Multiple sequence alignment - TraesCS4A01G332600

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 TraesCS4A01G332600 chr4A 100.000 4649 0 0 1 4649 616699796 616704444 0.000000e+00 8586.0
1 TraesCS4A01G332600 chr4A 80.350 2229 305 66 2 2160 615458359 615456194 0.000000e+00 1567.0
2 TraesCS4A01G332600 chr4A 80.917 1462 202 35 942 2372 632615670 632617085 0.000000e+00 1083.0
3 TraesCS4A01G332600 chr4A 86.376 734 58 18 4 716 616687929 616688641 0.000000e+00 763.0
4 TraesCS4A01G332600 chr4A 84.127 504 70 8 2782 3285 632617333 632617826 3.250000e-131 479.0
5 TraesCS4A01G332600 chr4A 74.355 1279 223 59 960 2185 615376144 615374918 9.180000e-122 448.0
6 TraesCS4A01G332600 chr4A 86.085 424 45 6 2373 2789 632617135 632617551 1.190000e-120 444.0
7 TraesCS4A01G332600 chr4A 98.655 223 3 0 2567 2789 616702577 616702799 3.370000e-106 396.0
8 TraesCS4A01G332600 chr4A 94.872 39 1 1 56 94 622941798 622941761 5.020000e-05 60.2
9 TraesCS4A01G332600 chr5D 84.789 2209 229 45 2 2160 552682711 552684862 0.000000e+00 2119.0
10 TraesCS4A01G332600 chr5D 87.399 1492 143 25 1320 2789 551409460 551407992 0.000000e+00 1672.0
11 TraesCS4A01G332600 chr5D 94.822 869 43 2 2786 3653 551408209 551407342 0.000000e+00 1354.0
12 TraesCS4A01G332600 chr5D 94.452 757 29 6 3893 4649 551407156 551406413 0.000000e+00 1153.0
13 TraesCS4A01G332600 chr5D 77.028 1171 216 29 1029 2190 552129691 552128565 1.420000e-174 623.0
14 TraesCS4A01G332600 chr5D 90.146 274 24 1 999 1272 551409722 551409452 2.060000e-93 353.0
15 TraesCS4A01G332600 chr5D 84.774 243 23 3 723 953 551410243 551410003 1.010000e-56 231.0
16 TraesCS4A01G332600 chr5D 94.872 39 1 1 56 94 546223650 546223687 5.020000e-05 60.2
17 TraesCS4A01G332600 chr5D 94.872 39 1 1 56 94 546228288 546228325 5.020000e-05 60.2
18 TraesCS4A01G332600 chr5D 94.872 39 1 1 56 94 546229450 546229487 5.020000e-05 60.2
19 TraesCS4A01G332600 chr5D 94.737 38 2 0 3651 3688 551407203 551407166 5.020000e-05 60.2
20 TraesCS4A01G332600 chr5B 87.716 1677 126 28 707 2372 703805153 703803546 0.000000e+00 1882.0
21 TraesCS4A01G332600 chr5B 81.473 2240 284 65 2 2171 697870139 697867961 0.000000e+00 1716.0
22 TraesCS4A01G332600 chr5B 91.652 1138 60 9 2786 3917 699612295 699611187 0.000000e+00 1543.0
23 TraesCS4A01G332600 chr5B 95.119 881 33 5 3776 4649 703794618 703793741 0.000000e+00 1380.0
24 TraesCS4A01G332600 chr5B 93.743 895 53 3 2781 3674 703798268 703797376 0.000000e+00 1339.0
25 TraesCS4A01G332600 chr5B 93.230 709 45 3 3915 4622 699609344 699608638 0.000000e+00 1040.0
26 TraesCS4A01G332600 chr5B 75.709 1799 306 79 602 2337 699282960 699281230 0.000000e+00 780.0
27 TraesCS4A01G332600 chr5B 95.291 361 15 1 2431 2789 699612435 699612075 5.220000e-159 571.0
28 TraesCS4A01G332600 chr5B 93.699 365 17 1 2431 2789 703798410 703798046 4.090000e-150 542.0
29 TraesCS4A01G332600 chr5B 91.954 348 21 3 2032 2372 699615001 699614654 9.050000e-132 481.0
30 TraesCS4A01G332600 chr5B 88.037 326 26 5 872 1196 699616410 699616097 1.580000e-99 374.0
31 TraesCS4A01G332600 chr5B 92.035 113 7 2 3665 3775 703794891 703794779 1.730000e-34 158.0
32 TraesCS4A01G332600 chr5B 90.789 76 6 1 723 798 699616536 699616462 2.960000e-17 100.0
33 TraesCS4A01G332600 chr5B 97.143 35 0 1 56 90 123803544 123803577 1.810000e-04 58.4
34 TraesCS4A01G332600 chr6D 79.091 1827 265 68 1010 2789 458990784 458989028 0.000000e+00 1149.0
35 TraesCS4A01G332600 chr6D 83.357 697 78 17 2785 3477 459062858 459062196 1.110000e-170 610.0
36 TraesCS4A01G332600 chr6D 81.746 630 92 13 2785 3412 69107099 69106491 5.370000e-139 505.0
37 TraesCS4A01G332600 chr6D 88.728 346 32 5 2446 2789 459062984 459062644 2.590000e-112 416.0
38 TraesCS4A01G332600 chr2B 80.028 1407 215 34 999 2372 781149700 781151073 0.000000e+00 981.0
39 TraesCS4A01G332600 chr2B 81.328 798 124 14 1597 2372 781085479 781084685 3.950000e-175 625.0
40 TraesCS4A01G332600 chr2B 81.876 629 89 11 2785 3412 781151308 781151912 1.490000e-139 507.0
41 TraesCS4A01G332600 chr2B 86.000 150 21 0 3898 4047 781083436 781083287 1.340000e-35 161.0
42 TraesCS4A01G332600 chr2A 79.685 1398 228 36 999 2372 776170804 776169439 0.000000e+00 957.0
43 TraesCS4A01G332600 chr2A 81.402 699 95 17 2785 3481 776169208 776168543 5.290000e-149 538.0
44 TraesCS4A01G332600 chr2A 81.818 627 76 27 2858 3479 776214582 776215175 4.180000e-135 492.0
45 TraesCS4A01G332600 chr2D 79.601 1402 232 30 999 2372 651431730 651433105 0.000000e+00 955.0
46 TraesCS4A01G332600 chr2D 82.222 630 89 14 2785 3412 651421987 651421379 5.330000e-144 521.0
47 TraesCS4A01G332600 chr2D 81.833 633 92 14 2782 3412 117632855 117633466 1.150000e-140 510.0
48 TraesCS4A01G332600 chr2D 76.144 306 63 9 174 475 546780546 546780247 8.060000e-33 152.0
49 TraesCS4A01G332600 chr2D 85.393 89 6 4 3567 3654 651597648 651597730 8.290000e-13 86.1
50 TraesCS4A01G332600 chr6B 83.070 697 80 17 2785 3477 698114702 698114040 2.390000e-167 599.0
51 TraesCS4A01G332600 chr6B 87.572 346 36 5 2446 2789 698114828 698114488 1.210000e-105 394.0
52 TraesCS4A01G332600 chr6B 97.143 35 0 1 56 90 563486573 563486540 1.810000e-04 58.4
53 TraesCS4A01G332600 chr6A 82.066 697 91 18 2785 3479 605343678 605343014 8.730000e-157 564.0
54 TraesCS4A01G332600 chr6A 86.994 346 37 6 2446 2789 605343803 605343464 2.620000e-102 383.0
55 TraesCS4A01G332600 chrUn 78.146 906 173 12 1316 2208 23720226 23719333 1.890000e-153 553.0
