Multiple sequence alignment - TraesCS1A01G283900

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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 TraesCS1A01G283900 chr1A 100.000 4304 0 0 1 4304 481672552 481676855 0.000000e+00 7949
1 TraesCS1A01G283900 chr1A 77.758 1115 186 44 1846 2935 480935277 480934200 2.820000e-176 628
2 TraesCS1A01G283900 chr1D 91.101 3551 201 45 85 3604 381017746 381021212 0.000000e+00 4700
3 TraesCS1A01G283900 chr1D 77.917 1114 186 42 1846 2935 379912116 379911039 1.310000e-179 640
4 TraesCS1A01G283900 chr1B 90.106 3578 194 66 78 3607 510807557 510811022 0.000000e+00 4499
5 TraesCS1A01G283900 chr1B 77.568 1110 197 35 1846 2935 509902455 509901378 1.310000e-174 623
6 TraesCS1A01G283900 chr7A 96.901 710 21 1 3596 4304 39132067 39131358 0.000000e+00 1188
7 TraesCS1A01G283900 chr7A 96.124 516 18 2 3790 4304 49058294 49058808 0.000000e+00 841
8 TraesCS1A01G283900 chr7A 96.875 160 5 0 3605 3764 49058138 49058297 7.090000e-68 268
9 TraesCS1A01G283900 chr7A 84.058 207 22 5 3609 3811 130383083 130382884 5.680000e-44 189
10 TraesCS1A01G283900 chr7A 86.047 172 15 8 4040 4208 49058839 49059004 4.420000e-40 176
11 TraesCS1A01G283900 chr7A 97.938 97 2 0 4208 4304 49058765 49058861 7.400000e-38 169
12 TraesCS1A01G283900 chr7A 85.612 139 18 2 3049 3186 149861049 149860912 1.250000e-30 145
13 TraesCS1A01G283900 chr4A 96.291 701 25 1 3605 4304 489422160 489421460 0.000000e+00 1149
14 TraesCS1A01G283900 chr4A 86.986 146 14 4 4063 4208 489421457 489421317 4.450000e-35 159
15 TraesCS1A01G283900 chr6A 95.863 701 28 1 3605 4304 498543738 498543038 0.000000e+00 1133
16 TraesCS1A01G283900 chr3D 83.100 1000 125 27 1958 2935 465027150 465026173 0.000000e+00 870
17 TraesCS1A01G283900 chr3D 80.924 996 151 29 1958 2935 464808955 464807981 0.000000e+00 750
18 TraesCS1A01G283900 chr3D 82.946 387 60 5 1447 1830 465027850 465027467 1.150000e-90 344
19 TraesCS1A01G283900 chr3A 82.834 1002 124 29 1958 2935 608347363 608346386 0.000000e+00 854
20 TraesCS1A01G283900 chr3A 79.940 997 159 25 1958 2935 608195753 608194779 0.000000e+00 695
21 TraesCS1A01G283900 chr3A 83.204 387 59 5 1447 1830 608348068 608347685 2.460000e-92 350
22 TraesCS1A01G283900 chr3A 74.237 524 110 19 1448 1958 596794327 596794838 3.400000e-46 196
23 TraesCS1A01G283900 chr3B 82.335 1002 129 29 1958 2935 618442173 618441196 0.000000e+00 826
24 TraesCS1A01G283900 chr3B 79.940 997 159 29 1958 2935 618155761 618154787 0.000000e+00 695
25 TraesCS1A01G283900 chr3B 82.171 387 63 5 1447 1830 618442878 618442495 1.150000e-85 327
26 TraesCS1A01G283900 chr3B 74.525 526 105 23 1448 1958 597545462 597545973 7.300000e-48 202
27 TraesCS1A01G283900 chr3B 95.050 101 5 0 1430 1530 618869549 618869649 4.450000e-35 159
28 TraesCS1A01G283900 chr7B 78.257 998 177 27 1958 2935 111943061 111944038 4.760000e-169 604
29 TraesCS1A01G283900 chr7D 78.398 986 171 27 1971 2935 149181908 149182872 1.710000e-168 603
30 TraesCS1A01G283900 chr7D 78.318 987 170 27 1971 2935 149085129 149084165 7.970000e-167 597
31 TraesCS1A01G283900 chr7D 85.612 139 18 2 3049 3186 149084088 149083951 1.250000e-30 145
32 TraesCS1A01G283900 chr4B 83.247 388 48 6 3870 4256 626459817 626459446 1.480000e-89 340
33 TraesCS1A01G283900 chr2A 78.261 529 101 13 1429 1950 185264917 185265438 1.150000e-85 327
34 TraesCS1A01G283900 chr2A 82.519 389 50 8 3870 4256 72712538 72712166 4.150000e-85 326
35 TraesCS1A01G283900 chr2A 87.417 151 15 4 3605 3751 705552291 705552441 2.060000e-38 171
36 TraesCS1A01G283900 chr2A 82.036 167 23 7 3020 3183 185270427 185270589 7.510000e-28 135
37 TraesCS1A01G283900 chr2A 82.237 152 21 6 3034 3183 185363058 185362911 4.520000e-25 126
38 TraesCS1A01G283900 chr5D 88.095 210 22 3 3603 3809 36210996 36210787 3.320000e-61 246
39 TraesCS1A01G283900 chr2D 87.500 208 23 3 3605 3809 43797804 43797597 2.000000e-58 237
40 TraesCS1A01G283900 chr2D 86.538 208 25 3 3605 3809 440329012 440329219 4.330000e-55 226
41 TraesCS1A01G283900 chr2D 80.838 167 25 7 3020 3183 165340654 165340816 1.630000e-24 124
42 TraesCS1A01G283900 chr2D 81.818 154 20 8 3033 3183 165483679 165483531 5.840000e-24 122
43 TraesCS1A01G283900 chr5A 80.745 322 40 10 3936 4256 16970208 16970508 9.310000e-57 231
44 TraesCS1A01G283900 chr2B 82.635 167 22 7 3020 3183 232289671 232289509 1.610000e-29 141


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 TraesCS1A01G283900 chr1A 481672552 481676855 4303 False 7949.0 7949 100.0000 1 4304 1 chr1A.!!$F1 4303
