Multiple sequence alignment - TraesCS4B01G253900

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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 TraesCS4B01G253900 chr4B 100.000 3132 0 0 1 3132 519402889 519406020 0.000000e+00 5784.0
1 TraesCS4B01G253900 chr4D 93.906 1526 81 8 801 2321 422548322 422549840 0.000000e+00 2292.0
2 TraesCS4B01G253900 chr4D 88.131 733 42 10 2443 3132 422549840 422550570 0.000000e+00 830.0
3 TraesCS4B01G253900 chr4D 81.325 332 29 18 433 759 422547071 422547374 4.040000e-59 239.0
4 TraesCS4B01G253900 chr4D 93.056 144 8 2 2307 2449 497646673 497646531 3.170000e-50 209.0
5 TraesCS4B01G253900 chr4A 93.085 1533 69 21 801 2321 41920453 41918946 0.000000e+00 2209.0
6 TraesCS4B01G253900 chr4A 86.856 776 69 16 4 772 41932071 41931322 0.000000e+00 837.0
7 TraesCS4B01G253900 chr4A 92.241 348 24 3 2443 2788 41918946 41918600 1.010000e-134 490.0
8 TraesCS4B01G253900 chr4A 97.083 240 7 0 2893 3132 41918061 41917822 3.760000e-109 405.0
9 TraesCS4B01G253900 chr6A 89.655 377 35 4 985 1360 530252937 530252564 7.860000e-131 477.0
10 TraesCS4B01G253900 chr6D 88.542 384 40 3 975 1358 385787100 385786721 2.200000e-126 462.0
11 TraesCS4B01G253900 chr6D 73.280 625 143 22 1497 2111 470030672 470030062 1.140000e-49 207.0
12 TraesCS4B01G253900 chr6B 87.047 386 46 3 975 1360 576269357 576268976 1.730000e-117 433.0
13 TraesCS4B01G253900 chr6B 96.241 133 5 0 2317 2449 707499520 707499652 5.260000e-53 219.0
14 TraesCS4B01G253900 chr6B 96.241 133 4 1 2315 2447 277700317 277700186 1.890000e-52 217.0
15 TraesCS4B01G253900 chr3A 96.992 133 4 0 2320 2452 371626586 371626718 1.130000e-54 224.0
16 TraesCS4B01G253900 chr3D 96.947 131 4 0 2316 2446 67064781 67064911 1.460000e-53 220.0
17 TraesCS4B01G253900 chr1B 96.947 131 4 0 2317 2447 56893365 56893235 1.460000e-53 220.0
18 TraesCS4B01G253900 chr5B 94.286 140 6 2 2313 2452 563340503 563340640 2.450000e-51 213.0
19 TraesCS4B01G253900 chr5B 92.105 152 9 3 2306 2455 252323496 252323646 8.800000e-51 211.0
20 TraesCS4B01G253900 chr5B 100.000 30 0 0 292 321 285596638 285596609 4.360000e-04 56.5
21 TraesCS4B01G253900 chrUn 94.574 129 7 0 2321 2449 36530802 36530674 1.900000e-47 200.0
22 TraesCS4B01G253900 chr2B 71.823 543 117 31 1516 2030 39978026 39977492 4.240000e-24 122.0
23 TraesCS4B01G253900 chr3B 95.000 40 1 1 70 109 736339533 736339495 9.380000e-06 62.1


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 TraesCS4B01G253900 chr4B 519402889 519406020 3131 False 5784.000000 5784 100.000000 1 3132 1 chr4B.!!$F1 3131
1 TraesCS4B01G253900 chr4D 422547071 422550570 3499 False 1120.333333 2292 87.787333 433 3132 3 chr4D.!!$F1 2699
2 TraesCS4B01G253900 chr4A 41917822 41920453 2631 True 1034.666667 2209 94.136333 801 3132 3 chr4A.!!$R2 2331
3 TraesCS4B01G253900 chr4A 41931322 41932071 749 True 837.000000 837 86.856000 4 772 1 chr4A.!!$R1 768
4 TraesCS4B01G253900 chr6D 470030062 470030672 610 True 207.000000 207 73.280000 1497 2111 1 chr6D.!!$R2 614

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
280 282 0.103208 GATCTCTGCATCGACGGGTT 59.897 55.0 0.0 0.0 0.00 4.11 F
922 1840 0.244450 TAACCAGCCGTTACCTGTCG 59.756 55.0 0.0 0.0 35.79 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 2151 0.824759 GGACGTTGGAGATGTAGCCT 59.175 55.0 0.00 0.0 0.00 4.58 R
2320 3261 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.0 13.64 0.0 46.06 3.85 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
28 29 2.434185 GCGTGATCGGACAAGCCA 60.434 61.111 8.71 0.00 38.81 4.75
31 32 1.375908 GTGATCGGACAAGCCAGCA 60.376 57.895 0.00 0.00 35.94 4.41
85 86 1.753463 CCGAGAAGCCTACTCCGGT 60.753 63.158 0.00 0.00 0.00 5.28
88 89 0.747283 GAGAAGCCTACTCCGGTCGA 60.747 60.000 0.00 0.00 0.00 4.20
110 111 1.069049 GTGCCACATTGAAGCCAGTTT 59.931 47.619 0.00 0.00 0.00 2.66
111 112 1.068895 TGCCACATTGAAGCCAGTTTG 59.931 47.619 0.00 0.00 0.00 2.93
112 113 1.787012 CCACATTGAAGCCAGTTTGC 58.213 50.000 0.00 0.00 0.00 3.68
113 114 1.606224 CCACATTGAAGCCAGTTTGCC 60.606 52.381 0.00 0.00 0.00 4.52
114 115 0.681175 ACATTGAAGCCAGTTTGCCC 59.319 50.000 0.00 0.00 0.00 5.36
115 116 0.388907 CATTGAAGCCAGTTTGCCCG 60.389 55.000 0.00 0.00 0.00 6.13
116 117 0.827507 ATTGAAGCCAGTTTGCCCGT 60.828 50.000 0.00 0.00 0.00 5.28
119 120 3.133365 AAGCCAGTTTGCCCGTCCT 62.133 57.895 0.00 0.00 0.00 3.85
156 157 2.024176 ATTTAAGCATGGCTCGACGT 57.976 45.000 0.00 0.00 38.25 4.34
170 171 1.403225 CGACGTCGTTCGCATCACAT 61.403 55.000 29.08 0.00 44.19 3.21
