Multiple sequence alignment - TraesCS4B01G288500

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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 TraesCS4B01G288500 chr4B 100.000 5551 0 0 1 5551 573397112 573391562 0.000000e+00 10251.0
1 TraesCS4B01G288500 chr4B 100.000 1600 0 0 5844 7443 573391269 573389670 0.000000e+00 2955.0
2 TraesCS4B01G288500 chr4D 91.882 3991 254 32 1374 5311 459079803 459075830 0.000000e+00 5511.0
3 TraesCS4B01G288500 chr4D 94.406 1001 33 10 376 1363 459081212 459080222 0.000000e+00 1517.0
4 TraesCS4B01G288500 chr4D 92.950 922 53 8 5846 6757 459075522 459074603 0.000000e+00 1332.0
5 TraesCS4B01G288500 chr4D 87.028 794 52 21 6686 7443 459074605 459073827 0.000000e+00 848.0
6 TraesCS4B01G288500 chr4D 85.174 317 27 8 4 319 459083538 459083241 2.610000e-79 307.0
7 TraesCS4B01G288500 chr4D 74.444 810 146 34 4755 5550 82232039 82231277 7.300000e-75 292.0
8 TraesCS4B01G288500 chr4D 74.439 579 106 26 4844 5399 207481197 207481756 2.100000e-50 211.0
9 TraesCS4B01G288500 chr4D 73.789 702 112 32 4313 4984 497254236 497254895 2.100000e-50 211.0
10 TraesCS4B01G288500 chr4D 94.231 52 3 0 331 382 459083097 459083046 6.190000e-11 80.5
11 TraesCS4B01G288500 chr4D 81.633 98 15 2 5877 5972 408787203 408787299 2.230000e-10 78.7
12 TraesCS4B01G288500 chr4D 81.000 100 15 3 5877 5974 98927268 98927171 8.010000e-10 76.8
13 TraesCS4B01G288500 chr4D 86.765 68 6 3 3653 3718 159644100 159644034 1.040000e-08 73.1
14 TraesCS4B01G288500 chr4A 91.462 3420 184 42 1374 4767 9615823 9619160 0.000000e+00 4599.0
15 TraesCS4B01G288500 chr4A 88.082 1225 82 30 164 1363 9613967 9615152 0.000000e+00 1395.0
16 TraesCS4B01G288500 chr4A 93.465 811 41 8 5967 6771 9620060 9620864 0.000000e+00 1194.0
17 TraesCS4B01G288500 chr4A 72.886 1206 217 61 4020 5179 638247419 638248560 1.560000e-81 315.0
18 TraesCS4B01G288500 chr4A 89.958 239 23 1 7016 7254 9621197 9621434 2.610000e-79 307.0
19 TraesCS4B01G288500 chr4A 74.860 712 145 19 4548 5251 692339392 692340077 7.300000e-75 292.0
20 TraesCS4B01G288500 chr4A 85.965 285 21 4 6765 7033 9620903 9621184 3.400000e-73 287.0
21 TraesCS4B01G288500 chr4A 84.689 209 27 2 4818 5023 9619179 9619385 3.520000e-48 204.0
22 TraesCS4B01G288500 chr4A 74.003 577 113 19 4844 5399 474086637 474087197 4.550000e-47 200.0
23 TraesCS4B01G288500 chr4A 96.939 98 3 0 7345 7442 9621473 9621570 1.660000e-36 165.0
24 TraesCS4B01G288500 chr4A 80.208 96 17 1 5877 5970 477047796 477047891 3.730000e-08 71.3
25 TraesCS4B01G288500 chr1A 76.441 1579 271 58 4033 5551 534053282 534054819 0.000000e+00 761.0
26 TraesCS4B01G288500 chr2A 75.359 1534 303 42 4026 5512 749052860 749054365 0.000000e+00 669.0
27 TraesCS4B01G288500 chr2A 77.310 974 161 32 4024 4947 565316799 565315836 3.080000e-143 520.0
28 TraesCS4B01G288500 chr2A 74.301 1109 216 33 4458 5551 498044815 498045869 8.990000e-109 405.0
29 TraesCS4B01G288500 chr2A 75.593 885 141 40 4210 5070 760931123 760931956 1.180000e-97 368.0
30 TraesCS4B01G288500 chr2A 79.658 526 90 8 4228 4741 598981760 598981240 5.490000e-96 363.0
31 TraesCS4B01G288500 chr2A 84.247 146 23 0 4459 4604 420404991 420405136 7.780000e-30 143.0
32 TraesCS4B01G288500 chr2A 90.291 103 7 1 3534 3636 746918334 746918235 1.690000e-26 132.0
33 TraesCS4B01G288500 chr2A 83.077 130 21 1 3395 3523 711885514 711885385 4.720000e-22 117.0
34 TraesCS4B01G288500 chr2A 79.592 98 17 3 5877 5972 445714589 445714685 4.820000e-07 67.6
35 TraesCS4B01G288500 chr2A 100.000 30 0 0 5849 5878 261217542 261217513 1.000000e-03 56.5
36 TraesCS4B01G288500 chr2B 78.175 1118 188 27 4341 5429 34077137 34078227 0.000000e+00 662.0
37 TraesCS4B01G288500 chr2B 73.916 1499 262 69 4104 5551 436962407 436963827 4.040000e-132 483.0
38 TraesCS4B01G288500 chr2B 88.393 112 9 2 3534 3645 646038054 646037947 1.690000e-26 132.0
39 TraesCS4B01G288500 chr2B 89.552 67 6 1 3654 3720 196268043 196268108 4.790000e-12 84.2
40 TraesCS4B01G288500 chr7D 77.232 1221 214 32 4215 5389 206683618 206682416 0.000000e+00 656.0
41 TraesCS4B01G288500 chr7D 81.614 223 32 6 4024 4238 254339931 254339710 7.680000e-40 176.0
42 TraesCS4B01G288500 chr7D 82.677 127 21 1 3398 3523 128915578 128915452 2.200000e-20 111.0
43 TraesCS4B01G288500 chr7D 97.561 41 1 0 7198 7238 168580959 168580919 3.730000e-08 71.3
44 TraesCS4B01G288500 chr7D 95.238 42 1 1 7198 7239 164195903 164195943 1.730000e-06 65.8
45 TraesCS4B01G288500 chr6D 76.797 1280 219 40 4019 5260 26005929 26004690 0.000000e+00 647.0
46 TraesCS4B01G288500 chr6D 87.037 108 13 1 3398 3504 6861617 6861724 3.650000e-23 121.0
47 TraesCS4B01G288500 chr6D 93.878 49 1 2 7191 7239 291236915 291236961 1.040000e-08 73.1
48 TraesCS4B01G288500 chr3D 77.324 1151 207 25 4373 5491 406410457 406411585 1.360000e-176 630.0
49 TraesCS4B01G288500 chr3D 77.904 1059 201 19 4514 5551 508310144 508309098 4.900000e-176 628.0
50 TraesCS4B01G288500 chr3D 80.645 341 61 4 4083 4420 613070974 613071312 7.410000e-65 259.0
