Multiple sequence alignment - TraesCS5A01G485900

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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 TraesCS5A01G485900 chr5A 100.000 4181 0 0 1 4181 657108266 657104086 0.000000e+00 7721.0
1 TraesCS5A01G485900 chr5A 100.000 709 0 0 4462 5170 657103805 657103097 0.000000e+00 1310.0
2 TraesCS5A01G485900 chr5A 89.213 788 55 15 2319 3088 534988468 534987693 0.000000e+00 957.0
3 TraesCS5A01G485900 chr5A 86.836 866 78 17 928 1765 534989996 534989139 0.000000e+00 935.0
4 TraesCS5A01G485900 chr5A 82.987 817 67 47 3391 4181 534987414 534986644 0.000000e+00 673.0
5 TraesCS5A01G485900 chr5A 87.302 504 58 6 4670 5170 637048188 637047688 5.810000e-159 571.0
6 TraesCS5A01G485900 chr5A 77.751 836 105 51 3365 4181 657182002 657181229 6.150000e-119 438.0
7 TraesCS5A01G485900 chr5A 88.110 328 36 3 2760 3086 657182589 657182264 2.260000e-103 387.0
8 TraesCS5A01G485900 chr5A 92.251 271 14 5 255 519 534990322 534990053 1.360000e-100 377.0
9 TraesCS5A01G485900 chr5A 95.139 144 7 0 3207 3350 534987634 534987491 1.450000e-55 228.0
10 TraesCS5A01G485900 chr5A 85.128 195 26 2 4465 4659 534986560 534986369 4.080000e-46 196.0
11 TraesCS5A01G485900 chr5A 92.537 134 10 0 3210 3343 657182217 657182084 5.280000e-45 193.0
12 TraesCS5A01G485900 chr5A 87.500 128 15 1 2105 2232 534988729 534988603 4.170000e-31 147.0
13 TraesCS5A01G485900 chr5A 90.566 106 10 0 2341 2446 657183086 657182981 1.940000e-29 141.0
14 TraesCS5A01G485900 chr5A 90.217 92 6 1 968 1059 657184682 657184594 3.270000e-22 117.0
15 TraesCS5A01G485900 chr5D 92.525 1913 75 32 2319 4181 528846866 528844972 0.000000e+00 2678.0
16 TraesCS5A01G485900 chr5D 84.586 1038 92 31 2105 3088 419366265 419367288 0.000000e+00 968.0
17 TraesCS5A01G485900 chr5D 88.039 510 57 4 4661 5168 417047114 417046607 7.410000e-168 601.0
18 TraesCS5A01G485900 chr5D 85.409 514 65 8 4661 5170 487530517 487531024 4.590000e-145 525.0
19 TraesCS5A01G485900 chr5D 87.472 447 36 10 928 1361 528848267 528847828 1.000000e-136 497.0
20 TraesCS5A01G485900 chr5D 85.141 498 51 13 1624 2115 419365664 419366144 6.020000e-134 488.0
21 TraesCS5A01G485900 chr5D 79.211 760 114 27 2323 3070 528880972 528880245 6.020000e-134 488.0
22 TraesCS5A01G485900 chr5D 81.525 590 55 36 3178 3718 419367306 419367890 2.210000e-118 436.0
23 TraesCS5A01G485900 chr5D 77.358 848 113 43 3364 4181 528879968 528879170 3.700000e-116 429.0
24 TraesCS5A01G485900 chr5D 85.195 385 31 13 3801 4181 419368042 419368404 6.320000e-99 372.0
25 TraesCS5A01G485900 chr5D 92.369 249 17 2 1 247 528849042 528848794 2.290000e-93 353.0
26 TraesCS5A01G485900 chr5D 95.312 192 9 0 4462 4653 528844883 528844692 6.500000e-79 305.0
27 TraesCS5A01G485900 chr5D 83.801 321 19 14 1650 1959 528847577 528847279 1.830000e-69 274.0
28 TraesCS5A01G485900 chr5D 85.859 198 25 2 4462 4659 419368492 419368686 1.890000e-49 207.0
29 TraesCS5A01G485900 chr5D 80.634 284 40 9 1415 1692 528882601 528882327 6.790000e-49 206.0
30 TraesCS5A01G485900 chr5D 91.852 135 9 2 3210 3343 528880181 528880048 2.460000e-43 187.0
31 TraesCS5A01G485900 chr5D 87.143 70 8 1 435 504 528848408 528848340 1.540000e-10 78.7
32 TraesCS5A01G485900 chr5B 92.891 844 34 15 3355 4181 665994183 665993349 0.000000e+00 1203.0
33 TraesCS5A01G485900 chr5B 89.317 805 48 17 2319 3087 665995226 665994424 0.000000e+00 976.0
34 TraesCS5A01G485900 chr5B 83.860 917 72 31 928 1811 665996843 665995970 0.000000e+00 804.0
35 TraesCS5A01G485900 chr5B 95.377 411 17 1 519 929 656783293 656783701 0.000000e+00 652.0
36 TraesCS5A01G485900 chr5B 79.369 761 112 28 2323 3070 666126674 666125946 1.290000e-135 494.0
37 TraesCS5A01G485900 chr5B 80.840 381 36 11 3350 3726 666125625 666125278 1.100000e-66 265.0
38 TraesCS5A01G485900 chr5B 93.182 176 7 2 3178 3349 665994401 665994227 2.390000e-63 254.0
39 TraesCS5A01G485900 chr5B 92.216 167 12 1 4462 4627 665993260 665993094 8.650000e-58 235.0
40 TraesCS5A01G485900 chr5B 82.283 254 17 15 1 247 665998015 665997783 1.470000e-45 195.0
41 TraesCS5A01G485900 chr5B 90.141 142 12 2 3210 3350 666125878 666125738 3.180000e-42 183.0
42 TraesCS5A01G485900 chr5B 86.420 162 17 3 1534 1692 666128284 666128125 6.880000e-39 172.0
43 TraesCS5A01G485900 chr5B 90.805 87 5 2 435 519 665996980 665996895 4.230000e-21 113.0
44 TraesCS5A01G485900 chr7D 95.377 411 18 1 519 929 404032781 404033190 0.000000e+00 652.0
45 TraesCS5A01G485900 chr7D 95.146 412 18 1 518 929 572205632 572205223 0.000000e+00 649.0
46 TraesCS5A01G485900 chr7D 95.134 411 18 1 519 929 375607270 375606862 0.000000e+00 647.0
47 TraesCS5A01G485900 chr7D 87.867 511 59 3 4662 5170 153060860 153061369 9.580000e-167 597.0
48 TraesCS5A01G485900 chr7D 87.921 505 53 7 4669 5170 517354316 517353817 5.770000e-164 588.0
49 TraesCS5A01G485900 chr7D 87.771 507 49 9 4669 5170 571879571 571879073 9.650000e-162 580.0
50 TraesCS5A01G485900 chr7A 95.377 411 17 1 519 929 104653385 104653793 0.000000e+00 652.0
