Multiple sequence alignment - TraesCS7A01G040500

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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 TraesCS7A01G040500 chr7A 100.000 4966 0 0 1 4966 18796324 18791359 0.000000e+00 9171.0
1 TraesCS7A01G040500 chr7A 85.811 148 19 2 1 147 84044052 84044198 6.660000e-34 156.0
2 TraesCS7A01G040500 chr7A 75.573 262 55 9 1 258 562325146 562324890 2.430000e-23 121.0
3 TraesCS7A01G040500 chr7D 92.180 3376 172 29 661 4010 18387124 18383815 0.000000e+00 4687.0
4 TraesCS7A01G040500 chr7D 91.830 869 61 8 4105 4966 18383806 18382941 0.000000e+00 1203.0
5 TraesCS7A01G040500 chr7D 74.206 504 101 18 39 522 375978496 375978002 3.050000e-42 183.0
6 TraesCS7A01G040500 chrUn 93.448 2732 138 16 1299 4010 50915912 50913202 0.000000e+00 4015.0
7 TraesCS7A01G040500 chrUn 90.308 681 61 4 4280 4955 50913126 50912446 0.000000e+00 887.0
8 TraesCS7A01G040500 chrUn 84.895 715 71 20 544 1243 50916605 50915913 0.000000e+00 688.0
9 TraesCS7A01G040500 chr3A 79.805 411 70 13 6 410 158163736 158163333 2.260000e-73 287.0
10 TraesCS7A01G040500 chr1D 79.481 385 74 3 29 411 441094176 441094557 8.190000e-68 268.0
11 TraesCS7A01G040500 chr1D 75.485 412 98 3 1 411 18676586 18676995 1.090000e-46 198.0
12 TraesCS7A01G040500 chr1D 75.787 413 79 17 1 410 193449929 193450323 6.560000e-44 189.0
13 TraesCS7A01G040500 chr1D 83.562 146 24 0 1 146 490583862 490583717 2.410000e-28 137.0
14 TraesCS7A01G040500 chr1D 79.545 88 14 4 427 514 203279371 203279454 5.370000e-05 60.2
15 TraesCS7A01G040500 chr6D 75.985 533 107 7 1 513 315366188 315365657 6.380000e-64 255.0
16 TraesCS7A01G040500 chr6D 78.218 202 30 13 1 194 55939256 55939061 3.140000e-22 117.0
17 TraesCS7A01G040500 chr2B 75.963 545 95 16 1 514 794000249 793999710 1.070000e-61 248.0
18 TraesCS7A01G040500 chr5A 77.053 414 86 7 3 410 131806124 131806534 3.870000e-56 230.0
19 TraesCS7A01G040500 chr1B 77.150 407 83 10 1 404 489687496 489687895 1.390000e-55 228.0
20 TraesCS7A01G040500 chr4B 76.513 413 87 9 1 409 500109063 500108657 3.010000e-52 217.0
21 TraesCS7A01G040500 chr7B 74.775 555 97 21 1 524 169467500 169466958 5.040000e-50 209.0
22 TraesCS7A01G040500 chr2A 82.993 147 25 0 1 147 744842730 744842876 3.120000e-27 134.0
23 TraesCS7A01G040500 chr2A 73.359 259 47 19 252 503 526114041 526114284 5.330000e-10 76.8
24 TraesCS7A01G040500 chr2A 100.000 29 0 0 487 515 151287663 151287691 2.000000e-03 54.7
25 TraesCS7A01G040500 chr5B 84.706 85 11 1 431 515 233816388 233816470 3.190000e-12 84.2
26 TraesCS7A01G040500 chr3D 93.617 47 2 1 429 475 338931323 338931278 8.920000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G040500 chr7A 18791359 18796324 4965 True 9171.000000 9171 100.000000 1 4966 1 chr7A.!!$R1 4965
1 TraesCS7A01G040500 chr7D 18382941 18387124 4183 True 2945.000000 4687 92.005000 661 4966 2 chr7D.!!$R2 4305
2 TraesCS7A01G040500 chrUn 50912446 50916605 4159 True 1863.333333 4015 89.550333 544 4955 3 chrUn.!!$R1 4411
3 TraesCS7A01G040500 chr6D 315365657 315366188 531 True 255.000000 255 75.985000 1 513 1 chr6D.!!$R2 512
4 TraesCS7A01G040500 chr2B 793999710 794000249 539 True 248.000000 248 75.963000 1 514 1 chr2B.!!$R1 513
5 TraesCS7A01G040500 chr7B 169466958 169467500 542 True 209.000000 209 74.775000 1 524 1 chr7B.!!$R1 523

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
476 517 0.034059 CACAGGAAACGAGGCAGACT 59.966 55.0 0.00 0.0 0.0 3.24 F
531 575 0.035056 GCAGCTGGGTATCCTTGTGT 60.035 55.0 17.12 0.0 0.0 3.72 F
1219 1278 0.040958 GCATCGGCCGCTAATTTGAG 60.041 55.0 23.51 0.0 0.0 3.02 F
1583 1660 0.542938 TGCCTGACCTGCTAGAGTGT 60.543 55.0 0.00 0.0 0.0 3.55 F
1584 1661 0.610687 GCCTGACCTGCTAGAGTGTT 59.389 55.0 0.00 0.0 0.0 3.32 F
2292 2370 0.901827 TCTTCAGAGGGTTGCGCATA 59.098 50.0 12.75 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1418 0.239347 GCAAGTGTAAGCAGCCAGTG 59.761 55.000 0.00 0.00 0.00 3.66 R
1565 1635 0.610687 AACACTCTAGCAGGTCAGGC 59.389 55.000 0.00 0.00 0.00 4.85 R
2706 2791 0.177141 CCATTGTACACGGACCGGAT 59.823 55.000 20.00 8.17 0.00 4.18 R
3475 3560 1.205417 GAAAAGATGCACCCACCATGG 59.795 52.381 11.19 11.19 37.25 3.66 R
3521 3606 2.445453 TGTTCAGAAAACACGAACGC 57.555 45.000 0.00 0.00 41.52 4.84 R
4200 4303 0.036732 TGCAATCTCTCCCCACACAC 59.963 55.000 0.00 0.00 0.00 3.82 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
46 47 1.410850 TTCATCGCCCCTCCCTCATC 61.411 60.000 0.00 0.00 0.00 2.92
47 48 1.840650 CATCGCCCCTCCCTCATCT 60.841 63.158 0.00 0.00 0.00 2.90
61 62 2.436646 ATCTGAGCCGGGCAAACG 60.437 61.111 23.09 6.54 0.00 3.60
70 71 0.381089 CCGGGCAAACGTTGTTGTAA 59.619 50.000 0.00 0.00 0.00 2.41
99 108 3.007635 TCGAGAAGTCATCGTGCTAAGA 58.992 45.455 0.00 0.00 40.95 2.10
103 112 0.456221 AGTCATCGTGCTAAGACCCG 59.544 55.000 0.00 0.00 0.00 5.28
105 114 0.454600 TCATCGTGCTAAGACCCGAC 59.545 55.000 0.00 0.00 31.43 4.79
109 118 1.352156 CGTGCTAAGACCCGACAAGC 61.352 60.000 0.00 0.00 0.00 4.01
116 125 3.819877 GACCCGACAAGCCCAACGT 62.820 63.158 0.00 0.00 0.00 3.99
118 127 1.740296 CCCGACAAGCCCAACGTAG 60.740 63.158 0.00 0.00 0.00 3.51
138 147 2.904866 GAACAGCAACCACCGCCA 60.905 61.111 0.00 0.00 0.00 5.69
