Multiple sequence alignment - TraesCS7B01G107100

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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 TraesCS7B01G107100 chr7B 100.000 4622 0 0 1 4622 123785390 123780769 0.000000e+00 8536.0
1 TraesCS7B01G107100 chr7B 94.595 111 6 0 4479 4589 695049285 695049395 6.150000e-39 172.0
2 TraesCS7B01G107100 chr7D 97.005 2771 69 6 914 3673 161482613 161479846 0.000000e+00 4645.0
3 TraesCS7B01G107100 chr7D 98.535 751 10 1 3735 4484 161479862 161479112 0.000000e+00 1325.0
4 TraesCS7B01G107100 chr7D 89.555 517 33 16 403 913 161483148 161482647 1.810000e-178 636.0
5 TraesCS7B01G107100 chr7D 90.351 342 20 8 1 332 161483513 161483175 1.970000e-118 436.0
6 TraesCS7B01G107100 chr7D 92.857 98 5 2 3194 3289 185552878 185552781 1.730000e-29 141.0
7 TraesCS7B01G107100 chr7D 90.291 103 9 1 3200 3301 231420157 231420055 2.900000e-27 134.0
8 TraesCS7B01G107100 chr7D 100.000 35 0 0 4588 4622 161479113 161479079 1.070000e-06 65.8
9 TraesCS7B01G107100 chr7D 88.000 50 4 1 3861 3910 187081900 187081947 1.800000e-04 58.4
10 TraesCS7B01G107100 chr7D 100.000 29 0 0 2995 3023 586784222 586784250 2.000000e-03 54.7
11 TraesCS7B01G107100 chr7A 90.419 1169 59 20 852 1986 162774504 162773355 0.000000e+00 1489.0
12 TraesCS7B01G107100 chr7A 92.162 791 39 10 34 816 162776074 162775299 0.000000e+00 1096.0
13 TraesCS7B01G107100 chr7A 91.392 395 29 3 3284 3673 162772432 162772038 1.890000e-148 536.0
14 TraesCS7B01G107100 chr7A 83.102 432 60 7 2524 2951 162773054 162772632 9.380000e-102 381.0
15 TraesCS7B01G107100 chr7A 90.877 285 23 2 1974 2257 162773337 162773055 3.380000e-101 379.0
16 TraesCS7B01G107100 chr7A 92.414 145 11 0 2284 2428 634932984 634933128 1.690000e-49 207.0
17 TraesCS7B01G107100 chr7A 91.724 145 10 2 3058 3201 162772573 162772430 2.820000e-47 200.0
18 TraesCS7B01G107100 chr7A 95.146 103 5 0 2423 2525 498590283 498590385 3.700000e-36 163.0
19 TraesCS7B01G107100 chr7A 100.000 28 0 0 2995 3022 234912141 234912168 8.000000e-03 52.8
20 TraesCS7B01G107100 chr5A 79.504 605 78 24 1594 2176 11945637 11946217 5.610000e-104 388.0
21 TraesCS7B01G107100 chr5A 86.905 84 7 4 3674 3757 123569718 123569639 1.770000e-14 91.6
22 TraesCS7B01G107100 chr2A 79.208 606 78 26 1594 2176 4023832 4024412 1.210000e-100 377.0
23 TraesCS7B01G107100 chr2A 92.857 98 6 1 3199 3295 498099530 498099433 1.730000e-29 141.0
24 TraesCS7B01G107100 chr2A 92.683 82 3 3 3672 3751 676079579 676079659 1.050000e-21 115.0
25 TraesCS7B01G107100 chr2A 97.059 34 1 0 2995 3028 2908899 2908866 1.800000e-04 58.4
26 TraesCS7B01G107100 chr6A 93.750 144 9 0 2285 2428 119757556 119757699 2.800000e-52 217.0
27 TraesCS7B01G107100 chr6A 100.000 30 0 0 3881 3910 346567131 346567102 6.460000e-04 56.5
28 TraesCS7B01G107100 chr5B 93.103 145 9 1 2286 2429 706457974 706458118 1.300000e-50 211.0
29 TraesCS7B01G107100 chr2D 93.571 140 9 0 2287 2426 630719577 630719438 4.690000e-50 209.0
30 TraesCS7B01G107100 chr2D 92.857 98 5 2 3202 3297 15682984 15682887 1.730000e-29 141.0
31 TraesCS7B01G107100 chr2D 93.827 81 1 4 3672 3750 136426751 136426829 8.120000e-23 119.0
32 TraesCS7B01G107100 chr2D 93.671 79 3 2 3672 3748 335683657 335683579 2.920000e-22 117.0
33 TraesCS7B01G107100 chr2D 91.667 84 4 3 3657 3739 529006647 529006728 3.780000e-21 113.0
34 TraesCS7B01G107100 chr2D 92.683 41 1 2 2995 3034 538315043 538315004 1.800000e-04 58.4
35 TraesCS7B01G107100 chr2D 100.000 30 0 0 3881 3910 607510265 607510236 6.460000e-04 56.5
36 TraesCS7B01G107100 chr6D 90.909 143 13 0 2284 2426 162248644 162248786 4.720000e-45 193.0
37 TraesCS7B01G107100 chr6D 93.137 102 5 2 2425 2526 327006505 327006604 1.040000e-31 148.0
38 TraesCS7B01G107100 chr6D 96.970 33 1 0 3878 3910 340997479 340997447 6.460000e-04 56.5
39 TraesCS7B01G107100 chr4B 92.913 127 9 0 2299 2425 663452960 663452834 7.900000e-43 185.0
40 TraesCS7B01G107100 chr4B 94.118 102 3 3 3194 3293 643774340 643774240 8.010000e-33 152.0
41 TraesCS7B01G107100 chr4B 95.556 90 3 1 3202 3290 104337414 104337325 4.820000e-30 143.0
42 TraesCS7B01G107100 chr4B 87.273 55 5 2 3883 3935 457413355 457413409 1.390000e-05 62.1
43 TraesCS7B01G107100 chr4B 85.484 62 5 3 2965 3022 673200693 673200632 1.390000e-05 62.1
44 TraesCS7B01G107100 chr4B 81.818 77 4 8 2959 3026 481601279 481601204 6.460000e-04 56.5
45 TraesCS7B01G107100 chr5D 93.333 120 7 1 4472 4590 555341184 555341065 4.750000e-40 176.0
46 TraesCS7B01G107100 chr5D 95.370 108 5 0 4482 4589 521523690 521523797 6.150000e-39 172.0
47 TraesCS7B01G107100 chr5D 90.909 110 8 2 2430 2538 113384628 113384736 3.730000e-31 147.0
48 TraesCS7B01G107100 chr5D 92.771 83 1 5 3672 3753 474217070 474217148 1.050000e-21 115.0
49 TraesCS7B01G107100 chr1B 95.370 108 5 0 4482 4589 113565123 113565230 6.150000e-39 172.0
50 TraesCS7B01G107100 chr1B 90.909 88 3 5 3672 3758 26635608 26635525 3.780000e-21 113.0
51 TraesCS7B01G107100 chr1B 97.143 35 0 1 2995 3029 586056777 586056810 1.800000e-04 58.4
52 TraesCS7B01G107100 chr4D 93.860 114 6 1 4476 4589 401095006 401095118 2.210000e-38 171.0
