Multiple sequence alignment - TraesCS3D01G540000

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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 TraesCS3D01G540000 chr3D 100.000 4902 0 0 1 4902 611562005 611566906 0.000000e+00 9053.0
1 TraesCS3D01G540000 chr3A 95.049 2444 72 16 2484 4902 746355539 746353120 0.000000e+00 3797.0
2 TraesCS3D01G540000 chr3A 84.187 898 83 26 571 1431 746357808 746356933 0.000000e+00 817.0
3 TraesCS3D01G540000 chr3A 87.868 272 20 7 2187 2448 746355807 746355539 1.710000e-79 307.0
4 TraesCS3D01G540000 chr3A 87.821 156 18 1 2033 2188 746356082 746355928 1.080000e-41 182.0
5 TraesCS3D01G540000 chr3B 95.847 1517 41 5 2484 3998 829285221 829286717 0.000000e+00 2433.0
6 TraesCS3D01G540000 chr3B 94.983 598 28 2 4061 4657 829286720 829287316 0.000000e+00 937.0
7 TraesCS3D01G540000 chr3B 85.419 775 68 21 695 1430 829283150 829283918 0.000000e+00 763.0
8 TraesCS3D01G540000 chr3B 91.667 516 43 0 1 516 829282463 829282978 0.000000e+00 715.0
9 TraesCS3D01G540000 chr3B 87.371 388 40 6 2065 2448 829284839 829285221 2.100000e-118 436.0
10 TraesCS3D01G540000 chr3B 88.000 150 18 0 1429 1578 829284042 829284191 1.400000e-40 178.0
11 TraesCS3D01G540000 chr3B 85.393 89 12 1 1 88 767457137 767457225 1.880000e-14 91.6
12 TraesCS3D01G540000 chr3B 90.769 65 6 0 135 199 25519936 25519872 2.430000e-13 87.9
13 TraesCS3D01G540000 chr4A 85.769 2108 211 47 1918 3985 13759219 13757161 0.000000e+00 2148.0
14 TraesCS3D01G540000 chr4A 78.116 361 45 17 851 1185 14020498 14020850 1.080000e-46 198.0
15 TraesCS3D01G540000 chr4A 86.022 93 12 1 4190 4282 13756769 13756678 1.120000e-16 99.0
16 TraesCS3D01G540000 chr4D 90.278 1512 124 12 2410 3916 453319702 453321195 0.000000e+00 1956.0
17 TraesCS3D01G540000 chr4D 90.625 64 6 0 136 199 47091487 47091424 8.740000e-13 86.1
18 TraesCS3D01G540000 chr4D 96.875 32 0 1 871 901 347444169 347444138 9.000000e-03 52.8
19 TraesCS3D01G540000 chr4B 90.703 1409 118 7 2534 3940 566979180 566980577 0.000000e+00 1864.0
20 TraesCS3D01G540000 chr4B 91.426 1283 107 2 2658 3940 566981810 566983089 0.000000e+00 1757.0
21 TraesCS3D01G540000 chr4B 79.661 295 33 13 851 1122 566601994 566601704 2.330000e-43 187.0
22 TraesCS3D01G540000 chr4B 90.000 90 8 1 4190 4279 566980859 566980947 1.120000e-21 115.0
23 TraesCS3D01G540000 chr4B 90.000 90 8 1 4190 4279 566983371 566983459 1.120000e-21 115.0
24 TraesCS3D01G540000 chr1A 80.769 260 43 4 205 459 153291865 153291608 3.870000e-46 196.0
25 TraesCS3D01G540000 chr5A 80.169 237 32 12 228 460 616713410 616713635 3.930000e-36 163.0
26 TraesCS3D01G540000 chr5A 79.237 236 36 10 228 460 616731453 616731678 8.500000e-33 152.0
27 TraesCS3D01G540000 chr1D 86.957 115 15 0 205 319 384527179 384527293 3.980000e-26 130.0
28 TraesCS3D01G540000 chr1D 96.875 32 0 1 871 901 288741561 288741592 9.000000e-03 52.8
29 TraesCS3D01G540000 chr1B 81.600 125 22 1 1 124 355730425 355730301 8.680000e-18 102.0
30 TraesCS3D01G540000 chr6A 81.356 118 21 1 1 117 259832109 259831992 1.450000e-15 95.3
31 TraesCS3D01G540000 chrUn 85.393 89 12 1 1 88 362471312 362471224 1.880000e-14 91.6
32 TraesCS3D01G540000 chr6B 81.250 112 19 2 1 110 464537386 464537275 6.760000e-14 89.8
33 TraesCS3D01G540000 chr6B 90.625 64 6 0 136 199 346882250 346882187 8.740000e-13 86.1
34 TraesCS3D01G540000 chr6B 89.062 64 7 0 136 199 345969249 345969312 4.070000e-11 80.5
35 TraesCS3D01G540000 chr7B 90.625 64 6 0 136 199 536196955 536197018 8.740000e-13 86.1
36 TraesCS3D01G540000 chr7B 80.357 112 19 3 1 110 3881224 3881114 1.130000e-11 82.4
37 TraesCS3D01G540000 chr7A 90.625 64 6 0 136 199 166094791 166094728 8.740000e-13 86.1
38 TraesCS3D01G540000 chr7A 79.661 118 23 1 1 117 621803772 621803889 3.140000e-12 84.2
39 TraesCS3D01G540000 chr7A 79.661 118 23 1 1 117 706591120 706591003 3.140000e-12 84.2
40 TraesCS3D01G540000 chr5B 89.062 64 7 0 136 199 247884980 247885043 4.070000e-11 80.5
41 TraesCS3D01G540000 chr2A 89.062 64 7 0 136 199 624441748 624441811 4.070000e-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 TraesCS3D01G540000 chr3D 611562005 611566906 4901 False 9053.000000 9053 100.000000 1 4902 1 chr3D.!!$F1 4901
1 TraesCS3D01G540000 chr3A 746353120 746357808 4688 True 1275.750000 3797 88.731250 571 4902 4 chr3A.!!$R1 4331
2 TraesCS3D01G540000 chr3B 829282463 829287316 4853 False 910.333333 2433 90.547833 1 4657 6 chr3B.!!$F2 4656
3 TraesCS3D01G540000 chr4A 13756678 13759219 2541 True 1123.500000 2148 85.895500 1918 4282 2 chr4A.!!$R1 2364
4 TraesCS3D01G540000 chr4D 453319702 453321195 1493 False 1956.000000 1956 90.278000 2410 3916 1 chr4D.!!$F1 1506
5 TraesCS3D01G540000 chr4B 566979180 566983459 4279 False 962.750000 1864 90.532250 2534 4279 4 chr4B.!!$F1 1745

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
534 562 0.105039 CAACATAGAGAGCCGACCCC 59.895 60.0 0.00 0.00 0.00 4.95 F
