Multiple sequence alignment - TraesCS1D01G351200

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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 TraesCS1D01G351200 chr1D 100.000 2541 0 0 1 2541 436607472 436610012 0.000000e+00 4693.0
1 TraesCS1D01G351200 chr1D 100.000 2430 0 0 5246 7675 436612717 436615146 0.000000e+00 4488.0
2 TraesCS1D01G351200 chr1D 100.000 2235 0 0 2745 4979 436610216 436612450 0.000000e+00 4128.0
3 TraesCS1D01G351200 chr1D 86.835 1542 147 25 999 2504 436329033 436330554 0.000000e+00 1672.0
4 TraesCS1D01G351200 chr1D 91.862 811 49 3 3245 4043 436330564 436331369 0.000000e+00 1116.0
5 TraesCS1D01G351200 chr1D 88.177 812 60 9 5480 6255 436332903 436333714 0.000000e+00 935.0
6 TraesCS1D01G351200 chr1D 83.210 1078 98 41 6112 7144 436334006 436335045 0.000000e+00 911.0
7 TraesCS1D01G351200 chr1D 84.674 659 34 20 4338 4964 436332005 436332628 5.130000e-166 595.0
8 TraesCS1D01G351200 chr1D 92.164 268 11 1 4046 4303 436331754 436332021 3.380000e-98 370.0
9 TraesCS1D01G351200 chr1D 83.709 399 43 11 2790 3168 200460481 200460085 2.630000e-94 357.0
10 TraesCS1D01G351200 chr1D 85.827 254 12 6 5246 5479 436332614 436332863 1.650000e-61 248.0
11 TraesCS1D01G351200 chr1D 79.585 289 28 13 7395 7675 436335287 436335552 2.200000e-40 178.0
12 TraesCS1D01G351200 chr1D 90.244 123 12 0 6133 6255 436333886 436334008 2.220000e-35 161.0
13 TraesCS1D01G351200 chr1D 96.970 33 1 0 4303 4335 259781361 259781393 1.000000e-03 56.5
14 TraesCS1D01G351200 chr1B 92.140 2570 156 24 2 2539 591419034 591421589 0.000000e+00 3585.0
15 TraesCS1D01G351200 chr1B 88.450 1974 77 41 5246 7144 591424264 591426161 0.000000e+00 2242.0
16 TraesCS1D01G351200 chr1B 95.809 1026 39 1 3247 4272 591422590 591423611 0.000000e+00 1653.0
17 TraesCS1D01G351200 chr1B 88.868 1069 80 9 3264 4303 593690770 593689712 0.000000e+00 1279.0
18 TraesCS1D01G351200 chr1B 88.986 1035 81 9 3296 4303 593737393 593736365 0.000000e+00 1249.0
19 TraesCS1D01G351200 chr1B 85.766 1096 121 17 999 2075 591351038 591352117 0.000000e+00 1127.0
20 TraesCS1D01G351200 chr1B 94.659 674 26 6 4299 4964 591423607 591424278 0.000000e+00 1037.0
21 TraesCS1D01G351200 chr1B 91.076 762 52 4 3258 4007 591352729 591353486 0.000000e+00 1016.0
22 TraesCS1D01G351200 chr1B 89.558 814 49 6 5478 6255 591355220 591356033 0.000000e+00 1000.0
23 TraesCS1D01G351200 chr1B 85.435 1023 76 22 5925 6905 593689166 593688175 0.000000e+00 996.0
24 TraesCS1D01G351200 chr1B 86.258 946 73 27 5991 6905 593735402 593734483 0.000000e+00 974.0
25 TraesCS1D01G351200 chr1B 83.605 860 85 29 6112 6950 591356750 591357574 0.000000e+00 756.0
26 TraesCS1D01G351200 chr1B 85.997 657 45 17 4338 4964 593736381 593735742 0.000000e+00 660.0
27 TraesCS1D01G351200 chr1B 89.744 429 22 11 2786 3198 591421831 591422253 5.270000e-146 529.0
28 TraesCS1D01G351200 chr1B 84.220 564 43 13 7151 7675 591426326 591426882 2.470000e-139 507.0
29 TraesCS1D01G351200 chr1B 90.566 371 26 5 4338 4702 593689728 593689361 4.160000e-132 483.0
30 TraesCS1D01G351200 chr1B 86.824 425 44 6 2092 2508 591352271 591352691 1.510000e-126 464.0
31 TraesCS1D01G351200 chr1B 88.438 320 19 6 4000 4301 591354053 591354372 3.380000e-98 370.0
32 TraesCS1D01G351200 chr1B 87.736 318 19 8 4667 4964 591354630 591354947 3.410000e-93 353.0
33 TraesCS1D01G351200 chr1B 95.385 195 9 0 7481 7675 593684268 593684074 2.080000e-80 311.0
34 TraesCS1D01G351200 chr1B 94.706 170 9 0 7506 7675 593722232 593722063 1.640000e-66 265.0
35 TraesCS1D01G351200 chr1B 96.732 153 4 1 5331 5482 591355034 591355186 3.550000e-63 254.0
36 TraesCS1D01G351200 chr1B 87.892 223 16 6 4338 4551 591354358 591354578 1.280000e-62 252.0
37 TraesCS1D01G351200 chr1B 92.208 154 11 1 5331 5483 593735655 593735502 4.660000e-52 217.0
38 TraesCS1D01G351200 chr1B 93.966 116 7 0 5368 5483 593689354 593689239 7.920000e-40 176.0
39 TraesCS1D01G351200 chr1B 88.028 142 17 0 5774 5915 591355720 591355861 1.320000e-37 169.0
40 TraesCS1D01G351200 chr1B 84.472 161 25 0 5770 5930 593689135 593688975 7.970000e-35 159.0
41 TraesCS1D01G351200 chr1B 91.860 86 7 0 7059 7144 593684843 593684758 3.760000e-23 121.0
42 TraesCS1D01G351200 chr1B 82.787 122 21 0 5809 5930 593735412 593735291 8.140000e-20 110.0
43 TraesCS1D01G351200 chr1B 88.732 71 4 1 5246 5316 593735756 593735690 4.940000e-12 84.2
44 TraesCS1D01G351200 chr1B 87.324 71 5 1 5246 5316 591354933 591354999 2.300000e-10 78.7
45 TraesCS1D01G351200 chr1A 92.146 1044 44 14 5246 6255 533691848 533692887 0.000000e+00 1439.0
46 TraesCS1D01G351200 chr1A 85.466 1383 138 26 999 2349 533665835 533667186 0.000000e+00 1382.0
47 TraesCS1D01G351200 chr1A 90.066 1067 72 11 3264 4303 533690131 533691190 0.000000e+00 1352.0
48 TraesCS1D01G351200 chr1A 89.231 1105 78 14 3226 4303 533667900 533668990 0.000000e+00 1343.0
49 TraesCS1D01G351200 chr1A 88.133 809 63 5 5480 6255 533669884 533670692 0.000000e+00 931.0
50 TraesCS1D01G351200 chr1A 86.707 835 38 29 6112 6900 533693170 533693977 0.000000e+00 859.0
51 TraesCS1D01G351200 chr1A 89.043 648 45 3 3682 4303 534821460 534820813 0.000000e+00 780.0
52 TraesCS1D01G351200 chr1A 87.976 657 46 13 4338 4964 534820829 534820176 0.000000e+00 745.0
53 TraesCS1D01G351200 chr1A 85.503 745 62 24 6112 6826 533670831 533671559 0.000000e+00 736.0
54 TraesCS1D01G351200 chr1A 89.081 577 35 11 4412 4964 533691290 533691862 0.000000e+00 691.0
55 TraesCS1D01G351200 chr1A 88.235 561 36 14 4433 4964 533669049 533669608 1.810000e-180 643.0
