Multiple sequence alignment - TraesCS2A01G016700

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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 TraesCS2A01G016700 chr2A 100.000 3455 0 0 1 3455 7740619 7744073 0.000000e+00 6381.0
1 TraesCS2A01G016700 chr2A 80.943 1506 254 15 971 2457 8413082 8414573 0.000000e+00 1160.0
2 TraesCS2A01G016700 chr2A 81.756 1025 172 10 1443 2463 8034406 8033393 0.000000e+00 843.0
3 TraesCS2A01G016700 chr2A 88.767 365 31 7 90 451 7732193 7732550 4.090000e-119 438.0
4 TraesCS2A01G016700 chr2A 88.728 346 33 3 2974 3316 8151068 8151410 5.330000e-113 418.0
5 TraesCS2A01G016700 chr2B 93.001 2329 125 19 774 3083 11389329 11391638 0.000000e+00 3363.0
6 TraesCS2A01G016700 chr2B 80.159 1507 265 22 976 2462 11907130 11905638 0.000000e+00 1096.0
7 TraesCS2A01G016700 chr2B 96.646 328 10 1 450 776 793364328 793364001 8.430000e-151 544.0
8 TraesCS2A01G016700 chr2B 95.495 333 14 1 444 776 87756059 87756390 6.570000e-147 531.0
9 TraesCS2A01G016700 chr2B 80.656 579 69 19 2768 3316 11402060 11402625 3.210000e-110 409.0
10 TraesCS2A01G016700 chr2B 84.561 421 50 11 2903 3316 11993852 11994264 1.490000e-108 403.0
11 TraesCS2A01G016700 chr2B 90.950 221 13 2 236 451 11389134 11389352 1.210000e-74 291.0
12 TraesCS2A01G016700 chr2B 80.645 310 41 14 2975 3275 212577587 212577886 4.490000e-54 222.0
13 TraesCS2A01G016700 chr2B 94.059 101 6 0 93 193 11388764 11388864 1.660000e-33 154.0
14 TraesCS2A01G016700 chr2B 82.609 115 14 4 1 114 11387233 11387342 2.840000e-16 97.1
15 TraesCS2A01G016700 chr2B 96.000 50 2 0 3078 3127 11396731 11396780 7.950000e-12 82.4
16 TraesCS2A01G016700 chr2B 91.667 48 2 2 8 53 11388707 11388754 8.000000e-07 65.8
17 TraesCS2A01G016700 chr2D 92.656 1811 112 7 777 2581 8665994 8667789 0.000000e+00 2588.0
18 TraesCS2A01G016700 chr2D 80.293 1502 261 14 976 2457 9008723 9010209 0.000000e+00 1101.0
19 TraesCS2A01G016700 chr2D 77.941 1496 285 23 994 2457 19587009 19588491 0.000000e+00 893.0
20 TraesCS2A01G016700 chr2D 96.707 334 10 1 445 777 308681367 308681700 3.900000e-154 555.0
21 TraesCS2A01G016700 chr2D 96.407 334 11 1 445 777 308677936 308678269 1.810000e-152 549.0
22 TraesCS2A01G016700 chr2D 81.913 575 58 18 2768 3316 8684792 8685346 8.800000e-121 444.0
23 TraesCS2A01G016700 chr2D 87.861 346 35 4 2974 3316 8838995 8838654 1.930000e-107 399.0
24 TraesCS2A01G016700 chr2D 82.803 471 48 19 1 451 8665557 8666014 1.160000e-104 390.0
25 TraesCS2A01G016700 chr2D 83.673 343 40 9 2977 3316 8959045 8958716 3.350000e-80 309.0
26 TraesCS2A01G016700 chr2D 82.173 359 55 7 96 451 8664331 8664683 2.020000e-77 300.0
27 TraesCS2A01G016700 chr2D 81.757 148 23 2 3169 3316 8837412 8837269 1.680000e-23 121.0
28 TraesCS2A01G016700 chr2D 81.203 133 25 0 3184 3316 8957460 8957328 1.310000e-19 108.0
29 TraesCS2A01G016700 chr3D 81.283 1325 220 10 1151 2457 564053738 564055052 0.000000e+00 1048.0
30 TraesCS2A01G016700 chr3D 83.610 421 56 10 2903 3316 564001482 564001068 1.950000e-102 383.0
31 TraesCS2A01G016700 chr3D 81.203 133 25 0 3184 3316 563999833 563999701 1.310000e-19 108.0
32 TraesCS2A01G016700 chrUn 81.791 1016 175 5 1443 2457 335085452 335086458 0.000000e+00 843.0
33 TraesCS2A01G016700 chrUn 81.791 1016 175 5 1443 2457 416897231 416896225 0.000000e+00 843.0
34 TraesCS2A01G016700 chr5A 96.657 329 11 0 448 776 661244060 661244388 6.520000e-152 547.0
35 TraesCS2A01G016700 chr6D 96.037 328 12 1 450 776 338921034 338920707 1.830000e-147 532.0
36 TraesCS2A01G016700 chr7B 95.719 327 14 0 450 776 73479798 73479472 8.490000e-146 527.0
37 TraesCS2A01G016700 chr4B 95.732 328 13 1 450 776 166832906 166833233 8.490000e-146 527.0
38 TraesCS2A01G016700 chr1B 95.719 327 14 0 450 776 220750281 220750607 8.490000e-146 527.0


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 TraesCS2A01G016700 chr2A 7740619 7744073 3454 False 6381.000000 6381 100.000000 1 3455 1 chr2A.!!$F2 3454
1 TraesCS2A01G016700 chr2A 8413082 8414573 1491 False 1160.000000 1160 80.943000 971 2457 1 chr2A.!!$F4 1486
2 TraesCS2A01G016700 chr2A 8033393 8034406 1013 True 843.000000 843 81.756000 1443 2463 1 chr2A.!!$R1 1020
3 TraesCS2A01G016700 chr2B 11905638 11907130 1492 True 1096.000000 1096 80.159000 976 2462 1 chr2B.!!$R1 1486
4 TraesCS2A01G016700 chr2B 11387233 11391638 4405 False 794.180000 3363 90.457200 1 3083 5 chr2B.!!$F6 3082
5 TraesCS2A01G016700 chr2B 11402060 11402625 565 False 409.000000 409 80.656000 2768 3316 1 chr2B.!!$F2 548
6 TraesCS2A01G016700 chr2D 9008723 9010209 1486 False 1101.000000 1101 80.293000 976 2457 1 chr2D.!!$F2 1481
7 TraesCS2A01G016700 chr2D 8664331 8667789 3458 False 1092.666667 2588 85.877333 1 2581 3 chr2D.!!$F4 2580
