Multiple sequence alignment - TraesCS5A01G448000

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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 TraesCS5A01G448000 chr5A 100.000 2981 0 0 1 2981 629696815 629699795 0.000000e+00 5505
1 TraesCS5A01G448000 chr5D 90.244 2378 185 17 16 2388 501786788 501784453 0.000000e+00 3062
2 TraesCS5A01G448000 chr5D 95.200 125 6 0 2846 2970 501784050 501783926 6.520000e-47 198
3 TraesCS5A01G448000 chr5B 89.562 1916 127 29 337 2233 625537558 625535697 0.000000e+00 2362
4 TraesCS5A01G448000 chr5B 89.358 1917 132 26 337 2233 630298150 630296286 0.000000e+00 2344
5 TraesCS5A01G448000 chr5B 83.271 269 35 7 2456 2717 625535686 625535421 3.840000e-59 239
6 TraesCS5A01G448000 chr5B 82.528 269 38 6 2456 2717 630296275 630296009 8.310000e-56 228


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 TraesCS5A01G448000 chr5A 629696815 629699795 2980 False 5505.0 5505 100.0000 1 2981 1 chr5A.!!$F1 2980
1 TraesCS5A01G448000 chr5D 501783926 501786788 2862 True 1630.0 3062 92.7220 16 2970 2 chr5D.!!$R1 2954
2 TraesCS5A01G448000 chr5B 625535421 625537558 2137 True 1300.5 2362 86.4165 337 2717 2 chr5B.!!$R1 2380
3 TraesCS5A01G448000 chr5B 630296009 630298150 2141 True 1286.0 2344 85.9430 337 2717 2 chr5B.!!$R2 2380

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
186 187 0.323633 TCAAGGCCCACACCATCATG 60.324 55.0 0.0 0.0 0.0 3.07 F
953 975 0.465705 TTCTCCATCACCATCCTCGC 59.534 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1840 0.546122 TCACCCTGCATGTACATCCC 59.454 55.0 5.07 0.6 0.0 3.85 R
2426 2483 0.103208 CTGATGCGAGTGGAGGGTAC 59.897 60.0 0.00 0.0 0.0 3.34 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
24 25 7.436536 GGAGCACATAAACATAAACATTTCG 57.563 36.000 0.00 0.00 0.00 3.46
31 32 5.897377 AAACATAAACATTTCGGAGAGGG 57.103 39.130 0.00 0.00 38.43 4.30
35 36 0.391263 AACATTTCGGAGAGGGCGTC 60.391 55.000 0.00 0.00 38.43 5.19
37 38 2.050350 ATTTCGGAGAGGGCGTCGA 61.050 57.895 0.00 0.00 38.43 4.20
41 42 3.069318 GGAGAGGGCGTCGAAGGT 61.069 66.667 0.00 0.00 0.00 3.50
42 43 1.751927 GGAGAGGGCGTCGAAGGTA 60.752 63.158 0.00 0.00 0.00 3.08
47 48 2.522638 GGGCGTCGAAGGTAATGCG 61.523 63.158 0.00 0.00 0.00 4.73
56 57 2.723618 CGAAGGTAATGCGGTCAAAACG 60.724 50.000 0.00 0.00 0.00 3.60
68 69 4.912766 GCGGTCAAAACGAATAAATCACAA 59.087 37.500 0.00 0.00 0.00 3.33
69 70 5.399892 GCGGTCAAAACGAATAAATCACAAA 59.600 36.000 0.00 0.00 0.00 2.83
72 73 7.324856 CGGTCAAAACGAATAAATCACAAATCA 59.675 33.333 0.00 0.00 0.00 2.57
96 97 9.120538 TCAACATATTTCAATTTCCTAGTAGCC 57.879 33.333 0.00 0.00 0.00 3.93
97 98 8.902806 CAACATATTTCAATTTCCTAGTAGCCA 58.097 33.333 0.00 0.00 0.00 4.75
112 113 5.552870 AGTAGCCATAAATGTCGGAGATT 57.447 39.130 0.00 0.00 40.67 2.40
185 186 0.409092 TTCAAGGCCCACACCATCAT 59.591 50.000 0.00 0.00 0.00 2.45
186 187 0.323633 TCAAGGCCCACACCATCATG 60.324 55.000 0.00 0.00 0.00 3.07
195 196 4.015764 CCCACACCATCATGACATTTACA 58.984 43.478 0.00 0.00 0.00 2.41
213 214 2.446435 ACAAAGGAAACCCATCCATCG 58.554 47.619 0.00 0.00 42.27 3.84
217 218 2.196595 AGGAAACCCATCCATCGAGAA 58.803 47.619 0.00 0.00 42.27 2.87
221 222 4.402474 GGAAACCCATCCATCGAGAAAATT 59.598 41.667 0.00 0.00 39.42 1.82
239 240 4.388577 AATTCCAAGGCTAAGACCAAGT 57.611 40.909 0.00 0.00 0.00 3.16
247 248 4.137543 AGGCTAAGACCAAGTCAAAACTG 58.862 43.478 0.00 0.00 35.36 3.16
274 275 6.082338 CACTCAATCAAAATCAAAGTCCTCG 58.918 40.000 0.00 0.00 0.00 4.63
275 276 5.182001 ACTCAATCAAAATCAAAGTCCTCGG 59.818 40.000 0.00 0.00 0.00 4.63
288 289 2.203126 CTCGGCTGAATGGGAGGC 60.203 66.667 0.00 0.00 0.00 4.70
305 306 3.046374 GAGGCCTCCAATCCTACCTTAA 58.954 50.000 23.19 0.00 31.71 1.85
421 422 1.283613 TGATGCCCAAGGTCGGTTTAT 59.716 47.619 0.00 0.00 0.00 1.40
429 430 5.656480 CCCAAGGTCGGTTTATAATTTTGG 58.344 41.667 0.00 0.00 33.95 3.28
436 437 4.712337 TCGGTTTATAATTTTGGCCATGGT 59.288 37.500 14.67 0.00 0.00 3.55
452 453 2.338984 GTCGAGGCGTCACAACCT 59.661 61.111 7.26 0.00 39.65 3.50
612 614 9.202273 CATATTATGCTCTTCCTTGAGTTAGAC 57.798 37.037 0.00 0.00 36.51 2.59
616 618 4.038763 TGCTCTTCCTTGAGTTAGACGAAA 59.961 41.667 0.00 0.00 36.51 3.46