56 TraesCS1D01G351200 chr1A 80.856 794 112 21 999 1785 533688543 533689303 8.580000e-164 588.0
57 TraesCS1D01G351200 chr1A 84.833 600 59 17 6333 6905 534819878 534819284 6.680000e-160 575.0
58 TraesCS1D01G351200 chr1A 80.278 791 116 20 1006 1788 534832230 534831472 1.870000e-155 560.0
59 TraesCS1D01G351200 chr1A 84.397 564 39 21 7152 7675 533694574 533695128 6.870000e-140 508.0
60 TraesCS1D01G351200 chr1A 90.649 385 31 2 3264 3648 534821842 534821463 2.470000e-139 507.0
61 TraesCS1D01G351200 chr1A 92.857 168 10 2 5314 5479 533669677 533669844 7.690000e-60 243.0
62 TraesCS1D01G351200 chr1A 94.156 154 8 1 5331 5483 534820089 534819936 4.630000e-57 233.0
63 TraesCS1D01G351200 chr1A 87.778 180 15 2 2101 2280 533667357 533667185 3.630000e-48 204.0
64 TraesCS1D01G351200 chr1A 87.342 158 16 2 2222 2376 533667511 533667667 2.200000e-40 178.0
65 TraesCS1D01G351200 chr1A 81.057 227 33 7 7058 7283 533671684 533671901 1.020000e-38 172.0
66 TraesCS1D01G351200 chr1A 85.625 160 21 2 5757 5915 533670365 533670523 4.760000e-37 167.0
67 TraesCS1D01G351200 chr1A 84.348 115 14 2 2284 2395 533690020 533690133 8.140000e-20 110.0
68 TraesCS1D01G351200 chr1A 88.732 71 4 1 5246 5316 534820190 534820124 4.940000e-12 84.2
69 TraesCS1D01G351200 chr2D 87.711 415 46 5 2789 3200 574415672 574415260 5.390000e-131 479.0
70 TraesCS1D01G351200 chr2D 78.003 641 113 21 3250 3874 617315470 617316098 2.020000e-100 377.0
71 TraesCS1D01G351200 chr2D 82.944 428 51 13 2786 3193 349566270 349566695 4.380000e-97 366.0
72 TraesCS1D01G351200 chr5D 86.946 429 42 13 2789 3210 53608646 53608225 3.240000e-128 470.0
73 TraesCS1D01G351200 chr3A 86.243 378 41 11 2850 3220 624709601 624709228 4.310000e-107 399.0
74 TraesCS1D01G351200 chr6D 88.344 326 36 2 2845 3168 341587436 341587761 2.600000e-104 390.0
75 TraesCS1D01G351200 chr7D 86.179 369 40 9 2845 3205 421971441 421971076 9.340000e-104 388.0
76 TraesCS1D01G351200 chr4B 85.674 356 41 8 2845 3194 94104262 94104613 4.380000e-97 366.0
77 TraesCS1D01G351200 chr3D 100.000 42 0 0 4547 4588 301973204 301973245 2.300000e-10 78.7
78 TraesCS1D01G351200 chr2A 95.833 48 2 0 4543 4590 124382090 124382043 2.300000e-10 78.7
79 TraesCS1D01G351200 chr3B 97.727 44 1 0 4545 4588 686338133 686338176 8.260000e-10 76.8


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 TraesCS1D01G351200 chr1D 436607472 436615146 7674 False 4436.333333 4693 100.000000 1 7675 3 chr1D.!!$F3 7674
1 TraesCS1D01G351200 chr1D 436329033 436335552 6519 False 687.333333 1672 86.953111 999 7675 9 chr1D.!!$F2 6676
2 TraesCS1D01G351200 chr1B 591419034 591426882 7848 False 1592.166667 3585 90.837000 2 7675 6 chr1B.!!$F2 7673
3 TraesCS1D01G351200 chr1B 593734483 593737393 2910 True 549.033333 1249 87.494667 3296 6905 6 chr1B.!!$R3 3609
4 TraesCS1D01G351200 chr1B 591351038 591357574 6536 False 530.881818 1127 88.452636 999 6950 11 chr1B.!!$F1 5951
5 TraesCS1D01G351200 chr1B 593684074 593690770 6696 True 503.571429 1279 90.078857 3264 7675 7 chr1B.!!$R2 4411
6 TraesCS1D01G351200 chr1A 533688543 533695128 6585 False 792.428571 1439 86.800143 999 7675 7 chr1A.!!$F2 6676
7 TraesCS1D01G351200 chr1A 533665835 533671901 6066 False 643.888889 1382 87.049889 999 7283 9 chr1A.!!$F1 6284
8 TraesCS1D01G351200 chr1A 534831472 534832230 758 True 560.000000 560 80.278000 1006 1788 1 chr1A.!!$R2 782
9 TraesCS1D01G351200 chr1A 534819284 534821842 2558 True 487.366667 780 89.231500 3264 6905 6 chr1A.!!$R3 3641
10 TraesCS1D01G351200 chr2D 617315470 617316098 628 False 377.000000 377 78.003000 3250 3874 1 chr2D.!!$F2 624

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
675 686 0.106719 GCAGCAGCCCCAAATACCTA 60.107 55.0 0.00 0.00 33.58 3.08 F
988 1001 0.376152 GCACAACATCAGATCCAGCG 59.624 55.0 0.00 0.00 0.00 5.18 F
1229 1255 0.533032 GGAGAGCTCACCACCACTAC 59.467 60.0 23.63 0.00 0.00 2.73 F
1601 1637 1.074752 GTAGAAGTGTCTGCTGCTGC 58.925 55.0 8.89 8.89 33.94 5.25 F
3442 4862 0.395586 ACTTGGGCTTGAACTGCACA 60.396 50.0 0.00 0.00 42.62 4.57 F
4951 7443 0.393537 AGATGGCACTAGCACAAGGC 60.394 55.0 0.00 0.00 44.61 4.35 F
5586 8140 0.319211 CTACACGCCGTGGAAGTTCA 60.319 55.0 22.60 0.00 37.94 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1770 0.178921 TCCCTCTGAGGTGCTCTTGT 60.179 55.000 21.70 0.00 31.93 3.16 R
1793 1832 1.147600 ACCGGTTGACCTGTTCCAC 59.852 57.895 0.00 0.00 28.50 4.02 R
3109 4033 0.322366 TCCGTTCAATGCATGCCTCA 60.322 50.000 16.68 0.00 0.00 3.86 R
3449 4869 0.250597 TGACTGCTTGCTGTGATGCT 60.251 50.000 9.74 0.00 0.00 3.79 R
5302 7794 0.730840 GTTACGGAGGCAAAATCCCG 59.269 55.000 0.00 0.00 46.65 5.14 R
6185 8784 0.033920 AGTCATCGCTGCTGTTGACA 59.966 50.000 23.81 0.00 40.69 3.58 R
7456 15311 0.250553 AATTCAGTCCGCCGGTTGAA 60.251 50.000 21.45 21.45 34.23 2.69 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
33 34 3.688673 GTCTTCAATCCTTGAGCTCCTTG 59.311 47.826 12.15 7.40 41.38 3.61
34 35 2.119801 TCAATCCTTGAGCTCCTTGC 57.880 50.000 12.15 0.00 43.29 4.01
76 81 4.223032 TCTCTCCCTACTGTGACATTTTCC 59.777 45.833 0.00 0.00 0.00 3.13
77 82 3.907474 TCTCCCTACTGTGACATTTTCCA 59.093 43.478 0.00 0.00 0.00 3.53
78 83 4.003648 CTCCCTACTGTGACATTTTCCAC 58.996 47.826 0.00 0.00 0.00 4.02
92 97 6.590068 ACATTTTCCACCATCACATTTTCAA 58.410 32.000 0.00 0.00 0.00 2.69
101 106 4.338879 CATCACATTTTCAACCTCCTCCT 58.661 43.478 0.00 0.00 0.00 3.69
121 126 3.679980 CCTCCCGTGAATCAATAATAGCG 59.320 47.826 0.00 0.00 0.00 4.26
207 212 2.099141 ACACCATCAATCACACTCGG 57.901 50.000 0.00 0.00 0.00 4.63
