Multiple sequence alignment - TraesCS6D01G283900

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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 TraesCS6D01G283900 chr6D 100.000 3152 0 0 1 3152 391338650 391335499 0.000000e+00 5821.0
1 TraesCS6D01G283900 chr6D 89.831 767 63 10 1 762 391506967 391506211 0.000000e+00 970.0
2 TraesCS6D01G283900 chr6D 93.976 83 3 2 802 884 391506227 391506147 1.190000e-24 124.0
3 TraesCS6D01G283900 chr6D 100.000 32 0 0 665 696 353364015 353363984 3.400000e-05 60.2
4 TraesCS6D01G283900 chr6A 91.960 2301 135 26 592 2879 537486656 537484393 0.000000e+00 3179.0
5 TraesCS6D01G283900 chr6A 90.423 1796 128 22 510 2296 537603109 537601349 0.000000e+00 2324.0
6 TraesCS6D01G283900 chr6A 90.423 1796 128 22 510 2296 537610232 537608472 0.000000e+00 2324.0
7 TraesCS6D01G283900 chr6A 88.280 529 38 9 1 526 537591419 537590912 2.080000e-171 612.0
8 TraesCS6D01G283900 chr6A 88.235 527 32 17 1 526 537610743 537610246 1.250000e-168 603.0
9 TraesCS6D01G283900 chr6A 88.046 527 33 12 1 526 537603620 537603123 5.820000e-167 597.0
10 TraesCS6D01G283900 chr6A 89.270 466 43 3 2316 2778 537466999 537466538 7.580000e-161 577.0
11 TraesCS6D01G283900 chr6A 88.451 381 43 1 2304 2684 537601194 537600815 2.860000e-125 459.0
12 TraesCS6D01G283900 chr6A 88.451 381 43 1 2304 2684 537608317 537607938 2.860000e-125 459.0
13 TraesCS6D01G283900 chr6B 96.669 1501 42 4 802 2296 584588976 584587478 0.000000e+00 2488.0
14 TraesCS6D01G283900 chr6B 90.220 1503 108 16 802 2296 584688146 584686675 0.000000e+00 1925.0
15 TraesCS6D01G283900 chr6B 93.759 721 33 4 1 711 584590052 584589334 0.000000e+00 1072.0
16 TraesCS6D01G283900 chr6B 90.082 736 64 3 2304 3039 584587298 584586572 0.000000e+00 946.0
17 TraesCS6D01G283900 chr6B 88.743 382 40 3 2304 2684 584686510 584686131 6.160000e-127 464.0
18 TraesCS6D01G283900 chr1B 80.851 141 21 5 1108 1244 683538543 683538405 4.300000e-19 106.0
19 TraesCS6D01G283900 chr1B 79.167 96 17 3 601 696 51128876 51128968 2.620000e-06 63.9
20 TraesCS6D01G283900 chr3A 100.000 32 0 0 665 696 83224190 83224221 3.400000e-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 TraesCS6D01G283900 chr6D 391335499 391338650 3151 True 5821.000000 5821 100.000000 1 3152 1 chr6D.!!$R2 3151
1 TraesCS6D01G283900 chr6D 391506147 391506967 820 True 547.000000 970 91.903500 1 884 2 chr6D.!!$R3 883
2 TraesCS6D01G283900 chr6A 537484393 537486656 2263 True 3179.000000 3179 91.960000 592 2879 1 chr6A.!!$R2 2287
3 TraesCS6D01G283900 chr6A 537607938 537610743 2805 True 1128.666667 2324 89.036333 1 2684 3 chr6A.!!$R5 2683
4 TraesCS6D01G283900 chr6A 537600815 537603620 2805 True 1126.666667 2324 88.973333 1 2684 3 chr6A.!!$R4 2683
5 TraesCS6D01G283900 chr6A 537590912 537591419 507 True 612.000000 612 88.280000 1 526 1 chr6A.!!$R3 525
6 TraesCS6D01G283900 chr6B 584586572 584590052 3480 True 1502.000000 2488 93.503333 1 3039 3 chr6B.!!$R1 3038
7 TraesCS6D01G283900 chr6B 584686131 584688146 2015 True 1194.500000 1925 89.481500 802 2684 2 chr6B.!!$R2 1882

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
704 758 0.457443 GCCAACAAGAATAGGCAGGC 59.543 55.0 0.00 0.0 46.26 4.85 F
