Multiple sequence alignment - TraesCS3D01G120600

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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 TraesCS3D01G120600 chr3D 100.000 7702 0 0 1 7702 76384334 76376633 0.000000e+00 14224.0
1 TraesCS3D01G120600 chr3A 96.337 7644 175 26 1 7558 90864398 90856774 0.000000e+00 12467.0
2 TraesCS3D01G120600 chr3B 96.528 5300 144 9 1 5283 123358201 123352925 0.000000e+00 8732.0
3 TraesCS3D01G120600 chr3B 96.976 1025 19 3 6153 7168 123351749 123350728 0.000000e+00 1711.0
4 TraesCS3D01G120600 chr3B 94.652 748 10 3 5337 6082 123352821 123352102 0.000000e+00 1133.0
5 TraesCS3D01G120600 chr3B 96.809 94 2 1 7557 7650 771179098 771179190 1.030000e-33 156.0
6 TraesCS3D01G120600 chr3B 93.137 102 6 1 7551 7652 29377104 29377004 1.730000e-31 148.0
7 TraesCS3D01G120600 chr3B 97.674 43 1 0 5305 5347 123352867 123352825 2.980000e-09 75.0
8 TraesCS3D01G120600 chr6A 80.089 447 71 13 5652 6094 573821992 573821560 4.490000e-82 316.0
9 TraesCS3D01G120600 chr1B 81.924 343 54 5 5652 5991 554655310 554655647 4.550000e-72 283.0
10 TraesCS3D01G120600 chr1B 79.885 348 56 6 2431 2773 60595716 60595378 7.720000e-60 243.0
11 TraesCS3D01G120600 chr1B 95.918 49 2 0 977 1025 249622188 249622236 6.410000e-11 80.5
12 TraesCS3D01G120600 chr5B 81.633 343 55 5 5652 5991 461888647 461888984 2.120000e-70 278.0
13 TraesCS3D01G120600 chr5B 80.290 345 57 5 2431 2773 35550010 35549675 4.610000e-62 250.0
14 TraesCS3D01G120600 chr5B 96.703 91 3 0 7556 7646 509185705 509185795 1.340000e-32 152.0
15 TraesCS3D01G120600 chr2B 81.579 342 55 7 5652 5990 501796787 501797123 7.610000e-70 276.0
16 TraesCS3D01G120600 chr2B 79.487 156 15 12 7557 7698 397939470 397939318 2.290000e-15 95.3
17 TraesCS3D01G120600 chr2B 96.491 57 1 1 7642 7698 240186252 240186307 8.230000e-15 93.5
18 TraesCS3D01G120600 chr6B 78.523 447 74 14 5652 6094 546034653 546034225 2.740000e-69 274.0
19 TraesCS3D01G120600 chr6B 82.231 242 37 4 5647 5886 645901996 645902233 3.640000e-48 204.0
20 TraesCS3D01G120600 chr6B 77.157 197 37 5 3538 3726 645810961 645810765 2.940000e-19 108.0
21 TraesCS3D01G120600 chr2A 76.957 447 72 19 5652 6094 398489193 398488774 7.780000e-55 226.0
22 TraesCS3D01G120600 chr2A 96.842 95 3 0 7554 7648 362443165 362443071 8.000000e-35 159.0
23 TraesCS3D01G120600 chr2A 95.789 95 4 0 7556 7650 693209979 693209885 3.720000e-33 154.0
24 TraesCS3D01G120600 chr2A 95.082 61 2 1 7642 7702 384892418 384892359 2.290000e-15 95.3
25 TraesCS3D01G120600 chr2A 82.418 91 15 1 3652 3742 398489564 398489475 2.300000e-10 78.7
26 TraesCS3D01G120600 chr2A 82.955 88 14 1 3652 3739 398833766 398833852 2.300000e-10 78.7
27 TraesCS3D01G120600 chr2D 90.517 116 9 2 7546 7660 531351197 531351311 1.340000e-32 152.0
28 TraesCS3D01G120600 chr2D 88.158 76 4 4 7625 7699 304990856 304990785 1.380000e-12 86.1
29 TraesCS3D01G120600 chr4D 85.517 145 13 7 7556 7696 116822000 116821860 2.240000e-30 145.0
30 TraesCS3D01G120600 chr7B 87.597 129 8 7 7532 7660 702244409 702244529 8.060000e-30 143.0
