Multiple sequence alignment - TraesCS2D01G508200

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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 TraesCS2D01G508200 chr2D 100.000 3377 0 0 1 3377 601264939 601261563 0.000000e+00 6237.0
1 TraesCS2D01G508200 chr2D 79.318 469 87 8 966 1427 601255532 601255067 1.510000e-83 320.0
2 TraesCS2D01G508200 chr2A 95.386 1517 62 2 919 2427 734654313 734652797 0.000000e+00 2407.0
3 TraesCS2D01G508200 chr2A 94.765 745 37 2 2407 3150 734652781 734652038 0.000000e+00 1158.0
4 TraesCS2D01G508200 chr2A 92.744 317 19 3 98 412 734658479 734658165 3.970000e-124 455.0
5 TraesCS2D01G508200 chr2A 87.500 272 16 8 533 790 734657859 734657592 7.080000e-77 298.0
6 TraesCS2D01G508200 chr2A 89.756 205 18 2 3176 3377 734651960 734651756 3.340000e-65 259.0
7 TraesCS2D01G508200 chr2A 85.593 118 16 1 423 539 579718118 579718235 4.580000e-24 122.0
8 TraesCS2D01G508200 chr7D 82.531 1391 232 10 984 2367 60705484 60704098 0.000000e+00 1212.0
9 TraesCS2D01G508200 chr7D 80.586 1365 253 7 1029 2385 62280168 62281528 0.000000e+00 1042.0
10 TraesCS2D01G508200 chr7D 80.873 1260 229 9 1133 2386 62260491 62259238 0.000000e+00 981.0
11 TraesCS2D01G508200 chr7D 80.544 1249 236 4 1141 2385 62122193 62123438 0.000000e+00 953.0
12 TraesCS2D01G508200 chr7D 81.250 112 15 4 423 532 191064262 191064155 6.000000e-13 86.1
13 TraesCS2D01G508200 chr7D 79.048 105 10 3 422 526 488806578 488806486 1.010000e-05 62.1
14 TraesCS2D01G508200 chr7A 81.747 1408 250 6 976 2378 65154751 65153346 0.000000e+00 1170.0
15 TraesCS2D01G508200 chr7A 81.105 1249 229 4 1141 2385 65442037 65443282 0.000000e+00 992.0
16 TraesCS2D01G508200 chr7A 79.518 1328 253 12 1070 2386 65329796 65328477 0.000000e+00 928.0
17 TraesCS2D01G508200 chr2B 81.548 1382 241 10 992 2371 731536644 731535275 0.000000e+00 1127.0
18 TraesCS2D01G508200 chr2B 86.940 268 34 1 2407 2673 731480921 731480654 1.970000e-77 300.0
19 TraesCS2D01G508200 chr2B 75.993 604 91 30 2816 3377 731476710 731476119 2.580000e-66 263.0
20 TraesCS2D01G508200 chr2B 88.889 90 9 1 431 520 587245934 587245846 3.560000e-20 110.0
21 TraesCS2D01G508200 chr5D 91.398 93 7 1 2 94 295079028 295079119 3.540000e-25 126.0
22 TraesCS2D01G508200 chr1D 89.216 102 10 1 426 526 11045629 11045528 3.540000e-25 126.0
23 TraesCS2D01G508200 chr1D 88.636 88 9 1 440 526 114116085 114116172 4.610000e-19 106.0
24 TraesCS2D01G508200 chr3B 84.762 105 14 2 426 528 41476645 41476749 1.660000e-18 104.0
25 TraesCS2D01G508200 chr3D 85.000 100 13 2 433 531 274360222 274360320 2.140000e-17 100.0
26 TraesCS2D01G508200 chr1A 85.000 80 11 1 453 531 329525565 329525486 2.790000e-11 80.5
27 TraesCS2D01G508200 chr6D 94.118 51 1 1 422 470 447892330 447892380 3.610000e-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 TraesCS2D01G508200 chr2D 601261563 601264939 3376 True 6237.0 6237 100.0000 1 3377 1 chr2D.!!$R2 3376
1 TraesCS2D01G508200 chr2A 734651756 734658479 6723 True 915.4 2407 92.0302 98 3377 5 chr2A.!!$R1 3279
2 TraesCS2D01G508200 chr7D 60704098 60705484 1386 True 1212.0 1212 82.5310 984 2367 1 chr7D.!!$R1 1383
3 TraesCS2D01G508200 chr7D 62280168 62281528 1360 False 1042.0 1042 80.5860 1029 2385 1 chr7D.!!$F2 1356
4 TraesCS2D01G508200 chr7D 62259238 62260491 1253 True 981.0 981 80.8730 1133 2386 1 chr7D.!!$R2 1253
5 TraesCS2D01G508200 chr7D 62122193 62123438 1245 False 953.0 953 80.5440 1141 2385 1 chr7D.!!$F1 1244
6 TraesCS2D01G508200 chr7A 65153346 65154751 1405 True 1170.0 1170 81.7470 976 2378 1 chr7A.!!$R1 1402
7 TraesCS2D01G508200 chr7A 65442037 65443282 1245 False 992.0 992 81.1050 1141 2385 1 chr7A.!!$F1 1244
8 TraesCS2D01G508200 chr7A 65328477 65329796 1319 True 928.0 928 79.5180 1070 2386 1 chr7A.!!$R2 1316
9 TraesCS2D01G508200 chr2B 731535275 731536644 1369 True 1127.0 1127 81.5480 992 2371 1 chr2B.!!$R2 1379
10 TraesCS2D01G508200 chr2B 731476119 731480921 4802 True 281.5 300 81.4665 2407 3377 2 chr2B.!!$R3 970

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
835 1062 0.031515 TTCCCTCTCGCTATCCCCAA 60.032 55.0 0.0 0.0 0.0 4.12 F
903 3094 0.107410 TTGGGTGTTGTCTCAAGCGT 60.107 50.0 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 5705 0.179009 GATGGATGCAGCTAGCCCAA 60.179 55.000 12.13 0.0 44.83 4.12 R
2786 6211 1.202903 AGTCGACCCAGTCTACACAGT 60.203 52.381 13.01 0.0 31.87 3.55 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
38 39 9.747898 AGTGTGGTACTTAATCCAATAAAATGA 57.252 29.630 0.00 0.00 35.67 2.57
46 47 7.759433 ACTTAATCCAATAAAATGAAAGGTGCG 59.241 33.333 0.00 0.00 0.00 5.34
47 48 5.659440 ATCCAATAAAATGAAAGGTGCGT 57.341 34.783 0.00 0.00 0.00 5.24