8 TraesCS2A01G016700 chr2D 19587009 19588491 1482 False 893.000000 893 77.941000 994 2457 1 chr2D.!!$F3 1463
9 TraesCS2A01G016700 chr2D 308677936 308681700 3764 False 552.000000 555 96.557000 445 777 2 chr2D.!!$F5 332
10 TraesCS2A01G016700 chr2D 8684792 8685346 554 False 444.000000 444 81.913000 2768 3316 1 chr2D.!!$F1 548
11 TraesCS2A01G016700 chr2D 8837269 8838995 1726 True 260.000000 399 84.809000 2974 3316 2 chr2D.!!$R1 342
12 TraesCS2A01G016700 chr2D 8957328 8959045 1717 True 208.500000 309 82.438000 2977 3316 2 chr2D.!!$R2 339
13 TraesCS2A01G016700 chr3D 564053738 564055052 1314 False 1048.000000 1048 81.283000 1151 2457 1 chr3D.!!$F1 1306
14 TraesCS2A01G016700 chr3D 563999701 564001482 1781 True 245.500000 383 82.406500 2903 3316 2 chr3D.!!$R1 413
15 TraesCS2A01G016700 chrUn 335085452 335086458 1006 False 843.000000 843 81.791000 1443 2457 1 chrUn.!!$F1 1014
16 TraesCS2A01G016700 chrUn 416896225 416897231 1006 True 843.000000 843 81.791000 1443 2457 1 chrUn.!!$R1 1014

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
779 3768 0.02877 CCGTTCTTTGCGCAAGTTCA 59.971 50.0 23.68 7.56 41.68 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2722 5759 0.622665 CTTCCTCCCTGGCAAGATGT 59.377 55.0 0.0 0.0 35.26 3.06 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
33 34 5.712152 AAAACAGGCCTGAAACATTCTAG 57.288 39.130 39.19 8.37 0.00 2.43
38 39 4.156739 CAGGCCTGAAACATTCTAGAAACC 59.843 45.833 29.88 0.84 0.00 3.27
42 43 5.106515 GCCTGAAACATTCTAGAAACCTCAC 60.107 44.000 9.71 1.22 0.00 3.51
47 48 8.188139 TGAAACATTCTAGAAACCTCACAAAAC 58.812 33.333 9.71 0.00 0.00 2.43
78 79 6.374333 GGAAGAATTGCGCCAAATAGGATATA 59.626 38.462 4.18 0.00 41.22 0.86
79 80 7.067494 GGAAGAATTGCGCCAAATAGGATATAT 59.933 37.037 4.18 0.00 41.22 0.86
161 2083 1.878656 CGGGGACTGACTGACTGACC 61.879 65.000 0.00 0.00 36.31 4.02
168 2090 3.628280 GACTGACTGACCGACCGGC 62.628 68.421 8.55 2.35 39.32 6.13
178 2100 2.427245 CCGACCGGCCTCTGAAGAT 61.427 63.158 0.00 0.00 0.00 2.40
181 2103 1.404843 GACCGGCCTCTGAAGATACT 58.595 55.000 0.00 0.00 0.00 2.12
198 2120 4.346418 AGATACTAAAGGAGTCAGGCATGG 59.654 45.833 0.00 0.00 39.81 3.66
203 2125 1.142748 GGAGTCAGGCATGGAGTCG 59.857 63.158 0.00 0.00 35.92 4.18
222 2144 1.640428 GCGGTTCTCATCATCGTTCA 58.360 50.000 0.00 0.00 0.00 3.18
224 2146 1.927174 CGGTTCTCATCATCGTTCACC 59.073 52.381 0.00 0.00 0.00 4.02
225 2147 2.673893 CGGTTCTCATCATCGTTCACCA 60.674 50.000 0.00 0.00 0.00 4.17
226 2148 3.535561 GGTTCTCATCATCGTTCACCAT 58.464 45.455 0.00 0.00 0.00 3.55
228 2150 2.554142 TCTCATCATCGTTCACCATGC 58.446 47.619 0.00 0.00 0.00 4.06
238 2385 0.675208 TTCACCATGCCGCGTAACAT 60.675 50.000 4.92 2.68 0.00 2.71
239 2386 1.087202 TCACCATGCCGCGTAACATC 61.087 55.000 4.92 0.00 0.00 3.06
242 2389 1.498865 CCATGCCGCGTAACATCTCC 61.499 60.000 4.92 0.00 0.00 3.71
244 2391 1.966901 ATGCCGCGTAACATCTCCCA 61.967 55.000 4.92 0.00 0.00 4.37
262 2409 3.261897 TCCCACAAAAGTTTCTTTGCCAA 59.738 39.130 0.00 0.00 39.46 4.52
325 2477 8.719645 TCTAGAAAAATCCCAAGAAATTCCAA 57.280 30.769 0.00 0.00 0.00 3.53
369 2521 9.793252 GTAGAGCACACATAATTGAATCAAAAT 57.207 29.630 0.00 0.00 0.00 1.82
387 2539 7.504924 TCAAAATATCCAACAAAAGACGAGT 57.495 32.000 0.00 0.00 0.00 4.18
664 3653 5.107104 CGCAAGCTAAGTGAAAACAGTCATA 60.107 40.000 0.00 0.00 0.00 2.15
704 3693 1.374343 CCGACGATCGTCCTCCTTCA 61.374 60.000 35.48 0.00 41.76 3.02
721 3710 4.346127 TCCTTCATTCATGGTCTCGATCAT 59.654 41.667 0.00 0.00 30.99 2.45
764 3753 6.870971 ATAATTATGCGATTACAACCCGTT 57.129 33.333 0.00 0.00 0.00 4.44
777 3766 1.358759 CCCGTTCTTTGCGCAAGTT 59.641 52.632 23.68 0.00 41.68 2.66
778 3767 0.660300 CCCGTTCTTTGCGCAAGTTC 60.660 55.000 23.68 13.56 41.68 3.01
779 3768 0.028770 CCGTTCTTTGCGCAAGTTCA 59.971 50.000 23.68 7.56 41.68 3.18
780 3769 1.334960 CCGTTCTTTGCGCAAGTTCAT 60.335 47.619 23.68 0.00 41.68 2.57
781 3770 1.710249 CGTTCTTTGCGCAAGTTCATG 59.290 47.619 23.68 10.26 41.68 3.07
782 3771 2.731217 GTTCTTTGCGCAAGTTCATGT 58.269 42.857 23.68 0.00 41.68 3.21
783 3772 2.404265 TCTTTGCGCAAGTTCATGTG 57.596 45.000 23.68 7.39 41.68 3.21
784 3773 1.001487 TCTTTGCGCAAGTTCATGTGG 60.001 47.619 23.68 6.41 41.68 4.17
785 3774 0.597118 TTTGCGCAAGTTCATGTGGC 60.597 50.000 23.68 0.00 41.68 5.01
786 3775 1.454572 TTGCGCAAGTTCATGTGGCT 61.455 50.000 21.02 0.00 41.68 4.75
787 3776 1.286880 GCGCAAGTTCATGTGGCTT 59.713 52.632 0.30 0.00 41.68 4.35
788 3777 1.005294 GCGCAAGTTCATGTGGCTTG 61.005 55.000 0.30 16.43 41.61 4.01
789 3778 0.387622 CGCAAGTTCATGTGGCTTGG 60.388 55.000 19.72 11.33 39.75 3.61
790 3779 0.961019 GCAAGTTCATGTGGCTTGGA 59.039 50.000 19.72 0.00 39.75 3.53
791 3780 1.336240 GCAAGTTCATGTGGCTTGGAC 60.336 52.381 19.72 7.87 39.75 4.02
792 3781 1.955778 CAAGTTCATGTGGCTTGGACA 59.044 47.619 14.33 0.00 36.79 4.02
