Multiple sequence alignment - TraesCS5A01G189200

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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 TraesCS5A01G189200 chr5A 100.000 6763 0 0 1 6763 391554896 391548134 0.000000e+00 12490
1 TraesCS5A01G189200 chr5A 97.761 134 3 0 256 389 391554510 391554377 1.470000e-56 231
2 TraesCS5A01G189200 chr5A 97.761 134 3 0 387 520 391554641 391554508 1.470000e-56 231
3 TraesCS5A01G189200 chr5A 96.875 64 2 0 2425 2488 391552411 391552348 2.580000e-19 108
4 TraesCS5A01G189200 chr5A 96.875 64 2 0 2486 2549 391552472 391552409 2.580000e-19 108
5 TraesCS5A01G189200 chr5D 95.459 1850 56 13 3410 5245 306186508 306188343 0.000000e+00 2926
6 TraesCS5A01G189200 chr5D 92.857 2002 69 25 534 2488 306183615 306185589 0.000000e+00 2837
7 TraesCS5A01G189200 chr5D 94.151 1419 57 14 5329 6739 306188715 306190115 0.000000e+00 2137
8 TraesCS5A01G189200 chr5D 91.435 934 40 25 2486 3409 306185526 306186429 0.000000e+00 1245
9 TraesCS5A01G189200 chr5D 93.902 82 3 2 5238 5318 306188587 306188667 9.210000e-24 122
10 TraesCS5A01G189200 chr5B 93.592 1623 66 16 3410 5011 351458733 351460338 0.000000e+00 2386
11 TraesCS5A01G189200 chr5B 92.728 1664 67 17 534 2178 351455738 351457366 0.000000e+00 2353
12 TraesCS5A01G189200 chr5B 90.411 1095 62 15 5331 6405 351460767 351461838 0.000000e+00 1400
13 TraesCS5A01G189200 chr5B 91.631 932 50 16 2486 3409 351457744 351458655 0.000000e+00 1264
14 TraesCS5A01G189200 chr5B 94.631 298 11 2 2193 2488 351457510 351457804 2.220000e-124 457
15 TraesCS5A01G189200 chr5B 93.204 309 12 4 6438 6737 351472636 351472944 4.810000e-121 446
16 TraesCS5A01G189200 chr5B 93.000 200 13 1 5047 5245 351460333 351460532 2.390000e-74 291
17 TraesCS5A01G189200 chr5B 83.577 274 32 2 39 312 351455086 351455346 1.880000e-60 244
18 TraesCS5A01G189200 chr7B 86.702 376 42 6 4553 4926 470521806 470522175 1.760000e-110 411
19 TraesCS5A01G189200 chr7B 91.724 145 12 0 2824 2968 470520028 470520172 1.150000e-47 202
20 TraesCS5A01G189200 chr7B 90.541 148 12 2 998 1145 470518373 470518518 1.920000e-45 195
21 TraesCS5A01G189200 chr7B 91.176 102 8 1 3937 4037 470520926 470521027 3.290000e-28 137
22 TraesCS5A01G189200 chr7A 85.638 376 46 6 4553 4926 545940219 545939850 8.220000e-104 388
23 TraesCS5A01G189200 chr7A 91.724 145 12 0 2824 2968 545941867 545941723 1.150000e-47 202
24 TraesCS5A01G189200 chr7A 92.481 133 10 0 1001 1133 545943530 545943398 2.490000e-44 191
25 TraesCS5A01G189200 chr7A 89.691 97 10 0 3941 4037 545941096 545941000 2.560000e-24 124
26 TraesCS5A01G189200 chr7D 85.372 376 48 4 4553 4926 451159238 451159608 3.830000e-102 383
27 TraesCS5A01G189200 chr7D 92.199 141 10 1 998 1137 451155832 451155972 1.490000e-46 198


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 TraesCS5A01G189200 chr5A 391548134 391554896 6762 True 2633.600000 12490 97.854400 1 6763 5 chr5A.!!$R1 6762
1 TraesCS5A01G189200 chr5D 306183615 306190115 6500 False 1853.400000 2926 93.560800 534 6739 5 chr5D.!!$F1 6205
2 TraesCS5A01G189200 chr5B 351455086 351461838 6752 False 1199.285714 2386 91.367143 39 6405 7 chr5B.!!$F2 6366
3 TraesCS5A01G189200 chr7B 470518373 470522175 3802 False 236.250000 411 90.035750 998 4926 4 chr7B.!!$F1 3928
4 TraesCS5A01G189200 chr7A 545939850 545943530 3680 True 226.250000 388 89.883500 1001 4926 4 chr7A.!!$R1 3925
5 TraesCS5A01G189200 chr7D 451155832 451159608 3776 False 290.500000 383 88.785500 998 4926 2 chr7D.!!$F1 3928

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
26 27 0.107214 CTCTCGCCTCTCTCCACTCT 60.107 60.000 0.00 0.0 0.00 3.24 F
27 28 0.107410 TCTCGCCTCTCTCCACTCTC 60.107 60.000 0.00 0.0 0.00 3.20 F
29 30 0.107410 TCGCCTCTCTCCACTCTCTC 60.107 60.000 0.00 0.0 0.00 3.20 F
35 36 0.172352 CTCTCCACTCTCTCGTTGGC 59.828 60.000 0.00 0.0 0.00 4.52 F
375 376 0.520404 CCGCATGGCTATCATTGCTC 59.480 55.000 0.00 0.0 32.92 4.26 F
827 1061 1.068281 CACTGACCCAGATCATCCTCG 59.932 57.143 0.45 0.0 35.18 4.63 F
1438 1790 1.610886 GGACGGCTACTGCTTTCCTTT 60.611 52.381 0.00 0.0 37.22 3.11 F
3101 4361 1.301677 GCTTCTGTGCTGGTGGTAGC 61.302 60.000 0.00 0.0 43.95 3.58 F
4055 5511 0.111061 TCAAACTGATGCCCTGCTGT 59.889 50.000 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2185 0.035317 CTTGACTAGCAGTGTGGCCA 59.965 55.000 0.00 0.0 0.00 5.36 R
1924 2289 6.763610 AGGCGATCCAAACTAATTCTTTAGAG 59.236 38.462 0.03 0.0 35.54 2.43 R
1926 2291 6.927294 AGGCGATCCAAACTAATTCTTTAG 57.073 37.500 0.00 0.0 36.84 1.85 R
2174 2897 7.775093 TCCTCATAGGTCCATGTTCATTTTTAG 59.225 37.037 0.00 0.0 36.53 1.85 R
2492 3347 7.712797 TCGTGTAAATCTAGAAGATACATGCA 58.287 34.615 19.97 0.0 33.41 3.96 R
2947 4149 3.319137 TCATACGCTGAAAAGTCTGCT 57.681 42.857 4.44 0.0 44.29 4.24 R
3273 4536 1.406751 CGATAGCACCATCAACACCCA 60.407 52.381 0.00 0.0 0.00 4.51 R
4956 6792 1.406898 TGCAAACCACGCTGATTGAAA 59.593 42.857 0.00 0.0 0.00 2.69 R
6122 8267 0.957395 CAGTGGCGCTGGAAATGTCT 60.957 55.000 20.17 0.0 41.42 3.41 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 1.757682 CCACTTACTCTCGCCTCTCT 58.242 55.000 0.00 0.00 0.00 3.10
20 21 1.673920 CCACTTACTCTCGCCTCTCTC 59.326 57.143 0.00 0.00 0.00 3.20
21 22 1.673920 CACTTACTCTCGCCTCTCTCC 59.326 57.143 0.00 0.00 0.00 3.71
22 23 1.282447 ACTTACTCTCGCCTCTCTCCA 59.718 52.381 0.00 0.00 0.00 3.86
