Multiple sequence alignment - TraesCS4D01G310100

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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 TraesCS4D01G310100 chr4D 100.000 3821 0 0 1 3821 477509656 477505836 0.000000e+00 7057.0
1 TraesCS4D01G310100 chr4D 81.105 561 92 9 1020 1573 504328866 504329419 1.630000e-118 436.0
2 TraesCS4D01G310100 chr4D 77.985 268 51 7 2537 2801 504330513 504330775 1.100000e-35 161.0
3 TraesCS4D01G310100 chr4A 88.889 2304 110 60 4 2256 684272315 684270107 0.000000e+00 2702.0
4 TraesCS4D01G310100 chr4A 88.084 1519 116 34 2253 3741 684270022 684268539 0.000000e+00 1742.0
5 TraesCS4D01G310100 chr4A 88.779 606 49 10 3140 3741 684398292 684398882 0.000000e+00 725.0
6 TraesCS4D01G310100 chr4B 94.002 1784 51 21 496 2256 602451099 602449349 0.000000e+00 2651.0
7 TraesCS4D01G310100 chr4B 90.000 900 44 22 2253 3144 602449242 602448381 0.000000e+00 1122.0
8 TraesCS4D01G310100 chr4B 87.946 448 40 10 3184 3629 602448395 602447960 2.040000e-142 516.0
9 TraesCS4D01G310100 chr4B 81.489 497 80 7 1020 1510 650960791 650961281 7.690000e-107 398.0
10 TraesCS4D01G310100 chr4B 84.533 375 35 16 4 377 602451606 602451254 2.180000e-92 350.0
11 TraesCS4D01G310100 chr4B 78.731 268 49 7 2537 2801 650962530 650962792 5.070000e-39 172.0
12 TraesCS4D01G310100 chr1B 80.658 1246 179 34 1015 2256 270792746 270793933 0.000000e+00 909.0
13 TraesCS4D01G310100 chr1D 80.578 1246 182 37 1015 2257 194927324 194926136 0.000000e+00 905.0
14 TraesCS4D01G310100 chr1D 86.010 193 22 5 3627 3818 473695546 473695734 6.470000e-48 202.0
15 TraesCS4D01G310100 chr1A 80.498 1246 181 37 1015 2256 243162856 243161669 0.000000e+00 898.0
16 TraesCS4D01G310100 chr6D 80.807 719 122 12 1022 1732 463549412 463548702 2.010000e-152 549.0
17 TraesCS4D01G310100 chr5A 80.570 561 95 9 1020 1573 688973634 688974187 1.640000e-113 420.0
18 TraesCS4D01G310100 chr5A 77.068 266 57 4 2537 2801 688975379 688975641 2.380000e-32 150.0
19 TraesCS4D01G310100 chr6A 81.455 275 47 4 2550 2822 610205979 610206251 4.970000e-54 222.0
20 TraesCS4D01G310100 chr7A 87.245 196 22 2 3626 3821 657446466 657446658 1.790000e-53 220.0
21 TraesCS4D01G310100 chr7B 88.679 53 3 3 3657 3707 460977943 460977994 1.150000e-05 62.1


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 TraesCS4D01G310100 chr4D 477505836 477509656 3820 True 7057.00 7057 100.00000 1 3821 1 chr4D.!!$R1 3820
1 TraesCS4D01G310100 chr4D 504328866 504330775 1909 False 298.50 436 79.54500 1020 2801 2 chr4D.!!$F1 1781
2 TraesCS4D01G310100 chr4A 684268539 684272315 3776 True 2222.00 2702 88.48650 4 3741 2 chr4A.!!$R1 3737
3 TraesCS4D01G310100 chr4A 684398292 684398882 590 False 725.00 725 88.77900 3140 3741 1 chr4A.!!$F1 601
4 TraesCS4D01G310100 chr4B 602447960 602451606 3646 True 1159.75 2651 89.12025 4 3629 4 chr4B.!!$R1 3625
5 TraesCS4D01G310100 chr4B 650960791 650962792 2001 False 285.00 398 80.11000 1020 2801 2 chr4B.!!$F1 1781
6 TraesCS4D01G310100 chr1B 270792746 270793933 1187 False 909.00 909 80.65800 1015 2256 1 chr1B.!!$F1 1241
7 TraesCS4D01G310100 chr1D 194926136 194927324 1188 True 905.00 905 80.57800 1015 2257 1 chr1D.!!$R1 1242
8 TraesCS4D01G310100 chr1A 243161669 243162856 1187 True 898.00 898 80.49800 1015 2256 1 chr1A.!!$R1 1241
9 TraesCS4D01G310100 chr6D 463548702 463549412 710 True 549.00 549 80.80700 1022 1732 1 chr6D.!!$R1 710
10 TraesCS4D01G310100 chr5A 688973634 688975641 2007 False 285.00 420 78.81900 1020 2801 2 chr5A.!!$F1 1781

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
175 187 0.036875 CCACCTCCACCTTTCCACTC 59.963 60.000 0.00 0.00 0.00 3.51 F
913 1047 0.043334 TTTCCCCTCTCCTAGCTGCT 59.957 55.000 7.57 7.57 0.00 4.24 F
914 1048 0.397816 TTCCCCTCTCCTAGCTGCTC 60.398 60.000 4.91 0.00 0.00 4.26 F
952 1086 2.251818 TCCAAGAGCAGAGTAGCTTGT 58.748 47.619 0.00 0.00 46.75 3.16 F
987 1121 2.300152 CTGTGTGGGCTAGACAAGAGAA 59.700 50.000 1.88 0.00 31.47 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2245 0.600255 CTTGTCCTTGTCGCCGTTCT 60.600 55.000 0.00 0.00 0.00 3.01 R
2476 3040 0.242017 GTTGCCAGGAGTACGTACGT 59.758 55.000 25.98 25.98 0.00 3.57 R
2479 3043 0.245539 GCAGTTGCCAGGAGTACGTA 59.754 55.000 0.00 0.00 34.31 3.57 R
2529 3097 2.441375 TGAATCACCACCAAAGGTCAGA 59.559 45.455 0.00 0.00 40.77 3.27 R
2985 3866 2.410053 GTCTGCTTTAGCGACAACAGAG 59.590 50.000 16.28 0.36 45.83 3.35 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
71 72 4.200283 CTGACCGCCGCTCTCCTC 62.200 72.222 0.00 0.00 0.00 3.71
79 80 4.465446 CGCTCTCCTCCCCTCCCA 62.465 72.222 0.00 0.00 0.00 4.37
154 166 3.448686 CTCCACTCGATCCAACATACAC 58.551 50.000 0.00 0.00 0.00 2.90
161 173 2.354704 CGATCCAACATACACACCACCT 60.355 50.000 0.00 0.00 0.00 4.00
162 174 2.851263 TCCAACATACACACCACCTC 57.149 50.000 0.00 0.00 0.00 3.85
163 175 1.349688 TCCAACATACACACCACCTCC 59.650 52.381 0.00 0.00 0.00 4.30
164 176 1.073125 CCAACATACACACCACCTCCA 59.927 52.381 0.00 0.00 0.00 3.86
165 177 2.151202 CAACATACACACCACCTCCAC 58.849 52.381 0.00 0.00 0.00 4.02
