Multiple sequence alignment - TraesCS2B01G246100

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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 TraesCS2B01G246100 chr2B 100.000 4610 0 0 1 4610 250525411 250520802 0.000000e+00 8514.0
1 TraesCS2B01G246100 chr2A 89.465 2468 114 60 1615 4008 209208059 209205664 0.000000e+00 2983.0
2 TraesCS2B01G246100 chr2A 86.844 1619 79 50 1 1576 209209661 209208134 0.000000e+00 1687.0
3 TraesCS2B01G246100 chr2D 88.011 2277 118 48 2342 4541 194657967 194655769 0.000000e+00 2549.0
4 TraesCS2B01G246100 chr2D 87.809 1296 55 45 310 1576 194659963 194658742 0.000000e+00 1423.0
5 TraesCS2B01G246100 chr2D 94.669 619 19 6 1610 2224 194658672 194658064 0.000000e+00 948.0
6 TraesCS2B01G246100 chr7B 94.953 1268 51 7 1943 3206 375545375 375544117 0.000000e+00 1975.0
7 TraesCS2B01G246100 chr7B 94.444 72 2 2 4540 4610 616797714 616797784 4.880000e-20 110.0
8 TraesCS2B01G246100 chr7B 89.744 78 2 2 4539 4610 116382313 116382236 1.370000e-15 95.3
9 TraesCS2B01G246100 chr4B 93.056 72 3 2 4540 4610 69928304 69928374 2.270000e-18 104.0
10 TraesCS2B01G246100 chr7D 86.486 74 8 2 4538 4610 519711952 519711880 3.820000e-11 80.5
11 TraesCS2B01G246100 chr6A 86.486 74 6 4 4539 4610 572023769 572023698 1.380000e-10 78.7
12 TraesCS2B01G246100 chr5B 100.000 35 0 0 4576 4610 134908121 134908155 1.070000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G246100 chr2B 250520802 250525411 4609 True 8514 8514 100.0000 1 4610 1 chr2B.!!$R1 4609
1 TraesCS2B01G246100 chr2A 209205664 209209661 3997 True 2335 2983 88.1545 1 4008 2 chr2A.!!$R1 4007
2 TraesCS2B01G246100 chr2D 194655769 194659963 4194 True 1640 2549 90.1630 310 4541 3 chr2D.!!$R1 4231
3 TraesCS2B01G246100 chr7B 375544117 375545375 1258 True 1975 1975 94.9530 1943 3206 1 chr7B.!!$R2 1263

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
940 1003 0.104409 ATTTATCCCTCCTCCGGCCT 60.104 55.000 0.0 0.0 0.00 5.19 F
941 1004 1.054406 TTTATCCCTCCTCCGGCCTG 61.054 60.000 0.0 0.0 0.00 4.85 F
2541 2715 1.741706 CAGCACCTCCAATGCAGTTAG 59.258 52.381 0.0 0.0 45.92 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2670 2849 1.184970 AAAGAAACCGGTGGGCATGG 61.185 55.0 8.52 0.00 36.48 3.66 R
2737 2916 1.846007 ACTCTGTGGCCTCTGACTAG 58.154 55.0 3.32 1.13 0.00 2.57 R
4104 4391 0.322098 TTGACGTGCTTGTATGGGGG 60.322 55.0 0.00 0.00 0.00 5.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.334960 CCGACTGCACCAAATGTTGAC 60.335 52.381 0.00 0.00 0.00 3.18
30 31 2.979813 GCACCAAATGTTGACAATCGAC 59.020 45.455 0.00 0.00 0.00 4.20
39 40 6.902224 ATGTTGACAATCGACGATTTATCA 57.098 33.333 20.12 21.19 33.44 2.15
83 84 6.569179 ACAATTTTCTATTAACACACGGCT 57.431 33.333 0.00 0.00 0.00 5.52
115 116 9.753674 AAGGTAATGTTTAAAGATGGATTCTGA 57.246 29.630 0.00 0.00 33.93 3.27
116 117 9.178758 AGGTAATGTTTAAAGATGGATTCTGAC 57.821 33.333 0.00 0.00 33.93 3.51
121 122 2.611225 AAGATGGATTCTGACTCCGC 57.389 50.000 9.21 4.53 35.41 5.54
138 139 5.357257 ACTCCGCGTCAATATTTAGAACAT 58.643 37.500 4.92 0.00 0.00 2.71
139 140 6.509656 ACTCCGCGTCAATATTTAGAACATA 58.490 36.000 4.92 0.00 0.00 2.29
140 141 6.420008 ACTCCGCGTCAATATTTAGAACATAC 59.580 38.462 4.92 0.00 0.00 2.39
255 257 4.752101 GGAGATAATTCGAATCCACCACAG 59.248 45.833 11.83 0.00 0.00 3.66
259 261 0.684535 TTCGAATCCACCACAGCAGA 59.315 50.000 0.00 0.00 0.00 4.26
260 262 0.684535 TCGAATCCACCACAGCAGAA 59.315 50.000 0.00 0.00 0.00 3.02
261 263 1.071542 TCGAATCCACCACAGCAGAAA 59.928 47.619 0.00 0.00 0.00 2.52
262 264 1.197721 CGAATCCACCACAGCAGAAAC 59.802 52.381 0.00 0.00 0.00 2.78
263 265 1.541588 GAATCCACCACAGCAGAAACC 59.458 52.381 0.00 0.00 0.00 3.27
264 266 0.251341 ATCCACCACAGCAGAAACCC 60.251 55.000 0.00 0.00 0.00 4.11
265 267 1.152777 CCACCACAGCAGAAACCCA 60.153 57.895 0.00 0.00 0.00 4.51
266 268 0.540365 CCACCACAGCAGAAACCCAT 60.540 55.000 0.00 0.00 0.00 4.00
267 269 0.599558 CACCACAGCAGAAACCCATG 59.400 55.000 0.00 0.00 0.00 3.66
268 270 0.478072 ACCACAGCAGAAACCCATGA 59.522 50.000 0.00 0.00 0.00 3.07
269 271 1.076024 ACCACAGCAGAAACCCATGAT 59.924 47.619 0.00 0.00 0.00 2.45
270 272 1.475280 CCACAGCAGAAACCCATGATG 59.525 52.381 0.00 0.00 38.73 3.07
271 273 1.475280 CACAGCAGAAACCCATGATGG 59.525 52.381 3.98 3.98 37.15 3.51
272 274 0.458669 CAGCAGAAACCCATGATGGC 59.541 55.000 5.79 0.00 35.79 4.40
273 275 0.333993 AGCAGAAACCCATGATGGCT 59.666 50.000 5.79 0.00 35.79 4.75
