Multiple sequence alignment - TraesCS5B01G006900

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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 TraesCS5B01G006900 chr5B 100.000 6261 0 0 1 6261 8170451 8176711 0.000000e+00 11562.0
1 TraesCS5B01G006900 chr5B 97.829 2533 37 7 984 3502 33271567 33269039 0.000000e+00 4357.0
2 TraesCS5B01G006900 chr5B 96.463 1866 50 8 1637 3502 32668391 32666542 0.000000e+00 3066.0
3 TraesCS5B01G006900 chr5B 98.165 763 12 1 4831 5593 33260006 33259246 0.000000e+00 1330.0
4 TraesCS5B01G006900 chr5B 96.656 598 18 2 4831 5428 32653669 32653074 0.000000e+00 992.0
5 TraesCS5B01G006900 chr5B 95.695 604 26 0 3517 4120 33261800 33261197 0.000000e+00 972.0
6 TraesCS5B01G006900 chr5B 78.995 1433 255 36 2097 3501 8087725 8089139 0.000000e+00 937.0
7 TraesCS5B01G006900 chr5B 97.191 534 12 3 5729 6261 576073633 576074164 0.000000e+00 900.0
8 TraesCS5B01G006900 chr5B 94.539 531 25 4 5733 6261 694726670 694726142 0.000000e+00 817.0
9 TraesCS5B01G006900 chr5B 93.657 536 26 8 5729 6261 665900861 665901391 0.000000e+00 795.0
10 TraesCS5B01G006900 chr5B 78.922 816 114 32 4831 5634 7936644 7935875 9.370000e-138 501.0
11 TraesCS5B01G006900 chr5B 76.769 947 164 37 929 1861 8086635 8087539 4.390000e-131 479.0
12 TraesCS5B01G006900 chr5B 91.946 298 24 0 4831 5128 338822268 338821971 9.710000e-113 418.0
13 TraesCS5B01G006900 chr5B 91.513 271 22 1 4300 4570 492681705 492681974 7.670000e-99 372.0
14 TraesCS5B01G006900 chr5B 94.931 217 10 1 602 817 32668624 32668408 7.770000e-89 339.0
15 TraesCS5B01G006900 chr5B 92.245 245 8 5 4121 4355 33260310 33260067 2.800000e-88 337.0
16 TraesCS5B01G006900 chr5B 91.964 224 13 4 4620 4841 32653918 32653698 6.100000e-80 309.0
17 TraesCS5B01G006900 chr5B 97.159 176 5 0 4135 4310 32661314 32661139 1.320000e-76 298.0
18 TraesCS5B01G006900 chr5B 81.737 334 42 10 4831 5160 8089842 8090160 1.730000e-65 261.0
19 TraesCS5B01G006900 chr5B 76.618 479 102 8 2255 2729 32565324 32565796 8.050000e-64 255.0
20 TraesCS5B01G006900 chr5B 95.455 132 6 0 602 733 33272162 33272031 1.770000e-50 211.0
21 TraesCS5B01G006900 chr5B 85.263 95 12 1 4636 4728 37374429 37374523 5.170000e-16 97.1
22 TraesCS5B01G006900 chr5B 97.826 46 1 0 5689 5734 7935856 7935811 5.200000e-11 80.5
23 TraesCS5B01G006900 chr5B 94.000 50 3 0 4567 4616 32661141 32661092 6.730000e-10 76.8
24 TraesCS5B01G006900 chr5B 100.000 29 0 0 670 698 33272184 33272156 3.000000e-03 54.7
25 TraesCS5B01G006900 chr5A 95.158 2375 79 10 1135 3502 6195445 6197790 0.000000e+00 3716.0
26 TraesCS5B01G006900 chr5A 92.494 826 42 10 4832 5649 5718657 5719470 0.000000e+00 1164.0
27 TraesCS5B01G006900 chr5A 79.117 1427 256 31 2098 3501 5992089 5993496 0.000000e+00 946.0
28 TraesCS5B01G006900 chr5A 79.515 908 153 20 2606 3501 4983992 4983106 3.210000e-172 616.0
29 TraesCS5B01G006900 chr5A 85.714 546 66 8 2882 3427 5702854 5703387 3.280000e-157 566.0
30 TraesCS5B01G006900 chr5A 80.915 634 80 19 4831 5453 4977014 4976411 4.420000e-126 462.0
31 TraesCS5B01G006900 chr5A 90.114 263 22 3 4570 4829 5718355 5718616 7.770000e-89 339.0
32 TraesCS5B01G006900 chr5A 81.138 334 45 9 4831 5160 5994193 5994512 1.040000e-62 252.0
33 TraesCS5B01G006900 chr5A 82.573 241 21 10 895 1128 5700707 5700933 6.410000e-45 193.0
34 TraesCS5B01G006900 chr5A 93.243 74 5 0 4656 4729 5994052 5994125 6.640000e-20 110.0
35 TraesCS5B01G006900 chr5A 97.143 35 1 0 672 706 562425901 562425935 6.780000e-05 60.2
36 TraesCS5B01G006900 chr5D 95.249 905 37 5 4831 5734 7591529 7590630 0.000000e+00 1428.0
37 TraesCS5B01G006900 chr5D 79.453 1426 252 30 2098 3501 7748226 7746820 0.000000e+00 972.0
38 TraesCS5B01G006900 chr5D 83.984 1024 125 17 2304 3322 7493047 7494036 0.000000e+00 946.0
39 TraesCS5B01G006900 chr5D 86.081 546 64 8 2882 3427 7600842 7600309 1.510000e-160 577.0
40 TraesCS5B01G006900 chr5D 95.437 263 12 0 4309 4571 533643423 533643161 2.700000e-113 420.0
41 TraesCS5B01G006900 chr5D 92.620 271 18 1 4307 4575 203290365 203290095 7.610000e-104 388.0
42 TraesCS5B01G006900 chr5D 81.791 335 41 10 4831 5160 7746120 7745801 4.810000e-66 263.0
43 TraesCS5B01G006900 chr5D 86.792 159 17 3 5212 5369 7499883 7500038 2.320000e-39 174.0
44 TraesCS5B01G006900 chr5D 95.000 80 3 1 3364 3443 7494046 7494124 2.370000e-24 124.0
45 TraesCS5B01G006900 chr5D 97.674 43 1 0 5692 5734 7735580 7735538 2.420000e-09 75.0
46 TraesCS5B01G006900 chr5D 76.027 146 31 4 2254 2397 7952042 7951899 8.710000e-09 73.1
47 TraesCS5B01G006900 chr1B 94.215 605 30 2 1 604 269218859 269218259 0.000000e+00 918.0
48 TraesCS5B01G006900 chr1B 94.050 605 31 2 1 604 25227708 25227108 0.000000e+00 913.0
49 TraesCS5B01G006900 chr1B 93.884 605 31 3 1 604 390272524 390273123 0.000000e+00 907.0
50 TraesCS5B01G006900 chr1B 93.884 605 32 2 1 604 644278244 644278844 0.000000e+00 907.0
51 TraesCS5B01G006900 chr2B 94.050 605 30 3 1 604 40323789 40324388 0.000000e+00 913.0
