Multiple sequence alignment - TraesCS2B01G179500

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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 TraesCS2B01G179500 chr2B 100.000 5471 0 0 1 5471 154232392 154237862 0.000000e+00 10104.0
1 TraesCS2B01G179500 chr2D 93.845 3103 124 25 2401 5471 102857942 102861009 0.000000e+00 4610.0
2 TraesCS2B01G179500 chr2D 90.818 2102 84 32 84 2150 102855859 102857886 0.000000e+00 2712.0
3 TraesCS2B01G179500 chr2D 100.000 30 0 0 2212 2241 102857908 102857937 7.660000e-04 56.5
4 TraesCS2B01G179500 chr2A 91.127 1961 114 23 2657 4578 101888235 101890174 0.000000e+00 2603.0
5 TraesCS2B01G179500 chr2A 86.748 1894 117 53 91 1935 101886039 101887847 0.000000e+00 1984.0
6 TraesCS2B01G179500 chr2A 87.773 687 59 16 4798 5471 101890245 101890919 0.000000e+00 780.0
7 TraesCS2B01G179500 chr2A 89.372 207 19 2 4592 4798 101890570 101890773 1.960000e-64 257.0
8 TraesCS2B01G179500 chr2A 79.389 262 36 13 2008 2259 101887870 101888123 9.420000e-38 169.0
9 TraesCS2B01G179500 chr2A 92.473 93 4 3 1 93 24556925 24556836 4.450000e-26 130.0
10 TraesCS2B01G179500 chr3A 80.939 362 43 19 94 439 708985744 708986095 4.200000e-66 263.0
11 TraesCS2B01G179500 chr3A 80.663 362 38 26 99 439 652833269 652833619 9.100000e-63 252.0
12 TraesCS2B01G179500 chr3A 75.105 237 46 12 4951 5178 221274993 221275225 1.250000e-16 99.0
13 TraesCS2B01G179500 chr3D 81.931 321 33 17 94 402 126385778 126385471 1.180000e-61 248.0
14 TraesCS2B01G179500 chr3D 80.387 362 37 22 94 439 517012007 517011664 1.520000e-60 244.0
15 TraesCS2B01G179500 chr3D 74.459 231 51 8 4955 5178 178651832 178652061 5.840000e-15 93.5
16 TraesCS2B01G179500 chr4A 79.189 370 53 20 73 428 516584682 516585041 9.160000e-58 235.0
17 TraesCS2B01G179500 chr4A 88.393 112 9 4 1 109 223857883 223857993 1.240000e-26 132.0
18 TraesCS2B01G179500 chr3B 79.614 363 47 22 93 439 680220112 680220463 9.160000e-58 235.0
19 TraesCS2B01G179500 chr3B 95.402 87 4 0 1 87 68406264 68406350 7.390000e-29 139.0
20 TraesCS2B01G179500 chr3B 97.531 81 2 0 1 81 611179016 611179096 7.390000e-29 139.0
21 TraesCS2B01G179500 chr3B 75.598 209 43 8 4977 5178 257098984 257099191 4.510000e-16 97.1
22 TraesCS2B01G179500 chr5D 79.387 359 50 19 98 439 549767705 549767354 1.190000e-56 231.0
23 TraesCS2B01G179500 chr5D 98.750 80 1 0 1 80 342697446 342697367 5.710000e-30 143.0
24 TraesCS2B01G179500 chr7D 98.734 79 1 0 1 79 13018532 13018454 2.050000e-29 141.0
25 TraesCS2B01G179500 chr4B 94.318 88 3 2 1 88 32425751 32425836 3.440000e-27 134.0
26 TraesCS2B01G179500 chr4B 92.473 93 5 2 1 92 68097483 68097392 1.240000e-26 132.0
27 TraesCS2B01G179500 chr1D 79.891 184 33 4 1753 1934 366723826 366724007 1.240000e-26 132.0
28 TraesCS2B01G179500 chr1A 80.110 181 33 3 1755 1934 465454635 465454457 1.240000e-26 132.0
29 TraesCS2B01G179500 chr1A 92.473 93 4 3 1 93 534363175 534363264 4.450000e-26 130.0
30 TraesCS2B01G179500 chr1B 79.661 177 34 2 1759 1934 491040846 491040671 5.750000e-25 126.0


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 TraesCS2B01G179500 chr2B 154232392 154237862 5470 False 10104.0 10104 100.000000 1 5471 1 chr2B.!!$F1 5470
1 TraesCS2B01G179500 chr2D 102855859 102861009 5150 False 2459.5 4610 94.887667 84 5471 3 chr2D.!!$F1 5387
2 TraesCS2B01G179500 chr2A 101886039 101890919 4880 False 1158.6 2603 86.881800 91 5471 5 chr2A.!!$F1 5380

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
854 900 0.031449 GTCCATCACTCGAGCCTAGC 59.969 60.0 13.61 0.00 0.00 3.42 F
1136 1207 0.107654 CACCCGGATCAACTTCCTCC 60.108 60.0 0.73 0.00 33.30 4.30 F
2373 2496 0.033504 TGAGACACCGAGCAACTTCC 59.966 55.0 0.00 0.00 0.00 3.46 F
2524 2647 0.038526 GTGGACAGGGTACACGTCAG 60.039 60.0 17.67 1.44 37.65 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2354 2477 0.033504 GGAAGTTGCTCGGTGTCTCA 59.966 55.000 0.0 0.0 0.00 3.27 R
2658 2785 0.035630 GCACACCTGGCAATCTCTCT 60.036 55.000 0.0 0.0 0.00 3.10 R
4234 4400 1.071314 AGGTTGGTCATGGTCCCCAA 61.071 55.000 0.0 0.0 36.95 4.12 R
4522 4691 3.318557 CCAGTTTTTAACCAAAGGCCGTA 59.681 43.478 0.0 0.0 0.00 4.02 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
65 66 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
66 67 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
67 68 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
68 69 7.975616 CCATTTTGATGACAAGTATTTTCGGAT 59.024 33.333 0.00 0.00 37.32 4.18
69 70 8.800972 CATTTTGATGACAAGTATTTTCGGATG 58.199 33.333 0.00 0.00 37.32 3.51
70 71 6.435430 TTGATGACAAGTATTTTCGGATGG 57.565 37.500 0.00 0.00 0.00 3.51
71 72 5.739959 TGATGACAAGTATTTTCGGATGGA 58.260 37.500 0.00 0.00 0.00 3.41
72 73 5.817296 TGATGACAAGTATTTTCGGATGGAG 59.183 40.000 0.00 0.00 0.00 3.86
73 74 4.513442 TGACAAGTATTTTCGGATGGAGG 58.487 43.478 0.00 0.00 0.00 4.30
74 75 3.877508 GACAAGTATTTTCGGATGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