274 276 1.188863 GCAGAAACCCATGATGGCTT 58.811 50.000 5.79 1.01 35.79 4.35
275 277 1.551883 GCAGAAACCCATGATGGCTTT 59.448 47.619 5.79 5.06 35.79 3.51
333 335 1.750778 GGAACGGTGGATAACGGACTA 59.249 52.381 0.00 0.00 33.48 2.59
334 336 2.223665 GGAACGGTGGATAACGGACTAG 60.224 54.545 0.00 0.00 33.48 2.57
341 343 4.759183 GGTGGATAACGGACTAGTAGTAGG 59.241 50.000 1.88 0.67 0.00 3.18
342 344 4.215185 GTGGATAACGGACTAGTAGTAGGC 59.785 50.000 1.88 5.69 32.73 3.93
436 440 2.814336 GTCATCCAGAATAATTCCGGGC 59.186 50.000 0.00 0.00 0.00 6.13
515 531 4.483711 GGTCGTTACCGCCAGTAC 57.516 61.111 0.00 0.00 35.62 2.73
516 532 1.153765 GGTCGTTACCGCCAGTACC 60.154 63.158 0.00 0.00 35.62 3.34
518 534 0.457337 GTCGTTACCGCCAGTACCAG 60.457 60.000 0.00 0.00 0.00 4.00
656 700 0.827507 AATTATCCCGGCCCATGCAC 60.828 55.000 0.00 0.00 40.13 4.57
711 755 2.102161 CACGCGCCCAAATAAGCC 59.898 61.111 5.73 0.00 0.00 4.35
712 756 2.045340 ACGCGCCCAAATAAGCCT 60.045 55.556 5.73 0.00 0.00 4.58
778 834 4.154347 GCCGTGAGCAGGAGGAGG 62.154 72.222 0.00 0.00 42.97 4.30
779 835 4.154347 CCGTGAGCAGGAGGAGGC 62.154 72.222 0.00 0.00 0.00 4.70
780 836 3.073735 CGTGAGCAGGAGGAGGCT 61.074 66.667 0.00 0.00 44.48 4.58
781 837 2.583520 GTGAGCAGGAGGAGGCTG 59.416 66.667 0.00 0.00 41.22 4.85
782 838 2.686470 TGAGCAGGAGGAGGCTGG 60.686 66.667 0.00 0.00 41.22 4.85
783 839 4.173924 GAGCAGGAGGAGGCTGGC 62.174 72.222 0.00 0.00 41.22 4.85
785 841 4.486503 GCAGGAGGAGGCTGGCAG 62.487 72.222 10.94 10.94 0.00 4.85
786 842 3.795041 CAGGAGGAGGCTGGCAGG 61.795 72.222 17.64 0.00 0.00 4.85
810 866 3.667282 AGGGACGACGACACCACG 61.667 66.667 0.00 0.00 39.31 4.94
818 874 2.011453 ACGACACCACGTCAAAAGC 58.989 52.632 0.00 0.00 45.70 3.51
821 877 1.822581 GACACCACGTCAAAAGCAAC 58.177 50.000 0.00 0.00 44.69 4.17
822 878 1.131504 GACACCACGTCAAAAGCAACA 59.868 47.619 0.00 0.00 44.69 3.33
827 885 0.751643 ACGTCAAAAGCAACAGGCCT 60.752 50.000 0.00 0.00 46.50 5.19
884 942 5.880332 TCCGATTCTCAAGTTTTAATCCCAG 59.120 40.000 0.00 0.00 0.00 4.45
915 978 4.742649 TCCGGCCTCTCTCTGCGT 62.743 66.667 0.00 0.00 0.00 5.24
934 997 3.808174 GCGTGTGTAATTTATCCCTCCTC 59.192 47.826 0.00 0.00 0.00 3.71
935 998 4.377897 CGTGTGTAATTTATCCCTCCTCC 58.622 47.826 0.00 0.00 0.00 4.30
936 999 4.377897 GTGTGTAATTTATCCCTCCTCCG 58.622 47.826 0.00 0.00 0.00 4.63
937 1000 3.389983 TGTGTAATTTATCCCTCCTCCGG 59.610 47.826 0.00 0.00 0.00 5.14
938 1001 2.370849 TGTAATTTATCCCTCCTCCGGC 59.629 50.000 0.00 0.00 0.00 6.13
939 1002 0.771755 AATTTATCCCTCCTCCGGCC 59.228 55.000 0.00 0.00 0.00 6.13
940 1003 0.104409 ATTTATCCCTCCTCCGGCCT 60.104 55.000 0.00 0.00 0.00 5.19
941 1004 1.054406 TTTATCCCTCCTCCGGCCTG 61.054 60.000 0.00 0.00 0.00 4.85
944 1007 4.860881 CCCTCCTCCGGCCTGCTA 62.861 72.222 0.00 0.00 0.00 3.49
945 1008 3.541713 CCTCCTCCGGCCTGCTAC 61.542 72.222 0.00 0.00 0.00 3.58
946 1009 3.905678 CTCCTCCGGCCTGCTACG 61.906 72.222 0.00 0.00 0.00 3.51
1046 1112 2.697425 CGTCACGCAGCTATGTGC 59.303 61.111 11.61 0.00 40.77 4.57
1155 1221 2.286523 CCTCGTCTGGGACCAGCTT 61.287 63.158 13.51 0.00 43.31 3.74
1261 1327 2.501128 CCATGGATGACGACGCCT 59.499 61.111 5.56 0.00 0.00 5.52
1431 1497 4.520179 TCTGTCGACCTGCTAGTGTAATA 58.480 43.478 14.12 0.00 0.00 0.98
1432 1498 4.945543 TCTGTCGACCTGCTAGTGTAATAA 59.054 41.667 14.12 0.00 0.00 1.40
1433 1499 5.593095 TCTGTCGACCTGCTAGTGTAATAAT 59.407 40.000 14.12 0.00 0.00 1.28
1472 1541 8.871629 TTGTTTTGGTACTATCATGGTTATGT 57.128 30.769 0.00 0.00 35.73 2.29
1476 1545 5.364778 TGGTACTATCATGGTTATGTGTGC 58.635 41.667 0.00 0.00 35.73 4.57
1550 1619 6.606395 AGAAGCAATTGCCAGAATCTATTTCT 59.394 34.615 26.45 19.59 41.22 2.52
1567 1637 8.645814 TCTATTTCTCAGTACAACCTACAGAA 57.354 34.615 0.00 0.00 0.00 3.02
1576 1646 7.936847 TCAGTACAACCTACAGAAACATTTCAT 59.063 33.333 7.10 0.00 39.61 2.57
1578 1648 8.784043 AGTACAACCTACAGAAACATTTCATTC 58.216 33.333 7.10 0.00 39.61 2.67
1579 1649 7.823745 ACAACCTACAGAAACATTTCATTCT 57.176 32.000 7.10 0.00 39.61 2.40
1581 1651 7.040409 ACAACCTACAGAAACATTTCATTCTCC 60.040 37.037 7.10 0.00 39.61 3.71
1582 1652 6.784031 ACCTACAGAAACATTTCATTCTCCT 58.216 36.000 7.10 0.00 39.61 3.69
1584 1654 8.043710 ACCTACAGAAACATTTCATTCTCCTAG 58.956 37.037 7.10 0.00 39.61 3.02
1585 1655 8.260818 CCTACAGAAACATTTCATTCTCCTAGA 58.739 37.037 7.10 0.00 39.61 2.43
1586 1656 9.658799 CTACAGAAACATTTCATTCTCCTAGAA 57.341 33.333 7.10 0.00 39.61 2.10
1599 1669 5.697473 TCTCCTAGAATGAATGCTCTACG 57.303 43.478 0.00 0.00 0.00 3.51
