Multiple sequence alignment - TraesCS1B01G471400

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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 TraesCS1B01G471400 chr1B 100.000 3315 0 0 2511 5825 679654949 679651635 0.000000e+00 6122.0
1 TraesCS1B01G471400 chr1B 100.000 2329 0 0 1 2329 679657459 679655131 0.000000e+00 4301.0
2 TraesCS1B01G471400 chr1B 77.350 2128 401 65 2725 4811 679709275 679707188 0.000000e+00 1184.0
3 TraesCS1B01G471400 chr1B 85.556 810 114 3 999 1805 679710581 679709772 0.000000e+00 845.0
4 TraesCS1B01G471400 chr1B 85.330 818 114 4 998 1809 679701926 679701109 0.000000e+00 841.0
5 TraesCS1B01G471400 chr1B 97.959 98 0 2 2511 2608 363151758 363151663 1.000000e-37 169.0
6 TraesCS1B01G471400 chr1B 100.000 89 0 0 2511 2599 245935401 245935489 1.300000e-36 165.0
7 TraesCS1B01G471400 chr1A 91.821 2262 172 8 2603 4860 586316439 586314187 0.000000e+00 3140.0
8 TraesCS1B01G471400 chr1A 91.821 2262 171 9 2603 4860 586346825 586344574 0.000000e+00 3140.0
9 TraesCS1B01G471400 chr1A 89.512 2174 117 50 207 2329 586348954 586346841 0.000000e+00 2649.0
10 TraesCS1B01G471400 chr1A 89.545 2152 118 48 229 2329 586318550 586316455 0.000000e+00 2628.0
11 TraesCS1B01G471400 chr1A 86.853 1179 126 22 3726 4884 586429427 586428258 0.000000e+00 1291.0
12 TraesCS1B01G471400 chr1A 78.607 2024 353 56 2811 4811 586924519 586922553 0.000000e+00 1266.0
13 TraesCS1B01G471400 chr1A 85.750 1207 133 20 606 1803 586520249 586519073 0.000000e+00 1240.0
14 TraesCS1B01G471400 chr1A 76.875 2240 450 56 2608 4811 586332746 586330539 0.000000e+00 1205.0
15 TraesCS1B01G471400 chr1A 77.465 2099 386 69 2811 4857 586518526 586516463 0.000000e+00 1175.0
16 TraesCS1B01G471400 chr1A 77.590 1776 338 41 2608 4363 586362496 586360761 0.000000e+00 1020.0
17 TraesCS1B01G471400 chr1A 82.953 1138 140 24 724 1810 586714482 586713348 0.000000e+00 977.0
18 TraesCS1B01G471400 chr1A 84.737 819 118 5 998 1812 586403487 586402672 0.000000e+00 813.0
19 TraesCS1B01G471400 chr1A 84.491 806 122 3 1007 1809 586366343 586365538 0.000000e+00 793.0
20 TraesCS1B01G471400 chr1A 82.718 758 76 26 5020 5737 586313768 586313026 1.780000e-174 623.0
21 TraesCS1B01G471400 chr1A 85.261 536 35 13 3 522 586520886 586520379 4.030000e-141 512.0
22 TraesCS1B01G471400 chr1A 90.476 63 5 1 32 94 550598210 550598149 1.350000e-11 82.4
23 TraesCS1B01G471400 chr1D 90.053 2272 195 14 2604 4859 487840423 487838167 0.000000e+00 2915.0
24 TraesCS1B01G471400 chr1D 91.749 1321 101 6 899 2214 487841911 487840594 0.000000e+00 1829.0
25 TraesCS1B01G471400 chr1D 78.937 2032 362 45 2811 4802 487895990 487893985 0.000000e+00 1321.0
26 TraesCS1B01G471400 chr1D 77.573 2118 396 59 2723 4811 488484080 488486147 0.000000e+00 1206.0
27 TraesCS1B01G471400 chr1D 81.542 791 74 37 4997 5741 487837523 487836759 2.340000e-163 586.0
28 TraesCS1B01G471400 chr1D 83.207 661 64 26 189 838 487842574 487841950 3.940000e-156 562.0
29 TraesCS1B01G471400 chr1D 95.699 93 4 0 25 117 487842683 487842591 3.640000e-32 150.0
30 TraesCS1B01G471400 chrUn 77.678 2110 405 50 2723 4811 8844812 8842748 0.000000e+00 1227.0
31 TraesCS1B01G471400 chrUn 83.004 912 140 8 999 1896 8846044 8845134 0.000000e+00 811.0
32 TraesCS1B01G471400 chr4A 79.029 906 165 19 2881 3771 728831393 728832288 1.080000e-166 597.0
33 TraesCS1B01G471400 chr4A 75.598 1254 254 38 2880 4111 728429651 728428428 1.820000e-159 573.0
34 TraesCS1B01G471400 chr4A 75.339 1253 259 37 2880 4111 729861884 729863107 1.830000e-154 556.0
35 TraesCS1B01G471400 chr7D 76.957 894 181 19 2891 3771 10471081 10470200 2.440000e-133 486.0
36 TraesCS1B01G471400 chr7D 95.833 48 2 0 48 95 62195011 62194964 1.740000e-10 78.7
37 TraesCS1B01G471400 chr4B 73.535 1092 259 24 2906 3976 646578596 646577514 7.080000e-104 388.0
38 TraesCS1B01G471400 chr4B 98.876 89 1 0 2511 2599 31525763 31525675 6.040000e-35 159.0
39 TraesCS1B01G471400 chr7A 100.000 89 0 0 2511 2599 539312480 539312392 1.300000e-36 165.0
40 TraesCS1B01G471400 chr6B 100.000 89 0 0 2511 2599 217172168 217172080 1.300000e-36 165.0
41 TraesCS1B01G471400 chr6B 98.889 90 0 1 2511 2600 359814929 359815017 6.040000e-35 159.0
42 TraesCS1B01G471400 chr2A 100.000 89 0 0 2511 2599 498099186 498099274 1.300000e-36 165.0
43 TraesCS1B01G471400 chr7B 98.837 86 1 0 2511 2596 231703794 231703709 2.810000e-33 154.0
44 TraesCS1B01G471400 chr2D 93.878 98 5 1 2511 2607 215831879 215831976 4.700000e-31 147.0


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 TraesCS1B01G471400 chr1B 679651635 679657459 5824 True 5211.500000 6122 100.000000 1 5825 2 chr1B.!!$R3 5824
1 TraesCS1B01G471400 chr1B 679707188 679710581 3393 True 1014.500000 1184 81.453000 999 4811 2 chr1B.!!$R4 3812
2 TraesCS1B01G471400 chr1B 679701109 679701926 817 True 841.000000 841 85.330000 998 1809 1 chr1B.!!$R2 811
3 TraesCS1B01G471400 chr1A 586344574 586348954 4380 True 2894.500000 3140 90.666500 207 4860 2 chr1A.!!$R8 4653
4 TraesCS1B01G471400 chr1A 586313026 586318550 5524 True 2130.333333 3140 88.028000 229 5737 3 chr1A.!!$R7 5508
5 TraesCS1B01G471400 chr1A 586428258 586429427 1169 True 1291.000000 1291 86.853000 3726 4884 1 chr1A.!!$R4 1158
6 TraesCS1B01G471400 chr1A 586922553 586924519 1966 True 1266.000000 1266 78.607000 2811 4811 1 chr1A.!!$R6 2000
