Multiple sequence alignment - TraesCS7D01G253900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G253900 chr7D 100.000 9798 0 0 1 9798 230651597 230661394 0.000000e+00 18094.0
1 TraesCS7D01G253900 chr7D 85.000 140 11 9 9664 9798 230668796 230668930 6.170000e-27 134.0
2 TraesCS7D01G253900 chr7D 100.000 31 0 0 4146 4176 16694460 16694490 3.820000e-04 58.4
3 TraesCS7D01G253900 chr7A 94.804 7409 239 42 1929 9225 243502296 243509670 0.000000e+00 11415.0
4 TraesCS7D01G253900 chr7A 94.469 1374 43 16 551 1908 243500947 243502303 0.000000e+00 2085.0
5 TraesCS7D01G253900 chr7A 91.379 348 19 5 9438 9782 243509907 243510246 5.360000e-127 466.0
6 TraesCS7D01G253900 chr7A 84.400 250 17 9 9226 9474 243643714 243643942 9.900000e-55 226.0
7 TraesCS7D01G253900 chr7A 92.908 141 8 1 9499 9639 243644023 243644161 4.640000e-48 204.0
8 TraesCS7D01G253900 chr7A 91.912 136 10 1 9229 9363 243509716 243509851 1.300000e-43 189.0
9 TraesCS7D01G253900 chr7A 92.035 113 8 1 3894 4006 721473685 721473574 3.660000e-34 158.0
10 TraesCS7D01G253900 chr7B 93.864 4384 171 38 4892 9225 202108085 202112420 0.000000e+00 6516.0
11 TraesCS7D01G253900 chr7B 93.794 2401 82 22 372 2730 202103068 202105443 0.000000e+00 3546.0
12 TraesCS7D01G253900 chr7B 94.993 2157 72 10 2732 4854 202105519 202107673 0.000000e+00 3352.0
13 TraesCS7D01G253900 chr7B 89.914 347 29 3 1 344 202102551 202102894 9.030000e-120 442.0
14 TraesCS7D01G253900 chr7B 91.120 259 11 6 9542 9798 202112478 202112726 3.390000e-89 340.0
15 TraesCS7D01G253900 chr7B 93.443 61 4 0 4264 4324 329084189 329084249 3.770000e-14 91.6
16 TraesCS7D01G253900 chr7B 92.063 63 5 0 4266 4328 604365599 604365661 1.360000e-13 89.8
17 TraesCS7D01G253900 chr5A 76.331 1183 254 21 2868 4030 487839842 487841018 2.340000e-170 610.0
18 TraesCS7D01G253900 chr5A 74.634 615 127 18 7100 7710 487843588 487844177 2.730000e-60 244.0
19 TraesCS7D01G253900 chr5D 76.227 1182 255 21 2869 4030 385944050 385945225 3.910000e-168 603.0
20 TraesCS7D01G253900 chr5D 74.146 615 130 18 7100 7710 385947348 385947937 2.750000e-55 228.0
21 TraesCS7D01G253900 chr5D 83.750 80 10 3 4328 4406 28168609 28168532 1.370000e-08 73.1
22 TraesCS7D01G253900 chr5B 75.842 1188 256 22 2868 4030 463846648 463847829 8.530000e-160 575.0
23 TraesCS7D01G253900 chr5B 74.675 616 125 22 7100 7710 463850151 463850740 2.730000e-60 244.0
24 TraesCS7D01G253900 chr2B 90.566 159 15 0 1387 1545 773077065 773077223 2.770000e-50 211.0
25 TraesCS7D01G253900 chr1B 81.004 279 31 11 1278 1546 444671632 444671898 1.670000e-47 202.0
26 TraesCS7D01G253900 chr1B 79.275 193 33 5 4142 4331 478483310 478483122 2.870000e-25 128.0
27 TraesCS7D01G253900 chr1B 90.769 65 6 0 4271 4335 660675970 660676034 4.870000e-13 87.9
28 TraesCS7D01G253900 chr1B 89.583 48 5 0 4128 4175 385647319 385647272 2.950000e-05 62.1
29 TraesCS7D01G253900 chr4D 90.000 70 7 0 4266 4335 498726616 498726685 3.770000e-14 91.6
30 TraesCS7D01G253900 chr4D 91.803 61 5 0 4271 4331 14867830 14867890 1.750000e-12 86.1
31 TraesCS7D01G253900 chr6D 93.103 58 4 0 4274 4331 5038749 5038692 1.750000e-12 86.1
32 TraesCS7D01G253900 chr1A 87.324 71 7 2 4256 4324 366124762 366124832 8.160000e-11 80.5


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 TraesCS7D01G253900 chr7D 230651597 230661394 9797 False 18094.00 18094 100.0000 1 9798 1 chr7D.!!$F2 9797
1 TraesCS7D01G253900 chr7A 243500947 243510246 9299 False 3538.75 11415 93.1410 551 9782 4 chr7A.!!$F1 9231
2 TraesCS7D01G253900 chr7B 202102551 202112726 10175 False 2839.20 6516 92.7370 1 9798 5 chr7B.!!$F3 9797
3 TraesCS7D01G253900 chr5A 487839842 487844177 4335 False 427.00 610 75.4825 2868 7710 2 chr5A.!!$F1 4842
4 TraesCS7D01G253900 chr5D 385944050 385947937 3887 False 415.50 603 75.1865 2869 7710 2 chr5D.!!$F1 4841
5 TraesCS7D01G253900 chr5B 463846648 463850740 4092 False 409.50 575 75.2585 2868 7710 2 chr5B.!!$F1 4842

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
146 149 0.033991 TCTCCTCCTCCTGGAACTCG 60.034 60.000 0.00 0.0 42.66 4.18 F
1871 2071 0.462759 CTCGCTTCCTTGATCACCCC 60.463 60.000 0.00 0.0 0.00 4.95 F
3493 3834 0.040058 TGGCTCAAGCAATGGATGGT 59.960 50.000 4.13 0.0 44.36 3.55 F
3609 3950 0.107703 TGCATAAAGGCACTCGGAGG 60.108 55.000 10.23 0.0 38.49 4.30 F
4874 5261 1.275421 TATGGAATGCACGGTGGGGA 61.275 55.000 10.60 0.0 0.00 4.81 F