51 TraesCS5A01G485900 chr7A 95.134 411 18 1 519 929 483653592 483654000 0.000000e+00 647.0
52 TraesCS5A01G485900 chr1B 95.377 411 17 1 519 929 313489943 313489535 0.000000e+00 652.0
53 TraesCS5A01G485900 chr6A 95.134 411 17 2 519 929 568003346 568002939 0.000000e+00 645.0
54 TraesCS5A01G485900 chr2B 95.134 411 17 2 519 929 97978468 97978061 0.000000e+00 645.0
55 TraesCS5A01G485900 chr4D 87.084 511 54 9 4669 5170 434931329 434930822 7.510000e-158 568.0
56 TraesCS5A01G485900 chr3B 86.745 513 63 5 4661 5170 245350340 245349830 2.700000e-157 566.0
57 TraesCS5A01G485900 chr7B 85.880 517 64 7 4657 5170 394774701 394775211 4.550000e-150 542.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G485900 chr5A 657103097 657108266 5169 True 4515.500000 7721 100.000000 1 5170 2 chr5A.!!$R3 5169
1 TraesCS5A01G485900 chr5A 637047688 637048188 500 True 571.000000 571 87.302000 4670 5170 1 chr5A.!!$R1 500
2 TraesCS5A01G485900 chr5A 534986369 534990322 3953 True 501.857143 957 88.436286 255 4659 7 chr5A.!!$R2 4404
3 TraesCS5A01G485900 chr5A 657181229 657184682 3453 True 255.200000 438 87.836200 968 4181 5 chr5A.!!$R4 3213
4 TraesCS5A01G485900 chr5D 528844692 528849042 4350 True 697.616667 2678 89.770333 1 4653 6 chr5D.!!$R2 4652
5 TraesCS5A01G485900 chr5D 417046607 417047114 507 True 601.000000 601 88.039000 4661 5168 1 chr5D.!!$R1 507
6 TraesCS5A01G485900 chr5D 487530517 487531024 507 False 525.000000 525 85.409000 4661 5170 1 chr5D.!!$F1 509
7 TraesCS5A01G485900 chr5D 419365664 419368686 3022 False 494.200000 968 84.461200 1624 4659 5 chr5D.!!$F2 3035
8 TraesCS5A01G485900 chr5D 528879170 528882601 3431 True 327.500000 488 82.263750 1415 4181 4 chr5D.!!$R3 2766
9 TraesCS5A01G485900 chr5B 665993094 665998015 4921 True 540.000000 1203 89.222000 1 4627 7 chr5B.!!$R1 4626
10 TraesCS5A01G485900 chr5B 666125278 666128284 3006 True 278.500000 494 84.192500 1534 3726 4 chr5B.!!$R2 2192
11 TraesCS5A01G485900 chr7D 153060860 153061369 509 False 597.000000 597 87.867000 4662 5170 1 chr7D.!!$F1 508
12 TraesCS5A01G485900 chr4D 434930822 434931329 507 True 568.000000 568 87.084000 4669 5170 1 chr4D.!!$R1 501
13 TraesCS5A01G485900 chr3B 245349830 245350340 510 True 566.000000 566 86.745000 4661 5170 1 chr3B.!!$R1 509
14 TraesCS5A01G485900 chr7B 394774701 394775211 510 False 542.000000 542 85.880000 4657 5170 1 chr7B.!!$F1 513

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
190 202 0.379669 CCAGCGGCATGATTGACTTC 59.620 55.0 1.45 0.0 0.00 3.01 F
1323 2075 0.173935 TCGTCGTGATTGCCCGTTAT 59.826 50.0 0.00 0.0 0.00 1.89 F
2158 3703 0.109412 GCTTGTGTCATGGCTTCTGC 60.109 55.0 0.00 0.0 38.76 4.26 F
2909 5400 0.644380 TCCTCTCCATGGGGATGTCT 59.356 55.0 16.66 0.0 43.91 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 3682 0.111061 AGAAGCCATGACACAAGCCA 59.889 50.0 0.00 0.0 0.00 4.75 R
2771 5262 0.254747 GGATCATCACCCGGTTCCAA 59.745 55.0 0.00 0.0 0.00 3.53 R
4059 6872 0.036388 TTCCAGATCGCCTGTGAACC 60.036 55.0 4.40 0.0 41.33 3.62 R
4742 7561 0.106335 TCCGTGCGGGTCAACTTTTA 59.894 50.0 10.94 0.0 37.00 1.52 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
88 89 5.183014 TCACATGGTCATATACGTGTCTC 57.817 43.478 0.00 0.00 0.00 3.36
123 124 5.670792 ATTTGTGTAGTGATAAGGTCGGA 57.329 39.130 0.00 0.00 0.00 4.55
125 126 6.778834 TTTGTGTAGTGATAAGGTCGGATA 57.221 37.500 0.00 0.00 0.00 2.59
126 127 6.971726 TTGTGTAGTGATAAGGTCGGATAT 57.028 37.500 0.00 0.00 0.00 1.63
132 138 9.350951 TGTAGTGATAAGGTCGGATATATATGG 57.649 37.037 0.00 0.00 0.00 2.74
190 202 0.379669 CCAGCGGCATGATTGACTTC 59.620 55.000 1.45 0.00 0.00 3.01
192 204 0.749454 AGCGGCATGATTGACTTCCC 60.749 55.000 1.45 0.00 0.00 3.97
236 248 3.005684 TCTTGAAATTTCGTGCTGGCAAT 59.994 39.130 13.34 0.00 0.00 3.56
238 250 3.058450 TGAAATTTCGTGCTGGCAATTG 58.942 40.909 13.34 0.00 0.00 2.32
240 252 0.390209 ATTTCGTGCTGGCAATTGGC 60.390 50.000 24.20 24.20 43.74 4.52
241 253 2.745906 TTTCGTGCTGGCAATTGGCG 62.746 55.000 25.00 19.95 46.16 5.69
243 255 4.360964 GTGCTGGCAATTGGCGCA 62.361 61.111 31.66 31.66 46.16 6.09
244 256 3.383681 TGCTGGCAATTGGCGCAT 61.384 55.556 31.66 0.00 46.16 4.73
245 257 2.050934 TGCTGGCAATTGGCGCATA 61.051 52.632 31.66 19.24 46.16 3.14
246 258 1.364901 GCTGGCAATTGGCGCATAT 59.635 52.632 29.53 0.00 46.16 1.78
247 259 0.597568 GCTGGCAATTGGCGCATATA 59.402 50.000 29.53 13.40 46.16 0.86
248 260 1.666888 GCTGGCAATTGGCGCATATAC 60.667 52.381 29.53 12.75 46.16 1.47
253 265 2.665519 GCAATTGGCGCATATACGAAGG 60.666 50.000 10.83 0.00 34.06 3.46
254 266 2.805671 CAATTGGCGCATATACGAAGGA 59.194 45.455 10.83 0.00 34.06 3.36
255 267 2.605837 TTGGCGCATATACGAAGGAA 57.394 45.000 10.83 0.00 34.06 3.36
263 310 4.386049 CGCATATACGAAGGAAATGTCTCC 59.614 45.833 0.00 0.00 33.21 3.71
303 350 5.384063 ACGAGACATATATCTTGGAGCTG 57.616 43.478 3.30 0.00 34.76 4.24
325 372 3.758554 GCCCTTCTTGAAATTCTGTGCTA 59.241 43.478 0.00 0.00 0.00 3.49
378 428 1.134098 GCAGAATTGTAGCTAGGCCCA 60.134 52.381 0.00 0.00 0.00 5.36