166 178 0.690762 ACATACACACCACCTCCACC 59.309 55.000 0.00 0.00 0.00 4.61
167 179 0.984230 CATACACACCACCTCCACCT 59.016 55.000 0.00 0.00 0.00 4.00
168 180 1.351017 CATACACACCACCTCCACCTT 59.649 52.381 0.00 0.00 0.00 3.50
175 187 0.036875 CCACCTCCACCTTTCCACTC 59.963 60.000 0.00 0.00 0.00 3.51
177 189 0.401395 ACCTCCACCTTTCCACTCCA 60.401 55.000 0.00 0.00 0.00 3.86
180 192 1.302511 CCACCTTTCCACTCCACCG 60.303 63.158 0.00 0.00 0.00 4.94
183 195 1.376037 CCTTTCCACTCCACCGCTC 60.376 63.158 0.00 0.00 0.00 5.03
214 226 2.989253 TCCTCGCTCTCGCCACAA 60.989 61.111 0.00 0.00 35.26 3.33
215 227 2.811317 CCTCGCTCTCGCCACAAC 60.811 66.667 0.00 0.00 35.26 3.32
216 228 2.049156 CTCGCTCTCGCCACAACA 60.049 61.111 0.00 0.00 35.26 3.33
217 229 2.049156 TCGCTCTCGCCACAACAG 60.049 61.111 0.00 0.00 35.26 3.16
218 230 2.049156 CGCTCTCGCCACAACAGA 60.049 61.111 0.00 0.00 0.00 3.41
219 231 1.664649 CGCTCTCGCCACAACAGAA 60.665 57.895 0.00 0.00 0.00 3.02
288 305 0.534412 AGTCCGAGGTCAGCAATCAG 59.466 55.000 0.00 0.00 0.00 2.90
290 307 0.532573 TCCGAGGTCAGCAATCAGTC 59.467 55.000 0.00 0.00 0.00 3.51
291 308 0.247460 CCGAGGTCAGCAATCAGTCA 59.753 55.000 0.00 0.00 0.00 3.41
292 309 1.638133 CGAGGTCAGCAATCAGTCAG 58.362 55.000 0.00 0.00 0.00 3.51
293 310 1.067283 CGAGGTCAGCAATCAGTCAGT 60.067 52.381 0.00 0.00 0.00 3.41
294 311 2.615869 GAGGTCAGCAATCAGTCAGTC 58.384 52.381 0.00 0.00 0.00 3.51
298 315 0.325933 CAGCAATCAGTCAGTCCCCA 59.674 55.000 0.00 0.00 0.00 4.96
300 317 1.168714 GCAATCAGTCAGTCCCCAAC 58.831 55.000 0.00 0.00 0.00 3.77
303 320 0.475632 ATCAGTCAGTCCCCAACCCA 60.476 55.000 0.00 0.00 0.00 4.51
304 321 0.696143 TCAGTCAGTCCCCAACCCAA 60.696 55.000 0.00 0.00 0.00 4.12
335 353 8.944029 CAATTTCTTAGATTTCTCTCTCAAGCA 58.056 33.333 0.00 0.00 32.66 3.91
337 355 8.908786 TTTCTTAGATTTCTCTCTCAAGCAAA 57.091 30.769 0.00 0.00 32.66 3.68
389 429 3.030652 CGTGTTCTTGGCACCACC 58.969 61.111 0.00 0.00 39.84 4.61
468 513 6.127869 TGTGTAGAACAGAGCTTGAGATCTAC 60.128 42.308 17.04 17.04 38.98 2.59
469 514 6.094881 GTGTAGAACAGAGCTTGAGATCTACT 59.905 42.308 20.94 2.66 38.98 2.57
470 515 5.835113 AGAACAGAGCTTGAGATCTACTC 57.165 43.478 0.00 0.74 38.98 2.59
471 516 4.644685 AGAACAGAGCTTGAGATCTACTCC 59.355 45.833 0.00 0.00 44.34 3.85
472 517 3.974719 ACAGAGCTTGAGATCTACTCCA 58.025 45.455 0.00 0.00 44.34 3.86
473 518 3.953612 ACAGAGCTTGAGATCTACTCCAG 59.046 47.826 0.00 0.00 44.34 3.86
474 519 3.953612 CAGAGCTTGAGATCTACTCCAGT 59.046 47.826 0.00 0.00 44.34 4.00
475 520 5.129634 CAGAGCTTGAGATCTACTCCAGTA 58.870 45.833 0.00 0.00 44.34 2.74
476 521 5.008613 CAGAGCTTGAGATCTACTCCAGTAC 59.991 48.000 0.00 0.00 44.34 2.73
477 522 3.880490 AGCTTGAGATCTACTCCAGTACG 59.120 47.826 0.00 0.00 44.34 3.67
478 523 3.628487 GCTTGAGATCTACTCCAGTACGT 59.372 47.826 0.00 0.00 44.34 3.57
479 524 4.815308 GCTTGAGATCTACTCCAGTACGTA 59.185 45.833 0.00 0.00 44.34 3.57
480 525 5.277442 GCTTGAGATCTACTCCAGTACGTAC 60.277 48.000 18.10 18.10 44.34 3.67
481 526 5.611128 TGAGATCTACTCCAGTACGTACT 57.389 43.478 22.45 22.45 44.34 2.73
482 527 6.721704 TGAGATCTACTCCAGTACGTACTA 57.278 41.667 26.95 12.60 44.34 1.82
567 645 3.426568 GCGGTGGTGCTCTGCTTC 61.427 66.667 0.00 0.00 34.72 3.86
568 646 2.345244 CGGTGGTGCTCTGCTTCT 59.655 61.111 0.00 0.00 0.00 2.85
569 647 2.031516 CGGTGGTGCTCTGCTTCTG 61.032 63.158 0.00 0.00 0.00 3.02
570 648 2.331132 GGTGGTGCTCTGCTTCTGC 61.331 63.158 0.00 0.00 40.20 4.26
571 649 1.302351 GTGGTGCTCTGCTTCTGCT 60.302 57.895 0.00 0.00 40.48 4.24
572 650 0.888285 GTGGTGCTCTGCTTCTGCTT 60.888 55.000 0.00 0.00 40.48 3.91
573 651 0.887836 TGGTGCTCTGCTTCTGCTTG 60.888 55.000 0.00 0.00 40.48 4.01
589 680 5.886992 TCTGCTTGCTTGATTGTTGATATG 58.113 37.500 0.00 0.00 0.00 1.78
647 747 3.786516 AATCCGACCGTTTTTGTGTTT 57.213 38.095 0.00 0.00 0.00 2.83
657 757 0.175989 TTTTGTGTTTCCCGGCCAAC 59.824 50.000 2.24 0.77 0.00 3.77
660 760 0.970937 TGTGTTTCCCGGCCAACAAA 60.971 50.000 16.00 9.85 34.70 2.83
662 762 0.175989 TGTTTCCCGGCCAACAAAAC 59.824 50.000 12.88 8.23 29.81 2.43
682 782 3.283751 ACCAAACTCATTTCGTCCACAA 58.716 40.909 0.00 0.00 0.00 3.33
727 830 3.200605 TCTGCTAATTGATCCTGCCTTCA 59.799 43.478 0.00 0.00 0.00 3.02
734 837 3.482156 TGATCCTGCCTTCATTAGCTC 57.518 47.619 0.00 0.00 0.00 4.09
785 888 4.580167 TCGGATTTTGCAGGATATTCTTGG 59.420 41.667 0.00 0.00 0.00 3.61
786 889 4.580167 CGGATTTTGCAGGATATTCTTGGA 59.420 41.667 0.00 0.00 0.00 3.53
787 890 5.067674 CGGATTTTGCAGGATATTCTTGGAA 59.932 40.000 0.00 0.00 32.45 3.53
872 986 2.031495 AACCTAGTCTGACTTGGCCT 57.969 50.000 29.86 18.66 43.50 5.19
873 987 1.270907 ACCTAGTCTGACTTGGCCTG 58.729 55.000 29.86 12.94 43.50 4.85
875 989 0.901124 CTAGTCTGACTTGGCCTGCT 59.099 55.000 16.53 0.00 0.00 4.24
877 991 2.033141 TCTGACTTGGCCTGCTGC 59.967 61.111 3.32 0.00 40.16 5.25
883 997 2.283101 TTGGCCTGCTGCGGATTT 60.283 55.556 10.70 0.00 42.61 2.17
887 1001 0.748005 GGCCTGCTGCGGATTTCTTA 60.748 55.000 10.70 0.00 42.61 2.10
894 1008 3.003480 GCTGCGGATTTCTTACTGTTCT 58.997 45.455 0.00 0.00 0.00 3.01
