Multiple sequence alignment - TraesCS1A01G181000

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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 TraesCS1A01G181000 chr1A 100.000 4825 0 0 1 4825 327018953 327014129 0.000000e+00 8911.0
1 TraesCS1A01G181000 chr1B 91.940 1588 60 34 700 2248 357638060 357639618 0.000000e+00 2161.0
2 TraesCS1A01G181000 chr1B 89.394 1254 75 28 3045 4287 357640859 357642065 0.000000e+00 1526.0
3 TraesCS1A01G181000 chr1B 93.045 532 27 6 58 582 357637182 357637710 0.000000e+00 769.0
4 TraesCS1A01G181000 chr1B 88.462 494 19 10 2479 2963 357640329 357640793 3.260000e-156 562.0
5 TraesCS1A01G181000 chr1B 87.277 448 37 12 4276 4705 357642090 357642535 1.210000e-135 494.0
6 TraesCS1A01G181000 chr1D 95.594 1339 24 13 700 2035 254794426 254793120 0.000000e+00 2113.0
7 TraesCS1A01G181000 chr1D 93.110 1103 51 10 3193 4287 254791590 254790505 0.000000e+00 1592.0
8 TraesCS1A01G181000 chr1D 91.525 649 29 10 9 638 254795250 254794609 0.000000e+00 870.0
9 TraesCS1A01G181000 chr1D 93.679 443 22 2 2688 3128 254792158 254791720 0.000000e+00 658.0
10 TraesCS1A01G181000 chr1D 88.262 443 26 15 4287 4703 254790471 254790029 1.550000e-139 507.0
11 TraesCS1A01G181000 chr1D 83.820 445 41 9 2052 2481 254793066 254792638 1.260000e-105 394.0
12 TraesCS1A01G181000 chr1D 91.429 210 9 4 2479 2687 254792460 254792259 3.680000e-71 279.0
13 TraesCS1A01G181000 chr1D 80.952 105 9 4 605 700 3853241 3853139 6.700000e-09 73.1
14 TraesCS1A01G181000 chr1D 97.368 38 1 0 665 702 57851379 57851342 1.120000e-06 65.8
15 TraesCS1A01G181000 chr1D 100.000 32 0 0 3125 3156 254791699 254791668 5.220000e-05 60.2
16 TraesCS1A01G181000 chr6B 85.589 798 107 6 995 1791 2772083 2772873 0.000000e+00 830.0
17 TraesCS1A01G181000 chr6B 85.607 799 103 11 996 1791 1133234 1132445 0.000000e+00 828.0
18 TraesCS1A01G181000 chr6B 85.569 589 83 2 3220 3807 1131985 1131398 2.470000e-172 616.0
19 TraesCS1A01G181000 chr6B 85.640 578 80 2 3213 3790 2772998 2773572 5.340000e-169 604.0
20 TraesCS1A01G181000 chr6B 94.872 39 2 0 669 707 239177124 239177086 1.450000e-05 62.1
21 TraesCS1A01G181000 chrUn 89.671 639 66 0 1153 1791 329195308 329194670 0.000000e+00 815.0
22 TraesCS1A01G181000 chrUn 86.340 571 76 2 3220 3789 329194289 329193720 5.300000e-174 621.0
23 TraesCS1A01G181000 chrUn 100.000 34 0 0 669 702 74074451 74074484 4.030000e-06 63.9
24 TraesCS1A01G181000 chr3B 80.374 107 9 7 605 701 224273164 224273060 2.410000e-08 71.3
25 TraesCS1A01G181000 chr3B 97.368 38 1 0 669 706 461421859 461421822 1.120000e-06 65.8
26 TraesCS1A01G181000 chr3A 100.000 35 0 0 669 703 270482714 270482680 1.120000e-06 65.8
27 TraesCS1A01G181000 chr6D 100.000 34 0 0 669 702 181351141 181351174 4.030000e-06 63.9
28 TraesCS1A01G181000 chr7B 94.872 39 2 0 669 707 324851568 324851530 1.450000e-05 62.1
29 TraesCS1A01G181000 chr2A 84.746 59 5 3 4768 4825 470245278 470245333 6.750000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G181000 chr1A 327014129 327018953 4824 True 8911.00 8911 100.000000 1 4825 1 chr1A.!!$R1 4824
1 TraesCS1A01G181000 chr1B 357637182 357642535 5353 False 1102.40 2161 90.023600 58 4705 5 chr1B.!!$F1 4647
2 TraesCS1A01G181000 chr1D 254790029 254795250 5221 True 809.15 2113 92.177375 9 4703 8 chr1D.!!$R3 4694
3 TraesCS1A01G181000 chr6B 1131398 1133234 1836 True 722.00 828 85.588000 996 3807 2 chr6B.!!$R2 2811
4 TraesCS1A01G181000 chr6B 2772083 2773572 1489 False 717.00 830 85.614500 995 3790 2 chr6B.!!$F1 2795
5 TraesCS1A01G181000 chrUn 329193720 329195308 1588 True 718.00 815 88.005500 1153 3789 2 chrUn.!!$R1 2636

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
813 1063 0.035820 TTCCAATCCTGTGCCCGTAC 60.036 55.0 0.00 0.0 0.00 3.67 F
1802 2061 0.036765 GGTAAGGACGCACACATCCA 60.037 55.0 0.00 0.0 37.47 3.41 F
1887 2154 0.435008 CAGCTGTTGCGTAGAACGAC 59.565 55.0 5.25 0.0 46.05 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 2646 0.752658 TACTCACAGCCATCCCATCG 59.247 55.0 0.00 0.0 0.00 3.84 R
2631 3820 0.961753 GTCCTTTTGGGCCTTGTCTG 59.038 55.0 4.53 0.0 38.54 3.51 R
3844 5223 0.251297 CATCAGGGCTTGGTGGTTCA 60.251 55.0 1.21 0.0 34.09 3.18 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
