Multiple sequence alignment - TraesCS1A01G356600

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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 TraesCS1A01G356600 chr1A 100.000 5145 0 0 431 5575 539720002 539725146 0.000000e+00 9502
1 TraesCS1A01G356600 chr1A 89.467 845 82 2 1170 2014 539428196 539427359 0.000000e+00 1061
2 TraesCS1A01G356600 chr1A 88.143 894 93 8 1128 2017 539616549 539615665 0.000000e+00 1051
3 TraesCS1A01G356600 chr1A 82.096 1145 149 22 2050 3182 539427272 539426172 0.000000e+00 928
4 TraesCS1A01G356600 chr1A 99.662 296 1 0 431 726 510356777 510357072 4.910000e-150 542
5 TraesCS1A01G356600 chr1A 86.172 499 57 10 3194 3688 285430669 285430179 3.820000e-146 529
6 TraesCS1A01G356600 chr1A 98.644 295 4 0 431 725 548724851 548724557 1.780000e-144 523
7 TraesCS1A01G356600 chr1A 100.000 282 0 0 1 282 539719572 539719853 6.400000e-144 521
8 TraesCS1A01G356600 chr1A 98.305 295 5 0 431 725 365015374 365015080 8.280000e-143 518
9 TraesCS1A01G356600 chr1A 99.291 282 2 0 1 282 510356494 510356775 1.390000e-140 510
10 TraesCS1A01G356600 chr1A 98.227 282 5 0 1 282 365015657 365015376 1.400000e-135 494
11 TraesCS1A01G356600 chr1A 97.872 282 6 0 1 282 548725134 548724853 6.490000e-134 488
12 TraesCS1A01G356600 chr1A 85.861 389 47 8 3667 4051 483937245 483937629 1.870000e-109 407
13 TraesCS1A01G356600 chr1A 88.172 279 33 0 2904 3182 535481112 535481390 3.220000e-87 333
14 TraesCS1A01G356600 chr6A 97.319 1529 40 1 4047 5575 605861780 605863307 0.000000e+00 2595
15 TraesCS1A01G356600 chr6A 94.118 1530 87 3 4046 5575 419642877 419644403 0.000000e+00 2324
16 TraesCS1A01G356600 chr6A 93.987 1530 89 3 4046 5575 419632683 419634209 0.000000e+00 2313
17 TraesCS1A01G356600 chr6A 93.791 1530 92 3 4046 5575 419600119 419601645 0.000000e+00 2296
18 TraesCS1A01G356600 chr6A 93.882 1520 89 4 4057 5575 419671574 419673090 0.000000e+00 2289
19 TraesCS1A01G356600 chr6A 86.056 502 62 6 3194 3692 448702927 448703423 2.960000e-147 532
20 TraesCS1A01G356600 chr2A 97.255 1530 42 0 4046 5575 633248893 633250422 0.000000e+00 2593
21 TraesCS1A01G356600 chr2A 98.644 295 4 0 431 725 35380418 35380712 1.780000e-144 523
22 TraesCS1A01G356600 chr2A 86.570 484 53 10 3194 3673 584069597 584070072 1.780000e-144 523
23 TraesCS1A01G356600 chr2A 97.872 282 6 0 1 282 35380135 35380416 6.490000e-134 488
24 TraesCS1A01G356600 chr4B 94.022 1539 84 7 4039 5574 644322892 644321359 0.000000e+00 2326
25 TraesCS1A01G356600 chr4B 89.723 866 71 10 1152 2013 660197468 660196617 0.000000e+00 1090
26 TraesCS1A01G356600 chr4B 99.661 295 1 0 431 725 573505515 573505809 1.770000e-149 540
27 TraesCS1A01G356600 chr4B 98.227 282 5 0 1 282 573505232 573505513 1.400000e-135 494
28 TraesCS1A01G356600 chr7D 87.215 1533 190 6 4046 5575 402332407 402330878 0.000000e+00 1740
29 TraesCS1A01G356600 chr7D 92.415 857 52 9 3194 4046 600888251 600889098 0.000000e+00 1210
30 TraesCS1A01G356600 chr7D 89.087 449 39 9 3194 3638 118601395 118600953 2.940000e-152 549
31 TraesCS1A01G356600 chr7D 87.371 388 38 10 3668 4050 474007797 474007416 8.580000e-118 435
32 TraesCS1A01G356600 chr2D 87.206 1532 191 5 4046 5575 75666429 75664901 0.000000e+00 1738
33 TraesCS1A01G356600 chr1B 95.364 1057 43 4 963 2014 603261186 603262241 0.000000e+00 1676
34 TraesCS1A01G356600 chr1B 93.159 804 50 1 2001 2799 603262276 603263079 0.000000e+00 1175
35 TraesCS1A01G356600 chr1B 88.552 891 89 8 1128 2014 603149431 603148550 0.000000e+00 1068
36 TraesCS1A01G356600 chr1B 81.842 1151 145 36 2048 3182 603092763 603091661 0.000000e+00 909
37 TraesCS1A01G356600 chr1B 82.152 762 96 20 2048 2797 603148450 603147717 7.940000e-173 617
38 TraesCS1A01G356600 chr1B 93.298 373 25 0 2810 3182 603263065 603263437 8.160000e-153 551
39 TraesCS1A01G356600 chr1B 99.664 298 1 0 431 728 488065563 488065860 3.800000e-151 545
40 TraesCS1A01G356600 chr1B 84.225 374 58 1 2810 3182 603147730 603147357 4.110000e-96 363
41 TraesCS1A01G356600 chr1B 92.377 223 13 2 980 1198 603254676 603254898 1.170000e-81 315
42 TraesCS1A01G356600 chr1D 96.004 1026 28 9 995 2014 443467534 443466516 0.000000e+00 1655
43 TraesCS1A01G356600 chr1D 95.371 1037 39 5 980 2014 443749358 443750387 0.000000e+00 1640
44 TraesCS1A01G356600 chr1D 94.937 790 35 1 2013 2797 443466469 443465680 0.000000e+00 1232
45 TraesCS1A01G356600 chr1D 91.269 859 59 12 3194 4047 62320941 62321788 0.000000e+00 1157
46 TraesCS1A01G356600 chr1D 89.529 850 78 5 1169 2014 443429533 443428691 0.000000e+00 1066
47 TraesCS1A01G356600 chr1D 88.686 875 89 6 1143 2014 443552709 443553576 0.000000e+00 1059
48 TraesCS1A01G356600 chr1D 81.589 793 110 20 2018 2797 443717313 443718082 1.710000e-174 623
49 TraesCS1A01G356600 chr1D 81.234 762 103 24 2048 2791 443428606 443427867 3.740000e-161 579
50 TraesCS1A01G356600 chr1D 93.834 373 23 0 2810 3182 443465692 443465320 3.770000e-156 562
