741344 CGACCGAAGAAAGAAACACATCT 59.259 43.478 0.00 0.00 0.00 2.90
861 2895 4.211374 CGACCGAAGAAAGAAACACATCTT 59.789 41.667 0.00 0.00 41.34 2.40
874 2908 7.260603 AGAAACACATCTTCAGAAACAAAAGG 58.739 34.615 0.00 0.00 0.00 3.11
909 2945 2.329379 GAGCGCGAGAGAGAAGAAAAA 58.671 47.619 12.10 0.00 0.00 1.94
970 3010 2.047844 CCTCGGTGCCAGTCAGTG 60.048 66.667 0.00 0.00 0.00 3.66
994 3034 1.386772 TTGGTGGTCCCCCAGTTCT 60.387 57.895 0.00 0.00 42.94 3.01
1239 3279 2.746277 GTCGCCTTCAACCCGCAT 60.746 61.111 0.00 0.00 0.00 4.73
1333 3374 5.503846 GCACATGGAAAACCAACATTTGTTC 60.504 40.000 0.00 0.00 35.83 3.18
1340 3381 6.255670 GGAAAACCAACATTTGTTCTCTGTTC 59.744 38.462 0.00 0.00 35.83 3.18
1374 3415 6.045955 GCTACAGGATTGAGAAGTTTAGGAG 58.954 44.000 0.00 0.00 0.00 3.69
1388 3429 0.601558 TAGGAGCGCGATATGTTCCC 59.398 55.000 12.10 0.00 0.00 3.97
1399 3440 4.449068 GCGATATGTTCCCAGTACTGATTG 59.551 45.833 24.68 12.00 0.00 2.67
1401 3442 5.463392 CGATATGTTCCCAGTACTGATTGTG 59.537 44.000 24.68 6.77 0.00 3.33
1422 3463 2.100631 GTGTCGAACAGGATGCGGG 61.101 63.158 0.00 0.00 42.53 6.13
1423 3464 2.511600 GTCGAACAGGATGCGGGG 60.512 66.667 0.00 0.00 42.53 5.73
1454 3495 4.074259 GGTGGTTTCCGGTAGTATTTTGT 58.926 43.478 0.00 0.00 0.00 2.83
1467 3508 7.550196 CGGTAGTATTTTGTGTAGGGTTTGTAT 59.450 37.037 0.00 0.00 0.00 2.29
1471 3512 9.796180 AGTATTTTGTGTAGGGTTTGTATTGTA 57.204 29.630 0.00 0.00 0.00 2.41
1509 3551 0.179097 CGGAGCTAAGAACAGAGGGC 60.179 60.000 0.00 0.00 0.00 5.19
1541 3583 2.609610 GTGGGGGACTGGGTGCTA 60.610 66.667 0.00 0.00 0.00 3.49
1542 3584 2.609610 TGGGGGACTGGGTGCTAC 60.610 66.667 0.00 0.00 0.00 3.58
1543 3585 2.285442 GGGGGACTGGGTGCTACT 60.285 66.667 0.00 0.00 0.00 2.57
1544 3586 1.002533 GGGGGACTGGGTGCTACTA 59.997 63.158 0.00 0.00 0.00 1.82
1545 3587 0.619543 GGGGGACTGGGTGCTACTAA 60.620 60.000 0.00 0.00 0.00 2.24
1556 3598 7.471041 ACTGGGTGCTACTAATAGATGAGATA 58.529 38.462 0.00 0.00 0.00 1.98
1571 3613 3.529533 TGAGATAAAGAAGAGCTGCAGC 58.470 45.455 31.53 31.53 42.49 5.25
1599 3641 7.412137 AAGCATTGAAAGAACTAAATTGCAC 57.588 32.000 0.00 0.00 0.00 4.57
1608 3650 8.782533 AAAGAACTAAATTGCACTTTTAGACG 57.217 30.769 24.71 8.83 38.40 4.18
1769 4983 1.929836 GTCTTCTGCAGCCGATTAGTG 59.070 52.381 9.47 0.00 0.00 2.74
1770 4984 1.824852 TCTTCTGCAGCCGATTAGTGA 59.175 47.619 9.47 0.00 0.00 3.41
1771 4985 2.432146 TCTTCTGCAGCCGATTAGTGAT 59.568 45.455 9.47 0.00 0.00 3.06
1772 4986 2.229675 TCTGCAGCCGATTAGTGATG 57.770 50.000 9.47 0.00 0.00 3.07
1773 4987 1.202568 TCTGCAGCCGATTAGTGATGG 60.203 52.381 9.47 0.00 0.00 3.51
1774 4988 0.179048 TGCAGCCGATTAGTGATGGG 60.179 55.000 0.00 0.00 36.75 4.00
1930 5144 6.420913 TTCTATGCCACCCTTAAGAGTATC 57.579 41.667 3.36 0.00 0.00 2.24
2140 5361 2.001812 CTGATGTCTCACCTTGGTCG 57.998 55.000 0.00 0.00 0.00 4.79
2141 5362 0.608130 TGATGTCTCACCTTGGTCGG 59.392 55.000 0.00 0.00 0.00 4.79
2173 5394 0.179124 CTGCGTTCTAGTCCTCCTGC 60.179 60.000 0.00 0.00 0.00 4.85
2194 5415 1.067283 TCTGTAGTCTGCTCTGCTTGC 60.067 52.381 0.00 0.00 0.00 4.01
2207 5428 3.403038 TCTGCTTGCCTCTGTTTTCTAC 58.597 45.455 0.00 0.00 0.00 2.59
2268 5608 5.466127 AGCCCCTAAAATGTAGAAATGGA 57.534 39.130 0.00 0.00 0.00 3.41
2673 6015 3.299503 ACAAAAGTTTCATGTCCTGCCT 58.700 40.909 0.00 0.00 0.00 4.75
2749 6091 2.365293 GGTGAGCCAAGGTGAATTTTGT 59.635 45.455 0.00 0.00 34.09 2.83
2757 6099 5.427378 CCAAGGTGAATTTTGTGGAAAACT 58.573 37.500 0.00 0.00 33.86 2.66
2770 6112 1.666189 GGAAAACTATGCGGAGTGAGC 59.334 52.381 0.00 0.00 0.00 4.26
2794 6136 1.271982 GGTGGAGGGGAGGAAAGAAAC 60.272 57.143 0.00 0.00 0.00 2.78
2801 6143 3.075148 GGGGAGGAAAGAAACGAGAAAG 58.925 50.000 0.00 0.00 0.00 2.62
2844 6403 6.288096 TGGGCCCAAGAAATATATAAAGGT 57.712 37.500 26.33 0.00 0.00 3.50
2893 6452 6.218746 CAAACTTGCTCTTGAGCCTTTAAAT 58.781 36.000 18.48 0.00 0.00 1.40
2894 6453 6.410942 AACTTGCTCTTGAGCCTTTAAATT 57.589 33.333 18.48 1.52 0.00 1.82
2921 6481 9.677567 TTTTACAGTGCACTCTAAAATCATTTC 57.322 29.630 26.52 0.00 26.83 2.17
3011 6571 7.977853 GCTCTGATGGTTTCACAATGATTTATT 59.022 33.333 0.00 0.00 0.00 1.40