51 TraesCS4B01G288500 chr3D 91.262 103 5 2 3532 3634 324307066 324307164 3.620000e-28 137.0
52 TraesCS4B01G288500 chr3D 90.588 85 7 1 3643 3726 67721208 67721292 2.200000e-20 111.0
53 TraesCS4B01G288500 chr3D 81.915 94 15 2 5877 5968 590560273 590560180 2.230000e-10 78.7
54 TraesCS4B01G288500 chr7A 75.504 1290 252 38 4022 5279 709421769 709420512 2.330000e-159 573.0
55 TraesCS4B01G288500 chr7A 78.905 493 82 14 5038 5520 444954101 444953621 1.560000e-81 315.0
56 TraesCS4B01G288500 chr6A 77.728 898 171 17 4044 4919 183950585 183951475 2.380000e-144 523.0
57 TraesCS4B01G288500 chr6A 97.143 35 1 0 5844 5878 449710942 449710976 8.060000e-05 60.2
58 TraesCS4B01G288500 chr3A 72.956 1468 268 74 4090 5492 728937683 728939086 7.000000e-105 392.0
59 TraesCS4B01G288500 chr3A 90.291 103 6 2 3532 3634 397145499 397145401 1.690000e-26 132.0
60 TraesCS4B01G288500 chr3B 74.356 776 158 24 4124 4874 475197425 475196666 7.300000e-75 292.0
61 TraesCS4B01G288500 chr3B 81.848 303 52 3 4083 4384 825975365 825975065 1.240000e-62 252.0
62 TraesCS4B01G288500 chr3B 81.448 221 37 4 4021 4238 417226087 417226306 2.130000e-40 178.0
63 TraesCS4B01G288500 chr3B 84.921 126 12 5 3398 3519 52361450 52361572 3.650000e-23 121.0
64 TraesCS4B01G288500 chr3B 83.740 123 17 2 3390 3510 590252195 590252074 6.100000e-21 113.0
65 TraesCS4B01G288500 chr6B 75.407 614 108 20 4026 4620 2926895 2927484 2.660000e-64 257.0
66 TraesCS4B01G288500 chr1B 77.670 412 83 5 4459 4865 50354052 50354459 7.460000e-60 243.0
67 TraesCS4B01G288500 chr1B 75.309 162 34 3 4644 4800 39114386 39114546 1.040000e-08 73.1
68 TraesCS4B01G288500 chr2D 86.719 128 16 1 3397 3523 535222760 535222633 2.800000e-29 141.0
69 TraesCS4B01G288500 chr2D 90.385 104 8 2 3534 3636 430605650 430605548 1.300000e-27 135.0
70 TraesCS4B01G288500 chr2D 96.104 77 3 0 3532 3608 12564950 12565026 7.840000e-25 126.0
71 TraesCS4B01G288500 chr2D 85.345 116 14 2 4341 4453 543517588 543517703 4.720000e-22 117.0
72 TraesCS4B01G288500 chr2D 82.979 94 14 1 5879 5970 555310032 555309939 4.790000e-12 84.2
73 TraesCS4B01G288500 chr2D 80.612 98 15 4 5877 5972 335120634 335120729 1.040000e-08 73.1
74 TraesCS4B01G288500 chr2D 80.645 93 16 1 5878 5968 630831549 630831641 3.730000e-08 71.3
75 TraesCS4B01G288500 chr2D 93.333 45 2 1 7199 7243 503137434 503137391 1.730000e-06 65.8
76 TraesCS4B01G288500 chr7B 88.785 107 11 1 3534 3640 72679395 72679290 6.060000e-26 130.0
77 TraesCS4B01G288500 chr7B 82.171 129 20 2 3397 3523 106108359 106108232 2.840000e-19 108.0
78 TraesCS4B01G288500 chr7B 97.561 41 1 0 7199 7239 107127393 107127433 3.730000e-08 71.3
79 TraesCS4B01G288500 chr5B 73.947 380 74 15 4397 4764 487495381 487495747 6.060000e-26 130.0
80 TraesCS4B01G288500 chr5D 90.476 84 6 2 3645 3726 498682631 498682714 7.900000e-20 110.0
81 TraesCS4B01G288500 chr1D 97.500 40 1 0 7203 7242 12067490 12067451 1.340000e-07 69.4
82 TraesCS4B01G288500 chr1D 95.349 43 2 0 7197 7239 275947615 275947657 1.340000e-07 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 TraesCS4B01G288500 chr4B 573389670 573397112 7442 True 6603.000000 10251 100.000000 1 7443 2 chr4B.!!$R1 7442
1 TraesCS4B01G288500 chr4D 459073827 459083538 9711 True 1599.250000 5511 90.945167 4 7443 6 chr4D.!!$R4 7439
2 TraesCS4B01G288500 chr4D 82231277 82232039 762 True 292.000000 292 74.444000 4755 5550 1 chr4D.!!$R1 795
3 TraesCS4B01G288500 chr4D 207481197 207481756 559 False 211.000000 211 74.439000 4844 5399 1 chr4D.!!$F1 555
4 TraesCS4B01G288500 chr4D 497254236 497254895 659 False 211.000000 211 73.789000 4313 4984 1 chr4D.!!$F3 671
5 TraesCS4B01G288500 chr4A 9613967 9621570 7603 False 1164.428571 4599 90.080000 164 7442 7 chr4A.!!$F5 7278
6 TraesCS4B01G288500 chr4A 638247419 638248560 1141 False 315.000000 315 72.886000 4020 5179 1 chr4A.!!$F3 1159
7 TraesCS4B01G288500 chr4A 692339392 692340077 685 False 292.000000 292 74.860000 4548 5251 1 chr4A.!!$F4 703
8 TraesCS4B01G288500 chr1A 534053282 534054819 1537 False 761.000000 761 76.441000 4033 5551 1 chr1A.!!$F1 1518
9 TraesCS4B01G288500 chr2A 749052860 749054365 1505 False 669.000000 669 75.359000 4026 5512 1 chr2A.!!$F4 1486
10 TraesCS4B01G288500 chr2A 565315836 565316799 963 True 520.000000 520 77.310000 4024 4947 1 chr2A.!!$R2 923
11 TraesCS4B01G288500 chr2A 498044815 498045869 1054 False 405.000000 405 74.301000 4458 5551 1 chr2A.!!$F3 1093
12 TraesCS4B01G288500 chr2A 760931123 760931956 833 False 368.000000 368 75.593000 4210 5070 1 chr2A.!!$F5 860
13 TraesCS4B01G288500 chr2A 598981240 598981760 520 True 363.000000 363 79.658000 4228 4741 1 chr2A.!!$R3 513
14 TraesCS4B01G288500 chr2B 34077137 34078227 1090 False 662.000000 662 78.175000 4341 5429 1 chr2B.!!$F1 1088
15 TraesCS4B01G288500 chr2B 436962407 436963827 1420 False 483.000000 483 73.916000 4104 5551 1 chr2B.!!$F3 1447
16 TraesCS4B01G288500 chr7D 206682416 206683618 1202 True 656.000000 656 77.232000 4215 5389 1 chr7D.!!$R3 1174