51 TraesCS1A01G356600 chr1D 84.572 538 66 14 3197 3726 378275365 378274837 8.280000e-143 518
52 TraesCS1A01G356600 chr1D 87.701 374 45 1 2810 3182 443554381 443554754 8.580000e-118 435
53 TraesCS1A01G356600 chr1D 87.366 372 47 0 2811 3182 443718071 443718442 1.440000e-115 427
54 TraesCS1A01G356600 chr7A 90.568 880 64 16 3189 4055 708599203 708600076 0.000000e+00 1147
55 TraesCS1A01G356600 chr7A 98.644 295 4 0 431 725 571355730 571356024 1.780000e-144 523
56 TraesCS1A01G356600 chr7A 98.936 282 3 0 1 282 571355447 571355728 6.450000e-139 505
57 TraesCS1A01G356600 chr3D 87.800 959 95 15 1063 2014 341493402 341494345 0.000000e+00 1103
58 TraesCS1A01G356600 chr3D 82.147 801 104 23 2016 2794 341494410 341495193 0.000000e+00 651
59 TraesCS1A01G356600 chr3D 83.896 385 43 9 2810 3175 341495183 341495567 3.200000e-92 350
60 TraesCS1A01G356600 chr3B 87.592 951 92 17 1074 2014 440228846 440229780 0.000000e+00 1079
61 TraesCS1A01G356600 chr3B 82.625 800 102 18 2016 2794 440229845 440230628 0.000000e+00 673
62 TraesCS1A01G356600 chr3B 99.661 295 1 0 431 725 146316040 146315746 1.770000e-149 540
63 TraesCS1A01G356600 chr3B 98.936 282 3 0 1 282 146316323 146316042 6.450000e-139 505
64 TraesCS1A01G356600 chr3A 87.080 952 97 16 1073 2014 461841708 461840773 0.000000e+00 1053
65 TraesCS1A01G356600 chr3A 81.592 1206 137 41 2017 3181 461840707 461839546 0.000000e+00 918
66 TraesCS1A01G356600 chr5D 88.679 848 62 15 3194 4035 445697038 445696219 0.000000e+00 1003
67 TraesCS1A01G356600 chr5D 86.423 383 41 10 3667 4045 41036027 41036402 5.200000e-110 409
68 TraesCS1A01G356600 chr4A 87.426 843 70 17 3190 4027 3070604 3071415 0.000000e+00 937
69 TraesCS1A01G356600 chrUn 100.000 282 0 0 1 282 374988963 374989244 6.400000e-144 521
70 TraesCS1A01G356600 chrUn 97.872 282 6 0 1 282 82661573 82661292 6.490000e-134 488
71 TraesCS1A01G356600 chr6B 97.966 295 6 0 431 725 45200677 45200383 3.850000e-141 512
72 TraesCS1A01G356600 chr6B 93.137 102 6 1 726 826 367267165 367267064 1.250000e-31 148
73 TraesCS1A01G356600 chr6B 88.506 87 10 0 849 935 633516842 633516928 7.640000e-19 106
74 TraesCS1A01G356600 chr5A 86.423 383 44 7 3668 4046 705763207 705763585 4.020000e-111 412
75 TraesCS1A01G356600 chr5B 85.870 92 13 0 849 940 354906971 354906880 1.280000e-16 99


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 TraesCS1A01G356600 chr1A 539719572 539725146 5574 False 5011.500000 9502 100.000000 1 5575 2 chr1A.!!$F4 5574
1 TraesCS1A01G356600 chr1A 539615665 539616549 884 True 1051.000000 1051 88.143000 1128 2017 1 chr1A.!!$R2 889
2 TraesCS1A01G356600 chr1A 539426172 539428196 2024 True 994.500000 1061 85.781500 1170 3182 2 chr1A.!!$R4 2012
3 TraesCS1A01G356600 chr1A 510356494 510357072 578 False 526.000000 542 99.476500 1 726 2 chr1A.!!$F3 725
4 TraesCS1A01G356600 chr1A 365015080 365015657 577 True 506.000000 518 98.266000 1 725 2 chr1A.!!$R3 724
5 TraesCS1A01G356600 chr1A 548724557 548725134 577 True 505.500000 523 98.258000 1 725 2 chr1A.!!$R5 724
6 TraesCS1A01G356600 chr6A 605861780 605863307 1527 False 2595.000000 2595 97.319000 4047 5575 1 chr6A.!!$F6 1528
7 TraesCS1A01G356600 chr6A 419642877 419644403 1526 False 2324.000000 2324 94.118000 4046 5575 1 chr6A.!!$F3 1529
8 TraesCS1A01G356600 chr6A 419632683 419634209 1526 False 2313.000000 2313 93.987000 4046 5575 1 chr6A.!!$F2 1529
9 TraesCS1A01G356600 chr6A 419600119 419601645 1526 False 2296.000000 2296 93.791000 4046 5575 1 chr6A.!!$F1 1529
10 TraesCS1A01G356600 chr6A 419671574 419673090 1516 False 2289.000000 2289 93.882000 4057 5575 1 chr6A.!!$F4 1518
11 TraesCS1A01G356600 chr2A 633248893 633250422 1529 False 2593.000000 2593 97.255000 4046 5575 1 chr2A.!!$F2 1529
12 TraesCS1A01G356600 chr2A 35380135 35380712 577 False 505.500000 523 98.258000 1 725 2 chr2A.!!$F3 724
13 TraesCS1A01G356600 chr4B 644321359 644322892 1533 True 2326.000000 2326 94.022000 4039 5574 1 chr4B.!!$R1 1535
14 TraesCS1A01G356600 chr4B 660196617 660197468 851 True 1090.000000 1090 89.723000 1152 2013 1 chr4B.!!$R2 861
15 TraesCS1A01G356600 chr4B 573505232 573505809 577 False 517.000000 540 98.944000 1 725 2 chr4B.!!$F1 724
16 TraesCS1A01G356600 chr7D 402330878 402332407 1529 True 1740.000000 1740 87.215000 4046 5575 1 chr7D.!!$R2 1529
17 TraesCS1A01G356600 chr7D 600888251 600889098 847 False 1210.000000 1210 92.415000 3194 4046 1 chr7D.!!$F1 852
18 TraesCS1A01G356600 chr2D 75664901 75666429 1528 True 1738.000000 1738 87.206000 4046 5575 1 chr2D.!!$R1 1529
19 TraesCS1A01G356600 chr1B 603261186 603263437 2251 False 1134.000000 1676 93.940333 963 3182 3 chr1B.!!$F3 2219
20 TraesCS1A01G356600 chr1B 603091661 603092763 1102 True 909.000000 909 81.842000 2048 3182 1 chr1B.!!$R1 1134
21 TraesCS1A01G356600 chr1B 603147357 603149431 2074 True 682.666667 1068 84.976333 1128 3182 3 chr1B.!!$R2 2054
22 TraesCS1A01G356600 chr1D 443749358 443750387 1029 False 1640.000000 1640 95.371000 980 2014 1 chr1D.!!$F2 1034
