Multiple sequence alignment - TraesCS2A01G493900

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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 TraesCS2A01G493900 chr2A 100.000 2453 0 0 1 2453 726084775 726087227 0.000000e+00 4530.0
1 TraesCS2A01G493900 chr2A 86.792 795 68 21 666 1454 726099999 726100762 0.000000e+00 852.0
2 TraesCS2A01G493900 chr2A 83.403 717 74 24 754 1459 726159156 726159838 7.450000e-175 623.0
3 TraesCS2A01G493900 chr2A 87.773 229 28 0 701 929 726121054 726121282 4.020000e-68 268.0
4 TraesCS2A01G493900 chr2A 84.889 225 26 5 1722 1940 726121499 726121721 1.140000e-53 220.0
5 TraesCS2A01G493900 chr2A 81.496 254 27 14 1186 1432 726296088 726296328 8.950000e-45 191.0
6 TraesCS2A01G493900 chr2A 78.182 220 17 12 1458 1648 726100816 726101033 7.170000e-21 111.0
7 TraesCS2A01G493900 chr2D 89.087 953 55 12 526 1459 591121138 591122060 0.000000e+00 1138.0
8 TraesCS2A01G493900 chr2D 86.358 821 66 22 666 1459 591177836 591178637 0.000000e+00 854.0
9 TraesCS2A01G493900 chr2D 90.945 508 34 8 950 1456 591275974 591276470 0.000000e+00 673.0
10 TraesCS2A01G493900 chr2D 81.574 521 72 8 1949 2452 591179568 591180081 2.270000e-110 409.0
11 TraesCS2A01G493900 chr2D 84.561 285 31 5 636 907 591275680 591275964 1.120000e-68 270.0
12 TraesCS2A01G493900 chr2D 81.496 254 33 12 1186 1432 591388841 591389087 1.920000e-46 196.0
13 TraesCS2A01G493900 chr2D 81.132 265 25 15 1458 1700 591122109 591122370 3.220000e-44 189.0
14 TraesCS2A01G493900 chr2B 86.270 823 69 24 666 1459 716977620 716978427 0.000000e+00 854.0
15 TraesCS2A01G493900 chr2B 82.375 800 91 28 682 1459 717009727 717010498 0.000000e+00 651.0
16 TraesCS2A01G493900 chr2B 82.353 510 88 2 1 509 775463557 775464065 2.240000e-120 442.0
17 TraesCS2A01G493900 chr2B 82.157 510 91 0 12 521 676741155 676740646 2.900000e-119 438.0
18 TraesCS2A01G493900 chr2B 97.143 35 1 0 1500 1534 717010586 717010620 2.630000e-05 60.2
19 TraesCS2A01G493900 chr4A 82.745 510 87 1 12 521 614059755 614060263 1.030000e-123 453.0
20 TraesCS2A01G493900 chr4A 82.353 510 89 1 12 521 614038686 614039194 2.240000e-120 442.0
21 TraesCS2A01G493900 chr4A 82.157 510 90 1 12 521 614080667 614081175 1.040000e-118 436.0
22 TraesCS2A01G493900 chrUn 82.353 510 90 0 12 521 41828962 41829471 6.220000e-121 444.0
23 TraesCS2A01G493900 chr1A 82.353 510 90 0 12 521 571876598 571877107 6.220000e-121 444.0
24 TraesCS2A01G493900 chr7A 82.157 510 91 0 12 521 217387542 217387033 2.900000e-119 438.0
25 TraesCS2A01G493900 chr1B 81.712 514 90 1 12 521 424548809 424549322 2.250000e-115 425.0


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 TraesCS2A01G493900 chr2A 726084775 726087227 2452 False 4530.0 4530 100.0000 1 2453 1 chr2A.!!$F1 2452
1 TraesCS2A01G493900 chr2A 726159156 726159838 682 False 623.0 623 83.4030 754 1459 1 chr2A.!!$F2 705
2 TraesCS2A01G493900 chr2A 726099999 726101033 1034 False 481.5 852 82.4870 666 1648 2 chr2A.!!$F4 982
3 TraesCS2A01G493900 chr2A 726121054 726121721 667 False 244.0 268 86.3310 701 1940 2 chr2A.!!$F5 1239
4 TraesCS2A01G493900 chr2D 591121138 591122370 1232 False 663.5 1138 85.1095 526 1700 2 chr2D.!!$F2 1174
5 TraesCS2A01G493900 chr2D 591177836 591180081 2245 False 631.5 854 83.9660 666 2452 2 chr2D.!!$F3 1786
6 TraesCS2A01G493900 chr2D 591275680 591276470 790 False 471.5 673 87.7530 636 1456 2 chr2D.!!$F4 820
7 TraesCS2A01G493900 chr2B 716977620 716978427 807 False 854.0 854 86.2700 666 1459 1 chr2B.!!$F1 793
8 TraesCS2A01G493900 chr2B 775463557 775464065 508 False 442.0 442 82.3530 1 509 1 chr2B.!!$F2 508
9 TraesCS2A01G493900 chr2B 676740646 676741155 509 True 438.0 438 82.1570 12 521 1 chr2B.!!$R1 509
10 TraesCS2A01G493900 chr2B 717009727 717010620 893 False 355.6 651 89.7590 682 1534 2 chr2B.!!$F3 852
11 TraesCS2A01G493900 chr4A 614059755 614060263 508 False 453.0 453 82.7450 12 521 1 chr4A.!!$F2 509
12 TraesCS2A01G493900 chr4A 614038686 614039194 508 False 442.0 442 82.3530 12 521 1 chr4A.!!$F1 509
13 TraesCS2A01G493900 chr4A 614080667 614081175 508 False 436.0 436 82.1570 12 521 1 chr4A.!!$F3 509
