Multiple sequence alignment - TraesCS4D01G086100

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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 TraesCS4D01G086100 chr4D 100.000 4106 0 0 1 4106 61595940 61591835 0.000000e+00 7583.0
1 TraesCS4D01G086100 chr4D 100.000 32 0 0 3529 3560 381882629 381882598 4.430000e-05 60.2
2 TraesCS4D01G086100 chr4B 92.707 2756 129 34 597 3334 91327060 91329761 0.000000e+00 3910.0
3 TraesCS4D01G086100 chr4B 91.803 1098 40 17 371 1466 91190110 91191159 0.000000e+00 1483.0
4 TraesCS4D01G086100 chr4B 97.379 725 18 1 1488 2212 91227971 91228694 0.000000e+00 1232.0
5 TraesCS4D01G086100 chr4B 96.175 549 18 3 3559 4106 91329986 91330532 0.000000e+00 894.0
6 TraesCS4D01G086100 chr4B 89.105 257 16 3 370 618 91326511 91326763 3.990000e-80 309.0
7 TraesCS4D01G086100 chr4B 95.706 163 4 2 3341 3500 91329825 91329987 4.070000e-65 259.0
8 TraesCS4D01G086100 chr4B 87.805 82 5 5 2461 2541 91228880 91228957 1.570000e-14 91.6
9 TraesCS4D01G086100 chr4B 100.000 34 0 0 3529 3562 670403282 670403249 3.430000e-06 63.9
10 TraesCS4D01G086100 chr4A 91.088 1728 85 32 815 2515 534792142 534790457 0.000000e+00 2274.0
11 TraesCS4D01G086100 chr4A 95.993 549 20 2 3559 4106 534789448 534788901 0.000000e+00 891.0
12 TraesCS4D01G086100 chr4A 88.215 577 48 4 2552 3125 534790458 534789899 0.000000e+00 671.0
13 TraesCS4D01G086100 chr4A 91.691 337 22 4 83 413 534792914 534792578 2.890000e-126 462.0
14 TraesCS4D01G086100 chr4A 97.546 163 1 2 3341 3500 534789609 534789447 4.040000e-70 276.0
15 TraesCS4D01G086100 chr4A 88.128 219 10 3 3114 3331 534789880 534789677 3.170000e-61 246.0
16 TraesCS4D01G086100 chr6D 93.714 175 11 0 1824 1998 358216793 358216619 3.150000e-66 263.0
17 TraesCS4D01G086100 chr6D 96.078 51 2 0 3 53 386176456 386176406 2.630000e-12 84.2
18 TraesCS4D01G086100 chrUn 93.567 171 11 0 1828 1998 209272496 209272326 5.270000e-64 255.0
19 TraesCS4D01G086100 chrUn 100.000 33 0 0 3528 3560 63534385 63534417 1.230000e-05 62.1
20 TraesCS4D01G086100 chr7B 93.567 171 11 0 1828 1998 642232629 642232459 5.270000e-64 255.0
21 TraesCS4D01G086100 chr7B 100.000 32 0 0 3529 3560 334774331 334774362 4.430000e-05 60.2
22 TraesCS4D01G086100 chr5D 98.113 53 1 0 1 53 540829043 540828991 4.370000e-15 93.5
23 TraesCS4D01G086100 chr5D 98.039 51 1 0 3 53 25300020 25299970 5.650000e-14 89.8
24 TraesCS4D01G086100 chr5D 100.000 29 0 0 3493 3521 538166863 538166835 2.000000e-03 54.7
25 TraesCS4D01G086100 chr3A 98.000 50 1 0 5 54 427203346 427203297 2.030000e-13 87.9
26 TraesCS4D01G086100 chr3A 89.706 68 4 2 3495 3561 67912114 67912179 2.630000e-12 84.2
27 TraesCS4D01G086100 chr7A 96.078 51 2 0 3 53 70750534 70750484 2.630000e-12 84.2
28 TraesCS4D01G086100 chr6A 96.078 51 2 0 3 53 101542602 101542552 2.630000e-12 84.2
29 TraesCS4D01G086100 chr6A 100.000 30 0 0 3492 3521 27342888 27342917 5.730000e-04 56.5
30 TraesCS4D01G086100 chr2A 96.078 51 2 0 3 53 392998738 392998788 2.630000e-12 84.2
31 TraesCS4D01G086100 chr2A 83.333 84 3 5 3489 3562 215751195 215751277 2.650000e-07 67.6
32 TraesCS4D01G086100 chr1B 95.918 49 2 0 3 51 313485296 313485344 3.400000e-11 80.5
33 TraesCS4D01G086100 chr1B 100.000 32 0 0 3529 3560 465681347 465681316 4.430000e-05 60.2
34 TraesCS4D01G086100 chr1B 100.000 28 0 0 3494 3521 292204985 292204958 7.000000e-03 52.8
35 TraesCS4D01G086100 chr1A 93.878 49 3 0 5 53 529649296 529649344 1.580000e-09 75.0
36 TraesCS4D01G086100 chr1A 92.105 38 2 1 3485 3521 480430739 480430702 7.000000e-03 52.8
37 TraesCS4D01G086100 chr1D 100.000 32 0 0 3529 3560 348128555 348128524 4.430000e-05 60.2
38 TraesCS4D01G086100 chr2D 94.737 38 0 2 3528 3563 88085357 88085394 1.590000e-04 58.4
39 TraesCS4D01G086100 chr6B 96.875 32 1 0 3491 3522 277158933 277158964 2.000000e-03 54.7
40 TraesCS4D01G086100 chr3B 96.970 33 0 1 3489 3521 623657657 623657626 2.000000e-03 54.7
41 TraesCS4D01G086100 chr3D 100.000 28 0 0 3494 3521 446429887 446429860 7.000000e-03 52.8
42 TraesCS4D01G086100 chr2B 96.875 32 0 1 3490 3521 488199258 488199288 7.000000e-03 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 TraesCS4D01G086100 chr4D 61591835 61595940 4105 True 7583.000000 7583 100.000000 1 4106 1 chr4D.!!$R1 4105
1 TraesCS4D01G086100 chr4B 91190110 91191159 1049 False 1483.000000 1483 91.803000 371 1466 1 chr4B.!!$F1 1095
2 TraesCS4D01G086100 chr4B 91326511 91330532 4021 False 1343.000000 3910 93.423250 370 4106 4 chr4B.!!$F3 3736
3 TraesCS4D01G086100 chr4B 91227971 91228957 986 False 661.800000 1232 92.592000 1488 2541 2 chr4B.!!$F2 1053
4 TraesCS4D01G086100 chr4A 534788901 534792914 4013 True 803.333333 2274 92.110167 83 4106 6 chr4A.!!$R1 4023

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
