Multiple sequence alignment - TraesCS2B01G133200

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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 TraesCS2B01G133200 chr2B 100.000 3650 0 0 1 3650 99759046 99755397 0.000000e+00 6741.0
1 TraesCS2B01G133200 chr2B 88.571 210 24 0 2345 2554 99756651 99756442 4.680000e-64 255.0
2 TraesCS2B01G133200 chr2B 88.571 210 24 0 2396 2605 99756702 99756493 4.680000e-64 255.0
3 TraesCS2B01G133200 chr2A 91.557 2440 122 39 572 2975 65327068 65324677 0.000000e+00 3288.0
4 TraesCS2B01G133200 chr2A 92.593 378 20 5 2967 3341 65324471 65324099 1.490000e-148 536.0
5 TraesCS2B01G133200 chr2A 94.521 219 11 1 3432 3650 65324096 65323879 1.620000e-88 337.0
6 TraesCS2B01G133200 chr2A 86.207 232 26 2 2391 2616 65325312 65325081 2.810000e-61 246.0
7 TraesCS2B01G133200 chr2A 82.203 236 12 4 106 322 65349505 65349281 3.750000e-40 176.0
8 TraesCS2B01G133200 chr2A 86.164 159 17 3 2442 2596 65325312 65325155 2.250000e-37 167.0
9 TraesCS2B01G133200 chr2A 90.244 82 7 1 356 436 65334593 65334512 4.980000e-19 106.0
10 TraesCS2B01G133200 chr2A 94.340 53 3 0 51 103 65349600 65349548 8.400000e-12 82.4
11 TraesCS2B01G133200 chr2A 93.750 48 2 1 324 370 65349262 65349215 1.820000e-08 71.3
12 TraesCS2B01G133200 chr2D 90.257 2063 116 37 632 2656 63690955 63688940 0.000000e+00 2617.0
13 TraesCS2B01G133200 chr2D 92.875 407 15 8 2800 3198 63688935 63688535 2.440000e-161 579.0
14 TraesCS2B01G133200 chr2D 91.184 397 21 3 3267 3650 63688519 63688124 8.980000e-146 527.0
15 TraesCS2B01G133200 chr2D 92.500 160 10 2 101 260 63691587 63691430 1.020000e-55 228.0
16 TraesCS2B01G133200 chr2D 87.845 181 22 0 2345 2525 63689199 63689019 2.860000e-51 213.0


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 TraesCS2B01G133200 chr2B 99755397 99759046 3649 True 2417.0 6741 92.380667 1 3650 3 chr2B.!!$R1 3649
1 TraesCS2B01G133200 chr2A 65323879 65327068 3189 True 914.8 3288 90.208400 572 3650 5 chr2A.!!$R2 3078
2 TraesCS2B01G133200 chr2D 63688124 63691587 3463 True 832.8 2617 90.932200 101 3650 5 chr2D.!!$R1 3549

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
564 779 0.037697 TCACGGCACTACATCACCAC 60.038 55.0 0.00 0.0 0.0 4.16 F
626 841 0.038166 GTCCATCTGCCCAAAGTCCA 59.962 55.0 0.00 0.0 0.0 4.02 F
1617 1873 0.178944 GGGGCCTAGTTTGGTTTGGT 60.179 55.0 0.84 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1669 0.249784 CGCACCCTCTGATGGAGATG 60.250 60.0 5.95 0.0 44.45 2.90 R
2571 2840 0.178767 TCTGGGCATCAGATTCCACG 59.821 55.0 1.14 0.0 46.71 4.94 R
2837 3106 0.526211 ACATTAGAGACAGACGCGCA 59.474 50.0 5.73 0.0 0.00 6.09 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
34 35 7.507733 AGTAGGAGTACTATAAACCATCACG 57.492 40.000 0.00 0.00 37.76 4.35
35 36 7.285566 AGTAGGAGTACTATAAACCATCACGA 58.714 38.462 0.00 0.00 37.76 4.35
36 37 6.388435 AGGAGTACTATAAACCATCACGAC 57.612 41.667 0.00 0.00 0.00 4.34
37 38 5.889853 AGGAGTACTATAAACCATCACGACA 59.110 40.000 0.00 0.00 0.00 4.35
38 39 6.550108 AGGAGTACTATAAACCATCACGACAT 59.450 38.462 0.00 0.00 0.00 3.06
39 40 7.722728 AGGAGTACTATAAACCATCACGACATA 59.277 37.037 0.00 0.00 0.00 2.29
40 41 8.521176 GGAGTACTATAAACCATCACGACATAT 58.479 37.037 0.00 0.00 0.00 1.78
41 42 9.557338 GAGTACTATAAACCATCACGACATATC 57.443 37.037 0.00 0.00 0.00 1.63
57 58 6.292389 GACATATCGATTGTTCCCTTTCTG 57.708 41.667 1.71 0.00 0.00 3.02
58 59 5.126067 ACATATCGATTGTTCCCTTTCTGG 58.874 41.667 1.71 0.00 0.00 3.86
59 60 3.721087 ATCGATTGTTCCCTTTCTGGT 57.279 42.857 0.00 0.00 0.00 4.00
60 61 3.053831 TCGATTGTTCCCTTTCTGGTC 57.946 47.619 0.00 0.00 0.00 4.02
61 62 2.084546 CGATTGTTCCCTTTCTGGTCC 58.915 52.381 0.00 0.00 0.00 4.46
62 63 2.084546 GATTGTTCCCTTTCTGGTCCG 58.915 52.381 0.00 0.00 0.00 4.79
63 64 0.109723 TTGTTCCCTTTCTGGTCCGG 59.890 55.000 0.00 0.00 0.00 5.14
64 65 1.002502 GTTCCCTTTCTGGTCCGGG 60.003 63.158 0.00 0.00 38.07 5.73
65 66 1.151987 TTCCCTTTCTGGTCCGGGA 60.152 57.895 0.00 0.00 43.75 5.14
66 67 0.549169 TTCCCTTTCTGGTCCGGGAT 60.549 55.000 0.00 0.00 44.73 3.85
67 68 0.981277 TCCCTTTCTGGTCCGGGATC 60.981 60.000 0.00 0.00 40.69 3.36
68 69 0.983378 CCCTTTCTGGTCCGGGATCT 60.983 60.000 9.08 0.00 39.08 2.75
69 70 1.691482 CCCTTTCTGGTCCGGGATCTA 60.691 57.143 9.08 0.00 39.08 1.98
70 71 1.413077 CCTTTCTGGTCCGGGATCTAC 59.587 57.143 9.08 0.00 0.00 2.59
71 72 2.108168 CTTTCTGGTCCGGGATCTACA 58.892 52.381 9.08 1.57 0.00 2.74
72 73 1.776662 TTCTGGTCCGGGATCTACAG 58.223 55.000 9.08 10.94 0.00 2.74
73 74 0.629596 TCTGGTCCGGGATCTACAGT 59.370 55.000 9.08 0.00 0.00 3.55
74 75 0.747255 CTGGTCCGGGATCTACAGTG 59.253 60.000 9.08 0.00 0.00 3.66
75 76 0.040646 TGGTCCGGGATCTACAGTGT 59.959 55.000 9.08 0.00 0.00 3.55
76 77 0.460311 GGTCCGGGATCTACAGTGTG 59.540 60.000 5.88 0.00 0.00 3.82
77 78 0.460311 GTCCGGGATCTACAGTGTGG 59.540 60.000 5.88 2.38 0.00 4.17
78 79 1.144057 CCGGGATCTACAGTGTGGC 59.856 63.158 5.88 0.00 0.00 5.01
79 80 1.226974 CGGGATCTACAGTGTGGCG 60.227 63.158 5.88 0.00 0.00 5.69
80 81 1.663379 CGGGATCTACAGTGTGGCGA 61.663 60.000 5.88 0.00 0.00 5.54
81 82 0.535335 GGGATCTACAGTGTGGCGAA 59.465 55.000 5.88 0.00 0.00 4.70
82 83 1.471676 GGGATCTACAGTGTGGCGAAG 60.472 57.143 5.88 0.00 0.00 3.79
