Multiple sequence alignment - TraesCS3D01G370000

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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 TraesCS3D01G370000 chr3D 100.000 3257 0 0 1 3257 482609154 482605898 0.000000e+00 6015.0
1 TraesCS3D01G370000 chr3D 96.774 124 2 1 2505 2626 359257717 359257840 4.260000e-49 206.0
2 TraesCS3D01G370000 chr3D 96.774 124 2 1 2505 2626 477355200 477355323 4.260000e-49 206.0
3 TraesCS3D01G370000 chr3D 92.701 137 6 3 2505 2639 523189066 523189200 9.220000e-46 195.0
4 TraesCS3D01G370000 chr3D 81.548 168 27 4 3052 3219 129018689 129018852 5.670000e-28 135.0
5 TraesCS3D01G370000 chr3B 92.609 2530 123 28 15 2503 644922215 644919709 0.000000e+00 3578.0
6 TraesCS3D01G370000 chr3B 86.224 617 78 7 2628 3238 644919713 644919098 0.000000e+00 662.0
7 TraesCS3D01G370000 chr3B 96.032 126 3 1 2505 2628 699701441 699701566 1.530000e-48 204.0
8 TraesCS3D01G370000 chr3A 93.966 2138 100 12 380 2501 625556616 625554492 0.000000e+00 3206.0
9 TraesCS3D01G370000 chr3A 86.445 391 42 9 1 382 625562140 625561752 5.030000e-113 418.0
10 TraesCS3D01G370000 chr3A 81.378 392 65 6 2839 3228 625540923 625540538 2.440000e-81 313.0
11 TraesCS3D01G370000 chr3A 84.459 148 20 3 2628 2772 625554489 625554342 3.390000e-30 143.0
12 TraesCS3D01G370000 chr3A 82.090 134 21 2 3087 3219 140812194 140812063 9.550000e-21 111.0
13 TraesCS3D01G370000 chr2A 94.203 138 4 3 2499 2633 718972018 718971882 1.180000e-49 207.0
14 TraesCS3D01G370000 chr7A 96.774 124 2 1 2505 2626 466311267 466311144 4.260000e-49 206.0
15 TraesCS3D01G370000 chr6D 96.774 124 2 1 2505 2626 345490426 345490303 4.260000e-49 206.0
16 TraesCS3D01G370000 chr2B 93.478 138 7 1 2498 2633 396725543 396725406 1.530000e-48 204.0
17 TraesCS3D01G370000 chr2B 76.963 191 42 2 2960 3149 455474611 455474422 1.240000e-19 108.0
18 TraesCS3D01G370000 chr4A 92.754 138 7 2 2498 2633 175649143 175649007 2.560000e-46 196.0
19 TraesCS3D01G370000 chr4A 84.733 131 15 5 3029 3157 189665174 189665301 3.410000e-25 126.0
20 TraesCS3D01G370000 chr4A 95.238 42 2 0 2073 2114 114092809 114092850 2.100000e-07 67.6
21 TraesCS3D01G370000 chr1D 93.103 116 8 0 1805 1920 436069978 436070093 1.550000e-38 171.0
22 TraesCS3D01G370000 chr1D 92.920 113 8 0 1808 1920 32736552 32736440 7.230000e-37 165.0
23 TraesCS3D01G370000 chr7D 92.920 113 8 0 1808 1920 527011279 527011391 7.230000e-37 165.0
24 TraesCS3D01G370000 chr2D 92.241 116 9 0 1805 1920 562843914 562844029 7.230000e-37 165.0
25 TraesCS3D01G370000 chr2D 81.119 143 26 1 3037 3179 2624739 2624598 2.660000e-21 113.0
26 TraesCS3D01G370000 chr7B 90.179 112 11 0 1810 1921 677704195 677704306 2.620000e-31 147.0
27 TraesCS3D01G370000 chr1B 89.474 114 12 0 1808 1921 52240261 52240148 9.420000e-31 145.0
28 TraesCS3D01G370000 chr4D 84.677 124 17 2 3079 3201 355718349 355718471 4.410000e-24 122.0
29 TraesCS3D01G370000 chr4B 83.088 136 21 2 3067 3201 439207690 439207824 4.410000e-24 122.0


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 TraesCS3D01G370000 chr3D 482605898 482609154 3256 True 6015.0 6015 100.0000 1 3257 1 chr3D.!!$R1 3256
1 TraesCS3D01G370000 chr3B 644919098 644922215 3117 True 2120.0 3578 89.4165 15 3238 2 chr3B.!!$R1 3223
2 TraesCS3D01G370000 chr3A 625554342 625556616 2274 True 1674.5 3206 89.2125 380 2772 2 chr3A.!!$R4 2392

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
179 180 0.110295 TCAGGAACCACACACATGGG 59.890 55.0 0.00 0.0 44.81 4.00 F
188 189 0.323360 ACACACATGGGGGATTTCCG 60.323 55.0 2.86 0.0 36.71 4.30 F
1642 1689 0.456312 CTCGTCCAACCTACAGTCGC 60.456 60.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1748 1.153289 CTCCTGGTTGAGCCCGATG 60.153 63.158 0.00 0.0 36.04 3.84 R
2163 2210 4.070552 ACCTCGTGCGCCTTCTCC 62.071 66.667 4.18 0.0 0.00 3.71 R
2572 2631 0.110295 TTGGGTCACTGACATGTGGG 59.890 55.000 1.15 0.0 38.40 4.61 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
90 91 3.465403 CGAGCCTCCCCACTCTGG 61.465 72.222 0.00 0.00 37.25 3.86
94 95 2.673523 CCTCCCCACTCTGGCAAG 59.326 66.667 0.00 0.00 35.79 4.01
95 96 2.227036 CCTCCCCACTCTGGCAAGT 61.227 63.158 0.00 0.00 35.79 3.16
97 98 0.984230 CTCCCCACTCTGGCAAGTTA 59.016 55.000 0.00 0.00 35.79 2.24
104 105 2.416547 CACTCTGGCAAGTTACCAATCG 59.583 50.000 0.00 0.00 36.56 3.34
111 112 2.364632 CAAGTTACCAATCGCATCCCA 58.635 47.619 0.00 0.00 0.00 4.37
121 122 2.265904 CGCATCCCATCCCATGCAG 61.266 63.158 4.87 0.00 44.88 4.41
124 125 2.089368 ATCCCATCCCATGCAGGCT 61.089 57.895 0.00 0.00 35.39 4.58
126 127 2.599032 CCATCCCATGCAGGCTCA 59.401 61.111 0.00 0.00 35.39 4.26
132 133 1.214589 CCATGCAGGCTCACTTTGC 59.785 57.895 0.00 0.00 38.30 3.68
171 172 4.698201 TGTAGACATTTCAGGAACCACA 57.302 40.909 0.00 0.00 0.00 4.17
172 173 4.385825 TGTAGACATTTCAGGAACCACAC 58.614 43.478 0.00 0.00 0.00 3.82
