Multiple sequence alignment - TraesCS3B01G285000

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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 TraesCS3B01G285000 chr3B 100.000 2838 0 0 1 2838 456555735 456552898 0.000000e+00 5241.0
1 TraesCS3B01G285000 chr3B 94.578 166 9 0 1388 1553 372838606 372838441 1.010000e-64 257.0
2 TraesCS3B01G285000 chr3B 94.578 166 9 0 1388 1553 755167560 755167395 1.010000e-64 257.0
3 TraesCS3B01G285000 chr3B 92.222 90 7 0 1282 1371 181288899 181288810 8.250000e-26 128.0
4 TraesCS3B01G285000 chr3D 95.256 1307 42 5 1551 2838 355630806 355629501 0.000000e+00 2052.0
5 TraesCS3B01G285000 chr3D 93.344 1292 63 12 1 1288 355632095 355630823 0.000000e+00 1888.0
6 TraesCS3B01G285000 chr3D 92.222 90 7 0 1282 1371 126949134 126949045 8.250000e-26 128.0
7 TraesCS3B01G285000 chr3A 95.069 1298 43 7 1558 2838 474435679 474434386 0.000000e+00 2023.0
8 TraesCS3B01G285000 chr3A 92.957 1292 68 12 1 1288 474437100 474435828 0.000000e+00 1860.0
9 TraesCS3B01G285000 chr3A 91.111 90 8 0 1282 1371 137579648 137579559 3.840000e-24 122.0
10 TraesCS3B01G285000 chr4A 96.386 166 6 0 1388 1553 665604122 665604287 1.000000e-69 274.0
11 TraesCS3B01G285000 chr4A 93.605 172 10 1 1382 1552 642589583 642589412 3.630000e-64 255.0
12 TraesCS3B01G285000 chr6B 95.758 165 7 0 1388 1552 147089440 147089604 1.680000e-67 267.0
13 TraesCS3B01G285000 chr1A 95.152 165 8 0 1388 1552 11628336 11628172 7.800000e-66 261.0
14 TraesCS3B01G285000 chr6D 94.118 170 9 1 1388 1556 153869403 153869234 1.010000e-64 257.0
15 TraesCS3B01G285000 chr4B 94.578 166 9 0 1388 1553 9545124 9545289 1.010000e-64 257.0
16 TraesCS3B01G285000 chr4B 94.118 170 9 1 1384 1552 429241915 429242084 1.010000e-64 257.0
17 TraesCS3B01G285000 chr5A 89.655 87 6 3 1287 1371 558163627 558163542 1.080000e-19 108.0
18 TraesCS3B01G285000 chr5D 89.412 85 8 1 1287 1371 441390845 441390762 3.870000e-19 106.0
19 TraesCS3B01G285000 chr5D 88.608 79 7 2 1287 1364 478164264 478164187 8.370000e-16 95.3
20 TraesCS3B01G285000 chr7D 85.556 90 9 3 1286 1372 237415167 237415079 1.080000e-14 91.6
21 TraesCS3B01G285000 chr7B 84.615 91 9 4 1286 1372 214074957 214074868 5.040000e-13 86.1
22 TraesCS3B01G285000 chr5B 83.908 87 10 4 1287 1371 585752884 585752800 2.340000e-11 80.5


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 TraesCS3B01G285000 chr3B 456552898 456555735 2837 True 5241.0 5241 100.000 1 2838 1 chr3B.!!$R3 2837
1 TraesCS3B01G285000 chr3D 355629501 355632095 2594 True 1970.0 2052 94.300 1 2838 2 chr3D.!!$R2 2837
2 TraesCS3B01G285000 chr3A 474434386 474437100 2714 True 1941.5 2023 94.013 1 2838 2 chr3A.!!$R2 2837

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
83 84 0.034089 AGGAGCAGGTAAATGGGCAC 60.034 55.0 0.0 0.0 0.0 5.01 F
943 945 0.543749 AGGGGCAGAGACACAATAGC 59.456 55.0 0.0 0.0 0.0 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1538 0.038744 AGTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30 R
2695 2841 1.797046 CGTCATAGTGGCATCATGCTC 59.203 52.381 10.11 3.42 44.28 4.26 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
63 64 4.657814 AGGTCACAGAACCAACCATAAT 57.342 40.909 0.00 0.00 42.12 1.28
70 71 4.227300 ACAGAACCAACCATAATAGGAGCA 59.773 41.667 0.00 0.00 0.00 4.26
83 84 0.034089 AGGAGCAGGTAAATGGGCAC 60.034 55.000 0.00 0.00 0.00 5.01
104 105 4.406648 CATGTAGCAGAAGGACATGGTA 57.593 45.455 0.00 0.00 44.34 3.25
116 117 3.007723 AGGACATGGTAGATGCATAGCAG 59.992 47.826 0.00 0.00 43.65 4.24
165 166 6.208644 GCATACGCCAATCTTATGAACATTT 58.791 36.000 0.00 0.00 30.80 2.32
170 171 5.163622 CGCCAATCTTATGAACATTTCCAGT 60.164 40.000 0.00 0.00 0.00 4.00
289 290 3.005791 GCACTTGCAGTTCCCTACATTTT 59.994 43.478 0.00 0.00 41.59 1.82
390 391 1.651240 CCCCATTCGCTCAGCAGTTG 61.651 60.000 0.00 0.00 0.00 3.16
422 423 1.165270 GGGTGGTGCACTGTATCAAC 58.835 55.000 17.98 8.20 34.40 3.18
426 427 3.304659 GGTGGTGCACTGTATCAACTTTG 60.305 47.826 17.98 0.00 34.40 2.77
