Multiple sequence alignment - TraesCS2D01G193500

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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 TraesCS2D01G193500 chr2D 100.000 6662 0 0 1 6662 138700377 138693716 0.000000e+00 12303.0
1 TraesCS2D01G193500 chr2D 92.360 589 35 4 1 586 438014001 438014582 0.000000e+00 830.0
2 TraesCS2D01G193500 chr2D 91.597 595 36 6 1 586 152028247 152028836 0.000000e+00 809.0
3 TraesCS2D01G193500 chr2D 91.540 591 43 4 1 586 577997735 577997147 0.000000e+00 808.0
4 TraesCS2D01G193500 chr2A 92.873 3999 194 30 2674 6604 162415532 162419507 0.000000e+00 5722.0
5 TraesCS2D01G193500 chr2A 89.882 2115 141 41 580 2667 162413364 162415432 0.000000e+00 2652.0
6 TraesCS2D01G193500 chr2A 88.372 86 10 0 2674 2759 162414912 162414997 3.290000e-18 104.0
7 TraesCS2D01G193500 chr2B 93.215 2093 91 12 2674 4724 197150874 197148791 0.000000e+00 3031.0
8 TraesCS2D01G193500 chr2B 90.980 1674 91 32 617 2272 197152975 197151344 0.000000e+00 2200.0
9 TraesCS2D01G193500 chr2B 91.418 1305 62 16 4709 5969 197148602 197147304 0.000000e+00 1744.0
10 TraesCS2D01G193500 chr2B 84.323 606 67 8 6002 6604 197147303 197146723 9.700000e-158 568.0
11 TraesCS2D01G193500 chr2B 90.831 349 31 1 2319 2666 197151331 197150983 3.640000e-127 466.0
12 TraesCS2D01G193500 chr2B 91.803 61 5 0 2674 2734 197151464 197151404 1.190000e-12 86.1
13 TraesCS2D01G193500 chr4D 92.230 592 35 6 1 586 296267447 296268033 0.000000e+00 828.0
14 TraesCS2D01G193500 chr6D 91.906 593 42 4 1 588 51405520 51404929 0.000000e+00 824.0
15 TraesCS2D01G193500 chr7D 92.334 587 26 8 12 587 94753410 94753988 0.000000e+00 817.0
16 TraesCS2D01G193500 chr7D 91.500 600 35 7 1 588 97944621 97944026 0.000000e+00 811.0
17 TraesCS2D01G193500 chr7D 93.939 66 4 0 2428 2493 79630361 79630296 4.250000e-17 100.0
18 TraesCS2D01G193500 chrUn 91.625 597 30 9 1 586 103941178 103940591 0.000000e+00 808.0
19 TraesCS2D01G193500 chrUn 86.120 317 38 3 2360 2675 36178708 36179019 2.980000e-88 337.0
20 TraesCS2D01G193500 chr1D 91.540 591 37 5 1 588 24138400 24138980 0.000000e+00 802.0
21 TraesCS2D01G193500 chr5D 79.295 227 37 8 2396 2619 502029297 502029078 4.160000e-32 150.0
22 TraesCS2D01G193500 chr7A 87.218 133 14 1 2405 2537 82510746 82510617 1.500000e-31 148.0
23 TraesCS2D01G193500 chr5B 91.667 48 4 0 2360 2407 245968606 245968653 4.310000e-07 67.6


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 TraesCS2D01G193500 chr2D 138693716 138700377 6661 True 12303.000000 12303 100.000000 1 6662 1 chr2D.!!$R1 6661
1 TraesCS2D01G193500 chr2D 438014001 438014582 581 False 830.000000 830 92.360000 1 586 1 chr2D.!!$F2 585
2 TraesCS2D01G193500 chr2D 152028247 152028836 589 False 809.000000 809 91.597000 1 586 1 chr2D.!!$F1 585
3 TraesCS2D01G193500 chr2D 577997147 577997735 588 True 808.000000 808 91.540000 1 586 1 chr2D.!!$R2 585
4 TraesCS2D01G193500 chr2A 162413364 162419507 6143 False 2826.000000 5722 90.375667 580 6604 3 chr2A.!!$F1 6024
5 TraesCS2D01G193500 chr2B 197146723 197152975 6252 True 1349.183333 3031 90.428333 617 6604 6 chr2B.!!$R1 5987
6 TraesCS2D01G193500 chr4D 296267447 296268033 586 False 828.000000 828 92.230000 1 586 1 chr4D.!!$F1 585
7 TraesCS2D01G193500 chr6D 51404929 51405520 591 True 824.000000 824 91.906000 1 588 1 chr6D.!!$R1 587
8 TraesCS2D01G193500 chr7D 94753410 94753988 578 False 817.000000 817 92.334000 12 587 1 chr7D.!!$F1 575
9 TraesCS2D01G193500 chr7D 97944026 97944621 595 True 811.000000 811 91.500000 1 588 1 chr7D.!!$R2 587
10 TraesCS2D01G193500 chrUn 103940591 103941178 587 True 808.000000 808 91.625000 1 586 1 chrUn.!!$R1 585
11 TraesCS2D01G193500 chr1D 24138400 24138980 580 False 802.000000 802 91.540000 1 588 1 chr1D.!!$F1 587

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
638 671 0.467804 CCTAGGGCAGAGGAGAAAGC 59.532 60.000 0.00 0.00 35.99 3.51 F
2242 2297 0.391597 GGGGTCTTCAGACGTGTTCA 59.608 55.000 0.00 0.00 45.65 3.18 F
2663 2723 0.035820 AAACCACGGCGTACCATCAT 60.036 50.000 14.22 0.00 34.57 2.45 F
2668 2736 1.142965 CGGCGTACCATCATGACCA 59.857 57.895 0.00 0.00 34.57 4.02 F
2671 2739 1.290203 GCGTACCATCATGACCACAG 58.710 55.000 0.00 0.00 0.00 3.66 F
2715 2876 1.299939 GGGAGAGGAGGGGTGATTTT 58.700 55.000 0.00 0.00 0.00 1.82 F
3941 4113 1.565156 GAACATGGCGACGCTGACAA 61.565 55.000 20.77 1.02 0.00 3.18 F
5170 5592 1.796796 GAACAGCGAGATTGTGCCC 59.203 57.895 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 2469 0.031314 CATCGAGCGCTGTACTGGAT 59.969 55.000 18.48 0.0 33.45 3.41 R
3941 4113 0.251653 TCTGGACGGCTACTCTGGTT 60.252 55.000 0.00 0.0 0.00 3.67 R
4187 4389 1.608590 CATTGTTTCTGCCCACGTCTT 59.391 47.619 0.00 0.0 0.00 3.01 R
4501 4703 2.036346 AGAACAAAATGAGGCCAACTGC 59.964 45.455 5.01 0.0 40.16 4.40 R
4876 5298 9.121658 CATGCCAGATAGATGCATTCTAATAAT 57.878 33.333 0.00 0.0 42.79 1.28 R
5107 5529 3.034635 AGACTCGTATTTCAGGATGCCT 58.965 45.455 0.00 0.0 34.76 4.75 R
5321 5743 0.598065 AAATGCCACGAAAGCCTCAC 59.402 50.000 0.00 0.0 0.00 3.51 R
6497 6966 0.029300 GCTCACGCAAAAGCAAGACA 59.971 50.000 0.00 0.0 38.42 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 319 2.649531 AATTTCCTCGGTTGTGGTGA 57.350 45.000 0.00 0.00 0.00 4.02