151 160 0.036732 ACCGCCATTGAAGAGAAGCA 59.963 50.000 0.00 0.00 0.00 3.91
154 163 2.945008 CCGCCATTGAAGAGAAGCATAA 59.055 45.455 0.00 0.00 0.00 1.90
162 183 7.255381 CCATTGAAGAGAAGCATAAATCGGAAT 60.255 37.037 0.00 0.00 0.00 3.01
167 188 5.636965 AGAGAAGCATAAATCGGAATGATCG 59.363 40.000 0.00 0.00 35.84 3.69
171 192 6.808008 AGCATAAATCGGAATGATCGAATT 57.192 33.333 0.00 0.00 40.15 2.17
173 194 7.651808 AGCATAAATCGGAATGATCGAATTTT 58.348 30.769 0.00 0.00 40.15 1.82
179 200 6.598753 TCGGAATGATCGAATTTTTAGACC 57.401 37.500 0.00 0.00 33.42 3.85
186 207 5.350365 TGATCGAATTTTTAGACCCACGAAG 59.650 40.000 0.00 0.00 32.69 3.79
193 214 2.281539 TAGACCCACGAAGACAGACA 57.718 50.000 0.00 0.00 0.00 3.41
196 217 2.169769 AGACCCACGAAGACAGACAAAA 59.830 45.455 0.00 0.00 0.00 2.44
197 218 3.139077 GACCCACGAAGACAGACAAAAT 58.861 45.455 0.00 0.00 0.00 1.82
198 219 2.878406 ACCCACGAAGACAGACAAAATG 59.122 45.455 0.00 0.00 0.00 2.32
199 220 2.226437 CCCACGAAGACAGACAAAATGG 59.774 50.000 0.00 0.00 0.00 3.16
204 225 6.094048 CCACGAAGACAGACAAAATGGATATT 59.906 38.462 0.00 0.00 0.00 1.28
233 254 5.653769 CCACATGGATCCACTAAAGACAAAT 59.346 40.000 18.99 0.00 37.39 2.32
247 268 0.035439 ACAAATGCCGACCGAATCCT 60.035 50.000 0.00 0.00 0.00 3.24
258 279 0.747255 CCGAATCCTGTGAGATCCGT 59.253 55.000 0.00 0.00 0.00 4.69
260 281 1.678627 CGAATCCTGTGAGATCCGTCT 59.321 52.381 0.00 0.00 37.42 4.18
261 282 2.879026 CGAATCCTGTGAGATCCGTCTA 59.121 50.000 0.00 0.00 33.97 2.59
271 292 3.194968 TGAGATCCGTCTAAGACAAACCC 59.805 47.826 0.00 0.00 33.97 4.11
277 298 2.290071 CGTCTAAGACAAACCCCCACAT 60.290 50.000 0.00 0.00 32.09 3.21
281 302 0.850100 AGACAAACCCCCACATGTCA 59.150 50.000 0.00 0.00 43.53 3.58
283 304 2.158325 AGACAAACCCCCACATGTCATT 60.158 45.455 0.00 0.00 43.53 2.57
285 306 2.246469 CAAACCCCCACATGTCATTCA 58.754 47.619 0.00 0.00 0.00 2.57
287 308 2.220653 ACCCCCACATGTCATTCAAG 57.779 50.000 0.00 0.00 0.00 3.02
295 316 4.641541 CCACATGTCATTCAAGGATGCTAA 59.358 41.667 0.00 0.00 0.00 3.09
309 330 2.267045 GCTAAAAGCACCACTGGGG 58.733 57.895 0.00 0.00 41.89 4.96
316 337 3.579302 CACCACTGGGGCAAGGGA 61.579 66.667 0.00 0.00 42.05 4.20
327 348 2.829592 CAAGGGATAGGCGGGGAC 59.170 66.667 0.00 0.00 0.00 4.46
344 365 3.954258 GGGGACAACCTTATTCCATCTTG 59.046 47.826 0.00 0.00 40.03 3.02
346 367 5.261216 GGGACAACCTTATTCCATCTTGAA 58.739 41.667 0.00 0.00 35.85 2.69
347 368 5.358160 GGGACAACCTTATTCCATCTTGAAG 59.642 44.000 0.00 0.00 35.85 3.02
401 426 6.715264 AGGACACAAACCCTAATAAAACTCAG 59.285 38.462 0.00 0.00 0.00 3.35
411 436 7.122799 ACCCTAATAAAACTCAGAAAAGCATCC 59.877 37.037 0.00 0.00 0.00 3.51
415 456 8.767478 AATAAAACTCAGAAAAGCATCCAATG 57.233 30.769 0.00 0.00 0.00 2.82
421 462 2.841881 AGAAAAGCATCCAATGGGCAAT 59.158 40.909 0.00 0.00 0.00 3.56
424 465 0.325860 AGCATCCAATGGGCAATGGT 60.326 50.000 0.00 0.00 37.94 3.55
476 517 0.034059 CACAGGAAACGAGGCAGACT 59.966 55.000 0.00 0.00 0.00 3.24
514 555 1.192146 AGGCACGAGAAACCCTAGCA 61.192 55.000 0.00 0.00 0.00 3.49
525 569 2.062070 CCCTAGCAGCTGGGTATCC 58.938 63.158 22.60 0.00 38.65 2.59
526 570 0.472734 CCCTAGCAGCTGGGTATCCT 60.473 60.000 22.60 5.14 38.65 3.24
527 571 1.428869 CCTAGCAGCTGGGTATCCTT 58.571 55.000 16.80 0.00 0.00 3.36
528 572 1.071385 CCTAGCAGCTGGGTATCCTTG 59.929 57.143 16.80 3.67 0.00 3.61
529 573 1.765314 CTAGCAGCTGGGTATCCTTGT 59.235 52.381 17.12 0.00 0.00 3.16
530 574 0.254178 AGCAGCTGGGTATCCTTGTG 59.746 55.000 17.12 0.00 0.00 3.33
531 575 0.035056 GCAGCTGGGTATCCTTGTGT 60.035 55.000 17.12 0.00 0.00 3.72
532 576 1.209504 GCAGCTGGGTATCCTTGTGTA 59.790 52.381 17.12 0.00 0.00 2.90
533 577 2.158755 GCAGCTGGGTATCCTTGTGTAT 60.159 50.000 17.12 0.00 0.00 2.29
534 578 3.470709 CAGCTGGGTATCCTTGTGTATG 58.529 50.000 5.57 0.00 0.00 2.39
535 579 3.134623 CAGCTGGGTATCCTTGTGTATGA 59.865 47.826 5.57 0.00 0.00 2.15
536 580 3.389329 AGCTGGGTATCCTTGTGTATGAG 59.611 47.826 0.00 0.00 0.00 2.90
537 581 3.733337 CTGGGTATCCTTGTGTATGAGC 58.267 50.000 0.00 0.00 0.00 4.26
538 582 2.102420 TGGGTATCCTTGTGTATGAGCG 59.898 50.000 0.00 0.00 0.00 5.03
539 583 2.364324 GGGTATCCTTGTGTATGAGCGA 59.636 50.000 0.00 0.00 0.00 4.93
540 584 3.181469 GGGTATCCTTGTGTATGAGCGAA 60.181 47.826 0.00 0.00 0.00 4.70
541 585 4.051922 GGTATCCTTGTGTATGAGCGAAG 58.948 47.826 0.00 0.00 0.00 3.79
571 615 7.046652 CCCACAATTATTGCATTGGTTAATCA 58.953 34.615 4.68 0.00 38.32 2.57
573 617 8.767085 CCACAATTATTGCATTGGTTAATCATC 58.233 33.333 4.68 0.00 38.32 2.92
574 618 9.315525 CACAATTATTGCATTGGTTAATCATCA 57.684 29.630 4.68 0.00 38.32 3.07
616 660 9.760077 ATTAACTAGGATTAAGGAATGTGTACG 57.240 33.333 0.00 0.00 0.00 3.67
618 662 7.598759 ACTAGGATTAAGGAATGTGTACGAT 57.401 36.000 0.00 0.00 0.00 3.73
623 667 8.794553 AGGATTAAGGAATGTGTACGATACTAG 58.205 37.037 0.00 0.00 0.00 2.57
652 696 9.003112 CACAACTTATTGCATTCTTATTCTTCG 57.997 33.333 0.00 0.00 39.66 3.79
747 802 4.081309 CAGCTGGTTCATGGGATCATTTTT 60.081 41.667 5.57 0.00 0.00 1.94
753 808 7.972301 TGGTTCATGGGATCATTTTTAAAAGT 58.028 30.769 0.14 0.00 0.00 2.66
873 928 0.611340 TAACATGCATGCCAGCCACA 60.611 50.000 26.53 0.00 0.00 4.17
875 930 3.458163 ATGCATGCCAGCCACAGC 61.458 61.111 16.68 0.00 40.32 4.40
946 1004 7.066307 TGTTCAGCATAGCAAGGATTAGATA 57.934 36.000 0.00 0.00 0.00 1.98
