Multiple sequence alignment - TraesCS3B01G280000

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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 TraesCS3B01G280000 chr3B 100.000 8013 0 0 1 8013 449815420 449807408 0.000000e+00 14798
1 TraesCS3B01G280000 chr3B 90.099 303 26 3 1902 2203 695588447 695588148 2.710000e-104 390
2 TraesCS3B01G280000 chr3D 96.170 3185 85 19 4177 7343 351126511 351123346 0.000000e+00 5171
3 TraesCS3B01G280000 chr3D 95.037 3083 113 20 684 3752 351130050 351126994 0.000000e+00 4809
4 TraesCS3B01G280000 chr3D 90.789 684 51 5 1 682 351133753 351133080 0.000000e+00 904
5 TraesCS3B01G280000 chr3D 95.223 314 12 2 3747 4058 351126964 351126652 2.010000e-135 494
6 TraesCS3B01G280000 chr3D 93.464 153 9 1 3993 4145 426452011 426451860 8.090000e-55 226
7 TraesCS3B01G280000 chr3D 92.903 155 10 1 3991 4145 71517832 71517679 2.910000e-54 224
8 TraesCS3B01G280000 chr7A 98.322 2324 36 2 2463 4786 193563019 193560699 0.000000e+00 4072
9 TraesCS3B01G280000 chr7A 93.421 152 9 1 3991 4142 187460681 187460831 2.910000e-54 224
10 TraesCS3B01G280000 chr7A 84.028 144 23 0 4532 4675 536518493 536518350 1.080000e-28 139
11 TraesCS3B01G280000 chr3A 91.674 2378 136 29 4999 7343 469408738 469406390 0.000000e+00 3238
12 TraesCS3B01G280000 chr3A 93.621 1160 48 9 746 1883 469416555 469415400 0.000000e+00 1709
13 TraesCS3B01G280000 chr3A 92.707 1097 60 12 2660 3752 469411187 469410107 0.000000e+00 1565
14 TraesCS3B01G280000 chr3A 89.286 980 62 9 3747 4724 469410077 469409139 0.000000e+00 1188
15 TraesCS3B01G280000 chr3A 92.485 652 39 6 1875 2517 469415364 469414714 0.000000e+00 924
16 TraesCS3B01G280000 chr3A 93.548 155 9 1 3991 4145 34532603 34532450 6.250000e-56 230
17 TraesCS3B01G280000 chr3A 86.709 158 20 1 2522 2678 469414633 469414476 2.970000e-39 174
18 TraesCS3B01G280000 chr7B 98.068 1242 21 1 2463 3704 712255248 712254010 0.000000e+00 2158
19 TraesCS3B01G280000 chr7B 98.310 1006 17 0 3781 4786 712254008 712253003 0.000000e+00 1764
20 TraesCS3B01G280000 chr7B 85.962 520 52 9 7349 7867 138876150 138875651 3.290000e-148 536
21 TraesCS3B01G280000 chr7B 93.548 155 9 1 3991 4145 152467761 152467608 6.250000e-56 230
22 TraesCS3B01G280000 chr7B 94.574 129 6 1 7874 8002 461475689 461475562 1.760000e-46 198
23 TraesCS3B01G280000 chr7B 86.111 144 20 0 4532 4675 487812469 487812326 1.080000e-33 156
24 TraesCS3B01G280000 chr4B 94.944 534 24 1 7343 7873 137125737 137125204 0.000000e+00 833
25 TraesCS3B01G280000 chr2A 91.698 530 38 4 7344 7873 403225042 403225565 0.000000e+00 730
26 TraesCS3B01G280000 chr2A 91.509 530 39 4 7344 7873 401257331 401257854 0.000000e+00 725
27 TraesCS3B01G280000 chr4D 90.182 550 34 5 7343 7873 381376755 381377303 0.000000e+00 699
28 TraesCS3B01G280000 chr4D 84.124 548 54 19 7344 7865 207694261 207693721 4.320000e-137 499
29 TraesCS3B01G280000 chr4D 83.756 394 58 5 7380 7769 358030025 358029634 1.270000e-97 368
30 TraesCS3B01G280000 chr4D 94.531 128 7 0 7870 7997 258894028 258894155 1.760000e-46 198
31 TraesCS3B01G280000 chr5A 88.604 351 33 6 7527 7873 375870662 375870315 3.460000e-113 420
32 TraesCS3B01G280000 chr1A 84.597 422 60 4 7343 7761 406081450 406081031 1.610000e-111 414
33 TraesCS3B01G280000 chr6B 83.256 430 64 7 7344 7769 410066744 410067169 9.750000e-104 388
34 TraesCS3B01G280000 chr6B 93.421 152 9 1 3991 4142 469774183 469774333 2.910000e-54 224
35 TraesCS3B01G280000 chr6B 93.284 134 8 1 7869 8002 178493535 178493403 6.340000e-46 196
36 TraesCS3B01G280000 chr6B 92.029 138 7 3 7860 7997 153239880 153239747 2.950000e-44 191
37 TraesCS3B01G280000 chr6D 94.079 152 8 1 3991 4142 304099298 304099448 6.250000e-56 230
38 TraesCS3B01G280000 chrUn 92.086 139 11 0 7859 7997 468101779 468101917 6.340000e-46 196
39 TraesCS3B01G280000 chr2B 92.086 139 11 0 7859 7997 77862994 77863132 6.340000e-46 196
40 TraesCS3B01G280000 chr2B 91.367 139 12 0 7859 7997 77818948 77819086 2.950000e-44 191
41 TraesCS3B01G280000 chr5D 90.411 146 11 3 7862 8006 393056410 393056267 1.060000e-43 189
42 TraesCS3B01G280000 chr4A 93.077 130 7 2 7870 7998 448542231 448542359 1.060000e-43 189
43 TraesCS3B01G280000 chr7D 85.417 144 21 0 4532 4675 463880525 463880668 5.010000e-32 150


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 TraesCS3B01G280000 chr3B 449807408 449815420 8012 True 14798.000000 14798 100.000000 1 8013 1 chr3B.!!$R1 8012
1 TraesCS3B01G280000 chr3D 351123346 351133753 10407 True 2844.500000 5171 94.304750 1 7343 4 chr3D.!!$R3 7342
2 TraesCS3B01G280000 chr7A 193560699 193563019 2320 True 4072.000000 4072 98.322000 2463 4786 1 chr7A.!!$R1 2323
3 TraesCS3B01G280000 chr3A 469406390 469416555 10165 True 1466.333333 3238 91.080333 746 7343 6 chr3A.!!$R2 6597
