Multiple sequence alignment - TraesCS2D01G204900

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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 TraesCS2D01G204900 chr2D 100.000 5153 0 0 1 5153 156828982 156823830 0.000000e+00 9516
1 TraesCS2D01G204900 chr2B 95.365 2524 83 12 2184 4692 214377751 214375247 0.000000e+00 3982
2 TraesCS2D01G204900 chr2B 94.378 1263 45 14 566 1822 214379511 214378269 0.000000e+00 1916
3 TraesCS2D01G204900 chr2B 93.863 554 32 2 16 569 214384998 214384447 0.000000e+00 833
4 TraesCS2D01G204900 chr2B 94.395 446 22 3 4692 5137 214375283 214374841 0.000000e+00 682
5 TraesCS2D01G204900 chr2B 94.144 222 4 4 1986 2199 214377987 214377767 3.850000e-86 329
6 TraesCS2D01G204900 chr2A 93.452 2520 77 25 2184 4692 166756748 166754306 0.000000e+00 3659
7 TraesCS2D01G204900 chr2A 93.482 1166 48 20 664 1822 166758251 166757107 0.000000e+00 1707
8 TraesCS2D01G204900 chr2A 85.915 355 40 3 303 657 166758824 166758480 2.270000e-98 370
9 TraesCS2D01G204900 chr2A 95.794 214 4 2 1991 2199 166756978 166756765 1.780000e-89 340
10 TraesCS2D01G204900 chr2A 86.909 275 22 9 4866 5137 166753547 166753284 3.900000e-76 296
11 TraesCS2D01G204900 chr2A 94.175 103 6 0 4692 4794 166754342 166754240 1.920000e-34 158
12 TraesCS2D01G204900 chrUn 100.000 40 0 0 1950 1989 171047859 171047898 1.990000e-09 75
13 TraesCS2D01G204900 chrUn 100.000 40 0 0 1950 1989 189396614 189396653 1.990000e-09 75
14 TraesCS2D01G204900 chrUn 100.000 40 0 0 1950 1989 399419405 399419366 1.990000e-09 75
15 TraesCS2D01G204900 chrUn 100.000 40 0 0 1950 1989 452446622 452446583 1.990000e-09 75
16 TraesCS2D01G204900 chr6D 100.000 40 0 0 1950 1989 124521654 124521693 1.990000e-09 75
17 TraesCS2D01G204900 chr6D 100.000 40 0 0 1950 1989 246423148 246423187 1.990000e-09 75
18 TraesCS2D01G204900 chr6D 100.000 40 0 0 1950 1989 369943972 369944011 1.990000e-09 75
19 TraesCS2D01G204900 chr6D 100.000 40 0 0 1950 1989 458902315 458902354 1.990000e-09 75
20 TraesCS2D01G204900 chr1D 100.000 40 0 0 1950 1989 43232585 43232546 1.990000e-09 75


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 TraesCS2D01G204900 chr2D 156823830 156828982 5152 True 9516.000000 9516 100.000000 1 5153 1 chr2D.!!$R1 5152
1 TraesCS2D01G204900 chr2B 214374841 214379511 4670 True 1727.250000 3982 94.570500 566 5137 4 chr2B.!!$R2 4571
2 TraesCS2D01G204900 chr2B 214384447 214384998 551 True 833.000000 833 93.863000 16 569 1 chr2B.!!$R1 553
3 TraesCS2D01G204900 chr2A 166753284 166758824 5540 True 1088.333333 3659 91.621167 303 5137 6 chr2A.!!$R1 4834

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
732 955 0.949105 CTTACCACGGGTGCTCACAC 60.949 60.000 5.90 0.0 46.66 3.82 F
1957 2382 0.394899 AAGGCAGGCAAGAGTATGGC 60.395 55.000 0.00 0.0 45.57 4.40 F
1978 2403 1.007238 TGGAAGGTCAGCCTAGCTAGT 59.993 52.381 19.31 0.0 46.33 2.57 F
3454 3947 0.179015 TCCGCAAGCCAACCACTTTA 60.179 50.000 0.00 0.0 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2419 0.247814 CTGCGCGGTGAGCTAAATTG 60.248 55.000 8.83 0.0 45.59 2.32 R
3290 3759 1.082496 GTGCACTCAACTCGCTTGC 60.082 57.895 10.32 0.0 0.00 4.01 R
3829 4336 2.092914 GTGGGAGGCACTTAGTAAGCAT 60.093 50.000 9.92 0.0 41.55 3.79 R
4695 5205 0.244994 AGCTCACGCTAGGTTCACAG 59.755 55.000 0.00 0.0 46.79 3.66 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
72 73 4.686972 TCGAGCTAATGTTGAGATTCCTG 58.313 43.478 0.00 0.00 0.00 3.86
87 88 6.615316 TGAGATTCCTGTGAAATAGGGACATA 59.385 38.462 0.00 0.00 46.62 2.29
134 135 2.791179 AGCCCCAATCCTATGATCCAAA 59.209 45.455 0.00 0.00 0.00 3.28
138 139 5.396485 CCCCAATCCTATGATCCAAATGAA 58.604 41.667 0.00 0.00 0.00 2.57
150 151 8.827832 ATGATCCAAATGAATTCTGTAGGAAA 57.172 30.769 7.05 3.65 37.49 3.13
173 174 6.408770 AAATCCTTAGGGTTCAAATCCTCT 57.591 37.500 0.00 0.00 39.27 3.69
230 231 6.442885 AGATCATAGGATTGAGATGCCATGTA 59.557 38.462 0.00 0.00 32.67 2.29
244 245 9.624373 GAGATGCCATGTATTATGAATTCCTAT 57.376 33.333 2.27 0.00 0.00 2.57
286 287 8.923270 AGGAATTTTGTGAGAAGTAAATTTGGA 58.077 29.630 0.00 0.00 32.14 3.53