947 1005 7.683578 TGTTCAGCATAGCAAGGATTAGATAT 58.316 34.615 0.00 0.00 0.00 1.63
1051 1110 0.752658 GGGTTGCTTGGTGCTTCTTT 59.247 50.000 0.00 0.00 43.37 2.52
1086 1145 0.531532 CCGTGATGATGTGCCCTCTC 60.532 60.000 0.00 0.00 0.00 3.20
1189 1248 7.812669 CAGGTACGCATAGTATCATGTATTCAA 59.187 37.037 0.00 0.00 38.90 2.69
1190 1249 8.029522 AGGTACGCATAGTATCATGTATTCAAG 58.970 37.037 0.00 0.00 38.90 3.02
1195 1254 7.062722 CGCATAGTATCATGTATTCAAGTGAGG 59.937 40.741 0.00 0.00 0.00 3.86
1219 1278 0.040958 GCATCGGCCGCTAATTTGAG 60.041 55.000 23.51 0.00 0.00 3.02
1243 1302 6.261158 AGTCAGTTAGCTTCTTCCAAAGTTTC 59.739 38.462 0.00 0.00 0.00 2.78
1258 1317 3.047613 AGTTTCGTTTTGCTTCGACAC 57.952 42.857 0.00 0.00 37.13 3.67
1357 1418 6.992123 TCACATATCCACTGATTTCCATGTAC 59.008 38.462 0.00 0.00 29.49 2.90
1359 1420 6.767902 ACATATCCACTGATTTCCATGTACAC 59.232 38.462 0.00 0.00 29.02 2.90
1444 1514 3.643595 CTTGGATGGAAGCCCGCCA 62.644 63.158 0.00 0.00 46.54 5.69
1468 1538 4.593956 CTTACCAATTGGAGAGAGGCTTT 58.406 43.478 31.22 6.81 38.94 3.51
1514 1584 6.536224 GCTCGTCTATCTAGAGGTTACTATCC 59.464 46.154 0.00 0.00 38.82 2.59
1565 1635 3.853307 GCTTCACACCTCGGTTCAAAATG 60.853 47.826 0.00 0.00 0.00 2.32
1566 1636 1.606668 TCACACCTCGGTTCAAAATGC 59.393 47.619 0.00 0.00 0.00 3.56
1567 1637 0.958822 ACACCTCGGTTCAAAATGCC 59.041 50.000 0.00 0.00 0.00 4.40
1573 1650 1.202879 TCGGTTCAAAATGCCTGACCT 60.203 47.619 0.00 0.00 0.00 3.85
1583 1660 0.542938 TGCCTGACCTGCTAGAGTGT 60.543 55.000 0.00 0.00 0.00 3.55
1584 1661 0.610687 GCCTGACCTGCTAGAGTGTT 59.389 55.000 0.00 0.00 0.00 3.32
1635 1712 9.695155 ACCACCAGCTAATACAAATTTACTTAT 57.305 29.630 0.00 0.00 0.00 1.73
1689 1766 5.390251 CGCATATCTACACCAAGATTGATGC 60.390 44.000 9.85 9.85 40.95 3.91
1697 1774 4.518970 ACACCAAGATTGATGCTAAACGTT 59.481 37.500 0.00 0.00 0.00 3.99
1754 1831 8.723942 AAATATATCATCTATTTCGGACCAGC 57.276 34.615 0.00 0.00 0.00 4.85
1848 1925 2.222819 CGCGCTTGGTTCATCTAACTTC 60.223 50.000 5.56 0.00 38.23 3.01
1930 2007 9.282247 GTAATCTGCAATGTTCTGTTATTCTTG 57.718 33.333 0.00 0.00 0.00 3.02
1939 2016 9.630098 AATGTTCTGTTATTCTTGCATAGTTTG 57.370 29.630 0.00 0.00 0.00 2.93
1957 2034 8.915654 CATAGTTTGGTTGATCAAAGCTTTTAC 58.084 33.333 10.35 4.62 37.31 2.01
2045 2122 9.155975 CTTGCACTAGTTCTGATTACTTACATT 57.844 33.333 0.00 0.00 0.00 2.71
2089 2166 3.810941 ACTGGAATAAAGTTTTCGTGCGA 59.189 39.130 0.00 0.00 0.00 5.10
2122 2199 1.462616 CGTCATTTTCTGGGGATGCA 58.537 50.000 0.00 0.00 0.00 3.96
2143 2221 4.498345 GCAGAGTACGAAGATCAAGTAGGG 60.498 50.000 0.00 0.00 0.00 3.53
2178 2256 3.932710 TGTGCTCTCGTTTGATATTCCAC 59.067 43.478 0.00 0.00 0.00 4.02
2184 2262 6.480524 TCTCGTTTGATATTCCACTGTTTG 57.519 37.500 0.00 0.00 0.00 2.93
2225 2303 7.739295 ACAATGATACGTTGTATTGTTCTGTC 58.261 34.615 14.37 0.00 39.88 3.51
2226 2304 7.386573 ACAATGATACGTTGTATTGTTCTGTCA 59.613 33.333 14.37 0.00 39.88 3.58
2227 2305 6.699895 TGATACGTTGTATTGTTCTGTCAC 57.300 37.500 0.00 0.00 0.00 3.67
2228 2306 6.452242 TGATACGTTGTATTGTTCTGTCACT 58.548 36.000 0.00 0.00 0.00 3.41
2229 2307 6.926826 TGATACGTTGTATTGTTCTGTCACTT 59.073 34.615 0.00 0.00 0.00 3.16
2230 2308 5.652744 ACGTTGTATTGTTCTGTCACTTC 57.347 39.130 0.00 0.00 0.00 3.01
2231 2309 5.357257 ACGTTGTATTGTTCTGTCACTTCT 58.643 37.500 0.00 0.00 0.00 2.85
2232 2310 5.234329 ACGTTGTATTGTTCTGTCACTTCTG 59.766 40.000 0.00 0.00 0.00 3.02
2233 2311 5.234329 CGTTGTATTGTTCTGTCACTTCTGT 59.766 40.000 0.00 0.00 0.00 3.41
2234 2312 6.562270 CGTTGTATTGTTCTGTCACTTCTGTC 60.562 42.308 0.00 0.00 0.00 3.51
2265 2343 6.921412 TGGATGGTGTTATTAGGATGGAAAT 58.079 36.000 0.00 0.00 0.00 2.17
2267 2345 8.506921 TGGATGGTGTTATTAGGATGGAAATAA 58.493 33.333 0.00 0.00 0.00 1.40
2292 2370 0.901827 TCTTCAGAGGGTTGCGCATA 59.098 50.000 12.75 0.00 0.00 3.14
2301 2379 1.383456 GGTTGCGCATATGGGAAGCA 61.383 55.000 22.86 8.96 35.90 3.91
2353 2431 6.540189 ACTTGCTAATGCTAAACAGGTCATAG 59.460 38.462 0.00 0.00 40.48 2.23
2451 2536 8.081633 TCTTGAACAATAATTGACCATGTGAAC 58.918 33.333 0.00 0.00 0.00 3.18
2515 2600 2.039746 TGGTTTAGCCACACTACTGCAT 59.960 45.455 0.00 0.00 43.61 3.96
2529 2614 8.022550 CACACTACTGCATTGTGATGATTTTAA 58.977 33.333 17.00 0.00 42.77 1.52
2536 2621 5.720239 CATTGTGATGATTTTAATGCACGC 58.280 37.500 0.00 0.00 35.16 5.34
2544 2629 3.569250 TTTTAATGCACGCTTTCCTCC 57.431 42.857 0.00 0.00 0.00 4.30
2608 2693 4.537135 TGACAAGTAAGGCCACTCTTAG 57.463 45.455 5.01 4.08 30.76 2.18
2616 2701 7.497773 AGTAAGGCCACTCTTAGAACTAAAT 57.502 36.000 5.01 0.00 30.76 1.40
2643 2728 3.618690 AGGTCACTTGCTATTCCACTC 57.381 47.619 0.00 0.00 0.00 3.51
2660 2745 5.603596 TCCACTCTACATGTTTTTACGTGT 58.396 37.500 2.30 8.09 42.00 4.49
2706 2791 4.966805 AGGATATGGACGGAGAAAGGTTTA 59.033 41.667 0.00 0.00 0.00 2.01
2753 2838 1.377994 CCTCCAGGTGAGCTGCTTT 59.622 57.895 6.05 0.00 39.98 3.51
2813 2898 8.801299 TCTTAGTCTATGATTGATCTAGCCTTG 58.199 37.037 0.00 0.00 0.00 3.61
3019 3104 4.020617 CCCAAGGACTGCCTCGCA 62.021 66.667 0.00 0.00 46.28 5.10
3043 3128 1.344065 TGGAACCACTGGATGTACGT 58.656 50.000 0.71 0.00 0.00 3.57
3047 3132 3.056322 GGAACCACTGGATGTACGTAGTT 60.056 47.826 0.71 0.00 37.78 2.24