37 38 5.675970 TGAAATTCAAAGTTCGCTCGTTAG 58.324 37.500 0.00 0.00 35.90 2.34
54 55 7.515371 CGCTCGTTAGAATTTCCTATCAGAAAC 60.515 40.741 0.00 0.00 38.51 2.78
99 103 5.502606 GTCGTTCAGAACAAGAAGGAAAAG 58.497 41.667 13.82 0.00 40.31 2.27
167 171 3.060602 GGAAGGAGAAGTTGAACACGAG 58.939 50.000 0.00 0.00 0.00 4.18
178 182 1.939934 TGAACACGAGTTTGCCTTCTG 59.060 47.619 0.00 0.00 38.30 3.02
317 324 1.131315 GCCTTCGGATGCTCACTTTTC 59.869 52.381 0.00 0.00 0.00 2.29
340 347 3.958798 CTGCCAGATTTGGGAAGATTCAT 59.041 43.478 4.15 0.00 44.95 2.57
430 437 1.010419 GCGGCCAATTTTGACTGCTG 61.010 55.000 2.24 0.06 39.47 4.41
448 455 2.474816 CTGCTAGTAATGGTCGCCTTC 58.525 52.381 0.00 0.00 0.00 3.46
528 540 3.855689 ACATAAGTGCATTGAACCTGC 57.144 42.857 0.00 0.00 40.10 4.85
533 545 2.034124 AGTGCATTGAACCTGCTTTGT 58.966 42.857 0.00 0.00 40.34 2.83
534 546 2.431782 AGTGCATTGAACCTGCTTTGTT 59.568 40.909 0.00 0.00 40.34 2.83
545 557 3.310501 ACCTGCTTTGTTTGTACGTACAC 59.689 43.478 27.36 17.35 35.64 2.90
558 570 0.036388 CGTACACATTCACCCTGGCT 60.036 55.000 0.00 0.00 0.00 4.75
568 580 4.041762 CCCTGGCTGGCCGGTTAA 62.042 66.667 14.55 0.00 40.80 2.01
581 593 3.159353 CCGGTTAAAGGGCAAATTAGC 57.841 47.619 0.00 0.00 0.00 3.09
612 636 6.424032 ACTGTCCCATAAAATTTACTCCCTC 58.576 40.000 0.00 0.00 0.00 4.30
613 637 6.217693 ACTGTCCCATAAAATTTACTCCCTCT 59.782 38.462 0.00 0.00 0.00 3.69
614 638 6.423182 TGTCCCATAAAATTTACTCCCTCTG 58.577 40.000 0.00 0.00 0.00 3.35
615 639 5.299531 GTCCCATAAAATTTACTCCCTCTGC 59.700 44.000 0.00 0.00 0.00 4.26
617 641 5.532779 CCCATAAAATTTACTCCCTCTGCTC 59.467 44.000 0.00 0.00 0.00 4.26
630 654 7.220740 ACTCCCTCTGCTCTTAAATATAAAGC 58.779 38.462 0.00 0.00 0.00 3.51
631 655 6.534634 TCCCTCTGCTCTTAAATATAAAGCC 58.465 40.000 0.00 0.00 31.96 4.35
635 702 8.907885 CCTCTGCTCTTAAATATAAAGCCTTTT 58.092 33.333 0.00 0.00 31.96 2.27
675 856 8.683615 TGTGAACTACATACAGAACGAATCTAT 58.316 33.333 0.00 0.00 33.09 1.98
716 966 3.829886 ACATCAACATTACACTTGCCG 57.170 42.857 0.00 0.00 0.00 5.69
752 1002 6.420588 TGACGTTACAATTTACAAAGAACGG 58.579 36.000 8.82 0.00 41.71 4.44
777 1027 8.266682 GGTACGATCTTTTTCTTTTTCTTTTGC 58.733 33.333 0.00 0.00 0.00 3.68
778 1028 7.234187 ACGATCTTTTTCTTTTTCTTTTGCC 57.766 32.000 0.00 0.00 0.00 4.52
804 1054 1.089920 CGTTGCTCCTTCCAATCCTG 58.910 55.000 0.00 0.00 0.00 3.86
813 1063 0.035820 TTCCAATCCTGTGCCCGTAC 60.036 55.000 0.00 0.00 0.00 3.67
814 1064 1.813753 CCAATCCTGTGCCCGTACG 60.814 63.158 8.69 8.69 0.00 3.67
815 1065 1.079405 CAATCCTGTGCCCGTACGT 60.079 57.895 15.21 0.00 0.00 3.57
816 1066 0.173935 CAATCCTGTGCCCGTACGTA 59.826 55.000 15.21 0.00 0.00 3.57
926 1179 1.679311 CTGCTAGCTTCCCCACACA 59.321 57.895 17.23 0.00 0.00 3.72
941 1194 2.200067 CACACAGCTCTTGATCGATCC 58.800 52.381 22.31 6.72 0.00 3.36
964 1217 1.445066 CGCGCTCTCTTCTCTGCAA 60.445 57.895 5.56 0.00 0.00 4.08
965 1218 1.010935 CGCGCTCTCTTCTCTGCAAA 61.011 55.000 5.56 0.00 0.00 3.68
966 1219 1.151668 GCGCTCTCTTCTCTGCAAAA 58.848 50.000 0.00 0.00 0.00 2.44
967 1220 1.532868 GCGCTCTCTTCTCTGCAAAAA 59.467 47.619 0.00 0.00 0.00 1.94
968 1221 2.412585 GCGCTCTCTTCTCTGCAAAAAG 60.413 50.000 0.00 0.00 0.00 2.27
1527 1786 2.126071 CAGGCGACGTTCGTGGAT 60.126 61.111 11.11 0.00 42.81 3.41
1802 2061 0.036765 GGTAAGGACGCACACATCCA 60.037 55.000 0.00 0.00 37.47 3.41
1803 2062 1.609580 GGTAAGGACGCACACATCCAA 60.610 52.381 0.00 0.00 37.47 3.53
1824 2083 6.043938 TCCAAGAAGTACTCCCAAGTTATGTT 59.956 38.462 0.00 0.00 36.92 2.71
1825 2084 6.149474 CCAAGAAGTACTCCCAAGTTATGTTG 59.851 42.308 0.00 0.00 36.92 3.33
1826 2085 5.246307 AGAAGTACTCCCAAGTTATGTTGC 58.754 41.667 0.00 0.00 36.92 4.17
1827 2086 4.634012 AGTACTCCCAAGTTATGTTGCA 57.366 40.909 0.00 0.00 36.92 4.08
1887 2154 0.435008 CAGCTGTTGCGTAGAACGAC 59.565 55.000 5.25 0.00 46.05 4.34
1942 2209 5.261216 CAAGCCTATCTCCCCAACTTAAAA 58.739 41.667 0.00 0.00 0.00 1.52
1943 2210 5.117406 AGCCTATCTCCCCAACTTAAAAG 57.883 43.478 0.00 0.00 0.00 2.27
1944 2211 4.540502 AGCCTATCTCCCCAACTTAAAAGT 59.459 41.667 0.00 0.00 42.04 2.66
1945 2212 4.882427 GCCTATCTCCCCAACTTAAAAGTC 59.118 45.833 0.00 0.00 38.57 3.01
2035 2306 5.353123 TCAACCGTCATCTTATTTAACTGGC 59.647 40.000 0.00 0.00 0.00 4.85