23 TraesCS1A01G356600 chr1D 62320941 62321788 847 False 1157.000000 1157 91.269000 3194 4047 1 chr1D.!!$F1 853
24 TraesCS1A01G356600 chr1D 443465320 443467534 2214 True 1149.666667 1655 94.925000 995 3182 3 chr1D.!!$R3 2187
25 TraesCS1A01G356600 chr1D 443427867 443429533 1666 True 822.500000 1066 85.381500 1169 2791 2 chr1D.!!$R2 1622
26 TraesCS1A01G356600 chr1D 443552709 443554754 2045 False 747.000000 1059 88.193500 1143 3182 2 chr1D.!!$F3 2039
27 TraesCS1A01G356600 chr1D 443717313 443718442 1129 False 525.000000 623 84.477500 2018 3182 2 chr1D.!!$F4 1164
28 TraesCS1A01G356600 chr1D 378274837 378275365 528 True 518.000000 518 84.572000 3197 3726 1 chr1D.!!$R1 529
29 TraesCS1A01G356600 chr7A 708599203 708600076 873 False 1147.000000 1147 90.568000 3189 4055 1 chr7A.!!$F1 866
30 TraesCS1A01G356600 chr7A 571355447 571356024 577 False 514.000000 523 98.790000 1 725 2 chr7A.!!$F2 724
31 TraesCS1A01G356600 chr3D 341493402 341495567 2165 False 701.333333 1103 84.614333 1063 3175 3 chr3D.!!$F1 2112
32 TraesCS1A01G356600 chr3B 440228846 440230628 1782 False 876.000000 1079 85.108500 1074 2794 2 chr3B.!!$F1 1720
33 TraesCS1A01G356600 chr3B 146315746 146316323 577 True 522.500000 540 99.298500 1 725 2 chr3B.!!$R1 724
34 TraesCS1A01G356600 chr3A 461839546 461841708 2162 True 985.500000 1053 84.336000 1073 3181 2 chr3A.!!$R1 2108
35 TraesCS1A01G356600 chr5D 445696219 445697038 819 True 1003.000000 1003 88.679000 3194 4035 1 chr5D.!!$R1 841
36 TraesCS1A01G356600 chr4A 3070604 3071415 811 False 937.000000 937 87.426000 3190 4027 1 chr4A.!!$F1 837

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
110 111 0.250038 CATCGGGGCACAGATCGAAT 60.250 55.0 0.00 0.0 35.25 3.34 F
771 772 0.535335 GTAGCCTTCCGTGGATGTCA 59.465 55.0 0.00 0.0 0.00 3.58 F
2342 2461 0.108585 ATCATAATGGTTCCGGCGCT 59.891 50.0 7.64 0.0 0.00 5.92 F
2580 2702 0.591741 GTTCACGTATCGGGAGCTCG 60.592 60.0 7.83 0.0 41.43 5.03 F
3921 4089 0.673437 CAGCACCAAAACCGGTCAAT 59.327 50.0 8.04 0.0 37.07 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1120 1127 0.522495 GCAGAACGAGAGAGACGAGC 60.522 60.000 0.0 0.0 34.70 5.03 R
2580 2702 0.318762 AAGTTCCCAGTCGCAGTCTC 59.681 55.000 0.0 0.0 0.00 3.36 R
3921 4089 1.064906 AGATTCGTCCCTGTCTCGGTA 60.065 52.381 0.0 0.0 0.00 4.02 R
4288 4461 2.281208 CCACTGCGTTTTCCGGGA 60.281 61.111 0.0 0.0 36.94 5.14 R
4952 5125 0.659957 GATCGGAAATGAGCCAGTGC 59.340 55.000 0.0 0.0 37.95 4.40 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
110 111 0.250038 CATCGGGGCACAGATCGAAT 60.250 55.000 0.00 0.00 35.25 3.34
726 727 3.192633 GGCCGCTTTTTAGATTTCAGGAA 59.807 43.478 0.00 0.00 0.00 3.36
727 728 4.321675 GGCCGCTTTTTAGATTTCAGGAAA 60.322 41.667 0.00 0.00 34.46 3.13
728 729 4.621460 GCCGCTTTTTAGATTTCAGGAAAC 59.379 41.667 0.00 0.00 32.51 2.78
729 730 5.768317 CCGCTTTTTAGATTTCAGGAAACA 58.232 37.500 0.00 0.00 32.51 2.83
730 731 6.212955 CCGCTTTTTAGATTTCAGGAAACAA 58.787 36.000 0.00 0.00 32.51 2.83
731 732 6.699642 CCGCTTTTTAGATTTCAGGAAACAAA 59.300 34.615 0.00 0.00 32.51 2.83
732 733 7.384932 CCGCTTTTTAGATTTCAGGAAACAAAT 59.615 33.333 0.00 0.00 32.51 2.32
733 734 9.405587 CGCTTTTTAGATTTCAGGAAACAAATA 57.594 29.630 0.00 0.00 32.51 1.40
741 742 9.883142 AGATTTCAGGAAACAAATAAACAAACA 57.117 25.926 0.00 0.00 32.51 2.83
757 758 9.908152 ATAAACAAACAAATAAGTGAAGTAGCC 57.092 29.630 0.00 0.00 0.00 3.93
758 759 7.582667 AACAAACAAATAAGTGAAGTAGCCT 57.417 32.000 0.00 0.00 0.00 4.58
759 760 7.582667 ACAAACAAATAAGTGAAGTAGCCTT 57.417 32.000 0.00 0.00 0.00 4.35
760 761 7.649057 ACAAACAAATAAGTGAAGTAGCCTTC 58.351 34.615 0.00 0.00 46.09 3.46
761 762 6.819397 AACAAATAAGTGAAGTAGCCTTCC 57.181 37.500 0.93 0.00 45.45 3.46
762 763 4.935808 ACAAATAAGTGAAGTAGCCTTCCG 59.064 41.667 0.93 0.00 45.45 4.30
763 764 4.820894 AATAAGTGAAGTAGCCTTCCGT 57.179 40.909 0.93 0.00 45.45 4.69
764 765 2.457366 AAGTGAAGTAGCCTTCCGTG 57.543 50.000 0.93 0.00 45.45 4.94
765 766 0.608640 AGTGAAGTAGCCTTCCGTGG 59.391 55.000 0.93 0.00 45.45 4.94
766 767 0.606604 GTGAAGTAGCCTTCCGTGGA 59.393 55.000 0.93 0.00 45.45 4.02
767 768 1.207329 GTGAAGTAGCCTTCCGTGGAT 59.793 52.381 0.93 0.00 45.45 3.41
768 769 1.207089 TGAAGTAGCCTTCCGTGGATG 59.793 52.381 0.93 0.00 45.45 3.51
769 770 1.207329 GAAGTAGCCTTCCGTGGATGT 59.793 52.381 0.00 0.00 41.09 3.06
770 771 0.824759 AGTAGCCTTCCGTGGATGTC 59.175 55.000 0.00 0.00 0.00 3.06
771 772 0.535335 GTAGCCTTCCGTGGATGTCA 59.465 55.000 0.00 0.00 0.00 3.58
772 773 0.535335 TAGCCTTCCGTGGATGTCAC 59.465 55.000 0.00 0.00 42.74 3.67
773 774 1.003839 GCCTTCCGTGGATGTCACA 60.004 57.895 0.00 0.00 46.36 3.58
774 775 0.605319 GCCTTCCGTGGATGTCACAA 60.605 55.000 0.00 0.00 46.36 3.33
775 776 1.156736 CCTTCCGTGGATGTCACAAC 58.843 55.000 0.00 0.00 46.36 3.32
776 777 1.270839 CCTTCCGTGGATGTCACAACT 60.271 52.381 0.00 0.00 46.36 3.16
777 778 2.494059 CTTCCGTGGATGTCACAACTT 58.506 47.619 0.00 0.00 46.36 2.66
