Multiple sequence alignment - TraesCS4A01G256500

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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 TraesCS4A01G256500 chr4A 100.000 3800 0 0 1 3800 568191908 568195707 0.000000e+00 7018
1 TraesCS4A01G256500 chr4B 92.047 2867 121 41 778 3576 48991367 48994194 0.000000e+00 3932
2 TraesCS4A01G256500 chr4B 81.804 632 51 30 6 595 48990488 48991097 4.440000e-129 472
3 TraesCS4A01G256500 chr4D 91.700 2506 112 49 783 3257 34088850 34091290 0.000000e+00 3387
4 TraesCS4A01G256500 chr4D 85.354 396 18 11 3284 3669 34091284 34091649 1.290000e-99 374
5 TraesCS4A01G256500 chr4D 81.047 401 24 26 234 592 34088320 34088710 4.840000e-69 272
6 TraesCS4A01G256500 chr3B 71.029 787 178 37 1844 2608 99501461 99502219 1.100000e-30 145
7 TraesCS4A01G256500 chr3B 83.193 119 12 7 1059 1173 99500820 99500934 6.720000e-18 102
8 TraesCS4A01G256500 chr3D 71.366 681 153 31 1946 2608 61803545 61804201 5.120000e-29 139
9 TraesCS4A01G256500 chr3A 70.923 791 172 42 1844 2608 70849172 70849930 2.380000e-27 134
10 TraesCS4A01G256500 chr2A 80.128 156 26 5 1024 1177 650243642 650243794 1.120000e-20 111
11 TraesCS4A01G256500 chr2D 83.193 119 16 4 1060 1176 505814510 505814626 5.190000e-19 106


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 TraesCS4A01G256500 chr4A 568191908 568195707 3799 False 7018.000000 7018 100.000000 1 3800 1 chr4A.!!$F1 3799
1 TraesCS4A01G256500 chr4B 48990488 48994194 3706 False 2202.000000 3932 86.925500 6 3576 2 chr4B.!!$F1 3570
2 TraesCS4A01G256500 chr4D 34088320 34091649 3329 False 1344.333333 3387 86.033667 234 3669 3 chr4D.!!$F1 3435

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
285 296 0.110486 TCCTGTTTCCCTCCAGTTGC 59.890 55.0 0.0 0.0 0.00 4.17 F
383 394 0.387565 TGTCGGCTTTTCTTTTGGCC 59.612 50.0 0.0 0.0 41.02 5.36 F
1229 1445 0.179100 TAGCTCGCCATTGTCTCTGC 60.179 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1204 1406 0.539051 ACAATGGCGAGCTAGCTTCT 59.461 50.0 20.42 0.0 37.29 2.85 R
2031 2265 0.616395 TGACGAGGTGGATGCCCTTA 60.616 55.0 0.00 0.0 30.60 2.69 R
3193 3430 0.029035 CGACCGATGTAACGAGGGAG 59.971 60.0 0.00 0.0 35.09 4.30 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
28 29 8.487313 ACACACGCATTAATAAAATACTCTCA 57.513 30.769 0.00 0.00 0.00 3.27
29 30 8.388103 ACACACGCATTAATAAAATACTCTCAC 58.612 33.333 0.00 0.00 0.00 3.51
30 31 8.387354 CACACGCATTAATAAAATACTCTCACA 58.613 33.333 0.00 0.00 0.00 3.58
31 32 8.388103 ACACGCATTAATAAAATACTCTCACAC 58.612 33.333 0.00 0.00 0.00 3.82
32 33 7.850982 CACGCATTAATAAAATACTCTCACACC 59.149 37.037 0.00 0.00 0.00 4.16
33 34 7.551262 ACGCATTAATAAAATACTCTCACACCA 59.449 33.333 0.00 0.00 0.00 4.17
47 48 0.396556 ACACCACACCACCTTTTCCC 60.397 55.000 0.00 0.00 0.00 3.97
77 78 2.979299 GCGAATGCAGTTCAGATAAGC 58.021 47.619 0.00 0.00 42.15 3.09
80 81 3.242543 CGAATGCAGTTCAGATAAGCCAC 60.243 47.826 0.00 0.00 36.60 5.01
81 82 2.857186 TGCAGTTCAGATAAGCCACA 57.143 45.000 0.00 0.00 0.00 4.17
91 92 3.002656 CAGATAAGCCACAGCCGTTATTG 59.997 47.826 0.00 0.00 41.25 1.90
134 135 1.268032 CGTATGCTGATTGGGCGAAAC 60.268 52.381 0.00 0.00 0.00 2.78
137 138 2.192664 TGCTGATTGGGCGAAACTAA 57.807 45.000 0.00 0.00 0.00 2.24
139 140 3.088532 TGCTGATTGGGCGAAACTAAAT 58.911 40.909 0.00 0.00 0.00 1.40
140 141 3.128589 TGCTGATTGGGCGAAACTAAATC 59.871 43.478 0.00 0.00 0.00 2.17
164 165 5.511088 CAAAGTTGCTTACTACTACACCG 57.489 43.478 0.00 0.00 35.54 4.94
167 168 4.330250 AGTTGCTTACTACTACACCGAGA 58.670 43.478 0.00 0.00 34.56 4.04
174 175 6.201044 GCTTACTACTACACCGAGAACGTATA 59.799 42.308 0.00 0.00 37.88 1.47
176 177 5.907207 ACTACTACACCGAGAACGTATAGA 58.093 41.667 0.00 0.00 37.88 1.98
179 180 7.812191 ACTACTACACCGAGAACGTATAGATAG 59.188 40.741 0.00 0.00 37.88 2.08
180 181 4.745837 ACACCGAGAACGTATAGATAGC 57.254 45.455 0.00 0.00 37.88 2.97
181 182 3.501445 ACACCGAGAACGTATAGATAGCC 59.499 47.826 0.00 0.00 37.88 3.93
186 197 4.093703 CGAGAACGTATAGATAGCCTGAGG 59.906 50.000 0.00 0.00 34.56 3.86
196 207 2.425143 TAGCCTGAGGAAGCCAAATG 57.575 50.000 0.65 0.00 0.00 2.32
197 208 0.969409 AGCCTGAGGAAGCCAAATGC 60.969 55.000 0.65 0.00 41.71 3.56
198 209 1.252904 GCCTGAGGAAGCCAAATGCA 61.253 55.000 0.65 0.00 44.83 3.96
199 210 0.815734 CCTGAGGAAGCCAAATGCAG 59.184 55.000 0.00 0.00 44.83 4.41
200 211 1.615116 CCTGAGGAAGCCAAATGCAGA 60.615 52.381 0.00 0.00 44.83 4.26
213 224 2.815647 GCAGACCAGCAGGCGTAC 60.816 66.667 0.00 0.00 39.06 3.67
272 283 6.591935 TGTACTGTCTCATTCTTTTCCTGTT 58.408 36.000 0.00 0.00 0.00 3.16
285 296 0.110486 TCCTGTTTCCCTCCAGTTGC 59.890 55.000 0.00 0.00 0.00 4.17
383 394 0.387565 TGTCGGCTTTTCTTTTGGCC 59.612 50.000 0.00 0.00 41.02 5.36
444 489 3.886044 TGTCAGTAAGCAGACACCG 57.114 52.632 0.00 0.00 39.65 4.94
462 507 3.399770 GCACACGTCGCAAGCGTA 61.400 61.111 14.57 0.00 45.43 4.42
514 564 4.164843 AGCCACAGTTCAGAAGGTAAAA 57.835 40.909 0.00 0.00 0.00 1.52
520 570 6.293626 CCACAGTTCAGAAGGTAAAATCAGTG 60.294 42.308 0.00 0.00 0.00 3.66