2043 2378 6.428465 TCATCTTATTTAACTGGCGTGAAACA 59.572 34.615 0.00 0.00 35.74 2.83
2049 2384 2.157834 ACTGGCGTGAAACAATCGTA 57.842 45.000 0.00 0.00 35.74 3.43
2050 2385 2.485903 ACTGGCGTGAAACAATCGTAA 58.514 42.857 0.00 0.00 35.74 3.18
2060 2395 2.199291 ACAATCGTAATCCGGACGTC 57.801 50.000 6.12 7.13 41.11 4.34
2066 2401 2.032550 TCGTAATCCGGACGTCTCATTC 59.967 50.000 16.46 0.00 41.11 2.67
2118 2457 0.877071 GCATCACTTGACACACCCAG 59.123 55.000 0.00 0.00 0.00 4.45
2122 2461 1.768275 TCACTTGACACACCCAGACAT 59.232 47.619 0.00 0.00 0.00 3.06
2124 2463 3.582647 TCACTTGACACACCCAGACATAT 59.417 43.478 0.00 0.00 0.00 1.78
2125 2464 4.041567 TCACTTGACACACCCAGACATATT 59.958 41.667 0.00 0.00 0.00 1.28
2130 2473 4.530553 TGACACACCCAGACATATTGTACT 59.469 41.667 0.00 0.00 0.00 2.73
2234 2577 4.741239 AGGACATCCCGGGGCTGT 62.741 66.667 21.96 21.96 40.87 4.40
2248 2591 3.492137 CGGGGCTGTATAGGTTCAACTAC 60.492 52.174 0.00 0.00 0.00 2.73
2249 2592 3.710165 GGGGCTGTATAGGTTCAACTACT 59.290 47.826 0.00 0.00 0.00 2.57
2251 2594 5.010820 GGGGCTGTATAGGTTCAACTACTAG 59.989 48.000 0.00 0.00 0.00 2.57
2308 2652 1.138266 ACGGTCTGGAATAACGATGGG 59.862 52.381 0.00 0.00 0.00 4.00
2311 2655 3.403038 GGTCTGGAATAACGATGGGATG 58.597 50.000 0.00 0.00 0.00 3.51
2382 2927 6.640518 ACAGCGATGAGTAATTAGGAGAAAA 58.359 36.000 8.12 0.00 0.00 2.29
2394 2939 1.093496 GGAGAAAATGGTACCCCGCG 61.093 60.000 10.07 0.00 0.00 6.46
2395 2940 1.712018 GAGAAAATGGTACCCCGCGC 61.712 60.000 10.07 0.00 0.00 6.86
2396 2941 1.747745 GAAAATGGTACCCCGCGCT 60.748 57.895 10.07 0.00 0.00 5.92
2397 2942 0.462403 GAAAATGGTACCCCGCGCTA 60.462 55.000 10.07 0.00 0.00 4.26
2401 2947 2.512286 GGTACCCCGCGCTAAACC 60.512 66.667 5.56 1.34 0.00 3.27
2414 2960 5.445939 CCGCGCTAAACCATTATGATATGAC 60.446 44.000 5.56 0.00 0.00 3.06
2416 2962 5.445939 GCGCTAAACCATTATGATATGACCG 60.446 44.000 0.00 0.00 0.00 4.79
2420 2966 7.766278 GCTAAACCATTATGATATGACCGATCT 59.234 37.037 0.00 0.00 0.00 2.75
2426 2972 9.822185 CCATTATGATATGACCGATCTTAATCA 57.178 33.333 0.00 0.00 34.15 2.57
2490 3670 6.155475 ACTTATGCCTAACTCTAGAAGCAG 57.845 41.667 0.00 0.00 29.36 4.24
2542 3726 1.087771 CGGCCATCACTTTACGGGAC 61.088 60.000 2.24 0.00 0.00 4.46
2678 3867 2.230994 GAGTCAGCGATGCTCACCCA 62.231 60.000 16.58 0.00 36.40 4.51
2685 3976 1.301716 GATGCTCACCCACACACGT 60.302 57.895 0.00 0.00 0.00 4.49
2686 3977 0.037697 GATGCTCACCCACACACGTA 60.038 55.000 0.00 0.00 0.00 3.57
2720 4011 1.518133 CTCGTCTGTAGCCAGCAGC 60.518 63.158 0.00 0.00 44.25 5.25
2745 4036 4.453136 GCTACTTATCTCTAGCTAGTGCGT 59.547 45.833 20.10 13.75 45.42 5.24
2852 4144 2.305853 CGCGAATGATGGAGCCTCG 61.306 63.158 0.00 0.00 0.00 4.63
2892 4184 1.226888 GTCCATGGACGACGCTACC 60.227 63.158 28.52 3.15 35.30 3.18
2943 4235 1.134694 GTTTTCGCGCCATCTGGTC 59.865 57.895 0.00 0.00 37.57 4.02
2953 4245 0.863799 CCATCTGGTCGATCATTGCG 59.136 55.000 0.00 0.00 0.00 4.85
2954 4246 0.234106 CATCTGGTCGATCATTGCGC 59.766 55.000 0.00 0.00 0.00 6.09
2955 4247 1.217585 ATCTGGTCGATCATTGCGCG 61.218 55.000 0.00 0.00 0.00 6.86
2956 4248 1.878069 CTGGTCGATCATTGCGCGA 60.878 57.895 12.10 0.00 0.00 5.87
2991 4303 6.245408 TGTTCCTCTTGCCAGTAATAATTGT 58.755 36.000 0.00 0.00 0.00 2.71
3050 4362 1.180029 TTGGTCCGTAGTAGTCCTGC 58.820 55.000 0.00 0.00 0.00 4.85
3088 4402 2.943653 CCGACGGTTTCTTGTGGC 59.056 61.111 5.48 0.00 0.00 5.01
3090 4404 0.320073 CCGACGGTTTCTTGTGGCTA 60.320 55.000 5.48 0.00 0.00 3.93
3199 4578 5.409520 TGTGAAATCTTGCAGCAAGTAGTAG 59.590 40.000 30.16 9.00 41.66 2.57
3222 4601 5.234329 AGTGACTAACAAGTGTTGACGATTG 59.766 40.000 6.94 0.00 38.90 2.67
3443 4822 3.782443 GTCACCTACCCGGGCCTG 61.782 72.222 24.08 11.72 36.97 4.85
3662 5041 3.842923 AGCAGCGAGATGGACCCG 61.843 66.667 0.00 0.00 0.00 5.28
3729 5108 3.307906 TCGGCTACAACGGCACCT 61.308 61.111 0.00 0.00 0.00 4.00
3816 5195 3.799755 CCGGCAAGTACGGCAAGC 61.800 66.667 13.38 2.89 45.34 4.01
3857 5236 2.010582 TTTGCGTGAACCACCAAGCC 62.011 55.000 0.00 0.00 40.08 4.35
3975 5359 1.207593 GCCAGTGTGTTAAGCAGCG 59.792 57.895 0.00 0.00 0.00 5.18
3993 5377 1.640428 CGCGCCTGATTAGTCTTTGA 58.360 50.000 0.00 0.00 0.00 2.69
3994 5378 1.999735 CGCGCCTGATTAGTCTTTGAA 59.000 47.619 0.00 0.00 0.00 2.69