7 TraesCS1B01G471400 chr1A 586330539 586332746 2207 True 1205.000000 1205 76.875000 2608 4811 1 chr1A.!!$R2 2203
8 TraesCS1B01G471400 chr1A 586713348 586714482 1134 True 977.000000 977 82.953000 724 1810 1 chr1A.!!$R5 1086
9 TraesCS1B01G471400 chr1A 586516463 586520886 4423 True 975.666667 1240 82.825333 3 4857 3 chr1A.!!$R10 4854
10 TraesCS1B01G471400 chr1A 586360761 586366343 5582 True 906.500000 1020 81.040500 1007 4363 2 chr1A.!!$R9 3356
11 TraesCS1B01G471400 chr1A 586402672 586403487 815 True 813.000000 813 84.737000 998 1812 1 chr1A.!!$R3 814
12 TraesCS1B01G471400 chr1D 487893985 487895990 2005 True 1321.000000 1321 78.937000 2811 4802 1 chr1D.!!$R1 1991
13 TraesCS1B01G471400 chr1D 487836759 487842683 5924 True 1208.400000 2915 88.450000 25 5741 5 chr1D.!!$R2 5716
14 TraesCS1B01G471400 chr1D 488484080 488486147 2067 False 1206.000000 1206 77.573000 2723 4811 1 chr1D.!!$F1 2088
15 TraesCS1B01G471400 chrUn 8842748 8846044 3296 True 1019.000000 1227 80.341000 999 4811 2 chrUn.!!$R1 3812
16 TraesCS1B01G471400 chr4A 728831393 728832288 895 False 597.000000 597 79.029000 2881 3771 1 chr4A.!!$F1 890
17 TraesCS1B01G471400 chr4A 728428428 728429651 1223 True 573.000000 573 75.598000 2880 4111 1 chr4A.!!$R1 1231
18 TraesCS1B01G471400 chr4A 729861884 729863107 1223 False 556.000000 556 75.339000 2880 4111 1 chr4A.!!$F2 1231
19 TraesCS1B01G471400 chr7D 10470200 10471081 881 True 486.000000 486 76.957000 2891 3771 1 chr7D.!!$R1 880
20 TraesCS1B01G471400 chr4B 646577514 646578596 1082 True 388.000000 388 73.535000 2906 3976 1 chr4B.!!$R2 1070

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
873 1037 0.469917 CATCAGGTACGATGCCCCTT 59.530 55.000 0.0 0.00 36.64 3.95 F
1467 1672 0.321671 CCATTGACCCTCGACTGTGT 59.678 55.000 0.0 0.00 0.00 3.72 F
1509 1714 2.280389 CTCGTGGGCATCGATGGG 60.280 66.667 26.0 2.75 36.73 4.00 F
2543 5385 0.040425 GCGGGCATATTTGTAAGGCG 60.040 55.000 0.0 0.00 0.00 5.52 F
3874 6765 0.038159 GGAGACCACACTTGACCTCG 60.038 60.000 0.0 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2524 5366 0.040425 CGCCTTACAAATATGCCCGC 60.040 55.0 0.00 0.0 0.00 6.13 R
2531 5373 0.106918 CCCCCAGCGCCTTACAAATA 60.107 55.0 2.29 0.0 0.00 1.40 R
3402 6271 0.594110 GATCGTCCCTCTCGATGTCC 59.406 60.0 5.58 0.0 45.90 4.02 R
4440 7379 0.670854 GAGTTGACGCCTCCTTCACC 60.671 60.0 0.00 0.0 0.00 4.02 R
5554 9103 0.108207 CTGAGATGCCTGGATGGTCC 59.892 60.0 0.00 0.0 38.35 4.46 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
120 121 6.715264 AGAAAGGTTGGTATTTTGGTGTCTAG 59.285 38.462 0.00 0.00 0.00 2.43
135 136 4.416620 GTGTCTAGATGAAAGACGGTGAG 58.583 47.826 0.00 0.00 45.19 3.51
164 165 5.243730 CAGTGAAAGTGAAAACCATGGGTAT 59.756 40.000 18.09 0.14 40.62 2.73
225 232 5.613812 TGTGCTTACGTGATTTATTTGTCG 58.386 37.500 0.00 0.00 0.00 4.35
249 256 6.808212 CGGAGTAGTTTATTTTAGTTCGTGGA 59.192 38.462 0.00 0.00 0.00 4.02
294 315 1.760480 GTGGTTGTGGGCCTGGTTT 60.760 57.895 4.53 0.00 0.00 3.27
297 318 3.222855 TTGTGGGCCTGGTTTGCG 61.223 61.111 4.53 0.00 0.00 4.85
331 355 1.791283 GTCGTCGTCGTCAACCTCG 60.791 63.158 1.33 0.00 38.33 4.63
394 428 4.277515 TGAGCTCTGCACAGAAATACTT 57.722 40.909 16.19 0.00 36.94 2.24
404 438 3.927142 CACAGAAATACTTCCGTGTCCTC 59.073 47.826 0.00 0.00 35.89 3.71
417 451 2.356382 CGTGTCCTCTATCACTCCTCAC 59.644 54.545 0.00 0.00 33.07 3.51
421 455 4.263949 TGTCCTCTATCACTCCTCACTCAA 60.264 45.833 0.00 0.00 0.00 3.02
436 470 3.144506 CACTCAATCACTTCCAGCACTT 58.855 45.455 0.00 0.00 0.00 3.16
439 473 2.106338 TCAATCACTTCCAGCACTTCCA 59.894 45.455 0.00 0.00 0.00 3.53
483 517 2.840102 CCGCCCCTACCTCCTCAG 60.840 72.222 0.00 0.00 0.00 3.35
484 518 2.279073 CGCCCCTACCTCCTCAGA 59.721 66.667 0.00 0.00 0.00 3.27
625 747 1.298713 CGCCTCCTCTCGTTCATCG 60.299 63.158 0.00 0.00 41.41 3.84
743 870 3.059597 CACCAACTAACTCTTGCTTCACG 60.060 47.826 0.00 0.00 0.00 4.35
765 899 2.964389 GAGAGCGCCCGAATCTGC 60.964 66.667 2.29 0.00 0.00 4.26
787 921 3.995506 CTCCCCGCCGCATTCCTTT 62.996 63.158 0.00 0.00 0.00 3.11
790 934 2.046285 CCCGCCGCATTCCTTTTCT 61.046 57.895 0.00 0.00 0.00 2.52
793 937 1.809869 GCCGCATTCCTTTTCTCCC 59.190 57.895 0.00 0.00 0.00 4.30
794 938 1.667154 GCCGCATTCCTTTTCTCCCC 61.667 60.000 0.00 0.00 0.00 4.81
795 939 1.037579 CCGCATTCCTTTTCTCCCCC 61.038 60.000 0.00 0.00 0.00 5.40
801 945 2.267961 CTTTTCTCCCCCGACCGG 59.732 66.667 0.00 0.00 0.00 5.28
841 999 2.226149 ATCTCCGACCTCCCCGTCTT 62.226 60.000 0.00 0.00 0.00 3.01
863 1022 3.260884 TCTTCCTTCACCACATCAGGTAC 59.739 47.826 0.00 0.00 40.77 3.34
873 1037 0.469917 CATCAGGTACGATGCCCCTT 59.530 55.000 0.00 0.00 36.64 3.95
895 1059 0.742281 CACTGCAGAGGATCCCAACG 60.742 60.000 23.35 0.00 33.66 4.10
914 1087 1.268539 CGCCTCGCCACCAATTAATTC 60.269 52.381 0.00 0.00 0.00 2.17
915 1088 2.024414 GCCTCGCCACCAATTAATTCT 58.976 47.619 0.00 0.00 0.00 2.40
922 1095 6.155827 TCGCCACCAATTAATTCTTTTTGAG 58.844 36.000 0.00 0.00 0.00 3.02
923 1096 6.015856 TCGCCACCAATTAATTCTTTTTGAGA 60.016 34.615 0.00 0.00 0.00 3.27
959 1136 1.271379 ACCAACTAACCGCTGCTTCAT 60.271 47.619 0.00 0.00 0.00 2.57
965 1142 1.609208 AACCGCTGCTTCATTCTGTT 58.391 45.000 0.00 0.00 0.00 3.16
994 1171 2.817396 GCCGAGCCAAGAGAGCAC 60.817 66.667 0.00 0.00 0.00 4.40
