Multiple sequence alignment - TraesCS2B01G456000

Loading Multiple Alignment...

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 TraesCS2B01G456000 chr2B 100.000 5449 0 0 1 5449 650481338 650486786 0.000000e+00 10063.0
1 TraesCS2B01G456000 chr2A 87.293 3990 262 101 1 3871 689170356 689166493 0.000000e+00 4333.0
2 TraesCS2B01G456000 chr2A 93.874 653 31 5 4034 4679 689165814 689165164 0.000000e+00 976.0
3 TraesCS2B01G456000 chr2A 93.015 544 29 7 4677 5216 689165024 689164486 0.000000e+00 785.0
4 TraesCS2B01G456000 chr2A 84.163 221 15 4 5249 5449 689162905 689162685 4.310000e-46 196.0
5 TraesCS2B01G456000 chr2A 84.158 101 15 1 320 420 680101593 680101692 4.490000e-16 97.1
6 TraesCS2B01G456000 chr2D 89.195 3082 164 70 836 3812 544684242 544687259 0.000000e+00 3690.0
7 TraesCS2B01G456000 chr2D 92.067 1437 84 16 4031 5449 544687730 544689154 0.000000e+00 1995.0
8 TraesCS2B01G456000 chr2D 88.427 674 67 8 1 670 544683578 544684244 0.000000e+00 802.0
9 TraesCS2B01G456000 chr5B 86.139 101 12 2 436 535 245968697 245968796 2.080000e-19 108.0
10 TraesCS2B01G456000 chr5B 83.000 100 12 5 322 419 692280601 692280697 9.720000e-13 86.1
11 TraesCS2B01G456000 chr7D 84.314 102 11 5 320 419 481179816 481179914 1.620000e-15 95.3
12 TraesCS2B01G456000 chr7B 84.314 102 11 5 320 419 506757894 506757992 1.620000e-15 95.3
13 TraesCS2B01G456000 chr7B 83.333 102 16 1 441 541 637237192 637237091 5.810000e-15 93.5
14 TraesCS2B01G456000 chr3A 83.019 106 17 1 314 419 444536740 444536636 1.620000e-15 95.3
15 TraesCS2B01G456000 chr3A 86.047 86 12 0 1324 1409 26012602 26012517 5.810000e-15 93.5
16 TraesCS2B01G456000 chr3D 82.407 108 17 2 431 536 329497251 329497144 5.810000e-15 93.5
17 TraesCS2B01G456000 chr3D 96.296 54 2 0 527 580 490833716 490833663 7.520000e-14 89.8
18 TraesCS2B01G456000 chr3D 82.178 101 16 2 436 535 39532372 39532471 9.720000e-13 86.1
19 TraesCS2B01G456000 chr3B 98.113 53 1 0 2196 2248 813189978 813190030 5.810000e-15 93.5
20 TraesCS2B01G456000 chr3B 98.113 53 1 0 2195 2247 823871727 823871779 5.810000e-15 93.5
21 TraesCS2B01G456000 chr3B 81.731 104 18 1 314 417 426999848 426999746 9.720000e-13 86.1
22 TraesCS2B01G456000 chr3B 79.389 131 20 7 441 569 752670211 752670086 9.720000e-13 86.1
23 TraesCS2B01G456000 chr6B 83.168 101 15 2 436 534 657620492 657620592 2.090000e-14 91.6
24 TraesCS2B01G456000 chrUn 84.884 86 13 0 1324 1409 37325595 37325680 2.700000e-13 87.9
25 TraesCS2B01G456000 chr1A 81.308 107 19 1 444 549 552203233 552203127 9.720000e-13 86.1
26 TraesCS2B01G456000 chr1A 76.389 144 27 4 441 582 488096931 488096793 2.720000e-08 71.3
27 TraesCS2B01G456000 chr1D 82.353 102 10 7 321 418 22626924 22626827 1.260000e-11 82.4


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 TraesCS2B01G456000 chr2B 650481338 650486786 5448 False 10063.000000 10063 100.000000 1 5449 1 chr2B.!!$F1 5448
1 TraesCS2B01G456000 chr2A 689162685 689170356 7671 True 1572.500000 4333 89.586250 1 5449 4 chr2A.!!$R1 5448
2 TraesCS2B01G456000 chr2D 544683578 544689154 5576 False 2162.333333 3690 89.896333 1 5449 3 chr2D.!!$F1 5448

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
602 605 0.035739 TGCCGGGTTTTCTGTAGGAC 59.964 55.0 2.18 0.00 0.0 3.85 F
1239 1308 0.248825 CTGATCCCTTCTCTCGTGCG 60.249 60.0 0.00 0.00 0.0 5.34 F
2058 2159 0.396811 CCCGAGGTGAAAAGTCTGGT 59.603 55.0 0.00 0.00 0.0 4.00 F
3774 3963 0.103572 CATTTGTGCTAGGCCCATGC 59.896 55.0 0.00 1.45 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2298 0.108424 GCGCATTCAGTCTGGTCTCT 60.108 55.0 0.30 0.00 0.00 3.10 R
2930 3093 0.029681 AGGATGTAGGAGCCATGGGT 60.030 55.0 18.33 18.33 29.50 4.51 R
3943 4172 0.238025 TAAGCGCGAGTACACGACAA 59.762 50.0 17.12 0.00 35.09 3.18 R
5251 7739 0.036388 TTCAGGCCATTCGTCTGTCC 60.036 55.0 5.01 0.00 0.00 4.02 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
27 28 5.237127 TCATCATGGACTAAATCGTGCATTC 59.763 40.000 0.00 0.00 42.27 2.67
73 74 4.671377 CGCCTTAAATTTTCAGCATGCTA 58.329 39.130 22.19 4.85 34.76 3.49
130 131 7.095355 TGACTTCGTTAATCTTGAAGCTTTACC 60.095 37.037 0.00 0.00 42.17 2.85
152 153 6.998802 ACCAGCCTAATATTCAGTAGATGAC 58.001 40.000 0.00 0.00 37.77 3.06
338 341 3.495331 TGGCTAATTGTCCATGTGTTGT 58.505 40.909 0.00 0.00 0.00 3.32
342 345 6.210385 TGGCTAATTGTCCATGTGTTGTAAAT 59.790 34.615 0.00 0.00 0.00 1.40
346 349 9.173021 CTAATTGTCCATGTGTTGTAAATAGGA 57.827 33.333 0.00 0.00 0.00 2.94
402 405 5.742453 GTGTTCGACATATATGCTATACCCG 59.258 44.000 12.79 5.60 0.00 5.28