48 49 5.461032 TCCAATAAAATGAAAGGTGCGTT 57.539 34.783 0.00 0.00 0.00 4.84
49 50 6.576662 TCCAATAAAATGAAAGGTGCGTTA 57.423 33.333 0.00 0.00 0.00 3.18
50 51 7.164230 TCCAATAAAATGAAAGGTGCGTTAT 57.836 32.000 0.00 0.00 0.00 1.89
51 52 8.282455 TCCAATAAAATGAAAGGTGCGTTATA 57.718 30.769 0.00 0.00 0.00 0.98
52 53 8.402472 TCCAATAAAATGAAAGGTGCGTTATAG 58.598 33.333 0.00 0.00 0.00 1.31
53 54 8.402472 CCAATAAAATGAAAGGTGCGTTATAGA 58.598 33.333 0.00 0.00 0.00 1.98
54 55 9.781834 CAATAAAATGAAAGGTGCGTTATAGAA 57.218 29.630 0.00 0.00 0.00 2.10
56 57 5.485662 AATGAAAGGTGCGTTATAGAAGC 57.514 39.130 0.00 0.00 0.00 3.86
57 58 3.932822 TGAAAGGTGCGTTATAGAAGCA 58.067 40.909 0.00 0.00 38.71 3.91
58 59 4.320023 TGAAAGGTGCGTTATAGAAGCAA 58.680 39.130 1.32 0.00 42.93 3.91
59 60 4.757657 TGAAAGGTGCGTTATAGAAGCAAA 59.242 37.500 1.32 0.00 42.93 3.68
60 61 4.946784 AAGGTGCGTTATAGAAGCAAAG 57.053 40.909 1.32 0.00 42.93 2.77
61 62 3.939066 AGGTGCGTTATAGAAGCAAAGT 58.061 40.909 1.32 0.00 42.93 2.66
62 63 3.684788 AGGTGCGTTATAGAAGCAAAGTG 59.315 43.478 1.32 0.00 42.93 3.16
63 64 3.417185 GTGCGTTATAGAAGCAAAGTGC 58.583 45.455 0.00 0.00 45.46 4.40
64 65 2.418628 TGCGTTATAGAAGCAAAGTGCC 59.581 45.455 0.00 0.00 46.52 5.01
65 66 2.418628 GCGTTATAGAAGCAAAGTGCCA 59.581 45.455 0.00 0.00 46.52 4.92
66 67 3.485877 GCGTTATAGAAGCAAAGTGCCAG 60.486 47.826 0.00 0.00 46.52 4.85
67 68 3.063997 CGTTATAGAAGCAAAGTGCCAGG 59.936 47.826 0.00 0.00 46.52 4.45
68 69 4.261801 GTTATAGAAGCAAAGTGCCAGGA 58.738 43.478 0.00 0.00 46.52 3.86
69 70 2.949177 TAGAAGCAAAGTGCCAGGAA 57.051 45.000 0.00 0.00 46.52 3.36
70 71 2.071778 AGAAGCAAAGTGCCAGGAAA 57.928 45.000 0.00 0.00 46.52 3.13
71 72 2.387757 AGAAGCAAAGTGCCAGGAAAA 58.612 42.857 0.00 0.00 46.52 2.29
72 73 2.363359 AGAAGCAAAGTGCCAGGAAAAG 59.637 45.455 0.00 0.00 46.52 2.27
73 74 1.780503 AGCAAAGTGCCAGGAAAAGT 58.219 45.000 0.00 0.00 46.52 2.66
74 75 1.410153 AGCAAAGTGCCAGGAAAAGTG 59.590 47.619 0.00 0.00 46.52 3.16
75 76 1.136891 GCAAAGTGCCAGGAAAAGTGT 59.863 47.619 0.00 0.00 37.42 3.55
76 77 2.813061 CAAAGTGCCAGGAAAAGTGTG 58.187 47.619 0.00 0.00 0.00 3.82
77 78 1.402787 AAGTGCCAGGAAAAGTGTGG 58.597 50.000 0.00 0.00 0.00 4.17
83 84 3.030668 CCAGGAAAAGTGTGGCATTTC 57.969 47.619 3.29 3.29 34.93 2.17
86 87 3.303881 GGAAAAGTGTGGCATTTCCTC 57.696 47.619 18.63 0.63 46.09 3.71
87 88 2.893489 GGAAAAGTGTGGCATTTCCTCT 59.107 45.455 18.63 0.00 46.09 3.69
88 89 4.079253 GGAAAAGTGTGGCATTTCCTCTA 58.921 43.478 18.63 0.00 46.09 2.43
89 90 4.522789 GGAAAAGTGTGGCATTTCCTCTAA 59.477 41.667 18.63 0.00 46.09 2.10
90 91 5.010617 GGAAAAGTGTGGCATTTCCTCTAAA 59.989 40.000 18.63 0.00 46.09 1.85
91 92 6.295292 GGAAAAGTGTGGCATTTCCTCTAAAT 60.295 38.462 18.63 0.00 46.09 1.40
92 93 6.670695 AAAGTGTGGCATTTCCTCTAAATT 57.329 33.333 0.00 0.00 35.54 1.82
93 94 5.649782 AGTGTGGCATTTCCTCTAAATTG 57.350 39.130 0.00 0.00 35.54 2.32
94 95 5.079643 AGTGTGGCATTTCCTCTAAATTGT 58.920 37.500 0.00 0.00 35.54 2.71
95 96 5.183904 AGTGTGGCATTTCCTCTAAATTGTC 59.816 40.000 0.00 0.00 35.54 3.18
96 97 5.048083 GTGTGGCATTTCCTCTAAATTGTCA 60.048 40.000 0.00 0.00 35.54 3.58
106 107 7.707624 TCCTCTAAATTGTCATGCAAGATTT 57.292 32.000 0.00 0.00 40.86 2.17
113 114 4.508461 TGTCATGCAAGATTTGAGGTTG 57.492 40.909 0.00 0.00 0.00 3.77
118 119 6.479660 GTCATGCAAGATTTGAGGTTGAAAAA 59.520 34.615 0.00 0.00 0.00 1.94
196 197 7.597288 AAAACTAGACAGCCCAAATTAGTTT 57.403 32.000 0.00 2.56 40.86 2.66
235 236 7.821134 ACCTCTTCAATATCTATGGGCTAAT 57.179 36.000 0.00 0.00 0.00 1.73
237 238 7.238514 ACCTCTTCAATATCTATGGGCTAATGT 59.761 37.037 0.00 0.00 0.00 2.71
294 295 4.751098 GTGCAATGTGAAAAACATGGACAT 59.249 37.500 0.00 0.00 44.51 3.06
340 343 2.033424 GGAAAGAGGATTTATGGCACGC 59.967 50.000 0.00 0.00 0.00 5.34
343 346 1.486310 AGAGGATTTATGGCACGCAGA 59.514 47.619 0.00 0.00 0.00 4.26
383 386 4.444056 CCTCGTGCACACTTTTTATTTTGG 59.556 41.667 18.64 0.00 0.00 3.28
435 438 7.639113 TTTTTGCGGGTAATCTTTCATATCT 57.361 32.000 0.00 0.00 0.00 1.98
436 439 7.639113 TTTTGCGGGTAATCTTTCATATCTT 57.361 32.000 0.00 0.00 0.00 2.40
437 440 7.639113 TTTGCGGGTAATCTTTCATATCTTT 57.361 32.000 0.00 0.00 0.00 2.52
438 441 7.639113 TTGCGGGTAATCTTTCATATCTTTT 57.361 32.000 0.00 0.00 0.00 2.27
439 442 7.026631 TGCGGGTAATCTTTCATATCTTTTG 57.973 36.000 0.00 0.00 0.00 2.44
440 443 6.826231 TGCGGGTAATCTTTCATATCTTTTGA 59.174 34.615 0.00 0.00 0.00 2.69
441 444 7.338196 TGCGGGTAATCTTTCATATCTTTTGAA 59.662 33.333 0.00 0.00 0.00 2.69
442 445 7.644157 GCGGGTAATCTTTCATATCTTTTGAAC 59.356 37.037 0.00 0.00 33.03 3.18
443 446 7.850982 CGGGTAATCTTTCATATCTTTTGAACG 59.149 37.037 0.00 0.00 33.03 3.95
444 447 8.889717 GGGTAATCTTTCATATCTTTTGAACGA 58.110 33.333 0.00 0.00 36.29 3.85
