Multiple sequence alignment - TraesCS4A01G222900

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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 TraesCS4A01G222900 chr4A 100.000 5471 0 0 1 5471 530814792 530820262 0.000000e+00 10104.0
1 TraesCS4A01G222900 chr4A 89.773 88 9 0 2368 2455 524285372 524285459 4.480000e-21 113.0
2 TraesCS4A01G222900 chr4A 92.982 57 3 1 2623 2678 530817360 530817416 1.260000e-11 82.4
3 TraesCS4A01G222900 chr4A 92.982 57 3 1 2569 2625 530817414 530817469 1.260000e-11 82.4
4 TraesCS4A01G222900 chr4D 93.164 2677 92 38 21 2625 65180936 65178279 0.000000e+00 3845.0
5 TraesCS4A01G222900 chr4D 94.244 2241 56 21 2623 4833 65178334 65176137 0.000000e+00 3356.0
6 TraesCS4A01G222900 chr4D 92.254 142 5 3 5128 5268 65175818 65175682 4.320000e-46 196.0
7 TraesCS4A01G222900 chr4D 87.500 112 12 2 5022 5132 10812510 10812400 1.600000e-25 128.0
8 TraesCS4A01G222900 chr4D 87.500 112 12 2 5022 5132 10830279 10830169 1.600000e-25 128.0
9 TraesCS4A01G222900 chr4D 93.590 78 2 2 5254 5331 65175664 65175590 4.480000e-21 113.0
10 TraesCS4A01G222900 chr4B 87.709 1497 96 39 252 1682 95862597 95861123 0.000000e+00 1664.0
11 TraesCS4A01G222900 chr4B 86.923 1430 88 41 2623 4030 95860296 95858944 0.000000e+00 1513.0
12 TraesCS4A01G222900 chr4B 92.394 802 44 8 1752 2551 95861117 95860331 0.000000e+00 1127.0
13 TraesCS4A01G222900 chr4B 88.486 799 52 27 4134 4905 95858932 95858147 0.000000e+00 929.0
14 TraesCS4A01G222900 chr4B 95.122 205 8 1 21 223 95862867 95862663 6.840000e-84 322.0
15 TraesCS4A01G222900 chr4B 90.338 207 8 7 5128 5330 95857987 95857789 1.510000e-65 261.0
16 TraesCS4A01G222900 chr4B 91.111 90 8 0 2368 2457 65499667 65499756 7.440000e-24 122.0
17 TraesCS4A01G222900 chr4B 96.154 52 2 0 4664 4715 95858440 95858389 9.760000e-13 86.1
18 TraesCS4A01G222900 chr6A 86.452 465 47 6 2927 3385 9585563 9585109 3.810000e-136 496.0
19 TraesCS4A01G222900 chr3A 86.422 464 50 7 2927 3385 712304933 712305388 3.810000e-136 496.0
20 TraesCS4A01G222900 chr3B 85.897 468 52 10 2928 3385 370958814 370958351 2.290000e-133 486.0
21 TraesCS4A01G222900 chr3B 86.777 121 14 2 5023 5142 99473661 99473780 3.440000e-27 134.0
22 TraesCS4A01G222900 chr7B 85.225 467 51 9 2927 3385 10685286 10685742 1.070000e-126 464.0
23 TraesCS4A01G222900 chr3D 85.028 354 37 7 2927 3274 112759828 112759485 4.060000e-91 346.0
24 TraesCS4A01G222900 chr3D 93.277 119 8 0 3267 3385 112758250 112758132 5.630000e-40 176.0
25 TraesCS4A01G222900 chr6B 85.083 181 22 3 2368 2548 471229663 471229838 4.350000e-41 180.0
26 TraesCS4A01G222900 chr6B 88.571 105 12 0 5019 5123 149018649 149018753 1.600000e-25 128.0
27 TraesCS4A01G222900 chr5B 93.333 90 6 0 2368 2457 18337548 18337637 3.440000e-27 134.0
28 TraesCS4A01G222900 chr5B 90.099 101 10 0 5023 5123 459489894 459489994 1.240000e-26 132.0
29 TraesCS4A01G222900 chr5B 79.762 84 13 2 1648 1731 8269057 8268978 2.130000e-04 58.4
30 TraesCS4A01G222900 chr5B 100.000 28 0 0 1704 1731 591529861 591529888 1.000000e-02 52.8
31 TraesCS4A01G222900 chr1A 87.179 117 13 2 5014 5130 558182596 558182710 1.240000e-26 132.0
32 TraesCS4A01G222900 chr1A 87.611 113 13 1 5018 5129 494096725 494096613 4.450000e-26 130.0
33 TraesCS4A01G222900 chr1A 87.719 57 5 2 5340 5395 451566487 451566432 1.270000e-06 65.8
34 TraesCS4A01G222900 chr7D 86.957 115 14 1 5015 5129 557836240 557836127 1.600000e-25 128.0
35 TraesCS4A01G222900 chr7D 91.209 91 7 1 2368 2457 58205116 58205026 7.440000e-24 122.0
36 TraesCS4A01G222900 chr7D 81.818 88 11 3 1648 1735 610922376 610922458 9.830000e-08 69.4
37 TraesCS4A01G222900 chr1B 84.091 132 18 3 5020 5149 624507041 624506911 2.070000e-24 124.0
38 TraesCS4A01G222900 chr7A 79.339 121 15 9 1624 1740 166738671 166738557 5.880000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G222900 chr4A 530814792 530820262 5470 False 3422.933333 10104 95.321333 1 5471 3 chr4A.!!$F2 5470
1 TraesCS4A01G222900 chr4D 65175590 65180936 5346 True 1877.500000 3845 93.313000 21 5331 4 chr4D.!!$R3 5310
2 TraesCS4A01G222900 chr4B 95857789 95862867 5078 True 843.157143 1664 91.018000 21 5330 7 chr4B.!!$R1 5309
3 TraesCS4A01G222900 chr3D 112758132 112759828 1696 True 261.000000 346 89.152500 2927 3385 2 chr3D.!!$R1 458

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
930 1050 0.321564 CTCACAATCGCAGGGGTTCA 60.322 55.000 0.00 0.0 0.00 3.18 F
1646 1778 1.885887 TGTTGTAGCCCTTTGCATGTC 59.114 47.619 0.00 0.0 44.83 3.06 F
2560 2714 2.887151 ACAGGACTGGCAGCTAAAAT 57.113 45.000 15.89 0.0 34.19 1.82 F
2993 3153 0.588252 TGCTGCTTGCTCGACTTTTC 59.412 50.000 0.00 0.0 43.37 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2596 2750 0.252696 TGCCATCTGTAGGTGTCCCT 60.253 55.0 0.00 0.0 45.51 4.20 R
2597 2751 0.618458 TTGCCATCTGTAGGTGTCCC 59.382 55.0 0.00 0.0 0.00 4.46 R
4108 5546 0.542702 CCAAGATTGGGTTGTGGCCT 60.543 55.0 3.32 0.0 44.70 5.19 R