17 TraesCS4B01G288500 chr6D 26004690 26005929 1239 True 647.000000 647 76.797000 4019 5260 1 chr6D.!!$R1 1241
18 TraesCS4B01G288500 chr3D 406410457 406411585 1128 False 630.000000 630 77.324000 4373 5491 1 chr3D.!!$F3 1118
19 TraesCS4B01G288500 chr3D 508309098 508310144 1046 True 628.000000 628 77.904000 4514 5551 1 chr3D.!!$R1 1037
20 TraesCS4B01G288500 chr7A 709420512 709421769 1257 True 573.000000 573 75.504000 4022 5279 1 chr7A.!!$R2 1257
21 TraesCS4B01G288500 chr6A 183950585 183951475 890 False 523.000000 523 77.728000 4044 4919 1 chr6A.!!$F1 875
22 TraesCS4B01G288500 chr3A 728937683 728939086 1403 False 392.000000 392 72.956000 4090 5492 1 chr3A.!!$F1 1402
23 TraesCS4B01G288500 chr3B 475196666 475197425 759 True 292.000000 292 74.356000 4124 4874 1 chr3B.!!$R1 750
24 TraesCS4B01G288500 chr6B 2926895 2927484 589 False 257.000000 257 75.407000 4026 4620 1 chr6B.!!$F1 594

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
86 87 0.250770 GAAGGTTTCTTCTGCGGGGT 60.251 55.000 0.00 0.00 44.43 4.95 F
90 91 0.321298 GTTTCTTCTGCGGGGTGCTA 60.321 55.000 0.00 0.00 46.63 3.49 F
195 197 0.464036 CGGGGGATGAAGACGAATCA 59.536 55.000 0.00 0.00 0.00 2.57 F
372 509 0.757188 ATTTTGTTCACGGGTGGGCA 60.757 50.000 0.00 0.00 0.00 5.36 F
400 2377 1.056660 TTTATGAGGAGATCCCGCCC 58.943 55.000 0.00 0.00 40.87 6.13 F
642 2626 1.406069 CGATCCGATTCCATCCCATCC 60.406 57.143 0.00 0.00 0.00 3.51 F
643 2627 1.912043 GATCCGATTCCATCCCATCCT 59.088 52.381 0.00 0.00 0.00 3.24 F
2284 4965 2.032979 CGTTTTCATGGCCAAACAAAGC 60.033 45.455 10.96 10.15 33.23 3.51 F
2622 5306 2.060980 AGGCAGCCCCTTACTCTCG 61.061 63.158 8.22 0.00 43.06 4.04 F
4409 7241 0.802607 GTTTCACCTCGGCGCTCTAG 60.803 60.000 7.64 1.96 0.00 2.43 F
5167 8172 1.250840 GGAAACCATGGTGGGAGTGC 61.251 60.000 20.60 0.00 43.37 4.40 F
5512 8545 0.035439 GGTCATTTCAGGCGGGAAGA 60.035 55.000 0.00 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 4386 2.159382 TCCTGATTGGAAAAACGAGGC 58.841 47.619 0.00 0.00 42.94 4.70 R
1989 4663 5.488341 TGGTAACTAAGAGCAGATGGAAAC 58.512 41.667 0.00 0.00 37.61 2.78 R
2132 4813 3.527533 TGTATCGCAATGTCCCTGTTAC 58.472 45.455 0.00 0.00 0.00 2.50 R
2284 4965 9.597170 CAATGGAGATGACTGGATTATACATAG 57.403 37.037 0.00 0.00 0.00 2.23 R
2514 5198 5.474876 CCTTAAATGTCTTGAAGGCTTCTGT 59.525 40.000 26.26 4.46 36.40 3.41 R
2605 5289 2.501610 CGAGAGTAAGGGGCTGCC 59.498 66.667 11.05 11.05 0.00 4.85 R
2747 5432 4.521639 ACATGTGTGATCAGAGCAATTGTT 59.478 37.500 7.40 0.00 0.00 2.83 R
4031 6731 1.321474 TTGTGGGTCGACGTTAGAGT 58.679 50.000 9.92 0.00 0.00 3.24 R
4652 7554 0.314935 GGGTAAGACCAACGACGACA 59.685 55.000 0.00 0.00 41.02 4.35 R
5430 8457 0.034896 AGCGGACACGACCTTGATTT 59.965 50.000 0.00 0.00 44.60 2.17 R
6397 9436 0.608640 CGAGTACTTGGGCCTTGTCT 59.391 55.000 4.53 3.51 0.00 3.41 R
7142 10343 2.672381 CCAGTGCACTTGTTTGTTTTGG 59.328 45.455 18.94 8.40 0.00 3.28 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
20 21 1.338973 GTACCGGTGTGAGACAACTGA 59.661 52.381 19.93 0.00 32.52 3.41
26 27 4.556233 CGGTGTGAGACAACTGAGAAATA 58.444 43.478 0.00 0.00 32.52 1.40
37 38 8.517878 AGACAACTGAGAAATAATGGATGTTTG 58.482 33.333 0.00 0.00 0.00 2.93
40 41 7.396540 ACTGAGAAATAATGGATGTTTGGTC 57.603 36.000 0.00 0.00 0.00 4.02
41 42 7.177878 ACTGAGAAATAATGGATGTTTGGTCT 58.822 34.615 0.00 0.00 0.00 3.85
73 74 0.602905 CTCTTCCAACGGCGAAGGTT 60.603 55.000 16.62 0.00 37.83 3.50
86 87 0.250770 GAAGGTTTCTTCTGCGGGGT 60.251 55.000 0.00 0.00 44.43 4.95
90 91 0.321298 GTTTCTTCTGCGGGGTGCTA 60.321 55.000 0.00 0.00 46.63 3.49
101 102 1.049289 GGGGTGCTAGTCCAGTAGGG 61.049 65.000 8.04 0.00 34.83 3.53
122 123 1.445582 GTCAACACGTAGGCTCCGG 60.446 63.158 4.08 0.00 0.00 5.14
130 131 1.464376 CGTAGGCTCCGGTGATGGAT 61.464 60.000 7.92 0.00 37.41 3.41
133 134 2.498941 GGCTCCGGTGATGGATCGA 61.499 63.158 7.92 0.00 37.41 3.59
138 139 1.224069 CCGGTGATGGATCGACATGC 61.224 60.000 0.00 0.00 0.00 4.06
162 163 2.629137 TGGAATACCATCATGCCAATGC 59.371 45.455 0.00 0.00 41.77 3.56
195 197 0.464036 CGGGGGATGAAGACGAATCA 59.536 55.000 0.00 0.00 0.00 2.57
222 224 9.573133 CATGGACTTTGATGTAACCTTTTAATC 57.427 33.333 0.00 0.00 0.00 1.75
231 233 9.349713 TGATGTAACCTTTTAATCTTTCTGTGT 57.650 29.630 0.00 0.00 0.00 3.72
371 508 1.249407 TATTTTGTTCACGGGTGGGC 58.751 50.000 0.00 0.00 0.00 5.36
372 509 0.757188 ATTTTGTTCACGGGTGGGCA 60.757 50.000 0.00 0.00 0.00 5.36
400 2377 1.056660 TTTATGAGGAGATCCCGCCC 58.943 55.000 0.00 0.00 40.87 6.13
430 2407 5.128171 AGCACATAGTACGGGTTGAGAATTA 59.872 40.000 0.00 0.00 0.00 1.40
434 2411 4.482952 AGTACGGGTTGAGAATTAAGGG 57.517 45.455 0.00 0.00 0.00 3.95
602 2586 4.032900 CGATCAGTTGTAAATCTTCCCACG 59.967 45.833 0.00 0.00 0.00 4.94
642 2626 1.406069 CGATCCGATTCCATCCCATCC 60.406 57.143 0.00 0.00 0.00 3.51
643 2627 1.912043 GATCCGATTCCATCCCATCCT 59.088 52.381 0.00 0.00 0.00 3.24
644 2628 2.713828 TCCGATTCCATCCCATCCTA 57.286 50.000 0.00 0.00 0.00 2.94
645 2629 3.205519 TCCGATTCCATCCCATCCTAT 57.794 47.619 0.00 0.00 0.00 2.57
646 2630 3.531059 TCCGATTCCATCCCATCCTATT 58.469 45.455 0.00 0.00 0.00 1.73
