Multiple sequence alignment - TraesCS5A01G411200

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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 TraesCS5A01G411200 chr5A 100.000 7292 0 0 1 7292 599815381 599808090 0.000000e+00 13466
1 TraesCS5A01G411200 chr5A 91.871 1267 83 7 3609 4864 93198055 93199312 0.000000e+00 1751
2 TraesCS5A01G411200 chr5A 98.333 60 1 0 7233 7292 673519158 673519217 1.000000e-18 106
3 TraesCS5A01G411200 chr5D 94.365 2715 118 22 3960 6661 480712185 480709493 0.000000e+00 4133
4 TraesCS5A01G411200 chr5D 88.948 1882 115 45 4 1857 480715947 480714131 0.000000e+00 2237
5 TraesCS5A01G411200 chr5D 95.135 966 42 5 2726 3687 480713153 480712189 0.000000e+00 1519
6 TraesCS5A01G411200 chr5D 92.760 884 56 8 2753 3633 494070941 494070063 0.000000e+00 1271
7 TraesCS5A01G411200 chr5D 91.882 850 61 8 2787 3633 493897475 493898319 0.000000e+00 1181
8 TraesCS5A01G411200 chr5D 91.212 330 19 4 2421 2742 480713494 480713167 2.410000e-119 440
9 TraesCS5A01G411200 chr5D 88.525 366 32 7 6878 7237 480708046 480707685 1.120000e-117 435
10 TraesCS5A01G411200 chr5D 94.203 207 10 2 6680 6885 480709435 480709230 1.530000e-81 315
11 TraesCS5A01G411200 chr5B 93.973 2688 108 25 3908 6561 589125903 589123236 0.000000e+00 4017
12 TraesCS5A01G411200 chr5B 93.106 1494 69 18 2421 3900 589127442 589125969 0.000000e+00 2158
13 TraesCS5A01G411200 chr5B 89.982 1697 91 40 4 1669 589129851 589128203 0.000000e+00 2119
14 TraesCS5A01G411200 chr5B 89.286 784 39 11 1724 2479 589128209 589127443 0.000000e+00 941
15 TraesCS5A01G411200 chr5B 87.435 191 19 4 926 1112 687949959 687949770 1.590000e-51 215
16 TraesCS5A01G411200 chr3A 91.713 1267 86 7 3609 4864 606013838 606015096 0.000000e+00 1740
17 TraesCS5A01G411200 chr3D 89.103 780 45 16 1719 2471 21935812 21936578 0.000000e+00 933
18 TraesCS5A01G411200 chr3D 100.000 56 0 0 7237 7292 609880368 609880313 3.600000e-18 104
19 TraesCS5A01G411200 chr1D 88.847 789 47 16 1719 2479 66759320 66760095 0.000000e+00 931
20 TraesCS5A01G411200 chrUn 88.086 789 53 23 1719 2479 93958142 93958917 0.000000e+00 898
21 TraesCS5A01G411200 chrUn 89.960 249 17 6 4624 4864 478806836 478807084 1.530000e-81 315
22 TraesCS5A01G411200 chrUn 91.005 189 14 3 926 1112 93957292 93957479 1.210000e-62 252
23 TraesCS5A01G411200 chr7D 87.563 788 50 20 1719 2479 568457988 568458754 0.000000e+00 869
24 TraesCS5A01G411200 chr7D 83.150 273 37 9 2928 3195 194692625 194692357 2.630000e-59 241
25 TraesCS5A01G411200 chr7D 100.000 59 0 0 7234 7292 450262530 450262472 7.730000e-20 110
26 TraesCS5A01G411200 chr2A 87.056 788 62 17 1719 2479 268560307 268559533 0.000000e+00 854
27 TraesCS5A01G411200 chr2A 77.264 1016 153 53 4560 5558 389435004 389435958 6.480000e-145 525
28 TraesCS5A01G411200 chr2A 87.222 180 19 4 926 1103 268561165 268560988 1.240000e-47 202
29 TraesCS5A01G411200 chr2A 86.061 165 20 2 1472 1633 389430775 389430939 2.700000e-39 174
30 TraesCS5A01G411200 chr2A 90.816 98 9 0 2957 3054 389432270 389432367 1.650000e-26 132
31 TraesCS5A01G411200 chr2A 98.361 61 0 1 7232 7292 502275683 502275624 1.000000e-18 106
32 TraesCS5A01G411200 chr7A 87.113 776 67 20 1719 2479 727858905 727859662 0.000000e+00 848
33 TraesCS5A01G411200 chr7A 92.647 68 5 0 7225 7292 33004325 33004392 1.670000e-16 99
34 TraesCS5A01G411200 chr7B 91.257 549 32 8 1934 2479 123397817 123398352 0.000000e+00 734
35 TraesCS5A01G411200 chr7B 88.180 533 44 13 2825 3341 740536722 740537251 1.040000e-172 617
36 TraesCS5A01G411200 chr7B 89.831 177 17 1 3150 3325 740538939 740539115 7.360000e-55 226
37 TraesCS5A01G411200 chr7B 88.827 179 16 3 937 1112 123385474 123385651 4.430000e-52 217
38 TraesCS5A01G411200 chr7B 91.791 134 10 1 1719 1851 123386304 123386437 1.250000e-42 185
39 TraesCS5A01G411200 chr2B 91.020 490 28 8 1993 2479 398111910 398112386 0.000000e+00 647
40 TraesCS5A01G411200 chr2B 90.984 488 28 9 1993 2479 71029553 71030025 1.710000e-180 643
41 TraesCS5A01G411200 chr2B 85.128 195 28 1 5377 5570 359621992 359621798 1.600000e-46 198
42 TraesCS5A01G411200 chr2B 85.455 165 21 3 1472 1633 359637743 359637579 1.260000e-37 169
43 TraesCS5A01G411200 chr2D 77.555 998 150 48 4560 5543 308475580 308476517 1.080000e-147 534
44 TraesCS5A01G411200 chr2D 86.061 165 20 2 1472 1633 308471300 308471464 2.700000e-39 174
45 TraesCS5A01G411200 chr2D 90.816 98 9 0 2957 3054 308472781 308472878 1.650000e-26 132
46 TraesCS5A01G411200 chr1A 90.052 191 14 4 926 1112 425126389 425126578 7.310000e-60 243
47 TraesCS5A01G411200 chr1B 87.766 188 13 8 926 1103 542805898 542806085 2.060000e-50 211
48 TraesCS5A01G411200 chr1B 89.143 175 10 6 926 1093 513972052 513972224 7.410000e-50 209
49 TraesCS5A01G411200 chr6A 95.385 65 3 0 7228 7292 114245803 114245867 3.600000e-18 104
50 TraesCS5A01G411200 chr4B 98.305 59 1 0 7234 7292 10429573 10429631 3.600000e-18 104
51 TraesCS5A01G411200 chr3B 100.000 56 0 0 7237 7292 754153275 754153220 3.600000e-18 104
52 TraesCS5A01G411200 chr3B 90.789 76 3 3 7218 7292 788206468 788206396 1.670000e-16 99