778 779 3.556213 CCTTCCGTGGATGTCACAACTTA 60.556 47.826 0.00 0.00 46.36 2.24
779 780 3.755112 TCCGTGGATGTCACAACTTAA 57.245 42.857 0.00 0.00 46.36 1.85
780 781 4.074627 TCCGTGGATGTCACAACTTAAA 57.925 40.909 0.00 0.00 46.36 1.52
781 782 4.647611 TCCGTGGATGTCACAACTTAAAT 58.352 39.130 0.00 0.00 46.36 1.40
782 783 4.454161 TCCGTGGATGTCACAACTTAAATG 59.546 41.667 0.00 0.00 46.36 2.32
783 784 4.454161 CCGTGGATGTCACAACTTAAATGA 59.546 41.667 0.00 0.00 46.36 2.57
784 785 5.390885 CCGTGGATGTCACAACTTAAATGAG 60.391 44.000 0.00 0.00 46.36 2.90
785 786 5.408299 CGTGGATGTCACAACTTAAATGAGA 59.592 40.000 0.00 0.00 46.36 3.27
786 787 6.603095 GTGGATGTCACAACTTAAATGAGAC 58.397 40.000 9.91 9.91 45.39 3.36
787 788 6.204688 GTGGATGTCACAACTTAAATGAGACA 59.795 38.462 17.39 17.39 46.97 3.41
819 820 4.731313 TCATCTAGATGAGGCCTAGACA 57.269 45.455 27.93 0.00 43.57 3.41
820 821 4.661222 TCATCTAGATGAGGCCTAGACAG 58.339 47.826 27.93 1.16 43.57 3.51
821 822 4.352298 TCATCTAGATGAGGCCTAGACAGA 59.648 45.833 27.93 5.57 43.57 3.41
822 823 4.093472 TCTAGATGAGGCCTAGACAGAC 57.907 50.000 4.42 0.00 38.08 3.51
823 824 2.080654 AGATGAGGCCTAGACAGACC 57.919 55.000 4.42 0.00 0.00 3.85
824 825 1.044611 GATGAGGCCTAGACAGACCC 58.955 60.000 4.42 0.00 0.00 4.46
825 826 0.639392 ATGAGGCCTAGACAGACCCT 59.361 55.000 4.42 0.00 0.00 4.34
826 827 1.305886 TGAGGCCTAGACAGACCCTA 58.694 55.000 4.42 0.00 0.00 3.53
827 828 1.860240 TGAGGCCTAGACAGACCCTAT 59.140 52.381 4.42 0.00 0.00 2.57
828 829 2.247635 TGAGGCCTAGACAGACCCTATT 59.752 50.000 4.42 0.00 0.00 1.73
829 830 3.310193 GAGGCCTAGACAGACCCTATTT 58.690 50.000 4.42 0.00 0.00 1.40
830 831 4.078805 TGAGGCCTAGACAGACCCTATTTA 60.079 45.833 4.42 0.00 0.00 1.40
831 832 4.892198 AGGCCTAGACAGACCCTATTTAA 58.108 43.478 1.29 0.00 0.00 1.52
832 833 5.477913 AGGCCTAGACAGACCCTATTTAAT 58.522 41.667 1.29 0.00 0.00 1.40
833 834 6.631107 AGGCCTAGACAGACCCTATTTAATA 58.369 40.000 1.29 0.00 0.00 0.98
834 835 7.080353 AGGCCTAGACAGACCCTATTTAATAA 58.920 38.462 1.29 0.00 0.00 1.40
835 836 7.016366 AGGCCTAGACAGACCCTATTTAATAAC 59.984 40.741 1.29 0.00 0.00 1.89
836 837 7.160049 GCCTAGACAGACCCTATTTAATAACC 58.840 42.308 0.00 0.00 0.00 2.85
837 838 7.016366 GCCTAGACAGACCCTATTTAATAACCT 59.984 40.741 0.00 0.00 0.00 3.50
838 839 8.586744 CCTAGACAGACCCTATTTAATAACCTC 58.413 40.741 0.00 0.00 0.00 3.85
839 840 9.369672 CTAGACAGACCCTATTTAATAACCTCT 57.630 37.037 0.00 0.00 0.00 3.69
841 842 9.725206 AGACAGACCCTATTTAATAACCTCTAA 57.275 33.333 0.00 0.00 0.00 2.10
842 843 9.761504 GACAGACCCTATTTAATAACCTCTAAC 57.238 37.037 0.00 0.00 0.00 2.34
843 844 8.712103 ACAGACCCTATTTAATAACCTCTAACC 58.288 37.037 0.00 0.00 0.00 2.85
844 845 8.155510 CAGACCCTATTTAATAACCTCTAACCC 58.844 40.741 0.00 0.00 0.00 4.11
845 846 7.853003 AGACCCTATTTAATAACCTCTAACCCA 59.147 37.037 0.00 0.00 0.00 4.51
846 847 8.591526 ACCCTATTTAATAACCTCTAACCCAT 57.408 34.615 0.00 0.00 0.00 4.00
847 848 8.445588 ACCCTATTTAATAACCTCTAACCCATG 58.554 37.037 0.00 0.00 0.00 3.66
848 849 8.665906 CCCTATTTAATAACCTCTAACCCATGA 58.334 37.037 0.00 0.00 0.00 3.07
856 857 9.628500 AATAACCTCTAACCCATGATAAGTTTC 57.372 33.333 0.00 0.00 0.00 2.78
857 858 6.893020 ACCTCTAACCCATGATAAGTTTCT 57.107 37.500 0.00 0.00 0.00 2.52
858 859 6.653989 ACCTCTAACCCATGATAAGTTTCTG 58.346 40.000 0.00 0.00 0.00 3.02
859 860 6.215636 ACCTCTAACCCATGATAAGTTTCTGT 59.784 38.462 0.00 0.00 0.00 3.41
860 861 7.402071 ACCTCTAACCCATGATAAGTTTCTGTA 59.598 37.037 0.00 0.00 0.00 2.74
861 862 8.265055 CCTCTAACCCATGATAAGTTTCTGTAA 58.735 37.037 0.00 0.00 0.00 2.41
862 863 9.667107 CTCTAACCCATGATAAGTTTCTGTAAA 57.333 33.333 0.00 0.00 0.00 2.01
881 882 9.021807 TCTGTAAATAAATAGATAGGGACTCGG 57.978 37.037 0.00 0.00 41.75 4.63
882 883 8.130671 TGTAAATAAATAGATAGGGACTCGGG 57.869 38.462 0.00 0.00 41.75 5.14
883 884 7.951806 TGTAAATAAATAGATAGGGACTCGGGA 59.048 37.037 0.00 0.00 41.75 5.14
884 885 6.854091 AATAAATAGATAGGGACTCGGGAC 57.146 41.667 0.00 0.00 41.75 4.46
885 886 4.472690 AAATAGATAGGGACTCGGGACT 57.527 45.455 0.00 0.00 41.75 3.85
886 887 4.472690 AATAGATAGGGACTCGGGACTT 57.527 45.455 0.00 0.00 41.75 3.01
887 888 5.595814 AATAGATAGGGACTCGGGACTTA 57.404 43.478 0.00 0.00 41.75 2.24
888 889 5.799978 ATAGATAGGGACTCGGGACTTAT 57.200 43.478 0.00 0.00 41.75 1.73
889 890 6.905067 ATAGATAGGGACTCGGGACTTATA 57.095 41.667 0.00 0.00 41.75 0.98
890 891 5.595814 AGATAGGGACTCGGGACTTATAA 57.404 43.478 0.00 0.00 41.75 0.98
891 892 5.961897 AGATAGGGACTCGGGACTTATAAA 58.038 41.667 0.00 0.00 41.75 1.40
892 893 6.563163 AGATAGGGACTCGGGACTTATAAAT 58.437 40.000 0.00 0.00 41.75 1.40
893 894 7.017531 AGATAGGGACTCGGGACTTATAAATT 58.982 38.462 0.00 0.00 41.75 1.82
894 895 8.175431 AGATAGGGACTCGGGACTTATAAATTA 58.825 37.037 0.00 0.00 41.75 1.40
895 896 8.731591 ATAGGGACTCGGGACTTATAAATTAA 57.268 34.615 0.00 0.00 41.75 1.40
896 897 7.063934 AGGGACTCGGGACTTATAAATTAAG 57.936 40.000 0.00 0.00 0.00 1.85
897 898 6.842807 AGGGACTCGGGACTTATAAATTAAGA 59.157 38.462 0.00 0.00 0.00 2.10
