Multiple sequence alignment - TraesCS6D01G117800

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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 TraesCS6D01G117800 chr6D 100.000 4987 0 0 1 4987 83487932 83492918 0.000000e+00 9210.0
1 TraesCS6D01G117800 chr6D 85.286 2569 261 69 1309 3834 83225661 83223167 0.000000e+00 2542.0
2 TraesCS6D01G117800 chr6D 84.162 543 68 12 416 949 122379213 122379746 1.240000e-140 510.0
3 TraesCS6D01G117800 chr6D 84.292 452 52 13 4548 4987 433634130 433634574 1.660000e-114 424.0
4 TraesCS6D01G117800 chr6D 81.343 268 46 4 4151 4416 327025154 327024889 1.090000e-51 215.0
5 TraesCS6D01G117800 chr6D 80.919 283 27 17 4442 4704 362908104 362908379 1.100000e-46 198.0
6 TraesCS6D01G117800 chr6D 83.246 191 18 8 4445 4623 362921856 362922044 3.990000e-36 163.0
7 TraesCS6D01G117800 chr6B 93.163 2472 140 16 967 3425 159283659 159286114 0.000000e+00 3602.0
8 TraesCS6D01G117800 chr6B 85.981 2461 244 57 1309 3735 158289819 158287426 0.000000e+00 2540.0
9 TraesCS6D01G117800 chr6B 88.067 1542 153 13 1795 3312 159371656 159373190 0.000000e+00 1799.0
10 TraesCS6D01G117800 chr6B 92.671 996 49 18 3459 4441 159286110 159287094 0.000000e+00 1413.0
11 TraesCS6D01G117800 chr6B 86.637 449 43 13 4549 4987 297288151 297288592 9.710000e-132 481.0
12 TraesCS6D01G117800 chr6B 86.637 449 43 13 4549 4987 297295665 297296106 9.710000e-132 481.0
13 TraesCS6D01G117800 chr6B 82.982 570 50 20 966 1507 159367732 159368282 5.840000e-129 472.0
14 TraesCS6D01G117800 chr6B 83.282 323 33 3 14 315 159283253 159283575 1.370000e-70 278.0
15 TraesCS6D01G117800 chr6A 88.031 1930 188 24 1656 3567 100426789 100424885 0.000000e+00 2244.0
16 TraesCS6D01G117800 chr6A 85.506 1711 161 37 1795 3476 100734175 100735827 0.000000e+00 1705.0
17 TraesCS6D01G117800 chr6A 89.091 385 38 4 1597 1980 100733293 100733674 4.520000e-130 475.0
18 TraesCS6D01G117800 chr6A 88.321 274 25 6 1180 1452 100733131 100733398 6.230000e-84 322.0
19 TraesCS6D01G117800 chr6A 81.116 233 23 5 5 217 100727680 100727911 3.090000e-37 167.0
20 TraesCS6D01G117800 chr6A 83.784 185 17 5 4445 4618 596149783 596149601 3.990000e-36 163.0
21 TraesCS6D01G117800 chr7A 92.634 543 38 1 4445 4987 183709909 183709369 0.000000e+00 780.0
22 TraesCS6D01G117800 chr7A 82.944 557 76 15 408 955 512186893 512187439 7.510000e-133 484.0
23 TraesCS6D01G117800 chr7A 87.850 107 4 5 4494 4600 183694194 183694097 3.150000e-22 117.0
24 TraesCS6D01G117800 chr4B 86.067 567 53 15 4442 4987 142040842 142041403 2.000000e-163 586.0
25 TraesCS6D01G117800 chr4B 85.983 478 51 11 418 890 657859927 657859461 9.640000e-137 497.0
26 TraesCS6D01G117800 chr4B 100.000 29 0 0 313 341 404525267 404525239 3.000000e-03 54.7
27 TraesCS6D01G117800 chr4A 84.473 541 66 11 417 949 45350510 45351040 7.400000e-143 518.0
28 TraesCS6D01G117800 chr4A 82.123 179 29 3 4146 4323 381817121 381817297 3.110000e-32 150.0
29 TraesCS6D01G117800 chr1D 83.919 541 68 13 418 949 379729186 379728656 2.680000e-137 499.0
30 TraesCS6D01G117800 chr1D 87.823 271 31 2 4146 4416 205342388 205342656 2.900000e-82 316.0
31 TraesCS6D01G117800 chr1A 83.453 556 72 13 405 949 430186221 430186767 2.680000e-137 499.0
32 TraesCS6D01G117800 chr1A 83.002 553 76 9 406 949 542714888 542715431 7.510000e-133 484.0
33 TraesCS6D01G117800 chr1A 79.630 270 30 14 4445 4701 553060693 553060436 2.390000e-38 171.0
34 TraesCS6D01G117800 chr1A 83.422 187 17 6 4445 4620 553053620 553053437 1.440000e-35 161.0
35 TraesCS6D01G117800 chr1B 83.393 560 64 20 4439 4987 467901689 467901148 4.490000e-135 492.0
36 TraesCS6D01G117800 chr3A 83.491 527 69 13 432 949 527609030 527608513 4.520000e-130 475.0
37 TraesCS6D01G117800 chr3A 80.345 290 30 16 4431 4704 327105471 327105193 1.420000e-45 195.0
38 TraesCS6D01G117800 chr2B 82.671 554 75 13 413 955 134604589 134605132 5.840000e-129 472.0
39 TraesCS6D01G117800 chr2B 85.398 452 49 10 4548 4987 178158591 178158145 2.120000e-123 453.0
40 TraesCS6D01G117800 chr2B 82.888 187 19 5 4445 4620 607076309 607076125 6.680000e-34 156.0
41 TraesCS6D01G117800 chr5D 82.238 563 64 28 4441 4987 368740377 368739835 2.120000e-123 453.0
42 TraesCS6D01G117800 chr4D 81.753 559 70 24 4443 4987 473839637 473840177 5.930000e-119 438.0
43 TraesCS6D01G117800 chr5B 89.401 217 18 4 4440 4655 52934995 52934783 8.230000e-68 268.0
44 TraesCS6D01G117800 chr7B 82.836 268 43 3 4150 4416 289233777 289233512 2.320000e-58 237.0
45 TraesCS6D01G117800 chr3D 81.132 265 46 4 4154 4416 229119058 229118796 5.060000e-50 209.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G117800 chr6D 83487932 83492918 4986 False 9210.000000 9210 100.000000 1 4987 1 chr6D.!!$F1 4986
1 TraesCS6D01G117800 chr6D 83223167 83225661 2494 True 2542.000000 2542 85.286000 1309 3834 1 chr6D.!!$R1 2525
2 TraesCS6D01G117800 chr6D 122379213 122379746 533 False 510.000000 510 84.162000 416 949 1 chr6D.!!$F2 533
3 TraesCS6D01G117800 chr6B 158287426 158289819 2393 True 2540.000000 2540 85.981000 1309 3735 1 chr6B.!!$R1 2426
