Multiple sequence alignment - TraesCS4D01G023500

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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 TraesCS4D01G023500 chr4D 100.000 4778 0 0 1 4778 10248441 10253218 0.000000e+00 8824.0
1 TraesCS4D01G023500 chr4D 84.382 1383 190 19 2411 3780 420942835 420944204 0.000000e+00 1334.0
2 TraesCS4D01G023500 chr4D 79.021 1349 245 30 2415 3745 47535724 47534396 0.000000e+00 889.0
3 TraesCS4D01G023500 chr4D 84.022 557 87 2 1860 2415 420942188 420942743 7.040000e-148 534.0
4 TraesCS4D01G023500 chr4D 84.410 449 65 3 1863 2307 47536516 47536069 2.040000e-118 436.0
5 TraesCS4D01G023500 chr4D 88.672 256 27 2 1150 1404 420940123 420940377 1.290000e-80 311.0
6 TraesCS4D01G023500 chr4B 94.741 2814 110 19 1854 4651 19736095 19738886 0.000000e+00 4342.0
7 TraesCS4D01G023500 chr4B 84.359 1381 192 17 2411 3779 518098126 518099494 0.000000e+00 1332.0
8 TraesCS4D01G023500 chr4B 89.014 801 58 24 616 1405 19735116 19735897 0.000000e+00 965.0
9 TraesCS4D01G023500 chr4B 78.206 1349 256 30 2412 3742 69378920 69380248 0.000000e+00 828.0
10 TraesCS4D01G023500 chr4B 84.926 544 77 5 1854 2394 518097469 518098010 3.250000e-151 545.0
11 TraesCS4D01G023500 chr4B 83.628 452 69 3 1860 2307 69378048 69378498 2.060000e-113 420.0
12 TraesCS4D01G023500 chr4B 86.713 286 35 3 1121 1404 518095400 518095684 9.980000e-82 315.0
13 TraesCS4D01G023500 chr4B 83.509 285 37 8 1123 1402 69375933 69376212 1.710000e-64 257.0
14 TraesCS4D01G023500 chr4B 92.571 175 6 4 135 307 19729972 19730141 1.330000e-60 244.0
15 TraesCS4D01G023500 chr4B 84.716 229 19 6 205 428 19735016 19735233 1.040000e-51 215.0
16 TraesCS4D01G023500 chr4B 82.902 193 12 10 637 824 19734578 19734754 2.300000e-33 154.0
17 TraesCS4D01G023500 chr4B 90.244 82 3 5 4 81 49100425 49100505 8.460000e-18 102.0
18 TraesCS4D01G023500 chr4B 83.871 93 9 5 4682 4769 19739166 19739257 3.060000e-12 84.2
19 TraesCS4D01G023500 chr4A 94.657 2508 111 14 1707 4208 593356977 593354487 0.000000e+00 3868.0
20 TraesCS4D01G023500 chr4A 84.325 1378 191 18 2415 3779 43233076 43231711 0.000000e+00 1325.0
21 TraesCS4D01G023500 chr4A 85.068 1259 96 39 329 1527 593358204 593356978 0.000000e+00 1199.0
22 TraesCS4D01G023500 chr4A 78.380 1346 260 25 2414 3745 550482521 550481193 0.000000e+00 845.0
23 TraesCS4D01G023500 chr4A 85.099 557 81 2 1860 2415 43233725 43233170 6.940000e-158 568.0
24 TraesCS4D01G023500 chr4A 83.964 449 67 4 1863 2307 550483256 550482809 4.420000e-115 425.0
25 TraesCS4D01G023500 chr4A 89.062 256 26 2 1150 1404 43235685 43235431 2.780000e-82 316.0
26 TraesCS4D01G023500 chr4A 90.957 188 9 5 73 257 593359185 593359003 3.690000e-61 246.0
27 TraesCS4D01G023500 chr4A 79.717 212 31 8 4576 4778 593354493 593354285 4.980000e-30 143.0
28 TraesCS4D01G023500 chr4A 89.899 99 6 1 243 337 593358987 593358889 1.810000e-24 124.0
29 TraesCS4D01G023500 chr4A 94.203 69 3 1 4 72 581324359 581324426 2.350000e-18 104.0
30 TraesCS4D01G023500 chr4A 87.000 100 4 3 338 428 593357899 593357800 2.350000e-18 104.0
31 TraesCS4D01G023500 chr4A 93.056 72 4 1 8 79 732742881 732742811 2.350000e-18 104.0
32 TraesCS4D01G023500 chr6D 78.413 542 96 20 3183 3715 389370151 389370680 2.760000e-87 333.0
33 TraesCS4D01G023500 chr6D 73.616 777 184 17 2414 3181 389369302 389370066 3.640000e-71 279.0
34 TraesCS4D01G023500 chr6D 79.635 329 53 11 1085 1409 389367204 389367522 1.730000e-54 224.0
35 TraesCS4D01G023500 chr7D 96.373 193 7 0 1524 1716 580554206 580554014 7.720000e-83 318.0
36 TraesCS4D01G023500 chr3D 96.875 192 3 3 1526 1715 6058058 6058248 7.720000e-83 318.0
37 TraesCS4D01G023500 chr6A 95.876 194 7 1 1524 1717 63210297 63210489 3.590000e-81 313.0
38 TraesCS4D01G023500 chr6A 83.636 220 26 7 1085 1302 535896378 535896589 1.050000e-46 198.0
39 TraesCS4D01G023500 chr1A 95.789 190 8 0 1525 1714 572357484 572357673 1.670000e-79 307.0
40 TraesCS4D01G023500 chr1A 94.819 193 8 2 1524 1716 133163744 133163554 2.790000e-77 300.0
41 TraesCS4D01G023500 chr7A 94.388 196 9 2 1523 1718 610448563 610448756 2.790000e-77 300.0
42 TraesCS4D01G023500 chr7A 90.789 76 5 2 4 79 154378490 154378417 3.040000e-17 100.0
43 TraesCS4D01G023500 chr3A 94.792 192 10 0 1525 1716 708640749 708640558 2.790000e-77 300.0
44 TraesCS4D01G023500 chr2A 94.792 192 10 0 1525 1716 763334173 763334364 2.790000e-77 300.0
45 TraesCS4D01G023500 chr5D 94.359 195 8 3 1523 1717 406201283 406201092 3.620000e-76 296.0
46 TraesCS4D01G023500 chr6B 73.067 776 190 16 2414 3181 582400060 582400824 1.710000e-64 257.0