14 TraesCS2A01G493900 chrUn 41828962 41829471 509 False 444.0 444 82.3530 12 521 1 chrUn.!!$F1 509
15 TraesCS2A01G493900 chr1A 571876598 571877107 509 False 444.0 444 82.3530 12 521 1 chr1A.!!$F1 509
16 TraesCS2A01G493900 chr7A 217387033 217387542 509 True 438.0 438 82.1570 12 521 1 chr7A.!!$R1 509
17 TraesCS2A01G493900 chr1B 424548809 424549322 513 False 425.0 425 81.7120 12 521 1 chr1B.!!$F1 509

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
92 97 0.038159 AACGCGAGGTTGAAGAGGAG 60.038 55.0 15.93 0.0 37.5 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 2063 0.109272 CCGTATGAGTGAGTGTGCGT 60.109 55.0 0.0 0.0 0.0 5.24 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
26 27 3.528597 ATAGAGTCTCCTTGGCGAAAC 57.471 47.619 0.00 0.00 0.00 2.78
44 45 2.510411 CCACGCCCATGCCTGATA 59.490 61.111 0.00 0.00 0.00 2.15
49 50 2.156098 GCCCATGCCTGATAGGGGA 61.156 63.158 0.00 0.00 41.63 4.81
50 51 1.719063 GCCCATGCCTGATAGGGGAA 61.719 60.000 0.00 0.00 41.63 3.97
74 79 0.611714 GTAGGCCGTTGAGGAGGAAA 59.388 55.000 0.00 0.00 45.00 3.13
82 87 1.469335 TTGAGGAGGAAACGCGAGGT 61.469 55.000 15.93 0.00 0.00 3.85
86 91 0.601841 GGAGGAAACGCGAGGTTGAA 60.602 55.000 15.93 0.00 44.23 2.69
92 97 0.038159 AACGCGAGGTTGAAGAGGAG 60.038 55.000 15.93 0.00 37.50 3.69
95 100 0.892063 GCGAGGTTGAAGAGGAGAGT 59.108 55.000 0.00 0.00 0.00 3.24
97 102 2.098443 GCGAGGTTGAAGAGGAGAGTAG 59.902 54.545 0.00 0.00 0.00 2.57
101 106 2.563179 GGTTGAAGAGGAGAGTAGTGCA 59.437 50.000 0.00 0.00 0.00 4.57
113 118 3.944015 AGAGTAGTGCAGCAATCCAATTC 59.056 43.478 0.00 0.00 0.00 2.17
115 120 0.813184 AGTGCAGCAATCCAATTCCG 59.187 50.000 0.00 0.00 0.00 4.30
125 130 5.835280 AGCAATCCAATTCCGGAATTTATCT 59.165 36.000 34.61 21.71 38.84 1.98
145 150 1.080569 GAAACCCCATGCGTTGCAG 60.081 57.895 0.00 0.00 43.65 4.41
146 151 1.523154 GAAACCCCATGCGTTGCAGA 61.523 55.000 0.00 0.00 43.65 4.26
149 154 2.703798 CCCCATGCGTTGCAGAAGG 61.704 63.158 0.00 0.00 43.65 3.46
155 160 0.749818 TGCGTTGCAGAAGGTCCAAA 60.750 50.000 0.00 0.00 33.32 3.28
161 166 4.082787 CGTTGCAGAAGGTCCAAAACATAT 60.083 41.667 0.00 0.00 0.00 1.78
169 174 5.472301 AGGTCCAAAACATATTCCCATCT 57.528 39.130 0.00 0.00 0.00 2.90
173 178 4.881273 TCCAAAACATATTCCCATCTGACG 59.119 41.667 0.00 0.00 0.00 4.35
191 196 1.342174 ACGGAGTCGACTGCCTTTTTA 59.658 47.619 28.43 0.00 29.74 1.52
197 202 3.432252 AGTCGACTGCCTTTTTAATGTCG 59.568 43.478 19.30 0.00 45.51 4.35
206 211 4.617223 GCCTTTTTAATGTCGAGCTTGAAC 59.383 41.667 4.86 0.97 0.00 3.18
209 214 6.360681 CCTTTTTAATGTCGAGCTTGAACAAG 59.639 38.462 4.86 9.82 41.24 3.16
212 217 2.154854 TGTCGAGCTTGAACAAGAGG 57.845 50.000 17.19 6.26 40.79 3.69
215 220 1.301677 CGAGCTTGAACAAGAGGGCC 61.302 60.000 17.19 0.00 40.79 5.80
216 221 0.250901 GAGCTTGAACAAGAGGGCCA 60.251 55.000 17.19 0.00 40.79 5.36
239 244 0.602638 TCTTGCACTTGTGTAGCCGG 60.603 55.000 0.00 0.00 0.00 6.13
243 248 2.048503 ACTTGTGTAGCCGGCGAC 60.049 61.111 30.24 30.24 0.00 5.19
244 249 2.261671 CTTGTGTAGCCGGCGACT 59.738 61.111 34.70 16.30 0.00 4.18
245 250 1.246056 ACTTGTGTAGCCGGCGACTA 61.246 55.000 34.70 23.09 0.00 2.59
314 319 2.171940 GCACTCTGCGCGTTTGAG 59.828 61.111 8.43 14.98 31.71 3.02
320 325 2.664851 TGCGCGTTTGAGACCAGG 60.665 61.111 8.43 0.00 0.00 4.45
322 327 2.030562 CGCGTTTGAGACCAGGGT 59.969 61.111 0.00 0.00 0.00 4.34
323 328 2.317609 CGCGTTTGAGACCAGGGTG 61.318 63.158 0.00 0.00 0.00 4.61
325 330 0.818040 GCGTTTGAGACCAGGGTGTT 60.818 55.000 0.00 0.00 0.00 3.32
330 335 1.434188 TGAGACCAGGGTGTTCATGT 58.566 50.000 0.00 0.00 0.00 3.21
335 340 0.178992 CCAGGGTGTTCATGTGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
338 343 1.282570 GGTGTTCATGTGTGGTGCG 59.717 57.895 0.00 0.00 0.00 5.34
341 346 0.105778 TGTTCATGTGTGGTGCGAGA 59.894 50.000 0.00 0.00 0.00 4.04
344 349 1.664649 CATGTGTGGTGCGAGACGT 60.665 57.895 0.00 0.00 0.00 4.34
346 351 0.109272 ATGTGTGGTGCGAGACGTAG 60.109 55.000 0.00 0.00 0.00 3.51
350 355 1.379443 TGGTGCGAGACGTAGGGAT 60.379 57.895 0.00 0.00 0.00 3.85
353 358 1.001597 GGTGCGAGACGTAGGGATAAG 60.002 57.143 0.00 0.00 0.00 1.73
355 360 2.553172 GTGCGAGACGTAGGGATAAGAT 59.447 50.000 0.00 0.00 0.00 2.40