589 617 0.179065 GGTCTAGCCGCGGGTAATTT 60.179 55.0 34.09 1.79 0.00 1.82 F
1276 1342 0.179129 CAAATTCAGCGGCCATGGTC 60.179 55.0 14.67 10.70 0.00 4.02 F
2732 5963 0.400594 GTTTGTCCCTGGTGCTAGGT 59.599 55.0 1.01 0.00 36.02 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2494 3211 0.538057 CACACAGCTTGTCCACCCAT 60.538 55.000 0.0 0.0 35.67 4.00 R
2561 3278 3.292460 AGGATGAAACAAAACCAACGGA 58.708 40.909 0.0 0.0 0.00 4.69 R
2941 6172 0.038343 TGCCAAATTTCTTCCGCAGC 60.038 50.000 0.0 0.0 0.00 5.25 R
3998 7235 1.580059 GGGTACTCCACATTCCAGGA 58.420 55.000 0.0 0.0 35.00 3.86 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
39 40 2.338813 CGACGAGACGAAGACAATCAAC 59.661 50.000 0.00 0.00 35.09 3.18
44 45 5.048921 ACGAGACGAAGACAATCAACTAGAA 60.049 40.000 0.00 0.00 0.00 2.10
47 48 6.513180 AGACGAAGACAATCAACTAGAACAA 58.487 36.000 0.00 0.00 0.00 2.83
75 76 0.895530 CTAAGGTCGTCTTGGAGGCA 59.104 55.000 4.52 0.00 36.21 4.75
90 91 1.869767 GAGGCATAATCGGCTGAACAG 59.130 52.381 0.00 0.00 42.77 3.16
122 123 1.731720 AAAATCTCAGCACTCCGAGC 58.268 50.000 0.00 0.00 0.00 5.03
160 161 4.046286 TGGAGGTAAGCAAATGAATGGT 57.954 40.909 0.00 0.00 0.00 3.55
174 175 2.830923 TGAATGGTTCGGATTTGGCATT 59.169 40.909 0.00 0.00 0.00 3.56
183 184 2.433970 CGGATTTGGCATTACCCCATTT 59.566 45.455 0.00 0.00 37.83 2.32
194 195 5.047092 GCATTACCCCATTTAGCTATGCATT 60.047 40.000 3.54 0.00 37.62 3.56
259 260 8.023706 CCTTCTTGATTGCTAATGATGATGATG 58.976 37.037 0.00 0.00 0.00 3.07
270 271 9.478768 GCTAATGATGATGATGATCTCGATTAT 57.521 33.333 0.00 0.00 0.00 1.28
275 276 8.419442 TGATGATGATGATCTCGATTATAAGGG 58.581 37.037 0.00 0.00 0.00 3.95
281 282 6.268825 TGATCTCGATTATAAGGGTGCTAC 57.731 41.667 0.00 0.00 0.00 3.58
285 286 6.513180 TCTCGATTATAAGGGTGCTACTTTG 58.487 40.000 0.00 0.00 0.00 2.77
293 294 2.308866 AGGGTGCTACTTTGCTACCAAT 59.691 45.455 0.00 0.00 36.53 3.16
295 296 3.343617 GGTGCTACTTTGCTACCAATGA 58.656 45.455 0.00 0.00 35.63 2.57
296 297 3.127030 GGTGCTACTTTGCTACCAATGAC 59.873 47.826 0.00 0.00 35.63 3.06
298 299 4.093556 GTGCTACTTTGCTACCAATGACTC 59.906 45.833 0.00 0.00 32.25 3.36
303 304 3.510388 TTGCTACCAATGACTCGAGAG 57.490 47.619 21.68 4.14 0.00 3.20
324 325 7.205515 AGAGATTCTAACATGTCCTTTGGAT 57.794 36.000 0.00 0.00 32.73 3.41
343 344 3.610911 GATGACCTAGGAACCCACTTTG 58.389 50.000 17.98 0.00 0.00 2.77
380 381 4.021229 CCCTGGGGTTTACAATAGGTTTC 58.979 47.826 4.27 0.00 0.00 2.78
387 388 5.388111 GGTTTACAATAGGTTTCTGCGTTC 58.612 41.667 0.00 0.00 0.00 3.95
391 392 4.251268 ACAATAGGTTTCTGCGTTCTACC 58.749 43.478 0.00 0.00 0.00 3.18
395 396 2.835764 AGGTTTCTGCGTTCTACCCATA 59.164 45.455 0.00 0.00 0.00 2.74
400 401 0.742505 TGCGTTCTACCCATAGTCGG 59.257 55.000 0.00 0.00 32.17 4.79
401 402 0.596859 GCGTTCTACCCATAGTCGGC 60.597 60.000 0.00 0.00 32.17 5.54
460 461 2.541466 AGTTAGGTGGACTCCTTCTGG 58.459 52.381 0.00 0.00 38.86 3.86
464 465 1.003233 GTGGACTCCTTCTGGTGCC 60.003 63.158 0.00 0.00 34.23 5.01
469 470 3.316573 CTCCTTCTGGTGCCGGGAC 62.317 68.421 19.24 19.24 34.23 4.46
472 473 3.316573 CTTCTGGTGCCGGGACTCC 62.317 68.421 26.18 11.11 0.00 3.85
493 494 3.319198 TCTTGCCGGGTCCACTCC 61.319 66.667 2.18 0.00 0.00 3.85
516 517 1.682451 CCGGCCGGGTCTTATCTTCA 61.682 60.000 37.42 0.00 0.00 3.02
517 518 0.177141 CGGCCGGGTCTTATCTTCAA 59.823 55.000 20.10 0.00 0.00 2.69
530 558 5.828328 TCTTATCTTCAACATAGAGAGCCGA 59.172 40.000 0.00 0.00 0.00 5.54
534 562 0.105039 CAACATAGAGAGCCGACCCC 59.895 60.000 0.00 0.00 0.00 4.95
553 581 1.148310 CTATGGCGCCCTAAATGACG 58.852 55.000 26.77 1.14 0.00 4.35
589 617 0.179065 GGTCTAGCCGCGGGTAATTT 60.179 55.000 34.09 1.79 0.00 1.82
591 619 0.249155 TCTAGCCGCGGGTAATTTCG 60.249 55.000 34.09 23.14 0.00 3.46
603 631 0.674269 TAATTTCGCCGACACCCACC 60.674 55.000 0.00 0.00 0.00 4.61
779 808 2.203743 ACGTCCGTTCCTTCCCCT 60.204 61.111 0.00 0.00 0.00 4.79
784 813 2.269241 CGTTCCTTCCCCTCTGCC 59.731 66.667 0.00 0.00 0.00 4.85
803 832 4.704103 TCCCACAGCCTCGCTCCT 62.704 66.667 0.00 0.00 36.40 3.69
811 840 1.752694 GCCTCGCTCCTCACTCTCT 60.753 63.158 0.00 0.00 0.00 3.10
835 877 2.928396 ACCCACCCCCTGTTCTCG 60.928 66.667 0.00 0.00 0.00 4.04
839 881 1.192146 CCACCCCCTGTTCTCGAAGA 61.192 60.000 0.00 0.00 0.00 2.87
1124 1183 2.541762 GCTGGCTTCGATCTGTTATGAC 59.458 50.000 0.00 0.00 0.00 3.06
1126 1185 2.766263 TGGCTTCGATCTGTTATGACCT 59.234 45.455 0.00 0.00 0.00 3.85
1132 1191 1.139058 GATCTGTTATGACCTGGGCGT 59.861 52.381 0.00 0.00 0.00 5.68
1165 1230 0.251121 TCATTTTTCGCCTGGCCTGA 60.251 50.000 14.12 2.16 0.00 3.86
1179 1244 2.370445 CCTGATGGCCGGAGTCCTT 61.370 63.158 5.05 0.00 0.00 3.36
1188 1253 0.618458 CCGGAGTCCTTGGATTTGGA 59.382 55.000 7.77 0.00 0.00 3.53
1218 1283 6.092670 CAGCACAACCGGGATTATAGAATATG 59.907 42.308 6.32 0.00 0.00 1.78
1240 1305 5.538118 TGTAAGAACATCATTGTCGTCAGT 58.462 37.500 0.00 0.00 34.06 3.41
1243 1308 5.348418 AGAACATCATTGTCGTCAGTTTG 57.652 39.130 0.00 0.00 34.06 2.93
1244 1309 4.816385 AGAACATCATTGTCGTCAGTTTGT 59.184 37.500 0.00 0.00 34.06 2.83
