Multiple sequence alignment - TraesCS4A01G422200

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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 TraesCS4A01G422200 chr4A 100.000 3382 0 0 1 3382 692395370 692391989 0.000000e+00 6246.0
1 TraesCS4A01G422200 chr4A 90.722 1261 106 3 1049 2309 705764475 705763226 0.000000e+00 1670.0
2 TraesCS4A01G422200 chr4A 91.038 915 71 10 1 911 694751408 694752315 0.000000e+00 1225.0
3 TraesCS4A01G422200 chr4A 94.198 586 29 2 1730 2310 694756276 694756861 0.000000e+00 889.0
4 TraesCS4A01G422200 chr4A 94.310 580 31 2 1120 1697 694755703 694756282 0.000000e+00 887.0
5 TraesCS4A01G422200 chr4A 84.642 586 56 15 2649 3224 705757376 705756815 1.370000e-153 553.0
6 TraesCS4A01G422200 chr4A 90.805 87 5 2 2484 2570 705757715 705757632 2.760000e-21 113.0
7 TraesCS4A01G422200 chr4A 94.737 57 3 0 909 965 694755478 694755534 4.650000e-14 89.8
8 TraesCS4A01G422200 chr4A 95.918 49 2 0 1071 1119 694755633 694755681 2.800000e-11 80.5
9 TraesCS4A01G422200 chr7A 92.761 1492 90 10 909 2386 32584131 32582644 0.000000e+00 2141.0
10 TraesCS4A01G422200 chr7A 92.017 238 14 1 679 911 32584392 32584155 2.520000e-86 329.0
11 TraesCS4A01G422200 chr7A 86.603 209 25 3 2690 2896 32582116 32581909 9.440000e-56 228.0
12 TraesCS4A01G422200 chr7A 86.517 89 11 1 3070 3158 32539610 32539523 2.780000e-16 97.1
13 TraesCS4A01G422200 chr7D 92.794 680 48 1 1301 1979 32566455 32565776 0.000000e+00 983.0
14 TraesCS4A01G422200 chr7D 91.019 412 23 1 1975 2386 32559921 32559524 8.250000e-151 544.0
15 TraesCS4A01G422200 chr7D 83.529 340 41 12 2885 3223 32505631 32505306 1.520000e-78 303.0
16 TraesCS4A01G422200 chr7D 92.547 161 11 1 3223 3382 134434668 134434508 2.620000e-56 230.0
17 TraesCS4A01G422200 chr7D 85.946 185 19 3 2718 2897 32505832 32505650 1.240000e-44 191.0
18 TraesCS4A01G422200 chr7D 75.366 410 89 12 5 407 168492926 168492522 1.600000e-43 187.0
19 TraesCS4A01G422200 chr6B 87.116 683 81 7 3 682 141088503 141089181 0.000000e+00 767.0
20 TraesCS4A01G422200 chr1D 86.823 683 80 9 3 682 437687892 437687217 0.000000e+00 754.0
21 TraesCS4A01G422200 chr1D 82.309 667 100 16 24 682 452661949 452662605 2.280000e-156 562.0
22 TraesCS4A01G422200 chr1D 77.480 373 69 14 8 372 451399362 451398997 3.420000e-50 209.0
23 TraesCS4A01G422200 chr6A 83.417 597 84 14 73 664 84901930 84902516 1.070000e-149 540.0
24 TraesCS4A01G422200 chr6D 74.821 699 142 23 8 682 458999182 458999870 5.520000e-73 285.0
25 TraesCS4A01G422200 chr2B 93.210 162 10 1 3222 3382 642972000 642971839 1.570000e-58 237.0
26 TraesCS4A01G422200 chr2B 92.547 161 11 1 3223 3382 73957714 73957554 2.620000e-56 230.0
27 TraesCS4A01G422200 chr2B 92.547 161 10 2 3223 3382 774836972 774837131 2.620000e-56 230.0
28 TraesCS4A01G422200 chr5B 92.593 162 11 1 3222 3382 65968024 65968185 7.300000e-57 231.0
29 TraesCS4A01G422200 chr2D 91.617 167 12 2 3218 3382 636210303 636210469 2.620000e-56 230.0
30 TraesCS4A01G422200 chr2D 91.667 168 9 2 3220 3382 351377208 351377041 9.440000e-56 228.0
31 TraesCS4A01G422200 chr1B 92.547 161 11 1 3223 3382 665819049 665819209 2.620000e-56 230.0
32 TraesCS4A01G422200 chr3D 91.124 169 13 2 3216 3382 352104149 352103981 9.440000e-56 228.0
33 TraesCS4A01G422200 chr3D 76.384 271 54 6 417 682 554356497 554356762 1.640000e-28 137.0
34 TraesCS4A01G422200 chr4D 73.032 686 140 32 23 676 132921302 132921974 2.060000e-47 200.0
35 TraesCS4A01G422200 chr3B 79.681 251 43 6 421 667 828776013 828775767 1.250000e-39 174.0
36 TraesCS4A01G422200 chr3B 72.014 561 119 24 28 563 478328056 478327509 7.610000e-27 132.0
37 TraesCS4A01G422200 chr5D 77.308 260 54 5 410 665 524489168 524489426 7.560000e-32 148.0
38 TraesCS4A01G422200 chr5D 77.519 258 47 10 432 682 545803259 545803006 9.780000e-31 145.0


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 TraesCS4A01G422200 chr4A 692391989 692395370 3381 True 6246.000000 6246 100.000000 1 3382 1 chr4A.!!$R1 3381
1 TraesCS4A01G422200 chr4A 705763226 705764475 1249 True 1670.000000 1670 90.722000 1049 2309 1 chr4A.!!$R2 1260
2 TraesCS4A01G422200 chr4A 694751408 694756861 5453 False 634.260000 1225 94.040200 1 2310 5 chr4A.!!$F1 2309
3 TraesCS4A01G422200 chr4A 705756815 705757715 900 True 333.000000 553 87.723500 2484 3224 2 chr4A.!!$R3 740
4 TraesCS4A01G422200 chr7A 32581909 32584392 2483 True 899.333333 2141 90.460333 679 2896 3 chr7A.!!$R2 2217
5 TraesCS4A01G422200 chr7D 32565776 32566455 679 True 983.000000 983 92.794000 1301 1979 1 chr7D.!!$R2 678
6 TraesCS4A01G422200 chr7D 32505306 32505832 526 True 247.000000 303 84.737500 2718 3223 2 chr7D.!!$R5 505