359 364 4.378666 GCGAGACGTAGGGATAAGATCTTC 60.379 50.000 12.24 0.00 0.00 2.87
362 367 3.220110 ACGTAGGGATAAGATCTTCGCA 58.780 45.455 12.24 0.00 0.00 5.10
383 388 1.284408 GATTTTGGCAACGGCGTGA 59.716 52.632 15.70 0.00 42.47 4.35
386 391 0.596083 TTTTGGCAACGGCGTGAATG 60.596 50.000 15.70 9.95 42.47 2.67
395 400 0.926155 CGGCGTGAATGAGACTGATG 59.074 55.000 0.00 0.00 0.00 3.07
397 402 1.134699 GGCGTGAATGAGACTGATGGA 60.135 52.381 0.00 0.00 0.00 3.41
434 439 1.330655 CCTCAGCGCCCTCCTTCTTA 61.331 60.000 2.29 0.00 0.00 2.10
439 444 2.506472 GCCCTCCTTCTTAGGCGG 59.494 66.667 0.00 0.00 44.68 6.13
440 445 2.506472 CCCTCCTTCTTAGGCGGC 59.494 66.667 0.00 0.00 43.88 6.53
442 447 1.144936 CCTCCTTCTTAGGCGGCAG 59.855 63.158 13.08 0.00 39.49 4.85
455 460 3.070576 GGCAGGACCACATTGGCC 61.071 66.667 0.00 0.00 42.67 5.36
472 477 0.525761 GCCGAGTTTAGCCATTGCAA 59.474 50.000 0.00 0.00 41.13 4.08
477 482 3.578688 GAGTTTAGCCATTGCAAGTTGG 58.421 45.455 13.76 13.76 41.13 3.77
483 488 0.390124 CCATTGCAAGTTGGCTGTGT 59.610 50.000 4.94 0.00 34.04 3.72
494 499 2.740055 GCTGTGTGCAGGGAGTCG 60.740 66.667 0.00 0.00 42.78 4.18
500 505 2.343758 TGCAGGGAGTCGAAGCAC 59.656 61.111 0.00 0.00 0.00 4.40
509 514 0.247736 AGTCGAAGCACTGGATGACC 59.752 55.000 0.00 0.00 0.00 4.02
511 516 0.904865 TCGAAGCACTGGATGACCCT 60.905 55.000 0.00 0.00 35.38 4.34
517 522 1.142465 GCACTGGATGACCCTCATGAT 59.858 52.381 0.00 0.00 37.20 2.45
521 526 2.436911 CTGGATGACCCTCATGATGTCA 59.563 50.000 22.94 22.94 42.65 3.58
522 527 2.845586 TGGATGACCCTCATGATGTCAA 59.154 45.455 23.93 11.28 41.85 3.18
523 528 3.266513 TGGATGACCCTCATGATGTCAAA 59.733 43.478 23.93 14.25 41.85 2.69
524 529 4.079615 TGGATGACCCTCATGATGTCAAAT 60.080 41.667 23.93 13.71 41.85 2.32
525 530 4.891756 GGATGACCCTCATGATGTCAAATT 59.108 41.667 23.93 13.17 41.85 1.82
526 531 5.361857 GGATGACCCTCATGATGTCAAATTT 59.638 40.000 23.93 12.90 41.85 1.82
527 532 6.127253 GGATGACCCTCATGATGTCAAATTTT 60.127 38.462 23.93 12.63 41.85 1.82
528 533 6.028146 TGACCCTCATGATGTCAAATTTTG 57.972 37.500 20.10 2.59 36.16 2.44
529 534 5.539574 TGACCCTCATGATGTCAAATTTTGT 59.460 36.000 20.10 0.00 36.16 2.83
530 535 6.029346 ACCCTCATGATGTCAAATTTTGTC 57.971 37.500 8.89 4.43 0.00 3.18
531 536 5.539574 ACCCTCATGATGTCAAATTTTGTCA 59.460 36.000 10.68 10.68 33.51 3.58
532 537 6.211986 ACCCTCATGATGTCAAATTTTGTCAT 59.788 34.615 17.80 17.80 41.05 3.06
538 543 9.628746 CATGATGTCAAATTTTGTCATGTAAGA 57.371 29.630 21.23 5.75 39.04 2.10
566 571 4.904241 AGTTGAAGAGATTAAGCTGCACT 58.096 39.130 0.00 0.00 0.00 4.40
572 577 3.056536 AGAGATTAAGCTGCACTGAACGA 60.057 43.478 0.00 0.00 0.00 3.85
639 660 6.837992 TGTGAACAAGTCTAACAGAAAACAC 58.162 36.000 0.00 0.00 0.00 3.32
662 686 7.041372 ACACAAAGTAACCTGTATCATGTGAAC 60.041 37.037 8.84 0.00 39.05 3.18
699 723 3.612539 CTGTAGACATCGATCACACTCG 58.387 50.000 0.00 0.00 39.99 4.18
841 903 3.825611 GCGATGCCGGTGCCATTT 61.826 61.111 1.90 0.00 36.33 2.32
846 908 4.481112 GCCGGTGCCATTTCTGCG 62.481 66.667 1.90 0.00 0.00 5.18
872 937 2.743718 CAACTCCAGTGGCCGACT 59.256 61.111 3.51 0.00 34.02 4.18
932 997 5.511373 CGCTCTCCAAATACTCCATCCAATA 60.511 44.000 0.00 0.00 0.00 1.90
940 1044 6.506538 AATACTCCATCCAATACTCAAGCT 57.493 37.500 0.00 0.00 0.00 3.74
967 1071 2.154462 CAAAGCAAACCCAGATCGTCT 58.846 47.619 0.00 0.00 0.00 4.18
968 1072 2.554032 CAAAGCAAACCCAGATCGTCTT 59.446 45.455 0.00 0.00 0.00 3.01
969 1073 2.100605 AGCAAACCCAGATCGTCTTC 57.899 50.000 0.00 0.00 0.00 2.87
970 1074 1.347707 AGCAAACCCAGATCGTCTTCA 59.652 47.619 0.00 0.00 0.00 3.02
971 1075 1.734465 GCAAACCCAGATCGTCTTCAG 59.266 52.381 0.00 0.00 0.00 3.02
972 1076 2.612972 GCAAACCCAGATCGTCTTCAGA 60.613 50.000 0.00 0.00 0.00 3.27
1111 1219 0.445436 CAACAAGGATGTGCTCGAGC 59.555 55.000 30.42 30.42 40.46 5.03
1113 1221 1.186200 ACAAGGATGTGCTCGAGCTA 58.814 50.000 35.27 24.94 42.66 3.32
1347 1455 3.796443 CGCGTCTCGTCCTCCGAA 61.796 66.667 0.00 0.00 46.75 4.30
1348 1456 2.564975 GCGTCTCGTCCTCCGAAA 59.435 61.111 0.00 0.00 46.75 3.46
1465 1644 2.120232 CCTCGTGATCGATCCTTTTCG 58.880 52.381 22.31 17.02 45.21 3.46
1540 1723 4.562425 CGCCGTGCCATACCCCAT 62.562 66.667 0.00 0.00 0.00 4.00