232 237 1.135859 GTTTGTTCCTGCTCAGCATCG 60.136 52.381 0.00 0.00 38.13 3.84
250 255 4.308265 CATCGCTGTGATCAGATTCATCT 58.692 43.478 0.00 0.00 43.76 2.90
258 265 7.272948 GCTGTGATCAGATTCATCTTGTTTTTC 59.727 37.037 0.00 0.00 43.76 2.29
291 298 9.829507 TGTTCATTTTCATTATTTTTCACACCT 57.170 25.926 0.00 0.00 0.00 4.00
334 341 7.410120 AGTCCCCAAGATTGTTTGATATTTC 57.590 36.000 0.00 0.00 0.00 2.17
335 342 6.381133 AGTCCCCAAGATTGTTTGATATTTCC 59.619 38.462 0.00 0.00 0.00 3.13
341 348 9.709495 CCAAGATTGTTTGATATTTCCTTTTCA 57.291 29.630 0.00 0.00 0.00 2.69
385 392 5.389859 TGGTCTTGGCTATTTGTTTGATG 57.610 39.130 0.00 0.00 0.00 3.07
396 403 7.390162 GGCTATTTGTTTGATGAAATTTGGGAA 59.610 33.333 0.00 0.00 0.00 3.97
430 438 1.064685 CCAGGGTTTATCACACCTCCC 60.065 57.143 0.00 0.00 34.36 4.30
471 482 2.636830 CAAGGCACTCACTTCCCTATG 58.363 52.381 0.00 0.00 38.49 2.23
519 530 7.665145 TCATTCTTGTTGGTTGTCATAGATTCA 59.335 33.333 0.00 0.00 0.00 2.57
525 536 7.450074 TGTTGGTTGTCATAGATTCAACTAGT 58.550 34.615 0.00 0.00 40.52 2.57
526 537 7.387673 TGTTGGTTGTCATAGATTCAACTAGTG 59.612 37.037 0.00 0.00 40.52 2.74
532 543 4.345257 TCATAGATTCAACTAGTGCCCCTC 59.655 45.833 0.00 0.00 0.00 4.30
539 550 0.642710 ACTAGTGCCCCTCCAGGTAT 59.357 55.000 0.00 0.00 0.00 2.73
547 558 2.039084 GCCCCTCCAGGTATATGAACAG 59.961 54.545 0.00 0.00 0.00 3.16
548 559 3.587498 CCCCTCCAGGTATATGAACAGA 58.413 50.000 0.00 0.00 0.00 3.41
579 590 1.190643 CACTCTGAGAAGAGTCCCCC 58.809 60.000 12.44 0.00 46.34 5.40
602 613 1.890876 TTTTCCACCTCCATGTCACG 58.109 50.000 0.00 0.00 0.00 4.35
612 623 1.418264 TCCATGTCACGAAGTTTCCCA 59.582 47.619 0.00 0.00 41.61 4.37
613 624 2.039746 TCCATGTCACGAAGTTTCCCAT 59.960 45.455 0.00 0.00 41.61 4.00
614 625 2.819608 CCATGTCACGAAGTTTCCCATT 59.180 45.455 0.00 0.00 41.61 3.16
656 667 4.042062 TGGCTCCAAATGATATACTCCCTG 59.958 45.833 0.00 0.00 0.00 4.45
660 671 3.755378 CCAAATGATATACTCCCTGCAGC 59.245 47.826 8.66 0.00 0.00 5.25
675 686 0.106719 GCAGCAGCCCCAAATACCTA 60.107 55.000 0.00 0.00 33.58 3.08
698 709 7.493971 CCTATCTATTTCTATTTCTGGCATCCG 59.506 40.741 0.00 0.00 0.00 4.18
753 764 8.567285 TCATTCCTTTTTCCTAAGAAGATGAC 57.433 34.615 0.00 0.00 32.35 3.06
754 765 8.163408 TCATTCCTTTTTCCTAAGAAGATGACA 58.837 33.333 0.00 0.00 32.35 3.58
763 774 6.753180 TCCTAAGAAGATGACATACATGAGC 58.247 40.000 0.00 0.00 39.56 4.26
771 782 6.228995 AGATGACATACATGAGCTGGTATTG 58.771 40.000 0.00 0.00 39.56 1.90
782 793 9.113838 ACATGAGCTGGTATTGAAAAATACTAG 57.886 33.333 14.26 14.26 43.13 2.57
846 857 1.275291 TGTCTTTCATCGGAGTGGGTC 59.725 52.381 0.00 0.00 0.00 4.46
868 879 3.425162 AACTCCCTGACAAATGAGACC 57.575 47.619 0.00 0.00 0.00 3.85
873 884 2.616510 CCCTGACAAATGAGACCTGGTC 60.617 54.545 19.20 19.20 0.00 4.02
912 925 4.755411 TGGCTAGTAAGATGCAACACTAC 58.245 43.478 0.00 0.00 0.00 2.73
919 932 1.831106 AGATGCAACACTACGGGATCA 59.169 47.619 0.00 0.00 32.54 2.92
920 933 2.236146 AGATGCAACACTACGGGATCAA 59.764 45.455 0.00 0.00 32.54 2.57
941 954 4.188948 ACTAGCGTTTATAGTCGACGAC 57.811 45.455 20.25 20.25 38.99 4.34
960 973 2.325761 ACTCACGTTTATCTCACGCAC 58.674 47.619 0.00 0.00 41.53 5.34
987 1000 0.737219 GGCACAACATCAGATCCAGC 59.263 55.000 0.00 0.00 0.00 4.85
988 1001 0.376152 GCACAACATCAGATCCAGCG 59.624 55.000 0.00 0.00 0.00 5.18
995 1008 2.208431 CATCAGATCCAGCGAAACTCC 58.792 52.381 0.00 0.00 0.00 3.85
1022 1035 2.029964 GTTCCACTTCCGTGCCGA 59.970 61.111 0.00 0.00 39.86 5.54
1094 1107 1.346068 GAGTGCAGGTGAACTCTCCTT 59.654 52.381 10.48 0.00 45.34 3.36
1228 1254 0.614979 GGGAGAGCTCACCACCACTA 60.615 60.000 28.36 0.00 0.00 2.74
1229 1255 0.533032 GGAGAGCTCACCACCACTAC 59.467 60.000 23.63 0.00 0.00 2.73
1601 1637 1.074752 GTAGAAGTGTCTGCTGCTGC 58.925 55.000 8.89 8.89 33.94 5.25
1653 1692 5.243507 ACATGATACATCTGTTGTTTTGGCA 59.756 36.000 0.00 0.00 39.87 4.92
1658 1697 1.412079 TCTGTTGTTTTGGCAGCCAT 58.588 45.000 17.09 0.00 31.53 4.40
1789 1828 1.334960 CCACTAAACTTGCGCAACCAG 60.335 52.381 21.02 12.86 0.00 4.00
1809 1848 3.637714 CGTGGAACAGGTCAACCG 58.362 61.111 0.00 0.00 41.80 4.44
1836 1875 4.460263 AGGATGCGGTAATAAAATGCAGA 58.540 39.130 0.00 0.00 39.17 4.26
1885 1924 7.285783 TCTCCGTACTGAAATACAAAATTCG 57.714 36.000 0.00 0.00 0.00 3.34
1930 1996 6.645306 TGTCCAATATCTAATTGGTCGAACA 58.355 36.000 14.66 0.00 46.47 3.18
1959 2025 9.971922 ATTTGAATCTTGTTCTTTAGGTGAAAG 57.028 29.630 0.00 0.00 45.23 2.62
2160 2424 4.445699 GGCTTGAGTCCATAGCCG 57.554 61.111 11.01 0.00 44.39 5.52
2164 2428 1.403814 CTTGAGTCCATAGCCGAGGA 58.596 55.000 0.00 0.00 0.00 3.71
2216 2480 4.481368 TGCCCTACTGATAATGTCGTTT 57.519 40.909 0.00 0.00 0.00 3.60
2273 2537 8.368668 CCTACATTTTACAGCCTAGCTAGTTAT 58.631 37.037 19.31 4.85 36.40 1.89
2296 2560 2.676342 GTGGCTTGGTTAGATGTAACGG 59.324 50.000 6.67 1.76 39.70 4.44
2316 2580 3.924686 CGGGTGACACTAGTAAATCACAC 59.075 47.826 24.45 22.03 42.66 3.82
2345 3068 9.449719 TCTTGAGGAAAATAAATAGGTCTCAAC 57.550 33.333 0.00 0.00 35.79 3.18
2440 3166 5.382618 AAGACTTGCAACAATCCAAGATC 57.617 39.130 0.00 0.00 40.59 2.75
2474 3200 8.296713 ACATGTCATCTTGTTACCAAATACAAC 58.703 33.333 0.00 0.00 31.46 3.32
2504 3257 8.579682 TCGTACTAACCTTCTACAAGTTTTTC 57.420 34.615 0.00 0.00 0.00 2.29
2772 3635 9.545105 CTTTTGTCAGATATAGCTTTGAGATCT 57.455 33.333 0.00 0.00 0.00 2.75
2879 3802 3.333680 TCATGGGGAACTTCTTTTAGGCT 59.666 43.478 0.00 0.00 0.00 4.58
2880 3803 4.538490 TCATGGGGAACTTCTTTTAGGCTA 59.462 41.667 0.00 0.00 0.00 3.93
2909 3832 8.661352 AATCTTAATCACCAACCAACTTTTTG 57.339 30.769 0.00 0.00 0.00 2.44