31 TraesCS3D01G120600 chr7A 88.889 117 12 1 7543 7658 341444534 341444650 8.060000e-30 143.0
32 TraesCS3D01G120600 chrUn 95.082 61 2 1 7642 7702 163394505 163394446 2.290000e-15 95.3
33 TraesCS3D01G120600 chrUn 95.082 61 2 1 7642 7702 325472517 325472458 2.290000e-15 95.3
34 TraesCS3D01G120600 chrUn 95.082 61 2 1 7642 7702 384522767 384522708 2.290000e-15 95.3
35 TraesCS3D01G120600 chrUn 96.552 58 1 1 7642 7699 386040264 386040320 2.290000e-15 95.3
36 TraesCS3D01G120600 chr1D 95.918 49 2 0 977 1025 169068240 169068192 6.410000e-11 80.5
37 TraesCS3D01G120600 chr1A 95.745 47 2 0 977 1023 225516976 225516930 8.290000e-10 76.8


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 TraesCS3D01G120600 chr3D 76376633 76384334 7701 True 14224.00 14224 100.0000 1 7702 1 chr3D.!!$R1 7701
1 TraesCS3D01G120600 chr3A 90856774 90864398 7624 True 12467.00 12467 96.3370 1 7558 1 chr3A.!!$R1 7557
2 TraesCS3D01G120600 chr3B 123350728 123358201 7473 True 2912.75 8732 96.4575 1 7168 4 chr3B.!!$R2 7167

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
559 598 0.252742 TTCTTCCTCCTCCACCTCCC 60.253 60.000 0.00 0.00 0.00 4.30 F
1227 1267 0.742281 CTGATGGTCCAGAGCCAACG 60.742 60.000 0.00 0.00 39.72 4.10 F
1317 1357 1.177401 GGAAAAAGAATGGCCGCTCT 58.823 50.000 0.00 0.00 0.00 4.09 F
2988 3028 1.527034 TTGTGCTGTTCAGCCTCATC 58.473 50.000 19.91 7.79 0.00 2.92 F
3335 3375 0.250727 GTCAGCTGCACCCCAAGTTA 60.251 55.000 9.47 0.00 0.00 2.24 F
3340 3380 1.278127 GCTGCACCCCAAGTTAGACTA 59.722 52.381 0.00 0.00 0.00 2.59 F
3777 3817 1.661112 GCACGTCATCACCTAAAGCTC 59.339 52.381 0.00 0.00 0.00 4.09 F
4932 4972 2.174319 GGCTCTTGACGAATCCCGC 61.174 63.158 0.00 0.00 43.32 6.13 F
6094 6187 1.075542 CAAATCAACGGCTCGTGCTA 58.924 50.000 9.61 0.00 39.99 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2392 1.644786 CCGGGTTGGCATCGAAAGAC 61.645 60.000 0.00 0.00 46.97 3.01 R
2590 2630 0.031716 TCAGTATCAGCCTCCCTGCT 60.032 55.000 0.00 0.00 44.00 4.24 R
3110 3150 0.036388 TGAAGTCCGGACATTCTGGC 60.036 55.000 35.00 12.57 42.73 4.85 R
4677 4717 3.768757 CCCCTTTCCACAAAATAGCATGA 59.231 43.478 0.00 0.00 0.00 3.07 R
5302 5350 6.154534 TCCCGAAGAAGATAGAAAACAGATGA 59.845 38.462 0.00 0.00 0.00 2.92 R
5303 5351 6.341316 TCCCGAAGAAGATAGAAAACAGATG 58.659 40.000 0.00 0.00 0.00 2.90 R
5719 5812 2.064762 GACTGCGATGATACCATCTGC 58.935 52.381 6.88 6.88 45.37 4.26 R
6398 6773 0.764271 TGTTCCAGTGATCAGGCACA 59.236 50.000 0.00 0.00 41.19 4.57 R
7284 7668 2.373224 TGCTCAACATGTCCAAACACA 58.627 42.857 0.00 0.00 38.48 3.72 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
40 41 6.093633 CACTAACAAGAAGGTTAATACAGGGC 59.906 42.308 0.00 0.00 33.18 5.19
57 67 1.106285 GGCCAACAGATTCATCCACC 58.894 55.000 0.00 0.00 0.00 4.61
97 107 0.885879 TATGATAGTACCTGCCGGCG 59.114 55.000 23.90 16.52 0.00 6.46
200 210 1.059006 AGTGGGGATGATGAGGAGGC 61.059 60.000 0.00 0.00 0.00 4.70
246 278 1.422531 CCCTGCAAGATCCTAGAGCT 58.577 55.000 0.00 0.00 34.07 4.09
247 279 1.767681 CCCTGCAAGATCCTAGAGCTT 59.232 52.381 0.00 0.00 38.93 3.74
