Multiple sequence alignment - TraesCS3A01G265700

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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 TraesCS3A01G265700 chr3A 100.000 6862 0 0 1 6862 490170600 490163739 0.000000e+00 12672.0
1 TraesCS3A01G265700 chr3A 97.778 90 1 1 6625 6713 32161399 32161310 3.310000e-33 154.0
2 TraesCS3A01G265700 chr3A 96.739 92 2 1 6622 6712 508202898 508202807 1.190000e-32 152.0
3 TraesCS3A01G265700 chr3D 96.136 3546 105 12 2650 6185 368884955 368881432 0.000000e+00 5760.0
4 TraesCS3A01G265700 chr3D 92.032 1506 75 15 1151 2656 368886461 368885001 0.000000e+00 2074.0
5 TraesCS3A01G265700 chr3D 95.526 447 15 4 678 1123 368887373 368886931 0.000000e+00 710.0
6 TraesCS3A01G265700 chr3D 87.829 608 41 12 1 581 532157124 532156523 0.000000e+00 682.0
7 TraesCS3A01G265700 chr3D 80.392 255 49 1 4676 4930 335673095 335673348 7.020000e-45 193.0
8 TraesCS3A01G265700 chr3D 90.984 122 7 4 6625 6743 368881081 368880961 1.980000e-35 161.0
9 TraesCS3A01G265700 chr3D 96.667 90 2 1 6622 6710 428437218 428437307 1.540000e-31 148.0
10 TraesCS3A01G265700 chr3D 92.941 85 6 0 6773 6857 368880962 368880878 2.600000e-24 124.0
11 TraesCS3A01G265700 chr3D 92.308 78 5 1 582 659 368887437 368887361 7.280000e-20 110.0
12 TraesCS3A01G265700 chr3B 94.775 3694 153 18 2650 6328 479903380 479899712 0.000000e+00 5716.0
13 TraesCS3A01G265700 chr3B 97.743 709 15 1 1743 2451 479904515 479903808 0.000000e+00 1219.0
14 TraesCS3A01G265700 chr3B 95.338 429 16 3 692 1119 479906330 479905905 0.000000e+00 678.0
15 TraesCS3A01G265700 chr3B 88.050 477 39 6 1155 1631 479905690 479905232 3.620000e-152 549.0
16 TraesCS3A01G265700 chr3B 97.253 182 5 0 2475 2656 479903607 479903426 6.680000e-80 309.0
17 TraesCS3A01G265700 chr3B 93.085 188 11 2 6670 6857 479899586 479899401 2.440000e-69 274.0
18 TraesCS3A01G265700 chr3B 97.727 88 1 1 6625 6711 560090365 560090452 4.290000e-32 150.0
19 TraesCS3A01G265700 chr3B 85.600 125 15 1 4519 4643 479901554 479901433 2.010000e-25 128.0
20 TraesCS3A01G265700 chr3B 97.143 35 1 0 6434 6468 479899659 479899625 7.430000e-05 60.2
21 TraesCS3A01G265700 chr4D 87.829 608 45 19 1 581 112102615 112103220 0.000000e+00 686.0
22 TraesCS3A01G265700 chr4D 85.207 169 22 3 1 168 374095180 374095346 3.290000e-38 171.0
23 TraesCS3A01G265700 chr4D 97.802 91 0 2 6625 6714 473811605 473811694 9.210000e-34 156.0
24 TraesCS3A01G265700 chr4D 86.486 74 8 2 470 542 329002493 329002421 5.710000e-11 80.5
25 TraesCS3A01G265700 chr7D 95.266 338 12 1 1 334 555670222 555670559 3.640000e-147 532.0
26 TraesCS3A01G265700 chr7D 90.385 260 25 0 322 581 555670574 555670833 6.590000e-90 342.0
27 TraesCS3A01G265700 chr7D 82.008 239 42 1 4677 4915 1972306 1972069 1.170000e-47 202.0
28 TraesCS3A01G265700 chr7D 76.733 202 32 4 105 293 489201687 489201886 1.580000e-16 99.0
29 TraesCS3A01G265700 chr4B 87.500 384 21 14 224 580 188201398 188201781 1.060000e-112 418.0
30 TraesCS3A01G265700 chr4B 97.333 225 6 0 1 225 188200872 188201096 3.880000e-102 383.0
31 TraesCS3A01G265700 chr4B 97.753 89 0 2 6625 6711 428838687 428838599 1.190000e-32 152.0
32 TraesCS3A01G265700 chr2B 82.625 259 44 1 4671 4929 757361622 757361365 1.930000e-55 228.0
33 TraesCS3A01G265700 chr2B 79.457 258 48 4 4676 4931 423002485 423002231 1.970000e-40 178.0
34 TraesCS3A01G265700 chr5A 81.679 262 47 1 4670 4931 397510397 397510137 4.170000e-52 217.0
35 TraesCS3A01G265700 chr5A 77.670 309 47 17 1 293 355375506 355375204 1.180000e-37 169.0
36 TraesCS3A01G265700 chr6D 80.545 257 44 5 4676 4930 460588009 460588261 7.020000e-45 193.0
37 TraesCS3A01G265700 chr2D 80.078 256 44 7 4677 4929 43503545 43503796 4.230000e-42 183.0
38 TraesCS3A01G265700 chr1D 87.417 151 18 1 1 150 276772820 276772970 9.150000e-39 172.0
39 TraesCS3A01G265700 chr1D 96.703 91 2 1 6625 6714 416592374 416592464 4.290000e-32 150.0
40 TraesCS3A01G265700 chr7A 98.824 85 1 0 6625 6709 49354173 49354089 1.190000e-32 152.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G265700 chr3A 490163739 490170600 6861 True 12672.000000 12672 100.000000 1 6862 1 chr3A.!!$R2 6861
1 TraesCS3A01G265700 chr3D 368880878 368887437 6559 True 1489.833333 5760 93.321167 582 6857 6 chr3D.!!$R2 6275
2 TraesCS3A01G265700 chr3D 532156523 532157124 601 True 682.000000 682 87.829000 1 581 1 chr3D.!!$R1 580
3 TraesCS3A01G265700 chr3B 479899401 479906330 6929 True 1116.650000 5716 93.623375 692 6857 8 chr3B.!!$R1 6165
4 TraesCS3A01G265700 chr4D 112102615 112103220 605 False 686.000000 686 87.829000 1 581 1 chr4D.!!$F1 580
5 TraesCS3A01G265700 chr7D 555670222 555670833 611 False 437.000000 532 92.825500 1 581 2 chr7D.!!$F2 580
6 TraesCS3A01G265700 chr4B 188200872 188201781 909 False 400.500000 418 92.416500 1 580 2 chr4B.!!$F1 579

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
854 1191 0.250124 CCAACAGACAGCCACCGTAA 60.250 55.000 0.00 0.00 0.00 3.18 F
1182 1961 0.023354 GCTGTGTAATTCGCGACGTC 59.977 55.000 9.15 5.18 0.00 4.34 F
1767 3178 0.033228 TGCATTTCCCCGTTGCTTTG 59.967 50.000 0.00 0.00 37.28 2.77 F
2510 4098 0.036732 TTTACCTGCCTGTCTGCCTG 59.963 55.000 0.00 0.00 0.00 4.85 F
2884 4524 1.980844 CGCACACAACAAGAATGATGC 59.019 47.619 0.00 0.00 32.93 3.91 F