627 630 4.969484 AGTTAGACGAAACCACAAATCCT 58.031 39.130 0.00 0.00 0.00 3.24
657 660 4.707448 TGGGAAACTTTTGCTACAAAGACA 59.293 37.500 9.67 0.00 0.00 3.41
698 709 1.343985 TGCCTACCTTGATCTAGCCCA 60.344 52.381 0.00 0.00 0.00 5.36
736 747 9.973661 TCTTCCCATCTTTATATGTTTTTCTCA 57.026 29.630 0.00 0.00 0.00 3.27
758 777 3.704061 ACTGAAGGACCTCTTAGAGATGC 59.296 47.826 11.32 0.00 35.50 3.91
783 802 4.164604 AGGGGGTCGTGTATGCTTTTATAA 59.835 41.667 0.00 0.00 0.00 0.98
785 804 6.043474 AGGGGGTCGTGTATGCTTTTATAATA 59.957 38.462 0.00 0.00 0.00 0.98
870 892 5.945144 AAAGGCATTGCTATTTCAAGGAT 57.055 34.783 8.82 0.00 30.08 3.24
916 938 1.933021 TAGGTTTTGAGGAGAGCGGA 58.067 50.000 0.00 0.00 0.00 5.54
926 948 2.096248 AGGAGAGCGGAGAGTTACTTG 58.904 52.381 0.00 0.00 0.00 3.16
933 955 2.735762 GCGGAGAGTTACTTGCGATTCT 60.736 50.000 11.01 0.00 0.00 2.40
943 965 3.942829 ACTTGCGATTCTTTCTCCATCA 58.057 40.909 0.00 0.00 0.00 3.07
953 975 0.465705 TTCTCCATCACCATCCTCGC 59.534 55.000 0.00 0.00 0.00 5.03
975 997 2.533266 TCTCTTCTGCTGCGAAAAGT 57.467 45.000 7.95 0.00 0.00 2.66
991 1013 5.173131 GCGAAAAGTACAACAAACAATCCAG 59.827 40.000 0.00 0.00 0.00 3.86
1017 1039 3.808728 TCAAATGGGTTCTCGATGGATC 58.191 45.455 0.00 0.00 0.00 3.36
1059 1081 9.912634 AATGATAATTTAGGTTATCCATTTGCG 57.087 29.630 4.69 0.00 39.32 4.85
1165 1187 7.398829 TCTTATACTTCATTTGGTGCCTTACA 58.601 34.615 0.00 0.00 0.00 2.41
1182 1204 8.190784 GTGCCTTACAAGCAATCAAGTAATTAT 58.809 33.333 0.00 0.00 43.02 1.28
1191 1213 9.950496 AAGCAATCAAGTAATTATCCGATCTAT 57.050 29.630 0.00 0.00 0.00 1.98
1259 1281 9.177304 CATATGATCTGTTTCATTTGTGTATGC 57.823 33.333 0.00 0.00 37.51 3.14
1260 1282 6.572167 TGATCTGTTTCATTTGTGTATGCA 57.428 33.333 0.00 0.00 0.00 3.96
1309 1331 9.082313 ACACATGGGAGGATTATTTGATAATTC 57.918 33.333 0.00 0.00 35.68 2.17
1324 1346 5.916318 TGATAATTCCCAACCATGATTTGC 58.084 37.500 0.00 0.00 0.00 3.68
1404 1426 8.783093 CCTCGACAATATTTTGATTTAGCCATA 58.217 33.333 2.69 0.00 36.64 2.74
1474 1496 6.405538 AGATTTTGTTTGTGTTCATGTTGGT 58.594 32.000 0.00 0.00 0.00 3.67
1483 1505 7.825331 TTGTGTTCATGTTGGTATAGGAAAA 57.175 32.000 0.00 0.00 0.00 2.29
1550 1572 3.391296 GCCTCCTTCTACCCATAACATCA 59.609 47.826 0.00 0.00 0.00 3.07
1580 1602 4.368315 CAATTCATCATGTCAATGCCTGG 58.632 43.478 0.00 0.00 33.47 4.45
1609 1631 2.058705 TCAAACATCCAGGTGTACCCA 58.941 47.619 0.00 0.00 36.42 4.51
1624 1646 3.103911 CCACTGTTCGCGACGACC 61.104 66.667 9.15 0.00 34.89 4.79
1722 1744 7.936496 AAAACAAAACAAAACTTCCATCCAT 57.064 28.000 0.00 0.00 0.00 3.41
1734 1756 5.222870 ACTTCCATCCATATTCAGGACTCT 58.777 41.667 0.00 0.00 38.13 3.24
1761 1783 1.225855 GACACACCGCACTTGATCAA 58.774 50.000 8.12 8.12 0.00 2.57
1857 1879 1.152368 AAAGCAGAACAGGGCAGCT 59.848 52.632 0.00 0.00 37.08 4.24
1861 1883 2.856000 AGAACAGGGCAGCTGGGT 60.856 61.111 17.12 0.00 0.00 4.51
1884 1906 6.286758 GTTGCTAGAGAATCATGATGAAGGA 58.713 40.000 9.46 1.45 37.82 3.36
1893 1915 8.043429 AGAATCATGATGAAGGAAAGAGGTAT 57.957 34.615 9.46 0.00 0.00 2.73
1959 1981 4.592942 ACTACATGCATGAACTGGACAAT 58.407 39.130 32.75 8.94 0.00 2.71
1960 1982 3.861276 ACATGCATGAACTGGACAATG 57.139 42.857 32.75 3.42 0.00 2.82
1971 1993 1.378514 GGACAATGTGCCCACCGAT 60.379 57.895 0.00 0.00 0.00 4.18
2013 2035 0.614697 TCGTCCATGAGAAGAGGCCA 60.615 55.000 5.01 0.00 0.00 5.36
2022 2044 0.182775 AGAAGAGGCCACCGTGTTTT 59.817 50.000 5.01 0.00 0.00 2.43
2073 2095 2.515057 AACAAACGTGCTCCGCCA 60.515 55.556 0.00 0.00 41.42 5.69
2091 2113 3.001838 CGCCACGCTTGCTATTATTGTTA 59.998 43.478 0.00 0.00 0.00 2.41
2092 2114 4.279659 GCCACGCTTGCTATTATTGTTAC 58.720 43.478 0.00 0.00 0.00 2.50
2093 2115 4.788521 GCCACGCTTGCTATTATTGTTACC 60.789 45.833 0.00 0.00 0.00 2.85
2159 2182 4.870363 TGTGGCTGAAAAGACTATTTTGC 58.130 39.130 0.00 0.00 0.00 3.68
2202 2225 6.558771 TGGTCACACATTTTAACATCTCTG 57.441 37.500 0.00 0.00 0.00 3.35
2258 2281 8.985315 ACTCATGATTAATCAAAAGCCTCATA 57.015 30.769 21.50 0.00 40.69 2.15
2271 2294 9.466497 TCAAAAGCCTCATATAGAAAAATGTCT 57.534 29.630 0.00 0.00 0.00 3.41
2275 2298 8.910351 AGCCTCATATAGAAAAATGTCTAACC 57.090 34.615 0.00 0.00 33.86 2.85
2276 2299 8.494433 AGCCTCATATAGAAAAATGTCTAACCA 58.506 33.333 0.00 0.00 33.86 3.67