427 428 2.884012 TGGTGCACTGTATCAACTTTGG 59.116 45.455 17.98 0.00 0.00 3.28
428 429 2.884639 GGTGCACTGTATCAACTTTGGT 59.115 45.455 17.98 0.00 0.00 3.67
429 430 3.317993 GGTGCACTGTATCAACTTTGGTT 59.682 43.478 17.98 0.00 35.86 3.67
430 431 4.517453 GGTGCACTGTATCAACTTTGGTTA 59.483 41.667 17.98 0.00 33.88 2.85
433 434 7.145323 GTGCACTGTATCAACTTTGGTTAAAT 58.855 34.615 10.32 0.00 33.88 1.40
434 435 7.114811 GTGCACTGTATCAACTTTGGTTAAATG 59.885 37.037 10.32 0.00 33.88 2.32
435 436 7.013750 TGCACTGTATCAACTTTGGTTAAATGA 59.986 33.333 0.00 0.00 33.88 2.57
436 437 8.028938 GCACTGTATCAACTTTGGTTAAATGAT 58.971 33.333 0.00 0.00 32.86 2.45
467 468 7.272037 TCACTCCTTCAACATTAAAGGTTTC 57.728 36.000 1.41 0.00 42.28 2.78
499 500 5.105392 ACCAAACAGGCACCATTATAACATG 60.105 40.000 0.00 0.00 43.14 3.21
510 511 7.064371 GCACCATTATAACATGCAGAGATAGAG 59.936 40.741 10.90 0.00 36.30 2.43
534 535 3.650281 TGTCATCACTATGCCATTGGT 57.350 42.857 4.26 0.00 32.76 3.67
543 544 5.948758 TCACTATGCCATTGGTATTTTGTGA 59.051 36.000 21.07 21.07 33.39 3.58
583 584 9.512588 AGAAATGGCTAGGACATAATCTAATTG 57.487 33.333 0.00 0.00 29.42 2.32
602 603 6.833342 AATTGTGACAATCTTTTTGCAGAC 57.167 33.333 11.70 0.00 0.00 3.51
614 615 4.503741 TTTTGCAGACTAAAGCCATCAC 57.496 40.909 0.00 0.00 0.00 3.06
705 706 7.643528 TCGAAGCTATATGTGACATTTCATC 57.356 36.000 2.29 0.00 33.11 2.92
706 707 6.646653 TCGAAGCTATATGTGACATTTCATCC 59.353 38.462 2.29 0.00 33.11 3.51
707 708 6.424812 CGAAGCTATATGTGACATTTCATCCA 59.575 38.462 2.29 0.00 33.11 3.41
708 709 7.041848 CGAAGCTATATGTGACATTTCATCCAA 60.042 37.037 2.29 0.00 33.11 3.53
709 710 8.701908 AAGCTATATGTGACATTTCATCCAAT 57.298 30.769 2.29 0.00 33.11 3.16
710 711 9.797642 AAGCTATATGTGACATTTCATCCAATA 57.202 29.630 2.29 0.00 33.11 1.90
711 712 9.970553 AGCTATATGTGACATTTCATCCAATAT 57.029 29.630 2.29 0.00 33.11 1.28
712 713 9.999009 GCTATATGTGACATTTCATCCAATATG 57.001 33.333 2.29 0.00 33.11 1.78
715 716 7.885009 ATGTGACATTTCATCCAATATGACA 57.115 32.000 0.00 0.00 33.11 3.58
716 717 7.700022 TGTGACATTTCATCCAATATGACAA 57.300 32.000 0.00 0.00 33.11 3.18
725 726 6.182627 TCATCCAATATGACAAGGATATGGC 58.817 40.000 0.00 0.00 38.77 4.40
726 727 5.581350 TCCAATATGACAAGGATATGGCA 57.419 39.130 0.00 0.00 43.89 4.92
728 729 4.154737 CCAATATGACAAGGATATGGCACG 59.845 45.833 0.00 0.00 42.20 5.34
740 741 4.082679 GGATATGGCACGGTTAACACAAAA 60.083 41.667 8.10 0.00 0.00 2.44
743 744 3.448686 TGGCACGGTTAACACAAAAATG 58.551 40.909 8.10 0.00 0.00 2.32
744 745 2.219903 GGCACGGTTAACACAAAAATGC 59.780 45.455 8.10 5.80 0.00 3.56
759 760 8.379902 ACACAAAAATGCTTTAAAAGAAGAACG 58.620 29.630 0.00 0.00 0.00 3.95
766 767 4.597079 CTTTAAAAGAAGAACGCACAGCA 58.403 39.130 0.00 0.00 0.00 4.41
833 834 5.263599 TGTGGGATATCAAGTTTCAGCATT 58.736 37.500 4.83 0.00 0.00 3.56
836 837 7.229306 TGTGGGATATCAAGTTTCAGCATTATC 59.771 37.037 4.83 0.00 0.00 1.75
848 849 5.627499 TCAGCATTATCCTGTTGAACAAC 57.373 39.130 10.28 10.28 41.50 3.32
913 914 1.555075 TCCTACAGCTTGACCCATCAC 59.445 52.381 0.00 0.00 33.38 3.06
917 918 0.679002 CAGCTTGACCCATCACCCAG 60.679 60.000 0.00 0.00 33.38 4.45
935 937 3.433740 CCCAGTATAAAAGGGGCAGAGAC 60.434 52.174 0.00 0.00 38.98 3.36
936 938 3.199946 CCAGTATAAAAGGGGCAGAGACA 59.800 47.826 0.00 0.00 0.00 3.41
943 945 0.543749 AGGGGCAGAGACACAATAGC 59.456 55.000 0.00 0.00 0.00 2.97
979 982 2.553247 CCTCCAGGGAAAACACTCCTTC 60.553 54.545 0.00 0.00 37.23 3.46
1008 1011 3.754965 AGCAGAGAACAACATGCCTAAA 58.245 40.909 0.00 0.00 39.51 1.85
1017 1020 3.709141 ACAACATGCCTAAACCCACTTTT 59.291 39.130 0.00 0.00 0.00 2.27
1018 1021 4.057432 CAACATGCCTAAACCCACTTTTG 58.943 43.478 0.00 0.00 0.00 2.44
1052 1055 6.580788 TCATCCTTCTAATTGCTCTCTTCAG 58.419 40.000 0.00 0.00 0.00 3.02
1091 1094 4.497473 TGTTTGCTATTTGTTCTTCCCG 57.503 40.909 0.00 0.00 0.00 5.14
1101 1105 7.066645 GCTATTTGTTCTTCCCGGTATTTTACT 59.933 37.037 0.00 0.00 0.00 2.24
1109 1113 3.451902 TCCCGGTATTTTACTCCGTCATT 59.548 43.478 0.00 0.00 42.30 2.57
1111 1115 5.305128 TCCCGGTATTTTACTCCGTCATTAT 59.695 40.000 0.00 0.00 42.30 1.28