6146 7035 0.622136 ATCAACTGATGCAGAGGCCA 59.378 50.000 5.01 0.0 40.13 5.36 F
7899 9167 3.378427 ACTCTCCTGTCACAAACAAAAGC 59.622 43.478 0.00 0.0 37.45 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2139 1.537202 GAGTGCCATTGCCGGATTATC 59.463 52.381 5.05 0.0 36.33 1.75 R
3609 3950 0.331616 ATAGCCCACCCACACCTTTC 59.668 55.000 0.00 0.0 0.00 2.62 R
4854 5241 0.819259 CCCCACCGTGCATTCCATAG 60.819 60.000 0.00 0.0 0.00 2.23 R
5138 6008 2.534349 CGTGGTAGCGTCATTACATCAC 59.466 50.000 0.00 0.0 0.00 3.06 R
6554 7445 1.736681 CAGAAGCTGTAGCAGAAAGGC 59.263 52.381 6.65 0.0 45.16 4.35 R
8097 9368 2.076863 GGAACGGAGAAACATCTGGTG 58.923 52.381 0.00 0.0 0.00 4.17 R
9383 10734 0.036858 GTCCAGAGACTGCCACCTTC 60.037 60.000 0.00 0.0 40.10 3.46 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
121 124 3.751479 TGCATCGCTTATCACCATAGT 57.249 42.857 0.00 0.00 0.00 2.12
146 149 0.033991 TCTCCTCCTCCTGGAACTCG 60.034 60.000 0.00 0.00 42.66 4.18
196 199 1.362406 GCTCAAGCCTAGGCAACGTC 61.362 60.000 34.70 16.78 44.88 4.34
224 227 4.512484 TCGATCAAGCATTTGTCCATGTA 58.488 39.130 0.00 0.00 35.73 2.29
227 230 3.355378 TCAAGCATTTGTCCATGTAGGG 58.645 45.455 0.00 0.00 35.73 3.53
254 257 0.838987 TAACCCTTTGTCGCCCTCCT 60.839 55.000 0.00 0.00 0.00 3.69
273 276 2.750657 CCCACCAGCCATCTCCTCC 61.751 68.421 0.00 0.00 0.00 4.30
281 285 0.465705 GCCATCTCCTCCGAATGACA 59.534 55.000 0.00 0.00 0.00 3.58
283 287 2.034878 CCATCTCCTCCGAATGACAGA 58.965 52.381 0.00 0.00 0.00 3.41
286 290 1.006043 TCTCCTCCGAATGACAGAGGT 59.994 52.381 8.01 0.00 46.15 3.85
298 302 1.352622 ACAGAGGTGGAAAGTGGGCA 61.353 55.000 0.00 0.00 0.00 5.36
301 305 0.690762 GAGGTGGAAAGTGGGCACTA 59.309 55.000 0.00 0.00 41.58 2.74
345 349 5.686771 GAACATTTTCGGCTAGATTTTGC 57.313 39.130 0.00 0.00 0.00 3.68
346 350 4.110036 ACATTTTCGGCTAGATTTTGCC 57.890 40.909 0.00 0.00 45.25 4.52
347 351 3.763897 ACATTTTCGGCTAGATTTTGCCT 59.236 39.130 7.11 0.00 46.42 4.75
348 352 4.220602 ACATTTTCGGCTAGATTTTGCCTT 59.779 37.500 7.11 0.00 46.42 4.35
349 353 4.434713 TTTTCGGCTAGATTTTGCCTTC 57.565 40.909 7.11 0.00 46.42 3.46
350 354 2.779755 TCGGCTAGATTTTGCCTTCA 57.220 45.000 7.11 0.00 46.42 3.02
351 355 2.356135 TCGGCTAGATTTTGCCTTCAC 58.644 47.619 7.11 0.00 46.42 3.18
352 356 1.062587 CGGCTAGATTTTGCCTTCACG 59.937 52.381 7.11 0.00 46.42 4.35
353 357 1.401905 GGCTAGATTTTGCCTTCACGG 59.598 52.381 1.33 0.00 45.26 4.94
355 359 2.747446 GCTAGATTTTGCCTTCACGGAA 59.253 45.455 0.00 0.00 33.16 4.30
356 360 3.190535 GCTAGATTTTGCCTTCACGGAAA 59.809 43.478 0.00 0.00 33.16 3.13
357 361 3.643159 AGATTTTGCCTTCACGGAAAC 57.357 42.857 0.00 0.00 26.46 2.78
358 362 2.955660 AGATTTTGCCTTCACGGAAACA 59.044 40.909 0.00 0.00 26.46 2.83
359 363 2.570442 TTTTGCCTTCACGGAAACAC 57.430 45.000 0.00 0.00 26.46 3.32
365 369 2.540973 GCCTTCACGGAAACACTGTTTC 60.541 50.000 21.79 21.79 35.72 2.78
368 372 4.527564 CTTCACGGAAACACTGTTTCATC 58.472 43.478 27.93 15.39 35.72 2.92
369 373 3.804036 TCACGGAAACACTGTTTCATCT 58.196 40.909 27.93 12.36 35.72 2.90
370 374 4.196193 TCACGGAAACACTGTTTCATCTT 58.804 39.130 27.93 11.79 35.72 2.40
405 555 5.418310 TGTTTTCGTCTTGCTTTTCCTAG 57.582 39.130 0.00 0.00 0.00 3.02
409 559 7.227910 TGTTTTCGTCTTGCTTTTCCTAGTTAT 59.772 33.333 0.00 0.00 0.00 1.89
419 569 5.360999 GCTTTTCCTAGTTATCCAGGCATTT 59.639 40.000 0.00 0.00 0.00 2.32
420 570 6.460261 GCTTTTCCTAGTTATCCAGGCATTTC 60.460 42.308 0.00 0.00 0.00 2.17
422 572 5.708736 TCCTAGTTATCCAGGCATTTCAA 57.291 39.130 0.00 0.00 0.00 2.69
424 574 6.064060 TCCTAGTTATCCAGGCATTTCAATG 58.936 40.000 0.00 0.00 39.40 2.82
493 643 3.750652 TGAGCAAACGTGAGCATTATCAA 59.249 39.130 13.99 0.00 0.00 2.57
847 1013 1.524621 GCACACTGTCACACCAGCT 60.525 57.895 0.00 0.00 35.83 4.24
848 1014 1.502163 GCACACTGTCACACCAGCTC 61.502 60.000 0.00 0.00 35.83 4.09
849 1015 0.882042 CACACTGTCACACCAGCTCC 60.882 60.000 0.00 0.00 35.83 4.70
850 1016 1.302033 CACTGTCACACCAGCTCCC 60.302 63.158 0.00 0.00 35.83 4.30
851 1017 2.348998 CTGTCACACCAGCTCCCC 59.651 66.667 0.00 0.00 0.00 4.81
906 1078 1.229209 TCCCTCTTCCGCTCCTGTT 60.229 57.895 0.00 0.00 0.00 3.16
1558 1753 4.988716 TGTGGGGCCTCGACGAGT 62.989 66.667 22.61 0.00 0.00 4.18
1732 1927 4.451150 GCATGGACCTCGCCACGA 62.451 66.667 0.00 0.00 41.56 4.35
1871 2071 0.462759 CTCGCTTCCTTGATCACCCC 60.463 60.000 0.00 0.00 0.00 4.95
1872 2072 0.909610 TCGCTTCCTTGATCACCCCT 60.910 55.000 0.00 0.00 0.00 4.79
1873 2073 0.830648 CGCTTCCTTGATCACCCCTA 59.169 55.000 0.00 0.00 0.00 3.53