3106 6667 7.905106 CCCCTTACACCCCTATATCTAGTAAAT 59.095 40.741 0.00 0.00 0.00 1.40
3586 7148 2.286872 CTGAATGCCTGGTCAGATGAC 58.713 52.381 6.92 4.33 43.32 3.06
3664 7226 2.549778 GCTCCTCATACAGGCCTTCATC 60.550 54.545 0.00 0.00 43.08 2.92
3745 7307 3.192844 GGATAAAGCGATCATACTCCGGA 59.807 47.826 2.93 2.93 0.00 5.14
3748 7310 0.178987 AGCGATCATACTCCGGACCT 60.179 55.000 0.00 0.00 0.00 3.85
3766 7328 0.321122 CTGACCCGCTTGCTCTTCTT 60.321 55.000 0.00 0.00 0.00 2.52
3779 7341 3.118261 TGCTCTTCTTATCTCGGGCATTT 60.118 43.478 0.00 0.00 0.00 2.32
3912 7474 1.153369 GATGCTCGGCCTGCACTTA 60.153 57.895 20.07 0.77 43.59 2.24
3922 7484 2.426522 GCCTGCACTTATGACAACTCA 58.573 47.619 0.00 0.00 0.00 3.41
3934 7496 2.295349 TGACAACTCACCTTCGGTAGAC 59.705 50.000 0.00 0.00 32.11 2.59
3988 7550 2.164624 CCGTGTTTTTCCCAACAGACAA 59.835 45.455 0.00 0.00 37.33 3.18
4068 7630 3.817084 CTGCAAAGGTTTGACAGATGAGA 59.183 43.478 15.81 0.00 40.98 3.27
4145 7707 8.480643 ACTTCTTCCTTGAATATAAACTGTCG 57.519 34.615 0.00 0.00 0.00 4.35
4150 7712 8.610248 TTCCTTGAATATAAACTGTCGTTTGA 57.390 30.769 1.04 0.00 42.94 2.69
4162 7724 3.921677 TGTCGTTTGACCAGGATTCTAC 58.078 45.455 0.00 0.00 44.86 2.59
4184 7746 2.897436 CTGAATCCACTCATTGCGAGA 58.103 47.619 0.00 0.00 45.45 4.04
4189 7751 3.333029 TCCACTCATTGCGAGAATTGA 57.667 42.857 0.00 0.00 45.45 2.57
4191 7753 3.624410 TCCACTCATTGCGAGAATTGATG 59.376 43.478 0.00 0.00 45.45 3.07
4192 7754 3.376234 CCACTCATTGCGAGAATTGATGT 59.624 43.478 0.00 0.00 45.45 3.06
4193 7755 4.571984 CCACTCATTGCGAGAATTGATGTA 59.428 41.667 0.00 0.00 45.45 2.29
4244 7806 3.101437 TGAAGGCCCGAGTACTTTGATA 58.899 45.455 0.00 0.00 0.00 2.15
4302 7876 4.134563 GCAAAAGGTGTAAAGACCTCTCA 58.865 43.478 0.00 0.00 46.29 3.27
4303 7877 4.762251 GCAAAAGGTGTAAAGACCTCTCAT 59.238 41.667 0.00 0.00 46.29 2.90
4304 7878 5.106515 GCAAAAGGTGTAAAGACCTCTCATC 60.107 44.000 0.00 0.00 46.29 2.92
4322 7896 0.602638 TCACAACATCACCAGGACGC 60.603 55.000 0.00 0.00 0.00 5.19
4323 7897 1.667830 ACAACATCACCAGGACGCG 60.668 57.895 3.53 3.53 0.00 6.01
4324 7898 2.047274 AACATCACCAGGACGCGG 60.047 61.111 12.47 0.00 0.00 6.46
4325 7899 4.760047 ACATCACCAGGACGCGGC 62.760 66.667 12.47 7.53 0.00 6.53
4344 7918 4.250464 CGGCTTATAGAGTTCAAACACCA 58.750 43.478 0.00 0.00 0.00 4.17
4350 7924 2.365582 AGAGTTCAAACACCACACCAC 58.634 47.619 0.00 0.00 0.00 4.16
4356 7930 1.476085 CAAACACCACACCACACACAT 59.524 47.619 0.00 0.00 0.00 3.21
4361 7935 3.145286 CACCACACCACACACATTATCA 58.855 45.455 0.00 0.00 0.00 2.15
4368 7942 4.996758 CACCACACACATTATCAACTCTCA 59.003 41.667 0.00 0.00 0.00 3.27
4372 7997 4.686091 ACACACATTATCAACTCTCACACG 59.314 41.667 0.00 0.00 0.00 4.49
4375 8000 5.862323 ACACATTATCAACTCTCACACGTAC 59.138 40.000 0.00 0.00 0.00 3.67
4465 8100 3.340789 GGTGGCTGAAACCGTGAC 58.659 61.111 0.00 0.00 0.00 3.67
4467 8102 0.034337 GGTGGCTGAAACCGTGACTA 59.966 55.000 0.00 0.00 0.00 2.59
4468 8103 1.338769 GGTGGCTGAAACCGTGACTAT 60.339 52.381 0.00 0.00 0.00 2.12
4470 8105 1.346395 TGGCTGAAACCGTGACTATGT 59.654 47.619 0.00 0.00 0.00 2.29
4471 8106 2.224426 TGGCTGAAACCGTGACTATGTT 60.224 45.455 0.00 0.00 0.00 2.71
4472 8107 2.812011 GGCTGAAACCGTGACTATGTTT 59.188 45.455 0.00 0.00 35.06 2.83
4554 8191 1.525077 GTGCAAAGGTGACGACCCA 60.525 57.895 0.00 0.00 44.40 4.51
4589 8226 3.494626 AGCGTTTCATCACTACAAGTGTG 59.505 43.478 6.93 5.44 46.03 3.82
4590 8227 3.493129 GCGTTTCATCACTACAAGTGTGA 59.507 43.478 6.93 7.37 46.03 3.58
4591 8228 4.608445 GCGTTTCATCACTACAAGTGTGAC 60.608 45.833 6.93 1.24 46.03 3.67
4592 8229 4.745125 CGTTTCATCACTACAAGTGTGACT 59.255 41.667 6.93 0.00 46.03 3.41
4593 8230 5.332581 CGTTTCATCACTACAAGTGTGACTG 60.333 44.000 6.93 2.42 46.03 3.51
4690 8329 1.535204 GCCACCACCCCTTTGTGATG 61.535 60.000 0.00 0.00 38.55 3.07
4705 8344 2.279741 GTGATGCTGGAGCGATGTAAA 58.720 47.619 0.00 0.00 45.83 2.01
4723 8362 6.757026 TGTAAAAACTTTTATTTGCCTCGC 57.243 33.333 0.00 0.00 35.35 5.03
4826 8476 5.109210 TGTACAAATCGCAGTCCTTCATAG 58.891 41.667 0.00 0.00 0.00 2.23