461 493 4.699522 GGTGCGAGAAACCCGGCT 62.700 66.667 0.00 0.00 0.00 5.52
559 598 0.252742 TTCTTCCTCCTCCACCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
611 650 1.972660 AAATTCTCGCCCCTCCTCCG 61.973 60.000 0.00 0.00 0.00 4.63
1149 1189 2.270527 GAGGCCTCTTCCAGCACC 59.729 66.667 26.25 0.00 0.00 5.01
1159 1199 3.655211 CCAGCACCCCCTCTGCTT 61.655 66.667 0.00 0.00 42.54 3.91
1227 1267 0.742281 CTGATGGTCCAGAGCCAACG 60.742 60.000 0.00 0.00 39.72 4.10
1317 1357 1.177401 GGAAAAAGAATGGCCGCTCT 58.823 50.000 0.00 0.00 0.00 4.09
1765 1805 2.806945 TGATGACCCATTGAGGAACC 57.193 50.000 0.00 0.00 41.22 3.62
2352 2392 7.171337 CACCCAAATTTTCCTGTGTTATCAAAG 59.829 37.037 0.00 0.00 0.00 2.77
2355 2395 8.143835 CCAAATTTTCCTGTGTTATCAAAGTCT 58.856 33.333 0.00 0.00 0.00 3.24
2444 2484 3.270877 GCCCAGAAGTTCATAACGATGT 58.729 45.455 5.50 0.00 36.23 3.06
2445 2485 3.689649 GCCCAGAAGTTCATAACGATGTT 59.310 43.478 5.50 0.00 36.23 2.71
2545 2585 8.024865 TCAACATTTCAGAACATGATTCACATC 58.975 33.333 0.00 0.00 37.89 3.06
2547 2587 8.118976 ACATTTCAGAACATGATTCACATCTT 57.881 30.769 0.00 0.00 37.89 2.40
2551 2591 9.897744 TTTCAGAACATGATTCACATCTTAAAC 57.102 29.630 0.00 0.00 37.89 2.01
2590 2630 2.819608 GTGGTTCTTGCTTCAGCCAATA 59.180 45.455 0.00 0.00 41.18 1.90
2643 2683 7.625498 TCCAGTGGAATATGTCATATTGGTA 57.375 36.000 20.43 6.01 35.68 3.25
2651 2691 9.686683 GGAATATGTCATATTGGTATTAAGCCT 57.313 33.333 20.43 0.00 35.68 4.58
2669 2709 5.712152 AGCCTTCCACTTAAATCTGTTTG 57.288 39.130 0.00 0.00 0.00 2.93
2696 2736 2.283145 ATTTCTGAAGCCTGCAGTGT 57.717 45.000 13.81 0.00 34.98 3.55
2718 2758 4.986054 TTGGCTTCCCAGTACTTTCTTA 57.014 40.909 0.00 0.00 43.37 2.10
2755 2795 5.010012 GGTTCATTGATTACCTTATGGCCTG 59.990 44.000 3.32 0.00 36.63 4.85
2896 2936 3.518590 GATTCTGGGCTGAATGCTTTTG 58.481 45.455 10.08 0.00 42.39 2.44
2962 3002 2.102578 GTTTGCATGGTAGGAGCCAAT 58.897 47.619 0.00 0.00 42.48 3.16
2988 3028 1.527034 TTGTGCTGTTCAGCCTCATC 58.473 50.000 19.91 7.79 0.00 2.92
3021 3061 2.821969 GACACAATGGAAGAACCTGCAT 59.178 45.455 0.00 0.00 39.86 3.96
3063 3103 5.063880 TCTTTGAAAAGGGAGCTGTCTAAC 58.936 41.667 0.00 0.00 36.67 2.34
3110 3150 5.009911 TCAAACAACTCATCAGTGGAAATGG 59.990 40.000 0.00 0.00 31.06 3.16
3144 3184 5.412594 CCGGACTTCAATGAATCTCTTTTCA 59.587 40.000 0.00 0.00 39.77 2.69
3185 3225 7.067494 ACCTTATCTGTGCAGATTTAATTGACC 59.933 37.037 18.34 0.00 45.31 4.02
3220 3260 8.577048 TGTTTTTCGGTTGATTATGGGTATTA 57.423 30.769 0.00 0.00 0.00 0.98
3335 3375 0.250727 GTCAGCTGCACCCCAAGTTA 60.251 55.000 9.47 0.00 0.00 2.24
3340 3380 1.278127 GCTGCACCCCAAGTTAGACTA 59.722 52.381 0.00 0.00 0.00 2.59
3362 3402 5.990120 ATACGTGAGGGTTAGTTAGTTGT 57.010 39.130 0.00 0.00 0.00 3.32
3580 3620 8.816640 AGTATTTTGTGCTGAAATTTTAGGTG 57.183 30.769 11.53 0.00 0.00 4.00
3606 3646 6.716628 TCCAGCCATTACCAGATGAAATTATC 59.283 38.462 0.00 0.00 0.00 1.75
3639 3679 3.350219 TCCTGTTGGCAGAGTTTATCC 57.650 47.619 0.00 0.00 45.28 2.59
3642 3682 3.054802 CCTGTTGGCAGAGTTTATCCTCT 60.055 47.826 0.00 0.00 45.28 3.69
3777 3817 1.661112 GCACGTCATCACCTAAAGCTC 59.339 52.381 0.00 0.00 0.00 4.09
