Multiple sequence alignment - TraesCS4B01G260300

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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 TraesCS4B01G260300 chr4B 100.000 5931 0 0 1 5931 527275360 527281290 0.000000e+00 10953.0
1 TraesCS4B01G260300 chr4D 92.352 5531 258 71 1 5482 429464394 429469808 0.000000e+00 7718.0
2 TraesCS4B01G260300 chr4D 91.892 148 6 3 5790 5931 429469996 429470143 1.010000e-47 202.0
3 TraesCS4B01G260300 chr4D 100.000 58 0 0 5720 5777 429469953 429470010 2.260000e-19 108.0
4 TraesCS4B01G260300 chr4D 95.000 40 1 1 5678 5717 473169099 473169137 1.780000e-05 62.1
5 TraesCS4B01G260300 chr4A 90.007 3032 162 65 2649 5627 37065456 37062513 0.000000e+00 3790.0
6 TraesCS4B01G260300 chr4A 93.612 1315 66 8 511 1816 37067662 37066357 0.000000e+00 1947.0
7 TraesCS4B01G260300 chr4A 94.595 814 19 9 1814 2606 37066275 37065466 0.000000e+00 1236.0
8 TraesCS4B01G260300 chr4A 93.396 106 5 2 5828 5931 37062406 37062301 7.960000e-34 156.0
9 TraesCS4B01G260300 chr4A 97.619 42 0 1 5676 5717 13521846 13521886 2.970000e-08 71.3
10 TraesCS4B01G260300 chr4A 97.297 37 0 1 5681 5717 358147970 358147935 1.780000e-05 62.1
11 TraesCS4B01G260300 chr3A 80.795 604 79 20 2847 3436 387283127 387283707 7.060000e-119 438.0
12 TraesCS4B01G260300 chr7B 80.198 606 79 25 2847 3436 351927612 351927032 3.310000e-112 416.0
13 TraesCS4B01G260300 chr3D 83.158 380 47 8 2847 3219 292037572 292037203 1.230000e-86 331.0
14 TraesCS4B01G260300 chr1D 79.189 370 50 12 2997 3365 46639592 46639249 1.290000e-56 231.0
15 TraesCS4B01G260300 chrUn 78.544 261 48 8 2750 3009 101291153 101291406 1.320000e-36 165.0
16 TraesCS4B01G260300 chrUn 100.000 33 0 0 5685 5717 15657159 15657127 1.780000e-05 62.1
17 TraesCS4B01G260300 chr1B 97.368 38 0 1 5680 5717 171407781 171407817 4.960000e-06 63.9
18 TraesCS4B01G260300 chr7D 91.304 46 3 1 5672 5717 620475434 620475390 1.780000e-05 62.1
19 TraesCS4B01G260300 chr6D 97.297 37 0 1 5681 5717 460463950 460463915 1.780000e-05 62.1
20 TraesCS4B01G260300 chr5B 97.222 36 0 1 5681 5716 275312041 275312007 6.420000e-05 60.2
21 TraesCS4B01G260300 chr5B 91.111 45 1 3 5681 5724 665750687 665750729 2.310000e-04 58.4


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 TraesCS4B01G260300 chr4B 527275360 527281290 5930 False 10953.00 10953 100.0000 1 5931 1 chr4B.!!$F1 5930
1 TraesCS4B01G260300 chr4D 429464394 429470143 5749 False 2676.00 7718 94.7480 1 5931 3 chr4D.!!$F2 5930
2 TraesCS4B01G260300 chr4A 37062301 37067662 5361 True 1782.25 3790 92.9025 511 5931 4 chr4A.!!$R2 5420
3 TraesCS4B01G260300 chr3A 387283127 387283707 580 False 438.00 438 80.7950 2847 3436 1 chr3A.!!$F1 589
4 TraesCS4B01G260300 chr7B 351927032 351927612 580 True 416.00 416 80.1980 2847 3436 1 chr7B.!!$R1 589

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
544 561 0.038526 AACCTTGACGTAGCACTCCG 60.039 55.0 0.00 0.00 0.00 4.63 F
1490 1516 0.028902 TCGACTACACATGGCGATCG 59.971 55.0 11.69 11.69 0.00 3.69 F
2967 3110 0.183492 TCTCCAGCCACTGCAACTTT 59.817 50.0 0.00 0.00 41.13 2.66 F
3585 3743 0.749454 GGGAATGACGGAGCAATGCT 60.749 55.0 7.79 7.79 43.88 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 2379 1.461127 GAGGCTGTAGACGCACAAAAG 59.539 52.381 0.00 0.0 0.00 2.27 R
