Multiple sequence alignment - TraesCS6B01G137200

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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 TraesCS6B01G137200 chr6B 100.000 4772 0 0 1 4772 134820000 134824771 0.000000e+00 8813
1 TraesCS6B01G137200 chr6D 93.790 1707 81 8 1107 2811 60542672 60544355 0.000000e+00 2542
2 TraesCS6B01G137200 chr6D 91.176 748 52 8 2840 3576 60544443 60545187 0.000000e+00 1003
3 TraesCS6B01G137200 chr6D 93.600 500 18 4 1 497 60540598 60541086 0.000000e+00 734
4 TraesCS6B01G137200 chr6D 88.618 615 26 14 497 1108 60542054 60542627 0.000000e+00 708
5 TraesCS6B01G137200 chr6D 93.249 474 23 5 4306 4772 60546037 60546508 0.000000e+00 689
6 TraesCS6B01G137200 chr6D 85.604 646 62 18 3582 4223 60545249 60545867 0.000000e+00 649
7 TraesCS6B01G137200 chr6A 91.687 1648 96 17 1199 2839 77533381 77534994 0.000000e+00 2246
8 TraesCS6B01G137200 chr6A 90.107 748 55 14 2842 3576 77535065 77535806 0.000000e+00 953
9 TraesCS6B01G137200 chr6A 88.721 727 32 17 504 1196 77532591 77533301 0.000000e+00 843
10 TraesCS6B01G137200 chr6A 93.145 496 24 3 1 496 77514128 77514613 0.000000e+00 719
11 TraesCS6B01G137200 chr6A 86.265 648 58 19 3582 4223 77535868 77536490 0.000000e+00 675
12 TraesCS6B01G137200 chr6A 84.979 466 52 15 4307 4772 77536654 77537101 1.570000e-124 457


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 TraesCS6B01G137200 chr6B 134820000 134824771 4771 False 8813.000000 8813 100.000000 1 4772 1 chr6B.!!$F1 4771
1 TraesCS6B01G137200 chr6D 60540598 60546508 5910 False 1054.166667 2542 91.006167 1 4772 6 chr6D.!!$F1 4771
2 TraesCS6B01G137200 chr6A 77532591 77537101 4510 False 1034.800000 2246 88.351800 504 4772 5 chr6A.!!$F2 4268

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
38 39 0.037605 GAGGGGCGACGAGAAGAAAA 60.038 55.0 0.0 0.0 0.00 2.29 F
116 117 0.038166 TCTTGGGGTCACATCTTGCC 59.962 55.0 0.0 0.0 0.00 4.52 F
170 171 0.093026 CGAACAATCACGCTTCGGTC 59.907 55.0 0.0 0.0 34.47 4.79 F
1085 2069 0.109226 CAGGTTCGTTCTCTCGTCCC 60.109 60.0 0.0 0.0 0.00 4.46 F
1488 2603 0.674534 ACGCTTATAGCCTCGGAAGG 59.325 55.0 0.0 0.0 46.44 3.46 F
3337 4522 0.166597 TGACGGTACTAGTTGTCGCG 59.833 55.0 0.0 0.0 34.11 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 2619 0.097674 CATTTCTCTCAAAGCCGCCG 59.902 55.000 0.0 0.0 0.00 6.46 R
1776 2892 1.355720 CCCAACAGAGTCAGGGGAAAT 59.644 52.381 0.0 0.0 41.49 2.17 R
1939 3055 1.461268 TGAGAGACCTGTTGGGCCA 60.461 57.895 0.0 0.0 44.45 5.36 R
2304 3420 0.873054 CTGCCTCTGACTGCAACAAG 59.127 55.000 0.0 0.0 36.98 3.16 R
3379 4564 0.381801 CGCAAAAGCAAGACAGGTGT 59.618 50.000 0.0 0.0 0.00 4.16 R
4380 5725 0.036388 TTGCTCCCAGTTTAGGCTCG 60.036 55.000 0.0 0.0 0.00 5.03 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
37 38 0.898789 AGAGGGGCGACGAGAAGAAA 60.899 55.000 0.00 0.00 0.00 2.52
38 39 0.037605 GAGGGGCGACGAGAAGAAAA 60.038 55.000 0.00 0.00 0.00 2.29
49 50 2.010497 GAGAAGAAAACCGGATCCAGC 58.990 52.381 9.46 0.00 0.00 4.85
116 117 0.038166 TCTTGGGGTCACATCTTGCC 59.962 55.000 0.00 0.00 0.00 4.52
142 143 1.278127 ACCTCGTACCATCACCAAAGG 59.722 52.381 0.00 0.00 0.00 3.11
170 171 0.093026 CGAACAATCACGCTTCGGTC 59.907 55.000 0.00 0.00 34.47 4.79
194 195 3.151912 AGCTTGACTCCTGCAAATTCT 57.848 42.857 0.00 0.00 0.00 2.40
213 214 8.392612 CAAATTCTGAGTCTTGCAAATTTTGTT 58.607 29.630 10.65 0.00 0.00 2.83
218 219 8.031864 TCTGAGTCTTGCAAATTTTGTTTTACA 58.968 29.630 10.65 0.00 0.00 2.41
219 220 8.715191 TGAGTCTTGCAAATTTTGTTTTACAT 57.285 26.923 10.65 0.00 0.00 2.29
220 221 9.160496 TGAGTCTTGCAAATTTTGTTTTACATT 57.840 25.926 10.65 0.00 0.00 2.71
314 315 1.495878 GCTCCGATGTATCTGCAGTG 58.504 55.000 14.67 0.00 0.00 3.66
326 327 1.000607 TCTGCAGTGTTACGTGAGACC 60.001 52.381 14.67 0.00 0.00 3.85
386 387 9.631257 TCATCTCCATTTTCTTATCTTGCAATA 57.369 29.630 0.00 0.00 0.00 1.90
403 404 9.330063 TCTTGCAATATGTTTAATCTCCTAGTG 57.670 33.333 0.00 0.00 0.00 2.74
435 439 4.026052 CTCTTGCATGTTTCCCCCTTAAT 58.974 43.478 0.00 0.00 0.00 1.40
451 455 1.134228 TAATACCGGGGGCTCCTTTC 58.866 55.000 6.32 0.00 0.00 2.62
453 457 2.850851 ATACCGGGGGCTCCTTTCCA 62.851 60.000 6.32 0.00 0.00 3.53
454 458 3.657350 CCGGGGGCTCCTTTCCAA 61.657 66.667 0.52 0.00 0.00 3.53
455 459 2.438795 CGGGGGCTCCTTTCCAAA 59.561 61.111 0.52 0.00 0.00 3.28
456 460 1.228737 CGGGGGCTCCTTTCCAAAA 60.229 57.895 0.52 0.00 0.00 2.44
457 461 0.830023 CGGGGGCTCCTTTCCAAAAA 60.830 55.000 0.52 0.00 0.00 1.94
497 501 1.486310 ACTGCTGTGTTCTTCCACTCA 59.514 47.619 0.00 0.00 36.30 3.41
499 503 2.483106 CTGCTGTGTTCTTCCACTCATG 59.517 50.000 0.00 0.00 36.30 3.07
581 1555 5.652014 TCAACCGATTGAAAATATTCAGGCT 59.348 36.000 0.00 0.00 45.82 4.58
598 1572 1.740025 GGCTATGAATGAATAGGCGCC 59.260 52.381 21.89 21.89 43.31 6.53
664 1638 3.296854 AGACGCTCTCTCTCTCTCTCTA 58.703 50.000 0.00 0.00 0.00 2.43
678 1652 6.268617 TCTCTCTCTCTATCTCTCTCTTCCAG 59.731 46.154 0.00 0.00 0.00 3.86
694 1668 1.621814 TCCAGACCACGACCTAAAAGG 59.378 52.381 0.00 0.00 42.49 3.11
700 1674 2.224450 ACCACGACCTAAAAGGAACCTG 60.224 50.000 0.00 0.00 37.67 4.00
701 1675 2.038033 CCACGACCTAAAAGGAACCTGA 59.962 50.000 0.00 0.00 37.67 3.86