289 290 9.492973 AATTTTGTGAGAAGTAAATTTGGATGG 57.507 29.630 0.00 0.00 28.64 3.51
331 332 8.869109 ACACATGAATTTTAGAAAATTGAGGGA 58.131 29.630 15.79 0.00 45.70 4.20
342 343 6.118852 AGAAAATTGAGGGAAGATAGAGCAC 58.881 40.000 0.00 0.00 0.00 4.40
357 358 6.550108 AGATAGAGCACGGGAGATAAACTAAA 59.450 38.462 0.00 0.00 0.00 1.85
399 400 9.838339 TCAAAGGAAAATAAAATAAGGTTTGCA 57.162 25.926 0.00 0.00 0.00 4.08
446 447 6.041296 GGGAATGGATTGCATGAGAATTTAGT 59.959 38.462 0.00 0.00 0.00 2.24
451 452 8.213518 TGGATTGCATGAGAATTTAGTAGTTC 57.786 34.615 0.00 0.00 0.00 3.01
465 466 6.526056 TTAGTAGTTCCATCTAGAGGGCTA 57.474 41.667 18.79 11.97 31.15 3.93
587 588 8.252417 CACTAGCATCTCAAGAAGCTATATCAT 58.748 37.037 15.12 0.57 46.17 2.45
680 903 4.188247 TCGATAGTTGAGGTCTTTGTGG 57.812 45.455 0.00 0.00 37.40 4.17
683 906 4.560716 CGATAGTTGAGGTCTTTGTGGTGA 60.561 45.833 0.00 0.00 0.00 4.02
717 940 4.396790 CCTAGGATCGAGTGATAGGCTTAC 59.603 50.000 1.05 0.00 34.09 2.34
732 955 0.949105 CTTACCACGGGTGCTCACAC 60.949 60.000 5.90 0.00 46.66 3.82
787 1010 2.250924 TCTGTCCAGTTGAGAGATGCA 58.749 47.619 0.00 0.00 38.39 3.96
788 1011 2.233186 TCTGTCCAGTTGAGAGATGCAG 59.767 50.000 0.00 0.00 38.39 4.41
805 1028 4.776795 TGCAGTTACATCGACTACAAGA 57.223 40.909 0.00 0.00 0.00 3.02
806 1029 4.482386 TGCAGTTACATCGACTACAAGAC 58.518 43.478 0.00 0.00 0.00 3.01
807 1030 4.022676 TGCAGTTACATCGACTACAAGACA 60.023 41.667 0.00 0.00 0.00 3.41
809 1032 6.127842 TGCAGTTACATCGACTACAAGACATA 60.128 38.462 0.00 0.00 0.00 2.29
836 1067 5.011635 TGGTTACTTCTGTCACATTAGCTCA 59.988 40.000 0.00 0.00 0.00 4.26
955 1187 7.431249 TCTACTAGCCGATTTTCGAATGTAAT 58.569 34.615 0.00 0.00 43.74 1.89
956 1188 6.920569 ACTAGCCGATTTTCGAATGTAATT 57.079 33.333 0.00 0.00 43.74 1.40
982 1214 7.473735 TTTTTGCCCAACATATATCACTCAA 57.526 32.000 0.00 0.00 0.00 3.02
983 1215 7.473735 TTTTGCCCAACATATATCACTCAAA 57.526 32.000 0.00 0.00 0.00 2.69
984 1216 7.658525 TTTGCCCAACATATATCACTCAAAT 57.341 32.000 0.00 0.00 0.00 2.32
985 1217 8.759481 TTTGCCCAACATATATCACTCAAATA 57.241 30.769 0.00 0.00 0.00 1.40
986 1218 8.759481 TTGCCCAACATATATCACTCAAATAA 57.241 30.769 0.00 0.00 0.00 1.40
1841 2266 3.698029 ATCATTTAACCATCACGCTGC 57.302 42.857 0.00 0.00 0.00 5.25
1859 2284 1.901833 TGCTGAGGCTCATGTGTAAGA 59.098 47.619 19.11 0.00 39.59 2.10
1860 2285 2.302733 TGCTGAGGCTCATGTGTAAGAA 59.697 45.455 19.11 0.00 39.59 2.52
1905 2330 2.685897 AGCGCAAACCACTTTCAGTTTA 59.314 40.909 11.47 0.00 34.52 2.01
1922 2347 7.825331 TCAGTTTATTGGATGGTGTACAAAA 57.175 32.000 0.00 0.00 33.40 2.44
1923 2348 7.881142 TCAGTTTATTGGATGGTGTACAAAAG 58.119 34.615 0.00 0.00 33.40 2.27
1925 2350 8.023128 CAGTTTATTGGATGGTGTACAAAAGAG 58.977 37.037 0.00 0.00 33.40 2.85
1926 2351 6.509418 TTATTGGATGGTGTACAAAAGAGC 57.491 37.500 0.00 0.00 33.40 4.09
1927 2352 3.500448 TGGATGGTGTACAAAAGAGCA 57.500 42.857 0.00 0.00 32.87 4.26
1928 2353 3.411446 TGGATGGTGTACAAAAGAGCAG 58.589 45.455 0.00 0.00 31.71 4.24
1929 2354 2.749621 GGATGGTGTACAAAAGAGCAGG 59.250 50.000 0.00 0.00 31.71 4.85
1930 2355 1.604604 TGGTGTACAAAAGAGCAGGC 58.395 50.000 0.00 0.00 0.00 4.85
1931 2356 0.881796 GGTGTACAAAAGAGCAGGCC 59.118 55.000 0.00 0.00 0.00 5.19
1932 2357 0.517316 GTGTACAAAAGAGCAGGCCG 59.483 55.000 0.00 0.00 0.00 6.13
1933 2358 0.605319 TGTACAAAAGAGCAGGCCGG 60.605 55.000 0.00 0.00 0.00 6.13
1934 2359 1.674322 TACAAAAGAGCAGGCCGGC 60.674 57.895 21.36 21.36 0.00 6.13
1935 2360 3.752339 CAAAAGAGCAGGCCGGCC 61.752 66.667 39.29 39.29 0.00 6.13
1954 2379 2.706339 CTGAAGGCAGGCAAGAGTAT 57.294 50.000 0.00 0.00 38.51 2.12
1955 2380 2.286872 CTGAAGGCAGGCAAGAGTATG 58.713 52.381 0.00 0.00 38.51 2.39
1956 2381 1.065199 TGAAGGCAGGCAAGAGTATGG 60.065 52.381 0.00 0.00 0.00 2.74
1957 2382 0.394899 AAGGCAGGCAAGAGTATGGC 60.395 55.000 0.00 0.00 45.57 4.40
1962 2387 3.882131 GGCAAGAGTATGGCTGGAA 57.118 52.632 0.00 0.00 42.22 3.53
1963 2388 1.673168 GGCAAGAGTATGGCTGGAAG 58.327 55.000 0.00 0.00 42.22 3.46
1964 2389 1.673168 GCAAGAGTATGGCTGGAAGG 58.327 55.000 0.00 0.00 0.00 3.46