3209 3360 0.723414 CTACTGTTGCATGTGCCTCG 59.277 55.000 2.07 0.0 41.18 4.63 R
4888 5084 0.764271 TCACCAGCCAGTCAATGACA 59.236 50.000 16.38 0.0 34.60 3.58 R
5188 5392 2.229543 TGCACAAAACCATGCAGAGATC 59.770 45.455 0.00 0.0 46.63 2.75 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 3.055530 TCCTTCTCTTCCACATCAAGAGC 60.056 47.826 4.81 0.00 44.56 4.09
129 130 4.454678 TCTGTTTGTCTCTTGTGCTTCAT 58.545 39.130 0.00 0.00 0.00 2.57
198 199 3.262420 CTCTGGTAATGAACTTGTCCGG 58.738 50.000 0.00 0.00 0.00 5.14
252 253 5.862845 AGTGAGTGACTGAATTTCATGAGT 58.137 37.500 0.00 0.00 31.75 3.41
283 284 0.668706 CGGAGCGGTCATCCATCATC 60.669 60.000 17.59 0.00 36.57 2.92
306 307 4.252971 TGTTGGTTAGGAGAACGAGAAG 57.747 45.455 0.00 0.00 0.00 2.85
323 324 2.628178 AGAAGACGAGTCATGTTGGTCA 59.372 45.455 13.95 0.00 0.00 4.02
374 375 4.082845 TGGTGACAAACTGAGGACAAAAA 58.917 39.130 0.00 0.00 37.44 1.94
418 435 3.057969 CAATAGTGCACAGGGACAAGA 57.942 47.619 21.04 0.00 37.91 3.02
419 436 3.411446 CAATAGTGCACAGGGACAAGAA 58.589 45.455 21.04 0.00 37.91 2.52
420 437 2.839486 TAGTGCACAGGGACAAGAAG 57.161 50.000 21.04 0.00 37.91 2.85
421 438 1.131638 AGTGCACAGGGACAAGAAGA 58.868 50.000 21.04 0.00 37.91 2.87
422 439 1.490490 AGTGCACAGGGACAAGAAGAA 59.510 47.619 21.04 0.00 37.91 2.52
423 440 1.876156 GTGCACAGGGACAAGAAGAAG 59.124 52.381 13.17 0.00 35.12 2.85
424 441 1.768275 TGCACAGGGACAAGAAGAAGA 59.232 47.619 0.00 0.00 0.00 2.87
425 442 2.373169 TGCACAGGGACAAGAAGAAGAT 59.627 45.455 0.00 0.00 0.00 2.40
426 443 3.582647 TGCACAGGGACAAGAAGAAGATA 59.417 43.478 0.00 0.00 0.00 1.98
427 444 4.041567 TGCACAGGGACAAGAAGAAGATAA 59.958 41.667 0.00 0.00 0.00 1.75
428 445 4.393371 GCACAGGGACAAGAAGAAGATAAC 59.607 45.833 0.00 0.00 0.00 1.89
429 446 5.551233 CACAGGGACAAGAAGAAGATAACA 58.449 41.667 0.00 0.00 0.00 2.41
430 447 5.641209 CACAGGGACAAGAAGAAGATAACAG 59.359 44.000 0.00 0.00 0.00 3.16
431 448 5.308237 ACAGGGACAAGAAGAAGATAACAGT 59.692 40.000 0.00 0.00 0.00 3.55
432 449 6.497259 ACAGGGACAAGAAGAAGATAACAGTA 59.503 38.462 0.00 0.00 0.00 2.74
433 450 6.814146 CAGGGACAAGAAGAAGATAACAGTAC 59.186 42.308 0.00 0.00 0.00 2.73
434 451 6.726764 AGGGACAAGAAGAAGATAACAGTACT 59.273 38.462 0.00 0.00 0.00 2.73
435 452 7.235812 AGGGACAAGAAGAAGATAACAGTACTT 59.764 37.037 0.00 0.00 0.00 2.24
436 453 7.332182 GGGACAAGAAGAAGATAACAGTACTTG 59.668 40.741 0.00 0.00 38.34 3.16
458 475 6.603237 TGTGTAGACATGAAGAACAACAAG 57.397 37.500 0.00 0.00 0.00 3.16
461 478 4.825546 AGACATGAAGAACAACAAGCTG 57.174 40.909 0.00 0.00 0.00 4.24
462 479 4.454678 AGACATGAAGAACAACAAGCTGA 58.545 39.130 0.00 0.00 0.00 4.26
502 519 9.540538 AGAGAGCTTATATACATGGATTACAGT 57.459 33.333 0.00 0.00 0.00 3.55
544 561 0.038526 AACCTTGACGTAGCACTCCG 60.039 55.000 0.00 0.00 0.00 4.63
545 562 1.805945 CCTTGACGTAGCACTCCGC 60.806 63.158 0.00 0.00 42.91 5.54
555 572 2.642139 AGCACTCCGCAAATTCATTG 57.358 45.000 0.00 0.00 46.13 2.82
559 576 0.526096 CTCCGCAAATTCATTGGCCG 60.526 55.000 0.00 0.00 39.54 6.13
614 632 4.871871 TCACTCAGAGAAGGAGTCCTAT 57.128 45.455 13.43 4.04 43.47 2.57