3048 3133 4.158394 GGAACCACTGGATGTACGTAGTTA 59.842 45.833 0.71 0.00 37.78 2.24
3049 3134 5.336690 GGAACCACTGGATGTACGTAGTTAA 60.337 44.000 0.71 0.00 37.78 2.01
3077 3162 4.070009 AGTCCCGAACCATTGTTTACTTC 58.930 43.478 0.00 0.00 33.97 3.01
3078 3163 3.816523 GTCCCGAACCATTGTTTACTTCA 59.183 43.478 0.00 0.00 33.97 3.02
3102 3187 6.833342 ATTTTCTTGCACACACAGATTTTC 57.167 33.333 0.00 0.00 0.00 2.29
3107 3192 4.031418 TGCACACACAGATTTTCTTGTG 57.969 40.909 13.43 13.43 39.32 3.33
3129 3214 6.423905 TGTGTCTTGCTCACTAGTAATTGAAC 59.576 38.462 0.00 0.00 36.83 3.18
3156 3241 5.216566 TCATTTGCTGACGTACTTAATGC 57.783 39.130 0.00 0.00 0.00 3.56
3201 3286 6.424509 CCTTCTGAGCTTATTAAGAGCATCAG 59.575 42.308 21.28 21.28 42.56 2.90
3260 3345 5.472137 TCTTGGCAGGTAATTAAGTGTCAAC 59.528 40.000 10.03 0.00 31.50 3.18
3319 3404 3.937079 TCTTGTAAGCATGCATCTGTCTG 59.063 43.478 21.98 2.99 0.00 3.51
3377 3462 8.762645 ACATTCTCCTTGTTGATCTGTAGATAA 58.237 33.333 0.00 0.00 34.37 1.75
3422 3507 2.026822 TCCTCTCCTGAAAAGTCATGGC 60.027 50.000 0.00 0.00 31.85 4.40
3424 3509 3.560882 CCTCTCCTGAAAAGTCATGGCTT 60.561 47.826 6.77 6.77 31.85 4.35
3443 3528 3.440173 GCTTACTTGCAAGGCTAACATCA 59.560 43.478 29.18 0.00 0.00 3.07
3475 3560 3.040147 TCCACACAAATCGAAGTCCTC 57.960 47.619 0.00 0.00 0.00 3.71
3482 3567 2.679837 CAAATCGAAGTCCTCCATGGTG 59.320 50.000 12.58 9.53 37.07 4.17
3521 3606 5.498393 TCTAGCATCGGGTAGGAATACTAG 58.502 45.833 0.00 0.00 43.65 2.57
3532 3617 4.184079 AGGAATACTAGCGTTCGTGTTT 57.816 40.909 0.00 0.00 0.00 2.83
3541 3626 2.417239 AGCGTTCGTGTTTTCTGAACAA 59.583 40.909 5.34 0.00 41.52 2.83
3543 3628 3.738399 CGTTCGTGTTTTCTGAACAACA 58.262 40.909 11.46 11.46 41.52 3.33
3549 3634 6.711579 TCGTGTTTTCTGAACAACATTCTAC 58.288 36.000 15.79 6.95 35.40 2.59
3658 3743 2.029110 CCCACTGCCAAACACCATTTAG 60.029 50.000 0.00 0.00 0.00 1.85
3733 3820 8.698973 TCTTCTTTATGGGTGTGTTTATCAAA 57.301 30.769 0.00 0.00 0.00 2.69
3903 3994 1.353694 ACTTCAGCAGAGGCCAAAGAT 59.646 47.619 5.01 0.00 42.56 2.40
3906 3997 3.272574 TCAGCAGAGGCCAAAGATTAG 57.727 47.619 5.01 0.00 42.56 1.73
4018 4118 3.008704 AGGGCCTTGTTTATACGTGAACT 59.991 43.478 0.00 0.00 0.00 3.01
4030 4130 8.645487 GTTTATACGTGAACTAGAGAAAGTTGG 58.355 37.037 0.00 0.00 39.78 3.77
4051 4151 6.418057 TGGCACAATAAGAGATTTGGTTTT 57.582 33.333 0.00 0.00 31.92 2.43
4052 4152 6.222389 TGGCACAATAAGAGATTTGGTTTTG 58.778 36.000 0.00 0.00 31.92 2.44
4053 4153 5.639082 GGCACAATAAGAGATTTGGTTTTGG 59.361 40.000 0.00 0.00 0.00 3.28
4054 4154 6.454795 GCACAATAAGAGATTTGGTTTTGGA 58.545 36.000 0.00 0.00 0.00 3.53
4055 4155 7.099120 GCACAATAAGAGATTTGGTTTTGGAT 58.901 34.615 0.00 0.00 0.00 3.41
4088 4188 9.897040 AACCATATGGAAATATTCATTAGGGTT 57.103 29.630 28.77 2.68 37.62 4.11
4089 4189 9.897040 ACCATATGGAAATATTCATTAGGGTTT 57.103 29.630 28.77 0.00 32.43 3.27
4094 4194 9.707957 ATGGAAATATTCATTAGGGTTTGTACA 57.292 29.630 0.00 0.00 0.00 2.90
4095 4195 9.535170 TGGAAATATTCATTAGGGTTTGTACAA 57.465 29.630 3.59 3.59 0.00 2.41
4100 4200 7.582667 ATTCATTAGGGTTTGTACAATAGCC 57.417 36.000 21.43 21.43 0.00 3.93
4101 4201 5.120399 TCATTAGGGTTTGTACAATAGCCG 58.880 41.667 22.10 13.95 34.70 5.52
4102 4202 4.822685 TTAGGGTTTGTACAATAGCCGA 57.177 40.909 22.10 17.96 34.70 5.54
4103 4203 3.261981 AGGGTTTGTACAATAGCCGAG 57.738 47.619 22.10 0.00 34.70 4.63
4104 4204 2.835764 AGGGTTTGTACAATAGCCGAGA 59.164 45.455 22.10 2.01 34.70 4.04
4105 4205 3.118738 AGGGTTTGTACAATAGCCGAGAG 60.119 47.826 22.10 0.00 34.70 3.20
4106 4206 3.369157 GGGTTTGTACAATAGCCGAGAGT 60.369 47.826 9.56 0.00 0.00 3.24
4107 4207 4.251268 GGTTTGTACAATAGCCGAGAGTT 58.749 43.478 9.56 0.00 0.00 3.01
4108 4208 4.329256 GGTTTGTACAATAGCCGAGAGTTC 59.671 45.833 9.56 0.00 0.00 3.01
4109 4209 3.795623 TGTACAATAGCCGAGAGTTCC 57.204 47.619 0.00 0.00 0.00 3.62
4110 4210 3.093814 TGTACAATAGCCGAGAGTTCCA 58.906 45.455 0.00 0.00 0.00 3.53
4111 4211 2.969628 ACAATAGCCGAGAGTTCCAG 57.030 50.000 0.00 0.00 0.00 3.86
4112 4212 1.134670 ACAATAGCCGAGAGTTCCAGC 60.135 52.381 0.00 0.00 0.00 4.85
4113 4213 0.103208 AATAGCCGAGAGTTCCAGCG 59.897 55.000 0.00 0.00 0.00 5.18
4137 4237 7.523219 CGTAATTTCTGTTTGTTGCCATACTA 58.477 34.615 0.00 0.00 0.00 1.82
4143 4243 7.575414 TCTGTTTGTTGCCATACTAGAAAAA 57.425 32.000 0.00 0.00 0.00 1.94
4144 4244 8.177119 TCTGTTTGTTGCCATACTAGAAAAAT 57.823 30.769 0.00 0.00 0.00 1.82
4224 4327 3.388024 GTGTGGGGAGAGATTGCACTATA 59.612 47.826 0.00 0.00 0.00 1.31
4315 4418 4.292186 AGCCGTTTGATATATCCATGCT 57.708 40.909 10.25 8.06 0.00 3.79
4335 4438 3.760684 GCTGAGTGAAATTGAATGAGGGT 59.239 43.478 0.00 0.00 0.00 4.34
4388 4493 6.824704 TGAAGCAATGAATGAGATACACATGA 59.175 34.615 0.00 0.00 0.00 3.07
4391 4496 9.516546 AAGCAATGAATGAGATACACATGATAT 57.483 29.630 0.00 0.00 0.00 1.63
4438 4543 6.039717 GCATGATACCTTGGTGAATACATGTT 59.960 38.462 2.30 0.00 36.19 2.71
4440 4545 6.480763 TGATACCTTGGTGAATACATGTTGT 58.519 36.000 2.30 0.00 0.00 3.32
4461 4567 1.066908 ACGTGGCAAGTCAAATGTTGG 59.933 47.619 0.00 0.00 0.00 3.77
4472 4578 3.190535 GTCAAATGTTGGCACGGTAGATT 59.809 43.478 0.00 0.00 34.79 2.40
4473 4579 3.438781 TCAAATGTTGGCACGGTAGATTC 59.561 43.478 0.00 0.00 0.00 2.52
4475 4581 4.481368 AATGTTGGCACGGTAGATTCTA 57.519 40.909 0.00 0.00 0.00 2.10