484 487 9.301153 AGTTGTGTTTTCATATTTGTGTTTCTC 57.699 29.630 0.00 0.00 0.00 2.87
487 490 7.971168 TGTGTTTTCATATTTGTGTTTCTCGTT 59.029 29.630 0.00 0.00 0.00 3.85
501 504 3.973206 TCTCGTTATGAGGGCTTTCAA 57.027 42.857 1.24 0.00 45.32 2.69
506 509 6.538742 TCTCGTTATGAGGGCTTTCAAATAAG 59.461 38.462 1.24 0.00 45.32 1.73
529 532 7.148733 AGATTCATTTTGAAACGTTTTGACG 57.851 32.000 15.89 2.70 40.12 4.35
530 533 6.970043 AGATTCATTTTGAAACGTTTTGACGA 59.030 30.769 15.89 5.01 40.12 4.20
531 534 6.547493 TTCATTTTGAAACGTTTTGACGAG 57.453 33.333 15.89 5.18 32.71 4.18
582 799 1.531739 GCGTGCCCCTTGGAATTTCA 61.532 55.000 0.00 0.00 0.00 2.69
612 829 8.884323 TGCTAGGAAGATGGTTGAGAATAATAT 58.116 33.333 0.00 0.00 0.00 1.28
641 868 2.363306 ATGGTTGAGAAGTTGGCACA 57.637 45.000 0.00 0.00 0.00 4.57
650 877 0.814010 AAGTTGGCACACACGGTCTC 60.814 55.000 0.00 0.00 39.29 3.36
670 897 4.326548 TCTCATACGTACTATCATCGCTCG 59.673 45.833 0.00 0.00 0.00 5.03
680 907 2.757686 TCATCGCTCGTGTACTGATC 57.242 50.000 0.00 0.00 0.00 2.92
688 915 5.178067 TCGCTCGTGTACTGATCGATATTTA 59.822 40.000 0.00 0.00 30.04 1.40
689 916 6.022208 CGCTCGTGTACTGATCGATATTTAT 58.978 40.000 0.00 0.00 33.26 1.40
708 935 6.985188 TTTATTTGATCTAGGTGTGCACTC 57.015 37.500 19.41 14.79 0.00 3.51
710 937 0.817654 TGATCTAGGTGTGCACTCCG 59.182 55.000 27.41 16.95 34.85 4.63
715 942 1.257750 TAGGTGTGCACTCCGCTGAT 61.258 55.000 27.41 15.18 43.06 2.90
727 954 4.026804 CACTCCGCTGATGTTACGTATTTC 60.027 45.833 0.00 0.00 0.00 2.17
760 987 5.185056 TCTTGTAATGGAAGATCGTGAGTGA 59.815 40.000 0.00 0.00 0.00 3.41
772 999 4.932268 TCGTGAGTGAAAAGAAACGTTT 57.068 36.364 14.57 14.57 33.07 3.60
785 1012 1.851658 AACGTTTGAAGGCATGCAAC 58.148 45.000 21.36 13.51 0.00 4.17
802 1029 2.539476 CAACGCCCTTGCATAAAATCC 58.461 47.619 0.00 0.00 37.32 3.01
803 1030 1.111277 ACGCCCTTGCATAAAATCCC 58.889 50.000 0.00 0.00 37.32 3.85
804 1031 0.389025 CGCCCTTGCATAAAATCCCC 59.611 55.000 0.00 0.00 37.32 4.81
805 1032 0.758734 GCCCTTGCATAAAATCCCCC 59.241 55.000 0.00 0.00 37.47 5.40
806 1033 1.969240 GCCCTTGCATAAAATCCCCCA 60.969 52.381 0.00 0.00 37.47 4.96
807 1034 1.762370 CCCTTGCATAAAATCCCCCAC 59.238 52.381 0.00 0.00 0.00 4.61
809 1036 2.465813 CTTGCATAAAATCCCCCACCA 58.534 47.619 0.00 0.00 0.00 4.17
810 1037 2.864885 TGCATAAAATCCCCCACCAT 57.135 45.000 0.00 0.00 0.00 3.55
811 1038 3.127791 TGCATAAAATCCCCCACCATT 57.872 42.857 0.00 0.00 0.00 3.16
812 1039 4.271807 TGCATAAAATCCCCCACCATTA 57.728 40.909 0.00 0.00 0.00 1.90
813 1040 3.964031 TGCATAAAATCCCCCACCATTAC 59.036 43.478 0.00 0.00 0.00 1.89
814 1041 4.223144 GCATAAAATCCCCCACCATTACT 58.777 43.478 0.00 0.00 0.00 2.24
816 1043 5.705400 CATAAAATCCCCCACCATTACTCT 58.295 41.667 0.00 0.00 0.00 3.24
817 1044 4.692523 AAAATCCCCCACCATTACTCTT 57.307 40.909 0.00 0.00 0.00 2.85
819 1046 1.591768 TCCCCCACCATTACTCTTCC 58.408 55.000 0.00 0.00 0.00 3.46
820 1047 0.551396 CCCCCACCATTACTCTTCCC 59.449 60.000 0.00 0.00 0.00 3.97
821 1048 1.596496 CCCCACCATTACTCTTCCCT 58.404 55.000 0.00 0.00 0.00 4.20
822 1049 1.490910 CCCCACCATTACTCTTCCCTC 59.509 57.143 0.00 0.00 0.00 4.30
824 1051 2.436173 CCCACCATTACTCTTCCCTCTC 59.564 54.545 0.00 0.00 0.00 3.20
825 1052 2.101582 CCACCATTACTCTTCCCTCTCG 59.898 54.545 0.00 0.00 0.00 4.04
826 1053 1.757699 ACCATTACTCTTCCCTCTCGC 59.242 52.381 0.00 0.00 0.00 5.03
827 1054 2.035632 CCATTACTCTTCCCTCTCGCT 58.964 52.381 0.00 0.00 0.00 4.93
829 1056 3.829601 CCATTACTCTTCCCTCTCGCTAT 59.170 47.826 0.00 0.00 0.00 2.97
831 1058 1.989706 ACTCTTCCCTCTCGCTATCC 58.010 55.000 0.00 0.00 0.00 2.59
832 1059 1.253100 CTCTTCCCTCTCGCTATCCC 58.747 60.000 0.00 0.00 0.00 3.85
834 1061 0.470080 CTTCCCTCTCGCTATCCCCA 60.470 60.000 0.00 0.00 0.00 4.96
835 1062 0.031515 TTCCCTCTCGCTATCCCCAA 60.032 55.000 0.00 0.00 0.00 4.12
837 1064 1.364171 CCTCTCGCTATCCCCAACG 59.636 63.158 0.00 0.00 0.00 4.10
838 1065 1.300233 CTCTCGCTATCCCCAACGC 60.300 63.158 0.00 0.00 0.00 4.84
839 1066 2.016393 CTCTCGCTATCCCCAACGCA 62.016 60.000 0.00 0.00 0.00 5.24
841 1068 2.125310 CGCTATCCCCAACGCACA 60.125 61.111 0.00 0.00 0.00 4.57
843 1070 1.498865 CGCTATCCCCAACGCACATC 61.499 60.000 0.00 0.00 0.00 3.06
844 1071 0.179045 GCTATCCCCAACGCACATCT 60.179 55.000 0.00 0.00 0.00 2.90
845 1072 1.586422 CTATCCCCAACGCACATCTG 58.414 55.000 0.00 0.00 0.00 2.90
846 1073 0.908910 TATCCCCAACGCACATCTGT 59.091 50.000 0.00 0.00 0.00 3.41
855 1082 2.171701 CACATCTGTGCACGCGTG 59.828 61.111 34.01 34.01 39.39 5.34
858 3049 1.282248 ACATCTGTGCACGCGTGTAC 61.282 55.000 41.37 41.37 44.73 2.90
863 3054 1.771044 GTGCACGCGTGTACACTAC 59.229 57.895 42.30 25.02 44.06 2.73
864 3055 0.935831 GTGCACGCGTGTACACTACA 60.936 55.000 42.30 27.05 44.06 2.74
874 3065 2.030371 TGTACACTACACGACCCAACA 58.970 47.619 0.00 0.00 32.89 3.33