956 980 4.626081 CCGCGACCATCCATCCCC 62.626 72.222 8.23 0.00 0.00 4.81
958 982 2.919043 GCGACCATCCATCCCCTT 59.081 61.111 0.00 0.00 0.00 3.95
960 984 1.451936 CGACCATCCATCCCCTTCC 59.548 63.158 0.00 0.00 0.00 3.46
961 985 1.056700 CGACCATCCATCCCCTTCCT 61.057 60.000 0.00 0.00 0.00 3.36
962 986 0.767998 GACCATCCATCCCCTTCCTC 59.232 60.000 0.00 0.00 0.00 3.71
963 987 0.699231 ACCATCCATCCCCTTCCTCC 60.699 60.000 0.00 0.00 0.00 4.30
1054 1078 2.676750 CGCAGGTATGGTTCTACAAGCA 60.677 50.000 0.00 0.00 44.02 3.91
1063 1087 1.026182 TTCTACAAGCATGCGCCCTG 61.026 55.000 13.01 10.93 39.83 4.45
1082 1106 2.188469 GCGGGCGGGTTCAGATTA 59.812 61.111 0.00 0.00 0.00 1.75
1100 1124 0.109458 TATCGAGTTTGACGCGCTGT 60.109 50.000 5.73 5.01 41.15 4.40
1277 1301 0.531974 GACGGTTGGCACTTGACAGA 60.532 55.000 0.00 0.00 32.66 3.41
1340 1364 6.146021 CAGCATGGTGTTATTTGTTTTTCTCC 59.854 38.462 16.80 0.00 0.00 3.71
1341 1365 5.988561 GCATGGTGTTATTTGTTTTTCTCCA 59.011 36.000 0.00 0.00 0.00 3.86
1342 1366 6.650390 GCATGGTGTTATTTGTTTTTCTCCAT 59.350 34.615 0.00 0.00 33.09 3.41
1344 1368 7.595819 TGGTGTTATTTGTTTTTCTCCATCT 57.404 32.000 0.00 0.00 0.00 2.90
1345 1369 7.432869 TGGTGTTATTTGTTTTTCTCCATCTG 58.567 34.615 0.00 0.00 0.00 2.90
1400 1424 5.820947 CCTTATGGTTATTTTACGTGAGCCT 59.179 40.000 0.00 0.00 0.00 4.58
1419 1443 5.463154 AGCCTAGTTCAGATTATGGAGTCT 58.537 41.667 0.00 0.00 0.00 3.24
1457 1483 4.157656 GCTTTGTGGTATCTTTGTATGGCA 59.842 41.667 0.00 0.00 0.00 4.92
1490 1516 0.028902 TCGACTACACATGGCGATCG 59.971 55.000 11.69 11.69 0.00 3.69
1507 1533 4.376861 GCGATCGCATTATTGATTGAACAC 59.623 41.667 33.89 0.00 41.49 3.32
1574 1600 4.020218 AGAGATGAAGGGACACGAAATTCA 60.020 41.667 0.00 0.00 34.64 2.57
1587 1613 9.226345 GGACACGAAATTCATTCTTATCATTTC 57.774 33.333 0.00 0.00 35.79 2.17
1638 1664 3.617368 GCCTAGGGCGAGAAGTCA 58.383 61.111 11.72 0.00 39.62 3.41
1643 1669 2.219458 CTAGGGCGAGAAGTCATACGA 58.781 52.381 0.00 0.00 0.00 3.43
1891 2006 2.858344 CCACGTAATGTTCATCCTCGTC 59.142 50.000 0.00 0.00 0.00 4.20
1973 2104 5.670361 TCCATAGTAGAATTAGCCCAAGGTT 59.330 40.000 0.00 0.00 0.00 3.50
2145 2278 2.428171 GCACATGCCATCATTAAGTGGT 59.572 45.455 0.00 0.00 37.81 4.16
2146 2279 3.735820 GCACATGCCATCATTAAGTGGTG 60.736 47.826 0.00 0.00 38.74 4.17
2168 2301 3.429085 GAGCACAGTTTTGACTTGTGTG 58.571 45.455 5.83 0.00 41.21 3.82
2246 2379 8.056407 AGCTTGATTCAAGTATTTACCCTTTC 57.944 34.615 23.66 6.12 42.77 2.62
2254 2387 7.430441 TCAAGTATTTACCCTTTCTTTTGTGC 58.570 34.615 0.00 0.00 0.00 4.57
2440 2573 3.515901 AGACAGGAGGTTTTAGCGAAGAT 59.484 43.478 0.00 0.00 0.00 2.40
2636 2769 5.681337 AGAAAAGCACTGCTCTTTTACTC 57.319 39.130 3.40 0.00 42.02 2.59
2640 2773 2.370189 AGCACTGCTCTTTTACTCACCT 59.630 45.455 0.00 0.00 30.62 4.00
2644 2777 3.388024 ACTGCTCTTTTACTCACCTGACA 59.612 43.478 0.00 0.00 0.00 3.58
2660 2793 4.037208 ACCTGACAAGATTCTTTGCTGTTG 59.963 41.667 0.00 0.00 0.00 3.33
2674 2807 1.471327 GCTGTTGGTTGTTGCACATGT 60.471 47.619 0.00 0.00 0.00 3.21
2679 2812 4.158579 TGTTGGTTGTTGCACATGTCTTTA 59.841 37.500 0.00 0.00 0.00 1.85
2680 2813 5.163468 TGTTGGTTGTTGCACATGTCTTTAT 60.163 36.000 0.00 0.00 0.00 1.40
2681 2814 5.119931 TGGTTGTTGCACATGTCTTTATC 57.880 39.130 0.00 0.00 0.00 1.75