47 TraesCS4D01G023500 chr6B 80.124 322 50 11 1085 1402 582397847 582398158 1.340000e-55 228.0
48 TraesCS4D01G023500 chr3B 87.940 199 16 4 2647 2838 104157461 104157658 1.340000e-55 228.0
49 TraesCS4D01G023500 chr3B 97.222 36 1 0 2391 2426 104157675 104157710 1.440000e-05 62.1
50 TraesCS4D01G023500 chr5B 92.105 76 4 2 8 82 617649893 617649819 6.540000e-19 106.0
51 TraesCS4D01G023500 chr2B 94.286 70 3 1 4 72 668434042 668433973 6.540000e-19 106.0
52 TraesCS4D01G023500 chr2B 95.385 65 3 0 8 72 80167064 80167128 2.350000e-18 104.0
53 TraesCS4D01G023500 chr5A 94.203 69 3 1 4 72 452517488 452517555 2.350000e-18 104.0
54 TraesCS4D01G023500 chr1D 94.203 69 3 1 4 72 225919274 225919341 2.350000e-18 104.0


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 TraesCS4D01G023500 chr4D 10248441 10253218 4777 False 8824.000000 8824 100.000000 1 4778 1 chr4D.!!$F1 4777
1 TraesCS4D01G023500 chr4D 420940123 420944204 4081 False 726.333333 1334 85.692000 1150 3780 3 chr4D.!!$F2 2630
2 TraesCS4D01G023500 chr4D 47534396 47536516 2120 True 662.500000 889 81.715500 1863 3745 2 chr4D.!!$R1 1882
3 TraesCS4D01G023500 chr4B 19734578 19739257 4679 False 1152.040000 4342 87.048800 205 4769 5 chr4B.!!$F3 4564
4 TraesCS4D01G023500 chr4B 518095400 518099494 4094 False 730.666667 1332 85.332667 1121 3779 3 chr4B.!!$F5 2658
5 TraesCS4D01G023500 chr4B 69375933 69380248 4315 False 501.666667 828 81.781000 1123 3742 3 chr4B.!!$F4 2619
6 TraesCS4D01G023500 chr4A 593354285 593359185 4900 True 947.333333 3868 87.883000 73 4778 6 chr4A.!!$R4 4705
7 TraesCS4D01G023500 chr4A 43231711 43235685 3974 True 736.333333 1325 86.162000 1150 3779 3 chr4A.!!$R2 2629
8 TraesCS4D01G023500 chr4A 550481193 550483256 2063 True 635.000000 845 81.172000 1863 3745 2 chr4A.!!$R3 1882
9 TraesCS4D01G023500 chr6D 389367204 389370680 3476 False 278.666667 333 77.221333 1085 3715 3 chr6D.!!$F1 2630
10 TraesCS4D01G023500 chr6B 582397847 582400824 2977 False 242.500000 257 76.595500 1085 3181 2 chr6B.!!$F1 2096

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
563 1529 0.392461 TATGTGCGGCCTGGTTTCTC 60.392 55.0 0.0 0.0 0.0 2.87 F
909 1912 0.598065 ACATGCAAGTCGGAAAAGCC 59.402 50.0 0.0 0.0 0.0 4.35 F
1641 3929 0.036765 TGCTGACGTGGGTTGTATCC 60.037 55.0 0.0 0.0 0.0 2.59 F
1643 3931 0.245539 CTGACGTGGGTTGTATCCGT 59.754 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 3910 0.036765 GGATACAACCCACGTCAGCA 60.037 55.000 0.0 0.0 0.00 4.41 R
2132 5651 2.281484 TCACCCTGGCGTTGAAGC 60.281 61.111 0.0 0.0 0.00 3.86 R
3472 8166 0.179045 AACTTGAGCTGTTCGCACCT 60.179 50.000 0.0 0.0 42.61 4.00 R
3789 8487 7.532884 CGCCAAAAACAGACTAACAATAACTAC 59.467 37.037 0.0 0.0 0.00 2.73 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
68 69 8.751242 TCATTCAGAAAATTGCTCATATTTCCA 58.249 29.630 0.00 0.00 33.35 3.53
71 72 7.894708 TCAGAAAATTGCTCATATTTCCAACA 58.105 30.769 0.00 0.00 33.35 3.33
106 107 8.612619 CCACAATCTACCATACATGTAACTTTC 58.387 37.037 10.14 0.00 0.00 2.62
253 488 9.199184 GCAAATACGATAAGAACAATATATGCG 57.801 33.333 0.00 0.00 0.00 4.73
284 549 6.907961 TCTACCTACCATGTAGTAGATGTGT 58.092 40.000 9.88 6.60 41.98 3.72
319 588 2.094675 CCACATTTGGGCCTAGTTCAG 58.905 52.381 4.53 0.00 39.57 3.02
414 1380 7.482654 TGAAATCCTACTATTCAAATCTGCG 57.517 36.000 0.00 0.00 30.60 5.18
438 1404 6.037830 CGTATCCCCGTGTAGAAATGAAAAAT 59.962 38.462 0.00 0.00 0.00 1.82
516 1482 5.557576 TTAGATGAGTTGCAGATATGGCT 57.442 39.130 0.00 0.00 0.00 4.75
555 1521 7.597288 TCTATGTAATATATATGTGCGGCCT 57.403 36.000 0.00 0.00 0.00 5.19
561 1527 1.961793 TATATGTGCGGCCTGGTTTC 58.038 50.000 0.00 0.00 0.00 2.78
563 1529 0.392461 TATGTGCGGCCTGGTTTCTC 60.392 55.000 0.00 0.00 0.00 2.87
606 1572 7.926674 TCAGATTTGAACATCTCATTTAGCA 57.073 32.000 0.00 0.00 32.78 3.49
611 1577 6.441093 TTGAACATCTCATTTAGCATCACC 57.559 37.500 0.00 0.00 32.78 4.02
618 1584 2.575735 TCATTTAGCATCACCTCACCCA 59.424 45.455 0.00 0.00 0.00 4.51
630 1596 4.904853 TCACCTCACCCACTTGCATATATA 59.095 41.667 0.00 0.00 0.00 0.86
631 1597 5.547666 TCACCTCACCCACTTGCATATATAT 59.452 40.000 0.00 0.00 0.00 0.86
632 1598 6.728632 TCACCTCACCCACTTGCATATATATA 59.271 38.462 0.00 0.00 0.00 0.86
633 1599 7.402941 TCACCTCACCCACTTGCATATATATAT 59.597 37.037 0.00 0.00 0.00 0.86
634 1600 8.704668 CACCTCACCCACTTGCATATATATATA 58.295 37.037 4.90 4.92 0.00 0.86
635 1601 9.452517 ACCTCACCCACTTGCATATATATATAT 57.547 33.333 9.12 9.12 0.00 0.86
682 1650 5.931724 TGCCATACATGTATAGTTGGATTCG 59.068 40.000 22.06 6.50 0.00 3.34
689 1657 8.087982 ACATGTATAGTTGGATTCGCATTAAG 57.912 34.615 0.00 0.00 0.00 1.85
692 1660 6.929049 TGTATAGTTGGATTCGCATTAAGAGG 59.071 38.462 0.00 0.00 0.00 3.69
