Multiple sequence alignment - TraesCS4A01G246000

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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 TraesCS4A01G246000 chr4A 100.000 3943 0 0 1 3943 556536589 556540531 0.000000e+00 7282.0
1 TraesCS4A01G246000 chr4A 95.082 61 3 0 3673 3733 675226986 675227046 3.240000e-16 97.1
2 TraesCS4A01G246000 chr4A 95.082 61 3 0 3673 3733 675295478 675295538 3.240000e-16 97.1
3 TraesCS4A01G246000 chr4D 89.810 3474 184 69 4 3372 43553125 43556533 0.000000e+00 4298.0
4 TraesCS4A01G246000 chr4D 93.204 309 16 3 3367 3673 43556568 43556873 2.160000e-122 449.0
5 TraesCS4A01G246000 chr4B 91.276 1811 74 39 2063 3823 63230615 63228839 0.000000e+00 2392.0
6 TraesCS4A01G246000 chr4B 86.052 2072 121 79 4 1996 63232687 63230705 0.000000e+00 2071.0
7 TraesCS4A01G246000 chr4B 94.215 121 7 0 3823 3943 63228878 63228758 6.730000e-43 185.0
8 TraesCS4A01G246000 chr5A 84.431 167 22 4 1001 1165 59596625 59596789 1.130000e-35 161.0
9 TraesCS4A01G246000 chr5D 84.049 163 22 4 1001 1161 68693709 68693869 1.900000e-33 154.0
10 TraesCS4A01G246000 chr5D 82.424 165 16 4 3673 3824 373397474 373397638 8.890000e-27 132.0
11 TraesCS4A01G246000 chr5D 97.059 34 1 0 3553 3586 482320842 482320875 1.530000e-04 58.4
12 TraesCS4A01G246000 chr5B 83.436 163 23 4 1001 1161 74633622 74633782 8.830000e-32 148.0
13 TraesCS4A01G246000 chrUn 95.082 61 3 0 3673 3733 330523842 330523902 3.240000e-16 97.1
14 TraesCS4A01G246000 chrUn 95.082 61 3 0 3673 3733 376008092 376008032 3.240000e-16 97.1
15 TraesCS4A01G246000 chr7A 91.667 60 5 0 3673 3732 271618710 271618769 2.520000e-12 84.2
16 TraesCS4A01G246000 chr7A 100.000 29 0 0 3561 3589 700161207 700161179 2.000000e-03 54.7
17 TraesCS4A01G246000 chr6B 95.000 40 2 0 3551 3590 37661032 37660993 3.290000e-06 63.9
18 TraesCS4A01G246000 chr7B 78.947 95 15 5 3498 3588 490685094 490685187 4.260000e-05 60.2


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 TraesCS4A01G246000 chr4A 556536589 556540531 3942 False 7282.000000 7282 100.000000 1 3943 1 chr4A.!!$F1 3942
1 TraesCS4A01G246000 chr4D 43553125 43556873 3748 False 2373.500000 4298 91.507000 4 3673 2 chr4D.!!$F1 3669
2 TraesCS4A01G246000 chr4B 63228758 63232687 3929 True 1549.333333 2392 90.514333 4 3943 3 chr4B.!!$R1 3939

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
759 823 0.107410 TCTCTCTCTCTCTCGGTGCC 60.107 60.0 0.00 0.0 0.00 5.01 F
1335 1447 0.315568 CGGCTCAGGTGTATCCTAGC 59.684 60.0 0.00 0.0 46.24 3.42 F
1456 1568 0.390735 ATCGCGGTACAACCAGTTCC 60.391 55.0 6.13 0.0 38.47 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1774 1.514087 GTTCACCGGGTCGCTCATA 59.486 57.895 6.32 0.0 0.0 2.15 R
2834 3018 1.800805 CAGACTGAGTTGGCATTCGT 58.199 50.000 0.00 0.0 0.0 3.85 R
2950 3134 3.270027 TCCCATATTTGTCACTTCGCAG 58.730 45.455 0.00 0.0 0.0 5.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.611673 CCTTTTCCATGTGAGCCGAGT 60.612 52.381 0.00 0.00 0.00 4.18
55 56 1.466167 CTTTTCCATGTGAGCCGAGTG 59.534 52.381 0.00 0.00 0.00 3.51
70 76 1.336440 CGAGTGGCAATGGTCAACAAA 59.664 47.619 0.00 0.00 0.00 2.83
71 77 2.030007 CGAGTGGCAATGGTCAACAAAT 60.030 45.455 0.00 0.00 0.00 2.32
72 78 3.578688 GAGTGGCAATGGTCAACAAATC 58.421 45.455 0.00 0.00 0.00 2.17
73 79 2.964464 AGTGGCAATGGTCAACAAATCA 59.036 40.909 0.00 0.00 0.00 2.57
74 80 3.006110 AGTGGCAATGGTCAACAAATCAG 59.994 43.478 0.00 0.00 0.00 2.90
