Multiple sequence alignment - TraesCS3A01G516700

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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 TraesCS3A01G516700 chr3A 100.000 5287 0 0 1 5287 734013013 734007727 0.000000e+00 9764.0
1 TraesCS3A01G516700 chr3D 91.931 2206 122 22 2357 4534 604369654 604367477 0.000000e+00 3037.0
2 TraesCS3A01G516700 chr3D 95.032 624 22 5 4670 5287 604367323 604366703 0.000000e+00 972.0
3 TraesCS3A01G516700 chr3D 85.328 702 73 18 1667 2359 604370360 604369680 0.000000e+00 699.0
4 TraesCS3A01G516700 chr3D 93.789 322 13 4 1 321 604372735 604372420 1.330000e-130 477.0
5 TraesCS3A01G516700 chr3D 83.864 440 44 14 339 771 604372004 604371585 1.380000e-105 394.0
6 TraesCS3A01G516700 chr3D 83.382 343 23 12 4347 4669 604376543 604376871 2.410000e-73 287.0
7 TraesCS3A01G516700 chr3D 83.067 313 14 17 1212 1505 604371199 604370907 1.140000e-61 248.0
8 TraesCS3A01G516700 chr3D 99.029 103 1 0 1067 1169 604371314 604371212 9.040000e-43 185.0
9 TraesCS3A01G516700 chr3D 83.951 162 11 7 795 943 604371601 604371442 1.990000e-29 141.0
10 TraesCS3A01G516700 chr3D 89.216 102 7 3 4570 4669 604367480 604367381 2.000000e-24 124.0
11 TraesCS3A01G516700 chr3D 97.436 39 1 0 3110 3148 535687334 535687372 3.420000e-07 67.6
12 TraesCS3A01G516700 chrUn 91.140 2043 124 30 2656 4668 42184815 42186830 0.000000e+00 2717.0
13 TraesCS3A01G516700 chrUn 84.909 1153 100 39 1237 2342 42183325 42184450 0.000000e+00 1098.0
14 TraesCS3A01G516700 chrUn 93.323 629 33 5 4665 5287 42186885 42187510 0.000000e+00 920.0
15 TraesCS3A01G516700 chrUn 79.275 883 79 39 339 1170 42182472 42183301 6.070000e-144 521.0
16 TraesCS3A01G516700 chrUn 91.049 324 23 2 1 321 42181762 42182082 2.920000e-117 433.0
17 TraesCS3A01G516700 chrUn 97.222 36 0 1 3110 3145 12355808 12355842 5.720000e-05 60.2
18 TraesCS3A01G516700 chr2A 79.627 643 59 31 1068 1675 635260233 635259628 3.840000e-106 396.0
19 TraesCS3A01G516700 chr7B 88.889 297 24 4 1 292 644739708 644740000 1.810000e-94 357.0
20 TraesCS3A01G516700 chr1A 100.000 46 0 0 3110 3155 561127823 561127868 9.430000e-13 86.1
21 TraesCS3A01G516700 chr5D 97.778 45 1 0 3110 3154 421483605 421483649 1.580000e-10 78.7
22 TraesCS3A01G516700 chr7D 86.111 72 9 1 5216 5287 466683698 466683768 5.680000e-10 76.8
23 TraesCS3A01G516700 chr3B 84.722 72 10 1 5216 5287 55716052 55715982 2.640000e-08 71.3
24 TraesCS3A01G516700 chr5A 93.182 44 2 1 3110 3152 641059906 641059949 4.420000e-06 63.9


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 TraesCS3A01G516700 chr3A 734007727 734013013 5286 True 9764.000000 9764 100.000000 1 5287 1 chr3A.!!$R1 5286
1 TraesCS3A01G516700 chr3D 604366703 604372735 6032 True 697.444444 3037 89.467444 1 5287 9 chr3D.!!$R1 5286
2 TraesCS3A01G516700 chrUn 42181762 42187510 5748 False 1137.800000 2717 87.939200 1 5287 5 chrUn.!!$F2 5286
3 TraesCS3A01G516700 chr2A 635259628 635260233 605 True 396.000000 396 79.627000 1068 1675 1 chr2A.!!$R1 607

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
486 913 0.031994 GGCCGTGCACTGATTTTTGT 59.968 50.000 16.19 0.0 0.00 2.83 F
991 1481 0.039617 CGCTAGGGCAAGAGATCTCG 60.040 60.000 16.97 5.2 38.60 4.04 F
1026 1516 0.106521 GCTTGCTTGGGCTTTTGGAA 59.893 50.000 0.00 0.0 39.59 3.53 F
1739 2667 0.251341 GCCTGTTCCATGGGACTGTT 60.251 55.000 24.02 0.0 0.00 3.16 F
3242 4383 1.273048 CCCCACATGTTCAACACCATG 59.727 52.381 0.00 0.0 43.21 3.66 F
3878 5032 0.459899 CGGGAGGAATCGATGACACA 59.540 55.000 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1470 2003 0.243636 CAAAGGGGTGAAATGTCGGC 59.756 55.000 0.0 0.0 0.0 5.54 R
1889 2829 1.580845 CCTCGGCACCTTTCAAGCTG 61.581 60.000 0.0 0.0 36.0 4.24 R
2704 3830 1.807814 ACCAAGTTCAGGGAGACACT 58.192 50.000 0.0 0.0 0.0 3.55 R
3732 4886 0.318441 CTCTTGTCCTGCTCCGTGAA 59.682 55.000 0.0 0.0 0.0 3.18 R
4129 5285 0.178068 ACTGGGCATACACATCGTCC 59.822 55.000 0.0 0.0 0.0 4.79 R
4727 5979 1.871039 CCCTGTTTTACTCGTGTGTGG 59.129 52.381 0.0 0.0 0.0 4.17 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
53 54 0.247736 AAGTCCAGCGAGCCTGTAAG 59.752 55.000 0.00 0.00 40.06 2.34
108 109 7.984050 TCAAATGCAAAACAATGGTTAAGAGAA 59.016 29.630 0.00 0.00 35.82 2.87
110 111 7.951530 ATGCAAAACAATGGTTAAGAGAAAG 57.048 32.000 0.00 0.00 35.82 2.62
133 134 7.369803 AGCAGAATAATGAACTTACACTGTG 57.630 36.000 6.19 6.19 32.79 3.66
162 163 1.461127 CGCCAAGAGTAAGTTGACAGC 59.539 52.381 0.00 0.00 0.00 4.40
164 165 2.481952 GCCAAGAGTAAGTTGACAGCAG 59.518 50.000 0.00 0.00 0.00 4.24
214 219 3.736252 CAGACGAGGAACACACAAGTTAG 59.264 47.826 0.00 0.00 0.00 2.34
215 220 3.383825 AGACGAGGAACACACAAGTTAGT 59.616 43.478 0.00 0.00 0.00 2.24
216 221 3.714391 ACGAGGAACACACAAGTTAGTC 58.286 45.455 0.00 0.00 0.00 2.59
241 246 4.934001 TCAAACACTTGAAGCAATTTGCAA 59.066 33.333 22.55 8.11 40.29 4.08
345 765 4.914983 TCATGAGAATGGATAAGCCCATC 58.085 43.478 0.00 0.00 45.69 3.51
395 819 3.039134 CCCCTGTTCCACGCAAAC 58.961 61.111 0.00 0.00 0.00 2.93
401 825 0.470766 TGTTCCACGCAAACCTAGGT 59.529 50.000 9.21 9.21 0.00 3.08
