Multiple sequence alignment - TraesCS6B01G424700

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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 TraesCS6B01G424700 chr6B 100.000 4793 0 0 1 4793 694126161 694121369 0.000000e+00 8852.0
1 TraesCS6B01G424700 chr6D 87.236 2413 234 38 1816 4203 456462511 456460148 0.000000e+00 2682.0
2 TraesCS6B01G424700 chr6D 86.103 1396 142 27 434 1815 456463905 456462548 0.000000e+00 1456.0
3 TraesCS6B01G424700 chr6D 85.185 621 58 12 4189 4793 456460133 456459531 1.480000e-169 606.0
4 TraesCS6B01G424700 chr6A 93.828 1604 80 12 3201 4793 603189462 603187867 0.000000e+00 2396.0
5 TraesCS6B01G424700 chr6A 82.891 1882 204 70 2 1815 603192618 603190787 0.000000e+00 1583.0
6 TraesCS6B01G424700 chr6A 85.049 1331 113 35 1816 3106 603190750 603189466 0.000000e+00 1277.0
7 TraesCS6B01G424700 chr3B 89.074 421 17 9 3100 3503 1441637 1441229 3.330000e-136 496.0
8 TraesCS6B01G424700 chr3B 100.000 46 0 0 3025 3070 1441680 1441635 8.550000e-13 86.1
9 TraesCS6B01G424700 chr7A 87.263 369 42 5 292 660 598321994 598322357 2.670000e-112 416.0
10 TraesCS6B01G424700 chr7A 91.968 249 17 2 1 249 598321751 598321996 3.550000e-91 346.0
11 TraesCS6B01G424700 chr7B 83.051 413 51 10 323 733 483311297 483310902 1.640000e-94 357.0
12 TraesCS6B01G424700 chr7B 82.334 317 37 11 416 730 416187359 416187658 1.710000e-64 257.0
13 TraesCS6B01G424700 chr2B 82.620 397 48 12 323 716 203581712 203581334 9.940000e-87 331.0
14 TraesCS6B01G424700 chr4B 81.360 397 56 10 320 714 473671192 473671572 1.680000e-79 307.0
15 TraesCS6B01G424700 chr4B 83.699 319 35 10 417 733 367070322 367070019 7.850000e-73 285.0
16 TraesCS6B01G424700 chr4B 83.648 318 34 11 415 730 363880132 363880433 2.820000e-72 283.0
17 TraesCS6B01G424700 chr4B 82.704 318 38 9 415 730 208020322 208020624 2.840000e-67 267.0
18 TraesCS6B01G424700 chr7D 89.714 175 17 1 1 175 75654861 75654688 6.240000e-54 222.0
19 TraesCS6B01G424700 chr5B 87.413 143 13 4 379 519 382324092 382324231 4.960000e-35 159.0
20 TraesCS6B01G424700 chr5B 88.983 118 6 3 616 733 435850041 435850151 6.470000e-29 139.0
21 TraesCS6B01G424700 chr1D 89.831 118 5 3 616 733 473888592 473888482 1.390000e-30 145.0
22 TraesCS6B01G424700 chr1D 86.923 130 12 3 604 733 487325615 487325491 1.800000e-29 141.0


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 TraesCS6B01G424700 chr6B 694121369 694126161 4792 True 8852.000000 8852 100.000000 1 4793 1 chr6B.!!$R1 4792
1 TraesCS6B01G424700 chr6D 456459531 456463905 4374 True 1581.333333 2682 86.174667 434 4793 3 chr6D.!!$R1 4359
2 TraesCS6B01G424700 chr6A 603187867 603192618 4751 True 1752.000000 2396 87.256000 2 4793 3 chr6A.!!$R1 4791
3 TraesCS6B01G424700 chr7A 598321751 598322357 606 False 381.000000 416 89.615500 1 660 2 chr7A.!!$F1 659

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
391 436 0.039798 ATCAGCACAGCAAAGCAACG 60.040 50.0 0.0 0.0 0.00 4.10 F
1228 1284 0.037046 TAGGTTTCGGTTTCGCCTCC 60.037 55.0 0.0 0.0 36.13 4.30 F
1541 1622 0.239347 GATTATGCGGGTGCTGATGC 59.761 55.0 0.0 0.0 43.34 3.91 F
2439 2556 0.457509 AGAGAGCTTCGTGTCGCATG 60.458 55.0 0.0 0.0 0.00 4.06 F
2785 2904 0.115547 TCCCTGGTGCTGTGGTACTA 59.884 55.0 0.0 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1957 0.034896 TCCAACCGTTCCAGAAGCTC 59.965 55.000 0.00 0.0 0.00 4.09 R
2713 2832 0.108662 GTGCTTAACATTGCTGGGCC 60.109 55.000 0.00 0.0 0.00 5.80 R
2757 2876 0.178921 AGCACCAGGGAGTCAGAGAA 60.179 55.000 0.00 0.0 0.00 2.87 R
3296 3455 1.153429 GCCGCAGTAAGAACCGGAT 60.153 57.895 9.46 0.0 43.20 4.18 R
4655 4866 0.764369 AGGTGGAGTCCAGAAGCACA 60.764 55.000 13.61 0.0 32.34 4.57 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
41 42 7.771183 AGATTAACACAAGCAACTGAGAAAAA 58.229 30.769 0.00 0.00 0.00 1.94
44 45 6.651755 AACACAAGCAACTGAGAAAAATTG 57.348 33.333 0.00 0.00 0.00 2.32
53 62 6.346359 GCAACTGAGAAAAATTGCAATCACTC 60.346 38.462 13.38 17.15 45.38 3.51
60 69 1.089920 ATTGCAATCACTCGACCTGC 58.910 50.000 5.99 0.00 35.04 4.85
83 92 1.336125 GATGCAACTGCCCTAATGCTC 59.664 52.381 0.00 0.00 41.18 4.26
107 116 7.054124 TCCATCCAAGATCTAATACAACAACC 58.946 38.462 0.00 0.00 0.00 3.77
110 119 4.574828 CCAAGATCTAATACAACAACCCCG 59.425 45.833 0.00 0.00 0.00 5.73
131 140 2.449464 CAGGCCATGAAACAATCAGGA 58.551 47.619 5.01 0.00 42.41 3.86
195 220 4.164822 ACCTCGAACAAAGCATGAATTG 57.835 40.909 0.00 2.91 0.00 2.32
235 264 5.238650 ACAAACATCTAGCAACAAGTGTACC 59.761 40.000 0.00 0.00 0.00 3.34
236 265 3.585862 ACATCTAGCAACAAGTGTACCG 58.414 45.455 0.00 0.00 0.00 4.02
272 301 2.307098 AGGAAAAGCTAGTCACAGGCAT 59.693 45.455 0.00 0.00 0.00 4.40
275 304 4.383118 GGAAAAGCTAGTCACAGGCATCTA 60.383 45.833 0.00 0.00 0.00 1.98