1601 1671 4.470602 TCCTAGAATGAATGCTCTACGGA 58.529 43.478 0.00 0.00 0.00 4.69
1602 1672 4.520874 TCCTAGAATGAATGCTCTACGGAG 59.479 45.833 0.00 0.00 42.18 4.63
1605 1675 3.701542 AGAATGAATGCTCTACGGAGACA 59.298 43.478 0.00 0.00 41.86 3.41
1606 1676 4.160439 AGAATGAATGCTCTACGGAGACAA 59.840 41.667 0.00 0.00 41.86 3.18
1607 1677 3.510388 TGAATGCTCTACGGAGACAAG 57.490 47.619 0.00 0.00 41.86 3.16
1671 1777 2.422479 CAGAACTGCATGTCCATTCAGG 59.578 50.000 10.83 0.00 36.58 3.86
1748 1854 2.356278 GGGGGCTTGCAGATGACA 59.644 61.111 0.00 0.00 0.00 3.58
1772 1878 3.370315 GCCTGAATCTGATGGACAAGACT 60.370 47.826 0.00 0.00 0.00 3.24
1835 1941 2.168496 GTGGCAGGTACTCACTCACTA 58.832 52.381 0.00 0.00 34.60 2.74
2284 2414 5.509716 TCAATGCTTTAGCTGAATGATGG 57.490 39.130 0.00 0.00 42.66 3.51
2293 2423 8.786898 GCTTTAGCTGAATGATGGATATTGTTA 58.213 33.333 0.00 0.00 38.21 2.41
2512 2684 2.386064 TTTCGGACGGTCTTGGGTGG 62.386 60.000 8.23 0.00 0.00 4.61
2541 2715 1.741706 CAGCACCTCCAATGCAGTTAG 59.258 52.381 0.00 0.00 45.92 2.34
2670 2849 3.515330 TTAATCTCGGACGGGTCTTTC 57.485 47.619 0.00 0.00 0.00 2.62
2828 3010 2.461110 GCGACAATAGCCCACACCG 61.461 63.158 0.00 0.00 0.00 4.94
2847 3029 3.053455 CCGAAACCTGATCTAATCGAGC 58.947 50.000 0.00 0.00 32.38 5.03
2940 3122 2.900547 CCCATTTAAGCCAGTGGGG 58.099 57.895 12.15 0.97 46.08 4.96
2995 3177 1.821753 AGGACTGACCGAACAGATCTG 59.178 52.381 21.37 21.37 44.74 2.90
3016 3198 0.527565 GGCGATGAGTGTTTGCCAAT 59.472 50.000 0.00 0.00 42.36 3.16
3032 3231 9.255304 TGTTTGCCAATAACAAGATAGAAAAAC 57.745 29.630 0.00 0.00 32.89 2.43
3043 3242 9.892130 AACAAGATAGAAAAACGGAGAAGATAT 57.108 29.630 0.00 0.00 0.00 1.63
3044 3243 9.319143 ACAAGATAGAAAAACGGAGAAGATATG 57.681 33.333 0.00 0.00 0.00 1.78
3089 3293 2.271800 CCACAGGTCGAAACTATGCTC 58.728 52.381 0.00 0.00 0.00 4.26
3237 3449 3.774734 AGTTCCATGGATGCATGCATAT 58.225 40.909 32.27 20.42 36.67 1.78
3238 3450 4.925836 AGTTCCATGGATGCATGCATATA 58.074 39.130 32.27 23.26 36.67 0.86
3239 3451 4.703575 AGTTCCATGGATGCATGCATATAC 59.296 41.667 32.27 24.95 36.67 1.47
3240 3452 4.579647 TCCATGGATGCATGCATATACT 57.420 40.909 32.27 12.25 36.67 2.12
3241 3453 4.266714 TCCATGGATGCATGCATATACTG 58.733 43.478 32.27 23.74 36.67 2.74
3266 3478 8.112822 TGCATAAGAGATACTCTATAGGAGCTT 58.887 37.037 0.00 0.00 45.48 3.74
3267 3479 8.621286 GCATAAGAGATACTCTATAGGAGCTTC 58.379 40.741 0.00 0.00 45.48 3.86
3268 3480 9.679661 CATAAGAGATACTCTATAGGAGCTTCA 57.320 37.037 0.00 0.00 45.48 3.02
3270 3482 8.807948 AAGAGATACTCTATAGGAGCTTCATC 57.192 38.462 0.00 0.00 45.48 2.92
3271 3483 8.162848 AGAGATACTCTATAGGAGCTTCATCT 57.837 38.462 0.00 0.00 45.48 2.90
3272 3484 8.049117 AGAGATACTCTATAGGAGCTTCATCTG 58.951 40.741 0.00 0.00 45.48 2.90
3273 3485 7.698912 AGATACTCTATAGGAGCTTCATCTGT 58.301 38.462 0.00 0.00 45.48 3.41
3274 3486 8.170061 AGATACTCTATAGGAGCTTCATCTGTT 58.830 37.037 0.00 0.00 45.48 3.16
3275 3487 6.648879 ACTCTATAGGAGCTTCATCTGTTC 57.351 41.667 0.00 0.00 45.48 3.18
3276 3488 6.132658 ACTCTATAGGAGCTTCATCTGTTCA 58.867 40.000 0.00 0.00 45.48 3.18
3288 3511 7.014326 AGCTTCATCTGTTCATCATGCATAAAT 59.986 33.333 0.00 0.00 0.00 1.40
3316 3539 4.081972 GGTGCATCTCTTTCAGAGTGTCTA 60.082 45.833 0.00 0.00 42.83 2.59
3328 3551 9.145865 CTTTCAGAGTGTCTATACCTTTCTTTC 57.854 37.037 0.00 0.00 0.00 2.62
3337 3560 6.824196 GTCTATACCTTTCTTTCCCTTTGGAG 59.176 42.308 0.00 0.00 43.07 3.86
3340 3563 2.893489 CCTTTCTTTCCCTTTGGAGTGG 59.107 50.000 0.00 0.00 43.07 4.00
3351 3574 4.324563 CCCTTTGGAGTGGAATGTCTGTAT 60.325 45.833 0.00 0.00 0.00 2.29
3354 3577 4.908601 TGGAGTGGAATGTCTGTATTGT 57.091 40.909 0.00 0.00 0.00 2.71
3368 3591 5.014202 TCTGTATTGTACCTAGTGCAGTGA 58.986 41.667 3.69 0.00 28.83 3.41
3369 3592 5.479027 TCTGTATTGTACCTAGTGCAGTGAA 59.521 40.000 3.69 0.00 28.83 3.18
3441 3672 1.541147 AGATGCCGTTTGTTGACATGG 59.459 47.619 0.00 0.00 0.00 3.66
3610 3841 3.068732 CGAGCCCATCATAGACTTCTGAA 59.931 47.826 0.00 0.00 0.00 3.02
3805 4072 1.273887 GCATCTCGCATGTACACGC 59.726 57.895 3.27 3.27 41.79 5.34
3908 4194 1.377594 TAGTGGTAGCTCGCACGGA 60.378 57.895 0.00 0.00 0.00 4.69
3909 4195 1.651240 TAGTGGTAGCTCGCACGGAC 61.651 60.000 0.00 0.00 0.00 4.79
3957 4243 5.536554 TGCAGATTCAAGATCTTTTCGAC 57.463 39.130 4.86 2.55 0.00 4.20
4027 4313 7.938140 TCCTCCTTGAAATGGTTATAGTTTG 57.062 36.000 0.00 0.00 31.98 2.93
4029 4315 7.610305 TCCTCCTTGAAATGGTTATAGTTTGTC 59.390 37.037 0.00 0.00 31.98 3.18