403 406 5.648960 TGTTCGACATATATGCTATACCCGA 59.351 40.000 12.79 7.56 0.00 5.14
414 417 8.998277 ATATGCTATACCCGACATATTCTAGT 57.002 34.615 0.00 0.00 33.06 2.57
486 489 3.726557 TGAGTACGGGTAGGAGAAGAA 57.273 47.619 0.00 0.00 0.00 2.52
489 492 4.834496 TGAGTACGGGTAGGAGAAGAAAAA 59.166 41.667 0.00 0.00 0.00 1.94
595 598 5.186797 TGATTGATTTAATGCCGGGTTTTCT 59.813 36.000 2.18 0.00 0.00 2.52
596 599 4.448537 TGATTTAATGCCGGGTTTTCTG 57.551 40.909 2.18 0.00 0.00 3.02
602 605 0.035739 TGCCGGGTTTTCTGTAGGAC 59.964 55.000 2.18 0.00 0.00 3.85
607 610 2.038033 CGGGTTTTCTGTAGGACAAGGA 59.962 50.000 0.00 0.00 0.00 3.36
610 613 4.891168 GGGTTTTCTGTAGGACAAGGAAAA 59.109 41.667 0.00 0.00 33.04 2.29
644 649 9.768662 GATTTGATTTAGATTATGCCAAACCAT 57.231 29.630 0.00 0.00 0.00 3.55
687 693 3.496784 TGGTGACGTACAACGCCAACT 62.497 52.381 15.91 0.00 42.24 3.16
698 704 2.817258 CAACGCCAACTTCCCTTCAATA 59.183 45.455 0.00 0.00 0.00 1.90
699 705 3.366052 ACGCCAACTTCCCTTCAATAT 57.634 42.857 0.00 0.00 0.00 1.28
700 706 4.497291 ACGCCAACTTCCCTTCAATATA 57.503 40.909 0.00 0.00 0.00 0.86
760 769 8.798402 TGATAATTTGACCTAAAATTCGTGGTT 58.202 29.630 0.00 0.00 39.73 3.67
775 786 9.751542 AAATTCGTGGTTAAACAATAAACATGA 57.248 25.926 0.00 4.48 38.09 3.07
789 800 4.882671 AAACATGACAGATGGAATACGC 57.117 40.909 0.00 0.00 0.00 4.42
791 802 3.872696 ACATGACAGATGGAATACGCAA 58.127 40.909 0.00 0.00 0.00 4.85
793 804 4.883585 ACATGACAGATGGAATACGCAATT 59.116 37.500 0.00 0.00 0.00 2.32
794 805 6.054941 ACATGACAGATGGAATACGCAATTA 58.945 36.000 0.00 0.00 0.00 1.40
795 806 6.203530 ACATGACAGATGGAATACGCAATTAG 59.796 38.462 0.00 0.00 0.00 1.73
796 807 5.912892 TGACAGATGGAATACGCAATTAGA 58.087 37.500 0.00 0.00 0.00 2.10
797 808 5.753438 TGACAGATGGAATACGCAATTAGAC 59.247 40.000 0.00 0.00 0.00 2.59
798 809 5.057149 ACAGATGGAATACGCAATTAGACC 58.943 41.667 0.00 0.00 0.00 3.85
799 810 4.452455 CAGATGGAATACGCAATTAGACCC 59.548 45.833 0.00 0.00 0.00 4.46
802 817 4.196193 TGGAATACGCAATTAGACCCTTG 58.804 43.478 0.00 0.00 0.00 3.61
807 822 2.943033 ACGCAATTAGACCCTTGTATGC 59.057 45.455 0.00 0.00 0.00 3.14
809 824 3.565482 CGCAATTAGACCCTTGTATGCAT 59.435 43.478 3.79 3.79 33.00 3.96
812 827 3.857157 TTAGACCCTTGTATGCATCCC 57.143 47.619 0.19 0.00 0.00 3.85
821 836 5.010012 CCCTTGTATGCATCCCTACATTTTC 59.990 44.000 0.19 0.00 0.00 2.29
822 837 5.010012 CCTTGTATGCATCCCTACATTTTCC 59.990 44.000 0.19 0.00 0.00 3.13
823 838 5.122707 TGTATGCATCCCTACATTTTCCA 57.877 39.130 0.19 0.00 0.00 3.53
824 839 5.132502 TGTATGCATCCCTACATTTTCCAG 58.867 41.667 0.19 0.00 0.00 3.86
825 840 3.017048 TGCATCCCTACATTTTCCAGG 57.983 47.619 0.00 0.00 0.00 4.45
828 843 3.207452 CCCTACATTTTCCAGGGGC 57.793 57.895 0.00 0.00 44.66 5.80
829 844 0.397114 CCCTACATTTTCCAGGGGCC 60.397 60.000 0.00 0.00 44.66 5.80
863 882 0.464554 GGTAGCAGCAAAGCCCTAGG 60.465 60.000 0.06 0.06 34.23 3.02
1060 1111 4.351874 TCGAGATCAAAATCCCATACCC 57.648 45.455 0.00 0.00 31.78 3.69
1062 1113 4.067896 CGAGATCAAAATCCCATACCCAG 58.932 47.826 0.00 0.00 31.78 4.45
1064 1115 3.205056 AGATCAAAATCCCATACCCAGCA 59.795 43.478 0.00 0.00 31.78 4.41
1221 1290 1.889530 GCTCCCGCAAGACAGGTACT 61.890 60.000 0.00 0.00 39.43 2.73
1236 1305 2.242708 AGGTACTGATCCCTTCTCTCGT 59.757 50.000 0.00 0.00 37.18 4.18
1237 1306 2.359531 GGTACTGATCCCTTCTCTCGTG 59.640 54.545 0.00 0.00 0.00 4.35
1239 1308 0.248825 CTGATCCCTTCTCTCGTGCG 60.249 60.000 0.00 0.00 0.00 5.34
1241 1310 3.417275 ATCCCTTCTCTCGTGCGCG 62.417 63.158 14.79 14.79 39.92 6.86
1271 1341 3.554692 CTCGCCGTCGTCCATTGC 61.555 66.667 0.00 0.00 36.96 3.56
1320 1390 0.595053 CGCGGATCAGATGCGTAGTT 60.595 55.000 23.44 0.00 46.32 2.24
1359 1429 2.407090 TGATCAGTTGAGTCAGTTGCG 58.593 47.619 0.00 0.00 0.00 4.85
1553 1631 7.092623 TGGCTGAGGTTTATTCAGGTTAATCTA 60.093 37.037 4.62 0.00 41.82 1.98
1576 1654 5.426504 ACAATTGCCTAGATGAACAGAGAG 58.573 41.667 5.05 0.00 0.00 3.20
1619 1697 3.703556 TGATAGATAGCCTAGCCATGCTC 59.296 47.826 0.00 0.00 40.44 4.26
1626 1704 3.418995 AGCCTAGCCATGCTCATTATTG 58.581 45.455 0.00 0.00 40.44 1.90
1648 1727 5.090139 TGTCTTCTTCATCTTTCCTCTCCT 58.910 41.667 0.00 0.00 0.00 3.69
1649 1729 6.256819 TGTCTTCTTCATCTTTCCTCTCCTA 58.743 40.000 0.00 0.00 0.00 2.94
1717 1798 5.178797 ACGCTTCAGTCTGCATAATTAGTT 58.821 37.500 0.00 0.00 0.00 2.24
1750 1834 1.264288 CTCCGCAAGAAACCACTGAAC 59.736 52.381 0.00 0.00 43.02 3.18
1753 1837 0.673985 GCAAGAAACCACTGAACCCC 59.326 55.000 0.00 0.00 0.00 4.95
1754 1838 2.026905 GCAAGAAACCACTGAACCCCA 61.027 52.381 0.00 0.00 0.00 4.96
1755 1839 2.383855 CAAGAAACCACTGAACCCCAA 58.616 47.619 0.00 0.00 0.00 4.12