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 TraesCS5A01G411200 chr5A 599808090 599815381 7291 True 13466.000000 13466 100.000000 1 7292 1 chr5A.!!$R1 7291
1 TraesCS5A01G411200 chr5A 93198055 93199312 1257 False 1751.000000 1751 91.871000 3609 4864 1 chr5A.!!$F1 1255
2 TraesCS5A01G411200 chr5D 480707685 480715947 8262 True 1513.166667 4133 92.064667 4 7237 6 chr5D.!!$R2 7233
3 TraesCS5A01G411200 chr5D 494070063 494070941 878 True 1271.000000 1271 92.760000 2753 3633 1 chr5D.!!$R1 880
4 TraesCS5A01G411200 chr5D 493897475 493898319 844 False 1181.000000 1181 91.882000 2787 3633 1 chr5D.!!$F1 846
5 TraesCS5A01G411200 chr5B 589123236 589129851 6615 True 2308.750000 4017 91.586750 4 6561 4 chr5B.!!$R2 6557
6 TraesCS5A01G411200 chr3A 606013838 606015096 1258 False 1740.000000 1740 91.713000 3609 4864 1 chr3A.!!$F1 1255
7 TraesCS5A01G411200 chr3D 21935812 21936578 766 False 933.000000 933 89.103000 1719 2471 1 chr3D.!!$F1 752
8 TraesCS5A01G411200 chr1D 66759320 66760095 775 False 931.000000 931 88.847000 1719 2479 1 chr1D.!!$F1 760
9 TraesCS5A01G411200 chrUn 93957292 93958917 1625 False 575.000000 898 89.545500 926 2479 2 chrUn.!!$F2 1553
10 TraesCS5A01G411200 chr7D 568457988 568458754 766 False 869.000000 869 87.563000 1719 2479 1 chr7D.!!$F1 760
11 TraesCS5A01G411200 chr2A 268559533 268561165 1632 True 528.000000 854 87.139000 926 2479 2 chr2A.!!$R2 1553
12 TraesCS5A01G411200 chr2A 389430775 389435958 5183 False 277.000000 525 84.713667 1472 5558 3 chr2A.!!$F1 4086
13 TraesCS5A01G411200 chr7A 727858905 727859662 757 False 848.000000 848 87.113000 1719 2479 1 chr7A.!!$F2 760
14 TraesCS5A01G411200 chr7B 123397817 123398352 535 False 734.000000 734 91.257000 1934 2479 1 chr7B.!!$F1 545
15 TraesCS5A01G411200 chr7B 740536722 740539115 2393 False 421.500000 617 89.005500 2825 3341 2 chr7B.!!$F3 516
16 TraesCS5A01G411200 chr7B 123385474 123386437 963 False 201.000000 217 90.309000 937 1851 2 chr7B.!!$F2 914
17 TraesCS5A01G411200 chr2D 308471300 308476517 5217 False 280.000000 534 84.810667 1472 5543 3 chr2D.!!$F1 4071

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
503 516 0.249155 CCGCATGCCAAACCATCATC 60.249 55.000 13.15 0.00 0.00 2.92 F
1242 1357 0.111704 CTCGTCGTGTTTGAAGTGCG 60.112 55.000 0.00 0.00 0.00 5.34 F
1756 2196 0.107017 TGCTTAGCTTCCATGGAGCC 60.107 55.000 24.08 15.96 0.00 4.70 F
2789 4249 1.271856 TTCGCACTACCAAGGGATCA 58.728 50.000 0.00 0.00 0.00 2.92 F
3060 4640 4.092968 GTGATTGGCTCGGTAAGTTTACAG 59.907 45.833 4.58 0.74 35.37 2.74 F
4157 8888 0.543749 ACTGCCTGTCTTATCCCTGC 59.456 55.000 0.00 0.00 0.00 4.85 F
5477 10280 1.482593 ACTTCGAAGATCCGCCTCAAT 59.517 47.619 31.08 1.21 35.04 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1584 0.108615 ACGCTCCAATCAGAACGAGG 60.109 55.000 0.00 0.00 0.00 4.63 R
3116 4697 2.358322 TCAAAGTCCAGGGGTCAAAC 57.642 50.000 0.00 0.00 0.00 2.93 R
3289 6821 3.251479 CCAAAATCTAAGCTTTGGCCC 57.749 47.619 3.20 0.00 43.70 5.80 R
3763 8351 3.944650 TCTACAGCAACTGAACAAGCAAA 59.055 39.130 0.78 0.00 35.18 3.68 R
4737 9532 4.516698 CAGATCACCGCCTAAAGCATAATT 59.483 41.667 0.00 0.00 44.04 1.40 R
5593 10398 1.699634 ACATGTTCACCACCTACTGCT 59.300 47.619 0.00 0.00 0.00 4.24 R
7271 13349 0.110869 TTTACCCCAAACGGACAGGG 59.889 55.000 1.66 1.66 45.75 4.45 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
89 91 2.194212 GCGGGATCTCACGGAGCTA 61.194 63.158 3.76 0.00 44.19 3.32
95 97 4.208686 CTCACGGAGCTACGCCCC 62.209 72.222 20.78 0.00 37.37 5.80
152 162 5.070770 TGCATCACACAATAAAATGTCCC 57.929 39.130 0.00 0.00 0.00 4.46
190 201 7.458397 ACTTGGTATGAATTGACACCTCTTTA 58.542 34.615 0.00 0.00 32.04 1.85
217 228 3.118992 TGTCACCGAGATGATTCCTTCAG 60.119 47.826 0.00 0.00 37.89 3.02
323 335 7.909777 TCGTTTCTTAAAGCGTAGATAGATG 57.090 36.000 0.00 0.00 39.73 2.90
331 343 4.792521 AGCGTAGATAGATGGATGAACC 57.207 45.455 0.00 0.00 39.54 3.62
362 374 4.106341 TCCCCATGAAGAAAGGAAGAAAGT 59.894 41.667 0.00 0.00 0.00 2.66
363 375 4.460731 CCCCATGAAGAAAGGAAGAAAGTC 59.539 45.833 0.00 0.00 0.00 3.01
364 376 5.072741 CCCATGAAGAAAGGAAGAAAGTCA 58.927 41.667 0.00 0.00 0.00 3.41
382 394 4.432712 AGTCAAACAAGGAACAAACATGC 58.567 39.130 0.00 0.00 0.00 4.06
384 396 3.129462 TCAAACAAGGAACAAACATGCGA 59.871 39.130 0.00 0.00 0.00 5.10
390 402 3.411446 AGGAACAAACATGCGAGAATCA 58.589 40.909 0.00 0.00 33.17 2.57
393 406 5.295292 AGGAACAAACATGCGAGAATCATAG 59.705 40.000 0.00 0.00 33.17 2.23
394 407 5.490139 AACAAACATGCGAGAATCATAGG 57.510 39.130 0.00 0.00 33.17 2.57
395 408 4.517285 ACAAACATGCGAGAATCATAGGT 58.483 39.130 0.00 0.00 33.17 3.08
396 409 4.333649 ACAAACATGCGAGAATCATAGGTG 59.666 41.667 0.00 0.00 33.17 4.00
397 410 2.487934 ACATGCGAGAATCATAGGTGC 58.512 47.619 0.00 0.00 33.17 5.01
398 411 2.103771 ACATGCGAGAATCATAGGTGCT 59.896 45.455 0.00 0.00 33.17 4.40
399 412 2.988010 TGCGAGAATCATAGGTGCTT 57.012 45.000 0.00 0.00 33.17 3.91
400 413 2.554142 TGCGAGAATCATAGGTGCTTG 58.446 47.619 0.00 0.00 33.17 4.01
401 414 1.869767 GCGAGAATCATAGGTGCTTGG 59.130 52.381 0.00 0.00 33.17 3.61
402 415 2.483714 GCGAGAATCATAGGTGCTTGGA 60.484 50.000 0.00 0.00 33.17 3.53
403 416 3.805108 GCGAGAATCATAGGTGCTTGGAT 60.805 47.826 0.00 0.00 33.17 3.41
