Multiple sequence alignment - TraesCS7B01G401200

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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 TraesCS7B01G401200 chr7B 100.000 3939 0 0 1 3939 667627057 667630995 0.000000e+00 7275
1 TraesCS7B01G401200 chr7D 89.368 1900 120 34 800 2675 593273666 593271825 0.000000e+00 2314
2 TraesCS7B01G401200 chr7D 91.352 1272 91 9 2671 3934 593271775 593270515 0.000000e+00 1722
3 TraesCS7B01G401200 chr7D 78.324 549 78 25 86 629 593274328 593273816 2.280000e-82 316
4 TraesCS7B01G401200 chr7A 93.340 1081 65 4 2695 3771 686109268 686108191 0.000000e+00 1591
5 TraesCS7B01G401200 chr7A 96.120 902 32 3 1775 2675 686110269 686109370 0.000000e+00 1469
6 TraesCS7B01G401200 chr7A 83.007 1124 84 48 728 1783 686111428 686110344 0.000000e+00 918
7 TraesCS7B01G401200 chr7A 81.518 606 78 18 73 673 686112016 686111440 5.960000e-128 468


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 TraesCS7B01G401200 chr7B 667627057 667630995 3938 False 7275.000000 7275 100.00000 1 3939 1 chr7B.!!$F1 3938
1 TraesCS7B01G401200 chr7D 593270515 593274328 3813 True 1450.666667 2314 86.34800 86 3934 3 chr7D.!!$R1 3848
2 TraesCS7B01G401200 chr7A 686108191 686112016 3825 True 1111.500000 1591 88.49625 73 3771 4 chr7A.!!$R1 3698

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
52 53 0.037326 CAAGAGCCTAGCCACGTTCA 60.037 55.0 0.0 0.0 0.0 3.18 F
928 970 0.468029 CAGCCTCTCCTCCTCCTCTC 60.468 65.0 0.0 0.0 0.0 3.20 F
1530 1611 0.255318 AGCTTTCTCCTGGGATGCTG 59.745 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1178 1224 0.106708 GCAGGAATCGATGCCCTACA 59.893 55.0 19.57 0.0 36.41 2.74 R
2733 3017 1.357907 CTGCTGACTTGTAGAGCTGC 58.642 55.0 0.00 0.0 33.66 5.25 R
3456 3744 0.177836 CAGGACACGGTGATATGCCA 59.822 55.0 16.29 0.0 0.00 4.92 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
21 22 4.425180 TTACTGTTAAGTTGCACCTCCA 57.575 40.909 0.00 0.00 37.88 3.86
22 23 3.290948 ACTGTTAAGTTGCACCTCCAA 57.709 42.857 0.00 0.00 30.14 3.53
23 24 3.626930 ACTGTTAAGTTGCACCTCCAAA 58.373 40.909 0.00 0.00 30.14 3.28
24 25 3.380320 ACTGTTAAGTTGCACCTCCAAAC 59.620 43.478 0.00 0.00 30.14 2.93
25 26 2.691011 TGTTAAGTTGCACCTCCAAACC 59.309 45.455 0.00 0.00 0.00 3.27
26 27 2.691011 GTTAAGTTGCACCTCCAAACCA 59.309 45.455 0.00 0.00 0.00 3.67
27 28 1.402787 AAGTTGCACCTCCAAACCAG 58.597 50.000 0.00 0.00 0.00 4.00
28 29 0.468029 AGTTGCACCTCCAAACCAGG 60.468 55.000 0.00 0.00 37.03 4.45
29 30 0.755327 GTTGCACCTCCAAACCAGGT 60.755 55.000 0.00 0.00 45.89 4.00
30 31 0.847373 TTGCACCTCCAAACCAGGTA 59.153 50.000 0.00 0.00 42.85 3.08
31 32 0.847373 TGCACCTCCAAACCAGGTAA 59.153 50.000 0.00 0.00 42.85 2.85
32 33 1.244816 GCACCTCCAAACCAGGTAAC 58.755 55.000 0.00 0.00 42.85 2.50
33 34 1.905637 CACCTCCAAACCAGGTAACC 58.094 55.000 0.00 0.00 42.85 2.85
34 35 1.144093 CACCTCCAAACCAGGTAACCA 59.856 52.381 0.00 0.00 42.85 3.67
35 36 1.854280 ACCTCCAAACCAGGTAACCAA 59.146 47.619 0.00 0.00 42.91 3.67
36 37 2.158519 ACCTCCAAACCAGGTAACCAAG 60.159 50.000 0.00 0.00 42.91 3.61
37 38 2.107552 CCTCCAAACCAGGTAACCAAGA 59.892 50.000 0.00 0.00 37.17 3.02
38 39 3.412386 CTCCAAACCAGGTAACCAAGAG 58.588 50.000 0.00 0.00 37.17 2.85
39 40 1.886542 CCAAACCAGGTAACCAAGAGC 59.113 52.381 0.00 0.00 37.17 4.09
40 41 1.886542 CAAACCAGGTAACCAAGAGCC 59.113 52.381 0.00 0.00 37.17 4.70
41 42 1.446016 AACCAGGTAACCAAGAGCCT 58.554 50.000 0.00 0.00 37.17 4.58
42 43 2.337359 ACCAGGTAACCAAGAGCCTA 57.663 50.000 0.00 0.00 37.17 3.93
43 44 2.188817 ACCAGGTAACCAAGAGCCTAG 58.811 52.381 0.00 0.00 37.17 3.02
44 45 1.134371 CCAGGTAACCAAGAGCCTAGC 60.134 57.143 0.00 0.00 37.17 3.42
45 46 1.134371 CAGGTAACCAAGAGCCTAGCC 60.134 57.143 0.00 0.00 37.17 3.93
46 47 0.909623 GGTAACCAAGAGCCTAGCCA 59.090 55.000 0.00 0.00 0.00 4.75
47 48 1.407025 GGTAACCAAGAGCCTAGCCAC 60.407 57.143 0.00 0.00 0.00 5.01
48 49 0.535335 TAACCAAGAGCCTAGCCACG 59.465 55.000 0.00 0.00 0.00 4.94
49 50 1.481056 AACCAAGAGCCTAGCCACGT 61.481 55.000 0.00 0.00 0.00 4.49
50 51 1.296715 CCAAGAGCCTAGCCACGTT 59.703 57.895 0.00 0.00 0.00 3.99
51 52 0.741221 CCAAGAGCCTAGCCACGTTC 60.741 60.000 0.00 0.00 0.00 3.95