694 1662 4.843728 AGTTGGATTCGCATTAAGAGGAA 58.156 39.130 0.00 0.00 0.00 3.36
695 1663 5.440610 AGTTGGATTCGCATTAAGAGGAAT 58.559 37.500 0.00 0.00 32.15 3.01
701 1669 7.080724 GGATTCGCATTAAGAGGAATGAAATC 58.919 38.462 0.40 7.77 38.83 2.17
702 1670 6.377327 TTCGCATTAAGAGGAATGAAATCC 57.623 37.500 0.40 0.00 38.83 3.01
720 1688 7.639039 TGAAATCCTACTATATTTTTGCTGCG 58.361 34.615 0.00 0.00 0.00 5.18
721 1689 7.282224 TGAAATCCTACTATATTTTTGCTGCGT 59.718 33.333 0.00 0.00 0.00 5.24
723 1691 7.653767 ATCCTACTATATTTTTGCTGCGTAC 57.346 36.000 0.00 0.00 0.00 3.67
724 1692 5.688621 TCCTACTATATTTTTGCTGCGTACG 59.311 40.000 11.84 11.84 0.00 3.67
730 1702 0.993532 TTTTGCTGCGTACGTATCCG 59.006 50.000 17.90 0.00 40.83 4.18
755 1727 6.851837 GCGCGTAGGATATATACTCACTATTG 59.148 42.308 8.43 0.00 0.00 1.90
757 1729 8.063038 CGCGTAGGATATATACTCACTATTGAC 58.937 40.741 0.00 0.00 0.00 3.18
809 1811 8.964476 ATTAATGTCCAGTAGAAATACACAGG 57.036 34.615 0.00 0.00 0.00 4.00
909 1912 0.598065 ACATGCAAGTCGGAAAAGCC 59.402 50.000 0.00 0.00 0.00 4.35
910 1913 0.883833 CATGCAAGTCGGAAAAGCCT 59.116 50.000 0.00 0.00 0.00 4.58
911 1914 2.083774 CATGCAAGTCGGAAAAGCCTA 58.916 47.619 0.00 0.00 0.00 3.93
912 1915 2.489938 TGCAAGTCGGAAAAGCCTAT 57.510 45.000 0.00 0.00 0.00 2.57
913 1916 3.620427 TGCAAGTCGGAAAAGCCTATA 57.380 42.857 0.00 0.00 0.00 1.31
914 1917 4.150897 TGCAAGTCGGAAAAGCCTATAT 57.849 40.909 0.00 0.00 0.00 0.86
915 1918 5.284861 TGCAAGTCGGAAAAGCCTATATA 57.715 39.130 0.00 0.00 0.00 0.86
950 1954 2.774234 TCTCCTGAATTCTCACATCCCC 59.226 50.000 7.05 0.00 0.00 4.81
952 1956 3.192944 TCCTGAATTCTCACATCCCCTT 58.807 45.455 7.05 0.00 0.00 3.95
953 1957 3.200825 TCCTGAATTCTCACATCCCCTTC 59.799 47.826 7.05 0.00 0.00 3.46
959 1963 2.744760 TCTCACATCCCCTTCTCTCTG 58.255 52.381 0.00 0.00 0.00 3.35
964 1968 1.138661 CATCCCCTTCTCTCTGTCTGC 59.861 57.143 0.00 0.00 0.00 4.26
981 1993 1.810030 GCACGTCGTCCATTCTCCC 60.810 63.158 0.00 0.00 0.00 4.30
987 1999 1.203994 GTCGTCCATTCTCCCGAAAGA 59.796 52.381 0.00 0.00 31.91 2.52
988 2000 1.897133 TCGTCCATTCTCCCGAAAGAA 59.103 47.619 2.53 2.53 39.49 2.52
989 2001 2.300723 TCGTCCATTCTCCCGAAAGAAA 59.699 45.455 3.97 0.00 38.69 2.52
996 2008 4.884668 TTCTCCCGAAAGAAAGAAGCTA 57.115 40.909 0.00 0.00 32.42 3.32
1034 2046 1.746615 GCATGGTCGTGCTCATGGT 60.747 57.895 7.82 0.00 41.82 3.55
1054 2066 1.433837 GACAATAATTCCGGCGGCGT 61.434 55.000 30.09 14.14 0.00 5.68
1067 2079 2.472059 CGGCGTTGCTGCATATGGT 61.472 57.895 1.84 0.00 36.28 3.55
1068 2080 1.157257 CGGCGTTGCTGCATATGGTA 61.157 55.000 1.84 0.00 36.28 3.25
1069 2081 1.238439 GGCGTTGCTGCATATGGTAT 58.762 50.000 1.84 0.00 36.28 2.73
1209 2224 4.335647 AAGGTGTCGCAGCTGGGG 62.336 66.667 28.30 11.75 41.59 4.96
1454 3115 3.877508 TGTCTGCGAGATCTTCTTCGATA 59.122 43.478 6.30 0.00 0.00 2.92
1459 3120 3.423867 GCGAGATCTTCTTCGATACAAGC 59.576 47.826 6.30 0.00 0.00 4.01
1462 3123 5.587289 GAGATCTTCTTCGATACAAGCAGT 58.413 41.667 0.00 0.00 0.00 4.40
1464 3125 4.521130 TCTTCTTCGATACAAGCAGTGT 57.479 40.909 0.00 0.00 44.82 3.55
1553 3841 9.678260 ATTTATCAGTTTTGCTAGAACTCATCT 57.322 29.630 0.00 0.00 42.48 2.90
1616 3904 5.243981 ACTGGATGTGATGCTATAAGATGC 58.756 41.667 0.00 0.00 0.00 3.91
1619 3907 4.092529 GGATGTGATGCTATAAGATGCGTG 59.907 45.833 0.00 0.00 0.00 5.34
1620 3908 4.058721 TGTGATGCTATAAGATGCGTGT 57.941 40.909 0.00 0.00 0.00 4.49
1622 3910 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
1623 3911 3.803778 TGATGCTATAAGATGCGTGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
1625 3913 2.205074 GCTATAAGATGCGTGTGTGCT 58.795 47.619 0.00 0.00 35.36 4.40
1626 3914 2.033407 GCTATAAGATGCGTGTGTGCTG 60.033 50.000 0.00 0.00 35.36 4.41
1628 3916 1.428448 TAAGATGCGTGTGTGCTGAC 58.572 50.000 0.00 0.00 35.36 3.51
1629 3917 1.560004 AAGATGCGTGTGTGCTGACG 61.560 55.000 0.00 0.00 38.63 4.35
1630 3918 2.280119 ATGCGTGTGTGCTGACGT 60.280 55.556 0.00 0.00 37.89 4.34
1631 3919 2.484631 GATGCGTGTGTGCTGACGTG 62.485 60.000 0.00 0.00 37.89 4.49
1633 3921 3.337889 CGTGTGTGCTGACGTGGG 61.338 66.667 0.00 0.00 0.00 4.61
1634 3922 2.203015 GTGTGTGCTGACGTGGGT 60.203 61.111 0.00 0.00 0.00 4.51
1637 3925 1.817941 GTGTGCTGACGTGGGTTGT 60.818 57.895 0.00 0.00 0.00 3.32
1639 3927 0.394938 TGTGCTGACGTGGGTTGTAT 59.605 50.000 0.00 0.00 0.00 2.29
1640 3928 1.076332 GTGCTGACGTGGGTTGTATC 58.924 55.000 0.00 0.00 0.00 2.24
1641 3929 0.036765 TGCTGACGTGGGTTGTATCC 60.037 55.000 0.00 0.00 0.00 2.59
1642 3930 1.082117 GCTGACGTGGGTTGTATCCG 61.082 60.000 0.00 0.00 0.00 4.18
1643 3931 0.245539 CTGACGTGGGTTGTATCCGT 59.754 55.000 0.00 0.00 0.00 4.69
