Multiple sequence alignment - TraesCS5B01G126000

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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 TraesCS5B01G126000 chr5B 100.000 6225 0 0 1 6225 229637433 229643657 0.000000e+00 11496.0
1 TraesCS5B01G126000 chr5B 85.479 303 41 3 5925 6225 434432182 434431881 4.690000e-81 313.0
2 TraesCS5B01G126000 chr5B 86.071 280 28 6 5510 5778 70695608 70695329 2.200000e-74 291.0
3 TraesCS5B01G126000 chr5B 89.474 171 11 7 5764 5931 400177642 400177476 6.320000e-50 209.0
4 TraesCS5B01G126000 chr5A 93.842 5732 237 56 1 5680 281060609 281066276 0.000000e+00 8523.0
5 TraesCS5B01G126000 chr5A 94.000 150 7 2 5772 5919 625659760 625659611 6.280000e-55 226.0
6 TraesCS5B01G126000 chr5A 90.798 163 10 5 5771 5931 278378163 278378322 4.890000e-51 213.0
7 TraesCS5B01G126000 chr5A 72.671 322 60 22 62 370 511876306 511876612 1.440000e-11 82.4
8 TraesCS5B01G126000 chr5D 96.164 4171 112 23 1620 5779 214715631 214719764 0.000000e+00 6772.0
9 TraesCS5B01G126000 chr5D 93.389 1074 41 14 495 1553 214714283 214715341 0.000000e+00 1563.0
10 TraesCS5B01G126000 chr5D 88.735 506 44 12 2 503 214713362 214713858 1.920000e-169 606.0
11 TraesCS5B01G126000 chr5D 90.000 310 24 4 5917 6225 214719749 214720052 1.630000e-105 394.0
12 TraesCS5B01G126000 chr5D 84.848 66 6 3 5508 5569 542299500 542299565 5.210000e-06 63.9
13 TraesCS5B01G126000 chr1B 88.387 310 35 1 5917 6225 46375412 46375721 7.620000e-99 372.0
14 TraesCS5B01G126000 chr1B 87.296 307 38 1 5920 6225 156846690 156846384 3.570000e-92 350.0
15 TraesCS5B01G126000 chr1B 88.519 270 28 3 5511 5778 156846947 156846679 2.160000e-84 324.0
16 TraesCS5B01G126000 chr1B 85.479 303 41 3 5925 6225 562478548 562478247 4.690000e-81 313.0
17 TraesCS5B01G126000 chr1B 85.813 289 30 7 5501 5778 46375138 46375426 4.720000e-76 296.0
18 TraesCS5B01G126000 chr1B 94.000 150 7 2 5771 5918 298489075 298489224 6.280000e-55 226.0
19 TraesCS5B01G126000 chr3A 86.928 306 37 3 5922 6225 550459061 550459365 2.150000e-89 340.0
20 TraesCS5B01G126000 chr3A 91.411 163 10 4 5764 5924 355068328 355068168 2.920000e-53 220.0
21 TraesCS5B01G126000 chr3B 86.129 310 41 2 5917 6225 117046198 117046506 3.600000e-87 333.0
22 TraesCS5B01G126000 chr3B 86.517 267 29 6 5516 5779 784451014 784450752 2.840000e-73 287.0
23 TraesCS5B01G126000 chr3B 93.464 153 7 3 5770 5920 187901815 187901664 2.260000e-54 224.0
24 TraesCS5B01G126000 chr3B 73.457 324 60 23 63 372 1318291 1318602 1.430000e-16 99.0
25 TraesCS5B01G126000 chr7B 85.430 302 43 1 5925 6225 568004710 568004409 4.690000e-81 313.0
26 TraesCS5B01G126000 chr7B 95.775 142 5 1 5779 5919 415978311 415978452 1.750000e-55 228.0
27 TraesCS5B01G126000 chr7B 76.596 141 16 12 5516 5645 595018606 595018472 1.870000e-05 62.1
28 TraesCS5B01G126000 chr2B 85.065 308 39 7 5924 6225 363827760 363828066 2.180000e-79 307.0
29 TraesCS5B01G126000 chr2B 79.623 265 46 6 1163 1423 582313983 582313723 3.830000e-42 183.0
30 TraesCS5B01G126000 chr2B 74.613 323 64 14 63 375 211622078 211622392 6.550000e-25 126.0
31 TraesCS5B01G126000 chrUn 86.429 280 28 6 5509 5778 67352397 67352118 1.310000e-76 298.0
32 TraesCS5B01G126000 chr6B 86.397 272 32 4 5510 5778 10690171 10690440 6.100000e-75 292.0
33 TraesCS5B01G126000 chr6A 86.121 281 28 7 5510 5779 77899550 77899270 6.100000e-75 292.0
34 TraesCS5B01G126000 chr4D 83.099 284 39 8 5504 5782 487093816 487093537 3.730000e-62 250.0
35 TraesCS5B01G126000 chr4D 72.812 320 55 21 63 370 99280543 99280244 5.170000e-11 80.5
36 TraesCS5B01G126000 chr7D 95.804 143 4 2 5778 5918 616052731 616052589 4.850000e-56 230.0
37 TraesCS5B01G126000 chr6D 93.960 149 7 2 5772 5918 332059977 332060125 2.260000e-54 224.0
38 TraesCS5B01G126000 chr2A 79.851 134 16 7 623 752 445716785 445716911 3.090000e-13 87.9
39 TraesCS5B01G126000 chr2D 85.294 68 8 1 5504 5569 309109022 309109089 1.120000e-07 69.4


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 TraesCS5B01G126000 chr5B 229637433 229643657 6224 False 11496.00 11496 100.0000 1 6225 1 chr5B.!!$F1 6224
1 TraesCS5B01G126000 chr5A 281060609 281066276 5667 False 8523.00 8523 93.8420 1 5680 1 chr5A.!!$F2 5679
2 TraesCS5B01G126000 chr5D 214713362 214720052 6690 False 2333.75 6772 92.0720 2 6225 4 chr5D.!!$F2 6223
3 TraesCS5B01G126000 chr1B 156846384 156846947 563 True 337.00 350 87.9075 5511 6225 2 chr1B.!!$R2 714
4 TraesCS5B01G126000 chr1B 46375138 46375721 583 False 334.00 372 87.1000 5501 6225 2 chr1B.!!$F2 724

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
573 1013 1.064906 ACAGATACTCCCTCCGTTCGA 60.065 52.381 0.00 0.00 0.00 3.71 F
911 1359 1.214062 CTCACTCTCCACGCCTCAC 59.786 63.158 0.00 0.00 0.00 3.51 F
