Multiple sequence alignment - TraesCS6B01G298000

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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 TraesCS6B01G298000 chr6B 100.000 5695 0 0 423 6117 534925968 534920274 0.000000e+00 10517.0
1 TraesCS6B01G298000 chr6B 100.000 155 0 0 1 155 534926390 534926236 2.790000e-73 287.0
2 TraesCS6B01G298000 chr6A 91.212 3607 169 57 2530 6062 497464926 497461394 0.000000e+00 4769.0
3 TraesCS6B01G298000 chr6A 87.636 1197 66 34 423 1558 497467116 497465941 0.000000e+00 1315.0
4 TraesCS6B01G298000 chr6A 86.230 915 56 27 1641 2511 497465912 497465024 0.000000e+00 928.0
5 TraesCS6B01G298000 chr6A 93.125 160 6 1 1 155 497467297 497467138 4.770000e-56 230.0
6 TraesCS6B01G298000 chr6A 98.246 57 1 0 6046 6102 497461379 497461323 3.900000e-17 100.0
7 TraesCS6B01G298000 chr6D 93.371 3168 140 33 2530 5657 346556351 346559488 0.000000e+00 4623.0
8 TraesCS6B01G298000 chr6D 88.222 2182 107 52 423 2511 346554125 346556249 0.000000e+00 2468.0
9 TraesCS6B01G298000 chr6D 95.720 257 10 1 5708 5963 346559489 346559745 4.410000e-111 412.0
10 TraesCS6B01G298000 chr6D 96.129 155 5 1 1 155 346553951 346554104 1.020000e-62 252.0
11 TraesCS6B01G298000 chr6D 100.000 36 0 0 6057 6092 346559845 346559880 3.960000e-07 67.6


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 TraesCS6B01G298000 chr6B 534920274 534926390 6116 True 5402.00 10517 100.0000 1 6117 2 chr6B.!!$R1 6116
1 TraesCS6B01G298000 chr6A 497461323 497467297 5974 True 1468.40 4769 91.2898 1 6102 5 chr6A.!!$R1 6101
2 TraesCS6B01G298000 chr6D 346553951 346559880 5929 False 1564.52 4623 94.6884 1 6092 5 chr6D.!!$F1 6091

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
589 607 0.250295 TGCATCCCTTAGCCGCATAC 60.250 55.0 0.00 0.00 0.00 2.39 F
1112 1156 0.029989 GACCCTTATCCCCTCACCCT 60.030 60.0 0.00 0.00 0.00 4.34 F
1495 1563 0.038251 ACGCGTGCTTTCTCATCAGA 60.038 50.0 12.93 0.00 0.00 3.27 F
1730 1813 0.179048 TGGCTATCCATCAACGGCTG 60.179 55.0 0.00 0.00 37.47 4.85 F
1890 1989 0.183971 TTACTGGGTTGGGTGGTGTG 59.816 55.0 0.00 0.00 0.00 3.82 F
2663 2917 0.041238 TGAACCGAGGAGTCCCAGAT 59.959 55.0 5.25 0.00 33.88 2.90 F
4532 4820 0.763035 ACCGGTTAGAAGGTGCACTT 59.237 50.0 17.98 6.12 43.65 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1446 0.031917 TACCACCCGGGCATCTCTAA 60.032 55.000 24.08 0.0 42.05 2.10 R
2236 2370 0.039074 AGAGAGTCGCAACGTCCTTG 60.039 55.000 0.00 0.0 0.00 3.61 R
2641 2895 0.406750 TGGGACTCCTCGGTTCACTA 59.593 55.000 0.00 0.0 0.00 2.74 R
2650 2904 1.145819 GCAGCATCTGGGACTCCTC 59.854 63.158 0.00 0.0 31.21 3.71 R
3753 4024 2.213499 CTTCGGGGTCATAATCTGCAC 58.787 52.381 0.00 0.0 0.00 4.57 R
4573 4861 1.078848 GAATGCCGTGCAGGAGACT 60.079 57.895 8.24 0.0 43.65 3.24 R
5899 6239 0.036732 GTCTGGGGCATCTGTCACAA 59.963 55.000 0.00 0.0 29.78 3.33 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
59 65 2.748465 CGTGAACCCTGTTTCTTTCCCT 60.748 50.000 0.00 0.00 0.00 4.20
589 607 0.250295 TGCATCCCTTAGCCGCATAC 60.250 55.000 0.00 0.00 0.00 2.39
606 624 3.733337 CATACCCTCGCTAGATTTGCTT 58.267 45.455 0.00 0.00 0.00 3.91
708 740 1.788308 GATTGTTCGTTCGTTCGTGGA 59.212 47.619 2.67 0.00 0.00 4.02
759 791 3.935240 AACAAATTAAAGGGAGGGGGT 57.065 42.857 0.00 0.00 0.00 4.95
760 792 3.184382 ACAAATTAAAGGGAGGGGGTG 57.816 47.619 0.00 0.00 0.00 4.61
761 793 2.725227 ACAAATTAAAGGGAGGGGGTGA 59.275 45.455 0.00 0.00 0.00 4.02
789 821 2.215196 GGATTAAAATCTGCGGCCGTA 58.785 47.619 28.70 23.09 35.73 4.02
791 823 1.371595 TTAAAATCTGCGGCCGTACC 58.628 50.000 28.70 11.04 0.00 3.34
915 955 9.057089 ACTAGTAGTTTTGAGATTGGTTTTGAG 57.943 33.333 0.00 0.00 0.00 3.02
917 957 8.293699 AGTAGTTTTGAGATTGGTTTTGAGTT 57.706 30.769 0.00 0.00 0.00 3.01
918 958 8.406297 AGTAGTTTTGAGATTGGTTTTGAGTTC 58.594 33.333 0.00 0.00 0.00 3.01
919 959 6.265577 AGTTTTGAGATTGGTTTTGAGTTCG 58.734 36.000 0.00 0.00 0.00 3.95
920 960 5.828299 TTTGAGATTGGTTTTGAGTTCGT 57.172 34.783 0.00 0.00 0.00 3.85
949 989 2.125512 GCCCGTTGCGATGTCTCT 60.126 61.111 0.00 0.00 0.00 3.10
963 1003 1.850345 TGTCTCTGGGGTTTCAGGTTT 59.150 47.619 0.00 0.00 35.58 3.27
1084 1128 2.317530 AGAGCCGGAAAGTAAGCATC 57.682 50.000 5.05 0.00 0.00 3.91
1086 1130 2.171448 AGAGCCGGAAAGTAAGCATCAT 59.829 45.455 5.05 0.00 0.00 2.45