173 174 3.576078 AGACATTTCAGGAACCACACA 57.424 42.857 0.00 0.00 0.00 3.72
174 175 3.214328 AGACATTTCAGGAACCACACAC 58.786 45.455 0.00 0.00 0.00 3.82
175 176 2.948979 GACATTTCAGGAACCACACACA 59.051 45.455 0.00 0.00 0.00 3.72
176 177 3.565307 ACATTTCAGGAACCACACACAT 58.435 40.909 0.00 0.00 0.00 3.21
177 178 3.318839 ACATTTCAGGAACCACACACATG 59.681 43.478 0.00 0.00 0.00 3.21
178 179 1.979855 TTCAGGAACCACACACATGG 58.020 50.000 0.00 0.00 46.10 3.66
179 180 0.110295 TCAGGAACCACACACATGGG 59.890 55.000 0.00 0.00 44.81 4.00
185 186 3.379617 CCACACACATGGGGGATTT 57.620 52.632 2.86 0.00 46.96 2.17
186 187 1.185315 CCACACACATGGGGGATTTC 58.815 55.000 2.86 0.00 46.96 2.17
187 188 1.185315 CACACACATGGGGGATTTCC 58.815 55.000 2.86 0.00 0.00 3.13
188 189 0.323360 ACACACATGGGGGATTTCCG 60.323 55.000 2.86 0.00 36.71 4.30
193 194 0.975040 CATGGGGGATTTCCGGCAAA 60.975 55.000 0.00 0.00 36.71 3.68
207 208 1.135517 CGGCAAAATTGGAACTACCGG 60.136 52.381 0.00 0.00 42.61 5.28
218 219 3.259123 TGGAACTACCGGTAGGAGTTTTC 59.741 47.826 37.97 30.22 42.61 2.29
231 232 1.396301 GAGTTTTCTGAGCTGCCGATG 59.604 52.381 0.00 0.00 0.00 3.84
234 235 2.541547 TTTCTGAGCTGCCGATGGGG 62.542 60.000 0.00 0.00 39.58 4.96
250 266 0.622136 GGGGGTTTACGGATGGAACT 59.378 55.000 0.00 0.00 0.00 3.01
251 267 1.407851 GGGGGTTTACGGATGGAACTC 60.408 57.143 0.00 0.00 0.00 3.01
252 268 1.648504 GGGTTTACGGATGGAACTCG 58.351 55.000 0.00 0.00 0.00 4.18
253 269 1.205417 GGGTTTACGGATGGAACTCGA 59.795 52.381 0.00 0.00 0.00 4.04
262 278 2.222886 GATGGAACTCGATCTCTCGGA 58.777 52.381 0.00 0.00 45.10 4.55
265 281 1.670791 GAACTCGATCTCTCGGAGGT 58.329 55.000 4.96 0.00 45.10 3.85
266 282 1.600485 GAACTCGATCTCTCGGAGGTC 59.400 57.143 4.96 4.59 45.10 3.85
288 305 4.079446 ACCAAGCAATCGGTGGTG 57.921 55.556 0.00 0.00 38.21 4.17
343 365 0.461548 TAGGACTGGATCAGCTTGCG 59.538 55.000 0.00 0.00 34.37 4.85
346 368 1.975363 GACTGGATCAGCTTGCGCAC 61.975 60.000 11.12 0.00 39.10 5.34
377 399 1.446099 TCAAAGCTAGCTCGCGGTG 60.446 57.895 19.65 11.27 34.40 4.94
401 424 2.358247 GAAAAGTCGAGGCCGCCA 60.358 61.111 13.15 0.00 35.37 5.69
424 447 2.836372 TGGGAGCTGCCATCTATCTATG 59.164 50.000 24.87 0.00 38.95 2.23
534 560 2.841389 CGTTAACGCACGAACGCT 59.159 55.556 16.05 0.00 43.15 5.07
633 660 1.965930 GCACGTGAATGTGGCTCCA 60.966 57.895 22.23 0.00 40.26 3.86
735 770 3.118334 TCCCGACGCCTTAAAATAATCCA 60.118 43.478 0.00 0.00 0.00 3.41
824 869 3.828875 AAACCCACAGATAGCTAGCTC 57.171 47.619 23.26 8.36 0.00 4.09
827 872 0.958091 CCACAGATAGCTAGCTCGCT 59.042 55.000 23.26 17.70 43.83 4.93
905 950 2.035576 CCGGCTTACTATATATCCCGCC 59.964 54.545 0.00 0.00 33.36 6.13
988 1035 1.227263 GGCCGAGCGAGCTAATCAA 60.227 57.895 0.00 0.00 0.00 2.57
1003 1050 4.442192 GCTAATCAACTCCGGAGAAGATGT 60.442 45.833 37.69 25.03 0.00 3.06
1407 1454 3.826282 CTCAGGAAGCTGGGGGAA 58.174 61.111 0.00 0.00 0.00 3.97
1443 1490 2.109126 GGACACGAGGGCAATGCTC 61.109 63.158 4.82 0.00 0.00 4.26
1635 1682 2.707849 GCTCCGCTCGTCCAACCTA 61.708 63.158 0.00 0.00 0.00 3.08
1642 1689 0.456312 CTCGTCCAACCTACAGTCGC 60.456 60.000 0.00 0.00 0.00 5.19
1842 1889 3.255379 GTCAAGATCGTCGGCGCC 61.255 66.667 19.07 19.07 38.14 6.53
2266 2313 1.275291 ACCCTTCGTGACGATCAATGT 59.725 47.619 9.08 0.00 35.23 2.71
2270 2317 3.501950 CTTCGTGACGATCAATGTCTCA 58.498 45.455 9.08 0.00 37.26 3.27
2278 2325 2.455032 GATCAATGTCTCACGACTCCG 58.545 52.381 0.00 0.00 40.86 4.63
2284 2331 2.675423 CTCACGACTCCGGTCCCA 60.675 66.667 0.00 0.00 39.15 4.37
2285 2332 2.987547 TCACGACTCCGGTCCCAC 60.988 66.667 0.00 0.00 39.15 4.61
2319 2366 5.010314 TGCTCAGCTGTTGATTCATTCTTTT 59.990 36.000 14.67 0.00 34.68 2.27
2320 2367 5.924825 GCTCAGCTGTTGATTCATTCTTTTT 59.075 36.000 14.67 0.00 34.68 1.94
2322 2369 7.281040 TCAGCTGTTGATTCATTCTTTTTCT 57.719 32.000 14.67 0.00 0.00 2.52
2323 2370 7.719483 TCAGCTGTTGATTCATTCTTTTTCTT 58.281 30.769 14.67 0.00 0.00 2.52
2340 2387 7.596995 TCTTTTTCTTTGTGTTGTTGTTACCTG 59.403 33.333 0.00 0.00 0.00 4.00
2347 2394 5.945155 TGTGTTGTTGTTACCTGTTCTTTC 58.055 37.500 0.00 0.00 0.00 2.62
2355 2404 9.575783 TGTTGTTACCTGTTCTTTCAAAATTAC 57.424 29.630 0.00 0.00 0.00 1.89
2364 2414 8.477419 TGTTCTTTCAAAATTACTTGGATCCT 57.523 30.769 14.23 0.00 0.00 3.24
2442 2492 6.539173 TGGTTGCTTACTTATTCTTTGGAGA 58.461 36.000 0.00 0.00 0.00 3.71
2460 2510 4.103785 TGGAGAATGATCCCATCTCTTTCC 59.896 45.833 15.13 4.84 38.72 3.13
2484 2538 5.716094 TCAGAGATGATTTTGCCATGTTTG 58.284 37.500 0.00 0.00 0.00 2.93
2516 2575 3.765349 TTTTTGCGGACGATGCTTC 57.235 47.368 0.00 0.00 0.00 3.86
2525 2584 4.513519 CGATGCTTCGGTGCCTTA 57.486 55.556 13.82 0.00 41.74 2.69
2526 2585 2.301505 CGATGCTTCGGTGCCTTAG 58.698 57.895 13.82 0.00 41.74 2.18
2527 2586 1.766143 CGATGCTTCGGTGCCTTAGC 61.766 60.000 13.82 0.00 41.74 3.09
2538 2597 2.489938 TGCCTTAGCACCTACCTTTG 57.510 50.000 0.00 0.00 46.52 2.77