75 76 3.521937 ACAAGTATTTTCGGATGGAGGGA 59.478 43.478 0.00 0.00 0.00 4.20
76 77 4.130118 CAAGTATTTTCGGATGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
77 78 3.385115 AGTATTTTCGGATGGAGGGAGT 58.615 45.455 0.00 0.00 0.00 3.85
78 79 4.553678 AGTATTTTCGGATGGAGGGAGTA 58.446 43.478 0.00 0.00 0.00 2.59
79 80 5.155905 AGTATTTTCGGATGGAGGGAGTAT 58.844 41.667 0.00 0.00 0.00 2.12
80 81 6.320518 AGTATTTTCGGATGGAGGGAGTATA 58.679 40.000 0.00 0.00 0.00 1.47
81 82 6.960542 AGTATTTTCGGATGGAGGGAGTATAT 59.039 38.462 0.00 0.00 0.00 0.86
82 83 8.120538 AGTATTTTCGGATGGAGGGAGTATATA 58.879 37.037 0.00 0.00 0.00 0.86
88 89 7.061054 TCGGATGGAGGGAGTATATACTTATG 58.939 42.308 16.46 0.00 36.50 1.90
178 186 9.927668 CCATTGTACTTGTAAGAAAAATTCCAT 57.072 29.630 0.00 0.00 0.00 3.41
306 316 6.279513 AGTCAACACTGGATTTTTGTTCAA 57.720 33.333 0.00 0.00 30.98 2.69
417 450 9.502091 TTTTTCTCATATAGGGTGTATATGCAC 57.498 33.333 14.90 14.90 37.64 4.57
426 459 3.275617 GTGTATATGCACCAGGAACCA 57.724 47.619 12.50 0.00 33.53 3.67
427 460 3.616219 GTGTATATGCACCAGGAACCAA 58.384 45.455 12.50 0.00 33.53 3.67
428 461 4.013728 GTGTATATGCACCAGGAACCAAA 58.986 43.478 12.50 0.00 33.53 3.28
580 625 0.392193 CGCAACCTGCTCTCCAATCT 60.392 55.000 0.00 0.00 42.25 2.40
613 658 1.208052 CTTCGGCAGATGGGAGAAAGA 59.792 52.381 0.00 0.00 0.00 2.52
620 665 4.759183 GGCAGATGGGAGAAAGAATATCAC 59.241 45.833 0.00 0.00 0.00 3.06
706 751 5.308825 TCTCCTTCTTCCACACTTTGAATC 58.691 41.667 0.00 0.00 0.00 2.52
708 753 3.189287 CCTTCTTCCACACTTTGAATCCG 59.811 47.826 0.00 0.00 0.00 4.18
731 776 4.821589 CGCCTCGCTTCCTCACCC 62.822 72.222 0.00 0.00 0.00 4.61
734 779 3.003173 CTCGCTTCCTCACCCCCA 61.003 66.667 0.00 0.00 0.00 4.96
737 782 2.936032 GCTTCCTCACCCCCACCT 60.936 66.667 0.00 0.00 0.00 4.00
738 783 2.539081 GCTTCCTCACCCCCACCTT 61.539 63.158 0.00 0.00 0.00 3.50
850 896 0.102120 CTCAGTCCATCACTCGAGCC 59.898 60.000 13.61 0.00 30.26 4.70
851 897 0.323816 TCAGTCCATCACTCGAGCCT 60.324 55.000 13.61 0.00 30.26 4.58
852 898 1.064685 TCAGTCCATCACTCGAGCCTA 60.065 52.381 13.61 0.00 30.26 3.93
853 899 1.336440 CAGTCCATCACTCGAGCCTAG 59.664 57.143 13.61 0.00 30.26 3.02
854 900 0.031449 GTCCATCACTCGAGCCTAGC 59.969 60.000 13.61 0.00 0.00 3.42
855 901 0.395724 TCCATCACTCGAGCCTAGCA 60.396 55.000 13.61 0.00 0.00 3.49
944 990 3.810896 GGCTCGCCGCGGAATTTT 61.811 61.111 33.48 0.00 40.44 1.82
990 1042 5.701290 CACCATACCTTTCTTTTTCTCTCGT 59.299 40.000 0.00 0.00 0.00 4.18
1030 1082 3.676605 ATCACGCCGACACCGACA 61.677 61.111 0.00 0.00 38.22 4.35
1031 1083 3.909258 ATCACGCCGACACCGACAC 62.909 63.158 0.00 0.00 38.22 3.67
1047 1099 4.148825 ACCGAGCGAGCCATCCAC 62.149 66.667 0.00 0.00 0.00 4.02
1050 1102 4.148825 GAGCGAGCCATCCACCGT 62.149 66.667 0.00 0.00 0.00 4.83
1051 1103 4.457496 AGCGAGCCATCCACCGTG 62.457 66.667 0.00 0.00 0.00 4.94
1089 1141 2.165030 CCAGCGAGCAAATCCAATCTTT 59.835 45.455 0.00 0.00 0.00 2.52
1122 1193 4.467084 CACCCGATCACCCACCCG 62.467 72.222 0.00 0.00 0.00 5.28
1136 1207 0.107654 CACCCGGATCAACTTCCTCC 60.108 60.000 0.73 0.00 33.30 4.30
1137 1208 1.272554 ACCCGGATCAACTTCCTCCC 61.273 60.000 0.73 0.00 33.30 4.30
1155 1227 1.885049 CCCCCTCTCATCTCTTTCCA 58.115 55.000 0.00 0.00 0.00 3.53
1160 1232 1.136695 CTCTCATCTCTTTCCAGCGCT 59.863 52.381 2.64 2.64 0.00 5.92
1281 1353 1.228063 AAGCTGCAGAGTGGTGGTG 60.228 57.895 20.43 0.00 0.00 4.17
1434 1510 2.344203 CGTCCTCTGCTTCCTCGGT 61.344 63.158 0.00 0.00 0.00 4.69
1935 2014 6.037830 TCAAGAACTTGCTTAACAACAGGTAC 59.962 38.462 9.38 0.00 40.24 3.34
1938 2017 6.260271 AGAACTTGCTTAACAACAGGTACTTC 59.740 38.462 0.00 0.00 31.72 3.01
1939 2018 5.681639 ACTTGCTTAACAACAGGTACTTCT 58.318 37.500 0.00 0.00 31.72 2.85
1940 2019 6.823497 ACTTGCTTAACAACAGGTACTTCTA 58.177 36.000 0.00 0.00 31.72 2.10
1942 2021 7.937394 ACTTGCTTAACAACAGGTACTTCTAAT 59.063 33.333 0.00 0.00 31.72 1.73
1945 2024 9.211485 TGCTTAACAACAGGTACTTCTAATTAC 57.789 33.333 0.00 0.00 34.60 1.89
1946 2025 8.378421 GCTTAACAACAGGTACTTCTAATTACG 58.622 37.037 0.00 0.00 34.60 3.18
1947 2026 9.415544 CTTAACAACAGGTACTTCTAATTACGT 57.584 33.333 0.00 0.00 34.60 3.57
1976 2055 3.738982 TCATGGAACTCGCTCTGAAAAA 58.261 40.909 0.00 0.00 0.00 1.94
1982 2061 5.080068 GGAACTCGCTCTGAAAAATTTACG 58.920 41.667 0.00 0.00 0.00 3.18
1992 2071 7.322938 GCTCTGAAAAATTTACGGTAACTTGAC 59.677 37.037 0.00 0.00 0.00 3.18
2013 2092 3.624861 ACATTGTCATCTCGGATGAAAGC 59.375 43.478 15.34 6.95 0.00 3.51
2157 2261 1.944177 AGCCTCTATATGTGCCGGAT 58.056 50.000 5.05 0.00 0.00 4.18
2190 2296 4.331968 CTGCAGGTTGGGTTCAGTAATTA 58.668 43.478 5.57 0.00 0.00 1.40
2191 2297 4.331968 TGCAGGTTGGGTTCAGTAATTAG 58.668 43.478 0.00 0.00 0.00 1.73
2192 2298 4.202524 TGCAGGTTGGGTTCAGTAATTAGT 60.203 41.667 0.00 0.00 0.00 2.24
2193 2299 4.156008 GCAGGTTGGGTTCAGTAATTAGTG 59.844 45.833 13.27 13.27 0.00 2.74
2194 2300 5.313712 CAGGTTGGGTTCAGTAATTAGTGT 58.686 41.667 17.79 0.00 0.00 3.55
2195 2301 6.469410 CAGGTTGGGTTCAGTAATTAGTGTA 58.531 40.000 17.79 7.72 0.00 2.90