23 24 1.673920 CTTACTCTCGCCTCTCTCCAC 59.326 57.143 0.00 0.00 0.00 4.02
24 25 0.913205 TACTCTCGCCTCTCTCCACT 59.087 55.000 0.00 0.00 0.00 4.00
25 26 0.393808 ACTCTCGCCTCTCTCCACTC 60.394 60.000 0.00 0.00 0.00 3.51
26 27 0.107214 CTCTCGCCTCTCTCCACTCT 60.107 60.000 0.00 0.00 0.00 3.24
27 28 0.107410 TCTCGCCTCTCTCCACTCTC 60.107 60.000 0.00 0.00 0.00 3.20
28 29 0.107214 CTCGCCTCTCTCCACTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
29 30 0.107410 TCGCCTCTCTCCACTCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
30 31 1.436195 CGCCTCTCTCCACTCTCTCG 61.436 65.000 0.00 0.00 0.00 4.04
31 32 0.393808 GCCTCTCTCCACTCTCTCGT 60.394 60.000 0.00 0.00 0.00 4.18
32 33 1.953311 GCCTCTCTCCACTCTCTCGTT 60.953 57.143 0.00 0.00 0.00 3.85
33 34 1.742831 CCTCTCTCCACTCTCTCGTTG 59.257 57.143 0.00 0.00 0.00 4.10
34 35 1.742831 CTCTCTCCACTCTCTCGTTGG 59.257 57.143 0.00 0.00 0.00 3.77
35 36 0.172352 CTCTCCACTCTCTCGTTGGC 59.828 60.000 0.00 0.00 0.00 4.52
36 37 1.216710 CTCCACTCTCTCGTTGGCC 59.783 63.158 0.00 0.00 0.00 5.36
37 38 1.533033 TCCACTCTCTCGTTGGCCA 60.533 57.895 0.00 0.00 0.00 5.36
38 39 1.374758 CCACTCTCTCGTTGGCCAC 60.375 63.158 3.88 0.00 0.00 5.01
47 48 3.712881 GTTGGCCACGACGAGCAC 61.713 66.667 3.88 0.00 0.00 4.40
101 102 2.237143 TCAAAGGCAAGATCTGGACGAT 59.763 45.455 0.00 0.00 34.25 3.73
104 105 1.137872 AGGCAAGATCTGGACGATGAC 59.862 52.381 0.00 0.00 30.84 3.06
111 112 3.371097 CTGGACGATGACCACCGGG 62.371 68.421 6.32 0.00 41.29 5.73
128 129 1.077429 GGTTCATCACCCCTCAGGC 60.077 63.158 0.00 0.00 40.19 4.85
129 130 1.685224 GTTCATCACCCCTCAGGCA 59.315 57.895 0.00 0.00 40.58 4.75
130 131 0.678048 GTTCATCACCCCTCAGGCAC 60.678 60.000 0.00 0.00 40.58 5.01
131 132 1.133181 TTCATCACCCCTCAGGCACA 61.133 55.000 0.00 0.00 40.58 4.57
132 133 1.377725 CATCACCCCTCAGGCACAC 60.378 63.158 0.00 0.00 40.58 3.82
133 134 1.847506 ATCACCCCTCAGGCACACA 60.848 57.895 0.00 0.00 40.58 3.72
137 138 1.379916 CCCCTCAGGCACACATTCA 59.620 57.895 0.00 0.00 0.00 2.57
153 154 1.321805 TTCATCAATGGCGGCAAGGG 61.322 55.000 18.31 8.75 0.00 3.95
155 156 3.667217 ATCAATGGCGGCAAGGGCT 62.667 57.895 18.31 0.00 40.87 5.19
157 158 4.052518 AATGGCGGCAAGGGCTCT 62.053 61.111 18.31 0.00 40.87 4.09
172 173 1.684248 GGCTCTGTTCCTGATGGCATT 60.684 52.381 0.00 0.00 0.00 3.56
176 177 3.952323 CTCTGTTCCTGATGGCATTGATT 59.048 43.478 0.00 0.00 0.00 2.57
208 209 4.642445 TTACCATTCTCGCAGTCGATTA 57.358 40.909 0.00 0.00 44.56 1.75
217 218 3.580731 TCGCAGTCGATTAACACATTGA 58.419 40.909 0.00 0.00 40.21 2.57
247 248 8.125978 ACCATTCACACATTCAATTTAGTCAT 57.874 30.769 0.00 0.00 0.00 3.06
248 249 8.246180 ACCATTCACACATTCAATTTAGTCATC 58.754 33.333 0.00 0.00 0.00 2.92
250 251 7.665561 TTCACACATTCAATTTAGTCATCGA 57.334 32.000 0.00 0.00 0.00 3.59
253 254 8.032451 TCACACATTCAATTTAGTCATCGACTA 58.968 33.333 0.00 0.00 41.51 2.59
259 260 9.877178 ATTCAATTTAGTCATCGACTAGAGTTT 57.123 29.630 0.00 0.00 44.46 2.66
260 261 9.706691 TTCAATTTAGTCATCGACTAGAGTTTT 57.293 29.630 0.00 0.00 44.46 2.43
269 270 4.817517 TCGACTAGAGTTTTAGGCTTTGG 58.182 43.478 0.00 0.00 0.00 3.28
274 275 6.362248 ACTAGAGTTTTAGGCTTTGGTTTGA 58.638 36.000 0.00 0.00 0.00 2.69
293 294 7.602753 GGTTTGAGACCTAACAAAGCATATTT 58.397 34.615 14.04 0.00 46.61 1.40
312 313 7.040409 GCATATTTAGTTAGGATTTGAGGGGTG 60.040 40.741 0.00 0.00 0.00 4.61
313 314 4.855298 TTAGTTAGGATTTGAGGGGTGG 57.145 45.455 0.00 0.00 0.00 4.61
314 315 2.929301 AGTTAGGATTTGAGGGGTGGA 58.071 47.619 0.00 0.00 0.00 4.02
315 316 2.846827 AGTTAGGATTTGAGGGGTGGAG 59.153 50.000 0.00 0.00 0.00 3.86
316 317 1.213296 TAGGATTTGAGGGGTGGAGC 58.787 55.000 0.00 0.00 0.00 4.70
317 318 1.076705 GGATTTGAGGGGTGGAGCC 60.077 63.158 0.00 0.00 0.00 4.70
318 319 1.575447 GGATTTGAGGGGTGGAGCCT 61.575 60.000 0.00 0.00 37.43 4.58
319 320 1.213296 GATTTGAGGGGTGGAGCCTA 58.787 55.000 0.00 0.00 37.43 3.93
321 322 1.562672 TTTGAGGGGTGGAGCCTAGC 61.563 60.000 0.00 0.00 37.43 3.42
322 323 3.164977 GAGGGGTGGAGCCTAGCC 61.165 72.222 0.00 0.00 37.43 3.93
345 346 3.437795 CAGCTTGGAGGCGCTTGG 61.438 66.667 7.64 0.00 33.45 3.61
346 347 3.640407 AGCTTGGAGGCGCTTGGA 61.640 61.111 7.64 0.00 37.29 3.53
347 348 3.130160 GCTTGGAGGCGCTTGGAG 61.130 66.667 7.64 0.44 0.00 3.86
348 349 3.130160 CTTGGAGGCGCTTGGAGC 61.130 66.667 7.64 0.00 38.02 4.70
357 358 4.858680 GCTTGGAGCGGGGTAGCC 62.859 72.222 1.07 1.07 38.01 3.93
358 359 4.530857 CTTGGAGCGGGGTAGCCG 62.531 72.222 4.56 1.59 38.01 5.52
374 375 2.637521 CCGCATGGCTATCATTGCT 58.362 52.632 0.00 0.00 32.92 3.91
375 376 0.520404 CCGCATGGCTATCATTGCTC 59.480 55.000 0.00 0.00 32.92 4.26
376 377 0.520404 CGCATGGCTATCATTGCTCC 59.480 55.000 0.00 0.00 32.92 4.70
377 378 1.881072 CGCATGGCTATCATTGCTCCT 60.881 52.381 0.00 0.00 32.92 3.69
378 379 2.236766 GCATGGCTATCATTGCTCCTT 58.763 47.619 0.00 0.00 32.92 3.36
379 380 2.030185 GCATGGCTATCATTGCTCCTTG 60.030 50.000 0.00 0.00 32.92 3.61
380 381 1.683943 TGGCTATCATTGCTCCTTGC 58.316 50.000 0.00 0.00 43.25 4.01
395 396 4.864806 GCTCCTTGCATTAAAGTTTTAGGC 59.135 41.667 4.42 4.42 42.31 3.93
396 397 5.336770 GCTCCTTGCATTAAAGTTTTAGGCT 60.337 40.000 11.86 0.00 42.31 4.58
397 398 6.664428 TCCTTGCATTAAAGTTTTAGGCTT 57.336 33.333 11.86 0.00 0.00 4.35
398 399 7.061566 TCCTTGCATTAAAGTTTTAGGCTTT 57.938 32.000 11.86 0.00 39.26 3.51