278 307 2.099921 AGCTAGTCACAGGCATCTAACG 59.900 50.000 0.00 0.00 0.00 3.18
284 313 2.101415 TCACAGGCATCTAACGAGGATG 59.899 50.000 10.76 10.76 42.25 3.51
287 316 2.363680 CAGGCATCTAACGAGGATGAGT 59.636 50.000 16.41 4.51 42.02 3.41
290 319 2.481969 GCATCTAACGAGGATGAGTGCA 60.482 50.000 16.41 0.00 42.02 4.57
338 367 2.820197 GTTTCAAGGCCCTAAAGTGGAG 59.180 50.000 0.00 0.00 0.00 3.86
377 406 2.201921 ATGATCCATCCAGCATCAGC 57.798 50.000 0.00 0.00 42.56 4.26
391 436 0.039798 ATCAGCACAGCAAAGCAACG 60.040 50.000 0.00 0.00 0.00 4.10
405 450 0.110823 GCAACGAGCAACCTTACACG 60.111 55.000 0.00 0.00 44.79 4.49
409 454 1.068127 ACGAGCAACCTTACACGAACT 59.932 47.619 0.00 0.00 0.00 3.01
440 485 6.835174 TGAATAGCTCCATTTCTAAGCATCT 58.165 36.000 0.00 0.00 38.51 2.90
517 567 0.370273 GCCACAAATCGCGACTACTG 59.630 55.000 12.93 9.05 0.00 2.74
532 582 4.929808 CGACTACTGGTAGCAAGAAAACAT 59.070 41.667 7.58 0.00 36.66 2.71
533 583 5.163953 CGACTACTGGTAGCAAGAAAACATG 60.164 44.000 7.58 0.00 36.66 3.21
534 584 5.621193 ACTACTGGTAGCAAGAAAACATGT 58.379 37.500 7.58 0.00 36.66 3.21
535 585 4.836125 ACTGGTAGCAAGAAAACATGTG 57.164 40.909 0.00 0.00 0.00 3.21
536 586 4.207165 ACTGGTAGCAAGAAAACATGTGT 58.793 39.130 0.00 0.00 0.00 3.72
537 587 4.644685 ACTGGTAGCAAGAAAACATGTGTT 59.355 37.500 0.00 0.00 40.50 3.32
539 589 4.202101 TGGTAGCAAGAAAACATGTGTTGG 60.202 41.667 5.84 0.00 38.44 3.77
540 590 3.457610 AGCAAGAAAACATGTGTTGGG 57.542 42.857 5.84 0.00 38.44 4.12
544 595 1.274798 GAAAACATGTGTTGGGCGCG 61.275 55.000 5.84 0.00 38.44 6.86
555 606 3.122323 GGGCGCGTCCAAATCGAA 61.122 61.111 27.96 0.00 36.21 3.71
561 614 0.179215 GCGTCCAAATCGAAGCACAG 60.179 55.000 0.00 0.00 37.24 3.66
607 660 0.656785 CTACGAGACTACCACGAGGC 59.343 60.000 0.00 0.00 39.06 4.70
689 742 2.029380 TCGCTTCGACATCTTGGAAGAA 60.029 45.455 4.34 0.00 39.56 2.52
690 743 2.346847 CGCTTCGACATCTTGGAAGAAG 59.653 50.000 4.34 0.00 39.56 2.85
691 744 3.589988 GCTTCGACATCTTGGAAGAAGA 58.410 45.455 7.13 0.00 39.56 2.87
697 750 0.922626 ATCTTGGAAGAAGAGGGGGC 59.077 55.000 0.00 0.00 38.77 5.80
795 848 3.505184 GGCCGTTATGCACCCACG 61.505 66.667 7.08 7.08 0.00 4.94
827 880 2.588856 ATCCCTAACTTCACCCGCGC 62.589 60.000 0.00 0.00 0.00 6.86
860 913 1.261619 GCTCGGTAAGCGATGAAATGG 59.738 52.381 0.00 0.00 42.21 3.16
861 914 2.550978 CTCGGTAAGCGATGAAATGGT 58.449 47.619 0.00 0.00 0.00 3.55
864 917 4.505808 TCGGTAAGCGATGAAATGGTAAA 58.494 39.130 0.00 0.00 0.00 2.01
865 918 5.120399 TCGGTAAGCGATGAAATGGTAAAT 58.880 37.500 0.00 0.00 0.00 1.40
866 919 6.282167 TCGGTAAGCGATGAAATGGTAAATA 58.718 36.000 0.00 0.00 0.00 1.40
867 920 6.201425 TCGGTAAGCGATGAAATGGTAAATAC 59.799 38.462 0.00 0.00 0.00 1.89
870 923 3.250040 AGCGATGAAATGGTAAATACGGC 59.750 43.478 0.00 0.00 0.00 5.68
871 924 3.794536 CGATGAAATGGTAAATACGGCG 58.205 45.455 4.80 4.80 0.00 6.46
872 925 3.246699 CGATGAAATGGTAAATACGGCGT 59.753 43.478 19.64 19.64 0.00 5.68
874 927 2.678836 TGAAATGGTAAATACGGCGTGG 59.321 45.455 24.86 0.00 0.00 4.94
875 928 2.406596 AATGGTAAATACGGCGTGGT 57.593 45.000 24.86 8.52 0.00 4.16
876 929 1.658994 ATGGTAAATACGGCGTGGTG 58.341 50.000 24.86 0.00 0.00 4.17
877 930 0.321021 TGGTAAATACGGCGTGGTGT 59.679 50.000 24.86 9.01 0.00 4.16
878 931 1.547820 TGGTAAATACGGCGTGGTGTA 59.452 47.619 24.86 7.93 0.00 2.90
886 939 2.358247 GCGTGGTGTAGGGTGGTG 60.358 66.667 0.00 0.00 0.00 4.17
902 956 0.322546 GGTGGATGAAAAGAGGGCGT 60.323 55.000 0.00 0.00 0.00 5.68
920 974 2.097629 GCGTGGAAGAAATTAGGGCTTC 59.902 50.000 0.00 0.00 37.80 3.86
934 988 4.653888 CTTCGGGTTTGGGGGCGT 62.654 66.667 0.00 0.00 0.00 5.68
966 1021 3.003763 GTCCCTGAGGAAGCCGGT 61.004 66.667 0.00 0.00 46.38 5.28
988 1044 2.363147 GCGAGGAGGGGTCTGAGT 60.363 66.667 0.00 0.00 0.00 3.41
989 1045 2.716017 GCGAGGAGGGGTCTGAGTG 61.716 68.421 0.00 0.00 0.00 3.51
990 1046 2.055042 CGAGGAGGGGTCTGAGTGG 61.055 68.421 0.00 0.00 0.00 4.00
998 1054 1.687493 GGTCTGAGTGGGAGGAGGG 60.687 68.421 0.00 0.00 0.00 4.30
1014 1070 2.908940 GGAATGGCGGCCATGGAG 60.909 66.667 33.56 9.81 44.40 3.86
1228 1284 0.037046 TAGGTTTCGGTTTCGCCTCC 60.037 55.000 0.00 0.00 36.13 4.30
1232 1288 2.459202 TTTCGGTTTCGCCTCCTCCC 62.459 60.000 0.00 0.00 36.13 4.30
1276 1335 4.470050 CTCGTCGCGCGCTGTTTC 62.470 66.667 30.48 12.96 41.07 2.78
1279 1338 4.349871 GTCGCGCGCTGTTTCGTT 62.350 61.111 30.48 0.00 0.00 3.85
1284 1343 0.928451 GCGCGCTGTTTCGTTTCTTT 60.928 50.000 26.67 0.00 0.00 2.52
1298 1357 3.429085 GTTTCTTTGATGTGCCGCATAG 58.571 45.455 0.00 0.00 38.06 2.23
1333 1414 4.424061 TTTGTGTGCTGAATGCTGTATC 57.576 40.909 0.00 0.00 43.37 2.24
1338 1419 3.055602 TGTGCTGAATGCTGTATCTGAGT 60.056 43.478 0.00 0.00 43.37 3.41
1373 1454 2.362077 ACCAGTTTGTTCCTGCATTGTC 59.638 45.455 0.00 0.00 0.00 3.18
1420 1501 2.036098 TCCGGGCAGTACGAGGAA 59.964 61.111 0.00 0.00 0.00 3.36
