Multiple sequence alignment - TraesCS4D01G300200

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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 TraesCS4D01G300200 chr4D 100.000 2378 0 0 1 2378 468701806 468704183 0.000000e+00 4392.0
1 TraesCS4D01G300200 chr4A 90.584 1370 83 20 801 2137 2786862 2785506 0.000000e+00 1773.0
2 TraesCS4D01G300200 chr4A 78.982 609 103 15 116 715 2787566 2786974 2.220000e-105 392.0
3 TraesCS4D01G300200 chr4B 90.687 1063 56 9 730 1751 588439810 588440870 0.000000e+00 1375.0
4 TraesCS4D01G300200 chr4B 88.235 187 11 4 2192 2378 588441284 588441459 1.850000e-51 213.0
5 TraesCS4D01G300200 chr4B 78.400 375 29 25 1788 2116 588440867 588441235 1.860000e-46 196.0
6 TraesCS4D01G300200 chr6A 83.945 218 15 6 1939 2137 506643072 506642856 8.680000e-45 191.0
7 TraesCS4D01G300200 chr3D 82.353 221 19 9 1936 2137 45759515 45759734 8.740000e-40 174.0
8 TraesCS4D01G300200 chr2B 82.673 202 29 3 1936 2137 406878283 406878478 8.740000e-40 174.0
9 TraesCS4D01G300200 chr2B 85.185 162 19 4 1981 2137 473772550 473772711 6.800000e-36 161.0
10 TraesCS4D01G300200 chr7B 82.353 221 17 4 1936 2137 387155883 387155666 3.140000e-39 172.0
11 TraesCS4D01G300200 chr7B 82.126 207 31 5 1936 2137 522151241 522151446 3.140000e-39 172.0
12 TraesCS4D01G300200 chr5A 82.673 202 28 4 1936 2137 295073176 295072982 3.140000e-39 172.0
13 TraesCS4D01G300200 chr5A 80.889 225 18 10 1935 2137 214918476 214918697 1.140000e-33 154.0
14 TraesCS4D01G300200 chr5B 81.818 198 15 7 1960 2137 211587128 211587324 1.900000e-31 147.0
15 TraesCS4D01G300200 chr5D 79.556 225 21 10 1935 2137 200643524 200643745 1.150000e-28 137.0
16 TraesCS4D01G300200 chr2A 92.632 95 6 1 2043 2137 586454807 586454900 4.120000e-28 135.0
17 TraesCS4D01G300200 chr2D 79.293 198 33 6 1936 2126 500397988 500397792 5.330000e-27 132.0
18 TraesCS4D01G300200 chr6B 83.673 98 13 3 439 536 6788596 6788690 3.260000e-14 89.8


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 TraesCS4D01G300200 chr4D 468701806 468704183 2377 False 4392.000000 4392 100.000 1 2378 1 chr4D.!!$F1 2377
1 TraesCS4D01G300200 chr4A 2785506 2787566 2060 True 1082.500000 1773 84.783 116 2137 2 chr4A.!!$R1 2021
2 TraesCS4D01G300200 chr4B 588439810 588441459 1649 False 594.666667 1375 85.774 730 2378 3 chr4B.!!$F1 1648

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
102 103 0.032117 TGAGGGATCCACCGAGACAT 60.032 55.0 15.23 0.0 40.11 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2246 0.108138 GTTCTGGCACGTGGATAGCT 60.108 55.0 18.88 0.0 0.0 3.32 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
25 26 2.930826 TCCTGGAAGAGGACAACAAC 57.069 50.000 0.00 0.00 46.96 3.32
26 27 1.070134 TCCTGGAAGAGGACAACAACG 59.930 52.381 0.00 0.00 46.96 4.10
27 28 1.202651 CCTGGAAGAGGACAACAACGT 60.203 52.381 0.00 0.00 46.33 3.99
28 29 2.561569 CTGGAAGAGGACAACAACGTT 58.438 47.619 0.00 0.00 34.07 3.99
29 30 2.285083 TGGAAGAGGACAACAACGTTG 58.715 47.619 26.20 26.20 0.00 4.10
30 31 2.093394 TGGAAGAGGACAACAACGTTGA 60.093 45.455 33.66 4.28 0.00 3.18
31 32 2.287103 GGAAGAGGACAACAACGTTGAC 59.713 50.000 33.66 19.54 0.00 3.18
32 33 1.567504 AGAGGACAACAACGTTGACG 58.432 50.000 33.66 23.97 46.33 4.35
33 34 0.580104 GAGGACAACAACGTTGACGG 59.420 55.000 33.66 22.37 44.95 4.79
34 35 1.010462 GGACAACAACGTTGACGGC 60.010 57.895 33.66 23.97 44.95 5.68
35 36 1.367195 GACAACAACGTTGACGGCG 60.367 57.895 33.66 17.76 44.95 6.46
36 37 1.754436 GACAACAACGTTGACGGCGA 61.754 55.000 33.66 0.00 44.95 5.54
37 38 1.083657 CAACAACGTTGACGGCGAG 60.084 57.895 33.66 11.19 44.95 5.03
38 39 2.241880 AACAACGTTGACGGCGAGG 61.242 57.895 33.66 5.07 44.95 4.63
39 40 4.072088 CAACGTTGACGGCGAGGC 62.072 66.667 23.90 2.67 44.95 4.70
61 62 4.680237 CGCAACCTGGCTCGGTGA 62.680 66.667 0.00 0.00 37.36 4.02
62 63 2.743928 GCAACCTGGCTCGGTGAG 60.744 66.667 0.00 0.00 37.36 3.51
71 72 2.048222 CTCGGTGAGCTTCCGCAA 60.048 61.111 21.22 8.74 46.49 4.85
72 73 2.357034 TCGGTGAGCTTCCGCAAC 60.357 61.111 21.22 2.57 46.49 4.17
73 74 3.423154 CGGTGAGCTTCCGCAACC 61.423 66.667 16.06 4.48 41.48 3.77
74 75 3.056328 GGTGAGCTTCCGCAACCC 61.056 66.667 0.00 0.00 38.51 4.11
75 76 2.032681 GTGAGCTTCCGCAACCCT 59.967 61.111 0.00 0.00 39.10 4.34
76 77 1.295423 GTGAGCTTCCGCAACCCTA 59.705 57.895 0.00 0.00 39.10 3.53
77 78 0.741221 GTGAGCTTCCGCAACCCTAG 60.741 60.000 0.00 0.00 39.10 3.02
78 79 1.192146 TGAGCTTCCGCAACCCTAGT 61.192 55.000 0.00 0.00 39.10 2.57
79 80 0.460459 GAGCTTCCGCAACCCTAGTC 60.460 60.000 0.00 0.00 39.10 2.59
80 81 1.192146 AGCTTCCGCAACCCTAGTCA 61.192 55.000 0.00 0.00 39.10 3.41
81 82 0.741221 GCTTCCGCAACCCTAGTCAG 60.741 60.000 0.00 0.00 35.78 3.51
82 83 0.608640 CTTCCGCAACCCTAGTCAGT 59.391 55.000 0.00 0.00 0.00 3.41
83 84 1.002087 CTTCCGCAACCCTAGTCAGTT 59.998 52.381 0.00 0.00 0.00 3.16
