Multiple sequence alignment - TraesCS2A01G588100

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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 TraesCS2A01G588100 chr2A 100.000 5682 0 0 1 5682 777522689 777528370 0.000000e+00 10493.0
1 TraesCS2A01G588100 chr2A 100.000 109 0 0 5968 6076 777528656 777528764 1.030000e-47 202.0
2 TraesCS2A01G588100 chr2D 93.791 4316 203 33 1405 5682 635224247 635219959 0.000000e+00 6425.0
3 TraesCS2A01G588100 chr2D 82.851 863 58 41 564 1410 635225160 635224372 0.000000e+00 691.0
4 TraesCS2A01G588100 chr2D 85.802 486 38 15 48 512 635225737 635225262 2.550000e-133 486.0
5 TraesCS2A01G588100 chr2D 96.330 109 4 0 5968 6076 635219932 635219824 4.840000e-41 180.0
6 TraesCS2A01G588100 chr2B 92.744 2591 138 27 1410 3956 779316595 779314011 0.000000e+00 3698.0
7 TraesCS2A01G588100 chr2B 91.437 1740 101 22 3966 5682 779313971 779312257 0.000000e+00 2344.0
8 TraesCS2A01G588100 chr2B 85.491 448 21 17 995 1406 779317150 779316711 1.570000e-115 427.0
9 TraesCS2A01G588100 chr2B 96.330 109 4 0 5968 6076 779312231 779312123 4.840000e-41 180.0
10 TraesCS2A01G588100 chr2B 84.444 135 18 3 48 180 779318037 779317904 4.940000e-26 130.0
11 TraesCS2A01G588100 chr2B 89.796 98 10 0 5977 6074 779289362 779289265 6.390000e-25 126.0
12 TraesCS2A01G588100 chr2B 76.190 210 24 13 304 507 779317836 779317647 3.020000e-13 87.9
13 TraesCS2A01G588100 chr7B 96.875 32 1 0 477 508 642984650 642984681 3.000000e-03 54.7
14 TraesCS2A01G588100 chr7B 96.875 32 1 0 477 508 642997928 642997959 3.000000e-03 54.7
15 TraesCS2A01G588100 chr7B 86.275 51 4 3 458 507 736650546 736650594 1.100000e-02 52.8
16 TraesCS2A01G588100 chr6B 92.308 39 2 1 470 508 26094109 26094146 3.000000e-03 54.7
17 TraesCS2A01G588100 chr5A 100.000 29 0 0 480 508 590613084 590613056 3.000000e-03 54.7
18 TraesCS2A01G588100 chr7D 100.000 28 0 0 477 504 240473688 240473715 1.100000e-02 52.8
19 TraesCS2A01G588100 chr5B 96.774 31 1 0 477 507 75979521 75979551 1.100000e-02 52.8
20 TraesCS2A01G588100 chr4B 96.774 31 1 0 477 507 59445989 59446019 1.100000e-02 52.8


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 TraesCS2A01G588100 chr2A 777522689 777528764 6075 False 5347.500000 10493 100.000000 1 6076 2 chr2A.!!$F1 6075
1 TraesCS2A01G588100 chr2D 635219824 635225737 5913 True 1945.500000 6425 89.693500 48 6076 4 chr2D.!!$R1 6028
2 TraesCS2A01G588100 chr2B 779312123 779318037 5914 True 1144.483333 3698 87.772667 48 6076 6 chr2B.!!$R2 6028

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
973 1430 0.036875 GGGACACAAGGAAGTGGGAG 59.963 60.0 0.00 0.00 43.72 4.30 F
1385 1891 0.039527 GTGCCACACCGAATTCCAAC 60.040 55.0 0.00 0.00 0.00 3.77 F
1414 2050 0.385223 GCAGAAAGTTGCGCACTGAG 60.385 55.0 24.26 7.41 35.12 3.35 F
3057 3720 0.733909 GCTTCCTCGCACAATTTGGC 60.734 55.0 0.78 1.02 0.00 4.52 F
3075 3738 0.169009 GCCAATCTGTTGTTCGAGCC 59.831 55.0 0.00 0.00 33.36 4.70 F
4225 4952 0.394625 GCCGCCTTGTATTGGGGTAA 60.395 55.0 0.00 0.00 36.96 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 2421 0.250252 TGTGCTCGGTGCTCAATGAA 60.250 50.0 4.53 0.0 41.46 2.57 R
3057 3720 0.443869 CGGCTCGAACAACAGATTGG 59.556 55.0 0.00 0.0 40.42 3.16 R
3075 3738 3.372954 CTTGCGAAGGATAAGGTAGTCG 58.627 50.0 0.00 0.0 0.00 4.18 R
4196 4923 0.466555 ACAAGGCGGCAGTAAACCAA 60.467 50.0 13.08 0.0 0.00 3.67 R
5056 5790 0.601046 CTATGCATGGGCGTCATCGT 60.601 55.0 10.16 0.0 45.35 3.73 R
6056 6808 0.463833 CTGAAATACCGTGGGGGCTC 60.464 60.0 0.00 0.0 40.62 4.70 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
17 18 4.068257 ACCTAGGGTTGCTAGGCC 57.932 61.111 14.81 0.00 45.86 5.19
18 19 2.064581 ACCTAGGGTTGCTAGGCCG 61.065 63.158 14.81 0.00 45.86 6.13
19 20 2.808206 CCTAGGGTTGCTAGGCCGG 61.808 68.421 0.00 0.00 37.70 6.13
20 21 3.462199 CTAGGGTTGCTAGGCCGGC 62.462 68.421 21.18 21.18 0.00 6.13
40 41 3.431725 GGCAACGCCTTCCCTTCG 61.432 66.667 0.00 0.00 46.69 3.79
41 42 4.103103 GCAACGCCTTCCCTTCGC 62.103 66.667 0.00 0.00 0.00 4.70
42 43 3.431725 CAACGCCTTCCCTTCGCC 61.432 66.667 0.00 0.00 0.00 5.54
43 44 3.637273 AACGCCTTCCCTTCGCCT 61.637 61.111 0.00 0.00 0.00 5.52
44 45 3.192103 AACGCCTTCCCTTCGCCTT 62.192 57.895 0.00 0.00 0.00 4.35
45 46 2.359975 CGCCTTCCCTTCGCCTTT 60.360 61.111 0.00 0.00 0.00 3.11
46 47 2.690778 CGCCTTCCCTTCGCCTTTG 61.691 63.158 0.00 0.00 0.00 2.77
181 183 0.315220 CGTCAGCGTCTACGTAGCTC 60.315 60.000 18.00 11.77 39.48 4.09
182 184 0.725686 GTCAGCGTCTACGTAGCTCA 59.274 55.000 18.00 0.00 39.48 4.26
183 185 0.725686 TCAGCGTCTACGTAGCTCAC 59.274 55.000 18.00 10.00 39.48 3.51
207 209 1.078143 GGGAGTCAGTCATGTGCCC 60.078 63.158 0.00 0.00 0.00 5.36
208 210 1.078143 GGAGTCAGTCATGTGCCCC 60.078 63.158 0.00 0.00 0.00 5.80
209 211 1.448540 GAGTCAGTCATGTGCCCCG 60.449 63.158 0.00 0.00 0.00 5.73
301 321 2.435693 CCCCGCCTCCGAATCTTCT 61.436 63.158 0.00 0.00 36.29 2.85