4032 4318 8.383175 TCCTTGAAATGGTTATAGTTTGTCTCT 58.617 33.333 0.00 0.00 31.98 3.10
4034 4320 9.442047 CTTGAAATGGTTATAGTTTGTCTCTCT 57.558 33.333 0.00 0.00 0.00 3.10
4035 4321 9.436957 TTGAAATGGTTATAGTTTGTCTCTCTC 57.563 33.333 0.00 0.00 0.00 3.20
4039 4325 6.178324 TGGTTATAGTTTGTCTCTCTCTCGA 58.822 40.000 0.00 0.00 0.00 4.04
4046 4332 5.010112 AGTTTGTCTCTCTCTCGAAACATGA 59.990 40.000 0.00 0.00 0.00 3.07
4050 4336 6.096036 TGTCTCTCTCTCGAAACATGATTTC 58.904 40.000 0.00 5.27 0.00 2.17
4085 4371 1.828979 TAATCCAAGCAACCGAACCC 58.171 50.000 0.00 0.00 0.00 4.11
4096 4382 2.882137 CAACCGAACCCATACAAAGTGT 59.118 45.455 0.00 0.00 0.00 3.55
4097 4383 2.500229 ACCGAACCCATACAAAGTGTG 58.500 47.619 0.00 0.00 0.00 3.82
4098 4384 1.810151 CCGAACCCATACAAAGTGTGG 59.190 52.381 6.01 6.01 43.08 4.17
4118 4405 1.548719 GGAAAACCCCCATACAAGCAC 59.451 52.381 0.00 0.00 0.00 4.40
4125 4412 1.883275 CCCCATACAAGCACGTCAAAA 59.117 47.619 0.00 0.00 0.00 2.44
4126 4413 2.095263 CCCCATACAAGCACGTCAAAAG 60.095 50.000 0.00 0.00 0.00 2.27
4127 4414 2.811431 CCCATACAAGCACGTCAAAAGA 59.189 45.455 0.00 0.00 0.00 2.52
4128 4415 3.440173 CCCATACAAGCACGTCAAAAGAT 59.560 43.478 0.00 0.00 0.00 2.40
4132 4419 7.081349 CCATACAAGCACGTCAAAAGATAAAA 58.919 34.615 0.00 0.00 0.00 1.52
4164 4452 2.307363 CGGACTGTGAAAACGCACT 58.693 52.632 0.00 0.00 39.49 4.40
4188 4476 0.519175 CGAAGCCGAGCATGAAAACG 60.519 55.000 0.00 0.00 38.22 3.60
4214 4502 0.316689 GCCACACCGAACAAGAAACG 60.317 55.000 0.00 0.00 0.00 3.60
4218 4506 3.682858 CCACACCGAACAAGAAACGATAT 59.317 43.478 0.00 0.00 0.00 1.63
4222 4510 6.475727 CACACCGAACAAGAAACGATATAGAT 59.524 38.462 0.00 0.00 0.00 1.98
4283 4571 2.301009 TCAGACCCCGGTTAGAGTTTTC 59.699 50.000 0.00 0.00 0.00 2.29
4316 4604 5.126396 GCTCCAGCTCAAAAGTAATTTGT 57.874 39.130 0.00 0.00 46.89 2.83
4333 4630 4.497473 TTTGTGTAGGATTCGCAAAAGG 57.503 40.909 0.00 0.00 40.62 3.11
4335 4632 1.810151 GTGTAGGATTCGCAAAAGGCA 59.190 47.619 0.00 0.00 45.17 4.75
4361 4658 2.919859 CTGCGACAGTCTGTGATAGTTG 59.080 50.000 11.04 0.00 0.00 3.16
4374 4671 4.464951 TGTGATAGTTGGTGTAGGTACTGG 59.535 45.833 0.00 0.00 41.52 4.00
4437 4734 5.828871 ACTACTACTGGACAGAAGGTGTAT 58.171 41.667 6.29 0.00 40.56 2.29
4464 4761 6.194796 AGTTTACATCCAACCATTGATTCG 57.805 37.500 0.00 0.00 0.00 3.34
4479 4776 6.093495 CCATTGATTCGGTAAGCACTTTAGAA 59.907 38.462 0.00 0.00 28.88 2.10
4543 4840 6.878317 AGTAATTCACTCAATCTTCCATCGA 58.122 36.000 0.00 0.00 28.33 3.59
4544 4841 6.983307 AGTAATTCACTCAATCTTCCATCGAG 59.017 38.462 0.00 0.00 28.33 4.04
4545 4842 5.604758 ATTCACTCAATCTTCCATCGAGA 57.395 39.130 0.00 0.00 0.00 4.04
4546 4843 5.405935 TTCACTCAATCTTCCATCGAGAA 57.594 39.130 0.00 0.00 0.00 2.87
4547 4844 5.405935 TCACTCAATCTTCCATCGAGAAA 57.594 39.130 0.00 0.00 0.00 2.52
4548 4845 5.982356 TCACTCAATCTTCCATCGAGAAAT 58.018 37.500 0.00 0.00 0.00 2.17
4549 4846 7.112452 TCACTCAATCTTCCATCGAGAAATA 57.888 36.000 0.00 0.00 0.00 1.40
4550 4847 7.555965 TCACTCAATCTTCCATCGAGAAATAA 58.444 34.615 0.00 0.00 0.00 1.40
4551 4848 7.708322 TCACTCAATCTTCCATCGAGAAATAAG 59.292 37.037 0.00 0.00 0.00 1.73
4552 4849 6.989169 ACTCAATCTTCCATCGAGAAATAAGG 59.011 38.462 0.00 0.00 0.00 2.69
4553 4850 6.291377 TCAATCTTCCATCGAGAAATAAGGG 58.709 40.000 0.00 0.00 0.00 3.95
4554 4851 6.099701 TCAATCTTCCATCGAGAAATAAGGGA 59.900 38.462 0.00 0.00 0.00 4.20
4555 4852 6.694445 ATCTTCCATCGAGAAATAAGGGAT 57.306 37.500 0.00 0.00 0.00 3.85
4556 4853 6.102897 TCTTCCATCGAGAAATAAGGGATC 57.897 41.667 0.00 0.00 0.00 3.36
4557 4854 4.521130 TCCATCGAGAAATAAGGGATCG 57.479 45.455 0.00 0.00 34.80 3.69
4558 4855 3.258372 TCCATCGAGAAATAAGGGATCGG 59.742 47.826 0.00 0.00 34.29 4.18
4559 4856 3.258372 CCATCGAGAAATAAGGGATCGGA 59.742 47.826 0.00 0.00 34.29 4.55
4560 4857 4.489810 CATCGAGAAATAAGGGATCGGAG 58.510 47.826 0.00 0.00 34.29 4.63
4561 4858 2.296471 TCGAGAAATAAGGGATCGGAGC 59.704 50.000 0.00 0.00 34.29 4.70
4562 4859 2.610727 CGAGAAATAAGGGATCGGAGCC 60.611 54.545 3.04 3.04 0.00 4.70
4563 4860 2.635427 GAGAAATAAGGGATCGGAGCCT 59.365 50.000 12.67 0.00 0.00 4.58
4564 4861 3.049344 AGAAATAAGGGATCGGAGCCTT 58.951 45.455 12.67 0.62 32.48 4.35
4565 4862 3.071747 AGAAATAAGGGATCGGAGCCTTC 59.928 47.826 12.67 7.60 30.45 3.46
4566 4863 1.353091 ATAAGGGATCGGAGCCTTCC 58.647 55.000 12.67 0.00 40.33 3.46
4569 4866 4.610714 GGATCGGAGCCTTCCCGC 62.611 72.222 4.74 0.00 46.10 6.13
