Multiple sequence alignment - TraesCS5D01G328900

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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 TraesCS5D01G328900 chr5D 100.000 3800 0 0 1 3800 421168921 421165122 0.000000e+00 7018.0
1 TraesCS5D01G328900 chr5D 94.025 569 12 6 3236 3800 421145528 421144978 0.000000e+00 843.0
2 TraesCS5D01G328900 chr5D 81.661 289 52 1 199 487 367696147 367696434 4.910000e-59 239.0
3 TraesCS5D01G328900 chr5D 88.166 169 13 2 1451 1619 452678382 452678221 1.080000e-45 195.0
4 TraesCS5D01G328900 chr5D 88.194 144 15 2 436 577 367696425 367696568 1.820000e-38 171.0
5 TraesCS5D01G328900 chr5A 92.631 1642 77 18 1621 3219 534457922 534459562 0.000000e+00 2322.0
6 TraesCS5D01G328900 chr5A 97.522 565 12 2 3236 3800 534459961 534460523 0.000000e+00 965.0
7 TraesCS5D01G328900 chr5A 86.230 748 65 14 711 1448 534457197 534457916 0.000000e+00 776.0
8 TraesCS5D01G328900 chr5A 86.792 212 15 6 2829 3027 534367163 534367374 1.370000e-54 224.0
9 TraesCS5D01G328900 chr5B 91.611 1359 79 16 1625 2950 507162952 507164308 0.000000e+00 1845.0
10 TraesCS5D01G328900 chr5B 89.720 749 40 16 710 1452 507162229 507162946 0.000000e+00 922.0
11 TraesCS5D01G328900 chr5B 95.575 565 22 3 3236 3800 507164793 507165354 0.000000e+00 902.0
12 TraesCS5D01G328900 chr5B 86.919 344 40 3 36 375 507121808 507122150 7.700000e-102 381.0
13 TraesCS5D01G328900 chr5B 89.778 225 22 1 370 593 507160578 507160802 1.730000e-73 287.0
14 TraesCS5D01G328900 chr5B 88.439 173 13 3 1447 1619 612672988 612672823 6.440000e-48 202.0
15 TraesCS5D01G328900 chr5B 89.506 162 10 4 1451 1612 418818833 418818679 8.330000e-47 198.0
16 TraesCS5D01G328900 chr5B 94.017 117 7 0 3103 3219 507164329 507164445 1.080000e-40 178.0
17 TraesCS5D01G328900 chr5B 72.474 574 126 22 64 624 600113742 600113188 5.080000e-34 156.0
18 TraesCS5D01G328900 chr5B 90.816 98 9 0 580 677 507161753 507161850 8.570000e-27 132.0
19 TraesCS5D01G328900 chr2A 79.522 586 104 13 1 576 670686760 670687339 1.640000e-108 403.0
20 TraesCS5D01G328900 chr7D 77.990 577 111 11 4 578 136398886 136398324 7.810000e-92 348.0
21 TraesCS5D01G328900 chr7D 76.820 522 104 8 75 581 594799699 594799180 1.040000e-70 278.0
22 TraesCS5D01G328900 chr1B 74.639 623 138 17 4 615 164717380 164716767 1.350000e-64 257.0
23 TraesCS5D01G328900 chr1B 86.857 175 16 5 1451 1625 49838518 49838685 5.010000e-44 189.0
24 TraesCS5D01G328900 chr1B 85.714 175 18 5 1451 1625 49836287 49836454 1.080000e-40 178.0
25 TraesCS5D01G328900 chr1A 88.636 176 13 3 1447 1622 181769592 181769424 1.380000e-49 207.0
26 TraesCS5D01G328900 chrUn 88.166 169 12 4 1445 1612 311695443 311695282 1.080000e-45 195.0
27 TraesCS5D01G328900 chr4A 87.574 169 13 6 1445 1612 714816885 714816724 5.010000e-44 189.0
28 TraesCS5D01G328900 chr4B 86.286 175 14 6 1449 1623 581175068 581174904 8.390000e-42 182.0
29 TraesCS5D01G328900 chr6B 72.118 373 83 14 114 474 704830621 704830258 4.040000e-15 93.5


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 TraesCS5D01G328900 chr5D 421165122 421168921 3799 True 7018.000000 7018 100.000000 1 3800 1 chr5D.!!$R2 3799
1 TraesCS5D01G328900 chr5D 421144978 421145528 550 True 843.000000 843 94.025000 3236 3800 1 chr5D.!!$R1 564
2 TraesCS5D01G328900 chr5A 534457197 534460523 3326 False 1354.333333 2322 92.127667 711 3800 3 chr5A.!!$F2 3089
3 TraesCS5D01G328900 chr5B 507160578 507165354 4776 False 711.000000 1845 91.919500 370 3800 6 chr5B.!!$F2 3430
4 TraesCS5D01G328900 chr2A 670686760 670687339 579 False 403.000000 403 79.522000 1 576 1 chr2A.!!$F1 575
5 TraesCS5D01G328900 chr7D 136398324 136398886 562 True 348.000000 348 77.990000 4 578 1 chr7D.!!$R1 574
6 TraesCS5D01G328900 chr7D 594799180 594799699 519 True 278.000000 278 76.820000 75 581 1 chr7D.!!$R2 506
7 TraesCS5D01G328900 chr1B 164716767 164717380 613 True 257.000000 257 74.639000 4 615 1 chr1B.!!$R1 611

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
808 2154 0.249073 CGAGCCCATCCGTACTCTTG 60.249 60.0 0.00 0.0 0.00 3.02 F
999 2347 0.188834 CCTAGGAGACGAAGGGGGAT 59.811 60.0 1.05 0.0 35.44 3.85 F
2125 3517 0.178921 TCCTTCTCCCACTGCTGTCT 60.179 55.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 3212 0.108138 GACCAAGAGCCGCTACATGT 60.108 55.0 2.69 2.69 0.00 3.21 R
2401 3797 0.320771 GCCTCGACTGAAGGAAGCAA 60.321 55.0 0.00 0.00 0.00 3.91 R