895 1009 3.437049 GCTGCGGATTTCTTACTGTTCTT 59.563 43.478 0.00 0.00 0.00 2.52
898 1012 4.454504 TGCGGATTTCTTACTGTTCTTTCC 59.545 41.667 0.00 0.00 0.00 3.13
899 1013 4.142665 GCGGATTTCTTACTGTTCTTTCCC 60.143 45.833 0.00 0.00 0.00 3.97
902 1016 5.648526 GGATTTCTTACTGTTCTTTCCCCTC 59.351 44.000 0.00 0.00 0.00 4.30
904 1018 5.485209 TTCTTACTGTTCTTTCCCCTCTC 57.515 43.478 0.00 0.00 0.00 3.20
907 1021 3.562108 ACTGTTCTTTCCCCTCTCCTA 57.438 47.619 0.00 0.00 0.00 2.94
913 1047 0.043334 TTTCCCCTCTCCTAGCTGCT 59.957 55.000 7.57 7.57 0.00 4.24
914 1048 0.397816 TTCCCCTCTCCTAGCTGCTC 60.398 60.000 4.91 0.00 0.00 4.26
938 1072 5.513788 CCAGGTTCTTGATCTTCTTCCAAGA 60.514 44.000 0.00 0.00 42.93 3.02
950 1084 3.169099 TCTTCCAAGAGCAGAGTAGCTT 58.831 45.455 0.00 0.00 46.75 3.74
951 1085 3.056250 TCTTCCAAGAGCAGAGTAGCTTG 60.056 47.826 0.00 0.00 46.75 4.01
952 1086 2.251818 TCCAAGAGCAGAGTAGCTTGT 58.748 47.619 0.00 0.00 46.75 3.16
953 1087 3.431415 TCCAAGAGCAGAGTAGCTTGTA 58.569 45.455 0.00 0.00 46.75 2.41
954 1088 3.193691 TCCAAGAGCAGAGTAGCTTGTAC 59.806 47.826 0.00 0.00 46.75 2.90
987 1121 2.300152 CTGTGTGGGCTAGACAAGAGAA 59.700 50.000 1.88 0.00 31.47 2.87
988 1122 2.300152 TGTGTGGGCTAGACAAGAGAAG 59.700 50.000 0.00 0.00 28.30 2.85
989 1123 2.563179 GTGTGGGCTAGACAAGAGAAGA 59.437 50.000 0.00 0.00 0.00 2.87
990 1124 2.828520 TGTGGGCTAGACAAGAGAAGAG 59.171 50.000 0.00 0.00 0.00 2.85
991 1125 3.093057 GTGGGCTAGACAAGAGAAGAGA 58.907 50.000 0.00 0.00 0.00 3.10
996 1130 5.040635 GGCTAGACAAGAGAAGAGAATTCG 58.959 45.833 0.00 0.00 0.00 3.34
999 1133 6.252655 GCTAGACAAGAGAAGAGAATTCGAAC 59.747 42.308 0.00 0.00 0.00 3.95
1557 1691 3.839432 CTCCTCGGCGTCTTCCCC 61.839 72.222 6.85 0.00 0.00 4.81
2450 3013 4.735369 TCCAATGTTCCAACAGGTAACAT 58.265 39.130 0.00 0.00 43.74 2.71
2452 3015 6.307776 TCCAATGTTCCAACAGGTAACATTA 58.692 36.000 16.89 7.32 46.65 1.90
2458 3022 7.429633 TGTTCCAACAGGTAACATTAACAATG 58.570 34.615 0.00 0.00 38.35 2.82
2464 3028 7.145932 ACAGGTAACATTAACAATGCTTCTC 57.854 36.000 0.00 0.00 42.69 2.87
2476 3040 4.402155 ACAATGCTTCTCAACTTTGGTTCA 59.598 37.500 0.00 0.00 32.73 3.18
2477 3041 4.574599 ATGCTTCTCAACTTTGGTTCAC 57.425 40.909 0.00 0.00 32.73 3.18
2479 3043 2.354821 GCTTCTCAACTTTGGTTCACGT 59.645 45.455 0.00 0.00 32.73 4.49
2534 3208 8.654230 TTTCTGAACAATAGAGCATATCTGAC 57.346 34.615 0.00 0.00 39.20 3.51
2859 3737 7.983307 AGAAACTGAACATAGTAGTACTACCG 58.017 38.462 25.97 18.01 36.75 4.02
2934 3815 6.345298 TCATGTAAAATCGATAGGCTTGTCA 58.655 36.000 0.00 0.00 0.00 3.58
2950 3831 2.080693 TGTCATGTAACCCGATTGTGC 58.919 47.619 0.00 0.00 0.00 4.57
2961 3842 2.223021 CCCGATTGTGCTTTGTGTATCG 60.223 50.000 0.00 0.00 35.81 2.92
2963 3844 2.785679 GATTGTGCTTTGTGTATCGCC 58.214 47.619 0.00 0.00 0.00 5.54
2964 3845 1.598882 TTGTGCTTTGTGTATCGCCA 58.401 45.000 0.00 0.00 0.00 5.69
2965 3846 1.155889 TGTGCTTTGTGTATCGCCAG 58.844 50.000 0.00 0.00 0.00 4.85
2966 3847 1.156736 GTGCTTTGTGTATCGCCAGT 58.843 50.000 0.00 0.00 0.00 4.00
2969 3850 3.374058 GTGCTTTGTGTATCGCCAGTAAT 59.626 43.478 0.00 0.00 0.00 1.89
2970 3851 4.006989 TGCTTTGTGTATCGCCAGTAATT 58.993 39.130 0.00 0.00 0.00 1.40
2985 3866 5.619981 GCCAGTAATTTCAGTGTTGTCATCC 60.620 44.000 0.00 0.00 0.00 3.51
3013 3894 3.195698 CTAAAGCAGACGGCCGGC 61.196 66.667 31.76 30.01 46.50 6.13
3014 3895 4.770874 TAAAGCAGACGGCCGGCC 62.771 66.667 36.69 36.69 46.50 6.13
3041 3923 3.322514 TGGCAGACCAAGCAGTAAC 57.677 52.632 0.00 0.00 45.37 2.50
3043 3925 0.960861 GGCAGACCAAGCAGTAACCC 60.961 60.000 0.00 0.00 35.26 4.11
3044 3926 0.036875 GCAGACCAAGCAGTAACCCT 59.963 55.000 0.00 0.00 0.00 4.34
3045 3927 1.813513 CAGACCAAGCAGTAACCCTG 58.186 55.000 0.00 0.00 44.53 4.45
3093 3984 5.564550 AGTTGCAGATAGGTTCTTGTTGAT 58.435 37.500 0.00 0.00 29.93 2.57
3101 3992 9.311916 CAGATAGGTTCTTGTTGATCTAAGAAG 57.688 37.037 15.73 11.85 41.90 2.85
3143 4036 7.922278 TCTGATTTCATTTTTGGTGTTTCAGAG 59.078 33.333 0.00 0.00 33.06 3.35
3157 4053 1.795768 TCAGAGTGAATCAACGTGGC 58.204 50.000 0.00 0.00 0.00 5.01
3186 4082 2.158841 CGTGCCGTACTTGCATAGTTTT 59.841 45.455 9.73 0.00 41.46 2.43
3187 4083 3.364565 CGTGCCGTACTTGCATAGTTTTT 60.365 43.478 9.73 0.00 41.46 1.94
3188 4084 3.911964 GTGCCGTACTTGCATAGTTTTTG 59.088 43.478 9.73 0.00 41.46 2.44
3192 4088 5.460748 GCCGTACTTGCATAGTTTTTGTTTT 59.539 36.000 6.82 0.00 38.33 2.43
3193 4089 6.637658 GCCGTACTTGCATAGTTTTTGTTTTA 59.362 34.615 6.82 0.00 38.33 1.52
3194 4090 7.327518 GCCGTACTTGCATAGTTTTTGTTTTAT 59.672 33.333 6.82 0.00 38.33 1.40
3195 4091 9.828852 CCGTACTTGCATAGTTTTTGTTTTATA 57.171 29.630 6.82 0.00 38.33 0.98
3201 4097 9.534565 TTGCATAGTTTTTGTTTTATAACAGCA 57.465 25.926 0.00 1.13 44.56 4.41
3202 4098 9.703892 TGCATAGTTTTTGTTTTATAACAGCAT 57.296 25.926 0.00 0.00 44.56 3.79
3231 4132 3.783191 TGCGTAGTTTGTTCACTACACA 58.217 40.909 10.73 5.05 46.66 3.72
3232 4133 4.373527 TGCGTAGTTTGTTCACTACACAT 58.626 39.130 10.73 0.00 46.66 3.21
3261 4162 7.716799 AAAATGGATGTATTGGTCTAGCAAA 57.283 32.000 0.00 0.00 0.00 3.68