1878 2557 0.322816 ACCTGCGATGCTGTTCCAAT 60.323 50.000 0.00 0.00 0.00 3.16 F
2657 3355 1.076332 GACCGTTGACTGAAATCGGG 58.924 55.000 6.84 0.00 44.54 5.14 F
3764 4466 0.252103 TCTACCTTTGCCTCGTCCCT 60.252 55.000 0.00 0.00 0.00 4.20 F
4500 5205 0.109873 CCCGCGACGCTAATAGTAGG 60.110 60.000 19.02 8.67 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 2429 0.460284 CACCTCTCGCCTACGCATTT 60.460 55.000 0.00 0.00 39.84 2.32 R
2628 3326 1.002900 AGTCAACGGTCATGCAAAACG 60.003 47.619 8.21 8.21 0.00 3.60 R
3040 3741 0.183492 TGCCAGGAATATGTGCTCCC 59.817 55.000 0.00 0.00 31.50 4.30 R
4337 5042 0.601558 GTTGCTGGAGTACTCGGTCA 59.398 55.000 16.56 10.50 0.00 4.02 R
5041 5747 0.314302 AGACGTTGAGGAACACGGAG 59.686 55.000 0.00 0.00 31.78 4.63 R
5795 6517 0.035056 CAGCCCTTTCCCACCACTAG 60.035 60.000 0.00 0.00 0.00 2.57 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
45 46 6.550843 GCCTGCTTTAGAGAAAGAAAGAATC 58.449 40.000 1.65 0.00 44.23 2.52
71 72 3.463329 ACTAGAGAAGATCTCAGGGCTCT 59.537 47.826 9.82 6.49 45.73 4.09
75 76 5.276440 AGAGAAGATCTCAGGGCTCTTTTA 58.724 41.667 9.82 0.00 45.73 1.52
76 77 5.904750 AGAGAAGATCTCAGGGCTCTTTTAT 59.095 40.000 9.82 0.00 45.73 1.40
78 79 6.591001 AGAAGATCTCAGGGCTCTTTTATTC 58.409 40.000 0.00 0.00 29.64 1.75
81 84 6.725364 AGATCTCAGGGCTCTTTTATTCAAA 58.275 36.000 0.00 0.00 0.00 2.69
122 125 4.989279 TGAAGGATTGAAATGCTTAGGC 57.011 40.909 9.44 0.00 45.40 3.93
157 160 7.325660 TGCTTGTTCTTTGATTCATAGGATC 57.674 36.000 4.57 0.00 0.00 3.36
173 176 7.615403 TCATAGGATCGGATCTAGGAATTTTG 58.385 38.462 16.96 4.03 0.00 2.44
266 270 6.582677 TTGTTATTTCCCGTGACATCAAAT 57.417 33.333 0.00 0.00 0.00 2.32
271 275 1.210967 TCCCGTGACATCAAATACCCC 59.789 52.381 0.00 0.00 0.00 4.95
274 278 3.118186 CCCGTGACATCAAATACCCCTTA 60.118 47.826 0.00 0.00 0.00 2.69
283 287 7.518188 ACATCAAATACCCCTTACTAATCCTG 58.482 38.462 0.00 0.00 0.00 3.86
287 291 8.069356 TCAAATACCCCTTACTAATCCTGTAGA 58.931 37.037 0.00 0.00 0.00 2.59
293 297 8.935741 ACCCCTTACTAATCCTGTAGAATTAAG 58.064 37.037 0.00 0.00 0.00 1.85
294 298 8.935741 CCCCTTACTAATCCTGTAGAATTAAGT 58.064 37.037 0.00 0.00 0.00 2.24
295 299 9.765795 CCCTTACTAATCCTGTAGAATTAAGTG 57.234 37.037 0.00 0.00 0.00 3.16
298 302 6.592870 ACTAATCCTGTAGAATTAAGTGGGC 58.407 40.000 0.00 0.00 0.00 5.36
299 303 5.450818 AATCCTGTAGAATTAAGTGGGCA 57.549 39.130 0.00 0.00 0.00 5.36
300 304 5.653255 ATCCTGTAGAATTAAGTGGGCAT 57.347 39.130 0.00 0.00 0.00 4.40
322 326 3.671079 TGCCACCCCATTCCTATACTTA 58.329 45.455 0.00 0.00 0.00 2.24
342 346 7.895975 ACTTACCCTATTCTTACGTTTTCAC 57.104 36.000 0.00 0.00 0.00 3.18
432 437 3.523157 TGATCTCTTGATTGTTGCCCCTA 59.477 43.478 0.00 0.00 32.19 3.53
448 453 9.041354 TGTTGCCCCTATTTATTAAGATTGTTT 57.959 29.630 0.00 0.00 0.00 2.83
452 457 7.145323 CCCCTATTTATTAAGATTGTTTGCCG 58.855 38.462 0.00 0.00 0.00 5.69
459 464 1.981256 AGATTGTTTGCCGGTTGTCT 58.019 45.000 1.90 0.00 0.00 3.41
496 501 9.654663 GTCACCAACTCACTTTTAATAGTAGAT 57.345 33.333 0.00 0.00 0.00 1.98
556 996 1.374758 GCACTCCCTCGGTTCACAG 60.375 63.158 0.00 0.00 0.00 3.66
563 1003 1.409427 CCCTCGGTTCACAGATACTCC 59.591 57.143 0.00 0.00 0.00 3.85
573 1013 1.064906 ACAGATACTCCCTCCGTTCGA 60.065 52.381 0.00 0.00 0.00 3.71
583 1023 5.047092 ACTCCCTCCGTTCGAAAATAACTAA 60.047 40.000 0.00 0.00 0.00 2.24
587 1027 6.757947 CCCTCCGTTCGAAAATAACTAACATA 59.242 38.462 0.00 0.00 0.00 2.29
590 1030 9.507280 CTCCGTTCGAAAATAACTAACATAGTA 57.493 33.333 0.00 0.00 38.26 1.82
834 1282 2.358247 GCTCCTCCGCGTCCAAAA 60.358 61.111 4.92 0.00 0.00 2.44
835 1283 2.677979 GCTCCTCCGCGTCCAAAAC 61.678 63.158 4.92 0.00 0.00 2.43
911 1359 1.214062 CTCACTCTCCACGCCTCAC 59.786 63.158 0.00 0.00 0.00 3.51
978 1426 2.040544 CCGGCGCAATTTCTGGAGT 61.041 57.895 10.83 0.00 0.00 3.85
1573 2026 4.842531 TCCCATGAGTATTTTGCTCTCA 57.157 40.909 0.00 0.00 41.43 3.27
1645 2321 6.152154 TCGCATCCATCCTTAACTATTCGATA 59.848 38.462 0.00 0.00 0.00 2.92
1750 2429 1.011333 GGCTCCTTTTGCGCGTATTA 58.989 50.000 8.43 0.00 0.00 0.98
1878 2557 0.322816 ACCTGCGATGCTGTTCCAAT 60.323 50.000 0.00 0.00 0.00 3.16
1970 2657 7.067859 TCAGCTGAATTTGGATTGAGATTTAGG 59.932 37.037 15.67 0.00 29.08 2.69
2203 2893 6.648310 CAGAGTAAAAGATCTTCTTCACAGCA 59.352 38.462 8.78 0.00 35.27 4.41
2246 2937 4.037208 CCAGAGAGCTGATTGTTTGTTTGT 59.963 41.667 0.00 0.00 45.17 2.83
2498 3191 6.827251 CAGGTACTACTCATCCTGTACTACAA 59.173 42.308 0.00 0.00 41.51 2.41
2572 3270 1.155042 GCAAGTGTCAGCCTTCTCTG 58.845 55.000 0.00 0.00 35.46 3.35
2657 3355 1.076332 GACCGTTGACTGAAATCGGG 58.924 55.000 6.84 0.00 44.54 5.14
2881 3580 3.411446 TCGAATGTCTTGTGAGGCAATT 58.589 40.909 0.00 0.00 41.61 2.32