421 471 1.227205 CTCTGCCAGATCTCCACGC 60.227 63.158 0.00 0.00 0.00 5.34
519 1207 3.521560 GTTGATCTCTTCATGCGGTGTA 58.478 45.455 0.00 0.00 33.34 2.90
520 1208 3.443099 TGATCTCTTCATGCGGTGTAG 57.557 47.619 0.00 0.00 0.00 2.74
523 1211 1.476891 TCTCTTCATGCGGTGTAGGAC 59.523 52.381 0.00 0.00 0.00 3.85
524 1212 1.204704 CTCTTCATGCGGTGTAGGACA 59.795 52.381 0.00 0.00 0.00 4.02
525 1213 1.621317 TCTTCATGCGGTGTAGGACAA 59.379 47.619 0.00 0.00 0.00 3.18
526 1214 2.037902 TCTTCATGCGGTGTAGGACAAA 59.962 45.455 0.00 0.00 0.00 2.83
527 1215 2.779755 TCATGCGGTGTAGGACAAAT 57.220 45.000 0.00 0.00 0.00 2.32
528 1216 2.355197 TCATGCGGTGTAGGACAAATG 58.645 47.619 0.00 0.00 0.00 2.32
529 1217 2.083774 CATGCGGTGTAGGACAAATGT 58.916 47.619 0.00 0.00 0.00 2.71
530 1218 2.264005 TGCGGTGTAGGACAAATGTT 57.736 45.000 0.00 0.00 0.00 2.71
531 1219 2.577700 TGCGGTGTAGGACAAATGTTT 58.422 42.857 0.00 0.00 0.00 2.83
532 1220 2.550606 TGCGGTGTAGGACAAATGTTTC 59.449 45.455 0.00 0.00 0.00 2.78
533 1221 2.095415 GCGGTGTAGGACAAATGTTTCC 60.095 50.000 0.00 0.00 0.00 3.13
534 1222 3.408634 CGGTGTAGGACAAATGTTTCCT 58.591 45.455 0.00 0.00 44.82 3.36
535 1223 4.571919 CGGTGTAGGACAAATGTTTCCTA 58.428 43.478 0.00 0.00 42.56 2.94
541 1229 4.469657 AGGACAAATGTTTCCTACAAGCA 58.530 39.130 0.00 0.00 40.70 3.91
542 1230 4.520492 AGGACAAATGTTTCCTACAAGCAG 59.480 41.667 0.00 0.00 40.70 4.24
543 1231 4.278419 GGACAAATGTTTCCTACAAGCAGT 59.722 41.667 0.00 0.00 40.89 4.40
544 1232 5.186996 ACAAATGTTTCCTACAAGCAGTG 57.813 39.130 0.00 0.00 40.89 3.66
545 1233 4.037923 ACAAATGTTTCCTACAAGCAGTGG 59.962 41.667 0.00 0.00 40.89 4.00
546 1234 3.508845 ATGTTTCCTACAAGCAGTGGT 57.491 42.857 0.00 0.00 40.89 4.16
547 1235 4.634012 ATGTTTCCTACAAGCAGTGGTA 57.366 40.909 0.00 0.00 40.89 3.25
548 1236 4.002906 TGTTTCCTACAAGCAGTGGTAG 57.997 45.455 0.00 0.00 37.36 3.18
549 1237 3.389983 TGTTTCCTACAAGCAGTGGTAGT 59.610 43.478 0.00 0.00 36.17 2.73
550 1238 4.141574 TGTTTCCTACAAGCAGTGGTAGTT 60.142 41.667 0.00 0.00 36.17 2.24
551 1239 5.070714 TGTTTCCTACAAGCAGTGGTAGTTA 59.929 40.000 0.00 0.00 36.17 2.24
552 1240 4.796038 TCCTACAAGCAGTGGTAGTTAC 57.204 45.455 0.00 0.00 36.17 2.50
553 1241 3.512724 TCCTACAAGCAGTGGTAGTTACC 59.487 47.826 0.00 1.25 46.62 2.85
563 1251 1.435577 GGTAGTTACCACCACTTGCG 58.564 55.000 3.45 0.00 45.73 4.85
564 1252 1.270465 GGTAGTTACCACCACTTGCGT 60.270 52.381 3.45 0.00 45.73 5.24
565 1253 2.486918 GTAGTTACCACCACTTGCGTT 58.513 47.619 0.00 0.00 0.00 4.84
566 1254 2.047002 AGTTACCACCACTTGCGTTT 57.953 45.000 0.00 0.00 0.00 3.60
567 1255 2.371306 AGTTACCACCACTTGCGTTTT 58.629 42.857 0.00 0.00 0.00 2.43
568 1256 2.098443 AGTTACCACCACTTGCGTTTTG 59.902 45.455 0.00 0.00 0.00 2.44
569 1257 1.752683 TACCACCACTTGCGTTTTGT 58.247 45.000 0.00 0.00 0.00 2.83
570 1258 1.752683 ACCACCACTTGCGTTTTGTA 58.247 45.000 0.00 0.00 0.00 2.41
571 1259 2.303175 ACCACCACTTGCGTTTTGTAT 58.697 42.857 0.00 0.00 0.00 2.29
572 1260 2.034053 ACCACCACTTGCGTTTTGTATG 59.966 45.455 0.00 0.00 0.00 2.39
573 1261 2.034053 CCACCACTTGCGTTTTGTATGT 59.966 45.455 0.00 0.00 0.00 2.29
574 1262 3.490078 CCACCACTTGCGTTTTGTATGTT 60.490 43.478 0.00 0.00 0.00 2.71
575 1263 3.485378 CACCACTTGCGTTTTGTATGTTG 59.515 43.478 0.00 0.00 0.00 3.33
576 1264 3.129638 ACCACTTGCGTTTTGTATGTTGT 59.870 39.130 0.00 0.00 0.00 3.32
577 1265 4.335874 ACCACTTGCGTTTTGTATGTTGTA 59.664 37.500 0.00 0.00 0.00 2.41
578 1266 5.009210 ACCACTTGCGTTTTGTATGTTGTAT 59.991 36.000 0.00 0.00 0.00 2.29
579 1267 5.341993 CCACTTGCGTTTTGTATGTTGTATG 59.658 40.000 0.00 0.00 0.00 2.39
580 1268 5.912396 CACTTGCGTTTTGTATGTTGTATGT 59.088 36.000 0.00 0.00 0.00 2.29
581 1269 7.072647 CACTTGCGTTTTGTATGTTGTATGTA 58.927 34.615 0.00 0.00 0.00 2.29
582 1270 7.268235 CACTTGCGTTTTGTATGTTGTATGTAG 59.732 37.037 0.00 0.00 0.00 2.74
583 1271 6.788684 TGCGTTTTGTATGTTGTATGTAGT 57.211 33.333 0.00 0.00 0.00 2.73
584 1272 7.886405 TGCGTTTTGTATGTTGTATGTAGTA 57.114 32.000 0.00 0.00 0.00 1.82
585 1273 8.481974 TGCGTTTTGTATGTTGTATGTAGTAT 57.518 30.769 0.00 0.00 0.00 2.12
586 1274 8.597227 TGCGTTTTGTATGTTGTATGTAGTATC 58.403 33.333 0.00 0.00 0.00 2.24
587 1275 8.814235 GCGTTTTGTATGTTGTATGTAGTATCT 58.186 33.333 0.00 0.00 0.00 1.98
591 1279 9.511144 TTTGTATGTTGTATGTAGTATCTGTCG 57.489 33.333 0.00 0.00 0.00 4.35
592 1280 8.441312 TGTATGTTGTATGTAGTATCTGTCGA 57.559 34.615 0.00 0.00 0.00 4.20
593 1281 8.895737 TGTATGTTGTATGTAGTATCTGTCGAA 58.104 33.333 0.00 0.00 0.00 3.71
594 1282 9.726232 GTATGTTGTATGTAGTATCTGTCGAAA 57.274 33.333 0.00 0.00 0.00 3.46
596 1284 8.851960 TGTTGTATGTAGTATCTGTCGAAATC 57.148 34.615 0.00 0.00 0.00 2.17
597 1285 7.642586 TGTTGTATGTAGTATCTGTCGAAATCG 59.357 37.037 0.00 0.00 41.45 3.34
611 1299 4.829808 TCGAAATCGAGAGTATGTACGTG 58.170 43.478 0.00 0.00 44.22 4.49
612 1300 4.330894 TCGAAATCGAGAGTATGTACGTGT 59.669 41.667 0.00 0.00 44.22 4.49
613 1301 5.519927 TCGAAATCGAGAGTATGTACGTGTA 59.480 40.000 0.00 0.00 44.22 2.90
614 1302 5.839753 CGAAATCGAGAGTATGTACGTGTAG 59.160 44.000 0.00 0.00 43.02 2.74
615 1303 6.509199 CGAAATCGAGAGTATGTACGTGTAGT 60.509 42.308 0.00 0.00 43.02 2.73
