Multiple sequence alignment - TraesCS2A01G369900

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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 TraesCS2A01G369900 chr2A 100.000 4526 0 0 458 4983 612758220 612762745 0.000000e+00 8359.0
1 TraesCS2A01G369900 chr2A 100.000 117 0 0 1 117 612757763 612757879 3.020000e-52 217.0
2 TraesCS2A01G369900 chr1B 93.478 3879 158 45 666 4474 529576186 529572333 0.000000e+00 5674.0
3 TraesCS2A01G369900 chr1B 87.758 1601 132 31 799 2368 529508467 529506900 0.000000e+00 1812.0
4 TraesCS2A01G369900 chr1B 84.814 1475 150 29 2688 4102 529503567 529502107 0.000000e+00 1415.0
5 TraesCS2A01G369900 chr1B 88.753 818 65 15 3761 4557 529439408 529438597 0.000000e+00 976.0
6 TraesCS2A01G369900 chr1B 86.997 746 59 14 3761 4477 529543835 529543099 0.000000e+00 806.0
7 TraesCS2A01G369900 chr1B 79.478 575 90 20 3602 4163 529432108 529431549 2.810000e-102 383.0
8 TraesCS2A01G369900 chr1B 93.069 202 14 0 466 667 529576693 529576492 3.770000e-76 296.0
9 TraesCS2A01G369900 chr1B 90.233 215 21 0 4572 4786 529467415 529467201 1.060000e-71 281.0
10 TraesCS2A01G369900 chr1B 83.516 273 27 7 4572 4843 529541739 529541484 6.450000e-59 239.0
11 TraesCS2A01G369900 chr1B 81.439 264 27 12 4572 4832 529553241 529552997 3.940000e-46 196.0
12 TraesCS2A01G369900 chr1B 82.090 201 28 5 4781 4978 529458572 529458377 1.110000e-36 165.0
13 TraesCS2A01G369900 chr1B 80.365 219 29 11 458 670 529509090 529508880 2.400000e-33 154.0
14 TraesCS2A01G369900 chr1B 89.076 119 11 2 4166 4283 529501609 529501492 4.020000e-31 147.0
15 TraesCS2A01G369900 chr1B 87.629 97 11 1 4748 4843 529437849 529437753 1.470000e-20 111.0
16 TraesCS2A01G369900 chr1B 95.385 65 3 0 4507 4571 529467527 529467463 2.450000e-18 104.0
17 TraesCS2A01G369900 chr1A 88.062 1667 146 32 799 2444 492200037 492198403 0.000000e+00 1927.0
18 TraesCS2A01G369900 chr1A 85.043 1872 194 46 2688 4494 492197745 492195895 0.000000e+00 1827.0
19 TraesCS2A01G369900 chr1A 86.763 831 68 18 3761 4570 492193147 492192338 0.000000e+00 887.0
20 TraesCS2A01G369900 chr1A 85.266 414 47 5 4572 4983 492195638 492195237 9.980000e-112 414.0
21 TraesCS2A01G369900 chr1A 85.973 221 18 2 463 670 492200658 492200438 1.810000e-54 224.0
22 TraesCS2A01G369900 chr1D 88.077 1669 138 33 799 2441 393440229 393441862 0.000000e+00 1923.0
23 TraesCS2A01G369900 chr1D 84.223 1705 172 40 2688 4317 393442522 393444204 0.000000e+00 1568.0
24 TraesCS2A01G369900 chr1D 87.644 1392 114 29 809 2164 393691485 393692854 0.000000e+00 1565.0
25 TraesCS2A01G369900 chr1D 84.314 1683 174 37 2704 4317 393693545 393695206 0.000000e+00 1563.0
26 TraesCS2A01G369900 chr1D 87.979 574 45 13 3761 4317 393476833 393477399 0.000000e+00 656.0
27 TraesCS2A01G369900 chr1D 86.598 291 19 11 4039 4317 393446270 393446552 2.250000e-78 303.0
28 TraesCS2A01G369900 chr1D 86.691 278 31 3 4572 4843 393473062 393473339 2.250000e-78 303.0
29 TraesCS2A01G369900 chr1D 86.239 109 10 3 4320 4423 393444243 393444351 4.080000e-21 113.0
30 TraesCS2A01G369900 chr1D 86.239 109 10 3 4320 4423 393695245 393695353 4.080000e-21 113.0
31 TraesCS2A01G369900 chr1D 94.340 53 2 1 4792 4843 393696954 393697006 4.140000e-11 80.5
32 TraesCS2A01G369900 chr4A 86.822 129 12 3 812 935 595422509 595422637 6.730000e-29 139.0
33 TraesCS2A01G369900 chr4A 87.143 70 1 4 458 527 702447217 702447156 6.920000e-09 73.1
34 TraesCS2A01G369900 chr4A 97.297 37 1 0 753 789 719682624 719682588 4.160000e-06 63.9
35 TraesCS2A01G369900 chr4D 84.507 142 15 4 812 946 7893679 7893538 3.130000e-27 134.0
36 TraesCS2A01G369900 chr3D 86.869 99 12 1 4632 4730 572018324 572018227 5.270000e-20 110.0
37 TraesCS2A01G369900 chr5D 87.143 70 1 4 458 527 480422567 480422628 6.920000e-09 73.1
38 TraesCS2A01G369900 chr2B 87.143 70 1 4 458 527 773634458 773634519 6.920000e-09 73.1
39 TraesCS2A01G369900 chr5A 86.567 67 4 2 458 524 598891814 598891875 8.950000e-08 69.4
40 TraesCS2A01G369900 chr7B 85.714 70 2 4 458 527 681707996 681707935 3.220000e-07 67.6
41 TraesCS2A01G369900 chr7B 97.297 37 1 0 753 789 72328273 72328237 4.160000e-06 63.9
42 TraesCS2A01G369900 chr4B 97.297 37 1 0 753 789 345463468 345463504 4.160000e-06 63.9
43 TraesCS2A01G369900 chr5B 90.000 50 2 2 478 527 502517126 502517172 1.500000e-05 62.1


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 TraesCS2A01G369900 chr2A 612757763 612762745 4982 False 4288.000 8359 100.00000 1 4983 2 chr2A.!!$F1 4982
1 TraesCS2A01G369900 chr1B 529572333 529576693 4360 True 2985.000 5674 93.27350 466 4474 2 chr1B.!!$R8 4008
2 TraesCS2A01G369900 chr1B 529501492 529509090 7598 True 882.000 1812 85.50325 458 4283 4 chr1B.!!$R6 3825
