Multiple sequence alignment - TraesCS7A01G083100

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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 TraesCS7A01G083100 chr7A 100.000 2582 0 0 1 2582 48011095 48013676 0.000000e+00 4769.0
1 TraesCS7A01G083100 chr7A 88.372 86 10 0 1250 1335 489704584 489704499 1.260000e-18 104.0
2 TraesCS7A01G083100 chr7A 88.889 45 3 2 2186 2229 77697859 77697816 1.000000e-03 54.7
3 TraesCS7A01G083100 chr7D 83.515 1377 146 26 1 1335 45758774 45760111 0.000000e+00 1210.0
4 TraesCS7A01G083100 chr7D 85.496 393 36 14 1491 1874 45760467 45760847 8.660000e-105 390.0
5 TraesCS7A01G083100 chr2D 86.576 812 97 5 2 804 27961243 27962051 0.000000e+00 885.0
6 TraesCS7A01G083100 chr2D 83.186 113 14 4 2181 2293 329404332 329404225 5.880000e-17 99.0
7 TraesCS7A01G083100 chr3B 86.330 812 98 7 2 803 474762970 474762162 0.000000e+00 872.0
8 TraesCS7A01G083100 chr3B 88.817 617 51 5 1973 2582 413838774 413839379 0.000000e+00 741.0
9 TraesCS7A01G083100 chr3B 85.333 300 34 3 1 291 814003322 814003620 4.180000e-78 302.0
10 TraesCS7A01G083100 chr5D 86.000 800 100 5 2 793 519705390 519706185 0.000000e+00 846.0
11 TraesCS7A01G083100 chr5D 85.612 139 12 3 2 132 289042487 289042625 3.460000e-29 139.0
12 TraesCS7A01G083100 chr5D 75.610 246 42 15 2181 2418 478167623 478167858 3.510000e-19 106.0
13 TraesCS7A01G083100 chr3D 85.965 798 101 4 2 791 590849398 590848604 0.000000e+00 843.0
14 TraesCS7A01G083100 chr6D 85.679 817 95 14 2 806 436297338 436296532 0.000000e+00 841.0
15 TraesCS7A01G083100 chr5B 85.609 813 102 8 2 803 328361846 328362654 0.000000e+00 839.0
16 TraesCS7A01G083100 chr5B 83.090 479 71 3 4 474 450666352 450665876 6.600000e-116 427.0
17 TraesCS7A01G083100 chr4D 86.494 770 79 12 35 791 503589381 503590138 0.000000e+00 822.0
18 TraesCS7A01G083100 chr1B 84.558 803 112 7 5 799 447208096 447207298 0.000000e+00 785.0
19 TraesCS7A01G083100 chr1B 82.090 469 44 14 1963 2401 623622668 623623126 5.250000e-97 364.0
20 TraesCS7A01G083100 chr1D 84.069 816 111 14 4 808 338649707 338648900 0.000000e+00 769.0
21 TraesCS7A01G083100 chr6B 83.171 820 121 8 5 816 210576607 210575797 0.000000e+00 734.0
22 TraesCS7A01G083100 chr6B 78.644 295 44 13 1962 2240 5046344 5046053 7.340000e-41 178.0
23 TraesCS7A01G083100 chr6B 81.818 220 23 11 2345 2562 5045742 5045538 4.420000e-38 169.0
24 TraesCS7A01G083100 chr1A 90.031 321 26 3 2267 2582 151353440 151353121 6.650000e-111 411.0
25 TraesCS7A01G083100 chr1A 87.869 305 31 4 1961 2260 151357667 151357364 1.140000e-93 353.0
26 TraesCS7A01G083100 chr4A 81.767 532 43 22 840 1335 658351583 658352096 1.860000e-106 396.0
27 TraesCS7A01G083100 chr4A 81.682 535 44 22 840 1338 658922764 658922248 1.860000e-106 396.0
28 TraesCS7A01G083100 chr4A 79.596 544 56 22 816 1335 658412461 658412973 3.180000e-89 339.0
29 TraesCS7A01G083100 chr4A 84.906 265 27 8 840 1100 658349949 658350204 3.300000e-64 255.0
30 TraesCS7A01G083100 chr4A 76.067 539 69 34 1331 1830 658413092 658413609 2.590000e-55 226.0
31 TraesCS7A01G083100 chr4A 76.722 421 48 26 1333 1718 658352211 658352616 3.390000e-44 189.0
32 TraesCS7A01G083100 chr4A 76.498 434 50 28 1333 1730 658922136 658921719 3.390000e-44 189.0
33 TraesCS7A01G083100 chr4A 89.535 86 9 0 1250 1335 614475232 614475317 2.720000e-20 110.0
34 TraesCS7A01G083100 chr2A 83.186 113 14 4 2181 2293 140641945 140641838 5.880000e-17 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G083100 chr7A 48011095 48013676 2581 False 4769.0 4769 100.000000 1 2582 1 chr7A.!!$F1 2581
1 TraesCS7A01G083100 chr7D 45758774 45760847 2073 False 800.0 1210 84.505500 1 1874 2 chr7D.!!$F1 1873
2 TraesCS7A01G083100 chr2D 27961243 27962051 808 False 885.0 885 86.576000 2 804 1 chr2D.!!$F1 802
3 TraesCS7A01G083100 chr3B 474762162 474762970 808 True 872.0 872 86.330000 2 803 1 chr3B.!!$R1 801
4 TraesCS7A01G083100 chr3B 413838774 413839379 605 False 741.0 741 88.817000 1973 2582 1 chr3B.!!$F1 609
5 TraesCS7A01G083100 chr5D 519705390 519706185 795 False 846.0 846 86.000000 2 793 1 chr5D.!!$F3 791
6 TraesCS7A01G083100 chr3D 590848604 590849398 794 True 843.0 843 85.965000 2 791 1 chr3D.!!$R1 789
7 TraesCS7A01G083100 chr6D 436296532 436297338 806 True 841.0 841 85.679000 2 806 1 chr6D.!!$R1 804