52 TraesCS5B01G006900 chr2B 93.740 607 32 3 1 606 225398937 225398336 0.000000e+00 905.0
53 TraesCS5B01G006900 chr2B 94.340 530 29 1 5733 6261 752878108 752878637 0.000000e+00 811.0
54 TraesCS5B01G006900 chr2B 91.304 276 21 3 4309 4583 420446665 420446938 2.130000e-99 374.0
55 TraesCS5B01G006900 chr6B 93.750 608 32 3 1 606 21063449 21064052 0.000000e+00 907.0
56 TraesCS5B01G006900 chr6B 92.720 261 19 0 4310 4570 676298205 676297945 1.650000e-100 377.0
57 TraesCS5B01G006900 chr4A 93.894 606 30 4 1 604 21229163 21229763 0.000000e+00 907.0
58 TraesCS5B01G006900 chr4A 97.191 534 12 3 5729 6261 661331288 661331819 0.000000e+00 900.0
59 TraesCS5B01G006900 chr4A 93.482 537 32 3 5726 6261 621758252 621757718 0.000000e+00 795.0
60 TraesCS5B01G006900 chr4A 87.522 569 64 5 3517 4078 677274649 677274081 0.000000e+00 651.0
61 TraesCS5B01G006900 chr4A 83.478 115 19 0 3198 3312 17846087 17845973 2.390000e-19 108.0
62 TraesCS5B01G006900 chr4A 97.368 38 1 0 667 704 528560559 528560596 1.460000e-06 65.8
63 TraesCS5B01G006900 chr3A 93.740 607 33 2 1 606 735598933 735599535 0.000000e+00 905.0
64 TraesCS5B01G006900 chr1A 97.026 538 13 3 5726 6261 556812914 556812378 0.000000e+00 902.0
65 TraesCS5B01G006900 chr1A 87.209 602 69 3 3517 4117 238080796 238081390 0.000000e+00 678.0
66 TraesCS5B01G006900 chr4B 96.604 530 17 1 5733 6261 647408439 647407910 0.000000e+00 878.0
67 TraesCS5B01G006900 chrUn 94.333 547 22 6 5722 6261 85702450 85702994 0.000000e+00 830.0
68 TraesCS5B01G006900 chrUn 85.788 584 64 10 3535 4111 27624567 27625138 8.980000e-168 601.0
69 TraesCS5B01G006900 chrUn 81.905 525 82 7 3597 4114 226735076 226734558 1.250000e-116 431.0
70 TraesCS5B01G006900 chrUn 81.609 522 83 7 3600 4114 274611069 274610554 2.700000e-113 420.0
71 TraesCS5B01G006900 chr6D 80.693 606 99 17 3517 4110 322712626 322712027 7.400000e-124 455.0
72 TraesCS5B01G006900 chr3D 79.085 612 110 15 3517 4117 69825357 69825961 7.560000e-109 405.0
73 TraesCS5B01G006900 chr3D 92.424 264 18 2 4307 4570 152235480 152235219 5.930000e-100 375.0
74 TraesCS5B01G006900 chr3B 80.762 525 88 7 3597 4114 803404063 803404581 1.260000e-106 398.0
75 TraesCS5B01G006900 chr3B 90.071 141 14 0 3517 3657 682811786 682811926 3.850000e-42 183.0
76 TraesCS5B01G006900 chr2D 92.701 274 19 1 4308 4580 170533477 170533750 1.640000e-105 394.0
77 TraesCS5B01G006900 chr2A 92.857 266 18 1 4306 4571 696827276 696827012 9.850000e-103 385.0
78 TraesCS5B01G006900 chr7D 92.424 264 20 0 4307 4570 552476168 552475905 1.650000e-100 377.0


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 TraesCS5B01G006900 chr5B 8170451 8176711 6260 False 11562.000000 11562 100.000000 1 6261 1 chr5B.!!$F1 6260
1 TraesCS5B01G006900 chr5B 32666542 32668624 2082 True 1702.500000 3066 95.697000 602 3502 2 chr5B.!!$R6 2900
2 TraesCS5B01G006900 chr5B 33269039 33272184 3145 True 1540.900000 4357 97.761333 602 3502 3 chr5B.!!$R8 2900
3 TraesCS5B01G006900 chr5B 576073633 576074164 531 False 900.000000 900 97.191000 5729 6261 1 chr5B.!!$F5 532
4 TraesCS5B01G006900 chr5B 33259246 33261800 2554 True 879.666667 1330 95.368333 3517 5593 3 chr5B.!!$R7 2076
5 TraesCS5B01G006900 chr5B 694726142 694726670 528 True 817.000000 817 94.539000 5733 6261 1 chr5B.!!$R2 528
6 TraesCS5B01G006900 chr5B 665900861 665901391 530 False 795.000000 795 93.657000 5729 6261 1 chr5B.!!$F6 532
7 TraesCS5B01G006900 chr5B 32653074 32653918 844 True 650.500000 992 94.310000 4620 5428 2 chr5B.!!$R4 808
8 TraesCS5B01G006900 chr5B 8086635 8090160 3525 False 559.000000 937 79.167000 929 5160 3 chr5B.!!$F7 4231
9 TraesCS5B01G006900 chr5B 7935811 7936644 833 True 290.750000 501 88.374000 4831 5734 2 chr5B.!!$R3 903
10 TraesCS5B01G006900 chr5A 6195445 6197790 2345 False 3716.000000 3716 95.158000 1135 3502 1 chr5A.!!$F1 2367
11 TraesCS5B01G006900 chr5A 5718355 5719470 1115 False 751.500000 1164 91.304000 4570 5649 2 chr5A.!!$F4 1079
12 TraesCS5B01G006900 chr5A 4983106 4983992 886 True 616.000000 616 79.515000 2606 3501 1 chr5A.!!$R2 895
13 TraesCS5B01G006900 chr5A 4976411 4977014 603 True 462.000000 462 80.915000 4831 5453 1 chr5A.!!$R1 622
14 TraesCS5B01G006900 chr5A 5992089 5994512 2423 False 436.000000 946 84.499333 2098 5160 3 chr5A.!!$F5 3062
15 TraesCS5B01G006900 chr5A 5700707 5703387 2680 False 379.500000 566 84.143500 895 3427 2 chr5A.!!$F3 2532
16 TraesCS5B01G006900 chr5D 7590630 7591529 899 True 1428.000000 1428 95.249000 4831 5734 1 chr5D.!!$R1 903
17 TraesCS5B01G006900 chr5D 7745801 7748226 2425 True 617.500000 972 80.622000 2098 5160 2 chr5D.!!$R7 3062
18 TraesCS5B01G006900 chr5D 7600309 7600842 533 True 577.000000 577 86.081000 2882 3427 1 chr5D.!!$R2 545
19 TraesCS5B01G006900 chr5D 7493047 7494124 1077 False 535.000000 946 89.492000 2304 3443 2 chr5D.!!$F2 1139
20 TraesCS5B01G006900 chr1B 269218259 269218859 600 True 918.000000 918 94.215000 1 604 1 chr1B.!!$R2 603
21 TraesCS5B01G006900 chr1B 25227108 25227708 600 True 913.000000 913 94.050000 1 604 1 chr1B.!!$R1 603
