Multiple sequence alignment - TraesCS5D01G102100

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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 TraesCS5D01G102100 chr5D 100.000 6708 0 0 1 6708 115027130 115020423 0.000000e+00 12388.0
1 TraesCS5D01G102100 chr5D 77.903 1240 176 43 4911 6110 114898230 114897049 0.000000e+00 682.0
2 TraesCS5D01G102100 chr5D 81.503 865 117 25 3634 4482 114899678 114898841 0.000000e+00 671.0
3 TraesCS5D01G102100 chr5D 80.435 184 30 6 319 499 36552660 36552840 1.170000e-27 135.0
4 TraesCS5D01G102100 chr5B 93.298 6491 276 60 11 6416 126300471 126294055 0.000000e+00 9430.0
5 TraesCS5D01G102100 chr5B 77.581 1240 180 45 4911 6110 126248444 126247263 0.000000e+00 660.0
6 TraesCS5D01G102100 chr5B 81.040 865 119 26 3634 4482 126249917 126249082 0.000000e+00 647.0
7 TraesCS5D01G102100 chr5B 95.294 170 7 1 6416 6584 112531426 112531595 1.110000e-67 268.0
8 TraesCS5D01G102100 chr5B 91.729 133 10 1 6576 6708 126294058 126293927 4.130000e-42 183.0
9 TraesCS5D01G102100 chr5A 94.363 2927 112 17 3513 6415 121115908 121113011 0.000000e+00 4442.0
10 TraesCS5D01G102100 chr5A 90.316 1394 97 27 387 1754 121119870 121118489 0.000000e+00 1792.0
11 TraesCS5D01G102100 chr5A 80.787 864 124 26 3634 4482 120759043 120758207 7.340000e-179 638.0
12 TraesCS5D01G102100 chr5A 87.578 322 35 4 3210 3528 121117658 121117339 1.060000e-97 368.0
13 TraesCS5D01G102100 chr5A 79.806 515 80 14 5600 6110 120753896 120753402 2.980000e-93 353.0
14 TraesCS5D01G102100 chr5A 88.288 222 22 2 2905 3122 121118066 121117845 5.160000e-66 263.0
15 TraesCS5D01G102100 chr5A 94.776 134 5 2 6576 6708 121112736 121112604 2.450000e-49 207.0
16 TraesCS5D01G102100 chr5A 87.755 98 12 0 2805 2902 121118193 121118096 1.530000e-21 115.0
17 TraesCS5D01G102100 chr1D 99.394 165 1 0 6413 6577 469874707 469874871 3.930000e-77 300.0
18 TraesCS5D01G102100 chr1D 92.982 57 4 0 3399 3455 100458185 100458129 4.310000e-12 84.2
19 TraesCS5D01G102100 chr7D 100.000 161 0 0 6416 6576 484298909 484299069 1.410000e-76 298.0
20 TraesCS5D01G102100 chr7D 93.878 49 2 1 3401 3449 119168412 119168365 9.330000e-09 73.1
21 TraesCS5D01G102100 chr4D 94.012 167 10 0 6416 6582 481370484 481370318 3.100000e-63 254.0
22 TraesCS5D01G102100 chr4D 85.714 63 8 1 3398 3460 7788648 7788587 1.560000e-06 65.8
23 TraesCS5D01G102100 chr4B 96.026 151 5 1 6430 6579 671182344 671182194 1.870000e-60 244.0
24 TraesCS5D01G102100 chr2D 93.293 164 10 1 6416 6578 403487925 403487762 2.420000e-59 241.0
25 TraesCS5D01G102100 chr2D 86.127 173 17 6 283 450 629736582 629736412 5.340000e-41 180.0
26 TraesCS5D01G102100 chr2A 91.463 164 13 1 6416 6578 102324539 102324376 2.430000e-54 224.0
27 TraesCS5D01G102100 chr3D 90.854 164 14 1 6416 6578 357158466 357158629 1.130000e-52 219.0
28 TraesCS5D01G102100 chr3A 90.854 164 14 1 6416 6578 476659461 476659624 1.130000e-52 219.0
29 TraesCS5D01G102100 chr2B 90.164 122 8 4 3421 3541 496963476 496963594 9.010000e-34 156.0
30 TraesCS5D01G102100 chr7B 87.500 80 9 1 3399 3477 496343632 496343711 2.580000e-14 91.6
31 TraesCS5D01G102100 chr1A 94.737 57 3 0 3399 3455 104946972 104947028 9.270000e-14 89.8
32 TraesCS5D01G102100 chr1B 91.228 57 5 0 3399 3455 151093978 151094034 2.010000e-10 78.7


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 TraesCS5D01G102100 chr5D 115020423 115027130 6707 True 12388.000000 12388 100.000000 1 6708 1 chr5D.!!$R1 6707
1 TraesCS5D01G102100 chr5D 114897049 114899678 2629 True 676.500000 682 79.703000 3634 6110 2 chr5D.!!$R2 2476
2 TraesCS5D01G102100 chr5B 126293927 126300471 6544 True 4806.500000 9430 92.513500 11 6708 2 chr5B.!!$R2 6697
3 TraesCS5D01G102100 chr5B 126247263 126249917 2654 True 653.500000 660 79.310500 3634 6110 2 chr5B.!!$R1 2476
4 TraesCS5D01G102100 chr5A 121112604 121119870 7266 True 1197.833333 4442 90.512667 387 6708 6 chr5A.!!$R3 6321
5 TraesCS5D01G102100 chr5A 120758207 120759043 836 True 638.000000 638 80.787000 3634 4482 1 chr5A.!!$R2 848

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
87 89 0.035056 CCTCCTCCTTCACGGCAAAT 60.035 55.0 0.00 0.00 0.00 2.32 F
523 527 0.036010 CCTTCCCATCTCGTGCACTT 60.036 55.0 16.19 0.00 0.00 3.16 F
945 952 0.233590 CAAATCCGTCGAAACACGCA 59.766 50.0 0.00 0.00 42.26 5.24 F
1907 1967 0.041663 CTAGTAGTGCTCGAGCTCGC 60.042 60.0 35.27 27.04 42.66 5.03 F