3265 4166 5.123186 TGGATGTATTGGTCTAGCAAAAACG 59.877 40.000 0.00 0.00 0.00 3.60
3269 4170 1.961793 TGGTCTAGCAAAAACGCACT 58.038 45.000 0.00 0.00 0.00 4.40
3293 4194 0.394192 AAGTCTGCTGCTGCTGTGTA 59.606 50.000 17.00 0.00 40.48 2.90
3294 4195 0.037512 AGTCTGCTGCTGCTGTGTAG 60.038 55.000 17.00 5.39 40.48 2.74
3318 4219 8.172352 AGAGTAAGATAATAGTGCTGGTAGTG 57.828 38.462 0.00 0.00 0.00 2.74
3321 4222 5.207110 AGATAATAGTGCTGGTAGTGCTG 57.793 43.478 0.00 0.00 0.00 4.41
3474 4375 2.968574 TGCTTCATTTGCAAAACCCCTA 59.031 40.909 17.19 0.00 37.51 3.53
3476 4377 3.006859 GCTTCATTTGCAAAACCCCTAGT 59.993 43.478 17.19 0.00 0.00 2.57
3489 4390 3.954662 ACCCCTAGTCACCATATGGATT 58.045 45.455 28.77 12.10 38.94 3.01
3566 4468 0.329261 TGGACCAGGCTTCTTCCATG 59.671 55.000 4.69 0.00 33.02 3.66
3587 4492 6.656693 CCATGTTGAGGTAGAAGACAAGAATT 59.343 38.462 0.00 0.00 0.00 2.17
3607 4512 8.608844 AGAATTAAAGTGACTGGTAGAACTTG 57.391 34.615 0.00 0.00 33.30 3.16
3654 4559 3.181484 ACTTTAGGAAACGGTGGCAAAAC 60.181 43.478 0.00 0.00 0.00 2.43
3708 4613 4.428615 AAATTTGTTACAATCGACCCGG 57.571 40.909 0.00 0.00 0.00 5.73
3715 4620 0.395312 ACAATCGACCCGGAACAACT 59.605 50.000 0.73 0.00 0.00 3.16
3735 4640 6.924060 ACAACTACATGGATTATTACTCTCGC 59.076 38.462 0.00 0.00 0.00 5.03
3741 4646 5.952526 TGGATTATTACTCTCGCGACATA 57.047 39.130 3.71 0.00 0.00 2.29
3742 4647 6.321848 TGGATTATTACTCTCGCGACATAA 57.678 37.500 3.71 4.47 0.00 1.90
3743 4648 6.379386 TGGATTATTACTCTCGCGACATAAG 58.621 40.000 3.71 2.93 0.00 1.73
3744 4649 6.016527 TGGATTATTACTCTCGCGACATAAGT 60.017 38.462 3.71 9.24 0.00 2.24
3745 4650 6.305877 GGATTATTACTCTCGCGACATAAGTG 59.694 42.308 3.71 0.00 0.00 3.16
3746 4651 4.895224 ATTACTCTCGCGACATAAGTGA 57.105 40.909 3.71 3.95 0.00 3.41
3747 4652 2.546195 ACTCTCGCGACATAAGTGAC 57.454 50.000 3.71 0.00 0.00 3.67
3748 4653 1.132643 ACTCTCGCGACATAAGTGACC 59.867 52.381 3.71 0.00 0.00 4.02
3749 4654 0.454600 TCTCGCGACATAAGTGACCC 59.545 55.000 3.71 0.00 0.00 4.46
3750 4655 0.172578 CTCGCGACATAAGTGACCCA 59.827 55.000 3.71 0.00 0.00 4.51
3751 4656 0.604073 TCGCGACATAAGTGACCCAA 59.396 50.000 3.71 0.00 0.00 4.12
3752 4657 0.999406 CGCGACATAAGTGACCCAAG 59.001 55.000 0.00 0.00 0.00 3.61
3753 4658 1.403647 CGCGACATAAGTGACCCAAGA 60.404 52.381 0.00 0.00 0.00 3.02
3754 4659 2.738643 CGCGACATAAGTGACCCAAGAT 60.739 50.000 0.00 0.00 0.00 2.40
3755 4660 3.270877 GCGACATAAGTGACCCAAGATT 58.729 45.455 0.00 0.00 0.00 2.40
3756 4661 3.689649 GCGACATAAGTGACCCAAGATTT 59.310 43.478 0.00 0.00 0.00 2.17
3757 4662 4.156008 GCGACATAAGTGACCCAAGATTTT 59.844 41.667 0.00 0.00 0.00 1.82
3758 4663 5.335661 GCGACATAAGTGACCCAAGATTTTT 60.336 40.000 0.00 0.00 0.00 1.94
3759 4664 6.314784 CGACATAAGTGACCCAAGATTTTTC 58.685 40.000 0.00 0.00 0.00 2.29
3760 4665 6.072728 CGACATAAGTGACCCAAGATTTTTCA 60.073 38.462 0.00 0.00 0.00 2.69
3761 4666 6.981722 ACATAAGTGACCCAAGATTTTTCAC 58.018 36.000 0.00 0.00 37.45 3.18
3762 4667 4.937201 AAGTGACCCAAGATTTTTCACC 57.063 40.909 0.00 0.00 37.84 4.02
3763 4668 3.230976 AGTGACCCAAGATTTTTCACCC 58.769 45.455 0.00 0.00 37.84 4.61
3764 4669 2.299013 GTGACCCAAGATTTTTCACCCC 59.701 50.000 0.00 0.00 32.12 4.95
3765 4670 1.544246 GACCCAAGATTTTTCACCCCG 59.456 52.381 0.00 0.00 0.00 5.73
3766 4671 0.894835 CCCAAGATTTTTCACCCCGG 59.105 55.000 0.00 0.00 0.00 5.73
3767 4672 0.246360 CCAAGATTTTTCACCCCGGC 59.754 55.000 0.00 0.00 0.00 6.13
3768 4673 0.109319 CAAGATTTTTCACCCCGGCG 60.109 55.000 0.00 0.00 0.00 6.46
3769 4674 1.248101 AAGATTTTTCACCCCGGCGG 61.248 55.000 21.46 21.46 37.81 6.13
3778 4683 4.958897 CCCCGGCGGTGAACCAAA 62.959 66.667 26.32 0.00 35.14 3.28
3779 4684 3.361977 CCCGGCGGTGAACCAAAG 61.362 66.667 26.32 1.35 35.14 2.77
3780 4685 2.281208 CCGGCGGTGAACCAAAGA 60.281 61.111 19.97 0.00 35.14 2.52
3781 4686 1.674322 CCGGCGGTGAACCAAAGAT 60.674 57.895 19.97 0.00 35.14 2.40
3782 4687 1.241315 CCGGCGGTGAACCAAAGATT 61.241 55.000 19.97 0.00 35.14 2.40
3783 4688 0.596082 CGGCGGTGAACCAAAGATTT 59.404 50.000 0.00 0.00 35.14 2.17
3784 4689 1.665735 CGGCGGTGAACCAAAGATTTG 60.666 52.381 0.00 0.00 37.90 2.32
3785 4690 1.418373 GCGGTGAACCAAAGATTTGC 58.582 50.000 0.00 0.00 36.86 3.68
3786 4691 1.934849 GCGGTGAACCAAAGATTTGCC 60.935 52.381 0.00 0.00 36.86 4.52
3787 4692 1.613437 CGGTGAACCAAAGATTTGCCT 59.387 47.619 0.00 0.00 36.86 4.75
3788 4693 2.351738 CGGTGAACCAAAGATTTGCCTC 60.352 50.000 0.00 0.08 36.86 4.70
3789 4694 2.029020 GGTGAACCAAAGATTTGCCTCC 60.029 50.000 0.00 0.00 36.86 4.30
3790 4695 1.885887 TGAACCAAAGATTTGCCTCCG 59.114 47.619 0.00 0.00 36.86 4.63
3791 4696 1.886542 GAACCAAAGATTTGCCTCCGT 59.113 47.619 0.00 0.00 36.86 4.69
3792 4697 1.534729 ACCAAAGATTTGCCTCCGTC 58.465 50.000 0.00 0.00 36.86 4.79
3793 4698 1.202879 ACCAAAGATTTGCCTCCGTCA 60.203 47.619 0.00 0.00 36.86 4.35
3794 4699 2.094675 CCAAAGATTTGCCTCCGTCAT 58.905 47.619 0.00 0.00 36.86 3.06
3795 4700 2.159338 CCAAAGATTTGCCTCCGTCATG 60.159 50.000 0.00 0.00 36.86 3.07
3796 4701 2.749076 CAAAGATTTGCCTCCGTCATGA 59.251 45.455 0.00 0.00 0.00 3.07