4005 5389 5.449107 TTAGTCTTTGAAGAGCGTACTGT 57.551 39.130 0.00 0.00 35.32 3.55
4006 5390 6.564709 TTAGTCTTTGAAGAGCGTACTGTA 57.435 37.500 0.00 0.00 35.32 2.74
4198 5586 9.226606 GCTAAAGCTCTAGATATCTAGTCAGAA 57.773 37.037 30.22 15.68 44.74 3.02
4224 5612 3.008813 ACAATGGCATGTCTCTGAACTCT 59.991 43.478 0.00 0.00 0.00 3.24
4225 5613 3.996921 ATGGCATGTCTCTGAACTCTT 57.003 42.857 0.00 0.00 0.00 2.85
4263 5651 3.360867 TCTGAACTAGGCAGAGAAGAGG 58.639 50.000 12.05 0.00 37.46 3.69
4454 5878 1.966451 GCCCAAGTTGTCCTCCACG 60.966 63.158 1.45 0.00 0.00 4.94
4457 5881 1.507141 CCAAGTTGTCCTCCACGTGC 61.507 60.000 10.91 0.00 0.00 5.34
4460 5884 1.668151 GTTGTCCTCCACGTGCCTC 60.668 63.158 10.91 0.00 0.00 4.70
4466 5890 1.373497 CTCCACGTGCCTCACTGTC 60.373 63.158 10.91 0.00 31.34 3.51
4475 5899 1.734477 CCTCACTGTCTTCACGCCG 60.734 63.158 0.00 0.00 0.00 6.46
4535 5959 1.878953 CCACCTGCGTTCAGTTAAGT 58.121 50.000 0.00 0.00 38.66 2.24
4540 5964 2.869801 CCTGCGTTCAGTTAAGTGTCAA 59.130 45.455 10.08 0.00 38.66 3.18
4561 5985 7.141363 GTCAAGCTTTGTTTATCAGTGTCAAT 58.859 34.615 0.00 0.00 0.00 2.57
4562 5986 7.649306 GTCAAGCTTTGTTTATCAGTGTCAATT 59.351 33.333 0.00 0.00 0.00 2.32
4563 5987 8.196771 TCAAGCTTTGTTTATCAGTGTCAATTT 58.803 29.630 0.00 0.00 0.00 1.82
4564 5988 8.819974 CAAGCTTTGTTTATCAGTGTCAATTTT 58.180 29.630 0.00 0.00 0.00 1.82
4565 5989 8.947055 AGCTTTGTTTATCAGTGTCAATTTTT 57.053 26.923 0.00 0.00 0.00 1.94
4613 6058 6.751157 ACATATATATTGACGAACGTGGGAA 58.249 36.000 4.19 0.00 0.00 3.97
4683 6136 1.135689 GTCACATGTCATCGGGTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
4705 6158 4.499696 GCGGTGGAATTTTGGAGATAATGG 60.500 45.833 0.00 0.00 0.00 3.16
4706 6159 4.037923 CGGTGGAATTTTGGAGATAATGGG 59.962 45.833 0.00 0.00 0.00 4.00
4707 6160 4.962362 GGTGGAATTTTGGAGATAATGGGT 59.038 41.667 0.00 0.00 0.00 4.51
4708 6161 6.133356 GGTGGAATTTTGGAGATAATGGGTA 58.867 40.000 0.00 0.00 0.00 3.69
4709 6162 6.782494 GGTGGAATTTTGGAGATAATGGGTAT 59.218 38.462 0.00 0.00 0.00 2.73
4710 6163 7.255942 GGTGGAATTTTGGAGATAATGGGTATG 60.256 40.741 0.00 0.00 0.00 2.39
4711 6164 7.287696 GTGGAATTTTGGAGATAATGGGTATGT 59.712 37.037 0.00 0.00 0.00 2.29
4712 6165 7.843760 TGGAATTTTGGAGATAATGGGTATGTT 59.156 33.333 0.00 0.00 0.00 2.71
4713 6166 8.360390 GGAATTTTGGAGATAATGGGTATGTTC 58.640 37.037 0.00 0.00 0.00 3.18
4714 6167 6.935741 TTTTGGAGATAATGGGTATGTTCG 57.064 37.500 0.00 0.00 0.00 3.95
4715 6168 4.002906 TGGAGATAATGGGTATGTTCGC 57.997 45.455 0.00 0.00 0.00 4.70
4716 6169 3.244422 TGGAGATAATGGGTATGTTCGCC 60.244 47.826 0.00 0.00 0.00 5.54
4717 6170 3.244422 GGAGATAATGGGTATGTTCGCCA 60.244 47.826 0.00 0.00 0.00 5.69
4718 6171 4.385825 GAGATAATGGGTATGTTCGCCAA 58.614 43.478 0.00 0.00 0.00 4.52
4719 6172 4.985538 AGATAATGGGTATGTTCGCCAAT 58.014 39.130 0.00 0.00 0.00 3.16
4720 6173 5.385198 AGATAATGGGTATGTTCGCCAATT 58.615 37.500 0.00 0.00 0.00 2.32
4721 6174 5.833131 AGATAATGGGTATGTTCGCCAATTT 59.167 36.000 0.00 0.00 0.00 1.82
4722 6175 3.799281 ATGGGTATGTTCGCCAATTTG 57.201 42.857 0.00 0.00 0.00 2.32
4723 6176 2.520069 TGGGTATGTTCGCCAATTTGT 58.480 42.857 0.00 0.00 0.00 2.83
4724 6177 2.894126 TGGGTATGTTCGCCAATTTGTT 59.106 40.909 0.00 0.00 0.00 2.83
4725 6178 3.057174 TGGGTATGTTCGCCAATTTGTTC 60.057 43.478 0.00 0.00 0.00 3.18
4726 6179 3.057174 GGGTATGTTCGCCAATTTGTTCA 60.057 43.478 0.00 0.00 0.00 3.18
4727 6180 4.551388 GGTATGTTCGCCAATTTGTTCAA 58.449 39.130 0.00 0.00 0.00 2.69
4728 6181 5.167845 GGTATGTTCGCCAATTTGTTCAAT 58.832 37.500 0.00 0.00 0.00 2.57
4729 6182 5.062058 GGTATGTTCGCCAATTTGTTCAATG 59.938 40.000 0.00 0.00 0.00 2.82
4730 6183 4.052159 TGTTCGCCAATTTGTTCAATGT 57.948 36.364 0.00 0.00 0.00 2.71
4731 6184 4.047822 TGTTCGCCAATTTGTTCAATGTC 58.952 39.130 0.00 0.00 0.00 3.06
4732 6185 2.927429 TCGCCAATTTGTTCAATGTCG 58.073 42.857 0.00 0.00 0.00 4.35
4733 6186 2.550180 TCGCCAATTTGTTCAATGTCGA 59.450 40.909 0.00 0.00 0.00 4.20
4734 6187 3.190327 TCGCCAATTTGTTCAATGTCGAT 59.810 39.130 0.00 0.00 0.00 3.59
4735 6188 3.301379 CGCCAATTTGTTCAATGTCGATG 59.699 43.478 0.00 0.00 0.00 3.84
4736 6189 4.236935 GCCAATTTGTTCAATGTCGATGT 58.763 39.130 0.00 0.00 0.00 3.06
4737 6190 4.685628 GCCAATTTGTTCAATGTCGATGTT 59.314 37.500 0.00 0.00 0.00 2.71