3040 3741 7.921786 TGTTTTCCTAGATAGAAACATGGTG 57.078 36.000 0.00 0.00 37.15 4.17
3568 4270 0.818445 CTCGCCCGCCTACTAGAAGA 60.818 60.000 0.00 0.00 0.00 2.87
3622 4324 5.762179 TTGTGTAGGTGAGGATGATTCTT 57.238 39.130 0.00 0.00 0.00 2.52
3668 4370 8.410141 GGATGAGGTTGCTATAGCTTATAGTAG 58.590 40.741 24.61 0.00 40.19 2.57
3669 4371 8.887264 ATGAGGTTGCTATAGCTTATAGTAGT 57.113 34.615 24.61 2.14 40.19 2.73
3670 4372 9.976776 ATGAGGTTGCTATAGCTTATAGTAGTA 57.023 33.333 24.61 0.00 40.19 1.82
3671 4373 9.451002 TGAGGTTGCTATAGCTTATAGTAGTAG 57.549 37.037 24.61 0.00 40.19 2.57
3672 4374 8.810990 AGGTTGCTATAGCTTATAGTAGTAGG 57.189 38.462 24.61 0.00 40.19 3.18
3673 4375 8.613034 AGGTTGCTATAGCTTATAGTAGTAGGA 58.387 37.037 24.61 0.00 40.19 2.94
3674 4376 8.676401 GGTTGCTATAGCTTATAGTAGTAGGAC 58.324 40.741 24.61 0.00 40.19 3.85
3675 4377 9.452287 GTTGCTATAGCTTATAGTAGTAGGACT 57.548 37.037 24.61 0.00 40.19 3.85
3764 4466 0.252103 TCTACCTTTGCCTCGTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
4144 4849 3.675790 ATGGTGGCCATGCTGGGT 61.676 61.111 9.72 0.00 43.39 4.51
4300 5005 3.699038 TGTTTCCCTTCACTTTTGACCAG 59.301 43.478 0.00 0.00 0.00 4.00
4302 5007 1.494721 TCCCTTCACTTTTGACCAGCT 59.505 47.619 0.00 0.00 0.00 4.24
4329 5034 1.904287 CACCATGGTTTCTTCGGGAA 58.096 50.000 16.84 0.00 0.00 3.97
4442 5147 0.790814 CGACAACCTCGCCTTTCTTC 59.209 55.000 0.00 0.00 35.06 2.87
4443 5148 1.605712 CGACAACCTCGCCTTTCTTCT 60.606 52.381 0.00 0.00 35.06 2.85
4500 5205 0.109873 CCCGCGACGCTAATAGTAGG 60.110 60.000 19.02 8.67 0.00 3.18
4501 5206 0.870393 CCGCGACGCTAATAGTAGGA 59.130 55.000 19.02 0.00 0.00 2.94
4502 5207 1.136029 CCGCGACGCTAATAGTAGGAG 60.136 57.143 19.02 0.00 0.00 3.69
4598 5303 8.405531 TGTCACTTTTCCTTAGTTTTCTTCATG 58.594 33.333 0.00 0.00 0.00 3.07
4599 5304 8.406297 GTCACTTTTCCTTAGTTTTCTTCATGT 58.594 33.333 0.00 0.00 0.00 3.21
4666 5372 2.435059 GGACTCTTGACGGCTGCC 60.435 66.667 9.11 9.11 0.00 4.85
4774 5480 2.104770 TATACCGCCGCTACGTCGTG 62.105 60.000 8.47 0.00 0.00 4.35
4846 5552 1.292541 GACCCTCGCGTTTCTCCTT 59.707 57.895 5.77 0.00 0.00 3.36
5330 6039 6.997239 TGTTCTAGATTTCGAGTAGCTGTA 57.003 37.500 0.00 0.00 0.00 2.74
5331 6040 7.569639 TGTTCTAGATTTCGAGTAGCTGTAT 57.430 36.000 0.00 0.00 0.00 2.29
5377 6086 7.781056 ACAAGGTAATGAAATGTGAAAACTGT 58.219 30.769 0.00 0.00 0.00 3.55
5410 6120 4.527944 GGGAAAGGAGATTTTACCTGGAG 58.472 47.826 0.00 0.00 37.93 3.86
5424 6134 1.302366 CTGGAGCTTGCATATGCGAA 58.698 50.000 22.21 15.65 45.83 4.70
5425 6135 1.878088 CTGGAGCTTGCATATGCGAAT 59.122 47.619 22.21 12.04 45.83 3.34
5506 6217 5.127682 ACTGCTTGTCTCCTTCATTTGTTTT 59.872 36.000 0.00 0.00 0.00 2.43
5514 6225 7.145985 GTCTCCTTCATTTGTTTTCTTTACCC 58.854 38.462 0.00 0.00 0.00 3.69
5573 6287 5.358298 TCACTGAATACATCCGAGATACG 57.642 43.478 0.00 0.00 42.18 3.06
5574 6288 5.061179 TCACTGAATACATCCGAGATACGA 58.939 41.667 0.00 0.00 45.77 3.43
5577 6294 6.695713 CACTGAATACATCCGAGATACGAAAA 59.304 38.462 0.00 0.00 45.77 2.29
5579 6296 7.926555 ACTGAATACATCCGAGATACGAAAAAT 59.073 33.333 0.00 0.00 45.77 1.82
5603 6325 4.326826 CACACACACCCAAGACAAGATAT 58.673 43.478 0.00 0.00 0.00 1.63
5634 6356 2.852075 ACCGACACACCACCCCAT 60.852 61.111 0.00 0.00 0.00 4.00
5650 6372 2.614057 CCCCATCGACAAACAATAGAGC 59.386 50.000 0.00 0.00 0.00 4.09
5658 6380 5.700832 TCGACAAACAATAGAGCAATGAACT 59.299 36.000 0.00 0.00 0.00 3.01
5727 6449 2.044806 GACCATGGATAGCCGCCACT 62.045 60.000 21.47 0.00 38.44 4.00
5730 6452 2.446848 ATGGATAGCCGCCACTGCT 61.447 57.895 0.00 0.00 42.81 4.24
5757 6479 8.514362 GATCAACGAAGATCAGGTTTTCACCG 62.514 46.154 14.09 0.00 43.07 4.94
5778 6500 3.182967 GAGAGCAATACGACAAGAGTGG 58.817 50.000 0.00 0.00 0.00 4.00
5779 6501 1.661112 GAGCAATACGACAAGAGTGGC 59.339 52.381 0.00 0.00 0.00 5.01
5780 6502 1.001974 AGCAATACGACAAGAGTGGCA 59.998 47.619 0.00 0.00 30.49 4.92
5781 6503 1.394917 GCAATACGACAAGAGTGGCAG 59.605 52.381 0.00 0.00 30.49 4.85
5782 6504 2.930887 GCAATACGACAAGAGTGGCAGA 60.931 50.000 0.00 0.00 30.49 4.26
5783 6505 2.656560 ATACGACAAGAGTGGCAGAC 57.343 50.000 0.00 0.00 30.49 3.51
5784 6506 1.617322 TACGACAAGAGTGGCAGACT 58.383 50.000 0.00 0.00 37.76 3.24
5785 6507 1.617322 ACGACAAGAGTGGCAGACTA 58.383 50.000 0.00 0.00 33.83 2.59
5786 6508 1.961394 ACGACAAGAGTGGCAGACTAA 59.039 47.619 0.00 0.00 33.83 2.24
5787 6509 2.029828 ACGACAAGAGTGGCAGACTAAG 60.030 50.000 0.00 0.00 33.83 2.18
5788 6510 2.672478 CGACAAGAGTGGCAGACTAAGG 60.672 54.545 0.00 0.00 33.83 2.69
5789 6511 1.002544 ACAAGAGTGGCAGACTAAGGC 59.997 52.381 0.00 0.00 33.83 4.35
5790 6512 1.002430 CAAGAGTGGCAGACTAAGGCA 59.998 52.381 0.00 0.00 39.41 4.75
5791 6513 1.577736 AGAGTGGCAGACTAAGGCAT 58.422 50.000 0.00 0.00 43.71 4.40
