Multiple sequence alignment - TraesCS1D01G110800

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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 TraesCS1D01G110800 chr1D 100.000 2555 0 0 1 2555 105952556 105950002 0.000000e+00 4719.0
1 TraesCS1D01G110800 chr1D 95.089 1344 58 3 357 1700 41893638 41894973 0.000000e+00 2109.0
2 TraesCS1D01G110800 chr1D 89.564 1102 65 26 651 1727 470157376 470156300 0.000000e+00 1352.0
3 TraesCS1D01G110800 chr1D 94.140 529 4 3 1728 2232 105341062 105340537 0.000000e+00 780.0
4 TraesCS1D01G110800 chr1D 96.610 354 12 0 5 358 41893137 41893490 2.830000e-164 588.0
5 TraesCS1D01G110800 chr1D 97.391 230 6 0 2003 2232 105920752 105920523 2.380000e-105 392.0
6 TraesCS1D01G110800 chr1D 85.784 204 14 9 2032 2232 105281908 105281717 4.310000e-48 202.0
7 TraesCS1D01G110800 chr1D 95.370 108 2 2 1980 2087 105156683 105156579 4.370000e-38 169.0
8 TraesCS1D01G110800 chr7A 95.976 1342 50 3 357 1698 727211432 727212769 0.000000e+00 2176.0
9 TraesCS1D01G110800 chr7A 96.350 274 9 1 85 358 727211012 727211284 1.390000e-122 449.0
10 TraesCS1D01G110800 chr7A 85.417 240 24 2 2316 2555 714038944 714039172 3.290000e-59 239.0
11 TraesCS1D01G110800 chr7A 87.662 154 15 2 358 507 114998032 114998185 2.610000e-40 176.0
12 TraesCS1D01G110800 chr2B 94.345 1344 57 6 357 1700 789863024 789861700 0.000000e+00 2043.0
13 TraesCS1D01G110800 chr2B 92.387 972 51 10 748 1696 799730783 799731754 0.000000e+00 1363.0
14 TraesCS1D01G110800 chr2B 86.372 1042 118 16 706 1731 246112112 246113145 0.000000e+00 1116.0
15 TraesCS1D01G110800 chr2B 96.721 366 9 3 1 363 789863488 789863123 7.820000e-170 606.0
16 TraesCS1D01G110800 chr2B 85.930 398 47 7 748 1138 658876226 658876621 1.410000e-112 416.0
17 TraesCS1D01G110800 chr2B 85.217 115 14 3 437 551 246111891 246112002 5.780000e-22 115.0
18 TraesCS1D01G110800 chr2A 93.219 988 43 10 357 1321 742042783 742041797 0.000000e+00 1432.0
19 TraesCS1D01G110800 chr2A 93.219 988 43 10 357 1321 742075271 742074285 0.000000e+00 1432.0
20 TraesCS1D01G110800 chr2A 93.219 988 43 10 357 1321 742107353 742106367 0.000000e+00 1432.0
21 TraesCS1D01G110800 chr2A 84.456 1306 139 37 457 1727 20528070 20529346 0.000000e+00 1229.0
22 TraesCS1D01G110800 chr2A 94.693 358 17 1 1 358 742075774 742075419 2.870000e-154 555.0
23 TraesCS1D01G110800 chr2A 94.693 358 17 1 1 358 742107856 742107501 2.870000e-154 555.0
24 TraesCS1D01G110800 chr2A 94.413 358 18 1 1 358 742043286 742042931 1.340000e-152 549.0
25 TraesCS1D01G110800 chr3B 88.900 1027 71 21 748 1741 804853125 804852109 0.000000e+00 1225.0
26 TraesCS1D01G110800 chr3B 88.554 332 33 3 2226 2555 340821143 340820815 5.120000e-107 398.0
27 TraesCS1D01G110800 chr3B 90.417 240 23 0 2316 2555 686566328 686566567 1.480000e-82 316.0
28 TraesCS1D01G110800 chr5B 90.870 920 54 16 835 1728 53740431 53739516 0.000000e+00 1206.0
29 TraesCS1D01G110800 chr4B 86.060 1033 115 17 706 1722 608974303 608975322 0.000000e+00 1083.0
30 TraesCS1D01G110800 chr1B 90.148 406 15 6 1827 2232 161401121 161401501 2.930000e-139 505.0
31 TraesCS1D01G110800 chr1B 86.614 254 25 6 1980 2231 161501335 161501581 3.240000e-69 272.0
32 TraesCS1D01G110800 chr1B 86.614 254 25 6 1980 2231 161553475 161553721 3.240000e-69 272.0
33 TraesCS1D01G110800 chr1B 86.275 255 26 6 1980 2232 161593688 161593935 4.190000e-68 268.0
34 TraesCS1D01G110800 chr3A 91.592 333 18 2 2233 2555 740403703 740403371 3.880000e-123 451.0
35 TraesCS1D01G110800 chr6B 91.561 237 20 0 2319 2555 19360422 19360186 6.820000e-86 327.0
36 TraesCS1D01G110800 chr7B 84.000 175 18 3 357 531 610788191 610788355 2.630000e-35 159.0
37 TraesCS1D01G110800 chr7B 93.976 83 4 1 2236 2317 587964191 587964109 9.600000e-25 124.0
38 TraesCS1D01G110800 chr1A 86.777 121 9 5 1 119 566702014 566702129 7.420000e-26 128.0
39 TraesCS1D01G110800 chr2D 81.818 121 15 5 1 119 586908801 586908916 7.530000e-16 95.3


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 TraesCS1D01G110800 chr1D 105950002 105952556 2554 True 4719.0 4719 100.0000 1 2555 1 chr1D.!!$R5 2554
1 TraesCS1D01G110800 chr1D 470156300 470157376 1076 True 1352.0 1352 89.5640 651 1727 1 chr1D.!!$R6 1076
2 TraesCS1D01G110800 chr1D 41893137 41894973 1836 False 1348.5 2109 95.8495 5 1700 2 chr1D.!!$F1 1695