4 TraesCS6D01G117800 chr6B 159283253 159287094 3841 False 1764.333333 3602 89.705333 14 4441 3 chr6B.!!$F3 4427
5 TraesCS6D01G117800 chr6B 159367732 159373190 5458 False 1135.500000 1799 85.524500 966 3312 2 chr6B.!!$F4 2346
6 TraesCS6D01G117800 chr6A 100424885 100426789 1904 True 2244.000000 2244 88.031000 1656 3567 1 chr6A.!!$R1 1911
7 TraesCS6D01G117800 chr6A 100733131 100735827 2696 False 834.000000 1705 87.639333 1180 3476 3 chr6A.!!$F2 2296
8 TraesCS6D01G117800 chr7A 183709369 183709909 540 True 780.000000 780 92.634000 4445 4987 1 chr7A.!!$R2 542
9 TraesCS6D01G117800 chr7A 512186893 512187439 546 False 484.000000 484 82.944000 408 955 1 chr7A.!!$F1 547
10 TraesCS6D01G117800 chr4B 142040842 142041403 561 False 586.000000 586 86.067000 4442 4987 1 chr4B.!!$F1 545
11 TraesCS6D01G117800 chr4A 45350510 45351040 530 False 518.000000 518 84.473000 417 949 1 chr4A.!!$F1 532
12 TraesCS6D01G117800 chr1D 379728656 379729186 530 True 499.000000 499 83.919000 418 949 1 chr1D.!!$R1 531
13 TraesCS6D01G117800 chr1A 430186221 430186767 546 False 499.000000 499 83.453000 405 949 1 chr1A.!!$F1 544
14 TraesCS6D01G117800 chr1A 542714888 542715431 543 False 484.000000 484 83.002000 406 949 1 chr1A.!!$F2 543
15 TraesCS6D01G117800 chr1B 467901148 467901689 541 True 492.000000 492 83.393000 4439 4987 1 chr1B.!!$R1 548
16 TraesCS6D01G117800 chr3A 527608513 527609030 517 True 475.000000 475 83.491000 432 949 1 chr3A.!!$R2 517
17 TraesCS6D01G117800 chr2B 134604589 134605132 543 False 472.000000 472 82.671000 413 955 1 chr2B.!!$F1 542
18 TraesCS6D01G117800 chr5D 368739835 368740377 542 True 453.000000 453 82.238000 4441 4987 1 chr5D.!!$R1 546
19 TraesCS6D01G117800 chr4D 473839637 473840177 540 False 438.000000 438 81.753000 4443 4987 1 chr4D.!!$F1 544

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
404 426 0.107214 CTCAGCTCTCCTCCTCGTCT 60.107 60.0 0.00 0.0 0.00 4.18 F
1724 2036 0.178995 TGACAAGATGTTGGCTGGCA 60.179 50.0 10.19 0.0 42.95 4.92 F
2426 6334 0.389817 CGTGCTTCGAGGACCATTCA 60.390 55.0 0.00 0.0 42.86 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 6210 0.748005 ATTGCCCTCCGGAAACATCG 60.748 55.0 5.23 0.0 25.02 3.84 R
3284 7193 0.035820 GGTAGCGGGTCCAAATGTGA 60.036 55.0 0.00 0.0 0.00 3.58 R
4008 7946 0.037882 CAGCAGAGACAAAGGCGAGA 60.038 55.0 0.00 0.0 0.00 4.04 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
24 25 0.318784 GTCACACGAGGTCACTGTCC 60.319 60.000 0.00 0.00 0.00 4.02
31 32 0.601558 GAGGTCACTGTCCGCTACAA 59.398 55.000 0.00 0.00 37.74 2.41
32 33 0.603569 AGGTCACTGTCCGCTACAAG 59.396 55.000 0.00 0.00 37.74 3.16
38 39 1.202582 ACTGTCCGCTACAAGCTAGTG 59.797 52.381 0.00 0.00 39.60 2.74
41 42 1.067776 GTCCGCTACAAGCTAGTGTGT 60.068 52.381 1.14 0.00 39.60 3.72
149 170 1.378382 CGGGCATGGTTGGATGACA 60.378 57.895 0.00 0.00 32.34 3.58
154 175 1.386533 CATGGTTGGATGACAGGCTC 58.613 55.000 0.00 0.00 0.00 4.70
168 189 3.093057 ACAGGCTCCGATATCACTATCC 58.907 50.000 3.12 0.00 31.67 2.59
169 190 2.098280 CAGGCTCCGATATCACTATCCG 59.902 54.545 3.12 0.00 31.67 4.18
173 194 3.082548 CTCCGATATCACTATCCGTGGT 58.917 50.000 3.12 0.00 43.94 4.16
185 206 4.129737 CGTGGTCGCATCCGAGGT 62.130 66.667 0.00 0.00 45.38 3.85
226 248 2.981859 ATTTGTCTCGGACGGCTTAT 57.018 45.000 0.00 0.00 34.95 1.73
228 250 3.872511 TTTGTCTCGGACGGCTTATAA 57.127 42.857 0.00 0.00 34.95 0.98
232 254 3.131577 TGTCTCGGACGGCTTATAAATGT 59.868 43.478 0.00 0.00 34.95 2.71
258 280 8.202137 TCCTAAACAAGTTACTATGTGCTATCC 58.798 37.037 0.00 0.00 0.00 2.59
268 290 1.167851 TGTGCTATCCAGTTGCTTGC 58.832 50.000 0.00 0.00 0.00 4.01
297 319 1.203052 CTTCGAGGGTAAAGCCGTGTA 59.797 52.381 0.00 0.00 38.44 2.90
308 330 7.071071 AGGGTAAAGCCGTGTATTAATTACCTA 59.929 37.037 10.56 0.00 40.25 3.08
326 348 9.788889 AATTACCTATTACAATACTTAGGGCAC 57.211 33.333 0.00 0.00 36.36 5.01
328 350 7.388638 ACCTATTACAATACTTAGGGCACAT 57.611 36.000 0.00 0.00 36.36 3.21
329 351 7.450903 ACCTATTACAATACTTAGGGCACATC 58.549 38.462 0.00 0.00 36.36 3.06
330 352 7.292591 ACCTATTACAATACTTAGGGCACATCT 59.707 37.037 0.00 0.00 36.36 2.90
332 354 4.156455 ACAATACTTAGGGCACATCTGG 57.844 45.455 0.00 0.00 0.00 3.86
333 355 3.780294 ACAATACTTAGGGCACATCTGGA 59.220 43.478 0.00 0.00 0.00 3.86
334 356 4.413520 ACAATACTTAGGGCACATCTGGAT 59.586 41.667 0.00 0.00 0.00 3.41
335 357 4.630644 ATACTTAGGGCACATCTGGATG 57.369 45.455 8.81 8.81 44.15 3.51
377 399 5.982890 ATATATGGCATTTACCCACTTGC 57.017 39.130 4.78 0.00 34.68 4.01
380 402 1.897423 GCATTTACCCACTTGCCCC 59.103 57.895 0.00 0.00 0.00 5.80
381 403 0.902516 GCATTTACCCACTTGCCCCA 60.903 55.000 0.00 0.00 0.00 4.96
382 404 0.894835 CATTTACCCACTTGCCCCAC 59.105 55.000 0.00 0.00 0.00 4.61
383 405 0.252057 ATTTACCCACTTGCCCCACC 60.252 55.000 0.00 0.00 0.00 4.61
384 406 1.656092 TTTACCCACTTGCCCCACCA 61.656 55.000 0.00 0.00 0.00 4.17
385 407 2.360439 TTACCCACTTGCCCCACCAC 62.360 60.000 0.00 0.00 0.00 4.16
386 408 3.902112 CCCACTTGCCCCACCACT 61.902 66.667 0.00 0.00 0.00 4.00
387 409 2.282462 CCACTTGCCCCACCACTC 60.282 66.667 0.00 0.00 0.00 3.51
388 410 2.515398 CACTTGCCCCACCACTCA 59.485 61.111 0.00 0.00 0.00 3.41