203 205 2.202987 CCCATCACAGCTCCGCTC 60.203 66.667 0.00 0.00 36.40 5.03
211 213 4.067512 AGCTCCGCTCCTCTCCCA 62.068 66.667 0.00 0.00 30.62 4.37
239 241 2.089980 CGTCGACCCTCCTCTCTTTTA 58.910 52.381 10.58 0.00 0.00 1.52
242 244 4.684877 GTCGACCCTCCTCTCTTTTATTC 58.315 47.826 3.51 0.00 0.00 1.75
245 247 4.684877 GACCCTCCTCTCTTTTATTCGAC 58.315 47.826 0.00 0.00 0.00 4.20
257 259 1.364721 TATTCGACGGTGCCAATGTG 58.635 50.000 0.00 0.00 0.00 3.21
258 260 0.605319 ATTCGACGGTGCCAATGTGT 60.605 50.000 0.00 0.00 0.00 3.72
280 282 0.103208 GATCTCTGCATCGACGGGTT 59.897 55.000 0.00 0.00 0.00 4.11
285 287 2.125512 GCATCGACGGGTTGCTCT 60.126 61.111 9.94 0.00 38.15 4.09
287 289 1.215382 CATCGACGGGTTGCTCTGA 59.785 57.895 0.00 0.00 0.00 3.27
289 291 0.537188 ATCGACGGGTTGCTCTGAAT 59.463 50.000 0.00 0.00 0.00 2.57
297 299 1.139853 GGTTGCTCTGAATCCGGATCT 59.860 52.381 19.43 8.17 0.00 2.75
301 303 1.876322 CTCTGAATCCGGATCTTGGC 58.124 55.000 19.43 5.88 0.00 4.52
333 335 1.109920 GCTCTCCTAGGCCATCGACA 61.110 60.000 5.01 0.00 0.00 4.35
346 348 4.429212 CGACATCCACGGCGACCA 62.429 66.667 16.62 0.00 0.00 4.02
361 363 0.840722 GACCACCTCCCTTGGGAAGA 60.841 60.000 11.03 0.00 38.59 2.87
415 417 3.827898 AGCAGTAGTCGCGCCTCC 61.828 66.667 0.00 0.00 0.00 4.30
418 420 2.829458 AGTAGTCGCGCCTCCTCC 60.829 66.667 0.00 0.00 0.00 4.30
420 422 2.516460 TAGTCGCGCCTCCTCCTC 60.516 66.667 0.00 0.00 0.00 3.71
421 423 3.339738 TAGTCGCGCCTCCTCCTCA 62.340 63.158 0.00 0.00 0.00 3.86
422 424 4.500116 GTCGCGCCTCCTCCTCAC 62.500 72.222 0.00 0.00 0.00 3.51
491 493 3.768632 GCAGTCGCTCAAGTACCG 58.231 61.111 0.00 0.00 34.30 4.02
535 538 1.300697 GTCAAGTGGAGCCGACGTT 60.301 57.895 0.00 0.00 0.00 3.99
550 553 2.840066 CGTTGCCGCTTTTCCACCA 61.840 57.895 0.00 0.00 0.00 4.17
551 554 1.665442 GTTGCCGCTTTTCCACCAT 59.335 52.632 0.00 0.00 0.00 3.55
573 576 3.818210 TGTCAAGGTTTGCATGAATACGT 59.182 39.130 0.00 0.00 0.00 3.57
606 609 6.017192 TGCATGATATTTGTCCATCCGTTTAG 60.017 38.462 0.00 0.00 0.00 1.85
607 610 6.204688 GCATGATATTTGTCCATCCGTTTAGA 59.795 38.462 0.00 0.00 0.00 2.10
608 611 7.571983 GCATGATATTTGTCCATCCGTTTAGAG 60.572 40.741 0.00 0.00 0.00 2.43
618 621 6.984474 GTCCATCCGTTTAGAGAAATGTATCA 59.016 38.462 0.00 0.00 30.70 2.15
619 622 7.169982 GTCCATCCGTTTAGAGAAATGTATCAG 59.830 40.741 0.00 0.00 30.70 2.90
620 623 6.986817 CCATCCGTTTAGAGAAATGTATCAGT 59.013 38.462 0.00 0.00 30.70 3.41
623 626 7.782049 TCCGTTTAGAGAAATGTATCAGTGAT 58.218 34.615 11.12 11.12 30.70 3.06
630 633 7.628234 AGAGAAATGTATCAGTGATGAAGGTT 58.372 34.615 16.15 3.58 0.00 3.50
646 649 2.486636 GGTTTAGGGCAAACGCTGGC 62.487 60.000 3.29 3.29 46.35 4.85
653 656 2.796227 GCAAACGCTGGCTTTGTAC 58.204 52.632 14.08 0.00 32.18 2.90
654 657 0.663269 GCAAACGCTGGCTTTGTACC 60.663 55.000 14.08 0.00 32.18 3.34
655 658 0.385473 CAAACGCTGGCTTTGTACCG 60.385 55.000 0.00 0.00 0.00 4.02
656 659 1.512156 AAACGCTGGCTTTGTACCGG 61.512 55.000 0.00 0.00 36.57 5.28
657 660 2.358247 CGCTGGCTTTGTACCGGT 60.358 61.111 13.98 13.98 35.84 5.28
658 661 1.964373 CGCTGGCTTTGTACCGGTT 60.964 57.895 15.04 0.00 35.84 4.44
659 662 0.671163 CGCTGGCTTTGTACCGGTTA 60.671 55.000 15.04 0.00 35.84 2.85
660 663 1.084289 GCTGGCTTTGTACCGGTTAG 58.916 55.000 15.04 6.89 35.84 2.34
675 679 4.838986 ACCGGTTAGATAGATGGCTTGTAT 59.161 41.667 0.00 0.00 0.00 2.29
686 690 0.532196 GGCTTGTATAGGTGTCCGCC 60.532 60.000 0.00 0.00 0.00 6.13
687 691 0.874607 GCTTGTATAGGTGTCCGCCG 60.875 60.000 0.00 0.00 0.00 6.46
703 707 4.099585 CGAAACGTCACGCGACCG 62.100 66.667 15.93 14.28 44.77 4.79
748 755 9.340223 CTTTAAGGGTCCCTAATCCTTCTATAT 57.660 37.037 12.06 0.00 40.86 0.86
749 756 8.912614 TTAAGGGTCCCTAATCCTTCTATATC 57.087 38.462 12.06 0.00 40.86 1.63
764 1598 7.552687 TCCTTCTATATCTGCACAATTCGTTTT 59.447 33.333 0.00 0.00 0.00 2.43
790 1639 3.290098 GTTGATACGCAACGCAAGG 57.710 52.632 0.00 0.00 46.50 3.61
792 1641 1.302383 TTGATACGCAACGCAAGGGG 61.302 55.000 0.00 0.00 46.39 4.79
793 1642 1.448893 GATACGCAACGCAAGGGGA 60.449 57.895 0.00 0.00 46.39 4.81
794 1643 1.702491 GATACGCAACGCAAGGGGAC 61.702 60.000 0.00 0.00 46.39 4.46
869 1784 2.141517 GTCGCATGATGAGCAGCTATT 58.858 47.619 0.00 0.00 0.00 1.73
914 1832 2.185387 ACTCCTGTATAACCAGCCGTT 58.815 47.619 0.00 0.00 38.57 4.44
922 1840 0.244450 TAACCAGCCGTTACCTGTCG 59.756 55.000 0.00 0.00 35.79 4.35
930 1848 0.866061 CGTTACCTGTCGCCATCGAG 60.866 60.000 0.00 0.00 46.46 4.04
933 1851 2.279502 TACCTGTCGCCATCGAGCAC 62.280 60.000 0.00 0.00 46.46 4.40