2539 2598 1.702957 TGCCTTAGCACCTACCTTTGT 59.297 47.619 0.00 0.00 46.52 2.83
2540 2599 2.084546 GCCTTAGCACCTACCTTTGTG 58.915 52.381 0.00 0.00 39.53 3.33
2541 2600 2.552373 GCCTTAGCACCTACCTTTGTGT 60.552 50.000 0.00 0.00 39.53 3.72
2542 2601 3.335579 CCTTAGCACCTACCTTTGTGTC 58.664 50.000 0.00 0.00 34.94 3.67
2543 2602 3.008049 CCTTAGCACCTACCTTTGTGTCT 59.992 47.826 0.00 0.00 34.94 3.41
2544 2603 4.222145 CCTTAGCACCTACCTTTGTGTCTA 59.778 45.833 0.00 0.00 34.94 2.59
2545 2604 5.104900 CCTTAGCACCTACCTTTGTGTCTAT 60.105 44.000 0.00 0.00 34.94 1.98
2546 2605 4.207891 AGCACCTACCTTTGTGTCTATG 57.792 45.455 0.00 0.00 34.94 2.23
2547 2606 3.838317 AGCACCTACCTTTGTGTCTATGA 59.162 43.478 0.00 0.00 34.94 2.15
2548 2607 3.933332 GCACCTACCTTTGTGTCTATGAC 59.067 47.826 0.00 0.00 34.94 3.06
2549 2608 4.562757 GCACCTACCTTTGTGTCTATGACA 60.563 45.833 0.00 0.00 40.50 3.58
2550 2609 5.734720 CACCTACCTTTGTGTCTATGACAT 58.265 41.667 3.65 0.00 44.63 3.06
2551 2610 5.582269 CACCTACCTTTGTGTCTATGACATG 59.418 44.000 3.65 0.00 44.63 3.21
2552 2611 5.248477 ACCTACCTTTGTGTCTATGACATGT 59.752 40.000 0.00 0.00 44.63 3.21
2553 2612 5.582269 CCTACCTTTGTGTCTATGACATGTG 59.418 44.000 1.15 0.00 44.63 3.21
2554 2613 4.326826 ACCTTTGTGTCTATGACATGTGG 58.673 43.478 1.15 0.00 44.63 4.17
2555 2614 3.691118 CCTTTGTGTCTATGACATGTGGG 59.309 47.826 1.15 2.15 44.63 4.61
2556 2615 2.401583 TGTGTCTATGACATGTGGGC 57.598 50.000 1.15 0.00 44.63 5.36
2557 2616 1.065491 TGTGTCTATGACATGTGGGCC 60.065 52.381 1.15 0.00 44.63 5.80
2558 2617 0.546122 TGTCTATGACATGTGGGCCC 59.454 55.000 17.59 17.59 37.67 5.80
2559 2618 0.546122 GTCTATGACATGTGGGCCCA 59.454 55.000 24.45 24.45 32.09 5.36
2560 2619 1.064758 GTCTATGACATGTGGGCCCAA 60.065 52.381 30.64 17.87 32.09 4.12
2561 2620 1.064758 TCTATGACATGTGGGCCCAAC 60.065 52.381 30.64 21.29 0.00 3.77
2562 2621 0.701147 TATGACATGTGGGCCCAACA 59.299 50.000 30.64 26.33 0.00 3.33
2563 2622 0.178938 ATGACATGTGGGCCCAACAA 60.179 50.000 30.64 16.52 0.00 2.83
2564 2623 0.827089 TGACATGTGGGCCCAACAAG 60.827 55.000 30.64 24.28 0.00 3.16
2565 2624 0.827507 GACATGTGGGCCCAACAAGT 60.828 55.000 30.64 27.21 0.00 3.16
2566 2625 1.114722 ACATGTGGGCCCAACAAGTG 61.115 55.000 30.64 22.61 0.00 3.16
2574 2633 3.305516 CCAACAAGTGGCTGGCCC 61.306 66.667 9.28 0.85 41.72 5.80
2575 2634 2.521465 CAACAAGTGGCTGGCCCA 60.521 61.111 9.28 0.00 42.79 5.36
2582 2641 3.578286 TGGCTGGCCCACATGTCA 61.578 61.111 9.28 0.00 39.18 3.58
2583 2642 2.753043 GGCTGGCCCACATGTCAG 60.753 66.667 0.00 7.70 0.00 3.51
2584 2643 2.034687 GCTGGCCCACATGTCAGT 59.965 61.111 12.37 0.00 0.00 3.41
2585 2644 2.338015 GCTGGCCCACATGTCAGTG 61.338 63.158 12.37 0.00 39.21 3.66
2586 2645 1.376086 CTGGCCCACATGTCAGTGA 59.624 57.895 0.00 0.00 42.05 3.41
2587 2646 0.957395 CTGGCCCACATGTCAGTGAC 60.957 60.000 16.68 16.68 42.05 3.67
2588 2647 1.675641 GGCCCACATGTCAGTGACC 60.676 63.158 20.43 2.99 42.05 4.02
2589 2648 1.675641 GCCCACATGTCAGTGACCC 60.676 63.158 20.43 0.00 42.05 4.46
2590 2649 1.760527 CCCACATGTCAGTGACCCA 59.239 57.895 20.43 3.20 42.05 4.51
2591 2650 0.110295 CCCACATGTCAGTGACCCAA 59.890 55.000 20.43 2.34 42.05 4.12
2592 2651 1.478471 CCCACATGTCAGTGACCCAAA 60.478 52.381 20.43 1.95 42.05 3.28
2593 2652 1.881973 CCACATGTCAGTGACCCAAAG 59.118 52.381 20.43 8.14 42.05 2.77
2594 2653 1.881973 CACATGTCAGTGACCCAAAGG 59.118 52.381 20.43 6.15 42.05 3.11
2595 2654 0.883833 CATGTCAGTGACCCAAAGGC 59.116 55.000 20.43 0.00 36.11 4.35
2596 2655 0.478072 ATGTCAGTGACCCAAAGGCA 59.522 50.000 20.43 0.00 36.11 4.75
2597 2656 0.179020 TGTCAGTGACCCAAAGGCAG 60.179 55.000 20.43 0.00 36.11 4.85
2598 2657 0.890996 GTCAGTGACCCAAAGGCAGG 60.891 60.000 12.54 0.00 36.11 4.85
2599 2658 1.151450 CAGTGACCCAAAGGCAGGT 59.849 57.895 0.00 0.00 39.75 4.00
2600 2659 1.151450 AGTGACCCAAAGGCAGGTG 59.849 57.895 0.00 0.00 36.17 4.00
2601 2660 2.203480 TGACCCAAAGGCAGGTGC 60.203 61.111 0.00 0.00 36.17 5.01
2619 2678 3.249687 CCTTTAAGGCACCGAAGCT 57.750 52.632 0.00 0.00 34.17 3.74
2620 2679 0.804989 CCTTTAAGGCACCGAAGCTG 59.195 55.000 0.00 0.00 34.17 4.24
2621 2680 0.169009 CTTTAAGGCACCGAAGCTGC 59.831 55.000 0.00 0.00 34.17 5.25
2622 2681 0.536233 TTTAAGGCACCGAAGCTGCA 60.536 50.000 1.02 0.00 36.27 4.41
2623 2682 0.322456 TTAAGGCACCGAAGCTGCAT 60.322 50.000 1.02 0.00 36.27 3.96
2624 2683 0.744414 TAAGGCACCGAAGCTGCATC 60.744 55.000 1.02 0.00 36.27 3.91
2625 2684 3.512516 GGCACCGAAGCTGCATCC 61.513 66.667 1.02 0.00 36.27 3.51
2626 2685 2.747460 GCACCGAAGCTGCATCCA 60.747 61.111 1.02 0.00 34.56 3.41
2627 2686 2.117156 GCACCGAAGCTGCATCCAT 61.117 57.895 1.02 0.00 34.56 3.41
2628 2687 1.660560 GCACCGAAGCTGCATCCATT 61.661 55.000 1.02 0.00 34.56 3.16
2629 2688 0.813184 CACCGAAGCTGCATCCATTT 59.187 50.000 1.02 0.00 0.00 2.32
2630 2689 1.203052 CACCGAAGCTGCATCCATTTT 59.797 47.619 1.02 0.00 0.00 1.82
2631 2690 1.895131 ACCGAAGCTGCATCCATTTTT 59.105 42.857 1.02 0.00 0.00 1.94