1644 3932 0.680618 TGACGTGGGTTGTATCCGTT 59.319 50.000 0.00 0.00 0.00 4.44
1645 3933 1.337074 TGACGTGGGTTGTATCCGTTC 60.337 52.381 0.00 0.00 0.00 3.95
1646 3934 0.971386 ACGTGGGTTGTATCCGTTCT 59.029 50.000 0.00 0.00 0.00 3.01
1648 3936 1.730064 CGTGGGTTGTATCCGTTCTTG 59.270 52.381 0.00 0.00 0.00 3.02
1649 3937 2.774687 GTGGGTTGTATCCGTTCTTGT 58.225 47.619 0.00 0.00 0.00 3.16
1652 3940 4.037089 GTGGGTTGTATCCGTTCTTGTTTT 59.963 41.667 0.00 0.00 0.00 2.43
1653 3941 4.276431 TGGGTTGTATCCGTTCTTGTTTTC 59.724 41.667 0.00 0.00 0.00 2.29
1654 3942 4.320714 GGGTTGTATCCGTTCTTGTTTTCC 60.321 45.833 0.00 0.00 0.00 3.13
1659 3947 2.294074 TCCGTTCTTGTTTTCCAGGTG 58.706 47.619 0.00 0.00 0.00 4.00
1660 3948 2.092861 TCCGTTCTTGTTTTCCAGGTGA 60.093 45.455 0.00 0.00 0.00 4.02
1661 3949 2.685897 CCGTTCTTGTTTTCCAGGTGAA 59.314 45.455 0.00 0.00 0.00 3.18
1663 3951 4.290155 CGTTCTTGTTTTCCAGGTGAATG 58.710 43.478 0.00 0.00 31.67 2.67
1664 3952 4.036262 CGTTCTTGTTTTCCAGGTGAATGA 59.964 41.667 0.00 0.00 31.67 2.57
1665 3953 5.523369 GTTCTTGTTTTCCAGGTGAATGAG 58.477 41.667 0.00 0.00 31.67 2.90
1666 3954 5.047566 TCTTGTTTTCCAGGTGAATGAGA 57.952 39.130 0.00 0.00 31.67 3.27
1667 3955 4.821805 TCTTGTTTTCCAGGTGAATGAGAC 59.178 41.667 0.00 0.00 31.67 3.36
1671 3959 3.874383 TTCCAGGTGAATGAGACCAAA 57.126 42.857 0.00 0.00 35.76 3.28
1672 3960 4.387026 TTCCAGGTGAATGAGACCAAAT 57.613 40.909 0.00 0.00 35.76 2.32
1673 3961 4.387026 TCCAGGTGAATGAGACCAAATT 57.613 40.909 0.00 0.00 35.76 1.82
1674 3962 5.512942 TCCAGGTGAATGAGACCAAATTA 57.487 39.130 0.00 0.00 35.76 1.40
1676 3964 4.094887 CCAGGTGAATGAGACCAAATTACG 59.905 45.833 0.00 0.00 35.76 3.18
1677 3965 4.695455 CAGGTGAATGAGACCAAATTACGT 59.305 41.667 0.00 0.00 35.76 3.57
1678 3966 4.935808 AGGTGAATGAGACCAAATTACGTC 59.064 41.667 0.00 0.00 35.76 4.34
1688 3976 7.589958 AGACCAAATTACGTCTCATCTAGAT 57.410 36.000 0.00 0.00 34.15 1.98
1689 3977 7.429633 AGACCAAATTACGTCTCATCTAGATG 58.570 38.462 24.32 24.32 45.40 2.90
1745 4551 5.169295 GTGTTGCTAAATCTTAGTCGACCT 58.831 41.667 13.01 2.17 0.00 3.85
1746 4552 5.062308 GTGTTGCTAAATCTTAGTCGACCTG 59.938 44.000 13.01 2.68 0.00 4.00
1747 4553 5.047590 TGTTGCTAAATCTTAGTCGACCTGA 60.048 40.000 13.01 8.54 0.00 3.86
1748 4554 5.250235 TGCTAAATCTTAGTCGACCTGAG 57.750 43.478 13.01 7.98 0.00 3.35
1795 5269 5.239744 TGAGATCTTACCTAGAGATTCGTGC 59.760 44.000 0.00 0.00 36.02 5.34
1849 5323 6.088173 TCATTCATCGGGTTATAATCGTACG 58.912 40.000 9.53 9.53 0.00 3.67
2200 5910 2.049156 CGTTCAGGAGCTGCGTGA 60.049 61.111 0.00 1.30 39.45 4.35
2859 7455 1.876714 GTGCATCGATACGGCGTGT 60.877 57.895 24.86 17.68 0.00 4.49
3423 8108 4.056125 CTGACCTCGACGGCAGCA 62.056 66.667 4.25 0.00 35.61 4.41
3460 8154 1.801332 CACTACGACGTGGAGGAGG 59.199 63.158 18.84 0.00 0.00 4.30
3789 8487 0.526662 ACGCCTGAACTAACTCTCCG 59.473 55.000 0.00 0.00 0.00 4.63
3793 8491 2.754002 GCCTGAACTAACTCTCCGTAGT 59.246 50.000 0.00 0.00 0.00 2.73
3794 8492 3.193056 GCCTGAACTAACTCTCCGTAGTT 59.807 47.826 0.00 0.00 42.31 2.24
3795 8493 4.397417 GCCTGAACTAACTCTCCGTAGTTA 59.603 45.833 0.00 0.00 40.20 2.24
3798 8496 6.973474 CCTGAACTAACTCTCCGTAGTTATTG 59.027 42.308 0.00 0.00 40.30 1.90
3805 8503 7.700022 AACTCTCCGTAGTTATTGTTAGTCT 57.300 36.000 0.00 0.00 37.93 3.24
3829 8531 0.323908 TTGGCGGGGGTAAAAGATGG 60.324 55.000 0.00 0.00 0.00 3.51
3845 8547 1.956477 GATGGATTGCATAGCGGGTTT 59.044 47.619 0.00 0.00 0.00 3.27
3869 8575 1.135939 GGCGACACAATTAACCGGC 59.864 57.895 0.00 0.00 38.52 6.13
3909 8615 3.476295 TCGAGCAACATCAAGAAATGC 57.524 42.857 0.00 0.00 37.28 3.56
3967 8676 8.156820 TGTCTGTTTCTAAATCCTCAATGAGAA 58.843 33.333 12.53 0.00 0.00 2.87
4001 8710 7.769220 ACATGATCAATGAGATTCTTGTTTCC 58.231 34.615 0.00 0.00 38.72 3.13
4004 8713 5.611796 TCAATGAGATTCTTGTTTCCGTG 57.388 39.130 0.00 0.00 0.00 4.94
4015 8724 5.556915 TCTTGTTTCCGTGTCCATAATCTT 58.443 37.500 0.00 0.00 0.00 2.40
4024 8733 6.432783 TCCGTGTCCATAATCTTGAATTGTTT 59.567 34.615 0.00 0.00 0.00 2.83
4025 8734 7.040062 TCCGTGTCCATAATCTTGAATTGTTTT 60.040 33.333 0.00 0.00 0.00 2.43
4026 8735 7.598493 CCGTGTCCATAATCTTGAATTGTTTTT 59.402 33.333 0.00 0.00 0.00 1.94
4027 8736 8.638565 CGTGTCCATAATCTTGAATTGTTTTTC 58.361 33.333 0.00 0.00 0.00 2.29
4083 8792 8.586273 CATGTCTTTGAATTAATAAAGCCAACG 58.414 33.333 6.01 0.00 34.67 4.10
4122 8831 6.685403 CACAACGTTAAGTTCTTACAAACCAG 59.315 38.462 0.00 0.00 42.02 4.00
4166 8877 0.165295 CACGACTCTAACACGAGCGA 59.835 55.000 0.00 0.00 35.79 4.93
4168 8879 1.202043 ACGACTCTAACACGAGCGATG 60.202 52.381 0.00 0.00 35.79 3.84
4195 8906 2.265467 TAAGGCCCCACAAGATCCGC 62.265 60.000 0.00 0.00 0.00 5.54
