Multiple sequence alignment - TraesCS3D01G292600

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 TraesCS3D01G292600 chr3D 100.000 7137 0 0 1 7137 402700850 402693714 0.000000e+00 13180.0
1 TraesCS3D01G292600 chr3D 87.811 1206 109 13 126 1321 402726321 402725144 0.000000e+00 1378.0
2 TraesCS3D01G292600 chr3D 90.090 111 10 1 1309 1419 402714340 402714231 7.460000e-30 143.0
3 TraesCS3D01G292600 chr3A 95.185 2887 98 14 2497 5368 523559709 523556849 0.000000e+00 4523.0
4 TraesCS3D01G292600 chr3A 91.816 1674 70 13 868 2501 523561318 523559672 0.000000e+00 2270.0
5 TraesCS3D01G292600 chr3A 88.746 1635 82 35 5223 6799 523556946 523555356 0.000000e+00 1906.0
6 TraesCS3D01G292600 chr3A 84.513 749 100 10 74 816 523566183 523565445 0.000000e+00 726.0
7 TraesCS3D01G292600 chr3A 81.269 662 58 40 6525 7131 523555644 523554994 6.480000e-130 475.0
8 TraesCS3D01G292600 chr3A 92.391 92 5 2 1 90 532199465 532199556 5.810000e-26 130.0
9 TraesCS3D01G292600 chr3A 91.579 95 5 3 1 93 598802712 598802619 2.090000e-25 128.0
10 TraesCS3D01G292600 chr3A 88.095 84 10 0 5222 5305 523556899 523556816 4.560000e-17 100.0
11 TraesCS3D01G292600 chr3B 93.820 2136 76 22 4415 6527 528174479 528172377 0.000000e+00 3162.0
12 TraesCS3D01G292600 chr3B 91.884 1072 52 11 823 1881 528177899 528176850 0.000000e+00 1465.0
13 TraesCS3D01G292600 chr3B 91.058 794 37 18 1880 2672 528176716 528175956 0.000000e+00 1042.0
14 TraesCS3D01G292600 chr3B 90.669 568 25 12 6582 7137 528147761 528147210 0.000000e+00 730.0
15 TraesCS3D01G292600 chr3B 92.903 465 22 7 4004 4463 528174936 528174478 0.000000e+00 665.0
16 TraesCS3D01G292600 chr3B 87.253 557 60 9 265 816 528179454 528178904 6.080000e-175 625.0
17 TraesCS3D01G292600 chr3B 91.814 452 25 6 2788 3228 528175940 528175490 2.830000e-173 619.0
18 TraesCS3D01G292600 chr3B 87.264 424 17 8 3229 3643 528175445 528175050 3.930000e-122 449.0
19 TraesCS3D01G292600 chr3B 93.519 108 7 0 1774 1881 528176849 528176742 2.060000e-35 161.0
20 TraesCS3D01G292600 chr3B 91.304 115 9 1 3704 3818 528175050 528174937 9.590000e-34 156.0
21 TraesCS3D01G292600 chr3B 83.838 99 14 2 5223 5320 528173615 528173518 7.620000e-15 93.5
22 TraesCS3D01G292600 chr4B 90.854 164 13 2 2244 2406 146469378 146469216 1.210000e-52 219.0
23 TraesCS3D01G292600 chr4B 89.157 166 17 1 2250 2414 366930143 366930308 9.380000e-49 206.0
24 TraesCS3D01G292600 chr5B 91.667 156 12 1 2252 2406 299602220 299602375 1.560000e-51 215.0
25 TraesCS3D01G292600 chr1D 90.683 161 13 2 2255 2414 7349704 7349863 5.610000e-51 213.0
26 TraesCS3D01G292600 chr1D 96.471 85 2 1 1 84 491533398 491533314 9.650000e-29 139.0
27 TraesCS3D01G292600 chr1D 88.182 110 5 6 1 104 168384822 168384715 2.700000e-24 124.0
28 TraesCS3D01G292600 chr7D 89.697 165 14 3 2250 2412 33102698 33102861 2.610000e-49 207.0
29 TraesCS3D01G292600 chr7D 95.402 87 2 2 1 85 361460961 361460875 3.470000e-28 137.0
30 TraesCS3D01G292600 chr7B 90.184 163 10 4 2255 2415 477814969 477814811 2.610000e-49 207.0
31 TraesCS3D01G292600 chr1A 85.279 197 23 5 2248 2438 240310289 240310093 1.570000e-46 198.0
32 TraesCS3D01G292600 chr1A 90.909 99 5 4 1 97 247243764 247243668 5.810000e-26 130.0
33 TraesCS3D01G292600 chr4D 96.429 84 3 0 1 84 498517644 498517561 9.650000e-29 139.0
34 TraesCS3D01G292600 chr5A 96.386 83 1 2 1 82 667231279 667231198 1.250000e-27 135.0
35 TraesCS3D01G292600 chr2B 93.182 88 3 3 1 86 373939753 373939839 7.520000e-25 126.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G292600 chr3D 402693714 402700850 7136 True 13180.00 13180 100.0000 1 7137 1 chr3D.!!$R1 7136
1 TraesCS3D01G292600 chr3D 402725144 402726321 1177 True 1378.00 1378 87.8110 126 1321 1 chr3D.!!$R3 1195
2 TraesCS3D01G292600 chr3A 523554994 523561318 6324 True 1854.80 4523 89.0222 868 7131 5 chr3A.!!$R3 6263
3 TraesCS3D01G292600 chr3A 523565445 523566183 738 True 726.00 726 84.5130 74 816 1 chr3A.!!$R1 742
4 TraesCS3D01G292600 chr3B 528172377 528179454 7077 True 843.75 3162 90.4657 265 6527 10 chr3B.!!$R2 6262
5 TraesCS3D01G292600 chr3B 528147210 528147761 551 True 730.00 730 90.6690 6582 7137 1 chr3B.!!$R1 555

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
173 174 0.106669 TCTCATGTCCTCGGTCCGAT 60.107 55.000 15.81 0.0 34.61 4.18 F
388 396 0.246086 CTCTCTGGTGCTGACTGGAC 59.754 60.000 0.00 0.0 36.19 4.02 F
1389 2429 0.521242 CGCGAGCAGTATTTGTTGGC 60.521 55.000 0.00 0.0 38.15 4.52 F