1820 1914 3.689649 ACTTTAATCGGCAATTCTTCGCT 59.310 39.130 0.00 0.00 0.00 4.93
2009 2110 1.418264 GTCCTCCCAAATCTAGCTCCC 59.582 57.143 0.00 0.00 0.00 4.30
2058 2159 0.396811 CCCGAGGTGAAAAGTCTGGT 59.603 55.000 0.00 0.00 0.00 4.00
2108 2214 4.248058 CCACCCATGCTGAAAATTTCTTC 58.752 43.478 7.29 0.00 0.00 2.87
2116 2222 7.095102 CCATGCTGAAAATTTCTTCGGAATTTT 60.095 33.333 7.29 5.51 38.41 1.82
2179 2304 3.660621 GCACTTGCACCAGAGACC 58.339 61.111 0.00 0.00 41.59 3.85
2191 2316 1.638133 CAGAGACCAGACTGAATGCG 58.362 55.000 3.32 0.00 36.38 4.73
2197 2322 2.437359 AGACTGAATGCGCTGCCC 60.437 61.111 9.73 0.00 0.00 5.36
2306 2432 1.068264 GCACAGTGTGAGATCTCGTCA 60.068 52.381 27.37 15.59 35.23 4.35
2310 2436 1.542030 AGTGTGAGATCTCGTCACCAC 59.458 52.381 30.02 23.08 43.19 4.16
2390 2523 3.832237 AAGTGTCGTGGGCCTGCTG 62.832 63.158 4.53 0.00 0.00 4.41
2443 2576 5.406175 GCCGCACGGTTAATAATTACTGATA 59.594 40.000 11.27 0.00 37.65 2.15
2481 2614 1.004044 ACCTGCACAGATCTTCCTTGG 59.996 52.381 0.00 0.00 0.00 3.61
2552 2687 0.455295 CGTGTCCTCTTCTCTCGCAC 60.455 60.000 0.00 0.00 0.00 5.34
2708 2849 1.153958 GCCAATGGTTCTCTTGCGC 60.154 57.895 0.00 0.00 0.00 6.09
2720 2861 2.124983 TTGCGCTCATCAGGAGGC 60.125 61.111 9.73 0.00 44.22 4.70
2730 2871 4.444022 GCTCATCAGGAGGCTTTCTATGAA 60.444 45.833 0.00 0.00 44.22 2.57
2731 2872 5.678583 CTCATCAGGAGGCTTTCTATGAAA 58.321 41.667 0.00 0.00 40.13 2.69
2800 2963 5.961396 ACTTGTCTAGAACTCGAGCTTAA 57.039 39.130 13.61 0.00 0.00 1.85
2801 2964 6.518208 ACTTGTCTAGAACTCGAGCTTAAT 57.482 37.500 13.61 0.00 0.00 1.40
2802 2965 6.926313 ACTTGTCTAGAACTCGAGCTTAATT 58.074 36.000 13.61 0.00 0.00 1.40
2806 2969 8.221965 TGTCTAGAACTCGAGCTTAATTATGA 57.778 34.615 13.61 0.00 0.00 2.15
2807 2970 8.851145 TGTCTAGAACTCGAGCTTAATTATGAT 58.149 33.333 13.61 0.00 0.00 2.45
2814 2977 7.445121 ACTCGAGCTTAATTATGATCATGGAA 58.555 34.615 18.72 5.91 0.00 3.53
2843 3006 2.690497 AGGATCATCGTAGGACACTGTG 59.310 50.000 6.19 6.19 0.00 3.66
2845 3008 3.119101 GGATCATCGTAGGACACTGTGTT 60.119 47.826 15.54 2.44 0.00 3.32
2854 3017 4.967084 AGGACACTGTGTTGTAATACCA 57.033 40.909 15.54 0.00 0.00 3.25
2867 3030 4.525996 TGTAATACCAGTACTCGTAGGCA 58.474 43.478 6.50 2.89 0.00 4.75
2948 3118 0.109342 CACCCATGGCTCCTACATCC 59.891 60.000 6.09 0.00 0.00 3.51
3018 3188 1.339055 TGATGATAGCCGGCCAATAGC 60.339 52.381 26.15 13.04 42.60 2.97
3179 3350 0.669619 TCGCCGTGTCAGTGAACTTA 59.330 50.000 0.00 0.00 0.00 2.24
3193 3364 2.104331 CTTACGGCGCTCCATCGT 59.896 61.111 6.90 10.89 40.40 3.73
3203 3374 2.002127 CTCCATCGTTCTCGCTTGC 58.998 57.895 0.00 0.00 36.96 4.01
3238 3414 4.253685 AGGGCGTATATATTCATGTGTGC 58.746 43.478 0.00 0.00 0.00 4.57
3303 3479 3.330267 GAAGAAGCTTCGTGGTGAGAAT 58.670 45.455 19.93 0.00 0.00 2.40
3310 3486 1.141881 CGTGGTGAGAATCCGAGGG 59.858 63.158 0.00 0.00 0.00 4.30
3313 3489 2.506472 GTGAGAATCCGAGGGGGC 59.494 66.667 0.00 0.00 34.94 5.80
3341 3521 3.804193 GGCTGAGGAAAAGGCGCG 61.804 66.667 0.00 0.00 0.00 6.86
3367 3547 4.692625 CGGTTTCTAGATAAGGATGCATGG 59.307 45.833 2.46 0.00 0.00 3.66
3473 3654 0.251742 TTTTGCTGGGGGTGAGATGG 60.252 55.000 0.00 0.00 0.00 3.51
3571 3754 1.818060 TCTGTGTGGTGCCAATAATGC 59.182 47.619 0.00 0.00 0.00 3.56
3572 3755 1.820519 CTGTGTGGTGCCAATAATGCT 59.179 47.619 0.00 0.00 0.00 3.79
3573 3756 3.016031 CTGTGTGGTGCCAATAATGCTA 58.984 45.455 0.00 0.00 0.00 3.49
3574 3757 3.630168 TGTGTGGTGCCAATAATGCTAT 58.370 40.909 0.00 0.00 0.00 2.97
3602 3785 7.132694 TGTATGCTGTTGTGTTCTTTAGATG 57.867 36.000 0.00 0.00 0.00 2.90
3605 3788 3.503748 GCTGTTGTGTTCTTTAGATGGCT 59.496 43.478 0.00 0.00 0.00 4.75
3657 3841 2.811317 GACTCGGCAGCTTCGGTG 60.811 66.667 6.41 0.00 0.00 4.94
3774 3963 0.103572 CATTTGTGCTAGGCCCATGC 59.896 55.000 0.00 1.45 0.00 4.06
3804 3993 1.021202 CAAGTTGTTCGACCTGCCAA 58.979 50.000 0.00 0.00 0.00 4.52
3822 4011 2.041620 CCAAGAAAGGAATGGACCTGGA 59.958 50.000 0.00 0.00 40.49 3.86
3841 4030 5.454755 CCTGGAGGAACAACACTTTCTTAGA 60.455 44.000 0.00 0.00 37.39 2.10
3850 4039 4.640771 ACACTTTCTTAGAGCCCAATCA 57.359 40.909 0.00 0.00 0.00 2.57
3859 4048 3.439857 AGAGCCCAATCAACTTGCTAA 57.560 42.857 0.00 0.00 33.20 3.09
3860 4049 3.350833 AGAGCCCAATCAACTTGCTAAG 58.649 45.455 0.00 0.00 33.20 2.18
3876 4065 7.951591 ACTTGCTAAGTTCACCATTTATTTGT 58.048 30.769 0.00 0.00 39.04 2.83
3877 4066 8.082242 ACTTGCTAAGTTCACCATTTATTTGTC 58.918 33.333 0.00 0.00 39.04 3.18
3880 4069 8.081633 TGCTAAGTTCACCATTTATTTGTCAAG 58.918 33.333 0.00 0.00 0.00 3.02
3881 4070 7.542130 GCTAAGTTCACCATTTATTTGTCAAGG 59.458 37.037 0.00 0.00 0.00 3.61