3130 4530 0.306533 ACACGCAAACACGGATCAAC 59.693 50.0 0.00 0.00 37.37 3.18 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
21 22 1.680651 CTCTCCGTCCACTGCTCCT 60.681 63.158 0.00 0.00 0.00 3.69
23 24 2.203640 TCCGTCCACTGCTCCTGT 60.204 61.111 0.00 0.00 0.00 4.00
29 30 1.451504 CCACTGCTCCTGTGGTTGA 59.548 57.895 11.68 0.00 44.70 3.18
35 36 0.393537 GCTCCTGTGGTTGATGGAGG 60.394 60.000 9.52 0.00 44.46 4.30
56 57 1.133761 GGGGTTGGCTCCTATTTCTCC 60.134 57.143 0.00 0.00 30.72 3.71
73 74 3.173965 TCTCCTCCTGTTGTTCCTTAGG 58.826 50.000 0.00 0.00 0.00 2.69
96 97 0.810016 AGGGCTTCGTCTTCGTCTAC 59.190 55.000 0.00 0.00 38.33 2.59
140 141 1.270412 TGTTGCGTCGAATAAGGTGGT 60.270 47.619 0.00 0.00 0.00 4.16
141 142 1.127951 GTTGCGTCGAATAAGGTGGTG 59.872 52.381 0.00 0.00 0.00 4.17
156 157 1.241990 TGGTGTCGGTCTCTTCCTCG 61.242 60.000 0.00 0.00 0.00 4.63
173 189 4.205584 GCCACAGCGACGTTTTTC 57.794 55.556 0.00 0.00 0.00 2.29
174 190 1.370051 GCCACAGCGACGTTTTTCC 60.370 57.895 0.00 0.00 0.00 3.13
175 191 1.782028 GCCACAGCGACGTTTTTCCT 61.782 55.000 0.00 0.00 0.00 3.36
180 196 2.554272 CGACGTTTTTCCTGGCGG 59.446 61.111 0.00 0.00 0.00 6.13
182 198 2.517402 ACGTTTTTCCTGGCGGCA 60.517 55.556 12.58 12.58 0.00 5.69
184 200 2.840066 CGTTTTTCCTGGCGGCACA 61.840 57.895 7.97 0.00 0.00 4.57
185 201 1.439644 GTTTTTCCTGGCGGCACAA 59.560 52.632 7.97 0.16 0.00 3.33
202 222 3.136763 CACAACTGAGCTGATGTGTCTT 58.863 45.455 0.00 0.00 38.62 3.01
212 232 3.248602 GCTGATGTGTCTTCTTGTCGTTT 59.751 43.478 0.00 0.00 0.00 3.60
225 245 0.305617 GTCGTTTGTTTGGACCGGTC 59.694 55.000 27.04 27.04 0.00 4.79
235 255 2.588034 GACCGGTCGGCCTTATGC 60.588 66.667 20.85 0.00 39.32 3.14
248 268 2.159462 GCCTTATGCTTCTTGTGTCTGC 60.159 50.000 0.00 0.00 36.87 4.26
249 269 3.341823 CCTTATGCTTCTTGTGTCTGCT 58.658 45.455 0.00 0.00 0.00 4.24
258 278 0.813610 TTGTGTCTGCTGGTTGTCGG 60.814 55.000 0.00 0.00 0.00 4.79
276 296 1.226603 GCTCTTATGGCGTCGTCGT 60.227 57.895 3.66 0.00 39.49 4.34
283 304 2.354305 GGCGTCGTCGTCAAGTGT 60.354 61.111 0.88 0.00 41.67 3.55
309 330 1.975660 TTGGTGCTGGTACAAGGTTC 58.024 50.000 0.00 0.00 38.70 3.62
339 360 1.282875 GCTGTGGACTTGGCGTTTC 59.717 57.895 0.00 0.00 0.00 2.78
363 385 1.091537 CAACAACAACGGCGGGATAT 58.908 50.000 13.24 0.00 0.00 1.63
532 563 4.039357 CCTCGTGTGCGTCTCGGT 62.039 66.667 4.04 0.00 39.49 4.69
542 573 4.057428 GTCTCGGTGGCGCTGACT 62.057 66.667 7.64 0.00 0.00 3.41
645 1640 3.518590 GGTGTTTACTGTACATCTCCCG 58.481 50.000 0.00 0.00 0.00 5.14
652 1647 2.233922 ACTGTACATCTCCCGGTCTTTG 59.766 50.000 0.00 0.00 0.00 2.77
658 1653 0.250295 TCTCCCGGTCTTTGTGCTTG 60.250 55.000 0.00 0.00 0.00 4.01
666 1661 2.479560 GGTCTTTGTGCTTGTTTTCGCT 60.480 45.455 0.00 0.00 0.00 4.93
667 1662 3.179048 GTCTTTGTGCTTGTTTTCGCTT 58.821 40.909 0.00 0.00 0.00 4.68
677 1672 2.993545 TGTTTTCGCTTGTGTATGTGC 58.006 42.857 0.00 0.00 0.00 4.57
679 1674 3.181496 TGTTTTCGCTTGTGTATGTGCAA 60.181 39.130 0.00 0.00 0.00 4.08
683 1678 2.551887 TCGCTTGTGTATGTGCAATTGT 59.448 40.909 7.40 0.00 0.00 2.71
684 1679 3.748568 TCGCTTGTGTATGTGCAATTGTA 59.251 39.130 7.40 0.00 0.00 2.41
685 1680 3.845775 CGCTTGTGTATGTGCAATTGTAC 59.154 43.478 18.59 18.59 0.00 2.90
686 1681 4.378356 CGCTTGTGTATGTGCAATTGTACT 60.378 41.667 24.30 13.86 0.00 2.73
688 1683 5.106555 GCTTGTGTATGTGCAATTGTACTCT 60.107 40.000 24.30 15.26 0.00 3.24
689 1684 5.861222 TGTGTATGTGCAATTGTACTCTG 57.139 39.130 24.30 0.00 0.00 3.35
690 1685 5.304778 TGTGTATGTGCAATTGTACTCTGT 58.695 37.500 24.30 12.10 0.00 3.41
692 1687 6.262049 TGTGTATGTGCAATTGTACTCTGTTT 59.738 34.615 24.30 7.75 0.00 2.83
694 1689 8.286800 GTGTATGTGCAATTGTACTCTGTTTTA 58.713 33.333 24.30 5.08 0.00 1.52
695 1690 9.008965 TGTATGTGCAATTGTACTCTGTTTTAT 57.991 29.630 24.30 11.37 0.00 1.40
740 2081 7.687941 TGTGAGGTCAAGAAAAGATATTTCC 57.312 36.000 0.00 0.00 0.00 3.13
808 2154 0.249073 CGAGCCCATCCGTACTCTTG 60.249 60.000 0.00 0.00 0.00 3.02
825 2171 3.173240 GCCGAGTCGAACACGAGC 61.173 66.667 15.64 2.71 34.12 5.03
933 2281 2.109304 ACCCCCAATTTCGAAGGAGAAA 59.891 45.455 5.92 0.00 43.28 2.52
936 2284 4.321974 CCCCCAATTTCGAAGGAGAAAAAG 60.322 45.833 3.58 0.00 42.52 2.27
937 2285 4.522789 CCCCAATTTCGAAGGAGAAAAAGA 59.477 41.667 3.58 0.00 42.52 2.52
938 2286 5.010617 CCCCAATTTCGAAGGAGAAAAAGAA 59.989 40.000 3.58 0.00 42.52 2.52
939 2287 6.152379 CCCAATTTCGAAGGAGAAAAAGAAG 58.848 40.000 3.58 0.00 42.52 2.85