537 587 2.125512 GGACTACGGCACAGGCAG 60.126 66.667 0.00 0.00 43.71 4.85
554 608 2.174360 GCAGCCCTCCAAAAAGAAGAT 58.826 47.619 0.00 0.00 0.00 2.40
555 609 2.094338 GCAGCCCTCCAAAAAGAAGATG 60.094 50.000 0.00 0.00 0.00 2.90
556 610 2.094338 CAGCCCTCCAAAAAGAAGATGC 60.094 50.000 0.00 0.00 0.00 3.91
559 613 3.694926 CCCTCCAAAAAGAAGATGCTCT 58.305 45.455 0.00 0.00 0.00 4.09
560 614 4.848357 CCCTCCAAAAAGAAGATGCTCTA 58.152 43.478 0.00 0.00 0.00 2.43
561 615 5.444176 CCCTCCAAAAAGAAGATGCTCTAT 58.556 41.667 0.00 0.00 0.00 1.98
562 616 5.890419 CCCTCCAAAAAGAAGATGCTCTATT 59.110 40.000 0.00 0.00 0.00 1.73
572 626 7.372260 AGAAGATGCTCTATTCAGTACCAAT 57.628 36.000 0.00 0.00 0.00 3.16
602 719 1.128200 ACCTACACTGTTGGTCTGCA 58.872 50.000 9.28 0.00 37.06 4.41
674 799 1.531149 ACACACGCACAAGAGTATTGC 59.469 47.619 0.00 0.00 0.00 3.56
741 921 1.338011 CGCCCCACTAAAAACTCCGTA 60.338 52.381 0.00 0.00 0.00 4.02
743 923 2.681344 GCCCCACTAAAAACTCCGTATG 59.319 50.000 0.00 0.00 0.00 2.39
744 924 3.871074 GCCCCACTAAAAACTCCGTATGT 60.871 47.826 0.00 0.00 0.00 2.29
745 925 3.937079 CCCCACTAAAAACTCCGTATGTC 59.063 47.826 0.00 0.00 0.00 3.06
746 926 4.323257 CCCCACTAAAAACTCCGTATGTCT 60.323 45.833 0.00 0.00 0.00 3.41
747 927 4.868734 CCCACTAAAAACTCCGTATGTCTC 59.131 45.833 0.00 0.00 0.00 3.36
748 928 5.475719 CCACTAAAAACTCCGTATGTCTCA 58.524 41.667 0.00 0.00 0.00 3.27
749 929 5.929992 CCACTAAAAACTCCGTATGTCTCAA 59.070 40.000 0.00 0.00 0.00 3.02
750 930 6.425721 CCACTAAAAACTCCGTATGTCTCAAA 59.574 38.462 0.00 0.00 0.00 2.69
751 931 7.041644 CCACTAAAAACTCCGTATGTCTCAAAA 60.042 37.037 0.00 0.00 0.00 2.44
752 932 8.339714 CACTAAAAACTCCGTATGTCTCAAAAA 58.660 33.333 0.00 0.00 0.00 1.94
774 954 5.830000 AAAAAGAGCTAAAAACTCCGTGT 57.170 34.783 0.00 0.00 34.56 4.49
775 955 5.830000 AAAAGAGCTAAAAACTCCGTGTT 57.170 34.783 0.00 0.00 41.29 3.32
776 956 6.930667 AAAAGAGCTAAAAACTCCGTGTTA 57.069 33.333 0.00 0.00 38.03 2.41
781 961 6.202379 AGAGCTAAAAACTCCGTGTTAAGAAC 59.798 38.462 0.00 0.00 38.03 3.01
862 1047 1.451028 GACATCAGCCACTGCCTCC 60.451 63.158 0.00 0.00 38.69 4.30
897 1099 6.245408 TCTTCTCTTCTCTAGCTCAGTCTTT 58.755 40.000 0.00 0.00 0.00 2.52
898 1100 5.895636 TCTCTTCTCTAGCTCAGTCTTTG 57.104 43.478 0.00 0.00 0.00 2.77
900 1102 5.414454 TCTCTTCTCTAGCTCAGTCTTTGAC 59.586 44.000 0.00 0.00 0.00 3.18
901 1103 4.461081 TCTTCTCTAGCTCAGTCTTTGACC 59.539 45.833 0.00 0.00 32.18 4.02
902 1104 3.767711 TCTCTAGCTCAGTCTTTGACCA 58.232 45.455 0.00 0.00 32.18 4.02
903 1105 3.761218 TCTCTAGCTCAGTCTTTGACCAG 59.239 47.826 0.00 0.00 32.18 4.00
915 1117 2.347697 TTGACCAGAACACTCGATCG 57.652 50.000 9.36 9.36 0.00 3.69
923 1125 0.457509 AACACTCGATCGCAGCTCAG 60.458 55.000 11.09 3.80 0.00 3.35
924 1126 2.103934 ACTCGATCGCAGCTCAGC 59.896 61.111 11.09 0.00 0.00 4.26
927 1129 2.657944 CGATCGCAGCTCAGCTCC 60.658 66.667 0.26 0.00 36.40 4.70
958 1160 1.529713 GAGCCCCCGGTTTCAAACA 60.530 57.895 1.93 0.00 0.00 2.83
1175 1377 2.202570 CGCCGAGAACCAGGTACG 60.203 66.667 0.00 0.00 0.00 3.67
1180 1382 1.747355 CCGAGAACCAGGTACGTACAT 59.253 52.381 26.02 17.76 0.00 2.29
1182 1384 3.242870 CCGAGAACCAGGTACGTACATAC 60.243 52.174 26.02 9.95 0.00 2.39
1183 1385 3.374988 CGAGAACCAGGTACGTACATACA 59.625 47.826 26.02 0.00 0.00 2.29
1184 1386 4.495349 CGAGAACCAGGTACGTACATACAG 60.495 50.000 26.02 13.95 0.00 2.74
1186 1388 4.397417 AGAACCAGGTACGTACATACAGAC 59.603 45.833 26.02 11.69 0.00 3.51
1189 1391 4.523943 ACCAGGTACGTACATACAGACAAA 59.476 41.667 26.02 0.00 0.00 2.83
1191 1393 6.103997 CCAGGTACGTACATACAGACAAATT 58.896 40.000 26.02 0.00 0.00 1.82
1192 1394 6.255020 CCAGGTACGTACATACAGACAAATTC 59.745 42.308 26.02 4.59 0.00 2.17
1193 1395 7.033791 CAGGTACGTACATACAGACAAATTCT 58.966 38.462 26.02 6.77 33.33 2.40
1194 1396 8.186163 CAGGTACGTACATACAGACAAATTCTA 58.814 37.037 26.02 0.00 31.12 2.10
1195 1397 8.742777 AGGTACGTACATACAGACAAATTCTAA 58.257 33.333 26.02 0.00 31.12 2.10
1198 1400 8.462143 ACGTACATACAGACAAATTCTAAGTG 57.538 34.615 0.00 0.00 31.12 3.16
1199 1401 7.544566 ACGTACATACAGACAAATTCTAAGTGG 59.455 37.037 0.00 0.00 31.12 4.00
1200 1402 6.743575 ACATACAGACAAATTCTAAGTGGC 57.256 37.500 0.00 0.00 31.12 5.01
1203 1405 4.691860 CAGACAAATTCTAAGTGGCTGG 57.308 45.455 2.45 0.00 43.47 4.85
1204 1406 4.326826 CAGACAAATTCTAAGTGGCTGGA 58.673 43.478 2.45 0.00 43.47 3.86
1205 1407 4.394300 CAGACAAATTCTAAGTGGCTGGAG 59.606 45.833 2.45 0.00 43.47 3.86
1206 1408 4.287067 AGACAAATTCTAAGTGGCTGGAGA 59.713 41.667 0.00 0.00 30.17 3.71
1229 1445 0.179100 TAGCTCGCCATTGTCTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
1259 1475 3.651480 AAATTCAGCTCGTGCGCGC 62.651 57.895 27.26 27.26 45.42 6.86
1486 1711 0.229753 GTCAAAGACTGACGCACGTG 59.770 55.000 12.28 12.28 44.95 4.49
1518 1743 0.374758 CATTGGCGAGGTTCATGTCG 59.625 55.000 0.00 0.00 39.25 4.35
1644 1869 1.889105 CGCATTCCTCATCCCCACG 60.889 63.158 0.00 0.00 0.00 4.94
1682 1907 4.194720 GCCGTGCCGTCTCTCGAT 62.195 66.667 0.00 0.00 42.86 3.59
1683 1908 2.024871 CCGTGCCGTCTCTCGATC 59.975 66.667 0.00 0.00 42.86 3.69