2196 2302 6.370718 CAGGTTGGGTTCAGTAATTAGTGTAC 59.629 42.308 17.79 17.55 0.00 2.90
2197 2303 6.271624 AGGTTGGGTTCAGTAATTAGTGTACT 59.728 38.462 22.06 1.69 31.85 2.73
2198 2304 6.370718 GGTTGGGTTCAGTAATTAGTGTACTG 59.629 42.308 22.06 12.62 46.55 2.74
2199 2305 6.045072 TGGGTTCAGTAATTAGTGTACTGG 57.955 41.667 22.06 0.00 45.65 4.00
2200 2306 5.544948 TGGGTTCAGTAATTAGTGTACTGGT 59.455 40.000 22.06 0.00 45.65 4.00
2201 2307 6.043474 TGGGTTCAGTAATTAGTGTACTGGTT 59.957 38.462 22.06 0.00 45.65 3.67
2202 2308 6.938596 GGGTTCAGTAATTAGTGTACTGGTTT 59.061 38.462 22.06 0.00 45.65 3.27
2203 2309 7.446319 GGGTTCAGTAATTAGTGTACTGGTTTT 59.554 37.037 22.06 0.00 45.65 2.43
2204 2310 8.501580 GGTTCAGTAATTAGTGTACTGGTTTTC 58.498 37.037 22.06 7.05 45.65 2.29
2205 2311 8.501580 GTTCAGTAATTAGTGTACTGGTTTTCC 58.498 37.037 17.79 0.00 45.65 3.13
2206 2312 7.163441 TCAGTAATTAGTGTACTGGTTTTCCC 58.837 38.462 17.79 0.00 45.65 3.97
2207 2313 7.016858 TCAGTAATTAGTGTACTGGTTTTCCCT 59.983 37.037 17.79 0.00 45.65 4.20
2208 2314 7.664318 CAGTAATTAGTGTACTGGTTTTCCCTT 59.336 37.037 11.54 0.00 43.12 3.95
2209 2315 8.883302 AGTAATTAGTGTACTGGTTTTCCCTTA 58.117 33.333 0.00 0.00 39.73 2.69
2210 2316 9.676861 GTAATTAGTGTACTGGTTTTCCCTTAT 57.323 33.333 0.00 0.00 39.73 1.73
2259 2365 4.215613 GCTTCCGTGAGTTTTAATTGAGGT 59.784 41.667 0.00 0.00 0.00 3.85
2262 2368 5.856156 TCCGTGAGTTTTAATTGAGGTACA 58.144 37.500 0.00 0.00 0.00 2.90
2265 2371 6.204108 CCGTGAGTTTTAATTGAGGTACACTT 59.796 38.462 0.00 0.00 0.00 3.16
2293 2416 4.040645 CTGGCTCAGGGTGCTCTA 57.959 61.111 0.00 0.00 0.00 2.43
2306 2429 4.577246 CTCTACGCCGGAGCTGCC 62.577 72.222 5.05 0.00 36.60 4.85
2342 2465 4.514577 CGGCCGGATCGTGCTCTT 62.515 66.667 20.10 0.00 0.00 2.85
2343 2466 2.125106 GGCCGGATCGTGCTCTTT 60.125 61.111 5.05 0.00 0.00 2.52
2344 2467 1.143183 GGCCGGATCGTGCTCTTTA 59.857 57.895 5.05 0.00 0.00 1.85
2345 2468 0.876342 GGCCGGATCGTGCTCTTTAG 60.876 60.000 5.05 0.00 0.00 1.85
2354 2477 2.184579 GCTCTTTAGCTCGCCGGT 59.815 61.111 1.90 0.00 45.85 5.28
2355 2478 2.167861 GCTCTTTAGCTCGCCGGTG 61.168 63.158 9.28 9.28 45.85 4.94
2356 2479 1.511305 CTCTTTAGCTCGCCGGTGA 59.489 57.895 18.43 18.43 0.00 4.02
2357 2480 0.526524 CTCTTTAGCTCGCCGGTGAG 60.527 60.000 35.59 35.59 39.05 3.51
2358 2481 0.963856 TCTTTAGCTCGCCGGTGAGA 60.964 55.000 41.88 23.77 38.28 3.27
2359 2482 0.802607 CTTTAGCTCGCCGGTGAGAC 60.803 60.000 41.88 31.82 38.28 3.36
2360 2483 1.529152 TTTAGCTCGCCGGTGAGACA 61.529 55.000 41.88 27.35 38.28 3.41
2361 2484 2.209064 TTAGCTCGCCGGTGAGACAC 62.209 60.000 41.88 26.70 38.28 3.67
2369 2492 3.952811 GGTGAGACACCGAGCAAC 58.047 61.111 5.17 0.00 44.95 4.17
2370 2493 1.367840 GGTGAGACACCGAGCAACT 59.632 57.895 5.17 0.00 44.95 3.16
2371 2494 0.249911 GGTGAGACACCGAGCAACTT 60.250 55.000 5.17 0.00 44.95 2.66
2372 2495 1.140816 GTGAGACACCGAGCAACTTC 58.859 55.000 0.00 0.00 0.00 3.01
2373 2496 0.033504 TGAGACACCGAGCAACTTCC 59.966 55.000 0.00 0.00 0.00 3.46
2374 2497 1.006102 AGACACCGAGCAACTTCCG 60.006 57.895 0.00 0.00 0.00 4.30
2375 2498 1.006571 GACACCGAGCAACTTCCGA 60.007 57.895 0.00 0.00 0.00 4.55
2376 2499 1.006102 ACACCGAGCAACTTCCGAG 60.006 57.895 0.00 0.00 0.00 4.63
2377 2500 1.738099 CACCGAGCAACTTCCGAGG 60.738 63.158 0.00 0.00 0.00 4.63
2378 2501 2.815647 CCGAGCAACTTCCGAGGC 60.816 66.667 0.00 0.00 0.00 4.70
2379 2502 2.262915 CGAGCAACTTCCGAGGCT 59.737 61.111 0.00 0.00 39.75 4.58
2380 2503 4.193653 GAGCAACTTCCGAGGCTC 57.806 61.111 3.87 3.87 44.97 4.70
2381 2504 1.807573 GAGCAACTTCCGAGGCTCG 60.808 63.158 29.16 29.16 42.72 5.03
2382 2505 3.491652 GCAACTTCCGAGGCTCGC 61.492 66.667 30.55 11.85 38.82 5.03
2383 2506 2.815647 CAACTTCCGAGGCTCGCC 60.816 66.667 30.55 0.00 38.82 5.54
2384 2507 4.436998 AACTTCCGAGGCTCGCCG 62.437 66.667 30.55 21.11 38.82 6.46
2446 2569 1.289066 CCCACGTGATCAGTGTCGT 59.711 57.895 19.30 12.16 37.88 4.34
2467 2590 1.741706 CTGCTGGATTGCGTTCATCTT 59.258 47.619 0.00 0.00 35.36 2.40
2470 2593 2.223203 GCTGGATTGCGTTCATCTTCTG 60.223 50.000 0.00 0.00 0.00 3.02
2514 2637 2.669569 CACGGCTTGTGGACAGGG 60.670 66.667 2.21 0.00 45.21 4.45
2515 2638 3.168528 ACGGCTTGTGGACAGGGT 61.169 61.111 0.00 0.00 0.00 4.34
2516 2639 1.839747 ACGGCTTGTGGACAGGGTA 60.840 57.895 0.00 0.00 0.00 3.69
2517 2640 1.375523 CGGCTTGTGGACAGGGTAC 60.376 63.158 0.00 0.00 0.00 3.34
2518 2641 1.758592 GGCTTGTGGACAGGGTACA 59.241 57.895 0.00 0.00 0.00 2.90
2519 2642 0.605589 GGCTTGTGGACAGGGTACAC 60.606 60.000 4.78 4.78 46.67 2.90
2522 2645 4.981415 GTGGACAGGGTACACGTC 57.019 61.111 10.44 10.44 37.65 4.34
2523 2646 2.043625 GTGGACAGGGTACACGTCA 58.956 57.895 17.67 1.64 37.65 4.35
2524 2647 0.038526 GTGGACAGGGTACACGTCAG 60.039 60.000 17.67 1.44 37.65 3.51
2525 2648 1.183030 TGGACAGGGTACACGTCAGG 61.183 60.000 17.67 0.00 0.00 3.86
2526 2649 1.590147 GACAGGGTACACGTCAGGG 59.410 63.158 13.05 0.00 0.00 4.45
2527 2650 0.896940 GACAGGGTACACGTCAGGGA 60.897 60.000 13.05 0.00 0.00 4.20