3797 4702 3.287867 AAGATTTGCCTCCGTCATGAT 57.712 42.857 0.00 0.00 0.00 2.45
3798 4703 2.569059 AGATTTGCCTCCGTCATGATG 58.431 47.619 8.03 8.03 0.00 3.07
3799 4704 2.171237 AGATTTGCCTCCGTCATGATGA 59.829 45.455 16.77 7.08 0.00 2.92
3800 4705 2.715749 TTTGCCTCCGTCATGATGAT 57.284 45.000 16.77 0.00 0.00 2.45
3801 4706 1.957668 TTGCCTCCGTCATGATGATG 58.042 50.000 16.77 7.67 33.30 3.07
3802 4707 0.832626 TGCCTCCGTCATGATGATGT 59.167 50.000 16.77 0.00 31.62 3.06
3803 4708 1.210234 TGCCTCCGTCATGATGATGTT 59.790 47.619 16.77 0.00 31.62 2.71
3804 4709 1.600957 GCCTCCGTCATGATGATGTTG 59.399 52.381 16.77 5.71 31.62 3.33
3805 4710 2.742856 GCCTCCGTCATGATGATGTTGA 60.743 50.000 16.77 3.78 31.62 3.18
3806 4711 3.129109 CCTCCGTCATGATGATGTTGAG 58.871 50.000 16.77 12.66 31.62 3.02
3807 4712 2.543012 CTCCGTCATGATGATGTTGAGC 59.457 50.000 16.77 0.00 31.62 4.26
3808 4713 2.093553 TCCGTCATGATGATGTTGAGCA 60.094 45.455 16.77 0.00 31.62 4.26
3809 4714 2.679336 CCGTCATGATGATGTTGAGCAA 59.321 45.455 16.77 0.00 31.62 3.91
3810 4715 3.127376 CCGTCATGATGATGTTGAGCAAA 59.873 43.478 16.77 0.00 31.62 3.68
3811 4716 4.379708 CCGTCATGATGATGTTGAGCAAAA 60.380 41.667 16.77 0.00 31.62 2.44
3812 4717 5.337554 CGTCATGATGATGTTGAGCAAAAT 58.662 37.500 9.46 0.00 0.00 1.82
3813 4718 5.229260 CGTCATGATGATGTTGAGCAAAATG 59.771 40.000 9.46 0.00 0.00 2.32
3814 4719 5.518847 GTCATGATGATGTTGAGCAAAATGG 59.481 40.000 0.00 0.00 0.00 3.16
3815 4720 5.186215 TCATGATGATGTTGAGCAAAATGGT 59.814 36.000 0.00 0.00 0.00 3.55
3816 4721 5.471556 TGATGATGTTGAGCAAAATGGTT 57.528 34.783 0.00 0.00 0.00 3.67
3817 4722 5.231702 TGATGATGTTGAGCAAAATGGTTG 58.768 37.500 0.00 0.00 0.00 3.77
3818 4723 3.992643 TGATGTTGAGCAAAATGGTTGG 58.007 40.909 0.00 0.00 0.00 3.77
3819 4724 3.387374 TGATGTTGAGCAAAATGGTTGGT 59.613 39.130 0.00 0.00 0.00 3.67
3820 4725 3.176552 TGTTGAGCAAAATGGTTGGTG 57.823 42.857 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.813724 GCCACCATGGGAGGGGAG 61.814 72.222 22.59 3.24 38.19 4.30
90 91 2.488153 GCCAGCTATAAATAAAGGGCCG 59.512 50.000 0.00 0.00 34.17 6.13
92 93 2.826128 GGGCCAGCTATAAATAAAGGGC 59.174 50.000 4.39 0.00 39.40 5.19
154 166 0.537371 GTGGAAAGGTGGAGGTGGTG 60.537 60.000 0.00 0.00 0.00 4.17
161 173 1.764571 CGGTGGAGTGGAAAGGTGGA 61.765 60.000 0.00 0.00 0.00 4.02
162 174 1.302511 CGGTGGAGTGGAAAGGTGG 60.303 63.158 0.00 0.00 0.00 4.61
163 175 1.966451 GCGGTGGAGTGGAAAGGTG 60.966 63.158 0.00 0.00 0.00 4.00
164 176 2.113243 GAGCGGTGGAGTGGAAAGGT 62.113 60.000 0.00 0.00 0.00 3.50
165 177 1.376037 GAGCGGTGGAGTGGAAAGG 60.376 63.158 0.00 0.00 0.00 3.11
166 178 1.376037 GGAGCGGTGGAGTGGAAAG 60.376 63.158 0.00 0.00 0.00 2.62
167 179 1.827399 GAGGAGCGGTGGAGTGGAAA 61.827 60.000 0.00 0.00 0.00 3.13
168 180 2.203788 AGGAGCGGTGGAGTGGAA 60.204 61.111 0.00 0.00 0.00 3.53
175 187 3.151022 GAGGAGGAGGAGCGGTGG 61.151 72.222 0.00 0.00 0.00 4.61
177 189 3.351885 AGGAGGAGGAGGAGCGGT 61.352 66.667 0.00 0.00 0.00 5.68
180 192 1.152546 GAGGAGGAGGAGGAGGAGC 60.153 68.421 0.00 0.00 0.00 4.70
183 195 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
214 226 1.000731 GTGCTCTCTGCTCTGTTCTGT 59.999 52.381 0.00 0.00 43.37 3.41
215 227 1.273048 AGTGCTCTCTGCTCTGTTCTG 59.727 52.381 0.00 0.00 43.01 3.02
216 228 1.631405 AGTGCTCTCTGCTCTGTTCT 58.369 50.000 0.00 0.00 43.01 3.01
288 305 0.185175 ACTTTGGGTTGGGGACTGAC 59.815 55.000 0.00 0.00 0.00 3.51
290 307 1.328279 GAACTTTGGGTTGGGGACTG 58.672 55.000 0.00 0.00 38.41 3.51
291 308 0.930726 TGAACTTTGGGTTGGGGACT 59.069 50.000 0.00 0.00 38.41 3.85
292 309 1.783071 TTGAACTTTGGGTTGGGGAC 58.217 50.000 0.00 0.00 38.41 4.46
293 310 2.785357 ATTGAACTTTGGGTTGGGGA 57.215 45.000 0.00 0.00 38.41 4.81
294 311 3.390967 AGAAATTGAACTTTGGGTTGGGG 59.609 43.478 0.00 0.00 38.41 4.96
298 315 9.764363 GAAATCTAAGAAATTGAACTTTGGGTT 57.236 29.630 0.00 0.00 41.40 4.11
300 317 9.631452 GAGAAATCTAAGAAATTGAACTTTGGG 57.369 33.333 0.00 0.00 0.00 4.12
329 346 5.660460 TGCGTTCTAGATAGATTTGCTTGA 58.340 37.500 0.00 0.00 31.40 3.02
330 347 5.973651 TGCGTTCTAGATAGATTTGCTTG 57.026 39.130 0.00 0.00 31.40 4.01
333 351 6.644592 AGATCTTGCGTTCTAGATAGATTTGC 59.355 38.462 0.00 0.00 35.46 3.68
335 353 7.014711 TGGAGATCTTGCGTTCTAGATAGATTT 59.985 37.037 0.00 0.00 35.46 2.17
337 355 6.007076 TGGAGATCTTGCGTTCTAGATAGAT 58.993 40.000 0.00 0.00 35.46 1.98
360 378 2.943345 GAACACGCACGCAGGACTG 61.943 63.158 0.00 0.00 0.00 3.51
361 379 2.644555 AAGAACACGCACGCAGGACT 62.645 55.000 0.00 0.00 0.00 3.85
407 447 3.219224 CAAATGGATTGGGGCCGG 58.781 61.111 0.00 0.00 35.27 6.13
431 476 1.226974 CTACACATGCTCGGGACCG 60.227 63.158 3.96 3.96 41.35 4.79
468 513 5.125097 ACATCCAAACTAGTACGTACTGGAG 59.875 44.000 36.48 27.86 38.08 3.86
469 514 5.012239 ACATCCAAACTAGTACGTACTGGA 58.988 41.667 36.48 31.21 38.08 3.86
470 515 5.100259 CACATCCAAACTAGTACGTACTGG 58.900 45.833 33.23 31.87 40.22 4.00
471 516 5.706916 ACACATCCAAACTAGTACGTACTG 58.293 41.667 33.23 24.68 37.10 2.74
472 517 5.972107 ACACATCCAAACTAGTACGTACT 57.028 39.130 29.62 29.62 40.24 2.73