4383 6029 1.421268 TGATGAAGCACTCAGGTTGGT 59.579 47.619 0.00 0.00 38.24 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 2489 0.522626 CAACAGCATTCGCCACATCA 59.477 50.000 0.0 0.0 39.83 3.07 R
2099 3510 1.134371 GTATCTCTTGGAGGTGCCCAC 60.134 57.143 0.0 0.0 35.62 4.61 R
2997 4640 1.269723 GCTAAACCCAACAAGAGGCAC 59.730 52.381 0.0 0.0 0.00 5.01 R
3785 5429 0.874390 TCGAAGCCAATGTTGCAGAC 59.126 50.000 0.0 0.0 0.00 3.51 R
4706 6352 4.003648 GGTCGAGATTTGTTTGGATCTGT 58.996 43.478 0.0 0.0 32.96 3.41 R
6373 8030 0.177604 CCTGCCTCACATCTGAGACC 59.822 60.000 0.0 0.0 46.32 3.85 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
109 110 1.266178 TCGCTCACCCTCTGAATTCA 58.734 50.000 8.12 8.12 0.00 2.57
293 597 2.358247 GCGGCGGGAACTGAAGAA 60.358 61.111 9.78 0.00 36.31 2.52
340 675 9.952188 TTATTACGTGTGAATCATTTGAACAAA 57.048 25.926 0.00 2.48 34.46 2.83
397 733 2.978824 GCCTCCGCCACTAACTGA 59.021 61.111 0.00 0.00 0.00 3.41
399 735 1.218316 CCTCCGCCACTAACTGACC 59.782 63.158 0.00 0.00 0.00 4.02
466 802 0.462937 ATGCCGGCGTACATGCTTTA 60.463 50.000 22.45 0.00 34.52 1.85
504 840 4.072131 GAGATTGCAAGTTAGGTGACCAA 58.928 43.478 3.63 0.00 0.00 3.67
512 848 2.173143 AGTTAGGTGACCAAAAACCCGA 59.827 45.455 3.63 0.00 37.13 5.14
518 854 4.650131 AGGTGACCAAAAACCCGAATTTTA 59.350 37.500 3.63 0.00 37.13 1.52
547 883 0.736053 GCACCAAACTGAACGTCCAA 59.264 50.000 0.00 0.00 0.00 3.53
561 897 3.074412 ACGTCCAAAGCAAGTTCTATGG 58.926 45.455 0.00 0.00 0.00 2.74
587 923 5.662208 TCCCGGTGATATTACCTCAACTTTA 59.338 40.000 14.25 0.00 38.62 1.85
604 940 4.956085 ACTTTAAACTTTGATGGGTTGGC 58.044 39.130 0.00 0.00 0.00 4.52
608 944 0.482446 ACTTTGATGGGTTGGCTCCA 59.518 50.000 2.26 0.00 38.82 3.86
717 1053 0.528684 GAGAACTGGAGCCGATTCCG 60.529 60.000 0.00 0.00 40.27 4.30
854 1191 0.250124 CCAACAGACAGCCACCGTAA 60.250 55.000 0.00 0.00 0.00 3.18
903 1240 3.879932 TCAGACGATACATGTAGCTCG 57.120 47.619 21.53 21.53 37.17 5.03
906 1243 2.031595 AGACGATACATGTAGCTCGCTG 60.032 50.000 22.57 9.39 34.60 5.18
925 1262 3.212685 CTGCTTCTTCTCAATCCATCCC 58.787 50.000 0.00 0.00 0.00 3.85
926 1263 2.092212 TGCTTCTTCTCAATCCATCCCC 60.092 50.000 0.00 0.00 0.00 4.81
1077 1414 2.044555 CGAGGGCCTCTACGACACA 61.045 63.158 29.81 0.00 0.00 3.72
1123 1460 0.094216 CGCGCAGATCAACAAGTGAG 59.906 55.000 8.75 0.00 40.43 3.51
1124 1461 0.179205 GCGCAGATCAACAAGTGAGC 60.179 55.000 0.30 0.00 43.33 4.26
1129 1466 2.777832 GATCAACAAGTGAGCTCCCT 57.222 50.000 12.15 0.78 39.67 4.20
1130 1467 3.895232 GATCAACAAGTGAGCTCCCTA 57.105 47.619 12.15 0.00 39.67 3.53
1131 1468 3.791245 GATCAACAAGTGAGCTCCCTAG 58.209 50.000 12.15 1.37 39.67 3.02
1140 1477 3.164977 GCTCCCTAGCCCACCCTC 61.165 72.222 0.00 0.00 43.40 4.30
1141 1478 2.446802 CTCCCTAGCCCACCCTCC 60.447 72.222 0.00 0.00 0.00 4.30
1142 1479 4.103928 TCCCTAGCCCACCCTCCC 62.104 72.222 0.00 0.00 0.00 4.30
1145 1482 4.475444 CTAGCCCACCCTCCCGGA 62.475 72.222 0.73 0.00 34.64 5.14
1146 1483 3.774336 TAGCCCACCCTCCCGGAT 61.774 66.667 0.73 0.00 34.64 4.18
1147 1484 3.341469 TAGCCCACCCTCCCGGATT 62.341 63.158 0.73 0.00 34.64 3.01
1148 1485 4.191015 GCCCACCCTCCCGGATTC 62.191 72.222 0.73 0.00 34.64 2.52
1149 1486 3.861797 CCCACCCTCCCGGATTCG 61.862 72.222 0.73 0.00 34.64 3.34
1182 1961 0.023354 GCTGTGTAATTCGCGACGTC 59.977 55.000 9.15 5.18 0.00 4.34
1185 1964 1.136113 TGTGTAATTCGCGACGTCGTA 60.136 47.619 35.48 22.95 42.22 3.43
1204 1983 1.742880 CCCGTGTGGATCTGTGCAG 60.743 63.158 0.00 0.00 37.49 4.41
1254 2033 4.637534 CGTGAGGATCCATTTGATTGTTCT 59.362 41.667 15.82 0.00 32.41 3.01
1269 2048 5.487488 TGATTGTTCTGGTATAGTGGGTTCT 59.513 40.000 0.00 0.00 0.00 3.01
1275 2054 6.027025 TCTGGTATAGTGGGTTCTAGTCAT 57.973 41.667 0.00 0.00 0.00 3.06
1282 2061 4.074970 AGTGGGTTCTAGTCATTTTGCTG 58.925 43.478 0.00 0.00 0.00 4.41
1283 2062 3.821033 GTGGGTTCTAGTCATTTTGCTGT 59.179 43.478 0.00 0.00 0.00 4.40
1284 2063 5.001232 GTGGGTTCTAGTCATTTTGCTGTA 58.999 41.667 0.00 0.00 0.00 2.74
1308 2087 2.338500 GAGAAGTCTTGCGGTTGGTAG 58.662 52.381 0.00 0.00 0.00 3.18
1317 2096 2.418692 TGCGGTTGGTAGTATGTTGTG 58.581 47.619 0.00 0.00 0.00 3.33
1319 2098 3.267483 GCGGTTGGTAGTATGTTGTGAT 58.733 45.455 0.00 0.00 0.00 3.06
1330 2109 9.489084 GGTAGTATGTTGTGATGCTTATCATTA 57.511 33.333 0.00 0.00 35.05 1.90
1351 2130 8.889717 TCATTAATTAGGGTCGAGAAAACAATC 58.110 33.333 0.00 0.00 0.00 2.67
1352 2131 5.796350 AATTAGGGTCGAGAAAACAATCG 57.204 39.130 0.00 0.00 40.26 3.34
1357 2136 4.159879 AGGGTCGAGAAAACAATCGTCTAT 59.840 41.667 0.00 0.00 39.86 1.98
1395 2174 3.678548 GTCAAAAAGCGTCCCAGTAGTAG 59.321 47.826 0.00 0.00 0.00 2.57
1397 2176 1.558233 AAAGCGTCCCAGTAGTAGCT 58.442 50.000 0.00 0.00 36.40 3.32
1398 2177 1.104630 AAGCGTCCCAGTAGTAGCTC 58.895 55.000 0.00 0.00 33.42 4.09
1399 2178 0.034380 AGCGTCCCAGTAGTAGCTCA 60.034 55.000 0.00 0.00 0.00 4.26
1400 2179 1.033574 GCGTCCCAGTAGTAGCTCAT 58.966 55.000 0.00 0.00 0.00 2.90
1401 2180 1.269309 GCGTCCCAGTAGTAGCTCATG 60.269 57.143 0.00 0.00 0.00 3.07
1402 2181 2.025155 CGTCCCAGTAGTAGCTCATGT 58.975 52.381 0.00 0.00 0.00 3.21
1419 2198 3.444742 TCATGTTCATGATTTGGGTGCTC 59.555 43.478 10.88 0.00 0.00 4.26
1437 2216 3.713248 TGCTCCAGAATATCAGGTCATGT 59.287 43.478 0.00 0.00 0.00 3.21
1466 2245 2.485814 GTCTGCCTGGATTTGAAGTCAC 59.514 50.000 0.00 0.00 0.00 3.67
1470 2249 2.350522 CCTGGATTTGAAGTCACGAGG 58.649 52.381 0.00 0.00 0.00 4.63
1490 2269 4.993028 AGGCACCTTGGTTATTGTAGAAA 58.007 39.130 0.00 0.00 0.00 2.52