2528 2651 0.470456 ACAGGGTACACGTCAGGGAA 60.470 55.000 0.00 0.00 0.00 3.97
2556 2679 2.111384 GGGAGGAGTAAGTGCAGATGA 58.889 52.381 0.00 0.00 0.00 2.92
2567 2690 1.448540 GCAGATGACGAGGTGGTGG 60.449 63.158 0.00 0.00 0.00 4.61
2568 2691 1.888436 GCAGATGACGAGGTGGTGGA 61.888 60.000 0.00 0.00 0.00 4.02
2571 2694 0.608640 GATGACGAGGTGGTGGAAGT 59.391 55.000 0.00 0.00 0.00 3.01
2577 2700 1.633774 GAGGTGGTGGAAGTGAGAGA 58.366 55.000 0.00 0.00 0.00 3.10
2605 2728 1.098050 AACTGCTCGATGAAATGCCC 58.902 50.000 0.00 0.00 0.00 5.36
2629 2756 6.399743 CATGAGAGAGATATGATGACAAGGG 58.600 44.000 0.00 0.00 0.00 3.95
2633 2760 3.327172 AGAGATATGATGACAAGGGCAGG 59.673 47.826 0.00 0.00 0.00 4.85
2634 2761 3.321039 AGATATGATGACAAGGGCAGGA 58.679 45.455 0.00 0.00 0.00 3.86
2636 2763 1.588239 ATGATGACAAGGGCAGGAGA 58.412 50.000 0.00 0.00 0.00 3.71
2637 2764 0.907486 TGATGACAAGGGCAGGAGAG 59.093 55.000 0.00 0.00 0.00 3.20
2647 2774 1.477558 GGGCAGGAGAGAGAGAGAGAG 60.478 61.905 0.00 0.00 0.00 3.20
2649 2776 2.486191 GGCAGGAGAGAGAGAGAGAGAG 60.486 59.091 0.00 0.00 0.00 3.20
2650 2777 2.486191 GCAGGAGAGAGAGAGAGAGAGG 60.486 59.091 0.00 0.00 0.00 3.69
2652 2779 2.022035 AGGAGAGAGAGAGAGAGAGGGA 60.022 54.545 0.00 0.00 0.00 4.20
2653 2780 2.370189 GGAGAGAGAGAGAGAGAGGGAG 59.630 59.091 0.00 0.00 0.00 4.30
2656 2783 3.051803 AGAGAGAGAGAGAGAGGGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2657 2784 3.312890 AGAGAGAGAGAGAGGGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2658 2785 3.051803 AGAGAGAGAGAGAGGGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2659 2786 3.312890 AGAGAGAGAGAGGGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2660 2787 3.051803 AGAGAGAGAGAGGGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2661 2788 3.312890 AGAGAGAGAGGGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2662 2789 3.051803 AGAGAGAGAGGGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2663 2790 3.312890 AGAGAGAGGGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2664 2791 3.051803 AGAGAGAGGGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2665 2792 3.906846 GAGAGAGGGAGAGAGAGAGAGAT 59.093 52.174 0.00 0.00 0.00 2.75
2689 2816 2.094659 GGTGTGCGATGACCTGTCG 61.095 63.158 0.00 0.00 41.77 4.35
2696 2823 0.458543 CGATGACCTGTCGAACCCAG 60.459 60.000 0.00 0.00 41.40 4.45
2708 2841 1.204704 CGAACCCAGTCAGCACAGATA 59.795 52.381 0.00 0.00 0.00 1.98
2709 2842 2.622436 GAACCCAGTCAGCACAGATAC 58.378 52.381 0.00 0.00 0.00 2.24
2719 2852 1.993369 GCACAGATACCGCTTTGGCC 61.993 60.000 0.00 0.00 43.94 5.36
2721 2854 0.676782 ACAGATACCGCTTTGGCCAC 60.677 55.000 3.88 0.00 43.94 5.01
2724 2857 1.702491 GATACCGCTTTGGCCACGTC 61.702 60.000 3.88 0.00 43.94 4.34
2810 2943 6.072673 AGGGACAAAACATTAACTTGTCGATC 60.073 38.462 7.79 0.00 46.42 3.69
2816 2949 5.862924 ACATTAACTTGTCGATCAGTTGG 57.137 39.130 17.95 11.64 0.00 3.77
2834 2968 6.072893 TCAGTTGGCGACTAAAAATAGGTTTC 60.073 38.462 7.16 0.00 36.65 2.78
2886 3020 1.135315 CGGCTTGGATTGGTCAATGTG 60.135 52.381 0.43 0.00 0.00 3.21
2888 3022 2.353011 GGCTTGGATTGGTCAATGTGTG 60.353 50.000 0.43 0.00 0.00 3.82
2890 3024 2.967745 TGGATTGGTCAATGTGTGGA 57.032 45.000 0.43 0.00 0.00 4.02
2891 3025 3.454719 TGGATTGGTCAATGTGTGGAT 57.545 42.857 0.43 0.00 0.00 3.41
2902 3057 6.314896 GGTCAATGTGTGGATTTTTGTTTTCA 59.685 34.615 0.00 0.00 0.00 2.69
3008 3167 3.574396 CCTTCTAGGATATTGTGCCGAGA 59.426 47.826 0.00 0.00 37.67 4.04
3028 3187 5.278266 CGAGAGGAATCAGAGGTATTGTCTC 60.278 48.000 0.00 0.00 0.00 3.36
3036 3195 4.948004 TCAGAGGTATTGTCTCGTATGTGT 59.052 41.667 0.00 0.00 36.45 3.72
3041 3200 1.414378 TTGTCTCGTATGTGTGTGCG 58.586 50.000 0.00 0.00 0.00 5.34
3049 3208 3.000825 TCGTATGTGTGTGCGCATTATTC 59.999 43.478 15.91 0.00 42.60 1.75
3063 3222 4.611355 CGCATTATTCGATTACCTTGCTGG 60.611 45.833 11.29 0.00 42.93 4.85
3082 3241 7.099266 TGCTGGGTTATAGAATCAACAATTG 57.901 36.000 3.24 3.24 0.00 2.32
3303 3466 3.402628 ACTGACGTTTTGCCTAGTCAT 57.597 42.857 0.00 0.00 41.92 3.06
3430 3593 2.679059 GCACTGGAATGCTAAGCTCTCA 60.679 50.000 0.00 0.00 42.62 3.27
3510 3673 3.900971 TGGGAACTTTCGGGTTAGTTTT 58.099 40.909 0.00 0.00 34.88 2.43
3767 3930 4.096984 AGCCTTATGAGCTTGTTAATGCAC 59.903 41.667 0.00 0.00 37.24 4.57
4091 4257 9.859427 GATTTTCATTTTATCTGGACATTCACA 57.141 29.630 0.00 0.00 0.00 3.58
4229 4395 5.122869 CGGAATAGATGATGGCGAAATTGAT 59.877 40.000 0.00 0.00 0.00 2.57
4234 4400 6.889301 AGATGATGGCGAAATTGATAACAT 57.111 33.333 0.00 0.00 0.00 2.71
4272 4441 7.070571 ACCAACCTTTCAGATGGAAAAATACAA 59.929 33.333 0.00 0.00 44.52 2.41
4281 4450 5.302823 AGATGGAAAAATACAATGGCCTAGC 59.697 40.000 3.32 0.00 0.00 3.42
4522 4691 5.513233 ACAACAGAATGATAAAGCCCTCAT 58.487 37.500 0.00 0.00 39.69 2.90
4599 4768 7.439056 ACACCATTTAAAGAAGCTTCACATTTG 59.561 33.333 27.57 16.21 0.00 2.32
4629 4798 7.937649 AGTTTGACTTAAGACAATACCAAACC 58.062 34.615 18.69 3.42 41.49 3.27
4683 4852 5.715070 AGTACTGGAGATCAAAGAAGAACG 58.285 41.667 0.00 0.00 0.00 3.95