56 TraesCS4A01G332600 chrUn 88.158 76 8 1 3567 3641 23717934 23717859 6.410000e-14 89.8
57 TraesCS4A01G332600 chr7D 86.111 108 15 0 3179 3286 180218937 180219044 2.940000e-22 117.0
58 TraesCS4A01G332600 chr7A 84.259 108 17 0 3179 3286 184586213 184586320 6.360000e-19 106.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G332600 chr4A 616699796 616704444 4648 False 4491.000000 8586 99.327500 1 4649 2 chr4A.!!$F2 4648
1 TraesCS4A01G332600 chr4A 615456194 615458359 2165 True 1567.000000 1567 80.350000 2 2160 1 chr4A.!!$R2 2158
2 TraesCS4A01G332600 chr4A 616687929 616688641 712 False 763.000000 763 86.376000 4 716 1 chr4A.!!$F1 712
3 TraesCS4A01G332600 chr4A 632615670 632617826 2156 False 668.666667 1083 83.709667 942 3285 3 chr4A.!!$F3 2343
4 TraesCS4A01G332600 chr4A 615374918 615376144 1226 True 448.000000 448 74.355000 960 2185 1 chr4A.!!$R1 1225
5 TraesCS4A01G332600 chr5D 552682711 552684862 2151 False 2119.000000 2119 84.789000 2 2160 1 chr5D.!!$F2 2158
6 TraesCS4A01G332600 chr5D 551406413 551410243 3830 True 803.866667 1672 91.055000 723 4649 6 chr5D.!!$R2 3926
7 TraesCS4A01G332600 chr5D 552128565 552129691 1126 True 623.000000 623 77.028000 1029 2190 1 chr5D.!!$R1 1161
8 TraesCS4A01G332600 chr5B 703803546 703805153 1607 True 1882.000000 1882 87.716000 707 2372 1 chr5B.!!$R3 1665
9 TraesCS4A01G332600 chr5B 697867961 697870139 2178 True 1716.000000 1716 81.473000 2 2171 1 chr5B.!!$R1 2169
10 TraesCS4A01G332600 chr5B 703793741 703798410 4669 True 854.750000 1380 93.649000 2431 4649 4 chr5B.!!$R5 2218
11 TraesCS4A01G332600 chr5B 699281230 699282960 1730 True 780.000000 780 75.709000 602 2337 1 chr5B.!!$R2 1735
12 TraesCS4A01G332600 chr5B 699608638 699616536 7898 True 684.833333 1543 91.825500 723 4622 6 chr5B.!!$R4 3899
13 TraesCS4A01G332600 chr6D 458989028 458990784 1756 True 1149.000000 1149 79.091000 1010 2789 1 chr6D.!!$R2 1779
14 TraesCS4A01G332600 chr6D 459062196 459062984 788 True 513.000000 610 86.042500 2446 3477 2 chr6D.!!$R3 1031
15 TraesCS4A01G332600 chr6D 69106491 69107099 608 True 505.000000 505 81.746000 2785 3412 1 chr6D.!!$R1 627
16 TraesCS4A01G332600 chr2B 781149700 781151912 2212 False 744.000000 981 80.952000 999 3412 2 chr2B.!!$F1 2413
17 TraesCS4A01G332600 chr2B 781083287 781085479 2192 True 393.000000 625 83.664000 1597 4047 2 chr2B.!!$R1 2450
18 TraesCS4A01G332600 chr2A 776168543 776170804 2261 True 747.500000 957 80.543500 999 3481 2 chr2A.!!$R1 2482
19 TraesCS4A01G332600 chr2A 776214582 776215175 593 False 492.000000 492 81.818000 2858 3479 1 chr2A.!!$F1 621
20 TraesCS4A01G332600 chr2D 651431730 651433105 1375 False 955.000000 955 79.601000 999 2372 1 chr2D.!!$F2 1373
21 TraesCS4A01G332600 chr2D 651421379 651421987 608 True 521.000000 521 82.222000 2785 3412 1 chr2D.!!$R2 627
22 TraesCS4A01G332600 chr2D 117632855 117633466 611 False 510.000000 510 81.833000 2782 3412 1 chr2D.!!$F1 630
23 TraesCS4A01G332600 chr6B 698114040 698114828 788 True 496.500000 599 85.321000 2446 3477 2 chr6B.!!$R2 1031
24 TraesCS4A01G332600 chr6A 605343014 605343803 789 True 473.500000 564 84.530000 2446 3479 2 chr6A.!!$R1 1033
25 TraesCS4A01G332600 chrUn 23717859 23720226 2367 True 321.400000 553 83.152000 1316 3641 2 chrUn.!!$R1 2325

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
187 188 0.034896 CTATGGCGGCGAGGGTAAAT 59.965 55.000 12.98 0.0 0.00 1.40 F
231 232 0.402566 AGCTCATGGATTAGCCCCCT 60.403 55.000 0.75 0.0 39.64 4.79 F
475 485 0.608308 GGCAGCGAGGTTAGGGTTTT 60.608 55.000 0.00 0.0 0.00 2.43 F
773 833 1.138859 CTAACCATGCACCTCATCGGA 59.861 52.381 0.00 0.0 36.31 4.55 F
2653 6171 0.112218 TGTCCTTCATGGGTTGGTGG 59.888 55.000 0.00 0.0 36.20 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 2777 0.032615 AACTCGAGCTCCTGGATCCT 60.033 55.0 13.61 0.0 0.0 3.24 R
1717 2821 0.694771 TGGGTGCAGAAATGAGCTCT 59.305 50.0 16.19 0.0 0.0 4.09 R
1774 2878 1.230635 CGAAGCACACTGGAGGGTTG 61.231 60.0 0.00 0.0 0.0 3.77 R
2735 6253 0.033504 TGGTCTTCTCGGCACTGTTC 59.966 55.0 0.00 0.0 0.0 3.18 R
4040 12459 0.030504 CGGTCACAACAAATGCAGCA 59.969 50.0 0.00 0.0 0.0 4.41 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
57 58 3.425422 GGCACGCCAATCCAGATC 58.575 61.111 2.36 0.00 35.81 2.75
139 140 0.603569 AGACAGTACGTGAGCCCAAG 59.396 55.000 0.00 0.00 0.00 3.61
150 151 3.125316 CGTGAGCCCAAGTTAATCTTCAC 59.875 47.826 0.00 0.00 33.63 3.18
169 170 0.984995 CGAGTTTTCTCCCCTTCCCT 59.015 55.000 0.00 0.00 43.49 4.20
178 179 4.626081 CCCTTCCCTATGGCGGCG 62.626 72.222 0.51 0.51 0.00 6.46
187 188 0.034896 CTATGGCGGCGAGGGTAAAT 59.965 55.000 12.98 0.00 0.00 1.40
209 210 0.608308 TCTCCTTCAGACTTCGCCGA 60.608 55.000 0.00 0.00 0.00 5.54
211 212 1.176619 TCCTTCAGACTTCGCCGACA 61.177 55.000 0.00 0.00 0.00 4.35
231 232 0.402566 AGCTCATGGATTAGCCCCCT 60.403 55.000 0.75 0.00 39.64 4.79
237 238 2.286935 TGGATTAGCCCCCTTCTCTT 57.713 50.000 0.00 0.00 34.97 2.85
246 247 0.895559 CCCCTTCTCTTTGCCGCTTT 60.896 55.000 0.00 0.00 0.00 3.51
302 311 4.341520 CCTTCACTCGGGCTAGTAGTTTAT 59.658 45.833 0.00 0.00 0.00 1.40
307 316 6.377996 TCACTCGGGCTAGTAGTTTATGTTAA 59.622 38.462 0.00 0.00 0.00 2.01
371 381 1.136884 CGCTTCGTCTTCGAGTTTGTG 60.137 52.381 0.00 0.00 46.81 3.33
383 393 2.576615 GAGTTTGTGTTCTGGGCTCTT 58.423 47.619 0.00 0.00 0.00 2.85
395 405 0.757188 GGGCTCTTCGATCCTCCTCA 60.757 60.000 0.00 0.00 0.00 3.86
