Multiple sequence alignment - TraesCS3B01G389800

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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 TraesCS3B01G389800 chr3B 100.000 4723 0 0 1 4723 613801432 613806154 0.000000e+00 8722.0
1 TraesCS3B01G389800 chr3B 91.176 102 6 3 1697 1796 590430928 590431028 8.240000e-28 135.0
2 TraesCS3B01G389800 chr3B 92.632 95 5 2 1703 1796 613803227 613803134 8.240000e-28 135.0
3 TraesCS3B01G389800 chr3B 86.207 116 12 4 2544 2657 613804088 613803975 6.420000e-24 122.0
4 TraesCS3B01G389800 chr3B 88.889 99 9 1 1700 1796 590431031 590430933 2.310000e-23 121.0
5 TraesCS3B01G389800 chr3B 92.308 65 4 1 1746 1809 667390053 667389989 1.810000e-14 91.6
6 TraesCS3B01G389800 chr3B 95.833 48 2 0 1699 1746 6965017 6964970 1.410000e-10 78.7
7 TraesCS3B01G389800 chr3B 81.443 97 10 5 2542 2631 513567944 513568039 6.560000e-09 73.1
8 TraesCS3B01G389800 chr3B 86.538 52 7 0 2602 2653 741579466 741579415 1.840000e-04 58.4
9 TraesCS3B01G389800 chr3D 87.791 1720 136 35 1 1704 462232499 462234160 0.000000e+00 1945.0
10 TraesCS3B01G389800 chr3D 91.634 777 58 6 3952 4723 462236264 462237038 0.000000e+00 1068.0
11 TraesCS3B01G389800 chr3D 85.257 1031 91 28 2949 3954 462235231 462236225 0.000000e+00 1005.0
12 TraesCS3B01G389800 chr3D 86.957 782 63 26 1795 2559 462234159 462234918 0.000000e+00 843.0
13 TraesCS3B01G389800 chr3D 86.631 187 23 2 2645 2831 462234924 462235108 6.200000e-49 206.0
14 TraesCS3B01G389800 chr3D 81.818 99 11 3 2554 2647 461663755 461663851 5.070000e-10 76.8
15 TraesCS3B01G389800 chr3D 81.443 97 10 5 2542 2631 393656560 393656655 6.560000e-09 73.1
16 TraesCS3B01G389800 chr3D 78.571 98 15 3 2556 2647 287478519 287478422 5.100000e-05 60.2
17 TraesCS3B01G389800 chr3A 84.869 1791 140 59 1 1746 605167779 605169483 0.000000e+00 1685.0
18 TraesCS3B01G389800 chr3A 92.430 753 36 9 1762 2498 605169532 605170279 0.000000e+00 1055.0
19 TraesCS3B01G389800 chr3A 95.312 576 27 0 4148 4723 605171954 605172529 0.000000e+00 915.0
20 TraesCS3B01G389800 chr3A 91.196 443 32 6 3008 3444 605170732 605171173 3.150000e-166 595.0
21 TraesCS3B01G389800 chr3A 80.000 665 69 32 3478 4114 605171174 605171802 2.610000e-117 433.0
22 TraesCS3B01G389800 chr3A 85.366 451 23 14 2551 2969 605170286 605170725 1.210000e-115 427.0
23 TraesCS3B01G389800 chr3A 85.345 116 9 7 2548 2657 130843827 130843940 3.860000e-21 113.0
24 TraesCS3B01G389800 chr3A 81.443 97 10 5 2542 2631 513606591 513606686 6.560000e-09 73.1
25 TraesCS3B01G389800 chr3A 95.556 45 2 0 2602 2646 722355883 722355927 6.560000e-09 73.1
26 TraesCS3B01G389800 chr1D 96.923 65 2 0 1253 1317 382725853 382725789 5.000000e-20 110.0
27 TraesCS3B01G389800 chr1D 84.091 88 8 3 2568 2649 283615479 283615392 3.920000e-11 80.5
28 TraesCS3B01G389800 chr1D 84.706 85 7 5 2556 2634 283615395 283615479 3.920000e-11 80.5
29 TraesCS3B01G389800 chr1D 100.000 31 0 0 2551 2581 376255243 376255213 1.840000e-04 58.4
30 TraesCS3B01G389800 chr1D 100.000 29 0 0 2553 2581 376239787 376239759 2.000000e-03 54.7
31 TraesCS3B01G389800 chr1D 100.000 29 0 0 2553 2581 376260408 376260380 2.000000e-03 54.7
32 TraesCS3B01G389800 chr1D 100.000 29 0 0 2553 2581 484117668 484117696 2.000000e-03 54.7
33 TraesCS3B01G389800 chr1D 96.774 31 1 0 2554 2584 110937755 110937725 9.000000e-03 52.8
34 TraesCS3B01G389800 chr1B 98.387 62 1 0 1256 1317 512636952 512636891 5.000000e-20 110.0
35 TraesCS3B01G389800 chr1B 96.667 60 2 0 1398 1457 512636779 512636720 3.010000e-17 100.0
36 TraesCS3B01G389800 chr1B 84.375 96 9 4 1703 1796 229367013 229366922 6.510000e-14 89.8
37 TraesCS3B01G389800 chr1B 92.308 52 4 0 1695 1746 302009904 302009955 1.820000e-09 75.0
38 TraesCS3B01G389800 chr1A 98.387 62 1 0 1256 1317 482780061 482780000 5.000000e-20 110.0
39 TraesCS3B01G389800 chr1A 98.361 61 1 0 1397 1457 482779886 482779826 1.800000e-19 108.0
40 TraesCS3B01G389800 chr1A 86.170 94 9 2 2554 2646 259202066 259202156 1.080000e-16 99.0
41 TraesCS3B01G389800 chr1A 91.045 67 6 0 1746 1812 41745155 41745221 1.810000e-14 91.6
42 TraesCS3B01G389800 chr1A 80.392 102 11 6 2553 2646 471731264 471731164 8.480000e-08 69.4
43 TraesCS3B01G389800 chr1A 79.592 98 14 3 2556 2647 249387632 249387535 1.100000e-06 65.8
44 TraesCS3B01G389800 chr4A 96.552 58 1 1 1743 1799 676418930 676418873 1.400000e-15 95.3
45 TraesCS3B01G389800 chr4A 94.118 51 2 1 1696 1746 646986597 646986548 5.070000e-10 76.8
46 TraesCS3B01G389800 chr7D 82.143 112 12 4 2548 2651 106921436 106921325 6.510000e-14 89.8
47 TraesCS3B01G389800 chr7D 95.455 44 1 1 2548 2590 107266162 107266119 8.480000e-08 69.4