4748 4917 6.072649 TCTAATCCGGGTTTCTTTTTCCTTT 58.927 36.000 4.62 0.00 0.00 3.11
4764 4933 4.385358 TCCTTTTGTTGCCTTCTTGTTC 57.615 40.909 0.00 0.00 0.00 3.18
4835 5004 2.224572 TGTGCCCGTGTACAAATAACCT 60.225 45.455 0.00 0.00 33.92 3.50
4953 5122 5.995282 TCAGTACACCCACTGTTCTAAATTG 59.005 40.000 0.00 0.00 45.11 2.32
4961 5130 5.393461 CCCACTGTTCTAAATTGATTGGAGC 60.393 44.000 0.00 0.00 31.65 4.70
5172 5352 8.661352 AGACAAAACCAAACCTTCAATTAATG 57.339 30.769 0.00 0.00 0.00 1.90
5246 5427 3.582647 TGAAGCTAGTTGTTCAGGGATGA 59.417 43.478 0.00 0.00 0.00 2.92
5393 5575 4.640771 TCCATGTCAGGGCTATAATTCC 57.359 45.455 0.00 0.00 0.00 3.01
5431 5613 5.591099 TCTTTCCAGCTGAAACAAAATGTC 58.409 37.500 17.39 0.00 38.04 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
41 42 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
42 43 7.312154 TCCGAAAATACTTGTCATCAAAATGG 58.688 34.615 0.00 0.00 33.42 3.16
43 44 8.800972 CATCCGAAAATACTTGTCATCAAAATG 58.199 33.333 0.00 0.00 32.87 2.32
44 45 7.975616 CCATCCGAAAATACTTGTCATCAAAAT 59.024 33.333 0.00 0.00 32.87 1.82
45 46 7.175816 TCCATCCGAAAATACTTGTCATCAAAA 59.824 33.333 0.00 0.00 32.87 2.44
46 47 6.657117 TCCATCCGAAAATACTTGTCATCAAA 59.343 34.615 0.00 0.00 32.87 2.69
47 48 6.176896 TCCATCCGAAAATACTTGTCATCAA 58.823 36.000 0.00 0.00 0.00 2.57
48 49 5.739959 TCCATCCGAAAATACTTGTCATCA 58.260 37.500 0.00 0.00 0.00 3.07
49 50 5.237344 CCTCCATCCGAAAATACTTGTCATC 59.763 44.000 0.00 0.00 0.00 2.92
50 51 5.126067 CCTCCATCCGAAAATACTTGTCAT 58.874 41.667 0.00 0.00 0.00 3.06
51 52 4.513442 CCTCCATCCGAAAATACTTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
52 53 3.877508 CCCTCCATCCGAAAATACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
53 54 3.521937 TCCCTCCATCCGAAAATACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
54 55 4.130118 CTCCCTCCATCCGAAAATACTTG 58.870 47.826 0.00 0.00 0.00 3.16
55 56 3.780850 ACTCCCTCCATCCGAAAATACTT 59.219 43.478 0.00 0.00 0.00 2.24
56 57 3.385115 ACTCCCTCCATCCGAAAATACT 58.615 45.455 0.00 0.00 0.00 2.12
57 58 3.840124 ACTCCCTCCATCCGAAAATAC 57.160 47.619 0.00 0.00 0.00 1.89
58 59 8.120538 AGTATATACTCCCTCCATCCGAAAATA 58.879 37.037 9.71 0.00 0.00 1.40
59 60 6.960542 AGTATATACTCCCTCCATCCGAAAAT 59.039 38.462 9.71 0.00 0.00 1.82
60 61 6.320518 AGTATATACTCCCTCCATCCGAAAA 58.679 40.000 9.71 0.00 0.00 2.29
61 62 5.900437 AGTATATACTCCCTCCATCCGAAA 58.100 41.667 9.71 0.00 0.00 3.46
62 63 5.531753 AGTATATACTCCCTCCATCCGAA 57.468 43.478 9.71 0.00 0.00 4.30
63 64 5.531753 AAGTATATACTCCCTCCATCCGA 57.468 43.478 15.72 0.00 34.99 4.55
64 65 6.834451 ACATAAGTATATACTCCCTCCATCCG 59.166 42.308 15.72 0.00 34.99 4.18
65 66 7.070074 CCACATAAGTATATACTCCCTCCATCC 59.930 44.444 15.72 0.00 34.99 3.51
66 67 7.070074 CCCACATAAGTATATACTCCCTCCATC 59.930 44.444 15.72 0.00 34.99 3.51
67 68 6.903534 CCCACATAAGTATATACTCCCTCCAT 59.096 42.308 15.72 1.38 34.99 3.41
68 69 6.047479 TCCCACATAAGTATATACTCCCTCCA 59.953 42.308 15.72 0.00 34.99 3.86
69 70 6.500336 TCCCACATAAGTATATACTCCCTCC 58.500 44.000 15.72 0.00 34.99 4.30
70 71 8.431910 TTTCCCACATAAGTATATACTCCCTC 57.568 38.462 15.72 0.00 34.99 4.30
71 72 8.808240 TTTTCCCACATAAGTATATACTCCCT 57.192 34.615 15.72 3.50 34.99 4.20
130 133 9.546428 AATGGAAGGTCAACTTTATTTCAAAAG 57.454 29.630 0.00 0.00 40.21 2.27
415 448 3.509967 GGAAATACCTTTGGTTCCTGGTG 59.490 47.826 0.00 0.00 37.09 4.17
416 449 3.501568 GGGAAATACCTTTGGTTCCTGGT 60.502 47.826 6.07 0.00 37.09 4.00
417 450 3.096852 GGGAAATACCTTTGGTTCCTGG 58.903 50.000 6.07 0.00 37.09 4.45
418 451 3.763897 CTGGGAAATACCTTTGGTTCCTG 59.236 47.826 6.07 0.00 37.09 3.86
419 452 3.660669 TCTGGGAAATACCTTTGGTTCCT 59.339 43.478 6.07 0.00 37.09 3.36
420 453 4.042271 TCTGGGAAATACCTTTGGTTCC 57.958 45.455 0.00 0.00 37.09 3.62
421 454 5.261216 TGATCTGGGAAATACCTTTGGTTC 58.739 41.667 0.00 0.00 37.09 3.62
422 455 5.269554 TGATCTGGGAAATACCTTTGGTT 57.730 39.130 0.00 0.00 37.09 3.67
423 456 4.946160 TGATCTGGGAAATACCTTTGGT 57.054 40.909 0.00 0.00 40.16 3.67
424 457 5.893255 TGAATGATCTGGGAAATACCTTTGG 59.107 40.000 0.00 0.00 38.98 3.28
425 458 6.183360 GGTGAATGATCTGGGAAATACCTTTG 60.183 42.308 0.00 0.00 38.98 2.77
426 459 5.893824 GGTGAATGATCTGGGAAATACCTTT 59.106 40.000 0.00 0.00 38.98 3.11
427 460 5.449553 GGTGAATGATCTGGGAAATACCTT 58.550 41.667 0.00 0.00 38.98 3.50
428 461 4.444876 CGGTGAATGATCTGGGAAATACCT 60.445 45.833 0.00 0.00 38.98 3.08
545 590 3.127030 GGTTGCGACTTTTCTAATCCTGG 59.873 47.826 3.59 0.00 0.00 4.45
613 658 6.266558 GTGAGGAGTGAGTATCTGGTGATATT 59.733 42.308 0.00 0.00 37.48 1.28
620 665 1.678627 CGGTGAGGAGTGAGTATCTGG 59.321 57.143 0.00 0.00 34.92 3.86
678 723 1.003696 GTGTGGAAGAAGGAGAAGGGG 59.996 57.143 0.00 0.00 0.00 4.79
718 763 3.319198 GTGGGGGTGAGGAAGCGA 61.319 66.667 0.00 0.00 0.00 4.93
719 764 4.410400 GGTGGGGGTGAGGAAGCG 62.410 72.222 0.00 0.00 0.00 4.68
731 776 4.738998 TGCATGGGCGAAGGTGGG 62.739 66.667 0.00 0.00 45.35 4.61