84 85 0.320374 TCCGCAACCCTAGTCAGTTG 59.680 55.000 11.30 11.30 44.93 3.16
85 86 0.320374 CCGCAACCCTAGTCAGTTGA 59.680 55.000 17.17 0.00 44.93 3.18
86 87 1.673033 CCGCAACCCTAGTCAGTTGAG 60.673 57.143 17.17 14.36 44.93 3.02
87 88 1.673033 CGCAACCCTAGTCAGTTGAGG 60.673 57.143 17.17 7.66 44.93 3.86
93 94 2.752030 CCTAGTCAGTTGAGGGATCCA 58.248 52.381 15.23 0.00 0.00 3.41
94 95 2.432510 CCTAGTCAGTTGAGGGATCCAC 59.567 54.545 15.23 7.66 0.00 4.02
95 96 1.280457 AGTCAGTTGAGGGATCCACC 58.720 55.000 15.23 4.80 38.08 4.61
96 97 0.108138 GTCAGTTGAGGGATCCACCG 60.108 60.000 15.23 0.00 40.11 4.94
97 98 0.252057 TCAGTTGAGGGATCCACCGA 60.252 55.000 15.23 0.97 40.11 4.69
98 99 0.176680 CAGTTGAGGGATCCACCGAG 59.823 60.000 15.23 0.00 40.11 4.63
99 100 0.041238 AGTTGAGGGATCCACCGAGA 59.959 55.000 15.23 0.00 40.11 4.04
100 101 0.175989 GTTGAGGGATCCACCGAGAC 59.824 60.000 15.23 0.33 40.11 3.36
101 102 0.252057 TTGAGGGATCCACCGAGACA 60.252 55.000 15.23 0.00 40.11 3.41
102 103 0.032117 TGAGGGATCCACCGAGACAT 60.032 55.000 15.23 0.00 40.11 3.06
103 104 0.676736 GAGGGATCCACCGAGACATC 59.323 60.000 15.23 0.00 40.11 3.06
104 105 0.760945 AGGGATCCACCGAGACATCC 60.761 60.000 15.23 0.00 40.11 3.51
105 106 0.760945 GGGATCCACCGAGACATCCT 60.761 60.000 15.23 0.00 40.11 3.24
106 107 0.676736 GGATCCACCGAGACATCCTC 59.323 60.000 6.95 0.00 38.55 3.71
107 108 1.403814 GATCCACCGAGACATCCTCA 58.596 55.000 0.00 0.00 42.06 3.86
108 109 1.967066 GATCCACCGAGACATCCTCAT 59.033 52.381 0.00 0.00 42.06 2.90
109 110 1.403814 TCCACCGAGACATCCTCATC 58.596 55.000 0.00 0.00 42.06 2.92
110 111 1.114627 CCACCGAGACATCCTCATCA 58.885 55.000 0.00 0.00 42.06 3.07
111 112 1.482182 CCACCGAGACATCCTCATCAA 59.518 52.381 0.00 0.00 42.06 2.57
112 113 2.544685 CACCGAGACATCCTCATCAAC 58.455 52.381 0.00 0.00 42.06 3.18
113 114 2.094026 CACCGAGACATCCTCATCAACA 60.094 50.000 0.00 0.00 42.06 3.33
114 115 2.567169 ACCGAGACATCCTCATCAACAA 59.433 45.455 0.00 0.00 42.06 2.83
130 131 0.664767 ACAACGTGCGAGAAGAGAGC 60.665 55.000 0.00 0.00 0.00 4.09
157 158 3.402110 TGTCCATGCATAGGAATAAGCG 58.598 45.455 16.37 0.00 36.80 4.68
164 165 5.483685 TGCATAGGAATAAGCGGAGTTAT 57.516 39.130 0.00 0.00 0.00 1.89
167 168 8.301252 TGCATAGGAATAAGCGGAGTTATATA 57.699 34.615 0.00 0.00 0.00 0.86
168 169 8.924303 TGCATAGGAATAAGCGGAGTTATATAT 58.076 33.333 0.00 0.00 0.00 0.86
250 251 7.717875 AGTTATAAACGCTCCCTTGCAAATATA 59.282 33.333 0.00 0.00 36.23 0.86
255 256 3.627577 CGCTCCCTTGCAAATATAGTGTT 59.372 43.478 0.00 0.00 0.00 3.32
257 258 4.202050 GCTCCCTTGCAAATATAGTGTTGG 60.202 45.833 0.00 0.00 0.00 3.77
258 259 3.699038 TCCCTTGCAAATATAGTGTTGGC 59.301 43.478 0.00 0.00 0.00 4.52
288 289 0.623723 GGGTTAGGGCATCTCCAACA 59.376 55.000 0.00 0.00 36.21 3.33
289 290 1.408822 GGGTTAGGGCATCTCCAACAG 60.409 57.143 0.00 0.00 36.21 3.16
291 292 0.918983 TTAGGGCATCTCCAACAGGG 59.081 55.000 0.00 0.00 36.21 4.45
294 295 0.107165 GGGCATCTCCAACAGGGTAC 60.107 60.000 0.00 0.00 38.11 3.34
318 319 0.466189 ATGCGCCCCTAAATGTCTGG 60.466 55.000 4.18 0.00 0.00 3.86
319 320 1.223487 GCGCCCCTAAATGTCTGGA 59.777 57.895 0.00 0.00 0.00 3.86
320 321 1.095807 GCGCCCCTAAATGTCTGGAC 61.096 60.000 0.00 0.00 0.00 4.02
323 324 2.019156 GCCCCTAAATGTCTGGACTGC 61.019 57.143 2.38 0.00 0.00 4.40
324 325 1.281867 CCCCTAAATGTCTGGACTGCA 59.718 52.381 2.38 0.00 0.00 4.41
325 326 2.092212 CCCCTAAATGTCTGGACTGCAT 60.092 50.000 2.38 0.00 0.00 3.96
326 327 2.947652 CCCTAAATGTCTGGACTGCATG 59.052 50.000 2.38 0.00 0.00 4.06
327 328 2.947652 CCTAAATGTCTGGACTGCATGG 59.052 50.000 0.00 0.00 0.00 3.66
328 329 2.592102 AAATGTCTGGACTGCATGGT 57.408 45.000 0.00 0.00 0.00 3.55
329 330 2.592102 AATGTCTGGACTGCATGGTT 57.408 45.000 0.00 0.00 0.00 3.67
378 380 9.174166 GGTACATCAAATATTTGTGGAGTAGTT 57.826 33.333 23.95 9.30 39.18 2.24
386 388 2.806608 TGTGGAGTAGTTCGGTTGTC 57.193 50.000 0.00 0.00 0.00 3.18
397 399 2.178912 TCGGTTGTCTGAAATCCCAC 57.821 50.000 0.00 0.00 0.00 4.61
401 403 3.550030 CGGTTGTCTGAAATCCCACAAAC 60.550 47.826 0.00 0.00 33.82 2.93
403 405 2.226330 TGTCTGAAATCCCACAAACCG 58.774 47.619 0.00 0.00 0.00 4.44
404 406 1.539827 GTCTGAAATCCCACAAACCGG 59.460 52.381 0.00 0.00 0.00 5.28
426 428 2.314549 AGGCAAATATGGGGAGGTTTGA 59.685 45.455 0.00 0.00 34.38 2.69
428 430 2.695147 GCAAATATGGGGAGGTTTGAGG 59.305 50.000 0.00 0.00 34.38 3.86
434 436 1.423921 TGGGGAGGTTTGAGGAAGTTC 59.576 52.381 0.00 0.00 0.00 3.01
436 438 1.610886 GGGAGGTTTGAGGAAGTTCGG 60.611 57.143 0.00 0.00 0.00 4.30
437 439 1.610886 GGAGGTTTGAGGAAGTTCGGG 60.611 57.143 0.00 0.00 0.00 5.14
443 445 2.027625 GAGGAAGTTCGGGCACACG 61.028 63.158 0.00 0.00 0.00 4.49
446 448 2.654912 GAAGTTCGGGCACACGACG 61.655 63.158 0.00 0.00 43.37 5.12
447 449 4.657824 AGTTCGGGCACACGACGG 62.658 66.667 0.00 0.00 43.37 4.79
451 453 4.953868 CGGGCACACGACGGACAA 62.954 66.667 0.00 0.00 35.47 3.18
