Multiple sequence alignment - TraesCS2A01G278400

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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 TraesCS2A01G278400 chr2A 100.000 5538 0 0 1 5538 461387278 461392815 0.000000e+00 10227.0
1 TraesCS2A01G278400 chr2D 93.742 3292 147 28 11 3288 347789900 347793146 0.000000e+00 4883.0
2 TraesCS2A01G278400 chr2D 93.016 1532 74 22 3368 4898 347793143 347794642 0.000000e+00 2206.0
3 TraesCS2A01G278400 chr2D 80.925 1232 176 25 1938 3118 347807276 347808499 0.000000e+00 918.0
4 TraesCS2A01G278400 chr2D 93.204 309 19 2 29 336 510200963 510200656 2.350000e-123 453.0
5 TraesCS2A01G278400 chr2D 96.512 86 2 1 4919 5003 347794627 347794712 2.080000e-29 141.0
6 TraesCS2A01G278400 chr2D 94.444 36 2 0 3345 3380 610495915 610495880 7.750000e-04 56.5
7 TraesCS2A01G278400 chr2B 93.522 2470 90 30 827 3261 412988966 412991400 0.000000e+00 3611.0
8 TraesCS2A01G278400 chr2B 95.470 1170 43 6 3368 4536 412991451 412992611 0.000000e+00 1858.0
9 TraesCS2A01G278400 chr2B 93.531 371 20 2 4528 4898 412992636 412993002 2.920000e-152 549.0
10 TraesCS2A01G278400 chr2B 94.444 36 2 0 3345 3380 745861415 745861380 7.750000e-04 56.5
11 TraesCS2A01G278400 chr5D 81.151 1321 187 36 1960 3240 449940975 449939677 0.000000e+00 1003.0
12 TraesCS2A01G278400 chr5D 79.590 1318 213 39 1960 3239 449936207 449934908 0.000000e+00 893.0
13 TraesCS2A01G278400 chr5D 80.317 1199 182 35 1960 3118 449983278 449982094 0.000000e+00 857.0
14 TraesCS2A01G278400 chr5D 94.079 304 16 2 29 331 123508712 123508410 1.410000e-125 460.0
15 TraesCS2A01G278400 chr5D 91.975 324 22 2 12 331 292349040 292348717 8.460000e-123 451.0
16 TraesCS2A01G278400 chr5D 91.950 323 20 5 11 331 281005471 281005789 1.090000e-121 448.0
17 TraesCS2A01G278400 chr5D 81.992 261 44 3 3409 3667 449934837 449934578 9.340000e-53 219.0
18 TraesCS2A01G278400 chr5D 81.923 260 45 2 3409 3667 449981918 449981660 9.340000e-53 219.0
19 TraesCS2A01G278400 chr5D 76.061 330 58 10 3762 4076 449939148 449938825 9.610000e-33 152.0
20 TraesCS2A01G278400 chr5D 76.036 338 53 17 3760 4077 449981461 449981132 3.460000e-32 150.0
21 TraesCS2A01G278400 chr5A 80.789 1343 194 41 1938 3239 569224765 569223446 0.000000e+00 992.0
22 TraesCS2A01G278400 chr5A 97.584 538 11 2 5002 5538 680753167 680753703 0.000000e+00 920.0
23 TraesCS2A01G278400 chr5A 79.803 1322 207 40 1957 3240 569151632 569152931 0.000000e+00 907.0
24 TraesCS2A01G278400 chr5A 80.234 1280 193 44 1987 3239 569183932 569182686 0.000000e+00 907.0
25 TraesCS2A01G278400 chr5A 94.424 538 27 3 5002 5538 701985673 701985138 0.000000e+00 824.0
26 TraesCS2A01G278400 chr5A 92.924 537 34 4 5004 5538 647551125 647551659 0.000000e+00 778.0
27 TraesCS2A01G278400 chr5A 82.625 259 45 0 3409 3667 569182615 569182357 4.320000e-56 230.0
28 TraesCS2A01G278400 chr5A 81.679 262 42 5 3409 3667 569152986 569153244 4.350000e-51 213.0
29 TraesCS2A01G278400 chr5A 81.298 262 43 5 3409 3667 569218478 569218220 2.020000e-49 207.0
30 TraesCS2A01G278400 chr5A 80.769 260 48 2 3409 3667 569223375 569223117 9.410000e-48 202.0
31 TraesCS2A01G278400 chr1A 97.412 541 12 2 4999 5538 302911824 302912363 0.000000e+00 920.0
32 TraesCS2A01G278400 chr7B 83.236 1032 140 25 2089 3092 733359501 733358475 0.000000e+00 917.0
33 TraesCS2A01G278400 chr7A 81.255 1195 163 41 2089 3228 726859482 726858294 0.000000e+00 909.0
34 TraesCS2A01G278400 chr7A 91.900 321 24 2 11 330 463344305 463344624 1.090000e-121 448.0
35 TraesCS2A01G278400 chr7A 80.672 476 71 11 3421 3886 726858223 726857759 3.170000e-92 350.0
36 TraesCS2A01G278400 chr3A 97.201 536 14 1 5004 5538 27908720 27908185 0.000000e+00 905.0
37 TraesCS2A01G278400 chr3A 97.201 536 14 1 5004 5538 715213483 715214018 0.000000e+00 905.0
38 TraesCS2A01G278400 chr3A 94.776 536 26 2 5004 5538 37632900 37633434 0.000000e+00 833.0
39 TraesCS2A01G278400 chr7D 80.936 1196 169 40 2086 3228 630713291 630714480 0.000000e+00 891.0
40 TraesCS2A01G278400 chr5B 79.456 1324 213 40 1960 3239 549949244 549947936 0.000000e+00 883.0
41 TraesCS2A01G278400 chr5B 81.978 1021 142 26 1960 2944 549954194 549953180 0.000000e+00 828.0
42 TraesCS2A01G278400 chr5B 80.682 264 51 0 3409 3672 549712309 549712572 7.270000e-49 206.0
43 TraesCS2A01G278400 chr6A 95.238 546 15 3 5004 5538 428285585 428286130 0.000000e+00 854.0
44 TraesCS2A01G278400 chr4A 93.738 543 31 3 4998 5538 521945171 521945712 0.000000e+00 811.0
45 TraesCS2A01G278400 chr1D 91.950 323 23 2 11 333 270312420 270312101 3.040000e-122 449.0
46 TraesCS2A01G278400 chr6D 91.331 323 24 3 11 330 101573004 101573325 6.590000e-119 438.0
47 TraesCS2A01G278400 chr4D 91.131 327 23 5 5 330 11309998 11309677 6.590000e-119 438.0
48 TraesCS2A01G278400 chr6B 94.231 52 0 3 3282 3332 259074097 259074146 5.950000e-10 76.8
49 TraesCS2A01G278400 chr6B 97.368 38 0 1 824 861 577919839 577919875 4.630000e-06 63.9