1246 1311 5.591643 ACATCATTGTCGTCAGTTTGTAC 57.408 39.130 0.00 0.00 0.00 2.90
1248 1313 5.405571 ACATCATTGTCGTCAGTTTGTACTC 59.594 40.000 0.00 0.00 30.26 2.59
1250 1315 4.038763 TCATTGTCGTCAGTTTGTACTCCT 59.961 41.667 0.00 0.00 30.26 3.69
1256 1322 4.954202 TCGTCAGTTTGTACTCCTATCCAT 59.046 41.667 0.00 0.00 30.26 3.41
1276 1342 0.179129 CAAATTCAGCGGCCATGGTC 60.179 55.000 14.67 10.70 0.00 4.02
1294 1381 2.635427 GGTCAGAAAGGAGAGGACAAGT 59.365 50.000 0.00 0.00 0.00 3.16
1315 1402 0.543749 GCTCACCATGGCTAAGGAGT 59.456 55.000 13.04 0.00 0.00 3.85
1320 1407 0.465097 CCATGGCTAAGGAGTGCTGG 60.465 60.000 0.00 0.00 0.00 4.85
1329 1416 2.583520 GAGTGCTGGCAGAGAGGG 59.416 66.667 20.86 0.00 0.00 4.30
1336 1423 2.843730 TGCTGGCAGAGAGGGTAAAATA 59.156 45.455 20.86 0.00 0.00 1.40
1338 1425 3.628032 GCTGGCAGAGAGGGTAAAATAAC 59.372 47.826 20.86 0.00 0.00 1.89
1388 1475 2.772515 AGCAGTCCAACCTAGGGATAAC 59.227 50.000 14.81 6.14 36.67 1.89
1414 1502 2.629336 AGTAATTCAGGCTAGGCTGC 57.371 50.000 35.07 22.91 0.00 5.25
1418 1506 1.992519 ATTCAGGCTAGGCTGCTGGG 61.993 60.000 35.07 16.53 0.00 4.45
1434 1715 6.294397 GGCTGCTGGGATTCTTAGATATTTTG 60.294 42.308 0.00 0.00 0.00 2.44
1463 1744 1.466167 GTCGTGCTGAATTGCTGATGT 59.534 47.619 0.00 0.00 0.00 3.06
1476 1757 3.151554 TGCTGATGTTGATGAAGCTTGT 58.848 40.909 2.10 0.00 34.92 3.16
1480 1761 4.392047 TGATGTTGATGAAGCTTGTCAGT 58.608 39.130 2.10 0.00 0.00 3.41
1485 1766 2.551032 TGATGAAGCTTGTCAGTTGCAG 59.449 45.455 2.10 0.00 0.00 4.41
1500 1781 4.512944 CAGTTGCAGTGTCAATGTAGAAGT 59.487 41.667 1.77 0.00 0.00 3.01
1549 1830 9.559958 GTGAAATCATTTTAGTGACATGTTAGG 57.440 33.333 0.00 0.00 0.00 2.69
1552 1833 7.865706 ATCATTTTAGTGACATGTTAGGGTC 57.134 36.000 0.00 0.00 34.63 4.46
1553 1834 6.774673 TCATTTTAGTGACATGTTAGGGTCA 58.225 36.000 0.00 0.00 41.44 4.02
1566 1847 6.928348 TGTTAGGGTCACTTTGATCTAAGA 57.072 37.500 21.42 0.00 31.09 2.10
1578 1859 8.886719 CACTTTGATCTAAGAGATATTGTGCAA 58.113 33.333 21.42 0.00 34.53 4.08
1579 1860 9.107177 ACTTTGATCTAAGAGATATTGTGCAAG 57.893 33.333 21.42 0.00 34.53 4.01
1580 1861 7.488187 TTGATCTAAGAGATATTGTGCAAGC 57.512 36.000 0.00 0.00 34.53 4.01
1581 1862 5.693555 TGATCTAAGAGATATTGTGCAAGCG 59.306 40.000 0.00 0.00 34.53 4.68
1586 2042 2.213499 AGATATTGTGCAAGCGCTACC 58.787 47.619 12.05 5.12 39.64 3.18
1657 2123 9.587772 TGATAAAGAGAGTATTCTTTTCCTTCG 57.412 33.333 6.35 0.00 43.08 3.79
1658 2124 8.950208 ATAAAGAGAGTATTCTTTTCCTTCGG 57.050 34.615 6.35 0.00 43.08 4.30
1659 2125 6.361768 AAGAGAGTATTCTTTTCCTTCGGT 57.638 37.500 0.00 0.00 33.74 4.69
1660 2126 6.361768 AGAGAGTATTCTTTTCCTTCGGTT 57.638 37.500 0.00 0.00 32.53 4.44
1661 2127 6.770542 AGAGAGTATTCTTTTCCTTCGGTTT 58.229 36.000 0.00 0.00 32.53 3.27
1662 2128 6.874664 AGAGAGTATTCTTTTCCTTCGGTTTC 59.125 38.462 0.00 0.00 32.53 2.78
1663 2129 5.638234 AGAGTATTCTTTTCCTTCGGTTTCG 59.362 40.000 0.00 0.00 37.82 3.46
1664 2130 4.694037 AGTATTCTTTTCCTTCGGTTTCGG 59.306 41.667 0.00 0.00 36.95 4.30
1665 2131 1.886886 TCTTTTCCTTCGGTTTCGGG 58.113 50.000 0.00 0.00 36.95 5.14
1666 2132 1.417145 TCTTTTCCTTCGGTTTCGGGA 59.583 47.619 0.00 0.00 36.95 5.14
1667 2133 2.158784 TCTTTTCCTTCGGTTTCGGGAA 60.159 45.455 0.00 0.00 35.80 3.97
1668 2134 2.345124 TTTCCTTCGGTTTCGGGAAA 57.655 45.000 0.00 0.00 41.19 3.13
1669 2135 2.572209 TTCCTTCGGTTTCGGGAAAT 57.428 45.000 0.00 0.00 35.07 2.17
1670 2136 2.103537 TCCTTCGGTTTCGGGAAATC 57.896 50.000 0.00 0.00 36.95 2.17
1671 2137 1.348366 TCCTTCGGTTTCGGGAAATCA 59.652 47.619 5.37 0.00 36.95 2.57
1672 2138 2.026636 TCCTTCGGTTTCGGGAAATCAT 60.027 45.455 5.37 0.00 36.95 2.45
1673 2139 2.752903 CCTTCGGTTTCGGGAAATCATT 59.247 45.455 5.37 0.00 36.95 2.57
1674 2140 3.192633 CCTTCGGTTTCGGGAAATCATTT 59.807 43.478 5.37 0.00 36.95 2.32
1675 2141 3.840890 TCGGTTTCGGGAAATCATTTG 57.159 42.857 5.37 0.00 36.95 2.32
1676 2142 2.490115 TCGGTTTCGGGAAATCATTTGG 59.510 45.455 5.37 0.00 36.95 3.28
1677 2143 2.416701 CGGTTTCGGGAAATCATTTGGG 60.417 50.000 5.37 0.00 31.06 4.12
1678 2144 2.565391 GGTTTCGGGAAATCATTTGGGT 59.435 45.455 0.00 0.00 31.92 4.51
1679 2145 3.007506 GGTTTCGGGAAATCATTTGGGTT 59.992 43.478 0.00 0.00 31.92 4.11
1680 2146 4.221041 GGTTTCGGGAAATCATTTGGGTTA 59.779 41.667 0.00 0.00 31.92 2.85
1681 2147 5.165676 GTTTCGGGAAATCATTTGGGTTAC 58.834 41.667 0.00 0.00 32.36 2.50
1682 2148 4.035612 TCGGGAAATCATTTGGGTTACA 57.964 40.909 0.00 0.00 0.00 2.41
1683 2149 4.013728 TCGGGAAATCATTTGGGTTACAG 58.986 43.478 0.00 0.00 0.00 2.74
1684 2150 3.761752 CGGGAAATCATTTGGGTTACAGT 59.238 43.478 0.00 0.00 0.00 3.55
1693 2159 7.033530 TCATTTGGGTTACAGTTTAGTGTTG 57.966 36.000 0.00 0.00 31.46 3.33
1699 2165 5.746721 GGGTTACAGTTTAGTGTTGCTTTTG 59.253 40.000 0.00 0.00 31.46 2.44
1719 2185 6.801539 TTTGGCTTAGAGTTGATGTGTAAG 57.198 37.500 0.00 0.00 0.00 2.34
1723 2189 4.690748 GCTTAGAGTTGATGTGTAAGTGCA 59.309 41.667 0.00 0.00 0.00 4.57
1725 2191 6.128172 GCTTAGAGTTGATGTGTAAGTGCAAT 60.128 38.462 0.00 0.00 0.00 3.56