3848 3888 6.652900 GCTCCTTCTGAAATTTCTGTAGAAGT 59.347 38.462 27.89 0.00 41.56 3.01
3944 3984 2.549754 GTCTGGATTGTGACAACAGTGG 59.450 50.000 13.45 0.01 37.67 4.00
4023 4063 4.342772 CTGGTGACAAACTTTGTTCTTCG 58.657 43.478 8.56 0.00 45.52 3.79
4095 4135 8.334734 CCTTCCATGGATATTCCTCAAGATAAT 58.665 37.037 17.06 0.00 37.46 1.28
4677 4717 3.559069 TGGTGCTACTAACCGCTATACT 58.441 45.455 0.00 0.00 40.86 2.12
4932 4972 2.174319 GGCTCTTGACGAATCCCGC 61.174 63.158 0.00 0.00 43.32 6.13
5004 5044 4.338118 AGGAAGTCTCAGCGAGATAAGAAG 59.662 45.833 10.65 0.00 40.98 2.85
5005 5045 4.097286 GGAAGTCTCAGCGAGATAAGAAGT 59.903 45.833 10.65 0.00 40.98 3.01
5691 5784 5.706833 GGGAAAGGATTGATTGTTGCATTTT 59.293 36.000 0.00 0.00 0.00 1.82
5719 5812 4.422840 CGGCTATCATGCTCTCATCTTAG 58.577 47.826 0.00 0.00 0.00 2.18
5761 5854 7.171508 CAGTCTAGCAAACAATGTTGAGACTTA 59.828 37.037 20.76 3.29 39.93 2.24
6094 6187 1.075542 CAAATCAACGGCTCGTGCTA 58.924 50.000 9.61 0.00 39.99 3.49
6123 6216 4.418392 CCTGCATTTGCTGATACAGTTTC 58.582 43.478 10.57 0.00 41.71 2.78
6398 6773 2.092914 CCAGAAAATAAGGCGAGGAGGT 60.093 50.000 0.00 0.00 0.00 3.85
6497 6872 2.640989 CGTGTGGACGTCGAGGAA 59.359 61.111 12.85 0.00 40.91 3.36
6665 7040 2.117423 TCCAGCAGGGACTCGTCA 59.883 61.111 0.00 0.00 42.15 4.35
6693 7074 1.979693 GACAGCAGGAGGGACGACT 60.980 63.158 0.00 0.00 0.00 4.18
6715 7096 2.050714 GTGACGCCTCGTTGTCGA 60.051 61.111 0.00 0.00 41.37 4.20
6871 7252 3.442076 TCTTCCTCCTCCTTACCTTGTC 58.558 50.000 0.00 0.00 0.00 3.18
6912 7293 4.115199 GCTGATGCCTCCCGGGTT 62.115 66.667 22.86 0.91 37.43 4.11
7182 7566 3.171388 ACATGGGCCGGGATCTCC 61.171 66.667 2.18 0.00 0.00 3.71
7202 7586 3.324108 GCGGTGGAGGTTGGGGTA 61.324 66.667 0.00 0.00 0.00 3.69
7253 7637 0.749454 GATTGGTTCAGCTCGGGCAT 60.749 55.000 11.40 0.00 41.70 4.40
7282 7666 2.718747 TTCCAAGGGTGTGTACGGCG 62.719 60.000 4.80 4.80 0.00 6.46
7283 7667 2.340809 CAAGGGTGTGTACGGCGA 59.659 61.111 16.62 0.00 0.00 5.54
7284 7668 1.079405 CAAGGGTGTGTACGGCGAT 60.079 57.895 16.62 0.00 0.00 4.58
7286 7670 1.823169 AAGGGTGTGTACGGCGATGT 61.823 55.000 16.62 0.00 0.00 3.06
7315 7702 7.157347 TGGACATGTTGAGCATAGATTATCTC 58.843 38.462 0.00 0.00 35.74 2.75
7369 7756 6.346359 GCTGAGATGAGATTTTGTTTGTTTGC 60.346 38.462 0.00 0.00 0.00 3.68
7558 7947 4.390129 TCATCTACTCCCTCCATCCTAC 57.610 50.000 0.00 0.00 0.00 3.18
7559 7948 3.990933 TCATCTACTCCCTCCATCCTACT 59.009 47.826 0.00 0.00 0.00 2.57
7560 7949 4.043561 TCATCTACTCCCTCCATCCTACTC 59.956 50.000 0.00 0.00 0.00 2.59
7561 7950 2.717515 TCTACTCCCTCCATCCTACTCC 59.282 54.545 0.00 0.00 0.00 3.85
7562 7951 0.563672 ACTCCCTCCATCCTACTCCC 59.436 60.000 0.00 0.00 0.00 4.30
7563 7952 0.863956 CTCCCTCCATCCTACTCCCT 59.136 60.000 0.00 0.00 0.00 4.20
7564 7953 0.861155 TCCCTCCATCCTACTCCCTC 59.139 60.000 0.00 0.00 0.00 4.30
7565 7954 0.178918 CCCTCCATCCTACTCCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
7566 7955 0.540830 CCTCCATCCTACTCCCTCCG 60.541 65.000 0.00 0.00 0.00 4.63
7567 7956 0.186386 CTCCATCCTACTCCCTCCGT 59.814 60.000 0.00 0.00 0.00 4.69
