Multiple sequence alignment - TraesCS1B01G308700

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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 TraesCS1B01G308700 chr1B 100.000 3937 0 0 1 3937 531206711 531202775 0.000000e+00 7271
1 TraesCS1B01G308700 chr1B 92.373 118 7 2 2996 3111 58710677 58710560 2.430000e-37 167
2 TraesCS1B01G308700 chr1D 93.938 3052 94 35 1 2998 391316750 391319764 0.000000e+00 4527
3 TraesCS1B01G308700 chr1D 94.140 529 19 6 3110 3633 391319763 391320284 0.000000e+00 795
4 TraesCS1B01G308700 chr1D 95.620 274 12 0 3664 3937 391322498 391322771 1.300000e-119 440
5 TraesCS1B01G308700 chr1D 93.277 119 6 2 2997 3113 222028542 222028424 1.450000e-39 174
6 TraesCS1B01G308700 chr1A 97.507 2567 64 0 432 2998 493823635 493821069 0.000000e+00 4386
7 TraesCS1B01G308700 chr1A 88.350 515 19 14 3110 3620 493821070 493820593 7.330000e-162 580
8 TraesCS1B01G308700 chr1A 94.203 276 15 1 3663 3937 493820591 493820316 1.690000e-113 420
9 TraesCS1B01G308700 chr1A 89.922 129 8 5 2992 3117 569891811 569891937 1.130000e-35 161
10 TraesCS1B01G308700 chr1A 88.776 98 10 1 3606 3703 563590743 563590839 6.910000e-23 119
11 TraesCS1B01G308700 chr3B 95.088 2565 120 1 440 2998 702692596 702690032 0.000000e+00 4034
12 TraesCS1B01G308700 chr3B 83.619 525 46 16 3108 3608 702690035 702689527 1.290000e-124 457
13 TraesCS1B01G308700 chr3B 91.667 120 8 2 2996 3113 201343457 201343576 8.750000e-37 165
14 TraesCS1B01G308700 chr3B 90.625 96 6 2 3611 3703 731134716 731134811 1.490000e-24 124
15 TraesCS1B01G308700 chr3A 94.815 2565 127 1 440 2998 665967174 665964610 0.000000e+00 3995
16 TraesCS1B01G308700 chr3A 85.492 386 25 12 3108 3480 665964613 665964246 1.340000e-99 374
17 TraesCS1B01G308700 chr3D 94.698 2565 130 1 440 2998 531367824 531365260 0.000000e+00 3978
18 TraesCS1B01G308700 chr3D 94.340 2562 138 2 440 2995 426440291 426442851 0.000000e+00 3921
19 TraesCS1B01G308700 chr3D 85.243 515 45 13 3108 3607 426442851 426443349 5.870000e-138 501
20 TraesCS1B01G308700 chr3D 84.100 522 46 18 3108 3608 531365263 531364758 1.660000e-128 470
21 TraesCS1B01G308700 chr4A 85.958 997 89 28 162 1118 590255894 590254909 0.000000e+00 1018
22 TraesCS1B01G308700 chrUn 97.076 342 10 0 2654 2995 480559231 480559572 9.490000e-161 577
23 TraesCS1B01G308700 chr4D 86.866 434 28 14 676 1103 12419533 12419943 3.590000e-125 459
24 TraesCS1B01G308700 chr4D 82.845 478 50 18 3146 3608 12419948 12420408 2.200000e-107 399
25 TraesCS1B01G308700 chr5D 92.562 121 7 2 2993 3111 47538500 47538620 5.230000e-39 172
26 TraesCS1B01G308700 chr5D 93.966 116 4 2 2997 3111 382258646 382258533 5.230000e-39 172
27 TraesCS1B01G308700 chr5D 90.526 95 4 3 3610 3703 491004692 491004602 1.920000e-23 121
28 TraesCS1B01G308700 chr5D 85.841 113 9 6 3606 3716 491004604 491004711 3.220000e-21 113
29 TraesCS1B01G308700 chr5B 92.437 119 7 2 2996 3112 594747112 594746994 6.770000e-38 169
30 TraesCS1B01G308700 chr2D 92.437 119 7 2 2995 3111 155565250 155565368 6.770000e-38 169
31 TraesCS1B01G308700 chr2D 87.736 106 5 5 3606 3710 376700736 376700834 2.490000e-22 117
32 TraesCS1B01G308700 chr6B 91.667 120 8 2 2995 3112 704015499 704015380 8.750000e-37 165