399 400 6.928492 TCCTTGCATTAAAGTTTTAGGCTTTG 59.072 34.615 11.86 3.32 36.88 2.77
400 401 6.147656 CCTTGCATTAAAGTTTTAGGCTTTGG 59.852 38.462 11.86 7.70 36.88 3.28
401 402 6.168270 TGCATTAAAGTTTTAGGCTTTGGT 57.832 33.333 11.86 0.00 36.88 3.67
402 403 6.587273 TGCATTAAAGTTTTAGGCTTTGGTT 58.413 32.000 11.86 0.00 36.88 3.67
403 404 7.051000 TGCATTAAAGTTTTAGGCTTTGGTTT 58.949 30.769 11.86 0.00 36.88 3.27
404 405 7.011857 TGCATTAAAGTTTTAGGCTTTGGTTTG 59.988 33.333 11.86 0.00 36.88 2.93
405 406 7.225734 GCATTAAAGTTTTAGGCTTTGGTTTGA 59.774 33.333 4.16 0.00 36.88 2.69
406 407 8.764287 CATTAAAGTTTTAGGCTTTGGTTTGAG 58.236 33.333 0.00 0.00 36.88 3.02
407 408 6.538945 AAAGTTTTAGGCTTTGGTTTGAGA 57.461 33.333 0.00 0.00 35.16 3.27
408 409 5.515797 AGTTTTAGGCTTTGGTTTGAGAC 57.484 39.130 0.00 0.00 0.00 3.36
418 419 6.093404 GCTTTGGTTTGAGACCTTATAAAGC 58.907 40.000 10.46 10.46 46.96 3.51
440 441 8.697507 AAGCATATTTAGTTAGGATTTGAGGG 57.302 34.615 0.00 0.00 0.00 4.30
441 442 7.234355 AGCATATTTAGTTAGGATTTGAGGGG 58.766 38.462 0.00 0.00 0.00 4.79
444 445 4.855298 TTAGTTAGGATTTGAGGGGTGG 57.145 45.455 0.00 0.00 0.00 4.61
476 477 3.437795 CAGCTTGGAGGCGCTTGG 61.438 66.667 7.64 0.00 33.45 3.61
478 479 3.130160 GCTTGGAGGCGCTTGGAG 61.130 66.667 7.64 0.44 0.00 3.86
479 480 3.130160 CTTGGAGGCGCTTGGAGC 61.130 66.667 7.64 0.00 38.02 4.70
489 490 4.530857 CTTGGAGCGGGGTAGCCG 62.531 72.222 4.56 1.59 38.01 5.52
525 751 3.302740 GCTCCTTGCATTAAAGTCGATCG 60.303 47.826 9.36 9.36 42.31 3.69
526 752 3.857052 TCCTTGCATTAAAGTCGATCGT 58.143 40.909 15.94 0.00 0.00 3.73
527 753 5.001237 TCCTTGCATTAAAGTCGATCGTA 57.999 39.130 15.94 0.00 0.00 3.43
528 754 5.597806 TCCTTGCATTAAAGTCGATCGTAT 58.402 37.500 15.94 1.69 0.00 3.06
529 755 6.046593 TCCTTGCATTAAAGTCGATCGTATT 58.953 36.000 15.94 10.93 0.00 1.89
530 756 6.537301 TCCTTGCATTAAAGTCGATCGTATTT 59.463 34.615 15.94 17.86 0.00 1.40
532 758 8.004344 CCTTGCATTAAAGTCGATCGTATTTAG 58.996 37.037 15.94 10.95 0.00 1.85
537 763 7.992180 TTAAAGTCGATCGTATTTAGGAACC 57.008 36.000 15.94 0.00 0.00 3.62
538 764 4.220533 AGTCGATCGTATTTAGGAACCG 57.779 45.455 15.94 0.00 0.00 4.44
555 781 4.454847 GGAACCGAGGGAGTAAAAAGAAAG 59.545 45.833 0.00 0.00 0.00 2.62
556 782 4.968971 ACCGAGGGAGTAAAAAGAAAGA 57.031 40.909 0.00 0.00 0.00 2.52
575 802 8.850007 AGAAAGAAAGGGAGTAGTATGTTTTC 57.150 34.615 0.00 0.00 0.00 2.29
608 836 2.461110 CGAAGATCCCCAAACGCCG 61.461 63.158 0.00 0.00 0.00 6.46
699 933 2.565834 TGGTCTATATAAAGCGGCCTCC 59.434 50.000 0.00 0.00 0.00 4.30
827 1061 1.068281 CACTGACCCAGATCATCCTCG 59.932 57.143 0.45 0.00 35.18 4.63
985 1219 4.468713 GTCGATAGGGTTAGGGTTAGAGT 58.531 47.826 0.00 0.00 0.00 3.24
1222 1493 2.135139 GAATGGATGATGCGTTCGCTA 58.865 47.619 17.63 5.43 0.00 4.26
1302 1636 6.017357 GTGGGTTCTATCGGGATTTAATGTTC 60.017 42.308 0.00 0.00 0.00 3.18
1438 1790 1.610886 GGACGGCTACTGCTTTCCTTT 60.611 52.381 0.00 0.00 37.22 3.11
1468 1820 8.870160 TGTGAACTTGAAATGTTTGAAATAGG 57.130 30.769 0.00 0.00 34.00 2.57
1469 1821 8.690884 TGTGAACTTGAAATGTTTGAAATAGGA 58.309 29.630 0.00 0.00 34.00 2.94
1470 1822 9.528018 GTGAACTTGAAATGTTTGAAATAGGAA 57.472 29.630 0.00 0.00 34.00 3.36
1471 1823 9.748708 TGAACTTGAAATGTTTGAAATAGGAAG 57.251 29.630 0.00 0.00 34.00 3.46
1472 1824 9.196552 GAACTTGAAATGTTTGAAATAGGAAGG 57.803 33.333 0.00 0.00 34.00 3.46
1473 1825 7.670364 ACTTGAAATGTTTGAAATAGGAAGGG 58.330 34.615 0.00 0.00 0.00 3.95
1474 1826 7.290014 ACTTGAAATGTTTGAAATAGGAAGGGT 59.710 33.333 0.00 0.00 0.00 4.34
1475 1827 6.991938 TGAAATGTTTGAAATAGGAAGGGTG 58.008 36.000 0.00 0.00 0.00 4.61
1476 1828 6.014669 TGAAATGTTTGAAATAGGAAGGGTGG 60.015 38.462 0.00 0.00 0.00 4.61
1597 1962 5.779241 TGAGATAGAAAGGGTGGAATGTT 57.221 39.130 0.00 0.00 0.00 2.71
1668 2033 9.787532 TTATTGCTTTCATTTAGTGTATCTTGC 57.212 29.630 0.00 0.00 0.00 4.01
1743 2108 4.142447 GGACTAAGCGTCTCAATGTACTCA 60.142 45.833 0.00 0.00 42.44 3.41
1909 2274 3.439129 CACATGTGTACTCGTAGTCTCCA 59.561 47.826 18.03 0.00 0.00 3.86
1969 2334 6.864685 TCGCCTACTTATTGATGGTTATTACG 59.135 38.462 0.00 0.00 0.00 3.18
2151 2870 3.065371 GCCATGTTTGTGTCCATAGCTAC 59.935 47.826 0.00 0.00 0.00 3.58
2163 2886 7.657354 TGTGTCCATAGCTACAAGCAATATAAG 59.343 37.037 0.00 0.00 45.56 1.73
2214 3065 8.312564 GGACCTATGAGGACAGGTATAAAATAC 58.687 40.741 0.00 0.00 45.32 1.89
2374 3227 5.015178 TCCCATATTTGACAAAAGAGGGACT 59.985 40.000 23.28 3.47 40.11 3.85
2505 3360 8.743085 AGTGAATGTAAATGCATGTATCTTCT 57.257 30.769 16.36 6.04 0.00 2.85
2506 3361 9.836864 AGTGAATGTAAATGCATGTATCTTCTA 57.163 29.630 16.36 6.36 0.00 2.10
2516 3371 7.930513 TGCATGTATCTTCTAGATTTACACG 57.069 36.000 10.43 5.85 36.20 4.49
2517 3372 7.712797 TGCATGTATCTTCTAGATTTACACGA 58.287 34.615 10.43 0.00 36.20 4.35
2518 3373 8.194769 TGCATGTATCTTCTAGATTTACACGAA 58.805 33.333 10.43 0.00 36.20 3.85
2947 4149 2.031012 CGTGCTGCCTCTGGTTCA 59.969 61.111 0.00 0.00 0.00 3.18
3002 4204 6.419710 GCATTGTTTGGTTCCAGTTAGTTTAC 59.580 38.462 0.00 0.00 0.00 2.01
3063 4322 8.607441 TGATGCTTATTCTATGTATTGTGTCC 57.393 34.615 0.00 0.00 0.00 4.02
3101 4361 1.301677 GCTTCTGTGCTGGTGGTAGC 61.302 60.000 0.00 0.00 43.95 3.58
3179 4439 6.183360 GGCAGTGTTCTTCTTAGACAAAAGTT 60.183 38.462 0.00 0.00 0.00 2.66
3273 4536 8.383374 TGGACTGTAATACTAAATTAGGGTGT 57.617 34.615 4.92 0.00 0.00 4.16