940 2288 6.016276 CCCAATTTCGAAGGAGAAAAAGAAGA 60.016 38.462 3.58 0.00 42.52 2.87
942 2290 7.920682 CCAATTTCGAAGGAGAAAAAGAAGAAA 59.079 33.333 0.00 0.00 42.52 2.52
946 2294 6.354130 TCGAAGGAGAAAAAGAAGAAAGGAA 58.646 36.000 0.00 0.00 0.00 3.36
947 2295 6.826741 TCGAAGGAGAAAAAGAAGAAAGGAAA 59.173 34.615 0.00 0.00 0.00 3.13
948 2296 7.502561 TCGAAGGAGAAAAAGAAGAAAGGAAAT 59.497 33.333 0.00 0.00 0.00 2.17
949 2297 8.784043 CGAAGGAGAAAAAGAAGAAAGGAAATA 58.216 33.333 0.00 0.00 0.00 1.40
951 2299 9.868160 AAGGAGAAAAAGAAGAAAGGAAATAGA 57.132 29.630 0.00 0.00 0.00 1.98
952 2300 9.868160 AGGAGAAAAAGAAGAAAGGAAATAGAA 57.132 29.630 0.00 0.00 0.00 2.10
976 2324 0.476771 ACAGAAAAGCGAGGGGGAAA 59.523 50.000 0.00 0.00 0.00 3.13
999 2347 0.188834 CCTAGGAGACGAAGGGGGAT 59.811 60.000 1.05 0.00 35.44 3.85
1073 2421 3.591835 CGGCAACAACGCAAGGGT 61.592 61.111 0.00 0.00 46.39 4.34
1091 2439 1.984570 TGACCGGCAGAGGGAAGAG 60.985 63.158 0.00 0.00 35.02 2.85
1102 2450 2.821810 GGAAGAGGAAGGCGCTGC 60.822 66.667 7.64 0.00 0.00 5.25
1106 2454 4.760047 GAGGAAGGCGCTGCGGAA 62.760 66.667 24.61 0.00 0.00 4.30
1151 2499 4.271816 CAGGAGGGACGATCGCCG 62.272 72.222 16.60 0.90 45.44 6.46
1282 2631 2.868999 CTTCGGCTCCTTCGACGACC 62.869 65.000 0.00 0.00 36.30 4.79
1308 2657 3.670991 GTGAGTGTCAGTCGAATCTGTTC 59.329 47.826 3.23 0.30 36.85 3.18
1311 2660 3.823873 AGTGTCAGTCGAATCTGTTCTCT 59.176 43.478 3.27 2.84 36.85 3.10
1318 2668 3.369451 GTCGAATCTGTTCTCTTCTTGCC 59.631 47.826 0.00 0.00 32.00 4.52
1336 2686 2.358582 TGCCGCGAATCAAATGATGAAT 59.641 40.909 8.23 0.00 42.54 2.57
1337 2687 3.181488 TGCCGCGAATCAAATGATGAATT 60.181 39.130 8.23 0.00 42.54 2.17
1340 2690 4.497842 CCGCGAATCAAATGATGAATTGGA 60.498 41.667 8.23 0.00 42.54 3.53
1343 2693 5.526115 CGAATCAAATGATGAATTGGAGGG 58.474 41.667 0.00 0.00 42.54 4.30
1419 2769 6.581542 CGGCACTAGTAGTAATTTAGGAATCG 59.418 42.308 1.57 0.00 0.00 3.34
1457 2813 9.990868 ATTTTGTTTTCCTACAATATACTCCCT 57.009 29.630 0.00 0.00 37.81 4.20
1458 2814 9.457436 TTTTGTTTTCCTACAATATACTCCCTC 57.543 33.333 0.00 0.00 37.81 4.30
1459 2815 7.133133 TGTTTTCCTACAATATACTCCCTCC 57.867 40.000 0.00 0.00 0.00 4.30
1460 2816 6.906901 TGTTTTCCTACAATATACTCCCTCCT 59.093 38.462 0.00 0.00 0.00 3.69
1461 2817 7.404980 TGTTTTCCTACAATATACTCCCTCCTT 59.595 37.037 0.00 0.00 0.00 3.36
1462 2818 8.272889 GTTTTCCTACAATATACTCCCTCCTTT 58.727 37.037 0.00 0.00 0.00 3.11
1463 2819 7.613551 TTCCTACAATATACTCCCTCCTTTC 57.386 40.000 0.00 0.00 0.00 2.62
1464 2820 6.082707 TCCTACAATATACTCCCTCCTTTCC 58.917 44.000 0.00 0.00 0.00 3.13
1465 2821 6.085416 CCTACAATATACTCCCTCCTTTCCT 58.915 44.000 0.00 0.00 0.00 3.36
1466 2822 7.075915 TCCTACAATATACTCCCTCCTTTCCTA 59.924 40.741 0.00 0.00 0.00 2.94
1467 2823 7.733501 CCTACAATATACTCCCTCCTTTCCTAA 59.266 40.741 0.00 0.00 0.00 2.69
1468 2824 9.155785 CTACAATATACTCCCTCCTTTCCTAAA 57.844 37.037 0.00 0.00 0.00 1.85
1469 2825 8.582891 ACAATATACTCCCTCCTTTCCTAAAT 57.417 34.615 0.00 0.00 0.00 1.40
1470 2826 9.684702 ACAATATACTCCCTCCTTTCCTAAATA 57.315 33.333 0.00 0.00 0.00 1.40
1475 2831 9.915564 ATACTCCCTCCTTTCCTAAATATAAGT 57.084 33.333 0.00 0.00 0.00 2.24
1476 2832 8.265108 ACTCCCTCCTTTCCTAAATATAAGTC 57.735 38.462 0.00 0.00 0.00 3.01
1477 2833 8.074991 ACTCCCTCCTTTCCTAAATATAAGTCT 58.925 37.037 0.00 0.00 0.00 3.24
1478 2834 8.871570 TCCCTCCTTTCCTAAATATAAGTCTT 57.128 34.615 0.00 0.00 0.00 3.01
1479 2835 9.292751 TCCCTCCTTTCCTAAATATAAGTCTTT 57.707 33.333 0.00 0.00 0.00 2.52
1480 2836 9.922477 CCCTCCTTTCCTAAATATAAGTCTTTT 57.078 33.333 0.00 0.00 0.00 2.27
1504 2860 8.725405 TTTTATAGATTTCAATGCGGACTACA 57.275 30.769 0.00 0.00 0.00 2.74
1505 2861 8.902540 TTTATAGATTTCAATGCGGACTACAT 57.097 30.769 0.00 0.00 0.00 2.29
1506 2862 9.990360 TTTATAGATTTCAATGCGGACTACATA 57.010 29.630 0.00 0.00 0.00 2.29
1507 2863 7.891183 ATAGATTTCAATGCGGACTACATAC 57.109 36.000 0.00 0.00 0.00 2.39
1508 2864 5.670485 AGATTTCAATGCGGACTACATACA 58.330 37.500 0.00 0.00 0.00 2.29
1509 2865 5.755375 AGATTTCAATGCGGACTACATACAG 59.245 40.000 0.00 0.00 0.00 2.74
1510 2866 4.729227 TTCAATGCGGACTACATACAGA 57.271 40.909 0.00 0.00 0.00 3.41
1511 2867 4.937201 TCAATGCGGACTACATACAGAT 57.063 40.909 0.00 0.00 0.00 2.90
1512 2868 6.399639 TTCAATGCGGACTACATACAGATA 57.600 37.500 0.00 0.00 0.00 1.98
1513 2869 5.769367 TCAATGCGGACTACATACAGATAC 58.231 41.667 0.00 0.00 0.00 2.24
1514 2870 5.300792 TCAATGCGGACTACATACAGATACA 59.699 40.000 0.00 0.00 0.00 2.29