8 TraesCS7A01G083100 chr5B 328361846 328362654 808 False 839.0 839 85.609000 2 803 1 chr5B.!!$F1 801
9 TraesCS7A01G083100 chr4D 503589381 503590138 757 False 822.0 822 86.494000 35 791 1 chr4D.!!$F1 756
10 TraesCS7A01G083100 chr1B 447207298 447208096 798 True 785.0 785 84.558000 5 799 1 chr1B.!!$R1 794
11 TraesCS7A01G083100 chr1D 338648900 338649707 807 True 769.0 769 84.069000 4 808 1 chr1D.!!$R1 804
12 TraesCS7A01G083100 chr6B 210575797 210576607 810 True 734.0 734 83.171000 5 816 1 chr6B.!!$R1 811
13 TraesCS7A01G083100 chr1A 151353121 151357667 4546 True 382.0 411 88.950000 1961 2582 2 chr1A.!!$R1 621
14 TraesCS7A01G083100 chr4A 658921719 658922764 1045 True 292.5 396 79.090000 840 1730 2 chr4A.!!$R1 890
15 TraesCS7A01G083100 chr4A 658412461 658413609 1148 False 282.5 339 77.831500 816 1830 2 chr4A.!!$F3 1014
16 TraesCS7A01G083100 chr4A 658349949 658352616 2667 False 280.0 396 81.131667 840 1718 3 chr4A.!!$F2 878

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
361 371 0.034574 AATAATGCCGCCAGTGTGGA 60.035 50.0 0.0 0.0 45.51 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 3785 0.03254 ACGTACAGTTCCCAACCGAC 59.967 55.0 0.0 0.0 0.0 4.79 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
22 23 3.216187 TGTTCAAATTCTCGGGACCAA 57.784 42.857 0.00 0.00 0.00 3.67
112 122 7.445402 GCCTAGCACCTGAGAAATGATTTAATA 59.555 37.037 0.00 0.00 0.00 0.98
116 126 9.412460 AGCACCTGAGAAATGATTTAATATTCA 57.588 29.630 0.00 0.00 0.00 2.57
267 277 7.067008 GTGCTATACCAGTTTTCACACCATTAT 59.933 37.037 0.00 0.00 0.00 1.28
291 301 4.473444 AGATCATGTGTTGTGGAAACCTT 58.527 39.130 0.00 0.00 0.00 3.50
343 353 5.826208 TCGATGCTAGTTATGTGGAGAGTAA 59.174 40.000 0.00 0.00 0.00 2.24
361 371 0.034574 AATAATGCCGCCAGTGTGGA 60.035 50.000 0.00 0.00 45.51 4.02
391 401 4.057432 GCTAGGAACTCATCTGATGAAGC 58.943 47.826 19.95 19.15 41.75 3.86
407 418 8.197439 TCTGATGAAGCTATTATTTCTTCGTGA 58.803 33.333 0.00 0.00 39.12 4.35
420 431 2.698797 TCTTCGTGAGACTTTCTGGGTT 59.301 45.455 0.00 0.00 41.84 4.11
422 433 4.342951 TCTTCGTGAGACTTTCTGGGTTAA 59.657 41.667 0.00 0.00 41.84 2.01
530 541 3.042887 GACTGGTTGTGATTTTGTTCGC 58.957 45.455 0.00 0.00 0.00 4.70
553 564 3.256631 TCTTTCCTTGCAAATGAGAAGGC 59.743 43.478 0.00 0.00 36.88 4.35
560 571 2.224597 TGCAAATGAGAAGGCTGACAGA 60.225 45.455 6.65 0.00 0.00 3.41
585 596 7.353414 TCTCCTCTCGTTGATATGAAGAAAT 57.647 36.000 0.00 0.00 0.00 2.17
598 609 9.547753 TGATATGAAGAAATAAGCCTTGAGTAC 57.452 33.333 0.00 0.00 0.00 2.73
605 616 5.700402 AATAAGCCTTGAGTACATCCAGT 57.300 39.130 0.00 0.00 0.00 4.00
646 657 2.627945 TGCGAAAATCAATCGGCTAGT 58.372 42.857 0.00 0.00 40.54 2.57
654 665 0.947244 CAATCGGCTAGTCAATGGGC 59.053 55.000 0.00 0.00 0.00 5.36
723 736 5.665459 AGATTCTTCTCAATAGTGTTCCGG 58.335 41.667 0.00 0.00 0.00 5.14
724 737 4.884668 TTCTTCTCAATAGTGTTCCGGT 57.115 40.909 0.00 0.00 0.00 5.28
727 740 5.258841 TCTTCTCAATAGTGTTCCGGTCTA 58.741 41.667 0.00 1.16 0.00 2.59
742 755 2.791158 CGGTCTATGTGGCGAATTTTGC 60.791 50.000 0.00 0.00 0.00 3.68
751 764 1.389784 GGCGAATTTTGCAATGAACGG 59.610 47.619 10.71 0.00 0.00 4.44
766 779 6.307077 GCAATGAACGGTTGTAATAACCTTTC 59.693 38.462 16.54 16.54 44.26 2.62
767 780 5.945466 TGAACGGTTGTAATAACCTTTCC 57.055 39.130 19.08 7.56 43.72 3.13
768 781 5.374921 TGAACGGTTGTAATAACCTTTCCA 58.625 37.500 19.08 9.33 43.72 3.53
824 837 4.473477 AAGACTCCCCGTTTTATCTCTG 57.527 45.455 0.00 0.00 0.00 3.35
825 838 3.709587 AGACTCCCCGTTTTATCTCTGA 58.290 45.455 0.00 0.00 0.00 3.27
831 844 4.530946 TCCCCGTTTTATCTCTGAGACTTT 59.469 41.667 10.00 0.00 0.00 2.66
864 879 1.851304 TCAATTCCAACAGCCATCCC 58.149 50.000 0.00 0.00 0.00 3.85
866 881 2.112998 CAATTCCAACAGCCATCCCAT 58.887 47.619 0.00 0.00 0.00 4.00
867 882 2.077687 ATTCCAACAGCCATCCCATC 57.922 50.000 0.00 0.00 0.00 3.51
869 884 1.825191 CCAACAGCCATCCCATCCG 60.825 63.158 0.00 0.00 0.00 4.18
870 885 1.224315 CAACAGCCATCCCATCCGA 59.776 57.895 0.00 0.00 0.00 4.55
873 888 1.526917 CAGCCATCCCATCCGAACC 60.527 63.158 0.00 0.00 0.00 3.62
875 890 1.526917 GCCATCCCATCCGAACCAG 60.527 63.158 0.00 0.00 0.00 4.00
936 957 1.276138 TCCAGCATACATATGGCTCCG 59.724 52.381 7.80 0.00 34.32 4.63
937 958 1.276138 CCAGCATACATATGGCTCCGA 59.724 52.381 7.80 0.00 34.32 4.55
960 983 4.415150 CCCCTCTGCACGCCACAT 62.415 66.667 0.00 0.00 0.00 3.21
985 1034 1.220206 CACGGGAGAAGCAGAGCAT 59.780 57.895 0.00 0.00 0.00 3.79