898 899 6.927936 GGGACTCGGGACTTATAAATTAAGAC 59.072 42.308 0.00 0.00 0.00 3.01
899 900 7.201983 GGGACTCGGGACTTATAAATTAAGACT 60.202 40.741 0.00 0.00 0.00 3.24
900 901 8.202811 GGACTCGGGACTTATAAATTAAGACTT 58.797 37.037 0.00 0.00 0.00 3.01
930 931 8.918202 ATGTCCTAGAACTTATGAAACAAACA 57.082 30.769 0.00 0.00 0.00 2.83
931 932 8.378172 TGTCCTAGAACTTATGAAACAAACAG 57.622 34.615 0.00 0.00 0.00 3.16
932 933 7.444183 TGTCCTAGAACTTATGAAACAAACAGG 59.556 37.037 0.00 0.00 0.00 4.00
933 934 6.940298 TCCTAGAACTTATGAAACAAACAGGG 59.060 38.462 0.00 0.00 0.00 4.45
934 935 5.453567 AGAACTTATGAAACAAACAGGGC 57.546 39.130 0.00 0.00 0.00 5.19
935 936 3.915437 ACTTATGAAACAAACAGGGCG 57.085 42.857 0.00 0.00 0.00 6.13
936 937 3.219281 ACTTATGAAACAAACAGGGCGT 58.781 40.909 0.00 0.00 0.00 5.68
937 938 4.391155 ACTTATGAAACAAACAGGGCGTA 58.609 39.130 0.00 0.00 0.00 4.42
938 939 4.822896 ACTTATGAAACAAACAGGGCGTAA 59.177 37.500 0.00 0.00 0.00 3.18
939 940 3.915437 ATGAAACAAACAGGGCGTAAG 57.085 42.857 0.00 0.00 43.44 2.34
940 941 2.645802 TGAAACAAACAGGGCGTAAGT 58.354 42.857 0.00 0.00 41.68 2.24
941 942 2.614983 TGAAACAAACAGGGCGTAAGTC 59.385 45.455 0.00 0.00 45.19 3.01
942 943 2.632987 AACAAACAGGGCGTAAGTCT 57.367 45.000 0.00 0.00 45.30 3.24
943 944 2.632987 ACAAACAGGGCGTAAGTCTT 57.367 45.000 0.00 0.00 45.30 3.01
944 945 3.756933 ACAAACAGGGCGTAAGTCTTA 57.243 42.857 0.00 0.00 45.30 2.10
945 946 4.281898 ACAAACAGGGCGTAAGTCTTAT 57.718 40.909 0.00 0.00 45.30 1.73
946 947 5.410355 ACAAACAGGGCGTAAGTCTTATA 57.590 39.130 0.00 0.00 45.30 0.98
947 948 5.416947 ACAAACAGGGCGTAAGTCTTATAG 58.583 41.667 0.00 0.00 45.30 1.31
948 949 5.046807 ACAAACAGGGCGTAAGTCTTATAGT 60.047 40.000 0.00 0.00 45.30 2.12
949 950 4.915158 ACAGGGCGTAAGTCTTATAGTC 57.085 45.455 0.00 0.00 45.30 2.59
950 951 3.635836 ACAGGGCGTAAGTCTTATAGTCC 59.364 47.826 11.56 11.56 45.30 3.85
951 952 3.635373 CAGGGCGTAAGTCTTATAGTCCA 59.365 47.826 18.14 0.00 45.30 4.02
952 953 3.635836 AGGGCGTAAGTCTTATAGTCCAC 59.364 47.826 18.14 0.00 45.30 4.02
953 954 3.635836 GGGCGTAAGTCTTATAGTCCACT 59.364 47.826 13.58 0.00 45.30 4.00
954 955 4.499357 GGGCGTAAGTCTTATAGTCCACTG 60.499 50.000 13.58 0.00 45.30 3.66
955 956 4.043073 GCGTAAGTCTTATAGTCCACTGC 58.957 47.826 0.00 0.00 41.68 4.40
956 957 4.280461 CGTAAGTCTTATAGTCCACTGCG 58.720 47.826 0.00 0.00 0.00 5.18
957 958 4.034858 CGTAAGTCTTATAGTCCACTGCGA 59.965 45.833 0.00 0.00 0.00 5.10
958 959 4.373348 AAGTCTTATAGTCCACTGCGAC 57.627 45.455 0.00 0.00 0.00 5.19
959 960 3.353557 AGTCTTATAGTCCACTGCGACA 58.646 45.455 0.00 0.00 35.07 4.35
960 961 3.954904 AGTCTTATAGTCCACTGCGACAT 59.045 43.478 0.00 0.00 35.07 3.06
961 962 4.036971 AGTCTTATAGTCCACTGCGACATC 59.963 45.833 0.00 0.00 35.07 3.06
962 963 3.951680 TCTTATAGTCCACTGCGACATCA 59.048 43.478 0.00 0.00 35.07 3.07
963 964 4.584743 TCTTATAGTCCACTGCGACATCAT 59.415 41.667 0.00 0.00 35.07 2.45
964 965 5.768164 TCTTATAGTCCACTGCGACATCATA 59.232 40.000 0.00 0.00 35.07 2.15
965 966 6.434340 TCTTATAGTCCACTGCGACATCATAT 59.566 38.462 0.00 0.00 35.07 1.78
966 967 3.103447 AGTCCACTGCGACATCATATG 57.897 47.619 0.00 0.00 35.07 1.78
967 968 2.138320 GTCCACTGCGACATCATATGG 58.862 52.381 2.13 0.00 32.74 2.74
971 972 3.197265 CACTGCGACATCATATGGACAA 58.803 45.455 2.13 0.00 33.60 3.18
983 984 1.338107 ATGGACAAGACGAGTGGACA 58.662 50.000 0.00 0.00 0.00 4.02
1120 1127 1.153939 CAGTCCAGCTCTCGTTCCG 60.154 63.158 0.00 0.00 0.00 4.30
1141 1148 1.062002 CTCGTCTCTCTCGTTCTGCTC 59.938 57.143 0.00 0.00 0.00 4.26
1513 1545 1.265454 ACCTTCTCATCACGGACCCC 61.265 60.000 0.00 0.00 0.00 4.95
2274 2375 4.283363 AGCATATATCTCAAGGTGCCTG 57.717 45.455 0.00 0.00 33.29 4.85
2339 2458 1.680735 TGCAATCATAATGGTTCCGGC 59.319 47.619 0.00 0.00 0.00 6.13
2342 2461 0.108585 ATCATAATGGTTCCGGCGCT 59.891 50.000 7.64 0.00 0.00 5.92
2395 2517 3.545124 TACCCAGCGGCCACACAAG 62.545 63.158 2.24 0.00 0.00 3.16
2456 2578 3.919216 TCTCGAGCTTCTCCTTTTCTTG 58.081 45.455 7.81 0.00 0.00 3.02
2495 2617 2.564947 GTTCCTGTCAGGACATGAGAGT 59.435 50.000 21.73 0.00 45.78 3.24
2507 2629 2.634940 ACATGAGAGTATCCCATTCCCG 59.365 50.000 0.00 0.00 33.66 5.14
2580 2702 0.591741 GTTCACGTATCGGGAGCTCG 60.592 60.000 7.83 0.00 41.43 5.03
2584 2706 1.159098 ACGTATCGGGAGCTCGAGAC 61.159 60.000 18.75 9.94 44.72 3.36
2744 2876 1.165270 GTGTTTGGGAGGATCAACCG 58.835 55.000 0.00 0.00 44.74 4.44
2783 2915 2.683933 GGGGTTCTGCTCCGAGGA 60.684 66.667 0.00 0.00 0.00 3.71
2794 2926 1.270358 GCTCCGAGGAGAAACACAAGT 60.270 52.381 22.32 0.00 44.53 3.16
2795 2927 2.807108 GCTCCGAGGAGAAACACAAGTT 60.807 50.000 22.32 0.00 44.53 2.66
2796 2928 2.802816 CTCCGAGGAGAAACACAAGTTG 59.197 50.000 13.69 0.00 44.53 3.16
2797 2929 2.169769 TCCGAGGAGAAACACAAGTTGT 59.830 45.455 1.64 1.64 41.74 3.32
2798 2930 5.216363 CTCCGAGGAGAAACACAAGTTGTT 61.216 45.833 13.69 0.00 44.53 2.83
2900 3032 4.807039 GCAAAGCGCTGGCATGGG 62.807 66.667 24.52 6.21 43.41 4.00
3017 3149 2.835701 GAACATCCTGCTCACGCGGA 62.836 60.000 12.47 3.82 45.62 5.54