75 81 3.005684 GTGGCAATGGTCAACAAATCAGA 59.994 43.478 0.00 0.00 0.00 3.27
76 82 3.640498 TGGCAATGGTCAACAAATCAGAA 59.360 39.130 0.00 0.00 0.00 3.02
77 83 4.100653 TGGCAATGGTCAACAAATCAGAAA 59.899 37.500 0.00 0.00 0.00 2.52
78 84 5.221682 TGGCAATGGTCAACAAATCAGAAAT 60.222 36.000 0.00 0.00 0.00 2.17
79 85 5.349543 GGCAATGGTCAACAAATCAGAAATC 59.650 40.000 0.00 0.00 0.00 2.17
80 86 5.927689 GCAATGGTCAACAAATCAGAAATCA 59.072 36.000 0.00 0.00 0.00 2.57
81 87 6.128742 GCAATGGTCAACAAATCAGAAATCAC 60.129 38.462 0.00 0.00 0.00 3.06
82 88 6.906157 ATGGTCAACAAATCAGAAATCACT 57.094 33.333 0.00 0.00 0.00 3.41
83 89 6.713762 TGGTCAACAAATCAGAAATCACTT 57.286 33.333 0.00 0.00 0.00 3.16
84 90 6.738114 TGGTCAACAAATCAGAAATCACTTC 58.262 36.000 0.00 0.00 0.00 3.01
85 91 6.320926 TGGTCAACAAATCAGAAATCACTTCA 59.679 34.615 0.00 0.00 36.40 3.02
88 94 5.712152 ACAAATCAGAAATCACTTCACCC 57.288 39.130 0.00 0.00 36.40 4.61
103 109 2.113139 CCCCACACCACACTGACC 59.887 66.667 0.00 0.00 0.00 4.02
190 196 7.006509 ACTAAACTAAACTAAAACCCTTCCCC 58.993 38.462 0.00 0.00 0.00 4.81
194 200 6.387127 ACTAAACTAAAACCCTTCCCCAAAT 58.613 36.000 0.00 0.00 0.00 2.32
196 202 8.181524 ACTAAACTAAAACCCTTCCCCAAATAT 58.818 33.333 0.00 0.00 0.00 1.28
197 203 9.703677 CTAAACTAAAACCCTTCCCCAAATATA 57.296 33.333 0.00 0.00 0.00 0.86
198 204 8.603898 AAACTAAAACCCTTCCCCAAATATAG 57.396 34.615 0.00 0.00 0.00 1.31
199 205 7.533923 ACTAAAACCCTTCCCCAAATATAGA 57.466 36.000 0.00 0.00 0.00 1.98
205 211 5.104409 CCCTTCCCCAAATATAGATCTCCT 58.896 45.833 0.00 0.00 0.00 3.69
213 219 1.822506 TATAGATCTCCTGCCGTCCG 58.177 55.000 0.00 0.00 0.00 4.79
337 354 3.873910 CCGGGGAGCAATATTATACAGG 58.126 50.000 0.00 0.00 0.00 4.00
383 400 3.265995 ACAAATGGGGACGGAGAATTACT 59.734 43.478 0.00 0.00 0.00 2.24
384 401 3.840124 AATGGGGACGGAGAATTACTC 57.160 47.619 0.00 0.00 44.24 2.59
404 421 2.504175 TCCTAATTTCTTCTCCACCCCG 59.496 50.000 0.00 0.00 0.00 5.73
458 488 0.457851 CTTCCACTAGCTGGTCTCCG 59.542 60.000 0.00 0.00 41.52 4.63
459 489 0.970937 TTCCACTAGCTGGTCTCCGG 60.971 60.000 0.00 0.00 41.52 5.14
460 490 1.682684 CCACTAGCTGGTCTCCGGT 60.683 63.158 0.00 0.00 34.90 5.28
503 533 4.517703 GTCCGTCGACTCCGAGCG 62.518 72.222 14.70 0.00 46.52 5.03
504 534 4.747529 TCCGTCGACTCCGAGCGA 62.748 66.667 14.70 9.83 46.52 4.93
534 564 1.927210 CGGTTCTGGATTCATCGCG 59.073 57.895 0.00 0.00 0.00 5.87
647 699 0.681243 GGAATCTTGGAGGGTGTGGC 60.681 60.000 0.00 0.00 0.00 5.01
697 749 2.023461 CGTCCGCACGCAACAAAA 59.977 55.556 0.00 0.00 39.69 2.44
740 792 4.162690 GCCGCGGGTTCATCCTCT 62.163 66.667 29.38 0.00 36.25 3.69
741 793 2.107141 CCGCGGGTTCATCCTCTC 59.893 66.667 20.10 0.00 36.25 3.20
742 794 2.427245 CCGCGGGTTCATCCTCTCT 61.427 63.158 20.10 0.00 36.25 3.10
743 795 1.066587 CGCGGGTTCATCCTCTCTC 59.933 63.158 0.00 0.00 36.25 3.20
744 796 1.388065 CGCGGGTTCATCCTCTCTCT 61.388 60.000 0.00 0.00 36.25 3.10
746 798 2.026905 GCGGGTTCATCCTCTCTCTCT 61.027 57.143 0.00 0.00 36.25 3.10
748 800 2.422803 CGGGTTCATCCTCTCTCTCTCT 60.423 54.545 0.00 0.00 36.25 3.10
759 823 0.107410 TCTCTCTCTCTCTCGGTGCC 60.107 60.000 0.00 0.00 0.00 5.01
776 840 2.435586 CCACTCCTGCCGCTTCTG 60.436 66.667 0.00 0.00 0.00 3.02
777 841 3.123620 CACTCCTGCCGCTTCTGC 61.124 66.667 0.00 0.00 0.00 4.26
778 842 4.400961 ACTCCTGCCGCTTCTGCC 62.401 66.667 0.00 0.00 35.36 4.85
856 930 1.153309 CCTGTGATGGCTGATGCGA 60.153 57.895 0.00 0.00 40.82 5.10
858 932 0.461516 CTGTGATGGCTGATGCGAGT 60.462 55.000 0.00 0.00 40.82 4.18
