Multiple sequence alignment - TraesCS3B01G424100

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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 TraesCS3B01G424100 chr3B 100.000 3665 0 0 1 3665 661827692 661824028 0.000000e+00 6769.0
1 TraesCS3B01G424100 chr3D 90.421 1806 96 32 949 2732 500542922 500541172 0.000000e+00 2305.0
2 TraesCS3B01G424100 chr3D 95.244 820 27 6 1 818 500543866 500543057 0.000000e+00 1288.0
3 TraesCS3B01G424100 chr3D 93.921 806 33 8 2190 2988 500534831 500534035 0.000000e+00 1203.0
4 TraesCS3B01G424100 chr3D 80.161 373 51 10 3026 3378 500540842 500540473 1.310000e-64 257.0
5 TraesCS3B01G424100 chr3D 81.967 244 31 9 2766 3000 500541170 500540931 1.040000e-45 195.0
6 TraesCS3B01G424100 chr3D 77.419 310 47 11 3089 3378 500534032 500533726 2.930000e-36 163.0
7 TraesCS3B01G424100 chr3D 86.087 115 1 7 816 920 500543030 500542921 3.870000e-20 110.0
8 TraesCS3B01G424100 chr3A 95.461 1322 39 6 1694 3000 639700786 639699471 0.000000e+00 2089.0
9 TraesCS3B01G424100 chr3A 85.978 1840 129 59 1 1795 639702536 639700781 0.000000e+00 1849.0
10 TraesCS3B01G424100 chr3A 78.075 374 59 13 3025 3378 639699377 639699007 7.970000e-52 215.0
11 TraesCS3B01G424100 chr6B 85.385 260 27 5 3417 3665 476814875 476815134 3.630000e-65 259.0
12 TraesCS3B01G424100 chr2B 86.567 201 19 2 3470 3662 717821988 717822188 7.970000e-52 215.0
13 TraesCS3B01G424100 chr2B 92.593 54 4 0 3486 3539 10991120 10991067 1.090000e-10 78.7


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 TraesCS3B01G424100 chr3B 661824028 661827692 3664 True 6769.000000 6769 100.000000 1 3665 1 chr3B.!!$R1 3664
1 TraesCS3B01G424100 chr3D 500540473 500543866 3393 True 831.000000 2305 86.776000 1 3378 5 chr3D.!!$R2 3377
2 TraesCS3B01G424100 chr3D 500533726 500534831 1105 True 683.000000 1203 85.670000 2190 3378 2 chr3D.!!$R1 1188
3 TraesCS3B01G424100 chr3A 639699007 639702536 3529 True 1384.333333 2089 86.504667 1 3378 3 chr3A.!!$R1 3377

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
877 912 0.102120 TTTGCAGGCCACAGAAAACG 59.898 50.0 5.01 0.0 0.00 3.6 F
1247 1326 0.248539 GTCTAGCCGTCTAGCCGTTG 60.249 60.0 0.00 0.0 41.59 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1928 0.529337 CAGTCATAGCAGACGCCTGG 60.529 60.0 0.00 0.0 43.24 4.45 R
3240 3527 0.255890 GGCAAGCTGATTGAGGGGTA 59.744 55.0 10.23 0.0 41.83 3.69 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
61 62 4.023707 CAGAACTGTTTCTCCACAACATCC 60.024 45.833 0.00 0.00 40.34 3.51
114 115 0.515127 TCGCACAATGTAACAAGCCG 59.485 50.000 0.00 0.00 0.00 5.52
224 225 0.682209 GGCTGTGGCATCTGTTGGAT 60.682 55.000 0.00 0.00 40.87 3.41
390 391 3.074369 TTCTGGGCGCCGATCTCA 61.074 61.111 22.54 11.52 0.00 3.27
471 474 2.251642 GCACACCTGGACCGACAAC 61.252 63.158 0.00 0.00 0.00 3.32
476 479 1.147376 CCTGGACCGACAACACCAA 59.853 57.895 0.00 0.00 31.85 3.67
523 529 2.515996 ATACCACCGAACACCTGGCG 62.516 60.000 0.00 0.00 0.00 5.69
740 746 3.164269 CGGAGGTGGGGGATGGAG 61.164 72.222 0.00 0.00 0.00 3.86
742 748 2.372688 GAGGTGGGGGATGGAGGA 59.627 66.667 0.00 0.00 0.00 3.71
844 879 4.371975 CGAAAGCGGAAAGTGGGA 57.628 55.556 0.00 0.00 0.00 4.37
876 911 1.538849 CCTTTGCAGGCCACAGAAAAC 60.539 52.381 5.01 0.00 31.53 2.43
877 912 0.102120 TTTGCAGGCCACAGAAAACG 59.898 50.000 5.01 0.00 0.00 3.60
878 913 2.050077 GCAGGCCACAGAAAACGC 60.050 61.111 5.01 0.00 0.00 4.84
879 914 2.555547 GCAGGCCACAGAAAACGCT 61.556 57.895 5.01 0.00 0.00 5.07
880 915 1.576421 CAGGCCACAGAAAACGCTC 59.424 57.895 5.01 0.00 0.00 5.03
920 965 3.685214 GACGGCTGTGATCGCGTCT 62.685 63.158 0.80 0.00 32.37 4.18
921 966 3.250323 CGGCTGTGATCGCGTCTG 61.250 66.667 5.77 1.29 0.00 3.51
922 967 2.887568 GGCTGTGATCGCGTCTGG 60.888 66.667 5.77 0.00 0.00 3.86
923 968 2.887568 GCTGTGATCGCGTCTGGG 60.888 66.667 5.77 0.00 0.00 4.45
924 969 2.202797 CTGTGATCGCGTCTGGGG 60.203 66.667 5.77 0.00 0.00 4.96
925 970 3.723235 CTGTGATCGCGTCTGGGGG 62.723 68.421 5.77 0.00 0.00 5.40
981 1027 2.050077 TCTGCGTCTGTGTGAGCG 60.050 61.111 0.00 0.00 0.00 5.03
982 1028 2.355126 CTGCGTCTGTGTGAGCGT 60.355 61.111 0.00 0.00 0.00 5.07
983 1029 2.354656 TGCGTCTGTGTGAGCGTC 60.355 61.111 0.00 0.00 0.00 5.19
