Multiple sequence alignment - TraesCS2B01G442400

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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 TraesCS2B01G442400 chr2B 100.000 8124 0 0 1 8124 635338351 635346474 0.000000e+00 15003.0
1 TraesCS2B01G442400 chr2D 94.954 6619 214 40 35 6569 534357713 534364295 0.000000e+00 10262.0
2 TraesCS2B01G442400 chr2D 93.526 1174 54 11 6563 7722 534364336 534365501 0.000000e+00 1727.0
3 TraesCS2B01G442400 chr2D 81.567 434 49 14 7718 8122 534366168 534366599 6.080000e-86 329.0
4 TraesCS2B01G442400 chr2D 87.019 208 24 3 7399 7604 544568159 544568365 1.760000e-56 231.0
5 TraesCS2B01G442400 chr2D 85.204 196 27 2 7409 7604 10736103 10735910 4.970000e-47 200.0
6 TraesCS2B01G442400 chr2D 83.575 207 33 1 7399 7604 47677813 47678019 8.320000e-45 193.0
7 TraesCS2B01G442400 chr2D 89.000 100 11 0 7651 7750 571042749 571042650 3.080000e-24 124.0
8 TraesCS2B01G442400 chr2D 97.436 39 1 0 2847 2885 534360614 534360652 5.260000e-07 67.6
9 TraesCS2B01G442400 chr2D 100.000 30 0 0 7599 7628 452615260 452615289 1.000000e-03 56.5
10 TraesCS2B01G442400 chr1B 89.193 2082 178 24 785 2845 545213417 545211362 0.000000e+00 2555.0
11 TraesCS2B01G442400 chr1B 88.084 2182 194 47 5157 7294 545208931 545206772 0.000000e+00 2529.0
12 TraesCS2B01G442400 chr1B 85.340 1487 153 27 3252 4711 545211090 545209642 0.000000e+00 1478.0
13 TraesCS2B01G442400 chr1B 86.111 180 18 5 435 608 545213760 545213582 3.870000e-43 187.0
14 TraesCS2B01G442400 chr1D 90.555 1927 170 9 927 2845 405372142 405370220 0.000000e+00 2540.0
15 TraesCS2B01G442400 chr1D 91.102 1416 107 17 5157 6569 405367781 405366382 0.000000e+00 1899.0
16 TraesCS2B01G442400 chr1D 84.488 1631 170 32 3128 4711 405370087 405368493 0.000000e+00 1533.0
17 TraesCS2B01G442400 chr1D 83.808 772 78 29 6563 7294 405366338 405365574 0.000000e+00 689.0
18 TraesCS2B01G442400 chr1D 79.320 353 30 20 435 776 405372622 405372302 2.970000e-49 207.0
19 TraesCS2B01G442400 chr1A 90.870 1413 107 16 5157 6568 500829889 500828498 0.000000e+00 1875.0
20 TraesCS2B01G442400 chr1A 90.330 1303 102 7 1544 2845 500834370 500833091 0.000000e+00 1687.0
21 TraesCS2B01G442400 chr1A 86.061 1485 148 21 3252 4711 500831836 500830386 0.000000e+00 1541.0
22 TraesCS2B01G442400 chr1A 85.884 758 68 23 6570 7294 500828449 500827698 0.000000e+00 771.0
23 TraesCS2B01G442400 chr1A 88.055 586 67 3 963 1546 500835114 500834530 0.000000e+00 691.0
24 TraesCS2B01G442400 chr1A 76.378 508 78 22 7642 8117 4667128 4666631 1.360000e-57 235.0
25 TraesCS2B01G442400 chr1A 80.282 355 32 22 435 774 500835650 500835319 4.900000e-57 233.0
26 TraesCS2B01G442400 chr5D 88.108 185 22 0 7420 7604 360549986 360549802 3.820000e-53 220.0
27 TraesCS2B01G442400 chr2A 87.047 193 24 1 7405 7596 13838300 13838108 4.940000e-52 217.0
28 TraesCS2B01G442400 chr2A 100.000 30 0 0 7599 7628 596513394 596513365 1.000000e-03 56.5
29 TraesCS2B01G442400 chr3D 83.491 212 31 4 7393 7604 433764439 433764646 2.310000e-45 195.0
30 TraesCS2B01G442400 chr3D 83.654 208 29 4 7400 7604 529756252 529756047 2.990000e-44 191.0
31 TraesCS2B01G442400 chr7B 83.654 208 31 3 7394 7601 121778178 121778382 8.320000e-45 193.0
32 TraesCS2B01G442400 chr3B 100.000 30 0 0 7599 7628 71312760 71312731 1.000000e-03 56.5
33 TraesCS2B01G442400 chr3A 100.000 30 0 0 7599 7628 57210702 57210673 1.000000e-03 56.5


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 TraesCS2B01G442400 chr2B 635338351 635346474 8123 False 15003.00 15003 100.000000 1 8124 1 chr2B.!!$F1 8123
1 TraesCS2B01G442400 chr2D 534357713 534366599 8886 False 3096.40 10262 91.870750 35 8122 4 chr2D.!!$F4 8087
2 TraesCS2B01G442400 chr1B 545206772 545213760 6988 True 1687.25 2555 87.182000 435 7294 4 chr1B.!!$R1 6859
3 TraesCS2B01G442400 chr1D 405365574 405372622 7048 True 1373.60 2540 85.854600 435 7294 5 chr1D.!!$R1 6859
4 TraesCS2B01G442400 chr1A 500827698 500835650 7952 True 1133.00 1875 86.913667 435 7294 6 chr1A.!!$R2 6859

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
24 25 0.856982 ACCATTGGAGGTTTCCCACA 59.143 50.000 10.37 0.0 43.33 4.17 F
1593 1853 0.886563 GCAGGCAAAGCATCTCAAGT 59.113 50.000 0.00 0.0 0.00 3.16 F
3280 4553 0.687354 TCTTCTTGGGTGAGAGTGCC 59.313 55.000 0.00 0.0 0.00 5.01 F
3476 4752 0.384309 CTAGGGTGCGAGCGAATACA 59.616 55.000 0.00 0.0 0.00 2.29 F