5792 6514 2.752030 AGAGTGGCAGACTAAGGCATA 58.248 47.619 0.00 0.00 43.71 3.14
5793 6515 2.697751 AGAGTGGCAGACTAAGGCATAG 59.302 50.000 0.00 0.00 43.71 2.23
5794 6516 1.139853 AGTGGCAGACTAAGGCATAGC 59.860 52.381 0.00 0.00 43.71 2.97
5795 6517 4.131040 AGTGGCAGACTAAGGCATAGCC 62.131 54.545 0.00 0.00 43.71 3.93
5805 6527 1.451936 GGCATAGCCTAGTGGTGGG 59.548 63.158 0.00 0.00 46.69 4.61
5806 6528 1.054406 GGCATAGCCTAGTGGTGGGA 61.054 60.000 0.00 0.00 46.69 4.37
5807 6529 0.837272 GCATAGCCTAGTGGTGGGAA 59.163 55.000 0.00 0.00 35.27 3.97
5808 6530 1.211949 GCATAGCCTAGTGGTGGGAAA 59.788 52.381 0.00 0.00 35.27 3.13
5809 6531 2.746472 GCATAGCCTAGTGGTGGGAAAG 60.746 54.545 0.00 0.00 35.27 2.62
5810 6532 1.580059 TAGCCTAGTGGTGGGAAAGG 58.420 55.000 0.00 0.00 35.27 3.11
5811 6533 1.208165 AGCCTAGTGGTGGGAAAGGG 61.208 60.000 0.00 0.00 35.27 3.95
5812 6534 1.303282 CCTAGTGGTGGGAAAGGGC 59.697 63.158 0.00 0.00 0.00 5.19
5813 6535 1.208165 CCTAGTGGTGGGAAAGGGCT 61.208 60.000 0.00 0.00 0.00 5.19
5814 6536 0.035056 CTAGTGGTGGGAAAGGGCTG 60.035 60.000 0.00 0.00 0.00 4.85
5815 6537 0.474854 TAGTGGTGGGAAAGGGCTGA 60.475 55.000 0.00 0.00 0.00 4.26
5816 6538 1.142688 AGTGGTGGGAAAGGGCTGAT 61.143 55.000 0.00 0.00 0.00 2.90
5817 6539 0.967380 GTGGTGGGAAAGGGCTGATG 60.967 60.000 0.00 0.00 0.00 3.07
5818 6540 2.054453 GGTGGGAAAGGGCTGATGC 61.054 63.158 0.00 0.00 38.76 3.91
5828 6550 3.731728 GCTGATGCCTCCCACCCA 61.732 66.667 0.00 0.00 0.00 4.51
5829 6551 2.273449 CTGATGCCTCCCACCCAC 59.727 66.667 0.00 0.00 0.00 4.61
5830 6552 3.338250 TGATGCCTCCCACCCACC 61.338 66.667 0.00 0.00 0.00 4.61
5831 6553 4.129148 GATGCCTCCCACCCACCC 62.129 72.222 0.00 0.00 0.00 4.61
5836 6558 2.858974 CTCCCACCCACCCAGGTT 60.859 66.667 0.00 0.00 38.39 3.50
5837 6559 2.856988 TCCCACCCACCCAGGTTC 60.857 66.667 0.00 0.00 38.39 3.62
5838 6560 3.182263 CCCACCCACCCAGGTTCA 61.182 66.667 0.00 0.00 38.39 3.18
5839 6561 2.773527 CCCACCCACCCAGGTTCAA 61.774 63.158 0.00 0.00 38.39 2.69
5840 6562 1.228552 CCACCCACCCAGGTTCAAG 60.229 63.158 0.00 0.00 38.39 3.02
5841 6563 1.228552 CACCCACCCAGGTTCAAGG 60.229 63.158 0.00 0.00 38.39 3.61
5842 6564 2.283173 CCCACCCAGGTTCAAGGC 60.283 66.667 0.00 0.00 34.66 4.35
5843 6565 2.520458 CCACCCAGGTTCAAGGCA 59.480 61.111 0.00 0.00 0.00 4.75
5844 6566 1.903404 CCACCCAGGTTCAAGGCAC 60.903 63.158 0.00 0.00 0.00 5.01
5845 6567 2.113139 ACCCAGGTTCAAGGCACG 59.887 61.111 0.00 0.00 0.00 5.34
5846 6568 2.429930 CCCAGGTTCAAGGCACGA 59.570 61.111 0.00 0.00 0.00 4.35
5847 6569 1.002134 CCCAGGTTCAAGGCACGAT 60.002 57.895 0.00 0.00 0.00 3.73
5848 6570 0.251916 CCCAGGTTCAAGGCACGATA 59.748 55.000 0.00 0.00 0.00 2.92
5849 6571 1.369625 CCAGGTTCAAGGCACGATAC 58.630 55.000 0.00 0.00 0.00 2.24
5850 6572 1.066143 CCAGGTTCAAGGCACGATACT 60.066 52.381 0.00 0.00 0.00 2.12
5851 6573 2.615493 CCAGGTTCAAGGCACGATACTT 60.615 50.000 0.00 0.00 0.00 2.24
5852 6574 2.416547 CAGGTTCAAGGCACGATACTTG 59.583 50.000 10.09 10.09 44.09 3.16
5853 6575 1.130561 GGTTCAAGGCACGATACTTGC 59.869 52.381 11.08 0.36 42.82 4.01
5854 6576 1.804151 GTTCAAGGCACGATACTTGCA 59.196 47.619 11.08 0.00 42.82 4.08
5855 6577 2.177394 TCAAGGCACGATACTTGCAA 57.823 45.000 0.00 0.00 42.82 4.08
5856 6578 2.710377 TCAAGGCACGATACTTGCAAT 58.290 42.857 0.00 0.00 42.82 3.56
5857 6579 3.081061 TCAAGGCACGATACTTGCAATT 58.919 40.909 0.00 0.00 42.82 2.32
5858 6580 3.505680 TCAAGGCACGATACTTGCAATTT 59.494 39.130 0.00 0.00 42.82 1.82
5859 6581 3.492421 AGGCACGATACTTGCAATTTG 57.508 42.857 0.00 0.00 42.12 2.32
5860 6582 2.164219 AGGCACGATACTTGCAATTTGG 59.836 45.455 0.00 0.00 42.12 3.28
5861 6583 2.163412 GGCACGATACTTGCAATTTGGA 59.837 45.455 0.00 0.00 42.12 3.53
5862 6584 3.181487 GGCACGATACTTGCAATTTGGAT 60.181 43.478 0.00 0.00 42.12 3.41
5863 6585 4.423732 GCACGATACTTGCAATTTGGATT 58.576 39.130 0.00 0.00 39.93 3.01
5864 6586 4.864247 GCACGATACTTGCAATTTGGATTT 59.136 37.500 0.00 0.00 39.93 2.17
5865 6587 5.220265 GCACGATACTTGCAATTTGGATTTG 60.220 40.000 0.00 0.00 39.93 2.32
5866 6588 5.863397 CACGATACTTGCAATTTGGATTTGT 59.137 36.000 0.00 0.00 0.00 2.83
5867 6589 6.365789 CACGATACTTGCAATTTGGATTTGTT 59.634 34.615 0.00 0.00 0.00 2.83
5868 6590 6.365789 ACGATACTTGCAATTTGGATTTGTTG 59.634 34.615 0.00 0.00 0.00 3.33
5869 6591 4.816786 ACTTGCAATTTGGATTTGTTGC 57.183 36.364 0.00 2.25 45.27 4.17
5874 6596 5.359716 GCAATTTGGATTTGTTGCATCAA 57.640 34.783 6.10 6.10 44.63 2.57
5875 6597 5.945155 GCAATTTGGATTTGTTGCATCAAT 58.055 33.333 10.87 0.00 44.63 2.57
5876 6598 6.383415 GCAATTTGGATTTGTTGCATCAATT 58.617 32.000 10.87 7.70 44.63 2.32
5877 6599 7.528307 GCAATTTGGATTTGTTGCATCAATTA 58.472 30.769 10.87 0.00 44.63 1.40