1028 1205 2.431942 AATCGTGACCGTGGCGAC 60.432 61.111 0.00 0.00 37.47 5.19
1353 1558 1.268352 GAGCGTCTTCGGATAGCTGAT 59.732 52.381 0.00 0.00 39.54 2.90
1416 1621 3.592059 TCGGCGCCAAAGGTATAATATC 58.408 45.455 28.98 0.00 0.00 1.63
1437 1642 2.103094 CGATGATTGGAAGCCTACCTCA 59.897 50.000 0.00 0.00 0.00 3.86
1449 1654 0.674895 CTACCTCAAGCACTGTGGCC 60.675 60.000 10.21 0.00 41.64 5.36
1450 1655 1.414866 TACCTCAAGCACTGTGGCCA 61.415 55.000 0.00 0.00 41.64 5.36
1465 1670 1.296715 GCCATTGACCCTCGACTGT 59.703 57.895 0.00 0.00 0.00 3.55
1467 1672 0.321671 CCATTGACCCTCGACTGTGT 59.678 55.000 0.00 0.00 0.00 3.72
1509 1714 2.280389 CTCGTGGGCATCGATGGG 60.280 66.667 26.00 2.75 36.73 4.00
1949 2194 9.252635 AGAGAAATAGAGAGGAAAATGCAAAAT 57.747 29.630 0.00 0.00 0.00 1.82
2271 5112 5.502382 GCGTATTTGTGATACACATGGACAG 60.502 44.000 5.43 0.00 44.16 3.51
2537 5379 1.981256 CCTAAGGCGGGCATATTTGT 58.019 50.000 3.78 0.00 0.00 2.83
2538 5380 3.134574 CCTAAGGCGGGCATATTTGTA 57.865 47.619 3.78 0.00 0.00 2.41
2539 5381 3.482436 CCTAAGGCGGGCATATTTGTAA 58.518 45.455 3.78 0.00 0.00 2.41
2540 5382 3.502211 CCTAAGGCGGGCATATTTGTAAG 59.498 47.826 3.78 0.00 0.00 2.34
2541 5383 1.981256 AGGCGGGCATATTTGTAAGG 58.019 50.000 3.78 0.00 0.00 2.69
2542 5384 0.313987 GGCGGGCATATTTGTAAGGC 59.686 55.000 0.00 0.00 0.00 4.35
2543 5385 0.040425 GCGGGCATATTTGTAAGGCG 60.040 55.000 0.00 0.00 0.00 5.52
2544 5386 0.040425 CGGGCATATTTGTAAGGCGC 60.040 55.000 0.00 0.00 0.00 6.53
2545 5387 1.318576 GGGCATATTTGTAAGGCGCT 58.681 50.000 7.64 0.00 34.95 5.92
2546 5388 1.001378 GGGCATATTTGTAAGGCGCTG 60.001 52.381 7.64 0.00 34.95 5.18
2547 5389 1.001378 GGCATATTTGTAAGGCGCTGG 60.001 52.381 7.64 0.00 0.00 4.85
2548 5390 1.001378 GCATATTTGTAAGGCGCTGGG 60.001 52.381 7.64 0.00 0.00 4.45
2549 5391 1.608590 CATATTTGTAAGGCGCTGGGG 59.391 52.381 7.64 0.00 0.00 4.96
2550 5392 0.106918 TATTTGTAAGGCGCTGGGGG 60.107 55.000 7.64 0.00 0.00 5.40
2579 5421 3.195698 GCCTAAGCGTCCAAGGCG 61.196 66.667 0.00 0.00 45.82 5.52
2580 5422 2.511600 CCTAAGCGTCCAAGGCGG 60.512 66.667 5.39 0.00 33.62 6.13
2581 5423 2.511600 CTAAGCGTCCAAGGCGGG 60.512 66.667 5.39 0.00 33.62 6.13
2582 5424 2.998480 TAAGCGTCCAAGGCGGGA 60.998 61.111 0.00 0.00 33.62 5.14
2599 5441 2.333926 GGGACGCCTTAAAAACAATGC 58.666 47.619 0.00 0.00 0.00 3.56
2654 5496 1.199615 TTCGGTACTCATCCATGCCA 58.800 50.000 0.00 0.00 0.00 4.92
2667 5511 8.168725 ACTCATCCATGCCATTAATAAAGAGAT 58.831 33.333 0.00 0.00 0.00 2.75
2973 5842 2.858745 ACCATTAAGTGTGCGTTTCCT 58.141 42.857 0.00 0.00 0.00 3.36
3021 5890 3.714391 AGTTACAACACGAGTGGAAGAC 58.286 45.455 8.19 0.61 34.19 3.01
3084 5953 3.181418 ACAAAATGGAACCCCTCAGTGAT 60.181 43.478 0.00 0.00 0.00 3.06
3250 6119 5.048991 GCCAATAAAGAAACGTCAAGGAAGA 60.049 40.000 0.00 0.00 0.00 2.87
3402 6271 3.576861 TGGTATGTATCCTGAGGACTGG 58.423 50.000 1.77 0.00 32.98 4.00
3453 6322 1.065199 TGGATAGCTGAAGGCCTTGTG 60.065 52.381 26.25 16.13 43.05 3.33
3536 6405 2.105477 ACAGAAGTGTGATTCAGCCTGT 59.895 45.455 0.00 0.00 34.75 4.00
3541 6410 3.614092 AGTGTGATTCAGCCTGTTATGG 58.386 45.455 0.00 0.00 0.00 2.74
3547 6419 5.701290 GTGATTCAGCCTGTTATGGTATACC 59.299 44.000 15.50 15.50 0.00 2.73
3563 6435 1.416243 TACCGTGAAGAGGTGGTGTT 58.584 50.000 0.00 0.00 42.83 3.32
3760 6647 6.653020 ACTATTGATGTCTGCCTATCACAAA 58.347 36.000 0.00 0.00 33.36 2.83
3835 6722 4.960469 AGTATCTCCGGGTGTTGAGAATTA 59.040 41.667 0.00 0.00 40.75 1.40
3836 6723 3.604875 TCTCCGGGTGTTGAGAATTAC 57.395 47.619 0.00 0.00 34.79 1.89
3874 6765 0.038159 GGAGACCACACTTGACCTCG 60.038 60.000 0.00 0.00 0.00 4.63
3877 6768 0.667792 GACCACACTTGACCTCGCTC 60.668 60.000 0.00 0.00 0.00 5.03
3942 6833 3.256558 GTCATGTTACGTACAACTCCCC 58.743 50.000 0.00 0.00 40.89 4.81
4155 7085 6.373005 TCCATGAAGGAAGTGAATTCAGTA 57.627 37.500 16.08 0.00 45.65 2.74
4245 7178 1.609208 AGCCAGAACGTGATGCTTTT 58.391 45.000 0.00 0.00 0.00 2.27
4307 7243 6.299805 TCATTTCAGTTCTGGCTATACTGT 57.700 37.500 10.78 0.00 40.08 3.55
4350 7286 4.952957 TCATTATCCAATCCTTTTCCGCAA 59.047 37.500 0.00 0.00 0.00 4.85
4440 7379 0.037326 TTCGCAACCTAGAGCTGTGG 60.037 55.000 0.00 0.00 0.00 4.17
4485 7424 5.351948 AGGTTAATCTTCTTGGAGAGCTC 57.648 43.478 5.27 5.27 0.00 4.09
4510 7449 2.049156 TCGTTGCACTCTGGCTCG 60.049 61.111 0.00 0.00 34.89 5.03
4655 7594 2.239654 TGCCCAACCTAAGATTCCTCTG 59.760 50.000 0.00 0.00 0.00 3.35
4668 7607 7.775053 AAGATTCCTCTGTATCTCTACATCC 57.225 40.000 0.00 0.00 37.24 3.51
4722 7664 1.045407 ACCTGTTACGCCTTGAGACA 58.955 50.000 0.00 0.00 0.00 3.41
4740 7691 1.139058 ACAATCTATCTGCGTGGGGTC 59.861 52.381 0.00 0.00 0.00 4.46
4745 7696 1.040893 TATCTGCGTGGGGTCGACAT 61.041 55.000 18.91 1.04 0.00 3.06
4834 7801 6.951198 TGGCCCTTCATTTTAGTTGATTTCTA 59.049 34.615 0.00 0.00 0.00 2.10
4835 7802 7.619302 TGGCCCTTCATTTTAGTTGATTTCTAT 59.381 33.333 0.00 0.00 0.00 1.98
4896 7908 2.523245 TGTTTTACTGATGGGCATGCA 58.477 42.857 21.36 0.00 0.00 3.96
4906 7918 4.025360 TGATGGGCATGCAGACTAATTTT 58.975 39.130 21.36 0.00 0.00 1.82
4913 7928 5.163519 GGCATGCAGACTAATTTTGTACCAT 60.164 40.000 21.36 0.00 0.00 3.55
4914 7929 5.745294 GCATGCAGACTAATTTTGTACCATG 59.255 40.000 14.21 10.59 0.00 3.66
4958 7973 8.029642 ACCTCTGAATATTATTAATTTCGGCG 57.970 34.615 0.00 0.00 0.00 6.46
4961 7976 7.802738 TCTGAATATTATTAATTTCGGCGTGG 58.197 34.615 6.85 0.00 0.00 4.94