1515 2871 4.830826 TGCGGACTACATACAGATACAG 57.169 45.455 0.00 0.00 0.00 2.74
1516 2872 3.568430 TGCGGACTACATACAGATACAGG 59.432 47.826 0.00 0.00 0.00 4.00
1517 2873 3.568853 GCGGACTACATACAGATACAGGT 59.431 47.826 0.00 0.00 0.00 4.00
1518 2874 4.556898 GCGGACTACATACAGATACAGGTG 60.557 50.000 0.00 0.00 0.00 4.00
1519 2875 4.579340 CGGACTACATACAGATACAGGTGT 59.421 45.833 0.00 0.00 0.00 4.16
1520 2876 5.761726 CGGACTACATACAGATACAGGTGTA 59.238 44.000 0.00 0.00 33.75 2.90
1521 2877 6.430308 CGGACTACATACAGATACAGGTGTAT 59.570 42.308 2.16 2.16 43.38 2.29
1522 2878 7.605309 CGGACTACATACAGATACAGGTGTATA 59.395 40.741 2.56 0.00 40.99 1.47
1523 2879 9.463902 GGACTACATACAGATACAGGTGTATAT 57.536 37.037 2.56 0.00 40.99 0.86
1561 2917 8.986991 AGAGTATAGATTCACTCATTTTGGTCT 58.013 33.333 4.70 0.00 42.99 3.85
1562 2918 8.954950 AGTATAGATTCACTCATTTTGGTCTG 57.045 34.615 0.00 0.00 0.00 3.51
1563 2919 8.543774 AGTATAGATTCACTCATTTTGGTCTGT 58.456 33.333 0.00 0.00 0.00 3.41
1564 2920 9.817809 GTATAGATTCACTCATTTTGGTCTGTA 57.182 33.333 0.00 0.00 0.00 2.74
1566 2922 7.621428 AGATTCACTCATTTTGGTCTGTATG 57.379 36.000 0.00 0.00 0.00 2.39
1567 2923 7.170965 AGATTCACTCATTTTGGTCTGTATGT 58.829 34.615 0.00 0.00 0.00 2.29
1568 2924 8.321353 AGATTCACTCATTTTGGTCTGTATGTA 58.679 33.333 0.00 0.00 0.00 2.29
1569 2925 7.905604 TTCACTCATTTTGGTCTGTATGTAG 57.094 36.000 0.00 0.00 0.00 2.74
1570 2926 7.004555 TCACTCATTTTGGTCTGTATGTAGT 57.995 36.000 0.00 0.00 0.00 2.73
1571 2927 7.097192 TCACTCATTTTGGTCTGTATGTAGTC 58.903 38.462 0.00 0.00 0.00 2.59
1572 2928 6.313905 CACTCATTTTGGTCTGTATGTAGTCC 59.686 42.308 0.00 0.00 0.00 3.85
1573 2929 5.416083 TCATTTTGGTCTGTATGTAGTCCG 58.584 41.667 0.00 0.00 0.00 4.79
1574 2930 4.877378 TTTTGGTCTGTATGTAGTCCGT 57.123 40.909 0.00 0.00 0.00 4.69
1575 2931 5.981088 TTTTGGTCTGTATGTAGTCCGTA 57.019 39.130 0.00 0.00 0.00 4.02
1576 2932 5.571784 TTTGGTCTGTATGTAGTCCGTAG 57.428 43.478 0.00 0.00 0.00 3.51
1577 2933 4.226427 TGGTCTGTATGTAGTCCGTAGT 57.774 45.455 0.00 0.00 0.00 2.73
1578 2934 3.943381 TGGTCTGTATGTAGTCCGTAGTG 59.057 47.826 0.00 0.00 0.00 2.74
1579 2935 3.314635 GGTCTGTATGTAGTCCGTAGTGG 59.685 52.174 0.00 0.00 40.09 4.00
1593 2949 5.752650 TCCGTAGTGGAATCTCTAGAAAGA 58.247 41.667 0.00 0.00 46.38 2.52
1594 2950 5.589452 TCCGTAGTGGAATCTCTAGAAAGAC 59.411 44.000 0.00 0.00 46.38 3.01
1595 2951 5.591067 CCGTAGTGGAATCTCTAGAAAGACT 59.409 44.000 0.00 0.00 42.00 3.24
1596 2952 6.095720 CCGTAGTGGAATCTCTAGAAAGACTT 59.904 42.308 0.00 0.00 42.00 3.01
1597 2953 7.282675 CCGTAGTGGAATCTCTAGAAAGACTTA 59.717 40.741 0.00 0.00 42.00 2.24
1598 2954 8.842280 CGTAGTGGAATCTCTAGAAAGACTTAT 58.158 37.037 0.00 0.00 0.00 1.73
1677 3036 1.072266 AGCCAACCCAGTCCATGTAA 58.928 50.000 0.00 0.00 0.00 2.41
1685 3048 2.436542 CCCAGTCCATGTAAATACCCGA 59.563 50.000 0.00 0.00 0.00 5.14
1702 3065 1.452110 CGACAATGCTTGGATGGACA 58.548 50.000 1.84 0.00 34.12 4.02
1725 3088 3.454719 AACATGGATGGTGATTGGTGA 57.545 42.857 0.00 0.00 0.00 4.02
1728 3091 3.511146 ACATGGATGGTGATTGGTGAAAC 59.489 43.478 0.00 0.00 0.00 2.78
1797 3185 2.897326 TGACAAGCTCCTAGTGTTGCTA 59.103 45.455 0.00 0.00 35.09 3.49
1799 3187 4.709886 TGACAAGCTCCTAGTGTTGCTATA 59.290 41.667 0.00 0.00 35.09 1.31
1804 3192 8.432805 ACAAGCTCCTAGTGTTGCTATATAATT 58.567 33.333 0.00 0.00 35.09 1.40
1840 3230 1.137086 CTACATGTAGCGGCTCTTGGT 59.863 52.381 19.55 4.11 0.00 3.67
1871 3261 3.550820 CATACATTCGAACCCATCCCAA 58.449 45.455 0.00 0.00 0.00 4.12
1927 3317 1.475403 ACATCCGAGTCACCGAGATT 58.525 50.000 0.00 0.00 0.00 2.40
1966 3356 2.487532 GCCTCTGCATGTCCATGGC 61.488 63.158 6.96 2.72 39.16 4.40
1978 3368 2.126228 CATGGCTTGGTTGCTGCG 60.126 61.111 0.00 0.00 0.00 5.18
2035 3425 1.781786 ATCGCACTAGGGATGACTGT 58.218 50.000 0.00 0.00 44.72 3.55
2086 3478 1.964552 ATCTAAGCATGCCTGTCTGC 58.035 50.000 15.66 0.00 38.69 4.26
2112 3504 5.204292 AGTTTGGCTTTCTTTCTTCCTTCT 58.796 37.500 0.00 0.00 0.00 2.85
2113 3505 5.300539 AGTTTGGCTTTCTTTCTTCCTTCTC 59.699 40.000 0.00 0.00 0.00 2.87
2114 3506 3.756117 TGGCTTTCTTTCTTCCTTCTCC 58.244 45.455 0.00 0.00 0.00 3.71
2115 3507 3.085533 GGCTTTCTTTCTTCCTTCTCCC 58.914 50.000 0.00 0.00 0.00 4.30
2116 3508 3.498661 GGCTTTCTTTCTTCCTTCTCCCA 60.499 47.826 0.00 0.00 0.00 4.37
2117 3509 3.504134 GCTTTCTTTCTTCCTTCTCCCAC 59.496 47.826 0.00 0.00 0.00 4.61