1587 1796 1.122019 GTCCCCCGATGCTACTGGAT 61.122 60.000 0.00 0.00 0.00 3.41
1606 1819 2.515926 TTATCCATCAGTCGAGCTGC 57.484 50.000 0.00 0.00 44.66 5.25
1756 2082 0.109272 ACGCACACTCACTCATACGG 60.109 55.000 0.00 0.00 0.00 4.02
1761 2087 1.544691 ACACTCACTCATACGGACACC 59.455 52.381 0.00 0.00 0.00 4.16
1801 2127 1.112950 GGGGACGGAGAGGAAAGTAG 58.887 60.000 0.00 0.00 0.00 2.57
1804 2130 2.094130 GGGACGGAGAGGAAAGTAGTTG 60.094 54.545 0.00 0.00 0.00 3.16
1808 2134 3.244112 ACGGAGAGGAAAGTAGTTGGTTG 60.244 47.826 0.00 0.00 0.00 3.77
1841 2167 8.062065 TGTGAAATGAGAAAAGTACTTGGTTT 57.938 30.769 9.34 0.00 0.00 3.27
1856 2182 6.367686 ACTTGGTTTGTTAGGTTTAAGTCG 57.632 37.500 0.00 0.00 0.00 4.18
1896 2222 9.987272 CTGATATGTTCATAGATAACCTGTTCA 57.013 33.333 0.00 0.00 32.72 3.18
1902 2228 7.606456 TGTTCATAGATAACCTGTTCAAAGGAC 59.394 37.037 0.00 0.00 40.02 3.85
1909 2235 2.093128 ACCTGTTCAAAGGACACGTCTT 60.093 45.455 0.00 0.00 40.02 3.01
1931 2257 3.181458 TGTCTTGCCCGAAAGAACTAGTT 60.181 43.478 8.13 8.13 37.90 2.24
1940 2266 3.250040 CGAAAGAACTAGTTGTTGGTGGG 59.750 47.826 17.83 3.63 39.30 4.61
1941 2267 4.457466 GAAAGAACTAGTTGTTGGTGGGA 58.543 43.478 17.83 0.00 39.30 4.37
1942 2268 3.771577 AGAACTAGTTGTTGGTGGGAG 57.228 47.619 14.14 0.00 39.30 4.30
1943 2269 3.314693 AGAACTAGTTGTTGGTGGGAGA 58.685 45.455 14.14 0.00 39.30 3.71
1944 2270 3.910627 AGAACTAGTTGTTGGTGGGAGAT 59.089 43.478 14.14 0.00 39.30 2.75
1945 2271 4.351111 AGAACTAGTTGTTGGTGGGAGATT 59.649 41.667 14.14 0.00 39.30 2.40
1946 2272 4.724279 ACTAGTTGTTGGTGGGAGATTT 57.276 40.909 0.00 0.00 0.00 2.17
1959 2648 2.076863 GGAGATTTACGCTGCAGTTGT 58.923 47.619 16.64 16.40 0.00 3.32
1976 2665 6.592798 CAGTTGTTGCTTCATTGTCATTTT 57.407 33.333 0.00 0.00 0.00 1.82
1979 2668 5.021033 TGTTGCTTCATTGTCATTTTGGT 57.979 34.783 0.00 0.00 0.00 3.67
1980 2669 6.154203 TGTTGCTTCATTGTCATTTTGGTA 57.846 33.333 0.00 0.00 0.00 3.25
1985 2674 5.713025 CTTCATTGTCATTTTGGTACCCTG 58.287 41.667 10.07 2.01 0.00 4.45
1991 2680 5.144100 TGTCATTTTGGTACCCTGATTTGT 58.856 37.500 10.07 0.00 0.00 2.83
1996 2685 1.173913 GGTACCCTGATTTGTGTGGC 58.826 55.000 0.00 0.00 0.00 5.01
2010 2699 0.610174 TGTGGCTGAGACATGGAGAC 59.390 55.000 0.00 0.00 0.00 3.36
2012 2701 1.142748 GGCTGAGACATGGAGACGG 59.857 63.158 0.00 0.00 0.00 4.79
2052 2741 4.188462 CCGTGACCTTATTCTGCAATGTA 58.812 43.478 0.00 0.00 0.00 2.29
2053 2742 4.034048 CCGTGACCTTATTCTGCAATGTAC 59.966 45.833 0.00 0.00 0.00 2.90
2054 2743 4.259810 CGTGACCTTATTCTGCAATGTACG 60.260 45.833 0.00 0.00 0.00 3.67
2055 2744 4.630069 GTGACCTTATTCTGCAATGTACGT 59.370 41.667 0.00 0.00 0.00 3.57
2056 2745 5.808540 GTGACCTTATTCTGCAATGTACGTA 59.191 40.000 0.00 0.00 0.00 3.57
2063 2752 8.710835 TTATTCTGCAATGTACGTATCTTTGA 57.289 30.769 18.77 4.68 0.00 2.69
2064 2753 7.609760 ATTCTGCAATGTACGTATCTTTGAA 57.390 32.000 18.77 12.27 0.00 2.69
2078 2767 1.444119 TTTGAAGAGGTGGTGCGTGC 61.444 55.000 0.00 0.00 0.00 5.34
2081 2770 4.996434 AGAGGTGGTGCGTGCTGC 62.996 66.667 0.00 0.00 46.70 5.25
2092 2781 2.282040 GTGCTGCAGTCCTTGGCT 60.282 61.111 16.64 0.00 0.00 4.75
2099 2788 1.941999 GCAGTCCTTGGCTTGATGGC 61.942 60.000 0.00 0.00 42.18 4.40
2107 2796 0.750546 TGGCTTGATGGCAGCAGATC 60.751 55.000 5.27 0.00 46.76 2.75
2109 2798 1.319541 GCTTGATGGCAGCAGATCAT 58.680 50.000 5.27 0.00 0.00 2.45
2112 2801 0.841289 TGATGGCAGCAGATCATGGA 59.159 50.000 0.00 0.00 0.00 3.41
2113 2802 1.213430 TGATGGCAGCAGATCATGGAA 59.787 47.619 0.00 0.00 0.00 3.53
2115 2804 1.466856 TGGCAGCAGATCATGGAAAC 58.533 50.000 0.00 0.00 0.00 2.78
2130 2819 0.784778 GAAACAGCGAAGGAGTGACG 59.215 55.000 0.00 0.00 0.00 4.35
2153 2842 0.943835 CGTGGTGCATTGTCTCGACA 60.944 55.000 0.00 0.00 39.98 4.35
2155 2844 2.162716 GGTGCATTGTCTCGACACC 58.837 57.895 3.66 3.66 43.57 4.16
2156 2845 2.912986 GTGCATTGTCTCGACACCA 58.087 52.632 0.00 0.00 41.67 4.17
2157 2846 1.442769 GTGCATTGTCTCGACACCAT 58.557 50.000 0.00 0.00 41.67 3.55
2158 2847 1.394917 GTGCATTGTCTCGACACCATC 59.605 52.381 0.00 0.00 41.67 3.51
2190 2886 5.357032 CCCAGATTTACCATTGAAGTACACC 59.643 44.000 0.00 0.00 0.00 4.16
2203 2899 3.873679 TACACCTGCGTCGGAGGGT 62.874 63.158 32.68 27.31 34.56 4.34