935 1853 2.125952 TGTCGCCATCGAGCACAG 60.126 61.111 0.00 0.00 46.46 3.66
958 1876 0.533755 GATCCCAGAAGCATCCCACG 60.534 60.000 0.00 0.00 0.00 4.94
959 1877 1.987807 ATCCCAGAAGCATCCCACGG 61.988 60.000 0.00 0.00 0.00 4.94
1013 1934 0.879400 CAGCTGATGGAGATCGCCAC 60.879 60.000 21.32 14.49 41.56 5.01
1394 2315 1.525077 TTTTTGCTCCAGCCGTCGT 60.525 52.632 0.00 0.00 41.18 4.34
1416 2338 2.953821 CTGCCGTGCGTCCATTTT 59.046 55.556 0.00 0.00 0.00 1.82
1425 2347 1.353609 GCGTCCATTTTGCATGGTGC 61.354 55.000 4.77 6.84 45.29 5.01
1792 2714 1.677552 CTGTTCACGGTAAGGGCCT 59.322 57.895 0.00 0.00 0.00 5.19
1981 2921 2.044946 GTCCTTCTGGGCGCCATT 60.045 61.111 30.85 0.00 30.82 3.16
2044 2984 1.300311 CACCAACGACGGCTACACA 60.300 57.895 0.00 0.00 0.00 3.72
2113 3053 0.771127 CCTTCTGTGGGGTGGAGAAA 59.229 55.000 0.00 0.00 0.00 2.52
2174 3115 2.440539 TTCTGAAGTCGTCAAGCTCC 57.559 50.000 0.00 0.00 35.22 4.70
2178 3119 1.061485 GAAGTCGTCAAGCTCCGTTC 58.939 55.000 0.00 0.00 0.00 3.95
2199 3140 0.321564 CCACACCATTCTGAAGCCGA 60.322 55.000 0.00 0.00 0.00 5.54
2200 3141 0.798776 CACACCATTCTGAAGCCGAC 59.201 55.000 0.00 0.00 0.00 4.79
2313 3254 5.294306 TCGATTAAGCACTTTGTGGATGATC 59.706 40.000 0.00 0.00 33.64 2.92
2320 3261 6.653020 AGCACTTTGTGGATGATCATTACTA 58.347 36.000 10.14 6.84 33.64 1.82
2321 3262 6.540189 AGCACTTTGTGGATGATCATTACTAC 59.460 38.462 10.14 6.79 33.64 2.73
2322 3263 6.540189 GCACTTTGTGGATGATCATTACTACT 59.460 38.462 10.14 0.00 33.64 2.57
2323 3264 7.254590 GCACTTTGTGGATGATCATTACTACTC 60.255 40.741 10.14 0.00 33.64 2.59
2324 3265 7.225538 CACTTTGTGGATGATCATTACTACTCC 59.774 40.741 10.14 5.98 0.00 3.85
2325 3266 5.808366 TGTGGATGATCATTACTACTCCC 57.192 43.478 10.14 4.30 0.00 4.30
2326 3267 5.467738 TGTGGATGATCATTACTACTCCCT 58.532 41.667 10.14 0.00 0.00 4.20
2327 3268 5.540337 TGTGGATGATCATTACTACTCCCTC 59.460 44.000 10.14 5.43 0.00 4.30
2328 3269 5.046950 GTGGATGATCATTACTACTCCCTCC 60.047 48.000 10.14 3.16 0.00 4.30
2329 3270 4.158764 GGATGATCATTACTACTCCCTCCG 59.841 50.000 10.14 0.00 0.00 4.63
2330 3271 4.180377 TGATCATTACTACTCCCTCCGT 57.820 45.455 0.00 0.00 0.00 4.69
2331 3272 4.142790 TGATCATTACTACTCCCTCCGTC 58.857 47.826 0.00 0.00 0.00 4.79
2332 3273 2.941480 TCATTACTACTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
2333 3274 1.607628 CATTACTACTCCCTCCGTCCG 59.392 57.143 0.00 0.00 0.00 4.79
2334 3275 0.107017 TTACTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
2335 3276 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
2336 3277 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
2337 3278 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
2338 3279 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2339 3280 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2340 3281 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2341 3282 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2342 3283 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2343 3284 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2344 3285 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2345 3286 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2346 3287 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2347 3288 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2348 3289 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2349 3290 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2350 3291 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2351 3292 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2352 3293 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2353 3294 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2354 3295 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2355 3296 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
2356 3297 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
2357 3298 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
2363 3304 6.860080 ACTTGTCATCAAAATGAATAGCAGG 58.140 36.000 0.00 0.00 43.42 4.85
2364 3305 5.840243 TGTCATCAAAATGAATAGCAGGG 57.160 39.130 0.00 0.00 43.42 4.45
2365 3306 4.646040 TGTCATCAAAATGAATAGCAGGGG 59.354 41.667 0.00 0.00 43.42 4.79
2366 3307 4.889409 GTCATCAAAATGAATAGCAGGGGA 59.111 41.667 0.00 0.00 43.42 4.81
2367 3308 5.537674 GTCATCAAAATGAATAGCAGGGGAT 59.462 40.000 0.00 0.00 43.42 3.85
2368 3309 5.537295 TCATCAAAATGAATAGCAGGGGATG 59.463 40.000 0.00 0.00 38.97 3.51