2910 3833 7.176589 TCTTAATCACCAACCAACTTTTTGT 57.823 32.000 0.00 0.00 0.00 2.83
2911 3834 8.294954 TCTTAATCACCAACCAACTTTTTGTA 57.705 30.769 0.00 0.00 0.00 2.41
2912 3835 8.192110 TCTTAATCACCAACCAACTTTTTGTAC 58.808 33.333 0.00 0.00 0.00 2.90
2913 3836 6.538945 AATCACCAACCAACTTTTTGTACT 57.461 33.333 0.00 0.00 0.00 2.73
2915 3838 5.956642 TCACCAACCAACTTTTTGTACTTC 58.043 37.500 0.00 0.00 0.00 3.01
3001 3925 5.882000 TCATGACCTGACATTTTGATACCAG 59.118 40.000 0.00 0.00 0.00 4.00
3012 3936 6.874134 ACATTTTGATACCAGTAGTCTGACAC 59.126 38.462 10.88 6.44 43.76 3.67
3029 3953 3.389656 TGACACATACTCTGTTGGAACCA 59.610 43.478 0.00 0.00 35.29 3.67
3037 3961 7.987458 ACATACTCTGTTGGAACCATATTAGTG 59.013 37.037 0.00 0.00 32.90 2.74
3042 3966 7.047891 TCTGTTGGAACCATATTAGTGTGATC 58.952 38.462 0.00 0.00 0.00 2.92
3043 3967 6.716284 TGTTGGAACCATATTAGTGTGATCA 58.284 36.000 0.00 0.00 0.00 2.92
3064 3988 7.499895 TGATCATTAGCATGCTTCATTAACTGA 59.500 33.333 28.02 16.10 0.00 3.41
3070 3994 4.790766 GCATGCTTCATTAACTGAATCCCG 60.791 45.833 11.37 0.00 42.87 5.14
3098 4022 7.658982 TGAAGGAATGATGATAGCATAGTGTTC 59.341 37.037 0.00 0.00 34.11 3.18
3109 4033 2.810274 GCATAGTGTTCGCATGGATCAT 59.190 45.455 0.00 0.00 0.00 2.45
3126 4050 1.402613 TCATGAGGCATGCATTGAACG 59.597 47.619 21.36 0.97 41.18 3.95
3137 4061 5.049474 GCATGCATTGAACGGAGATAACATA 60.049 40.000 14.21 0.00 0.00 2.29
3180 4104 3.738830 GTGGCATAGTCACCGGTATTA 57.261 47.619 6.87 0.00 31.24 0.98
3327 4747 4.805192 GTGTTTGTGTTTGATGCAGTTCAT 59.195 37.500 0.00 0.00 38.32 2.57
3399 4819 1.001068 TGTTGTTACCGCTTCGATGGA 59.999 47.619 5.93 0.00 0.00 3.41
3442 4862 0.395586 ACTTGGGCTTGAACTGCACA 60.396 50.000 0.00 0.00 42.62 4.57
3480 4900 1.436600 AGCAGTCAGAAGAACATGCG 58.563 50.000 0.00 0.00 35.98 4.73
3496 4916 1.266178 TGCGAGATCACCTCAAAGGA 58.734 50.000 0.00 0.00 42.06 3.36
3648 5070 9.472361 ACTGTAGCGTGGTTAACTATAATATTG 57.528 33.333 5.42 0.00 0.00 1.90
3775 5209 8.678199 AGCCTAACTTTGACTAATAAAATCTGC 58.322 33.333 0.00 0.00 0.00 4.26
3941 5376 8.718102 TGCTTGAAAGTAGGTATTATTCTGAC 57.282 34.615 0.00 0.00 0.00 3.51
3998 5434 2.683211 AGGGTCCAAACTGCAAATCT 57.317 45.000 0.00 0.00 0.00 2.40
4224 6622 6.223351 AGAGATTTTCTAAACCTAGGGACG 57.777 41.667 14.81 0.00 33.23 4.79
4371 6783 8.607441 TGGATGACAAGTATATGCATCTAAAC 57.393 34.615 0.19 0.00 35.76 2.01
4421 6876 4.082190 TGTTCCTTGTTCATCTAGGTCTCG 60.082 45.833 0.00 0.00 39.47 4.04
4681 7138 2.108168 GGGATGTGCCACTAGTGTCTA 58.892 52.381 21.18 4.62 38.95 2.59
4712 7169 1.480137 GTGCTAGTGCCATCTCAGTCT 59.520 52.381 0.00 0.00 38.71 3.24
4742 7208 1.912043 CTCTCCTTCCCTGACCATGTT 59.088 52.381 0.00 0.00 0.00 2.71
4864 7349 3.057596 GCCAAGGTTGATCGATTTGAACA 60.058 43.478 0.00 0.00 0.00 3.18
4871 7361 5.451908 GTTGATCGATTTGAACAGCTTGAA 58.548 37.500 0.00 0.00 30.37 2.69
4872 7362 5.687770 TGATCGATTTGAACAGCTTGAAA 57.312 34.783 0.00 0.00 0.00 2.69
4873 7363 6.070897 TGATCGATTTGAACAGCTTGAAAA 57.929 33.333 0.00 0.00 0.00 2.29
4949 7441 2.277969 CTGAGATGGCACTAGCACAAG 58.722 52.381 0.00 0.00 44.61 3.16
4950 7442 1.065926 TGAGATGGCACTAGCACAAGG 60.066 52.381 0.00 0.00 44.61 3.61
4951 7443 0.393537 AGATGGCACTAGCACAAGGC 60.394 55.000 0.00 0.00 44.61 4.35
4965 7457 5.768333 GCACAAGGCTATGAAAACATTTC 57.232 39.130 2.99 0.00 40.25 2.17
4966 7458 5.229423 GCACAAGGCTATGAAAACATTTCA 58.771 37.500 7.87 7.87 40.25 2.69
4967 7459 5.119125 GCACAAGGCTATGAAAACATTTCAC 59.881 40.000 7.61 0.00 40.25 3.18
4968 7460 5.634859 CACAAGGCTATGAAAACATTTCACC 59.365 40.000 7.61 5.50 0.00 4.02
4969 7461 5.170748 CAAGGCTATGAAAACATTTCACCC 58.829 41.667 7.61 8.63 0.00 4.61
4970 7462 3.443681 AGGCTATGAAAACATTTCACCCG 59.556 43.478 7.61 1.80 0.00 5.28
4971 7463 3.179048 GCTATGAAAACATTTCACCCGC 58.821 45.455 7.61 7.19 0.00 6.13
4972 7464 3.366883 GCTATGAAAACATTTCACCCGCA 60.367 43.478 7.61 0.00 0.00 5.69
4973 7465 3.742433 ATGAAAACATTTCACCCGCAA 57.258 38.095 7.61 0.00 0.00 4.85
4974 7466 3.526931 TGAAAACATTTCACCCGCAAA 57.473 38.095 1.57 0.00 0.00 3.68
4975 7467 3.861840 TGAAAACATTTCACCCGCAAAA 58.138 36.364 1.57 0.00 0.00 2.44
4976 7468 4.253685 TGAAAACATTTCACCCGCAAAAA 58.746 34.783 1.57 0.00 0.00 1.94
5268 7760 6.140303 AGCTATGAAAACATTAGTGGCATG 57.860 37.500 0.00 0.00 0.00 4.06
5269 7761 4.741676 GCTATGAAAACATTAGTGGCATGC 59.258 41.667 9.90 9.90 0.00 4.06
5270 7762 4.804868 ATGAAAACATTAGTGGCATGCA 57.195 36.364 21.36 2.54 0.00 3.96
5271 7763 4.804868 TGAAAACATTAGTGGCATGCAT 57.195 36.364 21.36 7.30 0.00 3.96
5302 7794 6.419413 TGAATACACCATTTTTGTTTCGAAGC 59.581 34.615 4.89 4.89 0.00 3.86
5316 7809 1.809869 GAAGCGGGATTTTGCCTCC 59.190 57.895 0.00 0.00 0.00 4.30
5319 7812 1.450669 GCGGGATTTTGCCTCCGTA 60.451 57.895 0.00 0.00 43.87 4.02
5320 7813 1.027792 GCGGGATTTTGCCTCCGTAA 61.028 55.000 0.00 0.00 43.87 3.18
5321 7814 0.730840 CGGGATTTTGCCTCCGTAAC 59.269 55.000 0.00 0.00 37.92 2.50
5322 7815 1.828979 GGGATTTTGCCTCCGTAACA 58.171 50.000 0.00 0.00 33.29 2.41
5328 7821 2.779755 TTGCCTCCGTAACATCACAT 57.220 45.000 0.00 0.00 0.00 3.21
5586 8140 0.319211 CTACACGCCGTGGAAGTTCA 60.319 55.000 22.60 0.00 37.94 3.18
5588 8142 1.278637 CACGCCGTGGAAGTTCAAC 59.721 57.895 9.90 2.31 0.00 3.18
5600 8154 2.169832 AGTTCAACATGGTGACCGAG 57.830 50.000 14.43 0.00 0.00 4.63
5661 8215 1.363807 CTCTGCGAGGTGTGTGACA 59.636 57.895 0.00 0.00 0.00 3.58
6134 8721 0.980423 GACAGGAGGTGAAGAAGGCT 59.020 55.000 0.00 0.00 0.00 4.58
6135 8722 0.689623 ACAGGAGGTGAAGAAGGCTG 59.310 55.000 0.00 0.00 0.00 4.85
6136 8723 0.676151 CAGGAGGTGAAGAAGGCTGC 60.676 60.000 0.00 0.00 0.00 5.25