2204 2900 2.482796 TACACCTGCGTCGGAGGGTA 62.483 60.000 32.68 26.41 34.56 3.69
2211 2916 2.728817 GTCGGAGGGTATCGCTGG 59.271 66.667 0.00 0.00 0.00 4.85
2213 2918 1.153061 TCGGAGGGTATCGCTGGAT 59.847 57.895 0.00 0.00 36.65 3.41
2225 2930 5.809562 GGTATCGCTGGATTATGAGATTCTG 59.190 44.000 0.00 0.00 34.00 3.02
2234 2939 5.512060 GGATTATGAGATTCTGGCAGCACTA 60.512 44.000 10.34 0.00 0.00 2.74
2237 2942 2.767960 TGAGATTCTGGCAGCACTATCA 59.232 45.455 10.34 6.81 0.00 2.15
2249 2954 1.071385 GCACTATCATCCCTCACCCTG 59.929 57.143 0.00 0.00 0.00 4.45
2250 2955 1.071385 CACTATCATCCCTCACCCTGC 59.929 57.143 0.00 0.00 0.00 4.85
2254 2959 0.548031 TCATCCCTCACCCTGCAATC 59.452 55.000 0.00 0.00 0.00 2.67
2274 2979 3.489731 CGCCACTTGTGCATCGAT 58.510 55.556 0.00 0.00 0.00 3.59
2276 2981 1.430632 GCCACTTGTGCATCGATGG 59.569 57.895 26.00 11.81 0.00 3.51
2295 3000 5.008019 CGATGGATGTTCTTGGTTTCATAGG 59.992 44.000 0.00 0.00 0.00 2.57
2299 3004 3.153919 TGTTCTTGGTTTCATAGGCCAC 58.846 45.455 5.01 0.00 31.19 5.01
2303 3008 2.787473 TGGTTTCATAGGCCACTCTG 57.213 50.000 5.01 0.00 0.00 3.35
2331 3036 1.151668 GGCTGCTTGTCTAGTGTGTG 58.848 55.000 0.00 0.00 0.00 3.82
2334 3039 2.212652 CTGCTTGTCTAGTGTGTGCAA 58.787 47.619 0.00 0.00 0.00 4.08
2346 3051 2.677836 GTGTGTGCAAGTTTCTCAGTCA 59.322 45.455 0.00 0.00 0.00 3.41
2352 3057 2.550978 CAAGTTTCTCAGTCACGTGGT 58.449 47.619 17.00 0.00 0.00 4.16
2357 3062 1.046472 TCTCAGTCACGTGGTTGGGT 61.046 55.000 17.00 0.00 0.00 4.51
2392 3097 3.662713 CGTGTTCACTTGCATCTTCTTCG 60.663 47.826 0.00 0.00 0.00 3.79
2393 3098 3.248602 GTGTTCACTTGCATCTTCTTCGT 59.751 43.478 0.00 0.00 0.00 3.85
2395 3100 4.214437 GTTCACTTGCATCTTCTTCGTTG 58.786 43.478 0.00 0.00 0.00 4.10
2397 3102 2.807967 CACTTGCATCTTCTTCGTTGGA 59.192 45.455 0.00 0.00 0.00 3.53
2399 3104 4.631377 CACTTGCATCTTCTTCGTTGGATA 59.369 41.667 0.00 0.00 0.00 2.59
2401 3106 5.705441 ACTTGCATCTTCTTCGTTGGATAAA 59.295 36.000 0.00 0.00 0.00 1.40
2407 3112 7.224753 GCATCTTCTTCGTTGGATAAATGACTA 59.775 37.037 0.00 0.00 33.40 2.59
2412 3117 4.928601 TCGTTGGATAAATGACTACTCGG 58.071 43.478 0.00 0.00 0.00 4.63
2413 3118 3.489785 CGTTGGATAAATGACTACTCGGC 59.510 47.826 0.00 0.00 0.00 5.54
2433 3139 4.432712 GGCGAGGATAATGTTGCATTTTT 58.567 39.130 0.00 0.00 0.00 1.94
2437 3143 7.141363 GCGAGGATAATGTTGCATTTTTCTAT 58.859 34.615 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.321996 GGTTTCGCCAAGGAGACTCT 59.678 55.000 1.74 0.00 42.68 3.24
32 33 0.111253 GTTCCCCTATCAGGCATGGG 59.889 60.000 0.00 0.00 39.37 4.00
44 45 2.286197 GGCCTACCTGGTTCCCCT 60.286 66.667 3.84 0.00 38.35 4.79
49 50 1.677552 CTCAACGGCCTACCTGGTT 59.322 57.895 3.84 0.00 38.35 3.67
50 51 2.291043 CCTCAACGGCCTACCTGGT 61.291 63.158 4.05 4.05 38.35 4.00
74 79 0.894184 TCTCCTCTTCAACCTCGCGT 60.894 55.000 5.77 0.00 0.00 6.01
82 87 2.232452 GCTGCACTACTCTCCTCTTCAA 59.768 50.000 0.00 0.00 0.00 2.69
83 88 1.821753 GCTGCACTACTCTCCTCTTCA 59.178 52.381 0.00 0.00 0.00 3.02
86 91 1.930251 TTGCTGCACTACTCTCCTCT 58.070 50.000 0.00 0.00 0.00 3.69
92 97 3.065925 GGAATTGGATTGCTGCACTACTC 59.934 47.826 0.00 0.00 0.00 2.59
95 100 2.016318 CGGAATTGGATTGCTGCACTA 58.984 47.619 0.00 0.00 0.00 2.74
97 102 0.179129 CCGGAATTGGATTGCTGCAC 60.179 55.000 0.00 0.00 0.00 4.57
101 106 5.835280 AGATAAATTCCGGAATTGGATTGCT 59.165 36.000 36.59 24.70 40.57 3.91
113 118 2.956333 GGGGTTTCCAGATAAATTCCGG 59.044 50.000 0.00 0.00 35.00 5.14
128 133 1.112315 TTCTGCAACGCATGGGGTTT 61.112 50.000 14.94 0.00 38.13 3.27
145 150 5.893824 AGATGGGAATATGTTTTGGACCTTC 59.106 40.000 0.00 0.00 0.00 3.46
146 151 5.658190 CAGATGGGAATATGTTTTGGACCTT 59.342 40.000 0.00 0.00 0.00 3.50
149 154 5.220854 CGTCAGATGGGAATATGTTTTGGAC 60.221 44.000 0.00 0.00 0.00 4.02
155 160 3.711704 ACTCCGTCAGATGGGAATATGTT 59.288 43.478 8.95 0.00 0.00 2.71
161 166 0.323087 TCGACTCCGTCAGATGGGAA 60.323 55.000 8.95 0.00 37.05 3.97
169 174 1.461091 AAAGGCAGTCGACTCCGTCA 61.461 55.000 16.96 0.00 37.05 4.35
173 178 3.751698 ACATTAAAAAGGCAGTCGACTCC 59.248 43.478 16.96 18.97 0.00 3.85
179 184 3.437049 AGCTCGACATTAAAAAGGCAGTC 59.563 43.478 0.00 0.00 0.00 3.51