404 417 4.561530 GCGAGAATCATAGGTGCTTGGATA 60.562 45.833 0.00 0.00 33.17 2.59
405 418 5.728471 CGAGAATCATAGGTGCTTGGATAT 58.272 41.667 0.00 0.00 33.17 1.63
406 419 5.809562 CGAGAATCATAGGTGCTTGGATATC 59.190 44.000 0.00 0.00 33.17 1.63
407 420 5.728471 AGAATCATAGGTGCTTGGATATCG 58.272 41.667 0.00 0.00 0.00 2.92
419 432 2.924903 TGGATATCGTATCGTGTTCGC 58.075 47.619 0.00 0.00 36.96 4.70
423 436 3.613702 CGTATCGTGTTCGCCCGC 61.614 66.667 0.00 0.00 36.96 6.13
449 462 1.098869 ACACATGTGACGTGCCAAAA 58.901 45.000 31.94 0.00 37.93 2.44
450 463 1.474478 ACACATGTGACGTGCCAAAAA 59.526 42.857 31.94 0.00 37.93 1.94
477 490 1.203523 GGAAACCATTTGCATGCCGTA 59.796 47.619 16.68 0.00 0.00 4.02
480 493 1.252175 ACCATTTGCATGCCGTAACA 58.748 45.000 16.68 0.00 0.00 2.41
489 502 2.744709 GCCGTAACACACCCGCAT 60.745 61.111 0.00 0.00 0.00 4.73
493 506 1.969064 GTAACACACCCGCATGCCA 60.969 57.895 13.15 0.00 0.00 4.92
503 516 0.249155 CCGCATGCCAAACCATCATC 60.249 55.000 13.15 0.00 0.00 2.92
533 546 5.874810 TCGCATCAAACTTTTCTAGTGCTAT 59.125 36.000 0.00 0.00 37.12 2.97
534 547 5.961843 CGCATCAAACTTTTCTAGTGCTATG 59.038 40.000 0.00 0.00 37.12 2.23
535 548 6.183360 CGCATCAAACTTTTCTAGTGCTATGA 60.183 38.462 0.00 0.00 37.12 2.15
656 674 3.430895 AGTTTCATAACGCGTGAACGAAT 59.569 39.130 14.98 0.00 39.39 3.34
657 675 4.622313 AGTTTCATAACGCGTGAACGAATA 59.378 37.500 14.98 0.00 39.39 1.75
658 676 5.118971 AGTTTCATAACGCGTGAACGAATAA 59.881 36.000 14.98 0.00 39.39 1.40
659 677 4.488518 TCATAACGCGTGAACGAATAAC 57.511 40.909 14.98 0.00 43.02 1.89
660 678 4.168014 TCATAACGCGTGAACGAATAACT 58.832 39.130 14.98 0.00 43.02 2.24
661 679 2.848562 AACGCGTGAACGAATAACTG 57.151 45.000 14.98 0.00 43.02 3.16
707 725 1.407656 AAAGTCACGACAGCTGGGGA 61.408 55.000 19.93 4.53 0.00 4.81
709 727 1.070786 GTCACGACAGCTGGGGAAA 59.929 57.895 19.93 0.00 0.00 3.13
714 732 1.133915 ACGACAGCTGGGGAAAAGAAA 60.134 47.619 19.93 0.00 0.00 2.52
715 733 1.537202 CGACAGCTGGGGAAAAGAAAG 59.463 52.381 19.93 0.00 0.00 2.62
716 734 1.889170 GACAGCTGGGGAAAAGAAAGG 59.111 52.381 19.93 0.00 0.00 3.11
1241 1356 0.232303 CCTCGTCGTGTTTGAAGTGC 59.768 55.000 0.00 0.00 0.00 4.40
1242 1357 0.111704 CTCGTCGTGTTTGAAGTGCG 60.112 55.000 0.00 0.00 0.00 5.34
1289 1407 8.957466 GTTATAATATCTGGGGATAGTTTTGGC 58.043 37.037 0.00 0.00 37.78 4.52
1319 1437 1.733360 GTTCAGCTCGACGACTAGAGT 59.267 52.381 0.00 0.00 36.88 3.24
1346 1464 3.487202 CGTGATGCCCGTTGGTCG 61.487 66.667 0.00 0.00 39.52 4.79
1348 1466 2.047655 TGATGCCCGTTGGTCGTC 60.048 61.111 0.00 0.00 37.94 4.20
1393 1528 0.801251 AGACGCTGCTTGATTTGCTC 59.199 50.000 0.00 0.00 0.00 4.26
1428 1574 4.036027 GTGTGATGAGATTGCGATGGAAAT 59.964 41.667 0.00 0.00 0.00 2.17
1438 1584 1.251762 GCGATGGAAATTTTAACGCGC 59.748 47.619 5.73 0.00 35.78 6.86
1464 1610 1.831106 TCTGATTGGAGCGTATGGTGT 59.169 47.619 0.00 0.00 0.00 4.16
1578 1938 0.606401 CGGAGCATGGGTTCAACACT 60.606 55.000 0.00 0.00 0.00 3.55
1654 2089 8.001292 AGGTAATTGATAGCCTGCTTTTCTATT 58.999 33.333 0.00 6.79 32.22 1.73
1661 2096 4.923415 AGCCTGCTTTTCTATTACCTGTT 58.077 39.130 0.00 0.00 0.00 3.16
1695 2132 4.060900 ACTTCTGCTGTATTCTGTGTGTG 58.939 43.478 0.00 0.00 0.00 3.82
1703 2140 3.752747 TGTATTCTGTGTGTGATGCAAGG 59.247 43.478 0.00 0.00 0.00 3.61
1756 2196 0.107017 TGCTTAGCTTCCATGGAGCC 60.107 55.000 24.08 15.96 0.00 4.70
1791 2231 3.249559 GCTGATGCTGCCACTAGATTTAC 59.750 47.826 0.00 0.00 36.03 2.01
1901 2398 5.872617 TGCTGTACATACGTTGCTCTTTTAT 59.127 36.000 0.00 0.00 0.00 1.40
2025 2522 3.005791 GGCTGCAAAGGTCATTGTACTTT 59.994 43.478 0.50 3.60 34.99 2.66
2083 2580 2.057922 AGTATCCATTGGCCCACTAGG 58.942 52.381 0.00 0.00 39.47 3.02
2093 2590 3.039011 TGGCCCACTAGGAGTTCTATTC 58.961 50.000 0.00 0.00 38.24 1.75
2096 2593 3.887716 GCCCACTAGGAGTTCTATTCGTA 59.112 47.826 0.00 0.00 38.24 3.43
2097 2594 4.023021 GCCCACTAGGAGTTCTATTCGTAG 60.023 50.000 0.00 0.00 38.24 3.51
2098 2595 5.131784 CCCACTAGGAGTTCTATTCGTAGT 58.868 45.833 0.00 2.74 43.30 2.73
2206 2703 6.170506 TCGACCTTGAACTATAAGTTGCATT 58.829 36.000 0.00 0.00 38.80 3.56
2319 2817 3.007940 ACAACACTTGCATGCCTAGTAGA 59.992 43.478 16.68 0.00 0.00 2.59
2333 2831 6.301486 TGCCTAGTAGATAAACCTCGATACA 58.699 40.000 0.00 0.00 0.00 2.29
2388 2888 7.651808 TCTGAATTTGGTTGAAGACTTGAATC 58.348 34.615 0.00 0.00 0.00 2.52
2399 2899 4.836125 AGACTTGAATCGTGCACAATTT 57.164 36.364 18.64 6.63 0.00 1.82
2493 3915 4.463186 TCTTACTGACCTTTCCTGCTAGAC 59.537 45.833 0.00 0.00 0.00 2.59
2619 4041 9.930693 CCTTCTAGTTTAACTTAAGACTGATGT 57.069 33.333 10.09 0.00 0.00 3.06
2789 4249 1.271856 TTCGCACTACCAAGGGATCA 58.728 50.000 0.00 0.00 0.00 2.92
2809 4269 7.605691 GGGATCAATATATGAACTCACTGAAGG 59.394 40.741 0.00 0.00 42.54 3.46
2813 4273 7.658982 TCAATATATGAACTCACTGAAGGATGC 59.341 37.037 0.00 0.00 34.30 3.91
3060 4640 4.092968 GTGATTGGCTCGGTAAGTTTACAG 59.907 45.833 4.58 0.74 35.37 2.74
3289 6821 6.538189 AAAATTTATCAACGTGCTTTTGGG 57.462 33.333 0.00 0.00 0.00 4.12
3722 8296 4.334552 TGCTTTCTATTGGACTTGATGCA 58.665 39.130 0.00 0.00 0.00 3.96
3816 8478 2.031420 CAGGCATCAGGTCATTAATGCG 60.031 50.000 10.76 0.00 44.23 4.73
3913 8641 9.780186 ATGATAGTTAAAACCTACTGGCTAATC 57.220 33.333 0.00 0.00 36.63 1.75