984 1030 2.354656 GCGTCTGTGTGAGCGTCA 60.355 61.111 0.00 0.00 0.00 4.35
985 1031 2.368105 GCGTCTGTGTGAGCGTCAG 61.368 63.158 0.00 0.00 0.00 3.51
987 1033 2.802683 GTCTGTGTGAGCGTCAGAC 58.197 57.895 8.41 8.41 46.70 3.51
988 1034 0.664767 GTCTGTGTGAGCGTCAGACC 60.665 60.000 11.85 0.00 46.85 3.85
989 1035 1.730902 CTGTGTGAGCGTCAGACCG 60.731 63.158 10.98 3.68 39.62 4.79
990 1036 2.335369 GTGTGAGCGTCAGACCGT 59.665 61.111 0.00 0.00 34.92 4.83
991 1037 1.729838 GTGTGAGCGTCAGACCGTC 60.730 63.158 0.00 0.00 34.92 4.79
1110 1174 2.172483 AATCGGTGAGTCGCTTGCCT 62.172 55.000 3.25 0.00 0.00 4.75
1111 1175 2.564553 ATCGGTGAGTCGCTTGCCTC 62.565 60.000 3.25 0.00 0.00 4.70
1112 1176 2.435059 GGTGAGTCGCTTGCCTCC 60.435 66.667 3.25 0.00 0.00 4.30
1113 1177 2.435059 GTGAGTCGCTTGCCTCCC 60.435 66.667 0.00 0.00 0.00 4.30
1181 1259 3.134458 CTCCGATTTACCTGATTCCTGC 58.866 50.000 0.00 0.00 0.00 4.85
1182 1260 2.771943 TCCGATTTACCTGATTCCTGCT 59.228 45.455 0.00 0.00 0.00 4.24
1183 1261 3.134458 CCGATTTACCTGATTCCTGCTC 58.866 50.000 0.00 0.00 0.00 4.26
1184 1262 3.134458 CGATTTACCTGATTCCTGCTCC 58.866 50.000 0.00 0.00 0.00 4.70
1185 1263 3.181461 CGATTTACCTGATTCCTGCTCCT 60.181 47.826 0.00 0.00 0.00 3.69
1186 1264 3.914426 TTTACCTGATTCCTGCTCCTC 57.086 47.619 0.00 0.00 0.00 3.71
1187 1265 2.856760 TACCTGATTCCTGCTCCTCT 57.143 50.000 0.00 0.00 0.00 3.69
1188 1266 1.494960 ACCTGATTCCTGCTCCTCTC 58.505 55.000 0.00 0.00 0.00 3.20
1247 1326 0.248539 GTCTAGCCGTCTAGCCGTTG 60.249 60.000 0.00 0.00 41.59 4.10
1270 1349 2.555757 GTGCTTCCAGTTTCAGCTGAAT 59.444 45.455 28.89 13.32 38.70 2.57
1273 1352 3.572584 CTTCCAGTTTCAGCTGAATTGC 58.427 45.455 28.89 20.56 38.70 3.56
1274 1353 1.888512 TCCAGTTTCAGCTGAATTGCC 59.111 47.619 28.89 16.66 38.70 4.52
1276 1355 2.352421 CCAGTTTCAGCTGAATTGCCAG 60.352 50.000 28.89 15.20 38.70 4.85
1285 1365 1.212751 GAATTGCCAGGTTCACGCC 59.787 57.895 0.00 0.00 0.00 5.68
1287 1367 0.827507 AATTGCCAGGTTCACGCCTT 60.828 50.000 0.00 0.00 36.58 4.35
1344 1424 0.605050 TAATGCGCCACTTGTGAGCA 60.605 50.000 19.49 19.49 42.28 4.26
1429 1510 3.501396 CGACATTTGCCTCGCCAT 58.499 55.556 0.00 0.00 0.00 4.40
1430 1511 1.353103 CGACATTTGCCTCGCCATC 59.647 57.895 0.00 0.00 0.00 3.51
1431 1512 1.091771 CGACATTTGCCTCGCCATCT 61.092 55.000 0.00 0.00 0.00 2.90
1432 1513 0.659957 GACATTTGCCTCGCCATCTC 59.340 55.000 0.00 0.00 0.00 2.75
1433 1514 0.254178 ACATTTGCCTCGCCATCTCT 59.746 50.000 0.00 0.00 0.00 3.10
1434 1515 0.942962 CATTTGCCTCGCCATCTCTC 59.057 55.000 0.00 0.00 0.00 3.20
1435 1516 0.531532 ATTTGCCTCGCCATCTCTCG 60.532 55.000 0.00 0.00 0.00 4.04
1436 1517 1.888436 TTTGCCTCGCCATCTCTCGT 61.888 55.000 0.00 0.00 0.00 4.18
1437 1518 1.035385 TTGCCTCGCCATCTCTCGTA 61.035 55.000 0.00 0.00 0.00 3.43
1438 1519 1.284408 GCCTCGCCATCTCTCGTAG 59.716 63.158 0.00 0.00 0.00 3.51
1439 1520 1.448922 GCCTCGCCATCTCTCGTAGT 61.449 60.000 0.00 0.00 0.00 2.73
1499 1580 3.459828 TGGTTATCCATTCCTGACCAGA 58.540 45.455 0.00 0.00 39.03 3.86
1514 1595 3.255395 TGACCAGACGTACCGTATTTTCA 59.745 43.478 0.00 0.00 41.37 2.69
1519 1600 4.795278 CAGACGTACCGTATTTTCAGTACC 59.205 45.833 0.00 0.00 41.37 3.34
1520 1601 4.458989 AGACGTACCGTATTTTCAGTACCA 59.541 41.667 0.00 0.00 41.37 3.25
1528 1609 6.426937 ACCGTATTTTCAGTACCATATGCATC 59.573 38.462 0.19 0.00 0.00 3.91
1536 1617 6.461640 TCAGTACCATATGCATCTCAATGAG 58.538 40.000 0.19 3.38 34.61 2.90
1552 1633 6.990939 TCTCAATGAGCTTATCCAGAATTCAG 59.009 38.462 8.44 0.00 0.00 3.02
1553 1634 5.530171 TCAATGAGCTTATCCAGAATTCAGC 59.470 40.000 8.44 6.66 0.00 4.26
1594 1675 3.660970 TTGGCTGGATATTGCTGGTAA 57.339 42.857 0.00 0.00 0.00 2.85
1595 1676 3.660970 TGGCTGGATATTGCTGGTAAA 57.339 42.857 0.00 0.00 0.00 2.01
1596 1677 3.287222 TGGCTGGATATTGCTGGTAAAC 58.713 45.455 0.00 0.00 0.00 2.01
1597 1678 3.287222 GGCTGGATATTGCTGGTAAACA 58.713 45.455 0.00 0.00 0.00 2.83
1611 1692 6.830873 CTGGTAAACAGTACAGTACCTACT 57.169 41.667 7.13 0.00 42.42 2.57
1612 1693 7.928307 CTGGTAAACAGTACAGTACCTACTA 57.072 40.000 7.13 2.43 42.42 1.82
1613 1694 8.517062 CTGGTAAACAGTACAGTACCTACTAT 57.483 38.462 7.13 0.00 42.42 2.12
1614 1695 8.511604 TGGTAAACAGTACAGTACCTACTATC 57.488 38.462 7.13 0.00 37.49 2.08
1615 1696 8.331740 TGGTAAACAGTACAGTACCTACTATCT 58.668 37.037 7.13 0.00 37.49 1.98