4 TraesCS3B01G280000 chr7B 712253003 712255248 2245 True 1961.000000 2158 98.189000 2463 4786 2 chr7B.!!$R5 2323
5 TraesCS3B01G280000 chr4B 137125204 137125737 533 True 833.000000 833 94.944000 7343 7873 1 chr4B.!!$R1 530
6 TraesCS3B01G280000 chr2A 403225042 403225565 523 False 730.000000 730 91.698000 7344 7873 1 chr2A.!!$F2 529
7 TraesCS3B01G280000 chr2A 401257331 401257854 523 False 725.000000 725 91.509000 7344 7873 1 chr2A.!!$F1 529
8 TraesCS3B01G280000 chr4D 381376755 381377303 548 False 699.000000 699 90.182000 7343 7873 1 chr4D.!!$F2 530
9 TraesCS3B01G280000 chr4D 207693721 207694261 540 True 499.000000 499 84.124000 7344 7865 1 chr4D.!!$R1 521

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
470 473 0.317160 TGATCACGACTGCTTCCGTT 59.683 50.000 0.00 0.0 36.83 4.44 F
1443 4504 0.107654 GTGAGGGAGGGACGGATTTG 60.108 60.000 0.00 0.0 0.00 2.32 F
1497 4558 0.543749 AGGCCGAGATTTTGCTAGCT 59.456 50.000 17.23 0.0 0.00 3.32 F
2908 9408 0.320683 TGCGCTCACATGTAGCAGTT 60.321 50.000 20.12 0.0 40.08 3.16 F
3822 10360 0.392863 TGCTGTAGCCATCAATGCGT 60.393 50.000 0.80 0.0 41.18 5.24 F
5260 12010 2.143925 GGACGCATATTTACCTCCTGC 58.856 52.381 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 4598 1.136336 GTTTTTACGCACCGAGCTCAG 60.136 52.381 15.4 4.66 42.61 3.35 R
2872 9372 1.339055 CGCAAGTCTCAGGGGAAATCA 60.339 52.381 0.0 0.00 0.00 2.57 R
3741 10246 7.981789 CGTGTGATGCCATATTAGGTAGATATT 59.018 37.037 0.0 0.00 0.00 1.28 R
5129 11879 0.107456 CTGTCCTCAGCCAACACTGT 59.893 55.000 0.0 0.00 38.84 3.55 R
5887 12647 0.818296 ACGTATGCCTCCTGTCTCAC 59.182 55.000 0.0 0.00 0.00 3.51 R
7285 14066 0.036164 AGGCCGCTGTTGATGTGTTA 59.964 50.000 0.0 0.00 0.00 2.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 95 4.747540 TGAAATGTTCTTGGTCATCACG 57.252 40.909 0.00 0.00 0.00 4.35
93 96 3.501828 TGAAATGTTCTTGGTCATCACGG 59.498 43.478 0.00 0.00 0.00 4.94
94 97 2.859165 ATGTTCTTGGTCATCACGGT 57.141 45.000 0.00 0.00 0.00 4.83
134 137 2.959707 CAGTAGGTAGCCAAGACCCTAG 59.040 54.545 0.00 0.00 37.73 3.02
164 167 0.991355 TGTTCTTGGTCACCACCCCT 60.991 55.000 0.00 0.00 42.99 4.79
166 169 0.991355 TTCTTGGTCACCACCCCTGT 60.991 55.000 0.00 0.00 42.99 4.00
173 176 1.757699 GTCACCACCCCTGTAGATCTC 59.242 57.143 0.00 0.00 0.00 2.75
190 193 1.002250 CTCGTCAAGGTTCACGTCGG 61.002 60.000 0.00 0.00 37.30 4.79
200 203 1.070776 GTTCACGTCGGTGCTTCTTTC 60.071 52.381 0.00 0.00 44.03 2.62
223 226 4.331168 CGATGAAGACAATCTGAAGGGAAC 59.669 45.833 0.00 0.00 0.00 3.62
260 263 5.182380 TGTCCGTGACAAGAAAGAAAAGTTT 59.818 36.000 4.51 0.00 39.78 2.66
286 289 6.060028 TGTCGCAAAGGATTCAAATATAGC 57.940 37.500 0.00 0.00 0.00 2.97
312 315 5.283457 AGTTCATAATGTCCTACCAGCTC 57.717 43.478 0.00 0.00 0.00 4.09
322 325 1.133790 CCTACCAGCTCAAGCATTTGC 59.866 52.381 4.59 0.00 45.16 3.68
354 357 4.215613 AGGTTTGTTACTTGCCGAATCTTC 59.784 41.667 0.00 0.00 0.00 2.87
382 385 5.055642 ACGATAGAATTGTCGTCAGTTCA 57.944 39.130 17.25 6.59 46.30 3.18
383 386 4.857588 ACGATAGAATTGTCGTCAGTTCAC 59.142 41.667 17.25 9.06 46.30 3.18
386 389 3.792401 AGAATTGTCGTCAGTTCACACA 58.208 40.909 17.25 0.00 40.95 3.72
405 408 6.209192 TCACACATGGAGCTTATCAACATTTT 59.791 34.615 0.00 0.00 0.00 1.82
409 412 7.762615 CACATGGAGCTTATCAACATTTTGAAT 59.237 33.333 0.00 0.00 45.01 2.57
421 424 6.723515 TCAACATTTTGAATGAAGATACCCCA 59.276 34.615 7.59 0.00 38.87 4.96
423 426 6.493166 ACATTTTGAATGAAGATACCCCAGA 58.507 36.000 7.59 0.00 0.00 3.86
426 429 5.779241 TTGAATGAAGATACCCCAGAAGT 57.221 39.130 0.00 0.00 0.00 3.01
428 431 4.080356 TGAATGAAGATACCCCAGAAGTGG 60.080 45.833 0.00 0.00 44.56 4.00
454 457 2.421775 TGCGGCGACAATGTTTAATGAT 59.578 40.909 12.98 0.00 0.00 2.45
455 458 3.035942 GCGGCGACAATGTTTAATGATC 58.964 45.455 12.98 0.00 0.00 2.92
458 461 4.028383 GGCGACAATGTTTAATGATCACG 58.972 43.478 0.00 0.00 0.00 4.35
470 473 0.317160 TGATCACGACTGCTTCCGTT 59.683 50.000 0.00 0.00 36.83 4.44
477 480 1.659098 CGACTGCTTCCGTTCCATAAC 59.341 52.381 0.00 0.00 0.00 1.89
511 514 5.521010 GGTTTATGTTCATGGTGCAATCATG 59.479 40.000 19.51 19.51 42.28 3.07
524 527 3.240069 GCAATCATGCGGAGATAAATGC 58.760 45.455 0.00 0.00 43.83 3.56
525 528 3.485633 CAATCATGCGGAGATAAATGCG 58.514 45.455 0.00 0.00 37.05 4.73
539 542 6.376978 AGATAAATGCGATAAATGCTTGCTC 58.623 36.000 0.00 0.00 0.00 4.26
557 560 3.112580 GCTCGAAGACTATGAAGAGTGC 58.887 50.000 0.00 0.00 0.00 4.40
559 562 4.676723 GCTCGAAGACTATGAAGAGTGCTT 60.677 45.833 0.00 0.00 36.96 3.91
570 573 9.717942 ACTATGAAGAGTGCTTTTATATCCATC 57.282 33.333 0.00 0.00 33.61 3.51
571 574 7.992754 ATGAAGAGTGCTTTTATATCCATCC 57.007 36.000 0.00 0.00 33.61 3.51
575 578 7.690301 GAAGAGTGCTTTTATATCCATCCAGGA 60.690 40.741 0.00 0.00 42.39 3.86
584 587 1.831286 CCATCCAGGAAGGCATGCC 60.831 63.158 30.12 30.12 41.22 4.40