2130 3313 0.106769 TCACCAGCAGGCTTTCACAA 60.107 50.000 0.00 0.0 39.06 3.33 F
2662 3846 1.000270 AAGCCACACACACCACCAA 60.000 52.632 0.00 0.0 0.00 3.67 F
4071 5336 0.034059 AGGACGTCTGGACTTGCTTG 59.966 55.000 16.46 0.0 27.22 4.01 F
4819 6143 0.538057 AGCAGCTGGCACTTGCTTTA 60.538 50.000 17.12 0.0 45.28 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 2170 1.006227 GAGGGGAAGGGAAGGGGAT 59.994 63.158 0.00 0.00 0.00 3.85 R
1481 2521 3.558033 GGGACACTTTAACCCAGTTTCA 58.442 45.455 0.00 0.00 42.81 2.69 R
2714 3898 0.964860 AGGCAACACACAAGCACACA 60.965 50.000 0.00 0.00 41.41 3.72 R
3374 4630 1.062525 CTTCGCTGGCCAAATACGC 59.937 57.895 7.01 5.17 0.00 4.42 R
4285 5550 1.178276 GATCTCAGTGACAGGGACGT 58.822 55.000 0.00 0.00 0.00 4.34 R
5444 6828 0.104356 TAGTTTGGTGGGGGAGTGGA 60.104 55.000 0.00 0.00 0.00 4.02 R
6513 7916 0.318441 TCCGAGCTGGAAAGACAGTG 59.682 55.000 0.00 0.00 46.38 3.66 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
20 21 1.863454 CTCTCGTTGCTATGCATCACC 59.137 52.381 0.19 0.00 38.76 4.02
21 22 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
22 23 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
23 24 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
24 25 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
25 26 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
26 27 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
27 28 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
28 29 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
29 30 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
30 31 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
31 32 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
32 33 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
33 34 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
34 35 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
35 36 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
36 37 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
44 45 1.405526 ATCTTGCGTGTGCGTAGGATT 60.406 47.619 0.00 0.00 44.18 3.01
45 46 2.935238 ATCTTGCGTGTGCGTAGGATTT 60.935 45.455 0.00 0.00 44.18 2.17
46 47 4.419949 ATCTTGCGTGTGCGTAGGATTTT 61.420 43.478 0.00 0.00 44.18 1.82
47 48 5.865159 ATCTTGCGTGTGCGTAGGATTTTT 61.865 41.667 0.00 0.00 44.18 1.94
71 72 7.798596 TTTGAAATTACTACGTTACCCAACA 57.201 32.000 0.00 0.00 34.05 3.33
72 73 7.424227 TTGAAATTACTACGTTACCCAACAG 57.576 36.000 0.00 0.00 34.05 3.16
80 81 1.405121 CGTTACCCAACAGTCCTAGCC 60.405 57.143 0.00 0.00 34.05 3.93
85 86 0.693049 CCAACAGTCCTAGCCTTGGT 59.307 55.000 0.00 0.00 0.00 3.67
97 98 2.854522 CCTTGGTTAAGGCTCGGTG 58.145 57.895 0.00 0.00 46.47 4.94
98 99 1.305930 CCTTGGTTAAGGCTCGGTGC 61.306 60.000 0.00 0.00 46.47 5.01
165 166 2.166907 TCCCTTCCTCTCATGTCCTC 57.833 55.000 0.00 0.00 0.00 3.71
167 168 0.749649 CCTTCCTCTCATGTCCTCGG 59.250 60.000 0.00 0.00 0.00 4.63
169 170 1.407258 CTTCCTCTCATGTCCTCGGTC 59.593 57.143 0.00 0.00 0.00 4.79
172 173 0.748367 CTCTCATGTCCTCGGTCCGA 60.748 60.000 14.54 14.54 0.00 4.55
173 174 0.106669 TCTCATGTCCTCGGTCCGAT 60.107 55.000 15.81 0.00 34.61 4.18
178 179 0.683179 TGTCCTCGGTCCGATGATGT 60.683 55.000 20.26 0.00 33.71 3.06
191 192 1.490693 ATGATGTCGATTGGCGTCGC 61.491 55.000 9.22 9.22 41.22 5.19
194 195 4.210304 GTCGATTGGCGTCGCTGC 62.210 66.667 18.11 1.39 41.22 5.25
219 220 2.747855 GTGAAGCTTCGGCCAGGG 60.748 66.667 21.11 0.00 43.01 4.45
261 268 6.811665 TCGTTTGTCTATGTTTCATCTAGGTG 59.188 38.462 0.00 0.00 0.00 4.00
304 312 3.697045 TGATGGTTCGTGTTTTGGTCTTT 59.303 39.130 0.00 0.00 0.00 2.52
349 357 2.706890 GGTTAGGTTCGGCTTCATCAA 58.293 47.619 0.00 0.00 0.00 2.57
350 358 3.279434 GGTTAGGTTCGGCTTCATCAAT 58.721 45.455 0.00 0.00 0.00 2.57
382 390 0.252239 TTAGGCCTCTCTGGTGCTGA 60.252 55.000 9.68 0.00 38.35 4.26
388 396 0.246086 CTCTCTGGTGCTGACTGGAC 59.754 60.000 0.00 0.00 36.19 4.02
422 432 2.928801 TGTTCAGCCTCTTAGTTGCA 57.071 45.000 0.00 0.00 0.00 4.08
431 441 3.873801 GCCTCTTAGTTGCATTCTTCCCA 60.874 47.826 0.00 0.00 0.00 4.37
485 495 0.799393 GCTTCTTTTGGCTCCGACTC 59.201 55.000 0.00 0.00 0.00 3.36
486 496 1.878102 GCTTCTTTTGGCTCCGACTCA 60.878 52.381 0.00 0.00 0.00 3.41
494 504 0.532573 GGCTCCGACTCATGACTTCA 59.467 55.000 0.00 0.00 0.00 3.02
499 509 4.753233 CTCCGACTCATGACTTCATTTCT 58.247 43.478 0.00 0.00 33.61 2.52
524 534 4.630111 TGTGTTAACAACGTTACCCTAGG 58.370 43.478 10.51 0.06 31.82 3.02
527 537 4.245660 GTTAACAACGTTACCCTAGGTCC 58.754 47.826 8.29 0.00 37.09 4.46
