Multiple sequence alignment - TraesCS3B01G514600

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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 TraesCS3B01G514600 chr3B 100.000 4258 0 0 1 4258 757287642 757283385 0.000000e+00 7864.0
1 TraesCS3B01G514600 chr3B 84.928 1453 167 31 665 2090 757457744 757456317 0.000000e+00 1423.0
2 TraesCS3B01G514600 chr3B 95.510 735 30 1 2124 2858 50677542 50676811 0.000000e+00 1171.0
3 TraesCS3B01G514600 chr3B 94.701 736 33 4 2124 2859 49114552 49113823 0.000000e+00 1138.0
4 TraesCS3B01G514600 chr3B 81.233 1103 161 27 999 2081 757279736 757280812 0.000000e+00 848.0
5 TraesCS3B01G514600 chr3B 85.567 97 10 3 1574 1668 22130160 22130066 9.740000e-17 99.0
6 TraesCS3B01G514600 chr3A 93.703 1604 83 8 529 2123 703100029 703098435 0.000000e+00 2386.0
7 TraesCS3B01G514600 chr3A 83.586 1517 159 41 650 2108 703135290 703133806 0.000000e+00 1339.0
8 TraesCS3B01G514600 chr3A 88.462 806 58 11 2853 3636 703098447 703097655 0.000000e+00 941.0
9 TraesCS3B01G514600 chr3A 87.903 620 70 3 999 1615 703006523 703007140 0.000000e+00 725.0
10 TraesCS3B01G514600 chr3A 78.867 724 112 26 1121 1819 702570427 702571134 6.490000e-123 451.0
11 TraesCS3B01G514600 chr3A 94.286 140 8 0 3641 3780 703097231 703097092 9.270000e-52 215.0
12 TraesCS3B01G514600 chr3A 77.119 118 17 7 1135 1247 21323962 21324074 4.600000e-05 60.2
13 TraesCS3B01G514600 chr3D 88.385 1498 110 28 671 2123 570278680 570277202 0.000000e+00 1744.0
14 TraesCS3B01G514600 chr3D 83.156 1128 160 22 999 2120 570270923 570272026 0.000000e+00 1003.0
15 TraesCS3B01G514600 chr3D 87.129 808 64 15 2853 3638 570277214 570276425 0.000000e+00 880.0
16 TraesCS3B01G514600 chr3D 83.804 531 51 14 1 519 31744211 31744718 4.980000e-129 472.0
17 TraesCS3B01G514600 chr3D 78.495 744 126 25 1090 1819 569976371 569977094 1.400000e-124 457.0
18 TraesCS3B01G514600 chr3D 95.122 205 8 2 3641 3845 570276251 570276049 5.310000e-84 322.0
19 TraesCS3B01G514600 chr3D 92.727 165 10 2 3843 4006 570275603 570275440 1.980000e-58 237.0
20 TraesCS3B01G514600 chr3D 86.957 115 15 0 3879 3993 570265597 570265711 3.460000e-26 130.0
21 TraesCS3B01G514600 chr3D 82.178 101 14 3 1571 1669 14999176 14999274 2.730000e-12 84.2
22 TraesCS3B01G514600 chr2B 95.418 742 29 3 2120 2859 727724358 727725096 0.000000e+00 1177.0
23 TraesCS3B01G514600 chr2B 93.750 736 43 1 2124 2859 301386411 301387143 0.000000e+00 1101.0
24 TraesCS3B01G514600 chr7B 95.380 736 29 3 2124 2858 32588049 32587318 0.000000e+00 1166.0
25 TraesCS3B01G514600 chr7B 86.415 530 56 8 1 519 558751541 558752065 2.220000e-157 566.0
26 TraesCS3B01G514600 chr6B 93.369 739 45 4 2124 2861 253225824 253226559 0.000000e+00 1090.0
27 TraesCS3B01G514600 chr6B 91.892 740 50 4 2124 2862 13239966 13239236 0.000000e+00 1026.0
28 TraesCS3B01G514600 chr6B 91.622 740 52 5 2124 2862 13307094 13306364 0.000000e+00 1014.0
29 TraesCS3B01G514600 chr6B 91.351 740 54 5 2124 2862 13262275 13261545 0.000000e+00 1003.0
30 TraesCS3B01G514600 chr4D 88.577 534 44 9 1 522 417804627 417805155 2.160000e-177 632.0
31 TraesCS3B01G514600 chr4D 88.506 522 42 12 12 520 401352175 401351659 2.180000e-172 616.0
32 TraesCS3B01G514600 chr4A 87.170 530 51 12 1 515 692423434 692423961 1.710000e-163 586.0
33 TraesCS3B01G514600 chr4A 86.604 530 54 12 1 515 692451547 692452074 1.720000e-158 569.0
34 TraesCS3B01G514600 chr4A 82.066 513 57 18 1 500 674463803 674464293 5.130000e-109 405.0
35 TraesCS3B01G514600 chrUn 86.713 429 40 12 102 515 442890318 442889892 1.080000e-125 460.0
36 TraesCS3B01G514600 chr2D 88.987 227 25 0 1 227 539014935 539015161 9.010000e-72 281.0
37 TraesCS3B01G514600 chr7D 86.235 247 29 3 1 245 62928345 62928588 3.270000e-66 263.0
38 TraesCS3B01G514600 chr6A 100.000 30 0 0 494 523 457071788 457071817 5.950000e-04 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 TraesCS3B01G514600 chr3B 757283385 757287642 4257 True 7864.000000 7864 100.000000 1 4258 1 chr3B.!!$R4 4257
1 TraesCS3B01G514600 chr3B 757456317 757457744 1427 True 1423.000000 1423 84.928000 665 2090 1 chr3B.!!$R5 1425
2 TraesCS3B01G514600 chr3B 50676811 50677542 731 True 1171.000000 1171 95.510000 2124 2858 1 chr3B.!!$R3 734
3 TraesCS3B01G514600 chr3B 49113823 49114552 729 True 1138.000000 1138 94.701000 2124 2859 1 chr3B.!!$R2 735
4 TraesCS3B01G514600 chr3B 757279736 757280812 1076 False 848.000000 848 81.233000 999 2081 1 chr3B.!!$F1 1082
5 TraesCS3B01G514600 chr3A 703133806 703135290 1484 True 1339.000000 1339 83.586000 650 2108 1 chr3A.!!$R1 1458
6 TraesCS3B01G514600 chr3A 703097092 703100029 2937 True 1180.666667 2386 92.150333 529 3780 3 chr3A.!!$R2 3251
7 TraesCS3B01G514600 chr3A 703006523 703007140 617 False 725.000000 725 87.903000 999 1615 1 chr3A.!!$F3 616
