Multiple sequence alignment - TraesCS5B01G425300

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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 TraesCS5B01G425300 chr5B 100.000 8017 0 0 1 8017 601329655 601337671 0.000000e+00 14805.0
1 TraesCS5B01G425300 chr5B 91.923 260 12 3 7751 8006 601344239 601344493 9.900000e-94 355.0
2 TraesCS5B01G425300 chr5A 92.393 4601 239 48 2875 7418 609206404 609210950 0.000000e+00 6455.0
3 TraesCS5B01G425300 chr5A 91.963 2837 120 41 49 2828 609203457 609206242 0.000000e+00 3877.0
4 TraesCS5B01G425300 chr5A 95.570 1377 56 3 5456 6832 609229015 609230386 0.000000e+00 2200.0
5 TraesCS5B01G425300 chr5A 93.316 778 43 5 4564 5336 609228236 609229009 0.000000e+00 1140.0
6 TraesCS5B01G425300 chr5A 86.154 455 57 2 6835 7289 609239691 609240139 3.360000e-133 486.0
7 TraesCS5B01G425300 chr5A 80.615 423 46 20 7583 7983 609240401 609240809 2.190000e-75 294.0
8 TraesCS5B01G425300 chr5A 79.787 282 6 15 7751 8016 609211357 609211603 3.000000e-34 158.0
9 TraesCS5B01G425300 chr5D 95.142 2388 75 10 4939 7318 488352495 488354849 0.000000e+00 3729.0
10 TraesCS5B01G425300 chr5D 96.654 2092 48 14 2875 4959 488350244 488352320 0.000000e+00 3456.0
11 TraesCS5B01G425300 chr5D 95.710 1282 52 3 1548 2828 488348799 488350078 0.000000e+00 2060.0
12 TraesCS5B01G425300 chr5D 89.774 753 36 15 858 1597 488348075 488348799 0.000000e+00 926.0
13 TraesCS5B01G425300 chr5D 83.164 689 34 30 1 665 488347338 488347968 9.090000e-154 555.0
14 TraesCS5B01G425300 chr5D 90.850 306 15 5 7684 7983 488355280 488355578 1.620000e-106 398.0
15 TraesCS5B01G425300 chr5D 88.930 271 16 2 7417 7673 488354924 488355194 1.000000e-83 322.0
16 TraesCS5B01G425300 chr5D 86.397 272 20 8 1 257 537938886 537938617 1.700000e-71 281.0
17 TraesCS5B01G425300 chr5D 96.970 33 1 0 2842 2874 488350144 488350176 1.000000e-03 56.5
18 TraesCS5B01G425300 chr1D 94.942 257 6 2 315 571 239784705 239784456 5.830000e-106 396.0
19 TraesCS5B01G425300 chr1D 85.662 272 22 10 1 257 239784969 239784700 3.690000e-68 270.0
20 TraesCS5B01G425300 chr7B 93.385 257 10 3 315 571 625272339 625272090 2.730000e-99 374.0
21 TraesCS5B01G425300 chr3B 93.385 257 10 3 315 571 62349721 62349472 2.730000e-99 374.0
22 TraesCS5B01G425300 chr2D 93.385 257 10 3 315 571 200393695 200393446 2.730000e-99 374.0
23 TraesCS5B01G425300 chr2D 86.029 272 21 8 1 257 42604124 42603855 7.930000e-70 276.0
24 TraesCS5B01G425300 chr2D 84.982 273 21 10 1 257 200393958 200393690 7.980000e-65 259.0
25 TraesCS5B01G425300 chr2B 93.333 255 9 4 315 569 346735860 346735614 3.530000e-98 370.0
26 TraesCS5B01G425300 chr4D 92.996 257 10 3 315 571 153051492 153051244 1.270000e-97 368.0
27 TraesCS5B01G425300 chr4D 86.397 272 20 9 1 257 153051756 153051487 1.700000e-71 281.0
28 TraesCS5B01G425300 chr3A 92.996 257 11 3 315 571 611009626 611009377 1.270000e-97 368.0
29 TraesCS5B01G425300 chr7A 86.765 272 19 9 1 257 151359782 151359513 3.660000e-73 287.0
30 TraesCS5B01G425300 chr7A 86.617 269 19 10 1 254 578331573 578331839 1.700000e-71 281.0
31 TraesCS5B01G425300 chr1B 84.758 269 24 8 1 254 632856770 632857036 3.710000e-63 254.0


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 TraesCS5B01G425300 chr5B 601329655 601337671 8016 False 14805.000000 14805 100.000000 1 8017 1 chr5B.!!$F1 8016
1 TraesCS5B01G425300 chr5A 609203457 609211603 8146 False 3496.666667 6455 88.047667 49 8016 3 chr5A.!!$F1 7967
2 TraesCS5B01G425300 chr5A 609228236 609230386 2150 False 1670.000000 2200 94.443000 4564 6832 2 chr5A.!!$F2 2268
3 TraesCS5B01G425300 chr5A 609239691 609240809 1118 False 390.000000 486 83.384500 6835 7983 2 chr5A.!!$F3 1148
4 TraesCS5B01G425300 chr5D 488347338 488355578 8240 False 1437.812500 3729 92.149250 1 7983 8 chr5D.!!$F1 7982
5 TraesCS5B01G425300 chr1D 239784456 239784969 513 True 333.000000 396 90.302000 1 571 2 chr1D.!!$R1 570
6 TraesCS5B01G425300 chr2D 200393446 200393958 512 True 316.500000 374 89.183500 1 571 2 chr2D.!!$R2 570
7 TraesCS5B01G425300 chr4D 153051244 153051756 512 True 324.500000 368 89.696500 1 571 2 chr4D.!!$R1 570

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
170 180 0.187361 TTTCACCCCAAACCTCCCAG 59.813 55.000 0.00 0.0 0.00 4.45 F
1399 1537 0.179078 TTTGGCCAGTTGCTTGCTTG 60.179 50.000 5.11 0.0 40.92 4.01 F
1403 1541 0.314935 GCCAGTTGCTTGCTTGCTTA 59.685 50.000 3.47 0.0 36.87 3.09 F