1503 2282 8.983724 GGTTATTGTAGAAATGATACTGAGCTC 58.016 37.037 6.82 6.82 0.00 4.09
1511 2290 3.000684 TGATACTGAGCTCTGTACGGT 57.999 47.619 29.10 17.45 34.01 4.83
1512 2291 3.353557 TGATACTGAGCTCTGTACGGTT 58.646 45.455 29.10 17.14 34.01 4.44
1513 2292 3.128764 TGATACTGAGCTCTGTACGGTTG 59.871 47.826 29.10 6.26 34.01 3.77
1514 2293 0.038159 ACTGAGCTCTGTACGGTTGC 60.038 55.000 23.17 12.29 0.00 4.17
1515 2294 0.038251 CTGAGCTCTGTACGGTTGCA 60.038 55.000 16.19 7.01 0.00 4.08
1516 2295 0.319555 TGAGCTCTGTACGGTTGCAC 60.320 55.000 16.19 14.87 0.00 4.57
1517 2296 1.004918 AGCTCTGTACGGTTGCACC 60.005 57.895 19.02 0.00 34.05 5.01
1518 2297 2.033194 GCTCTGTACGGTTGCACCC 61.033 63.158 14.35 0.00 33.75 4.61
1519 2298 1.369692 CTCTGTACGGTTGCACCCA 59.630 57.895 0.00 0.00 33.75 4.51
1520 2299 0.670546 CTCTGTACGGTTGCACCCAG 60.671 60.000 0.00 2.98 33.75 4.45
1521 2300 1.116536 TCTGTACGGTTGCACCCAGA 61.117 55.000 0.00 5.14 33.58 3.86
1581 2360 7.830940 TGAAACTTTCAAAACAGTAGTCGTA 57.169 32.000 1.47 0.00 36.59 3.43
1593 2372 8.876275 AAACAGTAGTCGTATGTTTTCACTAA 57.124 30.769 0.00 0.00 42.82 2.24
1613 2392 4.566545 AAAACATTGCATTCACGTCAGA 57.433 36.364 0.00 0.00 0.00 3.27
1615 2394 3.542712 ACATTGCATTCACGTCAGAAC 57.457 42.857 0.00 0.00 0.00 3.01
1635 2415 3.595819 GCCTTTTGCGGATCTGCT 58.404 55.556 26.32 0.00 35.36 4.24
1636 2416 1.885871 GCCTTTTGCGGATCTGCTT 59.114 52.632 26.32 0.00 35.36 3.91
1637 2417 0.244721 GCCTTTTGCGGATCTGCTTT 59.755 50.000 26.32 0.00 35.36 3.51
1638 2418 1.986698 CCTTTTGCGGATCTGCTTTG 58.013 50.000 26.32 13.61 35.36 2.77
1639 2419 1.541147 CCTTTTGCGGATCTGCTTTGA 59.459 47.619 26.32 4.02 35.36 2.69
1640 2420 2.415090 CCTTTTGCGGATCTGCTTTGAG 60.415 50.000 26.32 17.28 35.36 3.02
1641 2421 1.896220 TTTGCGGATCTGCTTTGAGT 58.104 45.000 26.32 0.00 35.36 3.41
1642 2422 1.442769 TTGCGGATCTGCTTTGAGTC 58.557 50.000 26.32 0.00 35.36 3.36
1643 2423 0.737367 TGCGGATCTGCTTTGAGTCG 60.737 55.000 26.32 2.26 35.36 4.18
1644 2424 2.002127 CGGATCTGCTTTGAGTCGC 58.998 57.895 0.00 0.00 0.00 5.19
1645 2425 0.737367 CGGATCTGCTTTGAGTCGCA 60.737 55.000 0.00 0.00 34.54 5.10
1646 2426 1.661341 GGATCTGCTTTGAGTCGCAT 58.339 50.000 0.00 0.00 35.32 4.73
1647 2427 2.012673 GGATCTGCTTTGAGTCGCATT 58.987 47.619 0.00 0.00 35.32 3.56
1648 2428 2.223203 GGATCTGCTTTGAGTCGCATTG 60.223 50.000 0.00 0.00 35.32 2.82
1649 2429 1.882912 TCTGCTTTGAGTCGCATTGT 58.117 45.000 0.00 0.00 35.32 2.71
1650 2430 1.532437 TCTGCTTTGAGTCGCATTGTG 59.468 47.619 0.00 0.00 35.32 3.33
1651 2431 0.040157 TGCTTTGAGTCGCATTGTGC 60.040 50.000 0.00 0.00 40.69 4.57
1663 2443 2.596851 ATTGTGCGAGAGGCCCTGT 61.597 57.895 0.00 0.00 42.61 4.00
1674 2454 1.815003 GAGGCCCTGTTCTTGTTGATG 59.185 52.381 0.00 0.00 0.00 3.07
1680 2460 4.556699 GCCCTGTTCTTGTTGATGTGTTAC 60.557 45.833 0.00 0.00 0.00 2.50
1683 2463 5.333339 CCTGTTCTTGTTGATGTGTTACTCG 60.333 44.000 0.00 0.00 0.00 4.18
1687 2467 6.466308 TCTTGTTGATGTGTTACTCGATTG 57.534 37.500 0.00 0.00 0.00 2.67
1691 2471 3.261580 TGATGTGTTACTCGATTGCAGG 58.738 45.455 0.00 0.00 0.00 4.85
1706 2486 5.345741 CGATTGCAGGTTTGAAGGTAAAATG 59.654 40.000 0.00 0.00 0.00 2.32
1709 2489 5.983540 TGCAGGTTTGAAGGTAAAATGTTT 58.016 33.333 0.00 0.00 0.00 2.83
1717 2497 5.537188 TGAAGGTAAAATGTTTGATGTGGC 58.463 37.500 0.00 0.00 0.00 5.01
1722 2502 5.062058 GGTAAAATGTTTGATGTGGCGAATG 59.938 40.000 0.00 0.00 0.00 2.67
1723 2503 2.282701 ATGTTTGATGTGGCGAATGC 57.717 45.000 0.00 0.00 41.71 3.56
1740 2520 6.751888 GGCGAATGCTGTTGATATTTAAAACT 59.248 34.615 0.00 0.00 42.25 2.66
1741 2521 7.913297 GGCGAATGCTGTTGATATTTAAAACTA 59.087 33.333 0.00 0.00 42.25 2.24
1766 3177 0.975887 ATGCATTTCCCCGTTGCTTT 59.024 45.000 0.00 0.00 37.28 3.51
1767 3178 0.033228 TGCATTTCCCCGTTGCTTTG 59.967 50.000 0.00 0.00 37.28 2.77
1802 3213 9.372189 AGTACTTAGGAGTAAAACCTTAACAGA 57.628 33.333 0.00 0.00 39.95 3.41
1808 3219 8.762481 AGGAGTAAAACCTTAACAGATGTTTT 57.238 30.769 3.14 0.00 41.99 2.43
1851 3262 9.716531 ATGATGTGATAGTTGATCGTGAATATT 57.283 29.630 0.00 0.00 37.38 1.28
1877 3288 6.119240 TGCAGGCATCTAGCTAATTTAGAT 57.881 37.500 7.63 3.47 44.79 1.98
1943 3354 8.417884 GCTATAAGTGAAGAGGTAGAGATTGTT 58.582 37.037 0.00 0.00 0.00 2.83
1956 3367 3.891977 AGAGATTGTTAGGCAGCTCGATA 59.108 43.478 0.00 0.00 36.27 2.92
2099 3510 1.270839 ACCTTTGACGACCCTGATGTG 60.271 52.381 0.00 0.00 0.00 3.21
2254 3665 1.243902 CCCAGCGGAAGTAAAGCAAA 58.756 50.000 0.00 0.00 0.00 3.68
2349 3760 2.747446 TCAGCGGTAATTTCCTTCAAGC 59.253 45.455 0.00 0.00 0.00 4.01
2436 3847 2.040145 TCTGTCTGCACCCATGAATGAA 59.960 45.455 0.00 0.00 0.00 2.57
2437 3848 2.821378 CTGTCTGCACCCATGAATGAAA 59.179 45.455 0.00 0.00 0.00 2.69
2439 3850 3.005684 TGTCTGCACCCATGAATGAAAAC 59.994 43.478 0.00 0.00 0.00 2.43
2510 4098 0.036732 TTTACCTGCCTGTCTGCCTG 59.963 55.000 0.00 0.00 0.00 4.85
2611 4199 4.582701 TGGTTTCAAAATGTGGCTACAG 57.417 40.909 9.38 0.00 40.79 2.74
2656 4244 4.082949 GGTGTATGCAAAGTGGAGTTAACC 60.083 45.833 0.88 0.00 0.00 2.85
2657 4245 4.760204 GTGTATGCAAAGTGGAGTTAACCT 59.240 41.667 0.88 0.00 0.00 3.50
2658 4246 5.001232 TGTATGCAAAGTGGAGTTAACCTC 58.999 41.667 0.88 0.00 39.67 3.85
2659 4247 3.569194 TGCAAAGTGGAGTTAACCTCA 57.431 42.857 0.88 0.00 42.40 3.86
2660 4248 3.476552 TGCAAAGTGGAGTTAACCTCAG 58.523 45.455 0.88 0.00 42.40 3.35
2661 4249 2.226674 GCAAAGTGGAGTTAACCTCAGC 59.773 50.000 0.88 0.00 42.40 4.26