50 TraesCS2A01G278400 chr4B 95.349 43 2 0 3337 3379 522687252 522687294 9.950000e-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 TraesCS2A01G278400 chr2A 461387278 461392815 5537 False 10227.000000 10227 100.000000 1 5538 1 chr2A.!!$F1 5537
1 TraesCS2A01G278400 chr2D 347789900 347794712 4812 False 2410.000000 4883 94.423333 11 5003 3 chr2D.!!$F2 4992
2 TraesCS2A01G278400 chr2D 347807276 347808499 1223 False 918.000000 918 80.925000 1938 3118 1 chr2D.!!$F1 1180
3 TraesCS2A01G278400 chr2B 412988966 412993002 4036 False 2006.000000 3611 94.174333 827 4898 3 chr2B.!!$F1 4071
4 TraesCS2A01G278400 chr5D 449934578 449940975 6397 True 566.750000 1003 79.698500 1960 4076 4 chr5D.!!$R3 2116
5 TraesCS2A01G278400 chr5D 449981132 449983278 2146 True 408.666667 857 79.425333 1960 4077 3 chr5D.!!$R4 2117
6 TraesCS2A01G278400 chr5A 680753167 680753703 536 False 920.000000 920 97.584000 5002 5538 1 chr5A.!!$F2 536
7 TraesCS2A01G278400 chr5A 701985138 701985673 535 True 824.000000 824 94.424000 5002 5538 1 chr5A.!!$R2 536
8 TraesCS2A01G278400 chr5A 647551125 647551659 534 False 778.000000 778 92.924000 5004 5538 1 chr5A.!!$F1 534
9 TraesCS2A01G278400 chr5A 569223117 569224765 1648 True 597.000000 992 80.779000 1938 3667 2 chr5A.!!$R4 1729
10 TraesCS2A01G278400 chr5A 569182357 569183932 1575 True 568.500000 907 81.429500 1987 3667 2 chr5A.!!$R3 1680
11 TraesCS2A01G278400 chr5A 569151632 569153244 1612 False 560.000000 907 80.741000 1957 3667 2 chr5A.!!$F3 1710
12 TraesCS2A01G278400 chr1A 302911824 302912363 539 False 920.000000 920 97.412000 4999 5538 1 chr1A.!!$F1 539
13 TraesCS2A01G278400 chr7B 733358475 733359501 1026 True 917.000000 917 83.236000 2089 3092 1 chr7B.!!$R1 1003
14 TraesCS2A01G278400 chr7A 726857759 726859482 1723 True 629.500000 909 80.963500 2089 3886 2 chr7A.!!$R1 1797
15 TraesCS2A01G278400 chr3A 27908185 27908720 535 True 905.000000 905 97.201000 5004 5538 1 chr3A.!!$R1 534
16 TraesCS2A01G278400 chr3A 715213483 715214018 535 False 905.000000 905 97.201000 5004 5538 1 chr3A.!!$F2 534
17 TraesCS2A01G278400 chr3A 37632900 37633434 534 False 833.000000 833 94.776000 5004 5538 1 chr3A.!!$F1 534
18 TraesCS2A01G278400 chr7D 630713291 630714480 1189 False 891.000000 891 80.936000 2086 3228 1 chr7D.!!$F1 1142
19 TraesCS2A01G278400 chr5B 549947936 549954194 6258 True 855.500000 883 80.717000 1960 3239 2 chr5B.!!$R1 1279
20 TraesCS2A01G278400 chr6A 428285585 428286130 545 False 854.000000 854 95.238000 5004 5538 1 chr6A.!!$F1 534
21 TraesCS2A01G278400 chr4A 521945171 521945712 541 False 811.000000 811 93.738000 4998 5538 1 chr4A.!!$F1 540

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
402 403 0.456628 GGCGACAAGACTCCTCCTAC 59.543 60.0 0.00 0.00 0.00 3.18 F
502 503 0.661552 CCGAACGGCGAAGAGAGATA 59.338 55.0 16.62 0.00 44.57 1.98 F
1716 1745 0.394762 TCCCATCCACTGCAGATTGC 60.395 55.0 23.35 0.00 45.29 3.56 F
3345 3642 0.677842 AGTAGTGACCGAAAACGGCT 59.322 50.0 8.59 1.15 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1360 0.039618 TTTCCAAGATCCAGGGCCAC 59.960 55.0 6.18 0.0 0.00 5.01 R
2375 2457 0.816825 ACAGTGTGTCCAAGCTGCTG 60.817 55.0 1.35 0.0 32.65 4.41 R
3539 3836 0.102844 CCCCATAAATTGCGCACCAG 59.897 55.0 11.12 0.0 0.00 4.00 R
4805 5311 0.041312 CCAAGTTTTGCCGACTCACG 60.041 55.0 0.00 0.0 42.18 4.35 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
81 82 0.542333 GCCCCCTCTGGTAGTTTCTC 59.458 60.000 0.00 0.00 0.00 2.87
82 83 1.902141 GCCCCCTCTGGTAGTTTCTCT 60.902 57.143 0.00 0.00 0.00 3.10
89 90 2.303022 TCTGGTAGTTTCTCTGCCCAAG 59.697 50.000 0.00 0.00 46.27 3.61
141 142 5.285651 CGTAAATTTGCAGGACTTTTGGAA 58.714 37.500 7.07 0.00 0.00 3.53
155 156 6.029346 ACTTTTGGAATTGTGCAGAATAGG 57.971 37.500 9.82 0.00 0.00 2.57
181 182 2.162681 CAGATTTGCTCCTTTCCGGTT 58.837 47.619 0.00 0.00 0.00 4.44
182 183 2.558359 CAGATTTGCTCCTTTCCGGTTT 59.442 45.455 0.00 0.00 0.00 3.27
299 300 8.818860 ACTGCCCATAATGCAATAAATATCAAT 58.181 29.630 0.00 0.00 38.46 2.57
339 340 1.192428 GGACGTATCAGGTCCCTTGT 58.808 55.000 6.76 0.00 44.94 3.16
349 350 3.164977 TCCCTTGTCGTGCACCCA 61.165 61.111 12.15 5.44 0.00 4.51
352 353 1.302431 CCTTGTCGTGCACCCATCA 60.302 57.895 12.15 2.58 0.00 3.07
387 388 3.691342 CGTGGGAAGTGAGGGCGA 61.691 66.667 0.00 0.00 0.00 5.54
401 402 0.683504 GGGCGACAAGACTCCTCCTA 60.684 60.000 0.00 0.00 0.00 2.94
402 403 0.456628 GGCGACAAGACTCCTCCTAC 59.543 60.000 0.00 0.00 0.00 3.18
423 424 1.617947 GGCACGTCCATCCTCTCCTT 61.618 60.000 0.00 0.00 34.01 3.36
430 431 3.541713 ATCCTCTCCTTCGGCGCC 61.542 66.667 19.07 19.07 0.00 6.53
470 471 2.432628 GTGTCGGTGAAGGCGGAG 60.433 66.667 0.00 0.00 0.00 4.63
501 502 1.030488 TCCGAACGGCGAAGAGAGAT 61.030 55.000 16.62 0.00 44.57 2.75
502 503 0.661552 CCGAACGGCGAAGAGAGATA 59.338 55.000 16.62 0.00 44.57 1.98
505 506 1.001158 GAACGGCGAAGAGAGATAGGG 60.001 57.143 16.62 0.00 0.00 3.53
506 507 0.824182 ACGGCGAAGAGAGATAGGGG 60.824 60.000 16.62 0.00 0.00 4.79
507 508 1.528292 CGGCGAAGAGAGATAGGGGG 61.528 65.000 0.00 0.00 0.00 5.40