4979 6597 0.810031 CCTTAACGCGGTGATCCAGG 60.810 60.0 7.07 0.0 0.00 4.45 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
17 18 3.927501 CCTCTCTCACCGACTCCC 58.072 66.667 0.00 0.00 0.00 4.30
18 19 1.304952 CCTCTCTCACCGACTCCCT 59.695 63.158 0.00 0.00 0.00 4.20
19 20 1.034838 CCTCTCTCACCGACTCCCTG 61.035 65.000 0.00 0.00 0.00 4.45
40 41 1.269831 CGATTCCCCGGTTCTGATCTC 60.270 57.143 0.00 0.00 0.00 2.75
43 44 1.689233 CCCCGGTTCTGATCTCCCA 60.689 63.158 0.00 0.00 0.00 4.37
211 214 1.731424 CGCACGAAATCGGTAGTGAGT 60.731 52.381 7.81 0.00 44.95 3.41
219 222 0.792640 TCGGTAGTGAGTCGTCGTTC 59.207 55.000 0.00 0.00 0.00 3.95
242 292 1.180907 CACACAGCTCTGCTCCTCTA 58.819 55.000 0.00 0.00 36.40 2.43
249 299 1.000771 TCTGCTCCTCTACTGCGGT 60.001 57.895 2.42 2.42 34.91 5.68
312 362 3.708451 TGATACAGCCTTCCTAGTCACA 58.292 45.455 0.00 0.00 0.00 3.58
405 455 1.739929 CGCACCTGTCGTTGCCATA 60.740 57.895 0.00 0.00 0.00 2.74
415 465 1.523938 GTTGCCATAGAGGGACGGC 60.524 63.158 0.00 0.00 45.11 5.68
474 524 2.586425 CTGACGGGGCCATCATTTATT 58.414 47.619 4.39 0.00 0.00 1.40
475 525 2.958355 CTGACGGGGCCATCATTTATTT 59.042 45.455 4.39 0.00 0.00 1.40
476 526 3.370104 TGACGGGGCCATCATTTATTTT 58.630 40.909 4.39 0.00 0.00 1.82
477 527 4.537751 TGACGGGGCCATCATTTATTTTA 58.462 39.130 4.39 0.00 0.00 1.52
478 528 5.144100 TGACGGGGCCATCATTTATTTTAT 58.856 37.500 4.39 0.00 0.00 1.40
479 529 6.307776 TGACGGGGCCATCATTTATTTTATA 58.692 36.000 4.39 0.00 0.00 0.98
539 599 1.602311 AGATTCAGATCCGGCATTGC 58.398 50.000 0.00 0.00 32.44 3.56
668 732 1.927895 AACTATGCTGCTGCGTACTC 58.072 50.000 12.96 0.00 43.34 2.59
670 734 0.598680 CTATGCTGCTGCGTACTCCC 60.599 60.000 12.96 0.00 43.34 4.30
697 764 2.096496 CACCAGCACCGATTCTTGATTC 59.904 50.000 0.00 0.00 0.00 2.52
754 845 6.828273 TGCCAATAGTATACATTGCTTGACTT 59.172 34.615 16.35 0.00 33.00 3.01
775 866 6.823497 ACTTGTACTCCAGTTTAGTTGCTTA 58.177 36.000 0.00 0.00 0.00 3.09
852 943 8.671384 CCAAGAGGGTTTATTCGTCATAAATA 57.329 34.615 6.03 0.00 39.16 1.40
887 1007 4.640201 TGGCTTTCTACTGCAATGGAATAC 59.360 41.667 0.00 0.00 0.00 1.89
888 1008 4.884164 GGCTTTCTACTGCAATGGAATACT 59.116 41.667 0.00 0.00 0.00 2.12
889 1009 5.220931 GGCTTTCTACTGCAATGGAATACTG 60.221 44.000 0.00 0.00 0.00 2.74
893 1013 7.418337 TTCTACTGCAATGGAATACTGACTA 57.582 36.000 0.00 0.00 0.00 2.59
905 1025 6.040955 TGGAATACTGACTATCTGCACCTTAG 59.959 42.308 0.00 0.00 0.00 2.18
919 1039 3.873952 GCACCTTAGTCATCCTCACAATC 59.126 47.826 0.00 0.00 0.00 2.67
923 1043 2.306341 AGTCATCCTCACAATCGCAG 57.694 50.000 0.00 0.00 0.00 5.18
929 1049 1.026718 CCTCACAATCGCAGGGGTTC 61.027 60.000 0.00 0.00 0.00 3.62
930 1050 0.321564 CTCACAATCGCAGGGGTTCA 60.322 55.000 0.00 0.00 0.00 3.18
980 1100 4.038522 TGCAGGAGCTCATCTGAATAGTAC 59.961 45.833 20.34 4.91 42.74 2.73
1011 1131 5.538433 AGAGCAGGGTATAATGAAGAGAGTC 59.462 44.000 0.00 0.00 0.00 3.36
1311 1431 3.331150 TGTAGTGTATTTTCGTGGCCAG 58.669 45.455 5.11 0.00 0.00 4.85
1404 1525 4.433615 TCGTCTCATATCTGAAAACAGGC 58.566 43.478 0.00 0.00 0.00 4.85
1505 1633 6.089417 CGTTCCAAAATAATTGAAGTTCAGGC 59.911 38.462 5.56 0.00 0.00 4.85
1646 1778 1.885887 TGTTGTAGCCCTTTGCATGTC 59.114 47.619 0.00 0.00 44.83 3.06
1684 1816 8.741603 TGGTCAAACTTAACTAAGCTTAACTT 57.258 30.769 7.74 4.66 42.76 2.66
1685 1817 9.835389 TGGTCAAACTTAACTAAGCTTAACTTA 57.165 29.630 7.74 3.72 39.97 2.24
1792 1927 9.973661 ATGCTACATTTATTATATGCCCTGTTA 57.026 29.630 0.00 0.00 0.00 2.41
2060 2196 3.084786 GTTCCTAGTGCATTGGCTTTCT 58.915 45.455 0.00 0.00 41.91 2.52
2440 2576 3.488721 GCACTGATGGTTGCTCAATGATC 60.489 47.826 0.00 0.00 0.00 2.92
2474 2610 5.493809 TGGTACAGGCACTTAACCTTTATC 58.506 41.667 0.00 0.00 40.34 1.75
2560 2714 2.887151 ACAGGACTGGCAGCTAAAAT 57.113 45.000 15.89 0.00 34.19 1.82
2568 2722 3.897505 ACTGGCAGCTAAAATGGACTTTT 59.102 39.130 15.89 0.00 40.21 2.27
2569 2723 4.344968 ACTGGCAGCTAAAATGGACTTTTT 59.655 37.500 15.89 2.24 38.09 1.94
2602 2756 9.856162 AAACAGTAAACTTTAATAGAAGGGACA 57.144 29.630 0.00 0.00 0.00 4.02
2603 2757 8.843885 ACAGTAAACTTTAATAGAAGGGACAC 57.156 34.615 0.00 0.00 0.00 3.67
2604 2758 7.881751 ACAGTAAACTTTAATAGAAGGGACACC 59.118 37.037 0.00 0.00 0.00 4.16
2615 2769 2.296920 GGGACACCTACAGATGGCA 58.703 57.895 0.00 0.00 0.00 4.92
2616 2770 0.618458 GGGACACCTACAGATGGCAA 59.382 55.000 0.00 0.00 0.00 4.52
2617 2771 1.679032 GGGACACCTACAGATGGCAAC 60.679 57.143 0.00 0.00 0.00 4.17
2752 2908 5.936956 TGGGTTTTCATTATTTTGGCATGTC 59.063 36.000 0.00 0.00 0.00 3.06
2788 2944 1.003355 ACCATGCAAGAGGGACACG 60.003 57.895 7.93 0.00 0.00 4.49
2794 2950 3.520290 TGCAAGAGGGACACGTATAAG 57.480 47.619 0.00 0.00 0.00 1.73
2810 2966 8.887717 ACACGTATAAGGATAATATACTCGACC 58.112 37.037 0.00 0.00 35.18 4.79
2943 3103 9.793252 ATATAACACTTGAAACAAATGATCTGC 57.207 29.630 0.00 0.00 0.00 4.26
2983 3143 1.559831 AAGTTTTTCGTGCTGCTTGC 58.440 45.000 0.00 0.00 43.25 4.01