302 322 1.522569 CCCGCCTCCGAATCTTCTT 59.477 57.895 0.00 0.00 36.29 2.52
366 386 5.184479 CGGCTAATGATTCATTCCATTCCAT 59.816 40.000 14.99 0.00 35.54 3.41
369 389 6.209986 GCTAATGATTCATTCCATTCCATCCA 59.790 38.462 14.99 0.00 35.54 3.41
370 390 7.093465 GCTAATGATTCATTCCATTCCATCCAT 60.093 37.037 14.99 0.00 35.54 3.41
408 438 5.988561 GTGAGATGCCAAGAAGATTAGTAGG 59.011 44.000 0.00 0.00 0.00 3.18
409 439 5.899547 TGAGATGCCAAGAAGATTAGTAGGA 59.100 40.000 0.00 0.00 0.00 2.94
410 440 6.041409 TGAGATGCCAAGAAGATTAGTAGGAG 59.959 42.308 0.00 0.00 0.00 3.69
422 452 2.049888 AGTAGGAGTACCACTACGCC 57.950 55.000 15.07 0.00 43.26 5.68
424 454 2.091994 AGTAGGAGTACCACTACGCCAT 60.092 50.000 15.07 0.69 43.53 4.40
433 463 1.070821 CACTACGCCATGTGACAGTG 58.929 55.000 0.00 0.00 36.38 3.66
434 464 0.670546 ACTACGCCATGTGACAGTGC 60.671 55.000 0.00 0.00 0.00 4.40
469 506 0.100682 CTGCTGGCATTTAGCTGCTG 59.899 55.000 13.43 0.00 44.79 4.41
475 512 1.033746 GCATTTAGCTGCTGCCTCCA 61.034 55.000 13.43 0.00 41.15 3.86
478 529 0.321919 TTTAGCTGCTGCCTCCACTG 60.322 55.000 13.43 0.00 40.80 3.66
481 532 2.436292 CTGCTGCCTCCACTGCTC 60.436 66.667 0.00 0.00 35.70 4.26
484 535 2.583520 CTGCCTCCACTGCTCCTC 59.416 66.667 0.00 0.00 0.00 3.71
487 538 2.730524 GCCTCCACTGCTCCTCCTC 61.731 68.421 0.00 0.00 0.00 3.71
511 620 2.563179 TCTTCTTCTTCTTCCTCCCGTG 59.437 50.000 0.00 0.00 0.00 4.94
534 643 1.675310 CTGTTGCCGCCATTCTCCA 60.675 57.895 0.00 0.00 0.00 3.86
537 646 4.802051 TGCCGCCATTCTCCAGCC 62.802 66.667 0.00 0.00 0.00 4.85
538 647 4.496336 GCCGCCATTCTCCAGCCT 62.496 66.667 0.00 0.00 0.00 4.58
539 648 2.203126 CCGCCATTCTCCAGCCTC 60.203 66.667 0.00 0.00 0.00 4.70
540 649 2.203126 CGCCATTCTCCAGCCTCC 60.203 66.667 0.00 0.00 0.00 4.30
541 650 2.203126 GCCATTCTCCAGCCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
544 653 1.144936 CATTCTCCAGCCTCCGTCC 59.855 63.158 0.00 0.00 0.00 4.79
545 654 1.306141 ATTCTCCAGCCTCCGTCCA 60.306 57.895 0.00 0.00 0.00 4.02
546 655 0.692419 ATTCTCCAGCCTCCGTCCAT 60.692 55.000 0.00 0.00 0.00 3.41
547 656 1.330655 TTCTCCAGCCTCCGTCCATC 61.331 60.000 0.00 0.00 0.00 3.51
549 658 3.083349 CCAGCCTCCGTCCATCCA 61.083 66.667 0.00 0.00 0.00 3.41
550 659 2.187946 CAGCCTCCGTCCATCCAC 59.812 66.667 0.00 0.00 0.00 4.02
552 661 1.613630 AGCCTCCGTCCATCCACTT 60.614 57.895 0.00 0.00 0.00 3.16
553 662 1.153349 GCCTCCGTCCATCCACTTC 60.153 63.158 0.00 0.00 0.00 3.01
555 713 0.978146 CCTCCGTCCATCCACTTCCT 60.978 60.000 0.00 0.00 0.00 3.36
559 717 0.905357 CGTCCATCCACTTCCTTCCT 59.095 55.000 0.00 0.00 0.00 3.36
560 718 2.108168 CGTCCATCCACTTCCTTCCTA 58.892 52.381 0.00 0.00 0.00 2.94
608 1051 4.959596 GCCGATCCGCTCCTGCTC 62.960 72.222 0.00 0.00 36.97 4.26
624 1067 3.719883 CTCCTGCTCCTGCTCTGCG 62.720 68.421 0.00 0.00 40.48 5.18
637 1080 1.173043 CTCTGCGTTCTCTCCTCACT 58.827 55.000 0.00 0.00 0.00 3.41
638 1081 1.543802 CTCTGCGTTCTCTCCTCACTT 59.456 52.381 0.00 0.00 0.00 3.16
639 1082 1.964223 TCTGCGTTCTCTCCTCACTTT 59.036 47.619 0.00 0.00 0.00 2.66
640 1083 2.365617 TCTGCGTTCTCTCCTCACTTTT 59.634 45.455 0.00 0.00 0.00 2.27
683 1134 2.045045 CGCCATTGGGGAGAAGCA 60.045 61.111 14.33 0.00 39.08 3.91
684 1135 1.678635 CGCCATTGGGGAGAAGCAA 60.679 57.895 14.33 0.00 39.08 3.91
685 1136 1.660560 CGCCATTGGGGAGAAGCAAG 61.661 60.000 14.33 0.00 39.08 4.01
686 1137 1.953231 GCCATTGGGGAGAAGCAAGC 61.953 60.000 4.53 0.00 40.01 4.01
705 1156 2.233431 AGCAGCAGCAGCCTAGATATAC 59.767 50.000 6.10 0.00 45.49 1.47
750 1207 1.740585 CGGAGAGCGAGAGAGAAAGAA 59.259 52.381 0.00 0.00 0.00 2.52
782 1239 1.353694 AGGATATCCATTGCTGCTCCC 59.646 52.381 23.81 0.00 38.89 4.30
797 1254 1.075226 TCCCCCTCCAAGATCTCCG 60.075 63.158 0.00 0.00 0.00 4.63
817 1274 4.840005 CCCTTTCGAGCTCCCCGC 62.840 72.222 8.47 0.00 39.57 6.13
818 1275 4.840005 CCTTTCGAGCTCCCCGCC 62.840 72.222 8.47 0.00 40.39 6.13
911 1368 0.963225 GAGAGGAATAGGAGGCGTCC 59.037 60.000 17.88 17.88 44.33 4.79
924 1381 2.951745 CGTCCGTCTGCGCATCTC 60.952 66.667 12.24 3.32 36.67 2.75
925 1382 2.492090 GTCCGTCTGCGCATCTCT 59.508 61.111 12.24 0.00 36.67 3.10
926 1383 1.587613 GTCCGTCTGCGCATCTCTC 60.588 63.158 12.24 0.00 36.67 3.20
927 1384 2.279120 CCGTCTGCGCATCTCTCC 60.279 66.667 12.24 0.00 36.67 3.71
928 1385 2.491621 CGTCTGCGCATCTCTCCA 59.508 61.111 12.24 0.00 0.00 3.86
929 1386 1.588403 CGTCTGCGCATCTCTCCAG 60.588 63.158 12.24 0.00 0.00 3.86
930 1387 1.515020 GTCTGCGCATCTCTCCAGT 59.485 57.895 12.24 0.00 0.00 4.00
931 1388 0.805322 GTCTGCGCATCTCTCCAGTG 60.805 60.000 12.24 0.00 0.00 3.66
932 1389 1.217511 CTGCGCATCTCTCCAGTGT 59.782 57.895 12.24 0.00 0.00 3.55
933 1390 0.805322 CTGCGCATCTCTCCAGTGTC 60.805 60.000 12.24 0.00 0.00 3.67
973 1430 0.036875 GGGACACAAGGAAGTGGGAG 59.963 60.000 0.00 0.00 43.72 4.30
982 1439 1.627834 AGGAAGTGGGAGCAAGAAGAG 59.372 52.381 0.00 0.00 0.00 2.85
985 1442 2.022718 AGTGGGAGCAAGAAGAGAGT 57.977 50.000 0.00 0.00 0.00 3.24
987 1444 1.620819 GTGGGAGCAAGAAGAGAGTGA 59.379 52.381 0.00 0.00 0.00 3.41