1 TraesCS1A01G283900 chr1A 480934200 480935277 1077 True 628.0 628 77.7580 1846 2935 1 chr1A.!!$R1 1089
2 TraesCS1A01G283900 chr1D 381017746 381021212 3466 False 4700.0 4700 91.1010 85 3604 1 chr1D.!!$F1 3519
3 TraesCS1A01G283900 chr1D 379911039 379912116 1077 True 640.0 640 77.9170 1846 2935 1 chr1D.!!$R1 1089
4 TraesCS1A01G283900 chr1B 510807557 510811022 3465 False 4499.0 4499 90.1060 78 3607 1 chr1B.!!$F1 3529
5 TraesCS1A01G283900 chr1B 509901378 509902455 1077 True 623.0 623 77.5680 1846 2935 1 chr1B.!!$R1 1089
6 TraesCS1A01G283900 chr7A 39131358 39132067 709 True 1188.0 1188 96.9010 3596 4304 1 chr7A.!!$R1 708
7 TraesCS1A01G283900 chr7A 49058138 49059004 866 False 363.5 841 94.2460 3605 4304 4 chr7A.!!$F1 699
8 TraesCS1A01G283900 chr4A 489421317 489422160 843 True 654.0 1149 91.6385 3605 4304 2 chr4A.!!$R1 699
9 TraesCS1A01G283900 chr6A 498543038 498543738 700 True 1133.0 1133 95.8630 3605 4304 1 chr6A.!!$R1 699
10 TraesCS1A01G283900 chr3D 464807981 464808955 974 True 750.0 750 80.9240 1958 2935 1 chr3D.!!$R1 977
11 TraesCS1A01G283900 chr3D 465026173 465027850 1677 True 607.0 870 83.0230 1447 2935 2 chr3D.!!$R2 1488
12 TraesCS1A01G283900 chr3A 608194779 608195753 974 True 695.0 695 79.9400 1958 2935 1 chr3A.!!$R1 977
13 TraesCS1A01G283900 chr3A 608346386 608348068 1682 True 602.0 854 83.0190 1447 2935 2 chr3A.!!$R2 1488
14 TraesCS1A01G283900 chr3B 618154787 618155761 974 True 695.0 695 79.9400 1958 2935 1 chr3B.!!$R1 977
15 TraesCS1A01G283900 chr3B 618441196 618442878 1682 True 576.5 826 82.2530 1447 2935 2 chr3B.!!$R2 1488
16 TraesCS1A01G283900 chr3B 597545462 597545973 511 False 202.0 202 74.5250 1448 1958 1 chr3B.!!$F1 510
17 TraesCS1A01G283900 chr7B 111943061 111944038 977 False 604.0 604 78.2570 1958 2935 1 chr7B.!!$F1 977
18 TraesCS1A01G283900 chr7D 149181908 149182872 964 False 603.0 603 78.3980 1971 2935 1 chr7D.!!$F1 964
19 TraesCS1A01G283900 chr7D 149083951 149085129 1178 True 371.0 597 81.9650 1971 3186 2 chr7D.!!$R1 1215
20 TraesCS1A01G283900 chr2A 185264917 185265438 521 False 327.0 327 78.2610 1429 1950 1 chr2A.!!$F1 521

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
210 212 0.032540 GCCTGGACAACAAAAGCCAG 59.967 55.000 0.0 0.0 45.81 4.85 F
903 913 0.037590 TCGACCAATGGTTTCCCAGG 59.962 55.000 6.3 0.0 46.15 4.45 F
904 914 0.251165 CGACCAATGGTTTCCCAGGT 60.251 55.000 6.3 0.0 46.15 4.00 F
1411 1434 0.742505 CGTACTGACCCTAATGGCGA 59.257 55.000 0.0 0.0 37.83 5.54 F
1412 1435 1.135527 CGTACTGACCCTAATGGCGAA 59.864 52.381 0.0 0.0 37.83 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1410 0.743097 ATTAGGGTCAGTACGTCGCC 59.257 55.000 0.00 0.00 0.00 5.54 R
1914 2040 1.415672 GGCCGGGGAGTCCATTCATA 61.416 60.000 12.30 0.00 34.36 2.15 R
2984 3269 1.999735 ACACAGTACATGTACATGCGC 59.000 47.619 32.02 23.72 41.41 6.09 R
3192 3499 0.380733 TCACCGACGATCGATCTTGG 59.619 55.000 24.34 21.44 43.74 3.61 R
3447 3756 0.381801 AAGGCACACACAAGCTTTCG 59.618 50.000 0.00 0.00 0.00 3.46 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
23 24 6.949352 GGATAAATGTCCTCATGTCATTGT 57.051 37.500 0.00 0.00 35.32 2.71
24 25 7.338800 GGATAAATGTCCTCATGTCATTGTT 57.661 36.000 0.00 0.00 35.32 2.83
25 26 7.198390 GGATAAATGTCCTCATGTCATTGTTG 58.802 38.462 0.00 0.00 35.32 3.33
26 27 4.445452 AATGTCCTCATGTCATTGTTGC 57.555 40.909 0.00 0.00 34.19 4.17
27 28 2.161855 TGTCCTCATGTCATTGTTGCC 58.838 47.619 0.00 0.00 0.00 4.52
28 29 2.161855 GTCCTCATGTCATTGTTGCCA 58.838 47.619 0.00 0.00 0.00 4.92
29 30 2.756760 GTCCTCATGTCATTGTTGCCAT 59.243 45.455 0.00 0.00 0.00 4.40
30 31 2.756207 TCCTCATGTCATTGTTGCCATG 59.244 45.455 0.00 0.00 0.00 3.66
31 32 2.494471 CCTCATGTCATTGTTGCCATGT 59.506 45.455 0.00 0.00 0.00 3.21
32 33 3.428452 CCTCATGTCATTGTTGCCATGTC 60.428 47.826 0.00 0.00 0.00 3.06
33 34 2.492881 TCATGTCATTGTTGCCATGTCC 59.507 45.455 0.00 0.00 0.00 4.02
34 35 0.880441 TGTCATTGTTGCCATGTCCG 59.120 50.000 0.00 0.00 0.00 4.79
35 36 1.164411 GTCATTGTTGCCATGTCCGA 58.836 50.000 0.00 0.00 0.00 4.55
36 37 1.745087 GTCATTGTTGCCATGTCCGAT 59.255 47.619 0.00 0.00 0.00 4.18
37 38 2.016318 TCATTGTTGCCATGTCCGATC 58.984 47.619 0.00 0.00 0.00 3.69
38 39 1.016627 ATTGTTGCCATGTCCGATCG 58.983 50.000 8.51 8.51 0.00 3.69
39 40 1.024046 TTGTTGCCATGTCCGATCGG 61.024 55.000 28.62 28.62 0.00 4.18
40 41 1.153449 GTTGCCATGTCCGATCGGA 60.153 57.895 32.59 32.59 42.90 4.55