1965 2390 1.065126 GCAAGAGTATGGCTGGAAGGT 60.065 52.381 0.00 0.00 0.00 3.50
1966 2391 2.911484 CAAGAGTATGGCTGGAAGGTC 58.089 52.381 0.00 0.00 0.00 3.85
1967 2392 2.237143 CAAGAGTATGGCTGGAAGGTCA 59.763 50.000 0.00 0.00 0.00 4.02
1968 2393 2.114616 AGAGTATGGCTGGAAGGTCAG 58.885 52.381 0.00 0.00 37.79 3.51
1975 2400 2.601664 CTGGAAGGTCAGCCTAGCT 58.398 57.895 0.00 0.00 46.33 3.32
1976 2401 1.781786 CTGGAAGGTCAGCCTAGCTA 58.218 55.000 0.00 0.00 46.33 3.32
1977 2402 1.686052 CTGGAAGGTCAGCCTAGCTAG 59.314 57.143 14.20 14.20 46.33 3.42
1978 2403 1.007238 TGGAAGGTCAGCCTAGCTAGT 59.993 52.381 19.31 0.00 46.33 2.57
1979 2404 1.684450 GGAAGGTCAGCCTAGCTAGTC 59.316 57.143 19.31 6.87 46.33 2.59
1980 2405 2.661718 GAAGGTCAGCCTAGCTAGTCT 58.338 52.381 19.31 9.44 46.33 3.24
1981 2406 2.838637 AGGTCAGCCTAGCTAGTCTT 57.161 50.000 19.31 1.77 44.90 3.01
1982 2407 2.383855 AGGTCAGCCTAGCTAGTCTTG 58.616 52.381 19.31 13.49 44.90 3.02
1983 2408 2.104170 GGTCAGCCTAGCTAGTCTTGT 58.896 52.381 19.31 0.00 36.40 3.16
1984 2409 2.100087 GGTCAGCCTAGCTAGTCTTGTC 59.900 54.545 19.31 11.19 36.40 3.18
1985 2410 2.755655 GTCAGCCTAGCTAGTCTTGTCA 59.244 50.000 19.31 0.00 36.40 3.58
1986 2411 3.193691 GTCAGCCTAGCTAGTCTTGTCAA 59.806 47.826 19.31 0.00 36.40 3.18
1987 2412 4.026744 TCAGCCTAGCTAGTCTTGTCAAT 58.973 43.478 19.31 0.00 36.40 2.57
1988 2413 4.098654 TCAGCCTAGCTAGTCTTGTCAATC 59.901 45.833 19.31 0.00 36.40 2.67
1989 2414 4.026744 AGCCTAGCTAGTCTTGTCAATCA 58.973 43.478 19.31 0.00 36.99 2.57
1990 2415 4.116238 GCCTAGCTAGTCTTGTCAATCAC 58.884 47.826 19.31 0.00 0.00 3.06
1991 2416 4.382040 GCCTAGCTAGTCTTGTCAATCACA 60.382 45.833 19.31 0.00 0.00 3.58
1992 2417 5.105752 CCTAGCTAGTCTTGTCAATCACAC 58.894 45.833 19.31 0.00 33.41 3.82
1993 2418 4.607293 AGCTAGTCTTGTCAATCACACA 57.393 40.909 0.00 0.00 33.41 3.72
1994 2419 4.310769 AGCTAGTCTTGTCAATCACACAC 58.689 43.478 0.00 0.00 33.41 3.82
1995 2420 4.058124 GCTAGTCTTGTCAATCACACACA 58.942 43.478 0.00 0.00 33.41 3.72
1996 2421 4.511454 GCTAGTCTTGTCAATCACACACAA 59.489 41.667 0.00 0.00 33.41 3.33
2006 2431 5.853282 GTCAATCACACACAATTTAGCTCAC 59.147 40.000 0.00 0.00 0.00 3.51
2210 2675 5.436175 CACCCACATGTTGACAAGGATATA 58.564 41.667 0.00 0.00 0.00 0.86
2211 2676 5.885352 CACCCACATGTTGACAAGGATATAA 59.115 40.000 0.00 0.00 0.00 0.98
2482 2951 5.178623 CGTTTGGTTCTCACATAGTTGCTAA 59.821 40.000 0.00 0.00 0.00 3.09
2951 3420 2.131854 TGGTCTCCACCTTCTTCCAAA 58.868 47.619 0.00 0.00 44.17 3.28
2952 3421 2.716424 TGGTCTCCACCTTCTTCCAAAT 59.284 45.455 0.00 0.00 44.17 2.32
2953 3422 3.140144 TGGTCTCCACCTTCTTCCAAATT 59.860 43.478 0.00 0.00 44.17 1.82
2997 3466 6.135290 TCTTCCAAATTCAAAGTGTCACAG 57.865 37.500 5.62 0.00 0.00 3.66
3221 3690 4.884961 ACTACATCATCTTCTACCCCTGT 58.115 43.478 0.00 0.00 0.00 4.00
3335 3804 0.387202 CTCATGGAAGATCGACGGCT 59.613 55.000 0.00 0.00 0.00 5.52
3410 3879 8.712228 ATAATTTTCTTTTGAGGGACAGAAGT 57.288 30.769 0.00 0.00 40.28 3.01
3415 3884 4.164221 TCTTTTGAGGGACAGAAGTTGAGT 59.836 41.667 0.00 0.00 40.28 3.41
3447 3940 0.451783 CATAGGTTCCGCAAGCCAAC 59.548 55.000 0.00 0.00 0.00 3.77
3448 3941 0.679960 ATAGGTTCCGCAAGCCAACC 60.680 55.000 10.99 10.99 44.75 3.77
3449 3942 2.058125 TAGGTTCCGCAAGCCAACCA 62.058 55.000 17.95 6.18 46.05 3.67
3450 3943 2.335011 GTTCCGCAAGCCAACCAC 59.665 61.111 0.00 0.00 0.00 4.16
3451 3944 2.193536 GTTCCGCAAGCCAACCACT 61.194 57.895 0.00 0.00 0.00 4.00
3452 3945 1.454847 TTCCGCAAGCCAACCACTT 60.455 52.632 0.00 0.00 0.00 3.16
3453 3946 1.040339 TTCCGCAAGCCAACCACTTT 61.040 50.000 0.00 0.00 0.00 2.66
3454 3947 0.179015 TCCGCAAGCCAACCACTTTA 60.179 50.000 0.00 0.00 0.00 1.85
3455 3948 0.887933 CCGCAAGCCAACCACTTTAT 59.112 50.000 0.00 0.00 0.00 1.40
3456 3949 1.135402 CCGCAAGCCAACCACTTTATC 60.135 52.381 0.00 0.00 0.00 1.75
3457 3950 1.539388 CGCAAGCCAACCACTTTATCA 59.461 47.619 0.00 0.00 0.00 2.15
3458 3951 2.414559 CGCAAGCCAACCACTTTATCAG 60.415 50.000 0.00 0.00 0.00 2.90
3459 3952 2.819608 GCAAGCCAACCACTTTATCAGA 59.180 45.455 0.00 0.00 0.00 3.27