793 3782 2.361757 CAAGTTCATGTGGCTTGGACAA 59.638 45.455 14.33 0.00 36.79 3.18
794 3783 2.233271 AGTTCATGTGGCTTGGACAAG 58.767 47.619 7.67 7.67 41.24 3.16
795 3784 1.956477 GTTCATGTGGCTTGGACAAGT 59.044 47.619 13.08 0.00 40.45 3.16
796 3785 2.362077 GTTCATGTGGCTTGGACAAGTT 59.638 45.455 13.08 0.00 40.45 2.66
840 3829 7.269724 CGTTTGGACGTTTAGAAAAATATCACC 59.730 37.037 0.00 0.00 44.08 4.02
846 3837 5.270853 GTTTAGAAAAATATCACCGCGCAT 58.729 37.500 8.75 0.00 0.00 4.73
944 3937 2.363406 GCAAGAGGCCAGCCCATT 60.363 61.111 5.01 0.00 36.58 3.16
945 3938 2.421399 GCAAGAGGCCAGCCCATTC 61.421 63.158 5.01 0.00 36.58 2.67
973 3966 1.122632 TTAGTCCAGTGACCGCCCAA 61.123 55.000 0.00 0.00 42.81 4.12
995 3997 5.184892 ACAGCTTTACCTCATCAATCCTT 57.815 39.130 0.00 0.00 0.00 3.36
998 4000 3.067320 GCTTTACCTCATCAATCCTTGCC 59.933 47.826 0.00 0.00 0.00 4.52
1011 4013 2.676121 TTGCCCATGGAGGTTGCG 60.676 61.111 15.22 0.00 34.66 4.85
1135 4137 2.746359 GGCTGCGGCATCTCCTAT 59.254 61.111 21.31 0.00 40.87 2.57
1146 4148 2.743183 GCATCTCCTATTGCGAGTTGGT 60.743 50.000 0.00 0.00 30.83 3.67
1164 4166 3.610619 TACCGTCGTCGAGGAGGCA 62.611 63.158 19.45 8.72 39.71 4.75
1197 4199 1.868713 TAACCAACTCCGGGATGCTA 58.131 50.000 0.00 0.00 0.00 3.49
1218 4220 1.065564 GCCCAGCTCAAGATGTTCTCT 60.066 52.381 0.00 0.00 34.96 3.10
1491 4511 4.499357 CGTAGGCCTTATGACACTTACCTC 60.499 50.000 12.58 0.00 0.00 3.85
1718 4751 0.109597 GGTGACAGCCTTTTGATGCG 60.110 55.000 0.00 0.00 0.00 4.73
1769 4802 7.341445 TGTTGGTAGTTATTGAGTTTGCTTT 57.659 32.000 0.00 0.00 0.00 3.51
1788 4821 5.945191 TGCTTTTGATGTAGGTGATGATGAA 59.055 36.000 0.00 0.00 0.00 2.57
1836 4869 1.076024 AGAATGGGCAGAGGAAGCAAA 59.924 47.619 0.00 0.00 0.00 3.68
1863 4896 8.777865 TCATCATTGTAAGTAGACTTCAAAGG 57.222 34.615 0.00 0.00 37.40 3.11
1939 4972 6.400091 CGACGAGTTGAGATACCTTTTCAAAG 60.400 42.308 0.00 0.00 33.10 2.77
2104 5140 4.291783 TGTTAAGTTTTGGCGTTGCATAC 58.708 39.130 0.00 0.00 0.00 2.39
2376 5412 6.614657 ACCCCCTCATAAATCATTTCCTAAG 58.385 40.000 0.00 0.00 0.00 2.18
2378 5414 6.717084 CCCCCTCATAAATCATTTCCTAAGTC 59.283 42.308 0.00 0.00 0.00 3.01
2399 5435 3.118408 TCTGTAACAAGTTGTGCTCAGGT 60.118 43.478 22.95 7.21 0.00 4.00
2401 5437 3.376859 TGTAACAAGTTGTGCTCAGGTTG 59.623 43.478 9.79 9.43 0.00 3.77
2417 5453 1.156736 GTTGCACATCAAGGTAGCGT 58.843 50.000 0.00 0.00 34.91 5.07
2419 5455 0.320050 TGCACATCAAGGTAGCGTCA 59.680 50.000 0.00 0.00 0.00 4.35
2436 5472 3.801997 ATGCCAGGGAGGAAGCGG 61.802 66.667 0.00 0.00 41.22 5.52
2464 5500 7.966812 AGGAGTGCCAATCTAATTTTCTTTTT 58.033 30.769 0.00 0.00 36.29 1.94
2466 5502 7.872483 GGAGTGCCAATCTAATTTTCTTTTTGA 59.128 33.333 0.00 0.00 0.00 2.69
2467 5503 9.260002 GAGTGCCAATCTAATTTTCTTTTTGAA 57.740 29.630 0.00 0.00 0.00 2.69
2557 5594 9.282247 CAACTAATGTGTTAGAGATTTCAATGC 57.718 33.333 2.47 0.00 39.77 3.56
2563 5600 9.836864 ATGTGTTAGAGATTTCAATGCTGTATA 57.163 29.630 0.00 0.00 0.00 1.47
2576 5613 7.744733 TCAATGCTGTATATTCTACCATCCAA 58.255 34.615 0.00 0.00 0.00 3.53
2577 5614 7.879677 TCAATGCTGTATATTCTACCATCCAAG 59.120 37.037 0.00 0.00 0.00 3.61
2590 5627 0.262876 ATCCAAGAATTCCCCTGCCC 59.737 55.000 0.65 0.00 0.00 5.36
2592 5629 0.041684 CCAAGAATTCCCCTGCCCTT 59.958 55.000 0.65 0.00 0.00 3.95
2595 5632 1.381735 GAATTCCCCTGCCCTTGGG 60.382 63.158 0.32 0.32 44.19 4.12
2596 5633 3.623934 AATTCCCCTGCCCTTGGGC 62.624 63.158 22.91 22.91 43.26 5.36
2722 5759 1.589630 CACCGAGGGTCGAACATGA 59.410 57.895 1.31 0.00 43.74 3.07
2745 5782 0.405585 CTTGCCAGGGAGGAAGGAAA 59.594 55.000 0.00 0.00 41.22 3.13
2749 5786 1.075536 GCCAGGGAGGAAGGAAAGAAA 59.924 52.381 0.00 0.00 41.22 2.52
2789 5828 1.377856 GGGAGGAAGCACAAGGAGC 60.378 63.158 0.00 0.00 0.00 4.70
2832 5871 2.700897 AGAGCTCGCATAATGTAACCCT 59.299 45.455 8.37 0.00 0.00 4.34
2833 5872 3.060602 GAGCTCGCATAATGTAACCCTC 58.939 50.000 0.00 0.00 0.00 4.30
2882 5922 0.749649 GTGTTTGTGTGGCCATGGAA 59.250 50.000 18.40 0.00 0.00 3.53
2967 6018 8.708378 TGTAGTATCAGATCAAATGAATCCTGT 58.292 33.333 0.00 3.24 0.00 4.00
3022 6085 4.516321 CGCACCATTGAATGAATCCTGATA 59.484 41.667 6.76 0.00 0.00 2.15
3023 6086 5.008911 CGCACCATTGAATGAATCCTGATAA 59.991 40.000 6.76 0.00 0.00 1.75
3026 6089 7.384115 GCACCATTGAATGAATCCTGATAAATG 59.616 37.037 6.76 0.00 0.00 2.32
3165 6238 3.494924 GGCCAAAACAGGAGAAAAGCATT 60.495 43.478 0.00 0.00 0.00 3.56
3169 6243 6.091305 GCCAAAACAGGAGAAAAGCATTATTC 59.909 38.462 0.00 0.00 0.00 1.75
3170 6244 7.153985 CCAAAACAGGAGAAAAGCATTATTCA 58.846 34.615 0.00 0.00 0.00 2.57
3181 6255 1.013596 CATTATTCACTTCGCCGCCA 58.986 50.000 0.00 0.00 0.00 5.69
3182 6256 1.003545 CATTATTCACTTCGCCGCCAG 60.004 52.381 0.00 0.00 0.00 4.85
3190 6264 3.899981 TTCGCCGCCAGCACTCAAT 62.900 57.895 0.00 0.00 44.04 2.57
