Multiple sequence alignment - TraesCS2B01G418200

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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 TraesCS2B01G418200 chr2B 100.000 4699 0 0 1 4699 598967156 598962458 0.000000e+00 8678.0
1 TraesCS2B01G418200 chr2B 100.000 34 0 0 4507 4540 598962620 598962587 3.930000e-06 63.9
2 TraesCS2B01G418200 chr2B 100.000 34 0 0 4537 4570 598962650 598962617 3.930000e-06 63.9
3 TraesCS2B01G418200 chr2D 93.178 2360 84 38 261 2563 509742330 509739991 0.000000e+00 3395.0
4 TraesCS2B01G418200 chr2D 93.544 1611 60 18 2721 4307 509739991 509738401 0.000000e+00 2359.0
5 TraesCS2B01G418200 chr2D 92.754 207 10 4 1 205 509742540 509742337 1.280000e-75 294.0
6 TraesCS2B01G418200 chr2D 92.547 161 12 0 4537 4697 509738180 509738020 1.020000e-56 231.0
7 TraesCS2B01G418200 chr2D 86.432 199 16 5 4342 4540 509738334 509738147 1.710000e-49 207.0
8 TraesCS2B01G418200 chr2A 92.828 1715 66 29 386 2067 653373699 653372009 0.000000e+00 2433.0
9 TraesCS2B01G418200 chr2A 93.584 1278 36 9 3033 4307 653370769 653369535 0.000000e+00 1864.0
10 TraesCS2B01G418200 chr2A 95.381 801 29 5 2064 2862 653371929 653371135 0.000000e+00 1267.0
11 TraesCS2B01G418200 chr2A 94.239 243 14 0 4298 4540 653369497 653369255 5.740000e-99 372.0
12 TraesCS2B01G418200 chr2A 88.479 217 15 6 1 207 653374092 653373876 2.170000e-63 254.0
13 TraesCS2B01G418200 chr2A 94.872 156 8 0 4537 4692 653369288 653369133 1.310000e-60 244.0
14 TraesCS2B01G418200 chr3D 89.147 129 10 3 80 205 485622983 485622856 1.750000e-34 158.0
15 TraesCS2B01G418200 chr3B 87.597 129 13 2 80 205 648708757 648708629 3.790000e-31 147.0
16 TraesCS2B01G418200 chr3A 83.824 136 12 5 80 205 634859154 634859019 2.300000e-23 121.0
17 TraesCS2B01G418200 chr3A 97.059 34 1 0 4489 4522 300495792 300495825 1.830000e-04 58.4
18 TraesCS2B01G418200 chr1B 97.059 34 1 0 61 94 26641220 26641253 1.830000e-04 58.4
19 TraesCS2B01G418200 chr1B 100.000 30 0 0 61 90 26641151 26641180 6.570000e-04 56.5


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 TraesCS2B01G418200 chr2B 598962458 598967156 4698 True 8678.000000 8678 100.0000 1 4699 1 chr2B.!!$R1 4698
1 TraesCS2B01G418200 chr2D 509738020 509742540 4520 True 1297.200000 3395 91.6910 1 4697 5 chr2D.!!$R1 4696
2 TraesCS2B01G418200 chr2A 653369133 653374092 4959 True 1072.333333 2433 93.2305 1 4692 6 chr2A.!!$R1 4691

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
963 1114 0.036010 CCCTGGAGCAATCTGTCGTT 60.036 55.0 0.0 0.0 0.0 3.85 F
2577 2992 0.108186 TCATTCAGTGGCGGTGCTAG 60.108 55.0 0.0 0.0 0.0 3.42 F
2720 3135 0.037326 CACGTAGCACCACCACTGAT 60.037 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2701 3116 0.037326 ATCAGTGGTGGTGCTACGTG 60.037 55.000 0.00 0.00 33.44 4.49 R
3602 4220 1.069022 GTGTGCGTGCAATCAATCTGT 60.069 47.619 0.00 0.00 0.00 3.41 R
4314 4984 1.131126 GTGCATGTGTACTGCCATGTC 59.869 52.381 16.61 11.78 40.42 3.06 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
57 62 4.495844 GCCCGATGTTTAGTAAATGCACTC 60.496 45.833 0.00 0.00 0.00 3.51
124 135 6.636705 ACAGTTATAGGTATTTGCACTTCGA 58.363 36.000 0.00 0.00 0.00 3.71
212 224 7.706159 TGAGCATCAACATTTGTGTATATTCC 58.294 34.615 0.00 0.00 45.97 3.01
213 225 7.042797 AGCATCAACATTTGTGTATATTCCC 57.957 36.000 0.00 0.00 0.00 3.97
214 226 6.835488 AGCATCAACATTTGTGTATATTCCCT 59.165 34.615 0.00 0.00 0.00 4.20
215 227 7.013655 AGCATCAACATTTGTGTATATTCCCTC 59.986 37.037 0.00 0.00 0.00 4.30
216 228 7.201812 GCATCAACATTTGTGTATATTCCCTCA 60.202 37.037 0.00 0.00 0.00 3.86
217 229 8.685427 CATCAACATTTGTGTATATTCCCTCAA 58.315 33.333 0.00 0.00 0.00 3.02
218 230 8.642935 TCAACATTTGTGTATATTCCCTCAAA 57.357 30.769 0.00 0.00 0.00 2.69
219 231 9.083422 TCAACATTTGTGTATATTCCCTCAAAA 57.917 29.630 0.00 0.00 0.00 2.44
220 232 9.703892 CAACATTTGTGTATATTCCCTCAAAAA 57.296 29.630 0.00 0.00 0.00 1.94
380 497 1.005037 CGCACTACTCAACCAGCCA 60.005 57.895 0.00 0.00 0.00 4.75
422 540 3.927142 CGTTCAGATCACAAACCTACCTC 59.073 47.826 0.00 0.00 0.00 3.85
424 542 3.516586 TCAGATCACAAACCTACCTCCA 58.483 45.455 0.00 0.00 0.00 3.86
425 543 4.104086 TCAGATCACAAACCTACCTCCAT 58.896 43.478 0.00 0.00 0.00 3.41
426 544 4.080919 TCAGATCACAAACCTACCTCCATG 60.081 45.833 0.00 0.00 0.00 3.66
463 583 4.658063 TGTAAATCCAACCTGATCCGTTT 58.342 39.130 0.00 0.00 0.00 3.60
468 588 2.500098 TCCAACCTGATCCGTTTAGAGG 59.500 50.000 0.00 0.00 0.00 3.69
488 608 2.583472 CCAAAGATTGGCACTCCCC 58.417 57.895 0.69 0.00 45.17 4.81
501 621 3.270877 GCACTCCCCACTACAACAATAG 58.729 50.000 0.00 0.00 0.00 1.73
511 631 5.334879 CCACTACAACAATAGCCACTTCAAC 60.335 44.000 0.00 0.00 0.00 3.18
515 635 7.883311 ACTACAACAATAGCCACTTCAACTTAT 59.117 33.333 0.00 0.00 0.00 1.73
516 636 9.378551 CTACAACAATAGCCACTTCAACTTATA 57.621 33.333 0.00 0.00 0.00 0.98