2277 2300 9.120538 GCCTCATATAGAAAAATGTCTAACCAA 57.879 33.333 0.00 0.00 33.86 3.67
2317 2340 4.659115 ACCGAGGCTAAAACCAAGTTTAT 58.341 39.130 0.00 0.00 34.43 1.40
2319 2342 6.240145 ACCGAGGCTAAAACCAAGTTTATTA 58.760 36.000 0.00 0.00 34.43 0.98
2375 2398 6.370453 AGTGTACCACCAACCTTATTTTCTT 58.630 36.000 0.00 0.00 34.49 2.52
2376 2399 6.837048 AGTGTACCACCAACCTTATTTTCTTT 59.163 34.615 0.00 0.00 34.49 2.52
2377 2400 8.000127 AGTGTACCACCAACCTTATTTTCTTTA 59.000 33.333 0.00 0.00 34.49 1.85
2380 2403 9.070179 GTACCACCAACCTTATTTTCTTTAGAA 57.930 33.333 0.00 0.00 0.00 2.10
2406 2463 8.774890 TCACTCAACTATATAGACTACGATCC 57.225 38.462 16.79 0.00 0.00 3.36
2408 2465 7.066043 CACTCAACTATATAGACTACGATCCCC 59.934 44.444 16.79 0.00 0.00 4.81
2409 2466 7.037442 ACTCAACTATATAGACTACGATCCCCT 60.037 40.741 16.79 0.00 0.00 4.79
2413 2470 2.875094 TAGACTACGATCCCCTAGCC 57.125 55.000 0.00 0.00 0.00 3.93
2425 2482 1.344763 CCCCTAGCCCTACTCGATTTG 59.655 57.143 0.00 0.00 0.00 2.32
2426 2483 1.344763 CCCTAGCCCTACTCGATTTGG 59.655 57.143 0.00 0.00 0.00 3.28
2427 2484 2.040178 CCTAGCCCTACTCGATTTGGT 58.960 52.381 2.84 0.00 0.00 3.67
2432 2489 2.395619 CCCTACTCGATTTGGTACCCT 58.604 52.381 10.07 0.00 0.00 4.34
2433 2490 2.364647 CCCTACTCGATTTGGTACCCTC 59.635 54.545 10.07 2.79 0.00 4.30
2436 2493 1.553704 ACTCGATTTGGTACCCTCCAC 59.446 52.381 10.07 0.00 37.20 4.02
2437 2494 1.831736 CTCGATTTGGTACCCTCCACT 59.168 52.381 10.07 0.00 37.20 4.00
2438 2495 1.829222 TCGATTTGGTACCCTCCACTC 59.171 52.381 10.07 0.00 37.20 3.51
2439 2496 1.470979 CGATTTGGTACCCTCCACTCG 60.471 57.143 10.07 5.80 37.20 4.18
2440 2497 0.252197 ATTTGGTACCCTCCACTCGC 59.748 55.000 10.07 0.00 37.20 5.03
2441 2498 1.122632 TTTGGTACCCTCCACTCGCA 61.123 55.000 10.07 0.00 37.20 5.10
2442 2499 0.907704 TTGGTACCCTCCACTCGCAT 60.908 55.000 10.07 0.00 37.20 4.73
2443 2500 1.327690 TGGTACCCTCCACTCGCATC 61.328 60.000 10.07 0.00 31.96 3.91
2444 2501 1.327690 GGTACCCTCCACTCGCATCA 61.328 60.000 0.00 0.00 0.00 3.07
2446 2503 1.676678 TACCCTCCACTCGCATCAGC 61.677 60.000 0.00 0.00 37.42 4.26
2448 2505 1.078918 CCTCCACTCGCATCAGCAA 60.079 57.895 0.00 0.00 42.27 3.91
2479 2539 4.706842 TCTGCCTAGAACAAAAAGAGGT 57.293 40.909 0.00 0.00 0.00 3.85
2482 2542 4.787551 TGCCTAGAACAAAAAGAGGTTGA 58.212 39.130 0.00 0.00 0.00 3.18
2499 2559 6.013842 AGGTTGATCGGAGAAATTTTTGAC 57.986 37.500 0.00 0.00 43.58 3.18
2518 2578 7.566760 TTTGACTAAAGTGTCACATCATTGT 57.433 32.000 5.62 0.00 45.32 2.71
2561 2621 7.391275 ACCAATTCATTTTGTGGATCCAAAATC 59.609 33.333 18.36 5.65 46.73 2.17
2576 2636 7.595130 GGATCCAAAATCGCAAATAGTAAATCC 59.405 37.037 6.95 0.00 0.00 3.01
2578 2638 7.254852 TCCAAAATCGCAAATAGTAAATCCAC 58.745 34.615 0.00 0.00 0.00 4.02
2599 2659 5.293569 CCACTATCCACGTGTATTCCTTTTC 59.706 44.000 15.65 0.00 0.00 2.29
2609 2671 3.325425 TGTATTCCTTTTCTCCGTCACCA 59.675 43.478 0.00 0.00 0.00 4.17
2621 2683 4.582656 TCTCCGTCACCAATTCATTTGTTT 59.417 37.500 0.00 0.00 33.15 2.83
2625 2687 5.980116 CCGTCACCAATTCATTTGTTTACAA 59.020 36.000 0.00 0.00 33.15 2.41
2645 2709 5.416947 ACAAAGGGTATGTACTAGCGAAAG 58.583 41.667 0.00 0.00 0.00 2.62
2654 2718 8.645487 GGTATGTACTAGCGAAAGTTTATATGC 58.355 37.037 0.00 0.00 0.00 3.14
2717 2783 6.890293 AGTTTACATCTTTATCCACTCCTCC 58.110 40.000 0.00 0.00 0.00 4.30
2718 2784 5.531122 TTACATCTTTATCCACTCCTCCG 57.469 43.478 0.00 0.00 0.00 4.63
2719 2785 3.643237 ACATCTTTATCCACTCCTCCGA 58.357 45.455 0.00 0.00 0.00 4.55
2720 2786 4.227197 ACATCTTTATCCACTCCTCCGAT 58.773 43.478 0.00 0.00 0.00 4.18
2721 2787 5.394738 ACATCTTTATCCACTCCTCCGATA 58.605 41.667 0.00 0.00 0.00 2.92
2722 2788 5.244178 ACATCTTTATCCACTCCTCCGATAC 59.756 44.000 0.00 0.00 0.00 2.24
2723 2789 4.800023 TCTTTATCCACTCCTCCGATACA 58.200 43.478 0.00 0.00 0.00 2.29
2724 2790 5.205821 TCTTTATCCACTCCTCCGATACAA 58.794 41.667 0.00 0.00 0.00 2.41
2725 2791 5.839063 TCTTTATCCACTCCTCCGATACAAT 59.161 40.000 0.00 0.00 0.00 2.71
2726 2792 5.468540 TTATCCACTCCTCCGATACAATG 57.531 43.478 0.00 0.00 0.00 2.82
2727 2793 1.412710 TCCACTCCTCCGATACAATGC 59.587 52.381 0.00 0.00 0.00 3.56
2728 2794 1.541233 CCACTCCTCCGATACAATGCC 60.541 57.143 0.00 0.00 0.00 4.40