508 509 1.668867 GCGAAGAGAGATAGGGGGC 59.331 63.158 0.00 0.00 0.00 5.80
509 510 1.115930 GCGAAGAGAGATAGGGGGCA 61.116 60.000 0.00 0.00 0.00 5.36
510 511 1.414158 CGAAGAGAGATAGGGGGCAA 58.586 55.000 0.00 0.00 0.00 4.52
599 600 2.277404 GGCCTCTCGGAGACCTCT 59.723 66.667 2.97 0.00 29.39 3.69
712 713 0.818040 GCGCCGGTCCCAAATATCTT 60.818 55.000 1.90 0.00 0.00 2.40
713 714 1.675552 CGCCGGTCCCAAATATCTTT 58.324 50.000 1.90 0.00 0.00 2.52
763 764 0.813184 CAAGCCTTAGTCGGTACCGA 59.187 55.000 32.61 32.61 46.87 4.69
790 791 1.360551 CTCGCTCCGACGGATCATT 59.639 57.895 18.71 0.00 0.00 2.57
791 792 0.661780 CTCGCTCCGACGGATCATTC 60.662 60.000 18.71 3.82 0.00 2.67
792 793 2.011349 CGCTCCGACGGATCATTCG 61.011 63.158 18.71 11.88 34.93 3.34
799 800 1.663445 CGACGGATCATTCGGCTCTAC 60.663 57.143 7.20 0.00 32.71 2.59
803 804 2.526432 GGATCATTCGGCTCTACCCTA 58.474 52.381 0.00 0.00 33.26 3.53
806 807 4.710375 GGATCATTCGGCTCTACCCTATTA 59.290 45.833 0.00 0.00 33.26 0.98
807 808 5.364157 GGATCATTCGGCTCTACCCTATTAT 59.636 44.000 0.00 0.00 33.26 1.28
879 883 1.376812 GCGGATCGGGTTCAACCTT 60.377 57.895 6.51 0.00 38.64 3.50
885 889 3.572682 GGATCGGGTTCAACCTTCTTTTT 59.427 43.478 6.51 0.00 38.64 1.94
890 894 6.566141 TCGGGTTCAACCTTCTTTTTAAAAG 58.434 36.000 6.51 10.89 38.64 2.27
946 950 1.017387 CATTTTCTCTGTAGCCGCCC 58.983 55.000 0.00 0.00 0.00 6.13
1051 1055 2.182030 CGCGGTGTTCTCCCTCTC 59.818 66.667 0.00 0.00 0.00 3.20
1091 1095 4.087892 CTACCTGCCTGCGGTGCT 62.088 66.667 13.42 0.00 35.98 4.40
1106 1110 2.618045 CGGTGCTGTTCTTATCCCCTTT 60.618 50.000 0.00 0.00 0.00 3.11
1109 1113 3.942115 GTGCTGTTCTTATCCCCTTTCTC 59.058 47.826 0.00 0.00 0.00 2.87
1120 1124 1.940613 CCCCTTTCTCGCCTTTTATCG 59.059 52.381 0.00 0.00 0.00 2.92
1164 1168 2.160417 CGCCACTTCTCTGGAATTTGAC 59.840 50.000 0.00 0.00 32.30 3.18
1252 1256 1.725973 GAGGTTCTGTTTTGCGCGC 60.726 57.895 27.26 27.26 0.00 6.86
1276 1280 5.356470 CAGAGGAGGGATGTCTTGAATTTTC 59.644 44.000 0.00 0.00 0.00 2.29
1277 1281 5.252630 AGAGGAGGGATGTCTTGAATTTTCT 59.747 40.000 0.00 0.00 0.00 2.52
1278 1282 5.896963 AGGAGGGATGTCTTGAATTTTCTT 58.103 37.500 0.00 0.00 0.00 2.52
1335 1341 1.207089 TGCGGTTCCTAATCACAGGAG 59.793 52.381 0.00 0.00 45.45 3.69
1354 1360 3.102276 GAGTCGTCAGTTGATTCGCTAG 58.898 50.000 0.00 0.00 0.00 3.42
1382 1388 3.099141 TGGATCTTGGAAAATGCCCTTC 58.901 45.455 0.00 0.00 0.00 3.46
1384 1390 1.544724 TCTTGGAAAATGCCCTTCCG 58.455 50.000 4.62 0.00 44.61 4.30
1395 1401 6.628919 AAATGCCCTTCCGTTTATATGTAC 57.371 37.500 0.00 0.00 0.00 2.90
1396 1402 5.562298 ATGCCCTTCCGTTTATATGTACT 57.438 39.130 0.00 0.00 0.00 2.73
1397 1403 4.952460 TGCCCTTCCGTTTATATGTACTC 58.048 43.478 0.00 0.00 0.00 2.59
1398 1404 4.202284 TGCCCTTCCGTTTATATGTACTCC 60.202 45.833 0.00 0.00 0.00 3.85
1399 1405 4.801914 GCCCTTCCGTTTATATGTACTCCC 60.802 50.000 0.00 0.00 0.00 4.30
1400 1406 4.591924 CCCTTCCGTTTATATGTACTCCCT 59.408 45.833 0.00 0.00 0.00 4.20
1401 1407 5.279356 CCCTTCCGTTTATATGTACTCCCTC 60.279 48.000 0.00 0.00 0.00 4.30
1402 1408 5.279356 CCTTCCGTTTATATGTACTCCCTCC 60.279 48.000 0.00 0.00 0.00 4.30
1403 1409 3.822735 TCCGTTTATATGTACTCCCTCCG 59.177 47.826 0.00 0.00 0.00 4.63
1404 1410 3.571401 CCGTTTATATGTACTCCCTCCGT 59.429 47.826 0.00 0.00 0.00 4.69
1405 1411 4.038402 CCGTTTATATGTACTCCCTCCGTT 59.962 45.833 0.00 0.00 0.00 4.44
1406 1412 5.452356 CCGTTTATATGTACTCCCTCCGTTT 60.452 44.000 0.00 0.00 0.00 3.60
1407 1413 5.689068 CGTTTATATGTACTCCCTCCGTTTC 59.311 44.000 0.00 0.00 0.00 2.78
1408 1414 6.576185 GTTTATATGTACTCCCTCCGTTTCA 58.424 40.000 0.00 0.00 0.00 2.69
1409 1415 6.795144 TTATATGTACTCCCTCCGTTTCAA 57.205 37.500 0.00 0.00 0.00 2.69
1410 1416 5.687166 ATATGTACTCCCTCCGTTTCAAA 57.313 39.130 0.00 0.00 0.00 2.69
1411 1417 4.569719 ATGTACTCCCTCCGTTTCAAAT 57.430 40.909 0.00 0.00 0.00 2.32
1412 1418 4.360951 TGTACTCCCTCCGTTTCAAATT 57.639 40.909 0.00 0.00 0.00 1.82
1413 1419 5.486735 TGTACTCCCTCCGTTTCAAATTA 57.513 39.130 0.00 0.00 0.00 1.40
1414 1420 5.240121 TGTACTCCCTCCGTTTCAAATTAC 58.760 41.667 0.00 0.00 0.00 1.89
1415 1421 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
1416 1422 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
1417 1423 4.286291 ACTCCCTCCGTTTCAAATTACTCT 59.714 41.667 0.00 0.00 0.00 3.24
1457 1463 3.006940 GTGGTCAGACACAACAGAACAA 58.993 45.455 2.17 0.00 40.99 2.83
1514 1525 6.263617 AGAAACGATTGGCCTTAAACTGTTTA 59.736 34.615 8.84 8.84 0.00 2.01
1521 1532 9.869757 GATTGGCCTTAAACTGTTTACATTATT 57.130 29.630 12.27 0.00 0.00 1.40
1522 1533 9.651913 ATTGGCCTTAAACTGTTTACATTATTG 57.348 29.630 12.27 0.00 0.00 1.90
1523 1534 8.410673 TGGCCTTAAACTGTTTACATTATTGA 57.589 30.769 12.27 0.00 0.00 2.57
1590 1601 8.557304 AGGGAATCCATGTTTGATTTCATTAT 57.443 30.769 0.09 0.00 32.74 1.28
1672 1701 5.361857 AGGGATAGAAATGGCAATCTTGTTG 59.638 40.000 10.87 0.00 0.00 3.33
1695 1724 6.112734 TGTGGTCGAGCATGTATTCTTTATT 58.887 36.000 21.66 0.00 0.00 1.40
1700 1729 7.064728 GGTCGAGCATGTATTCTTTATTATCCC 59.935 40.741 10.30 0.00 0.00 3.85