48 TraesCS3B01G389800 chr7D 92.683 41 3 0 2555 2595 414105345 414105305 5.100000e-05 60.2
49 TraesCS3B01G389800 chr7D 100.000 30 0 0 2618 2647 364420 364391 6.600000e-04 56.5
50 TraesCS3B01G389800 chr2D 82.243 107 12 4 2553 2653 24978592 24978697 8.420000e-13 86.1
51 TraesCS3B01G389800 chr2D 97.368 38 0 1 2547 2584 36364632 36364596 3.950000e-06 63.9
52 TraesCS3B01G389800 chr2D 96.875 32 1 0 2618 2649 472445886 472445917 2.000000e-03 54.7
53 TraesCS3B01G389800 chr6A 82.000 100 10 2 2556 2647 499792872 499792971 1.410000e-10 78.7
54 TraesCS3B01G389800 chr5D 81.000 100 16 3 1699 1796 530152627 530152529 5.070000e-10 76.8
55 TraesCS3B01G389800 chr5D 80.612 98 14 2 2549 2646 476613768 476613860 2.360000e-08 71.3
56 TraesCS3B01G389800 chr5D 89.796 49 3 2 2536 2584 561883404 561883358 1.420000e-05 62.1
57 TraesCS3B01G389800 chr5D 92.683 41 1 2 2546 2584 473792376 473792336 1.840000e-04 58.4
58 TraesCS3B01G389800 chr5D 94.444 36 2 0 2549 2584 14120454 14120419 6.600000e-04 56.5
59 TraesCS3B01G389800 chr6B 89.286 56 5 1 2598 2653 609840144 609840090 8.480000e-08 69.4
60 TraesCS3B01G389800 chr6B 92.857 42 3 0 2556 2597 714272143 714272102 1.420000e-05 62.1
61 TraesCS3B01G389800 chrUn 94.872 39 2 0 2556 2594 79688295 79688333 1.420000e-05 62.1
62 TraesCS3B01G389800 chrUn 90.244 41 4 0 2554 2594 321511881 321511921 2.000000e-03 54.7
63 TraesCS3B01G389800 chr7B 91.111 45 2 2 2604 2647 732651669 732651626 5.100000e-05 60.2
64 TraesCS3B01G389800 chr2A 87.500 48 6 0 2602 2649 613878683 613878730 6.600000e-04 56.5
65 TraesCS3B01G389800 chr2B 83.333 60 8 1 3933 3990 705331556 705331615 2.000000e-03 54.7


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 TraesCS3B01G389800 chr3B 613801432 613806154 4722 False 8722.000000 8722 100.0000 1 4723 1 chr3B.!!$F3 4722
1 TraesCS3B01G389800 chr3D 462232499 462237038 4539 False 1013.400000 1945 87.6540 1 4723 5 chr3D.!!$F3 4722
2 TraesCS3B01G389800 chr3A 605167779 605172529 4750 False 851.666667 1685 88.1955 1 4723 6 chr3A.!!$F4 4722

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
809 820 0.098025 ACACAAACGGAGCAAACACG 59.902 50.0 0.00 0.00 0.00 4.49 F
1217 1262 0.031585 ATGTATATGTGCCGCGTCGT 59.968 50.0 4.92 0.00 0.00 4.34 F
1323 1368 0.940519 CGTCGCCAAGGTACGTTTGA 60.941 55.0 0.00 1.61 32.16 2.69 F
2873 3029 0.901124 TGCCTTTGTGTTTGCTTGGT 59.099 45.0 0.00 0.00 0.00 3.67 F
3592 3775 0.033208 ATTGAATGGGGATGCGGTGT 60.033 50.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1864 0.187851 ATACTCCCTCCGTCCGGAAT 59.812 55.000 5.23 0.0 44.66 3.01 R
2311 2420 0.391793 GGTAGGCCAGCTCTGTGAAC 60.392 60.000 5.01 0.0 34.09 3.18 R
2928 3093 1.133790 CCAGGCAGCAGCTTATTTCAC 59.866 52.381 0.00 0.0 41.70 3.18 R
3677 3860 0.393808 GGCTCGAATTTGCCTGGGTA 60.394 55.000 6.18 0.0 45.26 3.69 R
4689 5044 1.079127 CAAGAACCCGGCGATGAGT 60.079 57.895 9.30 0.0 0.00 3.41 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
127 128 3.793144 CAAGCTCTTGGTCCGCGC 61.793 66.667 0.00 0.00 36.95 6.86
171 172 4.379243 CCAGGCGGCGAGACAACT 62.379 66.667 12.98 0.00 0.00 3.16
172 173 2.571757 CAGGCGGCGAGACAACTA 59.428 61.111 12.98 0.00 0.00 2.24
176 177 2.967397 CGGCGAGACAACTACCCA 59.033 61.111 0.00 0.00 0.00 4.51
189 190 0.737219 CTACCCAAGGTACTCGACGG 59.263 60.000 0.00 0.00 38.49 4.79
201 202 4.717629 CGACGGCGAACCTCAGCA 62.718 66.667 16.62 0.00 40.82 4.41
644 653 1.957765 GACGGTGGCTACCCCTTCTC 61.958 65.000 14.41 0.00 44.53 2.87
721 730 1.822250 GATGTTTCCGGCGATCGCTC 61.822 60.000 36.25 25.33 41.60 5.03
741 750 2.359975 CGAGGTTGGGGTTCAGGC 60.360 66.667 0.00 0.00 0.00 4.85
777 786 1.579626 CGCGACGAGAACGAGGTAC 60.580 63.158 0.00 0.00 42.66 3.34
779 788 1.579626 CGACGAGAACGAGGTACGC 60.580 63.158 0.00 0.00 46.94 4.42
794 805 1.300266 TACGCTCGTCGATGGACACA 61.300 55.000 8.67 0.00 43.61 3.72
805 816 1.606668 GATGGACACAAACGGAGCAAA 59.393 47.619 0.00 0.00 0.00 3.68
806 817 0.736053 TGGACACAAACGGAGCAAAC 59.264 50.000 0.00 0.00 0.00 2.93
807 818 0.736053 GGACACAAACGGAGCAAACA 59.264 50.000 0.00 0.00 0.00 2.83
808 819 1.533129 GGACACAAACGGAGCAAACAC 60.533 52.381 0.00 0.00 0.00 3.32
809 820 0.098025 ACACAAACGGAGCAAACACG 59.902 50.000 0.00 0.00 0.00 4.49
824 843 1.083806 ACACGTATGCTGCCACGATG 61.084 55.000 24.53 20.00 40.56 3.84
825 844 1.521457 ACGTATGCTGCCACGATGG 60.521 57.895 24.53 0.00 40.56 3.51
826 845 1.227234 CGTATGCTGCCACGATGGA 60.227 57.895 16.06 0.00 40.96 3.41
827 846 0.601046 CGTATGCTGCCACGATGGAT 60.601 55.000 16.06 0.00 40.96 3.41
828 847 1.151668 GTATGCTGCCACGATGGATC 58.848 55.000 8.04 0.00 40.96 3.36