22 TraesCS5B01G006900 chr1B 390272524 390273123 599 False 907.000000 907 93.884000 1 604 1 chr1B.!!$F1 603
23 TraesCS5B01G006900 chr1B 644278244 644278844 600 False 907.000000 907 93.884000 1 604 1 chr1B.!!$F2 603
24 TraesCS5B01G006900 chr2B 40323789 40324388 599 False 913.000000 913 94.050000 1 604 1 chr2B.!!$F1 603
25 TraesCS5B01G006900 chr2B 225398336 225398937 601 True 905.000000 905 93.740000 1 606 1 chr2B.!!$R1 605
26 TraesCS5B01G006900 chr2B 752878108 752878637 529 False 811.000000 811 94.340000 5733 6261 1 chr2B.!!$F3 528
27 TraesCS5B01G006900 chr6B 21063449 21064052 603 False 907.000000 907 93.750000 1 606 1 chr6B.!!$F1 605
28 TraesCS5B01G006900 chr4A 21229163 21229763 600 False 907.000000 907 93.894000 1 604 1 chr4A.!!$F1 603
29 TraesCS5B01G006900 chr4A 661331288 661331819 531 False 900.000000 900 97.191000 5729 6261 1 chr4A.!!$F3 532
30 TraesCS5B01G006900 chr4A 621757718 621758252 534 True 795.000000 795 93.482000 5726 6261 1 chr4A.!!$R2 535
31 TraesCS5B01G006900 chr4A 677274081 677274649 568 True 651.000000 651 87.522000 3517 4078 1 chr4A.!!$R3 561
32 TraesCS5B01G006900 chr3A 735598933 735599535 602 False 905.000000 905 93.740000 1 606 1 chr3A.!!$F1 605
33 TraesCS5B01G006900 chr1A 556812378 556812914 536 True 902.000000 902 97.026000 5726 6261 1 chr1A.!!$R1 535
34 TraesCS5B01G006900 chr1A 238080796 238081390 594 False 678.000000 678 87.209000 3517 4117 1 chr1A.!!$F1 600
35 TraesCS5B01G006900 chr4B 647407910 647408439 529 True 878.000000 878 96.604000 5733 6261 1 chr4B.!!$R1 528
36 TraesCS5B01G006900 chrUn 85702450 85702994 544 False 830.000000 830 94.333000 5722 6261 1 chrUn.!!$F2 539
37 TraesCS5B01G006900 chrUn 27624567 27625138 571 False 601.000000 601 85.788000 3535 4111 1 chrUn.!!$F1 576
38 TraesCS5B01G006900 chrUn 226734558 226735076 518 True 431.000000 431 81.905000 3597 4114 1 chrUn.!!$R1 517
39 TraesCS5B01G006900 chrUn 274610554 274611069 515 True 420.000000 420 81.609000 3600 4114 1 chrUn.!!$R2 514
40 TraesCS5B01G006900 chr6D 322712027 322712626 599 True 455.000000 455 80.693000 3517 4110 1 chr6D.!!$R1 593
41 TraesCS5B01G006900 chr3D 69825357 69825961 604 False 405.000000 405 79.085000 3517 4117 1 chr3D.!!$F1 600
42 TraesCS5B01G006900 chr3B 803404063 803404581 518 False 398.000000 398 80.762000 3597 4114 1 chr3B.!!$F2 517

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
202 204 0.032515 TCCCCATCTAGCTCCGTTCA 60.033 55.0 0.00 0.0 0.00 3.18 F
902 905 0.037734 AAAATCCCAGACGGACCCAC 59.962 55.0 0.00 0.0 46.09 4.61 F
1593 1895 0.613260 CCCTGTTCAAGACCCATCGA 59.387 55.0 0.00 0.0 0.00 3.59 F
3459 4024 0.106708 TGCGAGTTGAAGCACCTTCT 59.893 50.0 6.54 0.0 40.73 2.85 F
4125 4728 0.458669 GGTGTCGGTGTCGGATATGT 59.541 55.0 0.00 0.0 36.95 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1717 1.203052 CCCCGTTCTGCTTCGTACTTA 59.797 52.381 0.00 0.0 0.00 2.24 R
2458 2902 0.439985 CATCTTGACCAGAACGCACG 59.560 55.000 0.00 0.0 34.16 5.34 R
3506 4071 0.449388 CCCTGCGCTGAAAGTTGATC 59.551 55.000 16.65 0.0 35.30 2.92 R
4821 6344 1.878522 GTGTCACATAGCCCTCGCG 60.879 63.158 0.00 0.0 41.18 5.87 R
5634 7209 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.0 0.00 3.55 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
172 173 2.735772 GGCGGCTCCCTGAAGATGA 61.736 63.158 0.00 0.00 0.00 2.92
188 189 5.252863 TGAAGATGAAATAAAGGTCTCCCCA 59.747 40.000 0.00 0.00 34.66 4.96
202 204 0.032515 TCCCCATCTAGCTCCGTTCA 60.033 55.000 0.00 0.00 0.00 3.18
252 254 4.736896 GGCGGTGTGTCTCCGTCC 62.737 72.222 10.94 9.05 45.74 4.79
276 278 5.277683 CGATCTATCTTTGGTGGATTTGCTG 60.278 44.000 0.00 0.00 0.00 4.41
329 331 3.835978 TGTCTTCGGTTTGGATCCTTCTA 59.164 43.478 14.23 0.00 0.00 2.10
374 376 0.608308 GGTTACTGTTCTGGGGTGCC 60.608 60.000 0.00 0.00 0.00 5.01
380 382 4.974438 TTCTGGGGTGCCGGTCCT 62.974 66.667 15.33 0.00 0.00 3.85
381 383 3.549433 TTCTGGGGTGCCGGTCCTA 62.549 63.158 15.33 7.04 0.00 2.94
382 384 2.768344 CTGGGGTGCCGGTCCTAT 60.768 66.667 15.33 0.00 0.00 2.57
383 385 1.458777 CTGGGGTGCCGGTCCTATA 60.459 63.158 15.33 4.29 0.00 1.31
402 404 1.362224 ATATGGGGCCTTAGCACGAT 58.638 50.000 0.84 0.00 46.55 3.73
440 442 3.834726 CAACAAGTTGTGCCCGGA 58.165 55.556 9.79 0.00 35.92 5.14
441 443 1.654220 CAACAAGTTGTGCCCGGAG 59.346 57.895 9.79 0.00 35.92 4.63
622 624 1.359848 AGACCACTTAAATCGCGCTG 58.640 50.000 5.56 0.00 0.00 5.18
625 627 0.247814 CCACTTAAATCGCGCTGCTG 60.248 55.000 5.56 0.00 0.00 4.41
629 631 0.094558 TTAAATCGCGCTGCTGTTCG 59.905 50.000 5.56 0.00 0.00 3.95
717 719 0.179029 ACAAAACAGAGTGGTCGGGG 60.179 55.000 0.00 0.00 0.00 5.73
826 829 9.745018 ATTTCTATGGGATGATTATACAAGGTG 57.255 33.333 0.00 0.00 0.00 4.00
827 830 7.872061 TCTATGGGATGATTATACAAGGTGT 57.128 36.000 0.00 0.00 0.00 4.16
828 831 8.966155 TCTATGGGATGATTATACAAGGTGTA 57.034 34.615 0.00 0.00 37.24 2.90
829 832 9.387397 TCTATGGGATGATTATACAAGGTGTAA 57.613 33.333 0.00 0.00 36.31 2.41
