Multiple sequence alignment - TraesCS3D01G214100

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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 TraesCS3D01G214100 chr3D 100.000 7082 0 0 1 7082 289101323 289108404 0.000000e+00 13079.0
1 TraesCS3D01G214100 chr3D 76.481 540 77 33 3624 4135 98596440 98595923 1.530000e-61 248.0
2 TraesCS3D01G214100 chr3D 80.000 215 34 6 3127 3335 390078667 390078878 4.430000e-32 150.0
3 TraesCS3D01G214100 chr3D 91.398 93 7 1 2320 2411 4197114 4197022 7.460000e-25 126.0
4 TraesCS3D01G214100 chr3D 92.135 89 7 0 2323 2411 157099354 157099442 7.460000e-25 126.0
5 TraesCS3D01G214100 chr3D 91.209 91 7 1 2322 2411 429306332 429306242 9.650000e-24 122.0
6 TraesCS3D01G214100 chr3D 83.810 105 17 0 4488 4592 429780640 429780536 4.520000e-17 100.0
7 TraesCS3D01G214100 chr3B 95.609 4486 68 24 1675 6102 381754095 381758509 0.000000e+00 7073.0
8 TraesCS3D01G214100 chr3B 95.732 1570 49 6 1 1568 381752163 381753716 0.000000e+00 2512.0
9 TraesCS3D01G214100 chr3B 92.881 590 40 2 6495 7082 381759144 381759733 0.000000e+00 856.0
10 TraesCS3D01G214100 chr3B 97.806 319 7 0 6220 6538 381758827 381759145 1.040000e-152 551.0
11 TraesCS3D01G214100 chr3B 87.838 74 9 0 2627 2700 707251945 707252018 3.520000e-13 87.9
12 TraesCS3D01G214100 chr3A 96.269 3940 97 21 2308 6222 379821586 379825500 0.000000e+00 6416.0
13 TraesCS3D01G214100 chr3A 96.560 814 20 7 835 1642 379819737 379820548 0.000000e+00 1341.0
14 TraesCS3D01G214100 chr3A 94.768 669 12 4 1665 2313 379820884 379821549 0.000000e+00 1020.0
15 TraesCS3D01G214100 chr3A 88.378 826 65 12 1 805 379818730 379819545 0.000000e+00 965.0
16 TraesCS3D01G214100 chr3A 82.679 433 52 8 6659 7082 379826430 379826848 5.220000e-96 363.0
17 TraesCS3D01G214100 chr3A 94.964 139 6 1 6220 6358 379825609 379825746 4.300000e-52 217.0
18 TraesCS3D01G214100 chr3A 91.954 87 7 0 2325 2411 360822552 360822466 9.650000e-24 122.0
19 TraesCS3D01G214100 chr3A 94.595 74 4 0 6359 6432 379825785 379825858 1.610000e-21 115.0
20 TraesCS3D01G214100 chr3A 83.621 116 11 1 6467 6574 379825857 379825972 1.260000e-17 102.0
21 TraesCS3D01G214100 chr2A 77.000 1000 155 35 2660 3624 744053745 744052786 2.950000e-138 503.0
22 TraesCS3D01G214100 chr2A 78.829 444 71 15 3714 4149 195742385 195741957 1.950000e-70 278.0
23 TraesCS3D01G214100 chr7B 81.603 549 85 11 3624 4166 103579405 103579943 2.340000e-119 440.0
24 TraesCS3D01G214100 chr7B 92.045 88 7 0 2325 2412 103891527 103891440 2.680000e-24 124.0
25 TraesCS3D01G214100 chr2B 82.500 520 62 15 2836 3341 398710646 398710142 5.080000e-116 429.0
26 TraesCS3D01G214100 chr2B 81.272 566 73 25 3624 4166 398709972 398709417 1.830000e-115 427.0
27 TraesCS3D01G214100 chr2B 79.412 204 35 6 4386 4585 793184226 793184426 3.450000e-28 137.0
28 TraesCS3D01G214100 chr2B 80.714 140 22 4 4455 4591 198641627 198641490 3.490000e-18 104.0