48 49 0.158928 GTGTTTTCGCGAGAGTCACG 59.841 55.0 9.59 5.53 43.69 4.35 F
49 50 0.937699 TGTTTTCGCGAGAGTCACGG 60.938 55.0 9.59 2.55 43.69 4.94 F
276 283 0.949105 GAGAGAAAAACCGCGCTCCA 60.949 55.0 5.56 0.00 0.00 3.86 F
843 1246 0.951558 AGACACACGGTTTGGATTGC 59.048 50.0 0.00 0.00 0.00 3.56 F
1476 1901 0.324614 TCACCGTGATGCTGTTCCAT 59.675 50.0 0.00 0.00 0.00 3.41 F
2218 2680 0.525882 GCCGGCGACTACTCTTTCTC 60.526 60.0 12.58 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1464 0.608035 GACGCCATGGACCTTGGAAA 60.608 55.000 26.72 0.0 36.26 3.13 R
1043 1465 1.002624 GACGCCATGGACCTTGGAA 60.003 57.895 26.72 0.0 36.26 3.53 R
1183 1605 1.499049 GCAACGGAATCCTCGGATAC 58.501 55.000 0.00 0.0 33.97 2.24 R
2598 3107 0.096108 GCGCTCAAAGTAGCAGAAGC 59.904 55.000 0.00 0.0 42.91 3.86 R
2737 3246 0.110644 GTTGTTCGAGCTGCGGAAAG 60.111 55.000 10.05 0.0 41.33 2.62 R
3325 3864 0.680921 GGAAGCACAAGCATAGCCCA 60.681 55.000 0.00 0.0 45.49 5.36 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 4.073052 ATGGTTTTGCTTCCGCGA 57.927 50.000 8.23 0.00 39.65 5.87
18 19 2.336341 ATGGTTTTGCTTCCGCGAA 58.664 47.368 8.23 0.00 39.65 4.70
19 20 0.671251 ATGGTTTTGCTTCCGCGAAA 59.329 45.000 8.23 0.00 45.01 3.46
22 23 1.007849 TTTTGCTTCCGCGAAAGGC 60.008 52.632 8.23 8.27 42.97 4.35
23 24 1.729470 TTTTGCTTCCGCGAAAGGCA 61.729 50.000 8.23 11.21 42.97 4.75
24 25 2.400896 TTTGCTTCCGCGAAAGGCAC 62.401 55.000 8.23 0.00 43.84 5.01
25 26 4.445545 GCTTCCGCGAAAGGCACG 62.446 66.667 8.23 0.00 43.84 5.34
26 27 2.736995 CTTCCGCGAAAGGCACGA 60.737 61.111 8.23 0.00 43.84 4.35
27 28 2.047655 TTCCGCGAAAGGCACGAT 60.048 55.556 8.23 0.00 43.84 3.73
28 29 1.635663 CTTCCGCGAAAGGCACGATT 61.636 55.000 8.23 0.00 43.84 3.34
29 30 1.906994 TTCCGCGAAAGGCACGATTG 61.907 55.000 8.23 0.00 43.84 2.67
30 31 2.677003 CCGCGAAAGGCACGATTGT 61.677 57.895 8.23 0.00 43.84 2.71
40 41 3.719588 CACGATTGTGTTTTCGCGA 57.280 47.368 3.71 3.71 41.34 5.87
41 42 1.580439 CACGATTGTGTTTTCGCGAG 58.420 50.000 9.59 0.00 41.34 5.03
42 43 1.191425 CACGATTGTGTTTTCGCGAGA 59.809 47.619 9.59 0.43 41.34 4.04
43 44 1.455786 ACGATTGTGTTTTCGCGAGAG 59.544 47.619 9.59 0.00 43.69 3.20
44 45 1.455786 CGATTGTGTTTTCGCGAGAGT 59.544 47.619 9.59 0.00 43.69 3.24
45 46 2.470781 CGATTGTGTTTTCGCGAGAGTC 60.471 50.000 9.59 2.93 43.69 3.36
46 47 1.929230 TTGTGTTTTCGCGAGAGTCA 58.071 45.000 9.59 5.72 43.69 3.41
47 48 1.205657 TGTGTTTTCGCGAGAGTCAC 58.794 50.000 21.10 21.10 43.69 3.67
48 49 0.158928 GTGTTTTCGCGAGAGTCACG 59.841 55.000 9.59 5.53 43.69 4.35
49 50 0.937699 TGTTTTCGCGAGAGTCACGG 60.938 55.000 9.59 2.55 43.69 4.94
50 51 2.019951 TTTTCGCGAGAGTCACGGC 61.020 57.895 9.59 3.61 43.69 5.68
51 52 3.909258 TTTCGCGAGAGTCACGGCC 62.909 63.158 9.59 0.00 43.69 6.13
55 56 4.717629 CGAGAGTCACGGCCGCAA 62.718 66.667 28.58 11.20 0.00 4.85
56 57 2.811317 GAGAGTCACGGCCGCAAG 60.811 66.667 28.58 16.28 0.00 4.01
101 102 4.888038 AGAAACCGGTAAAGAAACACAC 57.112 40.909 8.00 0.00 0.00 3.82
104 105 4.625972 AACCGGTAAAGAAACACACAAG 57.374 40.909 8.00 0.00 0.00 3.16
106 107 4.263435 ACCGGTAAAGAAACACACAAGAA 58.737 39.130 4.49 0.00 0.00 2.52
107 108 4.701171 ACCGGTAAAGAAACACACAAGAAA 59.299 37.500 4.49 0.00 0.00 2.52
110 117 6.034150 CCGGTAAAGAAACACACAAGAAAAAC 59.966 38.462 0.00 0.00 0.00 2.43
113 120 8.766151 GGTAAAGAAACACACAAGAAAAACAAA 58.234 29.630 0.00 0.00 0.00 2.83
140 147 6.720012 AACATTGAAAACCAACACAGAAAC 57.280 33.333 0.00 0.00 37.63 2.78
148 155 3.436243 ACCAACACAGAAACCCAAAAGA 58.564 40.909 0.00 0.00 0.00 2.52
182 189 4.775253 ACTGAGAAAACCAAAGAAAACCCA 59.225 37.500 0.00 0.00 0.00 4.51
203 210 7.830739 ACCCAATAAAGAAACATAGAAAGCTG 58.169 34.615 0.00 0.00 0.00 4.24
237 244 6.183360 GCAAGAAAAACCAATGAAACCAACAT 60.183 34.615 0.00 0.00 0.00 2.71
250 257 6.126409 TGAAACCAACATAGAAAACAGACCT 58.874 36.000 0.00 0.00 0.00 3.85
267 274 7.971183 ACAGACCTAAGAATGAGAGAAAAAC 57.029 36.000 0.00 0.00 0.00 2.43
276 283 0.949105 GAGAGAAAAACCGCGCTCCA 60.949 55.000 5.56 0.00 0.00 3.86
279 286 2.903547 GAAAAACCGCGCTCCAGCA 61.904 57.895 5.56 0.00 42.21 4.41
281 288 1.805428 AAAAACCGCGCTCCAGCAAT 61.805 50.000 5.56 0.00 42.21 3.56
291 298 3.064545 GCGCTCCAGCAATAATCCATATC 59.935 47.826 0.00 0.00 42.21 1.63
302 309 3.314331 CCATATCGGGCCGGCTCT 61.314 66.667 26.87 9.45 0.00 4.09
335 342 1.128188 ACCTTTGGGCGAGAGGAAGT 61.128 55.000 13.11 0.00 34.61 3.01
641 1041 9.381027 GAAGTCCTTTTTCTGTTTTTGTTTTTG 57.619 29.630 0.00 0.00 0.00 2.44
731 1134 5.831103 ACCCACCAGATCTTCATTGTATTT 58.169 37.500 0.00 0.00 0.00 1.40
814 1217 1.860950 CGCATGCACGAAGCTTATAGT 59.139 47.619 19.57 0.00 45.94 2.12
815 1218 3.049912 CGCATGCACGAAGCTTATAGTA 58.950 45.455 19.57 0.00 45.94 1.82
816 1219 3.120286 CGCATGCACGAAGCTTATAGTAG 59.880 47.826 19.57 0.00 45.94 2.57