833 836 8.210946 TGGGATGATTATACAAGGTGTAAAGAG 58.789 37.037 0.00 0.00 36.31 2.85
834 837 7.661847 GGGATGATTATACAAGGTGTAAAGAGG 59.338 40.741 0.00 0.00 36.31 3.69
835 838 7.173390 GGATGATTATACAAGGTGTAAAGAGGC 59.827 40.741 0.00 0.00 36.31 4.70
836 839 6.953101 TGATTATACAAGGTGTAAAGAGGCA 58.047 36.000 0.00 0.00 36.31 4.75
837 840 7.398829 TGATTATACAAGGTGTAAAGAGGCAA 58.601 34.615 0.00 0.00 36.31 4.52
838 841 8.052748 TGATTATACAAGGTGTAAAGAGGCAAT 58.947 33.333 0.00 0.00 36.31 3.56
839 842 8.823220 ATTATACAAGGTGTAAAGAGGCAATT 57.177 30.769 0.00 0.00 36.31 2.32
840 843 9.914834 ATTATACAAGGTGTAAAGAGGCAATTA 57.085 29.630 0.00 0.00 36.31 1.40
841 844 9.914834 TTATACAAGGTGTAAAGAGGCAATTAT 57.085 29.630 0.00 0.00 36.31 1.28
843 846 9.914834 ATACAAGGTGTAAAGAGGCAATTATAA 57.085 29.630 0.00 0.00 36.31 0.98
844 847 8.823220 ACAAGGTGTAAAGAGGCAATTATAAT 57.177 30.769 0.00 0.00 0.00 1.28
845 848 9.255029 ACAAGGTGTAAAGAGGCAATTATAATT 57.745 29.630 4.81 4.81 0.00 1.40
868 871 7.971004 TTAGAAGAATATATATGCGTGCTCG 57.029 36.000 3.31 3.31 40.37 5.03
869 872 5.955488 AGAAGAATATATATGCGTGCTCGT 58.045 37.500 10.18 0.00 39.49 4.18
870 873 6.390721 AGAAGAATATATATGCGTGCTCGTT 58.609 36.000 10.18 0.79 39.49 3.85
871 874 6.868864 AGAAGAATATATATGCGTGCTCGTTT 59.131 34.615 10.18 0.43 39.49 3.60
872 875 6.395089 AGAATATATATGCGTGCTCGTTTG 57.605 37.500 10.18 0.00 39.49 2.93
873 876 5.926542 AGAATATATATGCGTGCTCGTTTGT 59.073 36.000 10.18 0.00 39.49 2.83
874 877 6.423905 AGAATATATATGCGTGCTCGTTTGTT 59.576 34.615 10.18 0.00 39.49 2.83
875 878 4.875544 ATATATGCGTGCTCGTTTGTTT 57.124 36.364 10.18 0.00 39.49 2.83
876 879 3.552604 ATATGCGTGCTCGTTTGTTTT 57.447 38.095 10.18 0.00 39.49 2.43
877 880 1.476074 ATGCGTGCTCGTTTGTTTTG 58.524 45.000 10.18 0.00 39.49 2.44
878 881 0.448197 TGCGTGCTCGTTTGTTTTGA 59.552 45.000 10.18 0.00 39.49 2.69
879 882 1.135660 TGCGTGCTCGTTTGTTTTGAA 60.136 42.857 10.18 0.00 39.49 2.69
880 883 1.914700 GCGTGCTCGTTTGTTTTGAAA 59.085 42.857 10.18 0.00 39.49 2.69
881 884 2.342948 GCGTGCTCGTTTGTTTTGAAAA 59.657 40.909 10.18 0.00 39.49 2.29
882 885 3.181539 GCGTGCTCGTTTGTTTTGAAAAA 60.182 39.130 10.18 0.00 39.49 1.94
900 903 3.664240 AAAAATCCCAGACGGACCC 57.336 52.632 0.00 0.00 46.09 4.46
901 904 0.774908 AAAAATCCCAGACGGACCCA 59.225 50.000 0.00 0.00 46.09 4.51
902 905 0.037734 AAAATCCCAGACGGACCCAC 59.962 55.000 0.00 0.00 46.09 4.61
903 906 1.848886 AAATCCCAGACGGACCCACC 61.849 60.000 0.00 0.00 46.09 4.61
937 940 1.899534 GAGTCCCTCCCCTCGATCG 60.900 68.421 9.36 9.36 0.00 3.69
947 950 1.140161 CCTCGATCGCCAAACCGTA 59.860 57.895 11.09 0.00 0.00 4.02
1425 1717 3.302347 CTTCGAGGACGCCAAGGCT 62.302 63.158 9.73 0.00 39.32 4.58
1593 1895 0.613260 CCCTGTTCAAGACCCATCGA 59.387 55.000 0.00 0.00 0.00 3.59
1805 2161 5.462068 GTGTTCTGGTTTATGGTTTGAAAGC 59.538 40.000 0.00 0.00 34.42 3.51
2093 2493 9.097257 CAAGGAAAAACACATTTCAACTATTGT 57.903 29.630 2.63 0.00 40.34 2.71
2094 2494 9.665719 AAGGAAAAACACATTTCAACTATTGTT 57.334 25.926 2.63 0.00 40.34 2.83
2458 2902 2.088950 TGGCTACTTTTACCGAGTGC 57.911 50.000 0.00 0.00 0.00 4.40
2855 3304 9.821240 AGTATGTATTCACTCATTATCTCCTCT 57.179 33.333 0.00 0.00 0.00 3.69
3459 4024 0.106708 TGCGAGTTGAAGCACCTTCT 59.893 50.000 6.54 0.00 40.73 2.85
3502 4067 5.599732 TCAACTTTCAACATCAATGGTTGG 58.400 37.500 5.55 0.00 44.38 3.77
3503 4068 5.362143 TCAACTTTCAACATCAATGGTTGGA 59.638 36.000 5.55 0.00 44.38 3.53
3504 4069 6.041865 TCAACTTTCAACATCAATGGTTGGAT 59.958 34.615 5.55 0.00 44.38 3.41
3505 4070 7.232330 TCAACTTTCAACATCAATGGTTGGATA 59.768 33.333 5.55 0.00 44.38 2.59
3506 4071 7.161773 ACTTTCAACATCAATGGTTGGATAG 57.838 36.000 5.55 3.96 44.38 2.08
3512 4077 6.949352 ACATCAATGGTTGGATAGATCAAC 57.051 37.500 0.00 0.00 42.53 3.18
3514 4079 7.121382 ACATCAATGGTTGGATAGATCAACTT 58.879 34.615 0.00 0.00 42.76 2.66
3515 4080 7.616935 ACATCAATGGTTGGATAGATCAACTTT 59.383 33.333 0.00 0.34 42.76 2.66
3543 4108 4.741239 GGACAGGGGAGGGAGCCA 62.741 72.222 0.00 0.00 0.00 4.75
3549 4114 2.150051 GGGGAGGGAGCCATCGATT 61.150 63.158 0.00 0.00 0.00 3.34
3648 4231 1.737838 TGGTGATGAGATTGCCGAAC 58.262 50.000 0.00 0.00 0.00 3.95
3898 4490 2.964925 GAACCGTCAGCACGTGCA 60.965 61.111 39.21 19.92 45.17 4.57
3901 4493 2.049526 CCGTCAGCACGTGCACTA 60.050 61.111 39.21 22.48 45.17 2.74
3923 4515 0.833287 GATGAGGCAGCCAGAGGTTA 59.167 55.000 15.80 0.00 0.00 2.85
4049 4648 2.930562 GGTGGTGGAGCTGGAGGT 60.931 66.667 0.00 0.00 0.00 3.85
4122 4725 3.055080 GCGGTGTCGGTGTCGGATA 62.055 63.158 0.00 0.00 36.95 2.59
4124 4727 0.594028 CGGTGTCGGTGTCGGATATG 60.594 60.000 0.00 0.00 36.95 1.78
4125 4728 0.458669 GGTGTCGGTGTCGGATATGT 59.541 55.000 0.00 0.00 36.95 2.29
4127 4730 2.542411 GGTGTCGGTGTCGGATATGTAC 60.542 54.545 0.00 0.00 36.95 2.90
4128 4731 2.097954 GTGTCGGTGTCGGATATGTACA 59.902 50.000 0.00 0.00 36.95 2.90
4129 4732 2.953648 TGTCGGTGTCGGATATGTACAT 59.046 45.455 13.93 13.93 36.95 2.29
4130 4733 4.023792 GTGTCGGTGTCGGATATGTACATA 60.024 45.833 17.65 17.65 36.95 2.29
