Multiple sequence alignment - TraesCS1D01G163100

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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 TraesCS1D01G163100 chr1D 100.000 5184 0 0 1 5184 233893088 233898271 0.000000e+00 9574.0
1 TraesCS1D01G163100 chr1B 90.388 2497 153 38 1 2449 368539327 368541784 0.000000e+00 3201.0
2 TraesCS1D01G163100 chr1B 88.971 943 62 22 4270 5184 368544494 368545422 0.000000e+00 1127.0
3 TraesCS1D01G163100 chr1B 90.275 874 59 13 3391 4261 368543430 368544280 0.000000e+00 1120.0
4 TraesCS1D01G163100 chr1B 93.151 584 36 4 2449 3030 368541824 368542405 0.000000e+00 854.0
5 TraesCS1D01G163100 chr1B 91.633 251 17 4 3074 3323 368542932 368543179 1.380000e-90 344.0
6 TraesCS1D01G163100 chr1B 93.939 66 3 1 3326 3390 368543221 368543286 1.190000e-16 99.0
7 TraesCS1D01G163100 chr1A 92.051 1799 103 20 671 2449 313752000 313750222 0.000000e+00 2494.0
8 TraesCS1D01G163100 chr1A 93.575 965 38 8 4228 5184 313748746 313747798 0.000000e+00 1417.0
9 TraesCS1D01G163100 chr1A 93.042 503 28 4 2458 2960 313750179 313749684 0.000000e+00 728.0
10 TraesCS1D01G163100 chr1A 86.085 539 44 6 1 510 313752682 313752146 7.590000e-153 551.0
11 TraesCS1D01G163100 chr1A 93.846 260 16 0 3832 4091 313749005 313748746 4.870000e-105 392.0
12 TraesCS1D01G163100 chr1A 91.561 237 16 4 3091 3326 313749357 313749124 1.800000e-84 324.0
13 TraesCS1D01G163100 chr7D 99.252 401 3 0 3460 3860 33677504 33677904 0.000000e+00 725.0
14 TraesCS1D01G163100 chr3D 84.545 220 23 6 156 373 219567786 219567576 1.890000e-49 207.0
15 TraesCS1D01G163100 chr3D 81.614 223 33 8 147 366 415532721 415532938 1.480000e-40 178.0
16 TraesCS1D01G163100 chr3B 84.091 220 25 6 156 373 293741151 293740940 2.450000e-48 204.0
17 TraesCS1D01G163100 chr3A 82.609 230 26 9 156 374 739144462 739144236 1.910000e-44 191.0
18 TraesCS1D01G163100 chr3A 95.349 43 2 0 733 775 26815684 26815642 9.310000e-08 69.4
19 TraesCS1D01G163100 chr5D 82.039 206 28 9 175 375 13891729 13891528 3.210000e-37 167.0
20 TraesCS1D01G163100 chr7A 83.234 167 24 4 156 321 651983223 651983386 3.230000e-32 150.0
21 TraesCS1D01G163100 chr6B 84.375 64 7 3 799 860 45598871 45598809 5.610000e-05 60.2


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 TraesCS1D01G163100 chr1D 233893088 233898271 5183 False 9574.000000 9574 100.000000 1 5184 1 chr1D.!!$F1 5183
1 TraesCS1D01G163100 chr1B 368539327 368545422 6095 False 1124.166667 3201 91.392833 1 5184 6 chr1B.!!$F1 5183
2 TraesCS1D01G163100 chr1A 313747798 313752682 4884 True 984.333333 2494 91.693333 1 5184 6 chr1A.!!$R1 5183

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
200 209 0.238289 CACGAACACATGGCAACTCC 59.762 55.0 0.0 0.0 37.61 3.85 F
1162 1278 0.248702 GCTACCTTCCTCTCGCTTCG 60.249 60.0 0.0 0.0 0.00 3.79 F
1199 1315 0.035056 ATTTTCCCGCTGACCCTCTG 60.035 55.0 0.0 0.0 0.00 3.35 F
2129 2251 0.396695 TCGGATCACCTACTGGACCC 60.397 60.0 0.0 0.0 37.04 4.46 F
3387 4076 0.179054 GAAGGGAATACGGCAGGGAC 60.179 60.0 0.0 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1316 0.101759 CTGGGCATGCCGAGAAATTG 59.898 55.0 37.56 15.22 43.43 2.32 R
2806 2969 0.332972 GCTGGATTGGAGAAAGGGGT 59.667 55.0 0.00 0.00 0.00 4.95 R
2807 2970 0.627986 AGCTGGATTGGAGAAAGGGG 59.372 55.0 0.00 0.00 0.00 4.79 R
3547 4380 1.136872 GACGCAGCAGTCTGATCGTC 61.137 60.0 19.60 19.60 43.28 4.20 R
5084 6172 0.738975 GGATGCGGTAAAAAGGGAGC 59.261 55.0 0.00 0.00 0.00 4.70 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
124 125 6.462500 AGAGCCATGCATATACTAAGTCAAG 58.538 40.000 0.00 0.00 0.00 3.02
199 208 0.385974 GCACGAACACATGGCAACTC 60.386 55.000 0.00 0.00 37.61 3.01
200 209 0.238289 CACGAACACATGGCAACTCC 59.762 55.000 0.00 0.00 37.61 3.85
201 210 0.889186 ACGAACACATGGCAACTCCC 60.889 55.000 0.00 0.00 37.61 4.30
274 304 6.847956 TGAATGGCAGTTTCAATTCTTTTG 57.152 33.333 1.15 0.00 30.44 2.44
412 444 8.372521 GTTTACAAATTCCATAATGCAACTTCG 58.627 33.333 0.00 0.00 0.00 3.79
443 475 7.340232 TGAAAGTTCAGCATATTATTCCAGCTT 59.660 33.333 0.00 0.00 32.35 3.74
483 515 3.232720 TGCATGGCAATACATCATCCT 57.767 42.857 0.00 0.00 34.76 3.24
555 644 3.383505 GTGCAAGTAAAAGACCCAAACCT 59.616 43.478 0.00 0.00 0.00 3.50
661 751 4.449405 TGCGTTCGTTCATTCATTTCAGTA 59.551 37.500 0.00 0.00 0.00 2.74
662 752 5.121611 TGCGTTCGTTCATTCATTTCAGTAT 59.878 36.000 0.00 0.00 0.00 2.12
709 799 7.112452 TCTGAAACATCTCATAATTCGGAGA 57.888 36.000 10.40 10.40 43.71 3.71
761 851 8.804912 AATGGTTGTAATTTAATACGGGTGTA 57.195 30.769 0.00 0.00 34.45 2.90
778 886 5.392811 CGGGTGTATTTTATTTACGGGCAAA 60.393 40.000 0.00 0.00 0.00 3.68
784 892 8.242053 TGTATTTTATTTACGGGCAAATTTCGA 58.758 29.630 4.93 0.00 30.84 3.71
786 894 5.883503 TTATTTACGGGCAAATTTCGAGT 57.116 34.783 4.93 0.00 30.84 4.18
788 896 5.883503 ATTTACGGGCAAATTTCGAGTAA 57.116 34.783 4.93 3.68 0.00 2.24
855 963 8.989980 GTATTTAGAAGGGAAACGATATCCAAG 58.010 37.037 0.00 0.00 38.80 3.61
865 973 0.251077 GATATCCAAGCAGGCCCCAG 60.251 60.000 0.00 0.00 37.29 4.45
883 991 6.012745 GCCCCAGGTATGAAATCATAGAAAT 58.987 40.000 3.40 0.00 39.29 2.17