8 TraesCS3B01G514600 chr3A 702570427 702571134 707 False 451.000000 451 78.867000 1121 1819 1 chr3A.!!$F2 698
9 TraesCS3B01G514600 chr3D 570270923 570272026 1103 False 1003.000000 1003 83.156000 999 2120 1 chr3D.!!$F5 1121
10 TraesCS3B01G514600 chr3D 570275440 570278680 3240 True 795.750000 1744 90.840750 671 4006 4 chr3D.!!$R1 3335
11 TraesCS3B01G514600 chr3D 31744211 31744718 507 False 472.000000 472 83.804000 1 519 1 chr3D.!!$F2 518
12 TraesCS3B01G514600 chr3D 569976371 569977094 723 False 457.000000 457 78.495000 1090 1819 1 chr3D.!!$F3 729
13 TraesCS3B01G514600 chr2B 727724358 727725096 738 False 1177.000000 1177 95.418000 2120 2859 1 chr2B.!!$F2 739
14 TraesCS3B01G514600 chr2B 301386411 301387143 732 False 1101.000000 1101 93.750000 2124 2859 1 chr2B.!!$F1 735
15 TraesCS3B01G514600 chr7B 32587318 32588049 731 True 1166.000000 1166 95.380000 2124 2858 1 chr7B.!!$R1 734
16 TraesCS3B01G514600 chr7B 558751541 558752065 524 False 566.000000 566 86.415000 1 519 1 chr7B.!!$F1 518
17 TraesCS3B01G514600 chr6B 253225824 253226559 735 False 1090.000000 1090 93.369000 2124 2861 1 chr6B.!!$F1 737
18 TraesCS3B01G514600 chr6B 13239236 13239966 730 True 1026.000000 1026 91.892000 2124 2862 1 chr6B.!!$R1 738
19 TraesCS3B01G514600 chr6B 13306364 13307094 730 True 1014.000000 1014 91.622000 2124 2862 1 chr6B.!!$R3 738
20 TraesCS3B01G514600 chr6B 13261545 13262275 730 True 1003.000000 1003 91.351000 2124 2862 1 chr6B.!!$R2 738
21 TraesCS3B01G514600 chr4D 417804627 417805155 528 False 632.000000 632 88.577000 1 522 1 chr4D.!!$F1 521
22 TraesCS3B01G514600 chr4D 401351659 401352175 516 True 616.000000 616 88.506000 12 520 1 chr4D.!!$R1 508
23 TraesCS3B01G514600 chr4A 692423434 692423961 527 False 586.000000 586 87.170000 1 515 1 chr4A.!!$F2 514
24 TraesCS3B01G514600 chr4A 692451547 692452074 527 False 569.000000 569 86.604000 1 515 1 chr4A.!!$F3 514

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
975 1059 0.102300 TCATCTCATGTACGCCACCG 59.898 55.0 0.00 0.0 41.14 4.94 F
2885 3053 0.040058 AAGGCATCAACTCCATGGCA 59.960 50.0 6.96 0.0 46.70 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2917 3085 0.103208 CCCTCCTCCATCGACGAAAG 59.897 60.0 0.00 0.0 0.00 2.62 R
4056 5118 0.250901 ACACAACTGGGCCAGATCAC 60.251 55.0 38.99 0.0 35.18 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
124 125 3.985877 CGCAGTGCAATCTGGGAA 58.014 55.556 16.83 0.00 46.57 3.97
154 155 4.976224 TTCTTCTCCGACAACGATGATA 57.024 40.909 0.00 0.00 42.66 2.15
155 156 5.515797 TTCTTCTCCGACAACGATGATAT 57.484 39.130 0.00 0.00 42.66 1.63
259 262 4.013728 TCTAGTTTGTGCTGTTTGGTTGT 58.986 39.130 0.00 0.00 0.00 3.32
291 294 8.717821 GTTATTTGTATCTGACTAGTTTGTGCA 58.282 33.333 0.00 0.00 0.00 4.57
320 326 3.884169 TGAACTTTGCTTGTATCGTTGC 58.116 40.909 0.00 0.00 0.00 4.17
343 351 7.930217 TGCATTATCTATTTGGTTGAACTAGC 58.070 34.615 0.00 0.00 0.00 3.42
350 358 7.446769 TCTATTTGGTTGAACTAGCTTGTGTA 58.553 34.615 0.36 0.00 0.00 2.90
363 371 0.179070 TTGTGTACTGGTTGCTCGCA 60.179 50.000 0.00 0.00 0.00 5.10
435 445 4.154347 GCCGCTGCTAGAGCCAGT 62.154 66.667 0.00 0.00 46.01 4.00
443 453 2.607442 TAGAGCCAGTGCCCTGCA 60.607 61.111 0.00 0.00 37.38 4.41
520 536 5.196809 CGTCTGTTGAAGATGCTCTAAAC 57.803 43.478 0.00 0.00 37.23 2.01
522 538 4.997395 GTCTGTTGAAGATGCTCTAAACCA 59.003 41.667 0.00 0.00 37.23 3.67
523 539 5.645497 GTCTGTTGAAGATGCTCTAAACCAT 59.355 40.000 0.00 0.00 37.23 3.55
524 540 6.150140 GTCTGTTGAAGATGCTCTAAACCATT 59.850 38.462 0.00 0.00 37.23 3.16
525 541 6.372659 TCTGTTGAAGATGCTCTAAACCATTC 59.627 38.462 0.00 0.00 0.00 2.67
526 542 5.415701 TGTTGAAGATGCTCTAAACCATTCC 59.584 40.000 0.00 0.00 0.00 3.01
527 543 5.178096 TGAAGATGCTCTAAACCATTCCA 57.822 39.130 0.00 0.00 0.00 3.53
711 729 2.654987 CGAGAGCTTCTTTTTGTTGCC 58.345 47.619 0.00 0.00 0.00 4.52
712 730 2.033299 CGAGAGCTTCTTTTTGTTGCCA 59.967 45.455 0.00 0.00 0.00 4.92
809 847 1.211449 CAGCTAGCTAGATCCGCCG 59.789 63.158 25.15 1.66 0.00 6.46
893 951 3.190849 CGTCGTGAGGCTGCCATG 61.191 66.667 22.65 6.67 0.00 3.66
935 1016 2.237392 CCTCTTCCTCTTCCACCGAATT 59.763 50.000 0.00 0.00 0.00 2.17
975 1059 0.102300 TCATCTCATGTACGCCACCG 59.898 55.000 0.00 0.00 41.14 4.94
1051 1155 1.035923 ATCTCGATCGACCACAGCAT 58.964 50.000 15.15 0.00 0.00 3.79
1103 1207 2.234908 CAAAAGACCTCCTCCTCATCGT 59.765 50.000 0.00 0.00 0.00 3.73
1202 1322 2.427245 CGGCCACCTCCCTCTACAG 61.427 68.421 2.24 0.00 0.00 2.74
1215 1335 1.414181 CTCTACAGCATCCCCGTCAAT 59.586 52.381 0.00 0.00 0.00 2.57
1276 1402 3.681835 GGTCCACCTGCGACGACT 61.682 66.667 0.00 0.00 0.00 4.18
1301 1427 2.683859 CCCACGACACGCTCGAGTA 61.684 63.158 15.13 0.00 46.14 2.59
1312 1438 1.465187 CGCTCGAGTACAACGACATCA 60.465 52.381 15.13 0.00 35.88 3.07