1489 1570 1.544246 GGTTTCCCCAAGGTGATTTCG 59.456 52.381 0.00 0.00 0.00 3.46
1493 1574 1.912731 TCCCCAAGGTGATTTCGATGA 59.087 47.619 0.00 0.00 0.00 2.92
1496 1577 3.347216 CCCAAGGTGATTTCGATGAACT 58.653 45.455 0.00 0.00 0.00 3.01
1502 1583 4.455877 AGGTGATTTCGATGAACTGTTTCC 59.544 41.667 0.00 0.00 0.00 3.13
1503 1584 4.379499 GGTGATTTCGATGAACTGTTTCCC 60.379 45.833 0.00 0.00 0.00 3.97
1504 1585 4.455877 GTGATTTCGATGAACTGTTTCCCT 59.544 41.667 0.00 0.00 0.00 4.20
1541 1622 0.239347 GATTATGCGGGTGCTGATGC 59.761 55.000 0.00 0.00 43.34 3.91
1549 1630 1.654954 GGGTGCTGATGCTCTGCTTG 61.655 60.000 13.26 0.00 41.21 4.01
1750 1831 5.053145 GCCAAGATTATGTGAAGTCGATCT 58.947 41.667 0.00 0.00 0.00 2.75
1762 1843 7.275183 TGTGAAGTCGATCTTGAATATGGATT 58.725 34.615 5.20 0.00 36.40 3.01
1774 1855 5.964758 TGAATATGGATTTGTCTGGTTTGC 58.035 37.500 0.00 0.00 0.00 3.68
1797 1878 3.876589 GACCAAGAGCGGCGGTGAA 62.877 63.158 19.47 0.00 31.63 3.18
1800 1881 1.080093 CAAGAGCGGCGGTGAAGTA 60.080 57.895 19.47 0.00 0.00 2.24
1805 1886 2.202756 CGGCGGTGAAGTAGGAGC 60.203 66.667 0.00 0.00 0.00 4.70
1840 1957 3.930229 TCATTCACGGATTCTGGTTAACG 59.070 43.478 0.00 0.00 0.00 3.18
1851 1968 2.631062 TCTGGTTAACGAGCTTCTGGAA 59.369 45.455 12.39 0.00 0.00 3.53
1869 1986 2.083774 GAACGGTTGGATTCAGCATCA 58.916 47.619 0.00 0.00 32.79 3.07
1957 2074 2.677289 CCAGGCAGCCCAGTGATCT 61.677 63.158 8.22 0.00 0.00 2.75
1968 2085 3.006323 GCCCAGTGATCTCTAGGTACATG 59.994 52.174 10.36 0.00 0.00 3.21
1982 2099 3.587506 AGGTACATGAGCCCTTAAACACT 59.412 43.478 0.00 0.00 0.00 3.55
1987 2104 4.202461 ACATGAGCCCTTAAACACTCTCAA 60.202 41.667 0.00 0.00 34.72 3.02
1988 2105 4.008074 TGAGCCCTTAAACACTCTCAAG 57.992 45.455 0.00 0.00 0.00 3.02
1989 2106 2.744741 GAGCCCTTAAACACTCTCAAGC 59.255 50.000 0.00 0.00 0.00 4.01
1991 2108 3.149981 GCCCTTAAACACTCTCAAGCTT 58.850 45.455 0.00 0.00 0.00 3.74
1992 2109 3.189495 GCCCTTAAACACTCTCAAGCTTC 59.811 47.826 0.00 0.00 0.00 3.86
1993 2110 4.646572 CCCTTAAACACTCTCAAGCTTCT 58.353 43.478 0.00 0.00 0.00 2.85
1994 2111 4.453819 CCCTTAAACACTCTCAAGCTTCTG 59.546 45.833 0.00 0.00 0.00 3.02
1995 2112 5.059833 CCTTAAACACTCTCAAGCTTCTGT 58.940 41.667 0.00 0.00 0.00 3.41
1996 2113 5.049818 CCTTAAACACTCTCAAGCTTCTGTG 60.050 44.000 0.00 6.08 0.00 3.66
1997 2114 2.540265 ACACTCTCAAGCTTCTGTGG 57.460 50.000 16.66 0.00 0.00 4.17
1998 2115 1.765314 ACACTCTCAAGCTTCTGTGGT 59.235 47.619 16.66 3.71 0.00 4.16
1999 2116 2.141517 CACTCTCAAGCTTCTGTGGTG 58.858 52.381 0.00 0.00 0.00 4.17
2000 2117 1.765314 ACTCTCAAGCTTCTGTGGTGT 59.235 47.619 0.00 0.00 0.00 4.16
2001 2118 2.141517 CTCTCAAGCTTCTGTGGTGTG 58.858 52.381 0.00 0.00 0.00 3.82
2003 2120 1.869767 CTCAAGCTTCTGTGGTGTGTC 59.130 52.381 0.00 0.00 0.00 3.67
2004 2121 0.947244 CAAGCTTCTGTGGTGTGTCC 59.053 55.000 0.00 0.00 0.00 4.02
2013 2130 3.829601 TCTGTGGTGTGTCCTTTGTTTTT 59.170 39.130 0.00 0.00 37.07 1.94
2029 2146 6.528537 TTGTTTTTCATGGTAGCATGCTAT 57.471 33.333 29.17 13.09 32.87 2.97
2030 2147 5.893687 TGTTTTTCATGGTAGCATGCTATG 58.106 37.500 29.17 23.52 40.85 2.23
2042 2159 4.275810 AGCATGCTATGGTTTGAACTCAT 58.724 39.130 21.21 0.00 37.84 2.90
2043 2160 4.708421 AGCATGCTATGGTTTGAACTCATT 59.292 37.500 21.21 0.00 37.84 2.57
2044 2161 5.887598 AGCATGCTATGGTTTGAACTCATTA 59.112 36.000 21.21 0.00 37.84 1.90
2045 2162 6.548622 AGCATGCTATGGTTTGAACTCATTAT 59.451 34.615 21.21 0.00 37.84 1.28
2073 2190 5.389859 TTCCGATGCAGAAAATCACAAAT 57.610 34.783 0.00 0.00 0.00 2.32
2080 2197 5.393124 TGCAGAAAATCACAAATCATCGAC 58.607 37.500 0.00 0.00 0.00 4.20
2081 2198 4.795278 GCAGAAAATCACAAATCATCGACC 59.205 41.667 0.00 0.00 0.00 4.79
2083 2200 6.025896 CAGAAAATCACAAATCATCGACCAG 58.974 40.000 0.00 0.00 0.00 4.00
2091 2208 5.180117 CACAAATCATCGACCAGTTTCTTCT 59.820 40.000 0.00 0.00 0.00 2.85
2110 2227 1.694150 CTGTGGAAACAGTGGAGAGGA 59.306 52.381 0.00 0.00 44.46 3.71
2113 2230 0.966920 GGAAACAGTGGAGAGGACGA 59.033 55.000 0.00 0.00 0.00 4.20
2143 2260 5.577164 GTCATACTTACTTGATGAACGCACT 59.423 40.000 0.00 0.00 31.62 4.40
2220 2337 6.325028 TGGATGAAGGTGTTTGAACCATTAAA 59.675 34.615 0.00 0.00 43.20 1.52
2267 2384 2.420129 GGCCTCGTTGAAGTCATGGTAT 60.420 50.000 0.00 0.00 0.00 2.73
2274 2391 6.206498 TCGTTGAAGTCATGGTATCTATTCG 58.794 40.000 0.00 0.00 0.00 3.34
2279 2396 3.641436 AGTCATGGTATCTATTCGTGGCA 59.359 43.478 0.00 0.00 0.00 4.92
2280 2397 3.741344 GTCATGGTATCTATTCGTGGCAC 59.259 47.826 7.79 7.79 0.00 5.01
2282 2399 3.452755 TGGTATCTATTCGTGGCACAG 57.547 47.619 19.09 10.60 41.80 3.66
2301 2418 5.220739 GCACAGCCTTTAATCATCTACACTG 60.221 44.000 0.00 0.00 0.00 3.66
2304 2421 6.372659 ACAGCCTTTAATCATCTACACTGTTG 59.627 38.462 0.00 0.00 30.94 3.33
2306 2423 7.549134 CAGCCTTTAATCATCTACACTGTTGTA 59.451 37.037 0.00 0.00 37.15 2.41