2892 3208 0.709992 TGGCCCCTTGCTTTAGGAAT 59.290 50.000 0.00 0.0 40.92 3.01 F
3886 4205 1.487976 CCCTCTGGCAGCATCTCTTTA 59.512 52.381 10.34 0.0 0.00 1.85 F
4919 5260 1.739466 CACCATTCATCAGTGGTTCCG 59.261 52.381 0.00 0.0 46.22 4.30 F
6453 7056 0.466189 CAGCAAGTCCACCAACAGGT 60.466 55.000 0.00 0.0 35.55 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2066 0.602638 GAAGACACGTGCCATGGACA 60.603 55.000 18.40 10.56 0.00 4.02 R
2967 3283 1.064906 CATGCATGGTCACTCCTCCTT 60.065 52.381 19.40 0.00 37.07 3.36 R
3001 3319 4.412528 AGGACCTAATTAAGTGATGGACCC 59.587 45.833 0.00 0.00 31.58 4.46 R
4830 5171 1.202348 GCTAACAATCCACCCAGTTGC 59.798 52.381 0.00 0.00 0.00 4.17 R
4923 5264 0.867746 CTGCTTCTTAGTGTTGCGCA 59.132 50.000 5.66 5.66 0.00 6.09 R
6463 7066 0.106419 TTGCCTCCGGTTCCTTTTGT 60.106 50.000 0.00 0.00 0.00 2.83 R
7638 8396 0.251787 GGCTGTGGAATCCCAAAGGT 60.252 55.000 0.00 0.00 46.08 3.50 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
39 41 5.578157 AACCTCCTAGCCTCAAACTAAAA 57.422 39.130 0.00 0.00 0.00 1.52
45 47 6.731467 TCCTAGCCTCAAACTAAAATGGATT 58.269 36.000 0.00 0.00 0.00 3.01
46 48 6.603201 TCCTAGCCTCAAACTAAAATGGATTG 59.397 38.462 0.00 0.00 0.00 2.67
47 49 5.665916 AGCCTCAAACTAAAATGGATTGG 57.334 39.130 0.00 0.00 0.00 3.16
90 97 2.299993 GCACAGCTATGCAGAGTACA 57.700 50.000 13.21 0.00 45.39 2.90
92 99 3.201290 GCACAGCTATGCAGAGTACAAT 58.799 45.455 13.21 0.00 45.39 2.71
99 106 6.744537 CAGCTATGCAGAGTACAATTCAAAAC 59.255 38.462 10.55 0.00 0.00 2.43
100 107 5.734498 GCTATGCAGAGTACAATTCAAAACG 59.266 40.000 10.55 0.00 0.00 3.60
103 110 5.507077 TGCAGAGTACAATTCAAAACGAAC 58.493 37.500 0.00 0.00 36.12 3.95
104 111 5.295787 TGCAGAGTACAATTCAAAACGAACT 59.704 36.000 0.00 0.00 36.12 3.01
105 112 5.846473 GCAGAGTACAATTCAAAACGAACTC 59.154 40.000 0.00 0.00 36.12 3.01
106 113 6.511121 GCAGAGTACAATTCAAAACGAACTCA 60.511 38.462 0.00 0.00 36.12 3.41
117 125 6.674066 TCAAAACGAACTCAAAACAGAACTT 58.326 32.000 0.00 0.00 0.00 2.66
170 180 0.187361 TTTCACCCCAAACCTCCCAG 59.813 55.000 0.00 0.00 0.00 4.45
272 303 2.202946 GACTCGCCCTAAGCAGCC 60.203 66.667 0.00 0.00 44.04 4.85
273 304 4.148825 ACTCGCCCTAAGCAGCCG 62.149 66.667 0.00 0.00 44.04 5.52
274 305 3.838271 CTCGCCCTAAGCAGCCGA 61.838 66.667 0.00 0.00 44.04 5.54
275 306 3.781770 CTCGCCCTAAGCAGCCGAG 62.782 68.421 2.67 2.67 44.04 4.63
276 307 4.899239 CGCCCTAAGCAGCCGAGG 62.899 72.222 3.49 3.49 44.04 4.63
655 703 4.147449 TCGGCGTCTGGGCTGATG 62.147 66.667 6.85 0.00 43.13 3.07
659 707 2.434884 CGTCTGGGCTGATGCGTT 60.435 61.111 0.00 0.00 40.82 4.84
660 708 2.743752 CGTCTGGGCTGATGCGTTG 61.744 63.158 0.00 0.00 40.82 4.10
661 709 1.672356 GTCTGGGCTGATGCGTTGT 60.672 57.895 0.00 0.00 40.82 3.32
662 710 1.672030 TCTGGGCTGATGCGTTGTG 60.672 57.895 0.00 0.00 40.82 3.33
663 711 3.332493 CTGGGCTGATGCGTTGTGC 62.332 63.158 0.00 0.00 46.70 4.57
664 712 3.058160 GGGCTGATGCGTTGTGCT 61.058 61.111 0.00 0.00 46.63 4.40
665 713 1.745115 GGGCTGATGCGTTGTGCTA 60.745 57.895 0.00 0.00 46.63 3.49
666 714 1.097547 GGGCTGATGCGTTGTGCTAT 61.098 55.000 0.00 0.00 46.63 2.97
667 715 0.734889 GGCTGATGCGTTGTGCTATT 59.265 50.000 0.00 0.00 46.63 1.73
668 716 1.133025 GGCTGATGCGTTGTGCTATTT 59.867 47.619 0.00 0.00 46.63 1.40
669 717 2.415893 GGCTGATGCGTTGTGCTATTTT 60.416 45.455 0.00 0.00 46.63 1.82
670 718 3.244976 GCTGATGCGTTGTGCTATTTTT 58.755 40.909 0.00 0.00 46.63 1.94
691 739 5.906113 TTTTTCTCTCTCTCTCTATGCGT 57.094 39.130 0.00 0.00 0.00 5.24
692 740 4.891627 TTTCTCTCTCTCTCTATGCGTG 57.108 45.455 0.00 0.00 0.00 5.34
693 741 2.844946 TCTCTCTCTCTCTATGCGTGG 58.155 52.381 0.00 0.00 0.00 4.94
773 866 4.754667 GCGAGGTTGGGGTCGGTC 62.755 72.222 0.00 0.00 36.67 4.79
801 894 0.394899 GATGGGCCTGAAAGTGGGAG 60.395 60.000 4.53 0.00 0.00 4.30
875 968 1.139058 CTAGGCCCATGAAGCGTAAGT 59.861 52.381 0.00 0.00 41.68 2.24
905 1000 5.914898 TTTGGGCTTCTAGCTTAATTTCC 57.085 39.130 0.00 0.00 41.99 3.13
906 1001 4.584638 TGGGCTTCTAGCTTAATTTCCA 57.415 40.909 0.00 0.00 41.99 3.53
909 1026 4.576873 GGGCTTCTAGCTTAATTTCCACTC 59.423 45.833 0.00 0.00 41.99 3.51
928 1045 1.667722 CAAAGGAACTGGGCCTTGC 59.332 57.895 4.53 0.00 44.72 4.01
933 1050 2.032681 AACTGGGCCTTGCTCGAC 59.967 61.111 4.53 0.00 0.00 4.20
1364 1502 0.538287 GTGCCTTGGCTCCTTCAACT 60.538 55.000 13.18 0.00 0.00 3.16
1365 1503 0.538057 TGCCTTGGCTCCTTCAACTG 60.538 55.000 13.18 0.00 0.00 3.16
1366 1504 0.250901 GCCTTGGCTCCTTCAACTGA 60.251 55.000 4.11 0.00 0.00 3.41