3182 3332 5.784177 CCAAGGTCGATGTGTATAGCTATT 58.216 41.667 12.39 0.00 0.00 1.73
3183 3333 6.223852 CCAAGGTCGATGTGTATAGCTATTT 58.776 40.000 12.39 0.00 0.00 1.40
3184 3334 6.706270 CCAAGGTCGATGTGTATAGCTATTTT 59.294 38.462 12.39 0.00 0.00 1.82
3185 3335 7.226720 CCAAGGTCGATGTGTATAGCTATTTTT 59.773 37.037 12.39 0.00 0.00 1.94
3186 3336 7.948278 AGGTCGATGTGTATAGCTATTTTTC 57.052 36.000 12.39 2.24 0.00 2.29
3187 3337 7.727181 AGGTCGATGTGTATAGCTATTTTTCT 58.273 34.615 12.39 0.00 0.00 2.52
3254 3404 4.468153 GTCTAGATTTGGTCCCTCAACTCT 59.532 45.833 0.00 0.00 39.14 3.24
3276 3426 2.113139 CCGGACAACTTGCACCCT 59.887 61.111 0.00 0.00 0.00 4.34
3277 3427 1.528309 CCGGACAACTTGCACCCTT 60.528 57.895 0.00 0.00 0.00 3.95
3278 3428 1.106944 CCGGACAACTTGCACCCTTT 61.107 55.000 0.00 0.00 0.00 3.11
3314 3464 2.434336 CGGACAAGATTCATCCCTGGTA 59.566 50.000 0.00 0.00 0.00 3.25
3413 3563 3.560481 TCCGCGTAATGTTTTCAAAGTCA 59.440 39.130 4.92 0.00 0.00 3.41
3494 3644 6.608610 GCGTACTTTTTCCAAGTTCACATAT 58.391 36.000 0.00 0.00 0.00 1.78
3619 3775 9.835389 TTTGGAAAGAGTTCATGAATTTGAAAT 57.165 25.926 12.12 0.00 37.36 2.17
3883 4051 7.892778 TTTACACGAATTTGAGTATGCACTA 57.107 32.000 0.00 0.00 34.21 2.74
3921 4089 0.673437 CAGCACCAAAACCGGTCAAT 59.327 50.000 8.04 0.00 37.07 2.57
3939 4108 2.068834 ATACCGAGACAGGGACGAAT 57.931 50.000 0.00 0.00 35.02 3.34
3991 4160 2.621526 GTTGTCCGGTTTTGGAGTTGAT 59.378 45.455 0.00 0.00 39.14 2.57
4091 4260 2.035066 GCCGGCTTCATTGATTTAGCAT 59.965 45.455 22.15 0.00 35.36 3.79
4187 4360 5.734855 TGAGTCTAATTTTCGCTAATGGC 57.265 39.130 0.00 0.00 37.64 4.40
4504 4677 0.948141 GTGCGAGAAACTGCAGCTCT 60.948 55.000 15.27 16.11 42.68 4.09
4725 4898 3.688272 CATCTGATAAGCTGTTTTGGCG 58.312 45.455 0.00 0.00 34.52 5.69
4952 5125 2.039084 ACAGAGCAGGGAAAGTTGTAGG 59.961 50.000 0.00 0.00 0.00 3.18
4955 5128 0.881796 GCAGGGAAAGTTGTAGGCAC 59.118 55.000 0.00 0.00 0.00 5.01
5191 5364 2.492012 CATGATCTAGAGGGCAGCAAC 58.508 52.381 0.00 0.00 0.00 4.17
5289 5462 8.655935 ATTTGTCCATTTCCTTCAGTATCTTT 57.344 30.769 0.00 0.00 0.00 2.52
5506 5679 4.222336 TGGGAAACTGACAATTTGACCAT 58.778 39.130 2.79 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 1.414919 AGTGACTTACCAAACGGCTGA 59.585 47.619 0.00 0.00 0.00 4.26
147 148 2.740055 CTTGTGCTTCCGCTCGCT 60.740 61.111 0.00 0.00 36.97 4.93
731 732 9.908152 GGCTACTTCACTTATTTGTTTGTTTAT 57.092 29.630 0.00 0.00 0.00 1.40
732 733 9.127277 AGGCTACTTCACTTATTTGTTTGTTTA 57.873 29.630 0.00 0.00 0.00 2.01
733 734 8.007405 AGGCTACTTCACTTATTTGTTTGTTT 57.993 30.769 0.00 0.00 0.00 2.83
734 735 7.582667 AGGCTACTTCACTTATTTGTTTGTT 57.417 32.000 0.00 0.00 0.00 2.83
735 736 7.582667 AAGGCTACTTCACTTATTTGTTTGT 57.417 32.000 0.00 0.00 28.54 2.83
750 751 1.207329 GACATCCACGGAAGGCTACTT 59.793 52.381 0.00 0.00 40.34 2.24
751 752 0.824759 GACATCCACGGAAGGCTACT 59.175 55.000 0.00 0.00 0.00 2.57
752 753 0.535335 TGACATCCACGGAAGGCTAC 59.465 55.000 0.00 0.00 0.00 3.58
753 754 0.535335 GTGACATCCACGGAAGGCTA 59.465 55.000 0.00 0.00 35.86 3.93
754 755 1.296715 GTGACATCCACGGAAGGCT 59.703 57.895 0.00 0.00 35.86 4.58
755 756 3.890674 GTGACATCCACGGAAGGC 58.109 61.111 0.00 0.00 35.86 4.35
762 763 6.204688 TGTCTCATTTAAGTTGTGACATCCAC 59.795 38.462 15.60 0.00 40.62 4.02
763 764 6.295249 TGTCTCATTTAAGTTGTGACATCCA 58.705 36.000 15.60 1.63 40.62 3.41
764 765 6.801539 TGTCTCATTTAAGTTGTGACATCC 57.198 37.500 15.60 0.00 40.62 3.51
798 799 4.352298 TCTGTCTAGGCCTCATCTAGATGA 59.648 45.833 29.17 29.17 43.25 2.92
799 800 4.458989 GTCTGTCTAGGCCTCATCTAGATG 59.541 50.000 24.32 24.32 43.25 2.90
800 801 4.508405 GGTCTGTCTAGGCCTCATCTAGAT 60.508 50.000 9.68 0.00 45.57 1.98
801 802 3.181438 GGTCTGTCTAGGCCTCATCTAGA 60.181 52.174 9.68 2.39 45.57 2.43
802 803 3.153919 GGTCTGTCTAGGCCTCATCTAG 58.846 54.545 9.68 0.00 45.57 2.43
803 804 3.231207 GGTCTGTCTAGGCCTCATCTA 57.769 52.381 9.68 0.00 45.57 1.98
804 805 2.080654 GGTCTGTCTAGGCCTCATCT 57.919 55.000 9.68 0.00 45.57 2.90
811 812 7.016366 AGGTTATTAAATAGGGTCTGTCTAGGC 59.984 40.741 0.00 0.00 0.00 3.93
812 813 8.493787 AGGTTATTAAATAGGGTCTGTCTAGG 57.506 38.462 0.00 0.00 0.00 3.02
813 814 9.369672 AGAGGTTATTAAATAGGGTCTGTCTAG 57.630 37.037 0.00 0.00 0.00 2.43
815 816 9.725206 TTAGAGGTTATTAAATAGGGTCTGTCT 57.275 33.333 0.00 0.00 0.00 3.41
816 817 9.761504 GTTAGAGGTTATTAAATAGGGTCTGTC 57.238 37.037 0.00 0.00 0.00 3.51
817 818 8.712103 GGTTAGAGGTTATTAAATAGGGTCTGT 58.288 37.037 0.00 0.00 0.00 3.41
818 819 8.155510 GGGTTAGAGGTTATTAAATAGGGTCTG 58.844 40.741 0.00 0.00 0.00 3.51
819 820 7.853003 TGGGTTAGAGGTTATTAAATAGGGTCT 59.147 37.037 0.00 0.00 0.00 3.85
820 821 8.037723 TGGGTTAGAGGTTATTAAATAGGGTC 57.962 38.462 0.00 0.00 0.00 4.46
821 822 8.445588 CATGGGTTAGAGGTTATTAAATAGGGT 58.554 37.037 0.00 0.00 0.00 4.34
822 823 8.665906 TCATGGGTTAGAGGTTATTAAATAGGG 58.334 37.037 0.00 0.00 0.00 3.53
830 831 9.628500 GAAACTTATCATGGGTTAGAGGTTATT 57.372 33.333 0.00 0.00 0.00 1.40