991 1040 1.411977 GGAGAAGCAGAGCATAGCAGA 59.588 52.381 0.00 0.00 0.00 4.26
995 1044 1.067084 GCAGAGCATAGCAGAGCGA 59.933 57.895 0.00 0.00 35.48 4.93
1004 1053 0.658368 TAGCAGAGCGACGAGATGTC 59.342 55.000 0.00 0.00 44.53 3.06
1176 2897 3.844090 GCGGAGGAGGCTCAGGAC 61.844 72.222 17.69 4.04 0.00 3.85
1177 2898 3.522731 CGGAGGAGGCTCAGGACG 61.523 72.222 17.69 10.92 0.00 4.79
1178 2899 2.363147 GGAGGAGGCTCAGGACGT 60.363 66.667 17.69 0.00 0.00 4.34
1179 2900 2.419739 GGAGGAGGCTCAGGACGTC 61.420 68.421 17.69 7.13 0.00 4.34
1180 2901 1.379309 GAGGAGGCTCAGGACGTCT 60.379 63.158 17.69 1.51 0.00 4.18
1181 2902 1.662438 GAGGAGGCTCAGGACGTCTG 61.662 65.000 17.69 11.66 44.68 3.51
1182 2903 2.716017 GGAGGCTCAGGACGTCTGG 61.716 68.421 17.69 8.07 43.53 3.86
1183 2904 1.979693 GAGGCTCAGGACGTCTGGT 60.980 63.158 16.46 0.00 43.53 4.00
1184 2905 1.534235 AGGCTCAGGACGTCTGGTT 60.534 57.895 16.46 0.00 43.53 3.67
1185 2906 1.079750 GGCTCAGGACGTCTGGTTC 60.080 63.158 16.46 0.00 43.53 3.62
1186 2907 1.666011 GCTCAGGACGTCTGGTTCA 59.334 57.895 16.46 0.00 43.53 3.18
1194 2915 2.741092 GTCTGGTTCAGGCACGGA 59.259 61.111 0.00 0.00 35.96 4.69
1209 2930 2.686835 GGAGCTCAGTGGGAGGCT 60.687 66.667 17.19 0.00 44.22 4.58
1435 3323 2.224670 ACAAATCAAACGCCTCCCACTA 60.225 45.455 0.00 0.00 0.00 2.74
1436 3324 2.109425 AATCAAACGCCTCCCACTAC 57.891 50.000 0.00 0.00 0.00 2.73
1437 3325 0.981183 ATCAAACGCCTCCCACTACA 59.019 50.000 0.00 0.00 0.00 2.74
1440 3328 2.159382 CAAACGCCTCCCACTACAATT 58.841 47.619 0.00 0.00 0.00 2.32
1443 3331 2.463752 ACGCCTCCCACTACAATTCTA 58.536 47.619 0.00 0.00 0.00 2.10
1446 3334 3.635373 CGCCTCCCACTACAATTCTACTA 59.365 47.826 0.00 0.00 0.00 1.82
1448 3336 4.404715 GCCTCCCACTACAATTCTACTACA 59.595 45.833 0.00 0.00 0.00 2.74
1449 3337 5.105064 GCCTCCCACTACAATTCTACTACAA 60.105 44.000 0.00 0.00 0.00 2.41
1451 3339 6.380274 CCTCCCACTACAATTCTACTACAAGA 59.620 42.308 0.00 0.00 0.00 3.02
1452 3340 7.093465 CCTCCCACTACAATTCTACTACAAGAA 60.093 40.741 0.00 0.00 39.71 2.52
1453 3341 8.375493 TCCCACTACAATTCTACTACAAGAAT 57.625 34.615 0.00 0.00 45.91 2.40
1455 3343 7.435488 CCCACTACAATTCTACTACAAGAATCG 59.565 40.741 0.00 0.00 43.75 3.34
1456 3344 8.188799 CCACTACAATTCTACTACAAGAATCGA 58.811 37.037 0.00 0.00 43.75 3.59
1457 3345 9.227490 CACTACAATTCTACTACAAGAATCGAG 57.773 37.037 0.00 1.78 43.75 4.04
1458 3346 8.958506 ACTACAATTCTACTACAAGAATCGAGT 58.041 33.333 0.00 0.00 43.75 4.18
1459 3347 9.790389 CTACAATTCTACTACAAGAATCGAGTT 57.210 33.333 0.00 0.00 43.75 3.01
1463 3388 8.690680 ATTCTACTACAAGAATCGAGTTGTTC 57.309 34.615 13.83 2.59 41.34 3.18
1474 3399 7.831753 AGAATCGAGTTGTTCTTCTTCATCTA 58.168 34.615 0.00 0.00 30.84 1.98
1486 3411 2.028476 TCTTCATCTAACGTGGTGGTGG 60.028 50.000 0.00 0.00 0.00 4.61
1525 3458 0.039180 TAGCACGGAGGAGGTGAAGA 59.961 55.000 0.00 0.00 37.60 2.87
1547 3480 3.188786 GCTCAAGTACTGGGCGCG 61.189 66.667 0.00 0.00 43.14 6.86
1583 3516 0.392729 GTCAGGCTCTGCAGCTGAAT 60.393 55.000 20.43 0.00 46.03 2.57
1587 3521 1.375098 GGCTCTGCAGCTGAATGACC 61.375 60.000 20.43 8.89 46.03 4.02
1589 3523 2.017623 GCTCTGCAGCTGAATGACCAT 61.018 52.381 20.43 0.00 43.09 3.55
1610 3544 1.682854 CAACAAGACAACAGGCCATGT 59.317 47.619 5.01 7.09 46.97 3.21
1615 3549 1.143684 AGACAACAGGCCATGTCAAGT 59.856 47.619 27.63 17.42 46.55 3.16
1616 3550 1.537202 GACAACAGGCCATGTCAAGTC 59.463 52.381 23.62 18.25 43.00 3.01
1617 3551 1.133823 ACAACAGGCCATGTCAAGTCA 60.134 47.619 5.01 0.00 43.00 3.41
1619 3553 1.901591 ACAGGCCATGTCAAGTCAAG 58.098 50.000 5.01 0.00 37.75 3.02
1621 3555 2.082231 CAGGCCATGTCAAGTCAAGAG 58.918 52.381 5.01 0.00 0.00 2.85
1624 3558 1.198637 GCCATGTCAAGTCAAGAGCAC 59.801 52.381 0.00 0.00 0.00 4.40
1625 3559 2.775890 CCATGTCAAGTCAAGAGCACT 58.224 47.619 0.00 0.00 0.00 4.40
1626 3560 2.740981 CCATGTCAAGTCAAGAGCACTC 59.259 50.000 0.00 0.00 0.00 3.51
1627 3561 3.396560 CATGTCAAGTCAAGAGCACTCA 58.603 45.455 0.00 0.00 0.00 3.41
1628 3562 3.103447 TGTCAAGTCAAGAGCACTCAG 57.897 47.619 0.00 0.00 0.00 3.35
1629 3563 1.797635 GTCAAGTCAAGAGCACTCAGC 59.202 52.381 0.00 0.00 46.19 4.26
1638 3572 2.350514 GCACTCAGCAGGCTCCTT 59.649 61.111 0.00 0.00 44.79 3.36
1649 3583 2.295885 CAGGCTCCTTGTCCATTGATC 58.704 52.381 0.00 0.00 0.00 2.92
1714 3680 1.267038 CGAAGCATGTTTCCGATGACG 60.267 52.381 15.65 0.32 39.43 4.35