4203 8914 1.134280 CCACAAGATCCGCCTCAAGAT 60.134 52.381 0.00 0.00 0.00 2.40
4217 8928 5.418676 GCCTCAAGATCTCCTATGAATAGC 58.581 45.833 0.00 0.00 0.00 2.97
4233 8944 4.509230 TGAATAGCGTGAAGATGCTTGATC 59.491 41.667 0.00 0.00 42.10 2.92
4248 8959 3.212685 CTTGATCTTGAGAAGGATGCCC 58.787 50.000 0.00 0.00 0.00 5.36
4255 8966 3.797353 GAAGGATGCCCGCCTCCA 61.797 66.667 12.72 0.00 33.76 3.86
4262 8973 4.115199 GCCCGCCTCCACCTCATT 62.115 66.667 0.00 0.00 0.00 2.57
4263 8974 2.124570 CCCGCCTCCACCTCATTG 60.125 66.667 0.00 0.00 0.00 2.82
4264 8975 2.671070 CCGCCTCCACCTCATTGT 59.329 61.111 0.00 0.00 0.00 2.71
4265 8976 1.450312 CCGCCTCCACCTCATTGTC 60.450 63.158 0.00 0.00 0.00 3.18
4284 8995 1.007238 TCCTGTCCTACCTCTTCCCTG 59.993 57.143 0.00 0.00 0.00 4.45
4299 9010 0.184451 CCCTGGAGTATGCCATTGCT 59.816 55.000 0.00 0.00 37.30 3.91
4305 9016 2.961062 GGAGTATGCCATTGCTGGAAAT 59.039 45.455 0.00 0.00 46.37 2.17
4365 9076 2.532250 GGAATGGTTCCCTCAATGGT 57.468 50.000 0.00 0.00 44.30 3.55
4384 9095 5.789643 TGGTAAGTTTGTTACGAGTAGGT 57.210 39.130 0.00 0.00 0.00 3.08
4409 9120 2.202566 GCGCCCAAGCTAAAGTACTAG 58.797 52.381 0.00 0.00 36.60 2.57
4411 9122 3.445857 CGCCCAAGCTAAAGTACTAGAC 58.554 50.000 0.00 0.00 36.60 2.59
4425 9137 5.251764 AGTACTAGACGTTCTCCAAGCTAA 58.748 41.667 0.00 0.00 0.00 3.09
4428 9140 0.992802 GACGTTCTCCAAGCTAAGCG 59.007 55.000 0.00 0.00 0.00 4.68
4430 9142 0.992802 CGTTCTCCAAGCTAAGCGAC 59.007 55.000 0.00 0.00 0.00 5.19
4455 9167 3.181967 CCCGCGAGCGTTCTTGAG 61.182 66.667 8.23 0.00 37.81 3.02
4456 9168 2.430921 CCGCGAGCGTTCTTGAGT 60.431 61.111 8.23 0.00 37.81 3.41
4474 9186 1.134670 AGTGGCGCAAGAATCTCTACC 60.135 52.381 10.83 0.00 43.02 3.18
4501 9213 4.654389 ATTTGGATTCCAATTTTGCCCA 57.346 36.364 18.62 1.94 43.55 5.36
4507 9219 4.216042 GGATTCCAATTTTGCCCAAAACAG 59.784 41.667 8.21 4.67 42.32 3.16
4510 9222 3.454082 TCCAATTTTGCCCAAAACAGTCT 59.546 39.130 8.21 0.00 42.32 3.24
4517 9229 2.685897 TGCCCAAAACAGTCTTGTACAC 59.314 45.455 0.00 0.00 36.23 2.90
4527 9239 3.555956 CAGTCTTGTACACAACTCCACAC 59.444 47.826 0.00 0.00 0.00 3.82
4543 9255 2.053627 CACACGAATTTTGCAAGAGCC 58.946 47.619 0.00 0.00 41.13 4.70
4548 9260 2.669434 CGAATTTTGCAAGAGCCCATTG 59.331 45.455 0.00 0.00 41.13 2.82
4573 9285 4.871933 CAGAATGTAGTTGGGGCTTTTT 57.128 40.909 0.00 0.00 0.00 1.94
4591 9303 3.458872 TGGAGCTCCACATAAAGCG 57.541 52.632 32.00 0.00 42.01 4.68
4603 9315 3.058570 CACATAAAGCGCAACACCTGTTA 60.059 43.478 11.47 0.00 36.32 2.41
4606 9318 0.179029 AAGCGCAACACCTGTTACCT 60.179 50.000 11.47 0.00 36.32 3.08
4616 9330 2.439507 CACCTGTTACCTAGGCCATGAT 59.560 50.000 9.30 0.00 38.96 2.45
4617 9331 2.439507 ACCTGTTACCTAGGCCATGATG 59.560 50.000 9.30 0.00 38.96 3.07
4651 9365 0.752009 TAGCGAAGGCCAGACGATCT 60.752 55.000 17.66 9.84 41.24 2.75
4675 9477 1.847818 TTTCACGACACGTTGAGGAG 58.152 50.000 0.00 0.00 38.32 3.69
4676 9478 0.031585 TTCACGACACGTTGAGGAGG 59.968 55.000 0.00 0.00 38.32 4.30
4677 9479 1.372997 CACGACACGTTGAGGAGGG 60.373 63.158 0.00 0.00 38.32 4.30
4678 9480 2.261671 CGACACGTTGAGGAGGGG 59.738 66.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.760077 GGAAATATGAGCAATTTTCTGAATGAT 57.240 29.630 0.00 0.00 0.00 2.45
42 43 8.751242 TGGAAATATGAGCAATTTTCTGAATGA 58.249 29.630 0.00 0.00 0.00 2.57
43 44 8.936070 TGGAAATATGAGCAATTTTCTGAATG 57.064 30.769 0.00 0.00 0.00 2.67
44 45 9.374838 GTTGGAAATATGAGCAATTTTCTGAAT 57.625 29.630 0.00 0.00 0.00 2.57
46 47 7.894708 TGTTGGAAATATGAGCAATTTTCTGA 58.105 30.769 0.00 0.00 0.00 3.27
47 48 8.712285 ATGTTGGAAATATGAGCAATTTTCTG 57.288 30.769 0.00 0.00 0.00 3.02
48 49 9.807649 GTATGTTGGAAATATGAGCAATTTTCT 57.192 29.630 0.00 0.00 0.00 2.52
49 50 9.807649 AGTATGTTGGAAATATGAGCAATTTTC 57.192 29.630 0.00 0.00 0.00 2.29
50 51 9.807649 GAGTATGTTGGAAATATGAGCAATTTT 57.192 29.630 0.00 0.00 0.00 1.82
51 52 8.970020 TGAGTATGTTGGAAATATGAGCAATTT 58.030 29.630 0.00 0.00 0.00 1.82
54 55 7.148086 GGTTGAGTATGTTGGAAATATGAGCAA 60.148 37.037 0.00 0.00 0.00 3.91
55 56 6.318648 GGTTGAGTATGTTGGAAATATGAGCA 59.681 38.462 0.00 0.00 0.00 4.26
57 58 6.828273 TGGGTTGAGTATGTTGGAAATATGAG 59.172 38.462 0.00 0.00 0.00 2.90
58 59 6.601613 GTGGGTTGAGTATGTTGGAAATATGA 59.398 38.462 0.00 0.00 0.00 2.15
59 60 6.376864 TGTGGGTTGAGTATGTTGGAAATATG 59.623 38.462 0.00 0.00 0.00 1.78
60 61 6.489603 TGTGGGTTGAGTATGTTGGAAATAT 58.510 36.000 0.00 0.00 0.00 1.28
61 62 5.882040 TGTGGGTTGAGTATGTTGGAAATA 58.118 37.500 0.00 0.00 0.00 1.40
63 64 4.171878 TGTGGGTTGAGTATGTTGGAAA 57.828 40.909 0.00 0.00 0.00 3.13
64 65 3.866703 TGTGGGTTGAGTATGTTGGAA 57.133 42.857 0.00 0.00 0.00 3.53
