Multiple sequence alignment - TraesCS3A01G075100

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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 TraesCS3A01G075100 chr3A 100.000 3968 0 0 1 3968 46833121 46837088 0.000000e+00 7328.0
1 TraesCS3A01G075100 chr3A 97.674 43 1 0 3378 3420 46836456 46836498 1.530000e-09 75.0
2 TraesCS3A01G075100 chr3A 97.674 43 1 0 3336 3378 46836498 46836540 1.530000e-09 75.0
3 TraesCS3A01G075100 chr3D 88.394 3455 247 73 1 3373 36011829 36015211 0.000000e+00 4017.0
4 TraesCS3A01G075100 chr3D 90.897 780 61 6 2317 3094 36167339 36168110 0.000000e+00 1038.0
5 TraesCS3A01G075100 chr3D 85.981 214 23 5 3379 3587 36015175 36015386 5.160000e-54 222.0
6 TraesCS3A01G075100 chr3D 85.047 214 25 5 3162 3373 36168216 36168424 1.120000e-50 211.0
7 TraesCS3A01G075100 chr3D 82.036 167 14 9 3752 3907 36015639 36015800 1.160000e-25 128.0
8 TraesCS3A01G075100 chr3D 90.909 77 7 0 3886 3962 36169003 36169079 1.950000e-18 104.0
9 TraesCS3A01G075100 chr3D 100.000 44 0 0 3925 3968 36015800 36015843 9.140000e-12 82.4
10 TraesCS3A01G075100 chr3B 89.690 1096 91 12 1700 2791 59034122 59035199 0.000000e+00 1378.0
11 TraesCS3A01G075100 chr3B 90.765 693 30 5 2784 3447 59036115 59036802 0.000000e+00 894.0
12 TraesCS3A01G075100 chr3B 88.582 543 47 9 1 543 59027772 59028299 0.000000e+00 645.0
13 TraesCS3A01G075100 chr3B 86.472 547 20 25 878 1423 59030717 59031210 5.800000e-153 551.0
14 TraesCS3A01G075100 chr3B 90.945 254 11 3 1420 1666 59033872 59034120 8.220000e-87 331.0
15 TraesCS3A01G075100 chr3B 90.496 242 20 2 1933 2171 570489252 570489011 2.300000e-82 316.0
16 TraesCS3A01G075100 chr3B 83.444 302 26 12 3682 3968 59038516 59038808 3.930000e-65 259.0
17 TraesCS3A01G075100 chr3B 88.095 210 13 3 3430 3639 59036812 59037009 5.120000e-59 239.0
18 TraesCS3A01G075100 chr3B 88.830 188 17 2 542 726 59028357 59028543 1.110000e-55 228.0
19 TraesCS3A01G075100 chrUn 80.292 685 78 33 1000 1677 359350285 359349651 7.770000e-127 464.0
20 TraesCS3A01G075100 chrUn 84.000 100 2 7 1726 1811 359349639 359349540 2.540000e-12 84.2
21 TraesCS3A01G075100 chr5D 80.292 685 78 33 1000 1677 553222246 553221612 7.770000e-127 464.0
22 TraesCS3A01G075100 chr5D 80.292 685 78 33 1000 1677 553256571 553255937 7.770000e-127 464.0
23 TraesCS3A01G075100 chr5D 90.083 242 21 2 1933 2171 553255829 553255588 1.070000e-80 311.0
24 TraesCS3A01G075100 chr5D 84.000 100 2 7 1726 1811 553221600 553221501 2.540000e-12 84.2
25 TraesCS3A01G075100 chr6B 79.970 664 77 33 1021 1677 699901425 699900811 4.710000e-119 438.0
26 TraesCS3A01G075100 chr6B 79.123 661 82 35 1021 1677 699822167 699821559 4.770000e-109 405.0
27 TraesCS3A01G075100 chr6B 90.574 244 18 3 1933 2171 699821450 699821207 6.400000e-83 318.0
28 TraesCS3A01G075100 chr6B 90.164 244 19 3 1933 2171 699861182 699860939 2.980000e-81 313.0
29 TraesCS3A01G075100 chr4A 91.358 243 17 3 1933 2171 743589280 743589038 2.960000e-86 329.0
30 TraesCS3A01G075100 chr4A 85.833 120 13 4 1174 1291 220151485 220151602 1.500000e-24 124.0
31 TraesCS3A01G075100 chr2B 90.612 245 20 2 1930 2171 263185365 263185609 4.950000e-84 322.0
32 TraesCS3A01G075100 chr5B 90.083 242 21 2 1933 2171 534952608 534952367 1.070000e-80 311.0
33 TraesCS3A01G075100 chr1A 79.195 298 28 16 3377 3650 306682387 306682674 4.080000e-40 176.0
34 TraesCS3A01G075100 chr1B 80.224 268 22 13 3377 3620 332093867 332093607 5.270000e-39 172.0
35 TraesCS3A01G075100 chr1B 89.720 107 9 1 3516 3620 337939415 337939521 6.920000e-28 135.0