417 841 4.341783 GTCCCTGGCAGCACAGCT 62.342 66.667 9.56 0.00 40.77 4.24
457 884 0.390866 AAGCGCACTGATCTGACTGG 60.391 55.000 11.47 0.00 0.00 4.00
467 894 3.349927 TGATCTGACTGGGCAAAATCAG 58.650 45.455 0.00 0.00 39.99 2.90
475 902 2.650196 GCAAAATCAGGCCGTGCA 59.350 55.556 0.00 0.00 35.28 4.57
476 903 1.734117 GCAAAATCAGGCCGTGCAC 60.734 57.895 6.82 6.82 35.28 4.57
478 905 0.387622 CAAAATCAGGCCGTGCACTG 60.388 55.000 16.19 9.93 36.07 3.66
479 906 0.537143 AAAATCAGGCCGTGCACTGA 60.537 50.000 16.19 12.09 46.62 3.41
480 907 2.993008 ATCAGGCCGTGCACTGAT 59.007 55.556 16.19 13.91 46.31 2.90
483 910 0.537143 TCAGGCCGTGCACTGATTTT 60.537 50.000 16.19 0.00 38.71 1.82
484 911 0.314935 CAGGCCGTGCACTGATTTTT 59.685 50.000 16.19 0.00 36.86 1.94
485 912 0.314935 AGGCCGTGCACTGATTTTTG 59.685 50.000 16.19 0.00 0.00 2.44
486 913 0.031994 GGCCGTGCACTGATTTTTGT 59.968 50.000 16.19 0.00 0.00 2.83
487 914 1.408422 GCCGTGCACTGATTTTTGTC 58.592 50.000 16.19 0.00 0.00 3.18
488 915 1.930371 GCCGTGCACTGATTTTTGTCC 60.930 52.381 16.19 0.00 0.00 4.02
490 917 1.335872 CGTGCACTGATTTTTGTCCCC 60.336 52.381 16.19 0.00 0.00 4.81
491 918 0.958091 TGCACTGATTTTTGTCCCCG 59.042 50.000 0.00 0.00 0.00 5.73
492 919 0.958822 GCACTGATTTTTGTCCCCGT 59.041 50.000 0.00 0.00 0.00 5.28
494 921 0.958822 ACTGATTTTTGTCCCCGTGC 59.041 50.000 0.00 0.00 0.00 5.34
517 944 3.135056 CTCGCCCACGCTACCTACC 62.135 68.421 0.00 0.00 39.84 3.18
519 946 1.825191 CGCCCACGCTACCTACCTA 60.825 63.158 0.00 0.00 0.00 3.08
520 947 1.738432 GCCCACGCTACCTACCTAC 59.262 63.158 0.00 0.00 0.00 3.18
521 948 2.028130 CCCACGCTACCTACCTACG 58.972 63.158 0.00 0.00 0.00 3.51
529 956 0.816825 TACCTACCTACGCAGAGCCG 60.817 60.000 0.00 0.00 0.00 5.52
582 1010 1.714899 CGCACCAACCAATCGGATCC 61.715 60.000 0.00 0.00 35.59 3.36
616 1044 1.813753 CGTCAATTCGCGACCCCAT 60.814 57.895 9.15 0.00 0.00 4.00
687 1118 4.933064 CGAGCTCGGCCCGATCAC 62.933 72.222 28.40 0.00 34.61 3.06
702 1133 1.128188 ATCACCCGGGGAATAGGAGC 61.128 60.000 27.92 0.00 0.00 4.70
723 1154 2.683933 GTCGGGGGCAGGAAGAGA 60.684 66.667 0.00 0.00 0.00 3.10
731 1162 1.506025 GGCAGGAAGAGAGATCCCTT 58.494 55.000 0.00 0.00 37.71 3.95
802 1233 4.796231 CGAGTCTTCCCGGCGGTG 62.796 72.222 26.32 16.42 0.00 4.94
803 1234 4.452733 GAGTCTTCCCGGCGGTGG 62.453 72.222 26.32 10.85 0.00 4.61
877 1309 0.961358 AACTCCTCTGACCGACCGAG 60.961 60.000 0.00 0.00 0.00 4.63
884 1316 4.477975 GACCGACCGAGCGACCTG 62.478 72.222 0.00 0.00 0.00 4.00
932 1384 4.418328 CGGCCGGATTTGGTGGGA 62.418 66.667 20.10 0.00 0.00 4.37
969 1458 1.747774 CTTGGTGGGCTTTGGTTGG 59.252 57.895 0.00 0.00 0.00 3.77
983 1472 4.424711 TTGGGGCGCTAGGGCAAG 62.425 66.667 30.16 0.00 44.56 4.01
991 1481 0.039617 CGCTAGGGCAAGAGATCTCG 60.040 60.000 16.97 5.20 38.60 4.04
992 1482 0.316841 GCTAGGGCAAGAGATCTCGG 59.683 60.000 16.97 14.03 38.54 4.63
993 1483 0.965439 CTAGGGCAAGAGATCTCGGG 59.035 60.000 16.97 13.69 34.09 5.14
994 1484 0.470080 TAGGGCAAGAGATCTCGGGG 60.470 60.000 16.97 11.31 34.09 5.73
995 1485 2.110006 GGCAAGAGATCTCGGGGC 59.890 66.667 21.23 21.23 34.09 5.80
996 1486 2.439104 GGCAAGAGATCTCGGGGCT 61.439 63.158 25.50 5.92 33.05 5.19
997 1487 1.227497 GCAAGAGATCTCGGGGCTG 60.227 63.158 21.45 14.39 34.09 4.85
998 1488 1.680522 GCAAGAGATCTCGGGGCTGA 61.681 60.000 21.45 0.00 34.09 4.26
999 1489 0.826715 CAAGAGATCTCGGGGCTGAA 59.173 55.000 16.97 0.00 34.09 3.02
1008 1498 2.997315 GGGGCTGAAGGGGTTTGC 60.997 66.667 0.00 0.00 0.00 3.68
1012 1502 1.005748 GCTGAAGGGGTTTGCTTGC 60.006 57.895 0.00 0.00 0.00 4.01
1026 1516 0.106521 GCTTGCTTGGGCTTTTGGAA 59.893 50.000 0.00 0.00 39.59 3.53
1027 1517 1.869774 CTTGCTTGGGCTTTTGGAAC 58.130 50.000 0.00 0.00 39.59 3.62
1030 1520 0.601046 GCTTGGGCTTTTGGAACAGC 60.601 55.000 0.00 0.00 35.74 4.40
1054 1551 4.214327 GGCGGAGAGGCGAAGAGG 62.214 72.222 0.00 0.00 35.04 3.69
1055 1552 3.141488 GCGGAGAGGCGAAGAGGA 61.141 66.667 0.00 0.00 0.00 3.71
1056 1553 3.115556 CGGAGAGGCGAAGAGGAG 58.884 66.667 0.00 0.00 0.00 3.69
1180 1680 4.857251 CGTAAGTGGGCCCTCATC 57.143 61.111 25.70 12.48 0.00 2.92
1181 1681 1.146263 CGTAAGTGGGCCCTCATCC 59.854 63.158 25.70 9.80 0.00 3.51
1182 1682 1.338136 CGTAAGTGGGCCCTCATCCT 61.338 60.000 25.70 8.00 0.00 3.24
1187 1687 3.174265 GGGCCCTCATCCTCCCTG 61.174 72.222 17.04 0.00 35.87 4.45
1192 1692 2.146061 CCTCATCCTCCCTGCCTCC 61.146 68.421 0.00 0.00 0.00 4.30
1258 1758 1.521457 CGCCGGCTTTGCTCATCTA 60.521 57.895 26.68 0.00 0.00 1.98
1264 1764 3.316283 CGGCTTTGCTCATCTATCTCTC 58.684 50.000 0.00 0.00 0.00 3.20
1266 1766 4.309099 GGCTTTGCTCATCTATCTCTCTG 58.691 47.826 0.00 0.00 0.00 3.35
1267 1767 4.202243 GGCTTTGCTCATCTATCTCTCTGT 60.202 45.833 0.00 0.00 0.00 3.41
1268 1768 4.984161 GCTTTGCTCATCTATCTCTCTGTC 59.016 45.833 0.00 0.00 0.00 3.51
1269 1769 4.827304 TTGCTCATCTATCTCTCTGTCG 57.173 45.455 0.00 0.00 0.00 4.35
1270 1770 3.814625 TGCTCATCTATCTCTCTGTCGT 58.185 45.455 0.00 0.00 0.00 4.34
1272 1772 3.120683 GCTCATCTATCTCTCTGTCGTCG 60.121 52.174 0.00 0.00 0.00 5.12
1273 1773 2.803386 TCATCTATCTCTCTGTCGTCGC 59.197 50.000 0.00 0.00 0.00 5.19