456 458 1.594293 CACACGACGGACAAGCCTT 60.594 57.895 0.00 0.00 0.00 4.35
457 459 1.594293 ACACGACGGACAAGCCTTG 60.594 57.895 2.11 2.11 0.00 3.61
461 463 1.084370 CGACGGACAAGCCTTGGATC 61.084 60.000 9.64 0.00 34.12 3.36
462 464 0.744771 GACGGACAAGCCTTGGATCC 60.745 60.000 9.64 4.20 34.12 3.36
463 465 1.452108 CGGACAAGCCTTGGATCCC 60.452 63.158 9.90 3.71 34.12 3.85
500 509 5.860648 TTTTTCCCCTCTACATCCTTTCT 57.139 39.130 0.00 0.00 0.00 2.52
501 510 5.437191 TTTTCCCCTCTACATCCTTTCTC 57.563 43.478 0.00 0.00 0.00 2.87
502 511 4.354208 TTCCCCTCTACATCCTTTCTCT 57.646 45.455 0.00 0.00 0.00 3.10
503 512 4.354208 TCCCCTCTACATCCTTTCTCTT 57.646 45.455 0.00 0.00 0.00 2.85
504 513 4.699994 TCCCCTCTACATCCTTTCTCTTT 58.300 43.478 0.00 0.00 0.00 2.52
505 514 5.101529 TCCCCTCTACATCCTTTCTCTTTT 58.898 41.667 0.00 0.00 0.00 2.27
508 517 6.345298 CCCTCTACATCCTTTCTCTTTTCTC 58.655 44.000 0.00 0.00 0.00 2.87
516 525 6.952605 TCCTTTCTCTTTTCTCCCTCAATA 57.047 37.500 0.00 0.00 0.00 1.90
543 552 2.951642 AGGGATGGACATTTATTGCACG 59.048 45.455 0.00 0.00 0.00 5.34
544 553 2.034558 GGGATGGACATTTATTGCACGG 59.965 50.000 0.00 0.00 0.00 4.94
546 555 1.468985 TGGACATTTATTGCACGGGG 58.531 50.000 0.00 0.00 0.00 5.73
550 559 1.548269 ACATTTATTGCACGGGGTTGG 59.452 47.619 0.00 0.00 0.00 3.77
575 584 1.112315 AGCCCTCTATCTGCTGTCCG 61.112 60.000 0.00 0.00 33.23 4.79
576 585 1.365633 CCCTCTATCTGCTGTCCGC 59.634 63.158 0.00 0.00 39.77 5.54
593 602 2.102420 TCCGCGGATATTTGATGTGTCT 59.898 45.455 27.28 0.00 0.00 3.41
596 605 3.183172 CGCGGATATTTGATGTGTCTGAG 59.817 47.826 0.00 0.00 0.00 3.35
598 607 4.025396 GCGGATATTTGATGTGTCTGAGTG 60.025 45.833 0.00 0.00 0.00 3.51
602 611 2.916702 TTGATGTGTCTGAGTGCAGT 57.083 45.000 0.00 0.00 42.84 4.40
604 613 1.688197 TGATGTGTCTGAGTGCAGTGA 59.312 47.619 0.00 0.00 42.84 3.41
606 615 0.249031 TGTGTCTGAGTGCAGTGACG 60.249 55.000 0.00 0.00 42.84 4.35
610 619 1.933853 GTCTGAGTGCAGTGACGTTTT 59.066 47.619 0.00 0.00 42.84 2.43
614 623 4.211164 TCTGAGTGCAGTGACGTTTTTATG 59.789 41.667 0.00 0.00 42.84 1.90
616 625 4.209452 AGTGCAGTGACGTTTTTATGTG 57.791 40.909 0.00 0.00 0.00 3.21
620 629 6.017440 AGTGCAGTGACGTTTTTATGTGTTAT 60.017 34.615 0.00 0.00 0.00 1.89
622 631 6.203915 TGCAGTGACGTTTTTATGTGTTATCT 59.796 34.615 0.00 0.00 0.00 1.98
626 635 7.439955 AGTGACGTTTTTATGTGTTATCTGTGA 59.560 33.333 0.00 0.00 0.00 3.58
628 637 7.095397 TGACGTTTTTATGTGTTATCTGTGAGG 60.095 37.037 0.00 0.00 0.00 3.86
629 638 6.708949 ACGTTTTTATGTGTTATCTGTGAGGT 59.291 34.615 0.00 0.00 0.00 3.85
630 639 7.095355 ACGTTTTTATGTGTTATCTGTGAGGTC 60.095 37.037 0.00 0.00 0.00 3.85
631 640 6.961359 TTTTATGTGTTATCTGTGAGGTCG 57.039 37.500 0.00 0.00 0.00 4.79
642 653 0.036306 GTGAGGTCGGACCCAACAAT 59.964 55.000 23.21 3.65 39.75 2.71
647 658 2.364002 AGGTCGGACCCAACAATTTTTG 59.636 45.455 23.21 0.00 39.75 2.44
654 665 5.432645 GGACCCAACAATTTTTGAGGAAAA 58.567 37.500 14.85 0.00 41.20 2.29
669 680 7.941431 TTGAGGAAAACAACCTAAAACACTA 57.059 32.000 0.00 0.00 37.93 2.74
683 694 9.702494 ACCTAAAACACTATACACTTACTGTTC 57.298 33.333 0.00 0.00 33.91 3.18
721 732 9.471084 AGTTTTTAAAAGATTAACAATGACCCG 57.529 29.630 0.14 0.00 30.86 5.28
722 733 9.251792 GTTTTTAAAAGATTAACAATGACCCGT 57.748 29.630 0.14 0.00 30.86 5.28
725 736 9.504708 TTTAAAAGATTAACAATGACCCGTAGA 57.495 29.630 0.00 0.00 30.86 2.59
726 737 9.675464 TTAAAAGATTAACAATGACCCGTAGAT 57.325 29.630 0.00 0.00 0.00 1.98
727 738 8.575649 AAAAGATTAACAATGACCCGTAGATT 57.424 30.769 0.00 0.00 0.00 2.40
728 739 7.787725 AAGATTAACAATGACCCGTAGATTC 57.212 36.000 0.00 0.00 0.00 2.52
729 740 7.125792 AGATTAACAATGACCCGTAGATTCT 57.874 36.000 0.00 0.00 0.00 2.40
731 742 6.978343 TTAACAATGACCCGTAGATTCTTG 57.022 37.500 0.00 0.00 0.00 3.02
732 743 4.819105 ACAATGACCCGTAGATTCTTGA 57.181 40.909 0.00 0.00 0.00 3.02
733 744 4.759782 ACAATGACCCGTAGATTCTTGAG 58.240 43.478 0.00 0.00 0.00 3.02
744 821 2.300152 AGATTCTTGAGCACGGAGTTGA 59.700 45.455 0.00 0.00 41.61 3.18
757 834 3.244422 ACGGAGTTGAAGATGCCTTTACA 60.244 43.478 0.00 0.00 37.78 2.41
767 844 1.600023 TGCCTTTACACGGGTTTCAG 58.400 50.000 0.00 0.00 0.00 3.02
799 876 0.951558 CCAATTTTCGGGCCGGATAG 59.048 55.000 27.98 11.28 0.00 2.08
824 901 7.057264 GGGGTTTCAGCTTAGAAGATATTTCT 58.943 38.462 0.00 5.76 0.00 2.52
839 916 3.713826 ATTTCTAGTTTTCGGCCCTGA 57.286 42.857 0.00 0.00 0.00 3.86
841 918 3.713826 TTCTAGTTTTCGGCCCTGATT 57.286 42.857 0.00 0.00 0.00 2.57
851 928 2.421399 GCCCTGATTCAGCCCAAGC 61.421 63.158 8.23 2.31 40.32 4.01
854 931 2.045045 TGATTCAGCCCAAGCCCG 60.045 61.111 0.00 0.00 41.25 6.13
918 998 2.284699 CCTTCCTCTCCCGTGGGT 60.285 66.667 4.53 0.00 36.47 4.51
980 1085 1.911454 AACTCCATCCATCCATCCCA 58.089 50.000 0.00 0.00 0.00 4.37
1384 1497 1.686587 CCACCATCATGTAGTAGCGGA 59.313 52.381 0.00 0.00 0.00 5.54
1430 1552 3.412386 GGTGTGTCCTGCTTCAGTTTAT 58.588 45.455 0.00 0.00 0.00 1.40