1114 1118 7.656948 CCCGGTATTTTACTCCGTCATTATTAA 59.343 37.037 0.00 0.00 42.30 1.40
1177 1181 7.822161 CCATAGTGGTGGAAATTGATAATGA 57.178 36.000 0.00 0.00 42.02 2.57
1292 1296 7.496346 TTCCATTCCATAGACATATACTCCC 57.504 40.000 0.00 0.00 0.00 4.30
1293 1297 6.815880 TCCATTCCATAGACATATACTCCCT 58.184 40.000 0.00 0.00 0.00 4.20
1294 1298 6.897966 TCCATTCCATAGACATATACTCCCTC 59.102 42.308 0.00 0.00 0.00 4.30
1295 1299 6.900186 CCATTCCATAGACATATACTCCCTCT 59.100 42.308 0.00 0.00 0.00 3.69
1296 1300 7.147759 CCATTCCATAGACATATACTCCCTCTG 60.148 44.444 0.00 0.00 0.00 3.35
1297 1301 6.470456 TCCATAGACATATACTCCCTCTGT 57.530 41.667 0.00 0.00 0.00 3.41
1298 1302 7.584396 TCCATAGACATATACTCCCTCTGTA 57.416 40.000 0.00 0.00 0.00 2.74
1299 1303 7.996788 TCCATAGACATATACTCCCTCTGTAA 58.003 38.462 0.00 0.00 0.00 2.41
1300 1304 8.453681 TCCATAGACATATACTCCCTCTGTAAA 58.546 37.037 0.00 0.00 0.00 2.01
1301 1305 8.524487 CCATAGACATATACTCCCTCTGTAAAC 58.476 40.741 0.00 0.00 0.00 2.01
1302 1306 9.303116 CATAGACATATACTCCCTCTGTAAACT 57.697 37.037 0.00 0.00 0.00 2.66
1305 1309 9.884814 AGACATATACTCCCTCTGTAAACTAAT 57.115 33.333 0.00 0.00 0.00 1.73
1306 1310 9.915629 GACATATACTCCCTCTGTAAACTAATG 57.084 37.037 0.00 0.00 0.00 1.90
1307 1311 9.435570 ACATATACTCCCTCTGTAAACTAATGT 57.564 33.333 0.00 0.00 0.00 2.71
1311 1315 9.710818 ATACTCCCTCTGTAAACTAATGTAAGA 57.289 33.333 0.00 0.00 0.00 2.10
1312 1316 7.838884 ACTCCCTCTGTAAACTAATGTAAGAC 58.161 38.462 0.00 0.00 0.00 3.01
1313 1317 7.453752 ACTCCCTCTGTAAACTAATGTAAGACA 59.546 37.037 0.00 0.00 0.00 3.41
1314 1318 8.375493 TCCCTCTGTAAACTAATGTAAGACAT 57.625 34.615 0.00 0.00 41.31 3.06
1316 1320 9.449719 CCCTCTGTAAACTAATGTAAGACATTT 57.550 33.333 9.92 0.00 45.80 2.32
1324 1328 9.816354 AAACTAATGTAAGACATTTTTGCAGTT 57.184 25.926 9.92 9.89 45.80 3.16
1325 1329 9.463443 AACTAATGTAAGACATTTTTGCAGTTC 57.537 29.630 9.92 0.00 45.80 3.01
1326 1330 8.629158 ACTAATGTAAGACATTTTTGCAGTTCA 58.371 29.630 9.92 0.00 45.80 3.18
1327 1331 9.462174 CTAATGTAAGACATTTTTGCAGTTCAA 57.538 29.630 9.92 0.00 45.80 2.69
1328 1332 8.715191 AATGTAAGACATTTTTGCAGTTCAAA 57.285 26.923 0.00 0.00 45.80 2.69
1329 1333 8.891671 ATGTAAGACATTTTTGCAGTTCAAAT 57.108 26.923 0.00 0.00 36.22 2.32
1330 1334 8.715191 TGTAAGACATTTTTGCAGTTCAAATT 57.285 26.923 0.00 0.00 43.53 1.82
1331 1335 8.602328 TGTAAGACATTTTTGCAGTTCAAATTG 58.398 29.630 0.00 0.00 43.53 2.32
1332 1336 7.846644 AAGACATTTTTGCAGTTCAAATTGA 57.153 28.000 9.36 0.00 43.53 2.57
1333 1337 7.846644 AGACATTTTTGCAGTTCAAATTGAA 57.153 28.000 4.03 4.03 43.53 2.69
1393 1397 9.571816 AGTATGTGAGTACTAACTAATACTCCC 57.428 37.037 13.93 0.00 44.50 4.30
1394 1398 9.571816 GTATGTGAGTACTAACTAATACTCCCT 57.428 37.037 11.79 0.00 44.50 4.20
1395 1399 8.694581 ATGTGAGTACTAACTAATACTCCCTC 57.305 38.462 11.79 0.00 44.50 4.30
1396 1400 7.059156 TGTGAGTACTAACTAATACTCCCTCC 58.941 42.308 11.79 0.00 44.50 4.30
1397 1401 6.204495 GTGAGTACTAACTAATACTCCCTCCG 59.796 46.154 2.77 0.00 44.50 4.63
1398 1402 6.126652 TGAGTACTAACTAATACTCCCTCCGT 60.127 42.308 0.00 0.00 44.50 4.69
1399 1403 6.667661 AGTACTAACTAATACTCCCTCCGTT 58.332 40.000 0.00 0.00 32.84 4.44
1400 1404 6.770303 AGTACTAACTAATACTCCCTCCGTTC 59.230 42.308 0.00 0.00 32.84 3.95
1401 1405 4.892345 ACTAACTAATACTCCCTCCGTTCC 59.108 45.833 0.00 0.00 0.00 3.62
1402 1406 3.684408 ACTAATACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
1403 1407 4.803329 ACTAATACTCCCTCCGTTCCTA 57.197 45.455 0.00 0.00 0.00 2.94
1404 1408 5.134725 ACTAATACTCCCTCCGTTCCTAA 57.865 43.478 0.00 0.00 0.00 2.69
1405 1409 5.522641 ACTAATACTCCCTCCGTTCCTAAA 58.477 41.667 0.00 0.00 0.00 1.85
1406 1410 6.141790 ACTAATACTCCCTCCGTTCCTAAAT 58.858 40.000 0.00 0.00 0.00 1.40
1407 1411 7.300658 ACTAATACTCCCTCCGTTCCTAAATA 58.699 38.462 0.00 0.00 0.00 1.40
1408 1412 7.954620 ACTAATACTCCCTCCGTTCCTAAATAT 59.045 37.037 0.00 0.00 0.00 1.28
1409 1413 9.471702 CTAATACTCCCTCCGTTCCTAAATATA 57.528 37.037 0.00 0.00 0.00 0.86
