Multiple sequence alignment - TraesCS3B01G334100

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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 TraesCS3B01G334100 chr3B 100.000 4395 0 0 1 4395 540459244 540463638 0.000000e+00 8117.0
1 TraesCS3B01G334100 chr3B 98.795 83 1 0 1442 1524 540460764 540460682 9.850000e-32 148.0
2 TraesCS3B01G334100 chr3B 86.957 69 7 2 2105 2172 614203059 614202992 4.710000e-10 76.8
3 TraesCS3B01G334100 chr3D 93.631 2795 123 24 1531 4286 414633472 414636250 0.000000e+00 4124.0
4 TraesCS3B01G334100 chr3D 95.103 1450 61 6 3 1443 414632018 414633466 0.000000e+00 2276.0
5 TraesCS3B01G334100 chr3A 92.080 2197 126 20 2105 4286 535808922 535806759 0.000000e+00 3049.0
6 TraesCS3B01G334100 chr3A 95.889 900 36 1 537 1435 535812273 535811374 0.000000e+00 1456.0
7 TraesCS3B01G334100 chr3A 93.542 542 30 2 3 539 535821112 535820571 0.000000e+00 802.0
8 TraesCS3B01G334100 chr3A 91.429 350 21 4 1740 2089 535809391 535809051 5.150000e-129 472.0
9 TraesCS3B01G334100 chr3A 89.855 207 19 2 1530 1736 535810781 535810577 9.370000e-67 265.0
10 TraesCS3B01G334100 chr3A 89.899 99 3 3 1433 1524 638201945 638201847 2.150000e-23 121.0
11 TraesCS3B01G334100 chr7D 78.404 639 127 9 2620 3251 154208975 154209609 5.290000e-109 405.0
12 TraesCS3B01G334100 chr5A 75.294 340 69 11 1073 1403 657651613 657651946 9.850000e-32 148.0
13 TraesCS3B01G334100 chr2B 93.407 91 5 1 1434 1523 744121695 744121605 2.760000e-27 134.0
14 TraesCS3B01G334100 chr2B 95.062 81 4 0 1442 1522 744121607 744121687 1.280000e-25 128.0
15 TraesCS3B01G334100 chr1D 95.181 83 4 0 1439 1521 293590599 293590681 9.920000e-27 132.0
16 TraesCS3B01G334100 chr1D 93.976 83 5 0 1442 1524 293590681 293590599 4.610000e-25 126.0
17 TraesCS3B01G334100 chr5B 86.842 114 13 2 4160 4271 384598873 384598760 4.610000e-25 126.0
18 TraesCS3B01G334100 chr7A 92.135 89 2 1 1442 1525 7584849 7584937 2.150000e-23 121.0
19 TraesCS3B01G334100 chr5D 92.857 84 5 1 1438 1521 7930352 7930270 2.150000e-23 121.0
20 TraesCS3B01G334100 chr1A 90.217 92 5 3 1435 1522 504616733 504616824 2.780000e-22 117.0
21 TraesCS3B01G334100 chr4B 88.732 71 6 2 2106 2174 633138195 633138265 7.830000e-13 86.1


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 TraesCS3B01G334100 chr3B 540459244 540463638 4394 False 8117.0 8117 100.00000 1 4395 1 chr3B.!!$F1 4394
1 TraesCS3B01G334100 chr3D 414632018 414636250 4232 False 3200.0 4124 94.36700 3 4286 2 chr3D.!!$F1 4283
2 TraesCS3B01G334100 chr3A 535806759 535812273 5514 True 1310.5 3049 92.31325 537 4286 4 chr3A.!!$R3 3749
3 TraesCS3B01G334100 chr3A 535820571 535821112 541 True 802.0 802 93.54200 3 539 1 chr3A.!!$R1 536
4 TraesCS3B01G334100 chr7D 154208975 154209609 634 False 405.0 405 78.40400 2620 3251 1 chr7D.!!$F1 631

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
252 260 0.321021 CTCCTGTTGCTCTGCTCAGT 59.679 55.000 11.53 0.0 32.84 3.41 F
770 778 0.806868 GACCGTGTGGATCGACTACA 59.193 55.000 9.41 0.0 39.21 2.74 F
1834 3607 0.249531 TGCGTTGGTAGCGAGTTTCA 60.250 50.000 0.00 0.0 37.44 2.69 F
3099 4997 1.001393 GGCGTTTCCATTGGGAGGA 60.001 57.895 2.09 0.0 46.01 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1206 0.950836 CCAACTTCATTGTGCCGTCA 59.049 50.000 0.0 0.0 36.47 4.35 R
2060 3833 1.134491 GGAGGGAGTACCATTCAACGG 60.134 57.143 0.0 0.0 43.89 4.44 R
3148 5046 1.643868 GGCGTTTGGCGTCATCATCA 61.644 55.000 0.0 0.0 45.83 3.07 R
3929 5839 0.323360 TTGGCCCACACCTTAGATGC 60.323 55.000 0.0 0.0 0.00 3.91 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
126 132 7.437748 AGGTCTCAATCTCATCTATAAAACCG 58.562 38.462 0.00 0.00 0.00 4.44
134 142 4.699637 TCATCTATAAAACCGCATCCGTT 58.300 39.130 0.00 0.00 0.00 4.44
137 145 4.116961 TCTATAAAACCGCATCCGTTCTG 58.883 43.478 0.00 0.00 0.00 3.02
143 151 0.374758 CCGCATCCGTTCTGTTCATG 59.625 55.000 0.00 0.00 0.00 3.07
161 169 6.258507 TGTTCATGATGATTAATCCACAGTCG 59.741 38.462 12.90 6.34 34.00 4.18
176 184 6.234920 TCCACAGTCGAATTCCATTTCTAAA 58.765 36.000 0.00 0.00 0.00 1.85
187 195 7.745620 ATTCCATTTCTAAAAACAGACGAGT 57.254 32.000 0.00 0.00 0.00 4.18
202 210 3.130693 AGACGAGTAGTAAGATGTTGGGC 59.869 47.826 0.00 0.00 0.00 5.36
252 260 0.321021 CTCCTGTTGCTCTGCTCAGT 59.679 55.000 11.53 0.00 32.84 3.41
258 266 2.001159 GTTGCTCTGCTCAGTGATGAG 58.999 52.381 11.36 11.36 38.86 2.90
400 408 4.832608 GGCATCGACCACCCGACC 62.833 72.222 0.00 0.00 41.70 4.79
433 441 2.342648 GAGTCCGCCTGGTTCGTT 59.657 61.111 0.00 0.00 36.30 3.85