2369 3310 4.870636 TCAAAATGAATAGCAGGGGATGT 58.129 39.130 0.00 0.00 0.00 3.06
2370 3311 6.012337 TCAAAATGAATAGCAGGGGATGTA 57.988 37.500 0.00 0.00 0.00 2.29
2371 3312 6.613699 TCAAAATGAATAGCAGGGGATGTAT 58.386 36.000 0.00 0.00 0.00 2.29
2372 3313 6.716628 TCAAAATGAATAGCAGGGGATGTATC 59.283 38.462 0.00 0.00 0.00 2.24
2373 3314 6.460103 AAATGAATAGCAGGGGATGTATCT 57.540 37.500 0.00 0.00 0.00 1.98
2374 3315 7.574021 AAATGAATAGCAGGGGATGTATCTA 57.426 36.000 0.00 0.00 0.00 1.98
2375 3316 6.805016 ATGAATAGCAGGGGATGTATCTAG 57.195 41.667 0.00 0.00 0.00 2.43
2376 3317 5.903923 TGAATAGCAGGGGATGTATCTAGA 58.096 41.667 0.00 0.00 0.00 2.43
2377 3318 6.506661 TGAATAGCAGGGGATGTATCTAGAT 58.493 40.000 10.73 10.73 0.00 1.98
2378 3319 6.382282 TGAATAGCAGGGGATGTATCTAGATG 59.618 42.308 15.79 0.00 0.00 2.90
2379 3320 4.139162 AGCAGGGGATGTATCTAGATGT 57.861 45.455 15.79 1.25 0.00 3.06
2380 3321 5.276694 AGCAGGGGATGTATCTAGATGTA 57.723 43.478 15.79 4.44 0.00 2.29
2381 3322 5.848004 AGCAGGGGATGTATCTAGATGTAT 58.152 41.667 15.79 9.11 0.00 2.29
2382 3323 6.267635 AGCAGGGGATGTATCTAGATGTATT 58.732 40.000 15.79 0.00 0.00 1.89
2383 3324 6.732862 AGCAGGGGATGTATCTAGATGTATTT 59.267 38.462 15.79 0.00 0.00 1.40
2384 3325 7.238514 AGCAGGGGATGTATCTAGATGTATTTT 59.761 37.037 15.79 0.00 0.00 1.82
2385 3326 8.540388 GCAGGGGATGTATCTAGATGTATTTTA 58.460 37.037 15.79 0.00 0.00 1.52
2387 3328 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
2409 3350 9.886132 TTAGTTCTAGATACATCCCTTTTTGTC 57.114 33.333 0.00 0.00 0.00 3.18
2410 3351 7.339482 AGTTCTAGATACATCCCTTTTTGTCC 58.661 38.462 0.00 0.00 0.00 4.02
2411 3352 6.884472 TCTAGATACATCCCTTTTTGTCCA 57.116 37.500 0.00 0.00 0.00 4.02
2412 3353 7.451731 TCTAGATACATCCCTTTTTGTCCAT 57.548 36.000 0.00 0.00 0.00 3.41
2413 3354 7.872138 TCTAGATACATCCCTTTTTGTCCATT 58.128 34.615 0.00 0.00 0.00 3.16
2414 3355 8.336235 TCTAGATACATCCCTTTTTGTCCATTT 58.664 33.333 0.00 0.00 0.00 2.32
2415 3356 7.797121 AGATACATCCCTTTTTGTCCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
2416 3357 7.614494 AGATACATCCCTTTTTGTCCATTTTG 58.386 34.615 0.00 0.00 0.00 2.44
2417 3358 5.885449 ACATCCCTTTTTGTCCATTTTGA 57.115 34.783 0.00 0.00 0.00 2.69
2418 3359 6.438186 ACATCCCTTTTTGTCCATTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
2419 3360 6.232692 ACATCCCTTTTTGTCCATTTTGATG 58.767 36.000 0.00 0.00 33.80 3.07
2420 3361 6.043012 ACATCCCTTTTTGTCCATTTTGATGA 59.957 34.615 0.00 0.00 32.39 2.92
2421 3362 5.852827 TCCCTTTTTGTCCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
2422 3363 5.365025 TCCCTTTTTGTCCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
2423 3364 6.054295 CCCTTTTTGTCCATTTTGATGACAA 58.946 36.000 0.00 0.00 34.47 3.18
2424 3365 6.203338 CCCTTTTTGTCCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.13 3.16
2425 3366 6.762661 CCTTTTTGTCCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.13 3.16
2426 3367 7.925483 CCTTTTTGTCCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.13 2.24
2427 3368 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
2428 3369 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
2429 3370 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
2430 3371 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
2431 3372 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
2432 3373 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
2433 3374 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
2434 3375 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2435 3376 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2436 3377 6.869315 TTTGATGACAAGTATTTTCGGACA 57.131 33.333 0.00 0.00 37.32 4.02
2437 3378 6.480524 TTGATGACAAGTATTTTCGGACAG 57.519 37.500 0.00 0.00 0.00 3.51
2438 3379 5.789521 TGATGACAAGTATTTTCGGACAGA 58.210 37.500 0.00 0.00 0.00 3.41
2439 3380 5.869344 TGATGACAAGTATTTTCGGACAGAG 59.131 40.000 0.00 0.00 0.00 3.35
2440 3381 4.566004 TGACAAGTATTTTCGGACAGAGG 58.434 43.478 0.00 0.00 0.00 3.69
2441 3382 3.933332 GACAAGTATTTTCGGACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2549 3491 6.976925 CCCATTTCAACTTTGAGAATATGCTC 59.023 38.462 3.43 3.43 38.61 4.26
2559 3501 6.915544 TTGAGAATATGCTCATCACTTCAC 57.084 37.500 14.45 0.00 43.84 3.18
2569 3511 3.885297 CTCATCACTTCACCAGTGGTTTT 59.115 43.478 13.62 0.00 45.46 2.43
2570 3512 5.042463 TCATCACTTCACCAGTGGTTTTA 57.958 39.130 13.62 0.00 45.46 1.52
2642 3584 4.637483 ATTTTATCATTGACCACGGCAG 57.363 40.909 0.00 0.00 0.00 4.85