4835 8485 4.681781 CGCAGTCCTTCATAGAACTCCAAT 60.682 45.833 0.00 0.00 0.00 3.16
4863 8513 2.607631 TTGGACCGTCTCGTTTCTTT 57.392 45.000 0.00 0.00 0.00 2.52
4907 8558 1.780919 AGGTCCCAAGGCTGTAAAAGT 59.219 47.619 0.00 0.00 0.00 2.66
4908 8559 2.177016 AGGTCCCAAGGCTGTAAAAGTT 59.823 45.455 0.00 0.00 0.00 2.66
4909 8560 2.963101 GGTCCCAAGGCTGTAAAAGTTT 59.037 45.455 0.00 0.00 0.00 2.66
4910 8561 3.386726 GGTCCCAAGGCTGTAAAAGTTTT 59.613 43.478 6.06 6.06 0.00 2.43
4911 8562 4.141801 GGTCCCAAGGCTGTAAAAGTTTTT 60.142 41.667 6.10 0.00 0.00 1.94
4933 8584 3.536158 TTTTAACATCAGTGCAGACGC 57.464 42.857 0.00 0.00 39.24 5.19
4943 8594 3.494336 GCAGACGCAAGCGCTCAT 61.494 61.111 12.06 0.00 44.19 2.90
4944 8595 2.167219 GCAGACGCAAGCGCTCATA 61.167 57.895 12.06 0.00 44.19 2.15
4945 8596 1.633171 CAGACGCAAGCGCTCATAC 59.367 57.895 12.06 1.58 44.19 2.39
4946 8597 1.078201 CAGACGCAAGCGCTCATACA 61.078 55.000 12.06 0.00 44.19 2.29
4947 8598 0.179100 AGACGCAAGCGCTCATACAT 60.179 50.000 12.06 0.00 44.19 2.29
4948 8599 1.067060 AGACGCAAGCGCTCATACATA 59.933 47.619 12.06 0.00 44.19 2.29
4949 8600 2.061773 GACGCAAGCGCTCATACATAT 58.938 47.619 12.06 0.00 44.19 1.78
4950 8601 1.794701 ACGCAAGCGCTCATACATATG 59.205 47.619 12.06 3.22 44.19 1.78
4951 8602 1.463034 CGCAAGCGCTCATACATATGC 60.463 52.381 12.06 13.77 35.30 3.14
4957 8608 3.559530 CGCTCATACATATGCGCATAC 57.440 47.619 31.17 15.14 42.77 2.39
4958 8609 2.923020 CGCTCATACATATGCGCATACA 59.077 45.455 31.17 19.39 42.77 2.29
4959 8610 3.553105 CGCTCATACATATGCGCATACAT 59.447 43.478 31.17 23.11 42.77 2.29
4960 8611 4.549489 CGCTCATACATATGCGCATACATG 60.549 45.833 31.17 28.57 42.77 3.21
4961 8612 4.260497 GCTCATACATATGCGCATACATGG 60.260 45.833 31.17 23.29 42.33 3.66
4962 8613 4.190772 TCATACATATGCGCATACATGGG 58.809 43.478 31.17 19.99 42.88 4.00
4963 8614 2.857186 ACATATGCGCATACATGGGA 57.143 45.000 31.17 10.90 42.66 4.37
4964 8615 3.138884 ACATATGCGCATACATGGGAA 57.861 42.857 31.17 10.09 42.66 3.97
4965 8616 2.813754 ACATATGCGCATACATGGGAAC 59.186 45.455 31.17 0.00 42.66 3.62
4966 8617 1.507562 TATGCGCATACATGGGAACG 58.492 50.000 25.78 0.00 42.66 3.95
4967 8618 0.463654 ATGCGCATACATGGGAACGT 60.464 50.000 24.02 0.00 42.66 3.99
4968 8619 1.087202 TGCGCATACATGGGAACGTC 61.087 55.000 5.66 0.00 42.66 4.34
4969 8620 0.810031 GCGCATACATGGGAACGTCT 60.810 55.000 0.30 0.00 42.66 4.18
4970 8621 1.651987 CGCATACATGGGAACGTCTT 58.348 50.000 0.00 0.00 42.66 3.01
4971 8622 1.593006 CGCATACATGGGAACGTCTTC 59.407 52.381 0.00 0.00 42.66 2.87
4972 8623 2.738643 CGCATACATGGGAACGTCTTCT 60.739 50.000 0.00 0.00 42.66 2.85
4973 8624 2.866762 GCATACATGGGAACGTCTTCTC 59.133 50.000 0.00 0.00 0.00 2.87
4974 8625 3.458189 CATACATGGGAACGTCTTCTCC 58.542 50.000 0.00 0.00 0.00 3.71
4979 8630 3.516578 GGAACGTCTTCTCCCACTG 57.483 57.895 0.00 0.00 0.00 3.66
4980 8631 0.966920 GGAACGTCTTCTCCCACTGA 59.033 55.000 0.00 0.00 0.00 3.41
4981 8632 1.343465 GGAACGTCTTCTCCCACTGAA 59.657 52.381 0.00 0.00 0.00 3.02
4982 8633 2.224209 GGAACGTCTTCTCCCACTGAAA 60.224 50.000 0.00 0.00 0.00 2.69
4983 8634 2.821991 ACGTCTTCTCCCACTGAAAG 57.178 50.000 0.00 0.00 42.29 2.62
4984 8635 1.270358 ACGTCTTCTCCCACTGAAAGC 60.270 52.381 0.00 0.00 37.60 3.51
4985 8636 1.433534 GTCTTCTCCCACTGAAAGCG 58.566 55.000 0.00 0.00 37.60 4.68
4986 8637 0.320771 TCTTCTCCCACTGAAAGCGC 60.321 55.000 0.00 0.00 37.60 5.92
4987 8638 0.603707 CTTCTCCCACTGAAAGCGCA 60.604 55.000 11.47 0.00 37.60 6.09
4988 8639 0.036732 TTCTCCCACTGAAAGCGCAT 59.963 50.000 11.47 0.00 37.60 4.73
4989 8640 0.391661 TCTCCCACTGAAAGCGCATC 60.392 55.000 11.47 8.39 37.60 3.91
4990 8641 1.699656 CTCCCACTGAAAGCGCATCG 61.700 60.000 11.47 6.82 37.60 3.84
5001 8652 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
5002 8653 1.300620 CGCATCGCCGGAAATCCTA 60.301 57.895 5.05 0.00 0.00 2.94
5003 8654 0.878523 CGCATCGCCGGAAATCCTAA 60.879 55.000 5.05 0.00 0.00 2.69
5004 8655 1.523758 GCATCGCCGGAAATCCTAAT 58.476 50.000 5.05 0.00 0.00 1.73
5005 8656 2.695359 GCATCGCCGGAAATCCTAATA 58.305 47.619 5.05 0.00 0.00 0.98