3 TraesCS1D01G110800 chr1D 105340537 105341062 525 True 780.0 780 94.1400 1728 2232 1 chr1D.!!$R3 504
4 TraesCS1D01G110800 chr7A 727211012 727212769 1757 False 1312.5 2176 96.1630 85 1698 2 chr7A.!!$F3 1613
5 TraesCS1D01G110800 chr2B 799730783 799731754 971 False 1363.0 1363 92.3870 748 1696 1 chr2B.!!$F2 948
6 TraesCS1D01G110800 chr2B 789861700 789863488 1788 True 1324.5 2043 95.5330 1 1700 2 chr2B.!!$R1 1699
7 TraesCS1D01G110800 chr2B 246111891 246113145 1254 False 615.5 1116 85.7945 437 1731 2 chr2B.!!$F3 1294
8 TraesCS1D01G110800 chr2A 20528070 20529346 1276 False 1229.0 1229 84.4560 457 1727 1 chr2A.!!$F1 1270
9 TraesCS1D01G110800 chr2A 742074285 742075774 1489 True 993.5 1432 93.9560 1 1321 2 chr2A.!!$R2 1320
10 TraesCS1D01G110800 chr2A 742106367 742107856 1489 True 993.5 1432 93.9560 1 1321 2 chr2A.!!$R3 1320
11 TraesCS1D01G110800 chr2A 742041797 742043286 1489 True 990.5 1432 93.8160 1 1321 2 chr2A.!!$R1 1320
12 TraesCS1D01G110800 chr3B 804852109 804853125 1016 True 1225.0 1225 88.9000 748 1741 1 chr3B.!!$R2 993
13 TraesCS1D01G110800 chr5B 53739516 53740431 915 True 1206.0 1206 90.8700 835 1728 1 chr5B.!!$R1 893
14 TraesCS1D01G110800 chr4B 608974303 608975322 1019 False 1083.0 1083 86.0600 706 1722 1 chr4B.!!$F1 1016

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
853 1072 0.250124 ACCGACACTTCATCGCCAAA 60.25 50.0 0.0 0.0 38.27 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2588 0.036765 TTGACCCGACTGATTTCCCG 60.037 55.0 0.0 0.0 0.0 5.14 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
83 84 6.018433 AGATTAATTTCCTGTAGCCACCAT 57.982 37.500 0.00 0.00 0.00 3.55
101 102 5.203528 CACCATCAATAAATCCCTCAACCT 58.796 41.667 0.00 0.00 0.00 3.50
122 123 6.059484 ACCTTCAAATTCGGTGAGAAAGTTA 58.941 36.000 0.00 0.00 42.91 2.24
440 593 4.677779 GCATCAAGCCCACAAATTACGATT 60.678 41.667 0.00 0.00 37.23 3.34
717 922 2.281070 CTGTTCACACGCCAGGCT 60.281 61.111 10.54 0.00 0.00 4.58
765 971 1.852942 GACTTCTTCAGCACGACACA 58.147 50.000 0.00 0.00 0.00 3.72
853 1072 0.250124 ACCGACACTTCATCGCCAAA 60.250 50.000 0.00 0.00 38.27 3.28
890 1112 2.673368 GTCTTCACCAACATCATCGTCC 59.327 50.000 0.00 0.00 0.00 4.79
1140 1411 1.608717 GACGGCACCCTCTGACATCT 61.609 60.000 0.00 0.00 0.00 2.90
1355 1642 1.962822 TCGTCACTAGCGTCCACGT 60.963 57.895 0.36 0.00 42.22 4.49
1364 1651 2.333938 CGTCCACGTCACTTCCGT 59.666 61.111 0.00 0.00 39.52 4.69
1516 1803 4.523173 AGACTTCAAATCCAGTCGTACTCA 59.477 41.667 0.00 0.00 43.69 3.41
1760 2060 5.759059 TGCTCCCTCAAACATTTCATATCT 58.241 37.500 0.00 0.00 0.00 1.98
1763 2063 5.508567 TCCCTCAAACATTTCATATCTGCA 58.491 37.500 0.00 0.00 0.00 4.41
1897 2221 2.823829 GCGTAATTGCTGGCCGGAG 61.824 63.158 18.31 0.00 0.00 4.63
2002 2326 2.550978 GCTTATACACACAGCGGATGT 58.449 47.619 0.00 0.00 45.43 3.06
2205 2529 3.322828 GGATAATACTACAAGGTCCGGCA 59.677 47.826 0.00 0.00 0.00 5.69
2213 2537 1.146263 AAGGTCCGGCATTCGATCC 59.854 57.895 0.00 0.00 42.43 3.36
2232 2556 5.661458 GATCCCTGGACCGTGTATTATATG 58.339 45.833 0.00 0.00 0.00 1.78
2233 2557 3.835978 TCCCTGGACCGTGTATTATATGG 59.164 47.826 0.00 0.00 0.00 2.74
2234 2558 3.596214 CCTGGACCGTGTATTATATGGC 58.404 50.000 0.00 0.00 0.00 4.40
2235 2559 3.250744 CTGGACCGTGTATTATATGGCG 58.749 50.000 0.00 0.00 0.00 5.69
2236 2560 1.997606 GGACCGTGTATTATATGGCGC 59.002 52.381 0.00 0.00 0.00 6.53
2237 2561 1.652124 GACCGTGTATTATATGGCGCG 59.348 52.381 0.00 0.00 35.04 6.86
2238 2562 1.000060 ACCGTGTATTATATGGCGCGT 60.000 47.619 8.43 0.00 33.66 6.01
2239 2563 1.388768 CCGTGTATTATATGGCGCGTG 59.611 52.381 8.43 0.00 33.66 5.34
2240 2564 1.201769 CGTGTATTATATGGCGCGTGC 60.202 52.381 13.78 13.78 41.71 5.34
2241 2565 2.066262 GTGTATTATATGGCGCGTGCT 58.934 47.619 21.89 4.17 42.25 4.40
2242 2566 3.247442 GTGTATTATATGGCGCGTGCTA 58.753 45.455 21.89 16.44 42.25 3.49
2243 2567 3.303495 GTGTATTATATGGCGCGTGCTAG 59.697 47.826 21.89 0.00 42.25 3.42
2244 2568 2.010145 ATTATATGGCGCGTGCTAGG 57.990 50.000 21.89 0.00 42.25 3.02
2245 2569 0.037697 TTATATGGCGCGTGCTAGGG 60.038 55.000 21.89 0.00 42.25 3.53
2246 2570 0.896479 TATATGGCGCGTGCTAGGGA 60.896 55.000 21.89 4.82 42.25 4.20
2247 2571 1.544825 ATATGGCGCGTGCTAGGGAT 61.545 55.000 21.89 7.10 42.25 3.85
2248 2572 2.154798 TATGGCGCGTGCTAGGGATC 62.155 60.000 21.89 2.27 42.25 3.36
2249 2573 4.221422 GGCGCGTGCTAGGGATCA 62.221 66.667 21.89 0.00 42.25 2.92