1326 1452 3.129502 ATCAACTGCATGCGCGCT 61.130 55.556 33.29 15.19 42.97 5.92
1358 1484 2.045708 CGCCCAACTGCCAGCATAA 61.046 57.895 0.00 0.00 0.00 1.90
1488 1614 3.958147 CTCTGCCAACGCCACCGAT 62.958 63.158 0.00 0.00 38.29 4.18
1762 1906 1.450134 TCCATCACGGACATGCTGC 60.450 57.895 0.00 0.00 39.64 5.25
1796 1940 0.179094 CTACGCAAGCACGGGGAATA 60.179 55.000 0.00 0.00 45.62 1.75
2103 2269 3.984732 GGCTTTGGGCTGGAGGGT 61.985 66.667 0.00 0.00 41.46 4.34
2375 2542 3.198582 GGAGACGGAGAAGACGGG 58.801 66.667 0.00 0.00 35.23 5.28
2520 2688 1.215647 CGTCCTGGTGCTAGTCCAC 59.784 63.158 5.00 0.00 35.00 4.02
2526 2694 3.807368 GTGCTAGTCCACCCCACT 58.193 61.111 0.00 0.00 0.00 4.00
2527 2695 2.986492 GTGCTAGTCCACCCCACTA 58.014 57.895 0.00 0.00 0.00 2.74
2672 2840 2.158900 CGTGATGGGCTTCCTGATTAGT 60.159 50.000 0.00 0.00 0.00 2.24
2682 2850 5.009110 GGCTTCCTGATTAGTTCTAATTGGC 59.991 44.000 6.54 5.66 0.00 4.52
2846 3014 1.819632 CCAAAAGCCCGCTCGCTAT 60.820 57.895 0.00 0.00 38.44 2.97
2867 3035 2.281970 CAGGCTGAGGCAGTGCAA 60.282 61.111 18.61 0.45 40.87 4.08
2885 3053 0.040058 AAGGCATCAACTCCATGGCA 59.960 50.000 6.96 0.00 46.70 4.92
2897 3065 1.820906 CATGGCACTGGTGATCGGG 60.821 63.158 4.79 0.00 0.00 5.14
2927 3095 1.674611 CGTGCTTCGCTTTCGTCGAT 61.675 55.000 0.00 0.00 35.75 3.59
2928 3096 0.246912 GTGCTTCGCTTTCGTCGATG 60.247 55.000 0.00 0.00 35.75 3.84
2929 3097 1.345176 GCTTCGCTTTCGTCGATGG 59.655 57.895 4.48 0.00 35.75 3.51
2946 3116 2.285743 GAGGAGGGGGACAAGGCT 60.286 66.667 0.00 0.00 0.00 4.58
3075 3245 3.330720 AACGGGAGGGGGCTCTTG 61.331 66.667 0.00 0.00 0.00 3.02
3087 3257 0.386838 GGCTCTTGTGCAGCAACTTT 59.613 50.000 0.00 0.00 38.77 2.66
3150 3320 2.113860 TGGATCTAGTGTTGCTTGGC 57.886 50.000 0.00 0.00 0.00 4.52
3249 3419 8.716674 ATTCACTCCTAAATGATAAATGCCAT 57.283 30.769 0.00 0.00 0.00 4.40
3252 3422 8.217111 TCACTCCTAAATGATAAATGCCATACA 58.783 33.333 0.00 0.00 0.00 2.29
3279 3449 2.095567 CGAACAAACTCCCTGCATCAAG 60.096 50.000 0.00 0.00 0.00 3.02
3309 3479 0.390340 CAGTACAGGAGCGCACACAT 60.390 55.000 11.47 0.00 0.00 3.21
3316 3486 0.166814 GGAGCGCACACATGTCTTTC 59.833 55.000 11.47 0.00 0.00 2.62
3317 3487 1.151668 GAGCGCACACATGTCTTTCT 58.848 50.000 11.47 0.00 0.00 2.52
3318 3488 1.532868 GAGCGCACACATGTCTTTCTT 59.467 47.619 11.47 0.00 0.00 2.52
3319 3489 1.949525 AGCGCACACATGTCTTTCTTT 59.050 42.857 11.47 0.00 0.00 2.52
3320 3490 2.358898 AGCGCACACATGTCTTTCTTTT 59.641 40.909 11.47 0.00 0.00 2.27
3321 3491 3.115554 GCGCACACATGTCTTTCTTTTT 58.884 40.909 0.30 0.00 0.00 1.94
3363 3540 4.997565 ACAAAATAAAGGCGATCATGGTG 58.002 39.130 0.00 0.00 0.00 4.17
3364 3541 4.704540 ACAAAATAAAGGCGATCATGGTGA 59.295 37.500 0.00 0.00 0.00 4.02
3365 3542 4.900635 AAATAAAGGCGATCATGGTGAC 57.099 40.909 0.00 0.00 0.00 3.67
3366 3543 1.934589 TAAAGGCGATCATGGTGACG 58.065 50.000 0.00 0.00 0.00 4.35
3367 3544 0.249120 AAAGGCGATCATGGTGACGA 59.751 50.000 0.00 0.00 0.00 4.20
3480 3673 2.713877 TCAGCATGATGCACTGCTTTA 58.286 42.857 20.71 6.52 46.22 1.85
3484 3677 2.919229 GCATGATGCACTGCTTTAACAC 59.081 45.455 13.36 0.00 44.26 3.32
3485 3678 3.612241 GCATGATGCACTGCTTTAACACA 60.612 43.478 13.36 0.00 44.26 3.72
3510 3703 8.473016 CAGCGTTAAAAATTTCGAACAACATTA 58.527 29.630 0.00 0.00 0.00 1.90
3621 3818 8.780249 TGTGCTAACTATAAGGTTGAAAGAAAC 58.220 33.333 0.00 0.00 0.00 2.78
3668 4284 1.009829 GGCTCTGCCGACACATAAAG 58.990 55.000 0.00 0.00 39.62 1.85
3757 4373 2.678336 GTGGTGATGAATCCGAAACCTC 59.322 50.000 0.00 0.00 0.00 3.85
3790 4406 5.268118 TCATTACTCAAGCGTCATCTCAT 57.732 39.130 0.00 0.00 0.00 2.90
3798 4414 0.659957 GCGTCATCTCATTTGGCCTC 59.340 55.000 3.32 0.00 0.00 4.70
3817 4433 5.695363 GGCCTCGTTCCTTGTTATTACTATC 59.305 44.000 0.00 0.00 0.00 2.08
3855 4916 7.201705 GCTCATAGTTTAGTTAAATCCCGCTTT 60.202 37.037 0.00 0.00 0.00 3.51
3877 4938 7.534239 GCTTTATACTGCAACAAAACTACTCAC 59.466 37.037 0.00 0.00 0.00 3.51
3880 4941 3.063452 ACTGCAACAAAACTACTCACGTG 59.937 43.478 9.94 9.94 0.00 4.49
3894 4955 2.011222 TCACGTGAACAAAAGACCACC 58.989 47.619 17.62 0.00 0.00 4.61
3949 5011 0.385029 GACTGCACATGGTTTGCACA 59.615 50.000 5.43 0.00 45.06 4.57
3972 5034 4.275936 AGAGAACAAGAACCGGTCAATTTG 59.724 41.667 8.04 12.73 0.00 2.32
3980 5042 2.604139 ACCGGTCAATTTGGTCCAAAT 58.396 42.857 22.00 22.00 44.62 2.32
3988 5050 5.046663 GTCAATTTGGTCCAAATGGGTACAT 60.047 40.000 26.94 9.65 42.32 2.29
4006 5068 3.453424 ACATTTGAAACTCGGTTTTGGC 58.547 40.909 3.96 0.00 35.77 4.52
4007 5069 2.588027 TTTGAAACTCGGTTTTGGCC 57.412 45.000 0.00 0.00 35.77 5.36
4008 5070 0.747852 TTGAAACTCGGTTTTGGCCC 59.252 50.000 0.00 0.00 35.77 5.80
4009 5071 0.106419 TGAAACTCGGTTTTGGCCCT 60.106 50.000 0.00 0.00 35.77 5.19
4010 5072 1.143277 TGAAACTCGGTTTTGGCCCTA 59.857 47.619 0.00 0.00 35.77 3.53
4011 5073 1.538512 GAAACTCGGTTTTGGCCCTAC 59.461 52.381 0.00 0.00 35.77 3.18