5006 8657 3.270877 GCATCGCCGGAAATCCTAATAT 58.729 45.455 5.05 0.00 0.00 1.28
5007 8658 4.439057 GCATCGCCGGAAATCCTAATATA 58.561 43.478 5.05 0.00 0.00 0.86
5008 8659 4.873827 GCATCGCCGGAAATCCTAATATAA 59.126 41.667 5.05 0.00 0.00 0.98
5009 8660 5.353123 GCATCGCCGGAAATCCTAATATAAA 59.647 40.000 5.05 0.00 0.00 1.40
5010 8661 6.038271 GCATCGCCGGAAATCCTAATATAAAT 59.962 38.462 5.05 0.00 0.00 1.40
5011 8662 7.415206 GCATCGCCGGAAATCCTAATATAAATT 60.415 37.037 5.05 0.00 0.00 1.82
5012 8663 7.605410 TCGCCGGAAATCCTAATATAAATTC 57.395 36.000 5.05 0.00 0.00 2.17
5013 8664 7.162761 TCGCCGGAAATCCTAATATAAATTCA 58.837 34.615 5.05 0.00 0.00 2.57
5014 8665 7.333423 TCGCCGGAAATCCTAATATAAATTCAG 59.667 37.037 5.05 0.00 0.00 3.02
5015 8666 7.414098 CGCCGGAAATCCTAATATAAATTCAGG 60.414 40.741 5.05 0.00 34.93 3.86
5016 8667 7.610305 GCCGGAAATCCTAATATAAATTCAGGA 59.390 37.037 5.05 0.00 39.63 3.86
5017 8668 9.515226 CCGGAAATCCTAATATAAATTCAGGAA 57.485 33.333 0.00 0.00 38.82 3.36
5030 8681 4.900635 ATTCAGGAATAATGCGAACACC 57.099 40.909 0.00 0.00 0.00 4.16
5031 8682 3.342377 TCAGGAATAATGCGAACACCA 57.658 42.857 0.00 0.00 0.00 4.17
5032 8683 3.270027 TCAGGAATAATGCGAACACCAG 58.730 45.455 0.00 0.00 0.00 4.00
5033 8684 2.355756 CAGGAATAATGCGAACACCAGG 59.644 50.000 0.00 0.00 0.00 4.45
5034 8685 2.238646 AGGAATAATGCGAACACCAGGA 59.761 45.455 0.00 0.00 0.00 3.86
5035 8686 2.354821 GGAATAATGCGAACACCAGGAC 59.645 50.000 0.00 0.00 0.00 3.85
5036 8687 3.270877 GAATAATGCGAACACCAGGACT 58.729 45.455 0.00 0.00 0.00 3.85
5037 8688 2.851263 TAATGCGAACACCAGGACTT 57.149 45.000 0.00 0.00 0.00 3.01
5038 8689 1.238439 AATGCGAACACCAGGACTTG 58.762 50.000 0.00 0.00 0.00 3.16
5039 8690 0.396435 ATGCGAACACCAGGACTTGA 59.604 50.000 0.00 0.00 0.00 3.02
5040 8691 0.179234 TGCGAACACCAGGACTTGAA 59.821 50.000 0.00 0.00 0.00 2.69
5041 8692 0.586802 GCGAACACCAGGACTTGAAC 59.413 55.000 0.00 0.00 0.00 3.18
5042 8693 1.226746 CGAACACCAGGACTTGAACC 58.773 55.000 0.00 0.00 0.00 3.62
5043 8694 1.202651 CGAACACCAGGACTTGAACCT 60.203 52.381 0.00 0.00 38.40 3.50
5051 8702 2.839228 AGGACTTGAACCTGATAGGCT 58.161 47.619 0.00 0.00 39.63 4.58
5052 8703 2.503356 AGGACTTGAACCTGATAGGCTG 59.497 50.000 0.00 0.00 39.63 4.85
5053 8704 2.420687 GGACTTGAACCTGATAGGCTGG 60.421 54.545 0.00 0.00 39.63 4.85
5054 8705 1.561542 ACTTGAACCTGATAGGCTGGG 59.438 52.381 0.00 0.00 39.63 4.45
5055 8706 0.918983 TTGAACCTGATAGGCTGGGG 59.081 55.000 0.00 0.00 39.63 4.96
5056 8707 0.044092 TGAACCTGATAGGCTGGGGA 59.956 55.000 0.00 0.00 39.63 4.81
5057 8708 1.345422 TGAACCTGATAGGCTGGGGAT 60.345 52.381 0.00 0.00 39.63 3.85
5058 8709 2.090210 TGAACCTGATAGGCTGGGGATA 60.090 50.000 0.00 0.00 39.63 2.59
5059 8710 2.031495 ACCTGATAGGCTGGGGATAC 57.969 55.000 0.00 0.00 39.63 2.24
5060 8711 1.509961 ACCTGATAGGCTGGGGATACT 59.490 52.381 0.00 0.00 39.63 2.12
5061 8712 2.728013 ACCTGATAGGCTGGGGATACTA 59.272 50.000 0.00 0.00 39.63 1.82
5062 8713 3.341280 ACCTGATAGGCTGGGGATACTAT 59.659 47.826 0.00 0.00 39.63 2.12
5063 8714 4.202945 ACCTGATAGGCTGGGGATACTATT 60.203 45.833 0.00 0.00 39.63 1.73
5064 8715 4.163078 CCTGATAGGCTGGGGATACTATTG 59.837 50.000 0.00 0.00 32.31 1.90
5065 8716 4.763355 TGATAGGCTGGGGATACTATTGT 58.237 43.478 0.00 0.00 0.00 2.71
5066 8717 4.777896 TGATAGGCTGGGGATACTATTGTC 59.222 45.833 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.351706 TTTTGCTACCACCGTCCTTT 57.648 45.000 0.00 0.00 0.00 3.11
8 9 2.351706 TTTTTGCTACCACCGTCCTT 57.648 45.000 0.00 0.00 0.00 3.36
44 45 6.512578 GCCAAATTTTTGCTACCATCGTTTTT 60.513 34.615 2.85 0.00 36.86 1.94
127 129 2.212652 GCCTTTTGTTTTTGCTGGGAG 58.787 47.619 0.00 0.00 0.00 4.30
129 131 0.936600 CGCCTTTTGTTTTTGCTGGG 59.063 50.000 0.00 0.00 0.00 4.45
226 229 4.781616 TCGGGTGATGGGCCGGTA 62.782 66.667 1.90 0.00 0.00 4.02
343 384 3.441608 CCCCATCCCTTGCCCCAT 61.442 66.667 0.00 0.00 0.00 4.00
384 425 2.923035 CGACCACCTCCACCACCT 60.923 66.667 0.00 0.00 0.00 4.00
429 470 5.529581 TCTTTTCCTCCAAATCACAAACC 57.470 39.130 0.00 0.00 0.00 3.27
430 471 6.805713 TCTTCTTTTCCTCCAAATCACAAAC 58.194 36.000 0.00 0.00 0.00 2.93