5878 6600 8.185505 GCAATTTGGATTTGTTGCATCAATTAT 58.814 29.630 10.87 3.04 44.63 1.28
5882 6604 8.929827 TTGGATTTGTTGCATCAATTATACTG 57.070 30.769 10.87 0.00 0.00 2.74
5883 6605 8.065473 TGGATTTGTTGCATCAATTATACTGT 57.935 30.769 10.87 0.00 0.00 3.55
5884 6606 9.183368 TGGATTTGTTGCATCAATTATACTGTA 57.817 29.630 10.87 0.00 0.00 2.74
5885 6607 9.669353 GGATTTGTTGCATCAATTATACTGTAG 57.331 33.333 10.87 0.00 0.00 2.74
5886 6608 9.669353 GATTTGTTGCATCAATTATACTGTAGG 57.331 33.333 10.87 0.00 0.00 3.18
5887 6609 7.566760 TTGTTGCATCAATTATACTGTAGGG 57.433 36.000 6.10 0.00 0.00 3.53
5888 6610 6.061441 TGTTGCATCAATTATACTGTAGGGG 58.939 40.000 0.00 0.00 0.00 4.79
5889 6611 5.904984 TGCATCAATTATACTGTAGGGGT 57.095 39.130 0.00 0.00 0.00 4.95
5890 6612 6.260700 TGCATCAATTATACTGTAGGGGTT 57.739 37.500 0.00 0.00 0.00 4.11
5891 6613 6.296026 TGCATCAATTATACTGTAGGGGTTC 58.704 40.000 0.00 0.00 0.00 3.62
5892 6614 5.705905 GCATCAATTATACTGTAGGGGTTCC 59.294 44.000 0.00 0.00 0.00 3.62
5893 6615 5.899631 TCAATTATACTGTAGGGGTTCCC 57.100 43.478 0.00 0.00 45.90 3.97
5905 6627 3.069079 GGGGTTCCCTTACAGTCTTTC 57.931 52.381 7.87 0.00 41.34 2.62
5906 6628 2.643304 GGGGTTCCCTTACAGTCTTTCT 59.357 50.000 7.87 0.00 41.34 2.52
5907 6629 3.842436 GGGGTTCCCTTACAGTCTTTCTA 59.158 47.826 7.87 0.00 41.34 2.10
5908 6630 4.473922 GGGGTTCCCTTACAGTCTTTCTAT 59.526 45.833 7.87 0.00 41.34 1.98
5909 6631 5.396548 GGGGTTCCCTTACAGTCTTTCTATC 60.397 48.000 7.87 0.00 41.34 2.08
5910 6632 5.189145 GGGTTCCCTTACAGTCTTTCTATCA 59.811 44.000 0.00 0.00 0.00 2.15
5911 6633 6.296259 GGGTTCCCTTACAGTCTTTCTATCAA 60.296 42.308 0.00 0.00 0.00 2.57
5912 6634 7.166167 GGTTCCCTTACAGTCTTTCTATCAAA 58.834 38.462 0.00 0.00 0.00 2.69
5913 6635 7.664318 GGTTCCCTTACAGTCTTTCTATCAAAA 59.336 37.037 0.00 0.00 0.00 2.44
5914 6636 9.063615 GTTCCCTTACAGTCTTTCTATCAAAAA 57.936 33.333 0.00 0.00 0.00 1.94
5941 6663 4.699522 AAGAGTGGGAACGCCGCC 62.700 66.667 0.00 0.00 43.65 6.13
5943 6665 4.778143 GAGTGGGAACGCCGCCAT 62.778 66.667 0.00 0.00 43.65 4.40
5944 6666 3.379865 GAGTGGGAACGCCGCCATA 62.380 63.158 0.00 0.00 43.65 2.74
5951 6673 3.447025 AACGCCGCCATAGAGCCTC 62.447 63.158 0.00 0.00 0.00 4.70
5959 6681 1.488393 GCCATAGAGCCTCCAGAAAGT 59.512 52.381 0.00 0.00 0.00 2.66
5965 6687 1.544691 GAGCCTCCAGAAAGTGTACGA 59.455 52.381 0.00 0.00 0.00 3.43
5973 6695 1.202440 AGAAAGTGTACGACGGCAACA 60.202 47.619 0.00 0.00 0.00 3.33
5975 6697 0.386476 AAGTGTACGACGGCAACAGA 59.614 50.000 0.00 0.00 0.00 3.41
5976 6698 0.318445 AGTGTACGACGGCAACAGAC 60.318 55.000 0.00 0.00 0.00 3.51
5977 6699 0.595567 GTGTACGACGGCAACAGACA 60.596 55.000 0.00 0.00 0.00 3.41
5978 6700 0.595567 TGTACGACGGCAACAGACAC 60.596 55.000 0.00 0.00 0.00 3.67
5979 6701 1.007038 TACGACGGCAACAGACACC 60.007 57.895 0.00 0.00 0.00 4.16
5980 6702 1.736365 TACGACGGCAACAGACACCA 61.736 55.000 0.00 0.00 0.00 4.17
5988 6716 0.746563 CAACAGACACCACCACCGTT 60.747 55.000 0.00 0.00 0.00 4.44
6065 6793 2.044758 ACCTTAACTCCGTCAACCACT 58.955 47.619 0.00 0.00 0.00 4.00
6079 6807 1.600636 CCACTCACAACCACGCCAT 60.601 57.895 0.00 0.00 0.00 4.40
6083 6811 0.677731 CTCACAACCACGCCATCCAT 60.678 55.000 0.00 0.00 0.00 3.41
6085 6813 1.074775 ACAACCACGCCATCCATGT 59.925 52.632 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 4.518970 GCCCTGAGATCTTCTCTAGTACTG 59.481 50.000 5.39 0.00 43.73 2.74
101 104 4.343231 TGCCTAAGCATTTCAATCCTTCA 58.657 39.130 0.00 0.00 46.52 3.02
133 136 6.037500 CGATCCTATGAATCAAAGAACAAGCA 59.962 38.462 0.00 0.00 0.00 3.91
137 140 6.233905 TCCGATCCTATGAATCAAAGAACA 57.766 37.500 0.00 0.00 0.00 3.18
157 160 8.662781 TTTCATAGACAAAATTCCTAGATCCG 57.337 34.615 0.00 0.00 0.00 4.18
245 249 6.459161 GGGTATTTGATGTCACGGGAAATAAC 60.459 42.308 0.00 0.00 0.00 1.89
246 250 5.591067 GGGTATTTGATGTCACGGGAAATAA 59.409 40.000 0.00 0.00 0.00 1.40
248 252 3.951680 GGGTATTTGATGTCACGGGAAAT 59.048 43.478 0.00 0.00 0.00 2.17
266 270 9.956558 TTAATTCTACAGGATTAGTAAGGGGTA 57.043 33.333 0.00 0.00 0.00 3.69
271 275 9.765795 CCCACTTAATTCTACAGGATTAGTAAG 57.234 37.037 0.00 0.00 0.00 2.34
274 278 6.157994 TGCCCACTTAATTCTACAGGATTAGT 59.842 38.462 0.00 0.00 0.00 2.24
283 287 4.307443 GGCAATGCCCACTTAATTCTAC 57.693 45.455 14.47 0.00 44.06 2.59
298 302 2.386829 ATAGGAATGGGGTGGCAATG 57.613 50.000 0.00 0.00 0.00 2.82
299 303 3.063650 AGTATAGGAATGGGGTGGCAAT 58.936 45.455 0.00 0.00 0.00 3.56
300 304 2.498441 AGTATAGGAATGGGGTGGCAA 58.502 47.619 0.00 0.00 0.00 4.52
311 315 9.646522 AACGTAAGAATAGGGTAAGTATAGGAA 57.353 33.333 0.00 0.00 43.62 3.36
322 326 6.373495 GGATTGTGAAAACGTAAGAATAGGGT 59.627 38.462 0.00 0.00 43.62 4.34
342 346 4.522022 GGGCCTCTTTGATTCATAGGATTG 59.478 45.833 0.84 0.00 0.00 2.67
432 437 7.382898 ACAACCGGCAAACAATCTTAATAAAT 58.617 30.769 0.00 0.00 0.00 1.40