528 538 2.014010 ACAACGTTACCCTAGGTCCA 57.986 50.000 8.29 0.00 37.09 4.02
537 547 3.286871 ACCCTAGGTCCAAGGTTAGTT 57.713 47.619 8.29 0.00 31.70 2.24
558 568 0.890683 GGAGAACCAAAGGTGCCATG 59.109 55.000 0.00 0.00 35.34 3.66
750 771 2.926165 GCAGAGTGCAAAGCAAGTAAG 58.074 47.619 0.00 0.00 44.26 2.34
751 772 2.919807 GCAGAGTGCAAAGCAAGTAAGC 60.920 50.000 0.00 0.00 44.26 3.09
752 773 2.291465 CAGAGTGCAAAGCAAGTAAGCA 59.709 45.455 0.00 0.00 41.47 3.91
753 774 2.951642 AGAGTGCAAAGCAAGTAAGCAA 59.048 40.909 0.00 0.00 41.47 3.91
767 788 6.074676 GCAAGTAAGCAACAGATGAAAACAAG 60.075 38.462 0.00 0.00 0.00 3.16
768 789 5.523369 AGTAAGCAACAGATGAAAACAAGC 58.477 37.500 0.00 0.00 0.00 4.01
786 807 8.681486 AAACAAGCATATGAATCATACAGCTA 57.319 30.769 23.43 0.00 38.88 3.32
787 808 8.859236 AACAAGCATATGAATCATACAGCTAT 57.141 30.769 23.43 15.85 38.88 2.97
822 1134 4.855298 TCCCCCTAAAAACTATGTCCAG 57.145 45.455 0.00 0.00 0.00 3.86
920 1939 7.482169 TCGATTACCAGCCTTCTCAATATAT 57.518 36.000 0.00 0.00 0.00 0.86
1045 2076 0.550147 ACACACCAGAGGGCCCTAAT 60.550 55.000 28.78 14.76 37.90 1.73
1046 2077 1.274184 ACACACCAGAGGGCCCTAATA 60.274 52.381 28.78 0.00 37.90 0.98
1047 2078 1.843851 CACACCAGAGGGCCCTAATAA 59.156 52.381 28.78 0.00 37.90 1.40
1048 2079 2.241176 CACACCAGAGGGCCCTAATAAA 59.759 50.000 28.78 0.00 37.90 1.40
1049 2080 2.923629 ACACCAGAGGGCCCTAATAAAA 59.076 45.455 28.78 0.00 37.90 1.52
1050 2081 3.335484 ACACCAGAGGGCCCTAATAAAAA 59.665 43.478 28.78 0.00 37.90 1.94
1051 2082 3.954258 CACCAGAGGGCCCTAATAAAAAG 59.046 47.826 28.78 10.32 37.90 2.27
1052 2083 3.596500 ACCAGAGGGCCCTAATAAAAAGT 59.403 43.478 28.78 11.01 37.90 2.66
1053 2084 4.791880 ACCAGAGGGCCCTAATAAAAAGTA 59.208 41.667 28.78 0.00 37.90 2.24
1054 2085 5.254501 ACCAGAGGGCCCTAATAAAAAGTAA 59.745 40.000 28.78 0.00 37.90 2.24
1135 2170 2.070039 CCTATCAACCGCCCTCCCA 61.070 63.158 0.00 0.00 0.00 4.37
1144 2184 3.502875 GCCCTCCCATCCCCTTCC 61.503 72.222 0.00 0.00 0.00 3.46
1389 2429 0.521242 CGCGAGCAGTATTTGTTGGC 60.521 55.000 0.00 0.00 38.15 4.52
1471 2511 1.004277 TCCGTTGGAGGAATTTGGGAG 59.996 52.381 0.00 0.00 37.36 4.30
1481 2521 5.026121 GAGGAATTTGGGAGGAAGGAAAAT 58.974 41.667 0.00 0.00 0.00 1.82
1654 2702 6.887376 ACTCGTGCATGTTTATACTTGTAG 57.113 37.500 5.68 0.00 33.28 2.74
1655 2703 6.395629 ACTCGTGCATGTTTATACTTGTAGT 58.604 36.000 5.68 0.00 33.28 2.73
1656 2704 7.541162 ACTCGTGCATGTTTATACTTGTAGTA 58.459 34.615 5.68 0.00 34.82 1.82
1699 2747 7.385752 CAGTGTTTTAGACTTTTGGGTCGTATA 59.614 37.037 0.00 0.00 40.76 1.47
1707 2755 7.674120 AGACTTTTGGGTCGTATACTTTAACT 58.326 34.615 0.56 0.00 40.76 2.24
1748 2796 0.459489 TTGTTCAAACCCTGCACAGC 59.541 50.000 0.00 0.00 32.53 4.40
1757 2805 3.433306 ACCCTGCACAGCTTATTGTTA 57.567 42.857 0.00 0.00 0.00 2.41
1801 2849 9.997172 AGATAGGAAAATTTAAGGGATCAGTTT 57.003 29.630 0.00 0.00 0.00 2.66
1830 2878 7.605410 ACAATTTGAATCATGCTGGAAATTC 57.395 32.000 2.79 0.00 0.00 2.17
1899 3082 3.187842 GGTTCCAGCGACGAACTTATTTT 59.812 43.478 0.00 0.00 39.65 1.82
2130 3313 0.106769 TCACCAGCAGGCTTTCACAA 60.107 50.000 0.00 0.00 39.06 3.33
2311 3494 8.162746 TGGATATTTCAATATGGACTACATGCA 58.837 33.333 0.00 0.00 40.82 3.96
2336 3519 6.319658 AGACTGAAATGAGTGAACAAACACAT 59.680 34.615 0.00 0.00 42.45 3.21
2337 3520 7.498900 AGACTGAAATGAGTGAACAAACACATA 59.501 33.333 0.00 0.00 42.45 2.29
2340 3523 8.854979 TGAAATGAGTGAACAAACACATAAAG 57.145 30.769 0.00 0.00 42.45 1.85
2341 3524 8.465999 TGAAATGAGTGAACAAACACATAAAGT 58.534 29.630 0.00 0.00 42.45 2.66
2595 3779 6.045955 GTCTCTGGATGAAACTATCTTGGAC 58.954 44.000 0.00 0.00 0.00 4.02
2662 3846 1.000270 AAGCCACACACACCACCAA 60.000 52.632 0.00 0.00 0.00 3.67
2684 3868 7.545265 ACCAACATCATATGCACAAATAAACAC 59.455 33.333 0.00 0.00 0.00 3.32
2731 3915 1.133363 CGTGTGTGCTTGTGTGTTGC 61.133 55.000 0.00 0.00 0.00 4.17
2817 4001 5.276868 CGTTTCGTTCATCATAGGGATCAAC 60.277 44.000 0.00 0.00 34.02 3.18
2857 4045 1.066573 ACACTCTCTCATCTTTGGCCG 60.067 52.381 0.00 0.00 0.00 6.13
2923 4111 8.283291 CACTTACATGTGAAGTTTACTCCTTTC 58.717 37.037 9.11 0.00 40.12 2.62
3291 4537 1.045407 AGCACAAGTTCGAGTGGGTA 58.955 50.000 4.88 0.00 36.29 3.69
3292 4538 1.145803 GCACAAGTTCGAGTGGGTAC 58.854 55.000 4.88 0.00 36.29 3.34
3293 4539 1.270147 GCACAAGTTCGAGTGGGTACT 60.270 52.381 4.88 0.00 40.66 2.73
3294 4540 2.805657 GCACAAGTTCGAGTGGGTACTT 60.806 50.000 4.88 0.00 37.25 2.24
3295 4541 3.553508 GCACAAGTTCGAGTGGGTACTTA 60.554 47.826 4.88 0.00 37.25 2.24