1659 2085 0.815213 TAATGTCCATCCTGCAGCGC 60.815 55.0 8.66 0.0 0.00 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 2103 0.108329 ACATAAGCGAACCACGAGGG 60.108 55.0 3.29 0.0 45.77 4.30 R
2925 3540 0.035915 GCTGAGGAACTGGAAGACCC 60.036 60.0 0.00 0.0 41.55 4.46 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
69 70 6.512514 AAAGCTCAATATCTCTGAATCCCT 57.487 37.500 0.00 0.00 0.00 4.20
90 91 5.371472 CCCTACCCTCCTTGATATTTTGGTA 59.629 44.000 0.00 0.00 0.00 3.25
193 194 0.677731 ATGTGGTGGCACAATCCTCG 60.678 55.000 20.82 0.00 44.16 4.63
225 227 4.943705 TGAAGCAGGACATGGAATAAACTC 59.056 41.667 0.00 0.00 0.00 3.01
274 280 2.169769 ACACTTCCTTTCAACCTGACGA 59.830 45.455 0.00 0.00 0.00 4.20
385 398 1.678101 GCATGCCCAGGTATTTCTCAC 59.322 52.381 6.36 0.00 0.00 3.51
580 625 3.541632 ACGAACAACAAACTGTCATCCT 58.458 40.909 0.00 0.00 0.00 3.24
639 692 4.943705 GCCACTTTAATTCCACTGATCTGA 59.056 41.667 6.60 0.00 0.00 3.27
660 714 7.923888 TCTGAGAAGACTGATTTTGACTTTTG 58.076 34.615 0.00 0.00 0.00 2.44
661 715 7.554118 TCTGAGAAGACTGATTTTGACTTTTGT 59.446 33.333 0.00 0.00 0.00 2.83
704 758 0.457443 GCCAACAAGAATAGGCAGGC 59.543 55.000 0.00 0.00 46.26 4.85
706 760 1.747355 CCAACAAGAATAGGCAGGCAG 59.253 52.381 0.00 0.00 0.00 4.85
707 761 2.618816 CCAACAAGAATAGGCAGGCAGA 60.619 50.000 0.00 0.00 0.00 4.26
708 762 2.681848 CAACAAGAATAGGCAGGCAGAG 59.318 50.000 0.00 0.00 0.00 3.35
709 763 2.191400 ACAAGAATAGGCAGGCAGAGA 58.809 47.619 0.00 0.00 0.00 3.10
710 764 2.776536 ACAAGAATAGGCAGGCAGAGAT 59.223 45.455 0.00 0.00 0.00 2.75
711 765 3.181456 ACAAGAATAGGCAGGCAGAGATC 60.181 47.826 0.00 0.00 0.00 2.75
712 766 1.977129 AGAATAGGCAGGCAGAGATCC 59.023 52.381 0.00 0.00 0.00 3.36
751 1165 5.590818 TGACTAATTCCCTTGTAGGAGAGT 58.409 41.667 0.00 0.00 37.67 3.24
752 1166 6.738635 TGACTAATTCCCTTGTAGGAGAGTA 58.261 40.000 0.00 0.00 37.67 2.59
753 1167 7.186972 TGACTAATTCCCTTGTAGGAGAGTAA 58.813 38.462 0.00 0.00 37.67 2.24
754 1168 7.676893 TGACTAATTCCCTTGTAGGAGAGTAAA 59.323 37.037 0.00 0.00 37.67 2.01
755 1169 7.849160 ACTAATTCCCTTGTAGGAGAGTAAAC 58.151 38.462 0.00 0.00 37.67 2.01
756 1170 6.697641 AATTCCCTTGTAGGAGAGTAAACA 57.302 37.500 0.00 0.00 37.67 2.83
757 1171 6.697641 ATTCCCTTGTAGGAGAGTAAACAA 57.302 37.500 0.00 0.00 37.67 2.83
758 1172 5.479124 TCCCTTGTAGGAGAGTAAACAAC 57.521 43.478 0.00 0.00 37.67 3.32
759 1173 5.152934 TCCCTTGTAGGAGAGTAAACAACT 58.847 41.667 0.00 0.00 38.41 3.16
760 1174 5.605488 TCCCTTGTAGGAGAGTAAACAACTT 59.395 40.000 0.00 0.00 36.48 2.66
761 1175 6.100714 TCCCTTGTAGGAGAGTAAACAACTTT 59.899 38.462 0.00 0.00 36.48 2.66
762 1176 6.771267 CCCTTGTAGGAGAGTAAACAACTTTT 59.229 38.462 0.00 0.00 36.48 2.27
763 1177 7.284716 CCCTTGTAGGAGAGTAAACAACTTTTT 59.715 37.037 0.00 0.00 36.48 1.94
790 1204 8.990163 TTTGGAATAGGAGAGTAAACAACTTT 57.010 30.769 0.00 0.00 39.07 2.66
791 1205 8.990163 TTGGAATAGGAGAGTAAACAACTTTT 57.010 30.769 0.00 0.00 39.07 2.27
792 1206 8.990163 TGGAATAGGAGAGTAAACAACTTTTT 57.010 30.769 0.00 0.00 39.07 1.94
1091 1514 1.049289 GCCCTCTTATCCACCTCGGT 61.049 60.000 0.00 0.00 35.57 4.69
1322 1748 1.612469 CTCAACTGCAGCGTCGACAG 61.612 60.000 15.27 7.41 37.45 3.51