595 603 7.922811 CCGACGTATAAGGGAAAGTTTATTAGT 59.077 37.037 0.00 0.00 0.00 2.24
613 621 1.068472 AGTGTGACGACGTTCATCTCC 60.068 52.381 0.13 0.00 0.00 3.71
619 627 4.143333 ACGTTCATCTCCGGCCCG 62.143 66.667 0.00 0.00 0.00 6.13
770 778 0.806868 GACCGTGTGGATCGACTACA 59.193 55.000 9.41 0.00 39.21 2.74
1107 1116 2.350863 ACAGGAGGTGGAAGAAGGAT 57.649 50.000 0.00 0.00 0.00 3.24
1197 1206 2.640316 AGAAGGCCACGAAGAACTTT 57.360 45.000 5.01 0.00 0.00 2.66
1265 1274 4.711949 CAGGCTTCCTGCGGCACT 62.712 66.667 0.00 0.00 45.13 4.40
1347 1356 0.733223 GCTTCGACGACTTCCTGGAC 60.733 60.000 0.00 0.00 0.00 4.02
1451 2040 9.601217 CATTCCTTTATTTATATACTCCCTCCG 57.399 37.037 0.00 0.00 0.00 4.63
1452 2041 8.731591 TTCCTTTATTTATATACTCCCTCCGT 57.268 34.615 0.00 0.00 0.00 4.69
1453 2042 8.731591 TCCTTTATTTATATACTCCCTCCGTT 57.268 34.615 0.00 0.00 0.00 4.44
1454 2043 9.162733 TCCTTTATTTATATACTCCCTCCGTTT 57.837 33.333 0.00 0.00 0.00 3.60
1455 2044 9.433153 CCTTTATTTATATACTCCCTCCGTTTC 57.567 37.037 0.00 0.00 0.00 2.78
1456 2045 9.991906 CTTTATTTATATACTCCCTCCGTTTCA 57.008 33.333 0.00 0.00 0.00 2.69
1460 2049 9.862149 ATTTATATACTCCCTCCGTTTCAAATT 57.138 29.630 0.00 0.00 0.00 1.82
1462 2051 9.768662 TTATATACTCCCTCCGTTTCAAATTAC 57.231 33.333 0.00 0.00 0.00 1.89
1463 2052 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
1464 2053 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
1465 2054 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
1466 2055 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
1467 2056 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
1468 2057 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
1469 2058 3.641648 TCCGTTTCAAATTACTCGTCGT 58.358 40.909 0.00 0.00 0.00 4.34
1470 2059 3.426191 TCCGTTTCAAATTACTCGTCGTG 59.574 43.478 0.00 0.00 0.00 4.35
1471 2060 3.422603 CCGTTTCAAATTACTCGTCGTGG 60.423 47.826 0.00 0.00 0.00 4.94
1472 2061 3.182972 CGTTTCAAATTACTCGTCGTGGT 59.817 43.478 0.00 0.00 0.00 4.16
1473 2062 4.318263 CGTTTCAAATTACTCGTCGTGGTT 60.318 41.667 0.00 0.00 0.00 3.67
1474 2063 5.504392 GTTTCAAATTACTCGTCGTGGTTT 58.496 37.500 0.00 0.00 0.00 3.27
1475 2064 5.738118 TTCAAATTACTCGTCGTGGTTTT 57.262 34.783 0.00 0.00 0.00 2.43
1476 2065 6.841443 TTCAAATTACTCGTCGTGGTTTTA 57.159 33.333 0.00 0.00 0.00 1.52
1477 2066 6.456447 TCAAATTACTCGTCGTGGTTTTAG 57.544 37.500 0.00 0.00 0.00 1.85
1478 2067 5.984926 TCAAATTACTCGTCGTGGTTTTAGT 59.015 36.000 0.00 0.00 0.00 2.24
1479 2068 6.479660 TCAAATTACTCGTCGTGGTTTTAGTT 59.520 34.615 0.00 0.00 0.00 2.24
1480 2069 6.849588 AATTACTCGTCGTGGTTTTAGTTT 57.150 33.333 0.00 0.00 0.00 2.66
1481 2070 7.945033 AATTACTCGTCGTGGTTTTAGTTTA 57.055 32.000 0.00 0.00 0.00 2.01
1482 2071 7.945033 ATTACTCGTCGTGGTTTTAGTTTAA 57.055 32.000 0.00 0.00 0.00 1.52
1483 2072 7.763172 TTACTCGTCGTGGTTTTAGTTTAAA 57.237 32.000 0.00 0.00 0.00 1.52
1484 2073 6.036246 ACTCGTCGTGGTTTTAGTTTAAAC 57.964 37.500 10.47 10.47 37.30 2.01
1485 2074 5.812127 ACTCGTCGTGGTTTTAGTTTAAACT 59.188 36.000 23.58 23.58 42.91 2.66
1486 2075 6.978080 ACTCGTCGTGGTTTTAGTTTAAACTA 59.022 34.615 21.52 21.52 40.37 2.24
1487 2076 7.491048 ACTCGTCGTGGTTTTAGTTTAAACTAA 59.509 33.333 28.77 28.77 46.58 2.24
1498 2087 7.763172 TTAGTTTAAACTAAAACCACGACGA 57.237 32.000 29.81 10.15 45.62 4.20
1499 2088 6.277918 AGTTTAAACTAAAACCACGACGAG 57.722 37.500 19.26 0.00 39.66 4.18
1500 2089 5.812127 AGTTTAAACTAAAACCACGACGAGT 59.188 36.000 19.26 0.00 39.66 4.18
1501 2090 6.978080 AGTTTAAACTAAAACCACGACGAGTA 59.022 34.615 19.26 0.00 39.66 2.59
1502 2091 7.491048 AGTTTAAACTAAAACCACGACGAGTAA 59.509 33.333 19.26 0.00 39.66 2.24
1503 2092 7.945033 TTAAACTAAAACCACGACGAGTAAT 57.055 32.000 0.00 0.00 0.00 1.89
1504 2093 6.849588 AAACTAAAACCACGACGAGTAATT 57.150 33.333 0.00 1.08 0.00 1.40
1505 2094 6.849588 AACTAAAACCACGACGAGTAATTT 57.150 33.333 0.00 0.34 0.00 1.82
1506 2095 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1507 2096 5.984926 ACTAAAACCACGACGAGTAATTTGA 59.015 36.000 0.00 0.00 0.00 2.69
1508 2097 5.738118 AAAACCACGACGAGTAATTTGAA 57.262 34.783 0.00 0.00 0.00 2.69
1509 2098 5.738118 AAACCACGACGAGTAATTTGAAA 57.262 34.783 0.00 0.00 0.00 2.69
1510 2099 4.720530 ACCACGACGAGTAATTTGAAAC 57.279 40.909 0.00 0.00 0.00 2.78
1511 2100 3.182972 ACCACGACGAGTAATTTGAAACG 59.817 43.478 0.00 0.00 0.00 3.60
1512 2101 3.422603 CCACGACGAGTAATTTGAAACGG 60.423 47.826 0.00 0.00 0.00 4.44
1513 2102 3.426191 CACGACGAGTAATTTGAAACGGA 59.574 43.478 0.00 0.00 0.00 4.69