1703 1732 8.607459 CGAGCATGTATTCTTTATTATCCCATC 58.393 37.037 0.00 0.00 0.00 3.51
1716 1745 0.394762 TCCCATCCACTGCAGATTGC 60.395 55.000 23.35 0.00 45.29 3.56
1749 1778 4.487714 TCTCTCAGTTGTGTTGAACCTT 57.512 40.909 0.00 0.00 0.00 3.50
1779 1808 1.415659 CTGCCTCCTTAGTCTCCCATG 59.584 57.143 0.00 0.00 0.00 3.66
1991 2021 5.163519 CCTTCATTTCACTTGTGAACACCTT 60.164 40.000 14.80 0.00 0.00 3.50
2375 2457 1.754234 ATTTGAGGCCGGCATGTCC 60.754 57.895 30.85 10.45 0.00 4.02
2944 3155 8.718656 AGTTTATCCTTCTCTAATTGCAGGTAT 58.281 33.333 0.00 0.00 0.00 2.73
3080 3314 2.338984 GAGGCGTCGGTGTTGTCT 59.661 61.111 0.00 0.00 0.00 3.41
3153 3417 4.616953 GCCTTCTCTGATAGTAACAGCTC 58.383 47.826 2.62 0.00 35.61 4.09
3293 3590 7.354751 AGAGTACTTCAATGATACTCCTTCC 57.645 40.000 16.24 0.00 43.90 3.46
3294 3591 6.039941 AGAGTACTTCAATGATACTCCTTCCG 59.960 42.308 16.24 0.00 43.90 4.30
3295 3592 5.657302 AGTACTTCAATGATACTCCTTCCGT 59.343 40.000 0.00 0.00 0.00 4.69
3296 3593 6.832384 AGTACTTCAATGATACTCCTTCCGTA 59.168 38.462 0.00 0.00 0.00 4.02
3297 3594 6.540438 ACTTCAATGATACTCCTTCCGTAA 57.460 37.500 0.00 0.00 0.00 3.18
3298 3595 6.942976 ACTTCAATGATACTCCTTCCGTAAA 58.057 36.000 0.00 0.00 0.00 2.01
3299 3596 7.042335 ACTTCAATGATACTCCTTCCGTAAAG 58.958 38.462 0.00 0.00 34.52 1.85
3300 3597 6.785337 TCAATGATACTCCTTCCGTAAAGA 57.215 37.500 0.00 0.00 37.12 2.52
3301 3598 7.177832 TCAATGATACTCCTTCCGTAAAGAA 57.822 36.000 0.00 0.00 37.12 2.52
3302 3599 7.617225 TCAATGATACTCCTTCCGTAAAGAAA 58.383 34.615 0.00 0.00 37.12 2.52
3303 3600 8.265055 TCAATGATACTCCTTCCGTAAAGAAAT 58.735 33.333 0.00 0.00 37.12 2.17
3304 3601 9.542462 CAATGATACTCCTTCCGTAAAGAAATA 57.458 33.333 0.00 0.00 37.12 1.40
3311 3608 8.755977 ACTCCTTCCGTAAAGAAATATAAGACA 58.244 33.333 0.00 0.00 37.12 3.41
3312 3609 9.765795 CTCCTTCCGTAAAGAAATATAAGACAT 57.234 33.333 0.00 0.00 37.12 3.06
3330 3627 9.814899 ATAAGACATTTGAGATCACTGAAGTAG 57.185 33.333 0.00 0.00 0.00 2.57
3331 3628 7.238486 AGACATTTGAGATCACTGAAGTAGT 57.762 36.000 0.00 0.00 41.36 2.73
3342 3639 3.378339 ACTGAAGTAGTGACCGAAAACG 58.622 45.455 0.00 0.00 38.49 3.60
3343 3640 2.729882 CTGAAGTAGTGACCGAAAACGG 59.270 50.000 7.12 7.12 0.00 4.44
3344 3641 1.458445 GAAGTAGTGACCGAAAACGGC 59.542 52.381 8.59 2.88 0.00 5.68
3345 3642 0.677842 AGTAGTGACCGAAAACGGCT 59.322 50.000 8.59 1.15 0.00 5.52
3346 3643 1.069668 AGTAGTGACCGAAAACGGCTT 59.930 47.619 8.59 0.00 0.00 4.35
3347 3644 2.297033 AGTAGTGACCGAAAACGGCTTA 59.703 45.455 8.59 0.00 0.00 3.09
3348 3645 1.505425 AGTGACCGAAAACGGCTTAC 58.495 50.000 8.59 5.68 0.00 2.34
3349 3646 1.202557 AGTGACCGAAAACGGCTTACA 60.203 47.619 8.59 2.26 0.00 2.41
3350 3647 1.802365 GTGACCGAAAACGGCTTACAT 59.198 47.619 8.59 0.00 0.00 2.29
3351 3648 2.224784 GTGACCGAAAACGGCTTACATT 59.775 45.455 8.59 0.00 0.00 2.71
3352 3649 2.879646 TGACCGAAAACGGCTTACATTT 59.120 40.909 8.59 0.00 0.00 2.32
3353 3650 3.231160 GACCGAAAACGGCTTACATTTG 58.769 45.455 8.59 0.00 0.00 2.32
3354 3651 2.619646 ACCGAAAACGGCTTACATTTGT 59.380 40.909 8.59 0.00 0.00 2.83
3355 3652 3.067040 ACCGAAAACGGCTTACATTTGTT 59.933 39.130 8.59 0.00 0.00 2.83
3356 3653 4.045783 CCGAAAACGGCTTACATTTGTTT 58.954 39.130 0.00 0.00 34.46 2.83
3357 3654 5.213675 CCGAAAACGGCTTACATTTGTTTA 58.786 37.500 0.00 0.00 32.84 2.01
3358 3655 5.115923 CCGAAAACGGCTTACATTTGTTTAC 59.884 40.000 0.00 0.00 32.84 2.01
3359 3656 5.681982 CGAAAACGGCTTACATTTGTTTACA 59.318 36.000 0.00 0.00 32.84 2.41
3360 3657 6.129561 CGAAAACGGCTTACATTTGTTTACAG 60.130 38.462 0.00 0.00 32.84 2.74
3361 3658 6.380095 AAACGGCTTACATTTGTTTACAGA 57.620 33.333 0.00 0.00 31.49 3.41
3362 3659 5.607119 ACGGCTTACATTTGTTTACAGAG 57.393 39.130 0.00 0.00 0.00 3.35
3363 3660 4.454504 ACGGCTTACATTTGTTTACAGAGG 59.545 41.667 0.00 0.00 0.00 3.69
3364 3661 4.142687 CGGCTTACATTTGTTTACAGAGGG 60.143 45.833 0.00 0.00 0.00 4.30
3365 3662 5.007682 GGCTTACATTTGTTTACAGAGGGA 58.992 41.667 0.00 0.00 0.00 4.20
3366 3663 5.123979 GGCTTACATTTGTTTACAGAGGGAG 59.876 44.000 0.00 0.00 0.00 4.30
3367 3664 5.705905 GCTTACATTTGTTTACAGAGGGAGT 59.294 40.000 0.00 0.00 0.00 3.85
3368 3665 6.877322 GCTTACATTTGTTTACAGAGGGAGTA 59.123 38.462 0.00 0.00 0.00 2.59
3369 3666 7.553044 GCTTACATTTGTTTACAGAGGGAGTAT 59.447 37.037 0.00 0.00 0.00 2.12
3388 3685 8.848182 GGGAGTATTATCTATCTTACCATACGG 58.152 40.741 0.00 0.00 38.77 4.02
3394 3691 9.939802 ATTATCTATCTTACCATACGGAAAACC 57.060 33.333 0.00 0.00 35.59 3.27
3395 3692 7.613551 ATCTATCTTACCATACGGAAAACCT 57.386 36.000 0.00 0.00 35.59 3.50
3396 3693 6.812998 TCTATCTTACCATACGGAAAACCTG 58.187 40.000 0.00 0.00 35.59 4.00
3482 3779 3.141488 CTGCCCGTCTAGCGACCT 61.141 66.667 7.94 0.00 44.77 3.85
3508 3805 3.843619 TGATCATGGTTCTGGGTCTTGTA 59.156 43.478 0.00 0.00 0.00 2.41
3539 3836 2.128035 CGGTCGGTCTTGCTATCATTC 58.872 52.381 0.00 0.00 0.00 2.67
3870 4288 7.062956 GCTTTATATTTTGCCTTTGTGTACCAC 59.937 37.037 0.00 0.00 34.56 4.16
3972 4399 4.515567 AGGAAACCTCTGAAAAATGTCGTC 59.484 41.667 0.00 0.00 0.00 4.20