817 1220 4.051922 GCATGCACGAAGCTTATAGTAGT 58.948 43.478 14.21 0.00 45.94 2.73
843 1246 0.951558 AGACACACGGTTTGGATTGC 59.048 50.000 0.00 0.00 0.00 3.56
893 1296 2.352960 GTCCGATTCCTGAACAGATTGC 59.647 50.000 3.19 0.00 0.00 3.56
895 1298 2.002586 CGATTCCTGAACAGATTGCGT 58.997 47.619 3.19 0.00 0.00 5.24
896 1299 2.029728 CGATTCCTGAACAGATTGCGTC 59.970 50.000 3.19 0.00 0.00 5.19
897 1300 2.542020 TTCCTGAACAGATTGCGTCA 57.458 45.000 3.19 0.00 0.00 4.35
898 1301 2.768253 TCCTGAACAGATTGCGTCAT 57.232 45.000 3.19 0.00 0.00 3.06
899 1302 2.349590 TCCTGAACAGATTGCGTCATG 58.650 47.619 3.19 0.00 0.00 3.07
900 1303 2.079158 CCTGAACAGATTGCGTCATGT 58.921 47.619 3.19 0.00 0.00 3.21
907 1310 1.470098 AGATTGCGTCATGTTTCCAGC 59.530 47.619 0.00 0.00 0.00 4.85
923 1333 2.815211 GCGCCGACTGCAGATCAA 60.815 61.111 23.35 0.00 41.33 2.57
938 1348 4.691175 CAGATCAATCTCGGTCTGATGTT 58.309 43.478 0.00 0.00 40.30 2.71
997 1418 1.006102 ACAAGCTCGAACCCGTCAG 60.006 57.895 0.00 0.00 37.05 3.51
1034 1456 2.278206 CTCACCTCGCGTGGATCG 60.278 66.667 32.11 19.19 43.23 3.69
1198 1620 1.666311 GCGAAGTATCCGAGGATTCCG 60.666 57.143 10.19 9.58 36.17 4.30
1199 1621 1.607628 CGAAGTATCCGAGGATTCCGT 59.392 52.381 10.19 0.33 36.17 4.69
1200 1622 2.034305 CGAAGTATCCGAGGATTCCGTT 59.966 50.000 10.19 0.00 36.17 4.44
1201 1623 3.381949 GAAGTATCCGAGGATTCCGTTG 58.618 50.000 10.19 0.00 36.17 4.10
1255 1677 1.615107 CCGAACGGAAGCACGAGAAC 61.615 60.000 7.53 0.00 37.50 3.01
1476 1901 0.324614 TCACCGTGATGCTGTTCCAT 59.675 50.000 0.00 0.00 0.00 3.41
1582 2007 2.142220 TGGTTCGCCAAGAGGTTCT 58.858 52.632 0.00 0.00 45.88 3.01
1698 2123 0.544357 TCAAGAGGGAAGGGCTCGAA 60.544 55.000 0.00 0.00 0.00 3.71
2212 2674 2.327244 CGTAGCCGGCGACTACTC 59.673 66.667 32.50 10.77 38.27 2.59
2213 2675 2.178890 CGTAGCCGGCGACTACTCT 61.179 63.158 32.50 11.79 38.27 3.24
2216 2678 0.737219 TAGCCGGCGACTACTCTTTC 59.263 55.000 23.20 0.00 0.00 2.62
2218 2680 0.525882 GCCGGCGACTACTCTTTCTC 60.526 60.000 12.58 0.00 0.00 2.87
2219 2681 1.096416 CCGGCGACTACTCTTTCTCT 58.904 55.000 9.30 0.00 0.00 3.10
2220 2682 1.473278 CCGGCGACTACTCTTTCTCTT 59.527 52.381 9.30 0.00 0.00 2.85
2221 2683 2.478200 CCGGCGACTACTCTTTCTCTTC 60.478 54.545 9.30 0.00 0.00 2.87
2222 2684 2.420722 CGGCGACTACTCTTTCTCTTCT 59.579 50.000 0.00 0.00 0.00 2.85
2223 2685 3.486209 CGGCGACTACTCTTTCTCTTCTC 60.486 52.174 0.00 0.00 0.00 2.87
2232 2694 8.643324 ACTACTCTTTCTCTTCTCTTTTTGCTA 58.357 33.333 0.00 0.00 0.00 3.49
2233 2695 9.651913 CTACTCTTTCTCTTCTCTTTTTGCTAT 57.348 33.333 0.00 0.00 0.00 2.97
2252 2714 6.219473 TGCTATGAATCAGTAGCTAGCTTTC 58.781 40.000 24.88 19.52 42.86 2.62
2267 2737 7.782049 AGCTAGCTTTCAAGTGTACATACATA 58.218 34.615 12.68 0.00 38.63 2.29
2292 2785 6.534475 AATGCCTTGTACATCATCACAAAT 57.466 33.333 0.00 0.00 34.43 2.32
2362 2855 4.483476 ACAGAAAGTTGCGACAATAACC 57.517 40.909 6.90 0.00 0.00 2.85
2445 2954 7.224297 AGAAACAATGCACTAGAAACCTAGAA 58.776 34.615 0.00 0.00 37.61 2.10
2453 2962 5.293079 GCACTAGAAACCTAGAATGAGCTTG 59.707 44.000 0.00 0.00 37.61 4.01
2461 2970 5.809001 ACCTAGAATGAGCTTGTTCAATCA 58.191 37.500 12.70 0.00 30.95 2.57
2506 3015 4.343526 ACACTGGGCACATCAAAATGTTTA 59.656 37.500 0.00 0.00 43.74 2.01
2507 3016 4.685628 CACTGGGCACATCAAAATGTTTAC 59.314 41.667 0.00 0.00 43.74 2.01
2530 3039 6.745116 ACTAAACAATACAAAGAAGGGTTGC 58.255 36.000 0.00 0.00 0.00 4.17
2531 3040 5.606348 AAACAATACAAAGAAGGGTTGCA 57.394 34.783 0.00 0.00 0.00 4.08
2532 3041 5.806654 AACAATACAAAGAAGGGTTGCAT 57.193 34.783 0.00 0.00 0.00 3.96
2533 3042 5.806654 ACAATACAAAGAAGGGTTGCATT 57.193 34.783 0.00 0.00 0.00 3.56
2534 3043 5.540911 ACAATACAAAGAAGGGTTGCATTG 58.459 37.500 8.03 8.03 42.02 2.82
2538 3047 3.181476 ACAAAGAAGGGTTGCATTGACAC 60.181 43.478 0.00 0.00 0.00 3.67
2540 3049 2.665165 AGAAGGGTTGCATTGACACAA 58.335 42.857 0.00 0.00 0.00 3.33
2541 3050 2.362077 AGAAGGGTTGCATTGACACAAC 59.638 45.455 0.00 0.00 44.29 3.32
2542 3051 0.667993 AGGGTTGCATTGACACAACG 59.332 50.000 0.00 0.00 45.62 4.10
2543 3052 0.665835 GGGTTGCATTGACACAACGA 59.334 50.000 0.00 0.00 45.62 3.85
2544 3053 1.066303 GGGTTGCATTGACACAACGAA 59.934 47.619 0.00 0.00 45.62 3.85
2558 3067 4.208355 CACAACGAAGGTGTAAACAATCG 58.792 43.478 7.85 7.85 35.90 3.34
2563 3072 5.717119 ACGAAGGTGTAAACAATCGACTAT 58.283 37.500 14.46 0.00 34.74 2.12
2568 3077 6.708285 AGGTGTAAACAATCGACTATCCTTT 58.292 36.000 0.00 0.00 0.00 3.11
2569 3078 6.594159 AGGTGTAAACAATCGACTATCCTTTG 59.406 38.462 0.00 0.00 0.00 2.77
2570 3079 6.248631 GTGTAAACAATCGACTATCCTTTGC 58.751 40.000 0.00 0.00 0.00 3.68
2585 3094 8.641541 ACTATCCTTTGCTTTTCTGAAATTTGA 58.358 29.630 3.31 0.00 0.00 2.69
2586 3095 7.958053 ATCCTTTGCTTTTCTGAAATTTGAG 57.042 32.000 3.31 0.00 0.00 3.02
2592 3101 5.128499 TGCTTTTCTGAAATTTGAGTTCCCA 59.872 36.000 3.31 0.00 0.00 4.37