473 518 6.261118 CCTACACATCCAAACTAGTACGTAC 58.739 44.000 18.10 18.10 0.00 3.67
474 519 5.357878 CCCTACACATCCAAACTAGTACGTA 59.642 44.000 0.00 0.00 0.00 3.57
475 520 4.159135 CCCTACACATCCAAACTAGTACGT 59.841 45.833 0.00 0.00 0.00 3.57
476 521 4.159135 ACCCTACACATCCAAACTAGTACG 59.841 45.833 0.00 0.00 0.00 3.67
477 522 5.672421 ACCCTACACATCCAAACTAGTAC 57.328 43.478 0.00 0.00 0.00 2.73
478 523 5.544948 ACAACCCTACACATCCAAACTAGTA 59.455 40.000 0.00 0.00 0.00 1.82
479 524 4.349930 ACAACCCTACACATCCAAACTAGT 59.650 41.667 0.00 0.00 0.00 2.57
480 525 4.906618 ACAACCCTACACATCCAAACTAG 58.093 43.478 0.00 0.00 0.00 2.57
481 526 4.986054 ACAACCCTACACATCCAAACTA 57.014 40.909 0.00 0.00 0.00 2.24
482 527 3.876309 ACAACCCTACACATCCAAACT 57.124 42.857 0.00 0.00 0.00 2.66
567 645 4.503007 GCATATCAACAATCAAGCAAGCAG 59.497 41.667 0.00 0.00 0.00 4.24
568 646 4.082136 TGCATATCAACAATCAAGCAAGCA 60.082 37.500 0.00 0.00 0.00 3.91
569 647 4.426416 TGCATATCAACAATCAAGCAAGC 58.574 39.130 0.00 0.00 0.00 4.01
570 648 6.200286 GGAATGCATATCAACAATCAAGCAAG 59.800 38.462 0.00 0.00 34.15 4.01
571 649 6.044046 GGAATGCATATCAACAATCAAGCAA 58.956 36.000 0.00 0.00 34.15 3.91
572 650 5.127356 TGGAATGCATATCAACAATCAAGCA 59.873 36.000 0.00 0.00 35.03 3.91
573 651 5.593968 TGGAATGCATATCAACAATCAAGC 58.406 37.500 0.00 0.00 0.00 4.01
589 680 0.662374 GCACAGCGCATATGGAATGC 60.662 55.000 11.47 1.59 41.79 3.56
633 732 0.456628 CCGGGAAACACAAAAACGGT 59.543 50.000 0.00 0.00 35.47 4.83
647 747 0.976073 TTTGGTTTTGTTGGCCGGGA 60.976 50.000 2.18 0.00 0.00 5.14
657 757 4.502645 GTGGACGAAATGAGTTTGGTTTTG 59.497 41.667 0.00 0.00 36.56 2.44
660 760 3.283751 TGTGGACGAAATGAGTTTGGTT 58.716 40.909 0.00 0.00 36.56 3.67
662 762 3.980646 TTGTGGACGAAATGAGTTTGG 57.019 42.857 0.00 0.00 0.00 3.28
727 830 6.002653 AGAGTTTTAAATCCGGGAGCTAAT 57.997 37.500 0.00 0.00 0.00 1.73
734 837 6.745116 ACAAAAGAAGAGTTTTAAATCCGGG 58.255 36.000 0.00 0.00 0.00 5.73
872 986 2.472695 ACAGTAAGAAATCCGCAGCA 57.527 45.000 0.00 0.00 0.00 4.41
873 987 3.003480 AGAACAGTAAGAAATCCGCAGC 58.997 45.455 0.00 0.00 0.00 5.25
875 989 4.454504 GGAAAGAACAGTAAGAAATCCGCA 59.545 41.667 0.00 0.00 0.00 5.69
877 991 4.395231 GGGGAAAGAACAGTAAGAAATCCG 59.605 45.833 0.00 0.00 0.00 4.18
883 997 3.838903 GGAGAGGGGAAAGAACAGTAAGA 59.161 47.826 0.00 0.00 0.00 2.10
887 1001 2.424684 AGGAGAGGGGAAAGAACAGT 57.575 50.000 0.00 0.00 0.00 3.55
894 1008 0.043334 AGCAGCTAGGAGAGGGGAAA 59.957 55.000 0.00 0.00 0.00 3.13
895 1009 0.397816 GAGCAGCTAGGAGAGGGGAA 60.398 60.000 0.00 0.00 0.00 3.97
898 1012 1.075674 TGGAGCAGCTAGGAGAGGG 60.076 63.158 0.00 0.00 0.00 4.30
899 1013 2.428834 CTGGAGCAGCTAGGAGAGG 58.571 63.158 0.00 0.00 0.00 3.69
907 1021 0.990374 ATCAAGAACCTGGAGCAGCT 59.010 50.000 0.00 0.00 0.00 4.24
913 1047 3.909995 TGGAAGAAGATCAAGAACCTGGA 59.090 43.478 0.00 0.00 0.00 3.86
914 1048 4.292186 TGGAAGAAGATCAAGAACCTGG 57.708 45.455 0.00 0.00 0.00 4.45
938 1072 3.345414 ACTACGTACAAGCTACTCTGCT 58.655 45.455 0.00 0.00 46.40 4.24
950 1084 5.106038 CCCACACAGAATTCTACTACGTACA 60.106 44.000 7.86 0.00 0.00 2.90
951 1085 5.338365 CCCACACAGAATTCTACTACGTAC 58.662 45.833 7.86 0.00 0.00 3.67
952 1086 4.142315 GCCCACACAGAATTCTACTACGTA 60.142 45.833 7.86 0.00 0.00 3.57
953 1087 3.368116 GCCCACACAGAATTCTACTACGT 60.368 47.826 7.86 0.00 0.00 3.57
954 1088 3.119101 AGCCCACACAGAATTCTACTACG 60.119 47.826 7.86 0.00 0.00 3.51
972 1106 5.351948 AATTCTCTTCTCTTGTCTAGCCC 57.648 43.478 0.00 0.00 0.00 5.19
987 1121 3.005554 CAGCACCATGTTCGAATTCTCT 58.994 45.455 0.00 0.00 0.00 3.10
988 1122 2.096496 CCAGCACCATGTTCGAATTCTC 59.904 50.000 0.00 0.00 0.00 2.87
989 1123 2.086869 CCAGCACCATGTTCGAATTCT 58.913 47.619 0.00 0.00 0.00 2.40
990 1124 1.468054 GCCAGCACCATGTTCGAATTC 60.468 52.381 0.00 0.00 0.00 2.17
991 1125 0.527565 GCCAGCACCATGTTCGAATT 59.472 50.000 0.00 0.00 0.00 2.17
1924 2121 3.121019 GTCGATGAGGACGGGGAG 58.879 66.667 0.00 0.00 0.00 4.30
2045 2242 2.030562 CCTTGTCGCCGTTCTGGT 59.969 61.111 0.00 0.00 41.21 4.00
2046 2243 2.027625 GTCCTTGTCGCCGTTCTGG 61.028 63.158 0.00 0.00 42.50 3.86
2047 2244 0.878523 TTGTCCTTGTCGCCGTTCTG 60.879 55.000 0.00 0.00 0.00 3.02
2048 2245 0.600255 CTTGTCCTTGTCGCCGTTCT 60.600 55.000 0.00 0.00 0.00 3.01
2049 2246 1.566018 CCTTGTCCTTGTCGCCGTTC 61.566 60.000 0.00 0.00 0.00 3.95
2050 2247 1.597027 CCTTGTCCTTGTCGCCGTT 60.597 57.895 0.00 0.00 0.00 4.44
2397 2723 2.582052 GAGAGGATGAGGATGACGAGT 58.418 52.381 0.00 0.00 0.00 4.18
2450 3013 6.463995 ACCAAAGTTGAGAAGCATTGTTAA 57.536 33.333 0.00 0.00 0.00 2.01
2451 3014 6.096141 TGAACCAAAGTTGAGAAGCATTGTTA 59.904 34.615 0.00 0.00 35.94 2.41
2452 3015 5.105392 TGAACCAAAGTTGAGAAGCATTGTT 60.105 36.000 0.00 0.00 35.94 2.83
2458 3022 2.354821 ACGTGAACCAAAGTTGAGAAGC 59.645 45.455 0.00 0.00 35.94 3.86
2464 3028 3.798337 AGTACGTACGTGAACCAAAGTTG 59.202 43.478 30.25 0.00 35.94 3.16
2476 3040 0.242017 GTTGCCAGGAGTACGTACGT 59.758 55.000 25.98 25.98 0.00 3.57
2477 3041 0.524862 AGTTGCCAGGAGTACGTACG 59.475 55.000 19.49 15.01 0.00 3.67
2479 3043 0.245539 GCAGTTGCCAGGAGTACGTA 59.754 55.000 0.00 0.00 34.31 3.57