930 1046 8.495148 GTTTTCAAACCAATTAGCCAAACATAG 58.505 33.333 0.00 0.00 32.82 2.23
977 1093 4.740902 ACCCAAAGAGGCAAAGAAGTAAT 58.259 39.130 0.00 0.00 35.39 1.89
1162 1278 0.248702 GCTACCTTCCTCTCGCTTCG 60.249 60.000 0.00 0.00 0.00 3.79
1196 1312 0.404040 TGAATTTTCCCGCTGACCCT 59.596 50.000 0.00 0.00 0.00 4.34
1197 1313 1.095600 GAATTTTCCCGCTGACCCTC 58.904 55.000 0.00 0.00 0.00 4.30
1199 1315 0.035056 ATTTTCCCGCTGACCCTCTG 60.035 55.000 0.00 0.00 0.00 3.35
1200 1316 2.748058 TTTTCCCGCTGACCCTCTGC 62.748 60.000 0.00 0.00 37.88 4.26
1202 1318 4.020617 CCCGCTGACCCTCTGCAA 62.021 66.667 0.00 0.00 40.74 4.08
1203 1319 2.270205 CCGCTGACCCTCTGCAAT 59.730 61.111 0.00 0.00 40.74 3.56
1204 1320 1.377725 CCGCTGACCCTCTGCAATT 60.378 57.895 0.00 0.00 40.74 2.32
1206 1322 0.449388 CGCTGACCCTCTGCAATTTC 59.551 55.000 0.00 0.00 40.74 2.17
1209 1325 2.005451 CTGACCCTCTGCAATTTCTCG 58.995 52.381 0.00 0.00 0.00 4.04
1210 1326 1.339055 TGACCCTCTGCAATTTCTCGG 60.339 52.381 0.00 0.00 0.00 4.63
1287 1405 4.355925 GACAGAACCGTCGCCTTT 57.644 55.556 0.00 0.00 0.00 3.11
1294 1412 0.604511 AACCGTCGCCTTTAAGGTGG 60.605 55.000 22.48 15.87 45.74 4.61
1500 1618 2.987149 CTGCGAAGTTGTAGGTACTGTG 59.013 50.000 0.00 0.00 41.52 3.66
1509 1627 6.642430 AGTTGTAGGTACTGTGTTGTTGTTA 58.358 36.000 0.00 0.00 41.52 2.41
1524 1645 3.880490 TGTTGTTATGTTCACTGGACCAC 59.120 43.478 0.00 0.00 0.00 4.16
1528 1649 4.251268 GTTATGTTCACTGGACCACCTAC 58.749 47.826 0.00 0.00 37.04 3.18
1548 1669 2.877168 ACAGCTCAAGAAACTGCTCAAG 59.123 45.455 0.00 0.00 34.72 3.02
1559 1680 3.492102 ACTGCTCAAGTTCAGGCTTTA 57.508 42.857 0.00 0.00 34.57 1.85
1560 1681 3.142174 ACTGCTCAAGTTCAGGCTTTAC 58.858 45.455 0.00 0.00 34.57 2.01
1561 1682 3.141398 CTGCTCAAGTTCAGGCTTTACA 58.859 45.455 0.00 0.00 0.00 2.41
1562 1683 3.141398 TGCTCAAGTTCAGGCTTTACAG 58.859 45.455 0.00 0.00 0.00 2.74
1563 1684 3.142174 GCTCAAGTTCAGGCTTTACAGT 58.858 45.455 0.00 0.00 0.00 3.55
1564 1685 4.202315 TGCTCAAGTTCAGGCTTTACAGTA 60.202 41.667 0.00 0.00 0.00 2.74
1565 1686 4.152580 GCTCAAGTTCAGGCTTTACAGTAC 59.847 45.833 0.00 0.00 0.00 2.73
1566 1687 5.542779 CTCAAGTTCAGGCTTTACAGTACT 58.457 41.667 0.00 0.00 0.00 2.73
1567 1688 5.539048 TCAAGTTCAGGCTTTACAGTACTC 58.461 41.667 0.00 0.00 0.00 2.59
1571 1692 5.071923 AGTTCAGGCTTTACAGTACTCCTTT 59.928 40.000 0.00 0.00 0.00 3.11
1573 1694 6.675413 TCAGGCTTTACAGTACTCCTTTTA 57.325 37.500 0.00 0.00 0.00 1.52
1650 1771 3.357079 GCCCAGACTGTTGCACCG 61.357 66.667 0.93 0.00 0.00 4.94
1653 1774 3.716006 CAGACTGTTGCACCGCCG 61.716 66.667 0.00 0.00 0.00 6.46
1744 1865 2.733956 TCACCCCTCAAATGGTAATGC 58.266 47.619 0.00 0.00 32.32 3.56
1755 1876 7.868415 CCTCAAATGGTAATGCTAGTACTAGAC 59.132 40.741 30.09 21.17 35.21 2.59
1779 1900 6.929606 ACTAGAGTGTAGTTTTGATGTGGTTC 59.070 38.462 0.00 0.00 0.00 3.62
1788 1909 5.304101 AGTTTTGATGTGGTTCATGGCTTTA 59.696 36.000 0.00 0.00 36.83 1.85
1789 1910 5.389859 TTTGATGTGGTTCATGGCTTTAG 57.610 39.130 0.00 0.00 36.83 1.85
1790 1911 4.032960 TGATGTGGTTCATGGCTTTAGT 57.967 40.909 0.00 0.00 36.83 2.24
1795 1916 4.037446 TGTGGTTCATGGCTTTAGTTTGAC 59.963 41.667 0.00 0.00 0.00 3.18
1842 1963 4.345859 TCATGAAACAAGAGGGTAACGT 57.654 40.909 0.00 0.00 37.60 3.99
1846 1967 3.872771 TGAAACAAGAGGGTAACGTTGTC 59.127 43.478 11.99 3.87 35.39 3.18
1892 2013 2.513666 TGATGCCACCCGAATCGC 60.514 61.111 0.00 0.00 0.00 4.58
1958 2079 1.016627 GCCTATGCAGCGAATTGTGA 58.983 50.000 0.00 0.00 37.47 3.58
1961 2082 3.250762 GCCTATGCAGCGAATTGTGAATA 59.749 43.478 0.00 0.00 37.47 1.75
2054 2175 6.100004 AGTCTACTGAATGTTTCATACGTGG 58.900 40.000 0.00 0.00 39.30 4.94
2111 2233 5.712152 AAATGATGTGTTTTCAGGAGGTC 57.288 39.130 0.00 0.00 0.00 3.85
2129 2251 0.396695 TCGGATCACCTACTGGACCC 60.397 60.000 0.00 0.00 37.04 4.46
2260 2383 5.643379 TGTTTGCCTTCTGATATGAAACC 57.357 39.130 0.00 0.00 0.00 3.27
2355 2478 2.575532 TGGCAGTTCTTGTCTTCCTTG 58.424 47.619 0.00 0.00 30.85 3.61
2371 2494 3.426615 TCCTTGGTTGTTGTTCTGTGTT 58.573 40.909 0.00 0.00 0.00 3.32
2373 2496 3.192422 CCTTGGTTGTTGTTCTGTGTTCA 59.808 43.478 0.00 0.00 0.00 3.18
2394 2517 3.611766 ATACTAACAGCCAGGTCACAC 57.388 47.619 0.00 0.00 0.00 3.82
2444 2567 2.228582 TGACACATTTTGATCCTTGCCG 59.771 45.455 0.00 0.00 0.00 5.69
2449 2572 3.763360 ACATTTTGATCCTTGCCGATTCA 59.237 39.130 0.00 0.00 0.00 2.57
2451 2574 5.105228 ACATTTTGATCCTTGCCGATTCAAT 60.105 36.000 0.00 0.00 0.00 2.57
2452 2575 6.096705 ACATTTTGATCCTTGCCGATTCAATA 59.903 34.615 0.00 0.00 0.00 1.90
2454 2577 4.422073 TGATCCTTGCCGATTCAATACT 57.578 40.909 0.00 0.00 0.00 2.12
2455 2578 4.129380 TGATCCTTGCCGATTCAATACTG 58.871 43.478 0.00 0.00 0.00 2.74
2456 2579 2.288666 TCCTTGCCGATTCAATACTGC 58.711 47.619 0.00 0.00 0.00 4.40
2474 2637 9.888878 CAATACTGCAATAATATGTTTCCTCTG 57.111 33.333 0.00 0.00 0.00 3.35
2649 2812 8.533569 TCTAGTTCACCATAGACATCATACAA 57.466 34.615 0.00 0.00 0.00 2.41
2662 2825 5.260424 ACATCATACAACTGGCATTGGTTA 58.740 37.500 12.20 0.92 33.63 2.85
2667 2830 2.562298 ACAACTGGCATTGGTTACATGG 59.438 45.455 12.20 0.00 33.63 3.66