3883 4072 7.595819 AGTTCACCATTTATTTGTCAAGGAA 57.404 32.000 0.00 0.00 0.00 3.36
3884 4073 7.433680 AGTTCACCATTTATTTGTCAAGGAAC 58.566 34.615 0.00 0.00 0.00 3.62
3886 4075 4.621034 CACCATTTATTTGTCAAGGAACGC 59.379 41.667 0.00 0.00 0.00 4.84
3887 4076 4.173256 CCATTTATTTGTCAAGGAACGCC 58.827 43.478 0.00 0.00 0.00 5.68
3888 4077 4.321601 CCATTTATTTGTCAAGGAACGCCA 60.322 41.667 0.00 0.00 36.29 5.69
3889 4078 4.920640 TTTATTTGTCAAGGAACGCCAA 57.079 36.364 0.00 0.00 36.29 4.52
3890 4079 4.497473 TTATTTGTCAAGGAACGCCAAG 57.503 40.909 0.00 0.00 36.29 3.61
3891 4080 2.045561 TTTGTCAAGGAACGCCAAGA 57.954 45.000 0.00 0.00 36.29 3.02
3892 4081 1.305201 TTGTCAAGGAACGCCAAGAC 58.695 50.000 0.00 0.00 39.36 3.01
3893 4082 0.878523 TGTCAAGGAACGCCAAGACG 60.879 55.000 0.00 0.00 40.82 4.18
3894 4083 0.599204 GTCAAGGAACGCCAAGACGA 60.599 55.000 0.00 0.00 36.29 4.20
3895 4084 0.319555 TCAAGGAACGCCAAGACGAG 60.320 55.000 0.00 0.00 36.29 4.18
3896 4085 0.319555 CAAGGAACGCCAAGACGAGA 60.320 55.000 0.00 0.00 36.29 4.04
3897 4086 0.391597 AAGGAACGCCAAGACGAGAA 59.608 50.000 0.00 0.00 36.29 2.87
3898 4087 0.391597 AGGAACGCCAAGACGAGAAA 59.608 50.000 0.00 0.00 36.29 2.52
3899 4088 0.790814 GGAACGCCAAGACGAGAAAG 59.209 55.000 0.00 0.00 36.70 2.62
3900 4089 0.790814 GAACGCCAAGACGAGAAAGG 59.209 55.000 0.00 0.00 36.70 3.11
3902 4091 0.600255 ACGCCAAGACGAGAAAGGTG 60.600 55.000 0.00 0.00 36.70 4.00
3915 4144 4.440802 CGAGAAAGGTGAAGTAGGAGATGG 60.441 50.000 0.00 0.00 0.00 3.51
3936 4165 6.561737 TGGTGACATGAAAAGCGTTTATAA 57.438 33.333 0.00 0.00 33.40 0.98
3937 4166 6.607689 TGGTGACATGAAAAGCGTTTATAAG 58.392 36.000 0.00 0.00 33.40 1.73
3939 4168 5.511729 GTGACATGAAAAGCGTTTATAAGGC 59.488 40.000 0.00 3.17 42.30 4.35
3941 4170 6.019779 ACATGAAAAGCGTTTATAAGGCAA 57.980 33.333 0.00 0.00 44.29 4.52
3942 4171 5.861787 ACATGAAAAGCGTTTATAAGGCAAC 59.138 36.000 0.00 0.00 44.29 4.17
3956 4185 0.782384 GGCAACTTGTCGTGTACTCG 59.218 55.000 10.97 10.97 0.00 4.18
3957 4186 0.161024 GCAACTTGTCGTGTACTCGC 59.839 55.000 12.30 8.31 0.00 5.03
3959 4188 1.273455 AACTTGTCGTGTACTCGCGC 61.273 55.000 12.30 0.00 45.60 6.86
3960 4189 1.442184 CTTGTCGTGTACTCGCGCT 60.442 57.895 12.30 0.00 45.60 5.92
3961 4190 1.002250 CTTGTCGTGTACTCGCGCTT 61.002 55.000 12.30 0.00 45.60 4.68
3962 4191 0.238025 TTGTCGTGTACTCGCGCTTA 59.762 50.000 12.30 0.00 45.60 3.09
3963 4192 0.448990 TGTCGTGTACTCGCGCTTAT 59.551 50.000 12.30 0.00 45.60 1.73
3964 4193 1.135603 TGTCGTGTACTCGCGCTTATT 60.136 47.619 12.30 0.00 45.60 1.40
3965 4194 1.916000 GTCGTGTACTCGCGCTTATTT 59.084 47.619 12.30 0.00 45.60 1.40
3966 4195 1.915350 TCGTGTACTCGCGCTTATTTG 59.085 47.619 12.30 0.00 45.60 2.32
3972 4201 2.683968 ACTCGCGCTTATTTGAGTTCA 58.316 42.857 5.56 0.00 38.48 3.18
4061 4837 2.430332 CTCCTGCTTTCCTCTCCACTAG 59.570 54.545 0.00 0.00 0.00 2.57
4076 4852 1.729586 ACTAGCAAAGTGTGGGGAGA 58.270 50.000 0.00 0.00 36.93 3.71
4355 5131 1.961180 GACCCTGAGGACGACATGGG 61.961 65.000 0.00 0.00 40.37 4.00
4364 5146 1.434622 GACGACATGGGATGCAGCTG 61.435 60.000 10.11 10.11 0.00 4.24
4391 5173 2.645802 GTGGCACCGGTCCATAATAAA 58.354 47.619 23.09 2.09 35.81 1.40
4396 5178 4.583073 GGCACCGGTCCATAATAAAAAGAT 59.417 41.667 2.59 0.00 0.00 2.40
4411 5193 3.237741 GATGAGGAGGAGGGCCGG 61.238 72.222 0.00 0.00 39.96 6.13
4414 5196 3.471806 GAGGAGGAGGGCCGGTTC 61.472 72.222 1.90 0.00 39.96 3.62
4490 5278 3.487211 TGCCAGGCATCAGTCAGT 58.513 55.556 11.22 0.00 31.71 3.41
4491 5279 1.297689 TGCCAGGCATCAGTCAGTC 59.702 57.895 11.22 0.00 31.71 3.51
4492 5280 1.297689 GCCAGGCATCAGTCAGTCA 59.702 57.895 6.55 0.00 0.00 3.41
4497 5285 1.078143 GCATCAGTCAGTCACCCCC 60.078 63.158 0.00 0.00 0.00 5.40
4558 5347 2.969677 TTCAGTTGCAGAGCGCGTCA 62.970 55.000 8.43 0.00 46.97 4.35
4603 5392 5.067023 TGTTTTCTGTACATGTTGCATGTCA 59.933 36.000 16.70 13.33 33.76 3.58
4718 5650 8.138365 TGTCGTTCATATGTCCTTTAATTAGC 57.862 34.615 1.90 0.00 0.00 3.09
4752 5684 6.310467 GCTATTCAACAGTGATGTTAAGTCGA 59.690 38.462 0.00 0.00 32.48 4.20
4793 5728 6.719370 TGCCTTACTCATTTCTTGGTGTTATT 59.281 34.615 0.00 0.00 0.00 1.40
4794 5729 7.885922 TGCCTTACTCATTTCTTGGTGTTATTA 59.114 33.333 0.00 0.00 0.00 0.98
4795 5730 8.903820 GCCTTACTCATTTCTTGGTGTTATTAT 58.096 33.333 0.00 0.00 0.00 1.28
4861 5796 1.003476 CAAGGCAATTTGTGGGGGC 60.003 57.895 0.00 0.00 0.00 5.80
4990 5925 0.968393 GGGCCGTTAATTCCCTTGCA 60.968 55.000 0.00 0.00 37.08 4.08
5078 6015 4.569162 GCATCGTGTTGCAGGTTATACTTA 59.431 41.667 0.00 0.00 42.31 2.24
5143 6080 1.133513 ACATGGGTTTGGCAGAAGTGA 60.134 47.619 0.00 0.00 0.00 3.41
