Multiple sequence alignment - TraesCS2A01G352300

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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 TraesCS2A01G352300 chr2A 100.000 7453 0 0 1 7453 592786301 592778849 0.000000e+00 13764.0
1 TraesCS2A01G352300 chr2A 88.462 208 22 2 3961 4166 388485997 388485790 4.460000e-62 250.0
2 TraesCS2A01G352300 chr2A 96.739 92 3 0 627 718 708034585 708034494 3.600000e-33 154.0
3 TraesCS2A01G352300 chr2A 91.525 59 3 2 3030 3086 89165448 89165390 6.200000e-11 80.5
4 TraesCS2A01G352300 chr2B 96.289 6171 170 34 717 6861 527889342 527883205 0.000000e+00 10072.0
5 TraesCS2A01G352300 chr2B 86.600 500 49 8 1 488 527890148 527889655 3.060000e-148 536.0
6 TraesCS2A01G352300 chr2B 78.360 439 63 19 7044 7451 527882191 527881754 9.600000e-64 255.0
7 TraesCS2A01G352300 chr2B 95.833 96 2 2 627 722 227115917 227115824 3.600000e-33 154.0
8 TraesCS2A01G352300 chr2B 93.000 100 7 0 626 725 479585319 479585220 6.030000e-31 147.0
9 TraesCS2A01G352300 chr2B 87.273 110 5 2 475 584 527889485 527889385 4.720000e-22 117.0
10 TraesCS2A01G352300 chr2D 96.412 2787 60 16 3407 6181 448141233 448138475 0.000000e+00 4556.0
11 TraesCS2A01G352300 chr2D 94.918 1771 55 11 1610 3364 448142975 448141224 0.000000e+00 2739.0
12 TraesCS2A01G352300 chr2D 95.497 866 24 6 709 1562 448143838 448142976 0.000000e+00 1369.0
13 TraesCS2A01G352300 chr2D 97.393 652 12 3 6193 6842 448138106 448137458 0.000000e+00 1105.0
14 TraesCS2A01G352300 chr2D 84.746 413 35 13 1 412 448151236 448150851 9.070000e-104 388.0
15 TraesCS2A01G352300 chr2D 78.829 444 59 17 7044 7453 448137164 448136722 4.430000e-67 267.0
16 TraesCS2A01G352300 chr2D 90.452 199 17 2 3959 4156 307808419 307808222 2.060000e-65 261.0
17 TraesCS2A01G352300 chr2D 89.764 127 10 1 506 629 448143961 448143835 7.740000e-35 159.0
18 TraesCS2A01G352300 chr2D 95.122 41 2 0 434 474 448150847 448150807 1.740000e-06 65.8
19 TraesCS2A01G352300 chr5D 91.584 202 15 2 3962 4162 322989740 322989540 2.050000e-70 278.0
20 TraesCS2A01G352300 chr7A 90.476 210 16 4 3959 4165 478160243 478160035 2.650000e-69 274.0
21 TraesCS2A01G352300 chr7D 90.686 204 15 4 3959 4161 416148684 416148484 1.230000e-67 268.0
22 TraesCS2A01G352300 chr7D 98.851 87 1 0 625 711 345777525 345777439 1.000000e-33 156.0
23 TraesCS2A01G352300 chr7D 85.401 137 12 7 2955 3086 112430077 112429944 1.300000e-27 135.0
24 TraesCS2A01G352300 chr6B 90.640 203 18 1 3961 4162 111124317 111124519 1.230000e-67 268.0
25 TraesCS2A01G352300 chr6D 89.151 212 20 3 3959 4168 27788578 27788788 2.060000e-65 261.0
26 TraesCS2A01G352300 chr6D 95.789 95 3 1 626 719 417354701 417354795 1.300000e-32 152.0
27 TraesCS2A01G352300 chr3D 97.778 90 2 0 625 714 505557307 505557396 1.000000e-33 156.0
28 TraesCS2A01G352300 chr3D 87.013 77 8 1 3012 3086 469482469 469482393 1.330000e-12 86.1
29 TraesCS2A01G352300 chr3B 94.845 97 3 2 626 720 748777176 748777080 4.660000e-32 150.0
30 TraesCS2A01G352300 chr3B 92.105 76 5 1 3012 3086 623827066 623826991 1.020000e-18 106.0
31 TraesCS2A01G352300 chr1A 95.652 92 4 0 627 718 551487855 551487764 1.680000e-31 148.0
32 TraesCS2A01G352300 chr1D 93.939 99 3 2 627 725 234329126 234329031 6.030000e-31 147.0
33 TraesCS2A01G352300 chr7B 84.672 137 13 7 2955 3086 72238825 72238692 6.070000e-26 130.0


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 TraesCS2A01G352300 chr2A 592778849 592786301 7452 True 13764.000000 13764 100.0000 1 7453 1 chr2A.!!$R3 7452
1 TraesCS2A01G352300 chr2B 527881754 527890148 8394 True 2745.000000 10072 87.1305 1 7451 4 chr2B.!!$R3 7450
2 TraesCS2A01G352300 chr2D 448136722 448143961 7239 True 1699.166667 4556 92.1355 506 7453 6 chr2D.!!$R2 6947

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
72 73 0.105778 GAAAGGAGGAGATCAGGGCG 59.894 60.000 0.00 0.0 0.00 6.13 F
1223 1429 0.510359 CTGCTCGTCAAGTGAGTTGC 59.490 55.000 0.00 0.0 35.94 4.17 F
1741 1952 0.591170 TAGTTTTTGCGCCTCACAGC 59.409 50.000 4.18 0.0 0.00 4.40 F
1757 1968 3.087031 CACAGCTCCATTGATGTTCCTT 58.913 45.455 0.00 0.0 34.05 3.36 F
3153 3379 2.158813 TGGTTCGACTTCAAGCTTTCCT 60.159 45.455 0.00 0.0 0.00 3.36 F
3690 3918 1.376424 CTGAGGACTGCGGCATTGT 60.376 57.895 1.75 0.0 0.00 2.71 F
4188 4418 2.496899 TTCATTCTCCACTGCCCTTC 57.503 50.000 0.00 0.0 0.00 3.46 F
5307 5546 4.015084 CTCCAAGTTGCTCATTTCCTCAT 58.985 43.478 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1943 1.022735 CATCAATGGAGCTGTGAGGC 58.977 55.0 0.00 0.00 0.00 4.70 R
2879 3105 0.320247 GCGCTGCTGCTATCCTGTAT 60.320 55.0 14.03 0.00 36.97 2.29 R
3153 3379 1.308069 GGAGCAGGCATTTCGAAGCA 61.308 55.0 11.04 0.00 0.00 3.91 R
3313 3540 1.755179 TCAATAGAGCAAAGGCCAGC 58.245 50.0 5.01 6.06 42.56 4.85 R
4217 4447 2.478335 CTTGGGTAAGGGCCTTGCGA 62.478 60.0 28.88 14.28 0.00 5.10 R