2727 2819 0.106015 GGCAGTTATGGGGAGCCAAT 60.106 55.0 0.00 0.00 44.59 3.16 F
3469 3734 0.179032 TGTCAACTCACCGTGCCATT 60.179 50.0 0.00 0.00 0.00 3.16 F
3796 5519 0.745845 CGTTTCCTGGATGGCCTCAG 60.746 60.0 3.32 9.26 35.26 3.35 F
4136 5859 1.095600 TCATCGTCGGAGGAAGAGTG 58.904 55.0 4.32 0.00 34.16 3.51 F
5557 8219 0.689412 TGGATGGCGGAGGTGTCATA 60.689 55.0 0.00 0.00 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 1959 0.172352 AGAAGAGGAAAGCGAGCTCG 59.828 55.000 31.37 31.37 43.27 5.03 R
1907 1967 4.227073 AGGAGATGGGAAAGAAGAGGAAAG 59.773 45.833 0.00 0.00 0.00 2.62 R
2734 2826 1.208165 ACCAGCCTAACAAGAGGGGG 61.208 60.000 0.00 0.00 37.06 5.40 R
3115 3274 0.180642 CATGGCTCATGCTCTCCACT 59.819 55.000 2.78 0.00 35.02 4.00 R
3831 5554 0.866427 CTGATAGCCGCATTGCTCTG 59.134 55.000 7.12 0.00 41.68 3.35 R
4747 6502 4.234574 GGATCAAAATTGTCCCGTGAAAC 58.765 43.478 0.00 0.00 0.00 2.78 R
5557 8219 1.202639 TGAACAGACGTTGATGCCTGT 60.203 47.619 0.00 0.00 41.14 4.00 R
5569 8231 2.565841 AGAAGGTTGTGCTGAACAGAC 58.434 47.619 5.97 2.49 40.74 3.51 R
6571 9239 0.249398 ATCGACCACACACCTAAGCC 59.751 55.000 0.00 0.00 0.00 4.35 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
26 27 1.138247 CCGTTTCGTCCGAGGTAGG 59.862 63.158 0.00 0.00 0.00 3.18
30 31 1.815003 GTTTCGTCCGAGGTAGGAGAA 59.185 52.381 0.00 0.00 41.68 2.87
58 59 2.404789 CGTGCATTGGCGATCACC 59.595 61.111 0.00 0.00 45.35 4.02
86 88 1.374947 CCTCCTCCTTCACGGCAAA 59.625 57.895 0.00 0.00 0.00 3.68
87 89 0.035056 CCTCCTCCTTCACGGCAAAT 60.035 55.000 0.00 0.00 0.00 2.32
92 94 0.676466 TCCTTCACGGCAAATCGCAT 60.676 50.000 0.00 0.00 45.17 4.73
95 97 1.585267 TTCACGGCAAATCGCATGCT 61.585 50.000 17.13 0.00 45.17 3.79
122 124 4.349342 AGTCACTTTCTTTCCTGACCATCT 59.651 41.667 0.00 0.00 34.71 2.90
137 139 6.465464 CCTGACCATCTGATCAATATCCAACT 60.465 42.308 0.00 0.00 0.00 3.16
153 155 2.559668 CCAACTGCCTCAATCATGTTGT 59.440 45.455 0.00 0.00 34.70 3.32
155 157 2.165167 ACTGCCTCAATCATGTTGTGG 58.835 47.619 17.51 17.51 36.46 4.17
164 166 4.038883 TCAATCATGTTGTGGCATGTTCAA 59.961 37.500 0.00 0.00 44.68 2.69
168 170 3.435105 TGTTGTGGCATGTTCAACTTC 57.565 42.857 20.87 5.64 41.05 3.01
177 180 3.569701 GCATGTTCAACTTCTTTCTCCCA 59.430 43.478 0.00 0.00 0.00 4.37
210 213 1.079127 CGCACGATGGTTCCTCCTT 60.079 57.895 0.00 0.00 37.07 3.36
348 351 3.444417 TCCCCGGCCATCCCTCTA 61.444 66.667 2.24 0.00 0.00 2.43
354 357 1.772156 GGCCATCCCTCTAAGCCCT 60.772 63.158 0.00 0.00 37.66 5.19
357 360 1.348008 CCATCCCTCTAAGCCCTGCA 61.348 60.000 0.00 0.00 0.00 4.41
361 364 1.639635 CCCTCTAAGCCCTGCACCAT 61.640 60.000 0.00 0.00 0.00 3.55
364 367 2.042464 CTCTAAGCCCTGCACCATCTA 58.958 52.381 0.00 0.00 0.00 1.98
366 369 2.369860 TCTAAGCCCTGCACCATCTATG 59.630 50.000 0.00 0.00 0.00 2.23
367 370 1.216064 AAGCCCTGCACCATCTATGA 58.784 50.000 0.00 0.00 0.00 2.15
377 380 5.263599 TGCACCATCTATGAAAAACTCCAT 58.736 37.500 0.00 0.00 0.00 3.41
378 381 5.357878 TGCACCATCTATGAAAAACTCCATC 59.642 40.000 0.00 0.00 0.00 3.51
381 384 5.817816 ACCATCTATGAAAAACTCCATCGAC 59.182 40.000 0.00 0.00 0.00 4.20
382 385 5.237344 CCATCTATGAAAAACTCCATCGACC 59.763 44.000 0.00 0.00 0.00 4.79
409 412 3.958798 GCACCTCCACCACTAAGATAGTA 59.041 47.826 0.00 0.00 37.23 1.82
418 421 6.289064 CACCACTAAGATAGTAAATGGGGTC 58.711 44.000 0.00 0.00 37.23 4.46
434 437 0.037160 GGTCGTGGCTTCCCCTTAAA 59.963 55.000 0.00 0.00 0.00 1.52
483 486 5.604650 CCCTAAGATAGATAATAGGGCTGGG 59.395 48.000 3.92 0.00 45.94 4.45
484 487 5.071115 CCTAAGATAGATAATAGGGCTGGGC 59.929 48.000 0.00 0.00 32.89 5.36
500 503 2.665603 GCCTTCTCCAGCGAGGTT 59.334 61.111 0.00 0.00 39.02 3.50
516 520 1.521681 GTTCGGCCTTCCCATCTCG 60.522 63.158 0.00 0.00 0.00 4.04
520 524 2.268920 GCCTTCCCATCTCGTGCA 59.731 61.111 0.00 0.00 0.00 4.57
523 527 0.036010 CCTTCCCATCTCGTGCACTT 60.036 55.000 16.19 0.00 0.00 3.16
526 530 1.215382 CCCATCTCGTGCACTTCGA 59.785 57.895 16.19 6.50 35.96 3.71
546 550 4.574828 TCGAAAGAAGGAAAAAGTGACTGG 59.425 41.667 0.00 0.00 37.03 4.00
549 553 0.668535 AAGGAAAAAGTGACTGGCGC 59.331 50.000 0.00 0.00 0.00 6.53
550 554 1.172812 AGGAAAAAGTGACTGGCGCC 61.173 55.000 22.73 22.73 0.00 6.53
551 555 1.452145 GGAAAAAGTGACTGGCGCCA 61.452 55.000 30.59 30.59 0.00 5.69
555 559 1.034838 AAAGTGACTGGCGCCACAAA 61.035 50.000 29.03 10.95 35.84 2.83
623 628 2.293399 ACAGCCAAGGAACACGAATTTC 59.707 45.455 0.00 0.00 0.00 2.17
624 629 2.293122 CAGCCAAGGAACACGAATTTCA 59.707 45.455 0.00 0.00 0.00 2.69