4570 4867 4.951963 GATCGGAGCCTTCCCGCG 62.952 72.222 0.00 0.00 46.10 6.46
4579 4876 4.521062 CTTCCCGCGCCTCCTCAG 62.521 72.222 0.00 0.00 0.00 3.35
4583 4880 3.764466 CCGCGCCTCCTCAGAGTT 61.764 66.667 0.00 0.00 38.58 3.01
4584 4881 2.262915 CGCGCCTCCTCAGAGTTT 59.737 61.111 0.00 0.00 38.58 2.66
4585 4882 1.511305 CGCGCCTCCTCAGAGTTTA 59.489 57.895 0.00 0.00 38.58 2.01
4586 4883 0.526524 CGCGCCTCCTCAGAGTTTAG 60.527 60.000 0.00 0.00 38.58 1.85
4587 4884 0.533032 GCGCCTCCTCAGAGTTTAGT 59.467 55.000 0.00 0.00 38.58 2.24
4588 4885 1.737363 GCGCCTCCTCAGAGTTTAGTG 60.737 57.143 0.00 0.00 38.58 2.74
4589 4886 1.134965 CGCCTCCTCAGAGTTTAGTGG 60.135 57.143 0.00 0.00 38.58 4.00
4590 4887 2.180276 GCCTCCTCAGAGTTTAGTGGA 58.820 52.381 0.00 0.00 38.58 4.02
4591 4888 2.769095 GCCTCCTCAGAGTTTAGTGGAT 59.231 50.000 0.00 0.00 38.58 3.41
4592 4889 3.198853 GCCTCCTCAGAGTTTAGTGGATT 59.801 47.826 0.00 0.00 38.58 3.01
4593 4890 4.682050 GCCTCCTCAGAGTTTAGTGGATTC 60.682 50.000 0.00 0.00 38.58 2.52
4594 4891 4.714308 CCTCCTCAGAGTTTAGTGGATTCT 59.286 45.833 0.00 0.00 38.58 2.40
4595 4892 5.395103 CCTCCTCAGAGTTTAGTGGATTCTG 60.395 48.000 0.00 0.00 38.58 3.02
4596 4893 4.467795 TCCTCAGAGTTTAGTGGATTCTGG 59.532 45.833 0.00 0.00 36.72 3.86
4597 4894 4.187694 CTCAGAGTTTAGTGGATTCTGGC 58.812 47.826 0.56 0.00 36.72 4.85
4598 4895 3.055094 TCAGAGTTTAGTGGATTCTGGCC 60.055 47.826 0.00 0.00 36.72 5.36
4599 4896 2.093447 AGAGTTTAGTGGATTCTGGCCG 60.093 50.000 0.00 0.00 0.00 6.13
4600 4897 1.628846 AGTTTAGTGGATTCTGGCCGT 59.371 47.619 0.00 0.00 0.00 5.68
4601 4898 2.007608 GTTTAGTGGATTCTGGCCGTC 58.992 52.381 0.00 0.00 0.00 4.79
4602 4899 0.539986 TTAGTGGATTCTGGCCGTCC 59.460 55.000 0.00 3.65 0.00 4.79
4603 4900 1.672854 TAGTGGATTCTGGCCGTCCG 61.673 60.000 0.00 0.00 34.72 4.79
4604 4901 2.682136 TGGATTCTGGCCGTCCGA 60.682 61.111 0.00 0.00 34.72 4.55
4605 4902 2.063979 TGGATTCTGGCCGTCCGAT 61.064 57.895 0.00 0.00 34.72 4.18
4606 4903 1.146263 GGATTCTGGCCGTCCGATT 59.854 57.895 0.00 0.00 34.14 3.34
4607 4904 0.880718 GGATTCTGGCCGTCCGATTC 60.881 60.000 0.00 0.00 34.14 2.52
4608 4905 1.215655 GATTCTGGCCGTCCGATTCG 61.216 60.000 0.00 0.00 34.14 3.34
4609 4906 1.956629 ATTCTGGCCGTCCGATTCGT 61.957 55.000 5.20 0.00 34.14 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.979813 GTCGATTGTCAACATTTGGTGC 59.020 45.455 0.00 0.00 31.48 5.01
23 24 8.278408 ACTCATTTCATGATAAATCGTCGATTG 58.722 33.333 20.62 8.45 38.85 2.67
83 84 8.424918 TCCATCTTTAAACATTACCTTTTTGCA 58.575 29.630 0.00 0.00 0.00 4.08
115 116 4.751060 TGTTCTAAATATTGACGCGGAGT 58.249 39.130 12.47 0.00 0.00 3.85
116 117 5.907197 ATGTTCTAAATATTGACGCGGAG 57.093 39.130 12.47 0.00 0.00 4.63
154 155 7.813148 TCAGCAAAATTACTACTATATCGGCTC 59.187 37.037 0.00 0.00 0.00 4.70
200 202 3.435275 AGCTTTTCTTCTCATTTCCCCC 58.565 45.455 0.00 0.00 0.00 5.40
201 203 6.590234 TTAAGCTTTTCTTCTCATTTCCCC 57.410 37.500 3.20 0.00 36.25 4.81
204 206 8.078596 TCTGCTTTAAGCTTTTCTTCTCATTTC 58.921 33.333 18.20 0.00 42.97 2.17
207 209 7.309073 CCTTCTGCTTTAAGCTTTTCTTCTCAT 60.309 37.037 18.20 0.00 42.97 2.90
208 210 6.016777 CCTTCTGCTTTAAGCTTTTCTTCTCA 60.017 38.462 18.20 0.00 42.97 3.27
262 264 2.554032 GACCGATTAAAGCCATCATGGG 59.446 50.000 5.62 0.00 38.19 4.00
263 265 2.224079 CGACCGATTAAAGCCATCATGG 59.776 50.000 0.00 0.00 41.55 3.66
264 266 2.872245 ACGACCGATTAAAGCCATCATG 59.128 45.455 0.00 0.00 0.00 3.07
265 267 3.194005 ACGACCGATTAAAGCCATCAT 57.806 42.857 0.00 0.00 0.00 2.45
266 268 2.675844 CAACGACCGATTAAAGCCATCA 59.324 45.455 0.00 0.00 0.00 3.07
267 269 2.676342 ACAACGACCGATTAAAGCCATC 59.324 45.455 0.00 0.00 0.00 3.51
268 270 2.418628 CACAACGACCGATTAAAGCCAT 59.581 45.455 0.00 0.00 0.00 4.40
269 271 1.801771 CACAACGACCGATTAAAGCCA 59.198 47.619 0.00 0.00 0.00 4.75
270 272 1.802365 ACACAACGACCGATTAAAGCC 59.198 47.619 0.00 0.00 0.00 4.35
271 273 2.412325 CCACACAACGACCGATTAAAGC 60.412 50.000 0.00 0.00 0.00 3.51
272 274 2.158841 CCCACACAACGACCGATTAAAG 59.841 50.000 0.00 0.00 0.00 1.85
273 275 2.144730 CCCACACAACGACCGATTAAA 58.855 47.619 0.00 0.00 0.00 1.52
274 276 1.343789 TCCCACACAACGACCGATTAA 59.656 47.619 0.00 0.00 0.00 1.40
275 277 0.967662 TCCCACACAACGACCGATTA 59.032 50.000 0.00 0.00 0.00 1.75
333 335 1.749634 CCGTTGCTACTGCCTACTACT 59.250 52.381 0.00 0.00 38.71 2.57
334 336 1.801765 GCCGTTGCTACTGCCTACTAC 60.802 57.143 3.44 0.00 38.71 2.73
373 377 4.705519 CAAAACGCCGGCTGCCTG 62.706 66.667 26.68 11.83 36.24 4.85