41 42 1.143838 TTGCCATGTCCGATCGGAG 59.856 57.895 36.38 24.74 46.16 4.63
42 43 1.326951 TTGCCATGTCCGATCGGAGA 61.327 55.000 36.38 34.67 46.16 3.71
43 44 1.300233 GCCATGTCCGATCGGAGAC 60.300 63.158 36.38 25.82 46.16 3.36
56 57 2.654802 GGAGACGGTCTGGACAAGA 58.345 57.895 16.72 0.00 0.00 3.02
57 58 1.187087 GGAGACGGTCTGGACAAGAT 58.813 55.000 16.72 0.00 37.23 2.40
58 59 1.550976 GGAGACGGTCTGGACAAGATT 59.449 52.381 16.72 0.00 37.23 2.40
59 60 2.028020 GGAGACGGTCTGGACAAGATTT 60.028 50.000 16.72 0.00 37.23 2.17
60 61 3.557264 GGAGACGGTCTGGACAAGATTTT 60.557 47.826 16.72 0.00 37.23 1.82
61 62 4.065789 GAGACGGTCTGGACAAGATTTTT 58.934 43.478 16.72 0.00 37.23 1.94
94 95 6.202188 TGACTAACGTCTGGACAAGAATTTTC 59.798 38.462 0.00 0.00 40.86 2.29
114 115 8.893563 ATTTTCATCCTAATTACCAAGACCAA 57.106 30.769 0.00 0.00 0.00 3.67
116 117 5.751586 TCATCCTAATTACCAAGACCAACC 58.248 41.667 0.00 0.00 0.00 3.77
129 130 2.509964 AGACCAACCAGTGAAGAAGGTT 59.490 45.455 0.00 0.00 46.03 3.50
137 138 5.123936 ACCAGTGAAGAAGGTTAAGACAAC 58.876 41.667 0.00 0.00 29.58 3.32
139 140 5.588648 CCAGTGAAGAAGGTTAAGACAACAA 59.411 40.000 0.00 0.00 0.00 2.83
152 153 7.148373 GGTTAAGACAACAACAAGTAGACAACA 60.148 37.037 0.00 0.00 0.00 3.33
154 155 5.242434 AGACAACAACAAGTAGACAACACA 58.758 37.500 0.00 0.00 0.00 3.72
168 170 5.121105 AGACAACACACTTAACAGGGTAAC 58.879 41.667 0.00 0.00 32.56 2.50
171 173 3.721035 ACACACTTAACAGGGTAACGAC 58.279 45.455 0.00 0.00 32.56 4.34
175 177 4.037446 ACACTTAACAGGGTAACGACGTAA 59.963 41.667 0.00 0.00 33.47 3.18
188 190 4.546637 CGTAAGTTCGTCGCCAGT 57.453 55.556 0.00 0.00 0.00 4.00
191 193 1.337821 GTAAGTTCGTCGCCAGTGAG 58.662 55.000 0.00 0.00 0.00 3.51
195 197 3.573772 TTCGTCGCCAGTGAGCCTG 62.574 63.158 0.00 0.00 41.15 4.85
210 212 0.032540 GCCTGGACAACAAAAGCCAG 59.967 55.000 0.00 0.00 45.81 4.85
224 226 5.990996 ACAAAAGCCAGGACAATAATTGTTG 59.009 36.000 12.84 12.84 45.52 3.33
237 239 1.821216 ATTGTTGACCCCGACATGAC 58.179 50.000 0.00 0.00 36.62 3.06
262 264 4.250464 GGTGATTTTGACGACAGATGGTA 58.750 43.478 0.00 0.00 0.00 3.25
269 271 2.289820 TGACGACAGATGGTACGATAGC 59.710 50.000 0.00 0.00 42.67 2.97
316 319 4.636435 AAAGGCACCGGTGGGACG 62.636 66.667 34.58 10.83 36.97 4.79
361 368 8.752766 TTACGATAATTACGGGAGATGAATTC 57.247 34.615 0.00 0.00 34.93 2.17
374 381 7.040478 CGGGAGATGAATTCCTGCATTTAATTA 60.040 37.037 2.27 0.00 34.50 1.40
390 397 7.331193 GCATTTAATTATCGTCCTACCTACAGG 59.669 40.741 0.00 0.00 42.17 4.00
392 399 7.756395 TTAATTATCGTCCTACCTACAGGAG 57.244 40.000 1.29 0.00 45.49 3.69
393 400 4.785346 TTATCGTCCTACCTACAGGAGT 57.215 45.455 1.29 0.00 45.49 3.85
394 401 5.894298 TTATCGTCCTACCTACAGGAGTA 57.106 43.478 1.29 0.00 45.49 2.59
395 402 3.550437 TCGTCCTACCTACAGGAGTAC 57.450 52.381 1.29 0.00 45.49 2.73
396 403 2.159043 TCGTCCTACCTACAGGAGTACG 60.159 54.545 1.29 6.58 45.49 3.67
398 405 2.941720 GTCCTACCTACAGGAGTACGTG 59.058 54.545 1.29 0.00 45.49 4.49
458 465 1.005394 TCGAGTTCGTCCTTTGGGC 60.005 57.895 1.07 0.00 40.80 5.36
462 469 2.033194 GTTCGTCCTTTGGGCGGAG 61.033 63.158 10.75 0.00 34.56 4.63
482 489 5.614668 CGGAGTATTATAAATGCCGTGCTTG 60.615 44.000 9.78 0.00 33.14 4.01
515 522 1.330080 GCAAATCGTGCGTGACAAGC 61.330 55.000 6.40 6.40 45.10 4.01
526 533 0.235926 GTGACAAGCAAGGAACGAGC 59.764 55.000 0.00 0.00 0.00 5.03
543 550 2.352225 CGAGCAAGAGCAGTAGTTGTCT 60.352 50.000 0.00 0.00 45.49 3.41
544 551 3.119814 CGAGCAAGAGCAGTAGTTGTCTA 60.120 47.826 0.00 0.00 45.49 2.59
545 552 4.420168 GAGCAAGAGCAGTAGTTGTCTAG 58.580 47.826 0.00 0.00 45.49 2.43
546 553 2.926838 GCAAGAGCAGTAGTTGTCTAGC 59.073 50.000 0.00 0.00 41.58 3.42
547 554 3.516615 CAAGAGCAGTAGTTGTCTAGCC 58.483 50.000 0.00 0.00 0.00 3.93
548 555 3.094484 AGAGCAGTAGTTGTCTAGCCT 57.906 47.619 0.00 0.00 0.00 4.58
549 556 4.237976 AGAGCAGTAGTTGTCTAGCCTA 57.762 45.455 0.00 0.00 0.00 3.93
550 557 4.204012 AGAGCAGTAGTTGTCTAGCCTAG 58.796 47.826 0.00 0.00 0.00 3.02
551 558 2.691011 AGCAGTAGTTGTCTAGCCTAGC 59.309 50.000 0.00 0.00 0.00 3.42
563 570 5.715279 TGTCTAGCCTAGCTTAAACAAGAGA 59.285 40.000 0.00 0.00 40.44 3.10
576 583 7.623089 GCTTAAACAAGAGAACACAGCTCATAG 60.623 40.741 0.00 0.00 34.85 2.23
577 584 4.199432 ACAAGAGAACACAGCTCATAGG 57.801 45.455 0.00 0.00 34.85 2.57
578 585 3.580458 ACAAGAGAACACAGCTCATAGGT 59.420 43.478 0.00 0.00 34.85 3.08
580 587 5.423610 ACAAGAGAACACAGCTCATAGGTAT 59.576 40.000 0.00 0.00 34.85 2.73
582 589 4.343526 AGAGAACACAGCTCATAGGTATGG 59.656 45.833 0.00 0.00 34.85 2.74