29 TraesCS3D01G214100 chr6B 82.353 493 46 19 2707 3163 184357346 184357833 2.400000e-104 390.0
30 TraesCS3D01G214100 chr6B 79.915 473 64 18 2719 3179 279923172 279922719 1.150000e-82 318.0
31 TraesCS3D01G214100 chr7A 79.855 551 90 15 3624 4166 138179868 138180405 4.010000e-102 383.0
32 TraesCS3D01G214100 chr7A 85.827 127 17 1 2628 2754 25118235 25118110 4.460000e-27 134.0
33 TraesCS3D01G214100 chr7A 90.217 92 7 2 2320 2411 8236005 8236094 1.250000e-22 119.0
34 TraesCS3D01G214100 chr7A 85.185 81 12 0 2626 2706 25118326 25118246 4.550000e-12 84.2
35 TraesCS3D01G214100 chr6A 81.385 462 61 11 2785 3232 521859973 521860423 3.140000e-93 353.0
36 TraesCS3D01G214100 chr6A 80.467 471 64 18 2721 3179 211713891 211714345 1.140000e-87 335.0
37 TraesCS3D01G214100 chr6D 81.116 466 62 16 2731 3185 157159002 157158552 4.070000e-92 350.0
38 TraesCS3D01G214100 chr6D 78.821 458 76 13 3699 4149 31804503 31804946 8.990000e-74 289.0
39 TraesCS3D01G214100 chr6D 83.234 167 22 6 4432 4593 415457732 415457567 1.590000e-31 148.0
40 TraesCS3D01G214100 chr6D 84.783 92 14 0 3624 3715 31804386 31804477 7.560000e-15 93.5
41 TraesCS3D01G214100 chr5D 80.255 471 69 17 3690 4153 326906303 326906756 4.090000e-87 333.0
42 TraesCS3D01G214100 chr5D 75.356 491 69 34 3015 3471 92172738 92172266 9.380000e-44 189.0
43 TraesCS3D01G214100 chr5D 73.995 423 103 7 6554 6974 408743575 408743158 1.580000e-36 165.0
44 TraesCS3D01G214100 chr5D 93.333 90 6 0 2323 2412 420277228 420277139 4.460000e-27 134.0
45 TraesCS3D01G214100 chr5D 88.235 51 4 1 2268 2316 128641829 128641779 7.670000e-05 60.2
46 TraesCS3D01G214100 chr4A 79.138 441 75 10 3714 4149 585593956 585593528 8.990000e-74 289.0
47 TraesCS3D01G214100 chr4A 78.065 310 43 16 3624 3908 573375763 573375454 9.440000e-39 172.0
48 TraesCS3D01G214100 chr4A 89.333 75 8 0 2626 2700 175216401 175216327 2.100000e-15 95.3
49 TraesCS3D01G214100 chr7D 78.693 352 48 20 2642 2989 10926916 10927244 7.200000e-50 209.0
50 TraesCS3D01G214100 chr7D 78.165 316 41 15 3127 3429 83752412 83752712 7.300000e-40 176.0
51 TraesCS3D01G214100 chr7D 81.935 155 16 9 3127 3269 460112735 460112581 3.470000e-23 121.0
52 TraesCS3D01G214100 chr7D 81.250 112 16 5 2644 2754 578797054 578796947 1.270000e-12 86.1
53 TraesCS3D01G214100 chr1D 82.915 199 31 1 3127 3325 221923199 221923394 7.300000e-40 176.0
54 TraesCS3D01G214100 chr1D 81.421 183 30 4 4409 4589 246946780 246946600 5.720000e-31 147.0
55 TraesCS3D01G214100 chr1D 91.860 86 7 0 3624 3709 485128852 485128937 3.470000e-23 121.0
56 TraesCS3D01G214100 chr1A 82.486 177 22 8 4433 4602 267143269 267143095 5.720000e-31 147.0
57 TraesCS3D01G214100 chr1A 90.698 86 8 0 3624 3709 582516624 582516709 1.610000e-21 115.0
58 TraesCS3D01G214100 chr1A 78.621 145 23 4 2941 3077 449664274 449664130 9.780000e-14 89.8
59 TraesCS3D01G214100 chr1A 88.571 70 6 2 2685 2754 463196979 463196912 4.550000e-12 84.2
60 TraesCS3D01G214100 chr1B 86.400 125 13 4 2625 2749 487173046 487172926 4.460000e-27 134.0