2712 2847 6.622962 CACATTTTGTTCGTTTTGTTGTATGC 59.377 34.615 0.00 0.00 0.00 3.14
2754 2896 8.426489 GGTTAACACCTATATTGTCCAGATACA 58.574 37.037 8.10 0.00 40.44 2.29
2756 2898 7.676683 AACACCTATATTGTCCAGATACAGT 57.323 36.000 0.00 0.00 0.00 3.55
2761 2903 9.601810 ACCTATATTGTCCAGATACAGTGATAA 57.398 33.333 0.00 0.00 0.00 1.75
2773 2915 8.735315 CAGATACAGTGATAAGGGTACAGATAG 58.265 40.741 0.00 0.00 0.00 2.08
2777 2919 5.069119 CAGTGATAAGGGTACAGATAGCACA 59.931 44.000 16.50 0.00 37.18 4.57
2967 3110 0.183492 TCTCCAGCCACTGCAACTTT 59.817 50.000 0.00 0.00 41.13 2.66
3010 3153 1.474077 GGATCAGTCACATTTGGGCAC 59.526 52.381 0.00 0.00 0.00 5.01
3011 3154 2.161855 GATCAGTCACATTTGGGCACA 58.838 47.619 0.00 0.00 0.00 4.57
3027 3170 2.570135 GCACAATCTGATCCCCTTCTC 58.430 52.381 0.00 0.00 0.00 2.87
3090 3235 7.413438 GCTTCCTCTGTATTCTTGTGTACAATG 60.413 40.741 0.00 0.00 35.02 2.82
3148 3293 1.612676 TGCATCTGCCTCCATAATGC 58.387 50.000 0.00 0.00 41.18 3.56
3239 3391 5.764686 ACATGCAACAGTAGACAATGAGAAA 59.235 36.000 0.00 0.00 0.00 2.52
3279 3432 6.460103 AGGGCACATAGGATAAAATCTCAT 57.540 37.500 0.00 0.00 0.00 2.90
3320 3473 2.766313 TGTCGTTCAGATTTGGTGAGG 58.234 47.619 0.00 0.00 0.00 3.86
3321 3474 2.104111 TGTCGTTCAGATTTGGTGAGGT 59.896 45.455 0.00 0.00 0.00 3.85
3323 3476 1.197721 CGTTCAGATTTGGTGAGGTGC 59.802 52.381 0.00 0.00 0.00 5.01
3325 3478 2.189594 TCAGATTTGGTGAGGTGCAG 57.810 50.000 0.00 0.00 0.00 4.41
3326 3479 1.421268 TCAGATTTGGTGAGGTGCAGT 59.579 47.619 0.00 0.00 0.00 4.40
3327 3480 1.538512 CAGATTTGGTGAGGTGCAGTG 59.461 52.381 0.00 0.00 0.00 3.66
3387 3542 1.845205 CCATAGGGGGAGGGAGCAG 60.845 68.421 0.00 0.00 0.00 4.24
3416 3574 2.224942 TGTCCTCTTCCTTCCTCGTACA 60.225 50.000 0.00 0.00 0.00 2.90
3525 3683 1.541233 CGGATGGTGGTGCTCTAATCC 60.541 57.143 0.00 0.00 0.00 3.01
3563 3721 1.109920 GGTGGCGCTCAGATCTAGGA 61.110 60.000 7.64 0.00 0.00 2.94
3585 3743 0.749454 GGGAATGACGGAGCAATGCT 60.749 55.000 7.79 7.79 43.88 3.79
3610 3768 1.551329 GGGTCTCTCCTTCTCTGGTGT 60.551 57.143 0.00 0.00 36.25 4.16
3621 3779 3.889692 CTGGTGTGGTGGGCTGGT 61.890 66.667 0.00 0.00 0.00 4.00
3682 3840 1.229400 TAACAAGGGGAGGGAGCGT 60.229 57.895 0.00 0.00 0.00 5.07
3726 3887 3.010420 GGAGGGATGAAACGAGAAAAGG 58.990 50.000 0.00 0.00 0.00 3.11
3727 3888 3.010420 GAGGGATGAAACGAGAAAAGGG 58.990 50.000 0.00 0.00 0.00 3.95
3728 3889 2.092323 GGGATGAAACGAGAAAAGGGG 58.908 52.381 0.00 0.00 0.00 4.79
3729 3890 2.290705 GGGATGAAACGAGAAAAGGGGA 60.291 50.000 0.00 0.00 0.00 4.81
3730 3891 3.010420 GGATGAAACGAGAAAAGGGGAG 58.990 50.000 0.00 0.00 0.00 4.30
3731 3892 3.307480 GGATGAAACGAGAAAAGGGGAGA 60.307 47.826 0.00 0.00 0.00 3.71
3732 3893 3.121738 TGAAACGAGAAAAGGGGAGAC 57.878 47.619 0.00 0.00 0.00 3.36
3769 3930 2.439135 CAGGTATGGATGGACACATGGA 59.561 50.000 0.00 0.00 37.47 3.41
3881 4043 4.102054 AGAAAAATCCGGGGATACGTATGT 59.898 41.667 13.97 0.00 33.97 2.29
3899 4061 1.446445 TGATACGTTTCGGCGGGTG 60.446 57.895 7.21 0.00 35.98 4.61
4004 4166 7.024340 ACAGATAAATGCACTGCTGAATTAG 57.976 36.000 1.98 0.00 35.38 1.73
4005 4167 6.600822 ACAGATAAATGCACTGCTGAATTAGT 59.399 34.615 1.98 0.00 35.38 2.24