6137 8724 1.377856 GGAGGTGAAGAAGGCTGCC 60.378 63.158 11.65 11.65 0.00 4.85
6138 8725 1.743252 GAGGTGAAGAAGGCTGCCG 60.743 63.158 13.96 0.00 0.00 5.69
6139 8726 3.435186 GGTGAAGAAGGCTGCCGC 61.435 66.667 13.96 9.78 0.00 6.53
6185 8784 1.201429 AGGAAGCCACCTCCATCGTT 61.201 55.000 0.00 0.00 34.98 3.85
6227 9698 2.282462 AAGAAACCAGCAGCGGGG 60.282 61.111 16.74 10.49 0.00 5.73
6340 9816 1.544691 GGAAGTAGACGAAGGTGCAGA 59.455 52.381 0.00 0.00 0.00 4.26
6416 9907 2.203771 GGGAGCCGTGGAGATCGAT 61.204 63.158 0.00 0.00 0.00 3.59
6572 10063 4.040047 TCAATCACATCTACACCAGGGAT 58.960 43.478 0.00 0.00 0.00 3.85
6625 10158 4.683334 GCGGGCAGTGAACAACGC 62.683 66.667 0.00 0.00 40.19 4.84
6630 10175 3.276091 CAGTGAACAACGCCGGCA 61.276 61.111 28.98 0.53 0.00 5.69
6668 10213 3.532155 GGAGCGGCTCAGGTCGAT 61.532 66.667 29.33 0.00 43.57 3.59
6702 10275 1.228003 TGCGTGAATTTGGGACGGT 60.228 52.632 0.00 0.00 33.68 4.83
6781 10391 2.158726 TCCAGTACAACTGTTGAACCCC 60.159 50.000 26.00 8.98 44.50 4.95
6918 10748 6.762661 TGGTAGTGTTTACTAACTTGTTGTCC 59.237 38.462 4.38 0.00 45.46 4.02
6933 10767 4.769688 TGTTGTCCAATCAGCCATACTAG 58.230 43.478 0.00 0.00 0.00 2.57
6934 10768 3.475566 TGTCCAATCAGCCATACTAGC 57.524 47.619 0.00 0.00 0.00 3.42
6935 10769 2.771372 TGTCCAATCAGCCATACTAGCA 59.229 45.455 0.00 0.00 0.00 3.49
6936 10770 3.199727 TGTCCAATCAGCCATACTAGCAA 59.800 43.478 0.00 0.00 0.00 3.91
6961 10795 1.900351 CCTGGTGAAGATCGCTCCA 59.100 57.895 10.57 10.57 0.00 3.86
6968 10802 1.012841 GAAGATCGCTCCAAGCCTTG 58.987 55.000 0.00 0.00 38.18 3.61
6975 10809 0.108472 GCTCCAAGCCTTGCCATTTC 60.108 55.000 0.00 0.00 34.48 2.17
6979 10813 2.308570 TCCAAGCCTTGCCATTTCTCTA 59.691 45.455 0.00 0.00 0.00 2.43
6982 10816 3.659183 AGCCTTGCCATTTCTCTACAT 57.341 42.857 0.00 0.00 0.00 2.29
7014 10848 6.942532 AACAGCAGTTTGAACTCAAGAATA 57.057 33.333 0.00 0.00 37.08 1.75
7042 10876 1.821332 GGCTGCTGAAAGATCCCCG 60.821 63.158 0.00 0.00 34.07 5.73
7077 14170 2.433970 CCATCAGGAGAAGGGAGAAGTC 59.566 54.545 0.00 0.00 36.89 3.01
7079 14172 1.719378 TCAGGAGAAGGGAGAAGTCCT 59.281 52.381 0.00 0.00 43.36 3.85
7086 14179 2.632763 AGGGAGAAGTCCTAAGCAGT 57.367 50.000 0.00 0.00 43.36 4.40
7087 14180 2.183679 AGGGAGAAGTCCTAAGCAGTG 58.816 52.381 0.00 0.00 43.36 3.66
7144 14409 2.855209 ATGAACAGAACTGCAGAGCT 57.145 45.000 23.35 13.92 0.00 4.09
7145 14410 1.875009 TGAACAGAACTGCAGAGCTG 58.125 50.000 27.13 27.13 34.65 4.24
7162 14585 2.159476 AGCTGCGCATACAAATCAACAG 60.159 45.455 12.24 0.00 0.00 3.16
7168 14591 3.373748 CGCATACAAATCAACAGGCAGTA 59.626 43.478 0.00 0.00 0.00 2.74
7208 14639 2.717639 ACAAGATGGTGTGGCCTATC 57.282 50.000 3.32 0.38 38.35 2.08
7222 14653 3.008375 TGGCCTATCCAGCATATCTTCAC 59.992 47.826 3.32 0.00 40.72 3.18
7272 14729 5.106357 GCAAGAAAAACTTTCTGCCCAAAAA 60.106 36.000 2.53 0.00 36.61 1.94
7283 14740 2.751806 CTGCCCAAAAAGACCAGATCTC 59.248 50.000 0.00 0.00 36.27 2.75
7284 14741 2.376518 TGCCCAAAAAGACCAGATCTCT 59.623 45.455 0.00 0.00 36.27 3.10
7286 14743 3.441922 GCCCAAAAAGACCAGATCTCTTC 59.558 47.826 0.00 0.00 36.27 2.87
7351 14812 4.189231 ACGGTAAACAGAGCACATTATCC 58.811 43.478 0.00 0.00 0.00 2.59
7352 14813 4.188462 CGGTAAACAGAGCACATTATCCA 58.812 43.478 0.00 0.00 0.00 3.41
7390 14877 2.026262 ACAGGCCAACAGACCGAATAAT 60.026 45.455 5.01 0.00 0.00 1.28
7403 14890 8.262227 ACAGACCGAATAATATGGACTAAAACA 58.738 33.333 0.00 0.00 0.00 2.83
7442 15297 4.011698 CCCATCACATGAGTTCATCACAA 58.988 43.478 0.00 0.00 41.91 3.33
7443 15298 4.095932 CCCATCACATGAGTTCATCACAAG 59.904 45.833 0.00 0.00 41.91 3.16
7445 15300 3.076621 TCACATGAGTTCATCACAAGGC 58.923 45.455 0.00 0.00 41.91 4.35
7446 15301 3.079578 CACATGAGTTCATCACAAGGCT 58.920 45.455 0.00 0.00 41.91 4.58
7447 15302 3.504906 CACATGAGTTCATCACAAGGCTT 59.495 43.478 0.00 0.00 41.91 4.35
7450 15305 2.886523 TGAGTTCATCACAAGGCTTTGG 59.113 45.455 13.65 2.32 38.66 3.28
7451 15306 2.887152 GAGTTCATCACAAGGCTTTGGT 59.113 45.455 13.65 0.00 38.66 3.67
7452 15307 4.072131 GAGTTCATCACAAGGCTTTGGTA 58.928 43.478 13.65 0.49 38.66 3.25
7453 15308 4.074970 AGTTCATCACAAGGCTTTGGTAG 58.925 43.478 13.65 2.78 38.66 3.18
7456 15311 3.157087 CATCACAAGGCTTTGGTAGGTT 58.843 45.455 13.65 0.00 38.66 3.50
7457 15312 3.306472 TCACAAGGCTTTGGTAGGTTT 57.694 42.857 13.65 0.00 38.66 3.27
7458 15313 3.219281 TCACAAGGCTTTGGTAGGTTTC 58.781 45.455 13.65 0.00 38.66 2.78
7459 15314 2.955660 CACAAGGCTTTGGTAGGTTTCA 59.044 45.455 13.65 0.00 38.66 2.69
7460 15315 3.383185 CACAAGGCTTTGGTAGGTTTCAA 59.617 43.478 13.65 0.00 38.66 2.69
7461 15316 3.383505 ACAAGGCTTTGGTAGGTTTCAAC 59.616 43.478 13.65 0.00 38.66 3.18
7462 15317 5.713130 ACAAGGCTTTGGTAGGTTTCAACC 61.713 45.833 13.65 0.00 42.83 3.77
7479 15334 0.953960 ACCGGCGGACTGAATTGTTC 60.954 55.000 35.78 0.00 0.00 3.18
7553 15408 2.270923 GCAGTGCGAGATACATCAACA 58.729 47.619 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.467769 AGGATTGAAGACCAGCATAATGG 58.532 43.478 0.00 0.00 46.47 3.16
33 34 0.250727 TGAAACACCTACTGCCCAGC 60.251 55.000 0.00 0.00 0.00 4.85
34 35 2.026822 AGATGAAACACCTACTGCCCAG 60.027 50.000 0.00 0.00 0.00 4.45
76 81 3.828451 AGGAGGTTGAAAATGTGATGGTG 59.172 43.478 0.00 0.00 0.00 4.17
77 82 4.082125 GAGGAGGTTGAAAATGTGATGGT 58.918 43.478 0.00 0.00 0.00 3.55
78 83 3.445096 GGAGGAGGTTGAAAATGTGATGG 59.555 47.826 0.00 0.00 0.00 3.51
92 97 0.688087 GATTCACGGGAGGAGGAGGT 60.688 60.000 0.00 0.00 0.00 3.85
101 106 3.659786 CCGCTATTATTGATTCACGGGA 58.340 45.455 0.00 0.00 35.85 5.14