3978 8706 1.137404 CTGCACCGCATGTTTAGGC 59.863 57.895 0.00 0.00 38.13 3.93
3994 8722 2.814805 AGGCCACTGCTGATTAATGT 57.185 45.000 5.01 0.00 37.74 2.71
4024 8752 2.930019 CAGGCACCTGTCAGGGGA 60.930 66.667 26.16 0.00 43.10 4.81
4092 8820 9.607285 CGTTCAACAAATACTATTTTAGCAACT 57.393 29.630 0.00 0.00 0.00 3.16
4157 8888 0.543749 ACTGCCTGTCTTATCCCTGC 59.456 55.000 0.00 0.00 0.00 4.85
4495 9244 3.587923 GCTTTTGCATGGCACATTTCTA 58.412 40.909 0.00 0.00 46.58 2.10
4536 9286 5.540911 TCAGGCAATCAACCAAATTTTCTC 58.459 37.500 0.00 0.00 0.00 2.87
4558 9308 7.281841 TCTCACATTACTATGCCATCATTCAA 58.718 34.615 0.00 0.00 35.03 2.69
4737 9532 7.094508 TGTTTCAGTTCTCTTGTTTTATGCA 57.905 32.000 0.00 0.00 0.00 3.96
4778 9573 2.752354 TCTGGTGTTGTTGGTTGTTCTG 59.248 45.455 0.00 0.00 0.00 3.02
5082 9878 2.884639 GTTGTAACCAATGTCCTGCTGT 59.115 45.455 0.00 0.00 32.11 4.40
5324 10127 8.822652 TGTTAGTTGTTTTACTACTCTTAGGC 57.177 34.615 0.00 0.00 35.83 3.93
5326 10129 9.138062 GTTAGTTGTTTTACTACTCTTAGGCTC 57.862 37.037 0.00 0.00 35.83 4.70
5327 10130 7.541916 AGTTGTTTTACTACTCTTAGGCTCT 57.458 36.000 0.00 0.00 28.27 4.09
5328 10131 7.964624 AGTTGTTTTACTACTCTTAGGCTCTT 58.035 34.615 0.00 0.00 28.27 2.85
5329 10132 9.086758 AGTTGTTTTACTACTCTTAGGCTCTTA 57.913 33.333 0.00 0.00 28.27 2.10
5330 10133 9.356433 GTTGTTTTACTACTCTTAGGCTCTTAG 57.644 37.037 0.00 0.00 0.00 2.18
5341 10144 3.378911 AGGCTCTTAGCTTATTCTCGC 57.621 47.619 0.00 0.00 41.99 5.03
5477 10280 1.482593 ACTTCGAAGATCCGCCTCAAT 59.517 47.619 31.08 1.21 35.04 2.57
5558 10363 7.012704 ACAGAAGGTATGCATACATCATTTGTC 59.987 37.037 32.19 20.52 39.87 3.18
5575 10380 7.919690 TCATTTGTCTTGTTCTTCACTGTAAG 58.080 34.615 0.00 0.00 42.29 2.34
5593 10398 7.055667 CTGTAAGTTATCTTGAGGCCATCTA 57.944 40.000 5.01 0.00 35.36 1.98
5619 10424 6.629515 GCAGTAGGTGGTGAACATGTTAGATA 60.630 42.308 11.95 0.00 0.00 1.98
5620 10425 6.980978 CAGTAGGTGGTGAACATGTTAGATAG 59.019 42.308 11.95 0.00 0.00 2.08
5629 10434 9.900710 GGTGAACATGTTAGATAGATACAGTAG 57.099 37.037 11.95 0.00 0.00 2.57
5640 10447 4.243793 AGATACAGTAGACTCCAGCACT 57.756 45.455 0.00 0.00 0.00 4.40
5676 10483 6.067217 AGGTTGTATACTGATGGCTTTTCT 57.933 37.500 4.17 0.00 0.00 2.52
5772 10579 6.892456 AGTGACAGAAGTCTCATATGGTAAGA 59.108 38.462 2.13 0.00 45.20 2.10
5773 10580 7.068103 AGTGACAGAAGTCTCATATGGTAAGAG 59.932 40.741 2.13 0.00 45.20 2.85
5808 10617 7.994425 TGGTGTTATCTTCAGCTTATTTTCA 57.006 32.000 0.00 0.00 34.86 2.69
5843 10652 9.492973 GCTAATTGGGCATAATAATTGTCATTT 57.507 29.630 0.00 0.00 0.00 2.32
6130 10939 7.916914 AGTGTCTTCTCTTTAGTACTCTCTC 57.083 40.000 0.00 0.00 0.00 3.20
6144 10953 9.678260 TTAGTACTCTCTCCGTAAAGAAATACT 57.322 33.333 0.00 0.00 32.45 2.12
6145 10954 8.578448 AGTACTCTCTCCGTAAAGAAATACTT 57.422 34.615 0.00 0.00 40.98 2.24
6147 10956 9.074443 GTACTCTCTCCGTAAAGAAATACTTTG 57.926 37.037 0.00 0.00 46.62 2.77
6148 10957 6.590677 ACTCTCTCCGTAAAGAAATACTTTGC 59.409 38.462 0.00 0.00 46.62 3.68
6252 11075 3.411446 TCACATGAACACCTTGGATGAC 58.589 45.455 0.00 0.00 0.00 3.06
6295 11118 3.975168 AGGCACGTGTTTACTAATCCT 57.025 42.857 18.38 8.56 0.00 3.24
6297 11120 2.676342 GGCACGTGTTTACTAATCCTGG 59.324 50.000 18.38 0.00 0.00 4.45
6332 11159 3.365565 CGTTTCGGTTGTTTGATAAGGGG 60.366 47.826 0.00 0.00 0.00 4.79
6430 11258 5.642063 ACTGTAATATAATCGGGAATTGCCG 59.358 40.000 30.34 30.34 37.63 5.69
6463 11292 3.243068 CCTGACCAGTGTAAACTTGTTGC 60.243 47.826 0.00 0.00 0.00 4.17
6485 11314 7.024340 TGCAAGCTTCTGATGATTCTATTTC 57.976 36.000 0.00 0.00 0.00 2.17
6568 11399 8.919145 TGTTTGAATCTGTAAATAACCTTTGGT 58.081 29.630 0.00 0.00 37.65 3.67
6598 11429 5.788450 TGTGAACACAATGGTTCTTTTGTT 58.212 33.333 5.11 0.76 45.74 2.83
6612 11443 6.420903 GGTTCTTTTGTTTATTGTGGCTTCTC 59.579 38.462 0.00 0.00 0.00 2.87
6615 11446 7.202526 TCTTTTGTTTATTGTGGCTTCTCTTG 58.797 34.615 0.00 0.00 0.00 3.02
6630 11464 5.679734 TTCTCTTGAGCTTTAAACTGCTG 57.320 39.130 6.68 0.00 39.91 4.41
6632 11466 5.126067 TCTCTTGAGCTTTAAACTGCTGTT 58.874 37.500 6.68 2.72 39.91 3.16
6661 11495 3.146066 GTCCTAGACACACCAAATGCAA 58.854 45.455 0.00 0.00 32.09 4.08
6677 11533 6.417327 CAAATGCAACTTTTGTAATTCGCAA 58.583 32.000 0.00 0.00 0.00 4.85
6678 11534 5.574815 ATGCAACTTTTGTAATTCGCAAC 57.425 34.783 0.00 0.00 0.00 4.17
6681 11555 5.578727 TGCAACTTTTGTAATTCGCAACTTT 59.421 32.000 0.00 0.00 0.00 2.66
6698 11572 5.567423 GCAACTTTTATCAGGGCTTCATGTT 60.567 40.000 0.00 0.00 0.00 2.71
6749 11623 5.619220 GTGATTTGGAGCTGGATCTATCTT 58.381 41.667 0.00 0.00 0.00 2.40
6761 11635 6.240549 TGGATCTATCTTCTTCCAACTTCC 57.759 41.667 0.00 0.00 35.38 3.46
6781 11655 1.068402 CGATTGTTGGTGCATTGCTGA 60.068 47.619 10.49 0.00 0.00 4.26
6839 11713 8.750515 TTGCATTGTGGAATGAGAATATTAGA 57.249 30.769 0.00 0.00 41.49 2.10
6856 11730 9.937175 GAATATTAGATGTAAAAGCAACTGGTC 57.063 33.333 0.00 0.00 0.00 4.02
6880 12945 2.896168 ACAGTTCGACTTTTCCACGAA 58.104 42.857 0.00 0.00 42.29 3.85
6899 12964 6.381801 CACGAAAAGCATCTAAACTTGGAAT 58.618 36.000 0.00 0.00 0.00 3.01
6900 12965 6.306356 CACGAAAAGCATCTAAACTTGGAATG 59.694 38.462 0.00 0.00 0.00 2.67
6901 12966 6.206634 ACGAAAAGCATCTAAACTTGGAATGA 59.793 34.615 0.00 0.00 0.00 2.57
6902 12967 6.744537 CGAAAAGCATCTAAACTTGGAATGAG 59.255 38.462 0.00 0.00 0.00 2.90