2729 2795 1.138859 CACTCCTCCGATACAATGCCA 59.861 52.381 0.00 0.00 0.00 4.92
2730 2796 1.837439 ACTCCTCCGATACAATGCCAA 59.163 47.619 0.00 0.00 0.00 4.52
2731 2797 2.439507 ACTCCTCCGATACAATGCCAAT 59.560 45.455 0.00 0.00 0.00 3.16
2732 2798 3.117888 ACTCCTCCGATACAATGCCAATT 60.118 43.478 0.00 0.00 0.00 2.32
2733 2799 3.885297 CTCCTCCGATACAATGCCAATTT 59.115 43.478 0.00 0.00 0.00 1.82
2734 2800 4.277476 TCCTCCGATACAATGCCAATTTT 58.723 39.130 0.00 0.00 0.00 1.82
2735 2801 4.709397 TCCTCCGATACAATGCCAATTTTT 59.291 37.500 0.00 0.00 0.00 1.94
2757 2823 8.904099 TTTTTAAACTTTGTTGAGGGTTTGAA 57.096 26.923 0.00 0.00 34.40 2.69
2758 2824 8.904099 TTTTAAACTTTGTTGAGGGTTTGAAA 57.096 26.923 0.00 0.00 35.98 2.69
2759 2825 7.892778 TTAAACTTTGTTGAGGGTTTGAAAC 57.107 32.000 0.00 0.00 34.40 2.78
2760 2826 5.476091 AACTTTGTTGAGGGTTTGAAACA 57.524 34.783 10.53 0.00 0.00 2.83
2761 2827 5.675684 ACTTTGTTGAGGGTTTGAAACAT 57.324 34.783 10.53 0.00 32.90 2.71
2762 2828 5.660460 ACTTTGTTGAGGGTTTGAAACATC 58.340 37.500 10.53 7.83 32.90 3.06
2763 2829 5.186797 ACTTTGTTGAGGGTTTGAAACATCA 59.813 36.000 10.53 10.27 32.90 3.07
2764 2830 5.867903 TTGTTGAGGGTTTGAAACATCAT 57.132 34.783 10.53 0.00 32.90 2.45
2765 2831 5.867903 TGTTGAGGGTTTGAAACATCATT 57.132 34.783 10.53 0.00 31.47 2.57
2786 2853 8.936070 TCATTTGCAAATAAAGAGAATCATGG 57.064 30.769 23.69 7.13 37.82 3.66
2789 2856 7.707624 TTGCAAATAAAGAGAATCATGGAGT 57.292 32.000 0.00 0.00 37.82 3.85
2790 2857 7.092137 TGCAAATAAAGAGAATCATGGAGTG 57.908 36.000 0.00 0.00 37.82 3.51
2796 2863 8.970859 ATAAAGAGAATCATGGAGTGGTAAAG 57.029 34.615 0.00 0.00 37.82 1.85
2800 2867 4.702131 AGAATCATGGAGTGGTAAAGTTGC 59.298 41.667 0.00 0.00 0.00 4.17
2806 2873 0.533308 AGTGGTAAAGTTGCGGCGAA 60.533 50.000 12.98 0.00 0.00 4.70
2808 2875 0.814410 TGGTAAAGTTGCGGCGAACA 60.814 50.000 12.98 0.00 0.00 3.18
2824 2891 2.727777 GAACACTTTGGTTTCTTCGGC 58.272 47.619 0.00 0.00 0.00 5.54
2825 2892 1.757682 ACACTTTGGTTTCTTCGGCA 58.242 45.000 0.00 0.00 0.00 5.69
2826 2893 1.676006 ACACTTTGGTTTCTTCGGCAG 59.324 47.619 0.00 0.00 0.00 4.85
2827 2894 0.668535 ACTTTGGTTTCTTCGGCAGC 59.331 50.000 0.00 0.00 0.00 5.25
2828 2895 0.954452 CTTTGGTTTCTTCGGCAGCT 59.046 50.000 0.00 0.00 0.00 4.24
2829 2896 2.151202 CTTTGGTTTCTTCGGCAGCTA 58.849 47.619 0.00 0.00 0.00 3.32
2830 2897 2.489938 TTGGTTTCTTCGGCAGCTAT 57.510 45.000 0.00 0.00 0.00 2.97
2831 2898 2.489938 TGGTTTCTTCGGCAGCTATT 57.510 45.000 0.00 0.00 0.00 1.73
2832 2899 3.620427 TGGTTTCTTCGGCAGCTATTA 57.380 42.857 0.00 0.00 0.00 0.98
2833 2900 4.150897 TGGTTTCTTCGGCAGCTATTAT 57.849 40.909 0.00 0.00 0.00 1.28
2834 2901 4.523083 TGGTTTCTTCGGCAGCTATTATT 58.477 39.130 0.00 0.00 0.00 1.40
2835 2902 4.947388 TGGTTTCTTCGGCAGCTATTATTT 59.053 37.500 0.00 0.00 0.00 1.40
2836 2903 5.417580 TGGTTTCTTCGGCAGCTATTATTTT 59.582 36.000 0.00 0.00 0.00 1.82
2837 2904 5.971792 GGTTTCTTCGGCAGCTATTATTTTC 59.028 40.000 0.00 0.00 0.00 2.29
2838 2905 5.403897 TTCTTCGGCAGCTATTATTTTCG 57.596 39.130 0.00 0.00 0.00 3.46
2839 2906 3.247648 TCTTCGGCAGCTATTATTTTCGC 59.752 43.478 0.00 0.00 0.00 4.70
2840 2907 1.871039 TCGGCAGCTATTATTTTCGCC 59.129 47.619 0.00 0.00 34.68 5.54
2841 2908 1.601903 CGGCAGCTATTATTTTCGCCA 59.398 47.619 6.72 0.00 37.95 5.69
2842 2909 2.226437 CGGCAGCTATTATTTTCGCCAT 59.774 45.455 6.72 0.00 37.95 4.40
2843 2910 3.667960 CGGCAGCTATTATTTTCGCCATC 60.668 47.826 6.72 0.00 37.95 3.51
2844 2911 3.253188 GGCAGCTATTATTTTCGCCATCA 59.747 43.478 1.33 0.00 37.98 3.07
2845 2912 4.222114 GCAGCTATTATTTTCGCCATCAC 58.778 43.478 0.00 0.00 0.00 3.06
2846 2913 4.023707 GCAGCTATTATTTTCGCCATCACT 60.024 41.667 0.00 0.00 0.00 3.41
2847 2914 5.506317 GCAGCTATTATTTTCGCCATCACTT 60.506 40.000 0.00 0.00 0.00 3.16
2848 2915 6.138761 CAGCTATTATTTTCGCCATCACTTC 58.861 40.000 0.00 0.00 0.00 3.01
2849 2916 5.050091 AGCTATTATTTTCGCCATCACTTCG 60.050 40.000 0.00 0.00 0.00 3.79
2850 2917 3.398954 TTATTTTCGCCATCACTTCGC 57.601 42.857 0.00 0.00 0.00 4.70
2879 2946 2.946752 GCCGTTCACGTTCGTTCCC 61.947 63.158 0.00 0.00 37.74 3.97
2911 2978 1.524961 CGGGTCCGATCCAATTCCA 59.475 57.895 2.83 0.00 42.83 3.53
2919 2986 0.588252 GATCCAATTCCATGACGCGG 59.412 55.000 12.47 0.00 0.00 6.46