1434 1556 5.687285 GTGTGTCCTGCTTCAGTTTATTTTG 59.313 40.000 0.00 0.00 0.00 2.44
1446 1568 7.928307 TCAGTTTATTTTGCTGCTTAGAGAT 57.072 32.000 0.00 0.00 0.00 2.75
1458 1580 6.097412 TGCTGCTTAGAGATTTCAGACATCTA 59.903 38.462 0.00 0.00 30.70 1.98
1597 1721 8.274248 CACATATCTTTTGTCGAGATGAATCAG 58.726 37.037 2.15 0.00 34.60 2.90
1617 1746 1.202498 GGGTTGCTAGCTAACCTACCG 60.202 57.143 30.76 0.00 45.42 4.02
1620 1749 1.843368 TGCTAGCTAACCTACCGTGT 58.157 50.000 17.23 0.00 0.00 4.49
1630 1759 1.278127 ACCTACCGTGTCCTGATTTGG 59.722 52.381 0.00 0.00 0.00 3.28
1648 1777 1.134521 TGGTAGGCGTAAATGAGGCTG 60.135 52.381 0.00 0.00 43.34 4.85
1649 1778 1.138266 GGTAGGCGTAAATGAGGCTGA 59.862 52.381 0.00 0.00 43.34 4.26
1655 1785 2.484264 GCGTAAATGAGGCTGAGTTTGT 59.516 45.455 0.00 0.00 35.98 2.83
1723 1853 3.250762 TCTGAAGTTGCTGTTGAATTCCG 59.749 43.478 2.27 0.00 0.00 4.30
1739 1869 2.620251 TCCGTATGCATTTCCCTGAG 57.380 50.000 3.54 0.00 0.00 3.35
1755 1885 3.431486 CCCTGAGGTTGCTGACTTAGATC 60.431 52.174 0.00 0.00 0.00 2.75
1757 1887 4.646945 CCTGAGGTTGCTGACTTAGATCTA 59.353 45.833 0.00 0.00 0.00 1.98
1835 1974 5.316167 TGTTGGATGAAATGCTGACTAGTT 58.684 37.500 0.00 0.00 34.76 2.24
1838 1977 5.748402 TGGATGAAATGCTGACTAGTTGAT 58.252 37.500 0.00 0.00 34.76 2.57
1882 2049 5.756347 AGTTGCGTAGTGTTGTGAATCTTTA 59.244 36.000 0.00 0.00 0.00 1.85
1925 2094 9.664332 AATAAATTTATTAGGCATTGCACACAA 57.336 25.926 19.57 0.00 34.41 3.33
1970 2140 3.354948 AAGGCATGCTGATACTGTCAA 57.645 42.857 18.92 0.00 36.14 3.18
1978 2148 3.194062 GCTGATACTGTCAAAGAGAGGC 58.806 50.000 0.00 0.00 36.14 4.70
2024 2194 3.955551 GGAGGAGTCCGTAAAGAGAGATT 59.044 47.826 2.76 0.00 31.37 2.40
2044 2214 6.878317 AGATTTGAAGGACTCGAATATCACA 58.122 36.000 0.00 0.00 38.14 3.58
2046 2216 6.968131 TTTGAAGGACTCGAATATCACAAG 57.032 37.500 0.00 0.00 0.00 3.16
2047 2217 5.011090 TGAAGGACTCGAATATCACAAGG 57.989 43.478 0.00 0.00 0.00 3.61
2049 2219 2.103263 AGGACTCGAATATCACAAGGGC 59.897 50.000 0.00 0.00 0.00 5.19
2050 2220 2.128035 GACTCGAATATCACAAGGGCG 58.872 52.381 0.00 0.00 0.00 6.13
2051 2221 0.861837 CTCGAATATCACAAGGGCGC 59.138 55.000 0.00 0.00 0.00 6.53
2052 2222 0.874175 TCGAATATCACAAGGGCGCG 60.874 55.000 0.00 0.00 0.00 6.86
2061 2246 1.669760 CAAGGGCGCGTGGAAGTTA 60.670 57.895 8.43 0.00 0.00 2.24
2103 2288 6.052840 CCATGACTTGGTTTCGATATCTTG 57.947 41.667 0.34 0.00 40.99 3.02
2109 2294 5.046159 ACTTGGTTTCGATATCTTGTGGGTA 60.046 40.000 0.34 0.00 0.00 3.69
2120 2305 7.040340 CGATATCTTGTGGGTATCAACTCTAGT 60.040 40.741 0.34 0.00 0.00 2.57
2126 2311 5.044328 TGTGGGTATCAACTCTAGTCTACCT 60.044 44.000 12.50 0.00 32.56 3.08
2127 2312 5.892686 GTGGGTATCAACTCTAGTCTACCTT 59.107 44.000 12.50 0.00 32.56 3.50
2128 2313 7.059156 GTGGGTATCAACTCTAGTCTACCTTA 58.941 42.308 12.50 4.59 32.56 2.69
2129 2314 7.559170 GTGGGTATCAACTCTAGTCTACCTTAA 59.441 40.741 12.50 0.00 32.56 1.85
2130 2315 7.559170 TGGGTATCAACTCTAGTCTACCTTAAC 59.441 40.741 12.50 2.63 32.56 2.01
2131 2316 7.779326 GGGTATCAACTCTAGTCTACCTTAACT 59.221 40.741 12.50 0.00 32.56 2.24
2132 2317 9.187996 GGTATCAACTCTAGTCTACCTTAACTT 57.812 37.037 8.28 0.00 30.87 2.66
2180 2365 5.866207 AGTCTACCTTAACTTGTTTGGGAG 58.134 41.667 9.61 9.61 0.00 4.30
2196 2381 2.031870 GGGAGTGAAAGGCTTTGTTGT 58.968 47.619 18.79 0.00 0.00 3.32
2197 2382 2.034685 GGGAGTGAAAGGCTTTGTTGTC 59.965 50.000 18.79 8.26 0.00 3.18
2221 2418 2.360852 CACAGGGAGGCTTGCTGG 60.361 66.667 0.00 0.00 0.00 4.85
2247 2444 0.108396 TAGTGCAGCAGCCAAAGTCA 59.892 50.000 0.00 0.00 41.13 3.41
2249 2446 0.388134 GTGCAGCAGCCAAAGTCATG 60.388 55.000 0.00 0.00 41.13 3.07
2290 2487 7.884257 TCTGAATCATTGCTTTGTTGACAATA 58.116 30.769 0.00 0.00 35.55 1.90
2291 2488 8.525316 TCTGAATCATTGCTTTGTTGACAATAT 58.475 29.630 0.00 0.00 35.55 1.28
2292 2489 9.146984 CTGAATCATTGCTTTGTTGACAATATT 57.853 29.630 0.00 0.00 35.55 1.28
2293 2490 9.491675 TGAATCATTGCTTTGTTGACAATATTT 57.508 25.926 0.00 0.00 35.55 1.40
2294 2491 9.749490 GAATCATTGCTTTGTTGACAATATTTG 57.251 29.630 0.00 0.00 35.55 2.32
2295 2492 9.491675 AATCATTGCTTTGTTGACAATATTTGA 57.508 25.926 0.00 0.00 35.55 2.69
2296 2493 8.883954 TCATTGCTTTGTTGACAATATTTGAA 57.116 26.923 0.00 0.00 35.55 2.69
2297 2494 8.980610 TCATTGCTTTGTTGACAATATTTGAAG 58.019 29.630 0.00 0.00 35.55 3.02
2298 2495 8.767085 CATTGCTTTGTTGACAATATTTGAAGT 58.233 29.630 0.00 0.00 35.55 3.01
2318 2515 8.177119 TGAAGTTTTTAACAGCTATGGAATGT 57.823 30.769 0.00 0.00 0.00 2.71
2350 2547 5.691754 GGCTCAATTGTTTTAACCTTCACAG 59.308 40.000 5.13 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.202651 ACGTTGTTGTCCTCTTCCAGG 60.203 52.381 0.00 0.00 45.15 4.45
8 9 2.240493 ACGTTGTTGTCCTCTTCCAG 57.760 50.000 0.00 0.00 0.00 3.86
9 10 2.093394 TCAACGTTGTTGTCCTCTTCCA 60.093 45.455 26.47 0.72 0.00 3.53
10 11 2.287103 GTCAACGTTGTTGTCCTCTTCC 59.713 50.000 26.47 0.06 0.00 3.46