3460 3953 3.366374 GCAAGCCAACCACTTTATCAGAC 60.366 47.826 0.00 0.00 0.00 3.51
3461 3954 3.073274 AGCCAACCACTTTATCAGACC 57.927 47.619 0.00 0.00 0.00 3.85
3462 3955 2.375174 AGCCAACCACTTTATCAGACCA 59.625 45.455 0.00 0.00 0.00 4.02
3463 3956 2.488153 GCCAACCACTTTATCAGACCAC 59.512 50.000 0.00 0.00 0.00 4.16
3464 3957 3.081804 CCAACCACTTTATCAGACCACC 58.918 50.000 0.00 0.00 0.00 4.61
3465 3958 3.497763 CCAACCACTTTATCAGACCACCA 60.498 47.826 0.00 0.00 0.00 4.17
3466 3959 3.418684 ACCACTTTATCAGACCACCAC 57.581 47.619 0.00 0.00 0.00 4.16
3467 3960 2.979678 ACCACTTTATCAGACCACCACT 59.020 45.455 0.00 0.00 0.00 4.00
3468 3961 3.008049 ACCACTTTATCAGACCACCACTC 59.992 47.826 0.00 0.00 0.00 3.51
3469 3962 3.007940 CCACTTTATCAGACCACCACTCA 59.992 47.826 0.00 0.00 0.00 3.41
3470 3963 4.504864 CCACTTTATCAGACCACCACTCAA 60.505 45.833 0.00 0.00 0.00 3.02
3471 3964 5.248640 CACTTTATCAGACCACCACTCAAT 58.751 41.667 0.00 0.00 0.00 2.57
3472 3965 6.406370 CACTTTATCAGACCACCACTCAATA 58.594 40.000 0.00 0.00 0.00 1.90
3481 3974 3.244875 ACCACCACTCAATAATGTCAGCA 60.245 43.478 0.00 0.00 0.00 4.41
3546 4047 0.798776 GAGCATCAAAGTCCACACCG 59.201 55.000 0.00 0.00 33.17 4.94
3584 4087 2.424601 CGAGCATCAAATGGGTGATTGT 59.575 45.455 0.00 0.00 36.04 2.71
3707 4210 5.347342 TGACTTGCAACTAAACATTGTTGG 58.653 37.500 2.13 2.36 42.48 3.77
3716 4219 7.566709 CAACTAAACATTGTTGGAAATTGCTC 58.433 34.615 2.13 0.00 39.64 4.26
3778 4285 7.822161 AACAATATGCTAGCAATCACCATTA 57.178 32.000 23.54 7.21 0.00 1.90
3781 4288 8.517878 ACAATATGCTAGCAATCACCATTATTC 58.482 33.333 23.54 0.00 0.00 1.75
3786 4293 6.152492 TGCTAGCAATCACCATTATTCAAACA 59.848 34.615 16.84 0.00 0.00 2.83
3794 4301 8.891671 ATCACCATTATTCAAACATTATTGGC 57.108 30.769 0.00 0.00 0.00 4.52
3855 4363 0.253327 CTAAGTGCCTCCCACCTTCC 59.747 60.000 0.00 0.00 45.83 3.46
4049 4557 6.323225 ATTCTTCAGAAAATGGAAGGCCATAG 59.677 38.462 5.01 0.00 44.25 2.23
4092 4600 4.999311 TCATGTCATCCAACAGAGAACAAG 59.001 41.667 0.00 0.00 31.50 3.16
4211 4721 7.065085 TGTGTACTCTATGTAGAACGAACCTAC 59.935 40.741 0.00 0.00 37.57 3.18
4226 4736 2.358615 TACGCAGCAGCAAGTGGG 60.359 61.111 0.82 0.00 42.27 4.61
4382 4892 4.810191 ACAGATGAGTTGGTCTCCTAAC 57.190 45.455 0.00 0.00 42.12 2.34
4449 4959 5.972107 CAGATTTGGACCTCTTTGTTCAT 57.028 39.130 0.00 0.00 0.00 2.57
4624 5134 2.103771 TCAATCTGCAGAGCTGGGATAC 59.896 50.000 22.96 0.00 0.00 2.24
4630 5140 2.136878 AGAGCTGGGATACTGGCCG 61.137 63.158 0.00 0.00 35.33 6.13
4676 5186 3.165058 TGGCTATGAACTTAGCGTGAG 57.835 47.619 11.58 0.00 44.52 3.51
4692 5202 4.871993 CGTGAGCTTAGCTTGATCAAAT 57.128 40.909 8.58 3.91 39.88 2.32
4693 5203 4.585364 CGTGAGCTTAGCTTGATCAAATG 58.415 43.478 8.58 0.00 39.88 2.32
4694 5204 4.495349 CGTGAGCTTAGCTTGATCAAATGG 60.495 45.833 8.58 0.00 39.88 3.16
4695 5205 3.379372 TGAGCTTAGCTTGATCAAATGGC 59.621 43.478 8.58 9.68 39.88 4.40
4696 5206 3.629087 AGCTTAGCTTGATCAAATGGCT 58.371 40.909 20.49 20.49 33.89 4.75
4697 5207 3.380637 AGCTTAGCTTGATCAAATGGCTG 59.619 43.478 23.72 13.24 33.89 4.85
4698 5208 3.129988 GCTTAGCTTGATCAAATGGCTGT 59.870 43.478 23.72 7.69 34.88 4.40
4699 5209 4.669318 CTTAGCTTGATCAAATGGCTGTG 58.331 43.478 23.72 15.03 34.88 3.66
4700 5210 2.799017 AGCTTGATCAAATGGCTGTGA 58.201 42.857 17.21 0.00 31.68 3.58
4701 5211 3.159472 AGCTTGATCAAATGGCTGTGAA 58.841 40.909 17.21 0.00 31.68 3.18
4702 5212 3.057033 AGCTTGATCAAATGGCTGTGAAC 60.057 43.478 17.21 0.00 31.68 3.18
4703 5213 3.841643 CTTGATCAAATGGCTGTGAACC 58.158 45.455 9.88 0.00 0.00 3.62
4704 5214 3.159213 TGATCAAATGGCTGTGAACCT 57.841 42.857 0.00 0.00 0.00 3.50
4705 5215 4.299586 TGATCAAATGGCTGTGAACCTA 57.700 40.909 0.00 0.00 0.00 3.08
4706 5216 4.264253 TGATCAAATGGCTGTGAACCTAG 58.736 43.478 0.00 0.00 0.00 3.02
4707 5217 2.436417 TCAAATGGCTGTGAACCTAGC 58.564 47.619 0.00 0.00 39.17 3.42
4708 5218 1.131126 CAAATGGCTGTGAACCTAGCG 59.869 52.381 0.00 0.00 40.78 4.26
4709 5219 0.324943 AATGGCTGTGAACCTAGCGT 59.675 50.000 0.00 0.00 40.78 5.07
4710 5220 0.391661 ATGGCTGTGAACCTAGCGTG 60.392 55.000 0.00 0.00 40.78 5.34