404 422 6.432936 CAATAAGATGGATATGTGTGTGTGC 58.567 40.000 0.00 0.00 0.00 4.57
406 424 1.003545 GATGGATATGTGTGTGTGCGC 60.004 52.381 0.00 0.00 0.00 6.09
473 497 1.272536 GGGAGGGAGAGAGTGTGTGTA 60.273 57.143 0.00 0.00 0.00 2.90
562 589 8.761689 ACTCTTAAAGTTAATATGGTCCCGTTA 58.238 33.333 0.00 0.00 33.03 3.18
638 671 0.467804 CCTAGGGCAGAGGAGAAAGC 59.532 60.000 0.00 0.00 35.99 3.51
666 699 2.416747 TCCAGTCATTTCAGCAGTTCG 58.583 47.619 0.00 0.00 0.00 3.95
807 841 1.817099 CCATCGAGAGGGCAGCAAC 60.817 63.158 0.00 0.00 0.00 4.17
809 843 0.674581 CATCGAGAGGGCAGCAACAA 60.675 55.000 0.00 0.00 0.00 2.83
918 958 4.354162 GTTTGCGCCCCCTACCCA 62.354 66.667 4.18 0.00 0.00 4.51
919 959 4.354162 TTTGCGCCCCCTACCCAC 62.354 66.667 4.18 0.00 0.00 4.61
942 982 2.892425 CTCCCGACTCGCCATTGC 60.892 66.667 0.00 0.00 0.00 3.56
1090 1130 2.806244 GGTATCCGTTTCCCGAATGATG 59.194 50.000 0.00 0.00 39.56 3.07
1103 1143 4.580167 CCCGAATGATGCTAGGATTTTTCA 59.420 41.667 15.48 4.81 0.00 2.69
1121 1161 0.688087 CAGACCAGGGAGGGGAGTAC 60.688 65.000 0.00 0.00 43.89 2.73
1195 1236 2.871022 GCAGTATCATCTTCACAGGCTG 59.129 50.000 14.16 14.16 0.00 4.85
1215 1260 1.086696 CGCTGTTCCTGTGGGTTATG 58.913 55.000 0.00 0.00 0.00 1.90
1216 1261 1.610624 CGCTGTTCCTGTGGGTTATGT 60.611 52.381 0.00 0.00 0.00 2.29
1217 1262 2.354303 CGCTGTTCCTGTGGGTTATGTA 60.354 50.000 0.00 0.00 0.00 2.29
1218 1263 3.681594 CGCTGTTCCTGTGGGTTATGTAT 60.682 47.826 0.00 0.00 0.00 2.29
1225 1270 4.342951 TCCTGTGGGTTATGTATTAGTCGG 59.657 45.833 0.00 0.00 0.00 4.79
1244 1289 6.098017 AGTCGGTTGTATTTCTAAGCAGTAC 58.902 40.000 0.00 0.00 0.00 2.73
1328 1377 5.596772 AGGTTCTAGATTCCTGCTCTCTTAC 59.403 44.000 13.91 0.00 0.00 2.34
1332 1381 6.427441 TCTAGATTCCTGCTCTCTTACTTGA 58.573 40.000 0.00 0.00 0.00 3.02
1334 1383 8.221251 TCTAGATTCCTGCTCTCTTACTTGATA 58.779 37.037 0.00 0.00 0.00 2.15
1335 1384 7.288810 AGATTCCTGCTCTCTTACTTGATAG 57.711 40.000 0.00 0.00 0.00 2.08
1341 1390 6.756074 CCTGCTCTCTTACTTGATAGTTCTTG 59.244 42.308 0.00 0.00 35.78 3.02
1368 1417 3.030291 TGTTTTGGTCAGCTTTCACCAT 58.970 40.909 9.31 0.00 42.42 3.55
1378 1427 7.450014 TGGTCAGCTTTCACCATTTTTCTTATA 59.550 33.333 5.03 0.00 37.78 0.98
1509 1560 2.810274 GTTCCTCTTACCCGTTTGTTCC 59.190 50.000 0.00 0.00 0.00 3.62
1523 1574 4.608445 CGTTTGTTCCGTTTCACAGAGATC 60.608 45.833 0.00 0.00 0.00 2.75
1532 1583 0.735471 TCACAGAGATCGAGAAGGCG 59.265 55.000 0.00 0.00 0.00 5.52
1637 1688 2.166664 GCAGTACCTCTTCGTCTTGGAT 59.833 50.000 0.00 0.00 0.00 3.41
1681 1732 3.432326 CCAGGTATTAGTTCAGCCAGGAC 60.432 52.174 0.00 0.00 0.00 3.85
1704 1755 3.728718 CGTACTTGGTGTTTTGAACATGC 59.271 43.478 0.00 0.00 44.35 4.06
1708 1759 4.099881 ACTTGGTGTTTTGAACATGCAGAT 59.900 37.500 0.00 0.00 44.35 2.90
1752 1803 8.008513 TGTCCTTATCTTATGAGTGGTACTTC 57.991 38.462 0.00 0.00 0.00 3.01
1804 1855 3.361281 ACAGACATCAGACATTGCCAT 57.639 42.857 0.00 0.00 0.00 4.40
1824 1875 6.591062 TGCCATTCTATGTTTGCATTTCTTTC 59.409 34.615 0.00 0.00 36.58 2.62
1882 1933 4.914291 GCACAACACGTGGTTAGC 57.086 55.556 21.57 15.74 46.45 3.09
1894 1945 2.134933 GGTTAGCGGAGAGGAGGGG 61.135 68.421 0.00 0.00 0.00 4.79
1909 1960 2.165641 GGAGGGGCGGTTTATTTTTCTG 59.834 50.000 0.00 0.00 0.00 3.02
1912 1963 2.297880 GGGGCGGTTTATTTTTCTGTGT 59.702 45.455 0.00 0.00 0.00 3.72
1929 1980 6.993786 TCTGTGTTTACTTGTTGACAATGA 57.006 33.333 0.00 0.00 35.02 2.57
1932 1983 8.465999 TCTGTGTTTACTTGTTGACAATGATTT 58.534 29.630 0.00 0.00 35.02 2.17
1942 1993 9.740239 CTTGTTGACAATGATTTGGGATATTAG 57.260 33.333 0.00 0.00 37.15 1.73
1945 1996 9.956720 GTTGACAATGATTTGGGATATTAGAAG 57.043 33.333 0.00 0.00 37.15 2.85
1947 1998 9.342308 TGACAATGATTTGGGATATTAGAAGAC 57.658 33.333 0.00 0.00 37.15 3.01
1948 1999 9.342308 GACAATGATTTGGGATATTAGAAGACA 57.658 33.333 0.00 0.00 37.15 3.41
1952 2003 8.607441 TGATTTGGGATATTAGAAGACATTCG 57.393 34.615 0.00 0.00 40.58 3.34
1953 2004 7.661437 TGATTTGGGATATTAGAAGACATTCGG 59.339 37.037 0.00 0.00 40.58 4.30
1954 2005 6.494666 TTGGGATATTAGAAGACATTCGGT 57.505 37.500 0.00 0.00 40.58 4.69
1966 2019 1.999735 ACATTCGGTCGTGCAGTATTG 59.000 47.619 0.00 0.00 0.00 1.90
1982 2036 6.712095 TGCAGTATTGTTCTTCTCATGACTTT 59.288 34.615 0.00 0.00 0.00 2.66
1983 2037 7.229306 TGCAGTATTGTTCTTCTCATGACTTTT 59.771 33.333 0.00 0.00 0.00 2.27
1984 2038 8.721478 GCAGTATTGTTCTTCTCATGACTTTTA 58.279 33.333 0.00 0.00 0.00 1.52
1986 2040 9.442047 AGTATTGTTCTTCTCATGACTTTTAGG 57.558 33.333 0.00 0.00 0.00 2.69
1987 2041 7.693969 ATTGTTCTTCTCATGACTTTTAGGG 57.306 36.000 0.00 0.00 0.00 3.53
1988 2042 6.187727 TGTTCTTCTCATGACTTTTAGGGT 57.812 37.500 0.00 0.00 0.00 4.34
1989 2043 6.601332 TGTTCTTCTCATGACTTTTAGGGTT 58.399 36.000 0.00 0.00 0.00 4.11
2025 2079 1.798813 AGTGCCGAAATCAACTTCGTC 59.201 47.619 5.17 0.00 45.31 4.20
2029 2083 2.223377 GCCGAAATCAACTTCGTCTTGT 59.777 45.455 5.17 0.00 45.31 3.16
2181 2236 4.421554 TGGCCAGGGGAGAGGAGG 62.422 72.222 0.00 0.00 0.00 4.30
2184 2239 3.700350 CCAGGGGAGAGGAGGGGT 61.700 72.222 0.00 0.00 0.00 4.95
2195 2250 4.270834 GAGAGGAGGGGTGGTTTATTTTC 58.729 47.826 0.00 0.00 0.00 2.29
2217 2272 8.649973 TTTCTCTCTCTTTACTTCTTGACAAC 57.350 34.615 0.00 0.00 0.00 3.32
2228 2283 6.051179 ACTTCTTGACAACTATTAGGGGTC 57.949 41.667 9.02 9.02 0.00 4.46
2231 2286 6.295719 TCTTGACAACTATTAGGGGTCTTC 57.704 41.667 14.29 0.00 0.00 2.87