3221 6305 1.230324 GTTCAGGAGTGACCAAGTGC 58.770 55.000 0.00 0.00 42.04 4.40
3228 6313 2.440409 GAGTGACCAAGTGCATCCAAT 58.560 47.619 0.00 0.00 0.00 3.16
3277 7754 9.965902 ATCATTTCCTTGTTGTCTCTAGTTTAT 57.034 29.630 0.00 0.00 0.00 1.40
3280 7757 7.435068 TTCCTTGTTGTCTCTAGTTTATTGC 57.565 36.000 0.00 0.00 0.00 3.56
3288 7765 6.113411 TGTCTCTAGTTTATTGCTTAAGCCC 58.887 40.000 24.30 5.74 41.18 5.19
3309 7786 4.879545 CCCAGTTTAAGCCGCTAATCTTAA 59.120 41.667 0.00 0.00 34.17 1.85
3316 7793 3.532542 AGCCGCTAATCTTAACTGAACC 58.467 45.455 0.00 0.00 0.00 3.62
3317 7794 3.055385 AGCCGCTAATCTTAACTGAACCA 60.055 43.478 0.00 0.00 0.00 3.67
3318 7795 3.309954 GCCGCTAATCTTAACTGAACCAG 59.690 47.826 0.00 0.00 37.52 4.00
3319 7796 3.309954 CCGCTAATCTTAACTGAACCAGC 59.690 47.826 0.00 0.00 34.37 4.85
3320 7797 4.184629 CGCTAATCTTAACTGAACCAGCT 58.815 43.478 0.00 0.00 34.37 4.24
3321 7798 5.348986 CGCTAATCTTAACTGAACCAGCTA 58.651 41.667 0.00 0.00 34.37 3.32
3322 7799 5.810587 CGCTAATCTTAACTGAACCAGCTAA 59.189 40.000 0.00 0.00 34.37 3.09
3323 7800 6.480320 CGCTAATCTTAACTGAACCAGCTAAT 59.520 38.462 0.00 0.00 34.37 1.73
3324 7801 7.306866 CGCTAATCTTAACTGAACCAGCTAATC 60.307 40.741 0.00 0.00 34.37 1.75
3325 7802 7.713073 GCTAATCTTAACTGAACCAGCTAATCT 59.287 37.037 0.00 0.00 34.37 2.40
3326 7803 9.606631 CTAATCTTAACTGAACCAGCTAATCTT 57.393 33.333 0.00 0.00 34.37 2.40
3327 7804 8.870075 AATCTTAACTGAACCAGCTAATCTTT 57.130 30.769 0.00 0.00 34.37 2.52
3328 7805 7.672983 TCTTAACTGAACCAGCTAATCTTTG 57.327 36.000 0.00 0.00 34.37 2.77
3329 7806 6.655003 TCTTAACTGAACCAGCTAATCTTTGG 59.345 38.462 0.00 0.00 34.37 3.28
3330 7807 3.084786 ACTGAACCAGCTAATCTTTGGC 58.915 45.455 0.00 0.00 35.35 4.52
3331 7808 2.083774 TGAACCAGCTAATCTTTGGCG 58.916 47.619 0.00 0.00 42.55 5.69
3332 7809 1.401905 GAACCAGCTAATCTTTGGCGG 59.598 52.381 0.00 5.45 42.55 6.13
3333 7810 2.408333 CCAGCTAATCTTTGGCGGG 58.592 57.895 0.94 0.94 44.72 6.13
3334 7811 3.476740 CAGCTAATCTTTGGCGGGA 57.523 52.632 0.00 0.00 42.55 5.14
3335 7812 1.750193 CAGCTAATCTTTGGCGGGAA 58.250 50.000 0.00 0.00 42.55 3.97
3336 7813 2.091541 CAGCTAATCTTTGGCGGGAAA 58.908 47.619 0.00 0.00 42.55 3.13
3337 7814 2.689983 CAGCTAATCTTTGGCGGGAAAT 59.310 45.455 0.00 0.00 42.55 2.17
3338 7815 2.952310 AGCTAATCTTTGGCGGGAAATC 59.048 45.455 0.00 0.00 42.55 2.17
3339 7816 2.687935 GCTAATCTTTGGCGGGAAATCA 59.312 45.455 0.00 0.00 0.00 2.57
3340 7817 3.319122 GCTAATCTTTGGCGGGAAATCAT 59.681 43.478 0.00 0.00 0.00 2.45
3341 7818 4.202151 GCTAATCTTTGGCGGGAAATCATT 60.202 41.667 0.00 0.00 0.00 2.57
3342 7819 4.824479 AATCTTTGGCGGGAAATCATTT 57.176 36.364 0.00 0.00 0.00 2.32
3343 7820 4.824479 ATCTTTGGCGGGAAATCATTTT 57.176 36.364 0.00 0.00 0.00 1.82
3344 7821 3.924144 TCTTTGGCGGGAAATCATTTTG 58.076 40.909 0.00 0.00 0.00 2.44
3345 7822 2.758736 TTGGCGGGAAATCATTTTGG 57.241 45.000 0.00 0.00 0.00 3.28
3346 7823 0.901124 TGGCGGGAAATCATTTTGGG 59.099 50.000 0.00 0.00 0.00 4.12
3347 7824 0.461870 GGCGGGAAATCATTTTGGGC 60.462 55.000 0.00 0.00 0.00 5.36
3348 7825 0.461870 GCGGGAAATCATTTTGGGCC 60.462 55.000 0.00 0.00 0.00 5.80
3349 7826 0.901124 CGGGAAATCATTTTGGGCCA 59.099 50.000 0.00 0.00 0.00 5.36
3350 7827 1.405391 CGGGAAATCATTTTGGGCCAC 60.405 52.381 5.23 0.00 0.00 5.01
3351 7828 1.908619 GGGAAATCATTTTGGGCCACT 59.091 47.619 5.23 0.00 0.00 4.00
3352 7829 2.093500 GGGAAATCATTTTGGGCCACTC 60.093 50.000 5.23 0.00 0.00 3.51
3353 7830 2.417243 GGAAATCATTTTGGGCCACTCG 60.417 50.000 5.23 0.00 0.00 4.18
3354 7831 1.185315 AATCATTTTGGGCCACTCGG 58.815 50.000 5.23 0.00 0.00 4.63
3355 7832 0.039618 ATCATTTTGGGCCACTCGGT 59.960 50.000 5.23 0.00 33.28 4.69
3356 7833 0.608035 TCATTTTGGGCCACTCGGTC 60.608 55.000 5.23 0.00 35.48 4.79
3362 7839 3.069778 GGCCACTCGGTCCTCTTT 58.930 61.111 0.00 0.00 33.28 2.52
3363 7840 1.376037 GGCCACTCGGTCCTCTTTG 60.376 63.158 0.00 0.00 33.28 2.77
3364 7841 1.671742 GCCACTCGGTCCTCTTTGA 59.328 57.895 0.00 0.00 33.28 2.69
3365 7842 0.390472 GCCACTCGGTCCTCTTTGAG 60.390 60.000 0.00 0.00 33.28 3.02
3376 7853 3.425162 CCTCTTTGAGGCCTTACTGTT 57.575 47.619 6.77 0.00 43.29 3.16
3377 7854 3.339141 CCTCTTTGAGGCCTTACTGTTC 58.661 50.000 6.77 0.00 43.29 3.18
3378 7855 3.244561 CCTCTTTGAGGCCTTACTGTTCA 60.245 47.826 6.77 0.00 43.29 3.18
3379 7856 4.389374 CTCTTTGAGGCCTTACTGTTCAA 58.611 43.478 6.77 1.15 0.00 2.69
3380 7857 4.985538 TCTTTGAGGCCTTACTGTTCAAT 58.014 39.130 6.77 0.00 0.00 2.57
3381 7858 5.385198 TCTTTGAGGCCTTACTGTTCAATT 58.615 37.500 6.77 0.00 0.00 2.32
3382 7859 5.833131 TCTTTGAGGCCTTACTGTTCAATTT 59.167 36.000 6.77 0.00 0.00 1.82
3383 7860 6.323739 TCTTTGAGGCCTTACTGTTCAATTTT 59.676 34.615 6.77 0.00 0.00 1.82
3384 7861 7.504238 TCTTTGAGGCCTTACTGTTCAATTTTA 59.496 33.333 6.77 0.00 0.00 1.52