1410 1414 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
1411 1415 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1412 1416 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1413 1417 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1414 1418 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1415 1419 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1416 1420 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1417 1421 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1418 1422 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
1435 1439 9.803315 AAGTCTTTTTAGAGGTTTCAATTGAAC 57.197 29.630 20.35 14.54 33.13 3.18
1436 1440 9.190317 AGTCTTTTTAGAGGTTTCAATTGAACT 57.810 29.630 20.35 14.82 33.13 3.01
1442 1446 8.740123 TTAGAGGTTTCAATTGAACTACAACA 57.260 30.769 20.35 1.32 41.52 3.33
1443 1447 7.823745 AGAGGTTTCAATTGAACTACAACAT 57.176 32.000 20.35 12.90 41.52 2.71
1444 1448 8.918202 AGAGGTTTCAATTGAACTACAACATA 57.082 30.769 20.35 0.00 41.52 2.29
1445 1449 8.784043 AGAGGTTTCAATTGAACTACAACATAC 58.216 33.333 20.35 11.95 41.52 2.39
1446 1450 7.581476 AGGTTTCAATTGAACTACAACATACG 58.419 34.615 20.35 0.00 41.52 3.06
1447 1451 6.799925 GGTTTCAATTGAACTACAACATACGG 59.200 38.462 20.35 0.00 41.52 4.02
1448 1452 7.308109 GGTTTCAATTGAACTACAACATACGGA 60.308 37.037 20.35 0.00 41.52 4.69
1449 1453 7.915293 TTCAATTGAACTACAACATACGGAT 57.085 32.000 16.91 0.00 41.52 4.18
1450 1454 7.302350 TCAATTGAACTACAACATACGGATG 57.698 36.000 5.94 5.94 41.52 3.51
1452 1456 8.035984 TCAATTGAACTACAACATACGGATGTA 58.964 33.333 15.10 0.00 45.93 2.29
1453 1457 8.826710 CAATTGAACTACAACATACGGATGTAT 58.173 33.333 15.10 8.21 45.93 2.29
1460 1464 9.511272 ACTACAACATACGGATGTATATAGACA 57.489 33.333 23.06 2.07 45.93 3.41
1491 1495 5.886960 AGTGTAGATTCACTCATTTTGCC 57.113 39.130 0.00 0.00 44.07 4.52
1492 1496 4.702131 AGTGTAGATTCACTCATTTTGCCC 59.298 41.667 0.00 0.00 44.07 5.36
1493 1497 4.016444 TGTAGATTCACTCATTTTGCCCC 58.984 43.478 0.00 0.00 0.00 5.80
1494 1498 3.173953 AGATTCACTCATTTTGCCCCA 57.826 42.857 0.00 0.00 0.00 4.96
1495 1499 3.716431 AGATTCACTCATTTTGCCCCAT 58.284 40.909 0.00 0.00 0.00 4.00
1496 1500 4.870636 AGATTCACTCATTTTGCCCCATA 58.129 39.130 0.00 0.00 0.00 2.74
1497 1501 5.461327 AGATTCACTCATTTTGCCCCATAT 58.539 37.500 0.00 0.00 0.00 1.78
1498 1502 5.303589 AGATTCACTCATTTTGCCCCATATG 59.696 40.000 0.00 0.00 0.00 1.78
1499 1503 3.979911 TCACTCATTTTGCCCCATATGT 58.020 40.909 1.24 0.00 0.00 2.29
1500 1504 5.122707 TCACTCATTTTGCCCCATATGTA 57.877 39.130 1.24 0.00 0.00 2.29
1501 1505 5.132502 TCACTCATTTTGCCCCATATGTAG 58.867 41.667 1.24 0.00 0.00 2.74
1502 1506 4.889409 CACTCATTTTGCCCCATATGTAGT 59.111 41.667 1.24 0.00 0.00 2.73
1503 1507 5.009010 CACTCATTTTGCCCCATATGTAGTC 59.991 44.000 1.24 0.00 0.00 2.59
1504 1508 4.469657 TCATTTTGCCCCATATGTAGTCC 58.530 43.478 1.24 0.00 0.00 3.85
1505 1509 3.306472 TTTTGCCCCATATGTAGTCCC 57.694 47.619 1.24 0.00 0.00 4.46
1506 1510 2.206322 TTGCCCCATATGTAGTCCCT 57.794 50.000 1.24 0.00 0.00 4.20
1507 1511 2.206322 TGCCCCATATGTAGTCCCTT 57.794 50.000 1.24 0.00 0.00 3.95
1508 1512 1.774254 TGCCCCATATGTAGTCCCTTG 59.226 52.381 1.24 0.00 0.00 3.61
1509 1513 1.774856 GCCCCATATGTAGTCCCTTGT 59.225 52.381 1.24 0.00 0.00 3.16
1510 1514 2.174854 GCCCCATATGTAGTCCCTTGTT 59.825 50.000 1.24 0.00 0.00 2.83
1511 1515 3.820557 CCCCATATGTAGTCCCTTGTTG 58.179 50.000 1.24 0.00 0.00 3.33
1512 1516 3.458118 CCCCATATGTAGTCCCTTGTTGA 59.542 47.826 1.24 0.00 0.00 3.18
1513 1517 4.080015 CCCCATATGTAGTCCCTTGTTGAA 60.080 45.833 1.24 0.00 0.00 2.69
1514 1518 5.505780 CCCATATGTAGTCCCTTGTTGAAA 58.494 41.667 1.24 0.00 0.00 2.69
1515 1519 6.129179 CCCATATGTAGTCCCTTGTTGAAAT 58.871 40.000 1.24 0.00 0.00 2.17
1516 1520 6.263168 CCCATATGTAGTCCCTTGTTGAAATC 59.737 42.308 1.24 0.00 0.00 2.17
1517 1521 7.056635 CCATATGTAGTCCCTTGTTGAAATCT 58.943 38.462 1.24 0.00 0.00 2.40
1518 1522 7.227512 CCATATGTAGTCCCTTGTTGAAATCTC 59.772 40.741 1.24 0.00 0.00 2.75
1519 1523 5.825593 TGTAGTCCCTTGTTGAAATCTCT 57.174 39.130 0.00 0.00 0.00 3.10
