Multiple sequence alignment - TraesCS2B01G628500

Loading Multiple Alignment...

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 TraesCS2B01G628500 chr2B 100.000 3144 0 0 1 3144 800026280 800029423 0.000000e+00 5806.0
1 TraesCS2B01G628500 chr2B 80.874 183 26 7 1 175 154189068 154188887 5.470000e-28 135.0
2 TraesCS2B01G628500 chr2D 91.480 1561 82 17 704 2232 641608784 641607243 0.000000e+00 2098.0
3 TraesCS2B01G628500 chr2D 87.358 791 72 16 782 1549 641959237 641958452 0.000000e+00 881.0
4 TraesCS2B01G628500 chr2D 89.362 705 50 14 1545 2238 641957919 641957229 0.000000e+00 863.0
5 TraesCS2B01G628500 chr2D 89.205 704 53 13 1545 2238 597904040 597903350 0.000000e+00 857.0
6 TraesCS2B01G628500 chr2D 86.564 454 32 13 782 1222 597922959 597922522 1.020000e-129 473.0
7 TraesCS2B01G628500 chr2D 94.881 293 15 0 1257 1549 597904891 597904599 2.860000e-125 459.0
8 TraesCS2B01G628500 chr2D 85.034 294 32 11 2286 2572 641607232 641606944 3.970000e-74 289.0
9 TraesCS2B01G628500 chr2D 81.865 193 28 5 1 188 585135813 585135623 4.200000e-34 156.0
10 TraesCS2B01G628500 chr2D 94.667 75 3 1 2631 2705 641606949 641606876 7.130000e-22 115.0
11 TraesCS2B01G628500 chr2A 90.039 1285 83 23 1318 2599 766710120 766708878 0.000000e+00 1622.0
12 TraesCS2B01G628500 chr2A 92.147 573 30 10 677 1237 766710780 766710211 0.000000e+00 795.0
13 TraesCS2B01G628500 chr2A 85.212 683 59 22 1 650 766711445 766710772 0.000000e+00 664.0
14 TraesCS2B01G628500 chr2A 78.404 426 50 19 2601 2987 766708844 766708422 4.050000e-59 239.0
15 TraesCS2B01G628500 chr3B 80.408 245 31 15 1 238 160832750 160832984 1.500000e-38 171.0
16 TraesCS2B01G628500 chr4D 76.751 357 45 22 1 329 451794524 451794870 6.980000e-37 165.0
17 TraesCS2B01G628500 chr7A 82.292 192 28 5 1 188 664165714 664165525 9.020000e-36 161.0
18 TraesCS2B01G628500 chr6A 82.796 186 21 9 1 177 558969829 558969646 4.200000e-34 156.0
19 TraesCS2B01G628500 chr6B 80.711 197 28 6 1 188 664164954 664165149 9.090000e-31 145.0
20 TraesCS2B01G628500 chr4A 81.215 181 27 5 1 175 596675639 596675818 4.230000e-29 139.0
21 TraesCS2B01G628500 chr7D 86.290 124 12 3 116 239 580000603 580000485 2.540000e-26 130.0
22 TraesCS2B01G628500 chr7D 76.140 285 44 16 298 571 178282128 178282399 9.150000e-26 128.0
23 TraesCS2B01G628500 chr5A 78.974 195 33 7 1 188 399304485 399304292 3.290000e-25 126.0
24 TraesCS2B01G628500 chr5A 78.808 151 19 11 266 411 546505602 546505744 4.320000e-14 89.8


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 TraesCS2B01G628500 chr2B 800026280 800029423 3143 False 5806 5806 100.000000 1 3144 1 chr2B.!!$F1 3143
1 TraesCS2B01G628500 chr2D 641957229 641959237 2008 True 872 881 88.360000 782 2238 2 chr2D.!!$R5 1456
2 TraesCS2B01G628500 chr2D 641606876 641608784 1908 True 834 2098 90.393667 704 2705 3 chr2D.!!$R4 2001
3 TraesCS2B01G628500 chr2D 597903350 597904891 1541 True 658 857 92.043000 1257 2238 2 chr2D.!!$R3 981
4 TraesCS2B01G628500 chr2A 766708422 766711445 3023 True 830 1622 86.450500 1 2987 4 chr2A.!!$R1 2986

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
891 926 0.036765 CGACCCCGATTTGGAAGTGA 60.037 55.0 0.0 0.0 42.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2540 3773 0.305922 GTGTTAGAGATGCATGCCGC 59.694 55.0 16.68 7.03 42.89 6.53 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
38 39 7.253817 CGTCGAGATCTTCAAAAACTAGATTCC 60.254 40.741 0.00 0.00 0.00 3.01
39 40 7.545965 GTCGAGATCTTCAAAAACTAGATTCCA 59.454 37.037 0.00 0.00 0.00 3.53
93 94 5.556355 AAAATCGGATAGAAAAACGGACC 57.444 39.130 0.00 0.00 0.00 4.46
94 95 2.282701 TCGGATAGAAAAACGGACCG 57.717 50.000 13.61 13.61 40.16 4.79
98 99 3.432933 CGGATAGAAAAACGGACCGAAAA 59.567 43.478 23.38 0.00 41.09 2.29
99 100 4.083908 CGGATAGAAAAACGGACCGAAAAA 60.084 41.667 23.38 0.00 41.09 1.94
154 156 3.414700 CACGGTTGTGCCTCTCGC 61.415 66.667 0.00 0.00 39.67 5.03
247 250 4.874977 GCCGTGCCTACCTCTCGC 62.875 72.222 0.00 0.00 0.00 5.03
252 255 2.413765 GCCTACCTCTCGCGGAAG 59.586 66.667 6.13 3.71 0.00 3.46
333 337 2.602257 CATAACCATGCCTCTCGTGA 57.398 50.000 0.00 0.00 33.49 4.35
334 338 2.905075 CATAACCATGCCTCTCGTGAA 58.095 47.619 0.00 0.00 33.49 3.18
336 340 1.813513 AACCATGCCTCTCGTGAAAG 58.186 50.000 0.00 0.00 33.49 2.62
351 374 3.724257 CGTGAAAGCGGAAGAAAGAAAAC 59.276 43.478 0.00 0.00 0.00 2.43
361 384 5.227184 CGGAAGAAAGAAAACAGAAAACACG 59.773 40.000 0.00 0.00 0.00 4.49
434 459 2.542595 GTGACTCGCGGAAGAAAAGAAA 59.457 45.455 6.13 0.00 0.00 2.52
463 488 6.976636 TTTTTCGTGCAAGAAAAGGAATTT 57.023 29.167 30.08 0.00 46.61 1.82
468 493 6.102663 TCGTGCAAGAAAAGGAATTTGAAAA 58.897 32.000 0.00 0.00 0.00 2.29
469 494 6.591834 TCGTGCAAGAAAAGGAATTTGAAAAA 59.408 30.769 0.00 0.00 0.00 1.94
500 525 2.223479 TGTGCAAAAGCGAAGAAAGACC 60.223 45.455 0.00 0.00 0.00 3.85
501 526 2.020720 TGCAAAAGCGAAGAAAGACCA 58.979 42.857 0.00 0.00 0.00 4.02
510 535 3.064820 GCGAAGAAAGACCAGTGAAAACA 59.935 43.478 0.00 0.00 0.00 2.83
554 582 2.483583 AAATCAAAAACGCGTGCAGA 57.516 40.000 14.98 9.61 0.00 4.26
560 588 4.352039 TCAAAAACGCGTGCAGAAAAATA 58.648 34.783 14.98 0.00 0.00 1.40
591 619 1.112315 ACGCTCTCAGCCTATCCCAG 61.112 60.000 0.00 0.00 38.18 4.45
593 621 1.643310 GCTCTCAGCCTATCCCAGAT 58.357 55.000 0.00 0.00 34.48 2.90
599 627 5.158141 TCTCAGCCTATCCCAGATAATTGT 58.842 41.667 0.00 0.00 0.00 2.71
621 649 1.738350 GGAAGTCTTTAAAGGAGCGCC 59.262 52.381 15.13 0.00 0.00 6.53