389 411 1.601759 CACTTGCCCCACCACTCAG 60.602 63.158 0.00 0.00 0.00 3.35
390 412 2.674380 CTTGCCCCACCACTCAGC 60.674 66.667 0.00 0.00 0.00 4.26
391 413 3.177884 TTGCCCCACCACTCAGCT 61.178 61.111 0.00 0.00 0.00 4.24
392 414 3.196207 TTGCCCCACCACTCAGCTC 62.196 63.158 0.00 0.00 0.00 4.09
393 415 3.325753 GCCCCACCACTCAGCTCT 61.326 66.667 0.00 0.00 0.00 4.09
394 416 2.985456 CCCCACCACTCAGCTCTC 59.015 66.667 0.00 0.00 0.00 3.20
395 417 2.664081 CCCCACCACTCAGCTCTCC 61.664 68.421 0.00 0.00 0.00 3.71
396 418 1.611851 CCCACCACTCAGCTCTCCT 60.612 63.158 0.00 0.00 0.00 3.69
397 419 1.612395 CCCACCACTCAGCTCTCCTC 61.612 65.000 0.00 0.00 0.00 3.71
398 420 1.612395 CCACCACTCAGCTCTCCTCC 61.612 65.000 0.00 0.00 0.00 4.30
399 421 0.614415 CACCACTCAGCTCTCCTCCT 60.614 60.000 0.00 0.00 0.00 3.69
400 422 0.324275 ACCACTCAGCTCTCCTCCTC 60.324 60.000 0.00 0.00 0.00 3.71
401 423 1.383456 CCACTCAGCTCTCCTCCTCG 61.383 65.000 0.00 0.00 0.00 4.63
402 424 0.679640 CACTCAGCTCTCCTCCTCGT 60.680 60.000 0.00 0.00 0.00 4.18
403 425 0.393808 ACTCAGCTCTCCTCCTCGTC 60.394 60.000 0.00 0.00 0.00 4.20
404 426 0.107214 CTCAGCTCTCCTCCTCGTCT 60.107 60.000 0.00 0.00 0.00 4.18
407 429 1.134220 CAGCTCTCCTCCTCGTCTACT 60.134 57.143 0.00 0.00 0.00 2.57
410 432 2.756207 GCTCTCCTCCTCGTCTACTTTT 59.244 50.000 0.00 0.00 0.00 2.27
455 477 3.255888 TGCCACTAGTTGTGTCTCACTAG 59.744 47.826 4.03 5.05 44.81 2.57
496 519 2.138596 ACAACTGCTCAAAAATGCCG 57.861 45.000 0.00 0.00 0.00 5.69
630 655 9.650371 CAAACTCGTTGACCATGTTATATAATG 57.350 33.333 0.00 0.00 39.87 1.90
649 674 7.915209 ATAATGAAATTACCCCTATACCCCA 57.085 36.000 0.00 0.00 42.43 4.96
650 675 6.813724 AATGAAATTACCCCTATACCCCAT 57.186 37.500 0.00 0.00 32.46 4.00
651 676 5.592587 TGAAATTACCCCTATACCCCATG 57.407 43.478 0.00 0.00 0.00 3.66
652 677 4.985583 TGAAATTACCCCTATACCCCATGT 59.014 41.667 0.00 0.00 0.00 3.21
654 679 3.728710 TTACCCCTATACCCCATGTCA 57.271 47.619 0.00 0.00 0.00 3.58
655 680 2.118403 ACCCCTATACCCCATGTCAG 57.882 55.000 0.00 0.00 0.00 3.51
656 681 0.693049 CCCCTATACCCCATGTCAGC 59.307 60.000 0.00 0.00 0.00 4.26
657 682 1.734655 CCCTATACCCCATGTCAGCT 58.265 55.000 0.00 0.00 0.00 4.24
658 683 1.625818 CCCTATACCCCATGTCAGCTC 59.374 57.143 0.00 0.00 0.00 4.09
659 684 2.614259 CCTATACCCCATGTCAGCTCT 58.386 52.381 0.00 0.00 0.00 4.09
660 685 2.564947 CCTATACCCCATGTCAGCTCTC 59.435 54.545 0.00 0.00 0.00 3.20
661 686 2.485966 ATACCCCATGTCAGCTCTCT 57.514 50.000 0.00 0.00 0.00 3.10
675 700 6.426633 TGTCAGCTCTCTTTATCTCTATCTCG 59.573 42.308 0.00 0.00 0.00 4.04
730 755 8.395633 GGAGTAAGCAAGCGAATAATTTTAGAA 58.604 33.333 0.00 0.00 0.00 2.10
764 789 3.368843 CGATGTTGGGATCAAGTGAGACT 60.369 47.826 0.00 0.00 32.92 3.24
816 842 4.620723 AGGTGACATGTTGGTCTATAGGA 58.379 43.478 0.00 0.00 38.61 2.94
822 848 9.391006 GTGACATGTTGGTCTATAGGAATTTTA 57.609 33.333 0.00 0.00 38.61 1.52
823 849 9.967451 TGACATGTTGGTCTATAGGAATTTTAA 57.033 29.630 0.00 0.00 38.61 1.52
882 908 4.789012 AATGGTGTCTAGTGGCATTTTG 57.211 40.909 0.00 0.00 0.00 2.44
895 922 1.862815 GCATTTTGAGCATGCGCCTAG 60.863 52.381 19.19 5.63 37.88 3.02
949 981 7.118390 CCCAATGACAAAACTAAGTAGTGAGAG 59.882 40.741 0.00 0.00 36.50 3.20
950 982 7.360438 CCAATGACAAAACTAAGTAGTGAGAGC 60.360 40.741 0.00 0.00 36.50 4.09
951 983 6.156748 TGACAAAACTAAGTAGTGAGAGCA 57.843 37.500 0.00 0.00 36.50 4.26
952 984 6.759272 TGACAAAACTAAGTAGTGAGAGCAT 58.241 36.000 0.00 0.00 36.50 3.79
954 986 8.364894 TGACAAAACTAAGTAGTGAGAGCATAA 58.635 33.333 0.00 0.00 36.50 1.90
955 987 9.204570 GACAAAACTAAGTAGTGAGAGCATAAA 57.795 33.333 0.00 0.00 36.50 1.40
956 988 9.726438 ACAAAACTAAGTAGTGAGAGCATAAAT 57.274 29.630 0.00 0.00 36.50 1.40
957 989 9.979270 CAAAACTAAGTAGTGAGAGCATAAATG 57.021 33.333 0.00 0.00 36.50 2.32
958 990 9.944376 AAAACTAAGTAGTGAGAGCATAAATGA 57.056 29.630 0.00 0.00 36.50 2.57
1027 1059 1.060729 TCACTCCCGGTTCAATTCCA 58.939 50.000 0.00 0.00 0.00 3.53
1029 1061 2.041081 TCACTCCCGGTTCAATTCCATT 59.959 45.455 0.00 0.00 0.00 3.16
1175 1216 3.428282 GTAAAGGCGGCCGGTGTG 61.428 66.667 29.38 0.00 0.00 3.82
1227 1268 3.391382 GCTCCACGGCACCTACCT 61.391 66.667 0.00 0.00 0.00 3.08
1334 1392 6.036735 GCGTTAGCAAAATCTGATAGGTTACA 59.963 38.462 0.00 0.00 44.35 2.41
1349 1644 9.560860 TGATAGGTTACAGATGATGGGTAATAT 57.439 33.333 0.00 0.00 30.56 1.28
1385 1680 8.435187 TGATAGCAAAATCTGATGGATTCTAGT 58.565 33.333 0.00 0.00 43.17 2.57
1386 1681 9.935241 GATAGCAAAATCTGATGGATTCTAGTA 57.065 33.333 0.00 0.00 43.17 1.82
1387 1682 9.941325 ATAGCAAAATCTGATGGATTCTAGTAG 57.059 33.333 0.00 0.00 43.17 2.57
1388 1683 8.027524 AGCAAAATCTGATGGATTCTAGTAGA 57.972 34.615 0.00 0.00 43.17 2.59
1410 1705 1.034838 TTGTTTTCCGGCTGTGTGCT 61.035 50.000 0.00 0.00 42.39 4.40
1421 1716 1.590238 GCTGTGTGCTGCTTATAGTCG 59.410 52.381 0.00 0.00 38.95 4.18
1431 1726 4.307432 CTGCTTATAGTCGTATTGTGGGG 58.693 47.826 0.00 0.00 0.00 4.96
1432 1727 3.962063 TGCTTATAGTCGTATTGTGGGGA 59.038 43.478 0.00 0.00 0.00 4.81
1434 1729 5.071250 TGCTTATAGTCGTATTGTGGGGAAT 59.929 40.000 0.00 0.00 0.00 3.01
1438 1733 4.295141 AGTCGTATTGTGGGGAATTTCA 57.705 40.909 0.00 0.00 0.00 2.69