3296 4542 3.985925 CACAAGTTCGAGTGGGTACTTAC 59.014 47.826 0.00 0.00 37.25 2.34
3297 4543 3.893813 ACAAGTTCGAGTGGGTACTTACT 59.106 43.478 0.00 2.84 37.25 2.24
3298 4544 4.235360 CAAGTTCGAGTGGGTACTTACTG 58.765 47.826 7.18 2.01 37.25 2.74
3374 4630 8.883954 TTTTGATGAGCTCAATACTAGATGAG 57.116 34.615 22.50 15.78 43.30 2.90
3478 4736 2.180086 TGGGCCTATCCTACTGATCTGT 59.820 50.000 4.53 10.33 34.76 3.41
3481 4739 4.221041 GGGCCTATCCTACTGATCTGTTAC 59.779 50.000 10.76 0.00 34.76 2.50
3749 5011 3.900941 AGTTTCGTGCATGTTCCAAATC 58.099 40.909 5.68 0.00 0.00 2.17
3818 5080 5.734720 TCATCATAAAGACACTTGGGAGTC 58.265 41.667 0.00 0.00 32.54 3.36
3873 5135 1.414181 CAGGCTTGATCTCGTACCCAT 59.586 52.381 0.00 0.00 0.00 4.00
3886 5148 4.885413 TCGTACCCATGGTATTAATTCCG 58.115 43.478 11.73 2.25 40.54 4.30
3903 5165 1.293498 CGGGCAAGCTACTGTCTGT 59.707 57.895 0.00 0.00 0.00 3.41
3905 5167 1.878102 CGGGCAAGCTACTGTCTGTTT 60.878 52.381 0.00 0.00 0.00 2.83
3989 5251 6.926313 ACCATTGTTCTAGTTCTACACTCTC 58.074 40.000 0.00 0.00 36.88 3.20
4071 5336 0.034059 AGGACGTCTGGACTTGCTTG 59.966 55.000 16.46 0.00 27.22 4.01
4120 5385 1.477014 GGCCAGGCCCTTGTATAAGTC 60.477 57.143 21.62 0.00 44.06 3.01
4184 5449 4.686191 ATCTGCACCTTCCAGATTCTAG 57.314 45.455 0.00 0.00 45.21 2.43
4285 5550 7.602644 GGACAGTGACACAACAGAAGATATAAA 59.397 37.037 8.59 0.00 0.00 1.40
4296 5561 5.421056 ACAGAAGATATAAACGTCCCTGTCA 59.579 40.000 0.00 0.00 28.87 3.58
4424 5691 1.273048 TGGCAAATTTGTAGCTGCAGG 59.727 47.619 17.12 0.00 36.50 4.85
4513 5820 9.629878 TTGTTAAGAAATACTGTTAAGAACCCA 57.370 29.630 0.00 0.00 0.00 4.51
4747 6071 4.739046 AAAGAAAGAAGATGTGCTGACG 57.261 40.909 0.00 0.00 0.00 4.35
4819 6143 0.538057 AGCAGCTGGCACTTGCTTTA 60.538 50.000 17.12 0.00 45.28 1.85
4960 6284 2.091541 GCTGTTAGCCAAGCCATTGTA 58.908 47.619 0.00 0.00 34.48 2.41
5002 6326 1.149174 AGGCAACCAGGACACACAG 59.851 57.895 0.00 0.00 37.17 3.66
5269 6593 0.738389 AGTTTCCAACACAACCAGCG 59.262 50.000 0.00 0.00 0.00 5.18
5306 6630 3.119708 GCCTAATGTTCAGCAGTTTCCAG 60.120 47.826 0.00 0.00 0.00 3.86
5350 6722 5.334414 CCAGTTGTCTAATGCTCAACAGTTC 60.334 44.000 9.35 0.00 42.33 3.01
5364 6748 1.462238 AGTTCCCTCCACCACAGCT 60.462 57.895 0.00 0.00 0.00 4.24
5365 6749 1.302832 GTTCCCTCCACCACAGCTG 60.303 63.158 13.48 13.48 0.00 4.24
5366 6750 3.196207 TTCCCTCCACCACAGCTGC 62.196 63.158 15.27 0.00 0.00 5.25
5367 6751 3.957586 CCCTCCACCACAGCTGCA 61.958 66.667 15.27 0.00 0.00 4.41
5368 6752 2.113774 CCTCCACCACAGCTGCAA 59.886 61.111 15.27 0.00 0.00 4.08
5369 6753 2.263741 CCTCCACCACAGCTGCAAC 61.264 63.158 15.27 0.00 0.00 4.17
5370 6754 2.203337 TCCACCACAGCTGCAACC 60.203 61.111 15.27 0.00 0.00 3.77
5371 6755 2.519063 CCACCACAGCTGCAACCA 60.519 61.111 15.27 0.00 0.00 3.67
5372 6756 2.723746 CACCACAGCTGCAACCAC 59.276 61.111 15.27 0.00 0.00 4.16
5373 6757 2.120282 CACCACAGCTGCAACCACA 61.120 57.895 15.27 0.00 0.00 4.17
5374 6758 1.825191 ACCACAGCTGCAACCACAG 60.825 57.895 15.27 0.00 40.80 3.66
5404 6788 1.829849 CCTCATCTTCCTCAGACAGCA 59.170 52.381 0.00 0.00 32.83 4.41
5444 6828 1.980765 TGCAAACTCAGATGAGACCCT 59.019 47.619 16.52 0.00 44.74 4.34
5500 6884 1.228831 CCACCAGCCATTGAACCCA 60.229 57.895 0.00 0.00 0.00 4.51
5518 6902 0.622665 CATCCCCTGAAACTCTGCCT 59.377 55.000 0.00 0.00 0.00 4.75
5578 6962 1.473965 CCATCAGGTGGGAGTCATTCG 60.474 57.143 0.00 0.00 44.79 3.34
5677 7061 4.748798 CCTCCTCCAGGCCAGGGT 62.749 72.222 15.24 0.00 34.56 4.34
5826 7210 2.439156 GATGCCTCCAGGTGGTGC 60.439 66.667 9.41 1.43 37.57 5.01
5904 7288 6.005066 TGGAGATATGATTGAGAAGGCAAA 57.995 37.500 0.00 0.00 0.00 3.68
6079 7463 3.357079 CTGGAAGCCGTGTGTGCC 61.357 66.667 0.00 0.00 0.00 5.01
6080 7464 4.182433 TGGAAGCCGTGTGTGCCA 62.182 61.111 0.00 0.00 0.00 4.92
6146 7533 5.936686 AAGATTTGATATGATGCCGTCTG 57.063 39.130 0.00 0.00 0.00 3.51
6179 7567 7.388224 TGTCCGTACAATGTACATACAAACATT 59.612 33.333 21.63 0.00 44.94 2.71
6197 7585 8.143193 ACAAACATTGAGCTTGAATTTCATGTA 58.857 29.630 12.33 0.00 0.00 2.29
6315 7708 4.460034 TCAGGTGATGTTTGCTAGTACGTA 59.540 41.667 0.00 0.00 0.00 3.57
6316 7709 4.561606 CAGGTGATGTTTGCTAGTACGTAC 59.438 45.833 18.10 18.10 0.00 3.67
6317 7710 3.545078 GGTGATGTTTGCTAGTACGTACG 59.455 47.826 19.49 15.01 0.00 3.67
6318 7711 4.161333 GTGATGTTTGCTAGTACGTACGT 58.839 43.478 25.98 25.98 0.00 3.57
6336 7735 7.687445 ACGTACGTTTTGAATTTTGTCTACTT 58.313 30.769 16.72 0.00 0.00 2.24