625 630 3.057315 CAGCCAAGGAACACGAATTTCAT 60.057 43.478 0.00 0.00 0.00 2.57
626 631 3.191371 AGCCAAGGAACACGAATTTCATC 59.809 43.478 0.00 0.00 0.00 2.92
627 632 3.057596 GCCAAGGAACACGAATTTCATCA 60.058 43.478 0.00 0.00 0.00 3.07
667 673 2.496470 AGAAGAAACGTAAGGGCGAGAT 59.504 45.455 0.00 0.00 46.39 2.75
945 952 0.233590 CAAATCCGTCGAAACACGCA 59.766 50.000 0.00 0.00 42.26 5.24
947 954 0.876777 AATCCGTCGAAACACGCACA 60.877 50.000 0.00 0.00 42.26 4.57
949 962 2.128128 CGTCGAAACACGCACAGC 60.128 61.111 0.00 0.00 42.26 4.40
986 1000 1.843368 TCCTTAATCCTCCACGTCGT 58.157 50.000 0.00 0.00 0.00 4.34
1075 1089 2.163509 CTTCCTCTTCGACAGGAGACA 58.836 52.381 11.34 0.00 41.27 3.41
1170 1184 2.678836 TGAGAGAGAGGAACGATTCGTC 59.321 50.000 12.80 6.18 39.99 4.20
1394 1408 4.899239 CCCATCTGCCCGCTCGAC 62.899 72.222 0.00 0.00 0.00 4.20
1400 1418 1.741401 CTGCCCGCTCGACATTTCA 60.741 57.895 0.00 0.00 0.00 2.69
1405 1423 1.471501 CCCGCTCGACATTTCATCTCA 60.472 52.381 0.00 0.00 0.00 3.27
1419 1437 0.250038 ATCTCAATCCATCGGGTGCG 60.250 55.000 0.00 0.00 34.93 5.34
1615 1637 3.132111 ACCGGGTGCCAATGATAATTTTC 59.868 43.478 6.32 0.00 0.00 2.29
1619 1641 5.519927 CGGGTGCCAATGATAATTTTCTTTC 59.480 40.000 0.00 0.00 0.00 2.62
1736 1772 6.547493 TCTTGTGTTCAAATTTTCGTTTCG 57.453 33.333 0.00 0.00 32.87 3.46
1765 1801 1.398390 GGCAGCCGTTTCTCATTACTG 59.602 52.381 0.00 0.00 0.00 2.74
1794 1830 7.092079 TCTAGCAACTGTTTAATTACGCTGTA 58.908 34.615 8.88 0.00 0.00 2.74
1810 1846 3.551046 CGCTGTAATAGGTCTAGCAGTGG 60.551 52.174 0.00 0.00 34.16 4.00
1815 1851 0.622136 TAGGTCTAGCAGTGGTCGGA 59.378 55.000 0.00 0.00 0.00 4.55
1899 1959 2.832733 AGTGGGTTTCCTAGTAGTGCTC 59.167 50.000 0.00 0.00 0.00 4.26
1907 1967 0.041663 CTAGTAGTGCTCGAGCTCGC 60.042 60.000 35.27 27.04 42.66 5.03
1913 1973 2.183046 GCTCGAGCTCGCTTTCCT 59.817 61.111 30.97 0.00 39.60 3.36
1944 2004 6.393897 TCCCATCTCCTATTAAACTCTGGAT 58.606 40.000 0.00 0.00 0.00 3.41
1945 2005 6.851836 TCCCATCTCCTATTAAACTCTGGATT 59.148 38.462 0.00 0.00 0.00 3.01
1957 2017 8.934023 TTAAACTCTGGATTTGGTGTATTTCT 57.066 30.769 0.00 0.00 0.00 2.52
1987 2047 9.881773 ATATCTTTAATGAAAAGGGGATAAGCA 57.118 29.630 0.00 0.00 44.10 3.91
1994 2054 0.107848 AAGGGGATAAGCACGGTTCG 60.108 55.000 0.00 0.00 0.00 3.95
1995 2055 0.974010 AGGGGATAAGCACGGTTCGA 60.974 55.000 0.00 0.00 0.00 3.71
2054 2114 7.229506 ACTTTCCACTAAGATTTTCTTCCTGTG 59.770 37.037 0.00 2.98 37.89 3.66
2057 2117 7.060421 TCCACTAAGATTTTCTTCCTGTGTTT 58.940 34.615 12.52 0.00 37.89 2.83
2058 2118 7.228706 TCCACTAAGATTTTCTTCCTGTGTTTC 59.771 37.037 12.52 0.00 37.89 2.78
2059 2119 7.013274 CCACTAAGATTTTCTTCCTGTGTTTCA 59.987 37.037 12.52 0.00 37.89 2.69
2060 2120 8.571336 CACTAAGATTTTCTTCCTGTGTTTCAT 58.429 33.333 0.00 0.00 37.89 2.57
2061 2121 9.793259 ACTAAGATTTTCTTCCTGTGTTTCATA 57.207 29.630 0.00 0.00 37.89 2.15
2340 2428 9.674068 TCATGTAACTAGTTAAAATGCCACATA 57.326 29.630 23.05 10.80 0.00 2.29
2404 2492 4.637483 ATTGGAATTATGAGGTGCAACG 57.363 40.909 0.00 0.00 38.12 4.10
2727 2819 0.106015 GGCAGTTATGGGGAGCCAAT 60.106 55.000 0.00 0.00 44.59 3.16
2728 2820 1.144913 GGCAGTTATGGGGAGCCAATA 59.855 52.381 0.00 0.00 44.59 1.90
2734 2826 4.102681 AGTTATGGGGAGCCAATACACTAC 59.897 45.833 0.00 0.00 0.00 2.73
2970 3125 9.731819 CTTGATGTATTTCCATGATTTCTTCAG 57.268 33.333 0.00 0.00 37.89 3.02
3032 3191 9.350357 TGCGTGTTTTGTTGTTATTTACTTTTA 57.650 25.926 0.00 0.00 0.00 1.52
3033 3192 9.823979 GCGTGTTTTGTTGTTATTTACTTTTAG 57.176 29.630 0.00 0.00 0.00 1.85
3115 3274 8.650490 AGCAAATTGGAAAATTTAGAGGAGAAA 58.350 29.630 0.00 0.00 31.67 2.52
3285 3543 4.330944 TCCAATAGACACGCCGATAAAT 57.669 40.909 0.00 0.00 0.00 1.40
3469 3734 0.179032 TGTCAACTCACCGTGCCATT 60.179 50.000 0.00 0.00 0.00 3.16
3623 5336 3.193691 ACATAGCAGTACCTATCCGATGC 59.806 47.826 0.00 0.00 0.00 3.91
3794 5517 2.115291 GCGTTTCCTGGATGGCCTC 61.115 63.158 3.32 0.00 35.26 4.70
3796 5519 0.745845 CGTTTCCTGGATGGCCTCAG 60.746 60.000 3.32 9.26 35.26 3.35
3852 5575 1.228063 AGCAATGCGGCTATCAGGG 60.228 57.895 0.00 0.00 43.70 4.45
3872 5595 1.606668 GTTGGCGTCTTTGATGGTGAA 59.393 47.619 0.00 0.00 0.00 3.18
4136 5859 1.095600 TCATCGTCGGAGGAAGAGTG 58.904 55.000 4.32 0.00 34.16 3.51
4402 6150 2.644798 ACCACAGGAGGCTTAAGAATGT 59.355 45.455 6.67 0.00 0.00 2.71
4506 6261 9.981114 TTCCCTAAAATTGTTTTTCTCATTCTC 57.019 29.630 0.00 0.00 36.47 2.87