3 TraesCS2A01G369900 chr1B 529437753 529439408 1655 True 543.500 976 88.19100 3761 4843 2 chr1B.!!$R4 1082
4 TraesCS2A01G369900 chr1B 529541484 529543835 2351 True 522.500 806 85.25650 3761 4843 2 chr1B.!!$R7 1082
5 TraesCS2A01G369900 chr1B 529431549 529432108 559 True 383.000 383 79.47800 3602 4163 1 chr1B.!!$R1 561
6 TraesCS2A01G369900 chr1A 492192338 492200658 8320 True 1055.800 1927 86.22140 463 4983 5 chr1A.!!$R1 4520
7 TraesCS2A01G369900 chr1D 393440229 393446552 6323 False 976.750 1923 86.28425 799 4423 4 chr1D.!!$F1 3624
8 TraesCS2A01G369900 chr1D 393691485 393697006 5521 False 830.375 1565 88.13425 809 4843 4 chr1D.!!$F3 4034
9 TraesCS2A01G369900 chr1D 393473062 393477399 4337 False 479.500 656 87.33500 3761 4843 2 chr1D.!!$F2 1082

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
98 99 0.318445 GCACTGCTTCTGTTGGCTTG 60.318 55.000 0.00 0.00 0.00 4.01 F
586 600 0.474184 CCCCTCCAATCGCTGGTAAT 59.526 55.000 3.62 0.00 46.51 1.89 F
1193 1571 0.610687 CCTTCTCGAACTTCTGCCCT 59.389 55.000 0.00 0.00 0.00 5.19 F
2320 2838 2.099405 TGTAGACTCGTGATCATGCCA 58.901 47.619 10.24 0.00 0.00 4.92 F
2515 3557 1.003233 CACTCCTAAAGGTGGACCCAC 59.997 57.143 10.61 10.61 45.49 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 2153 3.644966 TTGAGTGGGTCAACAAAGACT 57.355 42.857 0.00 0.0 40.45 3.24 R
2262 2780 1.176527 AGGACCATGGTGAAAATGCG 58.823 50.000 25.52 0.0 0.00 4.73 R
2403 3115 1.273327 ACCGGGGTTAACAACGTCTAG 59.727 52.381 6.32 6.9 0.00 2.43 R
3615 7208 0.179012 TGGACCTCACGGGAAAAACC 60.179 55.000 0.00 0.0 38.76 3.27 R
4148 8042 0.804544 TTATCGCGTCTTTGCCGAGG 60.805 55.000 5.77 0.0 0.00 4.63 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
27 28 4.789075 CGTCGCCGTCATCCCGTT 62.789 66.667 0.00 0.00 0.00 4.44
28 29 2.884207 GTCGCCGTCATCCCGTTC 60.884 66.667 0.00 0.00 0.00 3.95
29 30 4.137872 TCGCCGTCATCCCGTTCC 62.138 66.667 0.00 0.00 0.00 3.62
50 51 4.468689 CCTTTCCCCGCTCCGGTC 62.469 72.222 0.00 0.00 46.80 4.79
51 52 4.814294 CTTTCCCCGCTCCGGTCG 62.814 72.222 0.00 6.62 46.80 4.79
88 89 4.395583 GCCGTGCTGCACTGCTTC 62.396 66.667 32.68 12.00 40.49 3.86
89 90 2.667536 CCGTGCTGCACTGCTTCT 60.668 61.111 28.04 0.00 31.34 2.85
90 91 2.554775 CGTGCTGCACTGCTTCTG 59.445 61.111 28.04 8.99 31.34 3.02
91 92 2.249535 CGTGCTGCACTGCTTCTGT 61.250 57.895 28.04 0.00 31.34 3.41
92 93 1.779025 CGTGCTGCACTGCTTCTGTT 61.779 55.000 28.04 0.00 31.34 3.16
94 95 1.285023 GCTGCACTGCTTCTGTTGG 59.715 57.895 1.98 0.00 0.00 3.77
95 96 1.285023 CTGCACTGCTTCTGTTGGC 59.715 57.895 1.98 0.00 0.00 4.52
96 97 1.152902 TGCACTGCTTCTGTTGGCT 60.153 52.632 1.98 0.00 0.00 4.75
97 98 0.752743 TGCACTGCTTCTGTTGGCTT 60.753 50.000 1.98 0.00 0.00 4.35
98 99 0.318445 GCACTGCTTCTGTTGGCTTG 60.318 55.000 0.00 0.00 0.00 4.01
99 100 1.027357 CACTGCTTCTGTTGGCTTGT 58.973 50.000 0.00 0.00 0.00 3.16
100 101 1.027357 ACTGCTTCTGTTGGCTTGTG 58.973 50.000 0.00 0.00 0.00 3.33
101 102 0.318445 CTGCTTCTGTTGGCTTGTGC 60.318 55.000 0.00 0.00 38.76 4.57
103 104 1.283793 CTTCTGTTGGCTTGTGCGG 59.716 57.895 0.00 0.00 40.82 5.69
106 107 3.829272 CTGTTGGCTTGTGCGGTGC 62.829 63.158 0.00 0.00 40.82 5.01
555 569 2.045536 GCCTGCTGCTGCCTACTT 60.046 61.111 13.47 0.00 38.71 2.24
583 597 4.115199 GCCCCTCCAATCGCTGGT 62.115 66.667 3.62 0.00 46.51 4.00
584 598 2.742116 GCCCCTCCAATCGCTGGTA 61.742 63.158 3.62 0.00 46.51 3.25
585 599 1.912220 CCCCTCCAATCGCTGGTAA 59.088 57.895 3.62 0.00 46.51 2.85
586 600 0.474184 CCCCTCCAATCGCTGGTAAT 59.526 55.000 3.62 0.00 46.51 1.89
587 601 1.133792 CCCCTCCAATCGCTGGTAATT 60.134 52.381 3.62 0.00 46.51 1.40
588 602 2.654863 CCCTCCAATCGCTGGTAATTT 58.345 47.619 3.62 0.00 46.51 1.82
592 606 4.399303 CCTCCAATCGCTGGTAATTTTCTT 59.601 41.667 3.62 0.00 46.51 2.52
595 609 3.782889 ATCGCTGGTAATTTTCTTGCC 57.217 42.857 0.00 0.00 0.00 4.52
635 664 6.153170 TGGTGAATTGATGTATGCATTGTCTT 59.847 34.615 3.54 0.00 35.07 3.01
672 1035 9.667989 TGCATAGATGATTTAAATGTTCAATCG 57.332 29.630 5.17 0.00 30.69 3.34
680 1043 1.086696 AATGTTCAATCGTGGCTCCG 58.913 50.000 0.00 0.00 0.00 4.63
728 1095 9.699703 GAAACTACTCTTTCAGACTTTCAGTAT 57.300 33.333 0.00 0.00 31.46 2.12
744 1111 9.490379 ACTTTCAGTATTACTTTAGTGTTCAGG 57.510 33.333 0.00 0.00 0.00 3.86
1193 1571 0.610687 CCTTCTCGAACTTCTGCCCT 59.389 55.000 0.00 0.00 0.00 5.19
1388 1793 4.160439 TGTGGCTGTGTTCCAAAATTAACA 59.840 37.500 0.00 0.00 35.01 2.41
1390 1795 4.202202 TGGCTGTGTTCCAAAATTAACAGG 60.202 41.667 0.00 0.00 36.33 4.00
1393 1798 6.461788 GGCTGTGTTCCAAAATTAACAGGTAA 60.462 38.462 0.00 0.00 36.33 2.85
1740 2153 6.936335 CCTATATTAGTGGATGCACAATCACA 59.064 38.462 20.21 3.65 36.98 3.58