2118 3510 4.748239 GCTTTCTTTCTTCCTTCTCCCACT 60.748 45.833 0.00 0.00 0.00 4.00
2119 3511 4.357918 TTCTTTCTTCCTTCTCCCACTG 57.642 45.455 0.00 0.00 0.00 3.66
2120 3512 2.039084 TCTTTCTTCCTTCTCCCACTGC 59.961 50.000 0.00 0.00 0.00 4.40
2121 3513 1.734655 TTCTTCCTTCTCCCACTGCT 58.265 50.000 0.00 0.00 0.00 4.24
2122 3514 0.979665 TCTTCCTTCTCCCACTGCTG 59.020 55.000 0.00 0.00 0.00 4.41
2123 3515 0.689623 CTTCCTTCTCCCACTGCTGT 59.310 55.000 0.00 0.00 0.00 4.40
2124 3516 0.687354 TTCCTTCTCCCACTGCTGTC 59.313 55.000 0.00 0.00 0.00 3.51
2125 3517 0.178921 TCCTTCTCCCACTGCTGTCT 60.179 55.000 0.00 0.00 0.00 3.41
2126 3518 1.077169 TCCTTCTCCCACTGCTGTCTA 59.923 52.381 0.00 0.00 0.00 2.59
2134 3527 5.368816 TCTCCCACTGCTGTCTAGTATACTA 59.631 44.000 12.05 12.05 0.00 1.82
2232 3628 1.060553 CGTGCGCTCGTGTTAATTGAT 59.939 47.619 22.65 0.00 0.00 2.57
2286 3682 2.362077 GAGCAAAACAGAGCCTGGAAAA 59.638 45.455 0.00 0.00 35.51 2.29
2310 3706 4.370364 TGAACTGTTGGCTTTCAAAGTC 57.630 40.909 0.00 0.00 37.08 3.01
2320 3716 3.189495 GGCTTTCAAAGTCTTCAGCTACC 59.811 47.826 0.00 0.00 0.00 3.18
2348 3744 4.657504 AGCTTATCATTCTGATGAGGTGGA 59.342 41.667 11.36 0.00 45.43 4.02
2359 3755 1.262417 TGAGGTGGAATCTACACGCA 58.738 50.000 0.00 0.00 39.69 5.24
2401 3797 1.024046 TGAGTTTGCATATGCGCCGT 61.024 50.000 22.21 7.62 45.83 5.68
2622 4020 1.179174 GGGGACAGCTGTTGGTTTCC 61.179 60.000 22.65 15.88 39.18 3.13
2803 4201 1.267806 TGCTGCTTTCTGCTTAACAGC 59.732 47.619 5.88 5.88 46.76 4.40
2990 4388 6.975949 TGGTTATTATTACCTGTCCATTGGT 58.024 36.000 1.86 0.00 40.12 3.67
3070 4470 2.108168 GTACTGACAGCACCCCATCTA 58.892 52.381 1.25 0.00 0.00 1.98
3087 4487 4.511527 CATCTACTGATGGAACTTGCTGT 58.488 43.478 0.00 0.00 44.63 4.40
3099 4499 4.268405 GGAACTTGCTGTCAATGTTTTGTG 59.732 41.667 0.00 0.00 34.32 3.33
3108 4508 1.336440 CAATGTTTTGTGGCGGTCTCA 59.664 47.619 0.00 0.00 0.00 3.27
3251 5042 8.705594 AGCACACCTGAAACTATACATAACTAT 58.294 33.333 0.00 0.00 0.00 2.12
3434 5229 7.108841 ACCGATGATCTTAGCTAGTTTGTTA 57.891 36.000 0.00 0.00 0.00 2.41
3488 5283 2.302733 CAAAGGCCAGGCAATAAGGTTT 59.697 45.455 15.19 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.679305 GGAGCAGTGGACGGAGAGA 60.679 63.158 0.00 0.00 0.00 3.10
13 14 0.037303 CCATCAACCACAGGAGCAGT 59.963 55.000 0.00 0.00 0.00 4.40
21 22 3.506808 CCCCCTCCATCAACCACA 58.493 61.111 0.00 0.00 0.00 4.17
35 36 0.927029 AGAAATAGGAGCCAACCCCC 59.073 55.000 0.00 0.00 0.00 5.40
41 42 2.293184 ACAGGAGGAGAAATAGGAGCCA 60.293 50.000 0.00 0.00 0.00 4.75
49 50 4.731313 AAGGAACAACAGGAGGAGAAAT 57.269 40.909 0.00 0.00 0.00 2.17
56 57 5.246307 CCTAAACCTAAGGAACAACAGGAG 58.754 45.833 0.00 0.00 36.08 3.69
73 74 1.991264 GACGAAGACGAAGCCCTAAAC 59.009 52.381 0.00 0.00 42.66 2.01
140 141 2.341101 GGCGAGGAAGAGACCGACA 61.341 63.158 0.00 0.00 34.73 4.35
141 142 2.341101 TGGCGAGGAAGAGACCGAC 61.341 63.158 0.00 0.00 34.73 4.79
156 157 1.370051 GGAAAAACGTCGCTGTGGC 60.370 57.895 0.00 0.00 0.00 5.01
170 186 2.192861 CAGTTGTGCCGCCAGGAAA 61.193 57.895 0.00 0.00 41.02 3.13
173 189 3.052082 CTCAGTTGTGCCGCCAGG 61.052 66.667 0.00 0.00 41.62 4.45
174 190 3.730761 GCTCAGTTGTGCCGCCAG 61.731 66.667 0.00 0.00 0.00 4.85
175 191 4.254709 AGCTCAGTTGTGCCGCCA 62.255 61.111 2.82 0.00 35.33 5.69
180 196 1.196354 GACACATCAGCTCAGTTGTGC 59.804 52.381 12.72 0.00 40.93 4.57
182 198 3.070734 AGAAGACACATCAGCTCAGTTGT 59.929 43.478 0.00 0.00 0.00 3.32
184 200 4.063689 CAAGAAGACACATCAGCTCAGTT 58.936 43.478 0.00 0.00 0.00 3.16
185 201 3.070734 ACAAGAAGACACATCAGCTCAGT 59.929 43.478 0.00 0.00 0.00 3.41
202 222 1.666700 CGGTCCAAACAAACGACAAGA 59.333 47.619 0.00 0.00 0.00 3.02
212 232 4.629523 GGCCGACCGGTCCAAACA 62.630 66.667 28.52 0.00 37.65 2.83
225 245 1.398390 GACACAAGAAGCATAAGGCCG 59.602 52.381 0.00 0.00 46.50 6.13
235 255 2.289002 GACAACCAGCAGACACAAGAAG 59.711 50.000 0.00 0.00 0.00 2.85
248 268 1.656652 CCATAAGAGCCGACAACCAG 58.343 55.000 0.00 0.00 0.00 4.00
249 269 0.392461 GCCATAAGAGCCGACAACCA 60.392 55.000 0.00 0.00 0.00 3.67
258 278 1.201098 GACGACGACGCCATAAGAGC 61.201 60.000 7.30 0.00 43.96 4.09
263 283 0.455464 CACTTGACGACGACGCCATA 60.455 55.000 7.30 0.00 43.96 2.74
276 296 2.158769 AGCACCAATCTGTCACACTTGA 60.159 45.455 0.00 0.00 0.00 3.02
283 304 1.696884 TGTACCAGCACCAATCTGTCA 59.303 47.619 0.00 0.00 0.00 3.58
344 366 1.091537 ATATCCCGCCGTTGTTGTTG 58.908 50.000 0.00 0.00 0.00 3.33
345 367 1.091537 CATATCCCGCCGTTGTTGTT 58.908 50.000 0.00 0.00 0.00 2.83