4711 5221 1.292223 GGCTGTGAACCTAGCGTGA 59.708 57.895 0.00 0.00 40.78 4.35
4757 5267 1.983605 CTCAACGTGTGACGGTCATAC 59.016 52.381 23.23 23.23 36.37 2.39
4773 5283 6.183360 ACGGTCATACATAGATCAAACATGGA 60.183 38.462 0.00 0.00 0.00 3.41
4838 6031 1.720781 AGCAAAACCAGGGCTGAAAT 58.279 45.000 0.00 0.00 36.34 2.17
4850 6043 4.935808 CAGGGCTGAAATAGAACTAAACGT 59.064 41.667 0.00 0.00 0.00 3.99
4906 6099 3.963665 TCAATGTTTCCGCAAAGTCAAG 58.036 40.909 0.00 0.00 0.00 3.02
4935 6128 5.801947 GCAATCGACAATGAACTAGCAATTT 59.198 36.000 0.00 0.00 0.00 1.82
5007 6200 3.447918 TCCGGTATAGTTAAGCAGCAC 57.552 47.619 0.00 0.00 0.00 4.40
5009 6202 2.159014 CCGGTATAGTTAAGCAGCACCA 60.159 50.000 0.00 0.00 0.00 4.17
5047 6240 3.887621 ACCGCAGAGTAGCAATTCTAA 57.112 42.857 0.00 0.00 0.00 2.10
5092 6293 4.262592 GGGAATTCAACATCACTTTTGGCT 60.263 41.667 7.93 0.00 0.00 4.75
5106 6307 7.228590 TCACTTTTGGCTACCCATATTATACC 58.771 38.462 0.00 0.00 41.78 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.202818 TCCAATGCTCTCTCTCTCTCTCT 59.797 47.826 0.00 0.00 0.00 3.10
1 2 3.554934 TCCAATGCTCTCTCTCTCTCTC 58.445 50.000 0.00 0.00 0.00 3.20
2 3 3.668141 TCCAATGCTCTCTCTCTCTCT 57.332 47.619 0.00 0.00 0.00 3.10
3 4 4.942761 AATCCAATGCTCTCTCTCTCTC 57.057 45.455 0.00 0.00 0.00 3.20
4 5 4.588528 GGTAATCCAATGCTCTCTCTCTCT 59.411 45.833 0.00 0.00 0.00 3.10
5 6 4.262420 GGGTAATCCAATGCTCTCTCTCTC 60.262 50.000 0.00 0.00 35.00 3.20
6 7 3.645687 GGGTAATCCAATGCTCTCTCTCT 59.354 47.826 0.00 0.00 35.00 3.10
7 8 3.389329 TGGGTAATCCAATGCTCTCTCTC 59.611 47.826 0.00 0.00 43.84 3.20
8 9 3.387962 TGGGTAATCCAATGCTCTCTCT 58.612 45.455 0.00 0.00 43.84 3.10
9 10 3.845781 TGGGTAATCCAATGCTCTCTC 57.154 47.619 0.00 0.00 43.84 3.20
121 122 8.159447 CCTACAGAATTCATTTGGATCATAGGA 58.841 37.037 8.44 0.00 0.00 2.94
134 135 9.413734 CCTAAGGATTTTTCCTACAGAATTCAT 57.586 33.333 8.44 0.00 39.65 2.57
138 139 7.285340 ACCCTAAGGATTTTTCCTACAGAAT 57.715 36.000 0.00 0.00 39.65 2.40
150 151 6.408770 AGAGGATTTGAACCCTAAGGATTT 57.591 37.500 0.00 0.00 36.73 2.17
191 192 7.773489 TCCTATGATCTCTCTCAATTGTAGG 57.227 40.000 5.13 5.36 30.44 3.18
197 198 8.755028 CATCTCAATCCTATGATCTCTCTCAAT 58.245 37.037 0.00 0.00 0.00 2.57
199 200 6.153170 GCATCTCAATCCTATGATCTCTCTCA 59.847 42.308 0.00 0.00 0.00 3.27
286 287 5.260424 TGTGTGTTATTTCCTATGCACCAT 58.740 37.500 0.00 0.00 0.00 3.55
289 290 6.435430 TCATGTGTGTTATTTCCTATGCAC 57.565 37.500 0.00 0.00 0.00 4.57
331 332 4.896482 AGTTTATCTCCCGTGCTCTATCTT 59.104 41.667 0.00 0.00 0.00 2.40
342 343 3.264104 TGCGGTTTTAGTTTATCTCCCG 58.736 45.455 0.00 0.00 37.29 5.14
357 358 3.492482 CCTTTGAAAAGTCCAATGCGGTT 60.492 43.478 2.33 0.00 34.20 4.44
398 399 7.068103 TCCCATGCCAACATTTTATACTTAGTG 59.932 37.037 0.00 0.00 32.87 2.74
399 400 7.122715 TCCCATGCCAACATTTTATACTTAGT 58.877 34.615 0.00 0.00 32.87 2.24
446 447 5.600669 TGATAGCCCTCTAGATGGAACTA 57.399 43.478 17.48 10.24 0.00 2.24
451 452 7.911651 TCTTTTTATGATAGCCCTCTAGATGG 58.088 38.462 9.58 9.58 0.00 3.51
522 523 5.385198 ACTTCAGGGCTCTTTGAATTGTAA 58.615 37.500 0.00 0.00 33.25 2.41
569 570 9.806448 AGTTAGAGATGATATAGCTTCTTGAGA 57.194 33.333 7.71 0.00 0.00 3.27
680 903 3.713826 TCCTAGGTGGATTGGTTTCAC 57.286 47.619 9.08 0.00 40.56 3.18
700 923 2.293677 CGTGGTAAGCCTATCACTCGAT 59.706 50.000 4.29 0.00 37.05 3.59
717 940 1.101049 AAAAGTGTGAGCACCCGTGG 61.101 55.000 0.00 0.00 46.35 4.94
739 962 7.491254 TGTCGAAAAGCATGAAATAAATTCG 57.509 32.000 0.00 2.64 41.18 3.34
788 1011 9.343103 CCATATATGTCTTGTAGTCGATGTAAC 57.657 37.037 11.73 0.00 0.00 2.50
802 1025 8.758829 TGTGACAGAAGTAACCATATATGTCTT 58.241 33.333 11.73 9.75 37.34 3.01
807 1030 9.712305 GCTAATGTGACAGAAGTAACCATATAT 57.288 33.333 0.00 0.00 0.00 0.86
809 1032 7.796054 AGCTAATGTGACAGAAGTAACCATAT 58.204 34.615 0.00 0.00 0.00 1.78
836 1067 4.974399 TGACCCAAAACAAAAGTGGTTTT 58.026 34.783 0.00 0.00 42.13 2.43
1002 1240 1.671379 GACCGTTTGTCCCTCAGCC 60.671 63.158 0.00 0.00 38.09 4.85
1251 1489 3.008408 GAGGACGGGGAGAGGAGA 58.992 66.667 0.00 0.00 0.00 3.71