706 2690 2.689034 CCCTTCGCCCTCCTCCTT 60.689 66.667 0.00 0.00 0.00 3.36
1156 3142 4.096003 ACCATCCGGAACCCTGCG 62.096 66.667 9.01 0.00 35.59 5.18
1246 3236 9.337091 CCTCCGTTGTTAATTTATTGTTAACAG 57.663 33.333 8.56 2.80 46.58 3.16
1260 3250 9.571810 TTATTGTTAACAGCAGATGCAAAATAG 57.428 29.630 8.56 0.00 45.16 1.73
1363 3366 9.949174 CTCTATGATCAGCATGTAGACATATAC 57.051 37.037 0.09 0.00 37.87 1.47
1364 3367 8.616076 TCTATGATCAGCATGTAGACATATACG 58.384 37.037 0.09 0.00 37.87 3.06
1365 3368 6.575162 TGATCAGCATGTAGACATATACGT 57.425 37.500 0.00 0.00 37.40 3.57
1367 3370 8.281212 TGATCAGCATGTAGACATATACGTAT 57.719 34.615 13.54 13.54 37.40 3.06
1368 3371 8.739972 TGATCAGCATGTAGACATATACGTATT 58.260 33.333 14.33 0.00 37.40 1.89
1369 3372 9.574458 GATCAGCATGTAGACATATACGTATTT 57.426 33.333 14.33 2.61 37.40 1.40
1410 4074 8.076178 AGAGTTATGTTTGAACAGTGCATTTAC 58.924 33.333 2.77 0.00 43.04 2.01
1419 4083 9.891828 TTTGAACAGTGCATTTACAGTTATAAG 57.108 29.630 0.00 0.00 31.57 1.73
1457 4125 9.565213 GTTCTTTGAGTAAGCTTATTCGTAGTA 57.435 33.333 20.22 12.37 33.66 1.82
1629 4297 7.947890 ACAAGGGAGTTTTTCAAGGATAATACA 59.052 33.333 0.00 0.00 0.00 2.29
1681 4349 7.993183 CACATATGGACCTGGAAGTAAGTTAAT 59.007 37.037 7.80 0.00 0.00 1.40
1693 4366 6.148976 GGAAGTAAGTTAATGGACACCTTGTC 59.851 42.308 0.00 0.00 46.23 3.18
1712 4386 7.665974 ACCTTGTCTTTTTCCAACCTATAGAAG 59.334 37.037 0.00 0.00 0.00 2.85
1986 4660 3.181488 TGCACCTTGATTGTGTGTCAAAG 60.181 43.478 0.00 0.00 39.62 2.77
1987 4661 3.181487 GCACCTTGATTGTGTGTCAAAGT 60.181 43.478 0.00 0.00 39.62 2.66
1989 4663 4.799949 CACCTTGATTGTGTGTCAAAGTTG 59.200 41.667 0.00 0.00 39.62 3.16
1990 4664 4.462483 ACCTTGATTGTGTGTCAAAGTTGT 59.538 37.500 0.00 0.00 39.62 3.32
2006 4681 6.205464 TCAAAGTTGTTTCCATCTGCTCTTAG 59.795 38.462 0.00 0.00 0.00 2.18
2132 4813 3.006940 TGTATCCTTTGCGCAGGTTTAG 58.993 45.455 11.31 4.46 35.15 1.85
2284 4965 2.032979 CGTTTTCATGGCCAAACAAAGC 60.033 45.455 10.96 10.15 33.23 3.51
2316 4997 3.776417 TCCAGTCATCTCCATTGATGTCA 59.224 43.478 0.00 0.00 43.03 3.58
2514 5198 4.103153 AGTTTCCTGACTTCAGTCCATCAA 59.897 41.667 4.48 0.00 44.15 2.57
2540 5224 5.707764 AGAAGCCTTCAAGACATTTAAGGTC 59.292 40.000 7.29 1.13 40.52 3.85
2605 5289 7.438160 GGATTGTTCTAAAAGACAACCCAAAAG 59.562 37.037 0.00 0.00 26.79 2.27
2622 5306 2.060980 AGGCAGCCCCTTACTCTCG 61.061 63.158 8.22 0.00 43.06 4.04
2702 5387 8.718158 TGATCTATAGACTTGGATCTGAACAT 57.282 34.615 4.10 0.00 36.51 2.71
2735 5420 6.291955 GCATTCTCAAATCAAGTGTTTGTGTG 60.292 38.462 0.00 0.00 37.70 3.82
2849 5534 3.791953 TGATTGGGTAAGGTTTTCCGA 57.208 42.857 0.00 0.00 46.35 4.55
3090 5775 2.346766 TCATGAGGTTGCACACAAGT 57.653 45.000 0.00 0.00 36.16 3.16
3165 5850 2.288666 TCATAGGCCAATCTCAAACGC 58.711 47.619 5.01 0.00 0.00 4.84
3307 5992 5.830912 TCAGATTTTCACACGAAATTGCTT 58.169 33.333 0.00 0.00 40.75 3.91
3343 6028 4.901197 TGTCACCAAAAGGCAGTCTATA 57.099 40.909 0.00 0.00 0.00 1.31
3376 6061 2.708216 TTCCACAGTTGTGCTTCAGA 57.292 45.000 6.74 0.00 44.34 3.27
3377 6062 2.936919 TCCACAGTTGTGCTTCAGAT 57.063 45.000 6.74 0.00 44.34 2.90
3383 6068 2.414481 CAGTTGTGCTTCAGATTCTCCG 59.586 50.000 0.00 0.00 0.00 4.63
3387 6072 3.942829 TGTGCTTCAGATTCTCCGATTT 58.057 40.909 0.00 0.00 0.00 2.17
3424 6109 4.387437 CCCTCCTTCCCAAAATATAAGGCA 60.387 45.833 0.00 0.00 38.70 4.75
3441 6126 2.629137 AGGCACATTTGACTTTGCATGA 59.371 40.909 0.00 0.00 38.26 3.07
3603 6289 6.451064 CAACTTGTTTGGGACTAAAGAGTT 57.549 37.500 4.91 4.91 35.45 3.01
3604 6290 6.863275 CAACTTGTTTGGGACTAAAGAGTTT 58.137 36.000 6.94 0.00 35.45 2.66
3605 6291 6.451064 ACTTGTTTGGGACTAAAGAGTTTG 57.549 37.500 0.00 0.00 35.45 2.93
3606 6292 5.949952 ACTTGTTTGGGACTAAAGAGTTTGT 59.050 36.000 0.00 0.00 35.45 2.83
3607 6293 6.436218 ACTTGTTTGGGACTAAAGAGTTTGTT 59.564 34.615 0.00 0.00 35.45 2.83
3608 6294 7.612633 ACTTGTTTGGGACTAAAGAGTTTGTTA 59.387 33.333 0.00 0.00 35.45 2.41
3609 6295 7.324354 TGTTTGGGACTAAAGAGTTTGTTAC 57.676 36.000 0.00 0.00 35.45 2.50
3610 6296 7.114095 TGTTTGGGACTAAAGAGTTTGTTACT 58.886 34.615 0.00 0.00 40.71 2.24
3611 6297 8.266473 TGTTTGGGACTAAAGAGTTTGTTACTA 58.734 33.333 0.00 0.00 37.17 1.82
3612 6298 9.112725 GTTTGGGACTAAAGAGTTTGTTACTAA 57.887 33.333 0.00 0.00 37.17 2.24
3613 6299 9.683870 TTTGGGACTAAAGAGTTTGTTACTAAA 57.316 29.630 0.00 0.00 37.17 1.85
3614 6300 8.897872 TGGGACTAAAGAGTTTGTTACTAAAG 57.102 34.615 0.00 0.00 37.17 1.85
3627 6313 5.897050 TGTTACTAAAGGCTTTGTTGTTGG 58.103 37.500 22.32 0.00 0.00 3.77
3636 6322 2.414825 GCTTTGTTGTTGGTGTTGTTGG 59.585 45.455 0.00 0.00 0.00 3.77
3638 6324 4.810790 CTTTGTTGTTGGTGTTGTTGGTA 58.189 39.130 0.00 0.00 0.00 3.25
3642 6328 6.525578 TGTTGTTGGTGTTGTTGGTATTTA 57.474 33.333 0.00 0.00 0.00 1.40
3649 6335 9.997482 GTTGGTGTTGTTGGTATTTATATACAG 57.003 33.333 5.80 0.00 38.71 2.74
3715 6414 5.621197 ATCAATGCGCGCCTTATATTTTA 57.379 34.783 30.77 11.45 0.00 1.52
3733 6432 4.957606 TTTAGGAAGGAGGGGCATTTTA 57.042 40.909 0.00 0.00 0.00 1.52