831 832 9.004231 AGAAACTTATCATGGGTTAGAGGTTAT 57.996 33.333 0.00 0.00 0.00 1.89
832 833 8.265055 CAGAAACTTATCATGGGTTAGAGGTTA 58.735 37.037 0.00 0.00 0.00 2.85
833 834 7.112779 CAGAAACTTATCATGGGTTAGAGGTT 58.887 38.462 0.00 0.00 0.00 3.50
834 835 6.215636 ACAGAAACTTATCATGGGTTAGAGGT 59.784 38.462 0.00 0.00 0.00 3.85
835 836 6.653989 ACAGAAACTTATCATGGGTTAGAGG 58.346 40.000 0.00 0.00 0.00 3.69
836 837 9.667107 TTTACAGAAACTTATCATGGGTTAGAG 57.333 33.333 0.00 0.00 0.00 2.43
855 856 9.021807 CCGAGTCCCTATCTATTTATTTACAGA 57.978 37.037 0.00 0.00 0.00 3.41
856 857 8.251721 CCCGAGTCCCTATCTATTTATTTACAG 58.748 40.741 0.00 0.00 0.00 2.74
857 858 7.951806 TCCCGAGTCCCTATCTATTTATTTACA 59.048 37.037 0.00 0.00 0.00 2.41
858 859 8.249638 GTCCCGAGTCCCTATCTATTTATTTAC 58.750 40.741 0.00 0.00 0.00 2.01
859 860 8.175431 AGTCCCGAGTCCCTATCTATTTATTTA 58.825 37.037 0.00 0.00 0.00 1.40
860 861 7.017531 AGTCCCGAGTCCCTATCTATTTATTT 58.982 38.462 0.00 0.00 0.00 1.40
861 862 6.563163 AGTCCCGAGTCCCTATCTATTTATT 58.437 40.000 0.00 0.00 0.00 1.40
862 863 6.155247 AGTCCCGAGTCCCTATCTATTTAT 57.845 41.667 0.00 0.00 0.00 1.40
863 864 5.595814 AGTCCCGAGTCCCTATCTATTTA 57.404 43.478 0.00 0.00 0.00 1.40
864 865 4.472690 AGTCCCGAGTCCCTATCTATTT 57.527 45.455 0.00 0.00 0.00 1.40
865 866 4.472690 AAGTCCCGAGTCCCTATCTATT 57.527 45.455 0.00 0.00 0.00 1.73
866 867 5.799978 ATAAGTCCCGAGTCCCTATCTAT 57.200 43.478 0.00 0.00 0.00 1.98
867 868 6.708885 TTATAAGTCCCGAGTCCCTATCTA 57.291 41.667 0.00 0.00 0.00 1.98
868 869 5.595814 TTATAAGTCCCGAGTCCCTATCT 57.404 43.478 0.00 0.00 0.00 1.98
869 870 6.854091 ATTTATAAGTCCCGAGTCCCTATC 57.146 41.667 0.00 0.00 0.00 2.08
870 871 8.731591 TTAATTTATAAGTCCCGAGTCCCTAT 57.268 34.615 0.00 0.00 0.00 2.57
871 872 8.006564 TCTTAATTTATAAGTCCCGAGTCCCTA 58.993 37.037 0.00 0.00 0.00 3.53
872 873 6.842807 TCTTAATTTATAAGTCCCGAGTCCCT 59.157 38.462 0.00 0.00 0.00 4.20
873 874 6.927936 GTCTTAATTTATAAGTCCCGAGTCCC 59.072 42.308 0.00 0.00 0.00 4.46
874 875 7.724287 AGTCTTAATTTATAAGTCCCGAGTCC 58.276 38.462 0.00 0.00 0.00 3.85
904 905 9.349713 TGTTTGTTTCATAAGTTCTAGGACATT 57.650 29.630 3.42 0.00 0.00 2.71
905 906 8.918202 TGTTTGTTTCATAAGTTCTAGGACAT 57.082 30.769 3.42 0.00 0.00 3.06
906 907 7.444183 CCTGTTTGTTTCATAAGTTCTAGGACA 59.556 37.037 3.42 0.00 0.00 4.02
907 908 7.094762 CCCTGTTTGTTTCATAAGTTCTAGGAC 60.095 40.741 0.00 0.00 0.00 3.85
908 909 6.940298 CCCTGTTTGTTTCATAAGTTCTAGGA 59.060 38.462 0.00 0.00 0.00 2.94
909 910 6.349363 GCCCTGTTTGTTTCATAAGTTCTAGG 60.349 42.308 0.00 0.00 0.00 3.02
910 911 6.612306 GCCCTGTTTGTTTCATAAGTTCTAG 58.388 40.000 0.00 0.00 0.00 2.43
911 912 5.180492 CGCCCTGTTTGTTTCATAAGTTCTA 59.820 40.000 0.00 0.00 0.00 2.10
912 913 4.023193 CGCCCTGTTTGTTTCATAAGTTCT 60.023 41.667 0.00 0.00 0.00 3.01
913 914 4.226761 CGCCCTGTTTGTTTCATAAGTTC 58.773 43.478 0.00 0.00 0.00 3.01
914 915 3.634910 ACGCCCTGTTTGTTTCATAAGTT 59.365 39.130 0.00 0.00 0.00 2.66
915 916 3.219281 ACGCCCTGTTTGTTTCATAAGT 58.781 40.909 0.00 0.00 0.00 2.24
916 917 3.915437 ACGCCCTGTTTGTTTCATAAG 57.085 42.857 0.00 0.00 0.00 1.73
917 918 4.822896 ACTTACGCCCTGTTTGTTTCATAA 59.177 37.500 0.00 0.00 0.00 1.90
918 919 4.391155 ACTTACGCCCTGTTTGTTTCATA 58.609 39.130 0.00 0.00 0.00 2.15
919 920 3.219281 ACTTACGCCCTGTTTGTTTCAT 58.781 40.909 0.00 0.00 0.00 2.57
920 921 2.614983 GACTTACGCCCTGTTTGTTTCA 59.385 45.455 0.00 0.00 0.00 2.69
921 922 2.876550 AGACTTACGCCCTGTTTGTTTC 59.123 45.455 0.00 0.00 0.00 2.78
922 923 2.927028 AGACTTACGCCCTGTTTGTTT 58.073 42.857 0.00 0.00 0.00 2.83
923 924 2.632987 AGACTTACGCCCTGTTTGTT 57.367 45.000 0.00 0.00 0.00 2.83
924 925 2.632987 AAGACTTACGCCCTGTTTGT 57.367 45.000 0.00 0.00 0.00 2.83
925 926 5.416947 ACTATAAGACTTACGCCCTGTTTG 58.583 41.667 0.00 0.00 0.00 2.93
926 927 5.394993 GGACTATAAGACTTACGCCCTGTTT 60.395 44.000 0.00 0.00 0.00 2.83
927 928 4.099113 GGACTATAAGACTTACGCCCTGTT 59.901 45.833 0.00 0.00 0.00 3.16
928 929 3.635836 GGACTATAAGACTTACGCCCTGT 59.364 47.826 0.00 0.00 0.00 4.00
929 930 3.635373 TGGACTATAAGACTTACGCCCTG 59.365 47.826 0.00 0.00 0.00 4.45
930 931 3.635836 GTGGACTATAAGACTTACGCCCT 59.364 47.826 0.00 0.00 0.00 5.19
931 932 3.635836 AGTGGACTATAAGACTTACGCCC 59.364 47.826 0.00 0.00 0.00 6.13
932 933 4.608951 CAGTGGACTATAAGACTTACGCC 58.391 47.826 0.00 0.00 0.00 5.68
933 934 4.043073 GCAGTGGACTATAAGACTTACGC 58.957 47.826 0.00 0.00 0.00 4.42
934 935 4.034858 TCGCAGTGGACTATAAGACTTACG 59.965 45.833 0.00 0.00 0.00 3.18
935 936 5.163683 TGTCGCAGTGGACTATAAGACTTAC 60.164 44.000 11.48 0.00 37.81 2.34
936 937 4.945543 TGTCGCAGTGGACTATAAGACTTA 59.054 41.667 11.48 0.00 37.81 2.24
937 938 3.762288 TGTCGCAGTGGACTATAAGACTT 59.238 43.478 11.48 0.00 37.81 3.01
938 939 3.353557 TGTCGCAGTGGACTATAAGACT 58.646 45.455 11.48 0.00 37.81 3.24
939 940 3.777465 TGTCGCAGTGGACTATAAGAC 57.223 47.619 11.48 0.00 37.81 3.01
940 941 3.951680 TGATGTCGCAGTGGACTATAAGA 59.048 43.478 11.48 0.00 37.81 2.10
