Multiple sequence alignment - TraesCS7A01G213500

Loading Multiple Alignment...

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 TraesCS7A01G213500 chr7A 100.000 4935 0 0 1 4935 177322617 177327551 0.000000e+00 9114.0
1 TraesCS7A01G213500 chr7A 83.453 278 15 17 308 584 424976360 424976607 3.840000e-56 230.0
2 TraesCS7A01G213500 chr7A 100.000 33 0 0 1 33 54967618 54967586 1.480000e-05 62.1
3 TraesCS7A01G213500 chr7A 97.143 35 1 0 1 35 126751412 126751378 5.330000e-05 60.2
4 TraesCS7A01G213500 chr7B 93.125 2851 126 25 586 3396 140926946 140929766 0.000000e+00 4115.0
5 TraesCS7A01G213500 chr7B 90.142 1552 94 22 3392 4935 140929799 140931299 0.000000e+00 1964.0
6 TraesCS7A01G213500 chr7B 92.527 281 18 2 33 312 140926668 140926946 2.770000e-107 399.0
7 TraesCS7A01G213500 chr7D 94.983 1754 47 21 586 2317 175641047 175642781 0.000000e+00 2713.0
8 TraesCS7A01G213500 chr7D 94.265 1552 72 10 3392 4935 175644283 175645825 0.000000e+00 2357.0
9 TraesCS7A01G213500 chr7D 97.135 1082 28 3 2317 3396 175643170 175644250 0.000000e+00 1823.0
10 TraesCS7A01G213500 chr7D 92.883 281 18 2 33 312 175640768 175641047 1.650000e-109 407.0
11 TraesCS7A01G213500 chr7D 84.615 104 14 2 4684 4785 140840862 140840759 8.740000e-18 102.0
12 TraesCS7A01G213500 chr2D 84.477 277 15 11 310 586 541547537 541547289 1.060000e-61 248.0
13 TraesCS7A01G213500 chr2D 82.986 288 18 6 317 601 6521170 6521429 1.070000e-56 231.0
14 TraesCS7A01G213500 chr2D 92.105 152 10 1 308 459 515140995 515140846 3.870000e-51 213.0
15 TraesCS7A01G213500 chr5D 83.505 291 19 8 311 601 504232142 504232403 1.370000e-60 244.0
16 TraesCS7A01G213500 chr5D 93.919 148 9 0 309 456 441406635 441406782 1.790000e-54 224.0
17 TraesCS7A01G213500 chr5D 87.218 133 11 6 178 308 535006240 535006368 3.980000e-31 147.0
18 TraesCS7A01G213500 chr5D 85.455 110 12 2 4684 4789 437068545 437068436 1.450000e-20 111.0
19 TraesCS7A01G213500 chr4D 82.667 300 20 7 309 607 477414335 477414603 2.300000e-58 237.0
20 TraesCS7A01G213500 chr4D 92.617 149 11 0 308 456 489185594 489185742 1.080000e-51 215.0
21 TraesCS7A01G213500 chr4D 86.466 133 12 6 178 306 74079374 74079504 1.850000e-29 141.0
22 TraesCS7A01G213500 chr3D 83.509 285 16 12 312 596 581982238 581981985 2.300000e-58 237.0
23 TraesCS7A01G213500 chr3D 82.918 281 19 17 307 586 288046908 288047160 4.970000e-55 226.0
24 TraesCS7A01G213500 chr3D 93.878 147 9 0 310 456 563448935 563449081 6.430000e-54 222.0
25 TraesCS7A01G213500 chr3D 89.706 136 12 2 473 607 555181238 555181372 6.570000e-39 172.0
26 TraesCS7A01G213500 chr3D 87.218 133 11 6 178 306 288550588 288550458 3.980000e-31 147.0
27 TraesCS7A01G213500 chr3D 86.331 139 12 7 178 312 322435315 322435450 1.430000e-30 145.0
28 TraesCS7A01G213500 chr3B 78.250 400 66 14 1645 2030 640692001 640692393 2.300000e-58 237.0
29 TraesCS7A01G213500 chr3B 86.331 139 12 7 178 312 396271902 396272037 1.430000e-30 145.0
30 TraesCS7A01G213500 chr1B 83.275 287 18 9 313 598 451611931 451611674 2.300000e-58 237.0
31 TraesCS7A01G213500 chr1B 94.444 36 2 0 1 36 618003057 618003022 6.900000e-04 56.5
32 TraesCS7A01G213500 chr1B 94.286 35 2 0 1 35 628115004 628114970 2.000000e-03 54.7
33 TraesCS7A01G213500 chrUn 82.534 292 21 9 310 601 340490986 340491247 3.840000e-56 230.0
34 TraesCS7A01G213500 chr1A 82.373 295 20 14 304 596 218522004 218521740 1.380000e-55 228.0
35 TraesCS7A01G213500 chr1A 92.763 152 11 0 310 461 521902039 521902190 2.310000e-53 220.0
36 TraesCS7A01G213500 chr1A 92.248 129 6 2 473 601 314435786 314435910 3.920000e-41 180.0
37 TraesCS7A01G213500 chr1A 100.000 33 0 0 1 33 577983975 577983943 1.480000e-05 62.1
38 TraesCS7A01G213500 chr1A 100.000 32 0 0 1 32 34986925 34986956 5.330000e-05 60.2
39 TraesCS7A01G213500 chr1A 100.000 32 0 0 1 32 468600570 468600539 5.330000e-05 60.2
40 TraesCS7A01G213500 chr1A 100.000 32 0 0 1 32 470173318 470173287 5.330000e-05 60.2
41 TraesCS7A01G213500 chr1A 94.286 35 1 1 1 34 53913648 53913682 9.000000e-03 52.8
42 TraesCS7A01G213500 chr6B 91.720 157 12 1 304 459 659589549 659589705 2.990000e-52 217.0
43 TraesCS7A01G213500 chr6B 100.000 33 0 0 1 33 447958584 447958616 1.480000e-05 62.1
44 TraesCS7A01G213500 chr6B 100.000 33 0 0 1 33 716959201 716959169 1.480000e-05 62.1
45 TraesCS7A01G213500 chr2A 79.050 358 39 18 233 587 516889279 516889603 3.870000e-51 213.0
46 TraesCS7A01G213500 chr2A 100.000 36 0 0 1 36 740399308 740399343 3.190000e-07 67.6
47 TraesCS7A01G213500 chr2A 100.000 33 0 0 1 33 43159124 43159092 1.480000e-05 62.1
48 TraesCS7A01G213500 chr2B 90.385 156 15 0 304 459 244526299 244526144 6.480000e-49 206.0
49 TraesCS7A01G213500 chr2B 100.000 32 0 0 1 32 707716948 707716917 5.330000e-05 60.2
50 TraesCS7A01G213500 chr1D 80.972 247 41 6 178 421 468265392 468265149 1.810000e-44 191.0
51 TraesCS7A01G213500 chr6D 86.466 133 14 4 178 307 349988457 349988588 5.150000e-30 143.0