875 3066 2.034939 TGTACACTACACGACCCAACAG 59.965 50.000 0.00 0.00 32.89 3.16
879 3070 1.202486 ACTACACGACCCAACAGTGTG 60.202 52.381 10.27 0.00 46.94 3.82
880 3071 1.067974 CTACACGACCCAACAGTGTGA 59.932 52.381 10.27 0.00 46.94 3.58
881 3072 0.468226 ACACGACCCAACAGTGTGAT 59.532 50.000 0.00 0.00 45.99 3.06
883 3074 2.288825 ACACGACCCAACAGTGTGATAG 60.289 50.000 0.00 0.00 45.99 2.08
884 3075 1.968493 ACGACCCAACAGTGTGATAGT 59.032 47.619 0.00 0.00 0.00 2.12
892 3083 3.857157 ACAGTGTGATAGTTGGGTGTT 57.143 42.857 0.00 0.00 0.00 3.32
893 3084 3.476552 ACAGTGTGATAGTTGGGTGTTG 58.523 45.455 0.00 0.00 0.00 3.33
894 3085 3.118038 ACAGTGTGATAGTTGGGTGTTGT 60.118 43.478 0.00 0.00 0.00 3.32
895 3086 3.498397 CAGTGTGATAGTTGGGTGTTGTC 59.502 47.826 0.00 0.00 0.00 3.18
896 3087 3.391296 AGTGTGATAGTTGGGTGTTGTCT 59.609 43.478 0.00 0.00 0.00 3.41
898 3089 3.389656 TGTGATAGTTGGGTGTTGTCTCA 59.610 43.478 0.00 0.00 0.00 3.27
899 3090 4.141597 TGTGATAGTTGGGTGTTGTCTCAA 60.142 41.667 0.00 0.00 0.00 3.02
900 3091 4.452455 GTGATAGTTGGGTGTTGTCTCAAG 59.548 45.833 0.00 0.00 0.00 3.02
901 3092 1.680338 AGTTGGGTGTTGTCTCAAGC 58.320 50.000 0.00 0.00 0.00 4.01
902 3093 0.307760 GTTGGGTGTTGTCTCAAGCG 59.692 55.000 0.00 0.00 0.00 4.68
903 3094 0.107410 TTGGGTGTTGTCTCAAGCGT 60.107 50.000 0.00 0.00 0.00 5.07
904 3095 0.531974 TGGGTGTTGTCTCAAGCGTC 60.532 55.000 0.00 0.00 0.00 5.19
905 3096 0.531974 GGGTGTTGTCTCAAGCGTCA 60.532 55.000 0.00 0.00 0.00 4.35
907 3098 1.286501 GTGTTGTCTCAAGCGTCACA 58.713 50.000 0.00 0.00 0.00 3.58
982 4359 3.316868 GCTAACTGCTAAGATCCTCGTCT 59.683 47.826 0.00 0.00 38.95 4.18
1027 4404 2.320587 GCAACTGCCGTCCTCACAG 61.321 63.158 0.00 0.00 37.45 3.66
1033 4410 1.272490 CTGCCGTCCTCACAGAAGTTA 59.728 52.381 0.00 0.00 33.10 2.24
1055 4432 0.387622 CAATGGCTTTCCACTGCACG 60.388 55.000 0.00 0.00 46.92 5.34
1103 4480 9.194972 TGATATATGTCTCATCCATCTACTTCC 57.805 37.037 0.89 0.00 0.00 3.46
1105 4482 3.994317 TGTCTCATCCATCTACTTCCCA 58.006 45.455 0.00 0.00 0.00 4.37
1119 4499 3.690460 ACTTCCCATCGCTCTTTTGATT 58.310 40.909 0.00 0.00 0.00 2.57
1139 4519 2.661718 TGTCACGGCTACCATCTATCA 58.338 47.619 0.00 0.00 0.00 2.15
1892 5272 4.123506 GCACTCTCTAAAGACCTTATGGC 58.876 47.826 0.00 0.00 36.63 4.40
1893 5273 4.698575 CACTCTCTAAAGACCTTATGGCC 58.301 47.826 0.00 0.00 36.63 5.36
1964 5344 2.169352 TCCTACCAGCATCAGAGCTTTC 59.831 50.000 0.00 0.00 43.70 2.62
1998 5378 2.192664 TCTGCATGGCGAAAAAGGTA 57.807 45.000 0.00 0.00 0.00 3.08
2050 5430 5.115480 TCCCAAACTTTTCTGTTGCATTTC 58.885 37.500 0.00 0.00 0.00 2.17
2061 5441 4.341806 TCTGTTGCATTTCACCATTTCTGT 59.658 37.500 0.00 0.00 0.00 3.41
2217 5597 4.599041 TGGCATACATTGAAGCTAAAGGT 58.401 39.130 4.96 4.96 0.00 3.50
2253 5633 1.549203 ACAAGGTGTGGATGATTGGC 58.451 50.000 0.00 0.00 0.00 4.52
2301 5681 3.194861 CGTTGGGTGGATGTGTATACAG 58.805 50.000 5.62 0.00 40.79 2.74
2313 5693 4.655649 ATGTGTATACAGCCATCTTCTGGA 59.344 41.667 5.62 0.00 43.48 3.86
2325 5705 1.306141 TTCTGGAGCGGATGGACCT 60.306 57.895 0.00 0.00 36.31 3.85
2409 5834 7.705325 AGGTTAATCGCATCGACATAATATACC 59.295 37.037 0.00 0.00 39.18 2.73
2412 5837 4.740268 TCGCATCGACATAATATACCACC 58.260 43.478 0.00 0.00 0.00 4.61
2415 5840 4.630069 GCATCGACATAATATACCACCACC 59.370 45.833 0.00 0.00 0.00 4.61
2507 5932 1.139455 CCATTGCCCAAAAGCCTATGG 59.861 52.381 0.00 0.00 37.50 2.74
2510 5935 0.679640 TGCCCAAAAGCCTATGGTCG 60.680 55.000 0.00 0.00 34.79 4.79
2644 6069 5.923733 TGAGAACTCCCTGTCTCTAATTC 57.076 43.478 2.66 0.00 0.00 2.17
2778 6203 2.887568 GTGGCGAGCATGAGGACG 60.888 66.667 0.00 0.00 0.00 4.79
2807 6502 2.039480 ACTGTGTAGACTGGGTCGACTA 59.961 50.000 16.46 4.19 38.61 2.59
2868 10112 9.043548 AGTATATTAAGTACAACAGGTCCTTGT 57.956 33.333 1.84 1.84 35.92 3.16
2919 10166 3.885724 ATGAAATTTTTAGGGGTGCCG 57.114 42.857 0.00 0.00 0.00 5.69
2947 10194 1.080354 TCCTTCTGGATCCACCGGT 59.920 57.895 11.44 0.00 44.89 5.28
2975 10228 1.636570 GAAGCTCGGTCCCGCTTTTC 61.637 60.000 12.81 7.38 45.70 2.29
3058 10311 3.990318 AAGTCGTCGATGCAGATCATA 57.010 42.857 0.00 0.00 35.05 2.15
3093 10346 3.930229 CCGTGATTCTACGAACCAAATCA 59.070 43.478 9.29 0.00 46.46 2.57
3099 10352 2.301870 TCTACGAACCAAATCACTGCCT 59.698 45.455 0.00 0.00 0.00 4.75
3127 10380 6.235664 AGAAGGAAACGACAATAAAGGCTTA 58.764 36.000 0.00 0.00 0.00 3.09
3130 10383 8.570068 AAGGAAACGACAATAAAGGCTTATAA 57.430 30.769 0.00 0.00 0.00 0.98
3135 10388 8.975410 AACGACAATAAAGGCTTATAAAAACC 57.025 30.769 0.00 0.00 0.00 3.27
3143 10456 6.835819 AAGGCTTATAAAAACCCTGAAGAC 57.164 37.500 0.00 0.00 0.00 3.01
3155 10468 2.619074 CCCTGAAGACCCATCAGAAACC 60.619 54.545 5.16 0.00 45.74 3.27