3812 6511 5.637810 ACAATTTGATTTCTCGCGTCTAAGA 59.362 36.000 5.77 0.00 0.00 2.10
3863 6562 8.518430 TTGCATGGTATTTCTTTCAGCTATTA 57.482 30.769 0.00 0.00 0.00 0.98
3971 6670 8.102676 AACCTTTTAAGGGTAAGACGCTATTTA 58.897 33.333 12.87 0.00 46.58 1.40
3972 6671 7.913423 CCTTTTAAGGGTAAGACGCTATTTAC 58.087 38.462 0.32 0.00 40.76 2.01
4009 6709 9.270640 CTTGAATAGAAACTCATGCTTATAGCT 57.729 33.333 0.00 0.00 42.97 3.32
4031 6731 3.181438 TGCTACAAGTTTCCTTAGGGCAA 60.181 43.478 0.00 0.00 0.00 4.52
4203 6906 6.372103 ACACGAACGGATTTCATATAAACCAA 59.628 34.615 0.00 0.00 33.24 3.67
4236 7002 3.171277 GCAAACACGGCAGATTTCATAC 58.829 45.455 0.00 0.00 0.00 2.39
4284 7060 8.441312 TTTCGGACATACTTGAACTAAAAGTT 57.559 30.769 0.00 0.00 41.95 2.66
4408 7240 1.214589 GTTTCACCTCGGCGCTCTA 59.785 57.895 7.64 0.00 0.00 2.43
4409 7241 0.802607 GTTTCACCTCGGCGCTCTAG 60.803 60.000 7.64 1.96 0.00 2.43
4456 7341 3.241530 TTGCCTGCCTCCACGTCT 61.242 61.111 0.00 0.00 0.00 4.18
4512 7400 1.604378 CTGCAACTGGAGGGTAGGG 59.396 63.158 0.00 0.00 0.00 3.53
4557 7449 1.679977 GTGGTGACCTGCCATGCAT 60.680 57.895 2.11 0.00 38.13 3.96
4616 7509 4.980805 TTCGTGGTCGTGGCAGCC 62.981 66.667 3.66 3.66 38.33 4.85
4652 7554 1.757699 GGAGTTAGCGATGTCCTCCTT 59.242 52.381 7.58 0.00 38.90 3.36
4673 7579 1.444895 CGTCGTTGGTCTTACCCCG 60.445 63.158 0.00 0.00 37.50 5.73
4674 7580 1.667722 GTCGTTGGTCTTACCCCGT 59.332 57.895 0.00 0.00 37.50 5.28
4920 7841 1.705186 CCTCCCAAAACTTCTCCTCCA 59.295 52.381 0.00 0.00 0.00 3.86
4934 7873 1.988956 CTCCAGCTCCTCCTGCACT 60.989 63.158 0.00 0.00 0.00 4.40
5141 8142 2.298729 GTCTGTCTGAGAGAGCTTTGGT 59.701 50.000 4.56 0.00 0.00 3.67
5167 8172 1.250840 GGAAACCATGGTGGGAGTGC 61.251 60.000 20.60 0.00 43.37 4.40
5224 8232 1.523938 GTCTATGAACGGGGCTGCC 60.524 63.158 11.05 11.05 0.00 4.85
5241 8250 1.356527 GCCGTTTATATAGCGGGCGG 61.357 60.000 21.48 14.64 45.02 6.13
5292 8304 4.077184 TGGCGCCGGAGTAGGTTG 62.077 66.667 23.90 0.00 0.00 3.77
5301 8313 2.353406 CCGGAGTAGGTTGTTCGACAAT 60.353 50.000 0.00 0.00 40.59 2.71
5311 8323 4.271533 GGTTGTTCGACAATAGTGTGTCAA 59.728 41.667 0.00 0.00 46.90 3.18
5313 8325 5.590104 TGTTCGACAATAGTGTGTCAATG 57.410 39.130 0.00 0.00 46.90 2.82
5375 8402 2.802740 TACAGAGCAGTCGCGTGCAG 62.803 60.000 21.73 13.78 46.60 4.41
5430 8457 0.107897 ACATCGCTTCAATGCCGGTA 60.108 50.000 1.90 0.00 0.00 4.02
5431 8458 1.013596 CATCGCTTCAATGCCGGTAA 58.986 50.000 1.90 0.00 0.00 2.85
5433 8460 1.745232 TCGCTTCAATGCCGGTAAAT 58.255 45.000 1.90 0.00 0.00 1.40
5434 8461 1.668751 TCGCTTCAATGCCGGTAAATC 59.331 47.619 1.90 0.00 0.00 2.17
5435 8462 1.400142 CGCTTCAATGCCGGTAAATCA 59.600 47.619 1.90 0.00 0.00 2.57
5494 8527 2.590007 GCTATGGAGTGGCGCTGG 60.590 66.667 4.71 0.00 0.00 4.85
5512 8545 0.035439 GGTCATTTCAGGCGGGAAGA 60.035 55.000 0.00 0.00 0.00 2.87
5516 8549 1.899437 ATTTCAGGCGGGAAGAGCGA 61.899 55.000 0.00 0.00 35.00 4.93
5527 8560 0.452585 GAAGAGCGAGTAGGCGAGTT 59.547 55.000 0.00 0.00 38.18 3.01
5538 8571 1.660242 AGGCGAGTTAGGGGGTTTTA 58.340 50.000 0.00 0.00 0.00 1.52
5881 8914 1.263217 GTTGGATGACACAACACCGAC 59.737 52.381 3.65 0.00 45.62 4.79
5887 8920 1.338294 TGACACAACACCGACACAAGT 60.338 47.619 0.00 0.00 0.00 3.16
5890 8923 0.808453 ACAACACCGACACAAGTCCG 60.808 55.000 0.00 0.00 41.87 4.79
5921 8954 2.159627 GCACAATACTTCTGGACAACGG 59.840 50.000 0.00 0.00 0.00 4.44
5922 8955 3.399330 CACAATACTTCTGGACAACGGT 58.601 45.455 0.00 0.00 0.00 4.83
5923 8956 3.432252 CACAATACTTCTGGACAACGGTC 59.568 47.826 0.00 0.00 43.55 4.79
5937 8972 1.243342 ACGGTCCGAACGTATGTGGA 61.243 55.000 20.51 0.00 43.60 4.02
5951 8986 1.666872 GTGGACGGTTTGAGGGTCG 60.667 63.158 0.00 0.00 0.00 4.79
5953 8988 2.741211 GACGGTTTGAGGGTCGGC 60.741 66.667 0.00 0.00 0.00 5.54
5970 9005 3.168773 GCGTTGGAGATGCCCTTAA 57.831 52.632 0.00 0.00 34.03 1.85
5975 9010 3.206964 GTTGGAGATGCCCTTAACTAGC 58.793 50.000 0.00 0.00 34.97 3.42
6086 9121 9.034544 GGCATTTCATATTTTCAAGGTACAATC 57.965 33.333 0.00 0.00 0.00 2.67
6091 9126 8.062065 TCATATTTTCAAGGTACAATCCCAAC 57.938 34.615 0.00 0.00 0.00 3.77
6167 9202 2.888834 AACATGTTCTTTGGGTGTGC 57.111 45.000 4.92 0.00 0.00 4.57
6168 9203 1.774110 ACATGTTCTTTGGGTGTGCA 58.226 45.000 0.00 0.00 0.00 4.57
6206 9245 5.198274 GCGAATAAAAATAAGCCTCGTGAG 58.802 41.667 0.00 0.00 0.00 3.51
6254 9293 4.670765 AGAGCAAAATCATCAGGTTCCTT 58.329 39.130 0.00 0.00 0.00 3.36
6284 9323 7.686859 GCCTTCACTCTGGAAAAAGGTAAAAAT 60.687 37.037 0.00 0.00 38.97 1.82
6352 9391 2.197465 GGAGGTGGTTATCCTGAAGGT 58.803 52.381 0.00 0.00 35.20 3.50
6359 9398 5.280317 GGTGGTTATCCTGAAGGTGTTTCTA 60.280 44.000 0.00 0.00 36.71 2.10
6397 9436 2.025226 AGAGGATAGGGTGTTCGAGTCA 60.025 50.000 0.00 0.00 0.00 3.41
6519 9558 2.109425 ACTCCATAAAACCGACTGGC 57.891 50.000 0.00 0.00 39.70 4.85
6542 9581 3.048600 AGTTGGATTAGGATGCCTAGCA 58.951 45.455 0.00 0.00 44.86 3.49
6591 9630 3.213206 TCCTTGAGCAGAGCAGAAAAA 57.787 42.857 0.00 0.00 0.00 1.94
6703 9743 5.241662 ACAAATAGCTCTGACTTTGACTCC 58.758 41.667 0.00 0.00 33.79 3.85