7 TraesCS4A01G422200 chr6B 141088503 141089181 678 False 767.000000 767 87.116000 3 682 1 chr6B.!!$F1 679
8 TraesCS4A01G422200 chr1D 437687217 437687892 675 True 754.000000 754 86.823000 3 682 1 chr1D.!!$R1 679
9 TraesCS4A01G422200 chr1D 452661949 452662605 656 False 562.000000 562 82.309000 24 682 1 chr1D.!!$F1 658
10 TraesCS4A01G422200 chr6A 84901930 84902516 586 False 540.000000 540 83.417000 73 664 1 chr6A.!!$F1 591
11 TraesCS4A01G422200 chr6D 458999182 458999870 688 False 285.000000 285 74.821000 8 682 1 chr6D.!!$F1 674

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
76 105 0.256464 ACAACAAAAGGTCGGTCCCA 59.744 50.0 0.0 0.0 36.75 4.37 F
1157 4499 0.250513 GTCACCTTGGAAGCCTCGAT 59.749 55.0 0.0 0.0 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 4834 0.178767 CCACTCATTGATCTCGGCCA 59.821 55.0 2.24 0.0 0.0 5.36 R
2408 5761 0.110373 CCTTCCAACTTAACGCGTGC 60.110 55.0 14.98 0.0 0.0 5.34 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
41 70 1.080705 CCGGTTGTGAGTCGAGGAC 60.081 63.158 0.00 0.00 0.00 3.85
55 84 1.569479 GAGGACGGACTTGCAACTGC 61.569 60.000 0.00 0.00 42.50 4.40
61 90 0.317020 GGACTTGCAACTGCGACAAC 60.317 55.000 0.00 0.00 45.83 3.32
76 105 0.256464 ACAACAAAAGGTCGGTCCCA 59.744 50.000 0.00 0.00 36.75 4.37
103 133 6.110033 TGTTAGTTGAGAGTGCACTTACAAA 58.890 36.000 28.13 17.81 0.00 2.83
105 135 5.679734 AGTTGAGAGTGCACTTACAAATG 57.320 39.130 28.13 0.00 0.00 2.32
109 140 1.818674 GAGTGCACTTACAAATGGGGG 59.181 52.381 22.65 0.00 0.00 5.40
121 152 4.713553 ACAAATGGGGGAAAAATGTTGTC 58.286 39.130 0.00 0.00 0.00 3.18
126 157 2.024176 GGGAAAAATGTTGTCCCCCT 57.976 50.000 5.03 0.00 44.69 4.79
155 186 3.817647 AGTCAAGGATGAACTTGCAACTC 59.182 43.478 0.00 0.00 45.72 3.01
306 390 2.926200 CGAGTTGAAGGTAGACATGCAG 59.074 50.000 0.00 0.00 0.00 4.41
314 398 0.807667 GTAGACATGCAGCTGGGACG 60.808 60.000 17.12 0.00 0.00 4.79
351 436 3.434641 CCTAGTTACGAGTCGAGTGTGAA 59.565 47.826 21.50 0.40 0.00 3.18
353 438 3.625938 AGTTACGAGTCGAGTGTGAAAC 58.374 45.455 21.50 10.69 37.35 2.78
360 445 1.663643 GTCGAGTGTGAAACTGCAACA 59.336 47.619 0.00 0.00 40.07 3.33
362 447 1.933181 CGAGTGTGAAACTGCAACAGA 59.067 47.619 0.78 0.00 40.07 3.41
414 515 3.524095 TGATGGTGGACTTTTGGTCAT 57.476 42.857 0.00 0.00 46.16 3.06
443 544 5.413833 CAGTTACGAGTAGAGGGTGAACTTA 59.586 44.000 0.00 0.00 0.00 2.24
496 599 0.393077 CGAGTCAAGGGTGGACTTGT 59.607 55.000 5.92 0.00 45.21 3.16
562 667 3.321968 GGACTTGCAACTGGGAGAAAAAT 59.678 43.478 0.00 0.00 0.00 1.82
604 711 0.954452 GGGTGAACTTGCAACTGAGG 59.046 55.000 0.00 0.00 0.00 3.86
620 727 1.353022 TGAGGCAAAAATAGGTCGGGT 59.647 47.619 0.00 0.00 0.00 5.28
710 820 6.665992 AACGGCTAATATCAATCTAGGACA 57.334 37.500 0.00 0.00 0.00 4.02
794 904 9.851686 TTGCTTATGAGTGAAGGTTTGATATAT 57.148 29.630 0.00 0.00 0.00 0.86
876 991 7.102346 CCATTTATTTTGTTTCTACATGGGCA 58.898 34.615 0.00 0.00 33.44 5.36
893 1008 3.165890 GGGCACGCGTTTAGTAATTTTC 58.834 45.455 10.22 0.00 0.00 2.29
939 4223 6.818644 TGCTTATGACTTATGAGTGAAGGTTC 59.181 38.462 0.00 0.00 35.88 3.62
988 4300 4.020543 GCAGTATAAATTGGGGTGGTCAA 58.979 43.478 0.00 0.00 0.00 3.18
994 4306 4.787135 AAATTGGGGTGGTCAACAAAAT 57.213 36.364 0.00 0.00 0.00 1.82
1004 4316 6.377146 GGGTGGTCAACAAAATATGTGACTAT 59.623 38.462 0.00 0.00 42.99 2.12
1005 4317 7.415206 GGGTGGTCAACAAAATATGTGACTATC 60.415 40.741 0.00 0.00 42.99 2.08
1006 4318 7.336931 GGTGGTCAACAAAATATGTGACTATCT 59.663 37.037 0.00 0.00 42.99 1.98
1009 4321 8.946085 GGTCAACAAAATATGTGACTATCTTGA 58.054 33.333 0.00 0.00 42.99 3.02
1010 4322 9.979270 GTCAACAAAATATGTGACTATCTTGAG 57.021 33.333 0.00 0.00 42.99 3.02
1011 4323 8.668353 TCAACAAAATATGTGACTATCTTGAGC 58.332 33.333 0.00 0.00 42.99 4.26
1012 4324 8.671921 CAACAAAATATGTGACTATCTTGAGCT 58.328 33.333 0.00 0.00 42.99 4.09
1022 4338 5.952347 TGACTATCTTGAGCTTACTCTCCAA 59.048 40.000 0.00 0.00 43.85 3.53
1036 4352 5.643421 ACTCTCCAATTGCTATCCATCTT 57.357 39.130 0.00 0.00 0.00 2.40
1037 4353 5.374921 ACTCTCCAATTGCTATCCATCTTG 58.625 41.667 0.00 0.00 0.00 3.02
1062 4378 9.713684 TGGAAAAACTAATATCCATCTCCATTT 57.286 29.630 0.00 0.00 37.05 2.32
1112 4433 2.047655 GACGCCGTGATGGACCAA 60.048 61.111 0.00 0.00 42.00 3.67
1145 4487 1.985116 GCTCCTCCTCCGTCACCTT 60.985 63.158 0.00 0.00 0.00 3.50
1157 4499 0.250513 GTCACCTTGGAAGCCTCGAT 59.749 55.000 0.00 0.00 0.00 3.59
1274 4616 3.814577 CGACCAGATCGTCACCTTT 57.185 52.632 2.31 0.00 46.25 3.11
1544 4889 1.298859 GCGGCCTCGTCAAGAACATT 61.299 55.000 0.00 0.00 38.89 2.71
1634 4979 0.845102 GGAACTCCCCCTTCTTCCCA 60.845 60.000 0.00 0.00 0.00 4.37
1781 5126 4.446413 CCCTACCGCGGCGACTTT 62.446 66.667 28.58 7.06 0.00 2.66
2201 5547 1.194781 ACTTCGTGGCAGATCACCCT 61.195 55.000 0.00 0.00 34.36 4.34