1232 1733 2.805099 CAGTTGGTCTCAAGTGCTCTTC 59.195 50.000 0.00 0.00 44.33 2.87
1234 1735 2.805099 GTTGGTCTCAAGTGCTCTTCTG 59.195 50.000 0.00 0.00 32.92 3.02
1235 1736 2.319844 TGGTCTCAAGTGCTCTTCTGA 58.680 47.619 0.00 0.00 0.00 3.27
1236 1737 2.700371 TGGTCTCAAGTGCTCTTCTGAA 59.300 45.455 0.00 0.00 0.00 3.02
1237 1738 3.326006 TGGTCTCAAGTGCTCTTCTGAAT 59.674 43.478 0.00 0.00 0.00 2.57
1239 1740 4.867608 GGTCTCAAGTGCTCTTCTGAATAC 59.132 45.833 0.00 0.00 0.00 1.89
1247 1750 6.166982 AGTGCTCTTCTGAATACTAACAACC 58.833 40.000 0.00 0.00 0.00 3.77
1331 1837 7.242322 GGAACGAAATCCCTATTAGGAGTAT 57.758 40.000 11.52 0.00 39.95 2.12
1333 1839 7.579146 GGAACGAAATCCCTATTAGGAGTATCC 60.579 44.444 11.52 4.49 44.64 2.59
1369 1875 3.093717 AGTACTGTACTGTGTGTGTGC 57.906 47.619 19.09 0.00 37.69 4.57
1385 1891 0.039527 GTGCCACACCGAATTCCAAC 60.040 55.000 0.00 0.00 0.00 3.77
1414 2050 0.385223 GCAGAAAGTTGCGCACTGAG 60.385 55.000 24.26 7.41 35.12 3.35
1416 2052 1.331756 CAGAAAGTTGCGCACTGAGTT 59.668 47.619 11.12 1.25 35.12 3.01
1428 2064 4.466828 CGCACTGAGTTCCAAACATAAAG 58.533 43.478 0.00 0.00 0.00 1.85
1430 2066 4.261572 GCACTGAGTTCCAAACATAAAGCA 60.262 41.667 0.00 0.00 0.00 3.91
1432 2068 4.278419 ACTGAGTTCCAAACATAAAGCACC 59.722 41.667 0.00 0.00 0.00 5.01
1442 2078 6.816140 CCAAACATAAAGCACCCGATTTTAAT 59.184 34.615 0.00 0.00 31.94 1.40
1500 2136 2.418368 TCTTGTGCTTGTTCAGTGGT 57.582 45.000 0.00 0.00 0.00 4.16
1600 2236 6.377327 TTTGTTTGTCCTCTGTTCTCATTC 57.623 37.500 0.00 0.00 0.00 2.67
1635 2272 5.490139 TGCTCTGAAATGTTAGCTAATGC 57.510 39.130 9.88 0.00 35.95 3.56
1650 2287 5.506644 GCTAATGCTTTGCTCTGTTTTTC 57.493 39.130 0.00 0.00 36.03 2.29
1784 2421 1.203492 ACCAAAGAGGAGGTGGAGGAT 60.203 52.381 0.00 0.00 41.22 3.24
1932 2576 1.001181 TGCAAAGCTTCCTTGGAATGC 59.999 47.619 15.06 15.06 33.68 3.56
1943 2587 4.479158 TCCTTGGAATGCCTAAACTTGTT 58.521 39.130 0.00 0.00 34.31 2.83
1956 2600 6.223120 CCTAAACTTGTTTGGGAATCCTTTG 58.777 40.000 19.55 0.00 34.86 2.77
2067 2712 1.298667 GGCGGTAACCCATGTGACT 59.701 57.895 0.00 0.00 0.00 3.41
2109 2754 6.940298 TGTTGCTAGCTATACTCAAGGTTTTT 59.060 34.615 17.23 0.00 0.00 1.94
2132 2778 4.353489 TCCCCATTATCATGTGGATTAGCA 59.647 41.667 1.70 0.00 32.34 3.49
2163 2809 9.968743 CACCTTCGTTTGTTATATTTAGAAGAC 57.031 33.333 3.76 0.00 36.82 3.01
2349 3008 7.140705 TGTTGAAACACATCTGAATTCATGAC 58.859 34.615 14.50 3.28 33.17 3.06
2503 3162 9.814899 CGAAATAGCAGATCCTGAGATAATATT 57.185 33.333 0.00 0.00 32.44 1.28
2587 3246 4.681744 TCTTGTCTGAATTTTGCAACCAC 58.318 39.130 0.00 0.00 0.00 4.16
2666 3329 8.887717 CAAATGTTTTGAGAATCTAGGTAGGAG 58.112 37.037 0.00 0.00 34.92 3.69
2720 3383 8.138365 TGTTTTACTTCTGTAACTGTAGCAAG 57.862 34.615 0.00 0.00 38.26 4.01
2730 3393 6.049149 TGTAACTGTAGCAAGCAATATCCTC 58.951 40.000 0.00 0.00 0.00 3.71
2768 3431 6.106003 CACTGTATACTTAGCCATGTTGACA 58.894 40.000 4.17 0.00 0.00 3.58
2785 3448 5.221823 TGTTGACATTAACCTCCATCTGACA 60.222 40.000 0.00 0.00 0.00 3.58
2803 3466 7.067496 TCTGACAGTTCCTCTTCTAATTTGT 57.933 36.000 1.59 0.00 0.00 2.83
2807 3470 6.831976 ACAGTTCCTCTTCTAATTTGTCTGT 58.168 36.000 0.00 0.00 0.00 3.41
3045 3708 7.094805 TGTGTCATTATACAGTTTTGCTTCCTC 60.095 37.037 0.00 0.00 0.00 3.71
3057 3720 0.733909 GCTTCCTCGCACAATTTGGC 60.734 55.000 0.78 1.02 0.00 4.52
3075 3738 0.169009 GCCAATCTGTTGTTCGAGCC 59.831 55.000 0.00 0.00 33.36 4.70
3146 3810 3.205056 TGGGCCATCTTGGATAGAAATGT 59.795 43.478 0.00 0.00 40.96 2.71
3225 3890 5.246307 AGAAAGGCATACTGAAGTTACACC 58.754 41.667 0.00 0.00 0.00 4.16
3317 3982 5.175859 CCAACATACGACTTCCACACTTAT 58.824 41.667 0.00 0.00 0.00 1.73
3329 3994 5.386958 TCCACACTTATATGATACGCTCC 57.613 43.478 0.00 0.00 0.00 4.70
3399 4067 3.381045 CATGCTTGCCTGCTTATGAATG 58.619 45.455 0.00 0.00 0.00 2.67
3538 4209 8.691661 ATGTTGATGGTAAACTTTGAACTACT 57.308 30.769 0.00 0.00 0.00 2.57
3618 4306 2.961526 TTGTCGCAGGATCTAACCTC 57.038 50.000 0.00 0.00 38.32 3.85
3678 4370 3.879295 GCAGCCTGCTTCTTGTATATTCA 59.121 43.478 10.04 0.00 40.96 2.57
4116 4843 4.640771 TGGGAAATTCTGCTAGAAGTGT 57.359 40.909 0.00 0.00 37.69 3.55
4196 4923 5.716228 TCATGCTTCATCAAAAACCACCTAT 59.284 36.000 0.00 0.00 0.00 2.57
4225 4952 0.394625 GCCGCCTTGTATTGGGGTAA 60.395 55.000 0.00 0.00 36.96 2.85
4226 4953 1.752788 GCCGCCTTGTATTGGGGTAAT 60.753 52.381 0.00 0.00 36.96 1.89
4227 4954 1.953686 CCGCCTTGTATTGGGGTAATG 59.046 52.381 0.00 0.00 36.00 1.90
4228 4955 2.422235 CCGCCTTGTATTGGGGTAATGA 60.422 50.000 0.00 0.00 36.00 2.57
4238 4965 2.524306 TGGGGTAATGAAGCAGTTTGG 58.476 47.619 0.00 0.00 0.00 3.28
4240 4967 2.492088 GGGGTAATGAAGCAGTTTGGAC 59.508 50.000 0.00 0.00 0.00 4.02
4269 4999 5.536260 ACTACTTAGTTTCTCGTTGTTCCC 58.464 41.667 0.00 0.00 31.13 3.97
4272 5002 5.055144 ACTTAGTTTCTCGTTGTTCCCTTC 58.945 41.667 0.00 0.00 0.00 3.46
4278 5008 6.544564 AGTTTCTCGTTGTTCCCTTCATTTTA 59.455 34.615 0.00 0.00 0.00 1.52