83 84 1.476891 GGATCTACAGTGTGGCGAAGA 59.523 52.381 5.88 0.00 0.00 2.87
84 85 2.101582 GGATCTACAGTGTGGCGAAGAT 59.898 50.000 5.88 5.58 0.00 2.40
85 86 2.941453 TCTACAGTGTGGCGAAGATC 57.059 50.000 5.88 0.00 0.00 2.75
86 87 2.447443 TCTACAGTGTGGCGAAGATCT 58.553 47.619 5.88 0.00 0.00 2.75
87 88 2.826128 TCTACAGTGTGGCGAAGATCTT 59.174 45.455 7.95 7.95 0.00 2.40
88 89 1.800805 ACAGTGTGGCGAAGATCTTG 58.199 50.000 14.00 6.62 0.00 3.02
89 90 1.070758 ACAGTGTGGCGAAGATCTTGT 59.929 47.619 14.00 0.00 0.00 3.16
90 91 2.146342 CAGTGTGGCGAAGATCTTGTT 58.854 47.619 14.00 0.00 0.00 2.83
91 92 2.158449 CAGTGTGGCGAAGATCTTGTTC 59.842 50.000 14.00 0.00 0.00 3.18
92 93 1.464997 GTGTGGCGAAGATCTTGTTCC 59.535 52.381 14.00 11.02 0.00 3.62
93 94 1.071542 TGTGGCGAAGATCTTGTTCCA 59.928 47.619 14.00 13.46 0.00 3.53
94 95 1.734465 GTGGCGAAGATCTTGTTCCAG 59.266 52.381 14.00 0.00 0.00 3.86
95 96 0.729690 GGCGAAGATCTTGTTCCAGC 59.270 55.000 14.00 8.16 0.00 4.85
96 97 0.729690 GCGAAGATCTTGTTCCAGCC 59.270 55.000 14.00 0.00 0.00 4.85
97 98 1.373570 CGAAGATCTTGTTCCAGCCC 58.626 55.000 14.00 0.00 0.00 5.19
98 99 1.373570 GAAGATCTTGTTCCAGCCCG 58.626 55.000 14.00 0.00 0.00 6.13
99 100 0.984230 AAGATCTTGTTCCAGCCCGA 59.016 50.000 7.30 0.00 0.00 5.14
100 101 0.984230 AGATCTTGTTCCAGCCCGAA 59.016 50.000 0.00 0.00 0.00 4.30
101 102 1.065854 AGATCTTGTTCCAGCCCGAAG 60.066 52.381 0.00 0.00 0.00 3.79
122 123 0.813610 CACTGCGTGAAGGTGGTGAA 60.814 55.000 3.04 0.00 35.23 3.18
134 135 2.737376 GGTGAAGACCCGACGCAC 60.737 66.667 0.00 0.00 36.03 5.34
153 154 3.640000 ACACACGTGAGCAAGCGC 61.640 61.111 25.01 0.00 38.99 5.92
224 225 2.603953 GAACTTCCTTCCTTCGTACGG 58.396 52.381 16.52 0.00 0.00 4.02
230 231 0.242017 CTTCCTTCGTACGGTTCGGT 59.758 55.000 16.52 0.00 0.00 4.69
233 234 1.086696 CCTTCGTACGGTTCGGTCTA 58.913 55.000 16.52 0.00 0.00 2.59
235 236 2.286654 CCTTCGTACGGTTCGGTCTATC 60.287 54.545 16.52 0.00 0.00 2.08
238 239 1.070975 CGTACGGTTCGGTCTATCGAG 60.071 57.143 7.57 0.00 40.42 4.04
252 253 1.379527 ATCGAGGCGTTTGATTTCCC 58.620 50.000 0.00 0.00 0.00 3.97
255 256 1.654023 GAGGCGTTTGATTTCCCGGG 61.654 60.000 16.85 16.85 0.00 5.73
256 257 2.180769 GCGTTTGATTTCCCGGGC 59.819 61.111 18.49 1.20 0.00 6.13
257 258 2.631580 GCGTTTGATTTCCCGGGCA 61.632 57.895 18.49 0.00 0.00 5.36
258 259 1.211709 CGTTTGATTTCCCGGGCAC 59.788 57.895 18.49 7.37 0.00 5.01
259 260 1.211709 GTTTGATTTCCCGGGCACG 59.788 57.895 18.49 0.00 40.55 5.34
260 261 1.073373 TTTGATTTCCCGGGCACGA 59.927 52.632 18.49 3.66 44.60 4.35
261 262 0.322997 TTTGATTTCCCGGGCACGAT 60.323 50.000 18.49 6.51 44.60 3.73
262 263 0.322997 TTGATTTCCCGGGCACGATT 60.323 50.000 18.49 0.00 44.60 3.34
263 264 1.029408 TGATTTCCCGGGCACGATTG 61.029 55.000 18.49 0.00 44.60 2.67
303 517 0.531974 GCTCAACCACCGTGACAAGA 60.532 55.000 0.00 0.00 0.00 3.02
304 518 1.948104 CTCAACCACCGTGACAAGAA 58.052 50.000 0.00 0.00 0.00 2.52
311 525 1.257936 CACCGTGACAAGAAGTGTTCG 59.742 52.381 0.00 0.00 41.96 3.95
320 534 7.271868 CGTGACAAGAAGTGTTCGTACATAATA 59.728 37.037 0.00 0.00 41.96 0.98
321 535 8.918658 GTGACAAGAAGTGTTCGTACATAATAA 58.081 33.333 0.00 0.00 41.96 1.40
322 536 9.647797 TGACAAGAAGTGTTCGTACATAATAAT 57.352 29.630 0.00 0.00 41.96 1.28
348 562 6.375174 TCATTCATGTGAAAATAGTGTCCCTG 59.625 38.462 0.00 0.00 37.61 4.45
353 567 4.263462 TGTGAAAATAGTGTCCCTGCAGAT 60.263 41.667 17.39 0.00 0.00 2.90
354 568 4.702131 GTGAAAATAGTGTCCCTGCAGATT 59.298 41.667 17.39 1.59 0.00 2.40
376 590 2.556189 TCGCAGCTTATTTTTCAGGCAA 59.444 40.909 0.00 0.00 0.00 4.52
378 592 3.740321 CGCAGCTTATTTTTCAGGCAAAA 59.260 39.130 0.00 0.00 31.73 2.44
379 593 4.210955 CGCAGCTTATTTTTCAGGCAAAAA 59.789 37.500 0.00 0.00 45.88 1.94
388 603 6.293698 ATTTTTCAGGCAAAAAGCATTCTCT 58.706 32.000 2.56 0.00 45.20 3.10
389 604 6.426025 ATTTTTCAGGCAAAAAGCATTCTCTC 59.574 34.615 2.56 0.00 45.20 3.20
402 617 5.181748 AGCATTCTCTCATAAACGAAAGCT 58.818 37.500 0.00 0.00 36.12 3.74
407 622 3.250744 TCTCATAAACGAAAGCTGACGG 58.749 45.455 15.27 0.00 0.00 4.79
408 623 2.993899 CTCATAAACGAAAGCTGACGGT 59.006 45.455 15.27 7.52 0.00 4.83
426 641 1.671166 TGGACGGCCCATATCATCG 59.329 57.895 3.83 0.00 40.82 3.84
427 642 1.741770 GGACGGCCCATATCATCGC 60.742 63.158 0.00 0.00 34.14 4.58
428 643 1.005037 GACGGCCCATATCATCGCA 60.005 57.895 0.00 0.00 0.00 5.10
429 644 1.291877 GACGGCCCATATCATCGCAC 61.292 60.000 0.00 0.00 0.00 5.34
430 645 2.034879 CGGCCCATATCATCGCACC 61.035 63.158 0.00 0.00 0.00 5.01
431 646 1.073025 GGCCCATATCATCGCACCA 59.927 57.895 0.00 0.00 0.00 4.17
432 647 0.537143 GGCCCATATCATCGCACCAA 60.537 55.000 0.00 0.00 0.00 3.67
433 648 1.317613 GCCCATATCATCGCACCAAA 58.682 50.000 0.00 0.00 0.00 3.28
434 649 1.680735 GCCCATATCATCGCACCAAAA 59.319 47.619 0.00 0.00 0.00 2.44
435 650 2.543653 GCCCATATCATCGCACCAAAAC 60.544 50.000 0.00 0.00 0.00 2.43
436 651 2.286950 CCCATATCATCGCACCAAAACG 60.287 50.000 0.00 0.00 0.00 3.60
437 652 2.286950 CCATATCATCGCACCAAAACGG 60.287 50.000 0.00 0.00 42.50 4.44
438 653 0.730265 TATCATCGCACCAAAACGGC 59.270 50.000 0.00 0.00 39.03 5.68
439 654 1.933115 ATCATCGCACCAAAACGGCC 61.933 55.000 0.00 0.00 39.03 6.13
440 655 2.596046 ATCGCACCAAAACGGCCA 60.596 55.556 2.24 0.00 39.03 5.36
