Multiple sequence alignment - TraesCS6D01G074200

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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 TraesCS6D01G074200 chr6D 100.000 4672 0 0 1 4672 37906705 37902034 0.000000e+00 8628.0
1 TraesCS6D01G074200 chr6D 85.870 92 13 0 2544 2635 224765541 224765632 1.070000e-16 99.0
2 TraesCS6D01G074200 chr6A 92.742 1860 86 25 55 1880 49152821 49150977 0.000000e+00 2641.0
3 TraesCS6D01G074200 chr6A 88.571 945 57 23 2880 3799 49150036 49149118 0.000000e+00 1099.0
4 TraesCS6D01G074200 chr6A 86.132 923 77 25 3798 4672 49149081 49148162 0.000000e+00 948.0
5 TraesCS6D01G074200 chr6A 91.860 172 11 3 2625 2796 49150405 49150237 2.170000e-58 237.0
6 TraesCS6D01G074200 chr6A 96.364 55 0 1 1 55 49155573 49155521 6.440000e-14 89.8
7 TraesCS6D01G074200 chr6B 91.598 1452 81 21 418 1852 88656810 88655383 0.000000e+00 1967.0
8 TraesCS6D01G074200 chr6B 89.306 692 34 12 3126 3799 88654075 88653406 0.000000e+00 832.0
9 TraesCS6D01G074200 chr6B 86.325 702 46 24 1849 2546 88655110 88654455 0.000000e+00 719.0
10 TraesCS6D01G074200 chr6B 80.774 749 88 26 3899 4612 88648921 88648194 6.880000e-148 534.0
11 TraesCS6D01G074200 chr6B 96.850 254 8 0 2626 2879 88654454 88654201 4.320000e-115 425.0
12 TraesCS6D01G074200 chr6B 86.400 125 8 5 3780 3904 88653393 88653278 1.360000e-25 128.0
13 TraesCS6D01G074200 chr1A 77.211 667 104 23 1112 1751 404503584 404504229 3.460000e-91 346.0
14 TraesCS6D01G074200 chr1A 91.667 48 2 2 2727 2773 571725045 571725091 1.090000e-06 65.8
15 TraesCS6D01G074200 chr1A 85.714 63 7 2 2727 2788 571737790 571737851 1.090000e-06 65.8
16 TraesCS6D01G074200 chr1B 80.041 491 68 13 1112 1578 431449025 431448541 2.080000e-88 337.0
17 TraesCS6D01G074200 chr1B 88.710 62 5 2 2728 2788 662005492 662005552 1.800000e-09 75.0
18 TraesCS6D01G074200 chr1B 89.796 49 3 2 2726 2773 662020586 662020633 1.400000e-05 62.1
19 TraesCS6D01G074200 chr1D 75.610 656 83 34 1112 1737 318886378 318885770 2.160000e-63 254.0
20 TraesCS6D01G074200 chr1D 89.130 92 9 1 2541 2631 393970840 393970749 3.820000e-21 113.0
21 TraesCS6D01G074200 chr1D 89.583 48 3 2 2727 2773 475913521 475913567 5.050000e-05 60.2
22 TraesCS6D01G074200 chr5D 86.458 96 13 0 2537 2632 502881722 502881627 6.390000e-19 106.0
23 TraesCS6D01G074200 chr5D 85.714 98 12 2 2544 2640 423381395 423381299 8.270000e-18 102.0
24 TraesCS6D01G074200 chr3B 87.209 86 10 1 2544 2628 547120696 547120781 3.850000e-16 97.1
25 TraesCS6D01G074200 chr7B 83.696 92 15 0 2544 2635 526052812 526052903 2.320000e-13 87.9
26 TraesCS6D01G074200 chr7D 84.091 88 14 0 2544 2631 535726799 535726712 8.330000e-13 86.1
27 TraesCS6D01G074200 chr4B 84.706 85 13 0 2544 2628 217402168 217402252 8.330000e-13 86.1
28 TraesCS6D01G074200 chr3A 84.706 85 13 0 2544 2628 130447942 130448026 8.330000e-13 86.1
29 TraesCS6D01G074200 chr2D 100.000 29 0 0 3341 3369 153801626 153801598 2.000000e-03 54.7


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 TraesCS6D01G074200 chr6D 37902034 37906705 4671 True 8628.00 8628 100.0000 1 4672 1 chr6D.!!$R1 4671
1 TraesCS6D01G074200 chr6A 49148162 49155573 7411 True 1002.96 2641 91.1338 1 4672 5 chr6A.!!$R1 4671
2 TraesCS6D01G074200 chr6B 88653278 88656810 3532 True 814.20 1967 90.0958 418 3904 5 chr6B.!!$R2 3486
3 TraesCS6D01G074200 chr6B 88648194 88648921 727 True 534.00 534 80.7740 3899 4612 1 chr6B.!!$R1 713
4 TraesCS6D01G074200 chr1A 404503584 404504229 645 False 346.00 346 77.2110 1112 1751 1 chr1A.!!$F1 639
5 TraesCS6D01G074200 chr1D 318885770 318886378 608 True 254.00 254 75.6100 1112 1737 1 chr1D.!!$R1 625

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
401 3106 0.463620 ATCCTTTCAGAGCTCGCTCC 59.536 55.0 14.83 0.0 43.70 4.70 F
781 3491 0.676466 CCGACCAGCAATAGCCAACA 60.676 55.0 0.00 0.0 43.56 3.33 F
891 3602 0.676782 GGTGCCACGCTGTTTCCTAT 60.677 55.0 0.00 0.0 0.00 2.57 F
2086 5348 0.180406 AAGCGTTGGTGAGAAGTGGT 59.820 50.0 0.00 0.0 0.00 4.16 F