2246 5596 0.398696 TCAGTGGCGTGGTGGTATTT 59.601 50.000 0.00 0.00 0.00 1.40
2264 5614 0.608856 TTGCAGGCCATGTCGTCAAT 60.609 50.000 5.01 0.00 0.00 2.57
2271 5621 2.083774 GCCATGTCGTCAATCCTTTGA 58.916 47.619 0.00 0.00 39.54 2.69
2281 5631 3.376546 GTCAATCCTTTGAGCCACTGATC 59.623 47.826 0.00 0.00 42.41 2.92
2285 5635 2.159043 TCCTTTGAGCCACTGATCGATC 60.159 50.000 18.72 18.72 0.00 3.69
2323 5673 1.759459 GCTAGCCAGGCCGGAATAGT 61.759 60.000 16.53 0.00 36.56 2.12
2324 5674 0.034059 CTAGCCAGGCCGGAATAGTG 59.966 60.000 16.53 0.00 36.56 2.74
2363 5713 7.219484 ACTGATTTTTCTGTATCCTTGTTGG 57.781 36.000 0.00 0.00 37.10 3.77
2378 5731 1.134340 TGTTGGTGTAACAGCGGAAGT 60.134 47.619 0.00 0.00 44.07 3.01
2380 5733 3.132925 GTTGGTGTAACAGCGGAAGTAA 58.867 45.455 0.00 0.00 39.98 2.24
2386 5739 5.390567 GGTGTAACAGCGGAAGTAAAATGAG 60.391 44.000 0.00 0.00 39.98 2.90
2388 5741 2.778299 ACAGCGGAAGTAAAATGAGCA 58.222 42.857 0.00 0.00 0.00 4.26
2391 5744 1.790481 GCGGAAGTAAAATGAGCACGC 60.790 52.381 0.00 0.00 37.66 5.34
2392 5745 1.526986 CGGAAGTAAAATGAGCACGCG 60.527 52.381 3.53 3.53 0.00 6.01
2393 5746 1.463444 GGAAGTAAAATGAGCACGCGT 59.537 47.619 5.58 5.58 0.00 6.01
2396 5749 4.377635 GGAAGTAAAATGAGCACGCGTTTA 60.378 41.667 10.22 0.11 0.00 2.01
2397 5750 4.322101 AGTAAAATGAGCACGCGTTTAG 57.678 40.909 10.22 0.00 0.00 1.85
2398 5751 3.744426 AGTAAAATGAGCACGCGTTTAGT 59.256 39.130 10.22 3.88 0.00 2.24
2399 5752 4.925054 AGTAAAATGAGCACGCGTTTAGTA 59.075 37.500 10.22 0.00 0.00 1.82
2401 5754 4.939509 AAATGAGCACGCGTTTAGTAAT 57.060 36.364 10.22 0.00 0.00 1.89
2403 5756 4.939509 ATGAGCACGCGTTTAGTAATTT 57.060 36.364 10.22 0.00 0.00 1.82
2404 5757 4.735662 TGAGCACGCGTTTAGTAATTTT 57.264 36.364 10.22 0.00 0.00 1.82
2405 5758 5.842619 TGAGCACGCGTTTAGTAATTTTA 57.157 34.783 10.22 0.00 0.00 1.52
2406 5759 5.849858 TGAGCACGCGTTTAGTAATTTTAG 58.150 37.500 10.22 0.00 0.00 1.85
2407 5760 5.406175 TGAGCACGCGTTTAGTAATTTTAGT 59.594 36.000 10.22 0.00 0.00 2.24
2408 5761 5.614760 AGCACGCGTTTAGTAATTTTAGTG 58.385 37.500 10.22 0.00 0.00 2.74
2409 5762 4.259046 GCACGCGTTTAGTAATTTTAGTGC 59.741 41.667 10.22 0.00 43.06 4.40
2410 5763 5.375717 CACGCGTTTAGTAATTTTAGTGCA 58.624 37.500 10.22 0.00 0.00 4.57
2411 5764 5.279751 CACGCGTTTAGTAATTTTAGTGCAC 59.720 40.000 10.22 9.40 0.00 4.57
2412 5765 4.486025 CGCGTTTAGTAATTTTAGTGCACG 59.514 41.667 12.01 0.00 0.00 5.34
2413 5766 4.259046 GCGTTTAGTAATTTTAGTGCACGC 59.741 41.667 12.01 14.69 39.45 5.34
2414 5767 4.486025 CGTTTAGTAATTTTAGTGCACGCG 59.514 41.667 12.01 3.53 0.00 6.01
2415 5768 5.376537 GTTTAGTAATTTTAGTGCACGCGT 58.623 37.500 5.58 5.58 0.00 6.01
2416 5769 5.594724 TTAGTAATTTTAGTGCACGCGTT 57.405 34.783 10.22 0.00 0.00 4.84
2421 5774 3.948196 TTTTAGTGCACGCGTTAAGTT 57.052 38.095 10.22 0.00 0.00 2.66
2438 5791 7.631377 GCGTTAAGTTGGAAGGGATTACTAGTA 60.631 40.741 0.00 0.00 0.00 1.82
2439 5792 7.919621 CGTTAAGTTGGAAGGGATTACTAGTAG 59.080 40.741 2.23 0.00 0.00 2.57
2441 5794 9.551339 TTAAGTTGGAAGGGATTACTAGTAGAA 57.449 33.333 3.59 0.00 0.00 2.10
2443 5796 7.849160 AGTTGGAAGGGATTACTAGTAGAAAC 58.151 38.462 3.59 0.00 0.00 2.78
2447 5800 8.483758 TGGAAGGGATTACTAGTAGAAACAATC 58.516 37.037 3.59 4.20 0.00 2.67
2448 5801 8.706521 GGAAGGGATTACTAGTAGAAACAATCT 58.293 37.037 3.59 0.00 42.48 2.40
2475 5891 6.961554 CAGAAGCAACTTAATTCGTAATGTCC 59.038 38.462 0.00 0.00 0.00 4.02
2526 5958 6.586082 ACAGTTGTGTTCATTTCAGTTTTGAC 59.414 34.615 0.00 0.00 30.30 3.18
2527 5959 6.808212 CAGTTGTGTTCATTTCAGTTTTGACT 59.192 34.615 0.00 0.00 31.71 3.41
2556 5989 4.981806 TTCAAGTTGTGTAGCTGCTTTT 57.018 36.364 7.79 0.00 0.00 2.27
2578 6011 7.816945 TTTCTCTTTTCTGCTTTTGTTCAAG 57.183 32.000 0.00 0.00 0.00 3.02
2601 6137 4.365514 TGTTGGAAGCAATCTCTTGGTA 57.634 40.909 0.00 0.00 42.08 3.25
2633 6169 5.533528 TGGATCAGCAGATTGTTTATGGATG 59.466 40.000 0.00 0.00 33.72 3.51
2634 6170 5.048224 GGATCAGCAGATTGTTTATGGATGG 60.048 44.000 0.00 0.00 33.72 3.51
2659 6195 0.608130 GGGGTTTGAGGCAATGGTTC 59.392 55.000 0.00 0.00 0.00 3.62
2703 6400 6.381133 TCAGTACTGATGTATGAGGTTCACAT 59.619 38.462 21.74 0.00 35.65 3.21
2729 6506 8.716646 AAAAATAACACTCAAGTTCCCTTTTG 57.283 30.769 0.00 0.00 33.07 2.44
2782 6562 7.568349 TCTGGAATAACTTGTGCATTATCTCT 58.432 34.615 0.00 0.00 0.00 3.10
2798 6580 9.935241 GCATTATCTCTAAATCTGATTGTCCTA 57.065 33.333 3.22 0.00 0.00 2.94
2897 6682 7.120923 TGGGTCCAATTCTTGTAGATACTAC 57.879 40.000 0.00 0.00 0.00 2.73
2899 6684 8.063153 TGGGTCCAATTCTTGTAGATACTACTA 58.937 37.037 9.73 2.58 0.00 1.82
2900 6685 8.358895 GGGTCCAATTCTTGTAGATACTACTAC 58.641 40.741 9.73 0.00 41.90 2.73
2930 6743 0.610232 ACATGTCCAAGGCTCAAGGC 60.610 55.000 0.00 0.00 41.43 4.35