3306 4570 1.658114 CTATCGGACGCGGGATTGA 59.342 57.895 12.47 0.57 0.00 2.57
3315 4579 2.603008 CGGGATTGAAGGGGGCAT 59.397 61.111 0.00 0.00 0.00 4.40
3320 4584 1.560505 GATTGAAGGGGGCATTGTGT 58.439 50.000 0.00 0.00 0.00 3.72
3356 4620 3.616560 CGTATGTGAGCCAGTTAGGTTGT 60.617 47.826 0.00 0.00 40.61 3.32
3482 4825 9.807649 ATCTTGATTGGAATATTGCAAAGTTAC 57.192 29.630 23.76 13.85 41.79 2.50
3523 4866 3.696045 AGCCATTAAACTGCACATGGTA 58.304 40.909 0.00 0.00 38.81 3.25
3706 5056 4.749245 TCTCTCAAATTTCTTCCGTTGC 57.251 40.909 0.00 0.00 0.00 4.17
3709 5059 4.858935 TCTCAAATTTCTTCCGTTGCAAG 58.141 39.130 0.00 0.00 0.00 4.01
3802 5234 3.733077 GCAGGACAATAAGACAAGCATGC 60.733 47.826 10.51 10.51 0.00 4.06
4055 5511 0.111061 TCAAACTGATGCCCTGCTGT 59.889 50.000 0.00 0.00 0.00 4.40
4085 5541 7.982354 CCTTTTTGTTCCTAATGTTGGTTGTTA 59.018 33.333 0.00 0.00 0.00 2.41
4086 5542 9.541143 CTTTTTGTTCCTAATGTTGGTTGTTAT 57.459 29.630 0.00 0.00 0.00 1.89
4089 5545 9.968870 TTTGTTCCTAATGTTGGTTGTTATAAC 57.031 29.630 8.75 8.75 0.00 1.89
4195 5928 2.778299 TGGTTTCTGAAATCTGGACCG 58.222 47.619 14.01 0.00 0.00 4.79
4210 6033 6.303021 TCTGGACCGTTTTACATGTTTTAC 57.697 37.500 2.30 0.00 0.00 2.01
4513 6344 5.296780 CCTAAACATGTACTGGTTGGCTATG 59.703 44.000 0.00 0.00 34.95 2.23
4824 6657 5.746721 TGATATGTCGTTTATTGTGGAGTCG 59.253 40.000 0.00 0.00 0.00 4.18
4902 6735 6.496565 TGTGGGTTCATGTATTTGATTTCCTT 59.503 34.615 0.00 0.00 0.00 3.36
5006 6842 5.048083 GCATTATCCAAACAGAAACACCAGA 60.048 40.000 0.00 0.00 0.00 3.86
5018 6854 4.578928 AGAAACACCAGAACCACATGTTAC 59.421 41.667 0.00 0.00 37.29 2.50
5035 6871 9.559958 CACATGTTACTTTGGTTTCATCTTATC 57.440 33.333 0.00 0.00 0.00 1.75
5045 6881 6.349300 TGGTTTCATCTTATCTGTAGCTTCC 58.651 40.000 0.00 0.00 0.00 3.46
5064 6900 1.202110 CCGCACATGAAATCTGCTGTC 60.202 52.381 0.00 0.00 0.00 3.51
5089 6925 8.783093 TCAGTTACAATTAAGACCATGAAACTG 58.217 33.333 0.00 0.00 40.71 3.16
5146 6982 7.246674 TGGCGAGCTTTTATTCTACATTTAG 57.753 36.000 0.00 0.00 0.00 1.85
5162 6998 6.655078 ACATTTAGCTGGTCATTCTTGTTT 57.345 33.333 0.00 0.00 0.00 2.83
5221 7057 5.337578 ACAATTTGTTGCACCTTGTAGTT 57.662 34.783 0.00 0.00 0.00 2.24
5230 7066 2.476185 GCACCTTGTAGTTATTGCTGCG 60.476 50.000 0.00 0.00 0.00 5.18
5232 7068 3.623060 CACCTTGTAGTTATTGCTGCGAT 59.377 43.478 7.65 7.65 0.00 4.58
5283 7372 6.684897 AAGGAACATTGGAAATGGATCAAA 57.315 33.333 5.08 0.00 0.00 2.69
5284 7373 6.290294 AGGAACATTGGAAATGGATCAAAG 57.710 37.500 5.08 0.00 0.00 2.77
5506 7647 2.751259 ACACTTTGCCATGCTGACATAG 59.249 45.455 0.00 0.00 33.67 2.23
5531 7674 2.559668 AGCATTGTTGTATTGTGCAGCT 59.440 40.909 0.00 0.00 38.23 4.24
5667 7810 3.531207 CGGATGCTGAGGAGGCGA 61.531 66.667 0.00 0.00 0.00 5.54
5720 7863 4.437239 CAGAGGAGATTGCGTGTAAGATT 58.563 43.478 0.00 0.00 0.00 2.40
5815 7960 1.517242 CTCAAAGCTGCTCTTTCCGT 58.483 50.000 1.00 0.00 42.82 4.69
6050 8195 3.876320 CACATTTTTGTCCCACCCTTTTG 59.124 43.478 0.00 0.00 0.00 2.44
6058 8203 1.286553 TCCCACCCTTTTGTGTTGACT 59.713 47.619 0.00 0.00 34.35 3.41
6122 8267 5.584251 GGAGAACATGGCAGAAAAACAAAAA 59.416 36.000 0.00 0.00 0.00 1.94
6125 8270 6.313658 AGAACATGGCAGAAAAACAAAAAGAC 59.686 34.615 0.00 0.00 0.00 3.01
6136 8281 2.742774 ACAAAAAGACATTTCCAGCGC 58.257 42.857 0.00 0.00 0.00 5.92
6152 8297 4.030452 GCCACTGCCTCGTGTTGC 62.030 66.667 0.00 0.00 33.07 4.17
6158 8303 3.286751 GCCTCGTGTTGCTGGCAA 61.287 61.111 3.72 3.72 44.34 4.52
6204 8349 1.876799 TGGTAACATCGCCTGTTTGTG 59.123 47.619 8.23 0.00 45.98 3.33
6227 8372 0.938713 TTACTTTGTTGCCGACCGTG 59.061 50.000 0.00 0.00 0.00 4.94
6229 8374 1.027792 ACTTTGTTGCCGACCGTGTT 61.028 50.000 0.00 0.00 0.00 3.32
6230 8375 0.099791 CTTTGTTGCCGACCGTGTTT 59.900 50.000 0.00 0.00 0.00 2.83
6232 8377 0.938713 TTGTTGCCGACCGTGTTTAG 59.061 50.000 0.00 0.00 0.00 1.85
6233 8378 0.104487 TGTTGCCGACCGTGTTTAGA 59.896 50.000 0.00 0.00 0.00 2.10
6234 8379 1.270412 TGTTGCCGACCGTGTTTAGAT 60.270 47.619 0.00 0.00 0.00 1.98
6235 8380 2.029200 TGTTGCCGACCGTGTTTAGATA 60.029 45.455 0.00 0.00 0.00 1.98
6244 8389 5.505324 CGACCGTGTTTAGATACCCTAGAAG 60.505 48.000 0.00 0.00 0.00 2.85
6289 8435 2.030274 AGCAGGTGAATTAAACAACGGC 60.030 45.455 14.51 14.51 43.97 5.68
6301 8447 7.916914 ATTAAACAACGGCTACATTCTTACT 57.083 32.000 0.00 0.00 0.00 2.24
6311 8457 1.203928 CATTCTTACTGAGCTCGCCG 58.796 55.000 9.64 2.50 0.00 6.46
6323 8469 2.178273 TCGCCGTCACACGAGATG 59.822 61.111 0.00 0.00 46.05 2.90
6324 8470 2.178273 CGCCGTCACACGAGATGA 59.822 61.111 0.00 0.00 46.05 2.92
6326 8472 0.802222 CGCCGTCACACGAGATGAAT 60.802 55.000 0.00 0.00 46.05 2.57
6327 8473 1.359848 GCCGTCACACGAGATGAATT 58.640 50.000 0.00 0.00 46.05 2.17
6367 8519 0.464452 CAGGTTAACTAGGCCCCTCG 59.536 60.000 0.00 0.00 0.00 4.63
6394 8546 3.305720 TGGGTAGTTGAAGTCAGTCAGT 58.694 45.455 0.00 0.00 0.00 3.41
6405 8557 9.865484 GTTGAAGTCAGTCAGTAAAGAAATTAC 57.135 33.333 0.00 0.00 43.56 1.89
6414 8566 4.877323 GTAAAGAAATTACTGCCCGAGG 57.123 45.455 0.00 0.00 40.65 4.63
6415 8567 3.064958 GTAAAGAAATTACTGCCCGAGGC 59.935 47.826 7.87 7.87 40.77 4.70
6416 8568 5.161776 GTAAAGAAATTACTGCCCGAGGCT 61.162 45.833 14.76 0.00 41.95 4.58
6417 8569 5.913603 GTAAAGAAATTACTGCCCGAGGCTA 60.914 44.000 14.76 0.00 41.95 3.93
6418 8570 7.883760 GTAAAGAAATTACTGCCCGAGGCTAC 61.884 46.154 14.76 2.82 41.95 3.58