1684 1909 2.351322 CGTGCCGTCTCTCGATCG 60.351 66.667 9.36 9.36 42.86 3.69
1702 1932 3.870723 TCGACATTTTTCTCCACGTTG 57.129 42.857 0.00 0.00 0.00 4.10
1750 1984 2.219445 CGACGTGCATGTTCCATCATAG 59.781 50.000 13.92 0.00 0.00 2.23
1763 1997 6.150976 TGTTCCATCATAGCCTTTTAACAGTG 59.849 38.462 0.00 0.00 0.00 3.66
1764 1998 6.061022 TCCATCATAGCCTTTTAACAGTGA 57.939 37.500 0.00 0.00 0.00 3.41
1765 1999 5.880332 TCCATCATAGCCTTTTAACAGTGAC 59.120 40.000 0.00 0.00 0.00 3.67
1785 2019 5.181245 GTGACAACAAGTACACATGGCTAAT 59.819 40.000 0.00 0.00 32.25 1.73
1786 2020 6.370442 GTGACAACAAGTACACATGGCTAATA 59.630 38.462 0.00 0.00 32.25 0.98
1787 2021 6.937465 TGACAACAAGTACACATGGCTAATAA 59.063 34.615 0.00 0.00 0.00 1.40
1836 2070 4.680237 CTCAAGTGGCGCACCGGA 62.680 66.667 9.46 5.50 39.70 5.14
2268 2502 2.434185 GCGGCGACCAAGATGTCA 60.434 61.111 12.98 0.00 34.88 3.58
2669 2903 1.758440 TTCGTCCAGACCTGCAGCTT 61.758 55.000 8.66 0.00 0.00 3.74
2809 3043 3.061260 GAGCGGTAGACGGACCACC 62.061 68.421 4.56 0.00 44.51 4.61
2822 3056 0.249489 GACCACCACCGCATAGCTAG 60.249 60.000 0.00 0.00 0.00 3.42
2823 3057 1.595382 CCACCACCGCATAGCTAGC 60.595 63.158 6.62 6.62 0.00 3.42
2946 3183 5.819825 AGCCGATCAATTCCTTTAGTTTC 57.180 39.130 0.00 0.00 0.00 2.78
2958 3195 6.370186 TCCTTTAGTTTCTTCCCCTACTTC 57.630 41.667 0.00 0.00 0.00 3.01
2964 3201 0.905357 TCTTCCCCTACTTCTGCTGC 59.095 55.000 0.00 0.00 0.00 5.25
3090 3327 4.084745 CGGTATCGGATCGTGTATTTTTGG 60.085 45.833 0.00 0.00 0.00 3.28
3103 3340 4.278170 TGTATTTTTGGCTGGAGTGTTCTG 59.722 41.667 0.00 0.00 0.00 3.02
3127 3364 2.509651 TACCCCGGTTGTTCGCTGT 61.510 57.895 0.00 0.00 0.00 4.40
3128 3365 1.184322 TACCCCGGTTGTTCGCTGTA 61.184 55.000 0.00 0.00 0.00 2.74
3129 3366 2.030958 CCCCGGTTGTTCGCTGTAC 61.031 63.158 0.00 0.00 0.00 2.90
3151 3388 7.706179 TGTACTATTATTGTTGCCGGTTACTAC 59.294 37.037 1.90 0.00 0.00 2.73
3193 3430 7.014092 ACACTACTACTACTTTACATCTCGC 57.986 40.000 0.00 0.00 0.00 5.03
3196 3433 5.754543 ACTACTACTTTACATCTCGCTCC 57.245 43.478 0.00 0.00 0.00 4.70
3198 3435 3.633418 ACTACTTTACATCTCGCTCCCT 58.367 45.455 0.00 0.00 0.00 4.20
3199 3436 3.633065 ACTACTTTACATCTCGCTCCCTC 59.367 47.826 0.00 0.00 0.00 4.30
3201 3438 1.405821 CTTTACATCTCGCTCCCTCGT 59.594 52.381 0.00 0.00 0.00 4.18
3260 3516 2.976840 GCGGCGTTTCCAATGCTCA 61.977 57.895 9.37 0.00 42.98 4.26
3279 3535 4.720090 CTCAATTGTCAGCTGCAAAGTAG 58.280 43.478 21.71 15.91 0.00 2.57
3299 3555 1.890573 GCCCTCCATGTTGCTAAACCA 60.891 52.381 0.00 0.00 35.25 3.67
3396 3652 3.760035 CCACCACGAGCTAGCGGT 61.760 66.667 9.55 7.69 35.12 5.68
3397 3653 2.412323 CCACCACGAGCTAGCGGTA 61.412 63.158 9.55 0.00 35.12 4.02
3398 3654 1.064296 CACCACGAGCTAGCGGTAG 59.936 63.158 17.24 17.24 35.12 3.18
3488 3764 1.153127 TTGCGGTTGAAAGGTCCGT 60.153 52.632 0.00 0.00 45.11 4.69
3489 3765 1.440938 TTGCGGTTGAAAGGTCCGTG 61.441 55.000 0.00 0.00 45.11 4.94
3490 3766 1.890510 GCGGTTGAAAGGTCCGTGT 60.891 57.895 0.00 0.00 45.11 4.49
3491 3767 1.938861 CGGTTGAAAGGTCCGTGTG 59.061 57.895 0.00 0.00 39.51 3.82
3492 3768 1.503818 CGGTTGAAAGGTCCGTGTGG 61.504 60.000 0.00 0.00 39.51 4.17
3493 3769 0.464916 GGTTGAAAGGTCCGTGTGGT 60.465 55.000 0.00 0.00 36.30 4.16
3494 3770 0.942252 GTTGAAAGGTCCGTGTGGTC 59.058 55.000 0.00 0.00 36.30 4.02
3495 3771 0.179040 TTGAAAGGTCCGTGTGGTCC 60.179 55.000 0.00 0.00 43.14 4.46
3496 3772 1.666872 GAAAGGTCCGTGTGGTCCG 60.667 63.158 0.00 0.00 46.84 4.79
3497 3773 3.819877 AAAGGTCCGTGTGGTCCGC 62.820 63.158 0.00 0.00 46.84 5.54
3578 3854 3.567473 GCACGTTGCTTCTCCTCC 58.433 61.111 0.00 0.00 40.96 4.30
3579 3855 1.004440 GCACGTTGCTTCTCCTCCT 60.004 57.895 0.00 0.00 40.96 3.69
3580 3856 1.016653 GCACGTTGCTTCTCCTCCTC 61.017 60.000 0.00 0.00 40.96 3.71
3581 3857 0.390472 CACGTTGCTTCTCCTCCTCC 60.390 60.000 0.00 0.00 0.00 4.30
3582 3858 0.543174 ACGTTGCTTCTCCTCCTCCT 60.543 55.000 0.00 0.00 0.00 3.69
3583 3859 0.174617 CGTTGCTTCTCCTCCTCCTC 59.825 60.000 0.00 0.00 0.00 3.71
3584 3860 0.539518 GTTGCTTCTCCTCCTCCTCC 59.460 60.000 0.00 0.00 0.00 4.30
3585 3861 0.415429 TTGCTTCTCCTCCTCCTCCT 59.585 55.000 0.00 0.00 0.00 3.69
3586 3862 0.032615 TGCTTCTCCTCCTCCTCCTC 60.033 60.000 0.00 0.00 0.00 3.71
3587 3863 0.759060 GCTTCTCCTCCTCCTCCTCC 60.759 65.000 0.00 0.00 0.00 4.30
3588 3864 0.933700 CTTCTCCTCCTCCTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
3589 3865 1.290732 CTTCTCCTCCTCCTCCTCCTT 59.709 57.143 0.00 0.00 0.00 3.36
3607 3883 5.955355 CCTCCTTCTTCTTCTTCTTCTCCTA 59.045 44.000 0.00 0.00 0.00 2.94
3608 3884 6.127451 CCTCCTTCTTCTTCTTCTTCTCCTAC 60.127 46.154 0.00 0.00 0.00 3.18
3610 3886 7.013834 TCCTTCTTCTTCTTCTTCTCCTACTT 58.986 38.462 0.00 0.00 0.00 2.24
3618 3902 8.652290 TCTTCTTCTTCTCCTACTTTTAGCTTT 58.348 33.333 0.00 0.00 0.00 3.51
3620 3904 8.834749 TCTTCTTCTCCTACTTTTAGCTTTTC 57.165 34.615 0.00 0.00 0.00 2.29
3632 3916 7.986562 ACTTTTAGCTTTTCTTTTCGAGAACT 58.013 30.769 0.00 0.00 43.90 3.01
3633 3917 8.123575 ACTTTTAGCTTTTCTTTTCGAGAACTC 58.876 33.333 0.00 0.00 43.90 3.01