6397 7796 7.606858 TCATAGTGTGTACTACAGTCTACAC 57.393 40.000 15.70 15.70 41.92 2.90
6442 7844 0.519961 GCCGCACCTTTTTCGTACAT 59.480 50.000 0.00 0.00 0.00 2.29
6498 7901 5.921408 GCCTACGAAAATCACGAGAATATCT 59.079 40.000 0.00 0.00 34.70 1.98
6512 7915 0.905357 ATATCTGAGTATGGGCGCCC 59.095 55.000 39.40 39.40 0.00 6.13
6513 7916 1.192146 TATCTGAGTATGGGCGCCCC 61.192 60.000 41.75 26.88 45.71 5.80
6532 7964 0.318441 CACTGTCTTTCCAGCTCGGA 59.682 55.000 1.25 1.25 44.40 4.55
6564 7996 3.795688 TTCTCTGCTTGGATTGGAGTT 57.204 42.857 0.00 0.00 0.00 3.01
6644 8080 4.323257 GGAGAGAATAACCAAGTTCCCGAA 60.323 45.833 0.00 0.00 0.00 4.30
6840 8312 2.733945 CCAAACAAACGCCTGGGG 59.266 61.111 9.49 9.49 0.00 4.96
6841 8313 2.733945 CAAACAAACGCCTGGGGG 59.266 61.111 15.73 5.80 0.00 5.40
6859 8331 2.224548 GGGGGTAATGAATCCTTCTCGG 60.225 54.545 0.00 0.00 0.00 4.63
6882 8354 1.304217 TCCGGCGACTCCTTCTTCT 60.304 57.895 9.30 0.00 0.00 2.85
6886 8358 0.973496 GGCGACTCCTTCTTCTCCCT 60.973 60.000 0.00 0.00 0.00 4.20
6889 8361 1.491668 GACTCCTTCTTCTCCCTCCC 58.508 60.000 0.00 0.00 0.00 4.30
6951 8434 7.553760 GGCATATTTTGATTCCCAGATTTTGTT 59.446 33.333 0.00 0.00 0.00 2.83
6963 8463 4.021104 CCAGATTTTGTTTTCCCTCCCTTC 60.021 45.833 0.00 0.00 0.00 3.46
6966 8466 1.142060 TTGTTTTCCCTCCCTTCCGA 58.858 50.000 0.00 0.00 0.00 4.55
6990 8490 8.820933 CGAATCAGCTGTGATATAAAGAAGAAA 58.179 33.333 14.67 0.00 43.04 2.52
7109 8610 2.300850 TAAATCCTCCCCCGCGAACG 62.301 60.000 8.23 0.00 39.67 3.95
7127 8628 0.596082 CGCCTTGGTGACGGAATTTT 59.404 50.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.863454 GGTGATGCATAGCAACGAGAG 59.137 52.381 0.00 0.00 43.62 3.20
1 2 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
2 3 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
3 4 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
4 5 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
5 6 3.819337 AGATCATGGTGATGCATAGCAAC 59.181 43.478 0.00 0.00 43.62 4.17
6 7 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
7 8 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
8 9 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
9 10 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
10 11 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
11 12 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
12 13 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
13 14 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
14 15 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
15 16 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
16 17 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
17 18 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
18 19 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
19 20 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
20 21 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
21 22 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
22 23 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
23 24 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
24 25 0.175760 ATCCTACGCACACGCAAGAT 59.824 50.000 0.00 0.00 45.53 2.40
25 26 0.037697 AATCCTACGCACACGCAAGA 60.038 50.000 0.00 0.00 45.53 3.02
26 27 0.796312 AAATCCTACGCACACGCAAG 59.204 50.000 0.00 0.00 45.53 4.01
27 28 1.231221 AAAATCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
28 29 1.231221 AAAAATCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
45 46 8.680903 TGTTGGGTAACGTAGTAATTTCAAAAA 58.319 29.630 0.00 0.00 45.00 1.94
46 47 8.218338 TGTTGGGTAACGTAGTAATTTCAAAA 57.782 30.769 0.00 0.00 45.00 2.44
47 48 7.498570 ACTGTTGGGTAACGTAGTAATTTCAAA 59.501 33.333 0.00 0.00 45.00 2.69
48 49 6.991531 ACTGTTGGGTAACGTAGTAATTTCAA 59.008 34.615 0.00 0.00 45.00 2.69
49 50 6.523840 ACTGTTGGGTAACGTAGTAATTTCA 58.476 36.000 0.00 0.00 45.00 2.69
50 51 6.091305 GGACTGTTGGGTAACGTAGTAATTTC 59.909 42.308 0.00 0.00 45.00 2.17
51 52 5.934043 GGACTGTTGGGTAACGTAGTAATTT 59.066 40.000 0.00 0.00 45.00 1.82
52 53 5.246883 AGGACTGTTGGGTAACGTAGTAATT 59.753 40.000 0.00 0.00 45.00 1.40
53 54 4.774200 AGGACTGTTGGGTAACGTAGTAAT 59.226 41.667 0.00 0.00 45.00 1.89
54 55 4.151883 AGGACTGTTGGGTAACGTAGTAA 58.848 43.478 0.00 0.00 45.00 2.24
55 56 3.766545 AGGACTGTTGGGTAACGTAGTA 58.233 45.455 0.00 0.00 45.00 1.82
57 58 3.428589 GCTAGGACTGTTGGGTAACGTAG 60.429 52.174 0.00 0.00 39.71 3.51
58 59 2.493278 GCTAGGACTGTTGGGTAACGTA 59.507 50.000 0.00 0.00 39.71 3.57