2235 2290 5.187186 TGACAACTATTAGGGGTCTTCAGAC 59.813 44.000 14.29 0.00 44.04 3.51
2238 2293 3.700038 ACTATTAGGGGTCTTCAGACGTG 59.300 47.826 0.00 0.00 45.65 4.49
2239 2294 2.005370 TTAGGGGTCTTCAGACGTGT 57.995 50.000 0.00 0.00 45.65 4.49
2240 2295 2.005370 TAGGGGTCTTCAGACGTGTT 57.995 50.000 0.00 0.00 45.65 3.32
2241 2296 0.680061 AGGGGTCTTCAGACGTGTTC 59.320 55.000 0.00 0.00 45.65 3.18
2242 2297 0.391597 GGGGTCTTCAGACGTGTTCA 59.608 55.000 0.00 0.00 45.65 3.18
2243 2298 1.202604 GGGGTCTTCAGACGTGTTCAA 60.203 52.381 0.00 0.00 45.65 2.69
2244 2299 2.550208 GGGGTCTTCAGACGTGTTCAAT 60.550 50.000 0.00 0.00 45.65 2.57
2247 2302 3.560068 GGTCTTCAGACGTGTTCAATTGT 59.440 43.478 5.13 0.00 45.65 2.71
2248 2303 4.518217 GTCTTCAGACGTGTTCAATTGTG 58.482 43.478 5.13 0.00 35.12 3.33
2249 2304 3.002246 TCTTCAGACGTGTTCAATTGTGC 59.998 43.478 5.13 0.38 0.00 4.57
2251 2306 2.287644 TCAGACGTGTTCAATTGTGCAG 59.712 45.455 5.13 3.52 0.00 4.41
2253 2308 3.247411 CAGACGTGTTCAATTGTGCAGTA 59.753 43.478 5.13 0.00 0.00 2.74
2254 2309 4.065088 AGACGTGTTCAATTGTGCAGTAT 58.935 39.130 5.13 1.98 0.00 2.12
2257 2313 4.158384 CGTGTTCAATTGTGCAGTATTCC 58.842 43.478 5.13 0.00 0.00 3.01
2272 2328 5.163642 GCAGTATTCCTCTCGTCACTTTAGA 60.164 44.000 0.00 0.00 0.00 2.10
2273 2329 6.259638 CAGTATTCCTCTCGTCACTTTAGAC 58.740 44.000 0.00 0.00 35.19 2.59
2276 2334 5.373981 TTCCTCTCGTCACTTTAGACTTC 57.626 43.478 0.00 0.00 36.38 3.01
2295 2354 7.267128 AGACTTCTAGATTTTCAGATGCAGAG 58.733 38.462 0.00 0.00 0.00 3.35
2306 2365 3.194329 TCAGATGCAGAGATCAACTTCGT 59.806 43.478 0.00 0.00 0.00 3.85
2353 2412 5.935789 GTGCTTATACACCACAAGGAACTTA 59.064 40.000 0.00 0.00 39.93 2.24
2373 2432 6.712276 ACTTATGGATACTAGCTAATTGCCC 58.288 40.000 0.00 0.00 39.44 5.36
2377 2436 2.234300 TACTAGCTAATTGCCCGTGC 57.766 50.000 0.00 0.00 44.23 5.34
2410 2469 5.280676 GGGGGCATCAATATTCTAGTGATCA 60.281 44.000 0.00 0.00 41.06 2.92
2420 2479 9.636879 CAATATTCTAGTGATCATCCAGTACAG 57.363 37.037 0.00 0.00 0.00 2.74
2427 2486 1.029947 TCATCCAGTACAGCGCTCGA 61.030 55.000 7.13 0.00 0.00 4.04
2494 2553 4.839668 ACTCTCCATAGTTAGCGTGATC 57.160 45.455 0.00 0.00 0.00 2.92
2520 2579 5.049828 CACATCCAACGCTTGATGATACTA 58.950 41.667 13.58 0.00 0.00 1.82
2521 2580 5.176406 CACATCCAACGCTTGATGATACTAG 59.824 44.000 13.58 0.00 0.00 2.57
2534 2593 9.424319 CTTGATGATACTAGCCATAATTAACGT 57.576 33.333 0.00 0.00 0.00 3.99
2544 2603 5.542635 AGCCATAATTAACGTGATCCTCCTA 59.457 40.000 0.00 0.00 0.00 2.94
2571 2630 8.424918 TCCAAAGACTGATACTCTCCATAATTC 58.575 37.037 0.00 0.00 0.00 2.17
2585 2644 4.664536 TCCATAATTCACATGATCCTCCCA 59.335 41.667 0.00 0.00 0.00 4.37
2591 2650 2.173356 TCACATGATCCTCCCATCCAAC 59.827 50.000 0.00 0.00 0.00 3.77
2596 2655 2.158769 TGATCCTCCCATCCAACGAATG 60.159 50.000 0.00 0.00 0.00 2.67
2608 2667 4.948847 TCCAACGAATGATACTCTCCATG 58.051 43.478 0.00 0.00 0.00 3.66
2614 2673 8.491152 CAACGAATGATACTCTCCATGATTAAC 58.509 37.037 0.00 0.00 0.00 2.01
2618 2677 6.709018 TGATACTCTCCATGATTAACGTGA 57.291 37.500 0.00 0.00 37.69 4.35
2652 2712 1.478916 AGAAACCAAACCAAACCACGG 59.521 47.619 0.00 0.00 0.00 4.94
2663 2723 0.035820 AAACCACGGCGTACCATCAT 60.036 50.000 14.22 0.00 34.57 2.45
2667 2735 1.143183 ACGGCGTACCATCATGACC 59.857 57.895 12.58 0.00 34.57 4.02
2668 2736 1.142965 CGGCGTACCATCATGACCA 59.857 57.895 0.00 0.00 34.57 4.02
2671 2739 1.290203 GCGTACCATCATGACCACAG 58.710 55.000 0.00 0.00 0.00 3.66
2677 2838 4.412796 ACCATCATGACCACAGACTATG 57.587 45.455 0.00 0.00 0.00 2.23
2706 2867 1.458588 GTGGCTAGGGGAGAGGAGG 60.459 68.421 0.00 0.00 0.00 4.30
2715 2876 1.299939 GGGAGAGGAGGGGTGATTTT 58.700 55.000 0.00 0.00 0.00 1.82
2896 3058 6.208644 TGTGTTTTCTTCTGCTATTTTCAGC 58.791 36.000 0.00 0.00 42.15 4.26
2921 3083 8.983724 GCTATTACCTTTGTTTGCAAATTACAA 58.016 29.630 16.21 12.91 42.88 2.41
2941 3103 6.932901 ACAATGCATCTTGATTTTGTTACG 57.067 33.333 0.00 0.00 0.00 3.18
2965 3127 5.912955 GCTCCACATTGTTACTTTTGTGTAC 59.087 40.000 10.25 0.00 38.19 2.90
2969 3131 6.133392 CACATTGTTACTTTTGTGTACCTCG 58.867 40.000 0.00 0.00 35.79 4.63
3020 3182 5.167303 ACCTGATGTTCCTTAGTTTCTCC 57.833 43.478 0.00 0.00 0.00 3.71
3026 3188 3.075148 GTTCCTTAGTTTCTCCACTGGC 58.925 50.000 0.00 0.00 0.00 4.85
3027 3189 1.628846 TCCTTAGTTTCTCCACTGGCC 59.371 52.381 0.00 0.00 0.00 5.36
3269 3438 5.841810 CAGTTCCCTGTTTCTATGCAAAAA 58.158 37.500 0.00 0.00 33.80 1.94
3426 3595 1.621814 GAGGTACTACCCTGTGTTGCA 59.378 52.381 1.19 0.00 41.55 4.08
3501 3670 9.471084 TGCTCAATTGCTCATATTATTTGAATG 57.529 29.630 0.00 0.00 0.00 2.67
3521 3690 7.990917 TGAATGCTTTGTCACTTAACAACTAA 58.009 30.769 0.00 0.00 38.80 2.24
3547 3716 4.160329 AGTCACACCCATCTTCTTCAGTA 58.840 43.478 0.00 0.00 0.00 2.74
3571 3740 6.234177 ACAATTAGGCATAGCTATCCACTTC 58.766 40.000 18.59 2.32 0.00 3.01
3589 3758 8.306313 TCCACTTCTACTTCAAATATGCTCTA 57.694 34.615 0.00 0.00 0.00 2.43
3590 3759 8.417106 TCCACTTCTACTTCAAATATGCTCTAG 58.583 37.037 0.00 0.00 0.00 2.43
3629 3798 9.383519 AGAACTATCATGTTAATGTCGACATTT 57.616 29.630 39.86 25.78 43.48 2.32
3630 3799 9.988350 GAACTATCATGTTAATGTCGACATTTT 57.012 29.630 39.86 26.37 43.48 1.82
3680 3849 6.449698 TCTCAATTTGGTTCTGAAGCATTTC 58.550 36.000 21.40 0.00 38.87 2.17
3687 3856 5.976458 TGGTTCTGAAGCATTTCTTTGTTT 58.024 33.333 17.52 0.00 34.56 2.83