2704 3647 8.414003 GTCACACTTGATACCAGATTACAGATA 58.586 37.037 0.00 0.00 33.11 1.98
2724 3667 2.600439 AGCTAGATGGCTGCACTGA 58.400 52.632 0.50 0.00 41.43 3.41
2774 3717 2.214376 CCTACAGGTGGCCATGAAAA 57.786 50.000 9.72 0.00 0.00 2.29
2788 3731 6.606796 TGGCCATGAAAAATTCTTGCTAGATA 59.393 34.615 0.00 0.00 34.51 1.98
2816 3780 2.097825 CTGCCTTAGCCTGCAAAAGAT 58.902 47.619 5.99 0.00 36.98 2.40
2817 3781 1.820519 TGCCTTAGCCTGCAAAAGATG 59.179 47.619 5.99 0.00 38.69 2.90
2843 3811 5.792631 GCATGAGCAAATCAGCATTTTAAC 58.207 37.500 0.00 0.00 42.53 2.01
2847 3815 3.055167 AGCAAATCAGCATTTTAACCCCC 60.055 43.478 0.00 0.00 36.85 5.40
2851 3819 4.824479 ATCAGCATTTTAACCCCCTTTG 57.176 40.909 0.00 0.00 0.00 2.77
2853 3821 2.038295 CAGCATTTTAACCCCCTTTGCA 59.962 45.455 0.00 0.00 0.00 4.08
2855 3823 2.874052 GCATTTTAACCCCCTTTGCACC 60.874 50.000 0.00 0.00 0.00 5.01
2856 3824 2.176247 TTTTAACCCCCTTTGCACCA 57.824 45.000 0.00 0.00 0.00 4.17
2920 4297 3.866327 GCCTTTCACTTATCGAGGTCTTC 59.134 47.826 0.00 0.00 0.00 2.87
2933 4310 1.107114 GGTCTTCGAGGAGAGATGCA 58.893 55.000 0.00 0.00 0.00 3.96
2943 4320 4.038522 CGAGGAGAGATGCAGGAATTTCTA 59.961 45.833 0.00 0.00 0.00 2.10
2945 4322 4.718774 AGGAGAGATGCAGGAATTTCTACA 59.281 41.667 0.00 0.00 26.38 2.74
2948 4325 4.472833 AGAGATGCAGGAATTTCTACAGGT 59.527 41.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.335415 CCGATCACGCCACTCTGATAG 60.335 57.143 0.00 0.00 38.29 2.08
1 2 0.668535 CCGATCACGCCACTCTGATA 59.331 55.000 0.00 0.00 38.29 2.15
2 3 1.037579 TCCGATCACGCCACTCTGAT 61.038 55.000 0.00 0.00 38.29 2.90
11 12 2.434185 TGGCTTGTCCGATCACGC 60.434 61.111 0.00 0.00 37.80 5.34
31 32 4.722700 ATTGAAGCACCGCCGCCT 62.723 61.111 0.00 0.00 0.00 5.52
39 40 1.079875 CCGGCATTGCATTGAAGCAC 61.080 55.000 12.66 0.00 45.61 4.40
40 41 1.215912 CCGGCATTGCATTGAAGCA 59.784 52.632 12.66 0.00 43.99 3.91
64 65 2.413765 GAGTAGGCTTCTCGGGCG 59.586 66.667 5.34 0.00 36.85 6.13
85 86 0.804364 GCTTCAATGTGGCACATCGA 59.196 50.000 31.47 24.42 44.52 3.59
88 89 0.892755 CTGGCTTCAATGTGGCACAT 59.107 50.000 26.78 26.78 44.52 3.21
103 104 2.597510 AAGGACGGGCAAACTGGC 60.598 61.111 0.00 0.00 42.88 4.85
110 111 3.636231 CAGGTGGAAGGACGGGCA 61.636 66.667 0.00 0.00 0.00 5.36
111 112 4.410400 CCAGGTGGAAGGACGGGC 62.410 72.222 0.00 0.00 37.39 6.13
112 113 3.717294 CCCAGGTGGAAGGACGGG 61.717 72.222 0.00 0.00 37.39 5.28
113 114 4.410400 GCCCAGGTGGAAGGACGG 62.410 72.222 0.00 0.00 37.39 4.79
114 115 4.760047 CGCCCAGGTGGAAGGACG 62.760 72.222 0.00 0.00 37.39 4.79
156 157 5.049828 AGATATGAAATGTGATGCGAACGA 58.950 37.500 0.00 0.00 0.00 3.85
170 171 6.730447 TGTGATGGGGAAAAGAGATATGAAA 58.270 36.000 0.00 0.00 0.00 2.69
203 205 2.005960 GACGACGGTGATGGGAGAGG 62.006 65.000 0.00 0.00 0.00 3.69
211 213 2.360852 AGGGTCGACGACGGTGAT 60.361 61.111 20.92 2.91 40.21 3.06
239 241 0.605319 ACACATTGGCACCGTCGAAT 60.605 50.000 0.00 0.00 0.00 3.34
242 244 1.082169 CAACACATTGGCACCGTCG 60.082 57.895 0.00 0.00 31.63 5.12
257 259 1.203928 CGTCGATGCAGAGATCCAAC 58.796 55.000 0.00 0.00 0.00 3.77
258 260 0.103026 CCGTCGATGCAGAGATCCAA 59.897 55.000 0.00 0.00 0.00 3.53
262 264 0.179100 CAACCCGTCGATGCAGAGAT 60.179 55.000 0.00 0.00 0.00 2.75
267 269 2.434185 GAGCAACCCGTCGATGCA 60.434 61.111 10.33 0.00 42.45 3.96
280 282 1.139654 CCAAGATCCGGATTCAGAGCA 59.860 52.381 20.22 0.00 0.00 4.26
285 287 0.179084 GACGCCAAGATCCGGATTCA 60.179 55.000 20.22 0.00 0.00 2.57
287 289 0.462047 GTGACGCCAAGATCCGGATT 60.462 55.000 20.22 0.28 0.00 3.01
289 291 2.577059 GTGACGCCAAGATCCGGA 59.423 61.111 6.61 6.61 0.00 5.14
333 335 3.771160 GAGGTGGTCGCCGTGGAT 61.771 66.667 0.00 0.00 0.00 3.41
346 348 0.196118 TCCTTCTTCCCAAGGGAGGT 59.804 55.000 15.93 0.00 46.06 3.85
352 354 4.084011 GGATGATCTCCTTCTTCCCAAG 57.916 50.000 0.00 0.00 41.29 3.61
429 431 2.441348 TACTCCTCCATCGCGGCA 60.441 61.111 6.13 0.00 33.14 5.69
430 432 2.336809 CTACTCCTCCATCGCGGC 59.663 66.667 6.13 0.00 33.14 6.53
431 433 2.336809 GCTACTCCTCCATCGCGG 59.663 66.667 6.13 0.00 0.00 6.46
463 465 2.494677 GCGACTGCTAGAGGAGGAA 58.505 57.895 2.95 0.00 37.85 3.36
514 516 4.717629 TCGGCTCCACTTGACGCG 62.718 66.667 3.53 3.53 0.00 6.01
535 538 1.523154 GACATGGTGGAAAAGCGGCA 61.523 55.000 1.45 0.00 0.00 5.69
541 544 3.431486 GCAAACCTTGACATGGTGGAAAA 60.431 43.478 13.42 0.00 37.93 2.29
543 546 1.686052 GCAAACCTTGACATGGTGGAA 59.314 47.619 13.42 0.00 37.93 3.53
550 553 4.458989 ACGTATTCATGCAAACCTTGACAT 59.541 37.500 0.00 0.00 0.00 3.06
551 554 3.818210 ACGTATTCATGCAAACCTTGACA 59.182 39.130 0.00 0.00 0.00 3.58