5186 6767 3.189287 CCTAAAACTGAGCACTTCGCATT 59.811 43.478 0.00 0.0 46.13 3.56 F
6277 7871 3.269643 TCTCAGGAGGTATGAAGACTGGA 59.730 47.826 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1923 0.828762 TGCACAGGAAGCAGCCAAAT 60.829 50.000 0.00 0.00 37.02 2.32 R
3455 4731 0.952280 TATTCGCTCGCACCCTAGAG 59.048 55.000 0.00 0.00 37.54 2.43 R
4405 5702 0.960364 TCGGTGGAAGCCTGCAATTC 60.960 55.000 0.00 0.00 0.00 2.17 R
5460 7043 1.298116 CGGCGAAATGCTGCATCAG 60.298 57.895 16.55 11.06 44.47 2.90 R
6328 7922 1.252215 TACAGGGGTCGACAATGCGA 61.252 55.000 18.91 1.90 38.07 5.10 R
7715 9425 0.034380 CGGATAGGGGATCGGCTAGA 60.034 60.000 0.00 0.00 35.12 2.43 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
23 24 3.765968 ACCATTGGAGGTTTCCCAC 57.234 52.632 10.37 0.00 43.33 4.61
24 25 0.856982 ACCATTGGAGGTTTCCCACA 59.143 50.000 10.37 0.00 43.33 4.17
25 26 1.432807 ACCATTGGAGGTTTCCCACAT 59.567 47.619 10.37 0.00 43.33 3.21
26 27 1.826720 CCATTGGAGGTTTCCCACATG 59.173 52.381 0.00 0.00 43.33 3.21
27 28 2.557229 CCATTGGAGGTTTCCCACATGA 60.557 50.000 0.00 0.00 43.33 3.07
28 29 2.584835 TTGGAGGTTTCCCACATGAG 57.415 50.000 0.00 0.00 43.33 2.90
29 30 1.444933 TGGAGGTTTCCCACATGAGT 58.555 50.000 0.00 0.00 43.33 3.41
30 31 1.351017 TGGAGGTTTCCCACATGAGTC 59.649 52.381 0.00 0.00 43.33 3.36
31 32 1.630878 GGAGGTTTCCCACATGAGTCT 59.369 52.381 0.00 0.00 37.53 3.24
32 33 2.838202 GGAGGTTTCCCACATGAGTCTA 59.162 50.000 0.00 0.00 37.53 2.59
33 34 3.369576 GGAGGTTTCCCACATGAGTCTAC 60.370 52.174 0.00 0.00 37.53 2.59
47 48 5.194473 TGAGTCTACATGGAGGAGTAGTT 57.806 43.478 4.74 0.00 38.97 2.24
49 50 6.912426 TGAGTCTACATGGAGGAGTAGTTAT 58.088 40.000 4.74 0.00 38.97 1.89
50 51 7.355101 TGAGTCTACATGGAGGAGTAGTTATT 58.645 38.462 4.74 0.00 38.97 1.40
134 135 6.476706 GCTTAAATTTTGAGCCGCATAATCTT 59.523 34.615 13.40 0.00 29.49 2.40
235 237 3.057174 GCAACCATTTGATCCCGTTGTAA 60.057 43.478 0.00 0.00 36.91 2.41
237 239 5.163602 GCAACCATTTGATCCCGTTGTAATA 60.164 40.000 0.00 0.00 36.91 0.98
244 246 6.488769 TTGATCCCGTTGTAATACCTGTAT 57.511 37.500 0.00 0.00 0.00 2.29
245 247 7.600231 TTGATCCCGTTGTAATACCTGTATA 57.400 36.000 0.00 0.00 0.00 1.47
382 398 2.432300 CCCGTCGCCAGATAAGGGT 61.432 63.158 0.00 0.00 35.29 4.34
408 424 7.014326 TGTCCACTATAAATATGAGCTCTCGTT 59.986 37.037 16.19 6.52 0.00 3.85
423 439 2.482333 CGTTCAAACCCCGCCAACA 61.482 57.895 0.00 0.00 0.00 3.33
778 810 6.496338 AGAATTCGAACAATCCAGGTTTAC 57.504 37.500 0.00 0.00 0.00 2.01
779 811 6.238648 AGAATTCGAACAATCCAGGTTTACT 58.761 36.000 0.00 0.00 0.00 2.24
780 812 6.371825 AGAATTCGAACAATCCAGGTTTACTC 59.628 38.462 0.00 0.00 0.00 2.59
781 813 4.884668 TCGAACAATCCAGGTTTACTCT 57.115 40.909 0.00 0.00 0.00 3.24
884 965 3.724508 TGGTCAAACCTAAACGACGTA 57.275 42.857 0.00 0.00 39.58 3.57
885 966 3.641648 TGGTCAAACCTAAACGACGTAG 58.358 45.455 0.00 0.00 39.58 3.51
886 967 3.068024 TGGTCAAACCTAAACGACGTAGT 59.932 43.478 0.00 0.00 41.89 2.73
1072 1170 5.748152 GCAAGCACTAAATCACTTTTCACAA 59.252 36.000 0.00 0.00 0.00 3.33
1227 1325 3.066203 AGTTTAAGGCAAAGGTTGTGTCG 59.934 43.478 0.00 0.00 0.00 4.35
1359 1457 2.533266 GCTGTTGCTTCATATGTTGGC 58.467 47.619 1.90 6.50 36.03 4.52
1372 1470 1.279025 TGTTGGCCCCTACCTGATCC 61.279 60.000 0.00 0.00 0.00 3.36
1402 1500 5.165911 TGTCGACTACCTAAATAAGAGCG 57.834 43.478 17.92 0.00 0.00 5.03
1593 1853 0.886563 GCAGGCAAAGCATCTCAAGT 59.113 50.000 0.00 0.00 0.00 3.16
1611 1871 6.058553 TCAAGTGGAGAGATGATCAATGTT 57.941 37.500 0.00 0.00 0.00 2.71
1663 1923 4.605640 TTCAGTCGATCCATGCATGATA 57.394 40.909 28.31 15.61 0.00 2.15
1929 2189 6.373186 TTCTTATCGAAGATCGCAGAGTTA 57.627 37.500 0.00 0.00 45.12 2.24
1932 2192 4.902443 ATCGAAGATCGCAGAGTTAAGA 57.098 40.909 0.00 0.00 45.12 2.10
1947 2207 7.819900 GCAGAGTTAAGAAAGGTAGAGATGAAA 59.180 37.037 0.00 0.00 0.00 2.69
1986 2246 1.519455 CACCTCGGCGATGGTTCTC 60.519 63.158 22.58 0.00 33.75 2.87
2205 2465 5.324409 TCATTTATGTGCCTTGAGGAACTT 58.676 37.500 9.54 5.84 44.46 2.66
2394 2654 6.024552 TCTGGCAAATCAAGTTTATTGTCC 57.975 37.500 0.00 0.00 0.00 4.02
2981 3245 7.801752 TGTTTCTGTTGGAAAAATTGTTCAAC 58.198 30.769 10.53 11.94 44.34 3.18
3006 3270 9.843334 ACAAAAACGATTACACTTTTGTTAGAA 57.157 25.926 6.06 0.00 45.15 2.10
3010 3274 9.712359 AAACGATTACACTTTTGTTAGAACTTC 57.288 29.630 0.00 0.00 37.15 3.01
3011 3275 8.658499 ACGATTACACTTTTGTTAGAACTTCT 57.342 30.769 0.00 0.00 37.15 2.85
3012 3276 8.762426 ACGATTACACTTTTGTTAGAACTTCTC 58.238 33.333 0.00 0.00 37.15 2.87