4569 4799 3.464907 CATATCAGCAGAACCAGTCCTG 58.535 50.0 0.00 0.00 0.00 3.86 R
5974 6215 4.340666 TGACTAGCAGATGTTTTGCCAAAA 59.659 37.5 0.00 0.00 42.48 2.44 R
7055 8542 0.471617 CTCCCCAGAGCCGAATTGAT 59.528 55.0 0.00 0.00 32.13 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.107703 TTCATCGATTTCGCCAGGCT 60.108 50.000 10.54 0.00 39.60 4.58
72 73 0.105778 GAAAGGAGGAGATCAGGGCG 59.894 60.000 0.00 0.00 0.00 6.13
79 80 3.805891 GAGATCAGGGCGGCAGAGC 62.806 68.421 12.47 11.16 0.00 4.09
110 111 3.978687 AGTTTGTTACTGACTCACGGAG 58.021 45.455 0.03 0.03 35.19 4.63
119 120 3.574396 ACTGACTCACGGAGAAGAAATCA 59.426 43.478 7.76 0.46 33.32 2.57
121 122 3.254892 GACTCACGGAGAAGAAATCACC 58.745 50.000 7.76 0.00 35.61 4.02
122 123 2.028020 ACTCACGGAGAAGAAATCACCC 60.028 50.000 7.76 0.00 35.53 4.61
124 125 1.067142 CACGGAGAAGAAATCACCCGA 60.067 52.381 0.00 0.00 44.35 5.14
135 136 5.665459 AGAAATCACCCGAAGAGATAACTG 58.335 41.667 0.00 0.00 0.00 3.16
140 141 6.145338 TCACCCGAAGAGATAACTGATAAC 57.855 41.667 0.00 0.00 0.00 1.89
151 152 1.153647 CTGATAACGCGTGAGGCCA 60.154 57.895 14.98 4.10 38.94 5.36
156 157 1.240256 TAACGCGTGAGGCCATTTTT 58.760 45.000 14.98 0.00 38.94 1.94
163 164 3.425404 CGTGAGGCCATTTTTCATTACG 58.575 45.455 5.01 0.00 0.00 3.18
165 166 2.165437 TGAGGCCATTTTTCATTACGCC 59.835 45.455 5.01 0.00 35.08 5.68
174 175 4.768130 TTTTCATTACGCCCGATTTTGA 57.232 36.364 0.00 0.00 0.00 2.69
176 177 2.980568 TCATTACGCCCGATTTTGAGT 58.019 42.857 0.00 0.00 0.00 3.41
207 208 3.491766 TTCTTCTAGGGTGGGATCTGT 57.508 47.619 0.00 0.00 0.00 3.41
209 210 3.107601 TCTTCTAGGGTGGGATCTGTTG 58.892 50.000 0.00 0.00 0.00 3.33
212 213 1.622607 TAGGGTGGGATCTGTTGCCG 61.623 60.000 0.00 0.00 39.08 5.69
220 221 2.097466 GGGATCTGTTGCCGTGTAAATG 59.903 50.000 0.00 0.00 0.00 2.32
244 245 5.462068 GGATTACAGCTCAACCAAAACAAAC 59.538 40.000 0.00 0.00 0.00 2.93
252 254 6.925165 AGCTCAACCAAAACAAACATAATCTG 59.075 34.615 0.00 0.00 0.00 2.90
255 257 7.432869 TCAACCAAAACAAACATAATCTGGAG 58.567 34.615 0.00 0.00 0.00 3.86
256 258 5.783111 ACCAAAACAAACATAATCTGGAGC 58.217 37.500 0.00 0.00 0.00 4.70
269 271 5.923733 AATCTGGAGCTATCTATTACCGG 57.076 43.478 0.00 0.00 0.00 5.28
284 286 1.167155 ACCGGCGCAAACATGTTACA 61.167 50.000 12.39 0.00 0.00 2.41
288 290 2.728839 CGGCGCAAACATGTTACATTTT 59.271 40.909 12.39 0.00 0.00 1.82
295 297 6.855914 CGCAAACATGTTACATTTTACTGACT 59.144 34.615 12.39 0.00 0.00 3.41
314 316 5.989477 TGACTAATCAAACACATCCCTAGG 58.011 41.667 0.06 0.06 0.00 3.02
315 317 5.724370 TGACTAATCAAACACATCCCTAGGA 59.276 40.000 11.48 0.00 35.55 2.94
321 323 6.235231 TCAAACACATCCCTAGGATAGTTC 57.765 41.667 11.48 0.00 40.98 3.01
323 325 5.878406 AACACATCCCTAGGATAGTTCTG 57.122 43.478 11.48 0.00 40.98 3.02
392 394 9.063615 GGACTTAAAAAGAACCAACTAATCTCA 57.936 33.333 0.00 0.00 0.00 3.27
412 414 8.585471 ATCTCAACCATCAAACTATGTCAATT 57.415 30.769 0.00 0.00 0.00 2.32
413 415 8.044060 TCTCAACCATCAAACTATGTCAATTC 57.956 34.615 0.00 0.00 0.00 2.17
419 421 7.147846 ACCATCAAACTATGTCAATTCAATCCC 60.148 37.037 0.00 0.00 0.00 3.85
420 422 7.069085 CCATCAAACTATGTCAATTCAATCCCT 59.931 37.037 0.00 0.00 0.00 4.20
421 423 9.123902 CATCAAACTATGTCAATTCAATCCCTA 57.876 33.333 0.00 0.00 0.00 3.53
469 480 6.430616 TGCTCAAATGATGAACACTCAACATA 59.569 34.615 0.00 0.00 42.47 2.29
498 693 8.589335 AGTACTACCAAATATTAACATCAGCG 57.411 34.615 0.00 0.00 0.00 5.18
609 807 7.607607 TGCAATTAATACCATGCCTAGTATCAG 59.392 37.037 7.25 0.00 38.00 2.90
629 827 6.169557 TCAGTATGCATTTTATCCGGTACT 57.830 37.500 3.54 0.00 34.76 2.73
631 829 5.408604 CAGTATGCATTTTATCCGGTACTCC 59.591 44.000 3.54 0.00 0.00 3.85
632 830 3.202829 TGCATTTTATCCGGTACTCCC 57.797 47.619 0.00 0.00 0.00 4.30
634 832 3.181458 TGCATTTTATCCGGTACTCCCTC 60.181 47.826 0.00 0.00 0.00 4.30
635 833 3.071167 GCATTTTATCCGGTACTCCCTCT 59.929 47.826 0.00 0.00 0.00 3.69
636 834 4.632153 CATTTTATCCGGTACTCCCTCTG 58.368 47.826 0.00 0.00 0.00 3.35
637 835 3.393426 TTTATCCGGTACTCCCTCTGT 57.607 47.619 0.00 0.00 0.00 3.41
638 836 4.524802 TTTATCCGGTACTCCCTCTGTA 57.475 45.455 0.00 0.00 0.00 2.74
639 837 4.524802 TTATCCGGTACTCCCTCTGTAA 57.475 45.455 0.00 0.00 0.00 2.41
640 838 2.905415 TCCGGTACTCCCTCTGTAAA 57.095 50.000 0.00 0.00 0.00 2.01
641 839 2.450476 TCCGGTACTCCCTCTGTAAAC 58.550 52.381 0.00 0.00 0.00 2.01
642 840 2.042162 TCCGGTACTCCCTCTGTAAACT 59.958 50.000 0.00 0.00 0.00 2.66
643 841 3.266772 TCCGGTACTCCCTCTGTAAACTA 59.733 47.826 0.00 0.00 0.00 2.24
644 842 4.019174 CCGGTACTCCCTCTGTAAACTAA 58.981 47.826 0.00 0.00 0.00 2.24
645 843 4.648307 CCGGTACTCCCTCTGTAAACTAAT 59.352 45.833 0.00 0.00 0.00 1.73
646 844 5.829924 CCGGTACTCCCTCTGTAAACTAATA 59.170 44.000 0.00 0.00 0.00 0.98
647 845 6.492772 CCGGTACTCCCTCTGTAAACTAATAT 59.507 42.308 0.00 0.00 0.00 1.28
648 846 7.667219 CCGGTACTCCCTCTGTAAACTAATATA 59.333 40.741 0.00 0.00 0.00 0.86