640 672 1.407437 CCAATTAGTTGCTCCCGCTCT 60.407 52.381 0.00 0.00 36.97 4.09
641 673 1.667724 CAATTAGTTGCTCCCGCTCTG 59.332 52.381 0.00 0.00 36.97 3.35
642 674 0.179000 ATTAGTTGCTCCCGCTCTGG 59.821 55.000 0.00 0.00 36.97 3.86
643 675 0.902984 TTAGTTGCTCCCGCTCTGGA 60.903 55.000 0.00 0.00 42.00 3.86
649 681 2.438614 TCCCGCTCTGGAGAGTCG 60.439 66.667 5.57 8.92 43.85 4.18
650 682 4.200283 CCCGCTCTGGAGAGTCGC 62.200 72.222 5.57 0.00 43.85 5.19
651 683 3.137459 CCGCTCTGGAGAGTCGCT 61.137 66.667 5.57 0.00 43.85 4.93
652 684 2.407210 CGCTCTGGAGAGTCGCTC 59.593 66.667 5.57 0.00 43.85 5.03
653 685 2.402572 CGCTCTGGAGAGTCGCTCA 61.403 63.158 5.91 0.00 45.81 4.26
654 686 1.138671 GCTCTGGAGAGTCGCTCAC 59.861 63.158 5.91 3.38 45.81 3.51
655 687 1.427419 CTCTGGAGAGTCGCTCACG 59.573 63.158 5.91 0.00 45.81 4.35
656 688 2.202544 CTGGAGAGTCGCTCACGC 60.203 66.667 5.91 0.00 45.81 5.34
657 689 3.691744 CTGGAGAGTCGCTCACGCC 62.692 68.421 5.91 7.64 45.81 5.68
658 690 3.749064 GGAGAGTCGCTCACGCCA 61.749 66.667 5.91 0.00 45.81 5.69
659 691 2.202544 GAGAGTCGCTCACGCCAG 60.203 66.667 9.09 0.00 43.38 4.85
660 692 4.427661 AGAGTCGCTCACGCCAGC 62.428 66.667 9.09 0.00 39.84 4.85
749 782 2.822637 CCACCAGATGCCGGCCTAT 61.823 63.158 26.77 12.32 0.00 2.57
763 798 5.361857 TGCCGGCCTATATAGAATAGGTTAC 59.638 44.000 26.77 3.75 42.38 2.50
891 926 0.036765 CGACCCCGATTTGGAAGTGA 60.037 55.000 0.00 0.00 42.00 3.41
897 932 2.290323 CCCGATTTGGAAGTGACCTCTT 60.290 50.000 0.00 0.00 42.00 2.85
940 976 1.779025 CTCAGCCGCCAATCCAATCG 61.779 60.000 0.00 0.00 0.00 3.34
942 978 1.077787 AGCCGCCAATCCAATCGAA 60.078 52.632 0.00 0.00 0.00 3.71
945 981 0.593128 CCGCCAATCCAATCGAATCC 59.407 55.000 0.00 0.00 0.00 3.01
946 982 0.235665 CGCCAATCCAATCGAATCCG 59.764 55.000 0.00 0.00 37.07 4.18
947 983 0.040067 GCCAATCCAATCGAATCCGC 60.040 55.000 0.00 0.00 35.37 5.54
948 984 0.593128 CCAATCCAATCGAATCCGCC 59.407 55.000 0.00 0.00 35.37 6.13
949 985 0.593128 CAATCCAATCGAATCCGCCC 59.407 55.000 0.00 0.00 35.37 6.13
950 986 0.884704 AATCCAATCGAATCCGCCCG 60.885 55.000 0.00 0.00 35.37 6.13
952 988 3.649986 CAATCGAATCCGCCCGCC 61.650 66.667 0.00 0.00 35.37 6.13
957 993 4.256180 GAATCCGCCCGCCCAGAT 62.256 66.667 0.00 0.00 0.00 2.90
1106 1171 3.736100 CGGCCGCATGCTCAACAA 61.736 61.111 14.67 0.00 40.92 2.83
1115 1180 1.067295 ATGCTCAACAACCTCCAGGA 58.933 50.000 0.00 0.00 38.94 3.86
1247 1339 2.991250 ACACTTCCCCGATGAATCAAG 58.009 47.619 0.00 0.00 0.00 3.02
1665 2873 4.864334 CGGCAGGGACATGAGGGC 62.864 72.222 0.00 0.00 0.00 5.19
1666 2874 4.512914 GGCAGGGACATGAGGGCC 62.513 72.222 0.00 0.00 0.00 5.80
1833 3045 3.072468 CGCCTCCAAGGTCCCGTA 61.072 66.667 0.00 0.00 37.80 4.02
1973 3188 1.376424 AAGCATGCGACACCTCAGG 60.376 57.895 13.01 0.00 0.00 3.86
1974 3189 3.503363 GCATGCGACACCTCAGGC 61.503 66.667 0.00 0.00 32.85 4.85
1975 3190 2.267006 CATGCGACACCTCAGGCT 59.733 61.111 0.00 0.00 0.00 4.58
1980 3195 2.125753 GACACCTCAGGCTCAGCG 60.126 66.667 0.00 0.00 0.00 5.18
2211 3438 4.910195 TCAGTTTGTTGGAGCTCATGTAT 58.090 39.130 17.19 0.00 0.00 2.29
2214 3441 6.939730 TCAGTTTGTTGGAGCTCATGTATTAA 59.060 34.615 17.19 0.00 0.00 1.40
2215 3442 7.023575 CAGTTTGTTGGAGCTCATGTATTAAC 58.976 38.462 17.19 10.06 0.00 2.01
2238 3465 8.890124 AACAACAACATTCATTCATTCATTCA 57.110 26.923 0.00 0.00 0.00 2.57
2239 3466 9.496873 AACAACAACATTCATTCATTCATTCAT 57.503 25.926 0.00 0.00 0.00 2.57
2250 3477 8.508875 TCATTCATTCATTCATCCGATGTATTG 58.491 33.333 8.24 5.26 0.00 1.90
2251 3478 6.245115 TCATTCATTCATCCGATGTATTGC 57.755 37.500 8.24 0.00 0.00 3.56
2252 3479 5.999600 TCATTCATTCATCCGATGTATTGCT 59.000 36.000 8.24 0.00 0.00 3.91
2253 3480 7.160726 TCATTCATTCATCCGATGTATTGCTA 58.839 34.615 8.24 0.00 0.00 3.49
2254 3481 7.332678 TCATTCATTCATCCGATGTATTGCTAG 59.667 37.037 8.24 0.00 0.00 3.42
2255 3482 6.101650 TCATTCATCCGATGTATTGCTAGT 57.898 37.500 8.24 0.00 0.00 2.57
2256 3483 6.524734 TCATTCATCCGATGTATTGCTAGTT 58.475 36.000 8.24 0.00 0.00 2.24
2257 3484 6.992123 TCATTCATCCGATGTATTGCTAGTTT 59.008 34.615 8.24 0.00 0.00 2.66
2258 3485 8.147704 TCATTCATCCGATGTATTGCTAGTTTA 58.852 33.333 8.24 0.00 0.00 2.01
2259 3486 7.709269 TTCATCCGATGTATTGCTAGTTTAC 57.291 36.000 8.24 0.00 0.00 2.01
2260 3487 7.050970 TCATCCGATGTATTGCTAGTTTACT 57.949 36.000 8.24 0.00 0.00 2.24
2276 3503 9.064706 GCTAGTTTACTACTACCACTCATCATA 57.935 37.037 0.00 0.00 38.33 2.15
2278 3505 8.466617 AGTTTACTACTACCACTCATCATAGG 57.533 38.462 0.00 0.00 34.56 2.57
2279 3506 8.060075 AGTTTACTACTACCACTCATCATAGGT 58.940 37.037 0.00 0.00 34.56 3.08
2280 3507 8.693625 GTTTACTACTACCACTCATCATAGGTT 58.306 37.037 0.00 0.00 35.62 3.50
2281 3508 9.925545 TTTACTACTACCACTCATCATAGGTTA 57.074 33.333 0.00 0.00 35.62 2.85
2282 3509 9.925545 TTACTACTACCACTCATCATAGGTTAA 57.074 33.333 0.00 0.00 35.62 2.01
2283 3510 8.834004 ACTACTACCACTCATCATAGGTTAAA 57.166 34.615 0.00 0.00 35.62 1.52
2284 3511 8.915036 ACTACTACCACTCATCATAGGTTAAAG 58.085 37.037 0.00 0.00 35.62 1.85
2356 3588 4.512484 TGATAGCGTTGGTTTGATGATCA 58.488 39.130 0.00 0.00 0.00 2.92
2365 3597 7.083858 CGTTGGTTTGATGATCAACTACAATT 58.916 34.615 7.48 0.00 35.89 2.32
2374 3606 2.333926 TCAACTACAATTCGTGGCTCG 58.666 47.619 1.94 1.94 41.41 5.03
2408 3640 2.036958 TGGCACTATCAAATGACCGG 57.963 50.000 0.00 0.00 0.00 5.28
2409 3641 1.280710 TGGCACTATCAAATGACCGGT 59.719 47.619 6.92 6.92 0.00 5.28
2413 3645 4.377021 GCACTATCAAATGACCGGTGATA 58.623 43.478 14.63 11.77 34.01 2.15