4281 5011 6.234920 TCTCGTTGTTCCCTTCATTTTATCA 58.765 36.000 0.00 0.00 0.00 2.15
4285 5015 6.747280 CGTTGTTCCCTTCATTTTATCATGTC 59.253 38.462 0.00 0.00 0.00 3.06
4287 5017 5.656416 TGTTCCCTTCATTTTATCATGTCCC 59.344 40.000 0.00 0.00 0.00 4.46
4296 5026 9.865152 TTCATTTTATCATGTCCCTCATTATGA 57.135 29.630 0.00 0.00 34.09 2.15
4337 5067 0.534203 TCAGGTTTGCCGGACAGTTC 60.534 55.000 5.05 0.00 40.50 3.01
4361 5091 0.794473 GCAGTTACAGTACGTTGCCC 59.206 55.000 0.00 0.00 0.00 5.36
4464 5198 6.922247 ATCATCAAGATCCGATTATGCATC 57.078 37.500 0.19 0.00 28.20 3.91
4506 5240 3.376859 ACGTTCACATCTGCTGTTTTTCA 59.623 39.130 0.00 0.00 35.29 2.69
4536 5270 7.443259 AAATACGGCTAATACACTGTTTGTT 57.557 32.000 0.00 0.00 39.91 2.83
4538 5272 3.058501 ACGGCTAATACACTGTTTGTTGC 60.059 43.478 0.00 0.00 39.91 4.17
4539 5273 3.669557 CGGCTAATACACTGTTTGTTGCC 60.670 47.826 0.00 0.00 39.91 4.52
4540 5274 3.488489 GCTAATACACTGTTTGTTGCCG 58.512 45.455 0.00 0.00 39.91 5.69
4541 5275 3.187637 GCTAATACACTGTTTGTTGCCGA 59.812 43.478 0.00 0.00 39.91 5.54
4542 5276 4.142687 GCTAATACACTGTTTGTTGCCGAT 60.143 41.667 0.00 0.00 39.91 4.18
4543 5277 5.064198 GCTAATACACTGTTTGTTGCCGATA 59.936 40.000 0.00 0.00 39.91 2.92
4544 5278 4.939509 ATACACTGTTTGTTGCCGATAC 57.060 40.909 0.00 0.00 39.91 2.24
4545 5279 1.529438 ACACTGTTTGTTGCCGATACG 59.471 47.619 0.00 0.00 33.09 3.06
4546 5280 1.795872 CACTGTTTGTTGCCGATACGA 59.204 47.619 0.00 0.00 0.00 3.43
4547 5281 1.796459 ACTGTTTGTTGCCGATACGAC 59.204 47.619 0.00 0.00 0.00 4.34
4548 5282 1.795872 CTGTTTGTTGCCGATACGACA 59.204 47.619 0.00 0.00 31.96 4.35
4549 5283 2.210961 TGTTTGTTGCCGATACGACAA 58.789 42.857 0.00 2.80 41.21 3.18
4550 5284 2.032722 TGTTTGTTGCCGATACGACAAC 60.033 45.455 14.19 14.19 46.94 3.32
4574 5308 7.402054 ACATACAGATGGGATCAAAGTACAAA 58.598 34.615 0.00 0.00 37.39 2.83
4577 5311 4.096984 CAGATGGGATCAAAGTACAAAGCC 59.903 45.833 0.00 0.00 0.00 4.35
4639 5373 1.528129 GGCAAGGACACAAGGAAGAG 58.472 55.000 0.00 0.00 0.00 2.85
4673 5407 3.719214 GGCGACGATTCCACCATC 58.281 61.111 0.00 0.00 0.00 3.51
4676 5410 2.237751 CGACGATTCCACCATCCGC 61.238 63.158 0.00 0.00 0.00 5.54
4679 5413 1.449423 CGATTCCACCATCCGCACA 60.449 57.895 0.00 0.00 0.00 4.57
4746 5480 3.860681 GCCATGGCCATTCCGATT 58.139 55.556 27.24 0.00 37.80 3.34
4778 5512 1.819632 CAGGTTGCCGCCATACCTC 60.820 63.158 6.08 0.00 40.24 3.85
4790 5524 2.865670 GCCATACCTCAAGATCGAGCTG 60.866 54.545 2.80 0.00 0.00 4.24
4793 5527 1.140589 CCTCAAGATCGAGCTGCGT 59.859 57.895 2.80 0.00 41.80 5.24
4796 5530 1.880340 CAAGATCGAGCTGCGTCCC 60.880 63.158 2.80 0.00 41.80 4.46
4853 5587 1.079127 AAGCCACCATCTTCCGACG 60.079 57.895 0.00 0.00 0.00 5.12
4892 5626 4.853050 GGCGGCAGCTCTCAGCAT 62.853 66.667 9.17 0.00 45.56 3.79
4895 5629 3.574445 GGCAGCTCTCAGCATGCG 61.574 66.667 13.01 7.64 45.56 4.73
4960 5694 4.783621 GCCACCGAGCAGCCATGA 62.784 66.667 0.00 0.00 0.00 3.07
4964 5698 4.457496 CCGAGCAGCCATGACCGT 62.457 66.667 0.00 0.00 0.00 4.83
4972 5706 2.509336 CCATGACCGTGGCGTCTC 60.509 66.667 0.00 0.00 33.70 3.36
4979 5713 2.338620 CGTGGCGTCTCAAGGTCA 59.661 61.111 0.00 0.00 0.00 4.02
4997 5731 4.910585 GCGTCGATGCCGGGGATT 62.911 66.667 19.11 0.00 36.24 3.01
5001 5735 2.516930 CGATGCCGGGGATTGCTT 60.517 61.111 2.18 0.00 0.00 3.91
5003 5737 1.152881 GATGCCGGGGATTGCTTCT 60.153 57.895 2.18 0.00 0.00 2.85
5036 5770 1.606903 CCTCGACGATAGGCCTTAGT 58.393 55.000 12.58 9.14 46.50 2.24
5042 5776 1.218704 ACGATAGGCCTTAGTACCCCA 59.781 52.381 12.58 0.00 43.77 4.96
5046 5780 2.188731 GCCTTAGTACCCCACCGC 59.811 66.667 0.00 0.00 0.00 5.68
5063 5797 2.167861 GCCTCGGCTCAACGATGAC 61.168 63.158 0.00 0.00 42.62 3.06
5101 5838 7.658575 GGACACTGGACTTATTTTGTGTTACTA 59.341 37.037 0.00 0.00 38.52 1.82
5122 5860 7.894753 ACTATAGGATGATGATGACGATGAT 57.105 36.000 4.43 0.00 0.00 2.45
5129 5867 5.464030 TGATGATGACGATGATGACTGAT 57.536 39.130 0.00 0.00 0.00 2.90
5136 5874 4.641989 TGACGATGATGACTGATGAGAGAA 59.358 41.667 0.00 0.00 0.00 2.87
5141 5879 6.564312 CGATGATGACTGATGAGAGAAAATGC 60.564 42.308 0.00 0.00 0.00 3.56
5262 6000 3.005897 AGTGCGTGTCATCAGAACTTAGT 59.994 43.478 0.00 0.00 0.00 2.24
5263 6001 4.217767 AGTGCGTGTCATCAGAACTTAGTA 59.782 41.667 0.00 0.00 0.00 1.82
5264 6002 4.559251 GTGCGTGTCATCAGAACTTAGTAG 59.441 45.833 0.00 0.00 0.00 2.57
5265 6003 4.457949 TGCGTGTCATCAGAACTTAGTAGA 59.542 41.667 0.00 0.00 0.00 2.59
5296 6034 8.609176 GTTTGGTTTAAAGGAATTTCAAAGGAC 58.391 33.333 0.00 0.00 0.00 3.85
5299 6037 8.201464 TGGTTTAAAGGAATTTCAAAGGACTTC 58.799 33.333 0.00 0.00 0.00 3.01
5541 6279 4.216366 TGAGCGATCGAACATCTTCTAG 57.784 45.455 21.57 0.00 0.00 2.43
6013 6765 6.690194 ATGTCTGATCTTTCACAATTAGGC 57.310 37.500 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.822399 CCGGCCTAGCAACCCTAG 59.178 66.667 0.00 0.00 42.68 3.02
3 4 3.476419 GCCGGCCTAGCAACCCTA 61.476 66.667 18.11 0.00 0.00 3.53
24 25 4.103103 GCGAAGGGAAGGCGTTGC 62.103 66.667 1.57 1.57 0.00 4.17