734 779 3.142838 GCATGCATGGGCGAAGGT 61.143 61.111 27.34 0.00 45.35 3.50
850 896 3.304391 GCTAGTGCTAGTGCTAGTGCTAG 60.304 52.174 20.96 20.96 39.56 3.42
851 897 2.619177 GCTAGTGCTAGTGCTAGTGCTA 59.381 50.000 17.75 8.92 40.48 3.49
852 898 1.407258 GCTAGTGCTAGTGCTAGTGCT 59.593 52.381 17.75 8.36 40.48 4.40
853 899 1.135139 TGCTAGTGCTAGTGCTAGTGC 59.865 52.381 17.75 10.20 40.48 4.40
854 900 3.067320 TGATGCTAGTGCTAGTGCTAGTG 59.933 47.826 17.75 2.88 40.48 2.74
855 901 3.291584 TGATGCTAGTGCTAGTGCTAGT 58.708 45.455 17.75 5.58 40.48 2.57
964 1014 4.767409 AGAGAAAAAGAAAGGTATGGTGCC 59.233 41.667 0.00 0.00 0.00 5.01
973 1023 4.449405 GGTGAGACGAGAGAAAAAGAAAGG 59.551 45.833 0.00 0.00 0.00 3.11
990 1042 5.800296 TGAAAATTCAGGATTACGGTGAGA 58.200 37.500 0.00 0.00 32.50 3.27
1030 1082 4.148825 GTGGATGGCTCGCTCGGT 62.149 66.667 0.00 0.00 0.00 4.69
1031 1083 4.899239 GGTGGATGGCTCGCTCGG 62.899 72.222 0.00 0.00 0.00 4.63
1034 1086 4.457496 CACGGTGGATGGCTCGCT 62.457 66.667 0.00 0.00 0.00 4.93
1035 1087 4.451150 TCACGGTGGATGGCTCGC 62.451 66.667 8.50 0.00 0.00 5.03
1049 1101 1.671379 GAAAGTGGAGGGCGGTCAC 60.671 63.158 0.00 0.00 0.00 3.67
1050 1102 2.747686 GAAAGTGGAGGGCGGTCA 59.252 61.111 0.00 0.00 0.00 4.02
1051 1103 2.046217 GGAAAGTGGAGGGCGGTC 60.046 66.667 0.00 0.00 0.00 4.79
1136 1207 1.767681 CTGGAAAGAGATGAGAGGGGG 59.232 57.143 0.00 0.00 0.00 5.40
1137 1208 1.140652 GCTGGAAAGAGATGAGAGGGG 59.859 57.143 0.00 0.00 0.00 4.79
1140 1211 1.136695 AGCGCTGGAAAGAGATGAGAG 59.863 52.381 10.39 0.00 0.00 3.20
1141 1212 1.134877 CAGCGCTGGAAAGAGATGAGA 60.135 52.381 29.88 0.00 0.00 3.27
1143 1214 0.742281 GCAGCGCTGGAAAGAGATGA 60.742 55.000 36.47 0.00 0.00 2.92
1145 1216 1.451028 GGCAGCGCTGGAAAGAGAT 60.451 57.895 36.47 0.00 0.00 2.75
1146 1217 2.046892 GGCAGCGCTGGAAAGAGA 60.047 61.111 36.47 0.00 0.00 3.10
1147 1218 3.494336 CGGCAGCGCTGGAAAGAG 61.494 66.667 36.47 12.02 0.00 2.85
1148 1219 4.314440 ACGGCAGCGCTGGAAAGA 62.314 61.111 36.47 0.00 39.57 2.52
1180 1252 2.357034 GACTCTCCCGCGCAAACA 60.357 61.111 8.75 0.00 0.00 2.83
1191 1263 2.123342 CGCAAAGATCATCGGACTCTC 58.877 52.381 0.00 0.00 0.00 3.20
1301 1373 1.134560 GCTCCGAGTCCGACATTTACT 59.865 52.381 0.40 0.00 38.22 2.24
1302 1374 1.134560 AGCTCCGAGTCCGACATTTAC 59.865 52.381 0.40 0.00 38.22 2.01
1494 1570 0.329261 TGACCTTCCTGGCATCCTTG 59.671 55.000 0.00 0.00 40.22 3.61
1636 1715 3.077519 GCTGCTCCGGGTACGTCAT 62.078 63.158 0.00 0.00 38.78 3.06
1813 1892 3.255379 GAACATCTCCGTCGCCGC 61.255 66.667 0.00 0.00 0.00 6.53
1940 2019 8.814235 CGAGTTCCATGAATAGTAAACGTAATT 58.186 33.333 0.00 0.00 0.00 1.40
1942 2021 6.254157 GCGAGTTCCATGAATAGTAAACGTAA 59.746 38.462 0.00 0.00 0.00 3.18
1945 2024 4.804139 AGCGAGTTCCATGAATAGTAAACG 59.196 41.667 0.00 0.00 0.00 3.60
1946 2025 6.019479 CAGAGCGAGTTCCATGAATAGTAAAC 60.019 42.308 0.00 0.00 0.00 2.01
1947 2026 6.042777 CAGAGCGAGTTCCATGAATAGTAAA 58.957 40.000 0.00 0.00 0.00 2.01
1976 2055 7.606456 AGATGACAATGTCAAGTTACCGTAAAT 59.394 33.333 20.64 0.00 45.96 1.40
1982 2061 4.330074 CCGAGATGACAATGTCAAGTTACC 59.670 45.833 20.64 5.95 45.96 2.85
1992 2071 3.302935 CGCTTTCATCCGAGATGACAATG 60.303 47.826 13.90 6.60 0.00 2.82
2048 2127 4.330620 CCATAGCCAATGCAATTCACAAAC 59.669 41.667 0.00 0.00 41.13 2.93
2132 2217 4.141846 CCGGCACATATAGAGGCTATTCAT 60.142 45.833 0.00 0.00 0.00 2.57
2137 2222 2.597578 TCCGGCACATATAGAGGCTA 57.402 50.000 0.00 0.00 0.00 3.93
2174 2280 6.370718 CCAGTACACTAATTACTGAACCCAAC 59.629 42.308 10.43 0.00 46.44 3.77
2177 2283 6.046290 ACCAGTACACTAATTACTGAACCC 57.954 41.667 10.43 0.00 46.44 4.11
2190 2296 8.387813 TGAAATATAAGGGAAAACCAGTACACT 58.612 33.333 0.00 0.00 43.89 3.55
2191 2297 8.570068 TGAAATATAAGGGAAAACCAGTACAC 57.430 34.615 0.00 0.00 43.89 2.90
2192 2298 7.832187 CCTGAAATATAAGGGAAAACCAGTACA 59.168 37.037 0.00 0.00 43.89 2.90
2193 2299 7.832685 ACCTGAAATATAAGGGAAAACCAGTAC 59.167 37.037 4.53 0.00 43.89 2.73
2194 2300 7.935405 ACCTGAAATATAAGGGAAAACCAGTA 58.065 34.615 4.53 0.00 43.89 2.74
2195 2301 6.800890 ACCTGAAATATAAGGGAAAACCAGT 58.199 36.000 4.53 0.00 43.89 4.00
2196 2302 8.850156 CATACCTGAAATATAAGGGAAAACCAG 58.150 37.037 4.53 0.00 43.89 4.00
2197 2303 8.340757 ACATACCTGAAATATAAGGGAAAACCA 58.659 33.333 4.53 0.00 43.89 3.67
2198 2304 8.762481 ACATACCTGAAATATAAGGGAAAACC 57.238 34.615 4.53 0.00 37.94 3.27
2200 2306 9.116067 CGAACATACCTGAAATATAAGGGAAAA 57.884 33.333 4.53 0.00 37.94 2.29
2201 2307 8.269317 ACGAACATACCTGAAATATAAGGGAAA 58.731 33.333 0.00 0.00 37.94 3.13
2202 2308 7.798071 ACGAACATACCTGAAATATAAGGGAA 58.202 34.615 0.00 0.00 37.94 3.97
2203 2309 7.369551 ACGAACATACCTGAAATATAAGGGA 57.630 36.000 0.00 0.00 37.94 4.20
2204 2310 7.331193 GCTACGAACATACCTGAAATATAAGGG 59.669 40.741 0.00 0.00 37.94 3.95
2205 2311 7.331193 GGCTACGAACATACCTGAAATATAAGG 59.669 40.741 0.00 0.00 39.65 2.69
2206 2312 7.870954 TGGCTACGAACATACCTGAAATATAAG 59.129 37.037 0.00 0.00 0.00 1.73
2207 2313 7.728148 TGGCTACGAACATACCTGAAATATAA 58.272 34.615 0.00 0.00 0.00 0.98