33 TraesCS1B01G308700 chr4B 91.262 103 8 1 3606 3708 544445374 544445273 5.300000e-29 139
34 TraesCS1B01G308700 chr4B 88.776 98 9 1 3606 3703 11736831 11736926 6.910000e-23 119
35 TraesCS1B01G308700 chr7A 90.816 98 6 3 3610 3706 557893288 557893193 1.150000e-25 128
36 TraesCS1B01G308700 chr5A 82.895 152 17 6 3115 3265 450419375 450419518 1.150000e-25 128
37 TraesCS1B01G308700 chr2A 84.298 121 15 4 3610 3727 748086314 748086433 8.940000e-22 115


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 TraesCS1B01G308700 chr1B 531202775 531206711 3936 True 7271.000000 7271 100.000000 1 3937 1 chr1B.!!$R2 3936
1 TraesCS1B01G308700 chr1D 391316750 391322771 6021 False 1920.666667 4527 94.566000 1 3937 3 chr1D.!!$F1 3936
2 TraesCS1B01G308700 chr1A 493820316 493823635 3319 True 1795.333333 4386 93.353333 432 3937 3 chr1A.!!$R1 3505
3 TraesCS1B01G308700 chr3B 702689527 702692596 3069 True 2245.500000 4034 89.353500 440 3608 2 chr3B.!!$R1 3168
4 TraesCS1B01G308700 chr3A 665964246 665967174 2928 True 2184.500000 3995 90.153500 440 3480 2 chr3A.!!$R1 3040
5 TraesCS1B01G308700 chr3D 531364758 531367824 3066 True 2224.000000 3978 89.399000 440 3608 2 chr3D.!!$R1 3168
6 TraesCS1B01G308700 chr3D 426440291 426443349 3058 False 2211.000000 3921 89.791500 440 3607 2 chr3D.!!$F1 3167
7 TraesCS1B01G308700 chr4A 590254909 590255894 985 True 1018.000000 1018 85.958000 162 1118 1 chr4A.!!$R1 956
8 TraesCS1B01G308700 chr4D 12419533 12420408 875 False 429.000000 459 84.855500 676 3608 2 chr4D.!!$F1 2932

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
185 216 0.182299 CCAGGAATCAAGGAGGAGGC 59.818 60.000 0.00 0.0 0.00 4.70 F
398 447 2.027007 CCGGGACAAAACTGGGTATACA 60.027 50.000 5.01 0.0 0.00 2.29 F
1410 1525 1.063792 TGGTTCCCCATGATGATGTGG 60.064 52.381 0.00 0.0 35.17 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 1326 1.202855 AGCACACTGGTCAGAGCAAAT 60.203 47.619 3.41 0.0 0.00 2.32 R
2318 2433 0.447801 CACGCCAAACCATAGCAGAC 59.552 55.000 0.00 0.0 0.00 3.51 R
3088 3203 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.0 44.66 2.24 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
27 28 0.918258 TAATGCTGCCTCCACATGGA 59.082 50.000 0.00 0.00 43.08 3.41
28 29 0.682209 AATGCTGCCTCCACATGGAC 60.682 55.000 0.00 0.00 39.78 4.02
29 30 1.855441 ATGCTGCCTCCACATGGACA 61.855 55.000 0.00 0.00 39.78 4.02
30 31 1.077212 GCTGCCTCCACATGGACAT 60.077 57.895 0.00 0.00 39.78 3.06
31 32 1.381928 GCTGCCTCCACATGGACATG 61.382 60.000 10.57 10.57 44.15 3.21
32 33 0.750546 CTGCCTCCACATGGACATGG 60.751 60.000 15.94 0.00 42.91 3.66
33 34 1.304282 GCCTCCACATGGACATGGT 59.696 57.895 15.94 0.31 42.91 3.55
34 35 0.546122 GCCTCCACATGGACATGGTA 59.454 55.000 15.94 1.26 42.91 3.25
35 36 1.747206 GCCTCCACATGGACATGGTAC 60.747 57.143 15.94 0.00 42.91 3.34
178 209 2.093341 CCATTTTGCCCAGGAATCAAGG 60.093 50.000 0.00 0.00 0.00 3.61
185 216 0.182299 CCAGGAATCAAGGAGGAGGC 59.818 60.000 0.00 0.00 0.00 4.70
242 273 4.096003 CCGGCCCGATCTGTTGGT 62.096 66.667 3.71 0.00 0.00 3.67
296 327 2.657944 CTCCTCTGCGCTCGATGC 60.658 66.667 9.73 3.02 38.57 3.91
315 346 3.149196 TGCAAATGAAACAGAGGAGGAC 58.851 45.455 0.00 0.00 0.00 3.85