121 126 2.769095 ACCTCTTCATAGCTCTCAACCC 59.231 50.000 0.00 0.00 0.00 4.11
207 212 2.159462 GCTGAGCAGGAACAAACTATGC 60.159 50.000 0.00 0.00 37.15 3.14
232 237 5.814764 AACAAGATGAATCTGATCACAGC 57.185 39.130 0.00 0.00 43.17 4.40
238 243 9.293404 TGAGAAGAAAAACAAGATGAATCTGAT 57.707 29.630 0.00 0.00 37.19 2.90
240 245 9.343103 CATGAGAAGAAAAACAAGATGAATCTG 57.657 33.333 0.00 0.00 37.19 2.90
250 255 9.650539 TGAAAATGAACATGAGAAGAAAAACAA 57.349 25.926 0.00 0.00 0.00 2.83
289 296 1.298953 TGGAAGAAGGGGGATCAAGG 58.701 55.000 0.00 0.00 0.00 3.61
291 298 3.716872 GACTATGGAAGAAGGGGGATCAA 59.283 47.826 0.00 0.00 0.00 2.57
294 301 2.700540 GGGACTATGGAAGAAGGGGGAT 60.701 54.545 0.00 0.00 0.00 3.85
296 303 1.141185 GGGACTATGGAAGAAGGGGG 58.859 60.000 0.00 0.00 0.00 5.40
360 367 7.395772 TCATCAAACAAATAGCCAAGACCAATA 59.604 33.333 0.00 0.00 0.00 1.90
361 368 6.211184 TCATCAAACAAATAGCCAAGACCAAT 59.789 34.615 0.00 0.00 0.00 3.16
385 392 7.922811 GGTGATAAGATGTCATTCCCAAATTTC 59.077 37.037 0.00 0.00 0.00 2.17
396 403 5.456921 AAACCCTGGTGATAAGATGTCAT 57.543 39.130 0.00 0.00 0.00 3.06
430 438 2.358898 GGCTACCATACAACAAGGCATG 59.641 50.000 0.00 0.00 33.30 4.06
519 530 0.416231 TACCTGGAGGGGCACTAGTT 59.584 55.000 0.00 0.00 40.27 2.24
525 536 2.054799 GTTCATATACCTGGAGGGGCA 58.945 52.381 0.00 0.00 40.27 5.36
526 537 2.039084 CTGTTCATATACCTGGAGGGGC 59.961 54.545 0.00 0.00 40.27 5.80
532 543 4.347876 TGTCCCATCTGTTCATATACCTGG 59.652 45.833 0.00 0.00 0.00 4.45
539 550 3.837731 TGACAGTGTCCCATCTGTTCATA 59.162 43.478 20.43 0.00 43.64 2.15
547 558 1.895798 TCAGAGTGACAGTGTCCCATC 59.104 52.381 20.43 14.53 0.00 3.51
548 559 1.898472 CTCAGAGTGACAGTGTCCCAT 59.102 52.381 20.43 6.26 0.00 4.00
566 577 3.413327 GAAAAACAGGGGGACTCTTCTC 58.587 50.000 0.00 0.00 0.00 2.87
574 585 0.481128 GAGGTGGAAAAACAGGGGGA 59.519 55.000 0.00 0.00 0.00 4.81
579 590 3.004734 GTGACATGGAGGTGGAAAAACAG 59.995 47.826 0.00 0.00 0.00 3.16
614 625 3.749665 CAAAGTGAATTTGGCCTTCCA 57.250 42.857 3.32 0.00 43.88 3.53
656 667 0.106719 TAGGTATTTGGGGCTGCTGC 60.107 55.000 7.10 7.10 38.76 5.25
660 671 6.784031 AGAAATAGATAGGTATTTGGGGCTG 58.216 40.000 0.00 0.00 33.60 4.85
675 686 6.773638 ACGGATGCCAGAAATAGAAATAGAT 58.226 36.000 0.00 0.00 0.00 1.98
698 709 8.688747 AATAGAAGAGGAAATGGATTCATGAC 57.311 34.615 0.00 0.00 39.98 3.06
753 764 9.669353 GTATTTTTCAATACCAGCTCATGTATG 57.331 33.333 0.00 0.00 39.23 2.39
754 765 9.632638 AGTATTTTTCAATACCAGCTCATGTAT 57.367 29.630 0.00 0.00 44.23 2.29
763 774 9.627123 TTCCCATCTAGTATTTTTCAATACCAG 57.373 33.333 2.18 0.00 44.23 4.00
771 782 6.711194 GCCTACCTTCCCATCTAGTATTTTTC 59.289 42.308 0.00 0.00 0.00 2.29
782 793 0.181350 CACTGGCCTACCTTCCCATC 59.819 60.000 3.32 0.00 36.63 3.51
846 857 4.223923 AGGTCTCATTTGTCAGGGAGTTAG 59.776 45.833 0.00 0.00 0.00 2.34
882 893 5.994250 TGCATCTTACTAGCCAGAGAAAAT 58.006 37.500 0.00 0.00 0.00 1.82
912 925 4.868067 ACTATAAACGCTAGTTGATCCCG 58.132 43.478 0.00 0.00 41.05 5.14
919 932 4.331168 AGTCGTCGACTATAAACGCTAGTT 59.669 41.667 25.94 0.00 41.51 2.24
920 933 3.868077 AGTCGTCGACTATAAACGCTAGT 59.132 43.478 25.94 0.00 41.51 2.57
941 954 1.317611 CGTGCGTGAGATAAACGTGAG 59.682 52.381 0.00 0.00 42.93 3.51
1048 1061 4.157120 GGCCGACATAGCCGTGGT 62.157 66.667 0.00 0.00 41.41 4.16
1076 1089 1.517242 CAAGGAGAGTTCACCTGCAC 58.483 55.000 0.00 0.00 37.03 4.57
1094 1107 0.674581 CCAAAGAGCCGTCATCAGCA 60.675 55.000 0.00 0.00 0.00 4.41
1197 1223 3.603080 TCTCCCCGTGGTACCCCA 61.603 66.667 10.07 0.00 38.87 4.96
1228 1254 0.814457 GCTCGTCCAGATCTGACAGT 59.186 55.000 24.62 0.00 0.00 3.55
1229 1255 1.102154 AGCTCGTCCAGATCTGACAG 58.898 55.000 24.62 17.34 0.00 3.51
1258 1284 0.264955 TTATCCTCTCCTTCCCCGCT 59.735 55.000 0.00 0.00 0.00 5.52
1263 1289 2.365941 CGTTCCCTTATCCTCTCCTTCC 59.634 54.545 0.00 0.00 0.00 3.46
1333 1359 2.498077 CTCCTCCATGAGCTCACGA 58.502 57.895 20.97 16.31 0.00 4.35
1578 1614 3.812053 CAGCAGCAGACACTTCTACTTTT 59.188 43.478 0.00 0.00 0.00 2.27
1653 1692 0.969409 GCTTCTTGCTTCCCATGGCT 60.969 55.000 6.09 0.00 38.95 4.75
1658 1697 0.179004 TTTCGGCTTCTTGCTTCCCA 60.179 50.000 0.00 0.00 42.39 4.37
1677 1716 3.067106 CACCGTGCAAGTTAGATCTGTT 58.933 45.455 5.18 0.00 0.00 3.16
1678 1717 2.037251 ACACCGTGCAAGTTAGATCTGT 59.963 45.455 5.18 0.00 0.00 3.41
1731 1770 0.178921 TCCCTCTGAGGTGCTCTTGT 60.179 55.000 21.70 0.00 31.93 3.16
1771 1810 1.333619 CACTGGTTGCGCAAGTTTAGT 59.666 47.619 25.78 20.59 41.68 2.24
1789 1828 1.647084 GTTGACCTGTTCCACGCAC 59.353 57.895 0.00 0.00 0.00 5.34
1793 1832 1.147600 ACCGGTTGACCTGTTCCAC 59.852 57.895 0.00 0.00 28.50 4.02
1809 1848 2.922740 TTATTACCGCATCCTCCACC 57.077 50.000 0.00 0.00 0.00 4.61
1885 1924 7.084486 GGACATCATAAAGGAAACAACACTTC 58.916 38.462 0.00 0.00 0.00 3.01
1930 1996 8.912988 TCACCTAAAGAACAAGATTCAAATTGT 58.087 29.630 0.00 0.00 41.28 2.71
1959 2025 6.640907 ACGCTTGAGTGTTATTTCCAAATTTC 59.359 34.615 0.00 0.00 34.75 2.17
2017 2095 7.239763 TCGGAGATCCATATAACTTATGCAA 57.760 36.000 0.00 0.00 35.14 4.08
2188 2452 3.492102 TTATCAGTAGGGCATCAAGGC 57.508 47.619 0.00 0.00 43.27 4.35
2273 2537 4.382254 CCGTTACATCTAACCAAGCCACTA 60.382 45.833 0.00 0.00 30.00 2.74
2296 2560 4.890088 TGGTGTGATTTACTAGTGTCACC 58.110 43.478 23.51 20.47 40.07 4.02
2316 2580 8.986929 AGACCTATTTATTTTCCTCAAGATGG 57.013 34.615 0.00 0.00 0.00 3.51
2410 3133 2.571212 TGTTGCAAGTCTTACCACCAG 58.429 47.619 0.00 0.00 0.00 4.00
2440 3166 7.023575 GGTAACAAGATGACATGTAAAGCTTG 58.976 38.462 25.85 25.85 37.75 4.01
2474 3200 9.852091 AACTTGTAGAAGGTTAGTACGAATTAG 57.148 33.333 4.45 0.00 32.95 1.73