4006 4168 7.770433 ACAGATAAATGCACTGCTGAATTAGTA 59.230 33.333 1.98 0.00 35.38 1.82
4065 4229 5.590530 ACTGCTAGACATCCTAGAACTTG 57.409 43.478 0.00 0.00 46.17 3.16
4264 4428 6.061022 TCTTTATGGCAAGGATAAGTGTGA 57.939 37.500 0.00 0.00 0.00 3.58
4293 4457 8.310406 TGACTTGTGACTGTGATTACTAATTG 57.690 34.615 0.00 0.00 0.00 2.32
4372 4536 5.496133 TTCGCCTAGTATATCTATTCGCC 57.504 43.478 0.00 0.00 0.00 5.54
4410 4604 3.973206 TCATTCCCACTTGACGTATGT 57.027 42.857 0.00 0.00 0.00 2.29
4411 4605 5.408880 TTCATTCCCACTTGACGTATGTA 57.591 39.130 0.00 0.00 0.00 2.29
4412 4606 5.607939 TCATTCCCACTTGACGTATGTAT 57.392 39.130 0.00 0.00 0.00 2.29
4413 4607 6.718522 TCATTCCCACTTGACGTATGTATA 57.281 37.500 0.00 0.00 0.00 1.47
4414 4608 7.297936 TCATTCCCACTTGACGTATGTATAT 57.702 36.000 0.00 0.00 0.00 0.86
4415 4609 8.411991 TCATTCCCACTTGACGTATGTATATA 57.588 34.615 0.00 0.00 0.00 0.86
4416 4610 9.031537 TCATTCCCACTTGACGTATGTATATAT 57.968 33.333 0.00 0.00 0.00 0.86
4457 4651 3.942748 GCATAACAACTGGATCGGGTTTA 59.057 43.478 0.13 0.00 0.00 2.01
4458 4652 4.035208 GCATAACAACTGGATCGGGTTTAG 59.965 45.833 0.13 0.00 0.00 1.85
4459 4653 2.781681 ACAACTGGATCGGGTTTAGG 57.218 50.000 0.13 0.00 0.00 2.69
4460 4654 1.280998 ACAACTGGATCGGGTTTAGGG 59.719 52.381 0.13 0.00 0.00 3.53
4461 4655 1.280998 CAACTGGATCGGGTTTAGGGT 59.719 52.381 0.13 0.00 0.00 4.34
4462 4656 1.665137 ACTGGATCGGGTTTAGGGTT 58.335 50.000 0.00 0.00 0.00 4.11
4463 4657 1.990327 ACTGGATCGGGTTTAGGGTTT 59.010 47.619 0.00 0.00 0.00 3.27
4755 4951 5.468540 ACACACAGAAGCTACTATGAACA 57.531 39.130 0.00 0.00 0.00 3.18
4759 4955 6.475076 CACACAGAAGCTACTATGAACAGATC 59.525 42.308 0.00 0.00 0.00 2.75
4888 5084 4.899502 AGAACTCGACCAACATTGATTCT 58.100 39.130 0.00 0.00 0.00 2.40
4903 5099 3.340928 TGATTCTGTCATTGACTGGCTG 58.659 45.455 19.67 6.10 33.37 4.85
5164 5368 7.659652 ACAACTTACAGAAGTCTTTAGATGC 57.340 36.000 0.00 0.00 45.50 3.91
5188 5392 3.928375 GCATACTTGCTTGGTGAATTTGG 59.072 43.478 0.00 0.00 45.77 3.28
5359 5571 8.437742 CAGAAAAATTTGAAACATCATACAGGC 58.562 33.333 0.00 0.00 0.00 4.85
5361 5573 7.894376 AAAATTTGAAACATCATACAGGCAG 57.106 32.000 0.00 0.00 0.00 4.85
5362 5574 6.594788 AATTTGAAACATCATACAGGCAGT 57.405 33.333 0.00 0.00 0.00 4.40
5363 5575 7.701539 AATTTGAAACATCATACAGGCAGTA 57.298 32.000 0.00 0.00 37.06 2.74
5433 5645 3.902881 TTTGTGCTGTGAAAACCCAAT 57.097 38.095 0.00 0.00 0.00 3.16
5470 5682 7.201522 CGCTTTTCTCAGCACTATAAACATGTA 60.202 37.037 0.00 0.00 40.09 2.29
5544 5757 8.555166 AAACATGTTTTTAATACGTGACACAG 57.445 30.769 18.13 1.26 36.31 3.66
5566 5779 4.159135 AGTGCTGACATTTTCCCATCATTC 59.841 41.667 0.00 0.00 0.00 2.67
5576 5789 5.486735 TTTCCCATCATTCAAATGTGCTT 57.513 34.783 2.85 0.00 37.65 3.91
5635 5858 6.581712 GCTGCTATGGGGATTTGATTTTTAA 58.418 36.000 0.00 0.00 0.00 1.52
5665 5888 9.151177 ACATTCAAATCTAAATATGGGCATCTT 57.849 29.630 0.00 0.00 0.00 2.40
5667 5890 9.991906 ATTCAAATCTAAATATGGGCATCTTTG 57.008 29.630 0.00 0.00 0.00 2.77
5668 5891 8.765488 TCAAATCTAAATATGGGCATCTTTGA 57.235 30.769 0.00 0.00 0.00 2.69
5669 5892 9.370930 TCAAATCTAAATATGGGCATCTTTGAT 57.629 29.630 0.00 0.00 0.00 2.57
5670 5893 9.991906 CAAATCTAAATATGGGCATCTTTGATT 57.008 29.630 0.00 0.00 0.00 2.57