2950 6763 2.292267 CTTGTGCACTCACCCCATATC 58.708 52.381 19.41 0.00 42.46 1.63
2953 6766 2.224606 GTGCACTCACCCCATATCATG 58.775 52.381 10.32 0.00 37.24 3.07
2966 6779 5.286438 CCCATATCATGTTGTGCATTTGAG 58.714 41.667 0.00 0.00 35.19 3.02
2972 6785 5.845103 TCATGTTGTGCATTTGAGTTCAAT 58.155 33.333 0.00 0.00 35.19 2.57
3036 6849 2.869192 CTCTTCTTATCGCCTTTGCTCC 59.131 50.000 0.00 0.00 34.43 4.70
3042 6855 2.440539 ATCGCCTTTGCTCCGTATAG 57.559 50.000 0.00 0.00 34.43 1.31
3043 6856 0.249322 TCGCCTTTGCTCCGTATAGC 60.249 55.000 0.00 0.00 43.08 2.97
3053 6866 2.922758 GCTCCGTATAGCATTCAGTCGG 60.923 54.545 0.00 0.00 42.30 4.79
3056 6869 2.293677 CCGTATAGCATTCAGTCGGTCT 59.706 50.000 0.00 0.00 33.20 3.85
3059 6872 3.651803 ATAGCATTCAGTCGGTCTAGC 57.348 47.619 0.00 0.00 0.00 3.42
3150 6963 4.088648 GCAAAAACGATGTAGAATCACGG 58.911 43.478 0.00 0.00 0.00 4.94
3152 6965 2.596904 AACGATGTAGAATCACGGGG 57.403 50.000 0.00 0.00 0.00 5.73
3189 7002 5.087323 TGAGTTAATGGACTGACCTTCTCT 58.913 41.667 0.00 0.00 39.86 3.10
3190 7004 5.047021 TGAGTTAATGGACTGACCTTCTCTG 60.047 44.000 0.00 0.00 39.86 3.35
3194 7008 0.534873 GGACTGACCTTCTCTGCTCC 59.465 60.000 0.00 0.00 35.41 4.70
3206 7020 2.788807 TCTCTGCTCCCTAATCTCTCCT 59.211 50.000 0.00 0.00 0.00 3.69
3208 7022 1.885887 CTGCTCCCTAATCTCTCCTCG 59.114 57.143 0.00 0.00 0.00 4.63
3209 7023 1.215673 TGCTCCCTAATCTCTCCTCGT 59.784 52.381 0.00 0.00 0.00 4.18
3210 7024 1.883926 GCTCCCTAATCTCTCCTCGTC 59.116 57.143 0.00 0.00 0.00 4.20
3219 7033 5.959583 AATCTCTCCTCGTCCCTAATTTT 57.040 39.130 0.00 0.00 0.00 1.82
3235 7049 7.898014 CCTAATTTTAGGGGAGCAACTAATT 57.102 36.000 8.28 0.00 45.29 1.40
3236 7050 8.990163 CCTAATTTTAGGGGAGCAACTAATTA 57.010 34.615 8.28 0.00 45.29 1.40
3237 7051 9.416284 CCTAATTTTAGGGGAGCAACTAATTAA 57.584 33.333 8.28 0.00 45.29 1.40
3239 7053 6.746745 TTTTAGGGGAGCAACTAATTAACG 57.253 37.500 0.00 0.00 0.00 3.18
3240 7054 5.680594 TTAGGGGAGCAACTAATTAACGA 57.319 39.130 0.00 0.00 0.00 3.85
3241 7055 4.138487 AGGGGAGCAACTAATTAACGAG 57.862 45.455 0.00 0.00 0.00 4.18
3242 7056 2.612672 GGGGAGCAACTAATTAACGAGC 59.387 50.000 0.00 0.00 0.00 5.03
3243 7057 2.284417 GGGAGCAACTAATTAACGAGCG 59.716 50.000 0.00 0.00 0.00 5.03
3244 7058 2.285660 GGAGCAACTAATTAACGAGCGC 60.286 50.000 0.00 0.00 0.00 5.92
3245 7059 2.603560 GAGCAACTAATTAACGAGCGCT 59.396 45.455 11.27 11.27 0.00 5.92
3246 7060 2.603560 AGCAACTAATTAACGAGCGCTC 59.396 45.455 27.64 27.64 0.00 5.03
3247 7061 2.285660 GCAACTAATTAACGAGCGCTCC 60.286 50.000 30.66 13.79 0.00 4.70
3248 7062 3.187700 CAACTAATTAACGAGCGCTCCT 58.812 45.455 30.66 20.33 0.00 3.69
3249 7063 3.521947 ACTAATTAACGAGCGCTCCTT 57.478 42.857 30.66 26.03 0.00 3.36
3250 7064 3.445857 ACTAATTAACGAGCGCTCCTTC 58.554 45.455 30.66 8.16 0.00 3.46
3251 7065 1.278238 AATTAACGAGCGCTCCTTCG 58.722 50.000 30.66 22.24 0.00 3.79
3252 7066 0.527817 ATTAACGAGCGCTCCTTCGG 60.528 55.000 30.66 18.71 0.00 4.30
3253 7067 2.552585 TTAACGAGCGCTCCTTCGGG 62.553 60.000 30.66 17.99 0.00 5.14
3262 7076 2.927856 TCCTTCGGGAGCCTTGCA 60.928 61.111 0.00 0.00 39.58 4.08
3263 7077 2.034066 CCTTCGGGAGCCTTGCAA 59.966 61.111 0.00 0.00 37.25 4.08
3264 7078 2.335712 CCTTCGGGAGCCTTGCAAC 61.336 63.158 0.00 0.00 37.25 4.17
3265 7079 2.668212 TTCGGGAGCCTTGCAACG 60.668 61.111 0.00 0.00 0.00 4.10
3266 7080 3.171828 TTCGGGAGCCTTGCAACGA 62.172 57.895 0.00 0.00 0.00 3.85
3267 7081 2.436646 CGGGAGCCTTGCAACGAT 60.437 61.111 0.00 0.00 0.00 3.73
3268 7082 2.464459 CGGGAGCCTTGCAACGATC 61.464 63.158 5.28 5.28 0.00 3.69
3269 7083 1.377202 GGGAGCCTTGCAACGATCA 60.377 57.895 14.21 0.00 0.00 2.92
3270 7084 1.372087 GGGAGCCTTGCAACGATCAG 61.372 60.000 14.21 0.00 0.00 2.90
3271 7085 1.427020 GAGCCTTGCAACGATCAGC 59.573 57.895 8.54 0.00 0.00 4.26
3273 7087 2.099062 CCTTGCAACGATCAGCGC 59.901 61.111 0.00 0.00 46.04 5.92
3274 7088 2.099062 CTTGCAACGATCAGCGCC 59.901 61.111 2.29 0.00 46.04 6.53
3275 7089 2.667874 TTGCAACGATCAGCGCCA 60.668 55.556 2.29 0.00 46.04 5.69
3276 7090 1.985447 CTTGCAACGATCAGCGCCAT 61.985 55.000 2.29 0.00 46.04 4.40
3277 7091 1.585267 TTGCAACGATCAGCGCCATT 61.585 50.000 2.29 0.00 46.04 3.16
3278 7092 1.137404 GCAACGATCAGCGCCATTT 59.863 52.632 2.29 0.00 46.04 2.32
3279 7093 1.135699 GCAACGATCAGCGCCATTTG 61.136 55.000 2.29 0.00 46.04 2.32
3280 7094 0.523968 CAACGATCAGCGCCATTTGG 60.524 55.000 2.29 0.00 46.04 3.28
3290 7104 3.262936 CCATTTGGCGCGTTCTCA 58.737 55.556 8.43 0.00 0.00 3.27
3291 7105 1.135315 CCATTTGGCGCGTTCTCAG 59.865 57.895 8.43 0.00 0.00 3.35
3292 7106 1.577328 CCATTTGGCGCGTTCTCAGT 61.577 55.000 8.43 0.00 0.00 3.41
3293 7107 0.179215 CATTTGGCGCGTTCTCAGTC 60.179 55.000 8.43 0.00 0.00 3.51
3294 7108 0.602638 ATTTGGCGCGTTCTCAGTCA 60.603 50.000 8.43 0.00 0.00 3.41