7568 7957 0.635009 TCCATCCTACTCCCTCCGTT 59.365 55.000 0.00 0.00 0.00 4.44
7569 7958 1.041437 CCATCCTACTCCCTCCGTTC 58.959 60.000 0.00 0.00 0.00 3.95
7570 7959 1.041437 CATCCTACTCCCTCCGTTCC 58.959 60.000 0.00 0.00 0.00 3.62
7571 7960 0.635009 ATCCTACTCCCTCCGTTCCA 59.365 55.000 0.00 0.00 0.00 3.53
7572 7961 0.410663 TCCTACTCCCTCCGTTCCAA 59.589 55.000 0.00 0.00 0.00 3.53
7573 7962 1.203212 TCCTACTCCCTCCGTTCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
7574 7963 1.626825 CCTACTCCCTCCGTTCCAAAA 59.373 52.381 0.00 0.00 0.00 2.44
7575 7964 2.238898 CCTACTCCCTCCGTTCCAAAAT 59.761 50.000 0.00 0.00 0.00 1.82
7576 7965 3.453353 CCTACTCCCTCCGTTCCAAAATA 59.547 47.826 0.00 0.00 0.00 1.40
7577 7966 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
7578 7967 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
7579 7968 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
7580 7969 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
7581 7970 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
7582 7971 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
7583 7972 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
7584 7973 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
7585 7974 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
7586 7975 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
7587 7976 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
7588 7977 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
7589 7978 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
7590 7979 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
7591 7980 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
7592 7981 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
7593 7982 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
7594 7983 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
7595 7984 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
7632 8021 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
7633 8022 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
7634 8023 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
7635 8024 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
7636 8025 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
7637 8026 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
7638 8027 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
7639 8028 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
7640 8029 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
7641 8030 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
7642 8031 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
7643 8032 6.138263 TCTATTTTGGAACGGAGGGAGTATA 58.862 40.000 0.00 0.00 0.00 1.47
7644 8033 5.703730 ATTTTGGAACGGAGGGAGTATAA 57.296 39.130 0.00 0.00 0.00 0.98
7645 8034 5.703730 TTTTGGAACGGAGGGAGTATAAT 57.296 39.130 0.00 0.00 0.00 1.28
7646 8035 6.811634 TTTTGGAACGGAGGGAGTATAATA 57.188 37.500 0.00 0.00 0.00 0.98
7647 8036 7.383156 TTTTGGAACGGAGGGAGTATAATAT 57.617 36.000 0.00 0.00 0.00 1.28
