Multiple sequence alignment - TraesCS7D01G221800

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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 TraesCS7D01G221800 chr7D 100.000 2330 0 0 1 2330 182825088 182822759 0.000000e+00 4303.0
1 TraesCS7D01G221800 chr7D 95.103 633 22 9 1 628 235517142 235516514 0.000000e+00 989.0
2 TraesCS7D01G221800 chr7D 87.554 233 17 5 2100 2330 69445488 69445710 2.300000e-65 259.0
3 TraesCS7D01G221800 chr7B 89.421 1106 49 26 642 1740 151381401 151380357 0.000000e+00 1332.0
4 TraesCS7D01G221800 chr7B 83.221 149 23 2 1918 2065 151378134 151377987 4.040000e-28 135.0
5 TraesCS7D01G221800 chr7A 94.059 707 26 4 628 1330 188885491 188886185 0.000000e+00 1059.0
6 TraesCS7D01G221800 chr7A 84.556 259 23 8 1587 1844 188888252 188888494 8.320000e-60 241.0
7 TraesCS7D01G221800 chr7A 88.614 202 11 8 1409 1600 188886226 188886425 3.870000e-58 235.0
8 TraesCS7D01G221800 chr1A 94.945 633 19 11 1 627 321849709 321850334 0.000000e+00 979.0
9 TraesCS7D01G221800 chr1A 87.597 258 14 9 1386 1638 489155036 489154792 1.360000e-72 283.0
10 TraesCS7D01G221800 chr1A 92.308 52 3 1 1634 1684 489152944 489152893 3.210000e-09 73.1
11 TraesCS7D01G221800 chr6B 94.313 633 22 9 1 623 94333181 94332553 0.000000e+00 957.0
12 TraesCS7D01G221800 chr2B 94.268 628 30 6 1 627 51798968 51799590 0.000000e+00 955.0
13 TraesCS7D01G221800 chr2B 86.752 234 20 3 2097 2330 64038078 64037856 1.380000e-62 250.0
14 TraesCS7D01G221800 chr2D 93.939 627 27 10 1 623 324944542 324943923 0.000000e+00 937.0
15 TraesCS7D01G221800 chr5D 97.455 550 11 3 1 548 89496412 89495864 0.000000e+00 935.0
16 TraesCS7D01G221800 chr5D 92.417 633 38 8 1 627 45131016 45131644 0.000000e+00 894.0
17 TraesCS7D01G221800 chr5A 93.700 619 25 12 1 616 92199878 92200485 0.000000e+00 915.0
18 TraesCS7D01G221800 chr5A 86.498 237 25 1 2094 2330 137040548 137040777 1.070000e-63 254.0
19 TraesCS7D01G221800 chr3B 91.325 634 45 10 1 628 785866971 785867600 0.000000e+00 857.0
20 TraesCS7D01G221800 chr6D 86.752 785 67 17 916 1694 245571988 245571235 0.000000e+00 839.0
21 TraesCS7D01G221800 chr1B 90.213 235 21 2 2097 2330 595187272 595187505 2.910000e-79 305.0
22 TraesCS7D01G221800 chr4B 88.983 236 17 1 2095 2330 14527601 14527375 1.360000e-72 283.0
23 TraesCS7D01G221800 chr1D 88.285 239 17 4 2094 2330 428613249 428613478 2.280000e-70 276.0
24 TraesCS7D01G221800 chr3D 88.186 237 17 5 2096 2330 578905355 578905128 2.950000e-69 272.0
25 TraesCS7D01G221800 chr3D 88.136 236 17 4 2097 2330 572501887 572502113 1.060000e-68 270.0
26 TraesCS7D01G221800 chr5B 87.288 236 21 3 2096 2330 355617569 355617342 6.390000e-66 261.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G221800 chr7D 182822759 182825088 2329 True 4303.000000 4303 100.000000 1 2330 1 chr7D.!!$R1 2329
1 TraesCS7D01G221800 chr7D 235516514 235517142 628 True 989.000000 989 95.103000 1 628 1 chr7D.!!$R2 627
2 TraesCS7D01G221800 chr7B 151377987 151381401 3414 True 733.500000 1332 86.321000 642 2065 2 chr7B.!!$R1 1423
3 TraesCS7D01G221800 chr7A 188885491 188888494 3003 False 511.666667 1059 89.076333 628 1844 3 chr7A.!!$F1 1216
4 TraesCS7D01G221800 chr1A 321849709 321850334 625 False 979.000000 979 94.945000 1 627 1 chr1A.!!$F1 626
5 TraesCS7D01G221800 chr6B 94332553 94333181 628 True 957.000000 957 94.313000 1 623 1 chr6B.!!$R1 622
6 TraesCS7D01G221800 chr2B 51798968 51799590 622 False 955.000000 955 94.268000 1 627 1 chr2B.!!$F1 626
7 TraesCS7D01G221800 chr2D 324943923 324944542 619 True 937.000000 937 93.939000 1 623 1 chr2D.!!$R1 622
8 TraesCS7D01G221800 chr5D 89495864 89496412 548 True 935.000000 935 97.455000 1 548 1 chr5D.!!$R1 547
9 TraesCS7D01G221800 chr5D 45131016 45131644 628 False 894.000000 894 92.417000 1 627 1 chr5D.!!$F1 626
10 TraesCS7D01G221800 chr5A 92199878 92200485 607 False 915.000000 915 93.700000 1 616 1 chr5A.!!$F1 615
11 TraesCS7D01G221800 chr3B 785866971 785867600 629 False 857.000000 857 91.325000 1 628 1 chr3B.!!$F1 627
12 TraesCS7D01G221800 chr6D 245571235 245571988 753 True 839.000000 839 86.752000 916 1694 1 chr6D.!!$R1 778

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
828 915 0.90961 GTCATGTCCCCACCTCTCCA 60.91 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 6303 0.031449 GAAGCGCGGAGATTCTAGCT 59.969 55.0 8.83 0.0 41.7 3.32 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
418 430 4.142609 TGCAAAAACAATTAGCCCACAA 57.857 36.364 0.00 0.00 0.00 3.33
441 453 1.279271 AGCCAATTAGCTTCAGTCGGT 59.721 47.619 0.00 0.00 41.41 4.69
517 530 2.510238 CAGCTGTAGGCCGACTGC 60.510 66.667 31.43 31.43 42.72 4.40