517 637 8.807948 ACAACAATAGCCACTTCAACTTATAT 57.192 30.769 0.00 0.00 0.00 0.86
539 659 1.464997 CCTGTCCTAAAAAGTGCGCTC 59.535 52.381 9.73 4.74 0.00 5.03
579 706 1.134907 TCCGTCTGCCTCCGTTAAATC 60.135 52.381 0.00 0.00 0.00 2.17
584 711 1.208844 TGCCTCCGTTAAATCCCCCA 61.209 55.000 0.00 0.00 0.00 4.96
585 712 0.465642 GCCTCCGTTAAATCCCCCAG 60.466 60.000 0.00 0.00 0.00 4.45
721 864 0.532573 GTGTCTGCCCGAGAATCTGA 59.467 55.000 0.00 0.00 30.26 3.27
722 865 0.820226 TGTCTGCCCGAGAATCTGAG 59.180 55.000 0.00 0.00 30.26 3.35
786 930 4.680237 TGGCGCTTCGGGACACAG 62.680 66.667 7.64 0.00 0.00 3.66
915 1059 1.305213 GAAGGCATTGGGGGCTGAA 60.305 57.895 0.00 0.00 43.71 3.02
963 1114 0.036010 CCCTGGAGCAATCTGTCGTT 60.036 55.000 0.00 0.00 0.00 3.85
974 1125 0.790207 TCTGTCGTTGAATCGCTTGC 59.210 50.000 0.00 0.00 0.00 4.01
979 1130 1.539388 TCGTTGAATCGCTTGCCAATT 59.461 42.857 0.00 0.00 0.00 2.32
982 1133 1.255882 TGAATCGCTTGCCAATTGGT 58.744 45.000 25.19 2.83 37.57 3.67
995 1146 0.539438 AATTGGTTGCGGCTTGGAGA 60.539 50.000 0.00 0.00 0.00 3.71
1026 1177 1.001393 GGGGGCTTCGAACATGGAA 60.001 57.895 0.00 0.00 0.00 3.53
1137 1288 4.514577 CTCGTCGCCCGCCTCAAT 62.515 66.667 0.00 0.00 36.19 2.57
1314 1465 1.968493 ACCAAGAAGGAGAAGTACGCA 59.032 47.619 0.00 0.00 41.22 5.24
1371 1522 6.071896 GCACCAAGGTAGCTTAATCTCTTTTT 60.072 38.462 6.90 0.00 0.00 1.94
1402 1553 4.630505 TCAACTTGTACGTACTTGTTGCAA 59.369 37.500 33.55 24.59 38.56 4.08
1570 1722 5.106436 TGTGCAATGAATCTGAGATGTTGAC 60.106 40.000 15.32 11.69 0.00 3.18
1682 1855 5.009610 TGGAACAGTAGTTTTCCTTTCATGC 59.990 40.000 15.02 0.00 41.76 4.06
1751 1924 6.623767 GCTGTCTTGGATGGTGTTTATTCTTC 60.624 42.308 0.00 0.00 0.00 2.87
1845 2019 0.478072 AGGGTGGTCTTTGCATGTCA 59.522 50.000 0.00 0.00 0.00 3.58
1857 2031 5.535783 TCTTTGCATGTCAATCTCCTCAAAA 59.464 36.000 0.00 0.00 34.12 2.44
1878 2052 1.944709 GCTTTGGCGATTACCGGTATT 59.055 47.619 16.67 12.38 39.04 1.89
1920 2094 1.067776 CACCTTACCACAGACGAGTCC 60.068 57.143 0.00 0.00 0.00 3.85
1958 2132 8.968969 TCTTGCTAAGTTTTGGGTTAAAAGTTA 58.031 29.630 10.32 10.32 45.47 2.24
1989 2163 5.001874 GGAAGTTAAGGTTGAATTCCGTCT 58.998 41.667 2.27 0.00 0.00 4.18
2002 2176 6.435428 TGAATTCCGTCTAAACTTTCTTTGC 58.565 36.000 2.27 0.00 0.00 3.68
2007 2181 3.246699 CGTCTAAACTTTCTTTGCGTGGA 59.753 43.478 0.00 0.00 0.00 4.02
2025 2199 4.976116 CGTGGAAAACCTGTTCAGATTTTC 59.024 41.667 18.75 18.75 39.33 2.29
2099 2356 1.098050 GAGCATGGCAGAACGGAATT 58.902 50.000 0.00 0.00 0.00 2.17
2221 2479 6.469410 TGACCGTTTCCTGTTATTGAATAGT 58.531 36.000 0.00 0.00 0.00 2.12
2222 2480 7.613585 TGACCGTTTCCTGTTATTGAATAGTA 58.386 34.615 0.00 0.00 0.00 1.82
2306 2564 8.877808 AAGGATGTTTTGACTTTCAATTCTTC 57.122 30.769 0.00 0.00 36.11 2.87
2404 2662 5.496556 TGGTATGTCTTGGTGGTTGATTAG 58.503 41.667 0.00 0.00 0.00 1.73
2489 2747 5.047021 TGCACTCTAAGAGATGCTACAAAGT 60.047 40.000 16.53 0.00 37.48 2.66
2563 2978 8.648557 TTATCTGTTGCACTAGTATGTCATTC 57.351 34.615 0.00 0.00 0.00 2.67
2564 2979 6.036577 TCTGTTGCACTAGTATGTCATTCA 57.963 37.500 0.00 0.00 0.00 2.57
2565 2980 6.101997 TCTGTTGCACTAGTATGTCATTCAG 58.898 40.000 0.00 4.62 0.00 3.02
2566 2981 5.793817 TGTTGCACTAGTATGTCATTCAGT 58.206 37.500 0.00 0.00 0.00 3.41
2567 2982 5.639082 TGTTGCACTAGTATGTCATTCAGTG 59.361 40.000 13.08 13.08 0.00 3.66
2568 2983 4.758688 TGCACTAGTATGTCATTCAGTGG 58.241 43.478 16.61 0.00 0.00 4.00
2569 2984 3.557595 GCACTAGTATGTCATTCAGTGGC 59.442 47.826 16.61 9.48 0.00 5.01
2570 2985 3.798878 CACTAGTATGTCATTCAGTGGCG 59.201 47.826 0.00 0.00 34.28 5.69
2571 2986 2.315925 AGTATGTCATTCAGTGGCGG 57.684 50.000 0.00 0.00 34.28 6.13
2572 2987 1.555075 AGTATGTCATTCAGTGGCGGT 59.445 47.619 0.00 0.00 34.28 5.68
2573 2988 1.665679 GTATGTCATTCAGTGGCGGTG 59.334 52.381 0.00 0.00 34.28 4.94
2574 2989 1.308069 ATGTCATTCAGTGGCGGTGC 61.308 55.000 0.00 0.00 34.28 5.01
2575 2990 1.672356 GTCATTCAGTGGCGGTGCT 60.672 57.895 0.00 0.00 0.00 4.40
2576 2991 0.391130 GTCATTCAGTGGCGGTGCTA 60.391 55.000 0.00 0.00 0.00 3.49
2577 2992 0.108186 TCATTCAGTGGCGGTGCTAG 60.108 55.000 0.00 0.00 0.00 3.42
2578 2993 1.091771 CATTCAGTGGCGGTGCTAGG 61.092 60.000 0.00 0.00 0.00 3.02
2579 2994 1.264749 ATTCAGTGGCGGTGCTAGGA 61.265 55.000 0.00 0.00 0.00 2.94
2580 2995 1.476845 TTCAGTGGCGGTGCTAGGAA 61.477 55.000 0.00 0.00 0.00 3.36
2581 2996 1.221840 CAGTGGCGGTGCTAGGAAT 59.778 57.895 0.00 0.00 0.00 3.01
2582 2997 1.091771 CAGTGGCGGTGCTAGGAATG 61.092 60.000 0.00 0.00 0.00 2.67
2583 2998 1.819632 GTGGCGGTGCTAGGAATGG 60.820 63.158 0.00 0.00 0.00 3.16
2584 2999 1.992834 TGGCGGTGCTAGGAATGGA 60.993 57.895 0.00 0.00 0.00 3.41
2585 3000 1.223487 GGCGGTGCTAGGAATGGAA 59.777 57.895 0.00 0.00 0.00 3.53
2586 3001 0.815615 GGCGGTGCTAGGAATGGAAG 60.816 60.000 0.00 0.00 0.00 3.46
2587 3002 1.440145 GCGGTGCTAGGAATGGAAGC 61.440 60.000 0.00 0.00 0.00 3.86