3013 3277 8.979574 CGATTACACTTTTGTTAGAACTTCTCT 58.020 33.333 0.00 0.00 37.15 3.10
3015 3279 6.364945 ACACTTTTGTTAGAACTTCTCTGC 57.635 37.500 0.00 0.00 35.41 4.26
3016 3280 6.116126 ACACTTTTGTTAGAACTTCTCTGCT 58.884 36.000 0.00 0.00 35.41 4.24
3017 3281 6.599638 ACACTTTTGTTAGAACTTCTCTGCTT 59.400 34.615 0.00 0.00 35.41 3.91
3050 3314 8.619546 CAATTGTGGTGGTGTTGAAATTTTATT 58.380 29.630 0.00 0.00 0.00 1.40
3074 3338 4.119862 GCTGCTGGTTTAATCATCTCGTA 58.880 43.478 0.00 0.00 0.00 3.43
3156 3420 7.883391 AGCTATGTACTAGTACTGACACATT 57.117 36.000 28.56 8.65 37.00 2.71
3157 3421 8.975663 AGCTATGTACTAGTACTGACACATTA 57.024 34.615 28.56 9.88 37.00 1.90
3174 3441 8.614994 GACACATTATTAGTGGCATTTTGTAC 57.385 34.615 0.00 0.00 44.47 2.90
3183 3450 5.172205 AGTGGCATTTTGTACAAAACGTTT 58.828 33.333 30.66 15.76 42.32 3.60
3190 3457 5.640189 TTTGTACAAAACGTTTCCTGGAA 57.360 34.783 18.54 4.68 0.00 3.53
3209 3476 9.535170 TCCTGGAATACAAATATTACCAAAACA 57.465 29.630 0.00 0.00 31.25 2.83
3250 4516 8.870075 ATATATTTTCTTACTGATGAAGGGCC 57.130 34.615 0.00 0.00 0.00 5.80
3280 4553 0.687354 TCTTCTTGGGTGAGAGTGCC 59.313 55.000 0.00 0.00 0.00 5.01
3298 4571 4.095483 AGTGCCAATTAATCTCTTGCTTCG 59.905 41.667 0.00 0.00 0.00 3.79
3374 4647 7.113704 AGTGGTTTCGTATTTCTTTTAGTCG 57.886 36.000 0.00 0.00 0.00 4.18
3392 4668 9.585099 TTTTAGTCGTGTTAAACAACTCTTCTA 57.415 29.630 0.00 0.00 0.00 2.10
3416 4692 5.891551 AGTTTTGTGATTGGTCCAGTTTAGT 59.108 36.000 0.00 0.00 0.00 2.24
3421 4697 4.455877 GTGATTGGTCCAGTTTAGTCAAGG 59.544 45.833 0.00 0.00 0.00 3.61
3448 4724 7.843490 TTTGAGTTAATATGTCCTTTCTCGG 57.157 36.000 0.00 0.00 0.00 4.63
3449 4725 5.357257 TGAGTTAATATGTCCTTTCTCGGC 58.643 41.667 0.00 0.00 0.00 5.54
3476 4752 0.384309 CTAGGGTGCGAGCGAATACA 59.616 55.000 0.00 0.00 0.00 2.29
3557 4833 8.419076 TTGGATTTTTAGCTTCAAAAACAGTC 57.581 30.769 8.87 4.36 39.49 3.51
3596 4872 5.705441 TCATGTCGAATTTTTACCTTCAGCT 59.295 36.000 0.00 0.00 0.00 4.24
3772 5048 9.399403 GGAAAAGAATTCACTGAATTAACTGTC 57.601 33.333 15.58 10.71 41.56 3.51
3773 5049 9.399403 GAAAAGAATTCACTGAATTAACTGTCC 57.601 33.333 15.58 3.67 41.56 4.02
3788 5064 3.256960 TCCCCCACAAGGAGGCAC 61.257 66.667 0.00 0.00 38.24 5.01
4376 5673 5.894807 AGTTGAAGTCACATGTCCTTTTTG 58.105 37.500 0.00 0.00 0.00 2.44
4623 5922 5.828299 TTTCGATTTGAGTTCTTGTTGGT 57.172 34.783 0.00 0.00 0.00 3.67
4699 6000 4.142337 TGAATTATGCATGCACAGGAGTTG 60.142 41.667 25.37 0.00 0.00 3.16
4725 6164 5.705905 ACACCTTGAAGGCAAAATCTAGTAC 59.294 40.000 11.96 0.00 39.63 2.73
4728 6167 5.940470 CCTTGAAGGCAAAATCTAGTACAGT 59.060 40.000 0.00 0.00 32.73 3.55
4854 6325 3.511699 TGTGAGCAGTGCTACTAAATCG 58.488 45.455 19.77 0.00 39.88 3.34
4859 6330 5.073311 AGCAGTGCTACTAAATCGAGAAA 57.927 39.130 18.11 0.00 36.99 2.52
4918 6390 4.340617 TCCATGGTTTGTCAAATAGGTCC 58.659 43.478 12.58 0.00 0.00 4.46
5003 6475 6.136857 ACTTACATGAGCAGTAATAGAGGGA 58.863 40.000 0.00 0.00 31.64 4.20
5005 6477 6.266558 CTTACATGAGCAGTAATAGAGGGACT 59.733 42.308 0.00 0.00 33.94 3.85
5186 6767 3.189287 CCTAAAACTGAGCACTTCGCATT 59.811 43.478 0.00 0.00 46.13 3.56
5205 6786 4.154918 GCATTTTCAGGACCTAAGTGTCAG 59.845 45.833 0.00 0.00 36.97 3.51
5229 6810 4.568956 ACTGCAAATTTTAGGACCAATGC 58.431 39.130 0.00 0.00 0.00 3.56
5418 7001 5.989477 TCCAGCAATACTACATAAGTGCTT 58.011 37.500 0.00 0.00 39.39 3.91
5837 7420 9.201989 TCACTTATGGACTAAGTCTGAATATGT 57.798 33.333 0.00 0.00 45.61 2.29
5890 7473 8.664798 TGTAGTTTGGAAAACAGAATGATATCG 58.335 33.333 5.72 0.00 39.69 2.92
6030 7613 7.591057 TCATGTTCGTTTCTTCAGCTTTAAATG 59.409 33.333 0.00 0.00 0.00 2.32
6063 7646 6.595772 TTTGTTGTTGTTGCAAATCCATAC 57.404 33.333 0.00 0.00 0.00 2.39
6143 7734 8.932945 TTCATCAGTTAGTAATAGCAGTTCTG 57.067 34.615 0.00 0.00 0.00 3.02
6163 7754 7.770433 AGTTCTGATGTTGCTGCTAATACAATA 59.230 33.333 0.00 0.00 0.00 1.90
6277 7871 3.269643 TCTCAGGAGGTATGAAGACTGGA 59.730 47.826 0.00 0.00 0.00 3.86
6323 7917 6.098124 TGGAAAGTCAACCTTGATTCAAACAT 59.902 34.615 0.01 0.00 39.73 2.71
6502 8096 7.512130 TGGATGAGTATAGTGATGAGCAAATT 58.488 34.615 0.00 0.00 0.00 1.82
6658 8303 3.579335 AAGCTCGACTCTACAGGTTTC 57.421 47.619 0.00 0.00 0.00 2.78
6715 8383 7.275888 TGCTTTTCTTTATGATATGCCGAAT 57.724 32.000 0.00 0.00 0.00 3.34
6745 8413 7.814264 ACTTGAATCTTCTGAACTGAAATGT 57.186 32.000 0.00 0.00 0.00 2.71
6809 8477 2.593026 CTTGTTTGCTTGGGAAGGGTA 58.407 47.619 0.00 0.00 0.00 3.69