441 656 2.196925 ATCGCACCAAAACGGCCAA 61.197 52.632 2.24 0.00 39.03 4.52
442 657 1.739338 ATCGCACCAAAACGGCCAAA 61.739 50.000 2.24 0.00 39.03 3.28
443 658 1.519455 CGCACCAAAACGGCCAAAA 60.519 52.632 2.24 0.00 39.03 2.44
444 659 1.757346 CGCACCAAAACGGCCAAAAC 61.757 55.000 2.24 0.00 39.03 2.43
448 663 0.107654 CCAAAACGGCCAAAACCCAA 60.108 50.000 2.24 0.00 0.00 4.12
451 666 0.613777 AAACGGCCAAAACCCAACAA 59.386 45.000 2.24 0.00 0.00 2.83
455 670 1.474143 CGGCCAAAACCCAACAAACAT 60.474 47.619 2.24 0.00 0.00 2.71
456 671 2.224066 CGGCCAAAACCCAACAAACATA 60.224 45.455 2.24 0.00 0.00 2.29
459 674 3.558006 GCCAAAACCCAACAAACATACAC 59.442 43.478 0.00 0.00 0.00 2.90
462 677 5.171476 CAAAACCCAACAAACATACACACA 58.829 37.500 0.00 0.00 0.00 3.72
469 684 5.221224 CCAACAAACATACACACACTTCCAT 60.221 40.000 0.00 0.00 0.00 3.41
470 685 5.689383 ACAAACATACACACACTTCCATC 57.311 39.130 0.00 0.00 0.00 3.51
471 686 4.518970 ACAAACATACACACACTTCCATCC 59.481 41.667 0.00 0.00 0.00 3.51
472 687 4.365514 AACATACACACACTTCCATCCA 57.634 40.909 0.00 0.00 0.00 3.41
473 688 3.942829 ACATACACACACTTCCATCCAG 58.057 45.455 0.00 0.00 0.00 3.86
474 689 3.582647 ACATACACACACTTCCATCCAGA 59.417 43.478 0.00 0.00 0.00 3.86
475 690 4.041567 ACATACACACACTTCCATCCAGAA 59.958 41.667 0.00 0.00 0.00 3.02
477 692 2.224621 ACACACACTTCCATCCAGAAGG 60.225 50.000 6.28 0.00 46.24 3.46
478 693 1.271597 ACACACTTCCATCCAGAAGGC 60.272 52.381 6.28 0.00 46.24 4.35
479 694 1.067295 ACACTTCCATCCAGAAGGCA 58.933 50.000 6.28 0.00 46.24 4.75
480 695 1.425066 ACACTTCCATCCAGAAGGCAA 59.575 47.619 6.28 0.00 46.24 4.52
481 696 2.158475 ACACTTCCATCCAGAAGGCAAA 60.158 45.455 6.28 0.00 46.24 3.68
482 697 2.490903 CACTTCCATCCAGAAGGCAAAG 59.509 50.000 6.28 0.00 46.24 2.77
483 698 2.097825 CTTCCATCCAGAAGGCAAAGG 58.902 52.381 0.00 0.00 39.71 3.11
484 699 1.075601 TCCATCCAGAAGGCAAAGGT 58.924 50.000 0.00 0.00 33.74 3.50
485 700 1.428912 TCCATCCAGAAGGCAAAGGTT 59.571 47.619 0.00 0.00 33.74 3.50
486 701 2.158325 TCCATCCAGAAGGCAAAGGTTT 60.158 45.455 0.00 0.00 33.74 3.27
487 702 2.634453 CCATCCAGAAGGCAAAGGTTTT 59.366 45.455 0.00 0.00 33.74 2.43
488 703 3.306294 CCATCCAGAAGGCAAAGGTTTTC 60.306 47.826 0.00 0.00 33.74 2.29
489 704 2.316108 TCCAGAAGGCAAAGGTTTTCC 58.684 47.619 0.00 0.00 35.86 3.13
490 705 2.091333 TCCAGAAGGCAAAGGTTTTCCT 60.091 45.455 0.00 0.00 43.57 3.36
491 706 3.139397 TCCAGAAGGCAAAGGTTTTCCTA 59.861 43.478 0.00 0.00 41.85 2.94
492 707 4.386986 TCCAGAAGGCAAAGGTTTTCCTAA 60.387 41.667 0.00 0.00 41.85 2.69
493 708 5.870780 TCCAGAAGGCAAAGGTTTTCCTAAA 60.871 40.000 0.00 0.00 41.85 1.85
494 709 7.316955 TCCAGAAGGCAAAGGTTTTCCTAAAA 61.317 38.462 0.00 0.00 41.85 1.52
495 710 8.729733 TCCAGAAGGCAAAGGTTTTCCTAAAAA 61.730 37.037 0.00 0.00 41.85 1.94
522 737 5.459536 AAGAATTCCAGAAGGCAAAAGTC 57.540 39.130 0.65 0.00 33.74 3.01
527 742 4.431416 TCCAGAAGGCAAAAGTCTACAA 57.569 40.909 0.00 0.00 33.74 2.41
538 753 6.649557 GGCAAAAGTCTACAATACACTACACT 59.350 38.462 0.00 0.00 0.00 3.55
541 756 9.909644 CAAAAGTCTACAATACACTACACTACT 57.090 33.333 0.00 0.00 0.00 2.57
544 759 9.730705 AAGTCTACAATACACTACACTACTACA 57.269 33.333 0.00 0.00 0.00 2.74
545 760 9.902684 AGTCTACAATACACTACACTACTACAT 57.097 33.333 0.00 0.00 0.00 2.29
547 762 9.895138 TCTACAATACACTACACTACTACATCA 57.105 33.333 0.00 0.00 0.00 3.07
548 763 9.932699 CTACAATACACTACACTACTACATCAC 57.067 37.037 0.00 0.00 0.00 3.06
549 764 7.470079 ACAATACACTACACTACTACATCACG 58.530 38.462 0.00 0.00 0.00 4.35
550 765 4.959596 ACACTACACTACTACATCACGG 57.040 45.455 0.00 0.00 0.00 4.94
551 766 3.128242 ACACTACACTACTACATCACGGC 59.872 47.826 0.00 0.00 0.00 5.68
552 767 3.128068 CACTACACTACTACATCACGGCA 59.872 47.826 0.00 0.00 0.00 5.69
553 768 2.649331 ACACTACTACATCACGGCAC 57.351 50.000 0.00 0.00 0.00 5.01
554 769 2.168496 ACACTACTACATCACGGCACT 58.832 47.619 0.00 0.00 0.00 4.40
555 770 3.349927 ACACTACTACATCACGGCACTA 58.650 45.455 0.00 0.00 0.00 2.74
556 771 3.128242 ACACTACTACATCACGGCACTAC 59.872 47.826 0.00 0.00 0.00 2.73
557 772 3.128068 CACTACTACATCACGGCACTACA 59.872 47.826 0.00 0.00 0.00 2.74
558 773 3.952323 ACTACTACATCACGGCACTACAT 59.048 43.478 0.00 0.00 0.00 2.29
559 774 3.438297 ACTACATCACGGCACTACATC 57.562 47.619 0.00 0.00 0.00 3.06
560 775 2.758423 ACTACATCACGGCACTACATCA 59.242 45.455 0.00 0.00 0.00 3.07
561 776 2.010145 ACATCACGGCACTACATCAC 57.990 50.000 0.00 0.00 0.00 3.06
562 777 1.290203 CATCACGGCACTACATCACC 58.710 55.000 0.00 0.00 0.00 4.02
563 778 0.901827 ATCACGGCACTACATCACCA 59.098 50.000 0.00 0.00 0.00 4.17
564 779 0.037697 TCACGGCACTACATCACCAC 60.038 55.000 0.00 0.00 0.00 4.16
565 780 1.019278 CACGGCACTACATCACCACC 61.019 60.000 0.00 0.00 0.00 4.61
566 781 1.809619 CGGCACTACATCACCACCG 60.810 63.158 0.00 0.00 0.00 4.94
567 782 1.295423 GGCACTACATCACCACCGT 59.705 57.895 0.00 0.00 0.00 4.83
568 783 0.533491 GGCACTACATCACCACCGTA 59.467 55.000 0.00 0.00 0.00 4.02
569 784 1.636988 GCACTACATCACCACCGTAC 58.363 55.000 0.00 0.00 0.00 3.67
602 817 2.973899 CCAGACTCCGGTCACCAG 59.026 66.667 0.00 0.00 44.36 4.00
611 826 3.311110 GGTCACCAGAGCCGTCCA 61.311 66.667 0.00 0.00 36.27 4.02
625 840 1.026718 CGTCCATCTGCCCAAAGTCC 61.027 60.000 0.00 0.00 0.00 3.85