5672 5895 6.985117 TCTAAATATGGGCATCTTTGATTGC 58.015 36.000 0.00 0.00 38.14 3.56
5674 5897 5.617528 AATATGGGCATCTTTGATTGCAA 57.382 34.783 0.00 0.00 40.66 4.08
5704 5927 8.641499 TTTTGTTTTGTTGATAGCTTACCAAG 57.359 30.769 0.00 0.00 0.00 3.61
5718 5941 3.359002 CAAGCTGACCACTTGGCC 58.641 61.111 0.00 0.00 40.68 5.36
5719 5942 1.529010 CAAGCTGACCACTTGGCCA 60.529 57.895 0.00 0.00 40.68 5.36
5720 5943 1.108727 CAAGCTGACCACTTGGCCAA 61.109 55.000 19.25 19.25 40.68 4.52
5721 5944 0.396974 AAGCTGACCACTTGGCCAAA 60.397 50.000 20.91 1.89 39.32 3.28
5722 5945 0.178953 AGCTGACCACTTGGCCAAAT 60.179 50.000 20.91 6.63 39.32 2.32
5763 5986 6.873997 ACTATATGAATCACACGTCTTCCAA 58.126 36.000 0.00 0.00 0.00 3.53
5764 5987 7.327975 ACTATATGAATCACACGTCTTCCAAA 58.672 34.615 0.00 0.00 0.00 3.28
5765 5988 7.987458 ACTATATGAATCACACGTCTTCCAAAT 59.013 33.333 0.00 0.00 0.00 2.32
5766 5989 5.964958 ATGAATCACACGTCTTCCAAATT 57.035 34.783 0.00 0.00 0.00 1.82
5767 5990 5.356882 TGAATCACACGTCTTCCAAATTC 57.643 39.130 0.00 0.00 0.00 2.17
5768 5991 4.084066 TGAATCACACGTCTTCCAAATTCG 60.084 41.667 0.00 0.00 0.00 3.34
5769 5992 3.100658 TCACACGTCTTCCAAATTCGA 57.899 42.857 0.00 0.00 0.00 3.71
5770 5993 3.459145 TCACACGTCTTCCAAATTCGAA 58.541 40.909 0.00 0.00 0.00 3.71
5771 5994 3.493129 TCACACGTCTTCCAAATTCGAAG 59.507 43.478 3.35 8.33 38.47 3.79
5772 5995 2.806244 ACACGTCTTCCAAATTCGAAGG 59.194 45.455 3.35 0.00 37.83 3.46
5773 5996 3.064207 CACGTCTTCCAAATTCGAAGGA 58.936 45.455 3.35 1.84 37.83 3.36
5774 5997 3.496884 CACGTCTTCCAAATTCGAAGGAA 59.503 43.478 14.57 14.57 39.01 3.36
5775 5998 4.024387 CACGTCTTCCAAATTCGAAGGAAA 60.024 41.667 15.74 6.97 40.63 3.13
5776 5999 4.577283 ACGTCTTCCAAATTCGAAGGAAAA 59.423 37.500 15.74 3.28 40.63 2.29
5777 6000 5.240844 ACGTCTTCCAAATTCGAAGGAAAAT 59.759 36.000 15.74 2.77 40.63 1.82
5778 6001 5.795441 CGTCTTCCAAATTCGAAGGAAAATC 59.205 40.000 15.74 9.53 40.63 2.17
5779 6002 6.567701 CGTCTTCCAAATTCGAAGGAAAATCA 60.568 38.462 15.74 1.78 40.63 2.57
5780 6003 6.582672 GTCTTCCAAATTCGAAGGAAAATCAC 59.417 38.462 15.74 8.47 40.63 3.06
5781 6004 5.385509 TCCAAATTCGAAGGAAAATCACC 57.614 39.130 3.35 0.00 35.40 4.02
5782 6005 5.076873 TCCAAATTCGAAGGAAAATCACCT 58.923 37.500 3.35 0.00 39.69 4.00
5783 6006 5.183140 TCCAAATTCGAAGGAAAATCACCTC 59.817 40.000 3.35 0.00 36.67 3.85
5784 6007 5.048083 CCAAATTCGAAGGAAAATCACCTCA 60.048 40.000 3.35 0.00 36.67 3.86
5785 6008 6.446318 CAAATTCGAAGGAAAATCACCTCAA 58.554 36.000 3.35 0.00 36.67 3.02
5786 6009 6.648879 AATTCGAAGGAAAATCACCTCAAA 57.351 33.333 3.35 0.00 36.67 2.69
5787 6010 6.648879 ATTCGAAGGAAAATCACCTCAAAA 57.351 33.333 3.35 0.00 36.67 2.44
5788 6011 5.689383 TCGAAGGAAAATCACCTCAAAAG 57.311 39.130 0.00 0.00 36.67 2.27
5791 6014 6.320164 TCGAAGGAAAATCACCTCAAAAGAAA 59.680 34.615 0.00 0.00 36.67 2.52
5812 6035 8.183104 AGAAATCGAAGGAAAAGGAAATTTCT 57.817 30.769 17.42 0.00 38.92 2.52
5872 6098 1.486726 GGGTCATCCCGAGTTCTGAAT 59.513 52.381 0.00 0.00 44.74 2.57
5911 6139 2.038975 CCTCTCCTCGGTTCCCCA 59.961 66.667 0.00 0.00 0.00 4.96
5921 6149 1.303091 CGGTTCCCCACAATCGTTCC 61.303 60.000 0.00 0.00 0.00 3.62