2922 2989 1.656818 CCAATTCCATGACGCGGCTT 61.657 55.000 15.80 2.99 0.00 4.35
2949 3016 4.845307 TCCCACCACCCACACCCA 62.845 66.667 0.00 0.00 0.00 4.51
2979 3046 4.825679 CCCACCCCTCTCCCCTCC 62.826 77.778 0.00 0.00 0.00 4.30
2980 3047 4.825679 CCACCCCTCTCCCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.472163 CCGAAATGTTTATGTTTATGTGCTCC 59.528 38.462 0.00 0.00 0.00 4.70
1 2 7.247728 TCCGAAATGTTTATGTTTATGTGCTC 58.752 34.615 0.00 0.00 0.00 4.26
2 3 7.120579 TCTCCGAAATGTTTATGTTTATGTGCT 59.879 33.333 0.00 0.00 0.00 4.40
3 4 7.247728 TCTCCGAAATGTTTATGTTTATGTGC 58.752 34.615 0.00 0.00 0.00 4.57
4 5 7.910162 CCTCTCCGAAATGTTTATGTTTATGTG 59.090 37.037 0.00 0.00 0.00 3.21
5 6 7.067008 CCCTCTCCGAAATGTTTATGTTTATGT 59.933 37.037 0.00 0.00 0.00 2.29
6 7 7.417612 CCCTCTCCGAAATGTTTATGTTTATG 58.582 38.462 0.00 0.00 0.00 1.90
7 8 6.039382 GCCCTCTCCGAAATGTTTATGTTTAT 59.961 38.462 0.00 0.00 0.00 1.40
8 9 5.355910 GCCCTCTCCGAAATGTTTATGTTTA 59.644 40.000 0.00 0.00 0.00 2.01
9 10 4.157840 GCCCTCTCCGAAATGTTTATGTTT 59.842 41.667 0.00 0.00 0.00 2.83
10 11 3.694566 GCCCTCTCCGAAATGTTTATGTT 59.305 43.478 0.00 0.00 0.00 2.71
11 12 3.279434 GCCCTCTCCGAAATGTTTATGT 58.721 45.455 0.00 0.00 0.00 2.29
12 13 2.287915 CGCCCTCTCCGAAATGTTTATG 59.712 50.000 0.00 0.00 0.00 1.90
13 14 2.093128 ACGCCCTCTCCGAAATGTTTAT 60.093 45.455 0.00 0.00 0.00 1.40
14 15 1.276989 ACGCCCTCTCCGAAATGTTTA 59.723 47.619 0.00 0.00 0.00 2.01
19 20 1.601419 TTCGACGCCCTCTCCGAAAT 61.601 55.000 0.00 0.00 37.97 2.17
22 23 3.132139 CTTCGACGCCCTCTCCGA 61.132 66.667 0.00 0.00 0.00 4.55
24 25 1.318158 TTACCTTCGACGCCCTCTCC 61.318 60.000 0.00 0.00 0.00 3.71
31 32 1.749609 GACCGCATTACCTTCGACGC 61.750 60.000 0.00 0.00 0.00 5.19
35 36 2.723618 CGTTTTGACCGCATTACCTTCG 60.724 50.000 0.00 0.00 0.00 3.79
37 38 2.496111 TCGTTTTGACCGCATTACCTT 58.504 42.857 0.00 0.00 0.00 3.50
41 42 6.743627 GTGATTTATTCGTTTTGACCGCATTA 59.256 34.615 0.00 0.00 0.00 1.90
42 43 5.571357 GTGATTTATTCGTTTTGACCGCATT 59.429 36.000 0.00 0.00 0.00 3.56
47 48 8.514136 TGATTTGTGATTTATTCGTTTTGACC 57.486 30.769 0.00 0.00 0.00 4.02
72 73 9.646522 ATGGCTACTAGGAAATTGAAATATGTT 57.353 29.630 0.00 0.00 0.00 2.71
86 87 4.476297 TCCGACATTTATGGCTACTAGGA 58.524 43.478 0.00 0.00 32.20 2.94
158 159 3.821033 GGTGTGGGCCTTGAACATATATC 59.179 47.826 4.53 0.00 0.00 1.63
167 168 0.323633 CATGATGGTGTGGGCCTTGA 60.324 55.000 4.53 0.00 0.00 3.02
173 174 4.015764 TGTAAATGTCATGATGGTGTGGG 58.984 43.478 0.00 0.00 0.00 4.61
185 186 5.245075 GGATGGGTTTCCTTTGTAAATGTCA 59.755 40.000 0.00 0.00 32.68 3.58
186 187 5.245075 TGGATGGGTTTCCTTTGTAAATGTC 59.755 40.000 0.00 0.00 36.68 3.06
195 196 2.576191 TCTCGATGGATGGGTTTCCTTT 59.424 45.455 0.00 0.00 36.68 3.11
213 214 5.010282 TGGTCTTAGCCTTGGAATTTTCTC 58.990 41.667 0.00 0.00 0.00 2.87
217 218 4.740902 ACTTGGTCTTAGCCTTGGAATTT 58.259 39.130 0.00 0.00 0.00 1.82
221 222 2.334977 TGACTTGGTCTTAGCCTTGGA 58.665 47.619 0.00 0.00 33.15 3.53
239 240 2.942804 TGATTGAGTGCCCAGTTTTGA 58.057 42.857 0.00 0.00 0.00 2.69
247 248 4.886579 ACTTTGATTTTGATTGAGTGCCC 58.113 39.130 0.00 0.00 0.00 5.36
274 275 2.194326 GAGGCCTCCCATTCAGCC 59.806 66.667 23.19 0.00 46.13 4.85
275 276 2.194326 GGAGGCCTCCCATTCAGC 59.806 66.667 38.25 13.02 43.94 4.26
288 289 9.494055 TCTATATCATTAAGGTAGGATTGGAGG 57.506 37.037 0.00 0.00 0.00 4.30
353 354 0.599204 TCGCACCCGTTCTTTCTGAC 60.599 55.000 0.00 0.00 35.54 3.51
421 422 2.374184 CCTCGACCATGGCCAAAATTA 58.626 47.619 10.96 0.00 0.00 1.40
429 430 4.451150 TGACGCCTCGACCATGGC 62.451 66.667 13.04 3.65 45.25 4.40
436 437 0.038892 GTAAGGTTGTGACGCCTCGA 60.039 55.000 0.00 0.00 33.24 4.04
593 595 3.154710 TCGTCTAACTCAAGGAAGAGCA 58.845 45.455 0.00 0.00 39.26 4.26
627 630 4.751767 AGCAAAAGTTTCCCATCACAAA 57.248 36.364 0.00 0.00 0.00 2.83
657 660 2.019249 CAATGGTCGCATGTGGAGATT 58.981 47.619 6.39 0.00 0.00 2.40
734 745 4.659529 TCTCTAAGAGGTCCTTCAGTGA 57.340 45.455 0.00 0.00 36.34 3.41
735 746 4.441356 GCATCTCTAAGAGGTCCTTCAGTG 60.441 50.000 0.00 0.00 36.34 3.66
736 747 3.704061 GCATCTCTAAGAGGTCCTTCAGT 59.296 47.826 0.00 0.00 36.34 3.41
758 777 1.910580 AAGCATACACGACCCCCTGG 61.911 60.000 0.00 0.00 37.80 4.45