476 504 1.962807 CAAACCAAATCCAGACCAGCA 59.037 47.619 0.00 0.00 0.00 4.41
532 563 2.661537 CGTCAACAGTCAGCGCCA 60.662 61.111 2.29 0.00 0.00 5.69
542 573 0.317160 ATCTGAAGTCGCCGTCAACA 59.683 50.000 0.00 0.00 0.00 3.33
624 1619 3.518590 CGGGAGATGTACAGTAAACACC 58.481 50.000 0.33 0.00 0.00 4.16
625 1620 3.056322 ACCGGGAGATGTACAGTAAACAC 60.056 47.826 6.32 0.00 0.00 3.32
635 1630 1.066430 GCACAAAGACCGGGAGATGTA 60.066 52.381 6.32 0.00 0.00 2.29
645 1640 1.852280 GCGAAAACAAGCACAAAGACC 59.148 47.619 0.00 0.00 0.00 3.85
652 1647 1.908065 ACACAAGCGAAAACAAGCAC 58.092 45.000 0.00 0.00 35.48 4.40
658 1653 2.993545 TGCACATACACAAGCGAAAAC 58.006 42.857 0.00 0.00 0.00 2.43
666 1661 5.762711 ACAGAGTACAATTGCACATACACAA 59.237 36.000 11.35 0.00 0.00 3.33
667 1662 5.304778 ACAGAGTACAATTGCACATACACA 58.695 37.500 11.35 0.00 0.00 3.72
699 1694 8.689061 TGACCTCACATATTGTACGTATTAGTT 58.311 33.333 0.00 0.00 0.00 2.24
700 1695 8.229253 TGACCTCACATATTGTACGTATTAGT 57.771 34.615 0.00 0.00 0.00 2.24
701 1696 9.181805 CTTGACCTCACATATTGTACGTATTAG 57.818 37.037 0.00 0.00 0.00 1.73
703 1698 7.778083 TCTTGACCTCACATATTGTACGTATT 58.222 34.615 0.00 0.00 0.00 1.89
704 1699 7.342769 TCTTGACCTCACATATTGTACGTAT 57.657 36.000 0.00 0.00 0.00 3.06
705 1700 6.762702 TCTTGACCTCACATATTGTACGTA 57.237 37.500 0.00 0.00 0.00 3.57
706 1701 5.654603 TCTTGACCTCACATATTGTACGT 57.345 39.130 0.00 0.00 0.00 3.57
707 1702 6.961359 TTTCTTGACCTCACATATTGTACG 57.039 37.500 0.00 0.00 0.00 3.67
708 1703 8.547967 TCTTTTCTTGACCTCACATATTGTAC 57.452 34.615 0.00 0.00 0.00 2.90
808 2154 3.173240 GCTCGTGTTCGACTCGGC 61.173 66.667 0.00 7.74 41.35 5.54
825 2171 1.716378 CCGAACGCGAACACAAACG 60.716 57.895 15.93 6.10 40.82 3.60
922 2270 5.925509 TCCTTTCTTCTTTTTCTCCTTCGA 58.074 37.500 0.00 0.00 0.00 3.71
953 2301 1.686587 CCCCCTCGCTTTTCTGTTTTT 59.313 47.619 0.00 0.00 0.00 1.94
954 2302 1.133606 TCCCCCTCGCTTTTCTGTTTT 60.134 47.619 0.00 0.00 0.00 2.43
962 2310 2.741433 GGTTTTTCCCCCTCGCTTT 58.259 52.632 0.00 0.00 0.00 3.51
976 2324 1.569653 CCCTTCGTCTCCTAGGGTTT 58.430 55.000 9.46 0.00 43.07 3.27
989 2337 2.347490 CCGCCATATCCCCCTTCG 59.653 66.667 0.00 0.00 0.00 3.79
1066 2414 4.329545 TCTGCCGGTCACCCTTGC 62.330 66.667 1.90 0.00 0.00 4.01
1073 2421 1.984570 CTCTTCCCTCTGCCGGTCA 60.985 63.158 1.90 0.00 0.00 4.02
1106 2454 4.416738 GCTTCTTCTGGCGGGCCT 62.417 66.667 11.55 0.00 36.94 5.19
1151 2499 0.526524 CATGAACTCCTCGCGGTCTC 60.527 60.000 6.13 0.00 0.00 3.36
1230 2579 1.863662 GACAGTCCCAGAGTTCGCGA 61.864 60.000 3.71 3.71 0.00 5.87
1282 2631 4.149571 CAGATTCGACTGACACTCACTTTG 59.850 45.833 0.00 0.00 39.94 2.77
1308 2657 1.078709 TTGATTCGCGGCAAGAAGAG 58.921 50.000 6.13 0.00 0.00 2.85
1311 2660 1.809547 TCATTTGATTCGCGGCAAGAA 59.190 42.857 6.13 0.00 0.00 2.52
1318 2668 4.600032 TCCAATTCATCATTTGATTCGCG 58.400 39.130 0.00 0.00 33.34 5.87
1336 2686 0.391130 CATCGACTTTCGCCCTCCAA 60.391 55.000 0.00 0.00 40.21 3.53
1337 2687 1.218047 CATCGACTTTCGCCCTCCA 59.782 57.895 0.00 0.00 40.21 3.86
1340 2690 1.448540 CTGCATCGACTTTCGCCCT 60.449 57.895 0.00 0.00 40.21 5.19
1343 2693 2.464459 CCCCTGCATCGACTTTCGC 61.464 63.158 0.00 0.00 40.21 4.70
1452 2808 8.499288 AGACTTATATTTAGGAAAGGAGGGAG 57.501 38.462 0.00 0.00 0.00 4.30
1453 2809 8.871570 AAGACTTATATTTAGGAAAGGAGGGA 57.128 34.615 0.00 0.00 0.00 4.20
1454 2810 9.922477 AAAAGACTTATATTTAGGAAAGGAGGG 57.078 33.333 0.00 0.00 0.00 4.30
1478 2834 9.168451 TGTAGTCCGCATTGAAATCTATAAAAA 57.832 29.630 0.00 0.00 0.00 1.94
1479 2835 8.725405 TGTAGTCCGCATTGAAATCTATAAAA 57.275 30.769 0.00 0.00 0.00 1.52
1480 2836 8.902540 ATGTAGTCCGCATTGAAATCTATAAA 57.097 30.769 0.00 0.00 0.00 1.40
1481 2837 9.419297 GTATGTAGTCCGCATTGAAATCTATAA 57.581 33.333 0.00 0.00 0.00 0.98
1482 2838 8.581578 TGTATGTAGTCCGCATTGAAATCTATA 58.418 33.333 0.00 0.00 0.00 1.31
1483 2839 7.441836 TGTATGTAGTCCGCATTGAAATCTAT 58.558 34.615 0.00 0.00 0.00 1.98
1484 2840 6.811954 TGTATGTAGTCCGCATTGAAATCTA 58.188 36.000 0.00 0.00 0.00 1.98
1485 2841 5.670485 TGTATGTAGTCCGCATTGAAATCT 58.330 37.500 0.00 0.00 0.00 2.40
1486 2842 5.753438 TCTGTATGTAGTCCGCATTGAAATC 59.247 40.000 0.00 0.00 0.00 2.17
1487 2843 5.670485 TCTGTATGTAGTCCGCATTGAAAT 58.330 37.500 0.00 0.00 0.00 2.17
1488 2844 5.079689 TCTGTATGTAGTCCGCATTGAAA 57.920 39.130 0.00 0.00 0.00 2.69
1489 2845 4.729227 TCTGTATGTAGTCCGCATTGAA 57.271 40.909 0.00 0.00 0.00 2.69