3295 7109 0.602638 TTTGGCGCGTTCTCAGTCAT 60.603 50.000 8.43 0.00 0.00 3.06
3296 7110 0.602638 TTGGCGCGTTCTCAGTCATT 60.603 50.000 8.43 0.00 0.00 2.57
3297 7111 1.014044 TGGCGCGTTCTCAGTCATTC 61.014 55.000 8.43 0.00 0.00 2.67
3298 7112 1.341802 GCGCGTTCTCAGTCATTCG 59.658 57.895 8.43 0.00 0.00 3.34
3299 7113 1.341802 CGCGTTCTCAGTCATTCGC 59.658 57.895 0.00 0.00 40.19 4.70
3300 7114 1.710339 GCGTTCTCAGTCATTCGCC 59.290 57.895 0.00 0.00 38.16 5.54
3301 7115 1.014044 GCGTTCTCAGTCATTCGCCA 61.014 55.000 0.00 0.00 38.16 5.69
3302 7116 0.716108 CGTTCTCAGTCATTCGCCAC 59.284 55.000 0.00 0.00 0.00 5.01
3303 7117 0.716108 GTTCTCAGTCATTCGCCACG 59.284 55.000 0.00 0.00 0.00 4.94
3304 7118 0.317160 TTCTCAGTCATTCGCCACGT 59.683 50.000 0.00 0.00 0.00 4.49
3305 7119 0.388520 TCTCAGTCATTCGCCACGTG 60.389 55.000 9.08 9.08 0.00 4.49
3306 7120 0.667487 CTCAGTCATTCGCCACGTGT 60.667 55.000 15.65 0.00 0.00 4.49
3307 7121 0.666274 TCAGTCATTCGCCACGTGTC 60.666 55.000 15.65 0.00 0.00 3.67
3308 7122 1.733041 AGTCATTCGCCACGTGTCG 60.733 57.895 13.61 13.61 0.00 4.35
3309 7123 3.109547 TCATTCGCCACGTGTCGC 61.110 61.111 15.09 10.47 0.00 5.19
3315 7129 3.913573 GCCACGTGTCGCGCTATG 61.914 66.667 15.65 0.00 46.11 2.23
3316 7130 3.254654 CCACGTGTCGCGCTATGG 61.255 66.667 15.65 2.50 46.11 2.74
3317 7131 3.254654 CACGTGTCGCGCTATGGG 61.255 66.667 7.58 0.00 46.11 4.00
3333 7147 4.018409 GGCGCTCCCTCCAAATTT 57.982 55.556 7.64 0.00 0.00 1.82
3334 7148 2.276869 GGCGCTCCCTCCAAATTTT 58.723 52.632 7.64 0.00 0.00 1.82
3335 7149 1.470051 GGCGCTCCCTCCAAATTTTA 58.530 50.000 7.64 0.00 0.00 1.52
3336 7150 2.031870 GGCGCTCCCTCCAAATTTTAT 58.968 47.619 7.64 0.00 0.00 1.40
3337 7151 2.430694 GGCGCTCCCTCCAAATTTTATT 59.569 45.455 7.64 0.00 0.00 1.40
3338 7152 3.118775 GGCGCTCCCTCCAAATTTTATTT 60.119 43.478 7.64 0.00 0.00 1.40
3339 7153 4.503910 GCGCTCCCTCCAAATTTTATTTT 58.496 39.130 0.00 0.00 0.00 1.82
3340 7154 4.935205 GCGCTCCCTCCAAATTTTATTTTT 59.065 37.500 0.00 0.00 0.00 1.94
3358 7172 2.402640 TTTTATTTTTCCGCACGCGT 57.597 40.000 5.58 5.58 37.81 6.01
3359 7173 2.402640 TTTATTTTTCCGCACGCGTT 57.597 40.000 10.22 0.00 37.81 4.84
3360 7174 2.402640 TTATTTTTCCGCACGCGTTT 57.597 40.000 10.22 0.00 37.81 3.60
3361 7175 2.402640 TATTTTTCCGCACGCGTTTT 57.597 40.000 10.22 0.00 37.81 2.43
3362 7176 0.849579 ATTTTTCCGCACGCGTTTTG 59.150 45.000 10.22 0.00 37.81 2.44
3363 7177 1.140407 TTTTTCCGCACGCGTTTTGG 61.140 50.000 10.22 12.33 37.81 3.28
3364 7178 4.615834 TTCCGCACGCGTTTTGGC 62.616 61.111 10.22 9.51 37.81 4.52
3366 7180 4.622456 CCGCACGCGTTTTGGCTT 62.622 61.111 10.22 0.00 37.81 4.35
3367 7181 2.653766 CGCACGCGTTTTGGCTTT 60.654 55.556 10.22 0.00 34.35 3.51
3368 7182 2.227568 CGCACGCGTTTTGGCTTTT 61.228 52.632 10.22 0.00 34.35 2.27
3369 7183 1.747686 CGCACGCGTTTTGGCTTTTT 61.748 50.000 10.22 0.00 34.35 1.94
3370 7184 1.201343 GCACGCGTTTTGGCTTTTTA 58.799 45.000 10.22 0.00 0.00 1.52
3371 7185 1.588861 GCACGCGTTTTGGCTTTTTAA 59.411 42.857 10.22 0.00 0.00 1.52
3372 7186 2.029365 GCACGCGTTTTGGCTTTTTAAA 59.971 40.909 10.22 0.00 0.00 1.52
3373 7187 3.589314 CACGCGTTTTGGCTTTTTAAAC 58.411 40.909 10.22 0.00 0.00 2.01
3376 7190 3.845231 CGTTTTGGCTTTTTAAACGGG 57.155 42.857 10.48 0.00 46.06 5.28
3377 7191 3.188492 CGTTTTGGCTTTTTAAACGGGT 58.812 40.909 10.48 0.00 46.06 5.28
3378 7192 3.617706 CGTTTTGGCTTTTTAAACGGGTT 59.382 39.130 10.48 0.00 46.06 4.11
3379 7193 4.093115 CGTTTTGGCTTTTTAAACGGGTTT 59.907 37.500 10.48 2.05 46.06 3.27
3380 7194 5.390673 CGTTTTGGCTTTTTAAACGGGTTTT 60.391 36.000 10.48 0.00 46.06 2.43
3381 7195 6.380190 GTTTTGGCTTTTTAAACGGGTTTTT 58.620 32.000 1.70 0.00 34.23 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.036164 CTCACAACCGGGATCCAACA 59.964 55.000 15.23 0.00 0.00 3.33
41 70 1.771073 TTGTCGCAGTTGCAAGTCCG 61.771 55.000 11.45 11.45 42.21 4.79
61 90 0.951558 CAACTGGGACCGACCTTTTG 59.048 55.000 0.00 0.00 38.98 2.44
76 105 4.408182 AGTGCACTCTCAACTAACAACT 57.592 40.909 15.25 0.00 0.00 3.16
103 133 2.265367 GGGACAACATTTTTCCCCCAT 58.735 47.619 0.00 0.00 43.07 4.00
109 140 3.727726 CAACAGGGGGACAACATTTTTC 58.272 45.455 0.00 0.00 0.00 2.29
121 152 1.672356 CTTGACTCGCAACAGGGGG 60.672 63.158 0.00 0.00 31.96 5.40
126 157 2.143122 GTTCATCCTTGACTCGCAACA 58.857 47.619 0.00 0.00 31.96 3.33
155 186 2.004733 GACCCGACCTATTTTTGTCCG 58.995 52.381 0.00 0.00 0.00 4.79
217 301 3.406764 GTCTCACAACTCAGCCTCAATT 58.593 45.455 0.00 0.00 0.00 2.32
218 302 2.611473 CGTCTCACAACTCAGCCTCAAT 60.611 50.000 0.00 0.00 0.00 2.57
226 310 1.609072 CCACTCTCGTCTCACAACTCA 59.391 52.381 0.00 0.00 0.00 3.41
273 357 0.106708 TCAACTCGCAACTGAGGCTT 59.893 50.000 0.00 0.00 40.39 4.35