1514 2103 3.671928 ACGACGAGTAATTTGAAACGGAG 59.328 43.478 0.00 0.00 0.00 4.63
1515 2104 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
1516 2105 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
1517 2106 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
1518 2107 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
1519 2108 4.576879 GAGTAATTTGAAACGGAGGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
1520 2109 5.622914 CGAGTAATTTGAAACGGAGGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
1521 2110 5.485620 AGTAATTTGAAACGGAGGGAGTAC 58.514 41.667 0.00 0.00 0.00 2.73
1522 2111 4.360951 AATTTGAAACGGAGGGAGTACA 57.639 40.909 0.00 0.00 0.00 2.90
1523 2112 4.569719 ATTTGAAACGGAGGGAGTACAT 57.430 40.909 0.00 0.00 0.00 2.29
1524 2113 4.360951 TTTGAAACGGAGGGAGTACATT 57.639 40.909 0.00 0.00 0.00 2.71
1525 2114 4.360951 TTGAAACGGAGGGAGTACATTT 57.639 40.909 0.00 0.00 0.00 2.32
1526 2115 4.360951 TGAAACGGAGGGAGTACATTTT 57.639 40.909 0.00 0.00 0.00 1.82
1527 2116 4.320870 TGAAACGGAGGGAGTACATTTTC 58.679 43.478 0.00 0.00 0.00 2.29
1528 2117 3.345508 AACGGAGGGAGTACATTTTCC 57.654 47.619 0.00 0.00 0.00 3.13
1560 2149 4.042809 TGAATGGCTTTGTCTAGGAAAGGA 59.957 41.667 13.75 0.00 32.06 3.36
1561 2150 4.870021 ATGGCTTTGTCTAGGAAAGGAT 57.130 40.909 13.75 0.00 32.06 3.24
1794 3567 5.699458 ACTCACATACTCAAAACGTTAAGGG 59.301 40.000 0.00 0.00 0.00 3.95
1834 3607 0.249531 TGCGTTGGTAGCGAGTTTCA 60.250 50.000 0.00 0.00 37.44 2.69
1936 3709 6.088883 GCGTATTTGTTTGGTATTTTCTGGTG 59.911 38.462 0.00 0.00 0.00 4.17
1943 3716 3.592059 TGGTATTTTCTGGTGTCTACGC 58.408 45.455 0.00 0.00 0.00 4.42
1945 3718 3.864003 GGTATTTTCTGGTGTCTACGCTC 59.136 47.826 0.00 0.00 0.00 5.03
1946 3719 3.963428 ATTTTCTGGTGTCTACGCTCT 57.037 42.857 0.00 0.00 0.00 4.09
1955 3728 2.161211 GTGTCTACGCTCTTCGGTAACT 59.839 50.000 0.00 0.00 43.86 2.24
1956 3729 2.417933 TGTCTACGCTCTTCGGTAACTC 59.582 50.000 0.00 0.00 43.86 3.01
2060 3833 2.372837 TGTAGGGTTTGTGGTAGGTTCC 59.627 50.000 0.00 0.00 0.00 3.62
2086 3859 1.424638 ATGGTACTCCCTCCATTCCG 58.575 55.000 0.00 0.00 41.02 4.30
2142 4029 1.924524 CTTAAATCTCGAAAGCGCGGA 59.075 47.619 8.83 0.00 37.46 5.54
2157 4044 1.011968 GCGGACGCACTACATTGTGA 61.012 55.000 12.31 0.00 40.12 3.58
2200 4087 8.553696 GGTTTTCTATCGTCTTTCTGTTGTAAA 58.446 33.333 0.00 0.00 0.00 2.01
2217 4104 9.180678 CTGTTGTAAATCAATTTGTTCAGTACC 57.819 33.333 0.00 0.00 38.38 3.34
2277 4170 2.655090 TGATTGTGTGCTCCTTTCCA 57.345 45.000 0.00 0.00 0.00 3.53
2318 4211 7.724951 ACATTTTCAATGGGGTTGATGATTTTT 59.275 29.630 1.72 0.00 45.77 1.94
2391 4284 8.301720 CCATAACATGACAGGATTCATATTTGG 58.698 37.037 0.00 0.00 34.29 3.28
2427 4320 5.043281 TGCCCTGGGACCCTATTTATTAAAA 60.043 40.000 19.27 0.00 0.00 1.52
2428 4321 5.900699 GCCCTGGGACCCTATTTATTAAAAA 59.099 40.000 19.27 0.00 0.00 1.94
2532 4425 2.836262 TGTTTCAAATTTGCAGCCCTG 58.164 42.857 13.54 0.00 0.00 4.45
2797 4695 3.040477 TCATCATGAGTATGAGCCCACA 58.960 45.455 0.09 0.00 45.89 4.17
2812 4710 2.936993 GCCCACAGTTCTTCATCGTGAT 60.937 50.000 0.00 0.00 0.00 3.06
2824 4722 2.884639 TCATCGTGATATCAAGGCGAGA 59.115 45.455 18.20 13.63 35.03 4.04
2893 4791 4.021925 GCCTGCACGGTCCCTCTT 62.022 66.667 4.45 0.00 34.25 2.85
3099 4997 1.001393 GGCGTTTCCATTGGGAGGA 60.001 57.895 2.09 0.00 46.01 3.71
3148 5046 4.875713 GCCATGGCGGGGTTCGAT 62.876 66.667 23.48 0.00 42.43 3.59
3461 5359 5.176406 CGCACTTCACCTAGATGAATATGTG 59.824 44.000 11.61 11.61 37.93 3.21
3462 5360 6.051717 GCACTTCACCTAGATGAATATGTGT 58.948 40.000 15.51 2.17 37.93 3.72
3638 5541 5.562298 ACTGAGGTAGTGTTTGGTATTGT 57.438 39.130 0.00 0.00 38.49 2.71
3639 5542 5.937111 ACTGAGGTAGTGTTTGGTATTGTT 58.063 37.500 0.00 0.00 38.49 2.83
3780 5684 1.154413 GATGCGCAACAACTCGGTG 60.154 57.895 17.11 0.00 0.00 4.94
3783 5687 0.319986 TGCGCAACAACTCGGTGATA 60.320 50.000 8.16 0.00 0.00 2.15
3911 5816 6.149129 AGTATGAATACGATGCTCTTGTGA 57.851 37.500 0.00 0.00 38.28 3.58
3973 5883 6.282199 TCCACTTGGACTAACTTAGCTTAG 57.718 41.667 0.00 0.00 39.78 2.18
4068 5978 1.697432 TGTGGTAGAACCCAGGAACAG 59.303 52.381 0.00 0.00 37.50 3.16
4069 5979 1.003233 GTGGTAGAACCCAGGAACAGG 59.997 57.143 0.00 0.00 37.50 4.00
4072 5982 2.027100 GGTAGAACCCAGGAACAGGAAG 60.027 54.545 0.00 0.00 37.04 3.46
4073 5983 0.402121 AGAACCCAGGAACAGGAAGC 59.598 55.000 0.00 0.00 37.04 3.86
4078 5988 1.770324 CAGGAACAGGAAGCCCCTT 59.230 57.895 0.00 0.00 44.85 3.95
4079 5989 0.991920 CAGGAACAGGAAGCCCCTTA 59.008 55.000 0.00 0.00 44.85 2.69