4012 5074 0.475044 AACTCGGTTTTGGCCCTACA 59.525 50.000 0.00 0.00 0.00 2.74
4013 5075 0.036306 ACTCGGTTTTGGCCCTACAG 59.964 55.000 0.00 0.00 0.00 2.74
4014 5076 0.676782 CTCGGTTTTGGCCCTACAGG 60.677 60.000 0.00 0.00 39.47 4.00
4015 5077 1.128809 TCGGTTTTGGCCCTACAGGA 61.129 55.000 0.00 0.00 38.24 3.86
4016 5078 0.676782 CGGTTTTGGCCCTACAGGAG 60.677 60.000 0.00 0.00 38.24 3.69
4017 5079 0.323451 GGTTTTGGCCCTACAGGAGG 60.323 60.000 0.00 0.00 46.25 4.30
4023 5085 4.109656 CCCTACAGGAGGCCCCCT 62.110 72.222 0.00 0.00 45.17 4.79
4024 5086 2.722705 CCCTACAGGAGGCCCCCTA 61.723 68.421 5.01 0.00 45.17 3.53
4025 5087 1.316969 CCTACAGGAGGCCCCCTAA 59.683 63.158 5.01 0.00 38.96 2.69
4026 5088 0.327191 CCTACAGGAGGCCCCCTAAA 60.327 60.000 5.01 0.00 38.96 1.85
4027 5089 1.699257 CCTACAGGAGGCCCCCTAAAT 60.699 57.143 5.01 0.00 38.96 1.40
4028 5090 2.136026 CTACAGGAGGCCCCCTAAATT 58.864 52.381 5.01 0.00 34.07 1.82
4029 5091 0.631212 ACAGGAGGCCCCCTAAATTG 59.369 55.000 5.01 0.00 34.07 2.32
4030 5092 0.926293 CAGGAGGCCCCCTAAATTGA 59.074 55.000 5.01 0.00 34.07 2.57
4031 5093 1.133668 CAGGAGGCCCCCTAAATTGAG 60.134 57.143 5.01 0.00 34.07 3.02
4032 5094 0.927029 GGAGGCCCCCTAAATTGAGT 59.073 55.000 0.00 0.00 31.76 3.41
4033 5095 1.133761 GGAGGCCCCCTAAATTGAGTC 60.134 57.143 0.00 0.00 31.76 3.36
4034 5096 0.927029 AGGCCCCCTAAATTGAGTCC 59.073 55.000 0.00 0.00 28.47 3.85
4035 5097 0.927029 GGCCCCCTAAATTGAGTCCT 59.073 55.000 0.00 0.00 0.00 3.85
4036 5098 1.133761 GGCCCCCTAAATTGAGTCCTC 60.134 57.143 0.00 0.00 0.00 3.71
4037 5099 1.133761 GCCCCCTAAATTGAGTCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
4038 5100 2.493091 CCCCCTAAATTGAGTCCTCCT 58.507 52.381 0.00 0.00 0.00 3.69
4039 5101 3.665443 CCCCCTAAATTGAGTCCTCCTA 58.335 50.000 0.00 0.00 0.00 2.94
4040 5102 4.243643 CCCCCTAAATTGAGTCCTCCTAT 58.756 47.826 0.00 0.00 0.00 2.57
4041 5103 5.412384 CCCCCTAAATTGAGTCCTCCTATA 58.588 45.833 0.00 0.00 0.00 1.31
4042 5104 5.248705 CCCCCTAAATTGAGTCCTCCTATAC 59.751 48.000 0.00 0.00 0.00 1.47
4043 5105 5.248705 CCCCTAAATTGAGTCCTCCTATACC 59.751 48.000 0.00 0.00 0.00 2.73
4044 5106 5.844516 CCCTAAATTGAGTCCTCCTATACCA 59.155 44.000 0.00 0.00 0.00 3.25
4045 5107 6.239629 CCCTAAATTGAGTCCTCCTATACCAC 60.240 46.154 0.00 0.00 0.00 4.16
4046 5108 6.555360 CCTAAATTGAGTCCTCCTATACCACT 59.445 42.308 0.00 0.00 0.00 4.00
4047 5109 5.878406 AATTGAGTCCTCCTATACCACTG 57.122 43.478 0.00 0.00 0.00 3.66
4048 5110 4.332683 TTGAGTCCTCCTATACCACTGT 57.667 45.455 0.00 0.00 0.00 3.55
4049 5111 3.899726 TGAGTCCTCCTATACCACTGTC 58.100 50.000 0.00 0.00 0.00 3.51
4050 5112 3.528078 TGAGTCCTCCTATACCACTGTCT 59.472 47.826 0.00 0.00 0.00 3.41
4051 5113 3.886505 GAGTCCTCCTATACCACTGTCTG 59.113 52.174 0.00 0.00 0.00 3.51
4052 5114 3.269906 AGTCCTCCTATACCACTGTCTGT 59.730 47.826 0.00 0.00 0.00 3.41
4053 5115 4.477581 AGTCCTCCTATACCACTGTCTGTA 59.522 45.833 0.00 0.00 0.00 2.74
4054 5116 4.822896 GTCCTCCTATACCACTGTCTGTAG 59.177 50.000 0.00 0.00 0.00 2.74
4055 5117 4.141228 TCCTCCTATACCACTGTCTGTAGG 60.141 50.000 0.00 0.00 0.00 3.18
4056 5118 4.145807 CTCCTATACCACTGTCTGTAGGG 58.854 52.174 0.00 0.00 30.77 3.53
4057 5119 3.530564 TCCTATACCACTGTCTGTAGGGT 59.469 47.826 0.00 0.00 35.66 4.34
4058 5120 3.637229 CCTATACCACTGTCTGTAGGGTG 59.363 52.174 0.00 0.00 33.14 4.61
4059 5121 2.984435 TACCACTGTCTGTAGGGTGA 57.016 50.000 0.00 0.00 33.14 4.02
4060 5122 2.327325 ACCACTGTCTGTAGGGTGAT 57.673 50.000 0.00 0.00 32.12 3.06
4061 5123 2.180276 ACCACTGTCTGTAGGGTGATC 58.820 52.381 0.00 0.00 32.12 2.92
4062 5124 2.225394 ACCACTGTCTGTAGGGTGATCT 60.225 50.000 0.00 0.00 32.12 2.75
4063 5125 2.167281 CCACTGTCTGTAGGGTGATCTG 59.833 54.545 0.00 0.00 32.12 2.90
4064 5126 2.167281 CACTGTCTGTAGGGTGATCTGG 59.833 54.545 0.00 0.00 32.12 3.86
4065 5127 1.137872 CTGTCTGTAGGGTGATCTGGC 59.862 57.143 0.00 0.00 0.00 4.85
4066 5128 0.466124 GTCTGTAGGGTGATCTGGCC 59.534 60.000 0.00 0.00 0.00 5.36
4067 5129 0.691078 TCTGTAGGGTGATCTGGCCC 60.691 60.000 0.00 11.14 45.16 5.80
4071 5133 3.090765 GGGTGATCTGGCCCAGTT 58.909 61.111 11.27 1.42 44.23 3.16
4072 5134 1.379044 GGGTGATCTGGCCCAGTTG 60.379 63.158 11.27 0.00 44.23 3.16
4073 5135 1.380302 GGTGATCTGGCCCAGTTGT 59.620 57.895 11.27 0.00 32.61 3.32
4074 5136 0.962356 GGTGATCTGGCCCAGTTGTG 60.962 60.000 11.27 0.00 32.61 3.33
4075 5137 0.250901 GTGATCTGGCCCAGTTGTGT 60.251 55.000 11.27 0.00 32.61 3.72
4076 5138 0.478072 TGATCTGGCCCAGTTGTGTT 59.522 50.000 11.27 0.00 32.61 3.32
4077 5139 0.883833 GATCTGGCCCAGTTGTGTTG 59.116 55.000 11.27 0.00 32.61 3.33
4078 5140 1.181098 ATCTGGCCCAGTTGTGTTGC 61.181 55.000 11.27 0.00 32.61 4.17
4079 5141 1.829533 CTGGCCCAGTTGTGTTGCT 60.830 57.895 1.39 0.00 0.00 3.91
4080 5142 1.799258 CTGGCCCAGTTGTGTTGCTC 61.799 60.000 1.39 0.00 0.00 4.26