1721 3687 2.318578 TGTTTCCGATGACGTTACGAC 58.681 47.619 13.03 5.92 37.88 4.34
1739 3705 1.999735 GACAAGAATCGTTGCGGATGA 59.000 47.619 0.00 0.00 0.00 2.92
1749 3715 1.470098 GTTGCGGATGAATCTTGCTGT 59.530 47.619 8.70 0.00 32.21 4.40
1775 3748 1.603172 GGGAGCTGTACATCCGATTCG 60.603 57.143 8.99 0.00 36.38 3.34
1788 3761 1.871039 CCGATTCGGTGTTTCAGTTGT 59.129 47.619 17.08 0.00 42.73 3.32
1797 3774 3.059188 GGTGTTTCAGTTGTATGGTCGTG 60.059 47.826 0.00 0.00 0.00 4.35
1808 3785 1.428448 ATGGTCGTGTTCGTGTCATG 58.572 50.000 0.00 0.00 38.33 3.07
1813 3790 0.937699 CGTGTTCGTGTCATGTCGGT 60.938 55.000 0.00 0.00 0.00 4.69
1820 3797 0.872388 GTGTCATGTCGGTTGGGAAC 59.128 55.000 0.00 0.00 0.00 3.62
1827 3804 0.032540 GTCGGTTGGGAACTGTACGT 59.967 55.000 0.00 0.00 38.89 3.57
1828 3805 0.032403 TCGGTTGGGAACTGTACGTG 59.968 55.000 0.00 0.00 38.89 4.49
1840 3817 3.075884 ACTGTACGTGTGGTGTTTGTTT 58.924 40.909 0.00 0.00 0.00 2.83
1879 3856 5.997385 GCTACAGCTTCTCATCTAGAGTAC 58.003 45.833 0.00 0.00 40.67 2.73
1880 3857 5.763204 GCTACAGCTTCTCATCTAGAGTACT 59.237 44.000 0.00 0.00 40.67 2.73
1881 3858 6.932400 GCTACAGCTTCTCATCTAGAGTACTA 59.068 42.308 0.00 0.00 40.67 1.82
1882 3859 7.606456 GCTACAGCTTCTCATCTAGAGTACTAT 59.394 40.741 0.00 0.00 40.67 2.12
1883 3860 7.979444 ACAGCTTCTCATCTAGAGTACTATC 57.021 40.000 0.00 0.00 44.98 2.08
1884 3861 7.745717 ACAGCTTCTCATCTAGAGTACTATCT 58.254 38.462 0.00 0.00 44.98 1.98
1885 3862 8.876181 ACAGCTTCTCATCTAGAGTACTATCTA 58.124 37.037 0.00 0.00 44.98 1.98
1886 3863 9.371136 CAGCTTCTCATCTAGAGTACTATCTAG 57.629 40.741 11.28 11.28 46.85 2.43
1887 3864 8.540388 AGCTTCTCATCTAGAGTACTATCTAGG 58.460 40.741 15.52 4.92 45.93 3.02
1888 3865 8.319146 GCTTCTCATCTAGAGTACTATCTAGGT 58.681 40.741 15.52 8.62 45.93 3.08
1904 3881 9.435570 ACTATCTAGGTATAAACTCATGTGGTT 57.564 33.333 3.22 3.22 0.00 3.67
1905 3882 9.915629 CTATCTAGGTATAAACTCATGTGGTTC 57.084 37.037 0.41 0.00 0.00 3.62
1906 3883 7.727578 TCTAGGTATAAACTCATGTGGTTCA 57.272 36.000 0.41 0.00 0.00 3.18
1907 3884 8.141298 TCTAGGTATAAACTCATGTGGTTCAA 57.859 34.615 0.41 0.00 0.00 2.69
1908 3885 8.598916 TCTAGGTATAAACTCATGTGGTTCAAA 58.401 33.333 0.41 0.00 0.00 2.69
1909 3886 9.226606 CTAGGTATAAACTCATGTGGTTCAAAA 57.773 33.333 0.41 0.00 0.00 2.44
1910 3887 8.650143 AGGTATAAACTCATGTGGTTCAAAAT 57.350 30.769 0.41 0.00 0.00 1.82
1911 3888 9.747898 AGGTATAAACTCATGTGGTTCAAAATA 57.252 29.630 0.41 0.00 0.00 1.40
1915 3892 9.787532 ATAAACTCATGTGGTTCAAAATAATCG 57.212 29.630 0.41 0.00 0.00 3.34
1916 3893 6.817765 ACTCATGTGGTTCAAAATAATCGT 57.182 33.333 0.00 0.00 0.00 3.73
1917 3894 7.214467 ACTCATGTGGTTCAAAATAATCGTT 57.786 32.000 0.00 0.00 0.00 3.85
1918 3895 8.330466 ACTCATGTGGTTCAAAATAATCGTTA 57.670 30.769 0.00 0.00 0.00 3.18
1919 3896 8.234546 ACTCATGTGGTTCAAAATAATCGTTAC 58.765 33.333 0.00 0.00 0.00 2.50
1920 3897 7.531716 TCATGTGGTTCAAAATAATCGTTACC 58.468 34.615 0.00 0.00 0.00 2.85
1921 3898 5.929278 TGTGGTTCAAAATAATCGTTACCG 58.071 37.500 0.00 0.00 0.00 4.02
1931 3908 2.104267 TCGTTACCGAGCTAGCTGG 58.896 57.895 24.99 24.09 38.40 4.85
1932 3909 1.065928 CGTTACCGAGCTAGCTGGG 59.934 63.158 36.14 36.14 45.71 4.45
1933 3910 1.381928 CGTTACCGAGCTAGCTGGGA 61.382 60.000 41.94 27.61 43.43 4.37
1934 3911 0.386113 GTTACCGAGCTAGCTGGGAG 59.614 60.000 41.94 23.07 43.43 4.30
1935 3912 0.257905 TTACCGAGCTAGCTGGGAGA 59.742 55.000 41.94 28.98 43.43 3.71
1936 3913 0.478942 TACCGAGCTAGCTGGGAGAT 59.521 55.000 41.94 26.84 43.43 2.75
1937 3914 1.112315 ACCGAGCTAGCTGGGAGATG 61.112 60.000 41.94 21.78 43.43 2.90
1938 3915 1.664873 CGAGCTAGCTGGGAGATGG 59.335 63.158 24.99 0.00 0.00 3.51
1939 3916 1.814772 CGAGCTAGCTGGGAGATGGG 61.815 65.000 24.99 0.00 0.00 4.00
1940 3917 0.470833 GAGCTAGCTGGGAGATGGGA 60.471 60.000 24.99 0.00 0.00 4.37
1941 3918 0.193069 AGCTAGCTGGGAGATGGGAT 59.807 55.000 18.57 0.00 0.00 3.85
1942 3919 0.324285 GCTAGCTGGGAGATGGGATG 59.676 60.000 7.70 0.00 0.00 3.51
1943 3920 0.982704 CTAGCTGGGAGATGGGATGG 59.017 60.000 0.00 0.00 0.00 3.51
1944 3921 0.567687 TAGCTGGGAGATGGGATGGA 59.432 55.000 0.00 0.00 0.00 3.41
1945 3922 0.104037 AGCTGGGAGATGGGATGGAT 60.104 55.000 0.00 0.00 0.00 3.41
1946 3923 1.152917 AGCTGGGAGATGGGATGGATA 59.847 52.381 0.00 0.00 0.00 2.59
1947 3924 1.988107 GCTGGGAGATGGGATGGATAA 59.012 52.381 0.00 0.00 0.00 1.75
1948 3925 2.376518 GCTGGGAGATGGGATGGATAAA 59.623 50.000 0.00 0.00 0.00 1.40