431 472 7.069826 ACATCTTCTTTTCCTCCAAATCACAAA 59.930 33.333 0.00 0.00 0.00 2.83
432 473 6.550854 ACATCTTCTTTTCCTCCAAATCACAA 59.449 34.615 0.00 0.00 0.00 3.33
433 474 6.016024 CACATCTTCTTTTCCTCCAAATCACA 60.016 38.462 0.00 0.00 0.00 3.58
434 475 6.015940 ACACATCTTCTTTTCCTCCAAATCAC 60.016 38.462 0.00 0.00 0.00 3.06
435 476 6.016024 CACACATCTTCTTTTCCTCCAAATCA 60.016 38.462 0.00 0.00 0.00 2.57
446 487 2.948979 TCAACGCCACACATCTTCTTTT 59.051 40.909 0.00 0.00 0.00 2.27
451 2477 1.227999 CCGTCAACGCCACACATCTT 61.228 55.000 0.00 0.00 38.18 2.40
506 2532 3.000819 CGTCACTAGTGGGCCCCA 61.001 66.667 22.27 0.00 0.00 4.96
596 2623 3.672447 TCGACCGGCTGCGTGTTA 61.672 61.111 0.00 0.00 0.00 2.41
646 2674 9.931710 CGGTTTAGCAAAATTTAGTTAATTTCG 57.068 29.630 0.62 0.00 43.84 3.46
682 2710 8.578151 TGCTTTAACGGTTTAGTTAATTTCCAT 58.422 29.630 0.00 0.00 43.47 3.41
683 2711 7.938715 TGCTTTAACGGTTTAGTTAATTTCCA 58.061 30.769 0.00 0.00 43.47 3.53
699 2727 4.969816 AGGTTTCGATTGATGCTTTAACG 58.030 39.130 0.00 0.00 0.00 3.18
702 2730 8.958119 ATAGTAAGGTTTCGATTGATGCTTTA 57.042 30.769 0.00 0.00 0.00 1.85
751 2781 3.413327 TGCGAATAGTTTTGTTGCCCTA 58.587 40.909 0.00 0.00 0.00 3.53
754 2784 5.176590 TCATTTTGCGAATAGTTTTGTTGCC 59.823 36.000 0.00 0.00 0.00 4.52
755 2785 6.209129 TCATTTTGCGAATAGTTTTGTTGC 57.791 33.333 0.00 0.00 0.00 4.17
756 2786 8.486383 TCAATCATTTTGCGAATAGTTTTGTTG 58.514 29.630 0.00 0.00 0.00 3.33
806 2836 2.937149 GCGAAACTTCCAGATAACTCCC 59.063 50.000 0.00 0.00 0.00 4.30
812 2842 0.248012 TGCCGCGAAACTTCCAGATA 59.752 50.000 8.23 0.00 0.00 1.98
860 2894 8.980481 ATCTCTAGTTTCCTTTTGTTTCTGAA 57.020 30.769 0.00 0.00 0.00 3.02
861 2895 8.980481 AATCTCTAGTTTCCTTTTGTTTCTGA 57.020 30.769 0.00 0.00 0.00 3.27
874 2908 2.214467 CGCGCTCGAAATCTCTAGTTTC 59.786 50.000 5.56 0.00 38.10 2.78
909 2945 1.831290 GCCCCCAATTCCTTTCCTGTT 60.831 52.381 0.00 0.00 0.00 3.16
911 2947 0.252193 TGCCCCCAATTCCTTTCCTG 60.252 55.000 0.00 0.00 0.00 3.86
1239 3279 1.409064 GTGCGTACCTGGATGATGAGA 59.591 52.381 0.00 0.00 0.00 3.27
1333 3374 4.783055 TGTAGCCCTAGTCTAGAACAGAG 58.217 47.826 8.56 0.00 32.51 3.35
1340 3381 4.730966 TCAATCCTGTAGCCCTAGTCTAG 58.269 47.826 0.00 0.00 0.00 2.43
1374 3415 1.137513 GTACTGGGAACATATCGCGC 58.862 55.000 0.00 0.00 43.65 6.86
1388 3429 2.409715 CGACACAGCACAATCAGTACTG 59.590 50.000 17.17 17.17 45.41 2.74
1422 3463 1.663379 GGAAACCACCGCCAATAGCC 61.663 60.000 0.00 0.00 38.78 3.93
1423 3464 1.807226 GGAAACCACCGCCAATAGC 59.193 57.895 0.00 0.00 38.52 2.97
1454 3495 6.494146 CCCCTTTTTACAATACAAACCCTACA 59.506 38.462 0.00 0.00 0.00 2.74
1467 3508 3.501385 CCACTCCATCCCCCTTTTTACAA 60.501 47.826 0.00 0.00 0.00 2.41
1471 3512 0.252239 GCCACTCCATCCCCCTTTTT 60.252 55.000 0.00 0.00 0.00 1.94
1508 3550 1.672356 CACCCACACACTAGCCTGC 60.672 63.158 0.00 0.00 0.00 4.85
1509 3551 1.003355 CCACCCACACACTAGCCTG 60.003 63.158 0.00 0.00 0.00 4.85
1542 3584 9.357652 GCAGCTCTTCTTTATCTCATCTATTAG 57.642 37.037 0.00 0.00 0.00 1.73
1543 3585 8.864087 TGCAGCTCTTCTTTATCTCATCTATTA 58.136 33.333 0.00 0.00 0.00 0.98
1544 3586 7.733969 TGCAGCTCTTCTTTATCTCATCTATT 58.266 34.615 0.00 0.00 0.00 1.73
1545 3587 7.300556 TGCAGCTCTTCTTTATCTCATCTAT 57.699 36.000 0.00 0.00 0.00 1.98
1556 3598 4.412075 GGGCTGCAGCTCTTCTTT 57.588 55.556 35.82 0.00 38.82 2.52
1571 3613 7.276438 GCAATTTAGTTCTTTCAATGCTTAGGG 59.724 37.037 0.00 0.00 0.00 3.53
1713 3758 1.191535 CCATCGTGTCAGGAAGGGTA 58.808 55.000 8.60 0.00 0.00 3.69
1769 4983 2.057137 TAAGTTGCCATCAGCCCATC 57.943 50.000 0.00 0.00 42.71 3.51
1770 4984 2.102578 GTTAAGTTGCCATCAGCCCAT 58.897 47.619 0.00 0.00 42.71 4.00
1771 4985 1.202989 TGTTAAGTTGCCATCAGCCCA 60.203 47.619 0.00 0.00 42.71 5.36
1772 4986 1.474077 CTGTTAAGTTGCCATCAGCCC 59.526 52.381 0.00 0.00 42.71 5.19
1773 4987 1.474077 CCTGTTAAGTTGCCATCAGCC 59.526 52.381 0.00 0.00 42.71 4.85
1774 4988 1.474077 CCCTGTTAAGTTGCCATCAGC 59.526 52.381 0.00 0.00 44.14 4.26
1775 4989 3.071874 TCCCTGTTAAGTTGCCATCAG 57.928 47.619 0.00 0.00 0.00 2.90