4738 6191 5.177327 GCCAATTTGTTCAATGTCGATGTTT 59.823 36.000 0.00 0.00 0.00 2.83
4739 6192 6.292811 GCCAATTTGTTCAATGTCGATGTTTT 60.293 34.615 0.00 0.00 0.00 2.43
4740 6193 7.064674 CCAATTTGTTCAATGTCGATGTTTTG 58.935 34.615 0.00 0.00 0.00 2.44
4741 6194 7.042858 CCAATTTGTTCAATGTCGATGTTTTGA 60.043 33.333 0.00 0.00 0.00 2.69
4742 6195 6.804534 TTTGTTCAATGTCGATGTTTTGAC 57.195 33.333 0.00 0.00 36.87 3.18
4743 6196 5.749596 TGTTCAATGTCGATGTTTTGACT 57.250 34.783 0.00 0.00 37.20 3.41
4744 6197 6.130298 TGTTCAATGTCGATGTTTTGACTT 57.870 33.333 0.00 0.00 37.20 3.01
4745 6198 6.559810 TGTTCAATGTCGATGTTTTGACTTT 58.440 32.000 0.00 0.00 37.20 2.66
4746 6199 7.032580 TGTTCAATGTCGATGTTTTGACTTTT 58.967 30.769 0.00 0.00 37.20 2.27
4747 6200 8.184848 TGTTCAATGTCGATGTTTTGACTTTTA 58.815 29.630 0.00 0.00 37.20 1.52
4748 6201 8.469125 GTTCAATGTCGATGTTTTGACTTTTAC 58.531 33.333 0.00 0.00 37.20 2.01
4749 6202 7.925993 TCAATGTCGATGTTTTGACTTTTACT 58.074 30.769 0.00 0.00 37.20 2.24
4750 6203 8.402472 TCAATGTCGATGTTTTGACTTTTACTT 58.598 29.630 0.00 0.00 37.20 2.24
4751 6204 8.471457 CAATGTCGATGTTTTGACTTTTACTTG 58.529 33.333 0.00 0.00 37.20 3.16
4752 6205 6.491394 TGTCGATGTTTTGACTTTTACTTGG 58.509 36.000 0.00 0.00 37.20 3.61
4753 6206 5.398416 GTCGATGTTTTGACTTTTACTTGGC 59.602 40.000 0.00 0.00 33.98 4.52
4754 6207 5.066634 TCGATGTTTTGACTTTTACTTGGCA 59.933 36.000 0.00 0.00 0.00 4.92
4755 6208 5.920273 CGATGTTTTGACTTTTACTTGGCAT 59.080 36.000 0.00 0.00 0.00 4.40
4756 6209 7.041030 TCGATGTTTTGACTTTTACTTGGCATA 60.041 33.333 0.00 0.00 0.00 3.14
4757 6210 7.754924 CGATGTTTTGACTTTTACTTGGCATAT 59.245 33.333 0.00 0.00 0.00 1.78
4758 6211 9.423061 GATGTTTTGACTTTTACTTGGCATATT 57.577 29.630 0.00 0.00 0.00 1.28
4759 6212 9.777297 ATGTTTTGACTTTTACTTGGCATATTT 57.223 25.926 0.00 0.00 0.00 1.40
4789 6242 3.605895 TGCGGCATGTGCATCAAT 58.394 50.000 10.20 0.00 44.36 2.57
4790 6243 1.434287 TGCGGCATGTGCATCAATC 59.566 52.632 10.20 0.00 44.36 2.67
4791 6244 1.313812 TGCGGCATGTGCATCAATCA 61.314 50.000 10.20 0.00 44.36 2.57
4792 6245 0.179132 GCGGCATGTGCATCAATCAA 60.179 50.000 7.36 0.00 44.36 2.57
4793 6246 1.537348 GCGGCATGTGCATCAATCAAT 60.537 47.619 7.36 0.00 44.36 2.57
4794 6247 2.124122 CGGCATGTGCATCAATCAATG 58.876 47.619 7.36 0.00 44.36 2.82
4804 6257 4.505313 CATCAATCAATGCAGAGGATGG 57.495 45.455 10.29 3.84 33.29 3.51
4805 6258 3.937778 TCAATCAATGCAGAGGATGGA 57.062 42.857 0.00 0.00 0.00 3.41
4806 6259 3.816994 TCAATCAATGCAGAGGATGGAG 58.183 45.455 0.00 0.00 30.11 3.86
4807 6260 2.885266 CAATCAATGCAGAGGATGGAGG 59.115 50.000 0.00 0.00 30.11 4.30
4808 6261 1.883678 TCAATGCAGAGGATGGAGGA 58.116 50.000 0.00 0.00 30.11 3.71
4809 6262 2.415624 TCAATGCAGAGGATGGAGGAT 58.584 47.619 0.00 0.00 30.11 3.24
4810 6263 3.590714 TCAATGCAGAGGATGGAGGATA 58.409 45.455 0.00 0.00 30.11 2.59
4811 6264 3.326006 TCAATGCAGAGGATGGAGGATAC 59.674 47.826 0.00 0.00 30.11 2.24
4812 6265 2.477104 TGCAGAGGATGGAGGATACA 57.523 50.000 0.00 0.00 41.41 2.29
4813 6266 2.981921 TGCAGAGGATGGAGGATACAT 58.018 47.619 0.00 0.00 41.41 2.29
4814 6267 3.321039 TGCAGAGGATGGAGGATACATT 58.679 45.455 0.00 0.00 41.41 2.71
4815 6268 3.326006 TGCAGAGGATGGAGGATACATTC 59.674 47.826 0.00 0.00 41.41 2.67
4816 6269 3.582208 GCAGAGGATGGAGGATACATTCT 59.418 47.826 0.00 0.00 36.88 2.40
4817 6270 4.041444 GCAGAGGATGGAGGATACATTCTT 59.959 45.833 0.00 0.00 34.34 2.52
4818 6271 5.455899 GCAGAGGATGGAGGATACATTCTTT 60.456 44.000 0.00 0.00 34.34 2.52
4819 6272 6.599445 CAGAGGATGGAGGATACATTCTTTT 58.401 40.000 0.00 0.00 34.34 2.27
4820 6273 6.709846 CAGAGGATGGAGGATACATTCTTTTC 59.290 42.308 0.00 0.00 34.34 2.29
4821 6274 6.388100 AGAGGATGGAGGATACATTCTTTTCA 59.612 38.462 0.00 0.00 34.34 2.69
4822 6275 6.973642 AGGATGGAGGATACATTCTTTTCAA 58.026 36.000 0.00 0.00 29.87 2.69
4823 6276 7.413446 AGGATGGAGGATACATTCTTTTCAAA 58.587 34.615 0.00 0.00 29.87 2.69
4824 6277 7.895429 AGGATGGAGGATACATTCTTTTCAAAA 59.105 33.333 0.00 0.00 29.87 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.593825 ACTTTGAATTTCAGTACTACAATGCC 58.406 34.615 0.00 0.00 0.00 4.40
3 4 9.318041 CGAACTTTGAATTTCAGTACTACAATG 57.682 33.333 0.00 0.00 0.00 2.82