436 440 1.669115 CACAAGTGGCAGTCTCCGG 60.669 63.158 0.00 0.00 0.00 5.14
515 531 2.632377 GTGGTGGATGTCATGTACTGG 58.368 52.381 0.00 0.00 0.00 4.00
516 532 2.270923 CGTGGTGGATGTCATGTACTG 58.729 52.381 0.00 0.00 0.00 2.74
518 534 1.651987 CCGTGGTGGATGTCATGTAC 58.348 55.000 0.00 0.00 42.00 2.90
656 700 2.354199 GGACTCGGGTAAACTCTAGTCG 59.646 54.545 8.16 0.00 35.34 4.18
660 704 3.009916 AGTCAGGACTCGGGTAAACTCTA 59.990 47.826 0.00 0.00 36.92 2.43
711 755 2.513065 GATGGCACGCACGAACCAAG 62.513 60.000 11.56 0.00 35.41 3.61
712 756 2.593148 ATGGCACGCACGAACCAA 60.593 55.556 11.56 0.00 35.41 3.67
788 844 4.357947 TGTCGTCGTCCCTGCTGC 62.358 66.667 0.00 0.00 0.00 5.25
789 845 2.430921 GTGTCGTCGTCCCTGCTG 60.431 66.667 0.00 0.00 0.00 4.41
790 846 3.681835 GGTGTCGTCGTCCCTGCT 61.682 66.667 0.00 0.00 0.00 4.24
791 847 3.986006 TGGTGTCGTCGTCCCTGC 61.986 66.667 0.00 0.00 0.00 4.85
792 848 2.049433 GTGGTGTCGTCGTCCCTG 60.049 66.667 0.00 0.00 0.00 4.45
793 849 3.667282 CGTGGTGTCGTCGTCCCT 61.667 66.667 0.00 0.00 0.00 4.20
794 850 3.969802 ACGTGGTGTCGTCGTCCC 61.970 66.667 0.00 0.00 40.04 4.46
810 866 1.269778 GGAAGGCCTGTTGCTTTTGAC 60.270 52.381 5.69 0.00 39.73 3.18
818 874 4.438744 CGCTATAAAAAGGAAGGCCTGTTG 60.439 45.833 5.69 0.00 46.28 3.33
821 877 2.033424 GCGCTATAAAAAGGAAGGCCTG 59.967 50.000 5.69 0.00 46.28 4.85
827 885 1.937899 GGCTCGCGCTATAAAAAGGAA 59.062 47.619 5.56 0.00 36.09 3.36
884 942 2.892425 CGGAGGGAAGCACGATGC 60.892 66.667 0.00 0.00 45.46 3.91
915 978 4.682778 CGGAGGAGGGATAAATTACACA 57.317 45.455 0.00 0.00 0.00 3.72
1155 1221 2.757508 CAGGAGGAGCAGGCGAGA 60.758 66.667 0.00 0.00 0.00 4.04
1243 1309 2.588877 GGCGTCGTCATCCATGGG 60.589 66.667 13.02 0.00 0.00 4.00
1305 1371 1.139095 GACCACGTCCTCGACATCC 59.861 63.158 0.00 0.00 40.62 3.51
1431 1497 7.738847 ACCAAAACAAAGAATCAATGGAGATT 58.261 30.769 0.00 0.00 40.75 2.40
1432 1498 7.307131 ACCAAAACAAAGAATCAATGGAGAT 57.693 32.000 0.00 0.00 0.00 2.75
1433 1499 6.729690 ACCAAAACAAAGAATCAATGGAGA 57.270 33.333 0.00 0.00 0.00 3.71
1449 1515 8.181573 CACACATAACCATGATAGTACCAAAAC 58.818 37.037 0.00 0.00 35.96 2.43
1464 1533 0.394938 ACGGACAGCACACATAACCA 59.605 50.000 0.00 0.00 0.00 3.67
1472 1541 2.324014 AAAGGAGCACGGACAGCACA 62.324 55.000 0.00 0.00 0.00 4.57
1476 1545 1.884235 AAGAAAAGGAGCACGGACAG 58.116 50.000 0.00 0.00 0.00 3.51
1550 1619 7.276658 TGAAATGTTTCTGTAGGTTGTACTGA 58.723 34.615 6.99 0.00 38.02 3.41
1576 1646 5.010112 CCGTAGAGCATTCATTCTAGGAGAA 59.990 44.000 0.00 0.00 38.78 2.87
1578 1648 4.520874 TCCGTAGAGCATTCATTCTAGGAG 59.479 45.833 0.00 0.00 35.07 3.69
1579 1649 4.470602 TCCGTAGAGCATTCATTCTAGGA 58.529 43.478 0.00 0.00 35.07 2.94
1581 1651 5.009110 TGTCTCCGTAGAGCATTCATTCTAG 59.991 44.000 0.00 0.00 40.22 2.43
1582 1652 4.887655 TGTCTCCGTAGAGCATTCATTCTA 59.112 41.667 0.00 0.00 40.22 2.10
1584 1654 4.046938 TGTCTCCGTAGAGCATTCATTC 57.953 45.455 0.00 0.00 40.22 2.67
1585 1655 4.437239 CTTGTCTCCGTAGAGCATTCATT 58.563 43.478 0.00 0.00 40.22 2.57
1586 1656 3.739519 GCTTGTCTCCGTAGAGCATTCAT 60.740 47.826 0.00 0.00 40.22 2.57
1587 1657 2.417379 GCTTGTCTCCGTAGAGCATTCA 60.417 50.000 0.00 0.00 40.22 2.57
1588 1658 2.197577 GCTTGTCTCCGTAGAGCATTC 58.802 52.381 0.00 0.00 40.22 2.67
1589 1659 1.134670 GGCTTGTCTCCGTAGAGCATT 60.135 52.381 0.00 0.00 40.22 3.56
1590 1660 0.461961 GGCTTGTCTCCGTAGAGCAT 59.538 55.000 0.00 0.00 40.22 3.79
1592 1662 0.533032 AAGGCTTGTCTCCGTAGAGC 59.467 55.000 0.00 0.00 40.22 4.09
1594 1664 1.919240 TCAAGGCTTGTCTCCGTAGA 58.081 50.000 25.39 1.21 0.00 2.59
1595 1665 2.743636 TTCAAGGCTTGTCTCCGTAG 57.256 50.000 25.39 0.00 0.00 3.51
1596 1666 3.334691 CATTTCAAGGCTTGTCTCCGTA 58.665 45.455 25.39 2.73 0.00 4.02
1597 1667 2.154462 CATTTCAAGGCTTGTCTCCGT 58.846 47.619 25.39 5.93 0.00 4.69
1598 1668 1.135575 GCATTTCAAGGCTTGTCTCCG 60.136 52.381 25.39 13.06 32.08 4.63
1599 1669 1.888512 TGCATTTCAAGGCTTGTCTCC 59.111 47.619 25.39 12.43 36.52 3.71
1601 1671 3.057033 GTGATGCATTTCAAGGCTTGTCT 60.057 43.478 25.39 9.70 36.52 3.41
1602 1672 3.248266 GTGATGCATTTCAAGGCTTGTC 58.752 45.455 25.39 14.61 36.52 3.18
1605 1675 4.339872 TTTGTGATGCATTTCAAGGCTT 57.660 36.364 0.00 0.00 36.52 4.35
1606 1676 4.546829 ATTTGTGATGCATTTCAAGGCT 57.453 36.364 0.00 0.00 36.52 4.58
1607 1677 4.691685 TGAATTTGTGATGCATTTCAAGGC 59.308 37.500 0.00 4.26 36.03 4.35
1671 1777 5.274718 CACAGGTCGATGAGATACAGTTAC 58.725 45.833 0.00 0.00 0.00 2.50