4011 4444 2.773993 GGTTCGGATTAACCTGTGGA 57.226 50.000 0.00 0.00 44.67 4.02
4079 4513 2.104281 ACTGGGACAAAGAAGTAAGCGT 59.896 45.455 0.00 0.00 38.70 5.07
4108 4566 9.522804 GGTCATATTGTTTTGTGAGTTTTGTTA 57.477 29.630 0.00 0.00 0.00 2.41
4128 4586 3.708403 ATGTTGGCTTCTCAGTGATCA 57.292 42.857 0.00 0.00 0.00 2.92
4189 4662 3.720002 ACAGGGTTTTCAGTTCTTCCCTA 59.280 43.478 0.00 0.00 42.70 3.53
4193 4666 4.447325 GGGTTTTCAGTTCTTCCCTACCTT 60.447 45.833 0.00 0.00 32.89 3.50
4241 4714 6.183360 ACAAGACAAGATGCACAATTTTCTCA 60.183 34.615 0.00 0.00 0.00 3.27
4269 4742 1.152819 CCAGGGAGATGTGCATGGG 60.153 63.158 7.19 0.00 41.94 4.00
4283 4756 2.031870 GCATGGGGATAAGGAACCAAC 58.968 52.381 0.00 0.00 36.44 3.77
4390 4863 9.043079 GGTAAAAACAATTTGGATACGGAAAAA 57.957 29.630 0.78 0.00 42.51 1.94
4445 4918 9.978044 GTACTACCCTTGATAATGTAAGTAAGG 57.022 37.037 0.00 0.00 35.58 2.69
4458 4931 5.751586 TGTAAGTAAGGGCAGGGAATAAAG 58.248 41.667 0.00 0.00 0.00 1.85
4475 4948 9.232473 GGGAATAAAGTGTTTCTTCACTAGAAT 57.768 33.333 0.00 0.00 46.25 2.40
4596 5102 2.113860 TGGTAGTGCATTTCTGAGGC 57.886 50.000 0.00 0.00 0.00 4.70
4625 5131 3.630769 ACGCTAGTGATTACGATTGAGGA 59.369 43.478 10.99 0.00 0.00 3.71
4685 5191 4.522789 GCCAGGACAAATAAAACAAGGAGA 59.477 41.667 0.00 0.00 0.00 3.71
4693 5199 4.985044 ATAAAACAAGGAGACGACGTTG 57.015 40.909 0.13 0.00 40.16 4.10
4696 5202 1.315690 ACAAGGAGACGACGTTGAGA 58.684 50.000 10.51 0.00 38.48 3.27
4798 5304 1.010350 CGTAGTAGTAGCGTGGCCG 60.010 63.158 0.00 0.00 37.07 6.13
4898 5404 2.540383 TGTGTCCCTGATCTAGTGCTT 58.460 47.619 0.00 0.00 0.00 3.91
4899 5405 2.906389 TGTGTCCCTGATCTAGTGCTTT 59.094 45.455 0.00 0.00 0.00 3.51
4900 5406 3.055819 TGTGTCCCTGATCTAGTGCTTTC 60.056 47.826 0.00 0.00 0.00 2.62
4901 5407 3.196685 GTGTCCCTGATCTAGTGCTTTCT 59.803 47.826 0.00 0.00 0.00 2.52
4902 5408 3.840666 TGTCCCTGATCTAGTGCTTTCTT 59.159 43.478 0.00 0.00 0.00 2.52
4903 5409 4.287067 TGTCCCTGATCTAGTGCTTTCTTT 59.713 41.667 0.00 0.00 0.00 2.52
4904 5410 4.873259 GTCCCTGATCTAGTGCTTTCTTTC 59.127 45.833 0.00 0.00 0.00 2.62
4905 5411 4.780021 TCCCTGATCTAGTGCTTTCTTTCT 59.220 41.667 0.00 0.00 0.00 2.52
4906 5412 5.105146 TCCCTGATCTAGTGCTTTCTTTCTC 60.105 44.000 0.00 0.00 0.00 2.87
4907 5413 5.104982 CCCTGATCTAGTGCTTTCTTTCTCT 60.105 44.000 0.00 0.00 0.00 3.10
4908 5414 6.405538 CCTGATCTAGTGCTTTCTTTCTCTT 58.594 40.000 0.00 0.00 0.00 2.85
4909 5415 6.878389 CCTGATCTAGTGCTTTCTTTCTCTTT 59.122 38.462 0.00 0.00 0.00 2.52
4910 5416 7.390162 CCTGATCTAGTGCTTTCTTTCTCTTTT 59.610 37.037 0.00 0.00 0.00 2.27
4911 5417 8.092521 TGATCTAGTGCTTTCTTTCTCTTTTG 57.907 34.615 0.00 0.00 0.00 2.44
4912 5418 7.933577 TGATCTAGTGCTTTCTTTCTCTTTTGA 59.066 33.333 0.00 0.00 0.00 2.69
4913 5419 7.484035 TCTAGTGCTTTCTTTCTCTTTTGAC 57.516 36.000 0.00 0.00 0.00 3.18
4914 5420 7.047891 TCTAGTGCTTTCTTTCTCTTTTGACA 58.952 34.615 0.00 0.00 0.00 3.58
4915 5421 6.705863 AGTGCTTTCTTTCTCTTTTGACAT 57.294 33.333 0.00 0.00 0.00 3.06
4916 5422 6.733145 AGTGCTTTCTTTCTCTTTTGACATC 58.267 36.000 0.00 0.00 0.00 3.06
4917 5423 6.319658 AGTGCTTTCTTTCTCTTTTGACATCA 59.680 34.615 0.00 0.00 0.00 3.07
4918 5424 7.014038 AGTGCTTTCTTTCTCTTTTGACATCAT 59.986 33.333 0.00 0.00 0.00 2.45
4919 5425 7.650903 GTGCTTTCTTTCTCTTTTGACATCATT 59.349 33.333 0.00 0.00 0.00 2.57
4920 5426 7.864379 TGCTTTCTTTCTCTTTTGACATCATTC 59.136 33.333 0.00 0.00 0.00 2.67
4921 5427 7.328005 GCTTTCTTTCTCTTTTGACATCATTCC 59.672 37.037 0.00 0.00 0.00 3.01
4922 5428 8.469309 TTTCTTTCTCTTTTGACATCATTCCT 57.531 30.769 0.00 0.00 0.00 3.36
4923 5429 7.444629 TCTTTCTCTTTTGACATCATTCCTG 57.555 36.000 0.00 0.00 0.00 3.86
4924 5430 7.226441 TCTTTCTCTTTTGACATCATTCCTGA 58.774 34.615 0.00 0.00 35.41 3.86
4925 5431 7.886970 TCTTTCTCTTTTGACATCATTCCTGAT 59.113 33.333 0.00 0.00 43.02 2.90
4926 5432 7.621428 TTCTCTTTTGACATCATTCCTGATC 57.379 36.000 0.00 0.00 40.20 2.92
4927 5433 6.955364 TCTCTTTTGACATCATTCCTGATCT 58.045 36.000 0.00 0.00 40.20 2.75
4928 5434 8.082672 TCTCTTTTGACATCATTCCTGATCTA 57.917 34.615 0.00 0.00 40.20 1.98
4929 5435 8.202811 TCTCTTTTGACATCATTCCTGATCTAG 58.797 37.037 0.00 0.00 40.20 2.43
4930 5436 7.855375 TCTTTTGACATCATTCCTGATCTAGT 58.145 34.615 0.00 0.00 40.20 2.57
4931 5437 7.767659 TCTTTTGACATCATTCCTGATCTAGTG 59.232 37.037 0.00 0.00 40.20 2.74
4932 5438 6.550938 TTGACATCATTCCTGATCTAGTGT 57.449 37.500 0.00 0.00 40.20 3.55
4933 5439 6.550938 TGACATCATTCCTGATCTAGTGTT 57.449 37.500 0.00 0.00 40.20 3.32
4934 5440 7.660030 TGACATCATTCCTGATCTAGTGTTA 57.340 36.000 0.00 0.00 40.20 2.41
4935 5441 7.720442 TGACATCATTCCTGATCTAGTGTTAG 58.280 38.462 0.00 0.00 40.20 2.34
4936 5442 7.343057 TGACATCATTCCTGATCTAGTGTTAGT 59.657 37.037 0.00 0.00 40.20 2.24
4937 5443 7.495901 ACATCATTCCTGATCTAGTGTTAGTG 58.504 38.462 0.00 0.00 40.20 2.74
4938 5444 6.471233 TCATTCCTGATCTAGTGTTAGTGG 57.529 41.667 0.00 0.00 0.00 4.00
4939 5445 4.737855 TTCCTGATCTAGTGTTAGTGGC 57.262 45.455 0.00 0.00 0.00 5.01