644 723 5.991933 ATAGCGATCAGATCAGTATTGGT 57.008 39.130 11.12 1.54 0.00 3.67
662 741 5.939764 TTGGTAAGCTAGAGTGATGATGT 57.060 39.130 0.00 0.00 0.00 3.06
825 912 1.207791 GATGTCATGTCCCCACCTCT 58.792 55.000 0.00 0.00 0.00 3.69
828 915 0.909610 GTCATGTCCCCACCTCTCCA 60.910 60.000 0.00 0.00 0.00 3.86
852 940 3.053826 ACCTACATCCAAACCTATCCCC 58.946 50.000 0.00 0.00 0.00 4.81
870 958 1.807981 CAAACGCTGGCATGCATGG 60.808 57.895 27.34 13.04 0.00 3.66
912 1000 4.821589 CTCCCCTCGCGCTCCAAC 62.822 72.222 5.56 0.00 0.00 3.77
921 1009 3.423154 CGCTCCAACCCGAAGTGC 61.423 66.667 0.00 0.00 0.00 4.40
1334 1422 4.069869 CCAGTGCTGGTGAAGTGG 57.930 61.111 9.96 0.00 45.53 4.00
1335 1423 1.149174 CCAGTGCTGGTGAAGTGGT 59.851 57.895 9.96 0.00 45.53 4.16
1336 1424 1.168407 CCAGTGCTGGTGAAGTGGTG 61.168 60.000 9.96 0.00 45.53 4.17
1337 1425 0.179048 CAGTGCTGGTGAAGTGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
1369 1457 2.183478 TGGTATGGGCAATAGCATCG 57.817 50.000 9.68 0.00 42.84 3.84
1370 1458 0.804989 GGTATGGGCAATAGCATCGC 59.195 55.000 6.21 0.00 44.61 4.58
1371 1459 1.611673 GGTATGGGCAATAGCATCGCT 60.612 52.381 6.21 0.00 44.61 4.93
1372 1460 1.734465 GTATGGGCAATAGCATCGCTC 59.266 52.381 0.00 0.00 44.61 5.03
1373 1461 0.607489 ATGGGCAATAGCATCGCTCC 60.607 55.000 0.00 0.00 44.61 4.70
1374 1462 1.968540 GGGCAATAGCATCGCTCCC 60.969 63.158 0.00 0.00 44.61 4.30
1375 1463 1.227943 GGCAATAGCATCGCTCCCA 60.228 57.895 0.00 0.00 44.61 4.37
1376 1464 1.233285 GGCAATAGCATCGCTCCCAG 61.233 60.000 0.00 0.00 44.61 4.45
1377 1465 1.233285 GCAATAGCATCGCTCCCAGG 61.233 60.000 0.00 0.00 40.44 4.45
1378 1466 0.394192 CAATAGCATCGCTCCCAGGA 59.606 55.000 0.00 0.00 40.44 3.86
1379 1467 1.131638 AATAGCATCGCTCCCAGGAA 58.868 50.000 0.00 0.00 40.44 3.36
1380 1468 0.683973 ATAGCATCGCTCCCAGGAAG 59.316 55.000 0.00 0.00 40.44 3.46
1381 1469 0.687757 TAGCATCGCTCCCAGGAAGT 60.688 55.000 0.00 0.00 40.44 3.01
1384 1472 0.179089 CATCGCTCCCAGGAAGTCAG 60.179 60.000 0.00 0.00 0.00 3.51
1399 1487 0.247736 GTCAGGAACGTGGATGAGCT 59.752 55.000 0.00 0.00 0.00 4.09
1400 1488 0.247460 TCAGGAACGTGGATGAGCTG 59.753 55.000 0.00 0.00 0.00 4.24
1401 1489 1.078848 AGGAACGTGGATGAGCTGC 60.079 57.895 0.00 0.00 0.00 5.25
1402 1490 1.375908 GGAACGTGGATGAGCTGCA 60.376 57.895 1.02 0.00 0.00 4.41
1403 1491 0.955428 GGAACGTGGATGAGCTGCAA 60.955 55.000 1.02 0.00 0.00 4.08
1404 1492 0.166814 GAACGTGGATGAGCTGCAAC 59.833 55.000 1.02 0.00 0.00 4.17
1405 1493 1.568612 AACGTGGATGAGCTGCAACG 61.569 55.000 1.02 0.00 0.00 4.10
1406 1494 2.743752 CGTGGATGAGCTGCAACGG 61.744 63.158 1.02 0.00 0.00 4.44
1407 1495 2.747460 TGGATGAGCTGCAACGGC 60.747 61.111 1.02 0.00 41.68 5.68
1408 1496 3.512516 GGATGAGCTGCAACGGCC 61.513 66.667 1.02 0.00 40.13 6.13
1440 1538 1.402968 CCTCGGCGTAGTTAGTGCTAA 59.597 52.381 6.85 0.00 0.00 3.09
1450 1548 6.256686 CGTAGTTAGTGCTAAGTTAGTGGAG 58.743 44.000 11.51 0.00 31.68 3.86
1459 1557 4.021368 GCTAAGTTAGTGGAGAGGTTGTGA 60.021 45.833 11.51 0.00 0.00 3.58
1466 1564 0.693049 GGAGAGGTTGTGATGTGGGT 59.307 55.000 0.00 0.00 0.00 4.51
1537 1643 1.768684 GCCACTCTTGGTCCTGGTGA 61.769 60.000 0.00 0.00 45.98 4.02
1550 1656 3.189287 GTCCTGGTGATGTAGCTTTTGTG 59.811 47.826 0.00 0.00 0.00 3.33
1714 3663 7.796660 CGAAAATCTTGTAAATCTGACGTCAAA 59.203 33.333 20.49 6.93 0.00 2.69
1728 3677 2.299013 ACGTCAAAGAGACCATGCTACA 59.701 45.455 0.00 0.00 44.66 2.74
1740 3689 6.010219 AGACCATGCTACATTTTAACAGGTT 58.990 36.000 0.00 0.00 0.00 3.50
1742 3691 7.015195 AGACCATGCTACATTTTAACAGGTTTT 59.985 33.333 0.00 0.00 0.00 2.43
1743 3692 7.505258 ACCATGCTACATTTTAACAGGTTTTT 58.495 30.769 0.00 0.00 0.00 1.94
1778 3749 4.385825 GGGGGTTTTTCTTTCCATTTCAC 58.614 43.478 0.00 0.00 0.00 3.18
1790 5798 4.188247 TCCATTTCACGTAGAGTTCAGG 57.812 45.455 0.00 0.00 0.00 3.86
1823 5831 8.940397 TTTCCAGTGAAAGAATAATTTCTCCT 57.060 30.769 0.00 0.00 41.42 3.69
1855 5863 9.838339 AAATTTGTGATAGTACTCCCTTATCAG 57.162 33.333 0.00 0.00 0.00 2.90
1856 5864 6.978674 TTGTGATAGTACTCCCTTATCAGG 57.021 41.667 0.00 0.00 40.45 3.86
1875 5883 5.273208 TCAGGAGTAACTGATAAGCCTTCT 58.727 41.667 0.00 0.00 42.26 2.85
1881 5889 4.899352 AACTGATAAGCCTTCTGTGTCT 57.101 40.909 0.00 0.00 0.00 3.41
1882 5890 4.899352 ACTGATAAGCCTTCTGTGTCTT 57.101 40.909 0.00 0.00 0.00 3.01
1883 5891 5.234466 ACTGATAAGCCTTCTGTGTCTTT 57.766 39.130 0.00 0.00 0.00 2.52
1884 5892 5.625150 ACTGATAAGCCTTCTGTGTCTTTT 58.375 37.500 0.00 0.00 0.00 2.27
1885 5893 6.064717 ACTGATAAGCCTTCTGTGTCTTTTT 58.935 36.000 0.00 0.00 0.00 1.94
1912 5920 2.892784 GCTAGATAAGCCTTCCGTGT 57.107 50.000 0.00 0.00 46.25 4.49
1914 5922 2.100916 GCTAGATAAGCCTTCCGTGTCA 59.899 50.000 0.00 0.00 46.25 3.58