1654 2080 1.139058 AGACCGTAATGTCCATCCTGC 59.861 52.381 0.00 0.00 35.83 4.85
1659 2085 0.815213 TAATGTCCATCCTGCAGCGC 60.815 55.000 8.66 0.00 0.00 5.92
1677 2103 3.619054 GCTGATAAGCTCGGCGTC 58.381 61.111 6.85 0.00 45.96 5.19
1719 2145 2.421314 CAGGCAGTGACCACGACA 59.579 61.111 0.00 0.00 36.20 4.35
1722 2148 1.522806 GGCAGTGACCACGACAACA 60.523 57.895 0.00 0.00 36.20 3.33
1989 2415 1.661463 TGAAGGTGCTCCAGGAGAAT 58.339 50.000 21.89 0.00 35.89 2.40
2127 2553 1.605738 AGCTGCTTGCCAAGGGAAG 60.606 57.895 15.15 15.15 44.68 3.46
2168 2594 0.833287 TGAAGGATCCTGCTGTAGGC 59.167 55.000 21.10 1.92 46.87 3.93
2233 2659 7.096477 GCAATGTTTCATTCTTATTACCGCATC 60.096 37.037 0.00 0.00 0.00 3.91
2235 2661 5.883115 TGTTTCATTCTTATTACCGCATCCA 59.117 36.000 0.00 0.00 0.00 3.41
2244 2670 2.375014 TACCGCATCCAGATACTCCA 57.625 50.000 0.00 0.00 0.00 3.86
2341 2952 5.171476 AGTGCATCATATATCGGTTGCTAC 58.829 41.667 0.00 0.00 32.40 3.58
2462 3074 1.130054 AGTCACTGCATGGGTGAGGT 61.130 55.000 7.47 0.00 43.17 3.85
2517 3129 2.647299 TCCATGGTCAGCCTTTTCCTTA 59.353 45.455 12.58 0.00 35.27 2.69
2525 3137 4.762251 GTCAGCCTTTTCCTTATGTGAACT 59.238 41.667 0.00 0.00 0.00 3.01
2556 3168 4.389992 TGTCTCTTAGCATTTTCTTCAGCG 59.610 41.667 0.00 0.00 0.00 5.18
2599 3211 8.931385 ATAAATGTAATCATTGTTTGAGTGCC 57.069 30.769 0.00 0.00 42.60 5.01
2659 3271 3.207778 TCCCACTAAGTTTGGTTTGACG 58.792 45.455 0.00 0.00 31.46 4.35
2701 3316 9.585099 GAATTTGATGCATTCTGTTAATGGTTA 57.415 29.630 0.00 0.00 0.00 2.85
2779 3394 3.326006 TGGCTGAGAATTGACACTCTCTT 59.674 43.478 12.70 0.00 39.11 2.85
2843 3458 2.501723 CCACAGCTGGTATGGTAAGTCT 59.498 50.000 19.93 0.00 32.03 3.24
2844 3459 3.525537 CACAGCTGGTATGGTAAGTCTG 58.474 50.000 19.93 0.00 0.00 3.51
2845 3460 3.195610 CACAGCTGGTATGGTAAGTCTGA 59.804 47.826 19.93 0.00 0.00 3.27
2846 3461 3.195825 ACAGCTGGTATGGTAAGTCTGAC 59.804 47.826 19.93 0.00 0.00 3.51
2881 3496 4.951254 TCTGTTTACACGTTTGAGATGGA 58.049 39.130 0.00 0.00 0.00 3.41
2887 3502 6.715344 TTACACGTTTGAGATGGATGTTAC 57.285 37.500 0.00 0.00 0.00 2.50
2888 3503 4.894784 ACACGTTTGAGATGGATGTTACT 58.105 39.130 0.00 0.00 0.00 2.24
2889 3504 4.929808 ACACGTTTGAGATGGATGTTACTC 59.070 41.667 0.00 0.00 0.00 2.59
2890 3505 5.171476 CACGTTTGAGATGGATGTTACTCT 58.829 41.667 0.00 0.00 0.00 3.24
2891 3506 5.062683 CACGTTTGAGATGGATGTTACTCTG 59.937 44.000 0.00 0.00 0.00 3.35
2892 3507 4.568359 CGTTTGAGATGGATGTTACTCTGG 59.432 45.833 0.00 0.00 0.00 3.86
2893 3508 5.624509 CGTTTGAGATGGATGTTACTCTGGA 60.625 44.000 0.00 0.00 0.00 3.86
2907 3522 2.645297 ACTCTGGACTCTGGAGTAGTCA 59.355 50.000 3.03 2.83 44.25 3.41
2924 3539 0.404040 TCATTGGGGGAAGCTTCGTT 59.596 50.000 19.91 0.00 0.00 3.85
2925 3540 0.527565 CATTGGGGGAAGCTTCGTTG 59.472 55.000 19.91 7.31 0.00 4.10
2927 3542 2.361230 GGGGGAAGCTTCGTTGGG 60.361 66.667 19.91 0.00 0.00 4.12
2931 3546 0.250770 GGGAAGCTTCGTTGGGTCTT 60.251 55.000 19.91 0.00 0.00 3.01
2949 3564 2.731691 TTCCAGTTCCTCAGCACCGC 62.732 60.000 0.00 0.00 0.00 5.68
2956 3571 2.434884 CTCAGCACCGCGATTGGT 60.435 61.111 8.23 7.19 45.21 3.67
2990 3605 3.379372 GGTTACTACTGTACATCCTGCGA 59.621 47.826 0.00 0.00 0.00 5.10
3017 3632 1.302285 CCAGTGGCCAAGATGCTCT 59.698 57.895 7.24 0.00 0.00 4.09