52 TraesCS7A01G213500 chr5A 100.000 33 0 0 1 33 558335244 558335212 1.480000e-05 62.1
53 TraesCS7A01G213500 chr3A 100.000 33 0 0 1 33 715618913 715618881 1.480000e-05 62.1
54 TraesCS7A01G213500 chr3A 100.000 32 0 0 1 32 520412215 520412184 5.330000e-05 60.2
55 TraesCS7A01G213500 chr6A 96.970 33 1 0 1 33 139136136 139136168 6.900000e-04 56.5
56 TraesCS7A01G213500 chr6A 100.000 30 0 0 3 32 176295630 176295659 6.900000e-04 56.5
57 TraesCS7A01G213500 chr6A 92.308 39 2 1 1 38 596672476 596672438 2.000000e-03 54.7


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 TraesCS7A01G213500 chr7A 177322617 177327551 4934 False 9114.000000 9114 100.000000 1 4935 1 chr7A.!!$F1 4934
1 TraesCS7A01G213500 chr7B 140926668 140931299 4631 False 2159.333333 4115 91.931333 33 4935 3 chr7B.!!$F1 4902
2 TraesCS7A01G213500 chr7D 175640768 175645825 5057 False 1825.000000 2713 94.816500 33 4935 4 chr7D.!!$F1 4902

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
424 427 0.032130 ATGTCGAGCACTCAACACGT 59.968 50.000 0.0 0.0 0.00 4.49 F
425 428 0.179121 TGTCGAGCACTCAACACGTT 60.179 50.000 0.0 0.0 0.00 3.99 F
1578 1600 0.387929 TCGCAAGTCTGTCGGTTTCT 59.612 50.000 0.0 0.0 39.48 2.52 F
1579 1601 0.508641 CGCAAGTCTGTCGGTTTCTG 59.491 55.000 0.0 0.0 0.00 3.02 F
2211 2253 0.669318 TGGCACACTACTTGCTACGC 60.669 55.000 0.0 0.0 40.07 4.42 F
3191 3656 2.260247 TGCAGACAAGCAAGCATCC 58.740 52.632 0.0 0.0 42.46 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1259 0.172803 GCATCCAGAGGCAAAGCAAG 59.827 55.000 0.00 0.00 38.12 4.01 R
1799 1835 0.744414 ATTGAGTCATCGGGGCAACG 60.744 55.000 0.00 0.00 37.60 4.10 R
2424 2871 1.630878 AGGGTGCAGCCTAATATAGCC 59.369 52.381 35.44 4.39 37.43 3.93 R
2789 3251 2.609459 CACTAATAAAGCCTGGCACGAG 59.391 50.000 22.65 10.93 0.00 4.18 R
3721 4225 1.688772 ATGCAGGCATGACATCTTCC 58.311 50.000 0.62 0.00 35.03 3.46 R
4532 5038 1.001860 TGGCATAAACCTGCTTTTGGC 59.998 47.619 0.00 0.00 41.95 4.52 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
19 20 2.366167 CCTAGGCCTGGGAGCACT 60.366 66.667 30.85 0.00 32.26 4.40
20 21 1.075226 CCTAGGCCTGGGAGCACTA 60.075 63.158 30.85 0.00 32.26 2.74
21 22 1.118356 CCTAGGCCTGGGAGCACTAG 61.118 65.000 30.85 7.95 35.30 2.57
22 23 0.105964 CTAGGCCTGGGAGCACTAGA 60.106 60.000 17.99 0.00 36.52 2.43
23 24 0.563173 TAGGCCTGGGAGCACTAGAT 59.437 55.000 17.99 0.00 0.00 1.98
24 25 0.563173 AGGCCTGGGAGCACTAGATA 59.437 55.000 3.11 0.00 0.00 1.98
25 26 0.682292 GGCCTGGGAGCACTAGATAC 59.318 60.000 0.00 0.00 0.00 2.24
26 27 1.710816 GCCTGGGAGCACTAGATACT 58.289 55.000 0.00 0.00 0.00 2.12
27 28 2.043227 GCCTGGGAGCACTAGATACTT 58.957 52.381 0.00 0.00 0.00 2.24
28 29 2.436173 GCCTGGGAGCACTAGATACTTT 59.564 50.000 0.00 0.00 0.00 2.66
29 30 3.493524 GCCTGGGAGCACTAGATACTTTC 60.494 52.174 0.00 0.00 0.00 2.62
30 31 3.070302 CCTGGGAGCACTAGATACTTTCC 59.930 52.174 0.00 0.00 0.00 3.13
31 32 3.039011 TGGGAGCACTAGATACTTTCCC 58.961 50.000 0.00 4.81 42.49 3.97
138 139 7.384387 GCGGTGTTCTAGACTTATAAATAAGGG 59.616 40.741 12.99 2.79 43.07 3.95
148 149 6.592870 ACTTATAAATAAGGGTGGAGTGAGC 58.407 40.000 12.99 0.00 43.07 4.26
153 154 1.495579 AAGGGTGGAGTGAGCAGCAT 61.496 55.000 0.00 0.00 0.00 3.79
217 220 5.079406 CCGAAATCAAATGTACAAGACACG 58.921 41.667 0.00 5.85 42.17 4.49
254 257 5.178623 TGTTCACACATTTCAATCCGTAGTC 59.821 40.000 0.00 0.00 0.00 2.59
257 260 3.684788 ACACATTTCAATCCGTAGTCAGC 59.315 43.478 0.00 0.00 0.00 4.26
273 276 7.011389 CCGTAGTCAGCTCATTTTGAAATATCA 59.989 37.037 0.00 0.00 0.00 2.15
312 315 4.098960 TGTGAACGGAGGGAGTACATTATC 59.901 45.833 0.00 0.00 0.00 1.75
313 316 4.341520 GTGAACGGAGGGAGTACATTATCT 59.658 45.833 0.00 0.00 0.00 1.98
315 318 6.208994 GTGAACGGAGGGAGTACATTATCTAT 59.791 42.308 0.00 0.00 0.00 1.98
317 320 8.114102 TGAACGGAGGGAGTACATTATCTATAT 58.886 37.037 0.00 0.00 0.00 0.86
318 321 8.522542 AACGGAGGGAGTACATTATCTATATC 57.477 38.462 0.00 0.00 0.00 1.63
319 322 7.874252 ACGGAGGGAGTACATTATCTATATCT 58.126 38.462 0.00 0.00 0.00 1.98
361 364 6.983906 CCAAAGGGGCAGATCTAATTAATT 57.016 37.500 5.89 5.89 0.00 1.40
362 365 7.365497 CCAAAGGGGCAGATCTAATTAATTT 57.635 36.000 5.91 0.00 0.00 1.82
363 366 7.436933 CCAAAGGGGCAGATCTAATTAATTTC 58.563 38.462 5.91 0.00 0.00 2.17
364 367 7.069826 CCAAAGGGGCAGATCTAATTAATTTCA 59.930 37.037 5.91 0.00 0.00 2.69
365 368 7.830099 AAGGGGCAGATCTAATTAATTTCAG 57.170 36.000 5.91 0.00 0.00 3.02
366 369 7.154191 AGGGGCAGATCTAATTAATTTCAGA 57.846 36.000 5.91 4.62 0.00 3.27
367 370 7.001073 AGGGGCAGATCTAATTAATTTCAGAC 58.999 38.462 5.91 0.00 0.00 3.51
368 371 6.772716 GGGGCAGATCTAATTAATTTCAGACA 59.227 38.462 5.91 0.00 0.00 3.41
369 372 7.449704 GGGGCAGATCTAATTAATTTCAGACAT 59.550 37.037 5.91 0.00 0.00 3.06
370 373 8.510505 GGGCAGATCTAATTAATTTCAGACATC 58.489 37.037 5.91 0.60 0.00 3.06
371 374 9.060347 GGCAGATCTAATTAATTTCAGACATCA 57.940 33.333 5.91 0.00 0.00 3.07
389 392 5.643664 ACATCAAATCATGTCAATCCAACG 58.356 37.500 0.00 0.00 30.76 4.10