837 856 3.923614 CGATGGATCGTTCCGAGC 58.076 61.111 7.99 0.00 45.89 5.03
838 857 1.360551 CGATGGATCGTTCCGAGCT 59.639 57.895 7.99 0.00 45.89 4.09
963 988 1.376037 CCAGAAGGCAGGACGGAAC 60.376 63.158 0.00 0.00 0.00 3.62
966 991 1.671379 GAAGGCAGGACGGAACCAC 60.671 63.158 0.00 0.00 0.00 4.16
969 994 1.966451 GGCAGGACGGAACCACTTG 60.966 63.158 0.00 0.00 0.00 3.16
970 995 1.966451 GCAGGACGGAACCACTTGG 60.966 63.158 0.00 0.00 42.17 3.61
971 996 1.302511 CAGGACGGAACCACTTGGG 60.303 63.158 0.00 0.00 44.81 4.12
972 997 2.033602 GGACGGAACCACTTGGGG 59.966 66.667 0.00 0.00 42.91 4.96
973 998 2.033602 GACGGAACCACTTGGGGG 59.966 66.667 0.00 0.00 42.91 5.40
1015 1040 4.394712 GCAGGTGTCCAGGTCCGG 62.395 72.222 0.00 0.00 0.00 5.14
1188 1233 2.226330 GCTGATCTTCTCTCTCCGCTA 58.774 52.381 0.00 0.00 0.00 4.26
1210 1255 1.800586 CCGCTGTGATGTATATGTGCC 59.199 52.381 0.00 0.00 0.00 5.01
1217 1262 0.031585 ATGTATATGTGCCGCGTCGT 59.968 50.000 4.92 0.00 0.00 4.34
1323 1368 0.940519 CGTCGCCAAGGTACGTTTGA 60.941 55.000 0.00 1.61 32.16 2.69
1324 1369 1.435577 GTCGCCAAGGTACGTTTGAT 58.564 50.000 0.00 0.00 0.00 2.57
1325 1370 1.392510 GTCGCCAAGGTACGTTTGATC 59.607 52.381 0.00 0.00 0.00 2.92
1367 1415 2.494918 CGGACCGGGATCTGTGTC 59.505 66.667 6.32 0.00 0.00 3.67
1372 1421 1.822990 GACCGGGATCTGTGTCTTGTA 59.177 52.381 6.32 0.00 0.00 2.41
1376 1425 3.066900 CCGGGATCTGTGTCTTGTAGTAG 59.933 52.174 0.00 0.00 0.00 2.57
1471 1522 6.363357 GCAAAGATGTAAACTCAACACCATTC 59.637 38.462 0.00 0.00 0.00 2.67
1474 1525 4.447138 TGTAAACTCAACACCATTCCCT 57.553 40.909 0.00 0.00 0.00 4.20
1513 1565 8.702163 TTTTTGACCTGAAAACTCTTCATTTC 57.298 30.769 0.00 0.00 36.35 2.17
1542 1594 2.210961 CATGGAGCTATGTGTCTGCAG 58.789 52.381 7.63 7.63 34.24 4.41
1600 1653 6.106673 ACTAGTTAAATCCAGGAATGTGTCG 58.893 40.000 0.00 0.00 0.00 4.35
1603 1656 5.768164 AGTTAAATCCAGGAATGTGTCGTTT 59.232 36.000 0.00 0.00 0.00 3.60
1648 1702 2.508867 CATTCAATCCGTTTGCAGTCG 58.491 47.619 5.78 5.78 35.16 4.18
1660 1714 2.299993 TGCAGTCGCTTAGAATCAGG 57.700 50.000 0.00 0.00 39.64 3.86
1731 1785 3.055675 TCCGTCCGGAATTACTTGTCATT 60.056 43.478 5.23 0.00 42.05 2.57
1739 1793 6.475402 CCGGAATTACTTGTCATTAAAATGGC 59.525 38.462 0.00 0.29 41.30 4.40
1741 1795 7.220683 CGGAATTACTTGTCATTAAAATGGCTG 59.779 37.037 8.61 4.61 41.48 4.85
1746 1800 7.713764 ACTTGTCATTAAAATGGCTGAAAAC 57.286 32.000 8.61 0.00 41.48 2.43
1747 1801 7.271511 ACTTGTCATTAAAATGGCTGAAAACA 58.728 30.769 8.61 0.00 41.48 2.83
1748 1802 7.933033 ACTTGTCATTAAAATGGCTGAAAACAT 59.067 29.630 8.61 0.00 41.48 2.71
1749 1803 8.674263 TTGTCATTAAAATGGCTGAAAACATT 57.326 26.923 8.61 0.00 41.48 2.71
1750 1804 8.309163 TGTCATTAAAATGGCTGAAAACATTC 57.691 30.769 8.61 0.00 41.48 2.67
1751 1805 7.930325 TGTCATTAAAATGGCTGAAAACATTCA 59.070 29.630 8.61 0.00 41.48 2.57
1753 1807 9.504708 TCATTAAAATGGCTGAAAACATTCATT 57.495 25.926 3.00 0.00 36.36 2.57
1812 1899 4.133078 GGAGTATTTCCCAGCAGAATGAG 58.867 47.826 0.00 0.00 40.37 2.90
1818 1905 3.272574 TCCCAGCAGAATGAGATGTTC 57.727 47.619 0.00 0.00 39.69 3.18
1920 2016 4.767409 TCAGCATAGTGACTAGTGACTGTT 59.233 41.667 23.33 9.24 0.00 3.16
1921 2017 4.861462 CAGCATAGTGACTAGTGACTGTTG 59.139 45.833 23.33 19.79 0.00 3.33
1984 2080 4.446311 CCCTTCGATACATTGGGAATCCTT 60.446 45.833 0.00 0.00 40.23 3.36
2041 2146 5.013079 TCCTGATGGTGTTCTGTTCTGTAAT 59.987 40.000 0.00 0.00 34.23 1.89
2050 2155 9.817809 GGTGTTCTGTTCTGTAATATTATCTCA 57.182 33.333 0.00 0.00 0.00 3.27
2084 2189 5.394224 CGACCTCAAGCCTCTTGTTATCTAA 60.394 44.000 6.47 0.00 0.00 2.10
2182 2291 9.292846 CTGATCGAGATTTTTGCATTGATTTAA 57.707 29.630 0.00 0.00 0.00 1.52
2311 2420 4.514441 GGAGATGATGTTGTCCATAAGCTG 59.486 45.833 0.00 0.00 30.41 4.24
2346 2455 4.142425 GGCCTACCGCTATAAGTATGTCTC 60.142 50.000 0.00 0.00 37.74 3.36
2360 2469 6.095432 AGTATGTCTCTTTAGCTAGCCATG 57.905 41.667 12.13 0.99 0.00 3.66
2526 2638 9.770097 ATGTTGTAAATGTCCTCATATCTGTAG 57.230 33.333 0.00 0.00 33.49 2.74
2534 2646 4.081752 GTCCTCATATCTGTAGGAGCCATG 60.082 50.000 0.00 0.00 40.06 3.66
2540 2652 7.977818 TCATATCTGTAGGAGCCATGTATTTT 58.022 34.615 0.00 0.00 0.00 1.82
2546 2658 6.919721 TGTAGGAGCCATGTATTTTTGAAAC 58.080 36.000 0.00 0.00 0.00 2.78
2567 2679 5.952347 ACAAAAATACTACTCCCTCCGAT 57.048 39.130 0.00 0.00 0.00 4.18
2581 2693 5.952387 TCCCTCCGATCCAAATTAATTGAT 58.048 37.500 0.39 1.14 41.85 2.57
2594 2706 9.868277 CCAAATTAATTGATGCTGGTTTAGTAA 57.132 29.630 0.39 0.00 41.85 2.24
2703 2815 8.099364 TCATTTTCAAGTTGAACCTACTGATC 57.901 34.615 17.85 0.00 35.89 2.92
2872 3028 2.021355 TTGCCTTTGTGTTTGCTTGG 57.979 45.000 0.00 0.00 0.00 3.61
2873 3029 0.901124 TGCCTTTGTGTTTGCTTGGT 59.099 45.000 0.00 0.00 0.00 3.67