4972 8473 2.592861 GGCGTGGATCATGAGGGC 60.593 66.667 0.09 0.00 0.00 5.19
4986 8487 2.815158 TGAGGGCTATGTCAGTGTACA 58.185 47.619 0.00 0.00 0.00 2.90
4991 8492 4.019321 AGGGCTATGTCAGTGTACATTGTT 60.019 41.667 16.89 7.20 40.52 2.83
4992 8493 5.188948 AGGGCTATGTCAGTGTACATTGTTA 59.811 40.000 16.89 8.58 40.52 2.41
4993 8494 6.055588 GGGCTATGTCAGTGTACATTGTTAT 58.944 40.000 16.89 14.09 40.52 1.89
4994 8495 6.017934 GGGCTATGTCAGTGTACATTGTTATG 60.018 42.308 16.89 7.29 40.52 1.90
4995 8496 6.761242 GGCTATGTCAGTGTACATTGTTATGA 59.239 38.462 16.89 4.47 40.52 2.15
4996 8497 7.279981 GGCTATGTCAGTGTACATTGTTATGAA 59.720 37.037 16.89 0.00 40.52 2.57
4997 8498 8.116753 GCTATGTCAGTGTACATTGTTATGAAC 58.883 37.037 16.89 8.15 40.52 3.18
4998 8499 6.795098 TGTCAGTGTACATTGTTATGAACC 57.205 37.500 16.89 0.00 35.65 3.62
4999 8500 6.530120 TGTCAGTGTACATTGTTATGAACCT 58.470 36.000 16.89 0.00 35.65 3.50
5000 8501 6.426633 TGTCAGTGTACATTGTTATGAACCTG 59.573 38.462 16.89 6.78 35.65 4.00
5001 8502 5.937540 TCAGTGTACATTGTTATGAACCTGG 59.062 40.000 16.89 0.00 35.65 4.45
5002 8503 4.700213 AGTGTACATTGTTATGAACCTGGC 59.300 41.667 0.00 0.00 35.65 4.85
5042 8543 1.337823 ACTTCAGATCCGGTGGTTTCG 60.338 52.381 0.00 0.00 0.00 3.46
5064 8565 4.568359 CGGATACAAGGATTCAGAGTTGTG 59.432 45.833 0.00 0.00 34.92 3.33
5112 8617 1.448922 TTGTTGCCAACGCTACCCAC 61.449 55.000 2.68 0.00 39.64 4.61
5163 8668 1.195448 GCTGAACACCTGATCACAACG 59.805 52.381 0.00 0.00 0.00 4.10
5177 8682 0.249489 ACAACGAGTCAAAGAGCGCT 60.249 50.000 11.27 11.27 0.00 5.92
5185 8690 0.596577 TCAAAGAGCGCTACGTCAGT 59.403 50.000 11.50 0.00 0.00 3.41
5189 8694 3.036783 GAGCGCTACGTCAGTCCGT 62.037 63.158 11.50 0.00 44.50 4.69
5196 8701 4.003788 CGTCAGTCCGTTGGGCCT 62.004 66.667 4.53 0.00 0.00 5.19
5225 8730 5.596361 TGTCATTTACATTGGTGTTCACCTT 59.404 36.000 20.48 7.63 39.77 3.50
5228 8746 8.303876 GTCATTTACATTGGTGTTCACCTTAAT 58.696 33.333 20.48 11.35 39.77 1.40
5237 8755 4.437390 GGTGTTCACCTTAATTCATGCTCG 60.437 45.833 13.97 0.00 0.00 5.03
5251 8769 2.244651 GCTCGTGTGCCGTCTTGTT 61.245 57.895 0.00 0.00 37.94 2.83
5263 8801 0.883833 GTCTTGTTGCATGAGGTGGG 59.116 55.000 0.00 0.00 0.00 4.61
5267 8805 0.888736 TGTTGCATGAGGTGGGTTCG 60.889 55.000 0.00 0.00 0.00 3.95
5353 8894 3.431856 CAATTGGAGCGTCATCAACATG 58.568 45.455 0.00 0.00 0.00 3.21
5354 8895 0.804364 TTGGAGCGTCATCAACATGC 59.196 50.000 0.00 0.00 0.00 4.06
5382 8923 3.214328 CCTGCCATTTCCATAGGTACAC 58.786 50.000 0.00 0.00 0.00 2.90
5428 8971 8.547173 AGGGGAATGAAGCTTATTCATATCTAG 58.453 37.037 20.50 0.00 38.11 2.43
5481 9030 1.160137 GGCTGCTGGTTTCTGTAGTG 58.840 55.000 0.00 0.00 0.00 2.74
5501 9050 5.403246 AGTGCTACTGAATAGTCTTCAACG 58.597 41.667 0.00 0.00 38.36 4.10
5524 9073 0.882042 AACCGACTGCTCTGCACTTG 60.882 55.000 0.00 0.00 33.79 3.16
5534 9083 2.583868 TGCACTTGCGTCGTCGTT 60.584 55.556 3.66 0.00 45.83 3.85
5543 9092 1.268692 TGCGTCGTCGTTAACTGAAGT 60.269 47.619 3.71 0.00 39.49 3.01
5547 9096 3.625938 GTCGTCGTTAACTGAAGTGTCT 58.374 45.455 3.71 0.00 0.00 3.41
5548 9097 4.609113 CGTCGTCGTTAACTGAAGTGTCTA 60.609 45.833 3.71 0.00 0.00 2.59
5549 9098 4.610536 GTCGTCGTTAACTGAAGTGTCTAC 59.389 45.833 3.71 0.00 0.00 2.59
5550 9099 3.910767 CGTCGTTAACTGAAGTGTCTACC 59.089 47.826 3.71 0.00 0.00 3.18
5551 9100 4.555313 CGTCGTTAACTGAAGTGTCTACCA 60.555 45.833 3.71 0.00 0.00 3.25
5552 9101 4.916249 GTCGTTAACTGAAGTGTCTACCAG 59.084 45.833 3.71 0.00 0.00 4.00
5553 9102 4.581824 TCGTTAACTGAAGTGTCTACCAGT 59.418 41.667 3.71 0.00 41.14 4.00
5554 9103 4.680110 CGTTAACTGAAGTGTCTACCAGTG 59.320 45.833 3.71 0.00 39.52 3.66
5584 9133 6.373759 TCCAGGCATCTCAGTTAGTAATCTA 58.626 40.000 0.00 0.00 0.00 1.98
5667 9222 1.446907 ATGACTTGGAGCAGCTTTCG 58.553 50.000 0.00 0.00 0.00 3.46
5672 9227 2.037251 ACTTGGAGCAGCTTTCGTTCTA 59.963 45.455 0.00 0.00 0.00 2.10
5698 9255 3.567478 ATGTATCTGCTTCTTCCACCC 57.433 47.619 0.00 0.00 0.00 4.61
5707 9268 3.850173 TGCTTCTTCCACCCCTATAACTT 59.150 43.478 0.00 0.00 0.00 2.66
5708 9269 5.034200 TGCTTCTTCCACCCCTATAACTTA 58.966 41.667 0.00 0.00 0.00 2.24
5737 9298 7.994425 TCTGAATATCTCTCTGTAGCTAAGG 57.006 40.000 0.00 0.00 0.00 2.69
5741 9302 8.221251 TGAATATCTCTCTGTAGCTAAGGAGAA 58.779 37.037 20.34 14.43 34.93 2.87
5742 9303 8.635765 AATATCTCTCTGTAGCTAAGGAGAAG 57.364 38.462 20.34 15.91 34.93 2.85
5743 9304 5.702065 TCTCTCTGTAGCTAAGGAGAAGA 57.298 43.478 20.34 17.19 34.93 2.87
5744 9305 5.680619 TCTCTCTGTAGCTAAGGAGAAGAG 58.319 45.833 20.34 14.75 34.93 2.85
5745 9306 4.787551 TCTCTGTAGCTAAGGAGAAGAGG 58.212 47.826 18.71 2.18 32.76 3.69
5746 9307 3.292460 TCTGTAGCTAAGGAGAAGAGGC 58.708 50.000 0.00 0.00 0.00 4.70
5747 9308 3.053245 TCTGTAGCTAAGGAGAAGAGGCT 60.053 47.826 0.00 0.00 0.00 4.58
5748 9309 3.704061 CTGTAGCTAAGGAGAAGAGGCTT 59.296 47.826 0.00 0.00 0.00 4.35
5749 9310 4.868268 TGTAGCTAAGGAGAAGAGGCTTA 58.132 43.478 0.00 0.00 0.00 3.09
5750 9311 4.890581 TGTAGCTAAGGAGAAGAGGCTTAG 59.109 45.833 0.00 0.00 0.00 2.18
5751 9312 4.258457 AGCTAAGGAGAAGAGGCTTAGA 57.742 45.455 0.00 0.00 31.41 2.10
5752 9313 4.615513 AGCTAAGGAGAAGAGGCTTAGAA 58.384 43.478 0.00 0.00 31.41 2.10
5753 9314 4.649218 AGCTAAGGAGAAGAGGCTTAGAAG 59.351 45.833 0.00 0.00 31.41 2.85
5754 9315 4.647399 GCTAAGGAGAAGAGGCTTAGAAGA 59.353 45.833 0.00 0.00 31.41 2.87