4081 5143 1.827789 GGCCCAGTTGTGTTGCTCA 60.828 57.895 0.00 0.00 0.00 4.26
4082 5144 1.360192 GCCCAGTTGTGTTGCTCAC 59.640 57.895 5.83 5.83 46.31 3.51
4083 5145 1.103398 GCCCAGTTGTGTTGCTCACT 61.103 55.000 12.23 0.00 46.27 3.41
4084 5146 0.664761 CCCAGTTGTGTTGCTCACTG 59.335 55.000 12.23 0.00 46.27 3.66
4085 5147 0.664761 CCAGTTGTGTTGCTCACTGG 59.335 55.000 2.89 2.89 46.27 4.00
4086 5148 1.382522 CAGTTGTGTTGCTCACTGGT 58.617 50.000 12.23 0.00 46.27 4.00
4087 5149 1.745087 CAGTTGTGTTGCTCACTGGTT 59.255 47.619 12.23 0.00 46.27 3.67
4088 5150 2.164219 CAGTTGTGTTGCTCACTGGTTT 59.836 45.455 12.23 0.00 46.27 3.27
4089 5151 2.825532 AGTTGTGTTGCTCACTGGTTTT 59.174 40.909 12.23 0.00 46.27 2.43
4090 5152 2.923020 GTTGTGTTGCTCACTGGTTTTG 59.077 45.455 12.23 0.00 46.27 2.44
4091 5153 2.441410 TGTGTTGCTCACTGGTTTTGA 58.559 42.857 12.23 0.00 46.27 2.69
4092 5154 2.423185 TGTGTTGCTCACTGGTTTTGAG 59.577 45.455 12.23 0.00 46.27 3.02
4100 5162 5.039480 CTCACTGGTTTTGAGCATAACTG 57.961 43.478 4.31 1.75 34.41 3.16
4101 5163 4.460263 TCACTGGTTTTGAGCATAACTGT 58.540 39.130 4.31 2.22 0.00 3.55
4102 5164 4.887071 TCACTGGTTTTGAGCATAACTGTT 59.113 37.500 0.00 0.00 0.00 3.16
4103 5165 6.058833 TCACTGGTTTTGAGCATAACTGTTA 58.941 36.000 2.26 2.26 0.00 2.41
4104 5166 6.714810 TCACTGGTTTTGAGCATAACTGTTAT 59.285 34.615 7.22 7.22 0.00 1.89
4105 5167 7.880713 TCACTGGTTTTGAGCATAACTGTTATA 59.119 33.333 12.39 0.00 0.00 0.98
4106 5168 8.511321 CACTGGTTTTGAGCATAACTGTTATAA 58.489 33.333 12.39 1.65 0.00 0.98
4107 5169 9.243105 ACTGGTTTTGAGCATAACTGTTATAAT 57.757 29.630 12.39 4.81 0.00 1.28
4113 5175 9.772973 TTTGAGCATAACTGTTATAATATCGGT 57.227 29.630 12.39 5.43 0.00 4.69
4114 5176 9.772973 TTGAGCATAACTGTTATAATATCGGTT 57.227 29.630 12.39 4.68 35.33 4.44
4115 5177 9.772973 TGAGCATAACTGTTATAATATCGGTTT 57.227 29.630 12.39 0.00 33.55 3.27
4121 5183 7.492352 ACTGTTATAATATCGGTTTTCTGCC 57.508 36.000 0.00 0.00 0.00 4.85
4132 5194 4.908966 GGTTTTCTGCCGATTTCAATTG 57.091 40.909 0.00 0.00 0.00 2.32
4133 5195 4.555262 GGTTTTCTGCCGATTTCAATTGA 58.445 39.130 3.38 3.38 0.00 2.57
4134 5196 5.170748 GGTTTTCTGCCGATTTCAATTGAT 58.829 37.500 9.40 0.00 0.00 2.57
4135 5197 5.639082 GGTTTTCTGCCGATTTCAATTGATT 59.361 36.000 9.40 0.00 0.00 2.57
4136 5198 6.147656 GGTTTTCTGCCGATTTCAATTGATTT 59.852 34.615 9.40 0.00 0.00 2.17
4137 5199 7.307930 GGTTTTCTGCCGATTTCAATTGATTTT 60.308 33.333 9.40 0.00 0.00 1.82
4138 5200 6.949578 TTCTGCCGATTTCAATTGATTTTC 57.050 33.333 9.40 5.93 0.00 2.29
4139 5201 6.023357 TCTGCCGATTTCAATTGATTTTCA 57.977 33.333 9.40 2.75 0.00 2.69
4140 5202 6.632909 TCTGCCGATTTCAATTGATTTTCAT 58.367 32.000 9.40 0.00 0.00 2.57
4141 5203 7.098477 TCTGCCGATTTCAATTGATTTTCATT 58.902 30.769 9.40 0.00 0.00 2.57
4142 5204 7.603404 TCTGCCGATTTCAATTGATTTTCATTT 59.397 29.630 9.40 0.00 0.00 2.32
4143 5205 8.097078 TGCCGATTTCAATTGATTTTCATTTT 57.903 26.923 9.40 0.00 0.00 1.82
4144 5206 8.566260 TGCCGATTTCAATTGATTTTCATTTTT 58.434 25.926 9.40 0.00 0.00 1.94
4145 5207 9.054191 GCCGATTTCAATTGATTTTCATTTTTC 57.946 29.630 9.40 0.00 0.00 2.29
4168 5230 7.945033 TCTTTTCTTTTTCCATACAACATGC 57.055 32.000 0.00 0.00 0.00 4.06
4169 5231 7.495901 TCTTTTCTTTTTCCATACAACATGCA 58.504 30.769 0.00 0.00 0.00 3.96
4170 5232 8.149647 TCTTTTCTTTTTCCATACAACATGCAT 58.850 29.630 0.00 0.00 0.00 3.96
4171 5233 9.421806 CTTTTCTTTTTCCATACAACATGCATA 57.578 29.630 0.00 0.00 0.00 3.14
4172 5234 9.941325 TTTTCTTTTTCCATACAACATGCATAT 57.059 25.926 0.00 0.00 0.00 1.78
4173 5235 9.941325 TTTCTTTTTCCATACAACATGCATATT 57.059 25.926 0.00 0.00 0.00 1.28
4174 5236 9.941325 TTCTTTTTCCATACAACATGCATATTT 57.059 25.926 0.00 0.00 0.00 1.40
4175 5237 9.941325 TCTTTTTCCATACAACATGCATATTTT 57.059 25.926 0.00 0.00 0.00 1.82
4186 5248 8.739039 ACAACATGCATATTTTACTTTAGAGCA 58.261 29.630 0.00 0.00 0.00 4.26
4187 5249 9.571810 CAACATGCATATTTTACTTTAGAGCAA 57.428 29.630 0.00 0.00 32.83 3.91
4189 5251 9.573133 ACATGCATATTTTACTTTAGAGCAAAC 57.427 29.630 0.00 0.00 32.83 2.93
4190 5252 9.571810 CATGCATATTTTACTTTAGAGCAAACA 57.428 29.630 0.00 0.00 32.83 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.721706 CCGCCTTGCCCTCCTCTT 61.722 66.667 0.00 0.00 0.00 2.85
124 125 3.877559 TGTCGGAGAAGAATGATGCATT 58.122 40.909 0.00 0.00 39.69 3.56
154 155 2.878406 CAAGAAACACGTCTTCCCACAT 59.122 45.455 3.78 0.00 35.63 3.21
155 156 2.093394 TCAAGAAACACGTCTTCCCACA 60.093 45.455 3.78 0.00 35.63 4.17
277 280 3.616219 ACCAAACTGCACAAACTAGTCA 58.384 40.909 0.00 0.00 0.00 3.41
291 294 4.535526 ACAAGCAAAGTTCAACCAAACT 57.464 36.364 0.00 0.00 41.20 2.66
320 326 9.941664 CAAGCTAGTTCAACCAAATAGATAATG 57.058 33.333 0.00 0.00 35.06 1.90
343 351 0.512952 GCGAGCAACCAGTACACAAG 59.487 55.000 0.00 0.00 0.00 3.16
377 386 2.721231 GCTCCAACAACGCTGCAA 59.279 55.556 0.00 0.00 0.00 4.08