3669 3953 6.481643 TGGGGGACAAGAAAGAAATTAGTAG 58.518 40.000 0.00 0.00 0.00 2.57
3670 3954 6.045106 TGGGGGACAAGAAAGAAATTAGTAGT 59.955 38.462 0.00 0.00 0.00 2.73
3671 3955 6.598457 GGGGGACAAGAAAGAAATTAGTAGTC 59.402 42.308 0.00 0.00 0.00 2.59
3672 3956 6.313164 GGGGACAAGAAAGAAATTAGTAGTCG 59.687 42.308 0.00 0.00 0.00 4.18
3673 3957 6.872547 GGGACAAGAAAGAAATTAGTAGTCGT 59.127 38.462 0.00 0.00 0.00 4.34
3674 3958 7.148623 GGGACAAGAAAGAAATTAGTAGTCGTG 60.149 40.741 0.00 0.00 0.00 4.35
3675 3959 7.597743 GGACAAGAAAGAAATTAGTAGTCGTGA 59.402 37.037 0.00 0.00 0.00 4.35
3676 3960 8.882415 ACAAGAAAGAAATTAGTAGTCGTGAA 57.118 30.769 0.00 0.00 0.00 3.18
3677 3961 9.321562 ACAAGAAAGAAATTAGTAGTCGTGAAA 57.678 29.630 0.00 0.00 0.00 2.69
3683 3967 9.490379 AAGAAATTAGTAGTCGTGAAATTCACT 57.510 29.630 21.89 7.90 44.85 3.41
3708 3992 5.984695 AAAAACTAGAAGGAAATCAGGGC 57.015 39.130 0.00 0.00 0.00 5.19
3709 3993 4.936685 AAACTAGAAGGAAATCAGGGCT 57.063 40.909 0.00 0.00 0.00 5.19
3710 3994 6.388619 AAAACTAGAAGGAAATCAGGGCTA 57.611 37.500 0.00 0.00 0.00 3.93
3711 3995 5.622346 AACTAGAAGGAAATCAGGGCTAG 57.378 43.478 0.00 0.00 0.00 3.42
3712 3996 3.970640 ACTAGAAGGAAATCAGGGCTAGG 59.029 47.826 0.00 0.00 0.00 3.02
3713 3997 2.131023 AGAAGGAAATCAGGGCTAGGG 58.869 52.381 0.00 0.00 0.00 3.53
3714 3998 1.143889 GAAGGAAATCAGGGCTAGGGG 59.856 57.143 0.00 0.00 0.00 4.79
3715 3999 1.151679 GGAAATCAGGGCTAGGGGC 59.848 63.158 0.00 0.00 40.90 5.80
3724 4008 3.155750 GCTAGGGGCCAGATGGAG 58.844 66.667 4.39 0.00 37.39 3.86
3725 4009 1.768077 GCTAGGGGCCAGATGGAGT 60.768 63.158 4.39 0.00 37.39 3.85
3726 4010 2.049627 GCTAGGGGCCAGATGGAGTG 62.050 65.000 4.39 0.00 37.39 3.51
3727 4011 1.384502 TAGGGGCCAGATGGAGTGG 60.385 63.158 4.39 0.00 37.39 4.00
3728 4012 2.194951 TAGGGGCCAGATGGAGTGGT 62.195 60.000 4.39 0.00 37.40 4.16
3729 4013 1.692749 GGGGCCAGATGGAGTGGTA 60.693 63.158 4.39 0.00 37.40 3.25
3730 4014 1.527370 GGGCCAGATGGAGTGGTAC 59.473 63.158 4.39 0.00 37.40 3.34
3731 4015 1.271840 GGGCCAGATGGAGTGGTACA 61.272 60.000 4.39 0.00 37.40 2.90
3732 4016 0.839946 GGCCAGATGGAGTGGTACAT 59.160 55.000 2.18 0.00 38.04 2.29
3733 4017 1.212935 GGCCAGATGGAGTGGTACATT 59.787 52.381 2.18 0.00 38.04 2.71
3734 4018 2.292267 GCCAGATGGAGTGGTACATTG 58.708 52.381 2.18 0.00 38.04 2.82
3735 4019 2.092968 GCCAGATGGAGTGGTACATTGA 60.093 50.000 2.18 0.00 38.04 2.57
3736 4020 3.535561 CCAGATGGAGTGGTACATTGAC 58.464 50.000 0.00 0.00 38.04 3.18
3737 4021 3.190079 CAGATGGAGTGGTACATTGACG 58.810 50.000 0.00 0.00 44.52 4.35
3738 4022 3.096852 AGATGGAGTGGTACATTGACGA 58.903 45.455 0.00 0.00 44.52 4.20
3739 4023 3.706594 AGATGGAGTGGTACATTGACGAT 59.293 43.478 0.00 0.00 44.52 3.73
3740 4024 3.245518 TGGAGTGGTACATTGACGATG 57.754 47.619 0.75 0.75 44.52 3.84
3741 4025 2.829120 TGGAGTGGTACATTGACGATGA 59.171 45.455 9.78 0.00 44.52 2.92
3742 4026 3.187700 GGAGTGGTACATTGACGATGAC 58.812 50.000 9.78 3.70 44.52 3.06
3743 4027 2.852413 GAGTGGTACATTGACGATGACG 59.148 50.000 9.78 0.00 44.52 4.35
3744 4028 2.490509 AGTGGTACATTGACGATGACGA 59.509 45.455 9.78 0.00 44.52 4.20
3745 4029 3.057104 AGTGGTACATTGACGATGACGAA 60.057 43.478 9.78 0.00 44.52 3.85
3746 4030 3.676172 GTGGTACATTGACGATGACGAAA 59.324 43.478 9.78 0.00 44.52 3.46
3747 4031 4.150980 GTGGTACATTGACGATGACGAAAA 59.849 41.667 9.78 0.00 44.52 2.29
3748 4032 4.750598 TGGTACATTGACGATGACGAAAAA 59.249 37.500 9.78 0.00 42.66 1.94
3749 4033 5.410132 TGGTACATTGACGATGACGAAAAAT 59.590 36.000 9.78 0.00 42.66 1.82
3750 4034 5.732647 GGTACATTGACGATGACGAAAAATG 59.267 40.000 9.78 0.00 42.66 2.32
3751 4035 5.605564 ACATTGACGATGACGAAAAATGA 57.394 34.783 9.78 0.00 42.66 2.57
3752 4036 5.382303 ACATTGACGATGACGAAAAATGAC 58.618 37.500 9.78 0.00 42.66 3.06
3753 4037 3.698420 TGACGATGACGAAAAATGACG 57.302 42.857 0.00 0.00 42.66 4.35
3754 4038 3.310246 TGACGATGACGAAAAATGACGA 58.690 40.909 0.00 0.00 42.66 4.20
3755 4039 3.924073 TGACGATGACGAAAAATGACGAT 59.076 39.130 0.00 0.00 42.66 3.73
3756 4040 5.096849 TGACGATGACGAAAAATGACGATA 58.903 37.500 0.00 0.00 42.66 2.92
3757 4041 5.229260 TGACGATGACGAAAAATGACGATAG 59.771 40.000 0.00 0.00 42.66 2.08
3770 4054 2.431023 CGATAGTGGGAGGAGGTGG 58.569 63.158 0.00 0.00 0.00 4.61
3771 4055 1.749334 CGATAGTGGGAGGAGGTGGC 61.749 65.000 0.00 0.00 0.00 5.01
3772 4056 0.691078 GATAGTGGGAGGAGGTGGCA 60.691 60.000 0.00 0.00 0.00 4.92
3773 4057 0.029681 ATAGTGGGAGGAGGTGGCAT 60.030 55.000 0.00 0.00 0.00 4.40
3774 4058 0.982852 TAGTGGGAGGAGGTGGCATG 60.983 60.000 0.00 0.00 0.00 4.06
3775 4059 3.731728 TGGGAGGAGGTGGCATGC 61.732 66.667 9.90 9.90 0.00 4.06
3776 4060 4.512914 GGGAGGAGGTGGCATGCC 62.513 72.222 30.54 30.54 0.00 4.40
3777 4061 4.864334 GGAGGAGGTGGCATGCCG 62.864 72.222 30.87 0.00 39.42 5.69
3778 4062 4.864334 GAGGAGGTGGCATGCCGG 62.864 72.222 30.87 0.00 39.42 6.13
3784 4068 2.988684 GTGGCATGCCGGTGGAAA 60.989 61.111 30.87 9.56 39.42 3.13
3785 4069 2.037049 TGGCATGCCGGTGGAAAT 59.963 55.556 30.87 0.00 39.42 2.17