859 933 0.823460 TGTGATGGCTGATGCGAGTA 59.177 50.000 0.00 0.00 40.82 2.59
860 934 1.206849 TGTGATGGCTGATGCGAGTAA 59.793 47.619 0.00 0.00 40.82 2.24
861 935 2.158914 TGTGATGGCTGATGCGAGTAAT 60.159 45.455 0.00 0.00 40.82 1.89
862 936 3.069443 TGTGATGGCTGATGCGAGTAATA 59.931 43.478 0.00 0.00 40.82 0.98
863 937 3.430218 GTGATGGCTGATGCGAGTAATAC 59.570 47.826 0.00 0.00 40.82 1.89
864 938 3.069443 TGATGGCTGATGCGAGTAATACA 59.931 43.478 0.00 0.00 40.82 2.29
876 957 3.566322 CGAGTAATACAGAGTAGCAGCCT 59.434 47.826 0.00 0.00 0.00 4.58
929 1010 1.836166 TCTCTCCCATTTCCTGCTCTG 59.164 52.381 0.00 0.00 0.00 3.35
948 1029 1.443407 CAGATCTGCCGTGGTAGGG 59.557 63.158 10.38 0.00 0.00 3.53
949 1030 1.001760 AGATCTGCCGTGGTAGGGT 59.998 57.895 4.09 0.00 0.00 4.34
976 1057 2.103143 CGAGTAGCCGAGGTGCTG 59.897 66.667 0.00 0.00 42.77 4.41
983 1064 3.699894 CCGAGGTGCTGGTGAGCT 61.700 66.667 0.00 0.00 46.39 4.09
1037 1149 2.350895 CAACAGGATGGCCGTGGA 59.649 61.111 0.00 0.00 43.62 4.02
1056 1168 1.741032 GAGCTGCCACAGAGTGCTC 60.741 63.158 0.00 0.00 42.31 4.26
1157 1269 2.760385 GGTGGTCTCCCTCCTCGG 60.760 72.222 0.00 0.00 40.61 4.63
1158 1270 3.462678 GTGGTCTCCCTCCTCGGC 61.463 72.222 0.00 0.00 0.00 5.54
1159 1271 3.992641 TGGTCTCCCTCCTCGGCA 61.993 66.667 0.00 0.00 0.00 5.69
1160 1272 2.683933 GGTCTCCCTCCTCGGCAA 60.684 66.667 0.00 0.00 0.00 4.52
1161 1273 2.579738 GTCTCCCTCCTCGGCAAC 59.420 66.667 0.00 0.00 0.00 4.17
1215 1327 0.835941 ACCATCCTAGAGCCAAGCTG 59.164 55.000 0.00 0.00 39.88 4.24
1261 1373 1.277557 TCTTGAGCCAGAAGAGCTTCC 59.722 52.381 6.61 0.00 41.75 3.46
1317 1429 2.125912 CACCCTTCGACCAGCTCG 60.126 66.667 0.00 0.00 44.44 5.03
1320 1432 3.764466 CCTTCGACCAGCTCGGCT 61.764 66.667 2.50 0.00 43.16 5.52
1335 1447 0.315568 CGGCTCAGGTGTATCCTAGC 59.684 60.000 0.00 0.00 46.24 3.42
1337 1449 1.342819 GGCTCAGGTGTATCCTAGCAG 59.657 57.143 13.09 2.17 46.24 4.24
1341 1453 2.034878 CAGGTGTATCCTAGCAGCAGA 58.965 52.381 0.00 0.00 46.24 4.26
1342 1454 2.432146 CAGGTGTATCCTAGCAGCAGAA 59.568 50.000 0.00 0.00 46.24 3.02
1343 1455 3.107601 AGGTGTATCCTAGCAGCAGAAA 58.892 45.455 0.00 0.00 46.10 2.52
1361 1473 5.831702 AGAAACAGCATTCTGGATTCATC 57.168 39.130 12.92 0.00 44.54 2.92
1362 1474 5.258841 AGAAACAGCATTCTGGATTCATCA 58.741 37.500 12.92 0.00 44.54 3.07
1366 1478 3.315470 CAGCATTCTGGATTCATCACAGG 59.685 47.826 0.00 0.00 36.68 4.00
1401 1513 4.748144 GGGCCTCCCAAGCTGGTG 62.748 72.222 0.84 0.00 44.65 4.17
1437 1549 1.289066 CTTCCAGTTCGGCGACTCA 59.711 57.895 10.16 0.00 33.14 3.41
1449 1561 2.275703 CGACTCATCGCGGTACAAC 58.724 57.895 6.13 0.00 42.43 3.32
1456 1568 0.390735 ATCGCGGTACAACCAGTTCC 60.391 55.000 6.13 0.00 38.47 3.62
1457 1569 1.301087 CGCGGTACAACCAGTTCCA 60.301 57.895 0.00 0.00 38.47 3.53
1458 1570 1.289109 CGCGGTACAACCAGTTCCAG 61.289 60.000 0.00 0.00 38.47 3.86
1528 1640 1.541588 GAAGCAACAGTGGGATCAACC 59.458 52.381 0.00 0.00 38.08 3.77
1530 1642 1.168714 GCAACAGTGGGATCAACCTC 58.831 55.000 0.00 0.00 38.98 3.85
1602 1714 3.943381 TCATGTCATCTTTGAGCATGGAC 59.057 43.478 0.00 0.00 39.38 4.02
1608 1720 0.957395 CTTTGAGCATGGACGGCAGT 60.957 55.000 0.00 0.00 0.00 4.40
1645 1757 2.682269 GCCAAGTCTTCCTCCTTCCATC 60.682 54.545 0.00 0.00 0.00 3.51
1662 1774 3.790437 CTGATCGGTGGGCCTGCT 61.790 66.667 4.53 0.00 0.00 4.24
1680 1792 0.527817 CTATGAGCGACCCGGTGAAC 60.528 60.000 0.00 0.00 37.83 3.18
1823 1935 8.962111 GTGTTTCTGATTCTTTTGATTCAAGAC 58.038 33.333 0.00 0.00 38.06 3.01