1367 1505 1.819305 GCCTTGGCTCCTTCAACTGAA 60.819 52.381 4.11 0.00 0.00 3.02
1399 1537 0.179078 TTTGGCCAGTTGCTTGCTTG 60.179 50.000 5.11 0.00 40.92 4.01
1403 1541 0.314935 GCCAGTTGCTTGCTTGCTTA 59.685 50.000 3.47 0.00 36.87 3.09
1408 1546 4.114794 CAGTTGCTTGCTTGCTTAAAACT 58.885 39.130 3.47 2.31 0.00 2.66
1424 1562 9.542462 TGCTTAAAACTTAGAATAGATACGCAT 57.458 29.630 0.00 0.00 0.00 4.73
1444 1582 5.901884 CGCATTCCGTTTCTATATTGTTGAC 59.098 40.000 0.00 0.00 0.00 3.18
1458 1600 1.525077 TTGACGAACCTGCACACCC 60.525 57.895 0.00 0.00 0.00 4.61
1469 1611 2.006888 CTGCACACCCGATTTCGTAAT 58.993 47.619 0.00 0.00 37.74 1.89
1470 1612 3.191669 CTGCACACCCGATTTCGTAATA 58.808 45.455 0.00 0.00 37.74 0.98
1471 1613 3.191669 TGCACACCCGATTTCGTAATAG 58.808 45.455 0.00 0.00 37.74 1.73
1482 1624 9.745880 CCCGATTTCGTAATAGTAATAGCATAT 57.254 33.333 0.00 0.00 37.74 1.78
1507 1649 1.269448 CAGAACAATGGGACGGTTTGG 59.731 52.381 0.00 0.00 0.00 3.28
1579 1770 1.881973 GCTGCCTTTGATGTGAACTGA 59.118 47.619 0.00 0.00 0.00 3.41
1633 1824 4.155462 CAGTGTTGTTGGAGATGATTGGAG 59.845 45.833 0.00 0.00 0.00 3.86
1636 1827 5.122396 GTGTTGTTGGAGATGATTGGAGTAC 59.878 44.000 0.00 0.00 0.00 2.73
1694 1888 6.378280 TCAGGAAGAAGAAGAAGCAAAGTTTT 59.622 34.615 0.00 0.00 0.00 2.43
1698 1892 3.459232 AGAAGAAGCAAAGTTTTGGGC 57.541 42.857 6.72 0.00 38.57 5.36
1871 2066 3.554934 TGTTCAAGGACACTCATGCTTT 58.445 40.909 0.00 0.00 0.00 3.51
1886 2081 1.795170 GCTTTGTCCATGGCACGTGT 61.795 55.000 18.38 0.00 0.00 4.49
1900 2095 2.802816 GCACGTGTCTTCACAGATTCTT 59.197 45.455 18.38 0.00 44.02 2.52
1964 2160 7.857389 ACATCATATATGCGTGTTGTTTTGATC 59.143 33.333 7.92 0.00 0.00 2.92
1968 2164 6.735678 ATATGCGTGTTGTTTTGATCACTA 57.264 33.333 0.00 0.00 0.00 2.74
1986 2182 4.578105 TCACTAAATGCATGTGTTGTGTGA 59.422 37.500 13.54 12.82 33.82 3.58
1995 2191 4.983538 GCATGTGTTGTGTGATTTTCATCA 59.016 37.500 0.00 0.00 37.05 3.07
2025 2221 6.016610 TGTTTTACTAGCTGGTGGAATGTTTC 60.017 38.462 13.76 0.00 0.00 2.78
2055 2251 4.179298 GTTACGTTCTAATGGGTCCTGAC 58.821 47.826 0.00 0.00 0.00 3.51
2133 2329 3.170717 GACGATGGGGAATGGGAGTATA 58.829 50.000 0.00 0.00 0.00 1.47
2174 2370 5.771666 GGAGATCATATGGCAAGGAAATGAA 59.228 40.000 2.13 0.00 30.90 2.57
2214 2410 9.987272 AGAAAAAGATCAAAATACCAAAGAAGG 57.013 29.630 0.00 0.00 0.00 3.46
2246 2442 5.568620 AACCACTAAGTCAAGAGGTCAAT 57.431 39.130 0.00 0.00 39.24 2.57
2828 3024 6.806739 GCAAACAAATTGGTATCCTGAACTAC 59.193 38.462 0.00 0.00 39.54 2.73
2829 3025 7.523052 GCAAACAAATTGGTATCCTGAACTACA 60.523 37.037 0.00 0.00 39.54 2.74
2830 3026 7.687941 AACAAATTGGTATCCTGAACTACAG 57.312 36.000 0.00 0.00 45.36 2.74
2832 3028 6.879458 ACAAATTGGTATCCTGAACTACAGTC 59.121 38.462 0.00 0.00 44.40 3.51
2833 3029 6.620877 AATTGGTATCCTGAACTACAGTCA 57.379 37.500 0.00 0.00 44.40 3.41
2834 3030 5.401531 TTGGTATCCTGAACTACAGTCAC 57.598 43.478 0.00 0.00 44.40 3.67
2835 3031 4.412843 TGGTATCCTGAACTACAGTCACA 58.587 43.478 0.00 0.00 44.40 3.58
2838 3034 6.666113 TGGTATCCTGAACTACAGTCACATTA 59.334 38.462 0.00 0.00 44.40 1.90
2843 3090 9.823647 ATCCTGAACTACAGTCACATTAATTAG 57.176 33.333 0.00 0.00 44.40 1.73
2892 3208 0.709992 TGGCCCCTTGCTTTAGGAAT 59.290 50.000 0.00 0.00 40.92 3.01
2967 3283 3.706183 TGTGGGATTAACCAATGCATGA 58.294 40.909 0.00 0.00 43.34 3.07
3044 3362 5.181433 GTCCTCCTTGGTTACTGTGATTTTC 59.819 44.000 0.00 0.00 37.07 2.29
3829 4148 6.885376 TGGTGAACTTGTTAACTTCAAGGTTA 59.115 34.615 7.22 0.00 41.98 2.85
3851 4170 3.428413 TTTTTCTTCCTTCCCTACCGG 57.572 47.619 0.00 0.00 0.00 5.28
3886 4205 1.487976 CCCTCTGGCAGCATCTCTTTA 59.512 52.381 10.34 0.00 0.00 1.85
4069 4391 3.489059 CGTCCAATGCATGTTCCCATAAC 60.489 47.826 0.00 0.00 0.00 1.89
4280 4606 8.846211 TGCAATTAAGAGGTTATTAGTATTGGC 58.154 33.333 0.00 0.00 0.00 4.52
4312 4638 7.118971 GGAGACTAATTCTGCCAGCTATTAATG 59.881 40.741 0.00 0.00 36.69 1.90
4324 4650 7.611079 TGCCAGCTATTAATGTGATATATGCAA 59.389 33.333 0.00 0.00 0.00 4.08
4326 4652 8.127327 CCAGCTATTAATGTGATATATGCAAGC 58.873 37.037 0.00 0.00 0.00 4.01
4397 4723 5.634859 CAGTTTCACCTTAATTCATGTTGGC 59.365 40.000 0.00 0.00 0.00 4.52
4457 4783 4.274214 TCATATGTACTCAGTTCGTACCCG 59.726 45.833 1.90 0.00 37.11 5.28
4554 4895 5.479027 TCATACAATAGTATTAGCAGGCCGA 59.521 40.000 0.00 0.00 38.88 5.54
4555 4896 4.891992 ACAATAGTATTAGCAGGCCGAT 57.108 40.909 0.00 0.00 0.00 4.18