819 841 8.696043 TTCATCCTCCTATTTTTATCCACATG 57.304 34.615 0.00 0.00 0.00 3.21
910 932 0.170561 TCGCAAGTAACTCTCCGCTC 59.829 55.000 0.00 0.00 39.48 5.03
916 938 5.172205 GGAGAAAGAATCGCAAGTAACTCT 58.828 41.667 0.00 0.00 39.48 3.24
926 948 2.632377 TGGTGATGGAGAAAGAATCGC 58.368 47.619 0.00 0.00 0.00 4.58
933 955 1.134401 GCGAGGATGGTGATGGAGAAA 60.134 52.381 0.00 0.00 0.00 2.52
943 965 0.755686 GAAGAGATGGCGAGGATGGT 59.244 55.000 0.00 0.00 0.00 3.55
953 975 1.730501 TTTCGCAGCAGAAGAGATGG 58.269 50.000 0.00 0.00 0.00 3.51
975 997 6.951062 TGATTGACTGGATTGTTTGTTGTA 57.049 33.333 0.00 0.00 0.00 2.41
991 1013 4.201950 CCATCGAGAACCCATTTGATTGAC 60.202 45.833 0.00 0.00 0.00 3.18
1017 1039 1.958579 TCATTACATACCTCGGGTCGG 59.041 52.381 0.00 0.00 37.09 4.79
1059 1081 5.002464 AGTAATGTGCTTGATTTGCATCC 57.998 39.130 0.00 0.00 42.69 3.51
1135 1157 7.337942 AGGCACCAAATGAAGTATAAGAAGAAG 59.662 37.037 0.00 0.00 0.00 2.85
1137 1159 6.721318 AGGCACCAAATGAAGTATAAGAAGA 58.279 36.000 0.00 0.00 0.00 2.87
1165 1187 9.950496 ATAGATCGGATAATTACTTGATTGCTT 57.050 29.630 0.00 0.00 0.00 3.91
1257 1279 9.761504 TTGATTGATCTTTGATAAGTTTTTGCA 57.238 25.926 0.00 0.00 32.98 4.08
1309 1331 3.460103 GCAATAGCAAATCATGGTTGGG 58.540 45.455 10.75 0.29 40.93 4.12
1324 1346 6.093909 TGTGACACAAATGACCTATGCAATAG 59.906 38.462 5.62 0.00 46.56 1.73
1361 1383 4.811024 GTCGAGGTTCTTTGATGCATATGA 59.189 41.667 6.97 0.00 0.00 2.15
1376 1398 7.122055 TGGCTAAATCAAAATATTGTCGAGGTT 59.878 33.333 0.00 0.00 37.79 3.50
1404 1426 4.966965 TTGGTCATGTGTGTTTACGTTT 57.033 36.364 0.00 0.00 0.00 3.60
1408 1430 7.328249 CCATACATTTTGGTCATGTGTGTTTAC 59.672 37.037 8.42 0.00 40.39 2.01
1483 1505 8.318412 TGACTTTGTTGTATGACTATGTATGGT 58.682 33.333 0.00 0.00 0.00 3.55
1550 1572 9.366216 GCATTGACATGATGAATTGCATATTAT 57.634 29.630 0.00 0.00 37.34 1.28
1580 1602 5.473504 ACACCTGGATGTTTGAATCACTAAC 59.526 40.000 0.00 0.00 35.46 2.34
1609 1631 4.695231 CCGGTCGTCGCGAACAGT 62.695 66.667 12.06 0.00 44.54 3.55
1624 1646 4.508128 ATACCGACAGCCACGCCG 62.508 66.667 0.00 0.00 0.00 6.46
1633 1655 2.772287 TGCATCACACAAATACCGACA 58.228 42.857 0.00 0.00 0.00 4.35
1722 1744 6.152154 TGTGTCGAAATGTAGAGTCCTGAATA 59.848 38.462 0.00 0.00 0.00 1.75
1734 1756 1.141645 GTGCGGTGTGTCGAAATGTA 58.858 50.000 0.00 0.00 0.00 2.29
1761 1783 7.121168 TCAAATCTTGAGCGATGGTAGAAAAAT 59.879 33.333 0.00 0.00 34.08 1.82
1818 1840 0.546122 TCACCCTGCATGTACATCCC 59.454 55.000 5.07 0.60 0.00 3.85
1857 1879 4.409901 TCATCATGATTCTCTAGCAACCCA 59.590 41.667 5.16 0.00 0.00 4.51
1861 1883 6.490241 TCCTTCATCATGATTCTCTAGCAA 57.510 37.500 5.16 0.00 0.00 3.91
1884 1906 3.067684 CCGTGTTGGGAATACCTCTTT 57.932 47.619 0.00 0.00 41.11 2.52
1934 1956 4.194640 GTCCAGTTCATGCATGTAGTCAT 58.805 43.478 25.43 5.34 34.21 3.06
1959 1981 3.309436 CTTCCGATCGGTGGGCACA 62.309 63.158 32.15 9.80 36.47 4.57
1960 1982 1.952102 TACTTCCGATCGGTGGGCAC 61.952 60.000 32.15 0.00 36.47 5.01
1971 1993 3.319972 CCCGTAATTGGATCTACTTCCGA 59.680 47.826 0.00 0.00 38.74 4.55
2013 2035 2.039746 TGATGGATGGAGAAAACACGGT 59.960 45.455 0.00 0.00 0.00 4.83
2022 2044 5.248934 TGCATATATGTGTGATGGATGGAGA 59.751 40.000 14.14 0.00 0.00 3.71
2073 2095 4.814771 GGAGGTAACAATAATAGCAAGCGT 59.185 41.667 0.00 0.00 41.41 5.07
2077 2099 7.179269 ACAAAGGGAGGTAACAATAATAGCAA 58.821 34.615 0.00 0.00 41.41 3.91
2091 2113 5.664457 ACGGATATAGTAAACAAAGGGAGGT 59.336 40.000 0.00 0.00 0.00 3.85
2092 2114 5.989777 CACGGATATAGTAAACAAAGGGAGG 59.010 44.000 0.00 0.00 0.00 4.30
2093 2115 6.579865 ACACGGATATAGTAAACAAAGGGAG 58.420 40.000 0.00 0.00 0.00 4.30
2177 2200 7.882791 ACAGAGATGTTAAAATGTGTGACCATA 59.117 33.333 6.90 0.00 0.00 2.74
2289 2312 0.242825 GTTTTAGCCTCGGTTTGCCC 59.757 55.000 0.00 0.00 0.00 5.36
2324 2347 4.213564 CCACTTGGCTATGTTCTCTCTT 57.786 45.455 0.00 0.00 0.00 2.85
2325 2348 3.902881 CCACTTGGCTATGTTCTCTCT 57.097 47.619 0.00 0.00 0.00 3.10
2338 2361 4.481368 TGGTACACTAATAGCCACTTGG 57.519 45.455 0.00 0.00 38.53 3.61
2357 2380 8.802267 TGATTCTAAAGAAAATAAGGTTGGTGG 58.198 33.333 0.00 0.00 37.61 4.61
2377 2400 9.999660 TCGTAGTCTATATAGTTGAGTGATTCT 57.000 33.333 9.58 0.00 0.00 2.40
2380 2403 9.386010 GGATCGTAGTCTATATAGTTGAGTGAT 57.614 37.037 9.58 7.49 0.00 3.06