2252 2770 8.458843 GTTTGTGCATAGTACCAGATTATGTTT 58.541 33.333 0.00 0.00 31.85 2.83
2320 2838 2.099405 TGTAGACTCGTGATCATGCCA 58.901 47.619 10.24 0.00 0.00 4.92
2403 3115 7.095229 TGCTGACTAGTCATAAACAACATGTTC 60.095 37.037 25.35 0.00 38.10 3.18
2515 3557 1.003233 CACTCCTAAAGGTGGACCCAC 59.997 57.143 10.61 10.61 45.49 4.61
2540 3582 7.232534 ACATTTTTAAAGTCACCTCATGCCTAA 59.767 33.333 0.00 0.00 0.00 2.69
2637 3687 6.724893 AGCCCTACTTTTTGTTACACAATT 57.275 33.333 0.00 0.00 38.00 2.32
2836 6383 8.531982 ACTTATGATCACAGTACAGTAACACAT 58.468 33.333 7.48 1.04 0.00 3.21
2884 6431 5.357742 AGCCCACCCAAAAATGATATTTC 57.642 39.130 0.00 0.00 0.00 2.17
2989 6548 9.628500 AAGTTTGGTAAATAGAGTTCTGAAAGT 57.372 29.630 0.00 0.00 33.76 2.66
3362 6925 7.225538 ACTGCAGAGACTTTTGGAATTATATCG 59.774 37.037 23.35 0.00 0.00 2.92
3417 6981 8.432805 ACTTACTATCCCACTTCCTAATCAATG 58.567 37.037 0.00 0.00 0.00 2.82
3500 7068 4.320608 TTTTTCTTGTTCTGGGTGATGC 57.679 40.909 0.00 0.00 0.00 3.91
3512 7080 2.024414 GGGTGATGCCTGTTACAATCC 58.976 52.381 0.00 0.00 37.43 3.01
3518 7086 4.458989 TGATGCCTGTTACAATCCTTTGTC 59.541 41.667 0.00 0.00 42.43 3.18
3567 7135 5.687441 CGATACCTCCTTTTCCCATTGATCA 60.687 44.000 0.00 0.00 0.00 2.92
3644 7237 3.313012 CGTGAGGTCCACACTTGAATA 57.687 47.619 16.23 0.00 45.98 1.75
3687 7280 2.606308 GCAGACATGGTTGTTCAGCTTG 60.606 50.000 0.00 0.00 35.79 4.01
3759 7354 3.990318 GCTGGTTCTTGCCATTATACC 57.010 47.619 0.00 0.00 37.96 2.73
3772 7367 5.105023 TGCCATTATACCATGTTGTTTGCAT 60.105 36.000 0.00 0.00 0.00 3.96
4025 7632 4.803088 TCTGTTTTCTGACAAATTTTGCCG 59.197 37.500 9.04 0.00 0.00 5.69
4127 8015 0.040958 GCAGTTCTTGTTGCTCCACG 60.041 55.000 0.00 0.00 37.35 4.94
4146 8040 1.270094 CGTTGTAAGCCTGTCACTCCA 60.270 52.381 0.00 0.00 0.00 3.86
4147 8041 2.143925 GTTGTAAGCCTGTCACTCCAC 58.856 52.381 0.00 0.00 0.00 4.02
4148 8042 0.685097 TGTAAGCCTGTCACTCCACC 59.315 55.000 0.00 0.00 0.00 4.61
4149 8043 0.036294 GTAAGCCTGTCACTCCACCC 60.036 60.000 0.00 0.00 0.00 4.61
4150 8044 0.178903 TAAGCCTGTCACTCCACCCT 60.179 55.000 0.00 0.00 0.00 4.34
4233 11670 7.872061 AGGAACTACCATACCATGATCAATA 57.128 36.000 0.00 0.00 42.04 1.90
4250 11690 7.210174 TGATCAATAACAGGTCTTTATCGGAG 58.790 38.462 0.00 0.00 0.00 4.63
4283 11723 3.072915 TCAATCACAGGTGACCAGTTGAT 59.927 43.478 3.63 5.60 43.11 2.57
4341 11821 1.535462 GTTGCTAATGTGTTGCCTCGT 59.465 47.619 0.00 0.00 0.00 4.18
4484 11970 3.311110 TCCGGCGTGGAAGAAGCT 61.311 61.111 6.01 0.00 46.38 3.74
4489 11975 2.740055 CGTGGAAGAAGCTGCGCT 60.740 61.111 9.73 0.00 42.56 5.92
4490 11976 1.446099 CGTGGAAGAAGCTGCGCTA 60.446 57.895 9.73 0.00 38.25 4.26
4505 11991 7.548196 AGCTGCGCTATTTTTAGTTATACAA 57.452 32.000 9.73 0.00 36.99 2.41
4520 12285 7.159322 AGTTATACAATAGATAGACGCAGGG 57.841 40.000 0.00 0.00 0.00 4.45
4527 12292 1.209747 AGATAGACGCAGGGGGTTTTC 59.790 52.381 0.00 0.00 0.00 2.29
4567 13272 3.432252 CCCTCATTCGGTACATAAATCGC 59.568 47.826 0.00 0.00 0.00 4.58
4583 13918 0.181114 TCGCCGAGGGTAAGCTACTA 59.819 55.000 0.00 0.00 0.00 1.82
4606 13941 3.319755 ACATTTTGCAGAAAAGCCATCG 58.680 40.909 0.00 0.00 34.53 3.84
4607 13942 2.437200 TTTTGCAGAAAAGCCATCGG 57.563 45.000 0.00 0.00 0.00 4.18
4625 13960 6.016777 GCCATCGGAGAATCTCAAAATTATGT 60.017 38.462 12.79 0.00 43.58 2.29
4650 13985 6.127054 TGCAGGTACAATAGCTCTTTAGATGT 60.127 38.462 0.00 0.00 33.57 3.06
4656 13991 2.853731 AGCTCTTTAGATGTCCGTCG 57.146 50.000 0.00 0.00 0.00 5.12
4657 13992 2.366533 AGCTCTTTAGATGTCCGTCGA 58.633 47.619 0.00 0.00 0.00 4.20
4660 13995 4.113354 GCTCTTTAGATGTCCGTCGAATT 58.887 43.478 0.00 0.00 0.00 2.17
4675 14010 3.435671 GTCGAATTTGAGATCCAACGGTT 59.564 43.478 0.00 0.00 33.85 4.44
4677 14012 3.188460 CGAATTTGAGATCCAACGGTTGT 59.812 43.478 18.73 1.89 33.85 3.32
4681 14016 3.201353 TGAGATCCAACGGTTGTGAAA 57.799 42.857 18.73 3.04 0.00 2.69
4683 14018 4.141287 TGAGATCCAACGGTTGTGAAATT 58.859 39.130 18.73 6.69 0.00 1.82
4690 14025 5.707764 TCCAACGGTTGTGAAATTCATATCA 59.292 36.000 18.73 0.00 0.00 2.15
4692 14027 5.216566 ACGGTTGTGAAATTCATATCACG 57.783 39.130 0.00 4.59 46.99 4.35
4693 14028 4.094294 ACGGTTGTGAAATTCATATCACGG 59.906 41.667 0.00 0.35 46.99 4.94
4694 14029 4.094294 CGGTTGTGAAATTCATATCACGGT 59.906 41.667 0.00 0.00 46.99 4.83
4695 14030 5.292345 CGGTTGTGAAATTCATATCACGGTA 59.708 40.000 0.00 0.00 46.99 4.02
4696 14031 6.018262 CGGTTGTGAAATTCATATCACGGTAT 60.018 38.462 0.00 0.00 46.99 2.73
4697 14032 7.352739 GGTTGTGAAATTCATATCACGGTATC 58.647 38.462 0.00 0.00 46.99 2.24
4698 14033 7.011950 GGTTGTGAAATTCATATCACGGTATCA 59.988 37.037 0.00 0.00 46.99 2.15
4699 14034 7.477144 TGTGAAATTCATATCACGGTATCAC 57.523 36.000 0.00 0.00 46.99 3.06