2588 3003 0.179000 CGGTGCTAGGAATGGAAGCT 59.821 55.000 0.00 0.00 0.00 3.74
2589 3004 1.412710 CGGTGCTAGGAATGGAAGCTA 59.587 52.381 0.00 0.00 0.00 3.32
2590 3005 2.546795 CGGTGCTAGGAATGGAAGCTAG 60.547 54.545 0.00 0.00 0.00 3.42
2591 3006 2.436173 GGTGCTAGGAATGGAAGCTAGT 59.564 50.000 0.00 0.00 0.00 2.57
2592 3007 3.462021 GTGCTAGGAATGGAAGCTAGTG 58.538 50.000 0.00 0.00 0.00 2.74
2593 3008 3.133003 GTGCTAGGAATGGAAGCTAGTGA 59.867 47.826 0.00 0.00 0.00 3.41
2594 3009 3.969976 TGCTAGGAATGGAAGCTAGTGAT 59.030 43.478 0.00 0.00 0.00 3.06
2595 3010 4.202295 TGCTAGGAATGGAAGCTAGTGATG 60.202 45.833 0.00 0.00 0.00 3.07
2596 3011 4.202305 GCTAGGAATGGAAGCTAGTGATGT 60.202 45.833 0.00 0.00 0.00 3.06
2597 3012 4.414337 AGGAATGGAAGCTAGTGATGTC 57.586 45.455 0.00 0.00 0.00 3.06
2598 3013 3.776969 AGGAATGGAAGCTAGTGATGTCA 59.223 43.478 0.00 0.00 0.00 3.58
2599 3014 4.225942 AGGAATGGAAGCTAGTGATGTCAA 59.774 41.667 0.00 0.00 0.00 3.18
2600 3015 4.943705 GGAATGGAAGCTAGTGATGTCAAA 59.056 41.667 0.00 0.00 0.00 2.69
2601 3016 5.065731 GGAATGGAAGCTAGTGATGTCAAAG 59.934 44.000 0.00 0.00 0.00 2.77
2602 3017 3.338249 TGGAAGCTAGTGATGTCAAAGC 58.662 45.455 9.44 9.44 37.38 3.51
2603 3018 3.008375 TGGAAGCTAGTGATGTCAAAGCT 59.992 43.478 12.76 12.76 44.47 3.74
2604 3019 4.222810 TGGAAGCTAGTGATGTCAAAGCTA 59.777 41.667 16.80 4.44 42.87 3.32
2605 3020 5.104776 TGGAAGCTAGTGATGTCAAAGCTAT 60.105 40.000 16.80 10.16 42.87 2.97
2606 3021 6.098266 TGGAAGCTAGTGATGTCAAAGCTATA 59.902 38.462 16.80 7.76 42.87 1.31
2607 3022 7.158021 GGAAGCTAGTGATGTCAAAGCTATAT 58.842 38.462 16.80 6.38 42.87 0.86
2608 3023 7.117523 GGAAGCTAGTGATGTCAAAGCTATATG 59.882 40.741 16.80 0.00 42.87 1.78
2609 3024 5.931146 AGCTAGTGATGTCAAAGCTATATGC 59.069 40.000 15.57 2.00 42.29 3.14
2610 3025 5.698089 GCTAGTGATGTCAAAGCTATATGCA 59.302 40.000 9.97 0.00 45.94 3.96
2611 3026 6.370994 GCTAGTGATGTCAAAGCTATATGCAT 59.629 38.462 3.79 3.79 45.94 3.96
2612 3027 7.547019 GCTAGTGATGTCAAAGCTATATGCATA 59.453 37.037 9.27 9.27 45.94 3.14
2613 3028 7.664082 AGTGATGTCAAAGCTATATGCATAC 57.336 36.000 8.99 0.00 45.94 2.39
2614 3029 6.652481 AGTGATGTCAAAGCTATATGCATACC 59.348 38.462 8.99 0.63 45.94 2.73
2615 3030 5.939883 TGATGTCAAAGCTATATGCATACCC 59.060 40.000 8.99 0.26 45.94 3.69
2616 3031 5.303259 TGTCAAAGCTATATGCATACCCA 57.697 39.130 8.99 0.00 45.94 4.51
2617 3032 5.879763 TGTCAAAGCTATATGCATACCCAT 58.120 37.500 8.99 0.00 45.94 4.00
2618 3033 7.014988 TGTCAAAGCTATATGCATACCCATA 57.985 36.000 8.99 0.00 45.94 2.74
2619 3034 7.632861 TGTCAAAGCTATATGCATACCCATAT 58.367 34.615 8.99 0.00 45.94 1.78
2620 3035 8.767436 TGTCAAAGCTATATGCATACCCATATA 58.233 33.333 8.99 0.00 45.94 0.86
2621 3036 9.784531 GTCAAAGCTATATGCATACCCATATAT 57.215 33.333 8.99 0.00 45.94 0.86
2622 3037 9.783081 TCAAAGCTATATGCATACCCATATATG 57.217 33.333 8.99 5.68 45.94 1.78
2623 3038 9.565090 CAAAGCTATATGCATACCCATATATGT 57.435 33.333 8.99 0.00 45.94 2.29
2625 3040 9.565090 AAGCTATATGCATACCCATATATGTTG 57.435 33.333 8.99 5.14 45.94 3.33
2626 3041 8.937835 AGCTATATGCATACCCATATATGTTGA 58.062 33.333 8.99 0.00 45.94 3.18
2627 3042 9.730705 GCTATATGCATACCCATATATGTTGAT 57.269 33.333 8.99 0.00 38.98 2.57
2660 3075 9.891828 TTGTTAAATTCAAGTGTATTAGTGCAG 57.108 29.630 0.00 0.00 0.00 4.41
2661 3076 8.020819 TGTTAAATTCAAGTGTATTAGTGCAGC 58.979 33.333 0.00 0.00 0.00 5.25
2662 3077 6.824305 AAATTCAAGTGTATTAGTGCAGCT 57.176 33.333 0.00 0.00 0.00 4.24
2663 3078 7.921786 AAATTCAAGTGTATTAGTGCAGCTA 57.078 32.000 0.00 0.00 0.00 3.32
2664 3079 8.511604 AAATTCAAGTGTATTAGTGCAGCTAT 57.488 30.769 0.00 0.00 0.00 2.97
2665 3080 7.721286 ATTCAAGTGTATTAGTGCAGCTATC 57.279 36.000 0.00 0.00 0.00 2.08
2666 3081 6.220726 TCAAGTGTATTAGTGCAGCTATCA 57.779 37.500 0.00 0.00 0.00 2.15
2667 3082 6.042777 TCAAGTGTATTAGTGCAGCTATCAC 58.957 40.000 9.56 9.56 34.80 3.06
2668 3083 5.598416 AGTGTATTAGTGCAGCTATCACA 57.402 39.130 17.31 12.56 36.93 3.58
2669 3084 5.977635 AGTGTATTAGTGCAGCTATCACAA 58.022 37.500 17.31 11.12 36.93 3.33
2670 3085 6.406370 AGTGTATTAGTGCAGCTATCACAAA 58.594 36.000 17.31 5.52 36.93 2.83
2671 3086 7.050377 AGTGTATTAGTGCAGCTATCACAAAT 58.950 34.615 17.31 3.65 36.93 2.32
2672 3087 7.554118 AGTGTATTAGTGCAGCTATCACAAATT 59.446 33.333 17.31 3.12 36.93 1.82
2673 3088 8.184192 GTGTATTAGTGCAGCTATCACAAATTT 58.816 33.333 17.31 0.00 36.93 1.82
2674 3089 8.739039 TGTATTAGTGCAGCTATCACAAATTTT 58.261 29.630 17.31 2.25 36.93 1.82
2675 3090 9.013490 GTATTAGTGCAGCTATCACAAATTTTG 57.987 33.333 17.31 7.59 36.93 2.44
2676 3091 5.458041 AGTGCAGCTATCACAAATTTTGT 57.542 34.783 17.31 8.97 46.75 2.83
2704 3119 5.845953 GTCACTTGACATCATAAACAACACG 59.154 40.000 4.43 0.00 44.18 4.49
2705 3120 5.525745 TCACTTGACATCATAAACAACACGT 59.474 36.000 0.00 0.00 0.00 4.49
2706 3121 6.702282 TCACTTGACATCATAAACAACACGTA 59.298 34.615 0.00 0.00 0.00 3.57