5922 6150 0.037734 GGTTCCCCACAATCGTTCCT 59.962 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.067684 AGAAGAATTACCAACCCCACG 57.932 47.619 0.00 0.00 0.00 4.94
9 10 6.457159 TTAGAAGAAGAATTACCAACCCCA 57.543 37.500 0.00 0.00 0.00 4.96
81 82 6.603237 TTATTGTCATCAATCTTAGTGGCG 57.397 37.500 0.00 0.00 42.45 5.69
109 110 5.610398 TCTATGAAGCACAAGAGACAAACA 58.390 37.500 0.00 0.00 0.00 2.83
110 111 5.121454 CCTCTATGAAGCACAAGAGACAAAC 59.879 44.000 16.29 0.00 36.66 2.93
111 112 5.240891 CCTCTATGAAGCACAAGAGACAAA 58.759 41.667 16.29 0.00 36.66 2.83
112 113 4.323028 CCCTCTATGAAGCACAAGAGACAA 60.323 45.833 16.29 0.00 36.66 3.18
129 130 5.731187 TCATGGAGGAATTTTTCTCCCTCTA 59.269 40.000 13.92 8.44 46.71 2.43
198 199 3.065233 TGAGCATTCCAATTGTATGTCGC 59.935 43.478 15.26 11.22 0.00 5.19
266 267 2.141517 CAAGATGATGGATGACCGCTC 58.858 52.381 0.00 0.00 39.42 5.03
283 284 4.252971 TCTCGTTCTCCTAACCAACAAG 57.747 45.455 0.00 0.00 0.00 3.16
306 307 2.755650 ACTTGACCAACATGACTCGTC 58.244 47.619 0.00 0.00 0.00 4.20
323 324 5.180117 CACCTTCATCAATCTTCGACAACTT 59.820 40.000 0.00 0.00 0.00 2.66
409 426 6.726764 AGTACTGTTATCTTCTTCTTGTCCCT 59.273 38.462 0.00 0.00 0.00 4.20
410 427 6.937392 AGTACTGTTATCTTCTTCTTGTCCC 58.063 40.000 0.00 0.00 0.00 4.46
411 428 7.873505 ACAAGTACTGTTATCTTCTTCTTGTCC 59.126 37.037 0.00 0.00 38.61 4.02
412 429 8.704234 CACAAGTACTGTTATCTTCTTCTTGTC 58.296 37.037 0.00 0.00 40.16 3.18
413 430 8.204836 ACACAAGTACTGTTATCTTCTTCTTGT 58.795 33.333 0.00 0.00 41.93 3.16
414 431 8.594881 ACACAAGTACTGTTATCTTCTTCTTG 57.405 34.615 0.00 0.00 35.47 3.02
415 432 9.915629 CTACACAAGTACTGTTATCTTCTTCTT 57.084 33.333 0.00 0.00 35.47 2.52
416 433 9.298250 TCTACACAAGTACTGTTATCTTCTTCT 57.702 33.333 0.00 0.00 35.47 2.85
417 434 9.344309 GTCTACACAAGTACTGTTATCTTCTTC 57.656 37.037 0.00 0.00 35.47 2.87
418 435 8.857098 TGTCTACACAAGTACTGTTATCTTCTT 58.143 33.333 0.00 0.00 35.47 2.52
419 436 8.405418 TGTCTACACAAGTACTGTTATCTTCT 57.595 34.615 0.00 0.00 35.47 2.85
420 437 9.077674 CATGTCTACACAAGTACTGTTATCTTC 57.922 37.037 0.00 0.00 35.47 2.87
421 438 8.803235 TCATGTCTACACAAGTACTGTTATCTT 58.197 33.333 0.00 0.00 35.47 2.40
422 439 8.349568 TCATGTCTACACAAGTACTGTTATCT 57.650 34.615 0.00 0.00 35.47 1.98
423 440 8.981724 TTCATGTCTACACAAGTACTGTTATC 57.018 34.615 0.00 0.00 35.47 1.75
424 441 8.803235 TCTTCATGTCTACACAAGTACTGTTAT 58.197 33.333 0.00 0.00 35.47 1.89
425 442 8.173542 TCTTCATGTCTACACAAGTACTGTTA 57.826 34.615 0.00 0.00 35.47 2.41
426 443 7.050970 TCTTCATGTCTACACAAGTACTGTT 57.949 36.000 0.00 0.00 35.47 3.16
427 444 6.650427 TCTTCATGTCTACACAAGTACTGT 57.350 37.500 0.00 0.00 39.56 3.55
428 445 6.923508 TGTTCTTCATGTCTACACAAGTACTG 59.076 38.462 0.00 0.00 35.64 2.74
429 446 7.050970 TGTTCTTCATGTCTACACAAGTACT 57.949 36.000 0.00 0.00 35.64 2.73
430 447 7.223971 TGTTGTTCTTCATGTCTACACAAGTAC 59.776 37.037 0.00 6.51 35.64 2.73
431 448 7.269316 TGTTGTTCTTCATGTCTACACAAGTA 58.731 34.615 0.00 0.00 35.64 2.24
432 449 6.112734 TGTTGTTCTTCATGTCTACACAAGT 58.887 36.000 0.00 0.00 35.64 3.16
433 450 6.603237 TGTTGTTCTTCATGTCTACACAAG 57.397 37.500 0.00 0.00 35.64 3.16
434 451 6.458206 GCTTGTTGTTCTTCATGTCTACACAA 60.458 38.462 0.00 0.00 35.64 3.33
435 452 5.007626 GCTTGTTGTTCTTCATGTCTACACA 59.992 40.000 0.00 0.00 36.78 3.72