1370 1870 1.668793 TCGTCACGCTCGAGGTACA 60.669 57.895 15.58 0.00 33.38 2.90
1371 1871 1.022982 TCGTCACGCTCGAGGTACAT 61.023 55.000 15.58 0.00 33.38 2.29
1384 1905 0.824759 GGTACATCCTTCCTCACGCT 59.175 55.000 0.00 0.00 0.00 5.07
1403 1924 0.447406 TCAATCTCAAATGCCACGCG 59.553 50.000 3.53 3.53 0.00 6.01
1407 1932 2.358615 TCAAATGCCACGCGCTCT 60.359 55.556 5.73 0.00 38.78 4.09
1411 1936 0.447801 AAATGCCACGCGCTCTAAAG 59.552 50.000 5.73 0.00 38.78 1.85
1414 1939 0.391130 TGCCACGCGCTCTAAAGATT 60.391 50.000 5.73 0.00 38.78 2.40
1419 1947 4.357142 CCACGCGCTCTAAAGATTTACTA 58.643 43.478 5.73 0.00 0.00 1.82
1440 1969 1.404391 CTGCCCTTGATGTGATTGCTC 59.596 52.381 0.00 0.00 0.00 4.26
1474 2007 9.634021 ACAGATAGATAGATATATTCTTGCCGA 57.366 33.333 0.00 0.00 35.79 5.54
1505 2038 3.753272 CCCTTTGGATTGGATATACGCAG 59.247 47.826 0.00 0.00 0.00 5.18
1506 2039 4.504864 CCCTTTGGATTGGATATACGCAGA 60.505 45.833 0.00 0.00 0.00 4.26
1507 2040 5.063204 CCTTTGGATTGGATATACGCAGAA 58.937 41.667 0.00 0.00 0.00 3.02
1509 2042 6.293626 CCTTTGGATTGGATATACGCAGAAAG 60.294 42.308 0.00 0.00 0.00 2.62
1510 2043 5.290493 TGGATTGGATATACGCAGAAAGT 57.710 39.130 0.00 0.00 0.00 2.66
1514 2047 7.097192 GGATTGGATATACGCAGAAAGTCATA 58.903 38.462 0.00 0.00 0.00 2.15
1526 2080 6.481984 GCAGAAAGTCATATGTTCTAGTTGC 58.518 40.000 1.90 9.05 30.50 4.17
1560 2117 1.304381 ATCCGTGCTGCCACCATTT 60.304 52.632 0.00 0.00 38.79 2.32
1576 2133 6.035843 CCACCATTTCCGTCTGAATTTATTG 58.964 40.000 0.00 0.00 31.67 1.90
1617 2175 1.897560 AACTGGGAAGCAACTGTAGC 58.102 50.000 0.00 0.00 0.00 3.58
1665 2593 2.278854 TCGATGATGCGCTCAAATTGA 58.721 42.857 9.73 3.94 37.44 2.57
1694 2622 2.969821 AGTGGTTGTGGCTTATGGAA 57.030 45.000 0.00 0.00 0.00 3.53
1695 2623 3.456380 AGTGGTTGTGGCTTATGGAAT 57.544 42.857 0.00 0.00 0.00 3.01
1719 2647 4.482990 TGATGATAGGTGATAGCTGGTCA 58.517 43.478 0.00 0.00 0.00 4.02
1739 2667 0.251341 GCCTGTTCCATGGGACTGTT 60.251 55.000 24.02 0.00 0.00 3.16
1742 2670 3.761897 CCTGTTCCATGGGACTGTTAAA 58.238 45.455 24.02 1.41 0.00 1.52
1743 2671 3.506067 CCTGTTCCATGGGACTGTTAAAC 59.494 47.826 24.02 12.52 0.00 2.01
1744 2672 4.141287 CTGTTCCATGGGACTGTTAAACA 58.859 43.478 24.02 16.18 0.00 2.83
1745 2673 3.886505 TGTTCCATGGGACTGTTAAACAC 59.113 43.478 24.02 0.00 0.00 3.32
1746 2674 4.142038 GTTCCATGGGACTGTTAAACACT 58.858 43.478 16.69 0.00 0.00 3.55
1747 2675 5.163184 TGTTCCATGGGACTGTTAAACACTA 60.163 40.000 24.02 0.00 0.00 2.74
1759 2690 8.758633 ACTGTTAAACACTACTAGCTGTTATG 57.241 34.615 0.00 0.00 30.26 1.90
1776 2715 5.316167 TGTTATGTTCATTTGAGCCTCTGT 58.684 37.500 0.00 0.00 0.00 3.41
1792 2731 6.951971 AGCCTCTGTGTATCTTCTTATTGTT 58.048 36.000 0.00 0.00 0.00 2.83
1793 2732 7.044798 AGCCTCTGTGTATCTTCTTATTGTTC 58.955 38.462 0.00 0.00 0.00 3.18
1795 2734 7.331026 CCTCTGTGTATCTTCTTATTGTTCCA 58.669 38.462 0.00 0.00 0.00 3.53
1797 2736 8.722480 TCTGTGTATCTTCTTATTGTTCCATG 57.278 34.615 0.00 0.00 0.00 3.66
1798 2737 7.770433 TCTGTGTATCTTCTTATTGTTCCATGG 59.230 37.037 4.97 4.97 0.00 3.66
1799 2738 6.828273 TGTGTATCTTCTTATTGTTCCATGGG 59.172 38.462 13.02 0.00 0.00 4.00
1800 2739 7.054124 GTGTATCTTCTTATTGTTCCATGGGA 58.946 38.462 13.02 0.00 0.00 4.37
1801 2740 7.012421 GTGTATCTTCTTATTGTTCCATGGGAC 59.988 40.741 17.13 17.13 0.00 4.46
1802 2741 5.779241 TCTTCTTATTGTTCCATGGGACT 57.221 39.130 24.02 7.45 0.00 3.85
1803 2742 6.139679 TCTTCTTATTGTTCCATGGGACTT 57.860 37.500 24.02 13.70 0.00 3.01
1804 2743 7.265599 TCTTCTTATTGTTCCATGGGACTTA 57.734 36.000 24.02 12.40 0.00 2.24
1805 2744 7.872138 TCTTCTTATTGTTCCATGGGACTTAT 58.128 34.615 24.02 18.09 0.00 1.73
1806 2745 8.336235 TCTTCTTATTGTTCCATGGGACTTATT 58.664 33.333 24.02 8.56 0.00 1.40
1807 2746 9.627123 CTTCTTATTGTTCCATGGGACTTATTA 57.373 33.333 24.02 10.28 0.00 0.98
1808 2747 8.974060 TCTTATTGTTCCATGGGACTTATTAC 57.026 34.615 24.02 0.00 0.00 1.89
1815 2754 4.410883 TCCATGGGACTTATTACGGTCATT 59.589 41.667 13.02 0.00 34.49 2.57
1830 2770 6.385649 ACGGTCATTTCTTTTACATGTTGT 57.614 33.333 2.30 0.00 0.00 3.32
1874 2814 2.832129 TCTCAAGTGGCTCTCGGTTATT 59.168 45.455 0.00 0.00 0.00 1.40
1889 2829 5.516090 TCGGTTATTGAAAACAAGCTTGTC 58.484 37.500 31.20 19.52 41.31 3.18
1929 2869 1.447489 CTCTCGAAGCTGCAGGTGG 60.447 63.158 20.97 14.70 0.00 4.61
1979 2919 3.634504 TGATTGAACCCATCCAGGATTG 58.365 45.455 0.00 0.00 41.22 2.67
1984 2924 3.011595 TGAACCCATCCAGGATTGAATGT 59.988 43.478 0.00 0.00 41.22 2.71
2021 2961 4.519906 TTAGGGGAGAATTTTAGCCCAG 57.480 45.455 0.00 0.00 42.52 4.45
2023 2963 2.654896 AGGGGAGAATTTTAGCCCAGTT 59.345 45.455 0.00 0.00 42.52 3.16
2025 2965 3.563479 GGGGAGAATTTTAGCCCAGTTCA 60.563 47.826 0.00 0.00 42.52 3.18
2030 2970 6.272822 AGAATTTTAGCCCAGTTCATGAAC 57.727 37.500 27.69 27.69 41.45 3.18
2037 2977 3.956199 AGCCCAGTTCATGAACCATAATG 59.044 43.478 30.34 21.91 42.06 1.90
2039 2979 4.160252 GCCCAGTTCATGAACCATAATGTT 59.840 41.667 30.34 10.47 42.06 2.71
2040 2980 5.679638 GCCCAGTTCATGAACCATAATGTTC 60.680 44.000 30.34 13.67 43.90 3.18
2041 2981 5.449041 CCCAGTTCATGAACCATAATGTTCG 60.449 44.000 30.34 11.95 46.04 3.95