1521 1759 4.657824 ACGGTGCAGTCGAACCCG 62.658 66.667 15.12 11.66 44.06 5.28
1841 2266 5.021033 AGATTCTTACACATGAGCCTCAG 57.979 43.478 0.00 0.00 0.00 3.35
1859 2284 6.214819 TCAACACTAACCTAAGGCCTAAGATT 59.785 38.462 5.16 1.04 0.00 2.40
1860 2285 5.724854 TCAACACTAACCTAAGGCCTAAGAT 59.275 40.000 5.16 0.00 0.00 2.40
1905 2330 4.406456 TGCTCTTTTGTACACCATCCAAT 58.594 39.130 0.00 0.00 0.00 3.16
1935 2360 2.286872 CATACTCTTGCCTGCCTTCAG 58.713 52.381 0.00 0.00 40.02 3.02
1936 2361 1.065199 CCATACTCTTGCCTGCCTTCA 60.065 52.381 0.00 0.00 0.00 3.02
1937 2362 1.673168 CCATACTCTTGCCTGCCTTC 58.327 55.000 0.00 0.00 0.00 3.46
1938 2363 0.394899 GCCATACTCTTGCCTGCCTT 60.395 55.000 0.00 0.00 0.00 4.35
1939 2364 1.225704 GCCATACTCTTGCCTGCCT 59.774 57.895 0.00 0.00 0.00 4.75
1940 2365 1.099879 CAGCCATACTCTTGCCTGCC 61.100 60.000 0.00 0.00 0.00 4.85
1941 2366 1.099879 CCAGCCATACTCTTGCCTGC 61.100 60.000 0.00 0.00 0.00 4.85
1942 2367 0.543277 TCCAGCCATACTCTTGCCTG 59.457 55.000 0.00 0.00 0.00 4.85
1943 2368 1.211457 CTTCCAGCCATACTCTTGCCT 59.789 52.381 0.00 0.00 0.00 4.75
1944 2369 1.673168 CTTCCAGCCATACTCTTGCC 58.327 55.000 0.00 0.00 0.00 4.52
1945 2370 1.065126 ACCTTCCAGCCATACTCTTGC 60.065 52.381 0.00 0.00 0.00 4.01
1946 2371 2.237143 TGACCTTCCAGCCATACTCTTG 59.763 50.000 0.00 0.00 0.00 3.02
1947 2372 2.503356 CTGACCTTCCAGCCATACTCTT 59.497 50.000 0.00 0.00 0.00 2.85
1948 2373 2.114616 CTGACCTTCCAGCCATACTCT 58.885 52.381 0.00 0.00 0.00 3.24
1949 2374 2.611225 CTGACCTTCCAGCCATACTC 57.389 55.000 0.00 0.00 0.00 2.59
1963 2388 2.100087 GACAAGACTAGCTAGGCTGACC 59.900 54.545 29.93 16.75 41.95 4.02
1964 2389 2.755655 TGACAAGACTAGCTAGGCTGAC 59.244 50.000 29.93 21.76 41.95 3.51
1965 2390 3.087370 TGACAAGACTAGCTAGGCTGA 57.913 47.619 29.93 11.45 41.95 4.26
1966 2391 3.876274 TTGACAAGACTAGCTAGGCTG 57.124 47.619 29.93 23.36 41.95 4.85
1967 2392 4.026744 TGATTGACAAGACTAGCTAGGCT 58.973 43.478 24.19 24.19 45.60 4.58
1968 2393 4.116238 GTGATTGACAAGACTAGCTAGGC 58.884 47.826 24.35 22.21 0.00 3.93
1969 2394 5.105752 GTGTGATTGACAAGACTAGCTAGG 58.894 45.833 24.35 9.25 35.91 3.02
1970 2395 5.574830 GTGTGTGATTGACAAGACTAGCTAG 59.425 44.000 19.44 19.44 35.91 3.42
1971 2396 5.010617 TGTGTGTGATTGACAAGACTAGCTA 59.989 40.000 0.00 0.00 35.91 3.32
1972 2397 4.202253 TGTGTGTGATTGACAAGACTAGCT 60.202 41.667 0.00 0.00 35.91 3.32
1973 2398 4.058124 TGTGTGTGATTGACAAGACTAGC 58.942 43.478 0.00 0.00 35.91 3.42
1974 2399 6.791887 ATTGTGTGTGATTGACAAGACTAG 57.208 37.500 0.00 0.00 35.91 2.57
1975 2400 7.566760 AAATTGTGTGTGATTGACAAGACTA 57.433 32.000 0.00 0.00 35.91 2.59
1976 2401 6.455360 AAATTGTGTGTGATTGACAAGACT 57.545 33.333 0.00 0.00 35.91 3.24
1977 2402 6.360681 GCTAAATTGTGTGTGATTGACAAGAC 59.639 38.462 0.00 0.00 35.91 3.01
1978 2403 6.262944 AGCTAAATTGTGTGTGATTGACAAGA 59.737 34.615 0.00 0.00 35.91 3.02
1979 2404 6.441274 AGCTAAATTGTGTGTGATTGACAAG 58.559 36.000 0.00 0.00 35.91 3.16
1980 2405 6.039159 TGAGCTAAATTGTGTGTGATTGACAA 59.961 34.615 0.00 0.00 35.91 3.18
1981 2406 5.530543 TGAGCTAAATTGTGTGTGATTGACA 59.469 36.000 0.00 0.00 0.00 3.58
1982 2407 5.853282 GTGAGCTAAATTGTGTGTGATTGAC 59.147 40.000 0.00 0.00 0.00 3.18
1983 2408 5.048782 GGTGAGCTAAATTGTGTGTGATTGA 60.049 40.000 0.00 0.00 0.00 2.57
1984 2409 5.156355 GGTGAGCTAAATTGTGTGTGATTG 58.844 41.667 0.00 0.00 0.00 2.67
1985 2410 4.083324 CGGTGAGCTAAATTGTGTGTGATT 60.083 41.667 0.00 0.00 0.00 2.57
1986 2411 3.436704 CGGTGAGCTAAATTGTGTGTGAT 59.563 43.478 0.00 0.00 0.00 3.06
1987 2412 2.805671 CGGTGAGCTAAATTGTGTGTGA 59.194 45.455 0.00 0.00 0.00 3.58
1988 2413 2.665519 GCGGTGAGCTAAATTGTGTGTG 60.666 50.000 0.00 0.00 44.04 3.82
1989 2414 1.535462 GCGGTGAGCTAAATTGTGTGT 59.465 47.619 0.00 0.00 44.04 3.72
1990 2415 1.464023 CGCGGTGAGCTAAATTGTGTG 60.464 52.381 0.00 0.00 45.59 3.82
1991 2416 0.796312 CGCGGTGAGCTAAATTGTGT 59.204 50.000 0.00 0.00 45.59 3.72
1992 2417 0.521242 GCGCGGTGAGCTAAATTGTG 60.521 55.000 8.83 0.00 45.59 3.33
1993 2418 0.953471 TGCGCGGTGAGCTAAATTGT 60.953 50.000 8.83 0.00 45.59 2.71