1949 3926 3.011032 GCTGGGAGATGGGATGGATAAAT 59.989 47.826 0.00 0.00 0.00 1.40
1950 3927 4.228210 GCTGGGAGATGGGATGGATAAATA 59.772 45.833 0.00 0.00 0.00 1.40
1951 3928 5.281193 GCTGGGAGATGGGATGGATAAATAA 60.281 44.000 0.00 0.00 0.00 1.40
1952 3929 6.750930 GCTGGGAGATGGGATGGATAAATAAA 60.751 42.308 0.00 0.00 0.00 1.40
1953 3930 6.793478 TGGGAGATGGGATGGATAAATAAAG 58.207 40.000 0.00 0.00 0.00 1.85
1954 3931 6.190587 GGGAGATGGGATGGATAAATAAAGG 58.809 44.000 0.00 0.00 0.00 3.11
1955 3932 5.654209 GGAGATGGGATGGATAAATAAAGGC 59.346 44.000 0.00 0.00 0.00 4.35
1956 3933 5.256474 AGATGGGATGGATAAATAAAGGCG 58.744 41.667 0.00 0.00 0.00 5.52
1957 3934 3.761897 TGGGATGGATAAATAAAGGCGG 58.238 45.455 0.00 0.00 0.00 6.13
1958 3935 3.089284 GGGATGGATAAATAAAGGCGGG 58.911 50.000 0.00 0.00 0.00 6.13
1959 3936 3.499745 GGGATGGATAAATAAAGGCGGGT 60.500 47.826 0.00 0.00 0.00 5.28
1970 3947 2.044123 AAGGCGGGTGAGAAATCATC 57.956 50.000 0.00 0.00 0.00 2.92
1971 3948 0.181350 AGGCGGGTGAGAAATCATCC 59.819 55.000 0.00 0.00 37.53 3.51
1983 3960 3.721370 ATCATCCGCCTGGCCAACC 62.721 63.158 14.12 0.00 34.14 3.77
2026 4003 2.921754 CCGTCCGATTAGAACAACTCAC 59.078 50.000 0.00 0.00 0.00 3.51
2043 4020 0.179161 CACCTCCTCACGTCGTGATC 60.179 60.000 27.10 0.00 41.94 2.92
2049 4026 0.026933 CTCACGTCGTGATCCTCTCG 59.973 60.000 27.10 10.92 41.94 4.04
2068 4051 2.757099 CTGCATCCACAAGCCCCC 60.757 66.667 0.00 0.00 0.00 5.40
2161 4144 3.190849 CTGATGCACCTGCCGTCG 61.191 66.667 0.00 0.00 41.18 5.12
2276 8186 2.853080 AGCTTCATTACAGCTCCGGCT 61.853 52.381 0.00 0.00 44.77 5.52
2295 8205 0.726827 TTAAGCTTCATTGCCGCGAG 59.273 50.000 8.23 0.00 0.00 5.03
2353 8268 4.496670 GGCGACGCTTCACTGTAT 57.503 55.556 20.77 0.00 0.00 2.29
2359 8274 0.456221 ACGCTTCACTGTATCTCCGG 59.544 55.000 0.00 0.00 0.00 5.14
2506 8422 1.523711 CACGGGCATCGCAATACCT 60.524 57.895 0.00 0.00 43.89 3.08
2522 8438 2.029073 CTGTGACCTGACGGCGTT 59.971 61.111 16.19 0.00 0.00 4.84
2562 8478 1.073025 AAGGTGGATGCTGCAACGA 59.927 52.632 6.36 0.00 27.51 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.771749 TGATCCAACAAAATCAAAAGCCAATT 59.228 30.769 0.00 0.00 0.00 2.32
90 100 9.412460 TGAATATTAAATCATTTCTCAGGTGCT 57.588 29.630 0.00 0.00 0.00 4.40
112 122 5.275263 TGGATTCCTTCCCTTTTCTGAAT 57.725 39.130 3.95 0.00 44.77 2.57
116 126 3.771479 GCAATGGATTCCTTCCCTTTTCT 59.229 43.478 3.95 0.00 44.77 2.52
121 131 1.687368 GCAGCAATGGATTCCTTCCCT 60.687 52.381 3.95 0.00 44.77 4.20
258 268 7.067372 CCACAACACATGATCTTATAATGGTGT 59.933 37.037 0.00 0.00 0.00 4.16
267 277 5.630121 AGGTTTCCACAACACATGATCTTA 58.370 37.500 0.00 0.00 0.00 2.10
291 301 5.669904 TGACCTTGATATAATCAACTGGGGA 59.330 40.000 10.79 0.00 43.84 4.81
312 322 5.050769 CCACATAACTAGCATCGACATTGAC 60.051 44.000 0.00 0.00 0.00 3.18
343 353 0.464373 CTCCACACTGGCGGCATTAT 60.464 55.000 13.85 0.00 37.47 1.28
361 371 1.729586 TGAGTTCCTAGCAACCACCT 58.270 50.000 0.00 0.00 0.00 4.00
391 401 8.812329 CCAGAAAGTCTCACGAAGAAATAATAG 58.188 37.037 0.00 0.00 35.21 1.73
407 418 5.319043 TGGAACATTAACCCAGAAAGTCT 57.681 39.130 0.00 0.00 0.00 3.24
489 500 5.363868 CAGTCTCTGGAATAATGGACTGGTA 59.636 44.000 11.58 0.00 43.68 3.25
505 516 5.505173 AACAAAATCACAACCAGTCTCTG 57.495 39.130 0.00 0.00 0.00 3.35
520 531 3.068024 TGCAAGGAAAGAGCGAACAAAAT 59.932 39.130 0.00 0.00 0.00 1.82
530 541 4.617762 GCCTTCTCATTTGCAAGGAAAGAG 60.618 45.833 0.00 4.50 39.36 2.85
553 564 3.013219 TCAACGAGAGGAGATCTGTCAG 58.987 50.000 0.00 0.00 38.84 3.51
560 571 6.968263 TTCTTCATATCAACGAGAGGAGAT 57.032 37.500 0.00 0.00 34.05 2.75
585 596 5.897250 TCATACTGGATGTACTCAAGGCTTA 59.103 40.000 0.00 0.00 36.84 3.09
617 628 7.064490 AGCCGATTGATTTTCGCAATTTTAAAT 59.936 29.630 0.00 0.00 36.19 1.40
646 657 0.178967 TTTGTGAGCCAGCCCATTGA 60.179 50.000 0.00 0.00 0.00 2.57
654 665 2.287788 ACTTCGCAATTTTGTGAGCCAG 60.288 45.455 6.65 4.99 46.93 4.85
723 736 3.485947 TGCAAAATTCGCCACATAGAC 57.514 42.857 0.00 0.00 0.00 2.59
724 737 4.157472 TCATTGCAAAATTCGCCACATAGA 59.843 37.500 1.71 0.00 0.00 1.98
727 740 3.316071 TCATTGCAAAATTCGCCACAT 57.684 38.095 1.71 0.00 0.00 3.21
804 817 3.702045 CTCAGAGATAAAACGGGGAGTCT 59.298 47.826 0.00 0.00 0.00 3.24
805 818 3.700038 TCTCAGAGATAAAACGGGGAGTC 59.300 47.826 0.00 0.00 0.00 3.36
806 819 3.447944 GTCTCAGAGATAAAACGGGGAGT 59.552 47.826 2.64 0.00 0.00 3.85