2058 3004 6.986904 ATGTTCGAGAGTTTTTCTTATCCC 57.013 37.500 0.00 0.00 35.87 3.85
2059 3005 6.110411 TGTTCGAGAGTTTTTCTTATCCCT 57.890 37.500 0.00 0.00 35.87 4.20
2120 3066 4.568359 ACAAGAATCGATGAGGTCAAATCG 59.432 41.667 0.00 0.00 45.46 3.34
2190 3137 3.763897 TGCTATACACTCTCAACTGCTCA 59.236 43.478 0.00 0.00 0.00 4.26
2228 3176 9.502091 TGTTAGCTTACTTGATTTACTCATGTT 57.498 29.630 4.27 0.00 41.22 2.71
2239 3187 6.375174 TGATTTACTCATGTTGGATCTTGGTG 59.625 38.462 0.00 0.00 0.00 4.17
2243 3191 4.703575 ACTCATGTTGGATCTTGGTGATTG 59.296 41.667 0.00 0.00 35.14 2.67
2246 3194 5.539574 TCATGTTGGATCTTGGTGATTGTTT 59.460 36.000 0.00 0.00 35.14 2.83
2318 3266 7.791029 TCAGTTGAATACTCTTGGTATGCATA 58.209 34.615 1.16 1.16 43.71 3.14
2410 3535 6.459923 GGTGTCATCTTACTTCTCAGTTCTT 58.540 40.000 0.00 0.00 34.06 2.52
2414 3539 7.039714 TGTCATCTTACTTCTCAGTTCTTGCTA 60.040 37.037 0.00 0.00 34.06 3.49
2452 3578 7.838357 AATCAATCGATTCTGGCTGTTGTAAAC 60.838 37.037 7.92 0.00 42.00 2.01
2510 3636 4.789012 ATACCAACCTTGTCAAATGCAG 57.211 40.909 0.00 0.00 0.00 4.41
2528 3654 8.446273 CAAATGCAGTATATAACTCCATGTAGC 58.554 37.037 0.00 0.00 35.42 3.58
2529 3655 5.709966 TGCAGTATATAACTCCATGTAGCG 58.290 41.667 0.00 0.00 35.76 4.26
2530 3656 5.475564 TGCAGTATATAACTCCATGTAGCGA 59.524 40.000 0.00 0.00 35.76 4.93
2534 3660 8.391859 CAGTATATAACTCCATGTAGCGAGTAG 58.608 40.741 3.20 0.00 38.39 2.57
2535 3661 7.066043 AGTATATAACTCCATGTAGCGAGTAGC 59.934 40.741 3.20 0.00 38.39 3.58
2553 3679 2.571212 AGCGTTCATGTTGGAACTCAA 58.429 42.857 0.00 0.00 43.87 3.02
2569 3695 2.035066 ACTCAAAGAAGTGTTGCATGGC 59.965 45.455 0.00 0.00 0.00 4.40
2671 3797 8.791675 TGTACAATTCATTCATGCTTTTCTGTA 58.208 29.630 0.00 0.00 0.00 2.74
2704 3830 9.979578 AACTTGTTAATTGTGATTCATGCTTTA 57.020 25.926 0.00 0.00 0.00 1.85
2705 3831 9.630098 ACTTGTTAATTGTGATTCATGCTTTAG 57.370 29.630 0.00 0.00 0.00 1.85
2812 3938 6.757897 TTGGTCAATGCCAAGTCTATAAAG 57.242 37.500 5.29 0.00 42.98 1.85
2886 4023 6.538742 TGGCTCTGTTATGTAGCATTTCTAAC 59.461 38.462 0.00 0.00 38.01 2.34
2887 4024 6.538742 GGCTCTGTTATGTAGCATTTCTAACA 59.461 38.462 0.00 0.00 38.01 2.41
2900 4037 8.804688 AGCATTTCTAACAGTATTCGACTATC 57.195 34.615 0.00 0.00 35.64 2.08
2918 4055 8.239314 TCGACTATCGTCTTATTGTTACAACTT 58.761 33.333 0.00 0.00 41.35 2.66
3024 4161 5.673068 GCTTGCTCACAATAAGATCACTGTG 60.673 44.000 0.17 0.17 40.42 3.66
3033 4170 7.331687 CACAATAAGATCACTGTGTGTACATGA 59.668 37.037 7.79 0.00 35.97 3.07
3061 4198 8.424133 GGGCAATTTTATTTATTCATCTCCTGT 58.576 33.333 0.00 0.00 0.00 4.00
3062 4199 9.252962 GGCAATTTTATTTATTCATCTCCTGTG 57.747 33.333 0.00 0.00 0.00 3.66
3100 4237 9.912634 ATTGTTTCTTGTTAACATGGTCTTATG 57.087 29.630 18.40 0.00 35.60 1.90
3106 4243 4.699735 TGTTAACATGGTCTTATGCACCTG 59.300 41.667 3.59 0.00 34.66 4.00
3108 4245 4.568072 AACATGGTCTTATGCACCTGTA 57.432 40.909 0.00 0.00 34.66 2.74
3233 4374 2.420022 CTGATTTCGTCCCCACATGTTC 59.580 50.000 0.00 0.00 0.00 3.18
3242 4383 1.273048 CCCCACATGTTCAACACCATG 59.727 52.381 0.00 0.00 43.21 3.66
3329 4470 4.283467 AGGAACCTAAATTTGCAGGGAAAC 59.717 41.667 10.99 0.45 36.15 2.78
3376 4517 4.020662 AGCTAAAAAGGTGACCTCTCTCTG 60.021 45.833 3.76 0.00 30.89 3.35
3389 4540 4.078537 CCTCTCTCTGTGACTTCTCTTCA 58.921 47.826 0.00 0.00 0.00 3.02
3412 4563 8.492673 TCATTCCAGAGTGTATTGTAATTGTC 57.507 34.615 0.00 0.00 0.00 3.18
3585 4739 5.103000 GTGATCCCATCGATTCTAATACGG 58.897 45.833 0.00 0.00 0.00 4.02
3586 4740 5.014202 TGATCCCATCGATTCTAATACGGA 58.986 41.667 0.00 0.00 0.00 4.69
3587 4741 5.479027 TGATCCCATCGATTCTAATACGGAA 59.521 40.000 0.00 0.00 0.00 4.30
3653 4807 2.165998 GAAGAACCTGCTGCCAAAGAT 58.834 47.619 0.00 0.00 0.00 2.40
3686 4840 2.283388 ACCATTGCTGCCCCAGTG 60.283 61.111 0.00 0.00 33.43 3.66
3719 4873 7.905493 GCATTGTCGGATAGTAAGAAAAAGAAG 59.095 37.037 0.00 0.00 0.00 2.85
3732 4886 9.727859 GTAAGAAAAAGAAGAAGGAGAAGGTAT 57.272 33.333 0.00 0.00 0.00 2.73
3779 4933 2.554032 ACCGAAAAGCAAGGATGACAAG 59.446 45.455 0.00 0.00 0.00 3.16
3878 5032 0.459899 CGGGAGGAATCGATGACACA 59.540 55.000 0.00 0.00 0.00 3.72
3920 5074 1.301479 GTTTTCTGGAGACGGCGGT 60.301 57.895 13.24 0.00 36.33 5.68
3936 5090 2.439156 GTGTCCCAGAGCCCATGC 60.439 66.667 0.00 0.00 37.95 4.06
4168 5324 6.015688 CCCAGTGAGTAGTGTTAGTAAACTCA 60.016 42.308 9.95 9.95 43.08 3.41
4185 5341 4.935352 ACTCATGTTCTAGGATCTCTGC 57.065 45.455 0.00 0.00 0.00 4.26
4199 5355 2.588314 CTGCTGCGATGAGAGCCC 60.588 66.667 0.00 0.00 34.04 5.19
4258 5416 7.885922 TCTTTTGCACCTGAAATATGTAACCTA 59.114 33.333 0.00 0.00 0.00 3.08
4306 5464 7.905604 TTGTGAAACTTGAGACGATGATAAT 57.094 32.000 0.00 0.00 38.04 1.28
4311 5469 6.910536 AACTTGAGACGATGATAATTGGAC 57.089 37.500 0.00 0.00 0.00 4.02
4318 5476 4.067896 ACGATGATAATTGGACTCCATGC 58.932 43.478 0.00 0.00 31.53 4.06
4325 5483 0.770499 TTGGACTCCATGCTTGACCA 59.230 50.000 0.00 3.01 31.53 4.02
4468 5638 8.806146 TGCTCAGCATTAACATATACAGAGATA 58.194 33.333 0.00 0.00 31.71 1.98
4479 5649 9.823647 AACATATACAGAGATAAACTGGAACTG 57.176 33.333 0.00 0.00 39.38 3.16