1994 2419 0.247814 CTGCGCGGTGAGCTAAATTG 60.248 55.000 8.83 0.00 45.59 2.32
1995 2420 1.982073 GCTGCGCGGTGAGCTAAATT 61.982 55.000 19.23 0.00 45.59 1.82
1996 2421 2.464459 GCTGCGCGGTGAGCTAAAT 61.464 57.895 19.23 0.00 45.59 1.40
2006 2431 2.432456 TGAACTAGTGCTGCGCGG 60.432 61.111 13.18 13.18 0.00 6.46
2210 2675 4.415596 TCAAACCCACAGCCTCAAATATT 58.584 39.130 0.00 0.00 0.00 1.28
2211 2676 4.046286 TCAAACCCACAGCCTCAAATAT 57.954 40.909 0.00 0.00 0.00 1.28
2273 2739 3.459227 TGAATTCCATATCAGGTGAGCCA 59.541 43.478 2.27 0.00 37.19 4.75
2274 2740 4.090761 TGAATTCCATATCAGGTGAGCC 57.909 45.455 2.27 0.00 0.00 4.70
2482 2951 6.112927 ACCATAATTCTGTTGGTGCAAAAT 57.887 33.333 0.00 0.00 42.09 1.82
2628 3097 9.982651 TTGGCATGAAGTTAGTAGATAAGTATC 57.017 33.333 0.00 0.00 0.00 2.24
2772 3241 3.692791 CATGAACAGATGACATGCCTG 57.307 47.619 0.00 0.00 35.72 4.85
2784 3253 7.025963 GGAAAAGATTCTAACAGCATGAACAG 58.974 38.462 0.00 0.00 36.10 3.16
3113 3582 4.160065 GTCCTCTTAACCCACCTCTTCTAC 59.840 50.000 0.00 0.00 0.00 2.59
3190 3659 5.738909 AGAAGATGATGTAGTTGTTCAGGG 58.261 41.667 0.00 0.00 0.00 4.45
3290 3759 1.082496 GTGCACTCAACTCGCTTGC 60.082 57.895 10.32 0.00 0.00 4.01
3335 3804 5.908916 TCGAAACGATGTGTTGTTCAATA 57.091 34.783 0.00 0.00 40.84 1.90
3410 3879 5.069914 ACCTATGCACGACCATTATACTCAA 59.930 40.000 0.00 0.00 0.00 3.02
3415 3884 4.559906 CGGAACCTATGCACGACCATTATA 60.560 45.833 0.00 0.00 0.00 0.98
3447 3940 3.007940 TGAGTGGTGGTCTGATAAAGTGG 59.992 47.826 0.00 0.00 0.00 4.00
3448 3941 4.271696 TGAGTGGTGGTCTGATAAAGTG 57.728 45.455 0.00 0.00 0.00 3.16
3449 3942 4.974645 TTGAGTGGTGGTCTGATAAAGT 57.025 40.909 0.00 0.00 0.00 2.66
3450 3943 7.554118 ACATTATTGAGTGGTGGTCTGATAAAG 59.446 37.037 0.00 0.00 0.00 1.85
3451 3944 7.402054 ACATTATTGAGTGGTGGTCTGATAAA 58.598 34.615 0.00 0.00 0.00 1.40
3452 3945 6.957631 ACATTATTGAGTGGTGGTCTGATAA 58.042 36.000 0.00 0.00 0.00 1.75
3453 3946 6.156083 TGACATTATTGAGTGGTGGTCTGATA 59.844 38.462 0.00 0.00 0.00 2.15
3454 3947 5.045651 TGACATTATTGAGTGGTGGTCTGAT 60.046 40.000 0.00 0.00 0.00 2.90
3455 3948 4.285775 TGACATTATTGAGTGGTGGTCTGA 59.714 41.667 0.00 0.00 0.00 3.27
3456 3949 4.578871 TGACATTATTGAGTGGTGGTCTG 58.421 43.478 0.00 0.00 0.00 3.51
3457 3950 4.836825 CTGACATTATTGAGTGGTGGTCT 58.163 43.478 0.00 0.00 0.00 3.85
3458 3951 3.375299 GCTGACATTATTGAGTGGTGGTC 59.625 47.826 0.00 0.00 0.00 4.02
3459 3952 3.244875 TGCTGACATTATTGAGTGGTGGT 60.245 43.478 0.00 0.00 0.00 4.16
3460 3953 3.346315 TGCTGACATTATTGAGTGGTGG 58.654 45.455 0.00 0.00 0.00 4.61
3461 3954 5.106038 ACAATGCTGACATTATTGAGTGGTG 60.106 40.000 14.99 0.00 44.83 4.17
3462 3955 5.012239 ACAATGCTGACATTATTGAGTGGT 58.988 37.500 14.99 0.00 44.83 4.16
3463 3956 5.337554 CACAATGCTGACATTATTGAGTGG 58.662 41.667 14.99 3.02 44.83 4.00
3464 3957 5.106038 ACCACAATGCTGACATTATTGAGTG 60.106 40.000 14.99 6.94 44.83 3.51
3465 3958 5.012239 ACCACAATGCTGACATTATTGAGT 58.988 37.500 14.99 10.35 44.83 3.41
3466 3959 5.356190 AGACCACAATGCTGACATTATTGAG 59.644 40.000 14.99 9.26 44.83 3.02
3467 3960 5.124297 CAGACCACAATGCTGACATTATTGA 59.876 40.000 14.99 0.00 44.83 2.57
3468 3961 5.337554 CAGACCACAATGCTGACATTATTG 58.662 41.667 9.17 9.17 44.83 1.90
3469 3962 4.400251 CCAGACCACAATGCTGACATTATT 59.600 41.667 0.00 0.00 44.83 1.40
3470 3963 3.949754 CCAGACCACAATGCTGACATTAT 59.050 43.478 0.00 0.00 44.83 1.28
3471 3964 3.346315 CCAGACCACAATGCTGACATTA 58.654 45.455 0.00 0.00 44.83 1.90
3546 4047 2.452813 CGACTGTGGTGGCATACGC 61.453 63.158 0.00 0.00 37.44 4.42
3584 4087 3.330701 AGAGGCACCCTTGAGAAATGTAA 59.669 43.478 0.00 0.00 31.76 2.41
3623 4126 7.716799 ACTGGCAATCTTTATGGTAAAATGA 57.283 32.000 0.00 0.00 0.00 2.57
3778 4285 7.919385 AAGATAGGGCCAATAATGTTTGAAT 57.081 32.000 6.18 0.00 0.00 2.57
3781 4288 6.697019 CGAAAAGATAGGGCCAATAATGTTTG 59.303 38.462 6.18 0.00 0.00 2.93
3786 4293 6.833933 AGTTTCGAAAAGATAGGGCCAATAAT 59.166 34.615 13.10 0.00 0.00 1.28
3789 4296 4.600062 AGTTTCGAAAAGATAGGGCCAAT 58.400 39.130 13.10 0.00 0.00 3.16