4791 6546 4.113354 CGGCTAAGAAGGTACATTCTCAC 58.887 47.826 21.98 14.06 38.59 3.51
4796 6551 7.445945 GCTAAGAAGGTACATTCTCACCATAT 58.554 38.462 21.98 8.21 38.59 1.78
5557 8219 0.689412 TGGATGGCGGAGGTGTCATA 60.689 55.000 0.00 0.00 0.00 2.15
5569 8231 1.665679 GGTGTCATACAGGCATCAACG 59.334 52.381 0.00 0.00 31.65 4.10
6023 8691 4.927782 TTGTCTGCGCGCCCACTT 62.928 61.111 30.77 0.00 0.00 3.16
6202 8870 1.616159 CCTCCGCTCCCAAAAGAAAA 58.384 50.000 0.00 0.00 0.00 2.29
6245 8913 8.031864 TCAATTCAAAGAGTGCAAAGTTTAACA 58.968 29.630 0.00 0.00 0.00 2.41
6246 8914 7.755582 ATTCAAAGAGTGCAAAGTTTAACAC 57.244 32.000 11.26 11.26 0.00 3.32
6249 8917 4.273005 AGAGTGCAAAGTTTAACACGTG 57.727 40.909 15.48 15.48 38.08 4.49
6291 8959 1.777878 TCAGGTGGCTAGGGTTTTTCA 59.222 47.619 0.00 0.00 0.00 2.69
6294 8962 3.578282 CAGGTGGCTAGGGTTTTTCATTT 59.422 43.478 0.00 0.00 0.00 2.32
6338 9006 2.232298 CTCGCCTCTGGGTGTCTTCC 62.232 65.000 0.00 0.00 43.20 3.46
6344 9012 2.847234 TGGGTGTCTTCCGGCACT 60.847 61.111 9.40 0.00 36.03 4.40
6415 9083 3.431766 CCCAACCTACGGTTCAATCTAGG 60.432 52.174 0.00 0.00 43.05 3.02
6417 9085 2.395619 ACCTACGGTTCAATCTAGGGG 58.604 52.381 0.00 0.00 31.49 4.79
6419 9087 1.070289 CTACGGTTCAATCTAGGGGCC 59.930 57.143 0.00 0.00 0.00 5.80
6420 9088 0.620700 ACGGTTCAATCTAGGGGCCT 60.621 55.000 0.84 0.00 0.00 5.19
6421 9089 0.179045 CGGTTCAATCTAGGGGCCTG 60.179 60.000 0.84 0.00 0.00 4.85
6422 9090 1.213296 GGTTCAATCTAGGGGCCTGA 58.787 55.000 0.84 0.00 0.00 3.86
6427 9095 1.776667 CAATCTAGGGGCCTGATTGGA 59.223 52.381 25.23 10.98 41.70 3.53
6429 9097 2.212752 TCTAGGGGCCTGATTGGATT 57.787 50.000 0.84 0.00 38.35 3.01
6431 9099 1.496429 CTAGGGGCCTGATTGGATTGT 59.504 52.381 0.84 0.00 38.35 2.71
6433 9101 1.103398 GGGGCCTGATTGGATTGTCG 61.103 60.000 0.84 0.00 38.35 4.35
6435 9103 1.463674 GGCCTGATTGGATTGTCGTT 58.536 50.000 0.00 0.00 38.35 3.85
6436 9104 1.818674 GGCCTGATTGGATTGTCGTTT 59.181 47.619 0.00 0.00 38.35 3.60
6437 9105 2.231235 GGCCTGATTGGATTGTCGTTTT 59.769 45.455 0.00 0.00 38.35 2.43
6439 9107 3.244976 CCTGATTGGATTGTCGTTTTGC 58.755 45.455 0.00 0.00 38.35 3.68
6440 9108 3.305267 CCTGATTGGATTGTCGTTTTGCA 60.305 43.478 0.00 0.00 38.35 4.08
6441 9109 3.637432 TGATTGGATTGTCGTTTTGCAC 58.363 40.909 0.00 0.00 0.00 4.57
6442 9110 3.067320 TGATTGGATTGTCGTTTTGCACA 59.933 39.130 0.00 0.00 0.00 4.57
6443 9111 2.483583 TGGATTGTCGTTTTGCACAC 57.516 45.000 0.00 0.00 0.00 3.82
6445 9113 2.425312 TGGATTGTCGTTTTGCACACTT 59.575 40.909 0.00 0.00 0.00 3.16
6448 9116 5.038033 GGATTGTCGTTTTGCACACTTTTA 58.962 37.500 0.00 0.00 0.00 1.52
6449 9117 5.051973 GGATTGTCGTTTTGCACACTTTTAC 60.052 40.000 0.00 0.00 0.00 2.01
6450 9118 4.421033 TGTCGTTTTGCACACTTTTACA 57.579 36.364 0.00 0.00 0.00 2.41
6451 9119 4.159857 TGTCGTTTTGCACACTTTTACAC 58.840 39.130 0.00 0.00 0.00 2.90
6452 9120 3.544682 GTCGTTTTGCACACTTTTACACC 59.455 43.478 0.00 0.00 0.00 4.16
6453 9121 3.440872 TCGTTTTGCACACTTTTACACCT 59.559 39.130 0.00 0.00 0.00 4.00
6454 9122 3.545873 CGTTTTGCACACTTTTACACCTG 59.454 43.478 0.00 0.00 0.00 4.00
6455 9123 4.490743 GTTTTGCACACTTTTACACCTGT 58.509 39.130 0.00 0.00 0.00 4.00
6456 9124 5.642686 GTTTTGCACACTTTTACACCTGTA 58.357 37.500 0.00 0.00 0.00 2.74
6457 9125 5.899120 TTTGCACACTTTTACACCTGTAA 57.101 34.783 0.00 0.00 38.60 2.41
6470 9138 7.549147 TTACACCTGTAAAAGATACAGACCT 57.451 36.000 15.31 2.12 45.69 3.85
6471 9139 6.038997 ACACCTGTAAAAGATACAGACCTC 57.961 41.667 15.31 0.00 45.69 3.85
6472 9140 5.542635 ACACCTGTAAAAGATACAGACCTCA 59.457 40.000 15.31 0.00 45.69 3.86
6473 9141 6.042781 ACACCTGTAAAAGATACAGACCTCAA 59.957 38.462 15.31 0.00 45.69 3.02
6475 9143 7.278868 CACCTGTAAAAGATACAGACCTCAATC 59.721 40.741 15.31 0.00 45.69 2.67
6476 9144 6.477033 CCTGTAAAAGATACAGACCTCAATCG 59.523 42.308 15.31 0.00 45.69 3.34
6477 9145 6.338146 TGTAAAAGATACAGACCTCAATCGG 58.662 40.000 0.00 0.00 0.00 4.18
6478 9146 5.422214 AAAAGATACAGACCTCAATCGGT 57.578 39.130 0.00 0.00 40.80 4.69
6486 9154 2.409975 GACCTCAATCGGTCGTTTTCA 58.590 47.619 0.00 0.00 43.56 2.69
6489 9157 3.818773 ACCTCAATCGGTCGTTTTCATTT 59.181 39.130 0.00 0.00 29.14 2.32
6490 9158 4.083484 ACCTCAATCGGTCGTTTTCATTTC 60.083 41.667 0.00 0.00 29.14 2.17
6491 9159 4.154195 CCTCAATCGGTCGTTTTCATTTCT 59.846 41.667 0.00 0.00 0.00 2.52
6492 9160 5.029650 TCAATCGGTCGTTTTCATTTCTG 57.970 39.130 0.00 0.00 0.00 3.02
6493 9161 4.083537 TCAATCGGTCGTTTTCATTTCTGG 60.084 41.667 0.00 0.00 0.00 3.86