626 841 0.038166 GTCCATCTGCCCAAAGTCCA 59.962 55.000 0.00 0.00 0.00 4.02
628 843 1.358787 TCCATCTGCCCAAAGTCCAAT 59.641 47.619 0.00 0.00 0.00 3.16
630 845 3.011144 TCCATCTGCCCAAAGTCCAATTA 59.989 43.478 0.00 0.00 0.00 1.40
673 892 2.034305 CGGACCGACGAGGAAAAGATAT 59.966 50.000 8.64 0.00 45.00 1.63
920 1145 2.403586 GAAAATTCCGCCGAGCCG 59.596 61.111 0.00 0.00 0.00 5.52
942 1169 4.431131 CGCATTCCCCCACCAGCT 62.431 66.667 0.00 0.00 0.00 4.24
1052 1291 1.692749 CGAAATCCCTCCCCTCCCA 60.693 63.158 0.00 0.00 0.00 4.37
1053 1292 1.062488 CGAAATCCCTCCCCTCCCAT 61.062 60.000 0.00 0.00 0.00 4.00
1054 1293 0.774276 GAAATCCCTCCCCTCCCATC 59.226 60.000 0.00 0.00 0.00 3.51
1055 1294 0.702706 AAATCCCTCCCCTCCCATCC 60.703 60.000 0.00 0.00 0.00 3.51
1056 1295 1.627017 AATCCCTCCCCTCCCATCCT 61.627 60.000 0.00 0.00 0.00 3.24
1057 1296 2.054834 ATCCCTCCCCTCCCATCCTC 62.055 65.000 0.00 0.00 0.00 3.71
1058 1297 2.731461 CCCTCCCCTCCCATCCTCT 61.731 68.421 0.00 0.00 0.00 3.69
1059 1298 1.152139 CCTCCCCTCCCATCCTCTC 60.152 68.421 0.00 0.00 0.00 3.20
1060 1299 1.152139 CTCCCCTCCCATCCTCTCC 60.152 68.421 0.00 0.00 0.00 3.71
1061 1300 2.122189 CCCCTCCCATCCTCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
1062 1301 2.705410 CCCTCCCATCCTCTCCCA 59.295 66.667 0.00 0.00 0.00 4.37
1086 1325 1.433879 CTTCTCGGCTCGATTCGGT 59.566 57.895 6.18 0.00 34.61 4.69
1256 1498 4.070552 GACCACTCCGGCTCGCTT 62.071 66.667 0.00 0.00 39.03 4.68
1360 1602 3.744719 CCTCGCCTTCGTCGACCA 61.745 66.667 10.58 0.00 36.96 4.02
1428 1675 2.252714 CCTAGCTTAGGGTCCATCTCC 58.747 57.143 0.00 0.00 42.42 3.71
1429 1676 2.426414 CCTAGCTTAGGGTCCATCTCCA 60.426 54.545 0.00 0.00 42.42 3.86
1430 1677 2.503869 AGCTTAGGGTCCATCTCCAT 57.496 50.000 0.00 0.00 0.00 3.41
1431 1678 2.334023 AGCTTAGGGTCCATCTCCATC 58.666 52.381 0.00 0.00 0.00 3.51
1432 1679 2.050144 GCTTAGGGTCCATCTCCATCA 58.950 52.381 0.00 0.00 0.00 3.07
1433 1680 2.038295 GCTTAGGGTCCATCTCCATCAG 59.962 54.545 0.00 0.00 0.00 2.90
1434 1681 3.581101 CTTAGGGTCCATCTCCATCAGA 58.419 50.000 0.00 0.00 34.78 3.27
1504 1752 1.214589 CTGCCAAACTGCCATGCTC 59.785 57.895 0.00 0.00 0.00 4.26
1573 1821 1.139058 CCTTCCCGTTCCATCGAGAAT 59.861 52.381 0.00 0.00 28.49 2.40
1613 1869 0.404426 GAGTGGGGCCTAGTTTGGTT 59.596 55.000 0.84 0.00 0.00 3.67
1614 1870 0.857675 AGTGGGGCCTAGTTTGGTTT 59.142 50.000 0.84 0.00 0.00 3.27
1615 1871 0.966179 GTGGGGCCTAGTTTGGTTTG 59.034 55.000 0.84 0.00 0.00 2.93
1616 1872 0.178947 TGGGGCCTAGTTTGGTTTGG 60.179 55.000 0.84 0.00 0.00 3.28
1617 1873 0.178944 GGGGCCTAGTTTGGTTTGGT 60.179 55.000 0.84 0.00 0.00 3.67
1618 1874 0.966179 GGGCCTAGTTTGGTTTGGTG 59.034 55.000 0.84 0.00 0.00 4.17
1619 1875 0.317160 GGCCTAGTTTGGTTTGGTGC 59.683 55.000 0.00 0.00 0.00 5.01
1643 1899 1.523758 GGCTGTGTGGTCGAGAATTT 58.476 50.000 0.00 0.00 0.00 1.82
1645 1901 2.293399 GGCTGTGTGGTCGAGAATTTTT 59.707 45.455 0.00 0.00 0.00 1.94
1680 1937 0.802607 GAATCTGCCCGTGTCTCGAC 60.803 60.000 0.00 0.00 42.86 4.20
1752 2009 2.275089 CCGGGGAATCACATGCCA 59.725 61.111 0.00 0.00 31.30 4.92
1755 2012 2.120909 GGGGAATCACATGCCACGG 61.121 63.158 0.00 0.00 31.30 4.94
1790 2048 1.606668 GTTTTGTCACGGCAATCCAGA 59.393 47.619 0.00 0.00 0.00 3.86
1818 2076 2.884012 TGTCGTCAATTTCAAGCATGGT 59.116 40.909 0.00 0.00 0.00 3.55
1819 2077 3.236816 GTCGTCAATTTCAAGCATGGTG 58.763 45.455 0.00 0.00 0.00 4.17
1820 2078 2.228582 TCGTCAATTTCAAGCATGGTGG 59.771 45.455 0.00 0.00 0.00 4.61
1822 2080 3.552684 CGTCAATTTCAAGCATGGTGGTT 60.553 43.478 0.00 0.00 38.82 3.67
1834 2092 1.121378 TGGTGGTTGGTACTCGAACA 58.879 50.000 0.00 0.00 34.69 3.18
1842 2100 3.120321 TGGTACTCGAACAATGTTGCT 57.880 42.857 2.20 0.00 0.00 3.91
1843 2101 3.064207 TGGTACTCGAACAATGTTGCTC 58.936 45.455 2.20 0.00 0.00 4.26
1862 2125 3.262420 CTCGTTGCTGCTAATAAGTGGT 58.738 45.455 0.00 0.00 0.00 4.16
1863 2126 4.430007 CTCGTTGCTGCTAATAAGTGGTA 58.570 43.478 0.00 0.00 0.00 3.25
1870 2133 5.008911 TGCTGCTAATAAGTGGTATGCATTG 59.991 40.000 3.54 0.00 0.00 2.82
2469 2735 4.812476 TCGTCCGATGCCAAGCCG 62.812 66.667 0.00 0.00 0.00 5.52
2471 2737 3.195698 GTCCGATGCCAAGCCGAC 61.196 66.667 0.00 0.00 0.00 4.79
2528 2797 0.475906 GATGCCAAGCCTATGGGACT 59.524 55.000 0.00 0.00 44.11 3.85
2535 2804 0.475906 AGCCTATGGGACTTGATGCC 59.524 55.000 0.00 0.00 39.94 4.40
2571 2840 4.802051 TCGCCTGATGCCAAGCCC 62.802 66.667 0.00 0.00 36.24 5.19
2583 2852 0.107017 CCAAGCCCGTGGAATCTGAT 60.107 55.000 0.00 0.00 41.65 2.90
2656 2925 2.285368 CCCAGGCCTAGGGTGTGA 60.285 66.667 24.72 0.00 41.61 3.58
2670 2939 2.506438 GTGACGCCGTGCCTCTAC 60.506 66.667 0.00 0.00 0.00 2.59
2672 2941 4.509737 GACGCCGTGCCTCTACCC 62.510 72.222 0.00 0.00 0.00 3.69
2680 2949 2.365635 GCCTCTACCCTGCCCTGA 60.366 66.667 0.00 0.00 0.00 3.86
2691 2960 2.303549 CTGCCCTGATGGACGAGGTC 62.304 65.000 0.00 0.00 35.39 3.85
2729 2998 6.936900 CCGGAACTGAATAAGATAATGTGGAT 59.063 38.462 0.00 0.00 0.00 3.41
2751 3020 3.041946 CCAGGGCTAAGAAGATACTGGT 58.958 50.000 0.00 0.00 35.95 4.00
2764 3033 6.555360 AGAAGATACTGGTATCCTGGGTTTAG 59.445 42.308 14.77 0.00 42.13 1.85
2769 3038 1.761198 GGTATCCTGGGTTTAGCGTCT 59.239 52.381 0.00 0.00 0.00 4.18
2770 3039 2.223994 GGTATCCTGGGTTTAGCGTCTC 60.224 54.545 0.00 0.00 0.00 3.36