4632 4973 4.923871 CACTGTAGTTGTTCATAGCGACTT 59.076 41.667 0.00 0.00 33.12 3.01
4633 4974 6.072342 TCACTGTAGTTGTTCATAGCGACTTA 60.072 38.462 0.00 0.00 33.12 2.24
4673 5014 4.525100 GCTATACCCTAGGGACTTCTCAAG 59.475 50.000 35.38 18.10 41.75 3.02
4801 5142 3.766051 GGAAAAGGAACCTCGTACCTAGA 59.234 47.826 0.00 0.00 33.34 2.43
4830 5171 9.859427 TGTGCTGGATTTCTATTAATTGAAAAG 57.141 29.630 22.82 17.83 35.73 2.27
4842 5183 2.151502 TTGAAAAGCAACTGGGTGGA 57.848 45.000 0.00 0.00 0.00 4.02
4919 5260 1.739466 CACCATTCATCAGTGGTTCCG 59.261 52.381 0.00 0.00 46.22 4.30
4923 5264 2.631160 TTCATCAGTGGTTCCGTTGT 57.369 45.000 0.00 0.00 0.00 3.32
4949 5480 5.348724 CGCAACACTAAGAAGCAGAAATCTA 59.651 40.000 0.00 0.00 0.00 1.98
5031 5562 1.754234 GTTGGCCCTGGTATGCAGG 60.754 63.158 0.00 0.00 39.48 4.85
5143 5679 3.618594 TCTTCTCATGCGTTATGCTGAAC 59.381 43.478 0.00 0.00 46.63 3.18
5457 6017 6.339587 TCCATAACATGTTCCTGGTTTTTC 57.660 37.500 27.00 0.00 31.31 2.29
6453 7056 0.466189 CAGCAAGTCCACCAACAGGT 60.466 55.000 0.00 0.00 35.55 4.00
6454 7057 1.136828 AGCAAGTCCACCAACAGGTA 58.863 50.000 0.00 0.00 33.30 3.08
6455 7058 1.202770 AGCAAGTCCACCAACAGGTAC 60.203 52.381 0.00 0.00 33.30 3.34
6456 7059 1.476110 GCAAGTCCACCAACAGGTACA 60.476 52.381 0.00 0.00 33.30 2.90
6457 7060 2.925724 CAAGTCCACCAACAGGTACAA 58.074 47.619 0.00 0.00 33.30 2.41
6458 7061 3.486383 CAAGTCCACCAACAGGTACAAT 58.514 45.455 0.00 0.00 33.30 2.71
6459 7062 3.140325 AGTCCACCAACAGGTACAATG 57.860 47.619 0.00 0.00 33.30 2.82
6460 7063 2.708861 AGTCCACCAACAGGTACAATGA 59.291 45.455 4.48 0.00 33.30 2.57
6461 7064 3.330701 AGTCCACCAACAGGTACAATGAT 59.669 43.478 4.48 0.00 33.30 2.45
6462 7065 3.689649 GTCCACCAACAGGTACAATGATC 59.310 47.826 4.48 0.00 33.30 2.92
6463 7066 3.329225 TCCACCAACAGGTACAATGATCA 59.671 43.478 0.00 0.00 33.30 2.92
6464 7067 3.440173 CCACCAACAGGTACAATGATCAC 59.560 47.826 0.00 0.00 33.30 3.06
6465 7068 4.071423 CACCAACAGGTACAATGATCACA 58.929 43.478 0.00 0.00 33.30 3.58
6466 7069 4.518590 CACCAACAGGTACAATGATCACAA 59.481 41.667 0.00 0.00 33.30 3.33
6467 7070 5.009510 CACCAACAGGTACAATGATCACAAA 59.990 40.000 0.00 0.00 33.30 2.83
6468 7071 5.596361 ACCAACAGGTACAATGATCACAAAA 59.404 36.000 0.00 0.00 32.67 2.44
6469 7072 6.151691 CCAACAGGTACAATGATCACAAAAG 58.848 40.000 0.00 0.00 0.00 2.27
6470 7073 5.964958 ACAGGTACAATGATCACAAAAGG 57.035 39.130 0.00 0.00 0.00 3.11
6471 7074 5.630121 ACAGGTACAATGATCACAAAAGGA 58.370 37.500 0.00 0.00 0.00 3.36
6472 7075 6.068010 ACAGGTACAATGATCACAAAAGGAA 58.932 36.000 0.00 0.00 0.00 3.36
6473 7076 6.016276 ACAGGTACAATGATCACAAAAGGAAC 60.016 38.462 0.00 0.00 0.00 3.62
6474 7077 5.476945 AGGTACAATGATCACAAAAGGAACC 59.523 40.000 0.00 0.00 0.00 3.62
6475 7078 4.503741 ACAATGATCACAAAAGGAACCG 57.496 40.909 0.00 0.00 0.00 4.44
6476 7079 3.255642 ACAATGATCACAAAAGGAACCGG 59.744 43.478 0.00 0.00 0.00 5.28
6477 7080 2.940994 TGATCACAAAAGGAACCGGA 57.059 45.000 9.46 0.00 0.00 5.14
6478 7081 2.778299 TGATCACAAAAGGAACCGGAG 58.222 47.619 9.46 0.00 0.00 4.63
6592 7195 6.587990 AGACATTACGTTGAAGATGACTCTTG 59.412 38.462 0.00 0.00 41.87 3.02
6683 7286 4.878397 AGATGGCTAGCAACAAATAGTGAC 59.122 41.667 18.24 0.00 0.00 3.67
6695 7298 6.467723 ACAAATAGTGACGTTGATTCAGAC 57.532 37.500 0.00 0.00 0.00 3.51
6749 7352 3.819337 GAGTTGGTAAAGGTGGAAGGAAC 59.181 47.826 0.00 0.00 0.00 3.62
6755 7358 4.633126 GGTAAAGGTGGAAGGAACGATAAC 59.367 45.833 0.00 0.00 0.00 1.89
6784 7387 4.156739 TCCTGATGAGGATGATCGTTATCG 59.843 45.833 12.99 8.92 44.13 2.92
6853 7456 0.248843 AGCAGGAAGAGGAAGAAGCG 59.751 55.000 0.00 0.00 0.00 4.68
6875 7478 4.084328 CGTCACAGTGAAATCAGGAAGAAC 60.084 45.833 4.32 0.00 0.00 3.01
6881 7484 3.686726 GTGAAATCAGGAAGAACAGCGAT 59.313 43.478 0.00 0.00 0.00 4.58
6899 7502 0.534427 ATAGCGACGACGATCCCTCA 60.534 55.000 12.29 0.00 42.66 3.86
6902 7505 1.787057 GCGACGACGATCCCTCAGAT 61.787 60.000 12.29 0.00 42.66 2.90
6908 7511 2.095466 CGACGATCCCTCAGATTCTAGC 60.095 54.545 0.00 0.00 34.42 3.42
6912 7515 1.309950 TCCCTCAGATTCTAGCGACG 58.690 55.000 0.00 0.00 0.00 5.12
6915 7518 2.541999 CCCTCAGATTCTAGCGACGTTC 60.542 54.545 0.00 0.00 0.00 3.95
6927 7530 1.693083 CGACGTTCGGGATTTGAGCC 61.693 60.000 0.00 0.00 36.00 4.70
6935 7538 1.324740 GGGATTTGAGCCTGCATGCA 61.325 55.000 21.29 21.29 0.00 3.96
6936 7539 0.533491 GGATTTGAGCCTGCATGCAA 59.467 50.000 22.88 4.98 0.00 4.08
7007 7610 4.309950 AAGGGTCGCCGTGGTCAC 62.310 66.667 0.00 0.00 0.00 3.67