1827 1939 6.432162 TCTGATTCTTTTGATTCAAGACAGGG 59.568 38.462 0.00 0.00 38.06 4.45
1932 2044 8.854614 ATAAAATTGCTGATATACCTCCAGAC 57.145 34.615 0.00 0.00 0.00 3.51
1999 2111 4.042187 CCCCTCATCCCAGGTATTCTTTAG 59.958 50.000 0.00 0.00 0.00 1.85
2107 2252 9.216117 TGATAGAAATTAGTCATGATGATGCTG 57.784 33.333 0.00 0.00 0.00 4.41
2119 2264 6.877322 TCATGATGATGCTGTAATCACCATAG 59.123 38.462 0.00 0.53 38.52 2.23
2349 2495 7.535258 CGATGCCTTAATTGCTATGACATTAAC 59.465 37.037 0.00 0.00 0.00 2.01
2385 2531 4.202192 GGATGATGCCATTCTTTCTTTCCC 60.202 45.833 0.00 0.00 32.09 3.97
2389 2535 2.234414 TGCCATTCTTTCTTTCCCATGC 59.766 45.455 0.00 0.00 0.00 4.06
2470 2617 4.564041 AGATCATGCTATCGTGATTCACC 58.436 43.478 11.12 0.00 46.09 4.02
2471 2618 3.111853 TCATGCTATCGTGATTCACCC 57.888 47.619 11.12 0.00 33.54 4.61
2474 2621 1.134521 TGCTATCGTGATTCACCCACC 60.135 52.381 11.12 0.00 0.00 4.61
2475 2622 1.134521 GCTATCGTGATTCACCCACCA 60.135 52.381 11.12 0.00 0.00 4.17
2477 2624 3.244078 GCTATCGTGATTCACCCACCATA 60.244 47.826 11.12 0.59 0.00 2.74
2479 2626 5.337250 GCTATCGTGATTCACCCACCATATA 60.337 44.000 11.12 0.00 0.00 0.86
2514 2694 4.277672 CCTATCCAAATGACTTGCCTGATG 59.722 45.833 0.00 0.00 33.27 3.07
2518 2698 5.508567 TCCAAATGACTTGCCTGATGATAA 58.491 37.500 0.00 0.00 33.27 1.75
2521 2701 6.532657 CCAAATGACTTGCCTGATGATAAAAC 59.467 38.462 0.00 0.00 33.27 2.43
2551 2734 7.730364 AATATAGCTGTACAGTAATGGCAAC 57.270 36.000 23.44 4.14 0.00 4.17
2584 2767 2.553028 GGTCCTCTGAATTGGCACAGAA 60.553 50.000 7.58 0.00 42.39 3.02
2585 2768 3.350833 GTCCTCTGAATTGGCACAGAAT 58.649 45.455 7.58 0.00 42.39 2.40
2601 2784 8.210265 TGGCACAGAATTTTTCCTCTTTTTAAT 58.790 29.630 0.00 0.00 0.00 1.40
2613 2796 7.385778 TCCTCTTTTTAATAAACACCGGATG 57.614 36.000 9.46 5.32 0.00 3.51
2628 2811 1.860950 CGGATGTAGAAACATGGCTCG 59.139 52.381 0.00 0.00 46.49 5.03
2650 2833 9.486857 GCTCGTTGTACTTCTATTTTTATTTCC 57.513 33.333 0.00 0.00 0.00 3.13
2709 2893 4.042187 AGAAGACTAACCAATGGCTGAACT 59.958 41.667 0.00 0.00 0.00 3.01
2834 3018 3.516300 ACGAGGGTGAACATAACCATACA 59.484 43.478 0.00 0.00 39.65 2.29
2933 3117 1.261619 CTTGTTGGACAGACTGCGTTC 59.738 52.381 1.25 0.00 0.00 3.95
3067 3251 6.418057 TGCAAAAATGTTGTTCTCCCTTAT 57.582 33.333 0.00 0.00 0.00 1.73
3184 3368 7.637511 AGATAGAAATTGGGGGATGATATGTC 58.362 38.462 0.00 0.00 0.00 3.06
3264 3448 5.295540 GCACAAAAAGGCTGGTTTAAAATCA 59.704 36.000 0.00 0.00 0.00 2.57
3265 3449 6.183360 GCACAAAAAGGCTGGTTTAAAATCAA 60.183 34.615 0.00 0.00 0.00 2.57
3648 3880 2.774234 TGGAAAGCCATTGACCCAAAAA 59.226 40.909 0.00 0.00 39.92 1.94
3654 3886 2.223947 GCCATTGACCCAAAAAGTCGTT 60.224 45.455 0.00 0.00 37.04 3.85
3697 3929 1.444895 CTGTTTGGATTGCAGCCGC 60.445 57.895 3.59 0.00 39.24 6.53
3739 3971 0.320771 GTCGTTGACTGCTCCCACAT 60.321 55.000 0.00 0.00 0.00 3.21
3762 3994 2.796651 GCTTGAATCAGCGCCAGG 59.203 61.111 2.29 0.00 0.00 4.45
3767 4012 4.365111 AATCAGCGCCAGGGCCAA 62.365 61.111 6.18 0.00 37.98 4.52
3792 4037 0.676736 TGGTTGCCCCGTTCAATTTC 59.323 50.000 0.00 0.00 35.15 2.17
3800 4045 1.333619 CCCGTTCAATTTCTATGCCCG 59.666 52.381 0.00 0.00 0.00 6.13
3801 4046 1.268539 CCGTTCAATTTCTATGCCCGC 60.269 52.381 0.00 0.00 0.00 6.13
3802 4047 1.594518 CGTTCAATTTCTATGCCCGCG 60.595 52.381 0.00 0.00 0.00 6.46
3803 4048 0.380378 TTCAATTTCTATGCCCGCGC 59.620 50.000 0.00 0.00 0.00 6.86
3804 4049 1.369209 CAATTTCTATGCCCGCGCG 60.369 57.895 25.67 25.67 38.08 6.86