1091 1135 4.212214 GCCGGAAAGTAAGCATCATAAGAG 59.788 45.833 5.05 0.00 0.00 2.85
1098 1142 5.463154 AGTAAGCATCATAAGAGAGACCCT 58.537 41.667 0.00 0.00 0.00 4.34
1108 1152 2.227703 AGAGAGACCCTTATCCCCTCA 58.772 52.381 0.00 0.00 0.00 3.86
1112 1156 0.029989 GACCCTTATCCCCTCACCCT 60.030 60.000 0.00 0.00 0.00 4.34
1114 1158 1.203701 ACCCTTATCCCCTCACCCTTT 60.204 52.381 0.00 0.00 0.00 3.11
1117 1161 2.439880 CCTTATCCCCTCACCCTTTCTC 59.560 54.545 0.00 0.00 0.00 2.87
1118 1162 3.388913 CTTATCCCCTCACCCTTTCTCT 58.611 50.000 0.00 0.00 0.00 3.10
1122 1166 2.385765 TCCCCTCACCCTTTCTCTCTTA 59.614 50.000 0.00 0.00 0.00 2.10
1123 1167 2.769095 CCCCTCACCCTTTCTCTCTTAG 59.231 54.545 0.00 0.00 0.00 2.18
1124 1168 2.769095 CCCTCACCCTTTCTCTCTTAGG 59.231 54.545 0.00 0.00 0.00 2.69
1150 1194 6.001460 CCTGGTAGTGACATTTTTGGTCTAA 58.999 40.000 0.00 0.00 36.26 2.10
1166 1210 7.945033 TTGGTCTAAATTTTTGATCTGTTGC 57.055 32.000 0.00 0.00 0.00 4.17
1209 1254 6.753744 AGTTTATGTTCGTATCTTCGTTACCC 59.246 38.462 0.00 0.00 0.00 3.69
1210 1255 4.724074 ATGTTCGTATCTTCGTTACCCA 57.276 40.909 0.00 0.00 0.00 4.51
1214 1259 5.933463 TGTTCGTATCTTCGTTACCCATTTT 59.067 36.000 0.00 0.00 0.00 1.82
1218 1263 9.814899 TTCGTATCTTCGTTACCCATTTTTATA 57.185 29.630 0.00 0.00 0.00 0.98
1222 1267 7.760131 TCTTCGTTACCCATTTTTATACTCG 57.240 36.000 0.00 0.00 0.00 4.18
1257 1305 3.067883 GGTAGTGGTACTAGCTGTTAGCC 59.932 52.174 10.09 0.00 43.69 3.93
1344 1393 3.066342 GGCCCGAAATTAGGAGCTTTTAC 59.934 47.826 0.00 0.00 0.00 2.01
1345 1394 3.945921 GCCCGAAATTAGGAGCTTTTACT 59.054 43.478 0.00 0.00 0.00 2.24
1346 1395 4.398358 GCCCGAAATTAGGAGCTTTTACTT 59.602 41.667 0.00 0.00 0.00 2.24
1347 1396 5.676331 GCCCGAAATTAGGAGCTTTTACTTG 60.676 44.000 0.00 0.00 0.00 3.16
1348 1397 5.332707 CCGAAATTAGGAGCTTTTACTTGC 58.667 41.667 0.00 0.00 0.00 4.01
1349 1398 5.106317 CCGAAATTAGGAGCTTTTACTTGCA 60.106 40.000 0.00 0.00 0.00 4.08
1350 1399 6.378582 CGAAATTAGGAGCTTTTACTTGCAA 58.621 36.000 0.00 0.00 0.00 4.08
1351 1400 6.524586 CGAAATTAGGAGCTTTTACTTGCAAG 59.475 38.462 24.84 24.84 0.00 4.01
1354 1403 7.996098 ATTAGGAGCTTTTACTTGCAAGTTA 57.004 32.000 35.20 24.85 40.37 2.24
1366 1415 4.097892 ACTTGCAAGTTACAACCCTTTCAG 59.902 41.667 26.36 0.00 35.21 3.02
1388 1440 1.922135 GCTCAAATCAAAGCCGCCGA 61.922 55.000 0.00 0.00 32.22 5.54
1403 1455 0.878086 GCCGAGCCTGTTAGAGATGC 60.878 60.000 0.00 0.00 0.00 3.91
1429 1492 1.276989 TGGTACTGTCATTCGGAACCC 59.723 52.381 0.00 0.00 0.00 4.11
1438 1501 2.028112 TCATTCGGAACCCAGAAGTCAG 60.028 50.000 0.00 0.00 0.00 3.51
1447 1510 3.710722 AGAAGTCAGGGCCTGCGG 61.711 66.667 29.02 5.75 0.00 5.69
1476 1541 2.651105 TTCATCGCGTACCCCTGCA 61.651 57.895 5.77 0.00 0.00 4.41
1493 1561 2.153039 CACGCGTGCTTTCTCATCA 58.847 52.632 28.16 0.00 0.00 3.07
1495 1563 0.038251 ACGCGTGCTTTCTCATCAGA 60.038 50.000 12.93 0.00 0.00 3.27
1496 1564 0.644331 CGCGTGCTTTCTCATCAGAG 59.356 55.000 0.00 0.00 43.48 3.35
1498 1566 1.005340 CGTGCTTTCTCATCAGAGGC 58.995 55.000 0.00 0.00 42.34 4.70
1499 1567 1.405256 CGTGCTTTCTCATCAGAGGCT 60.405 52.381 0.00 0.00 42.34 4.58
1571 1648 0.868406 GAAAGACACGGCAACTGGAG 59.132 55.000 0.00 0.00 0.00 3.86
1572 1649 1.166531 AAAGACACGGCAACTGGAGC 61.167 55.000 0.00 0.00 0.00 4.70
1575 1652 0.737715 GACACGGCAACTGGAGCTAG 60.738 60.000 0.00 0.00 0.00 3.42
1576 1653 1.293498 CACGGCAACTGGAGCTAGT 59.707 57.895 0.00 0.00 0.00 2.57
1577 1654 0.530744 CACGGCAACTGGAGCTAGTA 59.469 55.000 0.00 0.00 0.00 1.82
1579 1656 2.361119 CACGGCAACTGGAGCTAGTATA 59.639 50.000 0.00 0.00 0.00 1.47
1580 1657 2.623889 ACGGCAACTGGAGCTAGTATAG 59.376 50.000 0.00 0.00 43.09 1.31
1581 1658 2.623889 CGGCAACTGGAGCTAGTATAGT 59.376 50.000 0.00 0.00 41.93 2.12
1582 1659 3.819337 CGGCAACTGGAGCTAGTATAGTA 59.181 47.826 0.00 0.00 41.93 1.82
1583 1660 4.320348 CGGCAACTGGAGCTAGTATAGTAC 60.320 50.000 0.00 0.00 41.93 2.73
1606 1683 6.879400 ACACTAGTTTATGATCTCCTTGTCC 58.121 40.000 0.00 0.00 0.00 4.02
1631 1709 0.320771 ATAGGATCCGGCATTCACGC 60.321 55.000 5.98 0.00 0.00 5.34
1696 1779 7.041440 CGATTACAGTATGGTTGCCATTAATCA 60.041 37.037 19.54 0.00 42.23 2.57
1730 1813 0.179048 TGGCTATCCATCAACGGCTG 60.179 55.000 0.00 0.00 37.47 4.85
1731 1814 1.510480 GGCTATCCATCAACGGCTGC 61.510 60.000 0.00 0.00 0.00 5.25