4480 5650 8.424918 ACATATACAGAGATAAACTGGAACTGG 58.575 37.037 0.00 0.00 39.38 4.00
4481 5651 8.642432 CATATACAGAGATAAACTGGAACTGGA 58.358 37.037 0.00 0.00 39.38 3.86
4587 5778 4.881850 CCAGTAATTCTTATTTGAGGCCGT 59.118 41.667 0.00 0.00 0.00 5.68
4609 5800 7.063544 GCCGTTAAGAGTCACCATTGATATATC 59.936 40.741 5.73 5.73 33.11 1.63
4630 5825 5.929697 TCTCATTGTCATGAAACTCACAC 57.070 39.130 0.00 0.00 39.04 3.82
4664 5859 3.084039 ACATTGAACATGGCAACGAGAT 58.916 40.909 5.54 0.00 42.51 2.75
4666 5861 1.737838 TGAACATGGCAACGAGATCC 58.262 50.000 0.00 0.00 42.51 3.36
4667 5862 1.003003 TGAACATGGCAACGAGATCCA 59.997 47.619 0.00 0.00 42.51 3.41
4668 5863 1.398390 GAACATGGCAACGAGATCCAC 59.602 52.381 0.00 0.00 42.51 4.02
4709 5961 0.517316 CGCTGTTTGACCTAAGCCAC 59.483 55.000 0.00 0.00 31.84 5.01
4727 5979 3.431233 GCCACTACAAAACTAACCTCGTC 59.569 47.826 0.00 0.00 0.00 4.20
4731 5983 3.547054 ACAAAACTAACCTCGTCCACA 57.453 42.857 0.00 0.00 0.00 4.17
4745 5997 2.217847 CGTCCACACACGAGTAAAACAG 59.782 50.000 0.00 0.00 42.69 3.16
4746 5998 2.542595 GTCCACACACGAGTAAAACAGG 59.457 50.000 0.00 0.00 0.00 4.00
4766 6018 3.915437 GGAAAATTTCCGAGCACAAGA 57.085 42.857 9.21 0.00 40.59 3.02
4770 6023 4.647424 AAATTTCCGAGCACAAGACAAA 57.353 36.364 0.00 0.00 0.00 2.83
4861 6116 2.252260 CGTTGGAACCGCTTGCTG 59.748 61.111 0.00 0.00 0.00 4.41
4895 6150 1.625616 CGGAACTTTATCGACTGCGT 58.374 50.000 0.00 0.00 38.98 5.24
4896 6151 1.990563 CGGAACTTTATCGACTGCGTT 59.009 47.619 0.00 0.00 38.98 4.84
4899 6154 4.418392 GGAACTTTATCGACTGCGTTAGA 58.582 43.478 0.00 0.00 38.98 2.10
4908 6163 1.464997 GACTGCGTTAGAAAGCAAGGG 59.535 52.381 4.48 0.00 42.54 3.95
5274 6535 3.004734 ACAATTACCTGCAGTGCAAAGTC 59.995 43.478 20.22 0.00 38.41 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 8.021396 AGTGTGCCGTCTTATTAAAAATTTCTC 58.979 33.333 0.00 0.00 0.00 2.87
71 72 0.030504 TGCATTTGACAAGTGTGCCG 59.969 50.000 11.77 0.00 35.03 5.69
73 74 3.370366 TGTTTTGCATTTGACAAGTGTGC 59.630 39.130 11.77 12.24 36.39 4.57
108 109 7.661437 TCACAGTGTAAGTTCATTATTCTGCTT 59.339 33.333 0.00 0.00 33.82 3.91
110 111 7.364522 TCACAGTGTAAGTTCATTATTCTGC 57.635 36.000 0.00 0.00 33.82 4.26
133 134 2.433868 TACTCTTGGCGTGTGTCTTC 57.566 50.000 0.00 0.00 0.00 2.87
162 163 1.378119 TCCTTGCTGCTGGATGCTG 60.378 57.895 10.08 0.00 43.37 4.41
164 165 2.758089 CGTCCTTGCTGCTGGATGC 61.758 63.158 16.85 7.00 43.25 3.91
214 219 3.398954 TTGCTTCAAGTGTTTGACGAC 57.601 42.857 0.00 0.00 42.79 4.34
215 220 4.630894 AATTGCTTCAAGTGTTTGACGA 57.369 36.364 0.00 0.00 42.79 4.20
216 221 4.548726 GCAAATTGCTTCAAGTGTTTGACG 60.549 41.667 11.19 0.00 40.96 4.35
256 261 7.924947 CACTCTGAGCAGTTCTTGATAATATCA 59.075 37.037 4.19 0.00 37.55 2.15
345 765 3.555547 TCCACATCGTTTGCATCTTATCG 59.444 43.478 0.00 0.00 0.00 2.92
395 819 2.688666 TGCTGCCAGGGACCTAGG 60.689 66.667 7.41 7.41 0.00 3.02
417 841 1.202769 CCTTAGGGGAAACGGGGTCA 61.203 60.000 0.00 0.00 37.23 4.02
457 884 2.125952 GCACGGCCTGATTTTGCC 60.126 61.111 0.00 0.00 44.41 4.52
467 894 0.031994 ACAAAAATCAGTGCACGGCC 59.968 50.000 12.54 0.00 0.00 6.13
470 897 1.335872 GGGGACAAAAATCAGTGCACG 60.336 52.381 12.01 6.78 0.00 5.34
471 898 1.335872 CGGGGACAAAAATCAGTGCAC 60.336 52.381 9.40 9.40 0.00 4.57
472 899 0.958091 CGGGGACAAAAATCAGTGCA 59.042 50.000 0.00 0.00 0.00 4.57
473 900 0.958822 ACGGGGACAAAAATCAGTGC 59.041 50.000 0.00 0.00 0.00 4.40
475 902 0.958822 GCACGGGGACAAAAATCAGT 59.041 50.000 0.00 0.00 0.00 3.41
476 903 0.243636 GGCACGGGGACAAAAATCAG 59.756 55.000 0.00 0.00 0.00 2.90
478 905 0.243636 CTGGCACGGGGACAAAAATC 59.756 55.000 0.00 0.00 30.64 2.17
479 906 1.815817 GCTGGCACGGGGACAAAAAT 61.816 55.000 0.00 0.00 30.64 1.82
480 907 2.494530 GCTGGCACGGGGACAAAAA 61.495 57.895 0.00 0.00 30.64 1.94
600 1028 2.112198 GCATGGGGTCGCGAATTGA 61.112 57.895 12.06 0.00 0.00 2.57
623 1051 2.269241 GCGGCTAGGGTTCTTGCT 59.731 61.111 0.00 0.00 40.66 3.91
624 1052 2.824489 GGCGGCTAGGGTTCTTGC 60.824 66.667 0.00 0.00 40.23 4.01
687 1118 2.520536 CCAGCTCCTATTCCCCGGG 61.521 68.421 15.80 15.80 0.00 5.73
690 1121 1.759459 CGACCCAGCTCCTATTCCCC 61.759 65.000 0.00 0.00 0.00 4.81
693 1124 1.749033 CCCGACCCAGCTCCTATTC 59.251 63.158 0.00 0.00 0.00 1.75
696 1127 4.475444 CCCCCGACCCAGCTCCTA 62.475 72.222 0.00 0.00 0.00 2.94
714 1145 3.922375 AGGTAAGGGATCTCTCTTCCTG 58.078 50.000 10.98 0.00 33.53 3.86
717 1148 4.100344 GTGGAAGGTAAGGGATCTCTCTTC 59.900 50.000 12.17 12.17 0.00 2.87
719 1150 3.648739 GTGGAAGGTAAGGGATCTCTCT 58.351 50.000 0.00 0.00 0.00 3.10
720 1151 2.362717 CGTGGAAGGTAAGGGATCTCTC 59.637 54.545 0.00 0.00 0.00 3.20
721 1152 2.389715 CGTGGAAGGTAAGGGATCTCT 58.610 52.381 0.00 0.00 0.00 3.10
723 1154 1.273666 ACCGTGGAAGGTAAGGGATCT 60.274 52.381 0.00 0.00 43.89 2.75
731 1162 1.514087 GCGATGACCGTGGAAGGTA 59.486 57.895 0.00 0.00 46.09 3.08
777 1208 4.856607 GGAAGACTCGCTCCGCCG 62.857 72.222 0.00 0.00 0.00 6.46
778 1209 4.516195 GGGAAGACTCGCTCCGCC 62.516 72.222 0.00 0.00 0.00 6.13
779 1210 4.856607 CGGGAAGACTCGCTCCGC 62.857 72.222 0.00 0.00 34.17 5.54
780 1211 4.194720 CCGGGAAGACTCGCTCCG 62.195 72.222 0.00 0.00 38.86 4.63