59 60 1.274447 GCTAGGACTGTTGGGTAACGT 59.726 52.381 0.00 0.00 39.71 3.99
60 61 1.405121 GGCTAGGACTGTTGGGTAACG 60.405 57.143 0.00 0.00 39.71 3.18
61 62 1.907255 AGGCTAGGACTGTTGGGTAAC 59.093 52.381 0.00 0.00 37.32 2.50
62 63 2.304761 CAAGGCTAGGACTGTTGGGTAA 59.695 50.000 0.00 0.00 0.00 2.85
63 64 1.906574 CAAGGCTAGGACTGTTGGGTA 59.093 52.381 0.00 0.00 0.00 3.69
64 65 0.693049 CAAGGCTAGGACTGTTGGGT 59.307 55.000 0.00 0.00 0.00 4.51
65 66 0.035056 CCAAGGCTAGGACTGTTGGG 60.035 60.000 0.00 0.00 35.07 4.12
66 67 0.693049 ACCAAGGCTAGGACTGTTGG 59.307 55.000 0.00 0.00 42.89 3.77
67 68 2.568623 AACCAAGGCTAGGACTGTTG 57.431 50.000 0.00 0.00 0.00 3.33
68 69 3.009143 CCTTAACCAAGGCTAGGACTGTT 59.991 47.826 0.00 0.00 44.90 3.16
69 70 2.572104 CCTTAACCAAGGCTAGGACTGT 59.428 50.000 0.00 0.00 44.90 3.55
70 71 3.268023 CCTTAACCAAGGCTAGGACTG 57.732 52.381 0.00 0.00 44.90 3.51
80 81 0.605319 TGCACCGAGCCTTAACCAAG 60.605 55.000 0.00 0.00 44.83 3.61
85 86 2.046314 GCCTGCACCGAGCCTTAA 60.046 61.111 0.00 0.00 44.83 1.85
112 113 3.559024 GATGATGCCATCGCCTCG 58.441 61.111 0.00 0.00 39.70 4.63
124 125 3.469008 TTATTCCACGCCTTCGATGAT 57.531 42.857 0.00 0.00 39.41 2.45
158 159 4.678423 TCATCGGACCGAGGACAT 57.322 55.556 26.22 3.91 41.59 3.06
172 173 1.490693 GCGACGCCAATCGACATCAT 61.491 55.000 9.14 0.00 45.13 2.45
173 174 2.164663 GCGACGCCAATCGACATCA 61.165 57.895 9.14 0.00 45.13 3.07
178 179 4.733371 TGCAGCGACGCCAATCGA 62.733 61.111 17.79 0.00 45.13 3.59
191 192 4.824166 GCTTCACGCGCCATGCAG 62.824 66.667 5.73 1.20 46.97 4.41
194 195 2.099062 GAAGCTTCACGCGCCATG 59.901 61.111 21.67 0.00 45.59 3.66
237 244 6.036083 CCACCTAGATGAAACATAGACAAACG 59.964 42.308 0.00 0.00 0.00 3.60
244 251 7.278868 GTCAAAGACCACCTAGATGAAACATAG 59.721 40.741 0.00 0.00 0.00 2.23
261 268 1.137513 CGTCCACTTCGTCAAAGACC 58.862 55.000 0.00 0.00 38.44 3.85
349 357 2.043227 GGCCTAACCTCACTAGCTCAT 58.957 52.381 0.00 0.00 34.51 2.90
350 358 1.486211 GGCCTAACCTCACTAGCTCA 58.514 55.000 0.00 0.00 34.51 4.26
382 390 2.134287 CATCCCCGATCCGTCCAGT 61.134 63.158 0.00 0.00 0.00 4.00
388 396 1.202639 TGAACAATCATCCCCGATCCG 60.203 52.381 0.00 0.00 0.00 4.18
422 432 6.494666 TTATATCGTTGTCCTGGGAAGAAT 57.505 37.500 0.00 0.00 0.00 2.40
431 441 7.817478 TCGAATTGCATATTATATCGTTGTCCT 59.183 33.333 0.00 0.00 0.00 3.85
473 483 0.976641 AAGTCATGAGTCGGAGCCAA 59.023 50.000 2.86 0.00 0.00 4.52
485 495 7.914871 TGTTAACACAACAGAAATGAAGTCATG 59.085 33.333 3.59 0.00 36.56 3.07
486 496 7.995289 TGTTAACACAACAGAAATGAAGTCAT 58.005 30.769 3.59 0.00 38.41 3.06
524 534 3.819337 GGTTCTCCAAACTAACCTTGGAC 59.181 47.826 0.13 0.00 45.88 4.02
544 554 1.607467 GCTCCATGGCACCTTTGGT 60.607 57.895 6.96 0.00 35.62 3.67
548 558 1.538687 GCAAAGCTCCATGGCACCTT 61.539 55.000 6.96 6.22 34.17 3.50
558 568 2.838974 GCGCTATGGGCAAAGCTCC 61.839 63.158 0.00 0.00 41.23 4.70
644 654 8.980596 TGTTCCCTTATAAAATGATTCTTGCAT 58.019 29.630 0.00 0.00 0.00 3.96
705 718 8.668353 GCTTGAAAGAAAAATTCCTTTTGACTT 58.332 29.630 0.00 0.00 37.36 3.01
712 725 6.982724 CACTCTGCTTGAAAGAAAAATTCCTT 59.017 34.615 0.00 0.00 0.00 3.36
713 726 6.510536 CACTCTGCTTGAAAGAAAAATTCCT 58.489 36.000 0.00 0.00 0.00 3.36
746 767 5.280945 TGCTTGTTTTCATCTGTTGCTTAC 58.719 37.500 0.00 0.00 0.00 2.34
747 768 5.512753 TGCTTGTTTTCATCTGTTGCTTA 57.487 34.783 0.00 0.00 0.00 3.09
748 769 4.389890 TGCTTGTTTTCATCTGTTGCTT 57.610 36.364 0.00 0.00 0.00 3.91
749 770 4.595762 ATGCTTGTTTTCATCTGTTGCT 57.404 36.364 0.00 0.00 0.00 3.91
750 771 6.094719 TCATATGCTTGTTTTCATCTGTTGC 58.905 36.000 0.00 0.00 0.00 4.17
751 772 8.697846 ATTCATATGCTTGTTTTCATCTGTTG 57.302 30.769 0.00 0.00 0.00 3.33
752 773 8.525316 TGATTCATATGCTTGTTTTCATCTGTT 58.475 29.630 0.00 0.00 0.00 3.16
753 774 8.058667 TGATTCATATGCTTGTTTTCATCTGT 57.941 30.769 0.00 0.00 0.00 3.41
767 788 9.814899 ACTAGAATAGCTGTATGATTCATATGC 57.185 33.333 18.68 18.68 44.39 3.14
786 807 6.668133 TTAGGGGGAAATGGAAACTAGAAT 57.332 37.500 0.00 0.00 0.00 2.40
787 808 6.471942 TTTAGGGGGAAATGGAAACTAGAA 57.528 37.500 0.00 0.00 0.00 2.10
832 1144 9.429359 TGTTTCTTCAGTTAAAAGCAATTTCAA 57.571 25.926 0.00 0.00 32.27 2.69
834 1146 8.050170 CGTGTTTCTTCAGTTAAAAGCAATTTC 58.950 33.333 0.00 0.00 32.27 2.17
1045 2076 8.917655 GTCTGTGCTGTTTGTTTTTACTTTTTA 58.082 29.630 0.00 0.00 0.00 1.52
1046 2077 7.655732 AGTCTGTGCTGTTTGTTTTTACTTTTT 59.344 29.630 0.00 0.00 0.00 1.94
1047 2078 7.151976 AGTCTGTGCTGTTTGTTTTTACTTTT 58.848 30.769 0.00 0.00 0.00 2.27
1048 2079 6.687604 AGTCTGTGCTGTTTGTTTTTACTTT 58.312 32.000 0.00 0.00 0.00 2.66