4700 14035 6.481976 TGTGAAATTCATATCACGGTATCACC 59.518 38.462 0.00 0.00 46.99 4.02
4701 14036 6.706270 GTGAAATTCATATCACGGTATCACCT 59.294 38.462 0.00 0.00 36.89 4.00
4702 14037 7.870954 GTGAAATTCATATCACGGTATCACCTA 59.129 37.037 0.00 0.00 36.89 3.08
4703 14038 8.425703 TGAAATTCATATCACGGTATCACCTAA 58.574 33.333 0.00 0.00 35.66 2.69
4704 14039 8.833231 AAATTCATATCACGGTATCACCTAAG 57.167 34.615 0.00 0.00 35.66 2.18
4705 14040 6.971726 TTCATATCACGGTATCACCTAAGT 57.028 37.500 0.00 0.00 35.66 2.24
4706 14041 6.971726 TCATATCACGGTATCACCTAAGTT 57.028 37.500 0.00 0.00 35.66 2.66
4707 14042 7.356089 TCATATCACGGTATCACCTAAGTTT 57.644 36.000 0.00 0.00 35.66 2.66
4708 14043 7.788026 TCATATCACGGTATCACCTAAGTTTT 58.212 34.615 0.00 0.00 35.66 2.43
4718 14053 5.836024 TCACCTAAGTTTTGGTATCACCT 57.164 39.130 0.00 0.00 39.58 4.00
4730 14065 4.013728 TGGTATCACCTGAAATTTTCCCG 58.986 43.478 6.68 0.00 39.58 5.14
4734 14069 4.627284 TCACCTGAAATTTTCCCGTCTA 57.373 40.909 6.68 0.00 0.00 2.59
4746 14081 1.666553 CCGTCTACGCAAACCAGCA 60.667 57.895 0.00 0.00 38.18 4.41
4756 14154 1.538047 CAAACCAGCAGCCAGTGTAT 58.462 50.000 0.00 0.00 0.00 2.29
4786 14184 1.227645 GATGTGGCGAGGCATGCTA 60.228 57.895 18.92 0.00 0.00 3.49
4832 15557 1.016627 CACATGCCAGTTATCCACCG 58.983 55.000 0.00 0.00 0.00 4.94
4833 15558 0.618458 ACATGCCAGTTATCCACCGT 59.382 50.000 0.00 0.00 0.00 4.83
4835 15560 1.401552 CATGCCAGTTATCCACCGTTG 59.598 52.381 0.00 0.00 0.00 4.10
4837 15562 0.676782 GCCAGTTATCCACCGTTGCT 60.677 55.000 0.00 0.00 0.00 3.91
4838 15563 1.406341 GCCAGTTATCCACCGTTGCTA 60.406 52.381 0.00 0.00 0.00 3.49
4840 15565 2.093658 CCAGTTATCCACCGTTGCTAGT 60.094 50.000 0.00 0.00 0.00 2.57
4841 15566 2.930040 CAGTTATCCACCGTTGCTAGTG 59.070 50.000 0.00 0.00 0.00 2.74
4842 15567 1.664151 GTTATCCACCGTTGCTAGTGC 59.336 52.381 0.00 0.00 40.20 4.40
4843 15568 0.179121 TATCCACCGTTGCTAGTGCG 60.179 55.000 0.00 0.00 43.34 5.34
4851 15576 1.026718 GTTGCTAGTGCGGCCAATCT 61.027 55.000 2.24 0.00 43.34 2.40
4852 15577 1.026182 TTGCTAGTGCGGCCAATCTG 61.026 55.000 2.24 0.00 43.34 2.90
4853 15578 2.182842 GCTAGTGCGGCCAATCTGG 61.183 63.158 2.24 0.00 41.55 3.86
4854 15579 1.524621 CTAGTGCGGCCAATCTGGG 60.525 63.158 2.24 0.00 38.19 4.45
4855 15580 2.257409 CTAGTGCGGCCAATCTGGGT 62.257 60.000 2.24 0.00 38.19 4.51
4856 15581 2.252072 TAGTGCGGCCAATCTGGGTC 62.252 60.000 2.24 0.00 38.19 4.46
4857 15582 3.329889 TGCGGCCAATCTGGGTCT 61.330 61.111 2.24 0.00 38.19 3.85
4858 15583 2.825836 GCGGCCAATCTGGGTCTG 60.826 66.667 2.24 0.00 38.19 3.51
4859 15584 2.989639 CGGCCAATCTGGGTCTGA 59.010 61.111 2.24 0.00 38.19 3.27
4860 15585 1.299648 CGGCCAATCTGGGTCTGAA 59.700 57.895 2.24 0.00 38.19 3.02
4862 15587 1.886222 CGGCCAATCTGGGTCTGAAAA 60.886 52.381 2.24 0.00 38.19 2.29
4864 15589 2.833943 GGCCAATCTGGGTCTGAAAAAT 59.166 45.455 0.00 0.00 38.19 1.82
4865 15590 3.118992 GGCCAATCTGGGTCTGAAAAATC 60.119 47.826 0.00 0.00 38.19 2.17
4866 15591 3.511146 GCCAATCTGGGTCTGAAAAATCA 59.489 43.478 0.00 0.00 38.19 2.57
4870 15595 6.424812 CCAATCTGGGTCTGAAAAATCAAAAC 59.575 38.462 0.00 0.00 32.67 2.43
4871 15596 5.181690 TCTGGGTCTGAAAAATCAAAACG 57.818 39.130 0.00 0.00 0.00 3.60
4872 15597 4.037446 TCTGGGTCTGAAAAATCAAAACGG 59.963 41.667 0.00 0.00 0.00 4.44
4873 15598 3.057019 GGGTCTGAAAAATCAAAACGGC 58.943 45.455 0.00 0.00 0.00 5.68
4874 15599 3.057019 GGTCTGAAAAATCAAAACGGCC 58.943 45.455 0.00 0.00 0.00 6.13
4875 15600 3.491792 GGTCTGAAAAATCAAAACGGCCA 60.492 43.478 2.24 0.00 0.00 5.36
4876 15601 4.116238 GTCTGAAAAATCAAAACGGCCAA 58.884 39.130 2.24 0.00 0.00 4.52
4877 15602 4.749598 GTCTGAAAAATCAAAACGGCCAAT 59.250 37.500 2.24 0.00 0.00 3.16
4880 15605 4.749099 TGAAAAATCAAAACGGCCAATCTG 59.251 37.500 2.24 0.00 0.00 2.90
4881 15606 3.317603 AAATCAAAACGGCCAATCTGG 57.682 42.857 2.24 0.00 41.55 3.86
4882 15607 1.185315 ATCAAAACGGCCAATCTGGG 58.815 50.000 2.24 0.00 38.19 4.45
4883 15608 0.178975 TCAAAACGGCCAATCTGGGT 60.179 50.000 2.24 0.00 38.19 4.51
4884 15609 0.243636 CAAAACGGCCAATCTGGGTC 59.756 55.000 2.24 0.00 38.19 4.46
4885 15610 0.112412 AAAACGGCCAATCTGGGTCT 59.888 50.000 2.24 0.00 38.19 3.85
4886 15611 0.609131 AAACGGCCAATCTGGGTCTG 60.609 55.000 2.24 0.00 38.19 3.51
4888 15613 1.299648 CGGCCAATCTGGGTCTGAA 59.700 57.895 2.24 0.00 38.19 3.02
4890 15615 1.886222 CGGCCAATCTGGGTCTGAAAA 60.886 52.381 2.24 0.00 38.19 2.29
4892 15617 2.833943 GGCCAATCTGGGTCTGAAAAAT 59.166 45.455 0.00 0.00 38.19 1.82
4893 15618 3.118992 GGCCAATCTGGGTCTGAAAAATC 60.119 47.826 0.00 0.00 38.19 2.17
4894 15619 3.428045 GCCAATCTGGGTCTGAAAAATCG 60.428 47.826 0.00 0.00 38.19 3.34