1520 1524 6.928348 TGTAGTCCCTTGTTGAAATCTCTA 57.072 37.500 0.00 0.00 0.00 2.43
1521 1525 7.311092 TGTAGTCCCTTGTTGAAATCTCTAA 57.689 36.000 0.00 0.00 0.00 2.10
1522 1526 7.741785 TGTAGTCCCTTGTTGAAATCTCTAAA 58.258 34.615 0.00 0.00 0.00 1.85
1523 1527 8.215050 TGTAGTCCCTTGTTGAAATCTCTAAAA 58.785 33.333 0.00 0.00 0.00 1.52
1524 1528 9.063615 GTAGTCCCTTGTTGAAATCTCTAAAAA 57.936 33.333 0.00 0.00 0.00 1.94
1525 1529 8.171164 AGTCCCTTGTTGAAATCTCTAAAAAG 57.829 34.615 0.00 0.00 0.00 2.27
1526 1530 7.998964 AGTCCCTTGTTGAAATCTCTAAAAAGA 59.001 33.333 0.00 0.00 0.00 2.52
1527 1531 8.076781 GTCCCTTGTTGAAATCTCTAAAAAGAC 58.923 37.037 0.00 0.00 0.00 3.01
1528 1532 7.998964 TCCCTTGTTGAAATCTCTAAAAAGACT 59.001 33.333 0.00 0.00 0.00 3.24
1529 1533 9.284968 CCCTTGTTGAAATCTCTAAAAAGACTA 57.715 33.333 0.00 0.00 0.00 2.59
1581 1710 9.745880 TCTAGCTCTTTATGTTTTCCTATAACG 57.254 33.333 0.00 0.00 0.00 3.18
1582 1711 7.787725 AGCTCTTTATGTTTTCCTATAACGG 57.212 36.000 0.00 0.00 0.00 4.44
1601 1730 2.223377 CGGTTGGTCACTTTTGCTAGAC 59.777 50.000 0.00 0.00 0.00 2.59
1616 1745 4.893608 TGCTAGACAACTTATGCTTCACA 58.106 39.130 0.00 0.00 0.00 3.58
1664 1793 4.676196 GCTTCAAATCGACAAATGCCAGAT 60.676 41.667 0.00 0.00 0.00 2.90
1693 1822 7.919690 CAGAATAACACTTCTGTTTTCACTCA 58.080 34.615 5.81 0.00 44.60 3.41
1727 1856 6.012658 TCCATGTATTCTTGTTCTTTGTGC 57.987 37.500 0.00 0.00 0.00 4.57
1789 1918 5.403558 TTCAGGACTATGACTATGGAGGA 57.596 43.478 0.00 0.00 0.00 3.71
1842 1971 1.755977 CGGGAGGAATGGCTAGAGAGT 60.756 57.143 0.00 0.00 0.00 3.24
1856 1985 4.439016 GCTAGAGAGTTAAGACCCTTCGTG 60.439 50.000 0.00 0.00 0.00 4.35
1900 2031 6.156256 AGTGTGGAGGTATTACTATGAAAGCA 59.844 38.462 0.00 0.00 0.00 3.91
1922 2053 3.460857 GTCATATGAGGGACCAGTCAC 57.539 52.381 5.42 0.00 0.00 3.67
1996 2127 3.377346 TCCAAATAGATCAGAGAGCGC 57.623 47.619 0.00 0.00 0.00 5.92
2011 2142 4.269123 AGAGAGCGCGATAGATATTACTCG 59.731 45.833 12.10 0.00 39.76 4.18
2042 2173 1.171308 TAGTCTAGCCGCGTGAAGTT 58.829 50.000 4.92 0.00 0.00 2.66
2173 2310 6.183360 GCTCTGTTCTCTTCTGTTTTGTTCTT 60.183 38.462 0.00 0.00 0.00 2.52
2174 2311 7.076842 TCTGTTCTCTTCTGTTTTGTTCTTG 57.923 36.000 0.00 0.00 0.00 3.02
2246 2392 5.982356 AGCACACTCATCACATATACAACT 58.018 37.500 0.00 0.00 0.00 3.16
2309 2455 6.611613 AATTGGAGAGTGAGTTGTGAGATA 57.388 37.500 0.00 0.00 0.00 1.98
2450 2596 1.229975 CGGTCACTGAGCACATGCAA 61.230 55.000 6.64 0.00 45.16 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.093288 CCACTCACATATCCACTGTGCT 60.093 50.000 1.29 0.00 42.93 4.40
63 64 1.211949 GTGCCCATTTACCTGCTCCTA 59.788 52.381 0.00 0.00 0.00 2.94
70 71 2.025416 TGCTACATGTGCCCATTTACCT 60.025 45.455 9.11 0.00 0.00 3.08
83 84 3.272574 ACCATGTCCTTCTGCTACATG 57.727 47.619 7.52 7.52 46.44 3.21
104 105 2.236766 GATTTGCCCTGCTATGCATCT 58.763 47.619 0.19 0.00 38.13 2.90
165 166 5.071788 ACATTTGAGACCTTCACTAACTGGA 59.928 40.000 0.00 0.00 34.94 3.86
170 171 6.173339 GGATCACATTTGAGACCTTCACTAA 58.827 40.000 0.00 0.00 34.94 2.24
229 230 1.038280 ACTAACGGATCCATCGGTCC 58.962 55.000 13.41 0.00 39.09 4.46
283 284 9.696917 GGAGTGAGAAAAATACAATGAAAATGT 57.303 29.630 0.00 0.00 34.81 2.71
289 290 7.453393 AGAGTGGAGTGAGAAAAATACAATGA 58.547 34.615 0.00 0.00 0.00 2.57
390 391 0.328258 ACCACCCACTATCAACTGGC 59.672 55.000 0.00 0.00 0.00 4.85
426 427 9.788960 GAAGGAGTGAAAATGTATCATTTAACC 57.211 33.333 7.91 7.56 0.00 2.85
430 431 8.859090 TGTTGAAGGAGTGAAAATGTATCATTT 58.141 29.630 2.42 2.42 0.00 2.32
433 434 8.408043 AATGTTGAAGGAGTGAAAATGTATCA 57.592 30.769 0.00 0.00 0.00 2.15
437 438 8.143835 CCTTTAATGTTGAAGGAGTGAAAATGT 58.856 33.333 9.95 0.00 44.27 2.71
438 439 8.143835 ACCTTTAATGTTGAAGGAGTGAAAATG 58.856 33.333 19.48 0.00 44.27 2.32
467 468 3.257873 TGGTGCCTGTTTGGTGAAATATG 59.742 43.478 0.00 0.00 38.35 1.78
499 500 3.069300 TGATGACAAGGCTCTATCTCTGC 59.931 47.826 0.00 0.00 0.00 4.26
534 535 8.846943 TCTTGAGCTGAGTATTTCACAAAATA 57.153 30.769 0.00 0.00 36.49 1.40