7004 8675 1.516365 CGGTGAGTCTCGTCCACTGT 61.516 60.000 12.38 0.00 33.70 3.55
7035 8716 7.147846 ACAGATTGAACTGACAAATCCTGTTTT 60.148 33.333 0.00 0.00 38.84 2.43
7059 8744 6.949578 TTCTCTCTTTGTTTGCTTGTTTTG 57.050 33.333 0.00 0.00 0.00 2.44
7113 8799 3.271014 GAGTACGACTCACCGGCA 58.729 61.111 0.00 0.00 44.45 5.69
7265 8962 4.292599 GTTTCCGGCTTAAAATTTGACGT 58.707 39.130 0.00 0.00 0.00 4.34
7331 9028 7.094508 AGTGATGTAACAAATTTGTGTGTGA 57.905 32.000 23.93 7.73 41.31 3.58
7389 9086 7.110155 AGTTTGAATCATATTACGGTGGAAGT 58.890 34.615 0.00 0.00 0.00 3.01
7390 9087 7.280205 AGTTTGAATCATATTACGGTGGAAGTC 59.720 37.037 0.00 0.00 0.00 3.01
7391 9088 5.607477 TGAATCATATTACGGTGGAAGTCC 58.393 41.667 0.00 0.00 0.00 3.85
7392 9089 5.365605 TGAATCATATTACGGTGGAAGTCCT 59.634 40.000 0.00 0.00 36.82 3.85
7394 9091 5.687166 TCATATTACGGTGGAAGTCCTTT 57.313 39.130 0.00 0.00 36.82 3.11
7395 9092 6.057321 TCATATTACGGTGGAAGTCCTTTT 57.943 37.500 0.00 0.00 36.82 2.27
7396 9093 6.478129 TCATATTACGGTGGAAGTCCTTTTT 58.522 36.000 0.00 0.00 36.82 1.94
7493 9190 1.208052 ACATCGAGGTTCATGGACCAG 59.792 52.381 25.54 17.83 42.35 4.00
7519 9216 4.481112 CATTGCGGCCGCCAGAAC 62.481 66.667 44.42 19.47 41.09 3.01
7546 9256 1.141019 GTCGCCGCTCTCATACCAA 59.859 57.895 0.00 0.00 0.00 3.67
7554 9264 0.815615 CTCTCATACCAAAGCCGGCC 60.816 60.000 26.15 5.07 0.00 6.13
7558 9268 0.466189 CATACCAAAGCCGGCCTGAT 60.466 55.000 26.15 11.04 0.00 2.90
7559 9269 0.258774 ATACCAAAGCCGGCCTGATT 59.741 50.000 26.15 8.05 0.00 2.57
7569 9279 1.135024 CCGGCCTGATTTTGTCAATGG 60.135 52.381 0.00 0.00 36.14 3.16
7574 9284 3.841643 CCTGATTTTGTCAATGGCAGTC 58.158 45.455 0.00 0.00 36.14 3.51
7577 9287 0.958091 TTTTGTCAATGGCAGTCGGG 59.042 50.000 0.00 0.00 0.00 5.14
7583 9293 0.036010 CAATGGCAGTCGGGAAGTCT 60.036 55.000 0.00 0.00 0.00 3.24
7584 9294 0.693049 AATGGCAGTCGGGAAGTCTT 59.307 50.000 0.00 0.00 0.00 3.01
7590 9300 1.006571 GTCGGGAAGTCTTCGTGCA 60.007 57.895 6.50 0.00 0.00 4.57
7628 9338 6.264518 GGCATTTCTAATCGATCCCCTAAAAA 59.735 38.462 0.00 0.00 0.00 1.94
7629 9339 7.363431 GCATTTCTAATCGATCCCCTAAAAAG 58.637 38.462 0.00 0.00 0.00 2.27
7630 9340 7.013369 GCATTTCTAATCGATCCCCTAAAAAGT 59.987 37.037 0.00 0.00 0.00 2.66
7631 9341 7.859325 TTTCTAATCGATCCCCTAAAAAGTG 57.141 36.000 0.00 0.00 0.00 3.16
7632 9342 5.365619 TCTAATCGATCCCCTAAAAAGTGC 58.634 41.667 0.00 0.00 0.00 4.40
7633 9343 3.644966 ATCGATCCCCTAAAAAGTGCA 57.355 42.857 0.00 0.00 0.00 4.57
7634 9344 2.706890 TCGATCCCCTAAAAAGTGCAC 58.293 47.619 9.40 9.40 0.00 4.57
7635 9345 1.396996 CGATCCCCTAAAAAGTGCACG 59.603 52.381 12.01 0.00 0.00 5.34
7636 9346 2.433436 GATCCCCTAAAAAGTGCACGT 58.567 47.619 12.01 5.01 0.00 4.49
7637 9347 1.600023 TCCCCTAAAAAGTGCACGTG 58.400 50.000 12.28 12.28 0.00 4.49
7638 9348 0.039527 CCCCTAAAAAGTGCACGTGC 60.040 55.000 33.11 33.11 42.50 5.34
7639 9349 0.385473 CCCTAAAAAGTGCACGTGCG 60.385 55.000 33.22 17.23 45.83 5.34
7662 9372 3.988517 CCTAAGGGCGTTTCTAATCGATC 59.011 47.826 0.00 0.00 0.00 3.69
7674 9384 4.628074 TCTAATCGATCCCCTAAAAAGCG 58.372 43.478 0.00 0.00 0.00 4.68
7693 9403 7.696992 AAAGCGATAAGGGAGTAAAAATTCA 57.303 32.000 0.00 0.00 0.00 2.57
7711 9421 6.742559 AATTCAGTTATAGTCCCATACGGT 57.257 37.500 0.00 0.00 0.00 4.83
7715 9425 3.901844 AGTTATAGTCCCATACGGTGCAT 59.098 43.478 0.00 0.00 0.00 3.96
7726 10107 4.683432 GGTGCATCTAGCCGATCC 57.317 61.111 0.00 0.00 44.83 3.36
7749 10130 3.640029 CCTATCCGGCTTAGTGGAGTAAA 59.360 47.826 0.00 0.00 37.76 2.01
7755 10136 5.413523 TCCGGCTTAGTGGAGTAAATTTTTC 59.586 40.000 0.00 0.00 0.00 2.29
7784 10165 5.770162 CCAACTCCCAATATACCCTCAAATC 59.230 44.000 0.00 0.00 0.00 2.17
7785 10166 5.584551 ACTCCCAATATACCCTCAAATCC 57.415 43.478 0.00 0.00 0.00 3.01
7800 10181 6.431722 CCTCAAATCCCCCTAAATTTACTCA 58.568 40.000 0.00 0.00 0.00 3.41
7801 10182 6.321435 CCTCAAATCCCCCTAAATTTACTCAC 59.679 42.308 0.00 0.00 0.00 3.51
7805 10186 3.784202 TCCCCCTAAATTTACTCACTCCC 59.216 47.826 0.00 0.00 0.00 4.30
7825 10206 0.179103 GCGGCGGCCTAGTAAAACTA 60.179 55.000 18.34 0.00 0.00 2.24
7843 10224 0.032017 TAGCACCTCTCTTCCTCCCC 60.032 60.000 0.00 0.00 0.00 4.81
7859 10240 2.632831 CCCCCACCACCATGTATCT 58.367 57.895 0.00 0.00 0.00 1.98
7860 10241 0.474184 CCCCCACCACCATGTATCTC 59.526 60.000 0.00 0.00 0.00 2.75
7861 10242 1.212375 CCCCACCACCATGTATCTCA 58.788 55.000 0.00 0.00 0.00 3.27
7870 10278 2.134287 ATGTATCTCACCGCCGCCT 61.134 57.895 0.00 0.00 0.00 5.52