3385 7862 6.817765 TGAGGCCTTACTGTTCAATTTTAG 57.182 37.500 6.77 0.00 0.00 1.85
3386 7863 6.539173 TGAGGCCTTACTGTTCAATTTTAGA 58.461 36.000 6.77 0.00 0.00 2.10
3387 7864 6.430000 TGAGGCCTTACTGTTCAATTTTAGAC 59.570 38.462 6.77 0.00 0.00 2.59
3388 7865 6.543735 AGGCCTTACTGTTCAATTTTAGACT 58.456 36.000 0.00 0.00 0.00 3.24
3389 7866 6.431234 AGGCCTTACTGTTCAATTTTAGACTG 59.569 38.462 0.00 0.00 0.00 3.51
3390 7867 6.206829 GGCCTTACTGTTCAATTTTAGACTGT 59.793 38.462 0.00 0.00 0.00 3.55
3391 7868 7.298854 GCCTTACTGTTCAATTTTAGACTGTC 58.701 38.462 0.00 0.00 0.00 3.51
3392 7869 7.173390 GCCTTACTGTTCAATTTTAGACTGTCT 59.827 37.037 15.57 15.57 0.00 3.41
3393 7870 8.713271 CCTTACTGTTCAATTTTAGACTGTCTC 58.287 37.037 14.62 0.00 0.00 3.36
3394 7871 9.261180 CTTACTGTTCAATTTTAGACTGTCTCA 57.739 33.333 14.62 0.00 0.00 3.27
3395 7872 9.778741 TTACTGTTCAATTTTAGACTGTCTCAT 57.221 29.630 14.62 2.54 0.00 2.90
3396 7873 8.092521 ACTGTTCAATTTTAGACTGTCTCATG 57.907 34.615 14.62 7.58 0.00 3.07
3397 7874 7.933577 ACTGTTCAATTTTAGACTGTCTCATGA 59.066 33.333 14.62 9.65 0.00 3.07
3398 7875 8.087982 TGTTCAATTTTAGACTGTCTCATGAC 57.912 34.615 14.62 4.72 43.20 3.06
3399 7876 7.933577 TGTTCAATTTTAGACTGTCTCATGACT 59.066 33.333 14.62 0.00 43.29 3.41
3400 7877 8.439286 GTTCAATTTTAGACTGTCTCATGACTC 58.561 37.037 14.62 5.59 43.29 3.36
3401 7878 6.808704 TCAATTTTAGACTGTCTCATGACTCG 59.191 38.462 14.62 0.00 43.29 4.18
3402 7879 4.703645 TTTAGACTGTCTCATGACTCGG 57.296 45.455 14.62 0.00 43.29 4.63
3403 7880 2.208132 AGACTGTCTCATGACTCGGT 57.792 50.000 4.06 6.57 43.29 4.69
3404 7881 3.351794 AGACTGTCTCATGACTCGGTA 57.648 47.619 4.06 0.00 43.29 4.02
3405 7882 3.687125 AGACTGTCTCATGACTCGGTAA 58.313 45.455 4.06 0.00 43.29 2.85
3406 7883 4.274147 AGACTGTCTCATGACTCGGTAAT 58.726 43.478 4.06 0.00 43.29 1.89
3407 7884 4.707448 AGACTGTCTCATGACTCGGTAATT 59.293 41.667 4.06 0.00 43.29 1.40
3408 7885 4.748892 ACTGTCTCATGACTCGGTAATTG 58.251 43.478 0.00 0.00 43.29 2.32
3409 7886 4.220821 ACTGTCTCATGACTCGGTAATTGT 59.779 41.667 0.00 0.00 43.29 2.71
3410 7887 5.147330 TGTCTCATGACTCGGTAATTGTT 57.853 39.130 0.00 0.00 43.29 2.83
3411 7888 5.168569 TGTCTCATGACTCGGTAATTGTTC 58.831 41.667 0.00 0.00 43.29 3.18
3412 7889 5.047306 TGTCTCATGACTCGGTAATTGTTCT 60.047 40.000 0.00 0.00 43.29 3.01
3413 7890 5.289675 GTCTCATGACTCGGTAATTGTTCTG 59.710 44.000 0.00 0.00 39.94 3.02
3414 7891 5.185056 TCTCATGACTCGGTAATTGTTCTGA 59.815 40.000 0.00 0.00 0.00 3.27
3415 7892 5.168569 TCATGACTCGGTAATTGTTCTGAC 58.831 41.667 0.00 0.00 0.00 3.51
3416 7893 4.866508 TGACTCGGTAATTGTTCTGACT 57.133 40.909 0.00 0.00 0.00 3.41
3417 7894 4.556233 TGACTCGGTAATTGTTCTGACTG 58.444 43.478 0.00 0.00 0.00 3.51
3418 7895 4.038763 TGACTCGGTAATTGTTCTGACTGT 59.961 41.667 0.00 0.00 0.00 3.55
3419 7896 5.242171 TGACTCGGTAATTGTTCTGACTGTA 59.758 40.000 0.00 0.00 0.00 2.74
3420 7897 5.467705 ACTCGGTAATTGTTCTGACTGTAC 58.532 41.667 0.00 0.00 0.00 2.90
3421 7898 5.243283 ACTCGGTAATTGTTCTGACTGTACT 59.757 40.000 0.00 0.00 0.00 2.73
3422 7899 5.706916 TCGGTAATTGTTCTGACTGTACTC 58.293 41.667 0.00 0.00 0.00 2.59
3423 7900 5.242171 TCGGTAATTGTTCTGACTGTACTCA 59.758 40.000 0.00 0.00 0.00 3.41
3424 7901 5.573282 CGGTAATTGTTCTGACTGTACTCAG 59.427 44.000 5.90 5.90 46.18 3.35
3436 7913 4.761235 CTGTACTCAGTACACGGAGAAA 57.239 45.455 14.00 1.91 42.99 2.52
3437 7914 5.117355 CTGTACTCAGTACACGGAGAAAA 57.883 43.478 14.00 0.00 42.99 2.29
3438 7915 5.710984 CTGTACTCAGTACACGGAGAAAAT 58.289 41.667 14.00 0.00 42.99 1.82
3439 7916 6.822667 TGTACTCAGTACACGGAGAAAATA 57.177 37.500 14.00 0.00 42.99 1.40
3440 7917 7.400599 TGTACTCAGTACACGGAGAAAATAT 57.599 36.000 14.00 0.00 42.99 1.28
3441 7918 8.510243 TGTACTCAGTACACGGAGAAAATATA 57.490 34.615 14.00 0.00 42.99 0.86
3442 7919 8.959548 TGTACTCAGTACACGGAGAAAATATAA 58.040 33.333 14.00 0.00 42.99 0.98
3443 7920 9.230932 GTACTCAGTACACGGAGAAAATATAAC 57.769 37.037 10.31 0.00 39.97 1.89
3444 7921 6.971184 ACTCAGTACACGGAGAAAATATAACG 59.029 38.462 15.10 0.00 39.97 3.18
3445 7922 7.087409 TCAGTACACGGAGAAAATATAACGA 57.913 36.000 0.00 0.00 0.00 3.85
3446 7923 7.537715 TCAGTACACGGAGAAAATATAACGAA 58.462 34.615 0.00 0.00 0.00 3.85
3447 7924 7.699391 TCAGTACACGGAGAAAATATAACGAAG 59.301 37.037 0.00 0.00 0.00 3.79
3448 7925 7.699391 CAGTACACGGAGAAAATATAACGAAGA 59.301 37.037 0.00 0.00 0.00 2.87
3449 7926 8.246180 AGTACACGGAGAAAATATAACGAAGAA 58.754 33.333 0.00 0.00 0.00 2.52
3450 7927 9.028185 GTACACGGAGAAAATATAACGAAGAAT 57.972 33.333 0.00 0.00 0.00 2.40
3452 7929 9.028185 ACACGGAGAAAATATAACGAAGAATAC 57.972 33.333 0.00 0.00 0.00 1.89
3453 7930 9.245962 CACGGAGAAAATATAACGAAGAATACT 57.754 33.333 0.00 0.00 0.00 2.12
3454 7931 9.813446 ACGGAGAAAATATAACGAAGAATACTT 57.187 29.630 0.00 0.00 39.24 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.156739 GGTTTCTAGAATGTTTCAGGCCTG 59.843 45.833 27.87 27.87 0.00 4.85