6434 8586 4.934515 AGGCTACTCGTTGATTTACTAGC 58.065 43.478 0.00 0.00 0.00 3.42
6481 8633 1.521681 GTGCCCGGAGATACTGTGC 60.522 63.158 0.73 0.00 0.00 4.57
6618 8770 0.602905 GGACACAAAGGACGGACAGG 60.603 60.000 0.00 0.00 0.00 4.00
6697 8849 3.115554 GCCGCGCTGATAATTTCATTTT 58.884 40.909 5.56 0.00 32.72 1.82
6729 8881 1.927569 GCCTCCCCCTTCCTTTCCTC 61.928 65.000 0.00 0.00 0.00 3.71
6748 8900 2.894858 CCCCCACACTCTCTCTCTC 58.105 63.158 0.00 0.00 0.00 3.20
6749 8901 0.686112 CCCCCACACTCTCTCTCTCC 60.686 65.000 0.00 0.00 0.00 3.71
6750 8902 0.040351 CCCCACACTCTCTCTCTCCA 59.960 60.000 0.00 0.00 0.00 3.86
6751 8903 1.551099 CCCCACACTCTCTCTCTCCAA 60.551 57.143 0.00 0.00 0.00 3.53
6752 8904 2.251818 CCCACACTCTCTCTCTCCAAA 58.748 52.381 0.00 0.00 0.00 3.28
6753 8905 2.634940 CCCACACTCTCTCTCTCCAAAA 59.365 50.000 0.00 0.00 0.00 2.44
6754 8906 3.262915 CCCACACTCTCTCTCTCCAAAAT 59.737 47.826 0.00 0.00 0.00 1.82
6755 8907 4.502962 CCACACTCTCTCTCTCCAAAATC 58.497 47.826 0.00 0.00 0.00 2.17
6756 8908 4.020751 CCACACTCTCTCTCTCCAAAATCA 60.021 45.833 0.00 0.00 0.00 2.57
6757 8909 5.512060 CCACACTCTCTCTCTCCAAAATCAA 60.512 44.000 0.00 0.00 0.00 2.57
6758 8910 5.994054 CACACTCTCTCTCTCCAAAATCAAA 59.006 40.000 0.00 0.00 0.00 2.69
6759 8911 6.654161 CACACTCTCTCTCTCCAAAATCAAAT 59.346 38.462 0.00 0.00 0.00 2.32
6760 8912 6.878389 ACACTCTCTCTCTCCAAAATCAAATC 59.122 38.462 0.00 0.00 0.00 2.17
6761 8913 6.877855 CACTCTCTCTCTCCAAAATCAAATCA 59.122 38.462 0.00 0.00 0.00 2.57
6762 8914 7.389884 CACTCTCTCTCTCCAAAATCAAATCAA 59.610 37.037 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.673920 GGAGAGAGGCGAGAGTAAGTG 59.326 57.143 0.00 0.00 0.00 3.16
2 3 1.282447 TGGAGAGAGGCGAGAGTAAGT 59.718 52.381 0.00 0.00 0.00 2.24
3 4 1.673920 GTGGAGAGAGGCGAGAGTAAG 59.326 57.143 0.00 0.00 0.00 2.34
4 5 1.282447 AGTGGAGAGAGGCGAGAGTAA 59.718 52.381 0.00 0.00 0.00 2.24
5 6 0.913205 AGTGGAGAGAGGCGAGAGTA 59.087 55.000 0.00 0.00 0.00 2.59
6 7 0.393808 GAGTGGAGAGAGGCGAGAGT 60.394 60.000 0.00 0.00 0.00 3.24
7 8 0.107214 AGAGTGGAGAGAGGCGAGAG 60.107 60.000 0.00 0.00 0.00 3.20
8 9 0.107410 GAGAGTGGAGAGAGGCGAGA 60.107 60.000 0.00 0.00 0.00 4.04
9 10 0.107214 AGAGAGTGGAGAGAGGCGAG 60.107 60.000 0.00 0.00 0.00 5.03
10 11 0.107410 GAGAGAGTGGAGAGAGGCGA 60.107 60.000 0.00 0.00 0.00 5.54
11 12 1.436195 CGAGAGAGTGGAGAGAGGCG 61.436 65.000 0.00 0.00 0.00 5.52
12 13 0.393808 ACGAGAGAGTGGAGAGAGGC 60.394 60.000 0.00 0.00 0.00 4.70
13 14 1.742831 CAACGAGAGAGTGGAGAGAGG 59.257 57.143 0.00 0.00 0.00 3.69
14 15 1.742831 CCAACGAGAGAGTGGAGAGAG 59.257 57.143 0.00 0.00 40.63 3.20
15 16 1.827681 CCAACGAGAGAGTGGAGAGA 58.172 55.000 0.00 0.00 40.63 3.10
16 17 0.172352 GCCAACGAGAGAGTGGAGAG 59.828 60.000 0.00 0.00 40.63 3.20
17 18 1.251527 GGCCAACGAGAGAGTGGAGA 61.252 60.000 0.00 0.00 40.63 3.71
18 19 1.216710 GGCCAACGAGAGAGTGGAG 59.783 63.158 0.00 0.00 40.63 3.86
19 20 1.533033 TGGCCAACGAGAGAGTGGA 60.533 57.895 0.61 0.00 40.63 4.02
20 21 1.374758 GTGGCCAACGAGAGAGTGG 60.375 63.158 7.24 0.00 40.96 4.00
21 22 4.268687 GTGGCCAACGAGAGAGTG 57.731 61.111 7.24 0.00 0.00 3.51
30 31 3.712881 GTGCTCGTCGTGGCCAAC 61.713 66.667 7.24 1.01 0.00 3.77
31 32 3.741830 TTGTGCTCGTCGTGGCCAA 62.742 57.895 7.24 0.00 0.00 4.52
32 33 4.228567 TTGTGCTCGTCGTGGCCA 62.229 61.111 0.00 0.00 0.00 5.36
33 34 3.414700 CTTGTGCTCGTCGTGGCC 61.415 66.667 0.00 0.00 0.00 5.36
34 35 1.687494 GATCTTGTGCTCGTCGTGGC 61.687 60.000 6.13 6.13 0.00 5.01
35 36 0.109086 AGATCTTGTGCTCGTCGTGG 60.109 55.000 0.00 0.00 0.00 4.94
36 37 0.987715 CAGATCTTGTGCTCGTCGTG 59.012 55.000 0.00 0.00 0.00 4.35
37 38 0.109086 CCAGATCTTGTGCTCGTCGT 60.109 55.000 0.00 0.00 0.00 4.34
38 39 0.171231 TCCAGATCTTGTGCTCGTCG 59.829 55.000 0.00 0.00 0.00 5.12
39 40 1.634702 GTCCAGATCTTGTGCTCGTC 58.365 55.000 0.00 0.00 0.00 4.20
40 41 0.109086 CGTCCAGATCTTGTGCTCGT 60.109 55.000 0.00 0.00 0.00 4.18
47 48 0.803768 CGCCTGTCGTCCAGATCTTG 60.804 60.000 0.00 0.00 44.49 3.02
66 67 1.926511 CTTTGATGCTCACCGCCACC 61.927 60.000 0.00 0.00 38.05 4.61
71 72 0.169672 CTTGCCTTTGATGCTCACCG 59.830 55.000 0.00 0.00 0.00 4.94
74 75 3.014623 CAGATCTTGCCTTTGATGCTCA 58.985 45.455 0.00 0.00 0.00 4.26
83 84 1.833630 TCATCGTCCAGATCTTGCCTT 59.166 47.619 0.00 0.00 37.52 4.35
92 93 2.348104 CCGGTGGTCATCGTCCAGA 61.348 63.158 2.89 0.00 35.49 3.86
93 94 2.184322 CCGGTGGTCATCGTCCAG 59.816 66.667 2.89 0.00 35.49 3.86
111 112 0.678048 GTGCCTGAGGGGTGATGAAC 60.678 60.000 0.00 0.00 37.43 3.18
120 121 1.340308 TGATGAATGTGTGCCTGAGGG 60.340 52.381 0.00 0.00 0.00 4.30
121 122 2.118313 TGATGAATGTGTGCCTGAGG 57.882 50.000 0.00 0.00 0.00 3.86
122 123 3.181490 CCATTGATGAATGTGTGCCTGAG 60.181 47.826 4.14 0.00 37.82 3.35
123 124 2.756207 CCATTGATGAATGTGTGCCTGA 59.244 45.455 4.14 0.00 37.82 3.86
124 125 2.737359 GCCATTGATGAATGTGTGCCTG 60.737 50.000 4.14 0.00 37.82 4.85
125 126 1.479323 GCCATTGATGAATGTGTGCCT 59.521 47.619 4.14 0.00 37.82 4.75
126 127 1.799917 CGCCATTGATGAATGTGTGCC 60.800 52.381 4.14 0.00 37.82 5.01
127 128 1.552226 CGCCATTGATGAATGTGTGC 58.448 50.000 4.14 0.00 37.82 4.57
128 129 1.799917 GCCGCCATTGATGAATGTGTG 60.800 52.381 4.14 2.77 37.82 3.82
129 130 0.457035 GCCGCCATTGATGAATGTGT 59.543 50.000 4.14 0.00 37.82 3.72
130 131 0.456628 TGCCGCCATTGATGAATGTG 59.543 50.000 4.14 0.00 37.82 3.21