6904 12969 5.441718 AGCATCTAAACTTGGAATGAGGA 57.558 39.130 0.00 0.00 0.00 3.71
6906 12971 5.649831 AGCATCTAAACTTGGAATGAGGAAC 59.350 40.000 0.00 0.00 0.00 3.62
6919 12986 3.667497 TGAGGAACTTGTGTAGCTGAG 57.333 47.619 0.00 0.00 41.55 3.35
6925 12992 1.336332 ACTTGTGTAGCTGAGCGAGTG 60.336 52.381 0.00 0.00 0.00 3.51
6926 12993 0.038251 TTGTGTAGCTGAGCGAGTGG 60.038 55.000 0.00 0.00 0.00 4.00
6984 13054 2.226437 CCATCTGTTCCAACCTTCAACG 59.774 50.000 0.00 0.00 0.00 4.10
7005 13075 6.716934 ACGATGAAATCCAGTCTGTAGTAT 57.283 37.500 0.00 0.00 41.39 2.12
7016 13086 6.382859 TCCAGTCTGTAGTATGAAGCCAAATA 59.617 38.462 0.00 0.00 0.00 1.40
7022 13092 8.046708 TCTGTAGTATGAAGCCAAATACACATT 58.953 33.333 0.00 0.00 32.69 2.71
7025 13095 7.466746 AGTATGAAGCCAAATACACATTTGT 57.533 32.000 8.75 0.00 46.45 2.83
7033 13103 7.599171 AGCCAAATACACATTTGTAAAGTACC 58.401 34.615 8.75 0.00 46.45 3.34
7056 13126 5.091910 CGGCCTTACGGATAAGAAATTTC 57.908 43.478 10.33 10.33 40.38 2.17
7090 13160 1.224592 GGGCCGTGACCATTCTGAT 59.775 57.895 0.00 0.00 0.00 2.90
7092 13162 1.017387 GGCCGTGACCATTCTGATTC 58.983 55.000 0.00 0.00 0.00 2.52
7099 13169 2.041485 TGACCATTCTGATTCCAAGCCA 59.959 45.455 0.00 0.00 0.00 4.75
7151 13221 5.635120 AGTTTCAAAAGAGTAGCTGGGAAT 58.365 37.500 0.00 0.00 0.00 3.01
7152 13222 6.779860 AGTTTCAAAAGAGTAGCTGGGAATA 58.220 36.000 0.00 0.00 0.00 1.75
7153 13223 7.231467 AGTTTCAAAAGAGTAGCTGGGAATAA 58.769 34.615 0.00 0.00 0.00 1.40
7154 13224 7.391833 AGTTTCAAAAGAGTAGCTGGGAATAAG 59.608 37.037 0.00 0.00 0.00 1.73
7155 13225 6.374417 TCAAAAGAGTAGCTGGGAATAAGT 57.626 37.500 0.00 0.00 0.00 2.24
7156 13226 6.173339 TCAAAAGAGTAGCTGGGAATAAGTG 58.827 40.000 0.00 0.00 0.00 3.16
7157 13227 6.013725 TCAAAAGAGTAGCTGGGAATAAGTGA 60.014 38.462 0.00 0.00 0.00 3.41
7158 13228 6.374417 AAAGAGTAGCTGGGAATAAGTGAA 57.626 37.500 0.00 0.00 0.00 3.18
7159 13229 5.346181 AGAGTAGCTGGGAATAAGTGAAC 57.654 43.478 0.00 0.00 0.00 3.18
7160 13230 4.777896 AGAGTAGCTGGGAATAAGTGAACA 59.222 41.667 0.00 0.00 0.00 3.18
7161 13231 5.248477 AGAGTAGCTGGGAATAAGTGAACAA 59.752 40.000 0.00 0.00 0.00 2.83
7162 13232 5.876357 AGTAGCTGGGAATAAGTGAACAAA 58.124 37.500 0.00 0.00 0.00 2.83
7180 13250 9.934190 GTGAACAAAAATATGCTTCAAATGTTT 57.066 25.926 0.00 0.00 0.00 2.83
7228 13306 5.128991 AGAACCTCTACGAATTTTCCTAGGG 59.871 44.000 9.46 0.00 0.00 3.53
7237 13315 5.708697 ACGAATTTTCCTAGGGTTTGGTTAG 59.291 40.000 9.46 0.79 0.00 2.34
7238 13316 5.124936 CGAATTTTCCTAGGGTTTGGTTAGG 59.875 44.000 9.46 0.00 36.18 2.69
7239 13317 3.444792 TTTCCTAGGGTTTGGTTAGGC 57.555 47.619 9.46 0.00 35.09 3.93
7240 13318 1.292085 TCCTAGGGTTTGGTTAGGCC 58.708 55.000 9.46 0.00 35.09 5.19
7249 13327 1.765074 TGGTTAGGCCAACTCCACC 59.235 57.895 5.01 1.53 45.94 4.61
7250 13328 1.376812 GGTTAGGCCAACTCCACCG 60.377 63.158 5.01 0.00 37.30 4.94
7251 13329 2.038837 GTTAGGCCAACTCCACCGC 61.039 63.158 5.01 0.00 34.06 5.68
7252 13330 3.599285 TTAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
7262 13340 4.944372 CCACCGCGCGACCCTATC 62.944 72.222 34.63 0.00 0.00 2.08
7263 13341 4.944372 CACCGCGCGACCCTATCC 62.944 72.222 34.63 0.00 0.00 2.59
7265 13343 4.647615 CCGCGCGACCCTATCCTG 62.648 72.222 34.63 6.11 0.00 3.86
7266 13344 3.900892 CGCGCGACCCTATCCTGT 61.901 66.667 28.94 0.00 0.00 4.00
7267 13345 2.027751 GCGCGACCCTATCCTGTC 59.972 66.667 12.10 0.00 0.00 3.51
7268 13346 2.728817 CGCGACCCTATCCTGTCC 59.271 66.667 0.00 0.00 0.00 4.02
7269 13347 2.728817 GCGACCCTATCCTGTCCG 59.271 66.667 0.00 0.00 0.00 4.79
7270 13348 2.857744 GCGACCCTATCCTGTCCGG 61.858 68.421 0.00 0.00 0.00 5.14
7271 13349 2.857744 CGACCCTATCCTGTCCGGC 61.858 68.421 0.00 0.00 0.00 6.13
7272 13350 2.446036 ACCCTATCCTGTCCGGCC 60.446 66.667 0.00 0.00 0.00 6.13
7273 13351 3.242291 CCCTATCCTGTCCGGCCC 61.242 72.222 0.00 0.00 0.00 5.80
7274 13352 2.122813 CCTATCCTGTCCGGCCCT 60.123 66.667 0.00 0.00 0.00 5.19
7275 13353 2.511452 CCTATCCTGTCCGGCCCTG 61.511 68.421 0.00 0.00 0.00 4.45
7276 13354 1.762460 CTATCCTGTCCGGCCCTGT 60.762 63.158 0.00 0.00 0.00 4.00
7277 13355 1.749334 CTATCCTGTCCGGCCCTGTC 61.749 65.000 0.00 0.00 0.00 3.51
7287 13365 4.280019 GCCCTGTCCGTTTGGGGT 62.280 66.667 0.00 0.00 41.19 4.95
7288 13366 2.897762 GCCCTGTCCGTTTGGGGTA 61.898 63.158 0.00 0.00 41.19 3.69
7289 13367 1.762471 CCCTGTCCGTTTGGGGTAA 59.238 57.895 0.00 0.00 37.37 2.85
7290 13368 0.110869 CCCTGTCCGTTTGGGGTAAA 59.889 55.000 0.00 0.00 37.37 2.01
7291 13369 1.479021 CCCTGTCCGTTTGGGGTAAAA 60.479 52.381 0.00 0.00 37.37 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.577313 GAGCGGCGGAATGGCTTC 61.577 66.667 9.78 0.00 42.02 3.86
106 109 7.479980 CAAAAATATGTAGGGAAAATGCTCGA 58.520 34.615 0.00 0.00 0.00 4.04
181 192 3.056821 TCGGTGACATGACTAAAGAGGTG 60.057 47.826 0.00 0.00 0.00 4.00
190 201 3.181471 GGAATCATCTCGGTGACATGACT 60.181 47.826 0.00 0.00 0.00 3.41
217 228 9.089123 CGTCTCTTTTCTTCGTAACATTTTTAC 57.911 33.333 0.00 0.00 0.00 2.01
323 335 2.716424 TGGGGATATTCCTGGTTCATCC 59.284 50.000 0.00 12.04 36.57 3.51
331 343 5.075493 CCTTTCTTCATGGGGATATTCCTG 58.925 45.833 0.00 0.00 36.57 3.86
362 374 3.129462 TCGCATGTTTGTTCCTTGTTTGA 59.871 39.130 0.00 0.00 0.00 2.69