334 365 4.856607 GAACGGAGCTCGCTCGGG 62.857 72.222 24.16 15.86 44.40 5.14
353 402 4.394712 GGTCAGGCGGGTGGAGTG 62.395 72.222 0.00 0.00 0.00 3.51
354 403 4.394712 GTCAGGCGGGTGGAGTGG 62.395 72.222 0.00 0.00 0.00 4.00
355 404 4.631740 TCAGGCGGGTGGAGTGGA 62.632 66.667 0.00 0.00 0.00 4.02
356 405 4.087892 CAGGCGGGTGGAGTGGAG 62.088 72.222 0.00 0.00 0.00 3.86
357 406 4.640690 AGGCGGGTGGAGTGGAGT 62.641 66.667 0.00 0.00 0.00 3.85
380 429 2.223711 GCATTTGGCCTGTAATAACCGG 60.224 50.000 3.32 0.00 36.11 5.28
398 447 2.027007 CCGGGACAAAACTGGGTATACA 60.027 50.000 5.01 0.00 0.00 2.29
402 451 5.395990 CGGGACAAAACTGGGTATACATACT 60.396 44.000 5.01 0.00 33.81 2.12
430 519 2.076207 TTACTTGGGGGATCGATCGA 57.924 50.000 21.86 21.86 0.00 3.59
1211 1326 1.406887 GCGGCTTCTAAGATCAACCCA 60.407 52.381 0.00 0.00 0.00 4.51
1410 1525 1.063792 TGGTTCCCCATGATGATGTGG 60.064 52.381 0.00 0.00 35.17 4.17
1503 1618 4.823442 TCAAAATGATGCAGTCTTCTGTGT 59.177 37.500 0.00 0.00 43.05 3.72
2021 2136 8.808529 ACTCAGAAAGAACACGATATAATTTCG 58.191 33.333 0.00 0.00 42.20 3.46
2114 2229 1.739067 ACAAGAGCGGTATTGAAGCC 58.261 50.000 26.87 0.00 0.00 4.35
2318 2433 1.001406 GGAGATATCCCTTCAGCACCG 59.999 57.143 0.00 0.00 0.00 4.94
2420 2535 2.227388 GGTGCTTGAGATTGAACCACAG 59.773 50.000 0.00 0.00 0.00 3.66
2516 2631 5.136105 AGGAAATCAATGAGGAACATAGGC 58.864 41.667 0.00 0.00 38.38 3.93
2546 2661 2.234168 GGAGACTGGTCTTAGTTGGGTC 59.766 54.545 4.67 0.00 40.61 4.46
2753 2868 3.185391 GCGAGAGATTGGCTTTAGCATAC 59.815 47.826 3.88 0.00 44.36 2.39
2774 2889 0.678048 GGCTTGTGATGACACCTCCC 60.678 60.000 0.00 0.00 45.40 4.30
2888 3003 8.498054 AAATTATTGTGAGAGACATCAATCGT 57.502 30.769 0.00 0.00 34.62 3.73
2961 3076 7.099266 TGTTCCATTGTCCATTCATGTATTC 57.901 36.000 0.00 0.00 0.00 1.75
3002 3117 7.771183 TGATTTGCATCAACTTTAATACTCCC 58.229 34.615 0.00 0.00 36.41 4.30
3003 3118 7.615365 TGATTTGCATCAACTTTAATACTCCCT 59.385 33.333 0.00 0.00 36.41 4.20
3004 3119 7.775053 TTTGCATCAACTTTAATACTCCCTT 57.225 32.000 0.00 0.00 0.00 3.95
3005 3120 7.775053 TTGCATCAACTTTAATACTCCCTTT 57.225 32.000 0.00 0.00 0.00 3.11
3006 3121 7.156876 TGCATCAACTTTAATACTCCCTTTG 57.843 36.000 0.00 0.00 0.00 2.77
3007 3122 6.719370 TGCATCAACTTTAATACTCCCTTTGT 59.281 34.615 0.00 0.00 0.00 2.83
3008 3123 7.094377 TGCATCAACTTTAATACTCCCTTTGTC 60.094 37.037 0.00 0.00 0.00 3.18
3009 3124 7.121315 GCATCAACTTTAATACTCCCTTTGTCT 59.879 37.037 0.00 0.00 0.00 3.41
3010 3125 7.979444 TCAACTTTAATACTCCCTTTGTCTG 57.021 36.000 0.00 0.00 0.00 3.51
3011 3126 6.940298 TCAACTTTAATACTCCCTTTGTCTGG 59.060 38.462 0.00 0.00 0.00 3.86
3012 3127 6.697641 ACTTTAATACTCCCTTTGTCTGGA 57.302 37.500 0.00 0.00 0.00 3.86
3013 3128 7.086685 ACTTTAATACTCCCTTTGTCTGGAA 57.913 36.000 0.00 0.00 0.00 3.53
3014 3129 7.523415 ACTTTAATACTCCCTTTGTCTGGAAA 58.477 34.615 0.00 0.00 0.00 3.13
3015 3130 8.170730 ACTTTAATACTCCCTTTGTCTGGAAAT 58.829 33.333 0.00 0.00 0.00 2.17
3016 3131 9.681062 CTTTAATACTCCCTTTGTCTGGAAATA 57.319 33.333 0.00 0.00 0.00 1.40
3017 3132 9.457436 TTTAATACTCCCTTTGTCTGGAAATAC 57.543 33.333 0.00 0.00 0.00 1.89
3018 3133 6.893020 ATACTCCCTTTGTCTGGAAATACT 57.107 37.500 0.00 0.00 0.00 2.12
3019 3134 5.584551 ACTCCCTTTGTCTGGAAATACTT 57.415 39.130 0.00 0.00 0.00 2.24