1874 2074 1.202580 CGCTTCCTTGATCACCCCTAG 60.203 57.143 0.00 0.00 0.00 3.02
1875 2075 1.475930 GCTTCCTTGATCACCCCTAGC 60.476 57.143 0.00 0.00 0.00 3.42
1904 2104 3.365364 GGTTTTCATTGACTGCTTCGAGG 60.365 47.826 0.00 0.00 0.00 4.63
1908 2108 3.329386 TCATTGACTGCTTCGAGGAAAG 58.671 45.455 0.00 0.00 0.00 2.62
1939 2139 7.888250 TGTATACTGGATATGAGCTATGAGG 57.112 40.000 4.17 0.00 0.00 3.86
2014 2214 7.806014 TGTTCAATTTAGCCGATTTTAAGTCAC 59.194 33.333 0.00 0.00 0.00 3.67
2446 2658 2.500098 TCATTTACCCTCCAGTTCCTCG 59.500 50.000 0.00 0.00 0.00 4.63
2566 2787 9.258826 CCATATGTTTCTTGATTTTTGTTGTGA 57.741 29.630 1.24 0.00 0.00 3.58
3027 3349 5.148651 AGGAACTATGTCACAGTTGGTAC 57.851 43.478 0.07 0.00 36.38 3.34
3175 3497 7.805071 CACATCAGTTTCTCAACTTCATTAACC 59.195 37.037 0.00 0.00 40.66 2.85
3319 3657 6.994496 TGATGCCAGAACAATTTATAGAGGAG 59.006 38.462 0.00 0.00 0.00 3.69
3377 3718 3.888930 CCAAGGCTCTGTCACCTTTTTAA 59.111 43.478 0.00 0.00 43.91 1.52
3493 3834 0.040058 TGGCTCAAGCAATGGATGGT 59.960 50.000 4.13 0.00 44.36 3.55
3609 3950 0.107703 TGCATAAAGGCACTCGGAGG 60.108 55.000 10.23 0.00 38.49 4.30
3811 4152 2.965147 TCTGGATGATATTCTGCGGACA 59.035 45.455 0.00 0.00 0.00 4.02
4056 4397 4.798882 ACCAAACCATTCACTTCACCTTA 58.201 39.130 0.00 0.00 0.00 2.69
4124 4466 9.149225 CTGTTAATGCATGCAAATAGGTTTTTA 57.851 29.630 26.68 12.24 0.00 1.52
4233 4575 6.259608 TGGTGAAGTACAAAATTGCCAAAATG 59.740 34.615 0.00 0.00 0.00 2.32
4246 4588 7.706100 ATTGCCAAAATGAAAATAAAGCCAT 57.294 28.000 0.00 0.00 0.00 4.40
4324 4687 3.980583 CGTATCCCGTGCTACCATT 57.019 52.632 0.00 0.00 0.00 3.16
4727 5110 7.292292 TCGTAAGACAAATTAATGGTCAAACG 58.708 34.615 23.67 23.67 45.01 3.60
4842 5229 6.975772 AGTTTTGTAAGTTGCTTAAAATGCGA 59.024 30.769 0.00 0.00 0.00 5.10
4854 5241 6.199342 TGCTTAAAATGCGAAACCAAACTTAC 59.801 34.615 0.00 0.00 0.00 2.34
4874 5261 1.275421 TATGGAATGCACGGTGGGGA 61.275 55.000 10.60 0.00 0.00 4.81
4875 5262 2.438434 GGAATGCACGGTGGGGAG 60.438 66.667 10.60 0.00 0.00 4.30
4877 5264 3.256960 AATGCACGGTGGGGAGGT 61.257 61.111 10.60 0.00 0.00 3.85
4878 5265 1.906105 GAATGCACGGTGGGGAGGTA 61.906 60.000 10.60 0.00 0.00 3.08
4879 5266 1.910580 AATGCACGGTGGGGAGGTAG 61.911 60.000 10.60 0.00 0.00 3.18
4880 5267 3.001406 GCACGGTGGGGAGGTAGT 61.001 66.667 10.60 0.00 0.00 2.73
4881 5268 1.683365 GCACGGTGGGGAGGTAGTA 60.683 63.158 10.60 0.00 0.00 1.82
5087 5957 7.413438 GGCATACTTTTCTATCACAGTTGTCAG 60.413 40.741 0.00 0.00 0.00 3.51
5179 6049 7.844009 ACCACGGAGAACTTATAGAAATTACA 58.156 34.615 0.00 0.00 0.00 2.41
5273 6143 6.300354 ACTTGTTATTCTGTTTCTGTTCCG 57.700 37.500 0.00 0.00 0.00 4.30
5520 6390 4.832266 TGGTACTGGCTTGTCATGAAATTT 59.168 37.500 0.00 0.00 0.00 1.82
5837 6721 7.125391 ACTGGGAATATTTCTGCTGGAAAATA 58.875 34.615 8.88 5.17 45.56 1.40
6032 6921 6.627395 TTCTGCTGAGCTAGTAATAGACTC 57.373 41.667 5.83 7.84 39.81 3.36
6033 6922 5.685728 TCTGCTGAGCTAGTAATAGACTCA 58.314 41.667 17.36 17.36 39.81 3.41
6146 7035 0.622136 ATCAACTGATGCAGAGGCCA 59.378 50.000 5.01 0.00 40.13 5.36
6436 7327 4.433936 CGCAATGCTGACTTCGATCATATC 60.434 45.833 2.94 0.00 0.00 1.63
7565 8814 4.976987 TGGAAAACGAAGAAACTGTTGTC 58.023 39.130 0.00 0.00 0.00 3.18
7668 8917 7.651704 AGGACGGAACAAAAACTGATTTTATTG 59.348 33.333 0.00 0.00 39.20 1.90
7740 9000 7.193595 AGTTTGTGTCTTTCGGTTTTGAATAG 58.806 34.615 0.00 0.00 0.00 1.73
7808 9068 5.823353 TGGTTTGGATTTTGTTTAGTCGTC 58.177 37.500 0.00 0.00 0.00 4.20
7899 9167 3.378427 ACTCTCCTGTCACAAACAAAAGC 59.622 43.478 0.00 0.00 37.45 3.51
7988 9256 7.607250 ACAGTTTTCCATCTGTTGTTTGTAAA 58.393 30.769 0.00 0.00 41.33 2.01
8020 9291 7.861630 TGTTCTTTTTCATTCTAGAGGAAACG 58.138 34.615 16.70 12.52 37.49 3.60
8033 9304 8.983307 TCTAGAGGAAACGAAATTAAGAGAAC 57.017 34.615 0.00 0.00 0.00 3.01
8039 9310 7.553044 AGGAAACGAAATTAAGAGAACTATGGG 59.447 37.037 0.00 0.00 0.00 4.00
8047 9318 4.618378 AAGAGAACTATGGGACCTCTCT 57.382 45.455 3.43 3.43 43.64 3.10
8056 9327 3.418684 TGGGACCTCTCTTTTACTTGC 57.581 47.619 0.00 0.00 0.00 4.01
8060 9331 4.327680 GGACCTCTCTTTTACTTGCATGT 58.672 43.478 10.40 10.40 0.00 3.21
8080 9351 4.030913 TGTTGGACCCTTCTCTATCGATT 58.969 43.478 1.71 0.00 0.00 3.34
8082 9353 5.839063 TGTTGGACCCTTCTCTATCGATTAT 59.161 40.000 1.71 0.00 0.00 1.28
8146 9417 8.845942 AACTAAAAATTAGACGAAACACAACC 57.154 30.769 4.24 0.00 0.00 3.77
8159 9430 5.965334 CGAAACACAACCTATATCACATTGC 59.035 40.000 0.00 0.00 0.00 3.56