583 590 4.290093 AGAACACAGCTCATAGGTATGGA 58.710 43.478 0.00 0.00 34.50 3.41
584 591 4.716784 AGAACACAGCTCATAGGTATGGAA 59.283 41.667 0.00 0.00 34.50 3.53
585 592 4.679373 ACACAGCTCATAGGTATGGAAG 57.321 45.455 0.00 0.00 34.50 3.46
586 593 4.290093 ACACAGCTCATAGGTATGGAAGA 58.710 43.478 0.00 0.00 34.50 2.87
587 594 4.904251 ACACAGCTCATAGGTATGGAAGAT 59.096 41.667 0.00 0.00 34.50 2.40
588 595 5.011533 ACACAGCTCATAGGTATGGAAGATC 59.988 44.000 0.00 0.00 34.50 2.75
589 596 5.011431 CACAGCTCATAGGTATGGAAGATCA 59.989 44.000 0.00 0.00 34.50 2.92
590 597 5.245751 ACAGCTCATAGGTATGGAAGATCAG 59.754 44.000 0.00 0.00 34.50 2.90
591 598 4.222588 AGCTCATAGGTATGGAAGATCAGC 59.777 45.833 0.00 0.00 34.50 4.26
592 599 4.020751 GCTCATAGGTATGGAAGATCAGCA 60.021 45.833 0.00 0.00 34.50 4.41
593 600 5.722263 CTCATAGGTATGGAAGATCAGCAG 58.278 45.833 0.00 0.00 34.50 4.24
608 615 3.141398 TCAGCAGCAGGTTGACTTTAAG 58.859 45.455 0.00 0.00 31.16 1.85
741 749 4.273318 CCCATGCTCATCATCATCATCAT 58.727 43.478 0.00 0.00 31.79 2.45
742 750 4.336713 CCCATGCTCATCATCATCATCATC 59.663 45.833 0.00 0.00 31.79 2.92
743 751 4.943705 CCATGCTCATCATCATCATCATCA 59.056 41.667 0.00 0.00 31.79 3.07
744 752 5.591877 CCATGCTCATCATCATCATCATCAT 59.408 40.000 0.00 0.00 31.79 2.45
745 753 6.238593 CCATGCTCATCATCATCATCATCATC 60.239 42.308 0.00 0.00 31.79 2.92
746 754 5.804639 TGCTCATCATCATCATCATCATCA 58.195 37.500 0.00 0.00 0.00 3.07
747 755 6.418101 TGCTCATCATCATCATCATCATCAT 58.582 36.000 0.00 0.00 0.00 2.45
748 756 6.540189 TGCTCATCATCATCATCATCATCATC 59.460 38.462 0.00 0.00 0.00 2.92
749 757 6.540189 GCTCATCATCATCATCATCATCATCA 59.460 38.462 0.00 0.00 0.00 3.07
750 758 7.228308 GCTCATCATCATCATCATCATCATCAT 59.772 37.037 0.00 0.00 0.00 2.45
751 759 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
752 760 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
753 761 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
754 762 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
755 763 8.489489 TCATCATCATCATCATCATCATCATCT 58.511 33.333 0.00 0.00 0.00 2.90
756 764 9.118300 CATCATCATCATCATCATCATCATCTT 57.882 33.333 0.00 0.00 0.00 2.40
757 765 8.723942 TCATCATCATCATCATCATCATCTTC 57.276 34.615 0.00 0.00 0.00 2.87
758 766 8.321353 TCATCATCATCATCATCATCATCTTCA 58.679 33.333 0.00 0.00 0.00 3.02
759 767 9.118300 CATCATCATCATCATCATCATCTTCAT 57.882 33.333 0.00 0.00 0.00 2.57
760 768 8.723942 TCATCATCATCATCATCATCTTCATC 57.276 34.615 0.00 0.00 0.00 2.92
761 769 8.543774 TCATCATCATCATCATCATCTTCATCT 58.456 33.333 0.00 0.00 0.00 2.90
764 772 8.375506 TCATCATCATCATCATCTTCATCTTCA 58.624 33.333 0.00 0.00 0.00 3.02
783 791 3.431856 TCATCGTCGTCGTAAATCCAAG 58.568 45.455 1.33 0.00 38.33 3.61
806 815 1.671901 AAAGCACACCCACCAAACGG 61.672 55.000 0.00 0.00 0.00 4.44
819 828 2.867975 ACCAAACGGTCGAAAGTAACTG 59.132 45.455 0.00 0.00 26.76 3.16
825 834 2.155155 CGGTCGAAAGTAACTGAACAGC 59.845 50.000 1.46 0.00 0.00 4.40
828 837 2.792674 TCGAAAGTAACTGAACAGCACG 59.207 45.455 1.46 0.00 0.00 5.34
840 849 1.921243 ACAGCACGGAAAACAAAAGC 58.079 45.000 0.00 0.00 0.00 3.51
841 850 1.476488 ACAGCACGGAAAACAAAAGCT 59.524 42.857 0.00 0.00 0.00 3.74
845 854 4.744631 CAGCACGGAAAACAAAAGCTATTT 59.255 37.500 0.00 0.00 0.00 1.40
868 877 2.409870 GCTTTGGCCCCACTCATCG 61.410 63.158 0.00 0.00 0.00 3.84
870 879 1.303236 TTTGGCCCCACTCATCGTG 60.303 57.895 0.00 0.00 43.41 4.35
898 908 6.226787 AGATATCTCATCGACCAATGGTTTC 58.773 40.000 6.30 0.00 35.25 2.78
903 913 0.037590 TCGACCAATGGTTTCCCAGG 59.962 55.000 6.30 0.00 46.15 4.45
904 914 0.251165 CGACCAATGGTTTCCCAGGT 60.251 55.000 6.30 0.00 46.15 4.00
905 915 1.256812 GACCAATGGTTTCCCAGGTG 58.743 55.000 6.30 0.00 46.15 4.00
906 916 2.669878 CCAATGGTTTCCCAGGTGG 58.330 57.895 0.00 0.00 46.15 4.61
907 917 1.543944 CCAATGGTTTCCCAGGTGGC 61.544 60.000 0.00 0.00 46.15 5.01
908 918 1.229177 AATGGTTTCCCAGGTGGCC 60.229 57.895 0.00 0.00 46.15 5.36
909 919 2.029892 AATGGTTTCCCAGGTGGCCA 62.030 55.000 0.00 0.00 46.15 5.36
910 920 2.283173 GGTTTCCCAGGTGGCCAG 60.283 66.667 5.11 0.00 0.00 4.85
911 921 2.283173 GTTTCCCAGGTGGCCAGG 60.283 66.667 5.11 3.35 0.00 4.45
924 934 5.958380 CAGGTGGCCAGGTATATATAGAGAA 59.042 44.000 5.11 0.00 0.00 2.87
932 942 5.886474 CAGGTATATATAGAGAACCCGAGCA 59.114 44.000 0.00 0.00 0.00 4.26
933 943 6.377429 CAGGTATATATAGAGAACCCGAGCAA 59.623 42.308 0.00 0.00 0.00 3.91
935 945 6.377712 GGTATATATAGAGAACCCGAGCAACT 59.622 42.308 0.00 0.00 0.00 3.16