1690 1796 3.440173 CCCAACATACTTAACCTGCACAG 59.560 47.826 0.00 0.00 0.00 3.66
1748 1854 1.588239 TGTCCATCAGATTCAGGCCT 58.412 50.000 0.00 0.00 0.00 5.19
1835 1941 1.548081 TGCAGTGCAGCCACATAAAT 58.452 45.000 15.37 0.00 44.53 1.40
1992 2098 3.588955 TGGTGAGATCGAACATGAACAG 58.411 45.455 0.00 0.00 0.00 3.16
2027 2133 8.358148 GTGGATGCTGCTAGTACTAACTTATTA 58.642 37.037 3.76 0.00 37.15 0.98
2284 2414 8.739972 ACAACATCAAGAACCCTTAACAATATC 58.260 33.333 0.00 0.00 0.00 1.63
2293 2423 6.375455 CAGCTATTACAACATCAAGAACCCTT 59.625 38.462 0.00 0.00 0.00 3.95
2338 2468 1.476845 TAGCCGTCTGCCACAAGGAA 61.477 55.000 0.00 0.00 42.71 3.36
2339 2469 1.264749 ATAGCCGTCTGCCACAAGGA 61.265 55.000 0.00 0.00 42.71 3.36
2445 2615 1.195900 TCGCACGAAAACTATTGTGGC 59.804 47.619 0.00 0.00 35.60 5.01
2447 2617 4.320667 TGATCGCACGAAAACTATTGTG 57.679 40.909 0.00 0.00 37.69 3.33
2512 2684 2.435059 GAGGTGCTGAAGGTCCGC 60.435 66.667 0.00 0.00 0.00 5.54
2670 2849 1.184970 AAAGAAACCGGTGGGCATGG 61.185 55.000 8.52 0.00 36.48 3.66
2737 2916 1.846007 ACTCTGTGGCCTCTGACTAG 58.154 55.000 3.32 1.13 0.00 2.57
2753 2932 9.738832 TTGTGGCTGTAATAAAACTAAAAACTC 57.261 29.630 0.00 0.00 0.00 3.01
2828 3010 4.433615 TGTGCTCGATTAGATCAGGTTTC 58.566 43.478 0.00 0.00 0.00 2.78
2847 3029 6.608002 AGTCTTAATTAGTCTAGTCCCCTGTG 59.392 42.308 0.00 0.00 0.00 3.66
2995 3177 1.210155 GGCAAACACTCATCGCCAC 59.790 57.895 0.00 0.00 42.50 5.01
3032 3231 5.126067 ACATGGGAAAACATATCTTCTCCG 58.874 41.667 0.00 0.00 0.00 4.63
3043 3242 2.091610 TGGGACAAGACATGGGAAAACA 60.092 45.455 0.00 0.00 31.92 2.83
3044 3243 2.296190 GTGGGACAAGACATGGGAAAAC 59.704 50.000 0.00 0.00 44.16 2.43
3249 3461 7.938140 ACAGATGAAGCTCCTATAGAGTATC 57.062 40.000 0.00 1.65 45.21 2.24
3250 3462 7.947332 TGAACAGATGAAGCTCCTATAGAGTAT 59.053 37.037 0.00 0.00 45.21 2.12
3251 3463 7.290813 TGAACAGATGAAGCTCCTATAGAGTA 58.709 38.462 0.00 0.00 45.21 2.59
3252 3464 6.132658 TGAACAGATGAAGCTCCTATAGAGT 58.867 40.000 0.00 0.00 45.21 3.24
3253 3465 6.647334 TGAACAGATGAAGCTCCTATAGAG 57.353 41.667 0.00 0.00 46.29 2.43
3254 3466 6.779539 TGATGAACAGATGAAGCTCCTATAGA 59.220 38.462 0.00 0.00 0.00 1.98
3255 3467 6.990798 TGATGAACAGATGAAGCTCCTATAG 58.009 40.000 0.00 0.00 0.00 1.31
3268 3480 9.976511 CCTAAAATTTATGCATGATGAACAGAT 57.023 29.630 10.16 0.00 0.00 2.90
3269 3481 8.970020 ACCTAAAATTTATGCATGATGAACAGA 58.030 29.630 10.16 0.00 0.00 3.41
3270 3482 9.027129 CACCTAAAATTTATGCATGATGAACAG 57.973 33.333 10.16 0.00 0.00 3.16
3271 3483 7.492020 GCACCTAAAATTTATGCATGATGAACA 59.508 33.333 10.16 0.00 36.30 3.18
3272 3484 7.492020 TGCACCTAAAATTTATGCATGATGAAC 59.508 33.333 10.16 0.00 41.18 3.18
3273 3485 7.554211 TGCACCTAAAATTTATGCATGATGAA 58.446 30.769 10.16 0.00 41.18 2.57
3274 3486 7.110043 TGCACCTAAAATTTATGCATGATGA 57.890 32.000 10.16 0.00 41.18 2.92
3316 3539 5.325239 CACTCCAAAGGGAAAGAAAGGTAT 58.675 41.667 0.00 0.00 44.38 2.73
3328 3551 2.224867 ACAGACATTCCACTCCAAAGGG 60.225 50.000 0.00 0.00 0.00 3.95
3337 3560 6.757010 CACTAGGTACAATACAGACATTCCAC 59.243 42.308 0.00 0.00 0.00 4.02
3340 3563 6.338146 TGCACTAGGTACAATACAGACATTC 58.662 40.000 0.00 0.00 0.00 2.67
3351 3574 4.283467 ACATCTTCACTGCACTAGGTACAA 59.717 41.667 0.00 0.00 0.00 2.41
3354 3577 6.129874 AGATACATCTTCACTGCACTAGGTA 58.870 40.000 0.00 0.00 31.97 3.08
3368 3591 7.877097 GCAGGTCTCAATTCATAGATACATCTT 59.123 37.037 0.00 0.00 38.32 2.40
3369 3592 7.385267 GCAGGTCTCAATTCATAGATACATCT 58.615 38.462 0.00 0.00 40.86 2.90
3441 3672 3.275338 GCGTATGCTCTGGCCTGC 61.275 66.667 3.32 6.66 38.39 4.85
3610 3841 1.697982 GGAGGAGTGGTTAGTTGGTGT 59.302 52.381 0.00 0.00 0.00 4.16
3641 3872 4.436183 GGTTGGTTAGTCGTAGTCGTAGTC 60.436 50.000 0.00 0.00 38.33 2.59
3709 3964 4.215399 ACATGAACCATAACCAACTCAACG 59.785 41.667 0.00 0.00 0.00 4.10
3743 3998 2.998493 TCCTCTCCAGGAAGAAGGC 58.002 57.895 7.17 0.00 46.84 4.35
3802 4069 3.942829 CATGGATTCCCTATACATGCGT 58.057 45.455 0.00 0.00 46.03 5.24
3957 4243 4.458295 TCACCGGTACTCTAAAGACTGAAG 59.542 45.833 6.87 0.00 0.00 3.02
4015 4301 6.178324 TCGAGAGAGAGACAAACTATAACCA 58.822 40.000 0.00 0.00 34.84 3.67
4016 4302 6.680874 TCGAGAGAGAGACAAACTATAACC 57.319 41.667 0.00 0.00 34.84 2.85
4027 4313 6.567769 GAAATCATGTTTCGAGAGAGAGAC 57.432 41.667 0.00 0.00 43.69 3.36
4039 4325 4.510038 AAAGCAGAGCGAAATCATGTTT 57.490 36.364 0.00 0.00 0.00 2.83
4046 4332 9.890629 TGGATTATATATAAAGCAGAGCGAAAT 57.109 29.630 9.20 0.00 0.00 2.17