5385 5903 2.182030 CTCGCCGTTGACCTCCTC 59.818 66.667 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.906105 TTGTGGGCCCCGATGTCTAC 61.906 60.000 22.27 8.70 0.00 2.59
4 5 2.438434 CTTGTGGGCCCCGATGTC 60.438 66.667 22.27 3.25 0.00 3.06
61 62 0.914902 AGAAACTACCAGAGGGGGCC 60.915 60.000 0.00 0.00 42.91 5.80
63 64 1.834263 CAGAGAAACTACCAGAGGGGG 59.166 57.143 0.00 0.00 42.91 5.40
127 128 2.224018 TGCACAATTCCAAAAGTCCTGC 60.224 45.455 0.00 0.00 0.00 4.85
141 142 4.713814 TCTGAGAGACCTATTCTGCACAAT 59.286 41.667 0.00 0.00 33.22 2.71
155 156 3.938334 GGAAAGGAGCAAATCTGAGAGAC 59.062 47.826 0.00 0.00 0.00 3.36
181 182 0.748005 GCCGGCAGCTGGAATTCTAA 60.748 55.000 25.86 0.00 38.99 2.10
182 183 1.153168 GCCGGCAGCTGGAATTCTA 60.153 57.895 25.86 0.00 38.99 2.10
255 256 9.681062 ATGGGCAGTTATTACATATTATGGTAC 57.319 33.333 8.48 0.00 33.60 3.34
265 266 6.975196 TTGCATTATGGGCAGTTATTACAT 57.025 33.333 0.00 0.00 43.05 2.29
273 274 7.779754 TGATATTTATTGCATTATGGGCAGT 57.220 32.000 0.00 0.00 43.05 4.40
299 300 8.031864 ACGTCCATTTTGCATCATGTTTTTATA 58.968 29.630 0.00 0.00 0.00 0.98
306 307 4.639755 TGATACGTCCATTTTGCATCATGT 59.360 37.500 0.00 0.00 0.00 3.21
310 311 3.627577 ACCTGATACGTCCATTTTGCATC 59.372 43.478 0.00 0.00 0.00 3.91
349 350 1.296715 GGCACTTGTCGGACCTGAT 59.703 57.895 5.55 0.00 0.00 2.90
352 353 2.915659 TCGGCACTTGTCGGACCT 60.916 61.111 5.55 0.00 44.30 3.85
358 359 2.981977 TTCCCACGTCGGCACTTGTC 62.982 60.000 0.00 0.00 0.00 3.18
387 388 0.971447 GCCGGTAGGAGGAGTCTTGT 60.971 60.000 1.90 0.00 41.02 3.16
401 402 3.771160 GAGGATGGACGTGCCGGT 61.771 66.667 4.04 0.00 40.66 5.28
402 403 3.432051 GAGAGGATGGACGTGCCGG 62.432 68.421 4.04 0.00 40.66 6.13
445 446 1.732259 CCTTCACCGACACATGCTAAC 59.268 52.381 0.00 0.00 0.00 2.34
447 448 0.391130 GCCTTCACCGACACATGCTA 60.391 55.000 0.00 0.00 0.00 3.49
501 502 3.525348 TTGACCCCCTTGCCCCCTA 62.525 63.158 0.00 0.00 0.00 3.53
502 503 4.959460 TTGACCCCCTTGCCCCCT 62.959 66.667 0.00 0.00 0.00 4.79
505 506 4.382541 CCCTTGACCCCCTTGCCC 62.383 72.222 0.00 0.00 0.00 5.36
508 509 3.268032 AGGCCCTTGACCCCCTTG 61.268 66.667 0.00 0.00 0.00 3.61
509 510 2.941583 GAGGCCCTTGACCCCCTT 60.942 66.667 0.00 0.00 0.00 3.95
545 546 3.141488 CTCTCCGGTGTCGAGGGG 61.141 72.222 0.00 0.00 39.00 4.79
623 624 1.671379 GGTCTTGGAGACGGTTGCC 60.671 63.158 2.33 0.00 45.96 4.52
627 628 0.900647 CAGGAGGTCTTGGAGACGGT 60.901 60.000 2.33 0.00 45.96 4.83
668 669 4.508128 ATGGTGCCCGCTACGACG 62.508 66.667 0.00 0.00 0.00 5.12
790 791 4.122337 TGGAATAATAGGGTAGAGCCGA 57.878 45.455 0.00 0.00 38.44 5.54
791 792 5.069251 CCTATGGAATAATAGGGTAGAGCCG 59.931 48.000 2.80 0.00 43.82 5.52
792 793 6.487299 CCTATGGAATAATAGGGTAGAGCC 57.513 45.833 2.80 0.00 43.82 4.70
863 864 2.491675 AAGAAGGTTGAACCCGATCC 57.508 50.000 11.41 0.00 39.75 3.36
866 867 6.377712 TCTTTTAAAAAGAAGGTTGAACCCGA 59.622 34.615 11.41 0.00 39.75 5.14
867 868 6.566141 TCTTTTAAAAAGAAGGTTGAACCCG 58.434 36.000 11.41 0.00 39.75 5.28
885 889 8.812972 ACTCTCACACCACATATAGTTCTTTTA 58.187 33.333 0.00 0.00 0.00 1.52
890 894 5.807520 CACACTCTCACACCACATATAGTTC 59.192 44.000 0.00 0.00 0.00 3.01
963 967 1.003233 GTCCTCCTCACACAAGGGC 60.003 63.158 0.00 0.00 37.02 5.19
1051 1055 1.419922 CGTGTTGAAGATTCCGCGG 59.580 57.895 22.12 22.12 0.00 6.46
1091 1095 2.093128 GGCGAGAAAGGGGATAAGAACA 60.093 50.000 0.00 0.00 0.00 3.18
1106 1110 3.128349 GCAATACCGATAAAAGGCGAGA 58.872 45.455 0.00 0.00 0.00 4.04
1109 1113 2.223377 GGAGCAATACCGATAAAAGGCG 59.777 50.000 0.00 0.00 0.00 5.52
1164 1168 0.517316 GCTACAACCAAAGCACGGAG 59.483 55.000 0.00 0.00 38.63 4.63
1252 1256 4.500499 AATTCAAGACATCCCTCCTCTG 57.500 45.455 0.00 0.00 0.00 3.35
1276 1280 3.359033 TGGCTTCTTGAATCCATCCAAG 58.641 45.455 2.22 0.00 40.68 3.61
1277 1281 3.454719 TGGCTTCTTGAATCCATCCAA 57.545 42.857 2.22 0.00 0.00 3.53
1278 1282 3.675348 ATGGCTTCTTGAATCCATCCA 57.325 42.857 11.59 3.16 34.43 3.41
1335 1341 2.594654 CACTAGCGAATCAACTGACGAC 59.405 50.000 0.00 0.00 0.00 4.34
1354 1360 0.039618 TTTCCAAGATCCAGGGCCAC 59.960 55.000 6.18 0.00 0.00 5.01
1382 1388 3.571401 ACGGAGGGAGTACATATAAACGG 59.429 47.826 0.00 0.00 0.00 4.44
1384 1390 6.576185 TGAAACGGAGGGAGTACATATAAAC 58.424 40.000 0.00 0.00 0.00 2.01
1395 1401 4.631813 CAGAGTAATTTGAAACGGAGGGAG 59.368 45.833 0.00 0.00 0.00 4.30
1396 1402 4.041198 ACAGAGTAATTTGAAACGGAGGGA 59.959 41.667 0.00 0.00 0.00 4.20
1397 1403 4.324267 ACAGAGTAATTTGAAACGGAGGG 58.676 43.478 0.00 0.00 0.00 4.30
1398 1404 5.581085 CCTACAGAGTAATTTGAAACGGAGG 59.419 44.000 0.00 0.00 0.00 4.30
1399 1405 6.090898 CACCTACAGAGTAATTTGAAACGGAG 59.909 42.308 0.00 0.00 0.00 4.63
1400 1406 5.929992 CACCTACAGAGTAATTTGAAACGGA 59.070 40.000 0.00 0.00 0.00 4.69
1401 1407 5.121768 CCACCTACAGAGTAATTTGAAACGG 59.878 44.000 0.00 0.00 0.00 4.44
1402 1408 5.699458 ACCACCTACAGAGTAATTTGAAACG 59.301 40.000 0.00 0.00 0.00 3.60
1403 1409 7.148457 GCTACCACCTACAGAGTAATTTGAAAC 60.148 40.741 0.00 0.00 0.00 2.78
1404 1410 6.877322 GCTACCACCTACAGAGTAATTTGAAA 59.123 38.462 0.00 0.00 0.00 2.69