25 26 3.431725 GGCGAAGGGAAGGCGTTG 61.432 66.667 0.00 0.00 0.00 4.10
26 27 2.692273 AAAGGCGAAGGGAAGGCGTT 62.692 55.000 0.00 0.00 36.45 4.84
27 28 3.192103 AAAGGCGAAGGGAAGGCGT 62.192 57.895 0.00 0.00 38.03 5.68
28 29 2.359975 AAAGGCGAAGGGAAGGCG 60.360 61.111 0.00 0.00 38.03 5.52
29 30 0.893727 TTCAAAGGCGAAGGGAAGGC 60.894 55.000 0.00 0.00 0.00 4.35
30 31 1.839424 ATTCAAAGGCGAAGGGAAGG 58.161 50.000 0.00 0.00 0.00 3.46
31 32 4.675408 GCTTAATTCAAAGGCGAAGGGAAG 60.675 45.833 0.00 0.00 0.00 3.46
32 33 3.192633 GCTTAATTCAAAGGCGAAGGGAA 59.807 43.478 0.00 0.00 0.00 3.97
33 34 2.752903 GCTTAATTCAAAGGCGAAGGGA 59.247 45.455 0.00 0.00 0.00 4.20
34 35 2.159240 GGCTTAATTCAAAGGCGAAGGG 60.159 50.000 0.00 0.00 41.48 3.95
35 36 3.150848 GGCTTAATTCAAAGGCGAAGG 57.849 47.619 0.00 0.00 41.48 3.46
41 42 3.119495 CGGTTGGAGGCTTAATTCAAAGG 60.119 47.826 0.00 0.00 0.00 3.11
42 43 3.673323 GCGGTTGGAGGCTTAATTCAAAG 60.673 47.826 0.00 0.00 0.00 2.77
43 44 2.230266 GCGGTTGGAGGCTTAATTCAAA 59.770 45.455 0.00 0.00 0.00 2.69
44 45 1.816224 GCGGTTGGAGGCTTAATTCAA 59.184 47.619 0.00 0.00 0.00 2.69
45 46 1.459450 GCGGTTGGAGGCTTAATTCA 58.541 50.000 0.00 0.00 0.00 2.57
46 47 0.738975 GGCGGTTGGAGGCTTAATTC 59.261 55.000 0.00 0.00 0.00 2.17
82 83 3.285215 GCCGATGGATGCAGCCTG 61.285 66.667 23.69 11.84 0.00 4.85
89 90 1.652563 CTGCATGTGCCGATGGATG 59.347 57.895 2.07 0.00 41.18 3.51
181 183 3.343788 GACTGACTCCCTCGCCGTG 62.344 68.421 0.00 0.00 0.00 4.94
182 184 3.063084 GACTGACTCCCTCGCCGT 61.063 66.667 0.00 0.00 0.00 5.68
183 185 2.418910 ATGACTGACTCCCTCGCCG 61.419 63.158 0.00 0.00 0.00 6.46
184 186 1.142748 CATGACTGACTCCCTCGCC 59.857 63.158 0.00 0.00 0.00 5.54
185 187 0.459237 CACATGACTGACTCCCTCGC 60.459 60.000 0.00 0.00 0.00 5.03
186 188 0.459237 GCACATGACTGACTCCCTCG 60.459 60.000 0.00 0.00 0.00 4.63
187 189 0.107945 GGCACATGACTGACTCCCTC 60.108 60.000 0.00 0.00 0.00 4.30
188 190 1.557269 GGGCACATGACTGACTCCCT 61.557 60.000 0.00 0.00 0.00 4.20
189 191 1.078143 GGGCACATGACTGACTCCC 60.078 63.158 0.00 0.00 0.00 4.30
190 192 1.078143 GGGGCACATGACTGACTCC 60.078 63.158 0.00 0.00 0.00 3.85
194 196 4.408821 GGCGGGGCACATGACTGA 62.409 66.667 0.00 0.00 0.00 3.41
237 250 3.589988 CTTCTGCAAGTACAGGTACAGG 58.410 50.000 11.78 4.64 38.48 4.00
287 304 0.530870 CGGGAAGAAGATTCGGAGGC 60.531 60.000 0.00 0.00 0.00 4.70
288 305 0.530870 GCGGGAAGAAGATTCGGAGG 60.531 60.000 0.00 0.00 0.00 4.30
289 306 0.175760 TGCGGGAAGAAGATTCGGAG 59.824 55.000 0.00 0.00 0.00 4.63
290 307 0.830648 ATGCGGGAAGAAGATTCGGA 59.169 50.000 0.00 0.00 0.00 4.55
291 308 1.221414 GATGCGGGAAGAAGATTCGG 58.779 55.000 0.00 0.00 0.00 4.30
293 310 3.737850 AGATGATGCGGGAAGAAGATTC 58.262 45.455 0.00 0.00 0.00 2.52
294 311 3.135348 TGAGATGATGCGGGAAGAAGATT 59.865 43.478 0.00 0.00 0.00 2.40
295 312 2.702478 TGAGATGATGCGGGAAGAAGAT 59.298 45.455 0.00 0.00 0.00 2.40
301 321 3.003394 ACAAATGAGATGATGCGGGAA 57.997 42.857 0.00 0.00 0.00 3.97
302 322 2.715749 ACAAATGAGATGATGCGGGA 57.284 45.000 0.00 0.00 0.00 5.14
366 386 2.755876 AGACCTCGCTCGCATGGA 60.756 61.111 0.00 0.00 0.00 3.41
369 389 2.182791 CACAGACCTCGCTCGCAT 59.817 61.111 0.00 0.00 0.00 4.73
370 390 2.982744 CTCACAGACCTCGCTCGCA 61.983 63.158 0.00 0.00 0.00 5.10
408 438 1.475280 TCACATGGCGTAGTGGTACTC 59.525 52.381 0.00 0.00 36.43 2.59
409 439 1.203994 GTCACATGGCGTAGTGGTACT 59.796 52.381 0.00 0.00 36.43 2.73
410 440 1.067425 TGTCACATGGCGTAGTGGTAC 60.067 52.381 0.00 0.00 36.43 3.34
422 452 1.376543 GGGATCTGCACTGTCACATG 58.623 55.000 0.00 0.00 0.00 3.21
424 454 0.837691 AGGGGATCTGCACTGTCACA 60.838 55.000 0.00 0.00 0.00 3.58
434 464 2.950309 CAGCAGATTGAAAGGGGATCTG 59.050 50.000 7.93 7.93 45.97 2.90
469 506 2.686835 AGGAGGAGCAGTGGAGGC 60.687 66.667 0.00 0.00 0.00 4.70
472 509 0.616111 GAAGGAGGAGGAGCAGTGGA 60.616 60.000 0.00 0.00 0.00 4.02
475 512 1.078656 AGAAGAAGGAGGAGGAGCAGT 59.921 52.381 0.00 0.00 0.00 4.40
478 529 2.466846 AGAAGAAGAAGGAGGAGGAGC 58.533 52.381 0.00 0.00 0.00 4.70
481 532 4.081142 GGAAGAAGAAGAAGAAGGAGGAGG 60.081 50.000 0.00 0.00 0.00 4.30
484 535 4.081142 GGAGGAAGAAGAAGAAGAAGGAGG 60.081 50.000 0.00 0.00 0.00 4.30
487 538 3.368948 CGGGAGGAAGAAGAAGAAGAAGG 60.369 52.174 0.00 0.00 0.00 3.46
511 620 2.533391 GAATGGCGGCAACAGTGAGC 62.533 60.000 18.31 0.00 0.00 4.26
534 643 1.613630 AAGTGGATGGACGGAGGCT 60.614 57.895 0.00 0.00 0.00 4.58
537 646 0.905357 AAGGAAGTGGATGGACGGAG 59.095 55.000 0.00 0.00 0.00 4.63
538 647 0.902531 GAAGGAAGTGGATGGACGGA 59.097 55.000 0.00 0.00 0.00 4.69
539 648 0.107654 GGAAGGAAGTGGATGGACGG 60.108 60.000 0.00 0.00 0.00 4.79
540 649 0.905357 AGGAAGGAAGTGGATGGACG 59.095 55.000 0.00 0.00 0.00 4.79
541 650 2.158885 GCTAGGAAGGAAGTGGATGGAC 60.159 54.545 0.00 0.00 0.00 4.02
544 653 1.839994 TGGCTAGGAAGGAAGTGGATG 59.160 52.381 0.00 0.00 0.00 3.51
545 654 2.122768 CTGGCTAGGAAGGAAGTGGAT 58.877 52.381 0.00 0.00 0.00 3.41
546 655 1.573108 CTGGCTAGGAAGGAAGTGGA 58.427 55.000 0.00 0.00 0.00 4.02