1616 1697 8.619546 GGTAAACAGTACAGTACCTACTATCTG 58.380 40.741 7.13 0.00 34.38 2.90
1617 1698 6.696441 AACAGTACAGTACCTACTATCTGC 57.304 41.667 7.13 0.00 34.13 4.26
1618 1699 6.003859 ACAGTACAGTACCTACTATCTGCT 57.996 41.667 7.13 0.00 34.13 4.24
1619 1700 7.134362 ACAGTACAGTACCTACTATCTGCTA 57.866 40.000 7.13 0.00 34.13 3.49
1620 1701 6.991531 ACAGTACAGTACCTACTATCTGCTAC 59.008 42.308 7.13 0.00 34.13 3.58
1621 1702 7.147514 ACAGTACAGTACCTACTATCTGCTACT 60.148 40.741 7.13 0.00 34.13 2.57
1622 1703 7.385752 CAGTACAGTACCTACTATCTGCTACTC 59.614 44.444 7.13 0.00 34.13 2.59
1623 1704 6.249911 ACAGTACCTACTATCTGCTACTCA 57.750 41.667 0.00 0.00 34.13 3.41
1624 1705 6.660800 ACAGTACCTACTATCTGCTACTCAA 58.339 40.000 0.00 0.00 34.13 3.02
1625 1706 6.543100 ACAGTACCTACTATCTGCTACTCAAC 59.457 42.308 0.00 0.00 34.13 3.18
1626 1707 6.768861 CAGTACCTACTATCTGCTACTCAACT 59.231 42.308 0.00 0.00 34.13 3.16
1627 1708 6.768861 AGTACCTACTATCTGCTACTCAACTG 59.231 42.308 0.00 0.00 34.13 3.16
1632 1713 2.462456 TCTGCTACTCAACTGCTTGG 57.538 50.000 0.00 0.00 0.00 3.61
1640 1721 0.674581 TCAACTGCTTGGCGGATCAG 60.675 55.000 5.30 0.00 38.46 2.90
1642 1723 0.613260 AACTGCTTGGCGGATCAGTA 59.387 50.000 5.30 0.00 38.68 2.74
1682 1774 0.801872 TGGCGATGAATTGGAACGTG 59.198 50.000 0.00 0.00 0.00 4.49
1692 1784 1.045407 TTGGAACGTGACCTAGCACT 58.955 50.000 12.20 0.00 36.65 4.40
1740 1928 1.537202 CTGTCTGCAACCCTAAAGCAC 59.463 52.381 0.00 0.00 34.13 4.40
1786 1974 7.074507 ACAAACTTACACACGACAATTTGTA 57.925 32.000 1.15 0.00 37.28 2.41
1891 2087 3.624861 CCCTGATACTAACTTGCTGCAAG 59.375 47.826 34.07 34.07 45.85 4.01
1914 2110 3.891977 TGTCCTACCTCATATCAGTGAGC 59.108 47.826 0.00 0.00 43.36 4.26
2360 2559 3.075641 GGAGTCCGGTGAGGGTCC 61.076 72.222 0.00 0.00 41.52 4.46
2539 2739 5.343249 GGATACTGTTTGATGATTTGCACC 58.657 41.667 0.00 0.00 0.00 5.01
2792 2994 2.026915 TGGAGCTTCTGCATGTGTACAT 60.027 45.455 0.00 0.00 42.74 2.29
2993 3210 3.120792 TCTATATTTGCGGTCGAACAGC 58.879 45.455 0.00 5.76 39.77 4.40
2997 3214 4.680237 TGCGGTCGAACAGCAGGG 62.680 66.667 14.44 0.00 43.96 4.45
3000 3217 2.747686 GGTCGAACAGCAGGGGAA 59.252 61.111 0.00 0.00 0.00 3.97
3001 3218 1.072505 GGTCGAACAGCAGGGGAAA 59.927 57.895 0.00 0.00 0.00 3.13
3003 3220 0.250338 GTCGAACAGCAGGGGAAAGT 60.250 55.000 0.00 0.00 0.00 2.66
3004 3221 0.472471 TCGAACAGCAGGGGAAAGTT 59.528 50.000 0.00 0.00 0.00 2.66
3005 3222 0.593128 CGAACAGCAGGGGAAAGTTG 59.407 55.000 0.00 0.00 0.00 3.16
3006 3223 0.315251 GAACAGCAGGGGAAAGTTGC 59.685 55.000 0.00 0.00 38.09 4.17
3007 3224 1.115326 AACAGCAGGGGAAAGTTGCC 61.115 55.000 0.00 0.00 38.58 4.52
3013 3230 3.991999 GGGAAAGTTGCCCGGTAC 58.008 61.111 2.05 0.00 35.50 3.34
3015 3232 0.675837 GGGAAAGTTGCCCGGTACTC 60.676 60.000 2.05 0.00 35.50 2.59
3016 3233 0.323957 GGAAAGTTGCCCGGTACTCT 59.676 55.000 0.00 0.00 0.00 3.24
3017 3234 1.439679 GAAAGTTGCCCGGTACTCTG 58.560 55.000 0.00 0.00 0.00 3.35
3018 3235 0.605589 AAAGTTGCCCGGTACTCTGC 60.606 55.000 0.00 0.00 0.00 4.26
3020 3237 3.307906 TTGCCCGGTACTCTGCGT 61.308 61.111 0.00 0.00 0.00 5.24
3021 3238 3.583276 TTGCCCGGTACTCTGCGTG 62.583 63.158 0.00 0.00 0.00 5.34
3022 3239 4.814294 GCCCGGTACTCTGCGTGG 62.814 72.222 0.00 0.00 0.00 4.94
3023 3240 3.066190 CCCGGTACTCTGCGTGGA 61.066 66.667 0.00 0.00 0.00 4.02
3068 3354 1.580437 CACATGCGCATGAACACCA 59.420 52.632 46.90 9.29 41.20 4.17
3082 3368 0.680601 ACACCATGGCGCATTCATCA 60.681 50.000 13.04 0.00 0.00 3.07
3108 3394 2.121645 CCATGGGCATCTTTCTGGC 58.878 57.895 2.85 0.00 40.76 4.85
3130 3417 0.613012 GGAGCTCCAGCAAAATGGGT 60.613 55.000 28.43 0.00 45.16 4.51
3141 3428 3.903090 AGCAAAATGGGTTCCTCATGAAA 59.097 39.130 0.00 0.00 33.94 2.69
3142 3429 4.533311 AGCAAAATGGGTTCCTCATGAAAT 59.467 37.500 0.00 0.00 33.94 2.17
3144 3431 5.797051 CAAAATGGGTTCCTCATGAAATGT 58.203 37.500 0.00 0.00 46.80 2.71
3146 3433 7.558604 CAAAATGGGTTCCTCATGAAATGTAT 58.441 34.615 0.00 0.00 46.80 2.29
3149 3436 4.080582 TGGGTTCCTCATGAAATGTATCGT 60.081 41.667 0.00 0.00 46.80 3.73
3155 3442 7.107639 TCCTCATGAAATGTATCGTTACAGA 57.892 36.000 11.67 2.64 46.80 3.41
3162 3449 5.670792 AATGTATCGTTACAGAGGGAACA 57.329 39.130 11.67 0.00 41.49 3.18