2707 3122 7.009440 CACTTGACATCATAAACAACACGTAG 58.991 38.462 0.00 0.00 0.00 3.51
2708 3123 5.524511 TGACATCATAAACAACACGTAGC 57.475 39.130 0.00 0.00 0.00 3.58
2709 3124 4.991687 TGACATCATAAACAACACGTAGCA 59.008 37.500 0.00 0.00 0.00 3.49
2710 3125 5.107259 TGACATCATAAACAACACGTAGCAC 60.107 40.000 0.00 0.00 0.00 4.40
2711 3126 4.153475 ACATCATAAACAACACGTAGCACC 59.847 41.667 0.00 0.00 0.00 5.01
2712 3127 3.729966 TCATAAACAACACGTAGCACCA 58.270 40.909 0.00 0.00 0.00 4.17
2713 3128 3.495377 TCATAAACAACACGTAGCACCAC 59.505 43.478 0.00 0.00 0.00 4.16
2714 3129 1.018910 AAACAACACGTAGCACCACC 58.981 50.000 0.00 0.00 0.00 4.61
2715 3130 0.107606 AACAACACGTAGCACCACCA 60.108 50.000 0.00 0.00 0.00 4.17
2716 3131 0.812412 ACAACACGTAGCACCACCAC 60.812 55.000 0.00 0.00 0.00 4.16
2717 3132 0.531974 CAACACGTAGCACCACCACT 60.532 55.000 0.00 0.00 0.00 4.00
2718 3133 0.531974 AACACGTAGCACCACCACTG 60.532 55.000 0.00 0.00 0.00 3.66
2719 3134 1.365999 CACGTAGCACCACCACTGA 59.634 57.895 0.00 0.00 0.00 3.41
2720 3135 0.037326 CACGTAGCACCACCACTGAT 60.037 55.000 0.00 0.00 0.00 2.90
2749 3164 6.566079 TCCTTTGGTCTTGTGATGAGATAT 57.434 37.500 0.00 0.00 0.00 1.63
2750 3165 7.675161 TCCTTTGGTCTTGTGATGAGATATA 57.325 36.000 0.00 0.00 0.00 0.86
2791 3214 6.192044 TGGAGCCAATCATCATATTGCATAT 58.808 36.000 0.00 0.00 35.85 1.78
2900 3323 7.358023 GCAAATCGTACCACTAAAAACAATGTG 60.358 37.037 0.00 0.00 0.00 3.21
2933 3364 7.340232 TGATTTATGGGCTGAATCCTTATATGC 59.660 37.037 0.00 0.00 30.66 3.14
2948 3379 1.173043 TATGCCCCTGAAAAGTTGCG 58.827 50.000 0.00 0.00 0.00 4.85
2951 3382 2.199652 CCCCTGAAAAGTTGCGCCA 61.200 57.895 4.18 0.00 0.00 5.69
2956 3387 3.220999 GAAAAGTTGCGCCACCCCC 62.221 63.158 8.18 0.00 0.00 5.40
2957 3388 3.749284 AAAAGTTGCGCCACCCCCT 62.749 57.895 8.18 0.00 0.00 4.79
2982 3418 3.317406 TGTCTATGACATGTGGGCCTAT 58.683 45.455 1.15 0.00 37.67 2.57
3167 3785 4.318121 GCTCTTGACACTTGTAGTTTCACG 60.318 45.833 0.00 0.00 34.94 4.35
3241 3859 9.074443 GTTACTAGATAAGTGACTGCTAAACAC 57.926 37.037 0.00 0.00 40.62 3.32
3242 3860 7.228314 ACTAGATAAGTGACTGCTAAACACA 57.772 36.000 0.00 0.00 36.93 3.72
3243 3861 7.667557 ACTAGATAAGTGACTGCTAAACACAA 58.332 34.615 0.00 0.00 36.93 3.33
3244 3862 6.787085 AGATAAGTGACTGCTAAACACAAC 57.213 37.500 0.00 0.00 37.05 3.32
3245 3863 6.288294 AGATAAGTGACTGCTAAACACAACA 58.712 36.000 0.00 0.00 37.05 3.33
3246 3864 4.616181 AAGTGACTGCTAAACACAACAC 57.384 40.909 0.00 0.00 37.05 3.32
3247 3865 2.607635 AGTGACTGCTAAACACAACACG 59.392 45.455 0.00 0.00 37.05 4.49
3248 3866 1.329292 TGACTGCTAAACACAACACGC 59.671 47.619 0.00 0.00 0.00 5.34
3249 3867 1.597663 GACTGCTAAACACAACACGCT 59.402 47.619 0.00 0.00 0.00 5.07
3250 3868 2.798283 GACTGCTAAACACAACACGCTA 59.202 45.455 0.00 0.00 0.00 4.26
3251 3869 3.199677 ACTGCTAAACACAACACGCTAA 58.800 40.909 0.00 0.00 0.00 3.09
3252 3870 3.623960 ACTGCTAAACACAACACGCTAAA 59.376 39.130 0.00 0.00 0.00 1.85
3253 3871 3.942739 TGCTAAACACAACACGCTAAAC 58.057 40.909 0.00 0.00 0.00 2.01
3254 3872 3.623960 TGCTAAACACAACACGCTAAACT 59.376 39.130 0.00 0.00 0.00 2.66
3255 3873 3.966218 GCTAAACACAACACGCTAAACTG 59.034 43.478 0.00 0.00 0.00 3.16
3256 3874 2.468532 AACACAACACGCTAAACTGC 57.531 45.000 0.00 0.00 0.00 4.40
3257 3875 1.663695 ACACAACACGCTAAACTGCT 58.336 45.000 0.00 0.00 0.00 4.24
3258 3876 2.828877 ACACAACACGCTAAACTGCTA 58.171 42.857 0.00 0.00 0.00 3.49
3259 3877 2.800544 ACACAACACGCTAAACTGCTAG 59.199 45.455 0.00 0.00 0.00 3.42
3320 3938 2.422803 GCAAATATGGTGGCTGGAGGTA 60.423 50.000 0.00 0.00 0.00 3.08
3353 3971 0.969409 ATTTCTGCTTCCCTGCTGGC 60.969 55.000 3.63 0.00 33.58 4.85
3580 4198 5.241728 TCATATCGAGTTCGGATGAGTTGAT 59.758 40.000 12.75 0.00 37.27 2.57
3602 4220 8.242729 TGATCAAGCTCAAGTTCTCTATGATA 57.757 34.615 0.00 0.00 0.00 2.15
3620 4238 3.063861 TGATACAGATTGATTGCACGCAC 59.936 43.478 0.00 0.00 0.00 5.34
3733 4351 2.679837 CTGTATCACTCCATGTGGCAAC 59.320 50.000 0.00 0.00 46.20 4.17
3775 4393 4.487714 TTTTCATAGCCATTCTCGTCCT 57.512 40.909 0.00 0.00 0.00 3.85
3778 4396 4.855715 TCATAGCCATTCTCGTCCTAAG 57.144 45.455 0.00 0.00 0.00 2.18
4114 4735 3.426191 CGTGATACAACGAAAACGGAGAA 59.574 43.478 0.00 0.00 46.49 2.87
4180 4801 5.947228 AATGAGAATTCAAGCTGAAACGA 57.053 34.783 8.44 0.00 40.12 3.85
4181 4802 4.732285 TGAGAATTCAAGCTGAAACGAC 57.268 40.909 8.44 0.00 40.12 4.34
4221 4842 8.677300 GCCTGAATTATGAGAAGTTTTCACATA 58.323 33.333 0.00 5.29 40.60 2.29
4236 4857 2.424246 TCACATATGTGTTCCTCGCGTA 59.576 45.455 30.03 8.78 45.76 4.42
4245 4866 1.869132 GTTCCTCGCGTAAACACCTTT 59.131 47.619 5.77 0.00 0.00 3.11
4314 4984 0.107081 TGGTGTGTACTTTCCCACGG 59.893 55.000 0.00 0.00 34.28 4.94
4378 5048 8.503458 TTTTCAAATTTGGTTGTGAACATGAT 57.497 26.923 17.90 0.00 30.00 2.45
4452 5122 7.553504 AATTTGGCTACTTTGGAAAACCTAT 57.446 32.000 0.00 0.00 0.00 2.57