378 387 3.648982 CGCTCCAACAACGCTGCA 61.649 61.111 0.00 0.00 0.00 4.41
379 388 4.389576 CCGCTCCAACAACGCTGC 62.390 66.667 0.00 0.00 0.00 5.25
380 389 3.726517 CCCGCTCCAACAACGCTG 61.727 66.667 0.00 0.00 0.00 5.18
381 390 4.250305 ACCCGCTCCAACAACGCT 62.250 61.111 0.00 0.00 0.00 5.07
383 392 3.411351 CGACCCGCTCCAACAACG 61.411 66.667 0.00 0.00 0.00 4.10
466 478 2.189342 GCACGCTAAAACAGTTTTGCA 58.811 42.857 19.77 1.66 43.14 4.08
491 507 0.249280 TCTTCAACAGACGCGCAAGA 60.249 50.000 5.73 3.01 43.02 3.02
492 508 0.792640 ATCTTCAACAGACGCGCAAG 59.207 50.000 5.73 0.15 32.83 4.01
623 639 2.092374 ATGCTCGTAGCGTCACGTA 58.908 52.632 0.00 0.00 46.26 3.57
711 729 2.284754 TCCAGATCTCTCCTCGGATG 57.715 55.000 0.00 0.00 0.00 3.51
712 730 2.291540 GGATCCAGATCTCTCCTCGGAT 60.292 54.545 6.95 9.23 37.92 4.18
809 847 1.298859 CTGCTCTGGGTGGCGTAAAC 61.299 60.000 0.00 0.00 0.00 2.01
893 951 2.165301 CGTGCCGGGATTCTCGTTC 61.165 63.158 2.18 0.00 0.00 3.95
935 1016 7.665559 AGATGATGTTTGCTGGTTTTCTAAGTA 59.334 33.333 0.00 0.00 0.00 2.24
975 1059 2.158638 ACGGGAGACTAGATGGGTAGAC 60.159 54.545 0.00 0.00 0.00 2.59
1103 1207 0.733150 CAGGATACACAGCGAGACGA 59.267 55.000 0.00 0.00 41.41 4.20
1202 1322 3.420943 CGGAATTGACGGGGATGC 58.579 61.111 0.00 0.00 0.00 3.91
1301 1427 1.069022 GCATGCAGTTGATGTCGTTGT 60.069 47.619 14.21 0.00 0.00 3.32
1312 1438 4.093952 GTGAGCGCGCATGCAGTT 62.094 61.111 35.10 10.81 42.97 3.16
1380 1506 2.746277 CAGCGGTAGGGGTTGTGC 60.746 66.667 0.00 0.00 0.00 4.57
1488 1614 1.836604 GCCCAAAGGGTTTCTGCCA 60.837 57.895 3.68 0.00 46.51 4.92
1494 1620 3.840132 ACCGGGCCCAAAGGGTTT 61.840 61.111 24.92 0.00 46.51 3.27
1644 1779 2.506345 GAGCGCGAACGAGTTAGCC 61.506 63.158 12.10 7.99 43.93 3.93
1694 1832 1.228063 CCGAAGATGGGCCAGATGG 60.228 63.158 13.78 5.49 38.53 3.51
1695 1833 1.895707 GCCGAAGATGGGCCAGATG 60.896 63.158 13.78 0.00 44.97 2.90
1696 1834 2.512896 GCCGAAGATGGGCCAGAT 59.487 61.111 13.78 0.00 44.97 2.90
1779 1923 1.743995 GTATTCCCCGTGCTTGCGT 60.744 57.895 0.00 0.00 0.00 5.24
2118 2284 2.872388 CGTGTCCACCCTGAGCACT 61.872 63.158 0.00 0.00 0.00 4.40
2119 2285 2.357517 CGTGTCCACCCTGAGCAC 60.358 66.667 0.00 0.00 0.00 4.40
2120 2286 3.625897 CCGTGTCCACCCTGAGCA 61.626 66.667 0.00 0.00 0.00 4.26
2121 2287 3.591254 GACCGTGTCCACCCTGAGC 62.591 68.421 0.00 0.00 0.00 4.26
2122 2288 2.657237 GACCGTGTCCACCCTGAG 59.343 66.667 0.00 0.00 0.00 3.35
2400 2567 0.626382 TCTCCATCTCTGTCCCTCGT 59.374 55.000 0.00 0.00 0.00 4.18
2444 2612 3.357079 CTTGCGCGGCTGTTCCTT 61.357 61.111 8.83 0.00 0.00 3.36
2520 2688 0.179045 CGCTCCTTCCAATAGTGGGG 60.179 60.000 9.77 3.64 46.01 4.96
2525 2693 1.595382 CCGCCGCTCCTTCCAATAG 60.595 63.158 0.00 0.00 0.00 1.73
2526 2694 2.504032 CCGCCGCTCCTTCCAATA 59.496 61.111 0.00 0.00 0.00 1.90
2632 2800 3.609807 CACGCATCACACATATAGATCGG 59.390 47.826 0.00 0.00 0.00 4.18
2846 3014 2.527624 ACTGCCTCAGCCTGGACA 60.528 61.111 0.00 0.00 38.69 4.02
2867 3035 0.682209 GTGCCATGGAGTTGATGCCT 60.682 55.000 18.40 0.00 0.00 4.75
2917 3085 0.103208 CCCTCCTCCATCGACGAAAG 59.897 60.000 0.00 0.00 0.00 2.62
2924 3092 1.689233 TTGTCCCCCTCCTCCATCG 60.689 63.158 0.00 0.00 0.00 3.84
2927 3095 2.124996 CCTTGTCCCCCTCCTCCA 59.875 66.667 0.00 0.00 0.00 3.86
2928 3096 3.412408 GCCTTGTCCCCCTCCTCC 61.412 72.222 0.00 0.00 0.00 4.30
2929 3097 2.285743 AGCCTTGTCCCCCTCCTC 60.286 66.667 0.00 0.00 0.00 3.71
3075 3245 4.979815 ACGGTAAAATTAAAGTTGCTGCAC 59.020 37.500 0.00 0.00 0.00 4.57
3087 3257 0.035247 AGGCGGGCACGGTAAAATTA 60.035 50.000 11.92 0.00 41.36 1.40
3150 3320 3.790820 CACAACACGATCACAAACTTTGG 59.209 43.478 6.47 0.00 34.12 3.28
3227 3397 8.394971 TGTATGGCATTTATCATTTAGGAGTG 57.605 34.615 4.78 0.00 0.00 3.51
3243 3413 7.041372 GGAGTTTGTTCGTTATATGTATGGCAT 60.041 37.037 4.88 4.88 41.42 4.40
3249 3419 5.813672 GCAGGGAGTTTGTTCGTTATATGTA 59.186 40.000 0.00 0.00 0.00 2.29
3252 3422 4.839121 TGCAGGGAGTTTGTTCGTTATAT 58.161 39.130 0.00 0.00 0.00 0.86
3254 3424 3.134574 TGCAGGGAGTTTGTTCGTTAT 57.865 42.857 0.00 0.00 0.00 1.89
3256 3426 1.880027 GATGCAGGGAGTTTGTTCGTT 59.120 47.619 0.00 0.00 0.00 3.85
3279 3449 4.483311 GCTCCTGTACTGTACTGTGTTAC 58.517 47.826 17.98 6.51 0.00 2.50
3318 3488 7.828712 TGTTAACCTCCTTTTTCGAAGAAAAA 58.171 30.769 16.60 16.60 45.90 1.94
3319 3489 7.393841 TGTTAACCTCCTTTTTCGAAGAAAA 57.606 32.000 2.48 4.07 45.90 2.29
3320 3490 7.393841 TTGTTAACCTCCTTTTTCGAAGAAA 57.606 32.000 2.48 4.40 45.90 2.52
3321 3491 7.393841 TTTGTTAACCTCCTTTTTCGAAGAA 57.606 32.000 2.48 0.00 45.90 2.52
3322 3492 7.393841 TTTTGTTAACCTCCTTTTTCGAAGA 57.606 32.000 2.48 0.00 0.00 2.87
3323 3493 9.738832 TTATTTTGTTAACCTCCTTTTTCGAAG 57.261 29.630 2.48 0.00 0.00 3.79
3363 3540 4.967437 AGTCGTCTATGTGTTTAGTCGTC 58.033 43.478 0.00 0.00 34.06 4.20