2678 2737 3.350219 TGGAGTGACCATAAGCCTTTC 57.650 47.619 0.00 0.00 44.64 2.62
2680 2739 4.101114 TGGAGTGACCATAAGCCTTTCTA 58.899 43.478 0.00 0.00 44.64 2.10
2681 2740 4.721776 TGGAGTGACCATAAGCCTTTCTAT 59.278 41.667 0.00 0.00 44.64 1.98
2683 2742 6.385759 TGGAGTGACCATAAGCCTTTCTATTA 59.614 38.462 0.00 0.00 44.64 0.98
2713 2774 0.587768 TGCAAATGCTGACACTCGTG 59.412 50.000 6.97 0.00 42.66 4.35
2732 2793 5.463286 TCGTGTAAATGTACGAACACTCAT 58.537 37.500 14.11 0.00 45.18 2.90
2779 2841 1.209504 CCCCGATGAGCACCTCTAAAA 59.790 52.381 0.00 0.00 0.00 1.52
2786 2848 6.100004 CGATGAGCACCTCTAAAAGACTAAA 58.900 40.000 0.00 0.00 0.00 1.85
2788 2850 5.548406 TGAGCACCTCTAAAAGACTAAACC 58.452 41.667 0.00 0.00 0.00 3.27
2790 2852 3.124806 GCACCTCTAAAAGACTAAACCGC 59.875 47.826 0.00 0.00 0.00 5.68
2791 2853 4.312443 CACCTCTAAAAGACTAAACCGCA 58.688 43.478 0.00 0.00 0.00 5.69
2794 2857 6.002082 ACCTCTAAAAGACTAAACCGCAAAT 58.998 36.000 0.00 0.00 0.00 2.32
2804 2867 6.092807 AGACTAAACCGCAAATCTTGAGATTC 59.907 38.462 6.70 0.00 43.41 2.52
2826 2889 3.123621 CACGAACTTAACACATGAGCCTC 59.876 47.826 0.00 0.00 0.00 4.70
2832 2895 4.021368 ACTTAACACATGAGCCTCGTAGTT 60.021 41.667 0.00 8.44 0.00 2.24
2833 2896 2.370281 ACACATGAGCCTCGTAGTTG 57.630 50.000 0.00 0.00 0.00 3.16
2851 2914 1.996798 TGACGAGAACCTTGTCTCCT 58.003 50.000 13.63 0.00 43.31 3.69
2854 2917 2.296471 GACGAGAACCTTGTCTCCTTGA 59.704 50.000 7.01 0.00 40.63 3.02
2905 2968 9.719355 AAATAAATCCAGGAAAATACAAACACC 57.281 29.630 0.00 0.00 0.00 4.16
2931 2994 3.181506 GCCAAGTCTAGATTTTGAAGCCG 60.182 47.826 17.01 5.62 0.00 5.52
2944 3007 2.198304 GAAGCCGGGTGGATTGACCT 62.198 60.000 7.07 0.00 45.88 3.85
2958 3021 4.276926 GGATTGACCTTATGATTGTCAGGC 59.723 45.833 0.00 0.00 39.89 4.85
2964 3027 4.660303 ACCTTATGATTGTCAGGCCATCTA 59.340 41.667 5.01 0.00 0.00 1.98
2968 3031 4.508551 TGATTGTCAGGCCATCTACAAT 57.491 40.909 18.97 18.97 43.36 2.71
2983 3047 1.161843 ACAATGCGTCCCCTAAAACG 58.838 50.000 0.00 0.00 41.68 3.60
2984 3048 0.450184 CAATGCGTCCCCTAAAACGG 59.550 55.000 0.00 0.00 39.24 4.44
2990 3054 1.516161 GTCCCCTAAAACGGACACAC 58.484 55.000 1.38 0.00 46.59 3.82
2996 3060 4.181578 CCCTAAAACGGACACACTATCTG 58.818 47.826 0.00 0.00 0.00 2.90
3001 3065 1.819288 ACGGACACACTATCTGTCAGG 59.181 52.381 0.00 0.00 39.97 3.86
3008 3072 1.678627 CACTATCTGTCAGGGGACTCG 59.321 57.143 0.00 0.00 44.61 4.18
3010 3074 1.950909 CTATCTGTCAGGGGACTCGTC 59.049 57.143 0.00 0.00 44.61 4.20
3026 3090 3.135457 TCCACGAGCGCGGATACA 61.135 61.111 15.86 0.00 43.17 2.29
3027 3091 2.655364 CCACGAGCGCGGATACAG 60.655 66.667 15.86 0.00 43.17 2.74
3028 3092 2.655364 CACGAGCGCGGATACAGG 60.655 66.667 15.86 0.00 43.17 4.00
3033 3097 4.221422 GCGCGGATACAGGAGCCA 62.221 66.667 8.83 0.00 30.53 4.75
3035 3099 2.280457 GCGGATACAGGAGCCAGC 60.280 66.667 0.00 0.00 30.53 4.85
3040 3104 0.036022 GATACAGGAGCCAGCCATCC 59.964 60.000 0.00 0.00 35.71 3.51
3042 3106 0.913934 TACAGGAGCCAGCCATCCAA 60.914 55.000 1.29 0.00 38.12 3.53
3063 3127 0.458889 CGCATTCCCTAAACGTCCGA 60.459 55.000 0.00 0.00 0.00 4.55
3065 3129 1.673626 GCATTCCCTAAACGTCCGACA 60.674 52.381 0.00 0.00 0.00 4.35
3066 3130 2.901249 CATTCCCTAAACGTCCGACAT 58.099 47.619 0.00 0.00 0.00 3.06
3067 3131 2.373540 TTCCCTAAACGTCCGACATG 57.626 50.000 0.00 0.00 0.00 3.21
3084 3148 2.305927 ACATGGTCCGACCTCTTTCATT 59.694 45.455 18.54 0.00 39.58 2.57
3085 3149 2.762535 TGGTCCGACCTCTTTCATTC 57.237 50.000 18.54 0.00 39.58 2.67
3087 3151 1.278127 GGTCCGACCTCTTTCATTCCA 59.722 52.381 10.59 0.00 34.73 3.53
3100 3164 6.880484 TCTTTCATTCCAAATGCATAGCAAT 58.120 32.000 0.00 0.00 43.62 3.56
3116 3180 8.415553 TGCATAGCAATATGAGCAAATTAAAGT 58.584 29.630 3.57 0.00 34.76 2.66
3122 3186 3.281341 TGAGCAAATTAAAGTGCGGTG 57.719 42.857 7.79 0.00 45.62 4.94
3168 3232 4.851639 AAAAGAGGTGCATCTCCATAGT 57.148 40.909 23.46 1.11 34.46 2.12
3181 3245 3.625764 TCTCCATAGTTTTTACATGCGCC 59.374 43.478 4.18 0.00 0.00 6.53
3192 3256 0.523072 ACATGCGCCTGATCACAAAC 59.477 50.000 19.95 0.00 0.00 2.93
3193 3257 0.521867 CATGCGCCTGATCACAAACG 60.522 55.000 6.88 0.00 0.00 3.60
3194 3258 0.955428 ATGCGCCTGATCACAAACGT 60.955 50.000 4.18 0.00 0.00 3.99
3200 3265 2.290641 GCCTGATCACAAACGTTTCAGT 59.709 45.455 20.05 11.07 33.56 3.41
3201 3266 3.243068 GCCTGATCACAAACGTTTCAGTT 60.243 43.478 20.05 8.67 33.56 3.16
3203 3268 4.035091 CCTGATCACAAACGTTTCAGTTCA 59.965 41.667 20.05 17.96 33.56 3.18
3206 3271 4.335082 TCACAAACGTTTCAGTTCAGTG 57.665 40.909 11.37 13.93 39.37 3.66
3212 3277 2.158813 ACGTTTCAGTTCAGTGGTCCAT 60.159 45.455 0.00 0.00 0.00 3.41
3213 3278 2.224079 CGTTTCAGTTCAGTGGTCCATG 59.776 50.000 0.00 0.00 0.00 3.66
3214 3279 1.896220 TTCAGTTCAGTGGTCCATGC 58.104 50.000 0.00 0.00 0.00 4.06
3218 3283 2.361757 CAGTTCAGTGGTCCATGCAAAA 59.638 45.455 0.00 0.00 0.00 2.44