36 TraesCS3A01G075100 chr1D 78.621 290 31 11 3377 3642 246002147 246002429 3.170000e-36 163.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G075100 chr3A 46833121 46837088 3967 False 2492.666667 7328 98.449333 1 3968 3 chr3A.!!$F1 3967
1 TraesCS3A01G075100 chr3D 36011829 36015843 4014 False 1112.350000 4017 89.102750 1 3968 4 chr3D.!!$F1 3967
2 TraesCS3A01G075100 chr3D 36167339 36169079 1740 False 451.000000 1038 88.951000 2317 3962 3 chr3D.!!$F2 1645
3 TraesCS3A01G075100 chr3B 59027772 59038808 11036 False 565.625000 1378 88.352875 1 3968 8 chr3B.!!$F1 3967
4 TraesCS3A01G075100 chrUn 359349540 359350285 745 True 274.100000 464 82.146000 1000 1811 2 chrUn.!!$R1 811
5 TraesCS3A01G075100 chr5D 553255588 553256571 983 True 387.500000 464 85.187500 1000 2171 2 chr5D.!!$R2 1171
6 TraesCS3A01G075100 chr5D 553221501 553222246 745 True 274.100000 464 82.146000 1000 1811 2 chr5D.!!$R1 811
7 TraesCS3A01G075100 chr6B 699900811 699901425 614 True 438.000000 438 79.970000 1021 1677 1 chr6B.!!$R2 656
8 TraesCS3A01G075100 chr6B 699821207 699822167 960 True 361.500000 405 84.848500 1021 2171 2 chr6B.!!$R3 1150

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
825 1638 0.026285 GGATTCAAACCGATCGCGTG 59.974 55.000 10.32 7.07 35.23 5.34 F
1302 3432 0.032615 ATGGAGGTCCGCTTCTCTCT 60.033 55.000 0.00 0.00 39.43 3.10 F
1955 6774 1.067071 GGTTGGTAAGGTCTCCTGTCG 60.067 57.143 0.00 0.00 32.13 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 7141 0.035458 AACCCAAGCGTCTCCTTCAG 59.965 55.0 0.00 0.0 0.0 3.02 R
2879 8629 0.179018 ACCTGCAGTCACCCAAGTTC 60.179 55.0 13.81 0.0 0.0 3.01 R
3371 9197 0.403655 TGCCCCTGTGTAAAGATGCA 59.596 50.0 0.00 0.0 0.0 3.96 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
25 26 0.872021 GCGCCTACCACTTGATCGAG 60.872 60.000 8.54 8.54 0.00 4.04
166 167 8.918202 TCAAGTTTTCAAACAGGTCTATATGT 57.082 30.769 5.26 0.00 41.30 2.29
170 171 9.396022 AGTTTTCAAACAGGTCTATATGTATGG 57.604 33.333 5.26 0.00 41.30 2.74
184 185 9.298250 TCTATATGTATGGTCCTTTACTGACTC 57.702 37.037 0.00 0.00 33.22 3.36
281 283 5.535406 AGACATCTACCATTCTTACTACGGG 59.465 44.000 0.00 0.00 0.00 5.28
369 371 2.107141 CCGCACTGTAGCTAGCCC 59.893 66.667 12.13 2.72 0.00 5.19
393 395 1.000739 ACCGATCCTCCCCGTTGTA 59.999 57.895 0.00 0.00 0.00 2.41
433 442 3.120546 AGTTTTGTTGCGATCGACAGATG 60.121 43.478 21.57 0.00 37.84 2.90
475 484 2.725815 GCGTGCGGCTGAAAACAC 60.726 61.111 0.00 0.00 39.11 3.32
509 518 0.108615 CGTGAGGCTTCTTGATCCGT 60.109 55.000 0.00 0.00 0.00 4.69
536 545 6.004928 GCTTTCGGCGTGTTTATTATTTTC 57.995 37.500 6.85 0.00 0.00 2.29
550 618 5.722021 ATTATTTTCCGGTTGAGCTGTTT 57.278 34.783 0.00 0.00 0.00 2.83
554 622 1.522668 TCCGGTTGAGCTGTTTGATG 58.477 50.000 0.00 0.00 0.00 3.07
578 647 0.992802 CGAAAGCTACTGAGAACGGC 59.007 55.000 0.00 0.00 0.00 5.68
605 674 1.443407 CAGAATCGTCTGCCCGGAT 59.557 57.895 0.73 0.00 44.74 4.18
613 682 0.101219 GTCTGCCCGGATTTTGCATC 59.899 55.000 0.73 0.00 33.97 3.91
614 683 1.064621 CTGCCCGGATTTTGCATCG 59.935 57.895 0.73 0.00 33.97 3.84
617 686 2.024588 CCGGATTTTGCATCGGCG 59.975 61.111 0.00 0.00 45.35 6.46
632 701 2.371923 GGCGTTTGAATTGCGTGCC 61.372 57.895 0.00 0.00 0.00 5.01
639 708 1.353103 GAATTGCGTGCCCGATGAG 59.647 57.895 0.00 0.00 35.63 2.90
665 734 3.061848 GCGTGTGGTGGGGATTGG 61.062 66.667 0.00 0.00 0.00 3.16
678 747 0.749049 GGATTGGGCAAGCTGGATTC 59.251 55.000 0.00 0.00 0.00 2.52
746 1544 2.786539 TAACTGCCACGAGCTGCTGG 62.787 60.000 7.01 8.90 43.85 4.85
771 1572 4.148645 TCGCTCACTCGCTCGTCG 62.149 66.667 0.00 0.00 40.15 5.12