68 69 5.013704 TGGTAGATTGTGGGTTGAGTATGTT 59.986 40.000 0.00 0.00 0.00 2.71
71 72 5.975988 ATGGTAGATTGTGGGTTGAGTAT 57.024 39.130 0.00 0.00 0.00 2.12
253 488 8.047911 TCTACTACATGGTAGGTAGATCTATGC 58.952 40.741 5.57 0.00 40.49 3.14
319 588 7.715265 TCTGCCATTTTATAAGATTCGAGTC 57.285 36.000 0.00 0.00 0.00 3.36
414 1380 6.746745 TTTTTCATTTCTACACGGGGATAC 57.253 37.500 0.00 0.00 0.00 2.24
460 1426 8.425577 TTTTTGCGAATCTAAATGTTTTTCCA 57.574 26.923 0.00 0.00 0.00 3.53
511 1477 8.657712 ACATAGATATATGTGCATATCAGCCAT 58.342 33.333 12.11 0.00 39.42 4.40
512 1478 8.026396 ACATAGATATATGTGCATATCAGCCA 57.974 34.615 12.11 0.00 39.42 4.75
542 1508 1.488812 AGAAACCAGGCCGCACATATA 59.511 47.619 0.00 0.00 0.00 0.86
543 1509 0.255890 AGAAACCAGGCCGCACATAT 59.744 50.000 0.00 0.00 0.00 1.78
544 1510 0.392461 GAGAAACCAGGCCGCACATA 60.392 55.000 0.00 0.00 0.00 2.29
555 1521 0.958091 CCAAATGTGGCGAGAAACCA 59.042 50.000 0.00 0.00 38.35 3.67
606 1572 0.700564 ATGCAAGTGGGTGAGGTGAT 59.299 50.000 0.00 0.00 0.00 3.06
660 1626 5.931724 TGCGAATCCAACTATACATGTATGG 59.068 40.000 25.48 24.38 0.00 2.74
664 1630 7.931407 TCTTAATGCGAATCCAACTATACATGT 59.069 33.333 2.69 2.69 0.00 3.21
668 1634 7.152645 TCCTCTTAATGCGAATCCAACTATAC 58.847 38.462 0.00 0.00 0.00 1.47
682 1650 9.732130 ATAGTAGGATTTCATTCCTCTTAATGC 57.268 33.333 0.00 0.00 42.71 3.56
694 1662 8.292448 CGCAGCAAAAATATAGTAGGATTTCAT 58.708 33.333 0.00 0.00 0.00 2.57
695 1663 7.282224 ACGCAGCAAAAATATAGTAGGATTTCA 59.718 33.333 0.00 0.00 0.00 2.69
701 1669 5.461078 ACGTACGCAGCAAAAATATAGTAGG 59.539 40.000 16.72 0.00 0.00 3.18
702 1670 6.506464 ACGTACGCAGCAAAAATATAGTAG 57.494 37.500 16.72 0.00 0.00 2.57
703 1671 7.326789 GGATACGTACGCAGCAAAAATATAGTA 59.673 37.037 16.72 0.00 0.00 1.82
705 1673 6.522761 GGATACGTACGCAGCAAAAATATAG 58.477 40.000 16.72 0.00 0.00 1.31
706 1674 6.456447 GGATACGTACGCAGCAAAAATATA 57.544 37.500 16.72 0.00 0.00 0.86
707 1675 5.338614 GGATACGTACGCAGCAAAAATAT 57.661 39.130 16.72 1.90 0.00 1.28
709 1677 3.668596 GGATACGTACGCAGCAAAAAT 57.331 42.857 16.72 0.00 0.00 1.82
724 1692 3.892918 ATATATCCTACGCGCGGATAC 57.107 47.619 35.22 0.00 44.05 2.24
730 1702 4.879104 AGTGAGTATATATCCTACGCGC 57.121 45.455 5.73 0.00 31.94 6.86
808 1810 9.520515 TCCTTCAAATATAAAATGCTAGGATCC 57.479 33.333 2.48 2.48 0.00 3.36
896 1899 7.133133 TCCTTTATATAGGCTTTTCCGACTT 57.867 36.000 4.43 0.00 40.77 3.01
909 1912 7.605691 CAGGAGAATGGCAGTTCCTTTATATAG 59.394 40.741 13.46 1.56 37.97 1.31
910 1913 7.292356 TCAGGAGAATGGCAGTTCCTTTATATA 59.708 37.037 13.46 0.00 37.97 0.86
911 1914 6.101734 TCAGGAGAATGGCAGTTCCTTTATAT 59.898 38.462 13.46 0.00 37.97 0.86
912 1915 5.428457 TCAGGAGAATGGCAGTTCCTTTATA 59.572 40.000 13.46 1.78 37.97 0.98
913 1916 4.228210 TCAGGAGAATGGCAGTTCCTTTAT 59.772 41.667 13.46 0.00 37.97 1.40
914 1917 3.587061 TCAGGAGAATGGCAGTTCCTTTA 59.413 43.478 13.46 5.43 37.97 1.85
915 1918 2.376518 TCAGGAGAATGGCAGTTCCTTT 59.623 45.455 13.46 0.00 37.97 3.11
950 1954 1.727535 CGACGTGCAGACAGAGAGAAG 60.728 57.143 0.00 0.00 0.00 2.85
952 1956 0.885150 ACGACGTGCAGACAGAGAGA 60.885 55.000 0.00 0.00 0.00 3.10
953 1957 0.453615 GACGACGTGCAGACAGAGAG 60.454 60.000 4.58 0.00 0.00 3.20
959 1963 0.388649 AGAATGGACGACGTGCAGAC 60.389 55.000 26.03 20.62 37.30 3.51
964 1968 1.516386 CGGGAGAATGGACGACGTG 60.516 63.158 4.58 0.00 0.00 4.49
981 1993 3.064545 CCATGGCTAGCTTCTTTCTTTCG 59.935 47.826 15.72 0.00 0.00 3.46
987 1999 3.197664 GCCCATGGCTAGCTTCTTT 57.802 52.632 15.72 0.00 46.69 2.52
988 2000 4.995594 GCCCATGGCTAGCTTCTT 57.004 55.556 15.72 0.00 46.69 2.52
1034 2046 1.433053 CGCCGCCGGAATTATTGTCA 61.433 55.000 7.68 0.00 0.00 3.58
1038 2050 1.725066 CAACGCCGCCGGAATTATT 59.275 52.632 7.68 0.00 39.22 1.40
1047 2059 3.585990 ATATGCAGCAACGCCGCC 61.586 61.111 0.00 0.00 0.00 6.13
1048 2060 2.352686 CATATGCAGCAACGCCGC 60.353 61.111 0.00 0.00 0.00 6.53
1054 2066 1.522668 GCCGATACCATATGCAGCAA 58.477 50.000 0.00 0.00 0.00 3.91
1060 2072 0.391130 CCACCGGCCGATACCATATG 60.391 60.000 30.73 8.96 0.00 1.78
1061 2073 1.980052 CCACCGGCCGATACCATAT 59.020 57.895 30.73 0.00 0.00 1.78
1062 2074 2.874664 GCCACCGGCCGATACCATA 61.875 63.158 30.73 0.00 44.06 2.74
1454 3115 4.281941 TCAGACAGAAGATACACTGCTTGT 59.718 41.667 0.00 0.00 42.84 3.16
1593 3881 5.243981 GCATCTTATAGCATCACATCCAGT 58.756 41.667 0.00 0.00 0.00 4.00
1594 3882 4.329256 CGCATCTTATAGCATCACATCCAG 59.671 45.833 0.00 0.00 0.00 3.86
1596 3884 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
1598 3886 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
1599 3887 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