4131 4734 4.763279 TGTCGGTGTCGGATATGTACATAT 59.237 41.667 25.08 25.08 34.50 1.78
4133 4736 6.600427 TGTCGGTGTCGGATATGTACATATAT 59.400 38.462 24.91 9.40 33.16 0.86
4334 5836 2.344025 CCTCCGTTCCTTTTTACTCCG 58.656 52.381 0.00 0.00 0.00 4.63
4335 5837 2.344025 CTCCGTTCCTTTTTACTCCGG 58.656 52.381 0.00 0.00 35.41 5.14
4336 5838 1.969923 TCCGTTCCTTTTTACTCCGGA 59.030 47.619 2.93 2.93 40.37 5.14
4337 5839 2.568509 TCCGTTCCTTTTTACTCCGGAT 59.431 45.455 3.57 0.00 38.02 4.18
4338 5840 3.768757 TCCGTTCCTTTTTACTCCGGATA 59.231 43.478 3.57 0.00 38.02 2.59
4339 5841 4.406649 TCCGTTCCTTTTTACTCCGGATAT 59.593 41.667 3.57 0.00 38.02 1.63
4340 5842 5.598005 TCCGTTCCTTTTTACTCCGGATATA 59.402 40.000 3.57 0.00 38.02 0.86
4341 5843 6.098124 TCCGTTCCTTTTTACTCCGGATATAA 59.902 38.462 3.57 4.21 38.02 0.98
4342 5844 6.762661 CCGTTCCTTTTTACTCCGGATATAAA 59.237 38.462 3.57 10.73 36.12 1.40
4343 5845 7.280652 CCGTTCCTTTTTACTCCGGATATAAAA 59.719 37.037 21.41 21.41 36.12 1.52
4344 5846 8.833493 CGTTCCTTTTTACTCCGGATATAAAAT 58.167 33.333 23.96 3.34 30.18 1.82
4352 5854 6.598753 ACTCCGGATATAAAATTTGTGTCG 57.401 37.500 3.57 0.00 0.00 4.35
4353 5855 6.342906 ACTCCGGATATAAAATTTGTGTCGA 58.657 36.000 3.57 0.00 0.00 4.20
4354 5856 6.479001 ACTCCGGATATAAAATTTGTGTCGAG 59.521 38.462 3.57 0.00 0.00 4.04
4355 5857 6.342906 TCCGGATATAAAATTTGTGTCGAGT 58.657 36.000 0.00 0.00 0.00 4.18
4356 5858 6.477688 TCCGGATATAAAATTTGTGTCGAGTC 59.522 38.462 0.00 0.00 0.00 3.36
4357 5859 6.256975 CCGGATATAAAATTTGTGTCGAGTCA 59.743 38.462 0.00 0.00 0.00 3.41
4358 5860 7.201574 CCGGATATAAAATTTGTGTCGAGTCAA 60.202 37.037 0.00 0.00 0.00 3.18
4359 5861 8.172484 CGGATATAAAATTTGTGTCGAGTCAAA 58.828 33.333 14.42 14.42 37.82 2.69
4360 5862 9.274065 GGATATAAAATTTGTGTCGAGTCAAAC 57.726 33.333 14.37 3.32 36.58 2.93
4363 5865 8.782533 ATAAAATTTGTGTCGAGTCAAACTTC 57.217 30.769 14.37 0.00 36.58 3.01
4364 5866 5.811399 AATTTGTGTCGAGTCAAACTTCA 57.189 34.783 14.37 0.00 36.58 3.02
4365 5867 4.593597 TTTGTGTCGAGTCAAACTTCAC 57.406 40.909 9.82 1.43 0.00 3.18
4366 5868 2.546778 TGTGTCGAGTCAAACTTCACC 58.453 47.619 0.00 0.00 0.00 4.02
4367 5869 2.093921 TGTGTCGAGTCAAACTTCACCA 60.094 45.455 0.00 0.00 0.00 4.17
4368 5870 2.933906 GTGTCGAGTCAAACTTCACCAA 59.066 45.455 0.00 0.00 0.00 3.67
4369 5871 2.933906 TGTCGAGTCAAACTTCACCAAC 59.066 45.455 0.00 0.00 0.00 3.77
4370 5872 3.195661 GTCGAGTCAAACTTCACCAACT 58.804 45.455 0.00 0.00 0.00 3.16
4371 5873 3.621715 GTCGAGTCAAACTTCACCAACTT 59.378 43.478 0.00 0.00 0.00 2.66
4372 5874 4.094442 GTCGAGTCAAACTTCACCAACTTT 59.906 41.667 0.00 0.00 0.00 2.66
4373 5875 5.292589 GTCGAGTCAAACTTCACCAACTTTA 59.707 40.000 0.00 0.00 0.00 1.85
4374 5876 5.875910 TCGAGTCAAACTTCACCAACTTTAA 59.124 36.000 0.00 0.00 0.00 1.52
4375 5877 5.963586 CGAGTCAAACTTCACCAACTTTAAC 59.036 40.000 0.00 0.00 0.00 2.01
4376 5878 6.203808 AGTCAAACTTCACCAACTTTAACC 57.796 37.500 0.00 0.00 0.00 2.85
4377 5879 5.712917 AGTCAAACTTCACCAACTTTAACCA 59.287 36.000 0.00 0.00 0.00 3.67
4378 5880 6.209788 AGTCAAACTTCACCAACTTTAACCAA 59.790 34.615 0.00 0.00 0.00 3.67
4379 5881 6.869388 GTCAAACTTCACCAACTTTAACCAAA 59.131 34.615 0.00 0.00 0.00 3.28
4380 5882 7.547722 GTCAAACTTCACCAACTTTAACCAAAT 59.452 33.333 0.00 0.00 0.00 2.32
4381 5883 8.097662 TCAAACTTCACCAACTTTAACCAAATT 58.902 29.630 0.00 0.00 0.00 1.82
4382 5884 8.726068 CAAACTTCACCAACTTTAACCAAATTT 58.274 29.630 0.00 0.00 0.00 1.82
4383 5885 9.945904 AAACTTCACCAACTTTAACCAAATTTA 57.054 25.926 0.00 0.00 0.00 1.40
4385 5887 9.541143 ACTTCACCAACTTTAACCAAATTTATG 57.459 29.630 0.00 0.00 0.00 1.90
4386 5888 9.541143 CTTCACCAACTTTAACCAAATTTATGT 57.459 29.630 0.00 0.00 0.00 2.29
4471 5973 9.936329 TGAATTTAAAGATATCCCTTTAGCCTT 57.064 29.630 0.00 0.00 39.10 4.35
4473 5975 9.715119 AATTTAAAGATATCCCTTTAGCCTTGT 57.285 29.630 0.00 0.00 39.10 3.16
4478 5980 8.697507 AAGATATCCCTTTAGCCTTGTAAATG 57.302 34.615 0.00 0.00 0.00 2.32
4479 5981 7.816411 AGATATCCCTTTAGCCTTGTAAATGT 58.184 34.615 0.00 0.00 0.00 2.71
4480 5982 8.282256 AGATATCCCTTTAGCCTTGTAAATGTT 58.718 33.333 0.00 0.00 0.00 2.71
4481 5983 5.975693 TCCCTTTAGCCTTGTAAATGTTG 57.024 39.130 0.00 0.00 0.00 3.33
4482 5984 5.636123 TCCCTTTAGCCTTGTAAATGTTGA 58.364 37.500 0.00 0.00 0.00 3.18
4483 5985 6.252995 TCCCTTTAGCCTTGTAAATGTTGAT 58.747 36.000 0.00 0.00 0.00 2.57
4484 5986 7.406916 TCCCTTTAGCCTTGTAAATGTTGATA 58.593 34.615 0.00 0.00 0.00 2.15
4485 5987 7.338449 TCCCTTTAGCCTTGTAAATGTTGATAC 59.662 37.037 0.00 0.00 0.00 2.24
4486 5988 7.339466 CCCTTTAGCCTTGTAAATGTTGATACT 59.661 37.037 0.00 0.00 0.00 2.12
4487 5989 8.739972 CCTTTAGCCTTGTAAATGTTGATACTT 58.260 33.333 0.00 0.00 0.00 2.24
4534 6036 8.861086 AGTAAAGATACTTTGACTTCAGACAGA 58.139 33.333 6.95 0.00 39.36 3.41
4535 6037 9.477484 GTAAAGATACTTTGACTTCAGACAGAA 57.523 33.333 6.95 0.00 34.41 3.02
4548 6050 7.462109 CTTCAGACAGAAGTTATATGCAGAC 57.538 40.000 0.00 0.00 46.97 3.51
4549 6051 6.782082 TCAGACAGAAGTTATATGCAGACT 57.218 37.500 0.00 0.00 0.00 3.24
4550 6052 7.881775 TCAGACAGAAGTTATATGCAGACTA 57.118 36.000 0.00 0.00 0.00 2.59