52 53 0.037326 CAAGAGCCTAGCCACGTTCA 60.037 55.000 0.00 0.00 0.00 3.18
53 54 0.685097 AAGAGCCTAGCCACGTTCAA 59.315 50.000 0.00 0.00 0.00 2.69
54 55 0.685097 AGAGCCTAGCCACGTTCAAA 59.315 50.000 0.00 0.00 0.00 2.69
55 56 1.071699 AGAGCCTAGCCACGTTCAAAA 59.928 47.619 0.00 0.00 0.00 2.44
56 57 1.877443 GAGCCTAGCCACGTTCAAAAA 59.123 47.619 0.00 0.00 0.00 1.94
92 93 0.995024 AAGAGCCTAGCCAATGGTGT 59.005 50.000 0.00 0.00 0.00 4.16
103 104 2.871236 GCCAATGGTGTCAAAATGGTGG 60.871 50.000 0.00 0.00 31.74 4.61
118 119 1.285950 GTGGAAACGAAGGCTTGCC 59.714 57.895 3.46 2.97 0.00 4.52
120 121 1.172180 TGGAAACGAAGGCTTGCCAG 61.172 55.000 14.54 7.26 0.00 4.85
236 243 1.292061 TGAACAAAGGACAACGACCG 58.708 50.000 0.00 0.00 0.00 4.79
239 246 2.663852 AAAGGACAACGACCGCGG 60.664 61.111 26.86 26.86 43.17 6.46
261 268 4.381185 GGCAACTTCATTGATTCAGATGCA 60.381 41.667 16.24 0.00 41.23 3.96
287 294 4.104086 ACTGGATCCATTCAAGTAGGTCA 58.896 43.478 16.63 0.00 36.81 4.02
296 303 5.652014 CCATTCAAGTAGGTCATGGCTTAAA 59.348 40.000 0.00 0.00 0.00 1.52
472 479 2.368655 ATGCGGACATTTTTCCTTGC 57.631 45.000 0.00 0.00 30.07 4.01
477 484 3.652274 CGGACATTTTTCCTTGCAACAT 58.348 40.909 0.00 0.00 32.88 2.71
491 498 9.806203 TTCCTTGCAACATATGAATATTTCTTG 57.194 29.630 10.38 1.97 0.00 3.02
505 512 9.499479 TGAATATTTCTTGCCAGATAGAAGATC 57.501 33.333 0.00 0.00 32.43 2.75
549 556 5.947503 TTTTTCTGTGCGAAATGAAGTTG 57.052 34.783 0.00 0.00 41.04 3.16
550 557 2.686558 TCTGTGCGAAATGAAGTTGC 57.313 45.000 0.00 0.00 0.00 4.17
556 563 4.208873 TGTGCGAAATGAAGTTGCATTTTC 59.791 37.500 11.86 0.00 45.63 2.29
560 567 6.644181 TGCGAAATGAAGTTGCATTTTCATAA 59.356 30.769 20.19 7.32 45.63 1.90
562 569 8.008844 GCGAAATGAAGTTGCATTTTCATAAAA 58.991 29.630 20.19 0.00 45.63 1.52
563 570 9.861138 CGAAATGAAGTTGCATTTTCATAAAAA 57.139 25.926 20.19 0.00 45.63 1.94
722 730 7.500720 AAACAAACCAGTATACCAGTTACAC 57.499 36.000 8.18 0.00 0.00 2.90
723 731 5.232463 ACAAACCAGTATACCAGTTACACG 58.768 41.667 8.18 0.00 0.00 4.49
724 732 4.460948 AACCAGTATACCAGTTACACGG 57.539 45.455 6.38 0.00 0.00 4.94
725 733 2.762327 ACCAGTATACCAGTTACACGGG 59.238 50.000 0.00 0.00 39.46 5.28
726 734 2.482490 CCAGTATACCAGTTACACGGGC 60.482 54.545 0.00 0.00 36.91 6.13
732 753 1.070786 CAGTTACACGGGCCACACT 59.929 57.895 4.39 0.00 0.00 3.55
735 756 1.010419 GTTACACGGGCCACACTACG 61.010 60.000 4.39 0.00 0.00 3.51
740 761 2.377310 CGGGCCACACTACGTTTCG 61.377 63.158 4.39 0.00 0.00 3.46
748 769 3.311106 CACACTACGTTTCGGTACATGT 58.689 45.455 2.69 2.69 0.00 3.21
768 789 1.460743 TGAAAAGCTTCAGACGATGCG 59.539 47.619 0.00 0.00 44.80 4.73
784 805 4.011517 CGGGCCCGTGTACCAAGT 62.012 66.667 36.64 0.00 34.35 3.16
787 808 2.281208 GCCCGTGTACCAAGTGCA 60.281 61.111 0.00 0.00 0.00 4.57
788 809 2.325082 GCCCGTGTACCAAGTGCAG 61.325 63.158 0.00 0.00 0.00 4.41
864 905 2.124277 ACAAACCGCTAATCCCCTTC 57.876 50.000 0.00 0.00 0.00 3.46
865 906 1.340697 ACAAACCGCTAATCCCCTTCC 60.341 52.381 0.00 0.00 0.00 3.46
898 940 2.579241 TAGTCTCGCTTGCGCTCGAC 62.579 60.000 9.73 14.72 34.93 4.20
927 969 1.620259 CAGCCTCTCCTCCTCCTCT 59.380 63.158 0.00 0.00 0.00 3.69
928 970 0.468029 CAGCCTCTCCTCCTCCTCTC 60.468 65.000 0.00 0.00 0.00 3.20
929 971 1.152546 GCCTCTCCTCCTCCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
930 972 1.655114 GCCTCTCCTCCTCCTCTCCT 61.655 65.000 0.00 0.00 0.00 3.69
1033 1075 0.958876 TCGCGCTCTCTGTACCTTCA 60.959 55.000 5.56 0.00 0.00 3.02
1076 1118 1.996755 GCGCTGCGAGTTACTTACC 59.003 57.895 28.07 0.00 0.00 2.85
1082 1124 4.679662 GCTGCGAGTTACTTACCAGATAA 58.320 43.478 10.49 0.00 0.00 1.75
1099 1145 1.875488 TAAGTGGAGAACCCTAGGCC 58.125 55.000 2.05 0.00 35.38 5.19
1134 1180 4.884257 GCGACCTGCGGCGGATTA 62.884 66.667 11.13 0.00 41.29 1.75
1154 1200 5.828299 TTATTGGCTAGTATTGGTTGTGC 57.172 39.130 0.00 0.00 0.00 4.57
1163 1209 3.702284 TATTGGTTGTGCGAGGGGTCG 62.702 57.143 0.00 0.00 0.00 4.79
1205 1251 1.960040 ATCGATTCCTGCGAGCCACA 61.960 55.000 0.00 0.00 41.49 4.17
1271 1322 0.732880 CGAGGTCACAGCCAGTAACG 60.733 60.000 0.00 0.00 0.00 3.18
1272 1323 0.601558 GAGGTCACAGCCAGTAACGA 59.398 55.000 0.00 0.00 0.00 3.85
1273 1324 1.000506 GAGGTCACAGCCAGTAACGAA 59.999 52.381 0.00 0.00 0.00 3.85