3020 3135 5.316987 ACTCCCTTTGTCTGGAAATACTTG 58.683 41.667 0.00 0.00 0.00 3.16
3021 3136 5.163088 ACTCCCTTTGTCTGGAAATACTTGT 60.163 40.000 0.00 0.00 0.00 3.16
3022 3137 5.313712 TCCCTTTGTCTGGAAATACTTGTC 58.686 41.667 0.00 0.00 0.00 3.18
3023 3138 4.154195 CCCTTTGTCTGGAAATACTTGTCG 59.846 45.833 0.00 0.00 0.00 4.35
3024 3139 4.755123 CCTTTGTCTGGAAATACTTGTCGT 59.245 41.667 0.00 0.00 0.00 4.34
3025 3140 5.238650 CCTTTGTCTGGAAATACTTGTCGTT 59.761 40.000 0.00 0.00 0.00 3.85
3026 3141 5.666969 TTGTCTGGAAATACTTGTCGTTG 57.333 39.130 0.00 0.00 0.00 4.10
3027 3142 4.951254 TGTCTGGAAATACTTGTCGTTGA 58.049 39.130 0.00 0.00 0.00 3.18
3028 3143 5.361427 TGTCTGGAAATACTTGTCGTTGAA 58.639 37.500 0.00 0.00 0.00 2.69
3029 3144 5.818336 TGTCTGGAAATACTTGTCGTTGAAA 59.182 36.000 0.00 0.00 0.00 2.69
3030 3145 6.485313 TGTCTGGAAATACTTGTCGTTGAAAT 59.515 34.615 0.00 0.00 0.00 2.17
3031 3146 6.797033 GTCTGGAAATACTTGTCGTTGAAATG 59.203 38.462 0.00 0.00 0.00 2.32
3032 3147 6.708502 TCTGGAAATACTTGTCGTTGAAATGA 59.291 34.615 0.00 0.00 0.00 2.57
3033 3148 7.390440 TCTGGAAATACTTGTCGTTGAAATGAT 59.610 33.333 0.00 0.00 0.00 2.45
3034 3149 8.554835 TGGAAATACTTGTCGTTGAAATGATA 57.445 30.769 0.00 0.00 0.00 2.15
3035 3150 9.173021 TGGAAATACTTGTCGTTGAAATGATAT 57.827 29.630 0.00 0.00 0.00 1.63
3077 3192 9.872684 AATTCTAGTACATCCATTTTCATCCAT 57.127 29.630 0.00 0.00 0.00 3.41
3078 3193 9.872684 ATTCTAGTACATCCATTTTCATCCATT 57.127 29.630 0.00 0.00 0.00 3.16
3079 3194 9.699410 TTCTAGTACATCCATTTTCATCCATTT 57.301 29.630 0.00 0.00 0.00 2.32
3083 3198 8.362639 AGTACATCCATTTTCATCCATTTATGC 58.637 33.333 0.00 0.00 0.00 3.14
3084 3199 6.218019 ACATCCATTTTCATCCATTTATGCG 58.782 36.000 0.00 0.00 0.00 4.73
3085 3200 6.040729 ACATCCATTTTCATCCATTTATGCGA 59.959 34.615 0.00 0.00 0.00 5.10
3086 3201 5.830912 TCCATTTTCATCCATTTATGCGAC 58.169 37.500 0.00 0.00 0.00 5.19
3087 3202 5.359292 TCCATTTTCATCCATTTATGCGACA 59.641 36.000 0.00 0.00 0.00 4.35
3088 3203 6.041511 CCATTTTCATCCATTTATGCGACAA 58.958 36.000 0.00 0.00 0.00 3.18
3089 3204 6.199531 CCATTTTCATCCATTTATGCGACAAG 59.800 38.462 0.00 0.00 0.00 3.16
3090 3205 5.895636 TTTCATCCATTTATGCGACAAGT 57.104 34.783 0.00 0.00 0.00 3.16
3091 3206 6.993786 TTTCATCCATTTATGCGACAAGTA 57.006 33.333 0.00 0.00 0.00 2.24
3092 3207 6.993786 TTCATCCATTTATGCGACAAGTAA 57.006 33.333 0.00 0.00 0.00 2.24
3093 3208 7.566760 TTCATCCATTTATGCGACAAGTAAT 57.433 32.000 0.00 0.00 0.00 1.89
3094 3209 7.566760 TCATCCATTTATGCGACAAGTAATT 57.433 32.000 0.00 0.00 0.00 1.40
3095 3210 7.639039 TCATCCATTTATGCGACAAGTAATTC 58.361 34.615 0.00 0.00 0.00 2.17
3096 3211 6.371809 TCCATTTATGCGACAAGTAATTCC 57.628 37.500 0.00 0.00 0.00 3.01
3097 3212 5.007234 TCCATTTATGCGACAAGTAATTCCG 59.993 40.000 0.00 0.00 0.00 4.30
3098 3213 4.868450 TTTATGCGACAAGTAATTCCGG 57.132 40.909 0.00 0.00 0.00 5.14
3099 3214 2.684001 ATGCGACAAGTAATTCCGGA 57.316 45.000 0.00 0.00 0.00 5.14
3100 3215 1.717194 TGCGACAAGTAATTCCGGAC 58.283 50.000 1.83 0.00 0.00 4.79
3101 3216 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
3102 3217 1.274596 CGACAAGTAATTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
3103 3218 1.135315 CGACAAGTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