818 831 8.964476 TTCTTGTTGTAAAAAGTCTCAGAGAT 57.036 30.769 2.64 0.00 0.00 2.75
831 844 9.311916 CTGTTGGAATTGATTTCTTGTTGTAAA 57.688 29.630 0.00 0.00 34.56 2.01
864 879 2.009774 GGATGTTGTCTGGTTCGGATG 58.990 52.381 0.00 0.00 0.00 3.51
866 881 1.052617 TGGATGTTGTCTGGTTCGGA 58.947 50.000 0.00 0.00 0.00 4.55
867 882 1.156736 GTGGATGTTGTCTGGTTCGG 58.843 55.000 0.00 0.00 0.00 4.30
869 884 2.568623 AGGTGGATGTTGTCTGGTTC 57.431 50.000 0.00 0.00 0.00 3.62
870 885 3.248024 TCTAGGTGGATGTTGTCTGGTT 58.752 45.455 0.00 0.00 0.00 3.67
873 888 3.118956 GGACTCTAGGTGGATGTTGTCTG 60.119 52.174 0.00 0.00 0.00 3.51
875 890 3.100671 AGGACTCTAGGTGGATGTTGTC 58.899 50.000 0.00 0.00 0.00 3.18
936 957 4.459089 GTGCAGAGGGGCGAGGTC 62.459 72.222 0.00 0.00 36.28 3.85
960 983 2.879233 GCTTCTCCCGTGTGGTGGA 61.879 63.158 0.00 0.00 34.77 4.02
985 1034 0.658368 GACATCTCGTCGCTCTGCTA 59.342 55.000 0.00 0.00 34.19 3.49
995 1044 1.078637 TCGGAGGTCGACATCTCGT 60.079 57.895 27.24 0.00 43.74 4.18
1004 1053 3.878519 GCTCGGAGTCGGAGGTCG 61.879 72.222 24.34 4.10 40.90 4.79
1060 1109 2.303549 GATGAGCAGGTGGAGGACGG 62.304 65.000 0.00 0.00 0.00 4.79
1135 2856 4.530857 GCTGGTCGCGGCCATACT 62.531 66.667 35.54 0.00 37.96 2.12
1166 2887 1.534235 AACCAGACGTCCTGAGCCT 60.534 57.895 13.01 0.00 45.78 4.58
1167 2888 1.079750 GAACCAGACGTCCTGAGCC 60.080 63.158 13.01 0.00 45.78 4.70
1169 2890 0.244994 CCTGAACCAGACGTCCTGAG 59.755 60.000 13.01 0.79 45.78 3.35
1170 2891 1.816863 GCCTGAACCAGACGTCCTGA 61.817 60.000 13.01 0.00 45.78 3.86
1171 2892 1.374758 GCCTGAACCAGACGTCCTG 60.375 63.158 13.01 9.80 42.55 3.86
1173 2894 1.668151 GTGCCTGAACCAGACGTCC 60.668 63.158 13.01 0.00 32.44 4.79
1175 2896 2.029073 CGTGCCTGAACCAGACGT 59.971 61.111 0.00 0.00 32.44 4.34
1176 2897 2.738521 CCGTGCCTGAACCAGACG 60.739 66.667 0.00 0.00 33.49 4.18
1177 2898 1.374758 CTCCGTGCCTGAACCAGAC 60.375 63.158 0.00 0.00 32.44 3.51
1178 2899 3.059982 CTCCGTGCCTGAACCAGA 58.940 61.111 0.00 0.00 32.44 3.86
1179 2900 2.743928 GCTCCGTGCCTGAACCAG 60.744 66.667 0.00 0.00 35.15 4.00
1180 2901 3.240134 GAGCTCCGTGCCTGAACCA 62.240 63.158 0.87 0.00 44.23 3.67
1181 2902 2.435059 GAGCTCCGTGCCTGAACC 60.435 66.667 0.87 0.00 44.23 3.62
1182 2903 1.739562 CTGAGCTCCGTGCCTGAAC 60.740 63.158 12.15 0.00 44.23 3.18
1183 2904 2.210013 ACTGAGCTCCGTGCCTGAA 61.210 57.895 12.15 0.00 44.23 3.02
1184 2905 2.601666 ACTGAGCTCCGTGCCTGA 60.602 61.111 12.15 0.00 44.23 3.86
1185 2906 2.433838 CACTGAGCTCCGTGCCTG 60.434 66.667 22.89 2.50 44.23 4.85
1186 2907 3.699894 CCACTGAGCTCCGTGCCT 61.700 66.667 27.40 0.00 44.23 4.75
1194 2915 3.715097 GCAGCCTCCCACTGAGCT 61.715 66.667 0.00 0.00 39.98 4.09
1406 3287 2.097444 GGCGTTTGATTTGTTTTGCTCG 60.097 45.455 0.00 0.00 0.00 5.03
1435 3323 8.088981 ACAACTCGATTCTTGTAGTAGAATTGT 58.911 33.333 11.43 5.46 43.18 2.71
1436 3324 8.467402 ACAACTCGATTCTTGTAGTAGAATTG 57.533 34.615 0.00 0.00 43.18 2.32
1437 3325 9.141400 GAACAACTCGATTCTTGTAGTAGAATT 57.859 33.333 0.00 0.00 43.18 2.17
1440 3328 7.450124 AGAACAACTCGATTCTTGTAGTAGA 57.550 36.000 4.28 0.00 30.88 2.59
1443 3331 6.750148 AGAAGAACAACTCGATTCTTGTAGT 58.250 36.000 14.72 0.00 43.54 2.73
1446 3334 6.049149 TGAAGAAGAACAACTCGATTCTTGT 58.951 36.000 14.72 9.19 43.54 3.16
1448 3336 7.158021 AGATGAAGAAGAACAACTCGATTCTT 58.842 34.615 10.69 10.69 45.61 2.52
1449 3337 6.696411 AGATGAAGAAGAACAACTCGATTCT 58.304 36.000 0.00 0.00 36.73 2.40
1451 3339 7.062371 CGTTAGATGAAGAAGAACAACTCGATT 59.938 37.037 0.00 0.00 0.00 3.34
1452 3340 6.528423 CGTTAGATGAAGAAGAACAACTCGAT 59.472 38.462 0.00 0.00 0.00 3.59
1453 3341 5.856986 CGTTAGATGAAGAAGAACAACTCGA 59.143 40.000 0.00 0.00 0.00 4.04
1455 3343 6.128795 CCACGTTAGATGAAGAAGAACAACTC 60.129 42.308 0.00 0.00 0.00 3.01
1456 3344 5.696724 CCACGTTAGATGAAGAAGAACAACT 59.303 40.000 0.00 0.00 0.00 3.16
1457 3345 5.465724 ACCACGTTAGATGAAGAAGAACAAC 59.534 40.000 0.00 0.00 0.00 3.32
1458 3346 5.465390 CACCACGTTAGATGAAGAAGAACAA 59.535 40.000 0.00 0.00 0.00 2.83
1459 3347 4.988540 CACCACGTTAGATGAAGAAGAACA 59.011 41.667 0.00 0.00 0.00 3.18
1463 3388 3.679980 CACCACCACGTTAGATGAAGAAG 59.320 47.826 0.00 0.00 0.00 2.85
1474 3399 3.413300 ACCCACCACCACCACGTT 61.413 61.111 0.00 0.00 0.00 3.99
1486 3411 2.912025 CCCTGCAACACCACCCAC 60.912 66.667 0.00 0.00 0.00 4.61
1525 3458 2.261671 CCAGTACTTGAGCCGCGT 59.738 61.111 4.92 0.00 0.00 6.01