1916 5924 3.914426 AGATAAGCCTTCCGTGTCAAT 57.086 42.857 0.00 0.00 0.00 2.57
1931 5944 5.237344 CCGTGTCAATAAGGATTCCTGATTC 59.763 44.000 11.88 3.92 32.58 2.52
1939 5952 2.571653 AGGATTCCTGATTCCAACACGA 59.428 45.455 3.86 0.00 34.24 4.35
1941 5954 3.600388 GATTCCTGATTCCAACACGAGT 58.400 45.455 0.00 0.00 0.00 4.18
1945 5958 4.312443 TCCTGATTCCAACACGAGTAAAC 58.688 43.478 0.00 0.00 0.00 2.01
1958 5971 6.788243 ACACGAGTAAACCCAAAGTAAAAAG 58.212 36.000 0.00 0.00 0.00 2.27
1959 5972 6.375174 ACACGAGTAAACCCAAAGTAAAAAGT 59.625 34.615 0.00 0.00 0.00 2.66
1960 5973 6.689669 CACGAGTAAACCCAAAGTAAAAAGTG 59.310 38.462 0.00 0.00 0.00 3.16
1962 5975 6.459161 CGAGTAAACCCAAAGTAAAAAGTGCT 60.459 38.462 0.00 0.00 0.00 4.40
1963 5976 7.254863 CGAGTAAACCCAAAGTAAAAAGTGCTA 60.255 37.037 0.00 0.00 0.00 3.49
1964 5977 7.709947 AGTAAACCCAAAGTAAAAAGTGCTAC 58.290 34.615 0.00 0.00 0.00 3.58
1965 5978 6.532988 AAACCCAAAGTAAAAAGTGCTACA 57.467 33.333 0.00 0.00 0.00 2.74
1966 5979 5.509716 ACCCAAAGTAAAAAGTGCTACAC 57.490 39.130 0.00 0.00 34.10 2.90
1969 5982 7.002276 ACCCAAAGTAAAAAGTGCTACACTAT 58.998 34.615 0.00 0.00 44.62 2.12
1970 5983 7.504574 ACCCAAAGTAAAAAGTGCTACACTATT 59.495 33.333 0.00 2.82 44.62 1.73
1971 5984 8.021396 CCCAAAGTAAAAAGTGCTACACTATTC 58.979 37.037 0.00 0.00 44.62 1.75
1972 5985 7.744715 CCAAAGTAAAAAGTGCTACACTATTCG 59.255 37.037 0.00 0.00 44.62 3.34
1978 5992 3.670625 AGTGCTACACTATTCGCCAAAA 58.329 40.909 0.00 0.00 43.46 2.44
1979 5993 4.069304 AGTGCTACACTATTCGCCAAAAA 58.931 39.130 0.00 0.00 43.46 1.94
2031 6045 3.750501 TCTGATGTACTACTCACCCCA 57.249 47.619 0.00 0.00 0.00 4.96
2034 6048 4.079154 TCTGATGTACTACTCACCCCATCT 60.079 45.833 0.00 0.00 32.07 2.90
2041 6055 6.493802 TGTACTACTCACCCCATCTCATAATC 59.506 42.308 0.00 0.00 0.00 1.75
2054 6068 7.872993 CCCATCTCATAATCTAAGAGCGTTTTA 59.127 37.037 0.00 0.00 0.00 1.52
2065 6079 9.865321 ATCTAAGAGCGTTTTATACACTAACAA 57.135 29.630 0.00 0.00 0.00 2.83
2066 6080 9.350357 TCTAAGAGCGTTTTATACACTAACAAG 57.650 33.333 0.00 0.00 0.00 3.16
2067 6081 9.350357 CTAAGAGCGTTTTATACACTAACAAGA 57.650 33.333 0.00 0.00 0.00 3.02
2068 6082 8.773404 AAGAGCGTTTTATACACTAACAAGAT 57.227 30.769 0.00 0.00 0.00 2.40
2069 6083 8.773404 AGAGCGTTTTATACACTAACAAGATT 57.227 30.769 0.00 0.00 0.00 2.40
2070 6084 9.865321 AGAGCGTTTTATACACTAACAAGATTA 57.135 29.630 0.00 0.00 0.00 1.75
2071 6085 9.897349 GAGCGTTTTATACACTAACAAGATTAC 57.103 33.333 0.00 0.00 0.00 1.89
2072 6086 9.426837 AGCGTTTTATACACTAACAAGATTACA 57.573 29.630 0.00 0.00 0.00 2.41
2073 6087 9.685005 GCGTTTTATACACTAACAAGATTACAG 57.315 33.333 0.00 0.00 0.00 2.74
2080 6094 9.944376 ATACACTAACAAGATTACAGTGACATT 57.056 29.630 7.01 0.00 39.13 2.71
2081 6095 8.677148 ACACTAACAAGATTACAGTGACATTT 57.323 30.769 7.01 0.00 39.13 2.32
2082 6096 9.772973 ACACTAACAAGATTACAGTGACATTTA 57.227 29.630 7.01 0.00 39.13 1.40
2087 6101 9.730420 AACAAGATTACAGTGACATTTAAACAC 57.270 29.630 0.00 0.00 35.15 3.32
2088 6102 9.120538 ACAAGATTACAGTGACATTTAAACACT 57.879 29.630 0.00 4.55 44.15 3.55
2089 6103 9.950680 CAAGATTACAGTGACATTTAAACACTT 57.049 29.630 7.10 3.63 41.93 3.16
2096 6110 9.609346 ACAGTGACATTTAAACACTTAACTAGT 57.391 29.630 7.10 0.00 41.93 2.57
2102 6116 9.716531 ACATTTAAACACTTAACTAGTACTCCC 57.283 33.333 0.00 0.00 34.56 4.30
2103 6117 9.939802 CATTTAAACACTTAACTAGTACTCCCT 57.060 33.333 0.00 0.00 34.56 4.20
2105 6119 6.602410 AAACACTTAACTAGTACTCCCTCC 57.398 41.667 0.00 0.00 34.56 4.30
2106 6120 4.268359 ACACTTAACTAGTACTCCCTCCG 58.732 47.826 0.00 0.00 34.56 4.63
2107 6121 4.263683 ACACTTAACTAGTACTCCCTCCGT 60.264 45.833 0.00 0.00 34.56 4.69
2108 6122 4.096081 CACTTAACTAGTACTCCCTCCGTG 59.904 50.000 0.00 0.00 34.56 4.94
2109 6123 1.472188 AACTAGTACTCCCTCCGTGC 58.528 55.000 0.00 0.00 0.00 5.34
2110 6124 0.395448 ACTAGTACTCCCTCCGTGCC 60.395 60.000 0.00 0.00 0.00 5.01
2111 6125 1.445716 CTAGTACTCCCTCCGTGCCG 61.446 65.000 0.00 0.00 0.00 5.69
2112 6126 1.913951 TAGTACTCCCTCCGTGCCGA 61.914 60.000 0.00 0.00 0.00 5.54
2113 6127 2.125961 GTACTCCCTCCGTGCCGAT 61.126 63.158 0.00 0.00 0.00 4.18
2114 6128 1.380785 TACTCCCTCCGTGCCGATT 60.381 57.895 0.00 0.00 0.00 3.34
2115 6129 0.974010 TACTCCCTCCGTGCCGATTT 60.974 55.000 0.00 0.00 0.00 2.17
2116 6130 0.974010 ACTCCCTCCGTGCCGATTTA 60.974 55.000 0.00 0.00 0.00 1.40
2117 6131 0.249489 CTCCCTCCGTGCCGATTTAG 60.249 60.000 0.00 0.00 0.00 1.85
2118 6132 0.974010 TCCCTCCGTGCCGATTTAGT 60.974 55.000 0.00 0.00 0.00 2.24
2119 6133 0.529992 CCCTCCGTGCCGATTTAGTC 60.530 60.000 0.00 0.00 0.00 2.59
2127 6141 4.527366 CGATTTAGTCGTTGCGCG 57.473 55.556 0.00 0.00 45.19 6.86
2128 6142 1.700029 CGATTTAGTCGTTGCGCGT 59.300 52.632 8.43 0.00 45.19 6.01