2416 3648 2.325583 TCAAATGACCGGTGATAGCC 57.674 50.000 14.63 0.00 0.00 3.93
2457 3689 8.785468 TTTACTACGCATTTTCTTTTTACCAC 57.215 30.769 0.00 0.00 0.00 4.16
2467 3699 9.965824 CATTTTCTTTTTACCACTATGTTCAGT 57.034 29.630 0.00 0.00 0.00 3.41
2534 3767 6.758886 AGAACAGATGTATTCCTCGATTCAAC 59.241 38.462 0.00 0.00 0.00 3.18
2538 3771 6.199908 CAGATGTATTCCTCGATTCAACTCAC 59.800 42.308 0.00 0.00 0.00 3.51
2540 3773 5.410924 TGTATTCCTCGATTCAACTCACTG 58.589 41.667 0.00 0.00 0.00 3.66
2543 3776 0.994995 CTCGATTCAACTCACTGCGG 59.005 55.000 0.00 0.00 0.00 5.69
2544 3777 1.014044 TCGATTCAACTCACTGCGGC 61.014 55.000 0.00 0.00 0.00 6.53
2545 3778 1.291184 CGATTCAACTCACTGCGGCA 61.291 55.000 1.29 1.29 0.00 5.69
2546 3779 1.089920 GATTCAACTCACTGCGGCAT 58.910 50.000 1.75 0.00 0.00 4.40
2561 3794 1.596260 CGGCATGCATCTCTAACACAG 59.404 52.381 21.36 0.00 0.00 3.66
2562 3795 2.739609 CGGCATGCATCTCTAACACAGA 60.740 50.000 21.36 0.00 0.00 3.41
2574 3807 3.709653 TCTAACACAGACCCTCAAACTGT 59.290 43.478 0.00 0.00 44.15 3.55
2586 3819 3.242870 CCTCAAACTGTCTGCAACTGTTC 60.243 47.826 17.65 0.00 45.89 3.18
2599 3832 1.597027 CTGTTCGAACTGGGCGGTT 60.597 57.895 27.32 0.00 0.00 4.44
2604 3869 0.464013 TCGAACTGGGCGGTTCAAAA 60.464 50.000 17.55 4.59 43.92 2.44
2608 3873 2.351706 ACTGGGCGGTTCAAAACTAA 57.648 45.000 0.00 0.00 0.00 2.24
2612 3877 1.612676 GGCGGTTCAAAACTAAGGGT 58.387 50.000 0.00 0.00 0.00 4.34
2626 3891 2.922503 GGGTTGGGGCTTTGTGGG 60.923 66.667 0.00 0.00 0.00 4.61
2638 3903 0.741915 TTTGTGGGCGTTCAAACCTC 59.258 50.000 0.00 0.00 0.00 3.85
2706 3971 3.461773 CCGCGTCCTCTCCCATGT 61.462 66.667 4.92 0.00 0.00 3.21
2710 3975 0.460987 GCGTCCTCTCCCATGTCAAG 60.461 60.000 0.00 0.00 0.00 3.02
2777 4042 3.244700 GCAGGATGGCTATCTACCACATT 60.245 47.826 10.15 0.00 40.82 2.71
2782 4047 4.137116 TGGCTATCTACCACATTCACAC 57.863 45.455 0.00 0.00 30.29 3.82
2783 4048 3.774766 TGGCTATCTACCACATTCACACT 59.225 43.478 0.00 0.00 30.29 3.55
2793 4070 1.303888 ATTCACACTGGCTGCCTGG 60.304 57.895 26.30 17.97 0.00 4.45
2794 4071 1.782201 ATTCACACTGGCTGCCTGGA 61.782 55.000 26.30 13.32 0.00 3.86
2811 4089 3.009723 CTGGAGGCATGAAAACATACGT 58.990 45.455 0.00 0.00 0.00 3.57
2832 4110 2.158813 TGTTGGAGAAACCCACTCTGAC 60.159 50.000 0.00 0.00 38.06 3.51
2844 4122 3.602513 CTCTGACGCCTGCTTGCCT 62.603 63.158 0.00 0.00 0.00 4.75
2846 4124 2.203337 TGACGCCTGCTTGCCTTT 60.203 55.556 0.00 0.00 0.00 3.11
2848 4126 2.519302 ACGCCTGCTTGCCTTTGT 60.519 55.556 0.00 0.00 0.00 2.83
2849 4127 2.256461 CGCCTGCTTGCCTTTGTC 59.744 61.111 0.00 0.00 0.00 3.18
2869 4147 2.073816 CGGTGCCCGCTATTTTATAGG 58.926 52.381 0.56 0.00 41.17 2.57
2873 4164 2.158740 TGCCCGCTATTTTATAGGCACA 60.159 45.455 0.00 0.00 45.08 4.57
2880 4171 3.896648 ATTTTATAGGCACAATCCGCG 57.103 42.857 0.00 0.00 0.00 6.46
2882 4173 0.105964 TTATAGGCACAATCCGCGCT 59.894 50.000 5.56 0.00 0.00 5.92
2906 4197 2.202810 CCTTCGCTTCCGCTCCTC 60.203 66.667 0.00 0.00 0.00 3.71
2907 4198 2.573869 CTTCGCTTCCGCTCCTCA 59.426 61.111 0.00 0.00 0.00 3.86
2914 4211 2.099652 CTTCCGCTCCTCACACCACA 62.100 60.000 0.00 0.00 0.00 4.17
2919 4216 1.975327 CTCCTCACACCACATCCGT 59.025 57.895 0.00 0.00 0.00 4.69
2928 4230 0.615331 ACCACATCCGTCATGAAGCT 59.385 50.000 0.00 0.00 36.21 3.74
2932 4234 3.244009 CCACATCCGTCATGAAGCTCTAT 60.244 47.826 0.00 0.00 36.21 1.98
2955 4257 2.164219 GTGACGTGGGATAACCTTACGA 59.836 50.000 19.99 2.90 43.51 3.43
2957 4259 1.133025 ACGTGGGATAACCTTACGACG 59.867 52.381 19.99 9.56 43.51 5.12
2965 4267 2.243602 AACCTTACGACGGAGCAAAA 57.756 45.000 0.00 0.00 0.00 2.44
2970 4272 2.228138 TACGACGGAGCAAAAACACT 57.772 45.000 0.00 0.00 0.00 3.55
2982 4284 4.926238 AGCAAAAACACTATCTCTCGACTG 59.074 41.667 0.00 0.00 0.00 3.51
2987 4289 5.749596 AACACTATCTCTCGACTGATCTG 57.250 43.478 0.00 0.00 0.00 2.90
2988 4290 4.133820 ACACTATCTCTCGACTGATCTGG 58.866 47.826 4.49 0.00 0.00 3.86
2989 4291 4.133820 CACTATCTCTCGACTGATCTGGT 58.866 47.826 4.49 0.00 0.00 4.00
2990 4292 5.163290 ACACTATCTCTCGACTGATCTGGTA 60.163 44.000 4.49 0.00 0.00 3.25
2991 4293 5.937540 CACTATCTCTCGACTGATCTGGTAT 59.062 44.000 4.49 0.00 0.00 2.73
2992 4294 7.100409 CACTATCTCTCGACTGATCTGGTATA 58.900 42.308 4.49 0.00 0.00 1.47
2993 4295 7.604545 CACTATCTCTCGACTGATCTGGTATAA 59.395 40.741 4.49 0.00 0.00 0.98
2994 4296 8.325787 ACTATCTCTCGACTGATCTGGTATAAT 58.674 37.037 4.49 0.00 0.00 1.28
2995 4297 6.809630 TCTCTCGACTGATCTGGTATAATG 57.190 41.667 4.49 0.00 0.00 1.90
2996 4298 6.534634 TCTCTCGACTGATCTGGTATAATGA 58.465 40.000 4.49 0.00 0.00 2.57
2997 4299 6.428465 TCTCTCGACTGATCTGGTATAATGAC 59.572 42.308 4.49 0.00 0.00 3.06
2998 4300 5.473846 TCTCGACTGATCTGGTATAATGACC 59.526 44.000 4.49 0.00 40.21 4.02
3011 4313 8.319057 TGGTATAATGACCAACTCTAATCAGT 57.681 34.615 0.00 0.00 46.70 3.41
3012 4314 8.204160 TGGTATAATGACCAACTCTAATCAGTG 58.796 37.037 0.00 0.00 46.70 3.66
3013 4315 7.171678 GGTATAATGACCAACTCTAATCAGTGC 59.828 40.741 0.00 0.00 39.51 4.40
3014 4316 4.833478 ATGACCAACTCTAATCAGTGCT 57.167 40.909 0.00 0.00 0.00 4.40
3015 4317 4.623932 TGACCAACTCTAATCAGTGCTT 57.376 40.909 0.00 0.00 0.00 3.91
3016 4318 4.569943 TGACCAACTCTAATCAGTGCTTC 58.430 43.478 0.00 0.00 0.00 3.86
3017 4319 3.589988 ACCAACTCTAATCAGTGCTTCG 58.410 45.455 0.00 0.00 0.00 3.79
3018 4320 3.006967 ACCAACTCTAATCAGTGCTTCGT 59.993 43.478 0.00 0.00 0.00 3.85
3019 4321 3.614616 CCAACTCTAATCAGTGCTTCGTC 59.385 47.826 0.00 0.00 0.00 4.20