3018 3633 1.030488 CCAGTGGCCAAGATGCTCTG 61.030 60.000 7.24 8.84 35.06 3.35
3032 3647 0.465278 GCTCTGGAGGGAAGGATTGC 60.465 60.000 0.00 0.00 34.72 3.56
3039 3654 2.505819 GGAGGGAAGGATTGCTCAGTAA 59.494 50.000 0.00 0.00 36.31 2.24
3040 3655 3.054361 GGAGGGAAGGATTGCTCAGTAAA 60.054 47.826 0.00 0.00 36.31 2.01
3041 3656 4.195416 GAGGGAAGGATTGCTCAGTAAAG 58.805 47.826 0.00 0.00 36.31 1.85
3042 3657 3.846588 AGGGAAGGATTGCTCAGTAAAGA 59.153 43.478 0.00 0.00 36.31 2.52
3043 3658 4.476479 AGGGAAGGATTGCTCAGTAAAGAT 59.524 41.667 0.00 0.00 36.31 2.40
3044 3659 4.578105 GGGAAGGATTGCTCAGTAAAGATG 59.422 45.833 0.00 0.00 36.31 2.90
3045 3660 5.189180 GGAAGGATTGCTCAGTAAAGATGT 58.811 41.667 0.00 0.00 31.69 3.06
3046 3661 5.065731 GGAAGGATTGCTCAGTAAAGATGTG 59.934 44.000 0.00 0.00 31.69 3.21
3047 3662 3.944015 AGGATTGCTCAGTAAAGATGTGC 59.056 43.478 0.00 0.00 37.60 4.57
3048 3663 3.944015 GGATTGCTCAGTAAAGATGTGCT 59.056 43.478 0.00 0.00 37.88 4.40
3049 3664 4.201891 GGATTGCTCAGTAAAGATGTGCTG 60.202 45.833 0.00 0.00 37.88 4.41
3050 3665 2.079158 TGCTCAGTAAAGATGTGCTGC 58.921 47.619 0.00 0.00 37.88 5.25
3051 3666 2.289882 TGCTCAGTAAAGATGTGCTGCT 60.290 45.455 0.00 0.00 37.88 4.24
3052 3667 2.351111 GCTCAGTAAAGATGTGCTGCTC 59.649 50.000 0.00 0.00 35.01 4.26
3053 3668 2.602211 CTCAGTAAAGATGTGCTGCTCG 59.398 50.000 0.00 0.00 0.00 5.03
3054 3669 2.231235 TCAGTAAAGATGTGCTGCTCGA 59.769 45.455 0.00 0.00 0.00 4.04
3055 3670 2.346847 CAGTAAAGATGTGCTGCTCGAC 59.653 50.000 0.00 0.00 0.00 4.20
3056 3671 2.232452 AGTAAAGATGTGCTGCTCGACT 59.768 45.455 0.00 0.00 0.00 4.18
3057 3672 1.436600 AAAGATGTGCTGCTCGACTG 58.563 50.000 0.00 0.00 0.00 3.51
3058 3673 0.605083 AAGATGTGCTGCTCGACTGA 59.395 50.000 0.00 0.00 0.00 3.41
3059 3674 0.822811 AGATGTGCTGCTCGACTGAT 59.177 50.000 0.00 0.00 0.00 2.90
3060 3675 0.928922 GATGTGCTGCTCGACTGATG 59.071 55.000 0.00 0.00 0.00 3.07
3061 3676 0.533951 ATGTGCTGCTCGACTGATGA 59.466 50.000 0.00 0.00 0.00 2.92
3062 3677 0.318120 TGTGCTGCTCGACTGATGAA 59.682 50.000 0.00 0.00 0.00 2.57
3063 3678 0.718343 GTGCTGCTCGACTGATGAAC 59.282 55.000 0.00 0.00 0.00 3.18
3064 3679 0.605083 TGCTGCTCGACTGATGAACT 59.395 50.000 0.00 0.00 0.00 3.01
3065 3680 0.997932 GCTGCTCGACTGATGAACTG 59.002 55.000 0.00 0.00 0.00 3.16
3066 3681 1.403382 GCTGCTCGACTGATGAACTGA 60.403 52.381 0.00 0.00 0.00 3.41
3067 3682 2.928301 GCTGCTCGACTGATGAACTGAA 60.928 50.000 0.00 0.00 0.00 3.02
3068 3683 2.922387 CTGCTCGACTGATGAACTGAAG 59.078 50.000 0.00 0.00 0.00 3.02
3069 3684 2.558359 TGCTCGACTGATGAACTGAAGA 59.442 45.455 0.00 0.00 0.00 2.87
3070 3685 3.005791 TGCTCGACTGATGAACTGAAGAA 59.994 43.478 0.00 0.00 0.00 2.52
3071 3686 3.611986 GCTCGACTGATGAACTGAAGAAG 59.388 47.826 0.00 0.00 0.00 2.85
3072 3687 4.804108 CTCGACTGATGAACTGAAGAAGT 58.196 43.478 0.00 0.00 42.60 3.01
3086 3701 6.709145 CTGAAGAAGTTCATCAGTCTGAAG 57.291 41.667 23.75 2.22 41.96 3.02
3087 3702 6.410942 TGAAGAAGTTCATCAGTCTGAAGA 57.589 37.500 6.64 5.02 37.79 2.87
3088 3703 6.219473 TGAAGAAGTTCATCAGTCTGAAGAC 58.781 40.000 6.64 6.12 40.28 3.01
3089 3704 6.041409 TGAAGAAGTTCATCAGTCTGAAGACT 59.959 38.462 6.64 7.17 45.52 3.24
3101 3716 5.028428 GTCTGAAGACTGAAATTGCACTC 57.972 43.478 3.13 0.00 41.65 3.51