2595 3104 5.627499 TTCTGAAATTTGAGTTCCCATCG 57.373 39.130 4.52 0.00 0.00 3.84
2597 3106 5.500234 TCTGAAATTTGAGTTCCCATCGAT 58.500 37.500 4.52 0.00 0.00 3.59
2598 3107 5.355071 TCTGAAATTTGAGTTCCCATCGATG 59.645 40.000 18.76 18.76 0.00 3.84
2599 3108 4.142403 TGAAATTTGAGTTCCCATCGATGC 60.142 41.667 20.25 6.26 0.00 3.91
2604 3113 2.208431 GAGTTCCCATCGATGCTTCTG 58.792 52.381 20.25 5.77 0.00 3.02
2616 3125 1.432514 TGCTTCTGCTACTTTGAGCG 58.567 50.000 0.00 0.00 45.99 5.03
2625 3134 1.661112 CTACTTTGAGCGCTACCAAGC 59.339 52.381 11.50 0.00 45.86 4.01
2629 3138 2.886124 GAGCGCTACCAAGCCGTC 60.886 66.667 11.50 0.00 46.68 4.79
2715 3224 2.363306 ATGACAACTGGTTCCTTGCA 57.637 45.000 0.00 0.00 0.00 4.08
2724 3233 3.181440 ACTGGTTCCTTGCATTCTCTTGA 60.181 43.478 0.00 0.00 0.00 3.02
2729 3238 6.319658 TGGTTCCTTGCATTCTCTTGATATTC 59.680 38.462 0.00 0.00 0.00 1.75
2737 3246 4.864916 TTCTCTTGATATTCGCAACTGC 57.135 40.909 0.00 0.00 37.78 4.40
2754 3263 2.317609 GCTTTCCGCAGCTCGAACA 61.318 57.895 7.07 0.00 41.67 3.18
2762 3271 1.845809 GCAGCTCGAACAACAGTGGG 61.846 60.000 0.00 0.00 0.00 4.61
2776 3285 6.454795 ACAACAGTGGGCATTTTATAACTTG 58.545 36.000 0.00 0.00 0.00 3.16
2841 3350 1.978782 CGCAAAGAGAAATCGCCAAAC 59.021 47.619 0.00 0.00 0.00 2.93
2864 3373 3.368843 CGGATGAAGTTGTGAGGTGAGAT 60.369 47.826 0.00 0.00 0.00 2.75
2909 3418 3.251004 GGGATTACGATCAATGCACCTTC 59.749 47.826 0.00 0.00 33.77 3.46
2988 3497 1.040646 AGACTCGGAGACACTGCAAA 58.959 50.000 12.86 0.00 0.00 3.68
2997 3506 4.669965 CGGAGACACTGCAAATTACATGTG 60.670 45.833 9.11 0.00 0.00 3.21
3005 3514 4.818642 TGCAAATTACATGTGGGTCAATG 58.181 39.130 9.11 0.00 0.00 2.82
3108 3617 7.801104 TGATGCAGGAGAATACTACCAAAATA 58.199 34.615 0.00 0.00 0.00 1.40
3170 3709 0.320421 GAACGCTTCAGTGTAGGGCA 60.320 55.000 12.82 0.00 37.87 5.36
3203 3742 2.388735 AGCTCGAGTGAATACATCCCA 58.611 47.619 15.13 0.00 0.00 4.37
3206 3745 3.722147 CTCGAGTGAATACATCCCAAGG 58.278 50.000 3.62 0.00 0.00 3.61
3209 3748 3.118775 CGAGTGAATACATCCCAAGGTCA 60.119 47.826 0.00 0.00 0.00 4.02
3289 3828 9.793252 CAAGCAAATTACATTTAGTAGATGCTT 57.207 29.630 13.52 13.52 46.64 3.91
3308 3847 2.391616 TGTGAGGCTGAATGCTACAG 57.608 50.000 0.00 0.00 42.39 2.74
3324 3863 3.487376 GCTACAGCGCATGAGCAATAAAA 60.487 43.478 23.73 1.92 42.27 1.52
3325 3864 3.788333 ACAGCGCATGAGCAATAAAAT 57.212 38.095 23.73 0.00 42.27 1.82
3326 3865 3.441163 ACAGCGCATGAGCAATAAAATG 58.559 40.909 23.73 12.92 42.27 2.32
3329 3868 2.129607 CGCATGAGCAATAAAATGGGC 58.870 47.619 0.00 0.00 42.27 5.36
3330 3869 2.223876 CGCATGAGCAATAAAATGGGCT 60.224 45.455 0.00 0.00 42.27 5.19
3331 3870 3.004629 CGCATGAGCAATAAAATGGGCTA 59.995 43.478 0.00 0.00 42.27 3.93
3332 3871 4.321452 CGCATGAGCAATAAAATGGGCTAT 60.321 41.667 0.00 0.00 42.27 2.97
3335 3933 4.217510 TGAGCAATAAAATGGGCTATGCT 58.782 39.130 0.00 0.00 36.59 3.79
3338 3936 4.406649 AGCAATAAAATGGGCTATGCTTGT 59.593 37.500 0.00 0.00 34.25 3.16
3339 3937 4.508861 GCAATAAAATGGGCTATGCTTGTG 59.491 41.667 0.00 0.00 0.00 3.33
3500 4101 3.944015 TCTACCGAGCCTTACTGAACTAC 59.056 47.826 0.00 0.00 0.00 2.73
3501 4102 2.805194 ACCGAGCCTTACTGAACTACT 58.195 47.619 0.00 0.00 0.00 2.57
3502 4103 2.754002 ACCGAGCCTTACTGAACTACTC 59.246 50.000 0.00 0.00 0.00 2.59
3503 4104 2.099427 CCGAGCCTTACTGAACTACTCC 59.901 54.545 0.00 0.00 0.00 3.85
3504 4105 2.099427 CGAGCCTTACTGAACTACTCCC 59.901 54.545 0.00 0.00 0.00 4.30
3505 4106 3.367321 GAGCCTTACTGAACTACTCCCT 58.633 50.000 0.00 0.00 0.00 4.20
3506 4107 3.367321 AGCCTTACTGAACTACTCCCTC 58.633 50.000 0.00 0.00 0.00 4.30
3507 4108 2.431419 GCCTTACTGAACTACTCCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
3508 4109 2.688958 CCTTACTGAACTACTCCCTCCG 59.311 54.545 0.00 0.00 0.00 4.63
3509 4110 3.354467 CTTACTGAACTACTCCCTCCGT 58.646 50.000 0.00 0.00 0.00 4.69
3510 4111 1.836802 ACTGAACTACTCCCTCCGTC 58.163 55.000 0.00 0.00 0.00 4.79
3511 4112 1.104630 CTGAACTACTCCCTCCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
3512 4113 0.324091 TGAACTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
3513 4114 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
3514 4115 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3515 4116 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3516 4117 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3517 4118 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3518 4119 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3519 4120 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3520 4121 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3521 4122 2.563179 CTCCCTCCGTCCCATAATGTAG 59.437 54.545 0.00 0.00 0.00 2.74
3522 4123 1.002087 CCCTCCGTCCCATAATGTAGC 59.998 57.143 0.00 0.00 0.00 3.58
3523 4124 1.691976 CCTCCGTCCCATAATGTAGCA 59.308 52.381 0.00 0.00 0.00 3.49