616 1304 7.306225 CGAAATCGAGAGTATGTACGTGTAGTA 60.306 40.741 0.00 0.00 43.02 1.82
617 1305 7.959689 AATCGAGAGTATGTACGTGTAGTAT 57.040 36.000 0.00 0.00 37.69 2.12
618 1306 6.760161 TCGAGAGTATGTACGTGTAGTATG 57.240 41.667 0.00 0.00 37.69 2.39
619 1307 6.276091 TCGAGAGTATGTACGTGTAGTATGT 58.724 40.000 0.00 0.00 37.69 2.29
620 1308 7.425606 TCGAGAGTATGTACGTGTAGTATGTA 58.574 38.462 0.00 0.00 37.69 2.29
621 1309 7.592903 TCGAGAGTATGTACGTGTAGTATGTAG 59.407 40.741 0.00 0.00 37.69 2.74
622 1310 7.380870 CGAGAGTATGTACGTGTAGTATGTAGT 59.619 40.741 0.00 0.00 37.69 2.73
623 1311 9.684448 GAGAGTATGTACGTGTAGTATGTAGTA 57.316 37.037 0.00 0.00 37.69 1.82
723 1411 8.833976 CATACAAATATGTACGCATTTCACAA 57.166 30.769 2.41 0.00 44.47 3.33
724 1412 9.283420 CATACAAATATGTACGCATTTCACAAA 57.717 29.630 2.41 0.00 44.47 2.83
733 1421 9.847706 ATGTACGCATTTCACAAATATAACAAA 57.152 25.926 0.00 0.00 29.54 2.83
734 1422 9.678941 TGTACGCATTTCACAAATATAACAAAA 57.321 25.926 0.00 0.00 0.00 2.44
737 1425 9.255304 ACGCATTTCACAAATATAACAAAAACT 57.745 25.926 0.00 0.00 0.00 2.66
752 1440 7.701539 AACAAAAACTATGGACTCATATGCA 57.298 32.000 0.00 0.00 35.53 3.96
753 1441 7.701539 ACAAAAACTATGGACTCATATGCAA 57.298 32.000 0.00 0.00 35.53 4.08
754 1442 8.297470 ACAAAAACTATGGACTCATATGCAAT 57.703 30.769 0.00 0.00 35.53 3.56
755 1443 8.752187 ACAAAAACTATGGACTCATATGCAATT 58.248 29.630 0.00 0.00 35.53 2.32
756 1444 9.590451 CAAAAACTATGGACTCATATGCAATTT 57.410 29.630 0.00 0.00 35.53 1.82
778 1466 6.492007 TTTTTCATGCAACTTGCTTTGAAA 57.508 29.167 25.47 25.47 45.25 2.69
779 1467 6.680874 TTTTCATGCAACTTGCTTTGAAAT 57.319 29.167 27.52 9.82 45.68 2.17
780 1468 7.783090 TTTTCATGCAACTTGCTTTGAAATA 57.217 28.000 27.52 20.61 45.68 1.40
781 1469 7.966246 TTTCATGCAACTTGCTTTGAAATAT 57.034 28.000 25.47 7.05 43.79 1.28
782 1470 7.585286 TTCATGCAACTTGCTTTGAAATATC 57.415 32.000 20.87 0.00 45.31 1.63
783 1471 6.927416 TCATGCAACTTGCTTTGAAATATCT 58.073 32.000 14.78 0.00 45.31 1.98
784 1472 7.380536 TCATGCAACTTGCTTTGAAATATCTT 58.619 30.769 14.78 0.00 45.31 2.40
785 1473 8.522003 TCATGCAACTTGCTTTGAAATATCTTA 58.478 29.630 14.78 0.00 45.31 2.10
786 1474 8.804743 CATGCAACTTGCTTTGAAATATCTTAG 58.195 33.333 14.78 0.00 45.31 2.18
787 1475 8.109705 TGCAACTTGCTTTGAAATATCTTAGA 57.890 30.769 14.78 0.00 45.31 2.10
788 1476 8.742777 TGCAACTTGCTTTGAAATATCTTAGAT 58.257 29.630 14.78 0.00 45.31 1.98
891 1579 1.511613 CACTGGGTGGTAGGATGGAT 58.488 55.000 0.00 0.00 0.00 3.41
893 1581 2.242196 CACTGGGTGGTAGGATGGATTT 59.758 50.000 0.00 0.00 0.00 2.17
898 1586 2.514160 GGTGGTAGGATGGATTTTCCCT 59.486 50.000 0.00 0.00 35.03 4.20
983 1685 5.506649 GGAGAGAGTCGTGAGTATCCATTTC 60.507 48.000 0.00 0.00 0.00 2.17
984 1686 4.950475 AGAGAGTCGTGAGTATCCATTTCA 59.050 41.667 0.00 0.00 0.00 2.69
985 1687 5.419155 AGAGAGTCGTGAGTATCCATTTCAA 59.581 40.000 0.00 0.00 0.00 2.69
986 1688 6.097554 AGAGAGTCGTGAGTATCCATTTCAAT 59.902 38.462 0.00 0.00 0.00 2.57
992 1694 7.441157 GTCGTGAGTATCCATTTCAATTCCATA 59.559 37.037 0.00 0.00 0.00 2.74
1059 1761 5.487433 CTTTTTCTTGTGGTTTTGGTCCTT 58.513 37.500 0.00 0.00 0.00 3.36
1062 1764 4.237976 TCTTGTGGTTTTGGTCCTTGTA 57.762 40.909 0.00 0.00 0.00 2.41
1119 1821 2.109181 GGTGGTATGAGGCGGCTC 59.891 66.667 30.53 30.53 0.00 4.70
1256 1964 6.151691 ACTTCATTCATGTCAAAATTGTCCG 58.848 36.000 0.00 0.00 0.00 4.79
1265 1991 1.810151 CAAAATTGTCCGACCATCCGT 59.190 47.619 0.00 0.00 0.00 4.69
1281 2007 3.309600 TCCGTTTTGGAGGGGTTTTAA 57.690 42.857 0.00 0.00 43.74 1.52
1302 2028 9.615295 TTTTAAACTTCGGTGCAAATTCTATAC 57.385 29.630 0.00 0.00 0.00 1.47
1303 2029 6.811253 AAACTTCGGTGCAAATTCTATACA 57.189 33.333 0.00 0.00 0.00 2.29
1309 2035 4.375005 CGGTGCAAATTCTATACATCGTCG 60.375 45.833 0.00 0.00 30.53 5.12
1316 2068 6.453643 AATTCTATACATCGTCGTGATTGC 57.546 37.500 0.00 0.00 34.13 3.56
1319 2071 0.526739 TACATCGTCGTGATTGCCCG 60.527 55.000 0.00 0.00 34.13 6.13
1323 2075 0.173935 TCGTCGTGATTGCCCGTTAT 59.826 50.000 0.00 0.00 0.00 1.89
1378 2139 2.688507 CTGGAACACGCATGTCTTAGT 58.311 47.619 0.00 0.00 38.45 2.24
1422 2198 3.366440 ACGTCTAGTGACCTCAAACAC 57.634 47.619 0.00 0.00 39.94 3.32
1598 2401 9.878667 TTCTCGATTTTCATATACCTTACACAA 57.121 29.630 0.00 0.00 0.00 3.33
1862 3121 8.510243 AATGATATCTAGTGTTCAATTGCACA 57.490 30.769 6.83 6.83 38.02 4.57
1864 3123 8.334263 TGATATCTAGTGTTCAATTGCACAAA 57.666 30.769 12.58 3.76 38.02 2.83
1865 3124 8.791675 TGATATCTAGTGTTCAATTGCACAAAA 58.208 29.630 12.58 3.42 38.02 2.44
1866 3125 9.624697 GATATCTAGTGTTCAATTGCACAAAAA 57.375 29.630 12.58 1.07 38.02 1.94
1870 3129 6.509317 AGTGTTCAATTGCACAAAAATACG 57.491 33.333 12.58 0.00 38.02 3.06
1874 3133 7.377397 GTGTTCAATTGCACAAAAATACGACTA 59.623 33.333 12.58 0.00 35.81 2.59
1893 3152 6.316390 ACGACTATTGAATTTGTTGGATCCTC 59.684 38.462 14.23 6.93 0.00 3.71
1902 3161 4.764679 TTGTTGGATCCTCACAAATTCG 57.235 40.909 21.33 0.00 0.00 3.34
1903 3162 4.014569 TGTTGGATCCTCACAAATTCGA 57.985 40.909 14.23 0.00 0.00 3.71