649 847 9.071276 CGGTACTCCCTCTGTAAACTAATATAA 57.929 37.037 0.00 0.00 0.00 0.98
653 851 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
655 853 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
706 904 9.774413 AACACTCTTATATTAATTTACGGAGGG 57.226 33.333 11.91 11.91 0.00 4.30
707 905 9.151177 ACACTCTTATATTAATTTACGGAGGGA 57.849 33.333 16.65 0.00 0.00 4.20
708 906 9.640963 CACTCTTATATTAATTTACGGAGGGAG 57.359 37.037 13.95 0.00 0.00 4.30
709 907 9.377238 ACTCTTATATTAATTTACGGAGGGAGT 57.623 33.333 13.95 0.00 0.00 3.85
715 913 6.549433 TTAATTTACGGAGGGAGTACATGT 57.451 37.500 2.69 2.69 0.00 3.21
738 936 2.806244 ACTAGCAAGCACTGGTTTTACG 59.194 45.455 0.00 0.00 36.95 3.18
790 988 4.180817 AGGGCAGTTTTGAAAAGAAAACG 58.819 39.130 0.00 0.00 46.19 3.60
868 1066 5.067805 CGAGAAGATCCCCAAAATAAAAGGG 59.932 44.000 0.00 0.00 42.44 3.95
941 1144 2.266055 CTCCCCCAACACTCGCTC 59.734 66.667 0.00 0.00 0.00 5.03
1223 1429 0.510359 CTGCTCGTCAAGTGAGTTGC 59.490 55.000 0.00 0.00 35.94 4.17
1342 1548 9.420551 ACTTTGAGAATTAAGTAGGTTCGTTAG 57.579 33.333 0.00 0.00 33.06 2.34
1367 1573 5.483685 TGTAGTGGAGATTACAAGTTGCT 57.516 39.130 1.81 0.00 0.00 3.91
1438 1644 7.312657 TGACATGTGAATATGCTTCTTCTTC 57.687 36.000 1.15 0.00 0.00 2.87
1450 1656 5.762045 TGCTTCTTCTTCAAATGTTAGTGC 58.238 37.500 0.00 0.00 0.00 4.40
1533 1743 9.605275 GTCCATATAGATATGCTTTATTCTGCA 57.395 33.333 4.28 0.00 43.67 4.41
1547 1757 8.504005 GCTTTATTCTGCAACACGGTATATTAT 58.496 33.333 0.00 0.00 0.00 1.28
1552 1762 4.200092 TGCAACACGGTATATTATGCCAA 58.800 39.130 10.86 0.00 34.32 4.52
1554 1764 5.300539 TGCAACACGGTATATTATGCCAATT 59.699 36.000 10.86 0.00 34.32 2.32
1555 1765 6.486993 TGCAACACGGTATATTATGCCAATTA 59.513 34.615 10.86 0.00 34.32 1.40
1557 1767 8.026607 GCAACACGGTATATTATGCCAATTATT 58.973 33.333 10.86 0.00 34.32 1.40
1558 1768 9.554724 CAACACGGTATATTATGCCAATTATTC 57.445 33.333 10.86 0.00 34.32 1.75
1560 1770 7.065324 ACACGGTATATTATGCCAATTATTCGG 59.935 37.037 10.86 0.00 34.32 4.30
1561 1771 7.065324 CACGGTATATTATGCCAATTATTCGGT 59.935 37.037 10.86 0.00 34.32 4.69
1562 1772 8.259411 ACGGTATATTATGCCAATTATTCGGTA 58.741 33.333 10.86 0.00 34.32 4.02
1564 1774 8.833493 GGTATATTATGCCAATTATTCGGTACC 58.167 37.037 0.16 0.16 34.86 3.34
1565 1775 7.875327 ATATTATGCCAATTATTCGGTACCC 57.125 36.000 6.25 0.00 0.00 3.69
1574 1784 7.681065 GCCAATTATTCGGTACCCATATAATGC 60.681 40.741 6.25 9.60 0.00 3.56
1644 1854 4.634184 ATGACAGCAGAATCAAGATTGC 57.366 40.909 0.00 0.00 0.00 3.56
1645 1855 3.414269 TGACAGCAGAATCAAGATTGCA 58.586 40.909 8.84 0.00 0.00 4.08
1646 1856 3.439129 TGACAGCAGAATCAAGATTGCAG 59.561 43.478 8.84 4.24 0.00 4.41
1648 1858 3.825014 ACAGCAGAATCAAGATTGCAGTT 59.175 39.130 8.84 0.00 0.00 3.16
1651 1861 3.675228 GCAGAATCAAGATTGCAGTTGGG 60.675 47.826 0.00 0.00 0.00 4.12
1652 1862 2.494870 AGAATCAAGATTGCAGTTGGGC 59.505 45.455 0.00 0.00 0.00 5.36
1653 1863 2.226962 ATCAAGATTGCAGTTGGGCT 57.773 45.000 5.88 0.00 34.04 5.19
1654 1864 1.538047 TCAAGATTGCAGTTGGGCTC 58.462 50.000 5.88 0.00 34.04 4.70
1655 1865 1.202915 TCAAGATTGCAGTTGGGCTCA 60.203 47.619 5.88 0.00 34.04 4.26
1656 1866 1.614903 CAAGATTGCAGTTGGGCTCAA 59.385 47.619 0.00 0.00 34.04 3.02
1664 1874 2.623416 GCAGTTGGGCTCAAAAAGTAGT 59.377 45.455 0.00 0.00 34.28 2.73
1666 1876 4.320275 GCAGTTGGGCTCAAAAAGTAGTAC 60.320 45.833 0.00 0.00 34.28 2.73
1684 1894 9.439500 AAGTAGTACTCACTGTTTTAACAACAA 57.561 29.630 2.58 0.00 38.66 2.83
1732 1943 2.414058 TGTGCACCATAGTTTTTGCG 57.586 45.000 15.69 0.00 37.82 4.85
1741 1952 0.591170 TAGTTTTTGCGCCTCACAGC 59.409 50.000 4.18 0.00 0.00 4.40
1757 1968 3.087031 CACAGCTCCATTGATGTTCCTT 58.913 45.455 0.00 0.00 34.05 3.36
1818 2029 6.892658 ATTCGGTATGCAAAAATAGCCATA 57.107 33.333 0.00 0.00 0.00 2.74
2389 2609 8.458573 TCCATTTTATAAACGCAAGGATGTAT 57.541 30.769 0.00 0.00 46.39 2.29
2610 2833 5.297527 AGAAAACGGTAACAAAACGGAATCT 59.702 36.000 0.00 0.00 0.00 2.40
2761 2986 3.260884 CGGTGGCCATACATACTATTCCT 59.739 47.826 9.72 0.00 0.00 3.36
2953 3179 4.333372 TGTAAAGAAACTCGACCAACCAAC 59.667 41.667 0.00 0.00 0.00 3.77
3153 3379 2.158813 TGGTTCGACTTCAAGCTTTCCT 60.159 45.455 0.00 0.00 0.00 3.36
3403 3630 6.458888 GGGCAGTAGCTCATCAAAATAAGTTC 60.459 42.308 0.00 0.00 42.33 3.01
3690 3918 1.376424 CTGAGGACTGCGGCATTGT 60.376 57.895 1.75 0.00 0.00 2.71
4092 4321 5.644977 GCAAAAAGCACCTATTTAGGAGT 57.355 39.130 10.61 0.00 46.38 3.85
4161 4391 3.128375 CGCAAACAAACAGGGCCT 58.872 55.556 0.00 0.00 0.00 5.19
4188 4418 2.496899 TTCATTCTCCACTGCCCTTC 57.503 50.000 0.00 0.00 0.00 3.46
4286 4516 4.058124 TGTAGCTAATGCGCCTCATTTAG 58.942 43.478 4.18 5.92 42.48 1.85
4569 4799 9.617975 GAAAGAAATAACCTGCTTATATGATGC 57.382 33.333 0.00 0.00 0.00 3.91
4695 4930 7.279750 TGATACACGCATCTTGGTTATACTA 57.720 36.000 0.00 0.00 0.00 1.82