23 24 7.123547 TGGTTTTGTGAGGTTTCTAGAATGTTT 59.876 33.333 5.89 0.00 0.00 2.83
27 28 6.601332 TCTGGTTTTGTGAGGTTTCTAGAAT 58.399 36.000 5.89 0.00 0.00 2.40
33 34 3.888930 TCCATCTGGTTTTGTGAGGTTTC 59.111 43.478 0.00 0.00 36.34 2.78
38 39 5.972107 ATTCTTCCATCTGGTTTTGTGAG 57.028 39.130 0.00 0.00 36.34 3.51
42 43 3.922240 CGCAATTCTTCCATCTGGTTTTG 59.078 43.478 0.00 0.00 36.34 2.44
47 48 0.383231 GGCGCAATTCTTCCATCTGG 59.617 55.000 10.83 0.00 0.00 3.86
78 79 4.371624 TTGTTCCTGTGATCAGTGGAAT 57.628 40.909 23.88 0.00 39.82 3.01
79 80 3.855255 TTGTTCCTGTGATCAGTGGAA 57.145 42.857 19.68 19.68 39.82 3.53
89 90 4.339247 AGTTGATCTGGTTTTGTTCCTGTG 59.661 41.667 0.00 0.00 0.00 3.66
161 2083 0.030908 GTATCTTCAGAGGCCGGTCG 59.969 60.000 1.90 0.00 0.00 4.79
168 2090 6.040391 CCTGACTCCTTTAGTATCTTCAGAGG 59.960 46.154 0.00 0.00 39.07 3.69
178 2100 3.706594 CTCCATGCCTGACTCCTTTAGTA 59.293 47.826 0.00 0.00 39.07 1.82
181 2103 2.501723 GACTCCATGCCTGACTCCTTTA 59.498 50.000 0.00 0.00 0.00 1.85
198 2120 1.482278 GATGATGAGAACCGCGACTC 58.518 55.000 8.23 13.96 0.00 3.36
203 2125 1.324736 GTGAACGATGATGAGAACCGC 59.675 52.381 0.00 0.00 0.00 5.68
222 2144 0.810031 GAGATGTTACGCGGCATGGT 60.810 55.000 12.47 1.66 0.00 3.55
224 2146 1.498865 GGGAGATGTTACGCGGCATG 61.499 60.000 12.47 0.00 0.00 4.06
225 2147 1.227556 GGGAGATGTTACGCGGCAT 60.228 57.895 12.47 12.02 0.00 4.40
226 2148 2.185867 GGGAGATGTTACGCGGCA 59.814 61.111 12.47 6.93 0.00 5.69
228 2150 0.390603 TTGTGGGAGATGTTACGCGG 60.391 55.000 12.47 0.00 0.00 6.46
238 2385 3.132111 GGCAAAGAAACTTTTGTGGGAGA 59.868 43.478 0.00 0.00 39.62 3.71
239 2386 3.118811 TGGCAAAGAAACTTTTGTGGGAG 60.119 43.478 0.00 0.00 39.62 4.30
242 2389 5.619625 TTTTGGCAAAGAAACTTTTGTGG 57.380 34.783 13.04 0.00 39.62 4.17
262 2409 1.760480 AGGGCGCCACTTGGTTTTT 60.760 52.632 30.85 0.00 37.57 1.94
325 2477 5.163457 GCTCTACTCTAGCAAATTCTGACCT 60.163 44.000 0.00 0.00 39.83 3.85
369 2521 4.202274 TGTCCACTCGTCTTTTGTTGGATA 60.202 41.667 0.00 0.00 0.00 2.59
528 3517 1.079127 ATTGGCTCGAGGAACCACG 60.079 57.895 15.58 4.45 31.83 4.94
634 3623 6.039616 TGTTTTCACTTAGCTTGCGATTTTT 58.960 32.000 0.00 0.00 0.00 1.94
704 3693 3.899980 TGGAGATGATCGAGACCATGAAT 59.100 43.478 0.00 0.00 0.00 2.57
764 3753 1.001487 CCACATGAACTTGCGCAAAGA 60.001 47.619 25.01 8.34 39.38 2.52
777 3766 1.955778 CAACTTGTCCAAGCCACATGA 59.044 47.619 0.00 0.00 41.99 3.07
778 3767 1.000060 CCAACTTGTCCAAGCCACATG 60.000 52.381 6.94 0.00 41.99 3.21
779 3768 1.331214 CCAACTTGTCCAAGCCACAT 58.669 50.000 6.94 0.00 41.99 3.21
780 3769 1.391157 GCCAACTTGTCCAAGCCACA 61.391 55.000 6.94 0.00 41.99 4.17
781 3770 1.109323 AGCCAACTTGTCCAAGCCAC 61.109 55.000 6.94 0.00 41.99 5.01
782 3771 0.396974 AAGCCAACTTGTCCAAGCCA 60.397 50.000 6.94 0.00 41.99 4.75
783 3772 0.315251 GAAGCCAACTTGTCCAAGCC 59.685 55.000 6.94 0.00 41.99 4.35
784 3773 1.268079 GAGAAGCCAACTTGTCCAAGC 59.732 52.381 6.94 0.00 39.66 4.01
790 3779 2.736670 ACAAGGAGAAGCCAACTTGT 57.263 45.000 0.00 0.00 46.11 3.16
791 3780 2.291741 GTGACAAGGAGAAGCCAACTTG 59.708 50.000 0.00 0.00 44.32 3.16
792 3781 2.576615 GTGACAAGGAGAAGCCAACTT 58.423 47.619 0.00 0.00 40.02 2.66
793 3782 1.541233 CGTGACAAGGAGAAGCCAACT 60.541 52.381 0.00 0.00 40.02 3.16
794 3783 0.868406 CGTGACAAGGAGAAGCCAAC 59.132 55.000 0.00 0.00 40.02 3.77
795 3784 0.884704 GCGTGACAAGGAGAAGCCAA 60.885 55.000 0.00 0.00 40.02 4.52
796 3785 1.301716 GCGTGACAAGGAGAAGCCA 60.302 57.895 0.00 0.00 40.02 4.75
840 3829 0.370273 GACTTGAGTGGTTATGCGCG 59.630 55.000 0.00 0.00 0.00 6.86
846 3837 2.684943 TGACTGGGACTTGAGTGGTTA 58.315 47.619 0.00 0.00 0.00 2.85
941 3934 9.099454 GGTCACTGGACTAATTTAACTAGAATG 57.901 37.037 0.00 0.00 43.77 2.67
942 3935 7.980099 CGGTCACTGGACTAATTTAACTAGAAT 59.020 37.037 0.00 0.00 43.77 2.40
943 3936 7.318141 CGGTCACTGGACTAATTTAACTAGAA 58.682 38.462 0.00 0.00 43.77 2.10
944 3937 6.626623 GCGGTCACTGGACTAATTTAACTAGA 60.627 42.308 0.00 0.00 43.77 2.43
945 3938 5.519206 GCGGTCACTGGACTAATTTAACTAG 59.481 44.000 0.00 0.00 43.77 2.57
973 3966 4.851639 AGGATTGATGAGGTAAAGCTGT 57.148 40.909 0.00 0.00 0.00 4.40
995 3997 2.982643 ATCGCAACCTCCATGGGCA 61.983 57.895 13.02 0.00 41.11 5.36
998 4000 0.107508 AGACATCGCAACCTCCATGG 60.108 55.000 4.97 4.97 42.93 3.66
1120 4122 1.563435 CGCAATAGGAGATGCCGCAG 61.563 60.000 0.00 0.00 43.43 5.18
1135 4137 1.372004 CGACGGTACCAACTCGCAA 60.372 57.895 13.54 0.00 0.00 4.85
1146 4148 2.821366 GCCTCCTCGACGACGGTA 60.821 66.667 7.55 0.00 40.21 4.02
1164 4166 1.818555 GGTTATGTACCGCCCGTCT 59.181 57.895 0.00 0.00 37.12 4.18
1197 4199 0.990374 AGAACATCTTGAGCTGGGCT 59.010 50.000 0.00 0.00 43.88 5.19
1284 4286 2.277120 CTAACCTCGTCGACGCCG 60.277 66.667 32.19 24.57 39.60 6.46