61 TraesCS3D01G214100 chr2D 77.880 217 38 10 4381 4592 208844168 208844379 7.460000e-25 126.0
62 TraesCS3D01G214100 chr2D 86.486 74 10 0 2626 2699 295898509 295898582 1.640000e-11 82.4
63 TraesCS3D01G214100 chr5A 80.952 84 14 2 50 132 830730 830648 1.650000e-06 65.8


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 TraesCS3D01G214100 chr3D 289101323 289108404 7081 False 13079.000 13079 100.00000 1 7082 1 chr3D.!!$F2 7081
1 TraesCS3D01G214100 chr3D 98595923 98596440 517 True 248.000 248 76.48100 3624 4135 1 chr3D.!!$R2 511
2 TraesCS3D01G214100 chr3B 381752163 381759733 7570 False 2748.000 7073 95.50700 1 7082 4 chr3B.!!$F2 7081
3 TraesCS3D01G214100 chr3A 379818730 379826848 8118 False 1317.375 6416 91.47925 1 7082 8 chr3A.!!$F1 7081
4 TraesCS3D01G214100 chr2A 744052786 744053745 959 True 503.000 503 77.00000 2660 3624 1 chr2A.!!$R2 964
5 TraesCS3D01G214100 chr7B 103579405 103579943 538 False 440.000 440 81.60300 3624 4166 1 chr7B.!!$F1 542
6 TraesCS3D01G214100 chr2B 398709417 398710646 1229 True 428.000 429 81.88600 2836 4166 2 chr2B.!!$R2 1330
7 TraesCS3D01G214100 chr7A 138179868 138180405 537 False 383.000 383 79.85500 3624 4166 1 chr7A.!!$F2 542

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
714 736 0.108804 CTGTGTCGAGGGTTGCGTAT 60.109 55.000 0.00 0.0 0.00 3.06 F
1650 1853 0.109272 TGATGAGTTCGAGTCCACGC 60.109 55.000 0.00 0.0 0.00 5.34 F
1651 1854 0.802607 GATGAGTTCGAGTCCACGCC 60.803 60.000 0.00 0.0 0.00 5.68 F
2624 3234 1.055849 TCACCTTGTGGCTAAGAGCA 58.944 50.000 0.21 0.0 44.75 4.26 F
3684 4469 0.252467 CCACCACCTTCCTCTCCTCT 60.252 60.000 0.00 0.0 0.00 3.69 F
3685 4470 1.007238 CCACCACCTTCCTCTCCTCTA 59.993 57.143 0.00 0.0 0.00 2.43 F
3687 4472 2.004589 ACCACCTTCCTCTCCTCTAGT 58.995 52.381 0.00 0.0 0.00 2.57 F
3688 4473 2.384029 ACCACCTTCCTCTCCTCTAGTT 59.616 50.000 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1863 0.106708 GTCATATCCCCGCAAGAGCA 59.893 55.000 0.00 0.0 42.27 4.26 R
2485 3085 1.195448 CAAAGTCTCAACGCGCAAGAT 59.805 47.619 5.73 0.0 43.02 2.40 R
3119 3764 1.343580 TGGTATGGGAGGTGATTCCGA 60.344 52.381 0.00 0.0 41.99 4.55 R
3686 4471 0.533032 CGAGGAGAGGAAGGTGGAAC 59.467 60.000 0.00 0.0 0.00 3.62 R
5436 6301 6.108687 TCCACTGCATAAGAGTAGTTCAATG 58.891 40.000 0.00 0.0 31.85 2.82 R
5850 6725 6.749118 GCACAAGATAAATGGCACTAAGAAAG 59.251 38.462 0.00 0.0 0.00 2.62 R
5936 6811 6.585695 ATTTAGTGTTCCGAGAGACAACTA 57.414 37.500 0.00 0.0 0.00 2.24 R
6087 6962 4.156556 ACAGCGCATGAAATAAACATCAGT 59.843 37.500 11.47 0.0 0.00 3.41 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
34 35 2.629909 GGGAGATCCTTTACCCTCACCT 60.630 54.545 0.00 0.00 39.28 4.00
93 94 6.085416 CCTAGTATCCCCTTCATACTCCTTT 58.915 44.000 0.00 0.00 37.99 3.11
219 223 1.166531 ACCTCGCAACCTTGTGAAGC 61.167 55.000 3.06 0.00 45.89 3.86
236 240 2.054453 GCCCCCAGGATCTTTGCAC 61.054 63.158 0.00 0.00 33.47 4.57