390 393 5.415389 ACATCAAATCATGTCAATCCAACGA 59.585 36.000 0.00 0.00 30.76 3.85
391 394 5.295431 TCAAATCATGTCAATCCAACGAC 57.705 39.130 0.00 0.00 0.00 4.34
392 395 4.155826 TCAAATCATGTCAATCCAACGACC 59.844 41.667 0.00 0.00 0.00 4.79
393 396 3.634397 ATCATGTCAATCCAACGACCT 57.366 42.857 0.00 0.00 0.00 3.85
394 397 4.753516 ATCATGTCAATCCAACGACCTA 57.246 40.909 0.00 0.00 0.00 3.08
395 398 4.123497 TCATGTCAATCCAACGACCTAG 57.877 45.455 0.00 0.00 0.00 3.02
396 399 3.767131 TCATGTCAATCCAACGACCTAGA 59.233 43.478 0.00 0.00 0.00 2.43
397 400 3.587797 TGTCAATCCAACGACCTAGAC 57.412 47.619 0.00 0.00 0.00 2.59
398 401 2.232941 TGTCAATCCAACGACCTAGACC 59.767 50.000 0.00 0.00 0.00 3.85
399 402 1.475280 TCAATCCAACGACCTAGACCG 59.525 52.381 0.00 0.00 0.00 4.79
400 403 0.175073 AATCCAACGACCTAGACCGC 59.825 55.000 0.00 0.00 0.00 5.68
401 404 0.683504 ATCCAACGACCTAGACCGCT 60.684 55.000 0.00 0.00 0.00 5.52
402 405 0.896940 TCCAACGACCTAGACCGCTT 60.897 55.000 0.00 0.00 0.00 4.68
403 406 0.458025 CCAACGACCTAGACCGCTTC 60.458 60.000 0.00 0.00 0.00 3.86
404 407 0.242825 CAACGACCTAGACCGCTTCA 59.757 55.000 0.00 0.00 0.00 3.02
405 408 0.963962 AACGACCTAGACCGCTTCAA 59.036 50.000 0.00 0.00 0.00 2.69
406 409 1.183549 ACGACCTAGACCGCTTCAAT 58.816 50.000 0.00 0.00 0.00 2.57
407 410 1.135083 ACGACCTAGACCGCTTCAATG 60.135 52.381 0.00 0.00 0.00 2.82
408 411 1.135083 CGACCTAGACCGCTTCAATGT 60.135 52.381 0.00 0.00 0.00 2.71
409 412 2.541556 GACCTAGACCGCTTCAATGTC 58.458 52.381 0.00 0.00 0.00 3.06
410 413 1.135083 ACCTAGACCGCTTCAATGTCG 60.135 52.381 0.00 0.00 34.24 4.35
411 414 1.134367 CCTAGACCGCTTCAATGTCGA 59.866 52.381 0.00 0.00 34.24 4.20
412 415 2.455032 CTAGACCGCTTCAATGTCGAG 58.545 52.381 0.00 0.00 34.24 4.04
413 416 0.737715 AGACCGCTTCAATGTCGAGC 60.738 55.000 0.00 0.00 34.24 5.03
414 417 1.005037 ACCGCTTCAATGTCGAGCA 60.005 52.632 0.00 0.00 36.22 4.26
415 418 1.291877 ACCGCTTCAATGTCGAGCAC 61.292 55.000 0.00 0.00 36.22 4.40
416 419 1.016130 CCGCTTCAATGTCGAGCACT 61.016 55.000 0.00 0.00 36.22 4.40
417 420 0.368227 CGCTTCAATGTCGAGCACTC 59.632 55.000 0.00 0.00 36.22 3.51
418 421 1.432514 GCTTCAATGTCGAGCACTCA 58.567 50.000 0.00 0.00 36.45 3.41
419 422 1.800586 GCTTCAATGTCGAGCACTCAA 59.199 47.619 0.00 0.00 36.45 3.02
420 423 2.412065 GCTTCAATGTCGAGCACTCAAC 60.412 50.000 0.00 0.00 36.45 3.18
421 424 2.524569 TCAATGTCGAGCACTCAACA 57.475 45.000 0.00 0.00 0.00 3.33
422 425 2.135139 TCAATGTCGAGCACTCAACAC 58.865 47.619 0.00 0.00 0.00 3.32
423 426 1.136529 CAATGTCGAGCACTCAACACG 60.137 52.381 0.00 0.00 0.00 4.49
424 427 0.032130 ATGTCGAGCACTCAACACGT 59.968 50.000 0.00 0.00 0.00 4.49
425 428 0.179121 TGTCGAGCACTCAACACGTT 60.179 50.000 0.00 0.00 0.00 3.99
426 429 0.928229 GTCGAGCACTCAACACGTTT 59.072 50.000 0.00 0.00 0.00 3.60
427 430 2.121786 GTCGAGCACTCAACACGTTTA 58.878 47.619 0.00 0.00 0.00 2.01
428 431 2.153247 GTCGAGCACTCAACACGTTTAG 59.847 50.000 0.00 0.00 0.00 1.85
429 432 1.136611 CGAGCACTCAACACGTTTAGC 60.137 52.381 0.00 0.00 0.00 3.09
442 445 3.515071 CGTTTAGCGTGCAGTTAGTTT 57.485 42.857 0.00 0.00 35.54 2.66
443 446 3.466836 CGTTTAGCGTGCAGTTAGTTTC 58.533 45.455 0.00 0.00 35.54 2.78
444 447 3.060138 CGTTTAGCGTGCAGTTAGTTTCA 60.060 43.478 0.00 0.00 35.54 2.69
445 448 4.551217 CGTTTAGCGTGCAGTTAGTTTCAA 60.551 41.667 0.00 0.00 35.54 2.69
446 449 4.725556 TTAGCGTGCAGTTAGTTTCAAG 57.274 40.909 0.00 0.00 0.00 3.02
447 450 1.264288 AGCGTGCAGTTAGTTTCAAGC 59.736 47.619 0.00 0.00 34.88 4.01
448 451 1.663161 GCGTGCAGTTAGTTTCAAGCC 60.663 52.381 0.00 0.00 0.00 4.35
449 452 1.601903 CGTGCAGTTAGTTTCAAGCCA 59.398 47.619 0.00 0.00 0.00 4.75
450 453 2.032799 CGTGCAGTTAGTTTCAAGCCAA 59.967 45.455 0.00 0.00 0.00 4.52
451 454 3.488384 CGTGCAGTTAGTTTCAAGCCAAA 60.488 43.478 0.00 0.00 0.00 3.28
452 455 4.620982 GTGCAGTTAGTTTCAAGCCAAAT 58.379 39.130 0.00 0.00 0.00 2.32
453 456 5.561919 CGTGCAGTTAGTTTCAAGCCAAATA 60.562 40.000 0.00 0.00 0.00 1.40
454 457 6.389906 GTGCAGTTAGTTTCAAGCCAAATAT 58.610 36.000 0.00 0.00 0.00 1.28
455 458 7.535139 GTGCAGTTAGTTTCAAGCCAAATATA 58.465 34.615 0.00 0.00 0.00 0.86
456 459 8.026607 GTGCAGTTAGTTTCAAGCCAAATATAA 58.973 33.333 0.00 0.00 0.00 0.98
457 460 8.748412 TGCAGTTAGTTTCAAGCCAAATATAAT 58.252 29.630 0.00 0.00 0.00 1.28
458 461 9.023967 GCAGTTAGTTTCAAGCCAAATATAATG 57.976 33.333 0.00 0.00 0.00 1.90
493 496 7.949903 GCAATGCCAAATATAATGTTGATCA 57.050 32.000 0.00 0.00 0.00 2.92
494 497 7.790000 GCAATGCCAAATATAATGTTGATCAC 58.210 34.615 0.00 0.00 0.00 3.06
495 498 7.438757 GCAATGCCAAATATAATGTTGATCACA 59.561 33.333 0.00 0.00 40.71 3.58
509 512 9.872721 AATGTTGATCACATAATAACATGCAAA 57.127 25.926 7.51 0.00 46.23 3.68
537 540 9.998106 AATATCCTACTTAATATCCACACACAC 57.002 33.333 0.00 0.00 0.00 3.82
538 541 7.676683 ATCCTACTTAATATCCACACACACT 57.323 36.000 0.00 0.00 0.00 3.55
539 542 7.490657 TCCTACTTAATATCCACACACACTT 57.509 36.000 0.00 0.00 0.00 3.16
540 543 8.598202 TCCTACTTAATATCCACACACACTTA 57.402 34.615 0.00 0.00 0.00 2.24