5755 9316 5.128008 GCTAAGGAGAAGAGGCTTAGAAGAA 59.872 44.000 0.00 0.00 31.41 2.52
5756 9317 5.675684 AAGGAGAAGAGGCTTAGAAGAAG 57.324 43.478 0.00 0.00 0.00 2.85
5757 9318 4.030216 AGGAGAAGAGGCTTAGAAGAAGG 58.970 47.826 0.00 0.00 0.00 3.46
5758 9319 3.772572 GGAGAAGAGGCTTAGAAGAAGGT 59.227 47.826 0.00 0.00 0.00 3.50
5759 9320 4.382577 GGAGAAGAGGCTTAGAAGAAGGTG 60.383 50.000 0.00 0.00 0.00 4.00
5760 9321 3.055458 AGAAGAGGCTTAGAAGAAGGTGC 60.055 47.826 0.00 0.00 0.00 5.01
5761 9322 2.260822 AGAGGCTTAGAAGAAGGTGCA 58.739 47.619 0.00 0.00 0.00 4.57
5762 9323 2.235898 AGAGGCTTAGAAGAAGGTGCAG 59.764 50.000 0.00 0.00 0.00 4.41
5763 9324 1.090728 GGCTTAGAAGAAGGTGCAGC 58.909 55.000 8.11 8.11 0.00 5.25
5764 9325 1.339535 GGCTTAGAAGAAGGTGCAGCT 60.340 52.381 13.85 13.85 0.00 4.24
5765 9326 1.736681 GCTTAGAAGAAGGTGCAGCTG 59.263 52.381 20.97 10.11 0.00 4.24
5766 9327 1.736681 CTTAGAAGAAGGTGCAGCTGC 59.263 52.381 31.89 31.89 42.50 5.25
5778 9339 0.168568 GCAGCTGCAGAGAAGAAAGC 59.831 55.000 33.36 0.20 41.59 3.51
5779 9340 1.520494 CAGCTGCAGAGAAGAAAGCA 58.480 50.000 20.43 0.00 36.32 3.91
5784 9345 3.758755 TGCAGAGAAGAAAGCAGAAGA 57.241 42.857 0.00 0.00 32.48 2.87
5785 9346 4.077300 TGCAGAGAAGAAAGCAGAAGAA 57.923 40.909 0.00 0.00 32.48 2.52
5786 9347 4.063689 TGCAGAGAAGAAAGCAGAAGAAG 58.936 43.478 0.00 0.00 32.48 2.85
5787 9348 4.202295 TGCAGAGAAGAAAGCAGAAGAAGA 60.202 41.667 0.00 0.00 32.48 2.87
5788 9349 4.152223 GCAGAGAAGAAAGCAGAAGAAGAC 59.848 45.833 0.00 0.00 0.00 3.01
5789 9350 4.385447 CAGAGAAGAAAGCAGAAGAAGACG 59.615 45.833 0.00 0.00 0.00 4.18
5790 9351 3.658709 AGAAGAAAGCAGAAGAAGACGG 58.341 45.455 0.00 0.00 0.00 4.79
5791 9352 1.802069 AGAAAGCAGAAGAAGACGGC 58.198 50.000 0.00 0.00 0.00 5.68
5792 9353 1.070758 AGAAAGCAGAAGAAGACGGCA 59.929 47.619 0.00 0.00 0.00 5.69
5793 9354 1.462670 GAAAGCAGAAGAAGACGGCAG 59.537 52.381 0.00 0.00 0.00 4.85
5794 9355 0.681733 AAGCAGAAGAAGACGGCAGA 59.318 50.000 0.00 0.00 0.00 4.26
5795 9356 0.681733 AGCAGAAGAAGACGGCAGAA 59.318 50.000 0.00 0.00 0.00 3.02
5796 9357 1.070758 AGCAGAAGAAGACGGCAGAAA 59.929 47.619 0.00 0.00 0.00 2.52
5797 9358 1.873591 GCAGAAGAAGACGGCAGAAAA 59.126 47.619 0.00 0.00 0.00 2.29
5798 9359 2.290641 GCAGAAGAAGACGGCAGAAAAA 59.709 45.455 0.00 0.00 0.00 1.94
5799 9360 3.608008 GCAGAAGAAGACGGCAGAAAAAG 60.608 47.826 0.00 0.00 0.00 2.27
5800 9361 3.058639 CAGAAGAAGACGGCAGAAAAAGG 60.059 47.826 0.00 0.00 0.00 3.11
5801 9362 2.640316 AGAAGACGGCAGAAAAAGGT 57.360 45.000 0.00 0.00 0.00 3.50
5802 9363 3.764237 AGAAGACGGCAGAAAAAGGTA 57.236 42.857 0.00 0.00 0.00 3.08
5803 9364 3.665190 AGAAGACGGCAGAAAAAGGTAG 58.335 45.455 0.00 0.00 0.00 3.18
5804 9365 3.323979 AGAAGACGGCAGAAAAAGGTAGA 59.676 43.478 0.00 0.00 0.00 2.59
5805 9366 3.041508 AGACGGCAGAAAAAGGTAGAC 57.958 47.619 0.00 0.00 0.00 2.59
5806 9367 2.633481 AGACGGCAGAAAAAGGTAGACT 59.367 45.455 0.00 0.00 0.00 3.24
5807 9368 3.830755 AGACGGCAGAAAAAGGTAGACTA 59.169 43.478 0.00 0.00 0.00 2.59
5808 9369 4.082136 AGACGGCAGAAAAAGGTAGACTAG 60.082 45.833 0.00 0.00 0.00 2.57
5809 9370 3.830755 ACGGCAGAAAAAGGTAGACTAGA 59.169 43.478 0.00 0.00 0.00 2.43
5810 9371 4.174762 CGGCAGAAAAAGGTAGACTAGAC 58.825 47.826 0.00 0.00 0.00 2.59
5811 9372 4.082136 CGGCAGAAAAAGGTAGACTAGACT 60.082 45.833 0.00 0.00 0.00 3.24
5812 9373 5.567025 CGGCAGAAAAAGGTAGACTAGACTT 60.567 44.000 0.00 0.00 0.00 3.01
5813 9374 6.231951 GGCAGAAAAAGGTAGACTAGACTTT 58.768 40.000 0.00 6.37 34.87 2.66
5814 9375 6.147985 GGCAGAAAAAGGTAGACTAGACTTTG 59.852 42.308 11.04 3.72 33.79 2.77
5815 9376 6.706716 GCAGAAAAAGGTAGACTAGACTTTGT 59.293 38.462 11.04 7.20 33.79 2.83
5816 9377 7.871463 GCAGAAAAAGGTAGACTAGACTTTGTA 59.129 37.037 11.04 0.00 33.79 2.41
5817 9378 9.194271 CAGAAAAAGGTAGACTAGACTTTGTAC 57.806 37.037 11.04 0.00 33.79 2.90
5818 9379 9.145442 AGAAAAAGGTAGACTAGACTTTGTACT 57.855 33.333 11.04 8.80 33.79 2.73
5819 9380 9.194271 GAAAAAGGTAGACTAGACTTTGTACTG 57.806 37.037 11.04 0.00 33.79 2.74
5820 9381 5.900865 AGGTAGACTAGACTTTGTACTGC 57.099 43.478 0.00 0.00 0.00 4.40
5821 9382 5.322754 AGGTAGACTAGACTTTGTACTGCA 58.677 41.667 0.00 0.00 0.00 4.41
5822 9383 5.952947 AGGTAGACTAGACTTTGTACTGCAT 59.047 40.000 0.00 0.00 0.00 3.96
5823 9384 6.437793 AGGTAGACTAGACTTTGTACTGCATT 59.562 38.462 0.00 0.00 0.00 3.56
5824 9385 7.038941 AGGTAGACTAGACTTTGTACTGCATTT 60.039 37.037 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 4.142271 ACTGAGATCTCACCGTCTTTCATC 60.142 45.833 21.67 0.00 35.46 2.92
135 136 6.376978 CATGGTTTTCACTTTCACTGAGATC 58.623 40.000 0.00 0.00 0.00 2.75
187 189 0.036010 GCACATACTGCAGTGGACCT 60.036 55.000 29.57 3.26 46.29 3.85
225 232 7.816513 AGTCCACGAACTAAAATAAACTACTCC 59.183 37.037 0.00 0.00 0.00 3.85
297 318 0.105039 CGACTTAGACAGATGCCCCC 59.895 60.000 0.00 0.00 0.00 5.40
394 428 1.564818 AGGAGTGATAGAGGACACGGA 59.435 52.381 0.00 0.00 41.22 4.69
404 438 5.850557 AGTGATTGAGTGAGGAGTGATAG 57.149 43.478 0.00 0.00 0.00 2.08
417 451 2.746362 GGAAGTGCTGGAAGTGATTGAG 59.254 50.000 0.00 0.00 35.30 3.02
421 455 2.107204 AGTTGGAAGTGCTGGAAGTGAT 59.893 45.455 0.00 0.00 35.30 3.06
436 470 1.553706 GGAACCCTAGACGAGTTGGA 58.446 55.000 0.00 0.00 0.00 3.53
439 473 1.602327 GGCGGAACCCTAGACGAGTT 61.602 60.000 0.00 0.00 0.00 3.01
483 517 1.424493 CGAGCAACGGAGCAAGGATC 61.424 60.000 4.18 0.00 38.46 3.36