599 602 2.078392 CATGCCAATTTTGAAGCCCAC 58.922 47.619 0.00 0.00 0.00 4.61
636 639 8.995027 ATTTGATTTACAGGATGCCATACTTA 57.005 30.769 0.00 0.00 42.53 2.24
679 682 7.977789 TCATGCACTGATTTCTGTAAACTTA 57.022 32.000 0.00 0.00 0.00 2.24
705 3737 8.856153 TTATATCAGTCAGTTAAAACTTGCCA 57.144 30.769 0.00 0.00 37.08 4.92
716 3748 3.436700 AAACTTGCCAGAGTTTTTCGG 57.563 42.857 0.00 0.00 45.05 4.30
823 3861 2.504244 CGTGACCCGCTCGACTTC 60.504 66.667 0.00 0.00 35.64 3.01
892 3930 1.977009 TCGATCTGCACCGTCCACT 60.977 57.895 0.00 0.00 0.00 4.00
976 4014 4.142687 GCTAGACAAAGCCGCTAATCAAAA 60.143 41.667 0.00 0.00 36.45 2.44
993 4031 2.193306 AAATCAAATCGCATCGCCAC 57.807 45.000 0.00 0.00 0.00 5.01
1246 4296 1.671054 CACCGGGTTGCGATTCTGT 60.671 57.895 6.32 0.00 0.00 3.41
1250 4300 0.110238 CGGGTTGCGATTCTGTGTTG 60.110 55.000 0.00 0.00 0.00 3.33
1267 4317 3.127533 GCAAATCGGCTCCGCTGT 61.128 61.111 2.96 0.00 39.59 4.40
1269 4319 3.127533 AAATCGGCTCCGCTGTGC 61.128 61.111 2.96 0.00 39.59 4.57
1327 4383 5.352846 GGTTCTTTATCTTCCTCTTGTGCTC 59.647 44.000 0.00 0.00 0.00 4.26
1443 4504 0.107654 GTGAGGGAGGGACGGATTTG 60.108 60.000 0.00 0.00 0.00 2.32
1472 4533 3.452990 TGTGTTGTCTCTAGGAACAACCA 59.547 43.478 25.40 21.31 41.00 3.67
1497 4558 0.543749 AGGCCGAGATTTTGCTAGCT 59.456 50.000 17.23 0.00 0.00 3.32
1503 4564 4.798574 CCGAGATTTTGCTAGCTTTTTGT 58.201 39.130 17.23 0.00 0.00 2.83
1537 4598 5.034797 GTGTTCTGAAACTGTGCCTTTTAC 58.965 41.667 0.00 0.00 36.30 2.01
1568 4629 5.732647 CGGTGCGTAAAAACTATTTCTCATG 59.267 40.000 0.00 0.00 0.00 3.07
1589 4650 6.476706 TCATGTATGTGAAATTCGAGCTAGTG 59.523 38.462 0.00 0.00 0.00 2.74
1603 4664 4.352887 GAGCTAGTGATGTCGAGTTAACC 58.647 47.826 0.88 0.00 0.00 2.85
1800 4861 5.822519 TCATGACTCCAGTGTTTTATATGCC 59.177 40.000 0.00 0.00 0.00 4.40
1814 4875 7.499563 TGTTTTATATGCCCGACAGCTTTATTA 59.500 33.333 0.00 0.00 0.00 0.98
1823 4884 6.417930 GCCCGACAGCTTTATTAATCAATTTC 59.582 38.462 0.00 0.00 0.00 2.17
1858 4919 6.434596 TGTGTGAAATGAAAAGATACAACCG 58.565 36.000 0.00 0.00 0.00 4.44
1980 5088 5.540337 TGTTGGTATATCAGGCTTCCTCTAG 59.460 44.000 0.00 0.00 0.00 2.43
1997 5105 7.452880 TCCTCTAGATTTCAAAAACATGGTG 57.547 36.000 0.00 0.00 0.00 4.17
2039 5147 1.362224 TGGAGGAAGGAACCCTTGAG 58.638 55.000 2.55 0.00 44.82 3.02
2055 5163 1.644509 TGAGATCGGGATGGGTATGG 58.355 55.000 0.00 0.00 0.00 2.74
2121 5229 9.277783 GATAATCTGGTAAAGATAATGCACACT 57.722 33.333 0.00 0.00 45.37 3.55
2221 5329 7.246171 AGTGAAGGTATACTCATTTCACACT 57.754 36.000 25.99 17.30 46.12 3.55
2278 5391 3.019564 CCTGAAGCTGTCATTTTAGGGG 58.980 50.000 0.00 0.00 35.07 4.79
2455 5571 7.912949 TTGTTCAGAAGTTTTCAATTCATCG 57.087 32.000 0.00 0.00 0.00 3.84
2761 9261 7.562454 TGTACAGTTTTTCCTTTTCTACCTG 57.438 36.000 0.00 0.00 0.00 4.00
2872 9372 6.095440 GTGCAATTCACTGGTGAGGTAATATT 59.905 38.462 3.62 0.00 42.38 1.28
2908 9408 0.320683 TGCGCTCACATGTAGCAGTT 60.321 50.000 20.12 0.00 40.08 3.16
3228 9729 5.118990 TGCAGAAGATTTCAGGCTACATAC 58.881 41.667 0.00 0.00 34.57 2.39
3822 10360 0.392863 TGCTGTAGCCATCAATGCGT 60.393 50.000 0.80 0.00 41.18 5.24
4352 10914 5.644644 GAGGAGGACAATTTTGCTATTGTG 58.355 41.667 14.28 0.00 45.98 3.33
4792 11357 2.493278 AGCAACACATAACCCTGAATGC 59.507 45.455 0.00 0.00 0.00 3.56
4835 11400 3.835395 ACCTTCTCCAAGAAATCTCGACT 59.165 43.478 0.00 0.00 33.19 4.18
4913 11581 6.563037 TGGGTAAACTGGCATATACTGTTA 57.437 37.500 0.00 0.00 31.13 2.41
4954 11622 8.365647 GGAGCTAAGTATTTACTATTGCAGGTA 58.634 37.037 0.00 0.00 34.99 3.08
5245 11995 4.523558 AGTTCCCTTACTCTATATGGACGC 59.476 45.833 0.00 0.00 0.00 5.19
5260 12010 2.143925 GGACGCATATTTACCTCCTGC 58.856 52.381 0.00 0.00 0.00 4.85
5347 12097 5.784578 ATATGTATACTGACTTGGCGACA 57.215 39.130 4.17 0.00 39.83 4.35
5586 12337 6.882610 ATCACTCAAAACAAGCTACATTCA 57.117 33.333 0.00 0.00 0.00 2.57
5615 12366 7.713764 ATTTGTTCAGTATTCTGGCAAAAAC 57.286 32.000 18.58 9.21 42.86 2.43
5621 12375 6.872920 TCAGTATTCTGGCAAAAACAAGTTT 58.127 32.000 0.00 0.00 41.59 2.66
5627 12381 7.589574 TTCTGGCAAAAACAAGTTTTCTAAC 57.410 32.000 10.96 4.14 41.45 2.34
5987 12747 0.108945 GGATGCAGCTTGTTGCCTTC 60.109 55.000 0.22 4.46 43.43 3.46
6063 12824 4.403752 ACGGAAAACCCTATACTGGTCTAC 59.596 45.833 0.00 0.00 34.15 2.59
6064 12825 4.202192 CGGAAAACCCTATACTGGTCTACC 60.202 50.000 0.00 0.00 34.15 3.18
6107 12879 7.500559 ACTCAGATCAATAATTTTGTAGCTCCC 59.499 37.037 0.00 0.00 0.00 4.30
6156 12928 8.604640 ATGTCTGATCTTGTTGCTAATATCTG 57.395 34.615 0.00 0.00 0.00 2.90
6411 13185 2.981784 TCCCATAATCTGCAGCCTACAT 59.018 45.455 9.47 0.00 0.00 2.29
6412 13186 4.167319 TCCCATAATCTGCAGCCTACATA 58.833 43.478 9.47 0.00 0.00 2.29
6414 13188 5.251468 TCCCATAATCTGCAGCCTACATAAT 59.749 40.000 9.47 0.00 0.00 1.28
6415 13189 5.587844 CCCATAATCTGCAGCCTACATAATC 59.412 44.000 9.47 0.00 0.00 1.75