2321 2438 6.101997 CACTGTTGTATACTCATTCTCTGCA 58.898 40.000 4.17 0.00 0.00 4.41
2322 2439 6.760298 CACTGTTGTATACTCATTCTCTGCAT 59.240 38.462 4.17 0.00 0.00 3.96
2325 2442 9.486497 CTGTTGTATACTCATTCTCTGCATTAT 57.514 33.333 4.17 0.00 0.00 1.28
2394 2511 3.282021 GAGATATGCTTGCTGGGTTTGA 58.718 45.455 0.00 0.00 0.00 2.69
2439 2556 0.457509 AGAGAGCTTCGTGTCGCATG 60.458 55.000 0.00 0.00 0.00 4.06
2544 2661 9.971922 CAGACAAGATTCTTAATTTGAAGGTTT 57.028 29.630 0.00 0.00 0.00 3.27
2596 2714 2.874086 GCTTGCTTTTGCCAAGTTTCAT 59.126 40.909 3.47 0.00 46.87 2.57
2625 2743 5.426504 TGCAAACATCAGTTTTGGTGAAAT 58.573 33.333 0.00 0.00 45.32 2.17
2690 2808 5.415415 CAGCTATGCACATTTAGGAAGAC 57.585 43.478 0.00 0.00 0.00 3.01
2691 2809 4.025396 CAGCTATGCACATTTAGGAAGACG 60.025 45.833 0.00 0.00 0.00 4.18
2699 2818 5.974751 GCACATTTAGGAAGACGTTCAAAAA 59.025 36.000 0.00 0.00 33.93 1.94
2720 2839 0.464554 GTTACTCCTCATGGCCCAGC 60.465 60.000 0.00 0.00 0.00 4.85
2722 2841 0.913934 TACTCCTCATGGCCCAGCAA 60.914 55.000 0.00 0.00 0.00 3.91
2755 2874 7.279981 GCACCATTGTGTCAACTATCTAATGTA 59.720 37.037 0.00 0.00 44.65 2.29
2757 2876 8.540388 ACCATTGTGTCAACTATCTAATGTACT 58.460 33.333 0.00 0.00 0.00 2.73
2761 2880 9.856488 TTGTGTCAACTATCTAATGTACTTCTC 57.144 33.333 0.00 0.00 0.00 2.87
2770 2889 6.080969 TCTAATGTACTTCTCTGACTCCCT 57.919 41.667 0.00 0.00 0.00 4.20
2771 2890 5.888724 TCTAATGTACTTCTCTGACTCCCTG 59.111 44.000 0.00 0.00 0.00 4.45
2772 2891 2.808919 TGTACTTCTCTGACTCCCTGG 58.191 52.381 0.00 0.00 0.00 4.45
2779 2898 1.004080 CTGACTCCCTGGTGCTGTG 60.004 63.158 0.00 0.00 0.00 3.66
2780 2899 2.348998 GACTCCCTGGTGCTGTGG 59.651 66.667 0.00 0.00 0.00 4.17
2785 2904 0.115547 TCCCTGGTGCTGTGGTACTA 59.884 55.000 0.00 0.00 0.00 1.82
2786 2905 0.981183 CCCTGGTGCTGTGGTACTAA 59.019 55.000 0.00 0.00 0.00 2.24
2794 2913 4.156008 GGTGCTGTGGTACTAAAAATCTGG 59.844 45.833 0.00 0.00 0.00 3.86
2796 2915 5.648092 GTGCTGTGGTACTAAAAATCTGGAT 59.352 40.000 0.00 0.00 0.00 3.41
2847 2966 4.476297 TCCAGAGTACAGTTACTGAACCA 58.524 43.478 20.07 0.00 38.77 3.67
2869 2988 1.271656 GCTTTGGCAGCTGACAAGAAT 59.728 47.619 32.49 0.00 44.95 2.40
2878 2997 4.320714 GCAGCTGACAAGAATTTGACATCA 60.321 41.667 20.43 0.00 38.08 3.07
2891 3010 7.816031 AGAATTTGACATCAACCATTCATTGAC 59.184 33.333 16.07 0.00 38.84 3.18
2900 3019 2.234661 ACCATTCATTGACGAGAGCTGA 59.765 45.455 0.00 0.00 0.00 4.26
2901 3020 3.264947 CCATTCATTGACGAGAGCTGAA 58.735 45.455 0.00 0.00 0.00 3.02
2902 3021 3.875727 CCATTCATTGACGAGAGCTGAAT 59.124 43.478 0.00 0.00 37.10 2.57
2903 3022 4.334759 CCATTCATTGACGAGAGCTGAATT 59.665 41.667 0.00 0.00 35.06 2.17
2904 3023 5.163683 CCATTCATTGACGAGAGCTGAATTT 60.164 40.000 0.00 0.00 35.06 1.82
2929 3078 2.812499 GCAATGGGATGCCTGCTG 59.188 61.111 9.86 3.30 40.49 4.41
2930 3079 2.812499 CAATGGGATGCCTGCTGC 59.188 61.111 4.35 0.00 41.77 5.25
2965 3117 5.835113 TTTATAAGGAGCATGCCTTTCAC 57.165 39.130 15.66 0.24 45.85 3.18
2966 3118 2.877097 TAAGGAGCATGCCTTTCACA 57.123 45.000 15.66 0.00 45.85 3.58
2994 3146 8.999431 GTTTCTCAGGAAGTAAAATATGTGACA 58.001 33.333 0.00 0.00 32.61 3.58
3059 3217 4.462483 TGTTGTTATCATCTTCCCTTTGCC 59.538 41.667 0.00 0.00 0.00 4.52
3069 3227 3.116900 TCTTCCCTTTGCCCTAAAACCTT 60.117 43.478 0.00 0.00 0.00 3.50
3073 3231 3.389656 CCCTTTGCCCTAAAACCTTTCAA 59.610 43.478 0.00 0.00 0.00 2.69
3077 3235 6.017192 CCTTTGCCCTAAAACCTTTCAATTTG 60.017 38.462 0.00 0.00 0.00 2.32
3087 3245 5.596836 ACCTTTCAATTTGTCAAAGCTGA 57.403 34.783 4.03 6.49 0.00 4.26
3151 3310 3.830755 TCTTGGTGTGGTCCTTCTAGTAC 59.169 47.826 0.00 0.00 0.00 2.73
3156 3315 4.081807 GGTGTGGTCCTTCTAGTACGAAAT 60.082 45.833 0.00 0.00 0.00 2.17
3157 3316 5.126061 GGTGTGGTCCTTCTAGTACGAAATA 59.874 44.000 0.00 0.00 0.00 1.40
3158 3317 6.032717 GTGTGGTCCTTCTAGTACGAAATAC 58.967 44.000 0.00 0.00 0.00 1.89
3162 3321 5.303845 GGTCCTTCTAGTACGAAATACCCAT 59.696 44.000 0.00 0.00 33.85 4.00
3165 3324 8.583296 GTCCTTCTAGTACGAAATACCCATATT 58.417 37.037 0.00 0.00 33.85 1.28
3181 3340 5.185635 ACCCATATTTTGATGTGTGGTTGAG 59.814 40.000 0.00 0.00 0.00 3.02
3182 3341 5.394443 CCCATATTTTGATGTGTGGTTGAGG 60.394 44.000 0.00 0.00 0.00 3.86
3185 3344 5.867903 ATTTTGATGTGTGGTTGAGGAAA 57.132 34.783 0.00 0.00 0.00 3.13
3215 3374 6.690194 ATGTGATCTCTTTAACCAAGCATC 57.310 37.500 0.00 0.00 31.70 3.91
3250 3409 9.739276 AACAGGAAAATGACATTCTTGAGTATA 57.261 29.630 0.05 0.00 37.34 1.47
3279 3438 5.163754 GCAGTCATTAGAAAGTAAACCGCAT 60.164 40.000 0.00 0.00 0.00 4.73
3280 3439 6.250819 CAGTCATTAGAAAGTAAACCGCATG 58.749 40.000 0.00 0.00 0.00 4.06
3296 3455 4.202315 ACCGCATGTATTATGGCTTCTACA 60.202 41.667 0.00 0.00 0.00 2.74
3300 3459 5.063944 GCATGTATTATGGCTTCTACATCCG 59.936 44.000 0.00 0.00 33.65 4.18