3104 3219 2.537401 GACAAGTAATTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3105 3220 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3106 3221 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3107 3222 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
3108 3223 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3271 3396 7.712639 TCTGTGCTCATCAATTCTACCTTAATC 59.287 37.037 0.00 0.00 0.00 1.75
3294 3419 1.600957 CTAGGTTGGCATCAATCAGCG 59.399 52.381 0.00 0.00 36.49 5.18
3423 3562 9.807921 ATGTACAGAATCTTTTTCTAAGGGAAA 57.192 29.630 0.33 0.00 41.58 3.13
3436 3575 7.654022 TTCTAAGGGAAAACACAAAGACAAT 57.346 32.000 0.00 0.00 0.00 2.71
3450 3589 1.550524 AGACAATAGGCTTGCGTCTCA 59.449 47.619 0.00 0.00 31.39 3.27
3500 3639 2.673523 CCAGGAGGGCAAGACAGG 59.326 66.667 0.00 0.00 0.00 4.00
3521 3666 2.930682 GACGCACATTAGGAAAGGAGAC 59.069 50.000 0.00 0.00 0.00 3.36
3633 3778 7.486647 TCTCCGTAAAGAAATATAAGAGCGTT 58.513 34.615 0.00 0.00 0.00 4.84
3634 3779 7.977853 TCTCCGTAAAGAAATATAAGAGCGTTT 59.022 33.333 0.00 0.00 0.00 3.60
3635 3780 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
3636 3781 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
3637 3782 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
3647 3792 7.811117 ATAAGAGCGTTTAGATCACTAGAGT 57.189 36.000 0.00 0.00 37.82 3.24
3648 3793 6.518208 AAGAGCGTTTAGATCACTAGAGTT 57.482 37.500 0.00 0.00 37.82 3.01
3649 3794 6.518208 AGAGCGTTTAGATCACTAGAGTTT 57.482 37.500 0.00 0.00 37.82 2.66
3650 3795 7.627298 AGAGCGTTTAGATCACTAGAGTTTA 57.373 36.000 0.00 0.00 37.82 2.01
3652 3797 7.553402 AGAGCGTTTAGATCACTAGAGTTTAGA 59.447 37.037 0.00 0.00 37.82 2.10
3653 3798 8.228035 AGCGTTTAGATCACTAGAGTTTAGAT 57.772 34.615 0.00 0.00 0.00 1.98
3654 3799 8.688151 AGCGTTTAGATCACTAGAGTTTAGATT 58.312 33.333 0.00 0.00 0.00 2.40
3655 3800 9.947669 GCGTTTAGATCACTAGAGTTTAGATTA 57.052 33.333 0.00 0.00 0.00 1.75
3681 6009 5.885881 ACTCTAGTGATCTAAACGCTCTTG 58.114 41.667 0.00 0.00 0.00 3.02
3767 6096 2.830370 GCGATGAAAGGCAGGGGG 60.830 66.667 0.00 0.00 0.00 5.40
3873 6202 9.941325 ATTATGCTCTACCATCTCTTAAGAATG 57.059 33.333 6.63 12.17 34.49 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.591835 GGAGAGGAGGAGCGCTCG 61.592 72.222 29.81 0.00 0.00 5.03
94 100 1.803334 TGATTCCGTAGCACAACCAC 58.197 50.000 0.00 0.00 0.00 4.16
97 103 3.994392 TCTTCTTGATTCCGTAGCACAAC 59.006 43.478 0.00 0.00 0.00 3.32
149 155 2.040145 CCTGGGCAAAATGGTGGATTTT 59.960 45.455 0.00 0.00 43.77 1.82
150 156 1.629861 CCTGGGCAAAATGGTGGATTT 59.370 47.619 0.00 0.00 35.65 2.17
151 157 1.203288 TCCTGGGCAAAATGGTGGATT 60.203 47.619 0.00 0.00 0.00 3.01
152 158 0.413037 TCCTGGGCAAAATGGTGGAT 59.587 50.000 0.00 0.00 0.00 3.41
153 159 0.189574 TTCCTGGGCAAAATGGTGGA 59.810 50.000 0.00 0.00 0.00 4.02
155 161 1.901159 TGATTCCTGGGCAAAATGGTG 59.099 47.619 0.00 0.00 0.00 4.17
156 162 2.323999 TGATTCCTGGGCAAAATGGT 57.676 45.000 0.00 0.00 0.00 3.55
157 163 2.093341 CCTTGATTCCTGGGCAAAATGG 60.093 50.000 0.00 0.00 0.00 3.16
158 164 2.833338 TCCTTGATTCCTGGGCAAAATG 59.167 45.455 0.00 0.00 0.00 2.32
178 209 2.185608 GCTCTCAACCGCCTCCTC 59.814 66.667 0.00 0.00 0.00 3.71
185 216 1.079543 CAGGTCAGGCTCTCAACCG 60.080 63.158 0.00 0.00 36.87 4.44