802 1614 1.372251 CCGATCTCGCCAGATTCCG 60.372 63.158 0.00 0.00 39.71 4.30
806 1618 2.076622 ATCTCGCCAGATTCCGTCCG 62.077 60.000 0.00 0.00 35.67 4.79
824 1637 2.380081 GGATTCAAACCGATCGCGT 58.620 52.632 10.32 6.50 35.23 6.01
825 1638 0.026285 GGATTCAAACCGATCGCGTG 59.974 55.000 10.32 7.07 35.23 5.34
826 1639 0.719465 GATTCAAACCGATCGCGTGT 59.281 50.000 10.32 1.28 35.23 4.49
827 1640 0.719465 ATTCAAACCGATCGCGTGTC 59.281 50.000 10.32 5.02 35.23 3.67
828 1641 1.610715 TTCAAACCGATCGCGTGTCG 61.611 55.000 22.90 22.90 38.75 4.35
874 1687 0.106894 GCCTCCTAATCCAACTCCCG 59.893 60.000 0.00 0.00 0.00 5.14
946 3058 0.240945 CGGCCATTATTTGATCCGCC 59.759 55.000 2.24 0.00 35.55 6.13
947 3059 1.620822 GGCCATTATTTGATCCGCCT 58.379 50.000 0.00 0.00 32.09 5.52
948 3060 1.541588 GGCCATTATTTGATCCGCCTC 59.458 52.381 0.00 0.00 32.09 4.70
949 3061 1.197721 GCCATTATTTGATCCGCCTCG 59.802 52.381 0.00 0.00 0.00 4.63
950 3062 1.197721 CCATTATTTGATCCGCCTCGC 59.802 52.381 0.00 0.00 0.00 5.03
991 3104 3.518998 GCGTCTGCGGCCTAGAGA 61.519 66.667 0.00 0.00 38.78 3.10
992 3105 3.064987 GCGTCTGCGGCCTAGAGAA 62.065 63.158 0.00 0.00 38.78 2.87
993 3106 1.226717 CGTCTGCGGCCTAGAGAAC 60.227 63.158 0.00 0.00 0.00 3.01
994 3107 1.890894 GTCTGCGGCCTAGAGAACA 59.109 57.895 0.00 0.00 0.00 3.18
995 3108 0.246635 GTCTGCGGCCTAGAGAACAA 59.753 55.000 0.00 0.00 0.00 2.83
996 3109 0.973632 TCTGCGGCCTAGAGAACAAA 59.026 50.000 0.00 0.00 0.00 2.83
997 3110 1.555075 TCTGCGGCCTAGAGAACAAAT 59.445 47.619 0.00 0.00 0.00 2.32
998 3111 2.764010 TCTGCGGCCTAGAGAACAAATA 59.236 45.455 0.00 0.00 0.00 1.40
1085 3215 0.960364 GGATGGTGCGCCTTCTTTCA 60.960 55.000 26.09 2.49 38.56 2.69
1087 3217 1.474077 GATGGTGCGCCTTCTTTCATT 59.526 47.619 21.65 0.00 36.37 2.57
1088 3218 0.597568 TGGTGCGCCTTCTTTCATTG 59.402 50.000 18.96 0.00 35.27 2.82
1089 3219 0.109132 GGTGCGCCTTCTTTCATTGG 60.109 55.000 9.68 0.00 0.00 3.16
1090 3220 0.881118 GTGCGCCTTCTTTCATTGGA 59.119 50.000 4.18 0.00 0.00 3.53
1092 3222 2.094545 GTGCGCCTTCTTTCATTGGATT 60.095 45.455 4.18 0.00 0.00 3.01
1093 3223 2.562298 TGCGCCTTCTTTCATTGGATTT 59.438 40.909 4.18 0.00 0.00 2.17
1094 3224 2.925563 GCGCCTTCTTTCATTGGATTTG 59.074 45.455 0.00 0.00 0.00 2.32
1095 3225 3.367292 GCGCCTTCTTTCATTGGATTTGA 60.367 43.478 0.00 0.00 0.00 2.69
1101 3231 6.984474 CCTTCTTTCATTGGATTTGATGGATG 59.016 38.462 0.00 0.00 0.00 3.51
1125 3255 3.179685 TGGATGGATGGATGGATCTCTC 58.820 50.000 0.00 0.00 0.00 3.20
1301 3431 0.103937 CATGGAGGTCCGCTTCTCTC 59.896 60.000 0.00 0.00 39.43 3.20
1302 3432 0.032615 ATGGAGGTCCGCTTCTCTCT 60.033 55.000 0.00 0.00 39.43 3.10
1428 6223 6.148976 CAGTAACTTTTACCCTCTTAAGGTGC 59.851 42.308 1.85 0.00 41.59 5.01
1495 6290 5.376625 TGAGTTAAGGCAGAGACAAAATGT 58.623 37.500 0.00 0.00 0.00 2.71
1496 6291 5.239306 TGAGTTAAGGCAGAGACAAAATGTG 59.761 40.000 0.00 0.00 0.00 3.21
1679 6482 3.323979 TGGTGTCCTAGTTCTTTCTGGAC 59.676 47.826 0.00 0.00 45.22 4.02
1902 6720 7.258441 TCGTCACTCTTTTGGTATCTATTCAG 58.742 38.462 0.00 0.00 0.00 3.02
1942 6761 7.836685 TGCATAATCTGAATTTTAGGGTTGGTA 59.163 33.333 0.00 0.00 0.00 3.25
1951 6770 3.572661 TTAGGGTTGGTAAGGTCTCCT 57.427 47.619 0.00 0.00 33.87 3.69
1955 6774 1.067071 GGTTGGTAAGGTCTCCTGTCG 60.067 57.143 0.00 0.00 32.13 4.35
2027 6848 2.551270 TGTGGAGCTTTCCTGAGGTAT 58.449 47.619 0.00 0.00 0.00 2.73
2029 6850 1.757118 TGGAGCTTTCCTGAGGTATCG 59.243 52.381 0.00 0.00 0.00 2.92
2037 6858 2.656002 TCCTGAGGTATCGTCCTTGAG 58.344 52.381 0.00 0.00 38.02 3.02
2042 6863 1.478510 AGGTATCGTCCTTGAGCACTG 59.521 52.381 0.00 0.00 33.52 3.66