4497 4603 3.627395 AGCATAAAGACCACCATCGAA 57.373 42.857 0.00 0.00 0.00 3.71
4606 4712 5.745227 ACCACTAGAACCATTAATGACAGG 58.255 41.667 17.23 2.46 0.00 4.00
4607 4713 5.250774 ACCACTAGAACCATTAATGACAGGT 59.749 40.000 17.23 3.14 35.47 4.00
4659 4765 6.865205 CAGTCATATAGCAACATCGATGAAGA 59.135 38.462 31.33 11.78 0.00 2.87
4742 4848 4.148348 CGATTACATAAACGACAGCCTAGC 59.852 45.833 0.00 0.00 34.02 3.42
4744 4850 1.209128 CATAAACGACAGCCTAGCCG 58.791 55.000 0.00 0.00 0.00 5.52
4759 4866 6.017109 CAGCCTAGCCGAATAAATACAAACAT 60.017 38.462 0.00 0.00 0.00 2.71
4767 4874 9.296400 GCCGAATAAATACAAACATTGTGTTAT 57.704 29.630 6.01 6.97 42.96 1.89
4789 4896 9.640963 GTTATACCCAACACATACATCTATCTC 57.359 37.037 0.00 0.00 0.00 2.75
4845 4952 4.848357 CCAAACTTGGGTCATAGAGTGAT 58.152 43.478 0.09 0.00 44.70 3.06
4855 4962 4.294232 GTCATAGAGTGATCACGTCCATG 58.706 47.826 19.85 18.98 39.48 3.66
4860 4967 2.363680 GAGTGATCACGTCCATGGAGAT 59.636 50.000 16.81 14.75 36.20 2.75
4863 4970 4.590647 AGTGATCACGTCCATGGAGATATT 59.409 41.667 16.81 0.00 36.20 1.28
4876 4983 6.669591 CCATGGAGATATTGATGTACCTAGGA 59.330 42.308 17.98 0.00 0.00 2.94
4925 5033 8.915057 AAGAATCATAGTAATCATGACCTTGG 57.085 34.615 0.00 0.00 35.33 3.61
4928 5036 4.660303 TCATAGTAATCATGACCTTGGCCT 59.340 41.667 3.32 0.00 0.00 5.19
4956 5064 4.916041 TCTGAAGTTCTGTCCAATGGAT 57.084 40.909 4.81 0.00 32.73 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.338136 GGAGGGGCGATGAAAGGAGA 61.338 60.000 0.00 0.00 0.00 3.71
23 24 2.375345 GGGAGGGGCGATGAAAGGA 61.375 63.158 0.00 0.00 0.00 3.36
24 25 2.193248 GGGAGGGGCGATGAAAGG 59.807 66.667 0.00 0.00 0.00 3.11
27 28 1.384502 ATGAGGGAGGGGCGATGAA 60.385 57.895 0.00 0.00 0.00 2.57
46 47 2.978010 AACGTTTGCCCGGCTCAG 60.978 61.111 11.61 2.21 0.00 3.35
47 48 3.283684 CAACGTTTGCCCGGCTCA 61.284 61.111 11.61 0.00 0.00 4.26
61 62 6.862090 ACTTCTCGACTGTCTATTACAACAAC 59.138 38.462 6.21 0.00 37.74 3.32
70 71 4.034626 CACGATGACTTCTCGACTGTCTAT 59.965 45.833 6.21 2.71 39.38 1.98
99 108 2.444700 CTACGTTGGGCTTGTCGGGT 62.445 60.000 0.00 0.00 0.00 5.28
103 112 0.320421 TCTGCTACGTTGGGCTTGTC 60.320 55.000 0.00 0.00 0.00 3.18
105 114 0.517316 GTTCTGCTACGTTGGGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
109 118 0.602638 TGCTGTTCTGCTACGTTGGG 60.603 55.000 0.00 0.00 0.00 4.12
116 125 0.602638 CGGTGGTTGCTGTTCTGCTA 60.603 55.000 3.65 0.00 0.00 3.49
118 127 2.639286 CGGTGGTTGCTGTTCTGC 59.361 61.111 0.00 0.00 0.00 4.26
138 147 7.500227 TCATTCCGATTTATGCTTCTCTTCAAT 59.500 33.333 0.00 0.00 0.00 2.57
154 163 7.255139 GGGTCTAAAAATTCGATCATTCCGATT 60.255 37.037 0.00 0.00 35.84 3.34
162 183 4.823157 TCGTGGGTCTAAAAATTCGATCA 58.177 39.130 0.00 0.00 0.00 2.92
167 188 5.699458 TCTGTCTTCGTGGGTCTAAAAATTC 59.301 40.000 0.00 0.00 0.00 2.17
171 192 3.385433 TGTCTGTCTTCGTGGGTCTAAAA 59.615 43.478 0.00 0.00 0.00 1.52
173 194 2.589720 TGTCTGTCTTCGTGGGTCTAA 58.410 47.619 0.00 0.00 0.00 2.10
179 200 3.138304 TCCATTTTGTCTGTCTTCGTGG 58.862 45.455 0.00 0.00 0.00 4.94
186 207 8.908786 TGGATCTAATATCCATTTTGTCTGTC 57.091 34.615 2.57 0.00 42.81 3.51
213 234 4.646492 GGCATTTGTCTTTAGTGGATCCAT 59.354 41.667 19.62 9.69 0.00 3.41
224 245 1.600023 TTCGGTCGGCATTTGTCTTT 58.400 45.000 0.00 0.00 0.00 2.52
233 254 2.225791 CTCACAGGATTCGGTCGGCA 62.226 60.000 0.00 0.00 0.00 5.69
247 268 4.321750 GGTTTGTCTTAGACGGATCTCACA 60.322 45.833 7.92 0.00 36.29 3.58
258 279 2.714250 ACATGTGGGGGTTTGTCTTAGA 59.286 45.455 0.00 0.00 0.00 2.10
260 281 2.443632 TGACATGTGGGGGTTTGTCTTA 59.556 45.455 1.15 0.00 39.33 2.10
261 282 1.216678 TGACATGTGGGGGTTTGTCTT 59.783 47.619 1.15 0.00 39.33 3.01
271 292 2.100252 GCATCCTTGAATGACATGTGGG 59.900 50.000 1.15 0.00 0.00 4.61
277 298 5.314923 GCTTTTAGCATCCTTGAATGACA 57.685 39.130 0.00 0.00 41.89 3.58
295 316 1.833934 CTTGCCCCAGTGGTGCTTT 60.834 57.895 17.97 0.00 36.04 3.51
305 326 3.488569 CGCCTATCCCTTGCCCCA 61.489 66.667 0.00 0.00 0.00 4.96
309 330 3.168528 TCCCCGCCTATCCCTTGC 61.169 66.667 0.00 0.00 0.00 4.01
316 337 1.815757 ATAAGGTTGTCCCCGCCTAT 58.184 50.000 0.00 0.00 31.43 2.57
327 348 5.067023 GCTCCTTCAAGATGGAATAAGGTTG 59.933 44.000 6.22 0.00 38.29 3.77
361 382 1.070758 TGTCCTGCTCAAAGAGGTGAC 59.929 52.381 0.00 0.00 0.00 3.67
364 385 1.131638 TGTGTCCTGCTCAAAGAGGT 58.868 50.000 0.00 0.00 0.00 3.85
401 426 2.766345 TTGCCCATTGGATGCTTTTC 57.234 45.000 3.62 0.00 0.00 2.29
411 436 0.756442 ATCCCGACCATTGCCCATTG 60.756 55.000 0.00 0.00 0.00 2.82
415 456 2.203351 GGATCCCGACCATTGCCC 60.203 66.667 0.00 0.00 0.00 5.36
421 462 1.672854 GACGTGATGGATCCCGACCA 61.673 60.000 9.90 0.00 41.83 4.02
424 465 1.107538 GGAGACGTGATGGATCCCGA 61.108 60.000 9.90 0.00 32.05 5.14
489 530 1.301479 GTTTCTCGTGCCTCCCGTT 60.301 57.895 0.00 0.00 0.00 4.44
514 555 3.384168 TCATACACAAGGATACCCAGCT 58.616 45.455 0.00 0.00 33.88 4.24
524 568 1.725641 TGCTTCGCTCATACACAAGG 58.274 50.000 0.00 0.00 0.00 3.61
525 569 3.242543 GGATTGCTTCGCTCATACACAAG 60.243 47.826 0.00 0.00 0.00 3.16
526 570 2.677836 GGATTGCTTCGCTCATACACAA 59.322 45.455 0.00 0.00 0.00 3.33
527 571 2.279741 GGATTGCTTCGCTCATACACA 58.720 47.619 0.00 0.00 0.00 3.72
528 572 1.599542 GGGATTGCTTCGCTCATACAC 59.400 52.381 0.00 0.00 34.56 2.90