296 327 2.744202 CCGTCCTCCTCTGTTTCATTTG 59.256 50.000 0.00 0.00 0.00 2.32
340 371 4.640690 ACTCCACTCCACCCGCCT 62.641 66.667 0.00 0.00 0.00 5.52
342 373 4.394712 CCACTCCACTCCACCCGC 62.395 72.222 0.00 0.00 0.00 6.13
378 427 3.337694 TGTATACCCAGTTTTGTCCCG 57.662 47.619 0.00 0.00 0.00 5.14
380 429 7.933215 AAAGTATGTATACCCAGTTTTGTCC 57.067 36.000 0.00 0.00 33.79 4.02
430 519 2.813908 GCGGGACTGCGAATTCGT 60.814 61.111 27.24 9.44 42.22 3.85
697 797 2.685380 AGAAGAGGTCCAGGCCGG 60.685 66.667 0.00 0.00 0.00 6.13
1211 1326 1.202855 AGCACACTGGTCAGAGCAAAT 60.203 47.619 3.41 0.00 0.00 2.32
1410 1525 9.057089 CAGGGATATCATAAAACTCCAAAGTAC 57.943 37.037 4.83 0.00 33.48 2.73
1492 1607 4.623932 TCATTAGGCAACACAGAAGACT 57.376 40.909 0.00 0.00 41.41 3.24
1955 2070 2.195727 TCCCTGATGCATCCACACTTA 58.804 47.619 23.67 2.32 0.00 2.24
2021 2136 7.066766 GCATATCCTGAGATTATGGAATTCCAC 59.933 40.741 29.32 16.31 40.42 4.02
2114 2229 5.931532 AGAGCAACAAAAGTGATATCGTTG 58.068 37.500 12.08 12.08 37.41 4.10
2240 2355 3.873952 GTCCTAGAAGCCTAACAATGCAG 59.126 47.826 0.00 0.00 0.00 4.41
2318 2433 0.447801 CACGCCAAACCATAGCAGAC 59.552 55.000 0.00 0.00 0.00 3.51
2420 2535 6.259550 AGCAAGACATAAGTTGTTTCATCC 57.740 37.500 0.00 0.00 39.18 3.51
2510 2625 2.959707 AGTCTCCTTCCTTACGCCTATG 59.040 50.000 0.00 0.00 0.00 2.23
2516 2631 2.448453 AGACCAGTCTCCTTCCTTACG 58.552 52.381 0.00 0.00 34.17 3.18
2546 2661 4.497006 GCATGAATTTCACCCTTCATCTCG 60.497 45.833 0.15 0.00 39.47 4.04
2753 2868 1.003355 AGGTGTCATCACAAGCCCG 60.003 57.895 0.98 0.00 45.45 6.13
2888 3003 6.882656 TGTTCCCTTGTCAAAATGATGAAAA 58.117 32.000 0.00 0.00 0.00 2.29
2961 3076 2.054232 ATCAATGAGCAGCTCCCTTG 57.946 50.000 20.16 20.71 0.00 3.61
2989 3104 6.697641 TCCAGACAAAGGGAGTATTAAAGT 57.302 37.500 0.00 0.00 0.00 2.66
2998 3113 5.316987 ACAAGTATTTCCAGACAAAGGGAG 58.683 41.667 0.00 0.00 34.02 4.30
2999 3114 5.313712 GACAAGTATTTCCAGACAAAGGGA 58.686 41.667 0.00 0.00 0.00 4.20
3000 3115 4.154195 CGACAAGTATTTCCAGACAAAGGG 59.846 45.833 0.00 0.00 0.00 3.95
3001 3116 4.755123 ACGACAAGTATTTCCAGACAAAGG 59.245 41.667 0.00 0.00 0.00 3.11
3002 3117 5.924475 ACGACAAGTATTTCCAGACAAAG 57.076 39.130 0.00 0.00 0.00 2.77
3003 3118 5.818336 TCAACGACAAGTATTTCCAGACAAA 59.182 36.000 0.00 0.00 0.00 2.83
3004 3119 5.361427 TCAACGACAAGTATTTCCAGACAA 58.639 37.500 0.00 0.00 0.00 3.18
3005 3120 4.951254 TCAACGACAAGTATTTCCAGACA 58.049 39.130 0.00 0.00 0.00 3.41
3006 3121 5.917541 TTCAACGACAAGTATTTCCAGAC 57.082 39.130 0.00 0.00 0.00 3.51
3007 3122 6.708502 TCATTTCAACGACAAGTATTTCCAGA 59.291 34.615 0.00 0.00 0.00 3.86
3008 3123 6.898041 TCATTTCAACGACAAGTATTTCCAG 58.102 36.000 0.00 0.00 0.00 3.86
3009 3124 6.869315 TCATTTCAACGACAAGTATTTCCA 57.131 33.333 0.00 0.00 0.00 3.53
3051 3166 9.872684 ATGGATGAAAATGGATGTACTAGAATT 57.127 29.630 0.00 0.00 0.00 2.17
3052 3167 9.872684 AATGGATGAAAATGGATGTACTAGAAT 57.127 29.630 0.00 0.00 0.00 2.40
3053 3168 9.699410 AAATGGATGAAAATGGATGTACTAGAA 57.301 29.630 0.00 0.00 0.00 2.10
3057 3172 8.362639 GCATAAATGGATGAAAATGGATGTACT 58.637 33.333 0.00 0.00 0.00 2.73
3058 3173 7.326789 CGCATAAATGGATGAAAATGGATGTAC 59.673 37.037 0.00 0.00 0.00 2.90