4530 5200 2.027929 TCCAAAATTGCATCAAGGGCTG 60.028 45.455 0.00 0.00 0.00 4.85
4531 5201 2.352388 CAAAATTGCATCAAGGGCTGG 58.648 47.619 0.00 0.00 0.00 4.85
4532 5202 1.941377 AAATTGCATCAAGGGCTGGA 58.059 45.000 0.00 0.00 0.00 3.86
4533 5203 1.941377 AATTGCATCAAGGGCTGGAA 58.059 45.000 0.00 0.00 0.00 3.53
4534 5204 1.941377 ATTGCATCAAGGGCTGGAAA 58.059 45.000 0.00 0.00 0.00 3.13
4535 5205 1.941377 TTGCATCAAGGGCTGGAAAT 58.059 45.000 0.00 0.00 0.00 2.17
4536 5206 2.824689 TGCATCAAGGGCTGGAAATA 57.175 45.000 0.00 0.00 0.00 1.40
4537 5207 3.317455 TGCATCAAGGGCTGGAAATAT 57.683 42.857 0.00 0.00 0.00 1.28
4538 5208 3.645434 TGCATCAAGGGCTGGAAATATT 58.355 40.909 0.00 0.00 0.00 1.28
4539 5209 4.032310 TGCATCAAGGGCTGGAAATATTT 58.968 39.130 0.00 0.00 0.00 1.40
4540 5210 4.099881 TGCATCAAGGGCTGGAAATATTTC 59.900 41.667 18.22 18.22 36.46 2.17
4557 5227 7.868906 AATATTTCCAAAATTGCATCAAGGG 57.131 32.000 0.00 0.00 0.00 3.95
4558 5228 2.766345 TCCAAAATTGCATCAAGGGC 57.234 45.000 0.00 0.00 0.00 5.19
4559 5229 2.259012 TCCAAAATTGCATCAAGGGCT 58.741 42.857 0.00 0.00 0.00 5.19
4668 5338 5.195185 GGGCCAATTCAAATTCAATTCCAT 58.805 37.500 4.39 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 109 7.225931 TCCATTCGAAGTGCAAATACCTATAAC 59.774 37.037 3.35 0.00 0.00 1.89
124 135 2.091333 ACTTGTGGTTGGGTTCTCCATT 60.091 45.455 0.00 0.00 46.52 3.16
279 396 9.125906 CAAGTTGTGCGTATTATAGGAGTATAC 57.874 37.037 0.00 0.00 0.00 1.47
380 497 1.218316 GGCTTCGAGTCGGGAACAT 59.782 57.895 13.54 0.00 0.00 2.71
422 540 9.669353 GATTTACAGTGTTTATCTATTGCATGG 57.331 33.333 0.00 0.00 0.00 3.66
424 542 9.407380 TGGATTTACAGTGTTTATCTATTGCAT 57.593 29.630 0.00 0.00 0.00 3.96
425 543 8.800370 TGGATTTACAGTGTTTATCTATTGCA 57.200 30.769 0.00 0.00 0.00 4.08
426 544 9.503427 GTTGGATTTACAGTGTTTATCTATTGC 57.497 33.333 0.00 0.00 0.00 3.56
487 607 4.323417 TGAAGTGGCTATTGTTGTAGTGG 58.677 43.478 0.00 0.00 0.00 4.00
488 608 5.470098 AGTTGAAGTGGCTATTGTTGTAGTG 59.530 40.000 0.00 0.00 0.00 2.74
501 621 5.758784 GGACAGGTATATAAGTTGAAGTGGC 59.241 44.000 0.00 0.00 0.00 5.01
511 631 7.307219 GCGCACTTTTTAGGACAGGTATATAAG 60.307 40.741 0.30 0.00 0.00 1.73
515 635 4.081309 AGCGCACTTTTTAGGACAGGTATA 60.081 41.667 11.47 0.00 0.00 1.47
516 636 3.007635 GCGCACTTTTTAGGACAGGTAT 58.992 45.455 0.30 0.00 0.00 2.73
517 637 2.038033 AGCGCACTTTTTAGGACAGGTA 59.962 45.455 11.47 0.00 0.00 3.08
579 706 0.548510 GGAGATTTCTGGACTGGGGG 59.451 60.000 0.00 0.00 0.00 5.40
584 711 0.827368 GGCGAGGAGATTTCTGGACT 59.173 55.000 0.00 0.00 0.00 3.85
585 712 0.827368 AGGCGAGGAGATTTCTGGAC 59.173 55.000 0.00 0.00 0.00 4.02
789 933 4.829518 GCCAAAACGATCCGCCGC 62.830 66.667 0.00 0.00 0.00 6.53
791 935 2.761195 GGAGCCAAAACGATCCGCC 61.761 63.158 0.00 0.00 0.00 6.13
792 936 2.791927 GGAGCCAAAACGATCCGC 59.208 61.111 0.00 0.00 0.00 5.54
794 938 0.463833 ATCCGGAGCCAAAACGATCC 60.464 55.000 11.34 0.00 0.00 3.36
888 1032 0.032813 CCAATGCCTTCCAGGTGGAT 60.033 55.000 0.00 0.00 44.98 3.41
889 1033 1.383799 CCAATGCCTTCCAGGTGGA 59.616 57.895 0.00 0.00 43.73 4.02
915 1059 2.919228 AGTTTCAGAACTTGTTCGGCT 58.081 42.857 8.40 0.00 43.48 5.52
963 1114 1.255882 ACCAATTGGCAAGCGATTCA 58.744 45.000 24.79 0.00 39.32 2.57
974 1125 1.374505 CCAAGCCGCAACCAATTGG 60.375 57.895 23.31 23.31 42.17 3.16
979 1130 2.032528 CTCTCCAAGCCGCAACCA 59.967 61.111 0.00 0.00 0.00 3.67
1019 1170 1.995626 CCCTCCGACCCTTCCATGT 60.996 63.158 0.00 0.00 0.00 3.21
1083 1234 2.283966 AGGTAGAGCAGCACGGGT 60.284 61.111 0.00 0.00 0.00 5.28
1086 1237 1.226435 GTCGAGGTAGAGCAGCACG 60.226 63.158 0.00 0.00 39.64 5.34
1257 1408 0.550147 ACCTACCATTGCCCTCCACT 60.550 55.000 0.00 0.00 0.00 4.00
1371 1522 7.545265 ACAAGTACGTACAAGTTGAAACTGTAA 59.455 33.333 26.55 0.00 39.66 2.41
1390 1541 5.494632 ACTAGTTGGTTTGCAACAAGTAC 57.505 39.130 11.39 2.18 35.18 2.73
1391 1542 6.114089 TGTACTAGTTGGTTTGCAACAAGTA 58.886 36.000 13.66 13.66 35.18 2.24
1392 1543 4.944930 TGTACTAGTTGGTTTGCAACAAGT 59.055 37.500 12.99 12.99 35.18 3.16
1393 1544 5.493133 TGTACTAGTTGGTTTGCAACAAG 57.507 39.130 0.00 0.00 35.18 3.16
1402 1553 3.771577 AGCAAGCTGTACTAGTTGGTT 57.228 42.857 0.00 1.31 29.86 3.67
1440 1591 5.048713 GCAACAAGTACAAGGAGCAAACTAT 60.049 40.000 0.00 0.00 0.00 2.12
1473 1624 3.882288 TGTCATGAAAGCAAGCTGTACAA 59.118 39.130 0.00 0.00 0.00 2.41
1474 1625 3.475575 TGTCATGAAAGCAAGCTGTACA 58.524 40.909 0.00 0.00 0.00 2.90
1531 1683 5.301551 TCATTGCACACAAACCAAATCTACT 59.698 36.000 0.00 0.00 39.77 2.57
1570 1722 8.517062 AATCTAAATTCTCAGAAACATCCCTG 57.483 34.615 0.00 0.00 0.00 4.45
1682 1855 3.245797 CAGAGACCAATACACACTGACG 58.754 50.000 0.00 0.00 0.00 4.35
1751 1924 3.521560 TCAGCATAAGTACCAGAAAGCG 58.478 45.455 0.00 0.00 0.00 4.68
1845 2019 2.229784 CGCCAAAGCTTTTGAGGAGATT 59.770 45.455 16.19 0.00 36.60 2.40
1857 2031 0.538118 TACCGGTAATCGCCAAAGCT 59.462 50.000 13.14 0.00 37.59 3.74