4050 4336 7.278646 TGCTTGGATTATATATAAAGCAGAGCG 59.721 37.037 19.00 4.01 37.15 5.03
4053 4339 9.231297 GGTTGCTTGGATTATATATAAAGCAGA 57.769 33.333 20.70 13.58 42.06 4.26
4055 4341 7.880713 TCGGTTGCTTGGATTATATATAAAGCA 59.119 33.333 19.00 19.00 39.85 3.91
4098 4384 1.548719 GTGCTTGTATGGGGGTTTTCC 59.451 52.381 0.00 0.00 39.75 3.13
4104 4391 0.322098 TTGACGTGCTTGTATGGGGG 60.322 55.000 0.00 0.00 0.00 5.40
4149 4437 1.944709 GGGTTAGTGCGTTTTCACAGT 59.055 47.619 0.00 0.00 39.35 3.55
4164 4452 1.153449 CATGCTCGGCTTCGGGTTA 60.153 57.895 0.00 0.00 36.60 2.85
4202 4490 7.588854 TCGGTAATCTATATCGTTTCTTGTTCG 59.411 37.037 0.00 0.00 0.00 3.95
4214 4502 7.310664 TCGGTTCATGTTCGGTAATCTATATC 58.689 38.462 0.00 0.00 0.00 1.63
4218 4506 4.987408 TCGGTTCATGTTCGGTAATCTA 57.013 40.909 0.00 0.00 0.00 1.98
4222 4510 2.224233 TGGTTCGGTTCATGTTCGGTAA 60.224 45.455 0.00 0.00 0.00 2.85
4267 4555 0.322648 ACCGAAAACTCTAACCGGGG 59.677 55.000 6.32 0.00 43.98 5.73
4302 4590 7.041030 TGCGAATCCTACACAAATTACTTTTGA 60.041 33.333 5.17 0.00 46.36 2.69
4304 4592 7.209471 TGCGAATCCTACACAAATTACTTTT 57.791 32.000 0.00 0.00 0.00 2.27
4316 4604 2.192664 TGCCTTTTGCGAATCCTACA 57.807 45.000 0.00 0.00 45.60 2.74
4361 4658 2.369532 TGGTTGAACCAGTACCTACACC 59.630 50.000 14.05 0.00 44.79 4.16
4528 4825 6.426328 CCCTTATTTCTCGATGGAAGATTGAG 59.574 42.308 0.00 0.00 0.00 3.02
4535 4832 4.262463 CCGATCCCTTATTTCTCGATGGAA 60.262 45.833 0.00 0.00 0.00 3.53
4541 4838 2.610727 GGCTCCGATCCCTTATTTCTCG 60.611 54.545 0.00 0.00 0.00 4.04
4542 4839 2.635427 AGGCTCCGATCCCTTATTTCTC 59.365 50.000 0.00 0.00 0.00 2.87
4543 4840 2.695585 AGGCTCCGATCCCTTATTTCT 58.304 47.619 0.00 0.00 0.00 2.52
4544 4841 3.403968 GAAGGCTCCGATCCCTTATTTC 58.596 50.000 1.42 0.00 41.36 2.17
4545 4842 2.106684 GGAAGGCTCCGATCCCTTATTT 59.893 50.000 1.42 0.00 41.36 1.40
4546 4843 1.700186 GGAAGGCTCCGATCCCTTATT 59.300 52.381 1.42 0.00 41.36 1.40
4547 4844 1.353091 GGAAGGCTCCGATCCCTTAT 58.647 55.000 1.42 0.00 41.36 1.73
4548 4845 2.836020 GGAAGGCTCCGATCCCTTA 58.164 57.895 1.42 0.00 41.36 2.69
4549 4846 3.648694 GGAAGGCTCCGATCCCTT 58.351 61.111 1.03 1.03 43.87 3.95
4562 4859 4.521062 CTGAGGAGGCGCGGGAAG 62.521 72.222 8.83 0.00 0.00 3.46
4566 4863 1.945354 TAAACTCTGAGGAGGCGCGG 61.945 60.000 8.83 0.00 43.46 6.46
4567 4864 0.526524 CTAAACTCTGAGGAGGCGCG 60.527 60.000 9.85 0.00 43.46 6.86
4568 4865 0.533032 ACTAAACTCTGAGGAGGCGC 59.467 55.000 9.85 0.00 43.46 6.53
4569 4866 1.134965 CCACTAAACTCTGAGGAGGCG 60.135 57.143 9.85 0.25 43.46 5.52
4570 4867 2.180276 TCCACTAAACTCTGAGGAGGC 58.820 52.381 9.85 0.00 43.46 4.70
4571 4868 4.714308 AGAATCCACTAAACTCTGAGGAGG 59.286 45.833 9.85 0.00 43.46 4.30
4572 4869 5.395103 CCAGAATCCACTAAACTCTGAGGAG 60.395 48.000 9.85 5.87 44.62 3.69
4573 4870 4.467795 CCAGAATCCACTAAACTCTGAGGA 59.532 45.833 9.85 0.00 36.44 3.71
4574 4871 4.764172 CCAGAATCCACTAAACTCTGAGG 58.236 47.826 9.85 0.00 36.44 3.86
4575 4872 4.187694 GCCAGAATCCACTAAACTCTGAG 58.812 47.826 2.45 2.45 36.44 3.35
4576 4873 3.055094 GGCCAGAATCCACTAAACTCTGA 60.055 47.826 0.00 0.00 36.44 3.27
4577 4874 3.274288 GGCCAGAATCCACTAAACTCTG 58.726 50.000 0.00 0.00 34.55 3.35
4578 4875 2.093447 CGGCCAGAATCCACTAAACTCT 60.093 50.000 2.24 0.00 0.00 3.24
4579 4876 2.280628 CGGCCAGAATCCACTAAACTC 58.719 52.381 2.24 0.00 0.00 3.01
4580 4877 1.628846 ACGGCCAGAATCCACTAAACT 59.371 47.619 2.24 0.00 0.00 2.66
4581 4878 2.007608 GACGGCCAGAATCCACTAAAC 58.992 52.381 2.24 0.00 0.00 2.01
4582 4879 1.065709 GGACGGCCAGAATCCACTAAA 60.066 52.381 0.00 0.00 32.35 1.85
4583 4880 0.539986 GGACGGCCAGAATCCACTAA 59.460 55.000 0.00 0.00 32.35 2.24
4584 4881 1.672854 CGGACGGCCAGAATCCACTA 61.673 60.000 8.76 0.00 32.35 2.74
4585 4882 2.990479 GGACGGCCAGAATCCACT 59.010 61.111 0.00 0.00 32.35 4.00
4586 4883 2.311688 ATCGGACGGCCAGAATCCAC 62.312 60.000 8.76 0.00 32.35 4.02
4587 4884 1.622607 AATCGGACGGCCAGAATCCA 61.623 55.000 8.76 0.00 32.35 3.41
4588 4885 0.880718 GAATCGGACGGCCAGAATCC 60.881 60.000 8.76 2.60 0.00 3.01
4589 4886 1.215655 CGAATCGGACGGCCAGAATC 61.216 60.000 8.76 7.64 0.00 2.52
4590 4887 1.227263 CGAATCGGACGGCCAGAAT 60.227 57.895 8.76 0.00 0.00 2.40
4591 4888 2.183300 CGAATCGGACGGCCAGAA 59.817 61.111 8.76 0.00 0.00 3.02
4592 4889 3.066190 ACGAATCGGACGGCCAGA 61.066 61.111 8.76 6.14 34.93 3.86


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

AutoCloner maintained by Alex Coulton.