7067 7670 0.173708 AGACTGGCGACTTCGGATTC 59.826 55.000 0.02 0.00 40.23 2.52
7152 7768 5.505173 TGCTTTCTTCTCCTTTTCTTGTG 57.495 39.130 0.00 0.00 0.00 3.33
7177 7793 2.026822 TCCTCTTTGCTGATGAGGTTCC 60.027 50.000 16.55 0.00 45.50 3.62
7182 7798 4.895297 TCTTTGCTGATGAGGTTCCTTTTT 59.105 37.500 0.00 0.00 0.00 1.94
7184 7800 2.813754 TGCTGATGAGGTTCCTTTTTCG 59.186 45.455 0.00 0.00 0.00 3.46
7228 7844 4.501400 GCAGAAGGCTTGTAATGGTTTTGT 60.501 41.667 3.46 0.00 40.25 2.83
7284 7900 1.200519 CCCTGGAATTCCACCGACTA 58.799 55.000 23.63 0.34 42.01 2.59
7289 7905 4.040461 CCTGGAATTCCACCGACTATATGT 59.960 45.833 23.63 0.00 42.01 2.29
7293 7912 5.465724 GGAATTCCACCGACTATATGTTCAC 59.534 44.000 20.04 0.00 35.64 3.18
7310 7929 4.036262 TGTTCACCACACTTGCTATTGAAC 59.964 41.667 0.00 0.00 41.03 3.18
7329 7948 4.097135 TGAACGAAAAGGCACATCTTCAAA 59.903 37.500 0.00 0.00 0.00 2.69
7333 7952 4.984161 CGAAAAGGCACATCTTCAAAACAT 59.016 37.500 0.00 0.00 0.00 2.71
7334 7953 5.117592 CGAAAAGGCACATCTTCAAAACATC 59.882 40.000 0.00 0.00 0.00 3.06
7335 7954 4.525912 AAGGCACATCTTCAAAACATCC 57.474 40.909 0.00 0.00 0.00 3.51
7353 7972 0.777446 CCTTTCCCTTCCCTCCAACA 59.223 55.000 0.00 0.00 0.00 3.33
7418 8127 2.286502 GGGAAGGGGGAAGCTCCT 60.287 66.667 0.00 0.00 36.57 3.69
7420 8129 1.925972 GGAAGGGGGAAGCTCCTGT 60.926 63.158 0.00 0.00 36.57 4.00
7421 8130 1.604915 GAAGGGGGAAGCTCCTGTC 59.395 63.158 0.00 0.00 36.57 3.51
7423 8132 0.551131 AAGGGGGAAGCTCCTGTCAT 60.551 55.000 0.00 0.00 36.57 3.06
7444 8188 5.652014 TCATCAGACCAACATAAATGGAACC 59.348 40.000 0.00 0.00 40.56 3.62
7568 8326 4.931002 CCCATTGCACTTTATTCCAAACAG 59.069 41.667 0.00 0.00 0.00 3.16
7638 8396 1.611977 AGCTACTGTGTGTTCGCTACA 59.388 47.619 0.00 0.00 34.15 2.74
7674 8432 3.053693 ACAGCCCAATTTCTGTATGGCTA 60.054 43.478 0.00 0.00 46.98 3.93
7675 8433 3.316308 CAGCCCAATTTCTGTATGGCTAC 59.684 47.826 0.00 0.00 46.98 3.58
7676 8434 2.623416 GCCCAATTTCTGTATGGCTACC 59.377 50.000 0.00 0.00 35.99 3.18
7677 8435 3.688414 GCCCAATTTCTGTATGGCTACCT 60.688 47.826 0.00 0.00 35.99 3.08
7680 8438 4.576463 CCAATTTCTGTATGGCTACCTGTC 59.424 45.833 0.00 0.00 0.00 3.51
7682 8440 4.737855 TTTCTGTATGGCTACCTGTCTC 57.262 45.455 0.00 0.00 0.00 3.36
7713 8550 4.813750 ACTGTATAACAAACGCTACCCT 57.186 40.909 0.00 0.00 0.00 4.34
7714 8551 5.920193 ACTGTATAACAAACGCTACCCTA 57.080 39.130 0.00 0.00 0.00 3.53
7716 8553 5.009854 TGTATAACAAACGCTACCCTACC 57.990 43.478 0.00 0.00 0.00 3.18
7717 8554 3.548745 ATAACAAACGCTACCCTACCC 57.451 47.619 0.00 0.00 0.00 3.69
7718 8555 1.058284 AACAAACGCTACCCTACCCA 58.942 50.000 0.00 0.00 0.00 4.51
7719 8556 1.282382 ACAAACGCTACCCTACCCAT 58.718 50.000 0.00 0.00 0.00 4.00
7720 8557 1.208776 ACAAACGCTACCCTACCCATC 59.791 52.381 0.00 0.00 0.00 3.51
7721 8558 1.208535 CAAACGCTACCCTACCCATCA 59.791 52.381 0.00 0.00 0.00 3.07
7818 8681 1.929836 GTGCGTGCCTTCTATCTCTTG 59.070 52.381 0.00 0.00 0.00 3.02
7820 8683 1.808133 GCGTGCCTTCTATCTCTTGGG 60.808 57.143 0.00 0.00 0.00 4.12
7849 8717 1.471119 AGATACGTTTGAGAGGGCGA 58.529 50.000 0.00 0.00 0.00 5.54
7949 8823 0.462759 CCGATTTGAGTCTCTGGCCC 60.463 60.000 0.00 0.00 0.00 5.80
7961 8835 1.380785 CTGGCCCATTCCTGTGCAT 60.381 57.895 0.00 0.00 0.00 3.96
8001 8891 3.709880 TTCCGCCGGAGCATACACG 62.710 63.158 5.05 0.00 39.83 4.49
8016 8906 4.215399 GCATACACGCACATAAATATGGGT 59.785 41.667 4.70 0.00 42.18 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 3.701040 GTGAGGTAATTGTGCCAATCCAT 59.299 43.478 1.57 0.00 30.37 3.41
45 47 1.143889 TGTGGTGAGGTAATTGTGCCA 59.856 47.619 0.00 0.00 30.37 4.92
46 48 1.904287 TGTGGTGAGGTAATTGTGCC 58.096 50.000 0.00 0.00 0.00 5.01
47 49 2.164219 CCATGTGGTGAGGTAATTGTGC 59.836 50.000 0.00 0.00 0.00 4.57
59 61 0.963856 AGCTGTGCATCCATGTGGTG 60.964 55.000 0.00 0.00 36.34 4.17
60 62 0.620030 TAGCTGTGCATCCATGTGGT 59.380 50.000 0.00 0.00 36.34 4.16
85 90 8.024285 TGTTTTGAGTTCGTTTTGAATTGTACT 58.976 29.630 0.00 0.00 39.21 2.73
90 97 7.812669 AGTTCTGTTTTGAGTTCGTTTTGAATT 59.187 29.630 0.00 0.00 39.21 2.17
92 99 6.674066 AGTTCTGTTTTGAGTTCGTTTTGAA 58.326 32.000 0.00 0.00 0.00 2.69
99 106 3.181501 TGGCAAGTTCTGTTTTGAGTTCG 60.182 43.478 0.00 0.00 0.00 3.95
100 107 4.370364 TGGCAAGTTCTGTTTTGAGTTC 57.630 40.909 0.00 0.00 0.00 3.01
103 110 4.354587 GAGTTGGCAAGTTCTGTTTTGAG 58.645 43.478 9.30 0.00 0.00 3.02
104 111 3.181501 CGAGTTGGCAAGTTCTGTTTTGA 60.182 43.478 9.30 0.00 0.00 2.69