6808 9964 4.431131 ACCGCCATTCCCAGCAGG 62.431 66.667 0.00 0.00 0.00 4.85
6922 10093 3.876914 TGCTATGTGTGCTTTGCCTATAC 59.123 43.478 0.00 0.00 0.00 1.47
6924 10095 2.753055 TGTGTGCTTTGCCTATACGA 57.247 45.000 0.00 0.00 0.00 3.43
6932 10103 3.877508 GCTTTGCCTATACGATTGGTCTT 59.122 43.478 0.00 0.00 0.00 3.01
7026 10197 9.595823 CATTTCTCTCAATCTAATGGCAAAATT 57.404 29.630 0.00 0.00 0.00 1.82
7053 10254 5.163395 CCTTGAATAGAGTTGAGGGGTCTAC 60.163 48.000 0.00 0.00 0.00 2.59
7101 10302 5.830457 CAGACCTGGTCTTGATATGACTAGA 59.170 44.000 26.37 0.00 41.37 2.43
7142 10343 2.873797 AAAGCGAGGCCCTTTGATC 58.126 52.632 0.00 0.00 31.71 2.92
7183 10384 6.925165 CACTGGTCACTTGAAGCAAATTATTT 59.075 34.615 0.00 0.00 0.00 1.40
7297 10513 4.998671 TGTTTCAATCTTTCTTGTGGCA 57.001 36.364 0.00 0.00 0.00 4.92
7300 10516 4.572985 TTCAATCTTTCTTGTGGCACTG 57.427 40.909 19.83 11.68 0.00 3.66
7302 10518 3.565482 TCAATCTTTCTTGTGGCACTGAC 59.435 43.478 19.83 0.00 0.00 3.51
7367 10583 4.212143 TCTTGTGACCCTGATGATCTTG 57.788 45.455 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.611977 CTCAGTTGTCTCACACCGGTA 59.388 52.381 6.87 0.00 0.00 4.02
7 8 6.768483 TCCATTATTTCTCAGTTGTCTCACA 58.232 36.000 0.00 0.00 0.00 3.58
10 11 7.856145 ACATCCATTATTTCTCAGTTGTCTC 57.144 36.000 0.00 0.00 0.00 3.36
17 18 7.636150 AGACCAAACATCCATTATTTCTCAG 57.364 36.000 0.00 0.00 0.00 3.35
20 21 7.454380 TCCAAAGACCAAACATCCATTATTTCT 59.546 33.333 0.00 0.00 0.00 2.52
26 27 5.186409 CAGATCCAAAGACCAAACATCCATT 59.814 40.000 0.00 0.00 0.00 3.16
37 38 1.065564 AGAGCTGCAGATCCAAAGACC 60.066 52.381 27.52 1.31 0.00 3.85
40 41 2.015587 GGAAGAGCTGCAGATCCAAAG 58.984 52.381 27.52 0.00 0.00 2.77
41 42 1.352017 TGGAAGAGCTGCAGATCCAAA 59.648 47.619 27.52 9.11 37.24 3.28
73 74 1.192146 ACTAGCACCCCGCAGAAGAA 61.192 55.000 0.00 0.00 46.13 2.52
86 87 1.756950 CGGCCCTACTGGACTAGCA 60.757 63.158 0.00 0.00 41.74 3.49
90 91 1.229082 TTGACGGCCCTACTGGACT 60.229 57.895 0.00 0.00 41.74 3.85
122 123 0.530650 ACCGCATGTCGATCCATCAC 60.531 55.000 10.48 0.00 41.67 3.06
130 131 0.179094 GGTATTCCACCGCATGTCGA 60.179 55.000 10.48 0.00 41.67 4.20
162 163 0.899717 CCCCCGAATGGCCATTATGG 60.900 60.000 30.73 30.26 41.55 2.74
195 197 6.976934 AAAAGGTTACATCAAAGTCCATGT 57.023 33.333 0.00 0.00 37.08 3.21
252 254 8.487313 AACACCCAGAAAAATTGAAAAGTTAC 57.513 30.769 0.00 0.00 30.03 2.50
326 328 0.683504 TACACCGGGAGAAGAGAGGC 60.684 60.000 6.32 0.00 0.00 4.70
371 508 8.345565 CGGGATCTCCTCATAAATAAAAACTTG 58.654 37.037 0.00 0.00 35.95 3.16
372 509 7.013369 GCGGGATCTCCTCATAAATAAAAACTT 59.987 37.037 0.00 0.00 35.95 2.66
400 2377 0.039437 CCGTACTATGTGCTAGCCCG 60.039 60.000 13.29 1.86 0.00 6.13
403 2380 2.100252 TCAACCCGTACTATGTGCTAGC 59.900 50.000 8.10 8.10 0.00 3.42
404 2381 3.630769 TCTCAACCCGTACTATGTGCTAG 59.369 47.826 0.00 0.00 0.00 3.42
405 2382 3.623703 TCTCAACCCGTACTATGTGCTA 58.376 45.455 0.00 0.00 0.00 3.49
406 2383 2.453521 TCTCAACCCGTACTATGTGCT 58.546 47.619 0.00 0.00 0.00 4.40
407 2384 2.953466 TCTCAACCCGTACTATGTGC 57.047 50.000 0.00 0.00 0.00 4.57
408 2385 6.479001 CCTTAATTCTCAACCCGTACTATGTG 59.521 42.308 0.00 0.00 0.00 3.21
409 2386 6.407752 CCCTTAATTCTCAACCCGTACTATGT 60.408 42.308 0.00 0.00 0.00 2.29
410 2387 5.989777 CCCTTAATTCTCAACCCGTACTATG 59.010 44.000 0.00 0.00 0.00 2.23
475 2456 1.309688 GGCTATGGGGCCCAGAAAA 59.690 57.895 31.98 14.92 45.92 2.29
476 2457 3.015383 GGCTATGGGGCCCAGAAA 58.985 61.111 31.98 17.52 45.92 2.52
484 2465 6.642707 TTTTATTTTCGTATGGCTATGGGG 57.357 37.500 0.00 0.00 0.00 4.96
602 2586 3.621268 TCGGATCGTGTTCATTCCATTTC 59.379 43.478 0.00 0.00 0.00 2.17
642 2626 4.357918 AGACGGGAATGGAATGGAATAG 57.642 45.455 0.00 0.00 0.00 1.73
643 2627 4.165180 TCAAGACGGGAATGGAATGGAATA 59.835 41.667 0.00 0.00 0.00 1.75
644 2628 3.053693 TCAAGACGGGAATGGAATGGAAT 60.054 43.478 0.00 0.00 0.00 3.01
645 2629 2.307392 TCAAGACGGGAATGGAATGGAA 59.693 45.455 0.00 0.00 0.00 3.53
646 2630 1.912731 TCAAGACGGGAATGGAATGGA 59.087 47.619 0.00 0.00 0.00 3.41
791 2777 4.803426 CGGGCGAGACACTCCTGC 62.803 72.222 0.00 0.00 0.00 4.85
792 2778 3.057547 CTCGGGCGAGACACTCCTG 62.058 68.421 0.00 0.00 44.53 3.86
969 2955 1.381327 ACCTGGACGACCGATGGAT 60.381 57.895 14.72 0.72 39.42 3.41
1156 3142 3.188011 GGCTTCTAGTTTGCCGCC 58.812 61.111 7.42 0.00 37.11 6.13
1246 3236 2.493278 ACACCACCTATTTTGCATCTGC 59.507 45.455 0.00 0.00 42.50 4.26
1363 3366 7.963981 ACTCTCATCAAACACACATAAATACG 58.036 34.615 0.00 0.00 0.00 3.06
1367 3370 9.283768 ACATAACTCTCATCAAACACACATAAA 57.716 29.630 0.00 0.00 0.00 1.40
1368 3371 8.846943 ACATAACTCTCATCAAACACACATAA 57.153 30.769 0.00 0.00 0.00 1.90
1369 3372 8.846943 AACATAACTCTCATCAAACACACATA 57.153 30.769 0.00 0.00 0.00 2.29
1371 3374 7.281999 TCAAACATAACTCTCATCAAACACACA 59.718 33.333 0.00 0.00 0.00 3.72
1372 3375 7.639039 TCAAACATAACTCTCATCAAACACAC 58.361 34.615 0.00 0.00 0.00 3.82
1385 4049 7.860373 TGTAAATGCACTGTTCAAACATAACTC 59.140 33.333 0.00 0.00 38.41 3.01
1391 4055 5.574891 ACTGTAAATGCACTGTTCAAACA 57.425 34.783 0.00 0.00 37.37 2.83