1732 1815 0.533755 GCTATCCATCAACGGCTGCT 60.534 55.000 0.00 0.00 0.00 4.24
1733 1816 1.959042 CTATCCATCAACGGCTGCTT 58.041 50.000 0.00 0.00 0.00 3.91
1758 1847 4.524316 TCGAACCCGTGAAGATTTCTTA 57.476 40.909 0.00 0.00 35.15 2.10
1830 1919 6.761714 CCGTTTGTATATTTCTGTAGCTTCCT 59.238 38.462 0.00 0.00 0.00 3.36
1846 1935 8.978472 TGTAGCTTCCTGTAGAGTTGTTTATAT 58.022 33.333 0.00 0.00 0.00 0.86
1872 1971 3.637273 GTGGAGTGGAGCGGGGTT 61.637 66.667 0.00 0.00 0.00 4.11
1873 1972 2.120940 TGGAGTGGAGCGGGGTTA 59.879 61.111 0.00 0.00 0.00 2.85
1874 1973 2.288025 TGGAGTGGAGCGGGGTTAC 61.288 63.158 0.00 0.00 0.00 2.50
1875 1974 1.988406 GGAGTGGAGCGGGGTTACT 60.988 63.158 0.00 0.00 0.00 2.24
1877 1976 2.240162 GAGTGGAGCGGGGTTACTGG 62.240 65.000 0.00 0.00 0.00 4.00
1878 1977 3.006728 TGGAGCGGGGTTACTGGG 61.007 66.667 0.00 0.00 0.00 4.45
1879 1978 3.007323 GGAGCGGGGTTACTGGGT 61.007 66.667 0.00 0.00 0.00 4.51
1880 1979 2.599757 GGAGCGGGGTTACTGGGTT 61.600 63.158 0.00 0.00 0.00 4.11
1881 1980 1.376812 GAGCGGGGTTACTGGGTTG 60.377 63.158 0.00 0.00 0.00 3.77
1882 1981 2.360726 GCGGGGTTACTGGGTTGG 60.361 66.667 0.00 0.00 0.00 3.77
1883 1982 2.353573 CGGGGTTACTGGGTTGGG 59.646 66.667 0.00 0.00 0.00 4.12
1884 1983 2.531601 CGGGGTTACTGGGTTGGGT 61.532 63.158 0.00 0.00 0.00 4.51
1885 1984 1.076014 GGGGTTACTGGGTTGGGTG 59.924 63.158 0.00 0.00 0.00 4.61
1886 1985 1.076014 GGGTTACTGGGTTGGGTGG 59.924 63.158 0.00 0.00 0.00 4.61
1887 1986 1.722110 GGGTTACTGGGTTGGGTGGT 61.722 60.000 0.00 0.00 0.00 4.16
1888 1987 0.538746 GGTTACTGGGTTGGGTGGTG 60.539 60.000 0.00 0.00 0.00 4.17
1889 1988 0.184211 GTTACTGGGTTGGGTGGTGT 59.816 55.000 0.00 0.00 0.00 4.16
1890 1989 0.183971 TTACTGGGTTGGGTGGTGTG 59.816 55.000 0.00 0.00 0.00 3.82
1891 1990 1.710996 TACTGGGTTGGGTGGTGTGG 61.711 60.000 0.00 0.00 0.00 4.17
1892 1991 3.808218 CTGGGTTGGGTGGTGTGGG 62.808 68.421 0.00 0.00 0.00 4.61
2012 2116 1.398958 GCAGGGCAGGTAGAGGAGAG 61.399 65.000 0.00 0.00 0.00 3.20
2040 2150 1.624336 ACGACTTGGCTAGTACCACA 58.376 50.000 0.53 0.00 40.19 4.17
2107 2217 2.495155 ATGCCTGCAGAATGTGTGTA 57.505 45.000 17.39 0.00 39.31 2.90
2129 2243 5.923733 ACACCTCGTGAGAATCTTTCTAT 57.076 39.130 0.00 0.00 40.87 1.98
2203 2317 7.051623 TCTGTATAGAAATGCGGGTTACAAAT 58.948 34.615 0.00 0.00 0.00 2.32
2252 2386 0.507358 GAACAAGGACGTTGCGACTC 59.493 55.000 7.77 0.00 40.15 3.36
2264 2398 2.662006 TGCGACTCTCTCAGGATTTG 57.338 50.000 0.00 0.00 0.00 2.32
2436 2607 7.351952 TGGGTCACAACTATGTAGTCTATACT 58.648 38.462 0.00 0.00 37.82 2.12
2511 2682 8.280258 TCCCTGAGATGGATTGTTATAATCTT 57.720 34.615 1.97 0.00 0.00 2.40
2537 2791 2.487762 TGCTTTATTGCTGTGCTGTACC 59.512 45.455 0.00 0.00 0.00 3.34
2543 2797 0.692476 TGCTGTGCTGTACCCATTCT 59.308 50.000 0.00 0.00 0.00 2.40
2544 2798 1.905894 TGCTGTGCTGTACCCATTCTA 59.094 47.619 0.00 0.00 0.00 2.10
2575 2829 3.232720 GGGGTTCTCTTTAAACCACCA 57.767 47.619 7.29 0.00 46.60 4.17
2586 2840 6.074648 TCTTTAAACCACCAGGAACATCAAT 58.925 36.000 0.00 0.00 38.69 2.57
2587 2841 5.720371 TTAAACCACCAGGAACATCAATG 57.280 39.130 0.00 0.00 38.69 2.82
2591 2845 2.173519 CACCAGGAACATCAATGGCTT 58.826 47.619 0.00 0.00 36.21 4.35
2616 2870 5.867716 ACTTGCGTTATCGTTCTAATGAAGT 59.132 36.000 0.00 0.00 39.49 3.01
2641 2895 7.999679 TGCTCATATGCACTTTTATAAGCTTT 58.000 30.769 3.20 0.00 38.12 3.51
2649 2903 7.590279 TGCACTTTTATAAGCTTTAGTGAACC 58.410 34.615 20.11 9.75 36.07 3.62
2650 2904 6.741358 GCACTTTTATAAGCTTTAGTGAACCG 59.259 38.462 20.11 2.46 36.07 4.44
2652 2906 8.169268 CACTTTTATAAGCTTTAGTGAACCGAG 58.831 37.037 3.20 0.00 36.07 4.63
2663 2917 0.041238 TGAACCGAGGAGTCCCAGAT 59.959 55.000 5.25 0.00 33.88 2.90
2669 2923 2.191641 GGAGTCCCAGATGCTGCC 59.808 66.667 0.00 0.00 0.00 4.85
2674 2928 2.123854 CCCAGATGCTGCCATGCT 60.124 61.111 0.00 0.00 0.00 3.79
2710 2964 4.439700 CGTTCCTCCTATCTAAGCAACGAA 60.440 45.833 0.00 0.00 38.05 3.85
2711 2965 5.602628 GTTCCTCCTATCTAAGCAACGAAT 58.397 41.667 0.00 0.00 0.00 3.34
2741 3001 8.978874 TGTACATATTCATAATTGCTCCAGTT 57.021 30.769 0.00 0.00 0.00 3.16
2791 3051 4.439700 CCTTAAACCATGATGAGCTGCAAG 60.440 45.833 1.02 0.00 0.00 4.01
2879 3139 7.619050 AGATCCAATAGCAGTTGTATATCCTG 58.381 38.462 0.00 0.00 0.00 3.86
2880 3140 6.994421 TCCAATAGCAGTTGTATATCCTGA 57.006 37.500 0.00 0.00 0.00 3.86