2129 6143 0.580676 CGATTTAGTCGTTGCGCGTG 60.581 55.000 8.43 0.00 45.19 5.34
2130 6144 0.852007 GATTTAGTCGTTGCGCGTGC 60.852 55.000 15.48 15.48 42.13 5.34
2131 6145 1.289109 ATTTAGTCGTTGCGCGTGCT 61.289 50.000 23.16 2.60 43.34 4.40
2132 6146 2.153219 TTTAGTCGTTGCGCGTGCTG 62.153 55.000 23.16 12.00 43.34 4.41
2133 6147 3.834447 TAGTCGTTGCGCGTGCTGT 62.834 57.895 23.16 2.74 43.34 4.40
2134 6148 2.460837 TAGTCGTTGCGCGTGCTGTA 62.461 55.000 23.16 4.66 43.34 2.74
2135 6149 3.399770 TCGTTGCGCGTGCTGTAC 61.400 61.111 23.16 15.54 43.34 2.90
2136 6150 3.697444 CGTTGCGCGTGCTGTACA 61.697 61.111 23.16 0.00 43.34 2.90
2137 6151 2.860293 GTTGCGCGTGCTGTACAT 59.140 55.556 23.16 0.00 43.34 2.29
2138 6152 1.206578 GTTGCGCGTGCTGTACATT 59.793 52.632 23.16 0.00 43.34 2.71
2139 6153 0.440758 GTTGCGCGTGCTGTACATTA 59.559 50.000 23.16 0.00 43.34 1.90
2140 6154 1.062002 GTTGCGCGTGCTGTACATTAT 59.938 47.619 23.16 0.00 43.34 1.28
2141 6155 0.649993 TGCGCGTGCTGTACATTATG 59.350 50.000 23.16 0.00 43.34 1.90
2142 6156 0.654472 GCGCGTGCTGTACATTATGC 60.654 55.000 15.02 11.63 38.39 3.14
2143 6157 0.649993 CGCGTGCTGTACATTATGCA 59.350 50.000 18.24 12.29 0.00 3.96
2144 6158 1.261354 CGCGTGCTGTACATTATGCAT 59.739 47.619 18.24 3.79 37.76 3.96
2145 6159 2.286359 CGCGTGCTGTACATTATGCATT 60.286 45.455 3.54 0.00 37.76 3.56
2146 6160 3.694734 GCGTGCTGTACATTATGCATTT 58.305 40.909 3.54 0.00 37.76 2.32
2147 6161 4.104776 GCGTGCTGTACATTATGCATTTT 58.895 39.130 3.54 0.00 37.76 1.82
2148 6162 4.027458 GCGTGCTGTACATTATGCATTTTG 60.027 41.667 3.54 5.73 37.76 2.44
2149 6163 4.027458 CGTGCTGTACATTATGCATTTTGC 60.027 41.667 3.54 0.19 45.29 3.68
2160 6174 1.851658 GCATTTTGCAAACACGTCCT 58.148 45.000 12.39 0.00 44.26 3.85
2161 6175 1.522258 GCATTTTGCAAACACGTCCTG 59.478 47.619 12.39 2.65 44.26 3.86
2162 6176 2.797792 GCATTTTGCAAACACGTCCTGA 60.798 45.455 12.39 0.00 44.26 3.86
2163 6177 3.641648 CATTTTGCAAACACGTCCTGAT 58.358 40.909 12.39 0.00 0.00 2.90
2164 6178 4.793071 CATTTTGCAAACACGTCCTGATA 58.207 39.130 12.39 0.00 0.00 2.15
2165 6179 3.889196 TTTGCAAACACGTCCTGATAC 57.111 42.857 8.05 0.00 0.00 2.24
2166 6180 2.831685 TGCAAACACGTCCTGATACT 57.168 45.000 0.00 0.00 0.00 2.12
2167 6181 3.120321 TGCAAACACGTCCTGATACTT 57.880 42.857 0.00 0.00 0.00 2.24
2168 6182 3.472652 TGCAAACACGTCCTGATACTTT 58.527 40.909 0.00 0.00 0.00 2.66
2169 6183 3.880490 TGCAAACACGTCCTGATACTTTT 59.120 39.130 0.00 0.00 0.00 2.27
2170 6184 5.057819 TGCAAACACGTCCTGATACTTTTA 58.942 37.500 0.00 0.00 0.00 1.52
2171 6185 5.527951 TGCAAACACGTCCTGATACTTTTAA 59.472 36.000 0.00 0.00 0.00 1.52
2172 6186 6.038382 TGCAAACACGTCCTGATACTTTTAAA 59.962 34.615 0.00 0.00 0.00 1.52
2173 6187 7.081976 GCAAACACGTCCTGATACTTTTAAAT 58.918 34.615 0.00 0.00 0.00 1.40
2174 6188 7.270579 GCAAACACGTCCTGATACTTTTAAATC 59.729 37.037 0.00 0.00 0.00 2.17
2175 6189 7.972832 AACACGTCCTGATACTTTTAAATCA 57.027 32.000 0.00 0.00 0.00 2.57
2176 6190 8.561738 AACACGTCCTGATACTTTTAAATCAT 57.438 30.769 0.00 0.00 31.95 2.45
2177 6191 8.561738 ACACGTCCTGATACTTTTAAATCATT 57.438 30.769 0.00 0.00 31.95 2.57
2178 6192 9.010029 ACACGTCCTGATACTTTTAAATCATTT 57.990 29.630 0.00 0.00 31.95 2.32
2179 6193 9.277565 CACGTCCTGATACTTTTAAATCATTTG 57.722 33.333 0.00 0.00 31.95 2.32
2180 6194 9.226606 ACGTCCTGATACTTTTAAATCATTTGA 57.773 29.630 0.00 0.00 31.95 2.69
2203 6217 2.756283 CGCCCTCGTCTCCTTCCT 60.756 66.667 0.00 0.00 0.00 3.36
2204 6218 2.776913 CGCCCTCGTCTCCTTCCTC 61.777 68.421 0.00 0.00 0.00 3.71
2205 6219 1.682684 GCCCTCGTCTCCTTCCTCA 60.683 63.158 0.00 0.00 0.00 3.86
2206 6220 1.671901 GCCCTCGTCTCCTTCCTCAG 61.672 65.000 0.00 0.00 0.00 3.35
2207 6221 0.323908 CCCTCGTCTCCTTCCTCAGT 60.324 60.000 0.00 0.00 0.00 3.41
2208 6222 1.551452 CCTCGTCTCCTTCCTCAGTT 58.449 55.000 0.00 0.00 0.00 3.16
2209 6223 1.474879 CCTCGTCTCCTTCCTCAGTTC 59.525 57.143 0.00 0.00 0.00 3.01
2210 6224 2.442413 CTCGTCTCCTTCCTCAGTTCT 58.558 52.381 0.00 0.00 0.00 3.01
2211 6225 2.422127 CTCGTCTCCTTCCTCAGTTCTC 59.578 54.545 0.00 0.00 0.00 2.87
2212 6226 1.474879 CGTCTCCTTCCTCAGTTCTCC 59.525 57.143 0.00 0.00 0.00 3.71
2213 6227 2.530701 GTCTCCTTCCTCAGTTCTCCA 58.469 52.381 0.00 0.00 0.00 3.86
2214 6228 2.232696 GTCTCCTTCCTCAGTTCTCCAC 59.767 54.545 0.00 0.00 0.00 4.02
2215 6229 1.552792 CTCCTTCCTCAGTTCTCCACC 59.447 57.143 0.00 0.00 0.00 4.61
2216 6230 0.247736 CCTTCCTCAGTTCTCCACCG 59.752 60.000 0.00 0.00 0.00 4.94
2217 6231 0.969894 CTTCCTCAGTTCTCCACCGT 59.030 55.000 0.00 0.00 0.00 4.83
2218 6232 0.966920 TTCCTCAGTTCTCCACCGTC 59.033 55.000 0.00 0.00 0.00 4.79
2219 6233 1.213013 CCTCAGTTCTCCACCGTCG 59.787 63.158 0.00 0.00 0.00 5.12
2220 6234 1.444553 CTCAGTTCTCCACCGTCGC 60.445 63.158 0.00 0.00 0.00 5.19