603 761 2.187424 GAGCAGGAGCAGGAGCAG 59.813 66.667 0.00 0.00 45.49 4.24
604 762 2.284478 AGAGCAGGAGCAGGAGCA 60.284 61.111 0.00 0.00 45.49 4.26
608 1051 3.602513 AACGCAGAGCAGGAGCAGG 62.603 63.158 0.00 0.00 45.49 4.85
624 1067 6.052360 AGAAGAACAAAAGTGAGGAGAGAAC 58.948 40.000 0.00 0.00 0.00 3.01
637 1080 2.227194 GGCGGGAGAAGAAGAACAAAA 58.773 47.619 0.00 0.00 0.00 2.44
638 1081 1.876416 CGGCGGGAGAAGAAGAACAAA 60.876 52.381 0.00 0.00 0.00 2.83
639 1082 0.320421 CGGCGGGAGAAGAAGAACAA 60.320 55.000 0.00 0.00 0.00 2.83
640 1083 1.292223 CGGCGGGAGAAGAAGAACA 59.708 57.895 0.00 0.00 0.00 3.18
664 1115 2.830370 CTTCTCCCCAATGGCGCC 60.830 66.667 22.73 22.73 0.00 6.53
665 1116 3.521796 GCTTCTCCCCAATGGCGC 61.522 66.667 0.00 0.00 0.00 6.53
666 1117 1.660560 CTTGCTTCTCCCCAATGGCG 61.661 60.000 0.00 0.00 0.00 5.69
667 1118 1.953231 GCTTGCTTCTCCCCAATGGC 61.953 60.000 0.00 0.00 0.00 4.40
668 1119 0.612732 TGCTTGCTTCTCCCCAATGG 60.613 55.000 0.00 0.00 0.00 3.16
669 1120 0.815734 CTGCTTGCTTCTCCCCAATG 59.184 55.000 0.00 0.00 0.00 2.82
670 1121 0.969409 GCTGCTTGCTTCTCCCCAAT 60.969 55.000 0.00 0.00 38.95 3.16
671 1122 1.604593 GCTGCTTGCTTCTCCCCAA 60.605 57.895 0.00 0.00 38.95 4.12
683 1134 1.126488 TATCTAGGCTGCTGCTGCTT 58.874 50.000 26.79 22.98 40.48 3.91
684 1135 1.350071 ATATCTAGGCTGCTGCTGCT 58.650 50.000 26.79 16.79 40.48 4.24
685 1136 2.615869 GTATATCTAGGCTGCTGCTGC 58.384 52.381 21.42 21.42 39.59 5.25
686 1137 2.873609 CGTATATCTAGGCTGCTGCTG 58.126 52.381 15.64 0.77 39.59 4.41
728 1179 0.805614 TTTCTCTCTCGCTCTCCGTG 59.194 55.000 0.00 0.00 38.35 4.94
731 1182 2.490115 TGTTCTTTCTCTCTCGCTCTCC 59.510 50.000 0.00 0.00 0.00 3.71
734 1185 3.249917 CCTTGTTCTTTCTCTCTCGCTC 58.750 50.000 0.00 0.00 0.00 5.03
736 1187 2.342179 CCCTTGTTCTTTCTCTCTCGC 58.658 52.381 0.00 0.00 0.00 5.03
737 1188 2.354203 CCCCCTTGTTCTTTCTCTCTCG 60.354 54.545 0.00 0.00 0.00 4.04
763 1220 1.615384 GGGGAGCAGCAATGGATATCC 60.615 57.143 15.39 15.39 0.00 2.59
764 1221 1.615384 GGGGGAGCAGCAATGGATATC 60.615 57.143 0.00 0.00 0.00 1.63
769 1226 2.123982 GAGGGGGAGCAGCAATGG 60.124 66.667 0.00 0.00 0.00 3.16
770 1227 2.123982 GGAGGGGGAGCAGCAATG 60.124 66.667 0.00 0.00 0.00 2.82
771 1228 2.220786 CTTGGAGGGGGAGCAGCAAT 62.221 60.000 0.00 0.00 0.00 3.56
772 1229 2.858476 TTGGAGGGGGAGCAGCAA 60.858 61.111 0.00 0.00 0.00 3.91
782 1239 1.403687 GGGACGGAGATCTTGGAGGG 61.404 65.000 0.00 0.00 0.00 4.30
797 1254 2.585153 GGGAGCTCGAAAGGGGAC 59.415 66.667 7.83 0.00 0.00 4.46
847 1304 2.664081 GCTCACCAGTCAGGGAGGG 61.664 68.421 0.00 0.00 43.89 4.30
887 1344 2.022718 CCTCCTATTCCTCTCCCAGG 57.977 60.000 0.00 0.00 45.15 4.45
911 1368 1.588403 CTGGAGAGATGCGCAGACG 60.588 63.158 18.32 0.00 44.07 4.18
913 1370 1.253593 ACACTGGAGAGATGCGCAGA 61.254 55.000 18.32 0.00 0.00 4.26
914 1371 0.805322 GACACTGGAGAGATGCGCAG 60.805 60.000 18.32 1.10 0.00 5.18
916 1373 1.875813 CGACACTGGAGAGATGCGC 60.876 63.158 0.00 0.00 0.00 6.09
917 1374 1.226802 CCGACACTGGAGAGATGCG 60.227 63.158 0.00 0.00 0.00 4.73
919 1376 1.468985 AGACCGACACTGGAGAGATG 58.531 55.000 0.00 0.00 0.00 2.90
920 1377 1.821753 CAAGACCGACACTGGAGAGAT 59.178 52.381 0.00 0.00 0.00 2.75
922 1379 0.244994 CCAAGACCGACACTGGAGAG 59.755 60.000 0.00 0.00 0.00 3.20
923 1380 0.469331 ACCAAGACCGACACTGGAGA 60.469 55.000 0.00 0.00 0.00 3.71
924 1381 0.393077 AACCAAGACCGACACTGGAG 59.607 55.000 0.00 0.00 0.00 3.86
925 1382 0.834612 AAACCAAGACCGACACTGGA 59.165 50.000 0.00 0.00 0.00 3.86
926 1383 1.226746 GAAACCAAGACCGACACTGG 58.773 55.000 0.00 0.00 0.00 4.00
927 1384 0.859232 CGAAACCAAGACCGACACTG 59.141 55.000 0.00 0.00 0.00 3.66
928 1385 0.878961 GCGAAACCAAGACCGACACT 60.879 55.000 0.00 0.00 0.00 3.55
929 1386 0.878961 AGCGAAACCAAGACCGACAC 60.879 55.000 0.00 0.00 0.00 3.67
930 1387 0.599204 GAGCGAAACCAAGACCGACA 60.599 55.000 0.00 0.00 0.00 4.35
931 1388 1.615107 CGAGCGAAACCAAGACCGAC 61.615 60.000 0.00 0.00 0.00 4.79
932 1389 1.372499 CGAGCGAAACCAAGACCGA 60.372 57.895 0.00 0.00 0.00 4.69
933 1390 3.011760 GCGAGCGAAACCAAGACCG 62.012 63.158 0.00 0.00 0.00 4.79
960 1417 2.157738 CTTCTTGCTCCCACTTCCTTG 58.842 52.381 0.00 0.00 0.00 3.61
961 1418 2.039613 CTCTTCTTGCTCCCACTTCCTT 59.960 50.000 0.00 0.00 0.00 3.36
973 1430 0.322975 TGCCCTCACTCTCTTCTTGC 59.677 55.000 0.00 0.00 0.00 4.01
982 1439 0.034670 ATCTTGCCTTGCCCTCACTC 60.035 55.000 0.00 0.00 0.00 3.51
985 1442 1.000521 CCATCTTGCCTTGCCCTCA 60.001 57.895 0.00 0.00 0.00 3.86
987 1444 2.363406 GCCATCTTGCCTTGCCCT 60.363 61.111 0.00 0.00 0.00 5.19
1189 1690 3.618690 TTGGTGTTTGGTGAAAAAGGG 57.381 42.857 0.00 0.00 0.00 3.95
1227 1728 7.360101 CGTTTGGGTTGTTAGTATTCAGAAGAG 60.360 40.741 0.00 0.00 0.00 2.85
1232 1733 4.379082 GCCGTTTGGGTTGTTAGTATTCAG 60.379 45.833 0.00 0.00 38.44 3.02
1234 1735 3.754850 AGCCGTTTGGGTTGTTAGTATTC 59.245 43.478 0.00 0.00 45.97 1.75
1235 1736 3.758425 AGCCGTTTGGGTTGTTAGTATT 58.242 40.909 0.00 0.00 45.97 1.89