2881 3141 7.559335 TCCAATAGCAGTTGTATATCCTGAT 57.441 36.000 0.00 0.00 0.00 2.90
2882 3142 7.389232 TCCAATAGCAGTTGTATATCCTGATG 58.611 38.462 0.00 0.00 0.00 3.07
2883 3143 6.093219 CCAATAGCAGTTGTATATCCTGATGC 59.907 42.308 0.00 0.00 0.00 3.91
2884 3144 4.970860 AGCAGTTGTATATCCTGATGCT 57.029 40.909 0.00 0.00 37.91 3.79
2948 3208 1.971167 GCCGTGGCATCTGACCAAA 60.971 57.895 5.89 0.00 39.39 3.28
2949 3209 1.315257 GCCGTGGCATCTGACCAAAT 61.315 55.000 5.89 0.00 39.39 2.32
2955 3215 5.410067 CGTGGCATCTGACCAAATATTTTT 58.590 37.500 0.00 0.00 39.39 1.94
2971 3231 8.394877 CAAATATTTTTAGTGCGTATGTCTCCA 58.605 33.333 0.00 0.00 0.00 3.86
3316 3576 5.764686 TCCAATCACATATACATTGAGTGCC 59.235 40.000 0.00 0.00 34.73 5.01
3330 3590 2.677836 TGAGTGCCGCTGATATTGAAAC 59.322 45.455 0.00 0.00 0.00 2.78
3471 3732 3.230134 TCACAAGCTGCCCAATTTAGTT 58.770 40.909 0.00 0.00 0.00 2.24
3486 3757 8.355169 CCCAATTTAGTTTACCATCATCATCAG 58.645 37.037 0.00 0.00 0.00 2.90
3501 3772 5.874261 TCATCATCAGTAAAATGAGCGTTCA 59.126 36.000 3.86 3.86 36.63 3.18
3716 3987 4.972440 GTGTTCTCTGTTTGCATGAAGTTC 59.028 41.667 0.00 0.00 0.00 3.01
3735 4006 9.996554 TGAAGTTCATCTGAGATGTAAAAACTA 57.003 29.630 20.60 9.20 0.00 2.24
3753 4024 6.582437 AAACTATTTTGTTTGGTTGCTTCG 57.418 33.333 0.00 0.00 38.54 3.79
3864 4135 4.320057 GCCACTGTGTTTTCATCTCTCTTG 60.320 45.833 7.08 0.00 0.00 3.02
3973 4245 7.760794 CCATAACAAATATTGCATATTCCGCAT 59.239 33.333 0.00 0.00 39.58 4.73
3981 4253 8.853126 AATATTGCATATTCCGCATATTATGCT 58.147 29.630 22.68 9.54 41.41 3.79
4052 4324 3.395941 AGGAAGTTCTGGACTCAATGGTT 59.604 43.478 2.25 0.00 37.72 3.67
4180 4452 4.142049 CCCTGAACAAGGTCTATCTCAGTC 60.142 50.000 0.00 0.00 45.78 3.51
4263 4535 4.281182 AGTCTATCAACGAACAAGTCCTGT 59.719 41.667 0.00 0.00 41.27 4.00
4451 4739 4.020485 GCCATAACCACGGACTATATTCCT 60.020 45.833 7.47 0.00 32.88 3.36
4532 4820 0.763035 ACCGGTTAGAAGGTGCACTT 59.237 50.000 17.98 6.12 43.65 3.16
4562 4850 3.264450 GGAACCAAAGGATCTCAGAGGAA 59.736 47.826 0.00 0.00 0.00 3.36
4573 4861 3.242867 TCTCAGAGGAAAGAAGCAGGAA 58.757 45.455 0.00 0.00 0.00 3.36
4577 4865 3.007831 CAGAGGAAAGAAGCAGGAAGTCT 59.992 47.826 0.00 0.00 0.00 3.24
4795 5086 1.888512 TGAAAGGGATGCTTGCTTGTC 59.111 47.619 0.00 0.00 0.00 3.18
4796 5087 1.888512 GAAAGGGATGCTTGCTTGTCA 59.111 47.619 0.00 0.00 0.00 3.58
5119 5411 1.030488 AGCAGCTCATGTGGTGATGC 61.030 55.000 26.32 18.02 41.19 3.91
5121 5413 1.450848 AGCTCATGTGGTGATGCGG 60.451 57.895 0.00 0.00 36.63 5.69
5122 5414 2.475466 GCTCATGTGGTGATGCGGG 61.475 63.158 0.00 0.00 35.97 6.13
5123 5415 2.438254 TCATGTGGTGATGCGGGC 60.438 61.111 0.00 0.00 0.00 6.13
5251 5554 3.485381 CGAGTCTTGCTGAATGCTGAATG 60.485 47.826 0.00 0.00 43.37 2.67
5252 5555 2.163815 AGTCTTGCTGAATGCTGAATGC 59.836 45.455 0.00 0.00 43.37 3.56
5253 5556 2.163815 GTCTTGCTGAATGCTGAATGCT 59.836 45.455 0.00 0.00 43.37 3.79
5254 5557 2.163613 TCTTGCTGAATGCTGAATGCTG 59.836 45.455 0.00 0.00 43.37 4.41
5255 5558 1.828979 TGCTGAATGCTGAATGCTGA 58.171 45.000 0.00 0.00 43.37 4.26
5256 5559 2.164338 TGCTGAATGCTGAATGCTGAA 58.836 42.857 0.00 0.00 43.37 3.02
5257 5560 2.758423 TGCTGAATGCTGAATGCTGAAT 59.242 40.909 0.00 0.00 43.37 2.57
5277 5580 2.012902 GCTGATGGCAACCCAGATGC 62.013 60.000 15.87 0.00 46.24 3.91
5322 5628 1.597742 CTGTTGTGTCTTGGTCAGGG 58.402 55.000 0.00 0.00 0.00 4.45
5370 5678 1.960040 TACCTGACGATGCCTGCCTG 61.960 60.000 0.00 0.00 0.00 4.85
5389 5697 1.914798 TGTGTGATGATGATGGGTGGA 59.085 47.619 0.00 0.00 0.00 4.02
5393 5701 1.134431 TGATGATGATGGGTGGACGTG 60.134 52.381 0.00 0.00 0.00 4.49
5396 5704 3.344137 ATGATGGGTGGACGTGGGC 62.344 63.158 0.00 0.00 0.00 5.36
5397 5705 4.028490 GATGGGTGGACGTGGGCA 62.028 66.667 0.00 0.00 0.00 5.36
5400 5708 3.315949 GGGTGGACGTGGGCAGTA 61.316 66.667 0.00 0.00 0.00 2.74
5401 5709 2.264794 GGTGGACGTGGGCAGTAG 59.735 66.667 0.00 0.00 0.00 2.57
5402 5710 2.434359 GTGGACGTGGGCAGTAGC 60.434 66.667 0.00 0.00 41.10 3.58
5403 5711 2.603473 TGGACGTGGGCAGTAGCT 60.603 61.111 0.00 0.00 41.70 3.32
5404 5712 2.184579 GGACGTGGGCAGTAGCTC 59.815 66.667 0.00 0.00 43.38 4.09
5416 5729 0.525668 AGTAGCTCGTATGCGTGTGC 60.526 55.000 2.37 6.77 43.20 4.57
5429 5742 2.359850 TGTGCACAAGATCGGCCC 60.360 61.111 19.28 0.00 0.00 5.80
5434 5747 1.817099 CACAAGATCGGCCCTGCTC 60.817 63.158 0.00 0.00 0.00 4.26