2521 3382 1.434188 TGACCCACCATCAGTGTCTT 58.566 50.000 0.00 0.00 45.74 3.01
2744 3607 6.540189 TCTCAAAGCTATATCTGACAAAAGCC 59.460 38.462 0.00 0.00 0.00 4.35
2745 3608 7.545362 TCTCAAAGCTATATCTGACAAAAGC 57.455 36.000 0.00 0.00 0.00 3.51
2746 3609 9.545105 AGATCTCAAAGCTATATCTGACAAAAG 57.455 33.333 0.00 0.00 0.00 2.27
2747 3610 9.322773 CAGATCTCAAAGCTATATCTGACAAAA 57.677 33.333 14.02 0.00 44.01 2.44
2748 3611 8.481314 ACAGATCTCAAAGCTATATCTGACAAA 58.519 33.333 21.10 0.00 44.01 2.83
2749 3612 7.924947 CACAGATCTCAAAGCTATATCTGACAA 59.075 37.037 21.10 0.00 44.01 3.18
2750 3613 7.069208 ACACAGATCTCAAAGCTATATCTGACA 59.931 37.037 21.10 0.00 44.01 3.58
2751 3614 7.432869 ACACAGATCTCAAAGCTATATCTGAC 58.567 38.462 21.10 0.00 44.01 3.51
2752 3615 7.594351 ACACAGATCTCAAAGCTATATCTGA 57.406 36.000 21.10 6.49 44.01 3.27
2753 3616 9.190858 GTTACACAGATCTCAAAGCTATATCTG 57.809 37.037 16.15 16.15 45.78 2.90
2754 3617 8.918116 TGTTACACAGATCTCAAAGCTATATCT 58.082 33.333 0.00 0.00 0.00 1.98
2755 3618 9.703892 ATGTTACACAGATCTCAAAGCTATATC 57.296 33.333 0.00 0.00 0.00 1.63
2756 3619 9.703892 GATGTTACACAGATCTCAAAGCTATAT 57.296 33.333 0.00 0.00 0.00 0.86
2757 3620 8.918116 AGATGTTACACAGATCTCAAAGCTATA 58.082 33.333 0.00 0.00 0.00 1.31
2758 3621 7.790027 AGATGTTACACAGATCTCAAAGCTAT 58.210 34.615 0.00 0.00 0.00 2.97
2759 3622 7.175347 AGATGTTACACAGATCTCAAAGCTA 57.825 36.000 0.00 0.00 0.00 3.32
2760 3623 6.047511 AGATGTTACACAGATCTCAAAGCT 57.952 37.500 0.00 0.00 0.00 3.74
2761 3624 6.734104 AAGATGTTACACAGATCTCAAAGC 57.266 37.500 0.00 0.00 0.00 3.51
2762 3625 8.763049 TGTAAGATGTTACACAGATCTCAAAG 57.237 34.615 11.18 0.00 42.99 2.77
2763 3626 9.208022 CTTGTAAGATGTTACACAGATCTCAAA 57.792 33.333 14.54 0.00 46.63 2.69
2764 3627 8.367911 ACTTGTAAGATGTTACACAGATCTCAA 58.632 33.333 14.54 0.00 46.63 3.02
2765 3628 7.896811 ACTTGTAAGATGTTACACAGATCTCA 58.103 34.615 14.54 0.00 46.63 3.27
2772 3635 7.929245 TGCTAAGAACTTGTAAGATGTTACACA 59.071 33.333 14.54 4.28 46.63 3.72
2785 3648 9.991906 TGTTACTACTTAATGCTAAGAACTTGT 57.008 29.630 0.07 0.00 38.35 3.16
2895 3818 9.280174 TCTATAGAAGTACAAAAAGTTGGTTGG 57.720 33.333 0.00 0.00 39.22 3.77
2955 3879 9.586435 CATGAATACTTAACCAAAAAGATTCCC 57.414 33.333 0.00 0.00 0.00 3.97
2960 3884 8.792633 CAGGTCATGAATACTTAACCAAAAAGA 58.207 33.333 0.00 0.00 0.00 2.52
2961 3885 8.792633 TCAGGTCATGAATACTTAACCAAAAAG 58.207 33.333 0.00 0.00 34.02 2.27
2962 3886 8.573035 GTCAGGTCATGAATACTTAACCAAAAA 58.427 33.333 0.00 0.00 40.43 1.94
2983 3907 6.536582 CAGACTACTGGTATCAAAATGTCAGG 59.463 42.308 0.00 0.00 40.14 3.86
3001 3925 5.183331 TCCAACAGAGTATGTGTCAGACTAC 59.817 44.000 1.31 0.00 44.43 2.73
3012 3936 7.987458 ACACTAATATGGTTCCAACAGAGTATG 59.013 37.037 0.00 0.00 0.00 2.39
3029 3953 8.859236 AAGCATGCTAATGATCACACTAATAT 57.141 30.769 23.00 0.00 35.67 1.28
3037 3961 7.590322 CAGTTAATGAAGCATGCTAATGATCAC 59.410 37.037 23.00 12.49 35.37 3.06
3064 3988 4.712051 TCATCATTCCTTCATCGGGATT 57.288 40.909 0.00 0.00 32.41 3.01
3070 3994 7.823310 ACACTATGCTATCATCATTCCTTCATC 59.177 37.037 0.00 0.00 34.22 2.92
3098 4022 0.521735 CATGCCTCATGATCCATGCG 59.478 55.000 17.54 0.00 43.81 4.73
3109 4033 0.322366 TCCGTTCAATGCATGCCTCA 60.322 50.000 16.68 0.00 0.00 3.86
3126 4050 2.706190 AGTGCCACCCTATGTTATCTCC 59.294 50.000 0.00 0.00 0.00 3.71
3327 4747 2.617021 GCCGACCCATTTACCTTCAAGA 60.617 50.000 0.00 0.00 0.00 3.02
3442 4862 2.723231 TGCTGTGATGCTGCAAACT 58.277 47.368 6.36 0.00 46.62 2.66
3449 4869 0.250597 TGACTGCTTGCTGTGATGCT 60.251 50.000 9.74 0.00 0.00 3.79
3480 4900 7.219484 TGAATTTTTCCTTTGAGGTGATCTC 57.781 36.000 0.00 0.00 42.74 2.75
3496 4916 6.664816 TGGCAGTCTTCCTCATATGAATTTTT 59.335 34.615 6.90 0.00 0.00 1.94
3941 5376 5.007385 ACGAGCACTTTACACTAATAGGG 57.993 43.478 0.00 0.00 0.00 3.53
3983 5419 9.595823 GTATTACTACTAGATTTGCAGTTTGGA 57.404 33.333 0.00 0.00 0.00 3.53
3998 5434 7.190335 ACACTTTGGCCATGTATTACTACTA 57.810 36.000 6.09 0.00 0.00 1.82
4271 6683 9.021807 CCATCCTCTATGAGCATGATTTATTTT 57.978 33.333 0.00 0.00 37.86 1.82
4532 6989 4.020218 TGAAGGGAGTACATCTGAACCTTG 60.020 45.833 0.00 0.00 37.01 3.61
4681 7138 2.558359 GGCACTAGCACAAAACTTGGAT 59.442 45.455 0.00 0.00 44.61 3.41
4712 7169 3.521126 CAGGGAAGGAGAGATTGGAAAGA 59.479 47.826 0.00 0.00 0.00 2.52
4871 7361 3.871485 TGTTTCATGTTTTGCTGGCTTT 58.129 36.364 0.00 0.00 0.00 3.51
4872 7362 3.540314 TGTTTCATGTTTTGCTGGCTT 57.460 38.095 0.00 0.00 0.00 4.35
4873 7363 3.069872 TGATGTTTCATGTTTTGCTGGCT 59.930 39.130 0.00 0.00 0.00 4.75
4874 7364 3.184986 GTGATGTTTCATGTTTTGCTGGC 59.815 43.478 0.00 0.00 33.56 4.85
4875 7365 4.370049 TGTGATGTTTCATGTTTTGCTGG 58.630 39.130 0.00 0.00 33.56 4.85
4949 7441 3.769536 CGGGTGAAATGTTTTCATAGCC 58.230 45.455 6.01 3.49 39.94 3.93
4950 7442 3.179048 GCGGGTGAAATGTTTTCATAGC 58.821 45.455 6.01 8.18 39.94 2.97
4951 7443 4.433186 TGCGGGTGAAATGTTTTCATAG 57.567 40.909 6.01 3.05 39.94 2.23
4952 7444 4.855715 TTGCGGGTGAAATGTTTTCATA 57.144 36.364 6.01 0.00 39.94 2.15
4953 7445 3.742433 TTGCGGGTGAAATGTTTTCAT 57.258 38.095 6.01 0.00 43.05 2.57
4954 7446 3.526931 TTTGCGGGTGAAATGTTTTCA 57.473 38.095 0.00 0.00 0.00 2.69
4955 7447 4.866682 TTTTTGCGGGTGAAATGTTTTC 57.133 36.364 0.00 0.00 0.00 2.29
5268 7760 7.975616 ACAAAAATGGTGTATTCAGACATATGC 59.024 33.333 1.58 0.00 0.00 3.14
5269 7761 9.859427 AACAAAAATGGTGTATTCAGACATATG 57.141 29.630 0.00 0.00 0.00 1.78
5271 7763 9.906660 GAAACAAAAATGGTGTATTCAGACATA 57.093 29.630 0.00 0.00 0.00 2.29
5302 7794 0.730840 GTTACGGAGGCAAAATCCCG 59.269 55.000 0.00 0.00 46.65 5.14