7885 10293 3.367743 CCTCCAACGACCGTCCGA 61.368 66.667 0.00 0.00 0.00 4.55
7904 10312 0.182775 ACCGGTTGGAATGGATAGCC 59.817 55.000 0.00 0.00 39.21 3.93
7905 10313 0.474184 CCGGTTGGAATGGATAGCCT 59.526 55.000 0.00 0.00 37.49 4.58
7907 10315 1.815408 CGGTTGGAATGGATAGCCTGG 60.815 57.143 0.00 0.00 34.31 4.45
7939 10347 3.061848 CCATCGGTGCCGGCTTTT 61.062 61.111 29.70 4.97 40.25 2.27
7945 10353 2.335011 GTGCCGGCTTTTCACCAC 59.665 61.111 29.70 11.08 0.00 4.16
7962 10370 1.748879 ACCGGAAATCACCCATGCG 60.749 57.895 9.46 0.00 0.00 4.73
7965 10373 2.408835 GAAATCACCCATGCGCCG 59.591 61.111 4.18 0.00 0.00 6.46
7990 10399 1.497991 CACGCGAAGAAGAGTTTGGA 58.502 50.000 15.93 0.00 0.00 3.53
8014 10423 1.819905 AAAAACCACCACGCCCAAG 59.180 52.632 0.00 0.00 0.00 3.61
8015 10424 2.304901 AAAAACCACCACGCCCAAGC 62.305 55.000 0.00 0.00 0.00 4.01
8016 10425 3.731766 AAACCACCACGCCCAAGCT 62.732 57.895 0.00 0.00 36.60 3.74
8017 10426 4.643387 ACCACCACGCCCAAGCTC 62.643 66.667 0.00 0.00 36.60 4.09
8019 10428 4.335647 CACCACGCCCAAGCTCCT 62.336 66.667 0.00 0.00 36.60 3.69
8020 10429 4.021925 ACCACGCCCAAGCTCCTC 62.022 66.667 0.00 0.00 36.60 3.71
8021 10430 4.785453 CCACGCCCAAGCTCCTCC 62.785 72.222 0.00 0.00 36.60 4.30
8029 10439 3.330720 AAGCTCCTCCCCCAACCG 61.331 66.667 0.00 0.00 0.00 4.44
8074 10484 1.817099 GGCTCTCCCGCAATGACAG 60.817 63.158 0.00 0.00 0.00 3.51
8076 10486 1.817099 CTCTCCCGCAATGACAGCC 60.817 63.158 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.142564 CATGTAGACTCATGTGGGAAACCTC 61.143 48.000 0.00 0.00 42.77 3.85
13 14 4.323792 CATGTAGACTCATGTGGGAAACCT 60.324 45.833 0.00 0.00 42.77 3.50
14 15 3.941483 CATGTAGACTCATGTGGGAAACC 59.059 47.826 0.00 0.00 42.71 3.27
15 16 3.941483 CCATGTAGACTCATGTGGGAAAC 59.059 47.826 11.49 0.00 42.29 2.78
16 17 3.843619 TCCATGTAGACTCATGTGGGAAA 59.156 43.478 11.49 0.00 42.29 3.13
17 18 3.449918 TCCATGTAGACTCATGTGGGAA 58.550 45.455 11.49 0.00 42.29 3.97
18 19 3.033909 CTCCATGTAGACTCATGTGGGA 58.966 50.000 11.49 0.00 42.29 4.37
19 20 2.103771 CCTCCATGTAGACTCATGTGGG 59.896 54.545 11.49 9.55 42.29 4.61
20 21 3.033909 TCCTCCATGTAGACTCATGTGG 58.966 50.000 11.49 12.06 42.29 4.17
21 22 3.703556 ACTCCTCCATGTAGACTCATGTG 59.296 47.826 11.49 0.00 42.29 3.21
22 23 3.987745 ACTCCTCCATGTAGACTCATGT 58.012 45.455 11.49 0.00 42.29 3.21
23 24 5.136828 ACTACTCCTCCATGTAGACTCATG 58.863 45.833 7.09 7.52 43.14 3.07
24 25 5.396057 ACTACTCCTCCATGTAGACTCAT 57.604 43.478 7.09 0.00 39.36 2.90
25 26 4.864483 ACTACTCCTCCATGTAGACTCA 57.136 45.455 7.09 0.00 39.36 3.41
26 27 7.502895 TCAATAACTACTCCTCCATGTAGACTC 59.497 40.741 7.09 0.00 39.36 3.36
27 28 7.355101 TCAATAACTACTCCTCCATGTAGACT 58.645 38.462 7.09 0.00 39.36 3.24
28 29 7.584122 TCAATAACTACTCCTCCATGTAGAC 57.416 40.000 7.09 0.00 39.36 2.59
29 30 8.603898 TTTCAATAACTACTCCTCCATGTAGA 57.396 34.615 7.09 0.00 39.36 2.59
30 31 9.838339 AATTTCAATAACTACTCCTCCATGTAG 57.162 33.333 0.00 0.00 41.18 2.74
32 33 9.838339 CTAATTTCAATAACTACTCCTCCATGT 57.162 33.333 0.00 0.00 0.00 3.21
99 100 7.247019 GGCTCAAAATTTAAGCTTCTAGACTG 58.753 38.462 19.31 0.00 36.29 3.51
112 113 5.748152 GCAAGATTATGCGGCTCAAAATTTA 59.252 36.000 0.00 0.00 36.45 1.40
134 135 2.273123 CTGGTGGCATGCCTAGCA 59.727 61.111 35.53 30.82 44.86 3.49
235 237 6.250711 TCACGTGGTATGGATATACAGGTAT 58.749 40.000 17.00 0.00 40.77 2.73
237 239 4.476297 TCACGTGGTATGGATATACAGGT 58.524 43.478 17.00 0.00 40.77 4.00
244 246 6.649141 GCTTTATTCATCACGTGGTATGGATA 59.351 38.462 17.00 14.04 0.00 2.59
245 247 5.470098 GCTTTATTCATCACGTGGTATGGAT 59.530 40.000 17.00 15.05 0.00 3.41
302 307 1.066257 GTCGCGCCCGTCCTATTTA 59.934 57.895 0.00 0.00 35.54 1.40
369 374 0.462047 GTGGACACCCTTATCTGGCG 60.462 60.000 0.00 0.00 0.00 5.69
370 375 0.912486 AGTGGACACCCTTATCTGGC 59.088 55.000 0.00 0.00 0.00 4.85
371 376 6.494666 TTTATAGTGGACACCCTTATCTGG 57.505 41.667 0.00 0.00 0.00 3.86
372 377 9.658799 CATATTTATAGTGGACACCCTTATCTG 57.341 37.037 0.00 0.00 0.00 2.90
374 379 9.877178 CTCATATTTATAGTGGACACCCTTATC 57.123 37.037 0.00 0.00 0.00 1.75
382 398 6.490381 ACGAGAGCTCATATTTATAGTGGACA 59.510 38.462 17.77 0.00 0.00 4.02
408 424 0.684805 AGTTTGTTGGCGGGGTTTGA 60.685 50.000 0.00 0.00 0.00 2.69
423 439 2.491675 GGATCTTTCCGTGGGAGTTT 57.508 50.000 0.00 0.00 31.21 2.66
729 755 4.039151 AGAAGAGTCAGCATCGTACATG 57.961 45.455 0.00 0.00 0.00 3.21
730 756 5.126779 TCTAGAAGAGTCAGCATCGTACAT 58.873 41.667 0.00 0.00 0.00 2.29