1236 1737 3.428413 AGCCGTTTGGGTTGTTAGTAT 57.572 42.857 0.00 0.00 45.97 2.12
1237 1738 2.934886 AGCCGTTTGGGTTGTTAGTA 57.065 45.000 0.00 0.00 45.97 1.82
1331 1837 8.890410 ACAGTACTAGGAAAAGTAATAGTGGA 57.110 34.615 0.00 0.00 33.85 4.02
1337 1843 9.086758 ACACAGTACAGTACTAGGAAAAGTAAT 57.913 33.333 13.12 0.00 37.23 1.89
1369 1875 1.544724 ATGGTTGGAATTCGGTGTGG 58.455 50.000 0.00 0.00 0.00 4.17
1385 1891 2.476854 GCAACTTTCTGCTCGCTTATGG 60.477 50.000 0.00 0.00 39.34 2.74
1414 2050 2.554893 TCGGGTGCTTTATGTTTGGAAC 59.445 45.455 0.00 0.00 0.00 3.62
1416 2052 2.570415 TCGGGTGCTTTATGTTTGGA 57.430 45.000 0.00 0.00 0.00 3.53
1447 2083 9.770097 GAATTAGTCCATCAAGTGATAATGAGA 57.230 33.333 0.00 0.00 32.63 3.27
1448 2084 9.551734 TGAATTAGTCCATCAAGTGATAATGAG 57.448 33.333 0.00 0.00 32.63 2.90
1451 2087 9.293404 CCATGAATTAGTCCATCAAGTGATAAT 57.707 33.333 0.00 0.00 32.63 1.28
1452 2088 7.229306 GCCATGAATTAGTCCATCAAGTGATAA 59.771 37.037 0.00 0.00 32.63 1.75
1453 2089 6.712095 GCCATGAATTAGTCCATCAAGTGATA 59.288 38.462 0.00 0.00 32.63 2.15
1500 2136 2.224209 GGTTCCGGTGAGTCTTCTTCAA 60.224 50.000 0.00 0.00 0.00 2.69
1600 2236 4.468765 TTCAGAGCATTCAGAGAAGAGG 57.531 45.455 0.00 0.00 0.00 3.69
1635 2272 6.377327 TTCTACAGGAAAAACAGAGCAAAG 57.623 37.500 0.00 0.00 0.00 2.77
1650 2287 3.310774 CCGAGCAACATCATTTCTACAGG 59.689 47.826 0.00 0.00 0.00 4.00
1784 2421 0.250252 TGTGCTCGGTGCTCAATGAA 60.250 50.000 4.53 0.00 41.46 2.57
1804 2441 4.967271 TGCGCTTGCGAGTCAGCA 62.967 61.111 19.55 14.12 46.54 4.41
1805 2442 3.716006 TTGCGCTTGCGAGTCAGC 61.716 61.111 19.55 7.01 43.34 4.26
1911 2551 2.548493 GCATTCCAAGGAAGCTTTGCAA 60.548 45.455 16.32 0.00 36.78 4.08
1932 2576 6.223120 CAAAGGATTCCCAAACAAGTTTAGG 58.777 40.000 4.09 4.09 33.51 2.69
1943 2587 3.172339 CAATCACCCAAAGGATTCCCAA 58.828 45.455 0.00 0.00 36.73 4.12
2067 2712 3.303725 GCAACATCGTCAAGCAACTGTAA 60.304 43.478 0.00 0.00 0.00 2.41
2163 2809 2.053865 AAGCCCACATTCATGCCCG 61.054 57.895 0.00 0.00 0.00 6.13
2231 2878 7.600375 TCGTGATTATCTCTAAATGCTTCATCC 59.400 37.037 0.00 0.00 0.00 3.51
2349 3008 2.344950 AGCTCACAGATCTTCTTTGCG 58.655 47.619 0.00 0.00 0.00 4.85
2503 3162 6.366340 TCTTCCTAACCAAACCATGTAACAA 58.634 36.000 0.00 0.00 0.00 2.83
2666 3329 7.702348 GGTGTATTTGATGCATTAGAAGGTTTC 59.298 37.037 0.00 0.00 0.00 2.78
2676 3339 4.782019 ACAACGGTGTATTTGATGCATT 57.218 36.364 2.99 0.00 35.72 3.56
2720 3383 4.554723 GCACCAATAACACGAGGATATTGC 60.555 45.833 12.12 3.00 36.27 3.56
2730 3393 1.234821 ACAGTGGCACCAATAACACG 58.765 50.000 15.27 0.00 38.78 4.49
2768 3431 4.785376 AGGAACTGTCAGATGGAGGTTAAT 59.215 41.667 6.91 0.00 37.18 1.40
2785 3448 8.429641 TGTTACAGACAAATTAGAAGAGGAACT 58.570 33.333 0.00 0.00 36.82 3.01
2803 3466 4.112634 GCATACGCAATCTCTGTTACAGA 58.887 43.478 14.77 14.77 36.72 3.41
3045 3708 1.337074 ACAGATTGGCCAAATTGTGCG 60.337 47.619 27.74 14.29 0.00 5.34
3057 3720 0.443869 CGGCTCGAACAACAGATTGG 59.556 55.000 0.00 0.00 40.42 3.16
3075 3738 3.372954 CTTGCGAAGGATAAGGTAGTCG 58.627 50.000 0.00 0.00 0.00 4.18
3225 3890 9.901724 GTGTGTGACTAATAAATATCAAGTTCG 57.098 33.333 0.00 0.00 0.00 3.95
3317 3982 3.511540 CCTCTTCCATGGAGCGTATCATA 59.488 47.826 15.53 0.00 0.00 2.15
3329 3994 5.157940 TCTTCTCAAACTCCTCTTCCATG 57.842 43.478 0.00 0.00 0.00 3.66
3538 4209 7.283127 AGCAGAAATATATCGCTGGAAGAAAAA 59.717 33.333 13.56 0.00 34.07 1.94
3678 4370 5.596763 TGAGGGGAAACTACCTACATTACT 58.403 41.667 0.00 0.00 37.18 2.24
3927 4621 5.048083 GGGAGTGTCATTTGAGCACATTAAA 60.048 40.000 12.52 0.00 35.75 1.52
4105 4832 3.435275 ACTCCTCATGACACTTCTAGCA 58.565 45.455 0.00 0.00 0.00 3.49
4107 4834 6.925211 TGTTAACTCCTCATGACACTTCTAG 58.075 40.000 7.22 0.00 0.00 2.43
4116 4843 7.015292 GGATACAGGTATGTTAACTCCTCATGA 59.985 40.741 7.22 0.00 41.01 3.07
4196 4923 0.466555 ACAAGGCGGCAGTAAACCAA 60.467 50.000 13.08 0.00 0.00 3.67
4225 4952 2.590821 AGCTTGTCCAAACTGCTTCAT 58.409 42.857 0.00 0.00 34.09 2.57
4226 4953 2.057137 AGCTTGTCCAAACTGCTTCA 57.943 45.000 0.00 0.00 34.09 3.02
4227 4954 3.142174 AGTAGCTTGTCCAAACTGCTTC 58.858 45.455 0.00 0.00 37.22 3.86
4228 4955 3.214696 AGTAGCTTGTCCAAACTGCTT 57.785 42.857 0.00 0.00 37.22 3.91
4238 4965 6.610456 ACGAGAAACTAAGTAGTAGCTTGTC 58.390 40.000 0.00 0.69 32.96 3.18
4240 4967 6.862090 ACAACGAGAAACTAAGTAGTAGCTTG 59.138 38.462 0.00 0.08 34.99 4.01
4278 5008 8.216423 GGCTTATATCATAATGAGGGACATGAT 58.784 37.037 0.00 0.00 39.39 2.45
4281 5011 7.037370 TGTGGCTTATATCATAATGAGGGACAT 60.037 37.037 0.00 0.00 41.45 3.06
4285 5015 8.051535 AGATTGTGGCTTATATCATAATGAGGG 58.948 37.037 0.00 0.00 0.00 4.30
4337 5067 2.987149 CAACGTACTGTAACTGCAGAGG 59.013 50.000 23.35 3.99 39.62 3.69
4361 5091 2.897855 CGTGACAAGCGCATAAACG 58.102 52.632 11.47 9.27 0.00 3.60
4464 5198 3.679389 GTGGAACTATATGCATCCCCAG 58.321 50.000 0.19 0.00 0.00 4.45
4478 5212 1.070758 AGCAGATGTGAACGTGGAACT 59.929 47.619 0.00 0.00 31.75 3.01