258 262 1.676014 GCACGTTCTAGCCCAGTCATT 60.676 52.381 0.00 0.00 0.00 2.57
326 330 2.224646 GGTGGATATGAGCTTTCTCCCC 60.225 54.545 0.00 0.00 38.58 4.81
341 345 3.850752 TCTCCCCAGGATCTTCATAGAC 58.149 50.000 0.00 0.00 31.99 2.59
360 364 1.272536 ACGAGTCCCTCAGCTTCCTTA 60.273 52.381 0.00 0.00 0.00 2.69
410 414 2.028020 CAGAAAGGCTCGAAGTAGGGTT 60.028 50.000 0.00 0.00 0.00 4.11
473 477 0.790207 GCTTTCGCATCTGAACGTCA 59.210 50.000 0.00 0.00 35.78 4.35
474 478 1.462541 GCTTTCGCATCTGAACGTCAC 60.463 52.381 0.00 0.00 35.78 3.67
653 675 0.679002 TTTCCGATCGTCCTCTCCGT 60.679 55.000 15.09 0.00 0.00 4.69
707 729 4.736739 TCGATCTGTGTCGAGGGT 57.263 55.556 0.00 0.00 44.87 4.34
712 734 1.816863 ATCTGTGTCGAGGGTTGCGT 61.817 55.000 0.00 0.00 0.00 5.24
714 736 0.108804 CTGTGTCGAGGGTTGCGTAT 60.109 55.000 0.00 0.00 0.00 3.06
774 796 1.201424 AGCCGAAACCCTAACCCTAG 58.799 55.000 0.00 0.00 0.00 3.02
804 826 2.202932 GTCGCCATGTGATCGCCT 60.203 61.111 3.31 0.00 0.00 5.52
805 827 2.106938 TCGCCATGTGATCGCCTC 59.893 61.111 3.31 0.00 0.00 4.70
806 828 2.969238 CGCCATGTGATCGCCTCC 60.969 66.667 3.31 0.00 0.00 4.30
807 829 2.592861 GCCATGTGATCGCCTCCC 60.593 66.667 3.31 0.00 0.00 4.30
808 830 2.910360 CCATGTGATCGCCTCCCA 59.090 61.111 3.31 0.00 0.00 4.37
809 831 1.524621 CCATGTGATCGCCTCCCAC 60.525 63.158 3.31 0.00 0.00 4.61
810 832 1.524002 CATGTGATCGCCTCCCACT 59.476 57.895 3.31 0.00 0.00 4.00
1606 1809 3.312697 GGTTTTGTCCTCTTCACAGTGTC 59.687 47.826 0.00 0.00 0.00 3.67
1609 1812 2.329267 TGTCCTCTTCACAGTGTCCAT 58.671 47.619 0.00 0.00 0.00 3.41
1642 1845 3.874392 TTCTGATGCTGATGAGTTCGA 57.126 42.857 0.00 0.00 0.00 3.71
1643 1846 3.433513 TCTGATGCTGATGAGTTCGAG 57.566 47.619 0.00 0.00 0.00 4.04
1644 1847 2.757314 TCTGATGCTGATGAGTTCGAGT 59.243 45.455 0.00 0.00 0.00 4.18
1645 1848 3.114809 CTGATGCTGATGAGTTCGAGTC 58.885 50.000 0.00 0.00 0.00 3.36
1646 1849 2.159184 TGATGCTGATGAGTTCGAGTCC 60.159 50.000 0.00 0.00 0.00 3.85
1647 1850 1.256812 TGCTGATGAGTTCGAGTCCA 58.743 50.000 0.00 0.00 0.00 4.02
1648 1851 1.067565 TGCTGATGAGTTCGAGTCCAC 60.068 52.381 0.00 0.00 0.00 4.02
1649 1852 1.901538 CTGATGAGTTCGAGTCCACG 58.098 55.000 0.00 0.00 0.00 4.94
1650 1853 0.109272 TGATGAGTTCGAGTCCACGC 60.109 55.000 0.00 0.00 0.00 5.34
1651 1854 0.802607 GATGAGTTCGAGTCCACGCC 60.803 60.000 0.00 0.00 0.00 5.68
1652 1855 2.126031 GAGTTCGAGTCCACGCCC 60.126 66.667 0.00 0.00 0.00 6.13
1653 1856 3.644399 GAGTTCGAGTCCACGCCCC 62.644 68.421 0.00 0.00 0.00 5.80
1654 1857 4.754667 GTTCGAGTCCACGCCCCC 62.755 72.222 0.00 0.00 0.00 5.40
1691 2207 2.036475 GGGATATGACAGACATGCGACT 59.964 50.000 0.00 0.00 39.77 4.18
1781 2297 9.511144 GTTAAAATTTACGAATGGAATACTGGG 57.489 33.333 0.00 0.00 0.00 4.45
1987 2541 4.081752 AGCAATAATCGAATTTGTGCCCAA 60.082 37.500 0.00 0.00 33.69 4.12
2352 2952 3.558321 CCTCCGTCCCAAAATAAGTGTCA 60.558 47.826 0.00 0.00 0.00 3.58
2461 3061 9.853177 AATACAAATTTCACCCAACCAAAATTA 57.147 25.926 0.00 0.00 32.55 1.40