3524 4125 2.104111 CCTCCGTCCCATAATGTAGCAA 59.896 50.000 0.00 0.00 0.00 3.91
3525 4126 3.393800 CTCCGTCCCATAATGTAGCAAG 58.606 50.000 0.00 0.00 0.00 4.01
3526 4127 1.873591 CCGTCCCATAATGTAGCAAGC 59.126 52.381 0.00 0.00 0.00 4.01
3527 4128 2.485479 CCGTCCCATAATGTAGCAAGCT 60.485 50.000 0.00 0.00 0.00 3.74
3528 4129 3.244078 CCGTCCCATAATGTAGCAAGCTA 60.244 47.826 0.00 0.00 0.00 3.32
3529 4130 4.377021 CGTCCCATAATGTAGCAAGCTAA 58.623 43.478 2.92 0.00 0.00 3.09
3530 4131 4.814234 CGTCCCATAATGTAGCAAGCTAAA 59.186 41.667 2.92 0.00 0.00 1.85
3531 4132 5.295787 CGTCCCATAATGTAGCAAGCTAAAA 59.704 40.000 2.92 0.00 0.00 1.52
3532 4133 6.183360 CGTCCCATAATGTAGCAAGCTAAAAA 60.183 38.462 2.92 0.00 0.00 1.94
3533 4134 6.972901 GTCCCATAATGTAGCAAGCTAAAAAC 59.027 38.462 2.92 0.00 0.00 2.43
3534 4135 5.971202 CCCATAATGTAGCAAGCTAAAAACG 59.029 40.000 2.92 0.00 0.00 3.60
3535 4136 6.404293 CCCATAATGTAGCAAGCTAAAAACGT 60.404 38.462 2.92 0.00 0.00 3.99
3536 4137 6.687105 CCATAATGTAGCAAGCTAAAAACGTC 59.313 38.462 2.92 0.00 0.00 4.34
3537 4138 5.941948 AATGTAGCAAGCTAAAAACGTCT 57.058 34.783 2.92 0.00 0.00 4.18
3538 4139 5.941948 ATGTAGCAAGCTAAAAACGTCTT 57.058 34.783 2.92 0.00 0.00 3.01
3539 4140 7.429636 AATGTAGCAAGCTAAAAACGTCTTA 57.570 32.000 2.92 0.00 0.00 2.10
3540 4141 6.219302 TGTAGCAAGCTAAAAACGTCTTAC 57.781 37.500 2.92 0.00 0.00 2.34
3541 4142 5.754406 TGTAGCAAGCTAAAAACGTCTTACA 59.246 36.000 2.92 0.00 0.00 2.41
3542 4143 5.941948 AGCAAGCTAAAAACGTCTTACAT 57.058 34.783 0.00 0.00 0.00 2.29
3543 4144 6.313744 AGCAAGCTAAAAACGTCTTACATT 57.686 33.333 0.00 0.00 0.00 2.71
3544 4145 7.429636 AGCAAGCTAAAAACGTCTTACATTA 57.570 32.000 0.00 0.00 0.00 1.90
3545 4146 8.040716 AGCAAGCTAAAAACGTCTTACATTAT 57.959 30.769 0.00 0.00 0.00 1.28
3546 4147 7.962918 AGCAAGCTAAAAACGTCTTACATTATG 59.037 33.333 0.00 0.00 0.00 1.90
3547 4148 7.218204 GCAAGCTAAAAACGTCTTACATTATGG 59.782 37.037 0.00 0.00 0.00 2.74
3548 4149 7.316544 AGCTAAAAACGTCTTACATTATGGG 57.683 36.000 0.00 0.00 0.00 4.00
3549 4150 7.107542 AGCTAAAAACGTCTTACATTATGGGA 58.892 34.615 0.00 0.00 0.00 4.37
3550 4151 7.065443 AGCTAAAAACGTCTTACATTATGGGAC 59.935 37.037 0.00 1.75 0.00 4.46
3626 4227 2.096069 TGTTCGACTCGTTTAGGTCTCG 60.096 50.000 0.00 0.00 0.00 4.04
3686 4288 5.376625 ACAGCCTTCAGTGTCAATTTCTTA 58.623 37.500 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.440214 CACAATCGTGCCTTTCGC 57.560 55.556 0.00 0.00 36.06 4.70
23 24 1.455786 CTCTCGCGAAAACACAATCGT 59.544 47.619 11.33 0.00 41.01 3.73
24 25 1.455786 ACTCTCGCGAAAACACAATCG 59.544 47.619 11.33 0.00 41.81 3.34
25 26 2.475111 TGACTCTCGCGAAAACACAATC 59.525 45.455 11.33 0.20 0.00 2.67
26 27 2.221055 GTGACTCTCGCGAAAACACAAT 59.779 45.455 21.45 1.18 0.00 2.71
27 28 1.591158 GTGACTCTCGCGAAAACACAA 59.409 47.619 21.45 1.34 0.00 3.33
28 29 1.205657 GTGACTCTCGCGAAAACACA 58.794 50.000 21.45 12.20 0.00 3.72
38 39 4.717629 TTGCGGCCGTGACTCTCG 62.718 66.667 28.70 0.00 0.00 4.04
39 40 2.811317 CTTGCGGCCGTGACTCTC 60.811 66.667 28.70 8.52 0.00 3.20
40 41 4.379243 CCTTGCGGCCGTGACTCT 62.379 66.667 28.70 0.00 0.00 3.24
41 42 3.876589 TTCCTTGCGGCCGTGACTC 62.877 63.158 28.70 10.19 0.00 3.36
42 43 2.951475 TTTTCCTTGCGGCCGTGACT 62.951 55.000 28.70 0.00 0.00 3.41
43 44 2.065906 TTTTTCCTTGCGGCCGTGAC 62.066 55.000 28.70 11.04 0.00 3.67
44 45 1.824329 TTTTTCCTTGCGGCCGTGA 60.824 52.632 28.70 15.44 0.00 4.35
45 46 2.725008 TTTTTCCTTGCGGCCGTG 59.275 55.556 28.70 16.85 0.00 4.94
72 73 9.872721 TGTTTCTTTACCGGTTTCTTTTTATTT 57.127 25.926 15.04 0.00 0.00 1.40
73 74 9.304731 GTGTTTCTTTACCGGTTTCTTTTTATT 57.695 29.630 15.04 0.00 0.00 1.40
74 75 8.468399 TGTGTTTCTTTACCGGTTTCTTTTTAT 58.532 29.630 15.04 0.00 0.00 1.40
75 76 7.754475 GTGTGTTTCTTTACCGGTTTCTTTTTA 59.246 33.333 15.04 0.00 0.00 1.52
76 77 6.587226 GTGTGTTTCTTTACCGGTTTCTTTTT 59.413 34.615 15.04 0.00 0.00 1.94
77 78 6.094719 GTGTGTTTCTTTACCGGTTTCTTTT 58.905 36.000 15.04 0.00 0.00 2.27
78 79 5.183522 TGTGTGTTTCTTTACCGGTTTCTTT 59.816 36.000 15.04 0.00 0.00 2.52
79 80 4.701171 TGTGTGTTTCTTTACCGGTTTCTT 59.299 37.500 15.04 0.00 0.00 2.52
80 81 4.263435 TGTGTGTTTCTTTACCGGTTTCT 58.737 39.130 15.04 0.00 0.00 2.52
81 82 4.619437 TGTGTGTTTCTTTACCGGTTTC 57.381 40.909 15.04 0.00 0.00 2.78
179 186 8.055279 TCAGCTTTCTATGTTTCTTTATTGGG 57.945 34.615 0.00 0.00 0.00 4.12
199 206 1.388547 TTCTTGCGGTTGTTTCAGCT 58.611 45.000 0.00 0.00 0.00 4.24
203 210 3.254892 TGGTTTTTCTTGCGGTTGTTTC 58.745 40.909 0.00 0.00 0.00 2.78
237 244 8.651589 TCTCTCATTCTTAGGTCTGTTTTCTA 57.348 34.615 0.00 0.00 0.00 2.10
250 257 3.124636 GCGCGGTTTTTCTCTCATTCTTA 59.875 43.478 8.83 0.00 0.00 2.10
267 274 1.571460 GATTATTGCTGGAGCGCGG 59.429 57.895 8.83 0.00 45.83 6.46
276 283 2.680805 CGGCCCGATATGGATTATTGCT 60.681 50.000 0.00 0.00 42.00 3.91