2716 2879 8.738199 TTAGTGTTTAACTAGTGATTGTCTCG 57.262 34.615 0.00 0.00 42.38 4.04
2733 2896 1.001406 CTCGGCCTTCCTGGTATCATC 59.999 57.143 0.00 0.00 38.35 2.92
2778 2941 9.958180 TGTAATCTATCTTTGGATTTCACTTGA 57.042 29.630 0.00 0.00 35.06 3.02
2806 2969 3.826524 TGTTTCTGGCTGAATAACCACA 58.173 40.909 7.68 6.13 34.24 4.17
2807 2970 3.568007 TGTTTCTGGCTGAATAACCACAC 59.432 43.478 7.68 2.31 34.24 3.82
2817 2980 3.245122 TGAATAACCACACCCCTTTCTCC 60.245 47.826 0.00 0.00 0.00 3.71
2829 2992 2.556114 CCCTTTCTCCAATCCAGCTGTT 60.556 50.000 13.81 0.00 0.00 3.16
2851 3014 8.948631 TGTTGGCTTTAATTACAAAATTGACA 57.051 26.923 0.00 0.00 36.02 3.58
2884 3047 4.789012 TTCTGCCCTTGAGCAAAATAAG 57.211 40.909 0.00 0.00 43.52 1.73
2895 3058 6.389830 TGAGCAAAATAAGAAGCTTCACAA 57.610 33.333 27.57 12.90 37.48 3.33
2924 3087 9.623000 AGTTGGTGAGTATTACTGTTTTAAGTT 57.377 29.630 0.00 0.00 0.00 2.66
2925 3088 9.874215 GTTGGTGAGTATTACTGTTTTAAGTTC 57.126 33.333 0.00 0.00 0.00 3.01
3002 3165 8.153550 AGCAGATGTACTTAATAATGGAAGAGG 58.846 37.037 0.00 0.00 0.00 3.69
3009 3172 7.741554 ACTTAATAATGGAAGAGGTCTGTCT 57.258 36.000 0.00 0.00 0.00 3.41
3046 3209 6.997239 ATATGAAAAGGTCCGTTTTACTCC 57.003 37.500 4.18 0.00 29.58 3.85
3047 3210 3.479489 TGAAAAGGTCCGTTTTACTCCC 58.521 45.455 4.18 0.00 29.58 4.30
3048 3211 3.117963 TGAAAAGGTCCGTTTTACTCCCA 60.118 43.478 4.18 0.00 29.58 4.37
3049 3212 3.581265 AAAGGTCCGTTTTACTCCCAA 57.419 42.857 0.00 0.00 0.00 4.12
3050 3213 2.556144 AGGTCCGTTTTACTCCCAAC 57.444 50.000 0.00 0.00 0.00 3.77
3051 3214 2.052468 AGGTCCGTTTTACTCCCAACT 58.948 47.619 0.00 0.00 0.00 3.16
3052 3215 3.242011 AGGTCCGTTTTACTCCCAACTA 58.758 45.455 0.00 0.00 0.00 2.24
3053 3216 3.842436 AGGTCCGTTTTACTCCCAACTAT 59.158 43.478 0.00 0.00 0.00 2.12
3054 3217 5.025453 AGGTCCGTTTTACTCCCAACTATA 58.975 41.667 0.00 0.00 0.00 1.31
3055 3218 5.484998 AGGTCCGTTTTACTCCCAACTATAA 59.515 40.000 0.00 0.00 0.00 0.98
3056 3219 6.157471 AGGTCCGTTTTACTCCCAACTATAAT 59.843 38.462 0.00 0.00 0.00 1.28
3057 3220 6.259387 GGTCCGTTTTACTCCCAACTATAATG 59.741 42.308 0.00 0.00 0.00 1.90
3058 3221 6.820152 GTCCGTTTTACTCCCAACTATAATGT 59.180 38.462 0.00 0.00 0.00 2.71
3059 3222 7.010830 GTCCGTTTTACTCCCAACTATAATGTC 59.989 40.741 0.00 0.00 0.00 3.06
3060 3223 6.819649 CCGTTTTACTCCCAACTATAATGTCA 59.180 38.462 0.00 0.00 0.00 3.58
3061 3224 7.011109 CCGTTTTACTCCCAACTATAATGTCAG 59.989 40.741 0.00 0.00 0.00 3.51
3062 3225 7.548075 CGTTTTACTCCCAACTATAATGTCAGT 59.452 37.037 0.00 0.00 0.00 3.41
3063 3226 9.880157 GTTTTACTCCCAACTATAATGTCAGTA 57.120 33.333 0.00 0.00 0.00 2.74
3064 3227 9.880157 TTTTACTCCCAACTATAATGTCAGTAC 57.120 33.333 0.00 0.00 0.00 2.73
3065 3228 8.598202 TTACTCCCAACTATAATGTCAGTACA 57.402 34.615 0.00 0.00 40.69 2.90
3067 3230 8.777578 ACTCCCAACTATAATGTCAGTACATA 57.222 34.615 0.00 0.00 45.79 2.29
3068 3231 9.209048 ACTCCCAACTATAATGTCAGTACATAA 57.791 33.333 0.00 0.00 45.79 1.90
3069 3232 9.698309 CTCCCAACTATAATGTCAGTACATAAG 57.302 37.037 0.00 0.00 45.79 1.73
3070 3233 8.148351 TCCCAACTATAATGTCAGTACATAAGC 58.852 37.037 0.00 0.00 45.79 3.09
3071 3234 8.150945 CCCAACTATAATGTCAGTACATAAGCT 58.849 37.037 0.00 0.00 45.79 3.74
3081 3729 8.420374 TGTCAGTACATAAGCTAAGTAAATGC 57.580 34.615 0.00 0.00 0.00 3.56
3089 3737 8.265055 ACATAAGCTAAGTAAATGCTCCTGTAA 58.735 33.333 0.00 0.00 35.85 2.41
3106 3754 7.043656 GCTCCTGTAAAACATACACACAAAAAC 60.044 37.037 0.00 0.00 0.00 2.43
3111 3759 6.959671 AAAACATACACACAAAAACCACTG 57.040 33.333 0.00 0.00 0.00 3.66
3125 3773 1.286553 ACCACTGTTGAAGGGTCCAAA 59.713 47.619 0.00 0.00 0.00 3.28
3158 3806 7.339482 TGTGTGGCAGTATACACCATTAATTA 58.661 34.615 17.67 3.40 44.94 1.40
3159 3807 7.829706 TGTGTGGCAGTATACACCATTAATTAA 59.170 33.333 17.67 0.00 44.94 1.40
3185 3833 4.795795 CAGTTTGTTCAACATTGCGTGTAA 59.204 37.500 0.00 0.00 41.14 2.41
3192 3840 5.879948 TCAACATTGCGTGTAATTTTGTG 57.120 34.783 8.65 0.00 41.14 3.33
3198 3847 7.197017 ACATTGCGTGTAATTTTGTGTTCTTA 58.803 30.769 0.00 0.00 39.91 2.10
3241 3890 4.376340 AACAGAGTTTTGTTGCCTGAAG 57.624 40.909 0.00 0.00 39.68 3.02
3250 3899 1.270571 TGTTGCCTGAAGTATCACGCA 60.271 47.619 0.00 0.00 43.05 5.24
3256 3905 2.427453 CCTGAAGTATCACGCACCTACT 59.573 50.000 0.00 0.00 0.00 2.57
3289 3939 5.703130 GGATGGGAAACAATAGTAGATGCTC 59.297 44.000 0.00 0.00 0.00 4.26
3306 3956 9.967346 GTAGATGCTCACTTATACACTCAATAA 57.033 33.333 0.00 0.00 0.00 1.40
3323 3973 6.372659 ACTCAATAATGTGAAGTAGGCACTTG 59.627 38.462 6.99 0.00 45.18 3.16
3360 4049 3.930848 GCTCTGCCCAGAAAATTCATTTG 59.069 43.478 0.00 0.00 36.94 2.32
3361 4050 3.929094 TCTGCCCAGAAAATTCATTTGC 58.071 40.909 0.00 0.00 33.91 3.68
3364 4053 4.066490 TGCCCAGAAAATTCATTTGCTTG 58.934 39.130 0.00 0.00 33.36 4.01
3386 4075 0.619255 TGAAGGGAATACGGCAGGGA 60.619 55.000 0.00 0.00 0.00 4.20
3387 4076 0.179054 GAAGGGAATACGGCAGGGAC 60.179 60.000 0.00 0.00 0.00 4.46
3388 4077 0.620700 AAGGGAATACGGCAGGGACT 60.621 55.000 0.00 0.00 43.88 3.85
3389 4078 1.049289 AGGGAATACGGCAGGGACTC 61.049 60.000 0.00 0.00 34.60 3.36