4081 5991 1.847088 AGGAACAGGAAGCCCCTTATC 59.153 52.381 0.00 0.00 44.85 1.75
4089 6000 2.376855 GGAAGCCCCTTATCTTAGCCAT 59.623 50.000 0.00 0.00 0.00 4.40
4109 6020 2.513753 TCCATTTTCTGCATCACGGTT 58.486 42.857 0.00 0.00 0.00 4.44
4117 6028 4.135747 TCTGCATCACGGTTCATTCATA 57.864 40.909 0.00 0.00 0.00 2.15
4279 6194 6.207614 GGGCTTAGAAAAACAACTCTCTTGAT 59.792 38.462 0.00 0.00 0.00 2.57
4297 6212 9.663904 TCTCTTGATTGAAATAACTTTTTCACG 57.336 29.630 0.00 0.00 43.38 4.35
4298 6213 9.663904 CTCTTGATTGAAATAACTTTTTCACGA 57.336 29.630 0.00 0.00 43.38 4.35
4304 6219 7.769719 TGAAATAACTTTTTCACGAATACGC 57.230 32.000 0.00 0.00 39.91 4.42
4305 6220 7.353497 TGAAATAACTTTTTCACGAATACGCA 58.647 30.769 0.00 0.00 39.91 5.24
4306 6221 8.018520 TGAAATAACTTTTTCACGAATACGCAT 58.981 29.630 0.00 0.00 39.91 4.73
4307 6222 7.719689 AATAACTTTTTCACGAATACGCATG 57.280 32.000 0.00 0.00 43.96 4.06
4308 6223 4.742438 ACTTTTTCACGAATACGCATGT 57.258 36.364 0.00 0.00 43.96 3.21
4309 6224 4.463209 ACTTTTTCACGAATACGCATGTG 58.537 39.130 4.30 4.30 43.96 3.21
4310 6225 4.024387 ACTTTTTCACGAATACGCATGTGT 60.024 37.500 17.35 17.35 43.96 3.72
4311 6226 5.177881 ACTTTTTCACGAATACGCATGTGTA 59.822 36.000 20.72 20.72 43.96 2.90
4312 6227 5.788055 TTTTCACGAATACGCATGTGTAT 57.212 34.783 23.19 23.19 43.96 2.29
4313 6228 5.383984 TTTCACGAATACGCATGTGTATC 57.616 39.130 27.48 19.82 43.96 2.24
4314 6229 4.035278 TCACGAATACGCATGTGTATCA 57.965 40.909 27.48 7.56 43.96 2.15
4315 6230 4.616953 TCACGAATACGCATGTGTATCAT 58.383 39.130 27.48 16.01 43.96 2.45
4316 6231 5.047188 TCACGAATACGCATGTGTATCATT 58.953 37.500 27.48 16.90 43.96 2.57
4317 6232 5.174943 TCACGAATACGCATGTGTATCATTC 59.825 40.000 27.48 22.09 43.96 2.67
4318 6233 4.447724 ACGAATACGCATGTGTATCATTCC 59.552 41.667 27.48 15.15 43.96 3.01
4319 6234 4.447389 CGAATACGCATGTGTATCATTCCA 59.553 41.667 27.48 4.64 34.01 3.53
4320 6235 5.120674 CGAATACGCATGTGTATCATTCCAT 59.879 40.000 27.48 13.40 34.01 3.41
4321 6236 6.486253 AATACGCATGTGTATCATTCCATC 57.514 37.500 27.48 0.00 34.01 3.51
4322 6237 3.141398 ACGCATGTGTATCATTCCATCC 58.859 45.455 10.90 0.00 34.09 3.51
4323 6238 3.140623 CGCATGTGTATCATTCCATCCA 58.859 45.455 0.00 0.00 34.09 3.41
4324 6239 3.754850 CGCATGTGTATCATTCCATCCAT 59.245 43.478 0.00 0.00 34.09 3.41
4325 6240 4.937015 CGCATGTGTATCATTCCATCCATA 59.063 41.667 0.00 0.00 34.09 2.74
4326 6241 5.064325 CGCATGTGTATCATTCCATCCATAG 59.936 44.000 0.00 0.00 34.09 2.23
4327 6242 6.175471 GCATGTGTATCATTCCATCCATAGA 58.825 40.000 0.00 0.00 34.09 1.98
4328 6243 6.656270 GCATGTGTATCATTCCATCCATAGAA 59.344 38.462 0.00 0.00 34.09 2.10
4329 6244 7.338703 GCATGTGTATCATTCCATCCATAGAAT 59.661 37.037 0.00 0.00 34.09 2.40
4330 6245 9.895138 CATGTGTATCATTCCATCCATAGAATA 57.105 33.333 0.00 0.00 34.09 1.75
4332 6247 9.948964 TGTGTATCATTCCATCCATAGAATAAG 57.051 33.333 0.00 0.00 31.55 1.73
4333 6248 9.950496 GTGTATCATTCCATCCATAGAATAAGT 57.050 33.333 0.00 0.00 31.55 2.24
4343 6258 9.838339 CCATCCATAGAATAAGTTAGAACAAGT 57.162 33.333 0.00 0.00 0.00 3.16
4350 6265 8.739649 AGAATAAGTTAGAACAAGTACGACAC 57.260 34.615 0.00 0.00 0.00 3.67
4351 6266 8.355169 AGAATAAGTTAGAACAAGTACGACACA 58.645 33.333 0.00 0.00 0.00 3.72
4352 6267 9.136952 GAATAAGTTAGAACAAGTACGACACAT 57.863 33.333 0.00 0.00 0.00 3.21
4353 6268 6.764877 AAGTTAGAACAAGTACGACACATG 57.235 37.500 0.00 0.00 32.04 3.21
4354 6269 6.080648 AGTTAGAACAAGTACGACACATGA 57.919 37.500 0.00 0.00 30.34 3.07
4355 6270 5.919141 AGTTAGAACAAGTACGACACATGAC 59.081 40.000 0.00 0.00 30.34 3.06
4356 6271 4.316205 AGAACAAGTACGACACATGACA 57.684 40.909 0.00 0.00 30.34 3.58
4357 6272 4.049186 AGAACAAGTACGACACATGACAC 58.951 43.478 0.00 0.00 30.34 3.67
4358 6273 3.446310 ACAAGTACGACACATGACACA 57.554 42.857 0.00 0.00 30.34 3.72
4359 6274 3.381045 ACAAGTACGACACATGACACAG 58.619 45.455 0.00 0.00 30.34 3.66
4360 6275 3.067601 ACAAGTACGACACATGACACAGA 59.932 43.478 0.00 0.00 30.34 3.41
4361 6276 4.237724 CAAGTACGACACATGACACAGAT 58.762 43.478 0.00 0.00 0.00 2.90
4362 6277 3.838120 AGTACGACACATGACACAGATG 58.162 45.455 0.00 0.00 0.00 2.90
4363 6278 1.432514 ACGACACATGACACAGATGC 58.567 50.000 0.00 0.00 0.00 3.91
4364 6279 1.270252 ACGACACATGACACAGATGCA 60.270 47.619 0.00 0.00 0.00 3.96
4365 6280 1.799994 CGACACATGACACAGATGCAA 59.200 47.619 0.00 0.00 0.00 4.08
4366 6281 2.159747 CGACACATGACACAGATGCAAG 60.160 50.000 0.00 0.00 0.00 4.01
4367 6282 3.069289 GACACATGACACAGATGCAAGA 58.931 45.455 0.00 0.00 0.00 3.02