279 286 1.408266 GCCGGCCCGATATGGATTATT 60.408 52.381 18.11 0.00 42.00 1.40
281 288 0.907704 AGCCGGCCCGATATGGATTA 60.908 55.000 26.15 0.00 42.00 1.75
302 309 2.545113 CCAAAGGTTGTTCTCGTCGAGA 60.545 50.000 20.85 20.85 36.86 4.04
309 316 0.875059 CTCGCCCAAAGGTTGTTCTC 59.125 55.000 0.00 0.00 34.57 2.87
317 324 0.036875 AACTTCCTCTCGCCCAAAGG 59.963 55.000 0.00 0.00 0.00 3.11
335 342 4.716784 CCAGGGCTATATATCACCTGCTAA 59.283 45.833 18.18 0.00 45.65 3.09
379 386 3.050089 TCTTCTCGAGACCTCCTATCCT 58.950 50.000 16.36 0.00 0.00 3.24
615 700 9.381027 CAAAAACAAAAACAGAAAAAGGACTTC 57.619 29.630 0.00 0.00 0.00 3.01
814 1217 0.800631 CCGTGTGTCTGTCGCTACTA 59.199 55.000 0.00 0.00 0.00 1.82
815 1218 1.170919 ACCGTGTGTCTGTCGCTACT 61.171 55.000 0.00 0.00 0.00 2.57
816 1219 0.318445 AACCGTGTGTCTGTCGCTAC 60.318 55.000 0.00 0.00 0.00 3.58
817 1220 0.386476 AAACCGTGTGTCTGTCGCTA 59.614 50.000 0.00 0.00 0.00 4.26
893 1296 2.480555 GGCGCTGGAAACATGACG 59.519 61.111 7.64 0.00 41.51 4.35
895 1298 2.032634 GTCGGCGCTGGAAACATGA 61.033 57.895 17.88 0.00 41.51 3.07
896 1299 2.034879 AGTCGGCGCTGGAAACATG 61.035 57.895 17.88 0.00 41.51 3.21
897 1300 2.034879 CAGTCGGCGCTGGAAACAT 61.035 57.895 17.88 0.00 41.51 2.71
898 1301 2.664851 CAGTCGGCGCTGGAAACA 60.665 61.111 17.88 0.00 39.59 2.83
899 1302 4.090057 GCAGTCGGCGCTGGAAAC 62.090 66.667 24.92 7.47 37.00 2.78
923 1333 1.469940 GCACGAACATCAGACCGAGAT 60.470 52.381 0.00 0.00 0.00 2.75
938 1348 3.751479 ATATATGCTGGAGTTGCACGA 57.249 42.857 0.00 0.00 43.59 4.35
997 1418 4.022762 TGAGGCAAGCGATCTATAAGACTC 60.023 45.833 0.00 0.00 0.00 3.36
1034 1456 2.604139 TGGACCTTGGAAATTGGAACC 58.396 47.619 0.00 0.00 0.00 3.62
1042 1464 0.608035 GACGCCATGGACCTTGGAAA 60.608 55.000 26.72 0.00 36.26 3.13
1043 1465 1.002624 GACGCCATGGACCTTGGAA 60.003 57.895 26.72 0.00 36.26 3.53
1044 1466 2.668632 GACGCCATGGACCTTGGA 59.331 61.111 26.72 0.00 36.26 3.53
1046 1468 3.499737 GCGACGCCATGGACCTTG 61.500 66.667 18.40 1.13 0.00 3.61
1047 1469 3.958147 CTGCGACGCCATGGACCTT 62.958 63.158 18.40 0.00 0.00 3.50
1048 1470 4.457496 CTGCGACGCCATGGACCT 62.457 66.667 18.40 0.00 0.00 3.85
1183 1605 1.499049 GCAACGGAATCCTCGGATAC 58.501 55.000 0.00 0.00 33.97 2.24
1199 1621 2.028778 GTTTGCGTGGCATGGCAA 59.971 55.556 25.11 20.42 46.52 4.52
1200 1622 2.911509 AGTTTGCGTGGCATGGCA 60.912 55.556 19.43 19.43 38.76 4.92
1201 1623 2.431260 CAGTTTGCGTGGCATGGC 60.431 61.111 13.29 13.29 38.76 4.40
1255 1677 4.831307 CGACGACGGCTTCTCGGG 62.831 72.222 0.00 0.00 35.37 5.14
1582 2007 4.651008 GACGACGTCGGGGTGCAA 62.651 66.667 37.89 0.00 44.95 4.08
2103 2529 4.814294 AACGATCGCCGCCTCACC 62.814 66.667 16.60 0.00 43.32 4.02
2212 2674 9.771915 GATTCATAGCAAAAAGAGAAGAGAAAG 57.228 33.333 0.00 0.00 0.00 2.62
2213 2675 9.288576 TGATTCATAGCAAAAAGAGAAGAGAAA 57.711 29.630 0.00 0.00 0.00 2.52
2216 2678 8.266392 ACTGATTCATAGCAAAAAGAGAAGAG 57.734 34.615 0.00 0.00 0.00 2.85
2218 2680 8.121708 GCTACTGATTCATAGCAAAAAGAGAAG 58.878 37.037 16.55 0.00 42.82 2.85
2219 2681 7.826252 AGCTACTGATTCATAGCAAAAAGAGAA 59.174 33.333 20.42 0.00 45.22 2.87
2220 2682 7.334090 AGCTACTGATTCATAGCAAAAAGAGA 58.666 34.615 20.42 0.00 45.22 3.10
2221 2683 7.551035 AGCTACTGATTCATAGCAAAAAGAG 57.449 36.000 20.42 0.00 45.22 2.85
2222 2684 7.225538 GCTAGCTACTGATTCATAGCAAAAAGA 59.774 37.037 20.42 6.70 45.22 2.52
2223 2685 7.226325 AGCTAGCTACTGATTCATAGCAAAAAG 59.774 37.037 17.69 15.14 45.22 2.27
2232 2694 6.538021 CACTTGAAAGCTAGCTACTGATTCAT 59.462 38.462 22.92 11.29 0.00 2.57
2233 2695 5.871524 CACTTGAAAGCTAGCTACTGATTCA 59.128 40.000 19.70 19.85 0.00 2.57
2252 2714 9.056005 ACAAGGCATTATATGTATGTACACTTG 57.944 33.333 0.00 5.15 39.30 3.16
2267 2737 7.643569 TTTGTGATGATGTACAAGGCATTAT 57.356 32.000 0.00 0.00 37.98 1.28
2362 2855 3.305335 GCATTTCAGTACACACCCCTTTG 60.305 47.826 0.00 0.00 0.00 2.77
2415 2924 7.665559 AGGTTTCTAGTGCATTGTTTCTTGATA 59.334 33.333 0.00 0.00 0.00 2.15
2445 2954 6.421485 AGGATAGTTGATTGAACAAGCTCAT 58.579 36.000 4.54 0.00 36.98 2.90
2453 2962 6.907212 CGCAAACATAGGATAGTTGATTGAAC 59.093 38.462 0.00 0.00 34.40 3.18
2461 2970 4.137116 TGCTCGCAAACATAGGATAGTT 57.863 40.909 0.00 0.00 0.00 2.24
2506 3015 6.322712 TGCAACCCTTCTTTGTATTGTTTAGT 59.677 34.615 0.00 0.00 0.00 2.24
2507 3016 6.744112 TGCAACCCTTCTTTGTATTGTTTAG 58.256 36.000 0.00 0.00 0.00 1.85
2521 3030 2.742774 GTTGTGTCAATGCAACCCTTC 58.257 47.619 0.00 0.00 39.07 3.46
2523 3032 0.667993 CGTTGTGTCAATGCAACCCT 59.332 50.000 0.00 0.00 41.16 4.34
2526 3035 2.223479 ACCTTCGTTGTGTCAATGCAAC 60.223 45.455 0.00 0.00 40.90 4.17
2527 3036 2.020720 ACCTTCGTTGTGTCAATGCAA 58.979 42.857 0.00 0.00 0.00 4.08
2528 3037 1.333308 CACCTTCGTTGTGTCAATGCA 59.667 47.619 0.00 0.00 0.00 3.96