3312 3471 2.098607 TCTACATCCGGTTCTTACTGCG 59.901 50.000 0.00 0.00 0.00 5.18
3374 3533 5.652014 CCTAAAATGTGTCCCTGCTGATTTA 59.348 40.000 0.00 0.00 0.00 1.40
3376 3535 7.502226 CCTAAAATGTGTCCCTGCTGATTTATA 59.498 37.037 0.00 0.00 0.00 0.98
3560 3724 8.044060 TGTACCAGTTCTCATCATGAAATTTC 57.956 34.615 11.41 11.41 0.00 2.17
3696 3860 1.134995 CATCCAGTGCTGCGAACTCTA 60.135 52.381 0.00 0.00 0.00 2.43
3897 4062 8.023128 AGTAAATTACTTTGCATGTGTGATGAC 58.977 33.333 0.00 0.00 34.86 3.06
4022 4187 8.674607 GGTCAAATACGAAGATTGAATAGGTTT 58.325 33.333 0.00 0.00 35.07 3.27
4085 4251 9.087424 TGATGAAATACAACTATCTTCTTGTCG 57.913 33.333 0.00 0.00 32.77 4.35
4086 4252 7.827819 TGAAATACAACTATCTTCTTGTCGG 57.172 36.000 0.00 0.00 32.77 4.79
4087 4253 6.816640 TGAAATACAACTATCTTCTTGTCGGG 59.183 38.462 0.00 0.00 32.77 5.14
4105 4271 2.735126 CGGGCACATGTTCAATTTAGGC 60.735 50.000 0.00 0.00 0.00 3.93
4221 4416 5.181811 TGGTTTGACTGATGTCTGCTAAATG 59.818 40.000 0.00 0.00 43.29 2.32
4255 4450 9.982291 CATTTATTTGGATTTTGAAGATGCAAG 57.018 29.630 3.16 0.00 36.43 4.01
4300 4495 1.202639 CGGCTGGTAGTATCATGGCAA 60.203 52.381 0.00 0.00 0.00 4.52
4373 4569 2.730382 TCTCATAAGGTGTCCACGCTA 58.270 47.619 0.00 0.00 0.00 4.26
4417 4613 9.127277 ACCATAAACTTGTTGTACAATACAGTT 57.873 29.630 12.26 15.77 37.48 3.16
4516 4712 7.889589 TCCACATATTGTAGATCTAATTGCG 57.110 36.000 3.40 0.00 0.00 4.85
4517 4713 7.666623 TCCACATATTGTAGATCTAATTGCGA 58.333 34.615 3.40 0.00 0.00 5.10
4539 4735 6.307155 CGAGTCAAAGTGTAAATCATGGAAC 58.693 40.000 0.00 0.00 0.00 3.62
4566 4773 3.406682 CAGCGGGACTGCATTTTTC 57.593 52.632 5.85 0.00 40.19 2.29
4625 4836 1.670295 TGCATAACCAATACGCAGCTG 59.330 47.619 10.11 10.11 0.00 4.24
4655 4866 7.790782 TTCTTCCCTATTATTTTGCCTGTTT 57.209 32.000 0.00 0.00 0.00 2.83
4664 4875 2.582728 TTTGCCTGTTTGTGCTTCTG 57.417 45.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.742053 GCTTGTGTTAATCTTGCCTCGA 59.258 45.455 0.00 0.00 0.00 4.04
13 14 4.858935 TCAGTTGCTTGTGTTAATCTTGC 58.141 39.130 0.00 0.00 0.00 4.01
20 21 6.255453 GCAATTTTTCTCAGTTGCTTGTGTTA 59.745 34.615 0.00 0.00 42.61 2.41
41 42 1.089920 GCAGGTCGAGTGATTGCAAT 58.910 50.000 12.83 12.83 37.45 3.56
44 45 1.446099 TCGCAGGTCGAGTGATTGC 60.446 57.895 0.00 0.00 43.16 3.56
60 69 1.600957 CATTAGGGCAGTTGCATCTCG 59.399 52.381 6.43 0.00 44.36 4.04
83 92 6.263168 GGGTTGTTGTATTAGATCTTGGATGG 59.737 42.308 0.00 0.00 0.00 3.51
107 116 1.606885 ATTGTTTCATGGCCTGCGGG 61.607 55.000 7.41 7.41 0.00 6.13
110 119 1.134907 CCTGATTGTTTCATGGCCTGC 60.135 52.381 3.32 0.00 32.72 4.85
114 123 3.091545 TCCTTCCTGATTGTTTCATGGC 58.908 45.455 0.00 0.00 32.72 4.40
131 140 2.522185 ACTGTGCATGATGCTTTCCTT 58.478 42.857 19.19 0.00 45.31 3.36
150 159 7.095313 GGTTTTACTCTGTTGTAAAGGAGCTAC 60.095 40.741 0.00 0.00 41.51 3.58
195 220 3.311322 TGTTTGTCAGTTCCGATGTGTTC 59.689 43.478 0.00 0.00 0.00 3.18
235 264 0.958091 TCCTGGTGAAAAATGGTGCG 59.042 50.000 0.00 0.00 0.00 5.34
236 265 3.467374 TTTCCTGGTGAAAAATGGTGC 57.533 42.857 0.00 0.00 39.98 5.01
272 301 3.023832 TGATGCACTCATCCTCGTTAGA 58.976 45.455 0.00 0.00 46.60 2.10
275 304 1.276138 TGTGATGCACTCATCCTCGTT 59.724 47.619 0.00 0.00 46.60 3.85
278 307 2.975732 TCTGTGATGCACTCATCCTC 57.024 50.000 0.00 0.00 46.60 3.71
284 313 5.583854 AGTGAAACATATCTGTGATGCACTC 59.416 40.000 0.00 0.00 41.43 3.51
287 316 5.355071 GGAAGTGAAACATATCTGTGATGCA 59.645 40.000 0.00 0.00 41.43 3.96
290 319 6.600822 CCTTGGAAGTGAAACATATCTGTGAT 59.399 38.462 0.00 0.00 41.43 3.06
293 322 4.702131 GCCTTGGAAGTGAAACATATCTGT 59.298 41.667 0.00 0.00 41.43 3.41
302 331 2.370349 TGAAACGCCTTGGAAGTGAAA 58.630 42.857 0.00 0.00 0.00 2.69
338 367 4.574828 TCATTTTCCTCGCCAGTAATTAGC 59.425 41.667 0.00 0.00 0.00 3.09
377 406 0.248580 TTGCTCGTTGCTTTGCTGTG 60.249 50.000 5.00 0.00 43.37 3.66
391 436 3.546670 CGATAGTTCGTGTAAGGTTGCTC 59.453 47.826 0.00 0.00 40.53 4.26
400 445 4.556104 GCTATTCAGCCGATAGTTCGTGTA 60.556 45.833 0.00 0.00 43.97 2.90
430 475 5.658634 AGATGTGGTGTAGAAGATGCTTAGA 59.341 40.000 0.00 0.00 0.00 2.10
440 485 2.301870 GGTGGTCAGATGTGGTGTAGAA 59.698 50.000 0.00 0.00 0.00 2.10
517 567 4.298332 CCAACACATGTTTTCTTGCTACC 58.702 43.478 0.00 0.00 35.83 3.18
532 582 4.858680 TTGGACGCGCCCAACACA 62.859 61.111 23.73 0.05 40.99 3.72
533 583 2.796245 GATTTGGACGCGCCCAACAC 62.796 60.000 27.22 18.59 45.13 3.32
534 584 2.596046 ATTTGGACGCGCCCAACA 60.596 55.556 27.22 17.48 45.13 3.33
535 585 2.178273 GATTTGGACGCGCCCAAC 59.822 61.111 27.22 12.75 45.13 3.77
536 586 3.427425 CGATTTGGACGCGCCCAA 61.427 61.111 23.73 23.73 43.90 4.12
537 587 3.885538 TTCGATTTGGACGCGCCCA 62.886 57.895 11.19 11.19 34.97 5.36
539 589 2.399611 CTTCGATTTGGACGCGCC 59.600 61.111 5.73 9.63 37.10 6.53