2792 6055 0.104356 TCCAGGTTCCCCAGGTAACA 60.104 55.0 4.70 0.0 38.53 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 5278 0.171679 TGCACATATTCGACCGACGT 59.828 50.0 0.0 0.0 43.13 4.34 R
2086 5348 0.175760 GCTCGGCCTCACTAACATCA 59.824 55.0 0.0 0.0 0.00 3.07 R
2416 5679 0.392461 TGGCTATTGAACGGCTGTCC 60.392 55.0 0.0 0.0 0.00 4.02 R
3627 7040 0.107945 GAGAAGATGCCGTCCAAGCT 60.108 55.0 0.0 0.0 0.00 3.74 R
3991 7452 0.112412 GGGAAGGGAGGAAAACTGCA 59.888 55.0 0.0 0.0 39.67 4.41 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
81 2783 3.128589 CCAAATGGGATTAAGTGTGGTCG 59.871 47.826 0.00 0.00 40.01 4.79
103 2805 4.157656 CGTCCCATTCCATTTGTATGTTGT 59.842 41.667 0.00 0.00 0.00 3.32
109 2811 8.093927 CCCATTCCATTTGTATGTTGTAGTTTT 58.906 33.333 0.00 0.00 0.00 2.43
110 2812 9.139174 CCATTCCATTTGTATGTTGTAGTTTTC 57.861 33.333 0.00 0.00 0.00 2.29
111 2813 9.912634 CATTCCATTTGTATGTTGTAGTTTTCT 57.087 29.630 0.00 0.00 0.00 2.52
135 2840 5.127519 TCCCATGTTGATGATTTCATTCCAC 59.872 40.000 0.00 0.00 36.57 4.02
150 2855 5.076182 TCATTCCACAAAATAAGCTGACCA 58.924 37.500 0.00 0.00 0.00 4.02
163 2868 7.713764 ATAAGCTGACCAAATTGAAAACAAC 57.286 32.000 0.00 0.00 0.00 3.32
181 2886 2.584608 CCGTGCCTAGAACCTGGG 59.415 66.667 0.00 0.00 35.09 4.45
221 2926 9.394767 ACATCATATATGCTTGTTTAACTGACA 57.605 29.630 7.92 0.00 0.00 3.58
238 2943 3.779759 TGACATTGTGTGGTTTGCTTTC 58.220 40.909 0.00 0.00 0.00 2.62
332 3037 7.766738 TGTCACTTACTGTCTTTTGTTGTCATA 59.233 33.333 0.00 0.00 0.00 2.15
401 3106 0.463620 ATCCTTTCAGAGCTCGCTCC 59.536 55.000 14.83 0.00 43.70 4.70
402 3107 0.900182 TCCTTTCAGAGCTCGCTCCA 60.900 55.000 14.83 0.00 43.70 3.86
472 3178 1.388547 TCAGTCTGGTGTTGGTTTGC 58.611 50.000 0.00 0.00 0.00 3.68
495 3202 4.014406 ACTTTATTAGTTGAAAGCCCGGG 58.986 43.478 19.09 19.09 36.34 5.73
496 3203 2.047002 TATTAGTTGAAAGCCCGGGC 57.953 50.000 39.29 39.29 42.33 6.13
499 3206 0.910566 TAGTTGAAAGCCCGGGCCTA 60.911 55.000 41.72 29.24 43.17 3.93
504 3211 2.479820 GAAAGCCCGGGCCTACTTGT 62.480 60.000 41.72 19.11 43.17 3.16
505 3212 2.764637 AAAGCCCGGGCCTACTTGTG 62.765 60.000 41.72 1.53 43.17 3.33
506 3213 4.029809 GCCCGGGCCTACTTGTGT 62.030 66.667 36.64 0.00 34.56 3.72
516 3223 2.731976 GCCTACTTGTGTCTTCGTTCTG 59.268 50.000 0.00 0.00 0.00 3.02
580 3290 4.527564 CAGTCAGTCTTTTTAGTTTGCGG 58.472 43.478 0.00 0.00 0.00 5.69
740 3450 1.347050 CCATGACCCAAACCATGCAAA 59.653 47.619 0.00 0.00 38.95 3.68
781 3491 0.676466 CCGACCAGCAATAGCCAACA 60.676 55.000 0.00 0.00 43.56 3.33
782 3492 1.382522 CGACCAGCAATAGCCAACAT 58.617 50.000 0.00 0.00 43.56 2.71
783 3493 1.745087 CGACCAGCAATAGCCAACATT 59.255 47.619 0.00 0.00 43.56 2.71
814 3525 7.452189 AGCTAGTAGTAAATTGATCTAGTCCCC 59.548 40.741 0.00 0.00 0.00 4.81
815 3526 7.452189 GCTAGTAGTAAATTGATCTAGTCCCCT 59.548 40.741 0.00 0.00 0.00 4.79
816 3527 7.604657 AGTAGTAAATTGATCTAGTCCCCTG 57.395 40.000 0.00 0.00 0.00 4.45
872 3583 3.181474 GCCCTAGTCTGCTAACCAAGTAG 60.181 52.174 0.00 0.00 39.16 2.57
884 3595 1.301716 CAAGTAGGTGCCACGCTGT 60.302 57.895 0.00 0.00 0.00 4.40
891 3602 0.676782 GGTGCCACGCTGTTTCCTAT 60.677 55.000 0.00 0.00 0.00 2.57
892 3603 1.406341 GGTGCCACGCTGTTTCCTATA 60.406 52.381 0.00 0.00 0.00 1.31
895 3606 1.933853 GCCACGCTGTTTCCTATACTG 59.066 52.381 0.00 0.00 0.00 2.74
906 3617 4.351874 TTCCTATACTGCTTATGGTGCC 57.648 45.455 0.00 0.00 0.00 5.01
929 3642 5.295152 CGTGGTTCCCTCACTTATATAACC 58.705 45.833 0.00 0.00 36.33 2.85
933 3646 5.539955 GGTTCCCTCACTTATATAACCCGTA 59.460 44.000 0.00 0.00 30.89 4.02
934 3647 6.450545 GTTCCCTCACTTATATAACCCGTAC 58.549 44.000 0.00 0.00 0.00 3.67
935 3648 4.761739 TCCCTCACTTATATAACCCGTACG 59.238 45.833 8.69 8.69 0.00 3.67
939 3665 4.752604 TCACTTATATAACCCGTACGCGTA 59.247 41.667 16.41 16.41 36.15 4.42
951 3677 3.120923 CCGTACGCGTAACACAAAATCTT 60.121 43.478 22.44 0.00 36.15 2.40
952 3678 4.448005 CGTACGCGTAACACAAAATCTTT 58.552 39.130 22.44 0.00 0.00 2.52
953 3679 4.313682 CGTACGCGTAACACAAAATCTTTG 59.686 41.667 22.44 0.00 0.00 2.77
954 3680 3.040099 ACGCGTAACACAAAATCTTTGC 58.960 40.909 11.67 0.00 0.00 3.68