5 6 7.225931 AGCGAACTTTGAATTTCAGTACTACAA 59.774 33.333 0.00 0.00 0.00 2.41
7 8 7.118422 AGCGAACTTTGAATTTCAGTACTAC 57.882 36.000 0.00 0.00 0.00 2.73
8 9 6.089016 CGAGCGAACTTTGAATTTCAGTACTA 59.911 38.462 0.00 0.00 0.00 1.82
9 10 5.107453 CGAGCGAACTTTGAATTTCAGTACT 60.107 40.000 0.00 0.00 0.00 2.73
10 11 5.073478 CGAGCGAACTTTGAATTTCAGTAC 58.927 41.667 0.00 0.00 0.00 2.73
11 12 4.748102 ACGAGCGAACTTTGAATTTCAGTA 59.252 37.500 0.00 0.00 0.00 2.74
12 13 3.560068 ACGAGCGAACTTTGAATTTCAGT 59.440 39.130 0.00 0.00 0.00 3.41
13 14 4.133856 ACGAGCGAACTTTGAATTTCAG 57.866 40.909 0.00 0.00 0.00 3.02
14 15 4.545823 AACGAGCGAACTTTGAATTTCA 57.454 36.364 0.00 0.00 0.00 2.69
15 16 5.912528 TCTAACGAGCGAACTTTGAATTTC 58.087 37.500 0.00 0.00 0.00 2.17
37 38 5.358160 CCACAGGGTTTCTGATAGGAAATTC 59.642 44.000 0.00 0.00 46.18 2.17
54 55 1.153489 CTCGATCACAGCCACAGGG 60.153 63.158 0.00 0.00 37.18 4.45
84 85 5.516696 GTGCAAGTTCTTTTCCTTCTTGTTC 59.483 40.000 0.00 0.00 38.09 3.18
99 103 0.856641 TCGCGTAACTGTGCAAGTTC 59.143 50.000 5.77 8.37 46.60 3.01
132 136 4.721132 TCTCCTTCCAAACCAAACGTATT 58.279 39.130 0.00 0.00 0.00 1.89
167 171 0.804989 CCATCGACCAGAAGGCAAAC 59.195 55.000 0.00 0.00 39.06 2.93
178 182 2.423446 CTAGCTGGCCCATCGACC 59.577 66.667 0.00 0.00 0.00 4.79
217 221 0.179148 CGTTCCATCACGATCACGGA 60.179 55.000 0.00 0.00 43.15 4.69
252 259 4.923942 CGCATCTGGGCTCGCCAT 62.924 66.667 10.51 0.00 37.98 4.40
317 324 2.449137 ATCTTCCCAAATCTGGCAGG 57.551 50.000 15.73 0.00 41.99 4.85
340 347 3.628942 CAGATTTCGAATGAATCTGGCCA 59.371 43.478 22.44 4.71 36.80 5.36
430 437 1.202382 ACGAAGGCGACCATTACTAGC 60.202 52.381 0.00 0.00 41.64 3.42
448 455 0.104304 AAACGCAGGCCTCCTATACG 59.896 55.000 0.00 2.49 29.64 3.06
528 540 5.905181 GGTGAATGTGTACGTACAAACAAAG 59.095 40.000 28.89 0.00 38.04 2.77
533 545 4.059511 CAGGGTGAATGTGTACGTACAAA 58.940 43.478 28.89 24.72 38.04 2.83
534 546 3.555377 CCAGGGTGAATGTGTACGTACAA 60.555 47.826 28.89 18.89 38.04 2.41
545 557 2.757099 GGCCAGCCAGGGTGAATG 60.757 66.667 20.97 4.58 38.09 2.67
558 570 0.543174 ATTTGCCCTTTAACCGGCCA 60.543 50.000 0.00 0.00 45.07 5.36
568 580 4.156008 CAGTTCGTAAGCTAATTTGCCCTT 59.844 41.667 8.30 0.33 37.18 3.95
644 711 8.683550 TCGTTCTGTATGTAGTTCACATTAAG 57.316 34.615 0.00 0.00 46.01 1.85
646 713 9.297586 GATTCGTTCTGTATGTAGTTCACATTA 57.702 33.333 0.00 0.00 46.01 1.90
714 964 6.038601 TGTAACGTCAATAATAATGCACGG 57.961 37.500 0.00 0.00 0.00 4.94
752 1002 8.266682 GGCAAAAGAAAAAGAAAAAGATCGTAC 58.733 33.333 0.00 0.00 0.00 3.67
765 1015 2.912986 GCCGGGGCAAAAGAAAAAG 58.087 52.632 2.18 0.00 41.49 2.27
789 1039 1.034292 GGCACAGGATTGGAAGGAGC 61.034 60.000 0.00 0.00 0.00 4.70
804 1054 0.803380 GTGGACATACGTACGGGCAC 60.803 60.000 21.06 9.03 0.00 5.01
814 1064 0.389426 AGCCGTGAACGTGGACATAC 60.389 55.000 1.75 0.00 37.74 2.39
815 1065 0.108992 GAGCCGTGAACGTGGACATA 60.109 55.000 1.75 0.00 37.74 2.29
816 1066 1.374252 GAGCCGTGAACGTGGACAT 60.374 57.895 1.75 0.00 37.74 3.06
926 1179 1.112315 AGCGGGATCGATCAAGAGCT 61.112 55.000 25.93 23.55 39.00 4.09
964 1217 4.827284 ACGGATGACTGGATGTTTTCTTTT 59.173 37.500 0.00 0.00 0.00 2.27
965 1218 4.398319 ACGGATGACTGGATGTTTTCTTT 58.602 39.130 0.00 0.00 0.00 2.52
966 1219 4.003648 GACGGATGACTGGATGTTTTCTT 58.996 43.478 0.00 0.00 0.00 2.52
967 1220 3.600388 GACGGATGACTGGATGTTTTCT 58.400 45.455 0.00 0.00 0.00 2.52
968 1221 2.678336 GGACGGATGACTGGATGTTTTC 59.322 50.000 0.00 0.00 0.00 2.29
1161 1420 3.691342 CCGTGCTCCCCGAACTCA 61.691 66.667 0.00 0.00 0.00 3.41
1729 1988 2.126463 CACGCTGTGGACGACGAT 60.126 61.111 0.00 0.00 0.00 3.73
1802 2061 5.705905 GCAACATAACTTGGGAGTACTTCTT 59.294 40.000 0.01 0.00 34.21 2.52
1803 2062 5.221843 TGCAACATAACTTGGGAGTACTTCT 60.222 40.000 0.01 0.00 34.21 2.85
1887 2154 3.078837 ACTTTTAACCAGCATACGTGGG 58.921 45.455 0.00 0.00 39.65 4.61
1944 2211 3.005050 ACGTATGGACTTTGTCGAACTGA 59.995 43.478 0.00 0.00 32.65 3.41
1945 2212 3.314553 ACGTATGGACTTTGTCGAACTG 58.685 45.455 0.00 0.00 32.65 3.16
2049 2384 0.815734 ACGAATGAGACGTCCGGATT 59.184 50.000 13.01 7.94 39.87 3.01
2050 2385 0.815734 AACGAATGAGACGTCCGGAT 59.184 50.000 13.01 0.00 43.16 4.18
2060 2395 4.245660 TCCTAACTTGCAGAACGAATGAG 58.754 43.478 0.00 0.00 0.00 2.90