7648 8037 8.495160 TTTTGGAACGGAGGGAGTATAATATA 57.505 34.615 0.00 0.00 0.00 0.86
7649 8038 8.495160 TTTGGAACGGAGGGAGTATAATATAA 57.505 34.615 0.00 0.00 0.00 0.98
7650 8039 7.713734 TGGAACGGAGGGAGTATAATATAAG 57.286 40.000 0.00 0.00 0.00 1.73
7651 8040 7.472741 TGGAACGGAGGGAGTATAATATAAGA 58.527 38.462 0.00 0.00 0.00 2.10
7652 8041 7.395489 TGGAACGGAGGGAGTATAATATAAGAC 59.605 40.741 0.00 0.00 0.00 3.01
7653 8042 6.998968 ACGGAGGGAGTATAATATAAGACG 57.001 41.667 0.00 0.00 0.00 4.18
7654 8043 6.479884 ACGGAGGGAGTATAATATAAGACGT 58.520 40.000 0.00 0.00 0.00 4.34
7655 8044 6.944862 ACGGAGGGAGTATAATATAAGACGTT 59.055 38.462 0.00 0.00 0.00 3.99
7656 8045 7.449704 ACGGAGGGAGTATAATATAAGACGTTT 59.550 37.037 0.00 0.00 0.00 3.60
7657 8046 8.302438 CGGAGGGAGTATAATATAAGACGTTTT 58.698 37.037 0.00 0.00 0.00 2.43
7658 8047 9.993454 GGAGGGAGTATAATATAAGACGTTTTT 57.007 33.333 0.00 0.00 0.00 1.94
7689 8078 9.998106 ACTACACTAGTGTCAATAAAACATCTT 57.002 29.630 31.11 4.33 43.74 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.947388 TGAATCTGTTGGCCCTGTATTAAC 59.053 41.667 0.00 0.00 0.00 2.01
40 41 2.025981 TCCTGGTGGATGAATCTGTTGG 60.026 50.000 0.00 0.00 37.46 3.77
57 67 2.435586 CGGCCAGTTCTGCTCCTG 60.436 66.667 2.24 0.00 0.00 3.86
328 360 3.048941 CTCCTTCGTCGGTCGGTCC 62.049 68.421 0.00 0.00 40.32 4.46
399 431 2.770868 ATCAGTGTGGGAGGGGAGCA 62.771 60.000 0.00 0.00 0.00 4.26
477 509 2.974285 TTATAGGGTTGGGGACAGGA 57.026 50.000 0.00 0.00 44.54 3.86
611 650 2.195956 GGGCTGGGGTTGATAGGC 59.804 66.667 0.00 0.00 36.39 3.93
793 833 1.157585 GAAAAGAGCGGTCTTGTCCC 58.842 55.000 29.33 16.18 42.59 4.46
947 987 0.319900 GACAAGAAGCTGCTCCACGA 60.320 55.000 1.00 0.00 0.00 4.35
1033 1073 3.107601 CTCCATCTAAACCCAGGAGTGA 58.892 50.000 0.00 0.00 40.71 3.41
1159 1199 1.272536 ACGCTTCCTCTTACTCCCTGA 60.273 52.381 0.00 0.00 0.00 3.86
1227 1267 1.357334 GTCACTCGAGCCGGATCTC 59.643 63.158 19.08 8.62 0.00 2.75
1765 1805 5.776744 TGATCTATCTGGTGATGACATTCG 58.223 41.667 0.00 0.00 34.32 3.34
2352 2392 1.644786 CCGGGTTGGCATCGAAAGAC 61.645 60.000 0.00 0.00 46.97 3.01
2355 2395 2.204865 ATCCCGGGTTGGCATCGAAA 62.205 55.000 22.86 0.00 35.87 3.46
2444 2484 3.094572 CTCCTTTCCCGAGGTACAGTAA 58.905 50.000 0.00 0.00 38.04 2.24
2445 2485 2.309755 TCTCCTTTCCCGAGGTACAGTA 59.690 50.000 0.00 0.00 38.04 2.74
2590 2630 0.031716 TCAGTATCAGCCTCCCTGCT 60.032 55.000 0.00 0.00 44.00 4.24
2643 2683 8.306761 CAAACAGATTTAAGTGGAAGGCTTAAT 58.693 33.333 0.00 0.00 37.97 1.40
2651 2691 6.463995 ACTTGCAAACAGATTTAAGTGGAA 57.536 33.333 0.00 0.00 29.37 3.53
2669 2709 3.922850 GCAGGCTTCAGAAATTAACTTGC 59.077 43.478 0.00 0.00 0.00 4.01
2696 2736 3.876309 AGAAAGTACTGGGAAGCCAAA 57.124 42.857 0.00 0.00 0.00 3.28
2718 2758 0.700564 ATGAACCATGCTGAGGGTGT 59.299 50.000 0.00 0.00 36.03 4.16
2896 2936 1.334779 GCATGGCGCTTCTGATTCATC 60.335 52.381 7.64 0.00 37.77 2.92
2988 3028 2.598589 CATTGTGTCTTGCCAATTCCG 58.401 47.619 0.00 0.00 0.00 4.30
3021 3061 6.936335 TCAAAGAGTGATATCTGAACTTTGCA 59.064 34.615 23.50 16.41 40.96 4.08