955 3681 3.039405 CGCGTAACACAAAATCTTTGCA 58.961 40.909 0.00 0.00 0.00 4.08
956 3682 3.121828 CGCGTAACACAAAATCTTTGCAC 60.122 43.478 0.00 0.00 0.00 4.57
957 3683 3.181575 GCGTAACACAAAATCTTTGCACC 59.818 43.478 0.00 0.00 0.00 5.01
958 3684 3.733727 CGTAACACAAAATCTTTGCACCC 59.266 43.478 0.00 0.00 0.00 4.61
959 3685 3.902881 AACACAAAATCTTTGCACCCA 57.097 38.095 0.00 0.00 0.00 4.51
960 3686 3.177997 ACACAAAATCTTTGCACCCAC 57.822 42.857 0.00 0.00 0.00 4.61
961 3687 2.765699 ACACAAAATCTTTGCACCCACT 59.234 40.909 0.00 0.00 0.00 4.00
962 3688 3.197549 ACACAAAATCTTTGCACCCACTT 59.802 39.130 0.00 0.00 0.00 3.16
966 3705 0.681175 ATCTTTGCACCCACTTTGCC 59.319 50.000 0.00 0.00 39.39 4.52
979 3718 1.635663 CTTTGCCCAACCTCGTAGCG 61.636 60.000 0.00 0.00 0.00 4.26
1069 3808 2.278013 GCCACCTCGATCGTCGTC 60.278 66.667 15.94 0.00 41.35 4.20
1603 4395 2.503375 CGTACGGCACTGTCGTCC 60.503 66.667 12.87 0.00 40.97 4.79
1856 4660 5.313280 AGTATAAGACTCGGTGAGGATCT 57.687 43.478 0.00 0.00 29.95 2.75
1869 4950 8.651589 TCGGTGAGGATCTATGACTTATAATT 57.348 34.615 0.00 0.00 34.92 1.40
1893 5154 2.677836 TCGTGTTGGCTATTCTTCATGC 59.322 45.455 0.00 0.00 0.00 4.06
1899 5160 1.598924 GGCTATTCTTCATGCGCTTGC 60.599 52.381 17.84 4.10 39.78 4.01
1907 5168 2.798976 TCATGCGCTTGCTTTCTTTT 57.201 40.000 17.84 0.00 40.12 2.27
1926 5187 1.262640 TAGGAACCAACGAGAGCCCC 61.263 60.000 0.00 0.00 0.00 5.80
1943 5204 2.504367 CCCCGCCTTTTCATATAGTGG 58.496 52.381 0.00 0.00 0.00 4.00
1946 5207 4.204012 CCCGCCTTTTCATATAGTGGAAA 58.796 43.478 0.00 0.00 34.16 3.13
1965 5226 5.420739 TGGAAATAAGGAATTGTACAAGGGC 59.579 40.000 14.65 5.61 0.00 5.19
1971 5232 3.826729 AGGAATTGTACAAGGGCTGAAAC 59.173 43.478 14.65 0.00 0.00 2.78
1976 5237 4.911514 TGTACAAGGGCTGAAACTTTTC 57.088 40.909 0.00 0.00 37.69 2.29
1978 5239 2.650322 ACAAGGGCTGAAACTTTTCGA 58.350 42.857 0.00 0.00 40.01 3.71
1991 5252 2.107041 TTTTCGAAGGGAGCTCGCCA 62.107 55.000 25.68 6.23 36.25 5.69
2086 5348 0.180406 AAGCGTTGGTGAGAAGTGGT 59.820 50.000 0.00 0.00 0.00 4.16
2128 5390 3.219928 GCGATCCGGAGCTGAGGA 61.220 66.667 19.08 8.98 41.30 3.71
2152 5414 3.502990 AACGTGTTAGCGGGCGTCA 62.503 57.895 0.00 0.00 36.51 4.35
2168 5430 2.345991 CACCGGTAGTGGGGTGTG 59.654 66.667 6.87 0.00 46.79 3.82
2169 5431 2.926242 ACCGGTAGTGGGGTGTGG 60.926 66.667 4.49 0.00 34.58 4.17
2170 5432 3.712907 CCGGTAGTGGGGTGTGGG 61.713 72.222 0.00 0.00 0.00 4.61
2171 5433 3.712907 CGGTAGTGGGGTGTGGGG 61.713 72.222 0.00 0.00 0.00 4.96
2177 5439 1.229400 GTGGGGTGTGGGGAGTCTA 60.229 63.158 0.00 0.00 0.00 2.59
2200 5462 1.847798 TTGACGGATTCAGGTGGGGG 61.848 60.000 0.00 0.00 34.94 5.40
2251 5514 1.209504 TCGGGGTTAGAGGAAATGCTG 59.790 52.381 0.00 0.00 0.00 4.41
2372 5635 1.878088 GGAAGAAGAAAACCGTGGTCC 59.122 52.381 0.00 0.00 0.00 4.46
2384 5647 1.134640 CCGTGGTCCGTTGGATATTGA 60.135 52.381 0.00 0.00 32.73 2.57
2385 5648 2.201732 CGTGGTCCGTTGGATATTGAG 58.798 52.381 0.00 0.00 32.73 3.02
2396 5659 6.265577 CGTTGGATATTGAGGGAAATTCAAC 58.734 40.000 0.00 0.00 37.38 3.18
2398 5661 7.260603 GTTGGATATTGAGGGAAATTCAACTG 58.739 38.462 0.00 0.00 37.38 3.16
2435 5698 0.392461 GGACAGCCGTTCAATAGCCA 60.392 55.000 0.00 0.00 0.00 4.75
2444 5707 3.888930 CCGTTCAATAGCCAACCCAATAT 59.111 43.478 0.00 0.00 0.00 1.28
2445 5708 4.340950 CCGTTCAATAGCCAACCCAATATT 59.659 41.667 0.00 0.00 0.00 1.28
2447 5710 6.208599 CCGTTCAATAGCCAACCCAATATTAT 59.791 38.462 0.00 0.00 0.00 1.28
2448 5711 7.255801 CCGTTCAATAGCCAACCCAATATTATT 60.256 37.037 0.00 0.00 0.00 1.40
2449 5712 8.141268 CGTTCAATAGCCAACCCAATATTATTT 58.859 33.333 0.00 0.00 0.00 1.40
2450 5713 9.830975 GTTCAATAGCCAACCCAATATTATTTT 57.169 29.630 0.00 0.00 0.00 1.82
2554 5817 6.874288 AGTACTAATTAATACTCGCTCCGT 57.126 37.500 0.76 0.00 0.00 4.69
2555 5818 6.896969 AGTACTAATTAATACTCGCTCCGTC 58.103 40.000 0.76 0.00 0.00 4.79
2556 5819 5.118642 ACTAATTAATACTCGCTCCGTCC 57.881 43.478 0.00 0.00 0.00 4.79
2557 5820 4.826183 ACTAATTAATACTCGCTCCGTCCT 59.174 41.667 0.00 0.00 0.00 3.85
2558 5821 6.000219 ACTAATTAATACTCGCTCCGTCCTA 59.000 40.000 0.00 0.00 0.00 2.94