2250 2574 2.202878 GCGCGTGCTAGGGATCAA 60.203 61.111 15.02 0.00 38.39 2.57
2251 2575 2.526120 GCGCGTGCTAGGGATCAAC 61.526 63.158 15.02 0.00 38.39 3.18
2252 2576 1.883084 CGCGTGCTAGGGATCAACC 60.883 63.158 0.00 0.00 38.08 3.77
2253 2577 1.883084 GCGTGCTAGGGATCAACCG 60.883 63.158 0.00 0.00 40.11 4.44
2254 2578 1.813859 CGTGCTAGGGATCAACCGA 59.186 57.895 0.00 0.00 40.11 4.69
2255 2579 0.527817 CGTGCTAGGGATCAACCGAC 60.528 60.000 0.00 0.00 40.11 4.79
2256 2580 0.824759 GTGCTAGGGATCAACCGACT 59.175 55.000 0.00 0.00 40.11 4.18
2257 2581 0.824109 TGCTAGGGATCAACCGACTG 59.176 55.000 0.00 0.00 40.11 3.51
2258 2582 1.112113 GCTAGGGATCAACCGACTGA 58.888 55.000 0.00 0.00 40.11 3.41
2259 2583 1.689273 GCTAGGGATCAACCGACTGAT 59.311 52.381 0.00 0.00 38.79 2.90
2260 2584 2.103263 GCTAGGGATCAACCGACTGATT 59.897 50.000 0.00 0.00 36.15 2.57
2261 2585 3.432326 GCTAGGGATCAACCGACTGATTT 60.432 47.826 0.00 0.00 36.15 2.17
2262 2586 3.268023 AGGGATCAACCGACTGATTTC 57.732 47.619 0.00 0.00 36.15 2.17
2263 2587 2.840651 AGGGATCAACCGACTGATTTCT 59.159 45.455 0.00 0.84 36.15 2.52
2264 2588 3.118592 AGGGATCAACCGACTGATTTCTC 60.119 47.826 0.00 0.00 36.15 2.87
2265 2589 2.860735 GGATCAACCGACTGATTTCTCG 59.139 50.000 0.00 0.00 36.15 4.04
2270 2594 2.380084 CCGACTGATTTCTCGGGAAA 57.620 50.000 13.89 13.89 44.84 3.13
2278 2602 2.380084 TTTCTCGGGAAATCAGTCGG 57.620 50.000 6.31 0.00 36.63 4.79
2279 2603 0.535335 TTCTCGGGAAATCAGTCGGG 59.465 55.000 0.00 0.00 0.00 5.14
2280 2604 0.613853 TCTCGGGAAATCAGTCGGGT 60.614 55.000 0.00 0.00 0.00 5.28
2281 2605 0.179108 CTCGGGAAATCAGTCGGGTC 60.179 60.000 0.00 0.00 0.00 4.46
2282 2606 0.901114 TCGGGAAATCAGTCGGGTCA 60.901 55.000 0.00 0.00 0.00 4.02
2283 2607 0.036765 CGGGAAATCAGTCGGGTCAA 60.037 55.000 0.00 0.00 0.00 3.18
2284 2608 1.406887 CGGGAAATCAGTCGGGTCAAT 60.407 52.381 0.00 0.00 0.00 2.57
2285 2609 2.017049 GGGAAATCAGTCGGGTCAATG 58.983 52.381 0.00 0.00 0.00 2.82
2286 2610 2.355716 GGGAAATCAGTCGGGTCAATGA 60.356 50.000 0.00 0.00 0.00 2.57
2287 2611 2.678336 GGAAATCAGTCGGGTCAATGAC 59.322 50.000 4.51 4.51 35.33 3.06
2296 2620 3.453559 GGTCAATGACCGTCCGATT 57.546 52.632 17.46 0.00 43.14 3.34
2297 2621 1.734163 GGTCAATGACCGTCCGATTT 58.266 50.000 17.46 0.00 43.14 2.17
2298 2622 2.081462 GGTCAATGACCGTCCGATTTT 58.919 47.619 17.46 0.00 43.14 1.82
2299 2623 2.159572 GGTCAATGACCGTCCGATTTTG 60.160 50.000 17.46 0.00 43.14 2.44
2300 2624 2.739913 GTCAATGACCGTCCGATTTTGA 59.260 45.455 1.10 0.00 0.00 2.69
2301 2625 3.374058 GTCAATGACCGTCCGATTTTGAT 59.626 43.478 1.10 0.00 0.00 2.57
2302 2626 4.569162 GTCAATGACCGTCCGATTTTGATA 59.431 41.667 1.10 0.00 0.00 2.15
2303 2627 5.236478 GTCAATGACCGTCCGATTTTGATAT 59.764 40.000 1.10 0.00 0.00 1.63
2304 2628 5.465390 TCAATGACCGTCCGATTTTGATATC 59.535 40.000 0.00 0.00 0.00 1.63
2305 2629 4.665833 TGACCGTCCGATTTTGATATCT 57.334 40.909 3.98 0.00 0.00 1.98
2306 2630 4.368315 TGACCGTCCGATTTTGATATCTG 58.632 43.478 3.98 0.00 0.00 2.90
2307 2631 3.131396 ACCGTCCGATTTTGATATCTGC 58.869 45.455 3.98 0.00 0.00 4.26
2308 2632 3.130633 CCGTCCGATTTTGATATCTGCA 58.869 45.455 3.98 0.00 0.00 4.41
2309 2633 3.748048 CCGTCCGATTTTGATATCTGCAT 59.252 43.478 3.98 0.00 0.00 3.96
2310 2634 4.377738 CCGTCCGATTTTGATATCTGCATG 60.378 45.833 3.98 0.00 0.00 4.06
2311 2635 4.470462 GTCCGATTTTGATATCTGCATGC 58.530 43.478 11.82 11.82 0.00 4.06
2312 2636 4.023792 GTCCGATTTTGATATCTGCATGCA 60.024 41.667 21.29 21.29 0.00 3.96
2313 2637 4.214758 TCCGATTTTGATATCTGCATGCAG 59.785 41.667 36.80 36.80 44.86 4.41
2314 2638 4.023450 CCGATTTTGATATCTGCATGCAGT 60.023 41.667 39.08 29.41 43.96 4.40
2315 2639 5.179929 CCGATTTTGATATCTGCATGCAGTA 59.820 40.000 39.08 30.33 43.96 2.74
2316 2640 6.128090 CCGATTTTGATATCTGCATGCAGTAT 60.128 38.462 39.08 32.71 43.96 2.12
2317 2641 6.741358 CGATTTTGATATCTGCATGCAGTATG 59.259 38.462 39.08 21.05 43.96 2.39
2318 2642 5.952526 TTTGATATCTGCATGCAGTATGG 57.047 39.130 39.08 20.69 43.96 2.74
2319 2643 4.628963 TGATATCTGCATGCAGTATGGT 57.371 40.909 39.08 24.43 43.96 3.55
2320 2644 4.572909 TGATATCTGCATGCAGTATGGTC 58.427 43.478 39.08 29.20 43.96 4.02
2321 2645 4.040706 TGATATCTGCATGCAGTATGGTCA 59.959 41.667 39.08 30.84 43.96 4.02
2322 2646 3.503800 ATCTGCATGCAGTATGGTCAT 57.496 42.857 39.08 24.43 43.96 3.06
2323 2647 3.286329 TCTGCATGCAGTATGGTCATT 57.714 42.857 39.08 0.00 43.96 2.57