3700 3869 7.587392 GCATTTCTTTGTTTTGGTGCTTTAATC 59.413 33.333 0.00 0.00 0.00 1.75
3701 3870 8.829612 CATTTCTTTGTTTTGGTGCTTTAATCT 58.170 29.630 0.00 0.00 0.00 2.40
3805 3974 5.097742 TGATTGAACTGATTACCCGTCAT 57.902 39.130 0.00 0.00 0.00 3.06
3819 3988 5.182169 ACCCGTCATTTTCCTGGTAAATA 57.818 39.130 10.45 0.00 0.00 1.40
3872 4041 9.730705 TCTTGATAGCATCATTATTTTAGAGGG 57.269 33.333 0.61 0.00 39.39 4.30
3894 4063 3.617735 TGTCGCCTGTGCCGGTTA 61.618 61.111 1.90 0.00 0.00 2.85
3911 4080 7.329717 GTGCCGGTTACATTTTTCATTTAATGA 59.670 33.333 1.90 3.20 36.03 2.57
3932 4101 2.539003 CCAAGTTCGAACATGGCGA 58.461 52.632 32.44 8.58 40.39 5.54
3941 4113 1.565156 GAACATGGCGACGCTGACAA 61.565 55.000 20.77 1.02 0.00 3.18
4044 4216 9.866655 TGTATTTTTCCAGCTATATTGGAGAAT 57.133 29.630 9.05 12.18 45.00 2.40
4091 4263 3.159472 TCGTTGGCTCCTGTTTAGTCTA 58.841 45.455 0.00 0.00 0.00 2.59
4105 4277 8.926710 CCTGTTTAGTCTATTGTTGTAGTCAAG 58.073 37.037 0.00 0.00 33.97 3.02
4136 4308 7.442364 TGCTTCTGCAGATACATTTTACTATCC 59.558 37.037 19.04 0.00 45.31 2.59
4187 4389 5.163322 GGATCATTTGTCAAATGGGCCAATA 60.163 40.000 29.34 14.59 46.40 1.90
4501 4703 1.804748 GACACGCCTTTAACTCTTGGG 59.195 52.381 0.00 0.00 0.00 4.12
4874 5296 7.719633 ACTGGTTGTAACACTCTTGAACATATT 59.280 33.333 0.00 0.00 0.00 1.28
4875 5297 8.458573 TGGTTGTAACACTCTTGAACATATTT 57.541 30.769 0.00 0.00 0.00 1.40
4876 5298 9.562408 TGGTTGTAACACTCTTGAACATATTTA 57.438 29.630 0.00 0.00 0.00 1.40
5130 5552 4.649674 AGGCATCCTGAAATACGAGTCTAA 59.350 41.667 0.00 0.00 29.57 2.10
5170 5592 1.796796 GAACAGCGAGATTGTGCCC 59.203 57.895 0.00 0.00 0.00 5.36
5321 5743 2.674852 CCACATCTGAATCAGGTTCACG 59.325 50.000 10.71 0.00 41.79 4.35
5335 5757 3.244105 CACGTGAGGCTTTCGTGG 58.756 61.111 26.06 14.37 46.99 4.94
5341 5763 0.597568 TGAGGCTTTCGTGGCATTTG 59.402 50.000 0.00 0.00 34.73 2.32
5378 5800 0.944386 CTGGCTGGTACACAACACAC 59.056 55.000 0.00 0.00 0.00 3.82
5385 5807 3.188492 TGGTACACAACACACACTAACG 58.812 45.455 0.00 0.00 0.00 3.18
5469 5895 8.629158 AGTTCATTAAGTTTATTTGAGTGCACA 58.371 29.630 21.04 0.00 0.00 4.57
5478 5904 7.981225 AGTTTATTTGAGTGCACAATCAACTTT 59.019 29.630 21.04 10.52 43.81 2.66
5483 5909 9.630098 ATTTGAGTGCACAATCAACTTTATTAG 57.370 29.630 21.04 0.00 43.81 1.73
5508 5947 3.971032 AGTACAAGCAAAGCAGTCAAC 57.029 42.857 0.00 0.00 0.00 3.18
5528 5968 2.287547 ACGTGTGTGGCATTTGATTCAC 60.288 45.455 0.00 0.00 0.00 3.18
5531 5971 2.964464 TGTGTGGCATTTGATTCACCTT 59.036 40.909 0.00 0.00 0.00 3.50
5550 5990 1.376466 GGGCTGACTTGGCTCTTGA 59.624 57.895 0.00 0.00 0.00 3.02
5561 6003 5.111293 ACTTGGCTCTTGATTGTGTTTTTG 58.889 37.500 0.00 0.00 0.00 2.44
5882 6347 5.755375 CCAACTATCTGTGCGTTTCATCTAT 59.245 40.000 0.00 0.00 0.00 1.98
5959 6424 1.501582 GTCCAGGTTAGGGCATCTCT 58.498 55.000 0.00 0.00 32.13 3.10
5969 6434 3.051940 AGGGCATCTCTAAGTCCATCA 57.948 47.619 0.00 0.00 0.00 3.07
5982 6447 0.250989 TCCATCAAAACGGACACCCC 60.251 55.000 0.00 0.00 0.00 4.95
5983 6448 1.248101 CCATCAAAACGGACACCCCC 61.248 60.000 0.00 0.00 0.00 5.40
5984 6449 0.251165 CATCAAAACGGACACCCCCT 60.251 55.000 0.00 0.00 0.00 4.79
5986 6451 1.138568 TCAAAACGGACACCCCCTAA 58.861 50.000 0.00 0.00 0.00 2.69
5987 6452 1.706305 TCAAAACGGACACCCCCTAAT 59.294 47.619 0.00 0.00 0.00 1.73
5988 6453 2.911636 TCAAAACGGACACCCCCTAATA 59.088 45.455 0.00 0.00 0.00 0.98
5990 6455 4.018233 TCAAAACGGACACCCCCTAATATT 60.018 41.667 0.00 0.00 0.00 1.28
5992 6457 2.766736 ACGGACACCCCCTAATATTGA 58.233 47.619 0.00 0.00 0.00 2.57
5993 6458 2.436911 ACGGACACCCCCTAATATTGAC 59.563 50.000 0.00 0.00 0.00 3.18
6074 6541 4.261801 CATCAAATGTCCGTCCTAGGTTT 58.738 43.478 9.08 0.00 0.00 3.27
6076 6543 3.325425 TCAAATGTCCGTCCTAGGTTTCA 59.675 43.478 9.08 3.30 0.00 2.69
6080 6547 3.170717 TGTCCGTCCTAGGTTTCATCTT 58.829 45.455 9.08 0.00 0.00 2.40
6139 6606 8.647143 ATTTATACAAAGTGCAAACATATGCC 57.353 30.769 1.58 0.00 45.83 4.40
6163 6630 4.418013 AACAATCAAAATGCGTCGATGA 57.582 36.364 9.31 0.00 0.00 2.92
6195 6662 8.829514 TTCATAAAGTTTTGTACTTGTGTTCG 57.170 30.769 0.00 0.00 46.34 3.95
6238 6705 2.440247 CCGCCAAACATCCTCCCC 60.440 66.667 0.00 0.00 0.00 4.81
6244 6711 0.033109 CAAACATCCTCCCCCTTCCC 60.033 60.000 0.00 0.00 0.00 3.97
6255 6722 2.115266 CCTTCCCCTGTTTGCGGT 59.885 61.111 0.00 0.00 0.00 5.68
6269 6736 3.998672 CGGTGGCGGGTAGTGTGT 61.999 66.667 0.00 0.00 0.00 3.72
6277 6744 3.110178 GGTAGTGTGTGTCGCCGC 61.110 66.667 0.00 0.00 0.00 6.53
6301 6768 4.645131 TTTGCGGGCGGCCACTAA 62.645 61.111 29.19 18.69 42.61 2.24
6358 6826 0.326264 GACATCTCTGCCACCACCTT 59.674 55.000 0.00 0.00 0.00 3.50
6362 6830 0.178921 TCTCTGCCACCACCTTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
6414 6883 1.070786 GGGAACTCAAGTGCGTGGA 59.929 57.895 0.00 0.00 0.00 4.02
6443 6912 2.940514 TGAAGTGGAGATAGTGGGGA 57.059 50.000 0.00 0.00 0.00 4.81
6450 6919 2.206223 GGAGATAGTGGGGAAAAGGGT 58.794 52.381 0.00 0.00 0.00 4.34
6467 6936 0.039527 GGTGGCTTTCGTGCGAAAAT 60.040 50.000 18.35 0.00 42.61 1.82
6488 6957 2.387757 AGTGCGGAAATGGCCAAATAT 58.612 42.857 10.96 0.00 0.00 1.28
6537 7006 0.544357 AGGGGTGTCGGATTCTGACA 60.544 55.000 21.71 21.71 43.68 3.58
6604 7073 1.208535 TCTACGGGAATTTGGACGCAT 59.791 47.619 0.00 0.00 0.00 4.73