3020 4322 4.237724 CAACTCTAATCAGTGCTTCGTCA 58.762 43.478 0.00 0.00 0.00 4.35
3021 4323 4.521130 ACTCTAATCAGTGCTTCGTCAA 57.479 40.909 0.00 0.00 0.00 3.18
3022 4324 4.489810 ACTCTAATCAGTGCTTCGTCAAG 58.510 43.478 0.00 0.00 0.00 3.02
3023 4325 4.021894 ACTCTAATCAGTGCTTCGTCAAGT 60.022 41.667 0.00 0.00 31.45 3.16
3024 4326 4.883083 TCTAATCAGTGCTTCGTCAAGTT 58.117 39.130 0.00 0.00 31.45 2.66
3025 4327 5.297547 TCTAATCAGTGCTTCGTCAAGTTT 58.702 37.500 0.00 0.00 31.45 2.66
3026 4328 4.474226 AATCAGTGCTTCGTCAAGTTTC 57.526 40.909 0.00 0.00 31.45 2.78
3027 4329 3.179443 TCAGTGCTTCGTCAAGTTTCT 57.821 42.857 0.00 0.00 31.45 2.52
3028 4330 4.316205 TCAGTGCTTCGTCAAGTTTCTA 57.684 40.909 0.00 0.00 31.45 2.10
3029 4331 4.689071 TCAGTGCTTCGTCAAGTTTCTAA 58.311 39.130 0.00 0.00 31.45 2.10
3030 4332 4.745125 TCAGTGCTTCGTCAAGTTTCTAAG 59.255 41.667 0.00 0.00 31.45 2.18
3031 4333 4.745125 CAGTGCTTCGTCAAGTTTCTAAGA 59.255 41.667 0.00 0.00 31.45 2.10
3032 4334 5.406780 CAGTGCTTCGTCAAGTTTCTAAGAT 59.593 40.000 0.00 0.00 31.45 2.40
3033 4335 6.586463 CAGTGCTTCGTCAAGTTTCTAAGATA 59.414 38.462 0.00 0.00 31.45 1.98
3034 4336 6.809196 AGTGCTTCGTCAAGTTTCTAAGATAG 59.191 38.462 0.00 0.00 31.45 2.08
3035 4337 6.807230 GTGCTTCGTCAAGTTTCTAAGATAGA 59.193 38.462 0.00 0.00 31.45 1.98
3036 4338 6.807230 TGCTTCGTCAAGTTTCTAAGATAGAC 59.193 38.462 0.00 0.00 31.09 2.59
3037 4339 6.807230 GCTTCGTCAAGTTTCTAAGATAGACA 59.193 38.462 0.00 0.00 31.09 3.41
3038 4340 7.328737 GCTTCGTCAAGTTTCTAAGATAGACAA 59.671 37.037 0.00 0.00 31.09 3.18
3039 4341 9.360093 CTTCGTCAAGTTTCTAAGATAGACAAT 57.640 33.333 0.00 0.00 33.84 2.71
3040 4342 8.912787 TCGTCAAGTTTCTAAGATAGACAATC 57.087 34.615 0.00 0.00 33.84 2.67
3041 4343 8.520351 TCGTCAAGTTTCTAAGATAGACAATCA 58.480 33.333 0.00 0.00 37.03 2.57
3042 4344 9.140286 CGTCAAGTTTCTAAGATAGACAATCAA 57.860 33.333 0.00 0.00 37.03 2.57
3047 4349 9.883142 AGTTTCTAAGATAGACAATCAAAGGAG 57.117 33.333 0.00 0.00 37.03 3.69
3048 4350 9.660180 GTTTCTAAGATAGACAATCAAAGGAGT 57.340 33.333 0.00 0.00 37.03 3.85
3049 4351 9.658799 TTTCTAAGATAGACAATCAAAGGAGTG 57.341 33.333 0.00 0.00 44.38 3.51
3050 4352 7.786030 TCTAAGATAGACAATCAAAGGAGTGG 58.214 38.462 0.00 0.00 43.17 4.00
3051 4353 5.365021 AGATAGACAATCAAAGGAGTGGG 57.635 43.478 0.00 0.00 43.17 4.61
3052 4354 4.785376 AGATAGACAATCAAAGGAGTGGGT 59.215 41.667 0.00 0.00 43.17 4.51
3053 4355 3.884037 AGACAATCAAAGGAGTGGGTT 57.116 42.857 0.00 0.00 43.17 4.11
3054 4356 3.756117 AGACAATCAAAGGAGTGGGTTC 58.244 45.455 0.00 0.00 43.17 3.62
3055 4357 3.138283 AGACAATCAAAGGAGTGGGTTCA 59.862 43.478 0.00 0.00 43.17 3.18
3056 4358 3.888930 GACAATCAAAGGAGTGGGTTCAA 59.111 43.478 0.00 0.00 43.17 2.69
3057 4359 4.482990 ACAATCAAAGGAGTGGGTTCAAT 58.517 39.130 0.00 0.00 43.17 2.57
3058 4360 4.901250 ACAATCAAAGGAGTGGGTTCAATT 59.099 37.500 0.00 0.00 43.17 2.32
3059 4361 5.366477 ACAATCAAAGGAGTGGGTTCAATTT 59.634 36.000 0.00 0.00 43.17 1.82
3060 4362 5.728637 ATCAAAGGAGTGGGTTCAATTTC 57.271 39.130 0.00 0.00 0.00 2.17
3061 4363 4.541705 TCAAAGGAGTGGGTTCAATTTCA 58.458 39.130 0.00 0.00 0.00 2.69
3062 4364 4.959210 TCAAAGGAGTGGGTTCAATTTCAA 59.041 37.500 0.00 0.00 0.00 2.69
3063 4365 5.602145 TCAAAGGAGTGGGTTCAATTTCAAT 59.398 36.000 0.00 0.00 0.00 2.57
3064 4366 6.099557 TCAAAGGAGTGGGTTCAATTTCAATT 59.900 34.615 0.00 0.00 0.00 2.32
3065 4367 5.728637 AGGAGTGGGTTCAATTTCAATTC 57.271 39.130 0.00 0.00 0.00 2.17
3066 4368 5.397360 AGGAGTGGGTTCAATTTCAATTCT 58.603 37.500 0.00 0.00 0.00 2.40
3067 4369 6.552008 AGGAGTGGGTTCAATTTCAATTCTA 58.448 36.000 0.00 0.00 0.00 2.10
3068 4370 7.184862 AGGAGTGGGTTCAATTTCAATTCTAT 58.815 34.615 0.00 0.00 0.00 1.98
3069 4371 7.340487 AGGAGTGGGTTCAATTTCAATTCTATC 59.660 37.037 0.00 0.00 0.00 2.08
3070 4372 7.088589 AGTGGGTTCAATTTCAATTCTATCG 57.911 36.000 0.00 0.00 0.00 2.92
3071 4373 6.095440 AGTGGGTTCAATTTCAATTCTATCGG 59.905 38.462 0.00 0.00 0.00 4.18
3072 4374 5.359576 TGGGTTCAATTTCAATTCTATCGGG 59.640 40.000 0.00 0.00 0.00 5.14
3073 4375 5.359860 GGGTTCAATTTCAATTCTATCGGGT 59.640 40.000 0.00 0.00 0.00 5.28
3074 4376 6.127451 GGGTTCAATTTCAATTCTATCGGGTT 60.127 38.462 0.00 0.00 0.00 4.11
3075 4377 7.067737 GGGTTCAATTTCAATTCTATCGGGTTA 59.932 37.037 0.00 0.00 0.00 2.85
3076 4378 8.463607 GGTTCAATTTCAATTCTATCGGGTTAA 58.536 33.333 0.00 0.00 0.00 2.01
3077 4379 9.285770 GTTCAATTTCAATTCTATCGGGTTAAC 57.714 33.333 0.00 0.00 0.00 2.01
3078 4380 8.568676 TCAATTTCAATTCTATCGGGTTAACA 57.431 30.769 8.10 0.00 0.00 2.41
3079 4381 9.015367 TCAATTTCAATTCTATCGGGTTAACAA 57.985 29.630 8.10 0.00 0.00 2.83
3080 4382 9.072294 CAATTTCAATTCTATCGGGTTAACAAC 57.928 33.333 8.10 0.00 0.00 3.32
3081 4383 6.411630 TTCAATTCTATCGGGTTAACAACG 57.588 37.500 8.10 11.39 0.00 4.10
3082 4384 5.481105 TCAATTCTATCGGGTTAACAACGT 58.519 37.500 17.65 10.27 0.00 3.99
3083 4385 5.933463 TCAATTCTATCGGGTTAACAACGTT 59.067 36.000 17.65 13.44 0.00 3.99
3084 4386 7.095910 TCAATTCTATCGGGTTAACAACGTTA 58.904 34.615 17.65 13.76 0.00 3.18
3085 4387 7.765360 TCAATTCTATCGGGTTAACAACGTTAT 59.235 33.333 17.65 10.08 0.00 1.89
3086 4388 7.704789 ATTCTATCGGGTTAACAACGTTATC 57.295 36.000 17.65 0.00 0.00 1.75
3087 4389 6.206395 TCTATCGGGTTAACAACGTTATCA 57.794 37.500 17.65 3.27 0.00 2.15
3088 4390 6.629128 TCTATCGGGTTAACAACGTTATCAA 58.371 36.000 17.65 0.00 0.00 2.57
3089 4391 4.988708 TCGGGTTAACAACGTTATCAAC 57.011 40.909 17.65 5.05 0.00 3.18