53 TraesCS7B01G107100 chr4D 94.444 36 0 1 3875 3910 372361600 372361567 2.000000e-03 54.7
54 TraesCS7B01G107100 chr4A 91.803 122 10 0 4476 4597 656482976 656483097 2.210000e-38 171.0
55 TraesCS7B01G107100 chr4A 93.204 103 7 0 2425 2527 60654185 60654287 8.010000e-33 152.0
56 TraesCS7B01G107100 chr4A 92.683 82 3 3 3672 3753 220752912 220752834 1.050000e-21 115.0
57 TraesCS7B01G107100 chr3D 94.545 110 6 0 4480 4589 107065385 107065494 2.210000e-38 171.0
58 TraesCS7B01G107100 chr3D 88.889 135 15 0 2287 2421 308761934 308762068 2.860000e-37 167.0
59 TraesCS7B01G107100 chr3D 90.000 110 7 4 3180 3286 303788434 303788542 6.240000e-29 139.0
60 TraesCS7B01G107100 chr1A 93.103 116 7 1 4474 4589 584968690 584968576 7.950000e-38 169.0
61 TraesCS7B01G107100 chr1A 86.508 126 14 3 2425 2548 16442904 16443028 8.070000e-28 135.0
62 TraesCS7B01G107100 chrUn 92.308 117 9 0 4482 4598 77885374 77885258 2.860000e-37 167.0
63 TraesCS7B01G107100 chrUn 93.137 102 5 2 2425 2526 476757008 476757107 1.040000e-31 148.0
64 TraesCS7B01G107100 chr3A 92.593 108 4 2 2425 2528 686191318 686191211 8.010000e-33 152.0
65 TraesCS7B01G107100 chr3A 89.474 114 10 1 2411 2522 177108964 177109077 4.820000e-30 143.0
66 TraesCS7B01G107100 chr6B 91.176 102 7 2 3187 3286 526034144 526034245 2.240000e-28 137.0
67 TraesCS7B01G107100 chr6B 93.827 81 2 3 3672 3752 81255867 81255944 8.120000e-23 119.0
68 TraesCS7B01G107100 chr3B 88.542 96 7 4 3672 3764 595691340 595691246 3.780000e-21 113.0
69 TraesCS7B01G107100 chr1D 94.595 37 1 1 3882 3918 322928430 322928395 6.460000e-04 56.5
70 TraesCS7B01G107100 chr2B 92.308 39 1 2 3873 3910 1273443 1273480 2.000000e-03 54.7
71 TraesCS7B01G107100 chr2B 94.286 35 1 1 2995 3029 641185530 641185497 8.000000e-03 52.8


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 TraesCS7B01G107100 chr7B 123780769 123785390 4621 True 8536.000000 8536 100.0000 1 4622 1 chr7B.!!$R1 4621
1 TraesCS7B01G107100 chr7D 161479079 161483513 4434 True 1421.560000 4645 95.0892 1 4622 5 chr7D.!!$R3 4621
2 TraesCS7B01G107100 chr7A 162772038 162776074 4036 True 680.166667 1489 89.9460 34 3673 6 chr7A.!!$R1 3639
3 TraesCS7B01G107100 chr5A 11945637 11946217 580 False 388.000000 388 79.5040 1594 2176 1 chr5A.!!$F1 582
4 TraesCS7B01G107100 chr2A 4023832 4024412 580 False 377.000000 377 79.2080 1594 2176 1 chr2A.!!$F1 582

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
768 793 0.945099 CGGACGATCGATCAGAAGGA 59.055 55.0 24.34 0.00 0.00 3.36 F
1787 2639 0.241213 TTCAGAACACGAGCTCCGAG 59.759 55.0 8.47 4.88 41.76 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 3137 1.003580 GAGGGAGTGGATTGTTGCTCA 59.996 52.381 0.0 0.0 0.0 4.26 R
3671 4574 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.0 0.0 0.0 3.85 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
42 52 8.635765 AATAGCTCTAGAAACAAATTCACCAA 57.364 30.769 0.00 0.00 40.72 3.67
147 157 4.988598 CGTGCTCCCGGTGCAGTT 62.989 66.667 17.93 0.00 41.41 3.16
148 158 2.594592 GTGCTCCCGGTGCAGTTT 60.595 61.111 17.93 0.00 41.41 2.66
180 190 4.527564 CCAACAAACGCTCTTAAGACAAG 58.472 43.478 0.00 0.00 0.00 3.16
183 193 4.694339 ACAAACGCTCTTAAGACAAGAGT 58.306 39.130 13.85 0.00 44.22 3.24
279 295 4.502171 TCACCACACAGCAACATAATTG 57.498 40.909 0.00 0.00 0.00 2.32
307 323 2.693591 TGTTCCTATGAGACGCCCTAAG 59.306 50.000 0.00 0.00 0.00 2.18
337 353 1.472376 GGTGCATCACTGGAGAGCTAC 60.472 57.143 0.00 0.00 34.40 3.58
350 366 2.100916 GAGAGCTACATGGACGCCTTAA 59.899 50.000 0.00 0.00 0.00 1.85
379 395 7.281324 TCTCAGCAGTCTCTACAATTACTAGTC 59.719 40.741 0.00 0.00 0.00 2.59
380 396 7.113437 TCAGCAGTCTCTACAATTACTAGTCT 58.887 38.462 0.00 0.00 0.00 3.24
405 428 6.661669 ACTAAACGTTATTCAACCGGAAAAG 58.338 36.000 9.46 0.00 39.39 2.27
526 550 3.044986 CAACAGGAACAACAATGAAGCG 58.955 45.455 0.00 0.00 0.00 4.68
758 782 4.271816 CCCCTGCTCGGACGATCG 62.272 72.222 14.88 14.88 33.16 3.69
759 783 3.209812 CCCTGCTCGGACGATCGA 61.210 66.667 24.34 0.00 37.60 3.59
760 784 2.556459 CCCTGCTCGGACGATCGAT 61.556 63.158 24.34 5.96 38.55 3.59
761 785 1.081774 CCTGCTCGGACGATCGATC 60.082 63.158 24.34 15.68 38.55 3.69
768 793 0.945099 CGGACGATCGATCAGAAGGA 59.055 55.000 24.34 0.00 0.00 3.36
778 803 3.449018 TCGATCAGAAGGAAGAGGAAAGG 59.551 47.826 0.00 0.00 0.00 3.11
790 815 1.077429 GGAAAGGCTTGGAGGCGAT 60.077 57.895 0.00 0.00 46.58 4.58
794 819 2.579684 AAGGCTTGGAGGCGATCGAC 62.580 60.000 21.57 18.32 46.58 4.20
816 841 2.726274 CGCGGCCCGATACTACTT 59.274 61.111 7.68 0.00 40.02 2.24
817 842 1.066918 CGCGGCCCGATACTACTTT 59.933 57.895 7.68 0.00 40.02 2.66
819 844 1.660167 GCGGCCCGATACTACTTTTT 58.340 50.000 7.68 0.00 0.00 1.94
875 1659 6.421801 CAGTTAATGGGCTTGTTTCAAGAAAG 59.578 38.462 12.77 0.00 0.00 2.62
879 1663 3.243839 TGGGCTTGTTTCAAGAAAGCATC 60.244 43.478 12.77 1.74 46.46 3.91
961 1778 3.535561 CTCTGGCTTATTACCACCACAG 58.464 50.000 0.00 0.00 32.49 3.66
967 1784 4.827284 GGCTTATTACCACCACAGCATAAT 59.173 41.667 0.00 0.00 0.00 1.28
974 1791 1.472082 CACCACAGCATAATTCGCCAA 59.528 47.619 0.00 0.00 0.00 4.52