3172 3459 2.158143 ACAGAGGGAACAACCTACTCCT 60.158 50.000 0.00 0.00 42.10 3.69
3184 3471 5.128499 ACAACCTACTCCTCTTGATCAGATG 59.872 44.000 0.00 0.00 0.00 2.90
3199 3486 6.286758 TGATCAGATGAAGGATCTTAGTTGC 58.713 40.000 0.00 0.00 39.64 4.17
3200 3487 5.682234 TCAGATGAAGGATCTTAGTTGCA 57.318 39.130 0.00 0.00 39.64 4.08
3206 3493 1.482593 AGGATCTTAGTTGCACCCTCG 59.517 52.381 0.00 0.00 0.00 4.63
3210 3497 0.391263 CTTAGTTGCACCCTCGTCCC 60.391 60.000 0.00 0.00 0.00 4.46
3212 3499 3.948719 GTTGCACCCTCGTCCCCA 61.949 66.667 0.00 0.00 0.00 4.96
3236 3523 2.856032 CGTGCCGCTCTTTGACAG 59.144 61.111 0.00 0.00 0.00 3.51
3239 3526 1.962822 TGCCGCTCTTTGACAGCAG 60.963 57.895 0.00 0.00 36.61 4.24
3240 3527 1.963338 GCCGCTCTTTGACAGCAGT 60.963 57.895 0.00 0.00 36.61 4.40
3241 3528 0.670546 GCCGCTCTTTGACAGCAGTA 60.671 55.000 0.00 0.00 36.61 2.74
3243 3530 1.071605 CGCTCTTTGACAGCAGTACC 58.928 55.000 0.00 0.00 36.61 3.34
3248 3550 1.347707 CTTTGACAGCAGTACCCCTCA 59.652 52.381 0.00 0.00 0.00 3.86
3302 3604 2.675423 ACGGTGTCGCTGCTCCTA 60.675 61.111 0.00 0.00 40.63 2.94
3305 3607 1.153745 GGTGTCGCTGCTCCTACTG 60.154 63.158 0.00 0.00 0.00 2.74
3336 3638 0.248012 TGCTCGGGCTCGACAAAATA 59.752 50.000 3.45 0.00 40.88 1.40
3378 3684 3.321111 TCACTTCACAAGGACCAGTAGTC 59.679 47.826 0.00 0.00 45.51 2.59
3385 3691 2.799371 GACCAGTAGTCCCGCTCG 59.201 66.667 0.00 0.00 39.84 5.03
3386 3692 3.412879 GACCAGTAGTCCCGCTCGC 62.413 68.421 0.00 0.00 39.84 5.03
3387 3693 4.208686 CCAGTAGTCCCGCTCGCC 62.209 72.222 0.00 0.00 0.00 5.54
3388 3694 4.554363 CAGTAGTCCCGCTCGCCG 62.554 72.222 0.00 0.00 0.00 6.46
3412 3718 4.243008 GCTAGCGCCTCTTCCCCC 62.243 72.222 2.29 0.00 0.00 5.40
3523 3829 4.699522 GGCTGTTCGGCGGTTCCT 62.700 66.667 7.21 0.00 0.00 3.36
3524 3830 3.423154 GCTGTTCGGCGGTTCCTG 61.423 66.667 7.21 0.00 0.00 3.86
3525 3831 2.742372 CTGTTCGGCGGTTCCTGG 60.742 66.667 7.21 0.00 0.00 4.45
3526 3832 4.323477 TGTTCGGCGGTTCCTGGG 62.323 66.667 7.21 0.00 0.00 4.45
3554 3860 4.514577 CGACACAGCGGGGGCTAG 62.515 72.222 0.00 0.00 0.00 3.42
3555 3861 4.162690 GACACAGCGGGGGCTAGG 62.163 72.222 0.00 0.00 0.00 3.02
3557 3863 4.473520 CACAGCGGGGGCTAGGTG 62.474 72.222 0.00 5.40 41.17 4.00
3564 3870 4.162690 GGGGCTAGGTGGAGCGTG 62.163 72.222 0.00 0.00 43.83 5.34
3565 3871 4.840005 GGGCTAGGTGGAGCGTGC 62.840 72.222 0.00 0.00 43.83 5.34
3566 3872 4.840005 GGCTAGGTGGAGCGTGCC 62.840 72.222 0.00 0.00 43.83 5.01
3567 3873 3.775654 GCTAGGTGGAGCGTGCCT 61.776 66.667 0.00 0.00 36.47 4.75
3568 3874 2.185350 CTAGGTGGAGCGTGCCTG 59.815 66.667 0.00 0.00 34.07 4.85
3569 3875 4.082523 TAGGTGGAGCGTGCCTGC 62.083 66.667 0.00 0.00 34.07 4.85
3588 3894 3.479203 CAGGGCGGCTATGGTGGA 61.479 66.667 9.56 0.00 0.00 4.02
3589 3895 2.448542 AGGGCGGCTATGGTGGAT 60.449 61.111 9.56 0.00 0.00 3.41
3590 3896 2.032681 GGGCGGCTATGGTGGATC 59.967 66.667 9.56 0.00 0.00 3.36
3591 3897 2.032681 GGCGGCTATGGTGGATCC 59.967 66.667 4.20 4.20 0.00 3.36
3592 3898 2.032681 GCGGCTATGGTGGATCCC 59.967 66.667 9.90 0.00 34.77 3.85
3593 3899 2.520536 GCGGCTATGGTGGATCCCT 61.521 63.158 9.90 0.00 34.77 4.20
3594 3900 1.674057 CGGCTATGGTGGATCCCTC 59.326 63.158 9.90 2.15 34.77 4.30
3595 3901 1.674057 GGCTATGGTGGATCCCTCG 59.326 63.158 9.90 0.00 34.77 4.63
3596 3902 0.832135 GGCTATGGTGGATCCCTCGA 60.832 60.000 9.90 0.00 34.77 4.04
3597 3903 1.270907 GCTATGGTGGATCCCTCGAT 58.729 55.000 9.90 7.91 34.77 3.59
3598 3904 1.205893 GCTATGGTGGATCCCTCGATC 59.794 57.143 9.90 0.00 43.73 3.69
3599 3905 2.813907 CTATGGTGGATCCCTCGATCT 58.186 52.381 9.90 0.00 43.90 2.75
3600 3906 1.638529 ATGGTGGATCCCTCGATCTC 58.361 55.000 9.90 0.00 43.90 2.75
3601 3907 0.823769 TGGTGGATCCCTCGATCTCG 60.824 60.000 9.90 0.00 43.90 4.04
3602 3908 3.211528 TGGTGGATCCCTCGATCTCGA 62.212 57.143 9.90 1.92 43.90 4.04
3613 3919 2.747436 TCGATCTCGATGCAGATTTGG 58.253 47.619 0.00 0.00 44.22 3.28
3614 3920 2.362077 TCGATCTCGATGCAGATTTGGA 59.638 45.455 0.00 0.00 44.22 3.53
3615 3921 3.006217 TCGATCTCGATGCAGATTTGGAT 59.994 43.478 0.00 0.00 44.22 3.41
3616 3922 3.367327 CGATCTCGATGCAGATTTGGATC 59.633 47.826 7.58 7.58 45.59 3.36
3620 3926 2.260844 GATGCAGATTTGGATCGGGA 57.739 50.000 1.93 0.00 41.40 5.14
3621 3927 1.876156 GATGCAGATTTGGATCGGGAC 59.124 52.381 1.93 0.00 41.40 4.46