2898 3062 4.081142 TGAAAGTCTGACTGGTTGAGAACA 60.081 41.667 11.71 0.00 0.00 3.18
2901 3065 4.843728 AGTCTGACTGGTTGAGAACAAAA 58.156 39.130 10.00 0.00 37.77 2.44
2918 3083 8.851541 AGAACAAAATTATTTTCATGGCATGT 57.148 26.923 25.62 10.23 0.00 3.21
2939 3104 8.764287 GCATGTTTTGTTTTAGTGAAATAAGCT 58.236 29.630 0.00 0.00 31.28 3.74
2943 3108 7.928908 TTTGTTTTAGTGAAATAAGCTGCTG 57.071 32.000 1.35 0.00 31.28 4.41
2946 3111 2.503895 AGTGAAATAAGCTGCTGCCT 57.496 45.000 12.44 1.33 40.80 4.75
2951 3116 1.467920 AATAAGCTGCTGCCTGGAAC 58.532 50.000 12.44 0.00 40.80 3.62
2972 3137 5.622770 ACGTTTCCAAATCCATGAACTAC 57.377 39.130 0.00 0.00 0.00 2.73
2978 3145 7.639113 TTCCAAATCCATGAACTACATTACC 57.361 36.000 0.00 0.00 37.07 2.85
2983 3150 4.460263 TCCATGAACTACATTACCATGCC 58.540 43.478 0.00 0.00 37.07 4.40
2993 3160 3.289836 CATTACCATGCCCAGACAATGA 58.710 45.455 0.00 0.00 0.00 2.57
3000 3167 4.202080 CCATGCCCAGACAATGAAATGTAG 60.202 45.833 0.00 0.00 32.57 2.74
3001 3168 4.299586 TGCCCAGACAATGAAATGTAGA 57.700 40.909 0.00 0.00 32.57 2.59
3004 3171 5.125900 TGCCCAGACAATGAAATGTAGATTG 59.874 40.000 0.00 0.00 32.57 2.67
3010 3177 7.337689 CAGACAATGAAATGTAGATTGGAAGGA 59.662 37.037 0.00 0.00 32.57 3.36
3041 3208 3.845781 TGAAGAAAGCTGGTCAGTTCT 57.154 42.857 0.00 0.00 0.00 3.01
3080 3247 5.633601 GCTTTTAATGCCAAGTTAGTCCAAC 59.366 40.000 0.00 0.00 37.41 3.77
3088 3255 3.191371 CCAAGTTAGTCCAACATTCTGCC 59.809 47.826 0.00 0.00 39.81 4.85
3158 3331 3.895041 TCCCTGAAATTTCCAGAAACCAC 59.105 43.478 15.48 0.00 33.65 4.16
3433 3608 3.069289 CAGCATCTGCACTGTGTTTCTA 58.931 45.455 9.86 0.00 45.16 2.10
3444 3619 5.163814 GCACTGTGTTTCTATCTGGTGAATC 60.164 44.000 9.86 0.00 0.00 2.52
3446 3621 5.934625 ACTGTGTTTCTATCTGGTGAATCAC 59.065 40.000 4.51 4.51 40.47 3.06
3458 3633 7.615582 TCTGGTGAATCACAGTATTCATTTC 57.384 36.000 15.86 0.00 45.13 2.17
3459 3634 6.313658 TCTGGTGAATCACAGTATTCATTTCG 59.686 38.462 15.86 0.00 45.13 3.46
3462 3637 6.961554 GGTGAATCACAGTATTCATTTCGTTC 59.038 38.462 15.86 0.00 45.13 3.95
3463 3638 6.678663 GTGAATCACAGTATTCATTTCGTTCG 59.321 38.462 8.74 0.00 45.13 3.95
3464 3639 6.367695 TGAATCACAGTATTCATTTCGTTCGT 59.632 34.615 0.00 0.00 40.17 3.85
3466 3641 4.387559 TCACAGTATTCATTTCGTTCGTGG 59.612 41.667 0.00 0.00 0.00 4.94
3467 3642 3.682858 ACAGTATTCATTTCGTTCGTGGG 59.317 43.478 0.00 0.00 0.00 4.61
3468 3643 3.930229 CAGTATTCATTTCGTTCGTGGGA 59.070 43.478 0.00 0.00 0.00 4.37
3469 3644 3.930848 AGTATTCATTTCGTTCGTGGGAC 59.069 43.478 0.00 0.00 0.00 4.46
3470 3645 2.536761 TTCATTTCGTTCGTGGGACT 57.463 45.000 0.00 0.00 0.00 3.85
3471 3646 3.663995 TTCATTTCGTTCGTGGGACTA 57.336 42.857 0.00 0.00 0.00 2.59
3472 3647 3.880047 TCATTTCGTTCGTGGGACTAT 57.120 42.857 0.00 0.00 0.00 2.12
3473 3648 3.517602 TCATTTCGTTCGTGGGACTATG 58.482 45.455 0.00 0.00 0.00 2.23
3474 3649 1.717194 TTTCGTTCGTGGGACTATGC 58.283 50.000 0.00 0.00 0.00 3.14
3476 3651 0.108992 TCGTTCGTGGGACTATGCAC 60.109 55.000 0.00 0.00 0.00 4.57
3563 3744 2.540383 TGCTATCCCTCCAGCGAATAT 58.460 47.619 0.00 0.00 40.79 1.28
3564 3745 2.906389 TGCTATCCCTCCAGCGAATATT 59.094 45.455 0.00 0.00 40.79 1.28
3568 3751 5.163405 GCTATCCCTCCAGCGAATATTGATA 60.163 44.000 0.00 0.00 0.00 2.15
3592 3775 0.033208 ATTGAATGGGGATGCGGTGT 60.033 50.000 0.00 0.00 0.00 4.16
3594 3777 0.621082 TGAATGGGGATGCGGTGTTA 59.379 50.000 0.00 0.00 0.00 2.41
3595 3778 1.214175 TGAATGGGGATGCGGTGTTAT 59.786 47.619 0.00 0.00 0.00 1.89
3596 3779 1.880027 GAATGGGGATGCGGTGTTATC 59.120 52.381 0.00 0.00 0.00 1.75
3597 3780 0.110486 ATGGGGATGCGGTGTTATCC 59.890 55.000 0.00 0.00 41.71 2.59
3604 3787 3.613702 CGGTGTTATCCGCGCGAC 61.614 66.667 34.63 22.09 43.96 5.19
3605 3788 2.507547 GGTGTTATCCGCGCGACA 60.508 61.111 34.63 24.69 0.00 4.35
3682 3865 8.187913 TCATGAAATGTTTGAAGAATTACCCA 57.812 30.769 0.00 0.00 46.80 4.51
3706 3889 2.871022 CAAATTCGAGCCTGGATCTCAG 59.129 50.000 10.61 4.67 43.00 3.35
3757 3940 4.320023 TCGGTTAATTGCTTGCTACTGAA 58.680 39.130 0.00 0.00 0.00 3.02
3758 3941 4.941263 TCGGTTAATTGCTTGCTACTGAAT 59.059 37.500 0.00 0.00 0.00 2.57
3759 3942 6.110033 TCGGTTAATTGCTTGCTACTGAATA 58.890 36.000 0.00 0.00 0.00 1.75
3760 3943 6.596106 TCGGTTAATTGCTTGCTACTGAATAA 59.404 34.615 0.00 0.00 0.00 1.40
3761 3944 7.282224 TCGGTTAATTGCTTGCTACTGAATAAT 59.718 33.333 0.00 0.00 0.00 1.28
3762 3945 7.376866 CGGTTAATTGCTTGCTACTGAATAATG 59.623 37.037 0.00 0.00 0.00 1.90
3763 3946 8.405531 GGTTAATTGCTTGCTACTGAATAATGA 58.594 33.333 0.00 0.00 0.00 2.57
3764 3947 9.956720 GTTAATTGCTTGCTACTGAATAATGAT 57.043 29.630 0.00 0.00 0.00 2.45
3765 3948 9.955208 TTAATTGCTTGCTACTGAATAATGATG 57.045 29.630 0.00 0.00 0.00 3.07