2703 4343 8.918202 AGCCTTAAATATGTCGATTTGGATTA 57.082 30.769 0.00 0.00 31.51 1.75
2754 4394 5.657474 TGTCATACCGAGAAACATACCTTC 58.343 41.667 0.00 0.00 0.00 3.46
2884 4524 1.980844 CGCACACAACAAGAATGATGC 59.019 47.619 0.00 0.00 32.93 3.91
2901 4541 3.512329 TGATGCTGAAATCACCAAGCATT 59.488 39.130 10.08 0.00 42.15 3.56
2979 4619 3.941483 GGGAACTGGAATCCGCATATATG 59.059 47.826 8.45 8.45 37.87 1.78
3051 4694 8.708378 TCAACTTGATGATATGGAACTACAGAT 58.292 33.333 0.00 0.00 0.00 2.90
3428 5072 3.785486 ACAAAGTTGCTGCCTTTCTTTC 58.215 40.909 0.00 0.00 29.89 2.62
3998 5642 7.049754 GCCAAGATAATGACAATTTTCCCAAT 58.950 34.615 0.00 0.00 0.00 3.16
4075 5719 2.408050 ACATGTCGCAGAAGAGAACAC 58.592 47.619 0.00 0.00 39.69 3.32
4191 5837 4.850680 TCATTTAGAAAATACCGTGCCCT 58.149 39.130 0.00 0.00 0.00 5.19
4383 6029 1.421268 TGATGAAGCACTCAGGTTGGT 59.579 47.619 0.00 0.00 38.24 3.67
4384 6030 1.808945 GATGAAGCACTCAGGTTGGTG 59.191 52.381 0.00 0.00 38.24 4.17
4448 6094 7.603024 GTGCTACTGGTAGTATCAAAACTCTTT 59.397 37.037 9.16 0.00 29.82 2.52
4559 6205 2.693591 TGCTATTGGAGTTAGAGACCGG 59.306 50.000 0.00 0.00 0.00 5.28
4585 6231 3.877508 GGTTTCTAGAGTTGTGTTGCTGT 59.122 43.478 0.00 0.00 0.00 4.40
4586 6232 4.335594 GGTTTCTAGAGTTGTGTTGCTGTT 59.664 41.667 0.00 0.00 0.00 3.16
4587 6233 5.526111 GGTTTCTAGAGTTGTGTTGCTGTTA 59.474 40.000 0.00 0.00 0.00 2.41
4779 6426 0.955428 GCTCCAACGGCAATCACTCA 60.955 55.000 0.00 0.00 0.00 3.41
4971 6618 9.435688 AAATGATTATTTTGTTTAGTTCCTGCC 57.564 29.630 0.00 0.00 32.70 4.85
5047 6694 7.847487 TGTAACTTGAGTTGTGTTTCTATTCG 58.153 34.615 6.64 0.00 38.90 3.34
5115 6762 2.158856 TGCTCTCATGCCTCTACATTGG 60.159 50.000 0.00 0.00 0.00 3.16
5142 6789 4.325972 TGTCCCGTTTTCCCTATTTGTAC 58.674 43.478 0.00 0.00 0.00 2.90
5211 6858 7.066163 GCTTTTGCTATTTATTTTTCCTGCCAT 59.934 33.333 0.00 0.00 43.35 4.40
5378 7025 6.368516 CACTTCCAAGTTTTGAAAGCAGAAAA 59.631 34.615 0.00 0.00 37.08 2.29
5433 7080 8.437360 TGAGGTATGATGTACTAAAGCATTTG 57.563 34.615 0.00 0.00 39.63 2.32
5436 7083 9.899661 AGGTATGATGTACTAAAGCATTTGTTA 57.100 29.630 0.00 0.00 39.63 2.41
5462 7109 5.697178 TCATCTTTTCGTCATTTGGTCGTTA 59.303 36.000 0.00 0.00 0.00 3.18
5505 7152 6.647067 GGGATACTGTTCACTAATCATACTGC 59.353 42.308 0.00 0.00 0.00 4.40
5564 7211 0.397187 TGTTGCTTACTAACGCCCCA 59.603 50.000 0.00 0.00 0.00 4.96
5657 7304 3.578688 GGATGACCTGACAAATGTTTGC 58.421 45.455 5.44 0.35 41.79 3.68
5881 7528 2.309136 ACCTTGGTTCCCATTGAAGG 57.691 50.000 0.00 0.00 34.81 3.46
5972 7619 4.217550 CACCTTCCCGTATGTTGTTTCAAT 59.782 41.667 0.00 0.00 0.00 2.57
6077 7733 4.133820 TCGGTGAGTGTTTGTTGATTGAT 58.866 39.130 0.00 0.00 0.00 2.57
6128 7784 6.696411 TGTGGAAGTGAAATTCTTTGTGTTT 58.304 32.000 0.00 0.00 0.00 2.83
6182 7838 5.296151 TCACTGTATTTCCATCTCCCATC 57.704 43.478 0.00 0.00 0.00 3.51
6192 7848 5.992564 TCCATCTCCCATCCATTTTCTAA 57.007 39.130 0.00 0.00 0.00 2.10
6199 7855 7.518188 TCTCCCATCCATTTTCTAATTACTCC 58.482 38.462 0.00 0.00 0.00 3.85
6217 7873 5.310720 ACTCCACGGAATAATTTTGAAGC 57.689 39.130 0.00 0.00 0.00 3.86
6221 7877 6.155827 TCCACGGAATAATTTTGAAGCTTTG 58.844 36.000 0.00 0.00 0.00 2.77
6222 7878 6.015856 TCCACGGAATAATTTTGAAGCTTTGA 60.016 34.615 0.00 0.00 0.00 2.69
6223 7879 6.813152 CCACGGAATAATTTTGAAGCTTTGAT 59.187 34.615 0.00 0.00 0.00 2.57
6224 7880 7.201461 CCACGGAATAATTTTGAAGCTTTGATG 60.201 37.037 0.00 0.00 0.00 3.07
6225 7881 7.329226 CACGGAATAATTTTGAAGCTTTGATGT 59.671 33.333 0.00 0.00 0.00 3.06
6238 7894 3.119495 GCTTTGATGTCCGCCTTTTACAT 60.119 43.478 0.00 0.00 36.57 2.29
6274 7931 1.370414 CGGCGCTTTGTGTTGAAGG 60.370 57.895 7.64 0.00 0.00 3.46
6292 7949 0.458716 GGAGTTGCGTCTCTAGTGGC 60.459 60.000 7.66 0.00 35.11 5.01
6297 7954 1.355916 GCGTCTCTAGTGGCTACGG 59.644 63.158 0.00 0.00 34.29 4.02
6298 7955 1.375098 GCGTCTCTAGTGGCTACGGT 61.375 60.000 0.00 0.00 34.29 4.83
6338 7995 1.029947 TCCGAGCACACGCAGATAGA 61.030 55.000 0.00 0.00 42.27 1.98
6344 8001 2.493675 AGCACACGCAGATAGAAGAGAA 59.506 45.455 0.00 0.00 42.27 2.87
6362 8019 0.249699 AACCGATCGTGTGTGAAGCA 60.250 50.000 15.09 0.00 0.00 3.91
6366 8023 2.095768 CCGATCGTGTGTGAAGCAATTT 60.096 45.455 15.09 0.00 0.00 1.82
6386 8043 3.490439 TTTTGCTGGTCTCAGATGTGA 57.510 42.857 0.00 0.00 43.49 3.58
6429 8086 2.237392 AGACCTGGAATTGCTCTGGTAC 59.763 50.000 0.00 0.00 33.22 3.34
6432 8089 2.290896 CCTGGAATTGCTCTGGTACCAA 60.291 50.000 17.11 0.00 0.00 3.67
6461 8139 4.463050 ACCTACTTCTCCTATCCTCAGG 57.537 50.000 0.00 0.00 37.00 3.86
6471 8161 8.713708 TTCTCCTATCCTCAGGAAAATACTAG 57.286 38.462 0.00 0.00 44.18 2.57
6473 8163 6.323737 TCCTATCCTCAGGAAAATACTAGGG 58.676 44.000 13.76 0.68 41.88 3.53
6507 8197 1.691976 ACATGGAAGTCGTGTCCTTGA 59.308 47.619 17.83 0.00 41.45 3.02
6508 8198 2.069273 CATGGAAGTCGTGTCCTTGAC 58.931 52.381 10.17 0.00 40.91 3.18
6509 8199 1.410004 TGGAAGTCGTGTCCTTGACT 58.590 50.000 0.00 0.00 46.98 3.41
6512 8202 3.290776 AGTCGTGTCCTTGACTTGC 57.709 52.632 0.00 0.00 42.61 4.01
6513 8203 0.753262 AGTCGTGTCCTTGACTTGCT 59.247 50.000 0.00 0.00 42.61 3.91
6520 8210 2.294233 TGTCCTTGACTTGCTTTCATGC 59.706 45.455 0.00 0.00 33.15 4.06
6533 8247 2.515926 TTCATGCGACCTCTGATAGC 57.484 50.000 0.00 0.00 0.00 2.97
6550 8264 6.372937 TCTGATAGCTCTACCTACGATCAATG 59.627 42.308 0.00 0.00 0.00 2.82
6563 8277 2.223611 CGATCAATGCTCTTCATGGCTC 59.776 50.000 0.00 0.00 35.13 4.70