573 576 5.048434 TGGACAAATATCATGCAAACACGAA 60.048 36.000 0.00 0.00 0.00 3.85
606 609 7.856145 AACCTTCATCACTGATACATTTCTC 57.144 36.000 0.00 0.00 0.00 2.87
607 610 9.388506 CTAAACCTTCATCACTGATACATTTCT 57.611 33.333 0.00 0.00 0.00 2.52
608 611 8.616076 CCTAAACCTTCATCACTGATACATTTC 58.384 37.037 0.00 0.00 0.00 2.17
618 621 3.806949 TTGCCCTAAACCTTCATCACT 57.193 42.857 0.00 0.00 0.00 3.41
619 622 3.365969 CGTTTGCCCTAAACCTTCATCAC 60.366 47.826 0.00 0.00 44.62 3.06
620 623 2.817258 CGTTTGCCCTAAACCTTCATCA 59.183 45.455 0.00 0.00 44.62 3.07
623 626 0.955905 GCGTTTGCCCTAAACCTTCA 59.044 50.000 0.00 0.00 44.62 3.02
630 633 0.825840 AAAGCCAGCGTTTGCCCTAA 60.826 50.000 0.00 0.00 44.31 2.69
646 649 4.989168 GCCATCTATCTAACCGGTACAAAG 59.011 45.833 8.00 3.44 0.00 2.77
647 650 4.652421 AGCCATCTATCTAACCGGTACAAA 59.348 41.667 8.00 0.00 0.00 2.83
648 651 4.220724 AGCCATCTATCTAACCGGTACAA 58.779 43.478 8.00 0.00 0.00 2.41
649 652 3.840991 AGCCATCTATCTAACCGGTACA 58.159 45.455 8.00 0.00 0.00 2.90
650 653 4.038883 ACAAGCCATCTATCTAACCGGTAC 59.961 45.833 8.00 0.00 0.00 3.34
651 654 4.220724 ACAAGCCATCTATCTAACCGGTA 58.779 43.478 8.00 0.00 0.00 4.02
652 655 3.039011 ACAAGCCATCTATCTAACCGGT 58.961 45.455 0.00 0.00 0.00 5.28
653 656 3.753294 ACAAGCCATCTATCTAACCGG 57.247 47.619 0.00 0.00 0.00 5.28
654 657 6.153000 ACCTATACAAGCCATCTATCTAACCG 59.847 42.308 0.00 0.00 0.00 4.44
655 658 7.038941 ACACCTATACAAGCCATCTATCTAACC 60.039 40.741 0.00 0.00 0.00 2.85
656 659 7.897864 ACACCTATACAAGCCATCTATCTAAC 58.102 38.462 0.00 0.00 0.00 2.34
657 660 7.178628 GGACACCTATACAAGCCATCTATCTAA 59.821 40.741 0.00 0.00 0.00 2.10
658 661 6.663953 GGACACCTATACAAGCCATCTATCTA 59.336 42.308 0.00 0.00 0.00 1.98
659 662 5.482175 GGACACCTATACAAGCCATCTATCT 59.518 44.000 0.00 0.00 0.00 1.98
660 663 5.622460 CGGACACCTATACAAGCCATCTATC 60.622 48.000 0.00 0.00 0.00 2.08
675 679 2.259204 CGTTTCGGCGGACACCTA 59.741 61.111 7.21 0.00 0.00 3.08
686 690 4.099585 CGGTCGCGTGACGTTTCG 62.100 66.667 21.89 15.71 46.49 3.46
687 691 4.405173 GCGGTCGCGTGACGTTTC 62.405 66.667 21.89 7.92 46.49 2.78
722 729 5.977821 AGAAGGATTAGGGACCCTTAAAG 57.022 43.478 20.96 0.00 40.14 1.85
792 1641 3.774959 ATCAGATCCCGTGCGCGTC 62.775 63.158 19.61 9.81 36.15 5.19
793 1642 3.838271 ATCAGATCCCGTGCGCGT 61.838 61.111 19.61 0.00 36.15 6.01
794 1643 3.333189 CATCAGATCCCGTGCGCG 61.333 66.667 13.88 13.88 37.95 6.86
795 1644 2.721971 ATCCATCAGATCCCGTGCGC 62.722 60.000 0.00 0.00 0.00 6.09
796 1645 0.668706 GATCCATCAGATCCCGTGCG 60.669 60.000 0.00 0.00 45.00 5.34
797 1646 3.223661 GATCCATCAGATCCCGTGC 57.776 57.895 0.00 0.00 45.00 5.34
869 1784 2.933287 AGCGGATTGGGTGTGGGA 60.933 61.111 0.00 0.00 0.00 4.37
922 1840 1.094073 ATCTTGCTGTGCTCGATGGC 61.094 55.000 0.00 0.00 0.00 4.40
930 1848 1.093159 CTTCTGGGATCTTGCTGTGC 58.907 55.000 0.00 0.00 0.00 4.57
933 1851 1.948145 GATGCTTCTGGGATCTTGCTG 59.052 52.381 0.00 0.00 39.30 4.41
935 1853 1.316651 GGATGCTTCTGGGATCTTGC 58.683 55.000 0.00 0.00 41.62 4.01
958 1876 1.302511 TCGTCTTGGCTTGGCTTCC 60.303 57.895 0.00 0.00 0.00 3.46
959 1877 1.869690 GTCGTCTTGGCTTGGCTTC 59.130 57.895 0.00 0.00 0.00 3.86
1230 2151 0.824759 GGACGTTGGAGATGTAGCCT 59.175 55.000 0.00 0.00 0.00 4.58
1400 2321 2.642129 CAAAATGGACGCACGGCA 59.358 55.556 0.00 0.00 0.00 5.69
1402 2323 1.072116 CATGCAAAATGGACGCACGG 61.072 55.000 0.00 0.00 38.73 4.94
1408 2329 1.353609 GCGCACCATGCAAAATGGAC 61.354 55.000 11.80 2.74 45.36 4.02
1425 2347 4.697756 ACACGGTCACCATGGGCG 62.698 66.667 18.09 6.92 0.00 6.13
1973 2913 3.567797 GAGCTCGTCAATGGCGCC 61.568 66.667 22.73 22.73 0.00 6.53
2113 3053 1.404391 ACTTACGAACGGCGATCATCT 59.596 47.619 16.62 0.00 44.57 2.90
2174 3115 2.455674 TCAGAATGGTGTGGAGAACG 57.544 50.000 0.00 0.00 36.16 3.95
2178 3119 1.457346 GGCTTCAGAATGGTGTGGAG 58.543 55.000 0.00 0.00 36.16 3.86
2226 3167 1.005037 ACTTCAGAATGGCGTCGCA 60.005 52.632 20.50 5.66 36.16 5.10
2232 3173 3.549794 AGCAATAGGACTTCAGAATGGC 58.450 45.455 0.00 0.00 36.16 4.40
2313 3254 1.607628 CGGACGGAGGGAGTAGTAATG 59.392 57.143 0.00 0.00 0.00 1.90
2320 3261 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2321 3262 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2322 3263 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2323 3264 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2324 3265 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2325 3266 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2326 3267 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2327 3268 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2328 3269 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2329 3270 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2330 3271 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