1583 3516 3.213506 CCTGTTGTCTTGTTGATGGTCA 58.786 45.455 0.00 0.00 0.00 4.02
1587 3521 1.955778 TGGCCTGTTGTCTTGTTGATG 59.044 47.619 3.32 0.00 0.00 3.07
1589 3523 1.955778 CATGGCCTGTTGTCTTGTTGA 59.044 47.619 3.32 0.00 0.00 3.18
1610 3544 1.413812 TGCTGAGTGCTCTTGACTTGA 59.586 47.619 0.68 0.00 43.37 3.02
1615 3549 1.004080 GCCTGCTGAGTGCTCTTGA 60.004 57.895 0.68 0.00 43.37 3.02
1616 3550 1.003597 AGCCTGCTGAGTGCTCTTG 60.004 57.895 0.68 0.00 43.37 3.02
1617 3551 1.296068 GAGCCTGCTGAGTGCTCTT 59.704 57.895 11.64 0.00 46.19 2.85
1621 3555 2.039405 CAAGGAGCCTGCTGAGTGC 61.039 63.158 0.00 0.00 43.25 4.40
1624 3558 1.078567 GGACAAGGAGCCTGCTGAG 60.079 63.158 0.00 0.00 0.00 3.35
1625 3559 1.203441 ATGGACAAGGAGCCTGCTGA 61.203 55.000 0.00 0.00 0.00 4.26
1626 3560 0.323178 AATGGACAAGGAGCCTGCTG 60.323 55.000 0.00 0.00 0.00 4.41
1627 3561 0.323178 CAATGGACAAGGAGCCTGCT 60.323 55.000 0.00 0.00 0.00 4.24
1628 3562 0.322816 TCAATGGACAAGGAGCCTGC 60.323 55.000 0.00 0.00 0.00 4.85
1629 3563 2.295885 GATCAATGGACAAGGAGCCTG 58.704 52.381 0.00 0.00 0.00 4.85
1630 3564 1.918262 TGATCAATGGACAAGGAGCCT 59.082 47.619 0.00 0.00 0.00 4.58
1631 3565 2.425143 TGATCAATGGACAAGGAGCC 57.575 50.000 0.00 0.00 0.00 4.70
1633 3567 3.284617 TGCATGATCAATGGACAAGGAG 58.715 45.455 0.00 0.00 36.71 3.69
1636 3570 5.006153 ACAATGCATGATCAATGGACAAG 57.994 39.130 0.00 0.00 39.72 3.16
1637 3571 4.439016 CGACAATGCATGATCAATGGACAA 60.439 41.667 0.00 0.00 39.72 3.18
1638 3572 3.065648 CGACAATGCATGATCAATGGACA 59.934 43.478 0.00 0.00 39.72 4.02
1649 3583 2.021793 CGACCGCGACAATGCATG 59.978 61.111 8.23 0.00 40.82 4.06
1721 3687 3.310774 AGATTCATCCGCAACGATTCTTG 59.689 43.478 0.00 0.00 0.00 3.02
1733 3699 2.079158 ACACACAGCAAGATTCATCCG 58.921 47.619 0.00 0.00 0.00 4.18
1739 3705 0.478072 TCCCCACACACAGCAAGATT 59.522 50.000 0.00 0.00 0.00 2.40
1749 3715 0.613260 GATGTACAGCTCCCCACACA 59.387 55.000 3.28 0.00 0.00 3.72
1775 3748 3.059188 CACGACCATACAACTGAAACACC 60.059 47.826 0.00 0.00 0.00 4.16
1782 3755 2.154963 CACGAACACGACCATACAACTG 59.845 50.000 0.00 0.00 0.00 3.16
1788 3761 2.029739 ACATGACACGAACACGACCATA 60.030 45.455 0.00 0.00 0.00 2.74
1797 3774 0.511221 CCAACCGACATGACACGAAC 59.489 55.000 0.00 0.00 0.00 3.95
1808 3785 0.032540 ACGTACAGTTCCCAACCGAC 59.967 55.000 0.00 0.00 0.00 4.79
1813 3790 0.831966 ACCACACGTACAGTTCCCAA 59.168 50.000 0.00 0.00 0.00 4.12
1820 3797 3.372822 AGAAACAAACACCACACGTACAG 59.627 43.478 0.00 0.00 0.00 2.74
1827 3804 2.163412 GAGCACAGAAACAAACACCACA 59.837 45.455 0.00 0.00 0.00 4.17
1828 3805 2.423538 AGAGCACAGAAACAAACACCAC 59.576 45.455 0.00 0.00 0.00 4.16
1840 3817 0.613012 TAGCTGGCTCAGAGCACAGA 60.613 55.000 30.33 16.43 44.75 3.41
1878 3855 9.435570 AACCACATGAGTTTATACCTAGATAGT 57.564 33.333 0.00 0.00 0.00 2.12
1879 3856 9.915629 GAACCACATGAGTTTATACCTAGATAG 57.084 37.037 0.00 0.00 0.00 2.08
1880 3857 9.429109 TGAACCACATGAGTTTATACCTAGATA 57.571 33.333 0.00 0.00 0.00 1.98
1881 3858 8.319057 TGAACCACATGAGTTTATACCTAGAT 57.681 34.615 0.00 0.00 0.00 1.98
1882 3859 7.727578 TGAACCACATGAGTTTATACCTAGA 57.272 36.000 0.00 0.00 0.00 2.43
1883 3860 8.786826 TTTGAACCACATGAGTTTATACCTAG 57.213 34.615 0.00 0.00 0.00 3.02
1884 3861 9.747898 ATTTTGAACCACATGAGTTTATACCTA 57.252 29.630 0.00 0.00 0.00 3.08
1885 3862 8.650143 ATTTTGAACCACATGAGTTTATACCT 57.350 30.769 0.00 0.00 0.00 3.08
1889 3866 9.787532 CGATTATTTTGAACCACATGAGTTTAT 57.212 29.630 0.00 0.00 0.00 1.40
1890 3867 8.788806 ACGATTATTTTGAACCACATGAGTTTA 58.211 29.630 0.00 0.00 0.00 2.01
1891 3868 7.657336 ACGATTATTTTGAACCACATGAGTTT 58.343 30.769 0.00 0.00 0.00 2.66
1892 3869 7.214467 ACGATTATTTTGAACCACATGAGTT 57.786 32.000 0.00 2.20 0.00 3.01
1893 3870 6.817765 ACGATTATTTTGAACCACATGAGT 57.182 33.333 0.00 0.00 0.00 3.41
1894 3871 7.696453 GGTAACGATTATTTTGAACCACATGAG 59.304 37.037 0.00 0.00 0.00 2.90
1895 3872 7.531716 GGTAACGATTATTTTGAACCACATGA 58.468 34.615 0.00 0.00 0.00 3.07
1896 3873 7.734538 GGTAACGATTATTTTGAACCACATG 57.265 36.000 0.00 0.00 0.00 3.21
1915 3892 0.386113 CTCCCAGCTAGCTCGGTAAC 59.614 60.000 25.36 0.00 0.00 2.50
1916 3893 0.257905 TCTCCCAGCTAGCTCGGTAA 59.742 55.000 25.36 13.48 0.00 2.85
1917 3894 0.478942 ATCTCCCAGCTAGCTCGGTA 59.521 55.000 25.36 16.30 0.00 4.02
1918 3895 1.112315 CATCTCCCAGCTAGCTCGGT 61.112 60.000 25.36 6.23 0.00 4.69