1904 3163 4.393834 TGTTGGATCCTCACAAATTCGAA 58.606 39.130 14.23 0.00 0.00 3.71
1905 3164 5.009631 TGTTGGATCCTCACAAATTCGAAT 58.990 37.500 14.23 4.39 0.00 3.34
1906 3165 5.476599 TGTTGGATCCTCACAAATTCGAATT 59.523 36.000 17.60 17.60 0.00 2.17
1907 3166 6.015519 TGTTGGATCCTCACAAATTCGAATTT 60.016 34.615 26.51 26.51 39.07 1.82
1908 3167 6.194796 TGGATCCTCACAAATTCGAATTTC 57.805 37.500 28.70 16.98 36.52 2.17
1952 3216 9.462606 AACTACCACAATATTCTCCCTAAAAAG 57.537 33.333 0.00 0.00 0.00 2.27
1975 3267 6.904498 AGCTACTAGTGCTACTATCAAATCG 58.096 40.000 15.39 0.00 39.21 3.34
2031 3323 6.350445 CCTGCAAATTCAACACTAATTAGGCT 60.350 38.462 16.73 0.00 32.39 4.58
2054 3346 9.748708 GGCTTTTATTATGTTGCTCAATGATAA 57.251 29.630 0.00 0.00 0.00 1.75
2083 3381 6.803807 GTCTTGCAATCTTCCAAACAATCTAC 59.196 38.462 0.00 0.00 0.00 2.59
2085 3383 7.882791 TCTTGCAATCTTCCAAACAATCTACTA 59.117 33.333 0.00 0.00 0.00 1.82
2158 3703 0.109412 GCTTGTGTCATGGCTTCTGC 60.109 55.000 0.00 0.00 38.76 4.26
2236 3785 8.709646 ACAGTGTTTTCGTAACTTGATCTATTC 58.290 33.333 0.00 0.00 0.00 1.75
2269 3851 5.127031 GCTATTTTTCTATGAAAGTGGGCCA 59.873 40.000 0.00 0.00 0.00 5.36
2403 4751 1.140312 ACCACATGGATTCGGGCTAT 58.860 50.000 4.53 0.00 38.94 2.97
2430 4778 1.609841 GGGAAGAACCGTTGGATCGTT 60.610 52.381 0.00 0.00 40.11 3.85
2472 4822 9.959721 ACTCAACATATAACCTAAAAGACATGT 57.040 29.630 0.00 0.00 0.00 3.21
2493 4873 5.976458 TGTATGTTGTGTCTGAGCATATGA 58.024 37.500 6.97 0.00 0.00 2.15
2494 4874 6.585416 TGTATGTTGTGTCTGAGCATATGAT 58.415 36.000 6.97 0.00 0.00 2.45
2495 4875 6.480981 TGTATGTTGTGTCTGAGCATATGATG 59.519 38.462 6.97 0.00 0.00 3.07
2658 5129 1.617536 ATCTTGAGCTCCAGCCCCA 60.618 57.895 12.15 0.00 43.38 4.96
2697 5172 1.760192 CATGCTCCCTCCCTTTCAAG 58.240 55.000 0.00 0.00 0.00 3.02
2771 5262 5.591877 GTGCCCATTATCAGATTTCTTCAGT 59.408 40.000 0.00 0.00 0.00 3.41
2909 5400 0.644380 TCCTCTCCATGGGGATGTCT 59.356 55.000 16.66 0.00 43.91 3.41
2931 5422 2.267006 CGGATCAGGTGCTGCTGT 59.733 61.111 0.00 0.00 0.00 4.40
3103 5603 9.004231 ACCCATCCAATAAAATTAGTACTCTCT 57.996 33.333 0.00 0.00 0.00 3.10
3104 5604 9.495572 CCCATCCAATAAAATTAGTACTCTCTC 57.504 37.037 0.00 0.00 0.00 3.20
3138 5638 6.257849 TCATCCATATTAGTTGTCGCTCAAAC 59.742 38.462 0.00 0.00 37.81 2.93
3140 5640 4.260212 CCATATTAGTTGTCGCTCAAACGG 60.260 45.833 0.00 0.00 37.81 4.44
3171 5671 5.209659 ACTAATTTGGACGGGAGAGAGTAT 58.790 41.667 0.00 0.00 0.00 2.12
3184 5687 6.347888 CGGGAGAGAGTATTAAAGTCGATCTC 60.348 46.154 0.00 0.00 32.09 2.75
3508 6151 9.368416 CTGGCAGGTATATATAGGAAGCTATAA 57.632 37.037 6.61 0.00 0.00 0.98
3573 6225 7.292713 TCTGTTAAACAGTATAGTCCACACA 57.707 36.000 0.00 0.00 46.03 3.72
3574 6226 7.375834 TCTGTTAAACAGTATAGTCCACACAG 58.624 38.462 0.00 0.00 46.03 3.66
3575 6227 7.231925 TCTGTTAAACAGTATAGTCCACACAGA 59.768 37.037 0.00 0.00 46.03 3.41
3580 6237 5.005740 ACAGTATAGTCCACACAGACGTAA 58.994 41.667 0.00 0.00 41.83 3.18
3751 6459 7.147983 TGGATTTATTAATTTAGCAACGCACCT 60.148 33.333 0.00 0.00 0.00 4.00
3793 6588 7.649306 TCGAGTTCTGAATGTCACATGTATATG 59.351 37.037 0.00 0.00 40.24 1.78
3956 6757 2.560542 AGAATGCGTATGGCTCTCCTAG 59.439 50.000 0.00 0.00 44.05 3.02
4045 6850 5.122239 TCATCATCGGTTCACTTCATGTTTC 59.878 40.000 0.00 0.00 0.00 2.78
4059 6872 0.375454 TGTTTCGTGTTCTTGCGTGG 59.625 50.000 0.00 0.00 0.00 4.94
4062 6875 0.745128 TTCGTGTTCTTGCGTGGGTT 60.745 50.000 0.00 0.00 0.00 4.11
4659 7474 2.676342 CCACCGCAATACCTGTACTTTC 59.324 50.000 0.00 0.00 0.00 2.62
4676 7491 4.666512 ACTTTCAGGATGCATTTGGTAGT 58.333 39.130 0.00 7.30 34.76 2.73
4735 7554 1.460504 GCCTGTTTGGTTACCTAGGC 58.539 55.000 9.30 18.04 43.20 3.93
4742 7561 0.621609 TGGTTACCTAGGCCGCATTT 59.378 50.000 9.30 0.00 0.00 2.32
4783 7602 0.322975 TCAAAGCACCTCTCAGCCTC 59.677 55.000 0.00 0.00 0.00 4.70
4789 7608 2.031624 GCACCTCTCAGCCTCCATCTA 61.032 57.143 0.00 0.00 0.00 1.98
4796 7616 4.813809 TCTCAGCCTCCATCTAGAAGAAT 58.186 43.478 0.00 0.00 0.00 2.40
4829 7649 1.306312 TTTCTACCGGGCCAGGCTA 60.306 57.895 23.25 12.30 33.69 3.93
4844 7664 2.109126 GCTAAGGCGAGCCACCTTG 61.109 63.158 17.18 2.86 46.99 3.61
4883 7705 1.579964 TTGCACAAGAGCATGCGAGG 61.580 55.000 13.01 6.10 45.19 4.63
4886 7708 3.570638 CAAGAGCATGCGAGGCGG 61.571 66.667 13.01 0.00 36.08 6.13
4901 7723 1.063417 AGGCGGTATACACCCTGTACT 60.063 52.381 11.52 0.00 42.43 2.73
4908 7730 5.121142 CGGTATACACCCTGTACTTTGTTTG 59.879 44.000 5.01 0.00 42.43 2.93
4920 7742 4.718940 ACTTTGTTTGTTCTTCCACCTG 57.281 40.909 0.00 0.00 0.00 4.00
4969 7792 5.093849 TCTTAGGTCCCTTTTAATCCACG 57.906 43.478 0.00 0.00 0.00 4.94
4973 7796 2.758423 GGTCCCTTTTAATCCACGCAAT 59.242 45.455 0.00 0.00 0.00 3.56
5017 7840 6.246420 ACTCTACATGAAAAAGATGTGCAC 57.754 37.500 10.75 10.75 35.62 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.303333 TGATACAGTCACACCTGTTCAAGTA 59.697 40.000 0.00 0.00 42.99 2.24
121 122 3.004524 GCTCGGTCCGTCCATATATATCC 59.995 52.174 11.88 0.00 35.57 2.59
123 124 2.617308 CGCTCGGTCCGTCCATATATAT 59.383 50.000 11.88 0.00 35.57 0.86