1274 1325 1.623811 AGGTCACAGCCAGTAACGAAT 59.376 47.619 0.00 0.00 0.00 3.34
1293 1344 0.537188 TCCCTTCCGATCTGCTGTTC 59.463 55.000 0.00 0.00 0.00 3.18
1402 1471 6.316319 TCAAAAGTCTGTCCGTTTTTGTTAC 58.684 36.000 7.99 0.00 39.96 2.50
1408 1477 5.568677 GTCTGTCCGTTTTTGTTACGTTTTT 59.431 36.000 0.00 0.00 37.30 1.94
1413 1482 4.027540 CCGTTTTTGTTACGTTTTTGCGAT 60.028 37.500 0.00 0.00 37.30 4.58
1423 1492 2.471103 CGTTTTTGCGATTCATTGCTGC 60.471 45.455 0.00 0.00 38.05 5.25
1424 1493 2.728690 TTTTGCGATTCATTGCTGCT 57.271 40.000 0.00 0.00 38.05 4.24
1425 1494 1.985334 TTTGCGATTCATTGCTGCTG 58.015 45.000 0.00 0.00 38.05 4.41
1497 1566 5.053811 TCGTCAAGAGCAGTGAAATTGTTA 58.946 37.500 0.00 0.00 0.00 2.41
1505 1586 6.040842 AGAGCAGTGAAATTGTTACCAATGTT 59.959 34.615 0.00 0.00 40.42 2.71
1506 1587 6.581712 AGCAGTGAAATTGTTACCAATGTTT 58.418 32.000 0.00 0.00 40.42 2.83
1507 1588 7.047271 AGCAGTGAAATTGTTACCAATGTTTT 58.953 30.769 0.00 0.00 40.42 2.43
1508 1589 7.011295 AGCAGTGAAATTGTTACCAATGTTTTG 59.989 33.333 0.00 0.00 40.42 2.44
1509 1590 7.201600 GCAGTGAAATTGTTACCAATGTTTTGT 60.202 33.333 0.00 0.00 40.42 2.83
1510 1591 9.307121 CAGTGAAATTGTTACCAATGTTTTGTA 57.693 29.630 0.00 0.00 40.42 2.41
1511 1592 9.877178 AGTGAAATTGTTACCAATGTTTTGTAA 57.123 25.926 0.00 0.00 40.42 2.41
1513 1594 8.821894 TGAAATTGTTACCAATGTTTTGTAAGC 58.178 29.630 0.00 0.00 40.42 3.09
1514 1595 8.956533 AAATTGTTACCAATGTTTTGTAAGCT 57.043 26.923 0.00 0.00 40.42 3.74
1515 1596 8.956533 AATTGTTACCAATGTTTTGTAAGCTT 57.043 26.923 3.48 3.48 40.42 3.74
1516 1597 8.956533 ATTGTTACCAATGTTTTGTAAGCTTT 57.043 26.923 3.20 0.00 39.81 3.51
1523 1604 5.712152 ATGTTTTGTAAGCTTTCTCCTGG 57.288 39.130 3.20 0.00 0.00 4.45
1524 1605 3.888930 TGTTTTGTAAGCTTTCTCCTGGG 59.111 43.478 3.20 0.00 0.00 4.45
1530 1611 0.255318 AGCTTTCTCCTGGGATGCTG 59.745 55.000 0.00 0.00 0.00 4.41
1540 1621 4.722700 GGATGCTGCCACGGGTGT 62.723 66.667 0.00 0.00 0.00 4.16
1542 1623 4.269523 ATGCTGCCACGGGTGTGT 62.270 61.111 0.00 0.00 44.92 3.72
1543 1624 4.927782 TGCTGCCACGGGTGTGTC 62.928 66.667 0.00 0.00 44.92 3.67
1544 1625 4.927782 GCTGCCACGGGTGTGTCA 62.928 66.667 0.00 0.00 44.92 3.58
1546 1627 1.295101 CTGCCACGGGTGTGTCATA 59.705 57.895 0.00 0.00 44.92 2.15
1580 1665 4.096081 GCAAAATTCTGTATCTGCTGCTCT 59.904 41.667 0.00 0.00 0.00 4.09
1603 1693 0.537371 GCACTGCAGTTAGGTTGGGT 60.537 55.000 18.94 0.00 0.00 4.51
1604 1694 1.271163 GCACTGCAGTTAGGTTGGGTA 60.271 52.381 18.94 0.00 0.00 3.69
1605 1695 2.699954 CACTGCAGTTAGGTTGGGTAG 58.300 52.381 18.94 0.00 0.00 3.18
1606 1696 2.038557 CACTGCAGTTAGGTTGGGTAGT 59.961 50.000 18.94 0.00 0.00 2.73
1607 1697 2.038557 ACTGCAGTTAGGTTGGGTAGTG 59.961 50.000 15.25 0.00 0.00 2.74
1608 1698 1.271163 TGCAGTTAGGTTGGGTAGTGC 60.271 52.381 0.00 0.00 37.44 4.40
1625 1715 6.239629 GGGTAGTGCTGCTATTACTAATCCTT 60.240 42.308 0.00 0.00 31.50 3.36
1626 1716 6.647067 GGTAGTGCTGCTATTACTAATCCTTG 59.353 42.308 0.00 0.00 31.50 3.61
1683 1784 3.990469 ACAGCACAGAATTGTACTTCTCG 59.010 43.478 0.00 0.00 35.25 4.04
1709 1810 5.705902 TGAATTCAGCATTTGACATGAGTG 58.294 37.500 3.38 0.00 34.94 3.51
1769 1870 0.877071 CTGCAACTTGTGGTAGCTGG 59.123 55.000 0.00 0.00 0.00 4.85
1780 1964 3.644265 TGTGGTAGCTGGTTCAGAACTAA 59.356 43.478 13.13 1.60 32.44 2.24
1821 2006 4.806952 ATTGAGGATTATTTTCCCGGGA 57.193 40.909 22.63 22.63 36.35 5.14
1846 2031 2.295909 TGCTGGGTTGCTGTATTTGAAC 59.704 45.455 0.00 0.00 0.00 3.18
1992 2178 2.835764 AGTACCCGCAAGAACATCCTTA 59.164 45.455 0.00 0.00 43.02 2.69
2250 2436 1.208259 CAAGCCGTTCTTGCAAAACC 58.792 50.000 0.00 0.00 44.85 3.27
2386 2574 5.675684 TGTCTCATTCTTGTACATGCCTA 57.324 39.130 0.00 0.00 0.00 3.93
2614 2802 0.332293 TTGATGGGCAATGCTCTGGA 59.668 50.000 6.67 0.00 0.00 3.86
2640 2828 7.931015 ATTTGGGAGACATACTGATAAGGTA 57.069 36.000 0.00 0.00 0.00 3.08
2675 2863 7.816640 TCAAATCTTTTACCACAGCTATTGTC 58.183 34.615 0.00 0.00 38.16 3.18
2677 2865 7.617041 AATCTTTTACCACAGCTATTGTCTC 57.383 36.000 0.00 0.00 38.16 3.36
2678 2866 6.109156 TCTTTTACCACAGCTATTGTCTCA 57.891 37.500 0.00 0.00 38.16 3.27
2733 3017 6.412362 AGATATAAACTGGTAGCACTCCTG 57.588 41.667 0.00 0.00 0.00 3.86