1104 1116 0.877071 TCACGACGAGGAAGTACCAC 59.123 55.000 0.00 0.00 42.04 4.16
1129 1141 6.702716 TCGATGTAAGTGTGTCCATACATA 57.297 37.500 0.00 0.00 38.67 2.29
1134 1146 5.815222 TGTAAGTGTGTCCATACATACATGC 59.185 40.000 7.78 1.19 46.83 4.06
1156 1174 6.484818 GCATGATGCATATGTACATGTGTA 57.515 37.500 27.08 24.57 44.26 2.90
1208 1226 6.204852 TCCTATACCTACGTGAAATCCCTA 57.795 41.667 0.00 0.00 0.00 3.53
1216 1234 1.801771 CGTGAAATCCCTACGCAAACA 59.198 47.619 0.00 0.00 0.00 2.83
1224 1242 4.185467 TCCCTACGCAAACATTTACGTA 57.815 40.909 8.98 8.98 40.32 3.57
1228 1246 5.004726 CCCTACGCAAACATTTACGTACTAC 59.995 44.000 5.87 0.00 40.32 2.73
1230 1248 6.966632 CCTACGCAAACATTTACGTACTACTA 59.033 38.462 5.87 0.00 40.32 1.82
1232 1250 6.381801 ACGCAAACATTTACGTACTACTAGT 58.618 36.000 0.00 0.00 38.29 2.57
1233 1251 6.863126 ACGCAAACATTTACGTACTACTAGTT 59.137 34.615 0.00 0.00 38.29 2.24
1234 1252 7.148918 ACGCAAACATTTACGTACTACTAGTTG 60.149 37.037 0.00 0.59 38.29 3.16
1235 1253 7.060979 CGCAAACATTTACGTACTACTAGTTGA 59.939 37.037 11.43 0.00 0.00 3.18
1236 1254 8.866956 GCAAACATTTACGTACTACTAGTTGAT 58.133 33.333 11.43 0.00 0.00 2.57
1268 1286 1.290203 CGTCTGCTGTTGAGTGTTGT 58.710 50.000 0.00 0.00 0.00 3.32
1297 1315 7.692908 AACAATTCCATCAAACTTTTACGTG 57.307 32.000 0.00 0.00 0.00 4.49
1303 1321 7.033530 TCCATCAAACTTTTACGTGTGAATT 57.966 32.000 0.00 0.00 34.96 2.17
1376 1399 2.512286 ATCGACCGTGCATGCAGG 60.512 61.111 28.99 28.99 0.00 4.85
1411 1434 0.742505 CGTACTGACCCTAATGGCGA 59.257 55.000 0.00 0.00 37.83 5.54
1412 1435 1.135527 CGTACTGACCCTAATGGCGAA 59.864 52.381 0.00 0.00 37.83 4.70
1840 1966 4.980805 TGTTCGGCGAGTGGTGGC 62.981 66.667 10.46 0.00 0.00 5.01
1914 2040 2.020131 CGTGTCCGACGCCTATACT 58.980 57.895 6.50 0.00 42.21 2.12
2916 3173 3.976701 CTGGGTCGCCATCCGCTTT 62.977 63.158 0.00 0.00 36.73 3.51
2984 3269 6.060136 TGGAGCTTGAATCCTCATTCATTAG 58.940 40.000 0.00 0.00 46.36 1.73
2994 3279 3.809279 CCTCATTCATTAGCGCATGTACA 59.191 43.478 11.47 0.00 0.00 2.90
2995 3280 4.453478 CCTCATTCATTAGCGCATGTACAT 59.547 41.667 11.47 1.41 0.00 2.29
2996 3281 5.347012 TCATTCATTAGCGCATGTACATG 57.653 39.130 28.07 28.07 41.60 3.21
2997 3282 4.815846 TCATTCATTAGCGCATGTACATGT 59.184 37.500 31.10 17.69 40.80 3.21
2998 3283 5.988561 TCATTCATTAGCGCATGTACATGTA 59.011 36.000 31.10 16.76 40.80 2.29
2999 3284 5.651172 TTCATTAGCGCATGTACATGTAC 57.349 39.130 31.10 25.99 40.80 2.90
3041 3326 5.414765 ACTGCTCATATGGACATATGCATTG 59.585 40.000 21.70 15.36 46.31 2.82
3045 3330 6.505044 TCATATGGACATATGCATTGCTTC 57.495 37.500 21.70 0.00 46.31 3.86
3046 3331 6.243148 TCATATGGACATATGCATTGCTTCT 58.757 36.000 21.70 0.00 46.31 2.85
3130 3437 2.281484 GCTGGTGCTGGACGGAAA 60.281 61.111 0.00 0.00 36.03 3.13
3192 3499 6.767902 TCTCCCAAAATGCTAGACATGATTAC 59.232 38.462 0.00 0.00 39.60 1.89
3225 3532 1.890489 TCGGTGAAGAAGATTGGTCGA 59.110 47.619 0.00 0.00 0.00 4.20
3226 3533 2.496070 TCGGTGAAGAAGATTGGTCGAT 59.504 45.455 0.00 0.00 0.00 3.59
3227 3534 2.860735 CGGTGAAGAAGATTGGTCGATC 59.139 50.000 0.00 0.00 0.00 3.69
3228 3535 2.860735 GGTGAAGAAGATTGGTCGATCG 59.139 50.000 9.36 9.36 0.00 3.69
3291 3598 4.724602 GCTCTCGCGTGTCCAGCA 62.725 66.667 5.77 0.00 34.19 4.41
3308 3616 3.242091 CCAGCAAGTTCGTCGTGATTATG 60.242 47.826 0.00 0.00 0.00 1.90
3325 3633 8.650714 CGTGATTATGTCCAATATAGTGATGTG 58.349 37.037 0.79 0.00 0.00 3.21
3447 3756 4.581409 TGGGCTTCTTTGTAAGTTGTAACC 59.419 41.667 0.00 0.00 0.00 2.85
3498 3807 8.870075 TCTATCTGTATGTATCTGCAGTGTAT 57.130 34.615 14.67 2.30 0.00 2.29
3499 3808 9.301897 TCTATCTGTATGTATCTGCAGTGTATT 57.698 33.333 14.67 0.10 0.00 1.89
3533 3842 7.559590 AAAGCCTAGATATGTTCATTGTCAC 57.440 36.000 0.00 0.00 0.00 3.67
3555 3864 6.416455 TCACGATAAATTTTGTTTGCACACTC 59.584 34.615 4.37 0.00 30.32 3.51
3662 3971 4.517453 TCGAAAACAGTCAAATTTCCCGAT 59.483 37.500 0.00 0.00 31.03 4.18
3725 4034 6.918022 CCAAAGAGCAAAAAGAACGTCTAAAT 59.082 34.615 0.00 0.00 0.00 1.40
3839 4148 0.664761 CGCCTGCAGTCCCATAATTG 59.335 55.000 13.81 0.00 0.00 2.32
4203 4512 9.802039 AAAGGTAAATTACACTGTAAATCTGGA 57.198 29.630 5.73 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.949352 ACAATGACATGAGGACATTTATCC 57.051 37.500 0.00 0.00 39.28 2.59
1 2 6.694411 GCAACAATGACATGAGGACATTTATC 59.306 38.462 0.00 0.00 34.15 1.75
2 3 6.406177 GGCAACAATGACATGAGGACATTTAT 60.406 38.462 0.00 0.00 33.41 1.40
3 4 5.105797 GGCAACAATGACATGAGGACATTTA 60.106 40.000 0.00 0.00 33.41 1.40
4 5 4.322198 GGCAACAATGACATGAGGACATTT 60.322 41.667 0.00 0.00 33.41 2.32