3766 3949 7.578310 ATTGCTTGCTACTGAATAATGATGT 57.422 32.000 0.00 0.00 0.00 3.06
3767 3950 7.395190 TTGCTTGCTACTGAATAATGATGTT 57.605 32.000 0.00 0.00 0.00 2.71
3768 3951 7.395190 TGCTTGCTACTGAATAATGATGTTT 57.605 32.000 0.00 0.00 0.00 2.83
3769 3952 7.252708 TGCTTGCTACTGAATAATGATGTTTG 58.747 34.615 0.00 0.00 0.00 2.93
3770 3953 7.094248 TGCTTGCTACTGAATAATGATGTTTGT 60.094 33.333 0.00 0.00 0.00 2.83
3771 3954 7.756722 GCTTGCTACTGAATAATGATGTTTGTT 59.243 33.333 0.00 0.00 0.00 2.83
3772 3955 9.630098 CTTGCTACTGAATAATGATGTTTGTTT 57.370 29.630 0.00 0.00 0.00 2.83
3773 3956 8.969121 TGCTACTGAATAATGATGTTTGTTTG 57.031 30.769 0.00 0.00 0.00 2.93
3848 4031 5.306678 TGCCTTCTTTTCCCATACAAAATGT 59.693 36.000 0.00 0.00 0.00 2.71
3905 4096 5.185056 GGTGGAATTGCTACCATTTAACAGT 59.815 40.000 11.72 0.00 46.68 3.55
3908 4099 6.071616 TGGAATTGCTACCATTTAACAGTTCC 60.072 38.462 8.21 8.21 43.54 3.62
3918 4109 5.105513 CCATTTAACAGTTCCCATTGTACCC 60.106 44.000 0.00 0.00 0.00 3.69
3950 4143 9.174166 TGCCTAGTTTAGAAAATTCCTAATGAC 57.826 33.333 2.36 0.35 0.00 3.06
3954 4147 8.494016 AGTTTAGAAAATTCCTAATGACTCCG 57.506 34.615 2.36 0.00 0.00 4.63
3967 4201 1.905894 TGACTCCGACCATCCAAATCA 59.094 47.619 0.00 0.00 0.00 2.57
3976 4210 9.448438 CTCCGACCATCCAAATCATATAAAATA 57.552 33.333 0.00 0.00 0.00 1.40
3977 4211 9.226606 TCCGACCATCCAAATCATATAAAATAC 57.773 33.333 0.00 0.00 0.00 1.89
3978 4212 8.458843 CCGACCATCCAAATCATATAAAATACC 58.541 37.037 0.00 0.00 0.00 2.73
4021 4255 4.225208 GAGCTTGAACAAGTGAAGATTGC 58.775 43.478 14.62 0.22 40.45 3.56
4023 4257 3.005155 GCTTGAACAAGTGAAGATTGCCT 59.995 43.478 14.62 0.00 40.45 4.75
4024 4258 4.791974 CTTGAACAAGTGAAGATTGCCTC 58.208 43.478 6.41 0.00 33.87 4.70
4033 4267 2.289382 TGAAGATTGCCTCACGTGCTTA 60.289 45.455 11.67 0.00 0.00 3.09
4036 4270 1.258982 GATTGCCTCACGTGCTTATCG 59.741 52.381 11.67 0.00 0.00 2.92
4045 4279 5.158101 TCACGTGCTTATCGTTTCAAAAA 57.842 34.783 11.67 0.00 39.55 1.94
4046 4280 5.753744 TCACGTGCTTATCGTTTCAAAAAT 58.246 33.333 11.67 0.00 39.55 1.82
4048 4282 6.693545 TCACGTGCTTATCGTTTCAAAAATTT 59.306 30.769 11.67 0.00 39.55 1.82
4059 4293 8.401046 TCGTTTCAAAAATTTCAGTAACAAGG 57.599 30.769 0.00 0.00 0.00 3.61
4133 4485 4.705507 ACTTAGTCCGTTTCTGCTATCTCA 59.294 41.667 0.00 0.00 0.00 3.27
4139 4491 2.796383 CGTTTCTGCTATCTCAGTCCGG 60.796 54.545 0.00 0.00 35.63 5.14
4140 4492 2.145397 TTCTGCTATCTCAGTCCGGT 57.855 50.000 0.00 0.00 35.63 5.28
4141 4493 2.145397 TCTGCTATCTCAGTCCGGTT 57.855 50.000 0.00 0.00 35.63 4.44
4142 4494 2.025155 TCTGCTATCTCAGTCCGGTTC 58.975 52.381 0.00 0.00 35.63 3.62
4143 4495 2.028130 CTGCTATCTCAGTCCGGTTCT 58.972 52.381 0.00 0.00 0.00 3.01
4144 4496 1.751351 TGCTATCTCAGTCCGGTTCTG 59.249 52.381 18.33 18.33 0.00 3.02
4163 4518 3.521529 ATATCCTCAGCACCGCGGC 62.522 63.158 28.58 12.97 0.00 6.53
4247 4602 0.895100 AGGTGCACAAATCGCATGGT 60.895 50.000 20.43 0.00 42.32 3.55
4250 4605 0.957362 TGCACAAATCGCATGGTGAA 59.043 45.000 0.00 0.00 33.55 3.18
4689 5044 0.035881 ACGTCGTCTCCTACACCTCA 59.964 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.031919 TTGCAATCGCTCGTGGGT 59.968 55.556 0.00 0.00 39.64 4.51
35 36 2.753966 CCCCTTGCAATCGCTCGTG 61.754 63.158 0.00 0.00 39.64 4.35
106 107 0.674895 GCGGACCAAGAGCTTGACAT 60.675 55.000 11.61 0.00 42.93 3.06
107 108 1.301716 GCGGACCAAGAGCTTGACA 60.302 57.895 11.61 0.00 42.93 3.58
171 172 1.315257 GCCGTCGAGTACCTTGGGTA 61.315 60.000 0.00 0.00 37.09 3.69
172 173 2.643232 GCCGTCGAGTACCTTGGGT 61.643 63.158 0.00 0.00 40.16 4.51
176 177 1.211190 GTTCGCCGTCGAGTACCTT 59.789 57.895 0.00 0.00 46.34 3.50
189 190 3.482783 GCTCGTGCTGAGGTTCGC 61.483 66.667 1.41 0.00 45.38 4.70
277 278 3.101428 GCGCGTTCCTCGACGAAA 61.101 61.111 8.43 0.00 45.47 3.46
412 420 4.129737 GCGAGGACCAGCGTGCTA 62.130 66.667 8.31 0.00 41.37 3.49
478 487 2.987547 TCGTTCGGCGACCTTCCT 60.988 61.111 10.16 0.00 45.68 3.36
551 560 2.031616 CGATCCATCAGCCGGCAT 59.968 61.111 31.54 12.49 0.00 4.40
622 631 3.782443 GGGGTAGCCACCGTCCTG 61.782 72.222 14.06 0.00 46.86 3.86
644 653 4.170062 CTTGGCCGATGCACGCAG 62.170 66.667 0.00 0.00 40.13 5.18
678 687 3.371034 TCGATGGGGAACAATCTGACTA 58.629 45.455 0.00 0.00 0.00 2.59
721 730 4.323477 TGAACCCCAACCTCGGCG 62.323 66.667 0.00 0.00 0.00 6.46
777 786 1.006825 TTTGTGTCCATCGACGAGCG 61.007 55.000 3.01 0.00 42.37 5.03
779 788 0.708370 CGTTTGTGTCCATCGACGAG 59.292 55.000 3.01 0.00 42.37 4.18
782 791 1.068474 CTCCGTTTGTGTCCATCGAC 58.932 55.000 0.00 0.00 39.66 4.20
794 805 1.069500 GCATACGTGTTTGCTCCGTTT 60.069 47.619 0.00 0.00 35.20 3.60
805 816 1.083806 CATCGTGGCAGCATACGTGT 61.084 55.000 17.64 8.19 40.87 4.49