1419 4083 7.750903 GCTTACTCAAAGAACCAAATGTGATAC 59.249 37.037 0.00 0.00 37.38 2.24
1423 4087 6.076981 AGCTTACTCAAAGAACCAAATGTG 57.923 37.500 0.00 0.00 37.38 3.21
1438 4106 7.918643 AGTGTCTACTACGAATAAGCTTACTC 58.081 38.462 8.70 6.59 34.74 2.59
1493 4161 6.805713 TCTGTAATCTGCATATTCAGTCGAA 58.194 36.000 16.39 0.00 35.63 3.71
1693 4366 5.294552 CGAGGCTTCTATAGGTTGGAAAAAG 59.705 44.000 0.00 0.00 0.00 2.27
1712 4386 2.159382 TCCTGATTGGAAAAACGAGGC 58.841 47.619 0.00 0.00 42.94 4.70
1986 4660 8.435624 TGGTAACTAAGAGCAGATGGAAACAAC 61.436 40.741 0.00 0.00 41.10 3.32
1987 4661 6.465178 TGGTAACTAAGAGCAGATGGAAACAA 60.465 38.462 0.00 0.00 41.10 2.83
1989 4663 5.488341 TGGTAACTAAGAGCAGATGGAAAC 58.512 41.667 0.00 0.00 37.61 2.78
1990 4664 5.755409 TGGTAACTAAGAGCAGATGGAAA 57.245 39.130 0.00 0.00 37.61 3.13
2132 4813 3.527533 TGTATCGCAATGTCCCTGTTAC 58.472 45.455 0.00 0.00 0.00 2.50
2284 4965 9.597170 CAATGGAGATGACTGGATTATACATAG 57.403 37.037 0.00 0.00 0.00 2.23
2514 5198 5.474876 CCTTAAATGTCTTGAAGGCTTCTGT 59.525 40.000 26.26 4.46 36.40 3.41
2540 5224 8.488651 AGATTAGGTTCCAAATTTACGTACTG 57.511 34.615 0.00 0.00 0.00 2.74
2605 5289 2.501610 CGAGAGTAAGGGGCTGCC 59.498 66.667 11.05 11.05 0.00 4.85
2622 5306 7.278875 AGAGACAATTCAAATGAGGATCTACC 58.721 38.462 0.00 0.00 34.92 3.18
2702 5387 4.736126 TGATTTGAGAATGCTACCTCGA 57.264 40.909 0.00 0.00 32.30 4.04
2747 5432 4.521639 ACATGTGTGATCAGAGCAATTGTT 59.478 37.500 7.40 0.00 0.00 2.83
3090 5775 5.185454 AGTTCATCTTTGTGTGTGAGTTCA 58.815 37.500 0.00 0.00 0.00 3.18
3128 5813 7.998383 TGGCCTATGAATTCAAGCTTCTATTTA 59.002 33.333 13.09 0.00 0.00 1.40
3165 5850 6.029346 AGCTTGGTGATTTAGGACAAATTG 57.971 37.500 0.00 0.00 0.00 2.32
3211 5896 9.459640 CAAATGGAAATTCTCACATATCATGAC 57.540 33.333 0.00 0.00 0.00 3.06
3216 5901 7.587037 TCCCAAATGGAAATTCTCACATATC 57.413 36.000 0.00 0.00 41.40 1.63
3233 5918 4.284178 AGAATACATGCAGCTTCCCAAAT 58.716 39.130 0.00 0.00 0.00 2.32
3275 5960 7.780008 TCGTGTGAAAATCTGAAAAGAACTA 57.220 32.000 0.00 0.00 0.00 2.24
3307 5992 5.497464 TGGTGACATAGTTGGAAGAATGA 57.503 39.130 0.00 0.00 33.40 2.57
3360 6045 3.188048 GGAGAATCTGAAGCACAACTGTG 59.812 47.826 5.45 5.45 41.60 3.66
3387 6072 5.222068 GGGAAGGAGGGAGTAGAAAAGAAAA 60.222 44.000 0.00 0.00 0.00 2.29
3424 6109 6.751157 TCAAAGATCATGCAAAGTCAAATGT 58.249 32.000 0.00 0.00 0.00 2.71
3441 6126 4.768448 TGGTCAAACTCATGCATCAAAGAT 59.232 37.500 0.00 0.00 0.00 2.40
3519 6205 5.997746 CCAACTCATGGTTTCACTTAGAGAA 59.002 40.000 0.00 0.00 44.85 2.87
3600 6286 7.165460 ACAACAAAGCCTTTAGTAACAAACT 57.835 32.000 0.00 0.00 42.62 2.66
3601 6287 7.201487 CCAACAACAAAGCCTTTAGTAACAAAC 60.201 37.037 0.00 0.00 0.00 2.93
3602 6288 6.814146 CCAACAACAAAGCCTTTAGTAACAAA 59.186 34.615 0.00 0.00 0.00 2.83
3603 6289 6.071278 ACCAACAACAAAGCCTTTAGTAACAA 60.071 34.615 0.00 0.00 0.00 2.83
3604 6290 5.419471 ACCAACAACAAAGCCTTTAGTAACA 59.581 36.000 0.00 0.00 0.00 2.41
3605 6291 5.746721 CACCAACAACAAAGCCTTTAGTAAC 59.253 40.000 0.00 0.00 0.00 2.50
3606 6292 5.419471 ACACCAACAACAAAGCCTTTAGTAA 59.581 36.000 0.00 0.00 0.00 2.24
3607 6293 4.951094 ACACCAACAACAAAGCCTTTAGTA 59.049 37.500 0.00 0.00 0.00 1.82
3608 6294 3.767131 ACACCAACAACAAAGCCTTTAGT 59.233 39.130 0.00 0.00 0.00 2.24
3609 6295 4.385358 ACACCAACAACAAAGCCTTTAG 57.615 40.909 0.00 0.00 0.00 1.85
3610 6296 4.021016 ACAACACCAACAACAAAGCCTTTA 60.021 37.500 0.00 0.00 0.00 1.85
3611 6297 3.244387 ACAACACCAACAACAAAGCCTTT 60.244 39.130 0.00 0.00 0.00 3.11
3612 6298 2.301583 ACAACACCAACAACAAAGCCTT 59.698 40.909 0.00 0.00 0.00 4.35
3613 6299 1.899142 ACAACACCAACAACAAAGCCT 59.101 42.857 0.00 0.00 0.00 4.58
3614 6300 2.378445 ACAACACCAACAACAAAGCC 57.622 45.000 0.00 0.00 0.00 4.35
3649 6335 9.173939 CACAACTTTGACTATGATTTTCACTTC 57.826 33.333 0.00 0.00 0.00 3.01
3693 6392 4.503741 AAAATATAAGGCGCGCATTGAT 57.496 36.364 37.76 27.13 0.00 2.57
3715 6414 4.669768 TGATATAAAATGCCCCTCCTTCCT 59.330 41.667 0.00 0.00 0.00 3.36
3863 6562 7.502060 TGTTCTCTCCAAAAGAATATCTCCT 57.498 36.000 0.00 0.00 35.35 3.69
3971 6670 7.899973 AGTTTCTATTCAAGCATCAAAATGGT 58.100 30.769 0.00 0.00 45.33 3.55
3972 6671 8.030692 TGAGTTTCTATTCAAGCATCAAAATGG 58.969 33.333 0.00 0.00 33.19 3.16
4031 6731 1.321474 TTGTGGGTCGACGTTAGAGT 58.679 50.000 9.92 0.00 0.00 3.24
4203 6906 3.612479 GCCGTGTTTGCATGAATCTCTTT 60.612 43.478 0.00 0.00 33.58 2.52
4512 7400 2.359975 CCCAAGAAGGTCACCGCC 60.360 66.667 0.00 0.00 34.66 6.13
4557 7449 1.065199 TCCGGTAGCGAGGAAGAGTAA 60.065 52.381 17.33 0.00 32.86 2.24
4652 7554 0.314935 GGGTAAGACCAACGACGACA 59.685 55.000 0.00 0.00 41.02 4.35
4673 7579 0.798771 GAGGCGACAGATGACGTGAC 60.799 60.000 0.00 0.00 35.76 3.67
4674 7580 1.241315 TGAGGCGACAGATGACGTGA 61.241 55.000 0.00 0.00 35.76 4.35
4745 7653 0.179176 CAGATCCGCCTCGATCGATC 60.179 60.000 19.78 15.68 42.94 3.69
4768 7681 1.810532 CTGCTCGAGTCCTACCACC 59.189 63.158 15.13 0.00 0.00 4.61
4849 7765 1.597854 CAAGAGCACCAACAGGCGA 60.598 57.895 0.00 0.00 34.54 5.54
4920 7841 1.118838 GACATAGTGCAGGAGGAGCT 58.881 55.000 0.00 0.00 0.00 4.09