2324 2648 2.946990 TCTGCATGCAGTATGGTCATTG 59.053 45.455 39.08 16.70 43.96 2.82
2325 2649 2.025898 TGCATGCAGTATGGTCATTGG 58.974 47.619 18.46 0.00 37.26 3.16
2326 2650 2.300433 GCATGCAGTATGGTCATTGGA 58.700 47.619 14.21 0.00 37.26 3.53
2327 2651 2.889045 GCATGCAGTATGGTCATTGGAT 59.111 45.455 14.21 0.00 37.26 3.41
2328 2652 3.319972 GCATGCAGTATGGTCATTGGATT 59.680 43.478 14.21 0.00 37.26 3.01
2329 2653 4.202182 GCATGCAGTATGGTCATTGGATTT 60.202 41.667 14.21 0.00 37.26 2.17
2330 2654 4.987408 TGCAGTATGGTCATTGGATTTG 57.013 40.909 0.00 0.00 35.86 2.32
2331 2655 3.700539 TGCAGTATGGTCATTGGATTTGG 59.299 43.478 0.00 0.00 35.86 3.28
2332 2656 3.701040 GCAGTATGGTCATTGGATTTGGT 59.299 43.478 0.00 0.00 35.86 3.67
2333 2657 4.202050 GCAGTATGGTCATTGGATTTGGTC 60.202 45.833 0.00 0.00 35.86 4.02
2334 2658 4.949238 CAGTATGGTCATTGGATTTGGTCA 59.051 41.667 0.00 0.00 0.00 4.02
2335 2659 5.418524 CAGTATGGTCATTGGATTTGGTCAA 59.581 40.000 0.00 0.00 0.00 3.18
2336 2660 6.097270 CAGTATGGTCATTGGATTTGGTCAAT 59.903 38.462 0.00 0.00 34.31 2.57
2337 2661 4.804868 TGGTCATTGGATTTGGTCAATG 57.195 40.909 9.08 9.08 46.77 2.82
2338 2662 3.055963 TGGTCATTGGATTTGGTCAATGC 60.056 43.478 10.19 6.56 45.69 3.56
2339 2663 3.055963 GGTCATTGGATTTGGTCAATGCA 60.056 43.478 10.19 0.00 45.69 3.96
2340 2664 3.928375 GTCATTGGATTTGGTCAATGCAC 59.072 43.478 10.19 6.89 42.51 4.57
2341 2665 3.577415 TCATTGGATTTGGTCAATGCACA 59.423 39.130 10.19 0.00 42.51 4.57
2342 2666 4.040095 TCATTGGATTTGGTCAATGCACAA 59.960 37.500 10.19 0.00 42.51 3.33
2343 2667 3.383620 TGGATTTGGTCAATGCACAAC 57.616 42.857 0.00 0.00 38.24 3.32
2344 2668 2.288091 TGGATTTGGTCAATGCACAACG 60.288 45.455 0.00 0.00 38.24 4.10
2345 2669 2.030363 GGATTTGGTCAATGCACAACGA 60.030 45.455 0.00 0.00 33.41 3.85
2346 2670 2.483583 TTTGGTCAATGCACAACGAC 57.516 45.000 0.00 0.00 0.00 4.34
2347 2671 0.306228 TTGGTCAATGCACAACGACG 59.694 50.000 0.00 0.00 0.00 5.12
2348 2672 1.440353 GGTCAATGCACAACGACGC 60.440 57.895 0.00 0.00 0.00 5.19
2349 2673 1.440353 GTCAATGCACAACGACGCC 60.440 57.895 0.00 0.00 0.00 5.68
2350 2674 2.126888 CAATGCACAACGACGCCC 60.127 61.111 0.00 0.00 0.00 6.13
2351 2675 2.281484 AATGCACAACGACGCCCT 60.281 55.556 0.00 0.00 0.00 5.19
2352 2676 2.616330 AATGCACAACGACGCCCTG 61.616 57.895 0.00 0.00 0.00 4.45
2355 2679 2.972505 CACAACGACGCCCTGCTT 60.973 61.111 0.00 0.00 0.00 3.91
2356 2680 2.665185 ACAACGACGCCCTGCTTC 60.665 61.111 0.00 0.00 0.00 3.86
2360 2684 3.479269 CGACGCCCTGCTTCGTTC 61.479 66.667 6.78 0.00 43.50 3.95
2361 2685 3.119096 GACGCCCTGCTTCGTTCC 61.119 66.667 0.00 0.00 39.22 3.62
2362 2686 3.591254 GACGCCCTGCTTCGTTCCT 62.591 63.158 0.00 0.00 39.22 3.36
2363 2687 2.815647 CGCCCTGCTTCGTTCCTC 60.816 66.667 0.00 0.00 0.00 3.71
2364 2688 2.815647 GCCCTGCTTCGTTCCTCG 60.816 66.667 0.00 0.00 41.41 4.63
2365 2689 2.657237 CCCTGCTTCGTTCCTCGT 59.343 61.111 0.00 0.00 40.80 4.18
2366 2690 1.738099 CCCTGCTTCGTTCCTCGTG 60.738 63.158 0.00 0.00 40.80 4.35
2367 2691 2.383527 CCTGCTTCGTTCCTCGTGC 61.384 63.158 0.00 0.00 40.80 5.34
2368 2692 2.357034 TGCTTCGTTCCTCGTGCC 60.357 61.111 0.00 0.00 40.80 5.01
2369 2693 3.479269 GCTTCGTTCCTCGTGCCG 61.479 66.667 0.00 0.00 40.80 5.69
2370 2694 3.479269 CTTCGTTCCTCGTGCCGC 61.479 66.667 0.00 0.00 40.80 6.53
2387 2711 4.799473 CCGCAACGCATGAGCACG 62.799 66.667 0.00 0.00 42.27 5.34
2388 2712 4.799473 CGCAACGCATGAGCACGG 62.799 66.667 0.00 0.00 42.27 4.94
2389 2713 3.422303 GCAACGCATGAGCACGGA 61.422 61.111 0.00 0.00 42.27 4.69
2390 2714 2.780643 CAACGCATGAGCACGGAG 59.219 61.111 0.00 0.00 42.27 4.63
2391 2715 2.434884 AACGCATGAGCACGGAGG 60.435 61.111 0.00 0.00 42.27 4.30
2392 2716 3.240134 AACGCATGAGCACGGAGGT 62.240 57.895 0.00 0.00 42.27 3.85
2393 2717 1.884075 AACGCATGAGCACGGAGGTA 61.884 55.000 0.00 0.00 42.27 3.08
2394 2718 1.589993 CGCATGAGCACGGAGGTAG 60.590 63.158 0.00 0.00 42.27 3.18
2395 2719 1.884926 GCATGAGCACGGAGGTAGC 60.885 63.158 0.00 0.00 41.58 3.58
2396 2720 1.589993 CATGAGCACGGAGGTAGCG 60.590 63.158 0.00 0.00 0.00 4.26
2397 2721 2.052690 ATGAGCACGGAGGTAGCGT 61.053 57.895 0.00 0.00 0.00 5.07
2398 2722 2.005960 ATGAGCACGGAGGTAGCGTC 62.006 60.000 0.00 0.00 0.00 5.19
2399 2723 2.675423 AGCACGGAGGTAGCGTCA 60.675 61.111 0.00 0.00 0.00 4.35
2400 2724 2.506438 GCACGGAGGTAGCGTCAC 60.506 66.667 0.00 0.00 0.00 3.67
2401 2725 2.991076 GCACGGAGGTAGCGTCACT 61.991 63.158 0.00 0.00 0.00 3.41