2734 3018 2.762535 TAAACTGGTAGCACTCCTGC 57.237 50.000 0.00 0.00 44.63 4.85
2740 3024 1.612395 GGTAGCACTCCTGCAGCTCT 61.612 60.000 8.66 2.61 46.97 4.09
2821 3105 6.225981 ACTCAGTCTTACATCACATATGCA 57.774 37.500 1.58 0.00 0.00 3.96
2825 3109 6.536224 TCAGTCTTACATCACATATGCAAGTG 59.464 38.462 1.58 10.11 37.10 3.16
2830 3114 7.769970 TCTTACATCACATATGCAAGTGAATGA 59.230 33.333 19.45 9.68 46.62 2.57
2832 3116 5.884232 ACATCACATATGCAAGTGAATGACT 59.116 36.000 19.45 4.86 46.62 3.41
2838 3122 3.144657 TGCAAGTGAATGACTGGATGT 57.855 42.857 0.00 0.00 34.02 3.06
2839 3123 2.815503 TGCAAGTGAATGACTGGATGTG 59.184 45.455 0.00 0.00 34.02 3.21
2978 3262 1.337703 TGGTTGATGCTTGCTGTTCAC 59.662 47.619 0.00 0.00 0.00 3.18
3076 3360 3.902881 AACTCTAGTTCTGCATCCTGG 57.097 47.619 0.00 0.00 31.64 4.45
3111 3395 3.791973 AACTTGCATGTTTGAAACGGA 57.208 38.095 11.92 0.00 0.00 4.69
3130 3414 4.581824 ACGGATGATTGCTTATTGCTGATT 59.418 37.500 0.00 0.00 43.37 2.57
3204 3488 5.861251 TGATCGTATTTGTGCAATTTGAACC 59.139 36.000 5.04 0.00 0.00 3.62
3205 3489 5.188327 TCGTATTTGTGCAATTTGAACCA 57.812 34.783 5.04 0.00 0.00 3.67
3283 3571 5.123820 TCCGCTCCATTTATGTCTTTTTCTG 59.876 40.000 0.00 0.00 0.00 3.02
3284 3572 5.106157 CCGCTCCATTTATGTCTTTTTCTGT 60.106 40.000 0.00 0.00 0.00 3.41
3355 3643 2.552315 CACTTGCACCGTTCATAGGTTT 59.448 45.455 0.00 0.00 40.59 3.27
3356 3644 3.004315 CACTTGCACCGTTCATAGGTTTT 59.996 43.478 0.00 0.00 40.59 2.43
3359 3647 3.215151 TGCACCGTTCATAGGTTTTTGA 58.785 40.909 0.00 0.00 40.59 2.69
3374 3662 4.211164 GGTTTTTGAATGCTGTTTACTGCC 59.789 41.667 8.91 0.00 39.65 4.85
3477 3765 1.539065 GGCATATCACCGTGTCCTGAG 60.539 57.143 0.00 0.00 0.00 3.35
3485 3773 1.691976 ACCGTGTCCTGAGTGAATGAA 59.308 47.619 0.00 0.00 0.00 2.57
3517 3805 6.357579 TGCATGTTTTAAGGGTTGATTGAT 57.642 33.333 0.00 0.00 0.00 2.57
3561 3849 5.948758 TGTGGCTGTTGGATATGTTTTGATA 59.051 36.000 0.00 0.00 0.00 2.15
3619 3907 9.020731 TGAACTATATATCTCGTGGAATTGCTA 57.979 33.333 0.00 0.00 0.00 3.49
3627 3915 1.405105 CGTGGAATTGCTAACCATGGG 59.595 52.381 18.09 0.00 37.14 4.00
3651 3939 5.220989 GCTCAGACATATGTGTTGCATGATT 60.221 40.000 14.43 0.00 39.09 2.57
3663 3951 6.374894 TGTGTTGCATGATTGAAGACATATGA 59.625 34.615 10.38 0.00 0.00 2.15
3730 4019 1.576356 GGAGCTAGATTTGGACTGCG 58.424 55.000 0.00 0.00 0.00 5.18
3751 4040 3.607078 CGTTGAACTAGCAAGCCAAGTTC 60.607 47.826 21.62 21.62 45.99 3.01
3761 4050 0.036010 AGCCAAGTTCGTGGATCAGG 60.036 55.000 8.81 0.00 41.65 3.86
3793 4082 1.621814 TCAACTCCACGGGGACTAAAG 59.378 52.381 0.00 0.00 38.64 1.85
3799 4088 1.425412 CACGGGGACTAAAGTGTTCG 58.575 55.000 0.00 0.00 0.00 3.95
3800 4089 0.319405 ACGGGGACTAAAGTGTTCGG 59.681 55.000 0.00 0.00 0.00 4.30
3814 4103 1.274167 TGTTCGGGCGTGATAAGTTCT 59.726 47.619 0.00 0.00 0.00 3.01
3824 4113 2.609459 GTGATAAGTTCTGGCATGTCGG 59.391 50.000 0.00 0.00 0.00 4.79
3827 4116 0.613260 AAGTTCTGGCATGTCGGCTA 59.387 50.000 0.00 0.00 41.89 3.93
3839 4128 3.769739 TGTCGGCTATGATTAAGGCAT 57.230 42.857 0.00 0.12 39.38 4.40
3848 4137 6.317391 GGCTATGATTAAGGCATTCTCATACC 59.683 42.308 10.53 12.05 39.24 2.73
3866 4155 0.107848 CCATAAGTTCGGTCGGCCTT 60.108 55.000 3.66 0.00 0.00 4.35
3872 4161 3.014085 TTCGGTCGGCCTTGGCTAG 62.014 63.158 3.66 6.48 0.00 3.42
3885 4176 1.666234 GGCTAGCCGCTCTATGCAC 60.666 63.158 20.16 0.00 43.06 4.57
3898 4189 2.490509 TCTATGCACGAACTTTCCGAGA 59.509 45.455 0.00 0.00 0.00 4.04
3900 4191 1.710013 TGCACGAACTTTCCGAGATC 58.290 50.000 0.00 0.00 0.00 2.75
3934 4225 5.003804 ACTAGCAAGGAATCATGAAACGTT 58.996 37.500 0.00 0.00 0.00 3.99
3935 4226 6.170506 ACTAGCAAGGAATCATGAAACGTTA 58.829 36.000 0.00 0.00 0.00 3.18
3936 4227 5.957842 AGCAAGGAATCATGAAACGTTAA 57.042 34.783 0.00 0.00 0.00 2.01
3937 4228 6.515272 AGCAAGGAATCATGAAACGTTAAT 57.485 33.333 0.00 0.00 0.00 1.40
3938 4229 6.324819 AGCAAGGAATCATGAAACGTTAATG 58.675 36.000 14.67 14.67 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.425180 TGGAGGTGCAACTTAACAGTAA 57.575 40.909 5.31 0.00 36.74 2.24
1 2 4.425180 TTGGAGGTGCAACTTAACAGTA 57.575 40.909 5.31 0.00 36.74 2.74
3 4 3.243401 GGTTTGGAGGTGCAACTTAACAG 60.243 47.826 20.09 0.00 36.74 3.16