2771 3040 1.568504 ATCCTGGGTTTAGCGTCTCA 58.431 50.000 0.00 0.00 0.00 3.27
2772 3041 1.568504 TCCTGGGTTTAGCGTCTCAT 58.431 50.000 0.00 0.00 0.00 2.90
2773 3042 1.480954 TCCTGGGTTTAGCGTCTCATC 59.519 52.381 0.00 0.00 0.00 2.92
2774 3043 1.482593 CCTGGGTTTAGCGTCTCATCT 59.517 52.381 0.00 0.00 0.00 2.90
2827 3096 8.763049 TGATAATGATGTTGTACTAGCTATGC 57.237 34.615 0.00 0.00 0.00 3.14
2829 3098 9.429359 GATAATGATGTTGTACTAGCTATGCTT 57.571 33.333 0.00 0.00 40.44 3.91
2830 3099 9.784531 ATAATGATGTTGTACTAGCTATGCTTT 57.215 29.630 0.00 0.00 40.44 3.51
2832 3101 8.594881 ATGATGTTGTACTAGCTATGCTTTAC 57.405 34.615 0.00 1.43 40.44 2.01
2833 3102 6.695713 TGATGTTGTACTAGCTATGCTTTACG 59.304 38.462 0.00 0.00 40.44 3.18
2836 3105 4.928601 TGTACTAGCTATGCTTTACGTGG 58.071 43.478 0.00 0.00 40.44 4.94
2837 3106 4.400251 TGTACTAGCTATGCTTTACGTGGT 59.600 41.667 0.00 0.00 40.44 4.16
2838 3107 3.782046 ACTAGCTATGCTTTACGTGGTG 58.218 45.455 0.00 0.00 40.44 4.17
2839 3108 1.369625 AGCTATGCTTTACGTGGTGC 58.630 50.000 0.00 0.00 33.89 5.01
2841 3110 0.026285 CTATGCTTTACGTGGTGCGC 59.974 55.000 0.00 0.00 46.11 6.09
3005 3493 0.809385 TTTTGGTGCGTCGTTTTCCA 59.191 45.000 0.00 0.00 0.00 3.53
3017 3505 4.612939 CGTCGTTTTCCATTTCTTCCCTTC 60.613 45.833 0.00 0.00 0.00 3.46
3081 3572 2.126580 CGTCGTCGACAGGTTCCC 60.127 66.667 24.13 0.00 39.71 3.97
3100 3591 2.626455 GCGAAACCATCCGCGATC 59.374 61.111 8.23 0.00 42.02 3.69
3201 3692 3.502455 CGACGGACGGACGGATGA 61.502 66.667 6.00 0.00 38.39 2.92
3330 3821 0.108186 CTCTGCATTACTCCCACGCA 60.108 55.000 0.00 0.00 0.00 5.24
3404 3895 3.964875 CAGTTGCGCTGCCCGTTT 61.965 61.111 9.73 0.00 38.52 3.60
3482 3982 2.654912 CTCCACGCGACCACGTTTC 61.655 63.158 15.93 0.00 45.75 2.78
3565 4065 1.597854 CTTCCACGGCAGAGCAACA 60.598 57.895 0.00 0.00 0.00 3.33
3572 4072 2.320587 GGCAGAGCAACAGGACACG 61.321 63.158 0.00 0.00 0.00 4.49
3578 4078 2.967076 CAACAGGACACGCACGCT 60.967 61.111 0.00 0.00 0.00 5.07
3619 4123 0.039437 GCGACCGATCACCGATGTAT 60.039 55.000 0.00 0.00 41.76 2.29
3633 4137 0.031585 ATGTATACGGCGTGCGTCAT 59.968 50.000 24.86 17.46 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.060347 CGTGATGGTTTATAGTACTCCTACTAA 57.940 37.037 0.00 0.00 38.66 2.24
9 10 8.432013 TCGTGATGGTTTATAGTACTCCTACTA 58.568 37.037 0.00 0.00 39.36 1.82
10 11 7.228308 GTCGTGATGGTTTATAGTACTCCTACT 59.772 40.741 0.00 0.00 37.04 2.57
11 12 7.012704 TGTCGTGATGGTTTATAGTACTCCTAC 59.987 40.741 0.00 0.00 0.00 3.18
12 13 7.056006 TGTCGTGATGGTTTATAGTACTCCTA 58.944 38.462 0.00 0.00 0.00 2.94
13 14 5.889853 TGTCGTGATGGTTTATAGTACTCCT 59.110 40.000 0.00 0.00 0.00 3.69
14 15 6.140303 TGTCGTGATGGTTTATAGTACTCC 57.860 41.667 0.00 0.00 0.00 3.85
15 16 9.557338 GATATGTCGTGATGGTTTATAGTACTC 57.443 37.037 0.00 0.00 0.00 2.59
16 17 8.235226 CGATATGTCGTGATGGTTTATAGTACT 58.765 37.037 3.37 0.00 42.78 2.73
17 18 8.378228 CGATATGTCGTGATGGTTTATAGTAC 57.622 38.462 3.37 0.00 42.78 2.73
34 35 5.237344 CCAGAAAGGGAACAATCGATATGTC 59.763 44.000 0.00 0.00 0.00 3.06
35 36 5.126067 CCAGAAAGGGAACAATCGATATGT 58.874 41.667 0.00 2.81 0.00 2.29
36 37 5.126067 ACCAGAAAGGGAACAATCGATATG 58.874 41.667 0.00 2.14 43.89 1.78
37 38 5.368989 GACCAGAAAGGGAACAATCGATAT 58.631 41.667 0.00 0.00 43.89 1.63
38 39 4.383770 GGACCAGAAAGGGAACAATCGATA 60.384 45.833 0.00 0.00 43.89 2.92
39 40 3.610911 GACCAGAAAGGGAACAATCGAT 58.389 45.455 0.00 0.00 43.89 3.59
40 41 2.290071 GGACCAGAAAGGGAACAATCGA 60.290 50.000 0.00 0.00 43.89 3.59
41 42 2.084546 GGACCAGAAAGGGAACAATCG 58.915 52.381 0.00 0.00 43.89 3.34
42 43 2.084546 CGGACCAGAAAGGGAACAATC 58.915 52.381 0.00 0.00 43.89 2.67
43 44 1.271926 CCGGACCAGAAAGGGAACAAT 60.272 52.381 0.00 0.00 43.89 2.71
44 45 0.109723 CCGGACCAGAAAGGGAACAA 59.890 55.000 0.00 0.00 43.89 2.83
45 46 1.758592 CCGGACCAGAAAGGGAACA 59.241 57.895 0.00 0.00 43.89 3.18
46 47 1.002502 CCCGGACCAGAAAGGGAAC 60.003 63.158 0.73 0.00 46.64 3.62
47 48 3.490851 CCCGGACCAGAAAGGGAA 58.509 61.111 0.73 0.00 46.64 3.97
49 50 0.983378 AGATCCCGGACCAGAAAGGG 60.983 60.000 0.73 0.00 43.89 3.95
50 51 1.413077 GTAGATCCCGGACCAGAAAGG 59.587 57.143 0.73 0.00 45.67 3.11
51 52 2.101582 CTGTAGATCCCGGACCAGAAAG 59.898 54.545 0.73 0.00 0.00 2.62
52 53 2.108168 CTGTAGATCCCGGACCAGAAA 58.892 52.381 0.73 0.00 0.00 2.52
53 54 1.006758 ACTGTAGATCCCGGACCAGAA 59.993 52.381 0.73 0.00 0.00 3.02
54 55 0.629596 ACTGTAGATCCCGGACCAGA 59.370 55.000 0.73 0.00 0.00 3.86
55 56 0.747255 CACTGTAGATCCCGGACCAG 59.253 60.000 0.73 1.63 0.00 4.00
56 57 0.040646 ACACTGTAGATCCCGGACCA 59.959 55.000 0.73 0.00 0.00 4.02
57 58 0.460311 CACACTGTAGATCCCGGACC 59.540 60.000 0.73 0.00 0.00 4.46
58 59 0.460311 CCACACTGTAGATCCCGGAC 59.540 60.000 0.73 0.00 0.00 4.79
59 60 1.327690 GCCACACTGTAGATCCCGGA 61.328 60.000 0.73 0.00 0.00 5.14
60 61 1.144057 GCCACACTGTAGATCCCGG 59.856 63.158 0.00 0.00 0.00 5.73
61 62 1.226974 CGCCACACTGTAGATCCCG 60.227 63.158 0.00 0.00 0.00 5.14
62 63 0.535335 TTCGCCACACTGTAGATCCC 59.465 55.000 0.00 0.00 0.00 3.85
63 64 1.476891 TCTTCGCCACACTGTAGATCC 59.523 52.381 0.00 0.00 0.00 3.36
64 65 2.941453 TCTTCGCCACACTGTAGATC 57.059 50.000 0.00 0.00 0.00 2.75
65 66 3.027412 AGATCTTCGCCACACTGTAGAT 58.973 45.455 0.00 0.00 0.00 1.98