3640 3946 2.271497 CCTCCAGAGGGCTGCAAG 59.729 66.667 5.74 0.00 44.87 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.413767 CGCCGATCGAAGTTGTCAGG 61.414 60.000 18.66 0.00 41.67 3.86
224 225 1.229428 CTTTGTGAGGCTTCGCTGAA 58.771 50.000 10.96 5.02 34.87 3.02
390 391 1.753078 CATGTGGGAGCAGCAGCAT 60.753 57.895 3.17 0.00 45.49 3.79
471 474 0.248296 CGGTGTTTCGTTGGTTGGTG 60.248 55.000 0.00 0.00 0.00 4.17
476 479 1.433837 GCTCACGGTGTTTCGTTGGT 61.434 55.000 8.17 0.00 41.86 3.67
728 734 1.421646 CTACATTCCTCCATCCCCCAC 59.578 57.143 0.00 0.00 0.00 4.61
729 735 1.010793 ACTACATTCCTCCATCCCCCA 59.989 52.381 0.00 0.00 0.00 4.96
740 746 7.363443 GGGCATCTAGATTCTAGACTACATTCC 60.363 44.444 22.58 11.89 0.00 3.01
742 748 6.439058 GGGGCATCTAGATTCTAGACTACATT 59.561 42.308 22.58 6.08 0.00 2.71
792 798 2.583593 GAGCCACGAGTCGGATGC 60.584 66.667 18.30 15.39 0.00 3.91
831 866 1.179174 GCCTTTTCCCACTTTCCGCT 61.179 55.000 0.00 0.00 0.00 5.52
896 941 4.129737 ATCACAGCCGTCCGTCCG 62.130 66.667 0.00 0.00 0.00 4.79
933 978 3.054503 CGAGAGACGACCACCCGT 61.055 66.667 0.00 0.00 46.43 5.28
934 979 4.477975 GCGAGAGACGACCACCCG 62.478 72.222 0.00 0.00 45.77 5.28
935 980 3.053849 GAGCGAGAGACGACCACCC 62.054 68.421 0.00 0.00 45.77 4.61
936 981 2.486042 GAGCGAGAGACGACCACC 59.514 66.667 0.00 0.00 45.77 4.61
937 982 1.984321 GAGGAGCGAGAGACGACCAC 61.984 65.000 0.00 0.00 45.77 4.16
938 983 1.745864 GAGGAGCGAGAGACGACCA 60.746 63.158 0.00 0.00 45.77 4.02
939 984 2.474612 GGAGGAGCGAGAGACGACC 61.475 68.421 0.00 0.00 45.77 4.79
940 985 2.815298 CGGAGGAGCGAGAGACGAC 61.815 68.421 0.00 0.00 45.77 4.34
941 986 2.511829 CGGAGGAGCGAGAGACGA 60.512 66.667 0.00 0.00 45.77 4.20
942 987 4.244802 GCGGAGGAGCGAGAGACG 62.245 72.222 0.00 0.00 45.66 4.18
943 988 3.894947 GGCGGAGGAGCGAGAGAC 61.895 72.222 0.00 0.00 38.18 3.36
981 1027 0.959553 TGGAGAACTGACGGTCTGAC 59.040 55.000 20.01 13.18 0.00 3.51
982 1028 1.546029 CATGGAGAACTGACGGTCTGA 59.454 52.381 20.01 0.00 0.00 3.27
983 1029 1.404717 CCATGGAGAACTGACGGTCTG 60.405 57.143 5.56 12.76 0.00 3.51
984 1030 0.898320 CCATGGAGAACTGACGGTCT 59.102 55.000 5.56 0.00 0.00 3.85
985 1031 0.741221 GCCATGGAGAACTGACGGTC 60.741 60.000 18.40 0.00 0.00 4.79
987 1033 1.811266 CGCCATGGAGAACTGACGG 60.811 63.158 18.40 0.00 0.00 4.79
988 1034 1.811266 CCGCCATGGAGAACTGACG 60.811 63.158 18.40 6.54 42.00 4.35
989 1035 2.109126 GCCGCCATGGAGAACTGAC 61.109 63.158 18.40 0.00 42.00 3.51
990 1036 2.268920 GCCGCCATGGAGAACTGA 59.731 61.111 18.40 0.00 42.00 3.41
991 1037 3.197790 CGCCGCCATGGAGAACTG 61.198 66.667 18.40 0.00 40.56 3.16
1112 1176 3.711782 AGGGGGAGGAGAAGGGGG 61.712 72.222 0.00 0.00 0.00 5.40
1113 1177 2.367512 CAGGGGGAGGAGAAGGGG 60.368 72.222 0.00 0.00 0.00 4.79
1125 1195 2.966309 GAAAACGTCGCTGCAGGGG 61.966 63.158 28.30 16.76 0.00 4.79
1181 1259 1.110442 CCCACAGTAGCAGAGAGGAG 58.890 60.000 0.00 0.00 0.00 3.69
1182 1260 0.972983 GCCCACAGTAGCAGAGAGGA 60.973 60.000 0.00 0.00 0.00 3.71
1183 1261 0.975040 AGCCCACAGTAGCAGAGAGG 60.975 60.000 0.00 0.00 0.00 3.69
1184 1262 0.175302 CAGCCCACAGTAGCAGAGAG 59.825 60.000 0.00 0.00 0.00 3.20
1185 1263 1.260538 CCAGCCCACAGTAGCAGAGA 61.261 60.000 0.00 0.00 0.00 3.10
1186 1264 1.220206 CCAGCCCACAGTAGCAGAG 59.780 63.158 0.00 0.00 0.00 3.35
1187 1265 1.536418 ACCAGCCCACAGTAGCAGA 60.536 57.895 0.00 0.00 0.00 4.26
1188 1266 1.376424 CACCAGCCCACAGTAGCAG 60.376 63.158 0.00 0.00 0.00 4.24
1247 1326 0.538287 AGCTGAAACTGGAAGCACCC 60.538 55.000 0.00 0.00 39.47 4.61
1270 1349 1.896660 GAAGGCGTGAACCTGGCAA 60.897 57.895 0.00 0.00 39.93 4.52
1273 1352 2.317609 CGTGAAGGCGTGAACCTGG 61.318 63.158 0.00 0.00 39.93 4.45
1274 1353 2.317609 CCGTGAAGGCGTGAACCTG 61.318 63.158 0.00 0.00 39.93 4.00
1287 1367 4.617520 TTTCCTGCGCTGCCGTGA 62.618 61.111 9.73 0.00 36.67 4.35
1344 1424 3.809832 CAGGATTTCACGTCAGTTTCAGT 59.190 43.478 0.00 0.00 0.00 3.41
1427 1508 5.240623 AGCAAGGAGAATACTACGAGAGATG 59.759 44.000 0.00 0.00 31.08 2.90
1428 1509 5.240623 CAGCAAGGAGAATACTACGAGAGAT 59.759 44.000 0.00 0.00 31.08 2.75
1429 1510 4.576873 CAGCAAGGAGAATACTACGAGAGA 59.423 45.833 0.00 0.00 31.08 3.10
1430 1511 4.576873 TCAGCAAGGAGAATACTACGAGAG 59.423 45.833 0.00 0.00 31.08 3.20