702 1676 3.326747 CACGACCTAAAAGGAACCTGAG 58.673 50.000 0.00 0.00 37.67 3.35
703 1677 3.006537 CACGACCTAAAAGGAACCTGAGA 59.993 47.826 0.00 0.00 37.67 3.27
765 1739 1.755380 CCCGTCTCTAACCTAACCTGG 59.245 57.143 0.00 0.00 0.00 4.45
781 1755 3.945434 GGCCATGCACGCATCTCG 61.945 66.667 0.44 0.00 45.38 4.04
855 1829 5.222278 ACTAGGATCAGGTTTTAGGAGGA 57.778 43.478 0.00 0.00 0.00 3.71
857 1831 4.354208 AGGATCAGGTTTTAGGAGGAGA 57.646 45.455 0.00 0.00 0.00 3.71
859 1833 6.044411 AGGATCAGGTTTTAGGAGGAGATA 57.956 41.667 0.00 0.00 0.00 1.98
860 1834 6.638953 AGGATCAGGTTTTAGGAGGAGATAT 58.361 40.000 0.00 0.00 0.00 1.63
861 1835 7.780822 AGGATCAGGTTTTAGGAGGAGATATA 58.219 38.462 0.00 0.00 0.00 0.86
898 1872 6.911250 TTTCGCAGGAGATCAGGTAATATA 57.089 37.500 0.00 0.00 0.00 0.86
899 1873 6.911250 TTCGCAGGAGATCAGGTAATATAA 57.089 37.500 0.00 0.00 0.00 0.98
900 1874 7.482169 TTCGCAGGAGATCAGGTAATATAAT 57.518 36.000 0.00 0.00 0.00 1.28
901 1875 8.589701 TTCGCAGGAGATCAGGTAATATAATA 57.410 34.615 0.00 0.00 0.00 0.98
902 1876 8.768501 TCGCAGGAGATCAGGTAATATAATAT 57.231 34.615 0.00 0.00 0.00 1.28
903 1877 9.201989 TCGCAGGAGATCAGGTAATATAATATT 57.798 33.333 0.00 0.00 0.00 1.28
936 1916 4.261994 CCGATCATCTCCCTCTTCTTCTTC 60.262 50.000 0.00 0.00 0.00 2.87
937 1917 4.584325 CGATCATCTCCCTCTTCTTCTTCT 59.416 45.833 0.00 0.00 0.00 2.85
938 1918 5.068987 CGATCATCTCCCTCTTCTTCTTCTT 59.931 44.000 0.00 0.00 0.00 2.52
939 1919 5.930837 TCATCTCCCTCTTCTTCTTCTTC 57.069 43.478 0.00 0.00 0.00 2.87
940 1920 4.714308 TCATCTCCCTCTTCTTCTTCTTCC 59.286 45.833 0.00 0.00 0.00 3.46
941 1921 3.093057 TCTCCCTCTTCTTCTTCTTCCG 58.907 50.000 0.00 0.00 0.00 4.30
942 1922 3.093057 CTCCCTCTTCTTCTTCTTCCGA 58.907 50.000 0.00 0.00 0.00 4.55
943 1923 3.704061 CTCCCTCTTCTTCTTCTTCCGAT 59.296 47.826 0.00 0.00 0.00 4.18
944 1924 4.097418 TCCCTCTTCTTCTTCTTCCGATT 58.903 43.478 0.00 0.00 0.00 3.34
945 1925 4.160626 TCCCTCTTCTTCTTCTTCCGATTC 59.839 45.833 0.00 0.00 0.00 2.52
946 1926 4.081420 CCCTCTTCTTCTTCTTCCGATTCA 60.081 45.833 0.00 0.00 0.00 2.57
1081 2065 1.469940 CCCATCAGGTTCGTTCTCTCG 60.470 57.143 0.00 0.00 0.00 4.04
1085 2069 0.109226 CAGGTTCGTTCTCTCGTCCC 60.109 60.000 0.00 0.00 0.00 4.46
1108 2093 2.751806 CTCCTTTCCTGTTCTGCATTCC 59.248 50.000 0.00 0.00 0.00 3.01
1120 2151 3.237746 TCTGCATTCCACCCAAATCAAA 58.762 40.909 0.00 0.00 0.00 2.69
1130 2161 6.188407 TCCACCCAAATCAAACCGATAATTA 58.812 36.000 0.00 0.00 32.51 1.40
1136 2167 9.593134 CCCAAATCAAACCGATAATTAATTGAA 57.407 29.630 11.05 0.00 32.51 2.69
1296 2406 5.185454 AGTGAGTGATCACAACAGTTTTCA 58.815 37.500 27.02 15.86 42.68 2.69
1297 2407 5.065218 AGTGAGTGATCACAACAGTTTTCAC 59.935 40.000 27.02 24.63 42.68 3.18
1301 2411 5.036737 GTGATCACAACAGTTTTCACCTTG 58.963 41.667 21.07 0.00 0.00 3.61
1303 2413 3.088532 TCACAACAGTTTTCACCTTGCT 58.911 40.909 0.00 0.00 0.00 3.91
1338 2453 7.407393 TTCATCATACATTCCTCATTTGCAA 57.593 32.000 0.00 0.00 0.00 4.08
1339 2454 7.407393 TCATCATACATTCCTCATTTGCAAA 57.593 32.000 15.44 15.44 0.00 3.68
1340 2455 7.259882 TCATCATACATTCCTCATTTGCAAAC 58.740 34.615 15.41 0.00 0.00 2.93
1341 2456 6.839124 TCATACATTCCTCATTTGCAAACT 57.161 33.333 15.41 0.99 0.00 2.66
1342 2457 6.623486 TCATACATTCCTCATTTGCAAACTG 58.377 36.000 15.41 13.63 0.00 3.16
1343 2458 3.656559 ACATTCCTCATTTGCAAACTGC 58.343 40.909 15.41 0.00 45.29 4.40
1423 2538 6.507900 TGCTCTCGTTGATTTTCCTATAGAG 58.492 40.000 0.00 0.00 0.00 2.43
1432 2547 1.621992 TTCCTATAGAGCAGGCCTCG 58.378 55.000 0.00 0.00 45.54 4.63
1477 2592 0.998669 TCGACGACGACACGCTTATA 59.001 50.000 5.75 0.00 43.81 0.98
1488 2603 0.674534 ACGCTTATAGCCTCGGAAGG 59.325 55.000 0.00 0.00 46.44 3.46
1571 2686 2.222027 GTAGCCTGAAGTTTGTGCTGT 58.778 47.619 0.00 0.00 33.63 4.40
1649 2764 7.552687 TCAAGGACATGACAGGAAATAATGTAC 59.447 37.037 0.00 0.00 33.12 2.90
1655 2770 5.785243 TGACAGGAAATAATGTACGTGTGA 58.215 37.500 0.00 0.00 32.83 3.58
1670 2785 7.341446 TGTACGTGTGATAAATTATTGCATCG 58.659 34.615 0.00 0.00 0.00 3.84
1744 2860 6.313905 GGTGTTCTTGTCCTGATATTACACTG 59.686 42.308 0.00 0.00 35.10 3.66
1762 2878 4.142469 ACACTGTTACTCCTTTGTTTGTGC 60.142 41.667 0.00 0.00 0.00 4.57
1776 2892 1.422977 TTGTGCTGAAGGGCTGGGTA 61.423 55.000 0.00 0.00 0.00 3.69
1815 2931 1.754226 GGCATTATTCCTTTGGCCGAA 59.246 47.619 5.01 5.01 0.00 4.30
1857 2973 6.572254 CCGAGTAATTTGTTACAGTTTTCACG 59.428 38.462 1.71 0.00 0.00 4.35
1955 3071 1.462238 ACTGGCCCAACAGGTCTCT 60.462 57.895 0.00 0.00 42.71 3.10
1956 3072 1.298014 CTGGCCCAACAGGTCTCTC 59.702 63.158 0.00 0.00 42.71 3.20
1984 3100 4.233005 GTTGCTCTTCTTTGAAGCATTCC 58.767 43.478 2.71 0.00 46.93 3.01
2021 3137 2.662791 CGAATTGTCGTTGGCTTGACAG 60.663 50.000 7.01 0.00 45.08 3.51
2091 3207 6.513230 GCAATGCAACCGAGTTGATTATATCA 60.513 38.462 17.49 7.03 45.28 2.15
2226 3342 2.309613 TGTGGCAAAACTGAGCAGAAT 58.690 42.857 4.21 0.00 0.00 2.40
2277 3393 6.185852 TCACAGATTTGCACAATGTAGATG 57.814 37.500 0.00 0.00 0.00 2.90
2278 3394 5.939296 TCACAGATTTGCACAATGTAGATGA 59.061 36.000 0.00 0.00 0.00 2.92
2279 3395 6.093082 TCACAGATTTGCACAATGTAGATGAG 59.907 38.462 0.00 0.00 0.00 2.90
2280 3396 6.093082 CACAGATTTGCACAATGTAGATGAGA 59.907 38.462 0.00 0.00 0.00 3.27