3805 4050 1.817941 AATTTCTATGCCCGCGCGT 60.818 52.632 29.95 12.94 38.08 6.01
3806 4051 1.373590 AATTTCTATGCCCGCGCGTT 61.374 50.000 29.95 12.80 38.08 4.84
3807 4052 2.047151 ATTTCTATGCCCGCGCGTTG 62.047 55.000 29.95 20.23 38.08 4.10
3815 4060 3.554692 CCGCGCGTTGGTGAGATC 61.555 66.667 29.95 0.00 0.00 2.75
3816 4061 2.809174 CGCGCGTTGGTGAGATCA 60.809 61.111 24.19 0.00 0.00 2.92
3817 4062 2.167219 CGCGCGTTGGTGAGATCAT 61.167 57.895 24.19 0.00 0.00 2.45
3818 4063 1.349627 GCGCGTTGGTGAGATCATG 59.650 57.895 8.43 0.00 0.00 3.07
3819 4064 2.009108 CGCGTTGGTGAGATCATGG 58.991 57.895 0.00 0.00 0.00 3.66
3820 4065 1.723870 GCGTTGGTGAGATCATGGC 59.276 57.895 0.00 0.00 0.00 4.40
3821 4066 2.009108 CGTTGGTGAGATCATGGCG 58.991 57.895 0.00 0.00 0.00 5.69
3822 4067 1.431488 CGTTGGTGAGATCATGGCGG 61.431 60.000 0.00 0.00 0.00 6.13
3823 4068 0.392998 GTTGGTGAGATCATGGCGGT 60.393 55.000 0.00 0.00 0.00 5.68
3824 4069 0.327924 TTGGTGAGATCATGGCGGTT 59.672 50.000 0.00 0.00 0.00 4.44
3825 4070 0.107703 TGGTGAGATCATGGCGGTTC 60.108 55.000 0.00 0.00 0.00 3.62
3826 4071 0.107703 GGTGAGATCATGGCGGTTCA 60.108 55.000 0.00 0.00 0.00 3.18
3827 4072 1.678728 GGTGAGATCATGGCGGTTCAA 60.679 52.381 0.00 0.00 0.00 2.69
3828 4073 2.292267 GTGAGATCATGGCGGTTCAAT 58.708 47.619 0.00 0.00 0.00 2.57
3829 4074 2.684881 GTGAGATCATGGCGGTTCAATT 59.315 45.455 0.00 0.00 0.00 2.32
3830 4075 3.129287 GTGAGATCATGGCGGTTCAATTT 59.871 43.478 0.00 0.00 0.00 1.82
3831 4076 3.378112 TGAGATCATGGCGGTTCAATTTC 59.622 43.478 0.00 0.00 0.00 2.17
3832 4077 3.624777 AGATCATGGCGGTTCAATTTCT 58.375 40.909 0.00 0.00 0.00 2.52
3833 4078 4.780815 AGATCATGGCGGTTCAATTTCTA 58.219 39.130 0.00 0.00 0.00 2.10
3834 4079 5.380043 AGATCATGGCGGTTCAATTTCTAT 58.620 37.500 0.00 0.00 0.00 1.98
3835 4080 4.898829 TCATGGCGGTTCAATTTCTATG 57.101 40.909 0.00 0.00 0.00 2.23
3836 4081 3.066621 TCATGGCGGTTCAATTTCTATGC 59.933 43.478 0.00 0.00 0.00 3.14
3837 4082 1.748493 TGGCGGTTCAATTTCTATGCC 59.252 47.619 0.00 0.00 41.56 4.40
3838 4083 1.067060 GGCGGTTCAATTTCTATGCCC 59.933 52.381 0.00 0.00 35.24 5.36
3839 4084 1.268539 GCGGTTCAATTTCTATGCCCG 60.269 52.381 0.00 0.00 36.05 6.13
3880 4125 1.137675 GGCAGAATCCTTGGCCAAATC 59.862 52.381 20.91 14.75 45.70 2.17
3927 4172 1.993956 CTGGGGTGTGATCCAAACAA 58.006 50.000 0.00 0.00 31.97 2.83
3935 4180 3.506067 GTGTGATCCAAACAACCCCTAAG 59.494 47.826 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.062587 CATGCGGACGATTTGTTCCTC 59.937 52.381 0.00 0.00 0.00 3.71
1 2 1.086696 CATGCGGACGATTTGTTCCT 58.913 50.000 0.00 0.00 0.00 3.36
2 3 0.802494 ACATGCGGACGATTTGTTCC 59.198 50.000 0.00 0.00 0.00 3.62
27 28 2.040278 CTCACATGGAAAAGGTCAGGGA 59.960 50.000 0.00 0.00 0.00 4.20
54 55 3.229293 TCTGATTTGTTGACCATTGCCA 58.771 40.909 0.00 0.00 0.00 4.92
55 56 3.940209 TCTGATTTGTTGACCATTGCC 57.060 42.857 0.00 0.00 0.00 4.52
70 76 3.074390 TGTGGGGTGAAGTGATTTCTGAT 59.926 43.478 0.00 0.00 36.71 2.90
71 77 2.441375 TGTGGGGTGAAGTGATTTCTGA 59.559 45.455 0.00 0.00 36.71 3.27
72 78 2.554032 GTGTGGGGTGAAGTGATTTCTG 59.446 50.000 0.00 0.00 36.71 3.02
73 79 2.489073 GGTGTGGGGTGAAGTGATTTCT 60.489 50.000 0.00 0.00 36.71 2.52
74 80 1.886542 GGTGTGGGGTGAAGTGATTTC 59.113 52.381 0.00 0.00 36.29 2.17
75 81 1.216678 TGGTGTGGGGTGAAGTGATTT 59.783 47.619 0.00 0.00 0.00 2.17
76 82 0.850100 TGGTGTGGGGTGAAGTGATT 59.150 50.000 0.00 0.00 0.00 2.57
77 83 0.110486 GTGGTGTGGGGTGAAGTGAT 59.890 55.000 0.00 0.00 0.00 3.06
78 84 1.275421 TGTGGTGTGGGGTGAAGTGA 61.275 55.000 0.00 0.00 0.00 3.41