2208 2314 7.014905 ACTGGCTACGAACATACCTGAAATATA 59.985 37.037 0.00 0.00 0.00 0.86
2209 2315 6.169557 TGGCTACGAACATACCTGAAATAT 57.830 37.500 0.00 0.00 0.00 1.28
2210 2316 5.128171 ACTGGCTACGAACATACCTGAAATA 59.872 40.000 0.00 0.00 0.00 1.40
2241 2347 6.780706 AGTGTACCTCAATTAAAACTCACG 57.219 37.500 0.00 0.00 0.00 4.35
2245 2351 8.918202 TGATGAAGTGTACCTCAATTAAAACT 57.082 30.769 0.00 0.00 34.40 2.66
2259 2365 2.905075 CCAGGCGATTGATGAAGTGTA 58.095 47.619 0.00 0.00 0.00 2.90
2262 2368 0.254178 AGCCAGGCGATTGATGAAGT 59.746 50.000 5.55 0.00 0.00 3.01
2265 2371 0.179065 CTGAGCCAGGCGATTGATGA 60.179 55.000 5.55 0.00 0.00 2.92
2325 2448 2.622903 TAAAGAGCACGATCCGGCCG 62.623 60.000 21.04 21.04 0.00 6.13
2326 2449 0.876342 CTAAAGAGCACGATCCGGCC 60.876 60.000 0.00 0.00 0.00 6.13
2327 2450 2.594541 CTAAAGAGCACGATCCGGC 58.405 57.895 0.00 0.00 0.00 6.13
2338 2461 0.526524 CTCACCGGCGAGCTAAAGAG 60.527 60.000 9.30 0.63 0.00 2.85
2339 2462 0.963856 TCTCACCGGCGAGCTAAAGA 60.964 55.000 14.87 0.00 32.75 2.52
2340 2463 0.802607 GTCTCACCGGCGAGCTAAAG 60.803 60.000 14.87 0.00 32.75 1.85
2341 2464 1.214589 GTCTCACCGGCGAGCTAAA 59.785 57.895 14.87 0.00 32.75 1.85
2342 2465 1.974875 TGTCTCACCGGCGAGCTAA 60.975 57.895 14.87 0.00 32.75 3.09
2343 2466 2.360726 TGTCTCACCGGCGAGCTA 60.361 61.111 14.87 3.13 32.75 3.32
2344 2467 4.057428 GTGTCTCACCGGCGAGCT 62.057 66.667 14.87 0.00 32.75 4.09
2353 2476 1.140816 GAAGTTGCTCGGTGTCTCAC 58.859 55.000 0.00 0.00 0.00 3.51
2354 2477 0.033504 GGAAGTTGCTCGGTGTCTCA 59.966 55.000 0.00 0.00 0.00 3.27
2355 2478 1.009389 CGGAAGTTGCTCGGTGTCTC 61.009 60.000 0.00 0.00 0.00 3.36
2356 2479 1.006102 CGGAAGTTGCTCGGTGTCT 60.006 57.895 0.00 0.00 0.00 3.41
2357 2480 1.006571 TCGGAAGTTGCTCGGTGTC 60.007 57.895 0.00 0.00 0.00 3.67
2358 2481 1.006102 CTCGGAAGTTGCTCGGTGT 60.006 57.895 0.00 0.00 0.00 4.16
2359 2482 1.738099 CCTCGGAAGTTGCTCGGTG 60.738 63.158 0.00 0.00 0.00 4.94
2360 2483 2.657237 CCTCGGAAGTTGCTCGGT 59.343 61.111 0.00 0.00 0.00 4.69
2361 2484 2.815647 GCCTCGGAAGTTGCTCGG 60.816 66.667 0.00 0.00 0.00 4.63
2362 2485 1.807573 GAGCCTCGGAAGTTGCTCG 60.808 63.158 0.00 0.00 42.43 5.03
2363 2486 1.807573 CGAGCCTCGGAAGTTGCTC 60.808 63.158 6.13 0.00 45.48 4.26
2364 2487 2.262915 CGAGCCTCGGAAGTTGCT 59.737 61.111 6.13 0.00 40.58 3.91
2365 2488 3.491652 GCGAGCCTCGGAAGTTGC 61.492 66.667 16.95 0.00 40.84 4.17
2366 2489 2.815647 GGCGAGCCTCGGAAGTTG 60.816 66.667 16.95 0.00 40.84 3.16
2367 2490 4.436998 CGGCGAGCCTCGGAAGTT 62.437 66.667 16.95 0.00 40.84 2.66
2446 2569 1.065926 AGATGAACGCAATCCAGCAGA 60.066 47.619 0.00 0.00 0.00 4.26
2467 2590 3.695606 GCACCAGAGCCGACCAGA 61.696 66.667 0.00 0.00 0.00 3.86
2511 2634 1.553704 GATTTCCCTGACGTGTACCCT 59.446 52.381 0.00 0.00 0.00 4.34
2512 2635 1.738030 CGATTTCCCTGACGTGTACCC 60.738 57.143 0.00 0.00 0.00 3.69
2513 2636 1.636988 CGATTTCCCTGACGTGTACC 58.363 55.000 0.00 0.00 0.00 3.34
2514 2637 1.636988 CCGATTTCCCTGACGTGTAC 58.363 55.000 0.00 0.00 0.00 2.90
2515 2638 0.108520 GCCGATTTCCCTGACGTGTA 60.109 55.000 0.00 0.00 0.00 2.90
2516 2639 1.375523 GCCGATTTCCCTGACGTGT 60.376 57.895 0.00 0.00 0.00 4.49
2517 2640 1.079127 AGCCGATTTCCCTGACGTG 60.079 57.895 0.00 0.00 0.00 4.49
2518 2641 1.079127 CAGCCGATTTCCCTGACGT 60.079 57.895 0.00 0.00 0.00 4.34
2519 2642 1.815421 CCAGCCGATTTCCCTGACG 60.815 63.158 0.00 0.00 0.00 4.35
2520 2643 1.452108 CCCAGCCGATTTCCCTGAC 60.452 63.158 0.00 0.00 0.00 3.51
2521 2644 1.615124 TCCCAGCCGATTTCCCTGA 60.615 57.895 0.00 0.00 0.00 3.86
2522 2645 1.153086 CTCCCAGCCGATTTCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
2523 2646 2.378634 CCTCCCAGCCGATTTCCCT 61.379 63.158 0.00 0.00 0.00 4.20
2524 2647 2.193248 CCTCCCAGCCGATTTCCC 59.807 66.667 0.00 0.00 0.00 3.97
2525 2648 1.147153 CTCCTCCCAGCCGATTTCC 59.853 63.158 0.00 0.00 0.00 3.13
2526 2649 1.120530 TACTCCTCCCAGCCGATTTC 58.879 55.000 0.00 0.00 0.00 2.17
2527 2650 1.486726 CTTACTCCTCCCAGCCGATTT 59.513 52.381 0.00 0.00 0.00 2.17
2528 2651 1.123928 CTTACTCCTCCCAGCCGATT 58.876 55.000 0.00 0.00 0.00 3.34
2556 2679 0.469331 TCTCACTTCCACCACCTCGT 60.469 55.000 0.00 0.00 0.00 4.18
2567 2690 2.089349 GCGGTGCGTCTCTCACTTC 61.089 63.158 0.00 0.00 34.97 3.01
2568 2691 2.049063 GCGGTGCGTCTCTCACTT 60.049 61.111 0.00 0.00 34.97 3.16
2571 2694 2.355837 GTTGCGGTGCGTCTCTCA 60.356 61.111 0.00 0.00 0.00 3.27
2605 2728 6.399743 CCCTTGTCATCATATCTCTCTCATG 58.600 44.000 0.00 0.00 0.00 3.07
2629 2756 2.486191 CCTCTCTCTCTCTCTCTCCTGC 60.486 59.091 0.00 0.00 0.00 4.85
2633 2760 3.309296 TCTCCCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
2634 2761 3.051803 TCTCTCCCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
2636 2763 3.051803 TCTCTCTCCCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
2637 2764 3.309296 TCTCTCTCCCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
2647 2774 2.887152 GCAATCTCTCTCTCTCTCCCTC 59.113 54.545 0.00 0.00 0.00 4.30