3102 3717 4.754114 GTCTGAAGACTGAAATTGCACTCT 59.246 41.667 3.13 0.00 41.65 3.24
3103 3718 4.753610 TCTGAAGACTGAAATTGCACTCTG 59.246 41.667 0.00 0.00 0.00 3.35
3104 3719 3.251729 TGAAGACTGAAATTGCACTCTGC 59.748 43.478 0.00 0.00 45.29 4.26
3116 3731 3.577649 GCACTCTGCAGTTAGTAGTGA 57.422 47.619 27.62 2.01 44.26 3.41
3117 3732 3.914312 GCACTCTGCAGTTAGTAGTGAA 58.086 45.455 27.62 1.05 44.26 3.18
3118 3733 3.675698 GCACTCTGCAGTTAGTAGTGAAC 59.324 47.826 27.62 12.99 44.26 3.18
3119 3734 4.559704 GCACTCTGCAGTTAGTAGTGAACT 60.560 45.833 27.62 0.00 44.26 3.01
3120 3735 5.335740 GCACTCTGCAGTTAGTAGTGAACTA 60.336 44.000 27.62 0.00 44.26 2.24
3121 3736 6.318628 CACTCTGCAGTTAGTAGTGAACTAG 58.681 44.000 21.88 7.11 41.70 2.57
3122 3737 6.149640 CACTCTGCAGTTAGTAGTGAACTAGA 59.850 42.308 21.88 0.00 41.70 2.43
3123 3738 6.887545 ACTCTGCAGTTAGTAGTGAACTAGAT 59.112 38.462 14.67 0.00 41.70 1.98
3124 3739 7.394923 ACTCTGCAGTTAGTAGTGAACTAGATT 59.605 37.037 14.67 0.00 41.70 2.40
3125 3740 7.763356 TCTGCAGTTAGTAGTGAACTAGATTC 58.237 38.462 14.67 0.00 41.70 2.52
3126 3741 7.612244 TCTGCAGTTAGTAGTGAACTAGATTCT 59.388 37.037 14.67 0.00 41.70 2.40
3127 3742 7.539436 TGCAGTTAGTAGTGAACTAGATTCTG 58.461 38.462 0.00 0.77 41.70 3.02
3128 3743 7.176865 TGCAGTTAGTAGTGAACTAGATTCTGT 59.823 37.037 0.00 0.00 41.70 3.41
3129 3744 8.030106 GCAGTTAGTAGTGAACTAGATTCTGTT 58.970 37.037 0.00 0.00 41.70 3.16
3130 3745 9.915629 CAGTTAGTAGTGAACTAGATTCTGTTT 57.084 33.333 0.00 0.00 41.70 2.83
3138 3753 9.832445 AGTGAACTAGATTCTGTTTAGTTTGAA 57.168 29.630 0.00 0.00 37.66 2.69
3139 3754 9.865484 GTGAACTAGATTCTGTTTAGTTTGAAC 57.135 33.333 0.00 0.00 37.66 3.18
3140 3755 9.832445 TGAACTAGATTCTGTTTAGTTTGAACT 57.168 29.630 0.00 1.60 37.66 3.01
3142 3757 8.608844 ACTAGATTCTGTTTAGTTTGAACTGG 57.391 34.615 6.64 0.00 40.07 4.00
3143 3758 8.429641 ACTAGATTCTGTTTAGTTTGAACTGGA 58.570 33.333 6.64 0.00 40.07 3.86
3144 3759 7.736447 AGATTCTGTTTAGTTTGAACTGGAG 57.264 36.000 6.64 0.00 40.07 3.86
3145 3760 7.283329 AGATTCTGTTTAGTTTGAACTGGAGT 58.717 34.615 6.64 0.00 40.07 3.85
3146 3761 8.429641 AGATTCTGTTTAGTTTGAACTGGAGTA 58.570 33.333 6.64 0.00 40.07 2.59
3147 3762 7.781548 TTCTGTTTAGTTTGAACTGGAGTAC 57.218 36.000 6.64 0.00 40.07 2.73
3148 3763 7.120923 TCTGTTTAGTTTGAACTGGAGTACT 57.879 36.000 6.64 0.00 40.07 2.73
3149 3764 6.984474 TCTGTTTAGTTTGAACTGGAGTACTG 59.016 38.462 0.00 0.00 40.07 2.74
3150 3765 5.526111 TGTTTAGTTTGAACTGGAGTACTGC 59.474 40.000 7.56 7.56 40.07 4.40
3151 3766 5.546621 TTAGTTTGAACTGGAGTACTGCT 57.453 39.130 15.92 0.00 40.07 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 6.328148 ACGATACCAAAATATCAAGGAGGGTA 59.672 38.462 0.00 0.00 31.98 3.69
90 91 1.681793 CTCGTGGGAGGTAATGACGAT 59.318 52.381 0.00 0.00 38.30 3.73
193 194 1.073284 TGTCCTGCTTCAAACTACCCC 59.927 52.381 0.00 0.00 0.00 4.95
317 323 5.731957 TGGGGCCTTTAAGTATTTGAAAC 57.268 39.130 0.84 0.00 0.00 2.78
580 625 5.084818 TCGATCAGCCATTTACTCTTTGA 57.915 39.130 0.00 0.00 0.00 2.69
639 692 8.055279 TCAACAAAAGTCAAAATCAGTCTTCT 57.945 30.769 0.00 0.00 0.00 2.85
660 714 2.954611 GGCCTTTCGTGCCTCAAC 59.045 61.111 0.00 0.00 45.70 3.18