1441 1736 4.881850 GTCGTATTGTGGGGAATTTCAGAT 59.118 41.667 0.00 0.00 0.00 2.90
1464 1759 5.627172 TCGATTATTTACTGCTGTTTGTGC 58.373 37.500 0.09 0.00 0.00 4.57
1477 1772 2.100749 TGTTTGTGCTGTCGAGAGAAGA 59.899 45.455 14.74 0.00 45.01 2.87
1494 1789 2.328819 AGATGCTGGCTGATTCTGTC 57.671 50.000 0.00 0.00 0.00 3.51
1516 1811 0.997932 CAGAATCTGACTCTGCGTGC 59.002 55.000 3.77 0.00 34.32 5.34
1552 1847 1.961277 CTCGCAGCCTTCAACCGTT 60.961 57.895 0.00 0.00 0.00 4.44
1581 1876 4.282449 TCCTAGCTATAGTGCGGCATAAAA 59.718 41.667 5.72 0.00 38.13 1.52
1592 1887 2.525055 CGGCATAAAATCCAACAACCG 58.475 47.619 0.00 0.00 0.00 4.44
1593 1888 2.094957 CGGCATAAAATCCAACAACCGT 60.095 45.455 0.00 0.00 33.64 4.83
1595 1890 3.924073 GGCATAAAATCCAACAACCGTTC 59.076 43.478 0.00 0.00 31.13 3.95
1603 1899 3.677190 TCCAACAACCGTTCGGATAATT 58.323 40.909 18.28 1.81 31.13 1.40
1710 2022 8.684386 TTAGATTGAATGTTTACTGGTGACAA 57.316 30.769 0.00 0.00 42.06 3.18
1715 2027 6.061441 TGAATGTTTACTGGTGACAAGATGT 58.939 36.000 0.00 0.00 42.06 3.06
1722 2034 0.883833 GGTGACAAGATGTTGGCTGG 59.116 55.000 10.19 0.00 42.95 4.85
1724 2036 0.178995 TGACAAGATGTTGGCTGGCA 60.179 50.000 10.19 0.00 42.95 4.92
1768 2082 1.372499 GTGCATGTGCTTGTGCTGG 60.372 57.895 6.55 0.00 41.78 4.85
1801 2115 1.203994 GGCTCAACGGTAGTGCTCTTA 59.796 52.381 0.00 0.00 0.00 2.10
1851 5732 8.632906 AACTTGTCAATTTTCAGATCATCTCT 57.367 30.769 0.00 0.00 33.14 3.10
1854 5735 9.985318 CTTGTCAATTTTCAGATCATCTCTAAC 57.015 33.333 0.00 0.00 31.13 2.34
1886 5767 2.036733 TGCCTTGACTTAACAGTAGCGT 59.963 45.455 0.00 0.00 31.22 5.07
1955 5837 8.633075 TTTCATAAATAGCACTAAAGCAATGC 57.367 30.769 0.00 0.00 39.74 3.56
2131 6039 4.520492 CACTCAACAAGCCTATGTCCTTTT 59.480 41.667 0.00 0.00 31.81 2.27
2302 6210 1.175983 TTTCACCCACGGCAATGGAC 61.176 55.000 7.04 0.00 43.02 4.02
2351 6259 1.077501 CGGTCATCCTGCATTGGGT 60.078 57.895 0.00 0.00 0.00 4.51
2376 6284 3.409026 ACATCCGCTTCCTCAATATCC 57.591 47.619 0.00 0.00 0.00 2.59
2385 6293 0.880278 CCTCAATATCCACACCGGCG 60.880 60.000 0.00 0.00 33.14 6.46
2404 6312 1.003839 TCTTCATCCGTGTGCACCC 60.004 57.895 15.69 0.48 0.00 4.61
2423 6331 2.579201 CCGTGCTTCGAGGACCAT 59.421 61.111 0.00 0.00 42.86 3.55
2426 6334 0.389817 CGTGCTTCGAGGACCATTCA 60.390 55.000 0.00 0.00 42.86 2.57
2492 6400 1.300775 CGCTGCTATCTGCCTCCTG 60.301 63.158 0.00 0.00 42.00 3.86
2597 6505 6.101734 TGAATGGCCCTTATGATCTTCTACTT 59.898 38.462 0.00 0.00 0.00 2.24
2717 6625 0.530650 ACAAGCACTGGACTCACACG 60.531 55.000 0.00 0.00 0.00 4.49
2852 6760 2.203788 AGTTCCTCCTCGTGGCCA 60.204 61.111 0.00 0.00 0.00 5.36
3159 7068 2.487934 GACTGCGGCAATATGATCTGT 58.512 47.619 3.44 0.00 0.00 3.41
3168 7077 3.881688 GCAATATGATCTGTGCAGAGGTT 59.118 43.478 11.47 0.00 41.33 3.50
3263 7172 2.159128 CCACATTGTCAGTTGTTGCCAA 60.159 45.455 0.00 0.00 0.00 4.52
3276 7185 1.944709 GTTGCCAACGTCTTTACTGGT 59.055 47.619 3.78 0.00 0.00 4.00
3284 7193 2.433239 ACGTCTTTACTGGTTCAGTGGT 59.567 45.455 10.46 0.00 45.01 4.16
3315 7224 1.202533 CCCGCTACCATCGTTCTCAAT 60.203 52.381 0.00 0.00 0.00 2.57
3340 7249 5.526115 TCGTTGGAATATAGTCGCTTTAGG 58.474 41.667 0.00 0.00 0.00 2.69
3358 7267 7.260603 GCTTTAGGACATAGAAATGTTTGCAT 58.739 34.615 0.00 0.00 46.49 3.96
3407 7321 8.865001 GCTATTCATCTTTCCAATATCTACGTC 58.135 37.037 0.00 0.00 0.00 4.34
3438 7353 1.535028 TGCTTTGCAGGTTATCACACG 59.465 47.619 0.00 0.00 33.32 4.49
3450 7365 1.308069 ATCACACGGCTTCATGTGGC 61.308 55.000 4.66 0.00 45.16 5.01
3458 7373 0.385974 GCTTCATGTGGCACGAACAC 60.386 55.000 13.77 1.17 39.26 3.32
3465 7380 1.376683 TGGCACGAACACTATGGCC 60.377 57.895 0.00 0.00 41.70 5.36
3478 7393 2.375174 ACTATGGCCACAGAAGGTTTGA 59.625 45.455 20.35 0.00 0.00 2.69
3579 7500 6.375455 TCAGAAATATTCTCCCTTTGAACTGC 59.625 38.462 0.00 0.00 38.11 4.40
3603 7524 5.122239 CGTTGAGCCTTTTATCATTCTGTCA 59.878 40.000 0.00 0.00 0.00 3.58
3614 7535 4.639078 TCATTCTGTCATTCAACTGGGA 57.361 40.909 0.00 0.00 0.00 4.37
3736 7671 1.737838 CCAGGTGCTCTAAATTGCGA 58.262 50.000 0.00 0.00 0.00 5.10
3748 7683 6.106877 TCTAAATTGCGAATGTAGAGTTGC 57.893 37.500 0.00 0.00 33.72 4.17
3774 7709 1.065199 CCATGTTCCAGGCTCAAGCTA 60.065 52.381 1.46 0.00 41.70 3.32
3789 7724 3.265737 TCAAGCTATTCAGGGCCAACTTA 59.734 43.478 6.18 0.00 0.00 2.24
3832 7770 8.855110 TCTGTTTTCTTCATTTTGGCAATAGTA 58.145 29.630 0.00 0.00 0.00 1.82
3836 7774 4.644685 TCTTCATTTTGGCAATAGTAGGGC 59.355 41.667 0.00 0.00 0.00 5.19
3848 7786 1.411041 AGTAGGGCGTAGAATGACCC 58.589 55.000 0.00 0.00 43.17 4.46
3869 7807 8.271458 TGACCCAGAGCTTCATTAATTATACAA 58.729 33.333 0.00 0.00 0.00 2.41
3898 7836 1.669115 CAGCTCACAACAGGGACCG 60.669 63.158 0.00 0.00 0.00 4.79
3900 7838 1.070786 GCTCACAACAGGGACCGAA 59.929 57.895 0.00 0.00 0.00 4.30
3906 7844 4.462133 TCACAACAGGGACCGAAAATAAA 58.538 39.130 0.00 0.00 0.00 1.40
3909 7847 5.048364 CACAACAGGGACCGAAAATAAATGA 60.048 40.000 0.00 0.00 0.00 2.57
3936 7874 6.766467 ACTACAACTTTGTCCTCGAGATTTTT 59.234 34.615 15.71 0.00 42.35 1.94
3945 7883 5.110598 GTCCTCGAGATTTTTAGGAAGGAC 58.889 45.833 15.71 4.89 39.77 3.85