484 518 1.448540 CGAGCAACGGAGCAAGGAT 60.449 57.895 4.18 0.00 38.46 3.24
618 740 0.321653 AAGGCACCTCACCGATGAAC 60.322 55.000 0.00 0.00 33.30 3.18
625 747 2.840753 TTGGGGAAGGCACCTCACC 61.841 63.158 2.85 0.00 40.44 4.02
743 870 3.438017 ATTCGGGCGCTCTCTCTGC 62.438 63.158 5.36 0.00 0.00 4.26
754 881 2.586357 GAGGACGCAGATTCGGGC 60.586 66.667 0.00 0.00 0.00 6.13
817 971 1.144936 GGGAGGTCGGAGATTGCTG 59.855 63.158 0.00 0.00 40.67 4.41
818 972 2.066999 GGGGAGGTCGGAGATTGCT 61.067 63.158 0.00 0.00 40.67 3.91
841 999 2.338809 ACCTGATGTGGTGAAGGAAGA 58.661 47.619 0.00 0.00 39.17 2.87
895 1059 2.024414 AGAATTAATTGGTGGCGAGGC 58.976 47.619 5.17 0.00 0.00 4.70
930 1103 4.214545 CAGCGGTTAGTTGGTGTCATAAAA 59.785 41.667 0.00 0.00 0.00 1.52
1149 1326 1.896694 CTCGAGCTTCTGAAGGGCT 59.103 57.895 18.38 11.28 39.16 5.19
1323 1522 1.140816 GAAGACGCTCTCGCAACTTT 58.859 50.000 0.00 0.00 39.84 2.66
1353 1558 1.478510 GTCTTGAGCTCTTCCATCCGA 59.521 52.381 16.19 0.00 0.00 4.55
1416 1621 2.103094 TGAGGTAGGCTTCCAATCATCG 59.897 50.000 13.03 0.00 0.00 3.84
1437 1642 1.181098 GGTCAATGGCCACAGTGCTT 61.181 55.000 8.16 0.00 42.13 3.91
1449 1654 1.432514 CACACAGTCGAGGGTCAATG 58.567 55.000 0.00 0.00 0.00 2.82
1450 1655 0.320771 GCACACAGTCGAGGGTCAAT 60.321 55.000 0.00 0.00 0.00 2.57
1465 1670 1.982395 CCTCCTGGTAGACCGCACA 60.982 63.158 0.00 0.00 39.43 4.57
1467 1672 3.075005 GCCTCCTGGTAGACCGCA 61.075 66.667 0.00 0.00 39.43 5.69
1509 1714 2.361737 GCAACCTCCTCCCTTGGC 60.362 66.667 0.00 0.00 0.00 4.52
2080 4801 2.107204 GGGTCATGAGGGCATTACAGAT 59.893 50.000 0.00 0.00 31.68 2.90
2149 4878 7.648039 AAAGGTATGAAGTGGTTGTTTAACA 57.352 32.000 0.00 0.00 38.58 2.41
2518 5360 1.981256 ACAAATATGCCCGCCTTAGG 58.019 50.000 0.00 0.00 0.00 2.69
2519 5361 3.502211 CCTTACAAATATGCCCGCCTTAG 59.498 47.826 0.00 0.00 0.00 2.18
2520 5362 3.482436 CCTTACAAATATGCCCGCCTTA 58.518 45.455 0.00 0.00 0.00 2.69
2521 5363 2.306847 CCTTACAAATATGCCCGCCTT 58.693 47.619 0.00 0.00 0.00 4.35
2522 5364 1.981256 CCTTACAAATATGCCCGCCT 58.019 50.000 0.00 0.00 0.00 5.52
2523 5365 0.313987 GCCTTACAAATATGCCCGCC 59.686 55.000 0.00 0.00 0.00 6.13
2524 5366 0.040425 CGCCTTACAAATATGCCCGC 60.040 55.000 0.00 0.00 0.00 6.13
2525 5367 0.040425 GCGCCTTACAAATATGCCCG 60.040 55.000 0.00 0.00 0.00 6.13
2526 5368 1.001378 CAGCGCCTTACAAATATGCCC 60.001 52.381 2.29 0.00 0.00 5.36
2527 5369 1.001378 CCAGCGCCTTACAAATATGCC 60.001 52.381 2.29 0.00 0.00 4.40
2528 5370 1.001378 CCCAGCGCCTTACAAATATGC 60.001 52.381 2.29 0.00 0.00 3.14
2529 5371 1.608590 CCCCAGCGCCTTACAAATATG 59.391 52.381 2.29 0.00 0.00 1.78
2530 5372 1.478654 CCCCCAGCGCCTTACAAATAT 60.479 52.381 2.29 0.00 0.00 1.28
2531 5373 0.106918 CCCCCAGCGCCTTACAAATA 60.107 55.000 2.29 0.00 0.00 1.40
2532 5374 1.379843 CCCCCAGCGCCTTACAAAT 60.380 57.895 2.29 0.00 0.00 2.32
2533 5375 2.034999 CCCCCAGCGCCTTACAAA 59.965 61.111 2.29 0.00 0.00 2.83
2563 5405 2.511600 CCGCCTTGGACGCTTAGG 60.512 66.667 0.00 0.00 42.00 2.69
2564 5406 2.511600 CCCGCCTTGGACGCTTAG 60.512 66.667 0.00 0.00 42.00 2.18
2565 5407 2.998480 TCCCGCCTTGGACGCTTA 60.998 61.111 0.00 0.00 42.00 3.09
2566 5408 4.699522 GTCCCGCCTTGGACGCTT 62.700 66.667 0.00 0.00 44.98 4.68
2578 5420 2.591133 CATTGTTTTTAAGGCGTCCCG 58.409 47.619 0.00 0.00 35.76 5.14
2579 5421 2.288518 TGCATTGTTTTTAAGGCGTCCC 60.289 45.455 0.00 0.00 39.98 4.46
2580 5422 2.729360 GTGCATTGTTTTTAAGGCGTCC 59.271 45.455 0.00 0.00 39.98 4.79
2581 5423 3.425193 CAGTGCATTGTTTTTAAGGCGTC 59.575 43.478 0.13 0.00 39.98 5.19
2582 5424 3.181480 ACAGTGCATTGTTTTTAAGGCGT 60.181 39.130 9.35 0.00 39.98 5.68
2583 5425 3.182173 CACAGTGCATTGTTTTTAAGGCG 59.818 43.478 12.76 0.00 39.98 5.52
2584 5426 4.119136 ACACAGTGCATTGTTTTTAAGGC 58.881 39.130 12.76 0.00 37.81 4.35
2585 5427 7.763172 TTTACACAGTGCATTGTTTTTAAGG 57.237 32.000 12.76 2.15 0.00 2.69
2588 5430 9.979270 CAAATTTTACACAGTGCATTGTTTTTA 57.021 25.926 12.76 1.82 0.00 1.52
2589 5431 7.484324 GCAAATTTTACACAGTGCATTGTTTTT 59.516 29.630 12.76 2.79 32.29 1.94
2590 5432 6.966066 GCAAATTTTACACAGTGCATTGTTTT 59.034 30.769 12.76 6.85 32.29 2.43
2591 5433 6.315891 AGCAAATTTTACACAGTGCATTGTTT 59.684 30.769 12.76 9.25 34.44 2.83
2592 5434 5.816777 AGCAAATTTTACACAGTGCATTGTT 59.183 32.000 12.76 7.13 34.44 2.83
2593 5435 5.358922 AGCAAATTTTACACAGTGCATTGT 58.641 33.333 9.35 9.35 34.44 2.71
2594 5436 5.910637 AGCAAATTTTACACAGTGCATTG 57.089 34.783 7.79 7.79 34.44 2.82
2595 5437 6.158598 CCTAGCAAATTTTACACAGTGCATT 58.841 36.000 0.00 0.00 34.44 3.56
2596 5438 5.336690 CCCTAGCAAATTTTACACAGTGCAT 60.337 40.000 0.00 0.00 34.44 3.96
2597 5439 4.022416 CCCTAGCAAATTTTACACAGTGCA 60.022 41.667 0.00 0.00 34.44 4.57
2598 5440 4.022329 ACCCTAGCAAATTTTACACAGTGC 60.022 41.667 0.00 0.00 0.00 4.40
2599 5441 5.705609 ACCCTAGCAAATTTTACACAGTG 57.294 39.130 0.00 0.00 0.00 3.66
2676 5520 3.425659 AGGCATTCCAGAACCTTTCTTC 58.574 45.455 0.00 0.00 38.11 2.87
3084 5953 7.939782 TCAACAATAGCATTCTTGAGTTTTGA 58.060 30.769 0.00 0.00 0.00 2.69
3402 6271 0.594110 GATCGTCCCTCTCGATGTCC 59.406 60.000 5.58 0.00 45.90 4.02
3523 6392 5.701290 GGTATACCATAACAGGCTGAATCAC 59.299 44.000 23.66 5.89 35.64 3.06
3536 6405 4.342951 CCACCTCTTCACGGTATACCATAA 59.657 45.833 21.76 10.81 35.14 1.90
3541 6410 2.494870 ACACCACCTCTTCACGGTATAC 59.505 50.000 0.00 0.00 32.37 1.47