5162 6099 8.576442 AGAAGTGATTTTTATCCGTTGACATTT 58.424 29.630 0.00 0.00 0.00 2.32
5191 6128 2.543031 CGATGCAATTCAGGCAAGATGG 60.543 50.000 0.00 0.00 45.60 3.51
5201 6141 3.511146 TCAGGCAAGATGGTTCCAAAATC 59.489 43.478 0.00 0.00 0.00 2.17
5203 7691 4.706476 CAGGCAAGATGGTTCCAAAATCTA 59.294 41.667 0.00 0.00 30.50 1.98
5205 7693 4.706962 GGCAAGATGGTTCCAAAATCTACT 59.293 41.667 0.00 0.00 30.50 2.57
5211 7699 8.349568 AGATGGTTCCAAAATCTACTAAAACC 57.650 34.615 0.00 0.00 36.34 3.27
5235 7723 0.320683 CCTCGAACCAGCACATGTCA 60.321 55.000 0.00 0.00 0.00 3.58
5236 7724 1.073964 CTCGAACCAGCACATGTCAG 58.926 55.000 0.00 0.00 0.00 3.51
5237 7725 0.392706 TCGAACCAGCACATGTCAGT 59.607 50.000 0.00 0.00 0.00 3.41
5239 7727 1.726791 CGAACCAGCACATGTCAGTAC 59.273 52.381 0.00 0.00 0.00 2.73
5247 7735 2.936993 GCACATGTCAGTACCCTTCTGG 60.937 54.545 0.00 0.00 41.37 3.86
5260 7748 2.168496 CCTTCTGGTAAGGACAGACGA 58.832 52.381 0.00 0.00 44.07 4.20
5301 7789 5.182001 ACAGTGCAGTTTGGAATAATCACTC 59.818 40.000 0.00 0.00 31.96 3.51
5305 7793 5.412594 TGCAGTTTGGAATAATCACTCTCAC 59.587 40.000 0.00 0.00 0.00 3.51
5323 7826 2.428890 TCACGGCAAGAAAAACACCATT 59.571 40.909 0.00 0.00 0.00 3.16
5332 7835 0.179124 AAAACACCATTGCGTGCGTT 60.179 45.000 5.51 0.00 37.25 4.84
5345 7848 1.959226 TGCGTTCTGACCCTTTCGC 60.959 57.895 0.00 0.00 43.14 4.70
5399 7902 0.916809 AATGGGTTAAGGGGGAGACG 59.083 55.000 0.00 0.00 0.00 4.18
5440 7948 6.127810 TCAAGCACTCTGAATAATGATTGC 57.872 37.500 0.00 0.00 38.13 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 0.182061 AGATGCACATAGGCCCACAG 59.818 55.000 0.00 0.00 0.00 3.66
244 246 7.345653 TGGTCAGAGTTGATCCAAGATATAAGT 59.654 37.037 0.00 0.00 33.27 2.24
252 254 3.054875 TCCATGGTCAGAGTTGATCCAAG 60.055 47.826 12.58 0.00 37.74 3.61
312 315 6.207691 ACACATGGACAATTAGCCATTTAC 57.792 37.500 8.18 0.00 42.03 2.01
316 319 4.088634 ACAACACATGGACAATTAGCCAT 58.911 39.130 0.00 5.62 45.47 4.40
318 321 5.637006 TTACAACACATGGACAATTAGCC 57.363 39.130 0.00 0.00 0.00 3.93
342 345 7.728532 TGAACCACTAGAATATGTATGCTCCTA 59.271 37.037 0.00 0.00 0.00 2.94
346 349 7.495934 GTGTTGAACCACTAGAATATGTATGCT 59.504 37.037 0.00 0.00 32.50 3.79
382 385 5.187687 TGTCGGGTATAGCATATATGTCGA 58.812 41.667 14.14 9.14 0.00 4.20
383 386 5.494632 TGTCGGGTATAGCATATATGTCG 57.505 43.478 14.14 7.33 0.00 4.35
392 395 7.534723 AAACTAGAATATGTCGGGTATAGCA 57.465 36.000 4.02 0.00 0.00 3.49
472 475 9.353999 CAAATTTTATTTTTCTTCTCCTACCCG 57.646 33.333 0.00 0.00 0.00 5.28
529 532 6.375736 TGTCCCGCATTAACTCAATTAAATCA 59.624 34.615 0.00 0.00 36.35 2.57
614 617 9.681692 TTTGGCATAATCTAAATCAAATCGATG 57.318 29.630 0.00 0.00 33.40 3.84
624 629 5.307716 CCCCATGGTTTGGCATAATCTAAAT 59.692 40.000 11.73 0.00 44.97 1.40
635 640 2.364186 CCTCCCCCATGGTTTGGC 60.364 66.667 11.73 0.00 44.97 4.52
644 649 2.931649 GGTTTCGTCCCTCCCCCA 60.932 66.667 0.00 0.00 0.00 4.96
698 704 9.594936 ACTTGACTAGCCAAATATCTCTACTAT 57.405 33.333 0.00 0.00 0.00 2.12
699 705 8.998277 ACTTGACTAGCCAAATATCTCTACTA 57.002 34.615 0.00 0.00 0.00 1.82
700 706 7.906199 ACTTGACTAGCCAAATATCTCTACT 57.094 36.000 0.00 0.00 0.00 2.57
763 772 7.467267 GCGTATTCCATCTGTCATGTTTATTGT 60.467 37.037 0.00 0.00 0.00 2.71
775 786 5.057149 GGTCTAATTGCGTATTCCATCTGT 58.943 41.667 0.00 0.00 0.00 3.41
787 798 2.942376 TGCATACAAGGGTCTAATTGCG 59.058 45.455 0.00 0.00 0.00 4.85
789 800 4.520492 GGGATGCATACAAGGGTCTAATTG 59.480 45.833 11.97 0.00 0.00 2.32
791 802 3.983410 AGGGATGCATACAAGGGTCTAAT 59.017 43.478 11.97 0.00 0.00 1.73
793 804 3.060479 AGGGATGCATACAAGGGTCTA 57.940 47.619 11.97 0.00 0.00 2.59
794 805 1.898863 AGGGATGCATACAAGGGTCT 58.101 50.000 11.97 0.00 0.00 3.85
795 806 2.438021 TGTAGGGATGCATACAAGGGTC 59.562 50.000 11.97 0.00 0.00 4.46
796 807 2.487775 TGTAGGGATGCATACAAGGGT 58.512 47.619 11.97 0.00 0.00 4.34
797 808 3.795688 ATGTAGGGATGCATACAAGGG 57.204 47.619 15.68 0.00 35.64 3.95
798 809 5.010012 GGAAAATGTAGGGATGCATACAAGG 59.990 44.000 15.68 0.00 35.64 3.61
799 810 5.593909 TGGAAAATGTAGGGATGCATACAAG 59.406 40.000 15.68 0.00 35.64 3.16
802 817 4.520492 CCTGGAAAATGTAGGGATGCATAC 59.480 45.833 0.00 0.00 0.00 2.39
812 827 0.751643 CCGGCCCCTGGAAAATGTAG 60.752 60.000 0.00 0.00 0.00 2.74
845 860 1.098129 GCCTAGGGCTTTGCTGCTAC 61.098 60.000 11.72 0.00 46.69 3.58
869 888 1.327690 TTATCTCTCGCGTGCCCCTT 61.328 55.000 5.77 0.00 0.00 3.95
892 911 1.302351 GTGTGCTCTGCTCTGCCTT 60.302 57.895 0.00 0.00 0.00 4.35
893 912 2.346739 GTGTGCTCTGCTCTGCCT 59.653 61.111 0.00 0.00 0.00 4.75
1018 1056 2.791927 GAATTGAACGCGCCTCCC 59.208 61.111 5.73 0.00 0.00 4.30