4934 7873 2.844946 CATGCCCGTTACATGGACATA 58.155 47.619 0.00 0.00 40.99 2.29
5141 8142 1.039068 CACCATGGTTTCCTTGCACA 58.961 50.000 16.84 0.00 0.00 4.57
5167 8172 3.368948 GGTACCTTTCTCCTCTTCTGCAG 60.369 52.174 7.63 7.63 0.00 4.41
5224 8232 1.924524 CATCCGCCCGCTATATAAACG 59.075 52.381 0.00 0.00 0.00 3.60
5241 8250 0.107831 TACCGCCTACCATTGCCATC 59.892 55.000 0.00 0.00 0.00 3.51
5301 8313 2.039613 TGCCCACATCATTGACACACTA 59.960 45.455 0.00 0.00 0.00 2.74
5311 8323 1.524002 CGTCTCCTGCCCACATCAT 59.476 57.895 0.00 0.00 0.00 2.45
5313 8325 2.187946 CCGTCTCCTGCCCACATC 59.812 66.667 0.00 0.00 0.00 3.06
5430 8457 0.034896 AGCGGACACGACCTTGATTT 59.965 50.000 0.00 0.00 44.60 2.17
5431 8458 0.389948 GAGCGGACACGACCTTGATT 60.390 55.000 0.00 0.00 44.60 2.57
5433 8460 1.901948 AGAGCGGACACGACCTTGA 60.902 57.895 0.00 0.00 44.60 3.02
5434 8461 1.734477 CAGAGCGGACACGACCTTG 60.734 63.158 0.00 0.00 44.60 3.61
5435 8462 2.651361 CAGAGCGGACACGACCTT 59.349 61.111 0.00 0.00 44.60 3.50
5494 8527 1.373570 CTCTTCCCGCCTGAAATGAC 58.626 55.000 0.00 0.00 0.00 3.06
5512 8545 1.102222 CCCTAACTCGCCTACTCGCT 61.102 60.000 0.00 0.00 0.00 4.93
5516 8549 0.042281 AACCCCCTAACTCGCCTACT 59.958 55.000 0.00 0.00 0.00 2.57
5527 8560 2.271777 CTGTCCCACTAAAACCCCCTA 58.728 52.381 0.00 0.00 0.00 3.53
5843 8876 1.144057 CACGGGCCTGTATCAGTCC 59.856 63.158 19.20 0.00 0.00 3.85
5844 8877 0.249398 AACACGGGCCTGTATCAGTC 59.751 55.000 19.20 0.00 0.00 3.51
5875 8908 3.403057 CGCGGACTTGTGTCGGTG 61.403 66.667 0.00 0.00 43.79 4.94
5890 8923 1.097547 AGTATTGTGCCATCCAGCGC 61.098 55.000 0.00 0.00 43.65 5.92
5893 8926 2.947652 CCAGAAGTATTGTGCCATCCAG 59.052 50.000 0.00 0.00 38.17 3.86
5900 8933 2.159627 CCGTTGTCCAGAAGTATTGTGC 59.840 50.000 0.00 0.00 38.17 4.57
5915 8948 0.314935 ACATACGTTCGGACCGTTGT 59.685 50.000 14.79 12.97 39.60 3.32
5921 8954 0.799534 CCGTCCACATACGTTCGGAC 60.800 60.000 12.72 12.72 43.73 4.79
5922 8955 1.243342 ACCGTCCACATACGTTCGGA 61.243 55.000 8.35 0.00 41.27 4.55
5923 8956 0.388907 AACCGTCCACATACGTTCGG 60.389 55.000 0.00 0.00 41.27 4.30
5924 8957 1.125384 CAAACCGTCCACATACGTTCG 59.875 52.381 0.00 0.00 41.27 3.95
5925 8958 2.406130 TCAAACCGTCCACATACGTTC 58.594 47.619 0.00 0.00 41.27 3.95
5926 8959 2.409975 CTCAAACCGTCCACATACGTT 58.590 47.619 0.00 0.00 41.27 3.99
5927 8960 1.337447 CCTCAAACCGTCCACATACGT 60.337 52.381 0.00 0.00 41.27 3.57
5928 8961 1.355971 CCTCAAACCGTCCACATACG 58.644 55.000 0.00 0.00 42.49 3.06
5929 8962 1.002773 ACCCTCAAACCGTCCACATAC 59.997 52.381 0.00 0.00 0.00 2.39
5930 8963 1.276989 GACCCTCAAACCGTCCACATA 59.723 52.381 0.00 0.00 0.00 2.29
5937 8972 4.675029 CGCCGACCCTCAAACCGT 62.675 66.667 0.00 0.00 0.00 4.83
5951 8986 0.393808 TTAAGGGCATCTCCAACGCC 60.394 55.000 0.00 0.00 45.47 5.68
5953 8988 2.403252 AGTTAAGGGCATCTCCAACG 57.597 50.000 0.00 0.00 36.21 4.10
5970 9005 8.870075 ACTATCTCATTTTTCAAAAGGCTAGT 57.130 30.769 0.00 0.00 30.40 2.57
6160 9195 1.339055 TGAACAGCTAGATGCACACCC 60.339 52.381 8.16 0.00 45.94 4.61
6161 9196 1.734465 GTGAACAGCTAGATGCACACC 59.266 52.381 20.16 8.42 45.94 4.16
6162 9197 2.414481 CAGTGAACAGCTAGATGCACAC 59.586 50.000 22.04 22.04 45.94 3.82
6167 9202 2.284263 TCGCAGTGAACAGCTAGATG 57.716 50.000 6.41 6.41 0.00 2.90
6168 9203 3.533606 ATTCGCAGTGAACAGCTAGAT 57.466 42.857 0.00 0.00 40.00 1.98
6254 9293 3.478857 TTTTCCAGAGTGAAGGCGTTA 57.521 42.857 0.00 0.00 0.00 3.18
6291 9330 9.953565 AGATGTAAGTAATTAAGGTGCAAACTA 57.046 29.630 0.00 0.00 0.00 2.24
6292 9331 8.863872 AGATGTAAGTAATTAAGGTGCAAACT 57.136 30.769 0.00 0.00 0.00 2.66
6347 9386 1.398390 CAGCGCCATAGAAACACCTTC 59.602 52.381 2.29 0.00 0.00 3.46
6352 9391 0.739462 CGGTCAGCGCCATAGAAACA 60.739 55.000 2.29 0.00 0.00 2.83
6359 9398 4.471908 TGCATCGGTCAGCGCCAT 62.472 61.111 2.29 0.00 0.00 4.40
6397 9436 0.608640 CGAGTACTTGGGCCTTGTCT 59.391 55.000 4.53 3.51 0.00 3.41
6429 9468 4.503910 CATCCGGTTCTACAACTTCATGA 58.496 43.478 0.00 0.00 32.50 3.07
6519 9558 3.817647 GCTAGGCATCCTAATCCAACTTG 59.182 47.826 0.00 0.00 35.49 3.16
6591 9630 9.070179 AGCAAATCAAATTAAAGCAATTCCTTT 57.930 25.926 0.00 0.00 35.74 3.11
6703 9743 5.261209 TGCTGAAATGAAATTAATCCCCG 57.739 39.130 0.00 0.00 33.67 5.73
6757 9868 2.820197 GGCGGAGGAGTTCAATCTTTTT 59.180 45.455 0.00 0.00 0.00 1.94
6894 10050 3.742369 GCAAAGCACACATAGCAACAAAT 59.258 39.130 0.00 0.00 0.00 2.32
6922 10093 3.062099 CCAACACGTATCAAGACCAATCG 59.938 47.826 0.00 0.00 0.00 3.34
6924 10095 4.015872 ACCAACACGTATCAAGACCAAT 57.984 40.909 0.00 0.00 0.00 3.16
6932 10103 2.675844 GCATAGCAACCAACACGTATCA 59.324 45.455 0.00 0.00 0.00 2.15
7015 10186 9.205513 ACTCTATTCAAGGATAATTTTGCCATT 57.794 29.630 0.00 0.00 0.00 3.16
7026 10197 5.538877 ACCCCTCAACTCTATTCAAGGATA 58.461 41.667 0.00 0.00 0.00 2.59
7101 10302 4.290622 CTTGCACCAGGGCCCAGT 62.291 66.667 27.56 18.91 0.00 4.00
7142 10343 2.672381 CCAGTGCACTTGTTTGTTTTGG 59.328 45.455 18.94 8.40 0.00 3.28


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

AutoCloner maintained by Alex Coulton.