2388 2411 6.183361 GGCTAGGGGATCGTAGTCTATATAGT 60.183 46.154 9.58 0.00 34.29 2.12
2389 2412 6.232692 GGCTAGGGGATCGTAGTCTATATAG 58.767 48.000 3.10 3.10 34.29 1.31
2390 2413 5.072872 GGGCTAGGGGATCGTAGTCTATATA 59.927 48.000 0.00 0.00 36.52 0.86
2391 2414 4.141205 GGGCTAGGGGATCGTAGTCTATAT 60.141 50.000 0.00 0.00 36.52 0.86
2392 2415 3.201708 GGGCTAGGGGATCGTAGTCTATA 59.798 52.174 0.00 0.00 36.52 1.31
2394 2417 1.353694 GGGCTAGGGGATCGTAGTCTA 59.646 57.143 0.00 0.00 36.52 2.59
2395 2418 0.112801 GGGCTAGGGGATCGTAGTCT 59.887 60.000 0.00 0.00 36.52 3.24
2401 2458 0.961358 CGAGTAGGGCTAGGGGATCG 60.961 65.000 0.00 0.00 0.00 3.69
2406 2463 1.344763 CCAAATCGAGTAGGGCTAGGG 59.655 57.143 0.00 0.00 0.00 3.53
2408 2465 3.005578 GGTACCAAATCGAGTAGGGCTAG 59.994 52.174 7.15 0.00 0.00 3.42
2409 2466 2.961062 GGTACCAAATCGAGTAGGGCTA 59.039 50.000 7.15 0.00 0.00 3.93
2426 2483 0.103208 CTGATGCGAGTGGAGGGTAC 59.897 60.000 0.00 0.00 0.00 3.34
2427 2484 1.676678 GCTGATGCGAGTGGAGGGTA 61.677 60.000 0.00 0.00 0.00 3.69
2432 2489 1.739466 GATTTTGCTGATGCGAGTGGA 59.261 47.619 0.00 0.00 43.34 4.02
2433 2490 1.469703 TGATTTTGCTGATGCGAGTGG 59.530 47.619 0.00 0.00 43.34 4.00
2436 2493 2.163010 AGGTTGATTTTGCTGATGCGAG 59.837 45.455 0.00 0.00 43.34 5.03
2437 2494 2.161855 AGGTTGATTTTGCTGATGCGA 58.838 42.857 0.00 0.00 43.34 5.10
2438 2495 2.642139 AGGTTGATTTTGCTGATGCG 57.358 45.000 0.00 0.00 43.34 4.73
2439 2496 3.924686 CAGAAGGTTGATTTTGCTGATGC 59.075 43.478 0.00 0.00 40.20 3.91
2440 2497 3.924686 GCAGAAGGTTGATTTTGCTGATG 59.075 43.478 0.00 0.00 0.00 3.07
2441 2498 3.056322 GGCAGAAGGTTGATTTTGCTGAT 60.056 43.478 0.00 0.00 0.00 2.90
2442 2499 2.297033 GGCAGAAGGTTGATTTTGCTGA 59.703 45.455 0.00 0.00 0.00 4.26
2443 2500 2.298163 AGGCAGAAGGTTGATTTTGCTG 59.702 45.455 2.60 0.00 0.00 4.41
2444 2501 2.601905 AGGCAGAAGGTTGATTTTGCT 58.398 42.857 2.60 0.00 0.00 3.91
2446 2503 5.241506 TGTTCTAGGCAGAAGGTTGATTTTG 59.758 40.000 0.00 0.00 41.48 2.44
2448 2505 4.985538 TGTTCTAGGCAGAAGGTTGATTT 58.014 39.130 0.00 0.00 41.48 2.17
2479 2539 8.846211 ACTTTAGTCAAAAATTTCTCCGATCAA 58.154 29.630 0.00 0.00 0.00 2.57
2482 2542 8.166422 ACACTTTAGTCAAAAATTTCTCCGAT 57.834 30.769 0.00 0.00 0.00 4.18
2499 2559 6.958255 TGACAACAATGATGTGACACTTTAG 58.042 36.000 7.20 0.00 40.46 1.85
2518 2578 3.254470 TGGTGACGAGAACTTTGACAA 57.746 42.857 0.00 0.00 0.00 3.18
2561 2621 6.346598 CGTGGATAGTGGATTTACTATTTGCG 60.347 42.308 0.00 0.00 42.38 4.85
2576 2636 6.106673 AGAAAAGGAATACACGTGGATAGTG 58.893 40.000 21.57 0.00 44.57 2.74
2578 2638 5.753921 GGAGAAAAGGAATACACGTGGATAG 59.246 44.000 21.57 0.00 0.00 2.08
2599 2659 4.503741 AACAAATGAATTGGTGACGGAG 57.496 40.909 0.00 0.00 43.66 4.63
2621 2683 6.153340 ACTTTCGCTAGTACATACCCTTTGTA 59.847 38.462 0.00 0.00 0.00 2.41
2625 2687 5.672421 AACTTTCGCTAGTACATACCCTT 57.328 39.130 0.00 0.00 0.00 3.95
2636 2700 7.222805 TGAACTCTGCATATAAACTTTCGCTAG 59.777 37.037 0.00 0.00 0.00 3.42
2688 2754 9.886132 GGAGTGGATAAAGATGTAAACTCTTTA 57.114 33.333 7.69 7.69 44.78 1.85
2700 2766 5.394738 TGTATCGGAGGAGTGGATAAAGAT 58.605 41.667 0.00 0.00 0.00 2.40
2708 2774 1.541233 GGCATTGTATCGGAGGAGTGG 60.541 57.143 0.00 0.00 0.00 4.00
2712 2778 3.576078 AATTGGCATTGTATCGGAGGA 57.424 42.857 0.00 0.00 0.00 3.71
2732 2798 8.904099 TTCAAACCCTCAACAAAGTTTAAAAA 57.096 26.923 0.00 0.00 31.50 1.94
2733 2799 8.775527 GTTTCAAACCCTCAACAAAGTTTAAAA 58.224 29.630 0.00 0.00 31.50 1.52
2734 2800 7.931948 TGTTTCAAACCCTCAACAAAGTTTAAA 59.068 29.630 0.00 0.00 31.50 1.52
2735 2801 7.442656 TGTTTCAAACCCTCAACAAAGTTTAA 58.557 30.769 0.00 0.00 31.50 1.52
2736 2802 6.994221 TGTTTCAAACCCTCAACAAAGTTTA 58.006 32.000 0.00 0.00 31.50 2.01
2737 2803 5.859495 TGTTTCAAACCCTCAACAAAGTTT 58.141 33.333 0.00 0.00 32.84 2.66
2738 2804 5.476091 TGTTTCAAACCCTCAACAAAGTT 57.524 34.783 0.00 0.00 0.00 2.66
2739 2805 5.186797 TGATGTTTCAAACCCTCAACAAAGT 59.813 36.000 0.00 0.00 33.02 2.66
2740 2806 5.659463 TGATGTTTCAAACCCTCAACAAAG 58.341 37.500 0.00 0.00 33.02 2.77
2741 2807 5.667539 TGATGTTTCAAACCCTCAACAAA 57.332 34.783 0.00 0.00 33.02 2.83
2742 2808 5.867903 ATGATGTTTCAAACCCTCAACAA 57.132 34.783 6.70 0.00 34.96 2.83