2563 5826 8.743085 ATTAATACTCGCTCCGTCCTATAATA 57.257 34.615 0.00 0.00 0.00 0.98
2564 5827 8.743085 TTAATACTCGCTCCGTCCTATAATAT 57.257 34.615 0.00 0.00 0.00 1.28
2565 5828 9.836864 TTAATACTCGCTCCGTCCTATAATATA 57.163 33.333 0.00 0.00 0.00 0.86
2566 5829 8.743085 AATACTCGCTCCGTCCTATAATATAA 57.257 34.615 0.00 0.00 0.00 0.98
2567 5830 6.680874 ACTCGCTCCGTCCTATAATATAAG 57.319 41.667 0.00 0.00 0.00 1.73
2568 5831 6.413052 ACTCGCTCCGTCCTATAATATAAGA 58.587 40.000 0.00 0.00 0.00 2.10
2569 5832 6.883217 ACTCGCTCCGTCCTATAATATAAGAA 59.117 38.462 0.00 0.00 0.00 2.52
2570 5833 7.081526 TCGCTCCGTCCTATAATATAAGAAC 57.918 40.000 0.00 0.00 0.00 3.01
2571 5834 5.964168 CGCTCCGTCCTATAATATAAGAACG 59.036 44.000 0.00 0.00 0.00 3.95
2572 5835 6.402983 CGCTCCGTCCTATAATATAAGAACGT 60.403 42.308 0.00 0.00 0.00 3.99
2573 5836 7.311408 GCTCCGTCCTATAATATAAGAACGTT 58.689 38.462 0.00 0.00 0.00 3.99
2574 5837 7.811713 GCTCCGTCCTATAATATAAGAACGTTT 59.188 37.037 0.46 0.00 0.00 3.60
2575 5838 9.688592 CTCCGTCCTATAATATAAGAACGTTTT 57.311 33.333 0.46 0.00 0.00 2.43
2622 5885 7.941795 ACATTTTTATATTACGAGACGGAGG 57.058 36.000 0.00 0.00 0.00 4.30
2623 5886 6.927381 ACATTTTTATATTACGAGACGGAGGG 59.073 38.462 0.00 0.00 0.00 4.30
2624 5887 6.713762 TTTTTATATTACGAGACGGAGGGA 57.286 37.500 0.00 0.00 0.00 4.20
2784 6047 3.787001 CTCGGCTCCAGGTTCCCC 61.787 72.222 0.00 0.00 0.00 4.81
2792 6055 0.104356 TCCAGGTTCCCCAGGTAACA 60.104 55.000 4.70 0.00 38.53 2.41
2921 6303 4.744570 CTGATTAGTCAGCAACTCCGTAA 58.255 43.478 1.91 0.00 44.86 3.18
2949 6331 3.008375 TGGAAGACTGGACATTTCTGGAG 59.992 47.826 0.00 0.00 0.00 3.86
2950 6332 2.777832 AGACTGGACATTTCTGGAGC 57.222 50.000 0.00 0.00 0.00 4.70
2951 6333 1.066573 AGACTGGACATTTCTGGAGCG 60.067 52.381 0.00 0.00 0.00 5.03
2955 6337 3.055094 ACTGGACATTTCTGGAGCGTAAT 60.055 43.478 0.00 0.00 0.00 1.89
2964 6346 5.496133 TTCTGGAGCGTAATAGAGTGTAC 57.504 43.478 0.00 0.00 0.00 2.90
2965 6347 4.520179 TCTGGAGCGTAATAGAGTGTACA 58.480 43.478 0.00 0.00 0.00 2.90
2966 6348 4.575236 TCTGGAGCGTAATAGAGTGTACAG 59.425 45.833 0.00 0.00 0.00 2.74
2967 6349 4.267536 TGGAGCGTAATAGAGTGTACAGT 58.732 43.478 1.90 1.90 0.00 3.55
2968 6350 4.095932 TGGAGCGTAATAGAGTGTACAGTG 59.904 45.833 8.23 0.00 0.00 3.66
2969 6351 4.096081 GGAGCGTAATAGAGTGTACAGTGT 59.904 45.833 8.23 6.77 0.00 3.55
2993 6385 8.033038 TGTAGTACACACTTCCAGAATTATGAC 58.967 37.037 0.54 0.00 36.14 3.06
3078 6472 9.676861 GGAGTACTTAATTACTTAACCCAACAT 57.323 33.333 6.91 0.00 32.17 2.71
3089 6483 1.107114 ACCCAACATTCGTGCAAACA 58.893 45.000 0.00 0.00 0.00 2.83
3090 6484 1.202359 ACCCAACATTCGTGCAAACAC 60.202 47.619 0.00 0.00 43.76 3.32
3173 6568 3.811722 TTGTGATGATCAAACTGCGTC 57.188 42.857 0.00 0.00 0.00 5.19
3178 6573 1.452110 TGATCAAACTGCGTCCATGG 58.548 50.000 4.97 4.97 0.00 3.66
3221 6616 1.610624 CGGTGCACCCACAAGAACTAT 60.611 52.381 29.95 0.00 43.88 2.12
3342 6737 1.600636 CCGCTGCTCAACTTTCCCA 60.601 57.895 0.00 0.00 0.00 4.37
3343 6738 1.576421 CGCTGCTCAACTTTCCCAC 59.424 57.895 0.00 0.00 0.00 4.61
3344 6739 1.856265 CGCTGCTCAACTTTCCCACC 61.856 60.000 0.00 0.00 0.00 4.61
3345 6740 1.856265 GCTGCTCAACTTTCCCACCG 61.856 60.000 0.00 0.00 0.00 4.94
3346 6741 1.856265 CTGCTCAACTTTCCCACCGC 61.856 60.000 0.00 0.00 0.00 5.68
3347 6742 2.626780 GCTCAACTTTCCCACCGCC 61.627 63.158 0.00 0.00 0.00 6.13
3609 7022 1.604438 CCGACGTCATGTTCAACTCCA 60.604 52.381 17.16 0.00 0.00 3.86
3627 7040 4.830765 GCGGTAGCACGGGCATCA 62.831 66.667 14.57 0.00 44.61 3.07
3630 7043 2.187946 GTAGCACGGGCATCAGCT 59.812 61.111 14.57 0.00 44.61 4.24
3694 7107 1.609208 GACGGCCATATGCAAGGAAT 58.391 50.000 2.24 0.00 43.89 3.01
3725 7138 8.141909 TGGATTATTCGTTCTCATAGTCGATTT 58.858 33.333 0.00 0.00 32.54 2.17
3745 7158 6.074623 CGATTTCGTACGTAGAGAAGTAGCTA 60.075 42.308 16.05 0.00 34.11 3.32
3746 7159 6.580963 TTTCGTACGTAGAGAAGTAGCTAG 57.419 41.667 16.05 0.00 0.00 3.42
3747 7160 4.047822 TCGTACGTAGAGAAGTAGCTAGC 58.952 47.826 16.05 6.62 0.00 3.42
3748 7161 3.801050 CGTACGTAGAGAAGTAGCTAGCA 59.199 47.826 18.83 0.00 0.00 3.49