6416 13190 6.413052 CCATAATCTGCAGCCTACATAATCT 58.587 40.000 9.47 0.00 0.00 2.40
6417 13191 6.883217 CCATAATCTGCAGCCTACATAATCTT 59.117 38.462 9.47 0.00 0.00 2.40
6418 13192 8.043113 CCATAATCTGCAGCCTACATAATCTTA 58.957 37.037 9.47 0.00 0.00 2.10
6419 13193 9.610705 CATAATCTGCAGCCTACATAATCTTAT 57.389 33.333 9.47 0.00 0.00 1.73
6556 13330 4.780021 ACTGTCATCAGAGGACTTGGTAAT 59.220 41.667 15.96 0.00 43.76 1.89
6577 13351 3.123804 TCTCGAACTTGCACTGACTTTC 58.876 45.455 0.00 0.00 0.00 2.62
6630 13404 7.020827 TCCTTATCAACTGAACTCTTGGAAT 57.979 36.000 0.00 0.00 0.00 3.01
6657 13432 2.027653 GCAGCTCTACCTTGAGTTCCTT 60.028 50.000 0.00 0.00 36.51 3.36
6819 13594 2.130272 TCTACAGTCGTGATGCCTCT 57.870 50.000 0.00 0.00 0.00 3.69
6856 13631 0.877213 GGCGCCATCATGGAAATTGC 60.877 55.000 24.80 2.23 40.96 3.56
7020 13795 3.503891 CAACATTGATGCTCAAATCGCA 58.496 40.909 3.27 0.00 40.12 5.10
7032 13807 5.933463 TGCTCAAATCGCATCATGTATCATA 59.067 36.000 0.00 0.00 31.40 2.15
7044 13819 6.676990 TCATGTATCATATTGCTGAGGACT 57.323 37.500 0.00 0.00 0.00 3.85
7179 13958 1.683917 CGGTCAGCTATTAGGCACTCT 59.316 52.381 0.00 0.00 41.75 3.24
7180 13959 2.885266 CGGTCAGCTATTAGGCACTCTA 59.115 50.000 0.00 0.00 41.75 2.43
7317 14098 5.932619 ACAGCGGCCTTATACATATATGA 57.067 39.130 19.63 3.73 0.00 2.15
7378 14159 2.686106 GACCCGGACCTGGCCTTA 60.686 66.667 0.73 0.00 0.00 2.69
7384 14165 1.677637 CGGACCTGGCCTTAGACCTC 61.678 65.000 3.32 0.00 0.00 3.85
7433 14214 0.755327 GCCATGGGTCGGCCTATTTT 60.755 55.000 15.13 0.00 44.22 1.82
7491 14272 0.610785 GAGGCCGACCCAAAATCCAA 60.611 55.000 0.00 0.00 36.11 3.53
7537 14319 1.271926 ACAAAGAAATAGCAGGGCGGT 60.272 47.619 0.00 0.00 0.00 5.68
7539 14321 0.912486 AAGAAATAGCAGGGCGGTCT 59.088 50.000 0.00 0.00 0.00 3.85
7546 14328 2.893398 CAGGGCGGTCTGTCTACC 59.107 66.667 0.00 0.00 36.08 3.18
7652 14479 6.403866 AATTTTGGATGTCAGCTGTGTAAA 57.596 33.333 14.67 6.50 0.00 2.01
7865 14697 6.038356 CCGTCGGTGAATACAAGTAACTTAT 58.962 40.000 2.08 0.00 0.00 1.73
7879 14711 9.145442 ACAAGTAACTTATAGAGTATTCCCTCC 57.855 37.037 0.00 0.00 37.72 4.30
7880 14712 7.999450 AGTAACTTATAGAGTATTCCCTCCG 57.001 40.000 0.00 0.00 37.72 4.63
7881 14713 7.525165 AGTAACTTATAGAGTATTCCCTCCGT 58.475 38.462 0.00 0.00 37.72 4.69
7882 14714 6.897706 AACTTATAGAGTATTCCCTCCGTC 57.102 41.667 0.00 0.00 37.72 4.79
7883 14715 5.323581 ACTTATAGAGTATTCCCTCCGTCC 58.676 45.833 0.00 0.00 36.65 4.79
7884 14716 2.671896 TAGAGTATTCCCTCCGTCCC 57.328 55.000 0.00 0.00 31.53 4.46
7885 14717 0.635009 AGAGTATTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 31.53 4.37
7886 14718 1.007963 AGAGTATTCCCTCCGTCCCAA 59.992 52.381 0.00 0.00 31.53 4.12
7887 14719 1.835531 GAGTATTCCCTCCGTCCCAAA 59.164 52.381 0.00 0.00 0.00 3.28
7888 14720 2.237893 GAGTATTCCCTCCGTCCCAAAA 59.762 50.000 0.00 0.00 0.00 2.44
7889 14721 2.850568 AGTATTCCCTCCGTCCCAAAAT 59.149 45.455 0.00 0.00 0.00 1.82
7890 14722 2.919772 ATTCCCTCCGTCCCAAAATT 57.080 45.000 0.00 0.00 0.00 1.82
7891 14723 2.209690 TTCCCTCCGTCCCAAAATTC 57.790 50.000 0.00 0.00 0.00 2.17
7892 14724 1.368374 TCCCTCCGTCCCAAAATTCT 58.632 50.000 0.00 0.00 0.00 2.40
7893 14725 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
7894 14726 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
7895 14727 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
7896 14728 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
7897 14729 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
7898 14730 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
7899 14731 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
7900 14732 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
7901 14733 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
7902 14734 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
7903 14735 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
7904 14736 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
7905 14737 8.487176 CGTCCCAAAATTCTTGTCTTAAATTTG 58.513 33.333 0.00 0.00 33.95 2.32
7906 14738 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
7907 14739 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
7908 14740 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
7929 14761 9.825109 TTGTCTAAATACGGATGTATCAATTCA 57.175 29.630 0.00 0.00 40.42 2.57
7930 14762 9.996554 TGTCTAAATACGGATGTATCAATTCAT 57.003 29.630 0.00 0.00 40.42 2.57
7932 14764 9.996554 TCTAAATACGGATGTATCAATTCATGT 57.003 29.630 0.00 0.00 40.42 3.21
7938 14770 8.506168 ACGGATGTATCAATTCATGTTTTAGT 57.494 30.769 0.00 0.00 0.00 2.24
7939 14771 9.607988 ACGGATGTATCAATTCATGTTTTAGTA 57.392 29.630 0.00 0.00 0.00 1.82
7952 14784 9.537192 TTCATGTTTTAGTATTAGGTACATCCG 57.463 33.333 0.00 0.00 41.99 4.18
7953 14785 8.698210 TCATGTTTTAGTATTAGGTACATCCGT 58.302 33.333 0.00 0.00 41.99 4.69