2485 3085 3.559655 GTGGCATCTACGTATTGCATTGA 59.440 43.478 23.85 6.88 38.12 2.57
2617 3227 3.365472 AGAAAAACTTCACCTTGTGGCT 58.635 40.909 0.00 0.00 36.63 4.75
2618 3228 4.532834 AGAAAAACTTCACCTTGTGGCTA 58.467 39.130 0.00 0.00 36.63 3.93
2619 3229 4.953579 AGAAAAACTTCACCTTGTGGCTAA 59.046 37.500 0.00 0.00 36.63 3.09
2620 3230 4.918810 AAAACTTCACCTTGTGGCTAAG 57.081 40.909 0.00 0.00 36.63 2.18
2621 3231 3.857157 AACTTCACCTTGTGGCTAAGA 57.143 42.857 4.07 0.00 36.63 2.10
2622 3232 3.409026 ACTTCACCTTGTGGCTAAGAG 57.591 47.619 4.07 0.00 36.63 2.85
2623 3233 2.079925 CTTCACCTTGTGGCTAAGAGC 58.920 52.381 4.07 0.00 41.46 4.09
2624 3234 1.055849 TCACCTTGTGGCTAAGAGCA 58.944 50.000 0.21 0.00 44.75 4.26
2625 3235 1.160137 CACCTTGTGGCTAAGAGCAC 58.840 55.000 0.21 0.00 44.75 4.40
2913 3537 6.435277 ACATGAACTCAACTTCCATAGCAAAT 59.565 34.615 0.00 0.00 0.00 2.32
3119 3764 4.552365 CGATGCCGCCACCTCCAT 62.552 66.667 0.00 0.00 0.00 3.41
3396 4043 2.418368 TGTTCATGTAGCCACCCATC 57.582 50.000 0.00 0.00 0.00 3.51
3675 4460 1.450312 CTCATCGGCCACCACCTTC 60.450 63.158 2.24 0.00 0.00 3.46
3676 4461 2.438434 CATCGGCCACCACCTTCC 60.438 66.667 2.24 0.00 0.00 3.46
3683 4468 1.904990 GCCACCACCTTCCTCTCCTC 61.905 65.000 0.00 0.00 0.00 3.71
3684 4469 0.252467 CCACCACCTTCCTCTCCTCT 60.252 60.000 0.00 0.00 0.00 3.69
3685 4470 1.007238 CCACCACCTTCCTCTCCTCTA 59.993 57.143 0.00 0.00 0.00 2.43
3686 4471 2.383855 CACCACCTTCCTCTCCTCTAG 58.616 57.143 0.00 0.00 0.00 2.43
3687 4472 2.004589 ACCACCTTCCTCTCCTCTAGT 58.995 52.381 0.00 0.00 0.00 2.57
3688 4473 2.384029 ACCACCTTCCTCTCCTCTAGTT 59.616 50.000 0.00 0.00 0.00 2.24
3690 4475 3.028130 CACCTTCCTCTCCTCTAGTTCC 58.972 54.545 0.00 0.00 0.00 3.62
3691 4476 2.655407 ACCTTCCTCTCCTCTAGTTCCA 59.345 50.000 0.00 0.00 0.00 3.53
3738 4565 2.716017 CCGCTCGGCTTCTCTCCTT 61.716 63.158 0.00 0.00 0.00 3.36
4753 5617 6.349611 CCTTTGATGCACAAGTAAACATAGCT 60.350 38.462 0.00 0.00 39.77 3.32
5850 6725 5.330455 TGACAGTTCTCTCATGTGTATCC 57.670 43.478 0.00 0.00 0.00 2.59
5936 6811 2.359967 GGTACCGGGAGCAGCTTCT 61.360 63.158 12.08 0.00 0.00 2.85
6087 6962 7.995289 ACGGAAATGATAGAACATAATTGCAA 58.005 30.769 0.00 0.00 0.00 4.08
6116 6991 9.398170 GATGTTTATTTCATGCGCTGTATATTT 57.602 29.630 9.73 0.00 0.00 1.40
6131 7006 7.591426 CGCTGTATATTTTAAGGAGAATTTGGC 59.409 37.037 0.00 0.00 0.00 4.52
6185 7060 7.141100 ACCTGAATTGAAACAGTATTAACGG 57.859 36.000 0.00 0.00 32.93 4.44
6443 7666 1.757118 TCTATCGCTTCCTTGACCCTG 59.243 52.381 0.00 0.00 0.00 4.45
6463 7686 1.377333 GCGGCTAGGGCAAACTCTT 60.377 57.895 0.00 0.00 40.87 2.85
6471 7694 1.707427 AGGGCAAACTCTTGTCTCCAT 59.293 47.619 0.00 0.00 37.32 3.41
6474 7697 3.307762 GGGCAAACTCTTGTCTCCATACT 60.308 47.826 0.00 0.00 37.32 2.12
6544 7809 2.586648 AATCCCGGTTTCTTTGCTCT 57.413 45.000 0.00 0.00 0.00 4.09
6618 8291 2.242564 GAATGGCGACGCTTTTTCTTC 58.757 47.619 20.77 9.68 0.00 2.87
6622 8295 0.507358 GCGACGCTTTTTCTTCGAGT 59.493 50.000 13.73 0.00 33.20 4.18