543 544 5.259632 AGCCATTTCTTGAGCTGAGTATTT 58.740 37.500 0.00 0.00 32.66 1.40
557 558 9.512588 CAATTAGATTATGTCCTAGCCATTTCT 57.487 33.333 0.00 5.32 0.00 2.52
583 584 6.142958 GCTTTAGTCTGCAAAAAGATTGTCAC 59.857 38.462 12.25 0.00 33.05 3.67
602 603 2.646930 TGCATGGAGTGATGGCTTTAG 58.353 47.619 0.00 0.00 0.00 1.85
614 615 2.158856 TCTTGGTCAGCTATGCATGGAG 60.159 50.000 15.09 2.86 0.00 3.86
705 706 4.154737 CGTGCCATATCCTTGTCATATTGG 59.845 45.833 0.00 0.00 0.00 3.16
706 707 4.154737 CCGTGCCATATCCTTGTCATATTG 59.845 45.833 0.00 0.00 0.00 1.90
707 708 4.202461 ACCGTGCCATATCCTTGTCATATT 60.202 41.667 0.00 0.00 0.00 1.28
708 709 3.327757 ACCGTGCCATATCCTTGTCATAT 59.672 43.478 0.00 0.00 0.00 1.78
709 710 2.703536 ACCGTGCCATATCCTTGTCATA 59.296 45.455 0.00 0.00 0.00 2.15
710 711 1.490490 ACCGTGCCATATCCTTGTCAT 59.510 47.619 0.00 0.00 0.00 3.06
711 712 0.908910 ACCGTGCCATATCCTTGTCA 59.091 50.000 0.00 0.00 0.00 3.58
712 713 2.038387 AACCGTGCCATATCCTTGTC 57.962 50.000 0.00 0.00 0.00 3.18
713 714 3.275999 GTTAACCGTGCCATATCCTTGT 58.724 45.455 0.00 0.00 0.00 3.16
714 715 3.064820 GTGTTAACCGTGCCATATCCTTG 59.935 47.826 2.48 0.00 0.00 3.61
715 716 3.275999 GTGTTAACCGTGCCATATCCTT 58.724 45.455 2.48 0.00 0.00 3.36
716 717 2.237643 TGTGTTAACCGTGCCATATCCT 59.762 45.455 2.48 0.00 0.00 3.24
725 726 5.710613 AAAGCATTTTTGTGTTAACCGTG 57.289 34.783 2.48 0.00 31.62 4.94
726 727 7.829378 TTTAAAGCATTTTTGTGTTAACCGT 57.171 28.000 2.48 0.00 40.09 4.83
740 741 5.587289 TGTGCGTTCTTCTTTTAAAGCATT 58.413 33.333 0.00 0.00 41.05 3.56
743 744 3.422217 GCTGTGCGTTCTTCTTTTAAAGC 59.578 43.478 0.00 0.00 0.00 3.51
744 745 4.597079 TGCTGTGCGTTCTTCTTTTAAAG 58.403 39.130 0.00 0.00 0.00 1.85
759 760 5.123979 AGCTACTTTAAAACCTATGCTGTGC 59.876 40.000 0.00 0.00 0.00 4.57
766 767 6.481643 TGGCTCAAGCTACTTTAAAACCTAT 58.518 36.000 1.46 0.00 41.70 2.57
833 834 5.943416 CCAGTAATGGTTGTTCAACAGGATA 59.057 40.000 15.89 2.98 0.00 2.59
836 837 3.888930 ACCAGTAATGGTTGTTCAACAGG 59.111 43.478 9.55 8.66 39.57 4.00
913 914 2.777692 TCTCTGCCCCTTTTATACTGGG 59.222 50.000 0.00 0.00 41.23 4.45
917 918 4.216411 TGTGTCTCTGCCCCTTTTATAC 57.784 45.455 0.00 0.00 0.00 1.47
943 945 1.339055 TGGAGGATTGTTGGCGAGAAG 60.339 52.381 0.00 0.00 0.00 2.85
979 982 1.731160 GTTGTTCTCTGCTAGCTGCTG 59.269 52.381 17.23 11.46 43.37 4.41
990 993 3.181434 TGGGTTTAGGCATGTTGTTCTCT 60.181 43.478 0.00 0.00 0.00 3.10
1008 1011 0.470766 TGGCGAGTACAAAAGTGGGT 59.529 50.000 0.00 0.00 0.00 4.51
1017 1020 2.388735 AGAAGGATGATGGCGAGTACA 58.611 47.619 0.00 0.00 0.00 2.90
1018 1021 4.585955 TTAGAAGGATGATGGCGAGTAC 57.414 45.455 0.00 0.00 0.00 2.73
1069 1072 4.082245 CCGGGAAGAACAAATAGCAAACAT 60.082 41.667 0.00 0.00 0.00 2.71
1163 1167 5.278957 CGGGGGAACATCATTATCAATTTCC 60.279 44.000 0.00 0.00 0.00 3.13
1177 1181 4.270008 CTTTATGAACTTCGGGGGAACAT 58.730 43.478 0.00 0.00 0.00 2.71
1286 1290 8.964772 GTCTTACATTAGTTTACAGAGGGAGTA 58.035 37.037 0.00 0.00 0.00 2.59
1287 1291 7.453752 TGTCTTACATTAGTTTACAGAGGGAGT 59.546 37.037 0.00 0.00 0.00 3.85
1288 1292 7.837863 TGTCTTACATTAGTTTACAGAGGGAG 58.162 38.462 0.00 0.00 0.00 4.30
1289 1293 7.786046 TGTCTTACATTAGTTTACAGAGGGA 57.214 36.000 0.00 0.00 0.00 4.20
1302 1306 9.809096 TTTGAACTGCAAAAATGTCTTACATTA 57.191 25.926 5.75 0.00 42.59 1.90
1303 1307 8.715191 TTTGAACTGCAAAAATGTCTTACATT 57.285 26.923 0.00 0.00 43.18 2.71
1367 1371 9.571816 GGGAGTATTAGTTAGTACTCACATACT 57.428 37.037 15.11 15.11 43.98 2.12
1368 1372 9.571816 AGGGAGTATTAGTTAGTACTCACATAC 57.428 37.037 19.76 9.07 45.77 2.39
1378 1382 4.892345 GGAACGGAGGGAGTATTAGTTAGT 59.108 45.833 0.00 0.00 0.00 2.24
1382 1386 3.684408 AGGAACGGAGGGAGTATTAGT 57.316 47.619 0.00 0.00 0.00 2.24
1387 1391 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
1388 1392 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
1389 1393 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
1390 1394 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1391 1395 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1392 1396 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