66 67 2.447443 AGATCTTCGCCACACTGTAGA 58.553 47.619 0.00 0.00 0.00 2.59
67 68 2.926200 CAAGATCTTCGCCACACTGTAG 59.074 50.000 4.57 0.00 0.00 2.74
68 69 2.299013 ACAAGATCTTCGCCACACTGTA 59.701 45.455 4.57 0.00 0.00 2.74
69 70 1.070758 ACAAGATCTTCGCCACACTGT 59.929 47.619 4.57 0.00 0.00 3.55
70 71 1.800805 ACAAGATCTTCGCCACACTG 58.199 50.000 4.57 0.00 0.00 3.66
71 72 2.417719 GAACAAGATCTTCGCCACACT 58.582 47.619 4.57 0.00 0.00 3.55
72 73 1.464997 GGAACAAGATCTTCGCCACAC 59.535 52.381 4.57 0.00 0.00 3.82
73 74 1.071542 TGGAACAAGATCTTCGCCACA 59.928 47.619 4.57 0.00 31.92 4.17
74 75 1.734465 CTGGAACAAGATCTTCGCCAC 59.266 52.381 4.57 0.00 38.70 5.01
75 76 1.945819 GCTGGAACAAGATCTTCGCCA 60.946 52.381 4.57 11.90 38.70 5.69
76 77 0.729690 GCTGGAACAAGATCTTCGCC 59.270 55.000 4.57 7.82 38.70 5.54
77 78 0.729690 GGCTGGAACAAGATCTTCGC 59.270 55.000 4.57 3.12 38.70 4.70
78 79 1.373570 GGGCTGGAACAAGATCTTCG 58.626 55.000 4.57 4.27 38.70 3.79
79 80 1.066143 TCGGGCTGGAACAAGATCTTC 60.066 52.381 4.57 0.00 38.70 2.87
80 81 0.984230 TCGGGCTGGAACAAGATCTT 59.016 50.000 0.88 0.88 38.70 2.40
81 82 0.984230 TTCGGGCTGGAACAAGATCT 59.016 50.000 0.00 0.00 38.70 2.75
82 83 1.373570 CTTCGGGCTGGAACAAGATC 58.626 55.000 0.00 0.00 38.70 2.75
83 84 0.035056 CCTTCGGGCTGGAACAAGAT 60.035 55.000 0.00 0.00 38.70 2.40
84 85 1.374947 CCTTCGGGCTGGAACAAGA 59.625 57.895 0.00 0.00 38.70 3.02
85 86 3.987404 CCTTCGGGCTGGAACAAG 58.013 61.111 0.00 0.00 38.70 3.16
122 123 4.295119 GTGTGGTGCGTCGGGTCT 62.295 66.667 0.00 0.00 0.00 3.85
134 135 2.633657 GCTTGCTCACGTGTGTGG 59.366 61.111 16.51 8.53 46.42 4.17
211 212 0.242017 ACCGAACCGTACGAAGGAAG 59.758 55.000 18.76 0.48 0.00 3.46
224 225 0.100146 AACGCCTCGATAGACCGAAC 59.900 55.000 0.00 0.00 42.67 3.95
233 234 1.379527 GGGAAATCAAACGCCTCGAT 58.620 50.000 0.00 0.00 0.00 3.59
235 236 1.423845 CGGGAAATCAAACGCCTCG 59.576 57.895 0.00 0.00 0.00 4.63
238 239 2.882132 CCCGGGAAATCAAACGCC 59.118 61.111 18.48 0.00 0.00 5.68
270 484 1.532868 GTTGAGCAGCATCGTCTTGTT 59.467 47.619 0.00 0.00 0.00 2.83
272 486 0.445436 GGTTGAGCAGCATCGTCTTG 59.555 55.000 0.00 0.00 0.00 3.02
277 491 3.181367 GGTGGTTGAGCAGCATCG 58.819 61.111 7.43 0.00 34.68 3.84
280 494 2.591429 CACGGTGGTTGAGCAGCA 60.591 61.111 12.14 0.00 0.00 4.41
320 534 8.253113 GGGACACTATTTTCACATGAATGAATT 58.747 33.333 0.00 0.00 38.37 2.17
321 535 7.616935 AGGGACACTATTTTCACATGAATGAAT 59.383 33.333 0.00 0.00 38.37 2.57
322 536 6.947733 AGGGACACTATTTTCACATGAATGAA 59.052 34.615 0.00 0.00 36.80 2.57
323 537 6.375174 CAGGGACACTATTTTCACATGAATGA 59.625 38.462 0.00 0.00 33.54 2.57
324 538 6.558009 CAGGGACACTATTTTCACATGAATG 58.442 40.000 0.00 0.00 33.54 2.67
325 539 5.126061 GCAGGGACACTATTTTCACATGAAT 59.874 40.000 0.00 0.00 33.54 2.57
326 540 4.458989 GCAGGGACACTATTTTCACATGAA 59.541 41.667 0.00 0.00 0.00 2.57
338 552 1.405526 GCGAAATCTGCAGGGACACTA 60.406 52.381 15.13 0.00 0.00 2.74
340 554 0.955428 TGCGAAATCTGCAGGGACAC 60.955 55.000 15.13 0.18 37.44 3.67
341 555 1.374568 TGCGAAATCTGCAGGGACA 59.625 52.632 15.13 1.32 37.44 4.02
348 562 4.858692 TGAAAAATAAGCTGCGAAATCTGC 59.141 37.500 0.00 0.00 0.00 4.26
353 567 3.005261 TGCCTGAAAAATAAGCTGCGAAA 59.995 39.130 0.00 0.00 0.00 3.46
354 568 2.556189 TGCCTGAAAAATAAGCTGCGAA 59.444 40.909 0.00 0.00 0.00 4.70
365 579 5.673514 AGAGAATGCTTTTTGCCTGAAAAA 58.326 33.333 0.00 0.00 40.52 1.94
376 590 6.803807 GCTTTCGTTTATGAGAGAATGCTTTT 59.196 34.615 7.39 0.00 39.28 2.27
378 592 5.645497 AGCTTTCGTTTATGAGAGAATGCTT 59.355 36.000 10.32 0.00 45.47 3.91
379 593 5.181748 AGCTTTCGTTTATGAGAGAATGCT 58.818 37.500 10.32 10.32 44.06 3.79
388 603 2.734606 CACCGTCAGCTTTCGTTTATGA 59.265 45.455 6.56 0.00 0.00 2.15
389 604 2.159707 CCACCGTCAGCTTTCGTTTATG 60.160 50.000 6.56 0.97 0.00 1.90
421 636 2.622011 GGCCGTTTTGGTGCGATGA 61.622 57.895 0.00 0.00 41.21 2.92
425 640 1.519455 TTTTGGCCGTTTTGGTGCG 60.519 52.632 0.00 0.00 41.21 5.34
426 641 1.433053 GGTTTTGGCCGTTTTGGTGC 61.433 55.000 0.00 0.00 41.21 5.01
427 642 0.812014 GGGTTTTGGCCGTTTTGGTG 60.812 55.000 0.00 0.00 41.21 4.17
428 643 1.265454 TGGGTTTTGGCCGTTTTGGT 61.265 50.000 0.00 0.00 41.21 3.67
429 644 0.107654 TTGGGTTTTGGCCGTTTTGG 60.108 50.000 0.00 0.00 42.50 3.28
430 645 1.010580 GTTGGGTTTTGGCCGTTTTG 58.989 50.000 0.00 0.00 0.00 2.44
431 646 0.613777 TGTTGGGTTTTGGCCGTTTT 59.386 45.000 0.00 0.00 0.00 2.43
432 647 0.613777 TTGTTGGGTTTTGGCCGTTT 59.386 45.000 0.00 0.00 0.00 3.60
433 648 0.613777 TTTGTTGGGTTTTGGCCGTT 59.386 45.000 0.00 0.00 0.00 4.44
434 649 0.108089 GTTTGTTGGGTTTTGGCCGT 60.108 50.000 0.00 0.00 0.00 5.68
435 650 0.108138 TGTTTGTTGGGTTTTGGCCG 60.108 50.000 0.00 0.00 0.00 6.13
436 651 2.340210 ATGTTTGTTGGGTTTTGGCC 57.660 45.000 0.00 0.00 0.00 5.36
437 652 3.558006 GTGTATGTTTGTTGGGTTTTGGC 59.442 43.478 0.00 0.00 0.00 4.52
438 653 4.568760 GTGTGTATGTTTGTTGGGTTTTGG 59.431 41.667 0.00 0.00 0.00 3.28
439 654 5.062809 GTGTGTGTATGTTTGTTGGGTTTTG 59.937 40.000 0.00 0.00 0.00 2.44
440 655 5.046950 AGTGTGTGTATGTTTGTTGGGTTTT 60.047 36.000 0.00 0.00 0.00 2.43
441 656 4.464597 AGTGTGTGTATGTTTGTTGGGTTT 59.535 37.500 0.00 0.00 0.00 3.27
442 657 4.020543 AGTGTGTGTATGTTTGTTGGGTT 58.979 39.130 0.00 0.00 0.00 4.11