6605 7074 2.431419 TCTACGGGAATTTGGACGCATA 59.569 45.455 0.00 0.00 0.00 3.14
6606 7075 1.663695 ACGGGAATTTGGACGCATAG 58.336 50.000 0.00 0.00 0.00 2.23
6607 7076 1.208535 ACGGGAATTTGGACGCATAGA 59.791 47.619 0.00 0.00 0.00 1.98
6608 7077 1.597663 CGGGAATTTGGACGCATAGAC 59.402 52.381 0.00 0.00 0.00 2.59
6609 7078 1.597663 GGGAATTTGGACGCATAGACG 59.402 52.381 0.00 0.00 39.50 4.18
6618 7087 2.665649 ACGCATAGACGTTTGATGGA 57.334 45.000 0.00 0.00 45.75 3.41
6619 7088 2.268298 ACGCATAGACGTTTGATGGAC 58.732 47.619 0.00 0.00 45.75 4.02
6620 7089 1.593006 CGCATAGACGTTTGATGGACC 59.407 52.381 0.00 0.00 0.00 4.46
6621 7090 1.940613 GCATAGACGTTTGATGGACCC 59.059 52.381 0.00 0.00 0.00 4.46
6622 7091 2.679639 GCATAGACGTTTGATGGACCCA 60.680 50.000 0.00 0.00 0.00 4.51
6623 7092 3.605634 CATAGACGTTTGATGGACCCAA 58.394 45.455 0.00 0.00 0.00 4.12
6624 7093 2.649531 AGACGTTTGATGGACCCAAA 57.350 45.000 0.00 0.00 0.00 3.28
6625 7094 2.938838 AGACGTTTGATGGACCCAAAA 58.061 42.857 0.00 0.00 35.57 2.44
6626 7095 3.496331 AGACGTTTGATGGACCCAAAAT 58.504 40.909 0.00 0.00 35.57 1.82
6627 7096 3.255642 AGACGTTTGATGGACCCAAAATG 59.744 43.478 0.00 0.00 35.57 2.32
6628 7097 2.962421 ACGTTTGATGGACCCAAAATGT 59.038 40.909 5.62 5.62 35.57 2.71
6629 7098 3.386402 ACGTTTGATGGACCCAAAATGTT 59.614 39.130 5.62 0.00 35.57 2.71
6630 7099 4.141824 ACGTTTGATGGACCCAAAATGTTT 60.142 37.500 5.62 0.00 35.57 2.83
6631 7100 4.447389 CGTTTGATGGACCCAAAATGTTTC 59.553 41.667 0.00 0.00 35.57 2.78
6632 7101 3.932545 TGATGGACCCAAAATGTTTCG 57.067 42.857 0.00 0.00 0.00 3.46
6633 7102 3.491342 TGATGGACCCAAAATGTTTCGA 58.509 40.909 0.00 0.00 0.00 3.71
6634 7103 3.254657 TGATGGACCCAAAATGTTTCGAC 59.745 43.478 0.00 0.00 0.00 4.20
6635 7104 2.656002 TGGACCCAAAATGTTTCGACA 58.344 42.857 0.00 0.00 0.00 4.35
6636 7105 3.024547 TGGACCCAAAATGTTTCGACAA 58.975 40.909 0.00 0.00 0.00 3.18
6637 7106 3.181485 TGGACCCAAAATGTTTCGACAAC 60.181 43.478 0.00 0.00 0.00 3.32
6638 7107 3.181485 GGACCCAAAATGTTTCGACAACA 60.181 43.478 13.12 13.12 34.31 3.33
6639 7108 4.500716 GGACCCAAAATGTTTCGACAACAT 60.501 41.667 15.64 15.64 42.19 2.71
6640 7109 4.367450 ACCCAAAATGTTTCGACAACATG 58.633 39.130 19.60 12.56 40.43 3.21
6641 7110 3.740321 CCCAAAATGTTTCGACAACATGG 59.260 43.478 19.60 17.89 40.43 3.66
6642 7111 4.367450 CCAAAATGTTTCGACAACATGGT 58.633 39.130 19.60 12.05 40.43 3.55
6643 7112 4.444056 CCAAAATGTTTCGACAACATGGTC 59.556 41.667 19.60 0.00 40.43 4.02
6644 7113 3.915437 AATGTTTCGACAACATGGTCC 57.085 42.857 19.60 0.00 40.43 4.46
6645 7114 1.222300 TGTTTCGACAACATGGTCCG 58.778 50.000 0.00 0.00 34.24 4.79
6646 7115 1.202545 TGTTTCGACAACATGGTCCGA 60.203 47.619 0.00 0.00 34.24 4.55
6647 7116 1.868498 GTTTCGACAACATGGTCCGAA 59.132 47.619 12.02 12.02 34.24 4.30
6648 7117 1.504359 TTCGACAACATGGTCCGAAC 58.496 50.000 12.02 0.00 34.24 3.95
6649 7118 0.665068 TCGACAACATGGTCCGAACG 60.665 55.000 2.59 0.00 34.24 3.95
6650 7119 0.942410 CGACAACATGGTCCGAACGT 60.942 55.000 0.00 0.00 34.24 3.99
6651 7120 1.223187 GACAACATGGTCCGAACGTT 58.777 50.000 0.00 0.00 0.00 3.99
6652 7121 2.406130 GACAACATGGTCCGAACGTTA 58.594 47.619 0.00 0.00 0.00 3.18
6653 7122 2.137523 ACAACATGGTCCGAACGTTAC 58.862 47.619 0.00 0.00 0.00 2.50
6654 7123 1.125384 CAACATGGTCCGAACGTTACG 59.875 52.381 0.00 2.19 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
404 422 1.732809 TCTCTCTCTCTAACACACGCG 59.267 52.381 3.53 3.53 0.00 6.01
406 424 2.680841 CCCTCTCTCTCTCTAACACACG 59.319 54.545 0.00 0.00 0.00 4.49
638 671 2.426024 CTGAAATGACTGGATTGCCCTG 59.574 50.000 0.00 0.00 39.53 4.45
666 699 0.036875 CTGAGTTTGACCCACCTCCC 59.963 60.000 0.00 0.00 0.00 4.30
790 824 0.674581 TTGTTGCTGCCCTCTCGATG 60.675 55.000 0.00 0.00 0.00 3.84
807 841 1.053835 AGGGGGTTTTGGTTGGCTTG 61.054 55.000 0.00 0.00 0.00 4.01
809 843 1.152333 GAGGGGGTTTTGGTTGGCT 60.152 57.895 0.00 0.00 0.00 4.75
905 941 3.655350 ATTTGTGGGTAGGGGGCGC 62.655 63.158 0.00 0.00 0.00 6.53
913 953 0.906775 GTCGGGAGGATTTGTGGGTA 59.093 55.000 0.00 0.00 0.00 3.69
918 958 1.218316 GCGAGTCGGGAGGATTTGT 59.782 57.895 15.52 0.00 0.00 2.83
919 959 1.521681 GGCGAGTCGGGAGGATTTG 60.522 63.158 15.52 0.00 0.00 2.32
1090 1130 3.054361 TCCCTGGTCTGAAAAATCCTAGC 60.054 47.826 0.00 0.00 0.00 3.42
1103 1143 1.704704 GTACTCCCCTCCCTGGTCT 59.295 63.158 0.00 0.00 0.00 3.85
1195 1236 0.676782 ATAACCCACAGGAACAGCGC 60.677 55.000 0.00 0.00 36.73 5.92
1215 1260 8.638685 TGCTTAGAAATACAACCGACTAATAC 57.361 34.615 0.00 0.00 0.00 1.89
1216 1261 8.472413 ACTGCTTAGAAATACAACCGACTAATA 58.528 33.333 0.00 0.00 0.00 0.98
1217 1262 7.328737 ACTGCTTAGAAATACAACCGACTAAT 58.671 34.615 0.00 0.00 0.00 1.73
1218 1263 6.694447 ACTGCTTAGAAATACAACCGACTAA 58.306 36.000 0.00 0.00 0.00 2.24
1244 1289 0.890683 GGTTTGCAGGGTCAATCAGG 59.109 55.000 0.00 0.00 0.00 3.86
1328 1377 7.095940 CCAAAACAACATGCAAGAACTATCAAG 60.096 37.037 0.00 0.00 0.00 3.02
1332 1381 6.160576 ACCAAAACAACATGCAAGAACTAT 57.839 33.333 0.00 0.00 0.00 2.12
1334 1383 4.081752 TGACCAAAACAACATGCAAGAACT 60.082 37.500 0.00 0.00 0.00 3.01
1335 1384 4.180057 TGACCAAAACAACATGCAAGAAC 58.820 39.130 0.00 0.00 0.00 3.01
1341 1390 2.514205 AGCTGACCAAAACAACATGC 57.486 45.000 0.00 0.00 0.00 4.06
1378 1427 7.272037 ACGTATTCCATCAAGTTGTTCTTTT 57.728 32.000 2.11 0.00 33.63 2.27