3059 3174 7.230309 TCGCATAAATGGATGAAAATGGATGTA 59.770 33.333 0.00 0.00 0.00 2.29
3060 3175 6.040729 TCGCATAAATGGATGAAAATGGATGT 59.959 34.615 0.00 0.00 0.00 3.06
3061 3176 6.364165 GTCGCATAAATGGATGAAAATGGATG 59.636 38.462 0.00 0.00 0.00 3.51
3062 3177 6.040729 TGTCGCATAAATGGATGAAAATGGAT 59.959 34.615 0.00 0.00 0.00 3.41
3063 3178 5.359292 TGTCGCATAAATGGATGAAAATGGA 59.641 36.000 0.00 0.00 0.00 3.41
3064 3179 5.590145 TGTCGCATAAATGGATGAAAATGG 58.410 37.500 0.00 0.00 0.00 3.16
3065 3180 6.753279 ACTTGTCGCATAAATGGATGAAAATG 59.247 34.615 0.00 0.00 0.00 2.32
3066 3181 6.866480 ACTTGTCGCATAAATGGATGAAAAT 58.134 32.000 0.00 0.00 0.00 1.82
3067 3182 6.266168 ACTTGTCGCATAAATGGATGAAAA 57.734 33.333 0.00 0.00 0.00 2.29
3068 3183 5.895636 ACTTGTCGCATAAATGGATGAAA 57.104 34.783 0.00 0.00 0.00 2.69
3069 3184 6.993786 TTACTTGTCGCATAAATGGATGAA 57.006 33.333 0.00 0.00 0.00 2.57
3070 3185 7.255104 GGAATTACTTGTCGCATAAATGGATGA 60.255 37.037 0.00 0.00 0.00 2.92
3071 3186 6.857964 GGAATTACTTGTCGCATAAATGGATG 59.142 38.462 0.00 0.00 0.00 3.51
3072 3187 6.293407 CGGAATTACTTGTCGCATAAATGGAT 60.293 38.462 0.00 0.00 0.00 3.41
3073 3188 5.007234 CGGAATTACTTGTCGCATAAATGGA 59.993 40.000 0.00 0.00 0.00 3.41
3074 3189 5.204833 CGGAATTACTTGTCGCATAAATGG 58.795 41.667 0.00 0.00 0.00 3.16
3075 3190 5.007234 TCCGGAATTACTTGTCGCATAAATG 59.993 40.000 0.00 0.00 0.00 2.32
3076 3191 5.007332 GTCCGGAATTACTTGTCGCATAAAT 59.993 40.000 5.23 0.00 0.00 1.40
3077 3192 4.330620 GTCCGGAATTACTTGTCGCATAAA 59.669 41.667 5.23 0.00 0.00 1.40
3078 3193 3.866910 GTCCGGAATTACTTGTCGCATAA 59.133 43.478 5.23 0.00 0.00 1.90
3079 3194 3.450578 GTCCGGAATTACTTGTCGCATA 58.549 45.455 5.23 0.00 0.00 3.14
3080 3195 2.277084 GTCCGGAATTACTTGTCGCAT 58.723 47.619 5.23 0.00 0.00 4.73
3081 3196 1.717194 GTCCGGAATTACTTGTCGCA 58.283 50.000 5.23 0.00 0.00 5.10
3082 3197 0.643820 CGTCCGGAATTACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
3083 3198 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
3084 3199 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3085 3200 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3086 3201 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3087 3202 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
3088 3203 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
3089 3204 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
3090 3205 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
3091 3206 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
3092 3207 0.187851 ATACTCCCTCCGTCCGGAAT 59.812 55.000 5.23 0.00 44.66 3.01
3093 3208 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
3094 3209 0.109342 GTATACTCCCTCCGTCCGGA 59.891 60.000 0.00 0.00 42.90 5.14
3095 3210 0.110104 AGTATACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
3096 3211 1.236628 CAGTATACTCCCTCCGTCCG 58.763 60.000 1.26 0.00 0.00 4.79
3097 3212 1.144503 TCCAGTATACTCCCTCCGTCC 59.855 57.143 1.26 0.00 0.00 4.79
3098 3213 2.653234 TCCAGTATACTCCCTCCGTC 57.347 55.000 1.26 0.00 0.00 4.79
3099 3214 3.231818 CAATCCAGTATACTCCCTCCGT 58.768 50.000 1.26 0.00 0.00 4.69
3100 3215 2.028930 GCAATCCAGTATACTCCCTCCG 60.029 54.545 1.26 0.00 0.00 4.63