2281 3397 6.093219 ACAGATTTGCACAATGTAGATGAGAC 59.907 38.462 0.00 0.00 0.00 3.36
2282 3398 6.093082 CAGATTTGCACAATGTAGATGAGACA 59.907 38.462 0.00 0.00 0.00 3.41
2283 3399 6.827251 AGATTTGCACAATGTAGATGAGACAT 59.173 34.615 0.00 0.00 39.22 3.06
2291 3407 6.379417 ACAATGTAGATGAGACATGAGAGTGA 59.621 38.462 0.00 0.00 37.59 3.41
2304 3420 5.873712 ACATGAGAGTGATCATTCTGTGTTC 59.126 40.000 23.91 10.73 37.84 3.18
2488 3604 5.178797 ACGCTTGCTACATCTACTTTGAAT 58.821 37.500 0.00 0.00 0.00 2.57
2490 3606 6.816640 ACGCTTGCTACATCTACTTTGAATTA 59.183 34.615 0.00 0.00 0.00 1.40
2517 3633 2.180769 CGCCGTCGTGAGGAATCA 59.819 61.111 0.00 0.00 0.00 2.57
2528 3644 6.128661 CGTCGTGAGGAATCAAATGAAGTAAA 60.129 38.462 0.00 0.00 0.00 2.01
2530 3646 8.879759 GTCGTGAGGAATCAAATGAAGTAAATA 58.120 33.333 0.00 0.00 0.00 1.40
2561 3677 8.704849 TTGCCCATACTTATATGCATAGTTTT 57.295 30.769 12.79 0.00 37.46 2.43
2562 3678 8.704849 TGCCCATACTTATATGCATAGTTTTT 57.295 30.769 12.79 0.00 37.46 1.94
2563 3679 8.792633 TGCCCATACTTATATGCATAGTTTTTC 58.207 33.333 12.79 0.00 37.46 2.29
2595 3711 6.036191 GCTTTACTGGACTTTCTATTTCTCCG 59.964 42.308 0.00 0.00 0.00 4.63
2598 3714 5.963594 ACTGGACTTTCTATTTCTCCGTAC 58.036 41.667 0.00 0.00 0.00 3.67
2599 3715 5.105432 ACTGGACTTTCTATTTCTCCGTACC 60.105 44.000 0.00 0.00 0.00 3.34
2705 3821 6.017400 TGAAGCTCCTGACATTTCAAAATC 57.983 37.500 0.00 0.00 0.00 2.17
2814 3930 9.290988 TCTCTTACTGATCCACTAGATGATTAC 57.709 37.037 0.00 0.00 34.42 1.89
2952 4137 7.315142 TCATCAGTGTTATTTTGCTTCCAATC 58.685 34.615 0.00 0.00 0.00 2.67
2967 4152 1.033746 CAATCGTGGGGAATGCTGCT 61.034 55.000 0.00 0.00 0.00 4.24
3039 4224 9.004717 AGAGAAGCTTAAAATTCTTAACAGTCC 57.995 33.333 0.00 0.00 35.93 3.85
3049 4234 5.767816 TTCTTAACAGTCCTTCCTTTTGC 57.232 39.130 0.00 0.00 0.00 3.68
3063 4248 6.294675 CCTTCCTTTTGCACAGATCACATAAA 60.295 38.462 0.00 0.00 0.00 1.40
3149 4334 2.604139 CATGTTTGGGGTAGGTTGGTT 58.396 47.619 0.00 0.00 0.00 3.67
3274 4459 4.193893 TGGATGATGGGCCAGCCG 62.194 66.667 20.74 0.00 45.08 5.52
3289 4474 1.734465 CAGCCGATGGACTTGAACTTC 59.266 52.381 0.00 0.00 0.00 3.01
3328 4513 4.441079 GCAAGCCTCTTAATGACGGTACTA 60.441 45.833 0.00 0.00 0.00 1.82
3337 4522 0.166597 TGACGGTACTAGTTGTCGCG 59.833 55.000 0.00 0.00 34.11 5.87
3360 4545 6.345487 GCGTTTTTGTTGCAGGTACTAAAATC 60.345 38.462 10.90 5.17 36.02 2.17
3363 4548 8.487176 GTTTTTGTTGCAGGTACTAAAATCATG 58.513 33.333 10.90 0.00 36.02 3.07
3375 4560 8.985805 GGTACTAAAATCATGTACCCTTATTCG 58.014 37.037 9.63 0.00 46.16 3.34
3378 4563 6.598753 AAAATCATGTACCCTTATTCGTCG 57.401 37.500 0.00 0.00 0.00 5.12
3379 4564 5.524971 AATCATGTACCCTTATTCGTCGA 57.475 39.130 0.00 0.00 0.00 4.20
3382 4567 3.492421 TGTACCCTTATTCGTCGACAC 57.508 47.619 17.16 2.35 0.00 3.67
3399 4589 4.141553 GACACCTGTCTTGCTTTTGCGT 62.142 50.000 0.00 0.00 44.26 5.24
3419 4609 6.831769 TGCGTGAATTCACTCTTCTATTTTC 58.168 36.000 30.45 5.56 44.34 2.29
3424 4614 8.663911 GTGAATTCACTCTTCTATTTTCCTCTG 58.336 37.037 27.66 0.00 43.25 3.35
3490 4680 8.409358 TGCTGTTTCTATGCTATCTGATAGTA 57.591 34.615 22.12 19.25 35.29 1.82
3517 4707 6.270815 TGCTAGTTTCTATGTACATTCCGAC 58.729 40.000 14.77 8.56 0.00 4.79
3545 4735 6.098409 GGATCCTGATGGTAAGTTCTTCACTA 59.902 42.308 3.84 0.00 32.58 2.74
3547 4737 5.187186 TCCTGATGGTAAGTTCTTCACTACC 59.813 44.000 0.00 0.00 32.58 3.18
3549 4739 4.768448 TGATGGTAAGTTCTTCACTACCGA 59.232 41.667 0.00 0.00 32.94 4.69
3559 4755 3.005472 TCTTCACTACCGAACTTCCTGTG 59.995 47.826 0.00 0.00 0.00 3.66
3560 4756 2.313317 TCACTACCGAACTTCCTGTGT 58.687 47.619 0.00 0.00 0.00 3.72
3564 4760 5.051816 CACTACCGAACTTCCTGTGTTTTA 58.948 41.667 0.00 0.00 0.00 1.52
3576 4772 8.571336 ACTTCCTGTGTTTTAATCTTTCAGATG 58.429 33.333 0.00 0.00 34.65 2.90
3579 4775 9.300681 TCCTGTGTTTTAATCTTTCAGATGAAT 57.699 29.630 0.00 0.00 34.65 2.57
3604 4856 4.325028 TGTGCTGCATGAATTTTCAGTT 57.675 36.364 5.27 0.00 41.08 3.16
3608 4860 5.691305 GTGCTGCATGAATTTTCAGTTGTTA 59.309 36.000 5.27 0.00 41.08 2.41
3627 4879 7.176690 AGTTGTTAGGCATTTAGCTACAAACAT 59.823 33.333 0.00 0.00 44.79 2.71
3630 4882 4.344104 AGGCATTTAGCTACAAACATGGT 58.656 39.130 0.00 0.00 44.79 3.55
3638 4890 4.848357 AGCTACAAACATGGTTGCTCTAT 58.152 39.130 23.39 6.09 42.22 1.98
3639 4891 5.256474 AGCTACAAACATGGTTGCTCTATT 58.744 37.500 23.39 5.33 42.22 1.73
3640 4892 5.124457 AGCTACAAACATGGTTGCTCTATTG 59.876 40.000 23.39 5.82 42.22 1.90
3643 4895 7.012327 GCTACAAACATGGTTGCTCTATTGATA 59.988 37.037 23.39 4.13 34.80 2.15
3644 4896 7.088589 ACAAACATGGTTGCTCTATTGATAC 57.911 36.000 23.39 0.00 31.29 2.24
3650 4902 9.277783 ACATGGTTGCTCTATTGATACTATTTC 57.722 33.333 0.00 0.00 0.00 2.17
3669 4921 9.739276 ACTATTTCCATGAATCTCAAACTACAA 57.261 29.630 0.00 0.00 0.00 2.41
3684 4936 8.974060 TCAAACTACAAATCCAGTAAGAAAGT 57.026 30.769 0.00 0.00 0.00 2.66
3694 4946 8.785329 AATCCAGTAAGAAAGTGAGAAAGATC 57.215 34.615 0.00 0.00 0.00 2.75
3695 4947 7.303182 TCCAGTAAGAAAGTGAGAAAGATCA 57.697 36.000 0.00 0.00 0.00 2.92
3696 4948 7.735917 TCCAGTAAGAAAGTGAGAAAGATCAA 58.264 34.615 0.00 0.00 0.00 2.57
3704 4956 8.954350 AGAAAGTGAGAAAGATCAATATTGTGG 58.046 33.333 14.97 0.00 0.00 4.17
3706 4958 7.621428 AGTGAGAAAGATCAATATTGTGGTG 57.379 36.000 14.97 0.00 0.00 4.17