2993 3153 0.588252 TGCTGCTTGCTCGACTTTTC 59.412 50.000 0.00 0.00 43.37 2.29
3233 3397 1.851304 CCCTCCAAATGCTTAAGCCA 58.149 50.000 24.30 12.86 41.18 4.75
3539 4945 7.353414 TGCCATTATATCATCTCTAGCTACC 57.647 40.000 0.00 0.00 0.00 3.18
3728 5134 5.985911 TCTTGGCCAGGTAATTTACTCTAC 58.014 41.667 15.41 0.00 0.00 2.59
3774 5184 5.978934 CATTCTTTGCTGCCAAATATTCC 57.021 39.130 0.00 0.00 39.98 3.01
3776 5186 4.724074 TCTTTGCTGCCAAATATTCCTG 57.276 40.909 0.00 0.00 39.98 3.86
3900 5319 7.448420 TCATTCTGAAATTACCATTTGGCAAA 58.552 30.769 16.01 16.01 39.32 3.68
3957 5377 2.012673 GGCAACATAGCTTGTCAGGAG 58.987 52.381 0.00 0.00 37.68 3.69
4065 5501 2.419673 TGGCTTTGTATGCTCAATCGTG 59.580 45.455 0.00 0.00 0.00 4.35
4066 5502 2.444351 GCTTTGTATGCTCAATCGTGC 58.556 47.619 0.00 0.00 0.00 5.34
4067 5503 2.792542 GCTTTGTATGCTCAATCGTGCC 60.793 50.000 0.00 0.00 0.00 5.01
4076 5514 0.901827 TCAATCGTGCCCTGCTTCTA 59.098 50.000 0.00 0.00 0.00 2.10
4077 5515 1.486310 TCAATCGTGCCCTGCTTCTAT 59.514 47.619 0.00 0.00 0.00 1.98
4108 5546 1.821936 CAAAGCCACAAGCCCACAA 59.178 52.632 0.00 0.00 45.47 3.33
4109 5547 0.249573 CAAAGCCACAAGCCCACAAG 60.250 55.000 0.00 0.00 45.47 3.16
4110 5548 1.402107 AAAGCCACAAGCCCACAAGG 61.402 55.000 0.00 0.00 45.47 3.61
4212 5650 3.194719 GCAGCCTGCATCAAGACC 58.805 61.111 12.82 0.00 44.26 3.85
4305 5743 4.752879 TACGACGGCAAGCTGGGC 62.753 66.667 4.10 4.10 0.00 5.36
4392 5830 1.070445 GATGCTGGAGGACCCATCG 59.930 63.158 0.00 0.00 45.57 3.84
4475 5913 3.730061 GCGTCATGGAATGCTTGAAGAAG 60.730 47.826 7.58 0.00 46.21 2.85
4476 5914 3.181503 CGTCATGGAATGCTTGAAGAAGG 60.182 47.826 0.00 0.00 46.21 3.46
4477 5915 3.129988 GTCATGGAATGCTTGAAGAAGGG 59.870 47.826 0.00 0.00 46.21 3.95
4599 6039 5.240183 GTGTATACCGTAGATGCACCTAGAA 59.760 44.000 0.00 0.00 34.82 2.10
4605 6045 1.479709 AGATGCACCTAGAAGTCGCT 58.520 50.000 0.00 0.00 0.00 4.93
4636 6077 5.398603 TCTTCCTTTTGTCAAAAACAGCA 57.601 34.783 11.73 0.00 39.58 4.41
4717 6192 4.020573 CCAGTGACACCTTGGATAGTTGTA 60.021 45.833 7.91 0.00 33.76 2.41
4718 6193 5.338381 CCAGTGACACCTTGGATAGTTGTAT 60.338 44.000 7.91 0.00 33.76 2.29
4770 6253 8.618702 TTTAACCAAGTATCCGACACAAAATA 57.381 30.769 0.00 0.00 0.00 1.40
4807 6290 8.119226 GGTTTCTAAATCAATCAAGATGAGACG 58.881 37.037 0.00 0.00 0.00 4.18
4923 6522 3.612955 GCAATAAAACAAGGGCACGCTTA 60.613 43.478 0.00 0.00 0.00 3.09
4925 6524 5.167845 CAATAAAACAAGGGCACGCTTAAT 58.832 37.500 0.00 0.00 0.00 1.40
4927 6526 4.857509 AAAACAAGGGCACGCTTAATTA 57.142 36.364 0.00 0.00 0.00 1.40
4932 6531 6.518208 ACAAGGGCACGCTTAATTATTTTA 57.482 33.333 0.00 0.00 0.00 1.52
4933 6532 6.560711 ACAAGGGCACGCTTAATTATTTTAG 58.439 36.000 0.00 0.00 0.00 1.85
4979 6597 2.051345 CGCACGTGTTTTGGCCTC 60.051 61.111 18.38 0.00 0.00 4.70
5025 6643 8.152309 GGTACGTTTAGATGTCTGATAGTACT 57.848 38.462 0.00 0.00 31.73 2.73
5026 6644 8.619546 GGTACGTTTAGATGTCTGATAGTACTT 58.380 37.037 0.00 0.00 31.73 2.24
5027 6645 9.649024 GTACGTTTAGATGTCTGATAGTACTTC 57.351 37.037 0.00 0.00 30.17 3.01
5028 6646 8.277490 ACGTTTAGATGTCTGATAGTACTTCA 57.723 34.615 0.00 4.22 0.00 3.02
5029 6647 8.904834 ACGTTTAGATGTCTGATAGTACTTCAT 58.095 33.333 0.00 0.00 0.00 2.57
5030 6648 9.388346 CGTTTAGATGTCTGATAGTACTTCATC 57.612 37.037 0.00 0.00 0.00 2.92
5031 6649 9.685828 GTTTAGATGTCTGATAGTACTTCATCC 57.314 37.037 0.00 0.09 33.16 3.51
5032 6650 6.567687 AGATGTCTGATAGTACTTCATCCG 57.432 41.667 0.00 0.00 33.16 4.18
5033 6651 6.065374 AGATGTCTGATAGTACTTCATCCGT 58.935 40.000 0.00 0.71 33.16 4.69
5034 6652 6.547880 AGATGTCTGATAGTACTTCATCCGTT 59.452 38.462 0.00 0.00 33.16 4.44
5035 6653 6.132791 TGTCTGATAGTACTTCATCCGTTC 57.867 41.667 0.00 0.00 0.00 3.95
5036 6654 5.067413 TGTCTGATAGTACTTCATCCGTTCC 59.933 44.000 0.00 0.00 0.00 3.62
5037 6655 4.275196 TCTGATAGTACTTCATCCGTTCCG 59.725 45.833 0.00 0.00 0.00 4.30
5038 6656 4.201657 TGATAGTACTTCATCCGTTCCGA 58.798 43.478 0.00 0.00 0.00 4.55
5039 6657 4.641541 TGATAGTACTTCATCCGTTCCGAA 59.358 41.667 0.00 0.00 0.00 4.30
5040 6658 5.301045 TGATAGTACTTCATCCGTTCCGAAT 59.699 40.000 0.00 0.00 0.00 3.34
5041 6659 4.467198 AGTACTTCATCCGTTCCGAATT 57.533 40.909 0.00 0.00 0.00 2.17
5042 6660 5.587388 AGTACTTCATCCGTTCCGAATTA 57.413 39.130 0.00 0.00 0.00 1.40
5043 6661 5.346522 AGTACTTCATCCGTTCCGAATTAC 58.653 41.667 0.00 0.00 0.00 1.89
5044 6662 4.467198 ACTTCATCCGTTCCGAATTACT 57.533 40.909 0.00 0.00 0.00 2.24
5045 6663 4.828829 ACTTCATCCGTTCCGAATTACTT 58.171 39.130 0.00 0.00 0.00 2.24
5046 6664 4.630069 ACTTCATCCGTTCCGAATTACTTG 59.370 41.667 0.00 0.00 0.00 3.16
5047 6665 4.196626 TCATCCGTTCCGAATTACTTGT 57.803 40.909 0.00 0.00 0.00 3.16
5048 6666 4.178540 TCATCCGTTCCGAATTACTTGTC 58.821 43.478 0.00 0.00 0.00 3.18
5049 6667 3.663995 TCCGTTCCGAATTACTTGTCA 57.336 42.857 0.00 0.00 0.00 3.58
5050 6668 3.319755 TCCGTTCCGAATTACTTGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