181 186 4.083324 TCAAGCTCGACATTAAAAAGGCAG 60.083 41.667 0.00 0.00 0.00 4.85
182 187 3.818210 TCAAGCTCGACATTAAAAAGGCA 59.182 39.130 0.00 0.00 0.00 4.75
191 196 3.070018 CCTCTTGTTCAAGCTCGACATT 58.930 45.455 7.58 0.00 0.00 2.71
197 202 0.250901 TGGCCCTCTTGTTCAAGCTC 60.251 55.000 0.00 0.00 0.00 4.09
206 211 0.676151 GCAAGACTCTGGCCCTCTTG 60.676 60.000 18.55 18.55 42.56 3.02
209 214 1.376553 GTGCAAGACTCTGGCCCTC 60.377 63.158 0.00 0.00 27.29 4.30
212 217 0.536006 ACAAGTGCAAGACTCTGGCC 60.536 55.000 2.77 0.00 31.73 5.36
215 220 2.478134 GCTACACAAGTGCAAGACTCTG 59.522 50.000 0.00 0.00 31.73 3.35
216 221 2.548920 GGCTACACAAGTGCAAGACTCT 60.549 50.000 0.00 0.00 31.73 3.24
239 244 2.875080 ATGTTCGCAACTTTAGTCGC 57.125 45.000 1.68 0.00 0.00 5.19
243 248 8.673626 AATTTCATGTATGTTCGCAACTTTAG 57.326 30.769 0.00 0.00 0.00 1.85
245 250 9.289303 GATAATTTCATGTATGTTCGCAACTTT 57.711 29.630 0.00 0.00 0.00 2.66
284 289 4.672542 GCGCAGAGTGCATTCATAAAGAAA 60.673 41.667 12.16 0.00 45.36 2.52
290 295 0.460109 ACGCGCAGAGTGCATTCATA 60.460 50.000 12.16 0.00 45.36 2.15
293 298 1.061799 CAAACGCGCAGAGTGCATTC 61.062 55.000 5.73 0.00 45.36 2.67
308 313 2.341846 TGAACACCCTGGTCTCAAAC 57.658 50.000 0.00 0.00 34.53 2.93
311 316 1.072173 CACATGAACACCCTGGTCTCA 59.928 52.381 0.00 1.23 34.53 3.27
314 319 1.238439 CACACATGAACACCCTGGTC 58.762 55.000 0.00 0.00 33.88 4.02
320 325 1.163420 TCGCACCACACATGAACACC 61.163 55.000 0.00 0.00 0.00 4.16
322 327 0.105778 TCTCGCACCACACATGAACA 59.894 50.000 0.00 0.00 0.00 3.18
323 328 0.512952 GTCTCGCACCACACATGAAC 59.487 55.000 0.00 0.00 0.00 3.18
325 330 1.372872 CGTCTCGCACCACACATGA 60.373 57.895 0.00 0.00 0.00 3.07
330 335 2.632544 CCCTACGTCTCGCACCACA 61.633 63.158 0.00 0.00 0.00 4.17
335 340 2.336945 TCTTATCCCTACGTCTCGCA 57.663 50.000 0.00 0.00 0.00 5.10
338 343 4.378666 GCGAAGATCTTATCCCTACGTCTC 60.379 50.000 8.25 0.00 0.00 3.36
341 346 3.220110 TGCGAAGATCTTATCCCTACGT 58.780 45.455 8.25 0.00 0.00 3.57
344 349 6.611613 ATCATTGCGAAGATCTTATCCCTA 57.388 37.500 8.25 0.00 0.00 3.53
346 351 6.566197 AAATCATTGCGAAGATCTTATCCC 57.434 37.500 8.25 0.00 0.00 3.85
350 355 5.125257 TGCCAAAATCATTGCGAAGATCTTA 59.875 36.000 8.25 0.00 0.00 2.10
353 358 3.772932 TGCCAAAATCATTGCGAAGATC 58.227 40.909 0.00 0.00 0.00 2.75
355 360 3.316283 GTTGCCAAAATCATTGCGAAGA 58.684 40.909 0.00 0.00 0.00 2.87
359 364 0.714994 CCGTTGCCAAAATCATTGCG 59.285 50.000 0.00 0.00 0.00 4.85
362 367 0.316841 ACGCCGTTGCCAAAATCATT 59.683 45.000 0.00 0.00 0.00 2.57
383 388 6.377080 TGACTATAGGTCCATCAGTCTCATT 58.623 40.000 4.43 0.00 43.89 2.57
386 391 5.626142 TCTGACTATAGGTCCATCAGTCTC 58.374 45.833 13.90 0.00 43.89 3.36
395 400 3.712218 AGGGCTTTTCTGACTATAGGTCC 59.288 47.826 4.43 0.00 43.89 4.46
397 402 4.362677 TGAGGGCTTTTCTGACTATAGGT 58.637 43.478 4.43 0.00 0.00 3.08
407 412 2.360475 GGCGCTGAGGGCTTTTCT 60.360 61.111 20.97 0.00 41.33 2.52
410 415 4.416738 GAGGGCGCTGAGGGCTTT 62.417 66.667 20.97 9.52 41.33 3.51
434 439 3.650950 AATGTGGTCCTGCCGCCT 61.651 61.111 0.00 0.00 46.96 5.52
438 443 3.070576 GGCCAATGTGGTCCTGCC 61.071 66.667 0.00 0.00 40.46 4.85
439 444 3.443045 CGGCCAATGTGGTCCTGC 61.443 66.667 2.24 0.00 39.48 4.85
440 445 1.746615 CTCGGCCAATGTGGTCCTG 60.747 63.158 2.24 0.00 39.48 3.86
442 447 0.893727 AAACTCGGCCAATGTGGTCC 60.894 55.000 2.24 0.00 39.48 4.46
455 460 3.236816 CAACTTGCAATGGCTAAACTCG 58.763 45.455 0.00 0.00 41.91 4.18
472 477 2.203394 CCCTGCACACAGCCAACT 60.203 61.111 0.00 0.00 43.02 3.16
477 482 2.715532 TTCGACTCCCTGCACACAGC 62.716 60.000 0.00 0.00 43.02 4.40
483 488 2.210013 AGTGCTTCGACTCCCTGCA 61.210 57.895 0.00 0.00 0.00 4.41
494 499 0.615331 TGAGGGTCATCCAGTGCTTC 59.385 55.000 0.00 0.00 38.24 3.86
500 505 2.436911 TGACATCATGAGGGTCATCCAG 59.563 50.000 22.31 0.00 34.28 3.86
509 514 7.094631 ACATGACAAAATTTGACATCATGAGG 58.905 34.615 28.69 17.17 42.53 3.86
511 516 9.628746 CTTACATGACAAAATTTGACATCATGA 57.371 29.630 28.69 17.22 42.53 3.07
526 531 9.996554 TCTTCAACTATCTTTCTTACATGACAA 57.003 29.630 0.00 0.00 0.00 3.18
527 532 9.645059 CTCTTCAACTATCTTTCTTACATGACA 57.355 33.333 0.00 0.00 0.00 3.58