2331 3272 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
2332 3273 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
2337 3278 8.627403 CCTGCTATTCATTTTGATGACAAGTAT 58.373 33.333 0.00 0.00 37.32 2.12
2338 3279 7.067372 CCCTGCTATTCATTTTGATGACAAGTA 59.933 37.037 0.00 0.00 37.32 2.24
2339 3280 6.127535 CCCTGCTATTCATTTTGATGACAAGT 60.128 38.462 0.00 0.00 37.32 3.16
2340 3281 6.270815 CCCTGCTATTCATTTTGATGACAAG 58.729 40.000 0.00 0.00 37.32 3.16
2341 3282 5.127519 CCCCTGCTATTCATTTTGATGACAA 59.872 40.000 0.00 0.00 0.00 3.18
2342 3283 4.646040 CCCCTGCTATTCATTTTGATGACA 59.354 41.667 0.00 0.00 0.00 3.58
2343 3284 4.889409 TCCCCTGCTATTCATTTTGATGAC 59.111 41.667 0.00 0.00 0.00 3.06
2344 3285 5.128033 TCCCCTGCTATTCATTTTGATGA 57.872 39.130 0.00 0.00 0.00 2.92
2345 3286 5.303589 ACATCCCCTGCTATTCATTTTGATG 59.696 40.000 0.00 0.00 33.80 3.07
2346 3287 5.461327 ACATCCCCTGCTATTCATTTTGAT 58.539 37.500 0.00 0.00 0.00 2.57
2347 3288 4.870636 ACATCCCCTGCTATTCATTTTGA 58.129 39.130 0.00 0.00 0.00 2.69
2348 3289 6.718454 AGATACATCCCCTGCTATTCATTTTG 59.282 38.462 0.00 0.00 0.00 2.44
2349 3290 6.856757 AGATACATCCCCTGCTATTCATTTT 58.143 36.000 0.00 0.00 0.00 1.82
2350 3291 6.460103 AGATACATCCCCTGCTATTCATTT 57.540 37.500 0.00 0.00 0.00 2.32
2351 3292 6.962311 TCTAGATACATCCCCTGCTATTCATT 59.038 38.462 0.00 0.00 0.00 2.57
2352 3293 6.506661 TCTAGATACATCCCCTGCTATTCAT 58.493 40.000 0.00 0.00 0.00 2.57
2353 3294 5.903923 TCTAGATACATCCCCTGCTATTCA 58.096 41.667 0.00 0.00 0.00 2.57
2354 3295 6.382570 ACATCTAGATACATCCCCTGCTATTC 59.617 42.308 4.54 0.00 0.00 1.75
2355 3296 6.267635 ACATCTAGATACATCCCCTGCTATT 58.732 40.000 4.54 0.00 0.00 1.73
2356 3297 5.848004 ACATCTAGATACATCCCCTGCTAT 58.152 41.667 4.54 0.00 0.00 2.97
2357 3298 5.276694 ACATCTAGATACATCCCCTGCTA 57.723 43.478 4.54 0.00 0.00 3.49
2358 3299 4.139162 ACATCTAGATACATCCCCTGCT 57.861 45.455 4.54 0.00 0.00 4.24
2359 3300 6.552445 AATACATCTAGATACATCCCCTGC 57.448 41.667 4.54 0.00 0.00 4.85
2361 3302 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
2383 3324 9.886132 GACAAAAAGGGATGTATCTAGAACTAA 57.114 33.333 0.00 0.00 0.00 2.24
2384 3325 8.483758 GGACAAAAAGGGATGTATCTAGAACTA 58.516 37.037 0.00 0.00 0.00 2.24
2385 3326 7.037586 TGGACAAAAAGGGATGTATCTAGAACT 60.038 37.037 0.00 0.00 0.00 3.01
2386 3327 7.110155 TGGACAAAAAGGGATGTATCTAGAAC 58.890 38.462 0.00 0.00 0.00 3.01
2387 3328 7.265599 TGGACAAAAAGGGATGTATCTAGAA 57.734 36.000 0.00 0.00 0.00 2.10
2388 3329 6.884472 TGGACAAAAAGGGATGTATCTAGA 57.116 37.500 0.00 0.00 0.00 2.43
2389 3330 8.525290 AAATGGACAAAAAGGGATGTATCTAG 57.475 34.615 0.00 0.00 0.00 2.43
2390 3331 8.748412 CAAAATGGACAAAAAGGGATGTATCTA 58.252 33.333 0.00 0.00 0.00 1.98
2391 3332 7.454380 TCAAAATGGACAAAAAGGGATGTATCT 59.546 33.333 0.00 0.00 0.00 1.98
2392 3333 7.610865 TCAAAATGGACAAAAAGGGATGTATC 58.389 34.615 0.00 0.00 0.00 2.24
2393 3334 7.552050 TCAAAATGGACAAAAAGGGATGTAT 57.448 32.000 0.00 0.00 0.00 2.29
2394 3335 6.985653 TCAAAATGGACAAAAAGGGATGTA 57.014 33.333 0.00 0.00 0.00 2.29
2395 3336 5.885449 TCAAAATGGACAAAAAGGGATGT 57.115 34.783 0.00 0.00 0.00 3.06
2396 3337 6.369615 GTCATCAAAATGGACAAAAAGGGATG 59.630 38.462 0.00 0.00 33.42 3.51
2397 3338 6.043012 TGTCATCAAAATGGACAAAAAGGGAT 59.957 34.615 0.00 0.00 33.42 3.85
2398 3339 5.365025 TGTCATCAAAATGGACAAAAAGGGA 59.635 36.000 0.00 0.00 33.42 4.20
2399 3340 5.609423 TGTCATCAAAATGGACAAAAAGGG 58.391 37.500 0.00 0.00 33.42 3.95
2400 3341 6.762661 ACTTGTCATCAAAATGGACAAAAAGG 59.237 34.615 7.70 0.11 34.98 3.11
2401 3342 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
2402 3343 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
2403 3344 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
2404 3345 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
2405 3346 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
2406 3347 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
2407 3348 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
2408 3349 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2409 3350 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2410 3351 7.807433 TGTCCGAAAATACTTGTCATCAAAATG 59.193 33.333 0.00 0.00 32.87 2.32