1019 1057 1.429148 ATCGAATTGAACGCGCCTCC 61.429 55.000 5.73 0.00 0.00 4.30
1021 1059 0.373716 GAATCGAATTGAACGCGCCT 59.626 50.000 5.73 0.00 0.00 5.52
1031 1082 5.822519 TGGGATTTTGATCTCGAATCGAATT 59.177 36.000 6.84 0.00 34.74 2.17
1060 1111 0.458197 CACCTCTCTCGCTCTTGCTG 60.458 60.000 0.00 0.00 36.97 4.41
1062 1113 1.153667 CCACCTCTCTCGCTCTTGC 60.154 63.158 0.00 0.00 0.00 4.01
1064 1115 2.355193 GCCCACCTCTCTCGCTCTT 61.355 63.158 0.00 0.00 0.00 2.85
1221 1290 1.809869 CGCACGAGAGAAGGGATCA 59.190 57.895 0.00 0.00 0.00 2.92
1222 1291 1.590259 GCGCACGAGAGAAGGGATC 60.590 63.158 0.30 0.00 0.00 3.36
1223 1292 2.496817 GCGCACGAGAGAAGGGAT 59.503 61.111 0.30 0.00 0.00 3.85
1224 1293 4.116328 CGCGCACGAGAGAAGGGA 62.116 66.667 8.75 0.00 43.93 4.20
1271 1341 4.227134 CCAGGGCCACGGATCGAG 62.227 72.222 6.18 0.00 0.00 4.04
1359 1429 6.542370 TGGCAACTATAAACCTCTAATTCAGC 59.458 38.462 0.00 0.00 37.61 4.26
1402 1472 7.584122 ACTCAACTGACTAAACTGAAGTAGA 57.416 36.000 0.00 0.00 0.00 2.59
1473 1550 1.308998 CTGTTTTGTCCCGCAGAGTT 58.691 50.000 0.00 0.00 0.00 3.01
1553 1631 5.046014 ACTCTCTGTTCATCTAGGCAATTGT 60.046 40.000 7.40 0.00 0.00 2.71
1576 1654 2.012673 CTGGCCTGCTGAGTATGAAAC 58.987 52.381 3.32 0.00 0.00 2.78
1593 1671 3.435275 TGGCTAGGCTATCTATCACTGG 58.565 50.000 18.18 0.00 0.00 4.00
1619 1697 9.393512 AGAGGAAAGATGAAGAAGACAATAATG 57.606 33.333 0.00 0.00 0.00 1.90
1626 1704 5.675684 AGGAGAGGAAAGATGAAGAAGAC 57.324 43.478 0.00 0.00 0.00 3.01
1717 1798 3.702548 TCTTGCGGAGGCTGTATAAACTA 59.297 43.478 0.00 0.00 40.82 2.24
1791 1884 7.681939 AGAATTGCCGATTAAAGTAAGTTCA 57.318 32.000 0.00 0.00 0.00 3.18
1846 1940 7.754851 AGTCTTTGACCCGTGTAAATTAAAT 57.245 32.000 0.00 0.00 32.18 1.40
2009 2110 5.565637 CGTGTGATAGAATATGTGAGAGGGG 60.566 48.000 0.00 0.00 0.00 4.79
2013 2114 4.537015 CGCGTGTGATAGAATATGTGAGA 58.463 43.478 0.00 0.00 0.00 3.27
2043 2144 2.104963 GAGGTCACCAGACTTTTCACCT 59.895 50.000 0.00 0.00 44.36 4.00
2058 2159 4.758674 CAGCAGAAATTGAGAAAGAGGTCA 59.241 41.667 0.00 0.00 0.00 4.02
2108 2214 4.492791 AACTGAACCCGTTAAAATTCCG 57.507 40.909 0.00 0.00 0.00 4.30
2116 2222 6.891908 AGAAGTATACCTAACTGAACCCGTTA 59.108 38.462 0.00 0.00 0.00 3.18
2172 2297 1.638133 CGCATTCAGTCTGGTCTCTG 58.362 55.000 0.00 0.00 0.00 3.35
2173 2298 0.108424 GCGCATTCAGTCTGGTCTCT 60.108 55.000 0.30 0.00 0.00 3.10
2174 2299 0.108424 AGCGCATTCAGTCTGGTCTC 60.108 55.000 11.47 0.00 0.00 3.36
2175 2300 0.390866 CAGCGCATTCAGTCTGGTCT 60.391 55.000 11.47 0.00 0.00 3.85
2176 2301 1.975363 GCAGCGCATTCAGTCTGGTC 61.975 60.000 11.47 0.00 0.00 4.02
2177 2302 2.037136 GCAGCGCATTCAGTCTGGT 61.037 57.895 11.47 0.00 0.00 4.00
2178 2303 2.758089 GGCAGCGCATTCAGTCTGG 61.758 63.158 11.47 0.00 0.00 3.86
2179 2304 2.758089 GGGCAGCGCATTCAGTCTG 61.758 63.158 11.47 0.00 0.00 3.51
2191 2316 1.973812 GGTTGACTTCCTGGGCAGC 60.974 63.158 0.00 0.00 0.00 5.25
2265 2391 1.678101 GGCGCTGCTAATTCATTCCTT 59.322 47.619 7.64 0.00 0.00 3.36
2390 2523 0.314302 ATGGCGCATCGTAGTAGACC 59.686 55.000 10.83 0.00 0.00 3.85
2443 2576 4.561326 GCAGGTGTGTGGCAAAGATAATTT 60.561 41.667 0.00 0.00 0.00 1.82
2481 2614 7.258441 TCTATATAGATAGATTTGCACGGTGC 58.742 38.462 25.55 25.55 40.47 5.01
2503 2636 6.390721 CAGCACTGCTACTACTTTTTCTCTA 58.609 40.000 2.39 0.00 36.40 2.43
2552 2687 1.699634 TCAAGACCAGACAAGGGAAGG 59.300 52.381 0.00 0.00 0.00 3.46
2670 2811 2.607750 TGGCAGACCACTCCCCTC 60.608 66.667 0.00 0.00 42.67 4.30
2678 2819 1.604308 CATTGGCAGTGGCAGACCA 60.604 57.895 19.65 5.30 46.51 4.02
2708 2849 4.952071 TCATAGAAAGCCTCCTGATGAG 57.048 45.455 0.00 0.00 41.07 2.90
2730 2871 3.064820 GTGTGGTCGAGTGTCACATTTTT 59.935 43.478 5.62 0.00 42.34 1.94
2731 2872 2.612212 GTGTGGTCGAGTGTCACATTTT 59.388 45.455 5.62 0.00 42.34 1.82
2800 2963 6.012245 TCCTGCCATAGTTCCATGATCATAAT 60.012 38.462 8.15 0.00 0.00 1.28
2801 2964 5.310331 TCCTGCCATAGTTCCATGATCATAA 59.690 40.000 8.15 0.00 0.00 1.90
2802 2965 4.845796 TCCTGCCATAGTTCCATGATCATA 59.154 41.667 8.15 0.00 0.00 2.15
2806 2969 3.654321 TGATCCTGCCATAGTTCCATGAT 59.346 43.478 0.00 0.00 0.00 2.45
2807 2970 3.047857 TGATCCTGCCATAGTTCCATGA 58.952 45.455 0.00 0.00 0.00 3.07
2814 2977 2.828520 CCTACGATGATCCTGCCATAGT 59.171 50.000 0.00 0.00 34.89 2.12
2843 3006 5.163622 TGCCTACGAGTACTGGTATTACAAC 60.164 44.000 16.86 5.54 0.00 3.32
2845 3008 4.336433 GTGCCTACGAGTACTGGTATTACA 59.664 45.833 16.86 12.54 0.00 2.41
2854 3017 3.243101 CGATCATTGTGCCTACGAGTACT 60.243 47.826 0.00 0.00 0.00 2.73
2930 3093 0.029681 AGGATGTAGGAGCCATGGGT 60.030 55.000 18.33 18.33 29.50 4.51