1919 3896 1.664873 CATCTCCCAGCTAGCTCGG 59.335 63.158 21.39 21.39 0.00 4.63
1920 3897 1.664873 CCATCTCCCAGCTAGCTCG 59.335 63.158 16.15 8.64 0.00 5.03
1921 3898 0.470833 TCCCATCTCCCAGCTAGCTC 60.471 60.000 16.15 0.00 0.00 4.09
1922 3899 0.193069 ATCCCATCTCCCAGCTAGCT 59.807 55.000 12.68 12.68 0.00 3.32
1923 3900 0.324285 CATCCCATCTCCCAGCTAGC 59.676 60.000 6.62 6.62 0.00 3.42
1924 3901 0.982704 CCATCCCATCTCCCAGCTAG 59.017 60.000 0.00 0.00 0.00 3.42
1925 3902 0.567687 TCCATCCCATCTCCCAGCTA 59.432 55.000 0.00 0.00 0.00 3.32
1926 3903 0.104037 ATCCATCCCATCTCCCAGCT 60.104 55.000 0.00 0.00 0.00 4.24
1927 3904 1.661463 TATCCATCCCATCTCCCAGC 58.339 55.000 0.00 0.00 0.00 4.85
1928 3905 4.942363 ATTTATCCATCCCATCTCCCAG 57.058 45.455 0.00 0.00 0.00 4.45
1929 3906 6.240556 CCTTTATTTATCCATCCCATCTCCCA 60.241 42.308 0.00 0.00 0.00 4.37
1930 3907 6.190587 CCTTTATTTATCCATCCCATCTCCC 58.809 44.000 0.00 0.00 0.00 4.30
1931 3908 5.654209 GCCTTTATTTATCCATCCCATCTCC 59.346 44.000 0.00 0.00 0.00 3.71
1932 3909 5.355350 CGCCTTTATTTATCCATCCCATCTC 59.645 44.000 0.00 0.00 0.00 2.75
1933 3910 5.256474 CGCCTTTATTTATCCATCCCATCT 58.744 41.667 0.00 0.00 0.00 2.90
1934 3911 4.399303 CCGCCTTTATTTATCCATCCCATC 59.601 45.833 0.00 0.00 0.00 3.51
1935 3912 4.344104 CCGCCTTTATTTATCCATCCCAT 58.656 43.478 0.00 0.00 0.00 4.00
1936 3913 3.499563 CCCGCCTTTATTTATCCATCCCA 60.500 47.826 0.00 0.00 0.00 4.37
1937 3914 3.089284 CCCGCCTTTATTTATCCATCCC 58.911 50.000 0.00 0.00 0.00 3.85
1938 3915 3.506067 CACCCGCCTTTATTTATCCATCC 59.494 47.826 0.00 0.00 0.00 3.51
1939 3916 4.394729 TCACCCGCCTTTATTTATCCATC 58.605 43.478 0.00 0.00 0.00 3.51
1940 3917 4.104102 TCTCACCCGCCTTTATTTATCCAT 59.896 41.667 0.00 0.00 0.00 3.41
1941 3918 3.456644 TCTCACCCGCCTTTATTTATCCA 59.543 43.478 0.00 0.00 0.00 3.41
1942 3919 4.081322 TCTCACCCGCCTTTATTTATCC 57.919 45.455 0.00 0.00 0.00 2.59
1943 3920 6.262273 TGATTTCTCACCCGCCTTTATTTATC 59.738 38.462 0.00 0.00 0.00 1.75
1944 3921 6.126409 TGATTTCTCACCCGCCTTTATTTAT 58.874 36.000 0.00 0.00 0.00 1.40
1945 3922 5.502079 TGATTTCTCACCCGCCTTTATTTA 58.498 37.500 0.00 0.00 0.00 1.40
1946 3923 4.340617 TGATTTCTCACCCGCCTTTATTT 58.659 39.130 0.00 0.00 0.00 1.40
1947 3924 3.963129 TGATTTCTCACCCGCCTTTATT 58.037 40.909 0.00 0.00 0.00 1.40
1948 3925 3.644966 TGATTTCTCACCCGCCTTTAT 57.355 42.857 0.00 0.00 0.00 1.40
1949 3926 3.541632 GATGATTTCTCACCCGCCTTTA 58.458 45.455 0.00 0.00 33.22 1.85
1950 3927 2.369394 GATGATTTCTCACCCGCCTTT 58.631 47.619 0.00 0.00 33.22 3.11
1951 3928 1.408822 GGATGATTTCTCACCCGCCTT 60.409 52.381 0.00 0.00 33.22 4.35
1952 3929 0.181350 GGATGATTTCTCACCCGCCT 59.819 55.000 0.00 0.00 33.22 5.52
1953 3930 2.707902 GGATGATTTCTCACCCGCC 58.292 57.895 0.00 0.00 33.22 6.13
1956 3933 0.181350 AGGCGGATGATTTCTCACCC 59.819 55.000 0.00 0.00 33.22 4.61
1957 3934 1.303309 CAGGCGGATGATTTCTCACC 58.697 55.000 0.00 0.00 33.22 4.02
1958 3935 1.303309 CCAGGCGGATGATTTCTCAC 58.697 55.000 0.00 0.00 33.22 3.51
1959 3936 0.464373 GCCAGGCGGATGATTTCTCA 60.464 55.000 0.00 0.00 35.41 3.27
1971 3948 4.341502 CAAACGGTTGGCCAGGCG 62.342 66.667 5.11 2.93 34.09 5.52
1983 3960 1.531677 CCACATGCGCCTAATCAAACG 60.532 52.381 4.18 0.00 0.00 3.60
2026 4003 1.032657 AGGATCACGACGTGAGGAGG 61.033 60.000 31.72 5.64 46.04 4.30
2043 4020 0.247460 TTGTGGATGCAGACGAGAGG 59.753 55.000 0.00 0.00 0.00 3.69
2049 4026 2.048603 GGGGCTTGTGGATGCAGAC 61.049 63.158 0.00 0.00 0.00 3.51
2175 4158 3.121030 GATGCAGCGGTCGTGCTT 61.121 61.111 14.87 10.63 44.46 3.91
2276 8186 0.726827 CTCGCGGCAATGAAGCTTAA 59.273 50.000 6.13 0.00 34.17 1.85
2278 8188 2.401766 CCTCGCGGCAATGAAGCTT 61.402 57.895 6.13 0.00 34.17 3.74
2317 8227 0.109597 CGGAGTTGCAATGAAGTGCC 60.110 55.000 0.59 0.00 44.26 5.01
2318 8228 0.109597 CCGGAGTTGCAATGAAGTGC 60.110 55.000 0.59 0.00 45.15 4.40
2320 8230 1.577328 CGCCGGAGTTGCAATGAAGT 61.577 55.000 5.05 0.00 0.00 3.01
2353 8268 1.153449 CAATAAGCACCGCCGGAGA 60.153 57.895 11.71 0.00 0.00 3.71
2489 8405 1.523711 CAGGTATTGCGATGCCCGT 60.524 57.895 16.85 0.00 38.69 5.28
2491 8407 0.463654 TCACAGGTATTGCGATGCCC 60.464 55.000 16.85 6.88 38.69 5.36
2506 8422 2.279851 CAACGCCGTCAGGTCACA 60.280 61.111 0.00 0.00 40.50 3.58
2532 8448 3.057548 CACCTTGCTGCATGCCGA 61.058 61.111 16.68 0.00 42.00 5.54


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

AutoCloner maintained by Alex Coulton.