11 12 2.034001 CGTCAACGTTGTTGTCCTCTTC 60.034 50.000 26.47 6.11 34.11 2.87
12 13 1.931172 CGTCAACGTTGTTGTCCTCTT 59.069 47.619 26.47 0.00 34.11 2.85
13 14 1.567504 CGTCAACGTTGTTGTCCTCT 58.432 50.000 26.47 0.00 34.11 3.69
14 15 0.580104 CCGTCAACGTTGTTGTCCTC 59.420 55.000 26.47 9.45 37.74 3.71
15 16 1.433837 GCCGTCAACGTTGTTGTCCT 61.434 55.000 26.47 0.00 37.74 3.85
16 17 1.010462 GCCGTCAACGTTGTTGTCC 60.010 57.895 26.47 9.93 37.74 4.02
17 18 1.367195 CGCCGTCAACGTTGTTGTC 60.367 57.895 26.47 14.56 37.74 3.18
18 19 1.758319 CTCGCCGTCAACGTTGTTGT 61.758 55.000 26.47 0.00 37.74 3.32
19 20 1.083657 CTCGCCGTCAACGTTGTTG 60.084 57.895 26.47 19.14 37.74 3.33
20 21 2.241880 CCTCGCCGTCAACGTTGTT 61.242 57.895 26.47 0.00 37.74 2.83
21 22 2.660552 CCTCGCCGTCAACGTTGT 60.661 61.111 26.47 0.00 37.74 3.32
22 23 4.072088 GCCTCGCCGTCAACGTTG 62.072 66.667 22.35 22.35 37.74 4.10
44 45 4.680237 TCACCGAGCCAGGTTGCG 62.680 66.667 0.00 0.00 43.00 4.85
45 46 2.743928 CTCACCGAGCCAGGTTGC 60.744 66.667 0.00 0.00 43.00 4.17
63 64 0.608640 ACTGACTAGGGTTGCGGAAG 59.391 55.000 0.00 0.00 0.00 3.46
64 65 1.053424 AACTGACTAGGGTTGCGGAA 58.947 50.000 0.00 0.00 0.00 4.30
65 66 0.320374 CAACTGACTAGGGTTGCGGA 59.680 55.000 10.81 0.00 36.78 5.54
66 67 0.320374 TCAACTGACTAGGGTTGCGG 59.680 55.000 15.76 0.39 41.53 5.69
67 68 1.673033 CCTCAACTGACTAGGGTTGCG 60.673 57.143 15.76 11.80 41.53 4.85
68 69 1.339151 CCCTCAACTGACTAGGGTTGC 60.339 57.143 15.76 0.00 44.34 4.17
69 70 2.770164 CCCTCAACTGACTAGGGTTG 57.230 55.000 14.93 14.93 44.34 3.77
73 74 2.432510 GTGGATCCCTCAACTGACTAGG 59.567 54.545 9.90 0.00 0.00 3.02
74 75 2.432510 GGTGGATCCCTCAACTGACTAG 59.567 54.545 9.90 0.00 0.00 2.57
75 76 2.467880 GGTGGATCCCTCAACTGACTA 58.532 52.381 9.90 0.00 0.00 2.59
76 77 1.280457 GGTGGATCCCTCAACTGACT 58.720 55.000 9.90 0.00 0.00 3.41
77 78 0.108138 CGGTGGATCCCTCAACTGAC 60.108 60.000 9.90 0.00 34.02 3.51
78 79 0.252057 TCGGTGGATCCCTCAACTGA 60.252 55.000 9.90 8.34 38.22 3.41
79 80 0.176680 CTCGGTGGATCCCTCAACTG 59.823 60.000 9.90 5.84 33.51 3.16
80 81 0.041238 TCTCGGTGGATCCCTCAACT 59.959 55.000 9.90 0.00 0.00 3.16
81 82 0.175989 GTCTCGGTGGATCCCTCAAC 59.824 60.000 9.90 0.00 0.00 3.18
82 83 0.252057 TGTCTCGGTGGATCCCTCAA 60.252 55.000 9.90 0.00 0.00 3.02
83 84 0.032117 ATGTCTCGGTGGATCCCTCA 60.032 55.000 9.90 0.00 0.00 3.86
84 85 0.676736 GATGTCTCGGTGGATCCCTC 59.323 60.000 9.90 2.15 0.00 4.30
85 86 0.760945 GGATGTCTCGGTGGATCCCT 60.761 60.000 9.90 0.00 0.00 4.20
86 87 0.760945 AGGATGTCTCGGTGGATCCC 60.761 60.000 9.90 0.00 35.85 3.85
87 88 0.676736 GAGGATGTCTCGGTGGATCC 59.323 60.000 4.20 4.20 35.51 3.36
88 89 1.403814 TGAGGATGTCTCGGTGGATC 58.596 55.000 0.00 0.00 45.32 3.36
89 90 1.967066 GATGAGGATGTCTCGGTGGAT 59.033 52.381 0.00 0.00 45.32 3.41
90 91 1.341976 TGATGAGGATGTCTCGGTGGA 60.342 52.381 0.00 0.00 45.32 4.02
91 92 1.114627 TGATGAGGATGTCTCGGTGG 58.885 55.000 0.00 0.00 45.32 4.61
92 93 2.094026 TGTTGATGAGGATGTCTCGGTG 60.094 50.000 0.00 0.00 45.32 4.94
93 94 2.179427 TGTTGATGAGGATGTCTCGGT 58.821 47.619 0.00 0.00 45.32 4.69
94 95 2.932614 GTTGTTGATGAGGATGTCTCGG 59.067 50.000 0.00 0.00 45.32 4.63
95 96 2.600420 CGTTGTTGATGAGGATGTCTCG 59.400 50.000 0.00 0.00 45.32 4.04
96 97 3.369147 CACGTTGTTGATGAGGATGTCTC 59.631 47.826 0.00 0.00 42.74 3.36
97 98 3.329386 CACGTTGTTGATGAGGATGTCT 58.671 45.455 0.00 0.00 0.00 3.41
98 99 2.159653 GCACGTTGTTGATGAGGATGTC 60.160 50.000 0.00 0.00 0.00 3.06
99 100 1.806542 GCACGTTGTTGATGAGGATGT 59.193 47.619 0.00 0.00 0.00 3.06
100 101 1.201954 CGCACGTTGTTGATGAGGATG 60.202 52.381 0.00 0.00 0.00 3.51
101 102 1.078709 CGCACGTTGTTGATGAGGAT 58.921 50.000 0.00 0.00 0.00 3.24
102 103 0.032815 TCGCACGTTGTTGATGAGGA 59.967 50.000 0.00 0.00 0.00 3.71
103 104 0.439985 CTCGCACGTTGTTGATGAGG 59.560 55.000 0.00 0.00 0.00 3.86
104 105 1.418373 TCTCGCACGTTGTTGATGAG 58.582 50.000 0.00 0.00 0.00 2.90
105 106 1.792367 CTTCTCGCACGTTGTTGATGA 59.208 47.619 0.00 0.00 0.00 2.92
106 107 1.792367 TCTTCTCGCACGTTGTTGATG 59.208 47.619 0.00 0.00 0.00 3.07
107 108 2.061773 CTCTTCTCGCACGTTGTTGAT 58.938 47.619 0.00 0.00 0.00 2.57
108 109 1.066454 TCTCTTCTCGCACGTTGTTGA 59.934 47.619 0.00 0.00 0.00 3.18
109 110 1.453524 CTCTCTTCTCGCACGTTGTTG 59.546 52.381 0.00 0.00 0.00 3.33
110 111 1.772182 CTCTCTTCTCGCACGTTGTT 58.228 50.000 0.00 0.00 0.00 2.83
111 112 0.664767 GCTCTCTTCTCGCACGTTGT 60.665 55.000 0.00 0.00 0.00 3.32
112 113 1.347817 GGCTCTCTTCTCGCACGTTG 61.348 60.000 0.00 0.00 0.00 4.10
113 114 1.080434 GGCTCTCTTCTCGCACGTT 60.080 57.895 0.00 0.00 0.00 3.99
114 115 1.806461 TTGGCTCTCTTCTCGCACGT 61.806 55.000 0.00 0.00 0.00 4.49
130 131 2.934887 TCCTATGCATGGACATGTTGG 58.065 47.619 12.26 10.14 40.80 3.77
222 223 2.284417 GCAAGGGAGCGTTTATAACTCG 59.716 50.000 5.27 5.27 0.00 4.18
231 232 3.627577 CACTATATTTGCAAGGGAGCGTT 59.372 43.478 0.00 0.00 37.31 4.84