5561 5878 3.809905 AGTTGGAGTTTTCAGACAGACC 58.190 45.455 0.00 0.00 0.00 3.85
5750 6070 2.034879 GTGTGAGCGTGTGATGGGG 61.035 63.158 0.00 0.00 0.00 4.96
5754 6074 1.224592 GAGCGTGTGATGGGGGAAT 59.775 57.895 0.00 0.00 0.00 3.01
5775 6095 3.191669 TGCGATTATTCCACGACGAAAT 58.808 40.909 0.00 1.07 0.00 2.17
5793 6113 2.985847 GCTCTTTTGGGCGCACCT 60.986 61.111 7.46 0.00 41.11 4.00
5794 6114 2.956987 CTCTTTTGGGCGCACCTG 59.043 61.111 7.46 0.00 41.11 4.00
5797 6117 3.846602 CTTTTGGGCGCACCTGCAC 62.847 63.158 7.46 0.00 42.21 4.57
5850 6171 3.753434 CGCTGAGAGCCTCCACGT 61.753 66.667 0.00 0.00 38.18 4.49
5851 6172 2.125753 GCTGAGAGCCTCCACGTG 60.126 66.667 9.08 9.08 34.48 4.49
5852 6173 2.125753 CTGAGAGCCTCCACGTGC 60.126 66.667 10.91 0.00 0.00 5.34
5853 6174 3.655810 CTGAGAGCCTCCACGTGCC 62.656 68.421 10.91 0.00 0.00 5.01
5854 6175 4.803426 GAGAGCCTCCACGTGCCG 62.803 72.222 10.91 2.42 0.00 5.69
5856 6177 3.755628 GAGCCTCCACGTGCCGTA 61.756 66.667 10.91 0.00 38.32 4.02
5857 6178 3.291101 GAGCCTCCACGTGCCGTAA 62.291 63.158 10.91 0.00 38.32 3.18
5858 6179 2.357760 GCCTCCACGTGCCGTAAA 60.358 61.111 10.91 0.00 38.32 2.01
5859 6180 2.388232 GCCTCCACGTGCCGTAAAG 61.388 63.158 10.91 0.00 38.32 1.85
5860 6181 1.005394 CCTCCACGTGCCGTAAAGT 60.005 57.895 10.91 0.00 38.32 2.66
5861 6182 1.289109 CCTCCACGTGCCGTAAAGTG 61.289 60.000 10.91 0.00 38.32 3.16
5862 6183 3.249999 CCACGTGCCGTAAAGTGG 58.750 61.111 10.91 5.53 46.52 4.00
5863 6184 3.249999 CACGTGCCGTAAAGTGGG 58.750 61.111 0.82 0.00 38.32 4.61
5864 6185 2.031465 ACGTGCCGTAAAGTGGGG 59.969 61.111 0.00 0.00 38.73 4.96
5865 6186 2.744709 CGTGCCGTAAAGTGGGGG 60.745 66.667 0.00 0.00 0.00 5.40
5866 6187 3.060000 GTGCCGTAAAGTGGGGGC 61.060 66.667 0.00 0.00 45.76 5.80
5914 6254 4.819783 TGTTGTGACAGATGCCCC 57.180 55.556 0.00 0.00 0.00 5.80
5963 6303 4.525576 CGCGCGCACTAGTCCGTA 62.526 66.667 32.61 0.00 0.00 4.02
5965 6305 2.789917 CGCGCACTAGTCCGTAGT 59.210 61.111 8.22 0.00 43.31 2.73
5966 6306 2.009108 CGCGCACTAGTCCGTAGTA 58.991 57.895 8.22 0.00 40.27 1.82
5968 6308 1.659491 CGCGCACTAGTCCGTAGTATG 60.659 57.143 8.22 0.00 40.27 2.39
5970 6310 1.334779 CGCACTAGTCCGTAGTATGCC 60.335 57.143 0.00 0.00 40.27 4.40
5971 6311 1.679680 GCACTAGTCCGTAGTATGCCA 59.320 52.381 0.00 0.00 40.27 4.92
5972 6312 2.296471 GCACTAGTCCGTAGTATGCCAT 59.704 50.000 0.00 0.00 40.27 4.40
5973 6313 3.857383 GCACTAGTCCGTAGTATGCCATG 60.857 52.174 0.00 0.00 40.27 3.66
5975 6315 4.517832 CACTAGTCCGTAGTATGCCATGTA 59.482 45.833 0.00 0.00 40.27 2.29
5976 6316 4.518211 ACTAGTCCGTAGTATGCCATGTAC 59.482 45.833 0.00 0.00 40.47 2.90
5978 6318 3.568853 AGTCCGTAGTATGCCATGTACTC 59.431 47.826 0.00 0.00 34.43 2.59
6102 6503 5.753438 CGCTGCTTGTTTTATCAGGTCTATA 59.247 40.000 0.00 0.00 0.00 1.31
6103 6504 6.257849 CGCTGCTTGTTTTATCAGGTCTATAA 59.742 38.462 0.00 0.00 0.00 0.98
6104 6505 7.201609 CGCTGCTTGTTTTATCAGGTCTATAAA 60.202 37.037 0.00 0.00 0.00 1.40
6105 6506 8.458843 GCTGCTTGTTTTATCAGGTCTATAAAA 58.541 33.333 0.00 0.00 36.77 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 65 1.611261 CGGTGGGTGGGAAGGACTA 60.611 63.158 0.00 0.00 0.00 2.59
589 607 2.478831 GAGAAGCAAATCTAGCGAGGG 58.521 52.381 0.00 0.00 37.01 4.30
606 624 9.787532 CGAAAAATAAAGAATTGCTAATGGAGA 57.212 29.630 0.00 0.00 0.00 3.71
759 791 4.628715 GCAGATTTTAATCCCCTCACCTCA 60.629 45.833 0.00 0.00 36.04 3.86
760 792 3.885901 GCAGATTTTAATCCCCTCACCTC 59.114 47.826 0.00 0.00 36.04 3.85
761 793 3.685550 CGCAGATTTTAATCCCCTCACCT 60.686 47.826 0.00 0.00 36.04 4.00
799 835 1.545706 GGCAAGAGAAGGAGACGGGT 61.546 60.000 0.00 0.00 0.00 5.28
913 953 2.591133 GCAGAAGAGTCAGACGAACTC 58.409 52.381 0.00 0.00 42.84 3.01
915 955 1.670380 GGGCAGAAGAGTCAGACGAAC 60.670 57.143 0.00 0.00 0.00 3.95
917 957 1.587043 CGGGCAGAAGAGTCAGACGA 61.587 60.000 0.00 0.00 0.00 4.20
918 958 1.153939 CGGGCAGAAGAGTCAGACG 60.154 63.158 0.00 0.00 0.00 4.18
919 959 0.318762 AACGGGCAGAAGAGTCAGAC 59.681 55.000 0.00 0.00 0.00 3.51
920 960 0.318441 CAACGGGCAGAAGAGTCAGA 59.682 55.000 0.00 0.00 0.00 3.27
949 989 1.045911 GCACCAAACCTGAAACCCCA 61.046 55.000 0.00 0.00 0.00 4.96
1084 1128 4.757692 AGGGGATAAGGGTCTCTCTTATG 58.242 47.826 6.62 0.00 37.50 1.90
1086 1130 3.797845 TGAGGGGATAAGGGTCTCTCTTA 59.202 47.826 0.00 0.00 0.00 2.10