2402 2726 1.154016 CACGGAGGTAGCGTCACTG 60.154 63.158 0.00 0.00 0.00 3.66
2403 2727 2.202623 CGGAGGTAGCGTCACTGC 60.203 66.667 0.00 0.00 0.00 4.40
2412 2736 3.268603 CGTCACTGCCGCACAACA 61.269 61.111 0.00 0.00 0.00 3.33
2413 2737 2.327940 GTCACTGCCGCACAACAC 59.672 61.111 0.00 0.00 0.00 3.32
2414 2738 2.124942 TCACTGCCGCACAACACA 60.125 55.556 0.00 0.00 0.00 3.72
2415 2739 1.746991 TCACTGCCGCACAACACAA 60.747 52.632 0.00 0.00 0.00 3.33
2416 2740 1.586042 CACTGCCGCACAACACAAC 60.586 57.895 0.00 0.00 0.00 3.32
2417 2741 2.352229 CTGCCGCACAACACAACG 60.352 61.111 0.00 0.00 0.00 4.10
2418 2742 2.818487 CTGCCGCACAACACAACGA 61.818 57.895 0.00 0.00 0.00 3.85
2419 2743 2.052237 GCCGCACAACACAACGAG 60.052 61.111 0.00 0.00 0.00 4.18
2420 2744 2.052237 CCGCACAACACAACGAGC 60.052 61.111 0.00 0.00 0.00 5.03
2421 2745 2.423517 CGCACAACACAACGAGCG 60.424 61.111 0.00 0.00 39.17 5.03
2422 2746 2.722188 GCACAACACAACGAGCGC 60.722 61.111 0.00 0.00 0.00 5.92
2423 2747 2.052237 CACAACACAACGAGCGCC 60.052 61.111 2.29 0.00 0.00 6.53
2424 2748 3.276846 ACAACACAACGAGCGCCC 61.277 61.111 2.29 0.00 0.00 6.13
2425 2749 4.368808 CAACACAACGAGCGCCCG 62.369 66.667 10.67 10.67 0.00 6.13
2467 2791 4.764336 CGCGCCAGCCACAACATG 62.764 66.667 0.00 0.00 41.18 3.21
2478 2802 3.017265 CCACAACATGGTCAAAGCTTC 57.983 47.619 0.00 0.00 44.46 3.86
2479 2803 2.361757 CCACAACATGGTCAAAGCTTCA 59.638 45.455 0.00 0.00 44.46 3.02
2480 2804 3.006110 CCACAACATGGTCAAAGCTTCAT 59.994 43.478 0.00 0.00 44.46 2.57
2481 2805 4.501915 CCACAACATGGTCAAAGCTTCATT 60.502 41.667 0.00 0.00 44.46 2.57
2482 2806 4.446385 CACAACATGGTCAAAGCTTCATTG 59.554 41.667 0.00 0.00 0.00 2.82
2483 2807 3.947910 ACATGGTCAAAGCTTCATTGG 57.052 42.857 0.00 0.00 0.00 3.16
2484 2808 3.499338 ACATGGTCAAAGCTTCATTGGA 58.501 40.909 0.00 0.00 0.00 3.53
2485 2809 3.508793 ACATGGTCAAAGCTTCATTGGAG 59.491 43.478 0.00 0.00 0.00 3.86
2486 2810 1.888512 TGGTCAAAGCTTCATTGGAGC 59.111 47.619 9.05 9.05 0.00 4.70
2487 2811 1.135575 GGTCAAAGCTTCATTGGAGCG 60.136 52.381 11.29 0.00 0.00 5.03
2488 2812 1.537202 GTCAAAGCTTCATTGGAGCGT 59.463 47.619 11.29 5.37 0.00 5.07
2489 2813 1.806542 TCAAAGCTTCATTGGAGCGTC 59.193 47.619 11.29 0.00 0.00 5.19
2490 2814 0.798776 AAAGCTTCATTGGAGCGTCG 59.201 50.000 11.29 0.00 0.00 5.12
2491 2815 1.639298 AAGCTTCATTGGAGCGTCGC 61.639 55.000 9.80 9.80 0.00 5.19
2492 2816 3.093278 CTTCATTGGAGCGTCGCC 58.907 61.111 14.86 5.33 0.00 5.54
2493 2817 2.802667 CTTCATTGGAGCGTCGCCG 61.803 63.158 14.86 0.00 37.07 6.46
2511 2835 4.111016 CCGCGACTAGCCACGACA 62.111 66.667 8.23 0.00 44.76 4.35
2512 2836 2.577112 CGCGACTAGCCACGACAG 60.577 66.667 0.00 0.00 44.76 3.51
2513 2837 2.567049 GCGACTAGCCACGACAGT 59.433 61.111 8.38 0.00 40.81 3.55
2515 2839 1.801913 CGACTAGCCACGACAGTGC 60.802 63.158 0.00 0.00 46.62 4.40
2516 2840 1.446272 GACTAGCCACGACAGTGCC 60.446 63.158 0.00 0.00 46.62 5.01
2517 2841 2.125512 CTAGCCACGACAGTGCCC 60.126 66.667 0.00 0.00 46.62 5.36
2518 2842 2.603473 TAGCCACGACAGTGCCCT 60.603 61.111 0.00 0.00 46.62 5.19
2519 2843 2.564553 CTAGCCACGACAGTGCCCTC 62.565 65.000 0.00 0.00 46.62 4.30
2521 2845 3.314331 CCACGACAGTGCCCTCCT 61.314 66.667 0.00 0.00 46.62 3.69
2522 2846 2.262915 CACGACAGTGCCCTCCTC 59.737 66.667 0.00 0.00 41.94 3.71
2523 2847 3.374402 ACGACAGTGCCCTCCTCG 61.374 66.667 0.00 0.00 0.00 4.63
2524 2848 4.803426 CGACAGTGCCCTCCTCGC 62.803 72.222 0.00 0.00 0.00 5.03
2525 2849 3.695606 GACAGTGCCCTCCTCGCA 61.696 66.667 0.00 0.00 0.00 5.10
2526 2850 3.655810 GACAGTGCCCTCCTCGCAG 62.656 68.421 0.00 0.00 36.78 5.18
2541 2865 3.576004 CAGCACTGCCTCTGAAGC 58.424 61.111 0.00 0.00 32.26 3.86
2542 2866 2.047465 AGCACTGCCTCTGAAGCG 60.047 61.111 0.00 0.00 0.00 4.68
2543 2867 3.797546 GCACTGCCTCTGAAGCGC 61.798 66.667 0.00 0.00 0.00 5.92
2544 2868 3.123620 CACTGCCTCTGAAGCGCC 61.124 66.667 2.29 0.00 0.00 6.53
2545 2869 4.749310 ACTGCCTCTGAAGCGCCG 62.749 66.667 2.29 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 8.434589 AATTTGAAGGTTGAGGGATTTATTGA 57.565 30.769 0.00 0.00 0.00 2.57
101 102 7.504924 ACATAACTTTCTCACCGAATTTGAA 57.495 32.000 0.00 0.00 0.00 2.69
122 123 4.895889 TGATCTGGACGAGGATTTCTACAT 59.104 41.667 0.00 0.00 0.00 2.29
193 197 0.328592 TCTCTGTAGGTGCCGAGACT 59.671 55.000 0.00 0.00 0.00 3.24
285 289 0.742505 ATGGCCAAGTGCATGAATCG 59.257 50.000 10.96 0.00 43.89 3.34