3166 10479 3.684788 CCATCAGAAACCTAAACCGACTG 59.315 47.826 0.00 0.00 0.00 3.51
3216 10531 4.043200 GCCTTGACCGTTGGCAGC 62.043 66.667 0.00 0.00 45.46 5.25
3230 10545 3.761481 GCAGCAAGCACACTAACAG 57.239 52.632 0.00 0.00 44.79 3.16
3236 10551 2.031682 GCAAGCACACTAACAGAACAGG 60.032 50.000 0.00 0.00 0.00 4.00
3242 10557 4.261197 GCACACTAACAGAACAGGAAAAGG 60.261 45.833 0.00 0.00 0.00 3.11
3267 10582 5.632034 AGGGAGAACATTATTCCTACACC 57.368 43.478 0.00 0.00 0.00 4.16
3316 10631 3.304659 CCAAACCAAACATGAAGACTCCG 60.305 47.826 0.00 0.00 0.00 4.63
3318 10633 2.494059 ACCAAACATGAAGACTCCGTG 58.506 47.619 0.00 0.00 0.00 4.94
3320 10635 2.738846 CCAAACATGAAGACTCCGTGAG 59.261 50.000 0.00 0.03 35.52 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.739972 GGATTAAGTACCACACTTTTCATTGAT 58.260 33.333 0.00 0.00 45.54 2.57
3 4 7.721842 TGGATTAAGTACCACACTTTTCATTGA 59.278 33.333 0.00 0.00 45.54 2.57
4 5 7.881142 TGGATTAAGTACCACACTTTTCATTG 58.119 34.615 0.00 0.00 45.54 2.82
5 6 8.472007 TTGGATTAAGTACCACACTTTTCATT 57.528 30.769 0.00 0.00 45.54 2.57
6 7 8.650143 ATTGGATTAAGTACCACACTTTTCAT 57.350 30.769 0.00 0.00 45.54 2.57
7 8 9.575868 TTATTGGATTAAGTACCACACTTTTCA 57.424 29.630 0.00 0.00 45.54 2.69
12 13 9.747898 TCATTTTATTGGATTAAGTACCACACT 57.252 29.630 0.00 0.00 40.05 3.55
20 21 7.759433 CGCACCTTTCATTTTATTGGATTAAGT 59.241 33.333 0.00 0.00 0.00 2.24
21 22 7.759433 ACGCACCTTTCATTTTATTGGATTAAG 59.241 33.333 0.00 0.00 0.00 1.85
22 23 7.607250 ACGCACCTTTCATTTTATTGGATTAA 58.393 30.769 0.00 0.00 0.00 1.40
23 24 7.164230 ACGCACCTTTCATTTTATTGGATTA 57.836 32.000 0.00 0.00 0.00 1.75
24 25 6.036577 ACGCACCTTTCATTTTATTGGATT 57.963 33.333 0.00 0.00 0.00 3.01
25 26 5.659440 ACGCACCTTTCATTTTATTGGAT 57.341 34.783 0.00 0.00 0.00 3.41
26 27 5.461032 AACGCACCTTTCATTTTATTGGA 57.539 34.783 0.00 0.00 0.00 3.53
27 28 8.402472 TCTATAACGCACCTTTCATTTTATTGG 58.598 33.333 0.00 0.00 0.00 3.16
28 29 9.781834 TTCTATAACGCACCTTTCATTTTATTG 57.218 29.630 0.00 0.00 0.00 1.90
30 31 8.129211 GCTTCTATAACGCACCTTTCATTTTAT 58.871 33.333 0.00 0.00 0.00 1.40
31 32 7.119992 TGCTTCTATAACGCACCTTTCATTTTA 59.880 33.333 0.00 0.00 0.00 1.52
32 33 6.072175 TGCTTCTATAACGCACCTTTCATTTT 60.072 34.615 0.00 0.00 0.00 1.82
33 34 5.414454 TGCTTCTATAACGCACCTTTCATTT 59.586 36.000 0.00 0.00 0.00 2.32
34 35 4.941263 TGCTTCTATAACGCACCTTTCATT 59.059 37.500 0.00 0.00 0.00 2.57
35 36 4.513442 TGCTTCTATAACGCACCTTTCAT 58.487 39.130 0.00 0.00 0.00 2.57
36 37 3.932822 TGCTTCTATAACGCACCTTTCA 58.067 40.909 0.00 0.00 0.00 2.69
37 38 4.939509 TTGCTTCTATAACGCACCTTTC 57.060 40.909 0.00 0.00 32.71 2.62
38 39 4.760204 ACTTTGCTTCTATAACGCACCTTT 59.240 37.500 0.00 0.00 32.71 3.11
39 40 4.154195 CACTTTGCTTCTATAACGCACCTT 59.846 41.667 0.00 0.00 32.71 3.50
40 41 3.684788 CACTTTGCTTCTATAACGCACCT 59.315 43.478 0.00 0.00 32.71 4.00
41 42 3.727970 GCACTTTGCTTCTATAACGCACC 60.728 47.826 0.00 0.00 40.96 5.01
42 43 3.417185 GCACTTTGCTTCTATAACGCAC 58.583 45.455 0.00 0.00 40.96 5.34
43 44 2.418628 GGCACTTTGCTTCTATAACGCA 59.581 45.455 0.00 0.00 44.28 5.24
44 45 2.418628 TGGCACTTTGCTTCTATAACGC 59.581 45.455 0.00 0.00 44.28 4.84
45 46 3.063997 CCTGGCACTTTGCTTCTATAACG 59.936 47.826 0.00 0.00 44.28 3.18
46 47 4.261801 TCCTGGCACTTTGCTTCTATAAC 58.738 43.478 0.00 0.00 44.28 1.89
47 48 4.568072 TCCTGGCACTTTGCTTCTATAA 57.432 40.909 0.00 0.00 44.28 0.98
48 49 4.568072 TTCCTGGCACTTTGCTTCTATA 57.432 40.909 0.00 0.00 44.28 1.31
49 50 3.439857 TTCCTGGCACTTTGCTTCTAT 57.560 42.857 0.00 0.00 44.28 1.98
50 51 2.949177 TTCCTGGCACTTTGCTTCTA 57.051 45.000 0.00 0.00 44.28 2.10
51 52 2.071778 TTTCCTGGCACTTTGCTTCT 57.928 45.000 0.00 0.00 44.28 2.85
52 53 2.101415 ACTTTTCCTGGCACTTTGCTTC 59.899 45.455 0.00 0.00 44.28 3.86
53 54 2.110578 ACTTTTCCTGGCACTTTGCTT 58.889 42.857 0.00 0.00 44.28 3.91
54 55 1.410153 CACTTTTCCTGGCACTTTGCT 59.590 47.619 0.00 0.00 44.28 3.91
55 56 1.136891 ACACTTTTCCTGGCACTTTGC 59.863 47.619 0.00 0.00 44.08 3.68
56 57 2.481795 CCACACTTTTCCTGGCACTTTG 60.482 50.000 0.00 0.00 0.00 2.77
57 58 1.756538 CCACACTTTTCCTGGCACTTT 59.243 47.619 0.00 0.00 0.00 2.66
58 59 1.402787 CCACACTTTTCCTGGCACTT 58.597 50.000 0.00 0.00 0.00 3.16
59 60 3.116091 CCACACTTTTCCTGGCACT 57.884 52.632 0.00 0.00 0.00 4.40
63 64 3.030668 GAAATGCCACACTTTTCCTGG 57.969 47.619 0.00 0.00 36.76 4.45
67 68 5.705609 TTAGAGGAAATGCCACACTTTTC 57.294 39.130 0.00 0.00 40.17 2.29
68 69 6.670695 ATTTAGAGGAAATGCCACACTTTT 57.329 33.333 0.00 0.00 36.35 2.27
69 70 6.041979 ACAATTTAGAGGAAATGCCACACTTT 59.958 34.615 0.00 0.00 37.82 2.66
70 71 5.539955 ACAATTTAGAGGAAATGCCACACTT 59.460 36.000 0.00 0.00 37.82 3.16
71 72 5.079643 ACAATTTAGAGGAAATGCCACACT 58.920 37.500 0.00 0.00 37.82 3.55