3786 4070 2.349672 TGGCATGCCGGTGGAAATG 61.350 57.895 30.87 1.11 39.42 2.32
3787 4071 2.350458 GGCATGCCGGTGGAAATGT 61.350 57.895 23.48 0.00 0.00 2.71
3788 4072 1.139520 GCATGCCGGTGGAAATGTC 59.860 57.895 6.36 0.00 0.00 3.06
3789 4073 1.315257 GCATGCCGGTGGAAATGTCT 61.315 55.000 6.36 0.00 0.00 3.41
3790 4074 1.176527 CATGCCGGTGGAAATGTCTT 58.823 50.000 1.90 0.00 0.00 3.01
3791 4075 1.133025 CATGCCGGTGGAAATGTCTTC 59.867 52.381 1.90 0.00 0.00 2.87
3792 4076 0.608035 TGCCGGTGGAAATGTCTTCC 60.608 55.000 1.90 0.00 39.03 3.46
3793 4077 0.322546 GCCGGTGGAAATGTCTTCCT 60.323 55.000 1.90 0.00 39.31 3.36
3794 4078 1.065709 GCCGGTGGAAATGTCTTCCTA 60.066 52.381 1.90 0.00 39.31 2.94
3795 4079 2.629051 CCGGTGGAAATGTCTTCCTAC 58.371 52.381 0.00 2.42 39.31 3.18
3796 4080 2.629051 CGGTGGAAATGTCTTCCTACC 58.371 52.381 5.20 9.17 39.31 3.18
3797 4081 2.027561 CGGTGGAAATGTCTTCCTACCA 60.028 50.000 17.59 0.00 38.51 3.25
3798 4082 3.558321 CGGTGGAAATGTCTTCCTACCAA 60.558 47.826 17.59 0.00 38.51 3.67
3799 4083 4.403734 GGTGGAAATGTCTTCCTACCAAA 58.596 43.478 14.84 0.00 38.49 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.595823 AGAGTATTTTATTAATGCGTGTGTAGT 57.404 29.630 0.00 0.00 0.00 2.73
2 3 9.589111 TGAGAGTATTTTATTAATGCGTGTGTA 57.411 29.630 0.00 0.00 0.00 2.90
3 4 8.388103 GTGAGAGTATTTTATTAATGCGTGTGT 58.612 33.333 0.00 0.00 0.00 3.72
4 5 8.387354 TGTGAGAGTATTTTATTAATGCGTGTG 58.613 33.333 0.00 0.00 0.00 3.82
12 13 8.158132 TGGTGTGGTGTGAGAGTATTTTATTAA 58.842 33.333 0.00 0.00 0.00 1.40
27 28 0.744281 GGAAAAGGTGGTGTGGTGTG 59.256 55.000 0.00 0.00 0.00 3.82
28 29 0.396556 GGGAAAAGGTGGTGTGGTGT 60.397 55.000 0.00 0.00 0.00 4.16
29 30 1.452145 CGGGAAAAGGTGGTGTGGTG 61.452 60.000 0.00 0.00 0.00 4.17
30 31 1.152839 CGGGAAAAGGTGGTGTGGT 60.153 57.895 0.00 0.00 0.00 4.16
31 32 0.466555 TTCGGGAAAAGGTGGTGTGG 60.467 55.000 0.00 0.00 0.00 4.17
32 33 0.666374 GTTCGGGAAAAGGTGGTGTG 59.334 55.000 0.00 0.00 0.00 3.82
33 34 0.466739 GGTTCGGGAAAAGGTGGTGT 60.467 55.000 0.00 0.00 0.00 4.16
47 48 2.089017 TGCATTCGCATCTGGTTCG 58.911 52.632 0.00 0.00 45.36 3.95
68 69 0.613260 AACGGCTGTGGCTTATCTGA 59.387 50.000 0.00 0.00 38.73 3.27
77 78 0.676466 TGCTCCAATAACGGCTGTGG 60.676 55.000 0.00 0.00 0.00 4.17
80 81 0.947244 GGATGCTCCAATAACGGCTG 59.053 55.000 0.00 0.00 36.28 4.85
81 82 0.546122 TGGATGCTCCAATAACGGCT 59.454 50.000 2.78 0.00 45.00 5.52
113 114 0.813610 TTCGCCCAATCAGCATACGG 60.814 55.000 0.00 0.00 0.00 4.02
115 116 2.017049 AGTTTCGCCCAATCAGCATAC 58.983 47.619 0.00 0.00 0.00 2.39
119 120 3.695816 GATTTAGTTTCGCCCAATCAGC 58.304 45.455 0.00 0.00 0.00 4.26
151 152 7.489160 TCTATACGTTCTCGGTGTAGTAGTAA 58.511 38.462 0.00 0.00 41.85 2.24
154 155 7.201427 GCTATCTATACGTTCTCGGTGTAGTAG 60.201 44.444 0.00 0.00 41.85 2.57
155 156 6.587990 GCTATCTATACGTTCTCGGTGTAGTA 59.412 42.308 0.00 0.00 41.85 1.82
156 157 5.407995 GCTATCTATACGTTCTCGGTGTAGT 59.592 44.000 0.00 0.00 41.85 2.73
157 158 5.163874 GGCTATCTATACGTTCTCGGTGTAG 60.164 48.000 0.00 0.00 41.85 2.74
164 165 5.247084 TCCTCAGGCTATCTATACGTTCTC 58.753 45.833 0.00 0.00 0.00 2.87
167 168 4.218852 GCTTCCTCAGGCTATCTATACGTT 59.781 45.833 0.00 0.00 0.00 3.99
180 181 0.815734 CTGCATTTGGCTTCCTCAGG 59.184 55.000 0.00 0.00 45.15 3.86
181 182 1.471684 GTCTGCATTTGGCTTCCTCAG 59.528 52.381 0.00 0.00 45.15 3.35
186 197 0.108945 GCTGGTCTGCATTTGGCTTC 60.109 55.000 0.00 0.00 45.15 3.86
196 207 2.815647 GTACGCCTGCTGGTCTGC 60.816 66.667 11.69 0.00 35.27 4.26
197 208 2.507102 CGTACGCCTGCTGGTCTG 60.507 66.667 11.69 4.49 35.27 3.51
198 209 4.436998 GCGTACGCCTGCTGGTCT 62.437 66.667 29.51 0.00 35.27 3.85
272 283 0.768221 ACAGGAGCAACTGGAGGGAA 60.768 55.000 11.63 0.00 42.75 3.97
285 296 2.578178 CGAAGCGCGAGACAGGAG 60.578 66.667 12.10 0.00 44.57 3.69
459 504 1.151777 GCACATGGGATCCACGTACG 61.152 60.000 15.01 15.01 35.80 3.67
460 505 0.178068 AGCACATGGGATCCACGTAC 59.822 55.000 15.23 1.83 35.80 3.67
461 506 0.177836 CAGCACATGGGATCCACGTA 59.822 55.000 15.23 0.00 35.80 3.57
462 507 1.078214 CAGCACATGGGATCCACGT 60.078 57.895 15.23 3.96 35.80 4.49
496 542 6.293626 CCACTGATTTTACCTTCTGAACTGTG 60.294 42.308 0.00 0.00 0.00 3.66
514 564 0.532573 CTGTGCCGTAGTCCACTGAT 59.467 55.000 0.00 0.00 34.16 2.90
520 570 2.125512 CTGCCTGTGCCGTAGTCC 60.126 66.667 0.00 0.00 36.33 3.85
537 587 2.165234 GAGCATCTTCTTTTTGGAGGGC 59.835 50.000 0.00 0.00 0.00 5.19
554 608 9.588096 TCTCTAATATTGGTACTGAATAGAGCA 57.412 33.333 0.00 0.00 36.61 4.26
560 614 9.440761 AGGTTCTCTCTAATATTGGTACTGAAT 57.559 33.333 0.00 0.00 0.00 2.57
561 615 8.840200 AGGTTCTCTCTAATATTGGTACTGAA 57.160 34.615 0.00 0.00 0.00 3.02
562 616 9.352191 GTAGGTTCTCTCTAATATTGGTACTGA 57.648 37.037 0.00 0.00 0.00 3.41
572 626 6.952358 ACCAACAGTGTAGGTTCTCTCTAATA 59.048 38.462 0.00 0.00 29.58 0.98
602 719 4.394712 CCGCGGTTTCCTCCTGCT 62.395 66.667 19.50 0.00 0.00 4.24
651 776 0.934496 TACTCTTGTGCGTGTGTTGC 59.066 50.000 0.00 0.00 0.00 4.17
674 799 1.446907 CCCAGTTAGCAGAGCACAAG 58.553 55.000 0.00 0.00 0.00 3.16