399 552 1.338960 TGCAGATGGTTCAATCGCTCA 60.339 47.619 0.00 0.00 31.65 4.26
440 593 3.904586 TGCAGTGTAGTCGATGCAA 57.095 47.368 6.65 0.00 45.09 4.08
717 922 1.960417 TTGCATCTCGTTTCACACCA 58.040 45.000 0.00 0.00 0.00 4.17
765 971 1.964373 GCGACGGGGTGTTGATGTT 60.964 57.895 0.00 0.00 33.36 2.71
794 1007 2.125512 GATGCGTCGCTTGGAGGT 60.126 61.111 19.50 0.00 33.10 3.85
819 1032 4.107051 GGTGGTGCAGCGACATGC 62.107 66.667 11.91 0.00 46.68 4.06
853 1072 4.999950 GTGAAGACCATGTTGATGAAGACT 59.000 41.667 0.00 0.00 0.00 3.24
890 1112 4.935495 AGGCAGTGGCGGTGTGTG 62.935 66.667 11.51 0.00 42.47 3.82
1140 1411 0.389296 CGTGGACGATACACCTTGCA 60.389 55.000 0.00 0.00 43.02 4.08
1208 1479 0.817654 TCGTCGTGGATGATGAAGCT 59.182 50.000 0.00 0.00 31.14 3.74
1296 1583 1.804151 GTTGTTGCCGATGAGTTGCTA 59.196 47.619 0.00 0.00 0.00 3.49
1364 1651 1.488705 ATTCCCTCCCGCAGTCACAA 61.489 55.000 0.00 0.00 0.00 3.33
1426 1713 1.543896 ATGGGTTGGCACCTAGGGT 60.544 57.895 14.81 0.00 43.65 4.34
1516 1803 1.756950 TAGCGGGAGTGAAGCGGAT 60.757 57.895 0.00 0.00 35.78 4.18
2002 2326 3.321648 ATCGTCCACCTGCAGCCA 61.322 61.111 8.66 0.00 0.00 4.75
2003 2327 2.821366 CATCGTCCACCTGCAGCC 60.821 66.667 8.66 0.00 0.00 4.85
2213 2537 3.596214 GCCATATAATACACGGTCCAGG 58.404 50.000 0.00 0.00 0.00 4.45
2232 2556 3.733344 TTGATCCCTAGCACGCGCC 62.733 63.158 5.73 0.00 39.83 6.53
2233 2557 2.202878 TTGATCCCTAGCACGCGC 60.203 61.111 5.73 0.00 38.99 6.86
2234 2558 1.883084 GGTTGATCCCTAGCACGCG 60.883 63.158 3.53 3.53 0.00 6.01
2235 2559 1.883084 CGGTTGATCCCTAGCACGC 60.883 63.158 0.00 0.00 0.00 5.34
2236 2560 0.527817 GTCGGTTGATCCCTAGCACG 60.528 60.000 0.00 0.00 0.00 5.34
2237 2561 0.824759 AGTCGGTTGATCCCTAGCAC 59.175 55.000 0.00 0.00 0.00 4.40
2238 2562 0.824109 CAGTCGGTTGATCCCTAGCA 59.176 55.000 0.00 0.00 0.00 3.49
2239 2563 1.112113 TCAGTCGGTTGATCCCTAGC 58.888 55.000 0.00 0.00 0.00 3.42
2240 2564 4.100189 AGAAATCAGTCGGTTGATCCCTAG 59.900 45.833 3.58 0.00 36.81 3.02
2241 2565 4.030913 AGAAATCAGTCGGTTGATCCCTA 58.969 43.478 3.58 0.00 36.81 3.53
2242 2566 2.840651 AGAAATCAGTCGGTTGATCCCT 59.159 45.455 3.58 2.32 36.81 4.20
2243 2567 3.198872 GAGAAATCAGTCGGTTGATCCC 58.801 50.000 3.58 0.00 36.81 3.85
2244 2568 2.860735 CGAGAAATCAGTCGGTTGATCC 59.139 50.000 3.58 0.77 36.81 3.36
2259 2583 1.066430 CCCGACTGATTTCCCGAGAAA 60.066 52.381 0.00 0.00 45.78 2.52
2260 2584 0.535335 CCCGACTGATTTCCCGAGAA 59.465 55.000 0.00 0.00 0.00 2.87
2261 2585 0.613853 ACCCGACTGATTTCCCGAGA 60.614 55.000 0.00 0.00 0.00 4.04
2262 2586 0.179108 GACCCGACTGATTTCCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
2263 2587 0.901114 TGACCCGACTGATTTCCCGA 60.901 55.000 0.00 0.00 0.00 5.14
2264 2588 0.036765 TTGACCCGACTGATTTCCCG 60.037 55.000 0.00 0.00 0.00 5.14
2265 2589 2.017049 CATTGACCCGACTGATTTCCC 58.983 52.381 0.00 0.00 0.00 3.97
2266 2590 2.678336 GTCATTGACCCGACTGATTTCC 59.322 50.000 5.44 0.00 0.00 3.13
2267 2591 2.678336 GGTCATTGACCCGACTGATTTC 59.322 50.000 23.00 0.00 46.19 2.17
2268 2592 2.711542 GGTCATTGACCCGACTGATTT 58.288 47.619 23.00 0.00 46.19 2.17
2269 2593 2.403252 GGTCATTGACCCGACTGATT 57.597 50.000 23.00 0.00 46.19 2.57
2279 2603 2.739913 TCAAAATCGGACGGTCATTGAC 59.260 45.455 10.76 8.34 0.00 3.18
2280 2604 3.046968 TCAAAATCGGACGGTCATTGA 57.953 42.857 10.76 8.93 0.00 2.57
2281 2605 5.466728 AGATATCAAAATCGGACGGTCATTG 59.533 40.000 10.76 6.93 0.00 2.82
2282 2606 5.466728 CAGATATCAAAATCGGACGGTCATT 59.533 40.000 10.76 0.00 0.00 2.57
2283 2607 4.991056 CAGATATCAAAATCGGACGGTCAT 59.009 41.667 10.76 0.00 0.00 3.06
2284 2608 4.368315 CAGATATCAAAATCGGACGGTCA 58.632 43.478 10.76 0.00 0.00 4.02
2285 2609 3.184581 GCAGATATCAAAATCGGACGGTC 59.815 47.826 5.32 0.00 0.00 4.79
2286 2610 3.131396 GCAGATATCAAAATCGGACGGT 58.869 45.455 5.32 0.00 0.00 4.83
2287 2611 3.130633 TGCAGATATCAAAATCGGACGG 58.869 45.455 5.32 0.00 0.00 4.79
2288 2612 4.705492 CATGCAGATATCAAAATCGGACG 58.295 43.478 5.32 0.00 0.00 4.79
2289 2613 4.023792 TGCATGCAGATATCAAAATCGGAC 60.024 41.667 18.46 0.00 0.00 4.79
2290 2614 4.136051 TGCATGCAGATATCAAAATCGGA 58.864 39.130 18.46 0.00 0.00 4.55
2291 2615 4.023450 ACTGCATGCAGATATCAAAATCGG 60.023 41.667 45.50 21.09 46.30 4.18
2292 2616 5.104562 ACTGCATGCAGATATCAAAATCG 57.895 39.130 45.50 21.51 46.30 3.34
2293 2617 7.027760 CCATACTGCATGCAGATATCAAAATC 58.972 38.462 45.50 2.37 46.30 2.17