3101 3216 3.007398 CAGCAATCCAGTATACTCCCTCC 59.993 52.174 1.26 0.00 0.00 4.30
3102 3217 3.898123 TCAGCAATCCAGTATACTCCCTC 59.102 47.826 1.26 0.00 0.00 4.30
3103 3218 3.928754 TCAGCAATCCAGTATACTCCCT 58.071 45.455 1.26 0.00 0.00 4.20
3104 3219 4.899352 ATCAGCAATCCAGTATACTCCC 57.101 45.455 1.26 0.00 0.00 4.30
3105 3220 5.858381 TCAATCAGCAATCCAGTATACTCC 58.142 41.667 1.26 0.00 0.00 3.85
3106 3221 7.792374 TTTCAATCAGCAATCCAGTATACTC 57.208 36.000 1.26 0.00 0.00 2.59
3107 3222 7.994911 TCATTTCAATCAGCAATCCAGTATACT 59.005 33.333 0.00 0.00 0.00 2.12
3108 3223 8.158169 TCATTTCAATCAGCAATCCAGTATAC 57.842 34.615 0.00 0.00 0.00 1.47
3174 3297 1.131883 GTGGCACATGATTCAGCTGAC 59.868 52.381 18.03 6.65 44.52 3.51
3271 3396 2.617308 CTGATTGATGCCAACCTAGCAG 59.383 50.000 0.00 0.00 44.90 4.24
3370 3501 6.475504 ACATCACACAGATATGTTCAGGAAA 58.524 36.000 0.00 0.00 34.43 3.13
3416 3555 5.221441 GCCTATTGTCTTTGTGTTTTCCCTT 60.221 40.000 0.00 0.00 0.00 3.95
3417 3556 4.280929 GCCTATTGTCTTTGTGTTTTCCCT 59.719 41.667 0.00 0.00 0.00 4.20
3418 3557 4.280929 AGCCTATTGTCTTTGTGTTTTCCC 59.719 41.667 0.00 0.00 0.00 3.97
3423 3562 3.304659 CGCAAGCCTATTGTCTTTGTGTT 60.305 43.478 0.00 0.00 0.00 3.32
3424 3563 2.226437 CGCAAGCCTATTGTCTTTGTGT 59.774 45.455 0.00 0.00 0.00 3.72
3425 3564 2.226437 ACGCAAGCCTATTGTCTTTGTG 59.774 45.455 0.00 0.00 45.62 3.33
3426 3565 2.484264 GACGCAAGCCTATTGTCTTTGT 59.516 45.455 0.00 0.00 45.62 2.83
3427 3566 2.744202 AGACGCAAGCCTATTGTCTTTG 59.256 45.455 0.00 0.00 45.62 2.77
3431 3570 2.010145 TGAGACGCAAGCCTATTGTC 57.990 50.000 0.00 0.00 45.62 3.18
3436 3575 3.819564 ATACATTGAGACGCAAGCCTA 57.180 42.857 0.00 0.00 40.42 3.93
3497 3636 2.009774 CCTTTCCTAATGTGCGTCCTG 58.990 52.381 0.00 0.00 0.00 3.86
3499 3638 2.093658 TCTCCTTTCCTAATGTGCGTCC 60.094 50.000 0.00 0.00 0.00 4.79
3500 3639 2.930682 GTCTCCTTTCCTAATGTGCGTC 59.069 50.000 0.00 0.00 0.00 5.19
3521 3666 6.426328 GGGATGTGCACTAATATTTCTCTCTG 59.574 42.308 19.41 0.00 0.00 3.35
3608 3753 7.035840 ACGCTCTTATATTTCTTTACGGAGA 57.964 36.000 0.00 0.00 0.00 3.71
3650 3795 8.776470 GCGTTTAGATCACTAGAGTAGTAATCT 58.224 37.037 5.33 5.33 44.17 2.40
3652 3797 8.680039 AGCGTTTAGATCACTAGAGTAGTAAT 57.320 34.615 0.00 0.00 37.23 1.89
3653 3798 7.986320 AGAGCGTTTAGATCACTAGAGTAGTAA 59.014 37.037 0.00 0.00 37.82 2.24
3654 3799 7.499292 AGAGCGTTTAGATCACTAGAGTAGTA 58.501 38.462 0.00 0.00 37.82 1.82
3655 3800 6.350906 AGAGCGTTTAGATCACTAGAGTAGT 58.649 40.000 0.00 0.00 37.82 2.73
3656 3801 6.854496 AGAGCGTTTAGATCACTAGAGTAG 57.146 41.667 0.00 0.00 37.82 2.57
3657 3802 6.598457 ACAAGAGCGTTTAGATCACTAGAGTA 59.402 38.462 0.00 0.00 37.82 2.59
3659 3804 5.885881 ACAAGAGCGTTTAGATCACTAGAG 58.114 41.667 0.00 0.00 37.82 2.43
3660 3805 5.899120 ACAAGAGCGTTTAGATCACTAGA 57.101 39.130 0.00 0.00 37.82 2.43
3661 3806 8.635877 AAATACAAGAGCGTTTAGATCACTAG 57.364 34.615 0.00 0.00 37.82 2.57
3768 6097 2.432174 AAAGGCAAGGGGAGAGGTGC 62.432 60.000 0.00 0.00 36.24 5.01
3770 6099 0.405973 GAAAAGGCAAGGGGAGAGGT 59.594 55.000 0.00 0.00 0.00 3.85
3782 6111 0.039165 CGCACAAAGGAGGAAAAGGC 60.039 55.000 0.00 0.00 0.00 4.35
3820 6149 6.035327 GCTGTAAATGATTTGCTTCAACCATC 59.965 38.462 7.48 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.