125 126 0.809385 CGCTCGGTCCGTCCATATAT 59.191 55.000 11.88 0.00 35.57 0.86
126 127 0.250424 TCGCTCGGTCCGTCCATATA 60.250 55.000 11.88 0.00 35.57 0.86
132 138 2.087009 CAACTTCGCTCGGTCCGTC 61.087 63.158 11.88 3.73 0.00 4.79
179 191 5.380043 GACACATATGGGGAAGTCAATCAT 58.620 41.667 10.35 0.00 0.00 2.45
190 202 1.541233 GGAGCTTCGACACATATGGGG 60.541 57.143 10.35 2.41 0.00 4.96
192 204 2.205074 GTGGAGCTTCGACACATATGG 58.795 52.381 7.80 0.00 35.30 2.74
236 248 2.605837 TTCCTTCGTATATGCGCCAA 57.394 45.000 4.18 0.00 0.00 4.52
238 250 2.806244 ACATTTCCTTCGTATATGCGCC 59.194 45.455 4.18 0.00 0.00 6.53
240 252 4.386049 GGAGACATTTCCTTCGTATATGCG 59.614 45.833 6.90 6.90 34.27 4.73
241 253 5.297547 TGGAGACATTTCCTTCGTATATGC 58.702 41.667 0.00 0.00 38.12 3.14
242 254 6.073548 GCTTGGAGACATTTCCTTCGTATATG 60.074 42.308 0.00 0.00 42.32 1.78
243 255 5.992217 GCTTGGAGACATTTCCTTCGTATAT 59.008 40.000 0.00 0.00 42.32 0.86
244 256 5.128827 AGCTTGGAGACATTTCCTTCGTATA 59.871 40.000 0.00 0.00 42.32 1.47
245 257 4.080863 AGCTTGGAGACATTTCCTTCGTAT 60.081 41.667 0.00 0.00 42.32 3.06
246 258 3.260884 AGCTTGGAGACATTTCCTTCGTA 59.739 43.478 0.00 0.00 42.32 3.43
247 259 2.039084 AGCTTGGAGACATTTCCTTCGT 59.961 45.455 0.00 0.00 42.32 3.85
248 260 2.675348 GAGCTTGGAGACATTTCCTTCG 59.325 50.000 0.00 0.00 42.32 3.79
303 350 2.560105 AGCACAGAATTTCAAGAAGGGC 59.440 45.455 0.00 0.00 0.00 5.19
325 372 6.601613 TCCTTCGTATATGTGCCAATTTTTCT 59.398 34.615 0.00 0.00 0.00 2.52
395 445 4.903649 TGGAGATCTGGCAGAGAATGAATA 59.096 41.667 23.24 1.72 33.12 1.75
421 471 4.955811 TCCAATGTATACCTGCCTACTG 57.044 45.455 0.00 0.00 0.00 2.74
488 1170 3.903714 TGAAGAGATCAACCTGGTCAAGA 59.096 43.478 0.00 0.00 34.30 3.02
504 1192 1.204704 TGTCCTACACCGCATGAAGAG 59.795 52.381 0.00 0.00 0.00 2.85
519 1207 4.469657 TGCTTGTAGGAAACATTTGTCCT 58.530 39.130 0.00 0.00 46.29 3.85
520 1208 4.278419 ACTGCTTGTAGGAAACATTTGTCC 59.722 41.667 0.00 0.00 38.10 4.02
523 1211 4.037923 ACCACTGCTTGTAGGAAACATTTG 59.962 41.667 0.00 0.00 38.10 2.32
524 1212 4.215109 ACCACTGCTTGTAGGAAACATTT 58.785 39.130 0.00 0.00 38.10 2.32
525 1213 3.832527 ACCACTGCTTGTAGGAAACATT 58.167 40.909 0.00 0.00 38.10 2.71
526 1214 3.508845 ACCACTGCTTGTAGGAAACAT 57.491 42.857 0.00 0.00 38.10 2.71
527 1215 3.389983 ACTACCACTGCTTGTAGGAAACA 59.610 43.478 0.00 0.00 38.98 2.83
528 1216 4.004196 ACTACCACTGCTTGTAGGAAAC 57.996 45.455 0.00 0.00 38.98 2.78
529 1217 4.699925 AACTACCACTGCTTGTAGGAAA 57.300 40.909 0.00 0.00 38.98 3.13
530 1218 4.020839 GGTAACTACCACTGCTTGTAGGAA 60.021 45.833 0.80 0.00 45.73 3.36
531 1219 3.512724 GGTAACTACCACTGCTTGTAGGA 59.487 47.826 0.80 0.00 45.73 2.94
532 1220 3.858247 GGTAACTACCACTGCTTGTAGG 58.142 50.000 0.80 0.00 45.73 3.18
544 1232 1.435577 CGCAAGTGGTGGTAACTACC 58.564 55.000 0.00 0.00 46.62 3.18
559 1247 7.192148 ACTACATACAACATACAAAACGCAA 57.808 32.000 0.00 0.00 0.00 4.85
560 1248 6.788684 ACTACATACAACATACAAAACGCA 57.211 33.333 0.00 0.00 0.00 5.24
561 1249 8.814235 AGATACTACATACAACATACAAAACGC 58.186 33.333 0.00 0.00 0.00 4.84
565 1253 9.511144 CGACAGATACTACATACAACATACAAA 57.489 33.333 0.00 0.00 0.00 2.83
566 1254 8.895737 TCGACAGATACTACATACAACATACAA 58.104 33.333 0.00 0.00 0.00 2.41
567 1255 8.441312 TCGACAGATACTACATACAACATACA 57.559 34.615 0.00 0.00 0.00 2.29
568 1256 9.726232 TTTCGACAGATACTACATACAACATAC 57.274 33.333 0.00 0.00 0.00 2.39
570 1258 9.464714 GATTTCGACAGATACTACATACAACAT 57.535 33.333 0.00 0.00 0.00 2.71
571 1259 7.642586 CGATTTCGACAGATACTACATACAACA 59.357 37.037 0.00 0.00 43.02 3.33
572 1260 7.854422 TCGATTTCGACAGATACTACATACAAC 59.146 37.037 0.00 0.00 44.22 3.32
573 1261 7.922837 TCGATTTCGACAGATACTACATACAA 58.077 34.615 0.00 0.00 44.22 2.41
574 1262 7.440255 TCTCGATTTCGACAGATACTACATACA 59.560 37.037 0.00 0.00 44.22 2.29
575 1263 7.794880 TCTCGATTTCGACAGATACTACATAC 58.205 38.462 0.00 0.00 44.22 2.39
576 1264 7.656542 ACTCTCGATTTCGACAGATACTACATA 59.343 37.037 11.41 0.00 44.22 2.29
577 1265 6.483974 ACTCTCGATTTCGACAGATACTACAT 59.516 38.462 11.41 0.00 44.22 2.29
578 1266 5.816258 ACTCTCGATTTCGACAGATACTACA 59.184 40.000 11.41 0.00 44.22 2.74
579 1267 6.289745 ACTCTCGATTTCGACAGATACTAC 57.710 41.667 11.41 0.00 44.22 2.73
580 1268 7.656542 ACATACTCTCGATTTCGACAGATACTA 59.343 37.037 11.41 0.00 44.22 1.82
581 1269 6.483974 ACATACTCTCGATTTCGACAGATACT 59.516 38.462 11.41 0.00 44.22 2.12
582 1270 6.660722 ACATACTCTCGATTTCGACAGATAC 58.339 40.000 11.41 0.00 44.22 2.24
583 1271 6.862711 ACATACTCTCGATTTCGACAGATA 57.137 37.500 11.41 2.50 44.22 1.98
584 1272 5.759506 ACATACTCTCGATTTCGACAGAT 57.240 39.130 11.41 0.20 44.22 2.90
585 1273 5.276726 CGTACATACTCTCGATTTCGACAGA 60.277 44.000 11.41 2.69 44.22 3.41
586 1274 4.899052 CGTACATACTCTCGATTTCGACAG 59.101 45.833 0.00 1.11 44.22 3.51
587 1275 4.330894 ACGTACATACTCTCGATTTCGACA 59.669 41.667 0.00 0.00 44.22 4.35
588 1276 4.665292 CACGTACATACTCTCGATTTCGAC 59.335 45.833 0.00 0.00 44.22 4.20
590 1278 4.585364 ACACGTACATACTCTCGATTTCG 58.415 43.478 0.00 0.00 41.45 3.46
591 1279 6.713520 ACTACACGTACATACTCTCGATTTC 58.286 40.000 0.00 0.00 0.00 2.17