6495 9163 3.207778 TCGGTCGTTTTCATTTCTGGTT 58.792 40.909 0.00 0.00 0.00 3.67
6496 9164 3.002862 TCGGTCGTTTTCATTTCTGGTTG 59.997 43.478 0.00 0.00 0.00 3.77
6497 9165 3.002862 CGGTCGTTTTCATTTCTGGTTGA 59.997 43.478 0.00 0.00 0.00 3.18
6498 9166 4.496673 CGGTCGTTTTCATTTCTGGTTGAA 60.497 41.667 0.00 0.00 0.00 2.69
6510 9178 8.252417 TCATTTCTGGTTGAAAATCATATGTGG 58.748 33.333 1.90 0.00 46.32 4.17
6515 9183 4.160252 GGTTGAAAATCATATGTGGCTGGT 59.840 41.667 1.90 0.00 0.00 4.00
6516 9184 4.987408 TGAAAATCATATGTGGCTGGTG 57.013 40.909 1.90 0.00 0.00 4.17
6517 9185 4.598022 TGAAAATCATATGTGGCTGGTGA 58.402 39.130 1.90 0.00 0.00 4.02
6518 9186 5.015515 TGAAAATCATATGTGGCTGGTGAA 58.984 37.500 1.90 0.00 0.00 3.18
6519 9187 5.479724 TGAAAATCATATGTGGCTGGTGAAA 59.520 36.000 1.90 0.00 0.00 2.69
6520 9188 6.154877 TGAAAATCATATGTGGCTGGTGAAAT 59.845 34.615 1.90 0.00 0.00 2.17
6521 9189 7.341512 TGAAAATCATATGTGGCTGGTGAAATA 59.658 33.333 1.90 0.00 0.00 1.40
6522 9190 6.639632 AATCATATGTGGCTGGTGAAATAC 57.360 37.500 1.90 0.00 0.00 1.89
6523 9191 5.109500 TCATATGTGGCTGGTGAAATACA 57.891 39.130 1.90 0.00 0.00 2.29
6542 9210 9.977762 GAAATACACTTGTAAAAGTAATACGGG 57.022 33.333 0.00 0.00 33.76 5.28
6543 9211 9.506018 AAATACACTTGTAAAAGTAATACGGGT 57.494 29.630 0.00 0.00 33.76 5.28
6545 9213 6.290605 ACACTTGTAAAAGTAATACGGGTGT 58.709 36.000 0.00 0.00 37.07 4.16
6548 9216 9.585099 CACTTGTAAAAGTAATACGGGTGTATA 57.415 33.333 0.00 0.00 40.42 1.47
6565 9233 7.528675 GGGTGTATAAATTTACCCCTATTCCA 58.471 38.462 13.90 0.00 45.65 3.53
6566 9234 8.005976 GGGTGTATAAATTTACCCCTATTCCAA 58.994 37.037 13.90 0.00 45.65 3.53
6567 9235 9.074576 GGTGTATAAATTTACCCCTATTCCAAG 57.925 37.037 0.00 0.00 0.00 3.61
6568 9236 8.573885 GTGTATAAATTTACCCCTATTCCAAGC 58.426 37.037 0.00 0.00 0.00 4.01
6569 9237 6.894339 ATAAATTTACCCCTATTCCAAGCG 57.106 37.500 0.00 0.00 0.00 4.68
6570 9238 2.721425 TTTACCCCTATTCCAAGCGG 57.279 50.000 0.00 0.00 0.00 5.52
6571 9239 0.841289 TTACCCCTATTCCAAGCGGG 59.159 55.000 0.00 0.00 39.85 6.13
6574 9242 2.757124 CCCTATTCCAAGCGGGGCT 61.757 63.158 0.00 0.00 42.56 5.19
6618 9400 3.190849 CGATGTCACGCCTGCCAG 61.191 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.890510 GGACGAAACGGCAACACCT 60.891 57.895 0.00 0.00 36.10 4.00
1 2 2.635338 GGACGAAACGGCAACACC 59.365 61.111 0.00 0.00 36.10 4.16
2 3 2.154427 CTCGGACGAAACGGCAACAC 62.154 60.000 0.00 0.00 36.10 3.32
3 4 1.952133 CTCGGACGAAACGGCAACA 60.952 57.895 0.00 0.00 36.10 3.33
4 5 2.664436 CCTCGGACGAAACGGCAAC 61.664 63.158 0.00 0.00 36.10 4.17
5 6 1.804396 TACCTCGGACGAAACGGCAA 61.804 55.000 0.00 0.00 36.10 4.52
6 7 2.203972 CTACCTCGGACGAAACGGCA 62.204 60.000 0.00 0.00 36.10 5.69
7 8 1.515736 CTACCTCGGACGAAACGGC 60.516 63.158 0.00 0.00 0.00 5.68
8 9 1.138247 CCTACCTCGGACGAAACGG 59.862 63.158 0.00 0.00 0.00 4.44
9 10 0.098376 CTCCTACCTCGGACGAAACG 59.902 60.000 0.00 0.00 0.00 3.60
26 27 4.443266 ACGCTGCCGCCTCTTCTC 62.443 66.667 0.00 0.00 38.22 2.87
75 77 1.135699 GCATGCGATTTGCCGTGAAG 61.136 55.000 0.00 0.00 45.60 3.02
86 88 3.465742 AAGTGACTGATAGCATGCGAT 57.534 42.857 13.54 13.54 0.00 4.58
87 89 2.967599 AAGTGACTGATAGCATGCGA 57.032 45.000 13.01 7.70 0.00 5.10
92 94 5.012046 TCAGGAAAGAAAGTGACTGATAGCA 59.988 40.000 0.00 0.00 30.75 3.49
95 97 5.306937 TGGTCAGGAAAGAAAGTGACTGATA 59.693 40.000 0.00 0.00 39.45 2.15
122 124 4.776435 TGAGGCAGTTGGATATTGATCA 57.224 40.909 0.00 0.00 33.27 2.92
153 155 3.569701 GGAGAAAGAAGTTGAACATGCCA 59.430 43.478 0.00 0.00 0.00 4.92
155 157 3.569701 TGGGAGAAAGAAGTTGAACATGC 59.430 43.478 0.00 0.00 0.00 4.06
164 166 5.513962 GGAAGAAGATGTGGGAGAAAGAAGT 60.514 44.000 0.00 0.00 0.00 3.01
168 170 3.615155 GGGAAGAAGATGTGGGAGAAAG 58.385 50.000 0.00 0.00 0.00 2.62
199 202 2.528127 TGCGGGAAGGAGGAACCA 60.528 61.111 0.00 0.00 42.04 3.67
200 203 2.269241 CTGCGGGAAGGAGGAACC 59.731 66.667 0.00 0.00 34.34 3.62
201 204 2.436824 GCTGCGGGAAGGAGGAAC 60.437 66.667 0.00 0.00 38.88 3.62
226 229 4.554036 GAGGCAGACGGATGGGGC 62.554 72.222 0.00 0.00 0.00 5.80
227 230 3.866582 GGAGGCAGACGGATGGGG 61.867 72.222 0.00 0.00 0.00 4.96
286 289 3.793888 GTTGAGGGTAGGGCGGGG 61.794 72.222 0.00 0.00 0.00 5.73
287 290 3.793888 GGTTGAGGGTAGGGCGGG 61.794 72.222 0.00 0.00 0.00 6.13
288 291 2.687566 AGGTTGAGGGTAGGGCGG 60.688 66.667 0.00 0.00 0.00 6.13
289 292 2.732619 GGAGGTTGAGGGTAGGGCG 61.733 68.421 0.00 0.00 0.00 6.13