528 533 9.862371 TCTCTTCAACTATCTTTCTTACATGAC 57.138 33.333 0.00 0.00 0.00 3.06
538 543 7.826252 TGCAGCTTAATCTCTTCAACTATCTTT 59.174 33.333 0.00 0.00 0.00 2.52
555 560 2.812358 TCTCGTTCAGTGCAGCTTAA 57.188 45.000 0.00 0.00 0.00 1.85
566 571 6.704050 TCACATACAAGAACATTTCTCGTTCA 59.296 34.615 5.89 0.00 44.22 3.18
639 660 7.672983 AGTTCACATGATACAGGTTACTTTG 57.327 36.000 0.00 0.00 0.00 2.77
662 686 4.210120 GTCTACAGCTCTGTGTTTCACAAG 59.790 45.833 12.43 0.13 44.08 3.16
699 723 1.666311 CCGGTGAAAGTGAGACGAGTC 60.666 57.143 0.00 0.00 0.00 3.36
846 908 0.804989 CACTGGAGTTGGCGGAAATC 59.195 55.000 0.00 0.00 0.00 2.17
932 997 1.336125 GCTTTGTTCTGCAGCTTGAGT 59.664 47.619 9.47 0.00 0.00 3.41
940 1044 1.136695 CTGGGTTTGCTTTGTTCTGCA 59.863 47.619 0.00 0.00 37.42 4.41
970 1074 1.249407 GACTGACCGGACTGAAGTCT 58.751 55.000 9.46 0.00 44.20 3.24
971 1075 0.959553 TGACTGACCGGACTGAAGTC 59.040 55.000 9.46 12.17 44.04 3.01
972 1076 1.341531 CTTGACTGACCGGACTGAAGT 59.658 52.381 9.46 0.77 0.00 3.01
1170 1278 4.086178 CGCCTCGACGACGACTGT 62.086 66.667 5.75 0.00 43.81 3.55
1171 1279 4.813526 CCGCCTCGACGACGACTG 62.814 72.222 5.75 1.86 43.81 3.51
1465 1644 2.436824 GCTCCTTCCGGGTTGCTC 60.437 66.667 0.00 0.00 36.25 4.26
1466 1645 3.249189 TGCTCCTTCCGGGTTGCT 61.249 61.111 0.00 0.00 36.90 3.91
1471 1650 4.479993 CTGGCTGCTCCTTCCGGG 62.480 72.222 0.00 0.00 35.26 5.73
1479 1658 0.532573 TGTACTACTGCTGGCTGCTC 59.467 55.000 17.45 0.00 43.37 4.26
1538 1721 0.809636 TAACTGTCGCGCCATGGATG 60.810 55.000 18.40 8.13 0.00 3.51
1539 1722 0.810031 GTAACTGTCGCGCCATGGAT 60.810 55.000 18.40 0.00 0.00 3.41
1540 1723 1.447140 GTAACTGTCGCGCCATGGA 60.447 57.895 18.40 0.00 0.00 3.41
1569 1778 0.399949 AATCCAGTAGCATCGGGGGA 60.400 55.000 0.00 0.00 0.00 4.81
1570 1779 1.348064 TAATCCAGTAGCATCGGGGG 58.652 55.000 0.00 0.00 0.00 5.40
1676 1889 0.110486 AGGGTACAGGCAACAGGTTG 59.890 55.000 7.77 7.77 43.14 3.77
1677 1890 0.110486 CAGGGTACAGGCAACAGGTT 59.890 55.000 0.00 0.00 41.41 3.50
1678 1891 1.060163 ACAGGGTACAGGCAACAGGT 61.060 55.000 0.00 0.00 41.41 4.00
1679 1892 0.981183 TACAGGGTACAGGCAACAGG 59.019 55.000 0.00 0.00 41.41 4.00
1686 1899 0.249398 GTGCAGGTACAGGGTACAGG 59.751 60.000 8.60 1.62 0.00 4.00
1724 1958 3.870422 TGCGTGCGTGTTGTGGTG 61.870 61.111 0.00 0.00 0.00 4.17
1725 1959 3.871574 GTGCGTGCGTGTTGTGGT 61.872 61.111 0.00 0.00 0.00 4.16
1737 2063 0.109272 CCGTATGAGTGAGTGTGCGT 60.109 55.000 0.00 0.00 0.00 5.24
1756 2082 2.262915 CTCCTCAGCCACGGTGTC 59.737 66.667 7.45 0.00 32.43 3.67
1761 2087 2.422231 CCTCTCCTCCTCAGCCACG 61.422 68.421 0.00 0.00 0.00 4.94
1875 2201 8.328758 TCCTTTGAACAGGTTATCTATGAACAT 58.671 33.333 0.00 0.00 35.15 2.71
1883 2209 4.202326 ACGTGTCCTTTGAACAGGTTATCT 60.202 41.667 0.00 0.00 41.51 1.98
1890 2216 2.936498 ACAAGACGTGTCCTTTGAACAG 59.064 45.455 0.00 0.00 34.38 3.16
1902 2228 0.878523 TTCGGGCAAGACAAGACGTG 60.879 55.000 0.00 0.00 0.00 4.49
1909 2235 2.367567 ACTAGTTCTTTCGGGCAAGACA 59.632 45.455 0.00 0.00 32.28 3.41
1931 2257 1.349688 AGCGTAAATCTCCCACCAACA 59.650 47.619 0.00 0.00 0.00 3.33
1940 2266 3.482786 CAACAACTGCAGCGTAAATCTC 58.517 45.455 15.27 0.00 0.00 2.75
1941 2267 3.542712 CAACAACTGCAGCGTAAATCT 57.457 42.857 15.27 0.00 0.00 2.40
1959 2648 5.537188 GGTACCAAAATGACAATGAAGCAA 58.463 37.500 7.15 0.00 0.00 3.91
1979 2668 1.702401 TCAGCCACACAAATCAGGGTA 59.298 47.619 0.00 0.00 0.00 3.69
1980 2669 0.478072 TCAGCCACACAAATCAGGGT 59.522 50.000 0.00 0.00 0.00 4.34
1985 2674 2.163010 CCATGTCTCAGCCACACAAATC 59.837 50.000 0.00 0.00 0.00 2.17
1991 2680 0.610174 GTCTCCATGTCTCAGCCACA 59.390 55.000 0.00 0.00 0.00 4.17
1996 2685 0.459237 GTGCCGTCTCCATGTCTCAG 60.459 60.000 0.00 0.00 0.00 3.35
2033 2722 4.827692 ACGTACATTGCAGAATAAGGTCA 58.172 39.130 0.00 0.00 0.00 4.02
2036 2725 7.715265 AAGATACGTACATTGCAGAATAAGG 57.285 36.000 0.00 0.00 0.00 2.69
2038 2727 8.710835 TCAAAGATACGTACATTGCAGAATAA 57.289 30.769 0.00 0.00 0.00 1.40
2042 2731 6.394809 TCTTCAAAGATACGTACATTGCAGA 58.605 36.000 12.03 12.03 0.00 4.26
2043 2732 6.237942 CCTCTTCAAAGATACGTACATTGCAG 60.238 42.308 0.00 4.00 33.93 4.41
2052 2741 3.864921 GCACCACCTCTTCAAAGATACGT 60.865 47.826 0.00 0.00 33.93 3.57