3708 4960 7.335422 AGTGAGAAAGATCAATATTGTGGTGAC 59.665 37.037 14.97 5.17 0.00 3.67
3712 4964 8.517878 AGAAAGATCAATATTGTGGTGACTTTG 58.482 33.333 14.97 0.00 30.19 2.77
3713 4965 7.765695 AAGATCAATATTGTGGTGACTTTGT 57.234 32.000 14.97 0.00 0.00 2.83
3732 4984 9.916397 GACTTTGTACAATTCACTAATATTCCG 57.084 33.333 9.56 0.00 0.00 4.30
3772 5024 5.124936 GGTAATAACCCTGCACAAAACTAGG 59.875 44.000 0.00 0.00 40.21 3.02
3778 5030 3.008049 CCCTGCACAAAACTAGGAGTACT 59.992 47.826 0.00 0.00 31.91 2.73
3805 5057 5.974156 TGATCCCATGGATTCTACAGAAA 57.026 39.130 15.22 0.00 43.27 2.52
3833 5085 3.374220 ACCATGTGACAACATTTGCAG 57.626 42.857 0.00 0.00 44.94 4.41
3840 5092 2.880268 TGACAACATTTGCAGTCAGGAG 59.120 45.455 0.44 0.00 36.20 3.69
3841 5093 1.610522 ACAACATTTGCAGTCAGGAGC 59.389 47.619 0.00 0.00 0.00 4.70
3842 5094 1.068055 CAACATTTGCAGTCAGGAGCC 60.068 52.381 0.00 0.00 0.00 4.70
3843 5095 0.111061 ACATTTGCAGTCAGGAGCCA 59.889 50.000 0.00 0.00 0.00 4.75
3844 5096 0.809385 CATTTGCAGTCAGGAGCCAG 59.191 55.000 0.00 0.00 0.00 4.85
3845 5097 0.323178 ATTTGCAGTCAGGAGCCAGG 60.323 55.000 0.00 0.00 0.00 4.45
3846 5098 1.418097 TTTGCAGTCAGGAGCCAGGA 61.418 55.000 0.00 0.00 0.00 3.86
3849 5101 1.908340 GCAGTCAGGAGCCAGGACAT 61.908 60.000 12.03 0.00 34.04 3.06
3899 5153 4.702131 GGCAGTGTTTCCTCACATTTAGAT 59.298 41.667 0.00 0.00 40.37 1.98
3909 5163 8.690203 TTCCTCACATTTAGATGTCTTTCAAA 57.310 30.769 0.00 0.00 44.55 2.69
3914 5168 7.809331 TCACATTTAGATGTCTTTCAAATGCAC 59.191 33.333 13.01 0.00 44.55 4.57
3934 5188 5.104982 TGCACCCATTCTTGAAACTCTTTTT 60.105 36.000 0.00 0.00 0.00 1.94
3935 5189 5.234972 GCACCCATTCTTGAAACTCTTTTTG 59.765 40.000 0.00 0.00 0.00 2.44
3943 5197 5.186797 TCTTGAAACTCTTTTTGGAAAGCCA 59.813 36.000 0.00 0.00 41.63 4.75
3962 5216 3.568007 GCCACACATCCAGTTTTGTAGAA 59.432 43.478 0.00 0.00 0.00 2.10
3968 5222 5.047802 CACATCCAGTTTTGTAGAAAGGCAT 60.048 40.000 0.00 0.00 0.00 4.40
3969 5223 6.150976 CACATCCAGTTTTGTAGAAAGGCATA 59.849 38.462 0.00 0.00 0.00 3.14
3971 5225 7.397192 ACATCCAGTTTTGTAGAAAGGCATAAT 59.603 33.333 0.00 0.00 0.00 1.28
3972 5226 7.391148 TCCAGTTTTGTAGAAAGGCATAATC 57.609 36.000 0.00 0.00 0.00 1.75
3973 5227 6.945435 TCCAGTTTTGTAGAAAGGCATAATCA 59.055 34.615 0.00 0.00 0.00 2.57
3974 5228 7.450014 TCCAGTTTTGTAGAAAGGCATAATCAA 59.550 33.333 0.00 0.00 0.00 2.57
3975 5229 7.756722 CCAGTTTTGTAGAAAGGCATAATCAAG 59.243 37.037 0.00 0.00 0.00 3.02
3976 5230 7.756722 CAGTTTTGTAGAAAGGCATAATCAAGG 59.243 37.037 0.00 0.00 0.00 3.61
3977 5231 7.451566 AGTTTTGTAGAAAGGCATAATCAAGGT 59.548 33.333 0.00 0.00 0.00 3.50
3978 5232 8.736244 GTTTTGTAGAAAGGCATAATCAAGGTA 58.264 33.333 0.00 0.00 0.00 3.08
3979 5233 8.871629 TTTGTAGAAAGGCATAATCAAGGTAA 57.128 30.769 0.00 0.00 0.00 2.85
4039 5293 5.767665 TGCTATTGTACCAGCAAAGAAAGAA 59.232 36.000 10.48 0.00 44.49 2.52
4040 5294 6.264292 TGCTATTGTACCAGCAAAGAAAGAAA 59.736 34.615 10.48 0.00 44.49 2.52
4041 5295 6.803807 GCTATTGTACCAGCAAAGAAAGAAAG 59.196 38.462 6.39 0.00 37.73 2.62
4117 5371 4.319046 GCAAGTGCAGGTATCATCATTACG 60.319 45.833 0.00 0.00 41.59 3.18
4134 5388 9.849607 CATCATTACGTAACATGTAAGATCAAC 57.150 33.333 10.81 0.00 33.56 3.18
4143 5398 6.515272 ACATGTAAGATCAACCAAACATCC 57.485 37.500 0.00 0.00 0.00 3.51
4175 5430 9.258629 TCAACTTATTCCATTCCATCAAATTCT 57.741 29.630 0.00 0.00 0.00 2.40
4193 5448 4.712122 TTCTAAACCCATCGAAATTGCC 57.288 40.909 0.00 0.00 0.00 4.52
4196 5451 1.094785 AACCCATCGAAATTGCCTCG 58.905 50.000 0.00 0.00 37.66 4.63
4230 5487 9.020644 AGAGGCTTATATATATACTCCCTCTGT 57.979 37.037 26.07 14.62 0.00 3.41
4231 5488 9.649316 GAGGCTTATATATATACTCCCTCTGTT 57.351 37.037 21.65 6.13 0.00 3.16
4232 5489 9.649316 AGGCTTATATATATACTCCCTCTGTTC 57.351 37.037 1.73 0.00 0.00 3.18
4233 5490 9.422681 GGCTTATATATATACTCCCTCTGTTCA 57.577 37.037 1.73 0.00 0.00 3.18
4238 5495 0.252558 TACTCCCTCTGTTCACCCCC 60.253 60.000 0.00 0.00 0.00 5.40
4239 5496 1.229658 CTCCCTCTGTTCACCCCCT 60.230 63.158 0.00 0.00 0.00 4.79
4240 5497 0.842467 CTCCCTCTGTTCACCCCCTT 60.842 60.000 0.00 0.00 0.00 3.95
4241 5498 0.840722 TCCCTCTGTTCACCCCCTTC 60.841 60.000 0.00 0.00 0.00 3.46
4242 5499 1.133809 CCCTCTGTTCACCCCCTTCA 61.134 60.000 0.00 0.00 0.00 3.02
4243 5500 0.995024 CCTCTGTTCACCCCCTTCAT 59.005 55.000 0.00 0.00 0.00 2.57
4244 5501 1.340405 CCTCTGTTCACCCCCTTCATG 60.340 57.143 0.00 0.00 0.00 3.07
4247 5504 2.162681 CTGTTCACCCCCTTCATGTTC 58.837 52.381 0.00 0.00 0.00 3.18
4248 5505 1.496857 TGTTCACCCCCTTCATGTTCA 59.503 47.619 0.00 0.00 0.00 3.18
4249 5506 2.091610 TGTTCACCCCCTTCATGTTCAA 60.092 45.455 0.00 0.00 0.00 2.69
4250 5507 2.962421 GTTCACCCCCTTCATGTTCAAA 59.038 45.455 0.00 0.00 0.00 2.69
4251 5508 3.541242 TCACCCCCTTCATGTTCAAAT 57.459 42.857 0.00 0.00 0.00 2.32
4252 5509 4.666412 TCACCCCCTTCATGTTCAAATA 57.334 40.909 0.00 0.00 0.00 1.40
4255 5512 4.158394 CACCCCCTTCATGTTCAAATACTG 59.842 45.833 0.00 0.00 0.00 2.74
4256 5513 3.701040 CCCCCTTCATGTTCAAATACTGG 59.299 47.826 0.00 0.00 0.00 4.00
4257 5514 3.131046 CCCCTTCATGTTCAAATACTGGC 59.869 47.826 0.00 0.00 0.00 4.85
4258 5515 4.019174 CCCTTCATGTTCAAATACTGGCT 58.981 43.478 0.00 0.00 0.00 4.75
4259 5516 4.096984 CCCTTCATGTTCAAATACTGGCTC 59.903 45.833 0.00 0.00 0.00 4.70