131 132 1.135527 CTTGCCGCCATTGATGAATGT 59.864 47.619 4.14 0.00 37.82 2.71
132 133 1.537348 CCTTGCCGCCATTGATGAATG 60.537 52.381 0.00 0.00 39.04 2.67
133 134 0.748450 CCTTGCCGCCATTGATGAAT 59.252 50.000 0.00 0.00 0.00 2.57
137 138 3.149648 GCCCTTGCCGCCATTGAT 61.150 61.111 0.00 0.00 0.00 2.57
153 154 1.404391 CAATGCCATCAGGAACAGAGC 59.596 52.381 0.00 0.00 36.89 4.09
155 156 3.657398 ATCAATGCCATCAGGAACAGA 57.343 42.857 0.00 0.00 36.89 3.41
157 158 4.096231 CGTAAATCAATGCCATCAGGAACA 59.904 41.667 0.00 0.00 36.89 3.18
160 161 2.618241 GCGTAAATCAATGCCATCAGGA 59.382 45.455 0.00 0.00 36.89 3.86
172 173 7.518211 CGAGAATGGTAATCAATGCGTAAATCA 60.518 37.037 0.00 0.00 0.00 2.57
176 177 4.025229 GCGAGAATGGTAATCAATGCGTAA 60.025 41.667 0.00 0.00 0.00 3.18
208 209 8.347004 TGTGTGAATGGTATAATCAATGTGTT 57.653 30.769 0.00 0.00 0.00 3.32
247 248 4.282703 ACCAAAGCCTAAAACTCTAGTCGA 59.717 41.667 0.00 0.00 0.00 4.20
248 249 4.566987 ACCAAAGCCTAAAACTCTAGTCG 58.433 43.478 0.00 0.00 0.00 4.18
250 251 6.362248 TCAAACCAAAGCCTAAAACTCTAGT 58.638 36.000 0.00 0.00 0.00 2.57
253 254 5.299531 GTCTCAAACCAAAGCCTAAAACTCT 59.700 40.000 0.00 0.00 0.00 3.24
269 270 9.774742 CTAAATATGCTTTGTTAGGTCTCAAAC 57.225 33.333 0.00 0.00 31.59 2.93
288 289 7.352522 TCCACCCCTCAAATCCTAACTAAATAT 59.647 37.037 0.00 0.00 0.00 1.28
293 294 4.037927 CTCCACCCCTCAAATCCTAACTA 58.962 47.826 0.00 0.00 0.00 2.24
304 305 2.365635 GCTAGGCTCCACCCCTCA 60.366 66.667 0.00 0.00 40.58 3.86
327 328 3.437795 CAAGCGCCTCCAAGCTGG 61.438 66.667 2.29 0.00 43.78 4.85
328 329 3.437795 CCAAGCGCCTCCAAGCTG 61.438 66.667 2.29 0.00 43.78 4.24
329 330 3.618780 CTCCAAGCGCCTCCAAGCT 62.619 63.158 2.29 0.00 46.97 3.74
331 332 3.130160 GCTCCAAGCGCCTCCAAG 61.130 66.667 2.29 0.00 0.00 3.61
340 341 4.858680 GGCTACCCCGCTCCAAGC 62.859 72.222 0.00 0.00 38.02 4.01
356 357 0.520404 GAGCAATGATAGCCATGCGG 59.480 55.000 0.24 0.00 35.72 5.69
357 358 0.520404 GGAGCAATGATAGCCATGCG 59.480 55.000 0.24 0.00 35.72 4.73
358 359 1.906990 AGGAGCAATGATAGCCATGC 58.093 50.000 0.00 0.00 35.24 4.06
359 360 2.030185 GCAAGGAGCAATGATAGCCATG 60.030 50.000 0.00 0.00 44.79 3.66
361 362 1.683943 GCAAGGAGCAATGATAGCCA 58.316 50.000 0.00 0.00 44.79 4.75
372 373 4.864806 GCCTAAAACTTTAATGCAAGGAGC 59.135 41.667 0.00 0.00 45.96 4.70
374 375 6.664428 AAGCCTAAAACTTTAATGCAAGGA 57.336 33.333 0.00 0.00 0.00 3.36
375 376 6.147656 CCAAAGCCTAAAACTTTAATGCAAGG 59.852 38.462 0.00 0.00 35.62 3.61
376 377 6.705825 ACCAAAGCCTAAAACTTTAATGCAAG 59.294 34.615 0.00 0.00 35.62 4.01
377 378 6.587273 ACCAAAGCCTAAAACTTTAATGCAA 58.413 32.000 0.00 0.00 35.62 4.08
378 379 6.168270 ACCAAAGCCTAAAACTTTAATGCA 57.832 33.333 0.00 0.00 35.62 3.96
379 380 7.225734 TCAAACCAAAGCCTAAAACTTTAATGC 59.774 33.333 0.00 0.00 35.62 3.56
380 381 8.655651 TCAAACCAAAGCCTAAAACTTTAATG 57.344 30.769 0.00 0.00 35.62 1.90
381 382 8.700973 TCTCAAACCAAAGCCTAAAACTTTAAT 58.299 29.630 0.00 0.00 35.62 1.40
382 383 7.977293 GTCTCAAACCAAAGCCTAAAACTTTAA 59.023 33.333 0.00 0.00 35.62 1.52
383 384 7.485810 GTCTCAAACCAAAGCCTAAAACTTTA 58.514 34.615 0.00 0.00 35.62 1.85
386 387 5.515797 GTCTCAAACCAAAGCCTAAAACT 57.484 39.130 0.00 0.00 0.00 2.66
414 415 9.136323 CCCTCAAATCCTAACTAAATATGCTTT 57.864 33.333 0.00 0.00 0.00 3.51
415 416 7.725844 CCCCTCAAATCCTAACTAAATATGCTT 59.274 37.037 0.00 0.00 0.00 3.91
416 417 7.147123 ACCCCTCAAATCCTAACTAAATATGCT 60.147 37.037 0.00 0.00 0.00 3.79
417 418 7.004691 ACCCCTCAAATCCTAACTAAATATGC 58.995 38.462 0.00 0.00 0.00 3.14
418 419 7.448469 CCACCCCTCAAATCCTAACTAAATATG 59.552 40.741 0.00 0.00 0.00 1.78
419 420 7.352522 TCCACCCCTCAAATCCTAACTAAATAT 59.647 37.037 0.00 0.00 0.00 1.28
420 421 6.679303 TCCACCCCTCAAATCCTAACTAAATA 59.321 38.462 0.00 0.00 0.00 1.40
421 422 5.494706 TCCACCCCTCAAATCCTAACTAAAT 59.505 40.000 0.00 0.00 0.00 1.40
422 423 4.853276 TCCACCCCTCAAATCCTAACTAAA 59.147 41.667 0.00 0.00 0.00 1.85
423 424 4.440808 TCCACCCCTCAAATCCTAACTAA 58.559 43.478 0.00 0.00 0.00 2.24
424 425 4.037927 CTCCACCCCTCAAATCCTAACTA 58.962 47.826 0.00 0.00 0.00 2.24
425 426 2.846827 CTCCACCCCTCAAATCCTAACT 59.153 50.000 0.00 0.00 0.00 2.24
426 427 2.684038 GCTCCACCCCTCAAATCCTAAC 60.684 54.545 0.00 0.00 0.00 2.34
427 428 1.564348 GCTCCACCCCTCAAATCCTAA 59.436 52.381 0.00 0.00 0.00 2.69
428 429 1.213296 GCTCCACCCCTCAAATCCTA 58.787 55.000 0.00 0.00 0.00 2.94
429 430 1.575447 GGCTCCACCCCTCAAATCCT 61.575 60.000 0.00 0.00 0.00 3.24
430 431 1.076705 GGCTCCACCCCTCAAATCC 60.077 63.158 0.00 0.00 0.00 3.01
431 432 1.141858 CTAGGCTCCACCCCTCAAATC 59.858 57.143 0.00 0.00 40.58 2.17
432 433 1.216990 CTAGGCTCCACCCCTCAAAT 58.783 55.000 0.00 0.00 40.58 2.32
433 434 1.562672 GCTAGGCTCCACCCCTCAAA 61.563 60.000 0.00 0.00 40.58 2.69
434 435 1.995626 GCTAGGCTCCACCCCTCAA 60.996 63.158 0.00 0.00 40.58 3.02
435 436 2.365635 GCTAGGCTCCACCCCTCA 60.366 66.667 0.00 0.00 40.58 3.86
436 437 3.164977 GGCTAGGCTCCACCCCTC 61.165 72.222 9.46 0.00 40.58 4.30
459 460 3.437795 CCAAGCGCCTCCAAGCTG 61.438 66.667 2.29 0.00 43.78 4.24
471 472 4.858680 GGCTACCCCGCTCCAAGC 62.859 72.222 0.00 0.00 38.02 4.01
489 490 3.613432 GCAAGGAGCAATTATAGCCATGC 60.613 47.826 0.00 0.00 44.79 4.06
490 491 4.170292 GCAAGGAGCAATTATAGCCATG 57.830 45.455 0.00 0.00 44.79 3.66
503 504 3.302740 CGATCGACTTTAATGCAAGGAGC 60.303 47.826 10.26 0.00 45.96 4.70