3090 4392 4.375272 TCGGGTTAACAACGTTATCAACA 58.625 39.130 17.65 0.00 0.00 3.33
3091 4393 4.448395 TCGGGTTAACAACGTTATCAACAG 59.552 41.667 17.65 3.97 0.00 3.16
3092 4394 4.211794 CGGGTTAACAACGTTATCAACAGT 59.788 41.667 8.10 0.00 0.00 3.55
3093 4395 5.404968 CGGGTTAACAACGTTATCAACAGTA 59.595 40.000 8.10 0.00 0.00 2.74
3094 4396 6.073873 CGGGTTAACAACGTTATCAACAGTAA 60.074 38.462 8.10 0.00 0.00 2.24
3095 4397 7.360269 CGGGTTAACAACGTTATCAACAGTAAT 60.360 37.037 8.10 0.00 0.00 1.89
3096 4398 7.747357 GGGTTAACAACGTTATCAACAGTAATG 59.253 37.037 8.10 0.00 0.00 1.90
3097 4399 8.497554 GGTTAACAACGTTATCAACAGTAATGA 58.502 33.333 8.10 0.00 0.00 2.57
3098 4400 9.525007 GTTAACAACGTTATCAACAGTAATGAG 57.475 33.333 0.00 0.00 0.00 2.90
3099 4401 7.956420 AACAACGTTATCAACAGTAATGAGA 57.044 32.000 0.00 0.00 0.00 3.27
3100 4402 8.547967 AACAACGTTATCAACAGTAATGAGAT 57.452 30.769 0.00 2.78 0.00 2.75
3101 4403 9.647797 AACAACGTTATCAACAGTAATGAGATA 57.352 29.630 0.00 1.80 0.00 1.98
3102 4404 9.817809 ACAACGTTATCAACAGTAATGAGATAT 57.182 29.630 0.00 0.00 0.00 1.63
3104 4406 9.477484 AACGTTATCAACAGTAATGAGATATCC 57.523 33.333 0.00 0.00 0.00 2.59
3105 4407 8.861086 ACGTTATCAACAGTAATGAGATATCCT 58.139 33.333 0.00 0.00 0.00 3.24
3106 4408 9.347934 CGTTATCAACAGTAATGAGATATCCTC 57.652 37.037 0.00 0.00 42.30 3.71
3111 4413 8.580720 TCAACAGTAATGAGATATCCTCTTAGC 58.419 37.037 0.00 0.00 42.44 3.09
3112 4414 8.363390 CAACAGTAATGAGATATCCTCTTAGCA 58.637 37.037 0.00 0.00 42.44 3.49
3113 4415 7.891561 ACAGTAATGAGATATCCTCTTAGCAC 58.108 38.462 0.00 0.00 42.44 4.40
3114 4416 7.728083 ACAGTAATGAGATATCCTCTTAGCACT 59.272 37.037 0.00 0.00 42.44 4.40
3115 4417 8.243426 CAGTAATGAGATATCCTCTTAGCACTC 58.757 40.741 0.00 0.00 42.44 3.51
3116 4418 8.170061 AGTAATGAGATATCCTCTTAGCACTCT 58.830 37.037 0.00 0.00 42.44 3.24
3117 4419 6.839124 ATGAGATATCCTCTTAGCACTCTG 57.161 41.667 0.00 0.00 42.44 3.35
3118 4420 5.700183 TGAGATATCCTCTTAGCACTCTGT 58.300 41.667 0.00 0.00 42.44 3.41
3119 4421 6.132658 TGAGATATCCTCTTAGCACTCTGTT 58.867 40.000 0.00 0.00 42.44 3.16
3120 4422 6.040278 TGAGATATCCTCTTAGCACTCTGTTG 59.960 42.308 0.00 0.00 42.44 3.33
3121 4423 6.132658 AGATATCCTCTTAGCACTCTGTTGA 58.867 40.000 0.00 0.00 0.00 3.18
3122 4424 4.734398 ATCCTCTTAGCACTCTGTTGAG 57.266 45.455 0.00 0.00 45.43 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.617959 AGTTTTTGAAGATCTCGACGTGA 58.382 39.130 0.00 1.62 0.00 4.35
10 11 4.974103 AGTTTTTGAAGATCTCGACGTG 57.026 40.909 0.00 0.00 0.00 4.49
11 12 6.010294 TCTAGTTTTTGAAGATCTCGACGT 57.990 37.500 0.00 0.00 0.00 4.34
38 39 7.922505 TTTTTCGTCAAAACCTATCAACATG 57.077 32.000 0.00 0.00 30.89 3.21
80 81 3.002144 CGGTTTTTCGGTCCGTTTTTCTA 59.998 43.478 11.88 0.00 39.51 2.10
82 83 2.110990 CGGTTTTTCGGTCCGTTTTTC 58.889 47.619 11.88 0.91 39.51 2.29
279 282 0.597568 CGCCATGCCTCTCAAAAACA 59.402 50.000 0.00 0.00 0.00 2.83
330 334 4.668289 TGTTTTCTTTCTTCCGCTTTCAC 58.332 39.130 0.00 0.00 0.00 3.18
331 335 4.638421 TCTGTTTTCTTTCTTCCGCTTTCA 59.362 37.500 0.00 0.00 0.00 2.69
333 337 5.576447 TTCTGTTTTCTTTCTTCCGCTTT 57.424 34.783 0.00 0.00 0.00 3.51
334 338 5.576447 TTTCTGTTTTCTTTCTTCCGCTT 57.424 34.783 0.00 0.00 0.00 4.68
336 340 5.004440 GTGTTTTCTGTTTTCTTTCTTCCGC 59.996 40.000 0.00 0.00 0.00 5.54
369 392 1.369091 CCCATGCCTCTCGAAAACGG 61.369 60.000 0.00 0.00 0.00 4.44
404 427 1.154908 CGCGAGTCACCGTTTTTCG 60.155 57.895 0.00 0.00 39.52 3.46
406 429 0.810823 TTCCGCGAGTCACCGTTTTT 60.811 50.000 8.23 0.00 0.00 1.94
412 435 0.790814 CTTTTCTTCCGCGAGTCACC 59.209 55.000 8.23 0.00 0.00 4.02
414 437 2.519377 TTCTTTTCTTCCGCGAGTCA 57.481 45.000 8.23 0.00 0.00 3.41
470 495 7.360776 TTTCTTCGCTTTTGCACAAGAATTTTT 60.361 29.630 16.70 0.00 45.49 1.94
471 496 6.091986 TTTCTTCGCTTTTGCACAAGAATTTT 59.908 30.769 16.70 0.00 45.49 1.82
472 497 5.580297 TTTCTTCGCTTTTGCACAAGAATTT 59.420 32.000 16.70 0.00 45.49 1.82
473 498 5.108517 TTTCTTCGCTTTTGCACAAGAATT 58.891 33.333 16.70 0.00 45.49 2.17
474 499 4.681744 TTTCTTCGCTTTTGCACAAGAAT 58.318 34.783 16.70 0.00 45.49 2.40
484 509 3.541632 TCACTGGTCTTTCTTCGCTTTT 58.458 40.909 0.00 0.00 0.00 2.27
485 510 3.194005 TCACTGGTCTTTCTTCGCTTT 57.806 42.857 0.00 0.00 0.00 3.51
490 515 7.883229 TTTTTGTTTTCACTGGTCTTTCTTC 57.117 32.000 0.00 0.00 0.00 2.87
540 568 5.704217 TTTATTTTTCTGCACGCGTTTTT 57.296 30.435 10.22 0.00 0.00 1.94
572 600 1.075970 TGGGATAGGCTGAGAGCGT 60.076 57.895 0.00 0.00 43.62 5.07
577 605 5.495926 ACAATTATCTGGGATAGGCTGAG 57.504 43.478 0.00 0.00 0.00 3.35
593 621 7.308348 CGCTCCTTTAAAGACTTCCAACAATTA 60.308 37.037 16.98 0.00 0.00 1.40
599 627 2.812011 GCGCTCCTTTAAAGACTTCCAA 59.188 45.455 16.98 0.00 0.00 3.53
666 698 3.184683 GAGCTCTCTTGTGGCGCG 61.185 66.667 6.43 0.00 0.00 6.86
667 699 3.184683 CGAGCTCTCTTGTGGCGC 61.185 66.667 12.85 0.00 0.00 6.53
668 700 2.507992 CCGAGCTCTCTTGTGGCG 60.508 66.667 12.85 0.00 0.00 5.69
669 701 2.817396 GCCGAGCTCTCTTGTGGC 60.817 66.667 12.85 12.13 35.04 5.01
670 702 1.447489 CTGCCGAGCTCTCTTGTGG 60.447 63.158 12.85 5.40 0.00 4.17
671 703 1.447489 CCTGCCGAGCTCTCTTGTG 60.447 63.158 12.85 0.00 0.00 3.33
672 704 2.977178 CCTGCCGAGCTCTCTTGT 59.023 61.111 12.85 0.00 0.00 3.16
673 705 2.511145 GCCTGCCGAGCTCTCTTG 60.511 66.667 12.85 0.00 0.00 3.02
674 706 2.683212 AGCCTGCCGAGCTCTCTT 60.683 61.111 12.85 0.00 34.91 2.85
736 769 4.835615 CCTATTCTATATAGGCCGGCATCT 59.164 45.833 30.85 19.77 35.26 2.90