3219 3284 2.362077 AGTTCAGTGGTCCATGCAAAAC 59.638 45.455 0.00 0.00 0.00 2.43
3220 3285 0.950836 TCAGTGGTCCATGCAAAACG 59.049 50.000 0.00 0.00 0.00 3.60
3221 3286 0.039256 CAGTGGTCCATGCAAAACGG 60.039 55.000 0.00 0.00 0.00 4.44
3222 3287 1.372872 GTGGTCCATGCAAAACGGC 60.373 57.895 0.00 0.00 0.00 5.68
3238 3303 1.278699 ACGGCATTTTTGCATTCCCAT 59.721 42.857 0.00 0.00 36.33 4.00
3239 3304 2.290197 ACGGCATTTTTGCATTCCCATT 60.290 40.909 0.00 0.00 36.33 3.16
3240 3305 2.096174 CGGCATTTTTGCATTCCCATTG 59.904 45.455 0.00 0.00 36.33 2.82
3241 3306 3.345414 GGCATTTTTGCATTCCCATTGA 58.655 40.909 0.00 0.00 36.33 2.57
3242 3307 3.375922 GGCATTTTTGCATTCCCATTGAG 59.624 43.478 0.00 0.00 36.33 3.02
3243 3308 4.255301 GCATTTTTGCATTCCCATTGAGA 58.745 39.130 0.00 0.00 34.41 3.27
3244 3309 4.879545 GCATTTTTGCATTCCCATTGAGAT 59.120 37.500 0.00 0.00 34.41 2.75
3245 3310 5.007332 GCATTTTTGCATTCCCATTGAGATC 59.993 40.000 0.00 0.00 34.41 2.75
3246 3311 4.741321 TTTTGCATTCCCATTGAGATCC 57.259 40.909 0.00 0.00 0.00 3.36
3247 3312 3.385314 TTGCATTCCCATTGAGATCCA 57.615 42.857 0.00 0.00 0.00 3.41
3248 3313 3.385314 TGCATTCCCATTGAGATCCAA 57.615 42.857 0.00 0.00 39.41 3.53
3249 3314 3.025978 TGCATTCCCATTGAGATCCAAC 58.974 45.455 0.00 0.00 37.63 3.77
3250 3315 3.294214 GCATTCCCATTGAGATCCAACT 58.706 45.455 0.00 0.00 37.63 3.16
3251 3316 3.317430 GCATTCCCATTGAGATCCAACTC 59.683 47.826 0.00 0.00 37.63 3.01
3252 3317 2.988010 TCCCATTGAGATCCAACTCG 57.012 50.000 0.00 0.00 39.49 4.18
3253 3318 2.187958 TCCCATTGAGATCCAACTCGT 58.812 47.619 0.00 0.00 39.49 4.18
3254 3319 2.168521 TCCCATTGAGATCCAACTCGTC 59.831 50.000 0.00 0.00 39.49 4.20
3255 3320 2.555199 CCATTGAGATCCAACTCGTCC 58.445 52.381 0.00 0.00 39.49 4.79
3256 3321 2.093500 CCATTGAGATCCAACTCGTCCA 60.093 50.000 0.00 0.00 39.49 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.668706 CAGGAGCATAGGGAATCGCG 60.669 60.000 0.00 0.00 0.00 5.87
1 2 0.952984 GCAGGAGCATAGGGAATCGC 60.953 60.000 0.00 0.00 41.58 4.58
2 3 0.321122 GGCAGGAGCATAGGGAATCG 60.321 60.000 0.00 0.00 44.61 3.34
3 4 1.063183 AGGCAGGAGCATAGGGAATC 58.937 55.000 0.00 0.00 44.61 2.52
4 5 2.422939 TAGGCAGGAGCATAGGGAAT 57.577 50.000 0.00 0.00 44.61 3.01
5 6 2.422939 ATAGGCAGGAGCATAGGGAA 57.577 50.000 0.00 0.00 40.73 3.97
6 7 2.260822 GAATAGGCAGGAGCATAGGGA 58.739 52.381 0.00 0.00 40.73 4.20
7 8 1.066573 CGAATAGGCAGGAGCATAGGG 60.067 57.143 0.00 0.00 40.73 3.53
8 9 1.620819 ACGAATAGGCAGGAGCATAGG 59.379 52.381 0.00 0.00 40.73 2.57
9 10 3.255888 TGTACGAATAGGCAGGAGCATAG 59.744 47.826 0.00 0.00 40.73 2.23
10 11 3.227614 TGTACGAATAGGCAGGAGCATA 58.772 45.455 0.00 0.00 44.61 3.14
11 12 2.039418 TGTACGAATAGGCAGGAGCAT 58.961 47.619 0.00 0.00 44.61 3.79
12 13 1.480789 TGTACGAATAGGCAGGAGCA 58.519 50.000 0.00 0.00 44.61 4.26
13 14 2.596904 TTGTACGAATAGGCAGGAGC 57.403 50.000 0.00 0.00 41.10 4.70
90 91 1.065551 GGGATGCGATTGGTAACTTGC 59.934 52.381 0.00 0.00 37.61 4.01
94 95 1.880027 GGATGGGATGCGATTGGTAAC 59.120 52.381 0.00 0.00 0.00 2.50
95 96 1.202879 GGGATGGGATGCGATTGGTAA 60.203 52.381 0.00 0.00 0.00 2.85
97 98 1.151450 GGGATGGGATGCGATTGGT 59.849 57.895 0.00 0.00 0.00 3.67
104 105 1.906824 CCTGCATGGGATGGGATGC 60.907 63.158 0.00 0.00 44.42 3.91
111 112 0.333993 AAAGTGAGCCTGCATGGGAT 59.666 50.000 0.00 0.00 36.00 3.85
121 122 1.372128 CCTTTGCGCAAAGTGAGCC 60.372 57.895 43.76 2.33 42.67 4.70
124 125 2.199652 CCCCCTTTGCGCAAAGTGA 61.200 57.895 43.76 23.53 44.66 3.41
126 127 3.615709 GCCCCCTTTGCGCAAAGT 61.616 61.111 43.76 0.00 44.66 2.66
132 133 4.729918 AGCTCAGCCCCCTTTGCG 62.730 66.667 0.00 0.00 0.00 4.85
142 143 3.373439 CCTGAAATGTCTACAAGCTCAGC 59.627 47.826 11.24 0.00 32.83 4.26
171 172 1.306296 CCGGAAATCCCCCATGTGT 59.694 57.895 0.00 0.00 0.00 3.72
172 173 2.127232 GCCGGAAATCCCCCATGTG 61.127 63.158 5.05 0.00 0.00 3.21
173 174 2.161713 TTGCCGGAAATCCCCCATGT 62.162 55.000 5.05 0.00 0.00 3.21
174 175 0.975040 TTTGCCGGAAATCCCCCATG 60.975 55.000 5.05 0.00 0.00 3.66
175 176 0.252467 TTTTGCCGGAAATCCCCCAT 60.252 50.000 5.05 0.00 0.00 4.00
176 177 0.252467 ATTTTGCCGGAAATCCCCCA 60.252 50.000 5.05 0.00 0.00 4.96
177 178 0.908910 AATTTTGCCGGAAATCCCCC 59.091 50.000 5.05 0.00 0.00 5.40
178 179 1.406751 CCAATTTTGCCGGAAATCCCC 60.407 52.381 5.05 0.00 0.00 4.81
179 180 1.552792 TCCAATTTTGCCGGAAATCCC 59.447 47.619 5.05 0.00 0.00 3.85
180 181 3.000041 GTTCCAATTTTGCCGGAAATCC 59.000 45.455 5.05 0.00 40.40 3.01
181 182 3.925379 AGTTCCAATTTTGCCGGAAATC 58.075 40.909 5.05 0.00 40.40 2.17
182 183 4.322424 GGTAGTTCCAATTTTGCCGGAAAT 60.322 41.667 5.05 0.00 40.40 2.17
183 184 3.006003 GGTAGTTCCAATTTTGCCGGAAA 59.994 43.478 5.05 0.00 40.40 3.13
184 185 2.559231 GGTAGTTCCAATTTTGCCGGAA 59.441 45.455 5.05 0.00 36.46 4.30
185 186 2.164338 GGTAGTTCCAATTTTGCCGGA 58.836 47.619 5.05 0.00 35.97 5.14
186 187 1.135517 CGGTAGTTCCAATTTTGCCGG 60.136 52.381 0.00 0.00 34.97 6.13