6564 8278 2.793288 TCAATGCTCTTCATGGCTCA 57.207 45.000 0.00 0.00 35.13 4.26
6565 8279 3.076079 TCAATGCTCTTCATGGCTCAA 57.924 42.857 0.00 0.00 35.13 3.02
6566 8280 3.014623 TCAATGCTCTTCATGGCTCAAG 58.985 45.455 0.00 0.00 35.13 3.02
6567 8281 2.753452 CAATGCTCTTCATGGCTCAAGT 59.247 45.455 0.00 0.00 35.13 3.16
6571 8285 4.397420 TGCTCTTCATGGCTCAAGTAAAA 58.603 39.130 0.00 0.00 0.00 1.52
6572 8286 4.826733 TGCTCTTCATGGCTCAAGTAAAAA 59.173 37.500 0.00 0.00 0.00 1.94
6597 8311 7.625828 AAAAATGCTGTTCATAGGTACCTAC 57.374 36.000 24.07 14.32 34.33 3.18
6598 8312 5.950544 AATGCTGTTCATAGGTACCTACA 57.049 39.130 24.07 18.11 34.33 2.74
6599 8313 5.950544 ATGCTGTTCATAGGTACCTACAA 57.049 39.130 24.07 16.12 32.59 2.41
6600 8314 5.748670 TGCTGTTCATAGGTACCTACAAA 57.251 39.130 24.07 17.06 0.00 2.83
6601 8315 6.116711 TGCTGTTCATAGGTACCTACAAAA 57.883 37.500 24.07 14.69 0.00 2.44
6602 8316 6.717289 TGCTGTTCATAGGTACCTACAAAAT 58.283 36.000 24.07 6.01 0.00 1.82
6603 8317 6.597672 TGCTGTTCATAGGTACCTACAAAATG 59.402 38.462 24.07 18.07 0.00 2.32
6604 8318 6.458342 GCTGTTCATAGGTACCTACAAAATGC 60.458 42.308 24.07 19.95 0.00 3.56
6605 8319 6.477253 TGTTCATAGGTACCTACAAAATGCA 58.523 36.000 24.07 13.01 0.00 3.96
6606 8320 6.943146 TGTTCATAGGTACCTACAAAATGCAA 59.057 34.615 24.07 11.59 0.00 4.08
6607 8321 7.613801 TGTTCATAGGTACCTACAAAATGCAAT 59.386 33.333 24.07 2.07 0.00 3.56
6608 8322 8.466798 GTTCATAGGTACCTACAAAATGCAATT 58.533 33.333 24.07 0.44 38.98 2.32
6609 8323 9.688091 TTCATAGGTACCTACAAAATGCAATTA 57.312 29.630 24.07 0.00 33.67 1.40
6610 8324 9.688091 TCATAGGTACCTACAAAATGCAATTAA 57.312 29.630 24.07 0.00 33.67 1.40
6611 8325 9.730420 CATAGGTACCTACAAAATGCAATTAAC 57.270 33.333 24.07 0.00 33.67 2.01
6612 8326 6.848451 AGGTACCTACAAAATGCAATTAACG 58.152 36.000 14.41 0.00 33.67 3.18
6613 8327 6.031471 GGTACCTACAAAATGCAATTAACGG 58.969 40.000 4.06 0.00 33.67 4.44
6614 8328 4.490743 ACCTACAAAATGCAATTAACGGC 58.509 39.130 0.00 0.00 33.67 5.68
6615 8329 3.545873 CCTACAAAATGCAATTAACGGCG 59.454 43.478 4.80 4.80 33.67 6.46
6616 8330 2.333014 ACAAAATGCAATTAACGGCGG 58.667 42.857 13.24 0.00 33.67 6.13
6617 8331 2.288518 ACAAAATGCAATTAACGGCGGT 60.289 40.909 13.24 7.51 33.67 5.68
6618 8332 1.989430 AAATGCAATTAACGGCGGTG 58.011 45.000 8.19 0.00 33.67 4.94
6619 8333 0.885196 AATGCAATTAACGGCGGTGT 59.115 45.000 8.19 0.00 32.46 4.16
6620 8334 0.170116 ATGCAATTAACGGCGGTGTG 59.830 50.000 8.19 3.95 0.00 3.82
6621 8335 0.885150 TGCAATTAACGGCGGTGTGA 60.885 50.000 8.19 0.00 0.00 3.58
6622 8336 0.450184 GCAATTAACGGCGGTGTGAT 59.550 50.000 8.19 0.00 0.00 3.06
6623 8337 1.793714 GCAATTAACGGCGGTGTGATG 60.794 52.381 8.19 2.26 0.00 3.07
6709 8424 6.384224 CACTATACTACAACGACTTTGGTGA 58.616 40.000 0.00 0.00 39.84 4.02
6714 8429 4.929808 ACTACAACGACTTTGGTGATGATC 59.070 41.667 0.00 0.00 39.84 2.92
6732 8447 7.172532 GTGATGATCGTCAGAGTCTTAGTCTAT 59.827 40.741 18.02 0.00 0.00 1.98
6740 8455 7.794810 CGTCAGAGTCTTAGTCTATTAATCGTG 59.205 40.741 0.00 0.00 0.00 4.35
6850 8565 3.875727 AGATCATCTCTGAATGTTTGGCG 59.124 43.478 0.00 0.00 34.37 5.69
6857 8572 3.206964 TCTGAATGTTTGGCGTTGTACA 58.793 40.909 0.00 0.00 0.00 2.90
6858 8573 3.818210 TCTGAATGTTTGGCGTTGTACAT 59.182 39.130 0.00 0.00 32.89 2.29
6859 8574 3.894920 TGAATGTTTGGCGTTGTACATG 58.105 40.909 0.00 0.00 31.98 3.21
6860 8575 3.316588 TGAATGTTTGGCGTTGTACATGT 59.683 39.130 2.69 2.69 31.98 3.21
6861 8576 4.515567 TGAATGTTTGGCGTTGTACATGTA 59.484 37.500 0.08 0.08 31.98 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
293 597 5.746990 AAGTACTGTAATTGCCTCTGTCT 57.253 39.130 0.00 0.00 0.00 3.41
340 675 4.751767 TTTTTGCAGAAACACCCTCAAT 57.248 36.364 0.00 0.00 0.00 2.57
395 731 0.105194 TCTTCCCACTGTCAGGGTCA 60.105 55.000 4.53 0.00 46.82 4.02
397 733 0.987294 CATCTTCCCACTGTCAGGGT 59.013 55.000 4.53 0.00 46.82 4.34
399 735 0.325933 TGCATCTTCCCACTGTCAGG 59.674 55.000 4.53 0.00 0.00 3.86
466 802 2.665649 TCTCGTGCAAATACGGTCAT 57.334 45.000 0.00 0.00 43.85 3.06
504 840 9.163899 TGCTAAAACTTTTAAAATTCGGGTTTT 57.836 25.926 21.59 21.59 38.41 2.43
518 854 5.575218 CGTTCAGTTTGGTGCTAAAACTTTT 59.425 36.000 8.61 0.00 43.60 2.27
547 883 1.407437 CGGGAGCCATAGAACTTGCTT 60.407 52.381 0.00 0.00 33.41 3.91
561 897 1.968493 TGAGGTAATATCACCGGGAGC 59.032 52.381 6.32 0.00 43.84 4.70
587 923 1.970640 GGAGCCAACCCATCAAAGTTT 59.029 47.619 0.00 0.00 0.00 2.66
608 944 0.884704 ATGCGAACGTGTTCCTTGCT 60.885 50.000 7.13 0.00 36.27 3.91
685 1021 5.050023 GCTCCAGTTCTCAAAACACTAGTTC 60.050 44.000 0.00 0.00 36.84 3.01
690 1026 2.576615 GGCTCCAGTTCTCAAAACACT 58.423 47.619 0.00 0.00 0.00 3.55
717 1053 7.661847 TGTTCTATCCTTCTTTCTCTTTTGACC 59.338 37.037 0.00 0.00 0.00 4.02
854 1191 0.688087 GGGGATTCAGACGAGAGGGT 60.688 60.000 0.00 0.00 0.00 4.34
903 1240 2.617774 GGATGGATTGAGAAGAAGCAGC 59.382 50.000 0.00 0.00 0.00 5.25
906 1243 2.580962 GGGGATGGATTGAGAAGAAGC 58.419 52.381 0.00 0.00 0.00 3.86
996 1333 3.352990 TAGGGGGTTCGCCATTGCC 62.353 63.158 8.11 0.00 39.05 4.52
997 1334 1.823899 CTAGGGGGTTCGCCATTGC 60.824 63.158 8.11 0.00 39.05 3.56
998 1335 1.823899 GCTAGGGGGTTCGCCATTG 60.824 63.158 8.11 3.35 39.05 2.82
1077 1414 2.546795 GCCGTCGAAGAAGATGATGGAT 60.547 50.000 0.00 0.00 40.52 3.41
1124 1461 2.446802 GGAGGGTGGGCTAGGGAG 60.447 72.222 0.00 0.00 0.00 4.30