8169 9441 7.517320 ACCTATATCACATTGCACCAAATAGA 58.483 34.615 0.00 0.00 0.00 1.98
8199 9471 4.202212 GGTAGGTTCAAGTTTGGTTGCATT 60.202 41.667 0.00 0.00 0.00 3.56
8238 9510 2.030007 TGGCTCTTTTCTGAAAATGCGG 60.030 45.455 22.51 11.69 33.48 5.69
8291 9573 3.118592 GCCTGGCTGTTCTGTAATCTACT 60.119 47.826 12.43 0.00 0.00 2.57
8293 9575 3.861840 TGGCTGTTCTGTAATCTACTGC 58.138 45.455 0.00 0.00 35.52 4.40
8313 9596 4.343231 TGCTGATCCTCCAATTTTTGCTA 58.657 39.130 0.00 0.00 0.00 3.49
8360 9644 2.097036 CTTCCATCATGCTTCAGCCAA 58.903 47.619 0.00 0.00 41.18 4.52
8377 9666 2.038557 GCCAAACCACTAACTCTCTCCA 59.961 50.000 0.00 0.00 0.00 3.86
8440 9729 2.363683 GAGCCTGGAGAAACAATGGAG 58.636 52.381 0.00 0.00 0.00 3.86
8494 9783 1.912110 GAAGAATTCGTCGACGGAGTG 59.088 52.381 35.05 9.62 36.29 3.51
8596 9885 0.719465 CCGTTACGCACAGGATCAAC 59.281 55.000 0.00 0.00 0.00 3.18
8644 9933 3.706373 CCCCCACCGGTCAGTCTG 61.706 72.222 2.59 0.00 0.00 3.51
8648 9937 2.047844 CACCGGTCAGTCTGCTGG 60.048 66.667 2.59 16.28 42.78 4.85
8689 9978 3.003763 GCCCCCTCGAGTGAAGGT 61.004 66.667 12.31 0.00 0.00 3.50
8691 9980 1.305381 CCCCCTCGAGTGAAGGTCT 60.305 63.158 12.31 0.00 0.00 3.85
8692 9981 1.608717 CCCCCTCGAGTGAAGGTCTG 61.609 65.000 12.31 0.00 0.00 3.51
8695 9984 1.248486 CCTCGAGTGAAGGTCTGACA 58.752 55.000 12.31 0.00 0.00 3.58
8801 10090 0.392461 TCTGCGGAACATGTAAGGGC 60.392 55.000 0.00 1.24 0.00 5.19
8852 10141 6.308015 TGATGTAGCAGTTTTGTATAGGGT 57.692 37.500 0.00 0.00 0.00 4.34
9038 10343 2.945668 GTGTGCTGTGGAAGAACTTTCT 59.054 45.455 0.00 0.00 35.13 2.52
9039 10344 4.127171 GTGTGCTGTGGAAGAACTTTCTA 58.873 43.478 0.00 0.00 35.13 2.10
9040 10345 4.757149 GTGTGCTGTGGAAGAACTTTCTAT 59.243 41.667 0.00 0.00 35.13 1.98
9041 10346 5.932303 GTGTGCTGTGGAAGAACTTTCTATA 59.068 40.000 0.00 0.00 35.13 1.31
9042 10347 6.595716 GTGTGCTGTGGAAGAACTTTCTATAT 59.404 38.462 0.00 0.00 35.13 0.86
9043 10348 7.764443 GTGTGCTGTGGAAGAACTTTCTATATA 59.236 37.037 0.00 0.00 35.13 0.86
9292 10643 1.550524 AGAGTCGCTTGATGCTTGGTA 59.449 47.619 0.00 0.00 40.11 3.25
9325 10676 0.467384 GCAGGCCTCAGCTCTGAATA 59.533 55.000 0.00 0.00 38.72 1.75
9346 10697 4.918810 ATTTTCAGGAAACACACCTCAC 57.081 40.909 0.00 0.00 35.35 3.51
9347 10698 3.644966 TTTCAGGAAACACACCTCACT 57.355 42.857 0.00 0.00 35.35 3.41
9348 10699 2.910688 TCAGGAAACACACCTCACTC 57.089 50.000 0.00 0.00 35.35 3.51
9349 10700 2.398588 TCAGGAAACACACCTCACTCT 58.601 47.619 0.00 0.00 35.35 3.24
9350 10701 2.365617 TCAGGAAACACACCTCACTCTC 59.634 50.000 0.00 0.00 35.35 3.20
9352 10703 1.270893 GGAAACACACCTCACTCTCCC 60.271 57.143 0.00 0.00 0.00 4.30
9353 10704 1.694696 GAAACACACCTCACTCTCCCT 59.305 52.381 0.00 0.00 0.00 4.20
9354 10705 1.343069 AACACACCTCACTCTCCCTC 58.657 55.000 0.00 0.00 0.00 4.30
9355 10706 0.485099 ACACACCTCACTCTCCCTCT 59.515 55.000 0.00 0.00 0.00 3.69
9356 10707 0.894141 CACACCTCACTCTCCCTCTG 59.106 60.000 0.00 0.00 0.00 3.35
9357 10708 0.780637 ACACCTCACTCTCCCTCTGA 59.219 55.000 0.00 0.00 0.00 3.27
9359 10710 1.824230 CACCTCACTCTCCCTCTGAAG 59.176 57.143 0.00 0.00 0.00 3.02
9360 10711 1.431243 ACCTCACTCTCCCTCTGAAGT 59.569 52.381 0.00 0.00 0.00 3.01
9361 10712 2.099405 CCTCACTCTCCCTCTGAAGTC 58.901 57.143 0.00 0.00 0.00 3.01
9362 10713 2.291540 CCTCACTCTCCCTCTGAAGTCT 60.292 54.545 0.00 0.00 0.00 3.24
9363 10714 3.053991 CCTCACTCTCCCTCTGAAGTCTA 60.054 52.174 0.00 0.00 0.00 2.59
9364 10715 4.568804 CCTCACTCTCCCTCTGAAGTCTAA 60.569 50.000 0.00 0.00 0.00 2.10
9365 10716 4.337145 TCACTCTCCCTCTGAAGTCTAAC 58.663 47.826 0.00 0.00 0.00 2.34
9366 10717 3.445805 CACTCTCCCTCTGAAGTCTAACC 59.554 52.174 0.00 0.00 0.00 2.85
9367 10718 3.335484 ACTCTCCCTCTGAAGTCTAACCT 59.665 47.826 0.00 0.00 0.00 3.50
9368 10719 4.540906 ACTCTCCCTCTGAAGTCTAACCTA 59.459 45.833 0.00 0.00 0.00 3.08
9369 10720 4.857679 TCTCCCTCTGAAGTCTAACCTAC 58.142 47.826 0.00 0.00 0.00 3.18
9370 10721 4.291513 TCTCCCTCTGAAGTCTAACCTACA 59.708 45.833 0.00 0.00 0.00 2.74
9371 10722 5.006896 TCCCTCTGAAGTCTAACCTACAA 57.993 43.478 0.00 0.00 0.00 2.41
9372 10723 5.017490 TCCCTCTGAAGTCTAACCTACAAG 58.983 45.833 0.00 0.00 0.00 3.16
9373 10724 4.773149 CCCTCTGAAGTCTAACCTACAAGT 59.227 45.833 0.00 0.00 0.00 3.16
9374 10725 5.246429 CCCTCTGAAGTCTAACCTACAAGTT 59.754 44.000 0.00 0.00 0.00 2.66
9375 10726 6.239629 CCCTCTGAAGTCTAACCTACAAGTTT 60.240 42.308 0.00 0.00 0.00 2.66