372 457 2.047179 GCAACTGAGGTCCGACCC 60.047 66.667 14.32 6.53 39.75 4.46
382 468 1.511850 CACCATCAACTCGCAACTGA 58.488 50.000 0.00 0.00 0.00 3.41
414 515 1.471119 CTCTACTCGTAACTGGGGCA 58.529 55.000 0.00 0.00 0.00 5.36
580 687 2.624838 CAGTTGCAAGTTCACCCTTGAT 59.375 45.455 3.38 0.00 43.65 2.57
604 711 2.124277 AGGACCCGACCTATTTTTGC 57.876 50.000 0.00 0.00 38.65 3.68
611 718 1.033746 CGCAACTAGGACCCGACCTA 61.034 60.000 0.00 0.00 41.00 3.08
620 727 0.671472 TCGTCGACTCGCAACTAGGA 60.671 55.000 14.70 0.00 0.00 2.94
794 904 1.756024 CCACCCCAACTTGTACCGA 59.244 57.895 0.00 0.00 0.00 4.69
876 991 5.406175 TGCACTAGAAAATTACTAAACGCGT 59.594 36.000 5.58 5.58 0.00 6.01
893 1008 0.527385 GGAGAGAGCGCTTGCACTAG 60.527 60.000 13.26 0.00 39.77 2.57
939 4223 5.183713 TGAAACCTTCACTCATAAGCAATGG 59.816 40.000 0.00 0.00 33.76 3.16
988 4300 8.798859 AAGCTCAAGATAGTCACATATTTTGT 57.201 30.769 0.00 0.00 39.91 2.83
994 4306 7.229707 GGAGAGTAAGCTCAAGATAGTCACATA 59.770 40.741 0.00 0.00 44.00 2.29
1004 4316 4.019860 AGCAATTGGAGAGTAAGCTCAAGA 60.020 41.667 7.72 0.00 44.00 3.02
1005 4317 4.260170 AGCAATTGGAGAGTAAGCTCAAG 58.740 43.478 7.72 0.00 44.00 3.02
1006 4318 4.292186 AGCAATTGGAGAGTAAGCTCAA 57.708 40.909 7.72 0.00 44.00 3.02
1009 4321 4.410228 TGGATAGCAATTGGAGAGTAAGCT 59.590 41.667 7.72 0.00 34.84 3.74
1010 4322 4.708177 TGGATAGCAATTGGAGAGTAAGC 58.292 43.478 7.72 0.00 0.00 3.09
1011 4323 6.767456 AGATGGATAGCAATTGGAGAGTAAG 58.233 40.000 7.72 0.00 0.00 2.34
1012 4324 6.753913 AGATGGATAGCAATTGGAGAGTAA 57.246 37.500 7.72 0.00 0.00 2.24
1036 4352 9.713684 AAATGGAGATGGATATTAGTTTTTCCA 57.286 29.630 0.00 0.00 42.18 3.53
1062 4378 1.672854 CCTACCATTGACGCGGAGGA 61.673 60.000 12.47 0.00 0.00 3.71
1489 4834 0.178767 CCACTCATTGATCTCGGCCA 59.821 55.000 2.24 0.00 0.00 5.36
1493 4838 3.111838 CTCGAACCACTCATTGATCTCG 58.888 50.000 0.00 0.00 0.00 4.04
1544 4889 1.807165 GCAATCGCGCTCAGAGACA 60.807 57.895 5.56 0.00 0.00 3.41
1653 4998 1.135083 CGAGGCGTTGACATAGAACCT 60.135 52.381 0.00 0.00 0.00 3.50
1654 4999 1.278238 CGAGGCGTTGACATAGAACC 58.722 55.000 0.00 0.00 0.00 3.62
1772 5117 3.777925 CTGTCGCCAAAGTCGCCG 61.778 66.667 0.00 0.00 0.00 6.46
1788 5133 3.284449 GGCAAACAACGGGTCGCT 61.284 61.111 0.00 0.00 0.00 4.93
2201 5547 1.628340 TCCATGAGGAAGAAGGCGAAA 59.372 47.619 0.00 0.00 42.23 3.46
2246 5596 1.002257 ATTGACGACATGGCCTGCA 60.002 52.632 3.32 0.00 0.00 4.41
2264 5614 1.266178 TCGATCAGTGGCTCAAAGGA 58.734 50.000 0.00 0.00 0.00 3.36
2271 5621 2.029828 GGTAATCGATCGATCAGTGGCT 60.030 50.000 29.48 15.23 33.08 4.75
2281 5631 1.000827 AGCAGAGCTGGTAATCGATCG 60.001 52.381 9.36 9.36 39.83 3.69
2285 5635 1.850377 CAGAGCAGAGCTGGTAATCG 58.150 55.000 1.72 0.00 39.88 3.34
2323 5673 8.940768 AAAAATCAGTTACTTTAGCAAAAGCA 57.059 26.923 0.00 0.00 45.06 3.91
2324 5674 9.249457 AGAAAAATCAGTTACTTTAGCAAAAGC 57.751 29.630 0.00 0.00 45.06 3.51
2344 5694 7.339721 TGTTACACCAACAAGGATACAGAAAAA 59.660 33.333 0.00 0.00 44.20 1.94
2347 5697 5.931294 TGTTACACCAACAAGGATACAGAA 58.069 37.500 0.00 0.00 44.20 3.02
2349 5699 4.154195 GCTGTTACACCAACAAGGATACAG 59.846 45.833 0.00 0.00 46.37 2.74
2363 5713 5.600908 TCATTTTACTTCCGCTGTTACAC 57.399 39.130 0.00 0.00 0.00 2.90
2378 5731 5.842619 TTACTAAACGCGTGCTCATTTTA 57.157 34.783 14.98 4.67 0.00 1.52
2380 5733 4.939509 ATTACTAAACGCGTGCTCATTT 57.060 36.364 14.98 4.35 0.00 2.32
2386 5739 4.259046 GCACTAAAATTACTAAACGCGTGC 59.741 41.667 14.98 1.21 37.47 5.34
2388 5741 5.376537 GTGCACTAAAATTACTAAACGCGT 58.623 37.500 5.58 5.58 0.00 6.01
2391 5744 4.486025 CGCGTGCACTAAAATTACTAAACG 59.514 41.667 16.19 0.00 0.00 3.60
2392 5745 5.376537 ACGCGTGCACTAAAATTACTAAAC 58.623 37.500 12.93 0.00 0.00 2.01
2393 5746 5.594724 ACGCGTGCACTAAAATTACTAAA 57.405 34.783 12.93 0.00 0.00 1.85
2396 5749 5.178067 ACTTAACGCGTGCACTAAAATTACT 59.822 36.000 14.98 0.00 0.00 2.24
2397 5750 5.376537 ACTTAACGCGTGCACTAAAATTAC 58.623 37.500 14.98 0.00 0.00 1.89
2398 5751 5.594724 ACTTAACGCGTGCACTAAAATTA 57.405 34.783 14.98 3.79 0.00 1.40
2399 5752 4.477302 ACTTAACGCGTGCACTAAAATT 57.523 36.364 14.98 4.75 0.00 1.82
2401 5754 3.546417 CCAACTTAACGCGTGCACTAAAA 60.546 43.478 14.98 1.36 0.00 1.52
2403 5756 1.527736 CCAACTTAACGCGTGCACTAA 59.472 47.619 14.98 6.74 0.00 2.24
2404 5757 1.141645 CCAACTTAACGCGTGCACTA 58.858 50.000 14.98 0.00 0.00 2.74
2405 5758 0.531090 TCCAACTTAACGCGTGCACT 60.531 50.000 14.98 0.00 0.00 4.40
2406 5759 0.305313 TTCCAACTTAACGCGTGCAC 59.695 50.000 14.98 6.82 0.00 4.57
2407 5760 0.584396 CTTCCAACTTAACGCGTGCA 59.416 50.000 14.98 0.00 0.00 4.57
2408 5761 0.110373 CCTTCCAACTTAACGCGTGC 60.110 55.000 14.98 0.00 0.00 5.34
2409 5762 0.515564 CCCTTCCAACTTAACGCGTG 59.484 55.000 14.98 2.11 0.00 5.34