3433 4266 4.952071 TCTTGATGCTCCAAGATAGAGG 57.048 45.455 14.45 0.00 45.25 3.69
3436 4269 6.452647 TCTTGATGCTCCAAGATAGAGGGAG 61.453 48.000 14.45 0.00 45.25 4.30
3459 4292 5.752892 CAGATGATTCTGGGTCAATGAAG 57.247 43.478 0.00 0.00 44.78 3.02
3460 4293 5.191426 CAGATGATTCTGGGTCAATGAAGT 58.809 41.667 0.00 0.00 44.78 3.01
3461 4294 5.296283 CAGATGATTCTGGGTCAATGAAGTC 59.704 44.000 0.00 0.00 44.78 3.01
3481 4314 5.810095 AGTCCTACTTCTTCCTTTCCAATG 58.190 41.667 0.00 0.00 0.00 2.82
3482 4315 4.944317 GTCCTACTTCTTCCTTTCCAATGG 59.056 45.833 0.00 0.00 0.00 3.16
3498 4331 4.044571 TCCAATGGAGAAATTCCCTCAAGT 59.955 41.667 0.00 0.00 46.19 3.16
3501 4334 4.722526 TGGAGAAATTCCCTCAAGTGAA 57.277 40.909 9.23 0.00 46.19 3.18
3506 4339 4.104738 AGAAATTCCCTCAAGTGAACTCCA 59.895 41.667 0.00 0.00 0.00 3.86
3510 4343 2.978978 TCCCTCAAGTGAACTCCATGAA 59.021 45.455 0.00 0.00 0.00 2.57
3522 4355 8.051535 AGTGAACTCCATGAATATGATCAAACT 58.948 33.333 0.00 0.00 36.36 2.66
3527 4360 6.661777 TCCATGAATATGATCAAACTGGTGA 58.338 36.000 0.00 0.00 36.36 4.02
3554 4387 6.978674 AAGAATTATCACCTAGGACGATCA 57.021 37.500 17.98 8.87 0.00 2.92
3564 4397 1.875813 GGACGATCAGACTGCTGCG 60.876 63.158 0.00 3.89 42.01 5.18
3567 4400 2.220224 CGATCAGACTGCTGCGTCG 61.220 63.158 15.24 11.68 42.01 5.12
3571 4404 3.753434 AGACTGCTGCGTCGGGAG 61.753 66.667 15.24 5.82 38.90 4.30
3572 4405 4.803426 GACTGCTGCGTCGGGAGG 62.803 72.222 10.79 0.00 32.35 4.30
3595 4428 8.814038 AGGATGTATTTTAGTTGATTTCTGCT 57.186 30.769 0.00 0.00 0.00 4.24
3672 4507 8.739039 TCGACCAGAATGATTTTATTTGAACAT 58.261 29.630 0.00 0.00 39.69 2.71
3673 4508 9.013490 CGACCAGAATGATTTTATTTGAACATC 57.987 33.333 0.00 0.00 39.69 3.06
3691 4527 8.515695 TGAACATCAAGATGCAAAATCTAGAT 57.484 30.769 9.85 0.00 42.39 1.98
3694 4530 8.289939 ACATCAAGATGCAAAATCTAGATTGT 57.710 30.769 18.61 10.66 42.39 2.71
3731 4567 2.376518 TCCTTGCTGGAAGAATTGACCT 59.623 45.455 10.73 0.00 42.94 3.85
3732 4568 2.490903 CCTTGCTGGAAGAATTGACCTG 59.509 50.000 10.73 0.00 38.35 4.00
3734 4570 0.813821 GCTGGAAGAATTGACCTGCC 59.186 55.000 0.00 0.00 40.84 4.85
3742 4578 4.796038 AGAATTGACCTGCCAAATTCTG 57.204 40.909 8.62 0.00 30.41 3.02
3749 4585 3.480470 ACCTGCCAAATTCTGATATCCG 58.520 45.455 0.00 0.00 0.00 4.18
3767 4603 1.247567 CGCAACCACCTTGATCCTTT 58.752 50.000 0.00 0.00 30.42 3.11
3938 4774 5.998363 GGTTTCAGTTTCAAGTCCAGTCTAT 59.002 40.000 0.00 0.00 0.00 1.98
3989 4825 1.443872 ATCTCGTGGTGTTCGTCGC 60.444 57.895 0.00 0.00 0.00 5.19
4018 4854 3.497227 GCTACCAAGGTTACAGGGAACAA 60.497 47.826 0.00 0.00 0.00 2.83
4074 4910 5.105392 TCAAACCAAGCTTGATGAAGTTTGT 60.105 36.000 33.19 19.16 44.65 2.83
4168 5004 2.871096 TGAAACTAACGGCCCTTGAT 57.129 45.000 0.00 0.00 0.00 2.57
4169 5005 3.149005 TGAAACTAACGGCCCTTGATT 57.851 42.857 0.00 0.00 0.00 2.57
4170 5006 2.817258 TGAAACTAACGGCCCTTGATTG 59.183 45.455 0.00 0.00 0.00 2.67
4171 5007 2.579410 AACTAACGGCCCTTGATTGT 57.421 45.000 0.00 0.00 0.00 2.71
4172 5008 1.821216 ACTAACGGCCCTTGATTGTG 58.179 50.000 0.00 0.00 0.00 3.33
4173 5009 1.094785 CTAACGGCCCTTGATTGTGG 58.905 55.000 0.00 0.00 0.00 4.17
4174 5010 0.402504 TAACGGCCCTTGATTGTGGT 59.597 50.000 0.00 0.00 0.00 4.16
4175 5011 0.469144 AACGGCCCTTGATTGTGGTT 60.469 50.000 0.00 0.00 0.00 3.67
4176 5012 0.469144 ACGGCCCTTGATTGTGGTTT 60.469 50.000 0.00 0.00 0.00 3.27
4177 5013 0.038343 CGGCCCTTGATTGTGGTTTG 60.038 55.000 0.00 0.00 0.00 2.93
4178 5014 1.047801 GGCCCTTGATTGTGGTTTGT 58.952 50.000 0.00 0.00 0.00 2.83
4179 5015 1.270252 GGCCCTTGATTGTGGTTTGTG 60.270 52.381 0.00 0.00 0.00 3.33
4180 5016 1.686052 GCCCTTGATTGTGGTTTGTGA 59.314 47.619 0.00 0.00 0.00 3.58
4189 5025 6.676950 TGATTGTGGTTTGTGATTGTATGAC 58.323 36.000 0.00 0.00 0.00 3.06
4252 5088 9.139734 AGTACCTGTCCAAATCTAAATATACGA 57.860 33.333 0.00 0.00 0.00 3.43
4288 5329 1.000506 GGTAGCAGACTTGGAACGTCA 59.999 52.381 0.00 0.00 33.89 4.35
4309 5350 4.035558 TCAAAAGCAACAACTCTAGCAGTG 59.964 41.667 0.00 0.00 34.56 3.66
4328 5369 3.207265 TGTAGTGCAACACATTGGAGT 57.793 42.857 0.00 0.00 42.06 3.85
4361 5402 0.034896 AGTGCAGACCGTAACCCAAG 59.965 55.000 0.00 0.00 0.00 3.61
4369 5410 3.075884 GACCGTAACCCAAGCAATTGTA 58.924 45.455 7.40 0.00 0.00 2.41
4451 5492 3.800506 ACGCTACACTAACACACTTGTTC 59.199 43.478 0.00 0.00 42.67 3.18
4464 5505 4.680110 CACACTTGTTCGTCTTACAGTAGG 59.320 45.833 0.00 0.00 0.00 3.18
4605 5646 6.279123 TCAAAACATTTGCATGCAAGTTAGA 58.721 32.000 30.25 25.51 37.24 2.10
4633 5674 3.686726 CCATCTTCGGTTTTCTGAGGAAG 59.313 47.826 0.00 0.00 42.96 3.46
4806 5878 3.389925 TTTTCAAGCATCAGCAAAGGG 57.610 42.857 0.00 0.00 45.49 3.95
4825 5897 1.202452 GGGCAGCATTACCAGCAAATC 60.202 52.381 0.00 0.00 0.00 2.17
4829 5901 0.455410 GCATTACCAGCAAATCGCCA 59.545 50.000 0.00 0.00 44.04 5.69
4839 5911 3.314913 CAGCAAATCGCCATAACCATACA 59.685 43.478 0.00 0.00 44.04 2.29
4909 5989 3.508402 GCAGGAGGATAGTTAGGCTAGAC 59.492 52.174 0.00 0.00 32.45 2.59
4910 5990 3.754323 CAGGAGGATAGTTAGGCTAGACG 59.246 52.174 0.00 0.00 32.45 4.18
4933 6013 5.049060 CGTGAAACCCAACAGAAACATATGA 60.049 40.000 10.38 0.00 0.00 2.15