187 188 1.135517 CCGGTAGTTCCAATTTTGCCG 60.136 52.381 0.00 0.00 37.92 5.69
188 189 1.890489 ACCGGTAGTTCCAATTTTGCC 59.110 47.619 4.49 0.00 35.57 4.52
193 194 3.447950 ACTCCTACCGGTAGTTCCAATT 58.552 45.455 33.97 12.63 35.57 2.32
207 208 2.351455 GGCAGCTCAGAAAACTCCTAC 58.649 52.381 0.00 0.00 0.00 3.18
218 219 4.559063 CCCCCATCGGCAGCTCAG 62.559 72.222 0.00 0.00 0.00 3.35
231 232 0.622136 AGTTCCATCCGTAAACCCCC 59.378 55.000 0.00 0.00 0.00 5.40
234 235 2.660189 TCGAGTTCCATCCGTAAACC 57.340 50.000 0.00 0.00 0.00 3.27
250 266 0.179043 CAGGACCTCCGAGAGATCGA 60.179 60.000 0.00 0.00 42.08 3.59
251 267 1.791103 GCAGGACCTCCGAGAGATCG 61.791 65.000 0.00 0.00 42.08 3.69
252 268 0.753479 TGCAGGACCTCCGAGAGATC 60.753 60.000 0.00 0.00 42.08 2.75
253 269 1.040339 GTGCAGGACCTCCGAGAGAT 61.040 60.000 0.00 0.00 42.08 2.75
287 304 3.060138 GCACGATCTTAACGTTTGACACA 60.060 43.478 5.91 0.00 42.07 3.72
288 305 3.183775 AGCACGATCTTAACGTTTGACAC 59.816 43.478 5.91 3.54 42.07 3.67
346 368 2.594303 TTTGACTGGCCAGGTGCG 60.594 61.111 35.42 12.80 42.61 5.34
353 375 1.086634 CGAGCTAGCTTTGACTGGCC 61.087 60.000 20.42 0.00 44.59 5.36
356 378 1.416813 CCGCGAGCTAGCTTTGACTG 61.417 60.000 20.42 6.07 34.40 3.51
377 399 1.157585 GCCTCGACTTTTCCTTCACC 58.842 55.000 0.00 0.00 0.00 4.02
401 424 2.346529 AGATAGATGGCAGCTCCCATT 58.653 47.619 11.43 3.69 45.41 3.16
534 560 6.549364 ACATTTTGGATAGTTGACTTTGTGGA 59.451 34.615 0.00 0.00 0.00 4.02
597 623 0.810426 GCTAGGCCCTCGCTTTGTAC 60.810 60.000 0.00 0.00 34.44 2.90
598 624 1.261938 TGCTAGGCCCTCGCTTTGTA 61.262 55.000 8.88 0.00 34.44 2.41
827 872 4.308899 GCTGGAGCTCTAGTTTATTCGA 57.691 45.455 25.84 0.00 38.21 3.71
878 923 5.658190 GGGATATATAGTAAGCCGGTTGGTA 59.342 44.000 1.90 0.00 37.67 3.25
988 1035 0.820871 GCTGACATCTTCTCCGGAGT 59.179 55.000 30.17 11.65 0.00 3.85
1047 1094 1.860641 TCGGGCAGAGGAAGTATGAA 58.139 50.000 0.00 0.00 0.00 2.57
1050 1097 2.243810 GAGATCGGGCAGAGGAAGTAT 58.756 52.381 0.00 0.00 0.00 2.12
1351 1398 4.443266 GGCGTCGGAGAGCAGCTT 62.443 66.667 0.00 0.00 36.95 3.74
1407 1454 3.958147 CTCGCACTCGGCCACCAAT 62.958 63.158 2.24 0.00 40.31 3.16
1443 1490 3.461773 ACGCCATCCTGGGACTCG 61.462 66.667 0.00 0.00 38.19 4.18
1701 1748 1.153289 CTCCTGGTTGAGCCCGATG 60.153 63.158 0.00 0.00 36.04 3.84
2163 2210 4.070552 ACCTCGTGCGCCTTCTCC 62.071 66.667 4.18 0.00 0.00 3.71
2266 2313 2.360852 GGGACCGGAGTCGTGAGA 60.361 66.667 9.46 0.00 44.54 3.27
2270 2317 2.675772 GAGTGGGACCGGAGTCGT 60.676 66.667 9.46 0.00 44.54 4.34
2278 2325 1.211457 AGCATTCTGATGAGTGGGACC 59.789 52.381 0.00 0.00 35.16 4.46
2284 2331 2.236644 ACAGCTGAGCATTCTGATGAGT 59.763 45.455 23.35 0.00 39.99 3.41
2285 2332 2.907634 ACAGCTGAGCATTCTGATGAG 58.092 47.619 23.35 0.00 39.99 2.90
2319 2366 5.968528 ACAGGTAACAACAACACAAAGAA 57.031 34.783 0.00 0.00 41.41 2.52
2320 2367 5.708230 AGAACAGGTAACAACAACACAAAGA 59.292 36.000 0.00 0.00 41.41 2.52
2322 2369 5.968528 AGAACAGGTAACAACAACACAAA 57.031 34.783 0.00 0.00 41.41 2.83
2323 2370 5.968528 AAGAACAGGTAACAACAACACAA 57.031 34.783 0.00 0.00 41.41 3.33
2340 2387 8.576442 TCAGGATCCAAGTAATTTTGAAAGAAC 58.424 33.333 15.82 0.00 0.00 3.01
2347 2394 4.098501 GCCCTCAGGATCCAAGTAATTTTG 59.901 45.833 15.82 0.00 33.47 2.44
2355 2404 0.107312 CAGTGCCCTCAGGATCCAAG 60.107 60.000 15.82 10.78 33.47 3.61
2364 2414 2.425592 CACGAACCAGTGCCCTCA 59.574 61.111 0.00 0.00 35.17 3.86
2384 2434 6.347402 CGGTGTCGATGTATTTCTCTTTTGTT 60.347 38.462 0.00 0.00 39.00 2.83
2442 2492 4.973856 TCTGAGGAAAGAGATGGGATCATT 59.026 41.667 0.00 0.00 32.98 2.57
2453 2503 5.066246 GGCAAAATCATCTCTGAGGAAAGAG 59.934 44.000 4.59 0.00 44.34 2.85
2460 2510 5.578005 AACATGGCAAAATCATCTCTGAG 57.422 39.130 0.00 0.00 34.12 3.35
2508 2567 1.766143 GCTAAGGCACCGAAGCATCG 61.766 60.000 3.96 3.96 42.52 3.84
2509 2568 0.744414 TGCTAAGGCACCGAAGCATC 60.744 55.000 13.05 0.00 44.28 3.91
2510 2569 1.299648 TGCTAAGGCACCGAAGCAT 59.700 52.632 13.05 0.00 44.28 3.79
2511 2570 2.747022 TGCTAAGGCACCGAAGCA 59.253 55.556 13.05 13.05 44.28 3.91
2520 2579 2.084546 CACAAAGGTAGGTGCTAAGGC 58.915 52.381 0.00 0.00 39.26 4.35
2521 2580 3.008049 AGACACAAAGGTAGGTGCTAAGG 59.992 47.826 0.00 0.00 38.57 2.69
2522 2581 4.273148 AGACACAAAGGTAGGTGCTAAG 57.727 45.455 0.00 0.00 38.57 2.18
2523 2582 5.482526 TCATAGACACAAAGGTAGGTGCTAA 59.517 40.000 0.00 0.00 38.57 3.09
2524 2583 5.020795 TCATAGACACAAAGGTAGGTGCTA 58.979 41.667 0.00 0.00 38.57 3.49
2525 2584 3.838317 TCATAGACACAAAGGTAGGTGCT 59.162 43.478 0.00 0.00 38.57 4.40
2526 2585 3.933332 GTCATAGACACAAAGGTAGGTGC 59.067 47.826 0.00 0.00 38.57 5.01
2527 2586 5.147330 TGTCATAGACACAAAGGTAGGTG 57.853 43.478 0.00 0.00 37.67 4.00
2528 2587 5.248477 ACATGTCATAGACACAAAGGTAGGT 59.752 40.000 1.43 0.00 45.65 3.08
2529 2588 5.582269 CACATGTCATAGACACAAAGGTAGG 59.418 44.000 0.00 0.00 45.65 3.18
2530 2589 5.582269 CCACATGTCATAGACACAAAGGTAG 59.418 44.000 0.00 0.00 45.65 3.18