3018 3188 3.934457 AAATGTAAAGGTTGCCTTCGG 57.066 42.857 0.45 0.00 43.92 4.30
3022 3192 6.176896 ACAAAACAAAATGTAAAGGTTGCCT 58.823 32.000 0.00 0.00 33.87 4.75
3179 3350 3.701604 GAGAACGATGGAGCGCCGT 62.702 63.158 2.29 0.00 38.24 5.68
3203 3374 2.186826 CGCCCTTTATTCCCAGCCG 61.187 63.158 0.00 0.00 0.00 5.52
3238 3414 1.787057 TTTACCACAAAGGCGCACGG 61.787 55.000 10.83 1.77 43.14 4.94
3303 3479 3.006728 AACATTCGCCCCCTCGGA 61.007 61.111 0.00 0.00 0.00 4.55
3310 3486 0.960364 TCAGCCAAGAACATTCGCCC 60.960 55.000 0.00 0.00 0.00 6.13
3313 3489 2.099141 TCCTCAGCCAAGAACATTCG 57.901 50.000 0.00 0.00 0.00 3.34
3341 3521 3.495001 GCATCCTTATCTAGAAACCGCAC 59.505 47.826 0.00 0.00 0.00 5.34
3386 3566 4.323868 CGATATTCTTCTACCGCGAAATCC 59.676 45.833 8.23 0.00 0.00 3.01
3470 3651 5.558818 GATGAAGTAGCATCTCATTCCCAT 58.441 41.667 0.00 0.00 41.09 4.00
3602 3785 2.038387 TCTGGATAAAAAGGCGAGCC 57.962 50.000 5.89 5.89 0.00 4.70
3605 3788 7.931578 TTTATTCTTCTGGATAAAAAGGCGA 57.068 32.000 0.00 0.00 0.00 5.54
3657 3841 1.139058 ACTTCCACCACTGGCGATATC 59.861 52.381 0.00 0.00 37.49 1.63
3774 3963 2.015227 AACAACTTGGCAACTGGCGG 62.015 55.000 0.00 0.00 46.16 6.13
3780 3969 1.021968 AGGTCGAACAACTTGGCAAC 58.978 50.000 1.87 0.00 0.00 4.17
3804 3993 1.918957 CCTCCAGGTCCATTCCTTTCT 59.081 52.381 0.00 0.00 35.37 2.52
3822 4011 4.390264 GGCTCTAAGAAAGTGTTGTTCCT 58.610 43.478 0.00 0.00 0.00 3.36
3841 4030 3.160679 ACTTAGCAAGTTGATTGGGCT 57.839 42.857 7.16 0.00 39.04 5.19
3859 4048 7.433680 GTTCCTTGACAAATAAATGGTGAACT 58.566 34.615 0.00 0.00 0.00 3.01
3860 4049 6.362283 CGTTCCTTGACAAATAAATGGTGAAC 59.638 38.462 0.00 0.00 0.00 3.18
3862 4051 5.563867 GCGTTCCTTGACAAATAAATGGTGA 60.564 40.000 0.00 0.00 0.00 4.02
3863 4052 4.621034 GCGTTCCTTGACAAATAAATGGTG 59.379 41.667 0.00 0.00 0.00 4.17
3864 4053 4.321675 GGCGTTCCTTGACAAATAAATGGT 60.322 41.667 0.00 0.00 0.00 3.55
3866 4055 4.804108 TGGCGTTCCTTGACAAATAAATG 58.196 39.130 0.00 0.00 0.00 2.32
3867 4056 5.242838 TCTTGGCGTTCCTTGACAAATAAAT 59.757 36.000 0.00 0.00 33.05 1.40
3870 4059 3.500680 GTCTTGGCGTTCCTTGACAAATA 59.499 43.478 0.00 0.00 33.05 1.40
3871 4060 2.293399 GTCTTGGCGTTCCTTGACAAAT 59.707 45.455 0.00 0.00 33.05 2.32
3872 4061 1.673920 GTCTTGGCGTTCCTTGACAAA 59.326 47.619 0.00 0.00 33.05 2.83
3873 4062 1.305201 GTCTTGGCGTTCCTTGACAA 58.695 50.000 0.00 0.00 36.26 3.18
3874 4063 0.878523 CGTCTTGGCGTTCCTTGACA 60.879 55.000 0.00 0.00 36.12 3.58
3875 4064 0.599204 TCGTCTTGGCGTTCCTTGAC 60.599 55.000 0.00 0.00 34.43 3.18
3876 4065 0.319555 CTCGTCTTGGCGTTCCTTGA 60.320 55.000 0.00 0.00 0.00 3.02
3877 4066 0.319555 TCTCGTCTTGGCGTTCCTTG 60.320 55.000 0.00 0.00 0.00 3.61
3880 4069 0.790814 CTTTCTCGTCTTGGCGTTCC 59.209 55.000 0.00 0.00 0.00 3.62
3881 4070 0.790814 CCTTTCTCGTCTTGGCGTTC 59.209 55.000 0.00 0.00 0.00 3.95
3883 4072 0.600255 CACCTTTCTCGTCTTGGCGT 60.600 55.000 0.00 0.00 0.00 5.68
3884 4073 0.319555 TCACCTTTCTCGTCTTGGCG 60.320 55.000 0.00 0.00 0.00 5.69
3886 4075 3.113260 ACTTCACCTTTCTCGTCTTGG 57.887 47.619 0.00 0.00 0.00 3.61
3887 4076 4.022242 TCCTACTTCACCTTTCTCGTCTTG 60.022 45.833 0.00 0.00 0.00 3.02
3888 4077 4.150359 TCCTACTTCACCTTTCTCGTCTT 58.850 43.478 0.00 0.00 0.00 3.01
3889 4078 3.759618 CTCCTACTTCACCTTTCTCGTCT 59.240 47.826 0.00 0.00 0.00 4.18
3890 4079 3.757493 TCTCCTACTTCACCTTTCTCGTC 59.243 47.826 0.00 0.00 0.00 4.20
3891 4080 3.764218 TCTCCTACTTCACCTTTCTCGT 58.236 45.455 0.00 0.00 0.00 4.18
3892 4081 4.440802 CCATCTCCTACTTCACCTTTCTCG 60.441 50.000 0.00 0.00 0.00 4.04
3893 4082 4.468153 ACCATCTCCTACTTCACCTTTCTC 59.532 45.833 0.00 0.00 0.00 2.87
3894 4083 4.223923 CACCATCTCCTACTTCACCTTTCT 59.776 45.833 0.00 0.00 0.00 2.52
3895 4084 4.223032 TCACCATCTCCTACTTCACCTTTC 59.777 45.833 0.00 0.00 0.00 2.62
3896 4085 4.020128 GTCACCATCTCCTACTTCACCTTT 60.020 45.833 0.00 0.00 0.00 3.11
3897 4086 3.515901 GTCACCATCTCCTACTTCACCTT 59.484 47.826 0.00 0.00 0.00 3.50
3898 4087 3.100671 GTCACCATCTCCTACTTCACCT 58.899 50.000 0.00 0.00 0.00 4.00
3899 4088 2.832129 TGTCACCATCTCCTACTTCACC 59.168 50.000 0.00 0.00 0.00 4.02
3900 4089 4.160439 TCATGTCACCATCTCCTACTTCAC 59.840 45.833 0.00 0.00 0.00 3.18
3902 4091 5.344743 TTCATGTCACCATCTCCTACTTC 57.655 43.478 0.00 0.00 0.00 3.01
3915 4144 5.511729 GCCTTATAAACGCTTTTCATGTCAC 59.488 40.000 0.00 0.00 0.00 3.67
3922 4151 5.918576 ACAAGTTGCCTTATAAACGCTTTTC 59.081 36.000 1.81 0.00 0.00 2.29
3928 4157 4.084223 ACACGACAAGTTGCCTTATAAACG 60.084 41.667 1.81 0.00 0.00 3.60
3929 4158 5.352643 ACACGACAAGTTGCCTTATAAAC 57.647 39.130 1.81 0.00 0.00 2.01