4896 15621 4.458989 CCAATCTGGGTCTGAAAAATCGAA 59.541 41.667 0.00 0.00 32.67 3.71
4897 15622 5.048083 CCAATCTGGGTCTGAAAAATCGAAA 60.048 40.000 0.00 0.00 32.67 3.46
4898 15623 5.886960 ATCTGGGTCTGAAAAATCGAAAG 57.113 39.130 0.00 0.00 0.00 2.62
4899 15624 3.502211 TCTGGGTCTGAAAAATCGAAAGC 59.498 43.478 0.00 0.00 0.00 3.51
4900 15625 3.486383 TGGGTCTGAAAAATCGAAAGCT 58.514 40.909 0.00 0.00 0.00 3.74
4901 15626 3.502211 TGGGTCTGAAAAATCGAAAGCTC 59.498 43.478 0.00 0.00 0.00 4.09
4917 16089 5.616424 CGAAAGCTCAAAAGAACTGGATCTG 60.616 44.000 0.00 0.00 0.00 2.90
4920 16092 5.568392 AGCTCAAAAGAACTGGATCTGATT 58.432 37.500 0.00 0.00 0.00 2.57
4921 16093 6.715280 AGCTCAAAAGAACTGGATCTGATTA 58.285 36.000 0.00 0.00 0.00 1.75
4922 16094 7.344913 AGCTCAAAAGAACTGGATCTGATTAT 58.655 34.615 0.00 0.00 0.00 1.28
4924 16096 7.255070 GCTCAAAAGAACTGGATCTGATTATCC 60.255 40.741 0.00 0.00 44.96 2.59
4947 16119 4.448537 AAATCATTTGAAAATCGCCGGA 57.551 36.364 5.05 0.00 0.00 5.14
4948 16120 4.448537 AATCATTTGAAAATCGCCGGAA 57.551 36.364 5.05 0.00 0.00 4.30
4949 16121 4.654091 ATCATTTGAAAATCGCCGGAAT 57.346 36.364 5.05 0.00 0.00 3.01
4950 16122 4.027572 TCATTTGAAAATCGCCGGAATC 57.972 40.909 5.05 0.00 0.00 2.52
4951 16123 3.441922 TCATTTGAAAATCGCCGGAATCA 59.558 39.130 5.05 0.00 0.00 2.57
4952 16124 3.485947 TTTGAAAATCGCCGGAATCAG 57.514 42.857 5.05 0.00 0.00 2.90
4954 16126 3.254470 TGAAAATCGCCGGAATCAGTA 57.746 42.857 5.05 0.00 0.00 2.74
4956 16128 2.981859 AAATCGCCGGAATCAGTAGT 57.018 45.000 5.05 0.00 0.00 2.73
4957 16129 2.225068 AATCGCCGGAATCAGTAGTG 57.775 50.000 5.05 0.00 0.00 2.74
4958 16130 0.249489 ATCGCCGGAATCAGTAGTGC 60.249 55.000 5.05 0.00 0.00 4.40
4960 16132 0.739462 CGCCGGAATCAGTAGTGCAA 60.739 55.000 5.05 0.00 0.00 4.08
4962 16134 1.599542 GCCGGAATCAGTAGTGCAATC 59.400 52.381 5.05 0.00 0.00 2.67
4964 16136 2.481276 CCGGAATCAGTAGTGCAATCGA 60.481 50.000 0.00 0.00 0.00 3.59
4967 16139 4.092821 CGGAATCAGTAGTGCAATCGAAAA 59.907 41.667 0.00 0.00 0.00 2.29
4968 16140 5.220662 CGGAATCAGTAGTGCAATCGAAAAT 60.221 40.000 0.00 0.00 0.00 1.82
4969 16141 6.195165 GGAATCAGTAGTGCAATCGAAAATC 58.805 40.000 0.00 0.00 0.00 2.17
4970 16142 4.840401 TCAGTAGTGCAATCGAAAATCG 57.160 40.909 0.00 0.00 42.10 3.34
4971 16143 4.242475 TCAGTAGTGCAATCGAAAATCGT 58.758 39.130 0.00 0.00 41.35 3.73
4972 16144 4.326278 TCAGTAGTGCAATCGAAAATCGTC 59.674 41.667 0.00 0.00 41.35 4.20
4974 16146 3.729526 AGTGCAATCGAAAATCGTCTG 57.270 42.857 0.00 0.51 41.35 3.51
4975 16147 2.416547 AGTGCAATCGAAAATCGTCTGG 59.583 45.455 0.00 0.00 41.35 3.86
4976 16148 2.415168 GTGCAATCGAAAATCGTCTGGA 59.585 45.455 0.00 0.00 41.35 3.86
4977 16149 2.672874 TGCAATCGAAAATCGTCTGGAG 59.327 45.455 0.00 0.00 41.35 3.86
4978 16150 2.930040 GCAATCGAAAATCGTCTGGAGA 59.070 45.455 0.00 0.00 41.35 3.71
4979 16151 3.242123 GCAATCGAAAATCGTCTGGAGAC 60.242 47.826 0.00 0.00 41.35 3.36
4981 16153 2.168496 TCGAAAATCGTCTGGAGACCT 58.832 47.619 1.15 0.00 41.86 3.85
4982 16154 2.163815 TCGAAAATCGTCTGGAGACCTC 59.836 50.000 1.15 0.00 41.86 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.137872 GGAACGGGATGACGGCGA 62.138 66.667 16.62 0.00 38.39 5.54
72 73 2.667536 AGAAGCAGTGCAGCACGG 60.668 61.111 20.26 20.26 39.64 4.94
73 74 1.779025 AACAGAAGCAGTGCAGCACG 61.779 55.000 19.96 15.24 39.64 5.34
74 75 0.317603 CAACAGAAGCAGTGCAGCAC 60.318 55.000 18.55 18.55 36.85 4.40
75 76 1.449726 CCAACAGAAGCAGTGCAGCA 61.450 55.000 19.20 0.00 36.85 4.41
76 77 1.285023 CCAACAGAAGCAGTGCAGC 59.715 57.895 19.20 8.56 0.00 5.25
77 78 1.170919 AGCCAACAGAAGCAGTGCAG 61.171 55.000 19.20 6.61 0.00 4.41
78 79 0.752743 AAGCCAACAGAAGCAGTGCA 60.753 50.000 19.20 0.00 0.00 4.57
79 80 0.318445 CAAGCCAACAGAAGCAGTGC 60.318 55.000 7.13 7.13 0.00 4.40
81 82 1.027357 CACAAGCCAACAGAAGCAGT 58.973 50.000 0.00 0.00 0.00 4.40
82 83 0.318445 GCACAAGCCAACAGAAGCAG 60.318 55.000 0.00 0.00 33.58 4.24
84 85 1.370900 CGCACAAGCCAACAGAAGC 60.371 57.895 0.00 0.00 37.52 3.86
85 86 1.283793 CCGCACAAGCCAACAGAAG 59.716 57.895 0.00 0.00 37.52 2.85
86 87 1.453015 ACCGCACAAGCCAACAGAA 60.453 52.632 0.00 0.00 37.52 3.02
87 88 2.186160 CACCGCACAAGCCAACAGA 61.186 57.895 0.00 0.00 37.52 3.41
88 89 2.332514 CACCGCACAAGCCAACAG 59.667 61.111 0.00 0.00 37.52 3.16
89 90 3.898509 GCACCGCACAAGCCAACA 61.899 61.111 0.00 0.00 37.52 3.33
90 91 4.980903 CGCACCGCACAAGCCAAC 62.981 66.667 0.00 0.00 37.52 3.77
457 458 1.803519 CTCGTCGGCTGTTCTGCTC 60.804 63.158 0.00 0.00 0.00 4.26
458 459 2.259818 CTCGTCGGCTGTTCTGCT 59.740 61.111 0.00 0.00 0.00 4.24
459 460 2.811317 CCTCGTCGGCTGTTCTGC 60.811 66.667 0.00 0.00 0.00 4.26
574 588 3.427503 CGGCAAGAAAATTACCAGCGATT 60.428 43.478 0.00 0.00 0.00 3.34