5 6 2.691011 TGGTTTGGAGGTGCAACTTAAC 59.309 45.455 5.31 11.01 36.74 2.01
6 7 2.955660 CTGGTTTGGAGGTGCAACTTAA 59.044 45.455 5.31 1.38 36.74 1.85
7 8 2.582052 CTGGTTTGGAGGTGCAACTTA 58.418 47.619 5.31 0.00 36.74 2.24
8 9 1.402787 CTGGTTTGGAGGTGCAACTT 58.597 50.000 5.31 0.00 36.74 2.66
9 10 0.468029 CCTGGTTTGGAGGTGCAACT 60.468 55.000 2.34 2.34 36.74 3.16
10 11 0.755327 ACCTGGTTTGGAGGTGCAAC 60.755 55.000 0.00 0.00 42.56 4.17
11 12 0.847373 TACCTGGTTTGGAGGTGCAA 59.153 50.000 3.84 0.00 43.99 4.08
12 13 0.847373 TTACCTGGTTTGGAGGTGCA 59.153 50.000 3.84 0.00 43.99 4.57
13 14 1.244816 GTTACCTGGTTTGGAGGTGC 58.755 55.000 3.84 0.00 43.99 5.01
14 15 1.144093 TGGTTACCTGGTTTGGAGGTG 59.856 52.381 3.84 0.00 43.99 4.00
15 16 1.525175 TGGTTACCTGGTTTGGAGGT 58.475 50.000 3.84 0.00 46.10 3.85
16 17 2.107552 TCTTGGTTACCTGGTTTGGAGG 59.892 50.000 3.84 0.00 36.57 4.30
17 18 3.412386 CTCTTGGTTACCTGGTTTGGAG 58.588 50.000 3.84 1.52 0.00 3.86
18 19 2.488347 GCTCTTGGTTACCTGGTTTGGA 60.488 50.000 3.84 0.00 0.00 3.53
19 20 1.886542 GCTCTTGGTTACCTGGTTTGG 59.113 52.381 3.84 0.00 0.00 3.28
20 21 1.886542 GGCTCTTGGTTACCTGGTTTG 59.113 52.381 3.84 0.00 0.00 2.93
21 22 1.780919 AGGCTCTTGGTTACCTGGTTT 59.219 47.619 3.84 0.00 0.00 3.27
22 23 1.446016 AGGCTCTTGGTTACCTGGTT 58.554 50.000 3.84 0.00 0.00 3.67
23 24 2.188817 CTAGGCTCTTGGTTACCTGGT 58.811 52.381 4.05 4.05 33.60 4.00
24 25 1.134371 GCTAGGCTCTTGGTTACCTGG 60.134 57.143 2.07 0.00 33.60 4.45
25 26 1.134371 GGCTAGGCTCTTGGTTACCTG 60.134 57.143 9.46 0.00 33.60 4.00
26 27 1.205055 GGCTAGGCTCTTGGTTACCT 58.795 55.000 9.46 0.00 36.27 3.08
27 28 0.909623 TGGCTAGGCTCTTGGTTACC 59.090 55.000 18.18 0.00 0.00 2.85
28 29 1.739371 CGTGGCTAGGCTCTTGGTTAC 60.739 57.143 18.18 3.53 0.00 2.50
29 30 0.535335 CGTGGCTAGGCTCTTGGTTA 59.465 55.000 18.18 0.00 0.00 2.85
30 31 1.296715 CGTGGCTAGGCTCTTGGTT 59.703 57.895 18.18 0.00 0.00 3.67
31 32 1.481056 AACGTGGCTAGGCTCTTGGT 61.481 55.000 18.18 4.83 0.00 3.67
32 33 0.741221 GAACGTGGCTAGGCTCTTGG 60.741 60.000 18.18 4.20 0.00 3.61
33 34 0.037326 TGAACGTGGCTAGGCTCTTG 60.037 55.000 18.18 6.94 0.00 3.02
34 35 0.685097 TTGAACGTGGCTAGGCTCTT 59.315 50.000 18.18 4.60 0.00 2.85
35 36 0.685097 TTTGAACGTGGCTAGGCTCT 59.315 50.000 18.18 0.00 0.00 4.09
36 37 1.519408 TTTTGAACGTGGCTAGGCTC 58.481 50.000 18.18 13.04 0.00 4.70
37 38 1.975660 TTTTTGAACGTGGCTAGGCT 58.024 45.000 18.18 0.00 0.00 4.58
67 68 3.259123 CCATTGGCTAGGCTCTTGTTTTT 59.741 43.478 18.18 0.00 0.00 1.94
68 69 2.827921 CCATTGGCTAGGCTCTTGTTTT 59.172 45.455 18.18 0.00 0.00 2.43
69 70 2.225117 ACCATTGGCTAGGCTCTTGTTT 60.225 45.455 18.18 0.00 0.00 2.83
70 71 1.355720 ACCATTGGCTAGGCTCTTGTT 59.644 47.619 18.18 0.00 0.00 2.83
71 72 0.995024 ACCATTGGCTAGGCTCTTGT 59.005 50.000 18.18 7.03 0.00 3.16
72 73 1.340405 ACACCATTGGCTAGGCTCTTG 60.340 52.381 18.18 11.49 0.00 3.02
73 74 0.995024 ACACCATTGGCTAGGCTCTT 59.005 50.000 18.18 0.00 0.00 2.85
74 75 0.543749 GACACCATTGGCTAGGCTCT 59.456 55.000 18.18 1.46 0.00 4.09
75 76 0.253044 TGACACCATTGGCTAGGCTC 59.747 55.000 18.18 5.22 0.00 4.70
76 77 0.698238 TTGACACCATTGGCTAGGCT 59.302 50.000 18.18 0.00 0.00 4.58
84 85 4.333913 TTCCACCATTTTGACACCATTG 57.666 40.909 0.00 0.00 0.00 2.82
92 93 2.035321 GCCTTCGTTTCCACCATTTTGA 59.965 45.455 0.00 0.00 0.00 2.69
103 104 1.081175 GCTGGCAAGCCTTCGTTTC 60.081 57.895 12.96 0.00 44.22 2.78
146 152 9.869757 CGTGGATATGTAATGTATCAGGAATTA 57.130 33.333 0.00 0.00 31.61 1.40
147 153 7.824289 CCGTGGATATGTAATGTATCAGGAATT 59.176 37.037 0.00 0.00 31.61 2.17
148 154 7.180229 TCCGTGGATATGTAATGTATCAGGAAT 59.820 37.037 0.00 0.00 31.49 3.01
149 155 6.495526 TCCGTGGATATGTAATGTATCAGGAA 59.504 38.462 0.00 0.00 31.49 3.36
150 156 6.014012 TCCGTGGATATGTAATGTATCAGGA 58.986 40.000 0.00 0.00 31.72 3.86
151 157 6.100004 GTCCGTGGATATGTAATGTATCAGG 58.900 44.000 0.00 0.00 31.61 3.86
152 158 6.100004 GGTCCGTGGATATGTAATGTATCAG 58.900 44.000 0.00 0.00 31.61 2.90
153 159 5.540719 TGGTCCGTGGATATGTAATGTATCA 59.459 40.000 0.00 0.00 31.61 2.15
154 160 6.032956 TGGTCCGTGGATATGTAATGTATC 57.967 41.667 0.00 0.00 0.00 2.24
155 161 5.778241 TCTGGTCCGTGGATATGTAATGTAT 59.222 40.000 0.00 0.00 0.00 2.29