1878 2052 1.000843 CTCCAATACCGCCGATCATCA 59.999 52.381 0.00 0.00 0.00 3.07
1958 2132 3.655777 TCAACCTTAACTTCCCATGGAGT 59.344 43.478 15.22 6.82 31.21 3.85
1989 2163 5.103687 GGTTTTCCACGCAAAGAAAGTTTA 58.896 37.500 0.00 0.00 40.31 2.01
2002 2176 4.568152 AAATCTGAACAGGTTTTCCACG 57.432 40.909 7.17 0.00 38.52 4.94
2099 2356 5.297547 AGAAAACTATGACGCAACAGAGAA 58.702 37.500 8.40 0.00 33.92 2.87
2234 2492 2.844451 GCAGAGGGCAAACAACGCA 61.844 57.895 0.00 0.00 43.97 5.24
2306 2564 2.746279 TGCACCTTATGGTTATGGGG 57.254 50.000 0.00 0.00 46.05 4.96
2329 2587 5.531122 TTTACCATAGCTAGTGCCTACTG 57.469 43.478 0.00 0.00 40.80 2.74
2338 2596 8.364142 AGCATTCTCTACTTTTACCATAGCTAG 58.636 37.037 0.00 0.00 0.00 3.42
2404 2662 2.484742 ACTACCAAACCCCGACATTC 57.515 50.000 0.00 0.00 0.00 2.67
2489 2747 4.014406 TGAGCTCCTGTTACGACTATGAA 58.986 43.478 12.15 0.00 0.00 2.57
2563 2978 1.091771 CATTCCTAGCACCGCCACTG 61.092 60.000 0.00 0.00 0.00 3.66
2564 2979 1.221840 CATTCCTAGCACCGCCACT 59.778 57.895 0.00 0.00 0.00 4.00
2565 2980 1.819632 CCATTCCTAGCACCGCCAC 60.820 63.158 0.00 0.00 0.00 5.01
2566 2981 1.558167 TTCCATTCCTAGCACCGCCA 61.558 55.000 0.00 0.00 0.00 5.69
2567 2982 0.815615 CTTCCATTCCTAGCACCGCC 60.816 60.000 0.00 0.00 0.00 6.13
2568 2983 1.440145 GCTTCCATTCCTAGCACCGC 61.440 60.000 0.00 0.00 35.05 5.68
2569 2984 0.179000 AGCTTCCATTCCTAGCACCG 59.821 55.000 0.00 0.00 37.37 4.94
2570 2985 2.436173 ACTAGCTTCCATTCCTAGCACC 59.564 50.000 0.00 0.00 37.37 5.01
2571 2986 3.133003 TCACTAGCTTCCATTCCTAGCAC 59.867 47.826 0.00 0.00 37.37 4.40
2572 2987 3.374764 TCACTAGCTTCCATTCCTAGCA 58.625 45.455 0.00 0.00 37.37 3.49
2573 2988 4.202305 ACATCACTAGCTTCCATTCCTAGC 60.202 45.833 0.00 0.00 33.53 3.42
2574 2989 5.069648 TGACATCACTAGCTTCCATTCCTAG 59.930 44.000 0.00 0.00 35.75 3.02
2575 2990 4.962362 TGACATCACTAGCTTCCATTCCTA 59.038 41.667 0.00 0.00 0.00 2.94
2576 2991 3.776969 TGACATCACTAGCTTCCATTCCT 59.223 43.478 0.00 0.00 0.00 3.36
2577 2992 4.142609 TGACATCACTAGCTTCCATTCC 57.857 45.455 0.00 0.00 0.00 3.01
2578 2993 5.448360 GCTTTGACATCACTAGCTTCCATTC 60.448 44.000 0.00 0.00 33.47 2.67
2579 2994 4.397417 GCTTTGACATCACTAGCTTCCATT 59.603 41.667 0.00 0.00 33.47 3.16
2580 2995 3.944015 GCTTTGACATCACTAGCTTCCAT 59.056 43.478 0.00 0.00 33.47 3.41
2581 2996 3.008375 AGCTTTGACATCACTAGCTTCCA 59.992 43.478 10.46 0.00 39.59 3.53
2582 2997 3.604582 AGCTTTGACATCACTAGCTTCC 58.395 45.455 10.46 0.00 39.59 3.46
2583 2998 7.359933 GCATATAGCTTTGACATCACTAGCTTC 60.360 40.741 17.94 5.09 41.48 3.86
2584 2999 6.426328 GCATATAGCTTTGACATCACTAGCTT 59.574 38.462 17.94 11.14 41.48 3.74
2585 3000 5.931146 GCATATAGCTTTGACATCACTAGCT 59.069 40.000 17.24 17.24 42.84 3.32
2586 3001 5.698089 TGCATATAGCTTTGACATCACTAGC 59.302 40.000 0.00 6.96 45.94 3.42
2587 3002 7.902387 ATGCATATAGCTTTGACATCACTAG 57.098 36.000 0.00 0.00 45.94 2.57
2588 3003 7.819415 GGTATGCATATAGCTTTGACATCACTA 59.181 37.037 10.16 0.00 45.94 2.74
2589 3004 6.652481 GGTATGCATATAGCTTTGACATCACT 59.348 38.462 10.16 0.00 45.94 3.41
2590 3005 6.128172 GGGTATGCATATAGCTTTGACATCAC 60.128 42.308 10.16 0.00 45.94 3.06
2591 3006 5.939883 GGGTATGCATATAGCTTTGACATCA 59.060 40.000 10.16 0.00 45.94 3.07
2592 3007 5.939883 TGGGTATGCATATAGCTTTGACATC 59.060 40.000 10.16 0.00 45.94 3.06
2593 3008 5.879763 TGGGTATGCATATAGCTTTGACAT 58.120 37.500 10.16 0.00 45.94 3.06
2594 3009 5.303259 TGGGTATGCATATAGCTTTGACA 57.697 39.130 10.16 0.00 45.94 3.58
2595 3010 9.784531 ATATATGGGTATGCATATAGCTTTGAC 57.215 33.333 10.16 0.00 45.94 3.18
2596 3011 9.783081 CATATATGGGTATGCATATAGCTTTGA 57.217 33.333 10.16 0.00 45.94 2.69
2597 3012 9.565090 ACATATATGGGTATGCATATAGCTTTG 57.435 33.333 16.96 4.67 45.94 2.77
2599 3014 9.565090 CAACATATATGGGTATGCATATAGCTT 57.435 33.333 16.96 0.00 45.94 3.74
2600 3015 8.937835 TCAACATATATGGGTATGCATATAGCT 58.062 33.333 16.96 0.00 45.94 3.32
2601 3016 9.730705 ATCAACATATATGGGTATGCATATAGC 57.269 33.333 16.96 0.00 45.96 2.97
2634 3049 9.891828 CTGCACTAATACACTTGAATTTAACAA 57.108 29.630 0.00 0.00 0.00 2.83
2635 3050 8.020819 GCTGCACTAATACACTTGAATTTAACA 58.979 33.333 0.00 0.00 0.00 2.41
2636 3051 8.237267 AGCTGCACTAATACACTTGAATTTAAC 58.763 33.333 1.02 0.00 0.00 2.01
2637 3052 8.335532 AGCTGCACTAATACACTTGAATTTAA 57.664 30.769 1.02 0.00 0.00 1.52
2638 3053 7.921786 AGCTGCACTAATACACTTGAATTTA 57.078 32.000 1.02 0.00 0.00 1.40
2639 3054 6.824305 AGCTGCACTAATACACTTGAATTT 57.176 33.333 1.02 0.00 0.00 1.82
2640 3055 7.770433 TGATAGCTGCACTAATACACTTGAATT 59.230 33.333 1.02 0.00 33.57 2.17
2641 3056 7.225538 GTGATAGCTGCACTAATACACTTGAAT 59.774 37.037 12.65 0.00 34.08 2.57
2642 3057 6.535150 GTGATAGCTGCACTAATACACTTGAA 59.465 38.462 12.65 0.00 34.08 2.69
2643 3058 6.042777 GTGATAGCTGCACTAATACACTTGA 58.957 40.000 12.65 0.00 34.08 3.02
2644 3059 5.812127 TGTGATAGCTGCACTAATACACTTG 59.188 40.000 18.48 0.00 35.95 3.16