4792 5027 5.944599 GGTATCTAATATCCTGTGTCGGAGA 59.055 44.000 0.00 0.00 36.31 3.71
4854 5089 9.418839 CTCATATCTTAGATACAGATCCATCCA 57.581 37.037 3.83 0.00 32.94 3.41
5307 5546 4.015084 CTCCAAGTTGCTCATTTCCTCAT 58.985 43.478 0.00 0.00 0.00 2.90
5576 5815 5.946377 AGGGTGTTGAAAGAGTATGATTTCC 59.054 40.000 0.00 0.00 35.08 3.13
5834 6074 8.547967 TTTTAGACACTTTTATCAGTAGGCAG 57.452 34.615 0.00 0.00 0.00 4.85
5902 6142 7.361457 AGGACTATCATTTCTTCCGACATTA 57.639 36.000 0.00 0.00 0.00 1.90
5970 6211 6.039717 TGGATTCATCTGCTAGCCAATTTTAC 59.960 38.462 13.29 0.00 0.00 2.01
5974 6215 7.466746 TCATCTGCTAGCCAATTTTACTTTT 57.533 32.000 13.29 0.00 0.00 2.27
6101 6342 2.287915 CCGTCCGCTTAATCAAATCCAG 59.712 50.000 0.00 0.00 0.00 3.86
6105 6346 5.064198 CGTCCGCTTAATCAAATCCAGTTTA 59.936 40.000 0.00 0.00 0.00 2.01
6169 6413 1.670811 GTACCCGTCAAGATGCCAATG 59.329 52.381 0.00 0.00 0.00 2.82
6201 6802 8.708742 TCATATCTAATCGACCTTTAATTTGCG 58.291 33.333 0.00 0.00 0.00 4.85
6272 6873 8.703743 TCATCATTCCTTTTTCCTTTCAAGAAA 58.296 29.630 0.00 0.00 0.00 2.52
6311 6912 5.988561 AGTTTCATTCATAGAGGAATCGAGC 59.011 40.000 0.00 0.00 35.37 5.03
6312 6913 5.798125 TTCATTCATAGAGGAATCGAGCT 57.202 39.130 0.00 0.00 35.37 4.09
6551 7152 1.384191 CCAGCCTTGGCCCTAGTTT 59.616 57.895 8.17 0.00 37.73 2.66
6575 7176 7.177832 TGTTCGTTTTAGATCCTTCCTCATA 57.822 36.000 0.00 0.00 0.00 2.15
6646 7249 2.514803 GTTGGAACATGTACAGGGCTT 58.485 47.619 12.79 0.00 39.30 4.35
6785 7390 8.134895 TGTGCAGTCTTTCCTTAAATTTAAGTG 58.865 33.333 27.93 20.56 38.73 3.16
6786 7391 7.595130 GTGCAGTCTTTCCTTAAATTTAAGTGG 59.405 37.037 27.93 18.87 38.73 4.00
6810 7417 1.075542 CTTGCCTTCGTTACATCGCA 58.924 50.000 0.00 0.00 0.00 5.10
6855 7467 4.094294 TGGTTGATGTCTAATTTGCTACGC 59.906 41.667 0.00 0.00 0.00 4.42
6861 7473 3.007635 GTCTAATTTGCTACGCCTTGGT 58.992 45.455 0.00 0.00 0.00 3.67
6863 7475 2.723124 AATTTGCTACGCCTTGGTTG 57.277 45.000 0.00 0.00 0.00 3.77
6864 7476 1.616159 ATTTGCTACGCCTTGGTTGT 58.384 45.000 0.00 0.00 0.00 3.32
6866 7478 1.169661 TTGCTACGCCTTGGTTGTGG 61.170 55.000 0.00 0.00 0.00 4.17
6869 7481 1.435577 CTACGCCTTGGTTGTGGTAC 58.564 55.000 0.00 0.00 0.00 3.34
6872 7484 1.234615 CGCCTTGGTTGTGGTACCTG 61.235 60.000 14.36 0.00 39.04 4.00
6873 7485 0.109723 GCCTTGGTTGTGGTACCTGA 59.890 55.000 14.36 0.00 39.04 3.86
6874 7486 1.882352 GCCTTGGTTGTGGTACCTGAG 60.882 57.143 14.36 0.74 39.04 3.35
6875 7487 1.697432 CCTTGGTTGTGGTACCTGAGA 59.303 52.381 14.36 0.00 39.04 3.27
6876 7488 2.289694 CCTTGGTTGTGGTACCTGAGAG 60.290 54.545 14.36 2.28 39.04 3.20
6877 7489 1.348064 TGGTTGTGGTACCTGAGAGG 58.652 55.000 14.36 0.00 42.49 3.69
6878 7490 1.132977 TGGTTGTGGTACCTGAGAGGA 60.133 52.381 14.36 0.00 37.67 3.71
6882 7494 3.184382 TGTGGTACCTGAGAGGAATGA 57.816 47.619 14.36 0.00 37.67 2.57
6883 7495 3.516586 TGTGGTACCTGAGAGGAATGAA 58.483 45.455 14.36 0.00 37.67 2.57
6884 7496 3.907474 TGTGGTACCTGAGAGGAATGAAA 59.093 43.478 14.36 0.00 37.67 2.69
6885 7497 4.536090 TGTGGTACCTGAGAGGAATGAAAT 59.464 41.667 14.36 0.00 37.67 2.17
6887 7499 6.386927 TGTGGTACCTGAGAGGAATGAAATAT 59.613 38.462 14.36 0.00 37.67 1.28
6888 7500 6.708054 GTGGTACCTGAGAGGAATGAAATATG 59.292 42.308 14.36 0.00 37.67 1.78
6890 7502 7.567250 TGGTACCTGAGAGGAATGAAATATGTA 59.433 37.037 14.36 0.00 37.67 2.29
6891 7503 7.873505 GGTACCTGAGAGGAATGAAATATGTAC 59.126 40.741 4.06 0.00 37.67 2.90
6893 7505 5.928839 CCTGAGAGGAATGAAATATGTACCG 59.071 44.000 0.00 0.00 37.67 4.02
6895 7507 6.749139 TGAGAGGAATGAAATATGTACCGAG 58.251 40.000 0.00 0.00 0.00 4.63
6896 7508 6.323996 TGAGAGGAATGAAATATGTACCGAGT 59.676 38.462 0.00 0.00 0.00 4.18
6897 7509 6.516718 AGAGGAATGAAATATGTACCGAGTG 58.483 40.000 0.00 0.00 0.00 3.51
6898 7510 6.323996 AGAGGAATGAAATATGTACCGAGTGA 59.676 38.462 0.00 0.00 0.00 3.41
6899 7511 7.015682 AGAGGAATGAAATATGTACCGAGTGAT 59.984 37.037 0.00 0.00 0.00 3.06
6900 7512 7.509546 AGGAATGAAATATGTACCGAGTGATT 58.490 34.615 0.00 0.00 0.00 2.57
6901 7513 8.647796 AGGAATGAAATATGTACCGAGTGATTA 58.352 33.333 0.00 0.00 0.00 1.75
6902 7514 9.268268 GGAATGAAATATGTACCGAGTGATTAA 57.732 33.333 0.00 0.00 0.00 1.40
6927 7539 2.917933 CCATATTGGTCCTCGCAAAGA 58.082 47.619 0.00 0.00 31.35 2.52
6929 7541 3.694072 CCATATTGGTCCTCGCAAAGAAA 59.306 43.478 0.00 0.00 31.35 2.52
6930 7542 4.339247 CCATATTGGTCCTCGCAAAGAAAT 59.661 41.667 0.00 0.00 31.35 2.17
6931 7543 5.163519 CCATATTGGTCCTCGCAAAGAAATT 60.164 40.000 0.00 0.00 31.35 1.82
6932 7544 3.641437 TTGGTCCTCGCAAAGAAATTG 57.359 42.857 0.00 0.00 42.21 2.32
6952 7579 9.392021 GAAATTGCTAGAGCTTTATATGCTTTC 57.608 33.333 2.72 0.00 41.30 2.62
6957 7584 5.764487 AGAGCTTTATATGCTTTCTTGGC 57.236 39.130 0.00 0.00 41.30 4.52
6960 7587 4.340381 AGCTTTATATGCTTTCTTGGCCAG 59.660 41.667 5.11 0.00 37.52 4.85
6974 7601 2.229792 TGGCCAGTTACTTGCTCAAAG 58.770 47.619 0.00 0.00 42.07 2.77