781 1212 4.516195 GCCGGGAAGACTCGCTCC 62.516 72.222 2.18 0.00 38.86 4.70
810 1241 4.803426 GGAGGCGACAGGTGCTCG 62.803 72.222 0.00 0.00 0.00 5.03
811 1242 3.363844 GAGGAGGCGACAGGTGCTC 62.364 68.421 0.00 0.00 0.00 4.26
812 1243 3.386237 GAGGAGGCGACAGGTGCT 61.386 66.667 0.00 0.00 0.00 4.40
813 1244 4.459089 GGAGGAGGCGACAGGTGC 62.459 72.222 0.00 0.00 0.00 5.01
814 1245 2.681778 AGGAGGAGGCGACAGGTG 60.682 66.667 0.00 0.00 0.00 4.00
815 1246 2.681778 CAGGAGGAGGCGACAGGT 60.682 66.667 0.00 0.00 0.00 4.00
816 1247 4.154347 GCAGGAGGAGGCGACAGG 62.154 72.222 0.00 0.00 0.00 4.00
877 1309 1.664965 GATGGTATCGGCAGGTCGC 60.665 63.158 0.00 0.00 41.28 5.19
883 1315 2.335011 CGCGAGATGGTATCGGCA 59.665 61.111 0.00 0.00 40.50 5.69
884 1316 3.106407 GCGCGAGATGGTATCGGC 61.106 66.667 12.10 0.00 40.50 5.54
885 1317 1.730902 CAGCGCGAGATGGTATCGG 60.731 63.158 12.10 0.00 45.32 4.18
918 1370 2.437716 CCGTCCCACCAAATCCGG 60.438 66.667 0.00 0.00 0.00 5.14
969 1458 2.723586 GATCTCTTGCCCTAGCGCCC 62.724 65.000 2.29 0.00 44.31 6.13
983 1472 1.745264 CCTTCAGCCCCGAGATCTC 59.255 63.158 13.05 13.05 0.00 2.75
991 1481 2.997315 GCAAACCCCTTCAGCCCC 60.997 66.667 0.00 0.00 0.00 5.80
992 1482 1.533994 AAGCAAACCCCTTCAGCCC 60.534 57.895 0.00 0.00 0.00 5.19
993 1483 1.667722 CAAGCAAACCCCTTCAGCC 59.332 57.895 0.00 0.00 0.00 4.85
994 1484 1.005748 GCAAGCAAACCCCTTCAGC 60.006 57.895 0.00 0.00 0.00 4.26
995 1485 1.043022 AAGCAAGCAAACCCCTTCAG 58.957 50.000 0.00 0.00 0.00 3.02
996 1486 0.752054 CAAGCAAGCAAACCCCTTCA 59.248 50.000 0.00 0.00 0.00 3.02
997 1487 0.033920 CCAAGCAAGCAAACCCCTTC 59.966 55.000 0.00 0.00 0.00 3.46
998 1488 1.410050 CCCAAGCAAGCAAACCCCTT 61.410 55.000 0.00 0.00 0.00 3.95
999 1489 1.838396 CCCAAGCAAGCAAACCCCT 60.838 57.895 0.00 0.00 0.00 4.79
1008 1498 1.138661 TGTTCCAAAAGCCCAAGCAAG 59.861 47.619 0.00 0.00 43.56 4.01
1012 1502 0.318955 CGCTGTTCCAAAAGCCCAAG 60.319 55.000 0.00 0.00 35.98 3.61
1042 1532 1.076339 CTCCCTCCTCTTCGCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
1044 1541 2.042435 CCTCCCTCCTCTTCGCCT 60.042 66.667 0.00 0.00 0.00 5.52
1049 1546 2.690510 GCTGGCCTCCCTCCTCTT 60.691 66.667 3.32 0.00 0.00 2.85
1054 1551 4.201122 CCATGGCTGGCCTCCCTC 62.201 72.222 13.05 0.00 35.23 4.30
1170 1670 3.174265 CAGGGAGGATGAGGGCCC 61.174 72.222 16.46 16.46 41.00 5.80
1171 1671 3.883549 GCAGGGAGGATGAGGGCC 61.884 72.222 0.00 0.00 0.00 5.80
1172 1672 3.883549 GGCAGGGAGGATGAGGGC 61.884 72.222 0.00 0.00 0.00 5.19
1173 1673 2.040043 AGGCAGGGAGGATGAGGG 60.040 66.667 0.00 0.00 0.00 4.30
1174 1674 2.146061 GGAGGCAGGGAGGATGAGG 61.146 68.421 0.00 0.00 0.00 3.86
1175 1675 2.146061 GGGAGGCAGGGAGGATGAG 61.146 68.421 0.00 0.00 0.00 2.90
1176 1676 2.040464 GGGAGGCAGGGAGGATGA 60.040 66.667 0.00 0.00 0.00 2.92
1177 1677 3.554342 CGGGAGGCAGGGAGGATG 61.554 72.222 0.00 0.00 0.00 3.51
1206 1706 3.959991 GACTGAAGCAGCCGGGACC 62.960 68.421 2.18 0.00 34.37 4.46
1207 1707 2.435059 GACTGAAGCAGCCGGGAC 60.435 66.667 2.18 0.00 34.37 4.46
1208 1708 2.922503 TGACTGAAGCAGCCGGGA 60.923 61.111 2.18 0.00 34.37 5.14
1209 1709 2.435586 CTGACTGAAGCAGCCGGG 60.436 66.667 2.18 0.00 34.37 5.73
1210 1710 0.886490 AAACTGACTGAAGCAGCCGG 60.886 55.000 0.00 0.00 36.86 6.13
1258 1758 0.449786 CACAGCGACGACAGAGAGAT 59.550 55.000 0.00 0.00 0.00 2.75
1282 1782 2.279517 CGACACCTATCCGGCAGC 60.280 66.667 0.00 0.00 35.61 5.25
1283 1783 1.226974 CACGACACCTATCCGGCAG 60.227 63.158 0.00 0.00 35.61 4.85
1287 1787 1.226974 CAGGCACGACACCTATCCG 60.227 63.158 0.00 0.00 35.10 4.18
1288 1788 1.144057 CCAGGCACGACACCTATCC 59.856 63.158 0.00 0.00 35.10 2.59
1370 1870 2.102252 GAGATTGAGCGTGAGGAAGGAT 59.898 50.000 0.00 0.00 0.00 3.24
1371 1871 1.478510 GAGATTGAGCGTGAGGAAGGA 59.521 52.381 0.00 0.00 0.00 3.36
1374 1874 3.401033 TTTGAGATTGAGCGTGAGGAA 57.599 42.857 0.00 0.00 0.00 3.36
1384 1905 0.447406 CGCGTGGCATTTGAGATTGA 59.553 50.000 0.00 0.00 0.00 2.57
1403 1924 5.919755 AGGGCAGTAGTAAATCTTTAGAGC 58.080 41.667 0.00 0.00 0.00 4.09
1407 1932 7.552687 CACATCAAGGGCAGTAGTAAATCTTTA 59.447 37.037 0.00 0.00 0.00 1.85
1411 1936 5.428253 TCACATCAAGGGCAGTAGTAAATC 58.572 41.667 0.00 0.00 0.00 2.17
1414 1939 5.185454 CAATCACATCAAGGGCAGTAGTAA 58.815 41.667 0.00 0.00 0.00 2.24
1419 1947 1.180029 GCAATCACATCAAGGGCAGT 58.820 50.000 0.00 0.00 0.00 4.40
1470 2003 0.243636 CAAAGGGGTGAAATGTCGGC 59.756 55.000 0.00 0.00 0.00 5.54
1474 2007 2.905736 CCAATCCAAAGGGGTGAAATGT 59.094 45.455 0.00 0.00 38.11 2.71
1505 2038 7.463383 CGACAGCAACTAGAACATATGACTTTC 60.463 40.741 10.38 3.03 0.00 2.62
1506 2039 6.311445 CGACAGCAACTAGAACATATGACTTT 59.689 38.462 10.38 0.00 0.00 2.66
1507 2040 5.807520 CGACAGCAACTAGAACATATGACTT 59.192 40.000 10.38 0.00 0.00 3.01
1509 2042 4.504461 CCGACAGCAACTAGAACATATGAC 59.496 45.833 10.38 3.20 0.00 3.06
1510 2043 4.401202 TCCGACAGCAACTAGAACATATGA 59.599 41.667 10.38 0.00 0.00 2.15
1514 2047 3.258372 TCTTCCGACAGCAACTAGAACAT 59.742 43.478 0.00 0.00 0.00 2.71
1560 2117 2.601314 CGCGACAATAAATTCAGACGGA 59.399 45.455 0.00 0.00 0.00 4.69