4261 5518 3.270027 TCATGTTCAAATACTGGCTCCG 58.730 45.455 0.00 0.00 0.00 4.63
4262 5519 2.851263 TGTTCAAATACTGGCTCCGT 57.149 45.000 0.00 0.00 0.00 4.69
4265 5522 0.539986 TCAAATACTGGCTCCGTCCC 59.460 55.000 0.00 0.00 0.00 4.46
4268 5525 0.325296 AATACTGGCTCCGTCCCTGA 60.325 55.000 0.00 0.00 0.00 3.86
4269 5526 0.105453 ATACTGGCTCCGTCCCTGAT 60.105 55.000 0.00 0.00 0.00 2.90
4270 5527 0.325296 TACTGGCTCCGTCCCTGATT 60.325 55.000 0.00 0.00 0.00 2.57
4272 5529 0.830648 CTGGCTCCGTCCCTGATTAA 59.169 55.000 0.00 0.00 0.00 1.40
4297 5554 9.674068 AAGGAGTTGTATTTTAGAGAGAAATCC 57.326 33.333 0.00 0.00 0.00 3.01
4298 5555 8.826765 AGGAGTTGTATTTTAGAGAGAAATCCA 58.173 33.333 0.00 0.00 0.00 3.41
4299 5556 8.884726 GGAGTTGTATTTTAGAGAGAAATCCAC 58.115 37.037 0.00 0.00 0.00 4.02
4300 5557 8.480643 AGTTGTATTTTAGAGAGAAATCCACG 57.519 34.615 0.00 0.00 0.00 4.94
4301 5558 8.095169 AGTTGTATTTTAGAGAGAAATCCACGT 58.905 33.333 0.00 0.00 0.00 4.49
4303 5560 9.932207 TTGTATTTTAGAGAGAAATCCACGTTA 57.068 29.630 0.00 0.00 0.00 3.18
4304 5561 9.932207 TGTATTTTAGAGAGAAATCCACGTTAA 57.068 29.630 0.00 0.00 0.00 2.01
4309 5654 2.004733 GAGAAATCCACGTTAACCCCG 58.995 52.381 0.00 0.00 0.00 5.73
4380 5725 1.078709 TGCATGCTTAAGACGCTCAC 58.921 50.000 20.33 0.00 0.00 3.51
4409 5754 0.745486 CTGGGAGCAATGCGACATCA 60.745 55.000 0.00 0.97 0.00 3.07
4422 5767 7.411696 GCAATGCGACATCAATGTTTGAAATAA 60.412 33.333 8.67 0.00 43.95 1.40
4430 5775 8.911662 ACATCAATGTTTGAAATAAAACGCTAC 58.088 29.630 0.00 0.00 43.95 3.58
4532 5883 5.645056 TCAGCATTAATGGATGGACCTTA 57.355 39.130 17.02 0.00 39.86 2.69
4604 5955 1.834263 ACTCTACATGGCAAGAGGGTC 59.166 52.381 16.74 0.00 42.94 4.46
4698 6050 4.393062 CCATCTGCGAGTTGTGTTCTATTT 59.607 41.667 0.00 0.00 0.00 1.40
4699 6051 5.106555 CCATCTGCGAGTTGTGTTCTATTTT 60.107 40.000 0.00 0.00 0.00 1.82
4711 6063 7.026631 TGTGTTCTATTTTGGTGTCTGAAAG 57.973 36.000 0.00 0.00 0.00 2.62
4756 6108 2.919228 AGTGGTGTTGACCTCTGTTTC 58.081 47.619 0.00 0.00 43.18 2.78
4762 6114 2.777692 TGTTGACCTCTGTTTCCTCCTT 59.222 45.455 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.595993 CTTCTCGTCGCCCCTCTTGA 61.596 60.000 0.00 0.00 0.00 3.02
37 38 1.299976 GGAGTTGCTGGATCCGGTT 59.700 57.895 21.88 5.66 0.00 4.44
38 39 1.903877 CTGGAGTTGCTGGATCCGGT 61.904 60.000 21.88 1.34 35.18 5.28
49 50 1.339535 GGCTTTCCTCTCCTGGAGTTG 60.340 57.143 22.50 15.89 40.30 3.16
93 94 2.554032 CAAGATGTGACCCCAAGAACAC 59.446 50.000 0.00 0.00 0.00 3.32
142 143 2.968655 GCGTGATTGTTCGTTTGGTAAC 59.031 45.455 0.00 0.00 0.00 2.50
170 171 0.603707 TTGCAGGAGTCAAGCTTCGG 60.604 55.000 0.00 0.00 0.00 4.30
194 195 8.715191 ATGTAAAACAAAATTTGCAAGACTCA 57.285 26.923 5.52 0.00 38.19 3.41
218 219 7.912719 AGAGGCTAGAAAACTTAGTTGAGAAT 58.087 34.615 0.00 0.00 0.00 2.40
219 220 7.304497 AGAGGCTAGAAAACTTAGTTGAGAA 57.696 36.000 0.00 0.00 0.00 2.87
220 221 6.349445 CGAGAGGCTAGAAAACTTAGTTGAGA 60.349 42.308 0.00 0.00 0.00 3.27
253 254 3.059352 ACAAGGAGCCACAGTTGATAC 57.941 47.619 0.00 0.00 0.00 2.24
314 315 5.572126 GTGATTTACTGAGGTCTCACGTAAC 59.428 44.000 15.63 10.19 35.28 2.50
345 346 6.303903 TGGAGATGATCATTCAAGAGACAA 57.696 37.500 10.14 0.00 34.96 3.18
386 387 7.458397 TGGAACAACACTAGGAGATTAAACAT 58.542 34.615 0.00 0.00 31.92 2.71
435 439 2.689771 GGAAAGGAGCCCCCGGTA 60.690 66.667 0.00 0.00 40.87 4.02
497 501 0.677842 GCGACCCTCCGTATAACCAT 59.322 55.000 0.00 0.00 0.00 3.55
499 503 1.008079 CGCGACCCTCCGTATAACC 60.008 63.158 0.00 0.00 0.00 2.85
501 505 1.168407 CCTCGCGACCCTCCGTATAA 61.168 60.000 3.71 0.00 0.00 0.98
502 506 1.598962 CCTCGCGACCCTCCGTATA 60.599 63.158 3.71 0.00 0.00 1.47
581 1555 1.004277 GGGGGCGCCTATTCATTCATA 59.996 52.381 28.56 0.00 0.00 2.15
598 1572 3.072211 GAGAACGTCAGTTTTAAGGGGG 58.928 50.000 0.00 0.00 41.34 5.40
678 1652 2.038164 AGGTTCCTTTTAGGTCGTGGTC 59.962 50.000 0.00 0.00 36.53 4.02
694 1668 2.491693 CACCTCTGTCTCTCTCAGGTTC 59.508 54.545 0.00 0.00 34.15 3.62
700 1674 4.502962 CAAAATCCACCTCTGTCTCTCTC 58.497 47.826 0.00 0.00 0.00 3.20
701 1675 3.262915 CCAAAATCCACCTCTGTCTCTCT 59.737 47.826 0.00 0.00 0.00 3.10
702 1676 3.008485 ACCAAAATCCACCTCTGTCTCTC 59.992 47.826 0.00 0.00 0.00 3.20
703 1677 2.982488 ACCAAAATCCACCTCTGTCTCT 59.018 45.455 0.00 0.00 0.00 3.10
765 1739 4.602696 GCGAGATGCGTGCATGGC 62.603 66.667 12.81 8.96 43.41 4.40
781 1755 1.826487 GAGGAGGAGGACGAGAGGC 60.826 68.421 0.00 0.00 39.70 4.70
898 1872 9.454859 GGAGATGATCGGGAGAAATTAAATATT 57.545 33.333 0.00 0.00 45.37 1.28
899 1873 8.049721 GGGAGATGATCGGGAGAAATTAAATAT 58.950 37.037 0.00 0.00 45.37 1.28
900 1874 7.237679 AGGGAGATGATCGGGAGAAATTAAATA 59.762 37.037 0.00 0.00 45.37 1.40
901 1875 6.044871 AGGGAGATGATCGGGAGAAATTAAAT 59.955 38.462 0.00 0.00 45.37 1.40
902 1876 5.369699 AGGGAGATGATCGGGAGAAATTAAA 59.630 40.000 0.00 0.00 45.37 1.52
903 1877 4.907875 AGGGAGATGATCGGGAGAAATTAA 59.092 41.667 0.00 0.00 45.37 1.40
936 1916 5.798132 TCCTCATGGATAATGAATCGGAAG 58.202 41.667 0.00 0.00 44.77 3.46
937 1917 5.823861 TCCTCATGGATAATGAATCGGAA 57.176 39.130 0.00 0.00 44.77 4.30
984 1964 1.068083 CATCGTCCTGATCCACGGG 59.932 63.158 8.57 0.00 45.93 5.28