5 6 3.194116 GGCAACAATGACATGAGGACATT 59.806 43.478 0.00 3.27 33.41 2.71
6 7 2.756760 GGCAACAATGACATGAGGACAT 59.243 45.455 0.00 0.00 33.41 3.06
7 8 2.161855 GGCAACAATGACATGAGGACA 58.838 47.619 0.00 0.00 33.41 4.02
8 9 2.927553 GGCAACAATGACATGAGGAC 57.072 50.000 0.00 0.00 33.41 3.85
18 19 4.446484 CCGATCGGACATGGCAACAATG 62.446 54.545 30.62 0.00 45.39 2.82
19 20 2.348440 CCGATCGGACATGGCAACAAT 61.348 52.381 30.62 0.00 45.39 2.71
20 21 1.024046 CCGATCGGACATGGCAACAA 61.024 55.000 30.62 0.00 45.39 2.83
21 22 1.449423 CCGATCGGACATGGCAACA 60.449 57.895 30.62 0.00 46.13 3.33
22 23 1.153449 TCCGATCGGACATGGCAAC 60.153 57.895 32.59 0.00 39.76 4.17
23 24 1.143838 CTCCGATCGGACATGGCAA 59.856 57.895 32.59 10.28 39.76 4.52
24 25 1.756561 TCTCCGATCGGACATGGCA 60.757 57.895 32.59 11.07 39.76 4.92
25 26 1.300233 GTCTCCGATCGGACATGGC 60.300 63.158 32.59 20.86 39.76 4.40
26 27 1.008424 CGTCTCCGATCGGACATGG 60.008 63.158 32.59 22.23 39.76 3.66
27 28 4.616592 CGTCTCCGATCGGACATG 57.383 61.111 32.59 23.71 39.76 3.21
33 34 1.818363 TCCAGACCGTCTCCGATCG 60.818 63.158 8.51 8.51 35.63 3.69
34 35 1.030488 TGTCCAGACCGTCTCCGATC 61.030 60.000 0.00 0.00 35.63 3.69
35 36 0.611062 TTGTCCAGACCGTCTCCGAT 60.611 55.000 0.00 0.00 35.63 4.18
36 37 1.228337 TTGTCCAGACCGTCTCCGA 60.228 57.895 0.00 0.00 35.63 4.55
37 38 1.213013 CTTGTCCAGACCGTCTCCG 59.787 63.158 0.00 0.00 0.00 4.63
38 39 1.187087 ATCTTGTCCAGACCGTCTCC 58.813 55.000 0.00 0.00 32.83 3.71
39 40 3.320673 AAATCTTGTCCAGACCGTCTC 57.679 47.619 0.00 0.00 32.83 3.36
40 41 3.771577 AAAATCTTGTCCAGACCGTCT 57.228 42.857 0.00 0.00 32.83 4.18
71 72 6.053005 TGAAAATTCTTGTCCAGACGTTAGT 58.947 36.000 0.00 0.00 0.00 2.24
72 73 6.539649 TGAAAATTCTTGTCCAGACGTTAG 57.460 37.500 0.00 0.00 0.00 2.34
73 74 6.148811 GGATGAAAATTCTTGTCCAGACGTTA 59.851 38.462 0.00 0.00 0.00 3.18
74 75 5.048713 GGATGAAAATTCTTGTCCAGACGTT 60.049 40.000 0.00 0.00 0.00 3.99
75 76 4.455877 GGATGAAAATTCTTGTCCAGACGT 59.544 41.667 0.00 0.00 0.00 4.34
76 77 4.697352 AGGATGAAAATTCTTGTCCAGACG 59.303 41.667 12.15 0.00 0.00 4.18
94 95 5.505780 TGGTTGGTCTTGGTAATTAGGATG 58.494 41.667 0.00 0.00 0.00 3.51
114 115 5.123936 GTTGTCTTAACCTTCTTCACTGGT 58.876 41.667 0.00 0.00 35.29 4.00
116 117 6.093495 TGTTGTTGTCTTAACCTTCTTCACTG 59.907 38.462 0.00 0.00 0.00 3.66
129 130 6.874664 TGTGTTGTCTACTTGTTGTTGTCTTA 59.125 34.615 0.00 0.00 0.00 2.10
137 138 7.067532 TGTTAAGTGTGTTGTCTACTTGTTG 57.932 36.000 0.00 0.00 36.22 3.33
139 140 5.815740 CCTGTTAAGTGTGTTGTCTACTTGT 59.184 40.000 0.00 0.00 36.22 3.16
152 153 2.362077 ACGTCGTTACCCTGTTAAGTGT 59.638 45.455 0.00 0.00 0.00 3.55
154 155 4.278419 ACTTACGTCGTTACCCTGTTAAGT 59.722 41.667 1.78 0.59 0.00 2.24
171 173 0.386352 TCACTGGCGACGAACTTACG 60.386 55.000 0.00 0.00 39.31 3.18
175 177 2.049063 GCTCACTGGCGACGAACT 60.049 61.111 0.00 0.00 0.00 3.01
188 190 1.032014 GCTTTTGTTGTCCAGGCTCA 58.968 50.000 0.00 0.00 0.00 4.26
191 193 0.032540 CTGGCTTTTGTTGTCCAGGC 59.967 55.000 0.00 0.00 41.71 4.85
195 197 1.398692 TGTCCTGGCTTTTGTTGTCC 58.601 50.000 0.00 0.00 0.00 4.02
196 198 3.733443 ATTGTCCTGGCTTTTGTTGTC 57.267 42.857 0.00 0.00 0.00 3.18
201 203 6.146021 GTCAACAATTATTGTCCTGGCTTTTG 59.854 38.462 11.24 3.04 44.59 2.44
210 212 3.128068 GTCGGGGTCAACAATTATTGTCC 59.872 47.826 11.24 8.22 44.59 4.02
222 224 2.047655 GCGTCATGTCGGGGTCAA 60.048 61.111 14.02 0.00 0.00 3.18
237 239 0.179250 CTGTCGTCAAAATCACCGCG 60.179 55.000 0.00 0.00 0.00 6.46
316 319 6.974622 TCGTAATATAAGGTGGAAAGACGTTC 59.025 38.462 0.00 0.00 35.28 3.95
317 320 6.866480 TCGTAATATAAGGTGGAAAGACGTT 58.134 36.000 0.00 0.00 0.00 3.99
318 321 6.455360 TCGTAATATAAGGTGGAAAGACGT 57.545 37.500 0.00 0.00 0.00 4.34
319 322 9.635520 ATTATCGTAATATAAGGTGGAAAGACG 57.364 33.333 0.00 0.00 0.00 4.18
346 353 2.115427 TGCAGGAATTCATCTCCCGTA 58.885 47.619 7.93 0.00 32.95 4.02
347 354 0.911769 TGCAGGAATTCATCTCCCGT 59.088 50.000 7.93 0.00 32.95 5.28
361 368 6.231211 AGGTAGGACGATAATTAAATGCAGG 58.769 40.000 0.00 0.00 0.00 4.85
374 381 3.494048 CGTACTCCTGTAGGTAGGACGAT 60.494 52.174 20.79 0.00 44.76 3.73
398 405 2.642139 ACATGCATTTGTGCTGTAGC 57.358 45.000 0.00 0.00 42.50 3.58
418 425 4.575885 AGGCTGTCGTGTTTATGTTATGT 58.424 39.130 0.00 0.00 0.00 2.29
419 426 4.259810 CGAGGCTGTCGTGTTTATGTTATG 60.260 45.833 0.00 0.00 44.20 1.90
420 427 3.863424 CGAGGCTGTCGTGTTTATGTTAT 59.137 43.478 0.00 0.00 44.20 1.89
421 428 3.247442 CGAGGCTGTCGTGTTTATGTTA 58.753 45.455 0.00 0.00 44.20 2.41