1091 1135 1.425694 GGTGAGGGGATAAGGGTCTC 58.574 60.000 0.00 0.00 0.00 3.36
1098 1142 3.014110 AGAGAGAAAGGGTGAGGGGATAA 59.986 47.826 0.00 0.00 0.00 1.75
1108 1152 3.445987 CAGGACCTAAGAGAGAAAGGGT 58.554 50.000 0.00 0.00 34.52 4.34
1112 1156 5.017490 CACTACCAGGACCTAAGAGAGAAA 58.983 45.833 0.00 0.00 0.00 2.52
1114 1158 3.850774 TCACTACCAGGACCTAAGAGAGA 59.149 47.826 0.00 0.00 0.00 3.10
1117 1161 3.698289 TGTCACTACCAGGACCTAAGAG 58.302 50.000 0.00 0.00 33.09 2.85
1118 1162 3.820195 TGTCACTACCAGGACCTAAGA 57.180 47.619 0.00 0.00 33.09 2.10
1122 1166 4.398319 CAAAAATGTCACTACCAGGACCT 58.602 43.478 0.00 0.00 33.09 3.85
1123 1167 3.506067 CCAAAAATGTCACTACCAGGACC 59.494 47.826 0.00 0.00 33.09 4.46
1124 1168 4.142038 ACCAAAAATGTCACTACCAGGAC 58.858 43.478 0.00 0.00 34.63 3.85
1150 1194 4.050553 CACCACGCAACAGATCAAAAATT 58.949 39.130 0.00 0.00 0.00 1.82
1165 1209 1.210155 GCCTTGATGAACACCACGC 59.790 57.895 0.00 0.00 0.00 5.34
1166 1210 0.518636 CTGCCTTGATGAACACCACG 59.481 55.000 0.00 0.00 0.00 4.94
1209 1254 5.696260 TCGTGCACTCGAGTATAAAAATG 57.304 39.130 19.57 4.28 34.85 2.32
1222 1267 1.419374 CACTACCAACTCGTGCACTC 58.581 55.000 16.19 0.00 0.00 3.51
1257 1305 2.668212 ACACACGGGCATCCAACG 60.668 61.111 0.00 0.00 0.00 4.10
1344 1393 4.610945 CTGAAAGGGTTGTAACTTGCAAG 58.389 43.478 24.84 24.84 32.09 4.01
1345 1394 3.181480 GCTGAAAGGGTTGTAACTTGCAA 60.181 43.478 0.00 0.00 32.09 4.08
1346 1395 2.360801 GCTGAAAGGGTTGTAACTTGCA 59.639 45.455 0.00 0.00 31.62 4.08
1347 1396 2.623416 AGCTGAAAGGGTTGTAACTTGC 59.377 45.455 0.00 0.00 0.00 4.01
1348 1397 3.550842 GCAGCTGAAAGGGTTGTAACTTG 60.551 47.826 20.43 0.00 0.00 3.16
1349 1398 2.623416 GCAGCTGAAAGGGTTGTAACTT 59.377 45.455 20.43 0.00 0.00 2.66
1350 1399 2.158608 AGCAGCTGAAAGGGTTGTAACT 60.159 45.455 20.43 0.00 0.00 2.24
1351 1400 2.226674 GAGCAGCTGAAAGGGTTGTAAC 59.773 50.000 20.43 0.00 0.00 2.50
1354 1403 0.183492 TGAGCAGCTGAAAGGGTTGT 59.817 50.000 20.43 0.00 0.00 3.32
1366 1415 3.025866 CGGCTTTGATTTGAGCAGC 57.974 52.632 0.00 0.00 40.63 5.25
1388 1440 1.690219 CCGGGCATCTCTAACAGGCT 61.690 60.000 0.00 0.00 0.00 4.58
1394 1446 0.031917 TACCACCCGGGCATCTCTAA 60.032 55.000 24.08 0.00 42.05 2.10
1403 1455 0.107848 GAATGACAGTACCACCCGGG 60.108 60.000 22.25 22.25 44.81 5.73
1429 1492 2.435586 CGCAGGCCCTGACTTCTG 60.436 66.667 16.85 0.00 32.44 3.02
1447 1510 3.044059 GCGATGAACAGTGGGCTGC 62.044 63.158 0.00 0.00 46.30 5.25
1476 1541 0.038251 TCTGATGAGAAAGCACGCGT 60.038 50.000 5.58 5.58 0.00 6.01
1481 1546 1.065636 CCAGCCTCTGATGAGAAAGCA 60.066 52.381 6.63 0.00 42.73 3.91
1486 1551 1.969200 GCAGCCAGCCTCTGATGAGA 61.969 60.000 2.12 0.00 42.73 3.27
1498 1566 3.054503 GCAGAGTGTGGCAGCCAG 61.055 66.667 16.83 2.48 32.34 4.85
1499 1567 3.563224 AGCAGAGTGTGGCAGCCA 61.563 61.111 11.22 11.22 0.00 4.75
1579 1656 8.596781 ACAAGGAGATCATAAACTAGTGTACT 57.403 34.615 0.00 0.00 0.00 2.73
1580 1657 7.921745 GGACAAGGAGATCATAAACTAGTGTAC 59.078 40.741 0.00 0.00 0.00 2.90
1581 1658 7.201794 CGGACAAGGAGATCATAAACTAGTGTA 60.202 40.741 0.00 0.00 0.00 2.90
1582 1659 6.405953 CGGACAAGGAGATCATAAACTAGTGT 60.406 42.308 0.00 0.00 0.00 3.55
1583 1660 5.980116 CGGACAAGGAGATCATAAACTAGTG 59.020 44.000 0.00 0.00 0.00 2.74
1631 1709 1.303317 CAGGGGAAGTTGAACGGGG 60.303 63.158 0.00 0.00 0.00 5.73
1696 1779 4.800554 CCAGAGGCAAAAGTCGGT 57.199 55.556 0.00 0.00 0.00 4.69
1717 1800 2.334946 GCAAGCAGCCGTTGATGGA 61.335 57.895 0.00 0.00 37.23 3.41
1730 1813 1.503818 TTCACGGGTTCGAAGCAAGC 61.504 55.000 26.94 10.42 40.11 4.01
1731 1814 0.512952 CTTCACGGGTTCGAAGCAAG 59.487 55.000 26.94 21.42 40.11 4.01
1732 1815 0.105224 TCTTCACGGGTTCGAAGCAA 59.895 50.000 26.94 12.71 38.80 3.91
1733 1816 0.320374 ATCTTCACGGGTTCGAAGCA 59.680 50.000 26.94 6.71 38.80 3.91
1758 1847 1.682087 GGCCAAAAAGTAGCCGGAGAT 60.682 52.381 5.05 0.00 36.84 2.75
1830 1919 9.251440 ACTCCACTGTATATAAACAACTCTACA 57.749 33.333 0.00 0.00 0.00 2.74
1846 1935 1.924731 CTCCACTCCACTCCACTGTA 58.075 55.000 0.00 0.00 0.00 2.74
1848 1937 1.294780 GCTCCACTCCACTCCACTG 59.705 63.158 0.00 0.00 0.00 3.66
1872 1971 1.710996 CCACACCACCCAACCCAGTA 61.711 60.000 0.00 0.00 0.00 2.74
1873 1972 2.600731 CACACCACCCAACCCAGT 59.399 61.111 0.00 0.00 0.00 4.00
1874 1973 2.203480 CCACACCACCCAACCCAG 60.203 66.667 0.00 0.00 0.00 4.45