540 590 2.276680 GCTTCGATTTGGACGCGC 60.277 61.111 5.73 0.00 0.00 6.86
544 595 0.874390 TGCTGTGCTTCGATTTGGAC 59.126 50.000 0.00 0.00 0.00 4.02
561 614 4.776647 GGTTGGATTGCGCGGTGC 62.777 66.667 8.83 6.58 46.70 5.01
570 623 1.276622 AGCGTACTCCTGGTTGGATT 58.723 50.000 0.00 0.00 45.16 3.01
583 636 1.005557 CGTGGTAGTCTCGTAGCGTAC 60.006 57.143 0.00 0.00 0.00 3.67
607 660 1.065273 GCATGATCTTGCTTGGCCG 59.935 57.895 22.66 0.00 39.57 6.13
650 703 2.094099 GCGAGGTACGGCGAAAATTTTA 59.906 45.455 16.62 0.00 42.83 1.52
652 705 0.445043 GCGAGGTACGGCGAAAATTT 59.555 50.000 16.62 0.00 42.83 1.82
653 706 0.390735 AGCGAGGTACGGCGAAAATT 60.391 50.000 16.62 0.00 42.83 1.82
654 707 0.390735 AAGCGAGGTACGGCGAAAAT 60.391 50.000 16.62 0.00 42.83 1.82
721 774 4.888325 CGCCTCCCATCCTCCCCT 62.888 72.222 0.00 0.00 0.00 4.79
795 848 2.303311 GTTAGGGATGAGATACAGGGGC 59.697 54.545 0.00 0.00 0.00 5.80
843 896 4.868450 TTTACCATTTCATCGCTTACCG 57.132 40.909 0.00 0.00 38.61 4.02
844 897 6.360329 CGTATTTACCATTTCATCGCTTACC 58.640 40.000 0.00 0.00 0.00 2.85
851 904 4.523813 CACGCCGTATTTACCATTTCATC 58.476 43.478 0.00 0.00 0.00 2.92
856 909 2.011222 CACCACGCCGTATTTACCATT 58.989 47.619 0.00 0.00 0.00 3.16
858 911 0.321021 ACACCACGCCGTATTTACCA 59.679 50.000 0.00 0.00 0.00 3.25
860 913 2.195922 CCTACACCACGCCGTATTTAC 58.804 52.381 0.00 0.00 0.00 2.01
861 914 1.136695 CCCTACACCACGCCGTATTTA 59.863 52.381 0.00 0.00 0.00 1.40
864 917 1.683365 ACCCTACACCACGCCGTAT 60.683 57.895 0.00 0.00 0.00 3.06
865 918 2.283101 ACCCTACACCACGCCGTA 60.283 61.111 0.00 0.00 0.00 4.02
866 919 3.998672 CACCCTACACCACGCCGT 61.999 66.667 0.00 0.00 0.00 5.68
867 920 4.752879 CCACCCTACACCACGCCG 62.753 72.222 0.00 0.00 0.00 6.46
870 923 1.550130 ATCCACCACCCTACACCACG 61.550 60.000 0.00 0.00 0.00 4.94
871 924 0.035439 CATCCACCACCCTACACCAC 60.035 60.000 0.00 0.00 0.00 4.16
872 925 0.178888 TCATCCACCACCCTACACCA 60.179 55.000 0.00 0.00 0.00 4.17
874 927 2.871096 TTTCATCCACCACCCTACAC 57.129 50.000 0.00 0.00 0.00 2.90
875 928 2.983192 TCTTTTCATCCACCACCCTACA 59.017 45.455 0.00 0.00 0.00 2.74
876 929 3.610911 CTCTTTTCATCCACCACCCTAC 58.389 50.000 0.00 0.00 0.00 3.18
877 930 2.576191 CCTCTTTTCATCCACCACCCTA 59.424 50.000 0.00 0.00 0.00 3.53
878 931 1.355720 CCTCTTTTCATCCACCACCCT 59.644 52.381 0.00 0.00 0.00 4.34
886 939 0.035439 TCCACGCCCTCTTTTCATCC 60.035 55.000 0.00 0.00 0.00 3.51
902 956 2.356741 CCCGAAGCCCTAATTTCTTCCA 60.357 50.000 0.00 0.00 34.32 3.53
920 974 3.215597 GAAAACGCCCCCAAACCCG 62.216 63.158 0.00 0.00 0.00 5.28
934 988 0.675522 GGGACGGATCGGCAAGAAAA 60.676 55.000 0.00 0.00 36.10 2.29
966 1021 0.830648 CAGACCCCTCCTCGCAATTA 59.169 55.000 0.00 0.00 0.00 1.40
988 1044 3.089874 CGCCATTCCCTCCTCCCA 61.090 66.667 0.00 0.00 0.00 4.37
989 1045 3.878667 CCGCCATTCCCTCCTCCC 61.879 72.222 0.00 0.00 0.00 4.30
990 1046 4.570874 GCCGCCATTCCCTCCTCC 62.571 72.222 0.00 0.00 0.00 4.30
998 1054 1.228367 ATCTCCATGGCCGCCATTC 60.228 57.895 22.88 0.00 42.23 2.67
1014 1070 2.107953 GCGAGCACCTCCTCCATC 59.892 66.667 0.00 0.00 0.00 3.51
1112 1168 4.452733 GGGCCTTCTGGACGTCGG 62.453 72.222 9.92 5.74 44.25 4.79
1228 1284 3.834799 GTCGTGTAGGGGCGGGAG 61.835 72.222 0.00 0.00 0.00 4.30
1264 1320 3.150485 GAAACGAAACAGCGCGCG 61.150 61.111 28.44 28.44 33.86 6.86
1265 1321 0.928451 AAAGAAACGAAACAGCGCGC 60.928 50.000 26.66 26.66 33.86 6.86
1273 1332 2.856720 GCGGCACATCAAAGAAACGAAA 60.857 45.455 0.00 0.00 0.00 3.46
1276 1335 0.040514 TGCGGCACATCAAAGAAACG 60.041 50.000 0.00 0.00 0.00 3.60
1277 1336 2.352503 ATGCGGCACATCAAAGAAAC 57.647 45.000 4.03 0.00 31.52 2.78
1278 1337 2.423185 CCTATGCGGCACATCAAAGAAA 59.577 45.455 4.03 0.00 40.38 2.52
1279 1338 2.016318 CCTATGCGGCACATCAAAGAA 58.984 47.619 4.03 0.00 40.38 2.52
1298 1357 3.451894 CAAATCCTGCGGGTGGCC 61.452 66.667 12.43 0.00 42.61 5.36
1356 1437 2.223479 ACACGACAATGCAGGAACAAAC 60.223 45.455 0.00 0.00 0.00 2.93
1373 1454 2.135933 GTTCCTGAAGACCTGAACACG 58.864 52.381 0.00 0.00 0.00 4.49
1420 1501 2.439701 TCGAACTCCCTCGCGGAT 60.440 61.111 6.13 0.00 41.00 4.18
1484 1565 6.884295 TCATAAGGGAAACAGTTCATCGAAAT 59.116 34.615 0.00 0.00 35.25 2.17
1487 1568 5.414789 TCATAAGGGAAACAGTTCATCGA 57.585 39.130 0.00 0.00 35.25 3.59
1489 1570 7.830739 ACATTTCATAAGGGAAACAGTTCATC 58.169 34.615 0.00 0.00 39.40 2.92
1493 1574 7.791029 ACAAACATTTCATAAGGGAAACAGTT 58.209 30.769 0.00 0.00 39.40 3.16
1496 1577 9.703892 CATAACAAACATTTCATAAGGGAAACA 57.296 29.630 0.00 0.00 39.40 2.83
1602 1683 5.125097 CAGAAAATGCTTTATGACCAGCTCT 59.875 40.000 0.00 0.00 36.10 4.09
1734 1815 8.421002 TCCATATTCAAGATCGACTTCACATAA 58.579 33.333 0.00 0.00 36.61 1.90
1750 1831 6.397272 GCAAACCAGACAAATCCATATTCAA 58.603 36.000 0.00 0.00 0.00 2.69
1762 1843 3.283684 CCGCGGCAAACCAGACAA 61.284 61.111 14.67 0.00 34.57 3.18