409 419 3.323691 TCCTCCTCAAGTTTGTCGATTGA 59.676 43.478 0.00 0.00 0.00 2.57
445 455 3.274095 GCTCTGGCTTAGATTCCTGTT 57.726 47.619 0.00 0.00 34.21 3.16
453 463 4.438148 GCTTAGATTCCTGTTGTCTCCTC 58.562 47.826 0.00 0.00 0.00 3.71
454 464 4.081420 GCTTAGATTCCTGTTGTCTCCTCA 60.081 45.833 0.00 0.00 0.00 3.86
475 485 0.608308 GGCAGCGAGGTTAGGGTTTT 60.608 55.000 0.00 0.00 0.00 2.43
539 551 9.793259 TTTGATCTAAGATGAACCTACAACTTT 57.207 29.630 0.00 0.00 35.27 2.66
585 621 4.963373 TGAAAATTCACCTACCTCACGAA 58.037 39.130 0.00 0.00 31.01 3.85
718 756 1.833630 TCGACAGCTCCAATCCATTCT 59.166 47.619 0.00 0.00 0.00 2.40
764 824 3.365832 CAAATCGATGCTAACCATGCAC 58.634 45.455 0.00 0.00 43.59 4.57
773 833 1.138859 CTAACCATGCACCTCATCGGA 59.861 52.381 0.00 0.00 36.31 4.55
840 900 2.423446 GCCGGATCCATCGAGCTT 59.577 61.111 13.41 0.00 0.00 3.74
949 1044 2.510238 GCATCTCAGCGCTCGGTT 60.510 61.111 7.13 0.00 0.00 4.44
1261 2333 3.426568 GGTTGCTCTCTGTGGCGC 61.427 66.667 0.00 0.00 0.00 6.53
1673 2777 2.319011 GATCGACGTGCCGTGCTCTA 62.319 60.000 4.94 0.00 41.37 2.43
1710 2814 3.222603 AGTTCTTTGGCTTTGGGTGTAG 58.777 45.455 0.00 0.00 0.00 2.74
1717 2821 3.178046 TGGCTTTGGGTGTAGACAGATA 58.822 45.455 0.00 0.00 0.00 1.98
1835 2939 8.706492 TCGTGTTGTAAGACTCTTTTCTAAAA 57.294 30.769 0.00 0.00 0.00 1.52
1990 3120 7.874528 TCTGCATCTACATACCATATGTTCTTG 59.125 37.037 6.78 4.32 33.76 3.02
2160 3299 0.183492 TTCCTTGAAGCTGCACCTGT 59.817 50.000 0.00 0.00 0.00 4.00
2161 3300 0.535780 TCCTTGAAGCTGCACCTGTG 60.536 55.000 0.00 0.00 0.00 3.66
2300 3493 8.366359 AGCAAGTTAATCTAATTTCCAACCAT 57.634 30.769 0.00 0.00 0.00 3.55
2346 3545 8.148351 ACTAAAAGTAGTGCATAGAAGACACAA 58.852 33.333 0.00 0.00 39.20 3.33
2391 3676 5.012239 TGTCTTCTCCAAAAATCCATCCTG 58.988 41.667 0.00 0.00 0.00 3.86
2399 3684 6.287525 TCCAAAAATCCATCCTGTGTTTTTC 58.712 36.000 0.00 0.00 31.70 2.29
2412 3802 4.519213 TGTGTTTTTCTCGAGGAGGAAAA 58.481 39.130 13.56 9.26 42.66 2.29
2611 6129 7.410991 ACTTGATAAGGGCCTAAACTTACATT 58.589 34.615 6.41 0.00 32.52 2.71
2612 6130 7.893833 ACTTGATAAGGGCCTAAACTTACATTT 59.106 33.333 6.41 0.00 32.52 2.32
2613 6131 8.658840 TTGATAAGGGCCTAAACTTACATTTT 57.341 30.769 6.41 0.00 32.52 1.82
2614 6132 9.756571 TTGATAAGGGCCTAAACTTACATTTTA 57.243 29.630 6.41 0.00 32.52 1.52
2615 6133 9.756571 TGATAAGGGCCTAAACTTACATTTTAA 57.243 29.630 6.41 0.00 32.52 1.52
2618 6136 7.418337 AGGGCCTAAACTTACATTTTAATGG 57.582 36.000 2.82 0.00 40.70 3.16
2619 6137 6.046593 GGGCCTAAACTTACATTTTAATGGC 58.953 40.000 0.84 0.00 40.70 4.40
2620 6138 6.351456 GGGCCTAAACTTACATTTTAATGGCA 60.351 38.462 0.84 0.00 40.70 4.92
2621 6139 7.100409 GGCCTAAACTTACATTTTAATGGCAA 58.900 34.615 0.00 0.88 40.70 4.52
2622 6140 7.768582 GGCCTAAACTTACATTTTAATGGCAAT 59.231 33.333 0.00 0.00 40.70 3.56
2623 6141 9.161629 GCCTAAACTTACATTTTAATGGCAATT 57.838 29.630 7.33 0.00 40.70 2.32
2628 6146 8.900983 ACTTACATTTTAATGGCAATTGTTGT 57.099 26.923 7.40 0.00 40.70 3.32
2629 6147 9.988815 ACTTACATTTTAATGGCAATTGTTGTA 57.011 25.926 7.40 0.00 40.70 2.41
2633 6151 9.282569 ACATTTTAATGGCAATTGTTGTAATGT 57.717 25.926 7.40 10.65 40.70 2.71
2636 6154 8.668510 TTTAATGGCAATTGTTGTAATGTTGT 57.331 26.923 7.40 0.00 0.00 3.32
2637 6155 6.783892 AATGGCAATTGTTGTAATGTTGTC 57.216 33.333 7.40 0.00 0.00 3.18
2638 6156 4.626042 TGGCAATTGTTGTAATGTTGTCC 58.374 39.130 7.40 0.00 0.00 4.02
2639 6157 4.343526 TGGCAATTGTTGTAATGTTGTCCT 59.656 37.500 7.40 0.00 0.00 3.85
2640 6158 5.163364 TGGCAATTGTTGTAATGTTGTCCTT 60.163 36.000 7.40 0.00 0.00 3.36
2641 6159 5.405269 GGCAATTGTTGTAATGTTGTCCTTC 59.595 40.000 7.40 0.00 0.00 3.46
2642 6160 5.982516 GCAATTGTTGTAATGTTGTCCTTCA 59.017 36.000 7.40 0.00 0.00 3.02
2643 6161 6.646240 GCAATTGTTGTAATGTTGTCCTTCAT 59.354 34.615 7.40 0.00 0.00 2.57
2644 6162 7.359431 GCAATTGTTGTAATGTTGTCCTTCATG 60.359 37.037 7.40 0.00 0.00 3.07
2645 6163 5.703978 TGTTGTAATGTTGTCCTTCATGG 57.296 39.130 0.00 0.00 37.10 3.66
2646 6164 4.522405 TGTTGTAATGTTGTCCTTCATGGG 59.478 41.667 0.00 0.00 36.20 4.00
2647 6165 4.380843 TGTAATGTTGTCCTTCATGGGT 57.619 40.909 0.00 0.00 36.20 4.51
2648 6166 4.735369 TGTAATGTTGTCCTTCATGGGTT 58.265 39.130 0.00 0.00 36.20 4.11
2649 6167 4.522405 TGTAATGTTGTCCTTCATGGGTTG 59.478 41.667 0.00 0.00 36.20 3.77
2650 6168 1.993956 TGTTGTCCTTCATGGGTTGG 58.006 50.000 0.00 0.00 36.20 3.77
2651 6169 1.216678 TGTTGTCCTTCATGGGTTGGT 59.783 47.619 0.00 0.00 36.20 3.67
2652 6170 1.613437 GTTGTCCTTCATGGGTTGGTG 59.387 52.381 0.00 0.00 36.20 4.17
2653 6171 0.112218 TGTCCTTCATGGGTTGGTGG 59.888 55.000 0.00 0.00 36.20 4.61
2654 6172 1.076549 TCCTTCATGGGTTGGTGGC 59.923 57.895 0.00 0.00 36.20 5.01
2655 6173 1.228831 CCTTCATGGGTTGGTGGCA 60.229 57.895 0.00 0.00 0.00 4.92
2656 6174 0.831288 CCTTCATGGGTTGGTGGCAA 60.831 55.000 0.00 0.00 0.00 4.52
2657 6175 0.604578 CTTCATGGGTTGGTGGCAAG 59.395 55.000 0.00 0.00 0.00 4.01
2658 6176 1.470996 TTCATGGGTTGGTGGCAAGC 61.471 55.000 0.00 0.00 0.00 4.01
2659 6177 1.909781 CATGGGTTGGTGGCAAGCT 60.910 57.895 0.00 0.00 33.52 3.74
2660 6178 1.152269 ATGGGTTGGTGGCAAGCTT 60.152 52.632 0.00 0.00 33.52 3.74
2661 6179 0.763986 ATGGGTTGGTGGCAAGCTTT 60.764 50.000 0.00 0.00 33.52 3.51
2662 6180 1.367471 GGGTTGGTGGCAAGCTTTC 59.633 57.895 0.00 0.00 33.52 2.62
2663 6181 1.398958 GGGTTGGTGGCAAGCTTTCA 61.399 55.000 0.00 0.00 33.52 2.69
2664 6182 0.681175 GGTTGGTGGCAAGCTTTCAT 59.319 50.000 0.00 0.00 0.00 2.57
2665 6183 1.070601 GGTTGGTGGCAAGCTTTCATT 59.929 47.619 0.00 0.00 0.00 2.57