3767 7180 3.382546 AGCATGATTTATGTCTGGTTGCC 59.617 43.478 0.00 0.00 39.08 4.52
3874 7327 7.668525 AAATTACTTTACAGCTGTGGTAGAC 57.331 36.000 29.57 0.00 0.00 2.59
3991 7452 4.322057 AACAGGGTGATTAGATGCCTTT 57.678 40.909 0.00 0.00 0.00 3.11
4036 7497 6.815089 TGGCATGTCAAAAACTCAATAAAGT 58.185 32.000 0.00 0.00 0.00 2.66
4122 7596 4.633565 CCACTCACTTGGATAAGAGCTTTC 59.366 45.833 0.00 0.00 39.24 2.62
4128 7602 5.814705 CACTTGGATAAGAGCTTTCCTACAG 59.185 44.000 0.00 0.00 37.36 2.74
4173 7686 3.719268 AGTTACATGATGAGGTGGCAA 57.281 42.857 0.00 0.00 0.00 4.52
4174 7687 4.240881 AGTTACATGATGAGGTGGCAAT 57.759 40.909 0.00 0.00 0.00 3.56
4175 7688 5.372343 AGTTACATGATGAGGTGGCAATA 57.628 39.130 0.00 0.00 0.00 1.90
4176 7689 5.945310 AGTTACATGATGAGGTGGCAATAT 58.055 37.500 0.00 0.00 0.00 1.28
4177 7690 6.000219 AGTTACATGATGAGGTGGCAATATC 59.000 40.000 0.00 0.00 0.00 1.63
4178 7691 4.719026 ACATGATGAGGTGGCAATATCT 57.281 40.909 0.00 0.00 0.00 1.98
4179 7692 4.395625 ACATGATGAGGTGGCAATATCTG 58.604 43.478 0.00 0.00 0.00 2.90
4180 7693 4.103627 ACATGATGAGGTGGCAATATCTGA 59.896 41.667 0.00 0.00 0.00 3.27
4201 7714 1.628340 TGCGAAAGAGAAGGGAATGGA 59.372 47.619 0.00 0.00 0.00 3.41
4389 7902 2.024941 AGTCCAGACATCCAAAATCCCC 60.025 50.000 0.00 0.00 0.00 4.81
4390 7903 1.064758 TCCAGACATCCAAAATCCCCG 60.065 52.381 0.00 0.00 0.00 5.73
4478 7999 0.328258 CCCACCTAAACCCCACTCAG 59.672 60.000 0.00 0.00 0.00 3.35
4483 8004 0.984230 CTAAACCCCACTCAGAGCCA 59.016 55.000 0.00 0.00 0.00 4.75
4493 8014 3.508793 CCACTCAGAGCCACATTTTTCAT 59.491 43.478 0.00 0.00 0.00 2.57
4505 8029 6.350906 CCACATTTTTCATAATCATGCCCTT 58.649 36.000 0.00 0.00 31.73 3.95
4510 8034 4.794311 TTCATAATCATGCCCTTCTCCA 57.206 40.909 0.00 0.00 31.73 3.86
4517 8041 1.489649 CATGCCCTTCTCCACTCTCAT 59.510 52.381 0.00 0.00 0.00 2.90
4528 8052 3.372897 TCCACTCTCATTCTCTGCTCAT 58.627 45.455 0.00 0.00 0.00 2.90
4535 8059 4.710865 TCTCATTCTCTGCTCATGAAGACT 59.289 41.667 0.00 0.00 0.00 3.24
4541 8065 0.321919 TGCTCATGAAGACTGCCACC 60.322 55.000 0.00 0.00 0.00 4.61
4606 8142 1.542375 ACATCACCCAGGCCTTCCT 60.542 57.895 0.00 0.00 45.66 3.36
4616 8152 3.971702 GCCTTCCTGGGTGCCACT 61.972 66.667 0.00 0.00 36.00 4.00
4634 8170 2.296471 CACTGATGTACTACCCCGGATC 59.704 54.545 0.73 0.00 0.00 3.36
4643 8179 2.170908 TACCCCGGATCTGGTCACCA 62.171 60.000 19.51 0.00 36.04 4.17
4645 8181 2.584608 CCGGATCTGGTCACCACC 59.415 66.667 12.93 0.00 44.10 4.61
4666 8202 2.281429 GTACCCTCCGCCCCTACT 59.719 66.667 0.00 0.00 0.00 2.57
4669 8205 2.578586 TACCCTCCGCCCCTACTGAC 62.579 65.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 2758 3.831911 ACCACACTTAATCCCATTTGGTG 59.168 43.478 0.00 0.00 34.78 4.17
81 2783 5.659440 ACAACATACAAATGGAATGGGAC 57.341 39.130 3.93 0.00 37.43 4.46
103 2805 7.669304 TGAAATCATCAACATGGGAGAAAACTA 59.331 33.333 0.00 0.00 34.30 2.24
109 2811 5.595542 GGAATGAAATCATCAACATGGGAGA 59.404 40.000 0.00 0.00 42.54 3.71
110 2812 5.361571 TGGAATGAAATCATCAACATGGGAG 59.638 40.000 0.00 0.00 42.54 4.30
111 2813 5.127519 GTGGAATGAAATCATCAACATGGGA 59.872 40.000 0.00 0.00 42.54 4.37
135 2840 8.610896 TGTTTTCAATTTGGTCAGCTTATTTTG 58.389 29.630 0.00 0.00 0.00 2.44
150 2855 2.169561 AGGCACGGGTTGTTTTCAATTT 59.830 40.909 0.00 0.00 42.08 1.82
163 2868 2.584608 CCAGGTTCTAGGCACGGG 59.415 66.667 0.00 0.00 0.00 5.28
181 2886 0.037590 TGATGTACCTGGGTGGCAAC 59.962 55.000 0.00 0.00 40.22 4.17
221 2926 3.387374 TCATGGAAAGCAAACCACACAAT 59.613 39.130 0.00 0.00 39.06 2.71
291 2996 6.998673 AGTAAGTGACAGCTATGGAAACTTTT 59.001 34.615 0.00 0.00 32.80 2.27
292 2997 6.428159 CAGTAAGTGACAGCTATGGAAACTTT 59.572 38.462 0.00 0.00 32.80 2.66
293 2998 5.934625 CAGTAAGTGACAGCTATGGAAACTT 59.065 40.000 0.00 0.00 34.14 2.66
332 3037 3.451178 ACAACAGGTACACAGACTTGAGT 59.549 43.478 0.00 0.00 31.24 3.41
472 3178 4.142469 CCCGGGCTTTCAACTAATAAAGTG 60.142 45.833 8.08 0.00 38.88 3.16
495 3202 2.731976 CAGAACGAAGACACAAGTAGGC 59.268 50.000 0.00 0.00 0.00 3.93
496 3203 4.238761 TCAGAACGAAGACACAAGTAGG 57.761 45.455 0.00 0.00 0.00 3.18