683 810 2.935481 AGCCCAGCCCAGTTAGCA 60.935 61.111 0.00 0.00 0.00 3.49
752 932 5.830000 ACACGGAGTTTTTAGCTCTTTTT 57.170 34.783 0.00 0.00 41.61 1.94
753 933 5.830000 AACACGGAGTTTTTAGCTCTTTT 57.170 34.783 0.00 0.00 41.61 2.27
754 934 6.764560 TCTTAACACGGAGTTTTTAGCTCTTT 59.235 34.615 0.00 0.00 41.61 2.52
755 935 6.285990 TCTTAACACGGAGTTTTTAGCTCTT 58.714 36.000 0.00 0.00 41.61 2.85
756 936 5.850614 TCTTAACACGGAGTTTTTAGCTCT 58.149 37.500 0.00 0.00 41.61 4.09
758 938 5.050567 CGTTCTTAACACGGAGTTTTTAGCT 60.051 40.000 0.80 0.00 41.61 3.32
759 939 5.135330 CGTTCTTAACACGGAGTTTTTAGC 58.865 41.667 0.80 0.00 41.61 3.09
770 950 0.160182 GCGTCACCGTTCTTAACACG 59.840 55.000 0.00 0.00 37.39 4.49
772 952 0.104487 TGGCGTCACCGTTCTTAACA 59.896 50.000 0.00 0.00 43.94 2.41
774 954 2.903284 GTGGCGTCACCGTTCTTAA 58.097 52.632 9.56 0.00 43.94 1.85
775 955 4.659480 GTGGCGTCACCGTTCTTA 57.341 55.556 9.56 0.00 43.94 2.10
831 1016 2.911484 CTGATGTCTAACTTGGGAGCC 58.089 52.381 0.00 0.00 0.00 4.70
862 1047 5.256474 AGAGAAGAGAAGAAGAGGAGTGAG 58.744 45.833 0.00 0.00 0.00 3.51
897 1099 0.109272 GCGATCGAGTGTTCTGGTCA 60.109 55.000 21.57 0.00 0.00 4.02
898 1100 0.109272 TGCGATCGAGTGTTCTGGTC 60.109 55.000 21.57 0.00 0.00 4.02
900 1102 1.416813 GCTGCGATCGAGTGTTCTGG 61.417 60.000 21.57 0.00 0.00 3.86
901 1103 0.457509 AGCTGCGATCGAGTGTTCTG 60.458 55.000 21.57 5.02 0.00 3.02
902 1104 0.179150 GAGCTGCGATCGAGTGTTCT 60.179 55.000 21.57 5.89 0.00 3.01
903 1105 0.456824 TGAGCTGCGATCGAGTGTTC 60.457 55.000 21.57 14.55 0.00 3.18
948 1150 2.670905 GTGTTTGGCTGTGTTTGAAACC 59.329 45.455 5.50 0.00 0.00 3.27
1175 1377 7.549488 AGCCACTTAGAATTTGTCTGTATGTAC 59.451 37.037 0.00 0.00 37.12 2.90
1180 1382 5.012664 TCCAGCCACTTAGAATTTGTCTGTA 59.987 40.000 0.00 0.00 37.12 2.74
1182 1384 4.326826 TCCAGCCACTTAGAATTTGTCTG 58.673 43.478 0.00 0.00 37.12 3.51
1183 1385 4.287067 TCTCCAGCCACTTAGAATTTGTCT 59.713 41.667 0.00 0.00 40.71 3.41
1184 1386 4.579869 TCTCCAGCCACTTAGAATTTGTC 58.420 43.478 0.00 0.00 0.00 3.18
1186 1388 4.142513 GCTTCTCCAGCCACTTAGAATTTG 60.143 45.833 0.00 0.00 43.65 2.32
1189 1391 3.274095 GCTTCTCCAGCCACTTAGAAT 57.726 47.619 0.00 0.00 43.65 2.40
1200 1402 1.067250 GGCGAGCTAGCTTCTCCAG 59.933 63.158 20.42 7.67 37.29 3.86
1203 1405 1.216122 CAATGGCGAGCTAGCTTCTC 58.784 55.000 20.42 11.49 37.29 2.87
1204 1406 0.539051 ACAATGGCGAGCTAGCTTCT 59.461 50.000 20.42 0.00 37.29 2.85
1205 1407 0.933796 GACAATGGCGAGCTAGCTTC 59.066 55.000 20.42 13.63 37.29 3.86
1206 1408 0.539051 AGACAATGGCGAGCTAGCTT 59.461 50.000 20.42 2.06 37.29 3.74
1259 1475 3.767230 CGAACGACAGCTGCACGG 61.767 66.667 28.21 13.57 0.00 4.94
1432 1649 6.379133 TCATTCAAAGCTTGATTAGAATGGCT 59.621 34.615 23.56 0.00 41.41 4.75
1518 1743 0.823460 CCCTGAAGTCTCTCTGCTCC 59.177 60.000 0.00 0.00 0.00 4.70
1644 1869 0.677842 CATACCCTGGGTAGTACGGC 59.322 60.000 28.25 0.00 41.83 5.68
1681 1906 3.364964 GCAACGTGGAGAAAAATGTCGAT 60.365 43.478 0.00 0.00 0.00 3.59
1682 1907 2.032377 GCAACGTGGAGAAAAATGTCGA 60.032 45.455 0.00 0.00 0.00 4.20
1683 1908 2.307049 GCAACGTGGAGAAAAATGTCG 58.693 47.619 0.00 0.00 0.00 4.35
1684 1909 2.307049 CGCAACGTGGAGAAAAATGTC 58.693 47.619 0.00 0.00 0.00 3.06
1750 1984 4.993905 ACTTGTTGTCACTGTTAAAAGGC 58.006 39.130 0.00 0.00 0.00 4.35
1763 1997 5.880054 ATTAGCCATGTGTACTTGTTGTC 57.120 39.130 0.00 0.00 0.00 3.18
1764 1998 6.150474 GGTTATTAGCCATGTGTACTTGTTGT 59.850 38.462 0.00 0.00 0.00 3.32
1765 1999 6.374333 AGGTTATTAGCCATGTGTACTTGTTG 59.626 38.462 0.00 0.00 0.00 3.33
2031 2265 0.616395 TGACGAGGTGGATGCCCTTA 60.616 55.000 0.00 0.00 30.60 2.69
2214 2448 2.737830 GAGGAGTAGATGGCGCCC 59.262 66.667 26.77 9.73 0.00 6.13
2400 2634 0.942962 CAATGCCGATCTCCTTGAGC 59.057 55.000 0.00 0.00 0.00 4.26
2644 2878 0.900647 CAGGTCTGGACGAACTCCCT 60.901 60.000 0.00 0.00 37.67 4.20
2802 3036 1.682451 TAGCTATGCGGTGGTGGTCC 61.682 60.000 0.00 0.00 0.00 4.46
2823 3057 2.047151 AATGCGGCGGTAATGCTTCG 62.047 55.000 9.78 0.00 34.52 3.79
2825 3059 0.661020 GTAATGCGGCGGTAATGCTT 59.339 50.000 9.78 0.00 34.52 3.91
2826 3060 1.164041 GGTAATGCGGCGGTAATGCT 61.164 55.000 9.78 0.00 34.52 3.79
2859 3096 1.105759 CCATAAGCTGGCTCCAAGGC 61.106 60.000 0.00 0.00 38.47 4.35
2887 3124 5.163844 CGTAGTAGCGCTATGTACTGATCAT 60.164 44.000 21.96 0.00 33.18 2.45
2913 3150 5.415077 GGAATTGATCGGCTACTAGCTACTA 59.585 44.000 7.99 0.00 41.99 1.82
2914 3151 4.218852 GGAATTGATCGGCTACTAGCTACT 59.781 45.833 7.99 0.00 41.99 2.57
2915 3152 4.218852 AGGAATTGATCGGCTACTAGCTAC 59.781 45.833 7.99 0.00 41.99 3.58
2931 3168 7.175797 AGTAGGGGAAGAAACTAAAGGAATTG 58.824 38.462 0.00 0.00 0.00 2.32
2946 3183 0.615331 TGCAGCAGAAGTAGGGGAAG 59.385 55.000 0.00 0.00 0.00 3.46
3000 3237 3.245668 AACAGTGCTCCTCGGGCAG 62.246 63.158 0.00 0.00 40.54 4.85
3090 3327 1.739562 CTCCGCAGAACACTCCAGC 60.740 63.158 0.00 0.00 0.00 4.85
3115 3352 6.657836 ACAATAATAGTACAGCGAACAACC 57.342 37.500 0.00 0.00 0.00 3.77
3127 3364 7.780064 TGTAGTAACCGGCAACAATAATAGTA 58.220 34.615 0.00 0.00 0.00 1.82