9376 10727 6.869388 CCTCTGAAGTCTAACCTACAAGTTTC 59.131 42.308 0.00 0.00 0.00 2.78
9377 10728 7.256012 CCTCTGAAGTCTAACCTACAAGTTTCT 60.256 40.741 0.00 0.00 0.00 2.52
9378 10729 8.019656 TCTGAAGTCTAACCTACAAGTTTCTT 57.980 34.615 0.00 0.00 0.00 2.52
9379 10730 8.142551 TCTGAAGTCTAACCTACAAGTTTCTTC 58.857 37.037 0.00 0.00 34.78 2.87
9380 10731 7.788026 TGAAGTCTAACCTACAAGTTTCTTCA 58.212 34.615 0.00 0.00 37.79 3.02
9381 10732 7.926555 TGAAGTCTAACCTACAAGTTTCTTCAG 59.073 37.037 0.00 0.00 36.72 3.02
9382 10733 7.598759 AGTCTAACCTACAAGTTTCTTCAGA 57.401 36.000 0.00 0.00 0.00 3.27
9383 10734 7.662897 AGTCTAACCTACAAGTTTCTTCAGAG 58.337 38.462 0.00 0.00 0.00 3.35
9384 10735 7.506261 AGTCTAACCTACAAGTTTCTTCAGAGA 59.494 37.037 0.00 0.00 0.00 3.10
9385 10736 8.142551 GTCTAACCTACAAGTTTCTTCAGAGAA 58.857 37.037 0.00 0.00 40.07 2.87
9386 10737 8.361139 TCTAACCTACAAGTTTCTTCAGAGAAG 58.639 37.037 0.39 0.39 42.55 2.85
9387 10738 5.859495 ACCTACAAGTTTCTTCAGAGAAGG 58.141 41.667 6.89 0.00 42.55 3.46
9388 10739 5.367060 ACCTACAAGTTTCTTCAGAGAAGGT 59.633 40.000 6.89 0.00 42.55 3.50
9389 10740 5.698545 CCTACAAGTTTCTTCAGAGAAGGTG 59.301 44.000 6.89 1.91 42.55 4.00
9390 10741 4.455606 ACAAGTTTCTTCAGAGAAGGTGG 58.544 43.478 6.89 0.00 42.55 4.61
9391 10742 3.133141 AGTTTCTTCAGAGAAGGTGGC 57.867 47.619 6.89 0.00 42.55 5.01
9400 10751 0.248843 GAGAAGGTGGCAGTCTCTGG 59.751 60.000 13.04 0.00 35.84 3.86
9417 10768 0.763604 TGGACCCACCAACCGAACTA 60.764 55.000 0.00 0.00 46.75 2.24
9420 10771 2.148768 GACCCACCAACCGAACTAAAG 58.851 52.381 0.00 0.00 0.00 1.85
9435 10786 2.037772 ACTAAAGGCTGTGGTGAGACAG 59.962 50.000 0.00 0.00 45.34 3.51
9451 10817 0.394216 ACAGGTCACAAGTGCAAGCA 60.394 50.000 0.00 0.00 0.00 3.91
9464 10830 0.032540 GCAAGCAGAACCAACTTGGG 59.967 55.000 12.62 0.00 43.37 4.12
9476 10843 4.286707 ACCAACTTGGGAAGCTAAAAGTT 58.713 39.130 12.62 9.12 43.37 2.66
9490 10857 6.010219 AGCTAAAAGTTTAGGAGATTTGGCA 58.990 36.000 11.73 0.00 39.15 4.92
9550 10917 1.524849 GCGGAAGATTGGAGAGGGC 60.525 63.158 0.00 0.00 0.00 5.19
9552 10919 1.626356 CGGAAGATTGGAGAGGGCCA 61.626 60.000 6.18 0.00 35.78 5.36
9622 10990 2.546368 CGACGGACAGATTTGGTCAAAA 59.454 45.455 0.00 0.00 37.00 2.44
9632 11000 1.576356 TTGGTCAAAATTTGGTGCGC 58.424 45.000 0.00 0.00 0.00 6.09
9635 11003 1.460359 GGTCAAAATTTGGTGCGCATG 59.540 47.619 15.91 4.97 0.00 4.06
9636 11004 2.402305 GTCAAAATTTGGTGCGCATGA 58.598 42.857 15.91 7.81 0.00 3.07
9637 11005 2.409378 GTCAAAATTTGGTGCGCATGAG 59.591 45.455 15.91 0.00 0.00 2.90
9684 11052 6.663953 AGTGTAGAGGATAAAGAGCAGTTGTA 59.336 38.462 0.00 0.00 0.00 2.41
9689 11057 6.381420 AGAGGATAAAGAGCAGTTGTAGCTAA 59.619 38.462 0.00 0.00 43.58 3.09
9690 11058 6.947464 AGGATAAAGAGCAGTTGTAGCTAAA 58.053 36.000 0.00 0.00 43.58 1.85
9718 11087 4.890158 TGGCTAATCTCACTGAACTCAA 57.110 40.909 0.00 0.00 0.00 3.02
9719 11088 4.569943 TGGCTAATCTCACTGAACTCAAC 58.430 43.478 0.00 0.00 0.00 3.18
9720 11089 4.284490 TGGCTAATCTCACTGAACTCAACT 59.716 41.667 0.00 0.00 0.00 3.16
9721 11090 4.867608 GGCTAATCTCACTGAACTCAACTC 59.132 45.833 0.00 0.00 0.00 3.01
9722 11091 5.473931 GCTAATCTCACTGAACTCAACTCA 58.526 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 8.948631 TGTCATCATCTTATAACTTTGAGTCC 57.051 34.615 0.00 0.00 0.00 3.85
82 85 8.177663 GCGATGCATGCTTAAAGTATACATAAT 58.822 33.333 20.33 0.00 26.72 1.28
103 106 3.990469 GGTGACTATGGTGATAAGCGATG 59.010 47.826 0.00 0.00 0.00 3.84
121 124 0.031716 CCAGGAGGAGGAGATGGTGA 60.032 60.000 0.00 0.00 36.89 4.02
146 149 2.778299 TGGTGGCTACAACAGATTGAC 58.222 47.619 1.52 0.00 39.97 3.18
196 199 2.098607 ACAAATGCTTGATCGAGGCATG 59.901 45.455 16.64 11.32 44.51 4.06
227 230 3.985279 GGCGACAAAGGGTTAATTCAAAC 59.015 43.478 0.00 0.00 0.00 2.93
241 244 2.528127 TGGGAGGAGGGCGACAAA 60.528 61.111 0.00 0.00 0.00 2.83
242 245 3.319198 GTGGGAGGAGGGCGACAA 61.319 66.667 0.00 0.00 0.00 3.18
254 257 1.690633 GAGGAGATGGCTGGTGGGA 60.691 63.158 0.00 0.00 0.00 4.37
273 276 2.738846 CACTTTCCACCTCTGTCATTCG 59.261 50.000 0.00 0.00 0.00 3.34
281 285 1.062488 AGTGCCCACTTTCCACCTCT 61.062 55.000 0.00 0.00 38.83 3.69
283 287 1.145571 TTAGTGCCCACTTTCCACCT 58.854 50.000 6.21 0.00 42.54 4.00
286 290 2.378547 AGGATTTAGTGCCCACTTTCCA 59.621 45.455 18.63 0.00 42.54 3.53
301 305 9.729281 TGTTCGGTTATTAGTCTTAAAGGATTT 57.271 29.630 0.00 0.00 43.42 2.17
344 348 1.021968 AACAGTGTTTCCGTGAAGGC 58.978 50.000 1.64 0.00 40.77 4.35