1125 1462 4.103928 GGGAGGGTGGGCTAGGGA 62.104 72.222 0.00 0.00 0.00 4.20
1185 1964 2.347490 GCACAGATCCACACGGGT 59.653 61.111 0.00 0.00 38.11 5.28
1242 2021 6.731467 ACCCACTATACCAGAACAATCAAAT 58.269 36.000 0.00 0.00 0.00 2.32
1244 2023 5.772393 ACCCACTATACCAGAACAATCAA 57.228 39.130 0.00 0.00 0.00 2.57
1254 2033 7.335627 CAAAATGACTAGAACCCACTATACCA 58.664 38.462 0.00 0.00 0.00 3.25
1269 2048 4.816392 TCTCGCTTACAGCAAAATGACTA 58.184 39.130 0.00 0.00 42.58 2.59
1275 2054 3.728845 AGACTTCTCGCTTACAGCAAAA 58.271 40.909 0.00 0.00 42.58 2.44
1282 2061 0.992802 CCGCAAGACTTCTCGCTTAC 59.007 55.000 1.86 0.00 43.02 2.34
1283 2062 0.601558 ACCGCAAGACTTCTCGCTTA 59.398 50.000 1.86 0.00 43.02 3.09
1284 2063 0.249911 AACCGCAAGACTTCTCGCTT 60.250 50.000 1.86 0.00 43.02 4.68
1292 2071 2.565834 ACATACTACCAACCGCAAGACT 59.434 45.455 0.00 0.00 43.02 3.24
1295 2074 3.071479 ACAACATACTACCAACCGCAAG 58.929 45.455 0.00 0.00 0.00 4.01
1317 2096 8.035394 TCTCGACCCTAATTAATGATAAGCATC 58.965 37.037 0.00 0.00 35.78 3.91
1319 2098 7.297936 TCTCGACCCTAATTAATGATAAGCA 57.702 36.000 0.00 0.00 0.00 3.91
1330 2109 5.243207 ACGATTGTTTTCTCGACCCTAATT 58.757 37.500 0.00 0.00 38.24 1.40
1331 2110 4.828829 ACGATTGTTTTCTCGACCCTAAT 58.171 39.130 0.00 0.00 38.24 1.73
1351 2130 1.070975 GCAGATCAGCGCAAATAGACG 60.071 52.381 11.47 0.00 0.00 4.18
1352 2131 1.262683 GGCAGATCAGCGCAAATAGAC 59.737 52.381 11.47 0.00 34.64 2.59
1357 2136 2.358615 ACGGCAGATCAGCGCAAA 60.359 55.556 11.47 0.00 34.64 3.68
1397 2176 5.649241 GGAGCACCCAAATCATGAACATGA 61.649 45.833 17.78 17.78 42.37 3.07
1398 2177 3.429822 GGAGCACCCAAATCATGAACATG 60.430 47.826 0.00 8.31 36.11 3.21
1399 2178 2.762327 GGAGCACCCAAATCATGAACAT 59.238 45.455 0.00 0.00 34.14 2.71
1400 2179 2.170166 GGAGCACCCAAATCATGAACA 58.830 47.619 0.00 0.00 34.14 3.18
1401 2180 2.165030 CTGGAGCACCCAAATCATGAAC 59.835 50.000 0.00 0.00 46.07 3.18
1402 2181 2.041485 TCTGGAGCACCCAAATCATGAA 59.959 45.455 0.00 0.00 46.07 2.57
1419 2198 9.212641 CTTTACATACATGACCTGATATTCTGG 57.787 37.037 0.00 0.00 40.80 3.86
1422 2201 9.988815 AGACTTTACATACATGACCTGATATTC 57.011 33.333 0.00 0.00 0.00 1.75
1424 2203 7.875041 GCAGACTTTACATACATGACCTGATAT 59.125 37.037 0.00 0.00 0.00 1.63
1425 2204 7.210174 GCAGACTTTACATACATGACCTGATA 58.790 38.462 0.00 0.00 0.00 2.15
1426 2205 6.051717 GCAGACTTTACATACATGACCTGAT 58.948 40.000 0.00 0.00 0.00 2.90
1437 2216 6.061022 TCAAATCCAGGCAGACTTTACATA 57.939 37.500 0.00 0.00 0.00 2.29
1466 2245 1.821216 ACAATAACCAAGGTGCCTCG 58.179 50.000 0.00 0.00 0.00 4.63
1470 2249 6.509418 TCATTTCTACAATAACCAAGGTGC 57.491 37.500 0.00 0.00 0.00 5.01
1490 2269 3.556999 ACCGTACAGAGCTCAGTATCAT 58.443 45.455 20.33 7.57 0.00 2.45
1513 2292 1.406539 CATTAGGTGCAATCTGGGTGC 59.593 52.381 0.00 0.00 42.55 5.01
1514 2293 3.003394 TCATTAGGTGCAATCTGGGTG 57.997 47.619 0.00 0.00 0.00 4.61
1515 2294 3.356290 GTTCATTAGGTGCAATCTGGGT 58.644 45.455 0.00 0.00 0.00 4.51
1516 2295 2.355756 CGTTCATTAGGTGCAATCTGGG 59.644 50.000 0.00 0.00 0.00 4.45
1517 2296 2.223340 GCGTTCATTAGGTGCAATCTGG 60.223 50.000 0.00 0.00 0.00 3.86
1518 2297 2.223340 GGCGTTCATTAGGTGCAATCTG 60.223 50.000 0.00 0.00 0.00 2.90
1519 2298 2.017049 GGCGTTCATTAGGTGCAATCT 58.983 47.619 0.00 0.00 0.00 2.40
1520 2299 1.742831 TGGCGTTCATTAGGTGCAATC 59.257 47.619 0.00 0.00 0.00 2.67
1521 2300 1.832883 TGGCGTTCATTAGGTGCAAT 58.167 45.000 0.00 0.00 0.00 3.56
1526 2305 6.843936 AATGAAGCATTGGCGTTCATTAGGT 61.844 40.000 17.37 3.55 45.37 3.08
1592 2371 4.566545 TCTGACGTGAATGCAATGTTTT 57.433 36.364 0.00 0.00 0.00 2.43
1593 2372 4.290155 GTTCTGACGTGAATGCAATGTTT 58.710 39.130 0.00 0.00 0.00 2.83
1613 2392 0.251341 AGATCCGCAAAAGGCTGGTT 60.251 50.000 0.00 0.00 41.67 3.67
1615 2394 1.805254 CAGATCCGCAAAAGGCTGG 59.195 57.895 0.00 0.00 41.67 4.85
1633 2413 2.716988 GCACAATGCGACTCAAAGC 58.283 52.632 0.00 0.00 31.71 3.51
1643 2423 3.512516 GGGCCTCTCGCACAATGC 61.513 66.667 0.84 0.00 42.24 3.56
1644 2424 2.110967 CAGGGCCTCTCGCACAATG 61.111 63.158 0.95 0.00 46.72 2.82
1645 2425 2.129555 AACAGGGCCTCTCGCACAAT 62.130 55.000 0.95 0.00 46.72 2.71
1646 2426 2.731691 GAACAGGGCCTCTCGCACAA 62.732 60.000 0.95 0.00 46.72 3.33
1647 2427 3.240134 GAACAGGGCCTCTCGCACA 62.240 63.158 0.95 0.00 46.72 4.57
1648 2428 2.435059 GAACAGGGCCTCTCGCAC 60.435 66.667 0.95 0.00 43.45 5.34
1649 2429 2.217038 AAGAACAGGGCCTCTCGCA 61.217 57.895 0.95 0.00 40.31 5.10
1650 2430 1.743252 CAAGAACAGGGCCTCTCGC 60.743 63.158 0.95 0.00 0.00 5.03
1651 2431 0.035458 AACAAGAACAGGGCCTCTCG 59.965 55.000 0.95 0.00 0.00 4.04
1652 2432 1.072331 TCAACAAGAACAGGGCCTCTC 59.928 52.381 0.95 3.07 0.00 3.20
1653 2433 1.140312 TCAACAAGAACAGGGCCTCT 58.860 50.000 0.95 0.00 0.00 3.69
1654 2434 1.815003 CATCAACAAGAACAGGGCCTC 59.185 52.381 0.95 0.00 0.00 4.70
1655 2435 1.145738 ACATCAACAAGAACAGGGCCT 59.854 47.619 0.00 0.00 0.00 5.19
1656 2436 1.270550 CACATCAACAAGAACAGGGCC 59.729 52.381 0.00 0.00 0.00 5.80
1657 2437 1.956477 ACACATCAACAAGAACAGGGC 59.044 47.619 0.00 0.00 0.00 5.19
1658 2438 4.821805 AGTAACACATCAACAAGAACAGGG 59.178 41.667 0.00 0.00 0.00 4.45
1663 2443 6.565811 GCAATCGAGTAACACATCAACAAGAA 60.566 38.462 0.00 0.00 0.00 2.52
1674 2454 3.496884 TCAAACCTGCAATCGAGTAACAC 59.503 43.478 0.00 0.00 0.00 3.32
1680 2460 2.154462 ACCTTCAAACCTGCAATCGAG 58.846 47.619 0.00 0.00 0.00 4.04