1021 1838 4.351054 CGTTCCCCTGCTTGCCCT 62.351 66.667 0.00 0.00 0.00 5.19
1362 2183 5.461526 GTTTGGGACTTGCTTACTGAAATC 58.538 41.667 0.00 0.00 0.00 2.17
1385 2211 1.738099 CTTCGCAGTTCCCGACCTG 60.738 63.158 0.00 0.00 34.01 4.00
1424 2250 1.216710 CCTGAAGCGTGAGGAGGAC 59.783 63.158 0.00 0.00 0.00 3.85
1464 2290 4.218200 TGGAGGTGATGCTTTGTTGTTATG 59.782 41.667 0.00 0.00 0.00 1.90
1465 2291 4.458989 GGAGGTGATGCTTTGTTGTTATGA 59.541 41.667 0.00 0.00 0.00 2.15
1475 2301 5.810074 GCTTTGTTGTTATGAACCAAAGTGT 59.190 36.000 15.93 0.00 40.10 3.55
1511 2342 1.556911 AGGAACATGCATCGAGGAAGT 59.443 47.619 0.00 0.00 0.00 3.01
1531 2362 4.564041 AGTGCAGTCAGTCTTGATACTTG 58.436 43.478 0.00 0.00 35.39 3.16
1552 2383 0.246635 TGAGTAACGCCCTCTTCTGC 59.753 55.000 0.00 0.00 0.00 4.26
1625 2456 0.527565 CTGGGTTTGATTTCAGCGGG 59.472 55.000 0.00 0.00 0.00 6.13
1693 2529 7.633018 AGGTAATTCATATCTTTGCTCCCTA 57.367 36.000 0.00 0.00 0.00 3.53
1696 2532 8.103305 GGTAATTCATATCTTTGCTCCCTATGA 58.897 37.037 0.00 0.00 0.00 2.15
1757 2609 6.780457 ACTGAAGGGAAATTTATGATGGTG 57.220 37.500 0.00 0.00 0.00 4.17
1758 2610 6.256053 ACTGAAGGGAAATTTATGATGGTGT 58.744 36.000 0.00 0.00 0.00 4.16
1781 2633 1.195674 GCTTCCTTTCAGAACACGAGC 59.804 52.381 0.00 0.00 0.00 5.03
1787 2639 0.241213 TTCAGAACACGAGCTCCGAG 59.759 55.000 8.47 4.88 41.76 4.63
1894 2754 6.258727 ACAAAGAAGGCATGTTCTATATGACG 59.741 38.462 0.00 0.00 38.60 4.35
2210 3101 7.636259 TTCCAACTTGCATTTTTATTTCGAG 57.364 32.000 0.00 0.00 0.00 4.04
2296 3188 6.206829 GGAATTACTTGTCTTAGTGCCTGTTT 59.793 38.462 0.00 0.00 0.00 2.83
2315 3207 2.561037 GGCAACCCACCAACTTCCG 61.561 63.158 0.00 0.00 0.00 4.30
2403 3295 2.507324 GAGCGGAGTTGCGGAGTC 60.507 66.667 0.00 0.00 40.67 3.36
2412 3304 1.203523 AGTTGCGGAGTCAGAGTGATC 59.796 52.381 0.00 0.00 0.00 2.92
2592 3489 7.016072 TCTCCCATGTGTGTCCATTAAAATTTT 59.984 33.333 8.75 8.75 0.00 1.82
2743 3640 0.255318 AGCTGCTTCCTGAATCCTGG 59.745 55.000 0.00 0.00 0.00 4.45
2978 3875 8.314021 TCAGTGCTCTGTAAAGAAATAAGATCA 58.686 33.333 15.01 0.00 41.91 2.92
3015 3912 8.705594 TGGAGTTATATTTCTTTACAGAGGGAG 58.294 37.037 0.00 0.00 0.00 4.30
3216 4114 3.614568 TCTATTACTCCCTCTGTCCCC 57.385 52.381 0.00 0.00 0.00 4.81
3389 4290 1.213678 CCAGAGGGAATCCAGATTGCA 59.786 52.381 13.02 0.00 40.36 4.08
3423 4324 5.301045 CCAGAAAGATACACAGTATCGGGTA 59.699 44.000 10.51 0.00 0.00 3.69
3640 4541 7.123247 CCTCCTGATGTCCAAGATTAACAAATT 59.877 37.037 0.00 0.00 0.00 1.82
3665 4568 7.341445 AGTTTTTAGTTTCAGGTTGTATGCA 57.659 32.000 0.00 0.00 0.00 3.96
3666 4569 7.425606 AGTTTTTAGTTTCAGGTTGTATGCAG 58.574 34.615 0.00 0.00 0.00 4.41
3667 4570 7.284489 AGTTTTTAGTTTCAGGTTGTATGCAGA 59.716 33.333 0.00 0.00 0.00 4.26
3668 4571 7.759489 TTTTAGTTTCAGGTTGTATGCAGAT 57.241 32.000 0.00 0.00 0.00 2.90
3669 4572 6.741992 TTAGTTTCAGGTTGTATGCAGATG 57.258 37.500 0.00 0.00 0.00 2.90
3670 4573 4.655963 AGTTTCAGGTTGTATGCAGATGT 58.344 39.130 0.00 0.00 0.00 3.06
3671 4574 5.804639 AGTTTCAGGTTGTATGCAGATGTA 58.195 37.500 0.00 0.00 0.00 2.29
3672 4575 5.643777 AGTTTCAGGTTGTATGCAGATGTAC 59.356 40.000 0.00 0.00 0.00 2.90
3673 4576 4.137116 TCAGGTTGTATGCAGATGTACC 57.863 45.455 0.00 0.00 0.00 3.34
3674 4577 3.774766 TCAGGTTGTATGCAGATGTACCT 59.225 43.478 6.26 6.26 35.00 3.08
3675 4578 4.122776 CAGGTTGTATGCAGATGTACCTC 58.877 47.826 8.48 0.00 32.45 3.85
3676 4579 4.033709 AGGTTGTATGCAGATGTACCTCT 58.966 43.478 6.26 0.00 28.75 3.69
3677 4580 5.069119 CAGGTTGTATGCAGATGTACCTCTA 59.931 44.000 8.48 0.00 32.45 2.43
3678 4581 5.303078 AGGTTGTATGCAGATGTACCTCTAG 59.697 44.000 0.00 0.00 28.75 2.43
3679 4582 4.855715 TGTATGCAGATGTACCTCTAGC 57.144 45.455 0.00 7.71 0.00 3.42
3680 4583 3.574396 TGTATGCAGATGTACCTCTAGCC 59.426 47.826 14.86 4.11 0.00 3.93
3681 4584 2.461300 TGCAGATGTACCTCTAGCCT 57.539 50.000 14.86 0.00 0.00 4.58
3682 4585 3.595190 TGCAGATGTACCTCTAGCCTA 57.405 47.619 14.86 1.86 0.00 3.93
3683 4586 3.223435 TGCAGATGTACCTCTAGCCTAC 58.777 50.000 14.86 0.00 0.00 3.18
3684 4587 2.559231 GCAGATGTACCTCTAGCCTACC 59.441 54.545 0.00 0.00 0.00 3.18
3685 4588 3.158676 CAGATGTACCTCTAGCCTACCC 58.841 54.545 0.00 0.00 0.00 3.69
3686 4589 2.110365 AGATGTACCTCTAGCCTACCCC 59.890 54.545 0.00 0.00 0.00 4.95
3687 4590 1.311880 TGTACCTCTAGCCTACCCCA 58.688 55.000 0.00 0.00 0.00 4.96
3688 4591 1.647506 TGTACCTCTAGCCTACCCCAA 59.352 52.381 0.00 0.00 0.00 4.12
3689 4592 2.037901 GTACCTCTAGCCTACCCCAAC 58.962 57.143 0.00 0.00 0.00 3.77
3690 4593 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
3691 4594 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
3692 4595 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
3693 4596 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
3694 4597 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
3695 4598 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
3696 4599 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
3707 4610 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
3708 4611 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
3709 4612 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