1288 4290 0.388134 TTGCTGCTAACCTCGTCGAC 60.388 55.000 5.18 5.18 0.00 4.20
1491 4511 4.055360 TGAACATGAAGTTGTCGGTGTAG 58.945 43.478 0.00 0.00 41.51 2.74
1769 4802 6.251255 TCCATTCATCATCACCTACATCAA 57.749 37.500 0.00 0.00 0.00 2.57
1788 4821 4.901250 ACCAATGAGTGAAACCTTTTCCAT 59.099 37.500 0.00 0.00 37.80 3.41
1966 4999 5.801531 TGTACTAGTTGTGGATGTTCTGT 57.198 39.130 0.00 0.00 0.00 3.41
2069 5105 7.657354 GCCAAAACTTAACATCAAGATTCCTTT 59.343 33.333 0.00 0.00 0.00 3.11
2104 5140 2.422519 CCATTCTCATCCCCTTGTCCAG 60.423 54.545 0.00 0.00 0.00 3.86
2334 5370 3.307480 GGGGTATCCTTGATTCCCATACG 60.307 52.174 17.35 0.00 47.00 3.06
2376 5412 3.248602 CCTGAGCACAACTTGTTACAGAC 59.751 47.826 15.53 1.75 29.82 3.51
2378 5414 3.206150 ACCTGAGCACAACTTGTTACAG 58.794 45.455 10.42 10.42 0.00 2.74
2382 5418 1.134946 GCAACCTGAGCACAACTTGTT 59.865 47.619 0.00 0.00 0.00 2.83
2399 5435 1.270571 TGACGCTACCTTGATGTGCAA 60.271 47.619 0.00 0.00 34.73 4.08
2401 5437 1.328680 CATGACGCTACCTTGATGTGC 59.671 52.381 0.00 0.00 0.00 4.57
2417 5453 3.001514 GCTTCCTCCCTGGCATGA 58.998 61.111 0.00 0.00 35.26 3.07
2419 5455 3.801997 CCGCTTCCTCCCTGGCAT 61.802 66.667 0.00 0.00 35.26 4.40
2464 5500 8.519526 ACAAGAGTTTCATTACACAAGTTTTCA 58.480 29.630 0.00 0.00 0.00 2.69
2466 5502 9.783256 GTACAAGAGTTTCATTACACAAGTTTT 57.217 29.630 0.00 0.00 0.00 2.43
2467 5503 9.174166 AGTACAAGAGTTTCATTACACAAGTTT 57.826 29.630 0.00 0.00 0.00 2.66
2557 5594 9.442047 GGAATTCTTGGATGGTAGAATATACAG 57.558 37.037 5.23 0.00 39.53 2.74
2563 5600 4.733988 AGGGGAATTCTTGGATGGTAGAAT 59.266 41.667 5.23 0.00 41.58 2.40
2576 5613 1.699752 CCAAGGGCAGGGGAATTCT 59.300 57.895 5.23 0.00 0.00 2.40
2577 5614 4.362479 CCAAGGGCAGGGGAATTC 57.638 61.111 0.00 0.00 0.00 2.17
2590 5627 3.415087 CCTCCTCCCCTGCCCAAG 61.415 72.222 0.00 0.00 0.00 3.61
2619 5656 3.105928 ATGATGGGTCAGGGGCCC 61.106 66.667 17.12 17.12 46.26 5.80
2634 5671 5.582269 GGTATATACACTATGCCTGCACATG 59.418 44.000 14.70 0.00 0.00 3.21
2635 5672 5.248248 TGGTATATACACTATGCCTGCACAT 59.752 40.000 14.70 0.00 31.99 3.21
2722 5759 0.622665 CTTCCTCCCTGGCAAGATGT 59.377 55.000 0.00 0.00 35.26 3.06
2832 5871 8.492748 GTTTTTCATGTATCAGAAGTACAACGA 58.507 33.333 0.00 0.00 35.84 3.85
2833 5872 8.279800 TGTTTTTCATGTATCAGAAGTACAACG 58.720 33.333 0.00 0.00 35.84 4.10
2945 5996 8.442632 TGAACAGGATTCATTTGATCTGATAC 57.557 34.615 10.80 0.00 0.00 2.24
3023 6086 9.628500 AGTTAAGTTTTCTCACCTTTCTACATT 57.372 29.630 0.00 0.00 0.00 2.71
3026 6089 8.658499 TCAGTTAAGTTTTCTCACCTTTCTAC 57.342 34.615 0.00 0.00 0.00 2.59
3076 6140 8.713271 CAGAGTCCTTAAAATAGACAACACTTC 58.287 37.037 0.00 0.00 32.82 3.01
3137 6201 2.745968 TCTCCTGTTTTGGCCAGTTTT 58.254 42.857 5.11 0.00 0.00 2.43
3140 6204 2.452600 TTTCTCCTGTTTTGGCCAGT 57.547 45.000 5.11 0.00 0.00 4.00
3165 6238 1.813753 GCTGGCGGCGAAGTGAATA 60.814 57.895 12.98 0.00 0.00 1.75
3181 6255 1.603802 CGTTGGTGAACATTGAGTGCT 59.396 47.619 0.00 0.00 31.78 4.40
3182 6256 1.334960 CCGTTGGTGAACATTGAGTGC 60.335 52.381 0.00 0.00 31.78 4.40
3190 6264 0.542333 TCCTGAACCGTTGGTGAACA 59.458 50.000 0.00 0.00 35.34 3.18
3221 6305 5.067954 TGAGTAGAATCATGCCATTGGATG 58.932 41.667 6.95 7.72 0.00 3.51
3228 6313 8.158789 TGATAAATGATGAGTAGAATCATGCCA 58.841 33.333 0.00 0.00 42.58 4.92
3280 7757 1.132453 GCGGCTTAAACTGGGCTTAAG 59.868 52.381 0.00 0.00 38.73 1.85
3288 7765 6.312918 TCAGTTAAGATTAGCGGCTTAAACTG 59.687 38.462 18.25 18.25 38.06 3.16
3298 7775 4.184629 AGCTGGTTCAGTTAAGATTAGCG 58.815 43.478 0.00 0.00 33.43 4.26
3309 7786 3.084786 GCCAAAGATTAGCTGGTTCAGT 58.915 45.455 0.00 0.00 33.43 3.41
3316 7793 1.750193 TTCCCGCCAAAGATTAGCTG 58.250 50.000 0.00 0.00 0.00 4.24
3317 7794 2.507407 TTTCCCGCCAAAGATTAGCT 57.493 45.000 0.00 0.00 0.00 3.32
3318 7795 2.687935 TGATTTCCCGCCAAAGATTAGC 59.312 45.455 0.00 0.00 0.00 3.09
3319 7796 5.520376 AATGATTTCCCGCCAAAGATTAG 57.480 39.130 0.00 0.00 0.00 1.73
3320 7797 5.930837 AAATGATTTCCCGCCAAAGATTA 57.069 34.783 0.00 0.00 0.00 1.75
3321 7798 4.824479 AAATGATTTCCCGCCAAAGATT 57.176 36.364 0.00 0.00 0.00 2.40
3322 7799 4.506758 CAAAATGATTTCCCGCCAAAGAT 58.493 39.130 0.00 0.00 0.00 2.40
3323 7800 3.306641 CCAAAATGATTTCCCGCCAAAGA 60.307 43.478 0.00 0.00 0.00 2.52
3324 7801 3.002102 CCAAAATGATTTCCCGCCAAAG 58.998 45.455 0.00 0.00 0.00 2.77
3325 7802 2.289945 CCCAAAATGATTTCCCGCCAAA 60.290 45.455 0.00 0.00 0.00 3.28
3326 7803 1.277557 CCCAAAATGATTTCCCGCCAA 59.722 47.619 0.00 0.00 0.00 4.52
3327 7804 0.901124 CCCAAAATGATTTCCCGCCA 59.099 50.000 0.00 0.00 0.00 5.69
3328 7805 0.461870 GCCCAAAATGATTTCCCGCC 60.462 55.000 0.00 0.00 0.00 6.13
3329 7806 0.461870 GGCCCAAAATGATTTCCCGC 60.462 55.000 0.00 0.00 0.00 6.13
3330 7807 0.901124 TGGCCCAAAATGATTTCCCG 59.099 50.000 0.00 0.00 0.00 5.14