443 658 3.626930 AGTGTGTGTATGTTTGTTGGGT 58.373 40.909 0.00 0.00 0.00 4.51
444 659 4.499019 GGAAGTGTGTGTATGTTTGTTGGG 60.499 45.833 0.00 0.00 0.00 4.12
448 663 4.518970 GGATGGAAGTGTGTGTATGTTTGT 59.481 41.667 0.00 0.00 0.00 2.83
451 666 4.041567 TCTGGATGGAAGTGTGTGTATGTT 59.958 41.667 0.00 0.00 0.00 2.71
455 670 3.007940 CCTTCTGGATGGAAGTGTGTGTA 59.992 47.826 0.00 0.00 40.56 2.90
456 671 2.224621 CCTTCTGGATGGAAGTGTGTGT 60.225 50.000 0.00 0.00 40.56 3.72
459 674 1.271543 TGCCTTCTGGATGGAAGTGTG 60.272 52.381 6.69 0.00 40.56 3.82
462 677 2.556114 CCTTTGCCTTCTGGATGGAAGT 60.556 50.000 6.69 0.00 40.56 3.01
469 684 2.091333 AGGAAAACCTTTGCCTTCTGGA 60.091 45.455 0.00 0.00 44.01 3.86
470 685 2.319844 AGGAAAACCTTTGCCTTCTGG 58.680 47.619 0.00 0.00 44.01 3.86
471 686 5.529581 TTTAGGAAAACCTTTGCCTTCTG 57.470 39.130 2.42 0.00 44.01 3.02
472 687 6.553953 TTTTTAGGAAAACCTTTGCCTTCT 57.446 33.333 2.42 0.00 44.01 2.85
497 712 6.653020 ACTTTTGCCTTCTGGAATTCTTTTT 58.347 32.000 5.23 0.00 34.57 1.94
498 713 6.098838 AGACTTTTGCCTTCTGGAATTCTTTT 59.901 34.615 5.23 0.00 34.57 2.27
499 714 5.600069 AGACTTTTGCCTTCTGGAATTCTTT 59.400 36.000 5.23 0.00 34.57 2.52
500 715 5.143369 AGACTTTTGCCTTCTGGAATTCTT 58.857 37.500 5.23 0.00 34.57 2.52
501 716 4.734266 AGACTTTTGCCTTCTGGAATTCT 58.266 39.130 5.23 0.00 34.57 2.40
502 717 5.473504 TGTAGACTTTTGCCTTCTGGAATTC 59.526 40.000 0.00 0.00 34.57 2.17
503 718 5.385198 TGTAGACTTTTGCCTTCTGGAATT 58.615 37.500 0.00 0.00 34.57 2.17
504 719 4.985538 TGTAGACTTTTGCCTTCTGGAAT 58.014 39.130 0.00 0.00 34.57 3.01
505 720 4.431416 TGTAGACTTTTGCCTTCTGGAA 57.569 40.909 0.00 0.00 34.57 3.53
506 721 4.431416 TTGTAGACTTTTGCCTTCTGGA 57.569 40.909 0.00 0.00 34.57 3.86
507 722 5.705441 TGTATTGTAGACTTTTGCCTTCTGG 59.295 40.000 0.00 0.00 0.00 3.86
508 723 6.428159 AGTGTATTGTAGACTTTTGCCTTCTG 59.572 38.462 0.00 0.00 0.00 3.02
509 724 6.534634 AGTGTATTGTAGACTTTTGCCTTCT 58.465 36.000 0.00 0.00 0.00 2.85
510 725 6.803154 AGTGTATTGTAGACTTTTGCCTTC 57.197 37.500 0.00 0.00 0.00 3.46
511 726 7.172703 GTGTAGTGTATTGTAGACTTTTGCCTT 59.827 37.037 0.00 0.00 33.90 4.35
512 727 6.649557 GTGTAGTGTATTGTAGACTTTTGCCT 59.350 38.462 0.00 0.00 33.90 4.75
513 728 6.649557 AGTGTAGTGTATTGTAGACTTTTGCC 59.350 38.462 0.00 0.00 33.90 4.52
518 733 9.730705 TGTAGTAGTGTAGTGTATTGTAGACTT 57.269 33.333 0.00 0.00 33.90 3.01
522 737 9.932699 GTGATGTAGTAGTGTAGTGTATTGTAG 57.067 37.037 0.00 0.00 0.00 2.74
527 742 5.008415 GCCGTGATGTAGTAGTGTAGTGTAT 59.992 44.000 0.00 0.00 0.00 2.29
538 753 3.949113 TGATGTAGTGCCGTGATGTAGTA 59.051 43.478 0.00 0.00 0.00 1.82
541 756 2.159156 GGTGATGTAGTGCCGTGATGTA 60.159 50.000 0.00 0.00 0.00 2.29
542 757 1.405526 GGTGATGTAGTGCCGTGATGT 60.406 52.381 0.00 0.00 0.00 3.06
543 758 1.290203 GGTGATGTAGTGCCGTGATG 58.710 55.000 0.00 0.00 0.00 3.07
544 759 0.901827 TGGTGATGTAGTGCCGTGAT 59.098 50.000 0.00 0.00 0.00 3.06
545 760 0.037697 GTGGTGATGTAGTGCCGTGA 60.038 55.000 0.00 0.00 0.00 4.35
546 761 1.019278 GGTGGTGATGTAGTGCCGTG 61.019 60.000 0.00 0.00 0.00 4.94
547 762 1.295423 GGTGGTGATGTAGTGCCGT 59.705 57.895 0.00 0.00 0.00 5.68
548 763 1.809619 CGGTGGTGATGTAGTGCCG 60.810 63.158 0.00 0.00 0.00 5.69
549 764 0.533491 TACGGTGGTGATGTAGTGCC 59.467 55.000 0.00 0.00 0.00 5.01
550 765 1.636988 GTACGGTGGTGATGTAGTGC 58.363 55.000 0.00 0.00 0.00 4.40
551 766 2.288961 GGTACGGTGGTGATGTAGTG 57.711 55.000 0.00 0.00 0.00 2.74
602 817 2.819984 TTTGGGCAGATGGACGGCTC 62.820 60.000 0.00 0.00 40.47 4.70
611 826 5.103771 AGAGATAATTGGACTTTGGGCAGAT 60.104 40.000 0.00 0.00 0.00 2.90
750 969 3.009714 AGAAGAAGGGCCCGGGTC 61.010 66.667 24.63 22.35 0.00 4.46
920 1145 2.785425 GGTGGGGGAATGCGAATGC 61.785 63.158 0.00 0.00 43.20 3.56
1052 1291 0.915364 GAAGCAAGGTGGGAGAGGAT 59.085 55.000 0.00 0.00 0.00 3.24
1053 1292 0.178891 AGAAGCAAGGTGGGAGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
1054 1293 0.251634 GAGAAGCAAGGTGGGAGAGG 59.748 60.000 0.00 0.00 0.00 3.69
1055 1294 0.108424 CGAGAAGCAAGGTGGGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
1056 1295 1.544825 CCGAGAAGCAAGGTGGGAGA 61.545 60.000 0.00 0.00 0.00 3.71
1057 1296 1.078848 CCGAGAAGCAAGGTGGGAG 60.079 63.158 0.00 0.00 0.00 4.30
1058 1297 3.068881 CCGAGAAGCAAGGTGGGA 58.931 61.111 0.00 0.00 0.00 4.37
1059 1298 2.747855 GCCGAGAAGCAAGGTGGG 60.748 66.667 0.00 0.00 0.00 4.61
1060 1299 1.743252 GAGCCGAGAAGCAAGGTGG 60.743 63.158 0.00 0.00 34.23 4.61
1061 1300 2.097038 CGAGCCGAGAAGCAAGGTG 61.097 63.158 0.00 0.00 34.23 4.00
1062 1301 1.608717 ATCGAGCCGAGAAGCAAGGT 61.609 55.000 3.76 0.00 39.91 3.50
1105 1344 0.596082 AACGCCCAAATTCAGAACCG 59.404 50.000 0.00 0.00 0.00 4.44
1174 1416 3.645975 CCACCACGTGCACGAACC 61.646 66.667 42.94 3.23 43.02 3.62
1409 1656 2.964209 TGGAGATGGACCCTAAGCTAG 58.036 52.381 0.00 0.00 0.00 3.42
1422 1669 0.249784 CGCACCCTCTGATGGAGATG 60.250 60.000 5.95 0.00 44.45 2.90
1424 1671 2.060383 CCGCACCCTCTGATGGAGA 61.060 63.158 5.95 0.00 44.45 3.71
1425 1672 2.503061 CCGCACCCTCTGATGGAG 59.497 66.667 5.95 0.00 41.51 3.86
1428 1675 2.513204 CAGCCGCACCCTCTGATG 60.513 66.667 0.00 0.00 0.00 3.07
1429 1676 4.479993 GCAGCCGCACCCTCTGAT 62.480 66.667 0.00 0.00 38.36 2.90
1573 1821 0.748729 ACGCACCAGAACGGGAAAAA 60.749 50.000 0.00 0.00 40.22 1.94