747 780 9.778993 GTCGATTTGCGTAACCTATTCTATATA 57.221 33.333 0.00 0.00 41.80 0.86
749 782 7.806487 CAGTCGATTTGCGTAACCTATTCTATA 59.194 37.037 0.00 0.00 41.80 1.31
868 903 1.781153 TTCCAAATCGGGGTCGGGTT 61.781 55.000 0.00 0.00 36.95 4.11
891 926 7.200434 TCAGCTTTATATGGAAAGAAGAGGT 57.800 36.000 2.70 0.00 38.48 3.85
897 932 6.327626 AGGTAGCTCAGCTTTATATGGAAAGA 59.672 38.462 3.31 0.00 40.44 2.52
940 976 4.256180 ATCTGGGCGGGCGGATTC 62.256 66.667 0.00 0.00 0.00 2.52
948 984 4.195334 CAAGGGGGATCTGGGCGG 62.195 72.222 0.00 0.00 0.00 6.13
949 985 4.883354 GCAAGGGGGATCTGGGCG 62.883 72.222 0.00 0.00 0.00 6.13
950 986 3.424105 AGCAAGGGGGATCTGGGC 61.424 66.667 0.00 0.00 0.00 5.36
952 988 1.530771 CAGAGCAAGGGGGATCTGG 59.469 63.158 0.75 0.00 45.17 3.86
954 990 0.915364 GAACAGAGCAAGGGGGATCT 59.085 55.000 0.00 0.00 32.90 2.75
956 992 1.575447 GGGAACAGAGCAAGGGGGAT 61.575 60.000 0.00 0.00 0.00 3.85
957 993 2.231380 GGGAACAGAGCAAGGGGGA 61.231 63.158 0.00 0.00 0.00 4.81
1106 1171 2.363147 GCTCGAGGTCCTGGAGGT 60.363 66.667 26.87 0.00 36.93 3.85
1222 1287 1.646912 TCATCGGGGAAGTGTTGGTA 58.353 50.000 0.00 0.00 0.00 3.25
1234 1326 4.579454 ATTGATTGCTTGATTCATCGGG 57.421 40.909 0.00 0.00 0.00 5.14
1247 1339 3.382865 GGGAGGAAGAAGGAATTGATTGC 59.617 47.826 0.00 0.00 0.00 3.56
1313 1421 2.202623 GTAGGTCCGCTCTGCACG 60.203 66.667 0.00 0.00 0.00 5.34
1314 1422 1.139947 GAGTAGGTCCGCTCTGCAC 59.860 63.158 8.64 0.00 0.00 4.57
1525 1633 4.457496 ACGATGCAGCTGTCGGGG 62.457 66.667 25.03 10.88 41.87 5.73
2214 3441 9.146984 GATGAATGAATGAATGAATGTTGTTGT 57.853 29.630 0.00 0.00 0.00 3.32
2215 3442 8.600625 GGATGAATGAATGAATGAATGTTGTTG 58.399 33.333 0.00 0.00 0.00 3.33
2238 3465 8.179509 AGTAGTAAACTAGCAATACATCGGAT 57.820 34.615 0.00 0.00 36.36 4.18
2239 3466 7.578310 AGTAGTAAACTAGCAATACATCGGA 57.422 36.000 0.00 0.00 36.36 4.55
2252 3479 9.570468 CCTATGATGAGTGGTAGTAGTAAACTA 57.430 37.037 0.00 0.00 39.80 2.24
2253 3480 8.060075 ACCTATGATGAGTGGTAGTAGTAAACT 58.940 37.037 0.00 0.00 42.62 2.66
2254 3481 8.235359 ACCTATGATGAGTGGTAGTAGTAAAC 57.765 38.462 0.00 0.00 0.00 2.01
2255 3482 8.834004 AACCTATGATGAGTGGTAGTAGTAAA 57.166 34.615 0.00 0.00 31.82 2.01
2256 3483 9.925545 TTAACCTATGATGAGTGGTAGTAGTAA 57.074 33.333 0.00 0.00 31.82 2.24
2257 3484 9.925545 TTTAACCTATGATGAGTGGTAGTAGTA 57.074 33.333 0.00 0.00 31.82 1.82
2258 3485 8.834004 TTTAACCTATGATGAGTGGTAGTAGT 57.166 34.615 0.00 0.00 31.82 2.73
2259 3486 9.132923 TCTTTAACCTATGATGAGTGGTAGTAG 57.867 37.037 0.00 0.00 31.82 2.57
2260 3487 9.483489 TTCTTTAACCTATGATGAGTGGTAGTA 57.517 33.333 0.00 0.00 31.82 1.82
2314 3546 9.471084 GCTATCAGAATAGATCATCATCATCAG 57.529 37.037 0.00 0.00 37.63 2.90
2331 3563 4.574892 TCATCAAACCAACGCTATCAGAA 58.425 39.130 0.00 0.00 0.00 3.02
2338 3570 3.149196 AGTTGATCATCAAACCAACGCT 58.851 40.909 0.29 0.00 42.47 5.07
2356 3588 2.066262 CACGAGCCACGAATTGTAGTT 58.934 47.619 7.86 0.00 45.77 2.24
2365 3597 1.872388 TGAAATTTCACGAGCCACGA 58.128 45.000 16.91 0.00 45.65 4.35
2374 3606 7.315142 TGATAGTGCCATCTTTGAAATTTCAC 58.685 34.615 20.35 7.93 36.83 3.18
2439 3671 7.593273 TGAACATAGTGGTAAAAAGAAAATGCG 59.407 33.333 0.00 0.00 0.00 4.73
2440 3672 8.810652 TGAACATAGTGGTAAAAAGAAAATGC 57.189 30.769 0.00 0.00 0.00 3.56
2506 3739 5.914898 TCGAGGAATACATCTGTTCTTGA 57.085 39.130 0.00 0.00 0.00 3.02
2513 3746 6.199908 GTGAGTTGAATCGAGGAATACATCTG 59.800 42.308 0.00 0.00 0.00 2.90
2516 3749 6.045318 CAGTGAGTTGAATCGAGGAATACAT 58.955 40.000 0.00 0.00 0.00 2.29
2520 3753 3.265791 GCAGTGAGTTGAATCGAGGAAT 58.734 45.455 0.00 0.00 0.00 3.01
2526 3759 1.291184 TGCCGCAGTGAGTTGAATCG 61.291 55.000 0.00 0.00 0.00 3.34
2540 3773 0.305922 GTGTTAGAGATGCATGCCGC 59.694 55.000 16.68 7.03 42.89 6.53
2543 3776 2.611292 GGTCTGTGTTAGAGATGCATGC 59.389 50.000 11.82 11.82 35.70 4.06
2544 3777 3.118482 AGGGTCTGTGTTAGAGATGCATG 60.118 47.826 2.46 0.00 35.70 4.06
2545 3778 3.110705 AGGGTCTGTGTTAGAGATGCAT 58.889 45.455 0.00 0.00 35.70 3.96
2546 3779 2.497675 GAGGGTCTGTGTTAGAGATGCA 59.502 50.000 0.00 0.00 35.70 3.96
2554 3787 3.709653 AGACAGTTTGAGGGTCTGTGTTA 59.290 43.478 1.78 0.00 41.58 2.41
2561 3794 1.604278 GTTGCAGACAGTTTGAGGGTC 59.396 52.381 0.00 0.00 0.00 4.46
2562 3795 1.212935 AGTTGCAGACAGTTTGAGGGT 59.787 47.619 0.00 0.00 0.00 4.34
2574 3807 1.581934 CCAGTTCGAACAGTTGCAGA 58.418 50.000 28.78 0.00 0.00 4.26
2599 3832 1.501604 AGCCCCAACCCTTAGTTTTGA 59.498 47.619 0.00 0.00 36.18 2.69
2604 3869 0.857675 ACAAAGCCCCAACCCTTAGT 59.142 50.000 0.00 0.00 0.00 2.24
2608 3873 2.201210 CCACAAAGCCCCAACCCT 59.799 61.111 0.00 0.00 0.00 4.34
2612 3877 4.531426 ACGCCCACAAAGCCCCAA 62.531 61.111 0.00 0.00 0.00 4.12
2626 3891 1.282875 GTGGCAGAGGTTTGAACGC 59.717 57.895 0.00 0.00 0.00 4.84
2638 3903 1.739929 TCCGTTGCGTATGTGGCAG 60.740 57.895 0.00 0.00 42.12 4.85
2670 3935 2.746277 CGCGGGAGAGGTTTTGGG 60.746 66.667 0.00 0.00 0.00 4.12
2701 3966 2.568090 GGCAACCGCTTGACATGG 59.432 61.111 0.00 0.00 35.17 3.66
2741 4006 3.179265 CTGCCGCGTCCAGTTACG 61.179 66.667 4.92 0.00 45.58 3.18
2743 4008 2.355986 ATCCTGCCGCGTCCAGTTA 61.356 57.895 18.72 9.80 0.00 2.24
2744 4009 3.706373 ATCCTGCCGCGTCCAGTT 61.706 61.111 18.72 6.96 0.00 3.16
2755 4020 1.694150 TGTGGTAGATAGCCATCCTGC 59.306 52.381 0.00 0.00 38.40 4.85
2756 4021 4.040829 TGAATGTGGTAGATAGCCATCCTG 59.959 45.833 0.00 0.00 38.40 3.86
2757 4022 4.040952 GTGAATGTGGTAGATAGCCATCCT 59.959 45.833 0.00 0.00 38.40 3.24