5051 6669 3.061322 CCGTTCCGAATTACTTGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
5052 6670 3.495377 CCGTTCCGAATTACTTGTCACAA 59.505 43.478 0.00 0.00 0.00 3.33
5053 6671 4.024725 CCGTTCCGAATTACTTGTCACAAA 60.025 41.667 0.00 0.00 0.00 2.83
5054 6672 5.503498 CGTTCCGAATTACTTGTCACAAAA 58.497 37.500 0.00 0.00 0.00 2.44
5055 6673 5.966503 CGTTCCGAATTACTTGTCACAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
5056 6674 6.635239 CGTTCCGAATTACTTGTCACAAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
5057 6675 7.357206 CGTTCCGAATTACTTGTCACAAAAATG 60.357 37.037 0.00 0.00 0.00 2.32
5058 6676 7.265647 TCCGAATTACTTGTCACAAAAATGA 57.734 32.000 0.00 0.00 0.00 2.57
5059 6677 7.708051 TCCGAATTACTTGTCACAAAAATGAA 58.292 30.769 0.00 0.00 0.00 2.57
5060 6678 8.356657 TCCGAATTACTTGTCACAAAAATGAAT 58.643 29.630 0.00 0.00 0.00 2.57
5061 6679 8.427012 CCGAATTACTTGTCACAAAAATGAATG 58.573 33.333 0.00 0.00 0.00 2.67
5062 6680 8.967218 CGAATTACTTGTCACAAAAATGAATGT 58.033 29.630 0.00 0.00 0.00 2.71
5107 6725 9.914131 TCTAGATACATCCATTTTTACGATGAG 57.086 33.333 3.44 0.00 37.44 2.90
5108 6726 9.698309 CTAGATACATCCATTTTTACGATGAGT 57.302 33.333 3.44 0.00 37.44 3.41
5114 6732 9.787532 ACATCCATTTTTACGATGAGTAATTTG 57.212 29.630 3.44 0.00 44.03 2.32
5115 6733 9.236691 CATCCATTTTTACGATGAGTAATTTGG 57.763 33.333 0.00 7.49 44.03 3.28
5116 6734 8.568676 TCCATTTTTACGATGAGTAATTTGGA 57.431 30.769 0.00 10.38 44.03 3.53
5117 6735 9.015367 TCCATTTTTACGATGAGTAATTTGGAA 57.985 29.630 11.32 0.00 44.03 3.53
5118 6736 9.072294 CCATTTTTACGATGAGTAATTTGGAAC 57.928 33.333 0.00 0.00 44.03 3.62
5119 6737 8.785101 CATTTTTACGATGAGTAATTTGGAACG 58.215 33.333 0.00 0.00 44.03 3.95
5120 6738 6.411630 TTTACGATGAGTAATTTGGAACGG 57.588 37.500 0.00 0.00 44.03 4.44
5121 6739 4.196626 ACGATGAGTAATTTGGAACGGA 57.803 40.909 0.00 0.00 0.00 4.69
5122 6740 4.181578 ACGATGAGTAATTTGGAACGGAG 58.818 43.478 0.00 0.00 0.00 4.63
5123 6741 4.081862 ACGATGAGTAATTTGGAACGGAGA 60.082 41.667 0.00 0.00 0.00 3.71
5124 6742 4.868171 CGATGAGTAATTTGGAACGGAGAA 59.132 41.667 0.00 0.00 0.00 2.87
5125 6743 5.350365 CGATGAGTAATTTGGAACGGAGAAA 59.650 40.000 0.00 0.00 0.00 2.52
5126 6744 6.455646 CGATGAGTAATTTGGAACGGAGAAAG 60.456 42.308 0.00 0.00 0.00 2.62
5183 6805 6.519679 TTGATTTGATTGAAGGGACATCAG 57.480 37.500 0.00 0.00 37.36 2.90
5197 6819 2.543012 GACATCAGATTGCATCGACCAG 59.457 50.000 0.00 0.00 0.00 4.00
5318 6972 1.077089 GAGCACTTCGTAAGTCGGCC 61.077 60.000 0.00 0.00 40.46 6.13
5321 6975 1.080025 ACTTCGTAAGTCGGCCTGC 60.080 57.895 0.00 0.00 37.02 4.85
5375 7029 9.825972 ACAACATCACAAGACTTTATTAATTCG 57.174 29.630 0.00 0.00 0.00 3.34
5376 7030 9.825972 CAACATCACAAGACTTTATTAATTCGT 57.174 29.630 0.00 0.00 0.00 3.85
5393 7047 8.618702 TTAATTCGTTACAATGTTTACAGGGA 57.381 30.769 0.00 0.00 0.00 4.20
5394 7048 5.927954 TTCGTTACAATGTTTACAGGGAC 57.072 39.130 0.00 0.00 0.00 4.46
5395 7049 4.958509 TCGTTACAATGTTTACAGGGACA 58.041 39.130 0.00 0.00 0.00 4.02
5396 7050 5.553123 TCGTTACAATGTTTACAGGGACAT 58.447 37.500 0.00 0.00 38.08 3.06
5397 7051 6.699366 TCGTTACAATGTTTACAGGGACATA 58.301 36.000 0.00 0.00 35.55 2.29
5398 7052 6.814644 TCGTTACAATGTTTACAGGGACATAG 59.185 38.462 0.00 0.00 35.55 2.23
5399 7053 6.036735 CGTTACAATGTTTACAGGGACATAGG 59.963 42.308 0.00 0.00 35.55 2.57
5400 7054 5.514500 ACAATGTTTACAGGGACATAGGT 57.486 39.130 0.00 0.00 35.55 3.08
5401 7055 6.630203 ACAATGTTTACAGGGACATAGGTA 57.370 37.500 0.00 0.00 35.55 3.08
5402 7056 7.208064 ACAATGTTTACAGGGACATAGGTAT 57.792 36.000 0.00 0.00 35.55 2.73
5403 7057 7.639378 ACAATGTTTACAGGGACATAGGTATT 58.361 34.615 0.00 0.00 35.55 1.89
5404 7058 8.113462 ACAATGTTTACAGGGACATAGGTATTT 58.887 33.333 0.00 0.00 35.55 1.40
5405 7059 8.966868 CAATGTTTACAGGGACATAGGTATTTT 58.033 33.333 0.00 0.00 35.55 1.82
5406 7060 9.541884 AATGTTTACAGGGACATAGGTATTTTT 57.458 29.630 0.00 0.00 35.55 1.94
5427 7081 6.930667 TTTTTGAGTAACTTAAGTCGGCTT 57.069 33.333 7.72 7.72 38.66 4.35
5428 7082 5.917541 TTTGAGTAACTTAAGTCGGCTTG 57.082 39.130 13.69 0.00 36.22 4.01
5429 7083 3.323243 TGAGTAACTTAAGTCGGCTTGC 58.677 45.455 13.69 0.00 36.22 4.01
5430 7084 3.006537 TGAGTAACTTAAGTCGGCTTGCT 59.993 43.478 13.69 1.38 36.22 3.91
5431 7085 3.586892 AGTAACTTAAGTCGGCTTGCTC 58.413 45.455 13.69 0.00 36.22 4.26
5432 7086 2.543777 AACTTAAGTCGGCTTGCTCA 57.456 45.000 13.69 0.00 36.22 4.26
5433 7087 2.543777 ACTTAAGTCGGCTTGCTCAA 57.456 45.000 13.69 0.00 36.22 3.02
5434 7088 3.059352 ACTTAAGTCGGCTTGCTCAAT 57.941 42.857 13.69 0.00 36.22 2.57
5435 7089 2.744202 ACTTAAGTCGGCTTGCTCAATG 59.256 45.455 13.69 0.00 36.22 2.82
5436 7090 2.760634 TAAGTCGGCTTGCTCAATGA 57.239 45.000 13.69 0.00 36.22 2.57
5437 7091 2.119801 AAGTCGGCTTGCTCAATGAT 57.880 45.000 0.00 0.00 32.92 2.45
5438 7092 2.988010 AGTCGGCTTGCTCAATGATA 57.012 45.000 0.00 0.00 0.00 2.15
5439 7093 3.266510 AGTCGGCTTGCTCAATGATAA 57.733 42.857 0.00 0.00 0.00 1.75
5440 7094 3.609853 AGTCGGCTTGCTCAATGATAAA 58.390 40.909 0.00 0.00 0.00 1.40