3710 4613 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
3711 4614 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
3712 4615 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
3713 4616 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
3714 4617 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
3715 4618 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
3716 4619 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
3717 4620 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
3718 4621 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
3719 4622 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
3720 4623 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
3721 4624 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
3722 4625 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
3723 4626 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
3724 4627 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
3725 4628 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
3726 4629 4.384940 AGGCTTTGTTGTTGTTGTTGTTT 58.615 34.783 0.00 0.00 0.00 2.83
3727 4630 4.213059 AGGCTTTGTTGTTGTTGTTGTTTG 59.787 37.500 0.00 0.00 0.00 2.93
3728 4631 4.024472 GGCTTTGTTGTTGTTGTTGTTTGT 60.024 37.500 0.00 0.00 0.00 2.83
3729 4632 5.504830 GGCTTTGTTGTTGTTGTTGTTTGTT 60.505 36.000 0.00 0.00 0.00 2.83
3730 4633 5.394904 GCTTTGTTGTTGTTGTTGTTTGTTG 59.605 36.000 0.00 0.00 0.00 3.33
3731 4634 6.422776 TTTGTTGTTGTTGTTGTTTGTTGT 57.577 29.167 0.00 0.00 0.00 3.32
3732 4635 6.422776 TTGTTGTTGTTGTTGTTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
3733 4636 6.422776 TGTTGTTGTTGTTGTTTGTTGTTT 57.577 29.167 0.00 0.00 0.00 2.83
3734 4637 6.250819 TGTTGTTGTTGTTGTTTGTTGTTTG 58.749 32.000 0.00 0.00 0.00 2.93
3735 4638 6.128282 TGTTGTTGTTGTTGTTTGTTGTTTGT 60.128 30.769 0.00 0.00 0.00 2.83
3736 4639 6.422776 TGTTGTTGTTGTTTGTTGTTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
3737 4640 6.250819 TGTTGTTGTTGTTTGTTGTTTGTTG 58.749 32.000 0.00 0.00 0.00 3.33
3738 4641 6.128282 TGTTGTTGTTGTTTGTTGTTTGTTGT 60.128 30.769 0.00 0.00 0.00 3.32
3739 4642 7.064134 TGTTGTTGTTGTTTGTTGTTTGTTGTA 59.936 29.630 0.00 0.00 0.00 2.41
3740 4643 7.715265 TGTTGTTGTTTGTTGTTTGTTGTAT 57.285 28.000 0.00 0.00 0.00 2.29
3741 4644 7.567571 TGTTGTTGTTTGTTGTTTGTTGTATG 58.432 30.769 0.00 0.00 0.00 2.39
3742 4645 6.158175 TGTTGTTTGTTGTTTGTTGTATGC 57.842 33.333 0.00 0.00 0.00 3.14
3987 4890 2.355756 GCTCATCAAGGCATTTTCGCTA 59.644 45.455 0.00 0.00 0.00 4.26
3994 4897 5.676552 TCAAGGCATTTTCGCTAAGGTATA 58.323 37.500 0.00 0.00 0.00 1.47
4216 5119 3.196039 CCATTTCTGGACATGGCAAATGA 59.804 43.478 19.43 1.96 46.37 2.57
4350 5253 2.368548 TCACAAAGCTAGCCTTGAGTGA 59.631 45.455 28.52 22.12 42.34 3.41
4355 5258 5.218139 CAAAGCTAGCCTTGAGTGAAAAAG 58.782 41.667 19.42 0.00 33.01 2.27
4356 5259 4.092116 AGCTAGCCTTGAGTGAAAAAGT 57.908 40.909 12.13 0.00 0.00 2.66
4421 5325 9.628500 AACTACCTTAAGAATTGAAAACTCAGT 57.372 29.630 3.36 0.00 0.00 3.41
4460 5364 2.418368 TGGTCACAAGCAAGTCAGTT 57.582 45.000 0.00 0.00 0.00 3.16
4483 5387 3.263425 AGCCAAATTCTTTCTCCGACCTA 59.737 43.478 0.00 0.00 0.00 3.08
4484 5388 3.374367 GCCAAATTCTTTCTCCGACCTAC 59.626 47.826 0.00 0.00 0.00 3.18
4485 5389 4.833390 CCAAATTCTTTCTCCGACCTACT 58.167 43.478 0.00 0.00 0.00 2.57
4486 5390 4.870991 CCAAATTCTTTCTCCGACCTACTC 59.129 45.833 0.00 0.00 0.00 2.59
4487 5391 4.739587 AATTCTTTCTCCGACCTACTCC 57.260 45.455 0.00 0.00 0.00 3.85
4488 5392 2.140839 TCTTTCTCCGACCTACTCCC 57.859 55.000 0.00 0.00 0.00 4.30
4489 5393 1.639628 TCTTTCTCCGACCTACTCCCT 59.360 52.381 0.00 0.00 0.00 4.20
4490 5394 2.025898 CTTTCTCCGACCTACTCCCTC 58.974 57.143 0.00 0.00 0.00 4.30
4491 5395 0.258194 TTCTCCGACCTACTCCCTCC 59.742 60.000 0.00 0.00 0.00 4.30
4492 5396 1.526455 CTCCGACCTACTCCCTCCG 60.526 68.421 0.00 0.00 0.00 4.63
4493 5397 2.268167 CTCCGACCTACTCCCTCCGT 62.268 65.000 0.00 0.00 0.00 4.69
4494 5398 1.379576 CCGACCTACTCCCTCCGTT 60.380 63.158 0.00 0.00 0.00 4.44
4495 5399 1.382692 CCGACCTACTCCCTCCGTTC 61.383 65.000 0.00 0.00 0.00 3.95
4496 5400 1.712977 CGACCTACTCCCTCCGTTCG 61.713 65.000 0.00 0.00 0.00 3.95
4497 5401 1.379576 ACCTACTCCCTCCGTTCGG 60.380 63.158 4.74 4.74 0.00 4.30
4498 5402 1.077212 CCTACTCCCTCCGTTCGGA 60.077 63.158 13.34 13.34 0.00 4.55
4499 5403 0.682209 CCTACTCCCTCCGTTCGGAA 60.682 60.000 14.79 0.04 33.41 4.30
4500 5404 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
4501 5405 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
4502 5406 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
4503 5407 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4504 5408 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4505 5409 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
4506 5410 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
4507 5411 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
4508 5412 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
4509 5413 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