5032 6120 5.023533 TGCAAATCTCCATGTAGTCCTAC 57.976 43.478 0.00 0.00 36.63 3.18
5057 6145 3.509575 ACAGCCAACTCTCTACTTCTCTG 59.490 47.826 0.00 0.00 0.00 3.35
5058 6146 3.509575 CAGCCAACTCTCTACTTCTCTGT 59.490 47.826 0.00 0.00 0.00 3.41
5061 6149 4.459685 GCCAACTCTCTACTTCTCTGTGTA 59.540 45.833 0.00 0.00 0.00 2.90
5062 6150 5.620429 GCCAACTCTCTACTTCTCTGTGTAC 60.620 48.000 0.00 0.00 0.00 2.90
5063 6151 5.708230 CCAACTCTCTACTTCTCTGTGTACT 59.292 44.000 0.00 0.00 0.00 2.73
5064 6152 6.879993 CCAACTCTCTACTTCTCTGTGTACTA 59.120 42.308 0.00 0.00 0.00 1.82
5065 6153 7.554835 CCAACTCTCTACTTCTCTGTGTACTAT 59.445 40.741 0.00 0.00 0.00 2.12
5066 6154 8.609176 CAACTCTCTACTTCTCTGTGTACTATC 58.391 40.741 0.00 0.00 0.00 2.08
5067 6155 7.277396 ACTCTCTACTTCTCTGTGTACTATCC 58.723 42.308 0.00 0.00 0.00 2.59
5084 6172 6.678568 ACTATCCACTATCCAATCCTTCAG 57.321 41.667 0.00 0.00 0.00 3.02
5100 6188 0.398696 TCAGCTCCCTTTTTACCGCA 59.601 50.000 0.00 0.00 0.00 5.69
5104 6192 1.953311 GCTCCCTTTTTACCGCATCCA 60.953 52.381 0.00 0.00 0.00 3.41
5123 6211 2.305928 CACCCATGTCAACTTTGGTCA 58.694 47.619 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 5.009210 GCACCACCTACTTTTGACAAATACA 59.991 40.000 0.50 0.00 0.00 2.29
158 167 3.026630 ACACGTGTGACACTTATCAGG 57.973 47.619 22.71 0.00 31.34 3.86
184 193 1.000274 GTTGGGAGTTGCCATGTGTTC 60.000 52.381 0.00 0.00 38.95 3.18
252 282 6.849588 ACAAAAGAATTGAAACTGCCATTC 57.150 33.333 0.00 0.00 0.00 2.67
257 287 7.277760 ACAAACCTACAAAAGAATTGAAACTGC 59.722 33.333 0.00 0.00 0.00 4.40
290 320 6.334202 ACAACTAAACTTGCCATTCGAAAAA 58.666 32.000 0.00 0.00 0.00 1.94
387 419 8.085296 ACGAAGTTGCATTATGGAATTTGTAAA 58.915 29.630 11.36 0.00 37.78 2.01
443 475 5.964887 GCAACACAGTGCAATTTAGAAAA 57.035 34.783 0.00 0.00 44.29 2.29
454 486 1.067749 TTGCCATGCAACACAGTGC 59.932 52.632 0.00 0.00 43.99 4.40
576 665 9.981460 AAGGTAGAATGTCTTCTAATTTGGAAT 57.019 29.630 0.00 0.00 43.77 3.01
637 727 3.550561 TGAAATGAATGAACGAACGCAC 58.449 40.909 0.00 0.00 0.00 5.34
686 776 6.423302 CCTCTCCGAATTATGAGATGTTTCAG 59.577 42.308 6.81 0.00 37.03 3.02
687 777 6.098266 TCCTCTCCGAATTATGAGATGTTTCA 59.902 38.462 6.81 0.00 37.03 2.69
709 799 2.372172 CGTGGCCTTATTATTCCCTCCT 59.628 50.000 3.32 0.00 0.00 3.69
761 851 7.317390 ACTCGAAATTTGCCCGTAAATAAAAT 58.683 30.769 0.00 0.00 30.47 1.82
767 857 5.686159 TTTACTCGAAATTTGCCCGTAAA 57.314 34.783 0.00 2.09 0.00 2.01
778 886 7.065283 CCGTCGTTTTAGTTTTTACTCGAAAT 58.935 34.615 0.00 0.00 0.00 2.17
784 892 3.059665 CGCCCGTCGTTTTAGTTTTTACT 60.060 43.478 0.00 0.00 0.00 2.24
786 894 2.222911 CCGCCCGTCGTTTTAGTTTTTA 59.777 45.455 0.00 0.00 36.19 1.52
788 896 0.587768 CCGCCCGTCGTTTTAGTTTT 59.412 50.000 0.00 0.00 36.19 2.43
855 963 0.106015 ATTTCATACCTGGGGCCTGC 60.106 55.000 0.84 0.00 0.00 4.85
883 991 3.261643 ACTCTGTGCATGGTGAGAATGTA 59.738 43.478 12.75 0.00 0.00 2.29
896 1004 4.734398 ATTGGTTTGAAAACTCTGTGCA 57.266 36.364 5.93 0.00 38.89 4.57
930 1046 3.501950 GATGCAAATTTCCGTGGAGTTC 58.498 45.455 0.00 0.00 0.00 3.01
1162 1278 5.871524 GGAAAATTCAGGAGAAAAGCAATCC 59.128 40.000 0.00 0.00 37.29 3.01
1196 1312 0.452987 GCATGCCGAGAAATTGCAGA 59.547 50.000 6.36 0.00 38.58 4.26
1197 1313 0.526954 GGCATGCCGAGAAATTGCAG 60.527 55.000 23.48 0.00 38.58 4.41
1199 1315 1.227060 GGGCATGCCGAGAAATTGC 60.227 57.895 29.90 9.36 36.85 3.56
1200 1316 0.101759 CTGGGCATGCCGAGAAATTG 59.898 55.000 37.56 15.22 43.43 2.32
1201 1317 0.323725 ACTGGGCATGCCGAGAAATT 60.324 50.000 43.91 25.64 43.43 1.82
1202 1318 0.749454 GACTGGGCATGCCGAGAAAT 60.749 55.000 43.91 28.13 43.43 2.17
1203 1319 1.377202 GACTGGGCATGCCGAGAAA 60.377 57.895 43.91 21.38 43.43 2.52
1204 1320 2.268920 GACTGGGCATGCCGAGAA 59.731 61.111 43.91 23.64 43.43 2.87
1206 1322 4.147449 TCGACTGGGCATGCCGAG 62.147 66.667 38.21 38.21 45.71 4.63
1209 1325 4.479993 AGCTCGACTGGGCATGCC 62.480 66.667 29.47 29.47 0.00 4.40
1210 1326 2.894387 GAGCTCGACTGGGCATGC 60.894 66.667 9.90 9.90 0.00 4.06
1287 1405 3.007182 CGGTTAACAGGAGAACCACCTTA 59.993 47.826 8.10 0.00 44.58 2.69
1294 1412 0.320160 ACGGCGGTTAACAGGAGAAC 60.320 55.000 13.24 0.00 0.00 3.01
1365 1483 3.255642 GGCACCAAGAAAAGCATAACTCA 59.744 43.478 0.00 0.00 0.00 3.41
1470 1588 2.803817 AACTTCGCAGGTGGACCGT 61.804 57.895 0.00 0.00 42.08 4.83
1500 1618 4.336993 TGGTCCAGTGAACATAACAACAAC 59.663 41.667 0.00 0.00 31.76 3.32
1509 1627 2.303022 CTGTAGGTGGTCCAGTGAACAT 59.697 50.000 0.00 0.00 41.12 2.71
1524 1645 2.999355 GAGCAGTTTCTTGAGCTGTAGG 59.001 50.000 0.00 0.00 38.69 3.18
1528 1649 2.877168 ACTTGAGCAGTTTCTTGAGCTG 59.123 45.455 0.00 0.00 39.38 4.24
1548 1669 4.538746 AGGAGTACTGTAAAGCCTGAAC 57.461 45.455 0.00 0.00 0.00 3.18
1571 1692 8.814931 ACACCTCCAATGAATGAAATGAAATAA 58.185 29.630 0.00 0.00 0.00 1.40
1573 1694 7.248743 ACACCTCCAATGAATGAAATGAAAT 57.751 32.000 0.00 0.00 0.00 2.17
1582 1703 4.229096 CGTTGAAACACCTCCAATGAATG 58.771 43.478 0.00 0.00 0.00 2.67
1584 1705 2.034053 GCGTTGAAACACCTCCAATGAA 59.966 45.455 0.00 0.00 0.00 2.57
1585 1706 1.606668 GCGTTGAAACACCTCCAATGA 59.393 47.619 0.00 0.00 0.00 2.57