3954 7892 5.757099 TTTTTAGGAAGGACCCTAGACAG 57.243 43.478 0.00 0.00 39.73 3.51
3974 7912 4.220602 ACAGTAAAGATTGCATTTGGGTCC 59.779 41.667 0.00 0.00 0.00 4.46
3977 7915 4.980339 AAAGATTGCATTTGGGTCCTTT 57.020 36.364 0.00 0.00 0.00 3.11
3978 7916 3.967332 AGATTGCATTTGGGTCCTTTG 57.033 42.857 0.00 0.00 0.00 2.77
3979 7917 2.027837 AGATTGCATTTGGGTCCTTTGC 60.028 45.455 0.00 0.00 0.00 3.68
3994 7932 1.334869 CTTTGCCTGTCACGAAGCTTT 59.665 47.619 0.00 0.00 0.00 3.51
3995 7933 2.248280 TTGCCTGTCACGAAGCTTTA 57.752 45.000 0.00 0.00 0.00 1.85
3996 7934 2.472695 TGCCTGTCACGAAGCTTTAT 57.527 45.000 0.00 0.00 0.00 1.40
3997 7935 3.603158 TGCCTGTCACGAAGCTTTATA 57.397 42.857 0.00 0.00 0.00 0.98
3998 7936 3.259064 TGCCTGTCACGAAGCTTTATAC 58.741 45.455 0.00 0.00 0.00 1.47
3999 7937 3.259064 GCCTGTCACGAAGCTTTATACA 58.741 45.455 0.00 2.69 0.00 2.29
4001 7939 4.201724 GCCTGTCACGAAGCTTTATACAAG 60.202 45.833 0.00 0.00 0.00 3.16
4002 7940 4.929808 CCTGTCACGAAGCTTTATACAAGT 59.070 41.667 0.00 0.00 0.00 3.16
4004 7942 6.034683 CCTGTCACGAAGCTTTATACAAGTAC 59.965 42.308 0.00 0.00 0.00 2.73
4006 7944 5.004156 GTCACGAAGCTTTATACAAGTACCG 59.996 44.000 0.00 0.00 0.00 4.02
4007 7945 5.097529 CACGAAGCTTTATACAAGTACCGA 58.902 41.667 0.00 0.00 0.00 4.69
4008 7946 5.747197 CACGAAGCTTTATACAAGTACCGAT 59.253 40.000 0.00 0.00 0.00 4.18
4009 7947 5.975939 ACGAAGCTTTATACAAGTACCGATC 59.024 40.000 0.00 0.00 0.00 3.69
4010 7948 6.183360 ACGAAGCTTTATACAAGTACCGATCT 60.183 38.462 0.00 0.00 0.00 2.75
4011 7949 6.360148 CGAAGCTTTATACAAGTACCGATCTC 59.640 42.308 0.00 0.00 0.00 2.75
4012 7950 5.759963 AGCTTTATACAAGTACCGATCTCG 58.240 41.667 0.00 0.00 39.44 4.04
4013 7951 4.382160 GCTTTATACAAGTACCGATCTCGC 59.618 45.833 0.00 0.00 38.18 5.03
4133 8080 1.763770 CCTTGGGTGCTGTCTCCTT 59.236 57.895 0.00 0.00 0.00 3.36
4153 8100 1.377856 GGGGGTTGCTCTCTTCTGC 60.378 63.158 0.00 0.00 0.00 4.26
4154 8101 1.682257 GGGGTTGCTCTCTTCTGCT 59.318 57.895 0.00 0.00 0.00 4.24
4155 8102 0.037447 GGGGTTGCTCTCTTCTGCTT 59.963 55.000 0.00 0.00 0.00 3.91
4156 8103 1.163554 GGGTTGCTCTCTTCTGCTTG 58.836 55.000 0.00 0.00 0.00 4.01
4157 8104 0.520847 GGTTGCTCTCTTCTGCTTGC 59.479 55.000 0.00 0.00 0.00 4.01
4158 8105 0.520847 GTTGCTCTCTTCTGCTTGCC 59.479 55.000 0.00 0.00 0.00 4.52
4187 8134 7.864108 TGAAACAATCATGAACTAGGGTATG 57.136 36.000 0.00 0.00 31.50 2.39
4197 8144 8.038944 TCATGAACTAGGGTATGAAGTTGTTAC 58.961 37.037 0.00 0.00 33.72 2.50
4202 8149 5.578157 AGGGTATGAAGTTGTTACCTGTT 57.422 39.130 9.58 0.00 36.45 3.16
4225 8174 9.579768 TGTTCGTAATAAAATTGATTCCCAATG 57.420 29.630 0.00 0.00 44.28 2.82
4322 8271 6.761242 CGTTCCTATAACCAATGATGAACTCA 59.239 38.462 0.00 0.00 38.53 3.41
4346 8295 9.692749 TCAATACTTTGTTCATATCCGTATCTC 57.307 33.333 0.00 0.00 34.32 2.75
4400 8349 0.542232 ACGGTACTTGCTCAGGGACT 60.542 55.000 0.00 0.00 43.88 3.85
4425 8374 4.646572 CAAGACTTAAGCTCCAGTTCCTT 58.353 43.478 1.29 0.00 0.00 3.36
4431 8380 1.343069 AGCTCCAGTTCCTTCTCGTT 58.657 50.000 0.00 0.00 0.00 3.85
4546 8497 2.125713 ATCGCAACCGTCGCATCA 60.126 55.556 0.00 0.00 35.54 3.07
4586 8548 2.160205 TCTGGATCGTCGTGTCTCTTT 58.840 47.619 0.00 0.00 0.00 2.52
4638 8600 5.553290 TCGACAGAAGACAGAGATTACAG 57.447 43.478 0.00 0.00 0.00 2.74
4659 8624 7.259290 ACAGTTTTCTCAAACACGTTATCAT 57.741 32.000 0.00 0.00 44.32 2.45
4663 8628 5.878332 TTCTCAAACACGTTATCATGCAT 57.122 34.783 0.00 0.00 0.00 3.96
4712 8686 2.304470 AGAGAAAAAGAGAGGGAGCACC 59.696 50.000 0.00 0.00 40.67 5.01
4750 8724 3.006940 CGGGGACAATTCGATGAAAGAA 58.993 45.455 0.00 0.00 0.00 2.52
4751 8725 3.438781 CGGGGACAATTCGATGAAAGAAA 59.561 43.478 0.00 0.00 0.00 2.52
4772 8746 5.806654 AAAATTATGCCTTGTGGACAGTT 57.193 34.783 0.00 0.00 34.57 3.16
4839 8813 8.729805 ACTCTGAAAAAGATGAATGGAGATAC 57.270 34.615 0.00 0.00 33.29 2.24
4858 8832 2.641305 ACTCTAACTATCGCTGGACGT 58.359 47.619 0.00 0.00 44.19 4.34
4920 8894 1.610624 CCCAAGCGGTACACAAGTGAT 60.611 52.381 7.28 0.00 0.00 3.06
4956 8930 5.862678 TTATTGTATCCCGACTCATCACA 57.137 39.130 0.00 0.00 0.00 3.58
4961 8935 2.153034 TCCCGACTCATCACATACCA 57.847 50.000 0.00 0.00 0.00 3.25
4966 8940 4.503817 CCCGACTCATCACATACCATGATT 60.504 45.833 0.00 0.00 34.49 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.389391 AGTGACCTCGTGTGACCTTG 59.611 55.000 0.00 0.00 30.41 3.61
7 8 1.371758 CGGACAGTGACCTCGTGTG 60.372 63.158 9.96 0.00 0.00 3.82
8 9 3.039988 CGGACAGTGACCTCGTGT 58.960 61.111 9.96 0.00 0.00 4.49
9 10 1.583495 TAGCGGACAGTGACCTCGTG 61.583 60.000 9.96 0.00 0.00 4.35
10 11 1.303074 TAGCGGACAGTGACCTCGT 60.303 57.895 9.96 0.00 0.00 4.18
11 12 1.136984 GTAGCGGACAGTGACCTCG 59.863 63.158 9.96 0.00 0.00 4.63
12 13 0.601558 TTGTAGCGGACAGTGACCTC 59.398 55.000 9.96 1.62 39.88 3.85
31 32 6.373216 TGTTCAACTAAAAACACACACTAGCT 59.627 34.615 0.00 0.00 30.73 3.32
32 33 6.548171 TGTTCAACTAAAAACACACACTAGC 58.452 36.000 0.00 0.00 30.73 3.42
38 39 5.155643 ACGGTTGTTCAACTAAAAACACAC 58.844 37.500 14.04 0.00 35.24 3.82
41 42 8.861101 CATAAAACGGTTGTTCAACTAAAAACA 58.139 29.630 14.04 0.00 37.31 2.83
126 147 0.112995 ATCCAACCATGCCCGCATAT 59.887 50.000 1.04 0.00 34.91 1.78