156 162 5.141910 TCTGGTCCGTGGATATGTAATGTA 58.858 41.667 0.00 0.00 0.00 2.29
157 163 3.964688 TCTGGTCCGTGGATATGTAATGT 59.035 43.478 0.00 0.00 0.00 2.71
158 164 4.280929 TCTCTGGTCCGTGGATATGTAATG 59.719 45.833 0.00 0.00 0.00 1.90
159 165 4.480115 TCTCTGGTCCGTGGATATGTAAT 58.520 43.478 0.00 0.00 0.00 1.89
160 166 3.905968 TCTCTGGTCCGTGGATATGTAA 58.094 45.455 0.00 0.00 0.00 2.41
167 173 2.434336 CCATTTATCTCTGGTCCGTGGA 59.566 50.000 0.00 0.00 0.00 4.02
222 229 2.663852 CCGCGGTCGTTGTCCTTT 60.664 61.111 19.50 0.00 0.00 3.11
236 243 2.162208 TCTGAATCAATGAAGTTGCCGC 59.838 45.455 0.00 0.00 37.74 6.53
239 246 4.740268 TGCATCTGAATCAATGAAGTTGC 58.260 39.130 8.68 8.68 37.74 4.17
240 247 7.061905 GTCTTTGCATCTGAATCAATGAAGTTG 59.938 37.037 8.76 0.00 39.25 3.16
241 248 7.039923 AGTCTTTGCATCTGAATCAATGAAGTT 60.040 33.333 8.76 0.00 0.00 2.66
261 268 5.251700 ACCTACTTGAATGGATCCAGTCTTT 59.748 40.000 34.86 23.37 41.06 2.52
287 294 7.438160 GTGAGCTTACAAAAACTTTTAAGCCAT 59.562 33.333 14.48 3.02 40.22 4.40
454 461 1.035923 TGCAAGGAAAAATGTCCGCA 58.964 45.000 0.00 0.00 43.03 5.69
537 544 9.861138 TTTTTATGAAAATGCAACTTCATTTCG 57.139 25.926 23.82 0.00 41.41 3.46
577 585 9.999009 TCACTTTAATACTACTGATGTTCGTAG 57.001 33.333 0.00 0.00 39.14 3.51
688 696 9.783256 GGTATACTGGTTTGTTTTTATCATGTC 57.217 33.333 2.25 0.00 0.00 3.06
690 698 9.787532 CTGGTATACTGGTTTGTTTTTATCATG 57.212 33.333 2.25 0.00 0.00 3.07
692 700 8.927675 ACTGGTATACTGGTTTGTTTTTATCA 57.072 30.769 2.25 0.00 0.00 2.15
706 714 2.482490 GGCCCGTGTAACTGGTATACTG 60.482 54.545 2.25 0.00 43.92 2.74
713 721 1.964373 GTGTGGCCCGTGTAACTGG 60.964 63.158 0.00 0.00 44.98 4.00
722 730 2.377310 CGAAACGTAGTGTGGCCCG 61.377 63.158 0.00 0.00 45.00 6.13
723 731 2.030958 CCGAAACGTAGTGTGGCCC 61.031 63.158 0.00 0.00 45.00 5.80
724 732 0.038343 TACCGAAACGTAGTGTGGCC 60.038 55.000 0.00 0.00 45.00 5.36
725 733 1.063031 GTACCGAAACGTAGTGTGGC 58.937 55.000 0.00 0.00 45.00 5.01
726 734 2.420628 TGTACCGAAACGTAGTGTGG 57.579 50.000 0.00 0.00 45.00 4.17
732 753 4.084433 GCTTTTCACATGTACCGAAACGTA 60.084 41.667 8.83 0.00 0.00 3.57
735 756 4.483476 AGCTTTTCACATGTACCGAAAC 57.517 40.909 8.83 1.16 0.00 2.78
740 761 4.377431 CGTCTGAAGCTTTTCACATGTACC 60.377 45.833 0.00 0.00 0.00 3.34
748 769 1.460743 CGCATCGTCTGAAGCTTTTCA 59.539 47.619 0.00 0.00 36.69 2.69
768 789 2.359478 CACTTGGTACACGGGCCC 60.359 66.667 13.57 13.57 39.29 5.80
784 805 5.240891 CCAGAATAGAGAACAGAAACTGCA 58.759 41.667 0.00 0.00 34.37 4.41
787 808 4.534103 AGCCCAGAATAGAGAACAGAAACT 59.466 41.667 0.00 0.00 0.00 2.66
788 809 4.837972 AGCCCAGAATAGAGAACAGAAAC 58.162 43.478 0.00 0.00 0.00 2.78
846 887 1.389555 GGAAGGGGATTAGCGGTTTG 58.610 55.000 0.00 0.00 0.00 2.93
865 906 2.610873 GAGACTAGGGTTCTATGGGGG 58.389 57.143 0.00 0.00 0.00 5.40
1009 1051 1.202313 GGTACAGAGAGCGCGAAATCT 60.202 52.381 12.10 9.80 0.00 2.40
1072 1114 4.695606 AGGGTTCTCCACTTATCTGGTAA 58.304 43.478 0.00 0.00 38.24 2.85
1073 1115 4.348020 AGGGTTCTCCACTTATCTGGTA 57.652 45.455 0.00 0.00 38.24 3.25
1074 1116 3.207044 AGGGTTCTCCACTTATCTGGT 57.793 47.619 0.00 0.00 38.24 4.00
1075 1117 3.643792 CCTAGGGTTCTCCACTTATCTGG 59.356 52.174 0.00 0.00 38.24 3.86
1076 1118 3.070302 GCCTAGGGTTCTCCACTTATCTG 59.930 52.174 11.72 0.00 38.24 2.90
1082 1124 1.307084 GGGCCTAGGGTTCTCCACT 60.307 63.158 11.72 0.00 38.24 4.00
1084 1126 2.365105 CGGGCCTAGGGTTCTCCA 60.365 66.667 11.72 0.00 38.24 3.86
1132 1178 4.334203 CGCACAACCAATACTAGCCAATAA 59.666 41.667 0.00 0.00 0.00 1.40
1134 1180 2.682856 CGCACAACCAATACTAGCCAAT 59.317 45.455 0.00 0.00 0.00 3.16
1165 1211 2.426023 CTACATACCGGCCCAGCC 59.574 66.667 0.00 0.00 46.75 4.85
1166 1212 2.426023 CCTACATACCGGCCCAGC 59.574 66.667 0.00 0.00 0.00 4.85
1167 1213 3.148084 CCCTACATACCGGCCCAG 58.852 66.667 0.00 0.00 0.00 4.45
1168 1214 3.165685 GCCCTACATACCGGCCCA 61.166 66.667 0.00 0.00 36.63 5.36
1169 1215 2.465055 GATGCCCTACATACCGGCCC 62.465 65.000 0.00 0.00 42.29 5.80
1170 1216 1.003718 GATGCCCTACATACCGGCC 60.004 63.158 0.00 0.00 42.29 6.13
1171 1217 1.374252 CGATGCCCTACATACCGGC 60.374 63.158 0.00 0.00 39.84 6.13
1172 1218 0.895530 ATCGATGCCCTACATACCGG 59.104 55.000 0.00 0.00 39.84 5.28