2768 4033 2.079158 CAGCCAGTGTGAATGTGGTAG 58.921 52.381 0.00 0.00 33.51 3.18
2770 4035 1.174712 GCAGCCAGTGTGAATGTGGT 61.175 55.000 0.00 0.00 33.51 4.16
2773 4038 0.892358 CAGGCAGCCAGTGTGAATGT 60.892 55.000 15.80 0.00 0.00 2.71
2777 4042 2.848679 TCCAGGCAGCCAGTGTGA 60.849 61.111 15.80 1.18 0.00 3.58
2805 4082 2.482721 GTGGGTTTCTCCAACACGTATG 59.517 50.000 0.00 0.00 42.46 2.39
2806 4083 2.370849 AGTGGGTTTCTCCAACACGTAT 59.629 45.455 0.00 0.00 42.46 3.06
2808 4085 0.544697 AGTGGGTTTCTCCAACACGT 59.455 50.000 0.00 0.00 42.46 4.49
2811 4089 2.123589 TCAGAGTGGGTTTCTCCAACA 58.876 47.619 0.00 0.00 42.50 3.33
2882 4173 4.344865 GGAAGCGAAGGGGGTGCA 62.345 66.667 0.00 0.00 0.00 4.57
2897 4188 1.888436 GATGTGGTGTGAGGAGCGGA 61.888 60.000 0.00 0.00 0.00 5.54
2900 4191 1.448540 CGGATGTGGTGTGAGGAGC 60.449 63.158 0.00 0.00 0.00 4.70
2906 4197 1.733912 CTTCATGACGGATGTGGTGTG 59.266 52.381 0.00 0.00 33.29 3.82
2907 4198 1.945819 GCTTCATGACGGATGTGGTGT 60.946 52.381 0.00 0.00 33.29 4.16
2914 4211 5.048364 GTCACTATAGAGCTTCATGACGGAT 60.048 44.000 6.78 0.00 0.00 4.18
2919 4216 4.036852 CCACGTCACTATAGAGCTTCATGA 59.963 45.833 6.78 0.00 0.00 3.07
2928 4230 5.057843 AGGTTATCCCACGTCACTATAGA 57.942 43.478 6.78 0.00 34.66 1.98
2932 4234 3.378112 CGTAAGGTTATCCCACGTCACTA 59.622 47.826 6.47 0.00 37.66 2.74
2939 4241 1.750778 TCCGTCGTAAGGTTATCCCAC 59.249 52.381 0.00 0.00 34.66 4.61
2955 4257 4.246458 GAGAGATAGTGTTTTTGCTCCGT 58.754 43.478 0.00 0.00 0.00 4.69
2957 4259 4.327627 GTCGAGAGATAGTGTTTTTGCTCC 59.672 45.833 0.00 0.00 45.19 4.70
2965 4267 4.578516 CCAGATCAGTCGAGAGATAGTGTT 59.421 45.833 0.00 0.00 45.19 3.32
2970 4272 8.322091 TCATTATACCAGATCAGTCGAGAGATA 58.678 37.037 0.00 0.00 45.19 1.98
2987 4289 7.171678 GCACTGATTAGAGTTGGTCATTATACC 59.828 40.741 0.00 0.00 40.19 2.73
2988 4290 7.928706 AGCACTGATTAGAGTTGGTCATTATAC 59.071 37.037 0.00 0.00 0.00 1.47
2989 4291 8.023021 AGCACTGATTAGAGTTGGTCATTATA 57.977 34.615 0.00 0.00 0.00 0.98
2990 4292 6.893583 AGCACTGATTAGAGTTGGTCATTAT 58.106 36.000 0.00 0.00 0.00 1.28
2991 4293 6.299805 AGCACTGATTAGAGTTGGTCATTA 57.700 37.500 0.00 0.00 0.00 1.90
2992 4294 5.171339 AGCACTGATTAGAGTTGGTCATT 57.829 39.130 0.00 0.00 0.00 2.57
2993 4295 4.833478 AGCACTGATTAGAGTTGGTCAT 57.167 40.909 0.00 0.00 0.00 3.06
2994 4296 4.569943 GAAGCACTGATTAGAGTTGGTCA 58.430 43.478 0.00 0.00 0.00 4.02
2995 4297 3.614616 CGAAGCACTGATTAGAGTTGGTC 59.385 47.826 0.00 0.00 0.00 4.02
2996 4298 3.006967 ACGAAGCACTGATTAGAGTTGGT 59.993 43.478 0.00 0.00 0.00 3.67
2997 4299 3.589988 ACGAAGCACTGATTAGAGTTGG 58.410 45.455 0.00 0.00 0.00 3.77
2998 4300 4.237724 TGACGAAGCACTGATTAGAGTTG 58.762 43.478 0.00 0.00 0.00 3.16
2999 4301 4.521130 TGACGAAGCACTGATTAGAGTT 57.479 40.909 0.00 0.00 0.00 3.01
3000 4302 4.021894 ACTTGACGAAGCACTGATTAGAGT 60.022 41.667 0.00 0.00 31.68 3.24
3001 4303 4.489810 ACTTGACGAAGCACTGATTAGAG 58.510 43.478 0.00 0.00 31.68 2.43
3002 4304 4.521130 ACTTGACGAAGCACTGATTAGA 57.479 40.909 0.00 0.00 31.68 2.10
3003 4305 5.406780 AGAAACTTGACGAAGCACTGATTAG 59.593 40.000 0.00 0.00 31.68 1.73
3004 4306 5.297547 AGAAACTTGACGAAGCACTGATTA 58.702 37.500 0.00 0.00 31.68 1.75
3005 4307 4.130118 AGAAACTTGACGAAGCACTGATT 58.870 39.130 0.00 0.00 31.68 2.57
3006 4308 3.733337 AGAAACTTGACGAAGCACTGAT 58.267 40.909 0.00 0.00 31.68 2.90
3007 4309 3.179443 AGAAACTTGACGAAGCACTGA 57.821 42.857 0.00 0.00 31.68 3.41
3008 4310 4.745125 TCTTAGAAACTTGACGAAGCACTG 59.255 41.667 0.00 0.00 31.68 3.66
3009 4311 4.945246 TCTTAGAAACTTGACGAAGCACT 58.055 39.130 0.00 0.00 31.68 4.40
3010 4312 5.847670 ATCTTAGAAACTTGACGAAGCAC 57.152 39.130 0.00 0.00 31.68 4.40
3011 4313 6.807230 GTCTATCTTAGAAACTTGACGAAGCA 59.193 38.462 0.00 0.00 36.40 3.91
3012 4314 6.807230 TGTCTATCTTAGAAACTTGACGAAGC 59.193 38.462 0.00 0.00 36.40 3.86
3013 4315 8.744008 TTGTCTATCTTAGAAACTTGACGAAG 57.256 34.615 0.00 0.00 36.40 3.79
3014 4316 9.355215 GATTGTCTATCTTAGAAACTTGACGAA 57.645 33.333 0.00 0.00 36.40 3.85
3015 4317 8.520351 TGATTGTCTATCTTAGAAACTTGACGA 58.480 33.333 0.00 0.00 36.40 4.20
3016 4318 8.689251 TGATTGTCTATCTTAGAAACTTGACG 57.311 34.615 0.00 0.00 36.40 4.35
3021 4323 9.883142 CTCCTTTGATTGTCTATCTTAGAAACT 57.117 33.333 0.00 0.00 36.40 2.66
3022 4324 9.660180 ACTCCTTTGATTGTCTATCTTAGAAAC 57.340 33.333 0.00 0.00 36.40 2.78
3023 4325 9.658799 CACTCCTTTGATTGTCTATCTTAGAAA 57.341 33.333 0.00 0.00 36.40 2.52
3024 4326 8.260818 CCACTCCTTTGATTGTCTATCTTAGAA 58.739 37.037 0.00 0.00 36.40 2.10
3025 4327 7.147655 CCCACTCCTTTGATTGTCTATCTTAGA 60.148 40.741 0.00 0.00 34.17 2.10
3026 4328 6.989169 CCCACTCCTTTGATTGTCTATCTTAG 59.011 42.308 0.00 0.00 34.17 2.18
3027 4329 6.443849 ACCCACTCCTTTGATTGTCTATCTTA 59.556 38.462 0.00 0.00 34.17 2.10
3028 4330 5.251700 ACCCACTCCTTTGATTGTCTATCTT 59.748 40.000 0.00 0.00 34.17 2.40
3029 4331 4.785376 ACCCACTCCTTTGATTGTCTATCT 59.215 41.667 0.00 0.00 34.17 1.98
3030 4332 5.104259 ACCCACTCCTTTGATTGTCTATC 57.896 43.478 0.00 0.00 0.00 2.08
3031 4333 5.014123 TGAACCCACTCCTTTGATTGTCTAT 59.986 40.000 0.00 0.00 0.00 1.98
3032 4334 4.349636 TGAACCCACTCCTTTGATTGTCTA 59.650 41.667 0.00 0.00 0.00 2.59
3033 4335 3.138283 TGAACCCACTCCTTTGATTGTCT 59.862 43.478 0.00 0.00 0.00 3.41
3034 4336 3.486383 TGAACCCACTCCTTTGATTGTC 58.514 45.455 0.00 0.00 0.00 3.18
3035 4337 3.593442 TGAACCCACTCCTTTGATTGT 57.407 42.857 0.00 0.00 0.00 2.71
3036 4338 5.473066 AATTGAACCCACTCCTTTGATTG 57.527 39.130 0.00 0.00 0.00 2.67