1788 1869 2.202756 GCTCCTACTTCACCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
1794 1875 0.116342 TGGTGGGAGCTCCTACTTCA 59.884 55.000 38.46 29.03 45.60 3.02
1797 1878 1.682684 CGTGGTGGGAGCTCCTACT 60.683 63.158 38.46 0.00 45.60 2.57
1824 1941 1.549170 AGCTCGTTAACCAGAATCCGT 59.451 47.619 4.23 0.00 0.00 4.69
1840 1957 0.034896 TCCAACCGTTCCAGAAGCTC 59.965 55.000 0.00 0.00 0.00 4.09
1851 1968 2.019249 CATGATGCTGAATCCAACCGT 58.981 47.619 0.00 0.00 34.00 4.83
1957 2074 5.027460 TGTTTAAGGGCTCATGTACCTAGA 58.973 41.667 6.13 0.00 33.37 2.43
1968 2085 2.744741 GCTTGAGAGTGTTTAAGGGCTC 59.255 50.000 0.00 0.00 0.00 4.70
1982 2099 1.486310 ACACACCACAGAAGCTTGAGA 59.514 47.619 2.10 0.00 0.00 3.27
1987 2104 0.839946 AAGGACACACCACAGAAGCT 59.160 50.000 0.00 0.00 42.04 3.74
1988 2105 1.334869 CAAAGGACACACCACAGAAGC 59.665 52.381 0.00 0.00 42.04 3.86
1989 2106 2.643551 ACAAAGGACACACCACAGAAG 58.356 47.619 0.00 0.00 42.04 2.85
1991 2108 2.799126 AACAAAGGACACACCACAGA 57.201 45.000 0.00 0.00 42.04 3.41
1992 2109 3.866883 AAAACAAAGGACACACCACAG 57.133 42.857 0.00 0.00 42.04 3.66
1993 2110 3.574396 TGAAAAACAAAGGACACACCACA 59.426 39.130 0.00 0.00 42.04 4.17
1994 2111 4.181309 TGAAAAACAAAGGACACACCAC 57.819 40.909 0.00 0.00 42.04 4.16
1995 2112 4.382470 CCATGAAAAACAAAGGACACACCA 60.382 41.667 0.00 0.00 42.04 4.17
1996 2113 4.119136 CCATGAAAAACAAAGGACACACC 58.881 43.478 0.00 0.00 39.35 4.16
1997 2114 4.754322 ACCATGAAAAACAAAGGACACAC 58.246 39.130 0.00 0.00 33.74 3.82
1998 2115 5.451242 GCTACCATGAAAAACAAAGGACACA 60.451 40.000 0.00 0.00 33.74 3.72
1999 2116 4.982295 GCTACCATGAAAAACAAAGGACAC 59.018 41.667 0.00 0.00 33.74 3.67
2000 2117 4.646945 TGCTACCATGAAAAACAAAGGACA 59.353 37.500 0.00 0.00 33.74 4.02
2001 2118 5.195001 TGCTACCATGAAAAACAAAGGAC 57.805 39.130 0.00 0.00 33.74 3.85
2029 2146 8.293867 CGGAAAGTTTATAATGAGTTCAAACCA 58.706 33.333 0.00 0.00 31.06 3.67
2030 2147 8.508875 TCGGAAAGTTTATAATGAGTTCAAACC 58.491 33.333 0.00 0.00 31.06 3.27
2042 2159 8.735315 TGATTTTCTGCATCGGAAAGTTTATAA 58.265 29.630 0.00 0.00 39.46 0.98
2043 2160 8.181573 GTGATTTTCTGCATCGGAAAGTTTATA 58.818 33.333 0.00 0.00 39.46 0.98
2044 2161 7.029563 GTGATTTTCTGCATCGGAAAGTTTAT 58.970 34.615 0.00 0.00 39.46 1.40
2045 2162 6.016693 TGTGATTTTCTGCATCGGAAAGTTTA 60.017 34.615 0.00 0.00 39.46 2.01
2053 2170 4.735985 TGATTTGTGATTTTCTGCATCGG 58.264 39.130 0.00 0.00 0.00 4.18
2073 2190 3.554960 CCACAGAAGAAACTGGTCGATGA 60.555 47.826 0.00 0.00 41.59 2.92
2091 2208 1.416401 GTCCTCTCCACTGTTTCCACA 59.584 52.381 0.00 0.00 0.00 4.17
2110 2227 7.817478 TCATCAAGTAAGTATGACAAACATCGT 59.183 33.333 0.00 0.00 40.07 3.73
2113 2230 8.443160 CGTTCATCAAGTAAGTATGACAAACAT 58.557 33.333 0.00 0.00 42.39 2.71
2143 2260 2.567169 AGATCCAGACACAATCCGAACA 59.433 45.455 0.00 0.00 0.00 3.18
2220 2337 7.655328 CACTCTGACAAGAATCTACAGAAACTT 59.345 37.037 12.81 0.00 37.20 2.66
2279 2396 6.054860 ACAGTGTAGATGATTAAAGGCTGT 57.945 37.500 0.00 0.00 0.00 4.40
2280 2397 6.372659 ACAACAGTGTAGATGATTAAAGGCTG 59.627 38.462 0.00 0.00 35.72 4.85
2282 2399 6.743575 ACAACAGTGTAGATGATTAAAGGC 57.256 37.500 0.00 0.00 35.72 4.35
2293 2410 8.678199 CAGAGAATGAGTATACAACAGTGTAGA 58.322 37.037 5.50 0.00 43.42 2.59
2296 2413 6.102663 GCAGAGAATGAGTATACAACAGTGT 58.897 40.000 5.50 3.04 42.09 3.55
2354 2471 9.445878 CATATCTCCTGTAAAGACAATGCATAT 57.554 33.333 0.00 0.00 34.35 1.78
2355 2472 7.388776 GCATATCTCCTGTAAAGACAATGCATA 59.611 37.037 0.00 0.00 41.10 3.14
2356 2473 6.206243 GCATATCTCCTGTAAAGACAATGCAT 59.794 38.462 13.33 0.00 41.10 3.96
2357 2474 5.528690 GCATATCTCCTGTAAAGACAATGCA 59.471 40.000 13.33 0.00 41.10 3.96
2358 2475 5.762218 AGCATATCTCCTGTAAAGACAATGC 59.238 40.000 11.49 11.49 41.41 3.56
2359 2476 7.637229 CAAGCATATCTCCTGTAAAGACAATG 58.363 38.462 0.00 0.00 34.35 2.82
2360 2477 6.261826 GCAAGCATATCTCCTGTAAAGACAAT 59.738 38.462 0.00 0.00 34.35 2.71
2394 2511 0.395724 GGGTCCCATCGCCTTGAAAT 60.396 55.000 1.78 0.00 0.00 2.17
2439 2556 6.838382 TGGATATAGGAAGGGAACTAAAAGC 58.162 40.000 0.00 0.00 42.68 3.51
2596 2714 5.936956 ACCAAAACTGATGTTTGCAAGAAAA 59.063 32.000 0.00 0.00 44.70 2.29
2699 2818 1.561542 CTGGGCCATGAGGAGTAACTT 59.438 52.381 6.72 0.00 36.89 2.66
2706 2825 1.076559 CATTGCTGGGCCATGAGGA 60.077 57.895 6.72 0.00 34.22 3.71
2712 2831 0.541530 TGCTTAACATTGCTGGGCCA 60.542 50.000 5.85 5.85 0.00 5.36
2713 2832 0.108662 GTGCTTAACATTGCTGGGCC 60.109 55.000 0.00 0.00 0.00 5.80
2715 2834 1.255882 TGGTGCTTAACATTGCTGGG 58.744 50.000 0.00 0.00 0.00 4.45
2755 2874 1.638529 CACCAGGGAGTCAGAGAAGT 58.361 55.000 0.00 0.00 0.00 3.01
2757 2876 0.178921 AGCACCAGGGAGTCAGAGAA 60.179 55.000 0.00 0.00 0.00 2.87
2761 2880 1.004080 CACAGCACCAGGGAGTCAG 60.004 63.158 0.00 0.00 0.00 3.51