3364 3541 6.148480 ACTTAGTCGTCTATGTGTTTAGTCGT 59.852 38.462 7.28 0.00 34.62 4.34
3365 3542 6.541086 ACTTAGTCGTCTATGTGTTTAGTCG 58.459 40.000 7.28 0.00 34.62 4.18
3366 3543 7.951706 GACTTAGTCGTCTATGTGTTTAGTC 57.048 40.000 11.79 6.39 35.58 2.59
3453 3646 2.082231 GTGCATCATGCTGACTTGAGT 58.918 47.619 11.84 0.00 45.31 3.41
3465 3658 3.366679 GCTGTGTTAAAGCAGTGCATCAT 60.367 43.478 19.20 2.50 40.52 2.45
3480 3673 5.800941 TGTTCGAAATTTTTAACGCTGTGTT 59.199 32.000 11.71 11.71 44.78 3.32
3484 3677 6.249478 TGTTGTTCGAAATTTTTAACGCTG 57.751 33.333 0.00 0.00 0.00 5.18
3485 3678 7.458038 AATGTTGTTCGAAATTTTTAACGCT 57.542 28.000 0.00 0.00 0.00 5.07
3597 3794 8.911918 TGTTTCTTTCAACCTTATAGTTAGCA 57.088 30.769 0.00 0.00 0.00 3.49
3757 4373 2.876091 TGAGTAATGAAGGCGTTCTCG 58.124 47.619 19.07 0.00 40.37 4.04
3790 4406 2.642154 TAACAAGGAACGAGGCCAAA 57.358 45.000 5.01 0.00 0.00 3.28
3830 4446 7.787725 AAGCGGGATTTAACTAAACTATGAG 57.212 36.000 0.00 0.00 0.00 2.90
3831 4447 9.841295 ATAAAGCGGGATTTAACTAAACTATGA 57.159 29.630 0.00 0.00 0.00 2.15
3835 4451 9.106070 CAGTATAAAGCGGGATTTAACTAAACT 57.894 33.333 0.00 0.00 0.00 2.66
3836 4452 7.854422 GCAGTATAAAGCGGGATTTAACTAAAC 59.146 37.037 0.00 0.00 0.00 2.01
3838 4454 7.049133 TGCAGTATAAAGCGGGATTTAACTAA 58.951 34.615 0.00 0.00 0.00 2.24
3839 4455 6.584488 TGCAGTATAAAGCGGGATTTAACTA 58.416 36.000 0.00 0.00 0.00 2.24
3840 4456 5.433526 TGCAGTATAAAGCGGGATTTAACT 58.566 37.500 0.00 0.00 0.00 2.24
3841 4457 5.744666 TGCAGTATAAAGCGGGATTTAAC 57.255 39.130 0.00 0.00 0.00 2.01
3842 4458 5.648526 TGTTGCAGTATAAAGCGGGATTTAA 59.351 36.000 0.00 0.00 0.00 1.52
3843 4459 5.186942 TGTTGCAGTATAAAGCGGGATTTA 58.813 37.500 0.00 0.00 0.00 1.40
3844 4460 4.013728 TGTTGCAGTATAAAGCGGGATTT 58.986 39.130 0.00 0.00 0.00 2.17
3845 4461 3.616219 TGTTGCAGTATAAAGCGGGATT 58.384 40.909 0.00 0.00 0.00 3.01
3846 4462 3.275617 TGTTGCAGTATAAAGCGGGAT 57.724 42.857 0.00 0.00 0.00 3.85
3847 4463 2.772077 TGTTGCAGTATAAAGCGGGA 57.228 45.000 0.00 0.00 0.00 5.14
3848 4464 3.840890 TTTGTTGCAGTATAAAGCGGG 57.159 42.857 0.00 0.00 0.00 6.13
3855 4916 6.218019 ACGTGAGTAGTTTTGTTGCAGTATA 58.782 36.000 0.00 0.00 46.88 1.47
3877 4938 1.740585 TGTGGTGGTCTTTTGTTCACG 59.259 47.619 0.00 0.00 0.00 4.35
3880 4941 3.428862 CCAACTGTGGTGGTCTTTTGTTC 60.429 47.826 0.00 0.00 40.42 3.18
3949 5011 3.771577 ATTGACCGGTTCTTGTTCTCT 57.228 42.857 9.42 0.00 0.00 3.10
3980 5042 3.495434 ACCGAGTTTCAAATGTACCCA 57.505 42.857 0.00 0.00 0.00 4.51
3988 5050 1.137282 GGGCCAAAACCGAGTTTCAAA 59.863 47.619 4.39 0.00 34.43 2.69
3989 5051 0.747852 GGGCCAAAACCGAGTTTCAA 59.252 50.000 4.39 0.00 34.43 2.69
3998 5060 0.323451 CCTCCTGTAGGGCCAAAACC 60.323 60.000 6.18 0.00 42.32 3.27
4006 5068 2.265890 TTAGGGGGCCTCCTGTAGGG 62.266 65.000 36.13 0.00 46.65 3.53
4008 5070 1.821088 ATTTAGGGGGCCTCCTGTAG 58.179 55.000 36.13 0.00 37.75 2.74
4009 5071 1.850345 CAATTTAGGGGGCCTCCTGTA 59.150 52.381 36.13 22.08 37.75 2.74
4010 5072 0.631212 CAATTTAGGGGGCCTCCTGT 59.369 55.000 36.13 17.47 37.75 4.00
4011 5073 0.926293 TCAATTTAGGGGGCCTCCTG 59.074 55.000 36.13 18.65 37.75 3.86
4012 5074 1.226311 CTCAATTTAGGGGGCCTCCT 58.774 55.000 31.61 31.61 40.79 3.69
4013 5075 0.927029 ACTCAATTTAGGGGGCCTCC 59.073 55.000 16.49 16.49 34.61 4.30
4014 5076 1.133761 GGACTCAATTTAGGGGGCCTC 60.134 57.143 0.84 0.00 34.61 4.70
4015 5077 0.927029 GGACTCAATTTAGGGGGCCT 59.073 55.000 0.84 0.00 37.71 5.19
4016 5078 0.927029 AGGACTCAATTTAGGGGGCC 59.073 55.000 0.00 0.00 0.00 5.80
4017 5079 1.133761 GGAGGACTCAATTTAGGGGGC 60.134 57.143 1.32 0.00 0.00 5.80
4018 5080 2.493091 AGGAGGACTCAATTTAGGGGG 58.507 52.381 1.32 0.00 0.00 5.40
4019 5081 5.248705 GGTATAGGAGGACTCAATTTAGGGG 59.751 48.000 1.32 0.00 0.00 4.79
4020 5082 5.844516 TGGTATAGGAGGACTCAATTTAGGG 59.155 44.000 1.32 0.00 0.00 3.53
4021 5083 6.555360 AGTGGTATAGGAGGACTCAATTTAGG 59.445 42.308 1.32 0.00 0.00 2.69
4022 5084 7.070074 ACAGTGGTATAGGAGGACTCAATTTAG 59.930 40.741 1.32 0.00 0.00 1.85
4023 5085 6.901300 ACAGTGGTATAGGAGGACTCAATTTA 59.099 38.462 1.32 0.00 0.00 1.40
4024 5086 5.726793 ACAGTGGTATAGGAGGACTCAATTT 59.273 40.000 1.32 0.00 0.00 1.82
4025 5087 5.281314 ACAGTGGTATAGGAGGACTCAATT 58.719 41.667 1.32 0.00 0.00 2.32
4026 5088 4.884961 ACAGTGGTATAGGAGGACTCAAT 58.115 43.478 1.32 0.00 0.00 2.57
4027 5089 4.017407 AGACAGTGGTATAGGAGGACTCAA 60.017 45.833 1.32 0.00 0.00 3.02
4028 5090 3.528078 AGACAGTGGTATAGGAGGACTCA 59.472 47.826 1.32 0.00 0.00 3.41
4029 5091 3.886505 CAGACAGTGGTATAGGAGGACTC 59.113 52.174 0.00 0.00 0.00 3.36
4030 5092 3.269906 ACAGACAGTGGTATAGGAGGACT 59.730 47.826 0.00 0.00 0.00 3.85
4031 5093 3.633418 ACAGACAGTGGTATAGGAGGAC 58.367 50.000 0.00 0.00 0.00 3.85
4032 5094 4.141228 CCTACAGACAGTGGTATAGGAGGA 60.141 50.000 0.00 0.00 32.47 3.71