3547 6419 3.040147 ACATAACACCACCTCTTCACG 57.960 47.619 0.00 0.00 0.00 4.35
3760 6647 6.404734 GCCCAGAAAAGTGTAAATGATCGAAT 60.405 38.462 0.00 0.00 0.00 3.34
3835 6722 6.322712 GTCTCCTCATCTAGGTTGTAATCTGT 59.677 42.308 0.00 0.00 46.62 3.41
3836 6723 6.239176 GGTCTCCTCATCTAGGTTGTAATCTG 60.239 46.154 0.00 0.00 46.62 2.90
3874 6765 5.183904 ACTGAAACAATTGACCAATAGGAGC 59.816 40.000 13.59 0.00 38.69 4.70
3877 6768 6.980593 TCAACTGAAACAATTGACCAATAGG 58.019 36.000 13.59 0.00 42.21 2.57
3942 6833 5.774498 AAACAAGCCCTTGAAGTTTAGAG 57.226 39.130 14.46 0.00 42.93 2.43
4155 7085 4.966805 TCTCCGAGACCCATAATAACCTTT 59.033 41.667 0.00 0.00 0.00 3.11
4245 7178 1.075482 CTTTCCAAGGGAGCTGGCA 59.925 57.895 0.00 0.00 33.63 4.92
4294 7227 7.222161 TCGTTATCTTCTACAGTATAGCCAGA 58.778 38.462 0.00 0.00 0.00 3.86
4295 7228 7.436430 TCGTTATCTTCTACAGTATAGCCAG 57.564 40.000 0.00 0.00 0.00 4.85
4307 7243 4.021229 TGAGCCCAGTTCGTTATCTTCTA 58.979 43.478 0.00 0.00 0.00 2.10
4350 7286 1.269621 CCGCCGATAAATTCCTCGAGT 60.270 52.381 12.31 0.00 37.05 4.18
4375 7311 9.531964 CCATACGGGAACTCTATGGAATTTCCA 62.532 44.444 20.09 20.09 45.94 3.53
4427 7366 1.270907 CTTCACCCACAGCTCTAGGT 58.729 55.000 0.00 0.00 0.00 3.08
4440 7379 0.670854 GAGTTGACGCCTCCTTCACC 60.671 60.000 0.00 0.00 0.00 4.02
4485 7424 3.934391 GAGTGCAACGAGGGACGGG 62.934 68.421 0.00 0.00 45.86 5.28
4499 7438 3.343788 GACGTCCCGAGCCAGAGTG 62.344 68.421 3.51 0.00 0.00 3.51
4518 7457 3.620488 AGCGCTTTCTTTTGGGATATGA 58.380 40.909 2.64 0.00 0.00 2.15
4645 7584 6.857848 TGGATGTAGAGATACAGAGGAATCT 58.142 40.000 0.00 0.00 35.15 2.40
4655 7594 4.261656 CGTGTTCCCTGGATGTAGAGATAC 60.262 50.000 0.00 0.00 0.00 2.24
4668 7607 1.301087 TACAACGCCGTGTTCCCTG 60.301 57.895 0.00 0.00 39.29 4.45
4722 7664 0.389391 CGACCCCACGCAGATAGATT 59.611 55.000 0.00 0.00 0.00 2.40
4740 7691 1.269778 ACTATGGCATCACCGATGTCG 60.270 52.381 1.65 0.00 46.34 4.35
4745 7696 1.136891 CAGACACTATGGCATCACCGA 59.863 52.381 1.65 0.00 43.94 4.69
4803 7766 4.677182 ACTAAAATGAAGGGCCAACAGAT 58.323 39.130 6.18 0.00 0.00 2.90
4834 7801 8.336806 CACAAATACAAACTGCATTTCAACAAT 58.663 29.630 0.00 0.00 0.00 2.71
4835 7802 7.547019 TCACAAATACAAACTGCATTTCAACAA 59.453 29.630 0.00 0.00 0.00 2.83
4839 7806 6.696583 CAGTCACAAATACAAACTGCATTTCA 59.303 34.615 0.00 0.00 31.87 2.69
4913 7928 9.599866 CAGAGGTTGATAAGATTACATTACACA 57.400 33.333 0.00 0.00 0.00 3.72
4914 7929 9.817809 TCAGAGGTTGATAAGATTACATTACAC 57.182 33.333 0.00 0.00 0.00 2.90
4932 7947 8.504005 CGCCGAAATTAATAATATTCAGAGGTT 58.496 33.333 0.00 0.00 0.00 3.50
4947 7962 3.536570 TCATGATCCACGCCGAAATTAA 58.463 40.909 0.00 0.00 0.00 1.40
4948 7963 3.130633 CTCATGATCCACGCCGAAATTA 58.869 45.455 0.00 0.00 0.00 1.40
4949 7964 1.942657 CTCATGATCCACGCCGAAATT 59.057 47.619 0.00 0.00 0.00 1.82
4955 7970 1.758440 TAGCCCTCATGATCCACGCC 61.758 60.000 0.00 0.00 0.00 5.68
4958 7973 2.369860 TGACATAGCCCTCATGATCCAC 59.630 50.000 0.00 0.00 0.00 4.02
4961 7976 3.070734 ACACTGACATAGCCCTCATGATC 59.929 47.826 0.00 0.00 0.00 2.92
4972 8473 8.604035 GGTTCATAACAATGTACACTGACATAG 58.396 37.037 11.94 0.00 39.16 2.23
4986 8487 5.360714 CACCATTAGCCAGGTTCATAACAAT 59.639 40.000 0.00 0.00 35.52 2.71
4991 8492 3.521531 TGACACCATTAGCCAGGTTCATA 59.478 43.478 0.00 0.00 35.52 2.15
4992 8493 2.308570 TGACACCATTAGCCAGGTTCAT 59.691 45.455 0.00 0.00 35.52 2.57
4993 8494 1.702401 TGACACCATTAGCCAGGTTCA 59.298 47.619 0.00 0.00 35.52 3.18
4994 8495 2.084546 GTGACACCATTAGCCAGGTTC 58.915 52.381 0.00 0.00 35.52 3.62
4995 8496 1.423541 TGTGACACCATTAGCCAGGTT 59.576 47.619 2.45 0.00 35.52 3.50
4996 8497 1.064003 TGTGACACCATTAGCCAGGT 58.936 50.000 2.45 0.00 39.10 4.00
4997 8498 1.453155 GTGTGACACCATTAGCCAGG 58.547 55.000 3.92 0.00 0.00 4.45
5023 8524 1.359848 CGAAACCACCGGATCTGAAG 58.640 55.000 9.46 0.00 0.00 3.02
5042 8543 4.333926 GCACAACTCTGAATCCTTGTATCC 59.666 45.833 0.00 0.00 0.00 2.59
5064 8565 4.120755 CCCCTGCTTCCTCCCTGC 62.121 72.222 0.00 0.00 0.00 4.85
5112 8617 5.174395 CAATGTAAAGAGTGAGTGGAGAGG 58.826 45.833 0.00 0.00 0.00 3.69
5163 8668 1.261097 GACGTAGCGCTCTTTGACTC 58.739 55.000 16.34 2.14 0.00 3.36
5185 8690 4.659172 CAAGGCAGGCCCAACGGA 62.659 66.667 6.70 0.00 36.58 4.69
5189 8694 0.471591 AAATGACAAGGCAGGCCCAA 60.472 50.000 6.70 0.00 36.58 4.12
5196 8701 3.894427 ACACCAATGTAAATGACAAGGCA 59.106 39.130 0.00 0.00 42.78 4.75
5237 8755 0.661187 CATGCAACAAGACGGCACAC 60.661 55.000 0.00 0.00 40.83 3.82
5251 8769 1.003839 GTCGAACCCACCTCATGCA 60.004 57.895 0.00 0.00 0.00 3.96
5263 8801 5.432885 TTGATTTGAAAAGGAGGTCGAAC 57.567 39.130 0.00 0.00 0.00 3.95
5267 8805 8.837788 ATTTGATTTGATTTGAAAAGGAGGTC 57.162 30.769 0.00 0.00 0.00 3.85
5304 8845 1.939934 CGGTCAGACTCAAACTGCAAA 59.060 47.619 0.00 0.00 35.61 3.68
5354 8895 4.481112 GAAATGGCAGGCGGCGTG 62.481 66.667 17.70 17.70 46.16 5.34
5449 8992 2.093500 CCAGCAGCCTCTATGTACACAA 60.093 50.000 0.00 0.00 0.00 3.33
5451 8994 1.482593 ACCAGCAGCCTCTATGTACAC 59.517 52.381 0.00 0.00 0.00 2.90
5456 8999 2.286872 CAGAAACCAGCAGCCTCTATG 58.713 52.381 0.00 0.00 0.00 2.23
5481 9030 4.745649 ACCGTTGAAGACTATTCAGTAGC 58.254 43.478 0.00 0.00 34.21 3.58
5501 9050 0.320421 TGCAGAGCAGTCGGTTAACC 60.320 55.000 15.13 15.13 33.32 2.85
5524 9073 1.121967 CACTTCAGTTAACGACGACGC 59.878 52.381 7.30 0.00 43.96 5.19