1405 1411 6.014070 TGCTACCACCTACAGAGTAATTTGAA 60.014 38.462 0.00 0.00 0.00 2.69
1406 1412 5.482526 TGCTACCACCTACAGAGTAATTTGA 59.517 40.000 0.00 0.00 0.00 2.69
1407 1413 5.581085 GTGCTACCACCTACAGAGTAATTTG 59.419 44.000 0.00 0.00 35.92 2.32
1408 1414 5.623824 CGTGCTACCACCTACAGAGTAATTT 60.624 44.000 0.00 0.00 38.79 1.82
1409 1415 4.142227 CGTGCTACCACCTACAGAGTAATT 60.142 45.833 0.00 0.00 38.79 1.40
1410 1416 3.380637 CGTGCTACCACCTACAGAGTAAT 59.619 47.826 0.00 0.00 38.79 1.89
1411 1417 2.751259 CGTGCTACCACCTACAGAGTAA 59.249 50.000 0.00 0.00 38.79 2.24
1412 1418 2.290514 ACGTGCTACCACCTACAGAGTA 60.291 50.000 0.00 0.00 38.79 2.59
1413 1419 1.174783 CGTGCTACCACCTACAGAGT 58.825 55.000 0.00 0.00 38.79 3.24
1414 1420 1.135373 CACGTGCTACCACCTACAGAG 60.135 57.143 0.82 0.00 38.79 3.35
1415 1421 0.885879 CACGTGCTACCACCTACAGA 59.114 55.000 0.82 0.00 38.79 3.41
1416 1422 0.885879 TCACGTGCTACCACCTACAG 59.114 55.000 11.67 0.00 38.79 2.74
1417 1423 0.885879 CTCACGTGCTACCACCTACA 59.114 55.000 11.67 0.00 38.79 2.74
1463 1469 7.781763 AGCGCGCATATCTTAAAATTTATTC 57.218 32.000 35.10 0.00 0.00 1.75
1466 1472 8.078959 TCTAAGCGCGCATATCTTAAAATTTA 57.921 30.769 35.10 16.23 0.00 1.40
1467 1473 6.954944 TCTAAGCGCGCATATCTTAAAATTT 58.045 32.000 35.10 15.94 0.00 1.82
1521 1532 6.714356 TGTCACACCTTTTGAACATATCATCA 59.286 34.615 0.00 0.00 38.03 3.07
1522 1533 7.094634 ACTGTCACACCTTTTGAACATATCATC 60.095 37.037 0.00 0.00 38.03 2.92
1523 1534 6.716628 ACTGTCACACCTTTTGAACATATCAT 59.283 34.615 0.00 0.00 38.03 2.45
1590 1601 9.584008 CAGAGGAATATAGTACCAAGGTAGTAA 57.416 37.037 15.69 7.74 39.18 2.24
1672 1701 6.604735 AATAAAGAATACATGCTCGACCAC 57.395 37.500 0.00 0.00 0.00 4.16
1695 1724 2.487805 GCAATCTGCAGTGGATGGGATA 60.488 50.000 14.67 0.00 44.26 2.59
1716 1745 5.980116 CACAACTGAGAGAATAACTATCCGG 59.020 44.000 0.00 0.00 36.16 5.14
1935 1965 2.182825 CGAACGTGGAAGAAGATACCG 58.817 52.381 0.00 0.00 0.00 4.02
1991 2021 4.893524 TCACACTCTACTTCTGAACAAGGA 59.106 41.667 0.00 0.00 0.00 3.36
2294 2344 7.106239 AGGTCCAACATATGTAAGAGACAAAG 58.894 38.462 9.21 0.00 42.78 2.77
2297 2347 5.128827 GGAGGTCCAACATATGTAAGAGACA 59.871 44.000 9.21 0.00 38.08 3.41
2375 2457 0.816825 ACAGTGTGTCCAAGCTGCTG 60.817 55.000 1.35 0.00 32.65 4.41
2944 3155 3.196039 TGGAGATGGACGACGGAAAATTA 59.804 43.478 0.00 0.00 0.00 1.40
2951 3163 1.134818 TCAATTGGAGATGGACGACGG 60.135 52.381 5.42 0.00 0.00 4.79
3080 3314 3.966665 TGCATATGACACCTCACCTGATA 59.033 43.478 6.97 0.00 0.00 2.15
3153 3417 6.672147 AGAGTATTTAAACTGCAGCAAGTTG 58.328 36.000 15.27 0.00 40.28 3.16
3304 3601 9.814899 CTACTTCAGTGATCTCAAATGTCTTAT 57.185 33.333 0.00 0.00 0.00 1.73
3305 3602 8.807118 ACTACTTCAGTGATCTCAAATGTCTTA 58.193 33.333 0.00 0.00 35.62 2.10
3306 3603 7.675062 ACTACTTCAGTGATCTCAAATGTCTT 58.325 34.615 0.00 0.00 35.62 3.01
3307 3604 7.238486 ACTACTTCAGTGATCTCAAATGTCT 57.762 36.000 0.00 0.00 35.62 3.41
3320 3617 3.181774 CGTTTTCGGTCACTACTTCAGTG 59.818 47.826 0.00 0.00 46.45 3.66
3321 3618 3.378339 CGTTTTCGGTCACTACTTCAGT 58.622 45.455 0.00 0.00 39.94 3.41
3335 3632 5.681982 TGTAAACAAATGTAAGCCGTTTTCG 59.318 36.000 0.00 0.00 43.67 3.46
3336 3633 6.913673 TCTGTAAACAAATGTAAGCCGTTTTC 59.086 34.615 0.00 0.00 32.42 2.29
3337 3634 6.797454 TCTGTAAACAAATGTAAGCCGTTTT 58.203 32.000 0.00 0.00 32.42 2.43
3338 3635 6.380095 TCTGTAAACAAATGTAAGCCGTTT 57.620 33.333 0.00 0.00 34.40 3.60
3339 3636 5.048991 CCTCTGTAAACAAATGTAAGCCGTT 60.049 40.000 0.00 0.00 0.00 4.44
3340 3637 4.454504 CCTCTGTAAACAAATGTAAGCCGT 59.545 41.667 0.00 0.00 0.00 5.68
3341 3638 4.142687 CCCTCTGTAAACAAATGTAAGCCG 60.143 45.833 0.00 0.00 0.00 5.52
3342 3639 5.007682 TCCCTCTGTAAACAAATGTAAGCC 58.992 41.667 0.00 0.00 0.00 4.35
3343 3640 5.705905 ACTCCCTCTGTAAACAAATGTAAGC 59.294 40.000 0.00 0.00 0.00 3.09
3344 3641 9.449719 AATACTCCCTCTGTAAACAAATGTAAG 57.550 33.333 0.00 0.00 0.00 2.34
3347 3644 9.614792 GATAATACTCCCTCTGTAAACAAATGT 57.385 33.333 0.00 0.00 0.00 2.71
3348 3645 9.838339 AGATAATACTCCCTCTGTAAACAAATG 57.162 33.333 0.00 0.00 0.00 2.32
3357 3654 8.679725 TGGTAAGATAGATAATACTCCCTCTGT 58.320 37.037 0.00 0.00 0.00 3.41
3358 3655 9.707957 ATGGTAAGATAGATAATACTCCCTCTG 57.292 37.037 0.00 0.00 0.00 3.35
3361 3658 9.629878 CGTATGGTAAGATAGATAATACTCCCT 57.370 37.037 0.00 0.00 0.00 4.20
3362 3659 8.848182 CCGTATGGTAAGATAGATAATACTCCC 58.152 40.741 0.00 0.00 0.00 4.30
3363 3660 9.624373 TCCGTATGGTAAGATAGATAATACTCC 57.376 37.037 0.00 0.00 36.30 3.85
3368 3665 9.939802 GGTTTTCCGTATGGTAAGATAGATAAT 57.060 33.333 0.00 0.00 36.30 1.28
3369 3666 9.151177 AGGTTTTCCGTATGGTAAGATAGATAA 57.849 33.333 0.00 0.00 46.35 1.75
3392 3689 9.678260 GAGGCAAGATAATAATGAATATCAGGT 57.322 33.333 0.00 0.00 32.17 4.00
3393 3690 9.902684 AGAGGCAAGATAATAATGAATATCAGG 57.097 33.333 0.00 0.00 32.17 3.86
3482 3779 4.040047 AGACCCAGAACCATGATCACATA 58.960 43.478 0.00 0.00 35.09 2.29
3539 3836 0.102844 CCCCATAAATTGCGCACCAG 59.897 55.000 11.12 0.00 0.00 4.00