290 293 2.376165 GGGAGGTTGAGGGTAGGGC 61.376 68.421 0.00 0.00 0.00 5.19
291 294 1.693103 GGGGAGGTTGAGGGTAGGG 60.693 68.421 0.00 0.00 0.00 3.53
292 295 1.693103 GGGGGAGGTTGAGGGTAGG 60.693 68.421 0.00 0.00 0.00 3.18
293 296 4.068257 GGGGGAGGTTGAGGGTAG 57.932 66.667 0.00 0.00 0.00 3.18
331 334 2.965226 CTTAGAGGGATGGCCGGGGA 62.965 65.000 2.18 0.00 33.83 4.81
333 336 3.151906 CTTAGAGGGATGGCCGGG 58.848 66.667 2.18 0.00 33.83 5.73
337 340 1.453669 CAGGGCTTAGAGGGATGGC 59.546 63.158 0.00 0.00 0.00 4.40
348 351 1.216064 TCATAGATGGTGCAGGGCTT 58.784 50.000 0.00 0.00 0.00 4.35
354 357 4.661222 TGGAGTTTTTCATAGATGGTGCA 58.339 39.130 0.00 0.00 0.00 4.57
357 360 5.817816 GTCGATGGAGTTTTTCATAGATGGT 59.182 40.000 0.00 0.00 30.25 3.55
361 364 4.383770 GGGGTCGATGGAGTTTTTCATAGA 60.384 45.833 0.00 0.00 0.00 1.98
364 367 2.620627 GGGGGTCGATGGAGTTTTTCAT 60.621 50.000 0.00 0.00 0.00 2.57
366 369 1.004394 AGGGGGTCGATGGAGTTTTTC 59.996 52.381 0.00 0.00 0.00 2.29
367 370 1.073098 AGGGGGTCGATGGAGTTTTT 58.927 50.000 0.00 0.00 0.00 1.94
382 385 4.351054 GTGGTGGAGGTGCAGGGG 62.351 72.222 0.00 0.00 0.00 4.79
409 412 1.304134 GGAAGCCACGACCCCATTT 60.304 57.895 0.00 0.00 0.00 2.32
434 437 7.945109 GGGGAAGTCATAGCCTTATTATCTTTT 59.055 37.037 0.00 0.00 0.00 2.27
444 447 2.889522 TAGGGGGAAGTCATAGCCTT 57.110 50.000 0.00 0.00 0.00 4.35
483 486 1.448717 GAACCTCGCTGGAGAAGGC 60.449 63.158 1.32 0.00 43.27 4.35
484 487 1.153745 CGAACCTCGCTGGAGAAGG 60.154 63.158 1.32 0.00 43.27 3.46
500 503 2.363795 ACGAGATGGGAAGGCCGA 60.364 61.111 0.00 0.00 33.83 5.54
506 509 0.389817 CGAAGTGCACGAGATGGGAA 60.390 55.000 12.01 0.00 0.00 3.97
516 520 3.963383 TTTCCTTCTTTCGAAGTGCAC 57.037 42.857 9.40 9.40 44.12 4.57
520 524 5.880887 AGTCACTTTTTCCTTCTTTCGAAGT 59.119 36.000 0.00 0.00 44.12 3.01
523 527 4.574828 CCAGTCACTTTTTCCTTCTTTCGA 59.425 41.667 0.00 0.00 0.00 3.71
526 530 3.066760 CGCCAGTCACTTTTTCCTTCTTT 59.933 43.478 0.00 0.00 0.00 2.52
594 599 4.499019 CGTGTTCCTTGGCTGTAACATTTT 60.499 41.667 0.00 0.00 34.62 1.82
605 610 3.057596 TGATGAAATTCGTGTTCCTTGGC 60.058 43.478 0.00 0.00 0.00 4.52
655 661 4.083565 AGATTCCTCTATCTCGCCCTTAC 58.916 47.826 0.00 0.00 28.74 2.34
667 673 5.481824 TCTTGAGTCTTGCAAGATTCCTCTA 59.518 40.000 35.31 27.44 44.81 2.43
945 952 5.123344 GGATAATTGTTTTACTGTCCGCTGT 59.877 40.000 0.00 0.00 0.00 4.40
947 954 5.497474 AGGATAATTGTTTTACTGTCCGCT 58.503 37.500 0.00 0.00 0.00 5.52
949 962 9.931210 GATTAAGGATAATTGTTTTACTGTCCG 57.069 33.333 0.00 0.00 31.83 4.79
956 969 9.116067 CGTGGAGGATTAAGGATAATTGTTTTA 57.884 33.333 0.00 0.00 31.83 1.52
957 970 7.614192 ACGTGGAGGATTAAGGATAATTGTTTT 59.386 33.333 0.00 0.00 31.83 2.43
986 1000 1.202568 CGGCCATTGAGATGTAGAGCA 60.203 52.381 2.24 0.00 0.00 4.26
1394 1408 4.023450 CACCCGATGGATTGAGATGAAATG 60.023 45.833 0.00 0.00 34.81 2.32
1400 1418 0.250038 CGCACCCGATGGATTGAGAT 60.250 55.000 0.00 0.00 36.29 2.75
1405 1423 4.467084 ACGCGCACCCGATGGATT 62.467 61.111 5.73 0.00 36.29 3.01
1419 1437 1.733399 AAGAAACGGAGCTCGACGC 60.733 57.895 7.83 0.00 42.43 5.19
1615 1637 7.875971 ACCTATACAAGCACAAAGAAAGAAAG 58.124 34.615 0.00 0.00 0.00 2.62
1619 1641 7.173218 TCTGAACCTATACAAGCACAAAGAAAG 59.827 37.037 0.00 0.00 0.00 2.62
1736 1772 2.945668 AGAAACGGCTGCCATATCTTTC 59.054 45.455 20.29 14.92 0.00 2.62
1765 1801 6.954297 GCGTAATTAAACAGTTGCTAGAAGAC 59.046 38.462 0.00 0.00 0.00 3.01
1794 1830 2.032620 CCGACCACTGCTAGACCTATT 58.967 52.381 0.00 0.00 0.00 1.73
1810 1846 7.818642 ACTAGACTATTACAGCATAATCCGAC 58.181 38.462 0.00 0.00 0.00 4.79
1815 1851 8.865090 AGCAAGACTAGACTATTACAGCATAAT 58.135 33.333 0.00 0.00 0.00 1.28
1881 1939 2.097825 TCGAGCACTACTAGGAAACCC 58.902 52.381 0.00 0.00 0.00 4.11
1899 1959 0.172352 AGAAGAGGAAAGCGAGCTCG 59.828 55.000 31.37 31.37 43.27 5.03
1907 1967 4.227073 AGGAGATGGGAAAGAAGAGGAAAG 59.773 45.833 0.00 0.00 0.00 2.62
1913 1973 8.393959 AGTTTAATAGGAGATGGGAAAGAAGA 57.606 34.615 0.00 0.00 0.00 2.87
2001 2061 7.617041 AGTCCATAATTAAACACTTGCTCTC 57.383 36.000 0.00 0.00 0.00 3.20
2003 2063 7.750903 GTCAAGTCCATAATTAAACACTTGCTC 59.249 37.037 19.47 14.28 40.27 4.26
2062 2122 9.868389 GATATTTTTATTGCCAAAGCTAAATGC 57.132 29.630 0.00 0.00 40.80 3.56
2165 2228 9.710900 AACATTCTCTTTGAAAAACAAGAACTT 57.289 25.926 0.00 0.00 39.77 2.66
2340 2428 7.496346 TGAACTTTACCATCTCTAGTGGAAT 57.504 36.000 4.93 0.00 39.12 3.01
2404 2492 9.691362 TTCTATTTCCTTTTGTACTTTTCATGC 57.309 29.630 0.00 0.00 0.00 4.06