700 754 1.270199 CCAATCTCGGATCTCTGCCTG 60.270 57.143 0.00 0.00 0.00 4.85
763 1177 8.990163 AGTTGTTTACTCTCCTATTCCAAAAA 57.010 30.769 0.00 0.00 28.23 1.94
764 1178 8.990163 AAGTTGTTTACTCTCCTATTCCAAAA 57.010 30.769 0.00 0.00 35.54 2.44
765 1179 8.990163 AAAGTTGTTTACTCTCCTATTCCAAA 57.010 30.769 0.00 0.00 35.54 3.28
766 1180 8.990163 AAAAGTTGTTTACTCTCCTATTCCAA 57.010 30.769 0.00 0.00 35.54 3.53
767 1181 8.990163 AAAAAGTTGTTTACTCTCCTATTCCA 57.010 30.769 0.00 0.00 35.54 3.53
791 1205 9.457436 AAGTTGTTTACTCTCCTTGACTAAAAA 57.543 29.630 0.00 0.00 35.54 1.94
792 1206 8.889717 CAAGTTGTTTACTCTCCTTGACTAAAA 58.110 33.333 0.00 0.00 35.54 1.52
793 1207 8.044908 ACAAGTTGTTTACTCTCCTTGACTAAA 58.955 33.333 1.64 0.00 35.54 1.85
794 1208 7.562135 ACAAGTTGTTTACTCTCCTTGACTAA 58.438 34.615 1.64 0.00 35.54 2.24
795 1209 7.120923 ACAAGTTGTTTACTCTCCTTGACTA 57.879 36.000 1.64 0.00 35.54 2.59
796 1210 5.990668 ACAAGTTGTTTACTCTCCTTGACT 58.009 37.500 1.64 0.00 35.54 3.41
797 1211 6.424207 CCTACAAGTTGTTTACTCTCCTTGAC 59.576 42.308 14.90 0.00 35.54 3.18
798 1212 6.325545 TCCTACAAGTTGTTTACTCTCCTTGA 59.674 38.462 14.90 0.00 35.54 3.02
799 1213 6.522054 TCCTACAAGTTGTTTACTCTCCTTG 58.478 40.000 14.90 0.00 35.54 3.61
800 1214 6.742559 TCCTACAAGTTGTTTACTCTCCTT 57.257 37.500 14.90 0.00 35.54 3.36
801 1215 6.742559 TTCCTACAAGTTGTTTACTCTCCT 57.257 37.500 14.90 0.00 35.54 3.69
802 1216 9.498176 TTTATTCCTACAAGTTGTTTACTCTCC 57.502 33.333 14.90 0.00 35.54 3.71
806 1220 9.063615 CCACTTTATTCCTACAAGTTGTTTACT 57.936 33.333 14.90 0.00 39.32 2.24
807 1221 8.843262 ACCACTTTATTCCTACAAGTTGTTTAC 58.157 33.333 14.90 0.00 0.00 2.01
808 1222 8.842280 CACCACTTTATTCCTACAAGTTGTTTA 58.158 33.333 14.90 0.00 26.96 2.01
809 1223 7.340999 ACACCACTTTATTCCTACAAGTTGTTT 59.659 33.333 14.90 0.00 26.96 2.83
1182 1608 1.069765 CTTGCAGTGGGAGACGTGT 59.930 57.895 0.00 0.00 0.00 4.49
1203 1629 2.345760 GGAGTCGGCGTTGGAGGTA 61.346 63.158 6.85 0.00 0.00 3.08
1677 2103 0.108329 ACATAAGCGAACCACGAGGG 60.108 55.000 3.29 0.00 45.77 4.30
1683 2109 1.271108 TGCCTGAACATAAGCGAACCA 60.271 47.619 0.00 0.00 0.00 3.67
1989 2415 5.821470 GCTCTGATCTTTCTGAATCAATCCA 59.179 40.000 0.00 0.00 30.48 3.41
2127 2553 4.410743 GCAACTTCAGCTGGCGGC 62.411 66.667 15.13 11.19 42.19 6.53
2168 2594 7.805071 GGTTAGTGAAGATTCAAAACATGTGAG 59.195 37.037 17.20 0.00 39.21 3.51
2233 2659 5.009510 CAGAGTACACATCTGGAGTATCTGG 59.990 48.000 0.00 0.00 40.44 3.86
2235 2661 4.582656 GCAGAGTACACATCTGGAGTATCT 59.417 45.833 11.37 0.00 43.61 1.98
2244 2670 2.672478 GCGAGTTGCAGAGTACACATCT 60.672 50.000 0.00 0.00 45.45 2.90
2341 2952 4.037208 AGCCAACAATCTTTCTCACAACTG 59.963 41.667 0.00 0.00 0.00 3.16
2462 3074 2.330440 ATGTATGATGGACAGCGCAA 57.670 45.000 11.47 0.00 0.00 4.85
2517 3129 7.550906 GCTAAGAGACAAATTCCTAGTTCACAT 59.449 37.037 0.00 0.00 0.00 3.21
2525 3137 9.520515 AAGAAAATGCTAAGAGACAAATTCCTA 57.479 29.630 0.00 0.00 0.00 2.94
2599 3211 1.999048 TTACCGTAACAGGTGATGCG 58.001 50.000 0.00 0.00 45.54 4.73
2641 3253 3.623960 TGGTCGTCAAACCAAACTTAGTG 59.376 43.478 0.00 0.00 46.26 2.74
2659 3271 6.801539 TCAAATTCAGTACTCACATTGGTC 57.198 37.500 0.00 0.00 0.00 4.02
2701 3316 5.820947 ACAAGTCGGAACTCAAAAACATAGT 59.179 36.000 0.00 0.00 33.48 2.12