1586 1707 1.662876 CGCGTTGAAACACCTCCAATG 60.663 52.381 0.00 0.00 0.00 2.82
1587 1708 0.591170 CGCGTTGAAACACCTCCAAT 59.409 50.000 0.00 0.00 0.00 3.16
1588 1709 0.745128 ACGCGTTGAAACACCTCCAA 60.745 50.000 5.58 0.00 0.00 3.53
1594 1715 1.980156 ACACAAAACGCGTTGAAACAC 59.020 42.857 27.34 0.00 32.59 3.32
1755 1876 6.929049 TGAACCACATCAAAACTACACTCTAG 59.071 38.462 0.00 0.00 0.00 2.43
1779 1900 6.449698 AGTTCATTGTCAAACTAAAGCCATG 58.550 36.000 0.00 0.00 34.05 3.66
1795 1916 3.384467 AGGAAACACCCACAAGTTCATTG 59.616 43.478 0.00 0.00 41.37 2.82
1833 1954 0.886563 CTCCTCGACAACGTTACCCT 59.113 55.000 0.00 0.00 40.69 4.34
1842 1963 1.186200 CATCCTCACCTCCTCGACAA 58.814 55.000 0.00 0.00 0.00 3.18
1846 1967 1.112315 CCCTCATCCTCACCTCCTCG 61.112 65.000 0.00 0.00 0.00 4.63
1892 2013 2.278857 CTCCGCAATCTCCGACGG 60.279 66.667 7.84 7.84 46.97 4.79
1896 2017 1.432270 GCTTTCCTCCGCAATCTCCG 61.432 60.000 0.00 0.00 0.00 4.63
1897 2018 1.432270 CGCTTTCCTCCGCAATCTCC 61.432 60.000 0.00 0.00 0.00 3.71
1958 2079 1.541233 CGAAGCGCTCCTCCCATTATT 60.541 52.381 12.06 0.00 0.00 1.40
1961 2082 2.187946 CGAAGCGCTCCTCCCATT 59.812 61.111 12.06 0.00 0.00 3.16
1999 2120 1.481772 AGCTCAGCTGATCTCAAGGAC 59.518 52.381 18.63 0.54 37.57 3.85
2054 2175 8.697292 AGGGACTCACACTAATAGAAGAAATAC 58.303 37.037 0.00 0.00 0.00 1.89
2111 2233 1.735376 CGGGTCCAGTAGGTGATCCG 61.735 65.000 0.00 0.00 39.05 4.18
2129 2251 6.866770 TCAGTAATTCTTCAGTCCTTACAACG 59.133 38.462 0.00 0.00 0.00 4.10
2260 2383 5.220662 CCTGTATATGTTCTTGTTTCCTGCG 60.221 44.000 0.00 0.00 0.00 5.18
2355 2478 6.131544 AGTATTGAACACAGAACAACAACC 57.868 37.500 0.00 0.00 0.00 3.77
2371 2494 3.580895 TGTGACCTGGCTGTTAGTATTGA 59.419 43.478 0.00 0.00 0.00 2.57
2373 2496 3.616560 CGTGTGACCTGGCTGTTAGTATT 60.617 47.826 0.00 0.00 0.00 1.89
2394 2517 2.972625 TCTCCAGTATTTCACTTGCCG 58.027 47.619 0.00 0.00 34.26 5.69
2426 2549 3.788333 ATCGGCAAGGATCAAAATGTG 57.212 42.857 0.00 0.00 0.00 3.21
2449 2572 8.571336 GCAGAGGAAACATATTATTGCAGTATT 58.429 33.333 0.00 0.00 0.00 1.89
2451 2574 7.282585 AGCAGAGGAAACATATTATTGCAGTA 58.717 34.615 0.00 0.00 0.00 2.74
2452 2575 6.125029 AGCAGAGGAAACATATTATTGCAGT 58.875 36.000 0.00 0.00 0.00 4.40
2454 2577 7.992608 TCTTAGCAGAGGAAACATATTATTGCA 59.007 33.333 0.00 0.00 0.00 4.08
2455 2578 8.383318 TCTTAGCAGAGGAAACATATTATTGC 57.617 34.615 0.00 0.00 0.00 3.56
2474 2637 8.430801 AATCGATCATATGCCTTATTCTTAGC 57.569 34.615 0.00 0.00 0.00 3.09
2649 2812 2.224992 TGTCCATGTAACCAATGCCAGT 60.225 45.455 0.00 0.00 0.00 4.00
2662 2825 9.632638 ACAAGCTAAATTATAAGATGTCCATGT 57.367 29.630 0.00 0.00 0.00 3.21
2698 2861 3.767673 AGGCCGAGACAATCACTAGTTAA 59.232 43.478 0.00 0.00 0.00 2.01
2699 2862 3.362706 AGGCCGAGACAATCACTAGTTA 58.637 45.455 0.00 0.00 0.00 2.24
2714 2877 1.048601 GATGATACCAGGAAGGCCGA 58.951 55.000 0.00 0.00 43.14 5.54
2716 2879 3.648545 AGTAAGATGATACCAGGAAGGCC 59.351 47.826 0.00 0.00 43.14 5.19
2778 2941 6.705825 GGTTATTCAGCCAGAAACAACAATTT 59.294 34.615 14.07 0.00 40.22 1.82
2788 2951 2.790433 GGTGTGGTTATTCAGCCAGAA 58.210 47.619 0.00 0.00 35.43 3.02
2806 2969 0.332972 GCTGGATTGGAGAAAGGGGT 59.667 55.000 0.00 0.00 0.00 4.95
2807 2970 0.627986 AGCTGGATTGGAGAAAGGGG 59.372 55.000 0.00 0.00 0.00 4.79
2829 2992 9.050601 CCTTTGTCAATTTTGTAATTAAAGCCA 57.949 29.630 0.00 0.00 31.49 4.75
2851 3014 3.549898 AGGGCAGAATCCTTTTCCTTT 57.450 42.857 0.00 0.00 0.00 3.11
2884 3047 3.565482 TCACCAACTCATTGTGAAGCTTC 59.435 43.478 19.89 19.89 33.60 3.86
2895 3058 9.787435 TTAAAACAGTAATACTCACCAACTCAT 57.213 29.630 0.00 0.00 0.00 2.90
2924 3087 4.756642 AGAGCACATGATTCAAACTTTCGA 59.243 37.500 0.00 0.00 0.00 3.71
2925 3088 5.039480 AGAGCACATGATTCAAACTTTCG 57.961 39.130 0.00 0.00 0.00 3.46
2930 3093 5.125100 TGGAAAGAGCACATGATTCAAAC 57.875 39.130 0.00 0.00 0.00 2.93
2960 3123 2.170166 CTGCTTTTAGGGTGCCAATGA 58.830 47.619 0.00 0.00 0.00 2.57
2994 3157 3.510459 TCATGAAGACAGACCTCTTCCA 58.490 45.455 0.00 0.00 43.90 3.53
3020 3183 9.768662 GGAGTAAAACGGACCTTTTCATATATA 57.231 33.333 0.00 0.00 0.00 0.86
3021 3184 7.718314 GGGAGTAAAACGGACCTTTTCATATAT 59.282 37.037 0.00 0.00 0.00 0.86
3022 3185 7.049754 GGGAGTAAAACGGACCTTTTCATATA 58.950 38.462 0.00 0.00 0.00 0.86
3023 3186 5.884232 GGGAGTAAAACGGACCTTTTCATAT 59.116 40.000 0.00 0.00 0.00 1.78
3024 3187 5.221884 TGGGAGTAAAACGGACCTTTTCATA 60.222 40.000 0.00 0.00 0.00 2.15
3025 3188 4.077108 GGGAGTAAAACGGACCTTTTCAT 58.923 43.478 0.00 0.00 0.00 2.57
3027 3190 3.479489 TGGGAGTAAAACGGACCTTTTC 58.521 45.455 0.00 0.00 0.00 2.29
3028 3191 3.581265 TGGGAGTAAAACGGACCTTTT 57.419 42.857 6.81 6.81 0.00 2.27
3029 3192 3.117776 AGTTGGGAGTAAAACGGACCTTT 60.118 43.478 0.00 0.00 0.00 3.11
3032 3195 2.556144 AGTTGGGAGTAAAACGGACC 57.444 50.000 0.00 0.00 0.00 4.46
3033 3196 6.820152 ACATTATAGTTGGGAGTAAAACGGAC 59.180 38.462 0.00 0.00 0.00 4.79
3034 3197 6.949715 ACATTATAGTTGGGAGTAAAACGGA 58.050 36.000 0.00 0.00 0.00 4.69
3035 3198 6.819649 TGACATTATAGTTGGGAGTAAAACGG 59.180 38.462 0.00 0.00 0.00 4.44
3036 3199 7.548075 ACTGACATTATAGTTGGGAGTAAAACG 59.452 37.037 0.00 0.00 0.00 3.60