2529 3038 1.333619 ACACCTTCGTTGTGTCAATGC 59.666 47.619 2.38 0.00 43.15 3.56
2530 3039 4.804608 TTACACCTTCGTTGTGTCAATG 57.195 40.909 9.86 0.00 43.15 2.82
2531 3040 4.636648 TGTTTACACCTTCGTTGTGTCAAT 59.363 37.500 9.86 0.00 43.15 2.57
2532 3041 4.001652 TGTTTACACCTTCGTTGTGTCAA 58.998 39.130 9.86 4.63 43.15 3.18
2533 3042 3.597255 TGTTTACACCTTCGTTGTGTCA 58.403 40.909 9.86 2.13 43.15 3.58
2534 3043 4.603231 TTGTTTACACCTTCGTTGTGTC 57.397 40.909 9.86 0.00 43.15 3.67
2538 3047 4.210537 AGTCGATTGTTTACACCTTCGTTG 59.789 41.667 0.00 0.00 0.00 4.10
2540 3049 3.986277 AGTCGATTGTTTACACCTTCGT 58.014 40.909 0.00 0.00 0.00 3.85
2541 3050 5.231568 GGATAGTCGATTGTTTACACCTTCG 59.768 44.000 0.00 0.00 0.00 3.79
2542 3051 6.338937 AGGATAGTCGATTGTTTACACCTTC 58.661 40.000 0.00 0.00 0.00 3.46
2543 3052 6.295719 AGGATAGTCGATTGTTTACACCTT 57.704 37.500 0.00 0.00 0.00 3.50
2544 3053 5.934402 AGGATAGTCGATTGTTTACACCT 57.066 39.130 0.00 0.00 0.00 4.00
2558 3067 8.919661 CAAATTTCAGAAAAGCAAAGGATAGTC 58.080 33.333 0.00 0.00 0.00 2.59
2563 3072 6.877236 ACTCAAATTTCAGAAAAGCAAAGGA 58.123 32.000 0.00 0.00 0.00 3.36
2568 3077 5.128499 TGGGAACTCAAATTTCAGAAAAGCA 59.872 36.000 0.00 0.00 0.00 3.91
2569 3078 5.600696 TGGGAACTCAAATTTCAGAAAAGC 58.399 37.500 0.00 0.00 0.00 3.51
2570 3079 6.583806 CGATGGGAACTCAAATTTCAGAAAAG 59.416 38.462 0.00 0.00 0.00 2.27
2585 3094 1.745141 GCAGAAGCATCGATGGGAACT 60.745 52.381 26.00 12.05 41.58 3.01
2586 3095 0.659957 GCAGAAGCATCGATGGGAAC 59.340 55.000 26.00 9.89 41.58 3.62
2592 3101 4.118410 CTCAAAGTAGCAGAAGCATCGAT 58.882 43.478 0.00 0.00 45.49 3.59
2595 3104 2.030213 CGCTCAAAGTAGCAGAAGCATC 59.970 50.000 0.00 0.00 45.49 3.91
2597 3106 1.432514 CGCTCAAAGTAGCAGAAGCA 58.567 50.000 0.00 0.00 45.49 3.91
2598 3107 0.096108 GCGCTCAAAGTAGCAGAAGC 59.904 55.000 0.00 0.00 42.91 3.86
2599 3108 1.719600 AGCGCTCAAAGTAGCAGAAG 58.280 50.000 2.64 0.00 42.91 2.85
2604 3113 1.661112 CTTGGTAGCGCTCAAAGTAGC 59.339 52.381 16.34 5.32 39.21 3.58
2629 3138 2.202298 GGCGGCATTTTCGTCACG 60.202 61.111 3.07 0.00 31.94 4.35
2687 3196 5.487488 AGGAACCAGTTGTCATATTAGGTCA 59.513 40.000 0.00 0.00 0.00 4.02
2715 3224 5.415415 GCAGTTGCGAATATCAAGAGAAT 57.585 39.130 0.00 0.00 0.00 2.40
2737 3246 0.110644 GTTGTTCGAGCTGCGGAAAG 60.111 55.000 10.05 0.00 41.33 2.62
2754 3263 5.478407 GCAAGTTATAAAATGCCCACTGTT 58.522 37.500 11.03 0.00 32.73 3.16
2762 3271 9.971922 ATCTTAATCTGGCAAGTTATAAAATGC 57.028 29.630 12.94 12.94 38.06 3.56
2841 3350 1.001974 TCACCTCACAACTTCATCCGG 59.998 52.381 0.00 0.00 0.00 5.14
2864 3373 8.998814 TCCCTATGTAGATATTTCTTTTGGTCA 58.001 33.333 0.00 0.00 33.17 4.02
2909 3418 8.945057 TGGAAAACTGAAAAATCAAAAAGAAGG 58.055 29.630 0.00 0.00 0.00 3.46
2981 3490 3.495331 TGACCCACATGTAATTTGCAGT 58.505 40.909 0.00 0.00 0.00 4.40
2988 3497 4.661222 TGTGTCATTGACCCACATGTAAT 58.339 39.130 14.05 0.00 34.37 1.89
2997 3506 3.665745 AGCATTTTGTGTCATTGACCC 57.334 42.857 14.05 3.24 0.00 4.46
3005 3514 7.760131 ATGCATATTGTTAGCATTTTGTGTC 57.240 32.000 0.00 0.00 45.98 3.67
3063 3572 7.173735 TGCATCATCCACAACTTAGCTTATATG 59.826 37.037 0.00 0.00 0.00 1.78
3064 3573 7.226441 TGCATCATCCACAACTTAGCTTATAT 58.774 34.615 0.00 0.00 0.00 0.86
3065 3574 6.591001 TGCATCATCCACAACTTAGCTTATA 58.409 36.000 0.00 0.00 0.00 0.98
3066 3575 5.439721 TGCATCATCCACAACTTAGCTTAT 58.560 37.500 0.00 0.00 0.00 1.73
3067 3576 4.842574 TGCATCATCCACAACTTAGCTTA 58.157 39.130 0.00 0.00 0.00 3.09
3068 3577 3.689347 TGCATCATCCACAACTTAGCTT 58.311 40.909 0.00 0.00 0.00 3.74
3069 3578 3.276857 CTGCATCATCCACAACTTAGCT 58.723 45.455 0.00 0.00 0.00 3.32
3108 3617 9.930693 TGGACAAAGTACTGTTTTGTTAAATTT 57.069 25.926 11.69 0.00 45.82 1.82
3203 3742 1.201429 ATTGACCTCGGGCTGACCTT 61.201 55.000 0.00 0.00 36.97 3.50
3206 3745 2.007608 GTAAATTGACCTCGGGCTGAC 58.992 52.381 0.00 0.00 0.00 3.51
3209 3748 1.628846 AGTGTAAATTGACCTCGGGCT 59.371 47.619 0.00 0.00 0.00 5.19
3308 3847 2.129607 CCCATTTTATTGCTCATGCGC 58.870 47.619 0.00 0.00 43.34 6.09
3309 3848 2.129607 GCCCATTTTATTGCTCATGCG 58.870 47.619 0.00 0.00 43.34 4.73
3324 3863 1.396653 GAAGCACAAGCATAGCCCAT 58.603 50.000 0.00 0.00 45.49 4.00
3325 3864 0.680921 GGAAGCACAAGCATAGCCCA 60.681 55.000 0.00 0.00 45.49 5.36
3326 3865 0.680921 TGGAAGCACAAGCATAGCCC 60.681 55.000 0.00 0.00 45.49 5.19
3329 3868 0.729116 CCGTGGAAGCACAAGCATAG 59.271 55.000 0.00 0.00 45.49 2.23
3330 3869 1.305219 GCCGTGGAAGCACAAGCATA 61.305 55.000 0.00 0.00 45.49 3.14
3331 3870 2.629656 GCCGTGGAAGCACAAGCAT 61.630 57.895 0.00 0.00 45.49 3.79
3332 3871 3.286751 GCCGTGGAAGCACAAGCA 61.287 61.111 0.00 0.00 45.49 3.91
3338 3936 4.695993 TCATGCGCCGTGGAAGCA 62.696 61.111 4.18 10.97 45.46 3.91
3339 3937 2.470801 TTTTCATGCGCCGTGGAAGC 62.471 55.000 4.18 0.00 0.00 3.86