2090 2427 0.894835 TCAAGTGATGCTACTGCCGA 59.105 50.000 0.00 0.00 38.71 5.54
2118 2457 5.527214 TGCATGGTAGCAAGTACAATATGTC 59.473 40.000 0.00 0.00 42.46 3.06
2302 2646 0.752658 TACTCACAGCCATCCCATCG 59.247 55.000 0.00 0.00 0.00 3.84
2308 2652 8.585881 TCCTAATAATTACTACTCACAGCCATC 58.414 37.037 0.00 0.00 0.00 3.51
2311 2655 8.179509 TCTCCTAATAATTACTACTCACAGCC 57.820 38.462 0.00 0.00 0.00 4.85
2346 2888 5.431765 ACTCATCGCTGTTCCATAATCTTT 58.568 37.500 0.00 0.00 0.00 2.52
2349 2891 7.426929 AATTACTCATCGCTGTTCCATAATC 57.573 36.000 0.00 0.00 0.00 1.75
2352 2894 6.266786 TCCTAATTACTCATCGCTGTTCCATA 59.733 38.462 0.00 0.00 0.00 2.74
2394 2939 7.766278 AGATCGGTCATATCATAATGGTTTAGC 59.234 37.037 0.00 0.00 0.00 3.09
2395 2940 9.658799 AAGATCGGTCATATCATAATGGTTTAG 57.341 33.333 0.00 0.00 0.00 1.85
2462 3009 9.628746 GCTTCTAGAGTTAGGCATAAGTAATAC 57.371 37.037 0.00 0.00 0.00 1.89
2490 3670 5.006746 CAGTGAATTACCCGCTACTGAATTC 59.993 44.000 0.00 0.00 38.16 2.17
2631 3820 0.961753 GTCCTTTTGGGCCTTGTCTG 59.038 55.000 4.53 0.00 38.54 3.51
2908 4200 4.107051 CGCGCAAGGAGCCAAAGG 62.107 66.667 8.75 0.00 41.38 3.11
2943 4235 3.260544 CTCGCTCGCGCAATGATCG 62.261 63.158 8.75 4.31 39.59 3.69
2954 4246 3.243892 GAACAGCTCGCTCGCTCG 61.244 66.667 0.00 0.00 38.41 5.03
2955 4247 2.883253 GGAACAGCTCGCTCGCTC 60.883 66.667 0.00 0.00 38.41 5.03
2956 4248 3.349481 GAGGAACAGCTCGCTCGCT 62.349 63.158 0.00 0.00 41.90 4.93
3012 4324 2.995258 CAAAGAAAATGAATGCGTGGGG 59.005 45.455 0.00 0.00 0.00 4.96
3018 4330 3.913089 ACGGACCAAAGAAAATGAATGC 58.087 40.909 0.00 0.00 0.00 3.56
3050 4362 3.274586 CGTGGAGCGATGCCATGG 61.275 66.667 7.63 7.63 44.77 3.66
3069 4383 2.549282 CACAAGAAACCGTCGGCG 59.451 61.111 12.28 0.29 37.95 6.46
3090 4404 3.668386 GCTAGGCACCAAAAGCGT 58.332 55.556 0.00 0.00 0.00 5.07
3161 4499 7.977853 GCAAGATTTCACATAGGTTGATCAATT 59.022 33.333 12.12 6.06 0.00 2.32
3162 4500 7.123098 TGCAAGATTTCACATAGGTTGATCAAT 59.877 33.333 12.12 0.00 0.00 2.57
3163 4501 6.433716 TGCAAGATTTCACATAGGTTGATCAA 59.566 34.615 3.38 3.38 0.00 2.57
3199 4578 5.432157 CAATCGTCAACACTTGTTAGTCAC 58.568 41.667 0.00 0.00 36.32 3.67
3302 4681 1.635663 CCACCTTGGCGTTCATCGTC 61.636 60.000 0.00 0.00 45.13 4.20
3831 5210 0.884704 TGGTTCACGCAAAGCCTCTC 60.885 55.000 0.00 0.00 0.00 3.20
3839 5218 2.485795 GGCTTGGTGGTTCACGCAA 61.486 57.895 0.00 0.00 34.83 4.85
3840 5219 2.904866 GGCTTGGTGGTTCACGCA 60.905 61.111 0.00 0.00 34.83 5.24
3842 5221 2.113139 AGGGCTTGGTGGTTCACG 59.887 61.111 0.00 0.00 34.83 4.35
3843 5222 0.251341 ATCAGGGCTTGGTGGTTCAC 60.251 55.000 0.00 0.00 0.00 3.18
3844 5223 0.251297 CATCAGGGCTTGGTGGTTCA 60.251 55.000 1.21 0.00 34.09 3.18
3845 5224 1.598701 GCATCAGGGCTTGGTGGTTC 61.599 60.000 12.13 0.00 38.41 3.62
3975 5359 3.262420 TCTTCAAAGACTAATCAGGCGC 58.738 45.455 0.00 0.00 33.60 6.53
3993 5377 3.868757 TGCATCTTACAGTACGCTCTT 57.131 42.857 0.00 0.00 0.00 2.85
3994 5378 3.381590 TGATGCATCTTACAGTACGCTCT 59.618 43.478 26.32 0.00 0.00 4.09
4049 5434 3.678289 TGACAAATCATCACTGACAGGG 58.322 45.455 7.51 2.02 33.22 4.45
4198 5586 3.959293 TCAGAGACATGCCATTGTGAAT 58.041 40.909 0.00 0.00 0.00 2.57
4199 5587 3.421919 TCAGAGACATGCCATTGTGAA 57.578 42.857 0.00 0.00 0.00 3.18
4201 5589 3.079578 AGTTCAGAGACATGCCATTGTG 58.920 45.455 0.00 0.00 0.00 3.33
4263 5651 4.225208 GCAGAAAAGAGACATGTTGCTTC 58.775 43.478 12.67 6.75 0.00 3.86
4436 5860 1.966451 CGTGGAGGACAACTTGGGC 60.966 63.158 0.00 0.00 0.00 5.36
4454 5878 1.560860 GCGTGAAGACAGTGAGGCAC 61.561 60.000 0.00 0.00 34.10 5.01
4457 5881 1.734477 CGGCGTGAAGACAGTGAGG 60.734 63.158 0.00 0.00 0.00 3.86
4460 5884 2.709125 TTCCCGGCGTGAAGACAGTG 62.709 60.000 6.01 0.00 0.00 3.66
4475 5899 1.384222 AAGGCGCAATTCCGATTCCC 61.384 55.000 10.83 0.00 0.00 3.97
4501 5925 1.014352 GGTGGCTATAAACTGGTGCG 58.986 55.000 0.00 0.00 0.00 5.34
4535 5959 5.588246 TGACACTGATAAACAAAGCTTGACA 59.412 36.000 0.00 0.00 0.00 3.58
4540 5964 8.947055 AAAAATTGACACTGATAAACAAAGCT 57.053 26.923 0.00 0.00 0.00 3.74
4591 6015 7.223260 TCTTCCCACGTTCGTCAATATATAT 57.777 36.000 0.00 0.00 0.00 0.86
4592 6016 6.638096 TCTTCCCACGTTCGTCAATATATA 57.362 37.500 0.00 0.00 0.00 0.86
4593 6017 5.524971 TCTTCCCACGTTCGTCAATATAT 57.475 39.130 0.00 0.00 0.00 0.86