6980 7607 4.520492 CCAGTTACTTGCTCAAAGGAATGT 59.480 41.667 0.00 0.00 40.92 2.71
7009 7636 4.021544 AGGGCACAATTTAGCGAAAAATGA 60.022 37.500 12.97 0.00 0.00 2.57
7011 7638 5.351189 GGGCACAATTTAGCGAAAAATGATT 59.649 36.000 12.97 0.00 0.00 2.57
7012 7639 6.533367 GGGCACAATTTAGCGAAAAATGATTA 59.467 34.615 12.97 0.00 0.00 1.75
7013 7640 7.064016 GGGCACAATTTAGCGAAAAATGATTAA 59.936 33.333 12.97 0.00 0.00 1.40
7014 7641 8.439286 GGCACAATTTAGCGAAAAATGATTAAA 58.561 29.630 12.97 0.00 0.00 1.52
7015 7642 9.804547 GCACAATTTAGCGAAAAATGATTAAAA 57.195 25.926 12.97 0.00 0.00 1.52
7020 7647 9.921637 ATTTAGCGAAAAATGATTAAAAGACCA 57.078 25.926 0.00 0.00 0.00 4.02
7048 8535 5.341407 GTTCTTCTGAACTCAAGCTCAAG 57.659 43.478 0.00 0.00 46.56 3.02
7049 8536 4.679373 TCTTCTGAACTCAAGCTCAAGT 57.321 40.909 0.00 0.00 0.00 3.16
7055 8542 3.206150 GAACTCAAGCTCAAGTGGACAA 58.794 45.455 1.99 0.00 0.00 3.18
7092 8579 2.869646 CATTTGCTTCCGCTCGCA 59.130 55.556 0.00 0.00 36.97 5.10
7097 8584 0.313672 TTGCTTCCGCTCGCAATTTT 59.686 45.000 0.00 0.00 40.84 1.82
7169 8657 9.917129 TTCTCGTCTAAATGTTATCTGTAAACA 57.083 29.630 0.00 0.00 40.85 2.83
7185 8673 5.080337 TGTAAACATTTAGGTGGAATGCCA 58.920 37.500 0.00 0.00 43.47 4.92
7227 8715 5.831702 AAAAATGCAAATTGGCTGACAAA 57.168 30.435 6.34 0.00 43.46 2.83
7229 8717 7.507733 AAAAATGCAAATTGGCTGACAAATA 57.492 28.000 6.34 0.00 43.46 1.40
7236 8726 3.608316 TTGGCTGACAAATATTTGGCC 57.392 42.857 27.40 27.23 45.65 5.36
7248 8738 7.602753 ACAAATATTTGGCCTTTCTTGACTAC 58.397 34.615 27.43 0.00 42.34 2.73
7257 8747 6.262273 TGGCCTTTCTTGACTACTTAACTTTG 59.738 38.462 3.32 0.00 0.00 2.77
7291 8804 9.232082 GTATAAAAATTATCATGCACGCTTTGA 57.768 29.630 0.00 0.00 0.00 2.69
7292 8805 6.393720 AAAAATTATCATGCACGCTTTGAC 57.606 33.333 0.00 0.00 0.00 3.18
7293 8806 4.700268 AATTATCATGCACGCTTTGACA 57.300 36.364 0.00 0.00 0.00 3.58
7294 8807 3.469899 TTATCATGCACGCTTTGACAC 57.530 42.857 0.00 0.00 0.00 3.67
7295 8808 1.527034 ATCATGCACGCTTTGACACT 58.473 45.000 0.00 0.00 0.00 3.55
7296 8809 2.162319 TCATGCACGCTTTGACACTA 57.838 45.000 0.00 0.00 0.00 2.74
7298 8811 2.223144 TCATGCACGCTTTGACACTAAC 59.777 45.455 0.00 0.00 0.00 2.34
7299 8812 0.579630 TGCACGCTTTGACACTAACG 59.420 50.000 0.00 0.00 0.00 3.18
7300 8813 0.580104 GCACGCTTTGACACTAACGT 59.420 50.000 0.00 0.00 0.00 3.99
7301 8814 2.279250 CACGCTTTGACACTAACGTG 57.721 50.000 0.00 0.00 46.63 4.49
7303 8816 2.542597 ACGCTTTGACACTAACGTGAA 58.457 42.857 0.00 0.00 43.97 3.18
7304 8817 2.283351 ACGCTTTGACACTAACGTGAAC 59.717 45.455 0.00 0.00 43.97 3.18
7305 8818 2.655577 CGCTTTGACACTAACGTGAACG 60.656 50.000 0.40 0.40 43.97 3.95
7368 8888 5.923684 TCTTTTGAATTTATTGTTCACCGCC 59.076 36.000 0.00 0.00 35.47 6.13
7376 8896 1.781025 TTGTTCACCGCCGAAGCAAG 61.781 55.000 0.00 0.00 39.83 4.01
7404 8924 0.541296 AGAGCCAAAACTGCCATGCT 60.541 50.000 0.00 0.00 0.00 3.79
7405 8925 0.319405 GAGCCAAAACTGCCATGCTT 59.681 50.000 0.00 0.00 0.00 3.91
7430 8951 7.871853 TGAACTCAAGGCTAAATTTAGTCAAC 58.128 34.615 27.07 14.83 37.83 3.18
7435 8956 7.156673 TCAAGGCTAAATTTAGTCAACTACGT 58.843 34.615 27.07 6.19 37.83 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.107703 AGCCTGGCGAAATCGATGAA 60.108 50.000 13.96 0.00 43.02 2.57
50 51 2.756907 CCCTGATCTCCTCCTTTCTCA 58.243 52.381 0.00 0.00 0.00 3.27
72 73 0.892814 ACTCCAGCAAAAGCTCTGCC 60.893 55.000 15.24 0.97 40.86 4.85
79 80 5.066505 AGTCAGTAACAAACTCCAGCAAAAG 59.933 40.000 0.00 0.00 35.76 2.27
110 111 6.256757 CAGTTATCTCTTCGGGTGATTTCTTC 59.743 42.308 0.00 0.00 31.60 2.87
119 120 4.499357 GCGTTATCAGTTATCTCTTCGGGT 60.499 45.833 0.00 0.00 0.00 5.28
121 122 3.664486 CGCGTTATCAGTTATCTCTTCGG 59.336 47.826 0.00 0.00 0.00 4.30
122 123 4.144902 CACGCGTTATCAGTTATCTCTTCG 59.855 45.833 10.22 0.00 0.00 3.79
124 125 5.244785 TCACGCGTTATCAGTTATCTCTT 57.755 39.130 10.22 0.00 0.00 2.85
135 136 1.014352 AAATGGCCTCACGCGTTATC 58.986 50.000 10.22 0.00 38.94 1.75
140 141 0.171007 ATGAAAAATGGCCTCACGCG 59.829 50.000 3.53 3.53 38.94 6.01
151 152 5.715070 TCAAAATCGGGCGTAATGAAAAAT 58.285 33.333 0.00 0.00 0.00 1.82
156 157 2.675844 CACTCAAAATCGGGCGTAATGA 59.324 45.455 0.00 0.00 0.00 2.57
163 164 2.091541 TGATTCCACTCAAAATCGGGC 58.908 47.619 0.00 0.00 35.16 6.13
165 166 7.092716 AGAAAATTGATTCCACTCAAAATCGG 58.907 34.615 0.00 0.00 38.55 4.18
174 175 6.660949 CACCCTAGAAGAAAATTGATTCCACT 59.339 38.462 0.00 0.00 0.00 4.00
176 177 5.951747 CCACCCTAGAAGAAAATTGATTCCA 59.048 40.000 0.00 0.00 0.00 3.53
207 208 3.127895 GCTGTAATCCATTTACACGGCAA 59.872 43.478 0.00 0.00 44.08 4.52
209 210 2.943033 AGCTGTAATCCATTTACACGGC 59.057 45.455 0.00 0.00 44.08 5.68
212 213 5.414454 TGGTTGAGCTGTAATCCATTTACAC 59.586 40.000 0.00 0.00 44.08 2.90
220 221 4.846779 TGTTTTGGTTGAGCTGTAATCC 57.153 40.909 0.00 0.00 0.00 3.01