2221 6235 1.867919 CTCAGTTCTCCACCGTCGCT 61.868 60.000 0.00 0.00 0.00 4.93
2222 6236 1.444553 CAGTTCTCCACCGTCGCTC 60.445 63.158 0.00 0.00 0.00 5.03
2223 6237 2.504244 GTTCTCCACCGTCGCTCG 60.504 66.667 0.00 0.00 39.52 5.03
2224 6238 4.415332 TTCTCCACCGTCGCTCGC 62.415 66.667 0.00 0.00 38.35 5.03
2250 6264 4.815108 GGTTCCGGCCACCATCCC 62.815 72.222 15.87 0.00 34.04 3.85
2251 6265 4.815108 GTTCCGGCCACCATCCCC 62.815 72.222 2.24 0.00 0.00 4.81
2255 6269 4.489771 CGGCCACCATCCCCTGTC 62.490 72.222 2.24 0.00 0.00 3.51
2256 6270 3.017581 GGCCACCATCCCCTGTCT 61.018 66.667 0.00 0.00 0.00 3.41
2257 6271 2.616458 GGCCACCATCCCCTGTCTT 61.616 63.158 0.00 0.00 0.00 3.01
2258 6272 1.077429 GCCACCATCCCCTGTCTTC 60.077 63.158 0.00 0.00 0.00 2.87
2259 6273 1.609783 CCACCATCCCCTGTCTTCC 59.390 63.158 0.00 0.00 0.00 3.46
2260 6274 0.916358 CCACCATCCCCTGTCTTCCT 60.916 60.000 0.00 0.00 0.00 3.36
2261 6275 0.543749 CACCATCCCCTGTCTTCCTC 59.456 60.000 0.00 0.00 0.00 3.71
2262 6276 0.621862 ACCATCCCCTGTCTTCCTCC 60.622 60.000 0.00 0.00 0.00 4.30
2263 6277 1.348775 CCATCCCCTGTCTTCCTCCC 61.349 65.000 0.00 0.00 0.00 4.30
2264 6278 1.004891 ATCCCCTGTCTTCCTCCCC 59.995 63.158 0.00 0.00 0.00 4.81
2265 6279 2.569373 ATCCCCTGTCTTCCTCCCCC 62.569 65.000 0.00 0.00 0.00 5.40
2266 6280 3.083997 CCCTGTCTTCCTCCCCCG 61.084 72.222 0.00 0.00 0.00 5.73
2267 6281 2.284699 CCTGTCTTCCTCCCCCGT 60.285 66.667 0.00 0.00 0.00 5.28
2268 6282 2.359967 CCTGTCTTCCTCCCCCGTC 61.360 68.421 0.00 0.00 0.00 4.79
2269 6283 2.284405 TGTCTTCCTCCCCCGTCC 60.284 66.667 0.00 0.00 0.00 4.79
2270 6284 3.082055 GTCTTCCTCCCCCGTCCC 61.082 72.222 0.00 0.00 0.00 4.46
2271 6285 4.410033 TCTTCCTCCCCCGTCCCC 62.410 72.222 0.00 0.00 0.00 4.81
2281 6295 2.043652 CCGTCCCCCGTTCTCCTA 60.044 66.667 0.00 0.00 33.66 2.94
2282 6296 1.683365 CCGTCCCCCGTTCTCCTAA 60.683 63.158 0.00 0.00 33.66 2.69
2283 6297 1.673808 CCGTCCCCCGTTCTCCTAAG 61.674 65.000 0.00 0.00 33.66 2.18
2284 6298 1.521141 GTCCCCCGTTCTCCTAAGC 59.479 63.158 0.00 0.00 0.00 3.09
2285 6299 1.079621 TCCCCCGTTCTCCTAAGCA 59.920 57.895 0.00 0.00 0.00 3.91
2286 6300 1.221021 CCCCCGTTCTCCTAAGCAC 59.779 63.158 0.00 0.00 0.00 4.40
2287 6301 1.221021 CCCCGTTCTCCTAAGCACC 59.779 63.158 0.00 0.00 0.00 5.01
2288 6302 1.221021 CCCGTTCTCCTAAGCACCC 59.779 63.158 0.00 0.00 0.00 4.61
2289 6303 1.550130 CCCGTTCTCCTAAGCACCCA 61.550 60.000 0.00 0.00 0.00 4.51
2290 6304 0.108138 CCGTTCTCCTAAGCACCCAG 60.108 60.000 0.00 0.00 0.00 4.45
2291 6305 0.741221 CGTTCTCCTAAGCACCCAGC 60.741 60.000 0.00 0.00 46.19 4.85
2301 6315 3.696306 GCACCCAGCTAGAATCTCC 57.304 57.895 0.00 0.00 41.15 3.71
2302 6316 0.249657 GCACCCAGCTAGAATCTCCG 60.250 60.000 0.00 0.00 41.15 4.63
2303 6317 0.249657 CACCCAGCTAGAATCTCCGC 60.250 60.000 0.00 0.00 0.00 5.54
2304 6318 1.006805 CCCAGCTAGAATCTCCGCG 60.007 63.158 0.00 0.00 0.00 6.46
2305 6319 1.663074 CCAGCTAGAATCTCCGCGC 60.663 63.158 0.00 0.00 0.00 6.86
2306 6320 1.361993 CAGCTAGAATCTCCGCGCT 59.638 57.895 5.56 0.00 0.00 5.92
2307 6321 0.249238 CAGCTAGAATCTCCGCGCTT 60.249 55.000 5.56 0.00 0.00 4.68
2308 6322 0.031449 AGCTAGAATCTCCGCGCTTC 59.969 55.000 5.56 1.38 0.00 3.86
2309 6323 0.249073 GCTAGAATCTCCGCGCTTCA 60.249 55.000 5.56 0.00 0.00 3.02
2310 6324 1.482278 CTAGAATCTCCGCGCTTCAC 58.518 55.000 5.56 0.00 0.00 3.18
2322 6336 4.760047 CTTCACGGGACCCAGCCG 62.760 72.222 12.15 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
418 430 2.622436 GACTGAAGCTAATTGGCTCGT 58.378 47.619 17.36 13.80 42.24 4.18
441 453 3.625897 CTGTCGGCCCACTGTGGA 61.626 66.667 27.94 5.03 40.96 4.02
517 530 1.033746 ACAGCAGGCCGATTGGATTG 61.034 55.000 1.98 0.75 37.49 2.67
644 723 5.590663 AGAACGACATCATCACTCTAGCTTA 59.409 40.000 0.00 0.00 0.00 3.09
662 741 1.614241 GGCCCTGCCTTCTAGAACGA 61.614 60.000 0.00 0.00 46.69 3.85
825 912 1.353022 GGTTTGGATGTAGGTGGTGGA 59.647 52.381 0.00 0.00 0.00 4.02
828 915 3.458487 GGATAGGTTTGGATGTAGGTGGT 59.542 47.826 0.00 0.00 0.00 4.16
852 940 1.807981 CCATGCATGCCAGCGTTTG 60.808 57.895 21.69 0.10 37.31 2.93
870 958 4.943705 TGAAGCTTGTGATTATGAAGGGTC 59.056 41.667 2.10 0.00 0.00 4.46
912 1000 1.376037 GGGAGTTGAGCACTTCGGG 60.376 63.158 0.00 0.00 35.01 5.14
913 1001 0.671781 CTGGGAGTTGAGCACTTCGG 60.672 60.000 0.00 0.00 35.01 4.30
914 1002 1.294659 GCTGGGAGTTGAGCACTTCG 61.295 60.000 0.00 0.00 35.01 3.79
921 1009 0.108898 CGAGTGAGCTGGGAGTTGAG 60.109 60.000 0.00 0.00 0.00 3.02
949 1037 1.684734 TCGGGGTAGAGTTGGGAGC 60.685 63.158 0.00 0.00 0.00 4.70
1334 1422 2.496942 CCATGGCTTGGTGGATCAC 58.503 57.895 11.13 0.00 40.99 3.06
1352 1440 1.734465 GAGCGATGCTATTGCCCATAC 59.266 52.381 0.00 0.00 39.88 2.39