941 942 4.307443 TGATGTCGCAGTGGACTATAAG 57.693 45.455 11.48 0.00 37.81 1.73
942 943 4.937201 ATGATGTCGCAGTGGACTATAA 57.063 40.909 11.48 1.08 37.81 0.98
943 944 5.105756 CCATATGATGTCGCAGTGGACTATA 60.106 44.000 3.65 8.62 37.81 1.31
944 945 4.322273 CCATATGATGTCGCAGTGGACTAT 60.322 45.833 3.65 5.41 37.81 2.12
945 946 3.005791 CCATATGATGTCGCAGTGGACTA 59.994 47.826 3.65 1.80 37.81 2.59
946 947 2.224137 CCATATGATGTCGCAGTGGACT 60.224 50.000 3.65 0.00 37.81 3.85
947 948 2.138320 CCATATGATGTCGCAGTGGAC 58.862 52.381 3.65 5.16 37.45 4.02
948 949 2.038659 TCCATATGATGTCGCAGTGGA 58.961 47.619 3.65 0.00 35.45 4.02
949 950 2.138320 GTCCATATGATGTCGCAGTGG 58.862 52.381 3.65 0.00 0.00 4.00
950 951 2.825205 TGTCCATATGATGTCGCAGTG 58.175 47.619 3.65 0.00 0.00 3.66
951 952 3.132824 TCTTGTCCATATGATGTCGCAGT 59.867 43.478 3.65 0.00 0.00 4.40
952 953 3.492383 GTCTTGTCCATATGATGTCGCAG 59.508 47.826 3.65 0.00 0.00 5.18
953 954 3.457234 GTCTTGTCCATATGATGTCGCA 58.543 45.455 3.65 0.00 0.00 5.10
954 955 2.472861 CGTCTTGTCCATATGATGTCGC 59.527 50.000 3.65 0.00 0.00 5.19
955 956 3.964909 TCGTCTTGTCCATATGATGTCG 58.035 45.455 3.65 0.46 0.00 4.35
956 957 4.742167 CACTCGTCTTGTCCATATGATGTC 59.258 45.833 3.65 0.00 0.00 3.06
957 958 4.442052 CCACTCGTCTTGTCCATATGATGT 60.442 45.833 3.65 0.00 0.00 3.06
958 959 4.053983 CCACTCGTCTTGTCCATATGATG 58.946 47.826 3.65 0.00 0.00 3.07
959 960 3.960755 TCCACTCGTCTTGTCCATATGAT 59.039 43.478 3.65 0.00 0.00 2.45
960 961 3.130516 GTCCACTCGTCTTGTCCATATGA 59.869 47.826 3.65 0.00 0.00 2.15
961 962 3.119137 TGTCCACTCGTCTTGTCCATATG 60.119 47.826 0.00 0.00 0.00 1.78
962 963 3.096852 TGTCCACTCGTCTTGTCCATAT 58.903 45.455 0.00 0.00 0.00 1.78
963 964 2.521126 TGTCCACTCGTCTTGTCCATA 58.479 47.619 0.00 0.00 0.00 2.74
964 965 1.338107 TGTCCACTCGTCTTGTCCAT 58.662 50.000 0.00 0.00 0.00 3.41
965 966 1.116308 TTGTCCACTCGTCTTGTCCA 58.884 50.000 0.00 0.00 0.00 4.02
966 967 1.499049 GTTGTCCACTCGTCTTGTCC 58.501 55.000 0.00 0.00 0.00 4.02
967 968 1.499049 GGTTGTCCACTCGTCTTGTC 58.501 55.000 0.00 0.00 0.00 3.18
971 972 1.471684 GATACGGTTGTCCACTCGTCT 59.528 52.381 0.00 0.00 35.02 4.18
1120 1127 0.522495 GCAGAACGAGAGAGACGAGC 60.522 60.000 0.00 0.00 34.70 5.03
2156 2257 1.221840 GGAGAAGGCGATGCAGGAA 59.778 57.895 0.00 0.00 0.00 3.36
2342 2461 1.067416 GTATGGCGAGACGATGGCA 59.933 57.895 0.00 0.00 45.22 4.92
2395 2517 1.632948 GGCGAAAACGTAGGACCAGC 61.633 60.000 0.00 0.00 0.00 4.85
2495 2617 1.148027 AGAGAGCTCGGGAATGGGATA 59.852 52.381 8.37 0.00 34.09 2.59
2507 2629 1.363443 CGATGCCTCCAGAGAGCTC 59.637 63.158 5.27 5.27 38.96 4.09
2580 2702 0.318762 AAGTTCCCAGTCGCAGTCTC 59.681 55.000 0.00 0.00 0.00 3.36
2584 2706 0.868406 GTTGAAGTTCCCAGTCGCAG 59.132 55.000 0.00 0.00 0.00 5.18
2798 2930 7.644986 ACAACTTGTGTTTCGATTTCAAAAA 57.355 28.000 0.00 0.00 37.01 1.94
2900 3032 1.696832 GCGATCTTGAACCGCTCACC 61.697 60.000 11.45 0.00 44.83 4.02
3017 3149 2.234908 CAGAGATCTTTGGGTCGAGGTT 59.765 50.000 5.33 0.00 0.00 3.50
3059 3191 4.129148 AATGGCCTTCCTCCCGGC 62.129 66.667 3.32 0.00 45.55 6.13
3254 3404 1.677052 GGTGCAAGTTGTCCGGTTTTA 59.323 47.619 0.00 0.00 0.00 1.52
3276 3426 6.374894 TCTTGTCCGGTTTCAGAAGTTAAAAA 59.625 34.615 0.00 0.00 0.00 1.94
3277 3427 5.881443 TCTTGTCCGGTTTCAGAAGTTAAAA 59.119 36.000 0.00 0.00 0.00 1.52
3278 3428 5.430007 TCTTGTCCGGTTTCAGAAGTTAAA 58.570 37.500 0.00 0.00 0.00 1.52
3621 3777 8.120465 CCACGTATTCTTTTAAGTTCGCATAAT 58.880 33.333 0.00 0.00 0.00 1.28
3780 3948 7.383029 CGTAGTTTTTCCAAGGTCGCATATATA 59.617 37.037 0.00 0.00 0.00 0.86
3782 3950 5.521010 CGTAGTTTTTCCAAGGTCGCATATA 59.479 40.000 0.00 0.00 0.00 0.86
3883 4051 1.843851 TGACTCACCCCAGTTTTGACT 59.156 47.619 0.00 0.00 0.00 3.41
3921 4089 1.064906 AGATTCGTCCCTGTCTCGGTA 60.065 52.381 0.00 0.00 0.00 4.02
3991 4160 6.928348 TTGGTGAAGTCTAGATTTAGTCCA 57.072 37.500 0.00 7.19 0.00 4.02
4051 4220 2.614057 GGCAATATGTCGGGTCTTTCAG 59.386 50.000 0.00 0.00 0.00 3.02
4091 4260 7.362056 GCTTGATCTTATGTTTCCACTGCTTTA 60.362 37.037 0.00 0.00 0.00 1.85
4288 4461 2.281208 CCACTGCGTTTTCCGGGA 60.281 61.111 0.00 0.00 36.94 5.14
4504 4677 5.719563 TGGAAACATCTACACACCTCATCTA 59.280 40.000 0.00 0.00 33.40 1.98
4684 4857 4.772231 ATGCCAGCAAGCCCCCAG 62.772 66.667 0.00 0.00 0.00 4.45
4725 4898 1.935933 ATCGCGAAGGAACATACACC 58.064 50.000 15.24 0.00 0.00 4.16
4822 4995 1.064389 AGCAATAGCCCCTCAGTTTCC 60.064 52.381 0.00 0.00 43.56 3.13
4952 5125 0.659957 GATCGGAAATGAGCCAGTGC 59.340 55.000 0.00 0.00 37.95 4.40
5118 5291 2.466982 CCGTGCGCTGAGAATGCAT 61.467 57.895 9.73 0.00 41.23 3.96
5119 5292 3.120385 CCGTGCGCTGAGAATGCA 61.120 61.111 9.73 0.00 36.02 3.96
5191 5364 2.945890 GCAAAGTATCCTGGGACAAGGG 60.946 54.545 0.00 0.00 38.70 3.95
5289 5462 3.006430 TGACTGCACTGAAGATACCGAAA 59.994 43.478 0.00 0.00 0.00 3.46
5506 5679 0.747255 GATCTGCTACAGGGCTTCGA 59.253 55.000 0.00 0.00 31.51 3.71


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

AutoCloner maintained by Alex Coulton.