1490 2846 4.937201 ATCTGTATGTAGTCCGCATTGA 57.063 40.909 0.00 0.00 0.00 2.57
1491 2847 5.528870 TGTATCTGTATGTAGTCCGCATTG 58.471 41.667 0.00 0.00 0.00 2.82
1492 2848 5.279006 CCTGTATCTGTATGTAGTCCGCATT 60.279 44.000 0.00 0.00 0.00 3.56
1493 2849 4.218635 CCTGTATCTGTATGTAGTCCGCAT 59.781 45.833 0.00 0.00 0.00 4.73
1494 2850 3.568430 CCTGTATCTGTATGTAGTCCGCA 59.432 47.826 0.00 0.00 0.00 5.69
1495 2851 3.568853 ACCTGTATCTGTATGTAGTCCGC 59.431 47.826 0.00 0.00 0.00 5.54
1496 2852 4.579340 ACACCTGTATCTGTATGTAGTCCG 59.421 45.833 0.00 0.00 0.00 4.79
1497 2853 7.762588 ATACACCTGTATCTGTATGTAGTCC 57.237 40.000 0.00 0.00 36.57 3.85
1535 2891 8.986991 AGACCAAAATGAGTGAATCTATACTCT 58.013 33.333 0.00 0.00 42.86 3.24
1536 2892 9.039870 CAGACCAAAATGAGTGAATCTATACTC 57.960 37.037 0.00 0.00 42.77 2.59
1537 2893 8.543774 ACAGACCAAAATGAGTGAATCTATACT 58.456 33.333 0.00 0.00 0.00 2.12
1538 2894 8.723942 ACAGACCAAAATGAGTGAATCTATAC 57.276 34.615 0.00 0.00 0.00 1.47
1540 2896 9.334947 CATACAGACCAAAATGAGTGAATCTAT 57.665 33.333 0.00 0.00 0.00 1.98
1541 2897 8.321353 ACATACAGACCAAAATGAGTGAATCTA 58.679 33.333 0.00 0.00 0.00 1.98
1542 2898 7.170965 ACATACAGACCAAAATGAGTGAATCT 58.829 34.615 0.00 0.00 0.00 2.40
1543 2899 7.383102 ACATACAGACCAAAATGAGTGAATC 57.617 36.000 0.00 0.00 0.00 2.52
1544 2900 8.103305 ACTACATACAGACCAAAATGAGTGAAT 58.897 33.333 0.00 0.00 0.00 2.57
1545 2901 7.450074 ACTACATACAGACCAAAATGAGTGAA 58.550 34.615 0.00 0.00 0.00 3.18
1546 2902 7.004555 ACTACATACAGACCAAAATGAGTGA 57.995 36.000 0.00 0.00 0.00 3.41
1547 2903 6.313905 GGACTACATACAGACCAAAATGAGTG 59.686 42.308 0.00 0.00 31.59 3.51
1548 2904 6.407202 GGACTACATACAGACCAAAATGAGT 58.593 40.000 0.00 0.00 31.59 3.41
1549 2905 5.520288 CGGACTACATACAGACCAAAATGAG 59.480 44.000 0.00 0.00 31.59 2.90
1550 2906 5.046878 ACGGACTACATACAGACCAAAATGA 60.047 40.000 0.00 0.00 31.59 2.57
1551 2907 5.175859 ACGGACTACATACAGACCAAAATG 58.824 41.667 0.00 0.00 31.59 2.32
1552 2908 5.416271 ACGGACTACATACAGACCAAAAT 57.584 39.130 0.00 0.00 31.59 1.82
1553 2909 4.877378 ACGGACTACATACAGACCAAAA 57.123 40.909 0.00 0.00 31.59 2.44
1554 2910 5.012239 ACTACGGACTACATACAGACCAAA 58.988 41.667 0.00 0.00 31.59 3.28
1555 2911 4.397103 CACTACGGACTACATACAGACCAA 59.603 45.833 0.00 0.00 31.59 3.67
1556 2912 3.943381 CACTACGGACTACATACAGACCA 59.057 47.826 0.00 0.00 31.59 4.02
1557 2913 3.314635 CCACTACGGACTACATACAGACC 59.685 52.174 0.00 0.00 36.56 3.85
1558 2914 4.194640 TCCACTACGGACTACATACAGAC 58.805 47.826 0.00 0.00 39.64 3.51
1559 2915 4.492494 TCCACTACGGACTACATACAGA 57.508 45.455 0.00 0.00 39.64 3.41
1560 2916 5.531659 AGATTCCACTACGGACTACATACAG 59.468 44.000 0.00 0.00 46.36 2.74
1561 2917 5.443283 AGATTCCACTACGGACTACATACA 58.557 41.667 0.00 0.00 46.36 2.29
1562 2918 5.764192 AGAGATTCCACTACGGACTACATAC 59.236 44.000 0.00 0.00 46.36 2.39
1563 2919 5.938279 AGAGATTCCACTACGGACTACATA 58.062 41.667 0.00 0.00 46.36 2.29
1564 2920 4.794334 AGAGATTCCACTACGGACTACAT 58.206 43.478 0.00 0.00 46.36 2.29
1565 2921 4.232188 AGAGATTCCACTACGGACTACA 57.768 45.455 0.00 0.00 46.36 2.74
1566 2922 5.609423 TCTAGAGATTCCACTACGGACTAC 58.391 45.833 0.00 0.00 46.36 2.73
1567 2923 5.883685 TCTAGAGATTCCACTACGGACTA 57.116 43.478 0.00 0.00 46.36 2.59
1568 2924 4.774660 TCTAGAGATTCCACTACGGACT 57.225 45.455 0.00 0.00 46.36 3.85
1569 2925 5.589452 TCTTTCTAGAGATTCCACTACGGAC 59.411 44.000 0.00 0.00 46.36 4.79
1570 2926 5.589452 GTCTTTCTAGAGATTCCACTACGGA 59.411 44.000 0.00 0.00 44.40 4.69
1571 2927 5.591067 AGTCTTTCTAGAGATTCCACTACGG 59.409 44.000 0.00 0.00 0.00 4.02
1572 2928 6.687081 AGTCTTTCTAGAGATTCCACTACG 57.313 41.667 0.00 0.00 0.00 3.51
1601 2957 9.798994 GACATAATCTACTCTTTCCGTTCTTAA 57.201 33.333 0.00 0.00 0.00 1.85
1602 2958 8.963725 TGACATAATCTACTCTTTCCGTTCTTA 58.036 33.333 0.00 0.00 0.00 2.10
1603 2959 7.837863 TGACATAATCTACTCTTTCCGTTCTT 58.162 34.615 0.00 0.00 0.00 2.52
1604 2960 7.339721 TCTGACATAATCTACTCTTTCCGTTCT 59.660 37.037 0.00 0.00 0.00 3.01
1605 2961 7.481642 TCTGACATAATCTACTCTTTCCGTTC 58.518 38.462 0.00 0.00 0.00 3.95
1606 2962 7.339721 TCTCTGACATAATCTACTCTTTCCGTT 59.660 37.037 0.00 0.00 0.00 4.44
1607 2963 6.829298 TCTCTGACATAATCTACTCTTTCCGT 59.171 38.462 0.00 0.00 0.00 4.69
1608 2964 7.136119 GTCTCTGACATAATCTACTCTTTCCG 58.864 42.308 0.00 0.00 32.09 4.30
1609 2965 7.286775 AGGTCTCTGACATAATCTACTCTTTCC 59.713 40.741 0.07 0.00 33.68 3.13