2666 6184 2.298729 GGTTGGTGGCAAGCTTTCATTA 59.701 45.455 0.00 0.00 0.00 1.90
2667 6185 3.244044 GGTTGGTGGCAAGCTTTCATTAA 60.244 43.478 0.00 0.00 0.00 1.40
2668 6186 3.658757 TGGTGGCAAGCTTTCATTAAC 57.341 42.857 0.00 0.00 0.00 2.01
2669 6187 2.961741 TGGTGGCAAGCTTTCATTAACA 59.038 40.909 0.00 0.00 0.00 2.41
2670 6188 3.577848 TGGTGGCAAGCTTTCATTAACAT 59.422 39.130 0.00 0.00 0.00 2.71
2671 6189 3.928375 GGTGGCAAGCTTTCATTAACATG 59.072 43.478 0.00 0.00 0.00 3.21
2672 6190 4.559153 GTGGCAAGCTTTCATTAACATGT 58.441 39.130 0.00 0.00 0.00 3.21
2673 6191 4.386652 GTGGCAAGCTTTCATTAACATGTG 59.613 41.667 0.00 0.00 0.00 3.21
2674 6192 4.039004 TGGCAAGCTTTCATTAACATGTGT 59.961 37.500 0.00 0.00 0.00 3.72
2675 6193 4.990426 GGCAAGCTTTCATTAACATGTGTT 59.010 37.500 0.00 3.64 41.73 3.32
2676 6194 6.155827 GGCAAGCTTTCATTAACATGTGTTA 58.844 36.000 0.00 1.62 39.31 2.41
2677 6195 6.813152 GGCAAGCTTTCATTAACATGTGTTAT 59.187 34.615 0.00 0.00 39.89 1.89
2678 6196 7.331687 GGCAAGCTTTCATTAACATGTGTTATT 59.668 33.333 0.00 1.24 39.89 1.40
2679 6197 8.711457 GCAAGCTTTCATTAACATGTGTTATTT 58.289 29.630 0.00 0.00 39.89 1.40
2693 6211 9.959721 ACATGTGTTATTTACTTTCTATGTCCT 57.040 29.630 0.00 0.00 0.00 3.85
2696 6214 8.726988 TGTGTTATTTACTTTCTATGTCCTTGC 58.273 33.333 0.00 0.00 0.00 4.01
2697 6215 8.947115 GTGTTATTTACTTTCTATGTCCTTGCT 58.053 33.333 0.00 0.00 0.00 3.91
2698 6216 9.515226 TGTTATTTACTTTCTATGTCCTTGCTT 57.485 29.630 0.00 0.00 0.00 3.91
2699 6217 9.774742 GTTATTTACTTTCTATGTCCTTGCTTG 57.225 33.333 0.00 0.00 0.00 4.01
2700 6218 9.733556 TTATTTACTTTCTATGTCCTTGCTTGA 57.266 29.630 0.00 0.00 0.00 3.02
2701 6219 8.635765 ATTTACTTTCTATGTCCTTGCTTGAA 57.364 30.769 0.00 0.00 0.00 2.69
2702 6220 7.672983 TTACTTTCTATGTCCTTGCTTGAAG 57.327 36.000 0.00 0.00 0.00 3.02
2703 6221 5.625150 ACTTTCTATGTCCTTGCTTGAAGT 58.375 37.500 0.00 0.00 0.00 3.01
2704 6222 6.064717 ACTTTCTATGTCCTTGCTTGAAGTT 58.935 36.000 0.00 0.00 0.00 2.66
2705 6223 7.224297 ACTTTCTATGTCCTTGCTTGAAGTTA 58.776 34.615 0.00 0.00 0.00 2.24
2706 6224 7.885399 ACTTTCTATGTCCTTGCTTGAAGTTAT 59.115 33.333 0.00 0.00 0.00 1.89
2707 6225 7.849804 TTCTATGTCCTTGCTTGAAGTTATC 57.150 36.000 0.00 0.00 0.00 1.75
2708 6226 7.187824 TCTATGTCCTTGCTTGAAGTTATCT 57.812 36.000 0.00 0.00 0.00 1.98
2709 6227 7.268586 TCTATGTCCTTGCTTGAAGTTATCTC 58.731 38.462 0.00 0.00 0.00 2.75
2710 6228 4.245660 TGTCCTTGCTTGAAGTTATCTCG 58.754 43.478 0.00 0.00 0.00 4.04
2711 6229 4.021456 TGTCCTTGCTTGAAGTTATCTCGA 60.021 41.667 0.00 0.00 0.00 4.04
2712 6230 4.327627 GTCCTTGCTTGAAGTTATCTCGAC 59.672 45.833 0.00 0.00 0.00 4.20
2713 6231 4.021456 TCCTTGCTTGAAGTTATCTCGACA 60.021 41.667 0.00 0.00 0.00 4.35
2714 6232 4.872691 CCTTGCTTGAAGTTATCTCGACAT 59.127 41.667 0.00 0.00 0.00 3.06
2715 6233 5.352569 CCTTGCTTGAAGTTATCTCGACATT 59.647 40.000 0.00 0.00 0.00 2.71
2716 6234 5.784750 TGCTTGAAGTTATCTCGACATTG 57.215 39.130 0.00 0.00 0.00 2.82
2717 6235 5.237815 TGCTTGAAGTTATCTCGACATTGT 58.762 37.500 0.00 0.00 0.00 2.71
2718 6236 5.700832 TGCTTGAAGTTATCTCGACATTGTT 59.299 36.000 0.00 0.00 0.00 2.83
2719 6237 6.017933 GCTTGAAGTTATCTCGACATTGTTG 58.982 40.000 0.00 0.00 0.00 3.33
2720 6238 6.347725 GCTTGAAGTTATCTCGACATTGTTGT 60.348 38.462 3.98 0.00 39.32 3.32
2721 6239 7.148639 GCTTGAAGTTATCTCGACATTGTTGTA 60.149 37.037 3.98 0.00 35.79 2.41
2722 6240 8.771920 TTGAAGTTATCTCGACATTGTTGTAT 57.228 30.769 3.98 2.78 35.79 2.29
2723 6241 8.407457 TGAAGTTATCTCGACATTGTTGTATC 57.593 34.615 3.98 0.00 35.79 2.24
2724 6242 8.032451 TGAAGTTATCTCGACATTGTTGTATCA 58.968 33.333 3.98 0.00 35.79 2.15
2725 6243 8.948631 AAGTTATCTCGACATTGTTGTATCAT 57.051 30.769 3.98 0.00 35.79 2.45
2726 6244 8.357796 AGTTATCTCGACATTGTTGTATCATG 57.642 34.615 3.98 0.00 35.79 3.07
2727 6245 8.197439 AGTTATCTCGACATTGTTGTATCATGA 58.803 33.333 0.00 0.00 35.79 3.07
2728 6246 6.834959 ATCTCGACATTGTTGTATCATGAC 57.165 37.500 0.00 0.00 35.79 3.06
2729 6247 4.798387 TCTCGACATTGTTGTATCATGACG 59.202 41.667 0.00 0.00 35.79 4.35
2730 6248 3.305897 TCGACATTGTTGTATCATGACGC 59.694 43.478 0.00 0.00 35.79 5.19
2731 6249 3.306973 CGACATTGTTGTATCATGACGCT 59.693 43.478 0.00 0.00 35.79 5.07
2732 6250 4.548916 CGACATTGTTGTATCATGACGCTC 60.549 45.833 0.00 0.00 35.79 5.03
2733 6251 3.306973 ACATTGTTGTATCATGACGCTCG 59.693 43.478 0.00 0.00 33.16 5.03
2734 6252 2.931512 TGTTGTATCATGACGCTCGA 57.068 45.000 0.00 0.00 0.00 4.04
2735 6253 2.797491 TGTTGTATCATGACGCTCGAG 58.203 47.619 8.45 8.45 0.00 4.04
2736 6254 2.422127 TGTTGTATCATGACGCTCGAGA 59.578 45.455 18.75 0.00 0.00 4.04
2737 6255 3.119637 TGTTGTATCATGACGCTCGAGAA 60.120 43.478 18.75 0.00 0.00 2.87
2738 6256 3.066369 TGTATCATGACGCTCGAGAAC 57.934 47.619 18.75 6.80 0.00 3.01
2739 6257 2.422127 TGTATCATGACGCTCGAGAACA 59.578 45.455 18.75 12.53 0.00 3.18
2740 6258 2.200792 ATCATGACGCTCGAGAACAG 57.799 50.000 18.75 6.35 0.00 3.16
2741 6259 0.881796 TCATGACGCTCGAGAACAGT 59.118 50.000 18.75 9.78 0.00 3.55
2742 6260 0.987715 CATGACGCTCGAGAACAGTG 59.012 55.000 18.75 4.90 0.00 3.66
2743 6261 0.734253 ATGACGCTCGAGAACAGTGC 60.734 55.000 18.75 0.00 0.00 4.40
2744 6262 2.049063 ACGCTCGAGAACAGTGCC 60.049 61.111 18.75 0.00 0.00 5.01
2745 6263 3.175240 CGCTCGAGAACAGTGCCG 61.175 66.667 18.75 3.26 0.00 5.69
2746 6264 2.258591 GCTCGAGAACAGTGCCGA 59.741 61.111 18.75 0.00 0.00 5.54
2747 6265 4.467232 CTCGAGAACAGTGCCGAG 57.533 61.111 6.58 5.36 41.71 4.63
2748 6266 4.074647 TCGAGAACAGTGCCGAGA 57.925 55.556 0.00 0.00 0.00 4.04