244 245 7.429633 CCGGTAATAGATAGCTCCAGATTATG 58.570 42.308 0.00 0.00 0.00 1.90
252 254 1.469423 GCGCCGGTAATAGATAGCTCC 60.469 57.143 1.90 0.00 0.00 4.70
255 257 2.074547 TTGCGCCGGTAATAGATAGC 57.925 50.000 4.18 0.00 0.00 2.97
256 258 3.386486 TGTTTGCGCCGGTAATAGATAG 58.614 45.455 4.18 0.00 0.00 2.08
267 269 1.975837 AATGTAACATGTTTGCGCCG 58.024 45.000 17.78 0.00 0.00 6.46
269 271 5.627367 TCAGTAAAATGTAACATGTTTGCGC 59.373 36.000 17.78 0.00 0.00 6.09
284 286 8.739972 GGGATGTGTTTGATTAGTCAGTAAAAT 58.260 33.333 0.00 0.00 35.39 1.82
288 290 6.620877 AGGGATGTGTTTGATTAGTCAGTA 57.379 37.500 0.00 0.00 35.39 2.74
295 297 7.931015 ACTATCCTAGGGATGTGTTTGATTA 57.069 36.000 9.46 0.00 43.06 1.75
298 300 5.964477 AGAACTATCCTAGGGATGTGTTTGA 59.036 40.000 9.46 0.00 43.06 2.69
314 316 7.440523 AGATTTGTGTGGTTTCAGAACTATC 57.559 36.000 0.00 0.00 36.03 2.08
370 372 9.191479 TGGTTGAGATTAGTTGGTTCTTTTTAA 57.809 29.630 0.00 0.00 0.00 1.52
371 373 8.754991 TGGTTGAGATTAGTTGGTTCTTTTTA 57.245 30.769 0.00 0.00 0.00 1.52
377 379 6.817765 TTGATGGTTGAGATTAGTTGGTTC 57.182 37.500 0.00 0.00 0.00 3.62
379 381 6.306987 AGTTTGATGGTTGAGATTAGTTGGT 58.693 36.000 0.00 0.00 0.00 3.67
382 384 9.167311 GACATAGTTTGATGGTTGAGATTAGTT 57.833 33.333 0.00 0.00 0.00 2.24
392 394 8.253113 GGATTGAATTGACATAGTTTGATGGTT 58.747 33.333 0.00 0.00 0.00 3.67
445 456 5.112220 TGTTGAGTGTTCATCATTTGAGC 57.888 39.130 0.00 0.00 35.27 4.26
480 675 8.794406 GTTGTTTACGCTGATGTTAATATTTGG 58.206 33.333 0.00 0.00 0.00 3.28
581 779 9.613428 GATACTAGGCATGGTATTAATTGCATA 57.387 33.333 8.83 7.78 33.61 3.14
609 807 4.694037 GGGAGTACCGGATAAAATGCATAC 59.306 45.833 9.46 0.00 36.97 2.39
612 810 2.775384 AGGGAGTACCGGATAAAATGCA 59.225 45.455 9.46 0.00 46.96 3.96
629 827 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
680 878 9.774413 CCCTCCGTAAATTAATATAAGAGTGTT 57.226 33.333 0.00 0.00 0.00 3.32
681 879 9.151177 TCCCTCCGTAAATTAATATAAGAGTGT 57.849 33.333 0.00 0.00 0.00 3.55
682 880 9.640963 CTCCCTCCGTAAATTAATATAAGAGTG 57.359 37.037 0.00 0.00 0.00 3.51
683 881 9.377238 ACTCCCTCCGTAAATTAATATAAGAGT 57.623 33.333 0.00 0.00 0.00 3.24
689 887 8.877195 ACATGTACTCCCTCCGTAAATTAATAT 58.123 33.333 0.00 0.00 0.00 1.28
690 888 8.253867 ACATGTACTCCCTCCGTAAATTAATA 57.746 34.615 0.00 0.00 0.00 0.98
691 889 7.133133 ACATGTACTCCCTCCGTAAATTAAT 57.867 36.000 0.00 0.00 0.00 1.40
692 890 6.549433 ACATGTACTCCCTCCGTAAATTAA 57.451 37.500 0.00 0.00 0.00 1.40
693 891 6.549433 AACATGTACTCCCTCCGTAAATTA 57.451 37.500 0.00 0.00 0.00 1.40
694 892 5.431179 AACATGTACTCCCTCCGTAAATT 57.569 39.130 0.00 0.00 0.00 1.82
695 893 5.659971 AGTAACATGTACTCCCTCCGTAAAT 59.340 40.000 0.00 0.00 0.00 1.40
696 894 5.018809 AGTAACATGTACTCCCTCCGTAAA 58.981 41.667 0.00 0.00 0.00 2.01
697 895 4.603131 AGTAACATGTACTCCCTCCGTAA 58.397 43.478 0.00 0.00 0.00 3.18
698 896 4.240881 AGTAACATGTACTCCCTCCGTA 57.759 45.455 0.00 0.00 0.00 4.02
699 897 3.097342 AGTAACATGTACTCCCTCCGT 57.903 47.619 0.00 0.00 0.00 4.69
700 898 3.004524 GCTAGTAACATGTACTCCCTCCG 59.995 52.174 0.00 0.00 0.00 4.63
701 899 3.958798 TGCTAGTAACATGTACTCCCTCC 59.041 47.826 0.00 0.00 0.00 4.30
702 900 5.593010 CTTGCTAGTAACATGTACTCCCTC 58.407 45.833 0.00 0.00 0.00 4.30
703 901 4.141914 GCTTGCTAGTAACATGTACTCCCT 60.142 45.833 0.00 0.00 0.00 4.20
704 902 4.120589 GCTTGCTAGTAACATGTACTCCC 58.879 47.826 0.00 0.00 0.00 4.30
705 903 4.567159 GTGCTTGCTAGTAACATGTACTCC 59.433 45.833 0.00 0.08 0.00 3.85
706 904 5.289675 CAGTGCTTGCTAGTAACATGTACTC 59.710 44.000 0.00 0.00 36.48 2.59
707 905 5.171476 CAGTGCTTGCTAGTAACATGTACT 58.829 41.667 0.00 6.02 38.20 2.73
708 906 4.330074 CCAGTGCTTGCTAGTAACATGTAC 59.670 45.833 0.00 0.00 0.00 2.90
709 907 4.020573 ACCAGTGCTTGCTAGTAACATGTA 60.021 41.667 0.00 0.00 0.00 2.29
710 908 3.244561 ACCAGTGCTTGCTAGTAACATGT 60.245 43.478 0.00 0.00 0.00 3.21
711 909 3.338249 ACCAGTGCTTGCTAGTAACATG 58.662 45.455 0.00 0.00 0.00 3.21
712 910 3.703001 ACCAGTGCTTGCTAGTAACAT 57.297 42.857 0.00 0.00 0.00 2.71
713 911 3.485463 AACCAGTGCTTGCTAGTAACA 57.515 42.857 0.00 0.00 0.00 2.41
714 912 4.830826 AAAACCAGTGCTTGCTAGTAAC 57.169 40.909 0.00 0.00 0.00 2.50
715 913 4.449743 CGTAAAACCAGTGCTTGCTAGTAA 59.550 41.667 0.00 0.00 0.00 2.24
874 1072 4.292306 AGTGGATGTGGGGAATAAAGAAGT 59.708 41.667 0.00 0.00 0.00 3.01
1342 1548 5.447818 GCAACTTGTAATCTCCACTACATGC 60.448 44.000 0.00 0.00 29.42 4.06
1367 1573 1.229400 AACCCAGAAGGAGGCGGTA 60.229 57.895 0.00 0.00 39.89 4.02
1402 1608 1.379044 CATGTCAACCTGAGGGGGC 60.379 63.158 2.38 0.00 40.03 5.80
1438 1644 7.274033 CACATGTCCAAATAGCACTAACATTTG 59.726 37.037 0.00 0.00 38.69 2.32
1450 1656 9.941664 GAGAACATTATTCACATGTCCAAATAG 57.058 33.333 0.00 0.00 33.54 1.73
1533 1743 8.447833 CGAATAATTGGCATAATATACCGTGTT 58.552 33.333 0.00 0.00 0.00 3.32
1560 1770 4.998672 TGCTTTACCGCATTATATGGGTAC 59.001 41.667 0.00 0.00 41.17 3.34