5441 7095 4.009675 AGTCGGCTTGCTCAATGATAAAA 58.990 39.130 0.00 0.00 0.00 1.52
5442 7096 4.095483 AGTCGGCTTGCTCAATGATAAAAG 59.905 41.667 0.00 0.00 0.00 2.27
5443 7097 4.094887 GTCGGCTTGCTCAATGATAAAAGA 59.905 41.667 4.54 0.00 0.00 2.52
5444 7098 4.094887 TCGGCTTGCTCAATGATAAAAGAC 59.905 41.667 4.54 1.20 0.00 3.01
5445 7099 4.142622 CGGCTTGCTCAATGATAAAAGACA 60.143 41.667 6.43 0.00 0.00 3.41
5446 7100 5.338365 GGCTTGCTCAATGATAAAAGACAG 58.662 41.667 4.54 0.00 0.00 3.51
5447 7101 5.124457 GGCTTGCTCAATGATAAAAGACAGA 59.876 40.000 4.54 0.00 0.00 3.41
5448 7102 6.256686 GCTTGCTCAATGATAAAAGACAGAG 58.743 40.000 4.54 0.00 0.00 3.35
5449 7103 6.128063 GCTTGCTCAATGATAAAAGACAGAGT 60.128 38.462 4.54 0.00 0.00 3.24
5450 7104 7.065085 GCTTGCTCAATGATAAAAGACAGAGTA 59.935 37.037 4.54 0.00 0.00 2.59
5451 7105 8.484641 TTGCTCAATGATAAAAGACAGAGTAG 57.515 34.615 0.00 0.00 0.00 2.57
5452 7106 7.615403 TGCTCAATGATAAAAGACAGAGTAGT 58.385 34.615 0.00 0.00 0.00 2.73
5453 7107 8.097038 TGCTCAATGATAAAAGACAGAGTAGTT 58.903 33.333 0.00 0.00 0.00 2.24
5454 7108 8.940952 GCTCAATGATAAAAGACAGAGTAGTTT 58.059 33.333 0.00 0.00 0.00 2.66
5460 7114 8.761497 TGATAAAAGACAGAGTAGTTTTCAACG 58.239 33.333 0.00 0.00 36.23 4.10
5461 7115 8.882415 ATAAAAGACAGAGTAGTTTTCAACGA 57.118 30.769 0.00 0.00 36.23 3.85
5462 7116 7.605410 AAAAGACAGAGTAGTTTTCAACGAA 57.395 32.000 0.00 0.00 36.23 3.85
5463 7117 7.605410 AAAGACAGAGTAGTTTTCAACGAAA 57.395 32.000 0.00 0.00 36.23 3.46
5464 7118 7.787725 AAGACAGAGTAGTTTTCAACGAAAT 57.212 32.000 0.00 0.00 36.23 2.17
5465 7119 7.409465 AGACAGAGTAGTTTTCAACGAAATC 57.591 36.000 0.00 0.00 36.23 2.17
5466 7120 6.984474 AGACAGAGTAGTTTTCAACGAAATCA 59.016 34.615 0.00 0.00 36.23 2.57
5467 7121 6.945072 ACAGAGTAGTTTTCAACGAAATCAC 58.055 36.000 0.00 0.00 36.23 3.06
5468 7122 6.761714 ACAGAGTAGTTTTCAACGAAATCACT 59.238 34.615 0.00 0.00 36.23 3.41
5469 7123 7.924412 ACAGAGTAGTTTTCAACGAAATCACTA 59.076 33.333 0.00 0.00 36.23 2.74
5470 7124 8.761497 CAGAGTAGTTTTCAACGAAATCACTAA 58.239 33.333 0.00 0.00 31.22 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.662438 GCAGGGAGTCGGTGAGAGAG 61.662 65.000 0.00 0.00 0.00 3.20
2 3 1.679305 GCAGGGAGTCGGTGAGAGA 60.679 63.158 0.00 0.00 0.00 3.10
3 4 2.888863 GCAGGGAGTCGGTGAGAG 59.111 66.667 0.00 0.00 0.00 3.20
4 5 2.838748 ATCGCAGGGAGTCGGTGAGA 62.839 60.000 0.00 0.38 33.90 3.27
5 6 1.949847 AATCGCAGGGAGTCGGTGAG 61.950 60.000 0.00 0.00 33.90 3.51
6 7 1.945354 GAATCGCAGGGAGTCGGTGA 61.945 60.000 0.00 0.00 34.81 4.02
7 8 1.519455 GAATCGCAGGGAGTCGGTG 60.519 63.158 0.00 0.00 29.08 4.94
8 9 2.722201 GGAATCGCAGGGAGTCGGT 61.722 63.158 8.65 0.00 40.60 4.69
9 10 2.107141 GGAATCGCAGGGAGTCGG 59.893 66.667 8.65 0.00 40.60 4.79
10 11 2.107141 GGGAATCGCAGGGAGTCG 59.893 66.667 8.65 0.00 40.60 4.18
11 12 2.506472 GGGGAATCGCAGGGAGTC 59.494 66.667 6.38 6.38 39.00 3.36
12 13 3.470888 CGGGGAATCGCAGGGAGT 61.471 66.667 0.00 0.00 0.00 3.85
13 14 4.241555 CCGGGGAATCGCAGGGAG 62.242 72.222 8.53 0.00 0.00 4.30
15 16 4.109675 AACCGGGGAATCGCAGGG 62.110 66.667 19.18 12.18 0.00 4.45
16 17 2.513897 GAACCGGGGAATCGCAGG 60.514 66.667 14.29 14.29 0.00 4.85
17 18 1.815421 CAGAACCGGGGAATCGCAG 60.815 63.158 6.32 0.00 0.00 5.18
18 19 1.622607 ATCAGAACCGGGGAATCGCA 61.623 55.000 6.32 0.00 0.00 5.10
19 20 0.880718 GATCAGAACCGGGGAATCGC 60.881 60.000 6.32 0.00 0.00 4.58
31 32 1.135094 GAGGCCATGGGAGATCAGAA 58.865 55.000 15.13 0.00 0.00 3.02
232 246 0.247736 AAACCGCAGTAGAGGAGCAG 59.752 55.000 0.00 0.00 38.21 4.24
233 247 0.246635 GAAACCGCAGTAGAGGAGCA 59.753 55.000 0.00 0.00 38.21 4.26
234 248 0.460459 GGAAACCGCAGTAGAGGAGC 60.460 60.000 0.00 0.00 38.21 4.70
237 287 4.496670 CGGAAACCGCAGTAGAGG 57.503 61.111 0.00 0.00 41.17 3.69
405 455 1.258445 AATTCTGTCGCCGTCCCTCT 61.258 55.000 0.00 0.00 0.00 3.69
438 488 2.606725 CGTCAGCTGGAAAGCTCAATAG 59.393 50.000 15.13 0.00 44.30 1.73
539 599 2.432628 GACCGACAGAGCCAACCG 60.433 66.667 0.00 0.00 0.00 4.44
590 654 2.869192 GACTTCGATGAAATCAGAGCCC 59.131 50.000 5.16 0.00 45.97 5.19
697 764 0.678684 AACGATTAAGGGCCAACGGG 60.679 55.000 6.18 0.00 37.18 5.28
754 845 6.183360 ACACTAAGCAACTAAACTGGAGTACA 60.183 38.462 0.00 0.00 0.00 2.90
830 921 9.847224 AACATATTTATGACGAATAAACCCTCT 57.153 29.630 4.63 0.00 42.22 3.69
844 935 7.701539 AGCCAGTTCACAAACATATTTATGA 57.298 32.000 4.63 0.00 37.88 2.15
846 937 8.806146 AGAAAGCCAGTTCACAAACATATTTAT 58.194 29.630 0.00 0.00 37.88 1.40
852 943 5.009010 CAGTAGAAAGCCAGTTCACAAACAT 59.991 40.000 0.00 0.00 37.88 2.71
887 1007 4.991153 TGACTAAGGTGCAGATAGTCAG 57.009 45.455 22.66 4.28 46.34 3.51
889 1009 4.586841 AGGATGACTAAGGTGCAGATAGTC 59.413 45.833 19.35 19.35 43.66 2.59
893 1013 3.133721 GTGAGGATGACTAAGGTGCAGAT 59.866 47.826 0.00 0.00 0.00 2.90
905 1025 1.293924 CCTGCGATTGTGAGGATGAC 58.706 55.000 0.00 0.00 0.00 3.06
929 1049 9.586435 GGGAAATAAAATATCAGTTCAGGTTTG 57.414 33.333 0.00 0.00 0.00 2.93