806 817 1.637934 CATCGTGGCAGCATACGTG 59.362 57.895 17.64 12.58 40.87 4.49
807 818 1.521457 CCATCGTGGCAGCATACGT 60.521 57.895 17.64 0.00 40.87 3.57
808 819 0.601046 ATCCATCGTGGCAGCATACG 60.601 55.000 13.55 13.55 37.47 3.06
809 820 1.151668 GATCCATCGTGGCAGCATAC 58.848 55.000 0.00 0.00 37.47 2.39
904 929 3.446873 TCGTTCTACGTGGGCCTTAATTA 59.553 43.478 4.53 0.00 43.14 1.40
951 976 1.966451 CAAGTGGTTCCGTCCTGCC 60.966 63.158 0.00 0.00 0.00 4.85
953 978 1.302511 CCCAAGTGGTTCCGTCCTG 60.303 63.158 0.00 0.00 0.00 3.86
954 979 2.526046 CCCCAAGTGGTTCCGTCCT 61.526 63.158 0.00 0.00 0.00 3.85
1188 1233 2.759191 CACATATACATCACAGCGGCT 58.241 47.619 0.00 0.00 0.00 5.52
1223 1268 3.914984 TCCAGAAGGAAAGTCAGCG 57.085 52.632 0.00 0.00 42.23 5.18
1358 1406 5.393243 GGGTCACTACTACAAGACACAGATC 60.393 48.000 0.00 0.00 34.62 2.75
1367 1415 4.822026 CCAGAAAGGGTCACTACTACAAG 58.178 47.826 0.00 0.00 0.00 3.16
1390 1439 0.310854 CCTTCGCCTGAAACACCAAC 59.689 55.000 0.00 0.00 32.66 3.77
1471 1522 1.324383 AAAACGTTGGGCACTAAGGG 58.676 50.000 0.00 0.00 38.98 3.95
1542 1594 2.096496 GTGCAGTTGACTACATCATGGC 59.904 50.000 0.00 0.00 37.11 4.40
1600 1653 7.923414 ATAGAACAGAACTGGGACAATAAAC 57.077 36.000 6.76 0.00 38.70 2.01
1603 1656 7.093068 TGCTAATAGAACAGAACTGGGACAATA 60.093 37.037 6.76 0.00 38.70 1.90
1648 1702 7.255277 CCAAAGTTATAAGGCCTGATTCTAAGC 60.255 40.741 8.29 0.00 0.00 3.09
1660 1714 6.517605 TGAAAACAACCCAAAGTTATAAGGC 58.482 36.000 0.00 0.00 36.18 4.35
1756 1810 9.236691 CGGAATTACTTGTCATTAAAATGGATG 57.763 33.333 3.00 0.00 37.03 3.51
1758 1812 7.612244 TCCGGAATTACTTGTCATTAAAATGGA 59.388 33.333 0.00 0.00 37.03 3.41
1759 1813 7.700656 GTCCGGAATTACTTGTCATTAAAATGG 59.299 37.037 5.23 0.00 37.03 3.16
1760 1814 7.428183 CGTCCGGAATTACTTGTCATTAAAATG 59.572 37.037 5.23 0.00 37.75 2.32
1761 1815 7.414762 CCGTCCGGAATTACTTGTCATTAAAAT 60.415 37.037 5.23 0.00 37.50 1.82
1763 1817 5.352016 CCGTCCGGAATTACTTGTCATTAAA 59.648 40.000 5.23 0.00 37.50 1.52
1764 1818 4.871557 CCGTCCGGAATTACTTGTCATTAA 59.128 41.667 5.23 0.00 37.50 1.40
1765 1819 4.160065 TCCGTCCGGAATTACTTGTCATTA 59.840 41.667 5.23 0.00 42.05 1.90
1777 1864 0.187851 ATACTCCCTCCGTCCGGAAT 59.812 55.000 5.23 0.00 44.66 3.01
1810 1897 6.629128 TCTGATGAGAGACTTTGAACATCTC 58.371 40.000 0.00 0.00 39.38 2.75
1881 1968 8.173775 CACTATGCTGAAAAATAGACTGTTCAG 58.826 37.037 7.69 7.69 46.33 3.02
1979 2075 7.671398 ACCAACAAAAGAGTGATAATCAAGGAT 59.329 33.333 0.00 0.00 0.00 3.24
1984 2080 7.815840 TGAACCAACAAAAGAGTGATAATCA 57.184 32.000 0.00 0.00 0.00 2.57
2041 2146 7.124147 TGAGGTCGCATATGGAATGAGATAATA 59.876 37.037 4.56 0.00 31.03 0.98
2050 2155 2.498167 GCTTGAGGTCGCATATGGAAT 58.502 47.619 4.56 0.00 0.00 3.01
2084 2189 5.217978 ACAAATCAATGCAACATCTTGGT 57.782 34.783 0.00 0.00 0.00 3.67
2188 2297 9.273016 TGCATTTTAGCCTAGATGTAATAGTTC 57.727 33.333 0.00 0.00 0.00 3.01
2311 2420 0.391793 GGTAGGCCAGCTCTGTGAAC 60.392 60.000 5.01 0.00 34.09 3.18
2346 2455 6.767902 TCAAACTTATCCATGGCTAGCTAAAG 59.232 38.462 15.72 10.99 0.00 1.85
2360 2469 8.560374 GCCAGTTGTATTAGATCAAACTTATCC 58.440 37.037 0.00 0.00 0.00 2.59
2518 2630 7.801104 TCAAAAATACATGGCTCCTACAGATA 58.199 34.615 0.00 0.00 0.00 1.98
2526 2638 7.489574 TTTTGTTTCAAAAATACATGGCTCC 57.510 32.000 0.00 0.00 0.00 4.70
2540 2652 6.428771 CGGAGGGAGTAGTATTTTTGTTTCAA 59.571 38.462 0.00 0.00 0.00 2.69
2546 2658 5.163343 TGGATCGGAGGGAGTAGTATTTTTG 60.163 44.000 0.00 0.00 0.00 2.44
2556 2668 5.104109 TCAATTAATTTGGATCGGAGGGAGT 60.104 40.000 0.00 0.00 35.92 3.85
2567 2679 8.133024 ACTAAACCAGCATCAATTAATTTGGA 57.867 30.769 18.51 6.74 35.92 3.53
2598 2710 8.630054 TTGATGCTGGTTTAGTACAACTTATT 57.370 30.769 0.00 0.00 0.00 1.40
2599 2711 8.807948 ATTGATGCTGGTTTAGTACAACTTAT 57.192 30.769 0.00 0.00 0.00 1.73
2600 2712 8.630054 AATTGATGCTGGTTTAGTACAACTTA 57.370 30.769 0.00 0.00 0.00 2.24
2601 2713 7.524717 AATTGATGCTGGTTTAGTACAACTT 57.475 32.000 0.00 0.00 0.00 2.66
2602 2714 8.630054 TTAATTGATGCTGGTTTAGTACAACT 57.370 30.769 0.00 0.00 0.00 3.16
2603 2715 9.855021 AATTAATTGATGCTGGTTTAGTACAAC 57.145 29.630 0.00 0.00 0.00 3.32
2605 2717 9.853555 CAAATTAATTGATGCTGGTTTAGTACA 57.146 29.630 0.39 0.00 41.85 2.90
2606 2718 9.301153 CCAAATTAATTGATGCTGGTTTAGTAC 57.699 33.333 0.39 0.00 41.85 2.73
2607 2719 9.249053 TCCAAATTAATTGATGCTGGTTTAGTA 57.751 29.630 13.18 0.00 41.85 1.82
2608 2720 8.133024 TCCAAATTAATTGATGCTGGTTTAGT 57.867 30.769 13.18 0.00 41.85 2.24
2609 2721 9.603921 AATCCAAATTAATTGATGCTGGTTTAG 57.396 29.630 13.18 0.00 41.85 1.85
2619 2731 7.134842 ACTCCCTCCAATCCAAATTAATTGAT 58.865 34.615 0.39 0.00 41.85 2.57