422 429 2.066262 CGAGGCTGTCGTGTTTATGTT 58.934 47.619 0.00 0.00 44.20 2.71
458 465 3.994392 AGCACGGCATTTATAATACTCCG 59.006 43.478 11.78 11.78 40.98 4.63
462 469 5.432885 ACCAAGCACGGCATTTATAATAC 57.567 39.130 0.00 0.00 0.00 1.89
515 522 0.795085 CTGCTCTTGCTCGTTCCTTG 59.205 55.000 0.00 0.00 40.48 3.61
526 533 3.194542 AGGCTAGACAACTACTGCTCTTG 59.805 47.826 0.00 0.00 0.00 3.02
543 550 6.164176 GTGTTCTCTTGTTTAAGCTAGGCTA 58.836 40.000 0.00 0.00 38.25 3.93
544 551 4.998033 GTGTTCTCTTGTTTAAGCTAGGCT 59.002 41.667 0.00 0.00 42.56 4.58
545 552 4.755123 TGTGTTCTCTTGTTTAAGCTAGGC 59.245 41.667 1.39 0.00 33.82 3.93
546 553 5.106908 GCTGTGTTCTCTTGTTTAAGCTAGG 60.107 44.000 1.39 0.00 33.82 3.02
547 554 5.698545 AGCTGTGTTCTCTTGTTTAAGCTAG 59.301 40.000 0.00 0.00 36.75 3.42
548 555 5.611374 AGCTGTGTTCTCTTGTTTAAGCTA 58.389 37.500 0.00 0.00 36.75 3.32
549 556 4.455606 AGCTGTGTTCTCTTGTTTAAGCT 58.544 39.130 0.00 0.00 33.82 3.74
550 557 4.273480 TGAGCTGTGTTCTCTTGTTTAAGC 59.727 41.667 0.00 0.00 33.82 3.09
551 558 5.991328 TGAGCTGTGTTCTCTTGTTTAAG 57.009 39.130 0.00 0.00 35.16 1.85
563 570 4.716784 TCTTCCATACCTATGAGCTGTGTT 59.283 41.667 0.00 0.00 35.75 3.32
576 583 2.492012 CTGCTGCTGATCTTCCATACC 58.508 52.381 0.00 0.00 0.00 2.73
577 584 2.158842 ACCTGCTGCTGATCTTCCATAC 60.159 50.000 8.20 0.00 0.00 2.39
578 585 2.121948 ACCTGCTGCTGATCTTCCATA 58.878 47.619 8.20 0.00 0.00 2.74
580 587 0.694771 AACCTGCTGCTGATCTTCCA 59.305 50.000 8.20 0.00 0.00 3.53
582 589 1.736681 GTCAACCTGCTGCTGATCTTC 59.263 52.381 8.20 0.00 0.00 2.87
583 590 1.350351 AGTCAACCTGCTGCTGATCTT 59.650 47.619 8.20 0.00 0.00 2.40
584 591 0.982704 AGTCAACCTGCTGCTGATCT 59.017 50.000 8.20 0.00 0.00 2.75
585 592 1.818642 AAGTCAACCTGCTGCTGATC 58.181 50.000 8.20 0.00 0.00 2.92
586 593 2.283145 AAAGTCAACCTGCTGCTGAT 57.717 45.000 8.20 0.00 0.00 2.90
587 594 2.928801 TAAAGTCAACCTGCTGCTGA 57.071 45.000 8.20 0.00 0.00 4.26
588 595 2.880890 ACTTAAAGTCAACCTGCTGCTG 59.119 45.455 0.00 0.00 0.00 4.41
589 596 3.214696 ACTTAAAGTCAACCTGCTGCT 57.785 42.857 0.00 0.00 0.00 4.24
590 597 3.550842 CCAACTTAAAGTCAACCTGCTGC 60.551 47.826 0.00 0.00 0.00 5.25
591 598 3.550842 GCCAACTTAAAGTCAACCTGCTG 60.551 47.826 0.00 0.00 0.00 4.41
592 599 2.623416 GCCAACTTAAAGTCAACCTGCT 59.377 45.455 0.00 0.00 0.00 4.24
593 600 2.288213 GGCCAACTTAAAGTCAACCTGC 60.288 50.000 0.00 0.00 0.00 4.85
608 615 1.109323 AGCTTTGGAGTGTGGCCAAC 61.109 55.000 7.24 8.61 44.58 3.77
741 749 7.545965 CGATGAAGATGAAGATGATGATGATGA 59.454 37.037 0.00 0.00 0.00 2.92
742 750 7.332182 ACGATGAAGATGAAGATGATGATGATG 59.668 37.037 0.00 0.00 0.00 3.07
743 751 7.387643 ACGATGAAGATGAAGATGATGATGAT 58.612 34.615 0.00 0.00 0.00 2.45
744 752 6.756221 ACGATGAAGATGAAGATGATGATGA 58.244 36.000 0.00 0.00 0.00 2.92
745 753 6.183359 CGACGATGAAGATGAAGATGATGATG 60.183 42.308 0.00 0.00 0.00 3.07
746 754 5.862860 CGACGATGAAGATGAAGATGATGAT 59.137 40.000 0.00 0.00 0.00 2.45
747 755 5.218139 CGACGATGAAGATGAAGATGATGA 58.782 41.667 0.00 0.00 0.00 2.92
748 756 4.981054 ACGACGATGAAGATGAAGATGATG 59.019 41.667 0.00 0.00 0.00 3.07
749 757 5.193663 ACGACGATGAAGATGAAGATGAT 57.806 39.130 0.00 0.00 0.00 2.45
750 758 4.602006 GACGACGATGAAGATGAAGATGA 58.398 43.478 0.00 0.00 0.00 2.92
751 759 3.420249 CGACGACGATGAAGATGAAGATG 59.580 47.826 0.00 0.00 42.66 2.90
752 760 3.065510 ACGACGACGATGAAGATGAAGAT 59.934 43.478 15.32 0.00 42.66 2.40
753 761 2.418976 ACGACGACGATGAAGATGAAGA 59.581 45.455 15.32 0.00 42.66 2.87
754 762 2.786854 ACGACGACGATGAAGATGAAG 58.213 47.619 15.32 0.00 42.66 3.02
755 763 2.913777 ACGACGACGATGAAGATGAA 57.086 45.000 15.32 0.00 42.66 2.57
756 764 4.345271 TTTACGACGACGATGAAGATGA 57.655 40.909 15.32 0.00 42.66 2.92
757 765 4.146616 GGATTTACGACGACGATGAAGATG 59.853 45.833 15.32 0.00 42.66 2.90
758 766 4.201980 TGGATTTACGACGACGATGAAGAT 60.202 41.667 15.32 0.00 42.66 2.40
759 767 3.127376 TGGATTTACGACGACGATGAAGA 59.873 43.478 15.32 0.00 42.66 2.87
760 768 3.431856 TGGATTTACGACGACGATGAAG 58.568 45.455 15.32 0.00 42.66 3.02
761 769 3.490800 TGGATTTACGACGACGATGAA 57.509 42.857 15.32 5.82 42.66 2.57
764 772 2.190981 GCTTGGATTTACGACGACGAT 58.809 47.619 15.32 0.00 42.66 3.73
783 791 1.954362 TTGGTGGGTGTGCTTTGTGC 61.954 55.000 0.00 0.00 43.25 4.57
806 815 3.361724 CGTGCTGTTCAGTTACTTTCGAC 60.362 47.826 1.78 0.00 0.00 4.20
819 828 2.281498 GCTTTTGTTTTCCGTGCTGTTC 59.719 45.455 0.00 0.00 0.00 3.18