5316 7809 2.621338 AGCAGACCATGTGATGTTACG 58.379 47.619 0.00 0.00 0.00 3.18
5319 7812 4.005650 CACTAAGCAGACCATGTGATGTT 58.994 43.478 0.00 0.00 0.00 2.71
5320 7813 3.603532 CACTAAGCAGACCATGTGATGT 58.396 45.455 0.00 0.00 0.00 3.06
5321 7814 2.941064 CCACTAAGCAGACCATGTGATG 59.059 50.000 0.00 0.00 0.00 3.07
5322 7815 2.840038 TCCACTAAGCAGACCATGTGAT 59.160 45.455 0.00 0.00 0.00 3.06
5328 7821 2.438021 ACAAACTCCACTAAGCAGACCA 59.562 45.455 0.00 0.00 0.00 4.02
5422 7937 3.950794 GATGCGGCAGGGACAACGA 62.951 63.158 9.25 0.00 0.00 3.85
5586 8140 1.292223 CGGACTCGGTCACCATGTT 59.708 57.895 0.00 0.00 33.68 2.71
5600 8154 2.047655 TCGCACAATGTCCCGGAC 60.048 61.111 10.96 10.96 0.00 4.79
5927 8499 4.012895 GCACCGACACCAACTGCG 62.013 66.667 0.00 0.00 0.00 5.18
6185 8784 0.033920 AGTCATCGCTGCTGTTGACA 59.966 50.000 23.81 0.00 40.69 3.58
6227 9698 1.757699 GACACTACCACCTCCATCTCC 59.242 57.143 0.00 0.00 0.00 3.71
6311 9787 1.138859 TCGTCTACTTCCATGGCCATG 59.861 52.381 34.82 34.82 38.51 3.66
6312 9788 1.496060 TCGTCTACTTCCATGGCCAT 58.504 50.000 14.09 14.09 0.00 4.40
6313 9789 1.207089 CTTCGTCTACTTCCATGGCCA 59.793 52.381 8.56 8.56 0.00 5.36
6314 9790 1.473434 CCTTCGTCTACTTCCATGGCC 60.473 57.143 6.96 0.00 0.00 5.36
6315 9791 1.207329 ACCTTCGTCTACTTCCATGGC 59.793 52.381 6.96 0.00 0.00 4.40
6340 9816 3.790437 CAGCACCATCTCCGGCCT 61.790 66.667 0.00 0.00 0.00 5.19
6463 9954 1.956170 AGCGTGACGAACAGCTTGG 60.956 57.895 10.10 0.00 35.90 3.61
6702 10275 3.443329 ACAACAAACTTCAGCACACATCA 59.557 39.130 0.00 0.00 0.00 3.07
6781 10391 1.202604 ACTCACACTTAACCCACACGG 60.203 52.381 0.00 0.00 37.81 4.94
6881 10535 7.970102 AGTAAACACTACCAAAAGATACTGGA 58.030 34.615 0.00 0.00 36.49 3.86
6918 10748 3.871006 TCGTTTGCTAGTATGGCTGATTG 59.129 43.478 0.00 0.00 46.01 2.67
6934 10768 1.522668 TCTTCACCAGGCATCGTTTG 58.477 50.000 0.00 0.00 0.00 2.93
6935 10769 2.359900 GATCTTCACCAGGCATCGTTT 58.640 47.619 0.00 0.00 0.00 3.60
6936 10770 1.740380 CGATCTTCACCAGGCATCGTT 60.740 52.381 0.00 0.00 33.29 3.85
6961 10795 3.439857 TGTAGAGAAATGGCAAGGCTT 57.560 42.857 0.00 0.00 0.00 4.35
6968 10802 9.440773 TGTTATCATGATATGTAGAGAAATGGC 57.559 33.333 16.06 0.00 0.00 4.40
6975 10809 9.486497 AAACTGCTGTTATCATGATATGTAGAG 57.514 33.333 22.69 15.55 34.96 2.43
6979 10813 8.400947 GTTCAAACTGCTGTTATCATGATATGT 58.599 33.333 16.06 6.30 34.96 2.29
6982 10816 7.823799 TGAGTTCAAACTGCTGTTATCATGATA 59.176 33.333 11.49 11.49 39.88 2.15
7042 10876 1.071385 CTGATGGGTGCTGTATCTCCC 59.929 57.143 0.00 0.00 39.58 4.30
7077 14170 1.906574 TCTGTAACCCCACTGCTTAGG 59.093 52.381 0.00 0.00 0.00 2.69
7079 14172 1.906574 CCTCTGTAACCCCACTGCTTA 59.093 52.381 0.00 0.00 0.00 3.09
7086 14179 2.602676 GCCTGCCTCTGTAACCCCA 61.603 63.158 0.00 0.00 0.00 4.96
7087 14180 1.926426 ATGCCTGCCTCTGTAACCCC 61.926 60.000 0.00 0.00 0.00 4.95
7144 14409 1.135431 GCCTGTTGATTTGTATGCGCA 60.135 47.619 14.96 14.96 0.00 6.09
7145 14410 1.135431 TGCCTGTTGATTTGTATGCGC 60.135 47.619 0.00 0.00 0.00 6.09
7146 14411 2.162208 ACTGCCTGTTGATTTGTATGCG 59.838 45.455 0.00 0.00 0.00 4.73
7162 14585 3.406764 CCATCCTTGAATAGCTACTGCC 58.593 50.000 0.00 0.00 40.80 4.85
7168 14591 4.141181 TGTTATGGCCATCCTTGAATAGCT 60.141 41.667 24.80 0.00 0.00 3.32
7200 14631 3.008375 GTGAAGATATGCTGGATAGGCCA 59.992 47.826 5.01 0.00 46.96 5.36
7208 14639 4.148128 AGTCCTTGTGAAGATATGCTGG 57.852 45.455 0.00 0.00 0.00 4.85
7222 14653 8.777865 TTTTATCTGAAGTCATGTAGTCCTTG 57.222 34.615 0.00 0.00 0.00 3.61
7272 14729 6.214412 ACCATGTAAAAGAAGAGATCTGGTCT 59.786 38.462 0.00 0.00 38.79 3.85
7286 14743 9.862585 GCAGAATGTTTTTAAACCATGTAAAAG 57.137 29.630 3.13 0.00 39.31 2.27
7304 14765 7.497249 GTCAATAAATCCAGTAGAGCAGAATGT 59.503 37.037 0.00 0.00 39.31 2.71
7306 14767 6.703607 CGTCAATAAATCCAGTAGAGCAGAAT 59.296 38.462 0.00 0.00 0.00 2.40
7351 14812 4.800471 GCCTGTTGAACACTTCTTTCTTTG 59.200 41.667 0.00 0.00 0.00 2.77
7352 14813 4.142160 GGCCTGTTGAACACTTCTTTCTTT 60.142 41.667 0.00 0.00 0.00 2.52
7403 14890 4.851540 TGATGGGGGTATGTATCACATCAT 59.148 41.667 3.68 0.00 39.88 2.45
7442 15297 2.594131 GGTTGAAACCTACCAAAGCCT 58.406 47.619 4.92 0.00 45.75 4.58
7453 15308 2.281276 AGTCCGCCGGTTGAAACC 60.281 61.111 1.63 1.88 45.76 3.27
7456 15311 0.250553 AATTCAGTCCGCCGGTTGAA 60.251 50.000 21.45 21.45 34.23 2.69
7457 15312 0.953471 CAATTCAGTCCGCCGGTTGA 60.953 55.000 1.63 5.99 0.00 3.18
7458 15313 1.234615 ACAATTCAGTCCGCCGGTTG 61.235 55.000 1.63 1.19 0.00 3.77
7459 15314 0.536460 AACAATTCAGTCCGCCGGTT 60.536 50.000 1.63 0.00 0.00 4.44
7460 15315 0.953960 GAACAATTCAGTCCGCCGGT 60.954 55.000 1.63 0.00 0.00 5.28
7461 15316 0.953471 TGAACAATTCAGTCCGCCGG 60.953 55.000 0.00 0.00 34.08 6.13
7462 15317 1.086696 ATGAACAATTCAGTCCGCCG 58.913 50.000 0.00 0.00 43.98 6.46
7463 15318 3.531538 TCTATGAACAATTCAGTCCGCC 58.468 45.455 0.00 0.00 43.98 6.13
7464 15319 5.741388 ATTCTATGAACAATTCAGTCCGC 57.259 39.130 0.00 0.00 43.98 5.54
7465 15320 8.331022 CAAGTATTCTATGAACAATTCAGTCCG 58.669 37.037 0.00 0.00 43.98 4.79
7466 15321 8.125448 GCAAGTATTCTATGAACAATTCAGTCC 58.875 37.037 0.00 0.00 43.98 3.85
7467 15322 8.887717 AGCAAGTATTCTATGAACAATTCAGTC 58.112 33.333 0.00 0.00 43.98 3.51
7468 15323 8.798859 AGCAAGTATTCTATGAACAATTCAGT 57.201 30.769 0.00 0.00 43.98 3.41
7479 15334 7.296628 AGGAAGGACTAGCAAGTATTCTATG 57.703 40.000 0.00 0.00 35.56 2.23
7553 15408 2.943199 GCCATACAGCTTCAAGGCTCTT 60.943 50.000 9.19 0.00 41.00 2.85


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

AutoCloner maintained by Alex Coulton.