1173 1219 2.607187 GAATCGATGCCCTACATACCG 58.393 52.381 0.00 0.00 39.84 4.02
1174 1220 2.567615 AGGAATCGATGCCCTACATACC 59.432 50.000 19.57 0.98 39.84 2.73
1178 1224 0.106708 GCAGGAATCGATGCCCTACA 59.893 55.000 19.57 0.00 36.41 2.74
1186 1232 1.227380 GTGGCTCGCAGGAATCGAT 60.227 57.895 0.00 0.00 35.25 3.59
1250 1296 0.541063 TTACTGGCTGTGACCTCGGA 60.541 55.000 7.34 0.00 0.00 4.55
1271 1322 1.139853 ACAGCAGATCGGAAGGGATTC 59.860 52.381 0.00 0.00 0.00 2.52
1272 1323 1.207791 ACAGCAGATCGGAAGGGATT 58.792 50.000 0.00 0.00 0.00 3.01
1273 1324 1.139853 GAACAGCAGATCGGAAGGGAT 59.860 52.381 0.00 0.00 0.00 3.85
1274 1325 0.537188 GAACAGCAGATCGGAAGGGA 59.463 55.000 0.00 0.00 0.00 4.20
1293 1344 3.324117 CATCACTGACTCACACCAGAAG 58.676 50.000 0.00 0.00 34.65 2.85
1358 1427 9.695526 CTTTTGATAACAATCCACAATCTCAAA 57.304 29.630 0.00 0.00 35.85 2.69
1360 1429 8.408043 ACTTTTGATAACAATCCACAATCTCA 57.592 30.769 0.00 0.00 35.85 3.27
1402 1471 2.471103 GCAGCAATGAATCGCAAAAACG 60.471 45.455 0.00 0.00 0.00 3.60
1408 1477 1.659622 CCCAGCAGCAATGAATCGCA 61.660 55.000 0.00 0.00 0.00 5.10
1413 1482 1.614903 CAAAGACCCAGCAGCAATGAA 59.385 47.619 0.00 0.00 0.00 2.57
1423 1492 1.133976 CCCATCTAGCCAAAGACCCAG 60.134 57.143 0.00 0.00 0.00 4.45
1424 1493 0.918983 CCCATCTAGCCAAAGACCCA 59.081 55.000 0.00 0.00 0.00 4.51
1425 1494 0.919710 ACCCATCTAGCCAAAGACCC 59.080 55.000 0.00 0.00 0.00 4.46
1497 1566 5.598417 AGGAGAAAGCTTACAAAACATTGGT 59.402 36.000 0.00 0.00 0.00 3.67
1505 1586 4.335416 CATCCCAGGAGAAAGCTTACAAA 58.665 43.478 0.00 0.00 0.00 2.83
1506 1587 3.873801 GCATCCCAGGAGAAAGCTTACAA 60.874 47.826 0.00 0.00 0.00 2.41
1507 1588 2.356125 GCATCCCAGGAGAAAGCTTACA 60.356 50.000 0.00 0.00 0.00 2.41
1508 1589 2.092699 AGCATCCCAGGAGAAAGCTTAC 60.093 50.000 0.00 0.00 0.00 2.34
1509 1590 2.092753 CAGCATCCCAGGAGAAAGCTTA 60.093 50.000 0.00 0.00 0.00 3.09
1510 1591 0.998145 AGCATCCCAGGAGAAAGCTT 59.002 50.000 0.00 0.00 0.00 3.74
1511 1592 0.255318 CAGCATCCCAGGAGAAAGCT 59.745 55.000 0.00 0.00 0.00 3.74
1512 1593 1.382692 GCAGCATCCCAGGAGAAAGC 61.383 60.000 0.00 0.00 0.00 3.51
1513 1594 0.750911 GGCAGCATCCCAGGAGAAAG 60.751 60.000 0.00 0.00 0.00 2.62
1514 1595 1.304282 GGCAGCATCCCAGGAGAAA 59.696 57.895 0.00 0.00 0.00 2.52
1515 1596 1.924939 TGGCAGCATCCCAGGAGAA 60.925 57.895 0.00 0.00 0.00 2.87
1516 1597 2.285592 TGGCAGCATCCCAGGAGA 60.286 61.111 0.00 0.00 0.00 3.71
1523 1604 4.722700 ACACCCGTGGCAGCATCC 62.723 66.667 0.00 0.00 34.19 3.51
1524 1605 3.434319 CACACCCGTGGCAGCATC 61.434 66.667 0.00 0.00 39.64 3.91
1537 1618 6.480524 TTGCAACTAGTGATTATGACACAC 57.519 37.500 0.00 0.00 40.25 3.82
1539 1620 8.970691 AATTTTGCAACTAGTGATTATGACAC 57.029 30.769 0.00 0.00 38.38 3.67
1540 1621 9.013229 AGAATTTTGCAACTAGTGATTATGACA 57.987 29.630 0.00 0.00 0.00 3.58
1542 1623 9.013229 ACAGAATTTTGCAACTAGTGATTATGA 57.987 29.630 0.00 0.00 0.00 2.15
1546 1627 9.236006 AGATACAGAATTTTGCAACTAGTGATT 57.764 29.630 0.00 0.00 0.00 2.57
1580 1665 3.146066 CCAACCTAACTGCAGTGCTTTA 58.854 45.455 22.49 8.02 0.00 1.85
1592 1682 1.003233 AGCAGCACTACCCAACCTAAC 59.997 52.381 0.00 0.00 0.00 2.34
1603 1693 7.597288 TCAAGGATTAGTAATAGCAGCACTA 57.403 36.000 0.00 0.00 34.64 2.74
1604 1694 6.485830 TCAAGGATTAGTAATAGCAGCACT 57.514 37.500 0.00 0.00 0.00 4.40
1605 1695 6.708054 ACATCAAGGATTAGTAATAGCAGCAC 59.292 38.462 0.00 0.00 0.00 4.40
1606 1696 6.830912 ACATCAAGGATTAGTAATAGCAGCA 58.169 36.000 0.00 0.00 0.00 4.41
1607 1697 8.833231 TTACATCAAGGATTAGTAATAGCAGC 57.167 34.615 0.00 0.00 0.00 5.25
1709 1810 6.591834 CACTAGGCTTATACCAACATGATAGC 59.408 42.308 0.00 0.00 0.00 2.97
1796 1980 5.362430 CCCGGGAAAATAATCCTCAATTCAA 59.638 40.000 18.48 0.00 39.57 2.69
1802 1986 3.389866 TCTCCCGGGAAAATAATCCTCA 58.610 45.455 26.68 0.00 39.57 3.86
1821 2006 2.814805 ATACAGCAACCCAGCAATCT 57.185 45.000 0.00 0.00 36.85 2.40
1846 2031 7.775397 AAAACAAATCAACAATTCAGACCAG 57.225 32.000 0.00 0.00 0.00 4.00
1992 2178 7.414266 AGCCTAACAAAAGAGAATTCCCTATT 58.586 34.615 0.65 0.00 0.00 1.73
2243 2429 3.193479 CCATCTTCCCTGTTAGGTTTTGC 59.807 47.826 0.00 0.00 31.93 3.68
2250 2436 3.133003 ACGATGACCATCTTCCCTGTTAG 59.867 47.826 8.20 0.00 35.72 2.34