1431 1512 4.524053 TCAGCAAGGAGAATACTACGAGA 58.476 43.478 0.00 0.00 31.08 4.04
1432 1513 4.576873 TCTCAGCAAGGAGAATACTACGAG 59.423 45.833 0.00 0.00 40.81 4.18
1433 1514 4.524053 TCTCAGCAAGGAGAATACTACGA 58.476 43.478 0.00 0.00 40.81 3.43
1434 1515 4.791411 GCTCTCAGCAAGGAGAATACTACG 60.791 50.000 4.63 0.00 42.99 3.51
1435 1516 4.340950 AGCTCTCAGCAAGGAGAATACTAC 59.659 45.833 0.00 0.00 45.56 2.73
1436 1517 4.541705 AGCTCTCAGCAAGGAGAATACTA 58.458 43.478 0.00 0.00 45.56 1.82
1437 1518 3.373830 AGCTCTCAGCAAGGAGAATACT 58.626 45.455 0.00 1.07 45.56 2.12
1438 1519 3.384467 AGAGCTCTCAGCAAGGAGAATAC 59.616 47.826 11.45 0.00 45.56 1.89
1439 1520 3.384146 CAGAGCTCTCAGCAAGGAGAATA 59.616 47.826 14.96 0.00 45.56 1.75
1514 1595 5.012871 AGCTCATTGAGATGCATATGGTACT 59.987 40.000 17.87 0.00 33.14 2.73
1519 1600 6.598064 TGGATAAGCTCATTGAGATGCATATG 59.402 38.462 17.87 0.00 33.14 1.78
1520 1601 6.718294 TGGATAAGCTCATTGAGATGCATAT 58.282 36.000 17.87 6.13 33.14 1.78
1528 1609 6.293516 GCTGAATTCTGGATAAGCTCATTGAG 60.294 42.308 9.40 9.40 0.00 3.02
1536 1617 6.140303 TGAATTGCTGAATTCTGGATAAGC 57.860 37.500 13.50 9.80 45.41 3.09
1552 1633 6.444633 CAATGGAGATAACTGGATGAATTGC 58.555 40.000 0.00 0.00 0.00 3.56
1553 1634 6.516194 GCCAATGGAGATAACTGGATGAATTG 60.516 42.308 2.05 0.00 0.00 2.32
1582 1663 7.046033 GGTACTGTACTGTTTACCAGCAATAT 58.954 38.462 16.79 0.00 45.68 1.28
1594 1675 6.424883 AGCAGATAGTAGGTACTGTACTGTT 58.575 40.000 16.79 6.65 41.52 3.16
1595 1676 6.003859 AGCAGATAGTAGGTACTGTACTGT 57.996 41.667 16.79 10.46 41.52 3.55
1596 1677 7.218614 AGTAGCAGATAGTAGGTACTGTACTG 58.781 42.308 16.79 6.57 44.61 2.74
1597 1678 7.070946 TGAGTAGCAGATAGTAGGTACTGTACT 59.929 40.741 16.79 11.59 45.82 2.73
1598 1679 7.215789 TGAGTAGCAGATAGTAGGTACTGTAC 58.784 42.308 9.46 9.46 45.82 2.90
1599 1680 7.370905 TGAGTAGCAGATAGTAGGTACTGTA 57.629 40.000 8.77 0.00 45.82 2.74
1600 1681 6.249911 TGAGTAGCAGATAGTAGGTACTGT 57.750 41.667 8.77 0.00 45.82 3.55
1601 1682 6.768861 AGTTGAGTAGCAGATAGTAGGTACTG 59.231 42.308 8.77 0.00 45.82 2.74
1603 1684 6.513720 GCAGTTGAGTAGCAGATAGTAGGTAC 60.514 46.154 0.00 0.00 38.60 3.34
1604 1685 5.531659 GCAGTTGAGTAGCAGATAGTAGGTA 59.468 44.000 0.00 0.00 0.00 3.08
1605 1686 4.339814 GCAGTTGAGTAGCAGATAGTAGGT 59.660 45.833 0.00 0.00 0.00 3.08
1606 1687 4.582656 AGCAGTTGAGTAGCAGATAGTAGG 59.417 45.833 0.00 0.00 0.00 3.18
1607 1688 5.766150 AGCAGTTGAGTAGCAGATAGTAG 57.234 43.478 0.00 0.00 0.00 2.57
1608 1689 5.163509 CCAAGCAGTTGAGTAGCAGATAGTA 60.164 44.000 0.00 0.00 35.46 1.82
1609 1690 4.382470 CCAAGCAGTTGAGTAGCAGATAGT 60.382 45.833 0.00 0.00 35.46 2.12
1610 1691 4.118410 CCAAGCAGTTGAGTAGCAGATAG 58.882 47.826 0.00 0.00 35.46 2.08
1611 1692 3.679917 GCCAAGCAGTTGAGTAGCAGATA 60.680 47.826 0.00 0.00 35.46 1.98
1612 1693 2.938756 GCCAAGCAGTTGAGTAGCAGAT 60.939 50.000 0.00 0.00 35.46 2.90
1613 1694 1.609061 GCCAAGCAGTTGAGTAGCAGA 60.609 52.381 0.00 0.00 35.46 4.26
1614 1695 0.801251 GCCAAGCAGTTGAGTAGCAG 59.199 55.000 0.00 0.00 35.46 4.24
1615 1696 0.950555 CGCCAAGCAGTTGAGTAGCA 60.951 55.000 0.00 0.00 35.46 3.49
1616 1697 1.639298 CCGCCAAGCAGTTGAGTAGC 61.639 60.000 0.00 0.00 35.46 3.58
1617 1698 0.037326 TCCGCCAAGCAGTTGAGTAG 60.037 55.000 0.00 0.00 35.46 2.57
1618 1699 0.613260 ATCCGCCAAGCAGTTGAGTA 59.387 50.000 0.00 0.00 35.46 2.59
1619 1700 0.674895 GATCCGCCAAGCAGTTGAGT 60.675 55.000 0.00 0.00 35.46 3.41
1620 1701 0.674581 TGATCCGCCAAGCAGTTGAG 60.675 55.000 0.00 0.00 35.46 3.02
1621 1702 0.674581 CTGATCCGCCAAGCAGTTGA 60.675 55.000 0.00 0.00 35.46 3.18
1622 1703 0.957395 ACTGATCCGCCAAGCAGTTG 60.957 55.000 0.00 0.00 38.34 3.16
1623 1704 0.613260 TACTGATCCGCCAAGCAGTT 59.387 50.000 8.92 0.00 41.43 3.16
1624 1705 0.108138 GTACTGATCCGCCAAGCAGT 60.108 55.000 8.68 8.68 43.40 4.40
1625 1706 1.148157 CGTACTGATCCGCCAAGCAG 61.148 60.000 0.00 0.00 34.65 4.24
1626 1707 1.153647 CGTACTGATCCGCCAAGCA 60.154 57.895 0.00 0.00 0.00 3.91
1627 1708 0.739813 AACGTACTGATCCGCCAAGC 60.740 55.000 0.00 0.00 0.00 4.01
1632 1713 0.713883 CACACAACGTACTGATCCGC 59.286 55.000 0.00 0.00 0.00 5.54
1642 1723 7.815549 TCGCCATATAATAATATCACACAACGT 59.184 33.333 0.00 0.00 0.00 3.99
1662 1753 1.401552 CACGTTCCAATTCATCGCCAT 59.598 47.619 0.00 0.00 0.00 4.40