2294 2618 6.492429 ACCATACTGCATGCAGATATCAAAAT 59.508 34.615 45.50 26.24 46.30 1.82
2295 2619 5.829391 ACCATACTGCATGCAGATATCAAAA 59.171 36.000 45.50 22.91 46.30 2.44
2296 2620 5.379187 ACCATACTGCATGCAGATATCAAA 58.621 37.500 45.50 24.10 46.30 2.69
2297 2621 4.976864 ACCATACTGCATGCAGATATCAA 58.023 39.130 45.50 25.59 46.30 2.57
2298 2622 4.040706 TGACCATACTGCATGCAGATATCA 59.959 41.667 45.50 34.00 46.30 2.15
2299 2623 4.572909 TGACCATACTGCATGCAGATATC 58.427 43.478 45.50 32.34 46.30 1.63
2300 2624 4.628963 TGACCATACTGCATGCAGATAT 57.371 40.909 45.50 33.61 46.30 1.63
2301 2625 4.628963 ATGACCATACTGCATGCAGATA 57.371 40.909 45.50 33.10 46.30 1.98
2302 2626 3.503800 ATGACCATACTGCATGCAGAT 57.496 42.857 45.50 31.74 46.30 2.90
2303 2627 2.946990 CAATGACCATACTGCATGCAGA 59.053 45.455 45.50 31.10 46.30 4.26
2305 2629 2.025898 CCAATGACCATACTGCATGCA 58.974 47.619 21.29 21.29 32.84 3.96
2306 2630 2.300433 TCCAATGACCATACTGCATGC 58.700 47.619 11.82 11.82 32.84 4.06
2307 2631 5.286438 CAAATCCAATGACCATACTGCATG 58.714 41.667 0.00 0.00 0.00 4.06
2308 2632 4.342951 CCAAATCCAATGACCATACTGCAT 59.657 41.667 0.00 0.00 0.00 3.96
2309 2633 3.700539 CCAAATCCAATGACCATACTGCA 59.299 43.478 0.00 0.00 0.00 4.41
2310 2634 3.701040 ACCAAATCCAATGACCATACTGC 59.299 43.478 0.00 0.00 0.00 4.40
2311 2635 4.949238 TGACCAAATCCAATGACCATACTG 59.051 41.667 0.00 0.00 0.00 2.74
2312 2636 5.191727 TGACCAAATCCAATGACCATACT 57.808 39.130 0.00 0.00 0.00 2.12
2313 2637 5.913137 TTGACCAAATCCAATGACCATAC 57.087 39.130 0.00 0.00 0.00 2.39
2321 2645 4.317488 GTTGTGCATTGACCAAATCCAAT 58.683 39.130 0.00 0.00 33.66 3.16
2322 2646 3.726607 GTTGTGCATTGACCAAATCCAA 58.273 40.909 0.00 0.00 0.00 3.53
2323 2647 2.288091 CGTTGTGCATTGACCAAATCCA 60.288 45.455 0.00 0.00 0.00 3.41
2324 2648 2.030363 TCGTTGTGCATTGACCAAATCC 60.030 45.455 0.00 0.00 0.00 3.01
2325 2649 2.979813 GTCGTTGTGCATTGACCAAATC 59.020 45.455 0.00 0.00 0.00 2.17
2326 2650 2.604373 CGTCGTTGTGCATTGACCAAAT 60.604 45.455 0.00 0.00 0.00 2.32
2327 2651 1.268285 CGTCGTTGTGCATTGACCAAA 60.268 47.619 0.00 0.00 0.00 3.28
2328 2652 0.306228 CGTCGTTGTGCATTGACCAA 59.694 50.000 0.00 0.00 0.00 3.67
2329 2653 1.938125 CGTCGTTGTGCATTGACCA 59.062 52.632 0.00 0.00 0.00 4.02
2330 2654 1.440353 GCGTCGTTGTGCATTGACC 60.440 57.895 0.00 0.00 0.00 4.02
2331 2655 1.440353 GGCGTCGTTGTGCATTGAC 60.440 57.895 0.00 0.00 0.00 3.18
2332 2656 2.612567 GGGCGTCGTTGTGCATTGA 61.613 57.895 0.00 0.00 0.00 2.57
2333 2657 2.126888 GGGCGTCGTTGTGCATTG 60.127 61.111 0.00 0.00 0.00 2.82
2334 2658 2.281484 AGGGCGTCGTTGTGCATT 60.281 55.556 0.00 0.00 0.00 3.56
2335 2659 3.049674 CAGGGCGTCGTTGTGCAT 61.050 61.111 0.00 0.00 0.00 3.96
2338 2662 2.954753 GAAGCAGGGCGTCGTTGTG 61.955 63.158 0.00 0.00 0.00 3.33
2339 2663 2.665185 GAAGCAGGGCGTCGTTGT 60.665 61.111 0.00 0.00 0.00 3.32
2344 2668 3.119096 GGAACGAAGCAGGGCGTC 61.119 66.667 0.00 0.00 40.23 5.19
2345 2669 3.591254 GAGGAACGAAGCAGGGCGT 62.591 63.158 0.00 0.00 43.39 5.68
2346 2670 2.815647 GAGGAACGAAGCAGGGCG 60.816 66.667 0.00 0.00 0.00 6.13
2347 2671 2.815647 CGAGGAACGAAGCAGGGC 60.816 66.667 0.00 0.00 45.77 5.19
2348 2672 1.738099 CACGAGGAACGAAGCAGGG 60.738 63.158 0.00 0.00 45.77 4.45
2349 2673 2.383527 GCACGAGGAACGAAGCAGG 61.384 63.158 0.00 0.00 45.77 4.85
2350 2674 2.383527 GGCACGAGGAACGAAGCAG 61.384 63.158 0.00 0.00 45.77 4.24
2351 2675 2.357034 GGCACGAGGAACGAAGCA 60.357 61.111 0.00 0.00 45.77 3.91
2370 2694 4.799473 CGTGCTCATGCGTTGCGG 62.799 66.667 0.00 0.00 43.34 5.69
2371 2695 4.799473 CCGTGCTCATGCGTTGCG 62.799 66.667 0.00 0.00 43.34 4.85
2372 2696 3.372676 CTCCGTGCTCATGCGTTGC 62.373 63.158 0.00 0.00 43.34 4.17
2373 2697 2.743752 CCTCCGTGCTCATGCGTTG 61.744 63.158 0.00 0.00 43.34 4.10
2374 2698 1.884075 TACCTCCGTGCTCATGCGTT 61.884 55.000 0.00 0.00 43.34 4.84
2375 2699 2.284798 CTACCTCCGTGCTCATGCGT 62.285 60.000 0.00 0.00 43.34 5.24
2376 2700 1.589993 CTACCTCCGTGCTCATGCG 60.590 63.158 0.00 0.00 43.34 4.73
2377 2701 1.884926 GCTACCTCCGTGCTCATGC 60.885 63.158 0.00 0.00 40.20 4.06
2378 2702 1.589993 CGCTACCTCCGTGCTCATG 60.590 63.158 0.00 0.00 0.00 3.07
2379 2703 2.005960 GACGCTACCTCCGTGCTCAT 62.006 60.000 0.00 0.00 39.30 2.90
2380 2704 2.675423 ACGCTACCTCCGTGCTCA 60.675 61.111 0.00 0.00 37.56 4.26
2381 2705 2.102553 GACGCTACCTCCGTGCTC 59.897 66.667 0.00 0.00 39.30 4.26