731 757 4.514401 TCTAGAAGAGTCAGCATCGTACA 58.486 43.478 0.00 0.00 0.00 2.90
778 810 3.311871 GCAATGAAGCACATCACCTAGAG 59.688 47.826 0.00 0.00 38.38 2.43
779 811 3.054875 AGCAATGAAGCACATCACCTAGA 60.055 43.478 0.00 0.00 38.38 2.43
780 812 3.276857 AGCAATGAAGCACATCACCTAG 58.723 45.455 0.00 0.00 38.38 3.02
781 813 3.354948 AGCAATGAAGCACATCACCTA 57.645 42.857 0.00 0.00 38.38 3.08
873 954 8.445193 AAATTAGAGAACACTACGTCGTTTAG 57.555 34.615 1.78 0.00 0.00 1.85
1227 1325 4.373116 TGCCCCGTCGCAGAGTTC 62.373 66.667 0.00 0.00 36.95 3.01
1335 1433 1.667724 ACATATGAAGCAACAGCGCTC 59.332 47.619 7.13 0.00 42.89 5.03
1359 1457 2.777459 AGTACTGGATCAGGTAGGGG 57.223 55.000 0.00 0.00 35.51 4.79
1372 1470 9.286946 CTTATTTAGGTAGTCGACAAAGTACTG 57.713 37.037 19.50 0.00 0.00 2.74
1402 1500 2.092699 AGCCCTCTTTACTGGATCTTGC 60.093 50.000 0.00 0.00 0.00 4.01
1593 1853 5.425196 TCACAACATTGATCATCTCTCCA 57.575 39.130 0.00 0.00 0.00 3.86
1611 1871 3.068064 TCGGCATCGAGGCTCACA 61.068 61.111 22.57 0.00 40.88 3.58
1663 1923 0.828762 TGCACAGGAAGCAGCCAAAT 60.829 50.000 0.00 0.00 37.02 2.32
1929 2189 6.394345 ACCCATTTCATCTCTACCTTTCTT 57.606 37.500 0.00 0.00 0.00 2.52
1932 2192 7.928873 TCTTTACCCATTTCATCTCTACCTTT 58.071 34.615 0.00 0.00 0.00 3.11
1947 2207 8.102484 AGGTGTATACATTCTTCTTTACCCAT 57.898 34.615 9.18 0.00 0.00 4.00
1986 2246 6.402222 AGCAGGAACACAAAAGTAGATAGAG 58.598 40.000 0.00 0.00 0.00 2.43
2205 2465 6.852420 AGCTTAGTTACAACATCACTAGGA 57.148 37.500 0.00 0.00 0.00 2.94
2394 2654 3.290308 GGTATCTCACCGAGTATGCAG 57.710 52.381 0.00 0.00 37.63 4.41
2514 2774 8.010697 TCATACCTCTCCCTATTCATTTCTGTA 58.989 37.037 0.00 0.00 0.00 2.74
2917 3180 5.049167 TGAAAGGTGAACATTGCAACAATC 58.951 37.500 0.00 0.32 0.00 2.67
2919 3182 4.462508 TGAAAGGTGAACATTGCAACAA 57.537 36.364 0.00 0.00 0.00 2.83
2948 3212 7.475771 TTTTTCCAACAGAAACATATTGTGC 57.524 32.000 0.00 0.00 44.20 4.57
3002 3266 5.670485 TGACAACAAAGCAGAGAAGTTCTA 58.330 37.500 5.09 0.00 33.83 2.10
3003 3267 4.517285 TGACAACAAAGCAGAGAAGTTCT 58.483 39.130 4.68 4.68 36.25 3.01
3004 3268 4.882671 TGACAACAAAGCAGAGAAGTTC 57.117 40.909 0.00 0.00 0.00 3.01
3005 3269 5.841957 ATTGACAACAAAGCAGAGAAGTT 57.158 34.783 0.00 0.00 39.54 2.66
3006 3270 5.126061 ACAATTGACAACAAAGCAGAGAAGT 59.874 36.000 13.59 0.00 39.54 3.01
3007 3271 5.457799 CACAATTGACAACAAAGCAGAGAAG 59.542 40.000 13.59 0.00 39.54 2.85
3008 3272 5.342433 CACAATTGACAACAAAGCAGAGAA 58.658 37.500 13.59 0.00 39.54 2.87
3009 3273 4.202040 CCACAATTGACAACAAAGCAGAGA 60.202 41.667 13.59 0.00 39.54 3.10
3010 3274 4.046462 CCACAATTGACAACAAAGCAGAG 58.954 43.478 13.59 0.00 39.54 3.35
3011 3275 3.446873 ACCACAATTGACAACAAAGCAGA 59.553 39.130 13.59 0.00 39.54 4.26
3012 3276 3.552699 CACCACAATTGACAACAAAGCAG 59.447 43.478 13.59 0.00 39.54 4.24
3013 3277 3.519579 CACCACAATTGACAACAAAGCA 58.480 40.909 13.59 0.00 39.54 3.91
3014 3278 2.865551 CCACCACAATTGACAACAAAGC 59.134 45.455 13.59 0.00 39.54 3.51
3015 3279 3.864583 CACCACCACAATTGACAACAAAG 59.135 43.478 13.59 0.00 39.54 2.77
3016 3280 3.259374 ACACCACCACAATTGACAACAAA 59.741 39.130 13.59 0.00 39.54 2.83
3017 3281 2.828520 ACACCACCACAATTGACAACAA 59.171 40.909 13.59 0.00 40.42 2.83
3050 3314 4.141937 ACGAGATGATTAAACCAGCAGCTA 60.142 41.667 0.00 0.00 0.00 3.32
3155 3419 8.136165 ACGTTTTGTACAAAATGCCACTAATAA 58.864 29.630 36.36 12.99 46.06 1.40
3156 3420 7.649973 ACGTTTTGTACAAAATGCCACTAATA 58.350 30.769 36.36 13.16 46.06 0.98
3157 3421 6.508777 ACGTTTTGTACAAAATGCCACTAAT 58.491 32.000 36.36 21.55 46.06 1.73
3161 3425 5.457650 AAACGTTTTGTACAAAATGCCAC 57.542 34.783 36.36 23.90 46.06 5.01
3168 3433 5.640189 TTCCAGGAAACGTTTTGTACAAA 57.360 34.783 17.01 17.01 0.00 2.83
3174 3441 8.980143 ATATTTGTATTCCAGGAAACGTTTTG 57.020 30.769 15.89 10.26 0.00 2.44
3183 3450 9.535170 TGTTTTGGTAATATTTGTATTCCAGGA 57.465 29.630 0.00 0.00 0.00 3.86
3190 3457 9.849166 CCGAGTTTGTTTTGGTAATATTTGTAT 57.151 29.630 0.00 0.00 0.00 2.29
3250 4516 8.340618 TCTCACCCAAGAAGAATTTGAAATAG 57.659 34.615 0.00 0.00 0.00 1.73
3280 4553 6.037500 TGGACATCGAAGCAAGAGATTAATTG 59.962 38.462 0.00 0.00 0.00 2.32
3298 4571 5.823045 AGAAATTCTTTACGGGATGGACATC 59.177 40.000 3.72 3.72 37.11 3.06
3331 4604 6.805713 ACCACTTTTCTTGGAAATGTAACTG 58.194 36.000 9.91 4.58 37.58 3.16
3351 4624 6.788930 CACGACTAAAAGAAATACGAAACCAC 59.211 38.462 0.00 0.00 0.00 4.16