345 349 2.680841 TGAAACAGTGTTTCCGTGAAGG 59.319 45.455 34.65 0.00 42.97 3.46
346 350 4.273480 AGATGAAACAGTGTTTCCGTGAAG 59.727 41.667 34.65 0.00 0.00 3.02
347 351 4.196193 AGATGAAACAGTGTTTCCGTGAA 58.804 39.130 34.65 21.92 0.00 3.18
348 352 3.804036 AGATGAAACAGTGTTTCCGTGA 58.196 40.909 34.65 22.23 0.00 4.35
349 353 4.552166 AAGATGAAACAGTGTTTCCGTG 57.448 40.909 34.65 0.00 0.00 4.94
350 354 4.638421 TCAAAGATGAAACAGTGTTTCCGT 59.362 37.500 34.65 26.41 30.99 4.69
351 355 5.168526 TCAAAGATGAAACAGTGTTTCCG 57.831 39.130 34.65 20.49 30.99 4.30
356 360 9.950496 AGACTATAATCAAAGATGAAACAGTGT 57.050 29.630 0.00 0.00 39.49 3.55
370 374 8.227791 GCAAGACGAAAACAAGACTATAATCAA 58.772 33.333 0.00 0.00 0.00 2.57
381 531 4.672409 AGGAAAAGCAAGACGAAAACAAG 58.328 39.130 0.00 0.00 0.00 3.16
389 539 5.175859 TGGATAACTAGGAAAAGCAAGACG 58.824 41.667 0.00 0.00 0.00 4.18
409 559 7.041107 GCTTTTTATACATTGAAATGCCTGGA 58.959 34.615 0.00 0.00 40.04 3.86
452 602 5.982516 TGCTCAAAGAAAACGTTTATTGCAT 59.017 32.000 15.03 0.00 0.00 3.96
480 630 6.913170 TCCTTTTCAACTTGATAATGCTCAC 58.087 36.000 0.00 0.00 0.00 3.51
530 680 6.568081 CGTTTACTGTAGCTATATTCGCTCCT 60.568 42.308 0.00 0.00 38.86 3.69
851 1017 2.245438 GAGGCAAGGGAACTCCGGAG 62.245 65.000 30.11 30.11 42.68 4.63
892 1064 1.292223 CGGAAACAGGAGCGGAAGA 59.708 57.895 0.00 0.00 0.00 2.87
906 1078 1.749638 GAGAGGAGAGGCGACGGAA 60.750 63.158 0.00 0.00 0.00 4.30
986 1159 4.899239 CCATGACGCCTCGGCCTC 62.899 72.222 0.00 1.14 37.98 4.70
988 1161 4.899239 CTCCATGACGCCTCGGCC 62.899 72.222 1.72 0.00 37.98 6.13
991 1164 4.899239 GGGCTCCATGACGCCTCG 62.899 72.222 20.05 0.00 45.57 4.63
992 1165 4.899239 CGGGCTCCATGACGCCTC 62.899 72.222 20.05 11.94 45.57 4.70
1654 1849 2.856032 CTTGTTCGCGCTGTCCAG 59.144 61.111 5.56 0.00 0.00 3.86
1871 2071 7.569957 GCAGTCAATGAAAACCAAAATTGCTAG 60.570 37.037 0.00 0.00 31.50 3.42
1872 2072 6.202570 GCAGTCAATGAAAACCAAAATTGCTA 59.797 34.615 0.00 0.00 31.50 3.49
1873 2073 5.007921 GCAGTCAATGAAAACCAAAATTGCT 59.992 36.000 0.00 0.00 31.50 3.91
1874 2074 5.007921 AGCAGTCAATGAAAACCAAAATTGC 59.992 36.000 0.00 0.00 31.50 3.56
1875 2075 6.607735 AGCAGTCAATGAAAACCAAAATTG 57.392 33.333 0.00 0.00 0.00 2.32
1904 2104 9.066892 TCATATCCAGTATACAATTTGCCTTTC 57.933 33.333 5.50 0.00 0.00 2.62
1908 2108 6.656693 AGCTCATATCCAGTATACAATTTGCC 59.343 38.462 5.50 0.00 0.00 4.52
1939 2139 1.537202 GAGTGCCATTGCCGGATTATC 59.463 52.381 5.05 0.00 36.33 1.75
2446 2658 6.169800 AGCTAGTTCTTTTCAGAAGATGGAC 58.830 40.000 0.00 0.00 39.86 4.02
2540 2753 9.258826 TCACAACAAAAATCAAGAAACATATGG 57.741 29.630 7.80 0.00 0.00 2.74
2566 2787 7.072562 AGTAGTCAATCAAGAGTCATATCCCT 58.927 38.462 0.00 0.00 0.00 4.20
2714 2962 6.183810 AGTGATTCAGATATCAATGCCTCA 57.816 37.500 5.32 0.00 36.37 3.86
3027 3349 1.915141 AGTGGGCAAAGAGAACATGG 58.085 50.000 0.00 0.00 0.00 3.66
3175 3497 2.051334 TTAGTTCCAATCGGCCATGG 57.949 50.000 7.63 7.63 38.09 3.66
3319 3657 5.538849 TTGTGGGTTTTACCTTGATTTCC 57.461 39.130 0.00 0.00 38.64 3.13
3377 3718 6.403878 CAATCAAGGCATTCCAAGATTTCTT 58.596 36.000 0.00 0.00 36.57 2.52
3493 3834 3.984838 GCAACCTGACCAAATTGCA 57.015 47.368 11.00 0.00 45.38 4.08
3609 3950 0.331616 ATAGCCCACCCACACCTTTC 59.668 55.000 0.00 0.00 0.00 2.62
3811 4152 1.280457 ACTCCCTCTTCGCCAATTCT 58.720 50.000 0.00 0.00 0.00 2.40
4056 4397 7.111247 TGATCTTTGAGGAACAAAACAACAT 57.889 32.000 0.00 0.00 45.97 2.71
4207 4549 5.344743 TTGGCAATTTTGTACTTCACCAA 57.655 34.783 0.00 0.00 32.50 3.67
4250 4603 8.417273 AGGCTATGTGTGTGTGTGTATATATA 57.583 34.615 0.00 0.00 0.00 0.86
4252 4605 6.724893 AGGCTATGTGTGTGTGTGTATATA 57.275 37.500 0.00 0.00 0.00 0.86
4324 4687 4.102815 TGCGGGCGCTTATGGGAA 62.103 61.111 7.64 0.00 42.51 3.97
4623 5006 3.181329 ACATAGTTGGACTGATGGGTGA 58.819 45.455 0.00 0.00 0.00 4.02
4726 5109 3.114065 GTTATGGACTCTAAAGCCGACG 58.886 50.000 0.00 0.00 0.00 5.12
4727 5110 4.388378 AGTTATGGACTCTAAAGCCGAC 57.612 45.455 0.00 0.00 31.20 4.79
4754 5140 1.617850 TCCATGGATTTTTGCAAGCGT 59.382 42.857 11.44 0.00 0.00 5.07
4842 5229 6.569610 CGTGCATTCCATAGTAAGTTTGGTTT 60.570 38.462 0.00 0.00 0.00 3.27
4854 5241 0.819259 CCCCACCGTGCATTCCATAG 60.819 60.000 0.00 0.00 0.00 2.23
5010 5880 6.134535 TCATCCCTAGTGGCTAAAAGAAAA 57.865 37.500 0.00 0.00 0.00 2.29
5012 5882 5.772393 TTCATCCCTAGTGGCTAAAAGAA 57.228 39.130 0.00 0.00 0.00 2.52
5138 6008 2.534349 CGTGGTAGCGTCATTACATCAC 59.466 50.000 0.00 0.00 0.00 3.06