1509 1560 3.175152 CCTTCTCGATCTCTGTGAAACG 58.825 50.000 0.00 0.00 42.39 3.60
1523 1574 0.882927 TTTTGTCCACCGCCTTCTCG 60.883 55.000 0.00 0.00 0.00 4.04
1532 1583 2.299013 GTTCCCCTGAATTTTGTCCACC 59.701 50.000 0.00 0.00 31.98 4.61
1604 1655 2.048222 TACTGCACAGTGAGCGGC 60.048 61.111 19.79 7.46 42.52 6.53
1637 1688 2.099592 CCAGAAGCAAAAGTTCAGTGCA 59.900 45.455 8.37 0.00 40.83 4.57
1681 1732 4.286910 CATGTTCAAAACACCAAGTACGG 58.713 43.478 0.00 0.00 45.50 4.02
1804 1855 6.012658 AGCGAAAGAAATGCAAACATAGAA 57.987 33.333 0.00 0.00 34.62 2.10
1824 1875 8.462143 ACATACGAATATTTTATACAGGAGCG 57.538 34.615 0.00 0.00 0.00 5.03
1868 1919 0.319211 TCTCCGCTAACCACGTGTTG 60.319 55.000 15.65 2.14 37.83 3.33
1894 1945 7.221259 ACAAGTAAACACAGAAAAATAAACCGC 59.779 33.333 0.00 0.00 0.00 5.68
1909 1960 7.042791 CCCAAATCATTGTCAACAAGTAAACAC 60.043 37.037 1.69 0.00 39.47 3.32
1912 1963 7.353414 TCCCAAATCATTGTCAACAAGTAAA 57.647 32.000 1.69 0.00 39.47 2.01
1929 1980 7.518188 ACCGAATGTCTTCTAATATCCCAAAT 58.482 34.615 0.00 0.00 0.00 2.32
1932 1983 5.278808 CGACCGAATGTCTTCTAATATCCCA 60.279 44.000 0.00 0.00 42.13 4.37
1942 1993 0.716108 CTGCACGACCGAATGTCTTC 59.284 55.000 0.00 0.00 42.13 2.87
1945 1996 1.922570 ATACTGCACGACCGAATGTC 58.077 50.000 0.00 0.00 40.81 3.06
1947 1998 1.999735 ACAATACTGCACGACCGAATG 59.000 47.619 0.00 0.00 0.00 2.67
1948 1999 2.380084 ACAATACTGCACGACCGAAT 57.620 45.000 0.00 0.00 0.00 3.34
1950 2001 1.271379 AGAACAATACTGCACGACCGA 59.729 47.619 0.00 0.00 0.00 4.69
1951 2002 1.710013 AGAACAATACTGCACGACCG 58.290 50.000 0.00 0.00 0.00 4.79
1952 2003 3.326747 AGAAGAACAATACTGCACGACC 58.673 45.455 0.00 0.00 0.00 4.79
1953 2004 3.987868 TGAGAAGAACAATACTGCACGAC 59.012 43.478 0.00 0.00 0.00 4.34
1954 2005 4.251543 TGAGAAGAACAATACTGCACGA 57.748 40.909 0.00 0.00 0.00 4.35
1955 2006 4.627035 TCATGAGAAGAACAATACTGCACG 59.373 41.667 0.00 0.00 0.00 5.34
1957 2008 5.798132 AGTCATGAGAAGAACAATACTGCA 58.202 37.500 0.00 0.00 0.00 4.41
1958 2009 6.734104 AAGTCATGAGAAGAACAATACTGC 57.266 37.500 0.00 0.00 0.00 4.40
1966 2019 7.511959 AAACCCTAAAAGTCATGAGAAGAAC 57.488 36.000 0.00 0.00 0.00 3.01
2003 2057 1.128692 CGAAGTTGATTTCGGCACTCC 59.871 52.381 1.27 0.00 44.56 3.85
2019 2073 4.672413 GCATTGTTTTCAGACAAGACGAAG 59.328 41.667 0.00 0.00 42.28 3.79
2025 2079 5.911280 CACTAGTGCATTGTTTTCAGACAAG 59.089 40.000 10.54 0.00 42.28 3.16
2112 2166 5.520748 AGGTTGTTGATCCAGGAAACTAT 57.479 39.130 0.00 0.00 40.21 2.12
2168 2223 2.366167 CACCCCTCCTCTCCCCTG 60.366 72.222 0.00 0.00 0.00 4.45
2181 2236 7.883833 AGTAAAGAGAGAGAAAATAAACCACCC 59.116 37.037 0.00 0.00 0.00 4.61
2195 2250 9.921637 AATAGTTGTCAAGAAGTAAAGAGAGAG 57.078 33.333 0.00 0.00 0.00 3.20
2217 2272 3.700038 ACACGTCTGAAGACCCCTAATAG 59.300 47.826 4.90 0.00 41.86 1.73
2228 2283 3.242706 TGCACAATTGAACACGTCTGAAG 60.243 43.478 13.59 0.00 0.00 3.02
2231 2286 2.032054 ACTGCACAATTGAACACGTCTG 59.968 45.455 13.59 0.00 0.00 3.51
2235 2290 4.083324 AGGAATACTGCACAATTGAACACG 60.083 41.667 13.59 6.45 0.00 4.49
2238 2293 5.446473 CGAGAGGAATACTGCACAATTGAAC 60.446 44.000 13.59 3.94 0.00 3.18
2239 2294 4.631377 CGAGAGGAATACTGCACAATTGAA 59.369 41.667 13.59 0.00 0.00 2.69
2240 2295 4.183865 CGAGAGGAATACTGCACAATTGA 58.816 43.478 13.59 0.00 0.00 2.57
2241 2296 3.935203 ACGAGAGGAATACTGCACAATTG 59.065 43.478 3.24 3.24 0.00 2.32
2242 2297 4.184629 GACGAGAGGAATACTGCACAATT 58.815 43.478 0.00 0.00 0.00 2.32
2243 2298 3.195610 TGACGAGAGGAATACTGCACAAT 59.804 43.478 0.00 0.00 0.00 2.71
2244 2299 2.560981 TGACGAGAGGAATACTGCACAA 59.439 45.455 0.00 0.00 0.00 3.33
2247 2302 2.447443 AGTGACGAGAGGAATACTGCA 58.553 47.619 0.00 0.00 0.00 4.41
2248 2303 3.512033 AAGTGACGAGAGGAATACTGC 57.488 47.619 0.00 0.00 0.00 4.40
2249 2304 6.094325 AGTCTAAAGTGACGAGAGGAATACTG 59.906 42.308 0.00 0.00 41.47 2.74
2251 2306 6.439675 AGTCTAAAGTGACGAGAGGAATAC 57.560 41.667 0.00 0.00 41.47 1.89
2253 2308 5.712917 AGAAGTCTAAAGTGACGAGAGGAAT 59.287 40.000 0.00 0.00 41.47 3.01
2254 2309 5.071370 AGAAGTCTAAAGTGACGAGAGGAA 58.929 41.667 0.00 0.00 41.47 3.36
2257 2313 6.971527 TCTAGAAGTCTAAAGTGACGAGAG 57.028 41.667 0.00 0.00 41.47 3.20
2272 2328 7.180322 TCTCTGCATCTGAAAATCTAGAAGT 57.820 36.000 0.00 0.00 0.00 3.01
2273 2329 7.927092 TGATCTCTGCATCTGAAAATCTAGAAG 59.073 37.037 0.00 0.00 0.00 2.85
2276 2334 7.711772 AGTTGATCTCTGCATCTGAAAATCTAG 59.288 37.037 0.00 0.00 0.00 2.43
2295 2354 7.572759 TGTTTTCAGACAATACGAAGTTGATC 58.427 34.615 0.00 0.00 37.78 2.92
2306 2365 8.717821 GCACTAGTGTATTGTTTTCAGACAATA 58.282 33.333 23.44 6.41 45.68 1.90
2353 2412 3.583086 ACGGGCAATTAGCTAGTATCCAT 59.417 43.478 0.00 0.00 44.79 3.41
2364 2423 0.243365 TGCAAAGCACGGGCAATTAG 59.757 50.000 14.57 3.05 44.61 1.73
2373 2432 4.341502 CCCCCGTTGCAAAGCACG 62.342 66.667 0.00 0.05 38.71 5.34
2377 2436 1.814772 TTGATGCCCCCGTTGCAAAG 61.815 55.000 0.00 2.09 42.92 2.77
2410 2469 0.031314 CATCGAGCGCTGTACTGGAT 59.969 55.000 18.48 0.00 33.45 3.41
2420 2479 1.852942 TGGAAAGTATCATCGAGCGC 58.147 50.000 0.00 0.00 0.00 5.92
2494 2553 1.399440 CATCAAGCGTTGGATGTGAGG 59.601 52.381 8.40 0.00 36.89 3.86
2506 2565 6.974932 AATTATGGCTAGTATCATCAAGCG 57.025 37.500 0.00 0.00 35.79 4.68
2520 2579 4.348168 AGGAGGATCACGTTAATTATGGCT 59.652 41.667 0.00 0.00 36.25 4.75