1409 1413 9.803315 GTTCAATTGAAACCTCTAAAAAGACTT 57.197 29.630 22.07 0.00 35.58 3.01
1410 1414 9.190317 AGTTCAATTGAAACCTCTAAAAAGACT 57.810 29.630 22.07 8.00 35.58 3.24
1416 1420 9.179909 TGTTGTAGTTCAATTGAAACCTCTAAA 57.820 29.630 22.07 11.47 38.38 1.85
1417 1421 8.740123 TGTTGTAGTTCAATTGAAACCTCTAA 57.260 30.769 22.07 11.41 38.38 2.10
1418 1422 8.918202 ATGTTGTAGTTCAATTGAAACCTCTA 57.082 30.769 22.07 15.46 38.38 2.43
1419 1423 7.823745 ATGTTGTAGTTCAATTGAAACCTCT 57.176 32.000 22.07 16.40 38.38 3.69
1420 1424 7.744715 CGTATGTTGTAGTTCAATTGAAACCTC 59.255 37.037 22.07 10.10 38.38 3.85
1421 1425 7.308348 CCGTATGTTGTAGTTCAATTGAAACCT 60.308 37.037 22.07 17.39 38.38 3.50
1422 1426 6.799925 CCGTATGTTGTAGTTCAATTGAAACC 59.200 38.462 22.07 11.16 38.38 3.27
1423 1427 7.577979 TCCGTATGTTGTAGTTCAATTGAAAC 58.422 34.615 22.07 17.37 38.38 2.78
1424 1428 7.731882 TCCGTATGTTGTAGTTCAATTGAAA 57.268 32.000 22.07 5.45 38.38 2.69
1425 1429 7.389330 ACATCCGTATGTTGTAGTTCAATTGAA 59.611 33.333 16.91 16.91 44.07 2.69
1426 1430 6.876789 ACATCCGTATGTTGTAGTTCAATTGA 59.123 34.615 3.38 3.38 44.07 2.57
1427 1431 7.072177 ACATCCGTATGTTGTAGTTCAATTG 57.928 36.000 0.00 0.00 44.07 2.32
1428 1432 8.958119 ATACATCCGTATGTTGTAGTTCAATT 57.042 30.769 0.00 0.00 44.07 2.32
1434 1438 9.511272 TGTCTATATACATCCGTATGTTGTAGT 57.489 33.333 0.00 0.00 44.07 2.73
1470 1474 4.142381 GGGGCAAAATGAGTGAATCTACAC 60.142 45.833 0.00 0.00 40.60 2.90
1471 1475 4.016444 GGGGCAAAATGAGTGAATCTACA 58.984 43.478 0.00 0.00 0.00 2.74
1472 1476 4.016444 TGGGGCAAAATGAGTGAATCTAC 58.984 43.478 0.00 0.00 0.00 2.59
1473 1477 4.314522 TGGGGCAAAATGAGTGAATCTA 57.685 40.909 0.00 0.00 0.00 1.98
1474 1478 3.173953 TGGGGCAAAATGAGTGAATCT 57.826 42.857 0.00 0.00 0.00 2.40
1475 1479 5.069516 ACATATGGGGCAAAATGAGTGAATC 59.930 40.000 7.80 0.00 0.00 2.52
1476 1480 4.964262 ACATATGGGGCAAAATGAGTGAAT 59.036 37.500 7.80 0.00 0.00 2.57
1477 1481 4.352009 ACATATGGGGCAAAATGAGTGAA 58.648 39.130 7.80 0.00 0.00 3.18
1478 1482 3.979911 ACATATGGGGCAAAATGAGTGA 58.020 40.909 7.80 0.00 0.00 3.41
1479 1483 4.889409 ACTACATATGGGGCAAAATGAGTG 59.111 41.667 7.80 0.00 0.00 3.51
1480 1484 5.129368 ACTACATATGGGGCAAAATGAGT 57.871 39.130 7.80 0.00 0.00 3.41
1481 1485 4.520492 GGACTACATATGGGGCAAAATGAG 59.480 45.833 7.80 0.00 0.00 2.90
1482 1486 4.469657 GGACTACATATGGGGCAAAATGA 58.530 43.478 7.80 0.00 0.00 2.57
1483 1487 3.573967 GGGACTACATATGGGGCAAAATG 59.426 47.826 7.80 0.00 0.00 2.32
1484 1488 3.467103 AGGGACTACATATGGGGCAAAAT 59.533 43.478 7.80 0.00 36.02 1.82
1485 1489 2.856231 AGGGACTACATATGGGGCAAAA 59.144 45.455 7.80 0.00 36.02 2.44
1486 1490 2.498441 AGGGACTACATATGGGGCAAA 58.502 47.619 7.80 0.00 36.02 3.68
1487 1491 2.174639 CAAGGGACTACATATGGGGCAA 59.825 50.000 7.80 0.00 38.49 4.52
1488 1492 1.774254 CAAGGGACTACATATGGGGCA 59.226 52.381 7.80 0.00 38.49 5.36
1489 1493 1.774856 ACAAGGGACTACATATGGGGC 59.225 52.381 7.80 1.38 38.49 5.80
1490 1494 3.458118 TCAACAAGGGACTACATATGGGG 59.542 47.826 7.80 1.74 38.49 4.96
1491 1495 4.771114 TCAACAAGGGACTACATATGGG 57.229 45.455 7.80 2.11 38.49 4.00
1492 1496 7.056635 AGATTTCAACAAGGGACTACATATGG 58.943 38.462 7.80 0.00 38.49 2.74
1493 1497 7.989741 AGAGATTTCAACAAGGGACTACATATG 59.010 37.037 0.00 0.00 38.49 1.78
1494 1498 8.095452 AGAGATTTCAACAAGGGACTACATAT 57.905 34.615 0.00 0.00 38.49 1.78
1495 1499 7.496346 AGAGATTTCAACAAGGGACTACATA 57.504 36.000 0.00 0.00 38.49 2.29
1496 1500 6.380079 AGAGATTTCAACAAGGGACTACAT 57.620 37.500 0.00 0.00 38.49 2.29
1497 1501 5.825593 AGAGATTTCAACAAGGGACTACA 57.174 39.130 0.00 0.00 38.49 2.74
1498 1502 8.617290 TTTTAGAGATTTCAACAAGGGACTAC 57.383 34.615 0.00 0.00 38.49 2.73
1499 1503 9.284968 CTTTTTAGAGATTTCAACAAGGGACTA 57.715 33.333 0.00 0.00 38.49 2.59
1501 1505 8.076781 GTCTTTTTAGAGATTTCAACAAGGGAC 58.923 37.037 0.00 0.00 0.00 4.46
1502 1506 7.998964 AGTCTTTTTAGAGATTTCAACAAGGGA 59.001 33.333 0.00 0.00 0.00 4.20