930 1050 9.547279 AGGGAAATAAAATATCAGTTCAGGTTT 57.453 29.630 0.00 0.00 0.00 3.27
980 1100 4.101585 TCATTATACCCTGCTCTGGTCAAG 59.898 45.833 0.00 0.00 37.31 3.02
1254 1374 0.458669 CCCATGCCTCATTCACAAGC 59.541 55.000 0.00 0.00 0.00 4.01
1287 1407 3.370061 GGCCACGAAAATACACTACAGAC 59.630 47.826 0.00 0.00 0.00 3.51
1311 1431 3.053896 GCAACGGTACCCACAGGC 61.054 66.667 6.25 0.00 36.11 4.85
1438 1562 9.634163 AACCGGACAATTTTCATTACTAATTTC 57.366 29.630 9.46 0.00 0.00 2.17
1448 1575 2.247358 AGGCAACCGGACAATTTTCAT 58.753 42.857 9.46 0.00 37.17 2.57
1450 1577 2.817844 ACTAGGCAACCGGACAATTTTC 59.182 45.455 9.46 0.00 37.17 2.29
1622 1754 1.256812 GCAAAGGGCTACAACACCAT 58.743 50.000 0.00 0.00 40.25 3.55
1646 1778 6.884280 AAGTTTGACCAACTCCATAGAAAG 57.116 37.500 0.00 0.00 45.77 2.62
2060 2196 8.286800 CACTATTTCAGGTTCGTTGTTCATTAA 58.713 33.333 0.00 0.00 0.00 1.40
2440 2576 1.755161 CCTGTACCATTCGACGATCG 58.245 55.000 14.88 14.88 42.10 3.69
2474 2610 9.424319 TGTAGAGTAGTTCTGAATTTAAAGCAG 57.576 33.333 12.35 12.35 36.61 4.24
2511 2648 2.299582 CCACCTCAATTGAATTGTGCCA 59.700 45.455 16.62 0.00 41.02 4.92
2576 2730 9.856162 TGTCCCTTCTATTAAAGTTTACTGTTT 57.144 29.630 0.00 0.00 0.00 2.83
2577 2731 9.281371 GTGTCCCTTCTATTAAAGTTTACTGTT 57.719 33.333 0.00 0.00 0.00 3.16
2578 2732 7.881751 GGTGTCCCTTCTATTAAAGTTTACTGT 59.118 37.037 0.00 0.00 0.00 3.55
2579 2733 8.101419 AGGTGTCCCTTCTATTAAAGTTTACTG 58.899 37.037 0.00 0.00 38.13 2.74
2580 2734 8.215954 AGGTGTCCCTTCTATTAAAGTTTACT 57.784 34.615 0.00 0.00 38.13 2.24
2581 2735 9.376075 GTAGGTGTCCCTTCTATTAAAGTTTAC 57.624 37.037 0.00 0.00 42.66 2.01
2582 2736 9.103582 TGTAGGTGTCCCTTCTATTAAAGTTTA 57.896 33.333 0.00 0.00 42.66 2.01
2583 2737 7.981142 TGTAGGTGTCCCTTCTATTAAAGTTT 58.019 34.615 0.00 0.00 42.66 2.66
2584 2738 7.456902 TCTGTAGGTGTCCCTTCTATTAAAGTT 59.543 37.037 0.00 0.00 42.66 2.66
2585 2739 6.958192 TCTGTAGGTGTCCCTTCTATTAAAGT 59.042 38.462 0.00 0.00 42.66 2.66
2586 2740 7.419711 TCTGTAGGTGTCCCTTCTATTAAAG 57.580 40.000 0.00 0.00 42.66 1.85
2587 2741 7.147549 CCATCTGTAGGTGTCCCTTCTATTAAA 60.148 40.741 0.00 0.00 42.66 1.52
2588 2742 6.326583 CCATCTGTAGGTGTCCCTTCTATTAA 59.673 42.308 0.00 0.00 42.66 1.40
2589 2743 5.839063 CCATCTGTAGGTGTCCCTTCTATTA 59.161 44.000 0.00 0.00 42.66 0.98
2590 2744 4.656112 CCATCTGTAGGTGTCCCTTCTATT 59.344 45.833 0.00 0.00 42.66 1.73
2591 2745 4.227197 CCATCTGTAGGTGTCCCTTCTAT 58.773 47.826 0.00 0.00 42.66 1.98
2592 2746 3.643237 CCATCTGTAGGTGTCCCTTCTA 58.357 50.000 0.00 0.00 42.66 2.10
2593 2747 2.472029 CCATCTGTAGGTGTCCCTTCT 58.528 52.381 0.00 0.00 42.66 2.85
2594 2748 1.134371 GCCATCTGTAGGTGTCCCTTC 60.134 57.143 0.00 0.00 42.66 3.46
2595 2749 0.912486 GCCATCTGTAGGTGTCCCTT 59.088 55.000 0.00 0.00 42.66 3.95
2596 2750 0.252696 TGCCATCTGTAGGTGTCCCT 60.253 55.000 0.00 0.00 45.51 4.20
2597 2751 0.618458 TTGCCATCTGTAGGTGTCCC 59.382 55.000 0.00 0.00 0.00 4.46
2598 2752 1.003118 TGTTGCCATCTGTAGGTGTCC 59.997 52.381 0.00 0.00 0.00 4.02
2599 2753 2.472695 TGTTGCCATCTGTAGGTGTC 57.527 50.000 0.00 0.00 0.00 3.67
2600 2754 2.884639 GTTTGTTGCCATCTGTAGGTGT 59.115 45.455 0.00 0.00 0.00 4.16
2601 2755 3.149196 AGTTTGTTGCCATCTGTAGGTG 58.851 45.455 0.00 0.00 0.00 4.00
2602 2756 3.508845 AGTTTGTTGCCATCTGTAGGT 57.491 42.857 0.00 0.00 0.00 3.08
2603 2757 4.853924 AAAGTTTGTTGCCATCTGTAGG 57.146 40.909 0.00 0.00 0.00 3.18
2604 2758 5.010012 AGGAAAAGTTTGTTGCCATCTGTAG 59.990 40.000 0.00 0.00 0.00 2.74
2605 2759 4.892934 AGGAAAAGTTTGTTGCCATCTGTA 59.107 37.500 0.00 0.00 0.00 2.74
2606 2760 3.706086 AGGAAAAGTTTGTTGCCATCTGT 59.294 39.130 0.00 0.00 0.00 3.41
2607 2761 4.326504 AGGAAAAGTTTGTTGCCATCTG 57.673 40.909 0.00 0.00 0.00 2.90
2608 2762 6.127196 TGTTTAGGAAAAGTTTGTTGCCATCT 60.127 34.615 0.00 0.00 0.00 2.90
2609 2763 6.045955 TGTTTAGGAAAAGTTTGTTGCCATC 58.954 36.000 0.00 0.00 0.00 3.51
2610 2764 5.983540 TGTTTAGGAAAAGTTTGTTGCCAT 58.016 33.333 0.00 0.00 0.00 4.40
2611 2765 5.046950 ACTGTTTAGGAAAAGTTTGTTGCCA 60.047 36.000 0.00 0.00 0.00 4.92
2612 2766 5.416083 ACTGTTTAGGAAAAGTTTGTTGCC 58.584 37.500 0.00 0.00 0.00 4.52
2613 2767 8.377681 GTTTACTGTTTAGGAAAAGTTTGTTGC 58.622 33.333 0.00 0.00 38.44 4.17
2614 2768 9.634163 AGTTTACTGTTTAGGAAAAGTTTGTTG 57.366 29.630 0.00 0.00 38.44 3.33
2724 2878 7.913674 TGCCAAAATAATGAAAACCCAATAC 57.086 32.000 0.00 0.00 0.00 1.89
2725 2879 8.105829 ACATGCCAAAATAATGAAAACCCAATA 58.894 29.630 0.00 0.00 0.00 1.90
2726 2880 6.947158 ACATGCCAAAATAATGAAAACCCAAT 59.053 30.769 0.00 0.00 0.00 3.16
2752 2908 6.042143 GCATGGTCTTGGTAAATTAATGGTG 58.958 40.000 0.00 0.00 0.00 4.17
2794 2950 9.186837 TCTCAATAAGGGTCGAGTATATTATCC 57.813 37.037 0.00 0.00 0.00 2.59
2810 2966 5.545723 ACATACTCCCTCCATCTCAATAAGG 59.454 44.000 0.00 0.00 0.00 2.69
2918 3078 8.791675 TGCAGATCATTTGTTTCAAGTGTTATA 58.208 29.630 0.00 0.00 0.00 0.98