4368 6283 3.072211 ACACATGACACAGATGCAAGAG 58.928 45.455 0.00 0.00 0.00 2.85
4369 6284 2.418976 CACATGACACAGATGCAAGAGG 59.581 50.000 0.00 0.00 0.00 3.69
4370 6285 1.400846 CATGACACAGATGCAAGAGGC 59.599 52.381 0.00 0.00 45.13 4.70
4381 6296 1.180029 GCAAGAGGCATGAACATGGT 58.820 50.000 15.15 0.00 43.97 3.55
4382 6297 1.135199 GCAAGAGGCATGAACATGGTG 60.135 52.381 15.15 0.00 43.97 4.17
4383 6298 2.165167 CAAGAGGCATGAACATGGTGT 58.835 47.619 15.15 0.00 39.16 4.16
4384 6299 2.119801 AGAGGCATGAACATGGTGTC 57.880 50.000 15.15 0.00 39.16 3.67
4385 6300 1.352017 AGAGGCATGAACATGGTGTCA 59.648 47.619 15.15 0.00 39.16 3.58
4386 6301 2.161855 GAGGCATGAACATGGTGTCAA 58.838 47.619 15.15 0.00 39.16 3.18
4387 6302 2.163010 GAGGCATGAACATGGTGTCAAG 59.837 50.000 15.15 0.00 39.16 3.02
4388 6303 2.161855 GGCATGAACATGGTGTCAAGA 58.838 47.619 15.15 0.00 39.16 3.02
4389 6304 2.163010 GGCATGAACATGGTGTCAAGAG 59.837 50.000 15.15 0.00 39.16 2.85
4390 6305 2.415090 GCATGAACATGGTGTCAAGAGC 60.415 50.000 15.15 1.16 39.16 4.09
4391 6306 2.636647 TGAACATGGTGTCAAGAGCA 57.363 45.000 0.00 0.00 0.00 4.26
4392 6307 2.497138 TGAACATGGTGTCAAGAGCAG 58.503 47.619 0.00 0.00 0.00 4.24
4393 6308 2.104622 TGAACATGGTGTCAAGAGCAGA 59.895 45.455 0.00 0.00 0.00 4.26
4394 6309 2.469274 ACATGGTGTCAAGAGCAGAG 57.531 50.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.565841 GGTCTGCCCATGATACTTGTC 58.434 52.381 0.00 0.00 0.00 3.18
1 2 1.134401 CGGTCTGCCCATGATACTTGT 60.134 52.381 0.00 0.00 0.00 3.16
40 41 3.444388 AGTAGATGAAACGGTCCAGACTC 59.556 47.826 0.00 0.00 0.00 3.36
42 43 3.870633 AGTAGATGAAACGGTCCAGAC 57.129 47.619 0.00 0.00 0.00 3.51
43 44 4.562757 CCAAAGTAGATGAAACGGTCCAGA 60.563 45.833 0.00 0.00 0.00 3.86
44 45 3.684788 CCAAAGTAGATGAAACGGTCCAG 59.315 47.826 0.00 0.00 0.00 3.86
45 46 3.325425 TCCAAAGTAGATGAAACGGTCCA 59.675 43.478 0.00 0.00 0.00 4.02
126 132 2.938451 TCATCATGAACAGAACGGATGC 59.062 45.455 0.00 0.00 33.84 3.91
134 142 7.341030 ACTGTGGATTAATCATCATGAACAGA 58.659 34.615 16.77 10.12 35.83 3.41
137 145 6.479990 TCGACTGTGGATTAATCATCATGAAC 59.520 38.462 17.07 4.42 32.79 3.18
143 151 6.483307 TGGAATTCGACTGTGGATTAATCATC 59.517 38.462 17.07 9.43 0.00 2.92
161 169 8.290325 ACTCGTCTGTTTTTAGAAATGGAATTC 58.710 33.333 0.00 0.00 33.67 2.17
176 184 6.157211 CCAACATCTTACTACTCGTCTGTTT 58.843 40.000 0.00 0.00 0.00 2.83
187 195 1.843851 CCCAGGCCCAACATCTTACTA 59.156 52.381 0.00 0.00 0.00 1.82
202 210 4.660771 AGAAGAAGGTTATGGTATCCCAGG 59.339 45.833 0.00 0.00 46.15 4.45
252 260 2.068821 GCCCAGGAGGAGCTCATCA 61.069 63.158 27.91 0.00 38.24 3.07
425 433 1.006571 GCGAGAGGACAACGAACCA 60.007 57.895 0.00 0.00 0.00 3.67
592 600 2.161012 GGAGATGAACGTCGTCACACTA 59.839 50.000 0.00 0.00 34.91 2.74
595 603 0.109919 CGGAGATGAACGTCGTCACA 60.110 55.000 0.00 2.87 34.91 3.58
662 670 0.818040 GACTTCACCGTGCCAACCTT 60.818 55.000 0.00 0.00 0.00 3.50
747 755 2.506217 CGATCCACACGGTCACGG 60.506 66.667 0.00 0.00 46.48 4.94
790 798 3.692406 GGGGCGACGAACACTCCT 61.692 66.667 0.00 0.00 0.00 3.69
1107 1116 3.251509 TTGGCCAGCTGCTCCAGA 61.252 61.111 20.49 12.24 40.92 3.86
1197 1206 0.950836 CCAACTTCATTGTGCCGTCA 59.049 50.000 0.00 0.00 36.47 4.35
1260 1269 2.818274 CGGCCCGTTTCTAGTGCC 60.818 66.667 0.00 0.00 38.74 5.01
1265 1274 1.186917 TTCTGGACGGCCCGTTTCTA 61.187 55.000 11.54 0.00 41.37 2.10
1347 1356 1.078759 GGTTGATGACGCTGACCTCG 61.079 60.000 0.00 0.00 0.00 4.63
1443 2032 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
1444 2033 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
1445 2034 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
1446 2035 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
1447 2036 3.671928 ACGACGAGTAATTTGAAACGGAG 59.328 43.478 0.00 0.00 0.00 4.63
1448 2037 3.426191 CACGACGAGTAATTTGAAACGGA 59.574 43.478 0.00 0.00 0.00 4.69
1449 2038 3.422603 CCACGACGAGTAATTTGAAACGG 60.423 47.826 0.00 0.00 0.00 4.44
1450 2039 3.182972 ACCACGACGAGTAATTTGAAACG 59.817 43.478 0.00 0.00 0.00 3.60
1451 2040 4.720530 ACCACGACGAGTAATTTGAAAC 57.279 40.909 0.00 0.00 0.00 2.78
1452 2041 5.738118 AAACCACGACGAGTAATTTGAAA 57.262 34.783 0.00 0.00 0.00 2.69
1453 2042 5.738118 AAAACCACGACGAGTAATTTGAA 57.262 34.783 0.00 0.00 0.00 2.69
1454 2043 5.984926 ACTAAAACCACGACGAGTAATTTGA 59.015 36.000 0.00 0.00 0.00 2.69
1455 2044 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1456 2045 6.849588 AACTAAAACCACGACGAGTAATTT 57.150 33.333 0.00 0.34 0.00 1.82
1457 2046 6.849588 AAACTAAAACCACGACGAGTAATT 57.150 33.333 0.00 1.08 0.00 1.40