2410 5763 0.393820 TCCCTTCCAACTTAACGCGT 59.606 50.000 5.58 5.58 0.00 6.01
2411 5764 1.734163 ATCCCTTCCAACTTAACGCG 58.266 50.000 3.53 3.53 0.00 6.01
2412 5765 4.259356 AGTAATCCCTTCCAACTTAACGC 58.741 43.478 0.00 0.00 0.00 4.84
2413 5766 6.637657 ACTAGTAATCCCTTCCAACTTAACG 58.362 40.000 0.00 0.00 0.00 3.18
2414 5767 8.975295 TCTACTAGTAATCCCTTCCAACTTAAC 58.025 37.037 3.76 0.00 0.00 2.01
2415 5768 9.551339 TTCTACTAGTAATCCCTTCCAACTTAA 57.449 33.333 3.76 0.00 0.00 1.85
2416 5769 9.551339 TTTCTACTAGTAATCCCTTCCAACTTA 57.449 33.333 3.76 0.00 0.00 2.24
2421 5774 7.801893 TTGTTTCTACTAGTAATCCCTTCCA 57.198 36.000 3.76 0.00 0.00 3.53
2497 5929 7.961325 AACTGAAATGAACACAACTGTTTTT 57.039 28.000 0.00 0.00 40.93 1.94
2498 5930 7.961325 AAACTGAAATGAACACAACTGTTTT 57.039 28.000 0.00 0.00 40.93 2.43
2501 5933 6.586082 GTCAAAACTGAAATGAACACAACTGT 59.414 34.615 0.00 0.00 0.00 3.55
2526 5958 7.746475 GCAGCTACACAACTTGAAATTACTAAG 59.254 37.037 0.00 0.00 0.00 2.18
2527 5959 7.444183 AGCAGCTACACAACTTGAAATTACTAA 59.556 33.333 0.00 0.00 0.00 2.24
2536 5969 4.199310 AGAAAAGCAGCTACACAACTTGA 58.801 39.130 0.00 0.00 0.00 3.02
2556 5989 6.515272 ACTTGAACAAAAGCAGAAAAGAGA 57.485 33.333 0.00 0.00 0.00 3.10
2578 6011 3.319122 ACCAAGAGATTGCTTCCAACAAC 59.681 43.478 0.00 0.00 32.95 3.32
2633 6169 0.623723 TGCCTCAAACCCCAGATACC 59.376 55.000 0.00 0.00 0.00 2.73
2634 6170 2.507407 TTGCCTCAAACCCCAGATAC 57.493 50.000 0.00 0.00 0.00 2.24
2678 6215 5.714806 TGTGAACCTCATACATCAGTACTGA 59.285 40.000 27.07 27.07 44.59 3.41
2683 6220 8.862325 TTTTTATGTGAACCTCATACATCAGT 57.138 30.769 0.00 0.00 36.52 3.41
2728 6505 5.453198 CCATACAGTCTATACATGCACACCA 60.453 44.000 0.00 0.00 0.00 4.17
2729 6506 4.991056 CCATACAGTCTATACATGCACACC 59.009 45.833 0.00 0.00 0.00 4.16
2897 6682 7.361799 GCCTTGGACATGTTTAGGTTAAAGTAG 60.362 40.741 17.79 0.00 0.00 2.57
2899 6684 5.243060 GCCTTGGACATGTTTAGGTTAAAGT 59.757 40.000 17.79 0.00 0.00 2.66
2900 6685 5.476945 AGCCTTGGACATGTTTAGGTTAAAG 59.523 40.000 17.79 7.04 0.00 1.85
2907 6720 3.441572 CCTTGAGCCTTGGACATGTTTAG 59.558 47.826 0.00 0.00 0.00 1.85
2913 6726 0.407139 AAGCCTTGAGCCTTGGACAT 59.593 50.000 0.00 0.00 45.47 3.06
2916 6729 0.538057 CACAAGCCTTGAGCCTTGGA 60.538 55.000 12.25 0.00 45.47 3.53
2930 6743 2.292267 GATATGGGGTGAGTGCACAAG 58.708 52.381 21.04 0.00 46.96 3.16
2950 6763 5.119588 GGATTGAACTCAAATGCACAACATG 59.880 40.000 0.00 0.00 39.60 3.21
2953 6766 4.619973 TGGATTGAACTCAAATGCACAAC 58.380 39.130 0.00 0.00 39.55 3.32
2966 6779 1.895131 ACAGTGGCCAATGGATTGAAC 59.105 47.619 34.31 6.34 40.14 3.18
2972 6785 2.307496 AATTGACAGTGGCCAATGGA 57.693 45.000 34.31 20.93 33.70 3.41
3036 6849 3.627732 AGACCGACTGAATGCTATACG 57.372 47.619 0.00 0.00 0.00 3.06
3042 6855 2.231215 ATGCTAGACCGACTGAATGC 57.769 50.000 0.00 0.00 0.00 3.56
3043 6856 4.837896 TCTATGCTAGACCGACTGAATG 57.162 45.455 0.00 0.00 0.00 2.67
3056 6869 9.374838 TCGATTAGAACGTATATGTCTATGCTA 57.625 33.333 0.00 0.00 0.00 3.49
3075 6888 9.834628 GAACTAGACTTGGAGATAATCGATTAG 57.165 37.037 21.55 11.34 0.00 1.73
3135 6948 3.588277 CCCCCGTGATTCTACATCG 57.412 57.895 0.00 0.00 0.00 3.84
3150 6963 7.230712 CCATTAACTCAATATAAACACTCCCCC 59.769 40.741 0.00 0.00 0.00 5.40
3152 6965 8.837389 GTCCATTAACTCAATATAAACACTCCC 58.163 37.037 0.00 0.00 0.00 4.30
3157 6970 9.391006 GGTCAGTCCATTAACTCAATATAAACA 57.609 33.333 0.00 0.00 35.97 2.83
3158 6971 9.614792 AGGTCAGTCCATTAACTCAATATAAAC 57.385 33.333 0.00 0.00 39.02 2.01
3162 6975 8.095452 AGAAGGTCAGTCCATTAACTCAATAT 57.905 34.615 0.00 0.00 39.02 1.28
3174 6987 1.261480 GAGCAGAGAAGGTCAGTCCA 58.739 55.000 0.00 0.00 39.02 4.02
3189 7002 1.215673 ACGAGGAGAGATTAGGGAGCA 59.784 52.381 0.00 0.00 0.00 4.26
3190 7004 1.883926 GACGAGGAGAGATTAGGGAGC 59.116 57.143 0.00 0.00 0.00 4.70
3194 7008 2.668144 AGGGACGAGGAGAGATTAGG 57.332 55.000 0.00 0.00 0.00 2.69
3219 7033 4.442472 GCTCGTTAATTAGTTGCTCCCCTA 60.442 45.833 0.00 0.00 0.00 3.53
3224 7038 2.603560 AGCGCTCGTTAATTAGTTGCTC 59.396 45.455 2.64 0.00 0.00 4.26
3225 7039 2.603560 GAGCGCTCGTTAATTAGTTGCT 59.396 45.455 23.61 7.90 31.95 3.91
3226 7040 2.285660 GGAGCGCTCGTTAATTAGTTGC 60.286 50.000 29.81 8.45 0.00 4.17
3227 7041 3.187700 AGGAGCGCTCGTTAATTAGTTG 58.812 45.455 29.81 0.00 0.00 3.16
3228 7042 3.521947 AGGAGCGCTCGTTAATTAGTT 57.478 42.857 29.81 3.47 0.00 2.24
3229 7043 3.445857 GAAGGAGCGCTCGTTAATTAGT 58.554 45.455 36.96 19.55 37.75 2.24
3230 7044 2.468040 CGAAGGAGCGCTCGTTAATTAG 59.532 50.000 36.96 23.67 37.75 1.73
3231 7045 2.456989 CGAAGGAGCGCTCGTTAATTA 58.543 47.619 36.96 0.00 37.75 1.40
3232 7046 1.278238 CGAAGGAGCGCTCGTTAATT 58.722 50.000 36.96 21.28 37.75 1.40