4033 5095 4.145807 CCTACAGACAGTGGTATAGGAGG 58.854 52.174 0.00 0.00 32.47 4.30
4034 5096 4.145807 CCCTACAGACAGTGGTATAGGAG 58.854 52.174 11.55 0.00 32.47 3.69
4035 5097 3.530564 ACCCTACAGACAGTGGTATAGGA 59.469 47.826 11.55 0.00 32.47 2.94
4036 5098 3.637229 CACCCTACAGACAGTGGTATAGG 59.363 52.174 0.00 0.30 0.00 2.57
4037 5099 4.533815 TCACCCTACAGACAGTGGTATAG 58.466 47.826 0.00 0.00 0.00 1.31
4038 5100 4.596354 TCACCCTACAGACAGTGGTATA 57.404 45.455 0.00 0.00 0.00 1.47
4039 5101 3.468071 TCACCCTACAGACAGTGGTAT 57.532 47.619 0.00 0.00 0.00 2.73
4040 5102 2.984435 TCACCCTACAGACAGTGGTA 57.016 50.000 0.00 0.00 0.00 3.25
4041 5103 2.180276 GATCACCCTACAGACAGTGGT 58.820 52.381 0.00 0.00 0.00 4.16
4042 5104 2.167281 CAGATCACCCTACAGACAGTGG 59.833 54.545 0.00 0.00 0.00 4.00
4043 5105 2.167281 CCAGATCACCCTACAGACAGTG 59.833 54.545 0.00 0.00 0.00 3.66
4044 5106 2.461695 CCAGATCACCCTACAGACAGT 58.538 52.381 0.00 0.00 0.00 3.55
4045 5107 1.137872 GCCAGATCACCCTACAGACAG 59.862 57.143 0.00 0.00 0.00 3.51
4046 5108 1.195115 GCCAGATCACCCTACAGACA 58.805 55.000 0.00 0.00 0.00 3.41
4047 5109 0.466124 GGCCAGATCACCCTACAGAC 59.534 60.000 0.00 0.00 0.00 3.51
4048 5110 0.691078 GGGCCAGATCACCCTACAGA 60.691 60.000 4.39 0.00 43.36 3.41
4049 5111 1.832912 GGGCCAGATCACCCTACAG 59.167 63.158 4.39 0.00 43.36 2.74
4050 5112 4.066614 GGGCCAGATCACCCTACA 57.933 61.111 4.39 0.00 43.36 2.74
4055 5117 0.962356 CACAACTGGGCCAGATCACC 60.962 60.000 38.99 0.00 35.18 4.02
4056 5118 0.250901 ACACAACTGGGCCAGATCAC 60.251 55.000 38.99 0.00 35.18 3.06
4057 5119 0.478072 AACACAACTGGGCCAGATCA 59.522 50.000 38.99 0.00 35.18 2.92
4058 5120 0.883833 CAACACAACTGGGCCAGATC 59.116 55.000 38.99 0.00 35.18 2.75
4059 5121 1.181098 GCAACACAACTGGGCCAGAT 61.181 55.000 38.99 26.17 35.18 2.90
4060 5122 1.827789 GCAACACAACTGGGCCAGA 60.828 57.895 38.99 0.86 35.18 3.86
4061 5123 1.799258 GAGCAACACAACTGGGCCAG 61.799 60.000 31.62 31.62 37.52 4.85
4062 5124 1.827789 GAGCAACACAACTGGGCCA 60.828 57.895 5.85 5.85 0.00 5.36
4063 5125 1.827789 TGAGCAACACAACTGGGCC 60.828 57.895 0.00 0.00 0.00 5.80
4064 5126 3.840437 TGAGCAACACAACTGGGC 58.160 55.556 0.00 0.00 0.00 5.36
4078 5140 4.516698 ACAGTTATGCTCAAAACCAGTGAG 59.483 41.667 0.00 0.00 44.48 3.51
4079 5141 4.460263 ACAGTTATGCTCAAAACCAGTGA 58.540 39.130 0.00 0.00 0.00 3.41
4080 5142 4.836125 ACAGTTATGCTCAAAACCAGTG 57.164 40.909 0.00 0.00 0.00 3.66
4081 5143 8.630054 TTATAACAGTTATGCTCAAAACCAGT 57.370 30.769 15.12 0.00 0.00 4.00
4087 5149 9.772973 ACCGATATTATAACAGTTATGCTCAAA 57.227 29.630 15.12 2.52 0.00 2.69
4088 5150 9.772973 AACCGATATTATAACAGTTATGCTCAA 57.227 29.630 15.12 2.86 0.00 3.02
4089 5151 9.772973 AAACCGATATTATAACAGTTATGCTCA 57.227 29.630 15.12 0.00 0.00 4.26
4095 5157 9.048446 GGCAGAAAACCGATATTATAACAGTTA 57.952 33.333 0.00 0.00 0.00 2.24
4096 5158 7.927048 GGCAGAAAACCGATATTATAACAGTT 58.073 34.615 0.00 0.00 0.00 3.16
4097 5159 7.492352 GGCAGAAAACCGATATTATAACAGT 57.508 36.000 0.00 0.00 0.00 3.55
4111 5173 4.555262 TCAATTGAAATCGGCAGAAAACC 58.445 39.130 5.45 0.00 0.00 3.27
4112 5174 6.710692 AATCAATTGAAATCGGCAGAAAAC 57.289 33.333 13.09 0.00 0.00 2.43
4113 5175 7.440556 TGAAAATCAATTGAAATCGGCAGAAAA 59.559 29.630 13.09 0.00 0.00 2.29
4114 5176 6.927936 TGAAAATCAATTGAAATCGGCAGAAA 59.072 30.769 13.09 0.00 0.00 2.52
4115 5177 6.453943 TGAAAATCAATTGAAATCGGCAGAA 58.546 32.000 13.09 0.00 0.00 3.02
4116 5178 6.023357 TGAAAATCAATTGAAATCGGCAGA 57.977 33.333 13.09 0.00 0.00 4.26
4117 5179 6.897259 ATGAAAATCAATTGAAATCGGCAG 57.103 33.333 13.09 0.00 0.00 4.85
4118 5180 7.670009 AAATGAAAATCAATTGAAATCGGCA 57.330 28.000 13.09 6.86 0.00 5.69
4119 5181 8.953507 AAAAATGAAAATCAATTGAAATCGGC 57.046 26.923 13.09 1.25 0.00 5.54
4142 5204 8.825745 GCATGTTGTATGGAAAAAGAAAAGAAA 58.174 29.630 0.00 0.00 0.00 2.52
4143 5205 7.984050 TGCATGTTGTATGGAAAAAGAAAAGAA 59.016 29.630 0.00 0.00 0.00 2.52
4144 5206 7.495901 TGCATGTTGTATGGAAAAAGAAAAGA 58.504 30.769 0.00 0.00 0.00 2.52
4145 5207 7.712264 TGCATGTTGTATGGAAAAAGAAAAG 57.288 32.000 0.00 0.00 0.00 2.27
4146 5208 9.941325 ATATGCATGTTGTATGGAAAAAGAAAA 57.059 25.926 10.16 0.00 0.00 2.29
4147 5209 9.941325 AATATGCATGTTGTATGGAAAAAGAAA 57.059 25.926 10.16 0.00 0.00 2.52
4148 5210 9.941325 AAATATGCATGTTGTATGGAAAAAGAA 57.059 25.926 10.16 0.00 0.00 2.52
4149 5211 9.941325 AAAATATGCATGTTGTATGGAAAAAGA 57.059 25.926 10.16 0.00 0.00 2.52
4160 5222 8.739039 TGCTCTAAAGTAAAATATGCATGTTGT 58.261 29.630 10.16 6.79 0.00 3.32
4161 5223 9.571810 TTGCTCTAAAGTAAAATATGCATGTTG 57.428 29.630 10.16 0.00 0.00 3.33
4163 5225 9.573133 GTTTGCTCTAAAGTAAAATATGCATGT 57.427 29.630 10.16 0.00 38.58 3.21
4164 5226 9.571810 TGTTTGCTCTAAAGTAAAATATGCATG 57.428 29.630 10.16 0.00 38.58 4.06


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

AutoCloner maintained by Alex Coulton.