149 170 2.291024 ACGGATAGTGATATCGGAGCCT 60.291 50.000 9.09 0.00 32.97 4.58
168 189 3.642778 AACCTCGGATGCGACCACG 62.643 63.158 4.75 0.00 42.93 4.94
169 190 0.953960 AAAACCTCGGATGCGACCAC 60.954 55.000 4.75 0.00 0.00 4.16
173 194 2.849081 GGAAAAACCTCGGATGCGA 58.151 52.632 9.57 9.57 35.41 5.10
203 224 1.135083 AGCCGTCCGAGACAAATACAG 60.135 52.381 5.15 0.00 32.09 2.74
214 235 3.102052 GGACATTTATAAGCCGTCCGA 57.898 47.619 11.87 0.00 37.04 4.55
228 250 7.883311 AGCACATAGTAACTTGTTTAGGACATT 59.117 33.333 0.00 0.00 38.26 2.71
232 254 8.202137 GGATAGCACATAGTAACTTGTTTAGGA 58.798 37.037 0.00 0.00 0.00 2.94
249 271 1.167851 GCAAGCAACTGGATAGCACA 58.832 50.000 0.00 0.00 0.00 4.57
281 303 6.203530 GGTAATTAATACACGGCTTTACCCTC 59.796 42.308 0.00 0.00 36.14 4.30
283 305 6.057533 AGGTAATTAATACACGGCTTTACCC 58.942 40.000 0.00 0.00 38.44 3.69
308 330 6.101150 TCCAGATGTGCCCTAAGTATTGTAAT 59.899 38.462 0.00 0.00 0.00 1.89
311 333 3.780294 TCCAGATGTGCCCTAAGTATTGT 59.220 43.478 0.00 0.00 0.00 2.71
326 348 1.179152 TGCCAAAGCACATCCAGATG 58.821 50.000 6.09 6.09 46.52 2.90
351 373 8.531146 GCAAGTGGGTAAATGCCATATATATTT 58.469 33.333 0.00 0.00 32.73 1.40
352 374 8.066612 GCAAGTGGGTAAATGCCATATATATT 57.933 34.615 0.00 0.00 32.73 1.28
353 375 7.645058 GCAAGTGGGTAAATGCCATATATAT 57.355 36.000 0.00 0.00 32.73 0.86
355 377 5.982890 GCAAGTGGGTAAATGCCATATAT 57.017 39.130 0.00 0.00 32.73 0.86
362 384 0.902516 TGGGGCAAGTGGGTAAATGC 60.903 55.000 0.00 0.00 38.06 3.56
363 385 0.894835 GTGGGGCAAGTGGGTAAATG 59.105 55.000 0.00 0.00 0.00 2.32
364 386 0.252057 GGTGGGGCAAGTGGGTAAAT 60.252 55.000 0.00 0.00 0.00 1.40
365 387 1.154221 GGTGGGGCAAGTGGGTAAA 59.846 57.895 0.00 0.00 0.00 2.01
366 388 2.085562 TGGTGGGGCAAGTGGGTAA 61.086 57.895 0.00 0.00 0.00 2.85
367 389 2.450699 TGGTGGGGCAAGTGGGTA 60.451 61.111 0.00 0.00 0.00 3.69
368 390 4.218686 GTGGTGGGGCAAGTGGGT 62.219 66.667 0.00 0.00 0.00 4.51
369 391 3.868200 GAGTGGTGGGGCAAGTGGG 62.868 68.421 0.00 0.00 0.00 4.61
370 392 2.282462 GAGTGGTGGGGCAAGTGG 60.282 66.667 0.00 0.00 0.00 4.00
371 393 1.601759 CTGAGTGGTGGGGCAAGTG 60.602 63.158 0.00 0.00 0.00 3.16
372 394 2.839098 CTGAGTGGTGGGGCAAGT 59.161 61.111 0.00 0.00 0.00 3.16
373 395 2.674380 GCTGAGTGGTGGGGCAAG 60.674 66.667 0.00 0.00 0.00 4.01
374 396 3.177884 AGCTGAGTGGTGGGGCAA 61.178 61.111 0.00 0.00 0.00 4.52
375 397 3.640407 GAGCTGAGTGGTGGGGCA 61.640 66.667 0.00 0.00 0.00 5.36
376 398 3.322318 GAGAGCTGAGTGGTGGGGC 62.322 68.421 0.00 0.00 0.00 5.80
377 399 2.664081 GGAGAGCTGAGTGGTGGGG 61.664 68.421 0.00 0.00 0.00 4.96
378 400 1.611851 AGGAGAGCTGAGTGGTGGG 60.612 63.158 0.00 0.00 0.00 4.61
379 401 1.612395 GGAGGAGAGCTGAGTGGTGG 61.612 65.000 0.00 0.00 0.00 4.61
380 402 0.614415 AGGAGGAGAGCTGAGTGGTG 60.614 60.000 0.00 0.00 0.00 4.17
381 403 0.324275 GAGGAGGAGAGCTGAGTGGT 60.324 60.000 0.00 0.00 0.00 4.16
382 404 1.383456 CGAGGAGGAGAGCTGAGTGG 61.383 65.000 0.00 0.00 0.00 4.00
383 405 0.679640 ACGAGGAGGAGAGCTGAGTG 60.680 60.000 0.00 0.00 0.00 3.51
384 406 0.393808 GACGAGGAGGAGAGCTGAGT 60.394 60.000 0.00 0.00 0.00 3.41
385 407 0.107214 AGACGAGGAGGAGAGCTGAG 60.107 60.000 0.00 0.00 0.00 3.35
386 408 1.134340 GTAGACGAGGAGGAGAGCTGA 60.134 57.143 0.00 0.00 0.00 4.26
387 409 1.134220 AGTAGACGAGGAGGAGAGCTG 60.134 57.143 0.00 0.00 0.00 4.24
388 410 1.209621 AGTAGACGAGGAGGAGAGCT 58.790 55.000 0.00 0.00 0.00 4.09
389 411 2.047002 AAGTAGACGAGGAGGAGAGC 57.953 55.000 0.00 0.00 0.00 4.09
410 432 6.402226 GCATAAACGTTCAAAACCCAAACAAA 60.402 34.615 0.00 0.00 0.00 2.83
413 435 4.025563 GGCATAAACGTTCAAAACCCAAAC 60.026 41.667 0.00 0.00 0.00 2.93
424 446 4.708601 CACAACTAGTGGCATAAACGTTC 58.291 43.478 0.00 0.00 44.69 3.95
496 519 3.254060 TGAGCAAGCATCTTAGAACGAC 58.746 45.455 0.00 0.00 0.00 4.34
627 652 6.105589 ACATGGGGTATAGGGGTAATTTCATT 59.894 38.462 0.00 0.00 0.00 2.57
630 655 5.073965 TGACATGGGGTATAGGGGTAATTTC 59.926 44.000 0.00 0.00 0.00 2.17
634 659 3.593942 CTGACATGGGGTATAGGGGTAA 58.406 50.000 0.00 0.00 0.00 2.85
648 673 8.114331 AGATAGAGATAAAGAGAGCTGACATG 57.886 38.462 0.00 0.00 0.00 3.21
649 674 7.119699 CGAGATAGAGATAAAGAGAGCTGACAT 59.880 40.741 0.00 0.00 0.00 3.06
650 675 6.426633 CGAGATAGAGATAAAGAGAGCTGACA 59.573 42.308 0.00 0.00 0.00 3.58
651 676 6.426937 ACGAGATAGAGATAAAGAGAGCTGAC 59.573 42.308 0.00 0.00 0.00 3.51
652 677 6.530120 ACGAGATAGAGATAAAGAGAGCTGA 58.470 40.000 0.00 0.00 0.00 4.26
654 679 8.946085 CATTACGAGATAGAGATAAAGAGAGCT 58.054 37.037 0.00 0.00 0.00 4.09
655 680 8.941977 TCATTACGAGATAGAGATAAAGAGAGC 58.058 37.037 0.00 0.00 0.00 4.09
675 700 4.497291 TGGGGTCCACACTTATCATTAC 57.503 45.455 0.00 0.00 0.00 1.89
739 764 3.750371 TCACTTGATCCCAACATCGTTT 58.250 40.909 0.00 0.00 0.00 3.60
744 769 3.584406 TGAGTCTCACTTGATCCCAACAT 59.416 43.478 0.00 0.00 0.00 2.71
779 804 5.136068 TGTCACCTCTTCCTCTATCTCAT 57.864 43.478 0.00 0.00 0.00 2.90
791 817 5.129485 CCTATAGACCAACATGTCACCTCTT 59.871 44.000 0.00 0.00 37.73 2.85
796 822 7.865706 AAATTCCTATAGACCAACATGTCAC 57.134 36.000 0.00 0.00 37.73 3.67
850 876 6.183360 CCACTAGACACCATTACTATCAGCTT 60.183 42.308 0.00 0.00 0.00 3.74