363 375 3.443037 TCGCATGTTTGTTCCTTGTTTG 58.557 40.909 0.00 0.00 0.00 2.93
364 376 3.380004 TCTCGCATGTTTGTTCCTTGTTT 59.620 39.130 0.00 0.00 0.00 2.83
382 394 3.459232 TCCAAGCACCTATGATTCTCG 57.541 47.619 0.00 0.00 30.06 4.04
384 396 5.247110 ACGATATCCAAGCACCTATGATTCT 59.753 40.000 0.00 0.00 30.06 2.40
390 402 4.705507 ACGATACGATATCCAAGCACCTAT 59.294 41.667 0.00 0.00 0.00 2.57
393 406 2.987149 CACGATACGATATCCAAGCACC 59.013 50.000 0.00 0.00 0.00 5.01
394 407 3.639538 ACACGATACGATATCCAAGCAC 58.360 45.455 0.00 0.00 0.00 4.40
395 408 4.295870 GAACACGATACGATATCCAAGCA 58.704 43.478 0.00 0.00 0.00 3.91
396 409 3.361053 CGAACACGATACGATATCCAAGC 59.639 47.826 0.00 0.00 0.00 4.01
397 410 3.361053 GCGAACACGATACGATATCCAAG 59.639 47.826 0.00 0.00 0.00 3.61
398 411 3.302555 GCGAACACGATACGATATCCAA 58.697 45.455 0.00 0.00 0.00 3.53
399 412 2.351060 GGCGAACACGATACGATATCCA 60.351 50.000 0.00 0.00 0.00 3.41
400 413 2.248487 GGCGAACACGATACGATATCC 58.752 52.381 0.00 0.00 0.00 2.59
401 414 2.248487 GGGCGAACACGATACGATATC 58.752 52.381 0.00 0.00 0.00 1.63
402 415 1.400629 CGGGCGAACACGATACGATAT 60.401 52.381 0.00 0.00 0.00 1.63
403 416 0.041047 CGGGCGAACACGATACGATA 60.041 55.000 0.00 0.00 0.00 2.92
404 417 1.298863 CGGGCGAACACGATACGAT 60.299 57.895 0.00 0.00 0.00 3.73
405 418 2.100797 CGGGCGAACACGATACGA 59.899 61.111 0.00 0.00 0.00 3.43
406 419 3.613702 GCGGGCGAACACGATACG 61.614 66.667 0.00 0.00 0.00 3.06
407 420 3.259751 GGCGGGCGAACACGATAC 61.260 66.667 0.00 0.00 0.00 2.24
423 436 3.566261 GTCACATGTGTGGCTCGG 58.434 61.111 24.63 0.00 46.41 4.63
449 462 4.953940 TGCAAATGGTTTCCTAGCTTTT 57.046 36.364 0.00 0.00 33.44 2.27
450 463 4.824289 CATGCAAATGGTTTCCTAGCTTT 58.176 39.130 0.00 0.00 0.00 3.51
477 490 2.130426 TTTGGCATGCGGGTGTGTT 61.130 52.632 12.44 0.00 0.00 3.32
480 493 3.302344 GGTTTGGCATGCGGGTGT 61.302 61.111 12.44 0.00 0.00 4.16
489 502 4.067192 CGATATCTGATGATGGTTTGGCA 58.933 43.478 0.00 0.00 34.32 4.92
493 506 5.554070 TGATGCGATATCTGATGATGGTTT 58.446 37.500 0.00 0.00 34.32 3.27
503 516 8.060679 CACTAGAAAAGTTTGATGCGATATCTG 58.939 37.037 0.00 0.00 35.76 2.90
533 546 0.391130 GCCACCACGCTTCATAGTCA 60.391 55.000 0.00 0.00 0.00 3.41
534 547 0.108138 AGCCACCACGCTTCATAGTC 60.108 55.000 0.00 0.00 34.73 2.59
535 548 0.391661 CAGCCACCACGCTTCATAGT 60.392 55.000 0.00 0.00 36.82 2.12
589 607 1.873591 CTCAGTTTGCCACGCTAAACT 59.126 47.619 0.00 0.00 45.25 2.66
621 639 5.501252 CGTTATGAAACTAAGCCGCGTAATT 60.501 40.000 4.92 0.00 33.15 1.40
626 644 1.591394 GCGTTATGAAACTAAGCCGCG 60.591 52.381 0.00 0.00 33.15 6.46
656 674 8.479689 TGGATCATTTATTCGTTCCTACAGTTA 58.520 33.333 0.00 0.00 0.00 2.24
657 675 7.280205 GTGGATCATTTATTCGTTCCTACAGTT 59.720 37.037 0.00 0.00 0.00 3.16
658 676 6.761714 GTGGATCATTTATTCGTTCCTACAGT 59.238 38.462 0.00 0.00 0.00 3.55
659 677 6.761242 TGTGGATCATTTATTCGTTCCTACAG 59.239 38.462 0.00 0.00 0.00 2.74
660 678 6.645306 TGTGGATCATTTATTCGTTCCTACA 58.355 36.000 0.00 0.00 0.00 2.74
661 679 6.202954 CCTGTGGATCATTTATTCGTTCCTAC 59.797 42.308 0.00 0.00 0.00 3.18
679 697 1.483004 TGTCGTGACTTTTCCTGTGGA 59.517 47.619 1.23 0.00 0.00 4.02
680 698 1.867233 CTGTCGTGACTTTTCCTGTGG 59.133 52.381 1.23 0.00 0.00 4.17
707 725 5.428253 GCTGGGTTTTTCTTCCTTTCTTTT 58.572 37.500 0.00 0.00 0.00 2.27
709 727 3.068165 CGCTGGGTTTTTCTTCCTTTCTT 59.932 43.478 0.00 0.00 0.00 2.52
714 732 1.179174 GGCGCTGGGTTTTTCTTCCT 61.179 55.000 7.64 0.00 0.00 3.36
715 733 1.289066 GGCGCTGGGTTTTTCTTCC 59.711 57.895 7.64 0.00 0.00 3.46
716 734 0.039165 CTGGCGCTGGGTTTTTCTTC 60.039 55.000 7.64 0.00 0.00 2.87
799 817 0.400975 TGCGTTTTTAGGGGTAGGCA 59.599 50.000 0.00 0.00 0.00 4.75
911 934 3.732849 GGAGCACAAGGGAGGGGG 61.733 72.222 0.00 0.00 0.00 5.40
916 939 1.984570 CGGAGAGGAGCACAAGGGA 60.985 63.158 0.00 0.00 0.00 4.20
917 940 2.581354 CGGAGAGGAGCACAAGGG 59.419 66.667 0.00 0.00 0.00 3.95
920 943 3.706373 GGGCGGAGAGGAGCACAA 61.706 66.667 0.00 0.00 36.65 3.33
1146 1259 2.368875 ACCAGAAGAGCGAAGGAAGAAA 59.631 45.455 0.00 0.00 0.00 2.52
1264 1382 7.827236 CGCCAAAACTATCCCCAGATATTATAA 59.173 37.037 0.00 0.00 34.44 0.98
1289 1407 0.596083 CGAGCTGAACCAGGCTATCG 60.596 60.000 0.00 0.00 39.05 2.92
1319 1437 1.270094 CGGGCATCACGCTAAATCCTA 60.270 52.381 0.00 0.00 41.91 2.94
1341 1459 2.506217 GCTGCGATTCGACGACCA 60.506 61.111 10.88 0.00 35.09 4.02
1393 1528 7.410087 GCAATCTCATCACACAAAATCGAAAAG 60.410 37.037 0.00 0.00 0.00 2.27
1438 1584 0.108615 ACGCTCCAATCAGAACGAGG 60.109 55.000 0.00 0.00 0.00 4.63
1464 1610 3.368013 CCGTGTAGGACTGCAATTACAGA 60.368 47.826 12.74 0.00 45.00 3.41
1578 1938 1.676635 GAGCTTGGTGATGCAGGCA 60.677 57.895 0.00 0.00 0.00 4.75
1676 2113 4.248058 CATCACACACAGAATACAGCAGA 58.752 43.478 0.00 0.00 0.00 4.26
1703 2140 9.677567 TGATAAACAAAATCTTCTAGTTTGCAC 57.322 29.630 0.00 0.00 44.93 4.57
1756 2196 4.496010 GCAGCATCAGCAAATCTAACTGAG 60.496 45.833 0.00 0.00 43.25 3.35
1791 2231 5.924786 TGTTTTGCAAATTTATTCGCATGG 58.075 33.333 13.65 0.00 33.71 3.66
1822 2263 1.602416 CCATGCACAACACGCAATCAA 60.602 47.619 0.00 0.00 43.84 2.57
1824 2265 0.733566 CCCATGCACAACACGCAATC 60.734 55.000 0.00 0.00 43.84 2.67