1776 4990 3.737559 ATCCCTGTTAAGTTGCCATCA 57.262 42.857 0.00 0.00 0.00 3.07
1980 5199 1.470979 CCTGGTCGGTGATTAGGAACG 60.471 57.143 0.00 0.00 0.00 3.95
2140 5361 7.479150 ACTAGAACGCAGACTTATAACTTACC 58.521 38.462 0.00 0.00 0.00 2.85
2141 5362 7.643371 GGACTAGAACGCAGACTTATAACTTAC 59.357 40.741 0.00 0.00 0.00 2.34
2173 5394 2.878580 CAAGCAGAGCAGACTACAGAG 58.121 52.381 0.00 0.00 0.00 3.35
2194 5415 5.359860 ACAACCCAAAAGTAGAAAACAGAGG 59.640 40.000 0.00 0.00 0.00 3.69
2207 5428 5.878332 AAGAAAGCAAAACAACCCAAAAG 57.122 34.783 0.00 0.00 0.00 2.27
2268 5608 9.399797 TCTACTGATTTAAAATGCTGATCACAT 57.600 29.630 0.00 0.00 0.00 3.21
2313 5653 7.641411 CGGCTGTGAATATTGTCTTGAAATAAG 59.359 37.037 0.00 0.00 0.00 1.73
2537 5879 9.223099 TGATTGCTAACTACATCAATCATATGG 57.777 33.333 11.14 0.00 45.47 2.74
2712 6054 2.046892 CCAGAAGAGGGTGCACCG 60.047 66.667 29.08 13.42 46.96 4.94
2749 6091 2.935238 GCTCACTCCGCATAGTTTTCCA 60.935 50.000 0.00 0.00 0.00 3.53
2757 6099 2.407616 CGTCGCTCACTCCGCATA 59.592 61.111 0.00 0.00 0.00 3.14
2770 6112 4.753662 TCCTCCCCTCCACCGTCG 62.754 72.222 0.00 0.00 0.00 5.12
2811 6370 2.247358 TCTTGGGCCCATTTTTCAGTC 58.753 47.619 29.23 0.00 0.00 3.51
2844 6403 5.588648 CAGACTCAGAAACCCTAAAACACAA 59.411 40.000 0.00 0.00 0.00 3.33
2921 6481 0.460987 CAACTCTAGCAGGGCCTTCG 60.461 60.000 1.32 0.00 0.00 3.79
3106 6667 6.209192 TCATTCTGAATCTGGCAAAGCTTTAA 59.791 34.615 12.25 0.00 0.00 1.52
3108 6669 4.525487 TCATTCTGAATCTGGCAAAGCTTT 59.475 37.500 5.69 5.69 0.00 3.51
3119 6681 6.011122 AGGCCAACTAATCATTCTGAATCT 57.989 37.500 5.01 0.00 0.00 2.40
3586 7148 3.409570 CATCCCATGCAGGAAGACATAG 58.590 50.000 0.00 0.00 40.04 2.23
3664 7226 2.666098 AATGAAGGACGTCCCGGGG 61.666 63.158 30.82 6.77 40.87 5.73
3745 7307 2.456287 GAAGAGCAAGCGGGTCAGGT 62.456 60.000 12.10 0.00 46.51 4.00
3748 7310 0.973632 TAAGAAGAGCAAGCGGGTCA 59.026 50.000 12.10 0.00 46.51 4.02
3766 7328 4.704540 ACAACATTTGAAATGCCCGAGATA 59.295 37.500 17.19 0.00 0.00 1.98
3779 7341 1.336440 CGGCCAACTCACAACATTTGA 59.664 47.619 2.24 0.00 0.00 2.69
3862 7424 2.263852 CCGCTCTCTCTTGCTGCA 59.736 61.111 0.00 0.00 0.00 4.41
3934 7496 4.663791 TGCTGTTGCACATCTCACAGATG 61.664 47.826 16.27 11.27 43.92 2.90
3961 7523 0.533308 TGGGAAAAACACGGTCCTCG 60.533 55.000 0.00 0.00 45.88 4.63
4068 7630 7.072454 ACTGGTAATGGTGATCTACATTATGGT 59.928 37.037 18.83 15.49 40.46 3.55
4145 7707 2.673368 CAGCGTAGAATCCTGGTCAAAC 59.327 50.000 0.00 0.00 0.00 2.93
4150 7712 3.460857 GATTCAGCGTAGAATCCTGGT 57.539 47.619 16.34 0.00 45.12 4.00
4162 7724 0.027194 CGCAATGAGTGGATTCAGCG 59.973 55.000 0.00 0.00 36.10 5.18
4219 7781 4.020039 TCAAAGTACTCGGGCCTTCAAATA 60.020 41.667 0.84 0.00 0.00 1.40
4302 7876 1.945819 GCGTCCTGGTGATGTTGTGAT 60.946 52.381 0.00 0.00 32.20 3.06
4303 7877 0.602638 GCGTCCTGGTGATGTTGTGA 60.603 55.000 0.00 0.00 32.20 3.58
4304 7878 1.868997 GCGTCCTGGTGATGTTGTG 59.131 57.895 0.00 0.00 32.20 3.33
4322 7896 4.092968 GTGGTGTTTGAACTCTATAAGCCG 59.907 45.833 0.00 0.00 0.00 5.52
4323 7897 5.001232 TGTGGTGTTTGAACTCTATAAGCC 58.999 41.667 0.00 0.00 0.00 4.35
4324 7898 5.106673 GGTGTGGTGTTTGAACTCTATAAGC 60.107 44.000 0.00 0.00 0.00 3.09
4325 7899 5.995282 TGGTGTGGTGTTTGAACTCTATAAG 59.005 40.000 0.00 0.00 0.00 1.73
4344 7918 4.973168 AGAGTTGATAATGTGTGTGGTGT 58.027 39.130 0.00 0.00 0.00 4.16
4350 7924 4.686091 ACGTGTGAGAGTTGATAATGTGTG 59.314 41.667 0.00 0.00 0.00 3.82
4356 7930 7.117236 GGAAAATGTACGTGTGAGAGTTGATAA 59.883 37.037 0.00 0.00 0.00 1.75
4361 7935 4.699637 TGGAAAATGTACGTGTGAGAGTT 58.300 39.130 0.00 0.00 0.00 3.01
4368 7942 1.073284 AGCCCTGGAAAATGTACGTGT 59.927 47.619 0.00 0.00 0.00 4.49
4372 7997 5.715434 TTTTACAGCCCTGGAAAATGTAC 57.285 39.130 13.05 0.00 45.51 2.90
4418 8053 1.730064 TCCTGAAACTAAATGCGCGTC 59.270 47.619 8.43 0.00 0.00 5.19
4420 8055 1.062587 CCTCCTGAAACTAAATGCGCG 59.937 52.381 0.00 0.00 0.00 6.86
4423 8058 1.401905 CGCCCTCCTGAAACTAAATGC 59.598 52.381 0.00 0.00 0.00 3.56
4448 8083 0.034337 TAGTCACGGTTTCAGCCACC 59.966 55.000 0.00 0.00 0.00 4.61