1561 1771 4.998672 GTGCTTTACCGCATTATATGGGTA 59.001 41.667 0.00 0.00 42.62 3.69
1562 1772 3.818773 GTGCTTTACCGCATTATATGGGT 59.181 43.478 0.00 0.00 42.62 4.51
1564 1774 4.419522 GGTGCTTTACCGCATTATATGG 57.580 45.455 0.00 0.00 42.62 2.74
1601 1811 3.394674 TTGATGACAACAAGGCGACTA 57.605 42.857 0.00 0.00 42.68 2.59
1634 1844 2.097825 GAGCCCAACTGCAATCTTGAT 58.902 47.619 0.00 0.00 0.00 2.57
1644 1854 5.063880 AGTACTACTTTTTGAGCCCAACTG 58.936 41.667 0.00 0.00 30.88 3.16
1645 1855 5.163237 TGAGTACTACTTTTTGAGCCCAACT 60.163 40.000 0.00 0.00 30.88 3.16
1646 1856 5.049612 GTGAGTACTACTTTTTGAGCCCAAC 60.050 44.000 0.00 0.00 30.88 3.77
1648 1858 4.347000 AGTGAGTACTACTTTTTGAGCCCA 59.653 41.667 0.00 0.00 34.74 5.36
1651 1861 6.846325 AACAGTGAGTACTACTTTTTGAGC 57.154 37.500 0.00 0.00 34.74 4.26
1664 1874 9.781834 CTCAAATTGTTGTTAAAACAGTGAGTA 57.218 29.630 13.19 0.00 40.50 2.59
1666 1876 7.222611 CCCTCAAATTGTTGTTAAAACAGTGAG 59.777 37.037 13.92 13.92 40.50 3.51
1684 1894 3.817647 GCGAATTCATAGAGCCCTCAAAT 59.182 43.478 6.22 0.00 0.00 2.32
1732 1943 1.022735 CATCAATGGAGCTGTGAGGC 58.977 55.000 0.00 0.00 0.00 4.70
1741 1952 6.921857 GCAAATATCAAGGAACATCAATGGAG 59.078 38.462 0.00 0.00 0.00 3.86
1757 1968 5.294734 TGCATACCTGAGAGCAAATATCA 57.705 39.130 0.00 0.00 33.48 2.15
1818 2029 4.438744 CGAACTGTTTTCTCTGGCAACTTT 60.439 41.667 0.00 0.00 37.61 2.66
2094 2314 6.925165 CCAACTTGTTACAGCATTGATTTCTT 59.075 34.615 6.81 0.00 0.00 2.52
2096 2316 5.634859 CCCAACTTGTTACAGCATTGATTTC 59.365 40.000 6.81 0.00 0.00 2.17
2265 2485 7.433708 AATTCCAACGCATAATCGAATATCA 57.566 32.000 0.00 0.00 0.00 2.15
2389 2609 5.142061 TCTGTTAATACGTGAAAGGAGCA 57.858 39.130 0.00 0.00 0.00 4.26
2610 2833 2.000048 AGGGGGAAGAAAACATGCCTA 59.000 47.619 0.00 0.00 0.00 3.93
2879 3105 0.320247 GCGCTGCTGCTATCCTGTAT 60.320 55.000 14.03 0.00 36.97 2.29
2882 3108 2.108566 AGCGCTGCTGCTATCCTG 59.891 61.111 10.39 0.00 45.14 3.86
2953 3179 3.598019 AAAATGCACCAATGGCTAGTG 57.402 42.857 0.00 0.00 34.58 2.74
3153 3379 1.308069 GGAGCAGGCATTTCGAAGCA 61.308 55.000 11.04 0.00 0.00 3.91
3313 3540 1.755179 TCAATAGAGCAAAGGCCAGC 58.245 50.000 5.01 6.06 42.56 4.85
3379 3606 6.317391 AGAACTTATTTTGATGAGCTACTGCC 59.683 38.462 0.00 0.00 40.80 4.85
3403 3630 9.449719 ACAGAGGGAGTGTAAAACAATATTTAG 57.550 33.333 0.00 0.00 0.00 1.85
3690 3918 3.818210 CACTTGTGTAACTATGGTGCCAA 59.182 43.478 0.00 0.00 38.04 4.52
3762 3990 6.503560 TTTAACTGAAAACTGTAGGGGAGA 57.496 37.500 0.00 0.00 0.00 3.71
3955 4183 3.625649 TGCCAAAGTGGAAAAGCTTTT 57.374 38.095 24.08 24.08 40.96 2.27
4066 4295 5.772672 TCCTAAATAGGTGCTTTTTGCTTCA 59.227 36.000 6.39 0.00 44.02 3.02
4103 4333 3.878699 CAGCTTTTCCACTTTGGCAAAAT 59.121 39.130 14.43 0.00 32.54 1.82
4161 4391 5.003804 GGCAGTGGAGAATGAAAAGACTAA 58.996 41.667 0.00 0.00 0.00 2.24
4217 4447 2.478335 CTTGGGTAAGGGCCTTGCGA 62.478 60.000 28.88 14.28 0.00 5.10
4286 4516 9.118236 GCTGTCAGTTACAAGTTTATTCAAATC 57.882 33.333 0.93 0.00 37.74 2.17
4483 4713 9.981114 CAAATAAAAACAAGGACCAAACTAGAT 57.019 29.630 0.00 0.00 0.00 1.98
4569 4799 3.464907 CATATCAGCAGAACCAGTCCTG 58.535 50.000 0.00 0.00 0.00 3.86
4695 4930 9.077885 ACTGAATCAAAGTGGTGTTAATTGTAT 57.922 29.630 0.00 0.00 0.00 2.29
4850 5085 7.248743 AGGATCACATTTTTGTTCAATGGAT 57.751 32.000 0.00 0.00 36.15 3.41
5219 5456 8.548025 TGGGAGATAAATCACTCTTGAACATAA 58.452 33.333 0.00 0.00 34.61 1.90
5307 5546 9.487790 CCAATTGCTACAGAAAGGAAATAAAAA 57.512 29.630 0.00 0.00 30.13 1.94
5884 6124 5.185454 TGTGCTAATGTCGGAAGAAATGAT 58.815 37.500 0.00 0.00 45.01 2.45
5974 6215 4.340666 TGACTAGCAGATGTTTTGCCAAAA 59.659 37.500 0.00 0.00 42.48 2.44
6169 6413 7.897575 AAAGGTCGATTAGATATGATGAAGC 57.102 36.000 0.00 0.00 0.00 3.86
6272 6873 3.159472 TGAAACTCAGCCATCATGCTTT 58.841 40.909 0.00 0.00 40.32 3.51
6311 6912 4.201676 TGTCGCGTGCAAATTATAACTCAG 60.202 41.667 5.77 0.00 0.00 3.35
6312 6913 3.680458 TGTCGCGTGCAAATTATAACTCA 59.320 39.130 5.77 0.00 0.00 3.41
6551 7152 5.477607 TGAGGAAGGATCTAAAACGAACA 57.522 39.130 0.00 0.00 0.00 3.18
6575 7176 8.541234 AGATCAACATCTGCAGATACATATGAT 58.459 33.333 28.27 26.60 38.03 2.45
6646 7249 2.816337 GCAGTAAAAGCAACCCCTGGTA 60.816 50.000 0.00 0.00 33.12 3.25
6785 7390 4.443394 CGATGTAACGAAGGCAAGTATACC 59.557 45.833 0.00 0.00 35.09 2.73
6786 7391 4.085210 GCGATGTAACGAAGGCAAGTATAC 60.085 45.833 0.00 0.00 35.09 1.47
6810 7417 5.512232 CCAAAAGAGAGCTCAACTTCCTACT 60.512 44.000 17.77 3.14 0.00 2.57
6855 7467 1.697432 TCTCAGGTACCACAACCAAGG 59.303 52.381 15.94 0.00 42.40 3.61
6861 7473 3.516586 TCATTCCTCTCAGGTACCACAA 58.483 45.455 15.94 0.00 36.53 3.33
6863 7475 4.553330 TTTCATTCCTCTCAGGTACCAC 57.447 45.455 15.94 0.00 36.53 4.16
6864 7476 6.386927 ACATATTTCATTCCTCTCAGGTACCA 59.613 38.462 15.94 0.00 36.53 3.25
6866 7478 7.873505 GGTACATATTTCATTCCTCTCAGGTAC 59.126 40.741 0.00 0.00 36.53 3.34