1726 2192 5.869753 AGAGTTGATGTGTAAGTGCAATC 57.130 39.130 0.00 0.00 0.00 2.67
1727 2193 4.697352 AGAGTTGATGTGTAAGTGCAATCC 59.303 41.667 0.00 0.00 0.00 3.01
1728 2194 3.758554 AGTTGATGTGTAAGTGCAATCCC 59.241 43.478 0.00 0.00 0.00 3.85
1729 2195 3.719268 TGATGTGTAAGTGCAATCCCT 57.281 42.857 0.00 0.00 0.00 4.20
1730 2196 3.346315 TGATGTGTAAGTGCAATCCCTG 58.654 45.455 0.00 0.00 0.00 4.45
1731 2197 2.949177 TGTGTAAGTGCAATCCCTGT 57.051 45.000 0.00 0.00 0.00 4.00
1739 2205 3.565307 AGTGCAATCCCTGTTTTTCTCA 58.435 40.909 0.00 0.00 0.00 3.27
1781 2247 7.517417 GCTTGAGAATTCCGTATGTACATTGAG 60.517 40.741 14.77 5.85 0.00 3.02
1796 2262 7.172342 TGTACATTGAGTTAGGGTTATTGCTT 58.828 34.615 0.00 0.00 0.00 3.91
1800 2266 4.993028 TGAGTTAGGGTTATTGCTTTGGT 58.007 39.130 0.00 0.00 0.00 3.67
1804 2270 3.525800 AGGGTTATTGCTTTGGTGTCT 57.474 42.857 0.00 0.00 0.00 3.41
1825 2291 3.726607 TGGTGCTTAATGCTTTTGGTTG 58.273 40.909 0.00 0.00 43.37 3.77
1830 2296 5.523552 GTGCTTAATGCTTTTGGTTGAAACT 59.476 36.000 0.00 0.00 43.37 2.66
1835 2301 8.600449 TTAATGCTTTTGGTTGAAACTTATGG 57.400 30.769 0.00 0.00 0.00 2.74
1846 2312 7.099120 GGTTGAAACTTATGGATCTTGCAATT 58.901 34.615 0.00 0.00 0.00 2.32
1849 2315 8.070034 TGAAACTTATGGATCTTGCAATTGAT 57.930 30.769 10.34 0.00 0.00 2.57
1851 2317 6.309712 ACTTATGGATCTTGCAATTGATCG 57.690 37.500 17.65 9.44 39.77 3.69
1854 2320 4.141233 TGGATCTTGCAATTGATCGAGA 57.859 40.909 17.65 7.51 39.77 4.04
1874 2346 6.706270 TCGAGAGAGCTTTTGACATAAAGTTT 59.294 34.615 0.00 0.00 34.86 2.66
1889 2361 7.611770 ACATAAAGTTTTTATCTTCCAAGGGC 58.388 34.615 0.00 0.00 0.00 5.19
1891 2363 2.492088 AGTTTTTATCTTCCAAGGGCGC 59.508 45.455 0.00 0.00 0.00 6.53
1913 2385 6.232788 CGCGGTCAAAATTATGTTCATTTTG 58.767 36.000 0.00 10.54 46.41 2.44
1914 2386 6.128956 CGCGGTCAAAATTATGTTCATTTTGT 60.129 34.615 14.61 0.00 45.71 2.83
1915 2387 7.008859 GCGGTCAAAATTATGTTCATTTTGTG 58.991 34.615 14.61 9.22 45.71 3.33
1936 2499 6.851609 TGTGATATTTTGGTGACATGTTAGC 58.148 36.000 12.50 12.50 42.32 3.09
1945 2508 2.973224 GTGACATGTTAGCGTTGCTTTG 59.027 45.455 0.00 0.00 40.44 2.77
1950 2513 3.811722 TGTTAGCGTTGCTTTGATCTG 57.188 42.857 0.00 0.00 40.44 2.90
1957 2520 3.242349 GCGTTGCTTTGATCTGAGAGATG 60.242 47.826 0.00 0.00 34.53 2.90
1962 2525 3.310227 GCTTTGATCTGAGAGATGCTGTG 59.690 47.826 0.00 0.00 34.53 3.66
1969 2532 1.345415 TGAGAGATGCTGTGCAAGTGA 59.655 47.619 0.00 0.00 43.62 3.41
1976 2539 2.426522 TGCTGTGCAAGTGATACTTCC 58.573 47.619 0.00 0.00 36.03 3.46
2022 2585 8.573885 CATGGAAATTTCATATGAGCAGTACAT 58.426 33.333 19.49 6.27 0.00 2.29
2030 2593 9.612066 TTTCATATGAGCAGTACATATTTGTGA 57.388 29.630 5.39 0.00 38.40 3.58
2031 2594 9.783081 TTCATATGAGCAGTACATATTTGTGAT 57.217 29.630 5.39 0.00 38.40 3.06
2054 2619 7.776500 TGATAATTCCATCTCTTTTCTGCATGA 59.224 33.333 0.00 0.00 0.00 3.07
2063 2633 6.470278 TCTCTTTTCTGCATGATCTTCTTCA 58.530 36.000 0.00 0.00 0.00 3.02
2107 2677 7.444792 GGGAGGATCATCTGATGCATTTATATC 59.555 40.741 12.78 8.38 44.10 1.63
2111 2681 8.613482 GGATCATCTGATGCATTTATATCTGTG 58.387 37.037 12.78 0.00 41.72 3.66
2135 2705 3.338249 TGAAGGAGCTTAATGAGTGTGC 58.662 45.455 0.00 0.00 0.00 4.57
2145 2715 5.355350 GCTTAATGAGTGTGCCTTTATCAGT 59.645 40.000 0.00 0.00 0.00 3.41
2176 2746 4.853924 AGTATCACAACCAAAGCCAAAG 57.146 40.909 0.00 0.00 0.00 2.77
2181 2751 1.490069 ACAACCAAAGCCAAAGCCAAT 59.510 42.857 0.00 0.00 41.25 3.16
2218 2910 5.908341 AGCTGCTAAATTCTCCTGTACTAC 58.092 41.667 0.00 0.00 0.00 2.73
2233 2925 8.071177 TCCTGTACTACTTTAATCCAAGTACC 57.929 38.462 8.10 0.00 41.05 3.34
2317 3023 5.183969 GGAACAAGAATAGTACTGGGTTCC 58.816 45.833 17.95 17.95 41.10 3.62
2323 3029 6.449830 AGAATAGTACTGGGTTCCAACTTT 57.550 37.500 5.39 0.00 30.80 2.66
2406 3120 3.244353 ACAGTTGACTGATCTGTTCCCTG 60.244 47.826 17.42 13.47 46.59 4.45
2461 3177 1.955778 TCGAACACGGTTACTCTTCCA 59.044 47.619 0.00 0.00 0.00 3.53
2464 3180 3.725490 GAACACGGTTACTCTTCCAGTT 58.275 45.455 0.00 0.00 36.43 3.16
2466 3182 2.696707 ACACGGTTACTCTTCCAGTTCA 59.303 45.455 0.00 0.00 36.43 3.18
2479 3195 7.013369 ACTCTTCCAGTTCAAAGTGTTATTTCC 59.987 37.037 0.00 0.00 26.56 3.13
2482 3198 6.126409 TCCAGTTCAAAGTGTTATTTCCACT 58.874 36.000 0.00 0.00 44.80 4.00
2507 3224 1.544724 TTGCTAATGGGTGGACAAGC 58.455 50.000 0.00 0.00 0.00 4.01
2517 3234 0.657840 GTGGACAAGCTGTGTGTGTC 59.342 55.000 6.90 6.90 41.96 3.67
2519 3236 1.065491 TGGACAAGCTGTGTGTGTCTT 60.065 47.619 13.66 0.00 41.96 3.01
2520 3237 2.017049 GGACAAGCTGTGTGTGTCTTT 58.983 47.619 13.66 0.00 41.96 2.52
2521 3238 2.223340 GGACAAGCTGTGTGTGTCTTTG 60.223 50.000 13.66 0.00 41.96 2.77
2522 3239 2.677836 GACAAGCTGTGTGTGTCTTTGA 59.322 45.455 8.01 0.00 41.96 2.69
2523 3240 3.282021 ACAAGCTGTGTGTGTCTTTGAT 58.718 40.909 0.00 0.00 39.72 2.57
2525 3242 4.512944 ACAAGCTGTGTGTGTCTTTGATAG 59.487 41.667 0.00 0.00 39.72 2.08
2564 3281 5.363939 AGCTAAGAGGATGATTTCTTTCCG 58.636 41.667 0.00 0.00 35.42 4.30