2831 2946 7.147976 GCAAAGTCAAACAGAAATGTTAGGAT 58.852 34.615 0.00 0.00 0.00 3.24
2832 2947 6.460953 GGCAAAGTCAAACAGAAATGTTAGGA 60.461 38.462 0.00 0.00 0.00 2.94
2833 2948 5.691754 GGCAAAGTCAAACAGAAATGTTAGG 59.308 40.000 0.00 0.00 0.00 2.69
2836 2951 5.343307 AGGCAAAGTCAAACAGAAATGTT 57.657 34.783 0.00 0.00 0.00 2.71
2838 2953 5.581874 ACAAAGGCAAAGTCAAACAGAAATG 59.418 36.000 0.00 0.00 0.00 2.32
2872 3028 3.531538 TCAACCAGTCAGACTTTCACAC 58.468 45.455 0.00 0.00 0.00 3.82
2873 3029 3.450817 TCTCAACCAGTCAGACTTTCACA 59.549 43.478 0.00 0.00 0.00 3.58
2918 3083 7.042791 GCAGCAGCTTATTTCACTAAAACAAAA 60.043 33.333 0.00 0.00 37.91 2.44
2928 3093 1.133790 CCAGGCAGCAGCTTATTTCAC 59.866 52.381 0.00 0.00 41.70 3.18
2939 3104 3.744559 GAAACGTTCCAGGCAGCA 58.255 55.556 0.00 0.00 0.00 4.41
2951 3116 5.621197 TGTAGTTCATGGATTTGGAAACG 57.379 39.130 0.00 0.00 0.00 3.60
2969 3134 3.558931 TGTCTGGGCATGGTAATGTAG 57.441 47.619 0.00 0.00 36.08 2.74
2972 3137 3.289836 TCATTGTCTGGGCATGGTAATG 58.710 45.455 0.00 0.00 36.82 1.90
2978 3145 3.880047 ACATTTCATTGTCTGGGCATG 57.120 42.857 0.00 0.00 0.00 4.06
2983 3150 7.395190 TTCCAATCTACATTTCATTGTCTGG 57.605 36.000 0.00 0.00 0.00 3.86
3000 3167 9.784531 TCTTCATCAGTTAATATCCTTCCAATC 57.215 33.333 0.00 0.00 0.00 2.67
3004 3171 8.563732 GCTTTCTTCATCAGTTAATATCCTTCC 58.436 37.037 0.00 0.00 0.00 3.46
3010 3177 8.049117 TGACCAGCTTTCTTCATCAGTTAATAT 58.951 33.333 0.00 0.00 0.00 1.28
3041 3208 7.931948 GGCATTAAAAGCTCTAGACCTATTACA 59.068 37.037 0.00 0.00 0.00 2.41
3080 3247 2.987413 TGCTAAAACACGGCAGAATG 57.013 45.000 0.00 0.00 40.87 2.67
3088 3255 3.126831 TGGCCAAATTTGCTAAAACACG 58.873 40.909 12.92 0.00 0.00 4.49
3158 3331 4.741676 GCAAAAGATGAAGACAACCAGTTG 59.258 41.667 8.95 8.95 45.58 3.16
3174 3347 5.336150 TCCACAAAAATGTCAGCAAAAGA 57.664 34.783 0.00 0.00 0.00 2.52
3308 3483 4.329545 GTGGAACCCGCTGAGGCA 62.330 66.667 0.00 0.00 39.21 4.75
3366 3541 3.007290 GGTTCACGGTAACTTTAGGTCCT 59.993 47.826 0.00 0.00 0.00 3.85
3433 3608 7.011763 CGAAATGAATACTGTGATTCACCAGAT 59.988 37.037 14.05 2.04 46.00 2.90
3444 3619 4.435518 CCCACGAACGAAATGAATACTGTG 60.436 45.833 0.14 0.00 0.00 3.66
3446 3621 3.930229 TCCCACGAACGAAATGAATACTG 59.070 43.478 0.14 0.00 0.00 2.74
3458 3633 2.369870 GTGCATAGTCCCACGAACG 58.630 57.895 0.00 0.00 0.00 3.95
3463 3638 1.521681 GCCTCGTGCATAGTCCCAC 60.522 63.158 0.00 0.00 40.77 4.61
3464 3639 1.264749 AAGCCTCGTGCATAGTCCCA 61.265 55.000 0.00 0.00 44.83 4.37
3466 3641 0.108138 ACAAGCCTCGTGCATAGTCC 60.108 55.000 0.00 0.00 44.83 3.85
3467 3642 1.281899 GACAAGCCTCGTGCATAGTC 58.718 55.000 0.00 3.82 44.83 2.59
3468 3643 0.608130 TGACAAGCCTCGTGCATAGT 59.392 50.000 0.00 0.00 44.83 2.12
3469 3644 1.596260 CATGACAAGCCTCGTGCATAG 59.404 52.381 0.00 0.00 44.83 2.23
3470 3645 1.655484 CATGACAAGCCTCGTGCATA 58.345 50.000 0.00 0.00 44.83 3.14
3471 3646 2.474561 CATGACAAGCCTCGTGCAT 58.525 52.632 0.00 0.00 44.83 3.96
3472 3647 3.970721 CATGACAAGCCTCGTGCA 58.029 55.556 0.00 0.00 44.83 4.57
3473 3648 2.482374 GCATGACAAGCCTCGTGC 59.518 61.111 0.00 5.38 43.99 5.34
3474 3649 1.642037 CCTGCATGACAAGCCTCGTG 61.642 60.000 0.00 0.00 0.00 4.35
3476 3651 1.078918 TCCTGCATGACAAGCCTCG 60.079 57.895 0.00 0.00 0.00 4.63
3563 3744 6.319405 CGCATCCCCATTCAATCATATATCAA 59.681 38.462 0.00 0.00 0.00 2.57
3564 3745 5.824097 CGCATCCCCATTCAATCATATATCA 59.176 40.000 0.00 0.00 0.00 2.15
3568 3751 3.245371 ACCGCATCCCCATTCAATCATAT 60.245 43.478 0.00 0.00 0.00 1.78
3592 3775 0.318360 CCATACTGTCGCGCGGATAA 60.318 55.000 31.69 7.56 0.00 1.75
3594 3777 2.027605 CCATACTGTCGCGCGGAT 59.972 61.111 31.69 15.20 0.00 4.18
3595 3778 4.865761 GCCATACTGTCGCGCGGA 62.866 66.667 31.69 16.18 0.00 5.54
3597 3780 3.913573 GTGCCATACTGTCGCGCG 61.914 66.667 26.76 26.76 0.00 6.86
3598 3781 2.296692 CTTGTGCCATACTGTCGCGC 62.297 60.000 0.00 0.00 0.00 6.86
3599 3782 0.735978 TCTTGTGCCATACTGTCGCG 60.736 55.000 0.00 0.00 0.00 5.87
3600 3783 1.438651 TTCTTGTGCCATACTGTCGC 58.561 50.000 0.00 0.00 0.00 5.19
3601 3784 3.436704 ACATTTCTTGTGCCATACTGTCG 59.563 43.478 0.00 0.00 37.11 4.35
3602 3785 5.156355 CAACATTTCTTGTGCCATACTGTC 58.844 41.667 0.00 0.00 38.99 3.51
3603 3786 4.584325 ACAACATTTCTTGTGCCATACTGT 59.416 37.500 0.00 0.00 38.99 3.55
3604 3787 4.919168 CACAACATTTCTTGTGCCATACTG 59.081 41.667 0.00 0.00 43.38 2.74
3605 3788 5.125100 CACAACATTTCTTGTGCCATACT 57.875 39.130 0.00 0.00 43.38 2.12
3613 3796 4.934602 CCAAACCAACACAACATTTCTTGT 59.065 37.500 0.00 0.00 41.53 3.16
3618 3801 6.294231 GGAAAAACCAAACCAACACAACATTT 60.294 34.615 0.00 0.00 38.79 2.32
3619 3802 5.182190 GGAAAAACCAAACCAACACAACATT 59.818 36.000 0.00 0.00 38.79 2.71