2069 6893 7.800380 GCGAGTTGTATCTTTTCATATTGGATG 59.200 37.037 0.00 0.00 0.00 3.51
2180 7004 2.205074 GTCATAAGCTGGTCCATCACG 58.795 52.381 0.00 0.00 0.00 4.35
2208 7032 7.505923 AGGTACTTCTTACAAATTTCCTTTGCT 59.494 33.333 0.00 0.00 42.07 3.91
2215 7039 7.504238 TCTTACAAATTTCCTTTGCTGAGGTTA 59.496 33.333 5.95 0.00 46.81 2.85
2220 7044 8.498358 CAAATTTCCTTTGCTGAGGTTAAAATC 58.502 33.333 5.95 0.00 37.98 2.17
2221 7045 6.723298 TTTCCTTTGCTGAGGTTAAAATCA 57.277 33.333 5.95 0.00 38.04 2.57
2236 7060 8.659527 AGGTTAAAATCAGAAATTTTGGATGGT 58.340 29.630 6.11 2.10 33.73 3.55
2238 7062 9.710900 GTTAAAATCAGAAATTTTGGATGGTCT 57.289 29.630 6.11 0.00 33.73 3.85
2239 7063 9.927668 TTAAAATCAGAAATTTTGGATGGTCTC 57.072 29.630 6.11 0.00 33.73 3.36
2240 7064 7.787623 AAATCAGAAATTTTGGATGGTCTCT 57.212 32.000 6.36 0.00 0.00 3.10
2241 7065 8.884124 AAATCAGAAATTTTGGATGGTCTCTA 57.116 30.769 6.36 0.00 0.00 2.43
2254 7078 9.607333 TTGGATGGTCTCTATCTATATTTGAGT 57.393 33.333 0.00 0.00 0.00 3.41
2272 7096 3.380954 TGAGTATGTACCATAACGCGGAA 59.619 43.478 12.47 0.00 0.00 4.30
2296 7122 9.294030 GAATTTGTTGGTTTCATGTAGATCATC 57.706 33.333 0.00 0.00 34.09 2.92
2305 7131 9.160496 GGTTTCATGTAGATCATCAGATATTCC 57.840 37.037 0.00 0.00 33.72 3.01
2315 7141 5.380043 TCATCAGATATTCCTTCTTTGGCC 58.620 41.667 0.00 0.00 0.00 5.36
2474 7300 3.507233 ACTTCATTCATTTGTCGTGGCAT 59.493 39.130 0.00 0.00 0.00 4.40
2557 7383 3.701542 TCGGTCTGATCTACATTGCTCTT 59.298 43.478 0.00 0.00 0.00 2.85
2597 7423 8.966069 AACTAGAATAACCAAAGAGGATTAGC 57.034 34.615 0.00 0.00 41.22 3.09
2676 7502 3.640029 TGACCAGGTATCCGAGAAATACC 59.360 47.826 0.00 4.48 46.06 2.73
2766 7592 6.628621 CGGTGTCTATGTTCCAGGTACATAAA 60.629 42.308 17.21 4.54 37.85 1.40
2817 8567 7.092716 GCATTTGTAGTGATTGTCATCCTTTT 58.907 34.615 0.00 0.00 0.00 2.27
2818 8568 7.599998 GCATTTGTAGTGATTGTCATCCTTTTT 59.400 33.333 0.00 0.00 0.00 1.94
2819 8569 8.918658 CATTTGTAGTGATTGTCATCCTTTTTG 58.081 33.333 0.00 0.00 0.00 2.44
2820 8570 7.815840 TTGTAGTGATTGTCATCCTTTTTGA 57.184 32.000 0.00 0.00 0.00 2.69
2821 8571 7.202016 TGTAGTGATTGTCATCCTTTTTGAC 57.798 36.000 0.00 0.00 43.04 3.18
2879 8629 3.796178 CCTCACGGAACATTTTGTTGTTG 59.204 43.478 0.00 0.00 41.28 3.33
2962 8712 3.140325 CCCTGTCAAAGGCAAAGACTA 57.860 47.619 0.00 0.00 45.89 2.59
3034 8787 4.504461 CCAGTCTCATGTTGTACGAATAGC 59.496 45.833 0.00 0.00 0.00 2.97
3068 8823 9.507329 AGTTGTCATTGTTAGACATGAATTACT 57.493 29.630 0.00 0.00 44.66 2.24
3199 9020 2.099141 TCTTTGGAAGTGCTCATCCG 57.901 50.000 5.65 0.00 38.63 4.18
3213 9034 2.849942 TCATCCGTTATGAGCCAATGG 58.150 47.619 0.00 0.00 39.77 3.16
3236 9057 7.445121 TGGCTATATCACATCTTAACAAGGAG 58.555 38.462 0.00 0.00 0.00 3.69
3246 9068 7.012327 CACATCTTAACAAGGAGAACTTTGTGA 59.988 37.037 0.00 0.00 43.65 3.58
3304 9126 6.535150 TGTGCTGTCTTTATTCTAGTACATGC 59.465 38.462 0.00 0.00 30.83 4.06
3344 9170 7.272037 ACAACATCCTTAACTTTTACACAGG 57.728 36.000 0.00 0.00 0.00 4.00
3345 9171 6.264518 ACAACATCCTTAACTTTTACACAGGG 59.735 38.462 0.00 0.00 0.00 4.45
3346 9172 5.321927 ACATCCTTAACTTTTACACAGGGG 58.678 41.667 0.00 0.00 0.00 4.79
3347 9173 3.758425 TCCTTAACTTTTACACAGGGGC 58.242 45.455 0.00 0.00 0.00 5.80
3348 9174 3.138653 TCCTTAACTTTTACACAGGGGCA 59.861 43.478 0.00 0.00 0.00 5.36
3350 9176 4.526650 CCTTAACTTTTACACAGGGGCAAT 59.473 41.667 0.00 0.00 0.00 3.56
3351 9177 5.712917 CCTTAACTTTTACACAGGGGCAATA 59.287 40.000 0.00 0.00 0.00 1.90
3352 9178 6.379988 CCTTAACTTTTACACAGGGGCAATAT 59.620 38.462 0.00 0.00 0.00 1.28