2580 3297 5.344884 TCTTTCCGTTGGTTTTGTTTCATC 58.655 37.500 0.00 0.00 0.00 2.92
2618 3337 8.195436 CCACATTCAGATGAATAAAAGCATCTT 58.805 33.333 7.71 0.00 46.65 2.40
2695 3414 2.024751 GGTAGATGGGGGCCTTAAAACA 60.025 50.000 0.84 0.00 0.00 2.83
2732 5963 0.400594 GTTTGTCCCTGGTGCTAGGT 59.599 55.000 1.01 0.00 36.02 3.08
2805 6036 1.545706 AAGGAGAGGTGCCGAACTCC 61.546 60.000 17.39 17.39 46.28 3.85
3395 6626 0.179004 AATGGTGCCGTTCACTGGAA 60.179 50.000 5.26 0.00 44.98 3.53
3423 6654 6.906157 ATATGATGGCAAATGGTTCCTAAG 57.094 37.500 0.00 0.00 0.00 2.18
3926 7157 5.815581 TGTATCTGCCTGTTTAGTGGAAAT 58.184 37.500 0.00 0.00 0.00 2.17
3998 7235 1.763545 GAAAGAACCCCTCGGCTAGAT 59.236 52.381 0.00 0.00 0.00 1.98
4110 7491 5.684704 TCTCTGAGATTTTGACCAAGTTGT 58.315 37.500 2.58 0.00 0.00 3.32
4179 7560 3.648067 TGTGAGATGAACAGGAACCTTCT 59.352 43.478 0.00 0.00 0.00 2.85
4180 7561 4.838423 TGTGAGATGAACAGGAACCTTCTA 59.162 41.667 0.00 0.00 0.00 2.10
4242 7671 4.155462 GCAGCAGAAGATTTCACTTGATCA 59.845 41.667 0.00 0.00 0.00 2.92
4247 7676 7.991460 AGCAGAAGATTTCACTTGATCATCATA 59.009 33.333 0.00 0.00 0.00 2.15
4261 7690 6.412214 TGATCATCATATCCATGGATGTGTC 58.588 40.000 36.39 29.17 42.09 3.67
4297 7726 3.128349 GCAGATTAGGCATGCCAAAATG 58.872 45.455 37.18 26.71 38.92 2.32
4371 7800 1.374560 GTTTGTGCCAAAACCAACCC 58.625 50.000 2.47 0.00 34.58 4.11
4500 7929 2.161012 GCATCTGACAAGTGGATGTGTG 59.839 50.000 11.63 0.00 39.04 3.82
4522 7951 6.493115 TGTGTTGTGGGTGAAAATGATTATCT 59.507 34.615 0.00 0.00 0.00 1.98
4527 7956 6.599244 TGTGGGTGAAAATGATTATCTGAGAC 59.401 38.462 0.00 0.00 0.00 3.36
4579 8008 5.629435 TCGCTGATGCTAATTACTAACATCG 59.371 40.000 0.00 0.00 36.33 3.84
4745 8174 6.799926 TGTGATTCTTTTGACGATCAATCA 57.200 33.333 0.00 0.00 36.11 2.57
4768 8197 2.670414 CGCAGAGGACAAAAGAGATGAC 59.330 50.000 0.00 0.00 0.00 3.06
4823 8264 8.046107 TGATATCTGATGTTCCATTTGTACACA 58.954 33.333 3.98 0.00 0.00 3.72
4842 8293 0.683973 ACCTGTGGTCAAGAGCAGAG 59.316 55.000 16.65 16.65 45.99 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.566523 AGTTGATTGTCTTCGTCTCGTC 58.433 45.455 0.00 0.00 0.00 4.20
22 23 6.150318 TGTTCTAGTTGATTGTCTTCGTCTC 58.850 40.000 0.00 0.00 0.00 3.36
24 25 6.764877 TTGTTCTAGTTGATTGTCTTCGTC 57.235 37.500 0.00 0.00 0.00 4.20
39 40 8.936864 ACGACCTTAGATGAAAAATTGTTCTAG 58.063 33.333 9.75 0.58 0.00 2.43
44 45 7.308589 CCAAGACGACCTTAGATGAAAAATTGT 60.309 37.037 0.00 0.00 32.86 2.71
47 48 6.472887 TCCAAGACGACCTTAGATGAAAAAT 58.527 36.000 0.00 0.00 32.86 1.82
58 59 1.568504 TATGCCTCCAAGACGACCTT 58.431 50.000 0.00 0.00 34.91 3.50
63 64 1.502231 CCGATTATGCCTCCAAGACG 58.498 55.000 0.00 0.00 0.00 4.18
75 76 3.704566 TGGAGTACTGTTCAGCCGATTAT 59.295 43.478 0.00 0.00 0.00 1.28
90 91 8.515414 AGTGCTGAGATTTTAAATTTGGAGTAC 58.485 33.333 0.00 0.00 0.00 2.73
160 161 1.006043 TGGGGTAATGCCAAATCCGAA 59.994 47.619 0.00 0.00 39.65 4.30
174 175 4.826733 CACAATGCATAGCTAAATGGGGTA 59.173 41.667 0.00 0.00 0.00 3.69
194 195 0.107066 CATGAGGGGCATAGCACACA 60.107 55.000 0.00 0.00 34.82 3.72
259 260 6.518208 AGTAGCACCCTTATAATCGAGATC 57.482 41.667 0.00 0.00 0.00 2.75
270 271 2.907696 TGGTAGCAAAGTAGCACCCTTA 59.092 45.455 0.00 0.00 35.91 2.69
275 276 4.003648 AGTCATTGGTAGCAAAGTAGCAC 58.996 43.478 12.00 1.69 36.85 4.40
281 282 3.849911 TCTCGAGTCATTGGTAGCAAAG 58.150 45.455 12.00 7.54 0.00 2.77
285 286 4.037446 AGAATCTCTCGAGTCATTGGTAGC 59.963 45.833 13.13 0.51 36.74 3.58
293 294 5.066634 GGACATGTTAGAATCTCTCGAGTCA 59.933 44.000 13.13 0.00 36.74 3.41
295 296 5.197451 AGGACATGTTAGAATCTCTCGAGT 58.803 41.667 13.13 0.00 0.00 4.18
296 297 5.766150 AGGACATGTTAGAATCTCTCGAG 57.234 43.478 5.93 5.93 0.00 4.04
298 299 5.521735 CCAAAGGACATGTTAGAATCTCTCG 59.478 44.000 0.00 0.00 0.00 4.04
303 304 6.038714 GGTCATCCAAAGGACATGTTAGAATC 59.961 42.308 0.00 0.00 37.94 2.52
324 325 2.414612 ACAAAGTGGGTTCCTAGGTCA 58.585 47.619 9.08 0.88 0.00 4.02
363 364 3.754850 ACGCAGAAACCTATTGTAAACCC 59.245 43.478 0.00 0.00 0.00 4.11
380 381 1.269102 CCGACTATGGGTAGAACGCAG 60.269 57.143 3.20 0.00 44.34 5.18
387 388 0.822532 AGGACGCCGACTATGGGTAG 60.823 60.000 0.00 0.00 0.00 3.18
391 392 0.030908 GAGAAGGACGCCGACTATGG 59.969 60.000 0.00 0.00 0.00 2.74
395 396 1.096416 CTTAGAGAAGGACGCCGACT 58.904 55.000 0.00 0.00 0.00 4.18
400 401 3.579335 ACAAGACTTAGAGAAGGACGC 57.421 47.619 0.00 0.00 36.95 5.19
401 402 5.862860 GGTTTACAAGACTTAGAGAAGGACG 59.137 44.000 0.00 0.00 36.95 4.79
475 476 2.047179 GAGTGGACCCGGCAAGAC 60.047 66.667 0.00 0.00 0.00 3.01
501 502 5.302059 TCTCTATGTTGAAGATAAGACCCGG 59.698 44.000 0.00 0.00 0.00 5.73
516 517 0.032017 AGGGGTCGGCTCTCTATGTT 60.032 55.000 0.00 0.00 0.00 2.71
517 518 0.851469 TAGGGGTCGGCTCTCTATGT 59.149 55.000 0.00 0.00 0.00 2.29
530 558 1.065997 ATTTAGGGCGCCATAGGGGT 61.066 55.000 30.85 9.69 39.65 4.95
534 562 1.148310 CGTCATTTAGGGCGCCATAG 58.852 55.000 30.85 14.33 0.00 2.23
540 568 2.200858 ATGATCGCGTCATTTAGGGCG 61.201 52.381 15.41 0.00 45.25 6.13