448 453 0.178301 TAACACACAGACAACCGGCA 59.822 50.000 0.00 0.00 0.00 5.69
452 457 4.689345 GGTGACTATAACACACAGACAACC 59.311 45.833 10.49 0.00 39.65 3.77
459 464 5.069914 AGTGAGTTGGTGACTATAACACACA 59.930 40.000 19.97 8.44 43.54 3.72
523 963 4.081198 AGGGAGTGCTTTTCAGTCATCTAG 60.081 45.833 2.67 0.00 45.00 2.43
524 964 3.840666 AGGGAGTGCTTTTCAGTCATCTA 59.159 43.478 2.67 0.00 45.00 1.98
556 996 3.515330 TTTTCGAACGGAGGGAGTATC 57.485 47.619 0.00 0.00 0.00 2.24
563 1003 6.657836 ATGTTAGTTATTTTCGAACGGAGG 57.342 37.500 0.00 0.00 31.85 4.30
714 1155 7.092716 CCTCCCTTCACAAATAAATGAAGTTG 58.907 38.462 11.80 4.52 46.93 3.16
721 1162 4.692523 ACCCCTCCCTTCACAAATAAAT 57.307 40.909 0.00 0.00 0.00 1.40
723 1164 5.043762 AGATACCCCTCCCTTCACAAATAA 58.956 41.667 0.00 0.00 0.00 1.40
770 1211 7.180322 AGAGAAGTCTGCTGAAGAAATATGA 57.820 36.000 0.00 0.00 36.40 2.15
820 1268 2.613506 GGTGTTTTGGACGCGGAGG 61.614 63.158 12.47 0.00 39.71 4.30
834 1282 3.622826 CGGGAGGGTTGACGGTGT 61.623 66.667 0.00 0.00 0.00 4.16
862 1310 6.282199 AGAGCACGGTTTATAAAGAGAGAA 57.718 37.500 0.00 0.00 0.00 2.87
911 1359 1.443802 GCTGGAGAAGAAACGGAAGG 58.556 55.000 0.00 0.00 0.00 3.46
978 1426 1.296392 CGTGAGGATCCAAGTGCCA 59.704 57.895 15.82 0.00 0.00 4.92
1145 1593 0.869454 CACGCGGCTCATCTCTTCTC 60.869 60.000 12.47 0.00 0.00 2.87
1146 1594 1.140589 CACGCGGCTCATCTCTTCT 59.859 57.895 12.47 0.00 0.00 2.85
1593 2046 2.545113 CCCCAATATGTGACGTACTCCG 60.545 54.545 0.00 0.00 44.03 4.63
1645 2321 9.486497 CACATGAAGCAAGATGTATAGATAACT 57.514 33.333 0.00 0.00 31.46 2.24
1662 2341 5.880054 ACCACAAAGTATACACATGAAGC 57.120 39.130 5.50 0.00 0.00 3.86
1750 2429 0.460284 CACCTCTCGCCTACGCATTT 60.460 55.000 0.00 0.00 39.84 2.32
1759 2438 1.153997 GAAGACGACACCTCTCGCC 60.154 63.158 0.00 0.00 37.15 5.54
1878 2557 9.643693 CGTACAAAGGATTTAGGTTTTCTACTA 57.356 33.333 0.00 0.00 35.03 1.82
1970 2657 3.125658 ACTCGCGAGTTTCTTCTACTCTC 59.874 47.826 34.98 0.00 38.83 3.20
2246 2937 1.675310 CAGCGAATTCCCCTGCACA 60.675 57.895 0.00 0.00 0.00 4.57
2572 3270 2.507324 GAGACGCGGCAAGAGACC 60.507 66.667 17.71 0.00 0.00 3.85
2628 3326 1.002900 AGTCAACGGTCATGCAAAACG 60.003 47.619 8.21 8.21 0.00 3.60
2630 3328 2.293170 TCAGTCAACGGTCATGCAAAA 58.707 42.857 0.00 0.00 0.00 2.44
2657 3355 3.133365 AACAGACAGGGTGTGGGGC 62.133 63.158 0.00 0.00 30.77 5.80
2871 3570 2.035066 AGCTTGTTCACAATTGCCTCAC 59.965 45.455 5.05 0.00 35.02 3.51
2872 3571 2.309613 AGCTTGTTCACAATTGCCTCA 58.690 42.857 5.05 0.00 35.02 3.86
2881 3580 3.879295 CTCTGGAGAAAAGCTTGTTCACA 59.121 43.478 17.74 15.13 0.00 3.58
3040 3741 0.183492 TGCCAGGAATATGTGCTCCC 59.817 55.000 0.00 0.00 31.50 4.30
3382 4083 3.699538 AGTAGAGCACGGTGACAATGATA 59.300 43.478 13.29 0.00 0.00 2.15
3388 4089 1.289066 GCAGTAGAGCACGGTGACA 59.711 57.895 13.29 0.00 0.00 3.58
3520 4221 7.362747 CCAAAAGTAGACTAGGATGAGTAACGT 60.363 40.741 0.00 0.00 0.00 3.99
3568 4270 5.136068 TCATAGGTGGTGAGATCTCTTCT 57.864 43.478 22.95 14.22 37.41 2.85
3583 4285 8.884323 ACCTACACAATCATATCATTCATAGGT 58.116 33.333 0.00 0.00 34.16 3.08
3584 4286 9.159364 CACCTACACAATCATATCATTCATAGG 57.841 37.037 0.00 0.00 0.00 2.57
3585 4287 9.933723 TCACCTACACAATCATATCATTCATAG 57.066 33.333 0.00 0.00 0.00 2.23
3622 4324 6.274436 TCATCCACCTTAGGCAATATATTCCA 59.726 38.462 0.00 1.89 0.00 3.53
3668 4370 6.297582 TCTAATACAGCTCCTACAGTCCTAC 58.702 44.000 0.00 0.00 0.00 3.18
3669 4371 6.511017 TCTAATACAGCTCCTACAGTCCTA 57.489 41.667 0.00 0.00 0.00 2.94
3670 4372 5.390087 TCTAATACAGCTCCTACAGTCCT 57.610 43.478 0.00 0.00 0.00 3.85
3671 4373 5.360144 TGTTCTAATACAGCTCCTACAGTCC 59.640 44.000 0.00 0.00 0.00 3.85
3672 4374 6.452494 TGTTCTAATACAGCTCCTACAGTC 57.548 41.667 0.00 0.00 0.00 3.51
3673 4375 5.361285 CCTGTTCTAATACAGCTCCTACAGT 59.639 44.000 0.00 0.00 43.31 3.55
3674 4376 5.594725 TCCTGTTCTAATACAGCTCCTACAG 59.405 44.000 0.00 0.00 43.31 2.74
3675 4377 5.516044 TCCTGTTCTAATACAGCTCCTACA 58.484 41.667 0.00 0.00 43.31 2.74
3735 4437 5.562890 CGAGGCAAAGGTAGAAAGGAAAAAG 60.563 44.000 0.00 0.00 0.00 2.27
3736 4438 4.277423 CGAGGCAAAGGTAGAAAGGAAAAA 59.723 41.667 0.00 0.00 0.00 1.94
3764 4466 3.070734 CCACATGACCAACATCCCAAAAA 59.929 43.478 0.00 0.00 37.07 1.94
4240 4945 1.316651 GATACGTACCGAGGAAGGCT 58.683 55.000 0.00 0.00 33.69 4.58
4300 5005 3.443045 CCATGGTGCCCGTGAAGC 61.443 66.667 2.57 0.00 42.73 3.86
4302 5007 1.152652 AAACCATGGTGCCCGTGAA 60.153 52.632 20.60 0.00 42.73 3.18
4329 5034 4.023980 TGGAGTACTCGGTCATGAATTCT 58.976 43.478 16.56 0.00 0.00 2.40
4337 5042 0.601558 GTTGCTGGAGTACTCGGTCA 59.398 55.000 16.56 10.50 0.00 4.02
4442 5147 1.675641 CCAGCCCGGAAAGTCCAAG 60.676 63.158 0.73 0.00 35.91 3.61