2749 6267 2.337361 TCGAGAACAGTGCCGAGAA 58.663 52.632 0.00 0.00 0.00 2.87
2750 6268 0.241213 TCGAGAACAGTGCCGAGAAG 59.759 55.000 0.00 0.00 0.00 2.85
2751 6269 0.241213 CGAGAACAGTGCCGAGAAGA 59.759 55.000 0.00 0.00 0.00 2.87
2752 6270 1.704070 GAGAACAGTGCCGAGAAGAC 58.296 55.000 0.00 0.00 0.00 3.01
2753 6271 0.318762 AGAACAGTGCCGAGAAGACC 59.681 55.000 0.00 0.00 0.00 3.85
2754 6272 0.033504 GAACAGTGCCGAGAAGACCA 59.966 55.000 0.00 0.00 0.00 4.02
2755 6273 0.468226 AACAGTGCCGAGAAGACCAA 59.532 50.000 0.00 0.00 0.00 3.67
2756 6274 0.687354 ACAGTGCCGAGAAGACCAAT 59.313 50.000 0.00 0.00 0.00 3.16
2757 6275 1.081892 CAGTGCCGAGAAGACCAATG 58.918 55.000 0.00 0.00 0.00 2.82
2758 6276 0.687354 AGTGCCGAGAAGACCAATGT 59.313 50.000 0.00 0.00 0.00 2.71
2759 6277 0.798776 GTGCCGAGAAGACCAATGTG 59.201 55.000 0.00 0.00 0.00 3.21
2760 6278 0.321564 TGCCGAGAAGACCAATGTGG 60.322 55.000 0.00 0.00 45.02 4.17
2770 6288 1.966762 CCAATGTGGTGTGGAAGCC 59.033 57.895 0.00 0.00 37.03 4.35
2771 6289 0.827089 CCAATGTGGTGTGGAAGCCA 60.827 55.000 0.00 0.00 37.03 4.75
2772 6290 1.259609 CAATGTGGTGTGGAAGCCAT 58.740 50.000 0.00 0.00 37.09 4.40
2773 6291 1.203052 CAATGTGGTGTGGAAGCCATC 59.797 52.381 0.00 0.00 37.09 3.51
2790 6308 3.369681 GCCATCCAAGGATTTGATGCAAA 60.370 43.478 0.00 0.00 37.75 3.68
2797 6315 5.114081 CAAGGATTTGATGCAAATTCCTCC 58.886 41.667 12.70 10.88 43.05 4.30
2802 6320 6.128200 GGATTTGATGCAAATTCCTCCAAAAC 60.128 38.462 6.82 0.00 43.05 2.43
2803 6321 5.549742 TTGATGCAAATTCCTCCAAAACT 57.450 34.783 0.00 0.00 0.00 2.66
2805 6323 5.299148 TGATGCAAATTCCTCCAAAACTTG 58.701 37.500 0.00 0.00 0.00 3.16
2806 6324 5.070180 TGATGCAAATTCCTCCAAAACTTGA 59.930 36.000 0.00 0.00 0.00 3.02
2807 6325 5.549742 TGCAAATTCCTCCAAAACTTGAT 57.450 34.783 0.00 0.00 0.00 2.57
2808 6326 6.662865 TGCAAATTCCTCCAAAACTTGATA 57.337 33.333 0.00 0.00 0.00 2.15
2809 6327 7.060383 TGCAAATTCCTCCAAAACTTGATAA 57.940 32.000 0.00 0.00 0.00 1.75
2811 6329 6.591448 GCAAATTCCTCCAAAACTTGATAAGG 59.409 38.462 0.00 0.00 0.00 2.69
2813 6331 3.697166 TCCTCCAAAACTTGATAAGGGC 58.303 45.455 0.00 0.00 0.00 5.19
2815 6333 3.564352 CCTCCAAAACTTGATAAGGGCCT 60.564 47.826 0.00 0.00 0.00 5.19
2825 6343 6.970191 ACTTGATAAGGGCCTAAACTTACAT 58.030 36.000 6.41 0.00 32.52 2.29
2844 6364 9.988815 ACTTACATTTTAATGGCAATTGTTGTA 57.011 25.926 7.40 0.00 40.70 2.41
2873 6394 1.470996 TTCATGGGTTGGTGGCAAGC 61.471 55.000 0.00 0.00 0.00 4.01
2931 6453 5.784750 TGCTTGAAGTTATCTCGACATTG 57.215 39.130 0.00 0.00 0.00 2.82
3296 6848 4.647399 GGTCAAGGAATGCTAGTAGTCTCT 59.353 45.833 8.18 1.51 0.00 3.10
3301 6853 7.616150 TCAAGGAATGCTAGTAGTCTCTTAACT 59.384 37.037 8.18 0.00 0.00 2.24
3483 7238 3.374058 CCAGTTTACCGAGTAATTGCCAG 59.626 47.826 0.00 0.00 0.00 4.85
3491 7246 4.275936 ACCGAGTAATTGCCAGATATTTGC 59.724 41.667 0.00 0.00 0.00 3.68
3499 7254 2.948315 TGCCAGATATTTGCGCATGTAA 59.052 40.909 12.75 2.29 0.00 2.41
3590 7353 1.837439 CTGTGTTATGCCTGGAGGGTA 59.163 52.381 0.00 0.00 37.43 3.69
3603 7366 4.829492 CCTGGAGGGTATCATTCAAATTCC 59.171 45.833 0.00 0.00 0.00 3.01
3654 7558 5.596845 TGACTGAAAAGGGTGCAAATTAAC 58.403 37.500 0.00 0.00 0.00 2.01
3659 7563 6.220201 TGAAAAGGGTGCAAATTAACTAAGC 58.780 36.000 0.00 0.00 0.00 3.09
3698 10096 3.519107 TGACTGGAAGCCTATCACATTGA 59.481 43.478 0.00 0.00 37.60 2.57
3728 10127 0.391793 GGCTGGCAGTAGAACAGGAC 60.392 60.000 17.16 0.00 32.98 3.85
3736 10135 1.065854 AGTAGAACAGGACAGCATGCC 60.066 52.381 15.66 0.00 42.53 4.40
3804 10364 5.923733 AGGATGTATCAAGAAACGAGACT 57.076 39.130 0.00 0.00 0.00 3.24
4045 12464 0.666913 CATTCCCTGCATACTGCTGC 59.333 55.000 0.34 0.00 45.31 5.25
4271 12694 1.269723 GCCTTCAGGTTTTAGGTGCAC 59.730 52.381 8.80 8.80 37.57 4.57
4306 12731 0.172127 TGCGCAGTTTGCAAGAAACA 59.828 45.000 5.66 0.00 45.36 2.83
4364 12789 7.655328 TGAAGTTTTTCAGCTTTTCTTTGAACA 59.345 29.630 0.00 0.00 38.37 3.18
4583 13008 8.827677 AGTATGAAGTTGTTCACAAGAAGTTAC 58.172 33.333 0.00 0.00 45.58 2.50
4621 13046 4.773742 ACGTTCTTCTTTCGAAGTGTTC 57.226 40.909 0.00 0.00 45.47 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.200716 CTCGAACGCAACTACACCCTA 59.799 52.381 0.00 0.00 0.00 3.53
55 56 6.263168 GGACATCCGATAAAATTGGAACAGAT 59.737 38.462 0.00 0.00 45.74 2.90
57 58 5.221048 GGGACATCCGATAAAATTGGAACAG 60.221 44.000 0.00 0.00 45.74 3.16
111 112 4.035324 GCTCACGTACTGTCTAAGAGCATA 59.965 45.833 12.28 0.00 44.60 3.14
139 140 5.121925 GGGGAGAAAACTCGTGAAGATTAAC 59.878 44.000 0.00 0.00 0.00 2.01
150 151 0.984995 AGGGAAGGGGAGAAAACTCG 59.015 55.000 0.00 0.00 0.00 4.18
169 170 0.470766 AATTTACCCTCGCCGCCATA 59.529 50.000 0.00 0.00 0.00 2.74
178 179 6.477253 AGTCTGAAGGAGAAAATTTACCCTC 58.523 40.000 6.45 6.53 30.26 4.30
187 188 2.767505 GGCGAAGTCTGAAGGAGAAAA 58.232 47.619 0.00 0.00 30.26 2.29
209 210 1.133668 GGGGCTAATCCATGAGCTTGT 60.134 52.381 0.00 0.00 38.79 3.16
211 212 0.480252 GGGGGCTAATCCATGAGCTT 59.520 55.000 0.00 0.00 38.79 3.74
254 263 1.001393 GATTTTCCTCCCCGCCACA 60.001 57.895 0.00 0.00 0.00 4.17
383 393 2.094700 CGACAAACTTGAGGAGGATCGA 60.095 50.000 0.00 0.00 34.37 3.59
395 405 5.060569 CGAATACGTCTCAATCGACAAACTT 59.939 40.000 0.00 0.00 35.65 2.66
433 443 5.046304 CCTTGAGGAGACAACAGGAATCTAA 60.046 44.000 0.00 0.00 37.39 2.10
435 445 3.262915 CCTTGAGGAGACAACAGGAATCT 59.737 47.826 0.00 0.00 37.39 2.40
445 455 1.881903 CTCGCTGCCTTGAGGAGACA 61.882 60.000 0.06 0.00 37.39 3.41