1049 2080 6.267496 AGTCTGTGCTGTTTGTTTTTACTT 57.733 33.333 0.00 0.00 0.00 2.24
1050 2081 5.897377 AGTCTGTGCTGTTTGTTTTTACT 57.103 34.783 0.00 0.00 0.00 2.24
1051 2082 7.913297 TGATTAGTCTGTGCTGTTTGTTTTTAC 59.087 33.333 0.00 0.00 0.00 2.01
1052 2083 7.990917 TGATTAGTCTGTGCTGTTTGTTTTTA 58.009 30.769 0.00 0.00 0.00 1.52
1053 2084 6.862209 TGATTAGTCTGTGCTGTTTGTTTTT 58.138 32.000 0.00 0.00 0.00 1.94
1054 2085 6.449635 TGATTAGTCTGTGCTGTTTGTTTT 57.550 33.333 0.00 0.00 0.00 2.43
1135 2170 1.006227 GAGGGGAAGGGAAGGGGAT 59.994 63.158 0.00 0.00 0.00 3.85
1144 2184 1.680314 GCTTGCTTGGAGGGGAAGG 60.680 63.158 0.00 0.00 33.69 3.46
1471 2511 4.955811 AACCCAGTTTCATTTTCCTTCC 57.044 40.909 0.00 0.00 0.00 3.46
1481 2521 3.558033 GGGACACTTTAACCCAGTTTCA 58.442 45.455 0.00 0.00 42.81 2.69
1654 2702 5.523916 ACACTGGATTGCGACATTTCTATAC 59.476 40.000 0.00 0.00 0.00 1.47
1655 2703 5.670485 ACACTGGATTGCGACATTTCTATA 58.330 37.500 0.00 0.00 0.00 1.31
1656 2704 4.517285 ACACTGGATTGCGACATTTCTAT 58.483 39.130 0.00 0.00 0.00 1.98
1699 2747 8.211629 GGTGATATATCCCAGTGAAGTTAAAGT 58.788 37.037 10.25 0.00 0.00 2.66
1707 2755 8.275187 ACAAATAGGTGATATATCCCAGTGAA 57.725 34.615 17.49 0.00 0.00 3.18
1757 2805 8.941995 TCCTATCTATTGACTAGCATTGTAGT 57.058 34.615 0.00 0.44 35.88 2.73
1786 2834 9.898152 AAATTGTTTTCAAACTGATCCCTTAAA 57.102 25.926 4.14 0.00 43.39 1.52
1795 2843 8.336806 GCATGATTCAAATTGTTTTCAAACTGA 58.663 29.630 0.00 0.00 43.39 3.41
1799 2847 7.498239 TCCAGCATGATTCAAATTGTTTTCAAA 59.502 29.630 0.00 0.00 40.46 2.69
1801 2849 6.522946 TCCAGCATGATTCAAATTGTTTTCA 58.477 32.000 0.00 0.00 39.69 2.69
1830 2878 4.624015 CAATACAAAGGGCATTGCTATGG 58.376 43.478 8.82 0.00 33.52 2.74
1899 3082 7.382898 TGAGCATTATAACCACAGCGATTATA 58.617 34.615 0.00 0.00 0.00 0.98
2130 3313 8.213679 TCAAGCTTATAGCAATAAATCTCCAGT 58.786 33.333 0.00 0.00 45.56 4.00
2217 3400 8.538701 ACTTCATGTAGATGTTTCTCAAGAGAT 58.461 33.333 6.32 0.00 37.29 2.75
2259 3442 8.786826 AAACATCTCATATTTGTAAACGGAGA 57.213 30.769 0.00 0.00 34.77 3.71
2309 3492 4.818534 TTGTTCACTCATTTCAGTCTGC 57.181 40.909 0.00 0.00 0.00 4.26
2311 3494 5.647658 TGTGTTTGTTCACTCATTTCAGTCT 59.352 36.000 0.00 0.00 38.90 3.24
2336 3519 8.492415 AATAGGATGTAGATAGGCACACTTTA 57.508 34.615 0.00 0.00 0.00 1.85
2337 3520 7.071196 TGAATAGGATGTAGATAGGCACACTTT 59.929 37.037 0.00 0.00 0.00 2.66
2340 3523 6.159988 GTGAATAGGATGTAGATAGGCACAC 58.840 44.000 0.00 0.00 0.00 3.82
2341 3524 5.838521 TGTGAATAGGATGTAGATAGGCACA 59.161 40.000 0.00 0.00 0.00 4.57
2662 3846 7.082700 TCGTGTTTATTTGTGCATATGATGT 57.917 32.000 6.97 0.00 0.00 3.06
2709 3893 4.236416 ACACAAGCACACACGCGC 62.236 61.111 5.73 0.00 36.85 6.86
2714 3898 0.964860 AGGCAACACACAAGCACACA 60.965 50.000 0.00 0.00 41.41 3.72
2731 3915 5.989477 TCCAGTATTTTCCTCATGTGTAGG 58.011 41.667 0.00 0.00 35.26 3.18
2737 3921 4.080356 TGTCCCTCCAGTATTTTCCTCATG 60.080 45.833 0.00 0.00 0.00 3.07
2794 3978 5.007724 GGTTGATCCCTATGATGAACGAAAC 59.992 44.000 0.00 0.00 45.33 2.78
2817 4001 2.044053 ATTGCCATCCACACGGGG 60.044 61.111 0.00 0.00 37.22 5.73
2857 4045 1.302832 GGATCATGGATGGCCCGTC 60.303 63.158 0.00 0.00 37.93 4.79
2910 4098 8.762481 AACATTTACAAGGAAAGGAGTAAACT 57.238 30.769 0.00 0.00 38.71 2.66
2923 4111 4.853924 ACTGGAGCAAACATTTACAAGG 57.146 40.909 0.00 0.00 0.00 3.61
3374 4630 1.062525 CTTCGCTGGCCAAATACGC 59.937 57.895 7.01 5.17 0.00 4.42
3376 4632 1.330829 GCTACTTCGCTGGCCAAATAC 59.669 52.381 7.01 0.00 0.00 1.89
3481 4739 7.340487 AGCTTGGGATTTCTAAATAACTGGAAG 59.660 37.037 0.00 0.00 42.29 3.46
3749 5011 4.717280 AGGTAGGACCAAAGGAGTGATAAG 59.283 45.833 0.00 0.00 41.95 1.73
3818 5080 6.018994 GGGATAACTCGTAGTTGCATGTAAAG 60.019 42.308 0.00 0.00 39.11 1.85
3873 5135 2.092103 AGCTTGCCCGGAATTAATACCA 60.092 45.455 0.73 0.00 0.00 3.25
3886 5148 1.807142 GAAACAGACAGTAGCTTGCCC 59.193 52.381 0.00 0.00 0.00 5.36
3942 5204 6.466470 GGTTAAAGGGCATCAGATTAGAGGAT 60.466 42.308 0.00 0.00 0.00 3.24
3956 5218 4.993028 ACTAGAACAATGGTTAAAGGGCA 58.007 39.130 0.00 0.00 37.36 5.36
3989 5251 4.665212 CAGTGTGCTTATAACTTGCCATG 58.335 43.478 0.00 0.00 0.00 3.66
4071 5336 2.019156 GCCACAGTAAGATGAAGGGCC 61.019 57.143 0.00 0.00 32.88 5.80
4102 5367 1.485066 ACGACTTATACAAGGGCCTGG 59.515 52.381 6.92 6.59 35.97 4.45
4120 5385 6.183360 ACAGGTTGATAATTGGCTCAAATACG 60.183 38.462 0.00 0.00 33.45 3.06
4184 5449 4.453819 GCTCTATGTTGAGATACCAATGGC 59.546 45.833 0.00 0.00 36.23 4.40