6632 8305 5.169738 GCTTTTTCTTCGAGTTTGTCTTTCG 59.830 40.000 0.00 0.00 35.76 3.46
6657 8330 4.934797 TTCAATCCTCCTTGAGTCCATT 57.065 40.909 0.00 0.00 36.55 3.16
6661 8334 2.257207 TCCTCCTTGAGTCCATTCGTT 58.743 47.619 0.00 0.00 0.00 3.85
6682 8355 3.928727 TGGACATAGTCGACGAAACTT 57.071 42.857 10.46 0.00 32.65 2.66
6705 8378 3.314541 ACGTAGATTCTTGCCGTCTTT 57.685 42.857 0.00 0.00 0.00 2.52
6716 8390 3.276091 CGTCTTTGTGGTGCGGCA 61.276 61.111 0.00 0.00 0.00 5.69
6739 8413 5.193099 AGGTTAGGGTTTATTGTCATGCT 57.807 39.130 0.00 0.00 0.00 3.79
6754 8428 3.254166 GTCATGCTGTGAGATTTGGTGTT 59.746 43.478 0.00 0.00 37.56 3.32
6757 8431 2.813754 TGCTGTGAGATTTGGTGTTAGC 59.186 45.455 0.00 0.00 0.00 3.09
6815 8489 1.920835 GACTCCAAGGCCCTGGTCT 60.921 63.158 20.21 6.28 37.74 3.85
6840 8514 0.721718 GGCACGTGCATGAAGACTAC 59.278 55.000 38.60 15.88 44.36 2.73
6844 8518 0.806102 CGTGCATGAAGACTACCCGG 60.806 60.000 0.00 0.00 0.00 5.73
6875 8549 4.095632 CGACAAGATCTAAGCTGACTCTGA 59.904 45.833 0.00 0.00 0.00 3.27
6917 8591 0.527817 GTGTTATCGGCTCGTCCTGG 60.528 60.000 0.00 0.00 0.00 4.45
6928 8602 0.892358 TCGTCCTGGCGTCAGTACTT 60.892 55.000 17.16 0.00 39.31 2.24
7078 8763 2.498078 GTTTGGGGAGACAAAACCAACA 59.502 45.455 0.00 0.00 42.24 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.876473 AGGATCTCCCTCCCAATAGGT 59.124 52.381 0.00 0.00 43.31 3.08
219 223 1.380380 GGTGCAAAGATCCTGGGGG 60.380 63.158 0.00 0.00 0.00 5.40
236 240 2.509336 CTGGGCTAGAACGTGCGG 60.509 66.667 0.00 0.00 0.00 5.69
258 262 1.745115 CTCGCCTCGGCCAATGAAA 60.745 57.895 2.24 0.00 37.98 2.69
306 310 2.439507 TGGGGAGAAAGCTCATATCCAC 59.560 50.000 13.36 10.87 43.14 4.02
326 330 3.254657 GGGACTCGTCTATGAAGATCCTG 59.745 52.174 0.00 0.00 33.30 3.86
360 364 2.443255 GGGAGGTATGGTGTTGATGGAT 59.557 50.000 0.00 0.00 0.00 3.41
410 414 0.386858 CGCGAAGAACAAGACTCCGA 60.387 55.000 0.00 0.00 0.00 4.55
473 477 2.668212 CGGCCACACCAATGACGT 60.668 61.111 2.24 0.00 39.03 4.34
474 478 2.668212 ACGGCCACACCAATGACG 60.668 61.111 2.24 0.00 39.03 4.35
499 503 4.232905 CTCAACCACTGGGGAGGA 57.767 61.111 1.10 0.00 41.15 3.71
653 675 3.395702 ACGGGGCGGTGCTAATGA 61.396 61.111 0.00 0.00 0.00 2.57
712 734 3.118884 GGTTGTGTCTAAGGAGGCGAATA 60.119 47.826 0.00 0.00 0.00 1.75
714 736 1.001633 GGTTGTGTCTAAGGAGGCGAA 59.998 52.381 0.00 0.00 0.00 4.70
723 745 1.689813 TGAGGCTTCGGTTGTGTCTAA 59.310 47.619 0.00 0.00 0.00 2.10
754 776 2.391678 CTAGGGTTAGGGTTTCGGCTA 58.608 52.381 0.00 0.00 0.00 3.93
774 796 4.395583 GCGACTGCAGCCTTGTGC 62.396 66.667 15.27 5.15 44.27 4.57
796 818 3.838271 GCGAGTGGGAGGCGATCA 61.838 66.667 0.00 0.00 0.00 2.92
946 1144 6.126825 TGGCCGGTACTTAATCTGGTTAATTA 60.127 38.462 1.90 0.00 32.12 1.40
947 1145 5.128205 GGCCGGTACTTAATCTGGTTAATT 58.872 41.667 1.90 0.00 32.12 1.40
959 1159 0.609662 GTCCTGTTGGCCGGTACTTA 59.390 55.000 1.90 0.00 0.00 2.24
989 1189 1.364626 CGGCAGCATCTTCTGTGGTC 61.365 60.000 0.00 0.00 36.49 4.02