2645 3060 5.977635 TGTGATAGCTGCACTAATACACTT 58.022 37.500 18.48 0.00 35.95 3.16
2646 3061 5.598416 TGTGATAGCTGCACTAATACACT 57.402 39.130 18.48 0.00 35.95 3.55
2647 3062 6.662414 TTTGTGATAGCTGCACTAATACAC 57.338 37.500 18.48 15.47 37.18 2.90
2648 3063 7.864108 AATTTGTGATAGCTGCACTAATACA 57.136 32.000 21.66 5.44 39.53 2.29
2649 3064 9.013490 CAAAATTTGTGATAGCTGCACTAATAC 57.987 33.333 21.66 3.46 39.53 1.89
2650 3065 8.739039 ACAAAATTTGTGATAGCTGCACTAATA 58.261 29.630 21.66 6.02 43.48 0.98
2651 3066 7.605449 ACAAAATTTGTGATAGCTGCACTAAT 58.395 30.769 10.91 18.27 43.48 1.73
2652 3067 6.980593 ACAAAATTTGTGATAGCTGCACTAA 58.019 32.000 10.91 17.27 43.48 2.24
2653 3068 6.573664 ACAAAATTTGTGATAGCTGCACTA 57.426 33.333 10.91 10.98 43.48 2.74
2654 3069 5.458041 ACAAAATTTGTGATAGCTGCACT 57.542 34.783 10.91 0.96 43.48 4.40
2680 3095 5.845953 CGTGTTGTTTATGATGTCAAGTGAC 59.154 40.000 4.43 4.43 44.97 3.67
2681 3096 5.525745 ACGTGTTGTTTATGATGTCAAGTGA 59.474 36.000 0.00 0.00 0.00 3.41
2682 3097 5.747565 ACGTGTTGTTTATGATGTCAAGTG 58.252 37.500 0.00 0.00 0.00 3.16
2683 3098 6.347402 GCTACGTGTTGTTTATGATGTCAAGT 60.347 38.462 0.00 0.00 0.00 3.16
2684 3099 6.015504 GCTACGTGTTGTTTATGATGTCAAG 58.984 40.000 0.00 0.00 0.00 3.02
2685 3100 5.467063 TGCTACGTGTTGTTTATGATGTCAA 59.533 36.000 0.00 0.00 0.00 3.18
2686 3101 4.991687 TGCTACGTGTTGTTTATGATGTCA 59.008 37.500 0.00 0.00 0.00 3.58
2687 3102 5.313623 GTGCTACGTGTTGTTTATGATGTC 58.686 41.667 0.00 0.00 0.00 3.06
2688 3103 4.153475 GGTGCTACGTGTTGTTTATGATGT 59.847 41.667 0.00 0.00 0.00 3.06
2689 3104 4.153296 TGGTGCTACGTGTTGTTTATGATG 59.847 41.667 0.00 0.00 0.00 3.07
2690 3105 4.153475 GTGGTGCTACGTGTTGTTTATGAT 59.847 41.667 0.00 0.00 0.00 2.45
2691 3106 3.495377 GTGGTGCTACGTGTTGTTTATGA 59.505 43.478 0.00 0.00 0.00 2.15
2692 3107 3.364565 GGTGGTGCTACGTGTTGTTTATG 60.365 47.826 0.00 0.00 0.00 1.90
2693 3108 2.809696 GGTGGTGCTACGTGTTGTTTAT 59.190 45.455 0.00 0.00 0.00 1.40
2694 3109 2.211806 GGTGGTGCTACGTGTTGTTTA 58.788 47.619 0.00 0.00 0.00 2.01
2695 3110 1.018910 GGTGGTGCTACGTGTTGTTT 58.981 50.000 0.00 0.00 0.00 2.83
2696 3111 0.107606 TGGTGGTGCTACGTGTTGTT 60.108 50.000 0.00 0.00 0.00 2.83
2697 3112 0.812412 GTGGTGGTGCTACGTGTTGT 60.812 55.000 0.00 0.00 0.00 3.32
2698 3113 0.531974 AGTGGTGGTGCTACGTGTTG 60.532 55.000 0.00 0.00 33.44 3.33
2699 3114 0.531974 CAGTGGTGGTGCTACGTGTT 60.532 55.000 0.00 0.00 33.44 3.32
2700 3115 1.069090 CAGTGGTGGTGCTACGTGT 59.931 57.895 0.00 0.00 33.44 4.49
2701 3116 0.037326 ATCAGTGGTGGTGCTACGTG 60.037 55.000 0.00 0.00 33.44 4.49
2702 3117 0.037326 CATCAGTGGTGGTGCTACGT 60.037 55.000 0.00 0.00 33.44 3.57
2703 3118 0.037326 ACATCAGTGGTGGTGCTACG 60.037 55.000 8.56 0.00 38.51 3.51
2704 3119 1.001974 TGACATCAGTGGTGGTGCTAC 59.998 52.381 8.56 0.00 38.51 3.58
2705 3120 1.347062 TGACATCAGTGGTGGTGCTA 58.653 50.000 8.56 0.00 38.51 3.49
2706 3121 0.694771 ATGACATCAGTGGTGGTGCT 59.305 50.000 8.56 0.00 38.51 4.40
2707 3122 1.470098 GAATGACATCAGTGGTGGTGC 59.530 52.381 8.56 0.00 38.51 5.01
2708 3123 2.086869 GGAATGACATCAGTGGTGGTG 58.913 52.381 8.56 0.00 41.05 4.17
2709 3124 1.988107 AGGAATGACATCAGTGGTGGT 59.012 47.619 8.56 0.00 0.00 4.16
2710 3125 2.795231 AGGAATGACATCAGTGGTGG 57.205 50.000 8.56 0.00 0.00 4.61
2711 3126 3.192001 CCAAAGGAATGACATCAGTGGTG 59.808 47.826 0.57 0.57 0.00 4.17
2712 3127 3.181429 ACCAAAGGAATGACATCAGTGGT 60.181 43.478 0.00 0.00 0.00 4.16
2713 3128 3.424703 ACCAAAGGAATGACATCAGTGG 58.575 45.455 0.00 0.00 0.00 4.00
2714 3129 4.330250 AGACCAAAGGAATGACATCAGTG 58.670 43.478 0.00 0.00 0.00 3.66
2715 3130 4.647564 AGACCAAAGGAATGACATCAGT 57.352 40.909 0.00 0.00 0.00 3.41
2716 3131 4.763793 ACAAGACCAAAGGAATGACATCAG 59.236 41.667 0.00 0.00 0.00 2.90
2717 3132 4.520111 CACAAGACCAAAGGAATGACATCA 59.480 41.667 0.00 0.00 0.00 3.07
2718 3133 4.761739 TCACAAGACCAAAGGAATGACATC 59.238 41.667 0.00 0.00 0.00 3.06
2719 3134 4.728772 TCACAAGACCAAAGGAATGACAT 58.271 39.130 0.00 0.00 0.00 3.06
2720 3135 4.163441 TCACAAGACCAAAGGAATGACA 57.837 40.909 0.00 0.00 0.00 3.58
2749 3164 6.782494 TGGCTCCAAGATTGTCTATATGACTA 59.218 38.462 6.79 1.24 45.54 2.59
2750 3165 5.604231 TGGCTCCAAGATTGTCTATATGACT 59.396 40.000 6.79 0.00 45.54 3.41
2791 3214 2.438021 ACTGAAGTGTTAGGTCTGGCAA 59.562 45.455 0.00 0.00 0.00 4.52
2900 3323 6.349944 GGATTCAGCCCATAAATCACATCATC 60.350 42.308 0.00 0.00 32.27 2.92
2933 3364 2.199652 TGGCGCAACTTTTCAGGGG 61.200 57.895 10.83 0.00 0.00 4.79
2948 3379 0.919710 ATAGACAGAAAGGGGGTGGC 59.080 55.000 0.00 0.00 0.00 5.01
2951 3382 2.915869 TGTCATAGACAGAAAGGGGGT 58.084 47.619 0.00 0.00 37.67 4.95
2956 3387 3.624861 GCCCACATGTCATAGACAGAAAG 59.375 47.826 0.00 0.00 46.04 2.62
2957 3388 3.609853 GCCCACATGTCATAGACAGAAA 58.390 45.455 0.00 0.00 46.04 2.52