2053 2742 2.673368 GCACCACCTCTTCAAAGATACG 59.327 50.000 0.00 0.00 33.93 3.06
2054 2743 2.673368 CGCACCACCTCTTCAAAGATAC 59.327 50.000 0.00 0.00 33.93 2.24
2055 2744 2.301870 ACGCACCACCTCTTCAAAGATA 59.698 45.455 0.00 0.00 33.93 1.98
2056 2745 1.072331 ACGCACCACCTCTTCAAAGAT 59.928 47.619 0.00 0.00 33.93 2.40
2063 2752 2.281070 CAGCACGCACCACCTCTT 60.281 61.111 0.00 0.00 0.00 2.85
2064 2753 4.996434 GCAGCACGCACCACCTCT 62.996 66.667 0.00 0.00 41.79 3.69
2078 2767 0.809385 CATCAAGCCAAGGACTGCAG 59.191 55.000 13.48 13.48 0.00 4.41
2081 2770 0.609957 TGCCATCAAGCCAAGGACTG 60.610 55.000 0.00 0.00 0.00 3.51
2085 2774 1.945354 CTGCTGCCATCAAGCCAAGG 61.945 60.000 0.00 0.00 0.00 3.61
2092 2781 1.213430 TCCATGATCTGCTGCCATCAA 59.787 47.619 13.46 0.00 32.76 2.57
2099 2788 1.063616 CGCTGTTTCCATGATCTGCTG 59.936 52.381 0.00 0.00 0.00 4.41
2100 2789 1.065926 TCGCTGTTTCCATGATCTGCT 60.066 47.619 0.00 0.00 0.00 4.24
2107 2796 1.466167 CACTCCTTCGCTGTTTCCATG 59.534 52.381 0.00 0.00 0.00 3.66
2109 2798 0.756294 TCACTCCTTCGCTGTTTCCA 59.244 50.000 0.00 0.00 0.00 3.53
2112 2801 0.387929 TCGTCACTCCTTCGCTGTTT 59.612 50.000 0.00 0.00 0.00 2.83
2113 2802 0.318784 GTCGTCACTCCTTCGCTGTT 60.319 55.000 0.00 0.00 0.00 3.16
2115 2804 0.455295 GAGTCGTCACTCCTTCGCTG 60.455 60.000 0.00 0.00 43.14 5.18
2117 2806 1.512310 CGAGTCGTCACTCCTTCGC 60.512 63.158 3.82 0.00 45.81 4.70
2121 2810 1.228184 ACCACGAGTCGTCACTCCT 60.228 57.895 16.86 0.00 45.81 3.69
2130 2819 1.071605 GAGACAATGCACCACGAGTC 58.928 55.000 0.00 0.00 0.00 3.36
2136 2825 0.602638 GGTGTCGAGACAATGCACCA 60.603 55.000 15.28 0.00 46.29 4.17
2160 2849 1.708341 ATGGTAAATCTGGGCATGCC 58.292 50.000 29.47 29.47 0.00 4.40
2161 2850 2.694628 TCAATGGTAAATCTGGGCATGC 59.305 45.455 9.90 9.90 0.00 4.06
2190 2886 2.331805 CGATACCCTCCGACGCAG 59.668 66.667 0.00 0.00 0.00 5.18
2203 2899 5.625426 GCCAGAATCTCATAATCCAGCGATA 60.625 44.000 0.00 0.00 0.00 2.92
2204 2900 4.829968 CCAGAATCTCATAATCCAGCGAT 58.170 43.478 0.00 0.00 0.00 4.58
2211 2916 4.387598 AGTGCTGCCAGAATCTCATAATC 58.612 43.478 0.00 0.00 0.00 1.75
2213 2918 3.920231 AGTGCTGCCAGAATCTCATAA 57.080 42.857 0.00 0.00 0.00 1.90
2225 2930 0.761187 TGAGGGATGATAGTGCTGCC 59.239 55.000 0.00 0.00 0.00 4.85
2234 2939 1.144503 GATTGCAGGGTGAGGGATGAT 59.855 52.381 0.00 0.00 0.00 2.45
2237 2942 0.549950 CAGATTGCAGGGTGAGGGAT 59.450 55.000 0.00 0.00 0.00 3.85
2249 2954 1.443194 CACAAGTGGCGCAGATTGC 60.443 57.895 10.83 0.00 40.69 3.56
2250 2955 1.443194 GCACAAGTGGCGCAGATTG 60.443 57.895 10.83 12.82 0.00 2.67
2254 2959 2.177531 GATGCACAAGTGGCGCAG 59.822 61.111 10.83 0.00 39.39 5.18
2274 2979 4.016444 GCCTATGAAACCAAGAACATCCA 58.984 43.478 0.00 0.00 0.00 3.41
2276 2981 4.016444 TGGCCTATGAAACCAAGAACATC 58.984 43.478 3.32 0.00 0.00 3.06
2287 2992 0.918983 CCCCAGAGTGGCCTATGAAA 59.081 55.000 3.32 0.00 35.79 2.69
2311 3016 0.319900 ACACACTAGACAAGCAGCCG 60.320 55.000 0.00 0.00 0.00 5.52
2314 3019 1.869774 TGCACACACTAGACAAGCAG 58.130 50.000 0.00 0.00 0.00 4.24
2321 3026 4.141937 ACTGAGAAACTTGCACACACTAGA 60.142 41.667 0.00 0.00 0.00 2.43
2331 3036 1.261619 CCACGTGACTGAGAAACTTGC 59.738 52.381 19.30 0.00 0.00 4.01
2334 3039 2.550978 CAACCACGTGACTGAGAAACT 58.449 47.619 19.30 0.00 0.00 2.66
2352 3057 1.231221 CGATTCAAACGTGGACCCAA 58.769 50.000 0.00 0.00 0.00 4.12
2364 3069 3.814842 AGATGCAAGTGAACACGATTCAA 59.185 39.130 8.16 0.00 36.20 2.69
2375 3080 2.807967 CCAACGAAGAAGATGCAAGTGA 59.192 45.455 0.00 0.00 0.00 3.41
2392 3097 3.489785 CGCCGAGTAGTCATTTATCCAAC 59.510 47.826 0.00 0.00 0.00 3.77
2393 3098 3.382227 TCGCCGAGTAGTCATTTATCCAA 59.618 43.478 0.00 0.00 0.00 3.53
2395 3100 3.566523 CTCGCCGAGTAGTCATTTATCC 58.433 50.000 5.82 0.00 0.00 2.59
2397 3102 3.220110 TCCTCGCCGAGTAGTCATTTAT 58.780 45.455 13.83 0.00 0.00 1.40
2399 3104 1.471119 TCCTCGCCGAGTAGTCATTT 58.529 50.000 13.83 0.00 0.00 2.32
2401 3106 2.563261 TATCCTCGCCGAGTAGTCAT 57.437 50.000 13.83 0.00 0.00 3.06
2407 3112 1.806623 GCAACATTATCCTCGCCGAGT 60.807 52.381 13.83 0.00 0.00 4.18
2412 3117 5.343249 AGAAAAATGCAACATTATCCTCGC 58.657 37.500 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.