2025 2522 0.963962 GACCCGTGTACTGGTCTTGA 59.036 55.000 15.65 0.00 43.97 3.02
2083 2580 9.367717 CATAGTACGAAACTACGAATAGAACTC 57.632 37.037 4.86 0.00 43.47 3.01
2093 2590 8.832487 ACAGTATTTCATAGTACGAAACTACG 57.168 34.615 0.00 0.00 43.47 3.51
2206 2703 6.892456 CCTCCATGGAAGTAGCATATAGACTA 59.108 42.308 17.00 0.00 38.35 2.59
2319 2817 9.607988 TGTGTCAAATATTGTATCGAGGTTTAT 57.392 29.630 0.00 0.00 0.00 1.40
2388 2888 5.918011 AGTGGTACAAATAAAATTGTGCACG 59.082 36.000 13.13 0.00 44.57 5.34
2399 2899 7.648039 AACAACCTCAAAGTGGTACAAATAA 57.352 32.000 0.00 0.00 44.16 1.40
2493 3915 4.756502 TGCAGAGAGATTCATGACTTCAG 58.243 43.478 0.00 0.00 0.00 3.02
2619 4041 8.175925 TCATCCAATTAACAAACTTCATGTGA 57.824 30.769 0.00 0.00 0.00 3.58
2773 4233 6.711277 TCATATATTGATCCCTTGGTAGTGC 58.289 40.000 0.00 0.00 0.00 4.40
2789 4249 6.648310 CGCATCCTTCAGTGAGTTCATATATT 59.352 38.462 0.00 0.00 0.00 1.28
2809 4269 4.932146 ACTAATACAAATTTGCCCGCATC 58.068 39.130 18.12 0.00 0.00 3.91
2813 4273 5.949735 ACAAGACTAATACAAATTTGCCCG 58.050 37.500 18.12 5.25 0.00 6.13
3060 4640 6.084326 TGCATTTCTTAAACTGTTTCTCCC 57.916 37.500 9.38 0.00 0.00 4.30
3116 4697 2.358322 TCAAAGTCCAGGGGTCAAAC 57.642 50.000 0.00 0.00 0.00 2.93
3127 4708 4.836125 TCATGTCAAAGCTTCAAAGTCC 57.164 40.909 0.00 0.00 0.00 3.85
3256 4907 7.461416 GCACGTTGATAAATTTTTCCATCTTCG 60.461 37.037 0.00 5.53 0.00 3.79
3289 6821 3.251479 CCAAAATCTAAGCTTTGGCCC 57.749 47.619 3.20 0.00 43.70 5.80
3763 8351 3.944650 TCTACAGCAACTGAACAAGCAAA 59.055 39.130 0.78 0.00 35.18 3.68
3802 8464 4.685169 AAGACAACGCATTAATGACCTG 57.315 40.909 19.73 13.18 0.00 4.00
3816 8478 4.212636 TCTTAGCGGCACTAAAAAGACAAC 59.787 41.667 1.45 0.00 40.36 3.32
3913 8641 6.656693 CCTAATTATATCCACTGAAAGGGCTG 59.343 42.308 0.00 0.00 34.45 4.85
4024 8752 6.266103 CCATCCTCCATGTTTAGTGCAATTAT 59.734 38.462 0.00 0.00 0.00 1.28
4092 8820 8.423906 AAGTTAAGACAGAGATTCTTACTCCA 57.576 34.615 0.00 0.00 35.69 3.86
4157 8888 5.321927 ACCCTGTTGAGGTATAAAACAAGG 58.678 41.667 0.00 0.00 40.00 3.61
4439 9188 7.476540 ACACATGTGACTACAGTAGGATTAA 57.523 36.000 31.94 0.00 40.79 1.40
4440 9189 8.762481 ATACACATGTGACTACAGTAGGATTA 57.238 34.615 31.94 8.98 40.79 1.75
4441 9190 7.661536 ATACACATGTGACTACAGTAGGATT 57.338 36.000 31.94 6.94 40.79 3.01
4495 9244 6.653020 TGCCTGATATTTCAATACTGACTGT 58.347 36.000 0.00 0.00 0.00 3.55
4536 9286 9.537192 AAAATTGAATGATGGCATAGTAATGTG 57.463 29.630 0.00 0.00 35.38 3.21
4737 9532 4.516698 CAGATCACCGCCTAAAGCATAATT 59.483 41.667 0.00 0.00 44.04 1.40
4778 9573 6.734104 AAGATAGAAACAGCAAGTGATGTC 57.266 37.500 2.18 0.00 44.74 3.06
5082 9878 2.950781 TCCACCACCTAATGTGCAAAA 58.049 42.857 0.00 0.00 44.01 2.44
5323 10126 3.243569 TGGAGCGAGAATAAGCTAAGAGC 60.244 47.826 0.00 0.00 44.69 4.09
5324 10127 4.576216 TGGAGCGAGAATAAGCTAAGAG 57.424 45.455 0.00 0.00 44.69 2.85
5326 10129 3.993081 CCATGGAGCGAGAATAAGCTAAG 59.007 47.826 5.56 0.00 44.69 2.18
5327 10130 3.388024 ACCATGGAGCGAGAATAAGCTAA 59.612 43.478 21.47 0.00 44.69 3.09
5328 10131 2.965831 ACCATGGAGCGAGAATAAGCTA 59.034 45.455 21.47 0.00 44.69 3.32
5330 10133 1.869767 CACCATGGAGCGAGAATAAGC 59.130 52.381 21.47 0.00 0.00 3.09
5558 10363 9.261180 TCAAGATAACTTACAGTGAAGAACAAG 57.739 33.333 0.00 0.00 34.70 3.16
5575 10380 4.202305 ACTGCTAGATGGCCTCAAGATAAC 60.202 45.833 3.32 0.00 0.00 1.89
5593 10398 1.699634 ACATGTTCACCACCTACTGCT 59.300 47.619 0.00 0.00 0.00 4.24
5619 10424 4.243793 AGTGCTGGAGTCTACTGTATCT 57.756 45.455 0.00 0.00 0.00 1.98
5620 10425 6.095720 ACTTTAGTGCTGGAGTCTACTGTATC 59.904 42.308 0.00 0.00 0.00 2.24
5629 10434 7.439655 CCTTTCATATACTTTAGTGCTGGAGTC 59.560 40.741 0.00 0.00 0.00 3.36
5663 10470 3.347077 AGACCAGAGAAAAGCCATCAG 57.653 47.619 0.00 0.00 0.00 2.90
5669 10476 5.506686 AAGTTCAAAGACCAGAGAAAAGC 57.493 39.130 0.00 0.00 0.00 3.51
5676 10483 5.825593 ACCTGATAAGTTCAAAGACCAGA 57.174 39.130 0.00 0.00 32.78 3.86
5772 10579 9.388506 CTGAAGATAACACCATTTAATGAGACT 57.611 33.333 6.50 0.00 0.00 3.24
5773 10580 8.125448 GCTGAAGATAACACCATTTAATGAGAC 58.875 37.037 6.50 0.00 0.00 3.36
5793 10602 9.798994 AGCAGAAATATTGAAAATAAGCTGAAG 57.201 29.630 0.00 0.00 0.00 3.02
5811 10620 9.715121 CAATTATTATGCCCAATTAGCAGAAAT 57.285 29.630 12.13 12.75 43.86 2.17
5817 10626 9.492973 AAATGACAATTATTATGCCCAATTAGC 57.507 29.630 0.00 0.00 0.00 3.09
5843 10652 2.151202 GTCCGAATTCCTGCAGAAACA 58.849 47.619 17.39 0.00 38.21 2.83
5890 10699 6.540551 TGGTTATGCATGCGTTTATTAGAAGA 59.459 34.615 19.31 0.00 0.00 2.87
5893 10702 6.667370 CATGGTTATGCATGCGTTTATTAGA 58.333 36.000 19.31 0.00 0.00 2.10
6130 10939 8.424731 GTGAAATTGCAAAGTATTTCTTTACGG 58.575 33.333 18.93 0.00 43.57 4.02
6143 10952 9.582431 AGATTCTTGATATGTGAAATTGCAAAG 57.418 29.630 1.71 0.00 0.00 2.77
6144 10953 9.361315 CAGATTCTTGATATGTGAAATTGCAAA 57.639 29.630 1.71 0.00 0.00 3.68
6145 10954 8.741841 TCAGATTCTTGATATGTGAAATTGCAA 58.258 29.630 0.00 0.00 0.00 4.08
6147 10956 8.186163 TGTCAGATTCTTGATATGTGAAATTGC 58.814 33.333 0.00 0.00 28.55 3.56
6295 11118 1.034838 AAACGTTGACAGCCTTGCCA 61.035 50.000 0.00 0.00 0.00 4.92
6297 11120 0.657368 CGAAACGTTGACAGCCTTGC 60.657 55.000 0.00 0.00 0.00 4.01