592 1280 6.674694 ACTACACGTACATACTCTCGATTT 57.325 37.500 0.00 0.00 0.00 2.17
593 1281 7.440556 ACATACTACACGTACATACTCTCGATT 59.559 37.037 0.00 0.00 0.00 3.34
594 1282 6.927936 ACATACTACACGTACATACTCTCGAT 59.072 38.462 0.00 0.00 0.00 3.59
595 1283 6.276091 ACATACTACACGTACATACTCTCGA 58.724 40.000 0.00 0.00 0.00 4.04
596 1284 6.522233 ACATACTACACGTACATACTCTCG 57.478 41.667 0.00 0.00 0.00 4.04
597 1285 8.586570 ACTACATACTACACGTACATACTCTC 57.413 38.462 0.00 0.00 0.00 3.20
695 1383 9.923786 GTGAAATGCGTACATATTTGTATGTAA 57.076 29.630 14.54 6.50 44.07 2.41
696 1384 9.099454 TGTGAAATGCGTACATATTTGTATGTA 57.901 29.630 14.54 11.55 44.07 2.29
697 1385 7.980062 TGTGAAATGCGTACATATTTGTATGT 58.020 30.769 14.54 6.36 44.07 2.29
698 1386 8.833976 TTGTGAAATGCGTACATATTTGTATG 57.166 30.769 10.25 10.25 44.71 2.39
707 1395 9.847706 TTTGTTATATTTGTGAAATGCGTACAT 57.152 25.926 0.00 0.00 38.49 2.29
708 1396 9.678941 TTTTGTTATATTTGTGAAATGCGTACA 57.321 25.926 0.00 0.00 32.38 2.90
711 1399 9.255304 AGTTTTTGTTATATTTGTGAAATGCGT 57.745 25.926 0.00 0.00 32.38 5.24
726 1414 9.407380 TGCATATGAGTCCATAGTTTTTGTTAT 57.593 29.630 6.97 0.00 38.53 1.89
727 1415 8.800370 TGCATATGAGTCCATAGTTTTTGTTA 57.200 30.769 6.97 0.00 38.53 2.41
728 1416 7.701539 TGCATATGAGTCCATAGTTTTTGTT 57.298 32.000 6.97 0.00 38.53 2.83
729 1417 7.701539 TTGCATATGAGTCCATAGTTTTTGT 57.298 32.000 6.97 0.00 38.53 2.83
730 1418 9.590451 AAATTGCATATGAGTCCATAGTTTTTG 57.410 29.630 6.97 0.00 38.53 2.44
859 1547 4.262113 CACCCAGTGGTAGTTACCCCAC 62.262 59.091 8.74 12.24 45.57 4.61
860 1548 0.194080 ACCCAGTGGTAGTTACCCCA 59.806 55.000 8.74 0.00 45.45 4.96
861 1549 0.616891 CACCCAGTGGTAGTTACCCC 59.383 60.000 8.74 0.00 45.57 4.95
872 1560 1.511613 ATCCATCCTACCACCCAGTG 58.488 55.000 0.00 0.00 0.00 3.66
873 1561 2.286935 AATCCATCCTACCACCCAGT 57.713 50.000 0.00 0.00 0.00 4.00
874 1562 3.555966 GAAAATCCATCCTACCACCCAG 58.444 50.000 0.00 0.00 0.00 4.45
875 1563 2.243736 GGAAAATCCATCCTACCACCCA 59.756 50.000 0.00 0.00 36.28 4.51
876 1564 2.424379 GGGAAAATCCATCCTACCACCC 60.424 54.545 0.00 0.00 38.64 4.61
877 1565 2.514160 AGGGAAAATCCATCCTACCACC 59.486 50.000 0.00 0.00 38.64 4.61
878 1566 3.953542 AGGGAAAATCCATCCTACCAC 57.046 47.619 0.00 0.00 38.64 4.16
937 1634 7.185856 TCTCCCTGGCACCTAGAACTATATATA 59.814 40.741 0.00 0.00 0.00 0.86
945 1642 0.827368 CTCTCCCTGGCACCTAGAAC 59.173 60.000 0.00 0.00 0.00 3.01
950 1647 1.305718 GACTCTCTCCCTGGCACCT 60.306 63.158 0.00 0.00 0.00 4.00
992 1694 3.517500 GACCTTCTCCTCCATCTTCAACT 59.482 47.826 0.00 0.00 0.00 3.16
1173 1878 1.361632 GTACGTACCGGCTCCCATC 59.638 63.158 15.00 0.00 0.00 3.51
1236 1941 4.858692 GGTCGGACAATTTTGACATGAATG 59.141 41.667 10.76 0.00 33.04 2.67
1237 1942 4.522405 TGGTCGGACAATTTTGACATGAAT 59.478 37.500 10.76 0.00 33.04 2.57
1256 1964 0.679960 CCCCTCCAAAACGGATGGTC 60.680 60.000 2.34 0.00 45.80 4.02
1265 1991 4.099727 CCGAAGTTTAAAACCCCTCCAAAA 59.900 41.667 0.00 0.00 0.00 2.44
1281 2007 6.238103 CGATGTATAGAATTTGCACCGAAGTT 60.238 38.462 0.00 0.00 0.00 2.66
1302 2028 1.358725 AACGGGCAATCACGACGATG 61.359 55.000 0.00 0.00 33.40 3.84
1303 2029 0.173935 TAACGGGCAATCACGACGAT 59.826 50.000 0.00 0.00 35.12 3.73
1309 2035 2.226330 TGGCATATAACGGGCAATCAC 58.774 47.619 0.00 0.00 36.57 3.06
1316 2068 4.142403 CCAGCAAATATGGCATATAACGGG 60.142 45.833 19.77 16.53 0.00 5.28
1344 2102 0.770499 TTCCAGCACTCACCAATCCA 59.230 50.000 0.00 0.00 0.00 3.41
1378 2139 7.879889 CGTACACGTGTGTTTAAGAAGAAACAA 60.880 37.037 30.83 1.27 41.83 2.83
1422 2198 7.967854 TCCGAATATTTGTTGCTTATGTCTTTG 59.032 33.333 1.99 0.00 0.00 2.77
1471 2253 0.947244 AAAAGACAGCTCTTGCCACG 59.053 50.000 0.00 0.00 36.80 4.94
1598 2401 9.836864 AAATCAAAAGGCTGAAAGTAGATTTTT 57.163 25.926 0.00 0.00 35.30 1.94
1646 2553 1.070134 ACTGCCTGAAACGCTTGAGTA 59.930 47.619 0.00 0.00 0.00 2.59
1648 2555 0.947244 AACTGCCTGAAACGCTTGAG 59.053 50.000 0.00 0.00 0.00 3.02
1698 2606 9.758651 CCTTTGGGCCTTTTTATATGTTATTAC 57.241 33.333 4.53 0.00 0.00 1.89
1699 2607 8.929487 CCCTTTGGGCCTTTTTATATGTTATTA 58.071 33.333 4.53 0.00 35.35 0.98
1700 2608 7.625682 TCCCTTTGGGCCTTTTTATATGTTATT 59.374 33.333 4.53 0.00 43.94 1.40
1704 2619 4.954089 TCCCTTTGGGCCTTTTTATATGT 58.046 39.130 4.53 0.00 43.94 2.29
1865 3124 8.621286 GGATCCAACAAATTCAATAGTCGTATT 58.379 33.333 6.95 0.00 0.00 1.89
1866 3125 7.993183 AGGATCCAACAAATTCAATAGTCGTAT 59.007 33.333 15.82 0.00 0.00 3.06
1870 3129 7.121168 TGTGAGGATCCAACAAATTCAATAGTC 59.879 37.037 15.82 0.00 0.00 2.59
1874 3133 6.669125 TTGTGAGGATCCAACAAATTCAAT 57.331 33.333 23.55 0.00 0.00 2.57
1902 3161 9.118236 GTTAGTGTGCAATTAAGAGTGAAATTC 57.882 33.333 0.00 0.00 0.00 2.17
1903 3162 8.850156 AGTTAGTGTGCAATTAAGAGTGAAATT 58.150 29.630 0.00 0.00 0.00 1.82
1904 3163 8.396272 AGTTAGTGTGCAATTAAGAGTGAAAT 57.604 30.769 0.00 0.00 0.00 2.17
1905 3164 7.801716 AGTTAGTGTGCAATTAAGAGTGAAA 57.198 32.000 0.00 0.00 0.00 2.69
1906 3165 7.386848 GGTAGTTAGTGTGCAATTAAGAGTGAA 59.613 37.037 0.00 0.00 0.00 3.18