5179 6049 6.627087 TTTATTCCCTCTCAGTTCTCACAT 57.373 37.500 0.00 0.00 0.00 3.21
6032 6921 3.546815 GCGATAAAAGCCATGCAGTACTG 60.547 47.826 18.93 18.93 0.00 2.74
6033 6922 2.614057 GCGATAAAAGCCATGCAGTACT 59.386 45.455 0.00 0.00 0.00 2.73
6307 7198 1.962807 CCACCCTGCAAGAACAATCAA 59.037 47.619 0.00 0.00 34.07 2.57
6554 7445 1.736681 CAGAAGCTGTAGCAGAAAGGC 59.263 52.381 6.65 0.00 45.16 4.35
6624 7808 9.125026 CAAGGCTGGATATTATTCTACAAAACT 57.875 33.333 0.00 0.00 0.00 2.66
7003 8187 3.816523 GTGGTGGAACATTTTAACCGAGA 59.183 43.478 0.00 0.00 44.52 4.04
7565 8814 7.372451 TCCACAGTTATTTGTTATTCGAAGG 57.628 36.000 3.35 0.00 0.00 3.46
7769 9029 4.450053 CAAACCAGGCAAATGGAAGAAAA 58.550 39.130 8.67 0.00 43.57 2.29
7776 9036 3.421919 AAATCCAAACCAGGCAAATGG 57.578 42.857 0.61 0.61 46.47 3.16
7808 9068 2.397549 CGGCAAAAGAAAGAAGCTTGG 58.602 47.619 2.10 0.00 0.00 3.61
7899 9167 8.091449 GGACTCTAGGTGGAAATATGATAAGTG 58.909 40.741 0.00 0.00 0.00 3.16
8015 9286 8.388853 GTCCCATAGTTCTCTTAATTTCGTTTC 58.611 37.037 0.00 0.00 0.00 2.78
8020 9291 7.797062 AGAGGTCCCATAGTTCTCTTAATTTC 58.203 38.462 0.00 0.00 31.52 2.17
8033 9304 5.119694 GCAAGTAAAAGAGAGGTCCCATAG 58.880 45.833 0.00 0.00 0.00 2.23
8036 9307 2.708861 TGCAAGTAAAAGAGAGGTCCCA 59.291 45.455 0.00 0.00 0.00 4.37
8039 9310 5.335191 CCAACATGCAAGTAAAAGAGAGGTC 60.335 44.000 0.00 0.00 0.00 3.85
8047 9318 3.571590 AGGGTCCAACATGCAAGTAAAA 58.428 40.909 0.00 0.00 0.00 1.52
8056 9327 3.384789 TCGATAGAGAAGGGTCCAACATG 59.615 47.826 0.00 0.00 42.67 3.21
8080 9351 9.201989 ACATCTGGTGTAGTTCTCAGATAAATA 57.798 33.333 0.00 0.00 42.85 1.40
8082 9353 7.482169 ACATCTGGTGTAGTTCTCAGATAAA 57.518 36.000 0.00 0.00 42.85 1.40
8097 9368 2.076863 GGAACGGAGAAACATCTGGTG 58.923 52.381 0.00 0.00 0.00 4.17
8146 9417 8.382030 TGTCTATTTGGTGCAATGTGATATAG 57.618 34.615 0.00 0.00 0.00 1.31
8159 9430 4.164221 ACCTACCTCCATGTCTATTTGGTG 59.836 45.833 0.00 0.00 34.48 4.17
8169 9441 4.398319 CAAACTTGAACCTACCTCCATGT 58.602 43.478 0.00 0.00 0.00 3.21
8238 9510 2.865551 CACACATTGACAAAACTTGGCC 59.134 45.455 0.00 0.00 38.13 5.36
8291 9573 3.167485 AGCAAAAATTGGAGGATCAGCA 58.833 40.909 0.00 0.00 36.25 4.41
8293 9575 5.416952 ACAGTAGCAAAAATTGGAGGATCAG 59.583 40.000 0.00 0.00 36.25 2.90
8313 9596 4.025040 TGAAATGAGATGGCAGAACAGT 57.975 40.909 0.00 0.00 0.00 3.55
8360 9644 4.804261 GCACATTGGAGAGAGTTAGTGGTT 60.804 45.833 0.00 0.00 0.00 3.67
8494 9783 3.443045 CACCATCCGCCTTGCACC 61.443 66.667 0.00 0.00 0.00 5.01
8569 9858 1.214373 TGTGCGTAACGGTTTCGGTC 61.214 55.000 19.06 6.36 41.39 4.79
8674 9963 0.612174 TCAGACCTTCACTCGAGGGG 60.612 60.000 16.20 13.77 42.73 4.79
8677 9966 2.155279 TCTGTCAGACCTTCACTCGAG 58.845 52.381 11.84 11.84 0.00 4.04
8689 9978 2.956333 TCTGGAAGAACGTTCTGTCAGA 59.044 45.455 35.08 35.08 42.31 3.27
8746 10035 1.448540 CTCTGAGGCGCCGAAATGT 60.449 57.895 23.20 0.68 0.00 2.71
8801 10090 4.551388 ACAAGCAAGAGAAACTAGACTCG 58.449 43.478 0.00 0.00 38.08 4.18
8852 10141 5.080969 GGTAAGCACACTATTACCTCACA 57.919 43.478 6.83 0.00 44.97 3.58
9252 10603 5.048154 ACTCTCGTGGTCATAGATCATGATG 60.048 44.000 14.30 0.00 45.37 3.07
9261 10612 1.018148 AGCGACTCTCGTGGTCATAG 58.982 55.000 0.00 0.00 42.81 2.23
9284 10635 1.270839 GCCTGAAGTGACTACCAAGCA 60.271 52.381 4.35 0.00 0.00 3.91
9292 10643 1.374190 CCTGCAGCCTGAAGTGACT 59.626 57.895 8.66 0.00 0.00 3.41
9325 10676 4.536765 AGTGAGGTGTGTTTCCTGAAAAT 58.463 39.130 0.00 0.00 35.20 1.82
9341 10692 2.099405 GACTTCAGAGGGAGAGTGAGG 58.901 57.143 0.00 0.00 0.00 3.86
9346 10697 3.976015 AGGTTAGACTTCAGAGGGAGAG 58.024 50.000 0.00 0.00 0.00 3.20
9347 10698 4.291513 TGTAGGTTAGACTTCAGAGGGAGA 59.708 45.833 0.00 0.00 0.00 3.71
9348 10699 4.601084 TGTAGGTTAGACTTCAGAGGGAG 58.399 47.826 0.00 0.00 0.00 4.30
9349 10700 4.669866 TGTAGGTTAGACTTCAGAGGGA 57.330 45.455 0.00 0.00 0.00 4.20
9350 10701 4.773149 ACTTGTAGGTTAGACTTCAGAGGG 59.227 45.833 0.00 0.00 0.00 4.30
9352 10703 7.662897 AGAAACTTGTAGGTTAGACTTCAGAG 58.337 38.462 0.00 0.00 0.00 3.35
9353 10704 7.598759 AGAAACTTGTAGGTTAGACTTCAGA 57.401 36.000 0.00 0.00 0.00 3.27
9354 10705 7.926555 TGAAGAAACTTGTAGGTTAGACTTCAG 59.073 37.037 0.00 0.00 38.03 3.02
9355 10706 7.788026 TGAAGAAACTTGTAGGTTAGACTTCA 58.212 34.615 0.00 0.00 39.05 3.02
9356 10707 8.142551 TCTGAAGAAACTTGTAGGTTAGACTTC 58.857 37.037 0.00 0.00 36.22 3.01
9357 10708 8.019656 TCTGAAGAAACTTGTAGGTTAGACTT 57.980 34.615 0.00 0.00 0.00 3.01