2516 2606 6.638610 TGTTTGTTGATTTTCAATGTCACCT 58.361 32.000 0.00 0.00 38.79 4.00
2524 2614 7.025963 GTGCCATTTTGTTTGTTGATTTTCAA 58.974 30.769 0.00 0.00 33.32 2.69
2727 2819 3.716431 CCTAACAAGAGGGGGTAGTGTA 58.284 50.000 0.00 0.00 32.39 2.90
2728 2820 2.547990 CCTAACAAGAGGGGGTAGTGT 58.452 52.381 0.00 0.00 32.39 3.55
2734 2826 1.208165 ACCAGCCTAACAAGAGGGGG 61.208 60.000 0.00 0.00 37.06 5.40
2970 3125 2.742053 TCATTGAGAAAGTACGGCAAGC 59.258 45.455 0.00 0.00 0.00 4.01
3032 3191 5.826208 CACGGGTAAGCCTTTTATTTATCCT 59.174 40.000 0.00 0.00 34.45 3.24
3033 3192 5.506815 GCACGGGTAAGCCTTTTATTTATCC 60.507 44.000 0.00 0.00 34.45 2.59
3115 3274 0.180642 CATGGCTCATGCTCTCCACT 59.819 55.000 2.78 0.00 35.02 4.00
3217 3475 9.409312 TCTGCAATTTTTACATGACAAATACAG 57.591 29.630 0.00 11.12 31.56 2.74
3285 3543 3.178046 TGCAGATCTGTTACCTTGGGTA 58.822 45.455 23.38 0.00 37.09 3.69
3369 3628 3.409026 ACTCACCAAAAGGCTAGACAG 57.591 47.619 0.00 0.00 0.00 3.51
3371 3630 5.488341 TGATAACTCACCAAAAGGCTAGAC 58.512 41.667 0.00 0.00 0.00 2.59
3406 3671 5.878406 AGAGTTAGTGGGGATCAACTATG 57.122 43.478 0.00 0.00 31.57 2.23
3469 3734 4.870636 AGGTGAATCTTTTCCCATGCATA 58.129 39.130 0.00 0.00 0.00 3.14
3623 5336 8.634444 ACATACTACTTTGTTCCTATAGAGCAG 58.366 37.037 0.00 0.00 37.00 4.24
3794 5517 4.641396 TGTCTGTGTAAATTGGAGTCCTG 58.359 43.478 11.33 0.00 0.00 3.86
3796 5519 5.305585 TCTTGTCTGTGTAAATTGGAGTCC 58.694 41.667 0.73 0.73 0.00 3.85
3831 5554 0.866427 CTGATAGCCGCATTGCTCTG 59.134 55.000 7.12 0.00 41.68 3.35
3852 5575 1.234821 TCACCATCAAAGACGCCAAC 58.765 50.000 0.00 0.00 0.00 3.77
3872 5595 3.679639 GCGGGCCTTCATTGATCATTTTT 60.680 43.478 0.84 0.00 0.00 1.94
4136 5859 1.667724 CCGATCTTCCTGTTCATGCAC 59.332 52.381 0.00 0.00 0.00 4.57
4402 6150 5.026121 AGTCCTCCACTGTGAAGATATGAA 58.974 41.667 9.86 0.00 32.26 2.57
4456 6206 6.119536 AGATTTTATACCATTTCACGGAGCA 58.880 36.000 0.00 0.00 0.00 4.26
4506 6261 9.387123 GAGAAAATAGCACAACAACTTCTAAAG 57.613 33.333 0.00 0.00 0.00 1.85
4747 6502 4.234574 GGATCAAAATTGTCCCGTGAAAC 58.765 43.478 0.00 0.00 0.00 2.78
4796 6551 9.519191 CCACATATGGTCCAAATATTAGATGAA 57.481 33.333 7.80 0.00 41.64 2.57
5557 8219 1.202639 TGAACAGACGTTGATGCCTGT 60.203 47.619 0.00 0.00 41.14 4.00
5569 8231 2.565841 AGAAGGTTGTGCTGAACAGAC 58.434 47.619 5.97 2.49 40.74 3.51
6245 8913 2.492090 GAGAGGAGATGCGCACGT 59.508 61.111 14.90 1.29 0.00 4.49
6246 8914 2.279120 GGAGAGGAGATGCGCACG 60.279 66.667 14.90 0.00 0.00 5.34
6249 8917 0.176680 TTTCAGGAGAGGAGATGCGC 59.823 55.000 0.00 0.00 0.00 6.09
6291 8959 3.683937 GGTGGCGGCTGCACAAAT 61.684 61.111 21.31 0.00 45.35 2.32
6310 8978 3.394836 AGAGGCGAGGGGAACTGC 61.395 66.667 0.00 0.00 0.00 4.40
6333 9001 3.390521 ATCGCCAGTGCCGGAAGA 61.391 61.111 5.05 0.00 0.00 2.87
6344 9012 4.041762 GGTTCCCCCACATCGCCA 62.042 66.667 0.00 0.00 0.00 5.69
6415 9083 0.394352 ACGACAATCCAATCAGGCCC 60.394 55.000 0.00 0.00 37.29 5.80
6417 9085 3.244976 CAAAACGACAATCCAATCAGGC 58.755 45.455 0.00 0.00 37.29 4.85
6419 9087 3.670055 GTGCAAAACGACAATCCAATCAG 59.330 43.478 0.00 0.00 0.00 2.90
6420 9088 3.067320 TGTGCAAAACGACAATCCAATCA 59.933 39.130 0.00 0.00 0.00 2.57
6421 9089 3.425193 GTGTGCAAAACGACAATCCAATC 59.575 43.478 0.00 0.00 0.00 2.67
6422 9090 3.068024 AGTGTGCAAAACGACAATCCAAT 59.932 39.130 0.00 0.00 0.00 3.16
6427 9095 5.287513 GTGTAAAAGTGTGCAAAACGACAAT 59.712 36.000 0.00 0.00 0.00 2.71
6429 9097 4.159857 GTGTAAAAGTGTGCAAAACGACA 58.840 39.130 0.00 0.00 0.00 4.35
6431 9099 3.440872 AGGTGTAAAAGTGTGCAAAACGA 59.559 39.130 0.00 0.00 0.00 3.85
6433 9101 4.490743 ACAGGTGTAAAAGTGTGCAAAAC 58.509 39.130 0.00 0.00 0.00 2.43
6435 9103 5.899120 TTACAGGTGTAAAAGTGTGCAAA 57.101 34.783 0.00 0.00 37.54 3.68
6436 9104 5.899120 TTTACAGGTGTAAAAGTGTGCAA 57.101 34.783 11.96 0.00 44.63 4.08
6445 9113 7.970102 AGGTCTGTATCTTTTACAGGTGTAAA 58.030 34.615 10.59 10.59 45.55 2.01
6448 9116 5.542635 TGAGGTCTGTATCTTTTACAGGTGT 59.457 40.000 11.65 0.00 43.67 4.16
6449 9117 6.037786 TGAGGTCTGTATCTTTTACAGGTG 57.962 41.667 11.65 0.00 43.67 4.00
6450 9118 6.681729 TTGAGGTCTGTATCTTTTACAGGT 57.318 37.500 11.65 0.00 43.67 4.00
6451 9119 6.477033 CGATTGAGGTCTGTATCTTTTACAGG 59.523 42.308 11.65 0.00 43.67 4.00
6452 9120 6.477033 CCGATTGAGGTCTGTATCTTTTACAG 59.523 42.308 6.45 6.45 44.56 2.74
6453 9121 6.070995 ACCGATTGAGGTCTGTATCTTTTACA 60.071 38.462 0.00 0.00 41.46 2.41