1361 1563 1.405121 CCGGTTTAGCACCTCCAGTAC 60.405 57.143 0.00 0.00 44.69 2.73
1652 1855 2.639327 CCGCAAGAGCAAAAGGGGG 61.639 63.158 0.00 0.00 42.27 5.40
1653 1856 2.639327 CCCGCAAGAGCAAAAGGGG 61.639 63.158 0.00 0.00 42.27 4.79
1654 1857 2.639327 CCCCGCAAGAGCAAAAGGG 61.639 63.158 0.00 0.00 42.27 3.95
1655 1858 0.967380 ATCCCCGCAAGAGCAAAAGG 60.967 55.000 0.00 0.00 42.27 3.11
1656 1859 1.750193 TATCCCCGCAAGAGCAAAAG 58.250 50.000 0.00 0.00 42.27 2.27
1657 1860 2.023673 CATATCCCCGCAAGAGCAAAA 58.976 47.619 0.00 0.00 42.27 2.44
1658 1861 1.211703 TCATATCCCCGCAAGAGCAAA 59.788 47.619 0.00 0.00 42.27 3.68
1659 1862 0.836606 TCATATCCCCGCAAGAGCAA 59.163 50.000 0.00 0.00 42.27 3.91
1660 1863 0.106708 GTCATATCCCCGCAAGAGCA 59.893 55.000 0.00 0.00 42.27 4.26
1661 1864 0.106708 TGTCATATCCCCGCAAGAGC 59.893 55.000 0.00 0.00 43.02 4.09
1662 1865 1.688735 TCTGTCATATCCCCGCAAGAG 59.311 52.381 0.00 0.00 43.02 2.85
1663 1866 1.412710 GTCTGTCATATCCCCGCAAGA 59.587 52.381 0.00 0.00 43.02 3.02
1707 2223 9.334947 CATAATCTGCCTAACCAAGATATATGG 57.665 37.037 5.64 5.64 43.84 2.74
1781 2297 2.746362 CTCAATTCTTGTGAGCAGTCCC 59.254 50.000 0.00 0.00 36.38 4.46
1987 2541 9.561069 AAGCGGTCTAGATAATAACAATGAAAT 57.439 29.630 0.00 0.00 0.00 2.17
2269 2823 7.411486 ACATCTTATATTATGACGGAGGGAG 57.589 40.000 2.69 0.00 0.00 4.30
2270 2824 7.792364 AACATCTTATATTATGACGGAGGGA 57.208 36.000 2.69 0.00 0.00 4.20
2461 3061 1.484653 TGCAATACGTAGATGCCACCT 59.515 47.619 24.85 0.00 39.31 4.00
2485 3085 1.195448 CAAAGTCTCAACGCGCAAGAT 59.805 47.619 5.73 0.00 43.02 2.40
2617 3227 4.541705 AGGAGATGCTCTTAGTGCTCTTA 58.458 43.478 7.78 0.00 0.00 2.10
2618 3228 3.373830 AGGAGATGCTCTTAGTGCTCTT 58.626 45.455 7.78 0.00 0.00 2.85
2619 3229 3.030873 AGGAGATGCTCTTAGTGCTCT 57.969 47.619 7.78 7.65 0.00 4.09
2620 3230 5.943416 TCTATAGGAGATGCTCTTAGTGCTC 59.057 44.000 7.78 3.40 0.00 4.26
2621 3231 5.886609 TCTATAGGAGATGCTCTTAGTGCT 58.113 41.667 7.78 0.00 0.00 4.40
2622 3232 6.773976 ATCTATAGGAGATGCTCTTAGTGC 57.226 41.667 0.00 0.00 43.71 4.40
3119 3764 1.343580 TGGTATGGGAGGTGATTCCGA 60.344 52.381 0.00 0.00 41.99 4.55
3396 4043 2.362889 GGTGCAATGGGAGGTGGG 60.363 66.667 0.00 0.00 0.00 4.61
3675 4460 2.838637 AGGTGGAACTAGAGGAGAGG 57.161 55.000 0.00 0.00 36.74 3.69
3676 4461 3.028130 GGAAGGTGGAACTAGAGGAGAG 58.972 54.545 0.00 0.00 36.74 3.20
3683 4468 3.028130 GAGGAGAGGAAGGTGGAACTAG 58.972 54.545 0.00 0.00 36.74 2.57
3684 4469 2.620886 CGAGGAGAGGAAGGTGGAACTA 60.621 54.545 0.00 0.00 36.74 2.24
3685 4470 1.893210 CGAGGAGAGGAAGGTGGAACT 60.893 57.143 0.00 0.00 36.74 3.01
3686 4471 0.533032 CGAGGAGAGGAAGGTGGAAC 59.467 60.000 0.00 0.00 0.00 3.62
3687 4472 0.614979 CCGAGGAGAGGAAGGTGGAA 60.615 60.000 0.00 0.00 0.00 3.53
3688 4473 1.000486 CCGAGGAGAGGAAGGTGGA 60.000 63.158 0.00 0.00 0.00 4.02
3690 4475 2.726351 GGCCGAGGAGAGGAAGGTG 61.726 68.421 0.00 0.00 0.00 4.00
3691 4476 2.364448 GGCCGAGGAGAGGAAGGT 60.364 66.667 0.00 0.00 0.00 3.50