3353 9179 7.558444 CCTTAACTTTTACACAGGGGCAATATA 59.442 37.037 0.00 0.00 0.00 0.86
3355 9181 5.822204 ACTTTTACACAGGGGCAATATACA 58.178 37.500 0.00 0.00 0.00 2.29
3356 9182 5.885912 ACTTTTACACAGGGGCAATATACAG 59.114 40.000 0.00 0.00 0.00 2.74
3358 9184 3.281727 ACACAGGGGCAATATACAGTG 57.718 47.619 0.00 0.00 0.00 3.66
3359 9185 2.092429 ACACAGGGGCAATATACAGTGG 60.092 50.000 0.00 0.00 0.00 4.00
3360 9186 2.172505 CACAGGGGCAATATACAGTGGA 59.827 50.000 0.00 0.00 0.00 4.02
3362 9188 4.041567 CACAGGGGCAATATACAGTGGATA 59.958 45.833 0.00 0.00 0.00 2.59
3363 9189 4.041691 ACAGGGGCAATATACAGTGGATAC 59.958 45.833 0.00 0.00 0.00 2.24
3436 9331 2.373335 TCTGGGGTTTGCAAGCTAAA 57.627 45.000 13.27 0.00 0.00 1.85
3446 9345 5.402270 GGTTTGCAAGCTAAATAAGTGTGTG 59.598 40.000 13.27 0.00 0.00 3.82
3565 9465 3.285290 TTCCTTAAGAGGTCCCTTCCA 57.715 47.619 3.36 0.00 43.97 3.53
3597 9503 8.241367 GTGTCCCTGTTAACCAATATTAAACAG 58.759 37.037 17.14 17.14 0.00 3.16
3598 9504 8.164733 TGTCCCTGTTAACCAATATTAAACAGA 58.835 33.333 21.71 9.67 31.68 3.41
3654 9601 5.893897 AAGCAGAAAATCTCAGATGGTTC 57.106 39.130 3.93 3.93 0.00 3.62
3705 11109 3.886123 AGCGAAACCAGGCTATATTGTT 58.114 40.909 0.00 0.00 37.83 2.83
3786 11239 3.189287 GGTGAGCACAGTATGGTTTGAAG 59.811 47.826 2.75 0.00 43.62 3.02
3793 11246 5.702865 CACAGTATGGTTTGAAGTGATTGG 58.297 41.667 0.00 0.00 43.62 3.16
3796 11249 2.765689 TGGTTTGAAGTGATTGGGGT 57.234 45.000 0.00 0.00 0.00 4.95
3838 11291 2.234908 ACACTCTGAATAGCCACACTCC 59.765 50.000 0.00 0.00 0.00 3.85
3839 11292 1.478510 ACTCTGAATAGCCACACTCCG 59.521 52.381 0.00 0.00 0.00 4.63
3850 11303 1.441729 ACACTCCGTGACACACCAG 59.558 57.895 6.37 0.35 36.96 4.00
3856 11309 2.972505 GTGACACACCAGGCCACG 60.973 66.667 5.01 0.00 0.00 4.94
3858 11311 4.626081 GACACACCAGGCCACGCT 62.626 66.667 5.01 0.00 0.00 5.07
3859 11312 4.935495 ACACACCAGGCCACGCTG 62.935 66.667 5.01 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.228245 TGGCAGGTGAGCAGAAACC 60.228 57.895 0.00 0.00 36.66 3.27
109 110 9.936759 GGTTTTATATTTGGTTGAAATCTTGGA 57.063 29.630 0.00 0.00 35.74 3.53
110 111 9.942850 AGGTTTTATATTTGGTTGAAATCTTGG 57.057 29.630 0.00 0.00 35.74 3.61
165 166 4.715527 ACGAGTCAGTAAAGGACCATAC 57.284 45.455 0.00 0.00 35.89 2.39
166 167 5.733620 AAACGAGTCAGTAAAGGACCATA 57.266 39.130 0.00 0.00 35.89 2.74
332 334 2.811514 GGCGATGATCCCCAGCTCA 61.812 63.158 0.00 0.00 0.00 4.26
369 371 2.190578 GGGAGGATCGGTGCCTTG 59.809 66.667 0.00 0.00 35.44 3.61
433 442 3.498774 ATGGTGGATGGATCTTACAGC 57.501 47.619 0.00 0.00 0.00 4.40
495 504 2.517450 CGCGACGGATCAAGAAGCC 61.517 63.158 0.00 0.00 0.00 4.35
497 506 1.078759 AAGCGCGACGGATCAAGAAG 61.079 55.000 12.10 0.00 0.00 2.85
536 545 1.069022 CACATCAAACAGCTCAACCGG 60.069 52.381 0.00 0.00 0.00 5.28
550 618 2.231235 TCAGTAGCTTTCGAGCACATCA 59.769 45.455 0.00 0.00 37.25 3.07
554 622 2.638556 TCTCAGTAGCTTTCGAGCAC 57.361 50.000 0.00 0.00 37.25 4.40
594 663 0.101219 GATGCAAAATCCGGGCAGAC 59.899 55.000 0.00 0.00 41.40 3.51
601 670 0.455972 AAACGCCGATGCAAAATCCG 60.456 50.000 0.00 0.00 37.32 4.18
605 674 2.430546 ATTCAAACGCCGATGCAAAA 57.569 40.000 0.00 0.00 37.32 2.44
613 682 2.706123 GCACGCAATTCAAACGCCG 61.706 57.895 0.00 0.00 0.00 6.46
614 683 2.371923 GGCACGCAATTCAAACGCC 61.372 57.895 0.00 0.00 0.00 5.68
617 686 0.109319 ATCGGGCACGCAATTCAAAC 60.109 50.000 1.67 0.00 40.69 2.93
632 701 2.885676 CGCGCCATTTCCTCATCGG 61.886 63.158 0.00 0.00 0.00 4.18
639 708 3.361977 ACCACACGCGCCATTTCC 61.362 61.111 5.73 0.00 0.00 3.13
665 734 3.521796 GCCCGAATCCAGCTTGCC 61.522 66.667 0.00 0.00 0.00 4.52