237 238 3.489059 CGCCAACACTATATTTGCAAGGG 60.489 47.826 0.00 0.00 0.00 3.95
250 251 2.617021 CCCCATAGTTAACGCCAACACT 60.617 50.000 0.00 0.00 0.00 3.55
255 256 2.171027 CCTAACCCCATAGTTAACGCCA 59.829 50.000 0.00 0.00 32.02 5.69
257 258 2.842457 CCCTAACCCCATAGTTAACGC 58.158 52.381 0.00 0.00 32.02 4.84
258 259 2.171027 TGCCCTAACCCCATAGTTAACG 59.829 50.000 0.00 0.00 32.02 3.18
288 289 2.590092 GGCGCATTGAGGTACCCT 59.410 61.111 10.83 0.00 36.03 4.34
289 290 2.516225 GGGCGCATTGAGGTACCC 60.516 66.667 10.83 0.32 0.00 3.69
291 292 0.179468 TTAGGGGCGCATTGAGGTAC 59.821 55.000 10.83 0.00 0.00 3.34
294 295 0.670162 CATTTAGGGGCGCATTGAGG 59.330 55.000 10.83 0.00 0.00 3.86
300 301 1.077787 CCAGACATTTAGGGGCGCA 60.078 57.895 10.83 0.00 0.00 6.09
304 305 1.281867 TGCAGTCCAGACATTTAGGGG 59.718 52.381 0.00 0.00 0.00 4.79
318 319 1.512926 AGTGTTCGAACCATGCAGTC 58.487 50.000 24.78 5.94 0.00 3.51
319 320 1.967319 AAGTGTTCGAACCATGCAGT 58.033 45.000 24.78 6.53 0.00 4.40
320 321 3.354089 AAAAGTGTTCGAACCATGCAG 57.646 42.857 24.78 0.00 0.00 4.41
351 352 8.548877 ACTACTCCACAAATATTTGATGTACCT 58.451 33.333 30.18 7.22 40.55 3.08
361 363 6.235664 ACAACCGAACTACTCCACAAATATT 58.764 36.000 0.00 0.00 0.00 1.28
363 365 5.011329 AGACAACCGAACTACTCCACAAATA 59.989 40.000 0.00 0.00 0.00 1.40
366 368 2.696707 AGACAACCGAACTACTCCACAA 59.303 45.455 0.00 0.00 0.00 3.33
367 369 2.035449 CAGACAACCGAACTACTCCACA 59.965 50.000 0.00 0.00 0.00 4.17
368 370 2.295349 TCAGACAACCGAACTACTCCAC 59.705 50.000 0.00 0.00 0.00 4.02
378 380 1.418264 TGTGGGATTTCAGACAACCGA 59.582 47.619 0.00 0.00 0.00 4.69
379 381 1.890876 TGTGGGATTTCAGACAACCG 58.109 50.000 0.00 0.00 0.00 4.44
386 388 1.812571 CTCCGGTTTGTGGGATTTCAG 59.187 52.381 0.00 0.00 0.00 3.02
397 399 1.408702 CCCATATTTGCCTCCGGTTTG 59.591 52.381 0.00 0.00 0.00 2.93
401 403 0.250901 CTCCCCATATTTGCCTCCGG 60.251 60.000 0.00 0.00 0.00 5.14
403 405 0.853530 ACCTCCCCATATTTGCCTCC 59.146 55.000 0.00 0.00 0.00 4.30
404 406 2.695147 CAAACCTCCCCATATTTGCCTC 59.305 50.000 0.00 0.00 0.00 4.70
407 409 2.695147 CCTCAAACCTCCCCATATTTGC 59.305 50.000 0.00 0.00 33.09 3.68
413 415 1.760405 ACTTCCTCAAACCTCCCCAT 58.240 50.000 0.00 0.00 0.00 4.00
415 417 1.610886 CGAACTTCCTCAAACCTCCCC 60.611 57.143 0.00 0.00 0.00 4.81
426 428 2.030562 CGTGTGCCCGAACTTCCT 59.969 61.111 0.00 0.00 0.00 3.36
428 430 2.654912 CGTCGTGTGCCCGAACTTC 61.655 63.158 0.00 0.00 38.80 3.01
434 436 4.953868 TTGTCCGTCGTGTGCCCG 62.954 66.667 0.00 0.00 0.00 6.13
436 438 3.712881 GCTTGTCCGTCGTGTGCC 61.713 66.667 0.00 0.00 0.00 5.01
437 439 3.712881 GGCTTGTCCGTCGTGTGC 61.713 66.667 0.00 0.00 0.00 4.57
443 445 0.744771 GGATCCAAGGCTTGTCCGTC 60.745 60.000 24.57 15.61 40.77 4.79
446 448 0.681243 GTGGGATCCAAGGCTTGTCC 60.681 60.000 24.57 23.37 34.18 4.02
447 449 0.681243 GGTGGGATCCAAGGCTTGTC 60.681 60.000 24.57 16.39 34.18 3.18
451 453 1.434513 TTGTGGTGGGATCCAAGGCT 61.435 55.000 15.23 0.00 39.34 4.58
456 458 1.364317 TGGGTTTGTGGTGGGATCCA 61.364 55.000 15.23 0.00 34.85 3.41
457 459 0.898326 GTGGGTTTGTGGTGGGATCC 60.898 60.000 1.92 1.92 0.00 3.36
461 463 1.199615 AAAAGTGGGTTTGTGGTGGG 58.800 50.000 0.00 0.00 0.00 4.61
482 491 4.354208 AAGAGAAAGGATGTAGAGGGGA 57.646 45.455 0.00 0.00 0.00 4.81
490 499 4.599241 TGAGGGAGAAAAGAGAAAGGATGT 59.401 41.667 0.00 0.00 0.00 3.06
491 500 5.171339 TGAGGGAGAAAAGAGAAAGGATG 57.829 43.478 0.00 0.00 0.00 3.51
492 501 5.850046 TTGAGGGAGAAAAGAGAAAGGAT 57.150 39.130 0.00 0.00 0.00 3.24
495 504 6.821160 GTCCTATTGAGGGAGAAAAGAGAAAG 59.179 42.308 0.00 0.00 43.94 2.62
496 505 6.272324 TGTCCTATTGAGGGAGAAAAGAGAAA 59.728 38.462 0.00 0.00 43.94 2.52
497 506 5.785423 TGTCCTATTGAGGGAGAAAAGAGAA 59.215 40.000 0.00 0.00 43.94 2.87
498 507 5.342017 TGTCCTATTGAGGGAGAAAAGAGA 58.658 41.667 0.00 0.00 43.94 3.10
499 508 5.683876 TGTCCTATTGAGGGAGAAAAGAG 57.316 43.478 0.00 0.00 43.94 2.85
500 509 5.045578 CCTTGTCCTATTGAGGGAGAAAAGA 60.046 44.000 0.00 0.00 43.94 2.52
501 510 5.189180 CCTTGTCCTATTGAGGGAGAAAAG 58.811 45.833 0.00 0.00 43.94 2.27
502 511 5.179452 CCTTGTCCTATTGAGGGAGAAAA 57.821 43.478 0.00 0.00 43.94 2.29
503 512 4.844349 CCTTGTCCTATTGAGGGAGAAA 57.156 45.455 0.00 0.00 43.94 2.52
516 525 5.203528 CAATAAATGTCCATCCCTTGTCCT 58.796 41.667 0.00 0.00 0.00 3.85
524 533 2.034558 CCCGTGCAATAAATGTCCATCC 59.965 50.000 0.00 0.00 0.00 3.51
563 572 1.545841 ATATCCGCGGACAGCAGATA 58.454 50.000 33.75 17.80 45.94 1.98
568 577 1.195448 CATCAAATATCCGCGGACAGC 59.805 52.381 33.75 0.00 43.95 4.40
571 580 2.210116 ACACATCAAATATCCGCGGAC 58.790 47.619 33.75 0.00 0.00 4.79
575 584 4.025396 CACTCAGACACATCAAATATCCGC 60.025 45.833 0.00 0.00 0.00 5.54
576 585 4.025396 GCACTCAGACACATCAAATATCCG 60.025 45.833 0.00 0.00 0.00 4.18
580 589 4.692155 CACTGCACTCAGACACATCAAATA 59.308 41.667 0.00 0.00 42.95 1.40
581 590 3.501062 CACTGCACTCAGACACATCAAAT 59.499 43.478 0.00 0.00 42.95 2.32