541 544 9.038072 TCCTACTTAATATCCACACACACTTAA 57.962 33.333 0.00 0.00 0.00 1.85
542 545 9.832445 CCTACTTAATATCCACACACACTTAAT 57.168 33.333 0.00 0.00 0.00 1.40
552 555 9.733556 ATCCACACACACTTAATATACTTTCAA 57.266 29.630 0.00 0.00 0.00 2.69
553 556 9.562408 TCCACACACACTTAATATACTTTCAAA 57.438 29.630 0.00 0.00 0.00 2.69
567 570 5.574815 ACTTTCAAATTAACGTGCATTGC 57.425 34.783 0.46 0.46 0.00 3.56
568 571 5.046529 ACTTTCAAATTAACGTGCATTGCA 58.953 33.333 7.38 7.38 35.60 4.08
579 582 2.328655 TGCATTGCACGTACACATTG 57.671 45.000 7.38 0.00 31.71 2.82
580 583 1.876156 TGCATTGCACGTACACATTGA 59.124 42.857 7.38 0.00 31.71 2.57
581 584 2.241722 GCATTGCACGTACACATTGAC 58.758 47.619 3.15 1.49 0.00 3.18
582 585 2.095768 GCATTGCACGTACACATTGACT 60.096 45.455 3.15 0.00 0.00 3.41
583 586 3.124466 GCATTGCACGTACACATTGACTA 59.876 43.478 3.15 0.00 0.00 2.59
584 587 4.724885 GCATTGCACGTACACATTGACTAG 60.725 45.833 3.15 0.00 0.00 2.57
585 588 3.653539 TGCACGTACACATTGACTAGT 57.346 42.857 0.00 0.00 0.00 2.57
586 589 3.985008 TGCACGTACACATTGACTAGTT 58.015 40.909 0.00 0.00 0.00 2.24
587 590 5.123805 TGCACGTACACATTGACTAGTTA 57.876 39.130 0.00 0.00 0.00 2.24
588 591 5.530712 TGCACGTACACATTGACTAGTTAA 58.469 37.500 2.16 2.16 0.00 2.01
589 592 5.984323 TGCACGTACACATTGACTAGTTAAA 59.016 36.000 3.97 0.00 0.00 1.52
590 593 6.479331 TGCACGTACACATTGACTAGTTAAAA 59.521 34.615 3.97 0.00 0.00 1.52
591 594 7.011202 TGCACGTACACATTGACTAGTTAAAAA 59.989 33.333 3.97 0.00 0.00 1.94
592 595 7.319615 GCACGTACACATTGACTAGTTAAAAAC 59.680 37.037 3.97 0.00 0.00 2.43
593 596 8.329583 CACGTACACATTGACTAGTTAAAAACA 58.670 33.333 3.97 0.00 0.00 2.83
626 629 3.536287 AGATCCCCTTGGAAGAAGAAGT 58.464 45.455 0.00 0.00 45.98 3.01
638 641 5.882557 TGGAAGAAGAAGTAATTCCATCTGC 59.117 40.000 8.93 7.42 44.75 4.26
648 651 6.613699 AGTAATTCCATCTGCCAATTCCATA 58.386 36.000 0.00 0.00 0.00 2.74
649 652 7.243824 AGTAATTCCATCTGCCAATTCCATAT 58.756 34.615 0.00 0.00 0.00 1.78
650 653 8.393259 AGTAATTCCATCTGCCAATTCCATATA 58.607 33.333 0.00 0.00 0.00 0.86
651 654 7.713734 AATTCCATCTGCCAATTCCATATAG 57.286 36.000 0.00 0.00 0.00 1.31
652 655 5.848286 TCCATCTGCCAATTCCATATAGT 57.152 39.130 0.00 0.00 0.00 2.12
653 656 6.950860 TCCATCTGCCAATTCCATATAGTA 57.049 37.500 0.00 0.00 0.00 1.82
654 657 6.950842 TCCATCTGCCAATTCCATATAGTAG 58.049 40.000 0.00 0.00 0.00 2.57
655 658 6.501805 TCCATCTGCCAATTCCATATAGTAGT 59.498 38.462 0.00 0.00 0.00 2.73
656 659 7.678171 TCCATCTGCCAATTCCATATAGTAGTA 59.322 37.037 0.00 0.00 0.00 1.82
659 662 9.769677 ATCTGCCAATTCCATATAGTAGTACTA 57.230 33.333 12.38 12.38 34.82 1.82
707 710 3.374988 CAGAATCATTAGCCAAAGCGTGA 59.625 43.478 0.00 0.00 46.67 4.35
790 793 2.747855 CCGCACCAAGAAGCCTCC 60.748 66.667 0.00 0.00 0.00 4.30
792 795 1.596934 CGCACCAAGAAGCCTCCTA 59.403 57.895 0.00 0.00 0.00 2.94
803 806 2.415608 GCCTCCTAAAAAGCGGCCC 61.416 63.158 0.00 0.00 34.75 5.80
829 832 0.665068 TCGGAATCAACACCACGACG 60.665 55.000 0.00 0.00 0.00 5.12
1222 1243 1.536284 CGGAGCTTGTAGATTCGGGTC 60.536 57.143 0.00 0.00 0.00 4.46
1231 1252 2.955477 AGATTCGGGTCGTTCTAACC 57.045 50.000 0.00 0.00 35.97 2.85
1236 1257 0.526954 CGGGTCGTTCTAACCATCGG 60.527 60.000 0.00 0.00 38.62 4.18
1238 1259 0.808847 GGTCGTTCTAACCATCGGGC 60.809 60.000 0.00 0.00 37.90 6.13
1247 1268 2.158561 AACCATCGGGCTTGCTTTGC 62.159 55.000 0.00 0.00 37.90 3.68
1349 1370 1.859080 GTGACACGCTTCTTTCTTCGT 59.141 47.619 0.00 0.00 35.35 3.85
1454 1476 4.518970 TCCCTGTGTACTTTTCTGAATTGC 59.481 41.667 0.00 0.00 0.00 3.56
1536 1558 9.258629 TCAGATTAGGGAATTTCATTGTCATTT 57.741 29.630 0.00 0.00 0.00 2.32
1567 1589 1.067821 CAGGGGTAGATCTCGCAAGTC 59.932 57.143 0.00 0.00 39.48 3.01
1577 1599 0.784778 CTCGCAAGTCTGTCGGTTTC 59.215 55.000 0.00 0.00 39.48 2.78
1578 1600 0.387929 TCGCAAGTCTGTCGGTTTCT 59.612 50.000 0.00 0.00 39.48 2.52
1579 1601 0.508641 CGCAAGTCTGTCGGTTTCTG 59.491 55.000 0.00 0.00 0.00 3.02
1580 1602 1.583054 GCAAGTCTGTCGGTTTCTGT 58.417 50.000 0.00 0.00 0.00 3.41
1581 1603 1.940613 GCAAGTCTGTCGGTTTCTGTT 59.059 47.619 0.00 0.00 0.00 3.16
1582 1604 3.128349 GCAAGTCTGTCGGTTTCTGTTA 58.872 45.455 0.00 0.00 0.00 2.41
1583 1605 3.558418 GCAAGTCTGTCGGTTTCTGTTAA 59.442 43.478 0.00 0.00 0.00 2.01
1584 1606 4.318831 GCAAGTCTGTCGGTTTCTGTTAAG 60.319 45.833 0.00 0.00 0.00 1.85
1585 1607 3.391049 AGTCTGTCGGTTTCTGTTAAGC 58.609 45.455 0.00 0.00 0.00 3.09
1586 1608 3.069729 AGTCTGTCGGTTTCTGTTAAGCT 59.930 43.478 0.00 0.00 0.00 3.74
1587 1609 3.808174 GTCTGTCGGTTTCTGTTAAGCTT 59.192 43.478 3.48 3.48 0.00 3.74
1722 1758 0.738389 CGCAAAGACACCACAAACCT 59.262 50.000 0.00 0.00 0.00 3.50
1916 1952 2.158813 ACTTGTCGAAAAAGAGGAGGCA 60.159 45.455 14.33 0.00 0.00 4.75
2015 2051 5.300034 TGCTGAGAAAGAAGCTTTGATCAAA 59.700 36.000 19.45 19.45 40.21 2.69
2021 2057 8.064336 AGAAAGAAGCTTTGATCAAATATGCT 57.936 30.769 21.44 21.44 32.83 3.79
2118 2160 6.382869 AGTGGAAATTGTGCTATATTCTGC 57.617 37.500 0.00 0.00 0.00 4.26
2202 2244 5.682943 TTGTTCTACAAATGGCACACTAC 57.317 39.130 0.00 0.00 34.97 2.73