690 762 1.146263 GCTCCCATCTACCCAACCG 59.854 63.158 0.00 0.00 0.00 4.44
749 1550 4.427661 AGCGAGTGAGCGAGTGGC 62.428 66.667 0.00 0.00 43.00 5.01
756 1557 2.872001 CACGACGAGCGAGTGAGC 60.872 66.667 0.00 0.00 44.57 4.26
771 1572 0.381089 AGATCGGATCGTTCGGACAC 59.619 55.000 12.08 4.56 34.45 3.67
802 1614 0.928229 CGATCGGTTTGAATCCGGAC 59.072 55.000 6.12 0.00 46.82 4.79
806 1618 0.026285 CACGCGATCGGTTTGAATCC 59.974 55.000 15.93 0.00 40.69 3.01
823 1636 2.105128 CTCTGCCGGGATCGACAC 59.895 66.667 2.18 0.00 39.00 3.67
824 1637 1.541310 AAACTCTGCCGGGATCGACA 61.541 55.000 2.18 0.00 39.00 4.35
825 1638 1.084370 CAAACTCTGCCGGGATCGAC 61.084 60.000 2.18 0.00 39.00 4.20
826 1639 1.218047 CAAACTCTGCCGGGATCGA 59.782 57.895 2.18 0.00 39.00 3.59
827 1640 0.673644 AACAAACTCTGCCGGGATCG 60.674 55.000 2.18 0.00 0.00 3.69
828 1641 0.804989 CAACAAACTCTGCCGGGATC 59.195 55.000 2.18 0.00 0.00 3.36
829 1642 0.609131 CCAACAAACTCTGCCGGGAT 60.609 55.000 2.18 0.00 0.00 3.85
830 1643 1.228124 CCAACAAACTCTGCCGGGA 60.228 57.895 2.18 0.00 0.00 5.14
831 1644 2.919494 GCCAACAAACTCTGCCGGG 61.919 63.158 2.18 0.00 0.00 5.73
832 1645 2.644992 GCCAACAAACTCTGCCGG 59.355 61.111 0.00 0.00 0.00 6.13
833 1646 2.133742 CTGGCCAACAAACTCTGCCG 62.134 60.000 7.01 0.00 45.12 5.69
874 1687 1.527311 GGAAGAAATAGCACGCGGATC 59.473 52.381 12.47 0.00 0.00 3.36
918 3030 0.465460 AATAATGGCCGCCGATGTGT 60.465 50.000 4.58 0.00 0.00 3.72
919 3031 0.667993 AAATAATGGCCGCCGATGTG 59.332 50.000 4.58 0.00 0.00 3.21
980 3093 4.261197 CCATTTATTTGTTCTCTAGGCCGC 60.261 45.833 0.00 0.00 0.00 6.53
982 3095 5.188327 GCCATTTATTTGTTCTCTAGGCC 57.812 43.478 0.00 0.00 32.50 5.19
983 3096 4.261197 CGGCCATTTATTTGTTCTCTAGGC 60.261 45.833 2.24 0.00 37.69 3.93
984 3097 4.275936 CCGGCCATTTATTTGTTCTCTAGG 59.724 45.833 2.24 0.00 0.00 3.02
985 3098 4.261197 GCCGGCCATTTATTTGTTCTCTAG 60.261 45.833 18.11 0.00 0.00 2.43
986 3099 3.630312 GCCGGCCATTTATTTGTTCTCTA 59.370 43.478 18.11 0.00 0.00 2.43
987 3100 2.427095 GCCGGCCATTTATTTGTTCTCT 59.573 45.455 18.11 0.00 0.00 3.10
988 3101 2.794631 CGCCGGCCATTTATTTGTTCTC 60.795 50.000 23.46 0.00 0.00 2.87
989 3102 1.134175 CGCCGGCCATTTATTTGTTCT 59.866 47.619 23.46 0.00 0.00 3.01
990 3103 1.135228 ACGCCGGCCATTTATTTGTTC 60.135 47.619 23.46 0.00 0.00 3.18
991 3104 0.892063 ACGCCGGCCATTTATTTGTT 59.108 45.000 23.46 0.00 0.00 2.83
992 3105 0.454196 GACGCCGGCCATTTATTTGT 59.546 50.000 23.46 9.49 0.00 2.83
993 3106 0.591236 CGACGCCGGCCATTTATTTG 60.591 55.000 23.46 5.65 0.00 2.32
994 3107 1.725066 CGACGCCGGCCATTTATTT 59.275 52.632 23.46 0.00 0.00 1.40
995 3108 3.416490 CGACGCCGGCCATTTATT 58.584 55.556 23.46 0.00 0.00 1.40
1039 3152 1.445582 CGACCCAGTTGTAGACGGC 60.446 63.158 0.00 0.00 0.00 5.68
1079 3209 6.196434 TCCATCCATCAAATCCAATGAAAGA 58.804 36.000 0.00 0.00 0.00 2.52
1085 3215 5.082633 TCCATCCATCCATCAAATCCAAT 57.917 39.130 0.00 0.00 0.00 3.16
1087 3217 4.412843 CATCCATCCATCCATCAAATCCA 58.587 43.478 0.00 0.00 0.00 3.41
1088 3218 3.767673 CCATCCATCCATCCATCAAATCC 59.232 47.826 0.00 0.00 0.00 3.01
1089 3219 4.669700 TCCATCCATCCATCCATCAAATC 58.330 43.478 0.00 0.00 0.00 2.17
1090 3220 4.752621 TCCATCCATCCATCCATCAAAT 57.247 40.909 0.00 0.00 0.00 2.32
1092 3222 3.245479 CCATCCATCCATCCATCCATCAA 60.245 47.826 0.00 0.00 0.00 2.57
1093 3223 2.310647 CCATCCATCCATCCATCCATCA 59.689 50.000 0.00 0.00 0.00 3.07
1094 3224 2.579400 TCCATCCATCCATCCATCCATC 59.421 50.000 0.00 0.00 0.00 3.51
1095 3225 2.651190 TCCATCCATCCATCCATCCAT 58.349 47.619 0.00 0.00 0.00 3.41