2382 2706 2.675423 TGACGCTACCTCCGTGCT 60.675 61.111 0.00 0.00 39.30 4.40
2383 2707 2.506438 GTGACGCTACCTCCGTGC 60.506 66.667 0.00 0.00 39.30 5.34
2384 2708 1.154016 CAGTGACGCTACCTCCGTG 60.154 63.158 0.00 0.00 39.30 4.94
2385 2709 2.991076 GCAGTGACGCTACCTCCGT 61.991 63.158 0.00 0.00 42.31 4.69
2386 2710 2.202623 GCAGTGACGCTACCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
2387 2711 2.184579 GGCAGTGACGCTACCTCC 59.815 66.667 0.00 0.00 0.00 4.30
2388 2712 2.202623 CGGCAGTGACGCTACCTC 60.203 66.667 4.90 0.00 0.00 3.85
2395 2719 3.268603 TGTTGTGCGGCAGTGACG 61.269 61.111 15.86 15.86 36.98 4.35
2396 2720 1.987704 TTGTGTTGTGCGGCAGTGAC 61.988 55.000 1.18 3.02 0.00 3.67
2397 2721 1.746991 TTGTGTTGTGCGGCAGTGA 60.747 52.632 1.18 0.00 0.00 3.41
2398 2722 1.586042 GTTGTGTTGTGCGGCAGTG 60.586 57.895 1.18 0.00 0.00 3.66
2399 2723 2.798009 GTTGTGTTGTGCGGCAGT 59.202 55.556 1.18 0.00 0.00 4.40
2400 2724 2.352229 CGTTGTGTTGTGCGGCAG 60.352 61.111 1.18 0.00 0.00 4.85
2401 2725 2.818487 CTCGTTGTGTTGTGCGGCA 61.818 57.895 0.00 0.00 0.00 5.69
2402 2726 2.052237 CTCGTTGTGTTGTGCGGC 60.052 61.111 0.00 0.00 0.00 6.53
2403 2727 2.052237 GCTCGTTGTGTTGTGCGG 60.052 61.111 0.00 0.00 0.00 5.69
2404 2728 2.423517 CGCTCGTTGTGTTGTGCG 60.424 61.111 0.00 0.00 37.57 5.34
2405 2729 2.722188 GCGCTCGTTGTGTTGTGC 60.722 61.111 0.00 0.00 0.00 4.57
2406 2730 2.052237 GGCGCTCGTTGTGTTGTG 60.052 61.111 7.64 0.00 0.00 3.33
2407 2731 3.276846 GGGCGCTCGTTGTGTTGT 61.277 61.111 7.64 0.00 0.00 3.32
2408 2732 4.368808 CGGGCGCTCGTTGTGTTG 62.369 66.667 24.35 0.00 0.00 3.33
2450 2774 4.764336 CATGTTGTGGCTGGCGCG 62.764 66.667 0.00 0.00 36.88 6.86
2451 2775 4.424566 CCATGTTGTGGCTGGCGC 62.425 66.667 7.94 7.94 42.12 6.53
2459 2783 3.713858 TGAAGCTTTGACCATGTTGTG 57.286 42.857 0.00 0.00 0.00 3.33
2460 2784 4.501915 CCAATGAAGCTTTGACCATGTTGT 60.502 41.667 0.00 0.00 0.00 3.32
2461 2785 3.991773 CCAATGAAGCTTTGACCATGTTG 59.008 43.478 0.00 0.00 0.00 3.33
2462 2786 3.896888 TCCAATGAAGCTTTGACCATGTT 59.103 39.130 0.00 0.00 0.00 2.71
2463 2787 3.499338 TCCAATGAAGCTTTGACCATGT 58.501 40.909 0.00 0.00 0.00 3.21
2464 2788 3.675228 GCTCCAATGAAGCTTTGACCATG 60.675 47.826 0.00 0.00 0.00 3.66
2465 2789 2.494870 GCTCCAATGAAGCTTTGACCAT 59.505 45.455 0.00 0.00 0.00 3.55
2466 2790 1.888512 GCTCCAATGAAGCTTTGACCA 59.111 47.619 0.00 0.00 0.00 4.02
2467 2791 1.135575 CGCTCCAATGAAGCTTTGACC 60.136 52.381 0.00 0.00 0.00 4.02
2468 2792 1.537202 ACGCTCCAATGAAGCTTTGAC 59.463 47.619 0.00 0.00 0.00 3.18
2469 2793 1.806542 GACGCTCCAATGAAGCTTTGA 59.193 47.619 0.00 0.00 0.00 2.69
2470 2794 1.464687 CGACGCTCCAATGAAGCTTTG 60.465 52.381 0.00 0.00 0.00 2.77
2471 2795 0.798776 CGACGCTCCAATGAAGCTTT 59.201 50.000 0.00 0.00 0.00 3.51
2472 2796 1.639298 GCGACGCTCCAATGAAGCTT 61.639 55.000 13.73 0.00 0.00 3.74
2473 2797 2.103042 GCGACGCTCCAATGAAGCT 61.103 57.895 13.73 0.00 0.00 3.74
2474 2798 2.401195 GCGACGCTCCAATGAAGC 59.599 61.111 13.73 0.00 0.00 3.86
2475 2799 3.093278 GGCGACGCTCCAATGAAG 58.907 61.111 20.77 0.00 0.00 3.02
2494 2818 4.111016 TGTCGTGGCTAGTCGCGG 62.111 66.667 28.13 11.38 40.57 6.46
2495 2819 2.577112 CTGTCGTGGCTAGTCGCG 60.577 66.667 23.73 23.73 40.44 5.87
2496 2820 1.801913 CACTGTCGTGGCTAGTCGC 60.802 63.158 0.00 0.00 37.50 5.19
2497 2821 1.801913 GCACTGTCGTGGCTAGTCG 60.802 63.158 0.00 0.00 41.51 4.18
2498 2822 4.170723 GCACTGTCGTGGCTAGTC 57.829 61.111 0.00 0.00 41.51 2.59
2504 2828 3.302347 GAGGAGGGCACTGTCGTGG 62.302 68.421 0.00 0.00 41.51 4.94
2505 2829 2.262915 GAGGAGGGCACTGTCGTG 59.737 66.667 0.00 0.00 44.07 4.35
2506 2830 3.374402 CGAGGAGGGCACTGTCGT 61.374 66.667 8.83 0.00 0.00 4.34
2507 2831 4.803426 GCGAGGAGGGCACTGTCG 62.803 72.222 12.10 12.10 34.47 4.35
2508 2832 3.655810 CTGCGAGGAGGGCACTGTC 62.656 68.421 0.00 0.00 36.24 3.51
2509 2833 3.699894 CTGCGAGGAGGGCACTGT 61.700 66.667 0.00 0.00 36.24 3.55
2524 2848 2.389020 CGCTTCAGAGGCAGTGCTG 61.389 63.158 16.11 5.74 0.00 4.41
2525 2849 2.047465 CGCTTCAGAGGCAGTGCT 60.047 61.111 16.11 0.33 0.00 4.40
2526 2850 3.797546 GCGCTTCAGAGGCAGTGC 61.798 66.667 6.55 6.55 39.24 4.40
2527 2851 3.123620 GGCGCTTCAGAGGCAGTG 61.124 66.667 7.64 0.00 40.00 3.66
2528 2852 4.749310 CGGCGCTTCAGAGGCAGT 62.749 66.667 7.64 0.00 40.24 4.40


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

AutoCloner maintained by Alex Coulton.