3063 3103 0.093535 CAGCGTATGTGCAGTCAACG 59.906 55.000 6.48 6.48 37.31 4.10
3110 3150 0.036388 TGAAGTCCGGACATTCTGGC 60.036 55.000 35.00 12.57 42.73 4.85
3220 3260 9.420118 TGTTTCTATTATAAAATCCTGGCATGT 57.580 29.630 0.00 0.00 0.00 3.21
3335 3375 6.657875 ACTAACTAACCCTCACGTATAGTCT 58.342 40.000 0.00 0.00 0.00 3.24
3340 3380 5.990120 ACAACTAACTAACCCTCACGTAT 57.010 39.130 0.00 0.00 0.00 3.06
3362 3402 2.394632 ACTCCACAGTGACTGGTACAA 58.605 47.619 17.92 0.00 38.70 2.41
3580 3620 3.281727 TTCATCTGGTAATGGCTGGAC 57.718 47.619 0.00 0.00 0.00 4.02
3606 3646 3.189287 GCCAACAGGAAATGTAGTCAGTG 59.811 47.826 0.00 0.00 43.00 3.66
3726 3766 3.924073 CGTCCACATGATTTCGAGTACAA 59.076 43.478 0.00 0.00 0.00 2.41
3777 3817 3.545703 AGTCAAGTTGGTTTCAGTGAGG 58.454 45.455 2.34 0.00 0.00 3.86
3848 3888 5.997129 TGTTGTGAAATAGACTGCTGATTCA 59.003 36.000 0.00 0.00 31.68 2.57
3944 3984 6.707608 TCTGCTTATCACATTGATATCACCAC 59.292 38.462 4.48 0.00 38.94 4.16
4023 4063 9.383519 TCTGGAGAGTTTGTAACATTATGATTC 57.616 33.333 0.00 0.00 0.00 2.52
4095 4135 6.896307 ACTCATCATCCAGAGCATCAGATATA 59.104 38.462 0.00 0.00 37.82 0.86
4677 4717 3.768757 CCCCTTTCCACAAAATAGCATGA 59.231 43.478 0.00 0.00 0.00 3.07
4932 4972 6.688813 CGTCACTATCCATGTCATATATCACG 59.311 42.308 0.00 0.00 0.00 4.35
5004 5044 7.120873 TCCTCTGTTAACTCAGACATAGTGTAC 59.879 40.741 7.22 0.00 39.20 2.90
5005 5045 7.173032 TCCTCTGTTAACTCAGACATAGTGTA 58.827 38.462 7.22 0.00 39.20 2.90
5302 5350 6.154534 TCCCGAAGAAGATAGAAAACAGATGA 59.845 38.462 0.00 0.00 0.00 2.92
5303 5351 6.341316 TCCCGAAGAAGATAGAAAACAGATG 58.659 40.000 0.00 0.00 0.00 2.90
5434 5524 7.894753 TCAATGGCATAGTTGGAATAATTCA 57.105 32.000 0.00 0.00 0.00 2.57
5691 5784 3.206150 GAGAGCATGATAGCCGGAAAAA 58.794 45.455 5.05 0.00 34.23 1.94
5697 5790 3.316071 AAGATGAGAGCATGATAGCCG 57.684 47.619 0.00 0.00 34.11 5.52
5719 5812 2.064762 GACTGCGATGATACCATCTGC 58.935 52.381 6.88 6.88 45.37 4.26
5740 5833 7.639039 CACTTAAGTCTCAACATTGTTTGCTA 58.361 34.615 4.77 0.00 0.00 3.49
5761 5854 2.826488 AGTCAGAGGGAGTATGCACTT 58.174 47.619 0.00 0.00 34.21 3.16
6398 6773 0.764271 TGTTCCAGTGATCAGGCACA 59.236 50.000 0.00 0.00 41.19 4.57
6912 7293 3.348119 TCTGCCAACAACACAGTTAACA 58.652 40.909 8.61 0.00 33.12 2.41
7054 7435 7.330262 TCTTCATATTTCATTTTCTTTGGGCC 58.670 34.615 0.00 0.00 0.00 5.80
7182 7566 4.722700 CCCAACCTCCACCGCTGG 62.723 72.222 0.00 0.00 39.23 4.85
7202 7586 2.763448 GGAAGAGCCACATGAGACTACT 59.237 50.000 0.00 0.00 36.34 2.57
7282 7666 3.004629 TGCTCAACATGTCCAAACACATC 59.995 43.478 0.00 0.00 38.48 3.06
7283 7667 2.957680 TGCTCAACATGTCCAAACACAT 59.042 40.909 0.00 0.00 38.48 3.21
7284 7668 2.373224 TGCTCAACATGTCCAAACACA 58.627 42.857 0.00 0.00 38.48 3.72
7286 7670 4.650734 TCTATGCTCAACATGTCCAAACA 58.349 39.130 0.00 0.00 40.06 2.83
7315 7702 3.311596 TCGACATATACAGACCACTGACG 59.688 47.826 0.00 0.00 46.03 4.35
7349 7736 7.434897 TGTGTAGCAAACAAACAAAATCTCATC 59.565 33.333 0.00 0.00 40.63 2.92
7369 7756 9.973450 AGCATGTCTAACTTAGATATTGTGTAG 57.027 33.333 5.53 0.00 34.87 2.74
7435 7822 7.712264 TTATCTTCAAATGCAAACCACTTTG 57.288 32.000 0.00 0.00 39.98 2.77