2211 2253 0.669318 TGGCACACTACTTGCTACGC 60.669 55.000 0.00 0.00 40.07 4.42
2404 2851 8.535335 AGAAAAGTGACACTACATGACTATCAT 58.465 33.333 8.91 0.00 37.65 2.45
2603 3050 3.889815 CATGTGGCCAATTCCTAGAAGA 58.110 45.455 7.24 0.00 0.00 2.87
2711 3166 9.586435 CCAAGTTGATTTTAAACTGAAGAAACT 57.414 29.630 3.87 0.00 37.90 2.66
2789 3251 5.603596 TCTGGATTGCAATGCATTTAATCC 58.396 37.500 33.63 33.63 40.56 3.01
2791 3253 5.603596 TGGATTGCAATGCATTTAATCCTC 58.396 37.500 36.12 24.49 40.70 3.71
2794 3256 4.031418 TGCAATGCATTTAATCCTCGTG 57.969 40.909 9.83 0.00 31.71 4.35
2967 3431 3.557508 GCAATTCCACTTTTTGCAATGC 58.442 40.909 0.00 0.00 43.95 3.56
2979 3443 7.584847 CACTTTTTGCAATGCAGTTGAATAAAG 59.415 33.333 19.32 19.32 44.01 1.85
3191 3656 2.260247 TGCAGACAAGCAAGCATCC 58.740 52.632 0.00 0.00 42.46 3.51
3254 3719 2.356227 GGTGGAAGATCTTCAAGGGGAC 60.356 54.545 31.29 18.15 41.20 4.46
3528 4030 8.678593 TGTCAACTGTGTAAATTGTATGGTAA 57.321 30.769 0.00 0.00 0.00 2.85
3589 4091 9.613428 ATGTTTAAGATTCGGATTCTACAATGA 57.387 29.630 3.07 0.00 0.00 2.57
3666 4168 2.536997 AATAGTGCGACCTGTGCCCC 62.537 60.000 0.00 0.00 0.00 5.80
3721 4225 7.817478 AGGAAACTTCAACAAAAGTAAAACTGG 59.183 33.333 0.00 0.00 38.52 4.00
3756 4260 5.827797 TGCCTGCATATTTACCCTCTTTAAG 59.172 40.000 0.00 0.00 0.00 1.85
4078 4582 0.390124 GACCGGTGTGACTGTAACCA 59.610 55.000 14.63 0.00 33.30 3.67
4101 4605 1.939934 CGAGCACTTGAAACTGGACAA 59.060 47.619 0.00 0.00 0.00 3.18
4115 4619 9.145865 TGAAACTGGACAATTGTTTTAGTTTTC 57.854 29.630 29.10 24.34 36.65 2.29
4117 4621 6.270064 ACTGGACAATTGTTTTAGTTTTCGG 58.730 36.000 13.36 0.00 0.00 4.30
4151 4655 0.861837 GTTCTGTGCTCTCCGTTGTG 59.138 55.000 0.00 0.00 0.00 3.33
4235 4739 9.502091 TGCTATCTAGTGTGATTTTAGTGTTTT 57.498 29.630 0.00 0.00 0.00 2.43
4255 4759 5.682943 TTTTAGACTTGGTTGAATGTCCG 57.317 39.130 0.00 0.00 0.00 4.79
4284 4788 7.431376 CACAGATTGCTGCTAAGTTTTATGATG 59.569 37.037 0.00 0.00 46.26 3.07
4428 4932 7.596749 AGTAAGTGCATTATAGTGACAACAC 57.403 36.000 0.00 0.00 46.24 3.32
4468 4972 3.932545 ACTTGTGAACACAGCAAAACA 57.067 38.095 7.67 0.00 42.94 2.83
4469 4973 4.454728 ACTTGTGAACACAGCAAAACAT 57.545 36.364 7.67 0.00 42.94 2.71
4486 4990 7.515957 CAAAACATCTTGCAATGAATCTACC 57.484 36.000 7.04 0.00 0.00 3.18
4532 5038 9.302345 CATATCCACACTAAGTGTAAAGTACAG 57.698 37.037 0.00 0.00 45.65 2.74
4535 5041 5.294356 CACACTAAGTGTAAAGTACAGCCA 58.706 41.667 0.00 0.00 45.65 4.75
4560 5066 2.738743 CAGGTTTATGCCACTCCCAAT 58.261 47.619 0.00 0.00 0.00 3.16
4575 5081 3.887110 CTCCCAATGCATGCTCTTAATGA 59.113 43.478 20.33 6.05 0.00 2.57
4650 5157 3.573967 CCAGGAAGGCTAAACAAACACAT 59.426 43.478 0.00 0.00 0.00 3.21
4661 5168 7.042992 GGCTAAACAAACACATCCAAAGTTTAC 60.043 37.037 0.00 0.00 34.03 2.01
4670 5177 5.120208 CACATCCAAAGTTTACCGAGTACAG 59.880 44.000 0.00 0.00 0.00 2.74
4712 5219 2.564947 AGTATCTGGATGGATTCGCCTC 59.435 50.000 0.00 0.00 37.63 4.70
4726 5233 2.031516 GCCTCCGGATGCGATGATG 61.032 63.158 16.23 0.00 0.00 3.07
4749 5256 4.747810 CCCTTCCTTGTAAATGATGCAAC 58.252 43.478 0.00 0.00 30.00 4.17
4818 5328 7.763172 AGCTTAGAGAGAATGTTATTTGACG 57.237 36.000 0.00 0.00 0.00 4.35
4874 5384 6.385537 TCAACTTAATTCGCTAGTTTCGAC 57.614 37.500 0.00 0.00 35.51 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.024984 TGCTCCCAGGCCTAGGGT 62.025 66.667 28.97 0.00 46.82 4.34
2 3 1.075226 TAGTGCTCCCAGGCCTAGG 60.075 63.158 11.64 11.64 0.00 3.02
3 4 0.105964 TCTAGTGCTCCCAGGCCTAG 60.106 60.000 3.98 0.00 35.95 3.02
4 5 0.563173 ATCTAGTGCTCCCAGGCCTA 59.437 55.000 3.98 0.00 0.00 3.93
5 6 0.563173 TATCTAGTGCTCCCAGGCCT 59.437 55.000 0.00 0.00 0.00 5.19
6 7 0.682292 GTATCTAGTGCTCCCAGGCC 59.318 60.000 0.00 0.00 0.00 5.19
7 8 1.710816 AGTATCTAGTGCTCCCAGGC 58.289 55.000 0.00 0.00 0.00 4.85
8 9 3.070302 GGAAAGTATCTAGTGCTCCCAGG 59.930 52.174 0.00 0.00 0.00 4.45
9 10 3.070302 GGGAAAGTATCTAGTGCTCCCAG 59.930 52.174 0.00 0.00 35.13 4.45
10 11 3.039011 GGGAAAGTATCTAGTGCTCCCA 58.961 50.000 0.00 0.00 35.13 4.37
11 12 2.369203 GGGGAAAGTATCTAGTGCTCCC 59.631 54.545 0.00 0.00 0.00 4.30
12 13 2.036089 CGGGGAAAGTATCTAGTGCTCC 59.964 54.545 0.00 0.00 0.00 4.70
13 14 2.694109 ACGGGGAAAGTATCTAGTGCTC 59.306 50.000 0.00 0.00 0.00 4.26
14 15 2.748388 ACGGGGAAAGTATCTAGTGCT 58.252 47.619 0.00 0.00 0.00 4.40
15 16 3.538634 AACGGGGAAAGTATCTAGTGC 57.461 47.619 0.00 0.00 0.00 4.40
16 17 6.401047 TCATAACGGGGAAAGTATCTAGTG 57.599 41.667 0.00 0.00 0.00 2.74
17 18 8.896722 ATATCATAACGGGGAAAGTATCTAGT 57.103 34.615 0.00 0.00 0.00 2.57
19 20 9.417561 CCTATATCATAACGGGGAAAGTATCTA 57.582 37.037 0.00 0.00 0.00 1.98
20 21 7.899709 ACCTATATCATAACGGGGAAAGTATCT 59.100 37.037 0.00 0.00 0.00 1.98
21 22 8.075761 ACCTATATCATAACGGGGAAAGTATC 57.924 38.462 0.00 0.00 0.00 2.24
22 23 8.445361 AACCTATATCATAACGGGGAAAGTAT 57.555 34.615 0.00 0.00 0.00 2.12
23 24 7.860649 AACCTATATCATAACGGGGAAAGTA 57.139 36.000 0.00 0.00 0.00 2.24