529 573 1.209261 TGGGATTGCTTCGCTCATACA 59.791 47.619 6.02 0.00 38.11 2.29
530 574 1.599542 GTGGGATTGCTTCGCTCATAC 59.400 52.381 6.02 0.00 38.11 2.39
531 575 1.209261 TGTGGGATTGCTTCGCTCATA 59.791 47.619 6.02 0.00 36.30 2.15
532 576 0.035152 TGTGGGATTGCTTCGCTCAT 60.035 50.000 6.02 0.00 36.30 2.90
533 577 0.250684 TTGTGGGATTGCTTCGCTCA 60.251 50.000 6.02 5.71 38.53 4.26
534 578 1.098050 ATTGTGGGATTGCTTCGCTC 58.902 50.000 6.02 3.62 38.11 5.03
535 579 1.549203 AATTGTGGGATTGCTTCGCT 58.451 45.000 6.02 0.00 38.11 4.93
536 580 3.715628 ATAATTGTGGGATTGCTTCGC 57.284 42.857 0.00 0.00 37.78 4.70
542 586 5.430007 ACCAATGCAATAATTGTGGGATTG 58.570 37.500 14.48 14.48 36.06 2.67
547 591 8.665643 ATGATTAACCAATGCAATAATTGTGG 57.334 30.769 0.00 0.00 36.06 4.17
594 638 7.598759 ATCGTACACATTCCTTAATCCTAGT 57.401 36.000 0.00 0.00 0.00 2.57
595 639 8.794553 AGTATCGTACACATTCCTTAATCCTAG 58.205 37.037 0.00 0.00 0.00 3.02
615 659 7.980742 TGCAATAAGTTGTGTACTAGTATCG 57.019 36.000 5.75 0.00 35.54 2.92
618 662 9.938280 AAGAATGCAATAAGTTGTGTACTAGTA 57.062 29.630 0.00 0.00 35.54 1.82
628 672 9.773328 TTCGAAGAATAAGAATGCAATAAGTTG 57.227 29.630 0.00 0.00 45.90 3.16
747 802 6.777213 ACAATGTGTAACCAACCACTTTTA 57.223 33.333 0.00 0.00 34.36 1.52
753 808 4.059511 CTCGTACAATGTGTAACCAACCA 58.940 43.478 0.00 0.00 34.21 3.67
873 928 0.556747 AGTCTATGACCTACCGGGCT 59.443 55.000 6.32 0.00 39.94 5.19
875 930 5.813383 TCTATTAGTCTATGACCTACCGGG 58.187 45.833 6.32 0.00 41.89 5.73
946 1004 1.759445 ACTACTGGCTCGATCTGCAAT 59.241 47.619 9.27 0.00 0.00 3.56
947 1005 1.135139 GACTACTGGCTCGATCTGCAA 59.865 52.381 9.27 0.00 0.00 4.08
1051 1110 1.990060 CGGAGGCCAGGAGAAGGAA 60.990 63.158 5.01 0.00 0.00 3.36
1086 1145 3.047877 GGCGGTGAGGACCAAACG 61.048 66.667 0.47 0.47 43.33 3.60
1189 1248 2.801631 GCCGATGCTAGCCCTCACT 61.802 63.158 13.29 0.00 33.53 3.41
1190 1249 2.280457 GCCGATGCTAGCCCTCAC 60.280 66.667 13.29 0.86 33.53 3.51
1195 1254 2.788191 ATTAGCGGCCGATGCTAGCC 62.788 60.000 33.48 8.41 45.00 3.93
1219 1278 6.378710 AAACTTTGGAAGAAGCTAACTGAC 57.621 37.500 0.00 0.00 0.00 3.51
1243 1302 2.476619 AGAGATGTGTCGAAGCAAAACG 59.523 45.455 0.00 0.00 0.00 3.60
1357 1418 0.239347 GCAAGTGTAAGCAGCCAGTG 59.761 55.000 0.00 0.00 0.00 3.66
1359 1420 1.171308 ATGCAAGTGTAAGCAGCCAG 58.829 50.000 0.00 0.00 44.94 4.85
1444 1514 2.092699 GCCTCTCTCCAATTGGTAAGCT 60.093 50.000 23.76 0.00 36.34 3.74
1474 1544 1.903294 GAGCCAGCTGTGAGATCCA 59.097 57.895 13.81 0.00 0.00 3.41
1565 1635 0.610687 AACACTCTAGCAGGTCAGGC 59.389 55.000 0.00 0.00 0.00 4.85
1566 1636 2.300152 TCAAACACTCTAGCAGGTCAGG 59.700 50.000 0.00 0.00 0.00 3.86
1567 1637 3.667497 TCAAACACTCTAGCAGGTCAG 57.333 47.619 0.00 0.00 0.00 3.51
1650 1727 9.974980 TGTAGATATGCGAATGAAAAGTACATA 57.025 29.630 0.00 0.00 0.00 2.29
1651 1728 8.765219 GTGTAGATATGCGAATGAAAAGTACAT 58.235 33.333 0.00 0.00 0.00 2.29
1689 1766 9.321590 GGTGTTTAATTAGTAAGCAACGTTTAG 57.678 33.333 0.00 0.00 35.03 1.85
1697 1774 4.755629 TGCGTGGTGTTTAATTAGTAAGCA 59.244 37.500 0.00 0.00 31.17 3.91
1748 1825 0.739813 ACCGCATTTACTCGCTGGTC 60.740 55.000 0.00 0.00 32.21 4.02
1754 1831 1.129811 GGGAAACACCGCATTTACTCG 59.870 52.381 0.00 0.00 40.11 4.18
1848 1925 0.659427 CATACTGCACCGCTTCCATG 59.341 55.000 0.00 0.00 0.00 3.66
1930 2007 5.064441 AGCTTTGATCAACCAAACTATGC 57.936 39.130 7.89 0.00 33.07 3.14
1939 2016 4.723248 CCGAGTAAAAGCTTTGATCAACC 58.277 43.478 13.54 2.30 0.00 3.77
2089 2166 2.957402 ATGACGCCCCATCACAATAT 57.043 45.000 0.00 0.00 0.00 1.28
2122 2199 3.633065 GCCCTACTTGATCTTCGTACTCT 59.367 47.826 0.00 0.00 0.00 3.24
2143 2221 5.452777 ACGAGAGCACAAAAAGAAAATAGC 58.547 37.500 0.00 0.00 0.00 2.97
2209 2287 5.234329 ACAGAAGTGACAGAACAATACAACG 59.766 40.000 0.00 0.00 0.00 4.10
2225 2303 5.122869 CACCATCCATTAAGTGACAGAAGTG 59.877 44.000 0.00 0.00 31.79 3.16
2226 2304 5.221925 ACACCATCCATTAAGTGACAGAAGT 60.222 40.000 0.00 0.00 34.33 3.01
2227 2305 5.248640 ACACCATCCATTAAGTGACAGAAG 58.751 41.667 0.00 0.00 34.33 2.85
2228 2306 5.241403 ACACCATCCATTAAGTGACAGAA 57.759 39.130 0.00 0.00 34.33 3.02
2229 2307 4.908601 ACACCATCCATTAAGTGACAGA 57.091 40.909 0.00 0.00 34.33 3.41
2230 2308 7.630242 AATAACACCATCCATTAAGTGACAG 57.370 36.000 0.00 0.00 34.33 3.51
2231 2309 7.773224 CCTAATAACACCATCCATTAAGTGACA 59.227 37.037 0.00 0.00 34.33 3.58
2232 2310 7.990886 TCCTAATAACACCATCCATTAAGTGAC 59.009 37.037 0.00 0.00 34.33 3.67
2233 2311 8.096621 TCCTAATAACACCATCCATTAAGTGA 57.903 34.615 0.00 0.00 34.33 3.41
2234 2312 8.786898 CATCCTAATAACACCATCCATTAAGTG 58.213 37.037 0.00 0.00 36.30 3.16
2265 2343 4.680708 CGCAACCCTCTGAAGAATAGCTTA 60.681 45.833 0.00 0.00 36.83 3.09
2267 2345 2.419297 CGCAACCCTCTGAAGAATAGCT 60.419 50.000 0.00 0.00 0.00 3.32
2292 2370 3.003394 TCGTCAATGATTGCTTCCCAT 57.997 42.857 0.00 0.00 0.00 4.00
2301 2379 5.089970 TCTCCATGAGTTCGTCAATGATT 57.910 39.130 0.00 0.00 39.19 2.57
2381 2459 5.526111 TCTTGGTAGCTTAGAACACAACAAC 59.474 40.000 0.00 0.00 0.00 3.32
2392 2470 9.717942 AGAAATATATGCTTCTTGGTAGCTTAG 57.282 33.333 0.00 0.00 39.38 2.18
2451 2536 1.135257 GGGCCTGATCGACGATGATAG 60.135 57.143 16.49 10.27 0.00 2.08
2515 2600 5.058149 AGCGTGCATTAAAATCATCACAA 57.942 34.783 0.00 0.00 0.00 3.33