3037 3200 8.788325 ACTGACATTATAGTTGGGAGTAAAAC 57.212 34.615 0.00 0.00 0.00 2.43
3038 3201 9.880157 GTACTGACATTATAGTTGGGAGTAAAA 57.120 33.333 0.00 0.00 0.00 1.52
3039 3202 9.038072 TGTACTGACATTATAGTTGGGAGTAAA 57.962 33.333 0.00 0.00 0.00 2.01
3040 3203 8.598202 TGTACTGACATTATAGTTGGGAGTAA 57.402 34.615 0.00 0.00 0.00 2.24
3041 3204 8.777578 ATGTACTGACATTATAGTTGGGAGTA 57.222 34.615 0.00 0.00 44.18 2.59
3042 3205 7.676683 ATGTACTGACATTATAGTTGGGAGT 57.323 36.000 0.00 0.00 44.18 3.85
3043 3206 9.698309 CTTATGTACTGACATTATAGTTGGGAG 57.302 37.037 0.00 0.00 44.18 4.30
3044 3207 8.148351 GCTTATGTACTGACATTATAGTTGGGA 58.852 37.037 0.00 0.00 44.18 4.37
3045 3208 8.150945 AGCTTATGTACTGACATTATAGTTGGG 58.849 37.037 0.00 0.00 44.18 4.12
3056 3219 8.258007 AGCATTTACTTAGCTTATGTACTGACA 58.742 33.333 0.00 0.00 36.00 3.58
3057 3220 8.649973 AGCATTTACTTAGCTTATGTACTGAC 57.350 34.615 0.00 0.00 34.37 3.51
3058 3221 7.926555 GGAGCATTTACTTAGCTTATGTACTGA 59.073 37.037 0.00 0.00 39.02 3.41
3059 3222 7.928706 AGGAGCATTTACTTAGCTTATGTACTG 59.071 37.037 0.00 0.00 39.02 2.74
3060 3223 7.928706 CAGGAGCATTTACTTAGCTTATGTACT 59.071 37.037 0.00 0.00 39.02 2.73
3061 3224 7.711339 ACAGGAGCATTTACTTAGCTTATGTAC 59.289 37.037 0.00 0.00 39.02 2.90
3062 3225 7.792032 ACAGGAGCATTTACTTAGCTTATGTA 58.208 34.615 0.00 0.00 39.02 2.29
3063 3226 6.653989 ACAGGAGCATTTACTTAGCTTATGT 58.346 36.000 0.00 0.00 39.02 2.29
3064 3227 8.662781 TTACAGGAGCATTTACTTAGCTTATG 57.337 34.615 0.00 0.00 39.02 1.90
3065 3228 9.681062 TTTTACAGGAGCATTTACTTAGCTTAT 57.319 29.630 0.00 0.00 39.02 1.73
3066 3229 8.943002 GTTTTACAGGAGCATTTACTTAGCTTA 58.057 33.333 0.00 0.00 39.02 3.09
3067 3230 7.447238 TGTTTTACAGGAGCATTTACTTAGCTT 59.553 33.333 0.00 0.00 39.02 3.74
3068 3231 6.940298 TGTTTTACAGGAGCATTTACTTAGCT 59.060 34.615 0.00 0.00 42.17 3.32
3069 3232 7.141100 TGTTTTACAGGAGCATTTACTTAGC 57.859 36.000 0.00 0.00 0.00 3.09
3071 3234 9.727859 TGTATGTTTTACAGGAGCATTTACTTA 57.272 29.630 0.00 0.00 0.00 2.24
3072 3235 8.512138 GTGTATGTTTTACAGGAGCATTTACTT 58.488 33.333 0.00 0.00 0.00 2.24
3081 3729 7.434013 GGTTTTTGTGTGTATGTTTTACAGGAG 59.566 37.037 0.00 0.00 0.00 3.69
3089 3737 6.031751 ACAGTGGTTTTTGTGTGTATGTTT 57.968 33.333 0.00 0.00 0.00 2.83
3106 3754 2.065899 TTTGGACCCTTCAACAGTGG 57.934 50.000 0.00 0.00 0.00 4.00
3111 3759 3.683365 ATGCAATTTGGACCCTTCAAC 57.317 42.857 0.00 0.00 0.00 3.18
3125 3773 5.239306 GTGTATACTGCCACACATATGCAAT 59.761 40.000 1.58 0.00 43.61 3.56
3158 3806 3.245754 CGCAATGTTGAACAAACTGCATT 59.754 39.130 21.91 2.66 38.99 3.56
3159 3807 2.796031 CGCAATGTTGAACAAACTGCAT 59.204 40.909 21.91 0.00 38.99 3.96
3185 3833 7.878495 TGGGTATCCCTATAAGAACACAAAAT 58.122 34.615 6.38 0.00 45.70 1.82
3198 3847 8.694171 TGTTGATACAATATGGGTATCCCTAT 57.306 34.615 18.21 0.00 45.70 2.57
3241 3890 6.183360 CCATATCTAGAGTAGGTGCGTGATAC 60.183 46.154 0.00 0.00 0.00 2.24
3250 3899 6.485388 TTCCCATCCATATCTAGAGTAGGT 57.515 41.667 0.00 0.00 0.00 3.08
3256 3905 8.742125 ACTATTGTTTCCCATCCATATCTAGA 57.258 34.615 0.00 0.00 0.00 2.43
3306 3956 5.483685 TCTTACAAGTGCCTACTTCACAT 57.516 39.130 0.00 0.00 45.12 3.21
3323 3973 3.429684 GGCAGAGCTACTCCAGTTCTTAC 60.430 52.174 0.00 0.00 41.68 2.34
3360 4049 2.415491 GCCGTATTCCCTTCAAACAAGC 60.415 50.000 0.00 0.00 0.00 4.01
3361 4050 2.817258 TGCCGTATTCCCTTCAAACAAG 59.183 45.455 0.00 0.00 0.00 3.16
3364 4053 1.743394 CCTGCCGTATTCCCTTCAAAC 59.257 52.381 0.00 0.00 0.00 2.93
3386 4075 3.436243 AGGTTCCATCTCTTCTTCGAGT 58.564 45.455 0.00 0.00 32.83 4.18
3387 4076 5.278758 GGATAGGTTCCATCTCTTCTTCGAG 60.279 48.000 0.00 0.00 44.74 4.04
3388 4077 4.585162 GGATAGGTTCCATCTCTTCTTCGA 59.415 45.833 0.00 0.00 44.74 3.71
3389 4078 4.877282 GGATAGGTTCCATCTCTTCTTCG 58.123 47.826 0.00 0.00 44.74 3.79
3420 4253 2.956132 TCTGCTCCCTCTATCTTGGAG 58.044 52.381 0.00 0.00 46.87 3.86
3457 4290 5.906772 TTGGAAAGGAAGAAGTAGGACTT 57.093 39.130 0.00 0.00 41.95 3.01
3458 4291 5.280727 CCATTGGAAAGGAAGAAGTAGGACT 60.281 44.000 0.00 0.00 0.00 3.85
3459 4292 4.944317 CCATTGGAAAGGAAGAAGTAGGAC 59.056 45.833 0.00 0.00 0.00 3.85
3460 4293 4.849810 TCCATTGGAAAGGAAGAAGTAGGA 59.150 41.667 1.94 0.00 0.00 2.94
3461 4294 5.045578 TCTCCATTGGAAAGGAAGAAGTAGG 60.046 44.000 6.88 0.00 32.57 3.18
3481 4314 4.657013 AGTTCACTTGAGGGAATTTCTCC 58.343 43.478 0.00 0.00 44.54 3.71
3482 4315 4.697828 GGAGTTCACTTGAGGGAATTTCTC 59.302 45.833 0.00 1.93 0.00 2.87
3498 4331 7.283807 CCAGTTTGATCATATTCATGGAGTTCA 59.716 37.037 0.00 0.00 28.73 3.18
3501 4334 6.544931 CACCAGTTTGATCATATTCATGGAGT 59.455 38.462 13.57 0.00 30.94 3.85
3522 4355 8.998814 TCCTAGGTGATAATTCTTAATTCACCA 58.001 33.333 19.31 7.45 43.20 4.17
3527 4360 9.930693 GATCGTCCTAGGTGATAATTCTTAATT 57.069 33.333 16.05 0.00 34.90 1.40
3535 4368 5.475220 CAGTCTGATCGTCCTAGGTGATAAT 59.525 44.000 16.05 2.85 0.00 1.28
3539 4372 2.644676 CAGTCTGATCGTCCTAGGTGA 58.355 52.381 9.08 8.78 0.00 4.02
3543 4376 1.268999 GCAGCAGTCTGATCGTCCTAG 60.269 57.143 3.32 0.00 42.95 3.02