6332 11159 1.065928 ACCGCGCTGTGAGCTATAC 59.934 57.895 2.79 0.00 39.60 1.47
6426 11254 2.367567 GGTCAGGGAAAGTATATCGGCA 59.632 50.000 0.00 0.00 0.00 5.69
6430 11258 5.615925 ACACTGGTCAGGGAAAGTATATC 57.384 43.478 7.28 0.00 35.36 1.63
6463 11292 6.259608 ACCGAAATAGAATCATCAGAAGCTTG 59.740 38.462 2.10 0.00 0.00 4.01
6485 11314 1.406887 CCAAAGGGTGATACAGGACCG 60.407 57.143 0.00 0.00 32.48 4.79
6568 11399 1.948834 CCATTGTGTTCACAGCTCACA 59.051 47.619 5.78 1.29 39.76 3.58
6598 11429 4.292186 AGCTCAAGAGAAGCCACAATAA 57.708 40.909 0.32 0.00 0.00 1.40
6612 11443 6.892310 AAAAACAGCAGTTTAAAGCTCAAG 57.108 33.333 7.72 0.00 46.79 3.02
6638 11472 2.744202 GCATTTGGTGTGTCTAGGACAG 59.256 50.000 0.27 0.00 43.57 3.51
6649 11483 6.019156 CGAATTACAAAAGTTGCATTTGGTGT 60.019 34.615 14.11 9.83 41.08 4.16
6661 11495 9.180678 CTGATAAAAGTTGCGAATTACAAAAGT 57.819 29.630 0.00 0.00 0.00 2.66
6677 11533 7.068716 GGATTAACATGAAGCCCTGATAAAAGT 59.931 37.037 0.00 0.00 0.00 2.66
6678 11534 7.068593 TGGATTAACATGAAGCCCTGATAAAAG 59.931 37.037 0.00 0.00 33.75 2.27
6681 11555 6.012337 TGGATTAACATGAAGCCCTGATAA 57.988 37.500 0.00 0.00 33.75 1.75
6698 11572 6.717289 ACCAGCAACTGTAATAACTGGATTA 58.283 36.000 13.45 0.00 46.10 1.75
6717 11591 1.130561 GCTCCAAATCACGTTACCAGC 59.869 52.381 0.00 0.00 0.00 4.85
6761 11635 1.068402 TCAGCAATGCACCAACAATCG 60.068 47.619 8.35 0.00 0.00 3.34
6781 11655 5.671329 GCTCGCATAAAGTTGAACGAATCTT 60.671 40.000 0.00 0.00 0.00 2.40
6839 11713 2.226330 TGCGACCAGTTGCTTTTACAT 58.774 42.857 11.20 0.00 40.60 2.29
6851 11725 4.336581 TCGAACTGTTGCGACCAG 57.663 55.556 0.45 1.98 36.01 4.00
6856 11730 1.329292 TGGAAAAGTCGAACTGTTGCG 59.671 47.619 0.00 1.96 36.66 4.85
6872 11746 5.278266 CCAAGTTTAGATGCTTTTCGTGGAA 60.278 40.000 0.00 0.00 0.00 3.53
6880 12945 6.248433 TCCTCATTCCAAGTTTAGATGCTTT 58.752 36.000 0.00 0.00 0.00 3.51
6899 12964 2.289072 GCTCAGCTACACAAGTTCCTCA 60.289 50.000 0.00 0.00 0.00 3.86
6900 12965 2.342179 GCTCAGCTACACAAGTTCCTC 58.658 52.381 0.00 0.00 0.00 3.71
6901 12966 1.337260 CGCTCAGCTACACAAGTTCCT 60.337 52.381 0.00 0.00 0.00 3.36
6902 12967 1.071605 CGCTCAGCTACACAAGTTCC 58.928 55.000 0.00 0.00 0.00 3.62
6904 12969 1.341531 ACTCGCTCAGCTACACAAGTT 59.658 47.619 0.00 0.00 0.00 2.66
6906 12971 1.344458 CACTCGCTCAGCTACACAAG 58.656 55.000 0.00 0.00 0.00 3.16
6919 12986 3.056304 GAGAAGCAAGATATCCACTCGC 58.944 50.000 0.00 0.00 0.00 5.03
6925 12992 6.540189 TGCTAGTTTTGAGAAGCAAGATATCC 59.460 38.462 0.00 0.00 41.74 2.59
6926 12993 7.545362 TGCTAGTTTTGAGAAGCAAGATATC 57.455 36.000 0.00 0.00 41.74 1.63
6958 13028 5.147032 TGAAGGTTGGAACAGATGGATTTT 58.853 37.500 0.00 0.00 42.39 1.82
6963 13033 2.226437 CGTTGAAGGTTGGAACAGATGG 59.774 50.000 0.00 0.00 42.39 3.51
6972 13042 3.505680 TGGATTTCATCGTTGAAGGTTGG 59.494 43.478 8.79 0.00 42.60 3.77
6984 13054 7.170658 GCTTCATACTACAGACTGGATTTCATC 59.829 40.741 7.51 0.00 0.00 2.92
7016 13086 2.815503 GCCGGGTACTTTACAAATGTGT 59.184 45.455 2.18 0.00 42.09 3.72
7022 13092 2.353605 CGTAAGGCCGGGTACTTTACAA 60.354 50.000 2.18 0.00 0.00 2.41
7050 13120 4.080751 CCTTTCATGGCTGGATGGAAATTT 60.081 41.667 0.00 0.00 28.29 1.82
7056 13126 1.397390 GCCCTTTCATGGCTGGATGG 61.397 60.000 0.00 0.00 45.70 3.51
7090 13160 2.584835 AGCACTTGTATGGCTTGGAA 57.415 45.000 0.00 0.00 33.21 3.53
7141 13211 7.775053 ATTTTTGTTCACTTATTCCCAGCTA 57.225 32.000 0.00 0.00 0.00 3.32
7152 13222 9.328845 ACATTTGAAGCATATTTTTGTTCACTT 57.671 25.926 0.00 0.00 0.00 3.16
7153 13223 8.891671 ACATTTGAAGCATATTTTTGTTCACT 57.108 26.923 0.00 0.00 0.00 3.41
7154 13224 9.934190 AAACATTTGAAGCATATTTTTGTTCAC 57.066 25.926 0.00 0.00 0.00 3.18
7184 13254 9.955102 AGGTTCTAGTACTTATTGTAAAAAGGG 57.045 33.333 0.00 0.00 32.25 3.95
7206 13284 4.781621 ACCCTAGGAAAATTCGTAGAGGTT 59.218 41.667 11.48 9.83 44.32 3.50
7245 13323 4.944372 GATAGGGTCGCGCGGTGG 62.944 72.222 31.69 0.71 0.00 4.61
7246 13324 4.944372 GGATAGGGTCGCGCGGTG 62.944 72.222 31.69 1.17 0.00 4.94
7248 13326 4.647615 CAGGATAGGGTCGCGCGG 62.648 72.222 31.69 11.75 0.00 6.46
7249 13327 3.825833 GACAGGATAGGGTCGCGCG 62.826 68.421 26.76 26.76 0.00 6.86
7250 13328 2.027751 GACAGGATAGGGTCGCGC 59.972 66.667 0.00 0.00 0.00 6.86
7251 13329 2.728817 GGACAGGATAGGGTCGCG 59.271 66.667 0.00 0.00 34.87 5.87
7252 13330 2.728817 CGGACAGGATAGGGTCGC 59.271 66.667 0.00 0.00 34.87 5.19
7253 13331 2.857744 GCCGGACAGGATAGGGTCG 61.858 68.421 5.05 0.00 45.00 4.79
7254 13332 2.508751 GGCCGGACAGGATAGGGTC 61.509 68.421 5.05 0.00 45.00 4.46
7255 13333 2.446036 GGCCGGACAGGATAGGGT 60.446 66.667 5.05 0.00 45.00 4.34
7256 13334 3.242291 GGGCCGGACAGGATAGGG 61.242 72.222 11.00 0.00 45.00 3.53
7257 13335 2.122813 AGGGCCGGACAGGATAGG 60.123 66.667 11.00 0.00 45.00 2.57
7258 13336 1.749334 GACAGGGCCGGACAGGATAG 61.749 65.000 11.00 0.00 45.00 2.08
7259 13337 1.760875 GACAGGGCCGGACAGGATA 60.761 63.158 11.00 0.00 45.00 2.59
7260 13338 3.083997 GACAGGGCCGGACAGGAT 61.084 66.667 11.00 0.00 45.00 3.24
7270 13348 2.414658 TTACCCCAAACGGACAGGGC 62.415 60.000 3.03 0.00 43.96 5.19
7271 13349 0.110869 TTTACCCCAAACGGACAGGG 59.889 55.000 1.66 1.66 45.75 4.45
7272 13350 1.984066 TTTTACCCCAAACGGACAGG 58.016 50.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.