105 112 3.108144 CGAGTTGGCAAGTTCTGTTTTG 58.892 45.455 9.30 0.00 0.00 2.44
106 113 3.013921 TCGAGTTGGCAAGTTCTGTTTT 58.986 40.909 9.30 0.00 0.00 2.43
117 125 1.375396 CAACCGGATCGAGTTGGCA 60.375 57.895 9.46 0.00 39.73 4.92
170 180 0.736053 TGGTTTCGTTGTGTGAAGCC 59.264 50.000 2.15 2.15 44.29 4.35
279 310 1.999002 GATTCCTCCCCCGGTTGGA 60.999 63.158 9.43 9.43 37.49 3.53
280 311 2.595655 GATTCCTCCCCCGGTTGG 59.404 66.667 0.00 0.00 0.00 3.77
281 312 2.189521 CGATTCCTCCCCCGGTTG 59.810 66.667 0.00 0.00 0.00 3.77
606 649 4.771356 TCGAACTCGAAGCGCCCG 62.771 66.667 2.29 8.90 46.30 6.13
669 717 5.393569 CCACGCATAGAGAGAGAGAGAAAAA 60.394 44.000 0.00 0.00 0.00 1.94
670 718 4.097135 CCACGCATAGAGAGAGAGAGAAAA 59.903 45.833 0.00 0.00 0.00 2.29
671 719 3.629855 CCACGCATAGAGAGAGAGAGAAA 59.370 47.826 0.00 0.00 0.00 2.52
672 720 3.210227 CCACGCATAGAGAGAGAGAGAA 58.790 50.000 0.00 0.00 0.00 2.87
673 721 2.171659 ACCACGCATAGAGAGAGAGAGA 59.828 50.000 0.00 0.00 0.00 3.10
674 722 2.290367 CACCACGCATAGAGAGAGAGAG 59.710 54.545 0.00 0.00 0.00 3.20
675 723 2.092914 TCACCACGCATAGAGAGAGAGA 60.093 50.000 0.00 0.00 0.00 3.10
676 724 2.293170 TCACCACGCATAGAGAGAGAG 58.707 52.381 0.00 0.00 0.00 3.20
677 725 2.420058 TCACCACGCATAGAGAGAGA 57.580 50.000 0.00 0.00 0.00 3.10
678 726 2.861750 GCATCACCACGCATAGAGAGAG 60.862 54.545 0.00 0.00 0.00 3.20
679 727 1.067669 GCATCACCACGCATAGAGAGA 59.932 52.381 0.00 0.00 0.00 3.10
680 728 1.495878 GCATCACCACGCATAGAGAG 58.504 55.000 0.00 0.00 0.00 3.20
681 729 0.104855 GGCATCACCACGCATAGAGA 59.895 55.000 0.00 0.00 38.86 3.10
682 730 0.105593 AGGCATCACCACGCATAGAG 59.894 55.000 0.00 0.00 43.14 2.43
683 731 0.541392 AAGGCATCACCACGCATAGA 59.459 50.000 0.00 0.00 43.14 1.98
684 732 0.659427 CAAGGCATCACCACGCATAG 59.341 55.000 0.00 0.00 43.14 2.23
685 733 0.035534 ACAAGGCATCACCACGCATA 60.036 50.000 0.00 0.00 43.14 3.14
686 734 1.303561 ACAAGGCATCACCACGCAT 60.304 52.632 0.00 0.00 43.14 4.73
687 735 2.112928 ACAAGGCATCACCACGCA 59.887 55.556 0.00 0.00 43.14 5.24
688 736 2.562912 CACAAGGCATCACCACGC 59.437 61.111 0.00 0.00 43.14 5.34
689 737 2.562912 GCACAAGGCATCACCACG 59.437 61.111 0.00 0.00 43.14 4.94
779 872 1.308069 CCACTTTCAGGCCCATCACG 61.308 60.000 0.00 0.00 0.00 4.35
819 912 4.503741 AGTTGTTTCATTCCATTCCGTG 57.496 40.909 0.00 0.00 0.00 4.94
905 1000 0.895559 GGCCCAGTTCCTTTGGAGTG 60.896 60.000 0.00 0.00 37.96 3.51
906 1001 1.068352 AGGCCCAGTTCCTTTGGAGT 61.068 55.000 0.00 0.00 37.96 3.85
909 1026 1.820010 GCAAGGCCCAGTTCCTTTGG 61.820 60.000 0.00 0.00 41.73 3.28
928 1045 3.594603 TTTAGGGCTTTCTCTGTCGAG 57.405 47.619 0.00 0.00 38.67 4.04
1164 1284 4.116585 TCGGCCTCCTCGAGCTCT 62.117 66.667 12.85 0.00 32.51 4.09
1309 1447 3.112709 GGAGACCTTGTCGCGTGC 61.113 66.667 5.77 0.57 37.67 5.34
1364 1502 6.061022 TGGCCAAATACTCTAGTTCATTCA 57.939 37.500 0.61 0.00 0.00 2.57
1365 1503 6.116126 ACTGGCCAAATACTCTAGTTCATTC 58.884 40.000 7.01 0.00 0.00 2.67
1366 1504 6.067217 ACTGGCCAAATACTCTAGTTCATT 57.933 37.500 7.01 0.00 0.00 2.57
1367 1505 5.700402 ACTGGCCAAATACTCTAGTTCAT 57.300 39.130 7.01 0.00 0.00 2.57
1383 1521 2.356673 GCAAGCAAGCAACTGGCC 60.357 61.111 0.00 0.00 46.50 5.36
1403 1541 7.709613 ACGGAATGCGTATCTATTCTAAGTTTT 59.290 33.333 0.00 0.00 34.52 2.43
1408 1546 7.431249 AGAAACGGAATGCGTATCTATTCTAA 58.569 34.615 8.92 0.00 34.52 2.10
1424 1562 6.091169 GGTTCGTCAACAATATAGAAACGGAA 59.909 38.462 0.00 0.00 33.70 4.30
1441 1579 2.110213 GGGTGTGCAGGTTCGTCA 59.890 61.111 0.00 0.00 0.00 4.35
1444 1582 1.234615 AAATCGGGTGTGCAGGTTCG 61.235 55.000 0.00 0.00 0.00 3.95
1482 1624 1.522668 CGTCCCATTGTTCTGCAGAA 58.477 50.000 25.16 25.16 0.00 3.02
1539 1681 5.336372 GCAGCAAATACCAACATCCTACAAA 60.336 40.000 0.00 0.00 0.00 2.83
1633 1824 9.042008 TCTTTGGCTTCTTATTATCAATCGTAC 57.958 33.333 0.00 0.00 0.00 3.67
1636 1827 7.442364 TCCTCTTTGGCTTCTTATTATCAATCG 59.558 37.037 0.00 0.00 35.26 3.34
1694 1888 2.371179 TCAATGCTTGGATTTTTGCCCA 59.629 40.909 0.00 0.00 0.00 5.36
1698 1892 8.508062 TCATTTTCATCAATGCTTGGATTTTTG 58.492 29.630 0.00 0.00 34.58 2.44
1722 1917 2.942804 TGGCAAGGACAATGTTCTTCA 58.057 42.857 3.49 0.00 27.27 3.02
1871 2066 0.602638 GAAGACACGTGCCATGGACA 60.603 55.000 18.40 10.56 0.00 4.02
1886 2081 3.071457 TGGACAGCAAGAATCTGTGAAGA 59.929 43.478 0.00 0.00 44.09 2.87
1926 2122 8.481314 ACGCATATATGATGTATCAAGAGGATT 58.519 33.333 17.10 0.00 40.69 3.01
1964 2160 4.857799 TCACACAACACATGCATTTAGTG 58.142 39.130 12.70 12.70 39.12 2.74