4465 8100 7.701809 TTTTGCCTTTTCGGTTAAAACATAG 57.298 32.000 0.00 0.00 33.49 2.23
4467 8102 6.986904 TTTTTGCCTTTTCGGTTAAAACAT 57.013 29.167 0.00 0.00 33.64 2.71
4502 8139 4.279420 AGGTGAAAAGAGCAAATCTGAACC 59.721 41.667 0.00 0.00 38.67 3.62
4510 8147 3.096092 ACCAACAGGTGAAAAGAGCAAA 58.904 40.909 0.00 0.00 33.38 3.68
4541 8178 1.064979 ACAACTTTGGGTCGTCACCTT 60.065 47.619 0.00 0.00 43.22 3.50
4543 8180 0.942252 GACAACTTTGGGTCGTCACC 59.058 55.000 0.00 0.00 42.90 4.02
4554 8191 1.329599 GAAACGCTCGGTGACAACTTT 59.670 47.619 0.00 0.00 0.00 2.66
4589 8226 1.893919 GCCTCTCTCACCCCACAGTC 61.894 65.000 0.00 0.00 0.00 3.51
4590 8227 1.915769 GCCTCTCTCACCCCACAGT 60.916 63.158 0.00 0.00 0.00 3.55
4591 8228 1.611851 AGCCTCTCTCACCCCACAG 60.612 63.158 0.00 0.00 0.00 3.66
4592 8229 1.610673 GAGCCTCTCTCACCCCACA 60.611 63.158 0.00 0.00 41.51 4.17
4593 8230 2.716017 CGAGCCTCTCTCACCCCAC 61.716 68.421 0.00 0.00 41.98 4.61
4682 8321 1.089112 CATCGCTCCAGCATCACAAA 58.911 50.000 0.00 0.00 42.21 2.83
4690 8329 3.831715 AAGTTTTTACATCGCTCCAGC 57.168 42.857 0.00 0.00 37.78 4.85
4705 8344 2.630580 TGGGCGAGGCAAATAAAAGTTT 59.369 40.909 0.00 0.00 0.00 2.66
4835 8485 5.524971 ACGAGACGGTCCAATGATAATTA 57.475 39.130 4.14 0.00 0.00 1.40
4848 8498 2.320745 AACCAAAGAAACGAGACGGT 57.679 45.000 0.00 0.00 0.00 4.83
4851 8501 6.851330 CACTTGATTAACCAAAGAAACGAGAC 59.149 38.462 0.00 0.00 0.00 3.36
4863 8513 3.142951 CCGGTGTTCACTTGATTAACCA 58.857 45.455 0.00 0.00 0.00 3.67
4889 8540 4.665833 AAAACTTTTACAGCCTTGGGAC 57.334 40.909 0.00 0.00 0.00 4.46
4912 8563 3.884169 GCGTCTGCACTGATGTTAAAAA 58.116 40.909 0.00 0.00 42.15 1.94
4913 8564 3.536158 GCGTCTGCACTGATGTTAAAA 57.464 42.857 0.00 0.00 42.15 1.52
4926 8577 2.167219 TATGAGCGCTTGCGTCTGC 61.167 57.895 13.26 0.00 45.69 4.26
4927 8578 1.078201 TGTATGAGCGCTTGCGTCTG 61.078 55.000 13.26 0.00 45.69 3.51
4928 8579 0.179100 ATGTATGAGCGCTTGCGTCT 60.179 50.000 13.26 13.17 45.69 4.18
4929 8580 1.487482 TATGTATGAGCGCTTGCGTC 58.513 50.000 13.26 12.36 45.69 5.19
4930 8581 1.794701 CATATGTATGAGCGCTTGCGT 59.205 47.619 13.26 3.97 45.69 5.24
4931 8582 1.463034 GCATATGTATGAGCGCTTGCG 60.463 52.381 13.26 10.90 37.67 4.85
4932 8583 1.463034 CGCATATGTATGAGCGCTTGC 60.463 52.381 13.26 14.20 43.80 4.01
4933 8584 2.498961 CGCATATGTATGAGCGCTTG 57.501 50.000 13.26 3.84 43.80 4.01
4939 8590 4.271776 CCCATGTATGCGCATATGTATGAG 59.728 45.833 31.79 23.74 35.75 2.90
4940 8591 4.081198 TCCCATGTATGCGCATATGTATGA 60.081 41.667 31.79 23.95 35.75 2.15
4941 8592 4.190772 TCCCATGTATGCGCATATGTATG 58.809 43.478 31.14 28.91 36.78 2.39
4942 8593 4.486125 TCCCATGTATGCGCATATGTAT 57.514 40.909 31.14 21.82 0.00 2.29
4943 8594 3.971245 TCCCATGTATGCGCATATGTA 57.029 42.857 31.14 20.69 0.00 2.29
4944 8595 2.813754 GTTCCCATGTATGCGCATATGT 59.186 45.455 31.14 20.06 0.00 2.29
4945 8596 2.159667 CGTTCCCATGTATGCGCATATG 60.160 50.000 31.14 25.70 0.00 1.78
4946 8597 2.076100 CGTTCCCATGTATGCGCATAT 58.924 47.619 31.14 16.30 0.00 1.78
4947 8598 1.202592 ACGTTCCCATGTATGCGCATA 60.203 47.619 25.78 25.78 0.00 3.14
4948 8599 0.463654 ACGTTCCCATGTATGCGCAT 60.464 50.000 28.23 28.23 0.00 4.73
4949 8600 1.078778 ACGTTCCCATGTATGCGCA 60.079 52.632 14.96 14.96 0.00 6.09
4950 8601 0.810031 AGACGTTCCCATGTATGCGC 60.810 55.000 0.00 0.00 0.00 6.09
4951 8602 1.593006 GAAGACGTTCCCATGTATGCG 59.407 52.381 0.00 0.00 0.00 4.73
4952 8603 2.866762 GAGAAGACGTTCCCATGTATGC 59.133 50.000 0.00 0.00 32.48 3.14
4953 8604 3.458189 GGAGAAGACGTTCCCATGTATG 58.542 50.000 0.00 0.00 32.48 2.39
4954 8605 3.821421 GGAGAAGACGTTCCCATGTAT 57.179 47.619 0.00 0.00 32.48 2.29
4961 8612 0.966920 TCAGTGGGAGAAGACGTTCC 59.033 55.000 0.00 0.00 32.48 3.62
4962 8613 2.814280 TTCAGTGGGAGAAGACGTTC 57.186 50.000 0.00 0.00 0.00 3.95
4963 8614 2.807108 GCTTTCAGTGGGAGAAGACGTT 60.807 50.000 0.00 0.00 0.00 3.99
4964 8615 1.270358 GCTTTCAGTGGGAGAAGACGT 60.270 52.381 0.00 0.00 0.00 4.34
4965 8616 1.433534 GCTTTCAGTGGGAGAAGACG 58.566 55.000 0.00 0.00 0.00 4.18
4966 8617 1.433534 CGCTTTCAGTGGGAGAAGAC 58.566 55.000 0.00 0.00 0.00 3.01