3500 4101 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3501 4102 2.605257 CTACATTATGGGACGGAGGGA 58.395 52.381 0.00 0.00 0.00 4.20
3502 4103 1.002087 GCTACATTATGGGACGGAGGG 59.998 57.143 0.00 0.00 0.00 4.30
3503 4104 1.691976 TGCTACATTATGGGACGGAGG 59.308 52.381 0.00 0.00 0.00 4.30
3504 4105 3.393800 CTTGCTACATTATGGGACGGAG 58.606 50.000 0.00 0.00 0.00 4.63
3505 4106 2.484770 GCTTGCTACATTATGGGACGGA 60.485 50.000 0.00 0.00 0.00 4.69
3506 4107 1.873591 GCTTGCTACATTATGGGACGG 59.126 52.381 0.00 0.00 0.00 4.79
3507 4108 2.838736 AGCTTGCTACATTATGGGACG 58.161 47.619 0.00 0.00 0.00 4.79
3508 4109 6.693315 TTTTAGCTTGCTACATTATGGGAC 57.307 37.500 1.37 0.00 0.00 4.46
3509 4110 6.183360 CGTTTTTAGCTTGCTACATTATGGGA 60.183 38.462 1.37 0.00 0.00 4.37
3510 4111 5.971202 CGTTTTTAGCTTGCTACATTATGGG 59.029 40.000 1.37 0.00 0.00 4.00
3511 4112 6.551736 ACGTTTTTAGCTTGCTACATTATGG 58.448 36.000 1.37 0.00 0.00 2.74
3512 4113 7.464358 AGACGTTTTTAGCTTGCTACATTATG 58.536 34.615 1.37 0.00 0.00 1.90
3513 4114 7.611213 AGACGTTTTTAGCTTGCTACATTAT 57.389 32.000 1.37 0.00 0.00 1.28
3514 4115 7.429636 AAGACGTTTTTAGCTTGCTACATTA 57.570 32.000 1.37 0.00 0.00 1.90
3515 4116 5.941948 AGACGTTTTTAGCTTGCTACATT 57.058 34.783 1.37 0.00 0.00 2.71
3516 4117 5.941948 AAGACGTTTTTAGCTTGCTACAT 57.058 34.783 1.37 0.00 0.00 2.29
3517 4118 5.754406 TGTAAGACGTTTTTAGCTTGCTACA 59.246 36.000 1.37 0.00 0.00 2.74
3518 4119 6.219302 TGTAAGACGTTTTTAGCTTGCTAC 57.781 37.500 1.37 0.00 0.00 3.58
3519 4120 7.429636 AATGTAAGACGTTTTTAGCTTGCTA 57.570 32.000 0.00 0.00 0.00 3.49
3520 4121 5.941948 ATGTAAGACGTTTTTAGCTTGCT 57.058 34.783 0.00 0.00 0.00 3.91
3521 4122 7.218204 CCATAATGTAAGACGTTTTTAGCTTGC 59.782 37.037 0.00 0.00 0.00 4.01
3522 4123 7.696453 CCCATAATGTAAGACGTTTTTAGCTTG 59.304 37.037 0.00 0.00 0.00 4.01
3523 4124 7.608761 TCCCATAATGTAAGACGTTTTTAGCTT 59.391 33.333 0.00 0.00 0.00 3.74
3524 4125 7.065443 GTCCCATAATGTAAGACGTTTTTAGCT 59.935 37.037 0.00 0.00 0.00 3.32
3525 4126 7.148373 TGTCCCATAATGTAAGACGTTTTTAGC 60.148 37.037 0.00 0.00 0.00 3.09
3526 4127 8.259049 TGTCCCATAATGTAAGACGTTTTTAG 57.741 34.615 0.00 0.00 0.00 1.85
3527 4128 8.095792 TCTGTCCCATAATGTAAGACGTTTTTA 58.904 33.333 0.00 0.00 0.00 1.52
3528 4129 6.938030 TCTGTCCCATAATGTAAGACGTTTTT 59.062 34.615 0.00 0.00 0.00 1.94
3529 4130 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
3530 4131 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
3531 4132 5.187186 ACTCTGTCCCATAATGTAAGACGTT 59.813 40.000 0.00 0.00 0.00 3.99
3532 4133 4.710375 ACTCTGTCCCATAATGTAAGACGT 59.290 41.667 0.00 0.00 0.00 4.34
3533 4134 5.263968 ACTCTGTCCCATAATGTAAGACG 57.736 43.478 0.00 0.00 0.00 4.18
3534 4135 7.349412 ACTACTCTGTCCCATAATGTAAGAC 57.651 40.000 0.00 0.00 0.00 3.01
3535 4136 9.656323 AATACTACTCTGTCCCATAATGTAAGA 57.344 33.333 0.00 0.00 0.00 2.10
3543 4144 8.627403 CGAACTTAAATACTACTCTGTCCCATA 58.373 37.037 0.00 0.00 0.00 2.74
3544 4145 7.341256 TCGAACTTAAATACTACTCTGTCCCAT 59.659 37.037 0.00 0.00 0.00 4.00
3545 4146 6.660521 TCGAACTTAAATACTACTCTGTCCCA 59.339 38.462 0.00 0.00 0.00 4.37
3546 4147 7.093322 TCGAACTTAAATACTACTCTGTCCC 57.907 40.000 0.00 0.00 0.00 4.46
3547 4148 6.692249 GCTCGAACTTAAATACTACTCTGTCC 59.308 42.308 0.00 0.00 0.00 4.02
3548 4149 7.474190 AGCTCGAACTTAAATACTACTCTGTC 58.526 38.462 0.00 0.00 0.00 3.51
3549 4150 7.393841 AGCTCGAACTTAAATACTACTCTGT 57.606 36.000 0.00 0.00 0.00 3.41
3550 4151 7.221067 CCAAGCTCGAACTTAAATACTACTCTG 59.779 40.741 0.00 0.00 0.00 3.35
3551 4152 7.259161 CCAAGCTCGAACTTAAATACTACTCT 58.741 38.462 0.00 0.00 0.00 3.24
3552 4153 6.019720 GCCAAGCTCGAACTTAAATACTACTC 60.020 42.308 0.00 0.00 0.00 2.59
3553 4154 5.811100 GCCAAGCTCGAACTTAAATACTACT 59.189 40.000 0.00 0.00 0.00 2.57
3554 4155 5.579511 TGCCAAGCTCGAACTTAAATACTAC 59.420 40.000 0.00 0.00 0.00 2.73
3555 4156 5.726397 TGCCAAGCTCGAACTTAAATACTA 58.274 37.500 0.00 0.00 0.00 1.82
3556 4157 4.575885 TGCCAAGCTCGAACTTAAATACT 58.424 39.130 0.00 0.00 0.00 2.12
3557 4158 4.939509 TGCCAAGCTCGAACTTAAATAC 57.060 40.909 0.00 0.00 0.00 1.89
3558 4159 5.545658 CTTGCCAAGCTCGAACTTAAATA 57.454 39.130 0.00 0.00 0.00 1.40
3559 4160 4.425577 CTTGCCAAGCTCGAACTTAAAT 57.574 40.909 0.00 0.00 0.00 1.40
3605 4206 2.096069 CGAGACCTAAACGAGTCGAACA 60.096 50.000 21.50 1.99 38.08 3.18
3626 4227 4.142687 GCTCGACTCTTATAGGCTCATCTC 60.143 50.000 0.00 0.00 0.00 2.75
3630 4231 3.142951 GAGCTCGACTCTTATAGGCTCA 58.857 50.000 11.33 0.00 42.62 4.26
3686 4288 2.033801 GTCACAACAGCTGATGCAACTT 59.966 45.455 23.35 0.00 42.74 2.66
3815 4417 5.297547 AGCATTTGTCTCGTCTTTAGAACA 58.702 37.500 0.00 0.00 0.00 3.18
3827 4429 8.140628 TCTCTACATGAATCTAGCATTTGTCTC 58.859 37.037 0.00 0.00 0.00 3.36
3948 4550 5.068636 CAGAATGTAGGAATGGAGAATGGG 58.931 45.833 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.