4551 6053 8.293699 TCAGACAGAAGTTATATGCAGACTAA 57.706 34.615 0.00 0.00 0.00 2.24
4552 6054 8.749354 TCAGACAGAAGTTATATGCAGACTAAA 58.251 33.333 0.00 0.00 0.00 1.85
4553 6055 9.371136 CAGACAGAAGTTATATGCAGACTAAAA 57.629 33.333 0.00 0.00 0.00 1.52
4554 6056 9.944376 AGACAGAAGTTATATGCAGACTAAAAA 57.056 29.630 0.00 0.00 0.00 1.94
4556 6058 9.944376 ACAGAAGTTATATGCAGACTAAAAAGA 57.056 29.630 0.00 0.00 0.00 2.52
4561 6063 8.665685 AGTTATATGCAGACTAAAAAGAAACGG 58.334 33.333 0.00 0.00 0.00 4.44
4562 6064 8.662141 GTTATATGCAGACTAAAAAGAAACGGA 58.338 33.333 0.00 0.00 0.00 4.69
4563 6065 5.613358 ATGCAGACTAAAAAGAAACGGAG 57.387 39.130 0.00 0.00 0.00 4.63
4564 6066 3.813166 TGCAGACTAAAAAGAAACGGAGG 59.187 43.478 0.00 0.00 0.00 4.30
4565 6067 3.188667 GCAGACTAAAAAGAAACGGAGGG 59.811 47.826 0.00 0.00 0.00 4.30
4566 6068 4.638304 CAGACTAAAAAGAAACGGAGGGA 58.362 43.478 0.00 0.00 0.00 4.20
4567 6069 4.691216 CAGACTAAAAAGAAACGGAGGGAG 59.309 45.833 0.00 0.00 0.00 4.30
4568 6070 4.347292 AGACTAAAAAGAAACGGAGGGAGT 59.653 41.667 0.00 0.00 0.00 3.85
4574 6076 5.952347 AAAGAAACGGAGGGAGTATATGT 57.048 39.130 0.00 0.00 0.00 2.29
4584 6086 6.095160 CGGAGGGAGTATATGTAGTATGTTCC 59.905 46.154 0.00 0.00 0.00 3.62
4596 6098 3.956744 AGTATGTTCCTTCAAAGGGAGC 58.043 45.455 8.89 0.00 46.47 4.70
4821 6344 1.760480 GTGAGGGAGAGGGAGAGGC 60.760 68.421 0.00 0.00 0.00 4.70
5011 6572 6.293081 CGACCATAGCACTATGAAAAAGATGG 60.293 42.308 17.35 4.38 44.22 3.51
5429 7001 1.624813 CATTCTGTTTGCATTGGGGGT 59.375 47.619 0.00 0.00 0.00 4.95
5430 7002 1.047002 TTCTGTTTGCATTGGGGGTG 58.953 50.000 0.00 0.00 0.00 4.61
5431 7003 0.831288 TCTGTTTGCATTGGGGGTGG 60.831 55.000 0.00 0.00 0.00 4.61
5471 7043 6.534475 TGATCAATCTTTTAGCTGGCAAAT 57.466 33.333 0.00 0.00 0.00 2.32
5634 7209 5.101628 GCAAATTCAAGTTCGGCATAATCA 58.898 37.500 0.00 0.00 0.00 2.57
5676 7255 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5677 7256 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5678 7257 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5679 7258 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5680 7259 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5681 7260 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
5685 7264 2.238363 GTGTGTGTGTGTGTGTTTTCG 58.762 47.619 0.00 0.00 0.00 3.46
5753 7332 0.544595 ACCGGAACAGGGCTCTAAGT 60.545 55.000 9.46 0.00 35.02 2.24
5869 7448 2.407616 CGCGTCTATGCCGACAGA 59.592 61.111 0.00 0.00 33.54 3.41
5924 7503 1.945354 GACTACGCCTACAGCTGCCA 61.945 60.000 15.27 0.20 40.39 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 1.736586 CGCCTGAACGGAGCTAGAT 59.263 57.895 0.00 0.00 33.16 1.98
250 252 5.368145 CAAATCCACCAAAGATAGATCGGA 58.632 41.667 0.00 0.00 0.00 4.55
252 254 4.818546 AGCAAATCCACCAAAGATAGATCG 59.181 41.667 0.00 0.00 0.00 3.69
276 278 0.109412 ACGAACAACGACGAGATCCC 60.109 55.000 0.00 0.00 45.77 3.85
329 331 5.277154 CCGCCGATGAAAAATAACGTAGATT 60.277 40.000 0.00 0.00 0.00 2.40
374 376 2.176247 AGGCCCCATATATAGGACCG 57.824 55.000 0.00 0.00 0.00 4.79
380 382 3.715287 TCGTGCTAAGGCCCCATATATA 58.285 45.455 0.00 0.00 37.74 0.86
381 383 2.546899 TCGTGCTAAGGCCCCATATAT 58.453 47.619 0.00 0.00 37.74 0.86
382 384 2.018355 TCGTGCTAAGGCCCCATATA 57.982 50.000 0.00 0.00 37.74 0.86
383 385 1.003580 CATCGTGCTAAGGCCCCATAT 59.996 52.381 0.00 0.00 37.74 1.78
402 404 2.581216 AGTAGACAGTCGGGAAGTCA 57.419 50.000 0.00 0.00 34.80 3.41
446 448 2.796193 CGTCATCGCCCCTCCATCA 61.796 63.158 0.00 0.00 0.00 3.07
544 546 5.877564 TCAATCATGGCAGTACAACGAATAA 59.122 36.000 0.00 0.00 0.00 1.40
625 627 0.876342 CTTAGATGAGCCCGGCGAAC 60.876 60.000 9.30 0.00 0.00 3.95
800 802 9.745018 CACCTTGTATAATCATCCCATAGAAAT 57.255 33.333 0.00 0.00 0.00 2.17
817 820 9.914834 TTATAATTGCCTCTTTACACCTTGTAT 57.085 29.630 0.00 0.00 32.20 2.29
818 821 9.914834 ATTATAATTGCCTCTTTACACCTTGTA 57.085 29.630 0.00 0.00 0.00 2.41
819 822 8.823220 ATTATAATTGCCTCTTTACACCTTGT 57.177 30.769 0.00 0.00 0.00 3.16
842 845 9.025020 CGAGCACGCATATATATTCTTCTAATT 57.975 33.333 0.00 0.00 0.00 1.40
843 846 8.191446 ACGAGCACGCATATATATTCTTCTAAT 58.809 33.333 2.62 0.00 43.96 1.73
844 847 7.535997 ACGAGCACGCATATATATTCTTCTAA 58.464 34.615 2.62 0.00 43.96 2.10
845 848 7.085052 ACGAGCACGCATATATATTCTTCTA 57.915 36.000 2.62 0.00 43.96 2.10
846 849 5.955488 ACGAGCACGCATATATATTCTTCT 58.045 37.500 2.62 0.00 43.96 2.85
847 850 6.633668 AACGAGCACGCATATATATTCTTC 57.366 37.500 2.62 0.00 43.96 2.87
848 851 6.423905 ACAAACGAGCACGCATATATATTCTT 59.576 34.615 2.62 0.00 43.96 2.52
849 852 5.926542 ACAAACGAGCACGCATATATATTCT 59.073 36.000 2.62 0.00 43.96 2.40
850 853 6.153212 ACAAACGAGCACGCATATATATTC 57.847 37.500 2.62 0.00 43.96 1.75
851 854 6.539649 AACAAACGAGCACGCATATATATT 57.460 33.333 2.62 0.00 43.96 1.28
852 855 6.539649 AAACAAACGAGCACGCATATATAT 57.460 33.333 2.62 0.00 43.96 0.86
853 856 5.977171 AAACAAACGAGCACGCATATATA 57.023 34.783 2.62 0.00 43.96 0.86