5534 9083 4.280174 GTCCACTGGTAGACACTTCAGTTA 59.720 45.833 0.00 0.00 38.27 2.24
5543 9092 1.203250 TGGATGGTCCACTGGTAGACA 60.203 52.381 0.00 0.00 42.67 3.41
5547 9096 1.271840 GCCTGGATGGTCCACTGGTA 61.272 60.000 0.00 0.00 42.67 3.25
5548 9097 2.606587 GCCTGGATGGTCCACTGGT 61.607 63.158 0.00 0.00 42.67 4.00
5549 9098 1.929860 ATGCCTGGATGGTCCACTGG 61.930 60.000 0.00 0.00 42.67 4.00
5550 9099 0.465097 GATGCCTGGATGGTCCACTG 60.465 60.000 0.00 0.00 42.67 3.66
5551 9100 0.622738 AGATGCCTGGATGGTCCACT 60.623 55.000 0.00 0.00 42.67 4.00
5552 9101 0.179034 GAGATGCCTGGATGGTCCAC 60.179 60.000 0.00 0.00 42.67 4.02
5553 9102 0.621280 TGAGATGCCTGGATGGTCCA 60.621 55.000 0.00 0.00 45.98 4.02
5554 9103 0.108207 CTGAGATGCCTGGATGGTCC 59.892 60.000 0.00 0.00 38.35 4.46
5617 9171 2.205074 GCTGGGAACATCAGACATACG 58.795 52.381 0.00 0.00 41.51 3.06
5619 9173 2.571202 TGTGCTGGGAACATCAGACATA 59.429 45.455 0.00 0.00 37.09 2.29
5620 9174 1.352017 TGTGCTGGGAACATCAGACAT 59.648 47.619 0.00 0.00 37.09 3.06
5621 9175 0.764271 TGTGCTGGGAACATCAGACA 59.236 50.000 0.00 0.00 37.09 3.41
5622 9176 1.896220 TTGTGCTGGGAACATCAGAC 58.104 50.000 0.00 0.00 37.09 3.51
5623 9177 2.224843 ACATTGTGCTGGGAACATCAGA 60.225 45.455 0.00 0.00 37.09 3.27
5630 9184 1.894466 CATTGGACATTGTGCTGGGAA 59.106 47.619 9.80 0.00 0.00 3.97
5672 9227 7.093112 GGGTGGAAGAAGCAGATACATATAGAT 60.093 40.741 0.00 0.00 0.00 1.98
5737 9298 4.754322 CACCTTCTTCTAAGCCTCTTCTC 58.246 47.826 0.00 0.00 0.00 2.87
5741 9302 2.235898 CTGCACCTTCTTCTAAGCCTCT 59.764 50.000 0.00 0.00 0.00 3.69
5742 9303 2.626840 CTGCACCTTCTTCTAAGCCTC 58.373 52.381 0.00 0.00 0.00 4.70
5743 9304 1.339535 GCTGCACCTTCTTCTAAGCCT 60.340 52.381 0.00 0.00 0.00 4.58
5744 9305 1.090728 GCTGCACCTTCTTCTAAGCC 58.909 55.000 0.00 0.00 0.00 4.35
5745 9306 1.736681 CAGCTGCACCTTCTTCTAAGC 59.263 52.381 0.00 0.00 0.00 3.09
5746 9307 1.736681 GCAGCTGCACCTTCTTCTAAG 59.263 52.381 33.36 0.00 41.59 2.18
5747 9308 1.813513 GCAGCTGCACCTTCTTCTAA 58.186 50.000 33.36 0.00 41.59 2.10
5748 9309 3.540211 GCAGCTGCACCTTCTTCTA 57.460 52.632 33.36 0.00 41.59 2.10
5749 9310 4.393693 GCAGCTGCACCTTCTTCT 57.606 55.556 33.36 0.00 41.59 2.85
5759 9320 0.168568 GCTTTCTTCTCTGCAGCTGC 59.831 55.000 31.89 31.89 42.50 5.25
5760 9321 1.465387 CTGCTTTCTTCTCTGCAGCTG 59.535 52.381 10.11 10.11 44.72 4.24
5761 9322 1.810959 CTGCTTTCTTCTCTGCAGCT 58.189 50.000 9.47 0.00 44.72 4.24
5764 9325 3.758755 TCTTCTGCTTTCTTCTCTGCA 57.241 42.857 0.00 0.00 0.00 4.41
5765 9326 4.152223 GTCTTCTTCTGCTTTCTTCTCTGC 59.848 45.833 0.00 0.00 0.00 4.26
5766 9327 4.385447 CGTCTTCTTCTGCTTTCTTCTCTG 59.615 45.833 0.00 0.00 0.00 3.35
5767 9328 4.555262 CGTCTTCTTCTGCTTTCTTCTCT 58.445 43.478 0.00 0.00 0.00 3.10
5768 9329 3.677596 CCGTCTTCTTCTGCTTTCTTCTC 59.322 47.826 0.00 0.00 0.00 2.87
5769 9330 3.658709 CCGTCTTCTTCTGCTTTCTTCT 58.341 45.455 0.00 0.00 0.00 2.85
5770 9331 2.158645 GCCGTCTTCTTCTGCTTTCTTC 59.841 50.000 0.00 0.00 0.00 2.87
5771 9332 2.147150 GCCGTCTTCTTCTGCTTTCTT 58.853 47.619 0.00 0.00 0.00 2.52
5772 9333 1.070758 TGCCGTCTTCTTCTGCTTTCT 59.929 47.619 0.00 0.00 0.00 2.52
5773 9334 1.462670 CTGCCGTCTTCTTCTGCTTTC 59.537 52.381 0.00 0.00 0.00 2.62
5774 9335 1.070758 TCTGCCGTCTTCTTCTGCTTT 59.929 47.619 0.00 0.00 0.00 3.51
5775 9336 0.681733 TCTGCCGTCTTCTTCTGCTT 59.318 50.000 0.00 0.00 0.00 3.91
5776 9337 0.681733 TTCTGCCGTCTTCTTCTGCT 59.318 50.000 0.00 0.00 0.00 4.24
5777 9338 1.512926 TTTCTGCCGTCTTCTTCTGC 58.487 50.000 0.00 0.00 0.00 4.26
5778 9339 3.058639 CCTTTTTCTGCCGTCTTCTTCTG 60.059 47.826 0.00 0.00 0.00 3.02
5779 9340 3.142174 CCTTTTTCTGCCGTCTTCTTCT 58.858 45.455 0.00 0.00 0.00 2.85
5780 9341 2.879026 ACCTTTTTCTGCCGTCTTCTTC 59.121 45.455 0.00 0.00 0.00 2.87
5781 9342 2.932261 ACCTTTTTCTGCCGTCTTCTT 58.068 42.857 0.00 0.00 0.00 2.52
5782 9343 2.640316 ACCTTTTTCTGCCGTCTTCT 57.360 45.000 0.00 0.00 0.00 2.85
5783 9344 3.432592 GTCTACCTTTTTCTGCCGTCTTC 59.567 47.826 0.00 0.00 0.00 2.87
5784 9345 3.071167 AGTCTACCTTTTTCTGCCGTCTT 59.929 43.478 0.00 0.00 0.00 3.01
5785 9346 2.633481 AGTCTACCTTTTTCTGCCGTCT 59.367 45.455 0.00 0.00 0.00 4.18
5786 9347 3.041508 AGTCTACCTTTTTCTGCCGTC 57.958 47.619 0.00 0.00 0.00 4.79
5787 9348 3.830755 TCTAGTCTACCTTTTTCTGCCGT 59.169 43.478 0.00 0.00 0.00 5.68
5788 9349 4.082136 AGTCTAGTCTACCTTTTTCTGCCG 60.082 45.833 0.00 0.00 0.00 5.69
5789 9350 5.408880 AGTCTAGTCTACCTTTTTCTGCC 57.591 43.478 0.00 0.00 0.00 4.85
5790 9351 6.706716 ACAAAGTCTAGTCTACCTTTTTCTGC 59.293 38.462 0.00 0.00 0.00 4.26
5791 9352 9.194271 GTACAAAGTCTAGTCTACCTTTTTCTG 57.806 37.037 0.00 0.00 0.00 3.02
5792 9353 9.145442 AGTACAAAGTCTAGTCTACCTTTTTCT 57.855 33.333 0.00 0.00 0.00 2.52
5793 9354 9.194271 CAGTACAAAGTCTAGTCTACCTTTTTC 57.806 37.037 0.00 0.00 0.00 2.29
5794 9355 7.656542 GCAGTACAAAGTCTAGTCTACCTTTTT 59.343 37.037 0.00 0.00 0.00 1.94
5795 9356 7.153315 GCAGTACAAAGTCTAGTCTACCTTTT 58.847 38.462 0.00 0.00 0.00 2.27
5796 9357 6.267014 TGCAGTACAAAGTCTAGTCTACCTTT 59.733 38.462 0.00 0.00 0.00 3.11
5797 9358 5.773680 TGCAGTACAAAGTCTAGTCTACCTT 59.226 40.000 0.00 0.00 0.00 3.50
5798 9359 5.322754 TGCAGTACAAAGTCTAGTCTACCT 58.677 41.667 0.00 0.00 0.00 3.08
5799 9360 5.640189 TGCAGTACAAAGTCTAGTCTACC 57.360 43.478 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.