499 3206 3.857052 TGTTCAGAACGAAGACACAAGT 58.143 40.909 8.80 0.00 33.09 3.16
536 3243 0.598158 GCGGACGACAACACCACTAA 60.598 55.000 0.00 0.00 0.00 2.24
580 3290 7.484959 CAGCCTTTTTCGTTTGTATAAGATTCC 59.515 37.037 0.00 0.00 0.00 3.01
740 3450 3.556423 GGTGGTCATTTTCTCACTACGGT 60.556 47.826 0.00 0.00 0.00 4.83
814 3525 0.321671 ACGGGTCATTGGTCAGTCAG 59.678 55.000 0.00 0.00 0.00 3.51
815 3526 0.762418 AACGGGTCATTGGTCAGTCA 59.238 50.000 0.00 0.00 0.00 3.41
816 3527 1.002087 AGAACGGGTCATTGGTCAGTC 59.998 52.381 0.00 0.00 0.00 3.51
872 3583 0.676782 ATAGGAAACAGCGTGGCACC 60.677 55.000 12.86 4.98 0.00 5.01
884 3595 4.714632 GGCACCATAAGCAGTATAGGAAA 58.285 43.478 0.00 0.00 0.00 3.13
891 3602 0.107897 CCACGGCACCATAAGCAGTA 60.108 55.000 0.00 0.00 38.32 2.74
892 3603 1.377202 CCACGGCACCATAAGCAGT 60.377 57.895 0.00 0.00 40.99 4.40
895 3606 1.654023 GGAACCACGGCACCATAAGC 61.654 60.000 0.00 0.00 0.00 3.09
929 3642 2.409378 AGATTTTGTGTTACGCGTACGG 59.591 45.455 20.44 9.73 46.04 4.02
933 3646 3.040099 GCAAAGATTTTGTGTTACGCGT 58.960 40.909 19.17 19.17 0.00 6.01
934 3647 3.039405 TGCAAAGATTTTGTGTTACGCG 58.961 40.909 3.53 3.53 0.00 6.01
935 3648 3.181575 GGTGCAAAGATTTTGTGTTACGC 59.818 43.478 0.00 0.00 0.00 4.42
939 3665 3.197549 AGTGGGTGCAAAGATTTTGTGTT 59.802 39.130 0.00 0.00 0.00 3.32
951 3677 1.687146 TTGGGCAAAGTGGGTGCAA 60.687 52.632 0.00 0.00 44.07 4.08
952 3678 2.042537 TTGGGCAAAGTGGGTGCA 60.043 55.556 0.00 0.00 44.07 4.57
953 3679 2.421314 GTTGGGCAAAGTGGGTGC 59.579 61.111 0.00 0.00 41.45 5.01
954 3680 1.457455 AGGTTGGGCAAAGTGGGTG 60.457 57.895 0.00 0.00 0.00 4.61
955 3681 1.152546 GAGGTTGGGCAAAGTGGGT 60.153 57.895 0.00 0.00 0.00 4.51
956 3682 2.268076 CGAGGTTGGGCAAAGTGGG 61.268 63.158 0.00 0.00 0.00 4.61
957 3683 0.250553 TACGAGGTTGGGCAAAGTGG 60.251 55.000 0.00 0.00 0.00 4.00
958 3684 1.156736 CTACGAGGTTGGGCAAAGTG 58.843 55.000 0.00 0.00 0.00 3.16
959 3685 0.605589 GCTACGAGGTTGGGCAAAGT 60.606 55.000 0.00 0.00 0.00 2.66
960 3686 1.635663 CGCTACGAGGTTGGGCAAAG 61.636 60.000 0.00 0.00 0.00 2.77
961 3687 1.669760 CGCTACGAGGTTGGGCAAA 60.670 57.895 0.00 0.00 0.00 3.68
962 3688 2.047655 CGCTACGAGGTTGGGCAA 60.048 61.111 0.00 0.00 0.00 4.52
1069 3808 1.595382 CCGCGATGCCTTCCCTTAG 60.595 63.158 8.23 0.00 0.00 2.18
1403 4166 1.301716 TTGAACGGCTCCTGCAGAC 60.302 57.895 17.39 3.85 41.91 3.51
1416 4188 2.268076 ACCGGCCAGCATGTTGAAC 61.268 57.895 11.60 2.64 0.00 3.18
1603 4395 2.091588 CCCACAAAATCTAACGACGACG 59.908 50.000 5.58 5.58 45.75 5.12
1856 4660 8.418662 AGCCAACACGACTAATTATAAGTCATA 58.581 33.333 7.45 0.00 42.91 2.15
1869 4950 4.794278 TGAAGAATAGCCAACACGACTA 57.206 40.909 0.00 0.00 0.00 2.59
1893 5154 3.004315 TGGTTCCTAAAAGAAAGCAAGCG 59.996 43.478 0.00 0.00 0.00 4.68
1899 5160 5.334182 GCTCTCGTTGGTTCCTAAAAGAAAG 60.334 44.000 0.00 0.00 0.00 2.62
1907 5168 1.262640 GGGGCTCTCGTTGGTTCCTA 61.263 60.000 0.00 0.00 0.00 2.94
1926 5187 7.444183 TCCTTATTTCCACTATATGAAAAGGCG 59.556 37.037 0.00 0.00 34.43 5.52
1943 5204 6.377146 TCAGCCCTTGTACAATTCCTTATTTC 59.623 38.462 9.13 0.00 0.00 2.17
1946 5207 5.450818 TCAGCCCTTGTACAATTCCTTAT 57.549 39.130 9.13 0.00 0.00 1.73
1965 5226 3.142174 AGCTCCCTTCGAAAAGTTTCAG 58.858 45.455 0.00 0.00 37.01 3.02
1971 5232 1.362406 GGCGAGCTCCCTTCGAAAAG 61.362 60.000 8.47 0.00 40.36 2.27
1976 5237 1.671054 TTTTGGCGAGCTCCCTTCG 60.671 57.895 18.49 5.50 40.85 3.79
1978 5239 1.603739 GGTTTTGGCGAGCTCCCTT 60.604 57.895 18.49 0.00 0.00 3.95
2012 5273 2.098607 ACATATTCGACCGACGTGTGAT 59.901 45.455 0.00 0.00 43.13 3.06
2017 5278 0.171679 TGCACATATTCGACCGACGT 59.828 50.000 0.00 0.00 43.13 4.34
2071 5333 2.851195 ACATCACCACTTCTCACCAAC 58.149 47.619 0.00 0.00 0.00 3.77
2086 5348 0.175760 GCTCGGCCTCACTAACATCA 59.824 55.000 0.00 0.00 0.00 3.07
2152 5414 2.926242 CCACACCCCACTACCGGT 60.926 66.667 13.98 13.98 0.00 5.28
2165 5427 2.036733 CGTCAACTTTAGACTCCCCACA 59.963 50.000 0.00 0.00 33.89 4.17
2166 5428 2.612221 CCGTCAACTTTAGACTCCCCAC 60.612 54.545 0.00 0.00 33.89 4.61