79 85 1.101049 GTGTGGTGTGGGGTGAAGTG 61.101 60.000 0.00 0.00 0.00 3.16
80 86 1.226262 GTGTGGTGTGGGGTGAAGT 59.774 57.895 0.00 0.00 0.00 3.01
81 87 0.819259 CAGTGTGGTGTGGGGTGAAG 60.819 60.000 0.00 0.00 0.00 3.02
82 88 1.225983 CAGTGTGGTGTGGGGTGAA 59.774 57.895 0.00 0.00 0.00 3.18
83 89 1.690985 TCAGTGTGGTGTGGGGTGA 60.691 57.895 0.00 0.00 0.00 4.02
84 90 1.525995 GTCAGTGTGGTGTGGGGTG 60.526 63.158 0.00 0.00 0.00 4.61
85 91 2.752807 GGTCAGTGTGGTGTGGGGT 61.753 63.158 0.00 0.00 0.00 4.95
88 94 1.594293 GTCGGTCAGTGTGGTGTGG 60.594 63.158 0.00 0.00 0.00 4.17
103 109 2.365635 AGGGAGGGACATGGGTCG 60.366 66.667 0.00 0.00 45.28 4.79
190 196 4.499183 GGACGGCAGGAGATCTATATTTG 58.501 47.826 0.00 0.00 0.00 2.32
194 200 1.073444 ACGGACGGCAGGAGATCTATA 59.927 52.381 0.00 0.00 0.00 1.31
196 202 0.818445 GACGGACGGCAGGAGATCTA 60.818 60.000 0.00 0.00 0.00 1.98
197 203 2.043852 ACGGACGGCAGGAGATCT 60.044 61.111 0.00 0.00 0.00 2.75
198 204 2.413765 GACGGACGGCAGGAGATC 59.586 66.667 0.00 0.00 0.00 2.75
199 205 3.518998 CGACGGACGGCAGGAGAT 61.519 66.667 0.00 0.00 38.46 2.75
251 268 2.865308 GGCGCCACGTTAGGAAAC 59.135 61.111 24.80 0.00 0.00 2.78
262 279 1.590525 CTAGTTTATCGCGGCGCCA 60.591 57.895 28.98 15.69 0.00 5.69
263 280 2.308039 CCTAGTTTATCGCGGCGCC 61.308 63.158 27.87 19.07 0.00 6.53
321 338 2.678336 GCCGGCCTGTATAATATTGCTC 59.322 50.000 18.11 0.00 0.00 4.26
322 339 2.711542 GCCGGCCTGTATAATATTGCT 58.288 47.619 18.11 0.00 0.00 3.91
356 373 1.544246 CTCCGTCCCCATTTGTTTTCC 59.456 52.381 0.00 0.00 0.00 3.13
383 400 2.504175 CGGGGTGGAGAAGAAATTAGGA 59.496 50.000 0.00 0.00 0.00 2.94
384 401 2.421529 CCGGGGTGGAGAAGAAATTAGG 60.422 54.545 0.00 0.00 42.00 2.69
385 402 2.919228 CCGGGGTGGAGAAGAAATTAG 58.081 52.381 0.00 0.00 42.00 1.73
647 699 3.724826 AACAACCCCACCACCACCG 62.725 63.158 0.00 0.00 0.00 4.94
697 749 3.917760 GCGACCCTAGCAGGCGAT 61.918 66.667 10.18 0.00 32.73 4.58
740 792 0.107410 GGCACCGAGAGAGAGAGAGA 60.107 60.000 0.00 0.00 0.00 3.10
741 793 1.101049 GGGCACCGAGAGAGAGAGAG 61.101 65.000 0.00 0.00 40.86 3.20
742 794 1.077357 GGGCACCGAGAGAGAGAGA 60.077 63.158 0.00 0.00 40.86 3.10
743 795 3.520402 GGGCACCGAGAGAGAGAG 58.480 66.667 0.00 0.00 40.86 3.20
759 823 2.435586 CAGAAGCGGCAGGAGTGG 60.436 66.667 1.45 0.00 0.00 4.00
839 913 0.461516 ACTCGCATCAGCCATCACAG 60.462 55.000 0.00 0.00 37.52 3.66
856 930 4.100189 CCAAGGCTGCTACTCTGTATTACT 59.900 45.833 0.00 0.00 0.00 2.24
858 932 4.030913 ACCAAGGCTGCTACTCTGTATTA 58.969 43.478 0.00 0.00 0.00 0.98
859 933 2.840651 ACCAAGGCTGCTACTCTGTATT 59.159 45.455 0.00 0.00 0.00 1.89
860 934 2.169352 CACCAAGGCTGCTACTCTGTAT 59.831 50.000 0.00 0.00 0.00 2.29
861 935 1.550524 CACCAAGGCTGCTACTCTGTA 59.449 52.381 0.00 0.00 0.00 2.74
862 936 0.322975 CACCAAGGCTGCTACTCTGT 59.677 55.000 0.00 0.00 0.00 3.41
863 937 0.610174 TCACCAAGGCTGCTACTCTG 59.390 55.000 0.00 0.00 0.00 3.35
864 938 0.901124 CTCACCAAGGCTGCTACTCT 59.099 55.000 0.00 0.00 0.00 3.24
876 957 4.758674 CAGATCTCAAGAAAAGCTCACCAA 59.241 41.667 0.00 0.00 0.00 3.67
945 1026 2.500815 TACTCGGCAGCTCTCACCCT 62.501 60.000 0.00 0.00 0.00 4.34
946 1027 2.010582 CTACTCGGCAGCTCTCACCC 62.011 65.000 0.00 0.00 0.00 4.61
947 1028 1.435515 CTACTCGGCAGCTCTCACC 59.564 63.158 0.00 0.00 0.00 4.02
948 1029 1.226831 GCTACTCGGCAGCTCTCAC 60.227 63.158 0.00 0.00 36.07 3.51
949 1030 2.418910 GGCTACTCGGCAGCTCTCA 61.419 63.158 0.00 0.00 39.09 3.27