1679 1771 2.039818 TCCTCTAGTGCTAGGTCACG 57.960 55.000 6.41 0.00 41.61 4.35
1682 1774 4.465886 TCAAGATCCTCTAGTGCTAGGTC 58.534 47.826 6.41 1.68 34.30 3.85
1708 1896 5.183904 GGGTTGCAGACAGAAATAAGATTGT 59.816 40.000 0.00 0.00 0.00 2.71
1740 1928 0.529337 CAGTCATAGCAGACGCCTGG 60.529 60.000 0.00 0.00 43.24 4.45
1746 1934 5.931441 AGTTTGTTTCAGTCATAGCAGAC 57.069 39.130 0.00 0.00 38.81 3.51
1751 1939 7.042992 TCGTGTGTAAGTTTGTTTCAGTCATAG 60.043 37.037 0.00 0.00 0.00 2.23
1786 1974 3.733337 ACAATGCGAGTCTTTCTCTGTT 58.267 40.909 0.00 0.00 40.75 3.16
1803 1991 7.557358 TGCTAATGGTTATCACATTCAGACAAT 59.443 33.333 0.00 0.00 39.18 2.71
1891 2087 4.261825 GCTCACTGATATGAGGTAGGACAC 60.262 50.000 5.02 0.00 45.35 3.67
1920 2116 3.885297 ACCTGAGAACAACCAGAAACATG 59.115 43.478 0.00 0.00 32.37 3.21
2113 2311 1.281867 CATCAGGCCCTCACCAACTTA 59.718 52.381 0.00 0.00 0.00 2.24
2220 2419 3.052036 CACACCACAAAACAATGCTAGC 58.948 45.455 8.10 8.10 0.00 3.42
2229 2428 8.376942 CAAACAACTAAATACACACCACAAAAC 58.623 33.333 0.00 0.00 0.00 2.43
2539 2739 2.355513 CCCAAGTGAAGATCCCAGTCTG 60.356 54.545 0.00 0.00 0.00 3.51
2993 3210 2.132089 TACCGGGCAACTTTCCCCTG 62.132 60.000 6.32 0.00 40.75 4.45
2997 3214 0.323957 AGAGTACCGGGCAACTTTCC 59.676 55.000 6.32 0.00 0.00 3.13
3000 3217 1.003718 GCAGAGTACCGGGCAACTT 60.004 57.895 6.32 0.00 0.00 2.66
3001 3218 2.663196 GCAGAGTACCGGGCAACT 59.337 61.111 6.32 6.20 0.00 3.16
3003 3220 3.307906 ACGCAGAGTACCGGGCAA 61.308 61.111 6.32 0.00 0.00 4.52
3004 3221 4.063967 CACGCAGAGTACCGGGCA 62.064 66.667 6.32 0.00 0.00 5.36
3005 3222 4.814294 CCACGCAGAGTACCGGGC 62.814 72.222 6.32 0.00 0.00 6.13
3006 3223 3.064987 CTCCACGCAGAGTACCGGG 62.065 68.421 6.32 0.00 0.00 5.73
3007 3224 2.490217 CTCCACGCAGAGTACCGG 59.510 66.667 0.00 0.00 0.00 5.28
3008 3225 2.202623 GCTCCACGCAGAGTACCG 60.203 66.667 4.42 0.00 38.92 4.02
3009 3226 2.970639 TGCTCCACGCAGAGTACC 59.029 61.111 4.42 0.00 45.47 3.34
3017 3234 0.745845 ATTGACTCCATGCTCCACGC 60.746 55.000 0.00 0.00 39.77 5.34
3018 3235 1.012086 CATTGACTCCATGCTCCACG 58.988 55.000 0.00 0.00 0.00 4.94
3020 3237 1.407851 GCTCATTGACTCCATGCTCCA 60.408 52.381 0.00 0.00 0.00 3.86
3021 3238 1.134159 AGCTCATTGACTCCATGCTCC 60.134 52.381 0.00 0.00 0.00 4.70
3022 3239 2.328819 AGCTCATTGACTCCATGCTC 57.671 50.000 0.00 0.00 0.00 4.26
3023 3240 2.366533 CAAGCTCATTGACTCCATGCT 58.633 47.619 0.00 0.00 41.83 3.79
3052 3338 2.952273 CATGGTGTTCATGCGCATG 58.048 52.632 38.48 38.48 45.58 4.06
3068 3354 1.033202 TGCAGTGATGAATGCGCCAT 61.033 50.000 4.18 0.00 45.54 4.40
3071 3357 1.206745 GCATGCAGTGATGAATGCGC 61.207 55.000 14.21 0.00 45.54 6.09
3102 3388 2.203983 TGGAGCTCCTGGCCAGAA 60.204 61.111 34.91 14.57 43.05 3.02
3108 3394 0.815734 CATTTTGCTGGAGCTCCTGG 59.184 55.000 33.21 25.46 42.66 4.45
3130 3417 7.552459 TCTGTAACGATACATTTCATGAGGAA 58.448 34.615 5.96 0.00 41.09 3.36
3141 3428 5.416947 GTTGTTCCCTCTGTAACGATACAT 58.583 41.667 5.96 0.00 41.09 2.29
3142 3429 4.322198 GGTTGTTCCCTCTGTAACGATACA 60.322 45.833 5.36 5.36 39.70 2.29
3144 3431 4.091549 AGGTTGTTCCCTCTGTAACGATA 58.908 43.478 0.00 0.00 36.75 2.92
3146 3433 2.322658 AGGTTGTTCCCTCTGTAACGA 58.677 47.619 0.00 0.00 36.75 3.85
3149 3436 3.836562 GGAGTAGGTTGTTCCCTCTGTAA 59.163 47.826 0.00 0.00 35.97 2.41
3155 3442 2.907042 CAAGAGGAGTAGGTTGTTCCCT 59.093 50.000 0.00 0.00 38.70 4.20
3162 3449 5.523588 TCATCTGATCAAGAGGAGTAGGTT 58.476 41.667 0.00 0.00 40.71 3.50
3172 3459 7.911130 ACTAAGATCCTTCATCTGATCAAGA 57.089 36.000 2.57 0.00 41.47 3.02
3184 3471 3.536570 GAGGGTGCAACTAAGATCCTTC 58.463 50.000 0.00 0.00 36.74 3.46
3200 3487 4.741239 ATGGCTGGGGACGAGGGT 62.741 66.667 0.00 0.00 0.00 4.34
3220 3507 2.180131 CTGCTGTCAAAGAGCGGCAC 62.180 60.000 1.45 0.00 41.47 5.01
3228 3515 1.347707 TGAGGGGTACTGCTGTCAAAG 59.652 52.381 0.00 0.00 0.00 2.77
3230 3517 1.429930 TTGAGGGGTACTGCTGTCAA 58.570 50.000 0.00 0.00 0.00 3.18
3231 3518 1.555075 GATTGAGGGGTACTGCTGTCA 59.445 52.381 0.00 0.00 0.00 3.58
3232 3519 1.555075 TGATTGAGGGGTACTGCTGTC 59.445 52.381 0.00 0.00 0.00 3.51
3233 3520 1.556911 CTGATTGAGGGGTACTGCTGT 59.443 52.381 0.66 0.66 0.00 4.40
3234 3521 1.745141 GCTGATTGAGGGGTACTGCTG 60.745 57.143 0.00 0.00 0.00 4.41