3331 7808 1.908619 AGTGGCCCAAAATGATTTCCC 59.091 47.619 0.00 0.00 0.00 3.97
3332 7809 2.417243 CGAGTGGCCCAAAATGATTTCC 60.417 50.000 0.00 0.00 0.00 3.13
3333 7810 2.417243 CCGAGTGGCCCAAAATGATTTC 60.417 50.000 0.00 0.00 0.00 2.17
3334 7811 1.550072 CCGAGTGGCCCAAAATGATTT 59.450 47.619 0.00 0.00 0.00 2.17
3335 7812 1.185315 CCGAGTGGCCCAAAATGATT 58.815 50.000 0.00 0.00 0.00 2.57
3336 7813 0.039618 ACCGAGTGGCCCAAAATGAT 59.960 50.000 0.00 0.00 39.70 2.45
3337 7814 0.608035 GACCGAGTGGCCCAAAATGA 60.608 55.000 0.00 0.00 39.70 2.57
3338 7815 1.595093 GGACCGAGTGGCCCAAAATG 61.595 60.000 0.00 0.00 37.81 2.32
3339 7816 1.304134 GGACCGAGTGGCCCAAAAT 60.304 57.895 0.00 0.00 37.81 1.82
3340 7817 2.114411 GGACCGAGTGGCCCAAAA 59.886 61.111 0.00 0.00 37.81 2.44
3341 7818 2.852075 AGGACCGAGTGGCCCAAA 60.852 61.111 0.00 0.00 41.07 3.28
3342 7819 3.319198 GAGGACCGAGTGGCCCAA 61.319 66.667 0.00 0.00 41.07 4.12
3343 7820 3.846405 AAGAGGACCGAGTGGCCCA 62.846 63.158 0.00 0.00 41.07 5.36
3344 7821 2.593956 AAAGAGGACCGAGTGGCCC 61.594 63.158 0.00 0.00 38.27 5.80
3345 7822 1.376037 CAAAGAGGACCGAGTGGCC 60.376 63.158 0.00 0.00 39.70 5.36
3346 7823 0.390472 CTCAAAGAGGACCGAGTGGC 60.390 60.000 0.00 0.00 39.70 5.01
3347 7824 3.822607 CTCAAAGAGGACCGAGTGG 57.177 57.895 0.00 0.00 42.84 4.00
3357 7834 4.008074 TGAACAGTAAGGCCTCAAAGAG 57.992 45.455 5.23 0.00 0.00 2.85
3358 7835 4.431416 TTGAACAGTAAGGCCTCAAAGA 57.569 40.909 5.23 0.00 0.00 2.52
3359 7836 5.712152 AATTGAACAGTAAGGCCTCAAAG 57.288 39.130 5.23 0.00 30.37 2.77
3360 7837 6.478512 AAAATTGAACAGTAAGGCCTCAAA 57.521 33.333 5.23 0.00 30.37 2.69
3361 7838 7.001674 TCTAAAATTGAACAGTAAGGCCTCAA 58.998 34.615 5.23 4.48 0.00 3.02
3362 7839 6.430000 GTCTAAAATTGAACAGTAAGGCCTCA 59.570 38.462 5.23 0.00 0.00 3.86
3363 7840 6.655425 AGTCTAAAATTGAACAGTAAGGCCTC 59.345 38.462 5.23 0.00 0.00 4.70
3364 7841 6.431234 CAGTCTAAAATTGAACAGTAAGGCCT 59.569 38.462 0.00 0.00 0.00 5.19
3365 7842 6.206829 ACAGTCTAAAATTGAACAGTAAGGCC 59.793 38.462 0.00 0.00 0.00 5.19
3366 7843 7.173390 AGACAGTCTAAAATTGAACAGTAAGGC 59.827 37.037 0.00 0.00 0.00 4.35
3367 7844 8.608844 AGACAGTCTAAAATTGAACAGTAAGG 57.391 34.615 0.00 0.00 0.00 2.69
3368 7845 9.261180 TGAGACAGTCTAAAATTGAACAGTAAG 57.739 33.333 2.00 0.00 0.00 2.34
3369 7846 9.778741 ATGAGACAGTCTAAAATTGAACAGTAA 57.221 29.630 2.00 0.00 0.00 2.24
3370 7847 9.208022 CATGAGACAGTCTAAAATTGAACAGTA 57.792 33.333 2.00 0.00 0.00 2.74
3371 7848 7.933577 TCATGAGACAGTCTAAAATTGAACAGT 59.066 33.333 2.00 0.00 0.00 3.55
3372 7849 8.226448 GTCATGAGACAGTCTAAAATTGAACAG 58.774 37.037 2.00 0.00 44.34 3.16
3373 7850 8.087982 GTCATGAGACAGTCTAAAATTGAACA 57.912 34.615 2.00 0.00 44.34 3.18
3389 7866 5.289675 CAGAACAATTACCGAGTCATGAGAC 59.710 44.000 0.00 0.00 45.31 3.36
3390 7867 5.185056 TCAGAACAATTACCGAGTCATGAGA 59.815 40.000 0.00 0.00 0.00 3.27
3391 7868 5.289675 GTCAGAACAATTACCGAGTCATGAG 59.710 44.000 0.00 0.00 0.00 2.90
3392 7869 5.047306 AGTCAGAACAATTACCGAGTCATGA 60.047 40.000 0.00 0.00 0.00 3.07
3393 7870 5.062683 CAGTCAGAACAATTACCGAGTCATG 59.937 44.000 0.00 0.00 0.00 3.07
3394 7871 5.171476 CAGTCAGAACAATTACCGAGTCAT 58.829 41.667 0.00 0.00 0.00 3.06
3395 7872 4.038763 ACAGTCAGAACAATTACCGAGTCA 59.961 41.667 0.00 0.00 0.00 3.41
3396 7873 4.557205 ACAGTCAGAACAATTACCGAGTC 58.443 43.478 0.00 0.00 0.00 3.36
3397 7874 4.602340 ACAGTCAGAACAATTACCGAGT 57.398 40.909 0.00 0.00 0.00 4.18
3398 7875 5.710984 AGTACAGTCAGAACAATTACCGAG 58.289 41.667 0.00 0.00 0.00 4.63
3399 7876 5.242171 TGAGTACAGTCAGAACAATTACCGA 59.758 40.000 0.00 0.00 0.00 4.69
3400 7877 5.466819 TGAGTACAGTCAGAACAATTACCG 58.533 41.667 0.00 0.00 0.00 4.02
3401 7878 6.952935 CTGAGTACAGTCAGAACAATTACC 57.047 41.667 8.14 0.00 46.02 2.85
3416 7893 5.717078 ATTTTCTCCGTGTACTGAGTACA 57.283 39.130 20.65 20.65 45.20 2.90
3417 7894 9.230932 GTTATATTTTCTCCGTGTACTGAGTAC 57.769 37.037 15.57 15.57 39.24 2.73
3418 7895 8.124823 CGTTATATTTTCTCCGTGTACTGAGTA 58.875 37.037 0.00 0.00 0.00 2.59
3419 7896 6.971184 CGTTATATTTTCTCCGTGTACTGAGT 59.029 38.462 0.00 0.00 0.00 3.41
3420 7897 7.191551 TCGTTATATTTTCTCCGTGTACTGAG 58.808 38.462 0.00 0.00 0.00 3.35
3421 7898 7.087409 TCGTTATATTTTCTCCGTGTACTGA 57.913 36.000 0.00 0.00 0.00 3.41
3422 7899 7.699391 TCTTCGTTATATTTTCTCCGTGTACTG 59.301 37.037 0.00 0.00 0.00 2.74
3423 7900 7.765307 TCTTCGTTATATTTTCTCCGTGTACT 58.235 34.615 0.00 0.00 0.00 2.73
3424 7901 7.975866 TCTTCGTTATATTTTCTCCGTGTAC 57.024 36.000 0.00 0.00 0.00 2.90
3426 7903 9.028185 GTATTCTTCGTTATATTTTCTCCGTGT 57.972 33.333 0.00 0.00 0.00 4.49
3427 7904 9.245962 AGTATTCTTCGTTATATTTTCTCCGTG 57.754 33.333 0.00 0.00 0.00 4.94
3428 7905 9.813446 AAGTATTCTTCGTTATATTTTCTCCGT 57.187 29.630 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.