2770 2889 4.759693 CAGATTTTTAGTACCACAGCACCA 59.240 41.667 0.00 0.00 0.00 4.17
2771 2890 4.156008 CCAGATTTTTAGTACCACAGCACC 59.844 45.833 0.00 0.00 0.00 5.01
2772 2891 5.001232 TCCAGATTTTTAGTACCACAGCAC 58.999 41.667 0.00 0.00 0.00 4.40
2779 2898 6.884836 AGTGTTCCATCCAGATTTTTAGTACC 59.115 38.462 0.00 0.00 0.00 3.34
2780 2899 7.923414 AGTGTTCCATCCAGATTTTTAGTAC 57.077 36.000 0.00 0.00 0.00 2.73
2785 2904 9.533831 AGTTATTAGTGTTCCATCCAGATTTTT 57.466 29.630 0.00 0.00 0.00 1.94
2823 2942 5.047306 TGGTTCAGTAACTGTACTCTGGATG 60.047 44.000 0.00 0.00 38.58 3.51
2829 2948 4.822026 AGCATGGTTCAGTAACTGTACTC 58.178 43.478 0.00 0.00 38.58 2.59
2831 2950 5.334879 CCAAAGCATGGTTCAGTAACTGTAC 60.335 44.000 11.16 0.00 44.85 2.90
2869 2988 5.240403 TCGTCAATGAATGGTTGATGTCAAA 59.760 36.000 0.00 0.00 41.26 2.69
2878 2997 3.005554 CAGCTCTCGTCAATGAATGGTT 58.994 45.455 0.00 0.00 0.00 3.67
2928 3077 8.856103 GCTCCTTATAAATTACCAATAAAGGCA 58.144 33.333 0.00 0.00 0.00 4.75
2929 3078 8.856103 TGCTCCTTATAAATTACCAATAAAGGC 58.144 33.333 0.00 0.00 0.00 4.35
2965 3117 8.454106 CACATATTTTACTTCCTGAGAAACCTG 58.546 37.037 0.00 0.00 0.00 4.00
2966 3118 8.383175 TCACATATTTTACTTCCTGAGAAACCT 58.617 33.333 0.00 0.00 0.00 3.50
3009 3161 7.657336 AGGCAACAAAGAAATTTAGATTTCGA 58.343 30.769 11.80 0.00 46.90 3.71
3020 3172 7.768120 TGATAACAACAAAGGCAACAAAGAAAT 59.232 29.630 0.00 0.00 41.41 2.17
3021 3173 7.099764 TGATAACAACAAAGGCAACAAAGAAA 58.900 30.769 0.00 0.00 41.41 2.52
3024 3176 6.925165 AGATGATAACAACAAAGGCAACAAAG 59.075 34.615 0.00 0.00 41.41 2.77
3027 3179 6.403866 AAGATGATAACAACAAAGGCAACA 57.596 33.333 0.00 0.00 41.41 3.33
3028 3180 5.863935 GGAAGATGATAACAACAAAGGCAAC 59.136 40.000 0.00 0.00 0.00 4.17
3029 3181 5.047377 GGGAAGATGATAACAACAAAGGCAA 60.047 40.000 0.00 0.00 0.00 4.52
3059 3217 7.495606 AGCTTTGACAAATTGAAAGGTTTTAGG 59.504 33.333 0.00 0.00 34.58 2.69
3073 3231 9.277783 GATGGTATACTATCAGCTTTGACAAAT 57.722 33.333 20.82 0.00 34.46 2.32
3077 3235 8.144478 TCAAGATGGTATACTATCAGCTTTGAC 58.856 37.037 25.66 2.19 42.36 3.18
3151 3310 6.917477 CCACACATCAAAATATGGGTATTTCG 59.083 38.462 0.00 0.00 41.59 3.46
3156 3315 6.249192 TCAACCACACATCAAAATATGGGTA 58.751 36.000 0.00 0.00 41.59 3.69
3157 3316 5.083122 TCAACCACACATCAAAATATGGGT 58.917 37.500 0.00 0.00 44.37 4.51
3158 3317 5.394443 CCTCAACCACACATCAAAATATGGG 60.394 44.000 0.00 0.00 36.29 4.00
3162 3321 6.968263 TTTCCTCAACCACACATCAAAATA 57.032 33.333 0.00 0.00 0.00 1.40
3165 3324 5.047021 TGTTTTTCCTCAACCACACATCAAA 60.047 36.000 0.00 0.00 0.00 2.69
3211 3370 2.479566 TCCTGTTGGAGTTGAGATGC 57.520 50.000 0.00 0.00 37.46 3.91
3215 3374 4.580167 TGTCATTTTCCTGTTGGAGTTGAG 59.420 41.667 0.00 0.00 44.24 3.02
3250 3409 6.206829 GGTTTACTTTCTAATGACTGCCTTGT 59.793 38.462 0.00 0.00 0.00 3.16
3279 3438 4.591498 ACCGGATGTAGAAGCCATAATACA 59.409 41.667 9.46 0.00 33.04 2.29
3280 3439 5.148651 ACCGGATGTAGAAGCCATAATAC 57.851 43.478 9.46 0.00 0.00 1.89
3296 3455 1.153429 GCCGCAGTAAGAACCGGAT 60.153 57.895 9.46 0.00 43.20 4.18
3300 3459 1.671054 TGCTGCCGCAGTAAGAACC 60.671 57.895 21.29 3.78 42.25 3.62
3454 3613 5.107220 GGAAACAGCTTCATCAAATTGCTTG 60.107 40.000 0.00 0.00 35.55 4.01
3527 3691 7.639113 TGATGAGAACTGGTACAAAAACTTT 57.361 32.000 0.00 0.00 38.70 2.66
3535 3699 7.665145 TGAAATTTCATGATGAGAACTGGTACA 59.335 33.333 16.91 0.00 31.01 2.90
3560 3724 5.535333 ACATTTCCTGAAATTGAAGCAGTG 58.465 37.500 2.42 0.00 38.84 3.66
3754 3918 4.277476 TGAGGTTGTTGAACATGGAAAGT 58.723 39.130 0.00 0.00 33.27 2.66
3897 4062 6.339194 TGTTTAACGTTCATCATATCACCG 57.661 37.500 2.82 0.00 0.00 4.94
4022 4187 2.375014 AGGCGGAAAAGGAGGAAAAA 57.625 45.000 0.00 0.00 0.00 1.94
4085 4251 2.735126 CGCCTAAATTGAACATGTGCCC 60.735 50.000 0.00 0.00 0.00 5.36
4086 4252 2.163412 TCGCCTAAATTGAACATGTGCC 59.837 45.455 0.00 0.00 0.00 5.01
4087 4253 3.485947 TCGCCTAAATTGAACATGTGC 57.514 42.857 0.00 0.00 0.00 4.57
4229 4424 9.982291 CTTGCATCTTCAAAATCCAAATAAATG 57.018 29.630 0.00 0.00 0.00 2.32
4255 4450 4.376146 CAGGCTAGATTAAAGAGACTGGC 58.624 47.826 8.83 0.00 41.83 4.85
4516 4712 7.440523 AGTTCCATGATTTACACTTTGACTC 57.559 36.000 0.00 0.00 0.00 3.36
4517 4713 8.918202 TTAGTTCCATGATTTACACTTTGACT 57.082 30.769 0.00 0.00 0.00 3.41
4539 4735 1.398390 GCAGTCCCGCTGTTGATTTAG 59.602 52.381 0.00 0.00 46.64 1.85
4566 4773 7.510549 TTTCTTCAGTAACTTCATCAAAGGG 57.489 36.000 0.00 0.00 39.47 3.95
4625 4836 8.478066 AGGCAAAATAATAGGGAAGAAAATGTC 58.522 33.333 0.00 0.00 0.00 3.06
4655 4866 0.764369 AGGTGGAGTCCAGAAGCACA 60.764 55.000 13.61 0.00 32.34 4.57
4664 4875 2.348998 CTGGTGCAGGTGGAGTCC 59.651 66.667 0.73 0.73 0.00 3.85
4725 4936 3.751175 TGAAAAGGAACAGCTGGAATACG 59.249 43.478 19.93 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.