3128 3365 6.642430 TGTAGTAACCGGCAACAATAATAGT 58.358 36.000 0.00 0.00 0.00 2.12
3129 3366 7.307751 CCATGTAGTAACCGGCAACAATAATAG 60.308 40.741 0.00 0.00 0.00 1.73
3177 3414 3.633065 GAGGGAGCGAGATGTAAAGTAGT 59.367 47.826 0.00 0.00 0.00 2.73
3182 3419 1.471119 ACGAGGGAGCGAGATGTAAA 58.529 50.000 0.00 0.00 34.83 2.01
3187 3424 1.609555 GATGTAACGAGGGAGCGAGAT 59.390 52.381 0.00 0.00 34.83 2.75
3188 3425 1.022735 GATGTAACGAGGGAGCGAGA 58.977 55.000 0.00 0.00 34.83 4.04
3189 3426 0.317103 CGATGTAACGAGGGAGCGAG 60.317 60.000 0.00 0.00 35.09 5.03
3191 3428 1.299165 CCGATGTAACGAGGGAGCG 60.299 63.158 0.00 0.00 35.09 5.03
3193 3430 0.029035 CGACCGATGTAACGAGGGAG 59.971 60.000 0.00 0.00 35.09 4.30
3196 3433 0.866061 CAGCGACCGATGTAACGAGG 60.866 60.000 0.00 0.00 35.09 4.63
3198 3435 0.179181 GACAGCGACCGATGTAACGA 60.179 55.000 13.35 0.00 45.31 3.85
3199 3436 0.455464 TGACAGCGACCGATGTAACG 60.455 55.000 13.35 0.00 45.31 3.18
3201 3438 0.455464 CGTGACAGCGACCGATGTAA 60.455 55.000 13.35 3.33 45.31 2.41
3248 3504 3.575256 AGCTGACAATTGAGCATTGGAAA 59.425 39.130 18.33 0.00 46.06 3.13
3260 3516 2.229784 GGCTACTTTGCAGCTGACAATT 59.770 45.455 20.43 12.84 39.09 2.32
3279 3535 0.817654 GGTTTAGCAACATGGAGGGC 59.182 55.000 0.00 0.00 34.15 5.19
3299 3555 2.473760 CCGAGATCGAGCGTGGACT 61.474 63.158 8.32 0.00 43.02 3.85
3396 3652 1.764571 AAAGGTGGTCACAGCCGCTA 61.765 55.000 0.00 0.00 46.03 4.26
3397 3653 3.120086 AAAGGTGGTCACAGCCGCT 62.120 57.895 3.40 0.00 46.03 5.52
3398 3654 2.594592 AAAGGTGGTCACAGCCGC 60.595 61.111 3.40 0.00 46.03 6.53
3399 3655 2.908073 GCAAAGGTGGTCACAGCCG 61.908 63.158 3.40 0.00 46.03 5.52
3400 3656 1.109323 AAGCAAAGGTGGTCACAGCC 61.109 55.000 3.40 0.00 46.03 4.85
3401 3657 1.604604 TAAGCAAAGGTGGTCACAGC 58.395 50.000 3.40 2.02 45.24 4.40
3469 3736 1.574428 CGGACCTTTCAACCGCAAG 59.426 57.895 0.00 0.00 40.19 4.01
3498 3774 2.938539 TTTTGTTCGGTTTGCGCGGG 62.939 55.000 8.83 0.00 0.00 6.13
3499 3775 1.140407 TTTTTGTTCGGTTTGCGCGG 61.140 50.000 8.83 0.00 0.00 6.46
3569 3845 0.933700 AGGAGGAGGAGGAGGAGAAG 59.066 60.000 0.00 0.00 0.00 2.85
3576 3852 2.657459 AGAAGAAGAAGGAGGAGGAGGA 59.343 50.000 0.00 0.00 0.00 3.71
3577 3853 3.114643 AGAAGAAGAAGGAGGAGGAGG 57.885 52.381 0.00 0.00 0.00 4.30
3578 3854 4.352893 AGAAGAAGAAGAAGGAGGAGGAG 58.647 47.826 0.00 0.00 0.00 3.69
3579 3855 4.412060 AGAAGAAGAAGAAGGAGGAGGA 57.588 45.455 0.00 0.00 0.00 3.71
3580 3856 4.777366 AGAAGAAGAAGAAGAAGGAGGAGG 59.223 45.833 0.00 0.00 0.00 4.30
3581 3857 5.105351 GGAGAAGAAGAAGAAGAAGGAGGAG 60.105 48.000 0.00 0.00 0.00 3.69
3582 3858 4.775253 GGAGAAGAAGAAGAAGAAGGAGGA 59.225 45.833 0.00 0.00 0.00 3.71
3583 3859 4.777366 AGGAGAAGAAGAAGAAGAAGGAGG 59.223 45.833 0.00 0.00 0.00 4.30
3584 3860 6.663523 AGTAGGAGAAGAAGAAGAAGAAGGAG 59.336 42.308 0.00 0.00 0.00 3.69
3585 3861 6.557568 AGTAGGAGAAGAAGAAGAAGAAGGA 58.442 40.000 0.00 0.00 0.00 3.36
3586 3862 6.850752 AGTAGGAGAAGAAGAAGAAGAAGG 57.149 41.667 0.00 0.00 0.00 3.46
3589 3865 8.308207 GCTAAAAGTAGGAGAAGAAGAAGAAGA 58.692 37.037 0.00 0.00 0.00 2.87
3607 3883 7.986562 AGTTCTCGAAAAGAAAAGCTAAAAGT 58.013 30.769 0.00 0.00 45.50 2.66
3608 3884 7.319144 CGAGTTCTCGAAAAGAAAAGCTAAAAG 59.681 37.037 15.87 0.00 45.50 2.27
3610 3886 6.257193 ACGAGTTCTCGAAAAGAAAAGCTAAA 59.743 34.615 25.45 0.00 45.50 1.85
3613 3889 4.120589 ACGAGTTCTCGAAAAGAAAAGCT 58.879 39.130 25.45 0.00 45.50 3.74
3614 3890 4.454403 ACGAGTTCTCGAAAAGAAAAGC 57.546 40.909 25.45 0.00 45.50 3.51
3632 3916 1.346722 GTCCCCCAAGAAGAAGAACGA 59.653 52.381 0.00 0.00 0.00 3.85
3633 3917 1.071699 TGTCCCCCAAGAAGAAGAACG 59.928 52.381 0.00 0.00 0.00 3.95
3634 3918 2.951229 TGTCCCCCAAGAAGAAGAAC 57.049 50.000 0.00 0.00 0.00 3.01
3645 3929 5.333566 ACTAATTTCTTTCTTGTCCCCCA 57.666 39.130 0.00 0.00 0.00 4.96
3686 3970 5.645201 AGCCCTGATTTCCTTCTAGTTTTT 58.355 37.500 0.00 0.00 0.00 1.94
3687 3971 5.262455 AGCCCTGATTTCCTTCTAGTTTT 57.738 39.130 0.00 0.00 0.00 2.43
3688 3972 4.936685 AGCCCTGATTTCCTTCTAGTTT 57.063 40.909 0.00 0.00 0.00 2.66
3689 3973 4.410555 CCTAGCCCTGATTTCCTTCTAGTT 59.589 45.833 0.00 0.00 0.00 2.24
3690 3974 3.970640 CCTAGCCCTGATTTCCTTCTAGT 59.029 47.826 0.00 0.00 0.00 2.57
3691 3975 3.326297 CCCTAGCCCTGATTTCCTTCTAG 59.674 52.174 0.00 0.00 0.00 2.43
3692 3976 3.318313 CCCTAGCCCTGATTTCCTTCTA 58.682 50.000 0.00 0.00 0.00 2.10
3693 3977 2.131023 CCCTAGCCCTGATTTCCTTCT 58.869 52.381 0.00 0.00 0.00 2.85
3694 3978 1.143889 CCCCTAGCCCTGATTTCCTTC 59.856 57.143 0.00 0.00 0.00 3.46
3695 3979 1.226311 CCCCTAGCCCTGATTTCCTT 58.774 55.000 0.00 0.00 0.00 3.36
3696 3980 1.356494 GCCCCTAGCCCTGATTTCCT 61.356 60.000 0.00 0.00 34.35 3.36
3697 3981 1.151679 GCCCCTAGCCCTGATTTCC 59.848 63.158 0.00 0.00 34.35 3.13
3698 3982 4.909678 GCCCCTAGCCCTGATTTC 57.090 61.111 0.00 0.00 34.35 2.17
3707 3991 1.768077 ACTCCATCTGGCCCCTAGC 60.768 63.158 0.00 0.00 42.60 3.42
3708 3992 1.414061 CCACTCCATCTGGCCCCTAG 61.414 65.000 0.00 0.00 34.44 3.02
3709 3993 1.384502 CCACTCCATCTGGCCCCTA 60.385 63.158 0.00 0.00 34.44 3.53