72 73 5.048083 TGACAATTTAGAGGAAATGCCACAC 60.048 40.000 0.00 0.00 37.82 3.82
73 74 5.076182 TGACAATTTAGAGGAAATGCCACA 58.924 37.500 0.00 0.00 37.82 4.17
74 75 5.643379 TGACAATTTAGAGGAAATGCCAC 57.357 39.130 0.00 0.00 37.82 5.01
75 76 5.394443 GCATGACAATTTAGAGGAAATGCCA 60.394 40.000 0.00 0.00 37.82 4.92
76 77 5.045872 GCATGACAATTTAGAGGAAATGCC 58.954 41.667 0.00 0.00 37.82 4.40
77 78 5.653507 TGCATGACAATTTAGAGGAAATGC 58.346 37.500 0.00 0.00 37.82 3.56
78 79 7.541162 TCTTGCATGACAATTTAGAGGAAATG 58.459 34.615 0.00 0.00 37.82 2.32
79 80 7.707624 TCTTGCATGACAATTTAGAGGAAAT 57.292 32.000 0.00 0.00 39.56 2.17
80 81 7.707624 ATCTTGCATGACAATTTAGAGGAAA 57.292 32.000 4.14 0.00 37.72 3.13
81 82 7.707624 AATCTTGCATGACAATTTAGAGGAA 57.292 32.000 4.14 0.00 37.72 3.36
82 83 7.394077 TCAAATCTTGCATGACAATTTAGAGGA 59.606 33.333 4.14 0.00 37.72 3.71
83 84 7.541162 TCAAATCTTGCATGACAATTTAGAGG 58.459 34.615 4.14 0.00 37.72 3.69
84 85 7.701078 CCTCAAATCTTGCATGACAATTTAGAG 59.299 37.037 4.14 10.30 37.72 2.43
85 86 7.177216 ACCTCAAATCTTGCATGACAATTTAGA 59.823 33.333 4.14 0.00 37.72 2.10
86 87 7.318141 ACCTCAAATCTTGCATGACAATTTAG 58.682 34.615 4.14 2.60 37.72 1.85
87 88 7.230849 ACCTCAAATCTTGCATGACAATTTA 57.769 32.000 4.14 0.00 37.72 1.40
88 89 6.105397 ACCTCAAATCTTGCATGACAATTT 57.895 33.333 4.14 0.00 37.72 1.82
89 90 5.733620 ACCTCAAATCTTGCATGACAATT 57.266 34.783 4.14 0.00 37.72 2.32
90 91 5.244402 TCAACCTCAAATCTTGCATGACAAT 59.756 36.000 4.14 0.00 37.72 2.71
91 92 4.583907 TCAACCTCAAATCTTGCATGACAA 59.416 37.500 4.14 0.00 36.62 3.18
92 93 4.143543 TCAACCTCAAATCTTGCATGACA 58.856 39.130 4.14 0.00 0.00 3.58
93 94 4.771590 TCAACCTCAAATCTTGCATGAC 57.228 40.909 4.14 0.00 0.00 3.06
94 95 5.787953 TTTCAACCTCAAATCTTGCATGA 57.212 34.783 4.57 4.57 0.00 3.07
95 96 6.847956 TTTTTCAACCTCAAATCTTGCATG 57.152 33.333 0.00 0.00 0.00 4.06
96 97 6.366877 CGATTTTTCAACCTCAAATCTTGCAT 59.633 34.615 0.00 0.00 35.57 3.96
106 107 4.377839 TGCAAACGATTTTTCAACCTCA 57.622 36.364 0.00 0.00 0.00 3.86
118 119 8.564574 TGTTTCTCTACTTAAAATGCAAACGAT 58.435 29.630 0.00 0.00 0.00 3.73
171 172 7.597288 AACTAATTTGGGCTGTCTAGTTTTT 57.403 32.000 0.00 0.00 0.00 1.94
196 197 4.646945 TGAAGAGGTTTTAATGCACCAACA 59.353 37.500 0.00 0.00 35.25 3.33
237 238 9.539825 GCACTCTCATTCAGATTATTAGAAAGA 57.460 33.333 0.00 0.00 0.00 2.52
294 295 3.308595 GCATTACATGTTGCACGCTAGTA 59.691 43.478 15.97 0.00 38.72 1.82
315 316 2.625314 GCCATAAATCCTCTTTCCTGGC 59.375 50.000 0.00 0.00 40.89 4.85
316 317 3.633986 GTGCCATAAATCCTCTTTCCTGG 59.366 47.826 0.00 0.00 0.00 4.45
317 318 3.313526 CGTGCCATAAATCCTCTTTCCTG 59.686 47.826 0.00 0.00 0.00 3.86
318 319 3.545703 CGTGCCATAAATCCTCTTTCCT 58.454 45.455 0.00 0.00 0.00 3.36
319 320 2.033424 GCGTGCCATAAATCCTCTTTCC 59.967 50.000 0.00 0.00 0.00 3.13
320 321 2.682856 TGCGTGCCATAAATCCTCTTTC 59.317 45.455 0.00 0.00 0.00 2.62
321 322 2.684881 CTGCGTGCCATAAATCCTCTTT 59.315 45.455 0.00 0.00 0.00 2.52
322 323 2.092968 TCTGCGTGCCATAAATCCTCTT 60.093 45.455 0.00 0.00 0.00 2.85
368 371 5.523438 TCGGAAGCCAAAATAAAAAGTGT 57.477 34.783 0.00 0.00 0.00 3.55
370 373 7.213678 TGAAATCGGAAGCCAAAATAAAAAGT 58.786 30.769 0.00 0.00 0.00 2.66
383 386 7.869800 AGATATGAAAGATTGAAATCGGAAGC 58.130 34.615 0.00 0.00 40.35 3.86
412 415 7.639113 AAGATATGAAAGATTACCCGCAAAA 57.361 32.000 0.00 0.00 0.00 2.44
413 416 7.639113 AAAGATATGAAAGATTACCCGCAAA 57.361 32.000 0.00 0.00 0.00 3.68
414 417 7.338196 TCAAAAGATATGAAAGATTACCCGCAA 59.662 33.333 0.00 0.00 0.00 4.85
417 420 7.850982 CGTTCAAAAGATATGAAAGATTACCCG 59.149 37.037 0.00 0.00 38.15 5.28
418 421 8.889717 TCGTTCAAAAGATATGAAAGATTACCC 58.110 33.333 1.68 0.00 39.33 3.69
440 443 8.751302 ACACAACTTAATTTGAACTTTTCGTT 57.249 26.923 12.06 0.00 38.91 3.85
441 444 8.751302 AACACAACTTAATTTGAACTTTTCGT 57.249 26.923 12.06 0.00 0.00 3.85
475 478 2.301870 AGCCCTCATAACGAGAAACACA 59.698 45.455 0.00 0.00 45.45 3.72
484 487 6.677781 TCTTATTTGAAAGCCCTCATAACG 57.322 37.500 0.00 0.00 0.00 3.18
487 490 9.425248 AATGAATCTTATTTGAAAGCCCTCATA 57.575 29.630 0.00 0.00 0.00 2.15
563 778 1.215382 GAAATTCCAAGGGGCACGC 59.785 57.895 0.00 0.00 43.76 5.34
565 780 4.696455 CATATTGAAATTCCAAGGGGCAC 58.304 43.478 0.00 0.00 0.00 5.01
566 781 3.134442 GCATATTGAAATTCCAAGGGGCA 59.866 43.478 0.00 0.00 0.00 5.36
570 785 7.503566 TCTTCCTAGCATATTGAAATTCCAAGG 59.496 37.037 0.00 0.00 0.00 3.61
571 786 8.455903 TCTTCCTAGCATATTGAAATTCCAAG 57.544 34.615 0.00 0.00 0.00 3.61
582 799 6.753913 TCTCAACCATCTTCCTAGCATATT 57.246 37.500 0.00 0.00 0.00 1.28
612 829 7.013274 GCCAACTTCTCAACCATAAGCATATTA 59.987 37.037 0.00 0.00 0.00 0.98
613 830 6.183360 GCCAACTTCTCAACCATAAGCATATT 60.183 38.462 0.00 0.00 0.00 1.28