2521 2580 4.642429 AGGAGGATCACGTTAATTATGGC 58.358 43.478 0.00 0.00 36.25 4.40
2534 2593 4.883759 TCAGTCTTTGGATAGGAGGATCA 58.116 43.478 0.00 0.00 36.25 2.92
2544 2603 7.921041 TTATGGAGAGTATCAGTCTTTGGAT 57.079 36.000 0.00 0.00 37.82 3.41
2571 2630 2.579873 GTTGGATGGGAGGATCATGTG 58.420 52.381 0.00 0.00 36.25 3.21
2585 2644 5.305386 TCATGGAGAGTATCATTCGTTGGAT 59.695 40.000 0.00 0.00 37.82 3.41
2591 2650 6.863645 ACGTTAATCATGGAGAGTATCATTCG 59.136 38.462 0.00 0.00 37.82 3.34
2596 2655 7.042658 GGTTTCACGTTAATCATGGAGAGTATC 60.043 40.741 0.00 0.00 0.00 2.24
2608 2667 8.071368 TCTATGTTTGTTGGTTTCACGTTAATC 58.929 33.333 0.00 0.00 0.00 1.75
2614 2673 5.457473 GGTTTCTATGTTTGTTGGTTTCACG 59.543 40.000 0.00 0.00 0.00 4.35
2618 2677 6.596106 GGTTTGGTTTCTATGTTTGTTGGTTT 59.404 34.615 0.00 0.00 0.00 3.27
2652 2712 1.134818 TCTGTGGTCATGATGGTACGC 60.135 52.381 0.00 0.00 0.00 4.42
2663 2723 1.696884 TGGCAACATAGTCTGTGGTCA 59.303 47.619 1.35 0.00 41.20 4.02
2801 2962 8.816894 CAAGAGAAATATCTATTACCTAGGGCA 58.183 37.037 14.81 0.00 34.96 5.36
2874 3035 6.639632 AGCTGAAAATAGCAGAAGAAAACA 57.360 33.333 0.00 0.00 46.07 2.83
2921 3083 5.314923 AGCGTAACAAAATCAAGATGCAT 57.685 34.783 0.00 0.00 0.00 3.96
2941 3103 4.932146 ACACAAAAGTAACAATGTGGAGC 58.068 39.130 9.28 0.00 45.65 4.70
2965 3127 5.008019 AGCTTGTGCACATTATATTTCGAGG 59.992 40.000 22.39 0.00 42.74 4.63
3020 3182 5.010282 AGTTAAATCCAACTAAGGCCAGTG 58.990 41.667 5.01 0.00 36.99 3.66
3026 3188 7.542130 GTCAATTGCAGTTAAATCCAACTAAGG 59.458 37.037 0.00 0.00 36.61 2.69
3027 3189 8.299570 AGTCAATTGCAGTTAAATCCAACTAAG 58.700 33.333 0.00 0.00 36.61 2.18
3131 3299 7.548075 GGTCAAGTCCTTGTCTATTCGATAAAA 59.452 37.037 6.90 0.00 41.16 1.52
3134 3302 5.892119 AGGTCAAGTCCTTGTCTATTCGATA 59.108 40.000 6.90 0.00 41.16 2.92
3223 3391 6.802608 TGTACCAGTATAATTCTTCAGACGG 58.197 40.000 0.00 0.00 0.00 4.79
3269 3438 8.395605 TGGGAATTACTGGGAGTTATAACTTTT 58.604 33.333 18.96 0.00 39.88 2.27
3270 3439 7.832685 GTGGGAATTACTGGGAGTTATAACTTT 59.167 37.037 18.96 7.05 39.88 2.66
3274 3443 8.626917 TTAGTGGGAATTACTGGGAGTTATAA 57.373 34.615 0.00 0.00 0.00 0.98
3311 3480 5.983118 GGTCCTACATTTTCCAAAAGTTGTG 59.017 40.000 2.59 0.00 0.00 3.33
3312 3481 5.659079 TGGTCCTACATTTTCCAAAAGTTGT 59.341 36.000 0.00 0.00 0.00 3.32
3372 3541 3.264450 GGACTCTTTCCTCCTCAATTGGA 59.736 47.826 5.42 0.00 41.95 3.53
3450 3619 6.761242 AGAACACAGTGGGAAAATTTTAAAGC 59.239 34.615 0.00 0.00 0.00 3.51
3521 3690 5.200483 TGAAGAAGATGGGTGTGACTTTTT 58.800 37.500 0.00 0.00 0.00 1.94
3547 3716 5.832539 AGTGGATAGCTATGCCTAATTGT 57.167 39.130 21.04 0.00 0.00 2.71
3589 3758 9.319060 ACATGATAGTTCTGATGGTATATGACT 57.681 33.333 0.00 0.00 0.00 3.41
3590 3759 9.935241 AACATGATAGTTCTGATGGTATATGAC 57.065 33.333 0.00 0.00 0.00 3.06
3597 3766 7.439356 CGACATTAACATGATAGTTCTGATGGT 59.561 37.037 0.00 0.00 34.11 3.55
3629 3798 6.760770 CAGTTGGCAAGGAAGTTATTTGAAAA 59.239 34.615 0.00 0.00 0.00 2.29
3630 3799 6.097554 TCAGTTGGCAAGGAAGTTATTTGAAA 59.902 34.615 0.00 0.00 0.00 2.69
3631 3800 5.596361 TCAGTTGGCAAGGAAGTTATTTGAA 59.404 36.000 0.00 0.00 0.00 2.69
3632 3801 5.136828 TCAGTTGGCAAGGAAGTTATTTGA 58.863 37.500 0.00 0.00 0.00 2.69
3680 3849 7.433680 ACCTAGATTAAAGCACCAAAACAAAG 58.566 34.615 0.00 0.00 0.00 2.77
3687 3856 4.993028 ACCAACCTAGATTAAAGCACCAA 58.007 39.130 0.00 0.00 0.00 3.67
3700 3869 1.902508 TCAAGCTCCAGACCAACCTAG 59.097 52.381 0.00 0.00 0.00 3.02
3701 3870 2.024176 TCAAGCTCCAGACCAACCTA 57.976 50.000 0.00 0.00 0.00 3.08
3733 3902 0.462581 CAAGATTAGCAGCCTCGCCA 60.463 55.000 0.00 0.00 0.00 5.69
3805 3974 4.159506 GCAGTGGCATATTTACCAGGAAAA 59.840 41.667 0.00 0.00 40.72 2.29
3931 4100 2.329379 CTACTCTGGTTTGTCAGCGTC 58.671 52.381 0.00 0.00 34.88 5.19
3932 4101 1.605712 GCTACTCTGGTTTGTCAGCGT 60.606 52.381 0.00 0.00 36.73 5.07
3941 4113 0.251653 TCTGGACGGCTACTCTGGTT 60.252 55.000 0.00 0.00 0.00 3.67
3969 4141 5.587844 ACAGGACAGATGAAAATGATGCTAC 59.412 40.000 0.00 0.00 0.00 3.58
4025 4197 7.514127 AGTTCCTATTCTCCAATATAGCTGGAA 59.486 37.037 0.00 0.00 42.43 3.53
4044 4216 6.620877 AGATTGTACACCATTGAGTTCCTA 57.379 37.500 0.00 0.00 0.00 2.94
4091 4263 4.899502 AGCAGCTACTTGACTACAACAAT 58.100 39.130 0.00 0.00 32.27 2.71
4136 4308 2.959465 AGACAGGGGACAAGGAAAAG 57.041 50.000 0.00 0.00 0.00 2.27
4187 4389 1.608590 CATTGTTTCTGCCCACGTCTT 59.391 47.619 0.00 0.00 0.00 3.01
4476 4678 2.891580 AGAGTTAAAGGCGTGTCTGAGA 59.108 45.455 0.00 0.00 0.00 3.27
4501 4703 2.036346 AGAACAAAATGAGGCCAACTGC 59.964 45.455 5.01 0.00 40.16 4.40
4876 5298 9.121658 CATGCCAGATAGATGCATTCTAATAAT 57.878 33.333 0.00 0.00 42.79 1.28
5107 5529 3.034635 AGACTCGTATTTCAGGATGCCT 58.965 45.455 0.00 0.00 34.76 4.75
5130 5552 2.101582 GAGTCGATGGAGCAACATAGGT 59.898 50.000 0.00 0.00 0.00 3.08
5170 5592 0.737715 CCACTTCCTCTTCGCTTCCG 60.738 60.000 0.00 0.00 0.00 4.30
5321 5743 0.598065 AAATGCCACGAAAGCCTCAC 59.402 50.000 0.00 0.00 0.00 3.51
5335 5757 1.881973 TGCAGGTCAGAGAACAAATGC 59.118 47.619 0.00 0.00 0.00 3.56
5341 5763 0.972883 AGGAGTGCAGGTCAGAGAAC 59.027 55.000 0.00 0.00 0.00 3.01
5378 5800 0.729116 CAATCTGCAGCCCGTTAGTG 59.271 55.000 9.47 0.00 0.00 2.74
5385 5807 1.474077 CTAAACACCAATCTGCAGCCC 59.526 52.381 9.47 0.00 0.00 5.19
5444 5870 8.795786 TGTGCACTCAAATAAACTTAATGAAC 57.204 30.769 19.41 0.00 0.00 3.18