1101 3231 2.851194 AGATCCATCCATCCATCCATCC 59.149 50.000 0.00 0.00 0.00 3.51
1125 3255 0.318107 CAGACCCAAAGCAAGCAACG 60.318 55.000 0.00 0.00 0.00 4.10
1301 3431 3.904800 GGGGGAAGAAGAGAAGAGAAG 57.095 52.381 0.00 0.00 0.00 2.85
1333 3463 3.368948 GCTAGGAGTCAACTCAAAGAGGG 60.369 52.174 11.99 0.00 44.60 4.30
1428 6223 8.112016 TCCTACTTGATCTATATGAGAAACCG 57.888 38.462 0.00 0.00 37.85 4.44
1828 6646 9.322776 CTGATACTTGACGATTTTTGAAGAAAG 57.677 33.333 0.00 0.00 0.00 2.62
1912 6730 7.775120 ACCCTAAAATTCAGATTATGCAACAG 58.225 34.615 0.00 0.00 0.00 3.16
1942 6761 1.758440 TTGCAGCGACAGGAGACCTT 61.758 55.000 0.00 0.00 0.00 3.50
1951 6770 2.281484 GGAAGGGTTGCAGCGACA 60.281 61.111 15.07 0.00 0.00 4.35
1955 6774 0.681175 ATTTGTGGAAGGGTTGCAGC 59.319 50.000 0.00 0.00 0.00 5.25
2027 6848 2.343758 GCCAGTGCTCAAGGACGA 59.656 61.111 0.00 0.00 41.53 4.20
2029 6850 1.739562 CTCGCCAGTGCTCAAGGAC 60.740 63.158 1.94 0.00 36.57 3.85
2037 6858 1.726853 AAGATACAACTCGCCAGTGC 58.273 50.000 0.00 0.00 31.06 4.40
2042 6863 6.260050 TCCAATATGAAAAGATACAACTCGCC 59.740 38.462 0.00 0.00 0.00 5.54
2083 6907 6.875726 TGATGAACCAACATTGTCAAACAAAA 59.124 30.769 0.00 0.00 41.96 2.44
2086 6910 5.126869 AGTGATGAACCAACATTGTCAAACA 59.873 36.000 0.00 0.00 0.00 2.83
2101 6925 8.119226 GCAAGATAGATGTACAAAGTGATGAAC 58.881 37.037 0.00 0.00 0.00 3.18
2180 7004 7.997773 AAGGAAATTTGTAAGAAGTACCTCC 57.002 36.000 0.00 0.00 30.94 4.30
2208 7032 9.709495 CATCCAAAATTTCTGATTTTAACCTCA 57.291 29.630 0.00 0.00 30.85 3.86
2215 7039 8.198807 AGAGACCATCCAAAATTTCTGATTTT 57.801 30.769 0.00 0.00 0.00 1.82
2220 7044 9.790344 ATAGATAGAGACCATCCAAAATTTCTG 57.210 33.333 0.00 0.00 0.00 3.02
2260 7084 2.094957 ACCAACAAATTCCGCGTTATGG 60.095 45.455 4.92 7.41 0.00 2.74
2266 7090 2.126914 TGAAACCAACAAATTCCGCG 57.873 45.000 0.00 0.00 0.00 6.46
2272 7096 8.352137 TGATGATCTACATGAAACCAACAAAT 57.648 30.769 0.00 0.00 39.56 2.32
2296 7122 4.785301 TCAGGCCAAAGAAGGAATATCTG 58.215 43.478 5.01 0.00 0.00 2.90
2305 7131 2.431454 GTCTCCTTCAGGCCAAAGAAG 58.569 52.381 19.85 19.85 40.64 2.85
2311 7137 2.217038 AAGCGTCTCCTTCAGGCCA 61.217 57.895 5.01 0.00 34.44 5.36
2315 7141 0.035458 AACCCAAGCGTCTCCTTCAG 59.965 55.000 0.00 0.00 0.00 3.02
2467 7293 2.948093 GCATACAAGCAATGCCACG 58.052 52.632 0.00 0.00 43.17 4.94
2474 7300 3.876914 GTGCTATACCTGCATACAAGCAA 59.123 43.478 11.09 0.00 45.13 3.91
2593 7419 8.801299 TCAAATGAATAACATGGAGTTTGCTAA 58.199 29.630 0.00 0.00 41.64 3.09
2594 7420 8.347004 TCAAATGAATAACATGGAGTTTGCTA 57.653 30.769 0.00 0.00 41.64 3.49
2676 7502 7.156876 TCCATTTGTTAGGCATCTTAACAAG 57.843 36.000 11.98 4.92 42.35 3.16
2766 7592 1.829849 GTAAAGGCGAGGTAAGAGGGT 59.170 52.381 0.00 0.00 0.00 4.34
2879 8629 0.179018 ACCTGCAGTCACCCAAGTTC 60.179 55.000 13.81 0.00 0.00 3.01
2962 8712 1.202855 AGGCTCACAGCAACTTCATGT 60.203 47.619 0.00 0.00 44.75 3.21
3008 8758 3.418047 TCGTACAACATGAGACTGGAGA 58.582 45.455 0.00 0.00 0.00 3.71
3011 8764 4.504461 GCTATTCGTACAACATGAGACTGG 59.496 45.833 0.00 0.00 0.00 4.00
3034 8787 5.050091 GTCTAACAATGACAACTCACACCAG 60.050 44.000 0.00 0.00 34.80 4.00
3068 8823 5.698545 TCATCATTGTTACAACACATGTCGA 59.301 36.000 0.00 0.00 42.70 4.20
3213 9034 8.983724 GTTCTCCTTGTTAAGATGTGATATAGC 58.016 37.037 0.00 0.00 0.00 2.97
3217 9038 9.219603 CAAAGTTCTCCTTGTTAAGATGTGATA 57.780 33.333 0.00 0.00 32.32 2.15
3221 9042 7.054124 TCACAAAGTTCTCCTTGTTAAGATGT 58.946 34.615 0.00 0.00 32.32 3.06
3246 9068 6.071447 TGCAATAATCAGTGTACCATTTGCTT 60.071 34.615 14.39 0.00 38.15 3.91