4510 5414 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
4511 5415 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
4512 5416 3.495377 CCGTTCGGAATTACTTGTCACAA 59.505 43.478 5.19 0.00 0.00 3.33
4513 5417 4.377022 CCGTTCGGAATTACTTGTCACAAG 60.377 45.833 16.42 16.42 0.00 3.16
4514 5418 4.446385 CGTTCGGAATTACTTGTCACAAGA 59.554 41.667 24.73 2.64 0.00 3.02
4515 5419 5.050634 CGTTCGGAATTACTTGTCACAAGAA 60.051 40.000 24.73 13.64 0.00 2.52
4516 5420 6.347402 CGTTCGGAATTACTTGTCACAAGAAT 60.347 38.462 24.73 15.18 0.00 2.40
4517 5421 6.480524 TCGGAATTACTTGTCACAAGAATG 57.519 37.500 24.73 7.96 0.00 2.67
4518 5422 6.227522 TCGGAATTACTTGTCACAAGAATGA 58.772 36.000 24.73 9.81 0.00 2.57
4519 5423 6.708502 TCGGAATTACTTGTCACAAGAATGAA 59.291 34.615 24.73 11.98 0.00 2.57
4520 5424 6.797033 CGGAATTACTTGTCACAAGAATGAAC 59.203 38.462 24.73 9.97 0.00 3.18
4521 5425 6.797033 GGAATTACTTGTCACAAGAATGAACG 59.203 38.462 24.73 0.00 0.00 3.95
4522 5426 6.861065 ATTACTTGTCACAAGAATGAACGT 57.139 33.333 24.73 2.24 0.00 3.99
4523 5427 7.956420 ATTACTTGTCACAAGAATGAACGTA 57.044 32.000 24.73 1.21 0.00 3.57
4524 5428 7.956420 TTACTTGTCACAAGAATGAACGTAT 57.044 32.000 24.73 0.00 0.00 3.06
4525 5429 6.467723 ACTTGTCACAAGAATGAACGTATC 57.532 37.500 24.73 0.00 0.00 2.24
4526 5430 6.223852 ACTTGTCACAAGAATGAACGTATCT 58.776 36.000 24.73 0.00 0.00 1.98
4527 5431 7.375834 ACTTGTCACAAGAATGAACGTATCTA 58.624 34.615 24.73 0.00 0.00 1.98
4528 5432 8.035394 ACTTGTCACAAGAATGAACGTATCTAT 58.965 33.333 24.73 0.00 0.00 1.98
4529 5433 9.516314 CTTGTCACAAGAATGAACGTATCTATA 57.484 33.333 12.63 0.00 0.00 1.31
4530 5434 9.863845 TTGTCACAAGAATGAACGTATCTATAA 57.136 29.630 0.00 0.00 0.00 0.98
4531 5435 9.297586 TGTCACAAGAATGAACGTATCTATAAC 57.702 33.333 0.00 0.00 0.00 1.89
4532 5436 8.469902 GTCACAAGAATGAACGTATCTATAACG 58.530 37.037 0.00 0.00 45.64 3.18
4533 5437 8.400186 TCACAAGAATGAACGTATCTATAACGA 58.600 33.333 2.27 0.00 42.90 3.85
4534 5438 9.016623 CACAAGAATGAACGTATCTATAACGAA 57.983 33.333 2.27 0.00 42.90 3.85
4535 5439 9.577110 ACAAGAATGAACGTATCTATAACGAAA 57.423 29.630 2.27 0.00 42.90 3.46
4564 5468 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
4565 5469 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
4566 5470 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
4567 5471 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
4568 5472 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
4569 5473 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
4570 5474 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
4571 5475 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
4572 5476 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
4573 5477 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
4574 5478 7.607991 ACATTCATTTCTTGGACGAGTAATTCT 59.392 33.333 0.00 0.00 0.00 2.40
4575 5479 6.968131 TCATTTCTTGGACGAGTAATTCTG 57.032 37.500 0.00 0.00 0.00 3.02
4576 5480 6.697395 TCATTTCTTGGACGAGTAATTCTGA 58.303 36.000 0.00 0.00 0.00 3.27
4577 5481 7.158697 TCATTTCTTGGACGAGTAATTCTGAA 58.841 34.615 0.00 0.00 0.00 3.02
4578 5482 6.780706 TTTCTTGGACGAGTAATTCTGAAC 57.219 37.500 0.00 0.00 0.00 3.18
4579 5483 4.482386 TCTTGGACGAGTAATTCTGAACG 58.518 43.478 0.00 0.00 0.00 3.95
4580 5484 3.226346 TGGACGAGTAATTCTGAACGG 57.774 47.619 0.00 0.00 0.00 4.44
4581 5485 2.821378 TGGACGAGTAATTCTGAACGGA 59.179 45.455 0.00 0.00 0.00 4.69
4582 5486 3.119602 TGGACGAGTAATTCTGAACGGAG 60.120 47.826 0.00 0.00 0.00 4.63
4583 5487 3.436496 GACGAGTAATTCTGAACGGAGG 58.564 50.000 0.00 0.00 0.00 4.30
4584 5488 2.165845 ACGAGTAATTCTGAACGGAGGG 59.834 50.000 0.00 0.00 0.00 4.30
4585 5489 2.426024 CGAGTAATTCTGAACGGAGGGA 59.574 50.000 0.00 0.00 0.00 4.20
4586 5490 3.489398 CGAGTAATTCTGAACGGAGGGAG 60.489 52.174 0.00 0.00 0.00 4.30
4587 5491 3.442076 AGTAATTCTGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.885399 AGTTGGTGAATTTGTTTCTAGAGCTAT 59.115 33.333 0.00 0.00 35.23 2.97
39 49 8.437360 TCTTACTTGATATATTGCACAGTTGG 57.563 34.615 0.00 0.00 0.00 3.77
147 157 0.463620 GTTTGTTGGGAGCAGGCAAA 59.536 50.000 0.00 0.00 0.00 3.68
148 158 1.733402 CGTTTGTTGGGAGCAGGCAA 61.733 55.000 0.00 0.00 0.00 4.52
279 295 5.220796 GGGCGTCTCATAGGAACAAATTAAC 60.221 44.000 0.00 0.00 0.00 2.01
307 323 5.368145 TCCAGTGATGCACCAAGTATATTC 58.632 41.667 0.00 0.00 34.49 1.75
337 353 3.242870 GCTGAGAATTTAAGGCGTCCATG 60.243 47.826 0.00 0.00 0.00 3.66
350 366 7.846066 AGTAATTGTAGAGACTGCTGAGAATT 58.154 34.615 0.00 0.00 0.00 2.17
379 395 6.949578 TTCCGGTTGAATAACGTTTAGTAG 57.050 37.500 5.91 0.00 37.69 2.57
380 396 7.571059 GCTTTTCCGGTTGAATAACGTTTAGTA 60.571 37.037 5.91 0.00 37.69 1.82
385 401 3.315749 TGCTTTTCCGGTTGAATAACGTT 59.684 39.130 5.88 5.88 37.69 3.99
526 550 2.717809 GAGCGTTCGCCGAACAGTC 61.718 63.158 27.37 18.99 42.05 3.51
591 615 2.265739 GGTAACCGACCGAACCCC 59.734 66.667 0.00 0.00 38.87 4.95
758 782 3.199727 AGCCTTTCCTCTTCCTTCTGATC 59.800 47.826 0.00 0.00 0.00 2.92
759 783 3.188773 AGCCTTTCCTCTTCCTTCTGAT 58.811 45.455 0.00 0.00 0.00 2.90
760 784 2.625639 AGCCTTTCCTCTTCCTTCTGA 58.374 47.619 0.00 0.00 0.00 3.27