2932 3092 8.920509 TGTATTTTCAGAATGCAGATCATTTG 57.079 30.769 0.00 0.00 44.95 2.32
3086 3246 6.920210 GGATATTTAGCTCCAACTGAAATTGC 59.080 38.462 0.00 0.00 0.00 3.56
3148 3311 7.674120 AGGATAACCGTATATACCCTGAAAAC 58.326 38.462 7.30 0.00 41.83 2.43
3233 3397 2.350863 AGTCCTTCCCTTCACCATCT 57.649 50.000 0.00 0.00 0.00 2.90
3539 4945 4.899239 GCCGATGACTGCTCCGGG 62.899 72.222 0.00 0.00 42.02 5.73
3611 5017 9.588096 TTCTCAAGTGCAGGATATACTATCTTA 57.412 33.333 0.00 0.00 0.00 2.10
3728 5134 3.684305 TCACTGAAATAATGACACTGGCG 59.316 43.478 0.00 0.00 0.00 5.69
3947 5366 8.876275 TTCAAAATCATTTTTCTCCTGACAAG 57.124 30.769 0.00 0.00 32.72 3.16
3957 5377 8.929746 GTTCCCAGAGATTCAAAATCATTTTTC 58.070 33.333 0.00 0.00 32.72 2.29
4065 5501 2.031682 CGTGCATAAATAGAAGCAGGGC 60.032 50.000 0.00 0.00 38.71 5.19
4066 5502 3.466836 TCGTGCATAAATAGAAGCAGGG 58.533 45.455 0.00 0.00 41.61 4.45
4067 5503 5.088141 CTTCGTGCATAAATAGAAGCAGG 57.912 43.478 0.00 0.00 42.37 4.85
4108 5546 0.542702 CCAAGATTGGGTTGTGGCCT 60.543 55.000 3.32 0.00 44.70 5.19
4109 5547 1.974543 CCAAGATTGGGTTGTGGCC 59.025 57.895 3.52 0.00 44.70 5.36
4236 5674 3.586961 TCGGAGAGCTCGATGGCG 61.587 66.667 8.37 0.00 37.29 5.69
4305 5743 1.205064 CTGCTTGCCGACGAACTTG 59.795 57.895 0.00 0.00 0.00 3.16
4356 5794 2.563261 TCATCCTCGCGACTAGGTAT 57.437 50.000 3.71 0.00 35.48 2.73
4392 5830 2.808523 TGGAGATCATCATGAGCGTC 57.191 50.000 0.09 0.00 37.94 5.19
4475 5913 1.796017 TTTCAAGAAACCCAACCCCC 58.204 50.000 0.00 0.00 0.00 5.40
4476 5914 3.916359 TTTTTCAAGAAACCCAACCCC 57.084 42.857 0.00 0.00 0.00 4.95
4511 5950 4.207955 ACTCCTTTTTCTGTTGAACCCTC 58.792 43.478 0.00 0.00 31.02 4.30
4599 6039 2.557490 AGGAAGAAAACGTAGAGCGACT 59.443 45.455 0.00 0.00 44.77 4.18
4605 6045 6.988622 TTGACAAAAGGAAGAAAACGTAGA 57.011 33.333 0.00 0.00 0.00 2.59
4717 6192 9.559958 CGAGTTTTTCTTCATAATTGTGCTTAT 57.440 29.630 0.00 0.00 0.00 1.73
4718 6193 8.564574 ACGAGTTTTTCTTCATAATTGTGCTTA 58.435 29.630 0.00 0.00 0.00 3.09
4807 6290 8.868744 TCAAACATAATAAAAATCACGTCGAC 57.131 30.769 5.18 5.18 0.00 4.20
4933 6532 1.515521 CTTGCGGTCAAGGGAACACC 61.516 60.000 4.81 0.00 44.53 4.16
4972 6590 2.669133 CGGTGATCCAGGAGGCCAA 61.669 63.158 5.01 0.00 33.74 4.52
4976 6594 1.672854 TAACGCGGTGATCCAGGAGG 61.673 60.000 7.07 0.00 0.00 4.30
4979 6597 0.810031 CCTTAACGCGGTGATCCAGG 60.810 60.000 7.07 0.00 0.00 4.45
5006 6624 8.568794 CGGATGAAGTACTATCAGACATCTAAA 58.431 37.037 0.00 0.00 34.86 1.85
5032 6650 7.646130 TCATTTTTGTGACAAGTAATTCGGAAC 59.354 33.333 0.00 0.00 0.00 3.62
5033 6651 7.708051 TCATTTTTGTGACAAGTAATTCGGAA 58.292 30.769 0.00 0.00 0.00 4.30
5034 6652 7.265647 TCATTTTTGTGACAAGTAATTCGGA 57.734 32.000 0.00 0.00 0.00 4.55
5035 6653 7.922505 TTCATTTTTGTGACAAGTAATTCGG 57.077 32.000 0.00 0.00 0.00 4.30
5036 6654 8.967218 ACATTCATTTTTGTGACAAGTAATTCG 58.033 29.630 0.00 0.00 0.00 3.34
5081 6699 9.914131 CTCATCGTAAAAATGGATGTATCTAGA 57.086 33.333 0.00 0.00 38.86 2.43
5082 6700 9.698309 ACTCATCGTAAAAATGGATGTATCTAG 57.302 33.333 0.80 0.00 38.86 2.43
5088 6706 9.787532 CAAATTACTCATCGTAAAAATGGATGT 57.212 29.630 0.80 0.00 41.17 3.06
5089 6707 9.236691 CCAAATTACTCATCGTAAAAATGGATG 57.763 33.333 0.00 0.00 41.17 3.51
5090 6708 9.184523 TCCAAATTACTCATCGTAAAAATGGAT 57.815 29.630 10.14 0.00 39.98 3.41
5091 6709 8.568676 TCCAAATTACTCATCGTAAAAATGGA 57.431 30.769 10.14 10.14 41.15 3.41
5092 6710 9.072294 GTTCCAAATTACTCATCGTAAAAATGG 57.928 33.333 0.00 0.00 41.17 3.16
5093 6711 8.785101 CGTTCCAAATTACTCATCGTAAAAATG 58.215 33.333 0.00 0.00 41.17 2.32
5094 6712 7.966204 CCGTTCCAAATTACTCATCGTAAAAAT 59.034 33.333 0.00 0.00 41.17 1.82
5095 6713 7.172875 TCCGTTCCAAATTACTCATCGTAAAAA 59.827 33.333 0.00 0.00 41.17 1.94
5096 6714 6.649973 TCCGTTCCAAATTACTCATCGTAAAA 59.350 34.615 0.00 0.00 41.17 1.52
5097 6715 6.164876 TCCGTTCCAAATTACTCATCGTAAA 58.835 36.000 0.00 0.00 41.17 2.01
5098 6716 5.722263 TCCGTTCCAAATTACTCATCGTAA 58.278 37.500 0.00 0.00 41.97 3.18
5099 6717 5.125900 TCTCCGTTCCAAATTACTCATCGTA 59.874 40.000 0.00 0.00 0.00 3.43
5100 6718 4.081862 TCTCCGTTCCAAATTACTCATCGT 60.082 41.667 0.00 0.00 0.00 3.73
5101 6719 4.430007 TCTCCGTTCCAAATTACTCATCG 58.570 43.478 0.00 0.00 0.00 3.84
5102 6720 6.371825 ACTTTCTCCGTTCCAAATTACTCATC 59.628 38.462 0.00 0.00 0.00 2.92
5103 6721 6.238648 ACTTTCTCCGTTCCAAATTACTCAT 58.761 36.000 0.00 0.00 0.00 2.90
5104 6722 5.617252 ACTTTCTCCGTTCCAAATTACTCA 58.383 37.500 0.00 0.00 0.00 3.41
5105 6723 7.845066 ATACTTTCTCCGTTCCAAATTACTC 57.155 36.000 0.00 0.00 0.00 2.59
5106 6724 8.631480 AAATACTTTCTCCGTTCCAAATTACT 57.369 30.769 0.00 0.00 0.00 2.24
5107 6725 8.727910 AGAAATACTTTCTCCGTTCCAAATTAC 58.272 33.333 0.00 0.00 46.62 1.89
5108 6726 8.857694 AGAAATACTTTCTCCGTTCCAAATTA 57.142 30.769 0.00 0.00 46.62 1.40
5109 6727 7.761038 AGAAATACTTTCTCCGTTCCAAATT 57.239 32.000 0.00 0.00 46.62 1.82
5110 6728 8.857694 TTAGAAATACTTTCTCCGTTCCAAAT 57.142 30.769 5.45 0.00 46.62 2.32