7954 14786 9.970395 CATGTTTTAGTATTAGGTACATCCGTA 57.030 33.333 0.00 0.00 41.99 4.02
7962 14794 8.600668 AGTATTAGGTACATCCGTATCTAGACA 58.399 37.037 0.00 0.00 41.33 3.41
7963 14795 9.224267 GTATTAGGTACATCCGTATCTAGACAA 57.776 37.037 0.00 0.00 41.33 3.18
7964 14796 8.701908 ATTAGGTACATCCGTATCTAGACAAA 57.298 34.615 0.00 0.00 41.33 2.83
7965 14797 8.701908 TTAGGTACATCCGTATCTAGACAAAT 57.298 34.615 0.00 0.00 41.33 2.32
7966 14798 6.982852 AGGTACATCCGTATCTAGACAAATG 58.017 40.000 0.00 0.00 37.29 2.32
7967 14799 6.550108 AGGTACATCCGTATCTAGACAAATGT 59.450 38.462 0.00 4.18 37.29 2.71
7968 14800 7.722728 AGGTACATCCGTATCTAGACAAATGTA 59.277 37.037 0.00 3.24 37.29 2.29
7969 14801 8.355169 GGTACATCCGTATCTAGACAAATGTAA 58.645 37.037 12.89 1.88 32.51 2.41
7970 14802 9.395707 GTACATCCGTATCTAGACAAATGTAAG 57.604 37.037 12.89 0.00 32.51 2.34
7971 14803 7.434492 ACATCCGTATCTAGACAAATGTAAGG 58.566 38.462 0.00 0.00 0.00 2.69
7972 14804 5.839621 TCCGTATCTAGACAAATGTAAGGC 58.160 41.667 0.00 0.00 0.00 4.35
7973 14805 5.361571 TCCGTATCTAGACAAATGTAAGGCA 59.638 40.000 0.00 0.00 0.00 4.75
7974 14806 5.462398 CCGTATCTAGACAAATGTAAGGCAC 59.538 44.000 0.00 0.00 0.00 5.01
7975 14807 5.173312 CGTATCTAGACAAATGTAAGGCACG 59.827 44.000 0.00 0.00 0.00 5.34
7976 14808 4.794278 TCTAGACAAATGTAAGGCACGA 57.206 40.909 0.00 0.00 0.00 4.35
7977 14809 5.142061 TCTAGACAAATGTAAGGCACGAA 57.858 39.130 0.00 0.00 0.00 3.85
7978 14810 5.730550 TCTAGACAAATGTAAGGCACGAAT 58.269 37.500 0.00 0.00 0.00 3.34
7979 14811 6.170506 TCTAGACAAATGTAAGGCACGAATT 58.829 36.000 0.00 0.00 0.00 2.17
7980 14812 5.705609 AGACAAATGTAAGGCACGAATTT 57.294 34.783 0.00 0.00 0.00 1.82
7981 14813 5.699839 AGACAAATGTAAGGCACGAATTTC 58.300 37.500 0.00 0.00 0.00 2.17
7982 14814 4.472286 ACAAATGTAAGGCACGAATTTCG 58.528 39.130 16.84 16.84 46.93 3.46
7983 14815 3.757745 AATGTAAGGCACGAATTTCGG 57.242 42.857 21.71 12.14 45.59 4.30
7999 14831 4.701286 GGGACGGAGGGAGTATGT 57.299 61.111 0.00 0.00 0.00 2.29
8000 14832 2.912020 GGGACGGAGGGAGTATGTT 58.088 57.895 0.00 0.00 0.00 2.71
8001 14833 1.201424 GGGACGGAGGGAGTATGTTT 58.799 55.000 0.00 0.00 0.00 2.83
8002 14834 1.134491 GGGACGGAGGGAGTATGTTTG 60.134 57.143 0.00 0.00 0.00 2.93
8003 14835 1.553704 GGACGGAGGGAGTATGTTTGT 59.446 52.381 0.00 0.00 0.00 2.83
8004 14836 2.762327 GGACGGAGGGAGTATGTTTGTA 59.238 50.000 0.00 0.00 0.00 2.41
8005 14837 3.387050 GGACGGAGGGAGTATGTTTGTAT 59.613 47.826 0.00 0.00 0.00 2.29
8006 14838 4.586001 GGACGGAGGGAGTATGTTTGTATA 59.414 45.833 0.00 0.00 0.00 1.47
8007 14839 5.069516 GGACGGAGGGAGTATGTTTGTATAA 59.930 44.000 0.00 0.00 0.00 0.98
8008 14840 6.239515 GGACGGAGGGAGTATGTTTGTATAAT 60.240 42.308 0.00 0.00 0.00 1.28
8009 14841 7.039504 GGACGGAGGGAGTATGTTTGTATAATA 60.040 40.741 0.00 0.00 0.00 0.98
8010 14842 8.431910 ACGGAGGGAGTATGTTTGTATAATAT 57.568 34.615 0.00 0.00 0.00 1.28
8011 14843 8.529476 ACGGAGGGAGTATGTTTGTATAATATC 58.471 37.037 0.00 0.00 0.00 1.63
8012 14844 8.750298 CGGAGGGAGTATGTTTGTATAATATCT 58.250 37.037 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 95 2.863740 GCTATAAATTTTGCCGCCAACC 59.136 45.455 0.00 0.00 0.00 3.77
93 96 3.516615 TGCTATAAATTTTGCCGCCAAC 58.483 40.909 0.00 0.00 0.00 3.77
94 97 3.194542 ACTGCTATAAATTTTGCCGCCAA 59.805 39.130 0.00 0.00 0.00 4.52
134 137 3.181448 TGACCAAGAACACTTCCTTACCC 60.181 47.826 0.00 0.00 0.00 3.69
164 167 3.119955 CGTGAACCTTGACGAGATCTACA 60.120 47.826 0.00 0.00 40.22 2.74
166 169 3.079578 ACGTGAACCTTGACGAGATCTA 58.920 45.455 3.99 0.00 40.22 1.98
173 176 1.299620 ACCGACGTGAACCTTGACG 60.300 57.895 0.00 0.00 43.40 4.35
200 203 4.128925 TCCCTTCAGATTGTCTTCATCG 57.871 45.455 0.00 0.00 0.00 3.84
223 226 2.556189 TCACGGACAACAATTCCAATGG 59.444 45.455 0.00 0.00 31.94 3.16
227 230 2.333688 TGTCACGGACAACAATTCCA 57.666 45.000 4.51 0.00 39.78 3.53
231 234 4.196193 TCTTTCTTGTCACGGACAACAAT 58.804 39.130 13.34 0.00 45.88 2.71
238 241 5.890424 AAACTTTTCTTTCTTGTCACGGA 57.110 34.783 0.00 0.00 0.00 4.69
239 242 7.700656 ACAATAAACTTTTCTTTCTTGTCACGG 59.299 33.333 0.00 0.00 29.20 4.94
260 263 8.289618 GCTATATTTGAATCCTTTGCGACAATA 58.710 33.333 0.00 0.00 0.00 1.90
286 289 5.986135 GCTGGTAGGACATTATGAACTAGTG 59.014 44.000 0.00 0.00 0.00 2.74
297 300 1.630369 TGCTTGAGCTGGTAGGACATT 59.370 47.619 4.44 0.00 42.66 2.71
306 309 4.470876 CGCAAATGCTTGAGCTGG 57.529 55.556 4.44 0.00 42.66 4.85
322 325 4.527564 CAAGTAACAAACCTTCTTGAGCG 58.472 43.478 0.00 0.00 38.06 5.03
328 331 3.202829 TCGGCAAGTAACAAACCTTCT 57.797 42.857 0.00 0.00 0.00 2.85
354 357 2.316792 CGACAATTCTATCGTAGCCCG 58.683 52.381 0.00 0.00 33.63 6.13
362 365 5.633601 TGTGTGAACTGACGACAATTCTATC 59.366 40.000 10.14 2.74 34.03 2.08
382 385 6.209192 TCAAAATGTTGATAAGCTCCATGTGT 59.791 34.615 0.00 0.00 38.88 3.72