6454 9122 6.338937 ACCGATTGAGGTCTGTATCTTTTAC 58.661 40.000 0.00 0.00 41.46 2.01
6455 9123 6.540438 ACCGATTGAGGTCTGTATCTTTTA 57.460 37.500 0.00 0.00 41.46 1.52
6456 9124 5.422214 ACCGATTGAGGTCTGTATCTTTT 57.578 39.130 0.00 0.00 41.46 2.27
6468 9136 4.154195 AGAAATGAAAACGACCGATTGAGG 59.846 41.667 0.00 0.00 37.30 3.86
6469 9137 5.082059 CAGAAATGAAAACGACCGATTGAG 58.918 41.667 0.00 0.00 0.00 3.02
6470 9138 4.083537 CCAGAAATGAAAACGACCGATTGA 60.084 41.667 0.00 0.00 0.00 2.57
6471 9139 4.158384 CCAGAAATGAAAACGACCGATTG 58.842 43.478 0.00 0.00 0.00 2.67
6472 9140 3.818773 ACCAGAAATGAAAACGACCGATT 59.181 39.130 0.00 0.00 0.00 3.34
6473 9141 3.408634 ACCAGAAATGAAAACGACCGAT 58.591 40.909 0.00 0.00 0.00 4.18
6475 9143 3.002862 TCAACCAGAAATGAAAACGACCG 59.997 43.478 0.00 0.00 0.00 4.79
6476 9144 4.561735 TCAACCAGAAATGAAAACGACC 57.438 40.909 0.00 0.00 0.00 4.79
6477 9145 6.879188 TTTTCAACCAGAAATGAAAACGAC 57.121 33.333 9.01 0.00 45.55 4.34
6484 9152 8.252417 CCACATATGATTTTCAACCAGAAATGA 58.748 33.333 10.38 0.00 45.15 2.57
6486 9154 7.043565 GCCACATATGATTTTCAACCAGAAAT 58.956 34.615 10.38 0.00 45.15 2.17
6489 9157 5.125900 CAGCCACATATGATTTTCAACCAGA 59.874 40.000 10.38 0.00 0.00 3.86
6490 9158 5.345702 CAGCCACATATGATTTTCAACCAG 58.654 41.667 10.38 0.00 0.00 4.00
6491 9159 4.160065 CCAGCCACATATGATTTTCAACCA 59.840 41.667 10.38 0.00 0.00 3.67
6492 9160 4.160252 ACCAGCCACATATGATTTTCAACC 59.840 41.667 10.38 0.00 0.00 3.77
6493 9161 5.104374 CACCAGCCACATATGATTTTCAAC 58.896 41.667 10.38 0.00 0.00 3.18
6495 9163 4.598022 TCACCAGCCACATATGATTTTCA 58.402 39.130 10.38 0.00 0.00 2.69
6496 9164 5.581126 TTCACCAGCCACATATGATTTTC 57.419 39.130 10.38 0.00 0.00 2.29
6497 9165 5.999205 TTTCACCAGCCACATATGATTTT 57.001 34.783 10.38 0.00 0.00 1.82
6498 9166 6.606796 TGTATTTCACCAGCCACATATGATTT 59.393 34.615 10.38 0.00 0.00 2.17
6499 9167 6.039717 GTGTATTTCACCAGCCACATATGATT 59.960 38.462 10.38 0.00 40.84 2.57
6516 9184 9.977762 CCCGTATTACTTTTACAAGTGTATTTC 57.022 33.333 4.49 0.00 43.54 2.17
6517 9185 9.506018 ACCCGTATTACTTTTACAAGTGTATTT 57.494 29.630 4.49 0.00 43.54 1.40
6518 9186 8.938906 CACCCGTATTACTTTTACAAGTGTATT 58.061 33.333 4.49 0.00 43.54 1.89
6519 9187 8.096414 ACACCCGTATTACTTTTACAAGTGTAT 58.904 33.333 4.49 1.46 43.54 2.29
6520 9188 7.441017 ACACCCGTATTACTTTTACAAGTGTA 58.559 34.615 4.49 0.00 43.54 2.90
6521 9189 6.290605 ACACCCGTATTACTTTTACAAGTGT 58.709 36.000 4.49 0.00 43.54 3.55
6522 9190 6.790285 ACACCCGTATTACTTTTACAAGTG 57.210 37.500 4.49 0.00 43.54 3.16
6531 9199 9.559732 GGGTAAATTTATACACCCGTATTACTT 57.440 33.333 10.47 0.00 41.24 2.24
6542 9210 8.573885 GCTTGGAATAGGGGTAAATTTATACAC 58.426 37.037 0.31 0.00 0.00 2.90
6543 9211 7.446013 CGCTTGGAATAGGGGTAAATTTATACA 59.554 37.037 0.31 0.00 0.00 2.29
6545 9213 6.943718 CCGCTTGGAATAGGGGTAAATTTATA 59.056 38.462 0.31 0.00 41.86 0.98
6548 9216 3.958147 CCGCTTGGAATAGGGGTAAATTT 59.042 43.478 0.00 0.00 41.86 1.82
6549 9217 3.562182 CCGCTTGGAATAGGGGTAAATT 58.438 45.455 0.00 0.00 41.86 1.82
6550 9218 2.158519 CCCGCTTGGAATAGGGGTAAAT 60.159 50.000 0.00 0.00 44.46 1.40
6551 9219 1.213430 CCCGCTTGGAATAGGGGTAAA 59.787 52.381 0.00 0.00 44.46 2.01
6552 9220 0.841289 CCCGCTTGGAATAGGGGTAA 59.159 55.000 0.00 0.00 44.46 2.85
6553 9221 2.535224 CCCGCTTGGAATAGGGGTA 58.465 57.895 0.00 0.00 44.46 3.69
6554 9222 3.331293 CCCGCTTGGAATAGGGGT 58.669 61.111 0.00 0.00 44.46 4.95
6556 9224 2.203351 GCCCCGCTTGGAATAGGG 60.203 66.667 0.00 0.00 43.41 3.53
6557 9225 2.919043 AGCCCCGCTTGGAATAGG 59.081 61.111 0.00 0.00 33.89 2.57
6566 9234 2.928396 ACACACCTAAGCCCCGCT 60.928 61.111 0.00 0.00 42.56 5.52
6567 9235 2.746277 CACACACCTAAGCCCCGC 60.746 66.667 0.00 0.00 0.00 6.13
6568 9236 2.046314 CCACACACCTAAGCCCCG 60.046 66.667 0.00 0.00 0.00 5.73
6569 9237 1.002502 GACCACACACCTAAGCCCC 60.003 63.158 0.00 0.00 0.00 5.80
6570 9238 1.375523 CGACCACACACCTAAGCCC 60.376 63.158 0.00 0.00 0.00 5.19
6571 9239 0.249398 ATCGACCACACACCTAAGCC 59.751 55.000 0.00 0.00 0.00 4.35
6572 9240 1.359848 CATCGACCACACACCTAAGC 58.640 55.000 0.00 0.00 0.00 3.09
6574 9242 1.001520 CACCATCGACCACACACCTAA 59.998 52.381 0.00 0.00 0.00 2.69
6618 9400 0.617820 TTCTACAGGTGGAGCCTCCC 60.618 60.000 8.62 0.00 46.96 4.30
6631 9413 2.561419 CCCGTCTCCTTGTTCTTCTACA 59.439 50.000 0.00 0.00 0.00 2.74
6633 9415 2.824341 GTCCCGTCTCCTTGTTCTTCTA 59.176 50.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.