5111 6729 8.680039 TTTAGAAATACTTTCTCCGTTCCAAA 57.320 30.769 5.45 0.00 46.62 3.28
5112 6730 8.152246 TCTTTAGAAATACTTTCTCCGTTCCAA 58.848 33.333 5.45 0.00 46.62 3.53
5113 6731 7.673180 TCTTTAGAAATACTTTCTCCGTTCCA 58.327 34.615 5.45 0.00 46.62 3.53
5114 6732 8.543862 TTCTTTAGAAATACTTTCTCCGTTCC 57.456 34.615 5.45 0.00 46.62 3.62
5116 6734 9.557061 ACTTTCTTTAGAAATACTTTCTCCGTT 57.443 29.630 5.45 0.00 46.62 4.44
5117 6735 9.557061 AACTTTCTTTAGAAATACTTTCTCCGT 57.443 29.630 5.45 0.00 46.62 4.69
5349 7003 9.825972 CGAATTAATAAAGTCTTGTGATGTTGT 57.174 29.630 0.00 0.00 0.00 3.32
5350 7004 9.825972 ACGAATTAATAAAGTCTTGTGATGTTG 57.174 29.630 0.00 0.00 0.00 3.33
5367 7021 9.233649 TCCCTGTAAACATTGTAACGAATTAAT 57.766 29.630 0.00 0.00 0.00 1.40
5368 7022 8.505625 GTCCCTGTAAACATTGTAACGAATTAA 58.494 33.333 0.00 0.00 0.00 1.40
5369 7023 7.660617 TGTCCCTGTAAACATTGTAACGAATTA 59.339 33.333 0.00 0.00 0.00 1.40
5370 7024 6.487331 TGTCCCTGTAAACATTGTAACGAATT 59.513 34.615 0.00 0.00 0.00 2.17
5371 7025 5.998981 TGTCCCTGTAAACATTGTAACGAAT 59.001 36.000 0.00 0.00 0.00 3.34
5372 7026 5.366460 TGTCCCTGTAAACATTGTAACGAA 58.634 37.500 0.00 0.00 0.00 3.85
5373 7027 4.958509 TGTCCCTGTAAACATTGTAACGA 58.041 39.130 0.00 0.00 0.00 3.85
5374 7028 5.873179 ATGTCCCTGTAAACATTGTAACG 57.127 39.130 0.00 0.00 32.24 3.18
5375 7029 6.882678 ACCTATGTCCCTGTAAACATTGTAAC 59.117 38.462 0.00 0.00 37.33 2.50
5376 7030 7.023171 ACCTATGTCCCTGTAAACATTGTAA 57.977 36.000 0.00 0.00 37.33 2.41
5377 7031 6.630203 ACCTATGTCCCTGTAAACATTGTA 57.370 37.500 0.00 0.00 37.33 2.41
5378 7032 5.514500 ACCTATGTCCCTGTAAACATTGT 57.486 39.130 0.00 0.00 37.33 2.71
5379 7033 8.519799 AAATACCTATGTCCCTGTAAACATTG 57.480 34.615 0.00 0.00 37.33 2.82
5380 7034 9.541884 AAAAATACCTATGTCCCTGTAAACATT 57.458 29.630 0.00 0.00 37.33 2.71
5404 7058 6.721321 CAAGCCGACTTAAGTTACTCAAAAA 58.279 36.000 10.02 0.00 33.74 1.94
5405 7059 5.277634 GCAAGCCGACTTAAGTTACTCAAAA 60.278 40.000 10.02 0.00 33.74 2.44
5406 7060 4.212636 GCAAGCCGACTTAAGTTACTCAAA 59.787 41.667 10.02 0.00 33.74 2.69
5407 7061 3.744426 GCAAGCCGACTTAAGTTACTCAA 59.256 43.478 10.02 0.00 33.74 3.02
5408 7062 3.006537 AGCAAGCCGACTTAAGTTACTCA 59.993 43.478 10.02 0.00 33.74 3.41
5409 7063 3.586892 AGCAAGCCGACTTAAGTTACTC 58.413 45.455 10.02 0.00 33.74 2.59
5410 7064 3.006537 TGAGCAAGCCGACTTAAGTTACT 59.993 43.478 10.02 4.95 33.74 2.24
5411 7065 3.323243 TGAGCAAGCCGACTTAAGTTAC 58.677 45.455 10.02 2.59 33.74 2.50
5412 7066 3.671008 TGAGCAAGCCGACTTAAGTTA 57.329 42.857 10.02 0.00 33.74 2.24
5413 7067 2.543777 TGAGCAAGCCGACTTAAGTT 57.456 45.000 10.02 0.00 33.74 2.66
5414 7068 2.543777 TTGAGCAAGCCGACTTAAGT 57.456 45.000 8.13 8.13 33.74 2.24
5415 7069 3.002791 TCATTGAGCAAGCCGACTTAAG 58.997 45.455 0.00 0.00 33.74 1.85
5416 7070 3.052455 TCATTGAGCAAGCCGACTTAA 57.948 42.857 0.00 0.00 33.74 1.85
5417 7071 2.760634 TCATTGAGCAAGCCGACTTA 57.239 45.000 0.00 0.00 33.74 2.24
5418 7072 2.119801 ATCATTGAGCAAGCCGACTT 57.880 45.000 0.00 0.00 36.19 3.01
5419 7073 2.988010 TATCATTGAGCAAGCCGACT 57.012 45.000 0.00 0.00 0.00 4.18
5420 7074 4.094887 TCTTTTATCATTGAGCAAGCCGAC 59.905 41.667 0.00 0.00 0.00 4.79
5421 7075 4.094887 GTCTTTTATCATTGAGCAAGCCGA 59.905 41.667 0.00 0.00 0.00 5.54
5422 7076 4.142622 TGTCTTTTATCATTGAGCAAGCCG 60.143 41.667 0.00 0.00 0.00 5.52
5423 7077 5.124457 TCTGTCTTTTATCATTGAGCAAGCC 59.876 40.000 0.00 0.00 0.00 4.35
5424 7078 6.128063 ACTCTGTCTTTTATCATTGAGCAAGC 60.128 38.462 0.00 0.00 0.00 4.01
5425 7079 7.375106 ACTCTGTCTTTTATCATTGAGCAAG 57.625 36.000 0.00 0.00 0.00 4.01
5426 7080 8.097038 ACTACTCTGTCTTTTATCATTGAGCAA 58.903 33.333 0.00 0.00 0.00 3.91
5427 7081 7.615403 ACTACTCTGTCTTTTATCATTGAGCA 58.385 34.615 0.00 0.00 0.00 4.26
5428 7082 8.485976 AACTACTCTGTCTTTTATCATTGAGC 57.514 34.615 0.00 0.00 0.00 4.26
5434 7088 8.761497 CGTTGAAAACTACTCTGTCTTTTATCA 58.239 33.333 0.00 0.00 46.99 2.15
5435 7089 8.975439 TCGTTGAAAACTACTCTGTCTTTTATC 58.025 33.333 0.00 0.00 46.99 1.75
5436 7090 8.882415 TCGTTGAAAACTACTCTGTCTTTTAT 57.118 30.769 0.00 0.00 46.99 1.40
5437 7091 8.706492 TTCGTTGAAAACTACTCTGTCTTTTA 57.294 30.769 0.00 0.00 46.99 1.52
5438 7092 7.605410 TTCGTTGAAAACTACTCTGTCTTTT 57.395 32.000 0.00 0.00 46.99 2.27
5439 7093 7.605410 TTTCGTTGAAAACTACTCTGTCTTT 57.395 32.000 0.00 0.00 46.99 2.52
5440 7094 7.494625 TGATTTCGTTGAAAACTACTCTGTCTT 59.505 33.333 0.00 0.00 46.99 3.01
5441 7095 6.984474 TGATTTCGTTGAAAACTACTCTGTCT 59.016 34.615 0.00 0.00 46.99 3.41
5442 7096 7.042658 AGTGATTTCGTTGAAAACTACTCTGTC 60.043 37.037 0.00 0.00 46.99 3.51
5443 7097 6.761714 AGTGATTTCGTTGAAAACTACTCTGT 59.238 34.615 0.00 0.00 46.99 3.41
5444 7098 7.178712 AGTGATTTCGTTGAAAACTACTCTG 57.821 36.000 0.00 0.00 46.99 3.35
5445 7099 8.882415 TTAGTGATTTCGTTGAAAACTACTCT 57.118 30.769 0.00 0.00 46.99 3.24


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

AutoCloner maintained by Alex Coulton.