383 386 6.623486 TCAAAATGTTGATAAGCTCCATGTG 58.377 36.000 0.00 0.00 38.88 3.21
386 389 8.070034 TCATTCAAAATGTTGATAAGCTCCAT 57.930 30.769 0.00 0.00 43.29 3.41
405 408 4.080356 CCACTTCTGGGGTATCTTCATTCA 60.080 45.833 0.00 0.00 33.23 2.57
421 424 2.040544 CGCCGCAATTCCCACTTCT 61.041 57.895 0.00 0.00 0.00 2.85
423 426 2.033448 TCGCCGCAATTCCCACTT 59.967 55.556 0.00 0.00 0.00 3.16
426 429 1.677300 ATTGTCGCCGCAATTCCCA 60.677 52.632 1.78 0.00 35.76 4.37
428 431 0.109319 AACATTGTCGCCGCAATTCC 60.109 50.000 4.42 0.00 37.00 3.01
454 457 1.006571 GGAACGGAAGCAGTCGTGA 60.007 57.895 0.00 0.00 39.70 4.35
455 458 0.670546 ATGGAACGGAAGCAGTCGTG 60.671 55.000 0.00 0.00 39.70 4.35
458 461 2.930682 GAGTTATGGAACGGAAGCAGTC 59.069 50.000 0.00 0.00 40.76 3.51
470 473 4.345859 AAACCACGACAAGAGTTATGGA 57.654 40.909 0.00 0.00 36.83 3.41
477 480 5.390885 CCATGAACATAAACCACGACAAGAG 60.391 44.000 0.00 0.00 0.00 2.85
511 514 4.091424 GCATTTATCGCATTTATCTCCGC 58.909 43.478 0.00 0.00 0.00 5.54
516 519 5.282310 CGAGCAAGCATTTATCGCATTTATC 59.718 40.000 0.00 0.00 0.00 1.75
517 520 5.049474 TCGAGCAAGCATTTATCGCATTTAT 60.049 36.000 0.00 0.00 33.57 1.40
518 521 4.272261 TCGAGCAAGCATTTATCGCATTTA 59.728 37.500 0.00 0.00 33.57 1.40
519 522 3.065233 TCGAGCAAGCATTTATCGCATTT 59.935 39.130 0.00 0.00 33.57 2.32
520 523 2.613595 TCGAGCAAGCATTTATCGCATT 59.386 40.909 0.00 0.00 33.57 3.56
521 524 2.212652 TCGAGCAAGCATTTATCGCAT 58.787 42.857 0.00 0.00 33.57 4.73
522 525 1.650825 TCGAGCAAGCATTTATCGCA 58.349 45.000 0.00 0.00 33.57 5.10
523 526 2.285220 TCTTCGAGCAAGCATTTATCGC 59.715 45.455 0.00 0.00 33.57 4.58
524 527 3.553511 AGTCTTCGAGCAAGCATTTATCG 59.446 43.478 0.00 0.00 34.80 2.92
525 528 6.422100 TCATAGTCTTCGAGCAAGCATTTATC 59.578 38.462 0.00 0.00 31.26 1.75
539 542 7.763172 ATAAAAGCACTCTTCATAGTCTTCG 57.237 36.000 0.00 0.00 0.00 3.79
557 560 5.634118 TGCCTTCCTGGATGGATATAAAAG 58.366 41.667 27.75 5.40 45.68 2.27
559 562 5.573219 CATGCCTTCCTGGATGGATATAAA 58.427 41.667 27.75 9.10 45.68 1.40
570 573 0.906775 AAATTGGCATGCCTTCCTGG 59.093 50.000 35.53 0.00 36.94 4.45
571 574 2.027929 TCAAAATTGGCATGCCTTCCTG 60.028 45.455 35.53 24.23 36.94 3.86
575 578 2.429478 GCTTCAAAATTGGCATGCCTT 58.571 42.857 35.53 21.06 36.94 4.35
584 587 5.110940 CCAAATTGTGGGCTTCAAAATTG 57.889 39.130 8.69 8.83 41.20 2.32
616 619 7.573710 TCAGTTAAGTATGGCATCCTGTAAAT 58.426 34.615 1.65 0.00 0.00 1.40
636 639 2.172505 TGATCATACGGCCCAATCAGTT 59.827 45.455 0.00 0.00 0.00 3.16
679 682 9.461312 TGGCAAGTTTTAACTGACTGATATAAT 57.539 29.630 0.00 0.00 39.66 1.28
682 685 7.168219 TCTGGCAAGTTTTAACTGACTGATAT 58.832 34.615 0.00 0.00 39.66 1.63
684 687 5.376625 TCTGGCAAGTTTTAACTGACTGAT 58.623 37.500 0.00 0.00 39.66 2.90
685 688 4.776349 TCTGGCAAGTTTTAACTGACTGA 58.224 39.130 0.00 0.92 39.66 3.41
686 689 4.576463 ACTCTGGCAAGTTTTAACTGACTG 59.424 41.667 0.00 0.00 39.66 3.51
687 690 4.781934 ACTCTGGCAAGTTTTAACTGACT 58.218 39.130 0.00 0.00 39.66 3.41
728 3764 5.418840 TGATTCAGGCCTATTCAGGTTTTTC 59.581 40.000 3.98 0.00 44.68 2.29
729 3765 5.332743 TGATTCAGGCCTATTCAGGTTTTT 58.667 37.500 3.98 0.00 44.68 1.94
730 3766 4.934356 TGATTCAGGCCTATTCAGGTTTT 58.066 39.130 3.98 0.00 44.68 2.43
731 3767 4.591321 TGATTCAGGCCTATTCAGGTTT 57.409 40.909 3.98 0.00 44.68 3.27
732 3768 4.228210 TCTTGATTCAGGCCTATTCAGGTT 59.772 41.667 3.98 0.00 44.68 3.50
733 3769 3.782523 TCTTGATTCAGGCCTATTCAGGT 59.217 43.478 3.98 0.00 44.68 4.00
734 3770 4.428294 TCTTGATTCAGGCCTATTCAGG 57.572 45.455 3.98 9.66 45.77 3.86
735 3771 4.820716 CCTTCTTGATTCAGGCCTATTCAG 59.179 45.833 3.98 0.00 0.00 3.02
736 3772 4.474651 TCCTTCTTGATTCAGGCCTATTCA 59.525 41.667 3.98 6.11 0.00 2.57
737 3773 5.041191 TCCTTCTTGATTCAGGCCTATTC 57.959 43.478 3.98 3.05 0.00 1.75
738 3774 5.444176 CTTCCTTCTTGATTCAGGCCTATT 58.556 41.667 3.98 0.00 0.00 1.73
823 3861 0.031616 AGGGGAAGCTCCTGGAGTAG 60.032 60.000 23.92 1.12 36.57 2.57
858 3896 2.008168 CGACGCGATCTAGCTGCTG 61.008 63.158 15.93 2.51 34.40 4.41
892 3930 0.458889 GCGTGGTGCGATAGGTTGTA 60.459 55.000 0.00 0.00 44.77 2.41
976 4014 0.659427 CTGTGGCGATGCGATTTGAT 59.341 50.000 0.00 0.00 0.00 2.57
1066 4104 1.552348 GATTCGATCGGAAGCGCAGG 61.552 60.000 16.41 0.00 38.24 4.85
1240 4290 1.888512 AGCCGATTTGCAACACAGAAT 59.111 42.857 0.00 0.00 0.00 2.40
1246 4296 3.262936 CGGAGCCGATTTGCAACA 58.737 55.556 2.00 0.00 42.83 3.33
1267 4317 1.391157 AAAGCCTGAAAACCTGCGCA 61.391 50.000 10.98 10.98 0.00 6.09
1269 4319 0.385974 CGAAAGCCTGAAAACCTGCG 60.386 55.000 0.00 0.00 0.00 5.18
1402 4463 4.765856 ACCTTGTCGTTGACTAGTCTACAT 59.234 41.667 28.73 10.74 34.56 2.29
1443 4504 2.028930 CCTAGAGACAACACACCCTGAC 60.029 54.545 0.00 0.00 0.00 3.51
1472 4533 3.356290 AGCAAAATCTCGGCCTTACATT 58.644 40.909 0.00 0.00 0.00 2.71
1497 4558 5.237344 CAGAACACCAAACCAAACACAAAAA 59.763 36.000 0.00 0.00 0.00 1.94