5458 5884 8.081633 CCTAATAAAGTTGATTGTGCACTCAAA 58.918 33.333 19.62 6.81 32.88 2.69
5478 5904 7.881232 ACTGCTTTGCTTGTACTAAACCTAATA 59.119 33.333 0.00 0.00 0.00 0.98
5483 5909 4.274950 TGACTGCTTTGCTTGTACTAAACC 59.725 41.667 0.00 0.00 0.00 3.27
5492 5918 1.202177 ACACGTTGACTGCTTTGCTTG 60.202 47.619 0.00 0.00 0.00 4.01
5508 5947 2.318578 GTGAATCAAATGCCACACACG 58.681 47.619 0.00 0.00 0.00 4.49
5528 5968 1.676967 GAGCCAAGTCAGCCCAAGG 60.677 63.158 0.00 0.00 0.00 3.61
5531 5971 1.073722 CAAGAGCCAAGTCAGCCCA 59.926 57.895 0.00 0.00 0.00 5.36
5550 5990 1.139455 AGCTGCCAGCAAAAACACAAT 59.861 42.857 20.53 0.00 45.56 2.71
5896 6361 4.677584 CTGGTTGAATTTCGGACAAAACA 58.322 39.130 5.46 0.00 0.00 2.83
5969 6434 4.018233 TCAATATTAGGGGGTGTCCGTTTT 60.018 41.667 0.00 0.00 35.00 2.43
6020 6487 3.891977 GGATGACTCACTCCACTAGCATA 59.108 47.826 0.00 0.00 0.00 3.14
6034 6501 5.233083 TGATGTATGGGATTGGATGACTC 57.767 43.478 0.00 0.00 0.00 3.36
6035 6502 5.651612 TTGATGTATGGGATTGGATGACT 57.348 39.130 0.00 0.00 0.00 3.41
6074 6541 4.397103 GTGCATGTCAAATGGAGAAGATGA 59.603 41.667 0.00 0.00 0.00 2.92
6076 6543 4.338012 TGTGCATGTCAAATGGAGAAGAT 58.662 39.130 0.00 0.00 0.00 2.40
6080 6547 6.829849 TCTATATGTGCATGTCAAATGGAGA 58.170 36.000 0.00 0.00 0.00 3.71
6139 6606 5.964751 TCATCGACGCATTTTGATTGTTATG 59.035 36.000 0.00 0.00 0.00 1.90
6187 6654 3.452474 CAATTTTTGGGCTCGAACACAA 58.548 40.909 0.00 0.00 0.00 3.33
6189 6656 1.792367 GCAATTTTTGGGCTCGAACAC 59.208 47.619 0.00 0.00 0.00 3.32
6195 6662 1.338105 GGACTGGCAATTTTTGGGCTC 60.338 52.381 0.00 0.00 0.00 4.70
6255 6722 2.738480 GACACACACTACCCGCCA 59.262 61.111 0.00 0.00 0.00 5.69
6395 6863 1.966451 CCACGCACTTGAGTTCCCC 60.966 63.158 0.00 0.00 0.00 4.81
6414 6883 3.228188 TCTCCACTTCATTTGGTGCTT 57.772 42.857 0.00 0.00 35.42 3.91
6419 6888 4.202441 CCCACTATCTCCACTTCATTTGG 58.798 47.826 0.00 0.00 35.18 3.28
6421 6890 4.111577 TCCCCACTATCTCCACTTCATTT 58.888 43.478 0.00 0.00 0.00 2.32
6426 6895 3.267031 CCTTTTCCCCACTATCTCCACTT 59.733 47.826 0.00 0.00 0.00 3.16
6443 6912 1.739667 GCACGAAAGCCACCCTTTT 59.260 52.632 0.00 0.00 43.64 2.27
6450 6919 2.095969 CACTATTTTCGCACGAAAGCCA 60.096 45.455 16.67 4.81 43.75 4.75
6467 6936 1.846007 ATTTGGCCATTTCCGCACTA 58.154 45.000 6.09 0.00 0.00 2.74
6488 6957 0.179009 AAAGCAAGACAGAGCCTGCA 60.179 50.000 2.50 0.00 34.37 4.41
6497 6966 0.029300 GCTCACGCAAAAGCAAGACA 59.971 50.000 0.00 0.00 38.42 3.41
6514 6983 0.032017 AGAATCCGACACCCCTAGCT 60.032 55.000 0.00 0.00 0.00 3.32
6517 6986 1.272816 TGTCAGAATCCGACACCCCTA 60.273 52.381 0.00 0.00 38.45 3.53
6604 7073 3.773418 TTTGGGTCCATCAAACGTCTA 57.227 42.857 0.00 0.00 0.00 2.59
6605 7074 2.649531 TTTGGGTCCATCAAACGTCT 57.350 45.000 0.00 0.00 0.00 4.18
6606 7075 3.005367 ACATTTTGGGTCCATCAAACGTC 59.995 43.478 0.00 0.00 34.34 4.34
6607 7076 2.962421 ACATTTTGGGTCCATCAAACGT 59.038 40.909 0.00 0.00 34.34 3.99
6608 7077 3.658757 ACATTTTGGGTCCATCAAACG 57.341 42.857 0.00 0.00 34.34 3.60
6609 7078 4.447389 CGAAACATTTTGGGTCCATCAAAC 59.553 41.667 0.00 0.00 34.34 2.93
6610 7079 4.342378 TCGAAACATTTTGGGTCCATCAAA 59.658 37.500 0.00 0.00 32.96 2.69
6611 7080 3.891977 TCGAAACATTTTGGGTCCATCAA 59.108 39.130 0.00 0.00 0.00 2.57
6612 7081 3.254657 GTCGAAACATTTTGGGTCCATCA 59.745 43.478 0.00 0.00 0.00 3.07
6613 7082 3.254657 TGTCGAAACATTTTGGGTCCATC 59.745 43.478 0.00 0.00 0.00 3.51
6614 7083 3.226777 TGTCGAAACATTTTGGGTCCAT 58.773 40.909 0.00 0.00 0.00 3.41
6615 7084 2.656002 TGTCGAAACATTTTGGGTCCA 58.344 42.857 0.00 0.00 0.00 4.02
6616 7085 3.181485 TGTTGTCGAAACATTTTGGGTCC 60.181 43.478 8.47 0.00 34.73 4.46
6617 7086 4.035278 TGTTGTCGAAACATTTTGGGTC 57.965 40.909 8.47 0.00 34.73 4.46
6618 7087 4.367450 CATGTTGTCGAAACATTTTGGGT 58.633 39.130 17.62 1.18 38.69 4.51
6619 7088 3.740321 CCATGTTGTCGAAACATTTTGGG 59.260 43.478 17.62 13.68 38.69 4.12
6620 7089 4.367450 ACCATGTTGTCGAAACATTTTGG 58.633 39.130 17.62 18.46 38.69 3.28
6621 7090 4.444056 GGACCATGTTGTCGAAACATTTTG 59.556 41.667 17.62 11.53 38.69 2.44
6622 7091 4.616953 GGACCATGTTGTCGAAACATTTT 58.383 39.130 17.62 10.83 38.69 1.82
6623 7092 3.304391 CGGACCATGTTGTCGAAACATTT 60.304 43.478 17.62 11.07 38.69 2.32
6624 7093 2.225491 CGGACCATGTTGTCGAAACATT 59.775 45.455 17.62 9.07 38.69 2.71
6625 7094 1.804151 CGGACCATGTTGTCGAAACAT 59.196 47.619 15.64 15.64 41.18 2.71
6626 7095 1.202545 TCGGACCATGTTGTCGAAACA 60.203 47.619 13.12 13.12 36.07 2.83
6627 7096 1.504359 TCGGACCATGTTGTCGAAAC 58.496 50.000 0.00 0.00 36.07 2.78
6628 7097 1.868498 GTTCGGACCATGTTGTCGAAA 59.132 47.619 10.43 0.00 36.07 3.46
6629 7098 1.504359 GTTCGGACCATGTTGTCGAA 58.496 50.000 0.00 6.40 36.07 3.71
6630 7099 0.665068 CGTTCGGACCATGTTGTCGA 60.665 55.000 0.00 0.00 36.07 4.20
6631 7100 0.942410 ACGTTCGGACCATGTTGTCG 60.942 55.000 0.00 0.00 36.07 4.35
6632 7101 1.223187 AACGTTCGGACCATGTTGTC 58.777 50.000 0.00 0.00 34.42 3.18
6633 7102 2.137523 GTAACGTTCGGACCATGTTGT 58.862 47.619 2.82 0.00 0.00 3.32
6634 7103 1.125384 CGTAACGTTCGGACCATGTTG 59.875 52.381 2.82 0.00 0.00 3.33
6635 7104 1.421382 CGTAACGTTCGGACCATGTT 58.579 50.000 2.82 0.00 0.00 2.71
6636 7105 3.111536 CGTAACGTTCGGACCATGT 57.888 52.632 2.82 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.