761 785 3.080319 CAAGCCTTTCCTCTTCCTTCTG 58.920 50.000 0.00 0.00 0.00 3.02
768 793 0.038890 GCCTCCAAGCCTTTCCTCTT 59.961 55.000 0.00 0.00 0.00 2.85
778 803 2.586357 GGTCGATCGCCTCCAAGC 60.586 66.667 11.09 0.00 0.00 4.01
875 1659 1.379642 CGAGCCCAGGGAAAAGATGC 61.380 60.000 10.89 0.00 0.00 3.91
879 1663 2.751837 GGCGAGCCCAGGGAAAAG 60.752 66.667 10.89 0.00 0.00 2.27
943 1760 1.352687 TGCTGTGGTGGTAATAAGCCA 59.647 47.619 0.00 0.00 0.00 4.75
948 1765 4.513692 GCGAATTATGCTGTGGTGGTAATA 59.486 41.667 0.00 0.00 0.00 0.98
961 1778 1.202348 GCTGCGTTGGCGAATTATGC 61.202 55.000 0.00 0.00 44.10 3.14
1335 2156 0.113580 TAAGCAAGTCCCAAACCCCC 59.886 55.000 0.00 0.00 0.00 5.40
1339 2160 4.911514 TTTCAGTAAGCAAGTCCCAAAC 57.088 40.909 0.00 0.00 0.00 2.93
1424 2250 3.066064 CCTCCACTTGTCTGATCTCGTAG 59.934 52.174 0.00 0.00 0.00 3.51
1464 2290 8.035984 AGCTACTATAGAAGAACACTTTGGTTC 58.964 37.037 6.78 0.00 45.87 3.62
1465 2291 7.908453 AGCTACTATAGAAGAACACTTTGGTT 58.092 34.615 6.78 0.00 0.00 3.67
1475 2301 7.505923 TGCATGTTCCTAGCTACTATAGAAGAA 59.494 37.037 6.78 0.00 0.00 2.52
1511 2342 4.871933 TCAAGTATCAAGACTGACTGCA 57.128 40.909 0.00 0.00 33.30 4.41
1514 2345 6.849085 ACTCATCAAGTATCAAGACTGACT 57.151 37.500 0.00 0.00 36.07 3.41
1531 2362 2.815478 CAGAAGAGGGCGTTACTCATC 58.185 52.381 6.06 3.89 37.43 2.92
1552 2383 5.645624 AGTACGACTGATGAGAATTGACAG 58.354 41.667 0.00 0.00 35.14 3.51
1625 2456 1.043224 CGTTGAACGACTGAGACGAC 58.957 55.000 13.13 5.48 46.05 4.34
1682 2513 2.617308 CAGCACATCATAGGGAGCAAAG 59.383 50.000 0.00 0.00 0.00 2.77
1686 2517 1.139654 TCACAGCACATCATAGGGAGC 59.860 52.381 0.00 0.00 0.00 4.70
1693 2529 4.768448 TGAATTCCTTTCACAGCACATCAT 59.232 37.500 2.27 0.00 39.44 2.45
1696 2532 5.733620 AATGAATTCCTTTCACAGCACAT 57.266 34.783 2.27 0.00 46.80 3.21
1757 2609 3.994392 TCGTGTTCTGAAAGGAAGCATAC 59.006 43.478 0.00 0.00 0.00 2.39
1758 2610 4.245660 CTCGTGTTCTGAAAGGAAGCATA 58.754 43.478 0.00 0.00 0.00 3.14
1781 2633 2.749076 TGTCATTTCCATTTGCTCGGAG 59.251 45.455 0.00 0.00 31.51 4.63
1787 2639 2.302733 AGGGGTTGTCATTTCCATTTGC 59.697 45.455 0.00 0.00 0.00 3.68
1894 2754 3.614092 TGAAGAATGGGCTCATGAGAAC 58.386 45.455 27.04 17.21 33.18 3.01
1973 2834 4.317488 TCAACGCGGGAGTTTTTAGTAAT 58.683 39.130 12.47 0.00 30.96 1.89
2245 3137 1.003580 GAGGGAGTGGATTGTTGCTCA 59.996 52.381 0.00 0.00 0.00 4.26
2296 3188 1.456705 GGAAGTTGGTGGGTTGCCA 60.457 57.895 0.00 0.00 0.00 4.92
2302 3194 1.544246 GGATTTTCGGAAGTTGGTGGG 59.456 52.381 0.00 0.00 0.00 4.61
2315 3207 2.615912 CTCCGCAGATCCTTGGATTTTC 59.384 50.000 3.43 0.00 0.00 2.29
2403 3295 1.470632 GCTCTGTTCGGGATCACTCTG 60.471 57.143 0.00 0.00 0.00 3.35
2412 3304 2.939103 CAAATCTAAGGCTCTGTTCGGG 59.061 50.000 0.00 0.00 0.00 5.14
2592 3489 4.884668 AAGAAAATGAGGACAGGACGTA 57.115 40.909 0.00 0.00 0.00 3.57
2743 3640 8.171840 GCTAATATTTGCTACGGATTCAGAATC 58.828 37.037 14.09 14.09 37.17 2.52
2765 3662 9.764363 CTAAATTAGGTATCATGTCAGTGCTAA 57.236 33.333 0.00 0.00 0.00 3.09
2985 3882 9.877178 CTCTGTAAAGAAATATAACTCCAGTGT 57.123 33.333 0.00 0.00 0.00 3.55
2990 3887 8.706521 ACTCCCTCTGTAAAGAAATATAACTCC 58.293 37.037 0.00 0.00 0.00 3.85
3389 4290 5.247110 TGTGTATCTTTCTGGAGAGCTTTCT 59.753 40.000 4.01 0.00 0.00 2.52
3423 4324 4.453480 TTCCACCACTGAATCCTCTTTT 57.547 40.909 0.00 0.00 0.00 2.27
3640 4541 8.453238 TGCATACAACCTGAAACTAAAAACTA 57.547 30.769 0.00 0.00 0.00 2.24
3649 4552 5.163754 GGTACATCTGCATACAACCTGAAAC 60.164 44.000 0.00 0.00 0.00 2.78
3665 4568 2.110365 GGGGTAGGCTAGAGGTACATCT 59.890 54.545 15.29 15.29 0.00 2.90
3666 4569 2.158355 TGGGGTAGGCTAGAGGTACATC 60.158 54.545 0.00 0.00 0.00 3.06
3667 4570 1.864251 TGGGGTAGGCTAGAGGTACAT 59.136 52.381 0.00 0.00 0.00 2.29
3668 4571 1.311880 TGGGGTAGGCTAGAGGTACA 58.688 55.000 0.00 0.00 0.00 2.90
3669 4572 2.037901 GTTGGGGTAGGCTAGAGGTAC 58.962 57.143 0.00 0.00 0.00 3.34
3670 4573 1.935196 AGTTGGGGTAGGCTAGAGGTA 59.065 52.381 0.00 0.00 0.00 3.08
3671 4574 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85
3672 4575 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
3673 4576 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
3674 4577 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
3675 4578 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
3676 4579 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
3677 4580 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
3686 4589 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
3687 4590 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
3688 4591 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
3689 4592 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
3690 4593 4.027437 ACAAAGCCTTTAGTCCCAAACAA 58.973 39.130 0.00 0.00 0.00 2.83
3691 4594 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
3692 4595 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
3693 4596 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
3694 4597 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
3695 4598 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