576 590 1.466950 CGGCAAGAAAATTACCAGCGA 59.533 47.619 0.00 0.00 0.00 4.93
577 591 1.467374 CCGGCAAGAAAATTACCAGCG 60.467 52.381 0.00 0.00 0.00 5.18
579 593 4.007659 ACTACCGGCAAGAAAATTACCAG 58.992 43.478 11.20 0.00 0.00 4.00
583 597 6.263617 AGACAAAACTACCGGCAAGAAAATTA 59.736 34.615 11.20 0.00 0.00 1.40
584 598 5.068591 AGACAAAACTACCGGCAAGAAAATT 59.931 36.000 11.20 0.00 0.00 1.82
585 599 4.583073 AGACAAAACTACCGGCAAGAAAAT 59.417 37.500 11.20 0.00 0.00 1.82
586 600 3.949113 AGACAAAACTACCGGCAAGAAAA 59.051 39.130 11.20 0.00 0.00 2.29
587 601 3.547746 AGACAAAACTACCGGCAAGAAA 58.452 40.909 11.20 0.00 0.00 2.52
588 602 3.202829 AGACAAAACTACCGGCAAGAA 57.797 42.857 11.20 0.00 0.00 2.52
592 606 1.950909 CCAAAGACAAAACTACCGGCA 59.049 47.619 0.00 0.00 0.00 5.69
595 609 4.886247 TTCACCAAAGACAAAACTACCG 57.114 40.909 0.00 0.00 0.00 4.02
635 664 9.612066 TTAAATCATCTATGCACTGTGACAATA 57.388 29.630 12.86 5.21 0.00 1.90
728 1095 5.534207 TCCGAACCTGAACACTAAAGTAA 57.466 39.130 0.00 0.00 0.00 2.24
734 1101 1.544691 GAGCTCCGAACCTGAACACTA 59.455 52.381 0.87 0.00 0.00 2.74
764 1132 6.834959 ACTAAATCAGCGACACTTGATATG 57.165 37.500 0.00 0.00 0.00 1.78
1193 1571 5.514500 AAAACCTCTAAATGTAGGGAGCA 57.486 39.130 0.00 0.00 37.18 4.26
1740 2153 3.644966 TTGAGTGGGTCAACAAAGACT 57.355 42.857 0.00 0.00 40.45 3.24
2018 2437 8.896744 CACATATACTCTTTCCACATTTCATGT 58.103 33.333 0.00 0.00 46.22 3.21
2260 2778 1.272212 GGACCATGGTGAAAATGCGTT 59.728 47.619 25.52 0.00 0.00 4.84
2262 2780 1.176527 AGGACCATGGTGAAAATGCG 58.823 50.000 25.52 0.00 0.00 4.73
2263 2781 3.119137 GGTAAGGACCATGGTGAAAATGC 60.119 47.826 25.52 5.40 46.12 3.56
2320 2838 3.494626 CAGTTCATGCGTGTAGACAAAGT 59.505 43.478 5.68 0.00 0.00 2.66
2403 3115 1.273327 ACCGGGGTTAACAACGTCTAG 59.727 52.381 6.32 6.90 0.00 2.43
2489 3531 3.263425 GTCCACCTTTAGGAGTGATCCAA 59.737 47.826 2.06 0.00 38.94 3.53
2515 3557 6.029346 AGGCATGAGGTGACTTTAAAAATG 57.971 37.500 0.00 0.00 46.94 2.32
2755 6294 7.706179 ACAAATGCACCAATATAACATTACAGC 59.294 33.333 0.00 0.00 31.05 4.40
3269 6832 0.615544 ATTGTGCCACTGGGAATGGG 60.616 55.000 0.00 0.00 37.73 4.00
3270 6833 0.533491 CATTGTGCCACTGGGAATGG 59.467 55.000 0.00 0.00 40.50 3.16
3362 6925 2.434359 CGGAAGCGGTTGTCCTCC 60.434 66.667 3.70 0.00 0.00 4.30
3417 6981 4.202151 ACTTCATCCAAGCCTGTTCAAAAC 60.202 41.667 0.00 0.00 35.17 2.43
3512 7080 5.909610 CAGTAGAAAAGAAAAGCCGACAAAG 59.090 40.000 0.00 0.00 0.00 2.77
3518 7086 5.607119 TTAGCAGTAGAAAAGAAAAGCCG 57.393 39.130 0.00 0.00 0.00 5.52
3615 7208 0.179012 TGGACCTCACGGGAAAAACC 60.179 55.000 0.00 0.00 38.76 3.27
3644 7237 9.135189 TCTGCTTGTATTTCTGGCATATAAAAT 57.865 29.630 0.00 0.00 32.39 1.82
3687 7280 7.331934 TGAGTAAGATACAATGTTCTGAGCAAC 59.668 37.037 0.00 0.00 0.00 4.17
3695 7288 7.201444 CCGTTGAGTGAGTAAGATACAATGTTC 60.201 40.741 0.00 0.00 0.00 3.18
3759 7354 7.359262 AGAATTCATGAATGCAAACAACATG 57.641 32.000 25.32 3.15 41.63 3.21
3791 7386 1.555075 TCCCATCAGGTCTGCAGTAAC 59.445 52.381 14.67 5.20 36.75 2.50
4034 7641 3.699038 ACCAAGCAAGAAAAACTGTAGCA 59.301 39.130 0.00 0.00 0.00 3.49
4035 7642 4.307443 ACCAAGCAAGAAAAACTGTAGC 57.693 40.909 0.00 0.00 0.00 3.58
4127 8015 2.143925 GTGGAGTGACAGGCTTACAAC 58.856 52.381 0.00 0.00 0.00 3.32
4147 8041 2.622903 TATCGCGTCTTTGCCGAGGG 62.623 60.000 5.77 0.00 0.00 4.30
4148 8042 0.804544 TTATCGCGTCTTTGCCGAGG 60.805 55.000 5.77 0.00 0.00 4.63
4149 8043 0.996462 TTTATCGCGTCTTTGCCGAG 59.004 50.000 5.77 0.00 0.00 4.63
4150 8044 1.647346 ATTTATCGCGTCTTTGCCGA 58.353 45.000 5.77 0.00 0.00 5.54
4211 11648 8.902540 TGTTATTGATCATGGTATGGTAGTTC 57.097 34.615 0.00 0.00 0.00 3.01
4283 11723 3.324268 TCACCCGACCAGTAACATAAACA 59.676 43.478 0.00 0.00 0.00 2.83
4432 11917 3.771160 GGATCCGCCGTGACCAGT 61.771 66.667 0.00 0.00 0.00 4.00
4505 11991 2.400467 AACCCCCTGCGTCTATCTAT 57.600 50.000 0.00 0.00 0.00 1.98
4520 12285 4.769859 TTAATAACAGCACCGAAAACCC 57.230 40.909 0.00 0.00 0.00 4.11
4527 12292 1.202098 GGGCGTTTAATAACAGCACCG 60.202 52.381 0.00 0.00 36.32 4.94
4567 13272 4.667519 ATGTTTAGTAGCTTACCCTCGG 57.332 45.455 0.00 0.00 0.00 4.63
4583 13918 4.211794 CGATGGCTTTTCTGCAAAATGTTT 59.788 37.500 0.00 0.00 30.91 2.83
4606 13941 6.096001 ACCTGCACATAATTTTGAGATTCTCC 59.904 38.462 11.12 0.00 0.00 3.71
4607 13942 7.093322 ACCTGCACATAATTTTGAGATTCTC 57.907 36.000 6.73 6.73 0.00 2.87
4625 13960 5.932619 TCTAAAGAGCTATTGTACCTGCA 57.067 39.130 0.00 0.00 0.00 4.41
4650 13985 3.259064 GTTGGATCTCAAATTCGACGGA 58.741 45.455 0.00 0.00 37.08 4.69
4656 13991 4.215399 TCACAACCGTTGGATCTCAAATTC 59.785 41.667 15.60 0.00 37.08 2.17
4657 13992 4.141287 TCACAACCGTTGGATCTCAAATT 58.859 39.130 15.60 0.00 37.08 1.82