1907 3166 6.872020 GGTAGTTAGTGTGCAATTAAGAGTGA 59.128 38.462 0.00 0.00 0.00 3.41
1908 3167 6.649141 TGGTAGTTAGTGTGCAATTAAGAGTG 59.351 38.462 0.00 0.00 0.00 3.51
1952 3216 6.670233 ACGATTTGATAGTAGCACTAGTAGC 58.330 40.000 0.00 1.88 33.66 3.58
2002 3294 7.894376 AATTAGTGTTGAATTTGCAGGATTG 57.106 32.000 2.52 0.00 0.00 2.67
2054 3346 2.957402 TGGAAGATTGCAAGACCTGT 57.043 45.000 4.94 0.00 0.00 4.00
2129 3674 2.647683 TGACACAAGCCATGGTTACA 57.352 45.000 14.67 1.33 0.00 2.41
2137 3682 0.111061 AGAAGCCATGACACAAGCCA 59.889 50.000 0.00 0.00 0.00 4.75
2158 3703 4.335082 TTTATCAAAATCGTGCAGGTCG 57.665 40.909 6.26 0.00 0.00 4.79
2256 3838 1.004745 AGATCGTTGGCCCACTTTCAT 59.995 47.619 5.29 0.00 0.00 2.57
2269 3851 3.184379 CACGTGTCATTCAACAGATCGTT 59.816 43.478 7.58 0.00 38.83 3.85
2308 4141 5.560183 GCCGTTACATATGGAGTACAATTGC 60.560 44.000 5.05 0.00 34.56 3.56
2403 4751 1.990160 AACGGTTCTTCCCTGCACCA 61.990 55.000 0.00 0.00 0.00 4.17
2457 4805 7.817418 ACACAACATACATGTCTTTTAGGTT 57.183 32.000 0.00 0.00 40.80 3.50
2509 4971 1.212751 GTTGGTCGGCTGATTTGGC 59.787 57.895 0.00 0.00 0.00 4.52
2518 4980 3.364441 TGCAGCATGTTGGTCGGC 61.364 61.111 11.80 0.00 39.31 5.54
2771 5262 0.254747 GGATCATCACCCGGTTCCAA 59.745 55.000 0.00 0.00 0.00 3.53
2909 5400 3.390521 AGCACCTGATCCGCGGAA 61.391 61.111 34.66 16.59 0.00 4.30
3102 5602 8.733458 CAACTAATATGGATGAGAGAGAGAGAG 58.267 40.741 0.00 0.00 0.00 3.20
3103 5603 8.224025 ACAACTAATATGGATGAGAGAGAGAGA 58.776 37.037 0.00 0.00 0.00 3.10
3104 5604 8.408043 ACAACTAATATGGATGAGAGAGAGAG 57.592 38.462 0.00 0.00 0.00 3.20
3105 5605 7.174080 CGACAACTAATATGGATGAGAGAGAGA 59.826 40.741 0.00 0.00 0.00 3.10
3106 5606 7.304735 CGACAACTAATATGGATGAGAGAGAG 58.695 42.308 0.00 0.00 0.00 3.20
3107 5607 6.294231 GCGACAACTAATATGGATGAGAGAGA 60.294 42.308 0.00 0.00 0.00 3.10
3108 5608 5.861251 GCGACAACTAATATGGATGAGAGAG 59.139 44.000 0.00 0.00 0.00 3.20
3109 5609 5.536538 AGCGACAACTAATATGGATGAGAGA 59.463 40.000 0.00 0.00 0.00 3.10
3138 5638 2.093783 GTCCAAATTAGTTGTCGCTCCG 59.906 50.000 0.00 0.00 35.23 4.63
3140 5640 2.093783 CCGTCCAAATTAGTTGTCGCTC 59.906 50.000 0.00 0.00 35.23 5.03
3171 5671 6.590292 GGTGAACAATGAGAGATCGACTTTAA 59.410 38.462 0.00 0.00 0.00 1.52
3184 5687 2.036958 TATGCCGGGTGAACAATGAG 57.963 50.000 2.18 0.00 0.00 2.90
3404 6047 0.744414 GCGGGAAGAAGCACTGCATA 60.744 55.000 3.30 0.00 36.53 3.14
3508 6151 5.537674 GGCTTGGATGATATCAGGTCAAATT 59.462 40.000 11.78 0.00 0.00 1.82
3564 6216 2.626266 TGTCATTACGTCTGTGTGGACT 59.374 45.455 0.00 0.00 34.38 3.85
3573 6225 7.667043 TTTGCTCTTTATTGTCATTACGTCT 57.333 32.000 0.00 0.00 0.00 4.18
3574 6226 7.962918 ACATTTGCTCTTTATTGTCATTACGTC 59.037 33.333 0.00 0.00 0.00 4.34
3575 6227 7.816640 ACATTTGCTCTTTATTGTCATTACGT 58.183 30.769 0.00 0.00 0.00 3.57
3751 6459 4.713824 ACTCGAACTTGGATCATCGTTA 57.286 40.909 0.00 0.00 36.70 3.18
3793 6588 9.935241 ACTCATAGGTACATATTGATCATTGAC 57.065 33.333 0.00 0.00 0.00 3.18
3933 6734 2.139118 GGAGAGCCATACGCATTCTTC 58.861 52.381 0.00 0.00 41.38 2.87
3934 6735 1.765314 AGGAGAGCCATACGCATTCTT 59.235 47.619 0.00 0.00 41.38 2.52
3935 6736 1.418334 AGGAGAGCCATACGCATTCT 58.582 50.000 0.00 0.00 41.38 2.40
3956 6757 5.725325 AGTAGGTACCTTGTTCTGAAGAC 57.275 43.478 22.11 7.91 0.00 3.01
4045 6850 1.278637 GAACCCACGCAAGAACACG 59.721 57.895 0.00 0.00 43.62 4.49
4059 6872 0.036388 TTCCAGATCGCCTGTGAACC 60.036 55.000 4.40 0.00 41.33 3.62
4062 6875 1.833630 AGATTTCCAGATCGCCTGTGA 59.166 47.619 4.40 0.00 41.33 3.58
4109 6922 0.616111 AGTCGATGGCCCTCACTTCT 60.616 55.000 8.86 0.00 0.00 2.85
4523 7337 7.886629 ATGCTGGTACATTGATTATTTCACT 57.113 32.000 0.00 0.00 38.20 3.41
4659 7474 2.357009 GCAGACTACCAAATGCATCCTG 59.643 50.000 0.00 0.13 38.54 3.86
4676 7491 2.597340 GGCTGGGCCTAATGCAGA 59.403 61.111 4.53 0.00 46.69 4.26
4700 7519 0.469144 AGGCCAAAAACATCCCACGT 60.469 50.000 5.01 0.00 0.00 4.49
4703 7522 1.799933 AACAGGCCAAAAACATCCCA 58.200 45.000 5.01 0.00 0.00 4.37
4735 7554 2.591133 CGGGTCAACTTTTAAATGCGG 58.409 47.619 1.19 0.00 0.00 5.69
4742 7561 0.106335 TCCGTGCGGGTCAACTTTTA 59.894 50.000 10.94 0.00 37.00 1.52
4783 7602 5.178996 CCGATTTGAGCATTCTTCTAGATGG 59.821 44.000 5.84 0.00 0.00 3.51
4789 7608 2.019984 GGCCGATTTGAGCATTCTTCT 58.980 47.619 0.00 0.00 0.00 2.85
4796 7616 0.605319 AGAAACGGCCGATTTGAGCA 60.605 50.000 35.90 0.00 0.00 4.26
4886 7708 7.443272 AGAACAAACAAAGTACAGGGTGTATAC 59.557 37.037 0.00 0.00 35.05 1.47
4901 7723 2.828520 TGCAGGTGGAAGAACAAACAAA 59.171 40.909 0.00 0.00 0.00 2.83
4908 7730 1.807142 GCTTACTGCAGGTGGAAGAAC 59.193 52.381 19.93 1.08 42.31 3.01
4920 7742 5.508994 GGAGATTAGAGAAGGAGCTTACTGC 60.509 48.000 0.00 0.00 43.29 4.40
4973 7796 8.579850 AGAGTTTATCTTAAATTGATGCACCA 57.420 30.769 0.00 0.00 32.99 4.17
5017 7840 6.865726 TCACAAAAATGAAACCATAACATCGG 59.134 34.615 0.00 0.00 0.00 4.18
5081 7905 8.415950 TCCAAAATAACTCCAAACATGTACAT 57.584 30.769 1.41 1.41 0.00 2.29
5085 7909 7.537596 TCATCCAAAATAACTCCAAACATGT 57.462 32.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.