1875 1974 3.826822 CCCACACCACCCAACCCA 61.827 66.667 0.00 0.00 0.00 4.51
1936 2035 0.105246 TTGCCCCCAAAGTCAATGGT 60.105 50.000 0.00 0.00 36.14 3.55
2012 2116 2.125106 CCAAGTCGTAGGCCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
2032 2136 1.717194 CCGTTACGCATTGTGGTACT 58.283 50.000 0.00 0.00 0.00 2.73
2040 2150 1.865865 CTATCCTGCCGTTACGCATT 58.134 50.000 0.00 0.00 38.30 3.56
2059 2169 1.359848 CCACATGTTCGTAGACAGGC 58.640 55.000 0.00 0.00 34.32 4.85
2107 2217 5.419155 TGATAGAAAGATTCTCACGAGGTGT 59.581 40.000 0.00 0.00 41.14 4.16
2230 2364 0.878523 TCGCAACGTCCTTGTTCAGG 60.879 55.000 0.00 0.00 45.64 3.86
2231 2365 0.232303 GTCGCAACGTCCTTGTTCAG 59.768 55.000 0.00 0.00 31.73 3.02
2236 2370 0.039074 AGAGAGTCGCAACGTCCTTG 60.039 55.000 0.00 0.00 0.00 3.61
2248 2382 9.606631 ATTTACAATACAAATCCTGAGAGAGTC 57.393 33.333 0.00 0.00 0.00 3.36
2388 2552 8.697292 CCCAGACTTAGCTTAATCTAAACTACT 58.303 37.037 0.00 0.00 0.00 2.57
2436 2607 3.081804 TCTTGTGCATCTCTCTACGACA 58.918 45.455 0.00 0.00 0.00 4.35
2511 2682 4.278170 ACAGCACAGCAATAAAGCAAACTA 59.722 37.500 0.00 0.00 36.85 2.24
2514 2685 3.731652 ACAGCACAGCAATAAAGCAAA 57.268 38.095 0.00 0.00 36.85 3.68
2515 2686 3.057596 GGTACAGCACAGCAATAAAGCAA 60.058 43.478 0.00 0.00 36.85 3.91
2516 2687 2.487762 GGTACAGCACAGCAATAAAGCA 59.512 45.455 0.00 0.00 36.85 3.91
2517 2688 2.159379 GGGTACAGCACAGCAATAAAGC 60.159 50.000 0.00 0.00 0.00 3.51
2518 2689 3.081061 TGGGTACAGCACAGCAATAAAG 58.919 45.455 0.00 0.00 0.00 1.85
2519 2690 3.147553 TGGGTACAGCACAGCAATAAA 57.852 42.857 0.00 0.00 0.00 1.40
2520 2691 2.869101 TGGGTACAGCACAGCAATAA 57.131 45.000 0.00 0.00 0.00 1.40
2521 2692 3.054434 AGAATGGGTACAGCACAGCAATA 60.054 43.478 0.00 0.00 31.73 1.90
2522 2693 2.094675 GAATGGGTACAGCACAGCAAT 58.905 47.619 0.00 0.00 31.73 3.56
2523 2694 1.073763 AGAATGGGTACAGCACAGCAA 59.926 47.619 0.00 0.00 31.73 3.91
2526 2697 3.470709 CCATAGAATGGGTACAGCACAG 58.529 50.000 0.00 0.00 46.86 3.66
2527 2698 3.558931 CCATAGAATGGGTACAGCACA 57.441 47.619 0.00 0.00 46.86 4.57
2537 2791 5.033982 ACCCCCGGTTAACCATAGAATGG 62.034 52.174 24.14 14.33 45.04 3.16
2543 2797 1.839354 GAGAACCCCCGGTTAACCATA 59.161 52.381 24.14 0.00 46.95 2.74
2544 2798 0.622136 GAGAACCCCCGGTTAACCAT 59.378 55.000 24.14 2.88 46.95 3.55
2554 2808 2.158430 TGGTGGTTTAAAGAGAACCCCC 60.158 50.000 3.79 2.49 44.73 5.40
2575 2829 3.445096 GCAAGTAAGCCATTGATGTTCCT 59.555 43.478 0.00 0.00 0.00 3.36
2616 2870 7.572523 AAGCTTATAAAAGTGCATATGAGCA 57.427 32.000 18.53 0.00 41.21 4.26
2641 2895 0.406750 TGGGACTCCTCGGTTCACTA 59.593 55.000 0.00 0.00 0.00 2.74
2649 2903 1.440893 CAGCATCTGGGACTCCTCG 59.559 63.158 0.00 0.00 0.00 4.63
2650 2904 1.145819 GCAGCATCTGGGACTCCTC 59.854 63.158 0.00 0.00 31.21 3.71
2652 2906 1.992519 ATGGCAGCATCTGGGACTCC 61.993 60.000 0.00 0.00 31.21 3.85
2663 2917 6.513230 CGATAATTAAAGTAAGCATGGCAGCA 60.513 38.462 10.71 0.00 36.85 4.41
2669 2923 8.283291 GGAGGAACGATAATTAAAGTAAGCATG 58.717 37.037 0.00 0.00 0.00 4.06
2703 2957 6.771076 TGAATATGTACAAGTCATTCGTTGC 58.229 36.000 0.00 0.00 0.00 4.17
2711 2965 9.056005 GGAGCAATTATGAATATGTACAAGTCA 57.944 33.333 0.00 4.26 0.00 3.41
2730 2990 4.162131 ACCAAGAACAAAAACTGGAGCAAT 59.838 37.500 0.00 0.00 0.00 3.56
2741 3001 3.133183 GCCCCAGTTAACCAAGAACAAAA 59.867 43.478 0.88 0.00 0.00 2.44
2791 3051 9.937175 CCTTATTAGCAGTAATTTAAGCAAGAC 57.063 33.333 5.30 0.00 31.04 3.01
2806 3066 5.088141 GCATATATGCGCCTTATTAGCAG 57.912 43.478 21.33 0.00 44.67 4.24
2879 3139 6.972328 TGCAAAGAACGGATTAAAATAGCATC 59.028 34.615 0.00 0.00 0.00 3.91
2880 3140 6.862209 TGCAAAGAACGGATTAAAATAGCAT 58.138 32.000 0.00 0.00 0.00 3.79
2881 3141 6.260870 TGCAAAGAACGGATTAAAATAGCA 57.739 33.333 0.00 0.00 0.00 3.49
2882 3142 7.755582 ATTGCAAAGAACGGATTAAAATAGC 57.244 32.000 1.71 0.00 0.00 2.97
2884 3144 9.959749 GGATATTGCAAAGAACGGATTAAAATA 57.040 29.630 1.71 0.00 0.00 1.40
3021 3281 3.181479 GCCATTGTATGTCGTCACCTCTA 60.181 47.826 0.00 0.00 0.00 2.43
3307 3567 3.198409 TCAATATCAGCGGCACTCAAT 57.802 42.857 1.45 0.00 0.00 2.57
3316 3576 4.576053 TCCTTCATGGTTTCAATATCAGCG 59.424 41.667 0.00 0.00 37.07 5.18
3330 3590 4.553323 CTTTGCAAACTTCTCCTTCATGG 58.447 43.478 8.05 0.00 37.10 3.66
3471 3732 7.041848 CGCTCATTTTACTGATGATGATGGTAA 60.042 37.037 0.00 0.00 33.39 2.85