3547 4380 1.136872 GACGCAGCAGTCTGATCGTC 61.137 60.000 19.60 19.60 43.28 4.20
3554 4387 3.753434 CTCCCGACGCAGCAGTCT 61.753 66.667 13.23 0.00 38.90 3.24
3564 4397 5.667466 TCAACTAAAATACATCCTCCCGAC 58.333 41.667 0.00 0.00 0.00 4.79
3567 4400 8.624776 CAGAAATCAACTAAAATACATCCTCCC 58.375 37.037 0.00 0.00 0.00 4.30
3572 4405 9.657121 GCTAGCAGAAATCAACTAAAATACATC 57.343 33.333 10.63 0.00 0.00 3.06
3641 4475 9.410556 CAAATAAAATCATTCTGGTCGAAAACT 57.589 29.630 0.00 0.00 34.79 2.66
3643 4477 9.973450 TTCAAATAAAATCATTCTGGTCGAAAA 57.027 25.926 0.00 0.00 34.79 2.29
3648 4482 9.859427 TGATGTTCAAATAAAATCATTCTGGTC 57.141 29.630 0.00 0.00 0.00 4.02
3691 4527 6.978080 GCAAGGACTTTGACTTCATTTTACAA 59.022 34.615 0.74 0.00 39.21 2.41
3694 4530 6.239008 CCAGCAAGGACTTTGACTTCATTTTA 60.239 38.462 0.74 0.00 41.22 1.52
3729 4565 2.227388 GCGGATATCAGAATTTGGCAGG 59.773 50.000 7.08 0.00 0.00 4.85
3731 4567 2.929641 TGCGGATATCAGAATTTGGCA 58.070 42.857 7.08 0.00 0.00 4.92
3732 4568 3.550842 GGTTGCGGATATCAGAATTTGGC 60.551 47.826 7.08 0.00 0.00 4.52
3734 4570 4.498009 GGTGGTTGCGGATATCAGAATTTG 60.498 45.833 7.08 0.00 0.00 2.32
3742 4578 2.325583 TCAAGGTGGTTGCGGATATC 57.674 50.000 0.00 0.00 35.94 1.63
3749 4585 3.572255 TGTAAAAGGATCAAGGTGGTTGC 59.428 43.478 0.00 0.00 35.94 4.17
3989 4825 1.906105 TAACCTTGGTAGCTGGCCGG 61.906 60.000 7.41 7.41 0.00 6.13
4136 4972 9.048446 GGCCGTTAGTTTCATATCACTAATTAA 57.952 33.333 0.00 0.00 37.71 1.40
4140 4976 5.129815 AGGGCCGTTAGTTTCATATCACTAA 59.870 40.000 0.00 0.00 33.89 2.24
4143 4979 3.805207 AGGGCCGTTAGTTTCATATCAC 58.195 45.455 0.00 0.00 0.00 3.06
4150 4986 2.817844 ACAATCAAGGGCCGTTAGTTTC 59.182 45.455 10.98 0.00 0.00 2.78
4151 4987 2.556622 CACAATCAAGGGCCGTTAGTTT 59.443 45.455 10.98 2.18 0.00 2.66
4158 4994 0.038343 CAAACCACAATCAAGGGCCG 60.038 55.000 0.00 0.00 0.00 6.13
4159 4995 1.047801 ACAAACCACAATCAAGGGCC 58.952 50.000 0.00 0.00 0.00 5.80
4168 5004 6.096141 ACAAGTCATACAATCACAAACCACAA 59.904 34.615 0.00 0.00 0.00 3.33
4169 5005 5.592282 ACAAGTCATACAATCACAAACCACA 59.408 36.000 0.00 0.00 0.00 4.17
4170 5006 6.072112 ACAAGTCATACAATCACAAACCAC 57.928 37.500 0.00 0.00 0.00 4.16
4171 5007 6.707440 AACAAGTCATACAATCACAAACCA 57.293 33.333 0.00 0.00 0.00 3.67
4172 5008 9.691362 AATAAACAAGTCATACAATCACAAACC 57.309 29.630 0.00 0.00 0.00 3.27
4175 5011 9.891828 GACAATAAACAAGTCATACAATCACAA 57.108 29.630 0.00 0.00 32.68 3.33
4176 5012 9.061435 TGACAATAAACAAGTCATACAATCACA 57.939 29.630 0.00 0.00 37.36 3.58
4177 5013 9.546909 CTGACAATAAACAAGTCATACAATCAC 57.453 33.333 0.00 0.00 41.02 3.06
4178 5014 8.236586 GCTGACAATAAACAAGTCATACAATCA 58.763 33.333 0.00 0.00 41.02 2.57
4179 5015 8.454106 AGCTGACAATAAACAAGTCATACAATC 58.546 33.333 0.00 0.00 41.02 2.67
4180 5016 8.340618 AGCTGACAATAAACAAGTCATACAAT 57.659 30.769 0.00 0.00 41.02 2.71
4189 5025 5.911280 CACACTGAAGCTGACAATAAACAAG 59.089 40.000 0.00 0.00 0.00 3.16
4252 5088 2.423538 GCTACCAACCGATTCAAGCAAT 59.576 45.455 0.00 0.00 0.00 3.56
4288 5329 3.947834 ACACTGCTAGAGTTGTTGCTTTT 59.052 39.130 0.00 0.00 29.75 2.27
4309 5350 3.542712 CACTCCAATGTGTTGCACTAC 57.457 47.619 0.00 0.00 35.11 2.73
4328 5369 5.646606 GGTCTGCACTTTGTAAAGAAAACA 58.353 37.500 11.07 3.28 39.31 2.83
4361 5402 6.113411 ACTCTTACCTGGTGTATACAATTGC 58.887 40.000 10.23 0.00 0.00 3.56
4369 5410 9.975218 AATTTTATCAACTCTTACCTGGTGTAT 57.025 29.630 10.23 0.00 0.00 2.29
4441 5482 4.680110 CCTACTGTAAGACGAACAAGTGTG 59.320 45.833 0.00 0.00 37.43 3.82
4605 5646 2.299297 AGAAAACCGAAGATGGACGTCT 59.701 45.455 16.46 0.00 0.00 4.18
4633 5674 5.679734 TTTCTGTTTGCTGATCTTGTCTC 57.320 39.130 0.00 0.00 0.00 3.36
4806 5878 1.534595 CGATTTGCTGGTAATGCTGCC 60.535 52.381 0.00 0.00 0.00 4.85
4839 5911 7.174107 AGATAGTTTTGCAATGGTAAGCATT 57.826 32.000 0.00 0.00 40.94 3.56
4909 5989 3.708563 ATGTTTCTGTTGGGTTTCACG 57.291 42.857 0.00 0.00 0.00 4.35
4910 5990 6.325919 TCATATGTTTCTGTTGGGTTTCAC 57.674 37.500 1.90 0.00 0.00 3.18
5032 6120 3.057174 AGAAGTAGAGAGTTGGCTGTTCG 60.057 47.826 0.00 0.00 0.00 3.95
5057 6145 6.919775 AGGATTGGATAGTGGATAGTACAC 57.080 41.667 0.00 0.00 39.10 2.90
5058 6146 7.073208 TGAAGGATTGGATAGTGGATAGTACA 58.927 38.462 0.00 0.00 0.00 2.90
5061 6149 5.012561 GCTGAAGGATTGGATAGTGGATAGT 59.987 44.000 0.00 0.00 0.00 2.12
5062 6150 5.248020 AGCTGAAGGATTGGATAGTGGATAG 59.752 44.000 0.00 0.00 0.00 2.08
5063 6151 5.158141 AGCTGAAGGATTGGATAGTGGATA 58.842 41.667 0.00 0.00 0.00 2.59
5064 6152 3.979347 AGCTGAAGGATTGGATAGTGGAT 59.021 43.478 0.00 0.00 0.00 3.41
5065 6153 3.387962 AGCTGAAGGATTGGATAGTGGA 58.612 45.455 0.00 0.00 0.00 4.02
5066 6154 3.495806 GGAGCTGAAGGATTGGATAGTGG 60.496 52.174 0.00 0.00 0.00 4.00
5067 6155 3.495806 GGGAGCTGAAGGATTGGATAGTG 60.496 52.174 0.00 0.00 0.00 2.74
5084 6172 0.738975 GGATGCGGTAAAAAGGGAGC 59.261 55.000 0.00 0.00 0.00 4.70
5100 6188 2.158325 ACCAAAGTTGACATGGGTGGAT 60.158 45.455 0.00 0.00 38.58 3.41
5104 6192 2.306847 GTGACCAAAGTTGACATGGGT 58.693 47.619 0.00 0.00 38.58 4.51


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

AutoCloner maintained by Alex Coulton.