1354 1442 0.607489 GGAGCGATGCTATTGCCCAT 60.607 55.000 0.00 0.00 39.88 4.00
1356 1444 1.968540 GGGAGCGATGCTATTGCCC 60.969 63.158 0.00 0.00 39.88 5.36
1357 1445 1.227943 TGGGAGCGATGCTATTGCC 60.228 57.895 0.00 0.00 39.88 4.52
1358 1446 1.233285 CCTGGGAGCGATGCTATTGC 61.233 60.000 0.00 0.00 39.88 3.56
1359 1447 0.394192 TCCTGGGAGCGATGCTATTG 59.606 55.000 0.00 0.00 39.88 1.90
1361 1449 0.683973 CTTCCTGGGAGCGATGCTAT 59.316 55.000 0.00 0.00 39.88 2.97
1363 1451 1.965754 GACTTCCTGGGAGCGATGCT 61.966 60.000 0.58 0.00 43.88 3.79
1364 1452 1.522580 GACTTCCTGGGAGCGATGC 60.523 63.158 0.58 0.00 0.00 3.91
1365 1453 0.179089 CTGACTTCCTGGGAGCGATG 60.179 60.000 0.58 0.00 0.00 3.84
1366 1454 1.333636 CCTGACTTCCTGGGAGCGAT 61.334 60.000 0.58 0.00 0.00 4.58
1367 1455 1.984570 CCTGACTTCCTGGGAGCGA 60.985 63.158 0.58 0.00 0.00 4.93
1368 1456 1.544825 TTCCTGACTTCCTGGGAGCG 61.545 60.000 0.58 0.00 34.88 5.03
1369 1457 0.035915 GTTCCTGACTTCCTGGGAGC 60.036 60.000 0.58 0.00 34.88 4.70
1370 1458 0.247736 CGTTCCTGACTTCCTGGGAG 59.752 60.000 0.00 0.00 34.88 4.30
1371 1459 0.471211 ACGTTCCTGACTTCCTGGGA 60.471 55.000 0.00 0.00 34.88 4.37
1372 1460 0.320771 CACGTTCCTGACTTCCTGGG 60.321 60.000 0.00 0.00 34.88 4.45
1373 1461 0.320771 CCACGTTCCTGACTTCCTGG 60.321 60.000 0.00 0.00 35.40 4.45
1374 1462 0.679505 TCCACGTTCCTGACTTCCTG 59.320 55.000 0.00 0.00 0.00 3.86
1375 1463 1.276421 CATCCACGTTCCTGACTTCCT 59.724 52.381 0.00 0.00 0.00 3.36
1376 1464 1.275291 TCATCCACGTTCCTGACTTCC 59.725 52.381 0.00 0.00 0.00 3.46
1377 1465 2.611518 CTCATCCACGTTCCTGACTTC 58.388 52.381 0.00 0.00 0.00 3.01
1378 1466 1.338200 GCTCATCCACGTTCCTGACTT 60.338 52.381 0.00 0.00 0.00 3.01
1379 1467 0.247736 GCTCATCCACGTTCCTGACT 59.752 55.000 0.00 0.00 0.00 3.41
1380 1468 0.247736 AGCTCATCCACGTTCCTGAC 59.752 55.000 0.00 0.00 0.00 3.51
1381 1469 0.247460 CAGCTCATCCACGTTCCTGA 59.753 55.000 0.00 0.00 0.00 3.86
1384 1472 0.955428 TTGCAGCTCATCCACGTTCC 60.955 55.000 0.00 0.00 0.00 3.62
1399 1487 3.215568 CCAACACAGGCCGTTGCA 61.216 61.111 14.55 0.00 41.94 4.08
1400 1488 3.216292 ACCAACACAGGCCGTTGC 61.216 61.111 14.55 0.00 41.94 4.17
1401 1489 2.058829 GACACCAACACAGGCCGTTG 62.059 60.000 13.38 13.38 42.73 4.10
1402 1490 1.822186 GACACCAACACAGGCCGTT 60.822 57.895 0.00 0.00 0.00 4.44
1403 1491 2.203153 GACACCAACACAGGCCGT 60.203 61.111 0.00 0.00 0.00 5.68
1404 1492 2.978010 GGACACCAACACAGGCCG 60.978 66.667 0.00 0.00 0.00 6.13
1405 1493 1.600916 GAGGACACCAACACAGGCC 60.601 63.158 0.00 0.00 0.00 5.19
1406 1494 1.961277 CGAGGACACCAACACAGGC 60.961 63.158 0.00 0.00 0.00 4.85
1407 1495 1.301716 CCGAGGACACCAACACAGG 60.302 63.158 0.00 0.00 0.00 4.00
1408 1496 1.961277 GCCGAGGACACCAACACAG 60.961 63.158 0.00 0.00 0.00 3.66
1440 1538 3.904339 ACATCACAACCTCTCCACTAACT 59.096 43.478 0.00 0.00 0.00 2.24
1450 1548 0.400213 TGGACCCACATCACAACCTC 59.600 55.000 0.00 0.00 0.00 3.85
1459 1557 4.082523 CGACGGCTGGACCCACAT 62.083 66.667 0.00 0.00 33.26 3.21
1624 3572 2.971915 CGTATGTCTATTTCGAGTCCGC 59.028 50.000 0.00 0.00 35.37 5.54
1626 3574 3.975670 CAGCGTATGTCTATTTCGAGTCC 59.024 47.826 0.00 0.00 0.00 3.85
1714 3663 5.882557 CCTGTTAAAATGTAGCATGGTCTCT 59.117 40.000 0.00 0.00 0.00 3.10
1756 3705 4.385825 GTGAAATGGAAAGAAAAACCCCC 58.614 43.478 0.00 0.00 0.00 5.40
1757 3706 4.055360 CGTGAAATGGAAAGAAAAACCCC 58.945 43.478 0.00 0.00 0.00 4.95
1758 3707 4.689071 ACGTGAAATGGAAAGAAAAACCC 58.311 39.130 0.00 0.00 0.00 4.11
1759 3708 6.731164 TCTACGTGAAATGGAAAGAAAAACC 58.269 36.000 0.00 0.00 0.00 3.27
1761 3710 7.562454 ACTCTACGTGAAATGGAAAGAAAAA 57.438 32.000 0.00 0.00 0.00 1.94
1778 3749 6.183360 TGGAAATCTGTATCCTGAACTCTACG 60.183 42.308 0.00 0.00 36.64 3.51
1832 5840 7.130099 TCCTGATAAGGGAGTACTATCACAAA 58.870 38.462 0.00 0.00 0.00 2.83
1852 5860 5.127845 CAGAAGGCTTATCAGTTACTCCTGA 59.872 44.000 0.00 0.00 45.06 3.86
1853 5861 5.105146 ACAGAAGGCTTATCAGTTACTCCTG 60.105 44.000 0.00 1.06 0.00 3.86
1854 5862 5.026790 ACAGAAGGCTTATCAGTTACTCCT 58.973 41.667 0.00 0.00 0.00 3.69
1855 5863 5.112686 CACAGAAGGCTTATCAGTTACTCC 58.887 45.833 0.00 0.00 0.00 3.85
1856 5864 5.725362 ACACAGAAGGCTTATCAGTTACTC 58.275 41.667 0.00 0.00 0.00 2.59
1859 5867 6.360370 AAGACACAGAAGGCTTATCAGTTA 57.640 37.500 0.00 0.00 0.00 2.24
1895 5903 6.462487 CCTTATTGACACGGAAGGCTTATCTA 60.462 42.308 0.00 0.00 32.54 1.98
1896 5904 3.914426 ATTGACACGGAAGGCTTATCT 57.086 42.857 0.00 0.00 0.00 1.98
1897 5905 4.511826 CCTTATTGACACGGAAGGCTTATC 59.488 45.833 0.00 0.00 32.54 1.75
1898 5906 4.163458 TCCTTATTGACACGGAAGGCTTAT 59.837 41.667 0.00 0.00 38.69 1.73
1899 5907 3.516300 TCCTTATTGACACGGAAGGCTTA 59.484 43.478 0.00 0.00 38.69 3.09
1900 5908 2.304761 TCCTTATTGACACGGAAGGCTT 59.695 45.455 0.00 0.00 38.69 4.35