1968 2164 5.816258 TGAAAATCACACAACACATGCATTT 59.184 32.000 0.00 0.00 0.00 2.32
1995 2191 6.969993 TCCACCAGCTAGTAAAACATTTTT 57.030 33.333 0.00 0.00 0.00 1.94
2025 2221 6.038356 ACCCATTAGAACGTAACGTATTCTG 58.962 40.000 12.17 1.72 39.99 3.02
2055 2251 7.601856 TGAAATAGCCCAAGAAACAACAATAG 58.398 34.615 0.00 0.00 0.00 1.73
2133 2329 0.911769 TCCGCTGGTCCATCTTCAAT 59.088 50.000 0.00 0.00 0.00 2.57
2214 2410 5.086104 TGACTTAGTGGTTTATCCTCTGC 57.914 43.478 0.00 0.00 39.91 4.26
2838 3034 9.377238 AGTAGGTCGGGAATAAGTATTCTAATT 57.623 33.333 10.17 0.00 41.33 1.40
2843 3090 6.264970 AGTGAGTAGGTCGGGAATAAGTATTC 59.735 42.308 2.92 2.92 40.96 1.75
2892 3208 9.899661 ATGTGACTGTACTTAATATTTGCCTAA 57.100 29.630 0.00 0.00 0.00 2.69
2967 3283 1.064906 CATGCATGGTCACTCCTCCTT 60.065 52.381 19.40 0.00 37.07 3.36
2997 3315 5.104485 ACCTAATTAAGTGATGGACCCTGTC 60.104 44.000 0.00 0.00 0.00 3.51
3001 3319 4.412528 AGGACCTAATTAAGTGATGGACCC 59.587 45.833 0.00 0.00 31.58 4.46
3044 3362 6.002704 AGCTTAATCCATTTGGCTCATCTAG 58.997 40.000 0.00 0.00 34.44 2.43
3851 4170 3.055747 CCAGAGGGAAAGTCAAGTAGTCC 60.056 52.174 0.00 0.00 35.59 3.85
3886 4205 9.890629 TGATAAAGTACTATTCTTGCAACAGAT 57.109 29.630 0.00 0.00 0.00 2.90
4069 4391 7.149569 ACACTTCACAAGTTCATATGGAATG 57.850 36.000 2.13 0.00 40.46 2.67
4280 4606 5.201713 TGGCAGAATTAGTCTCCTAATCG 57.798 43.478 0.00 0.00 41.91 3.34
4312 4638 7.953158 TCAGTCTAAAGCTTGCATATATCAC 57.047 36.000 0.00 0.00 0.00 3.06
4324 4650 6.260271 GTGTTGGTTACTTTCAGTCTAAAGCT 59.740 38.462 0.00 0.00 39.59 3.74
4326 4652 6.292703 CGGTGTTGGTTACTTTCAGTCTAAAG 60.293 42.308 0.00 0.00 41.35 1.85
4397 4723 2.222027 GAAGGCGTTTGAGATATGGGG 58.778 52.381 0.00 0.00 0.00 4.96
4457 4783 3.562505 CAATGCTTCTTGTGCTGAGTTC 58.437 45.455 0.00 0.00 0.00 3.01
4546 4887 4.826556 AGATTATTAGAGAATCGGCCTGC 58.173 43.478 0.00 0.00 42.67 4.85
4583 4924 7.241042 ACAAGCTAGATACCTACAGAACAAA 57.759 36.000 0.00 0.00 0.00 2.83
4773 5114 3.775910 ACGAGGTTCCTTTTCCTCTCTA 58.224 45.455 9.11 0.00 45.57 2.43
4777 5118 2.566279 AGGTACGAGGTTCCTTTTCCTC 59.434 50.000 0.00 0.00 44.65 3.71
4801 5142 8.985315 TCAATTAATAGAAATCCAGCACAGAT 57.015 30.769 0.00 0.00 0.00 2.90
4830 5171 1.202348 GCTAACAATCCACCCAGTTGC 59.798 52.381 0.00 0.00 0.00 4.17
4923 5264 0.867746 CTGCTTCTTAGTGTTGCGCA 59.132 50.000 5.66 5.66 0.00 6.09
5031 5562 6.876257 AGTCACATAACCTGAGAAAACTCATC 59.124 38.462 0.00 0.00 32.39 2.92
5052 5583 5.509498 AGATTAAATGCTTAGGCCAAGTCA 58.491 37.500 5.01 9.51 36.55 3.41
5131 5662 3.189287 AGAAGCCAAAGTTCAGCATAACG 59.811 43.478 0.50 0.00 34.46 3.18
5143 5679 6.790285 AAAAATGTTATGCAGAAGCCAAAG 57.210 33.333 0.00 0.00 41.13 2.77
5376 5936 6.902341 TGAGATGTAAGAAAGCATTCACAAC 58.098 36.000 4.27 0.03 38.06 3.32
5691 6267 7.928167 TGAAACAGAGCACATAGATGGTATTAG 59.072 37.037 0.00 0.00 0.00 1.73
6011 6587 6.929625 TCCTCTCTCATTTTAGACTTCAGTG 58.070 40.000 0.00 0.00 0.00 3.66
6027 6603 9.303116 TGAAATATACCTACAGAATCCTCTCTC 57.697 37.037 0.00 0.00 0.00 3.20
6028 6604 9.661954 TTGAAATATACCTACAGAATCCTCTCT 57.338 33.333 0.00 0.00 0.00 3.10
6416 6992 0.767375 TGCCTGAAGGACTTCTGCTT 59.233 50.000 19.88 0.00 40.14 3.91
6453 7056 4.457603 CCGGTTCCTTTTGTGATCATTGTA 59.542 41.667 0.00 0.00 0.00 2.41
6454 7057 3.255642 CCGGTTCCTTTTGTGATCATTGT 59.744 43.478 0.00 0.00 0.00 2.71
6455 7058 3.505680 TCCGGTTCCTTTTGTGATCATTG 59.494 43.478 0.00 0.00 0.00 2.82
6456 7059 3.758554 CTCCGGTTCCTTTTGTGATCATT 59.241 43.478 0.00 0.00 0.00 2.57
6457 7060 3.347216 CTCCGGTTCCTTTTGTGATCAT 58.653 45.455 0.00 0.00 0.00 2.45
6458 7061 2.552155 CCTCCGGTTCCTTTTGTGATCA 60.552 50.000 0.00 0.00 0.00 2.92
6459 7062 2.084546 CCTCCGGTTCCTTTTGTGATC 58.915 52.381 0.00 0.00 0.00 2.92
6460 7063 1.886655 GCCTCCGGTTCCTTTTGTGAT 60.887 52.381 0.00 0.00 0.00 3.06
6461 7064 0.536460 GCCTCCGGTTCCTTTTGTGA 60.536 55.000 0.00 0.00 0.00 3.58
6462 7065 0.821711 TGCCTCCGGTTCCTTTTGTG 60.822 55.000 0.00 0.00 0.00 3.33
6463 7066 0.106419 TTGCCTCCGGTTCCTTTTGT 60.106 50.000 0.00 0.00 0.00 2.83
6464 7067 1.202348 GATTGCCTCCGGTTCCTTTTG 59.798 52.381 0.00 0.00 0.00 2.44
6465 7068 1.545841 GATTGCCTCCGGTTCCTTTT 58.454 50.000 0.00 0.00 0.00 2.27
6466 7069 0.323451 GGATTGCCTCCGGTTCCTTT 60.323 55.000 0.00 0.00 33.29 3.11
6467 7070 1.303282 GGATTGCCTCCGGTTCCTT 59.697 57.895 0.00 0.00 33.29 3.36
6468 7071 2.998949 GGATTGCCTCCGGTTCCT 59.001 61.111 0.00 0.00 33.29 3.36