3233 7047 2.959275 CGAAGGAGCGCTCGTTAAT 58.041 52.632 36.96 21.62 37.75 1.40
3234 7048 4.470876 CGAAGGAGCGCTCGTTAA 57.529 55.556 36.96 0.00 37.75 2.01
3247 7061 2.680913 CGTTGCAAGGCTCCCGAAG 61.681 63.158 6.16 0.00 0.00 3.79
3248 7062 2.463589 ATCGTTGCAAGGCTCCCGAA 62.464 55.000 14.22 0.00 0.00 4.30
3249 7063 2.852495 GATCGTTGCAAGGCTCCCGA 62.852 60.000 14.22 11.74 0.00 5.14
3250 7064 2.436646 ATCGTTGCAAGGCTCCCG 60.437 61.111 14.22 6.41 0.00 5.14
3251 7065 1.372087 CTGATCGTTGCAAGGCTCCC 61.372 60.000 17.51 6.71 0.00 4.30
3252 7066 1.986575 GCTGATCGTTGCAAGGCTCC 61.987 60.000 17.51 8.73 0.00 4.70
3253 7067 1.427020 GCTGATCGTTGCAAGGCTC 59.573 57.895 14.22 14.31 0.00 4.70
3254 7068 2.393768 CGCTGATCGTTGCAAGGCT 61.394 57.895 14.22 4.59 0.00 4.58
3255 7069 2.099062 CGCTGATCGTTGCAAGGC 59.901 61.111 14.22 2.25 0.00 4.35
3256 7070 2.099062 GCGCTGATCGTTGCAAGG 59.901 61.111 12.91 12.91 41.07 3.61
3257 7071 1.985447 ATGGCGCTGATCGTTGCAAG 61.985 55.000 7.64 0.00 41.07 4.01
3258 7072 1.585267 AATGGCGCTGATCGTTGCAA 61.585 50.000 7.64 0.00 41.07 4.08
3259 7073 1.585267 AAATGGCGCTGATCGTTGCA 61.585 50.000 7.64 0.00 41.07 4.08
3260 7074 1.135699 CAAATGGCGCTGATCGTTGC 61.136 55.000 7.64 0.00 41.07 4.17
3261 7075 0.523968 CCAAATGGCGCTGATCGTTG 60.524 55.000 7.64 3.72 41.07 4.10
3262 7076 1.802636 CCAAATGGCGCTGATCGTT 59.197 52.632 7.64 0.00 41.07 3.85
3263 7077 3.501396 CCAAATGGCGCTGATCGT 58.499 55.556 7.64 0.00 41.07 3.73
3273 7087 1.135315 CTGAGAACGCGCCAAATGG 59.865 57.895 5.73 0.00 38.53 3.16
3274 7088 0.179215 GACTGAGAACGCGCCAAATG 60.179 55.000 5.73 0.00 0.00 2.32
3275 7089 0.602638 TGACTGAGAACGCGCCAAAT 60.603 50.000 5.73 0.00 0.00 2.32
3276 7090 0.602638 ATGACTGAGAACGCGCCAAA 60.603 50.000 5.73 0.00 0.00 3.28
3277 7091 0.602638 AATGACTGAGAACGCGCCAA 60.603 50.000 5.73 0.00 0.00 4.52
3278 7092 1.005037 AATGACTGAGAACGCGCCA 60.005 52.632 5.73 0.00 0.00 5.69
3279 7093 1.710339 GAATGACTGAGAACGCGCC 59.290 57.895 5.73 0.00 0.00 6.53
3280 7094 1.341802 CGAATGACTGAGAACGCGC 59.658 57.895 5.73 0.00 0.00 6.86
3281 7095 1.341802 GCGAATGACTGAGAACGCG 59.658 57.895 3.53 3.53 37.06 6.01
3282 7096 1.014044 TGGCGAATGACTGAGAACGC 61.014 55.000 0.00 0.00 44.18 4.84
3283 7097 0.716108 GTGGCGAATGACTGAGAACG 59.284 55.000 0.00 0.00 0.00 3.95
3284 7098 0.716108 CGTGGCGAATGACTGAGAAC 59.284 55.000 0.00 0.00 0.00 3.01
3285 7099 0.317160 ACGTGGCGAATGACTGAGAA 59.683 50.000 0.00 0.00 0.00 2.87
3286 7100 0.388520 CACGTGGCGAATGACTGAGA 60.389 55.000 7.95 0.00 0.00 3.27
3287 7101 0.667487 ACACGTGGCGAATGACTGAG 60.667 55.000 21.57 0.00 0.00 3.35
3288 7102 0.666274 GACACGTGGCGAATGACTGA 60.666 55.000 21.57 0.00 0.00 3.41
3289 7103 1.781555 GACACGTGGCGAATGACTG 59.218 57.895 21.57 0.00 0.00 3.51
3290 7104 4.261888 GACACGTGGCGAATGACT 57.738 55.556 21.57 0.00 0.00 3.41
3298 7112 3.913573 CATAGCGCGACACGTGGC 61.914 66.667 21.57 17.52 46.11 5.01
3299 7113 3.254654 CCATAGCGCGACACGTGG 61.255 66.667 21.57 6.15 46.11 4.94
3300 7114 3.254654 CCCATAGCGCGACACGTG 61.255 66.667 15.48 15.48 46.11 4.49
3316 7130 1.470051 TAAAATTTGGAGGGAGCGCC 58.530 50.000 2.29 0.00 0.00 6.53
3317 7131 3.801114 AATAAAATTTGGAGGGAGCGC 57.199 42.857 0.00 0.00 0.00 5.92
3338 7152 2.728922 ACGCGTGCGGAAAAATAAAAA 58.271 38.095 12.93 0.00 44.69 1.94
3339 7153 2.402640 ACGCGTGCGGAAAAATAAAA 57.597 40.000 12.93 0.00 44.69 1.52
3340 7154 2.402640 AACGCGTGCGGAAAAATAAA 57.597 40.000 14.98 0.00 44.69 1.40
3341 7155 2.402640 AAACGCGTGCGGAAAAATAA 57.597 40.000 14.98 0.00 44.69 1.40
3342 7156 2.044860 CAAAACGCGTGCGGAAAAATA 58.955 42.857 14.98 0.00 44.69 1.40
3343 7157 0.849579 CAAAACGCGTGCGGAAAAAT 59.150 45.000 14.98 0.00 44.69 1.82
3344 7158 1.140407 CCAAAACGCGTGCGGAAAAA 61.140 50.000 14.98 0.00 44.69 1.94
3345 7159 1.586564 CCAAAACGCGTGCGGAAAA 60.587 52.632 14.98 0.00 44.69 2.29
3346 7160 2.024871 CCAAAACGCGTGCGGAAA 59.975 55.556 14.98 0.00 44.69 3.13
3347 7161 4.615834 GCCAAAACGCGTGCGGAA 62.616 61.111 21.99 0.00 44.69 4.30
3349 7163 4.622456 AAGCCAAAACGCGTGCGG 62.622 61.111 14.98 15.28 44.69 5.69
3350 7164 1.747686 AAAAAGCCAAAACGCGTGCG 61.748 50.000 14.98 13.39 46.03 5.34
3351 7165 1.201343 TAAAAAGCCAAAACGCGTGC 58.799 45.000 14.98 12.59 0.00 5.34
3352 7166 3.589314 GTTTAAAAAGCCAAAACGCGTG 58.411 40.909 14.98 0.00 0.00 5.34
3353 7167 2.279397 CGTTTAAAAAGCCAAAACGCGT 59.721 40.909 5.58 5.58 45.83 6.01
3354 7168 2.869636 CGTTTAAAAAGCCAAAACGCG 58.130 42.857 3.53 3.53 45.83 6.01
3357 7171 5.548706 AAACCCGTTTAAAAAGCCAAAAC 57.451 34.783 0.00 0.00 0.00 2.43
3358 7172 6.570672 AAAAACCCGTTTAAAAAGCCAAAA 57.429 29.167 0.00 0.00 31.63 2.44


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

AutoCloner maintained by Alex Coulton.