553 581 1.895707 CCAGAAGGCCCATGATCGC 60.896 63.158 0.00 0.00 0.00 4.58
556 584 2.053244 CTAGACCAGAAGGCCCATGAT 58.947 52.381 0.00 0.00 39.06 2.45
562 590 2.501610 CGGCTAGACCAGAAGGCC 59.498 66.667 0.00 0.00 39.03 5.19
589 617 3.402095 TTTTGGTGGGTGTCGGCGA 62.402 57.895 4.99 4.99 0.00 5.54
591 619 1.104577 TTCTTTTGGTGGGTGTCGGC 61.105 55.000 0.00 0.00 0.00 5.54
594 622 4.400529 ACATTTTCTTTTGGTGGGTGTC 57.599 40.909 0.00 0.00 0.00 3.67
686 715 9.177608 CCACTAAAATATGGATTCTTTGTCTCA 57.822 33.333 0.00 0.00 38.34 3.27
688 717 8.960591 CACCACTAAAATATGGATTCTTTGTCT 58.039 33.333 0.00 0.00 39.46 3.41
690 719 7.363793 GGCACCACTAAAATATGGATTCTTTGT 60.364 37.037 0.00 0.00 39.46 2.83
691 720 6.980397 GGCACCACTAAAATATGGATTCTTTG 59.020 38.462 0.00 0.00 39.46 2.77
692 721 6.183360 CGGCACCACTAAAATATGGATTCTTT 60.183 38.462 0.00 0.00 39.46 2.52
695 724 4.578928 ACGGCACCACTAAAATATGGATTC 59.421 41.667 0.00 0.00 39.46 2.52
696 725 4.338118 CACGGCACCACTAAAATATGGATT 59.662 41.667 0.00 0.00 39.46 3.01
697 726 3.882888 CACGGCACCACTAAAATATGGAT 59.117 43.478 0.00 0.00 39.46 3.41
758 787 1.595357 GGAAGGAACGGACGTGGAT 59.405 57.895 0.00 0.00 0.00 3.41
779 808 4.664267 AGGCTGTGGGAGGGCAGA 62.664 66.667 0.00 0.00 34.87 4.26
784 813 4.154347 GAGCGAGGCTGTGGGAGG 62.154 72.222 0.00 0.00 39.88 4.30
798 827 1.334384 GGGGGAAGAGAGTGAGGAGC 61.334 65.000 0.00 0.00 0.00 4.70
803 832 1.229529 GGGTGGGGGAAGAGAGTGA 60.230 63.158 0.00 0.00 0.00 3.41
891 933 1.090625 GCCGACTGTAGAGAGCTCGA 61.091 60.000 8.37 0.00 34.09 4.04
894 936 2.115911 CCGCCGACTGTAGAGAGCT 61.116 63.158 0.00 0.00 0.00 4.09
895 937 2.054140 CTCCGCCGACTGTAGAGAGC 62.054 65.000 0.00 0.00 0.00 4.09
896 938 1.440938 CCTCCGCCGACTGTAGAGAG 61.441 65.000 0.00 0.00 0.00 3.20
897 939 1.451567 CCTCCGCCGACTGTAGAGA 60.452 63.158 0.00 0.00 0.00 3.10
898 940 1.030488 TTCCTCCGCCGACTGTAGAG 61.030 60.000 0.00 0.00 0.00 2.43
899 941 1.001764 TTCCTCCGCCGACTGTAGA 60.002 57.895 0.00 0.00 0.00 2.59
941 996 2.202623 CTGTCCACGCTCGTAGGC 60.203 66.667 0.00 0.00 0.00 3.93
1124 1183 2.482333 CCTAGAGACGACGCCCAGG 61.482 68.421 0.00 0.00 0.00 4.45
1126 1185 0.896940 AAACCTAGAGACGACGCCCA 60.897 55.000 0.00 0.00 0.00 5.36
1132 1191 5.107220 GCGAAAAATGAAAACCTAGAGACGA 60.107 40.000 0.00 0.00 0.00 4.20
1165 1230 1.281925 AATCCAAGGACTCCGGCCAT 61.282 55.000 2.24 0.00 0.00 4.40
1175 1240 2.947243 GCTGATGCTCCAAATCCAAGGA 60.947 50.000 0.00 0.00 36.03 3.36
1179 1244 1.272037 TGTGCTGATGCTCCAAATCCA 60.272 47.619 0.00 0.00 40.48 3.41
1188 1253 2.202236 ATCCCGGTTGTGCTGATGCT 62.202 55.000 0.00 0.00 40.48 3.79
1218 1283 6.467723 AACTGACGACAATGATGTTCTTAC 57.532 37.500 0.00 0.00 40.74 2.34
1227 1292 4.038763 AGGAGTACAAACTGACGACAATGA 59.961 41.667 0.00 0.00 35.56 2.57
1232 1297 4.157289 TGGATAGGAGTACAAACTGACGAC 59.843 45.833 0.00 0.00 35.56 4.34
1235 1300 6.222038 TGATGGATAGGAGTACAAACTGAC 57.778 41.667 0.00 0.00 35.56 3.51
1240 1305 7.283127 GCTGAATTTGATGGATAGGAGTACAAA 59.717 37.037 0.00 0.00 0.00 2.83
1243 1308 5.406780 CGCTGAATTTGATGGATAGGAGTAC 59.593 44.000 0.00 0.00 0.00 2.73
1244 1309 5.511373 CCGCTGAATTTGATGGATAGGAGTA 60.511 44.000 0.00 0.00 0.00 2.59
1246 1311 3.750130 CCGCTGAATTTGATGGATAGGAG 59.250 47.826 0.00 0.00 0.00 3.69
1248 1313 2.227388 GCCGCTGAATTTGATGGATAGG 59.773 50.000 0.00 0.00 0.00 2.57
1250 1315 2.229792 GGCCGCTGAATTTGATGGATA 58.770 47.619 0.00 0.00 0.00 2.59
1256 1322 0.611618 ACCATGGCCGCTGAATTTGA 60.612 50.000 13.04 0.00 0.00 2.69
1276 1342 3.513515 AGCTACTTGTCCTCTCCTTTCTG 59.486 47.826 0.00 0.00 0.00 3.02
1294 1381 2.042464 CTCCTTAGCCATGGTGAGCTA 58.958 52.381 14.67 5.43 40.56 3.32
1315 1402 1.064003 TTTTACCCTCTCTGCCAGCA 58.936 50.000 0.00 0.00 0.00 4.41
1320 1407 4.501071 TGTCGTTATTTTACCCTCTCTGC 58.499 43.478 0.00 0.00 0.00 4.26
1336 1423 5.182487 TGCCAATCATGTAGTAATGTCGTT 58.818 37.500 0.00 0.00 0.00 3.85
1338 1425 5.929697 ATGCCAATCATGTAGTAATGTCG 57.070 39.130 0.00 0.00 33.26 4.35
1356 1443 2.614057 GTTGGACTGCTATGTGTATGCC 59.386 50.000 0.00 0.00 0.00 4.40
1388 1475 4.320641 GCCTAGCCTGAATTACTACTCTCG 60.321 50.000 0.00 0.00 0.00 4.04
1408 1495 1.885049 TCTAAGAATCCCAGCAGCCT 58.115 50.000 0.00 0.00 0.00 4.58
1434 1715 1.438651 TTCAGCACGACTGCCATTAC 58.561 50.000 5.50 0.00 46.76 1.89
1457 1738 4.454847 ACTGACAAGCTTCATCAACATCAG 59.545 41.667 10.41 9.08 37.62 2.90
1459 1740 5.152097 CAACTGACAAGCTTCATCAACATC 58.848 41.667 10.41 0.00 0.00 3.06
1463 1744 2.950975 TGCAACTGACAAGCTTCATCAA 59.049 40.909 10.41 0.00 0.00 2.57
1476 1757 4.335400 TCTACATTGACACTGCAACTGA 57.665 40.909 0.00 0.00 0.00 3.41
1480 1761 4.273235 CACACTTCTACATTGACACTGCAA 59.727 41.667 0.00 0.00 0.00 4.08
1485 1766 6.584942 TCGATTACACACTTCTACATTGACAC 59.415 38.462 0.00 0.00 0.00 3.67
1519 1800 9.814899 ACATGTCACTAAAATGATTTCACAAAA 57.185 25.926 0.00 0.00 0.00 2.44
1520 1801 9.814899 AACATGTCACTAAAATGATTTCACAAA 57.185 25.926 0.00 0.00 0.00 2.83
1549 1830 9.039870 CACAATATCTCTTAGATCAAAGTGACC 57.960 37.037 0.00 0.00 36.20 4.02