1601 2159 0.764890 ACAGCTACAGTTGCTTCCCA 59.235 50.000 6.78 0.00 38.92 4.37
1617 2175 6.047870 AGCTCTCTGTAGCATCATTTTACAG 58.952 40.000 4.87 4.87 45.30 2.74
1665 2593 3.264450 AGCCACAACCACTAGCTAAATCT 59.736 43.478 0.00 0.00 30.46 2.40
1694 2622 6.899631 TGACCAGCTATCACCTATCATCATAT 59.100 38.462 0.00 0.00 0.00 1.78
1695 2623 6.256053 TGACCAGCTATCACCTATCATCATA 58.744 40.000 0.00 0.00 0.00 2.15
1722 2650 6.966490 TAGTGTTTAACAGTCCCATGGAACAG 60.966 42.308 15.22 1.49 35.62 3.16
1739 2667 9.938280 AATGAACATAACAGCTAGTAGTGTTTA 57.062 29.630 17.50 8.78 37.77 2.01
1742 2670 8.094548 TCAAATGAACATAACAGCTAGTAGTGT 58.905 33.333 0.00 0.00 31.61 3.55
1743 2671 8.479313 TCAAATGAACATAACAGCTAGTAGTG 57.521 34.615 0.00 0.00 0.00 2.74
1744 2672 7.278868 GCTCAAATGAACATAACAGCTAGTAGT 59.721 37.037 0.00 0.00 0.00 2.73
1745 2673 7.254590 GGCTCAAATGAACATAACAGCTAGTAG 60.255 40.741 0.00 0.00 0.00 2.57
1746 2674 6.538742 GGCTCAAATGAACATAACAGCTAGTA 59.461 38.462 0.00 0.00 0.00 1.82
1747 2675 5.355350 GGCTCAAATGAACATAACAGCTAGT 59.645 40.000 0.00 0.00 0.00 2.57
1759 2690 5.181748 AGATACACAGAGGCTCAAATGAAC 58.818 41.667 18.26 3.38 0.00 3.18
1792 2731 3.376636 TGACCGTAATAAGTCCCATGGA 58.623 45.455 15.22 0.00 31.76 3.41
1793 2732 3.830744 TGACCGTAATAAGTCCCATGG 57.169 47.619 4.14 4.14 31.76 3.66
1795 2734 6.248569 AGAAATGACCGTAATAAGTCCCAT 57.751 37.500 0.00 0.00 31.76 4.00
1797 2736 6.997239 AAAGAAATGACCGTAATAAGTCCC 57.003 37.500 0.00 0.00 31.76 4.46
1798 2737 8.938906 TGTAAAAGAAATGACCGTAATAAGTCC 58.061 33.333 0.00 0.00 31.76 3.85
1804 2743 8.573035 ACAACATGTAAAAGAAATGACCGTAAT 58.427 29.630 0.00 0.00 0.00 1.89
1805 2744 7.932335 ACAACATGTAAAAGAAATGACCGTAA 58.068 30.769 0.00 0.00 0.00 3.18
1806 2745 7.499321 ACAACATGTAAAAGAAATGACCGTA 57.501 32.000 0.00 0.00 0.00 4.02
1807 2746 6.385649 ACAACATGTAAAAGAAATGACCGT 57.614 33.333 0.00 0.00 0.00 4.83
1808 2747 7.021196 CCTACAACATGTAAAAGAAATGACCG 58.979 38.462 0.00 0.00 31.67 4.79
1815 2754 7.201839 GGACAAACCCTACAACATGTAAAAGAA 60.202 37.037 0.00 0.00 31.67 2.52
1830 2770 2.357760 GCACGCGGACAAACCCTA 60.358 61.111 12.47 0.00 34.64 3.53
1889 2829 1.580845 CCTCGGCACCTTTCAAGCTG 61.581 60.000 0.00 0.00 36.00 4.24
2014 2954 4.853468 TTATGGTTCATGAACTGGGCTA 57.147 40.909 31.81 16.34 40.94 3.93
2018 2958 5.353956 TCGAACATTATGGTTCATGAACTGG 59.646 40.000 31.81 18.97 45.82 4.00
2021 2961 6.313905 ACTCTCGAACATTATGGTTCATGAAC 59.686 38.462 27.16 27.16 45.82 3.18
2023 2963 5.977635 ACTCTCGAACATTATGGTTCATGA 58.022 37.500 6.82 0.00 45.82 3.07
2025 2965 7.687941 AAAACTCTCGAACATTATGGTTCAT 57.312 32.000 6.82 0.00 45.82 2.57
2030 2970 9.922305 GATAAGAAAAACTCTCGAACATTATGG 57.078 33.333 0.00 0.00 31.02 2.74
2037 2977 5.163844 GCAGGGATAAGAAAAACTCTCGAAC 60.164 44.000 0.00 0.00 31.02 3.95
2039 2979 4.223032 AGCAGGGATAAGAAAAACTCTCGA 59.777 41.667 0.00 0.00 31.02 4.04
2040 2980 4.508662 AGCAGGGATAAGAAAAACTCTCG 58.491 43.478 0.00 0.00 31.02 4.04
2041 2981 5.707764 ACAAGCAGGGATAAGAAAAACTCTC 59.292 40.000 0.00 0.00 31.02 3.20
2075 3021 7.507733 TGTCAATTTATTTTTGCCAGCATTT 57.492 28.000 0.00 0.00 0.00 2.32
2120 3066 3.696306 GGCTCCTAGGCTTGTCATC 57.304 57.895 2.96 0.00 37.85 2.92
2190 3137 6.128138 AGTAAGCTAACAACAGGGAAAGAT 57.872 37.500 0.00 0.00 0.00 2.40
2228 3176 3.005684 GCACAAACAATCACCAAGATCCA 59.994 43.478 0.00 0.00 35.39 3.41
2239 3187 4.172505 TGTTGTTGTCTGCACAAACAATC 58.827 39.130 15.86 11.63 44.32 2.67
2243 3191 5.339990 AGTAATGTTGTTGTCTGCACAAAC 58.660 37.500 0.00 0.00 44.32 2.93
2246 3194 4.036262 GGAAGTAATGTTGTTGTCTGCACA 59.964 41.667 0.00 0.00 0.00 4.57
2351 3446 5.435686 AACATTGAAGGTATGCAGTCCTA 57.564 39.130 11.99 0.00 33.27 2.94
2381 3504 4.763279 TGAGAAGTAAGATGACACCGTACA 59.237 41.667 0.00 0.00 0.00 2.90
2382 3505 5.106237 ACTGAGAAGTAAGATGACACCGTAC 60.106 44.000 0.00 0.00 0.00 3.67
2384 3507 3.827302 ACTGAGAAGTAAGATGACACCGT 59.173 43.478 0.00 0.00 0.00 4.83
2386 3509 6.031751 AGAACTGAGAAGTAAGATGACACC 57.968 41.667 0.00 0.00 0.00 4.16
2387 3510 6.128688 GCAAGAACTGAGAAGTAAGATGACAC 60.129 42.308 0.00 0.00 0.00 3.67
2391 3516 8.715191 ATTAGCAAGAACTGAGAAGTAAGATG 57.285 34.615 0.00 0.00 0.00 2.90
2432 3558 3.734463 TGTTTACAACAGCCAGAATCGA 58.266 40.909 0.00 0.00 36.25 3.59
2435 3561 5.133221 ACTCTTGTTTACAACAGCCAGAAT 58.867 37.500 0.00 0.00 43.27 2.40
2478 3604 5.838529 ACAAGGTTGGTATTTTGTACTTGC 58.161 37.500 0.00 0.00 38.02 4.01
2510 3636 7.188157 GCTACTCGCTACATGGAGTTATATAC 58.812 42.308 6.84 0.00 43.02 1.47
2528 3654 1.990799 TCCAACATGAACGCTACTCG 58.009 50.000 0.00 0.00 45.38 4.18
2529 3655 3.724295 GTTCCAACATGAACGCTACTC 57.276 47.619 0.00 0.00 35.70 2.59
2671 3797 8.805175 TGAATCACAATTAACAAGTTCATGGAT 58.195 29.630 0.00 0.00 0.00 3.41
2704 3830 1.807814 ACCAAGTTCAGGGAGACACT 58.192 50.000 0.00 0.00 0.00 3.55
2705 3831 2.640316 AACCAAGTTCAGGGAGACAC 57.360 50.000 0.00 0.00 0.00 3.67
2854 3980 2.162681 ACATAACAGAGCCACCAAAGC 58.837 47.619 0.00 0.00 0.00 3.51
2855 3981 3.375299 GCTACATAACAGAGCCACCAAAG 59.625 47.826 0.00 0.00 0.00 2.77
2857 3983 2.304470 TGCTACATAACAGAGCCACCAA 59.696 45.455 0.00 0.00 35.24 3.67