3324 9150 4.157840 GCCCCTGTGTAAAAGTTAAGGATG 59.842 45.833 0.00 0.00 0.00 3.51
3334 9160 5.650266 CACTGTATATTGCCCCTGTGTAAAA 59.350 40.000 0.00 0.00 0.00 1.52
3337 9163 3.135712 CCACTGTATATTGCCCCTGTGTA 59.864 47.826 0.00 0.00 0.00 2.90
3338 9164 2.092429 CCACTGTATATTGCCCCTGTGT 60.092 50.000 0.00 0.00 0.00 3.72
3339 9165 2.172505 TCCACTGTATATTGCCCCTGTG 59.827 50.000 0.00 0.00 0.00 3.66
3340 9166 2.487775 TCCACTGTATATTGCCCCTGT 58.512 47.619 0.00 0.00 0.00 4.00
3341 9167 3.795688 ATCCACTGTATATTGCCCCTG 57.204 47.619 0.00 0.00 0.00 4.45
3342 9168 4.239495 TGTATCCACTGTATATTGCCCCT 58.761 43.478 0.00 0.00 0.00 4.79
3343 9169 4.634012 TGTATCCACTGTATATTGCCCC 57.366 45.455 0.00 0.00 0.00 5.80
3344 9170 8.677300 CAATAATGTATCCACTGTATATTGCCC 58.323 37.037 0.00 0.00 0.00 5.36
3345 9171 9.231297 ACAATAATGTATCCACTGTATATTGCC 57.769 33.333 0.00 0.00 38.24 4.52
3348 9174 9.791801 TGCACAATAATGTATCCACTGTATATT 57.208 29.630 0.00 0.00 37.82 1.28
3350 9176 9.435688 GATGCACAATAATGTATCCACTGTATA 57.564 33.333 0.00 0.00 37.82 1.47
3351 9177 8.159447 AGATGCACAATAATGTATCCACTGTAT 58.841 33.333 0.00 0.00 41.22 2.29
3352 9178 7.508687 AGATGCACAATAATGTATCCACTGTA 58.491 34.615 0.00 0.00 41.22 2.74
3353 9179 6.359804 AGATGCACAATAATGTATCCACTGT 58.640 36.000 0.00 0.00 41.22 3.55
3355 9181 7.886629 AAAGATGCACAATAATGTATCCACT 57.113 32.000 0.00 0.00 41.22 4.00
3356 9182 8.620416 TGTAAAGATGCACAATAATGTATCCAC 58.380 33.333 0.00 0.00 41.22 4.02
3370 9196 0.811281 GCCCCTGTGTAAAGATGCAC 59.189 55.000 0.00 0.00 41.92 4.57
3371 9197 0.403655 TGCCCCTGTGTAAAGATGCA 59.596 50.000 0.00 0.00 0.00 3.96
3372 9198 1.544724 TTGCCCCTGTGTAAAGATGC 58.455 50.000 0.00 0.00 0.00 3.91
3373 9199 6.061441 TGTATATTGCCCCTGTGTAAAGATG 58.939 40.000 0.00 0.00 0.00 2.90
3374 9200 6.126478 ACTGTATATTGCCCCTGTGTAAAGAT 60.126 38.462 0.00 0.00 0.00 2.40
3375 9201 5.190925 ACTGTATATTGCCCCTGTGTAAAGA 59.809 40.000 0.00 0.00 0.00 2.52
3376 9202 5.296780 CACTGTATATTGCCCCTGTGTAAAG 59.703 44.000 0.00 0.00 0.00 1.85
3436 9331 3.369892 GGAGCAGATGTCCACACACTTAT 60.370 47.826 0.00 0.00 34.48 1.73
3446 9345 4.744795 TCTCTTTTAGGAGCAGATGTCC 57.255 45.455 0.00 0.00 33.70 4.02
3565 9465 9.541884 AATATTGGTTAACAGGGACACTAAATT 57.458 29.630 8.10 0.00 0.00 1.82
3644 9566 1.354368 GGAAACCCCTGAACCATCTGA 59.646 52.381 0.00 0.00 0.00 3.27
3665 9612 3.001330 CGCTTTTGCTAAGATACGAAGGG 59.999 47.826 0.00 0.00 44.80 3.95
3670 9617 4.142988 TGGTTTCGCTTTTGCTAAGATACG 60.143 41.667 3.72 0.00 44.80 3.06
3675 9622 2.922335 GCCTGGTTTCGCTTTTGCTAAG 60.922 50.000 0.00 0.00 44.80 2.18
3705 11109 6.821665 ACAAGATAGCCGAGCTTTTTGTATAA 59.178 34.615 3.71 0.00 40.44 0.98
3764 11217 2.778299 TCAAACCATACTGTGCTCACC 58.222 47.619 0.00 0.00 0.00 4.02
3786 11239 5.741011 TCTTCAGTTATACACCCCAATCAC 58.259 41.667 0.00 0.00 0.00 3.06
3793 11246 4.081642 TGCACTCTCTTCAGTTATACACCC 60.082 45.833 0.00 0.00 0.00 4.61
3796 11249 5.926542 GTGTTGCACTCTCTTCAGTTATACA 59.073 40.000 0.00 0.00 0.00 2.29
3838 11291 2.972505 GTGGCCTGGTGTGTCACG 60.973 66.667 3.32 0.00 34.83 4.35
3839 11292 2.972505 CGTGGCCTGGTGTGTCAC 60.973 66.667 3.32 0.00 0.00 3.67
3850 11303 3.050275 GACAGGAACAGCGTGGCC 61.050 66.667 0.00 0.00 34.29 5.36
3856 11309 4.516698 TCAGAAAATTCAGACAGGAACAGC 59.483 41.667 0.00 0.00 0.00 4.40
3858 11311 6.260936 GTCTTCAGAAAATTCAGACAGGAACA 59.739 38.462 7.06 0.00 35.04 3.18
3859 11312 6.293680 GGTCTTCAGAAAATTCAGACAGGAAC 60.294 42.308 11.77 1.84 36.39 3.62
3892 11456 1.369091 CGACTTGGCGAGGAATTGGG 61.369 60.000 6.71 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.