4967 8618 0.320771 GCGCTTTCAGTGGGAGAAGA 60.321 55.000 0.00 0.00 0.00 2.87
4968 8619 0.603707 TGCGCTTTCAGTGGGAGAAG 60.604 55.000 9.73 0.00 0.00 2.85
4969 8620 0.036732 ATGCGCTTTCAGTGGGAGAA 59.963 50.000 9.73 0.00 0.00 2.87
4970 8621 0.391661 GATGCGCTTTCAGTGGGAGA 60.392 55.000 9.73 0.00 0.00 3.71
4971 8622 1.699656 CGATGCGCTTTCAGTGGGAG 61.700 60.000 9.73 0.00 0.00 4.30
4972 8623 1.741401 CGATGCGCTTTCAGTGGGA 60.741 57.895 9.73 0.00 0.00 4.37
4973 8624 2.787249 CGATGCGCTTTCAGTGGG 59.213 61.111 9.73 0.00 0.00 4.61
4984 8635 0.878523 TTAGGATTTCCGGCGATGCG 60.879 55.000 9.30 0.00 42.08 4.73
4985 8636 1.523758 ATTAGGATTTCCGGCGATGC 58.476 50.000 9.30 0.00 42.08 3.91
4986 8637 6.978343 TTTATATTAGGATTTCCGGCGATG 57.022 37.500 9.30 0.00 42.08 3.84
4987 8638 7.827236 TGAATTTATATTAGGATTTCCGGCGAT 59.173 33.333 9.30 0.00 42.08 4.58
4988 8639 7.162761 TGAATTTATATTAGGATTTCCGGCGA 58.837 34.615 9.30 0.00 42.08 5.54
4989 8640 7.372451 TGAATTTATATTAGGATTTCCGGCG 57.628 36.000 0.00 0.00 42.08 6.46
4990 8641 7.610305 TCCTGAATTTATATTAGGATTTCCGGC 59.390 37.037 0.00 0.00 42.08 6.13
4991 8642 9.515226 TTCCTGAATTTATATTAGGATTTCCGG 57.485 33.333 0.00 0.00 42.08 5.14
5004 8655 8.564574 GGTGTTCGCATTATTCCTGAATTTATA 58.435 33.333 0.00 0.00 32.50 0.98
5005 8656 7.068103 TGGTGTTCGCATTATTCCTGAATTTAT 59.932 33.333 0.00 0.00 32.50 1.40
5006 8657 6.375736 TGGTGTTCGCATTATTCCTGAATTTA 59.624 34.615 0.00 0.00 32.50 1.40
5007 8658 5.184864 TGGTGTTCGCATTATTCCTGAATTT 59.815 36.000 0.00 0.00 32.50 1.82
5008 8659 4.704540 TGGTGTTCGCATTATTCCTGAATT 59.295 37.500 0.00 0.00 32.50 2.17
5009 8660 4.269183 TGGTGTTCGCATTATTCCTGAAT 58.731 39.130 0.00 0.00 34.93 2.57
5010 8661 3.680490 TGGTGTTCGCATTATTCCTGAA 58.320 40.909 0.00 0.00 0.00 3.02
5011 8662 3.270027 CTGGTGTTCGCATTATTCCTGA 58.730 45.455 0.00 0.00 0.00 3.86
5012 8663 2.355756 CCTGGTGTTCGCATTATTCCTG 59.644 50.000 0.00 0.00 0.00 3.86
5013 8664 2.238646 TCCTGGTGTTCGCATTATTCCT 59.761 45.455 0.00 0.00 0.00 3.36
5014 8665 2.354821 GTCCTGGTGTTCGCATTATTCC 59.645 50.000 0.00 0.00 0.00 3.01
5015 8666 3.270877 AGTCCTGGTGTTCGCATTATTC 58.729 45.455 0.00 0.00 0.00 1.75
5016 8667 3.350219 AGTCCTGGTGTTCGCATTATT 57.650 42.857 0.00 0.00 0.00 1.40
5017 8668 3.009723 CAAGTCCTGGTGTTCGCATTAT 58.990 45.455 0.00 0.00 0.00 1.28
5018 8669 2.037902 TCAAGTCCTGGTGTTCGCATTA 59.962 45.455 0.00 0.00 0.00 1.90
5019 8670 1.202758 TCAAGTCCTGGTGTTCGCATT 60.203 47.619 0.00 0.00 0.00 3.56
5020 8671 0.396435 TCAAGTCCTGGTGTTCGCAT 59.604 50.000 0.00 0.00 0.00 4.73
5021 8672 0.179234 TTCAAGTCCTGGTGTTCGCA 59.821 50.000 0.00 0.00 0.00 5.10
5022 8673 0.586802 GTTCAAGTCCTGGTGTTCGC 59.413 55.000 0.00 0.00 0.00 4.70
5023 8674 1.202651 AGGTTCAAGTCCTGGTGTTCG 60.203 52.381 0.00 0.00 33.62 3.95
5024 8675 2.222027 CAGGTTCAAGTCCTGGTGTTC 58.778 52.381 4.27 0.00 46.03 3.18
5025 8676 2.348411 CAGGTTCAAGTCCTGGTGTT 57.652 50.000 4.27 0.00 46.03 3.32
5031 8682 2.503356 CAGCCTATCAGGTTCAAGTCCT 59.497 50.000 0.00 0.00 37.80 3.85
5032 8683 2.420687 CCAGCCTATCAGGTTCAAGTCC 60.421 54.545 0.00 0.00 37.80 3.85
5033 8684 2.420687 CCCAGCCTATCAGGTTCAAGTC 60.421 54.545 0.00 0.00 37.80 3.01
5034 8685 1.561542 CCCAGCCTATCAGGTTCAAGT 59.438 52.381 0.00 0.00 37.80 3.16
5035 8686 1.133976 CCCCAGCCTATCAGGTTCAAG 60.134 57.143 0.00 0.00 37.80 3.02
5036 8687 0.918983 CCCCAGCCTATCAGGTTCAA 59.081 55.000 0.00 0.00 37.80 2.69
5037 8688 0.044092 TCCCCAGCCTATCAGGTTCA 59.956 55.000 0.00 0.00 37.80 3.18
5038 8689 1.439543 ATCCCCAGCCTATCAGGTTC 58.560 55.000 0.00 0.00 37.80 3.62
5039 8690 2.089925 AGTATCCCCAGCCTATCAGGTT 60.090 50.000 0.00 0.00 37.80 3.50
5040 8691 1.509961 AGTATCCCCAGCCTATCAGGT 59.490 52.381 0.00 0.00 37.80 4.00
5041 8692 2.334006 AGTATCCCCAGCCTATCAGG 57.666 55.000 0.00 0.00 38.80 3.86
5042 8693 4.780021 ACAATAGTATCCCCAGCCTATCAG 59.220 45.833 0.00 0.00 0.00 2.90
5043 8694 4.763355 ACAATAGTATCCCCAGCCTATCA 58.237 43.478 0.00 0.00 0.00 2.15
5044 8695 5.346181 GACAATAGTATCCCCAGCCTATC 57.654 47.826 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.