1600 3888 3.804325 ACACACGCATCTTATAGCATCAC 59.196 43.478 0.00 0.00 0.00 3.06
1602 3890 3.363378 GCACACACGCATCTTATAGCATC 60.363 47.826 0.00 0.00 0.00 3.91
1603 3891 2.545526 GCACACACGCATCTTATAGCAT 59.454 45.455 0.00 0.00 0.00 3.79
1604 3892 1.933181 GCACACACGCATCTTATAGCA 59.067 47.619 0.00 0.00 0.00 3.49
1605 3893 2.033407 CAGCACACACGCATCTTATAGC 60.033 50.000 0.00 0.00 0.00 2.97
1606 3894 3.243877 GTCAGCACACACGCATCTTATAG 59.756 47.826 0.00 0.00 0.00 1.31
1607 3895 3.186909 GTCAGCACACACGCATCTTATA 58.813 45.455 0.00 0.00 0.00 0.98
1608 3896 2.002586 GTCAGCACACACGCATCTTAT 58.997 47.619 0.00 0.00 0.00 1.73
1609 3897 1.428448 GTCAGCACACACGCATCTTA 58.572 50.000 0.00 0.00 0.00 2.10
1611 3899 2.023771 CGTCAGCACACACGCATCT 61.024 57.895 0.00 0.00 0.00 2.90
1612 3900 2.310233 ACGTCAGCACACACGCATC 61.310 57.895 0.00 0.00 39.73 3.91
1614 3902 3.261216 CACGTCAGCACACACGCA 61.261 61.111 0.00 0.00 39.73 5.24
1615 3903 4.000557 CCACGTCAGCACACACGC 62.001 66.667 0.00 0.00 39.73 5.34
1616 3904 3.337889 CCCACGTCAGCACACACG 61.338 66.667 0.00 0.00 41.90 4.49
1619 3907 0.531090 TACAACCCACGTCAGCACAC 60.531 55.000 0.00 0.00 0.00 3.82
1620 3908 0.394938 ATACAACCCACGTCAGCACA 59.605 50.000 0.00 0.00 0.00 4.57
1622 3910 0.036765 GGATACAACCCACGTCAGCA 60.037 55.000 0.00 0.00 0.00 4.41
1623 3911 1.082117 CGGATACAACCCACGTCAGC 61.082 60.000 0.00 0.00 0.00 4.26
1625 3913 0.680618 AACGGATACAACCCACGTCA 59.319 50.000 0.00 0.00 36.69 4.35
1626 3914 1.067354 AGAACGGATACAACCCACGTC 60.067 52.381 0.00 0.00 36.69 4.34
1628 3916 1.730064 CAAGAACGGATACAACCCACG 59.270 52.381 0.00 0.00 0.00 4.94
1629 3917 2.774687 ACAAGAACGGATACAACCCAC 58.225 47.619 0.00 0.00 0.00 4.61
1630 3918 3.495434 AACAAGAACGGATACAACCCA 57.505 42.857 0.00 0.00 0.00 4.51
1631 3919 4.320714 GGAAAACAAGAACGGATACAACCC 60.321 45.833 0.00 0.00 0.00 4.11
1633 3921 5.427036 TGGAAAACAAGAACGGATACAAC 57.573 39.130 0.00 0.00 0.00 3.32
1634 3922 4.517453 CCTGGAAAACAAGAACGGATACAA 59.483 41.667 0.00 0.00 0.00 2.41
1637 3925 4.069304 CACCTGGAAAACAAGAACGGATA 58.931 43.478 0.00 0.00 0.00 2.59
1639 3927 2.092861 TCACCTGGAAAACAAGAACGGA 60.093 45.455 0.00 0.00 0.00 4.69
1640 3928 2.294074 TCACCTGGAAAACAAGAACGG 58.706 47.619 0.00 0.00 0.00 4.44
1641 3929 4.036262 TCATTCACCTGGAAAACAAGAACG 59.964 41.667 0.00 0.00 39.39 3.95
1642 3930 5.299279 TCTCATTCACCTGGAAAACAAGAAC 59.701 40.000 0.00 0.00 39.39 3.01
1643 3931 5.299279 GTCTCATTCACCTGGAAAACAAGAA 59.701 40.000 0.00 0.00 39.39 2.52
1644 3932 4.821805 GTCTCATTCACCTGGAAAACAAGA 59.178 41.667 0.00 0.00 39.39 3.02
1645 3933 4.022849 GGTCTCATTCACCTGGAAAACAAG 60.023 45.833 0.00 0.00 39.39 3.16
1646 3934 3.888930 GGTCTCATTCACCTGGAAAACAA 59.111 43.478 0.00 0.00 39.39 2.83
1648 3936 3.486383 TGGTCTCATTCACCTGGAAAAC 58.514 45.455 0.00 0.00 39.39 2.43
1649 3937 3.874383 TGGTCTCATTCACCTGGAAAA 57.126 42.857 0.00 0.00 39.39 2.29
1652 3940 4.387026 AATTTGGTCTCATTCACCTGGA 57.613 40.909 0.00 0.00 34.66 3.86
1653 3941 4.094887 CGTAATTTGGTCTCATTCACCTGG 59.905 45.833 0.00 0.00 34.66 4.45
1654 3942 4.695455 ACGTAATTTGGTCTCATTCACCTG 59.305 41.667 0.00 0.00 34.66 4.00
1664 3952 7.285629 TCATCTAGATGAGACGTAATTTGGTCT 59.714 37.037 27.93 9.96 45.71 3.85
1665 3953 7.426410 TCATCTAGATGAGACGTAATTTGGTC 58.574 38.462 27.93 1.46 42.42 4.02
1666 3954 7.348080 TCATCTAGATGAGACGTAATTTGGT 57.652 36.000 27.93 0.00 42.42 3.67
1721 4033 4.927425 GGTCGACTAAGATTTAGCAACACA 59.073 41.667 16.46 0.00 0.00 3.72
1745 4551 8.655935 TGGATATAATATCAAGTCTCAGCTCA 57.344 34.615 0.00 0.00 0.00 4.26
1746 4552 9.531942 CATGGATATAATATCAAGTCTCAGCTC 57.468 37.037 0.00 0.00 0.00 4.09
1747 4553 9.264653 TCATGGATATAATATCAAGTCTCAGCT 57.735 33.333 0.00 0.00 0.00 4.24
1748 4554 9.531942 CTCATGGATATAATATCAAGTCTCAGC 57.468 37.037 0.00 0.00 0.00 4.26
1827 5301 5.860182 CACGTACGATTATAACCCGATGAAT 59.140 40.000 24.41 0.00 0.00 2.57
1828 5302 5.214417 CACGTACGATTATAACCCGATGAA 58.786 41.667 24.41 0.00 0.00 2.57
1849 5323 2.671351 CGATCGCCTACATACCATCCAC 60.671 54.545 0.26 0.00 0.00 4.02
2132 5651 2.281484 TCACCCTGGCGTTGAAGC 60.281 61.111 0.00 0.00 0.00 3.86
3381 8060 0.459078 CGAGCAGGCTCTTCTGATGA 59.541 55.000 18.23 0.00 40.69 2.92
3472 8166 0.179045 AACTTGAGCTGTTCGCACCT 60.179 50.000 0.00 0.00 42.61 4.00
3789 8487 7.532884 CGCCAAAAACAGACTAACAATAACTAC 59.467 37.037 0.00 0.00 0.00 2.73
3793 8491 5.278561 CCCGCCAAAAACAGACTAACAATAA 60.279 40.000 0.00 0.00 0.00 1.40
3794 8492 4.216687 CCCGCCAAAAACAGACTAACAATA 59.783 41.667 0.00 0.00 0.00 1.90
3795 8493 3.005367 CCCGCCAAAAACAGACTAACAAT 59.995 43.478 0.00 0.00 0.00 2.71