2167 5429 1.621814 CCGTCAACTTTAGACTCCCCA 59.378 52.381 0.00 0.00 33.89 4.96
2168 5430 1.897802 TCCGTCAACTTTAGACTCCCC 59.102 52.381 0.00 0.00 33.89 4.81
2169 5431 3.889520 ATCCGTCAACTTTAGACTCCC 57.110 47.619 0.00 0.00 33.89 4.30
2170 5432 4.817517 TGAATCCGTCAACTTTAGACTCC 58.182 43.478 0.00 0.00 33.89 3.85
2171 5433 4.865365 CCTGAATCCGTCAACTTTAGACTC 59.135 45.833 0.00 0.00 35.22 3.36
2177 5439 2.504367 CCACCTGAATCCGTCAACTTT 58.496 47.619 0.00 0.00 35.22 2.66
2200 5462 3.049080 GCTGATGACCCTCCCCCAC 62.049 68.421 0.00 0.00 0.00 4.61
2251 5514 1.677633 AATGTGTAGCCGTTGCCCC 60.678 57.895 0.00 0.00 38.69 5.80
2257 5520 1.002624 CCCACCAATGTGTAGCCGT 60.003 57.895 0.00 0.00 41.09 5.68
2333 5596 1.609061 CCTCATTCAACACCTGCTCGT 60.609 52.381 0.00 0.00 0.00 4.18
2341 5604 6.209361 GGTTTTCTTCTTCCTCATTCAACAC 58.791 40.000 0.00 0.00 0.00 3.32
2372 5635 6.095440 AGTTGAATTTCCCTCAATATCCAACG 59.905 38.462 0.00 0.00 35.36 4.10
2416 5679 0.392461 TGGCTATTGAACGGCTGTCC 60.392 55.000 0.00 0.00 0.00 4.02
2420 5683 0.679960 GGGTTGGCTATTGAACGGCT 60.680 55.000 0.00 0.00 0.00 5.52
2423 5686 5.514274 AATATTGGGTTGGCTATTGAACG 57.486 39.130 0.00 0.00 0.00 3.95
2474 5737 8.098286 TGCACAAACTAGCTAATTAGGTCTTTA 58.902 33.333 19.99 2.79 35.39 1.85
2547 5810 5.964168 CGTTCTTATATTATAGGACGGAGCG 59.036 44.000 0.00 0.00 39.22 5.03
2548 5811 6.850555 ACGTTCTTATATTATAGGACGGAGC 58.149 40.000 13.99 0.00 45.45 4.70
2549 5812 9.688592 AAAACGTTCTTATATTATAGGACGGAG 57.311 33.333 0.00 4.83 45.45 4.63
2596 5859 8.823818 CCTCCGTCTCGTAATATAAAAATGTTT 58.176 33.333 0.00 0.00 0.00 2.83
2597 5860 7.440255 CCCTCCGTCTCGTAATATAAAAATGTT 59.560 37.037 0.00 0.00 0.00 2.71
2598 5861 6.927381 CCCTCCGTCTCGTAATATAAAAATGT 59.073 38.462 0.00 0.00 0.00 2.71
2599 5862 7.149973 TCCCTCCGTCTCGTAATATAAAAATG 58.850 38.462 0.00 0.00 0.00 2.32
2600 5863 7.015001 ACTCCCTCCGTCTCGTAATATAAAAAT 59.985 37.037 0.00 0.00 0.00 1.82
2601 5864 6.322201 ACTCCCTCCGTCTCGTAATATAAAAA 59.678 38.462 0.00 0.00 0.00 1.94
2602 5865 5.829924 ACTCCCTCCGTCTCGTAATATAAAA 59.170 40.000 0.00 0.00 0.00 1.52
2603 5866 5.380043 ACTCCCTCCGTCTCGTAATATAAA 58.620 41.667 0.00 0.00 0.00 1.40
2604 5867 4.978099 ACTCCCTCCGTCTCGTAATATAA 58.022 43.478 0.00 0.00 0.00 0.98
2605 5868 4.630644 ACTCCCTCCGTCTCGTAATATA 57.369 45.455 0.00 0.00 0.00 0.86
2606 5869 3.505480 ACTCCCTCCGTCTCGTAATAT 57.495 47.619 0.00 0.00 0.00 1.28
2607 5870 4.630644 ATACTCCCTCCGTCTCGTAATA 57.369 45.455 0.00 0.00 0.00 0.98
2608 5871 3.505480 ATACTCCCTCCGTCTCGTAAT 57.495 47.619 0.00 0.00 0.00 1.89
2609 5872 3.287867 AATACTCCCTCCGTCTCGTAA 57.712 47.619 0.00 0.00 0.00 3.18
2610 5873 4.422073 TTAATACTCCCTCCGTCTCGTA 57.578 45.455 0.00 0.00 0.00 3.43
2611 5874 3.287867 TTAATACTCCCTCCGTCTCGT 57.712 47.619 0.00 0.00 0.00 4.18
2612 5875 4.850347 AATTAATACTCCCTCCGTCTCG 57.150 45.455 0.00 0.00 0.00 4.04
2642 5905 4.192317 GCTGTCCCTCCTAAAACATACAG 58.808 47.826 0.00 0.00 36.92 2.74
2670 5933 1.021390 GCACCAACATCGTCTCCCTG 61.021 60.000 0.00 0.00 0.00 4.45
2784 6047 7.624360 TGATAAGTAGCCATTTTGTTACCTG 57.376 36.000 0.00 0.00 0.00 4.00
2792 6055 5.944007 ACGGAAGTTGATAAGTAGCCATTTT 59.056 36.000 0.00 0.00 46.40 1.82
2897 6279 4.632367 ACGGAGTTGCTGACTAATCAGGT 61.632 47.826 2.97 0.00 46.85 4.00
2915 6297 4.224147 TCCAGTCTTCCATGAAATTACGGA 59.776 41.667 0.00 0.00 0.00 4.69
2921 6303 6.152323 CAGAAATGTCCAGTCTTCCATGAAAT 59.848 38.462 0.00 0.00 0.00 2.17
2949 6331 6.116680 ACTACACTGTACACTCTATTACGC 57.883 41.667 0.00 0.00 0.00 4.42
2950 6332 8.189709 TGTACTACACTGTACACTCTATTACG 57.810 38.462 3.72 0.00 45.16 3.18
2967 6349 8.033038 GTCATAATTCTGGAAGTGTGTACTACA 58.967 37.037 7.23 0.00 35.69 2.74
2968 6350 8.251721 AGTCATAATTCTGGAAGTGTGTACTAC 58.748 37.037 7.23 0.00 35.69 2.73
2969 6351 8.251026 CAGTCATAATTCTGGAAGTGTGTACTA 58.749 37.037 7.23 0.00 35.69 1.82
2987 6379 5.582269 GTGCTACTGAAATCTGCAGTCATAA 59.418 40.000 14.67 0.00 44.85 1.90
2993 6385 3.332919 AGTGTGCTACTGAAATCTGCAG 58.667 45.455 7.63 7.63 38.49 4.41
3024 6418 6.707440 TGGTCAAACTGAGAGCAAAATTTA 57.293 33.333 0.00 0.00 40.19 1.40