3794 4301 5.186198 ACATGGAGTTTCGAAAAGATAGGG 58.814 41.667 13.10 2.90 0.00 3.53
3829 4336 2.092914 GTGGGAGGCACTTAGTAAGCAT 60.093 50.000 9.92 0.00 41.55 3.79
4017 4525 9.762933 CCTTCCATTTTCTGAAGAATGTTTTTA 57.237 29.630 16.62 4.78 40.30 1.52
4053 4561 0.897621 ATGACACCGAGATGACAGCA 59.102 50.000 0.00 0.00 0.00 4.41
4211 4721 2.749044 ATCCCACTTGCTGCTGCG 60.749 61.111 11.21 0.00 43.34 5.18
4226 4736 4.455190 AGCAGCAAGTTTCTCTTTGAGATC 59.545 41.667 0.00 0.00 38.56 2.75
4382 4892 3.790820 CACCAAACAAACACATCTCAACG 59.209 43.478 0.00 0.00 0.00 4.10
4449 4959 0.807275 CCGATCGCACTGCAATCTCA 60.807 55.000 10.32 0.00 0.00 3.27
4525 5035 8.147058 GTCACCATACTGAATCTTACTGATGAT 58.853 37.037 0.00 0.00 35.21 2.45
4624 5134 2.670934 AAGCTCAAGTGCGGCCAG 60.671 61.111 2.24 0.00 38.13 4.85
4630 5140 1.003116 CCATATCGCAAGCTCAAGTGC 60.003 52.381 0.00 0.00 37.40 4.40
4676 5186 3.129988 ACAGCCATTTGATCAAGCTAAGC 59.870 43.478 17.42 12.93 31.23 3.09
4677 5187 4.397103 TCACAGCCATTTGATCAAGCTAAG 59.603 41.667 17.42 13.48 31.23 2.18
4678 5188 4.334552 TCACAGCCATTTGATCAAGCTAA 58.665 39.130 17.42 0.51 31.23 3.09
4679 5189 3.954200 TCACAGCCATTTGATCAAGCTA 58.046 40.909 17.42 0.86 31.23 3.32
4680 5190 2.799017 TCACAGCCATTTGATCAAGCT 58.201 42.857 13.36 13.36 0.00 3.74
4681 5191 3.248266 GTTCACAGCCATTTGATCAAGC 58.752 45.455 8.41 9.04 0.00 4.01
4682 5192 3.508793 AGGTTCACAGCCATTTGATCAAG 59.491 43.478 8.41 0.00 0.00 3.02
4683 5193 3.499338 AGGTTCACAGCCATTTGATCAA 58.501 40.909 3.38 3.38 0.00 2.57
4684 5194 3.159213 AGGTTCACAGCCATTTGATCA 57.841 42.857 0.00 0.00 0.00 2.92
4685 5195 3.065925 GCTAGGTTCACAGCCATTTGATC 59.934 47.826 0.00 0.00 0.00 2.92
4686 5196 3.019564 GCTAGGTTCACAGCCATTTGAT 58.980 45.455 0.00 0.00 0.00 2.57
4687 5197 2.436417 GCTAGGTTCACAGCCATTTGA 58.564 47.619 0.00 0.00 0.00 2.69
4688 5198 1.131126 CGCTAGGTTCACAGCCATTTG 59.869 52.381 0.00 0.00 34.15 2.32
4689 5199 1.271379 ACGCTAGGTTCACAGCCATTT 60.271 47.619 0.00 0.00 34.15 2.32
4690 5200 0.324943 ACGCTAGGTTCACAGCCATT 59.675 50.000 0.00 0.00 34.15 3.16
4691 5201 0.391661 CACGCTAGGTTCACAGCCAT 60.392 55.000 0.00 0.00 34.15 4.40
4692 5202 1.005037 CACGCTAGGTTCACAGCCA 60.005 57.895 0.00 0.00 34.15 4.75
4693 5203 0.737715 CTCACGCTAGGTTCACAGCC 60.738 60.000 0.00 0.00 34.15 4.85
4694 5204 1.355066 GCTCACGCTAGGTTCACAGC 61.355 60.000 0.00 0.00 0.00 4.40
4695 5205 0.244994 AGCTCACGCTAGGTTCACAG 59.755 55.000 0.00 0.00 46.79 3.66
4696 5206 2.351777 AGCTCACGCTAGGTTCACA 58.648 52.632 0.00 0.00 46.79 3.58
4706 5216 1.645034 TGATCAAGCTAAGCTCACGC 58.355 50.000 0.00 0.00 38.25 5.34
4707 5217 3.681897 AGTTTGATCAAGCTAAGCTCACG 59.318 43.478 21.72 0.00 38.25 4.35
4708 5218 5.388944 CAAGTTTGATCAAGCTAAGCTCAC 58.611 41.667 23.05 8.83 38.25 3.51
4709 5219 4.083110 GCAAGTTTGATCAAGCTAAGCTCA 60.083 41.667 27.39 4.93 38.25 4.26
4710 5220 4.155644 AGCAAGTTTGATCAAGCTAAGCTC 59.844 41.667 29.71 17.08 38.06 4.09
4711 5221 4.077822 AGCAAGTTTGATCAAGCTAAGCT 58.922 39.130 29.71 29.71 42.56 3.74
4757 5267 7.699391 GTGTTGTCAATCCATGTTTGATCTATG 59.301 37.037 10.47 0.00 35.68 2.23
4773 5283 5.183713 CACTTACCATCCATGTGTTGTCAAT 59.816 40.000 0.00 0.00 0.00 2.57
4816 6009 1.494960 TCAGCCCTGGTTTTGCTTTT 58.505 45.000 0.00 0.00 31.77 2.27
4878 6071 5.006552 ACTTTGCGGAAACATTGAACATTTG 59.993 36.000 0.00 0.00 0.00 2.32
4906 6099 3.900941 AGTTCATTGTCGATTGCAAACC 58.099 40.909 1.71 0.00 0.00 3.27
4935 6128 6.988522 TGATTAATGCTGCTTACTATACCGA 58.011 36.000 0.00 0.00 0.00 4.69
5007 6200 3.181493 GGTTGATGCTCAGTTGCTTATGG 60.181 47.826 0.00 0.00 0.00 2.74
5009 6202 2.679837 CGGTTGATGCTCAGTTGCTTAT 59.320 45.455 0.00 0.00 0.00 1.73
5064 6265 8.096414 CCAAAAGTGATGTTGAATTCCCTATTT 58.904 33.333 2.27 0.00 0.00 1.40
5065 6266 7.614494 CCAAAAGTGATGTTGAATTCCCTATT 58.386 34.615 2.27 0.00 0.00 1.73
5092 6293 8.418662 GCTATGAACATCGGTATAATATGGGTA 58.581 37.037 0.00 0.00 0.00 3.69
5106 6307 1.299850 TCGCCGGCTATGAACATCG 60.300 57.895 26.68 4.37 0.00 3.84


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

AutoCloner maintained by Alex Coulton.