1613 1869 2.031919 CACAGCCCTACGCACCAA 59.968 61.111 0.00 0.00 41.38 3.67
1614 1870 3.238497 ACACAGCCCTACGCACCA 61.238 61.111 0.00 0.00 41.38 4.17
1615 1871 2.742372 CACACAGCCCTACGCACC 60.742 66.667 0.00 0.00 41.38 5.01
1616 1872 2.742372 CCACACAGCCCTACGCAC 60.742 66.667 0.00 0.00 41.38 5.34
1617 1873 3.234630 GACCACACAGCCCTACGCA 62.235 63.158 0.00 0.00 41.38 5.24
1618 1874 2.434359 GACCACACAGCCCTACGC 60.434 66.667 0.00 0.00 37.98 4.42
1619 1875 2.126071 CGACCACACAGCCCTACG 60.126 66.667 0.00 0.00 0.00 3.51
1680 1937 4.381411 GAATCAAAGGAATCTAGTCGGGG 58.619 47.826 0.00 0.00 0.00 5.73
1731 1988 3.020647 ATGTGATTCCCCGGGGCA 61.021 61.111 36.68 27.51 34.68 5.36
1735 1992 2.120909 GTGGCATGTGATTCCCCGG 61.121 63.158 0.00 0.00 0.00 5.73
1752 2009 5.123027 ACAAAACAAAATGAAATGCAACCGT 59.877 32.000 0.00 0.00 0.00 4.83
1755 2012 6.192500 CGTGACAAAACAAAATGAAATGCAAC 59.808 34.615 0.00 0.00 0.00 4.17
1790 2048 4.260784 GCTTGAAATTGACGACAAGTGTCT 60.261 41.667 9.63 0.00 42.66 3.41
1818 2076 3.478857 ACATTGTTCGAGTACCAACCA 57.521 42.857 0.00 0.00 0.00 3.67
1819 2077 3.608474 GCAACATTGTTCGAGTACCAACC 60.608 47.826 0.00 0.00 0.00 3.77
1820 2078 3.250040 AGCAACATTGTTCGAGTACCAAC 59.750 43.478 0.00 0.00 0.00 3.77
1822 2080 3.064207 GAGCAACATTGTTCGAGTACCA 58.936 45.455 0.00 0.00 0.00 3.25
1823 2081 3.724295 GAGCAACATTGTTCGAGTACC 57.276 47.619 0.00 0.00 0.00 3.34
1842 2100 3.328382 ACCACTTATTAGCAGCAACGA 57.672 42.857 0.00 0.00 0.00 3.85
1843 2101 4.552767 GCATACCACTTATTAGCAGCAACG 60.553 45.833 0.00 0.00 0.00 4.10
1870 2133 3.070576 GTCCACCTGCCATTGCCC 61.071 66.667 0.00 0.00 36.33 5.36
2100 2363 1.505353 GTAGCGCACGTACAGGTCT 59.495 57.895 11.47 0.00 0.00 3.85
2469 2735 1.524621 CTGGGCATCATGTCCCGTC 60.525 63.158 5.62 0.00 42.76 4.79
2471 2737 1.524621 GTCTGGGCATCATGTCCCG 60.525 63.158 5.62 0.00 42.76 5.14
2477 2743 1.383109 TCGGAGGTCTGGGCATCAT 60.383 57.895 0.00 0.00 0.00 2.45
2506 2775 2.263741 CCATAGGCTTGGCATCGGC 61.264 63.158 0.00 0.00 40.13 5.54
2521 2790 1.341383 GGTCTTGGCATCAAGTCCCAT 60.341 52.381 9.99 0.00 46.40 4.00
2528 2797 0.250234 CTCCTCGGTCTTGGCATCAA 59.750 55.000 0.00 0.00 0.00 2.57
2535 2804 0.682855 AGCTCTCCTCCTCGGTCTTG 60.683 60.000 0.00 0.00 0.00 3.02
2536 2805 0.395173 GAGCTCTCCTCCTCGGTCTT 60.395 60.000 6.43 0.00 34.35 3.01
2543 2812 2.296945 ATCAGGCGAGCTCTCCTCCT 62.297 60.000 22.56 14.02 37.27 3.69
2559 2828 2.497792 ATTCCACGGGCTTGGCATCA 62.498 55.000 0.00 0.00 36.48 3.07
2571 2840 0.178767 TCTGGGCATCAGATTCCACG 59.821 55.000 1.14 0.00 46.71 4.94
2651 2920 3.277211 TAGAGGCACGGCGTCACAC 62.277 63.158 10.85 4.55 44.54 3.82
2666 2935 0.691078 GTCCATCAGGGCAGGGTAGA 60.691 60.000 0.00 0.00 40.10 2.59
2670 2939 3.083349 TCGTCCATCAGGGCAGGG 61.083 66.667 0.00 0.00 40.51 4.45
2672 2941 2.303549 GACCTCGTCCATCAGGGCAG 62.304 65.000 0.00 0.00 40.51 4.85
2680 2949 2.711922 GGCGACAGACCTCGTCCAT 61.712 63.158 0.00 0.00 35.99 3.41
2729 2998 3.309296 CCAGTATCTTCTTAGCCCTGGA 58.691 50.000 0.00 0.00 40.29 3.86
2751 3020 2.742348 TGAGACGCTAAACCCAGGATA 58.258 47.619 0.00 0.00 0.00 2.59
2825 3094 3.707700 CGCGCACCACGTAAAGCA 61.708 61.111 8.75 0.00 46.11 3.91
2826 3095 3.624831 GACGCGCACCACGTAAAGC 62.625 63.158 5.73 0.00 45.24 3.51
2827 3096 2.019951 AGACGCGCACCACGTAAAG 61.020 57.895 5.73 0.00 45.24 1.85
2829 3098 2.731721 CAGACGCGCACCACGTAA 60.732 61.111 5.73 0.00 45.24 3.18
2830 3099 3.884581 GACAGACGCGCACCACGTA 62.885 63.158 5.73 0.00 45.24 3.57
2833 3102 2.196382 TAGAGACAGACGCGCACCAC 62.196 60.000 5.73 0.00 0.00 4.16
2836 3105 0.917259 CATTAGAGACAGACGCGCAC 59.083 55.000 5.73 0.00 0.00 5.34
2837 3106 0.526211 ACATTAGAGACAGACGCGCA 59.474 50.000 5.73 0.00 0.00 6.09
2838 3107 1.584308 GAACATTAGAGACAGACGCGC 59.416 52.381 5.73 0.00 0.00 6.86
2839 3108 3.102276 GAGAACATTAGAGACAGACGCG 58.898 50.000 3.53 3.53 0.00 6.01
2841 3110 3.127203 ACGGAGAACATTAGAGACAGACG 59.873 47.826 0.00 0.00 0.00 4.18
2843 3112 3.119459 GCACGGAGAACATTAGAGACAGA 60.119 47.826 0.00 0.00 0.00 3.41
2844 3113 3.119316 AGCACGGAGAACATTAGAGACAG 60.119 47.826 0.00 0.00 0.00 3.51
2845 3114 2.826128 AGCACGGAGAACATTAGAGACA 59.174 45.455 0.00 0.00 0.00 3.41
2879 3149 1.016130 ACGAAGGCGACATCAAGCAG 61.016 55.000 0.00 0.00 41.64 4.24
3005 3493 5.300286 CGGAGCATAAATGAAGGGAAGAAAT 59.700 40.000 0.00 0.00 0.00 2.17
3017 3505 1.134098 ACAGACCCCGGAGCATAAATG 60.134 52.381 0.73 0.00 0.00 2.32
3048 3536 2.092148 CGACAAGCGCTTTCGACG 59.908 61.111 32.22 24.66 38.10 5.12
3100 3591 1.485838 GCACGAGGACATGATCGCAG 61.486 60.000 15.91 11.51 42.61 5.18
3109 3600 4.724602 GCAGCGAGCACGAGGACA 62.725 66.667 8.01 0.00 44.79 4.02
3187 3678 1.206745 CGAAATCATCCGTCCGTCCG 61.207 60.000 0.00 0.00 0.00 4.79
3201 3692 1.601903 TGCGCAACTTCAACTCGAAAT 59.398 42.857 8.16 0.00 31.71 2.17
3242 3733 4.821589 GAGTGCGCCGGAAGAGGG 62.822 72.222 5.05 0.00 0.00 4.30
3330 3821 1.153628 GGAGCATAACAGGTCGCGT 60.154 57.895 5.77 0.00 36.90 6.01
3416 3907 2.125912 GCTCTCGCCGAAGCAAGA 60.126 61.111 13.74 0.00 39.83 3.02
3578 4078 2.563179 GGAGAGGAGATAATTGCCGCTA 59.437 50.000 0.00 0.00 31.77 4.26
3583 4083 1.000163 TCGCGGAGAGGAGATAATTGC 60.000 52.381 6.13 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.