1503 4564 4.282195 AGTTTCAGAACACCAAACCAAACA 59.718 37.500 0.00 0.00 38.26 2.83
1537 4598 1.136336 GTTTTTACGCACCGAGCTCAG 60.136 52.381 15.40 4.66 42.61 3.35
1568 4629 6.477033 ACATCACTAGCTCGAATTTCACATAC 59.523 38.462 0.00 0.00 0.00 2.39
1589 4650 6.202188 TCAGAAACAAAGGTTAACTCGACATC 59.798 38.462 5.42 0.00 35.82 3.06
1603 4664 7.488322 TGGAAAATGGTACTTCAGAAACAAAG 58.512 34.615 0.00 0.00 0.00 2.77
1800 4861 6.918022 GGGAAATTGATTAATAAAGCTGTCGG 59.082 38.462 0.00 0.00 0.00 4.79
1814 4875 4.946157 CACAGTGCTCTAGGGAAATTGATT 59.054 41.667 0.00 0.00 0.00 2.57
1823 4884 2.839486 TTTCACACAGTGCTCTAGGG 57.161 50.000 0.00 0.00 32.98 3.53
1980 5088 4.574013 TGCAACCACCATGTTTTTGAAATC 59.426 37.500 0.00 0.00 0.00 2.17
2039 5147 3.721087 AAATCCATACCCATCCCGATC 57.279 47.619 0.00 0.00 0.00 3.69
2121 5229 8.445275 TGCAATACAAAGAGAACTGTTAGAAA 57.555 30.769 0.00 0.00 0.00 2.52
2278 5391 6.128117 TGTTGACGATTTCTTGGTATTTAGGC 60.128 38.462 0.00 0.00 0.00 3.93
2455 5571 7.765695 TGAATAAAAGATCCCATCAATAGGC 57.234 36.000 0.00 0.00 0.00 3.93
2872 9372 1.339055 CGCAAGTCTCAGGGGAAATCA 60.339 52.381 0.00 0.00 0.00 2.57
3741 10246 7.981789 CGTGTGATGCCATATTAGGTAGATATT 59.018 37.037 0.00 0.00 0.00 1.28
4352 10914 3.756434 TGTTTACTCCCATAGCTGCAAAC 59.244 43.478 1.02 1.05 0.00 2.93
4857 11422 4.877378 AAATTTGGCTCTGCAAATCTGA 57.123 36.364 0.00 0.00 31.42 3.27
5089 11839 5.239359 TCTATGACATTGTCTTTGCATGC 57.761 39.130 11.82 11.82 33.15 4.06
5090 11840 9.961265 AATTATCTATGACATTGTCTTTGCATG 57.039 29.630 17.26 0.00 33.15 4.06
5120 11870 3.149196 CAGCCAACACTGTAACCAGAAT 58.851 45.455 0.00 0.00 41.50 2.40
5129 11879 0.107456 CTGTCCTCAGCCAACACTGT 59.893 55.000 0.00 0.00 38.84 3.55
5347 12097 1.536922 CGACCAGCACGCTCATAGATT 60.537 52.381 0.00 0.00 0.00 2.40
5456 12206 8.876275 ATATGTCATGTCATAAAACATTTGGC 57.124 30.769 15.12 0.00 37.78 4.52
5520 12270 8.816894 TCACACTATTCTTCCTCAGTTAAATCT 58.183 33.333 0.00 0.00 0.00 2.40
5586 12337 9.995003 TTTGCCAGAATACTGAACAAATTTTAT 57.005 25.926 0.00 0.00 46.03 1.40
5887 12647 0.818296 ACGTATGCCTCCTGTCTCAC 59.182 55.000 0.00 0.00 0.00 3.51
6063 12824 9.868277 GATCTGAGTTAATTATGATACTCCAGG 57.132 37.037 10.95 4.21 36.94 4.45
6094 12866 4.373156 ACTCAGTTGGGAGCTACAAAAT 57.627 40.909 0.00 0.00 38.50 1.82
6156 12928 4.623932 TTGGTGGATATATCTGCCAGAC 57.376 45.455 20.10 7.37 34.23 3.51
6325 13099 0.107263 TCATGCCTTCGCCAATAGCA 60.107 50.000 0.00 0.00 44.04 3.49
6419 13193 8.967918 ACCGATCCATATTCTCGAATAAGAATA 58.032 33.333 8.36 8.36 46.75 1.75
6420 13194 7.841956 ACCGATCCATATTCTCGAATAAGAAT 58.158 34.615 3.70 4.70 45.59 2.40
6421 13195 7.228314 ACCGATCCATATTCTCGAATAAGAA 57.772 36.000 3.70 0.00 39.49 2.52
6556 13330 2.890808 AAGTCAGTGCAAGTTCGAGA 57.109 45.000 0.00 0.00 0.00 4.04
6630 13404 1.908619 TCAAGGTAGAGCTGCCATCAA 59.091 47.619 7.37 0.00 37.85 2.57
6657 13432 2.325583 ACTTCCGCTCAAACTTGTCA 57.674 45.000 0.00 0.00 0.00 3.58
6819 13594 3.334691 CGCCCAAATTCTGACTTAGTGA 58.665 45.455 0.00 0.00 0.00 3.41
6856 13631 3.182173 CCGCTTTATTGCACAACAACAAG 59.818 43.478 0.00 0.00 42.27 3.16
6973 13748 6.912591 CCCAAATTGCTAGATAAATCACGTTC 59.087 38.462 0.00 0.00 0.00 3.95
6977 13752 6.147864 TGCCCAAATTGCTAGATAAATCAC 57.852 37.500 0.00 0.00 0.00 3.06
7020 13795 7.255199 AGTCCTCAGCAATATGATACATGAT 57.745 36.000 0.00 0.00 0.00 2.45
7032 13807 3.689347 TGCAACAATAGTCCTCAGCAAT 58.311 40.909 0.00 0.00 0.00 3.56
7044 13819 3.534357 TTCCCCTTCCTTGCAACAATA 57.466 42.857 0.00 0.00 0.00 1.90
7285 14066 0.036164 AGGCCGCTGTTGATGTGTTA 59.964 50.000 0.00 0.00 0.00 2.41
7428 14209 7.870445 GTGAGGCCACAAACTTTTGATAAAATA 59.130 33.333 3.76 0.00 42.72 1.40
7433 14214 4.278170 CAGTGAGGCCACAAACTTTTGATA 59.722 41.667 3.76 0.00 45.54 2.15
7537 14319 2.885135 TTGGTCCTACGGTAGACAGA 57.115 50.000 16.59 2.84 0.00 3.41
7644 14471 6.018669 GGAAGACAAGACAAGACTTTACACAG 60.019 42.308 0.00 0.00 0.00 3.66
7652 14479 3.181461 CCACTGGAAGACAAGACAAGACT 60.181 47.826 0.00 0.00 37.43 3.24
7865 14697 1.854939 TGGGACGGAGGGAATACTCTA 59.145 52.381 0.00 0.00 37.63 2.43
7873 14705 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
7874 14706 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
7875 14707 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
7876 14708 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
7877 14709 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
7878 14710 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
7879 14711 8.487176 CAAATTTAAGACAAGAATTTTGGGACG 58.513 33.333 0.00 0.00 32.35 4.79
7880 14712 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
7881 14713 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
7882 14714 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
7903 14735 9.825109 TGAATTGATACATCCGTATTTAGACAA 57.175 29.630 0.00 0.00 38.48 3.18