1901 5909 1.906574 TCCTTATTGACACGGAAGGCT 59.093 47.619 4.86 0.00 38.69 4.58
1903 5911 3.877508 GGAATCCTTATTGACACGGAAGG 59.122 47.826 0.00 3.69 39.94 3.46
1904 5912 4.572389 CAGGAATCCTTATTGACACGGAAG 59.428 45.833 0.00 0.00 0.00 3.46
1907 5915 4.137116 TCAGGAATCCTTATTGACACGG 57.863 45.455 0.00 0.00 0.00 4.94
1909 5917 6.122277 TGGAATCAGGAATCCTTATTGACAC 58.878 40.000 13.00 0.00 36.64 3.67
1910 5918 6.325993 TGGAATCAGGAATCCTTATTGACA 57.674 37.500 13.00 9.12 36.64 3.58
1912 5920 6.603201 GTGTTGGAATCAGGAATCCTTATTGA 59.397 38.462 13.00 2.50 36.64 2.57
1914 5922 5.590259 CGTGTTGGAATCAGGAATCCTTATT 59.410 40.000 8.35 8.35 36.64 1.40
1916 5924 4.224147 TCGTGTTGGAATCAGGAATCCTTA 59.776 41.667 0.00 0.00 36.64 2.69
1931 5944 2.946990 ACTTTGGGTTTACTCGTGTTGG 59.053 45.455 0.00 0.00 0.00 3.77
1939 5952 6.785337 AGCACTTTTTACTTTGGGTTTACT 57.215 33.333 0.00 0.00 0.00 2.24
1941 5954 7.339976 AGTGTAGCACTTTTTACTTTGGGTTTA 59.660 33.333 0.00 0.00 42.59 2.01
1945 5958 5.767816 AGTGTAGCACTTTTTACTTTGGG 57.232 39.130 0.00 0.00 42.59 4.12
1958 5971 4.413495 TTTTTGGCGAATAGTGTAGCAC 57.587 40.909 0.00 0.00 34.10 4.40
2041 6055 9.350357 TCTTGTTAGTGTATAAAACGCTCTTAG 57.650 33.333 0.00 0.00 46.05 2.18
2054 6068 9.944376 AATGTCACTGTAATCTTGTTAGTGTAT 57.056 29.630 0.00 0.00 39.66 2.29
2070 6084 9.609346 ACTAGTTAAGTGTTTAAATGTCACTGT 57.391 29.630 9.87 1.99 41.37 3.55
2076 6090 9.716531 GGGAGTACTAGTTAAGTGTTTAAATGT 57.283 33.333 0.00 0.00 39.39 2.71
2077 6091 9.939802 AGGGAGTACTAGTTAAGTGTTTAAATG 57.060 33.333 0.00 0.00 39.39 2.32
2079 6093 8.588472 GGAGGGAGTACTAGTTAAGTGTTTAAA 58.412 37.037 0.00 0.00 39.39 1.52
2080 6094 7.094205 CGGAGGGAGTACTAGTTAAGTGTTTAA 60.094 40.741 0.00 0.00 39.39 1.52
2081 6095 6.375455 CGGAGGGAGTACTAGTTAAGTGTTTA 59.625 42.308 0.00 0.00 39.39 2.01
2082 6096 5.184671 CGGAGGGAGTACTAGTTAAGTGTTT 59.815 44.000 0.00 0.00 39.39 2.83
2083 6097 4.704057 CGGAGGGAGTACTAGTTAAGTGTT 59.296 45.833 0.00 0.00 39.39 3.32
2084 6098 4.263683 ACGGAGGGAGTACTAGTTAAGTGT 60.264 45.833 0.00 0.00 39.39 3.55
2085 6099 4.096081 CACGGAGGGAGTACTAGTTAAGTG 59.904 50.000 0.00 0.00 39.39 3.16
2086 6100 4.268359 CACGGAGGGAGTACTAGTTAAGT 58.732 47.826 0.00 0.00 42.62 2.24
2087 6101 3.066481 GCACGGAGGGAGTACTAGTTAAG 59.934 52.174 0.00 0.00 0.00 1.85
2088 6102 3.019564 GCACGGAGGGAGTACTAGTTAA 58.980 50.000 0.00 0.00 0.00 2.01
2089 6103 2.648059 GCACGGAGGGAGTACTAGTTA 58.352 52.381 0.00 0.00 0.00 2.24
2090 6104 1.472188 GCACGGAGGGAGTACTAGTT 58.528 55.000 0.00 0.00 0.00 2.24
2091 6105 0.395448 GGCACGGAGGGAGTACTAGT 60.395 60.000 0.00 0.00 0.00 2.57
2092 6106 2.416901 GGCACGGAGGGAGTACTAG 58.583 63.158 0.00 0.00 0.00 2.57
2093 6107 4.672251 GGCACGGAGGGAGTACTA 57.328 61.111 0.00 0.00 0.00 1.82
2120 6134 0.440758 TAATGTACAGCACGCGCAAC 59.559 50.000 5.73 0.00 42.27 4.17
2121 6135 1.061857 CATAATGTACAGCACGCGCAA 59.938 47.619 5.73 0.00 42.27 4.85
2122 6136 0.649993 CATAATGTACAGCACGCGCA 59.350 50.000 5.73 0.00 42.27 6.09
2123 6137 0.654472 GCATAATGTACAGCACGCGC 60.654 55.000 5.73 0.00 38.99 6.86
2124 6138 0.649993 TGCATAATGTACAGCACGCG 59.350 50.000 3.53 3.53 31.05 6.01
2125 6139 3.338818 AATGCATAATGTACAGCACGC 57.661 42.857 9.43 6.44 40.14 5.34
2126 6140 4.027458 GCAAAATGCATAATGTACAGCACG 60.027 41.667 9.43 1.65 44.26 5.34
2127 6141 5.379757 GCAAAATGCATAATGTACAGCAC 57.620 39.130 9.43 0.00 44.26 4.40
2141 6155 1.522258 CAGGACGTGTTTGCAAAATGC 59.478 47.619 14.67 5.49 45.29 3.56
2142 6156 3.077229 TCAGGACGTGTTTGCAAAATG 57.923 42.857 14.67 11.85 0.00 2.32
2143 6157 4.518970 AGTATCAGGACGTGTTTGCAAAAT 59.481 37.500 14.67 2.96 0.00 1.82
2144 6158 3.880490 AGTATCAGGACGTGTTTGCAAAA 59.120 39.130 14.67 1.61 0.00 2.44
2145 6159 3.472652 AGTATCAGGACGTGTTTGCAAA 58.527 40.909 8.05 8.05 0.00 3.68
2146 6160 3.120321 AGTATCAGGACGTGTTTGCAA 57.880 42.857 0.00 0.00 0.00 4.08
2147 6161 2.831685 AGTATCAGGACGTGTTTGCA 57.168 45.000 0.00 0.00 0.00 4.08
2148 6162 4.483476 AAAAGTATCAGGACGTGTTTGC 57.517 40.909 0.00 0.00 0.00 3.68
2149 6163 8.286800 TGATTTAAAAGTATCAGGACGTGTTTG 58.713 33.333 0.00 0.00 0.00 2.93
2150 6164 8.385898 TGATTTAAAAGTATCAGGACGTGTTT 57.614 30.769 0.00 0.00 0.00 2.83
2151 6165 7.972832 TGATTTAAAAGTATCAGGACGTGTT 57.027 32.000 0.00 0.00 0.00 3.32
2152 6166 8.561738 AATGATTTAAAAGTATCAGGACGTGT 57.438 30.769 0.00 0.00 34.52 4.49
2153 6167 9.277565 CAAATGATTTAAAAGTATCAGGACGTG 57.722 33.333 0.00 0.00 34.52 4.49
2154 6168 9.226606 TCAAATGATTTAAAAGTATCAGGACGT 57.773 29.630 0.00 0.00 34.52 4.34
2186 6200 2.756283 AGGAAGGAGACGAGGGCG 60.756 66.667 0.00 0.00 44.79 6.13
2187 6201 1.671901 CTGAGGAAGGAGACGAGGGC 61.672 65.000 0.00 0.00 0.00 5.19