3392 4668 5.891551 ACTAAACTGGACCAATCACAAAACT 59.108 36.000 0.00 0.00 0.00 2.66
3416 4692 9.753674 AAGGACATATTAACTCAAATTCCTTGA 57.246 29.630 0.00 0.00 41.93 3.02
3421 4697 9.922305 CGAGAAAGGACATATTAACTCAAATTC 57.078 33.333 0.00 0.00 0.00 2.17
3448 4724 1.032657 TCGCACCCTAGAGTCTCTGC 61.033 60.000 12.92 6.78 0.00 4.26
3449 4725 1.021202 CTCGCACCCTAGAGTCTCTG 58.979 60.000 12.92 2.82 0.00 3.35
3455 4731 0.952280 TATTCGCTCGCACCCTAGAG 59.048 55.000 0.00 0.00 37.54 2.43
3527 4803 7.856145 TTTTGAAGCTAAAAATCCAAGCAAA 57.144 28.000 3.70 0.00 38.75 3.68
3596 4872 8.210265 TGTTTCTAGCATACCATGATAACATCA 58.790 33.333 0.00 0.00 44.55 3.07
3691 4967 9.651913 GCTTGTATTATTTTCCCATCTTTCAAA 57.348 29.630 0.00 0.00 0.00 2.69
3773 5049 0.181350 GATAGTGCCTCCTTGTGGGG 59.819 60.000 0.00 0.00 35.33 4.96
3788 5064 6.393990 GCTCCAACATGTCCATAGTAGATAG 58.606 44.000 0.00 0.00 0.00 2.08
3845 5121 2.102578 GGTGCTTCCACTGGCATTAAT 58.897 47.619 0.00 0.00 41.75 1.40
3852 5128 1.299976 GGTAGGGTGCTTCCACTGG 59.700 63.158 0.00 0.00 41.75 4.00
4376 5673 7.238571 TCAACTTTCAACGTTAAGAACAGAAC 58.761 34.615 15.89 0.00 0.00 3.01
4405 5702 0.960364 TCGGTGGAAGCCTGCAATTC 60.960 55.000 0.00 0.00 0.00 2.17
4601 5898 5.828299 ACCAACAAGAACTCAAATCGAAA 57.172 34.783 0.00 0.00 0.00 3.46
4672 5973 4.576053 TCCTGTGCATGCATAATTCACTAC 59.424 41.667 25.64 7.17 0.00 2.73
4699 6000 2.893489 AGATTTTGCCTTCAAGGTGTCC 59.107 45.455 5.03 0.00 37.80 4.02
4854 6325 3.626217 ACGAAACAGAAACAGGGTTTCTC 59.374 43.478 18.58 9.21 44.98 2.87
4859 6330 4.710324 TCATAACGAAACAGAAACAGGGT 58.290 39.130 0.00 0.00 0.00 4.34
5003 6475 7.295340 ACTTCCATAAGTTAAAAGTCCCAAGT 58.705 34.615 3.93 0.00 43.60 3.16
5005 6477 8.219178 TGTACTTCCATAAGTTAAAAGTCCCAA 58.781 33.333 10.31 0.00 43.60 4.12
5101 6583 7.232534 ACCTTACTTAATTGGCATTCAAAGTCA 59.767 33.333 11.19 3.75 39.05 3.41
5186 6767 3.323979 GTCCTGACACTTAGGTCCTGAAA 59.676 47.826 0.00 0.00 36.97 2.69
5205 6786 4.864704 TTGGTCCTAAAATTTGCAGTCC 57.135 40.909 0.00 0.00 0.00 3.85
5229 6810 8.567948 TCTTAATCTGCTTAACCAAAAGTTCAG 58.432 33.333 0.00 0.00 40.05 3.02
5418 7001 4.783227 AGTTAACCTCTGCAATTCCCTAGA 59.217 41.667 0.88 0.00 0.00 2.43
5460 7043 1.298116 CGGCGAAATGCTGCATCAG 60.298 57.895 16.55 11.06 44.47 2.90
5837 7420 2.355310 CGACAATAGCCCACCCTTGTAA 60.355 50.000 0.00 0.00 32.28 2.41
5890 7473 8.827677 GTCATGTACTGTAATATTCTTTCCACC 58.172 37.037 0.00 0.00 0.00 4.61
6090 7673 8.742554 AAATTACTATGTGCAACTAAAACTGC 57.257 30.769 0.00 0.00 38.04 4.40
6143 7734 7.140705 TGCAATATTGTATTAGCAGCAACATC 58.859 34.615 16.61 0.00 0.00 3.06
6163 7754 6.766467 GCACTTAGGGTACTAATAACTGCAAT 59.234 38.462 0.00 0.00 38.44 3.56
6277 7871 3.384467 CACCACCTGTTCTTCCAACAATT 59.616 43.478 0.00 0.00 0.00 2.32
6323 7917 2.011222 GGGGTCGACAATGCGAAATAA 58.989 47.619 18.91 0.00 42.55 1.40
6328 7922 1.252215 TACAGGGGTCGACAATGCGA 61.252 55.000 18.91 1.90 38.07 5.10
6551 8146 4.287238 CGCATAAGTTATGGGGTCAAAC 57.713 45.455 25.02 7.23 43.15 2.93
6715 8383 9.559732 TTCAGTTCAGAAGATTCAAGTTATTGA 57.440 29.630 0.00 0.00 43.72 2.57
6745 8413 4.527038 AGTTTTCTCCATTCTCCGTGACTA 59.473 41.667 0.00 0.00 0.00 2.59
6809 8477 8.541234 ACTAAGATCCGTCTCCTCTTTAAAATT 58.459 33.333 0.00 0.00 32.15 1.82
6910 8578 1.705337 CGTGATGACGGTGCATTCCC 61.705 60.000 0.00 0.00 42.18 3.97
7004 8675 7.502226 AGGATTTGTCAGTTCAATCTGTTAACA 59.498 33.333 8.28 8.28 36.85 2.41
7035 8716 7.116233 GTCAAAACAAGCAAACAAAGAGAGAAA 59.884 33.333 0.00 0.00 0.00 2.52
7059 8744 7.803189 CCTGTTTTACACAACATGACAATAGTC 59.197 37.037 0.00 0.00 39.07 2.59
7113 8799 5.703130 GGATGAACTGTCTTCTAGCAACTTT 59.297 40.000 0.00 0.00 0.00 2.66
7323 9020 1.013596 CCGCAAGAACTTCACACACA 58.986 50.000 0.00 0.00 43.02 3.72
7331 9028 8.082852 CACTATATCTATGTACCGCAAGAACTT 58.917 37.037 0.00 0.00 43.02 2.66
7368 9065 5.365605 AGGACTTCCACCGTAATATGATTCA 59.634 40.000 0.00 0.00 38.89 2.57
7481 9178 0.669318 TCGTTCGCTGGTCCATGAAC 60.669 55.000 19.91 19.91 37.84 3.18
7493 9190 4.811761 GCCGCAATGGTCGTTCGC 62.812 66.667 0.00 0.00 41.21 4.70
7522 9219 3.482783 GAGAGCGGCGACAACAGC 61.483 66.667 12.98 0.00 0.00 4.40
7523 9220 0.179137 TATGAGAGCGGCGACAACAG 60.179 55.000 12.98 0.00 0.00 3.16
7524 9221 0.457853 GTATGAGAGCGGCGACAACA 60.458 55.000 12.98 5.33 0.00 3.33
7546 9256 0.539438 TGACAAAATCAGGCCGGCTT 60.539 50.000 28.56 18.19 31.91 4.35
7554 9264 3.495193 CGACTGCCATTGACAAAATCAG 58.505 45.455 10.49 10.49 38.99 2.90