4443 5148 2.434331 CCAGCCCGGAAAGTCCAA 59.566 61.111 0.73 0.00 35.91 3.53
4500 5205 7.118101 CCCGTGTCTACACTCTCTATAATACTC 59.882 44.444 11.22 0.00 44.34 2.59
4501 5206 6.935771 CCCGTGTCTACACTCTCTATAATACT 59.064 42.308 11.22 0.00 44.34 2.12
4502 5207 6.709846 ACCCGTGTCTACACTCTCTATAATAC 59.290 42.308 11.22 0.00 44.34 1.89
4563 5268 2.290641 AGGAAAAGTGACATTGTCGTGC 59.709 45.455 11.97 5.25 34.95 5.34
4666 5372 3.997064 CTCCGTGAAGAGCGCCAGG 62.997 68.421 2.29 0.00 0.00 4.45
4846 5552 2.903357 GCGATGAGGGAGAAGGCA 59.097 61.111 0.00 0.00 0.00 4.75
5038 5744 1.671379 GTTGAGGAACACGGAGGCC 60.671 63.158 0.00 0.00 31.78 5.19
5041 5747 0.314302 AGACGTTGAGGAACACGGAG 59.686 55.000 0.00 0.00 31.78 4.63
5330 6039 5.221843 TGTTAGCTCCTTTGTTGTACTCCAT 60.222 40.000 0.00 0.00 0.00 3.41
5331 6040 4.101898 TGTTAGCTCCTTTGTTGTACTCCA 59.898 41.667 0.00 0.00 0.00 3.86
5377 6086 0.338467 TCCTTTCCCCGATCCTCTCA 59.662 55.000 0.00 0.00 0.00 3.27
5424 6134 8.165239 TGTACATTTTAGAAGAACTTGTGCAT 57.835 30.769 0.00 0.00 0.00 3.96
5425 6135 7.561021 TGTACATTTTAGAAGAACTTGTGCA 57.439 32.000 0.00 0.00 0.00 4.57
5514 6225 0.392706 AAAGCGGGGAAGCCTTTTTG 59.607 50.000 0.00 0.00 38.01 2.44
5573 6287 2.593346 TGGGTGTGTGTGCATTTTTC 57.407 45.000 0.00 0.00 0.00 2.29
5574 6288 2.499289 TCTTGGGTGTGTGTGCATTTTT 59.501 40.909 0.00 0.00 0.00 1.94
5577 6294 1.032014 GTCTTGGGTGTGTGTGCATT 58.968 50.000 0.00 0.00 0.00 3.56
5579 6296 0.322906 TTGTCTTGGGTGTGTGTGCA 60.323 50.000 0.00 0.00 0.00 4.57
5634 6356 5.700832 AGTTCATTGCTCTATTGTTTGTCGA 59.299 36.000 0.00 0.00 0.00 4.20
5650 6372 2.217750 TCGTTGTGGTCCAGTTCATTG 58.782 47.619 0.00 0.00 0.00 2.82
5658 6380 1.227823 CTGGCTTCGTTGTGGTCCA 60.228 57.895 0.00 0.00 0.00 4.02
5730 6452 3.868757 AACCTGATCTTCGTTGATCGA 57.131 42.857 12.85 0.00 44.12 3.59
5757 6479 3.182967 CCACTCTTGTCGTATTGCTCTC 58.817 50.000 0.00 0.00 0.00 3.20
5758 6480 2.675317 GCCACTCTTGTCGTATTGCTCT 60.675 50.000 0.00 0.00 0.00 4.09
5765 6487 1.617322 AGTCTGCCACTCTTGTCGTA 58.383 50.000 0.00 0.00 0.00 3.43
5788 6510 0.837272 TTCCCACCACTAGGCTATGC 59.163 55.000 0.00 0.00 39.06 3.14
5789 6511 2.158755 CCTTTCCCACCACTAGGCTATG 60.159 54.545 0.00 0.00 39.06 2.23
5790 6512 2.127708 CCTTTCCCACCACTAGGCTAT 58.872 52.381 0.00 0.00 39.06 2.97
5791 6513 1.580059 CCTTTCCCACCACTAGGCTA 58.420 55.000 0.00 0.00 39.06 3.93
5792 6514 1.208165 CCCTTTCCCACCACTAGGCT 61.208 60.000 0.00 0.00 39.06 4.58
5793 6515 1.303282 CCCTTTCCCACCACTAGGC 59.697 63.158 0.00 0.00 39.06 3.93
5794 6516 1.208165 AGCCCTTTCCCACCACTAGG 61.208 60.000 0.00 0.00 42.21 3.02
5795 6517 0.035056 CAGCCCTTTCCCACCACTAG 60.035 60.000 0.00 0.00 0.00 2.57
5796 6518 0.474854 TCAGCCCTTTCCCACCACTA 60.475 55.000 0.00 0.00 0.00 2.74
5797 6519 1.142688 ATCAGCCCTTTCCCACCACT 61.143 55.000 0.00 0.00 0.00 4.00
5798 6520 0.967380 CATCAGCCCTTTCCCACCAC 60.967 60.000 0.00 0.00 0.00 4.16
5799 6521 1.383799 CATCAGCCCTTTCCCACCA 59.616 57.895 0.00 0.00 0.00 4.17
5800 6522 2.054453 GCATCAGCCCTTTCCCACC 61.054 63.158 0.00 0.00 33.58 4.61
5801 6523 3.608432 GCATCAGCCCTTTCCCAC 58.392 61.111 0.00 0.00 33.58 4.61
5811 6533 3.731728 TGGGTGGGAGGCATCAGC 61.732 66.667 0.00 0.00 41.10 4.26
5812 6534 2.273449 GTGGGTGGGAGGCATCAG 59.727 66.667 0.00 0.00 0.00 2.90
5813 6535 3.338250 GGTGGGTGGGAGGCATCA 61.338 66.667 0.00 0.00 0.00 3.07
5814 6536 4.129148 GGGTGGGTGGGAGGCATC 62.129 72.222 0.00 0.00 0.00 3.91
5819 6541 2.858974 AACCTGGGTGGGTGGGAG 60.859 66.667 0.00 0.00 39.85 4.30
5820 6542 2.856988 GAACCTGGGTGGGTGGGA 60.857 66.667 0.00 0.00 39.85 4.37
5821 6543 2.713531 CTTGAACCTGGGTGGGTGGG 62.714 65.000 0.00 0.00 39.85 4.61
5822 6544 1.228552 CTTGAACCTGGGTGGGTGG 60.229 63.158 0.00 0.00 39.85 4.61
5823 6545 1.228552 CCTTGAACCTGGGTGGGTG 60.229 63.158 0.00 0.00 39.85 4.61
5824 6546 3.146828 GCCTTGAACCTGGGTGGGT 62.147 63.158 0.00 0.00 42.05 4.51
5825 6547 2.283173 GCCTTGAACCTGGGTGGG 60.283 66.667 0.00 0.00 41.11 4.61
5826 6548 1.903404 GTGCCTTGAACCTGGGTGG 60.903 63.158 0.00 0.00 42.93 4.61
5827 6549 2.260869 CGTGCCTTGAACCTGGGTG 61.261 63.158 0.00 0.00 0.00 4.61
5828 6550 1.779061 ATCGTGCCTTGAACCTGGGT 61.779 55.000 0.00 0.00 0.00 4.51
5829 6551 0.251916 TATCGTGCCTTGAACCTGGG 59.748 55.000 0.00 0.00 0.00 4.45
5830 6552 1.066143 AGTATCGTGCCTTGAACCTGG 60.066 52.381 0.00 0.00 0.00 4.45
5831 6553 2.386661 AGTATCGTGCCTTGAACCTG 57.613 50.000 0.00 0.00 0.00 4.00
5832 6554 2.699954 CAAGTATCGTGCCTTGAACCT 58.300 47.619 5.24 0.00 40.36 3.50
5833 6555 1.130561 GCAAGTATCGTGCCTTGAACC 59.869 52.381 12.55 0.00 40.36 3.62
5834 6556 1.804151 TGCAAGTATCGTGCCTTGAAC 59.196 47.619 12.55 0.64 41.49 3.18
5835 6557 2.177394 TGCAAGTATCGTGCCTTGAA 57.823 45.000 12.55 2.25 41.49 2.69