2900 4037 4.435121 GGCGGAAGTTGTAACAATAAGACG 60.435 45.833 0.00 0.00 0.00 4.18
2918 4055 1.895798 GAGACATGGATATCTGGCGGA 59.104 52.381 0.00 0.00 0.00 5.54
3024 4161 9.816354 ATAAATAAAATTGCCCTTCATGTACAC 57.184 29.630 0.00 0.00 0.00 2.90
3033 4170 9.217336 AGGAGATGAATAAATAAAATTGCCCTT 57.783 29.630 0.00 0.00 0.00 3.95
3080 4217 5.414454 GGTGCATAAGACCATGTTAACAAGA 59.586 40.000 13.23 0.00 33.25 3.02
3100 4237 1.593196 TGTCTGCAAGTTACAGGTGC 58.407 50.000 3.24 0.00 38.78 5.01
3106 4243 5.412594 TCTGATGGAATTGTCTGCAAGTTAC 59.587 40.000 0.00 0.00 38.10 2.50
3108 4245 4.217118 GTCTGATGGAATTGTCTGCAAGTT 59.783 41.667 0.00 0.00 38.10 2.66
3233 4374 4.789012 ATCTAAGCAAACCATGGTGTTG 57.211 40.909 20.60 22.93 40.33 3.33
3242 4383 8.495148 CAATGGTTAAAACAATCTAAGCAAACC 58.505 33.333 0.00 0.00 38.57 3.27
3329 4470 2.019984 GTGCCTTTCTCAGCAATAGGG 58.980 52.381 0.00 0.00 41.48 3.53
3376 4517 4.928615 CACTCTGGAATGAAGAGAAGTCAC 59.071 45.833 7.42 0.00 43.27 3.67
3389 4540 7.103641 ACGACAATTACAATACACTCTGGAAT 58.896 34.615 0.00 0.00 0.00 3.01
3431 4582 7.884877 ACAATTTTCATGACCTGAGAGAATACA 59.115 33.333 0.00 0.00 34.68 2.29
3432 4583 8.180267 CACAATTTTCATGACCTGAGAGAATAC 58.820 37.037 0.00 0.00 34.68 1.89
3434 4585 6.349944 GCACAATTTTCATGACCTGAGAGAAT 60.350 38.462 0.00 0.00 34.68 2.40
3585 4739 5.067413 ACCGTTTCCTTTTCTCCTTCTTTTC 59.933 40.000 0.00 0.00 0.00 2.29
3586 4740 4.954202 ACCGTTTCCTTTTCTCCTTCTTTT 59.046 37.500 0.00 0.00 0.00 2.27
3587 4741 4.533815 ACCGTTTCCTTTTCTCCTTCTTT 58.466 39.130 0.00 0.00 0.00 2.52
3626 4780 0.676151 CAGCAGGTTCTTCAGGGCTC 60.676 60.000 0.00 0.00 0.00 4.70
3653 4807 1.990060 GGTGGCAGCTGGAGGAGTA 60.990 63.158 17.12 0.00 0.00 2.59
3719 4873 3.738590 GCTCCGTGAATACCTTCTCCTTC 60.739 52.174 0.00 0.00 32.29 3.46
3732 4886 0.318441 CTCTTGTCCTGCTCCGTGAA 59.682 55.000 0.00 0.00 0.00 3.18
3878 5032 2.604046 ACTCTGCAAACGACACTTCT 57.396 45.000 0.00 0.00 0.00 2.85
3920 5074 3.731728 GGCATGGGCTCTGGGACA 61.732 66.667 0.00 0.00 40.87 4.02
3936 5090 1.296715 CCTGGGTCTTGTCCTTCGG 59.703 63.158 0.00 0.00 0.00 4.30
4100 5254 2.119495 ACTAGGCACCACTAATCCCAG 58.881 52.381 0.00 0.00 0.00 4.45
4129 5285 0.178068 ACTGGGCATACACATCGTCC 59.822 55.000 0.00 0.00 0.00 4.79
4168 5324 2.035704 CGCAGCAGAGATCCTAGAACAT 59.964 50.000 0.00 0.00 0.00 2.71
4185 5341 0.461548 TACAAGGGCTCTCATCGCAG 59.538 55.000 0.00 0.00 0.00 5.18
4199 5355 4.639310 AGAAATTCAGATGCTGCCTACAAG 59.361 41.667 0.00 0.00 0.00 3.16
4306 5464 0.770499 TGGTCAAGCATGGAGTCCAA 59.230 50.000 17.71 0.00 36.95 3.53
4311 5469 2.414994 ATGAGTGGTCAAGCATGGAG 57.585 50.000 0.00 0.00 35.88 3.86
4468 5638 4.347000 TGCTAACTACTCCAGTTCCAGTTT 59.653 41.667 0.00 0.00 44.48 2.66
4476 5646 2.234908 CAGCCTTGCTAACTACTCCAGT 59.765 50.000 0.00 0.00 36.40 4.00
4477 5647 2.898705 CAGCCTTGCTAACTACTCCAG 58.101 52.381 0.00 0.00 36.40 3.86
4478 5648 1.066143 GCAGCCTTGCTAACTACTCCA 60.066 52.381 0.00 0.00 46.95 3.86
4479 5649 1.657822 GCAGCCTTGCTAACTACTCC 58.342 55.000 0.00 0.00 46.95 3.85
4560 5745 7.228706 CGGCCTCAAATAAGAATTACTGGTTAT 59.771 37.037 0.00 0.00 30.46 1.89
4609 5800 4.516321 TGGTGTGAGTTTCATGACAATGAG 59.484 41.667 0.00 0.00 43.64 2.90
4614 5807 2.942376 GTGTGGTGTGAGTTTCATGACA 59.058 45.455 0.00 0.00 0.00 3.58
4628 5823 3.127589 TCAATGTTCAGTACGTGTGGTG 58.872 45.455 0.00 0.00 0.00 4.17
4629 5824 3.462483 TCAATGTTCAGTACGTGTGGT 57.538 42.857 0.00 0.00 0.00 4.16
4630 5825 3.558006 TGTTCAATGTTCAGTACGTGTGG 59.442 43.478 0.00 0.00 0.00 4.17
4664 5859 1.905894 TGATGAAATGTCTCGGGTGGA 59.094 47.619 0.00 0.00 0.00 4.02
4666 5861 1.667724 GCTGATGAAATGTCTCGGGTG 59.332 52.381 0.00 0.00 0.00 4.61
4667 5862 1.278985 TGCTGATGAAATGTCTCGGGT 59.721 47.619 0.00 0.00 0.00 5.28
4668 5863 2.028420 TGCTGATGAAATGTCTCGGG 57.972 50.000 0.00 0.00 0.00 5.14
4700 5952 5.557866 AGGTTAGTTTTGTAGTGGCTTAGG 58.442 41.667 0.00 0.00 0.00 2.69
4709 5961 4.446719 GTGTGGACGAGGTTAGTTTTGTAG 59.553 45.833 0.00 0.00 0.00 2.74
4727 5979 1.871039 CCCTGTTTTACTCGTGTGTGG 59.129 52.381 0.00 0.00 0.00 4.17
4731 5983 6.459670 AAATTTTCCCTGTTTTACTCGTGT 57.540 33.333 0.00 0.00 0.00 4.49
4746 5998 3.004315 TGTCTTGTGCTCGGAAATTTTCC 59.996 43.478 16.80 16.80 46.62 3.13
4765 6017 7.110155 TGTTCCAGTTCTCCCTAATATTTGTC 58.890 38.462 0.00 0.00 0.00 3.18
4766 6018 7.027874 TGTTCCAGTTCTCCCTAATATTTGT 57.972 36.000 0.00 0.00 0.00 2.83
4770 6023 5.071115 GCTCTGTTCCAGTTCTCCCTAATAT 59.929 44.000 0.00 0.00 32.61 1.28
4861 6116 2.676342 AGTTCCGCCGTATGAATTTGTC 59.324 45.455 0.00 0.00 0.00 3.18
4895 6150 6.015434 GTGAATTCCTTTCCCTTGCTTTCTAA 60.015 38.462 2.27 0.00 33.04 2.10
4896 6151 5.476945 GTGAATTCCTTTCCCTTGCTTTCTA 59.523 40.000 2.27 0.00 33.04 2.10
4899 6154 3.966665 TGTGAATTCCTTTCCCTTGCTTT 59.033 39.130 2.27 0.00 33.04 3.51
4967 6225 5.312178 TCCTTGATTTCCCTCTAGGTTTCAA 59.688 40.000 0.00 0.00 38.71 2.69
4968 6226 4.849810 TCCTTGATTTCCCTCTAGGTTTCA 59.150 41.667 0.00 0.00 38.71 2.69


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

AutoCloner maintained by Alex Coulton.