24 25 6.758806 AACCTATATCATAACGGGGAAAGT 57.241 37.500 0.00 0.00 0.00 2.66
25 26 8.996271 GTAAAACCTATATCATAACGGGGAAAG 58.004 37.037 0.00 0.00 0.00 2.62
26 27 7.656948 CGTAAAACCTATATCATAACGGGGAAA 59.343 37.037 0.00 0.00 0.00 3.13
27 28 7.015098 TCGTAAAACCTATATCATAACGGGGAA 59.985 37.037 0.00 0.00 0.00 3.97
28 29 6.493115 TCGTAAAACCTATATCATAACGGGGA 59.507 38.462 0.00 0.00 0.00 4.81
29 30 6.587608 GTCGTAAAACCTATATCATAACGGGG 59.412 42.308 0.00 0.00 0.00 5.73
30 31 7.147312 TGTCGTAAAACCTATATCATAACGGG 58.853 38.462 0.00 0.00 0.00 5.28
31 32 8.752766 ATGTCGTAAAACCTATATCATAACGG 57.247 34.615 0.00 0.00 0.00 4.44
138 139 0.321919 TTCCATGCTGCTCACTCCAC 60.322 55.000 0.00 0.00 0.00 4.02
193 195 5.107259 CGTGTCTTGTACATTTGATTTCGGA 60.107 40.000 0.00 0.00 41.10 4.55
194 196 5.079406 CGTGTCTTGTACATTTGATTTCGG 58.921 41.667 0.00 0.00 41.10 4.30
254 257 8.975410 TGTTCTTGATATTTCAAAATGAGCTG 57.025 30.769 0.00 0.00 41.22 4.24
273 276 8.786826 TCCGTTCACAAATATAAGATGTTCTT 57.213 30.769 0.00 0.00 40.35 2.52
319 322 9.649316 CCCTTTGGGTCTTTTTATATTGGTATA 57.351 33.333 0.00 0.00 38.25 1.47
321 324 7.964666 CCCTTTGGGTCTTTTTATATTGGTA 57.035 36.000 0.00 0.00 38.25 3.25
322 325 6.867519 CCCTTTGGGTCTTTTTATATTGGT 57.132 37.500 0.00 0.00 38.25 3.67
338 341 6.983906 AATTAATTAGATCTGCCCCTTTGG 57.016 37.500 5.18 0.00 37.09 3.28
339 342 8.010733 TGAAATTAATTAGATCTGCCCCTTTG 57.989 34.615 5.18 0.00 0.00 2.77
340 343 8.061304 TCTGAAATTAATTAGATCTGCCCCTTT 58.939 33.333 5.18 0.00 0.00 3.11
341 344 7.503902 GTCTGAAATTAATTAGATCTGCCCCTT 59.496 37.037 5.18 0.00 0.00 3.95
342 345 7.001073 GTCTGAAATTAATTAGATCTGCCCCT 58.999 38.462 5.18 0.00 0.00 4.79
343 346 6.772716 TGTCTGAAATTAATTAGATCTGCCCC 59.227 38.462 5.18 0.00 0.00 5.80
344 347 7.807977 TGTCTGAAATTAATTAGATCTGCCC 57.192 36.000 5.18 0.00 0.00 5.36
345 348 9.060347 TGATGTCTGAAATTAATTAGATCTGCC 57.940 33.333 5.18 0.00 0.00 4.85
366 369 5.415389 TCGTTGGATTGACATGATTTGATGT 59.585 36.000 0.00 0.00 39.34 3.06
367 370 5.740569 GTCGTTGGATTGACATGATTTGATG 59.259 40.000 0.00 0.00 35.20 3.07
368 371 5.163622 GGTCGTTGGATTGACATGATTTGAT 60.164 40.000 0.00 0.00 36.83 2.57
369 372 4.155826 GGTCGTTGGATTGACATGATTTGA 59.844 41.667 0.00 0.00 36.83 2.69
370 373 4.156556 AGGTCGTTGGATTGACATGATTTG 59.843 41.667 0.00 0.00 36.83 2.32
371 374 4.335416 AGGTCGTTGGATTGACATGATTT 58.665 39.130 0.00 0.00 36.83 2.17
372 375 3.955471 AGGTCGTTGGATTGACATGATT 58.045 40.909 0.00 0.00 36.83 2.57
373 376 3.634397 AGGTCGTTGGATTGACATGAT 57.366 42.857 0.00 0.00 36.83 2.45
374 377 3.767131 TCTAGGTCGTTGGATTGACATGA 59.233 43.478 0.00 0.00 36.83 3.07
375 378 3.865745 GTCTAGGTCGTTGGATTGACATG 59.134 47.826 0.00 0.00 36.83 3.21
376 379 3.118738 GGTCTAGGTCGTTGGATTGACAT 60.119 47.826 0.00 0.00 36.83 3.06
377 380 2.232941 GGTCTAGGTCGTTGGATTGACA 59.767 50.000 0.00 0.00 36.83 3.58
378 381 2.734492 CGGTCTAGGTCGTTGGATTGAC 60.734 54.545 0.00 0.00 0.00 3.18
379 382 1.475280 CGGTCTAGGTCGTTGGATTGA 59.525 52.381 0.00 0.00 0.00 2.57
380 383 1.922570 CGGTCTAGGTCGTTGGATTG 58.077 55.000 0.00 0.00 0.00 2.67
381 384 0.175073 GCGGTCTAGGTCGTTGGATT 59.825 55.000 7.30 0.00 0.00 3.01
382 385 0.683504 AGCGGTCTAGGTCGTTGGAT 60.684 55.000 7.30 0.00 0.00 3.41
383 386 0.896940 AAGCGGTCTAGGTCGTTGGA 60.897 55.000 0.00 0.00 0.00 3.53
384 387 0.458025 GAAGCGGTCTAGGTCGTTGG 60.458 60.000 0.00 0.00 0.00 3.77
385 388 0.242825 TGAAGCGGTCTAGGTCGTTG 59.757 55.000 0.00 0.00 0.00 4.10
386 389 0.963962 TTGAAGCGGTCTAGGTCGTT 59.036 50.000 0.00 0.00 0.00 3.85
387 390 1.135083 CATTGAAGCGGTCTAGGTCGT 60.135 52.381 0.00 0.00 0.00 4.34
388 391 1.135083 ACATTGAAGCGGTCTAGGTCG 60.135 52.381 0.00 0.00 0.00 4.79
389 392 2.541556 GACATTGAAGCGGTCTAGGTC 58.458 52.381 4.60 4.60 36.05 3.85
390 393 1.135083 CGACATTGAAGCGGTCTAGGT 60.135 52.381 0.00 0.00 0.00 3.08
391 394 1.134367 TCGACATTGAAGCGGTCTAGG 59.866 52.381 0.00 0.00 0.00 3.02
392 395 2.455032 CTCGACATTGAAGCGGTCTAG 58.545 52.381 0.00 0.00 0.00 2.43
393 396 1.469251 GCTCGACATTGAAGCGGTCTA 60.469 52.381 0.00 0.00 0.00 2.59
394 397 0.737715 GCTCGACATTGAAGCGGTCT 60.738 55.000 0.00 0.00 0.00 3.85
395 398 1.014044 TGCTCGACATTGAAGCGGTC 61.014 55.000 0.00 0.00 0.00 4.79
396 399 1.005037 TGCTCGACATTGAAGCGGT 60.005 52.632 0.00 0.00 0.00 5.68
397 400 1.016130 AGTGCTCGACATTGAAGCGG 61.016 55.000 0.00 0.00 0.00 5.52
398 401 0.368227 GAGTGCTCGACATTGAAGCG 59.632 55.000 0.00 0.00 0.00 4.68
399 402 1.432514 TGAGTGCTCGACATTGAAGC 58.567 50.000 0.00 0.00 0.00 3.86
400 403 2.802247 TGTTGAGTGCTCGACATTGAAG 59.198 45.455 16.03 0.00 46.09 3.02
401 404 2.832563 TGTTGAGTGCTCGACATTGAA 58.167 42.857 16.03 0.00 46.09 2.69
402 405 2.524569 TGTTGAGTGCTCGACATTGA 57.475 45.000 16.03 0.00 46.09 2.57
407 410 0.928229 AAACGTGTTGAGTGCTCGAC 59.072 50.000 11.61 11.61 42.86 4.20
408 411 2.390938 CTAAACGTGTTGAGTGCTCGA 58.609 47.619 0.00 0.00 0.00 4.04
409 412 1.136611 GCTAAACGTGTTGAGTGCTCG 60.137 52.381 0.00 0.00 0.00 5.03
410 413 1.136611 CGCTAAACGTGTTGAGTGCTC 60.137 52.381 0.00 0.00 36.87 4.26