1081 2065 2.027653 CAGAACAGGAAAGGAGAGGGAC 60.028 54.545 0.00 0.00 0.00 4.46
1085 2069 2.847327 TGCAGAACAGGAAAGGAGAG 57.153 50.000 0.00 0.00 0.00 3.20
1108 2093 8.816144 CAATTAATTATCGGTTTGATTTGGGTG 58.184 33.333 0.00 0.00 38.57 4.61
1136 2167 8.967664 ATTGCCATGTTAATTATTGCAATCTT 57.032 26.923 16.86 13.13 40.67 2.40
1211 2321 5.990386 CCATCTGTGAATCAATAGAGACCAG 59.010 44.000 5.05 0.00 0.00 4.00
1216 2326 5.990386 CCTGTCCATCTGTGAATCAATAGAG 59.010 44.000 5.05 0.00 0.00 2.43
1301 2411 1.575244 TGATGAATGCGCTAGACAGC 58.425 50.000 9.73 7.33 44.90 4.40
1303 2413 4.320608 TGTATGATGAATGCGCTAGACA 57.679 40.909 9.73 4.21 0.00 3.41
1310 2425 5.874895 ATGAGGAATGTATGATGAATGCG 57.125 39.130 0.00 0.00 0.00 4.73
1423 2538 1.522580 GGAGAATGTCGAGGCCTGC 60.523 63.158 12.00 0.00 0.00 4.85
1488 2603 2.811317 CGGTTCTGCGAGACAGCC 60.811 66.667 0.00 0.00 46.76 4.85
1504 2619 0.097674 CATTTCTCTCAAAGCCGCCG 59.902 55.000 0.00 0.00 0.00 6.46
1571 2686 3.620488 ACAGGTTGAGCTTTGACTTGAA 58.380 40.909 12.04 0.00 0.00 2.69
1649 2764 7.110628 CACTTCGATGCAATAATTTATCACACG 59.889 37.037 0.00 0.00 0.00 4.49
1662 2777 5.375417 TTGATGAAACACTTCGATGCAAT 57.625 34.783 0.00 0.00 33.94 3.56
1663 2778 4.827304 TTGATGAAACACTTCGATGCAA 57.173 36.364 0.00 0.00 33.94 4.08
1664 2779 5.375417 AATTGATGAAACACTTCGATGCA 57.625 34.783 0.00 0.00 33.94 3.96
1670 2785 8.856490 ACTAACACAAATTGATGAAACACTTC 57.144 30.769 0.00 0.00 0.00 3.01
1719 2834 6.313905 CAGTGTAATATCAGGACAAGAACACC 59.686 42.308 0.00 0.00 36.28 4.16
1722 2838 7.907214 AACAGTGTAATATCAGGACAAGAAC 57.093 36.000 0.00 0.00 0.00 3.01
1744 2860 4.893424 TCAGCACAAACAAAGGAGTAAC 57.107 40.909 0.00 0.00 0.00 2.50
1762 2878 2.058593 GGAAATACCCAGCCCTTCAG 57.941 55.000 0.00 0.00 0.00 3.02
1776 2892 1.355720 CCCAACAGAGTCAGGGGAAAT 59.644 52.381 0.00 0.00 41.49 2.17
1815 2931 2.280592 GTGGCGAAACCCAGTCGT 60.281 61.111 0.00 0.00 40.64 4.34
1857 2973 3.068024 TCAACAAGGATCACCAAACAAGC 59.932 43.478 0.00 0.00 38.94 4.01
1939 3055 1.461268 TGAGAGACCTGTTGGGCCA 60.461 57.895 0.00 0.00 44.45 5.36
1955 3071 4.406648 TCAAAGAAGAGCAACAGAGTGA 57.593 40.909 0.00 0.00 0.00 3.41
1956 3072 4.554330 GCTTCAAAGAAGAGCAACAGAGTG 60.554 45.833 10.72 0.00 0.00 3.51
1984 3100 4.271049 ACAATTCGAATGCTACTTGGATCG 59.729 41.667 12.25 0.00 0.00 3.69
2021 3137 2.927477 CCAACTGCATGCACATGAAATC 59.073 45.455 18.46 0.00 41.20 2.17
2091 3207 3.012560 GCTCCTTAGCGCATGGATT 57.987 52.632 11.47 0.00 39.39 3.01
2226 3342 3.228188 AGAATGGTCACCTTGCTGAAA 57.772 42.857 0.00 0.00 0.00 2.69
2277 3393 5.749588 CACAGAATGATCACTCTCATGTCTC 59.250 44.000 3.12 0.00 39.69 3.36
2278 3394 5.187381 ACACAGAATGATCACTCTCATGTCT 59.813 40.000 12.62 0.00 39.69 3.41
2279 3395 5.417811 ACACAGAATGATCACTCTCATGTC 58.582 41.667 12.62 0.00 39.69 3.06
2280 3396 5.417754 ACACAGAATGATCACTCTCATGT 57.582 39.130 12.62 12.62 39.69 3.21
2281 3397 6.107343 AGAACACAGAATGATCACTCTCATG 58.893 40.000 3.12 8.38 39.69 3.07
2282 3398 6.297080 AGAACACAGAATGATCACTCTCAT 57.703 37.500 3.12 0.00 39.69 2.90
2283 3399 5.735285 AGAACACAGAATGATCACTCTCA 57.265 39.130 3.12 0.00 39.69 3.27
2291 3407 4.581824 ACTGCAACAAGAACACAGAATGAT 59.418 37.500 0.00 0.00 39.69 2.45
2304 3420 0.873054 CTGCCTCTGACTGCAACAAG 59.127 55.000 0.00 0.00 36.98 3.16
2488 3604 0.940519 CGACGGCGACTGGTTGTTAA 60.941 55.000 16.62 0.00 40.82 2.01
2490 3606 2.660552 CGACGGCGACTGGTTGTT 60.661 61.111 16.62 0.00 40.82 2.83
2517 3633 8.088463 TGGGCAATCCATTATTTACTTCATTT 57.912 30.769 0.00 0.00 41.46 2.32
2561 3677 6.716628 AGAAAGTCCAGTAAAGCATCATTGAA 59.283 34.615 0.00 0.00 0.00 2.69
2562 3678 6.240894 AGAAAGTCCAGTAAAGCATCATTGA 58.759 36.000 0.00 0.00 0.00 2.57
2563 3679 6.506500 AGAAAGTCCAGTAAAGCATCATTG 57.493 37.500 0.00 0.00 0.00 2.82
2571 3687 7.097834 ACGGAGAAATAGAAAGTCCAGTAAAG 58.902 38.462 0.00 0.00 0.00 1.85
2575 3691 5.105432 GGTACGGAGAAATAGAAAGTCCAGT 60.105 44.000 0.00 0.00 0.00 4.00
2595 3711 7.986562 ACTCAGAAACTTGAAAAAGAAGGTAC 58.013 34.615 0.00 0.00 0.00 3.34
2598 3714 8.458843 TGTAACTCAGAAACTTGAAAAAGAAGG 58.541 33.333 0.00 0.00 0.00 3.46
2628 3744 1.690209 CCCTGGTCCCATCAAATGCAT 60.690 52.381 0.00 0.00 0.00 3.96
2639 3755 1.229529 TCACCTCTTCCCTGGTCCC 60.230 63.158 0.00 0.00 33.75 4.46
2919 4104 6.366877 GCAAAATAACACTGATGAATGCAACT 59.633 34.615 0.00 0.00 0.00 3.16
2925 4110 7.230849 TGGAAGCAAAATAACACTGATGAAT 57.769 32.000 0.00 0.00 0.00 2.57
2952 4137 1.675310 TTCAGCAGCATTCCCCACG 60.675 57.895 0.00 0.00 0.00 4.94
2967 4152 2.837532 TGACAGCACTAGCATGTTCA 57.162 45.000 0.00 0.00 45.49 3.18
3033 4218 2.092429 TCTGTGCAAAAGGAAGGACTGT 60.092 45.455 0.00 0.00 0.00 3.55
3039 4224 4.778534 ATGTGATCTGTGCAAAAGGAAG 57.221 40.909 0.00 0.00 0.00 3.46
3047 4232 5.764686 ACAAGAACTTTATGTGATCTGTGCA 59.235 36.000 0.00 0.00 0.00 4.57
3048 4233 6.246420 ACAAGAACTTTATGTGATCTGTGC 57.754 37.500 0.00 0.00 0.00 4.57
3063 4248 9.041354 AGATCCTACAAGAGAAATACAAGAACT 57.959 33.333 0.00 0.00 0.00 3.01
3076 4261 3.135530 CCCAGGGAAAGATCCTACAAGAG 59.864 52.174 0.00 0.00 45.77 2.85
3149 4334 1.944024 CAGTAAGGCACAAACGGTTCA 59.056 47.619 0.00 0.00 0.00 3.18
3191 4376 6.152323 AGAGCAATCTGTCAGCAAAACAATAT 59.848 34.615 0.00 0.00 0.00 1.28
3328 4513 1.264672 GCAACAAAAACGCGACAACT 58.735 45.000 15.93 0.00 0.00 3.16