2717 3332 4.094442 GCCCAAAGATTTAGTACAAGTCGG 59.906 45.833 0.00 0.00 0.00 4.79
2718 3333 4.935808 AGCCCAAAGATTTAGTACAAGTCG 59.064 41.667 0.00 0.00 0.00 4.18
2747 3362 0.465460 TTCTCAGCCAGCCGTGTTTT 60.465 50.000 0.00 0.00 0.00 2.43
2752 3367 0.674895 GTCAATTCTCAGCCAGCCGT 60.675 55.000 0.00 0.00 0.00 5.68
2779 3394 1.413812 ACCATCAGCATCGACATAGCA 59.586 47.619 0.00 0.00 0.00 3.49
2843 3458 8.236586 GTGTAAACAGATCAGCAAAATATGTCA 58.763 33.333 0.00 0.00 28.83 3.58
2844 3459 7.426456 CGTGTAAACAGATCAGCAAAATATGTC 59.574 37.037 0.00 0.00 28.83 3.06
2845 3460 7.094805 ACGTGTAAACAGATCAGCAAAATATGT 60.095 33.333 0.00 0.00 30.19 2.29
2846 3461 7.243487 ACGTGTAAACAGATCAGCAAAATATG 58.757 34.615 0.00 0.00 0.00 1.78
2881 3496 4.054359 ACTCCAGAGTCCAGAGTAACAT 57.946 45.455 10.22 0.00 39.06 2.71
2887 3502 3.358111 TGACTACTCCAGAGTCCAGAG 57.642 52.381 3.00 5.65 42.29 3.35
2888 3503 4.019858 CAATGACTACTCCAGAGTCCAGA 58.980 47.826 3.00 0.00 42.29 3.86
2889 3504 3.131933 CCAATGACTACTCCAGAGTCCAG 59.868 52.174 3.00 0.00 42.29 3.86
2890 3505 3.099905 CCAATGACTACTCCAGAGTCCA 58.900 50.000 3.00 2.16 42.29 4.02
2891 3506 2.432510 CCCAATGACTACTCCAGAGTCC 59.567 54.545 3.00 0.00 42.29 3.85
2892 3507 2.432510 CCCCAATGACTACTCCAGAGTC 59.567 54.545 3.00 0.00 42.54 3.36
2893 3508 2.472029 CCCCAATGACTACTCCAGAGT 58.528 52.381 5.50 5.50 45.02 3.24
2907 3522 0.611896 CCAACGAAGCTTCCCCCAAT 60.612 55.000 20.62 0.00 0.00 3.16
2924 3539 1.352083 CTGAGGAACTGGAAGACCCA 58.648 55.000 0.00 0.00 41.55 4.51
2925 3540 0.035915 GCTGAGGAACTGGAAGACCC 60.036 60.000 0.00 0.00 41.55 4.46
2927 3542 1.609320 GGTGCTGAGGAACTGGAAGAC 60.609 57.143 0.00 0.00 41.55 3.01
2931 3546 3.059982 CGGTGCTGAGGAACTGGA 58.940 61.111 0.00 0.00 41.55 3.86
2949 3564 0.179192 CATTGTGCCGACACCAATCG 60.179 55.000 0.00 0.00 46.86 3.34
2956 3571 2.300723 AGTAGTAACCATTGTGCCGACA 59.699 45.455 0.00 0.00 0.00 4.35
2961 3576 5.293569 GGATGTACAGTAGTAACCATTGTGC 59.706 44.000 0.33 0.00 30.67 4.57
3017 3632 0.914644 CTGAGCAATCCTTCCCTCCA 59.085 55.000 0.00 0.00 0.00 3.86
3018 3633 0.915364 ACTGAGCAATCCTTCCCTCC 59.085 55.000 0.00 0.00 0.00 4.30
3032 3647 2.602211 CGAGCAGCACATCTTTACTGAG 59.398 50.000 0.00 0.00 31.67 3.35
3039 3654 0.605083 TCAGTCGAGCAGCACATCTT 59.395 50.000 0.00 0.00 0.00 2.40
3040 3655 0.822811 ATCAGTCGAGCAGCACATCT 59.177 50.000 0.00 0.00 0.00 2.90
3041 3656 0.928922 CATCAGTCGAGCAGCACATC 59.071 55.000 0.00 0.00 0.00 3.06
3042 3657 0.533951 TCATCAGTCGAGCAGCACAT 59.466 50.000 0.00 0.00 0.00 3.21
3043 3658 0.318120 TTCATCAGTCGAGCAGCACA 59.682 50.000 0.00 0.00 0.00 4.57
3044 3659 0.718343 GTTCATCAGTCGAGCAGCAC 59.282 55.000 0.00 0.00 0.00 4.40
3045 3660 0.605083 AGTTCATCAGTCGAGCAGCA 59.395 50.000 0.00 0.00 0.00 4.41
3046 3661 0.997932 CAGTTCATCAGTCGAGCAGC 59.002 55.000 0.00 0.00 0.00 5.25
3047 3662 2.643933 TCAGTTCATCAGTCGAGCAG 57.356 50.000 0.00 0.00 0.00 4.24
3048 3663 2.558359 TCTTCAGTTCATCAGTCGAGCA 59.442 45.455 0.00 0.00 0.00 4.26
3049 3664 3.223423 TCTTCAGTTCATCAGTCGAGC 57.777 47.619 0.00 0.00 0.00 5.03
3050 3665 4.804108 ACTTCTTCAGTTCATCAGTCGAG 58.196 43.478 0.00 0.00 27.32 4.04
3051 3666 4.855715 ACTTCTTCAGTTCATCAGTCGA 57.144 40.909 0.00 0.00 27.32 4.20