1552 1833 8.429493 TGCACAATATCTCTTAGATCAAAGTG 57.571 34.615 0.00 0.00 36.20 3.16
1553 1834 9.107177 CTTGCACAATATCTCTTAGATCAAAGT 57.893 33.333 0.00 0.00 36.20 2.66
1554 1835 8.068977 GCTTGCACAATATCTCTTAGATCAAAG 58.931 37.037 0.00 0.00 36.20 2.77
1566 1847 2.158900 AGGTAGCGCTTGCACAATATCT 60.159 45.455 18.68 0.00 42.66 1.98
1622 2088 9.950496 AGAATACTCTCTTTATCACAAATGTGT 57.050 29.630 12.87 4.14 45.76 3.72
1631 2097 9.587772 CGAAGGAAAAGAATACTCTCTTTATCA 57.412 33.333 0.00 0.00 43.33 2.15
1653 2119 4.165779 CAAATGATTTCCCGAAACCGAAG 58.834 43.478 0.00 0.00 32.51 3.79
1654 2120 3.057174 CCAAATGATTTCCCGAAACCGAA 60.057 43.478 0.00 0.00 32.51 4.30
1655 2121 2.490115 CCAAATGATTTCCCGAAACCGA 59.510 45.455 0.00 0.00 32.51 4.69
1656 2122 2.416701 CCCAAATGATTTCCCGAAACCG 60.417 50.000 0.00 0.00 32.51 4.44
1657 2123 2.565391 ACCCAAATGATTTCCCGAAACC 59.435 45.455 0.00 0.00 32.51 3.27
1658 2124 3.953712 ACCCAAATGATTTCCCGAAAC 57.046 42.857 0.00 0.00 32.51 2.78
1659 2125 4.833380 TGTAACCCAAATGATTTCCCGAAA 59.167 37.500 0.00 0.00 34.46 3.46
1660 2126 4.408276 TGTAACCCAAATGATTTCCCGAA 58.592 39.130 0.00 0.00 0.00 4.30
1661 2127 4.013728 CTGTAACCCAAATGATTTCCCGA 58.986 43.478 0.00 0.00 0.00 5.14
1662 2128 3.761752 ACTGTAACCCAAATGATTTCCCG 59.238 43.478 0.00 0.00 0.00 5.14
1663 2129 5.738619 AACTGTAACCCAAATGATTTCCC 57.261 39.130 0.00 0.00 0.00 3.97
1664 2130 7.812669 CACTAAACTGTAACCCAAATGATTTCC 59.187 37.037 0.00 0.00 0.00 3.13
1665 2131 8.357402 ACACTAAACTGTAACCCAAATGATTTC 58.643 33.333 0.00 0.00 0.00 2.17
1666 2132 8.245195 ACACTAAACTGTAACCCAAATGATTT 57.755 30.769 0.00 0.00 0.00 2.17
1667 2133 7.833285 ACACTAAACTGTAACCCAAATGATT 57.167 32.000 0.00 0.00 0.00 2.57
1668 2134 7.657336 CAACACTAAACTGTAACCCAAATGAT 58.343 34.615 0.00 0.00 0.00 2.45
1669 2135 6.460399 GCAACACTAAACTGTAACCCAAATGA 60.460 38.462 0.00 0.00 0.00 2.57
1670 2136 5.689961 GCAACACTAAACTGTAACCCAAATG 59.310 40.000 0.00 0.00 0.00 2.32
1671 2137 5.596772 AGCAACACTAAACTGTAACCCAAAT 59.403 36.000 0.00 0.00 0.00 2.32
1672 2138 4.951094 AGCAACACTAAACTGTAACCCAAA 59.049 37.500 0.00 0.00 0.00 3.28
1673 2139 4.528920 AGCAACACTAAACTGTAACCCAA 58.471 39.130 0.00 0.00 0.00 4.12
1674 2140 4.159244 AGCAACACTAAACTGTAACCCA 57.841 40.909 0.00 0.00 0.00 4.51
1675 2141 5.509716 AAAGCAACACTAAACTGTAACCC 57.490 39.130 0.00 0.00 0.00 4.11
1676 2142 5.746721 CCAAAAGCAACACTAAACTGTAACC 59.253 40.000 0.00 0.00 0.00 2.85
1677 2143 5.231357 GCCAAAAGCAACACTAAACTGTAAC 59.769 40.000 0.00 0.00 42.97 2.50
1678 2144 5.344884 GCCAAAAGCAACACTAAACTGTAA 58.655 37.500 0.00 0.00 42.97 2.41
1679 2145 4.927422 GCCAAAAGCAACACTAAACTGTA 58.073 39.130 0.00 0.00 42.97 2.74
1680 2146 3.780902 GCCAAAAGCAACACTAAACTGT 58.219 40.909 0.00 0.00 42.97 3.55
1693 2159 4.022849 ACACATCAACTCTAAGCCAAAAGC 60.023 41.667 0.00 0.00 44.25 3.51
1699 2165 4.093556 GCACTTACACATCAACTCTAAGCC 59.906 45.833 0.00 0.00 0.00 4.35
1719 2185 3.319122 ACTGAGAAAAACAGGGATTGCAC 59.681 43.478 0.00 0.00 39.38 4.57
1723 2189 5.310409 TCTGACTGAGAAAAACAGGGATT 57.690 39.130 0.00 0.00 39.38 3.01
1725 2191 4.771114 TTCTGACTGAGAAAAACAGGGA 57.229 40.909 0.00 0.00 37.78 4.20
1739 2205 1.331756 CAAGCAACGCTGTTTCTGACT 59.668 47.619 0.00 0.00 39.62 3.41
1752 2218 4.946784 ACATACGGAATTCTCAAGCAAC 57.053 40.909 5.23 0.00 0.00 4.17
1781 2247 4.765339 AGACACCAAAGCAATAACCCTAAC 59.235 41.667 0.00 0.00 0.00 2.34
1796 2262 1.885887 GCATTAAGCACCAGACACCAA 59.114 47.619 0.00 0.00 44.79 3.67
1825 2291 7.377928 CGATCAATTGCAAGATCCATAAGTTTC 59.622 37.037 18.13 0.00 37.87 2.78
1830 2296 6.290605 TCTCGATCAATTGCAAGATCCATAA 58.709 36.000 18.13 5.75 37.87 1.90
1835 2301 4.084433 GCTCTCTCGATCAATTGCAAGATC 60.084 45.833 15.38 15.38 37.79 2.75
1846 2312 3.942130 TGTCAAAAGCTCTCTCGATCA 57.058 42.857 0.00 0.00 0.00 2.92
1849 2315 5.784177 ACTTTATGTCAAAAGCTCTCTCGA 58.216 37.500 0.00 0.00 39.59 4.04
1863 2331 7.759886 GCCCTTGGAAGATAAAAACTTTATGTC 59.240 37.037 0.00 0.00 0.00 3.06
1864 2332 7.576856 CGCCCTTGGAAGATAAAAACTTTATGT 60.577 37.037 0.00 0.00 0.00 2.29
1865 2333 6.751888 CGCCCTTGGAAGATAAAAACTTTATG 59.248 38.462 0.00 0.00 0.00 1.90
1866 2334 6.627287 GCGCCCTTGGAAGATAAAAACTTTAT 60.627 38.462 0.00 0.00 0.00 1.40
1867 2335 5.336134 GCGCCCTTGGAAGATAAAAACTTTA 60.336 40.000 0.00 0.00 0.00 1.85
1868 2336 4.560716 GCGCCCTTGGAAGATAAAAACTTT 60.561 41.667 0.00 0.00 0.00 2.66
1874 2346 0.746563 CCGCGCCCTTGGAAGATAAA 60.747 55.000 0.00 0.00 0.00 1.40
1889 2361 6.388259 AAAATGAACATAATTTTGACCGCG 57.612 33.333 0.00 0.00 36.21 6.46
1913 2385 5.965334 CGCTAACATGTCACCAAAATATCAC 59.035 40.000 0.00 0.00 0.00 3.06
1914 2386 5.645929 ACGCTAACATGTCACCAAAATATCA 59.354 36.000 0.00 0.00 0.00 2.15
1915 2387 6.119144 ACGCTAACATGTCACCAAAATATC 57.881 37.500 0.00 0.00 0.00 1.63
1923 2486 1.156736 AGCAACGCTAACATGTCACC 58.843 50.000 0.00 0.00 36.99 4.02
1936 2499 3.242349 GCATCTCTCAGATCAAAGCAACG 60.242 47.826 0.00 0.00 31.32 4.10