3696 4599 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
3697 4600 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
3698 4601 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
3699 4602 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
3700 4603 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
3701 4604 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
3702 4605 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
3703 4606 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
3704 4607 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
3705 4608 4.024472 ACAAACAACAACAACAACAAAGCC 60.024 37.500 0.00 0.00 0.00 4.35
3706 4609 5.089396 ACAAACAACAACAACAACAAAGC 57.911 34.783 0.00 0.00 0.00 3.51
3707 4610 6.481984 ACAACAAACAACAACAACAACAAAG 58.518 32.000 0.00 0.00 0.00 2.77
3708 4611 6.422776 ACAACAAACAACAACAACAACAAA 57.577 29.167 0.00 0.00 0.00 2.83
3709 4612 6.422776 AACAACAAACAACAACAACAACAA 57.577 29.167 0.00 0.00 0.00 2.83
3710 4613 6.128282 ACAAACAACAAACAACAACAACAACA 60.128 30.769 0.00 0.00 0.00 3.33
3711 4614 6.251549 ACAAACAACAAACAACAACAACAAC 58.748 32.000 0.00 0.00 0.00 3.32
3712 4615 6.422776 ACAAACAACAAACAACAACAACAA 57.577 29.167 0.00 0.00 0.00 2.83
3713 4616 6.128282 ACAACAAACAACAAACAACAACAACA 60.128 30.769 0.00 0.00 0.00 3.33
3714 4617 6.251549 ACAACAAACAACAAACAACAACAAC 58.748 32.000 0.00 0.00 0.00 3.32
3715 4618 6.422776 ACAACAAACAACAAACAACAACAA 57.577 29.167 0.00 0.00 0.00 2.83
3716 4619 7.567571 CATACAACAAACAACAAACAACAACA 58.432 30.769 0.00 0.00 0.00 3.33
3717 4620 6.518054 GCATACAACAAACAACAAACAACAAC 59.482 34.615 0.00 0.00 0.00 3.32
3718 4621 6.202762 TGCATACAACAAACAACAAACAACAA 59.797 30.769 0.00 0.00 0.00 2.83
3719 4622 5.696270 TGCATACAACAAACAACAAACAACA 59.304 32.000 0.00 0.00 0.00 3.33
3720 4623 6.090088 TCTGCATACAACAAACAACAAACAAC 59.910 34.615 0.00 0.00 0.00 3.32
3721 4624 6.159293 TCTGCATACAACAAACAACAAACAA 58.841 32.000 0.00 0.00 0.00 2.83
3722 4625 5.714047 TCTGCATACAACAAACAACAAACA 58.286 33.333 0.00 0.00 0.00 2.83
3723 4626 6.255453 ACATCTGCATACAACAAACAACAAAC 59.745 34.615 0.00 0.00 0.00 2.93
3724 4627 6.336566 ACATCTGCATACAACAAACAACAAA 58.663 32.000 0.00 0.00 0.00 2.83
3725 4628 5.900425 ACATCTGCATACAACAAACAACAA 58.100 33.333 0.00 0.00 0.00 2.83
3726 4629 5.512753 ACATCTGCATACAACAAACAACA 57.487 34.783 0.00 0.00 0.00 3.33
3727 4630 6.434596 TGTACATCTGCATACAACAAACAAC 58.565 36.000 0.00 0.00 0.00 3.32
3728 4631 6.625873 TGTACATCTGCATACAACAAACAA 57.374 33.333 0.00 0.00 0.00 2.83
3729 4632 6.816134 ATGTACATCTGCATACAACAAACA 57.184 33.333 1.41 0.00 35.05 2.83
3730 4633 7.083858 ACAATGTACATCTGCATACAACAAAC 58.916 34.615 9.23 0.00 35.05 2.93
3731 4634 7.213216 ACAATGTACATCTGCATACAACAAA 57.787 32.000 9.23 0.00 35.05 2.83
3732 4635 6.128035 GGACAATGTACATCTGCATACAACAA 60.128 38.462 9.23 0.00 35.05 2.83
3733 4636 5.353956 GGACAATGTACATCTGCATACAACA 59.646 40.000 9.23 0.00 35.05 3.33
3734 4637 5.220854 GGGACAATGTACATCTGCATACAAC 60.221 44.000 9.23 0.00 35.05 3.32
3735 4638 4.881273 GGGACAATGTACATCTGCATACAA 59.119 41.667 9.23 0.00 35.05 2.41
3736 4639 4.164030 AGGGACAATGTACATCTGCATACA 59.836 41.667 9.23 0.61 35.82 2.29
3737 4640 4.708177 AGGGACAATGTACATCTGCATAC 58.292 43.478 9.23 0.00 0.00 2.39
3738 4641 6.126911 TGTTAGGGACAATGTACATCTGCATA 60.127 38.462 9.23 2.33 34.69 3.14
3739 4642 3.939740 AGGGACAATGTACATCTGCAT 57.060 42.857 9.23 0.00 0.00 3.96
3740 4643 4.019771 TGTTAGGGACAATGTACATCTGCA 60.020 41.667 9.23 3.28 34.69 4.41
3741 4644 4.513442 TGTTAGGGACAATGTACATCTGC 58.487 43.478 9.23 2.73 34.69 4.26
3742 4645 7.050377 AGAATGTTAGGGACAATGTACATCTG 58.950 38.462 9.23 11.79 42.62 2.90
4245 5148 5.719563 TCACCCATAAATCTGTACTGTGAGA 59.280 40.000 0.00 0.00 0.00 3.27
4350 5253 4.223144 AGCCACTTCCCATACAACTTTTT 58.777 39.130 0.00 0.00 0.00 1.94
4355 5258 2.489938 TGAGCCACTTCCCATACAAC 57.510 50.000 0.00 0.00 0.00 3.32
4356 5259 3.737559 AATGAGCCACTTCCCATACAA 57.262 42.857 0.00 0.00 0.00 2.41
4460 5364 3.263425 AGGTCGGAGAAAGAATTTGGCTA 59.737 43.478 0.00 0.00 39.27 3.93
4483 5387 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
4484 5388 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
4485 5389 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
4486 5390 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
4487 5391 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
4488 5392 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
4489 5393 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
4490 5394 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
4491 5395 4.446385 TCTTGTGACAAGTAATTCCGAACG 59.554 41.667 23.17 0.00 0.00 3.95
4492 5396 5.917541 TCTTGTGACAAGTAATTCCGAAC 57.082 39.130 23.17 0.00 0.00 3.95
4493 5397 6.708502 TCATTCTTGTGACAAGTAATTCCGAA 59.291 34.615 23.17 9.57 0.00 4.30
4494 5398 6.227522 TCATTCTTGTGACAAGTAATTCCGA 58.772 36.000 23.17 12.47 0.00 4.55
4495 5399 6.480524 TCATTCTTGTGACAAGTAATTCCG 57.519 37.500 23.17 10.82 0.00 4.30
4496 5400 6.797033 CGTTCATTCTTGTGACAAGTAATTCC 59.203 38.462 23.17 9.25 0.00 3.01