976 1057 6.619801 TTTTACTTTCTTGAGAAGCTCACC 57.380 37.500 0.00 0.00 40.46 4.02
983 1064 7.448469 CCTCCTCCATTTTTACTTTCTTGAGAA 59.552 37.037 0.00 0.00 0.00 2.87
1037 1149 2.169937 GAGCACTCTGTGGCAGCTCT 62.170 60.000 14.71 0.00 46.06 4.09
1158 1270 4.973360 CCGTTGCCGTTGCCGTTG 62.973 66.667 0.00 0.00 36.33 4.10
1164 1276 3.456431 TTCGTTGCCGTTGCCGTTG 62.456 57.895 0.00 0.00 36.33 4.10
1165 1277 3.175976 CTTCGTTGCCGTTGCCGTT 62.176 57.895 0.00 0.00 36.33 4.44
1166 1278 3.645975 CTTCGTTGCCGTTGCCGT 61.646 61.111 0.00 0.00 36.33 5.68
1197 1309 0.108207 CCAGCTTGGCTCTAGGATGG 59.892 60.000 0.00 0.00 36.40 3.51
1198 1310 0.835941 ACCAGCTTGGCTCTAGGATG 59.164 55.000 2.50 0.00 42.67 3.51
1199 1311 0.835941 CACCAGCTTGGCTCTAGGAT 59.164 55.000 2.50 0.00 42.67 3.24
1215 1327 1.376553 GGTCTGCCTTCTGCTCACC 60.377 63.158 0.00 0.00 42.00 4.02
1236 1348 0.693049 TCTTCTGGCTCAAGAACCCC 59.307 55.000 0.00 0.00 32.75 4.95
1261 1373 1.896660 CCGGGGTGTTGTTGTCCAG 60.897 63.158 0.00 0.00 0.00 3.86
1341 1453 4.768448 TGTGATGAATCCAGAATGCTGTTT 59.232 37.500 0.00 0.00 40.63 2.83
1342 1454 4.338012 TGTGATGAATCCAGAATGCTGTT 58.662 39.130 0.00 0.00 40.63 3.16
1343 1455 3.945921 CTGTGATGAATCCAGAATGCTGT 59.054 43.478 0.00 0.00 40.63 4.40
1419 1531 0.108615 ATGAGTCGCCGAACTGGAAG 60.109 55.000 0.00 0.00 42.00 3.46
1437 1549 0.390735 GGAACTGGTTGTACCGCGAT 60.391 55.000 8.23 0.00 42.58 4.58
1446 1558 1.954528 CTGCTGCTGGAACTGGTTG 59.045 57.895 0.00 0.00 0.00 3.77
1449 1561 1.654954 GATGCTGCTGCTGGAACTGG 61.655 60.000 17.00 0.00 40.48 4.00
1456 1568 2.485582 GTGCTGATGCTGCTGCTG 59.514 61.111 17.00 0.77 40.48 4.41
1457 1569 2.750637 GGTGCTGATGCTGCTGCT 60.751 61.111 17.00 2.26 40.48 4.24
1458 1570 3.052620 CTGGTGCTGATGCTGCTGC 62.053 63.158 8.89 8.89 40.48 5.25
1528 1640 1.242076 CTGGGGCTGTCAAACTTGAG 58.758 55.000 0.00 0.00 37.98 3.02
1530 1642 0.670162 CACTGGGGCTGTCAAACTTG 59.330 55.000 0.00 0.00 0.00 3.16
1608 1720 4.746309 GCATCCAGGCTGGCCACA 62.746 66.667 29.02 12.18 37.47 4.17
1645 1757 1.762522 ATAGCAGGCCCACCGATCAG 61.763 60.000 0.00 0.00 42.76 2.90
1662 1774 1.514087 GTTCACCGGGTCGCTCATA 59.486 57.895 6.32 0.00 0.00 2.15
1823 1935 5.771666 AGATAACAATTATCATGGTGCCCTG 59.228 40.000 10.40 0.00 43.52 4.45
1827 1939 6.942576 AGGGTAGATAACAATTATCATGGTGC 59.057 38.462 10.40 0.00 43.52 5.01
1844 1956 4.971924 ACTTCCTGCTGAAATAGGGTAGAT 59.028 41.667 0.00 0.00 34.76 1.98
1932 2044 4.021894 CCATACTTCCTCCAGGAGTATTCG 60.022 50.000 15.86 0.00 46.36 3.34
2107 2252 6.683974 AAGTTGATGTGCTATGGTGATTAC 57.316 37.500 0.00 0.00 0.00 1.89
2119 2264 5.587289 TCTTTACCAACAAAGTTGATGTGC 58.413 37.500 11.19 0.00 36.94 4.57
2349 2495 5.056480 TGGCATCATCCACGAAGTAATTAG 58.944 41.667 0.00 0.00 41.61 1.73
2385 2531 8.945481 TTGATATATTTTCCAAAAGTGGCATG 57.055 30.769 0.00 0.00 45.54 4.06
2518 2698 7.979444 ACTGTACAGCTATATTTGTGTGTTT 57.021 32.000 22.90 0.00 0.00 2.83
2521 2701 8.551205 CCATTACTGTACAGCTATATTTGTGTG 58.449 37.037 22.90 3.83 0.00 3.82
2536 2719 6.503589 TTTATGTGGTTGCCATTACTGTAC 57.496 37.500 0.00 0.00 35.28 2.90
2551 2734 7.040201 CCAATTCAGAGGACCATATTTATGTGG 60.040 40.741 4.18 4.18 43.81 4.17
2566 2749 4.796038 AAATTCTGTGCCAATTCAGAGG 57.204 40.909 0.00 0.00 40.91 3.69
2584 2767 9.483916 CCGGTGTTTATTAAAAAGAGGAAAAAT 57.516 29.630 0.00 0.00 0.00 1.82
2585 2768 8.693625 TCCGGTGTTTATTAAAAAGAGGAAAAA 58.306 29.630 0.00 0.00 0.00 1.94
2601 2784 4.938832 CCATGTTTCTACATCCGGTGTTTA 59.061 41.667 13.65 2.19 43.07 2.01