515 741 5.039333 CGGTTCCTAAATACGATCGACTTT 58.961 41.667 24.34 20.59 0.00 2.66
516 742 4.336433 TCGGTTCCTAAATACGATCGACTT 59.664 41.667 24.34 13.46 0.00 3.01
517 743 3.879295 TCGGTTCCTAAATACGATCGACT 59.121 43.478 24.34 5.14 0.00 4.18
518 744 4.214980 TCGGTTCCTAAATACGATCGAC 57.785 45.455 24.34 5.64 0.00 4.20
525 751 5.859205 TTACTCCCTCGGTTCCTAAATAC 57.141 43.478 0.00 0.00 0.00 1.89
526 752 6.872585 TTTTACTCCCTCGGTTCCTAAATA 57.127 37.500 0.00 0.00 0.00 1.40
527 753 5.767277 TTTTACTCCCTCGGTTCCTAAAT 57.233 39.130 0.00 0.00 0.00 1.40
528 754 5.307716 TCTTTTTACTCCCTCGGTTCCTAAA 59.692 40.000 0.00 0.00 0.00 1.85
529 755 4.840115 TCTTTTTACTCCCTCGGTTCCTAA 59.160 41.667 0.00 0.00 0.00 2.69
530 756 4.419282 TCTTTTTACTCCCTCGGTTCCTA 58.581 43.478 0.00 0.00 0.00 2.94
532 758 3.690475 TCTTTTTACTCCCTCGGTTCC 57.310 47.619 0.00 0.00 0.00 3.62
537 763 5.181433 CCCTTTCTTTCTTTTTACTCCCTCG 59.819 44.000 0.00 0.00 0.00 4.63
538 764 6.304624 TCCCTTTCTTTCTTTTTACTCCCTC 58.695 40.000 0.00 0.00 0.00 4.30
555 781 8.850007 AAGAAGAAAACATACTACTCCCTTTC 57.150 34.615 0.00 0.00 0.00 2.62
556 782 8.661345 AGAAGAAGAAAACATACTACTCCCTTT 58.339 33.333 0.00 0.00 0.00 3.11
638 866 1.751927 CTGGGAGATGCTGTTGCCC 60.752 63.158 0.00 0.00 38.71 5.36
640 868 1.246056 TTGCTGGGAGATGCTGTTGC 61.246 55.000 0.00 0.00 40.20 4.17
641 869 0.809385 CTTGCTGGGAGATGCTGTTG 59.191 55.000 0.00 0.00 0.00 3.33
642 870 0.403271 ACTTGCTGGGAGATGCTGTT 59.597 50.000 0.00 0.00 0.00 3.16
643 871 0.403271 AACTTGCTGGGAGATGCTGT 59.597 50.000 0.00 0.00 0.00 4.40
644 872 1.093159 GAACTTGCTGGGAGATGCTG 58.907 55.000 0.00 0.00 0.00 4.41
645 873 0.392193 CGAACTTGCTGGGAGATGCT 60.392 55.000 0.00 0.00 0.00 3.79
699 933 2.689034 AAGGAGGAGCGAAGGGGG 60.689 66.667 0.00 0.00 0.00 5.40
706 940 3.787001 GGTGGGGAAGGAGGAGCG 61.787 72.222 0.00 0.00 0.00 5.03
963 1197 4.277921 CACTCTAACCCTAACCCTATCGAC 59.722 50.000 0.00 0.00 0.00 4.20
985 1219 2.367377 CATCTCAGCCCCTCCCCA 60.367 66.667 0.00 0.00 0.00 4.96
1184 1418 1.570813 TCCACTGCGCAATAGAATCG 58.429 50.000 13.05 0.00 0.00 3.34
1222 1493 1.341209 TCGTCTCATCACAAGCACACT 59.659 47.619 0.00 0.00 0.00 3.55
1302 1636 7.864686 TCAATCGCAATGAGATAACTAAATGG 58.135 34.615 0.00 0.00 0.00 3.16
1318 1655 5.335583 CCTTTAACTGGACAATCAATCGCAA 60.336 40.000 0.00 0.00 0.00 4.85
1463 1815 3.737263 ACTAGCTTCCACCCTTCCTATT 58.263 45.455 0.00 0.00 0.00 1.73
1466 1818 2.627217 CCTACTAGCTTCCACCCTTCCT 60.627 54.545 0.00 0.00 0.00 3.36
1467 1819 1.763545 CCTACTAGCTTCCACCCTTCC 59.236 57.143 0.00 0.00 0.00 3.46
1468 1820 1.763545 CCCTACTAGCTTCCACCCTTC 59.236 57.143 0.00 0.00 0.00 3.46
1469 1821 1.365028 TCCCTACTAGCTTCCACCCTT 59.635 52.381 0.00 0.00 0.00 3.95
1470 1822 1.016415 TCCCTACTAGCTTCCACCCT 58.984 55.000 0.00 0.00 0.00 4.34
1471 1823 2.104669 ATCCCTACTAGCTTCCACCC 57.895 55.000 0.00 0.00 0.00 4.61
1472 1824 4.020128 CCATAATCCCTACTAGCTTCCACC 60.020 50.000 0.00 0.00 0.00 4.61
1473 1825 4.593634 ACCATAATCCCTACTAGCTTCCAC 59.406 45.833 0.00 0.00 0.00 4.02
1474 1826 4.827789 ACCATAATCCCTACTAGCTTCCA 58.172 43.478 0.00 0.00 0.00 3.53
1475 1827 5.827326 AACCATAATCCCTACTAGCTTCC 57.173 43.478 0.00 0.00 0.00 3.46
1476 1828 6.497606 AGGTAACCATAATCCCTACTAGCTTC 59.502 42.308 0.00 0.00 37.17 3.86
1583 1948 4.569719 ATCTCGTAACATTCCACCCTTT 57.430 40.909 0.00 0.00 0.00 3.11
1743 2108 6.648310 CACAACTAGAACAAGAGTGACATGAT 59.352 38.462 0.00 0.00 31.99 2.45
1820 2185 0.035317 CTTGACTAGCAGTGTGGCCA 59.965 55.000 0.00 0.00 0.00 5.36
1924 2289 6.763610 AGGCGATCCAAACTAATTCTTTAGAG 59.236 38.462 0.03 0.00 35.54 2.43
1926 2291 6.927294 AGGCGATCCAAACTAATTCTTTAG 57.073 37.500 0.00 0.00 36.84 1.85
2174 2897 7.775093 TCCTCATAGGTCCATGTTCATTTTTAG 59.225 37.037 0.00 0.00 36.53 1.85
2479 3334 9.182214 AGAAGATACATGCATTTACATTCACTT 57.818 29.630 15.77 7.36 0.00 3.16
2480 3335 8.743085 AGAAGATACATGCATTTACATTCACT 57.257 30.769 15.77 4.81 0.00 3.41
2490 3345 8.982685 CGTGTAAATCTAGAAGATACATGCATT 58.017 33.333 16.02 0.00 32.89 3.56
2491 3346 8.360390 TCGTGTAAATCTAGAAGATACATGCAT 58.640 33.333 19.97 0.00 33.41 3.96
2492 3347 7.712797 TCGTGTAAATCTAGAAGATACATGCA 58.287 34.615 19.97 0.00 33.41 3.96
2493 3348 8.575565 TTCGTGTAAATCTAGAAGATACATGC 57.424 34.615 19.97 9.73 33.41 4.06
2947 4149 3.319137 TCATACGCTGAAAAGTCTGCT 57.681 42.857 4.44 0.00 44.29 4.24
3063 4322 9.683069 ACAGAAGCATTACACAGAAAATAAAAG 57.317 29.630 0.00 0.00 0.00 2.27
3101 4361 2.563976 CAAAACGACTGAGCGAACATG 58.436 47.619 3.50 0.00 34.83 3.21
3273 4536 1.406751 CGATAGCACCATCAACACCCA 60.407 52.381 0.00 0.00 0.00 4.51
3306 4570 1.533753 CACCACACAATGCCCCCTT 60.534 57.895 0.00 0.00 0.00 3.95
3315 4579 4.885270 CCCGCCACCACCACACAA 62.885 66.667 0.00 0.00 0.00 3.33
3482 4825 7.639113 TGGCTATAAGTGGAATTTGGTTAAG 57.361 36.000 0.00 0.00 0.00 1.85
3523 4866 5.648092 GTGGACAAGACTACCAAATTAGCAT 59.352 40.000 0.00 0.00 35.40 3.79
3690 5040 9.950680 ATATATACTTGCAACGGAAGAAATTTG 57.049 29.630 0.00 0.00 0.00 2.32
3709 5059 9.167311 CCCTGGTTTTGCATCTAGAATATATAC 57.833 37.037 0.00 0.00 0.00 1.47
4055 5511 7.013834 ACCAACATTAGGAACAAAAAGGGATA 58.986 34.615 0.00 0.00 0.00 2.59
4195 5928 8.884726 ACAACAATTGGGTAAAACATGTAAAAC 58.115 29.630 10.83 0.00 34.12 2.43
4210 6033 3.367703 GCTCATGGAAGACAACAATTGGG 60.368 47.826 10.83 4.09 34.12 4.12
4513 6344 2.273370 TTCGAGACGGACAATGCTAC 57.727 50.000 0.00 0.00 0.00 3.58