615 832 4.640201 GCCAACTTCTCAACCATAAGCATA 59.360 41.667 0.00 0.00 0.00 3.14
616 833 3.445096 GCCAACTTCTCAACCATAAGCAT 59.555 43.478 0.00 0.00 0.00 3.79
617 834 2.819608 GCCAACTTCTCAACCATAAGCA 59.180 45.455 0.00 0.00 0.00 3.91
618 835 2.819608 TGCCAACTTCTCAACCATAAGC 59.180 45.455 0.00 0.00 0.00 3.09
619 836 3.820467 TGTGCCAACTTCTCAACCATAAG 59.180 43.478 0.00 0.00 0.00 1.73
620 837 3.568007 GTGTGCCAACTTCTCAACCATAA 59.432 43.478 0.00 0.00 0.00 1.90
641 868 4.445453 TGATAGTACGTATGAGACCGTGT 58.555 43.478 0.00 0.00 37.91 4.49
650 877 4.082447 CACGAGCGATGATAGTACGTATG 58.918 47.826 0.00 0.00 0.00 2.39
680 907 8.223769 GTGCACACCTAGATCAAATAAATATCG 58.776 37.037 13.17 0.00 0.00 2.92
688 915 3.679917 CGGAGTGCACACCTAGATCAAAT 60.680 47.826 27.50 0.00 0.00 2.32
689 916 2.353704 CGGAGTGCACACCTAGATCAAA 60.354 50.000 27.50 0.00 0.00 2.69
708 935 3.489785 GGAGAAATACGTAACATCAGCGG 59.510 47.826 0.00 0.00 0.00 5.52
710 937 4.439057 TGGGAGAAATACGTAACATCAGC 58.561 43.478 0.00 0.00 0.00 4.26
715 942 6.479972 AGATCATGGGAGAAATACGTAACA 57.520 37.500 0.00 0.00 0.00 2.41
727 954 5.933617 TCTTCCATTACAAGATCATGGGAG 58.066 41.667 10.00 10.00 43.04 4.30
760 987 3.555547 GCATGCCTTCAAACGTTTCTTTT 59.444 39.130 11.37 0.00 0.00 2.27
785 1012 0.389025 GGGGATTTTATGCAAGGGCG 59.611 55.000 0.00 0.00 45.35 6.13
790 1017 2.630889 TGGTGGGGGATTTTATGCAA 57.369 45.000 0.00 0.00 0.00 4.08
791 1018 2.864885 ATGGTGGGGGATTTTATGCA 57.135 45.000 0.00 0.00 0.00 3.96
793 1020 5.705400 AGAGTAATGGTGGGGGATTTTATG 58.295 41.667 0.00 0.00 0.00 1.90
795 1022 5.340528 GGAAGAGTAATGGTGGGGGATTTTA 60.341 44.000 0.00 0.00 0.00 1.52
797 1024 3.052869 GGAAGAGTAATGGTGGGGGATTT 60.053 47.826 0.00 0.00 0.00 2.17
799 1026 2.136026 GGAAGAGTAATGGTGGGGGAT 58.864 52.381 0.00 0.00 0.00 3.85
800 1027 1.591768 GGAAGAGTAATGGTGGGGGA 58.408 55.000 0.00 0.00 0.00 4.81
801 1028 0.551396 GGGAAGAGTAATGGTGGGGG 59.449 60.000 0.00 0.00 0.00 5.40
802 1029 1.490910 GAGGGAAGAGTAATGGTGGGG 59.509 57.143 0.00 0.00 0.00 4.96
803 1030 2.436173 GAGAGGGAAGAGTAATGGTGGG 59.564 54.545 0.00 0.00 0.00 4.61
804 1031 2.101582 CGAGAGGGAAGAGTAATGGTGG 59.898 54.545 0.00 0.00 0.00 4.61
805 1032 2.482142 GCGAGAGGGAAGAGTAATGGTG 60.482 54.545 0.00 0.00 0.00 4.17
806 1033 1.757699 GCGAGAGGGAAGAGTAATGGT 59.242 52.381 0.00 0.00 0.00 3.55
807 1034 2.035632 AGCGAGAGGGAAGAGTAATGG 58.964 52.381 0.00 0.00 0.00 3.16
809 1036 4.083565 GGATAGCGAGAGGGAAGAGTAAT 58.916 47.826 0.00 0.00 0.00 1.89
810 1037 3.488363 GGATAGCGAGAGGGAAGAGTAA 58.512 50.000 0.00 0.00 0.00 2.24
811 1038 2.224818 GGGATAGCGAGAGGGAAGAGTA 60.225 54.545 0.00 0.00 0.00 2.59
812 1039 1.479757 GGGATAGCGAGAGGGAAGAGT 60.480 57.143 0.00 0.00 0.00 3.24
813 1040 1.253100 GGGATAGCGAGAGGGAAGAG 58.747 60.000 0.00 0.00 0.00 2.85
814 1041 0.178958 GGGGATAGCGAGAGGGAAGA 60.179 60.000 0.00 0.00 0.00 2.87
816 1043 0.031515 TTGGGGATAGCGAGAGGGAA 60.032 55.000 0.00 0.00 0.00 3.97
817 1044 0.759436 GTTGGGGATAGCGAGAGGGA 60.759 60.000 0.00 0.00 0.00 4.20
819 1046 1.364171 CGTTGGGGATAGCGAGAGG 59.636 63.158 0.00 0.00 0.00 3.69
820 1047 1.300233 GCGTTGGGGATAGCGAGAG 60.300 63.158 0.00 0.00 0.00 3.20
821 1048 2.055633 TGCGTTGGGGATAGCGAGA 61.056 57.895 0.00 0.00 0.00 4.04
822 1049 1.883084 GTGCGTTGGGGATAGCGAG 60.883 63.158 0.00 0.00 0.00 5.03
824 1051 1.498865 GATGTGCGTTGGGGATAGCG 61.499 60.000 0.00 0.00 0.00 4.26
825 1052 0.179045 AGATGTGCGTTGGGGATAGC 60.179 55.000 0.00 0.00 0.00 2.97
826 1053 1.134401 ACAGATGTGCGTTGGGGATAG 60.134 52.381 0.00 0.00 0.00 2.08
827 1054 0.908910 ACAGATGTGCGTTGGGGATA 59.091 50.000 0.00 0.00 0.00 2.59
829 1056 1.302431 CACAGATGTGCGTTGGGGA 60.302 57.895 0.00 0.00 39.39 4.81
839 1066 1.006688 TACACGCGTGCACAGATGT 60.007 52.632 37.35 18.73 0.00 3.06
841 1068 1.006688 TGTACACGCGTGCACAGAT 60.007 52.632 35.01 20.18 32.35 2.90
846 1073 1.359475 TGTAGTGTACACGCGTGCA 59.641 52.632 37.35 24.66 35.15 4.57
847 1074 4.231753 TGTAGTGTACACGCGTGC 57.768 55.556 37.35 23.10 36.20 5.34
854 1081 2.030371 TGTTGGGTCGTGTAGTGTACA 58.970 47.619 0.00 0.00 36.08 2.90
855 1082 2.035066 ACTGTTGGGTCGTGTAGTGTAC 59.965 50.000 0.00 0.00 0.00 2.90
858 3049 1.202486 ACACTGTTGGGTCGTGTAGTG 60.202 52.381 0.00 0.00 39.86 2.74
859 3050 1.117150 ACACTGTTGGGTCGTGTAGT 58.883 50.000 0.00 0.00 39.86 2.73
863 3054 2.288825 ACTATCACACTGTTGGGTCGTG 60.289 50.000 0.00 0.00 34.92 4.35
864 3055 1.968493 ACTATCACACTGTTGGGTCGT 59.032 47.619 0.00 0.00 0.00 4.34
871 3062 3.857157 ACACCCAACTATCACACTGTT 57.143 42.857 0.00 0.00 0.00 3.16
874 3065 3.391296 AGACAACACCCAACTATCACACT 59.609 43.478 0.00 0.00 0.00 3.55
875 3066 3.740115 AGACAACACCCAACTATCACAC 58.260 45.455 0.00 0.00 0.00 3.82
879 3070 3.437049 GCTTGAGACAACACCCAACTATC 59.563 47.826 0.00 0.00 0.00 2.08