4285 5550 1.178276 GATCTCAGTGACAGGGACGT 58.822 55.000 0.00 0.00 0.00 4.34
4296 5561 4.482952 TCATGTGCATTCAGATCTCAGT 57.517 40.909 0.00 0.00 0.00 3.41
4424 5691 8.818141 ATGTGTACTGTATATGTATGCTTCAC 57.182 34.615 0.00 0.00 0.00 3.18
4507 5814 3.135530 ACTGGCTAGATCATCTTGGGTTC 59.864 47.826 3.17 0.00 0.00 3.62
4512 5819 7.798596 AAAATGTACTGGCTAGATCATCTTG 57.201 36.000 3.17 0.00 0.00 3.02
4513 5820 7.831193 ACAAAAATGTACTGGCTAGATCATCTT 59.169 33.333 3.17 0.00 0.00 2.40
4747 6071 0.251341 TTGGCTCAGGGAAAGAAGGC 60.251 55.000 0.00 0.00 0.00 4.35
4960 6284 2.642807 AGCTTGGTGTTGTGGGTAGTAT 59.357 45.455 0.00 0.00 0.00 2.12
5002 6326 2.808543 CTCTTGTTGTACTTGCTGACCC 59.191 50.000 0.00 0.00 0.00 4.46
5039 6363 3.009473 ACATCTTGAGCTTGAGGCCTTAA 59.991 43.478 6.77 8.64 43.05 1.85
5140 6464 3.123620 CGAGAGGGTTGCTGCTGC 61.124 66.667 8.89 8.89 40.20 5.25
5141 6465 1.294659 GAACGAGAGGGTTGCTGCTG 61.295 60.000 0.00 0.00 0.00 4.41
5142 6466 1.004440 GAACGAGAGGGTTGCTGCT 60.004 57.895 0.00 0.00 0.00 4.24
5285 6609 4.691860 CTGGAAACTGCTGAACATTAGG 57.308 45.455 0.00 0.00 0.00 2.69
5350 6722 3.496309 TTGCAGCTGTGGTGGAGGG 62.496 63.158 16.64 0.00 32.39 4.30
5364 6748 0.388659 GTTGGATTGCTGTGGTTGCA 59.611 50.000 0.00 0.00 38.80 4.08
5365 6749 0.319813 GGTTGGATTGCTGTGGTTGC 60.320 55.000 0.00 0.00 0.00 4.17
5366 6750 0.318120 GGGTTGGATTGCTGTGGTTG 59.682 55.000 0.00 0.00 0.00 3.77
5367 6751 0.188342 AGGGTTGGATTGCTGTGGTT 59.812 50.000 0.00 0.00 0.00 3.67
5368 6752 0.251341 GAGGGTTGGATTGCTGTGGT 60.251 55.000 0.00 0.00 0.00 4.16
5369 6753 0.251297 TGAGGGTTGGATTGCTGTGG 60.251 55.000 0.00 0.00 0.00 4.17
5370 6754 1.747355 GATGAGGGTTGGATTGCTGTG 59.253 52.381 0.00 0.00 0.00 3.66
5371 6755 1.637553 AGATGAGGGTTGGATTGCTGT 59.362 47.619 0.00 0.00 0.00 4.40
5372 6756 2.431954 AGATGAGGGTTGGATTGCTG 57.568 50.000 0.00 0.00 0.00 4.41
5373 6757 2.357569 GGAAGATGAGGGTTGGATTGCT 60.358 50.000 0.00 0.00 0.00 3.91
5374 6758 2.027385 GGAAGATGAGGGTTGGATTGC 58.973 52.381 0.00 0.00 0.00 3.56
5375 6759 3.054139 TGAGGAAGATGAGGGTTGGATTG 60.054 47.826 0.00 0.00 0.00 2.67
5404 6788 2.886523 CACATGAGGATGTTGTGGTTGT 59.113 45.455 0.00 0.00 41.12 3.32
5444 6828 0.104356 TAGTTTGGTGGGGGAGTGGA 60.104 55.000 0.00 0.00 0.00 4.02
5500 6884 0.622665 CAGGCAGAGTTTCAGGGGAT 59.377 55.000 0.00 0.00 0.00 3.85
5578 6962 4.024048 CCACCGTATGAATATTGCACTTCC 60.024 45.833 0.00 0.00 0.00 3.46
5677 7061 2.282887 GGAGGCGGCCCAAAAGAA 60.283 61.111 17.02 0.00 0.00 2.52
5744 7128 2.766345 TACGATGTGTTGTAACCCCC 57.234 50.000 0.00 0.00 0.00 5.40
5745 7129 2.940410 CCATACGATGTGTTGTAACCCC 59.060 50.000 0.00 0.00 0.00 4.95
5826 7210 1.077930 CCTGGATGGCTCACACCAG 60.078 63.158 16.12 16.12 44.71 4.00
5893 7277 1.619654 CCATGGTGTTTGCCTTCTCA 58.380 50.000 2.57 0.00 0.00 3.27
6079 7463 0.606096 TATCACGACACCACCCTGTG 59.394 55.000 0.00 0.00 42.05 3.66
6080 7464 1.480954 GATATCACGACACCACCCTGT 59.519 52.381 0.00 0.00 0.00 4.00
6179 7567 4.016444 GGGGTACATGAAATTCAAGCTCA 58.984 43.478 0.00 0.00 0.00 4.26
6397 7796 0.319555 TGGAAGAGCGAACCGTTCAG 60.320 55.000 11.74 5.59 39.43 3.02
6469 7872 1.404986 CGTGATTTTCGTAGGCTGGGA 60.405 52.381 0.00 0.00 0.00 4.37
6512 7915 0.671781 CCGAGCTGGAAAGACAGTGG 60.672 60.000 0.00 0.00 42.00 4.00
6513 7916 0.318441 TCCGAGCTGGAAAGACAGTG 59.682 55.000 0.00 0.00 46.38 3.66
6514 7917 2.746697 TCCGAGCTGGAAAGACAGT 58.253 52.632 0.00 0.00 46.38 3.55
6532 7964 6.819284 TCCAAGCAGAGAAATGAAAATGTTT 58.181 32.000 0.00 0.00 0.00 2.83
6564 7996 6.323482 CCATTCTCTTCTGTCTCTCCAATCTA 59.677 42.308 0.00 0.00 0.00 1.98
6759 8205 2.876645 CGCTCGGCTTCTCACGAC 60.877 66.667 0.00 0.00 35.04 4.34
6859 8331 3.591254 AAGGAGTCGCCGGAGCAAC 62.591 63.158 5.05 0.00 43.43 4.17
6872 8344 0.692756 GGGGGAGGGAGAAGAAGGAG 60.693 65.000 0.00 0.00 0.00 3.69
6889 8361 0.251916 TGGATAAGAACACGCAGGGG 59.748 55.000 0.00 0.00 0.00 4.79
6925 8397 7.049754 ACAAAATCTGGGAATCAAAATATGCC 58.950 34.615 0.00 0.00 0.00 4.40
6926 8398 8.496707 AACAAAATCTGGGAATCAAAATATGC 57.503 30.769 0.00 0.00 0.00 3.14
6951 8434 1.559682 CTGATTCGGAAGGGAGGGAAA 59.440 52.381 0.00 0.00 0.00 3.13
6963 8463 6.925718 TCTTCTTTATATCACAGCTGATTCGG 59.074 38.462 23.35 4.27 38.21 4.30
6990 8490 1.546029 GCGGCTCAATCTTCCCTTTTT 59.454 47.619 0.00 0.00 0.00 1.94
6991 8491 1.177401 GCGGCTCAATCTTCCCTTTT 58.823 50.000 0.00 0.00 0.00 2.27
7109 8610 2.817844 AGTAAAATTCCGTCACCAAGGC 59.182 45.455 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.