4738 6571 3.853475 AGGTTTGTACGTAAGGAATCGG 58.147 45.455 0.00 0.00 46.39 4.18
4956 6792 1.406898 TGCAAACCACGCTGATTGAAA 59.593 42.857 0.00 0.00 0.00 2.69
5018 6854 7.856145 AGCTACAGATAAGATGAAACCAAAG 57.144 36.000 0.00 0.00 0.00 2.77
5064 6900 8.783093 TCAGTTTCATGGTCTTAATTGTAACTG 58.217 33.333 12.29 12.29 43.23 3.16
5146 6982 4.202050 ACAAGTGAAACAAGAATGACCAGC 60.202 41.667 0.00 0.00 41.43 4.85
5162 6998 7.279615 TCCTTTTCAGAGTTAATGACAAGTGA 58.720 34.615 3.86 0.05 34.23 3.41
5245 7081 7.116805 CCAATGTTCCTTTTCAACTGCTTTATC 59.883 37.037 0.00 0.00 0.00 1.75
5321 7410 8.321353 TGATGAGTGAAAATAGTACTCCAACAT 58.679 33.333 0.00 1.84 39.98 2.71
5323 7412 8.723942 ATGATGAGTGAAAATAGTACTCCAAC 57.276 34.615 0.00 0.00 39.98 3.77
5378 7506 8.341903 TGCAACATAAATACCATCAAATAGTCG 58.658 33.333 0.00 0.00 0.00 4.18
5478 7619 4.463539 TCAGCATGGCAAAGTGTAATTGAT 59.536 37.500 0.00 0.00 36.16 2.57
5506 7647 2.518949 CACAATACAACAATGCTCGGC 58.481 47.619 0.00 0.00 0.00 5.54
5512 7653 4.300803 ACAAGCTGCACAATACAACAATG 58.699 39.130 1.02 0.00 0.00 2.82
5531 7674 3.505386 ACCATGATGCCCTTTGTTACAA 58.495 40.909 0.00 0.00 0.00 2.41
5585 7728 1.412710 GACCCTGAGGCGTATGATTCA 59.587 52.381 0.00 0.00 36.11 2.57
5667 7810 4.431416 TGGGCTTACCATTTGTATCGAT 57.569 40.909 2.16 2.16 46.80 3.59
5720 7863 2.657297 GGCAATGTGGAAGCCTTCA 58.343 52.632 6.80 0.00 44.92 3.02
5947 8092 8.860088 ACAAAATGTTCTACTCTTGGCTTATTT 58.140 29.630 0.00 0.00 0.00 1.40
6050 8195 6.757010 ACCATTTCGTCTATCATAGTCAACAC 59.243 38.462 0.00 0.00 0.00 3.32
6058 8203 7.915293 AAACAACACCATTTCGTCTATCATA 57.085 32.000 0.00 0.00 0.00 2.15
6122 8267 0.957395 CAGTGGCGCTGGAAATGTCT 60.957 55.000 20.17 0.00 41.42 3.41
6125 8270 2.180017 GCAGTGGCGCTGGAAATG 59.820 61.111 27.70 4.27 45.14 2.32
6136 8281 2.281070 AGCAACACGAGGCAGTGG 60.281 61.111 15.64 2.57 45.80 4.00
6152 8297 5.805994 GCAGTTTACTACTACTAGTTGCCAG 59.194 44.000 0.00 2.87 34.56 4.85
6204 8349 0.385098 GTCGGCAACAAAGTAACGCC 60.385 55.000 0.00 0.00 39.45 5.68
6207 8352 0.939419 ACGGTCGGCAACAAAGTAAC 59.061 50.000 0.00 0.00 0.00 2.50
6227 8372 4.049869 GCGCACTTCTAGGGTATCTAAAC 58.950 47.826 0.30 0.00 0.00 2.01
6229 8374 3.293337 TGCGCACTTCTAGGGTATCTAA 58.707 45.455 5.66 0.00 0.00 2.10
6230 8375 2.940158 TGCGCACTTCTAGGGTATCTA 58.060 47.619 5.66 0.00 0.00 1.98
6232 8377 2.821991 ATGCGCACTTCTAGGGTATC 57.178 50.000 14.90 0.00 0.00 2.24
6233 8378 3.832490 TGATATGCGCACTTCTAGGGTAT 59.168 43.478 14.90 2.56 0.00 2.73
6234 8379 3.227614 TGATATGCGCACTTCTAGGGTA 58.772 45.455 14.90 0.00 0.00 3.69
6235 8380 2.039418 TGATATGCGCACTTCTAGGGT 58.961 47.619 14.90 0.00 0.00 4.34
6289 8435 3.376540 GGCGAGCTCAGTAAGAATGTAG 58.623 50.000 15.40 0.00 0.00 2.74
6301 8447 4.700365 CGTGTGACGGCGAGCTCA 62.700 66.667 16.62 3.73 38.08 4.26
6311 8457 5.408604 AGTTGGTTAATTCATCTCGTGTGAC 59.591 40.000 0.00 0.00 0.00 3.67
6321 8467 4.273318 GAGGGAGCAGTTGGTTAATTCAT 58.727 43.478 0.00 0.00 0.00 2.57
6323 8469 3.017442 GGAGGGAGCAGTTGGTTAATTC 58.983 50.000 0.00 0.00 0.00 2.17
6324 8470 2.649816 AGGAGGGAGCAGTTGGTTAATT 59.350 45.455 0.00 0.00 0.00 1.40
6326 8472 1.742308 AGGAGGGAGCAGTTGGTTAA 58.258 50.000 0.00 0.00 0.00 2.01
6327 8473 1.628846 GAAGGAGGGAGCAGTTGGTTA 59.371 52.381 0.00 0.00 0.00 2.85
6367 8519 3.997021 CTGACTTCAACTACCCATGTGTC 59.003 47.826 0.00 0.00 0.00 3.67
6412 8564 4.401519 TGCTAGTAAATCAACGAGTAGCCT 59.598 41.667 5.71 0.00 40.10 4.58
6413 8565 4.679662 TGCTAGTAAATCAACGAGTAGCC 58.320 43.478 5.71 0.00 40.10 3.93
6414 8566 4.740695 CCTGCTAGTAAATCAACGAGTAGC 59.259 45.833 0.00 0.00 40.86 3.58
6415 8567 5.892568 ACCTGCTAGTAAATCAACGAGTAG 58.107 41.667 0.00 0.00 35.58 2.57
6416 8568 5.651139 AGACCTGCTAGTAAATCAACGAGTA 59.349 40.000 0.00 0.00 0.00 2.59
6417 8569 4.463186 AGACCTGCTAGTAAATCAACGAGT 59.537 41.667 0.00 0.00 0.00 4.18
6418 8570 5.000012 AGACCTGCTAGTAAATCAACGAG 58.000 43.478 0.00 0.00 0.00 4.18
6420 8572 4.567159 GGAAGACCTGCTAGTAAATCAACG 59.433 45.833 0.00 0.00 0.00 4.10
6421 8573 5.488341 TGGAAGACCTGCTAGTAAATCAAC 58.512 41.667 0.00 0.00 37.04 3.18
6422 8574 5.755409 TGGAAGACCTGCTAGTAAATCAA 57.245 39.130 0.00 0.00 37.04 2.57
6424 8576 7.604545 GGAATATGGAAGACCTGCTAGTAAATC 59.395 40.741 0.00 0.00 37.04 2.17
6425 8577 7.072454 TGGAATATGGAAGACCTGCTAGTAAAT 59.928 37.037 0.00 0.00 37.04 1.40
6426 8578 6.385759 TGGAATATGGAAGACCTGCTAGTAAA 59.614 38.462 0.00 0.00 37.04 2.01
6427 8579 5.903010 TGGAATATGGAAGACCTGCTAGTAA 59.097 40.000 0.00 0.00 37.04 2.24
6428 8580 5.464069 TGGAATATGGAAGACCTGCTAGTA 58.536 41.667 0.00 0.00 37.04 1.82
6429 8581 4.298626 TGGAATATGGAAGACCTGCTAGT 58.701 43.478 0.00 0.00 37.04 2.57
6430 8582 4.963318 TGGAATATGGAAGACCTGCTAG 57.037 45.455 0.00 0.00 37.04 3.42
6431 8583 5.132648 ACATTGGAATATGGAAGACCTGCTA 59.867 40.000 0.00 0.00 37.04 3.49
6432 8584 4.079558 ACATTGGAATATGGAAGACCTGCT 60.080 41.667 0.00 0.00 37.04 4.24
6433 8585 4.037208 CACATTGGAATATGGAAGACCTGC 59.963 45.833 0.00 0.00 37.04 4.85
6434 8586 5.439721 TCACATTGGAATATGGAAGACCTG 58.560 41.667 0.00 0.00 37.04 4.00
6595 8747 1.959226 CCGTCCTTTGTGTCCACGG 60.959 63.158 0.00 0.00 43.71 4.94
6637 8789 2.669569 GCAAGTTGCGAGCAGGGA 60.670 61.111 12.95 0.00 31.71 4.20


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

AutoCloner maintained by Alex Coulton.