3089 6483 4.152759 GCAAATTGCAAACATGCACATAGT 59.847 37.500 22.13 0.00 45.32 2.12
3090 6484 4.643953 GCAAATTGCAAACATGCACATAG 58.356 39.130 22.13 0.00 45.32 2.23
3134 6529 6.683715 TCACAAACTCAGATTGTCACGTATA 58.316 36.000 0.00 0.00 38.90 1.47
3139 6534 5.929697 TCATCACAAACTCAGATTGTCAC 57.070 39.130 0.00 0.00 38.90 3.67
3178 6573 3.679824 AGTAGCTCCTGTTGGTTACAC 57.320 47.619 0.00 0.00 32.10 2.90
3221 6616 4.296593 TTGGCGTCGCACCCGTAA 62.297 61.111 20.50 1.16 35.54 3.18
3449 6844 0.447801 GGTGCATTGATGTCGACACC 59.552 55.000 22.71 12.88 40.64 4.16
3480 6875 3.521796 GAAGCTTGCCGGCATCCC 61.522 66.667 33.25 20.89 34.17 3.85
3531 6944 3.106407 GGACACGCTCGTCTGCAC 61.106 66.667 0.00 0.00 36.12 4.57
3609 7022 4.530857 GATGCCCGTGCTACCGCT 62.531 66.667 0.00 0.00 38.71 5.52
3618 7031 2.045926 GTCCAAGCTGATGCCCGT 60.046 61.111 0.00 0.00 40.80 5.28
3620 7033 2.825836 CCGTCCAAGCTGATGCCC 60.826 66.667 0.00 0.00 40.80 5.36
3623 7036 0.463295 AGATGCCGTCCAAGCTGATG 60.463 55.000 0.00 0.00 0.00 3.07
3624 7037 0.254178 AAGATGCCGTCCAAGCTGAT 59.746 50.000 0.00 0.00 0.00 2.90
3627 7040 0.107945 GAGAAGATGCCGTCCAAGCT 60.108 55.000 0.00 0.00 0.00 3.74
3630 7043 1.902508 AGAAGAGAAGATGCCGTCCAA 59.097 47.619 0.00 0.00 0.00 3.53
3694 7107 8.183104 ACTATGAGAACGAATAATCCAGATCA 57.817 34.615 0.00 0.00 0.00 2.92
3725 7138 4.047822 GCTAGCTACTTCTCTACGTACGA 58.952 47.826 24.41 4.69 0.00 3.43
3745 7158 3.382546 GGCAACCAGACATAAATCATGCT 59.617 43.478 0.00 0.00 38.29 3.79
3746 7159 3.709987 GGCAACCAGACATAAATCATGC 58.290 45.455 0.00 0.00 38.29 4.06
3874 7327 9.538508 TCCGCATATAAGATCAAGATCAATATG 57.461 33.333 23.91 23.91 42.19 1.78
3991 7452 0.112412 GGGAAGGGAGGAAAACTGCA 59.888 55.000 0.00 0.00 39.67 4.41
3994 7455 1.076438 CAGGGGAAGGGAGGAAAACT 58.924 55.000 0.00 0.00 0.00 2.66
4000 7461 2.697644 ATGCCAGGGGAAGGGAGG 60.698 66.667 0.00 0.00 0.00 4.30
4036 7497 0.687920 TGTTACATCGGTGCCCTTGA 59.312 50.000 0.00 0.00 0.00 3.02
4122 7596 5.133941 TGTAGATTGGTCTCTAGCTGTAGG 58.866 45.833 0.00 0.00 35.87 3.18
4155 7660 5.999600 CAGATATTGCCACCTCATCATGTAA 59.000 40.000 0.00 0.00 0.00 2.41
4173 7686 4.590647 TCCCTTCTCTTTCGCATCAGATAT 59.409 41.667 0.00 0.00 0.00 1.63
4174 7687 3.960755 TCCCTTCTCTTTCGCATCAGATA 59.039 43.478 0.00 0.00 0.00 1.98
4175 7688 2.768527 TCCCTTCTCTTTCGCATCAGAT 59.231 45.455 0.00 0.00 0.00 2.90
4176 7689 2.179427 TCCCTTCTCTTTCGCATCAGA 58.821 47.619 0.00 0.00 0.00 3.27
4177 7690 2.680312 TCCCTTCTCTTTCGCATCAG 57.320 50.000 0.00 0.00 0.00 2.90
4178 7691 3.273434 CATTCCCTTCTCTTTCGCATCA 58.727 45.455 0.00 0.00 0.00 3.07
4179 7692 2.615912 CCATTCCCTTCTCTTTCGCATC 59.384 50.000 0.00 0.00 0.00 3.91
4180 7693 2.239654 TCCATTCCCTTCTCTTTCGCAT 59.760 45.455 0.00 0.00 0.00 4.73
4201 7714 2.158475 TGAATTTCAGGGTGTGAGCCTT 60.158 45.455 0.00 0.00 45.25 4.35
4269 7782 0.836400 TGGTGAGTCCCCTTGGAGAC 60.836 60.000 0.00 0.00 42.85 3.36
4321 7834 4.755411 CGTTGGATGCCTAGAAAGTTCTA 58.245 43.478 0.00 1.02 38.70 2.10
4322 7835 3.600388 CGTTGGATGCCTAGAAAGTTCT 58.400 45.455 0.00 0.00 41.24 3.01
4389 7902 2.350458 CCACCAATTTGGGGCCTCG 61.350 63.158 19.39 0.00 40.43 4.63
4390 7903 3.712287 CCACCAATTTGGGGCCTC 58.288 61.111 19.39 0.00 40.43 4.70
4411 7928 1.117142 ACGTCCAGAGTTCCCCGAAA 61.117 55.000 0.00 0.00 0.00 3.46
4478 7999 5.464389 GGCATGATTATGAAAAATGTGGCTC 59.536 40.000 0.85 0.00 36.36 4.70
4483 8004 7.418254 GGAGAAGGGCATGATTATGAAAAATGT 60.418 37.037 0.85 0.00 36.36 2.71
4493 8014 3.387962 AGAGTGGAGAAGGGCATGATTA 58.612 45.455 0.00 0.00 0.00 1.75
4505 8029 3.023119 GAGCAGAGAATGAGAGTGGAGA 58.977 50.000 0.00 0.00 0.00 3.71
4510 8034 4.710865 TCTTCATGAGCAGAGAATGAGAGT 59.289 41.667 0.00 0.00 32.23 3.24
4517 8041 2.354503 GGCAGTCTTCATGAGCAGAGAA 60.355 50.000 6.27 0.00 0.00 2.87
4528 8052 4.680237 CGGCGGTGGCAGTCTTCA 62.680 66.667 0.00 0.00 42.47 3.02
4606 8142 1.553248 GTAGTACATCAGTGGCACCCA 59.447 52.381 15.27 0.48 0.00 4.51
4616 8152 2.594131 CAGATCCGGGGTAGTACATCA 58.406 52.381 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.