3486 3757 4.083537 TGTCATGGTGAACGCTCATTTTAC 60.084 41.667 0.00 0.00 33.05 2.01
3501 3772 3.511146 CCAAAAATAGTGGCTGTCATGGT 59.489 43.478 0.00 0.00 0.00 3.55
3735 4006 2.607180 GCACGAAGCAACCAAACAAAAT 59.393 40.909 0.00 0.00 44.79 1.82
3753 4024 2.213499 CTTCGGGGTCATAATCTGCAC 58.787 52.381 0.00 0.00 0.00 4.57
3899 4170 8.303780 AGAGATGAAGATTGTGTTAGATCTGA 57.696 34.615 5.18 0.00 33.12 3.27
3931 4203 7.624360 TTGTTATGGCTAGATCGATGTTTTT 57.376 32.000 0.54 0.00 0.00 1.94
3932 4204 7.624360 TTTGTTATGGCTAGATCGATGTTTT 57.376 32.000 0.54 0.00 0.00 2.43
3973 4245 5.621197 AACTGTCGCAAACAAGCATAATA 57.379 34.783 0.00 0.00 37.45 0.98
3981 4253 3.791973 AATCCAAACTGTCGCAAACAA 57.208 38.095 0.00 0.00 37.45 2.83
4012 4284 4.916983 TCCTGCATATTTGGTTGCATAC 57.083 40.909 0.00 0.00 46.87 2.39
4052 4324 2.095110 CACGTACCAATACTCCGTGTCA 60.095 50.000 0.00 0.00 42.72 3.58
4180 4452 3.160679 ACACAATCCTTTTCCTCTGGG 57.839 47.619 0.00 0.00 0.00 4.45
4263 4535 3.181429 GCCATGGGAATAGGGATCTGAAA 60.181 47.826 15.13 0.00 0.00 2.69
4357 4640 8.992073 CCAATCAAGTATTCATTACGATCATCA 58.008 33.333 0.00 0.00 35.84 3.07
4451 4739 9.144747 CTCAGAGAAACAAAGATTTCTTCGATA 57.855 33.333 2.51 0.00 46.57 2.92
4532 4820 3.903090 AGATCCTTTGGTTCCATGCAAAA 59.097 39.130 0.00 0.00 0.00 2.44
4573 4861 1.078848 GAATGCCGTGCAGGAGACT 60.079 57.895 8.24 0.00 43.65 3.24
5123 5415 4.317444 TGTACAACACCCCGCCCG 62.317 66.667 0.00 0.00 0.00 6.13
5129 5421 1.613255 CCATCACCCTGTACAACACCC 60.613 57.143 0.00 0.00 0.00 4.61
5277 5580 0.662374 CTCCGTTGCAAAAGCAGCAG 60.662 55.000 0.00 0.00 43.75 4.24
5322 5628 0.454196 AACCAACCAAGCACACGAAC 59.546 50.000 0.00 0.00 0.00 3.95
5370 5678 2.292267 GTCCACCCATCATCATCACAC 58.708 52.381 0.00 0.00 0.00 3.82
5389 5697 1.035932 ATACGAGCTACTGCCCACGT 61.036 55.000 0.00 0.00 42.58 4.49
5393 5701 1.661821 CGCATACGAGCTACTGCCC 60.662 63.158 0.00 0.00 43.93 5.36
5396 5704 1.191944 CACACGCATACGAGCTACTG 58.808 55.000 0.00 0.00 43.93 2.74
5397 5705 0.525668 GCACACGCATACGAGCTACT 60.526 55.000 0.00 0.00 43.93 2.57
5400 5708 2.261361 TGCACACGCATACGAGCT 59.739 55.556 0.00 0.00 45.36 4.09
5416 5729 1.817099 GAGCAGGGCCGATCTTGTG 60.817 63.158 0.00 0.00 0.00 3.33
5429 5742 2.805353 CGTGAACCCGTCGAGCAG 60.805 66.667 0.00 0.00 0.00 4.24
5434 5747 2.798262 GTCGTCGTGAACCCGTCG 60.798 66.667 0.00 0.00 39.95 5.12
5505 5819 4.641396 TCAGATTTGACACGTTCCATTCT 58.359 39.130 0.00 0.00 0.00 2.40
5754 6074 2.281140 TTCGTCGTGGAATAATCGCA 57.719 45.000 0.00 0.00 0.00 5.10
5775 6095 3.294493 GGTGCGCCCAAAAGAGCA 61.294 61.111 4.45 0.00 37.26 4.26
5793 6113 3.705934 TTTGTCACGGGCAGGTGCA 62.706 57.895 4.01 0.00 44.36 4.57
5794 6114 2.904866 TTTGTCACGGGCAGGTGC 60.905 61.111 3.33 0.00 37.83 5.01
5797 6117 2.281761 AGCTTTGTCACGGGCAGG 60.282 61.111 0.00 0.00 0.00 4.85
5850 6171 4.708386 CGCCCCCACTTTACGGCA 62.708 66.667 0.00 0.00 41.71 5.69
5852 6173 4.404098 AGCGCCCCCACTTTACGG 62.404 66.667 2.29 0.00 0.00 4.02
5853 6174 3.124921 CAGCGCCCCCACTTTACG 61.125 66.667 2.29 0.00 0.00 3.18
5854 6175 3.440415 GCAGCGCCCCCACTTTAC 61.440 66.667 2.29 0.00 0.00 2.01
5855 6176 4.733542 GGCAGCGCCCCCACTTTA 62.734 66.667 2.29 0.00 44.06 1.85
5883 6223 1.004918 CAACAGGTGGACCGAGGTC 60.005 63.158 13.61 13.61 43.87 3.85
5899 6239 0.036732 GTCTGGGGCATCTGTCACAA 59.963 55.000 0.00 0.00 29.78 3.33
5963 6303 5.367937 AGAAATCTGGAGTACATGGCATACT 59.632 40.000 0.00 0.08 35.54 2.12
5965 6305 5.894298 AGAAATCTGGAGTACATGGCATA 57.106 39.130 0.00 0.00 0.00 3.14
5966 6306 4.785346 AGAAATCTGGAGTACATGGCAT 57.215 40.909 0.00 0.00 0.00 4.40
5968 6308 3.557595 CGAAGAAATCTGGAGTACATGGC 59.442 47.826 0.00 0.00 0.00 4.40
5970 6310 4.806247 GGACGAAGAAATCTGGAGTACATG 59.194 45.833 0.00 0.00 0.00 3.21
5971 6311 4.440250 CGGACGAAGAAATCTGGAGTACAT 60.440 45.833 0.00 0.00 0.00 2.29
5972 6312 3.119602 CGGACGAAGAAATCTGGAGTACA 60.120 47.826 0.00 0.00 0.00 2.90
5973 6313 3.436496 CGGACGAAGAAATCTGGAGTAC 58.564 50.000 0.00 0.00 0.00 2.73
5975 6315 1.204941 CCGGACGAAGAAATCTGGAGT 59.795 52.381 0.00 0.00 43.17 3.85
5976 6316 1.927895 CCGGACGAAGAAATCTGGAG 58.072 55.000 0.00 0.00 43.17 3.86
5978 6318 0.391130 TGCCGGACGAAGAAATCTGG 60.391 55.000 5.05 0.00 43.33 3.86


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

AutoCloner maintained by Alex Coulton.