3235 3522 0.543749 GCTGATTGAGGGGTACTGCT 59.456 55.000 0.00 0.00 0.00 4.24
3236 3523 0.543749 AGCTGATTGAGGGGTACTGC 59.456 55.000 0.00 0.00 0.00 4.40
3239 3526 1.383523 GCAAGCTGATTGAGGGGTAC 58.616 55.000 10.23 0.00 41.83 3.34
3240 3527 0.255890 GGCAAGCTGATTGAGGGGTA 59.744 55.000 10.23 0.00 41.83 3.69
3241 3528 1.000396 GGCAAGCTGATTGAGGGGT 60.000 57.895 10.23 0.00 41.83 4.95
3243 3530 0.465097 ATCGGCAAGCTGATTGAGGG 60.465 55.000 10.23 0.00 41.83 4.30
3248 3550 2.421424 GTCAAAGATCGGCAAGCTGATT 59.579 45.455 16.79 1.15 41.66 2.57
3284 3586 2.697761 TAGGAGCAGCGACACCGTC 61.698 63.158 0.00 0.00 38.24 4.79
3314 3616 0.464036 TTTGTCGAGCCCGAGCATAT 59.536 50.000 0.00 0.00 46.52 1.78
3315 3617 0.248012 TTTTGTCGAGCCCGAGCATA 59.752 50.000 0.00 0.00 46.52 3.14
3325 3627 7.812648 TGGAGTAAACCAAATATTTTGTCGAG 58.187 34.615 5.46 0.00 36.96 4.04
3336 3638 7.259088 AGTGAGATACTGGAGTAAACCAAAT 57.741 36.000 0.00 0.00 38.49 2.32
3395 3701 4.243008 GGGGGAAGAGGCGCTAGC 62.243 72.222 7.64 4.06 44.18 3.42
3506 3812 4.699522 AGGAACCGCCGAACAGCC 62.700 66.667 0.00 0.00 43.43 4.85
3507 3813 3.423154 CAGGAACCGCCGAACAGC 61.423 66.667 0.00 0.00 43.43 4.40
3508 3814 2.742372 CCAGGAACCGCCGAACAG 60.742 66.667 0.00 0.00 43.43 3.16
3509 3815 4.323477 CCCAGGAACCGCCGAACA 62.323 66.667 0.00 0.00 43.43 3.18
3547 3853 4.162690 CACGCTCCACCTAGCCCC 62.163 72.222 0.00 0.00 39.43 5.80
3548 3854 4.840005 GCACGCTCCACCTAGCCC 62.840 72.222 0.00 0.00 39.43 5.19
3549 3855 4.840005 GGCACGCTCCACCTAGCC 62.840 72.222 0.00 0.00 39.43 3.93
3550 3856 3.775654 AGGCACGCTCCACCTAGC 61.776 66.667 0.00 0.00 39.21 3.42
3551 3857 2.185350 CAGGCACGCTCCACCTAG 59.815 66.667 0.00 0.00 30.84 3.02
3552 3858 4.082523 GCAGGCACGCTCCACCTA 62.083 66.667 0.00 0.00 30.84 3.08
3571 3877 2.738213 GATCCACCATAGCCGCCCTG 62.738 65.000 0.00 0.00 0.00 4.45
3572 3878 2.448542 ATCCACCATAGCCGCCCT 60.449 61.111 0.00 0.00 0.00 5.19
3573 3879 2.032681 GATCCACCATAGCCGCCC 59.967 66.667 0.00 0.00 0.00 6.13
3574 3880 2.032681 GGATCCACCATAGCCGCC 59.967 66.667 6.95 0.00 38.79 6.13
3575 3881 2.032681 GGGATCCACCATAGCCGC 59.967 66.667 15.23 0.00 41.20 6.53
3576 3882 1.674057 GAGGGATCCACCATAGCCG 59.326 63.158 15.23 0.00 41.20 5.52
3577 3883 0.832135 TCGAGGGATCCACCATAGCC 60.832 60.000 15.23 0.00 41.20 3.93
3578 3884 1.205893 GATCGAGGGATCCACCATAGC 59.794 57.143 15.23 0.00 42.72 2.97
3594 3900 2.747436 TCCAAATCTGCATCGAGATCG 58.253 47.619 0.00 0.00 41.45 3.69
3595 3901 3.367327 CGATCCAAATCTGCATCGAGATC 59.633 47.826 0.00 0.02 40.48 2.75
3596 3902 3.324117 CGATCCAAATCTGCATCGAGAT 58.676 45.455 0.00 0.00 40.48 2.75
3597 3903 2.546584 CCGATCCAAATCTGCATCGAGA 60.547 50.000 0.00 0.00 40.48 4.04
3598 3904 1.797046 CCGATCCAAATCTGCATCGAG 59.203 52.381 0.00 0.00 40.48 4.04
3599 3905 1.541015 CCCGATCCAAATCTGCATCGA 60.541 52.381 0.00 0.00 40.48 3.59
3600 3906 0.870393 CCCGATCCAAATCTGCATCG 59.130 55.000 0.00 0.00 38.28 3.84
3601 3907 1.876156 GTCCCGATCCAAATCTGCATC 59.124 52.381 0.00 0.00 0.00 3.91
3602 3908 1.811558 CGTCCCGATCCAAATCTGCAT 60.812 52.381 0.00 0.00 0.00 3.96
3603 3909 0.461870 CGTCCCGATCCAAATCTGCA 60.462 55.000 0.00 0.00 0.00 4.41
3604 3910 1.776034 GCGTCCCGATCCAAATCTGC 61.776 60.000 0.00 0.00 0.00 4.26
3605 3911 1.160329 GGCGTCCCGATCCAAATCTG 61.160 60.000 0.00 0.00 0.00 2.90
3606 3912 1.146263 GGCGTCCCGATCCAAATCT 59.854 57.895 0.00 0.00 0.00 2.40
3607 3913 0.880718 GAGGCGTCCCGATCCAAATC 60.881 60.000 0.00 0.00 35.76 2.17
3608 3914 1.146263 GAGGCGTCCCGATCCAAAT 59.854 57.895 0.00 0.00 35.76 2.32
3609 3915 2.582436 GAGGCGTCCCGATCCAAA 59.418 61.111 0.00 0.00 35.76 3.28
3610 3916 3.467226 GGAGGCGTCCCGATCCAA 61.467 66.667 14.75 0.00 36.76 3.53
3611 3917 4.770362 TGGAGGCGTCCCGATCCA 62.770 66.667 22.25 0.26 43.15 3.41
3612 3918 3.917760 CTGGAGGCGTCCCGATCC 61.918 72.222 22.25 0.00 43.15 3.36
3613 3919 2.833582 TCTGGAGGCGTCCCGATC 60.834 66.667 22.25 0.00 43.15 3.69
3614 3920 2.835431 CTCTGGAGGCGTCCCGAT 60.835 66.667 22.25 0.00 43.15 4.18
3624 3930 2.438075 GCTTGCAGCCCTCTGGAG 60.438 66.667 0.00 0.00 41.73 3.86
3625 3931 4.399395 CGCTTGCAGCCCTCTGGA 62.399 66.667 0.00 0.00 38.18 3.86


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

AutoCloner maintained by Alex Coulton.