2509 3077 7.712639 GGTCAGATATGCTCTATTGTTCAGAAA 59.287 37.037 0.00 0.00 31.13 2.52
2510 3078 7.070447 AGGTCAGATATGCTCTATTGTTCAGAA 59.930 37.037 0.00 0.00 31.13 3.02
2524 3092 2.684881 CACCACCAAAGGTCAGATATGC 59.315 50.000 0.00 0.00 40.77 3.14
2525 3093 4.220693 TCACCACCAAAGGTCAGATATG 57.779 45.455 0.00 0.00 40.77 1.78
2527 3095 4.288366 TGAATCACCACCAAAGGTCAGATA 59.712 41.667 0.00 0.00 40.77 1.98
2528 3096 3.074390 TGAATCACCACCAAAGGTCAGAT 59.926 43.478 0.00 0.00 40.77 2.90
2529 3097 2.441375 TGAATCACCACCAAAGGTCAGA 59.559 45.455 0.00 0.00 40.77 3.27
2534 3208 3.254166 CAGAACTGAATCACCACCAAAGG 59.746 47.826 0.00 0.00 0.00 3.11
2766 3639 2.986306 GACGACGATGGTGGACGGT 61.986 63.158 0.00 0.00 0.00 4.83
2824 3697 4.370364 TGTTCAGTTTCTTGCTTGGTTC 57.630 40.909 0.00 0.00 0.00 3.62
2934 3815 3.057596 CACAAAGCACAATCGGGTTACAT 60.058 43.478 0.00 0.00 0.00 2.29
2950 3831 6.128282 ACTGAAATTACTGGCGATACACAAAG 60.128 38.462 0.00 0.00 0.00 2.77
2961 3842 4.829064 TGACAACACTGAAATTACTGGC 57.171 40.909 0.00 0.00 0.00 4.85
2963 3844 6.652481 AGAGGATGACAACACTGAAATTACTG 59.348 38.462 0.00 0.00 0.00 2.74
2964 3845 6.652481 CAGAGGATGACAACACTGAAATTACT 59.348 38.462 0.00 0.00 0.00 2.24
2965 3846 6.428159 ACAGAGGATGACAACACTGAAATTAC 59.572 38.462 12.53 0.00 0.00 1.89
2966 3847 6.533730 ACAGAGGATGACAACACTGAAATTA 58.466 36.000 12.53 0.00 0.00 1.40
2969 3850 4.422073 ACAGAGGATGACAACACTGAAA 57.578 40.909 12.53 0.00 0.00 2.69
2970 3851 4.129380 CAACAGAGGATGACAACACTGAA 58.871 43.478 12.53 0.00 0.00 3.02
2985 3866 2.410053 GTCTGCTTTAGCGACAACAGAG 59.590 50.000 16.28 0.36 45.83 3.35
3013 3894 2.264794 GTCTGCCACCCGTACTGG 59.735 66.667 1.12 1.12 37.55 4.00
3014 3895 2.107041 TTGGTCTGCCACCCGTACTG 62.107 60.000 0.00 0.00 46.18 2.74
3038 3920 4.825085 AGAAATCTGAAAAACGCAGGGTTA 59.175 37.500 2.78 0.00 38.08 2.85
3039 3921 3.636764 AGAAATCTGAAAAACGCAGGGTT 59.363 39.130 0.00 0.00 41.76 4.11
3040 3922 3.222603 AGAAATCTGAAAAACGCAGGGT 58.777 40.909 0.00 0.00 34.20 4.34
3041 3923 3.253188 TGAGAAATCTGAAAAACGCAGGG 59.747 43.478 0.00 0.00 34.20 4.45
3043 3925 5.514279 AGTTGAGAAATCTGAAAAACGCAG 58.486 37.500 0.00 0.00 34.71 5.18
3044 3926 5.499139 AGTTGAGAAATCTGAAAAACGCA 57.501 34.783 0.00 0.00 0.00 5.24
3045 3927 5.173854 CCAAGTTGAGAAATCTGAAAAACGC 59.826 40.000 3.87 0.00 0.00 4.84
3046 3928 6.494842 TCCAAGTTGAGAAATCTGAAAAACG 58.505 36.000 3.87 0.00 0.00 3.60
3047 3929 7.484140 ACTCCAAGTTGAGAAATCTGAAAAAC 58.516 34.615 3.87 0.00 36.22 2.43
3048 3930 7.645058 ACTCCAAGTTGAGAAATCTGAAAAA 57.355 32.000 3.87 0.00 36.22 1.94
3143 4036 1.803334 TACAGGCCACGTTGATTCAC 58.197 50.000 5.01 0.00 0.00 3.18
3187 4083 9.444534 CGCAAATGTATATGCTGTTATAAAACA 57.555 29.630 0.00 0.00 43.17 2.83
3188 4084 9.445786 ACGCAAATGTATATGCTGTTATAAAAC 57.554 29.630 0.00 0.00 40.39 2.43
3192 4088 9.483916 AACTACGCAAATGTATATGCTGTTATA 57.516 29.630 0.00 0.00 40.39 0.98
3193 4089 7.962964 ACTACGCAAATGTATATGCTGTTAT 57.037 32.000 0.00 0.00 40.39 1.89
3194 4090 7.780008 AACTACGCAAATGTATATGCTGTTA 57.220 32.000 0.00 0.00 40.39 2.41
3195 4091 6.677781 AACTACGCAAATGTATATGCTGTT 57.322 33.333 0.00 0.00 40.39 3.16
3196 4092 6.093495 ACAAACTACGCAAATGTATATGCTGT 59.907 34.615 0.00 0.00 40.39 4.40
3197 4093 6.486248 ACAAACTACGCAAATGTATATGCTG 58.514 36.000 0.00 0.00 40.39 4.41
3198 4094 6.677781 ACAAACTACGCAAATGTATATGCT 57.322 33.333 0.00 0.00 40.39 3.79
3199 4095 6.964370 TGAACAAACTACGCAAATGTATATGC 59.036 34.615 0.00 0.00 39.17 3.14
3200 4096 8.175069 AGTGAACAAACTACGCAAATGTATATG 58.825 33.333 0.00 0.00 0.00 1.78
3201 4097 8.263940 AGTGAACAAACTACGCAAATGTATAT 57.736 30.769 0.00 0.00 0.00 0.86
3202 4098 7.661127 AGTGAACAAACTACGCAAATGTATA 57.339 32.000 0.00 0.00 0.00 1.47
3248 4149 2.884639 AGTGCGTTTTTGCTAGACCAAT 59.115 40.909 0.00 0.00 35.36 3.16
3261 4162 2.135933 GCAGACTTCTGTAGTGCGTTT 58.864 47.619 8.04 0.00 45.45 3.60
3265 4166 1.074752 GCAGCAGACTTCTGTAGTGC 58.925 55.000 8.04 10.33 45.45 4.40
3269 4170 0.972134 AGCAGCAGCAGACTTCTGTA 59.028 50.000 3.17 0.00 45.45 2.74
3293 4194 7.255660 GCACTACCAGCACTATTATCTTACTCT 60.256 40.741 0.00 0.00 0.00 3.24
3294 4195 6.864165 GCACTACCAGCACTATTATCTTACTC 59.136 42.308 0.00 0.00 0.00 2.59
3318 4219 5.186996 TCAATCTGTTTTCCAACTTCAGC 57.813 39.130 0.00 0.00 33.58 4.26
3321 4222 6.015940 ACCTGATCAATCTGTTTTCCAACTTC 60.016 38.462 0.00 0.00 33.58 3.01
3431 4332 4.520492 CAGACTTTAGGAAGTTGGCACATT 59.480 41.667 0.00 0.00 45.88 2.71
3432 4333 4.074970 CAGACTTTAGGAAGTTGGCACAT 58.925 43.478 0.00 0.00 45.88 3.21
3433 4334 3.476552 CAGACTTTAGGAAGTTGGCACA 58.523 45.455 0.00 0.00 45.88 4.57
3489 4390 6.672266 TGGCTTATACCATGTTTGGAAAAA 57.328 33.333 0.00 0.00 46.92 1.94
3493 4394 4.099266 GCATTGGCTTATACCATGTTTGGA 59.901 41.667 0.00 0.00 40.47 3.53
3566 4468 9.274206 ACTTTAATTCTTGTCTTCTACCTCAAC 57.726 33.333 0.00 0.00 0.00 3.18
3587 4492 4.504340 GCCCAAGTTCTACCAGTCACTTTA 60.504 45.833 0.00 0.00 0.00 1.85
3607 4512 1.338107 AAAAAGTGCCTACCTTGCCC 58.662 50.000 0.00 0.00 0.00 5.36