825 834 5.047188 ACCAAATAGCTTTTGTTTTCCGTG 58.953 37.500 15.52 0.00 0.00 4.94
828 837 5.527214 AGCAACCAAATAGCTTTTGTTTTCC 59.473 36.000 15.52 6.11 34.37 3.13
840 849 1.066215 GGGGCCAAAGCAACCAAATAG 60.066 52.381 4.39 0.00 42.56 1.73
841 850 0.980423 GGGGCCAAAGCAACCAAATA 59.020 50.000 4.39 0.00 42.56 1.40
845 854 2.841988 GTGGGGCCAAAGCAACCA 60.842 61.111 4.39 0.00 43.00 3.67
868 877 5.316327 TGGTCGATGAGATATCTATGCAC 57.684 43.478 4.89 0.00 0.00 4.57
870 879 5.752472 CCATTGGTCGATGAGATATCTATGC 59.248 44.000 4.89 0.00 0.00 3.14
898 908 2.038863 TATATACCTGGCCACCTGGG 57.961 55.000 13.74 10.61 45.34 4.45
903 913 5.128991 GGGTTCTCTATATATACCTGGCCAC 59.871 48.000 0.00 0.00 0.00 5.01
904 914 5.278061 GGGTTCTCTATATATACCTGGCCA 58.722 45.833 4.71 4.71 0.00 5.36
905 915 4.341520 CGGGTTCTCTATATATACCTGGCC 59.658 50.000 0.00 0.00 32.73 5.36
906 916 5.198965 TCGGGTTCTCTATATATACCTGGC 58.801 45.833 9.59 0.00 36.21 4.85
907 917 5.299782 GCTCGGGTTCTCTATATATACCTGG 59.700 48.000 9.59 0.00 36.21 4.45
908 918 5.886474 TGCTCGGGTTCTCTATATATACCTG 59.114 44.000 4.59 4.59 36.74 4.00
909 919 6.075949 TGCTCGGGTTCTCTATATATACCT 57.924 41.667 2.41 0.00 0.00 3.08
910 920 6.377712 AGTTGCTCGGGTTCTCTATATATACC 59.622 42.308 0.00 0.00 0.00 2.73
911 921 7.393841 AGTTGCTCGGGTTCTCTATATATAC 57.606 40.000 0.00 0.00 0.00 1.47
924 934 4.722193 CAATGGAGTTGCTCGGGT 57.278 55.556 0.00 0.00 0.00 5.28
932 942 2.028748 GCTTGGTGATTGCAATGGAGTT 60.029 45.455 18.59 0.00 0.00 3.01
933 943 1.547372 GCTTGGTGATTGCAATGGAGT 59.453 47.619 18.59 0.00 0.00 3.85
935 945 1.546923 CTGCTTGGTGATTGCAATGGA 59.453 47.619 18.59 1.16 36.22 3.41
1023 1035 4.856607 GCCGCGACGAGGAGAAGG 62.857 72.222 22.59 2.12 0.00 3.46
1104 1116 5.407502 TGTATGGACACACTTACATCGAAG 58.592 41.667 0.00 0.00 0.00 3.79
1255 1273 5.705813 TTGTTACGTACAACACTCAACAG 57.294 39.130 3.40 0.00 41.73 3.16
1268 1286 9.881529 GTAAAAGTTTGATGGAATTGTTACGTA 57.118 29.630 0.00 0.00 0.00 3.57
1297 1315 3.396491 GCAGAGCAGTGCAATTCAC 57.604 52.632 19.20 0.00 43.41 3.18
1322 1340 2.034939 TCTGCTTGCAACAACCTCAATG 59.965 45.455 0.00 0.00 0.00 2.82
1387 1410 0.743097 ATTAGGGTCAGTACGTCGCC 59.257 55.000 0.00 0.00 0.00 5.54
1402 1425 1.774639 GCCATGCATTTCGCCATTAG 58.225 50.000 0.00 0.00 41.33 1.73
1411 1434 2.403186 CGTACGCGCCATGCATTT 59.597 55.556 5.73 0.00 46.97 2.32
1422 1445 2.125269 ATTCCCACCTGCGTACGC 60.125 61.111 32.49 32.49 42.35 4.42
1435 1458 3.374330 CGTCACGCTCGTCATTCC 58.626 61.111 0.00 0.00 0.00 3.01
1911 2037 2.605257 CCGGGGAGTCCATTCATAGTA 58.395 52.381 12.30 0.00 34.36 1.82
1914 2040 1.415672 GGCCGGGGAGTCCATTCATA 61.416 60.000 12.30 0.00 34.36 2.15
2984 3269 1.999735 ACACAGTACATGTACATGCGC 59.000 47.619 32.02 23.72 41.41 6.09
2994 3279 4.193826 AGCTTTGATCGACACAGTACAT 57.806 40.909 0.00 0.00 0.00 2.29
2995 3280 3.660501 AGCTTTGATCGACACAGTACA 57.339 42.857 0.00 0.00 0.00 2.90
2996 3281 5.061064 CAGTTAGCTTTGATCGACACAGTAC 59.939 44.000 0.00 0.00 0.00 2.73
2997 3282 5.161358 CAGTTAGCTTTGATCGACACAGTA 58.839 41.667 0.00 0.00 0.00 2.74
2998 3283 3.990469 CAGTTAGCTTTGATCGACACAGT 59.010 43.478 0.00 0.00 0.00 3.55
2999 3284 3.181526 GCAGTTAGCTTTGATCGACACAG 60.182 47.826 0.00 0.00 41.15 3.66
3024 3309 5.353400 CGAGAAGCAATGCATATGTCCATAT 59.647 40.000 8.35 0.00 34.50 1.78
3045 3330 1.935873 CATGAACCATACACCTGCGAG 59.064 52.381 0.00 0.00 0.00 5.03
3046 3331 2.011548 GCATGAACCATACACCTGCGA 61.012 52.381 0.00 0.00 0.00 5.10
3164 3471 4.156455 TGTCTAGCATTTTGGGAGATCC 57.844 45.455 0.00 0.00 0.00 3.36
3173 3480 8.757982 ATCTTGGTAATCATGTCTAGCATTTT 57.242 30.769 8.73 0.00 35.19 1.82
3192 3499 0.380733 TCACCGACGATCGATCTTGG 59.619 55.000 24.34 21.44 43.74 3.61
3291 3598 4.182693 TGGACATAATCACGACGAACTT 57.817 40.909 0.00 0.00 0.00 2.66
3337 3646 6.258160 CGAATCGCCTGAAAAATGAATTAGT 58.742 36.000 0.00 0.00 0.00 2.24
3447 3756 0.381801 AAGGCACACACAAGCTTTCG 59.618 50.000 0.00 0.00 0.00 3.46
3472 3781 7.588497 ACACTGCAGATACATACAGATAGAA 57.412 36.000 23.35 0.00 34.25 2.10
3473 3782 8.870075 ATACACTGCAGATACATACAGATAGA 57.130 34.615 23.35 0.00 34.25 1.98
3533 3842 6.991485 AGAGTGTGCAAACAAAATTTATCG 57.009 33.333 10.29 0.00 0.00 2.92
3588 3897 7.862675 AGACAGTCCCTTGTTAAATAGCTAAT 58.137 34.615 0.00 0.00 0.00 1.73
3662 3971 8.533569 TCATACAGGTGTAGTCTATTGATTGA 57.466 34.615 0.00 0.00 33.52 2.57
3725 4034 1.276989 GTCAGATGTTTACCCGGTCCA 59.723 52.381 0.00 0.00 0.00 4.02
4061 4370 7.639113 TTTACCCATCAATTCCAGTGTATTC 57.361 36.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.