7442 7829 9.807649 ACCAGATTATTATCTTCAAATGCAAAC 57.192 29.630 0.00 0.00 39.11 2.93
7558 7947 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
7559 7948 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
7560 7949 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
7561 7950 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
7562 7951 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
7563 7952 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
7564 7953 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
7565 7954 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
7566 7955 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
7567 7956 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
7568 7957 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
7569 7958 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
7606 7995 8.717821 CGTTCCAAAATAGATGACTCAACTTTA 58.282 33.333 0.00 0.00 0.00 1.85
7607 7996 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
7608 7997 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
7609 7998 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
7610 7999 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
7611 8000 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
7612 8001 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
7613 8002 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
7614 8003 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
7615 8004 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
7616 8005 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
7617 8006 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
7618 8007 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
7619 8008 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
7620 8009 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
7621 8010 6.811634 TTATACTCCCTCCGTTCCAAAATA 57.188 37.500 0.00 0.00 0.00 1.40
7622 8011 5.703730 TTATACTCCCTCCGTTCCAAAAT 57.296 39.130 0.00 0.00 0.00 1.82
7623 8012 5.703730 ATTATACTCCCTCCGTTCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
7624 8013 8.495160 TTATATTATACTCCCTCCGTTCCAAA 57.505 34.615 0.00 0.00 0.00 3.28
7625 8014 7.951806 TCTTATATTATACTCCCTCCGTTCCAA 59.048 37.037 0.00 0.00 0.00 3.53
7626 8015 7.395489 GTCTTATATTATACTCCCTCCGTTCCA 59.605 40.741 0.00 0.00 0.00 3.53
7627 8016 7.414984 CGTCTTATATTATACTCCCTCCGTTCC 60.415 44.444 0.00 0.00 0.00 3.62
7628 8017 7.120432 ACGTCTTATATTATACTCCCTCCGTTC 59.880 40.741 0.00 0.00 0.00 3.95
7629 8018 6.944862 ACGTCTTATATTATACTCCCTCCGTT 59.055 38.462 0.00 0.00 0.00 4.44
7630 8019 6.479884 ACGTCTTATATTATACTCCCTCCGT 58.520 40.000 0.00 0.00 0.00 4.69
7631 8020 6.998968 ACGTCTTATATTATACTCCCTCCG 57.001 41.667 0.00 0.00 0.00 4.63
7632 8021 9.993454 AAAAACGTCTTATATTATACTCCCTCC 57.007 33.333 0.00 0.00 0.00 4.30
7663 8052 9.998106 AAGATGTTTTATTGACACTAGTGTAGT 57.002 29.630 27.98 18.09 45.05 2.73


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

AutoCloner maintained by Alex Coulton.