9359 10710 7.659186 TCTCTGAAGAAACTTGTAGGTTAGAC 58.341 38.462 0.00 0.00 0.00 2.59
9360 10711 7.834881 TCTCTGAAGAAACTTGTAGGTTAGA 57.165 36.000 0.00 0.00 0.00 2.10
9361 10712 7.600752 CCTTCTCTGAAGAAACTTGTAGGTTAG 59.399 40.741 8.69 0.00 40.95 2.34
9362 10713 7.070821 ACCTTCTCTGAAGAAACTTGTAGGTTA 59.929 37.037 8.69 0.00 40.95 2.85
9363 10714 6.126739 ACCTTCTCTGAAGAAACTTGTAGGTT 60.127 38.462 8.69 0.00 40.95 3.50
9364 10715 5.367060 ACCTTCTCTGAAGAAACTTGTAGGT 59.633 40.000 8.69 0.00 40.95 3.08
9365 10716 5.698545 CACCTTCTCTGAAGAAACTTGTAGG 59.301 44.000 8.69 0.00 40.95 3.18
9366 10717 5.698545 CCACCTTCTCTGAAGAAACTTGTAG 59.301 44.000 8.69 0.00 40.95 2.74
9367 10718 5.611374 CCACCTTCTCTGAAGAAACTTGTA 58.389 41.667 8.69 0.00 40.95 2.41
9368 10719 4.455606 CCACCTTCTCTGAAGAAACTTGT 58.544 43.478 8.69 0.00 40.95 3.16
9369 10720 3.251972 GCCACCTTCTCTGAAGAAACTTG 59.748 47.826 8.69 0.00 40.95 3.16
9370 10721 3.117888 TGCCACCTTCTCTGAAGAAACTT 60.118 43.478 8.69 0.00 40.95 2.66
9371 10722 2.439507 TGCCACCTTCTCTGAAGAAACT 59.560 45.455 8.69 0.00 40.95 2.66
9372 10723 2.810852 CTGCCACCTTCTCTGAAGAAAC 59.189 50.000 8.69 0.00 40.95 2.78
9373 10724 2.439507 ACTGCCACCTTCTCTGAAGAAA 59.560 45.455 8.69 0.00 40.95 2.52
9374 10725 2.037772 GACTGCCACCTTCTCTGAAGAA 59.962 50.000 8.69 0.00 39.22 2.52
9375 10726 1.620819 GACTGCCACCTTCTCTGAAGA 59.379 52.381 8.69 0.00 0.00 2.87
9376 10727 1.622811 AGACTGCCACCTTCTCTGAAG 59.377 52.381 0.70 0.70 0.00 3.02
9377 10728 1.620819 GAGACTGCCACCTTCTCTGAA 59.379 52.381 0.00 0.00 34.16 3.02
9378 10729 1.203112 AGAGACTGCCACCTTCTCTGA 60.203 52.381 0.00 0.00 43.63 3.27
9379 10730 1.265236 AGAGACTGCCACCTTCTCTG 58.735 55.000 0.00 0.00 43.63 3.35
9380 10731 1.265236 CAGAGACTGCCACCTTCTCT 58.735 55.000 0.00 0.00 45.72 3.10
9381 10732 0.248843 CCAGAGACTGCCACCTTCTC 59.751 60.000 0.00 0.00 36.76 2.87
9382 10733 0.178921 TCCAGAGACTGCCACCTTCT 60.179 55.000 0.00 0.00 0.00 2.85
9383 10734 0.036858 GTCCAGAGACTGCCACCTTC 60.037 60.000 0.00 0.00 40.10 3.46
9384 10735 1.484444 GGTCCAGAGACTGCCACCTT 61.484 60.000 0.00 0.00 43.05 3.50
9385 10736 1.915769 GGTCCAGAGACTGCCACCT 60.916 63.158 0.00 0.00 43.05 4.00
9386 10737 2.665603 GGTCCAGAGACTGCCACC 59.334 66.667 0.00 0.00 43.05 4.61
9387 10738 2.217038 TGGGTCCAGAGACTGCCAC 61.217 63.158 0.00 0.00 43.05 5.01
9388 10739 2.204034 TGGGTCCAGAGACTGCCA 59.796 61.111 0.00 0.00 43.05 4.92
9389 10740 2.665603 GTGGGTCCAGAGACTGCC 59.334 66.667 0.00 0.00 43.05 4.85
9390 10741 2.217038 TGGTGGGTCCAGAGACTGC 61.217 63.158 0.00 0.00 43.05 4.40
9391 10742 4.215370 TGGTGGGTCCAGAGACTG 57.785 61.111 0.00 0.00 43.05 3.51
9400 10751 2.148768 CTTTAGTTCGGTTGGTGGGTC 58.851 52.381 0.00 0.00 0.00 4.46
9408 10759 1.142262 ACCACAGCCTTTAGTTCGGTT 59.858 47.619 0.00 0.00 0.00 4.44
9417 10768 0.109342 CCTGTCTCACCACAGCCTTT 59.891 55.000 0.00 0.00 42.29 3.11
9420 10771 1.004440 GACCTGTCTCACCACAGCC 60.004 63.158 0.00 0.00 42.29 4.85
9435 10786 1.024271 TTCTGCTTGCACTTGTGACC 58.976 50.000 4.79 0.00 0.00 4.02
9451 10817 3.876309 TTAGCTTCCCAAGTTGGTTCT 57.124 42.857 20.54 12.89 35.17 3.01
9464 10830 7.030165 GCCAAATCTCCTAAACTTTTAGCTTC 58.970 38.462 0.00 0.00 38.99 3.86
9476 10843 5.092554 TGTACGAATGCCAAATCTCCTAA 57.907 39.130 0.00 0.00 0.00 2.69
9490 10857 6.293698 ACCCAAGTTAGTTTTCTGTACGAAT 58.706 36.000 0.00 0.00 0.00 3.34
9622 10990 2.113860 ACTACTCATGCGCACCAAAT 57.886 45.000 14.90 0.00 0.00 2.32
9632 11000 8.194104 AGACTAGATGCAACTAAACTACTCATG 58.806 37.037 5.14 0.00 0.00 3.07
9635 11003 8.895737 ACTAGACTAGATGCAACTAAACTACTC 58.104 37.037 16.55 0.00 0.00 2.59
9636 11004 8.679100 CACTAGACTAGATGCAACTAAACTACT 58.321 37.037 16.55 3.61 0.00 2.57
9637 11005 8.460428 ACACTAGACTAGATGCAACTAAACTAC 58.540 37.037 16.55 0.00 0.00 2.73
9684 11052 4.871822 AGATTAGCCAAACCCATTTAGCT 58.128 39.130 0.00 0.00 43.87 3.32
9689 11057 4.019174 CAGTGAGATTAGCCAAACCCATT 58.981 43.478 0.00 0.00 0.00 3.16
9690 11058 3.266772 TCAGTGAGATTAGCCAAACCCAT 59.733 43.478 0.00 0.00 0.00 4.00
9718 11087 2.027745 ACGCTTGATCATTGGAGTGAGT 60.028 45.455 11.66 0.21 0.00 3.41
9719 11088 2.625737 ACGCTTGATCATTGGAGTGAG 58.374 47.619 11.66 0.00 0.00 3.51
9720 11089 2.768253 ACGCTTGATCATTGGAGTGA 57.232 45.000 11.66 0.00 0.00 3.41
9721 11090 3.837213 AAACGCTTGATCATTGGAGTG 57.163 42.857 0.00 0.00 0.00 3.51
9722 11091 4.943705 ACATAAACGCTTGATCATTGGAGT 59.056 37.500 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.