3738 4565 7.032598 AGGTAGAAATTGAAAGATGGAGGAA 57.967 36.000 0.00 0.00 0.00 3.36
4205 5050 2.591715 GTGCAAGAGTGGGTGCGT 60.592 61.111 0.00 0.00 43.93 5.24
4257 5102 3.782443 CCTACCTTTCCCGCCGCT 61.782 66.667 0.00 0.00 0.00 5.52
4315 5169 2.037367 CGACTCCCCAGACCCTGA 59.963 66.667 0.00 0.00 32.44 3.86
4376 5231 1.370414 CGAACGCCAACTGCCAAAG 60.370 57.895 0.00 0.00 36.24 2.77
4450 5305 6.149308 ACTCAGATGTAAAATGCATCACGAAA 59.851 34.615 0.00 0.00 43.66 3.46
4753 5617 6.527722 GCTCGCAGTGAAATCAAAATGAAATA 59.472 34.615 0.00 0.00 0.00 1.40
5036 5900 8.417106 TGTAACAAAATGAGGAGCAACAATAAA 58.583 29.630 0.00 0.00 0.00 1.40
5037 5901 7.865385 GTGTAACAAAATGAGGAGCAACAATAA 59.135 33.333 0.00 0.00 36.32 1.40
5436 6301 6.108687 TCCACTGCATAAGAGTAGTTCAATG 58.891 40.000 0.00 0.00 31.85 2.82
5850 6725 6.749118 GCACAAGATAAATGGCACTAAGAAAG 59.251 38.462 0.00 0.00 0.00 2.62
5936 6811 6.585695 ATTTAGTGTTCCGAGAGACAACTA 57.414 37.500 0.00 0.00 0.00 2.24
6087 6962 4.156556 ACAGCGCATGAAATAAACATCAGT 59.843 37.500 11.47 0.00 0.00 3.41
6116 6991 2.543037 GGGGGCCAAATTCTCCTTAA 57.457 50.000 4.39 0.00 0.00 1.85
6185 7060 0.790814 GCGGTGCACTCAGTAAGAAC 59.209 55.000 17.98 0.00 0.00 3.01
6443 7666 4.426313 AGTTTGCCCTAGCCGCCC 62.426 66.667 0.00 0.00 38.69 6.13
6449 7672 2.303022 TGGAGACAAGAGTTTGCCCTAG 59.697 50.000 0.00 0.00 37.85 3.02
6463 7686 1.133761 AGCCTCGCTAGTATGGAGACA 60.134 52.381 0.00 0.00 41.07 3.41
6471 7694 1.776662 AATCCACAGCCTCGCTAGTA 58.223 50.000 0.00 0.00 36.40 1.82
6474 7697 0.744414 GCAAATCCACAGCCTCGCTA 60.744 55.000 0.00 0.00 36.40 4.26
6618 8291 4.725556 TGAAATCCGAAAGACAAACTCG 57.274 40.909 0.00 0.00 0.00 4.18
6645 8318 2.778299 TCCAAACGAATGGACTCAAGG 58.222 47.619 9.39 0.00 44.52 3.61
6657 8330 1.805943 TCGTCGACTATGTCCAAACGA 59.194 47.619 14.70 11.04 36.71 3.85
6661 8334 3.928727 AGTTTCGTCGACTATGTCCAA 57.071 42.857 14.70 0.00 0.00 3.53
6682 8355 2.230508 AGACGGCAAGAATCTACGTTGA 59.769 45.455 1.33 1.33 37.96 3.18
6705 8378 1.599518 CTAACCTTGCCGCACCACA 60.600 57.895 0.00 0.00 0.00 4.17
6716 8390 5.418840 CAGCATGACAATAAACCCTAACCTT 59.581 40.000 0.00 0.00 39.69 3.50
6739 8413 3.146066 GTGGCTAACACCAAATCTCACA 58.854 45.455 0.00 0.00 44.49 3.58
6754 8428 4.080919 ACTTGCATACATCTGAAGTGGCTA 60.081 41.667 11.04 4.98 0.00 3.93
6757 8431 4.005650 ACACTTGCATACATCTGAAGTGG 58.994 43.478 12.56 0.00 45.08 4.00
6815 8489 0.250945 TTCATGCACGTGCCCCTTAA 60.251 50.000 35.72 18.09 41.18 1.85
6825 8499 0.806102 CCGGGTAGTCTTCATGCACG 60.806 60.000 0.00 0.00 0.00 5.34
6840 8514 1.811266 CTTGTCGATGACAGCCGGG 60.811 63.158 2.18 0.00 43.69 5.73
6844 8518 3.489047 GCTTAGATCTTGTCGATGACAGC 59.511 47.826 0.00 0.00 43.69 4.40
6875 8549 5.107133 CGTCTTTTGTCGTCACCCTTATAT 58.893 41.667 0.00 0.00 0.00 0.86
6917 8591 2.592194 TCGAATGACAAGTACTGACGC 58.408 47.619 0.00 0.00 0.00 5.19
6928 8602 8.518702 TCAAAATTATGAAACCATCGAATGACA 58.481 29.630 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.