2188 6202 0.323908 ACTGAGGAAGGAGACGAGGG 60.324 60.000 0.00 0.00 0.00 4.30
2189 6203 1.474879 GAACTGAGGAAGGAGACGAGG 59.525 57.143 0.00 0.00 0.00 4.63
2190 6204 2.422127 GAGAACTGAGGAAGGAGACGAG 59.578 54.545 0.00 0.00 0.00 4.18
2191 6205 2.438411 GAGAACTGAGGAAGGAGACGA 58.562 52.381 0.00 0.00 0.00 4.20
2192 6206 1.474879 GGAGAACTGAGGAAGGAGACG 59.525 57.143 0.00 0.00 0.00 4.18
2193 6207 2.232696 GTGGAGAACTGAGGAAGGAGAC 59.767 54.545 0.00 0.00 0.00 3.36
2194 6208 2.530701 GTGGAGAACTGAGGAAGGAGA 58.469 52.381 0.00 0.00 0.00 3.71
2195 6209 1.552792 GGTGGAGAACTGAGGAAGGAG 59.447 57.143 0.00 0.00 0.00 3.69
2196 6210 1.645710 GGTGGAGAACTGAGGAAGGA 58.354 55.000 0.00 0.00 0.00 3.36
2197 6211 0.247736 CGGTGGAGAACTGAGGAAGG 59.752 60.000 0.00 0.00 37.33 3.46
2198 6212 0.969894 ACGGTGGAGAACTGAGGAAG 59.030 55.000 0.00 0.00 38.65 3.46
2199 6213 0.966920 GACGGTGGAGAACTGAGGAA 59.033 55.000 0.00 0.00 38.65 3.36
2200 6214 1.241990 CGACGGTGGAGAACTGAGGA 61.242 60.000 0.00 0.00 38.65 3.71
2201 6215 1.213013 CGACGGTGGAGAACTGAGG 59.787 63.158 0.00 0.00 38.65 3.86
2202 6216 1.444553 GCGACGGTGGAGAACTGAG 60.445 63.158 0.00 0.00 38.65 3.35
2203 6217 1.863662 GAGCGACGGTGGAGAACTGA 61.864 60.000 3.31 0.00 38.65 3.41
2204 6218 1.444553 GAGCGACGGTGGAGAACTG 60.445 63.158 3.31 0.00 41.37 3.16
2205 6219 2.963371 GAGCGACGGTGGAGAACT 59.037 61.111 3.31 0.00 0.00 3.01
2206 6220 2.504244 CGAGCGACGGTGGAGAAC 60.504 66.667 3.31 0.00 38.46 3.01
2207 6221 4.415332 GCGAGCGACGGTGGAGAA 62.415 66.667 13.41 0.00 42.83 2.87
2233 6247 4.815108 GGGATGGTGGCCGGAACC 62.815 72.222 17.60 17.60 38.26 3.62
2234 6248 4.815108 GGGGATGGTGGCCGGAAC 62.815 72.222 5.05 1.43 0.00 3.62
2238 6252 4.489771 GACAGGGGATGGTGGCCG 62.490 72.222 0.00 0.00 0.00 6.13
2239 6253 2.558380 GAAGACAGGGGATGGTGGCC 62.558 65.000 0.00 0.00 0.00 5.36
2240 6254 1.077429 GAAGACAGGGGATGGTGGC 60.077 63.158 0.00 0.00 0.00 5.01
2241 6255 0.916358 AGGAAGACAGGGGATGGTGG 60.916 60.000 0.00 0.00 0.00 4.61
2242 6256 0.543749 GAGGAAGACAGGGGATGGTG 59.456 60.000 0.00 0.00 0.00 4.17
2243 6257 0.621862 GGAGGAAGACAGGGGATGGT 60.622 60.000 0.00 0.00 0.00 3.55
2244 6258 1.348775 GGGAGGAAGACAGGGGATGG 61.349 65.000 0.00 0.00 0.00 3.51
2245 6259 1.348775 GGGGAGGAAGACAGGGGATG 61.349 65.000 0.00 0.00 0.00 3.51
2246 6260 1.004891 GGGGAGGAAGACAGGGGAT 59.995 63.158 0.00 0.00 0.00 3.85
2247 6261 2.454941 GGGGAGGAAGACAGGGGA 59.545 66.667 0.00 0.00 0.00 4.81
2248 6262 2.692741 GGGGGAGGAAGACAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
2249 6263 3.083997 CGGGGGAGGAAGACAGGG 61.084 72.222 0.00 0.00 0.00 4.45
2250 6264 2.284699 ACGGGGGAGGAAGACAGG 60.285 66.667 0.00 0.00 0.00 4.00
2251 6265 2.359967 GGACGGGGGAGGAAGACAG 61.360 68.421 0.00 0.00 0.00 3.51
2252 6266 2.284405 GGACGGGGGAGGAAGACA 60.284 66.667 0.00 0.00 0.00 3.41
2253 6267 3.082055 GGGACGGGGGAGGAAGAC 61.082 72.222 0.00 0.00 0.00 3.01
2254 6268 4.410033 GGGGACGGGGGAGGAAGA 62.410 72.222 0.00 0.00 0.00 2.87
2266 6280 1.262640 TGCTTAGGAGAACGGGGGAC 61.263 60.000 0.00 0.00 0.00 4.46
2267 6281 1.079621 TGCTTAGGAGAACGGGGGA 59.920 57.895 0.00 0.00 0.00 4.81
2268 6282 1.221021 GTGCTTAGGAGAACGGGGG 59.779 63.158 0.00 0.00 0.00 5.40
2269 6283 1.221021 GGTGCTTAGGAGAACGGGG 59.779 63.158 0.00 0.00 31.55 5.73
2270 6284 1.221021 GGGTGCTTAGGAGAACGGG 59.779 63.158 0.00 0.00 31.55 5.28
2271 6285 0.108138 CTGGGTGCTTAGGAGAACGG 60.108 60.000 0.00 0.00 31.55 4.44
2272 6286 0.741221 GCTGGGTGCTTAGGAGAACG 60.741 60.000 0.00 0.00 38.95 3.95
2273 6287 3.160872 GCTGGGTGCTTAGGAGAAC 57.839 57.895 0.00 0.00 38.95 3.01
2283 6297 0.249657 CGGAGATTCTAGCTGGGTGC 60.250 60.000 0.00 0.00 43.29 5.01
2284 6298 0.249657 GCGGAGATTCTAGCTGGGTG 60.250 60.000 0.00 0.00 0.00 4.61
2285 6299 1.739338 CGCGGAGATTCTAGCTGGGT 61.739 60.000 0.00 0.00 0.00 4.51
2286 6300 1.006805 CGCGGAGATTCTAGCTGGG 60.007 63.158 0.00 0.00 0.00 4.45
2287 6301 1.663074 GCGCGGAGATTCTAGCTGG 60.663 63.158 8.83 0.00 0.00 4.85
2288 6302 0.249238 AAGCGCGGAGATTCTAGCTG 60.249 55.000 8.83 6.58 34.94 4.24
2289 6303 0.031449 GAAGCGCGGAGATTCTAGCT 59.969 55.000 8.83 0.00 41.70 3.32
2290 6304 0.249073 TGAAGCGCGGAGATTCTAGC 60.249 55.000 8.83 4.12 44.95 3.42
2291 6305 1.482278 GTGAAGCGCGGAGATTCTAG 58.518 55.000 8.83 0.00 44.95 2.43
2292 6306 0.248498 CGTGAAGCGCGGAGATTCTA 60.248 55.000 8.83 0.00 44.95 2.10
2293 6307 1.517257 CGTGAAGCGCGGAGATTCT 60.517 57.895 8.83 0.00 44.95 2.40
2294 6308 2.998667 CGTGAAGCGCGGAGATTC 59.001 61.111 8.83 2.68 44.93 2.52
2305 6319 4.760047 CGGCTGGGTCCCGTGAAG 62.760 72.222 2.65 0.00 40.84 3.02


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

AutoCloner maintained by Alex Coulton.