911 943 3.226777 TGTCATTGGGAATTTCAACCGT 58.773 40.909 0.00 0.00 0.00 4.83
913 945 6.054941 AGTTTTGTCATTGGGAATTTCAACC 58.945 36.000 0.00 0.00 0.00 3.77
925 957 7.171508 TGCTCTCACTACTTAGTTTTGTCATTG 59.828 37.037 0.00 0.00 33.46 2.82
1027 1059 0.771755 GCCTAGGGATTTCGGGGAAT 59.228 55.000 11.72 0.00 0.00 3.01
1029 1061 1.768888 GGCCTAGGGATTTCGGGGA 60.769 63.158 11.72 0.00 0.00 4.81
1133 1174 3.303135 AGGAAGGTCGCACGCTGA 61.303 61.111 0.00 0.00 0.00 4.26
1175 1216 4.445545 CTTTTGGTCGCCGCTCGC 62.446 66.667 0.00 0.00 38.27 5.03
1177 1218 4.103103 GCCTTTTGGTCGCCGCTC 62.103 66.667 0.00 0.00 42.99 5.03
1189 1230 3.670377 GACTTTGCGCCCGCCTTT 61.670 61.111 4.18 0.00 41.09 3.11
1334 1392 9.874205 CACAAACAAAAATATTACCCATCATCT 57.126 29.630 0.00 0.00 0.00 2.90
1349 1644 8.939201 TCAGATTTTGCTATCACAAACAAAAA 57.061 26.923 4.13 0.00 43.07 1.94
1350 1645 8.980610 CATCAGATTTTGCTATCACAAACAAAA 58.019 29.630 0.00 0.00 43.72 2.44
1356 1651 7.558807 AGAATCCATCAGATTTTGCTATCACAA 59.441 33.333 0.00 0.00 45.52 3.33
1385 1680 3.886505 ACACAGCCGGAAAACAAAATCTA 59.113 39.130 5.05 0.00 0.00 1.98
1386 1681 2.693074 ACACAGCCGGAAAACAAAATCT 59.307 40.909 5.05 0.00 0.00 2.40
1387 1682 2.794350 CACACAGCCGGAAAACAAAATC 59.206 45.455 5.05 0.00 0.00 2.17
1388 1683 2.820330 CACACAGCCGGAAAACAAAAT 58.180 42.857 5.05 0.00 0.00 1.82
1410 1705 3.962063 TCCCCACAATACGACTATAAGCA 59.038 43.478 0.00 0.00 0.00 3.91
1421 1716 5.123227 TCGATCTGAAATTCCCCACAATAC 58.877 41.667 0.00 0.00 0.00 1.89
1431 1726 9.591404 CAGCAGTAAATAATCGATCTGAAATTC 57.409 33.333 12.33 0.00 0.00 2.17
1432 1727 9.113838 ACAGCAGTAAATAATCGATCTGAAATT 57.886 29.630 12.33 0.43 0.00 1.82
1434 1729 8.492673 AACAGCAGTAAATAATCGATCTGAAA 57.507 30.769 12.33 0.00 0.00 2.69
1438 1733 7.677276 GCACAAACAGCAGTAAATAATCGATCT 60.677 37.037 0.00 0.00 0.00 2.75
1441 1736 5.411361 AGCACAAACAGCAGTAAATAATCGA 59.589 36.000 0.00 0.00 0.00 3.59
1464 1759 1.802136 GCCAGCATCTTCTCTCGACAG 60.802 57.143 0.00 0.00 0.00 3.51
1477 1772 2.026542 TGAAGACAGAATCAGCCAGCAT 60.027 45.455 0.00 0.00 0.00 3.79
1494 1789 2.922387 CACGCAGAGTCAGATTCTGAAG 59.078 50.000 23.63 18.04 42.46 3.02
1507 1802 4.731503 GCACAAGCGCACGCAGAG 62.732 66.667 18.24 8.92 44.88 3.35
1581 1876 3.337694 TTATCCGAACGGTTGTTGGAT 57.662 42.857 17.72 17.72 42.91 3.41
1647 1945 2.332063 ATGAGCAGAACATAACGGGG 57.668 50.000 0.00 0.00 0.00 5.73
1710 2022 2.362120 GCCTGCCAGCCAACATCT 60.362 61.111 0.00 0.00 0.00 2.90
1715 2027 3.573229 AGTCAGCCTGCCAGCCAA 61.573 61.111 0.00 0.00 0.00 4.52
1722 2034 1.024271 TTTGACAACAGTCAGCCTGC 58.976 50.000 0.00 0.00 45.68 4.85
1724 2036 3.567164 CAGATTTTGACAACAGTCAGCCT 59.433 43.478 0.00 0.00 42.72 4.58
1768 2082 2.463876 GTTGAGCCAAAAGAAGCACAC 58.536 47.619 0.00 0.00 29.07 3.82
1801 2115 3.646162 TCATACCCTATCCGAAGTTGCAT 59.354 43.478 0.00 0.00 0.00 3.96
1886 5767 9.823647 TTTTTCTTCTAATTTTGCCATGTACAA 57.176 25.926 0.00 0.00 0.00 2.41
1955 5837 4.046462 CACAACTCAAACTTGCTCAATGG 58.954 43.478 0.00 0.00 0.00 3.16
2007 5891 6.543430 AGACTTATCAGCTGAGTTCTGATT 57.457 37.500 22.96 4.95 45.99 2.57
2131 6039 1.219124 GCATTCAGCGACTCCCAGA 59.781 57.895 0.00 0.00 0.00 3.86
2255 6163 3.050354 AACCACACCACGGCCAAGA 62.050 57.895 2.24 0.00 0.00 3.02
2267 6175 4.555709 AAGCGCGGGTCAACCACA 62.556 61.111 8.83 0.00 40.22 4.17
2302 6210 0.748005 ATTGCCCTCCGGAAACATCG 60.748 55.000 5.23 0.00 25.02 3.84
2339 6247 1.302949 GTAGCCACCCAATGCAGGA 59.697 57.895 0.00 0.00 0.00 3.86
2351 6259 0.975556 TGAGGAAGCGGATGTAGCCA 60.976 55.000 0.00 0.00 34.64 4.75
2376 6284 2.100631 GGATGAAGACGCCGGTGTG 61.101 63.158 28.44 7.22 0.00 3.82
2385 6293 1.298859 GGGTGCACACGGATGAAGAC 61.299 60.000 20.43 0.00 0.00 3.01
2597 6505 4.077184 GCCGTGTGGACCATCCGA 62.077 66.667 15.11 0.00 40.17 4.55
2717 6625 0.179702 TGCCACTCATCATCCAGCTC 59.820 55.000 0.00 0.00 0.00 4.09
2852 6760 2.779755 TCATTTGTGGCGGTGTAGAT 57.220 45.000 0.00 0.00 0.00 1.98
3159 7068 3.059982 CGACCAGGAACCTCTGCA 58.940 61.111 0.00 0.00 33.64 4.41
3168 7077 2.430248 TCACATAGTAGCGACCAGGA 57.570 50.000 0.00 0.00 0.00 3.86
3263 7172 2.433239 ACCACTGAACCAGTAAAGACGT 59.567 45.455 0.00 0.00 43.43 4.34
3284 7193 0.035820 GGTAGCGGGTCCAAATGTGA 60.036 55.000 0.00 0.00 0.00 3.58
3315 7224 4.913335 AAGCGACTATATTCCAACGAGA 57.087 40.909 0.00 0.00 0.00 4.04
3358 7267 4.322273 CCTTCAACTGATCACTGCAGACTA 60.322 45.833 23.35 5.21 36.86 2.59
3407 7321 1.220529 TGCAAAGCAGAGACGTTCAG 58.779 50.000 0.00 0.00 33.32 3.02
3438 7353 1.210155 GTTCGTGCCACATGAAGCC 59.790 57.895 0.00 0.00 39.60 4.35
3450 7365 1.078709 CTGTGGCCATAGTGTTCGTG 58.921 55.000 20.76 0.00 0.00 4.35
3458 7373 3.012518 CTCAAACCTTCTGTGGCCATAG 58.987 50.000 22.80 22.80 0.00 2.23
3465 7380 6.615088 CCAAATACATCTCAAACCTTCTGTG 58.385 40.000 0.00 0.00 0.00 3.66
3478 7393 4.559300 GCAAACACACAGCCAAATACATCT 60.559 41.667 0.00 0.00 0.00 2.90
3579 7500 5.122239 TGACAGAATGATAAAAGGCTCAACG 59.878 40.000 0.00 0.00 39.69 4.10
3603 7524 2.949447 AGCAGTGTTTCCCAGTTGAAT 58.051 42.857 0.00 0.00 0.00 2.57
3629 7550 1.274728 AGTCACAGGCAGAAGCTACAG 59.725 52.381 0.00 0.00 41.70 2.74