4497 5401 7.352739 ACGTTCATTCTTGTGACAAGTAATTC 58.647 34.615 23.17 10.79 0.00 2.17
4498 5402 7.259290 ACGTTCATTCTTGTGACAAGTAATT 57.741 32.000 23.17 5.87 0.00 1.40
4499 5403 6.861065 ACGTTCATTCTTGTGACAAGTAAT 57.139 33.333 23.17 17.58 0.00 1.89
4500 5404 7.870954 AGATACGTTCATTCTTGTGACAAGTAA 59.129 33.333 23.17 16.30 0.00 2.24
4501 5405 7.375834 AGATACGTTCATTCTTGTGACAAGTA 58.624 34.615 23.17 15.54 0.00 2.24
4502 5406 6.223852 AGATACGTTCATTCTTGTGACAAGT 58.776 36.000 23.17 3.94 0.00 3.16
4503 5407 6.712241 AGATACGTTCATTCTTGTGACAAG 57.288 37.500 18.84 18.84 0.00 3.16
4504 5408 9.863845 TTATAGATACGTTCATTCTTGTGACAA 57.136 29.630 0.00 0.00 0.00 3.18
4505 5409 9.297586 GTTATAGATACGTTCATTCTTGTGACA 57.702 33.333 0.00 0.00 0.00 3.58
4506 5410 8.469902 CGTTATAGATACGTTCATTCTTGTGAC 58.530 37.037 0.00 0.00 34.47 3.67
4507 5411 8.400186 TCGTTATAGATACGTTCATTCTTGTGA 58.600 33.333 0.00 0.00 39.84 3.58
4508 5412 8.556517 TCGTTATAGATACGTTCATTCTTGTG 57.443 34.615 0.00 0.00 39.84 3.33
4509 5413 9.577110 TTTCGTTATAGATACGTTCATTCTTGT 57.423 29.630 0.00 0.00 39.84 3.16
4538 5442 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
4539 5443 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
4540 5444 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
4541 5445 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
4542 5446 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
4543 5447 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
4544 5448 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
4545 5449 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
4546 5450 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
4547 5451 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
4548 5452 7.607991 AGAATTACTCGTCCAAGAAATGAATGT 59.392 33.333 0.00 0.00 0.00 2.71
4549 5453 7.907045 CAGAATTACTCGTCCAAGAAATGAATG 59.093 37.037 0.00 0.00 0.00 2.67
4550 5454 7.824289 TCAGAATTACTCGTCCAAGAAATGAAT 59.176 33.333 0.00 0.00 0.00 2.57
4551 5455 7.158697 TCAGAATTACTCGTCCAAGAAATGAA 58.841 34.615 0.00 0.00 0.00 2.57
4552 5456 6.697395 TCAGAATTACTCGTCCAAGAAATGA 58.303 36.000 0.00 0.00 0.00 2.57
4553 5457 6.968131 TCAGAATTACTCGTCCAAGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
4554 5458 6.090898 CGTTCAGAATTACTCGTCCAAGAAAT 59.909 38.462 0.00 0.00 0.00 2.17
4555 5459 5.404366 CGTTCAGAATTACTCGTCCAAGAAA 59.596 40.000 0.00 0.00 0.00 2.52
4556 5460 4.921515 CGTTCAGAATTACTCGTCCAAGAA 59.078 41.667 0.00 0.00 0.00 2.52
4557 5461 4.482386 CGTTCAGAATTACTCGTCCAAGA 58.518 43.478 0.00 0.00 0.00 3.02
4558 5462 3.612860 CCGTTCAGAATTACTCGTCCAAG 59.387 47.826 0.00 0.00 0.00 3.61
4559 5463 3.256383 TCCGTTCAGAATTACTCGTCCAA 59.744 43.478 0.00 0.00 0.00 3.53
4560 5464 2.821378 TCCGTTCAGAATTACTCGTCCA 59.179 45.455 0.00 0.00 0.00 4.02
4561 5465 3.436496 CTCCGTTCAGAATTACTCGTCC 58.564 50.000 0.00 0.00 0.00 4.79
4562 5466 3.436496 CCTCCGTTCAGAATTACTCGTC 58.564 50.000 0.00 0.00 0.00 4.20
4563 5467 2.165845 CCCTCCGTTCAGAATTACTCGT 59.834 50.000 0.00 0.00 0.00 4.18
4564 5468 2.426024 TCCCTCCGTTCAGAATTACTCG 59.574 50.000 0.00 0.00 0.00 4.18
4565 5469 3.447944 ACTCCCTCCGTTCAGAATTACTC 59.552 47.826 0.00 0.00 0.00 2.59
4566 5470 3.442076 ACTCCCTCCGTTCAGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
4567 5471 3.889520 ACTCCCTCCGTTCAGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
4568 5472 6.363167 TTTTACTCCCTCCGTTCAGAATTA 57.637 37.500 0.00 0.00 0.00 1.40
4569 5473 4.903045 TTTACTCCCTCCGTTCAGAATT 57.097 40.909 0.00 0.00 0.00 2.17
4570 5474 4.903045 TTTTACTCCCTCCGTTCAGAAT 57.097 40.909 0.00 0.00 0.00 2.40
4571 5475 4.575885 CATTTTACTCCCTCCGTTCAGAA 58.424 43.478 0.00 0.00 0.00 3.02
4572 5476 3.618997 GCATTTTACTCCCTCCGTTCAGA 60.619 47.826 0.00 0.00 0.00 3.27
4573 5477 2.678336 GCATTTTACTCCCTCCGTTCAG 59.322 50.000 0.00 0.00 0.00 3.02
4574 5478 2.039216 TGCATTTTACTCCCTCCGTTCA 59.961 45.455 0.00 0.00 0.00 3.18
4575 5479 2.706890 TGCATTTTACTCCCTCCGTTC 58.293 47.619 0.00 0.00 0.00 3.95
4576 5480 2.871096 TGCATTTTACTCCCTCCGTT 57.129 45.000 0.00 0.00 0.00 4.44
4577 5481 2.039879 ACTTGCATTTTACTCCCTCCGT 59.960 45.455 0.00 0.00 0.00 4.69
4578 5482 2.678336 GACTTGCATTTTACTCCCTCCG 59.322 50.000 0.00 0.00 0.00 4.63
4579 5483 3.686016 TGACTTGCATTTTACTCCCTCC 58.314 45.455 0.00 0.00 0.00 4.30
4580 5484 4.702131 ACATGACTTGCATTTTACTCCCTC 59.298 41.667 0.00 0.00 34.15 4.30
4581 5485 4.666512 ACATGACTTGCATTTTACTCCCT 58.333 39.130 0.00 0.00 34.15 4.20
4582 5486 4.702131 AGACATGACTTGCATTTTACTCCC 59.298 41.667 0.00 0.00 34.15 4.30
4583 5487 5.886960 AGACATGACTTGCATTTTACTCC 57.113 39.130 0.00 0.00 34.15 3.85
4584 5488 9.334693 CTAAAAGACATGACTTGCATTTTACTC 57.665 33.333 11.17 0.00 34.15 2.59
4585 5489 9.066892 TCTAAAAGACATGACTTGCATTTTACT 57.933 29.630 11.17 0.00 34.15 2.24
4586 5490 9.846248 ATCTAAAAGACATGACTTGCATTTTAC 57.154 29.630 11.17 0.00 34.15 2.01
4587 5491 9.844790 CATCTAAAAGACATGACTTGCATTTTA 57.155 29.630 11.17 5.30 34.15 1.52


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

AutoCloner maintained by Alex Coulton.