6869 7481 5.928839 CGGTACATATTTCATTCCTCTCAGG 59.071 44.000 0.00 0.00 36.46 3.86
6872 7484 6.642950 CACTCGGTACATATTTCATTCCTCTC 59.357 42.308 0.00 0.00 0.00 3.20
6873 7485 6.323996 TCACTCGGTACATATTTCATTCCTCT 59.676 38.462 0.00 0.00 0.00 3.69
6874 7486 6.513180 TCACTCGGTACATATTTCATTCCTC 58.487 40.000 0.00 0.00 0.00 3.71
6875 7487 6.479972 TCACTCGGTACATATTTCATTCCT 57.520 37.500 0.00 0.00 0.00 3.36
6876 7488 7.730364 AATCACTCGGTACATATTTCATTCC 57.270 36.000 0.00 0.00 0.00 3.01
6907 7519 2.917933 TCTTTGCGAGGACCAATATGG 58.082 47.619 0.00 0.00 45.02 2.74
6908 7520 4.963276 TTTCTTTGCGAGGACCAATATG 57.037 40.909 0.00 0.00 0.00 1.78
6910 7522 5.309323 CAATTTCTTTGCGAGGACCAATA 57.691 39.130 0.00 0.00 0.00 1.90
6912 7524 3.641437 CAATTTCTTTGCGAGGACCAA 57.359 42.857 0.00 0.00 0.00 3.67
6922 7534 9.178427 GCATATAAAGCTCTAGCAATTTCTTTG 57.822 33.333 4.54 0.00 45.16 2.77
6924 7536 8.688747 AGCATATAAAGCTCTAGCAATTTCTT 57.311 30.769 4.54 0.00 45.16 2.52
6925 7537 8.688747 AAGCATATAAAGCTCTAGCAATTTCT 57.311 30.769 4.54 0.00 42.53 2.52
6926 7538 9.392021 GAAAGCATATAAAGCTCTAGCAATTTC 57.608 33.333 4.54 0.00 42.53 2.17
6927 7539 9.129532 AGAAAGCATATAAAGCTCTAGCAATTT 57.870 29.630 4.54 0.00 42.53 1.82
6929 7541 8.566260 CAAGAAAGCATATAAAGCTCTAGCAAT 58.434 33.333 4.54 0.00 42.53 3.56
6930 7542 7.012704 CCAAGAAAGCATATAAAGCTCTAGCAA 59.987 37.037 4.54 0.00 42.53 3.91
6931 7543 6.484643 CCAAGAAAGCATATAAAGCTCTAGCA 59.515 38.462 4.54 0.00 42.53 3.49
6932 7544 6.567511 GCCAAGAAAGCATATAAAGCTCTAGC 60.568 42.308 3.81 0.00 42.53 3.42
6934 7546 5.765182 GGCCAAGAAAGCATATAAAGCTCTA 59.235 40.000 0.00 0.00 42.53 2.43
6936 7548 4.339247 TGGCCAAGAAAGCATATAAAGCTC 59.661 41.667 0.61 0.00 42.53 4.09
6937 7549 4.280819 TGGCCAAGAAAGCATATAAAGCT 58.719 39.130 0.61 0.00 45.97 3.74
6938 7550 4.098501 ACTGGCCAAGAAAGCATATAAAGC 59.901 41.667 7.01 0.00 0.00 3.51
6942 7569 6.001449 AGTAACTGGCCAAGAAAGCATATA 57.999 37.500 7.01 0.00 0.00 0.86
6944 7571 4.301072 AGTAACTGGCCAAGAAAGCATA 57.699 40.909 7.01 0.00 0.00 3.14
6952 7579 1.896220 TGAGCAAGTAACTGGCCAAG 58.104 50.000 7.01 3.48 28.98 3.61
6957 7584 4.520492 ACATTCCTTTGAGCAAGTAACTGG 59.480 41.667 0.00 0.00 0.00 4.00
6960 7587 7.435068 TCTAACATTCCTTTGAGCAAGTAAC 57.565 36.000 0.00 0.00 0.00 2.50
6974 7601 5.405935 AATTGTGCCCTTTCTAACATTCC 57.594 39.130 0.00 0.00 0.00 3.01
6980 7607 4.328536 TCGCTAAATTGTGCCCTTTCTAA 58.671 39.130 0.00 0.00 0.00 2.10
7030 8517 3.134623 TCCACTTGAGCTTGAGTTCAGAA 59.865 43.478 0.60 0.00 36.65 3.02
7044 8531 2.487762 GCCGAATTGATTGTCCACTTGA 59.512 45.455 0.00 0.00 0.00 3.02
7045 8532 2.489329 AGCCGAATTGATTGTCCACTTG 59.511 45.455 0.00 0.00 0.00 3.16
7046 8533 2.749621 GAGCCGAATTGATTGTCCACTT 59.250 45.455 0.00 0.00 0.00 3.16
7047 8534 2.026822 AGAGCCGAATTGATTGTCCACT 60.027 45.455 0.00 0.00 0.00 4.00
7048 8535 2.096496 CAGAGCCGAATTGATTGTCCAC 59.904 50.000 0.00 0.00 0.00 4.02
7049 8536 2.358957 CAGAGCCGAATTGATTGTCCA 58.641 47.619 0.00 0.00 0.00 4.02
7055 8542 0.471617 CTCCCCAGAGCCGAATTGAT 59.528 55.000 0.00 0.00 32.13 2.57
7164 8652 6.672266 TTTGGCATTCCACCTAAATGTTTA 57.328 33.333 0.00 0.00 43.33 2.01
7168 8656 3.055963 TGCTTTGGCATTCCACCTAAATG 60.056 43.478 0.00 0.00 44.28 2.32
7169 8657 3.172339 TGCTTTGGCATTCCACCTAAAT 58.828 40.909 0.00 0.00 44.28 1.40
7170 8658 2.603021 TGCTTTGGCATTCCACCTAAA 58.397 42.857 0.00 0.00 44.28 1.85
7216 8704 3.172339 AGGCCAAATATTTGTCAGCCAA 58.828 40.909 31.44 0.00 42.07 4.52
7218 8706 3.893326 AAGGCCAAATATTTGTCAGCC 57.107 42.857 26.80 26.80 40.83 4.85
7220 8708 6.587608 GTCAAGAAAGGCCAAATATTTGTCAG 59.412 38.462 23.24 11.73 36.45 3.51
7225 8713 8.422577 AAGTAGTCAAGAAAGGCCAAATATTT 57.577 30.769 5.01 0.00 0.00 1.40
7227 8715 8.957466 GTTAAGTAGTCAAGAAAGGCCAAATAT 58.043 33.333 5.01 0.00 0.00 1.28
7229 8717 7.004691 AGTTAAGTAGTCAAGAAAGGCCAAAT 58.995 34.615 5.01 0.00 0.00 2.32
7265 8778 9.232082 TCAAAGCGTGCATGATAATTTTTATAC 57.768 29.630 10.93 0.00 0.00 1.47
7266 8779 9.232082 GTCAAAGCGTGCATGATAATTTTTATA 57.768 29.630 10.93 0.00 0.00 0.98
7273 8786 3.691118 AGTGTCAAAGCGTGCATGATAAT 59.309 39.130 10.93 0.00 0.00 1.28
7276 8789 1.527034 AGTGTCAAAGCGTGCATGAT 58.473 45.000 10.93 0.00 0.00 2.45
7282 8795 2.279250 CACGTTAGTGTCAAAGCGTG 57.721 50.000 10.12 10.12 43.15 5.34
7342 8862 7.757624 GGCGGTGAACAATAAATTCAAAAGATA 59.242 33.333 0.00 0.00 37.80 1.98
7343 8863 6.589907 GGCGGTGAACAATAAATTCAAAAGAT 59.410 34.615 0.00 0.00 37.80 2.40
7345 8865 5.164100 CGGCGGTGAACAATAAATTCAAAAG 60.164 40.000 0.00 0.00 37.80 2.27
7404 8924 8.349983 GTTGACTAAATTTAGCCTTGAGTTCAA 58.650 33.333 22.45 17.94 34.09 2.69
7405 8925 7.719633 AGTTGACTAAATTTAGCCTTGAGTTCA 59.280 33.333 22.45 13.86 34.09 3.18


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

AutoCloner maintained by Alex Coulton.