3798 8496 1.268625 CCCCGCCAAAAACAGACTAAC 59.731 52.381 0.00 0.00 0.00 2.34
3805 8503 1.413077 CTTTTACCCCCGCCAAAAACA 59.587 47.619 0.00 0.00 0.00 2.83
3829 8531 2.529151 CAACAAACCCGCTATGCAATC 58.471 47.619 0.00 0.00 0.00 2.67
3845 8547 0.945099 TTAATTGTGTCGCCGCAACA 59.055 45.000 0.00 0.00 43.39 3.33
3869 8575 1.927895 ACAATTAGCTCTTCGAGGCG 58.072 50.000 0.00 0.00 0.00 5.52
3917 8623 9.547753 ACAATTCCATTACATAGCTACACTAAG 57.452 33.333 0.00 0.00 33.57 2.18
3996 8705 5.873179 TTCAAGATTATGGACACGGAAAC 57.127 39.130 0.00 0.00 0.00 2.78
4001 8710 8.519492 AAAAACAATTCAAGATTATGGACACG 57.481 30.769 0.00 0.00 0.00 4.49
4024 8733 7.607250 TGTGCCTGTTTTCTAAAAGAAAGAAA 58.393 30.769 2.65 0.00 44.14 2.52
4025 8734 7.164230 TGTGCCTGTTTTCTAAAAGAAAGAA 57.836 32.000 2.65 0.00 44.14 2.52
4026 8735 6.767524 TGTGCCTGTTTTCTAAAAGAAAGA 57.232 33.333 2.65 0.00 44.14 2.52
4027 8736 6.476706 CCTTGTGCCTGTTTTCTAAAAGAAAG 59.523 38.462 2.65 0.00 44.14 2.62
4122 8831 9.748708 TGATTTGTATTTCTGCTTTATTATGCC 57.251 29.630 0.00 0.00 0.00 4.40
4166 8877 3.393687 TGTGGGGCCTTAGTTATCTCAT 58.606 45.455 0.84 0.00 0.00 2.90
4168 8879 3.454812 TCTTGTGGGGCCTTAGTTATCTC 59.545 47.826 0.84 0.00 0.00 2.75
4195 8906 5.184864 ACGCTATTCATAGGAGATCTTGAGG 59.815 44.000 0.00 0.00 0.00 3.86
4203 8914 5.565637 GCATCTTCACGCTATTCATAGGAGA 60.566 44.000 0.00 0.00 0.00 3.71
4233 8944 1.821332 GGCGGGCATCCTTCTCAAG 60.821 63.158 0.00 0.00 0.00 3.02
4238 8949 3.797353 TGGAGGCGGGCATCCTTC 61.797 66.667 22.98 0.00 46.05 3.46
4248 8959 1.450312 GGACAATGAGGTGGAGGCG 60.450 63.158 0.00 0.00 0.00 5.52
4255 8966 2.188817 GGTAGGACAGGACAATGAGGT 58.811 52.381 0.00 0.00 0.00 3.85
4261 8972 2.537143 GGAAGAGGTAGGACAGGACAA 58.463 52.381 0.00 0.00 0.00 3.18
4262 8973 1.273098 GGGAAGAGGTAGGACAGGACA 60.273 57.143 0.00 0.00 0.00 4.02
4263 8974 1.007359 AGGGAAGAGGTAGGACAGGAC 59.993 57.143 0.00 0.00 0.00 3.85
4264 8975 1.007238 CAGGGAAGAGGTAGGACAGGA 59.993 57.143 0.00 0.00 0.00 3.86
4265 8976 1.490574 CAGGGAAGAGGTAGGACAGG 58.509 60.000 0.00 0.00 0.00 4.00
4284 8995 2.057137 TTCCAGCAATGGCATACTCC 57.943 50.000 0.00 0.00 44.61 3.85
4335 9046 0.701731 AACCATTCCGTCCCATCCAA 59.298 50.000 0.00 0.00 0.00 3.53
4336 9047 0.254747 GAACCATTCCGTCCCATCCA 59.745 55.000 0.00 0.00 0.00 3.41
4364 9075 7.219726 GCTATGACCTACTCGTAACAAACTTAC 59.780 40.741 0.00 0.00 0.00 2.34
4365 9076 7.253422 GCTATGACCTACTCGTAACAAACTTA 58.747 38.462 0.00 0.00 0.00 2.24
4384 9095 1.209504 ACTTTAGCTTGGGCGCTATGA 59.790 47.619 7.64 0.00 41.71 2.15
4409 9120 0.992802 CGCTTAGCTTGGAGAACGTC 59.007 55.000 1.76 0.00 0.00 4.34
4411 9122 0.992802 GTCGCTTAGCTTGGAGAACG 59.007 55.000 1.76 0.00 0.00 3.95
4443 9155 3.016474 GCGCCACTCAAGAACGCTC 62.016 63.158 0.00 0.00 45.71 5.03
4447 9159 2.616969 TCTTGCGCCACTCAAGAAC 58.383 52.632 4.18 0.00 44.70 3.01
4450 9162 1.396301 GAGATTCTTGCGCCACTCAAG 59.604 52.381 4.18 0.62 41.57 3.02
4455 9167 1.291132 GGTAGAGATTCTTGCGCCAC 58.709 55.000 4.18 0.00 0.00 5.01
4456 9168 0.901827 TGGTAGAGATTCTTGCGCCA 59.098 50.000 4.18 0.00 0.00 5.69
4501 9213 5.123344 GTGGAGTTGTGTACAAGACTGTTTT 59.877 40.000 15.00 0.00 36.96 2.43
4507 9219 2.538449 CGTGTGGAGTTGTGTACAAGAC 59.462 50.000 0.00 0.00 36.39 3.01
4510 9222 2.963548 TCGTGTGGAGTTGTGTACAA 57.036 45.000 0.00 0.00 0.00 2.41
4517 9229 3.077229 TGCAAAATTCGTGTGGAGTTG 57.923 42.857 0.00 0.00 0.00 3.16
4527 9239 2.660189 ATGGGCTCTTGCAAAATTCG 57.340 45.000 0.00 0.00 41.91 3.34
4543 9255 4.158394 CCCAACTACATTCTGTTCCAATGG 59.842 45.833 0.00 0.00 35.82 3.16
4548 9260 2.092323 GCCCCAACTACATTCTGTTCC 58.908 52.381 0.00 0.00 0.00 3.62
4560 9272 0.105504 AGCTCCAAAAAGCCCCAACT 60.106 50.000 0.00 0.00 43.56 3.16
4573 9285 0.744414 GCGCTTTATGTGGAGCTCCA 60.744 55.000 32.00 32.00 45.30 3.86
4591 9303 1.450025 GCCTAGGTAACAGGTGTTGC 58.550 55.000 11.31 4.04 38.90 4.17
4603 9315 4.046286 TCAAAAACATCATGGCCTAGGT 57.954 40.909 11.31 0.00 0.00 3.08
4606 9318 4.415596 ACCTTCAAAAACATCATGGCCTA 58.584 39.130 3.32 0.00 0.00 3.93
4616 9330 6.674066 CCTTCGCTATTAACCTTCAAAAACA 58.326 36.000 0.00 0.00 0.00 2.83
4617 9331 5.571741 GCCTTCGCTATTAACCTTCAAAAAC 59.428 40.000 0.00 0.00 0.00 2.43
4656 9458 1.537348 CCTCCTCAACGTGTCGTGAAA 60.537 52.381 0.00 0.00 39.99 2.69
4684 9486 3.314357 CGTAATTTTAGCTACTTGCCCCC 59.686 47.826 0.00 0.00 44.23 5.40
4685 9487 4.193865 TCGTAATTTTAGCTACTTGCCCC 58.806 43.478 0.00 0.00 44.23 5.80
4686 9488 5.806366 TTCGTAATTTTAGCTACTTGCCC 57.194 39.130 0.00 0.00 44.23 5.36
4687 9489 7.011828 TGATTCGTAATTTTAGCTACTTGCC 57.988 36.000 0.00 0.00 44.23 4.52


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

AutoCloner maintained by Alex Coulton.