4660 13995 2.920724 TCACAACCGTTGGATCTCAA 57.079 45.000 15.60 0.00 34.12 3.02
4675 14010 6.481976 GGTGATACCGTGATATGAATTTCACA 59.518 38.462 0.15 0.00 41.85 3.58
4677 14012 6.826668 AGGTGATACCGTGATATGAATTTCA 58.173 36.000 0.75 0.75 44.90 2.69
4681 14016 7.540474 ACTTAGGTGATACCGTGATATGAAT 57.460 36.000 0.00 0.00 44.90 2.57
4683 14018 6.971726 AACTTAGGTGATACCGTGATATGA 57.028 37.500 0.00 0.00 44.90 2.15
4690 14025 4.628963 ACCAAAACTTAGGTGATACCGT 57.371 40.909 0.00 0.00 44.90 4.83
4692 14027 6.541278 GGTGATACCAAAACTTAGGTGATACC 59.459 42.308 0.00 0.00 38.42 2.73
4693 14028 7.280205 CAGGTGATACCAAAACTTAGGTGATAC 59.720 40.741 0.28 0.00 41.95 2.24
4694 14029 7.181305 TCAGGTGATACCAAAACTTAGGTGATA 59.819 37.037 0.28 0.00 41.95 2.15
4695 14030 6.012858 TCAGGTGATACCAAAACTTAGGTGAT 60.013 38.462 0.28 0.00 41.95 3.06
4696 14031 5.308497 TCAGGTGATACCAAAACTTAGGTGA 59.692 40.000 0.28 0.00 41.95 4.02
4697 14032 5.556915 TCAGGTGATACCAAAACTTAGGTG 58.443 41.667 0.28 0.00 41.95 4.00
4698 14033 5.836024 TCAGGTGATACCAAAACTTAGGT 57.164 39.130 0.28 0.00 41.95 3.08
4699 14034 7.703058 ATTTCAGGTGATACCAAAACTTAGG 57.297 36.000 0.28 0.00 41.95 2.69
4700 14035 9.981114 AAAATTTCAGGTGATACCAAAACTTAG 57.019 29.630 0.28 0.00 41.95 2.18
4701 14036 9.974980 GAAAATTTCAGGTGATACCAAAACTTA 57.025 29.630 0.11 0.00 41.95 2.24
4702 14037 7.931407 GGAAAATTTCAGGTGATACCAAAACTT 59.069 33.333 8.09 0.00 41.95 2.66
4703 14038 7.441836 GGAAAATTTCAGGTGATACCAAAACT 58.558 34.615 8.09 0.00 41.95 2.66
4704 14039 6.649141 GGGAAAATTTCAGGTGATACCAAAAC 59.351 38.462 8.09 0.00 41.95 2.43
4705 14040 6.517529 CGGGAAAATTTCAGGTGATACCAAAA 60.518 38.462 8.09 1.57 41.95 2.44
4706 14041 5.047660 CGGGAAAATTTCAGGTGATACCAAA 60.048 40.000 8.09 0.00 41.95 3.28
4707 14042 4.461081 CGGGAAAATTTCAGGTGATACCAA 59.539 41.667 8.09 0.00 41.95 3.67
4708 14043 4.013728 CGGGAAAATTTCAGGTGATACCA 58.986 43.478 8.09 0.00 41.95 3.25
4718 14053 2.768698 TGCGTAGACGGGAAAATTTCA 58.231 42.857 8.09 0.00 40.23 2.69
4730 14065 1.497722 GCTGCTGGTTTGCGTAGAC 59.502 57.895 0.00 0.00 35.36 2.59
4734 14069 3.289834 CTGGCTGCTGGTTTGCGT 61.290 61.111 0.00 0.00 35.36 5.24
4756 14154 3.597255 TCGCCACATCGTTTATTTACCA 58.403 40.909 0.00 0.00 0.00 3.25
4765 14163 2.108514 CATGCCTCGCCACATCGTT 61.109 57.895 0.00 0.00 0.00 3.85
4766 14164 2.512286 CATGCCTCGCCACATCGT 60.512 61.111 0.00 0.00 0.00 3.73
4786 14184 7.930325 CACATGACCTATAGAATTCACACATCT 59.070 37.037 8.44 0.00 0.00 2.90
4832 15557 1.026718 AGATTGGCCGCACTAGCAAC 61.027 55.000 0.00 0.00 42.27 4.17
4833 15558 1.026182 CAGATTGGCCGCACTAGCAA 61.026 55.000 0.00 0.00 42.27 3.91
4835 15560 2.182842 CCAGATTGGCCGCACTAGC 61.183 63.158 0.00 0.00 37.42 3.42
4837 15562 2.252072 GACCCAGATTGGCCGCACTA 62.252 60.000 0.00 0.00 35.79 2.74
4838 15563 3.628646 GACCCAGATTGGCCGCACT 62.629 63.158 0.00 0.00 35.79 4.40
4840 15565 3.329889 AGACCCAGATTGGCCGCA 61.330 61.111 0.00 0.00 35.79 5.69
4841 15566 2.819984 TTCAGACCCAGATTGGCCGC 62.820 60.000 0.00 0.00 35.79 6.53
4842 15567 0.322456 TTTCAGACCCAGATTGGCCG 60.322 55.000 0.00 0.00 35.79 6.13
4843 15568 1.923356 TTTTCAGACCCAGATTGGCC 58.077 50.000 0.00 0.00 35.79 5.36
4844 15569 3.511146 TGATTTTTCAGACCCAGATTGGC 59.489 43.478 0.00 0.00 35.79 4.52
4845 15570 5.726980 TTGATTTTTCAGACCCAGATTGG 57.273 39.130 0.00 0.00 37.25 3.16
4846 15571 6.144402 CGTTTTGATTTTTCAGACCCAGATTG 59.856 38.462 0.00 0.00 0.00 2.67
4851 15576 3.491792 GCCGTTTTGATTTTTCAGACCCA 60.492 43.478 0.00 0.00 0.00 4.51
4852 15577 3.057019 GCCGTTTTGATTTTTCAGACCC 58.943 45.455 0.00 0.00 0.00 4.46
4853 15578 3.057019 GGCCGTTTTGATTTTTCAGACC 58.943 45.455 0.00 0.00 0.00 3.85
4854 15579 3.712187 TGGCCGTTTTGATTTTTCAGAC 58.288 40.909 0.00 0.00 0.00 3.51
4855 15580 4.392921 TTGGCCGTTTTGATTTTTCAGA 57.607 36.364 0.00 0.00 0.00 3.27
4856 15581 4.990426 AGATTGGCCGTTTTGATTTTTCAG 59.010 37.500 0.00 0.00 0.00 3.02
4857 15582 4.749099 CAGATTGGCCGTTTTGATTTTTCA 59.251 37.500 0.00 0.00 0.00 2.69
4858 15583 4.152223 CCAGATTGGCCGTTTTGATTTTTC 59.848 41.667 0.00 0.00 0.00 2.29
4859 15584 4.064388 CCAGATTGGCCGTTTTGATTTTT 58.936 39.130 0.00 0.00 0.00 1.94
4860 15585 3.556843 CCCAGATTGGCCGTTTTGATTTT 60.557 43.478 0.00 0.00 35.79 1.82
4862 15587 1.550072 CCCAGATTGGCCGTTTTGATT 59.450 47.619 0.00 0.00 35.79 2.57
4864 15589 0.178975 ACCCAGATTGGCCGTTTTGA 60.179 50.000 0.00 0.00 35.79 2.69
4865 15590 0.243636 GACCCAGATTGGCCGTTTTG 59.756 55.000 0.00 0.00 35.79 2.44
4866 15591 0.112412 AGACCCAGATTGGCCGTTTT 59.888 50.000 0.00 0.00 35.79 2.43
4870 15595 0.322456 TTTCAGACCCAGATTGGCCG 60.322 55.000 0.00 0.00 35.79 6.13
4871 15596 1.923356 TTTTCAGACCCAGATTGGCC 58.077 50.000 0.00 0.00 35.79 5.36