2531 2590 5.487433 CCACATGTCATAGACACAAAGGTA 58.513 41.667 0.00 0.00 45.65 3.08
2532 2591 4.326826 CCACATGTCATAGACACAAAGGT 58.673 43.478 0.00 0.00 45.65 3.50
2533 2592 3.691118 CCCACATGTCATAGACACAAAGG 59.309 47.826 0.00 3.02 45.65 3.11
2534 2593 3.127548 GCCCACATGTCATAGACACAAAG 59.872 47.826 0.00 0.00 45.65 2.77
2535 2594 3.081061 GCCCACATGTCATAGACACAAA 58.919 45.455 0.00 0.00 45.65 2.83
2536 2595 2.617788 GGCCCACATGTCATAGACACAA 60.618 50.000 0.00 0.00 45.65 3.33
2537 2596 1.065491 GGCCCACATGTCATAGACACA 60.065 52.381 0.00 0.00 45.65 3.72
2538 2597 1.668419 GGCCCACATGTCATAGACAC 58.332 55.000 0.00 0.00 45.65 3.67
2539 2598 0.546122 GGGCCCACATGTCATAGACA 59.454 55.000 19.95 1.95 46.90 3.41
2540 2599 0.546122 TGGGCCCACATGTCATAGAC 59.454 55.000 24.45 0.00 0.00 2.59
2541 2600 1.064758 GTTGGGCCCACATGTCATAGA 60.065 52.381 28.70 1.58 0.00 1.98
2542 2601 1.340893 TGTTGGGCCCACATGTCATAG 60.341 52.381 28.70 0.00 0.00 2.23
2543 2602 0.701147 TGTTGGGCCCACATGTCATA 59.299 50.000 28.70 3.51 0.00 2.15
2544 2603 0.178938 TTGTTGGGCCCACATGTCAT 60.179 50.000 28.70 0.00 0.00 3.06
2545 2604 0.827089 CTTGTTGGGCCCACATGTCA 60.827 55.000 28.70 15.83 0.00 3.58
2546 2605 0.827507 ACTTGTTGGGCCCACATGTC 60.828 55.000 28.70 13.28 0.00 3.06
2547 2606 1.114722 CACTTGTTGGGCCCACATGT 61.115 55.000 28.70 27.05 0.00 3.21
2548 2607 1.667151 CACTTGTTGGGCCCACATG 59.333 57.895 28.70 26.43 0.00 3.21
2549 2608 1.533753 CCACTTGTTGGGCCCACAT 60.534 57.895 28.70 9.27 42.54 3.21
2550 2609 2.123511 CCACTTGTTGGGCCCACA 60.124 61.111 28.70 22.97 42.54 4.17
2558 2617 2.521465 TGGGCCAGCCACTTGTTG 60.521 61.111 11.50 0.00 37.98 3.33
2559 2618 2.521708 GTGGGCCAGCCACTTGTT 60.522 61.111 6.40 0.00 37.98 2.83
2560 2619 3.150903 ATGTGGGCCAGCCACTTGT 62.151 57.895 6.40 0.00 38.79 3.16
2561 2620 2.283388 ATGTGGGCCAGCCACTTG 60.283 61.111 6.40 0.00 38.79 3.16
2562 2621 2.283388 CATGTGGGCCAGCCACTT 60.283 61.111 6.40 0.00 38.79 3.16
2563 2622 3.574074 GACATGTGGGCCAGCCACT 62.574 63.158 6.40 0.00 38.79 4.00
2564 2623 3.064324 GACATGTGGGCCAGCCAC 61.064 66.667 6.40 4.05 37.98 5.01
2565 2624 3.572447 CTGACATGTGGGCCAGCCA 62.572 63.158 6.40 1.84 37.98 4.75
2566 2625 2.753043 CTGACATGTGGGCCAGCC 60.753 66.667 6.40 0.00 0.00 4.85
2567 2626 2.034687 ACTGACATGTGGGCCAGC 59.965 61.111 6.40 2.28 0.00 4.85
2568 2627 0.957395 GTCACTGACATGTGGGCCAG 60.957 60.000 6.40 6.93 38.40 4.85
2569 2628 1.073025 GTCACTGACATGTGGGCCA 59.927 57.895 1.15 0.00 38.40 5.36
2570 2629 1.675641 GGTCACTGACATGTGGGCC 60.676 63.158 1.15 0.00 38.40 5.80
2571 2630 1.675641 GGGTCACTGACATGTGGGC 60.676 63.158 1.15 0.00 38.40 5.36
2572 2631 0.110295 TTGGGTCACTGACATGTGGG 59.890 55.000 1.15 0.00 38.40 4.61
2573 2632 1.881973 CTTTGGGTCACTGACATGTGG 59.118 52.381 1.15 0.00 38.40 4.17
2574 2633 1.881973 CCTTTGGGTCACTGACATGTG 59.118 52.381 1.15 0.00 39.15 3.21
2575 2634 1.819305 GCCTTTGGGTCACTGACATGT 60.819 52.381 11.34 0.00 33.68 3.21
2576 2635 0.883833 GCCTTTGGGTCACTGACATG 59.116 55.000 11.34 0.00 33.68 3.21
2577 2636 0.478072 TGCCTTTGGGTCACTGACAT 59.522 50.000 11.34 0.00 33.68 3.06
2578 2637 0.179020 CTGCCTTTGGGTCACTGACA 60.179 55.000 11.34 0.00 33.68 3.58
2579 2638 0.890996 CCTGCCTTTGGGTCACTGAC 60.891 60.000 0.00 0.00 34.45 3.51
2580 2639 1.352622 ACCTGCCTTTGGGTCACTGA 61.353 55.000 0.00 0.00 34.45 3.41
2581 2640 1.151450 ACCTGCCTTTGGGTCACTG 59.849 57.895 0.00 0.00 34.45 3.66
2582 2641 1.151450 CACCTGCCTTTGGGTCACT 59.849 57.895 0.00 0.00 32.95 3.41
2583 2642 2.564721 GCACCTGCCTTTGGGTCAC 61.565 63.158 0.00 0.00 32.95 3.67
2584 2643 2.203480 GCACCTGCCTTTGGGTCA 60.203 61.111 0.00 0.00 32.95 4.02
2601 2660 0.804989 CAGCTTCGGTGCCTTAAAGG 59.195 55.000 0.00 0.00 38.80 3.11
2610 2669 0.813184 AAATGGATGCAGCTTCGGTG 59.187 50.000 0.22 0.00 0.00 4.94
2611 2670 1.549203 AAAATGGATGCAGCTTCGGT 58.451 45.000 0.22 0.00 0.00 4.69
2612 2671 2.660189 AAAAATGGATGCAGCTTCGG 57.340 45.000 0.22 0.00 0.00 4.30
2628 2687 9.591792 CATCAGATCACTAGTCATGAGTAAAAA 57.408 33.333 11.38 0.71 0.00 1.94
2629 2688 8.200120 CCATCAGATCACTAGTCATGAGTAAAA 58.800 37.037 11.38 1.04 0.00 1.52
2630 2689 7.343057 ACCATCAGATCACTAGTCATGAGTAAA 59.657 37.037 11.38 1.36 0.00 2.01
2631 2690 6.836007 ACCATCAGATCACTAGTCATGAGTAA 59.164 38.462 11.38 0.00 0.00 2.24
2632 2691 6.264067 CACCATCAGATCACTAGTCATGAGTA 59.736 42.308 9.88 9.88 0.00 2.59
2633 2692 5.068855 CACCATCAGATCACTAGTCATGAGT 59.931 44.000 8.40 8.40 0.00 3.41
2646 2705 2.419297 GGTCACTCCACACCATCAGATC 60.419 54.545 0.00 0.00 35.97 2.75
2700 2761 3.106242 ACATTTACACGAGTGTCAGCA 57.894 42.857 12.54 0.00 43.74 4.41
2703 2764 4.486574 TCGTACATTTACACGAGTGTCA 57.513 40.909 12.54 0.00 43.74 3.58
2713 2774 9.297586 TCATAAGATGAGTGTTCGTACATTTAC 57.702 33.333 0.00 0.00 33.57 2.01
2732 2793 5.104776 AGGTCTGCTTGCATAGTTCATAAGA 60.105 40.000 0.00 0.00 0.00 2.10