3629 4534 3.818180 TGCCACCGTTTCCTAAAGTAAA 58.182 40.909 0.00 0.00 0.00 2.01
3632 4537 2.351706 TTGCCACCGTTTCCTAAAGT 57.648 45.000 0.00 0.00 0.00 2.66
3635 4540 2.376109 TGTTTTGCCACCGTTTCCTAA 58.624 42.857 0.00 0.00 0.00 2.69
3636 4541 2.054232 TGTTTTGCCACCGTTTCCTA 57.946 45.000 0.00 0.00 0.00 2.94
3637 4542 1.408969 ATGTTTTGCCACCGTTTCCT 58.591 45.000 0.00 0.00 0.00 3.36
3638 4543 2.232756 AATGTTTTGCCACCGTTTCC 57.767 45.000 0.00 0.00 0.00 3.13
3654 4559 9.956720 CTTCTTAATTAATAGGTGAGGCAAATG 57.043 33.333 0.00 0.00 0.00 2.32
3689 4594 3.337694 TCCGGGTCGATTGTAACAAAT 57.662 42.857 0.00 0.00 0.00 2.32
3698 4603 1.619827 TGTAGTTGTTCCGGGTCGATT 59.380 47.619 0.00 0.00 0.00 3.34
3708 4613 8.969267 CGAGAGTAATAATCCATGTAGTTGTTC 58.031 37.037 0.00 0.00 0.00 3.18
3715 4620 5.239963 TGTCGCGAGAGTAATAATCCATGTA 59.760 40.000 10.24 0.00 43.49 2.29
3735 4640 5.880054 AAAATCTTGGGTCACTTATGTCG 57.120 39.130 0.00 0.00 0.00 4.35
3741 4646 3.641436 GGGTGAAAAATCTTGGGTCACTT 59.359 43.478 0.00 0.00 38.87 3.16
3742 4647 3.230976 GGGTGAAAAATCTTGGGTCACT 58.769 45.455 0.00 0.00 38.87 3.41
3743 4648 2.299013 GGGGTGAAAAATCTTGGGTCAC 59.701 50.000 0.00 0.00 38.28 3.67
3744 4649 2.604139 GGGGTGAAAAATCTTGGGTCA 58.396 47.619 0.00 0.00 0.00 4.02
3745 4650 1.544246 CGGGGTGAAAAATCTTGGGTC 59.456 52.381 0.00 0.00 0.00 4.46
3746 4651 1.627864 CGGGGTGAAAAATCTTGGGT 58.372 50.000 0.00 0.00 0.00 4.51
3747 4652 0.894835 CCGGGGTGAAAAATCTTGGG 59.105 55.000 0.00 0.00 0.00 4.12
3748 4653 0.246360 GCCGGGGTGAAAAATCTTGG 59.754 55.000 2.18 0.00 0.00 3.61
3749 4654 0.109319 CGCCGGGGTGAAAAATCTTG 60.109 55.000 11.01 0.00 0.00 3.02
3750 4655 1.248101 CCGCCGGGGTGAAAAATCTT 61.248 55.000 18.27 0.00 0.00 2.40
3751 4656 1.677633 CCGCCGGGGTGAAAAATCT 60.678 57.895 18.27 0.00 0.00 2.40
3752 4657 2.882132 CCGCCGGGGTGAAAAATC 59.118 61.111 18.27 0.00 0.00 2.17
3761 4666 4.958897 TTTGGTTCACCGCCGGGG 62.959 66.667 12.43 12.43 43.62 5.73
3762 4667 3.361977 CTTTGGTTCACCGCCGGG 61.362 66.667 8.57 0.00 39.43 5.73
3763 4668 1.241315 AATCTTTGGTTCACCGCCGG 61.241 55.000 0.00 0.00 39.43 6.13
3764 4669 0.596082 AAATCTTTGGTTCACCGCCG 59.404 50.000 0.00 0.00 39.43 6.46
3765 4670 1.934849 GCAAATCTTTGGTTCACCGCC 60.935 52.381 4.93 0.00 38.57 6.13
3766 4671 1.418373 GCAAATCTTTGGTTCACCGC 58.582 50.000 4.93 0.00 38.57 5.68
3767 4672 1.613437 AGGCAAATCTTTGGTTCACCG 59.387 47.619 4.93 0.00 38.57 4.94
3768 4673 2.029020 GGAGGCAAATCTTTGGTTCACC 60.029 50.000 4.93 0.00 38.57 4.02
3769 4674 2.351738 CGGAGGCAAATCTTTGGTTCAC 60.352 50.000 4.93 0.00 38.57 3.18
3770 4675 1.885887 CGGAGGCAAATCTTTGGTTCA 59.114 47.619 4.93 0.00 38.57 3.18
3771 4676 1.886542 ACGGAGGCAAATCTTTGGTTC 59.113 47.619 4.93 0.00 38.57 3.62
3772 4677 1.886542 GACGGAGGCAAATCTTTGGTT 59.113 47.619 4.93 0.00 38.57 3.67
3773 4678 1.202879 TGACGGAGGCAAATCTTTGGT 60.203 47.619 4.93 0.00 38.57 3.67
3774 4679 1.533625 TGACGGAGGCAAATCTTTGG 58.466 50.000 4.93 0.00 38.57 3.28
3775 4680 2.749076 TCATGACGGAGGCAAATCTTTG 59.251 45.455 0.00 0.00 41.03 2.77
3776 4681 3.071874 TCATGACGGAGGCAAATCTTT 57.928 42.857 0.00 0.00 0.00 2.52
3777 4682 2.787473 TCATGACGGAGGCAAATCTT 57.213 45.000 0.00 0.00 0.00 2.40
3778 4683 2.171237 TCATCATGACGGAGGCAAATCT 59.829 45.455 0.00 0.00 0.00 2.40
3779 4684 2.564771 TCATCATGACGGAGGCAAATC 58.435 47.619 0.00 0.00 0.00 2.17
3780 4685 2.715749 TCATCATGACGGAGGCAAAT 57.284 45.000 0.00 0.00 0.00 2.32
3781 4686 2.291365 CATCATCATGACGGAGGCAAA 58.709 47.619 0.00 0.00 30.57 3.68
3782 4687 1.210234 ACATCATCATGACGGAGGCAA 59.790 47.619 0.00 0.00 33.72 4.52
3783 4688 0.832626 ACATCATCATGACGGAGGCA 59.167 50.000 0.00 0.00 33.72 4.75
3784 4689 1.600957 CAACATCATCATGACGGAGGC 59.399 52.381 0.00 0.00 33.72 4.70
3785 4690 3.129109 CTCAACATCATCATGACGGAGG 58.871 50.000 0.00 3.25 33.72 4.30
3786 4691 2.543012 GCTCAACATCATCATGACGGAG 59.457 50.000 0.00 0.00 33.72 4.63
3787 4692 2.093553 TGCTCAACATCATCATGACGGA 60.094 45.455 0.00 0.00 33.72 4.69
3788 4693 2.282407 TGCTCAACATCATCATGACGG 58.718 47.619 0.00 0.00 33.72 4.79
3789 4694 4.345271 TTTGCTCAACATCATCATGACG 57.655 40.909 0.00 0.00 33.72 4.35
3790 4695 5.518847 CCATTTTGCTCAACATCATCATGAC 59.481 40.000 0.00 0.00 33.72 3.06
3791 4696 5.186215 ACCATTTTGCTCAACATCATCATGA 59.814 36.000 0.00 0.00 33.72 3.07
3792 4697 5.416083 ACCATTTTGCTCAACATCATCATG 58.584 37.500 0.00 0.00 35.92 3.07
3793 4698 5.670792 ACCATTTTGCTCAACATCATCAT 57.329 34.783 0.00 0.00 0.00 2.45
3794 4699 5.231702 CAACCATTTTGCTCAACATCATCA 58.768 37.500 0.00 0.00 0.00 3.07
3795 4700 4.628333 CCAACCATTTTGCTCAACATCATC 59.372 41.667 0.00 0.00 0.00 2.92
3796 4701 4.040706 ACCAACCATTTTGCTCAACATCAT 59.959 37.500 0.00 0.00 0.00 2.45
3797 4702 3.387374 ACCAACCATTTTGCTCAACATCA 59.613 39.130 0.00 0.00 0.00 3.07
3798 4703 3.742369 CACCAACCATTTTGCTCAACATC 59.258 43.478 0.00 0.00 0.00 3.06
3799 4704 3.731089 CACCAACCATTTTGCTCAACAT 58.269 40.909 0.00 0.00 0.00 2.71
3800 4705 3.176552 CACCAACCATTTTGCTCAACA 57.823 42.857 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.