2515 2703 6.151985 AGTGTGGTGAAATTGACAAAACACTA 59.848 34.615 20.46 11.19 40.75 2.74
2614 2802 7.643123 ACCTTATCAGTATGTCTCCCAAATTT 58.357 34.615 0.00 0.00 37.40 1.82
2654 2842 6.711277 TGAGACAATAGCTGTGGTAAAAGAT 58.289 36.000 0.00 0.00 38.84 2.40
2660 2848 6.070824 TCAGAAATGAGACAATAGCTGTGGTA 60.071 38.462 0.00 0.00 38.84 3.25
2733 3017 1.357907 CTGCTGACTTGTAGAGCTGC 58.642 55.000 0.00 0.00 33.66 5.25
2734 3018 1.405256 CCCTGCTGACTTGTAGAGCTG 60.405 57.143 0.00 0.00 33.66 4.24
2740 3024 2.605257 ACAGTACCCTGCTGACTTGTA 58.395 47.619 0.00 0.00 42.81 2.41
2799 3083 6.760298 ACTTGCATATGTGATGTAAGACTGAG 59.240 38.462 18.36 0.00 41.98 3.35
2821 3105 6.715280 AGTTATCACATCCAGTCATTCACTT 58.285 36.000 0.00 0.00 30.26 3.16
2825 3109 7.651304 CAGAGTAGTTATCACATCCAGTCATTC 59.349 40.741 0.00 0.00 0.00 2.67
2830 3114 6.859112 AACAGAGTAGTTATCACATCCAGT 57.141 37.500 0.00 0.00 0.00 4.00
2832 3116 6.371548 GCAAAACAGAGTAGTTATCACATCCA 59.628 38.462 0.00 0.00 0.00 3.41
2838 3122 6.145534 CGAACAGCAAAACAGAGTAGTTATCA 59.854 38.462 0.00 0.00 0.00 2.15
2839 3123 6.145696 ACGAACAGCAAAACAGAGTAGTTATC 59.854 38.462 0.00 0.00 0.00 1.75
2978 3262 6.625873 AACTAGGAAGTTCTTTTTCAGCAG 57.374 37.500 2.25 0.00 42.42 4.24
3076 3360 8.867112 ACATGCAAGTTAATCATTCATTCATC 57.133 30.769 0.00 0.00 0.00 2.92
3130 3414 1.918293 AACGGCAGGATCAGGACCA 60.918 57.895 0.00 0.00 0.00 4.02
3261 3549 5.942872 ACAGAAAAAGACATAAATGGAGCG 58.057 37.500 0.00 0.00 0.00 5.03
3283 3571 4.455533 TGGCACTCAACATGAACATCTAAC 59.544 41.667 0.00 0.00 0.00 2.34
3284 3572 4.650734 TGGCACTCAACATGAACATCTAA 58.349 39.130 0.00 0.00 0.00 2.10
3355 3643 4.662468 TTGGCAGTAAACAGCATTCAAA 57.338 36.364 0.00 0.00 0.00 2.69
3356 3644 4.340666 TCTTTGGCAGTAAACAGCATTCAA 59.659 37.500 0.00 0.00 0.00 2.69
3359 3647 4.099266 TGTTCTTTGGCAGTAAACAGCATT 59.901 37.500 6.56 0.00 0.00 3.56
3374 3662 4.165779 ACAAACTGCGAAGTTGTTCTTTG 58.834 39.130 10.24 5.68 39.78 2.77
3456 3744 0.177836 CAGGACACGGTGATATGCCA 59.822 55.000 16.29 0.00 0.00 4.92
3477 3765 5.706916 ACATGCAAGTTGATCTTCATTCAC 58.293 37.500 7.16 0.00 33.63 3.18
3485 3773 5.539955 ACCCTTAAAACATGCAAGTTGATCT 59.460 36.000 8.27 0.00 0.00 2.75
3517 3805 3.774766 ACATCAGTACCTACCAGCAATCA 59.225 43.478 0.00 0.00 0.00 2.57
3561 3849 7.148606 CGCAAATACAACCATCACATTTCAAAT 60.149 33.333 0.00 0.00 0.00 2.32
3619 3907 2.511218 ACATATGTCTGAGCCCATGGTT 59.489 45.455 11.73 0.00 0.00 3.67
3627 3915 3.624410 TCATGCAACACATATGTCTGAGC 59.376 43.478 15.60 13.00 38.45 4.26
3651 3939 5.805486 GCGTTAGTCACTTCATATGTCTTCA 59.195 40.000 1.90 0.00 0.00 3.02
3663 3951 3.498397 CCAAGTTCATGCGTTAGTCACTT 59.502 43.478 0.00 0.00 0.00 3.16
3724 4013 1.136224 GCTTGCTAGTTCAACGCAGTC 60.136 52.381 0.00 0.00 45.00 3.51
3730 4019 3.607078 CGAACTTGGCTTGCTAGTTCAAC 60.607 47.826 24.96 11.40 44.98 3.18
3751 4040 1.683943 AATCAATGGCCTGATCCACG 58.316 50.000 3.32 0.00 39.25 4.94
3761 4050 3.674753 CGTGGAGTTGAAAAATCAATGGC 59.325 43.478 0.00 0.00 43.89 4.40
3793 4082 1.392510 GAACTTATCACGCCCGAACAC 59.607 52.381 0.00 0.00 0.00 3.32
3799 4088 0.392461 TGCCAGAACTTATCACGCCC 60.392 55.000 0.00 0.00 0.00 6.13
3800 4089 1.331756 CATGCCAGAACTTATCACGCC 59.668 52.381 0.00 0.00 0.00 5.68
3814 4103 3.402110 CTTAATCATAGCCGACATGCCA 58.598 45.455 0.00 0.00 0.00 4.92
3824 4113 6.881065 TGGTATGAGAATGCCTTAATCATAGC 59.119 38.462 20.10 20.10 45.13 2.97
3827 4116 9.458727 CTTATGGTATGAGAATGCCTTAATCAT 57.541 33.333 6.98 6.98 35.01 2.45
3839 4128 4.202080 CCGACCGAACTTATGGTATGAGAA 60.202 45.833 0.00 0.00 38.99 2.87
3848 4137 1.006832 CAAGGCCGACCGAACTTATG 58.993 55.000 0.00 0.00 42.76 1.90
3852 4141 4.699522 GCCAAGGCCGACCGAACT 62.700 66.667 0.00 0.00 42.76 3.01
3877 4168 2.490509 TCTCGGAAAGTTCGTGCATAGA 59.509 45.455 0.00 0.00 0.00 1.98
3885 4176 3.499048 TCTTTCGATCTCGGAAAGTTCG 58.501 45.455 16.39 4.47 44.82 3.95
3911 4202 4.579869 ACGTTTCATGATTCCTTGCTAGT 58.420 39.130 0.00 0.00 0.00 2.57
3912 4203 5.551760 AACGTTTCATGATTCCTTGCTAG 57.448 39.130 0.00 0.00 0.00 3.42
3913 4204 7.471721 CATTAACGTTTCATGATTCCTTGCTA 58.528 34.615 5.91 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.