411 414 0.859232 CGCTAAACGTGTTGAGTGCT 59.141 50.000 0.00 0.00 36.87 4.40
412 415 3.345087 CGCTAAACGTGTTGAGTGC 57.655 52.632 0.00 0.00 36.87 4.40
423 426 4.461992 TGAAACTAACTGCACGCTAAAC 57.538 40.909 0.00 0.00 0.00 2.01
424 427 4.553938 GCTTGAAACTAACTGCACGCTAAA 60.554 41.667 0.00 0.00 0.00 1.85
425 428 3.059188 GCTTGAAACTAACTGCACGCTAA 60.059 43.478 0.00 0.00 0.00 3.09
426 429 2.478894 GCTTGAAACTAACTGCACGCTA 59.521 45.455 0.00 0.00 0.00 4.26
427 430 1.264288 GCTTGAAACTAACTGCACGCT 59.736 47.619 0.00 0.00 0.00 5.07
428 431 1.663161 GGCTTGAAACTAACTGCACGC 60.663 52.381 0.00 0.00 0.00 5.34
429 432 1.601903 TGGCTTGAAACTAACTGCACG 59.398 47.619 0.00 0.00 0.00 5.34
430 433 3.708563 TTGGCTTGAAACTAACTGCAC 57.291 42.857 0.00 0.00 0.00 4.57
431 434 4.935352 ATTTGGCTTGAAACTAACTGCA 57.065 36.364 0.00 0.00 0.00 4.41
432 435 9.023967 CATTATATTTGGCTTGAAACTAACTGC 57.976 33.333 0.00 0.00 0.00 4.40
469 472 7.438757 TGTGATCAACATTATATTTGGCATTGC 59.561 33.333 0.00 0.00 32.36 3.56
470 473 8.874744 TGTGATCAACATTATATTTGGCATTG 57.125 30.769 0.00 0.00 32.36 2.82
511 514 9.998106 GTGTGTGTGGATATTAAGTAGGATATT 57.002 33.333 0.00 0.00 0.00 1.28
512 515 9.381038 AGTGTGTGTGGATATTAAGTAGGATAT 57.619 33.333 0.00 0.00 0.00 1.63
513 516 8.777578 AGTGTGTGTGGATATTAAGTAGGATA 57.222 34.615 0.00 0.00 0.00 2.59
514 517 7.676683 AGTGTGTGTGGATATTAAGTAGGAT 57.323 36.000 0.00 0.00 0.00 3.24
515 518 7.490657 AAGTGTGTGTGGATATTAAGTAGGA 57.509 36.000 0.00 0.00 0.00 2.94
516 519 9.832445 ATTAAGTGTGTGTGGATATTAAGTAGG 57.168 33.333 0.00 0.00 0.00 3.18
526 529 9.733556 TTGAAAGTATATTAAGTGTGTGTGGAT 57.266 29.630 0.00 0.00 0.00 3.41
527 530 9.562408 TTTGAAAGTATATTAAGTGTGTGTGGA 57.438 29.630 0.00 0.00 0.00 4.02
541 544 9.019764 GCAATGCACGTTAATTTGAAAGTATAT 57.980 29.630 0.00 0.00 0.00 0.86
542 545 8.023706 TGCAATGCACGTTAATTTGAAAGTATA 58.976 29.630 2.72 0.00 31.71 1.47
543 546 6.865726 TGCAATGCACGTTAATTTGAAAGTAT 59.134 30.769 2.72 0.00 31.71 2.12
544 547 6.209361 TGCAATGCACGTTAATTTGAAAGTA 58.791 32.000 2.72 0.00 31.71 2.24
545 548 5.046529 TGCAATGCACGTTAATTTGAAAGT 58.953 33.333 2.72 0.00 31.71 2.66
546 549 5.573296 TGCAATGCACGTTAATTTGAAAG 57.427 34.783 2.72 0.00 31.71 2.62
560 563 1.876156 TCAATGTGTACGTGCAATGCA 59.124 42.857 8.25 2.72 35.60 3.96
561 564 2.095768 AGTCAATGTGTACGTGCAATGC 60.096 45.455 8.25 0.00 0.00 3.56
562 565 3.811722 AGTCAATGTGTACGTGCAATG 57.188 42.857 8.25 8.35 0.00 2.82
563 566 4.566004 ACTAGTCAATGTGTACGTGCAAT 58.434 39.130 8.25 1.77 0.00 3.56
564 567 3.985008 ACTAGTCAATGTGTACGTGCAA 58.015 40.909 8.25 0.00 0.00 4.08
565 568 3.653539 ACTAGTCAATGTGTACGTGCA 57.346 42.857 0.82 0.82 0.00 4.57
566 569 6.456447 TTTAACTAGTCAATGTGTACGTGC 57.544 37.500 0.00 0.00 0.00 5.34
567 570 8.329583 TGTTTTTAACTAGTCAATGTGTACGTG 58.670 33.333 0.00 0.00 0.00 4.49
568 571 8.422973 TGTTTTTAACTAGTCAATGTGTACGT 57.577 30.769 0.00 0.00 0.00 3.57
569 572 9.705471 TTTGTTTTTAACTAGTCAATGTGTACG 57.295 29.630 0.00 0.00 0.00 3.67
587 590 9.159254 AGGGGATCTTATCTTCTTTTTGTTTTT 57.841 29.630 0.00 0.00 0.00 1.94
588 591 8.727100 AGGGGATCTTATCTTCTTTTTGTTTT 57.273 30.769 0.00 0.00 0.00 2.43
589 592 8.588472 CAAGGGGATCTTATCTTCTTTTTGTTT 58.412 33.333 0.00 0.00 33.68 2.83
590 593 7.179160 CCAAGGGGATCTTATCTTCTTTTTGTT 59.821 37.037 0.00 0.00 35.59 2.83
591 594 6.665248 CCAAGGGGATCTTATCTTCTTTTTGT 59.335 38.462 0.00 0.00 35.59 2.83
592 595 6.891908 TCCAAGGGGATCTTATCTTCTTTTTG 59.108 38.462 0.00 0.00 38.64 2.44
593 596 7.044496 TCCAAGGGGATCTTATCTTCTTTTT 57.956 36.000 0.00 0.00 38.64 1.94
598 601 5.896073 TCTTCCAAGGGGATCTTATCTTC 57.104 43.478 0.00 0.00 44.48 2.87
603 606 5.101529 ACTTCTTCTTCCAAGGGGATCTTA 58.898 41.667 0.00 0.00 44.48 2.10
626 629 8.393259 ACTATATGGAATTGGCAGATGGAATTA 58.607 33.333 0.00 0.00 0.00 1.40
636 639 8.951614 ACTAGTACTACTATATGGAATTGGCA 57.048 34.615 0.00 0.00 29.08 4.92
648 651 7.713734 TGCAAGTGGAAACTAGTACTACTAT 57.286 36.000 15.41 7.11 29.08 2.12
649 652 7.395206 TCATGCAAGTGGAAACTAGTACTACTA 59.605 37.037 15.41 5.27 0.00 1.82
650 653 6.210784 TCATGCAAGTGGAAACTAGTACTACT 59.789 38.462 11.30 11.30 0.00 2.57
651 654 6.395629 TCATGCAAGTGGAAACTAGTACTAC 58.604 40.000 0.00 2.11 0.00 2.73
652 655 6.599356 TCATGCAAGTGGAAACTAGTACTA 57.401 37.500 1.89 1.89 0.00 1.82
653 656 5.483685 TCATGCAAGTGGAAACTAGTACT 57.516 39.130 0.00 0.00 0.00 2.73
654 657 5.106673 GGTTCATGCAAGTGGAAACTAGTAC 60.107 44.000 0.00 0.00 0.00 2.73
655 658 5.001232 GGTTCATGCAAGTGGAAACTAGTA 58.999 41.667 0.00 0.00 0.00 1.82
656 659 3.821033 GGTTCATGCAAGTGGAAACTAGT 59.179 43.478 0.00 0.00 0.00 2.57
659 662 2.362077 GTGGTTCATGCAAGTGGAAACT 59.638 45.455 0.00 0.00 0.00 2.66
790 793 2.746803 CGACCGGGCCGCTTTTTAG 61.747 63.158 23.20 7.57 0.00 1.85
803 806 1.080366 TGTTGATTCCGACCGACCG 60.080 57.895 0.00 0.00 0.00 4.79
1176 1197 1.978454 GGAGCATGAAATCCCTCCAG 58.022 55.000 9.25 0.00 40.10 3.86
1222 1243 1.006832 CAAGCCCGATGGTTAGAACG 58.993 55.000 0.00 0.00 32.24 3.95