3037 4339 5.602145 TGAAATTGAACCCACTCCTTTGATT 59.398 36.000 0.00 0.00 0.00 2.57
3038 4340 5.147032 TGAAATTGAACCCACTCCTTTGAT 58.853 37.500 0.00 0.00 0.00 2.57
3039 4341 4.541705 TGAAATTGAACCCACTCCTTTGA 58.458 39.130 0.00 0.00 0.00 2.69
3040 4342 4.935352 TGAAATTGAACCCACTCCTTTG 57.065 40.909 0.00 0.00 0.00 2.77
3041 4343 6.327365 AGAATTGAAATTGAACCCACTCCTTT 59.673 34.615 0.00 0.00 0.00 3.11
3042 4344 5.840693 AGAATTGAAATTGAACCCACTCCTT 59.159 36.000 0.00 0.00 0.00 3.36
3043 4345 5.397360 AGAATTGAAATTGAACCCACTCCT 58.603 37.500 0.00 0.00 0.00 3.69
3044 4346 5.728637 AGAATTGAAATTGAACCCACTCC 57.271 39.130 0.00 0.00 0.00 3.85
3045 4347 7.189512 CGATAGAATTGAAATTGAACCCACTC 58.810 38.462 0.00 0.00 39.76 3.51
3046 4348 6.095440 CCGATAGAATTGAAATTGAACCCACT 59.905 38.462 0.00 0.00 39.76 4.00
3047 4349 6.265577 CCGATAGAATTGAAATTGAACCCAC 58.734 40.000 0.00 0.00 39.76 4.61
3048 4350 5.359576 CCCGATAGAATTGAAATTGAACCCA 59.640 40.000 0.00 0.00 39.76 4.51
3049 4351 5.359860 ACCCGATAGAATTGAAATTGAACCC 59.640 40.000 0.00 0.00 39.76 4.11
3050 4352 6.451064 ACCCGATAGAATTGAAATTGAACC 57.549 37.500 0.00 0.00 39.76 3.62
3051 4353 9.285770 GTTAACCCGATAGAATTGAAATTGAAC 57.714 33.333 0.00 0.00 39.76 3.18
3052 4354 9.015367 TGTTAACCCGATAGAATTGAAATTGAA 57.985 29.630 2.48 0.00 39.76 2.69
3053 4355 8.568676 TGTTAACCCGATAGAATTGAAATTGA 57.431 30.769 2.48 0.00 39.76 2.57
3054 4356 9.072294 GTTGTTAACCCGATAGAATTGAAATTG 57.928 33.333 2.48 0.00 39.76 2.32
3055 4357 7.966204 CGTTGTTAACCCGATAGAATTGAAATT 59.034 33.333 2.48 0.00 39.76 1.82
3056 4358 7.120138 ACGTTGTTAACCCGATAGAATTGAAAT 59.880 33.333 18.20 0.00 39.76 2.17
3057 4359 6.427547 ACGTTGTTAACCCGATAGAATTGAAA 59.572 34.615 18.20 0.00 39.76 2.69
3058 4360 5.933463 ACGTTGTTAACCCGATAGAATTGAA 59.067 36.000 18.20 0.00 39.76 2.69
3059 4361 5.481105 ACGTTGTTAACCCGATAGAATTGA 58.519 37.500 18.20 0.00 39.76 2.57
3060 4362 5.789710 ACGTTGTTAACCCGATAGAATTG 57.210 39.130 18.20 0.00 39.76 2.32
3061 4363 7.765360 TGATAACGTTGTTAACCCGATAGAATT 59.235 33.333 11.99 6.55 39.76 2.17
3062 4364 7.267128 TGATAACGTTGTTAACCCGATAGAAT 58.733 34.615 11.99 6.73 39.76 2.40
3063 4365 6.629128 TGATAACGTTGTTAACCCGATAGAA 58.371 36.000 11.99 4.48 39.76 2.10
3064 4366 6.206395 TGATAACGTTGTTAACCCGATAGA 57.794 37.500 11.99 3.42 39.76 1.98
3065 4367 6.310956 TGTTGATAACGTTGTTAACCCGATAG 59.689 38.462 23.38 1.61 0.00 2.08
3066 4368 6.162079 TGTTGATAACGTTGTTAACCCGATA 58.838 36.000 23.38 12.44 0.00 2.92
3067 4369 4.996122 TGTTGATAACGTTGTTAACCCGAT 59.004 37.500 23.38 10.93 0.00 4.18
3068 4370 4.375272 TGTTGATAACGTTGTTAACCCGA 58.625 39.130 23.38 8.19 0.00 5.14
3069 4371 4.211794 ACTGTTGATAACGTTGTTAACCCG 59.788 41.667 23.38 17.97 0.00 5.28
3070 4372 5.678132 ACTGTTGATAACGTTGTTAACCC 57.322 39.130 23.38 6.70 0.00 4.11
3071 4373 8.497554 TCATTACTGTTGATAACGTTGTTAACC 58.502 33.333 23.38 10.87 0.00 2.85
3072 4374 9.525007 CTCATTACTGTTGATAACGTTGTTAAC 57.475 33.333 20.82 20.82 0.00 2.01
3073 4375 9.478768 TCTCATTACTGTTGATAACGTTGTTAA 57.521 29.630 11.99 4.38 0.00 2.01
3074 4376 9.647797 ATCTCATTACTGTTGATAACGTTGTTA 57.352 29.630 11.99 0.00 0.00 2.41
3075 4377 7.956420 TCTCATTACTGTTGATAACGTTGTT 57.044 32.000 11.99 0.00 0.00 2.83
3076 4378 9.817809 ATATCTCATTACTGTTGATAACGTTGT 57.182 29.630 11.99 3.45 0.00 3.32
3078 4380 9.477484 GGATATCTCATTACTGTTGATAACGTT 57.523 33.333 5.88 5.88 0.00 3.99
3079 4381 8.861086 AGGATATCTCATTACTGTTGATAACGT 58.139 33.333 2.05 0.00 0.00 3.99
3080 4382 9.347934 GAGGATATCTCATTACTGTTGATAACG 57.652 37.037 2.05 0.00 42.02 3.18
3085 4387 8.580720 GCTAAGAGGATATCTCATTACTGTTGA 58.419 37.037 2.05 0.00 44.81 3.18
3086 4388 8.363390 TGCTAAGAGGATATCTCATTACTGTTG 58.637 37.037 2.05 0.00 44.81 3.33
3087 4389 8.364142 GTGCTAAGAGGATATCTCATTACTGTT 58.636 37.037 2.05 0.00 44.81 3.16
3088 4390 7.728083 AGTGCTAAGAGGATATCTCATTACTGT 59.272 37.037 2.05 0.00 44.81 3.55
3089 4391 8.121305 AGTGCTAAGAGGATATCTCATTACTG 57.879 38.462 2.05 0.00 44.81 2.74
3090 4392 8.170061 AGAGTGCTAAGAGGATATCTCATTACT 58.830 37.037 2.05 0.00 44.81 2.24
3091 4393 8.243426 CAGAGTGCTAAGAGGATATCTCATTAC 58.757 40.741 2.05 0.00 44.81 1.89
3092 4394 7.947332 ACAGAGTGCTAAGAGGATATCTCATTA 59.053 37.037 2.05 0.00 44.81 1.90
3093 4395 6.782000 ACAGAGTGCTAAGAGGATATCTCATT 59.218 38.462 2.05 0.00 44.81 2.57
3094 4396 6.314120 ACAGAGTGCTAAGAGGATATCTCAT 58.686 40.000 2.05 0.00 44.81 2.90
3095 4397 5.700183 ACAGAGTGCTAAGAGGATATCTCA 58.300 41.667 2.05 0.00 44.81 3.27
3096 4398 6.264292 TCAACAGAGTGCTAAGAGGATATCTC 59.736 42.308 2.05 0.00 37.23 2.75
3097 4399 6.132658 TCAACAGAGTGCTAAGAGGATATCT 58.867 40.000 2.05 0.00 41.27 1.98
3098 4400 6.040391 ACTCAACAGAGTGCTAAGAGGATATC 59.960 42.308 0.00 0.00 40.95 1.63
3099 4401 5.896678 ACTCAACAGAGTGCTAAGAGGATAT 59.103 40.000 0.00 0.00 40.95 1.63
3100 4402 5.265191 ACTCAACAGAGTGCTAAGAGGATA 58.735 41.667 0.00 0.00 40.95 2.59
3101 4403 4.093011 ACTCAACAGAGTGCTAAGAGGAT 58.907 43.478 0.00 0.00 40.95 3.24
3102 4404 3.501349 ACTCAACAGAGTGCTAAGAGGA 58.499 45.455 0.00 0.00 40.95 3.71
3103 4405 3.951775 ACTCAACAGAGTGCTAAGAGG 57.048 47.619 0.00 0.00 40.95 3.69
3104 4406 7.897575 ATAAAACTCAACAGAGTGCTAAGAG 57.102 36.000 0.00 0.00 41.62 2.85
3105 4407 8.677148 AAATAAAACTCAACAGAGTGCTAAGA 57.323 30.769 0.00 0.00 41.62 2.10


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

AutoCloner maintained by Alex Coulton.