3337 4522 7.995463 TGATTTTAGTACCTGCAACAAAAAC 57.005 32.000 0.00 0.00 0.00 2.43
3360 4545 3.795101 GTGTCGACGAATAAGGGTACATG 59.205 47.826 11.62 0.00 0.00 3.21
3363 4548 2.424956 AGGTGTCGACGAATAAGGGTAC 59.575 50.000 11.62 0.00 0.00 3.34
3367 4552 2.527100 GACAGGTGTCGACGAATAAGG 58.473 52.381 11.62 0.00 35.12 2.69
3378 4563 1.597937 CGCAAAAGCAAGACAGGTGTC 60.598 52.381 1.60 1.60 45.08 3.67
3379 4564 0.381801 CGCAAAAGCAAGACAGGTGT 59.618 50.000 0.00 0.00 0.00 4.16
3382 4567 0.662619 TCACGCAAAAGCAAGACAGG 59.337 50.000 0.00 0.00 0.00 4.00
3399 4589 8.597167 TCAGAGGAAAATAGAAGAGTGAATTCA 58.403 33.333 3.38 3.38 0.00 2.57
3419 4609 2.511218 TCCCATCCTGGAAATTCAGAGG 59.489 50.000 0.00 4.41 40.96 3.69
3424 4614 3.968265 TGAAGTCCCATCCTGGAAATTC 58.032 45.455 0.00 0.00 40.96 2.17
3490 4680 6.284459 GGAATGTACATAGAAACTAGCAGCT 58.716 40.000 9.21 0.00 0.00 4.24
3517 4707 3.713764 AGAACTTACCATCAGGATCCTGG 59.286 47.826 35.95 25.74 43.75 4.45
3545 4735 5.374071 AGATTAAAACACAGGAAGTTCGGT 58.626 37.500 0.00 0.00 0.00 4.69
3547 4737 7.414436 TGAAAGATTAAAACACAGGAAGTTCG 58.586 34.615 0.00 0.00 0.00 3.95
3549 4739 8.519799 TCTGAAAGATTAAAACACAGGAAGTT 57.480 30.769 0.00 0.00 38.67 2.66
3576 4772 7.966111 TGAAAATTCATGCAGCACAAATATTC 58.034 30.769 0.00 0.00 31.01 1.75
3579 4775 6.457355 ACTGAAAATTCATGCAGCACAAATA 58.543 32.000 0.00 0.00 36.46 1.40
3604 4856 6.127758 CCATGTTTGTAGCTAAATGCCTAACA 60.128 38.462 9.51 9.51 44.23 2.41
3608 4860 4.344104 ACCATGTTTGTAGCTAAATGCCT 58.656 39.130 0.00 0.00 44.23 4.75
3627 4879 7.801104 TGGAAATAGTATCAATAGAGCAACCA 58.199 34.615 0.00 0.00 0.00 3.67
3643 4895 9.739276 TTGTAGTTTGAGATTCATGGAAATAGT 57.261 29.630 0.00 0.00 0.00 2.12
3650 4902 7.121759 ACTGGATTTGTAGTTTGAGATTCATGG 59.878 37.037 0.00 0.00 0.00 3.66
3664 4916 8.833231 TTCTCACTTTCTTACTGGATTTGTAG 57.167 34.615 0.00 0.00 0.00 2.74
3669 4921 8.378565 TGATCTTTCTCACTTTCTTACTGGATT 58.621 33.333 0.00 0.00 0.00 3.01
3671 4923 7.303182 TGATCTTTCTCACTTTCTTACTGGA 57.697 36.000 0.00 0.00 0.00 3.86
3684 4936 7.397221 AGTCACCACAATATTGATCTTTCTCA 58.603 34.615 22.16 0.00 0.00 3.27
3694 4946 9.128107 GAATTGTACAAAGTCACCACAATATTG 57.872 33.333 13.23 14.01 38.52 1.90
3695 4947 8.855110 TGAATTGTACAAAGTCACCACAATATT 58.145 29.630 13.23 0.00 38.52 1.28
3696 4948 8.296713 GTGAATTGTACAAAGTCACCACAATAT 58.703 33.333 28.75 4.26 38.52 1.28
3706 4958 9.916397 CGGAATATTAGTGAATTGTACAAAGTC 57.084 33.333 13.23 13.23 0.00 3.01
3762 5014 6.681729 TCATCCAAGTACTCCTAGTTTTGT 57.318 37.500 0.00 0.00 0.00 2.83
3772 5024 3.648067 TCCATGGGATCATCCAAGTACTC 59.352 47.826 13.02 0.00 40.62 2.59
3778 5030 4.664536 TGTAGAATCCATGGGATCATCCAA 59.335 41.667 13.02 0.00 42.27 3.53
3805 5057 7.596494 CAAATGTTGTCACATGGTAGAAATCT 58.404 34.615 0.00 0.00 43.34 2.40
3833 5085 1.222936 CCATGTCCTGGCTCCTGAC 59.777 63.158 0.00 0.00 38.47 3.51
3840 5092 4.718961 ACATAAATAGTCCATGTCCTGGC 58.281 43.478 0.00 0.00 45.52 4.85
3842 5094 8.739039 TCAAAAACATAAATAGTCCATGTCCTG 58.261 33.333 0.00 0.00 31.82 3.86
3843 5095 8.739972 GTCAAAAACATAAATAGTCCATGTCCT 58.260 33.333 0.00 0.00 31.82 3.85
3844 5096 8.739972 AGTCAAAAACATAAATAGTCCATGTCC 58.260 33.333 0.00 0.00 31.82 4.02
3859 5111 6.581712 ACACTGCCAAATTAGTCAAAAACAT 58.418 32.000 0.00 0.00 0.00 2.71
3876 5130 4.072131 TCTAAATGTGAGGAAACACTGCC 58.928 43.478 0.00 0.00 40.87 4.85
3899 5153 3.896888 AGAATGGGTGCATTTGAAAGACA 59.103 39.130 0.00 0.00 0.00 3.41
3909 5163 3.771216 AGAGTTTCAAGAATGGGTGCAT 58.229 40.909 0.00 0.00 0.00 3.96
3914 5168 6.160576 TCCAAAAAGAGTTTCAAGAATGGG 57.839 37.500 0.00 0.00 0.00 4.00
3934 5188 0.478072 ACTGGATGTGTGGCTTTCCA 59.522 50.000 0.00 0.00 40.85 3.53
3935 5189 1.620822 AACTGGATGTGTGGCTTTCC 58.379 50.000 0.00 0.00 0.00 3.13
3943 5197 4.278419 GCCTTTCTACAAAACTGGATGTGT 59.722 41.667 0.00 0.00 0.00 3.72
3990 5244 7.241042 AGAATACTTCAGCCTACACAACTTA 57.759 36.000 0.00 0.00 0.00 2.24
4004 5258 6.538742 GCTGGTACAATAGCAAGAATACTTCA 59.461 38.462 10.11 0.00 38.70 3.02
4007 5261 5.989477 TGCTGGTACAATAGCAAGAATACT 58.011 37.500 14.00 0.00 46.06 2.12
4017 5271 8.099364 TCTTTCTTTCTTTGCTGGTACAATAG 57.901 34.615 0.00 0.00 38.70 1.73
4021 5275 5.885912 ACTTCTTTCTTTCTTTGCTGGTACA 59.114 36.000 0.00 0.00 0.00 2.90
4076 5330 4.809426 ACTTGCTGCGATTAGTTGGTATAC 59.191 41.667 0.00 0.00 0.00 1.47
4077 5331 4.808895 CACTTGCTGCGATTAGTTGGTATA 59.191 41.667 0.00 0.00 0.00 1.47
4078 5332 3.623060 CACTTGCTGCGATTAGTTGGTAT 59.377 43.478 0.00 0.00 0.00 2.73
4106 5360 9.981114 TGATCTTACATGTTACGTAATGATGAT 57.019 29.630 25.44 18.16 0.00 2.45
4117 5371 7.968405 GGATGTTTGGTTGATCTTACATGTTAC 59.032 37.037 2.30 0.00 0.00 2.50
4134 5388 2.504367 AGTTGAGAACCGGATGTTTGG 58.496 47.619 9.46 0.00 37.29 3.28
4143 5398 4.941263 TGGAATGGAATAAGTTGAGAACCG 59.059 41.667 0.00 0.00 0.00 4.44
4175 5430 2.680841 CGAGGCAATTTCGATGGGTTTA 59.319 45.455 0.00 0.00 40.36 2.01
4193 5448 9.787435 ATATATATAAGCCTCTAAGGAGTCGAG 57.213 37.037 0.00 0.00 37.67 4.04
4213 5470 6.500336 GGGGTGAACAGAGGGAGTATATATA 58.500 44.000 0.00 0.00 0.00 0.86
4216 5473 3.588569 GGGGTGAACAGAGGGAGTATAT 58.411 50.000 0.00 0.00 0.00 0.86