6477 7080 2.727343 GGGATCATCCGAGGATTGCCT 61.727 57.143 1.12 0.00 39.50 4.75
6478 7081 0.322008 GGGATCATCCGAGGATTGCC 60.322 60.000 1.12 0.30 37.43 4.52
6479 7082 0.397941 TGGGATCATCCGAGGATTGC 59.602 55.000 1.12 0.00 37.43 3.56
6592 7195 3.323979 TCTTCCACTACCTTTCTCACCAC 59.676 47.826 0.00 0.00 0.00 4.16
6683 7286 2.476619 AGTTTCTGCGTCTGAATCAACG 59.523 45.455 11.57 11.57 41.68 4.10
6695 7298 0.457853 TCGGGAATCGAGTTTCTGCG 60.458 55.000 0.00 0.00 43.74 5.18
6749 7352 1.609072 TCATCAGGAGGAGCGTTATCG 59.391 52.381 0.00 0.00 40.37 2.92
6784 7387 1.205893 CAGACCTACTGCTGGACCTTC 59.794 57.143 0.00 0.00 39.86 3.46
6853 7456 4.816385 TGTTCTTCCTGATTTCACTGTGAC 59.184 41.667 10.56 0.00 0.00 3.67
6875 7478 1.055405 GATCGTCGTCGCTATCGCTG 61.055 60.000 0.00 0.00 36.96 5.18
6881 7484 1.153309 TGAGGGATCGTCGTCGCTA 60.153 57.895 12.08 2.77 40.93 4.26
6887 7490 2.095466 GCTAGAATCTGAGGGATCGTCG 60.095 54.545 0.00 0.00 32.76 5.12
6890 7493 2.095466 GTCGCTAGAATCTGAGGGATCG 60.095 54.545 0.00 0.00 37.05 3.69
6892 7495 1.883275 CGTCGCTAGAATCTGAGGGAT 59.117 52.381 0.00 0.00 37.05 3.85
6893 7496 1.309950 CGTCGCTAGAATCTGAGGGA 58.690 55.000 0.00 0.00 32.72 4.20
6899 7502 0.381089 CCCGAACGTCGCTAGAATCT 59.619 55.000 0.00 0.00 38.82 2.40
6902 7505 0.813184 AATCCCGAACGTCGCTAGAA 59.187 50.000 0.00 0.00 38.82 2.10
6908 7511 1.693083 GGCTCAAATCCCGAACGTCG 61.693 60.000 0.00 0.00 40.07 5.12
6912 7515 0.960364 TGCAGGCTCAAATCCCGAAC 60.960 55.000 0.00 0.00 0.00 3.95
6915 7518 1.731700 CATGCAGGCTCAAATCCCG 59.268 57.895 0.00 0.00 0.00 5.14
6927 7530 1.088340 CGACTCCTCCTTGCATGCAG 61.088 60.000 21.50 14.51 0.00 4.41
6935 7538 1.896465 CTTCTTGACCGACTCCTCCTT 59.104 52.381 0.00 0.00 0.00 3.36
6936 7539 1.551452 CTTCTTGACCGACTCCTCCT 58.449 55.000 0.00 0.00 0.00 3.69
7007 7610 1.001624 TTCAGCTGCATCACGAATCG 58.998 50.000 9.47 0.00 0.00 3.34
7067 7670 4.082787 ACCACATTTGCTTTTATCGTCCAG 60.083 41.667 0.00 0.00 0.00 3.86
7177 7793 6.094048 TGCAAGAAATCTCTATCCCGAAAAAG 59.906 38.462 0.00 0.00 0.00 2.27
7182 7798 4.753516 TTGCAAGAAATCTCTATCCCGA 57.246 40.909 0.00 0.00 0.00 5.14
7184 7800 4.641989 TGCTTTGCAAGAAATCTCTATCCC 59.358 41.667 0.00 0.00 34.76 3.85
7221 7837 9.575783 TGTGAACAACTCTAAATTAACAAAACC 57.424 29.630 0.00 0.00 0.00 3.27
7228 7844 8.999431 GGTGAGATGTGAACAACTCTAAATTAA 58.001 33.333 18.07 0.00 43.53 1.40
7244 7860 0.692476 TGGACCAAGGGTGAGATGTG 59.308 55.000 0.00 0.00 35.25 3.21
7284 7900 6.179756 TCAATAGCAAGTGTGGTGAACATAT 58.820 36.000 0.00 0.00 41.97 1.78
7289 7905 3.249799 CGTTCAATAGCAAGTGTGGTGAA 59.750 43.478 0.00 0.00 36.66 3.18
7293 7912 4.481930 TTTCGTTCAATAGCAAGTGTGG 57.518 40.909 0.00 0.00 0.00 4.17
7310 7929 4.358851 TGTTTTGAAGATGTGCCTTTTCG 58.641 39.130 0.00 0.00 0.00 3.46
7329 7948 1.641192 GGAGGGAAGGGAAAGGATGTT 59.359 52.381 0.00 0.00 0.00 2.71
7333 7952 1.073098 GTTGGAGGGAAGGGAAAGGA 58.927 55.000 0.00 0.00 0.00 3.36
7334 7953 0.777446 TGTTGGAGGGAAGGGAAAGG 59.223 55.000 0.00 0.00 0.00 3.11
7335 7954 1.705186 TCTGTTGGAGGGAAGGGAAAG 59.295 52.381 0.00 0.00 0.00 2.62
7353 7972 8.546644 GGAGGATCGATGGAACAAATTCTTTCT 61.547 40.741 0.54 0.00 37.99 2.52
7392 8101 2.609610 CCCCTTCCCTCACCCGAA 60.610 66.667 0.00 0.00 0.00 4.30
7418 8127 5.814481 TCCATTTATGTTGGTCTGATGACA 58.186 37.500 0.00 0.00 44.61 3.58
7420 8129 5.652014 GGTTCCATTTATGTTGGTCTGATGA 59.348 40.000 0.00 0.00 35.64 2.92
7421 8130 5.653769 AGGTTCCATTTATGTTGGTCTGATG 59.346 40.000 0.00 0.00 35.64 3.07
7423 8132 5.255397 AGGTTCCATTTATGTTGGTCTGA 57.745 39.130 0.00 0.00 35.64 3.27
7444 8188 6.463995 AAGAAGGAAGCTACTGACTGATAG 57.536 41.667 0.00 0.00 0.00 2.08
7545 8303 4.892433 TGTTTGGAATAAAGTGCAATGGG 58.108 39.130 0.00 0.00 0.00 4.00
7568 8326 3.435186 GCCAAAGTGCGAGGCTCC 61.435 66.667 9.32 2.37 44.92 4.70
7609 8367 2.224621 ACACACAGTAGCTCAAAGCCAT 60.225 45.455 0.00 0.00 43.77 4.40
7638 8396 0.251787 GGCTGTGGAATCCCAAAGGT 60.252 55.000 0.00 0.00 46.08 3.50
7708 8545 0.399949 CTGGCCTGATGGGTAGGGTA 60.400 60.000 3.32 0.00 35.80 3.69
7713 8550 2.042762 AGGCTGGCCTGATGGGTA 59.957 61.111 14.77 0.00 46.22 3.69
7818 8681 4.159135 TCAAACGTATCTACAGAGGAACCC 59.841 45.833 0.00 0.00 0.00 4.11
7820 8683 6.192234 TCTCAAACGTATCTACAGAGGAAC 57.808 41.667 0.00 0.00 0.00 3.62
7961 8835 2.125326 CCGAGTCGGCCTGTGGATA 61.125 63.158 20.50 0.00 41.17 2.59


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

AutoCloner maintained by Alex Coulton.