1610 2966 8.232913 AGGTCTCTGACATAATCTACTCTTTC 57.767 38.462 0.07 0.00 33.68 2.62
1611 2967 8.058847 AGAGGTCTCTGACATAATCTACTCTTT 58.941 37.037 0.00 0.00 38.75 2.52
1612 2968 7.582719 AGAGGTCTCTGACATAATCTACTCTT 58.417 38.462 0.00 0.00 38.75 2.85
1613 2969 7.149202 AGAGGTCTCTGACATAATCTACTCT 57.851 40.000 0.00 0.00 38.75 3.24
1614 2970 7.817418 AAGAGGTCTCTGACATAATCTACTC 57.183 40.000 0.77 0.00 40.36 2.59
1615 2971 7.417342 GCAAAGAGGTCTCTGACATAATCTACT 60.417 40.741 0.77 0.00 40.36 2.57
1616 2972 6.699642 GCAAAGAGGTCTCTGACATAATCTAC 59.300 42.308 0.77 0.00 40.36 2.59
1617 2973 6.381133 TGCAAAGAGGTCTCTGACATAATCTA 59.619 38.462 0.77 0.00 40.36 1.98
1618 2974 5.188555 TGCAAAGAGGTCTCTGACATAATCT 59.811 40.000 0.77 0.00 40.36 2.40
1619 2975 5.423015 TGCAAAGAGGTCTCTGACATAATC 58.577 41.667 0.77 0.00 40.36 1.75
1623 2979 3.996921 ATGCAAAGAGGTCTCTGACAT 57.003 42.857 0.77 3.63 40.36 3.06
1677 3036 2.799126 TCCAAGCATTGTCGGGTATT 57.201 45.000 0.00 0.00 46.99 1.89
1685 3048 2.596346 TGTTGTCCATCCAAGCATTGT 58.404 42.857 0.00 0.00 46.99 2.71
1702 3065 3.258872 CACCAATCACCATCCATGTTGTT 59.741 43.478 0.00 0.00 0.00 2.83
1721 3084 5.503846 GCAAAATTGTGATTGTGGTTTCACC 60.504 40.000 0.00 0.00 42.98 4.02
1722 3085 5.294060 AGCAAAATTGTGATTGTGGTTTCAC 59.706 36.000 0.00 0.00 37.84 3.18
1723 3086 5.426504 AGCAAAATTGTGATTGTGGTTTCA 58.573 33.333 0.00 0.00 37.84 2.69
1724 3087 5.989551 AGCAAAATTGTGATTGTGGTTTC 57.010 34.783 0.00 0.00 37.84 2.78
1725 3088 5.296531 GGAAGCAAAATTGTGATTGTGGTTT 59.703 36.000 3.29 0.00 46.13 3.27
1728 3091 4.449743 CAGGAAGCAAAATTGTGATTGTGG 59.550 41.667 3.29 0.00 32.13 4.17
1729 3092 4.084223 GCAGGAAGCAAAATTGTGATTGTG 60.084 41.667 3.29 2.79 44.79 3.33
1731 3094 4.657075 GCAGGAAGCAAAATTGTGATTG 57.343 40.909 3.29 0.00 44.79 2.67
1758 3141 1.350684 TCAGCAGGAAACTACATGCCA 59.649 47.619 0.00 0.00 46.56 4.92
1760 3143 2.426522 TGTCAGCAGGAAACTACATGC 58.573 47.619 0.00 0.00 45.89 4.06
1761 3144 3.120060 GCTTGTCAGCAGGAAACTACATG 60.120 47.826 0.00 0.00 46.49 3.21
1822 3212 0.108138 GACCAAGAGCCGCTACATGT 60.108 55.000 2.69 2.69 0.00 3.21
1827 3217 1.689233 ATGGGACCAAGAGCCGCTA 60.689 57.895 0.00 0.00 0.00 4.26
1840 3230 0.884259 CGAATGTATGGCGCATGGGA 60.884 55.000 14.90 0.00 0.00 4.37
1927 3317 2.237143 CCACTGGAGACCATCTTTGCTA 59.763 50.000 0.00 0.00 30.82 3.49
1966 3356 2.032528 TCCCTCGCAGCAACCAAG 59.967 61.111 0.00 0.00 0.00 3.61
1978 3368 3.131400 GGTTGTGATCTACAGAGTCCCTC 59.869 52.174 0.00 0.00 41.10 4.30
1987 3377 2.831685 AGTTGCGGTTGTGATCTACA 57.168 45.000 0.00 0.00 37.56 2.74
1999 3389 1.394917 CGATTGAAGAGGAAGTTGCGG 59.605 52.381 0.00 0.00 0.00 5.69
2035 3425 1.850345 ACTTCTTGGGTGAGGGTTTGA 59.150 47.619 0.00 0.00 0.00 2.69
2086 3478 6.641169 AGGAAGAAAGAAAGCCAAACTAAG 57.359 37.500 0.00 0.00 0.00 2.18
2089 3481 5.204292 AGAAGGAAGAAAGAAAGCCAAACT 58.796 37.500 0.00 0.00 0.00 2.66
2112 3504 4.521536 AGTATACTAGACAGCAGTGGGA 57.478 45.455 2.75 0.00 0.00 4.37
2113 3505 5.692613 GTAGTATACTAGACAGCAGTGGG 57.307 47.826 12.99 0.00 38.91 4.61
2145 3538 9.811995 CATCATCATCAGTTAATCAACCAAATT 57.188 29.630 0.00 0.00 35.05 1.82
2232 3628 2.214347 TGAACTTCAAACGCAATCGGA 58.786 42.857 0.00 0.00 40.69 4.55
2286 3682 4.646492 ACTTTGAAAGCCAACAGTTCATCT 59.354 37.500 4.57 0.00 33.85 2.90
2348 3744 1.656652 GCAGGTGATGCGTGTAGATT 58.343 50.000 0.00 0.00 46.99 2.40
2401 3797 0.320771 GCCTCGACTGAAGGAAGCAA 60.321 55.000 0.00 0.00 0.00 3.91
2803 4201 1.290324 CGACACCCTCCAGACACAG 59.710 63.158 0.00 0.00 0.00 3.66
2990 4388 5.672503 TGCAGGTTTACTTGTACAGTTGTA 58.327 37.500 0.00 0.00 36.88 2.41
3070 4470 2.936919 TGACAGCAAGTTCCATCAGT 57.063 45.000 0.00 0.00 0.00 3.41
3087 4487 1.606668 GAGACCGCCACAAAACATTGA 59.393 47.619 0.00 0.00 0.00 2.57
3099 4499 1.599542 GATACTGCATTTGAGACCGCC 59.400 52.381 0.00 0.00 0.00 6.13
3129 4529 0.721155 CACGCAAACACGGATCAACG 60.721 55.000 0.00 0.00 37.37 4.10
3130 4530 0.306533 ACACGCAAACACGGATCAAC 59.693 50.000 0.00 0.00 37.37 3.18
3219 4621 1.024271 GTTTCAGGTGTGCTGAGCAA 58.976 50.000 9.51 0.00 41.47 3.91
3221 4623 2.169832 TAGTTTCAGGTGTGCTGAGC 57.830 50.000 0.00 0.00 31.98 4.26
3222 4624 4.820897 TGTATAGTTTCAGGTGTGCTGAG 58.179 43.478 0.00 0.00 31.98 3.35
3678 5473 3.201487 TGAACCTGCATCAGAGGATCAAT 59.799 43.478 0.14 0.00 38.92 2.57


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

AutoCloner maintained by Alex Coulton.