3934 4163 3.645884 GAGTACACGACAAGTTGCCTTA 58.354 45.455 1.81 0.00 0.00 2.69
3935 4164 2.480845 GAGTACACGACAAGTTGCCTT 58.519 47.619 1.81 0.00 0.00 4.35
3936 4165 1.602165 CGAGTACACGACAAGTTGCCT 60.602 52.381 6.90 0.00 35.09 4.75
3937 4166 0.782384 CGAGTACACGACAAGTTGCC 59.218 55.000 6.90 0.00 35.09 4.52
3939 4168 0.429736 CGCGAGTACACGACAAGTTG 59.570 55.000 17.12 0.00 35.09 3.16
3941 4170 1.728426 GCGCGAGTACACGACAAGT 60.728 57.895 17.12 0.00 35.09 3.16
3942 4171 1.002250 AAGCGCGAGTACACGACAAG 61.002 55.000 17.12 5.39 35.09 3.16
3943 4172 0.238025 TAAGCGCGAGTACACGACAA 59.762 50.000 17.12 0.00 35.09 3.18
3944 4173 0.448990 ATAAGCGCGAGTACACGACA 59.551 50.000 17.12 0.00 35.09 4.35
3945 4174 1.542544 AATAAGCGCGAGTACACGAC 58.457 50.000 17.12 7.41 35.09 4.34
3946 4175 1.915350 CAAATAAGCGCGAGTACACGA 59.085 47.619 17.12 0.00 35.09 4.35
3947 4176 1.915350 TCAAATAAGCGCGAGTACACG 59.085 47.619 12.10 8.44 0.00 4.49
3948 4177 2.921754 ACTCAAATAAGCGCGAGTACAC 59.078 45.455 12.10 0.00 36.97 2.90
3952 4181 2.683968 TGAACTCAAATAAGCGCGAGT 58.316 42.857 12.10 4.44 40.38 4.18
3955 4184 4.002267 TGAATGAACTCAAATAAGCGCG 57.998 40.909 0.00 0.00 0.00 6.86
3956 4185 4.558860 GGTTGAATGAACTCAAATAAGCGC 59.441 41.667 0.00 0.00 37.08 5.92
3957 4186 5.698832 TGGTTGAATGAACTCAAATAAGCG 58.301 37.500 0.00 0.00 37.08 4.68
3958 4187 7.945033 TTTGGTTGAATGAACTCAAATAAGC 57.055 32.000 0.00 0.00 37.08 3.09
4061 4837 0.673985 GGTTTCTCCCCACACTTTGC 59.326 55.000 0.00 0.00 0.00 3.68
4076 4852 3.011566 TGTTGTCACTGTCATGGGTTT 57.988 42.857 0.00 0.00 0.00 3.27
4166 4942 1.832608 ACAGGTCTGCACGTCCTCA 60.833 57.895 0.00 0.00 0.00 3.86
4296 5072 4.175489 CGACGACGATGACCGGCT 62.175 66.667 0.00 0.00 46.22 5.52
4297 5073 4.170062 TCGACGACGATGACCGGC 62.170 66.667 5.75 0.00 43.81 6.13
4355 5131 1.588082 CACCAAACCCAGCTGCATC 59.412 57.895 8.66 0.00 0.00 3.91
4364 5146 4.906537 ACCGGTGCCACCAAACCC 62.907 66.667 15.45 0.00 38.47 4.11
4391 5173 1.341156 CGGCCCTCCTCCTCATCTTT 61.341 60.000 0.00 0.00 0.00 2.52
4396 5178 4.332543 AACCGGCCCTCCTCCTCA 62.333 66.667 0.00 0.00 0.00 3.86
4411 5193 5.476614 CCACAGGGTACTTACTTACTGAAC 58.523 45.833 0.00 0.00 0.00 3.18
4484 5272 1.616628 GGGATGGGGGTGACTGACT 60.617 63.158 0.00 0.00 0.00 3.41
4485 5273 2.680370 GGGGATGGGGGTGACTGAC 61.680 68.421 0.00 0.00 0.00 3.51
4558 5347 3.845781 TTCAGACTTTCAGAGGCTTGT 57.154 42.857 0.00 0.00 42.85 3.16
4718 5650 3.434641 CACTGTTGAATAGCAGGTGACAG 59.565 47.826 0.00 0.00 39.22 3.51
4793 5728 4.504864 CCCTTCATTTCGCCATACCAGATA 60.505 45.833 0.00 0.00 0.00 1.98
4794 5729 3.480470 CCTTCATTTCGCCATACCAGAT 58.520 45.455 0.00 0.00 0.00 2.90
4795 5730 2.421388 CCCTTCATTTCGCCATACCAGA 60.421 50.000 0.00 0.00 0.00 3.86
4861 5796 1.751351 TCGTGCTCCTCCATTACTCTG 59.249 52.381 0.00 0.00 0.00 3.35
5053 5990 1.155889 TAACCTGCAACACGATGCTG 58.844 50.000 12.30 11.43 46.54 4.41
5078 6015 3.194116 CAGAAGCTGGTGCCAAACAATAT 59.806 43.478 0.00 0.00 40.80 1.28
5143 6080 8.356657 TCTTGTCAAATGTCAACGGATAAAAAT 58.643 29.630 0.00 0.00 0.00 1.82
5162 6099 2.743664 CCTGAATTGCATCGTCTTGTCA 59.256 45.455 0.00 0.00 0.00 3.58
5191 6128 7.360691 GGTCTCGGTTTTAGTAGATTTTGGAAC 60.361 40.741 0.00 0.00 0.00 3.62
5220 7708 2.076863 GGTACTGACATGTGCTGGTTC 58.923 52.381 1.15 0.00 0.00 3.62
5221 7709 1.271379 GGGTACTGACATGTGCTGGTT 60.271 52.381 1.15 0.00 0.00 3.67
5223 7711 0.615331 AGGGTACTGACATGTGCTGG 59.385 55.000 1.15 0.00 0.00 4.85
5239 7727 1.204941 CGTCTGTCCTTACCAGAAGGG 59.795 57.143 3.58 0.00 40.44 3.95
5247 7735 1.207329 AGGCCATTCGTCTGTCCTTAC 59.793 52.381 5.01 0.00 0.00 2.34
5251 7739 0.036388 TTCAGGCCATTCGTCTGTCC 60.036 55.000 5.01 0.00 0.00 4.02
5256 7744 2.151202 TGTTTCTTCAGGCCATTCGTC 58.849 47.619 5.01 0.00 0.00 4.20
5258 7746 2.293122 TGTTGTTTCTTCAGGCCATTCG 59.707 45.455 5.01 0.00 0.00 3.34
5260 7748 3.068590 CACTGTTGTTTCTTCAGGCCATT 59.931 43.478 5.01 0.00 34.02 3.16
5301 7789 1.403679 TGGTGTTTTTCTTGCCGTGAG 59.596 47.619 0.00 0.00 0.00 3.51
5305 7793 1.526464 GCAATGGTGTTTTTCTTGCCG 59.474 47.619 0.00 0.00 36.96 5.69
5323 7826 2.933878 AAAGGGTCAGAACGCACGCA 62.934 55.000 0.00 0.00 40.65 5.24
5332 7835 0.319555 CGAACAGCGAAAGGGTCAGA 60.320 55.000 0.00 0.00 44.57 3.27
5345 7848 2.811317 GCTGTCTCCGGCGAACAG 60.811 66.667 23.51 23.51 32.22 3.16
5395 7898 1.556911 AGGACATGCTTTCATCCGTCT 59.443 47.619 0.00 0.00 30.59 4.18
5399 7902 4.023365 GCTTGATAGGACATGCTTTCATCC 60.023 45.833 0.00 0.00 37.75 3.51


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

AutoCloner maintained by Alex Coulton.