1683 2463 6.223120 ACATTTTACCTTCAAACCTGCAATC 58.777 36.000 0.00 0.00 0.00 2.67
1687 2467 6.045955 TCAAACATTTTACCTTCAAACCTGC 58.954 36.000 0.00 0.00 0.00 4.85
1691 2471 7.518211 GCCACATCAAACATTTTACCTTCAAAC 60.518 37.037 0.00 0.00 0.00 2.93
1706 2486 1.068333 ACAGCATTCGCCACATCAAAC 60.068 47.619 0.00 0.00 39.83 2.93
1709 2489 0.522626 CAACAGCATTCGCCACATCA 59.477 50.000 0.00 0.00 39.83 3.07
1740 2520 4.037446 GCAACGGGGAAATGCATTATCTTA 59.963 41.667 13.39 0.00 39.81 2.10
1741 2521 3.181476 GCAACGGGGAAATGCATTATCTT 60.181 43.478 13.39 0.00 39.81 2.40
1802 3213 9.829507 TCATGAAGGACAACAAATTAAAAACAT 57.170 25.926 0.00 0.00 0.00 2.71
1808 3219 8.175925 TCACATCATGAAGGACAACAAATTAA 57.824 30.769 0.00 0.00 33.02 1.40
1851 3262 7.679783 TCTAAATTAGCTAGATGCCTGCATAA 58.320 34.615 4.30 0.00 44.23 1.90
1877 3288 2.552599 TTGTGCGGATAAAGGTGTCA 57.447 45.000 0.00 0.00 0.00 3.58
1943 3354 1.717032 ATTGGGTATCGAGCTGCCTA 58.283 50.000 0.00 0.00 0.00 3.93
1956 3367 7.154656 GCTTCTTTAAATGACTTCAATTGGGT 58.845 34.615 5.42 5.18 0.00 4.51
2099 3510 1.134371 GTATCTCTTGGAGGTGCCCAC 60.134 57.143 0.00 0.00 35.62 4.61
2254 3665 3.449018 AGTTGATGATCTTACCGCAGAGT 59.551 43.478 0.00 0.00 0.00 3.24
2461 3872 5.689068 CCAGCAGAAAAAGAAGCACTAAAAG 59.311 40.000 0.00 0.00 0.00 2.27
2510 4098 4.371786 CCTTTTCTTCTTCTTTTGGCACC 58.628 43.478 0.00 0.00 0.00 5.01
2884 4524 6.565247 GCTTTTGAAATGCTTGGTGATTTCAG 60.565 38.462 8.35 0.00 44.99 3.02
2901 4541 9.844790 CTATTTCAGTATGTGATTGCTTTTGAA 57.155 29.630 0.00 0.00 37.40 2.69
2997 4640 1.269723 GCTAAACCCAACAAGAGGCAC 59.730 52.381 0.00 0.00 0.00 5.01
3428 5072 3.116300 GACTCATGTGCACCATACTACG 58.884 50.000 15.69 0.00 30.71 3.51
3519 5163 1.864711 CGGTTAGCGTGATTGGGTATG 59.135 52.381 0.00 0.00 0.00 2.39
3785 5429 0.874390 TCGAAGCCAATGTTGCAGAC 59.126 50.000 0.00 0.00 0.00 3.51
3998 5642 7.988599 TGTCTTCAAGTTTAAGGTACAAAGCTA 59.011 33.333 0.00 0.00 31.75 3.32
4075 5719 6.969828 AAAGAGGTATAAAAAGCACGAGAG 57.030 37.500 0.00 0.00 0.00 3.20
4383 6029 7.692460 ATGCAAATATGAGTGAAAGAGTTCA 57.308 32.000 0.00 0.00 41.57 3.18
4384 6030 8.976986 AAATGCAAATATGAGTGAAAGAGTTC 57.023 30.769 0.00 0.00 0.00 3.01
4448 6094 9.710900 ATCTCGTACAAATTCAGATATTATGCA 57.289 29.630 0.00 0.00 0.00 3.96
4530 6176 5.616270 TCTAACTCCAATAGCAACACAACA 58.384 37.500 0.00 0.00 0.00 3.33
4559 6205 5.239525 AGCAACACAACTCTAGAAACCAATC 59.760 40.000 0.00 0.00 0.00 2.67
4585 6231 8.707796 ATCAATCCGGTCTCTAACTCTAATAA 57.292 34.615 0.00 0.00 0.00 1.40
4586 6232 8.707796 AATCAATCCGGTCTCTAACTCTAATA 57.292 34.615 0.00 0.00 0.00 0.98
4587 6233 7.604657 AATCAATCCGGTCTCTAACTCTAAT 57.395 36.000 0.00 0.00 0.00 1.73
4706 6352 4.003648 GGTCGAGATTTGTTTGGATCTGT 58.996 43.478 0.00 0.00 32.96 3.41
4779 6426 9.847706 TGATATTAATTGCATGTTAAACACGTT 57.152 25.926 8.36 0.00 0.00 3.99
4838 6485 8.828688 AGGTAGGATATCAATTAAGCGTTAAC 57.171 34.615 4.83 0.00 0.00 2.01
4921 6568 9.528489 TTTGCCTTATTTGAAGGAAACTAGTAT 57.472 29.630 7.54 0.00 42.68 2.12
4971 6618 0.516877 ACGGCGACATGACAAATGTG 59.483 50.000 16.62 0.00 31.52 3.21
5047 6694 0.530870 CTCTAGCCCGCAAAGGTAGC 60.531 60.000 0.00 0.00 38.74 3.58
5115 6762 6.071784 ACAAATAGGGAAAACGGGACATTAAC 60.072 38.462 0.00 0.00 0.00 2.01
5123 6770 4.329392 ACAGTACAAATAGGGAAAACGGG 58.671 43.478 0.00 0.00 0.00 5.28
5142 6789 4.929808 AGAACTGTTTATTGCGGTAGACAG 59.070 41.667 13.77 13.77 40.63 3.51
5211 6858 2.730715 GCACGCTGACTGACAAACAAAA 60.731 45.455 0.00 0.00 0.00 2.44
5272 6919 1.134401 ACCATATGTGCCAGAGGAACG 60.134 52.381 1.24 0.00 32.81 3.95
5273 6920 2.717639 ACCATATGTGCCAGAGGAAC 57.282 50.000 1.24 0.00 0.00 3.62
5348 6995 5.234972 GCTTTCAAAACTTGGAAGTGGAATG 59.765 40.000 8.78 2.78 46.03 2.67
5378 7025 9.270640 GTTCTAAGATTTATGCTGATGAGTGAT 57.729 33.333 0.00 0.00 0.00 3.06
5433 7080 6.899114 ACCAAATGACGAAAAGATGAGTAAC 58.101 36.000 0.00 0.00 0.00 2.50
5436 7083 4.152402 CGACCAAATGACGAAAAGATGAGT 59.848 41.667 0.00 0.00 0.00 3.41
5462 7109 8.917088 CAGTATCCCTGAATGAAATAAAACCAT 58.083 33.333 0.00 0.00 44.49 3.55
5564 7211 6.874134 CAGTAGCTACCTGTTGATACAAAAGT 59.126 38.462 20.31 0.00 32.92 2.66
5657 7304 1.262417 CCATTCATCGAAGCATCACGG 59.738 52.381 0.00 0.00 0.00 4.94
5904 7551 9.885934 GGAATAAAACACAAACAAACAAAAAGT 57.114 25.926 0.00 0.00 0.00 2.66
5942 7589 5.130350 CAACATACGGGAAGGTGGAAATAT 58.870 41.667 0.00 0.00 0.00 1.28
5972 7619 2.367241 ACATACATACATACTGCCGCCA 59.633 45.455 0.00 0.00 0.00 5.69
6058 7713 7.489113 ACTGAAAATCAATCAACAAACACTCAC 59.511 33.333 0.00 0.00 0.00 3.51
6128 7784 7.666623 TGTCCATACATAGCATTTCGAGAATA 58.333 34.615 0.00 0.00 0.00 1.75
6182 7838 6.995511 TTCCGTGGAGTAATTAGAAAATGG 57.004 37.500 0.00 0.00 0.00 3.16
6192 7848 7.339466 AGCTTCAAAATTATTCCGTGGAGTAAT 59.661 33.333 10.01 10.01 38.23 1.89
6199 7855 7.329226 ACATCAAAGCTTCAAAATTATTCCGTG 59.671 33.333 0.00 0.00 0.00 4.94
6217 7873 4.662145 GATGTAAAAGGCGGACATCAAAG 58.338 43.478 14.84 0.00 45.74 2.77
6221 7877 2.277084 ACGATGTAAAAGGCGGACATC 58.723 47.619 11.58 11.58 43.91 3.06
6222 7878 2.277084 GACGATGTAAAAGGCGGACAT 58.723 47.619 0.00 0.00 36.52 3.06
6223 7879 1.001068 TGACGATGTAAAAGGCGGACA 59.999 47.619 0.00 0.00 0.00 4.02
6224 7880 1.717194 TGACGATGTAAAAGGCGGAC 58.283 50.000 0.00 0.00 0.00 4.79
6225 7881 2.459060 TTGACGATGTAAAAGGCGGA 57.541 45.000 0.00 0.00 0.00 5.54
6238 7894 2.413796 GCCGTACATGAAACATTGACGA 59.586 45.455 0.00 0.00 0.00 4.20