1458 2047 7.945033 TTAAACTAAAACCACGACGAGTAAT 57.055 32.000 0.00 0.00 0.00 1.89
1459 2048 7.491048 AGTTTAAACTAAAACCACGACGAGTAA 59.509 33.333 19.26 0.00 39.66 2.24
1460 2049 6.978080 AGTTTAAACTAAAACCACGACGAGTA 59.022 34.615 19.26 0.00 39.66 2.59
1461 2050 5.812127 AGTTTAAACTAAAACCACGACGAGT 59.188 36.000 19.26 0.00 39.66 4.18
1462 2051 6.277918 AGTTTAAACTAAAACCACGACGAG 57.722 37.500 19.26 0.00 39.66 4.18
1463 2052 7.763172 TTAGTTTAAACTAAAACCACGACGA 57.237 32.000 29.81 10.15 45.62 4.20
1474 2063 7.491048 ACTCGTCGTGGTTTTAGTTTAAACTAA 59.509 33.333 28.77 28.77 46.58 2.24
1475 2064 6.978080 ACTCGTCGTGGTTTTAGTTTAAACTA 59.022 34.615 21.52 21.52 40.37 2.24
1476 2065 5.812127 ACTCGTCGTGGTTTTAGTTTAAACT 59.188 36.000 23.58 23.58 42.91 2.66
1477 2066 6.036246 ACTCGTCGTGGTTTTAGTTTAAAC 57.964 37.500 10.47 10.47 37.30 2.01
1478 2067 7.763172 TTACTCGTCGTGGTTTTAGTTTAAA 57.237 32.000 0.00 0.00 0.00 1.52
1479 2068 7.945033 ATTACTCGTCGTGGTTTTAGTTTAA 57.055 32.000 0.00 0.00 0.00 1.52
1480 2069 7.945033 AATTACTCGTCGTGGTTTTAGTTTA 57.055 32.000 0.00 0.00 0.00 2.01
1481 2070 6.849588 AATTACTCGTCGTGGTTTTAGTTT 57.150 33.333 0.00 0.00 0.00 2.66
1482 2071 6.479660 TCAAATTACTCGTCGTGGTTTTAGTT 59.520 34.615 0.00 0.00 0.00 2.24
1483 2072 5.984926 TCAAATTACTCGTCGTGGTTTTAGT 59.015 36.000 0.00 0.00 0.00 2.24
1484 2073 6.456447 TCAAATTACTCGTCGTGGTTTTAG 57.544 37.500 0.00 0.00 0.00 1.85
1485 2074 6.841443 TTCAAATTACTCGTCGTGGTTTTA 57.159 33.333 0.00 0.00 0.00 1.52
1486 2075 5.738118 TTCAAATTACTCGTCGTGGTTTT 57.262 34.783 0.00 0.00 0.00 2.43
1487 2076 5.504392 GTTTCAAATTACTCGTCGTGGTTT 58.496 37.500 0.00 0.00 0.00 3.27
1488 2077 4.318263 CGTTTCAAATTACTCGTCGTGGTT 60.318 41.667 0.00 0.00 0.00 3.67
1489 2078 3.182972 CGTTTCAAATTACTCGTCGTGGT 59.817 43.478 0.00 0.00 0.00 4.16
1490 2079 3.422603 CCGTTTCAAATTACTCGTCGTGG 60.423 47.826 0.00 0.00 0.00 4.94
1491 2080 3.426191 TCCGTTTCAAATTACTCGTCGTG 59.574 43.478 0.00 0.00 0.00 4.35
1492 2081 3.641648 TCCGTTTCAAATTACTCGTCGT 58.358 40.909 0.00 0.00 0.00 4.34
1493 2082 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
1494 2083 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
1495 2084 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
1496 2085 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
1497 2086 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
1498 2087 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
1499 2088 5.240121 TGTACTCCCTCCGTTTCAAATTAC 58.760 41.667 0.00 0.00 0.00 1.89
1500 2089 5.486735 TGTACTCCCTCCGTTTCAAATTA 57.513 39.130 0.00 0.00 0.00 1.40
1501 2090 4.360951 TGTACTCCCTCCGTTTCAAATT 57.639 40.909 0.00 0.00 0.00 1.82
1502 2091 4.569719 ATGTACTCCCTCCGTTTCAAAT 57.430 40.909 0.00 0.00 0.00 2.32
1503 2092 4.360951 AATGTACTCCCTCCGTTTCAAA 57.639 40.909 0.00 0.00 0.00 2.69
1504 2093 4.360951 AAATGTACTCCCTCCGTTTCAA 57.639 40.909 0.00 0.00 0.00 2.69
1505 2094 4.320870 GAAAATGTACTCCCTCCGTTTCA 58.679 43.478 0.00 0.00 0.00 2.69
1506 2095 3.688185 GGAAAATGTACTCCCTCCGTTTC 59.312 47.826 0.00 0.00 0.00 2.78
1507 2096 3.329814 AGGAAAATGTACTCCCTCCGTTT 59.670 43.478 0.00 0.00 31.50 3.60
1508 2097 2.910977 AGGAAAATGTACTCCCTCCGTT 59.089 45.455 0.00 0.00 31.50 4.44
1509 2098 2.547990 AGGAAAATGTACTCCCTCCGT 58.452 47.619 0.00 0.00 31.50 4.69
1510 2099 3.532542 GAAGGAAAATGTACTCCCTCCG 58.467 50.000 0.00 0.00 31.50 4.63
1511 2100 3.523972 AGGAAGGAAAATGTACTCCCTCC 59.476 47.826 8.01 8.01 41.15 4.30
1512 2101 4.846168 AGGAAGGAAAATGTACTCCCTC 57.154 45.455 0.00 0.00 31.50 4.30
1513 2102 4.852697 AGAAGGAAGGAAAATGTACTCCCT 59.147 41.667 0.00 0.00 31.50 4.20
1514 2103 5.180810 AGAAGGAAGGAAAATGTACTCCC 57.819 43.478 0.00 0.00 31.50 4.30
1515 2104 6.238648 TCAAGAAGGAAGGAAAATGTACTCC 58.761 40.000 0.00 0.00 0.00 3.85
1516 2105 7.745620 TTCAAGAAGGAAGGAAAATGTACTC 57.254 36.000 0.00 0.00 0.00 2.59
1517 2106 7.177392 CCATTCAAGAAGGAAGGAAAATGTACT 59.823 37.037 0.00 0.00 30.52 2.73
1518 2107 7.315890 CCATTCAAGAAGGAAGGAAAATGTAC 58.684 38.462 0.00 0.00 30.52 2.90
1519 2108 6.071391 GCCATTCAAGAAGGAAGGAAAATGTA 60.071 38.462 0.00 0.00 30.52 2.29
1520 2109 5.279657 GCCATTCAAGAAGGAAGGAAAATGT 60.280 40.000 0.00 0.00 30.52 2.71
1521 2110 5.046807 AGCCATTCAAGAAGGAAGGAAAATG 60.047 40.000 0.00 0.00 30.52 2.32
1522 2111 5.089434 AGCCATTCAAGAAGGAAGGAAAAT 58.911 37.500 0.00 0.00 30.52 1.82
1523 2112 4.482990 AGCCATTCAAGAAGGAAGGAAAA 58.517 39.130 0.00 0.00 30.52 2.29