1503 1507 8.171164 AGTCTTTTTAGAGATTTCAACAAGGG 57.829 34.615 0.00 0.00 0.00 3.95
1517 1521 9.090692 CCGTTCCGAAATATTAGTCTTTTTAGA 57.909 33.333 0.00 0.00 0.00 2.10
1518 1522 9.090692 TCCGTTCCGAAATATTAGTCTTTTTAG 57.909 33.333 0.00 0.00 0.00 1.85
1519 1523 9.090692 CTCCGTTCCGAAATATTAGTCTTTTTA 57.909 33.333 0.00 0.00 0.00 1.52
1520 1524 7.065443 CCTCCGTTCCGAAATATTAGTCTTTTT 59.935 37.037 0.00 0.00 0.00 1.94
1521 1525 6.537660 CCTCCGTTCCGAAATATTAGTCTTTT 59.462 38.462 0.00 0.00 0.00 2.27
1522 1526 6.047231 CCTCCGTTCCGAAATATTAGTCTTT 58.953 40.000 0.00 0.00 0.00 2.52
1523 1527 5.452917 CCCTCCGTTCCGAAATATTAGTCTT 60.453 44.000 0.00 0.00 0.00 3.01
1524 1528 4.038883 CCCTCCGTTCCGAAATATTAGTCT 59.961 45.833 0.00 0.00 0.00 3.24
1525 1529 4.038402 TCCCTCCGTTCCGAAATATTAGTC 59.962 45.833 0.00 0.00 0.00 2.59
1526 1530 3.962718 TCCCTCCGTTCCGAAATATTAGT 59.037 43.478 0.00 0.00 0.00 2.24
1527 1531 4.038883 ACTCCCTCCGTTCCGAAATATTAG 59.961 45.833 0.00 0.00 0.00 1.73
1528 1532 3.962718 ACTCCCTCCGTTCCGAAATATTA 59.037 43.478 0.00 0.00 0.00 0.98
1529 1533 2.770232 ACTCCCTCCGTTCCGAAATATT 59.230 45.455 0.00 0.00 0.00 1.28
1530 1534 2.395619 ACTCCCTCCGTTCCGAAATAT 58.604 47.619 0.00 0.00 0.00 1.28
1531 1535 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1532 1536 1.479730 GTACTCCCTCCGTTCCGAAAT 59.520 52.381 0.00 0.00 0.00 2.17
1533 1537 0.890683 GTACTCCCTCCGTTCCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
1534 1538 0.038744 AGTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
1535 1539 0.038744 AAGTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
1536 1540 0.893447 AAAGTACTCCCTCCGTTCCG 59.107 55.000 0.00 0.00 0.00 4.30
1537 1541 2.177734 AGAAAGTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 0.00 3.62
1538 1542 3.181488 GCTAGAAAGTACTCCCTCCGTTC 60.181 52.174 0.00 0.00 0.00 3.95
1539 1543 2.759535 GCTAGAAAGTACTCCCTCCGTT 59.240 50.000 0.00 0.00 0.00 4.44
1540 1544 2.025131 AGCTAGAAAGTACTCCCTCCGT 60.025 50.000 0.00 0.00 0.00 4.69
1541 1545 2.619646 GAGCTAGAAAGTACTCCCTCCG 59.380 54.545 0.00 0.00 0.00 4.63
1542 1546 3.905968 AGAGCTAGAAAGTACTCCCTCC 58.094 50.000 0.00 0.00 0.00 4.30
1543 1547 5.925506 AAAGAGCTAGAAAGTACTCCCTC 57.074 43.478 0.00 0.00 0.00 4.30
1544 1548 6.898521 ACATAAAGAGCTAGAAAGTACTCCCT 59.101 38.462 0.00 0.00 0.00 4.20
1545 1549 7.114866 ACATAAAGAGCTAGAAAGTACTCCC 57.885 40.000 0.00 0.00 0.00 4.30
1546 1550 9.438228 AAAACATAAAGAGCTAGAAAGTACTCC 57.562 33.333 0.00 0.00 0.00 3.85
1548 1552 9.438228 GGAAAACATAAAGAGCTAGAAAGTACT 57.562 33.333 0.00 0.00 0.00 2.73
1549 1553 9.438228 AGGAAAACATAAAGAGCTAGAAAGTAC 57.562 33.333 0.00 0.00 0.00 2.73
1576 1705 3.219281 AGCAAAAGTGACCAACCGTTAT 58.781 40.909 0.00 0.00 0.00 1.89
1581 1710 3.211045 TGTCTAGCAAAAGTGACCAACC 58.789 45.455 0.00 0.00 0.00 3.77
1582 1711 4.335594 AGTTGTCTAGCAAAAGTGACCAAC 59.664 41.667 1.86 0.00 39.03 3.77
1626 1755 9.764363 TCGATTTGAAGCATAAACTGTAGATAT 57.236 29.630 0.00 0.00 0.00 1.63
1683 1812 9.241317 CATGGAATTAAGCATATGAGTGAAAAC 57.759 33.333 6.97 0.00 0.00 2.43
1789 1918 2.507058 TGGATCATGCCTAGAGTTTGCT 59.493 45.455 0.00 0.00 0.00 3.91
1842 1971 3.181458 GGGATATGCACGAAGGGTCTTAA 60.181 47.826 0.00 0.00 0.00 1.85
1856 1985 3.688185 CACTGTCATATGCAGGGATATGC 59.312 47.826 22.64 10.43 46.68 3.14
1875 2004 6.156256 TGCTTTCATAGTAATACCTCCACACT 59.844 38.462 0.00 0.00 0.00 3.55
1996 2127 8.899427 TTAGGGGATACGAGTAATATCTATCG 57.101 38.462 0.00 0.00 40.86 2.92
2011 2142 4.142204 GCGGCTAGACTATTTAGGGGATAC 60.142 50.000 0.00 0.00 0.00 2.24
2042 2173 3.213206 AGTGCCAATGAACAAGTCTCA 57.787 42.857 0.00 0.00 0.00 3.27
2115 2252 8.338259 AGCTCACAAGAAATTATTATAACTGCG 58.662 33.333 0.00 0.00 0.00 5.18
2149 2286 6.917217 AGAACAAAACAGAAGAGAACAGAG 57.083 37.500 0.00 0.00 0.00 3.35
2680 2826 4.158786 TCATGCTCAAAAATCCCCTTTCA 58.841 39.130 0.00 0.00 0.00 2.69
2695 2841 1.797046 CGTCATAGTGGCATCATGCTC 59.203 52.381 10.11 3.42 44.28 4.26


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

AutoCloner maintained by Alex Coulton.