3710 3994 2.194951 TACCACTCCATCTGGCCCCT 62.195 60.000 0.00 0.00 34.44 4.79
3711 3995 1.692749 TACCACTCCATCTGGCCCC 60.693 63.158 0.00 0.00 34.44 5.80
3712 3996 1.271840 TGTACCACTCCATCTGGCCC 61.272 60.000 0.00 0.00 34.44 5.80
3713 3997 0.839946 ATGTACCACTCCATCTGGCC 59.160 55.000 0.00 0.00 34.44 5.36
3714 3998 2.092968 TCAATGTACCACTCCATCTGGC 60.093 50.000 0.00 0.00 34.44 4.85
3715 3999 3.535561 GTCAATGTACCACTCCATCTGG 58.464 50.000 0.00 0.00 34.62 3.86
3716 4000 3.119137 TCGTCAATGTACCACTCCATCTG 60.119 47.826 0.00 0.00 0.00 2.90
3717 4001 3.096852 TCGTCAATGTACCACTCCATCT 58.903 45.455 0.00 0.00 0.00 2.90
3718 4002 3.520290 TCGTCAATGTACCACTCCATC 57.480 47.619 0.00 0.00 0.00 3.51
3719 4003 3.450817 TCATCGTCAATGTACCACTCCAT 59.549 43.478 0.00 0.00 36.68 3.41
3720 4004 2.829120 TCATCGTCAATGTACCACTCCA 59.171 45.455 0.00 0.00 36.68 3.86
3721 4005 3.187700 GTCATCGTCAATGTACCACTCC 58.812 50.000 0.00 0.00 36.68 3.85
3722 4006 2.852413 CGTCATCGTCAATGTACCACTC 59.148 50.000 0.00 0.00 36.68 3.51
3723 4007 2.490509 TCGTCATCGTCAATGTACCACT 59.509 45.455 0.00 0.00 36.68 4.00
3724 4008 2.871133 TCGTCATCGTCAATGTACCAC 58.129 47.619 0.00 0.00 36.68 4.16
3725 4009 3.579335 TTCGTCATCGTCAATGTACCA 57.421 42.857 0.00 0.00 36.68 3.25
3726 4010 4.914312 TTTTCGTCATCGTCAATGTACC 57.086 40.909 0.00 0.00 36.68 3.34
3727 4011 6.461698 GTCATTTTTCGTCATCGTCAATGTAC 59.538 38.462 0.00 0.00 36.68 2.90
3728 4012 6.530567 GTCATTTTTCGTCATCGTCAATGTA 58.469 36.000 0.00 0.00 36.68 2.29
3729 4013 5.382303 GTCATTTTTCGTCATCGTCAATGT 58.618 37.500 0.00 0.00 36.68 2.71
3730 4014 4.488449 CGTCATTTTTCGTCATCGTCAATG 59.512 41.667 0.00 0.00 38.33 2.82
3731 4015 4.387559 TCGTCATTTTTCGTCATCGTCAAT 59.612 37.500 0.00 0.00 38.33 2.57
3732 4016 3.736759 TCGTCATTTTTCGTCATCGTCAA 59.263 39.130 0.00 0.00 38.33 3.18
3733 4017 3.310246 TCGTCATTTTTCGTCATCGTCA 58.690 40.909 0.00 0.00 38.33 4.35
3734 4018 3.965209 TCGTCATTTTTCGTCATCGTC 57.035 42.857 0.00 0.00 38.33 4.20
3735 4019 5.004440 CACTATCGTCATTTTTCGTCATCGT 59.996 40.000 0.00 0.00 38.33 3.73
3736 4020 5.415366 CACTATCGTCATTTTTCGTCATCG 58.585 41.667 0.00 0.00 38.55 3.84
3737 4021 5.276868 CCCACTATCGTCATTTTTCGTCATC 60.277 44.000 0.00 0.00 0.00 2.92
3738 4022 4.570772 CCCACTATCGTCATTTTTCGTCAT 59.429 41.667 0.00 0.00 0.00 3.06
3739 4023 3.930229 CCCACTATCGTCATTTTTCGTCA 59.070 43.478 0.00 0.00 0.00 4.35
3740 4024 4.178540 TCCCACTATCGTCATTTTTCGTC 58.821 43.478 0.00 0.00 0.00 4.20
3741 4025 4.181578 CTCCCACTATCGTCATTTTTCGT 58.818 43.478 0.00 0.00 0.00 3.85
3742 4026 3.555956 CCTCCCACTATCGTCATTTTTCG 59.444 47.826 0.00 0.00 0.00 3.46
3743 4027 4.766375 TCCTCCCACTATCGTCATTTTTC 58.234 43.478 0.00 0.00 0.00 2.29
3744 4028 4.384208 CCTCCTCCCACTATCGTCATTTTT 60.384 45.833 0.00 0.00 0.00 1.94
3745 4029 3.134804 CCTCCTCCCACTATCGTCATTTT 59.865 47.826 0.00 0.00 0.00 1.82
3746 4030 2.700897 CCTCCTCCCACTATCGTCATTT 59.299 50.000 0.00 0.00 0.00 2.32
3747 4031 2.320781 CCTCCTCCCACTATCGTCATT 58.679 52.381 0.00 0.00 0.00 2.57
3748 4032 1.218196 ACCTCCTCCCACTATCGTCAT 59.782 52.381 0.00 0.00 0.00 3.06
3749 4033 0.629596 ACCTCCTCCCACTATCGTCA 59.370 55.000 0.00 0.00 0.00 4.35
3750 4034 1.033574 CACCTCCTCCCACTATCGTC 58.966 60.000 0.00 0.00 0.00 4.20
3751 4035 0.397254 CCACCTCCTCCCACTATCGT 60.397 60.000 0.00 0.00 0.00 3.73
3752 4036 1.749334 GCCACCTCCTCCCACTATCG 61.749 65.000 0.00 0.00 0.00 2.92
3753 4037 0.691078 TGCCACCTCCTCCCACTATC 60.691 60.000 0.00 0.00 0.00 2.08
3754 4038 0.029681 ATGCCACCTCCTCCCACTAT 60.030 55.000 0.00 0.00 0.00 2.12
3755 4039 0.982852 CATGCCACCTCCTCCCACTA 60.983 60.000 0.00 0.00 0.00 2.74
3756 4040 2.125912 ATGCCACCTCCTCCCACT 59.874 61.111 0.00 0.00 0.00 4.00
3757 4041 2.273449 CATGCCACCTCCTCCCAC 59.727 66.667 0.00 0.00 0.00 4.61
3758 4042 3.731728 GCATGCCACCTCCTCCCA 61.732 66.667 6.36 0.00 0.00 4.37
3759 4043 4.512914 GGCATGCCACCTCCTCCC 62.513 72.222 32.08 0.00 35.81 4.30
3760 4044 4.864334 CGGCATGCCACCTCCTCC 62.864 72.222 34.93 6.13 35.37 4.30
3761 4045 4.864334 CCGGCATGCCACCTCCTC 62.864 72.222 34.93 6.89 35.37 3.71
3767 4051 2.350458 ATTTCCACCGGCATGCCAC 61.350 57.895 34.93 10.80 35.37 5.01
3768 4052 2.037049 ATTTCCACCGGCATGCCA 59.963 55.556 34.93 15.34 35.37 4.92
3769 4053 2.283472 GACATTTCCACCGGCATGCC 62.283 60.000 27.67 27.67 0.00 4.40
3770 4054 1.139520 GACATTTCCACCGGCATGC 59.860 57.895 9.90 9.90 0.00 4.06
3771 4055 1.133025 GAAGACATTTCCACCGGCATG 59.867 52.381 0.00 0.00 0.00 4.06
3772 4056 1.463674 GAAGACATTTCCACCGGCAT 58.536 50.000 0.00 0.00 0.00 4.40
3773 4057 0.608035 GGAAGACATTTCCACCGGCA 60.608 55.000 0.00 0.00 38.45 5.69
3774 4058 0.322546 AGGAAGACATTTCCACCGGC 60.323 55.000 0.00 0.00 41.00 6.13
3775 4059 2.629051 GTAGGAAGACATTTCCACCGG 58.371 52.381 0.00 0.00 41.00 5.28
3776 4060 2.027561 TGGTAGGAAGACATTTCCACCG 60.028 50.000 8.51 0.00 39.98 4.94
3777 4061 3.713826 TGGTAGGAAGACATTTCCACC 57.286 47.619 8.51 12.39 41.00 4.61


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

AutoCloner maintained by Alex Coulton.