3620 3803 4.697828 GGAAAAACCAAACCAACACAACAT 59.302 37.500 0.00 0.00 38.79 2.71
3621 3804 4.065789 GGAAAAACCAAACCAACACAACA 58.934 39.130 0.00 0.00 38.79 3.33
3622 3805 4.320023 AGGAAAAACCAAACCAACACAAC 58.680 39.130 0.00 0.00 42.04 3.32
3623 3806 4.625607 AGGAAAAACCAAACCAACACAA 57.374 36.364 0.00 0.00 42.04 3.33
3626 3809 5.104735 AGCAATAGGAAAAACCAAACCAACA 60.105 36.000 0.00 0.00 42.04 3.33
3627 3810 5.236263 CAGCAATAGGAAAAACCAAACCAAC 59.764 40.000 0.00 0.00 42.04 3.77
3628 3811 5.129485 TCAGCAATAGGAAAAACCAAACCAA 59.871 36.000 0.00 0.00 42.04 3.67
3631 3814 6.223120 ACATCAGCAATAGGAAAAACCAAAC 58.777 36.000 0.00 0.00 42.04 2.93
3632 3815 6.418057 ACATCAGCAATAGGAAAAACCAAA 57.582 33.333 0.00 0.00 42.04 3.28
3677 3860 0.393808 GGCTCGAATTTGCCTGGGTA 60.394 55.000 6.18 0.00 45.26 3.69
3679 3862 3.200522 GGCTCGAATTTGCCTGGG 58.799 61.111 6.18 0.00 45.26 4.45
3706 3889 0.539986 TATGGAGGCCGTGAAAGACC 59.460 55.000 0.00 0.00 0.00 3.85
3708 3891 3.426787 TTTTATGGAGGCCGTGAAAGA 57.573 42.857 0.00 0.00 0.00 2.52
3730 3913 3.878778 AGCAAGCAATTAACCGAGAGAT 58.121 40.909 0.00 0.00 0.00 2.75
3757 3940 7.222417 CACACACACACAAACAAACATCATTAT 59.778 33.333 0.00 0.00 0.00 1.28
3758 3941 6.529477 CACACACACACAAACAAACATCATTA 59.471 34.615 0.00 0.00 0.00 1.90
3759 3942 5.348179 CACACACACACAAACAAACATCATT 59.652 36.000 0.00 0.00 0.00 2.57
3760 3943 4.863689 CACACACACACAAACAAACATCAT 59.136 37.500 0.00 0.00 0.00 2.45
3761 3944 4.233005 CACACACACACAAACAAACATCA 58.767 39.130 0.00 0.00 0.00 3.07
3762 3945 4.233789 ACACACACACACAAACAAACATC 58.766 39.130 0.00 0.00 0.00 3.06
3763 3946 4.250116 ACACACACACACAAACAAACAT 57.750 36.364 0.00 0.00 0.00 2.71
3764 3947 3.717400 ACACACACACACAAACAAACA 57.283 38.095 0.00 0.00 0.00 2.83
3765 3948 5.688176 AGTAAACACACACACACAAACAAAC 59.312 36.000 0.00 0.00 0.00 2.93
3766 3949 5.687730 CAGTAAACACACACACACAAACAAA 59.312 36.000 0.00 0.00 0.00 2.83
3767 3950 5.215903 CAGTAAACACACACACACAAACAA 58.784 37.500 0.00 0.00 0.00 2.83
3768 3951 4.788690 CAGTAAACACACACACACAAACA 58.211 39.130 0.00 0.00 0.00 2.83
3769 3952 3.606346 GCAGTAAACACACACACACAAAC 59.394 43.478 0.00 0.00 0.00 2.93
3770 3953 3.253432 TGCAGTAAACACACACACACAAA 59.747 39.130 0.00 0.00 0.00 2.83
3771 3954 2.814336 TGCAGTAAACACACACACACAA 59.186 40.909 0.00 0.00 0.00 3.33
3772 3955 2.418280 CTGCAGTAAACACACACACACA 59.582 45.455 5.25 0.00 0.00 3.72
3773 3956 2.791158 GCTGCAGTAAACACACACACAC 60.791 50.000 16.64 0.00 0.00 3.82
3872 4063 2.699954 AGCAATTCCACCGTAACAGAG 58.300 47.619 0.00 0.00 0.00 3.35
3905 4096 3.096092 GCATCAAAGGGTACAATGGGAA 58.904 45.455 0.00 0.00 0.00 3.97
3908 4099 2.738743 AGGCATCAAAGGGTACAATGG 58.261 47.619 0.00 0.00 0.00 3.16
3918 4109 8.743714 AGGAATTTTCTAAACTAGGCATCAAAG 58.256 33.333 0.00 0.00 0.00 2.77
3950 4143 7.744087 TTTTATATGATTTGGATGGTCGGAG 57.256 36.000 0.00 0.00 0.00 4.63
3976 4210 7.288810 TCAAGTGCTTATTTGATTCAAAGGT 57.711 32.000 16.34 4.54 36.76 3.50
3977 4211 6.309737 GCTCAAGTGCTTATTTGATTCAAAGG 59.690 38.462 16.34 10.34 36.76 3.11
3978 4212 7.088905 AGCTCAAGTGCTTATTTGATTCAAAG 58.911 34.615 16.34 5.29 40.93 2.77
4004 4238 3.565482 GTGAGGCAATCTTCACTTGTTCA 59.435 43.478 1.07 0.00 0.00 3.18
4014 4248 2.472695 TAAGCACGTGAGGCAATCTT 57.527 45.000 22.23 13.24 0.00 2.40
4021 4255 2.333926 TGAAACGATAAGCACGTGAGG 58.666 47.619 22.23 3.09 43.16 3.86
4023 4257 4.797693 TTTTGAAACGATAAGCACGTGA 57.202 36.364 22.23 0.00 43.16 4.35
4024 4258 6.432802 AATTTTTGAAACGATAAGCACGTG 57.567 33.333 12.28 12.28 43.16 4.49
4033 4267 9.030301 CCTTGTTACTGAAATTTTTGAAACGAT 57.970 29.630 0.00 0.00 0.00 3.73
4036 4270 9.366216 AGACCTTGTTACTGAAATTTTTGAAAC 57.634 29.630 0.00 0.00 0.00 2.78
4076 4310 5.186215 TGATGTGTAAAATACAGAGACGGGA 59.814 40.000 0.00 0.00 39.77 5.14
4120 4469 2.457598 ACCGGACTGAGATAGCAGAAA 58.542 47.619 9.46 0.00 39.20 2.52
4133 4485 3.314307 TGAGGATATCAGAACCGGACT 57.686 47.619 9.46 3.91 32.77 3.85
4143 4495 1.363807 CGCGGTGCTGAGGATATCA 59.636 57.895 4.83 0.00 36.21 2.15
4144 4496 1.373497 CCGCGGTGCTGAGGATATC 60.373 63.158 19.50 0.00 0.00 1.63
4159 4514 1.095807 GTGTAGGGAGATTTGGCCGC 61.096 60.000 0.00 0.00 0.00 6.53
4163 4518 3.954258 GGATTTGGTGTAGGGAGATTTGG 59.046 47.826 0.00 0.00 0.00 3.28
4247 4602 3.379445 GCCGGTCCGAGGAGTTCA 61.379 66.667 14.39 0.00 0.00 3.18
4277 4632 3.320879 CTGGATGCGCTGGGTCAGT 62.321 63.158 9.73 0.00 33.43 3.41
4334 4689 1.806623 GCATTCCGTCGAGCAGGTTAT 60.807 52.381 0.00 0.00 0.00 1.89
4597 4952 1.794151 TTGGCGTAGTGGTCGACGAA 61.794 55.000 9.92 0.00 43.34 3.85
4689 5044 1.079127 CAAGAACCCGGCGATGAGT 60.079 57.895 9.30 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.