1945 2508 2.598686 TGCACAGCATCTCTCAGATC 57.401 50.000 0.00 0.00 31.32 2.75
1950 2513 2.090400 TCACTTGCACAGCATCTCTC 57.910 50.000 0.00 0.00 38.76 3.20
1962 2525 5.488341 TCTAACCAAGGAAGTATCACTTGC 58.512 41.667 2.68 2.68 45.40 4.01
1969 2532 6.195600 TGGTGTTTCTAACCAAGGAAGTAT 57.804 37.500 0.00 0.00 44.72 2.12
2005 2568 9.783081 ATCACAAATATGTACTGCTCATATGAA 57.217 29.630 6.90 0.00 37.82 2.57
2025 2588 7.394077 TGCAGAAAAGAGATGGAATTATCACAA 59.606 33.333 0.00 0.00 0.00 3.33
2026 2589 6.885918 TGCAGAAAAGAGATGGAATTATCACA 59.114 34.615 0.00 0.00 0.00 3.58
2027 2590 7.325660 TGCAGAAAAGAGATGGAATTATCAC 57.674 36.000 0.00 0.00 0.00 3.06
2030 2593 8.707796 ATCATGCAGAAAAGAGATGGAATTAT 57.292 30.769 0.00 0.00 0.00 1.28
2031 2594 7.997223 AGATCATGCAGAAAAGAGATGGAATTA 59.003 33.333 0.00 0.00 0.00 1.40
2032 2595 6.834451 AGATCATGCAGAAAAGAGATGGAATT 59.166 34.615 0.00 0.00 0.00 2.17
2033 2596 6.366340 AGATCATGCAGAAAAGAGATGGAAT 58.634 36.000 0.00 0.00 0.00 3.01
2063 2633 9.440761 GATCCTCCCTATATAACTATTCCATGT 57.559 37.037 0.00 0.00 0.00 3.21
2082 2652 8.212312 AGATATAAATGCATCAGATGATCCTCC 58.788 37.037 15.12 0.00 31.21 4.30
2126 2696 5.882557 CCTAAACTGATAAAGGCACACTCAT 59.117 40.000 0.00 0.00 0.00 2.90
2127 2697 5.012664 TCCTAAACTGATAAAGGCACACTCA 59.987 40.000 0.00 0.00 0.00 3.41
2145 2715 8.736244 GCTTTGGTTGTGATACTAATTCCTAAA 58.264 33.333 0.00 0.00 0.00 1.85
2176 2746 6.038714 AGCAGCTAAAGTTATAACAGATTGGC 59.961 38.462 17.65 18.99 0.00 4.52
2218 2910 9.996554 AAAAAGGAATTGGTACTTGGATTAAAG 57.003 29.630 0.00 0.00 0.00 1.85
2261 2955 5.745294 CCGCATGAGAAAGGAACAAAATATG 59.255 40.000 0.00 0.00 0.00 1.78
2262 2956 5.652014 TCCGCATGAGAAAGGAACAAAATAT 59.348 36.000 0.00 0.00 0.00 1.28
2269 2971 2.100605 ACTCCGCATGAGAAAGGAAC 57.899 50.000 7.21 0.00 44.42 3.62
2272 2974 2.005451 CTGAACTCCGCATGAGAAAGG 58.995 52.381 7.21 0.00 44.42 3.11
2317 3023 4.044426 GCTGTGACTTGGCTTAAAAGTTG 58.956 43.478 0.00 0.00 37.98 3.16
2323 3029 1.142870 AGTGGCTGTGACTTGGCTTAA 59.857 47.619 4.74 0.00 0.00 1.85
2448 3164 4.211374 CACTTTGAACTGGAAGAGTAACCG 59.789 45.833 0.00 0.00 37.43 4.44
2452 3168 8.974060 AAATAACACTTTGAACTGGAAGAGTA 57.026 30.769 0.00 0.00 37.43 2.59
2479 3195 6.545666 TGTCCACCCATTAGCAAAATATAGTG 59.454 38.462 0.00 0.00 0.00 2.74
2482 3198 6.040391 GCTTGTCCACCCATTAGCAAAATATA 59.960 38.462 0.00 0.00 0.00 0.86
2494 3211 0.538057 CACACAGCTTGTCCACCCAT 60.538 55.000 0.00 0.00 35.67 4.00
2507 3224 8.310406 TCATTTACTATCAAAGACACACACAG 57.690 34.615 0.00 0.00 0.00 3.66
2547 3264 4.010349 ACCAACGGAAAGAAATCATCCTC 58.990 43.478 0.00 0.00 0.00 3.71
2549 3266 4.783764 AACCAACGGAAAGAAATCATCC 57.216 40.909 0.00 0.00 0.00 3.51
2555 3272 5.539048 TGAAACAAAACCAACGGAAAGAAA 58.461 33.333 0.00 0.00 0.00 2.52
2556 3273 5.135508 TGAAACAAAACCAACGGAAAGAA 57.864 34.783 0.00 0.00 0.00 2.52
2557 3274 4.785511 TGAAACAAAACCAACGGAAAGA 57.214 36.364 0.00 0.00 0.00 2.52
2561 3278 3.292460 AGGATGAAACAAAACCAACGGA 58.708 40.909 0.00 0.00 0.00 4.69
2564 3281 6.735678 ACAAAAGGATGAAACAAAACCAAC 57.264 33.333 0.00 0.00 0.00 3.77
2619 3338 9.316730 GCAAACACATTGACCAATCATATAAAT 57.683 29.630 0.00 0.00 41.85 1.40
2620 3339 8.309656 TGCAAACACATTGACCAATCATATAAA 58.690 29.630 0.00 0.00 41.85 1.40
2695 3414 5.057149 ACAAACTTTCTAGCATTGACGACT 58.943 37.500 0.00 0.00 0.00 4.18
2732 5963 1.270274 GACATCAGGTTGCATGCACAA 59.730 47.619 22.58 3.29 0.00 3.33
2941 6172 0.038343 TGCCAAATTTCTTCCGCAGC 60.038 50.000 0.00 0.00 0.00 5.25
3395 6626 6.783977 AGGAACCATTTGCCATCATATACAAT 59.216 34.615 0.00 0.00 0.00 2.71
3609 6840 2.674852 CTGTCCATGAATCTTGTCCACG 59.325 50.000 0.00 0.00 0.00 4.94
3971 7207 3.153919 CCGAGGGGTTCTTTCAAAATCA 58.846 45.455 0.00 0.00 0.00 2.57
3998 7235 1.580059 GGGTACTCCACATTCCAGGA 58.420 55.000 0.00 0.00 35.00 3.86
4110 7491 6.925718 CGCTCTCCTCTTTCATAAACATCATA 59.074 38.462 0.00 0.00 0.00 2.15
4145 7526 6.057533 TGTTCATCTCACAATGAAAGACTGT 58.942 36.000 1.17 0.00 44.83 3.55
4151 7532 5.241506 GGTTCCTGTTCATCTCACAATGAAA 59.758 40.000 1.17 0.00 44.83 2.69
4242 7671 7.087895 AGAAAGACACATCCATGGATATGAT 57.912 36.000 34.42 21.15 36.36 2.45
4247 7676 3.698040 GCAAGAAAGACACATCCATGGAT 59.302 43.478 22.15 22.15 34.81 3.41
4261 7690 5.636543 CCTAATCTGCCAAAAAGCAAGAAAG 59.363 40.000 0.00 0.00 43.52 2.62
4500 7929 7.121168 TCTCAGATAATCATTTTCACCCACAAC 59.879 37.037 0.00 0.00 0.00 3.32
4527 7956 4.055360 TCACTACGAGACCACACAAAATG 58.945 43.478 0.00 0.00 0.00 2.32
4532 7961 1.816835 GGATCACTACGAGACCACACA 59.183 52.381 0.00 0.00 0.00 3.72
4745 8174 3.196469 TCATCTCTTTTGTCCTCTGCGAT 59.804 43.478 0.00 0.00 0.00 4.58
4768 8197 0.389556 ATGCTATCAGCGGCTCATCG 60.390 55.000 0.00 0.00 46.26 3.84
4808 8249 3.004315 CCACAGGTGTGTACAAATGGAAC 59.996 47.826 9.22 0.00 44.21 3.62
4823 8264 0.683973 CTCTGCTCTTGACCACAGGT 59.316 55.000 0.00 0.00 39.44 4.00
4842 8293 0.666913 CAAGTCATGCCCTGCTATGC 59.333 55.000 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.