2608 2791 1.860950 CGAGCCATGTTTCTACATCCG 59.139 52.381 0.00 0.00 43.07 4.18
2613 2796 4.243270 AGTACAACGAGCCATGTTTCTAC 58.757 43.478 0.00 0.00 0.00 2.59
2650 2833 6.568869 TCAAACTTAGAAACATGTTGGGTTG 58.431 36.000 12.82 14.01 0.00 3.77
2709 2893 2.645297 TGTAGTACCCCCTGCATTTTGA 59.355 45.455 0.00 0.00 0.00 2.69
2774 2958 2.106074 TGGATCATCCACGCAACGC 61.106 57.895 0.66 0.00 42.67 4.84
2834 3018 1.800805 CAGACTGAGTTGGCATTCGT 58.199 50.000 0.00 0.00 0.00 3.85
2881 3065 5.385198 AGTTGGCATTTCCTGAAAAGAGTA 58.615 37.500 0.00 0.00 33.56 2.59
2950 3134 3.270027 TCCCATATTTGTCACTTCGCAG 58.730 45.455 0.00 0.00 0.00 5.18
3067 3251 7.348815 ACATTTCATCATTCTGATTACCTCCA 58.651 34.615 0.00 0.00 34.28 3.86
3648 3880 1.816835 TCGCTGGAATCTACAACGACT 59.183 47.619 0.00 0.00 32.28 4.18
3654 3886 4.442893 CCCTTACATTCGCTGGAATCTACA 60.443 45.833 0.00 0.00 40.90 2.74
3697 3929 0.250252 AAAATTGGTTGGGCAAGCCG 60.250 50.000 4.80 0.00 37.97 5.52
3722 3954 1.915614 GCATGTGGGAGCAGTCAACG 61.916 60.000 0.00 0.00 0.00 4.10
3800 4045 1.349627 CATGATCTCACCAACGCGC 59.650 57.895 5.73 0.00 0.00 6.86
3801 4046 2.009108 CCATGATCTCACCAACGCG 58.991 57.895 3.53 3.53 0.00 6.01
3802 4047 1.723870 GCCATGATCTCACCAACGC 59.276 57.895 0.00 0.00 0.00 4.84
3803 4048 1.431488 CCGCCATGATCTCACCAACG 61.431 60.000 0.00 0.00 0.00 4.10
3804 4049 0.392998 ACCGCCATGATCTCACCAAC 60.393 55.000 0.00 0.00 0.00 3.77
3805 4050 0.327924 AACCGCCATGATCTCACCAA 59.672 50.000 0.00 0.00 0.00 3.67
3806 4051 0.107703 GAACCGCCATGATCTCACCA 60.108 55.000 0.00 0.00 0.00 4.17
3807 4052 0.107703 TGAACCGCCATGATCTCACC 60.108 55.000 0.00 0.00 0.00 4.02
3808 4053 1.737838 TTGAACCGCCATGATCTCAC 58.262 50.000 0.00 0.00 0.00 3.51
3809 4054 2.715749 ATTGAACCGCCATGATCTCA 57.284 45.000 0.00 0.00 0.00 3.27
3810 4055 3.629398 AGAAATTGAACCGCCATGATCTC 59.371 43.478 0.00 0.00 0.00 2.75
3811 4056 3.624777 AGAAATTGAACCGCCATGATCT 58.375 40.909 0.00 0.00 0.00 2.75
3812 4057 5.455392 CATAGAAATTGAACCGCCATGATC 58.545 41.667 0.00 0.00 0.00 2.92
3813 4058 4.261741 GCATAGAAATTGAACCGCCATGAT 60.262 41.667 0.00 0.00 0.00 2.45
3814 4059 3.066621 GCATAGAAATTGAACCGCCATGA 59.933 43.478 0.00 0.00 0.00 3.07
3815 4060 3.374745 GCATAGAAATTGAACCGCCATG 58.625 45.455 0.00 0.00 0.00 3.66
3816 4061 2.362077 GGCATAGAAATTGAACCGCCAT 59.638 45.455 0.00 0.00 38.20 4.40
3817 4062 1.748493 GGCATAGAAATTGAACCGCCA 59.252 47.619 0.00 0.00 38.20 5.69
3818 4063 1.067060 GGGCATAGAAATTGAACCGCC 59.933 52.381 0.00 0.00 37.57 6.13
3819 4064 1.268539 CGGGCATAGAAATTGAACCGC 60.269 52.381 0.00 0.00 32.28 5.68
3820 4065 1.268539 GCGGGCATAGAAATTGAACCG 60.269 52.381 0.00 0.00 38.42 4.44
3821 4066 1.268539 CGCGGGCATAGAAATTGAACC 60.269 52.381 0.00 0.00 0.00 3.62
3822 4067 1.859998 GCGCGGGCATAGAAATTGAAC 60.860 52.381 20.76 0.00 39.62 3.18
3823 4068 0.380378 GCGCGGGCATAGAAATTGAA 59.620 50.000 20.76 0.00 39.62 2.69
3824 4069 1.771073 CGCGCGGGCATAGAAATTGA 61.771 55.000 24.84 0.00 39.92 2.57
3825 4070 1.369209 CGCGCGGGCATAGAAATTG 60.369 57.895 24.84 0.26 39.92 2.32
3826 4071 1.373590 AACGCGCGGGCATAGAAATT 61.374 50.000 35.22 12.15 39.92 1.82
3827 4072 1.817941 AACGCGCGGGCATAGAAAT 60.818 52.632 35.22 5.42 39.92 2.17
3828 4073 2.435234 AACGCGCGGGCATAGAAA 60.435 55.556 35.22 0.00 39.92 2.52
3829 4074 3.192230 CAACGCGCGGGCATAGAA 61.192 61.111 35.22 0.00 39.92 2.10
3895 4140 4.619320 CCCAGCCAGCCCACCAAA 62.619 66.667 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.