2529 2614 1.003839 TTCGGAGGAAAGCGTGCAT 60.004 52.632 0.00 0.00 0.00 3.96
2536 2621 1.160137 CTGCAACCTTCGGAGGAAAG 58.840 55.000 19.39 6.62 46.74 2.62
2544 2629 3.559238 AGCATTTAACTGCAACCTTCG 57.441 42.857 18.69 0.00 44.77 3.79
2616 2701 8.934697 AGTGGAATAGCAAGTGACCTATATTTA 58.065 33.333 0.00 0.00 0.00 1.40
2623 2708 3.177228 AGAGTGGAATAGCAAGTGACCT 58.823 45.455 0.00 0.00 0.00 3.85
2631 2716 7.064134 CGTAAAAACATGTAGAGTGGAATAGCA 59.936 37.037 0.00 0.00 0.00 3.49
2674 2759 1.068588 CGTCCATATCCTTTCTGCCGA 59.931 52.381 0.00 0.00 0.00 5.54
2690 2775 2.547826 CGGATAAACCTTTCTCCGTCC 58.452 52.381 13.68 0.00 45.93 4.79
2706 2791 0.177141 CCATTGTACACGGACCGGAT 59.823 55.000 20.00 8.17 0.00 4.18
2753 2838 9.810545 CTTTTTGGTTTAAAGTATTTGTCTCCA 57.189 29.630 0.00 0.00 39.63 3.86
2813 2898 6.206829 ACACAAATTAGAAGAGGGCTAAACAC 59.793 38.462 0.00 0.00 32.16 3.32
2991 3076 2.168313 CAGTCCTTGGGCAAAACTTTGT 59.832 45.455 4.23 0.00 40.24 2.83
3019 3104 3.814504 ACATCCAGTGGTTCCATCTTT 57.185 42.857 9.54 0.00 0.00 2.52
3043 3128 6.855763 TGGTTCGGGACTTCTAATTAACTA 57.144 37.500 0.00 0.00 0.00 2.24
3046 3131 6.478129 ACAATGGTTCGGGACTTCTAATTAA 58.522 36.000 0.00 0.00 0.00 1.40
3047 3132 6.057321 ACAATGGTTCGGGACTTCTAATTA 57.943 37.500 0.00 0.00 0.00 1.40
3048 3133 4.918588 ACAATGGTTCGGGACTTCTAATT 58.081 39.130 0.00 0.00 0.00 1.40
3049 3134 4.569719 ACAATGGTTCGGGACTTCTAAT 57.430 40.909 0.00 0.00 0.00 1.73
3077 3162 6.592798 AAATCTGTGTGTGCAAGAAAATTG 57.407 33.333 0.00 0.00 0.00 2.32
3078 3163 7.043565 AGAAAATCTGTGTGTGCAAGAAAATT 58.956 30.769 0.00 0.00 0.00 1.82
3102 3187 6.646653 TCAATTACTAGTGAGCAAGACACAAG 59.353 38.462 5.39 0.00 40.25 3.16
3107 3192 6.868864 TCTGTTCAATTACTAGTGAGCAAGAC 59.131 38.462 5.39 0.00 38.73 3.01
3129 3214 5.536554 AAGTACGTCAGCAAATGATTCTG 57.463 39.130 0.00 0.00 40.92 3.02
3156 3241 6.712547 AGAAGGAAAGAAACACTAGGAACATG 59.287 38.462 0.00 0.00 0.00 3.21
3201 3286 2.802719 TGAGAATAAAAGTGGGGGTGC 58.197 47.619 0.00 0.00 0.00 5.01
3293 3378 5.005740 ACAGATGCATGCTTACAAGAGAAA 58.994 37.500 20.33 0.00 0.00 2.52
3294 3379 4.582869 ACAGATGCATGCTTACAAGAGAA 58.417 39.130 20.33 0.00 0.00 2.87
3295 3380 4.081254 AGACAGATGCATGCTTACAAGAGA 60.081 41.667 20.33 0.00 0.00 3.10
3296 3381 4.034163 CAGACAGATGCATGCTTACAAGAG 59.966 45.833 20.33 3.38 0.00 2.85
3350 3435 6.401394 TCTACAGATCAACAAGGAGAATGTG 58.599 40.000 0.00 0.00 0.00 3.21
3377 3462 9.614792 GGATTCATCTGGTACTAGTACATTTTT 57.385 33.333 29.38 11.00 37.78 1.94
3422 3507 4.937620 TCTGATGTTAGCCTTGCAAGTAAG 59.062 41.667 24.35 10.95 0.00 2.34
3424 3509 4.222810 TCTCTGATGTTAGCCTTGCAAGTA 59.777 41.667 24.35 9.08 0.00 2.24
3475 3560 1.205417 GAAAAGATGCACCCACCATGG 59.795 52.381 11.19 11.19 37.25 3.66
3482 3567 3.202097 GCTAGAGAGAAAAGATGCACCC 58.798 50.000 0.00 0.00 0.00 4.61
3521 3606 2.445453 TGTTCAGAAAACACGAACGC 57.555 45.000 0.00 0.00 41.52 4.84
3523 3608 6.027749 AGAATGTTGTTCAGAAAACACGAAC 58.972 36.000 11.00 0.00 39.00 3.95
3532 3617 8.134202 TCCTAGATGTAGAATGTTGTTCAGAA 57.866 34.615 0.00 0.00 0.00 3.02
3549 3634 8.834465 CACCATTGTTCTCTTTAATCCTAGATG 58.166 37.037 0.00 0.00 0.00 2.90
3560 3645 3.593442 TCACCCACCATTGTTCTCTTT 57.407 42.857 0.00 0.00 0.00 2.52
3562 3647 2.915604 AGATCACCCACCATTGTTCTCT 59.084 45.455 0.00 0.00 0.00 3.10
3565 3650 3.071874 TCAGATCACCCACCATTGTTC 57.928 47.619 0.00 0.00 0.00 3.18
3818 3909 5.911752 TGAAAAGCAAAAGCTAACAATCCA 58.088 33.333 0.00 0.00 0.00 3.41
3825 3916 4.990426 GGCAGAATGAAAAGCAAAAGCTAA 59.010 37.500 0.00 0.00 39.69 3.09
3828 3919 2.156310 CGGCAGAATGAAAAGCAAAAGC 59.844 45.455 0.00 0.00 39.69 3.51
3832 3923 2.819019 TGATCGGCAGAATGAAAAGCAA 59.181 40.909 0.00 0.00 39.69 3.91
3860 3951 1.610038 CAATCTCCAACAGCTTGTGCA 59.390 47.619 0.00 0.00 42.74 4.57
3923 4014 2.223876 GCATGTTGGGTTGCATGGATAG 60.224 50.000 6.65 0.00 41.82 2.08
4018 4118 7.004555 TCTCTTATTGTGCCAACTTTCTCTA 57.995 36.000 0.00 0.00 0.00 2.43
4030 4130 6.454795 TCCAAAACCAAATCTCTTATTGTGC 58.545 36.000 0.00 0.00 0.00 4.57
4063 4163 9.897040 AAACCCTAATGAATATTTCCATATGGT 57.103 29.630 21.28 5.10 36.34 3.55
4069 4169 9.535170 TTGTACAAACCCTAATGAATATTTCCA 57.465 29.630 5.64 0.00 0.00 3.53
4074 4174 9.297037 GGCTATTGTACAAACCCTAATGAATAT 57.703 33.333 13.23 0.00 0.00 1.28
4075 4175 7.442969 CGGCTATTGTACAAACCCTAATGAATA 59.557 37.037 13.23 0.00 0.00 1.75
4076 4176 6.262273 CGGCTATTGTACAAACCCTAATGAAT 59.738 38.462 13.23 0.00 0.00 2.57
4077 4177 5.587043 CGGCTATTGTACAAACCCTAATGAA 59.413 40.000 13.23 0.00 0.00 2.57
4078 4178 5.104859 TCGGCTATTGTACAAACCCTAATGA 60.105 40.000 13.23 4.63 0.00 2.57
4079 4179 5.120399 TCGGCTATTGTACAAACCCTAATG 58.880 41.667 13.23 2.48 0.00 1.90
4080 4180 5.129815 TCTCGGCTATTGTACAAACCCTAAT 59.870 40.000 13.23 0.00 0.00 1.73
4081 4181 4.467082 TCTCGGCTATTGTACAAACCCTAA 59.533 41.667 13.23 3.99 0.00 2.69
4082 4182 4.025360 TCTCGGCTATTGTACAAACCCTA 58.975 43.478 13.23 4.76 0.00 3.53
4083 4183 2.835764 TCTCGGCTATTGTACAAACCCT 59.164 45.455 13.23 0.00 0.00 4.34
4084 4184 3.195661 CTCTCGGCTATTGTACAAACCC 58.804 50.000 13.23 11.71 0.00 4.11
4085 4185 3.858247 ACTCTCGGCTATTGTACAAACC 58.142 45.455 13.23 13.17 0.00 3.27