5836 6558 2.177394 TTGCAAGTATCGTGCCTTGA 57.823 45.000 0.00 0.00 41.49 3.02
5837 6559 3.492421 AATTGCAAGTATCGTGCCTTG 57.508 42.857 4.94 0.00 41.49 3.61
5838 6560 3.367292 CCAAATTGCAAGTATCGTGCCTT 60.367 43.478 4.94 0.00 41.49 4.35
5839 6561 2.164219 CCAAATTGCAAGTATCGTGCCT 59.836 45.455 4.94 0.00 41.49 4.75
5840 6562 2.163412 TCCAAATTGCAAGTATCGTGCC 59.837 45.455 4.94 0.00 41.49 5.01
5841 6563 3.485947 TCCAAATTGCAAGTATCGTGC 57.514 42.857 4.94 1.17 42.55 5.34
5842 6564 5.863397 ACAAATCCAAATTGCAAGTATCGTG 59.137 36.000 4.94 0.00 0.00 4.35
5843 6565 6.024552 ACAAATCCAAATTGCAAGTATCGT 57.975 33.333 4.94 0.00 0.00 3.73
5844 6566 6.670452 GCAACAAATCCAAATTGCAAGTATCG 60.670 38.462 4.94 0.00 45.38 2.92
5845 6567 6.536688 GCAACAAATCCAAATTGCAAGTATC 58.463 36.000 4.94 0.00 45.38 2.24
5846 6568 6.484818 GCAACAAATCCAAATTGCAAGTAT 57.515 33.333 4.94 0.00 45.38 2.12
5847 6569 5.921004 GCAACAAATCCAAATTGCAAGTA 57.079 34.783 4.94 0.00 45.38 2.24
5848 6570 4.816786 GCAACAAATCCAAATTGCAAGT 57.183 36.364 4.94 0.00 45.38 3.16
5852 6574 5.359716 TTGATGCAACAAATCCAAATTGC 57.640 34.783 6.97 0.94 46.08 3.56
5856 6578 9.368674 CAGTATAATTGATGCAACAAATCCAAA 57.631 29.630 13.75 0.00 33.44 3.28
5857 6579 8.530311 ACAGTATAATTGATGCAACAAATCCAA 58.470 29.630 13.75 0.00 33.44 3.53
5858 6580 8.065473 ACAGTATAATTGATGCAACAAATCCA 57.935 30.769 13.75 0.00 33.44 3.41
5859 6581 9.669353 CTACAGTATAATTGATGCAACAAATCC 57.331 33.333 13.75 1.07 33.44 3.01
5860 6582 9.669353 CCTACAGTATAATTGATGCAACAAATC 57.331 33.333 13.75 0.00 33.44 2.17
5861 6583 8.632679 CCCTACAGTATAATTGATGCAACAAAT 58.367 33.333 13.75 8.00 33.44 2.32
5862 6584 7.068103 CCCCTACAGTATAATTGATGCAACAAA 59.932 37.037 13.75 0.00 33.44 2.83
5863 6585 6.545666 CCCCTACAGTATAATTGATGCAACAA 59.454 38.462 12.12 12.12 0.00 2.83
5864 6586 6.061441 CCCCTACAGTATAATTGATGCAACA 58.939 40.000 0.00 0.00 0.00 3.33
5865 6587 6.062095 ACCCCTACAGTATAATTGATGCAAC 58.938 40.000 0.00 0.00 0.00 4.17
5866 6588 6.260700 ACCCCTACAGTATAATTGATGCAA 57.739 37.500 0.00 0.00 0.00 4.08
5867 6589 5.904984 ACCCCTACAGTATAATTGATGCA 57.095 39.130 0.00 0.00 0.00 3.96
5868 6590 5.705905 GGAACCCCTACAGTATAATTGATGC 59.294 44.000 0.00 0.00 0.00 3.91
5888 6610 8.617290 TTTTGATAGAAAGACTGTAAGGGAAC 57.383 34.615 0.00 0.00 39.30 3.62
5913 6635 4.212636 CGTTCCCACTCTTGTCGTATTTTT 59.787 41.667 0.00 0.00 0.00 1.94
5914 6636 3.744426 CGTTCCCACTCTTGTCGTATTTT 59.256 43.478 0.00 0.00 0.00 1.82
5915 6637 3.323243 CGTTCCCACTCTTGTCGTATTT 58.677 45.455 0.00 0.00 0.00 1.40
5916 6638 2.929592 GCGTTCCCACTCTTGTCGTATT 60.930 50.000 0.00 0.00 0.00 1.89
5917 6639 1.403780 GCGTTCCCACTCTTGTCGTAT 60.404 52.381 0.00 0.00 0.00 3.06
5918 6640 0.038892 GCGTTCCCACTCTTGTCGTA 60.039 55.000 0.00 0.00 0.00 3.43
5919 6641 1.300697 GCGTTCCCACTCTTGTCGT 60.301 57.895 0.00 0.00 0.00 4.34
5920 6642 2.027625 GGCGTTCCCACTCTTGTCG 61.028 63.158 0.00 0.00 0.00 4.35
5921 6643 2.027625 CGGCGTTCCCACTCTTGTC 61.028 63.158 0.00 0.00 0.00 3.18
5922 6644 2.030562 CGGCGTTCCCACTCTTGT 59.969 61.111 0.00 0.00 0.00 3.16
5923 6645 3.423154 GCGGCGTTCCCACTCTTG 61.423 66.667 9.37 0.00 0.00 3.02
5924 6646 4.699522 GGCGGCGTTCCCACTCTT 62.700 66.667 9.37 0.00 0.00 2.85
5926 6648 3.379865 TATGGCGGCGTTCCCACTC 62.380 63.158 9.74 0.00 33.17 3.51
5927 6649 3.385749 CTATGGCGGCGTTCCCACT 62.386 63.158 9.74 1.02 33.17 4.00
5928 6650 2.895372 CTATGGCGGCGTTCCCAC 60.895 66.667 9.74 0.00 33.17 4.61
5929 6651 3.078196 TCTATGGCGGCGTTCCCA 61.078 61.111 9.74 8.13 35.21 4.37
5930 6652 2.280186 CTCTATGGCGGCGTTCCC 60.280 66.667 9.74 1.13 0.00 3.97
5941 6663 3.902881 ACACTTTCTGGAGGCTCTATG 57.097 47.619 15.23 5.67 0.00 2.23
5943 6665 2.753452 CGTACACTTTCTGGAGGCTCTA 59.247 50.000 15.23 7.55 0.00 2.43
5944 6666 1.546476 CGTACACTTTCTGGAGGCTCT 59.454 52.381 15.23 0.00 0.00 4.09
5951 6673 0.319211 TGCCGTCGTACACTTTCTGG 60.319 55.000 0.00 0.00 0.00 3.86
5959 6681 0.595567 GTGTCTGTTGCCGTCGTACA 60.596 55.000 0.00 0.00 0.00 2.90
5965 6687 2.203153 GGTGGTGTCTGTTGCCGT 60.203 61.111 0.00 0.00 0.00 5.68
5973 6695 2.508928 CCAACGGTGGTGGTGTCT 59.491 61.111 12.69 0.00 40.42 3.41
6002 6730 0.036306 GGGTACACCACTTGTCCAGG 59.964 60.000 0.00 0.00 39.91 4.45
6065 6793 0.959867 CATGGATGGCGTGGTTGTGA 60.960 55.000 0.00 0.00 0.00 3.58
6103 6831 1.552348 GGAGCGTGCGTCTCATATGC 61.552 60.000 14.28 0.00 40.81 3.14
6104 6832 1.271446 CGGAGCGTGCGTCTCATATG 61.271 60.000 14.28 0.00 32.38 1.78
6105 6833 1.008424 CGGAGCGTGCGTCTCATAT 60.008 57.895 14.28 0.00 32.38 1.78
6106 6834 2.407616 CGGAGCGTGCGTCTCATA 59.592 61.111 14.28 0.00 32.38 2.15
6161 6890 1.150536 GGGTTGTCTGGTTGCAGGA 59.849 57.895 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.