854 857 4.875544 AAACAAACGAGCACGCATATAT 57.124 36.364 2.62 0.00 43.96 0.86
855 858 4.152580 TCAAAACAAACGAGCACGCATATA 59.847 37.500 2.62 0.00 43.96 0.86
856 859 3.058570 TCAAAACAAACGAGCACGCATAT 60.059 39.130 2.62 0.00 43.96 1.78
857 860 2.288186 TCAAAACAAACGAGCACGCATA 59.712 40.909 2.62 0.00 43.96 3.14
858 861 1.064803 TCAAAACAAACGAGCACGCAT 59.935 42.857 2.62 0.00 43.96 4.73
859 862 0.448197 TCAAAACAAACGAGCACGCA 59.552 45.000 2.62 0.00 43.96 5.24
860 863 1.540407 TTCAAAACAAACGAGCACGC 58.460 45.000 2.62 0.00 43.96 5.34
861 864 4.554162 TTTTTCAAAACAAACGAGCACG 57.446 36.364 0.76 0.76 45.75 5.34
895 898 4.139234 GCGTCTACGGGTGGGTCC 62.139 72.222 4.49 0.00 40.23 4.46
896 899 4.487412 CGCGTCTACGGGTGGGTC 62.487 72.222 10.99 0.00 45.50 4.46
925 928 1.521681 GTTTGGCGATCGAGGGGAG 60.522 63.158 21.57 0.00 0.00 4.30
926 929 2.582436 GTTTGGCGATCGAGGGGA 59.418 61.111 21.57 0.00 0.00 4.81
927 930 2.513897 GGTTTGGCGATCGAGGGG 60.514 66.667 21.57 0.00 0.00 4.79
928 931 2.287457 TACGGTTTGGCGATCGAGGG 62.287 60.000 21.57 2.32 0.00 4.30
929 932 0.249322 ATACGGTTTGGCGATCGAGG 60.249 55.000 21.57 1.22 0.00 4.63
930 933 1.521423 GAATACGGTTTGGCGATCGAG 59.479 52.381 21.57 2.73 0.00 4.04
1084 1305 1.611851 AGTGGAGAGCTGTCCCCTG 60.612 63.158 26.07 0.00 35.49 4.45
1425 1717 1.203052 CCCCGTTCTGCTTCGTACTTA 59.797 52.381 0.00 0.00 0.00 2.24
1593 1895 5.477984 TGCTTGTTCAAGAATAGGAAGCAAT 59.522 36.000 15.52 0.00 40.87 3.56
1708 2010 7.797121 TGGCCAGATATGAAATCAGATACTA 57.203 36.000 0.00 0.00 0.00 1.82
1805 2161 1.332028 GCGGTTTTGCTATGATCGTCG 60.332 52.381 0.00 0.00 0.00 5.12
2369 2813 1.540115 TCCTGGAGATAGAGGAGGCT 58.460 55.000 0.00 0.00 33.18 4.58
2458 2902 0.439985 CATCTTGACCAGAACGCACG 59.560 55.000 0.00 0.00 34.16 5.34
2847 3296 8.499406 AGAGTACTAACACAGAATAGAGGAGAT 58.501 37.037 0.00 0.00 0.00 2.75
2855 3304 9.856488 GAATCACAAGAGTACTAACACAGAATA 57.144 33.333 0.00 0.00 0.00 1.75
2924 3471 7.134815 AGATCAAATAAGTATCACGCAAATGC 58.865 34.615 0.00 0.00 37.78 3.56
3214 3770 7.028962 CACGAATTCCAATTTTCTCAGCATTA 58.971 34.615 0.00 0.00 0.00 1.90
3215 3771 5.865552 CACGAATTCCAATTTTCTCAGCATT 59.134 36.000 0.00 0.00 0.00 3.56
3459 4024 7.058525 AGTTGATCTATCCAAGCATGAATCAA 58.941 34.615 0.00 0.00 0.00 2.57
3502 4067 3.247173 CCTGCGCTGAAAGTTGATCTATC 59.753 47.826 16.65 0.00 35.30 2.08
3503 4068 3.201290 CCTGCGCTGAAAGTTGATCTAT 58.799 45.455 16.65 0.00 35.30 1.98
3504 4069 2.621338 CCTGCGCTGAAAGTTGATCTA 58.379 47.619 16.65 0.00 35.30 1.98
3505 4070 1.446907 CCTGCGCTGAAAGTTGATCT 58.553 50.000 16.65 0.00 35.30 2.75
3506 4071 0.449388 CCCTGCGCTGAAAGTTGATC 59.551 55.000 16.65 0.00 35.30 2.92
3512 4077 2.747855 GTCCCCCTGCGCTGAAAG 60.748 66.667 16.65 0.00 0.00 2.62
3514 4079 4.020617 CTGTCCCCCTGCGCTGAA 62.021 66.667 16.65 0.00 0.00 3.02
3543 4108 2.717639 ACCTGCTTGGCTAAATCGAT 57.282 45.000 0.00 0.00 40.22 3.59
3898 4490 2.025767 CTGGCTGCCTCATCGCTAGT 62.026 60.000 21.03 0.00 0.00 2.57
3901 4493 3.079478 TCTGGCTGCCTCATCGCT 61.079 61.111 21.03 0.00 0.00 4.93
3923 4515 1.603739 GGCTCCCTTTTCGCCACTT 60.604 57.895 0.00 0.00 43.25 3.16
3987 4579 4.491409 GCTCTCCTTTCCCGGCCC 62.491 72.222 0.00 0.00 0.00 5.80
4296 5798 5.602978 ACGGAGGGAGTACTATCAAATGAAT 59.397 40.000 0.00 0.00 0.00 2.57
4334 5836 9.274065 GTTTGACTCGACACAAATTTTATATCC 57.726 33.333 13.01 0.00 38.09 2.59
4337 5839 9.872757 GAAGTTTGACTCGACACAAATTTTATA 57.127 29.630 15.74 0.00 36.56 0.98
4338 5840 8.402472 TGAAGTTTGACTCGACACAAATTTTAT 58.598 29.630 15.74 1.99 36.56 1.40
4339 5841 7.694784 GTGAAGTTTGACTCGACACAAATTTTA 59.305 33.333 15.74 11.68 36.56 1.52
4340 5842 6.526674 GTGAAGTTTGACTCGACACAAATTTT 59.473 34.615 15.74 12.58 36.56 1.82
4341 5843 6.027749 GTGAAGTTTGACTCGACACAAATTT 58.972 36.000 15.04 15.04 38.15 1.82
4342 5844 5.448632 GGTGAAGTTTGACTCGACACAAATT 60.449 40.000 13.01 8.08 38.09 1.82
4343 5845 4.035208 GGTGAAGTTTGACTCGACACAAAT 59.965 41.667 13.01 2.04 38.09 2.32
4344 5846 3.372822 GGTGAAGTTTGACTCGACACAAA 59.627 43.478 7.79 7.79 32.54 2.83
4345 5847 2.933906 GGTGAAGTTTGACTCGACACAA 59.066 45.455 0.00 0.00 32.54 3.33
4346 5848 2.093921 TGGTGAAGTTTGACTCGACACA 60.094 45.455 0.00 0.00 32.54 3.72
4347 5849 2.546778 TGGTGAAGTTTGACTCGACAC 58.453 47.619 0.00 0.00 0.00 3.67
4348 5850 2.933906 GTTGGTGAAGTTTGACTCGACA 59.066 45.455 0.00 0.00 0.00 4.35
4349 5851 3.195661 AGTTGGTGAAGTTTGACTCGAC 58.804 45.455 0.00 0.00 0.00 4.20
4350 5852 3.536956 AGTTGGTGAAGTTTGACTCGA 57.463 42.857 0.00 0.00 0.00 4.04
4351 5853 4.616181 AAAGTTGGTGAAGTTTGACTCG 57.384 40.909 0.00 0.00 34.10 4.18
4352 5854 6.127842 TGGTTAAAGTTGGTGAAGTTTGACTC 60.128 38.462 0.00 0.00 39.36 3.36
4353 5855 5.712917 TGGTTAAAGTTGGTGAAGTTTGACT 59.287 36.000 0.00 0.00 39.36 3.41
4354 5856 5.956642 TGGTTAAAGTTGGTGAAGTTTGAC 58.043 37.500 0.00 0.00 38.98 3.18
4355 5857 6.591750 TTGGTTAAAGTTGGTGAAGTTTGA 57.408 33.333 0.00 0.00 35.80 2.69
4356 5858 7.841915 ATTTGGTTAAAGTTGGTGAAGTTTG 57.158 32.000 0.00 0.00 35.80 2.93
4357 5859 8.856153 AAATTTGGTTAAAGTTGGTGAAGTTT 57.144 26.923 0.00 0.00 38.16 2.66