2411 3352 7.881142 TGTCCGAAAATACTTGTCATCAAAAT 58.119 30.769 0.00 0.00 32.87 1.82
2412 3353 7.227711 TCTGTCCGAAAATACTTGTCATCAAAA 59.772 33.333 0.00 0.00 32.87 2.44
2413 3354 6.708502 TCTGTCCGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
2414 3355 6.227522 TCTGTCCGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
2415 3356 5.789521 TCTGTCCGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
2416 3357 5.292101 CCTCTGTCCGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
2417 3358 5.178797 CCTCTGTCCGAAAATACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
2418 3359 4.562757 CCCTCTGTCCGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
2419 3360 3.933332 CCCTCTGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2420 3361 3.581332 TCCCTCTGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2421 3362 4.184629 CTCCCTCTGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2422 3363 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
2423 3364 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
2424 3365 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
2425 3366 3.379372 CGTACTCCCTCTGTCCGAAAATA 59.621 47.826 0.00 0.00 0.00 1.40
2426 3367 2.165845 CGTACTCCCTCTGTCCGAAAAT 59.834 50.000 0.00 0.00 0.00 1.82
2427 3368 1.542915 CGTACTCCCTCTGTCCGAAAA 59.457 52.381 0.00 0.00 0.00 2.29
2428 3369 1.171308 CGTACTCCCTCTGTCCGAAA 58.829 55.000 0.00 0.00 0.00 3.46
2429 3370 0.325933 TCGTACTCCCTCTGTCCGAA 59.674 55.000 0.00 0.00 0.00 4.30
2430 3371 0.392193 GTCGTACTCCCTCTGTCCGA 60.392 60.000 0.00 0.00 0.00 4.55
2431 3372 0.675837 TGTCGTACTCCCTCTGTCCG 60.676 60.000 0.00 0.00 0.00 4.79
2432 3373 1.765230 ATGTCGTACTCCCTCTGTCC 58.235 55.000 0.00 0.00 0.00 4.02
2433 3374 3.066481 GGTAATGTCGTACTCCCTCTGTC 59.934 52.174 0.00 0.00 0.00 3.51
2434 3375 3.022406 GGTAATGTCGTACTCCCTCTGT 58.978 50.000 0.00 0.00 0.00 3.41
2435 3376 2.033049 CGGTAATGTCGTACTCCCTCTG 59.967 54.545 0.00 0.00 0.00 3.35
2436 3377 2.295885 CGGTAATGTCGTACTCCCTCT 58.704 52.381 0.00 0.00 0.00 3.69
2437 3378 1.336125 CCGGTAATGTCGTACTCCCTC 59.664 57.143 0.00 0.00 0.00 4.30
2438 3379 1.396653 CCGGTAATGTCGTACTCCCT 58.603 55.000 0.00 0.00 0.00 4.20
2439 3380 0.249197 GCCGGTAATGTCGTACTCCC 60.249 60.000 1.90 0.00 0.00 4.30
2440 3381 0.743097 AGCCGGTAATGTCGTACTCC 59.257 55.000 1.90 0.00 0.00 3.85
2441 3382 1.402968 TCAGCCGGTAATGTCGTACTC 59.597 52.381 1.90 0.00 0.00 2.59
2559 3501 5.106317 ACATCGTGCTTAATAAAACCACTGG 60.106 40.000 0.00 0.00 0.00 4.00
2565 3507 7.483375 TGTTGCATACATCGTGCTTAATAAAAC 59.517 33.333 0.00 0.00 42.92 2.43
2569 3511 6.670077 TTGTTGCATACATCGTGCTTAATA 57.330 33.333 0.00 0.00 42.92 0.98
2570 3512 5.559427 TTGTTGCATACATCGTGCTTAAT 57.441 34.783 0.00 0.00 42.92 1.40
2618 3560 4.460731 TGCCGTGGTCAATGATAAAATTCA 59.539 37.500 0.00 0.00 0.00 2.57
2642 3584 1.470098 CAGAGGTTAGCATGTTGGTGC 59.530 52.381 0.00 0.00 45.38 5.01
2660 3602 4.035792 TGTGACCGGAATGTTTTTGTACAG 59.964 41.667 9.46 0.00 0.00 2.74
2724 3667 3.683822 CGTGCCATTTTGGTTGCATTTAT 59.316 39.130 0.00 0.00 40.46 1.40
2736 3679 4.281898 AGGTAGTTAGTCGTGCCATTTT 57.718 40.909 0.00 0.00 0.00 1.82
2788 3731 2.757314 GCAGGCTAAGGCAGAAAATTCT 59.243 45.455 0.00 0.00 40.87 2.40
2821 3785 5.292589 GGGTTAAAATGCTGATTTGCTCATG 59.707 40.000 0.00 0.00 31.83 3.07
2822 3786 5.422145 GGGTTAAAATGCTGATTTGCTCAT 58.578 37.500 0.00 0.00 31.83 2.90
2823 3787 4.322650 GGGGTTAAAATGCTGATTTGCTCA 60.323 41.667 0.00 0.00 31.83 4.26
2836 3804 2.695585 TGGTGCAAAGGGGGTTAAAAT 58.304 42.857 0.00 0.00 0.00 1.82
2843 3811 3.558958 CCTTATTTTTGGTGCAAAGGGGG 60.559 47.826 2.19 0.00 34.72 5.40
2847 3815 5.178061 GGATCCCTTATTTTTGGTGCAAAG 58.822 41.667 0.00 0.00 34.72 2.77
2851 3819 2.481276 GCGGATCCCTTATTTTTGGTGC 60.481 50.000 6.06 0.00 0.00 5.01
2853 3821 3.288092 GAGCGGATCCCTTATTTTTGGT 58.712 45.455 6.06 0.00 0.00 3.67
2855 3823 3.990318 GGAGCGGATCCCTTATTTTTG 57.010 47.619 6.06 0.00 43.01 2.44
2920 4297 2.906691 AATTCCTGCATCTCTCCTCG 57.093 50.000 0.00 0.00 0.00 4.63
2933 4310 2.239907 GGCCTCACCTGTAGAAATTCCT 59.760 50.000 0.00 0.00 34.51 3.36
2943 4320 0.977627 TCGATGATGGCCTCACCTGT 60.978 55.000 3.32 0.00 40.22 4.00
2945 4322 0.977627 TGTCGATGATGGCCTCACCT 60.978 55.000 3.32 0.00 40.22 4.00
2948 4325 1.141665 CGTGTCGATGATGGCCTCA 59.858 57.895 3.32 5.76 38.53 3.86


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

AutoCloner maintained by Alex Coulton.