880 3071 3.412386 GCTTGAGACAACACCCAACTAT 58.588 45.455 0.00 0.00 0.00 2.12
881 3072 2.805295 CGCTTGAGACAACACCCAACTA 60.805 50.000 0.00 0.00 0.00 2.24
883 3074 0.307760 CGCTTGAGACAACACCCAAC 59.692 55.000 0.00 0.00 0.00 3.77
884 3075 0.107410 ACGCTTGAGACAACACCCAA 60.107 50.000 0.00 0.00 0.00 4.12
892 3083 2.407090 CAATCTGTGACGCTTGAGACA 58.593 47.619 0.00 0.00 0.00 3.41
893 3084 1.127582 GCAATCTGTGACGCTTGAGAC 59.872 52.381 0.00 0.00 0.00 3.36
894 3085 1.001293 AGCAATCTGTGACGCTTGAGA 59.999 47.619 0.00 0.00 0.00 3.27
895 3086 1.436600 AGCAATCTGTGACGCTTGAG 58.563 50.000 0.00 0.00 0.00 3.02
896 3087 2.741759 TAGCAATCTGTGACGCTTGA 57.258 45.000 0.00 0.00 35.93 3.02
898 3089 7.041780 CCTTTTATATAGCAATCTGTGACGCTT 60.042 37.037 0.00 0.00 35.93 4.68
899 3090 6.425114 CCTTTTATATAGCAATCTGTGACGCT 59.575 38.462 0.00 0.00 38.51 5.07
900 3091 6.423905 TCCTTTTATATAGCAATCTGTGACGC 59.576 38.462 0.00 0.00 0.00 5.19
901 3092 7.946655 TCCTTTTATATAGCAATCTGTGACG 57.053 36.000 0.00 0.00 0.00 4.35
902 3093 9.937175 GTTTCCTTTTATATAGCAATCTGTGAC 57.063 33.333 0.00 0.00 0.00 3.67
903 3094 9.679661 TGTTTCCTTTTATATAGCAATCTGTGA 57.320 29.630 0.00 0.00 0.00 3.58
1027 4404 4.846779 TGGAAAGCCATTGTGTAACTTC 57.153 40.909 0.00 0.00 39.92 3.01
1055 4432 1.322442 GGATTGGGGCATAGTCTTGC 58.678 55.000 0.00 0.00 42.01 4.01
1103 4480 3.725895 CGTGACAATCAAAAGAGCGATGG 60.726 47.826 0.00 0.00 0.00 3.51
1105 4482 2.416547 CCGTGACAATCAAAAGAGCGAT 59.583 45.455 0.00 0.00 0.00 4.58
1119 4499 2.661718 TGATAGATGGTAGCCGTGACA 58.338 47.619 0.00 0.00 0.00 3.58
1242 4622 6.316140 CGGTAGAATCATCAATCAAAGGTGAA 59.684 38.462 0.00 0.00 37.30 3.18
1892 5272 3.490759 GTGCATCACCAGCGACGG 61.491 66.667 0.00 0.00 33.85 4.79
1893 5273 2.433145 AGTGCATCACCAGCGACG 60.433 61.111 0.00 0.00 34.49 5.12
1998 5378 4.080638 GGTCTGATCTTCCTCCAATGAAGT 60.081 45.833 0.00 0.00 40.10 3.01
2061 5441 3.236391 GGCCCACCGACATGGATA 58.764 61.111 0.00 0.00 43.02 2.59
2205 5585 3.513912 TCTTCATCCGACCTTTAGCTTCA 59.486 43.478 0.00 0.00 0.00 3.02
2217 5597 2.559698 TGTTGCCTTTCTTCATCCGA 57.440 45.000 0.00 0.00 0.00 4.55
2253 5633 1.942657 CATTCATACCCTGCACCGAAG 59.057 52.381 0.00 0.00 0.00 3.79
2313 5693 4.115199 GCCCAAGGTCCATCCGCT 62.115 66.667 0.00 0.00 41.99 5.52
2325 5705 0.179009 GATGGATGCAGCTAGCCCAA 60.179 55.000 12.13 0.00 44.83 4.12
2392 5781 4.630069 GGTGGTGGTATATTATGTCGATGC 59.370 45.833 0.00 0.00 0.00 3.91
2409 5834 5.047590 TGTTGATGTAGTAGTAGTGGTGGTG 60.048 44.000 0.00 0.00 0.00 4.17
2412 5837 7.101652 AGATGTTGATGTAGTAGTAGTGGTG 57.898 40.000 0.00 0.00 0.00 4.17
2507 5932 1.544691 TCTGCCCTCTCTAAACACGAC 59.455 52.381 0.00 0.00 0.00 4.34
2510 5935 5.105310 TGACTATTCTGCCCTCTCTAAACAC 60.105 44.000 0.00 0.00 0.00 3.32
2644 6069 5.574815 AAATTGCACTTTTTCGGAAATCG 57.425 34.783 3.67 1.43 40.90 3.34
2748 6173 2.282407 CTCGCCACACATCATCATCAA 58.718 47.619 0.00 0.00 0.00 2.57
2778 6203 2.868583 CCAGTCTACACAGTATGCATGC 59.131 50.000 11.82 11.82 42.53 4.06
2786 6211 1.202903 AGTCGACCCAGTCTACACAGT 60.203 52.381 13.01 0.00 31.87 3.55
2820 10064 1.580845 CCTTCGGCCTTTGCACAGAG 61.581 60.000 0.17 0.00 40.13 3.35
2856 10100 4.196971 GAGTGTGTTTACAAGGACCTGTT 58.803 43.478 0.00 0.00 38.82 3.16
2910 10157 3.069778 GAAGACTTCGGCACCCCT 58.930 61.111 0.00 0.00 0.00 4.79
3026 10279 2.736995 CGACTTTTCGGCCGCAGA 60.737 61.111 23.51 3.32 41.89 4.26
3099 10352 5.472137 CCTTTATTGTCGTTTCCTTCTCCAA 59.528 40.000 0.00 0.00 0.00 3.53
3112 10365 7.700656 CAGGGTTTTTATAAGCCTTTATTGTCG 59.299 37.037 3.50 0.00 45.06 4.35
3114 10367 8.658840 TCAGGGTTTTTATAAGCCTTTATTGT 57.341 30.769 3.50 0.00 45.06 2.71
3127 10380 5.015178 TCTGATGGGTCTTCAGGGTTTTTAT 59.985 40.000 9.79 0.00 40.80 1.40
3130 10383 2.716424 TCTGATGGGTCTTCAGGGTTTT 59.284 45.455 9.79 0.00 40.80 2.43
3135 10388 2.307098 AGGTTTCTGATGGGTCTTCAGG 59.693 50.000 9.79 0.00 40.80 3.86
3143 10456 3.007635 GTCGGTTTAGGTTTCTGATGGG 58.992 50.000 0.00 0.00 0.00 4.00
3155 10468 2.604046 CTGGGATCCAGTCGGTTTAG 57.396 55.000 15.23 0.00 45.82 1.85
3166 10479 0.394565 CGATGGGTCTTCTGGGATCC 59.605 60.000 1.92 1.92 37.04 3.36
3216 10531 3.466836 TCCTGTTCTGTTAGTGTGCTTG 58.533 45.455 0.00 0.00 0.00 4.01
3225 10540 4.042435 CCCTACCCTTTTCCTGTTCTGTTA 59.958 45.833 0.00 0.00 0.00 2.41
3230 10545 2.910977 TCTCCCTACCCTTTTCCTGTTC 59.089 50.000 0.00 0.00 0.00 3.18
3236 10551 6.546403 GGAATAATGTTCTCCCTACCCTTTTC 59.454 42.308 0.00 0.00 0.00 2.29
3242 10557 6.464039 GGTGTAGGAATAATGTTCTCCCTACC 60.464 46.154 0.00 0.00 43.19 3.18
3267 10582 4.114997 GGCGGCAACATTGTCCCG 62.115 66.667 18.98 18.98 0.00 5.14


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

AutoCloner maintained by Alex Coulton.