4536 5270 2.424246 TCTGTATGTTGTCGTATCGGCA 59.576 45.455 0.00 0.00 40.58 5.69
4538 5272 3.981416 CCATCTGTATGTTGTCGTATCGG 59.019 47.826 0.00 0.00 0.00 4.18
4539 5273 3.981416 CCCATCTGTATGTTGTCGTATCG 59.019 47.826 0.00 0.00 0.00 2.92
4540 5274 5.196341 TCCCATCTGTATGTTGTCGTATC 57.804 43.478 0.00 0.00 0.00 2.24
4541 5275 5.304357 TGATCCCATCTGTATGTTGTCGTAT 59.696 40.000 0.00 0.00 0.00 3.06
4542 5276 4.647399 TGATCCCATCTGTATGTTGTCGTA 59.353 41.667 0.00 0.00 0.00 3.43
4543 5277 3.450817 TGATCCCATCTGTATGTTGTCGT 59.549 43.478 0.00 0.00 0.00 4.34
4544 5278 4.058721 TGATCCCATCTGTATGTTGTCG 57.941 45.455 0.00 0.00 0.00 4.35
4545 5279 5.882557 ACTTTGATCCCATCTGTATGTTGTC 59.117 40.000 0.00 0.00 0.00 3.18
4546 5280 5.819991 ACTTTGATCCCATCTGTATGTTGT 58.180 37.500 0.00 0.00 0.00 3.32
4547 5281 6.823182 TGTACTTTGATCCCATCTGTATGTTG 59.177 38.462 0.00 0.00 0.00 3.33
4548 5282 6.957631 TGTACTTTGATCCCATCTGTATGTT 58.042 36.000 0.00 0.00 0.00 2.71
4549 5283 6.560003 TGTACTTTGATCCCATCTGTATGT 57.440 37.500 0.00 0.00 0.00 2.29
4550 5284 7.467811 GCTTTGTACTTTGATCCCATCTGTATG 60.468 40.741 0.00 0.00 0.00 2.39
4551 5285 6.543831 GCTTTGTACTTTGATCCCATCTGTAT 59.456 38.462 0.00 0.00 0.00 2.29
4552 5286 5.880332 GCTTTGTACTTTGATCCCATCTGTA 59.120 40.000 0.00 0.00 0.00 2.74
4577 5311 2.124570 CTGTTGGGGATCAGGGCG 60.125 66.667 0.00 0.00 0.00 6.13
4673 5407 2.740055 GTGCTGGTCTCTGTGCGG 60.740 66.667 0.00 0.00 0.00 5.69
4676 5410 1.665916 CACGGTGCTGGTCTCTGTG 60.666 63.158 0.00 0.00 38.65 3.66
4679 5413 2.737180 CACACGGTGCTGGTCTCT 59.263 61.111 8.30 0.00 0.00 3.10
4746 5480 1.485294 AACCTGGGTGTCGTGGCATA 61.485 55.000 0.00 0.00 0.00 3.14
4778 5512 1.880340 GGGACGCAGCTCGATCTTG 60.880 63.158 11.64 0.00 41.67 3.02
4816 5550 4.864334 GCATGCCCTGTCCCGGAG 62.864 72.222 6.36 0.00 0.00 4.63
4820 5554 2.757099 CTTGGCATGCCCTGTCCC 60.757 66.667 33.44 7.62 34.56 4.46
4821 5555 3.455469 GCTTGGCATGCCCTGTCC 61.455 66.667 33.44 13.57 34.56 4.02
4822 5556 3.455469 GGCTTGGCATGCCCTGTC 61.455 66.667 33.44 22.82 44.32 3.51
4835 5569 1.079127 CGTCGGAAGATGGTGGCTT 60.079 57.895 0.00 0.00 45.19 4.35
4960 5694 3.222354 GACCTTGAGACGCCACGGT 62.222 63.158 1.76 1.76 40.79 4.83
4964 5698 2.343758 GCTGACCTTGAGACGCCA 59.656 61.111 0.00 0.00 0.00 5.69
4971 5705 1.446099 GCATCGACGCTGACCTTGA 60.446 57.895 2.28 0.00 0.00 3.02
4972 5706 2.456119 GGCATCGACGCTGACCTTG 61.456 63.158 2.49 0.00 0.00 3.61
4997 5731 1.725641 CTATCGTTGCCACAGAAGCA 58.274 50.000 0.00 0.00 38.81 3.91
5046 5780 1.874019 CGTCATCGTTGAGCCGAGG 60.874 63.158 0.00 0.00 40.68 4.63
5056 5790 0.601046 CTATGCATGGGCGTCATCGT 60.601 55.000 10.16 0.00 45.35 3.73
5063 5797 1.146930 AGTGTCCTATGCATGGGCG 59.853 57.895 23.60 2.01 45.35 6.13
5101 5838 6.380560 AGTCATCATCGTCATCATCATCCTAT 59.619 38.462 0.00 0.00 0.00 2.57
5115 5852 5.588958 TTTCTCTCATCAGTCATCATCGT 57.411 39.130 0.00 0.00 0.00 3.73
5122 5860 5.423290 TCCTAGCATTTTCTCTCATCAGTCA 59.577 40.000 0.00 0.00 0.00 3.41
5129 5867 8.198807 TGATATGATCCTAGCATTTTCTCTCA 57.801 34.615 0.00 0.00 0.00 3.27
5228 5966 7.433680 TGATGACACGCACTAGTATAATTGAT 58.566 34.615 0.00 0.00 0.00 2.57
5232 5970 6.635030 TCTGATGACACGCACTAGTATAAT 57.365 37.500 0.00 0.00 0.00 1.28
5233 5971 6.095021 AGTTCTGATGACACGCACTAGTATAA 59.905 38.462 0.00 0.00 0.00 0.98
5262 6000 5.549742 TCCTTTAAACCAAACCGTCTCTA 57.450 39.130 0.00 0.00 0.00 2.43
5263 6001 4.426736 TCCTTTAAACCAAACCGTCTCT 57.573 40.909 0.00 0.00 0.00 3.10
5264 6002 5.700722 ATTCCTTTAAACCAAACCGTCTC 57.299 39.130 0.00 0.00 0.00 3.36
5265 6003 6.097129 TGAAATTCCTTTAAACCAAACCGTCT 59.903 34.615 0.00 0.00 0.00 4.18
5296 6034 6.484977 GCTGGGATTAACTTTCCTCTATGAAG 59.515 42.308 0.00 0.00 33.53 3.02
5299 6037 4.752101 CGCTGGGATTAACTTTCCTCTATG 59.248 45.833 0.00 0.00 33.53 2.23
5426 6164 3.573967 CACAAAAATCTTGGTAGCCCACT 59.426 43.478 0.00 0.00 41.67 4.00
5514 6252 3.862267 AGATGTTCGATCGCTCAAAAGAG 59.138 43.478 11.09 0.00 0.00 2.85
5516 6254 4.328440 AGAAGATGTTCGATCGCTCAAAAG 59.672 41.667 11.09 0.00 37.79 2.27
5518 6256 3.849911 AGAAGATGTTCGATCGCTCAAA 58.150 40.909 11.09 0.00 37.79 2.69
5562 6301 5.489792 TGTTTAGAGAGAAATGCTGACCT 57.510 39.130 0.00 0.00 0.00 3.85
5563 6302 5.470098 TGTTGTTTAGAGAGAAATGCTGACC 59.530 40.000 0.00 0.00 0.00 4.02
5564 6303 6.545504 TGTTGTTTAGAGAGAAATGCTGAC 57.454 37.500 0.00 0.00 0.00 3.51
5646 6396 0.961019 AGTTACACTTGCGTCCGGTA 59.039 50.000 0.00 0.00 0.00 4.02
5650 6400 6.890558 TGTAATTTTAGTTACACTTGCGTCC 58.109 36.000 0.00 0.00 39.08 4.79
5651 6401 8.277713 TCTTGTAATTTTAGTTACACTTGCGTC 58.722 33.333 0.00 0.00 42.49 5.19
5652 6402 8.066000 GTCTTGTAATTTTAGTTACACTTGCGT 58.934 33.333 0.00 0.00 42.49 5.24
6013 6765 9.831737 AATTCTTTTACTGAAATCAGACATTCG 57.168 29.630 16.93 1.80 46.59 3.34
6056 6808 0.463833 CTGAAATACCGTGGGGGCTC 60.464 60.000 0.00 0.00 40.62 4.70


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

AutoCloner maintained by Alex Coulton.