593 602 3.874543 ACATAAAAACGTCACTGCACTCA 59.125 39.130 0.00 0.00 0.00 3.41
596 605 3.947626 ACACATAAAAACGTCACTGCAC 58.052 40.909 0.00 0.00 0.00 4.57
598 607 6.519761 CAGATAACACATAAAAACGTCACTGC 59.480 38.462 0.00 0.00 0.00 4.40
602 611 7.095397 CCTCACAGATAACACATAAAAACGTCA 60.095 37.037 0.00 0.00 0.00 4.35
604 613 6.708949 ACCTCACAGATAACACATAAAAACGT 59.291 34.615 0.00 0.00 0.00 3.99
606 615 7.234384 CGACCTCACAGATAACACATAAAAAC 58.766 38.462 0.00 0.00 0.00 2.43
610 619 4.707934 TCCGACCTCACAGATAACACATAA 59.292 41.667 0.00 0.00 0.00 1.90
614 623 2.416972 GGTCCGACCTCACAGATAACAC 60.417 54.545 10.59 0.00 34.73 3.32
616 625 1.136500 GGGTCCGACCTCACAGATAAC 59.864 57.143 17.27 0.00 38.64 1.89
620 629 1.152419 TTGGGTCCGACCTCACAGA 60.152 57.895 17.27 0.00 38.64 3.41
622 631 1.338890 TTGTTGGGTCCGACCTCACA 61.339 55.000 17.27 15.87 38.64 3.58
626 635 2.364002 CAAAAATTGTTGGGTCCGACCT 59.636 45.455 17.27 0.00 38.64 3.85
628 637 3.552068 CCTCAAAAATTGTTGGGTCCGAC 60.552 47.826 7.47 0.44 0.00 4.79
629 638 2.625790 CCTCAAAAATTGTTGGGTCCGA 59.374 45.455 7.47 0.00 0.00 4.55
630 639 2.625790 TCCTCAAAAATTGTTGGGTCCG 59.374 45.455 7.47 0.00 0.00 4.79
631 640 4.681074 TTCCTCAAAAATTGTTGGGTCC 57.319 40.909 7.47 0.00 0.00 4.46
642 653 8.151596 AGTGTTTTAGGTTGTTTTCCTCAAAAA 58.848 29.630 0.00 0.00 36.60 1.94
647 658 9.059260 TGTATAGTGTTTTAGGTTGTTTTCCTC 57.941 33.333 0.00 0.00 36.60 3.71
654 665 9.485206 CAGTAAGTGTATAGTGTTTTAGGTTGT 57.515 33.333 0.00 0.00 0.00 3.32
706 717 7.494625 TCAAGAATCTACGGGTCATTGTTAATC 59.505 37.037 0.00 0.00 0.00 1.75
707 718 7.335627 TCAAGAATCTACGGGTCATTGTTAAT 58.664 34.615 0.00 0.00 0.00 1.40
709 720 6.288941 TCAAGAATCTACGGGTCATTGTTA 57.711 37.500 0.00 0.00 0.00 2.41
711 722 4.759782 CTCAAGAATCTACGGGTCATTGT 58.240 43.478 0.00 0.00 0.00 2.71
712 723 3.557595 GCTCAAGAATCTACGGGTCATTG 59.442 47.826 0.00 0.00 0.00 2.82
715 726 2.094182 GTGCTCAAGAATCTACGGGTCA 60.094 50.000 0.00 0.00 0.00 4.02
716 727 2.541556 GTGCTCAAGAATCTACGGGTC 58.458 52.381 0.00 0.00 0.00 4.46
717 728 1.135083 CGTGCTCAAGAATCTACGGGT 60.135 52.381 0.00 0.00 0.00 5.28
719 730 1.560923 CCGTGCTCAAGAATCTACGG 58.439 55.000 7.09 7.09 43.93 4.02
720 731 2.159366 ACTCCGTGCTCAAGAATCTACG 60.159 50.000 0.00 0.00 0.00 3.51
721 732 3.512033 ACTCCGTGCTCAAGAATCTAC 57.488 47.619 0.00 0.00 0.00 2.59
722 733 3.509967 TCAACTCCGTGCTCAAGAATCTA 59.490 43.478 0.00 0.00 0.00 1.98
723 734 2.300152 TCAACTCCGTGCTCAAGAATCT 59.700 45.455 0.00 0.00 0.00 2.40
724 735 2.688507 TCAACTCCGTGCTCAAGAATC 58.311 47.619 0.00 0.00 0.00 2.52
725 736 2.839486 TCAACTCCGTGCTCAAGAAT 57.161 45.000 0.00 0.00 0.00 2.40
726 737 2.102420 TCTTCAACTCCGTGCTCAAGAA 59.898 45.455 0.00 0.00 0.00 2.52
727 738 1.686587 TCTTCAACTCCGTGCTCAAGA 59.313 47.619 0.00 0.00 0.00 3.02
728 739 2.154854 TCTTCAACTCCGTGCTCAAG 57.845 50.000 0.00 0.00 0.00 3.02
729 740 2.416747 CATCTTCAACTCCGTGCTCAA 58.583 47.619 0.00 0.00 0.00 3.02
731 742 0.723981 GCATCTTCAACTCCGTGCTC 59.276 55.000 0.00 0.00 0.00 4.26
732 743 0.674895 GGCATCTTCAACTCCGTGCT 60.675 55.000 0.00 0.00 33.38 4.40
733 744 0.674895 AGGCATCTTCAACTCCGTGC 60.675 55.000 0.00 0.00 0.00 5.34
744 821 2.579410 AACCCGTGTAAAGGCATCTT 57.421 45.000 0.00 0.00 32.39 2.40
757 834 2.851263 TGTCTTATGCTGAAACCCGT 57.149 45.000 0.00 0.00 0.00 5.28
767 844 5.519927 CCCGAAAATTGGAAATGTCTTATGC 59.480 40.000 0.00 0.00 0.00 3.14
799 876 7.057264 AGAAATATCTTCTAAGCTGAAACCCC 58.943 38.462 0.00 0.00 29.15 4.95
824 901 2.939640 GCTGAATCAGGGCCGAAAACTA 60.940 50.000 12.66 0.00 31.21 2.24
839 916 2.044946 GTCGGGCTTGGGCTGAAT 60.045 61.111 4.23 0.00 44.85 2.57
851 928 3.161450 ATGATGGTCGGGGTCGGG 61.161 66.667 0.00 0.00 36.95 5.14
854 931 0.676736 GAGAGATGATGGTCGGGGTC 59.323 60.000 0.00 0.00 0.00 4.46
899 976 1.612442 CCCACGGGAGAGGAAGGAA 60.612 63.158 0.00 0.00 43.94 3.36
996 1109 2.717044 CCACGCGTCCACCATCCTA 61.717 63.158 9.86 0.00 0.00 2.94
1384 1497 1.152756 GGATAAGGGGCACGGCAAT 60.153 57.895 0.00 0.00 0.00 3.56
1430 1552 5.764686 TGTCTGAAATCTCTAAGCAGCAAAA 59.235 36.000 0.00 0.00 0.00 2.44
1434 1556 5.358922 AGATGTCTGAAATCTCTAAGCAGC 58.641 41.667 4.45 0.00 27.78 5.25
1458 1580 4.181578 GCGGATATATAAACGACAGCCAT 58.818 43.478 12.05 0.00 0.00 4.40
1490 1613 3.944015 CCCATTTCACTCAGATTCTCCAC 59.056 47.826 0.00 0.00 0.00 4.02
1597 1721 1.202498 CGGTAGGTTAGCTAGCAACCC 60.202 57.143 29.67 20.68 45.55 4.11
1617 1746 1.338769 ACGCCTACCAAATCAGGACAC 60.339 52.381 0.00 0.00 33.42 3.67
1620 1749 3.985019 TTTACGCCTACCAAATCAGGA 57.015 42.857 0.00 0.00 33.42 3.86
1630 1759 2.159085 ACTCAGCCTCATTTACGCCTAC 60.159 50.000 0.00 0.00 0.00 3.18
1648 1777 7.886338 AGTATTTCATCCAAAAGGACAAACTC 58.114 34.615 0.00 0.00 0.00 3.01
1649 1778 7.839680 AGTATTTCATCCAAAAGGACAAACT 57.160 32.000 0.00 0.00 0.00 2.66
1675 1805 9.466497 AGAAACACATATGGATTTCAATAGTGT 57.534 29.630 24.48 8.39 38.29 3.55