1524 2113 4.118168 AGCCATTCAAGAAGGAAGGAAA 57.882 40.909 0.00 0.00 30.52 3.13
1525 2114 3.814504 AGCCATTCAAGAAGGAAGGAA 57.185 42.857 0.00 0.00 30.52 3.36
1526 2115 3.814504 AAGCCATTCAAGAAGGAAGGA 57.185 42.857 0.00 0.00 30.52 3.36
1527 2116 3.575687 ACAAAGCCATTCAAGAAGGAAGG 59.424 43.478 0.00 0.00 0.00 3.46
1528 2117 4.522022 AGACAAAGCCATTCAAGAAGGAAG 59.478 41.667 0.00 0.00 0.00 3.46
1560 2149 4.669809 TTCGCCCGGTGCCCAAAT 62.670 61.111 0.00 0.00 36.24 2.32
1561 2150 4.896829 TTTCGCCCGGTGCCCAAA 62.897 61.111 0.00 1.97 36.24 3.28
1794 3567 2.506438 GTAGTCCTCCGCACGTGC 60.506 66.667 30.42 30.42 37.78 5.34
1936 3709 2.677337 AGAGTTACCGAAGAGCGTAGAC 59.323 50.000 0.00 0.00 38.67 2.59
1943 3716 4.971220 GCGAGAAATAGAGTTACCGAAGAG 59.029 45.833 0.00 0.00 0.00 2.85
1945 3718 4.043073 GGCGAGAAATAGAGTTACCGAAG 58.957 47.826 0.00 0.00 0.00 3.79
1946 3719 3.181483 GGGCGAGAAATAGAGTTACCGAA 60.181 47.826 0.00 0.00 0.00 4.30
1955 3728 2.104792 CCAAGATGGGGCGAGAAATAGA 59.895 50.000 0.00 0.00 32.67 1.98
1956 3729 2.158755 ACCAAGATGGGGCGAGAAATAG 60.159 50.000 0.87 0.00 43.37 1.73
2060 3833 1.134491 GGAGGGAGTACCATTCAACGG 60.134 57.143 0.00 0.00 43.89 4.44
2111 3997 8.398665 GCTTTCGAGATTTAAGTTTGACCATAT 58.601 33.333 0.00 0.00 0.00 1.78
2126 4012 2.158959 CGTCCGCGCTTTCGAGATT 61.159 57.895 5.56 0.00 37.73 2.40
2142 4029 4.024048 CCTCTTTTTCACAATGTAGTGCGT 60.024 41.667 0.00 0.00 39.35 5.24
2157 4044 6.853490 AGAAAACCTGATACTCCCTCTTTTT 58.147 36.000 0.00 0.00 0.00 1.94
2200 4087 4.943705 AGCATCGGTACTGAACAAATTGAT 59.056 37.500 8.82 0.00 0.00 2.57
2217 4104 7.854534 TCAATGATATACAAAACTCAGCATCG 58.145 34.615 0.00 0.00 0.00 3.84
2253 4146 6.604171 TGGAAAGGAGCACACAATCATATAT 58.396 36.000 0.00 0.00 0.00 0.86
2404 4297 4.734843 TTAATAAATAGGGTCCCAGGGC 57.265 45.455 11.55 0.00 0.00 5.19
2428 4321 9.492973 ACATATTTCTGCAAATTTAGCTGTTTT 57.507 25.926 0.00 0.00 33.95 2.43
2797 4695 5.053145 GCCTTGATATCACGATGAAGAACT 58.947 41.667 10.63 0.00 0.00 3.01
2812 4710 3.561310 GCATGATGTTTCTCGCCTTGATA 59.439 43.478 0.00 0.00 0.00 2.15
2824 4722 2.684881 GGTGGAATCGAGCATGATGTTT 59.315 45.455 0.00 0.00 0.00 2.83
2974 4872 3.242903 CGAACGCATAGATGTCAGTCTCT 60.243 47.826 0.00 0.00 0.00 3.10
3148 5046 1.643868 GGCGTTTGGCGTCATCATCA 61.644 55.000 0.00 0.00 45.83 3.07
3461 5359 4.102649 GTGTTACACTCCAAAACAAGCAC 58.897 43.478 8.41 0.00 35.08 4.40
3462 5360 3.181505 CGTGTTACACTCCAAAACAAGCA 60.182 43.478 13.86 0.00 35.08 3.91
3638 5541 6.988580 TGTGCAAACAAAATCATAATCCACAA 59.011 30.769 0.00 0.00 0.00 3.33
3639 5542 6.519382 TGTGCAAACAAAATCATAATCCACA 58.481 32.000 0.00 0.00 0.00 4.17
3672 5575 8.597662 TGTCAAACAAACACTAAGATAGGTAC 57.402 34.615 0.00 0.00 0.00 3.34
3783 5687 8.884124 TCTTTAAAATCCTTCATCCACTCAAT 57.116 30.769 0.00 0.00 0.00 2.57
3928 5838 1.453928 GGCCCACACCTTAGATGCC 60.454 63.158 0.00 0.00 0.00 4.40
3929 5839 0.323360 TTGGCCCACACCTTAGATGC 60.323 55.000 0.00 0.00 0.00 3.91
3973 5883 1.331756 CAGAGGCACCGCAAACATATC 59.668 52.381 0.00 0.00 0.00 1.63
4068 5978 1.774856 TGGCTAAGATAAGGGGCTTCC 59.225 52.381 0.00 0.00 0.00 3.46
4069 5979 3.560239 GGATGGCTAAGATAAGGGGCTTC 60.560 52.174 0.00 0.00 0.00 3.86
4072 5982 1.705186 TGGATGGCTAAGATAAGGGGC 59.295 52.381 0.00 0.00 0.00 5.80
4073 5983 4.664688 AATGGATGGCTAAGATAAGGGG 57.335 45.455 0.00 0.00 0.00 4.79
4078 5988 5.693961 TGCAGAAAATGGATGGCTAAGATA 58.306 37.500 0.00 0.00 0.00 1.98
4079 5989 4.539726 TGCAGAAAATGGATGGCTAAGAT 58.460 39.130 0.00 0.00 0.00 2.40
4081 5991 4.340097 TGATGCAGAAAATGGATGGCTAAG 59.660 41.667 0.00 0.00 40.55 2.18
4089 6000 2.198827 ACCGTGATGCAGAAAATGGA 57.801 45.000 0.00 0.00 0.00 3.41
4189 6104 9.464714 CGTTAAGATATGTGCTAGTCAACTAAT 57.535 33.333 0.00 0.00 0.00 1.73
4214 6129 2.917933 TCCTTATCCTCCAACATTGCG 58.082 47.619 0.00 0.00 0.00 4.85
4286 6201 4.909305 CACATGCGTATTCGTGAAAAAGTT 59.091 37.500 0.00 0.00 39.49 2.66
4287 6202 4.024387 ACACATGCGTATTCGTGAAAAAGT 60.024 37.500 10.25 0.00 39.49 2.66
4288 6203 4.463209 ACACATGCGTATTCGTGAAAAAG 58.537 39.130 10.25 0.00 39.49 2.27
4289 6204 4.475763 ACACATGCGTATTCGTGAAAAA 57.524 36.364 10.25 0.00 39.49 1.94
4290 6205 5.348997 TGATACACATGCGTATTCGTGAAAA 59.651 36.000 7.77 0.00 39.49 2.29
4291 6206 4.865365 TGATACACATGCGTATTCGTGAAA 59.135 37.500 7.77 0.36 39.49 2.69
4292 6207 4.425520 TGATACACATGCGTATTCGTGAA 58.574 39.130 7.77 0.00 39.49 3.18
4293 6208 4.035278 TGATACACATGCGTATTCGTGA 57.965 40.909 7.77 0.00 39.49 4.35
4294 6209 4.972286 ATGATACACATGCGTATTCGTG 57.028 40.909 7.77 3.00 37.87 4.35