4086 4186 4.329256 GGAACTCTCGGCTATTGTACAAAC 59.671 45.833 13.23 5.29 0.00 2.93
4087 4187 4.020928 TGGAACTCTCGGCTATTGTACAAA 60.021 41.667 13.23 1.56 0.00 2.83
4088 4188 3.512329 TGGAACTCTCGGCTATTGTACAA 59.488 43.478 11.41 11.41 0.00 2.41
4089 4189 3.093814 TGGAACTCTCGGCTATTGTACA 58.906 45.455 0.00 0.00 0.00 2.90
4090 4190 3.707793 CTGGAACTCTCGGCTATTGTAC 58.292 50.000 0.00 0.00 0.00 2.90
4091 4191 2.100916 GCTGGAACTCTCGGCTATTGTA 59.899 50.000 0.00 0.00 0.00 2.41
4092 4192 1.134670 GCTGGAACTCTCGGCTATTGT 60.135 52.381 0.00 0.00 0.00 2.71
4093 4193 1.576356 GCTGGAACTCTCGGCTATTG 58.424 55.000 0.00 0.00 0.00 1.90
4094 4194 0.103208 CGCTGGAACTCTCGGCTATT 59.897 55.000 0.00 0.00 0.00 1.73
4095 4195 1.038130 ACGCTGGAACTCTCGGCTAT 61.038 55.000 0.00 0.00 0.00 2.97
4096 4196 0.393402 TACGCTGGAACTCTCGGCTA 60.393 55.000 0.00 0.00 0.00 3.93
4097 4197 1.248785 TTACGCTGGAACTCTCGGCT 61.249 55.000 0.00 0.00 0.00 5.52
4098 4198 0.179108 ATTACGCTGGAACTCTCGGC 60.179 55.000 0.00 0.00 0.00 5.54
4099 4199 2.295253 AATTACGCTGGAACTCTCGG 57.705 50.000 0.00 0.00 0.00 4.63
4100 4200 3.304559 CAGAAATTACGCTGGAACTCTCG 59.695 47.826 0.00 0.00 0.00 4.04
4101 4201 4.246458 ACAGAAATTACGCTGGAACTCTC 58.754 43.478 0.00 0.00 36.47 3.20
4102 4202 4.273148 ACAGAAATTACGCTGGAACTCT 57.727 40.909 0.00 0.00 36.47 3.24
4103 4203 5.147162 CAAACAGAAATTACGCTGGAACTC 58.853 41.667 0.00 0.00 36.47 3.01
4104 4204 4.578928 ACAAACAGAAATTACGCTGGAACT 59.421 37.500 0.00 0.00 36.47 3.01
4105 4205 4.855531 ACAAACAGAAATTACGCTGGAAC 58.144 39.130 0.00 0.00 36.47 3.62
4106 4206 5.277825 CAACAAACAGAAATTACGCTGGAA 58.722 37.500 0.00 0.00 36.47 3.53
4107 4207 4.791411 GCAACAAACAGAAATTACGCTGGA 60.791 41.667 0.00 0.00 36.47 3.86
4108 4208 3.425193 GCAACAAACAGAAATTACGCTGG 59.575 43.478 0.00 0.00 36.47 4.85
4109 4209 3.425193 GGCAACAAACAGAAATTACGCTG 59.575 43.478 0.00 0.00 38.10 5.18
4110 4210 3.638484 GGCAACAAACAGAAATTACGCT 58.362 40.909 0.00 0.00 0.00 5.07
4168 4271 3.380004 AGTGCAATCAAAACCTCGTCAAA 59.620 39.130 0.00 0.00 0.00 2.69
4172 4275 4.072131 ACATAGTGCAATCAAAACCTCGT 58.928 39.130 0.00 0.00 0.00 4.18
4200 4303 0.036732 TGCAATCTCTCCCCACACAC 59.963 55.000 0.00 0.00 0.00 3.82
4202 4305 0.326264 AGTGCAATCTCTCCCCACAC 59.674 55.000 0.00 0.00 0.00 3.82
4205 4308 8.860517 ATAATATATAGTGCAATCTCTCCCCA 57.139 34.615 0.00 0.00 0.00 4.96
4234 4337 5.755861 GCAACTTAGGTTTGCAAAACCATAA 59.244 36.000 23.36 14.79 42.69 1.90
4243 4346 6.588719 AATATGAAGCAACTTAGGTTTGCA 57.411 33.333 9.55 0.00 34.42 4.08
4289 4392 6.402550 GCATGGATATATCAAACGGCTAAGTG 60.403 42.308 14.60 0.00 0.00 3.16
4290 4393 5.643777 GCATGGATATATCAAACGGCTAAGT 59.356 40.000 14.60 0.00 0.00 2.24
4315 4418 7.723616 TCTTTAACCCTCATTCAATTTCACTCA 59.276 33.333 0.00 0.00 0.00 3.41
4335 4438 5.646360 GCCACCTTTAGTAGCATGTCTTTAA 59.354 40.000 0.00 0.00 32.74 1.52
4362 4465 7.337436 TCATGTGTATCTCATTCATTGCTTCAA 59.663 33.333 0.00 0.00 0.00 2.69
4418 4523 6.537301 CGTACAACATGTATTCACCAAGGTAT 59.463 38.462 0.00 0.00 35.05 2.73
4438 4543 2.566913 ACATTTGACTTGCCACGTACA 58.433 42.857 0.00 0.00 0.00 2.90
4440 4545 2.292016 CCAACATTTGACTTGCCACGTA 59.708 45.455 0.00 0.00 0.00 3.57
4461 4567 6.479001 TCTTTATGCTTTAGAATCTACCGTGC 59.521 38.462 0.00 0.00 0.00 5.34
4472 4578 5.105106 TCGATGGTGGTCTTTATGCTTTAGA 60.105 40.000 0.00 0.00 0.00 2.10
4473 4579 5.116180 TCGATGGTGGTCTTTATGCTTTAG 58.884 41.667 0.00 0.00 0.00 1.85
4475 4581 3.950397 TCGATGGTGGTCTTTATGCTTT 58.050 40.909 0.00 0.00 0.00 3.51
4497 4603 1.379776 ATCATGGATGGGCTGGCTAT 58.620 50.000 0.00 0.00 0.00 2.97
4549 4655 4.826733 TCAATCAGGTTGTAGCATGTGTTT 59.173 37.500 0.00 0.00 38.95 2.83
4584 4690 5.745227 ACCTGTCATTAATGGTTCTAGTGG 58.255 41.667 15.36 8.86 0.00 4.00
4598 4704 7.633789 ACTTTCATACCAGAATACCTGTCATT 58.366 34.615 0.00 0.00 41.33 2.57
4628 4734 7.854534 TCGATGTTGCTATATGACTGATTTTG 58.145 34.615 0.00 0.00 0.00 2.44
4633 4739 6.331369 TCATCGATGTTGCTATATGACTGA 57.669 37.500 24.09 0.00 0.00 3.41
4636 4742 7.543520 TCATCTTCATCGATGTTGCTATATGAC 59.456 37.037 24.09 0.00 41.17 3.06
4659 4765 4.222810 GCTTGGAAAACCCCATAAGTTCAT 59.777 41.667 0.00 0.00 35.87 2.57
4684 4790 8.507249 ACATAAGCTTTATCAACTCTTGTGTTC 58.493 33.333 3.20 0.00 36.26 3.18
4732 4838 4.628074 TGTATTTATTCGGCTAGGCTGTC 58.372 43.478 15.11 0.00 36.18 3.51
4734 4840 5.295787 TGTTTGTATTTATTCGGCTAGGCTG 59.704 40.000 15.11 8.17 36.06 4.85
4767 4874 8.002459 TGTAGAGATAGATGTATGTGTTGGGTA 58.998 37.037 0.00 0.00 0.00 3.69
4781 4888 7.755666 AGAGCCTAGAGATGTAGAGATAGAT 57.244 40.000 0.00 0.00 0.00 1.98
4789 4896 4.724399 TCCTCAAGAGCCTAGAGATGTAG 58.276 47.826 0.00 0.00 0.00 2.74
4835 4942 3.319122 TCCATGGACGTGATCACTCTATG 59.681 47.826 26.52 26.52 32.69 2.23
4845 4952 4.344968 ACATCAATATCTCCATGGACGTGA 59.655 41.667 11.44 7.57 0.00 4.35
4855 4962 9.702253 TTATCTCCTAGGTACATCAATATCTCC 57.298 37.037 9.08 0.00 0.00 3.71
4860 4967 8.901841 TCTCCTTATCTCCTAGGTACATCAATA 58.098 37.037 9.08 0.00 33.15 1.90
4863 4970 6.781857 TCTCCTTATCTCCTAGGTACATCA 57.218 41.667 9.08 0.00 33.15 3.07
4917 5024 1.918262 AGAATGATCAGGCCAAGGTCA 59.082 47.619 12.84 12.84 0.00 4.02


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

AutoCloner maintained by Alex Coulton.