6274 7931 0.528470 AGCCACTAGAGACGCAACTC 59.472 55.000 0.00 0.00 37.19 3.01
6292 7949 0.249120 TCAGGGATGCACAACCGTAG 59.751 55.000 0.00 0.00 0.00 3.51
6297 7954 1.885871 GCCTTCAGGGATGCACAAC 59.114 57.895 0.00 0.00 37.23 3.32
6298 7955 1.675310 CGCCTTCAGGGATGCACAA 60.675 57.895 0.00 0.00 37.23 3.33
6328 7985 2.366533 TCGGTTCTCTTCTATCTGCGT 58.633 47.619 0.00 0.00 0.00 5.24
6329 7986 3.560503 GATCGGTTCTCTTCTATCTGCG 58.439 50.000 0.00 0.00 0.00 5.18
6338 7995 1.611977 TCACACACGATCGGTTCTCTT 59.388 47.619 20.98 0.00 0.00 2.85
6344 8001 0.249699 TTGCTTCACACACGATCGGT 60.250 50.000 20.98 11.61 0.00 4.69
6366 8023 3.405831 CTCACATCTGAGACCAGCAAAA 58.594 45.455 0.00 0.00 46.32 2.44
6373 8030 0.177604 CCTGCCTCACATCTGAGACC 59.822 60.000 0.00 0.00 46.32 3.85
6380 8037 4.864334 CCGCCCCTGCCTCACATC 62.864 72.222 0.00 0.00 0.00 3.06
6432 8089 9.930158 GAGGATAGGAGAAGTAGGTTATGATAT 57.070 37.037 0.00 0.00 0.00 1.63
6461 8139 9.315363 TCTTCATCTAGATCCCCTAGTATTTTC 57.685 37.037 1.03 0.00 44.15 2.29
6471 8161 4.163427 TCCATGTCTTCATCTAGATCCCC 58.837 47.826 1.03 0.00 31.15 4.81
6473 8163 6.418057 ACTTCCATGTCTTCATCTAGATCC 57.582 41.667 1.03 0.00 31.15 3.36
6507 8197 1.160137 GAGGTCGCATGAAAGCAAGT 58.840 50.000 0.00 0.00 0.00 3.16
6508 8198 1.129998 CAGAGGTCGCATGAAAGCAAG 59.870 52.381 0.00 0.00 0.00 4.01
6509 8199 1.159285 CAGAGGTCGCATGAAAGCAA 58.841 50.000 0.00 0.00 0.00 3.91
6510 8200 0.321346 TCAGAGGTCGCATGAAAGCA 59.679 50.000 0.00 0.00 0.00 3.91
6511 8201 1.661341 ATCAGAGGTCGCATGAAAGC 58.339 50.000 0.00 0.00 0.00 3.51
6512 8202 2.799412 GCTATCAGAGGTCGCATGAAAG 59.201 50.000 0.00 0.00 0.00 2.62
6513 8203 2.432146 AGCTATCAGAGGTCGCATGAAA 59.568 45.455 0.00 0.00 0.00 2.69
6533 8247 5.009110 TGAAGAGCATTGATCGTAGGTAGAG 59.991 44.000 0.00 0.00 0.00 2.43
6550 8264 5.376854 TTTTTACTTGAGCCATGAAGAGC 57.623 39.130 0.00 0.00 0.00 4.09
6573 8287 7.172342 TGTAGGTACCTATGAACAGCATTTTT 58.828 34.615 24.36 0.00 38.44 1.94
6574 8288 6.717289 TGTAGGTACCTATGAACAGCATTTT 58.283 36.000 24.36 0.00 38.44 1.82
6575 8289 6.308015 TGTAGGTACCTATGAACAGCATTT 57.692 37.500 24.36 0.00 38.44 2.32
6576 8290 5.950544 TGTAGGTACCTATGAACAGCATT 57.049 39.130 24.36 0.00 38.44 3.56
6577 8291 5.950544 TTGTAGGTACCTATGAACAGCAT 57.049 39.130 24.36 0.00 41.08 3.79
6578 8292 5.748670 TTTGTAGGTACCTATGAACAGCA 57.251 39.130 24.36 12.78 0.00 4.41
6579 8293 6.458342 GCATTTTGTAGGTACCTATGAACAGC 60.458 42.308 24.36 19.16 0.00 4.40
6580 8294 6.597672 TGCATTTTGTAGGTACCTATGAACAG 59.402 38.462 24.36 14.15 0.00 3.16
6581 8295 6.477253 TGCATTTTGTAGGTACCTATGAACA 58.523 36.000 24.36 17.15 0.00 3.18
6582 8296 6.995511 TGCATTTTGTAGGTACCTATGAAC 57.004 37.500 24.36 14.68 0.00 3.18
6583 8297 8.588290 AATTGCATTTTGTAGGTACCTATGAA 57.412 30.769 24.36 17.88 0.00 2.57
6584 8298 9.688091 TTAATTGCATTTTGTAGGTACCTATGA 57.312 29.630 24.36 13.19 0.00 2.15
6585 8299 9.730420 GTTAATTGCATTTTGTAGGTACCTATG 57.270 33.333 24.36 19.04 0.00 2.23
6586 8300 8.617809 CGTTAATTGCATTTTGTAGGTACCTAT 58.382 33.333 24.36 6.61 0.00 2.57
6587 8301 7.066043 CCGTTAATTGCATTTTGTAGGTACCTA 59.934 37.037 18.10 18.10 0.00 3.08
6588 8302 6.127842 CCGTTAATTGCATTTTGTAGGTACCT 60.128 38.462 20.57 20.57 0.00 3.08
6589 8303 6.031471 CCGTTAATTGCATTTTGTAGGTACC 58.969 40.000 2.73 2.73 0.00 3.34
6590 8304 5.513849 GCCGTTAATTGCATTTTGTAGGTAC 59.486 40.000 0.00 0.00 0.00 3.34
6591 8305 5.642686 GCCGTTAATTGCATTTTGTAGGTA 58.357 37.500 0.00 0.00 0.00 3.08
6592 8306 4.490743 GCCGTTAATTGCATTTTGTAGGT 58.509 39.130 0.00 0.00 0.00 3.08
6593 8307 3.545873 CGCCGTTAATTGCATTTTGTAGG 59.454 43.478 0.00 0.91 0.00 3.18
6594 8308 3.545873 CCGCCGTTAATTGCATTTTGTAG 59.454 43.478 0.00 0.00 0.00 2.74
6595 8309 3.057456 ACCGCCGTTAATTGCATTTTGTA 60.057 39.130 0.00 0.00 0.00 2.41
6596 8310 2.288518 ACCGCCGTTAATTGCATTTTGT 60.289 40.909 0.00 0.00 0.00 2.83
6597 8311 2.091899 CACCGCCGTTAATTGCATTTTG 59.908 45.455 0.00 0.00 0.00 2.44
6598 8312 2.288518 ACACCGCCGTTAATTGCATTTT 60.289 40.909 0.00 0.00 0.00 1.82
6599 8313 1.271102 ACACCGCCGTTAATTGCATTT 59.729 42.857 0.00 0.00 0.00 2.32
6600 8314 0.885196 ACACCGCCGTTAATTGCATT 59.115 45.000 0.00 0.00 0.00 3.56
6601 8315 0.170116 CACACCGCCGTTAATTGCAT 59.830 50.000 0.00 0.00 0.00 3.96
6602 8316 0.885150 TCACACCGCCGTTAATTGCA 60.885 50.000 0.00 0.00 0.00 4.08
6603 8317 0.450184 ATCACACCGCCGTTAATTGC 59.550 50.000 0.00 0.00 0.00 3.56
6604 8318 1.735018 TCATCACACCGCCGTTAATTG 59.265 47.619 0.00 0.00 0.00 2.32
6605 8319 2.102070 TCATCACACCGCCGTTAATT 57.898 45.000 0.00 0.00 0.00 1.40
6606 8320 2.102070 TTCATCACACCGCCGTTAAT 57.898 45.000 0.00 0.00 0.00 1.40
6607 8321 1.880271 TTTCATCACACCGCCGTTAA 58.120 45.000 0.00 0.00 0.00 2.01
6608 8322 1.880271 TTTTCATCACACCGCCGTTA 58.120 45.000 0.00 0.00 0.00 3.18
6609 8323 1.025812 TTTTTCATCACACCGCCGTT 58.974 45.000 0.00 0.00 0.00 4.44
6610 8324 2.709170 TTTTTCATCACACCGCCGT 58.291 47.368 0.00 0.00 0.00 5.68
6709 8424 9.562408 TTAATAGACTAAGACTCTGACGATCAT 57.438 33.333 0.00 0.00 0.00 2.45
6714 8429 7.794810 CACGATTAATAGACTAAGACTCTGACG 59.205 40.741 2.28 0.00 0.00 4.35
6732 8447 9.038803 CATGAGATGATCTTTCTTCACGATTAA 57.961 33.333 0.00 0.00 0.00 1.40
6770 8485 0.952280 TCCTATAGCTGGCGAGTTCG 59.048 55.000 0.00 0.00 43.27 3.95


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

AutoCloner maintained by Alex Coulton.