4359 5861 9.541143 CATAAATTTGGTTAAAGTTGGTGAAGT 57.459 29.630 0.00 0.00 35.19 3.01
4360 5862 9.541143 ACATAAATTTGGTTAAAGTTGGTGAAG 57.459 29.630 0.00 0.00 35.19 3.02
4445 5947 9.936329 AAGGCTAAAGGGATATCTTTAAATTCA 57.064 29.630 2.05 0.00 38.34 2.57
4447 5949 9.715119 ACAAGGCTAAAGGGATATCTTTAAATT 57.285 29.630 2.05 0.00 38.34 1.82
4452 5954 9.136323 CATTTACAAGGCTAAAGGGATATCTTT 57.864 33.333 2.05 0.00 39.86 2.52
4453 5955 8.282256 ACATTTACAAGGCTAAAGGGATATCTT 58.718 33.333 2.05 0.00 0.00 2.40
4454 5956 7.816411 ACATTTACAAGGCTAAAGGGATATCT 58.184 34.615 2.05 0.00 0.00 1.98
4455 5957 8.352942 CAACATTTACAAGGCTAAAGGGATATC 58.647 37.037 0.00 0.00 0.00 1.63
4456 5958 8.058847 TCAACATTTACAAGGCTAAAGGGATAT 58.941 33.333 0.00 0.00 0.00 1.63
4457 5959 7.406916 TCAACATTTACAAGGCTAAAGGGATA 58.593 34.615 0.00 0.00 0.00 2.59
4458 5960 6.252995 TCAACATTTACAAGGCTAAAGGGAT 58.747 36.000 0.00 0.00 0.00 3.85
4459 5961 5.636123 TCAACATTTACAAGGCTAAAGGGA 58.364 37.500 0.00 0.00 0.00 4.20
4460 5962 5.975693 TCAACATTTACAAGGCTAAAGGG 57.024 39.130 0.00 0.00 0.00 3.95
4461 5963 8.281212 AGTATCAACATTTACAAGGCTAAAGG 57.719 34.615 0.00 0.00 0.00 3.11
4508 6010 8.861086 TCTGTCTGAAGTCAAAGTATCTTTACT 58.139 33.333 0.00 0.00 40.48 2.24
4509 6011 9.477484 TTCTGTCTGAAGTCAAAGTATCTTTAC 57.523 33.333 0.00 0.00 0.00 2.01
4510 6012 9.698309 CTTCTGTCTGAAGTCAAAGTATCTTTA 57.302 33.333 10.51 0.00 45.26 1.85
4511 6013 8.600449 CTTCTGTCTGAAGTCAAAGTATCTTT 57.400 34.615 10.51 0.00 45.26 2.52
4525 6027 7.175347 AGTCTGCATATAACTTCTGTCTGAA 57.825 36.000 0.00 0.00 0.00 3.02
4526 6028 6.782082 AGTCTGCATATAACTTCTGTCTGA 57.218 37.500 0.00 0.00 0.00 3.27
4527 6029 8.932945 TTTAGTCTGCATATAACTTCTGTCTG 57.067 34.615 0.00 0.00 0.00 3.51
4528 6030 9.944376 TTTTTAGTCTGCATATAACTTCTGTCT 57.056 29.630 0.00 0.00 0.00 3.41
4530 6032 9.944376 TCTTTTTAGTCTGCATATAACTTCTGT 57.056 29.630 0.00 0.00 0.00 3.41
4535 6037 8.665685 CCGTTTCTTTTTAGTCTGCATATAACT 58.334 33.333 0.00 0.00 0.00 2.24
4536 6038 8.662141 TCCGTTTCTTTTTAGTCTGCATATAAC 58.338 33.333 0.00 0.00 0.00 1.89
4537 6039 8.780846 TCCGTTTCTTTTTAGTCTGCATATAA 57.219 30.769 0.00 0.00 0.00 0.98
4538 6040 7.494625 CCTCCGTTTCTTTTTAGTCTGCATATA 59.505 37.037 0.00 0.00 0.00 0.86
4539 6041 6.316390 CCTCCGTTTCTTTTTAGTCTGCATAT 59.684 38.462 0.00 0.00 0.00 1.78
4540 6042 5.642063 CCTCCGTTTCTTTTTAGTCTGCATA 59.358 40.000 0.00 0.00 0.00 3.14
4541 6043 4.455877 CCTCCGTTTCTTTTTAGTCTGCAT 59.544 41.667 0.00 0.00 0.00 3.96
4542 6044 3.813166 CCTCCGTTTCTTTTTAGTCTGCA 59.187 43.478 0.00 0.00 0.00 4.41
4543 6045 3.188667 CCCTCCGTTTCTTTTTAGTCTGC 59.811 47.826 0.00 0.00 0.00 4.26
4544 6046 4.638304 TCCCTCCGTTTCTTTTTAGTCTG 58.362 43.478 0.00 0.00 0.00 3.51
4545 6047 4.347292 ACTCCCTCCGTTTCTTTTTAGTCT 59.653 41.667 0.00 0.00 0.00 3.24
4546 6048 4.639334 ACTCCCTCCGTTTCTTTTTAGTC 58.361 43.478 0.00 0.00 0.00 2.59
4547 6049 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
4548 6050 7.985752 ACATATACTCCCTCCGTTTCTTTTTAG 59.014 37.037 0.00 0.00 0.00 1.85
4549 6051 7.854337 ACATATACTCCCTCCGTTTCTTTTTA 58.146 34.615 0.00 0.00 0.00 1.52
4550 6052 6.718294 ACATATACTCCCTCCGTTTCTTTTT 58.282 36.000 0.00 0.00 0.00 1.94
4551 6053 6.309389 ACATATACTCCCTCCGTTTCTTTT 57.691 37.500 0.00 0.00 0.00 2.27
4552 6054 5.952347 ACATATACTCCCTCCGTTTCTTT 57.048 39.130 0.00 0.00 0.00 2.52
4553 6055 6.134754 ACTACATATACTCCCTCCGTTTCTT 58.865 40.000 0.00 0.00 0.00 2.52
4554 6056 5.703310 ACTACATATACTCCCTCCGTTTCT 58.297 41.667 0.00 0.00 0.00 2.52
4555 6057 7.176340 ACATACTACATATACTCCCTCCGTTTC 59.824 40.741 0.00 0.00 0.00 2.78
4556 6058 7.008941 ACATACTACATATACTCCCTCCGTTT 58.991 38.462 0.00 0.00 0.00 3.60
4557 6059 6.550163 ACATACTACATATACTCCCTCCGTT 58.450 40.000 0.00 0.00 0.00 4.44
4558 6060 6.137104 ACATACTACATATACTCCCTCCGT 57.863 41.667 0.00 0.00 0.00 4.69
4559 6061 6.095160 GGAACATACTACATATACTCCCTCCG 59.905 46.154 0.00 0.00 0.00 4.63
4560 6062 7.183460 AGGAACATACTACATATACTCCCTCC 58.817 42.308 0.00 0.00 29.02 4.30
4561 6063 8.653036 AAGGAACATACTACATATACTCCCTC 57.347 38.462 0.00 0.00 29.02 4.30
4562 6064 8.232412 TGAAGGAACATACTACATATACTCCCT 58.768 37.037 0.00 0.00 29.02 4.20
4563 6065 8.418597 TGAAGGAACATACTACATATACTCCC 57.581 38.462 0.00 0.00 29.02 4.30
4821 6344 1.878522 GTGTCACATAGCCCTCGCG 60.879 63.158 0.00 0.00 41.18 5.87
4829 6352 5.237127 TGCAAAAGTCAAGAGTGTCACATAG 59.763 40.000 5.62 0.00 0.00 2.23
5011 6572 8.015658 GCAATCCATAGAATTAACATACCGAAC 58.984 37.037 0.00 0.00 0.00 3.95
5340 6908 4.262894 GGACAATCTCCTGTACAACCTTCA 60.263 45.833 0.00 0.00 35.89 3.02
5471 7043 1.810151 GCCAGCGATCAGTGGTTAAAA 59.190 47.619 11.14 0.00 36.10 1.52
5634 7209 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
5685 7264 8.495148 CACCCATAATTTAAAGTTTTTGTCTGC 58.505 33.333 0.00 0.00 0.00 4.26
5753 7332 2.036604 TCGGCATATATTTGGCTGTCGA 59.963 45.455 15.78 6.40 42.72 4.20


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

AutoCloner maintained by Alex Coulton.