3736 7671 5.001232 ACATGGTAAACGCAACTCTACATT 58.999 37.500 0.00 0.00 0.00 2.71
3748 7683 1.737793 GAGCCTGGAACATGGTAAACG 59.262 52.381 0.00 0.00 38.20 3.60
3774 7709 2.619074 GCAGTCTAAGTTGGCCCTGAAT 60.619 50.000 0.00 0.00 0.00 2.57
3789 7724 5.730296 AACAGAGTGTAACATAGCAGTCT 57.270 39.130 0.00 0.00 43.75 3.24
3832 7770 0.325296 TCTGGGTCATTCTACGCCCT 60.325 55.000 0.00 0.00 41.59 5.19
3836 7774 2.166459 TGAAGCTCTGGGTCATTCTACG 59.834 50.000 0.00 0.00 0.00 3.51
3869 7807 6.823689 CCCTGTTGTGAGCTGTATTATAACTT 59.176 38.462 0.00 0.00 0.00 2.66
3887 7825 5.637006 TCATTTATTTTCGGTCCCTGTTG 57.363 39.130 0.00 0.00 0.00 3.33
3906 7844 5.607477 TCGAGGACAAAGTTGTAGTTTCAT 58.393 37.500 0.00 0.00 42.43 2.57
3909 7847 5.272283 TCTCGAGGACAAAGTTGTAGTTT 57.728 39.130 13.56 0.00 42.43 2.66
3927 7865 4.489306 AGGGTCCTTCCTAAAAATCTCG 57.511 45.455 0.00 0.00 34.92 4.04
3936 7874 5.254737 TCTTTACTGTCTAGGGTCCTTCCTA 59.745 44.000 0.00 0.00 38.30 2.94
3945 7883 6.183360 CCAAATGCAATCTTTACTGTCTAGGG 60.183 42.308 0.00 0.00 0.00 3.53
3954 7892 5.405935 AAGGACCCAAATGCAATCTTTAC 57.594 39.130 0.00 0.00 0.00 2.01
3974 7912 0.947244 AAGCTTCGTGACAGGCAAAG 59.053 50.000 0.00 0.00 0.00 2.77
3977 7915 2.472695 ATAAAGCTTCGTGACAGGCA 57.527 45.000 0.00 0.00 0.00 4.75
3978 7916 3.259064 TGTATAAAGCTTCGTGACAGGC 58.741 45.455 0.00 0.00 0.00 4.85
3979 7917 4.929808 ACTTGTATAAAGCTTCGTGACAGG 59.070 41.667 0.00 5.46 0.00 4.00
3994 7932 3.748083 AGGCGAGATCGGTACTTGTATA 58.252 45.455 4.18 0.00 40.23 1.47
3995 7933 2.584236 AGGCGAGATCGGTACTTGTAT 58.416 47.619 4.18 0.00 40.23 2.29
3996 7934 2.048444 AGGCGAGATCGGTACTTGTA 57.952 50.000 4.18 0.00 40.23 2.41
3997 7935 1.183549 AAGGCGAGATCGGTACTTGT 58.816 50.000 4.18 0.00 40.23 3.16
3998 7936 1.927174 CAAAGGCGAGATCGGTACTTG 59.073 52.381 4.18 0.00 40.23 3.16
3999 7937 1.549170 ACAAAGGCGAGATCGGTACTT 59.451 47.619 4.18 0.00 40.23 2.24
4001 7939 1.134560 AGACAAAGGCGAGATCGGTAC 59.865 52.381 4.18 0.00 40.23 3.34
4002 7940 1.404391 GAGACAAAGGCGAGATCGGTA 59.596 52.381 4.18 0.00 40.23 4.02
4004 7942 0.457851 AGAGACAAAGGCGAGATCGG 59.542 55.000 4.18 0.00 40.23 4.18
4006 7944 1.134848 AGCAGAGACAAAGGCGAGATC 60.135 52.381 0.00 0.00 0.00 2.75
4007 7945 0.901124 AGCAGAGACAAAGGCGAGAT 59.099 50.000 0.00 0.00 0.00 2.75
4008 7946 0.037882 CAGCAGAGACAAAGGCGAGA 60.038 55.000 0.00 0.00 0.00 4.04
4009 7947 1.633852 GCAGCAGAGACAAAGGCGAG 61.634 60.000 0.00 0.00 0.00 5.03
4010 7948 1.669115 GCAGCAGAGACAAAGGCGA 60.669 57.895 0.00 0.00 0.00 5.54
4011 7949 1.509644 TTGCAGCAGAGACAAAGGCG 61.510 55.000 0.00 0.00 0.00 5.52
4012 7950 0.670162 TTTGCAGCAGAGACAAAGGC 59.330 50.000 0.00 0.00 0.00 4.35
4013 7951 2.031333 GTCTTTGCAGCAGAGACAAAGG 60.031 50.000 31.65 2.79 46.51 3.11
4142 8089 2.105466 CGGGCAAGCAGAAGAGAGC 61.105 63.158 0.00 0.00 0.00 4.09
4150 8097 1.007387 GTTTCAACCGGGCAAGCAG 60.007 57.895 6.32 0.00 0.00 4.24
4153 8100 1.339610 TGATTGTTTCAACCGGGCAAG 59.660 47.619 6.32 0.00 0.00 4.01
4154 8101 1.403814 TGATTGTTTCAACCGGGCAA 58.596 45.000 6.32 1.30 0.00 4.52
4155 8102 1.271934 CATGATTGTTTCAACCGGGCA 59.728 47.619 6.32 0.00 38.03 5.36
4156 8103 1.543802 TCATGATTGTTTCAACCGGGC 59.456 47.619 6.32 0.00 38.03 6.13
4157 8104 3.255642 AGTTCATGATTGTTTCAACCGGG 59.744 43.478 6.32 0.00 38.03 5.73
4158 8105 4.503741 AGTTCATGATTGTTTCAACCGG 57.496 40.909 0.00 0.00 38.03 5.28
4197 8144 7.767261 TGGGAATCAATTTTATTACGAACAGG 58.233 34.615 0.00 0.00 0.00 4.00
4202 8149 8.744652 ACACATTGGGAATCAATTTTATTACGA 58.255 29.630 0.00 0.00 43.04 3.43
4219 8168 1.880819 GCAAGCCTCCACACATTGGG 61.881 60.000 0.00 0.00 46.92 4.12
4225 8174 2.042686 TATCATGCAAGCCTCCACAC 57.957 50.000 0.00 0.00 0.00 3.82
4297 8246 6.761242 TGAGTTCATCATTGGTTATAGGAACG 59.239 38.462 0.00 0.00 38.62 3.95
4400 8349 4.322801 GGAACTGGAGCTTAAGTCTTGCTA 60.323 45.833 4.02 0.00 37.16 3.49
4529 8480 2.125713 TGATGCGACGGTTGCGAT 60.126 55.556 15.25 9.83 34.24 4.58
4546 8497 1.265454 GGAGACATCGGTTCCAGGGT 61.265 60.000 0.00 0.00 0.00 4.34
4586 8548 7.496156 ACAGGGGGCTTATATATATCTCCTA 57.504 40.000 0.00 0.00 0.00 2.94
4638 8600 5.912396 TGCATGATAACGTGTTTGAGAAAAC 59.088 36.000 0.00 0.00 35.65 2.43
4659 8624 0.320050 TCGCTGGTTGTCTACATGCA 59.680 50.000 0.00 0.00 0.00 3.96
4663 8628 0.243907 GCTCTCGCTGGTTGTCTACA 59.756 55.000 0.00 0.00 0.00 2.74
4695 8669 2.868899 CAAGGTGCTCCCTCTCTTTTT 58.131 47.619 0.00 0.00 45.47 1.94
4739 8713 7.541783 CACAAGGCATAATTTTTCTTTCATCGA 59.458 33.333 0.00 0.00 0.00 3.59
4750 8724 5.070313 ACAACTGTCCACAAGGCATAATTTT 59.930 36.000 0.00 0.00 33.74 1.82
4751 8725 4.588528 ACAACTGTCCACAAGGCATAATTT 59.411 37.500 0.00 0.00 33.74 1.82
4772 8746 4.020573 CCTCAGTATGGAGTTTGTGGTACA 60.021 45.833 0.00 0.00 36.16 2.90
4839 8813 2.612672 TCACGTCCAGCGATAGTTAGAG 59.387 50.000 0.00 0.00 44.77 2.43
4858 8832 5.247337 TCCAGTACCAACAATCACTGTATCA 59.753 40.000 0.00 0.00 37.23 2.15
4920 8894 6.716628 GGGATACAATAAAGCATCCTCAATCA 59.283 38.462 0.00 0.00 37.65 2.57


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

AutoCloner maintained by Alex Coulton.