2649 2776 1.963515 GGCAATCTCTCTCTCTCTCCC 59.036 57.143 0.00 0.00 0.00 4.30
2650 2777 2.624838 CTGGCAATCTCTCTCTCTCTCC 59.375 54.545 0.00 0.00 0.00 3.71
2652 2779 2.024080 ACCTGGCAATCTCTCTCTCTCT 60.024 50.000 0.00 0.00 0.00 3.10
2653 2780 2.101249 CACCTGGCAATCTCTCTCTCTC 59.899 54.545 0.00 0.00 0.00 3.20
2656 2783 1.554160 CACACCTGGCAATCTCTCTCT 59.446 52.381 0.00 0.00 0.00 3.10
2657 2784 2.011046 GCACACCTGGCAATCTCTCTC 61.011 57.143 0.00 0.00 0.00 3.20
2658 2785 0.035630 GCACACCTGGCAATCTCTCT 60.036 55.000 0.00 0.00 0.00 3.10
2659 2786 1.364626 CGCACACCTGGCAATCTCTC 61.365 60.000 0.00 0.00 0.00 3.20
2660 2787 1.376424 CGCACACCTGGCAATCTCT 60.376 57.895 0.00 0.00 0.00 3.10
2661 2788 0.745845 ATCGCACACCTGGCAATCTC 60.746 55.000 0.00 0.00 0.00 2.75
2662 2789 1.028330 CATCGCACACCTGGCAATCT 61.028 55.000 0.00 0.00 0.00 2.40
2663 2790 1.026182 TCATCGCACACCTGGCAATC 61.026 55.000 0.00 0.00 0.00 2.67
2664 2791 1.002257 TCATCGCACACCTGGCAAT 60.002 52.632 0.00 0.00 0.00 3.56
2665 2792 1.965930 GTCATCGCACACCTGGCAA 60.966 57.895 0.00 0.00 0.00 4.52
2689 2816 2.622436 GTATCTGTGCTGACTGGGTTC 58.378 52.381 0.00 0.00 0.00 3.62
2696 2823 1.394917 CAAAGCGGTATCTGTGCTGAC 59.605 52.381 0.00 0.00 39.30 3.51
2742 2875 5.359576 ACTTGCACTTCAACTTATCAAACCA 59.640 36.000 0.00 0.00 0.00 3.67
2748 2881 5.461526 GGGAAACTTGCACTTCAACTTATC 58.538 41.667 0.00 0.00 0.00 1.75
2750 2883 3.314080 CGGGAAACTTGCACTTCAACTTA 59.686 43.478 0.00 0.00 0.00 2.24
2783 2916 6.095720 TCGACAAGTTAATGTTTTGTCCCTTT 59.904 34.615 10.05 0.00 44.79 3.11
2810 2943 5.622770 AACCTATTTTTAGTCGCCAACTG 57.377 39.130 0.00 0.00 39.11 3.16
2816 2949 7.360575 TGAAGAGAAACCTATTTTTAGTCGC 57.639 36.000 0.00 0.00 0.00 5.19
2853 2987 3.086282 TCCAAGCCGGTCCTAAAAATTC 58.914 45.455 1.90 0.00 35.57 2.17
2855 2989 2.891191 TCCAAGCCGGTCCTAAAAAT 57.109 45.000 1.90 0.00 35.57 1.82
2886 3020 7.538303 ACAAGTCATGAAAACAAAAATCCAC 57.462 32.000 0.00 0.00 0.00 4.02
2888 3022 8.764287 CCTAACAAGTCATGAAAACAAAAATCC 58.236 33.333 0.00 0.00 0.00 3.01
2890 3024 7.714813 CCCCTAACAAGTCATGAAAACAAAAAT 59.285 33.333 0.00 0.00 0.00 1.82
2891 3025 7.044798 CCCCTAACAAGTCATGAAAACAAAAA 58.955 34.615 0.00 0.00 0.00 1.94
2902 3057 0.625849 CCTGCCCCCTAACAAGTCAT 59.374 55.000 0.00 0.00 0.00 3.06
3008 3167 4.282496 ACGAGACAATACCTCTGATTCCT 58.718 43.478 0.00 0.00 0.00 3.36
3028 3187 3.279950 GAATAATGCGCACACACATACG 58.720 45.455 14.90 0.00 0.00 3.06
3036 3195 3.462982 AGGTAATCGAATAATGCGCACA 58.537 40.909 14.90 3.44 0.00 4.57
3041 3200 4.320494 CCCAGCAAGGTAATCGAATAATGC 60.320 45.833 0.00 0.00 34.66 3.56
3049 3208 5.209818 TCTATAACCCAGCAAGGTAATCG 57.790 43.478 0.00 0.00 40.05 3.34
3082 3241 4.870363 AGCAACATTTACATCACCACAAC 58.130 39.130 0.00 0.00 0.00 3.32
3176 3339 1.633432 CTTACAGGTCCAACATCCCCA 59.367 52.381 0.00 0.00 0.00 4.96
3213 3376 7.836685 TGTCCCTAGTATGATCTTCATCCTATC 59.163 40.741 0.00 0.00 38.26 2.08
3251 3414 2.113860 TATCCAAGCTGAGCAACACC 57.886 50.000 7.39 0.00 0.00 4.16
3289 3452 7.094805 TGAGATGTTTACATGACTAGGCAAAAC 60.095 37.037 14.85 14.85 36.57 2.43
3303 3466 7.477144 CACTACAAAGTGTGAGATGTTTACA 57.523 36.000 0.00 0.00 46.76 2.41
3767 3930 5.915196 GCAGCTAACAAGTTCCAGTAAAAAG 59.085 40.000 0.00 0.00 0.00 2.27
3984 4150 4.142447 ACTTCAAGCATGTGAATGATCTGC 60.142 41.667 0.00 0.00 36.92 4.26
4076 4242 7.491372 GTCTTTACGATTGTGAATGTCCAGATA 59.509 37.037 0.00 0.00 0.00 1.98
4229 4395 1.996291 TGGTCATGGTCCCCAATGTTA 59.004 47.619 0.00 0.00 36.95 2.41
4234 4400 1.071314 AGGTTGGTCATGGTCCCCAA 61.071 55.000 0.00 0.00 36.95 4.12
4281 4450 7.116662 CACATGATTTGGTAACTGAACAAATGG 59.883 37.037 5.34 0.00 42.84 3.16
4522 4691 3.318557 CCAGTTTTTAACCAAAGGCCGTA 59.681 43.478 0.00 0.00 0.00 4.02
4599 4768 9.052759 TGGTATTGTCTTAAGTCAAACTTCTTC 57.947 33.333 17.11 1.55 39.51 2.87
4629 4798 5.278957 CCCCACAGTTCCAAATTAAGTGAAG 60.279 44.000 2.05 0.00 32.66 3.02
4683 4852 3.181476 ACAACCAGCTTCACATTTTGGTC 60.181 43.478 0.00 0.00 41.08 4.02
4748 4917 2.750166 TGTTCGAACAAGAAGGCAACAA 59.250 40.909 27.94 0.00 35.67 2.83
4764 4933 2.350772 GCCAAAGTTCCTCACATGTTCG 60.351 50.000 0.00 0.00 0.00 3.95
4813 4982 2.750712 GGTTATTTGTACACGGGCACAT 59.249 45.455 0.00 0.00 0.00 3.21
4835 5004 6.882140 TGCCCTTCAAACGAGAAATATCTTAA 59.118 34.615 0.00 0.00 35.54 1.85
4953 5122 6.338214 TCTGACATATCTACAGCTCCAATC 57.662 41.667 0.00 0.00 0.00 2.67
4961 5130 8.867935 CAAGTTTGACTTCTGACATATCTACAG 58.132 37.037 0.00 0.00 36.03 2.74
5172 5352 2.620627 CCAAGTACTCCCCCATTTCCAC 60.621 54.545 0.00 0.00 0.00 4.02
5218 5399 5.335191 CCCTGAACAACTAGCTTCACATTTC 60.335 44.000 0.00 0.00 0.00 2.17
5246 5427 8.095169 GGAAAATACCGGATTAGATGTAGATGT 58.905 37.037 9.46 0.00 0.00 3.06
5393 5575 3.381272 TGGAAAGAGCTTTTGTGTTCTGG 59.619 43.478 0.00 0.00 32.11 3.86
5431 5613 1.065551 TCGGTCACGACATATCAGCTG 59.934 52.381 7.63 7.63 45.59 4.24


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

AutoCloner maintained by Alex Coulton.