453 463 1.450312 CCCTAACCTCGCTGCCTTG 60.450 63.158 0.00 0.00 0.00 3.61
454 464 1.489560 AACCCTAACCTCGCTGCCTT 61.490 55.000 0.00 0.00 0.00 4.35
487 498 1.279527 CTAAAACTCGCCGTCGTGCA 61.280 55.000 6.53 0.00 36.96 4.57
488 499 1.280206 ACTAAAACTCGCCGTCGTGC 61.280 55.000 0.00 0.00 36.96 5.34
489 500 0.433492 CACTAAAACTCGCCGTCGTG 59.567 55.000 0.00 0.00 36.96 4.35
490 501 0.031178 ACACTAAAACTCGCCGTCGT 59.969 50.000 0.00 0.00 36.96 4.34
539 551 6.729100 CACTCCCACCCAAATACTCCTATATA 59.271 42.308 0.00 0.00 0.00 0.86
614 650 5.104776 TGTGCTATAGAAAGAAGGCAGTCAT 60.105 40.000 3.21 0.00 0.00 3.06
718 756 4.166725 AGGCTGATTGGATAGTGGATTTGA 59.833 41.667 0.00 0.00 0.00 2.69
764 824 0.669932 GCTGCTGCTATCCGATGAGG 60.670 60.000 8.53 0.00 37.53 3.86
949 1044 7.657023 GGTTGAAACCCTAGATAGAAGTAGA 57.343 40.000 0.36 0.00 43.43 2.59
1505 2609 2.811317 CCACGAGAAGGCGACTGC 60.811 66.667 0.00 0.00 42.68 4.40
1506 2610 2.811317 GCCACGAGAAGGCGACTG 60.811 66.667 0.00 0.00 43.15 3.51
1673 2777 0.032615 AACTCGAGCTCCTGGATCCT 60.033 55.000 13.61 0.00 0.00 3.24
1710 2814 4.507388 GTGCAGAAATGAGCTCTATCTGTC 59.493 45.833 28.43 23.45 39.68 3.51
1717 2821 0.694771 TGGGTGCAGAAATGAGCTCT 59.305 50.000 16.19 0.00 0.00 4.09
1774 2878 1.230635 CGAAGCACACTGGAGGGTTG 61.231 60.000 0.00 0.00 0.00 3.77
1990 3120 6.743575 AATACACAGCTGAAATTGGTAGAC 57.256 37.500 23.35 0.00 0.00 2.59
2130 3268 5.385617 CAGCTTCAAGGAAAAATAGTGTCG 58.614 41.667 0.00 0.00 0.00 4.35
2202 3377 5.940617 ACATGCTAAGATGTGGGCTAAATA 58.059 37.500 0.00 0.00 35.17 1.40
2346 3545 1.818060 TGCCTCGCTGCAAAATTACAT 59.182 42.857 0.00 0.00 38.56 2.29
2391 3676 4.261072 GGTTTTCCTCCTCGAGAAAAACAC 60.261 45.833 27.21 19.63 32.35 3.32
2399 3684 2.014068 GCCATGGTTTTCCTCCTCGAG 61.014 57.143 14.67 5.13 41.38 4.04
2412 3802 2.191375 CGATGCAGAGGCCATGGT 59.809 61.111 14.67 0.00 40.13 3.55
2611 6129 8.668510 ACAACATTACAACAATTGCCATTAAA 57.331 26.923 5.05 0.00 0.00 1.52
2612 6130 7.386299 GGACAACATTACAACAATTGCCATTAA 59.614 33.333 5.05 0.00 0.00 1.40
2613 6131 6.870965 GGACAACATTACAACAATTGCCATTA 59.129 34.615 5.05 0.00 0.00 1.90
2614 6132 5.700373 GGACAACATTACAACAATTGCCATT 59.300 36.000 5.05 0.00 0.00 3.16
2615 6133 5.011943 AGGACAACATTACAACAATTGCCAT 59.988 36.000 5.05 0.00 0.00 4.40
2616 6134 4.343526 AGGACAACATTACAACAATTGCCA 59.656 37.500 5.05 0.00 0.00 4.92
2617 6135 4.881920 AGGACAACATTACAACAATTGCC 58.118 39.130 5.05 0.00 0.00 4.52
2618 6136 5.982516 TGAAGGACAACATTACAACAATTGC 59.017 36.000 5.05 0.00 0.00 3.56
2619 6137 7.116662 CCATGAAGGACAACATTACAACAATTG 59.883 37.037 3.24 3.24 41.22 2.32
2620 6138 7.153985 CCATGAAGGACAACATTACAACAATT 58.846 34.615 0.00 0.00 41.22 2.32
2621 6139 6.295236 CCCATGAAGGACAACATTACAACAAT 60.295 38.462 0.00 0.00 41.22 2.71
2622 6140 5.010516 CCCATGAAGGACAACATTACAACAA 59.989 40.000 0.00 0.00 41.22 2.83
2623 6141 4.522405 CCCATGAAGGACAACATTACAACA 59.478 41.667 0.00 0.00 41.22 3.33
2624 6142 4.522789 ACCCATGAAGGACAACATTACAAC 59.477 41.667 0.00 0.00 41.22 3.32
2625 6143 4.735369 ACCCATGAAGGACAACATTACAA 58.265 39.130 0.00 0.00 41.22 2.41
2626 6144 4.380843 ACCCATGAAGGACAACATTACA 57.619 40.909 0.00 0.00 41.22 2.41
2627 6145 4.082245 CCAACCCATGAAGGACAACATTAC 60.082 45.833 0.00 0.00 41.22 1.89
2628 6146 4.085733 CCAACCCATGAAGGACAACATTA 58.914 43.478 0.00 0.00 41.22 1.90
2629 6147 2.899256 CCAACCCATGAAGGACAACATT 59.101 45.455 0.00 0.00 41.22 2.71
2630 6148 2.158325 ACCAACCCATGAAGGACAACAT 60.158 45.455 0.00 0.00 41.22 2.71
2631 6149 1.216678 ACCAACCCATGAAGGACAACA 59.783 47.619 0.00 0.00 41.22 3.33
2632 6150 1.613437 CACCAACCCATGAAGGACAAC 59.387 52.381 0.00 0.00 41.22 3.32
2633 6151 1.480312 CCACCAACCCATGAAGGACAA 60.480 52.381 0.00 0.00 41.22 3.18
2634 6152 0.112218 CCACCAACCCATGAAGGACA 59.888 55.000 0.00 0.00 41.22 4.02
2635 6153 1.250840 GCCACCAACCCATGAAGGAC 61.251 60.000 0.00 0.00 41.22 3.85
2636 6154 1.076549 GCCACCAACCCATGAAGGA 59.923 57.895 0.00 0.00 41.22 3.36
2637 6155 0.831288 TTGCCACCAACCCATGAAGG 60.831 55.000 0.00 0.00 37.03 3.46
2638 6156 0.604578 CTTGCCACCAACCCATGAAG 59.395 55.000 0.00 0.00 0.00 3.02
2639 6157 1.470996 GCTTGCCACCAACCCATGAA 61.471 55.000 0.00 0.00 0.00 2.57
2640 6158 1.907807 GCTTGCCACCAACCCATGA 60.908 57.895 0.00 0.00 0.00 3.07
2641 6159 1.474332 AAGCTTGCCACCAACCCATG 61.474 55.000 0.00 0.00 0.00 3.66
2642 6160 0.763986 AAAGCTTGCCACCAACCCAT 60.764 50.000 0.00 0.00 0.00 4.00
2643 6161 1.382420 AAAGCTTGCCACCAACCCA 60.382 52.632 0.00 0.00 0.00 4.51
2644 6162 1.367471 GAAAGCTTGCCACCAACCC 59.633 57.895 0.00 0.00 0.00 4.11
2645 6163 0.681175 ATGAAAGCTTGCCACCAACC 59.319 50.000 0.00 0.00 0.00 3.77
2646 6164 2.531522 AATGAAAGCTTGCCACCAAC 57.468 45.000 0.00 0.00 0.00 3.77
2647 6165 3.386078 TGTTAATGAAAGCTTGCCACCAA 59.614 39.130 0.00 0.00 0.00 3.67
2648 6166 2.961741 TGTTAATGAAAGCTTGCCACCA 59.038 40.909 0.00 0.00 0.00 4.17
2649 6167 3.658757 TGTTAATGAAAGCTTGCCACC 57.341 42.857 0.00 0.00 0.00 4.61
2650 6168 4.386652 CACATGTTAATGAAAGCTTGCCAC 59.613 41.667 0.00 0.00 37.24 5.01
2651 6169 4.039004 ACACATGTTAATGAAAGCTTGCCA 59.961 37.500 0.00 1.44 37.24 4.92
2652 6170 4.559153 ACACATGTTAATGAAAGCTTGCC 58.441 39.130 0.00 0.00 37.24 4.52
2653 6171 7.816945 ATAACACATGTTAATGAAAGCTTGC 57.183 32.000 8.47 0.00 42.93 4.01
2667 6185 9.959721 AGGACATAGAAAGTAAATAACACATGT 57.040 29.630 0.00 0.00 0.00 3.21
2670 6188 8.726988 GCAAGGACATAGAAAGTAAATAACACA 58.273 33.333 0.00 0.00 0.00 3.72