4872 15597 3.428045 CGATTTTTCAGACCCAGATTGGC 60.428 47.826 0.00 0.00 35.79 4.52
4873 15598 4.009675 TCGATTTTTCAGACCCAGATTGG 58.990 43.478 0.00 0.00 37.25 3.16
4874 15599 5.627499 TTCGATTTTTCAGACCCAGATTG 57.373 39.130 0.00 0.00 0.00 2.67
4875 15600 5.335976 GCTTTCGATTTTTCAGACCCAGATT 60.336 40.000 0.00 0.00 0.00 2.40
4876 15601 4.156739 GCTTTCGATTTTTCAGACCCAGAT 59.843 41.667 0.00 0.00 0.00 2.90
4877 15602 3.502211 GCTTTCGATTTTTCAGACCCAGA 59.498 43.478 0.00 0.00 0.00 3.86
4880 15605 3.502211 TGAGCTTTCGATTTTTCAGACCC 59.498 43.478 0.00 0.00 0.00 4.46
4881 15606 4.749245 TGAGCTTTCGATTTTTCAGACC 57.251 40.909 0.00 0.00 0.00 3.85
4882 15607 6.912591 TCTTTTGAGCTTTCGATTTTTCAGAC 59.087 34.615 0.00 0.00 0.00 3.51
4883 15608 7.026631 TCTTTTGAGCTTTCGATTTTTCAGA 57.973 32.000 0.00 0.00 0.00 3.27
4884 15609 7.433425 AGTTCTTTTGAGCTTTCGATTTTTCAG 59.567 33.333 0.00 0.00 36.59 3.02
4885 15610 7.220683 CAGTTCTTTTGAGCTTTCGATTTTTCA 59.779 33.333 0.00 0.00 37.94 2.69
4886 15611 7.306225 CCAGTTCTTTTGAGCTTTCGATTTTTC 60.306 37.037 0.00 0.00 37.94 2.29
4888 15613 5.979517 CCAGTTCTTTTGAGCTTTCGATTTT 59.020 36.000 0.00 0.00 37.94 1.82
4890 15615 4.821805 TCCAGTTCTTTTGAGCTTTCGATT 59.178 37.500 0.00 0.00 37.94 3.34
4892 15617 3.804036 TCCAGTTCTTTTGAGCTTTCGA 58.196 40.909 0.00 0.00 37.94 3.71
4893 15618 4.453819 AGATCCAGTTCTTTTGAGCTTTCG 59.546 41.667 0.00 0.00 37.94 3.46
4894 15619 5.471456 TCAGATCCAGTTCTTTTGAGCTTTC 59.529 40.000 0.00 0.00 37.94 2.62
4896 15621 4.978099 TCAGATCCAGTTCTTTTGAGCTT 58.022 39.130 0.00 0.00 37.94 3.74
4897 15622 4.630644 TCAGATCCAGTTCTTTTGAGCT 57.369 40.909 0.00 0.00 40.74 4.09
4898 15623 5.893897 AATCAGATCCAGTTCTTTTGAGC 57.106 39.130 0.00 0.00 0.00 4.26
4899 15624 8.152309 GGATAATCAGATCCAGTTCTTTTGAG 57.848 38.462 0.00 0.00 44.34 3.02
4917 16089 9.853921 GCGATTTTCAAATGATTTTGGATAATC 57.146 29.630 9.38 9.38 42.10 1.75
4920 16092 6.475076 CGGCGATTTTCAAATGATTTTGGATA 59.525 34.615 0.00 0.00 42.10 2.59
4921 16093 5.291614 CGGCGATTTTCAAATGATTTTGGAT 59.708 36.000 0.00 0.00 42.10 3.41
4922 16094 4.624882 CGGCGATTTTCAAATGATTTTGGA 59.375 37.500 0.00 0.00 42.10 3.53
4924 16096 4.624882 TCCGGCGATTTTCAAATGATTTTG 59.375 37.500 9.30 0.00 42.98 2.44
4926 16098 4.448537 TCCGGCGATTTTCAAATGATTT 57.551 36.364 9.30 0.00 0.00 2.17
4928 16100 4.097741 TGATTCCGGCGATTTTCAAATGAT 59.902 37.500 9.30 0.00 0.00 2.45
4929 16101 3.441922 TGATTCCGGCGATTTTCAAATGA 59.558 39.130 9.30 0.00 0.00 2.57
4930 16102 3.768406 TGATTCCGGCGATTTTCAAATG 58.232 40.909 9.30 0.00 0.00 2.32
4932 16104 2.817258 ACTGATTCCGGCGATTTTCAAA 59.183 40.909 9.30 0.00 0.00 2.69
4934 16106 2.107950 ACTGATTCCGGCGATTTTCA 57.892 45.000 9.30 5.04 0.00 2.69
4935 16107 3.001330 CACTACTGATTCCGGCGATTTTC 59.999 47.826 9.30 0.00 0.00 2.29
4936 16108 2.936498 CACTACTGATTCCGGCGATTTT 59.064 45.455 9.30 0.00 0.00 1.82
4937 16109 2.550978 CACTACTGATTCCGGCGATTT 58.449 47.619 9.30 0.00 0.00 2.17
4938 16110 1.806623 GCACTACTGATTCCGGCGATT 60.807 52.381 9.30 0.00 0.00 3.34
4940 16112 1.141019 GCACTACTGATTCCGGCGA 59.859 57.895 9.30 0.00 0.00 5.54
4941 16113 0.739462 TTGCACTACTGATTCCGGCG 60.739 55.000 0.00 0.00 0.00 6.46
4942 16114 1.599542 GATTGCACTACTGATTCCGGC 59.400 52.381 0.00 0.00 0.00 6.13
4943 16115 1.860950 CGATTGCACTACTGATTCCGG 59.139 52.381 0.00 0.00 0.00 5.14
4944 16116 2.809446 TCGATTGCACTACTGATTCCG 58.191 47.619 0.00 0.00 0.00 4.30
4945 16117 5.545658 TTTTCGATTGCACTACTGATTCC 57.454 39.130 0.00 0.00 0.00 3.01
4946 16118 5.898606 CGATTTTCGATTGCACTACTGATTC 59.101 40.000 0.00 0.00 43.74 2.52
4947 16119 5.351465 ACGATTTTCGATTGCACTACTGATT 59.649 36.000 3.62 0.00 43.74 2.57
4948 16120 4.870426 ACGATTTTCGATTGCACTACTGAT 59.130 37.500 3.62 0.00 43.74 2.90
4949 16121 4.242475 ACGATTTTCGATTGCACTACTGA 58.758 39.130 3.62 0.00 43.74 3.41
4950 16122 4.327357 AGACGATTTTCGATTGCACTACTG 59.673 41.667 3.62 0.00 43.74 2.74
4951 16123 4.327357 CAGACGATTTTCGATTGCACTACT 59.673 41.667 3.62 0.00 43.74 2.57
4952 16124 4.492570 CCAGACGATTTTCGATTGCACTAC 60.493 45.833 3.62 0.00 43.74 2.73
4954 16126 2.416547 CCAGACGATTTTCGATTGCACT 59.583 45.455 3.62 0.00 43.74 4.40
4956 16128 2.672874 CTCCAGACGATTTTCGATTGCA 59.327 45.455 3.62 0.00 43.74 4.08
4957 16129 2.930040 TCTCCAGACGATTTTCGATTGC 59.070 45.455 3.62 0.00 43.74 3.56
4958 16130 3.307242 GGTCTCCAGACGATTTTCGATTG 59.693 47.826 3.62 1.89 43.74 2.67
4960 16132 2.761208 AGGTCTCCAGACGATTTTCGAT 59.239 45.455 3.62 0.00 43.74 3.59
4962 16134 2.531206 GAGGTCTCCAGACGATTTTCG 58.469 52.381 0.60 0.00 45.65 3.46


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

AutoCloner maintained by Alex Coulton.