4217 5474 2.359994 GGGGGTGAACAGAGGGAGTATA 60.360 54.545 0.00 0.00 0.00 1.47
4218 5475 1.625508 GGGGGTGAACAGAGGGAGTAT 60.626 57.143 0.00 0.00 0.00 2.12
4219 5476 0.252558 GGGGGTGAACAGAGGGAGTA 60.253 60.000 0.00 0.00 0.00 2.59
4220 5477 1.539124 GGGGGTGAACAGAGGGAGT 60.539 63.158 0.00 0.00 0.00 3.85
4221 5478 0.842467 AAGGGGGTGAACAGAGGGAG 60.842 60.000 0.00 0.00 0.00 4.30
4222 5479 0.840722 GAAGGGGGTGAACAGAGGGA 60.841 60.000 0.00 0.00 0.00 4.20
4223 5480 1.133809 TGAAGGGGGTGAACAGAGGG 61.134 60.000 0.00 0.00 0.00 4.30
4224 5481 0.995024 ATGAAGGGGGTGAACAGAGG 59.005 55.000 0.00 0.00 0.00 3.69
4227 5484 2.162681 GAACATGAAGGGGGTGAACAG 58.837 52.381 0.00 0.00 0.00 3.16
4228 5485 1.496857 TGAACATGAAGGGGGTGAACA 59.503 47.619 0.00 0.00 0.00 3.18
4230 5487 3.320610 TTTGAACATGAAGGGGGTGAA 57.679 42.857 0.00 0.00 0.00 3.18
4231 5488 3.541242 ATTTGAACATGAAGGGGGTGA 57.459 42.857 0.00 0.00 0.00 4.02
4232 5489 4.158394 CAGTATTTGAACATGAAGGGGGTG 59.842 45.833 0.00 0.00 0.00 4.61
4233 5490 4.344104 CAGTATTTGAACATGAAGGGGGT 58.656 43.478 0.00 0.00 0.00 4.95
4235 5492 3.131046 GCCAGTATTTGAACATGAAGGGG 59.869 47.826 0.00 0.00 0.00 4.79
4238 5495 4.201851 CGGAGCCAGTATTTGAACATGAAG 60.202 45.833 0.00 0.00 0.00 3.02
4239 5496 3.689161 CGGAGCCAGTATTTGAACATGAA 59.311 43.478 0.00 0.00 0.00 2.57
4240 5497 3.270027 CGGAGCCAGTATTTGAACATGA 58.730 45.455 0.00 0.00 0.00 3.07
4241 5498 3.009723 ACGGAGCCAGTATTTGAACATG 58.990 45.455 0.00 0.00 0.00 3.21
4242 5499 3.270877 GACGGAGCCAGTATTTGAACAT 58.729 45.455 0.00 0.00 0.00 2.71
4243 5500 2.614481 GGACGGAGCCAGTATTTGAACA 60.614 50.000 0.00 0.00 0.00 3.18
4244 5501 2.007608 GGACGGAGCCAGTATTTGAAC 58.992 52.381 0.00 0.00 0.00 3.18
4247 5504 0.541863 AGGGACGGAGCCAGTATTTG 59.458 55.000 0.00 0.00 0.00 2.32
4248 5505 0.541863 CAGGGACGGAGCCAGTATTT 59.458 55.000 0.00 0.00 0.00 1.40
4249 5506 0.325296 TCAGGGACGGAGCCAGTATT 60.325 55.000 0.00 0.00 0.00 1.89
4250 5507 0.105453 ATCAGGGACGGAGCCAGTAT 60.105 55.000 0.00 0.00 35.10 2.12
4251 5508 0.325296 AATCAGGGACGGAGCCAGTA 60.325 55.000 0.00 0.00 35.10 2.74
4252 5509 0.325296 TAATCAGGGACGGAGCCAGT 60.325 55.000 0.00 0.00 35.10 4.00
4255 5512 0.106894 CCTTAATCAGGGACGGAGCC 59.893 60.000 0.00 0.00 39.39 4.70
4256 5513 1.069358 CTCCTTAATCAGGGACGGAGC 59.931 57.143 0.00 0.00 44.12 4.70
4257 5514 2.389715 ACTCCTTAATCAGGGACGGAG 58.610 52.381 0.00 0.00 44.12 4.63
4258 5515 2.500098 CAACTCCTTAATCAGGGACGGA 59.500 50.000 0.00 0.00 44.12 4.69
4259 5516 2.236395 ACAACTCCTTAATCAGGGACGG 59.764 50.000 0.00 0.00 44.12 4.79
4261 5518 7.939784 AAAATACAACTCCTTAATCAGGGAC 57.060 36.000 0.00 0.00 44.12 4.46
4262 5519 9.053472 TCTAAAATACAACTCCTTAATCAGGGA 57.947 33.333 0.00 0.00 44.12 4.20
4272 5529 8.826765 TGGATTTCTCTCTAAAATACAACTCCT 58.173 33.333 0.00 0.00 34.71 3.69
4275 5532 8.095169 ACGTGGATTTCTCTCTAAAATACAACT 58.905 33.333 0.00 0.00 38.37 3.16
4276 5533 8.252964 ACGTGGATTTCTCTCTAAAATACAAC 57.747 34.615 0.00 0.00 38.37 3.32
4277 5534 8.842358 AACGTGGATTTCTCTCTAAAATACAA 57.158 30.769 0.00 0.00 38.37 2.41
4280 5537 9.374838 GGTTAACGTGGATTTCTCTCTAAAATA 57.625 33.333 0.00 0.00 0.00 1.40
4281 5538 7.336176 GGGTTAACGTGGATTTCTCTCTAAAAT 59.664 37.037 0.00 0.00 0.00 1.82
4282 5539 6.652062 GGGTTAACGTGGATTTCTCTCTAAAA 59.348 38.462 0.00 0.00 0.00 1.52
4283 5540 6.168389 GGGTTAACGTGGATTTCTCTCTAAA 58.832 40.000 0.00 0.00 0.00 1.85
4284 5541 5.337813 GGGGTTAACGTGGATTTCTCTCTAA 60.338 44.000 0.00 0.00 0.00 2.10
4286 5543 3.055312 GGGGTTAACGTGGATTTCTCTCT 60.055 47.826 0.00 0.00 0.00 3.10
4287 5544 3.268330 GGGGTTAACGTGGATTTCTCTC 58.732 50.000 0.00 0.00 0.00 3.20
4289 5546 2.004733 CGGGGTTAACGTGGATTTCTC 58.995 52.381 0.00 0.00 0.00 2.87
4290 5547 1.348696 ACGGGGTTAACGTGGATTTCT 59.651 47.619 0.00 0.00 43.78 2.52
4291 5548 1.812235 ACGGGGTTAACGTGGATTTC 58.188 50.000 0.00 0.00 43.78 2.17
4292 5549 3.272581 CATACGGGGTTAACGTGGATTT 58.727 45.455 0.00 0.00 45.20 2.17
4294 5551 1.832998 ACATACGGGGTTAACGTGGAT 59.167 47.619 0.00 0.00 45.20 3.41
4295 5552 1.265236 ACATACGGGGTTAACGTGGA 58.735 50.000 0.00 0.00 45.20 4.02
4296 5553 2.481795 CCTACATACGGGGTTAACGTGG 60.482 54.545 0.00 0.00 45.20 4.94
4297 5554 2.481795 CCCTACATACGGGGTTAACGTG 60.482 54.545 0.00 0.00 45.20 4.49
4299 5556 2.514205 CCCTACATACGGGGTTAACG 57.486 55.000 0.00 0.00 38.08 3.18
4309 5654 3.173668 TGCGATGTGAACCCTACATAC 57.826 47.619 0.00 0.00 38.78 2.39
4380 5725 0.036388 TTGCTCCCAGTTTAGGCTCG 60.036 55.000 0.00 0.00 0.00 5.03
4385 5730 1.398390 GTCGCATTGCTCCCAGTTTAG 59.602 52.381 7.12 0.00 0.00 1.85
4387 5732 0.537143 TGTCGCATTGCTCCCAGTTT 60.537 50.000 7.12 0.00 0.00 2.66
4391 5736 0.322366 TTGATGTCGCATTGCTCCCA 60.322 50.000 7.12 0.86 0.00 4.37
4495 5846 8.844244 CATTAATGCTGAAATAGGTTCTAGCTT 58.156 33.333 1.74 0.00 39.31 3.74
4546 5897 9.037737 CAATTGCATATATCCTGTTTTTCTTGG 57.962 33.333 0.00 0.00 0.00 3.61
4604 5955 2.967362 ACAATCATGGTGCATGCTTTG 58.033 42.857 20.33 10.84 41.18 2.77
4622 5973 5.827267 TCTTGAAAGTGAACCATGATGAACA 59.173 36.000 0.00 0.00 0.00 3.18
4698 6050 3.537580 AGCGTAAACTTTCAGACACCAA 58.462 40.909 0.00 0.00 0.00 3.67
4699 6051 3.188159 AGCGTAAACTTTCAGACACCA 57.812 42.857 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.