2671 6189 8.947115 AGCAAGGACATAGAAAGTAAATAACAC 58.053 33.333 0.00 0.00 0.00 3.32
2672 6190 9.515226 AAGCAAGGACATAGAAAGTAAATAACA 57.485 29.630 0.00 0.00 0.00 2.41
2673 6191 9.774742 CAAGCAAGGACATAGAAAGTAAATAAC 57.225 33.333 0.00 0.00 0.00 1.89
2674 6192 9.733556 TCAAGCAAGGACATAGAAAGTAAATAA 57.266 29.630 0.00 0.00 0.00 1.40
2675 6193 9.733556 TTCAAGCAAGGACATAGAAAGTAAATA 57.266 29.630 0.00 0.00 0.00 1.40
2676 6194 8.635765 TTCAAGCAAGGACATAGAAAGTAAAT 57.364 30.769 0.00 0.00 0.00 1.40
2677 6195 7.719633 ACTTCAAGCAAGGACATAGAAAGTAAA 59.280 33.333 0.00 0.00 36.26 2.01
2678 6196 7.224297 ACTTCAAGCAAGGACATAGAAAGTAA 58.776 34.615 0.00 0.00 36.26 2.24
2679 6197 6.769512 ACTTCAAGCAAGGACATAGAAAGTA 58.230 36.000 0.00 0.00 36.26 2.24
2680 6198 5.625150 ACTTCAAGCAAGGACATAGAAAGT 58.375 37.500 0.00 0.00 36.26 2.66
2681 6199 6.566197 AACTTCAAGCAAGGACATAGAAAG 57.434 37.500 0.00 0.00 36.26 2.62
2682 6200 8.103305 AGATAACTTCAAGCAAGGACATAGAAA 58.897 33.333 0.00 0.00 36.26 2.52
2683 6201 7.624549 AGATAACTTCAAGCAAGGACATAGAA 58.375 34.615 0.00 0.00 36.26 2.10
2684 6202 7.187824 AGATAACTTCAAGCAAGGACATAGA 57.812 36.000 0.00 0.00 36.26 1.98
2685 6203 6.199908 CGAGATAACTTCAAGCAAGGACATAG 59.800 42.308 0.00 0.00 36.26 2.23
2686 6204 6.042777 CGAGATAACTTCAAGCAAGGACATA 58.957 40.000 0.00 0.00 36.26 2.29
2687 6205 4.872691 CGAGATAACTTCAAGCAAGGACAT 59.127 41.667 0.00 0.00 36.26 3.06
2688 6206 4.021456 TCGAGATAACTTCAAGCAAGGACA 60.021 41.667 0.00 0.00 36.26 4.02
2689 6207 4.327627 GTCGAGATAACTTCAAGCAAGGAC 59.672 45.833 0.00 0.00 36.26 3.85
2690 6208 4.021456 TGTCGAGATAACTTCAAGCAAGGA 60.021 41.667 0.00 0.00 36.26 3.36
2691 6209 4.245660 TGTCGAGATAACTTCAAGCAAGG 58.754 43.478 0.00 0.00 36.26 3.61
2692 6210 6.128445 ACAATGTCGAGATAACTTCAAGCAAG 60.128 38.462 0.00 0.00 38.21 4.01
2693 6211 5.700832 ACAATGTCGAGATAACTTCAAGCAA 59.299 36.000 0.00 0.00 0.00 3.91
2694 6212 5.237815 ACAATGTCGAGATAACTTCAAGCA 58.762 37.500 0.00 0.00 0.00 3.91
2695 6213 5.786401 ACAATGTCGAGATAACTTCAAGC 57.214 39.130 0.00 0.00 0.00 4.01
2696 6214 7.121974 ACAACAATGTCGAGATAACTTCAAG 57.878 36.000 0.00 0.00 33.41 3.02
2697 6215 8.771920 ATACAACAATGTCGAGATAACTTCAA 57.228 30.769 0.00 0.00 41.05 2.69
2698 6216 8.032451 TGATACAACAATGTCGAGATAACTTCA 58.968 33.333 0.00 0.00 41.05 3.02
2699 6217 8.407457 TGATACAACAATGTCGAGATAACTTC 57.593 34.615 0.00 0.00 41.05 3.01
2700 6218 8.820933 CATGATACAACAATGTCGAGATAACTT 58.179 33.333 0.00 0.00 41.05 2.66
2701 6219 8.197439 TCATGATACAACAATGTCGAGATAACT 58.803 33.333 0.00 0.00 41.05 2.24
2702 6220 8.269424 GTCATGATACAACAATGTCGAGATAAC 58.731 37.037 0.00 0.00 41.05 1.89
2703 6221 7.167468 CGTCATGATACAACAATGTCGAGATAA 59.833 37.037 0.00 0.00 41.05 1.75
2704 6222 6.636850 CGTCATGATACAACAATGTCGAGATA 59.363 38.462 0.00 0.00 41.05 1.98
2705 6223 5.460091 CGTCATGATACAACAATGTCGAGAT 59.540 40.000 0.00 0.00 41.05 2.75
2706 6224 4.798387 CGTCATGATACAACAATGTCGAGA 59.202 41.667 0.00 0.00 41.05 4.04
2707 6225 4.548916 GCGTCATGATACAACAATGTCGAG 60.549 45.833 0.00 0.00 41.05 4.04
2708 6226 3.305897 GCGTCATGATACAACAATGTCGA 59.694 43.478 0.00 0.00 41.05 4.20
2709 6227 3.306973 AGCGTCATGATACAACAATGTCG 59.693 43.478 0.00 0.00 41.05 4.35
2710 6228 4.548916 CGAGCGTCATGATACAACAATGTC 60.549 45.833 0.00 0.00 41.05 3.06
2711 6229 3.306973 CGAGCGTCATGATACAACAATGT 59.693 43.478 0.00 0.00 43.74 2.71
2712 6230 3.551485 TCGAGCGTCATGATACAACAATG 59.449 43.478 0.00 0.00 0.00 2.82
2713 6231 3.780902 TCGAGCGTCATGATACAACAAT 58.219 40.909 0.00 0.00 0.00 2.71
2714 6232 3.119637 TCTCGAGCGTCATGATACAACAA 60.120 43.478 7.81 0.00 0.00 2.83
2715 6233 2.422127 TCTCGAGCGTCATGATACAACA 59.578 45.455 7.81 0.00 0.00 3.33
2716 6234 3.066369 TCTCGAGCGTCATGATACAAC 57.934 47.619 7.81 0.00 0.00 3.32
2717 6235 3.119637 TGTTCTCGAGCGTCATGATACAA 60.120 43.478 7.81 0.00 0.00 2.41
2718 6236 2.422127 TGTTCTCGAGCGTCATGATACA 59.578 45.455 7.81 0.00 0.00 2.29
2719 6237 3.039405 CTGTTCTCGAGCGTCATGATAC 58.961 50.000 7.81 0.00 0.00 2.24
2720 6238 2.683362 ACTGTTCTCGAGCGTCATGATA 59.317 45.455 7.81 0.00 0.00 2.15
2721 6239 1.474478 ACTGTTCTCGAGCGTCATGAT 59.526 47.619 7.81 0.00 0.00 2.45
2722 6240 0.881796 ACTGTTCTCGAGCGTCATGA 59.118 50.000 7.81 0.00 0.00 3.07
2723 6241 0.987715 CACTGTTCTCGAGCGTCATG 59.012 55.000 7.81 0.00 0.00 3.07
2724 6242 0.734253 GCACTGTTCTCGAGCGTCAT 60.734 55.000 7.81 0.00 0.00 3.06
2725 6243 1.371758 GCACTGTTCTCGAGCGTCA 60.372 57.895 7.81 5.76 0.00 4.35
2726 6244 2.089349 GGCACTGTTCTCGAGCGTC 61.089 63.158 7.81 0.95 0.00 5.19
2727 6245 2.049063 GGCACTGTTCTCGAGCGT 60.049 61.111 7.81 0.00 0.00 5.07
2728 6246 3.175240 CGGCACTGTTCTCGAGCG 61.175 66.667 7.81 0.00 0.00 5.03
2729 6247 1.803519 CTCGGCACTGTTCTCGAGC 60.804 63.158 7.81 0.00 41.69 5.03
2730 6248 4.467232 CTCGGCACTGTTCTCGAG 57.533 61.111 5.93 5.93 42.09 4.04
2731 6249 0.241213 CTTCTCGGCACTGTTCTCGA 59.759 55.000 0.00 0.00 0.00 4.04
2732 6250 0.241213 TCTTCTCGGCACTGTTCTCG 59.759 55.000 0.00 0.00 0.00 4.04
2733 6251 1.670380 GGTCTTCTCGGCACTGTTCTC 60.670 57.143 0.00 0.00 0.00 2.87
2734 6252 0.318762 GGTCTTCTCGGCACTGTTCT 59.681 55.000 0.00 0.00 0.00 3.01
2735 6253 0.033504 TGGTCTTCTCGGCACTGTTC 59.966 55.000 0.00 0.00 0.00 3.18
2736 6254 0.468226 TTGGTCTTCTCGGCACTGTT 59.532 50.000 0.00 0.00 0.00 3.16
2737 6255 0.687354 ATTGGTCTTCTCGGCACTGT 59.313 50.000 0.00 0.00 0.00 3.55
2738 6256 1.081892 CATTGGTCTTCTCGGCACTG 58.918 55.000 0.00 0.00 0.00 3.66