2743 2809 5.867903 AATGATGTTTCAAACCCTCAACA 57.132 34.783 6.70 0.00 34.96 3.33
2744 2810 5.050159 GCAAATGATGTTTCAAACCCTCAAC 60.050 40.000 6.70 0.00 34.96 3.18
2745 2811 5.055812 GCAAATGATGTTTCAAACCCTCAA 58.944 37.500 6.70 0.00 34.96 3.02
2746 2812 4.100653 TGCAAATGATGTTTCAAACCCTCA 59.899 37.500 0.00 1.58 34.96 3.86
2747 2813 4.630111 TGCAAATGATGTTTCAAACCCTC 58.370 39.130 0.00 0.00 34.96 4.30
2748 2814 4.686191 TGCAAATGATGTTTCAAACCCT 57.314 36.364 0.00 0.00 34.96 4.34
2749 2815 5.747951 TTTGCAAATGATGTTTCAAACCC 57.252 34.783 8.05 0.00 34.96 4.11
2750 2816 9.384682 CTTTATTTGCAAATGATGTTTCAAACC 57.615 29.630 30.43 0.00 34.96 3.27
2753 2819 9.761504 TCTCTTTATTTGCAAATGATGTTTCAA 57.238 25.926 30.43 13.94 34.96 2.69
2754 2820 9.761504 TTCTCTTTATTTGCAAATGATGTTTCA 57.238 25.926 30.43 8.73 36.00 2.69
2757 2823 9.932207 TGATTCTCTTTATTTGCAAATGATGTT 57.068 25.926 30.43 10.17 0.00 2.71
2760 2826 9.542462 CCATGATTCTCTTTATTTGCAAATGAT 57.458 29.630 30.43 11.61 0.00 2.45
2761 2827 8.751242 TCCATGATTCTCTTTATTTGCAAATGA 58.249 29.630 30.43 21.88 0.00 2.57
2762 2828 8.936070 TCCATGATTCTCTTTATTTGCAAATG 57.064 30.769 30.43 16.50 0.00 2.32
2763 2829 8.755977 ACTCCATGATTCTCTTTATTTGCAAAT 58.244 29.630 26.72 26.72 0.00 2.32
2764 2830 8.030692 CACTCCATGATTCTCTTTATTTGCAAA 58.969 33.333 15.44 15.44 0.00 3.68
2765 2831 7.363181 CCACTCCATGATTCTCTTTATTTGCAA 60.363 37.037 0.00 0.00 0.00 4.08
2786 2853 0.947180 TCGCCGCAACTTTACCACTC 60.947 55.000 0.00 0.00 0.00 3.51
2789 2856 0.814410 TGTTCGCCGCAACTTTACCA 60.814 50.000 7.06 0.00 0.00 3.25
2790 2857 0.385098 GTGTTCGCCGCAACTTTACC 60.385 55.000 7.06 0.00 0.00 2.85
2796 2863 1.657181 CCAAAGTGTTCGCCGCAAC 60.657 57.895 0.00 0.00 0.00 4.17
2800 2867 0.661020 AGAAACCAAAGTGTTCGCCG 59.339 50.000 0.00 0.00 0.00 6.46
2806 2873 1.676006 CTGCCGAAGAAACCAAAGTGT 59.324 47.619 0.00 0.00 0.00 3.55
2808 2875 0.668535 GCTGCCGAAGAAACCAAAGT 59.331 50.000 0.00 0.00 0.00 2.66
2824 2891 5.679734 AGTGATGGCGAAAATAATAGCTG 57.320 39.130 0.00 0.00 0.00 4.24
2825 2892 5.050091 CGAAGTGATGGCGAAAATAATAGCT 60.050 40.000 0.00 0.00 0.00 3.32
2826 2893 5.140177 CGAAGTGATGGCGAAAATAATAGC 58.860 41.667 0.00 0.00 0.00 2.97
2827 2894 5.140177 GCGAAGTGATGGCGAAAATAATAG 58.860 41.667 0.00 0.00 0.00 1.73
2828 2895 4.024387 GGCGAAGTGATGGCGAAAATAATA 60.024 41.667 0.00 0.00 32.79 0.98
2829 2896 3.243068 GGCGAAGTGATGGCGAAAATAAT 60.243 43.478 0.00 0.00 32.79 1.28
2830 2897 2.096819 GGCGAAGTGATGGCGAAAATAA 59.903 45.455 0.00 0.00 32.79 1.40
2831 2898 1.668751 GGCGAAGTGATGGCGAAAATA 59.331 47.619 0.00 0.00 32.79 1.40
2832 2899 0.451783 GGCGAAGTGATGGCGAAAAT 59.548 50.000 0.00 0.00 32.79 1.82
2833 2900 0.605319 AGGCGAAGTGATGGCGAAAA 60.605 50.000 0.00 0.00 32.79 2.29
2834 2901 0.605319 AAGGCGAAGTGATGGCGAAA 60.605 50.000 0.00 0.00 32.79 3.46
2835 2902 1.003839 AAGGCGAAGTGATGGCGAA 60.004 52.632 0.00 0.00 32.79 4.70
2836 2903 1.741401 CAAGGCGAAGTGATGGCGA 60.741 57.895 0.00 0.00 32.79 5.54
2837 2904 1.970917 GACAAGGCGAAGTGATGGCG 61.971 60.000 0.00 0.00 32.79 5.69
2838 2905 0.955428 TGACAAGGCGAAGTGATGGC 60.955 55.000 0.00 0.00 0.00 4.40
2839 2906 0.798776 GTGACAAGGCGAAGTGATGG 59.201 55.000 0.00 0.00 0.00 3.51
2840 2907 0.798776 GGTGACAAGGCGAAGTGATG 59.201 55.000 0.00 0.00 0.00 3.07
2841 2908 0.687354 AGGTGACAAGGCGAAGTGAT 59.313 50.000 0.00 0.00 0.00 3.06
2842 2909 0.249868 CAGGTGACAAGGCGAAGTGA 60.250 55.000 0.00 0.00 0.00 3.41
2843 2910 1.845809 GCAGGTGACAAGGCGAAGTG 61.846 60.000 0.00 0.00 0.00 3.16
2844 2911 1.598130 GCAGGTGACAAGGCGAAGT 60.598 57.895 0.00 0.00 0.00 3.01
2845 2912 2.328099 GGCAGGTGACAAGGCGAAG 61.328 63.158 0.00 0.00 0.00 3.79
2846 2913 2.281484 GGCAGGTGACAAGGCGAA 60.281 61.111 0.00 0.00 0.00 4.70
2849 2916 2.594592 AACGGCAGGTGACAAGGC 60.595 61.111 0.00 0.00 0.00 4.35
2850 2917 1.227823 TGAACGGCAGGTGACAAGG 60.228 57.895 0.00 0.00 0.00 3.61
2911 2978 3.118454 CCGTGAAAGCCGCGTCAT 61.118 61.111 4.92 0.00 46.53 3.06
2919 2986 1.671379 GTGGGAGGTCCGTGAAAGC 60.671 63.158 0.00 0.00 38.76 3.51
2922 2989 2.122769 TGGTGGGAGGTCCGTGAA 60.123 61.111 0.00 0.00 38.76 3.18


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

AutoCloner maintained by Alex Coulton.