3043 3661 6.422100 CCATACTCAATGCACTAGTCATGTAC 59.578 42.308 0.00 0.00 33.92 2.90
3143 3761 3.802139 TGAAACTACAAGTGTCAAGAGCG 59.198 43.478 0.00 0.00 39.39 5.03
3167 3785 2.159282 TCGGAAGAGAAAGTACGGATGC 60.159 50.000 0.00 0.00 34.84 3.91
3240 3858 1.798813 GCTAGCAGTTTAGCGTGTTGT 59.201 47.619 10.63 0.00 36.97 3.32
3241 3859 2.510615 GCTAGCAGTTTAGCGTGTTG 57.489 50.000 10.63 0.00 36.97 3.33
3247 3865 5.363979 ACAGAAAAAGCTAGCAGTTTAGC 57.636 39.130 18.83 11.74 45.05 3.09
3248 3866 7.861630 TGTAACAGAAAAAGCTAGCAGTTTAG 58.138 34.615 18.83 13.58 0.00 1.85
3249 3867 7.713507 TCTGTAACAGAAAAAGCTAGCAGTTTA 59.286 33.333 18.83 0.00 37.57 2.01
3250 3868 6.542370 TCTGTAACAGAAAAAGCTAGCAGTTT 59.458 34.615 18.83 15.82 37.57 2.66
3251 3869 6.055588 TCTGTAACAGAAAAAGCTAGCAGTT 58.944 36.000 18.83 7.72 37.57 3.16
3252 3870 5.611374 TCTGTAACAGAAAAAGCTAGCAGT 58.389 37.500 18.83 0.47 37.57 4.40
3253 3871 6.734104 ATCTGTAACAGAAAAAGCTAGCAG 57.266 37.500 18.83 0.20 44.04 4.24
3254 3872 6.149474 GGAATCTGTAACAGAAAAAGCTAGCA 59.851 38.462 18.83 0.00 44.04 3.49
3255 3873 6.149474 TGGAATCTGTAACAGAAAAAGCTAGC 59.851 38.462 6.62 6.62 44.04 3.42
3256 3874 7.672983 TGGAATCTGTAACAGAAAAAGCTAG 57.327 36.000 0.00 0.00 44.04 3.42
3257 3875 9.383519 CTATGGAATCTGTAACAGAAAAAGCTA 57.616 33.333 0.00 0.00 44.04 3.32
3258 3876 7.885399 ACTATGGAATCTGTAACAGAAAAAGCT 59.115 33.333 0.00 0.00 44.04 3.74
3259 3877 7.965107 CACTATGGAATCTGTAACAGAAAAAGC 59.035 37.037 0.00 0.00 44.04 3.51
3320 3938 2.686118 GCAGAAATCAATCTCCCCAGCT 60.686 50.000 0.00 0.00 0.00 4.24
3353 3971 3.367910 GCCGGAAGAGAAGGCTATATGAG 60.368 52.174 5.05 0.00 46.83 2.90
3580 4198 7.340487 TCTGTATCATAGAGAACTTGAGCTTGA 59.660 37.037 0.00 0.00 0.00 3.02
3602 4220 1.069022 GTGTGCGTGCAATCAATCTGT 60.069 47.619 0.00 0.00 0.00 3.41
3620 4238 2.228822 GACACATAGGCCACCTTTTGTG 59.771 50.000 19.67 19.67 44.65 3.33
3775 4393 6.416415 TGAAGGAATATTTACAACGGGCTTA 58.584 36.000 0.00 0.00 0.00 3.09
3778 4396 5.767816 ATGAAGGAATATTTACAACGGGC 57.232 39.130 0.00 0.00 0.00 6.13
3858 4476 4.473559 TCCTCCTGACCCCAACTTATTTAG 59.526 45.833 0.00 0.00 0.00 1.85
4060 4680 1.607148 GCAAAGAGCGGGTTACACTTT 59.393 47.619 0.00 0.00 0.00 2.66
4104 4724 1.340114 GGAGCTCCCATTCTCCGTTTT 60.340 52.381 23.19 0.00 39.43 2.43
4221 4842 2.157834 TGTTTACGCGAGGAACACAT 57.842 45.000 15.93 0.00 36.69 3.21
4222 4843 3.663644 TGTTTACGCGAGGAACACA 57.336 47.368 15.93 3.54 36.69 3.72
4236 4857 6.009908 ACCTACCTAGTTTCAAAGGTGTTT 57.990 37.500 4.29 0.00 45.75 2.83
4241 4862 6.059484 TCACAAACCTACCTAGTTTCAAAGG 58.941 40.000 0.00 0.00 35.28 3.11
4245 4866 7.558444 ACAAAATCACAAACCTACCTAGTTTCA 59.442 33.333 0.00 0.00 35.28 2.69
4314 4984 1.131126 GTGCATGTGTACTGCCATGTC 59.869 52.381 16.61 11.78 40.42 3.06
4504 5174 5.047872 GCCCTTGATGCAATTTTGGAAATTT 60.048 36.000 0.00 0.00 30.51 1.82
4531 5201 8.400186 CCCTTGATGCAATTTTGGAAATATTTC 58.600 33.333 18.22 18.22 36.46 2.17
4532 5202 7.148035 GCCCTTGATGCAATTTTGGAAATATTT 60.148 33.333 0.00 0.00 30.51 1.40
4533 5203 6.319405 GCCCTTGATGCAATTTTGGAAATATT 59.681 34.615 0.00 0.00 30.51 1.28
4534 5204 5.824097 GCCCTTGATGCAATTTTGGAAATAT 59.176 36.000 0.00 0.00 30.51 1.28
4535 5205 5.045724 AGCCCTTGATGCAATTTTGGAAATA 60.046 36.000 0.00 0.00 30.51 1.40
4536 5206 4.011698 GCCCTTGATGCAATTTTGGAAAT 58.988 39.130 0.00 0.00 30.51 2.17
4537 5207 3.072768 AGCCCTTGATGCAATTTTGGAAA 59.927 39.130 0.00 0.00 30.51 3.13
4538 5208 2.638855 AGCCCTTGATGCAATTTTGGAA 59.361 40.909 0.00 0.00 30.51 3.53
4539 5209 2.027929 CAGCCCTTGATGCAATTTTGGA 60.028 45.455 0.00 0.00 0.00 3.53
4540 5210 2.352388 CAGCCCTTGATGCAATTTTGG 58.648 47.619 0.00 0.00 0.00 3.28
4541 5211 2.027929 TCCAGCCCTTGATGCAATTTTG 60.028 45.455 0.00 0.00 0.00 2.44
4542 5212 2.259012 TCCAGCCCTTGATGCAATTTT 58.741 42.857 0.00 0.00 0.00 1.82
4543 5213 1.941377 TCCAGCCCTTGATGCAATTT 58.059 45.000 0.00 0.00 0.00 1.82
4544 5214 1.941377 TTCCAGCCCTTGATGCAATT 58.059 45.000 0.00 0.00 0.00 2.32
4545 5215 1.941377 TTTCCAGCCCTTGATGCAAT 58.059 45.000 0.00 0.00 0.00 3.56
4546 5216 1.941377 ATTTCCAGCCCTTGATGCAA 58.059 45.000 0.00 0.00 0.00 4.08
4547 5217 2.824689 TATTTCCAGCCCTTGATGCA 57.175 45.000 0.00 0.00 0.00 3.96
4548 5218 4.677673 AAATATTTCCAGCCCTTGATGC 57.322 40.909 0.00 0.00 0.00 3.91
4549 5219 6.642430 TGAAAAATATTTCCAGCCCTTGATG 58.358 36.000 0.10 0.00 43.54 3.07
4550 5220 6.872585 TGAAAAATATTTCCAGCCCTTGAT 57.127 33.333 0.10 0.00 43.54 2.57
4551 5221 6.872585 ATGAAAAATATTTCCAGCCCTTGA 57.127 33.333 0.10 0.00 43.54 3.02
4552 5222 8.423349 TCATATGAAAAATATTTCCAGCCCTTG 58.577 33.333 1.98 0.00 43.54 3.61
4553 5223 8.551682 TCATATGAAAAATATTTCCAGCCCTT 57.448 30.769 1.98 0.00 43.54 3.95
4554 5224 8.731591 ATCATATGAAAAATATTTCCAGCCCT 57.268 30.769 9.99 0.00 43.54 5.19


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

AutoCloner maintained by Alex Coulton.