2739 6257 0.687354 ACATTGGTCTTCTCGGCACT 59.313 50.000 0.00 0.00 0.00 4.40
2740 6258 0.798776 CACATTGGTCTTCTCGGCAC 59.201 55.000 0.00 0.00 0.00 5.01
2741 6259 0.321564 CCACATTGGTCTTCTCGGCA 60.322 55.000 0.00 0.00 31.35 5.69
2742 6260 2.471255 CCACATTGGTCTTCTCGGC 58.529 57.895 0.00 0.00 31.35 5.54
2751 6269 4.757746 ATGGCTTCCACACCACATTGGT 62.758 50.000 0.00 0.00 43.70 3.67
2752 6270 0.827089 TGGCTTCCACACCACATTGG 60.827 55.000 0.00 0.00 45.02 3.16
2753 6271 1.203052 GATGGCTTCCACACCACATTG 59.797 52.381 0.00 0.00 39.19 2.82
2754 6272 1.549203 GATGGCTTCCACACCACATT 58.451 50.000 0.00 0.00 39.19 2.71
2755 6273 0.323725 GGATGGCTTCCACACCACAT 60.324 55.000 14.15 0.00 44.74 3.21
2756 6274 1.074775 GGATGGCTTCCACACCACA 59.925 57.895 14.15 0.00 44.74 4.17
2757 6275 4.002797 GGATGGCTTCCACACCAC 57.997 61.111 14.15 0.00 44.74 4.16
2764 6282 2.738743 TCAAATCCTTGGATGGCTTCC 58.261 47.619 12.30 12.30 45.69 3.46
2765 6283 3.492137 GCATCAAATCCTTGGATGGCTTC 60.492 47.826 2.56 0.00 33.01 3.86
2766 6284 2.433239 GCATCAAATCCTTGGATGGCTT 59.567 45.455 2.56 0.00 33.01 4.35
2767 6285 2.037144 GCATCAAATCCTTGGATGGCT 58.963 47.619 2.56 0.00 33.01 4.75
2768 6286 1.758280 TGCATCAAATCCTTGGATGGC 59.242 47.619 2.56 3.86 33.01 4.40
2769 6287 4.475051 TTTGCATCAAATCCTTGGATGG 57.525 40.909 2.56 0.00 33.01 3.51
2770 6288 5.526111 GGAATTTGCATCAAATCCTTGGATG 59.474 40.000 2.56 0.00 42.32 3.51
2771 6289 5.427481 AGGAATTTGCATCAAATCCTTGGAT 59.573 36.000 2.40 0.00 42.32 3.41
2772 6290 4.778958 AGGAATTTGCATCAAATCCTTGGA 59.221 37.500 2.40 0.00 42.32 3.53
2773 6291 5.093849 AGGAATTTGCATCAAATCCTTGG 57.906 39.130 2.40 0.00 42.32 3.61
2774 6292 5.114081 GGAGGAATTTGCATCAAATCCTTG 58.886 41.667 8.77 0.00 42.32 3.61
2775 6293 4.778958 TGGAGGAATTTGCATCAAATCCTT 59.221 37.500 8.77 0.72 42.32 3.36
2776 6294 4.355549 TGGAGGAATTTGCATCAAATCCT 58.644 39.130 7.36 7.36 42.32 3.24
2777 6295 4.741321 TGGAGGAATTTGCATCAAATCC 57.259 40.909 5.39 8.28 42.32 3.01
2778 6296 6.652062 AGTTTTGGAGGAATTTGCATCAAATC 59.348 34.615 5.39 8.23 42.32 2.17
2779 6297 6.536447 AGTTTTGGAGGAATTTGCATCAAAT 58.464 32.000 8.56 0.00 44.62 2.32
2780 6298 5.927819 AGTTTTGGAGGAATTTGCATCAAA 58.072 33.333 0.00 5.19 37.75 2.69
2783 6301 5.540911 TCAAGTTTTGGAGGAATTTGCATC 58.459 37.500 0.00 0.00 0.00 3.91
2790 6308 4.711846 GCCCTTATCAAGTTTTGGAGGAAT 59.288 41.667 0.00 0.00 31.63 3.01
2797 6315 6.590234 AGTTTAGGCCCTTATCAAGTTTTG 57.410 37.500 0.00 0.00 0.00 2.44
2802 6320 7.881775 AATGTAAGTTTAGGCCCTTATCAAG 57.118 36.000 0.00 0.00 0.00 3.02
2803 6321 8.658840 AAAATGTAAGTTTAGGCCCTTATCAA 57.341 30.769 0.00 0.00 29.22 2.57
2807 6325 8.973182 CCATTAAAATGTAAGTTTAGGCCCTTA 58.027 33.333 0.00 0.00 37.68 2.69
2808 6326 7.580688 GCCATTAAAATGTAAGTTTAGGCCCTT 60.581 37.037 0.00 0.00 39.98 3.95
2809 6327 6.127168 GCCATTAAAATGTAAGTTTAGGCCCT 60.127 38.462 0.00 0.00 39.98 5.19
2811 6329 6.635755 TGCCATTAAAATGTAAGTTTAGGCC 58.364 36.000 0.00 0.00 43.06 5.19
2825 6343 7.277981 ACAACGTTACAACAATTGCCATTAAAA 59.722 29.630 5.05 0.00 31.36 1.52
2832 6352 3.047093 GGACAACGTTACAACAATTGCC 58.953 45.455 5.05 0.00 31.36 4.52
2844 6364 1.953686 CAACCCATGAAGGACAACGTT 59.046 47.619 0.00 0.00 41.22 3.99
2931 6453 3.066369 TCTCGAGCGTCATGATACAAC 57.934 47.619 7.81 0.00 0.00 3.32
3177 6711 0.779997 AGCTTCACCCACCTTGGATT 59.220 50.000 0.00 0.00 40.96 3.01
3296 6848 2.038863 TCCAAGCCTGGGAGAGTTAA 57.961 50.000 0.35 0.00 43.71 2.01
3483 7238 7.627585 ATTTGTCATTACATGCGCAAATATC 57.372 32.000 17.11 7.02 40.34 1.63
3491 7246 5.740569 CCTCAAGAATTTGTCATTACATGCG 59.259 40.000 0.00 0.00 34.97 4.73
3499 7254 4.074970 AGAACGCCTCAAGAATTTGTCAT 58.925 39.130 0.00 0.00 35.73 3.06
3590 7353 3.624777 ACGCCTCAGGAATTTGAATGAT 58.375 40.909 0.00 0.00 0.00 2.45
3603 7366 1.151668 CCAAACAGAGAACGCCTCAG 58.848 55.000 7.96 2.88 44.40 3.35
3698 10096 1.779092 ACTGCCAGCCATTATCCAGAT 59.221 47.619 0.00 0.00 0.00 2.90
3728 10127 5.258456 AGATTATTGTCAAAGGCATGCTG 57.742 39.130 18.92 8.46 0.00 4.41
3736 10135 9.003658 AGACCAAACTGTAGATTATTGTCAAAG 57.996 33.333 0.00 0.00 0.00 2.77
3773 10333 7.915397 CGTTTCTTGATACATCCTTTTTATGGG 59.085 37.037 0.00 0.00 0.00 4.00
3774 10334 8.673711 TCGTTTCTTGATACATCCTTTTTATGG 58.326 33.333 0.00 0.00 0.00 2.74
4038 12457 1.067516 GGTCACAACAAATGCAGCAGT 59.932 47.619 0.00 0.00 0.00 4.40
4039 12458 1.774639 GGTCACAACAAATGCAGCAG 58.225 50.000 0.00 0.00 0.00 4.24
4040 12459 0.030504 CGGTCACAACAAATGCAGCA 59.969 50.000 0.00 0.00 0.00 4.41
4041 12460 0.310543 TCGGTCACAACAAATGCAGC 59.689 50.000 0.00 0.00 0.00 5.25
4042 12461 2.725759 CGATCGGTCACAACAAATGCAG 60.726 50.000 7.38 0.00 0.00 4.41
4043 12462 1.196581 CGATCGGTCACAACAAATGCA 59.803 47.619 7.38 0.00 0.00 3.96
4044 12463 1.196808 ACGATCGGTCACAACAAATGC 59.803 47.619 20.98 0.00 0.00 3.56
4045 12464 3.103793 GACGATCGGTCACAACAAATG 57.896 47.619 20.98 0.00 45.36 2.32
4138 12557 4.841443 ATCATGCATATTGTTGACGCAT 57.159 36.364 0.00 0.00 43.81 4.73
4271 12694 1.265095 GCGCACATTCATATGAGTGGG 59.735 52.381 26.33 25.89 44.63 4.61
4543 12968 7.601130 ACAACTTCATACTTACTACAATTCGCA 59.399 33.333 0.00 0.00 0.00 5.10
4560 12985 6.601613 TGGTAACTTCTTGTGAACAACTTCAT 59.398 34.615 0.00 0.00 36.66 2.57
4583 13008 8.936864 AGAAGAACGTATTGAATTTAGAACTGG 58.063 33.333 0.00 0.00 0.00 4.00
4621 13046 2.492012 CTGCAATCTTAGCCCTAGCAG 58.508 52.381 0.00 0.00 43.56 4.24


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

AutoCloner maintained by Alex Coulton.