7558 9268 0.958091 CCCGACTGCCATTGACAAAA 59.042 50.000 0.00 0.00 0.00 2.44
7559 9269 0.109532 TCCCGACTGCCATTGACAAA 59.890 50.000 0.00 0.00 0.00 2.83
7569 9279 1.009389 CACGAAGACTTCCCGACTGC 61.009 60.000 9.63 0.00 0.00 4.40
7574 9284 2.372690 CGTGCACGAAGACTTCCCG 61.373 63.158 34.93 1.26 43.02 5.14
7577 9287 1.201825 GCACGTGCACGAAGACTTC 59.798 57.895 42.94 19.21 43.02 3.01
7583 9293 4.649310 TAGGCGCACGTGCACGAA 62.649 61.111 42.94 20.25 43.02 3.85
7584 9294 4.649310 TTAGGCGCACGTGCACGA 62.649 61.111 42.94 23.27 43.02 4.35
7597 9307 4.938226 GGATCGATTAGAAATGCCCTTAGG 59.062 45.833 0.00 0.00 0.00 2.69
7615 9325 1.396996 CGTGCACTTTTTAGGGGATCG 59.603 52.381 16.19 0.00 0.00 3.69
7628 9338 2.738521 CTTAGGCGCACGTGCACT 60.739 61.111 37.03 32.95 42.21 4.40
7629 9339 3.788766 CCTTAGGCGCACGTGCAC 61.789 66.667 37.03 29.08 42.21 4.57
7649 9359 6.511282 CGCTTTTTAGGGGATCGATTAGAAAC 60.511 42.308 0.00 0.00 0.00 2.78
7662 9372 3.118000 ACTCCCTTATCGCTTTTTAGGGG 60.118 47.826 0.00 0.00 44.67 4.79
7693 9403 3.302161 TGCACCGTATGGGACTATAACT 58.698 45.455 5.82 0.00 40.75 2.24
7715 9425 0.034380 CGGATAGGGGATCGGCTAGA 60.034 60.000 0.00 0.00 35.12 2.43
7726 10107 0.969894 CTCCACTAAGCCGGATAGGG 59.030 60.000 5.05 7.93 41.48 3.53
7749 10130 9.628500 GTATATTGGGAGTTGGAGTAGAAAAAT 57.372 33.333 0.00 0.00 0.00 1.82
7755 10136 5.155905 AGGGTATATTGGGAGTTGGAGTAG 58.844 45.833 0.00 0.00 0.00 2.57
7761 10142 5.770162 GGATTTGAGGGTATATTGGGAGTTG 59.230 44.000 0.00 0.00 0.00 3.16
7774 10155 4.710197 AAATTTAGGGGGATTTGAGGGT 57.290 40.909 0.00 0.00 0.00 4.34
7784 10165 3.433173 CGGGAGTGAGTAAATTTAGGGGG 60.433 52.174 0.00 0.00 0.00 5.40
7785 10166 3.805207 CGGGAGTGAGTAAATTTAGGGG 58.195 50.000 0.00 0.00 0.00 4.79
7805 10186 2.509786 TTTTACTAGGCCGCCGCG 60.510 61.111 5.59 5.59 35.02 6.46
7815 10196 6.254522 AGGAAGAGAGGTGCTAGTTTTACTA 58.745 40.000 0.00 0.00 0.00 1.82
7825 10206 1.306568 GGGGAGGAAGAGAGGTGCT 60.307 63.158 0.00 0.00 0.00 4.40
7843 10224 1.134098 GGTGAGATACATGGTGGTGGG 60.134 57.143 0.00 0.00 0.00 4.61
7846 10227 0.178068 GCGGTGAGATACATGGTGGT 59.822 55.000 0.00 0.00 0.00 4.16
7851 10232 1.956170 GGCGGCGGTGAGATACATG 60.956 63.158 9.78 0.00 0.00 3.21
7852 10233 2.088674 GAGGCGGCGGTGAGATACAT 62.089 60.000 9.78 0.00 0.00 2.29
7853 10234 2.758327 AGGCGGCGGTGAGATACA 60.758 61.111 9.78 0.00 0.00 2.29
7854 10235 2.027751 GAGGCGGCGGTGAGATAC 59.972 66.667 9.78 0.00 0.00 2.24
7870 10278 3.673484 GGTCGGACGGTCGTTGGA 61.673 66.667 1.43 0.00 0.00 3.53
7885 10293 0.182775 GGCTATCCATTCCAACCGGT 59.817 55.000 0.00 0.00 0.00 5.28
7890 10298 0.185901 GGCCAGGCTATCCATTCCAA 59.814 55.000 12.43 0.00 33.74 3.53
7923 10331 2.331893 TGAAAAGCCGGCACCGATG 61.332 57.895 31.54 0.00 42.83 3.84
7925 10333 2.975799 GTGAAAAGCCGGCACCGA 60.976 61.111 31.54 4.98 42.83 4.69
7929 10337 2.909965 GGTGGTGAAAAGCCGGCA 60.910 61.111 31.54 3.61 0.00 5.69
7934 10342 1.611491 TGATTTCCGGTGGTGAAAAGC 59.389 47.619 0.00 0.00 35.52 3.51
7939 10347 1.377229 GGGTGATTTCCGGTGGTGA 59.623 57.895 0.00 0.00 0.00 4.02
7944 10352 1.748879 CGCATGGGTGATTTCCGGT 60.749 57.895 0.00 0.00 0.00 5.28
7945 10353 3.110139 CGCATGGGTGATTTCCGG 58.890 61.111 0.00 0.00 0.00 5.14
7948 10356 2.408835 CGGCGCATGGGTGATTTC 59.591 61.111 10.83 0.00 0.00 2.17
7965 10373 3.423154 CTTCTTCGCGTGGGTGGC 61.423 66.667 5.77 0.00 0.00 5.01
7967 10375 0.600255 AACTCTTCTTCGCGTGGGTG 60.600 55.000 5.77 0.00 0.00 4.61
7968 10376 0.106149 AAACTCTTCTTCGCGTGGGT 59.894 50.000 5.77 0.00 0.00 4.51
8003 10412 4.021925 GAGGAGCTTGGGCGTGGT 62.022 66.667 0.00 0.00 44.37 4.16
8004 10413 4.785453 GGAGGAGCTTGGGCGTGG 62.785 72.222 0.00 0.00 44.37 4.94
8009 10418 2.941025 TTGGGGGAGGAGCTTGGG 60.941 66.667 0.00 0.00 0.00 4.12
8010 10419 2.356667 GTTGGGGGAGGAGCTTGG 59.643 66.667 0.00 0.00 0.00 3.61
8012 10421 3.330720 CGGTTGGGGGAGGAGCTT 61.331 66.667 0.00 0.00 0.00 3.74
8015 10424 3.787001 GAGCGGTTGGGGGAGGAG 61.787 72.222 0.00 0.00 0.00 3.69
8019 10428 2.938798 ATTGGAGCGGTTGGGGGA 60.939 61.111 0.00 0.00 0.00 4.81
8020 10429 2.755469 CATTGGAGCGGTTGGGGG 60.755 66.667 0.00 0.00 0.00 5.40
8021 10430 2.755469 CCATTGGAGCGGTTGGGG 60.755 66.667 0.00 0.00 0.00 4.96
8089 10499 2.237751 CGTTTAGCTCCGGCCGATG 61.238 63.158 30.73 19.78 39.73 3.84
8102 10512 2.420628 TCGGTTTTCGAGCTCGTTTA 57.579 45.000 33.33 18.29 43.74 2.01


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

AutoCloner maintained by Alex Coulton.