3064 3679 6.219473 GTCTTCAGACTGATGAACTTCTTCA 58.781 40.000 19.50 7.06 41.65 3.02
3065 3680 6.704512 GTCTTCAGACTGATGAACTTCTTC 57.295 41.667 19.50 5.25 41.65 2.87
3079 3694 4.754114 AGAGTGCAATTTCAGTCTTCAGAC 59.246 41.667 9.35 0.00 42.41 3.51
3080 3695 4.753610 CAGAGTGCAATTTCAGTCTTCAGA 59.246 41.667 12.11 0.00 42.41 3.27
3081 3696 4.613167 GCAGAGTGCAATTTCAGTCTTCAG 60.613 45.833 12.11 4.07 42.41 3.02
3082 3697 3.251729 GCAGAGTGCAATTTCAGTCTTCA 59.748 43.478 12.11 0.00 42.41 3.02
3083 3698 3.819537 GCAGAGTGCAATTTCAGTCTTC 58.180 45.455 12.11 4.94 42.41 2.87
3084 3699 3.911661 GCAGAGTGCAATTTCAGTCTT 57.088 42.857 12.11 0.00 42.41 3.01
3093 3708 9.569086 AGTTCACTACTAACTGCAGAGTGCAAT 62.569 40.741 23.35 9.89 44.00 3.56
3094 3709 8.355457 AGTTCACTACTAACTGCAGAGTGCAA 62.355 42.308 23.35 14.73 44.00 4.08
3095 3710 6.958596 AGTTCACTACTAACTGCAGAGTGCA 61.959 44.000 23.35 10.69 43.06 4.57
3096 3711 3.577649 TCACTACTAACTGCAGAGTGC 57.422 47.619 23.35 0.00 45.29 4.40
3097 3712 5.127693 AGTTCACTACTAACTGCAGAGTG 57.872 43.478 23.35 21.81 35.87 3.51
3098 3713 6.239396 TCTAGTTCACTACTAACTGCAGAGT 58.761 40.000 23.35 16.88 38.84 3.24
3099 3714 6.745159 TCTAGTTCACTACTAACTGCAGAG 57.255 41.667 23.35 11.11 38.84 3.35
3100 3715 7.612244 AGAATCTAGTTCACTACTAACTGCAGA 59.388 37.037 23.35 0.00 38.84 4.26
3101 3716 7.700234 CAGAATCTAGTTCACTACTAACTGCAG 59.300 40.741 13.48 13.48 38.84 4.41
3102 3717 7.176865 ACAGAATCTAGTTCACTACTAACTGCA 59.823 37.037 0.00 0.00 38.84 4.41
3103 3718 7.540299 ACAGAATCTAGTTCACTACTAACTGC 58.460 38.462 0.00 0.00 38.84 4.40
3104 3719 9.915629 AAACAGAATCTAGTTCACTACTAACTG 57.084 33.333 0.00 0.00 38.84 3.16
3112 3727 9.832445 TTCAAACTAAACAGAATCTAGTTCACT 57.168 29.630 0.00 0.00 39.39 3.41
3113 3728 9.865484 GTTCAAACTAAACAGAATCTAGTTCAC 57.135 33.333 0.00 0.00 39.39 3.18
3114 3729 9.832445 AGTTCAAACTAAACAGAATCTAGTTCA 57.168 29.630 0.00 0.00 37.06 3.18
3116 3731 9.057089 CCAGTTCAAACTAAACAGAATCTAGTT 57.943 33.333 0.00 0.00 37.08 2.24
3117 3732 8.429641 TCCAGTTCAAACTAAACAGAATCTAGT 58.570 33.333 0.00 0.00 37.08 2.57
3118 3733 8.833231 TCCAGTTCAAACTAAACAGAATCTAG 57.167 34.615 0.00 0.00 37.08 2.43
3119 3734 8.429641 ACTCCAGTTCAAACTAAACAGAATCTA 58.570 33.333 0.00 0.00 37.08 1.98
3120 3735 7.283329 ACTCCAGTTCAAACTAAACAGAATCT 58.717 34.615 0.00 0.00 37.08 2.40
3121 3736 7.497925 ACTCCAGTTCAAACTAAACAGAATC 57.502 36.000 0.00 0.00 37.08 2.52
3122 3737 8.211629 AGTACTCCAGTTCAAACTAAACAGAAT 58.788 33.333 0.00 0.00 37.08 2.40
3123 3738 7.494625 CAGTACTCCAGTTCAAACTAAACAGAA 59.505 37.037 0.00 0.00 37.08 3.02
3124 3739 6.984474 CAGTACTCCAGTTCAAACTAAACAGA 59.016 38.462 0.00 0.00 37.08 3.41
3125 3740 6.292919 GCAGTACTCCAGTTCAAACTAAACAG 60.293 42.308 0.00 0.00 37.08 3.16
3126 3741 5.526111 GCAGTACTCCAGTTCAAACTAAACA 59.474 40.000 0.00 0.00 37.08 2.83
3127 3742 5.758784 AGCAGTACTCCAGTTCAAACTAAAC 59.241 40.000 0.00 0.00 37.08 2.01
3128 3743 5.925509 AGCAGTACTCCAGTTCAAACTAAA 58.074 37.500 0.00 0.00 37.08 1.85
3129 3744 5.546621 AGCAGTACTCCAGTTCAAACTAA 57.453 39.130 0.00 0.00 37.08 2.24


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

AutoCloner maintained by Alex Coulton.