2779 2841 4.894784 TCTCAAGATTTGCGGTTTAGTCT 58.105 39.130 0.00 0.00 0.00 3.24
2786 2848 2.416547 CGTGAATCTCAAGATTTGCGGT 59.583 45.455 6.70 0.00 44.14 5.68
2788 2850 3.997319 TCGTGAATCTCAAGATTTGCG 57.003 42.857 16.64 16.64 44.14 4.85
2790 2852 8.282592 TGTTAAGTTCGTGAATCTCAAGATTTG 58.717 33.333 6.70 1.65 44.14 2.32
2791 2853 8.283291 GTGTTAAGTTCGTGAATCTCAAGATTT 58.717 33.333 6.70 0.00 44.14 2.17
2794 2857 6.277605 TGTGTTAAGTTCGTGAATCTCAAGA 58.722 36.000 0.00 0.00 33.23 3.02
2804 2867 3.067106 AGGCTCATGTGTTAAGTTCGTG 58.933 45.455 0.00 0.00 0.00 4.35
2832 2895 1.996798 AGGAGACAAGGTTCTCGTCA 58.003 50.000 0.00 0.00 42.74 4.35
2833 2896 2.296471 TCAAGGAGACAAGGTTCTCGTC 59.704 50.000 0.00 0.00 42.74 4.20
2891 2954 4.264460 TGGCATGGGTGTTTGTATTTTC 57.736 40.909 0.00 0.00 0.00 2.29
2902 2965 3.287867 AATCTAGACTTGGCATGGGTG 57.712 47.619 0.00 0.00 0.00 4.61
2905 2968 5.678107 GCTTCAAAATCTAGACTTGGCATGG 60.678 44.000 13.75 0.00 0.00 3.66
2931 2994 4.536765 ACAATCATAAGGTCAATCCACCC 58.463 43.478 0.00 0.00 37.09 4.61
2944 3007 5.628797 TGTAGATGGCCTGACAATCATAA 57.371 39.130 3.32 0.00 0.00 1.90
2958 3021 0.469917 AGGGGACGCATTGTAGATGG 59.530 55.000 0.00 0.00 0.00 3.51
2964 3027 1.161843 CGTTTTAGGGGACGCATTGT 58.838 50.000 0.00 0.00 32.11 2.71
2968 3031 1.004679 GTCCGTTTTAGGGGACGCA 60.005 57.895 0.00 0.00 42.91 5.24
2983 3047 1.482593 CCCCTGACAGATAGTGTGTCC 59.517 57.143 3.32 0.00 43.19 4.02
2984 3048 2.166664 GTCCCCTGACAGATAGTGTGTC 59.833 54.545 3.32 0.75 40.56 3.67
2990 3054 1.950909 GACGAGTCCCCTGACAGATAG 59.049 57.143 3.32 0.00 44.33 2.08
3010 3074 2.655364 CTGTATCCGCGCTCGTGG 60.655 66.667 15.06 15.06 46.45 4.94
3011 3075 2.655364 CCTGTATCCGCGCTCGTG 60.655 66.667 5.56 0.00 0.00 4.35
3012 3076 2.827190 TCCTGTATCCGCGCTCGT 60.827 61.111 5.56 0.00 0.00 4.18
3015 3079 3.917760 GGCTCCTGTATCCGCGCT 61.918 66.667 5.56 0.00 0.00 5.92
3016 3080 4.221422 TGGCTCCTGTATCCGCGC 62.221 66.667 0.00 0.00 0.00 6.86
3018 3082 2.280457 GCTGGCTCCTGTATCCGC 60.280 66.667 0.00 0.00 0.00 5.54
3026 3090 2.679716 GTTGGATGGCTGGCTCCT 59.320 61.111 16.43 0.00 32.47 3.69
3027 3091 2.440980 GGTTGGATGGCTGGCTCC 60.441 66.667 2.00 7.66 0.00 4.70
3028 3092 2.825836 CGGTTGGATGGCTGGCTC 60.826 66.667 2.00 0.00 0.00 4.70
3033 3097 1.754234 GGAATGCGGTTGGATGGCT 60.754 57.895 0.00 0.00 0.00 4.75
3035 3099 0.182537 TAGGGAATGCGGTTGGATGG 59.817 55.000 0.00 0.00 0.00 3.51
3040 3104 1.129811 GACGTTTAGGGAATGCGGTTG 59.870 52.381 0.00 0.00 0.00 3.77
3042 3106 0.392060 GGACGTTTAGGGAATGCGGT 60.392 55.000 0.00 0.00 0.00 5.68
3063 3127 1.348064 TGAAAGAGGTCGGACCATGT 58.652 50.000 27.87 12.02 41.95 3.21
3065 3129 2.092914 GGAATGAAAGAGGTCGGACCAT 60.093 50.000 27.87 13.95 41.95 3.55
3066 3130 1.278127 GGAATGAAAGAGGTCGGACCA 59.722 52.381 27.87 7.51 41.95 4.02
3067 3131 1.278127 TGGAATGAAAGAGGTCGGACC 59.722 52.381 19.61 19.61 38.99 4.46
3084 3148 4.828387 TGCTCATATTGCTATGCATTTGGA 59.172 37.500 3.54 0.00 38.76 3.53
3085 3149 5.128992 TGCTCATATTGCTATGCATTTGG 57.871 39.130 3.54 0.00 38.76 3.28
3087 3151 9.767228 TTAATTTGCTCATATTGCTATGCATTT 57.233 25.926 3.54 0.00 38.76 2.32
3100 3164 4.457603 ACACCGCACTTTAATTTGCTCATA 59.542 37.500 7.11 0.00 36.54 2.15
3116 3180 2.395360 GGCGCTATGAAACACCGCA 61.395 57.895 7.64 0.00 45.78 5.69
3122 3186 0.582005 GTGATCGGGCGCTATGAAAC 59.418 55.000 7.64 2.81 0.00 2.78
3168 3232 2.816672 TGTGATCAGGCGCATGTAAAAA 59.183 40.909 22.69 1.79 0.00 1.94
3181 3245 5.155509 TGAACTGAAACGTTTGTGATCAG 57.844 39.130 20.10 20.15 43.39 2.90
3192 3256 1.948104 TGGACCACTGAACTGAAACG 58.052 50.000 0.00 0.00 0.00 3.60
3193 3257 2.030805 GCATGGACCACTGAACTGAAAC 60.031 50.000 0.00 0.00 0.00 2.78
3194 3258 2.229792 GCATGGACCACTGAACTGAAA 58.770 47.619 0.00 0.00 0.00 2.69
3200 3265 1.336440 CGTTTTGCATGGACCACTGAA 59.664 47.619 0.00 0.00 0.00 3.02
3201 3266 0.950836 CGTTTTGCATGGACCACTGA 59.049 50.000 0.00 0.00 0.00 3.41
3203 3268 1.805428 GCCGTTTTGCATGGACCACT 61.805 55.000 0.00 0.00 32.27 4.00
3206 3271 3.046870 TGCCGTTTTGCATGGACC 58.953 55.556 0.00 0.00 36.04 4.46
3214 3279 3.553532 GGAATGCAAAAATGCCGTTTTG 58.446 40.909 14.49 14.49 46.62 2.44
3218 3283 0.683973 TGGGAATGCAAAAATGCCGT 59.316 45.000 0.00 0.00 0.00 5.68
3219 3284 2.027003 ATGGGAATGCAAAAATGCCG 57.973 45.000 0.00 0.00 0.00 5.69
3220 3285 3.345414 TCAATGGGAATGCAAAAATGCC 58.655 40.909 0.00 0.00 0.00 4.40
3221 3286 4.255301 TCTCAATGGGAATGCAAAAATGC 58.745 39.130 0.00 0.00 0.00 3.56
3222 3287 5.526111 GGATCTCAATGGGAATGCAAAAATG 59.474 40.000 0.00 0.00 0.00 2.32
3226 3291 3.710724 TGGATCTCAATGGGAATGCAAA 58.289 40.909 0.00 0.00 0.00 3.68
3231 3296 3.200825 ACGAGTTGGATCTCAATGGGAAT 59.799 43.478 0.00 0.00 37.73 3.01
3232 3297 2.571653 ACGAGTTGGATCTCAATGGGAA 59.428 45.455 0.00 0.00 37.73 3.97


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

AutoCloner maintained by Alex Coulton.