1231 1252 2.182537 GGCAAAGCAAGCCCGATG 59.817 61.111 2.95 0.00 46.50 3.84
1238 1259 0.172803 GCATCCAGAGGCAAAGCAAG 59.827 55.000 0.00 0.00 38.12 4.01
1247 1268 1.117749 TCCGATCCTGCATCCAGAGG 61.118 60.000 0.00 0.00 41.77 3.69
1454 1476 4.078516 GAACCACTCCCGGGGTCG 62.079 72.222 23.50 12.83 36.05 4.79
1536 1558 5.535029 AGATCTACCCCTGTAAACCATGTA 58.465 41.667 0.00 0.00 0.00 2.29
1537 1559 4.371681 AGATCTACCCCTGTAAACCATGT 58.628 43.478 0.00 0.00 0.00 3.21
1567 1589 4.813296 AAAGCTTAACAGAAACCGACAG 57.187 40.909 0.00 0.00 0.00 3.51
1585 1607 4.616835 GCCATCTCAACAAGGCTACAAAAG 60.617 45.833 0.00 0.00 43.70 2.27
1586 1608 3.255642 GCCATCTCAACAAGGCTACAAAA 59.744 43.478 0.00 0.00 43.70 2.44
1587 1609 2.819608 GCCATCTCAACAAGGCTACAAA 59.180 45.455 0.00 0.00 43.70 2.83
1799 1835 0.744414 ATTGAGTCATCGGGGCAACG 60.744 55.000 0.00 0.00 37.60 4.10
1916 1952 1.751924 GTACTCTCGGCAGACCTCAAT 59.248 52.381 0.00 0.00 0.00 2.57
2015 2051 9.956720 GCATTTTGTAACTGAGAATTAGCATAT 57.043 29.630 0.00 0.00 0.00 1.78
2021 2057 8.637986 ACCTTTGCATTTTGTAACTGAGAATTA 58.362 29.630 0.00 0.00 0.00 1.40
2118 2160 2.038295 AGGAAACTCTGGCTCACTGAAG 59.962 50.000 0.00 0.00 32.90 3.02
2404 2851 6.569179 AGCCGAATTTTTGACTAGCTTTAA 57.431 33.333 0.00 0.00 0.00 1.52
2406 2853 6.759497 ATAGCCGAATTTTTGACTAGCTTT 57.241 33.333 0.00 0.00 0.00 3.51
2418 2865 4.455877 GTGCAGCCTAATATAGCCGAATTT 59.544 41.667 0.00 0.00 0.00 1.82
2424 2871 1.630878 AGGGTGCAGCCTAATATAGCC 59.369 52.381 35.44 4.39 37.43 3.93
2603 3050 9.491675 TGTAATTGCAAGAAATGTTTGATGAAT 57.508 25.926 4.94 0.00 0.00 2.57
2711 3166 3.067742 GCCTGTCTGCTATTCGTACCTTA 59.932 47.826 0.00 0.00 0.00 2.69
2789 3251 2.609459 CACTAATAAAGCCTGGCACGAG 59.391 50.000 22.65 10.93 0.00 4.18
2791 3253 2.627945 TCACTAATAAAGCCTGGCACG 58.372 47.619 22.65 3.10 0.00 5.34
2794 3256 6.207691 TGAAATTCACTAATAAAGCCTGGC 57.792 37.500 11.65 11.65 0.00 4.85
2857 3320 4.076394 TGAGGATTAAAACTTTGGACCGG 58.924 43.478 0.00 0.00 0.00 5.28
3191 3656 6.857437 ACCTCCCATTCCAATTTTTCTAAG 57.143 37.500 0.00 0.00 0.00 2.18
3528 4030 6.835174 TCAAGCCAGAAATGATAAGCTAGAT 58.165 36.000 0.00 0.00 0.00 1.98
3589 4091 8.220755 TGATAGCCTAAATTGTTAGCGAATTT 57.779 30.769 0.00 0.00 36.19 1.82
3622 4124 4.969359 ACATATCCTAGCAGTGTTACCCTT 59.031 41.667 0.00 0.00 0.00 3.95
3666 4168 2.486918 TCATAGTGATCTTGCATGGCG 58.513 47.619 0.00 0.00 0.00 5.69
3721 4225 1.688772 ATGCAGGCATGACATCTTCC 58.311 50.000 0.62 0.00 35.03 3.46
3756 4260 4.483476 AAGAGCAACGTTTGATGGTTAC 57.517 40.909 0.00 0.00 0.00 2.50
4078 4582 2.808543 GTCCAGTTTCAAGTGCTCGATT 59.191 45.455 0.00 0.00 0.00 3.34
4115 4619 3.623060 CAGAACCAGGTAAATGTGATCCG 59.377 47.826 0.00 0.00 0.00 4.18
4117 4621 4.142600 GCACAGAACCAGGTAAATGTGATC 60.143 45.833 25.46 11.97 40.27 2.92
4151 4655 9.967346 GCCAAAGTTTTCCTTCTAATATAATCC 57.033 33.333 0.00 0.00 31.27 3.01
4235 4739 3.558321 CCCGGACATTCAACCAAGTCTAA 60.558 47.826 0.73 0.00 0.00 2.10
4284 4788 5.333568 GCATCAGCAGTTCAAAAATTCCAAC 60.334 40.000 0.00 0.00 41.58 3.77
4334 4838 4.257536 TCGTGATTGCACAAATATGACG 57.742 40.909 1.53 1.53 45.41 4.35
4468 4972 6.182627 TGTTCTGGTAGATTCATTGCAAGAT 58.817 36.000 4.94 0.00 0.00 2.40
4469 4973 5.559770 TGTTCTGGTAGATTCATTGCAAGA 58.440 37.500 4.94 0.00 0.00 3.02
4477 4981 4.318332 CTGCAACTGTTCTGGTAGATTCA 58.682 43.478 0.00 0.00 0.00 2.57
4482 4986 2.175878 AGCTGCAACTGTTCTGGTAG 57.824 50.000 1.02 0.00 0.00 3.18
4483 4987 2.897326 TCTAGCTGCAACTGTTCTGGTA 59.103 45.455 1.02 0.53 0.00 3.25
4486 4990 3.593096 TGATCTAGCTGCAACTGTTCTG 58.407 45.455 1.02 0.00 0.00 3.02
4532 5038 1.001860 TGGCATAAACCTGCTTTTGGC 59.998 47.619 0.00 0.00 41.95 4.52
4535 5041 2.562738 GGAGTGGCATAAACCTGCTTTT 59.437 45.455 0.00 0.00 41.95 2.27
4560 5066 7.767659 GTGAGGATATATCATTAAGAGCATGCA 59.232 37.037 21.98 0.00 0.00 3.96
4575 5081 8.695456 GTTTGTTTGGGAATTGTGAGGATATAT 58.305 33.333 0.00 0.00 0.00 0.86
4590 5097 5.648960 AGAGAAAAACTACGTTTGTTTGGGA 59.351 36.000 16.38 0.00 37.64 4.37
4611 5118 2.005451 CTGGGCGACTTTTCATGAGAG 58.995 52.381 0.00 0.95 0.00 3.20
4650 5157 3.322828 AGCTGTACTCGGTAAACTTTGGA 59.677 43.478 0.00 0.00 0.00 3.53
4661 5168 4.338682 AGGTATCTTTACAGCTGTACTCGG 59.661 45.833 26.02 15.19 0.00 4.63
4670 5177 5.141910 ACTAGGAGGAGGTATCTTTACAGC 58.858 45.833 0.00 0.00 0.00 4.40
4712 5219 3.052082 GGGCATCATCGCATCCGG 61.052 66.667 0.00 0.00 34.56 5.14
4726 5233 2.760092 TGCATCATTTACAAGGAAGGGC 59.240 45.455 0.00 0.00 0.00 5.19
4749 5256 9.736414 ATAATAATCTCCTCCATTCAATCACAG 57.264 33.333 0.00 0.00 0.00 3.66
4796 5306 8.918961 AGTCGTCAAATAACATTCTCTCTAAG 57.081 34.615 0.00 0.00 0.00 2.18
4808 5318 4.094090 AGGAGTCGAGTCGTCAAATAAC 57.906 45.455 13.12 1.06 0.00 1.89
4818 5328 1.543358 ACGGGTTTAAGGAGTCGAGTC 59.457 52.381 12.02 12.02 0.00 3.36
4874 5384 4.070581 ACGAGCATTTTCTGTTCAATCG 57.929 40.909 0.00 0.00 34.97 3.34


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

AutoCloner maintained by Alex Coulton.