3870 4288 6.850752 AAAATAAGTACCATTCCACCAAGG 57.149 37.500 0.00 0.00 39.47 3.61
3972 4399 2.086869 CACAGCCCCTAACAGTTCATG 58.913 52.381 0.00 0.00 0.00 3.07
4079 4513 3.818210 ACTCACAAAACAATATGACCGCA 59.182 39.130 0.00 0.00 0.00 5.69
4108 4566 3.708403 TGATCACTGAGAAGCCAACAT 57.292 42.857 0.00 0.00 0.00 2.71
4189 4662 4.074970 CTCATGTTGCCAAGTCTAAAGGT 58.925 43.478 0.00 0.00 0.00 3.50
4193 4666 4.065088 GTGTCTCATGTTGCCAAGTCTAA 58.935 43.478 0.00 0.00 0.00 2.10
4241 4714 3.117738 CACATCTCCCTGGCTAATTTCCT 60.118 47.826 0.00 0.00 0.00 3.36
4269 4742 3.622166 TTCCTCGTTGGTTCCTTATCC 57.378 47.619 0.00 0.00 37.07 2.59
4283 4756 4.082245 ACCATTTTAGCAACCAATTCCTCG 60.082 41.667 0.00 0.00 0.00 4.63
4390 4863 7.657761 CGCCTCTACTCATCCTAACATTTTTAT 59.342 37.037 0.00 0.00 0.00 1.40
4391 4864 6.984474 CGCCTCTACTCATCCTAACATTTTTA 59.016 38.462 0.00 0.00 0.00 1.52
4392 4865 5.817816 CGCCTCTACTCATCCTAACATTTTT 59.182 40.000 0.00 0.00 0.00 1.94
4443 4916 3.076032 AGAAACACTTTATTCCCTGCCCT 59.924 43.478 0.00 0.00 0.00 5.19
4444 4917 3.431415 AGAAACACTTTATTCCCTGCCC 58.569 45.455 0.00 0.00 0.00 5.36
4445 4918 4.522789 TGAAGAAACACTTTATTCCCTGCC 59.477 41.667 0.88 0.00 39.46 4.85
4446 4919 5.461526 GTGAAGAAACACTTTATTCCCTGC 58.538 41.667 0.00 0.00 39.46 4.85
4567 5073 3.648339 ATGCACTACCAAGCACAAAAG 57.352 42.857 0.00 0.00 44.49 2.27
4596 5102 3.003378 TCGTAATCACTAGCGTCCTCATG 59.997 47.826 0.00 0.00 0.00 3.07
4625 5131 4.954826 AGCCTTTTCTAGATACGTAGTGGT 59.045 41.667 0.08 0.00 45.73 4.16
4685 5191 1.202371 TCTGCAAAGTCTCAACGTCGT 60.202 47.619 0.00 0.00 0.00 4.34
4693 5199 3.911661 AGCACATTTCTGCAAAGTCTC 57.088 42.857 0.00 0.00 39.86 3.36
4696 5202 4.304110 CATGAAGCACATTTCTGCAAAGT 58.696 39.130 0.00 0.00 39.86 2.66
4800 5306 3.818121 TTTGCCGACTCACGTGGGG 62.818 63.158 21.67 14.90 39.22 4.96
4802 5308 1.157870 AGTTTTGCCGACTCACGTGG 61.158 55.000 17.00 9.11 40.78 4.94
4803 5309 0.655733 AAGTTTTGCCGACTCACGTG 59.344 50.000 9.94 9.94 40.78 4.49
4804 5310 0.655733 CAAGTTTTGCCGACTCACGT 59.344 50.000 0.00 0.00 40.78 4.49
4805 5311 0.041312 CCAAGTTTTGCCGACTCACG 60.041 55.000 0.00 0.00 42.18 4.35
4873 5379 1.137086 CTAGATCAGGGACACAACGGG 59.863 57.143 0.00 0.00 0.00 5.28
4898 5404 7.720957 TCAGGAATGATGTCAAAAGAGAAAGAA 59.279 33.333 0.00 0.00 0.00 2.52
4899 5405 7.226441 TCAGGAATGATGTCAAAAGAGAAAGA 58.774 34.615 0.00 0.00 0.00 2.52
4900 5406 7.444629 TCAGGAATGATGTCAAAAGAGAAAG 57.555 36.000 0.00 0.00 0.00 2.62
4901 5407 7.886970 AGATCAGGAATGATGTCAAAAGAGAAA 59.113 33.333 0.00 0.00 0.00 2.52
4902 5408 7.400439 AGATCAGGAATGATGTCAAAAGAGAA 58.600 34.615 0.00 0.00 0.00 2.87
4903 5409 6.955364 AGATCAGGAATGATGTCAAAAGAGA 58.045 36.000 0.00 0.00 0.00 3.10
4904 5410 7.986320 ACTAGATCAGGAATGATGTCAAAAGAG 59.014 37.037 0.00 0.00 0.00 2.85
4905 5411 7.767659 CACTAGATCAGGAATGATGTCAAAAGA 59.232 37.037 0.00 0.00 0.00 2.52
4906 5412 7.551974 ACACTAGATCAGGAATGATGTCAAAAG 59.448 37.037 0.00 0.00 0.00 2.27
4907 5413 7.397221 ACACTAGATCAGGAATGATGTCAAAA 58.603 34.615 0.00 0.00 0.00 2.44
4908 5414 6.950842 ACACTAGATCAGGAATGATGTCAAA 58.049 36.000 0.00 0.00 0.00 2.69
4909 5415 6.550938 ACACTAGATCAGGAATGATGTCAA 57.449 37.500 0.00 0.00 0.00 3.18
4910 5416 6.550938 AACACTAGATCAGGAATGATGTCA 57.449 37.500 0.00 0.00 0.00 3.58
4911 5417 7.651304 CACTAACACTAGATCAGGAATGATGTC 59.349 40.741 0.00 0.00 0.00 3.06
4912 5418 7.418368 CCACTAACACTAGATCAGGAATGATGT 60.418 40.741 0.00 0.00 0.00 3.06
4913 5419 6.927936 CCACTAACACTAGATCAGGAATGATG 59.072 42.308 0.00 0.00 0.00 3.07
4914 5420 6.463614 GCCACTAACACTAGATCAGGAATGAT 60.464 42.308 0.00 0.00 0.00 2.45
4915 5421 5.163405 GCCACTAACACTAGATCAGGAATGA 60.163 44.000 0.00 0.00 0.00 2.57
4916 5422 5.053145 GCCACTAACACTAGATCAGGAATG 58.947 45.833 0.00 0.00 0.00 2.67
4917 5423 4.716784 TGCCACTAACACTAGATCAGGAAT 59.283 41.667 0.00 0.00 0.00 3.01
4918 5424 4.093743 TGCCACTAACACTAGATCAGGAA 58.906 43.478 0.00 0.00 0.00 3.36
4919 5425 3.708451 TGCCACTAACACTAGATCAGGA 58.292 45.455 0.00 0.00 0.00 3.86
4920 5426 4.626042 GATGCCACTAACACTAGATCAGG 58.374 47.826 0.00 0.00 0.00 3.86
4921 5427 4.294232 CGATGCCACTAACACTAGATCAG 58.706 47.826 0.00 0.00 0.00 2.90
4922 5428 3.490933 GCGATGCCACTAACACTAGATCA 60.491 47.826 0.00 0.00 0.00 2.92
4923 5429 3.053455 GCGATGCCACTAACACTAGATC 58.947 50.000 0.00 0.00 0.00 2.75
4924 5430 2.695666 AGCGATGCCACTAACACTAGAT 59.304 45.455 0.00 0.00 0.00 1.98
4925 5431 2.100197 AGCGATGCCACTAACACTAGA 58.900 47.619 0.00 0.00 0.00 2.43
4926 5432 2.196749 CAGCGATGCCACTAACACTAG 58.803 52.381 0.00 0.00 0.00 2.57
4927 5433 1.739035 GCAGCGATGCCACTAACACTA 60.739 52.381 16.30 0.00 0.00 2.74
4928 5434 1.021390 GCAGCGATGCCACTAACACT 61.021 55.000 16.30 0.00 0.00 3.55
4929 5435 1.425428 GCAGCGATGCCACTAACAC 59.575 57.895 16.30 0.00 0.00 3.32
4930 5436 2.100031 CGCAGCGATGCCACTAACA 61.100 57.895 21.52 0.00 0.00 2.41
4931 5437 2.703409 CGCAGCGATGCCACTAAC 59.297 61.111 21.52 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.