4596 6041 3.446161 AGATCTTCCCACGTTCGTCAATA 59.554 43.478 0.00 0.00 0.00 1.90
4613 6058 7.480760 AGCTAGAGTTTTCAAGAAGAGATCT 57.519 36.000 0.00 0.00 41.32 2.75
4683 6136 4.037923 CCCATTATCTCCAAAATTCCACCG 59.962 45.833 0.00 0.00 0.00 4.94
4705 6158 4.167554 TGAACAAATTGGCGAACATACC 57.832 40.909 0.00 0.00 0.00 2.73
4706 6159 5.633182 ACATTGAACAAATTGGCGAACATAC 59.367 36.000 0.00 0.00 0.00 2.39
4707 6160 5.777802 ACATTGAACAAATTGGCGAACATA 58.222 33.333 0.00 0.00 0.00 2.29
4708 6161 4.630111 ACATTGAACAAATTGGCGAACAT 58.370 34.783 0.00 0.00 0.00 2.71
4709 6162 4.047822 GACATTGAACAAATTGGCGAACA 58.952 39.130 0.00 0.00 0.00 3.18
4710 6163 3.119463 CGACATTGAACAAATTGGCGAAC 59.881 43.478 9.80 0.00 32.70 3.95
4711 6164 3.003793 TCGACATTGAACAAATTGGCGAA 59.996 39.130 14.05 2.25 35.37 4.70
4712 6165 2.550180 TCGACATTGAACAAATTGGCGA 59.450 40.909 12.88 12.88 35.69 5.54
4713 6166 2.927429 TCGACATTGAACAAATTGGCG 58.073 42.857 9.27 9.27 32.42 5.69
4714 6167 4.236935 ACATCGACATTGAACAAATTGGC 58.763 39.130 0.00 0.00 0.00 4.52
4715 6168 6.768029 AAACATCGACATTGAACAAATTGG 57.232 33.333 0.00 0.00 0.00 3.16
4716 6169 7.788846 GTCAAAACATCGACATTGAACAAATTG 59.211 33.333 5.82 0.00 33.93 2.32
4717 6170 7.706179 AGTCAAAACATCGACATTGAACAAATT 59.294 29.630 5.82 0.00 33.93 1.82
4718 6171 7.202526 AGTCAAAACATCGACATTGAACAAAT 58.797 30.769 5.82 0.00 33.93 2.32
4719 6172 6.559810 AGTCAAAACATCGACATTGAACAAA 58.440 32.000 5.82 0.00 33.93 2.83
4720 6173 6.130298 AGTCAAAACATCGACATTGAACAA 57.870 33.333 5.82 0.00 33.93 2.83
4721 6174 5.749596 AGTCAAAACATCGACATTGAACA 57.250 34.783 5.82 0.00 33.93 3.18
4722 6175 7.449934 AAAAGTCAAAACATCGACATTGAAC 57.550 32.000 5.82 2.66 33.93 3.18
4723 6176 8.402472 AGTAAAAGTCAAAACATCGACATTGAA 58.598 29.630 5.82 0.00 33.93 2.69
4724 6177 7.925993 AGTAAAAGTCAAAACATCGACATTGA 58.074 30.769 0.00 0.00 34.48 2.57
4725 6178 8.471457 CAAGTAAAAGTCAAAACATCGACATTG 58.529 33.333 0.00 0.00 34.48 2.82
4726 6179 7.647715 CCAAGTAAAAGTCAAAACATCGACATT 59.352 33.333 0.00 0.00 34.48 2.71
4727 6180 7.138736 CCAAGTAAAAGTCAAAACATCGACAT 58.861 34.615 0.00 0.00 34.48 3.06
4728 6181 6.491394 CCAAGTAAAAGTCAAAACATCGACA 58.509 36.000 0.00 0.00 34.48 4.35
4729 6182 5.398416 GCCAAGTAAAAGTCAAAACATCGAC 59.602 40.000 0.00 0.00 0.00 4.20
4730 6183 5.066634 TGCCAAGTAAAAGTCAAAACATCGA 59.933 36.000 0.00 0.00 0.00 3.59
4731 6184 5.277825 TGCCAAGTAAAAGTCAAAACATCG 58.722 37.500 0.00 0.00 0.00 3.84
4732 6185 8.986477 ATATGCCAAGTAAAAGTCAAAACATC 57.014 30.769 0.00 0.00 0.00 3.06
4733 6186 9.777297 AAATATGCCAAGTAAAAGTCAAAACAT 57.223 25.926 0.00 0.00 0.00 2.71
4772 6225 1.313812 TGATTGATGCACATGCCGCA 61.314 50.000 12.33 12.33 44.94 5.69
4773 6226 0.179132 TTGATTGATGCACATGCCGC 60.179 50.000 0.49 0.00 41.18 6.53
4774 6227 2.124122 CATTGATTGATGCACATGCCG 58.876 47.619 0.49 0.00 41.18 5.69
4783 6236 4.142038 TCCATCCTCTGCATTGATTGATG 58.858 43.478 0.00 0.00 0.00 3.07
4784 6237 4.399219 CTCCATCCTCTGCATTGATTGAT 58.601 43.478 0.00 0.00 0.00 2.57
4785 6238 3.434596 CCTCCATCCTCTGCATTGATTGA 60.435 47.826 0.00 0.00 0.00 2.57
4786 6239 2.885266 CCTCCATCCTCTGCATTGATTG 59.115 50.000 0.00 0.00 0.00 2.67
4787 6240 2.781757 TCCTCCATCCTCTGCATTGATT 59.218 45.455 0.00 0.00 0.00 2.57
4788 6241 2.415624 TCCTCCATCCTCTGCATTGAT 58.584 47.619 0.00 0.00 0.00 2.57
4789 6242 1.883678 TCCTCCATCCTCTGCATTGA 58.116 50.000 0.00 0.00 0.00 2.57
4790 6243 2.953284 ATCCTCCATCCTCTGCATTG 57.047 50.000 0.00 0.00 0.00 2.82
4791 6244 3.321039 TGTATCCTCCATCCTCTGCATT 58.679 45.455 0.00 0.00 0.00 3.56
4792 6245 2.981921 TGTATCCTCCATCCTCTGCAT 58.018 47.619 0.00 0.00 0.00 3.96
4793 6246 2.477104 TGTATCCTCCATCCTCTGCA 57.523 50.000 0.00 0.00 0.00 4.41
4794 6247 3.582208 AGAATGTATCCTCCATCCTCTGC 59.418 47.826 0.00 0.00 0.00 4.26
4795 6248 5.822132 AAGAATGTATCCTCCATCCTCTG 57.178 43.478 0.00 0.00 0.00 3.35
4796 6249 6.388100 TGAAAAGAATGTATCCTCCATCCTCT 59.612 38.462 0.00 0.00 0.00 3.69
4797 6250 6.595682 TGAAAAGAATGTATCCTCCATCCTC 58.404 40.000 0.00 0.00 0.00 3.71
4798 6251 6.581388 TGAAAAGAATGTATCCTCCATCCT 57.419 37.500 0.00 0.00 0.00 3.24
4799 6252 7.645058 TTTGAAAAGAATGTATCCTCCATCC 57.355 36.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.