4295 6210 4.447724 GGAATGATACACATGCGTATTCGT 59.552 41.667 7.77 1.35 39.39 3.85
4296 6211 4.447389 TGGAATGATACACATGCGTATTCG 59.553 41.667 7.77 0.00 39.39 3.34
4297 6212 5.922739 TGGAATGATACACATGCGTATTC 57.077 39.130 7.77 4.02 39.39 1.75
4298 6213 5.412594 GGATGGAATGATACACATGCGTATT 59.587 40.000 7.77 0.00 39.39 1.89
4299 6214 4.937620 GGATGGAATGATACACATGCGTAT 59.062 41.667 6.08 6.08 39.39 3.06
4300 6215 4.202305 TGGATGGAATGATACACATGCGTA 60.202 41.667 0.00 0.00 39.39 4.42
4301 6216 3.141398 GGATGGAATGATACACATGCGT 58.859 45.455 0.00 0.00 39.39 5.24
4302 6217 3.140623 TGGATGGAATGATACACATGCG 58.859 45.455 0.00 0.00 39.39 4.73
4303 6218 6.175471 TCTATGGATGGAATGATACACATGC 58.825 40.000 0.00 0.00 39.39 4.06
4304 6219 8.803397 ATTCTATGGATGGAATGATACACATG 57.197 34.615 0.00 0.00 36.75 3.21
4306 6221 9.948964 CTTATTCTATGGATGGAATGATACACA 57.051 33.333 8.14 0.00 38.28 3.72
4307 6222 9.950496 ACTTATTCTATGGATGGAATGATACAC 57.050 33.333 8.14 0.00 38.28 2.90
4317 6232 9.838339 ACTTGTTCTAACTTATTCTATGGATGG 57.162 33.333 0.00 0.00 0.00 3.51
4324 6239 9.831737 GTGTCGTACTTGTTCTAACTTATTCTA 57.168 33.333 0.00 0.00 0.00 2.10
4325 6240 8.355169 TGTGTCGTACTTGTTCTAACTTATTCT 58.645 33.333 0.00 0.00 0.00 2.40
4326 6241 8.511465 TGTGTCGTACTTGTTCTAACTTATTC 57.489 34.615 0.00 0.00 0.00 1.75
4327 6242 8.922676 CATGTGTCGTACTTGTTCTAACTTATT 58.077 33.333 0.00 0.00 31.66 1.40
4328 6243 8.301720 TCATGTGTCGTACTTGTTCTAACTTAT 58.698 33.333 0.00 0.00 36.23 1.73
4329 6244 7.592533 GTCATGTGTCGTACTTGTTCTAACTTA 59.407 37.037 0.00 0.00 36.23 2.24
4330 6245 6.420008 GTCATGTGTCGTACTTGTTCTAACTT 59.580 38.462 0.00 0.00 36.23 2.66
4331 6246 5.919141 GTCATGTGTCGTACTTGTTCTAACT 59.081 40.000 0.00 0.00 36.23 2.24
4332 6247 5.688621 TGTCATGTGTCGTACTTGTTCTAAC 59.311 40.000 0.00 0.00 36.23 2.34
4333 6248 5.688621 GTGTCATGTGTCGTACTTGTTCTAA 59.311 40.000 0.00 0.00 36.23 2.10
4334 6249 5.217393 GTGTCATGTGTCGTACTTGTTCTA 58.783 41.667 0.00 0.00 36.23 2.10
4335 6250 4.049186 GTGTCATGTGTCGTACTTGTTCT 58.951 43.478 0.00 0.00 36.23 3.01
4336 6251 3.799963 TGTGTCATGTGTCGTACTTGTTC 59.200 43.478 0.00 5.00 36.23 3.18
4337 6252 3.787785 TGTGTCATGTGTCGTACTTGTT 58.212 40.909 0.00 0.00 36.23 2.83
4338 6253 3.067601 TCTGTGTCATGTGTCGTACTTGT 59.932 43.478 0.00 0.00 36.23 3.16
4339 6254 3.638484 TCTGTGTCATGTGTCGTACTTG 58.362 45.455 0.00 0.00 36.16 3.16
4340 6255 4.237724 CATCTGTGTCATGTGTCGTACTT 58.762 43.478 0.00 0.00 0.00 2.24
4341 6256 3.838120 CATCTGTGTCATGTGTCGTACT 58.162 45.455 0.00 0.00 0.00 2.73
4342 6257 2.345641 GCATCTGTGTCATGTGTCGTAC 59.654 50.000 0.00 0.00 0.00 3.67
4343 6258 2.029470 TGCATCTGTGTCATGTGTCGTA 60.029 45.455 0.00 0.00 0.00 3.43
4344 6259 1.270252 TGCATCTGTGTCATGTGTCGT 60.270 47.619 0.00 0.00 0.00 4.34
4345 6260 1.431496 TGCATCTGTGTCATGTGTCG 58.569 50.000 0.00 0.00 0.00 4.35
4346 6261 3.069289 TCTTGCATCTGTGTCATGTGTC 58.931 45.455 0.00 0.00 0.00 3.67
4347 6262 3.072211 CTCTTGCATCTGTGTCATGTGT 58.928 45.455 0.00 0.00 0.00 3.72
4348 6263 2.418976 CCTCTTGCATCTGTGTCATGTG 59.581 50.000 0.00 0.00 0.00 3.21
4349 6264 2.708051 CCTCTTGCATCTGTGTCATGT 58.292 47.619 0.00 0.00 0.00 3.21
4350 6265 1.400846 GCCTCTTGCATCTGTGTCATG 59.599 52.381 0.00 0.00 40.77 3.07
4351 6266 1.747709 GCCTCTTGCATCTGTGTCAT 58.252 50.000 0.00 0.00 40.77 3.06
4352 6267 3.238232 GCCTCTTGCATCTGTGTCA 57.762 52.632 0.00 0.00 40.77 3.58
4362 6277 1.135199 CACCATGTTCATGCCTCTTGC 60.135 52.381 7.21 0.00 41.77 4.01
4363 6278 2.163010 GACACCATGTTCATGCCTCTTG 59.837 50.000 7.21 2.54 0.00 3.02
4364 6279 2.224843 TGACACCATGTTCATGCCTCTT 60.225 45.455 7.21 0.00 0.00 2.85
4365 6280 1.352017 TGACACCATGTTCATGCCTCT 59.648 47.619 7.21 0.00 0.00 3.69
4366 6281 1.825090 TGACACCATGTTCATGCCTC 58.175 50.000 7.21 2.65 0.00 4.70
4367 6282 2.165167 CTTGACACCATGTTCATGCCT 58.835 47.619 7.21 0.00 0.00 4.75
4368 6283 2.161855 TCTTGACACCATGTTCATGCC 58.838 47.619 7.21 0.00 0.00 4.40
4369 6284 2.415090 GCTCTTGACACCATGTTCATGC 60.415 50.000 7.21 0.00 0.00 4.06
4370 6285 2.815503 TGCTCTTGACACCATGTTCATG 59.184 45.455 5.88 5.88 0.00 3.07
4371 6286 3.079578 CTGCTCTTGACACCATGTTCAT 58.920 45.455 0.00 0.00 0.00 2.57
4372 6287 2.104622 TCTGCTCTTGACACCATGTTCA 59.895 45.455 0.00 0.00 0.00 3.18
4373 6288 2.740981 CTCTGCTCTTGACACCATGTTC 59.259 50.000 0.00 0.00 0.00 3.18
4374 6289 2.775890 CTCTGCTCTTGACACCATGTT 58.224 47.619 0.00 0.00 0.00 2.71
4375 6290 2.469274 CTCTGCTCTTGACACCATGT 57.531 50.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.