7904 14736 9.996554 ATGAATTGATACATCCGTATTTAGACA 57.003 29.630 0.00 0.00 38.48 3.41
7906 14738 9.996554 ACATGAATTGATACATCCGTATTTAGA 57.003 29.630 0.00 0.00 38.48 2.10
7912 14744 9.607988 ACTAAAACATGAATTGATACATCCGTA 57.392 29.630 0.00 0.00 0.00 4.02
7913 14745 8.506168 ACTAAAACATGAATTGATACATCCGT 57.494 30.769 0.00 0.00 0.00 4.69
7926 14758 9.537192 CGGATGTACCTAATACTAAAACATGAA 57.463 33.333 0.00 0.00 34.56 2.57
7927 14759 8.698210 ACGGATGTACCTAATACTAAAACATGA 58.302 33.333 0.00 0.00 34.56 3.07
7928 14760 8.882415 ACGGATGTACCTAATACTAAAACATG 57.118 34.615 0.00 0.00 34.56 3.21
7936 14768 8.600668 TGTCTAGATACGGATGTACCTAATACT 58.399 37.037 0.00 0.00 34.56 2.12
7937 14769 8.783833 TGTCTAGATACGGATGTACCTAATAC 57.216 38.462 0.00 0.00 36.31 1.89
7938 14770 9.797642 TTTGTCTAGATACGGATGTACCTAATA 57.202 33.333 0.00 0.00 36.31 0.98
7939 14771 8.701908 TTTGTCTAGATACGGATGTACCTAAT 57.298 34.615 0.00 0.00 36.31 1.73
7940 14772 8.573885 CATTTGTCTAGATACGGATGTACCTAA 58.426 37.037 0.00 0.00 36.31 2.69
7941 14773 7.722728 ACATTTGTCTAGATACGGATGTACCTA 59.277 37.037 0.00 0.00 36.31 3.08
7942 14774 6.550108 ACATTTGTCTAGATACGGATGTACCT 59.450 38.462 0.00 0.00 36.31 3.08
7943 14775 6.746120 ACATTTGTCTAGATACGGATGTACC 58.254 40.000 0.00 0.00 32.26 3.34
7944 14776 9.395707 CTTACATTTGTCTAGATACGGATGTAC 57.604 37.037 14.05 0.00 33.35 2.90
7945 14777 8.573885 CCTTACATTTGTCTAGATACGGATGTA 58.426 37.037 11.94 11.94 32.86 2.29
7946 14778 7.434492 CCTTACATTTGTCTAGATACGGATGT 58.566 38.462 13.29 13.29 34.19 3.06
7947 14779 6.366332 GCCTTACATTTGTCTAGATACGGATG 59.634 42.308 0.00 0.85 0.00 3.51
7948 14780 6.041637 TGCCTTACATTTGTCTAGATACGGAT 59.958 38.462 0.00 0.00 0.00 4.18
7949 14781 5.361571 TGCCTTACATTTGTCTAGATACGGA 59.638 40.000 0.00 0.00 0.00 4.69
7950 14782 5.462398 GTGCCTTACATTTGTCTAGATACGG 59.538 44.000 0.00 0.00 0.00 4.02
7951 14783 5.173312 CGTGCCTTACATTTGTCTAGATACG 59.827 44.000 0.00 0.00 0.00 3.06
7952 14784 6.270815 TCGTGCCTTACATTTGTCTAGATAC 58.729 40.000 0.00 0.00 0.00 2.24
7953 14785 6.459670 TCGTGCCTTACATTTGTCTAGATA 57.540 37.500 0.00 0.00 0.00 1.98
7954 14786 5.339008 TCGTGCCTTACATTTGTCTAGAT 57.661 39.130 0.00 0.00 0.00 1.98
7955 14787 4.794278 TCGTGCCTTACATTTGTCTAGA 57.206 40.909 0.00 0.00 0.00 2.43
7956 14788 6.422776 AATTCGTGCCTTACATTTGTCTAG 57.577 37.500 0.00 0.00 0.00 2.43
7957 14789 6.401688 CGAAATTCGTGCCTTACATTTGTCTA 60.402 38.462 7.29 0.00 34.72 2.59
7958 14790 5.616866 CGAAATTCGTGCCTTACATTTGTCT 60.617 40.000 7.29 0.00 34.72 3.41
7959 14791 4.553429 CGAAATTCGTGCCTTACATTTGTC 59.447 41.667 7.29 0.00 34.72 3.18
7960 14792 4.472286 CGAAATTCGTGCCTTACATTTGT 58.528 39.130 7.29 0.00 34.72 2.83
7961 14793 3.851403 CCGAAATTCGTGCCTTACATTTG 59.149 43.478 14.58 0.00 38.40 2.32
7962 14794 3.119637 CCCGAAATTCGTGCCTTACATTT 60.120 43.478 14.58 0.00 38.40 2.32
7963 14795 2.422127 CCCGAAATTCGTGCCTTACATT 59.578 45.455 14.58 0.00 38.40 2.71
7964 14796 2.014128 CCCGAAATTCGTGCCTTACAT 58.986 47.619 14.58 0.00 38.40 2.29
7965 14797 1.002201 TCCCGAAATTCGTGCCTTACA 59.998 47.619 14.58 0.00 38.40 2.41
7966 14798 1.395954 GTCCCGAAATTCGTGCCTTAC 59.604 52.381 14.58 0.00 38.40 2.34
7967 14799 1.729284 GTCCCGAAATTCGTGCCTTA 58.271 50.000 14.58 0.00 38.40 2.69
7968 14800 1.296056 CGTCCCGAAATTCGTGCCTT 61.296 55.000 14.58 0.00 38.40 4.35
7969 14801 1.740296 CGTCCCGAAATTCGTGCCT 60.740 57.895 14.58 0.00 38.40 4.75
7970 14802 2.746803 CCGTCCCGAAATTCGTGCC 61.747 63.158 14.58 0.47 38.40 5.01
7971 14803 1.693083 CTCCGTCCCGAAATTCGTGC 61.693 60.000 14.58 3.20 38.40 5.34
7972 14804 1.082117 CCTCCGTCCCGAAATTCGTG 61.082 60.000 14.58 2.73 38.40 4.35
7973 14805 1.217244 CCTCCGTCCCGAAATTCGT 59.783 57.895 14.58 0.00 38.40 3.85
7974 14806 1.520787 CCCTCCGTCCCGAAATTCG 60.521 63.158 8.62 8.62 40.07 3.34
7975 14807 0.179081 CTCCCTCCGTCCCGAAATTC 60.179 60.000 0.00 0.00 0.00 2.17
7976 14808 0.908180 ACTCCCTCCGTCCCGAAATT 60.908 55.000 0.00 0.00 0.00 1.82
7977 14809 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
7978 14810 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.000 0.00 0.00 0.00 3.46
7979 14811 0.754217 CATACTCCCTCCGTCCCGAA 60.754 60.000 0.00 0.00 0.00 4.30
7980 14812 1.152819 CATACTCCCTCCGTCCCGA 60.153 63.158 0.00 0.00 0.00 5.14
7981 14813 1.041447 AACATACTCCCTCCGTCCCG 61.041 60.000 0.00 0.00 0.00 5.14
7982 14814 1.134491 CAAACATACTCCCTCCGTCCC 60.134 57.143 0.00 0.00 0.00 4.46
7983 14815 1.553704 ACAAACATACTCCCTCCGTCC 59.446 52.381 0.00 0.00 0.00 4.79
7984 14816 4.667519 ATACAAACATACTCCCTCCGTC 57.332 45.455 0.00 0.00 0.00 4.79
7985 14817 6.742559 ATTATACAAACATACTCCCTCCGT 57.257 37.500 0.00 0.00 0.00 4.69
7986 14818 8.750298 AGATATTATACAAACATACTCCCTCCG 58.250 37.037 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.