1680 1810 8.812513 TCAGAGAAACACATATGGATTTCAAT 57.187 30.769 24.48 15.19 34.22 2.57
1695 1825 4.260985 TCAACAGCAACTTCAGAGAAACA 58.739 39.130 0.00 0.00 0.00 2.83
1723 1853 2.099756 GCAACCTCAGGGAAATGCATAC 59.900 50.000 0.00 0.00 38.77 2.39
1739 1869 9.202273 CTCAAATATAGATCTAAGTCAGCAACC 57.798 37.037 6.52 0.00 0.00 3.77
1864 2004 7.964604 AAGGTCTAAAGATTCACAACACTAC 57.035 36.000 0.00 0.00 0.00 2.73
1868 2008 8.287439 TGAAAAAGGTCTAAAGATTCACAACA 57.713 30.769 0.00 0.00 0.00 3.33
1899 2068 9.664332 TTGTGTGCAATGCCTAATAAATTTATT 57.336 25.926 23.28 23.28 37.19 1.40
1900 2069 9.316730 CTTGTGTGCAATGCCTAATAAATTTAT 57.683 29.630 1.53 4.81 33.65 1.40
1901 2070 7.763528 CCTTGTGTGCAATGCCTAATAAATTTA 59.236 33.333 1.53 0.00 33.65 1.40
1902 2071 6.594937 CCTTGTGTGCAATGCCTAATAAATTT 59.405 34.615 1.53 0.00 33.65 1.82
1925 2094 0.613260 TCCACTATGCGCAAACTCCT 59.387 50.000 17.11 0.00 0.00 3.69
1970 2140 1.381463 GTCTACCCCGGCCTCTCTT 60.381 63.158 0.00 0.00 0.00 2.85
1978 2148 0.688487 TCAACTTTGGTCTACCCCGG 59.312 55.000 0.00 0.00 34.29 5.73
2024 2194 5.419542 CCTTGTGATATTCGAGTCCTTCAA 58.580 41.667 0.00 0.00 0.00 2.69
2044 2214 1.375523 CTAACTTCCACGCGCCCTT 60.376 57.895 5.73 0.00 0.00 3.95
2046 2216 2.567564 TAGCTAACTTCCACGCGCCC 62.568 60.000 5.73 0.00 0.00 6.13
2047 2217 0.529992 ATAGCTAACTTCCACGCGCC 60.530 55.000 5.73 0.00 0.00 6.53
2049 2219 1.202371 TGGATAGCTAACTTCCACGCG 60.202 52.381 10.01 3.53 34.65 6.01
2050 2220 2.596904 TGGATAGCTAACTTCCACGC 57.403 50.000 10.01 0.00 34.65 5.34
2061 2246 0.108138 GTTCTGGCACGTGGATAGCT 60.108 55.000 18.88 0.00 0.00 3.32
2103 2288 5.447757 AGGTAGACTAGAGTTGATACCCAC 58.552 45.833 0.00 0.00 34.86 4.61
2143 2328 9.034544 GTTAAGGTAGACTACTCGTTTCAAAAA 57.965 33.333 12.31 0.00 0.00 1.94
2144 2329 8.416329 AGTTAAGGTAGACTACTCGTTTCAAAA 58.584 33.333 12.31 0.00 0.00 2.44
2145 2330 7.945134 AGTTAAGGTAGACTACTCGTTTCAAA 58.055 34.615 12.31 0.00 0.00 2.69
2146 2331 7.516198 AGTTAAGGTAGACTACTCGTTTCAA 57.484 36.000 12.31 0.00 0.00 2.69
2147 2332 7.013655 ACAAGTTAAGGTAGACTACTCGTTTCA 59.986 37.037 12.31 0.00 0.00 2.69
2148 2333 7.366513 ACAAGTTAAGGTAGACTACTCGTTTC 58.633 38.462 12.31 0.00 0.00 2.78
2149 2334 7.282332 ACAAGTTAAGGTAGACTACTCGTTT 57.718 36.000 12.31 5.36 0.00 3.60
2150 2335 6.890979 ACAAGTTAAGGTAGACTACTCGTT 57.109 37.500 12.31 6.62 0.00 3.85
2151 2336 6.890979 AACAAGTTAAGGTAGACTACTCGT 57.109 37.500 12.31 4.18 0.00 4.18
2152 2337 6.585322 CCAAACAAGTTAAGGTAGACTACTCG 59.415 42.308 12.31 0.00 0.00 4.18
2153 2338 6.872547 CCCAAACAAGTTAAGGTAGACTACTC 59.127 42.308 12.31 3.20 0.00 2.59
2154 2339 6.556116 TCCCAAACAAGTTAAGGTAGACTACT 59.444 38.462 12.31 0.00 0.00 2.57
2155 2340 6.762333 TCCCAAACAAGTTAAGGTAGACTAC 58.238 40.000 3.86 3.86 0.00 2.73
2156 2341 6.556116 ACTCCCAAACAAGTTAAGGTAGACTA 59.444 38.462 4.67 0.00 0.00 2.59
2157 2342 5.368816 ACTCCCAAACAAGTTAAGGTAGACT 59.631 40.000 4.67 0.00 0.00 3.24
2158 2343 5.469084 CACTCCCAAACAAGTTAAGGTAGAC 59.531 44.000 4.67 0.00 0.00 2.59
2159 2344 5.367352 TCACTCCCAAACAAGTTAAGGTAGA 59.633 40.000 4.67 0.00 0.00 2.59
2160 2345 5.617252 TCACTCCCAAACAAGTTAAGGTAG 58.383 41.667 4.38 1.32 0.00 3.18
2161 2346 5.633655 TCACTCCCAAACAAGTTAAGGTA 57.366 39.130 4.38 0.00 0.00 3.08
2162 2347 4.513406 TCACTCCCAAACAAGTTAAGGT 57.487 40.909 4.38 0.00 0.00 3.50
2163 2348 5.221244 CCTTTCACTCCCAAACAAGTTAAGG 60.221 44.000 0.00 0.00 32.64 2.69
2164 2349 5.736207 GCCTTTCACTCCCAAACAAGTTAAG 60.736 44.000 0.00 0.00 0.00 1.85
2165 2350 4.098807 GCCTTTCACTCCCAAACAAGTTAA 59.901 41.667 0.00 0.00 0.00 2.01
2166 2351 3.634910 GCCTTTCACTCCCAAACAAGTTA 59.365 43.478 0.00 0.00 0.00 2.24
2180 2365 2.844122 ACGACAACAAAGCCTTTCAC 57.156 45.000 0.00 0.00 0.00 3.18
2196 2381 2.425592 CCTCCCTGTGTGCAACGA 59.574 61.111 0.00 0.00 42.39 3.85
2197 2382 3.357079 GCCTCCCTGTGTGCAACG 61.357 66.667 0.00 0.00 42.39 4.10
2221 2418 1.092345 GGCTGCTGCACTAGTAAGGC 61.092 60.000 17.89 0.00 41.91 4.35
2226 2423 0.109342 ACTTTGGCTGCTGCACTAGT 59.891 50.000 17.89 12.75 41.91 2.57
2265 2462 5.771153 TGTCAACAAAGCAATGATTCAGA 57.229 34.783 0.00 0.00 0.00 3.27
2267 2464 9.491675 AAATATTGTCAACAAAGCAATGATTCA 57.508 25.926 0.00 0.00 39.55 2.57
2268 2465 9.749490 CAAATATTGTCAACAAAGCAATGATTC 57.251 29.630 0.00 0.00 39.55 2.52
2271 2468 8.883954 TTCAAATATTGTCAACAAAGCAATGA 57.116 26.923 0.00 0.00 39.55 2.57
2274 2471 8.715191 AACTTCAAATATTGTCAACAAAGCAA 57.285 26.923 0.00 0.00 39.55 3.91
2291 2488 9.474920 CATTCCATAGCTGTTAAAAACTTCAAA 57.525 29.630 0.00 0.00 0.00 2.69
2292 2489 8.637986 ACATTCCATAGCTGTTAAAAACTTCAA 58.362 29.630 0.00 0.00 0.00 2.69
2293 2490 8.177119 ACATTCCATAGCTGTTAAAAACTTCA 57.823 30.769 0.00 0.00 0.00 3.02
2318 2515 9.030452 AGGTTAAAACAATTGAGCCATGTAATA 57.970 29.630 13.59 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.