436 453 5.237344 AGCTTGTTGTTCTTCATGTCTACAC 59.763 40.000 0.00 0.00 0.00 2.90
502 519 9.485206 GGTTCAAGAAAGAGTACATACAGTAAA 57.515 33.333 0.00 0.00 33.72 2.01
503 520 8.867097 AGGTTCAAGAAAGAGTACATACAGTAA 58.133 33.333 0.00 0.00 33.72 2.24
504 521 8.418597 AGGTTCAAGAAAGAGTACATACAGTA 57.581 34.615 0.00 0.00 0.00 2.74
505 522 7.304497 AGGTTCAAGAAAGAGTACATACAGT 57.696 36.000 0.00 0.00 0.00 3.55
506 523 7.872993 TCAAGGTTCAAGAAAGAGTACATACAG 59.127 37.037 0.00 0.00 0.00 2.74
507 524 7.656137 GTCAAGGTTCAAGAAAGAGTACATACA 59.344 37.037 0.00 0.00 0.00 2.29
508 525 7.148787 CGTCAAGGTTCAAGAAAGAGTACATAC 60.149 40.741 0.00 0.00 0.00 2.39
544 561 2.166579 CCGCGGCCAATGAATTTGC 61.167 57.895 14.67 0.00 33.73 3.68
545 562 0.453793 TACCGCGGCCAATGAATTTG 59.546 50.000 28.58 0.00 34.93 2.32
555 572 1.918868 CTGTTTCCTTTACCGCGGCC 61.919 60.000 28.58 0.00 0.00 6.13
559 576 4.779987 CAGTTTACTGTTTCCTTTACCGC 58.220 43.478 1.69 0.00 39.09 5.68
614 632 6.127535 CCGAATAGGACTGTTGTTAGTTAGGA 60.128 42.308 0.00 0.00 45.00 2.94
649 667 7.201670 GGTTTATCTACATCCTTTGTAAACGGG 60.202 40.741 0.00 0.00 40.27 5.28
709 728 4.142708 GGTTGGTGCCTTGTTTTTCTTTTG 60.143 41.667 0.00 0.00 0.00 2.44
963 987 2.904866 CTCCCTCTCCTCCGCGAG 60.905 72.222 8.23 2.69 0.00 5.03
1047 1071 2.438254 CCAGGGCGCATGCTTGTA 60.438 61.111 17.13 0.00 42.25 2.41
1066 1090 0.944311 CGATAATCTGAACCCGCCCG 60.944 60.000 0.00 0.00 0.00 6.13
1082 1106 1.372997 ACAGCGCGTCAAACTCGAT 60.373 52.632 8.43 0.00 0.00 3.59
1260 1284 1.002468 CTTTCTGTCAAGTGCCAACCG 60.002 52.381 0.00 0.00 0.00 4.44
1277 1301 4.520492 CACCTTCATACAGGTCAAAGCTTT 59.480 41.667 5.69 5.69 44.63 3.51
1340 1364 4.257267 TGATTACCGGCACTATCAGATG 57.743 45.455 0.00 0.00 0.00 2.90
1341 1365 6.351371 CCTTATGATTACCGGCACTATCAGAT 60.351 42.308 0.00 0.00 31.20 2.90
1342 1366 5.047306 CCTTATGATTACCGGCACTATCAGA 60.047 44.000 0.00 0.00 31.20 3.27
1344 1368 4.836175 TCCTTATGATTACCGGCACTATCA 59.164 41.667 0.00 6.09 0.00 2.15
1345 1369 5.401531 TCCTTATGATTACCGGCACTATC 57.598 43.478 0.00 0.00 0.00 2.08
1380 1404 5.985911 ACTAGGCTCACGTAAAATAACCAT 58.014 37.500 0.00 0.00 0.00 3.55
1400 1424 6.630413 GCCACAAGACTCCATAATCTGAACTA 60.630 42.308 0.00 0.00 0.00 2.24
1419 1443 3.825160 AAGCGCCTCGAAGCCACAA 62.825 57.895 2.29 0.00 0.00 3.33
1490 1516 4.892655 TCGACGTGTTCAATCAATAATGC 58.107 39.130 0.00 0.00 0.00 3.56
1507 1533 6.919188 ACACAATTAAATAGTTCGATCGACG 58.081 36.000 19.26 0.00 44.09 5.12
1574 1600 6.676558 ACCCCATCACAGAAATGATAAGAAT 58.323 36.000 0.00 0.00 37.20 2.40
1587 1613 3.891366 GGGATAAATTGACCCCATCACAG 59.109 47.826 0.00 0.00 36.92 3.66
1638 1664 9.363763 CATAGCTATCATGAGAAAATGTCGTAT 57.636 33.333 2.34 0.00 0.00 3.06
1643 1669 7.512130 TGACCATAGCTATCATGAGAAAATGT 58.488 34.615 2.34 0.00 0.00 2.71
1726 1752 8.845413 TTAATTAATGCATATTGGAAATGGCC 57.155 30.769 0.00 0.00 0.00 5.36
1759 1785 2.746362 GAGTTCATTGAGCAGAACAGGG 59.254 50.000 3.25 0.00 44.94 4.45
1950 2065 5.568620 ACCTTGGGCTAATTCTACTATGG 57.431 43.478 0.00 0.00 0.00 2.74
1973 2104 9.988815 GATTAGATTCCAAGAGAAGCATTACTA 57.011 33.333 0.00 0.00 43.58 1.82
2098 2229 2.062773 TCCTTTAACCCAAGCCCCTA 57.937 50.000 0.00 0.00 0.00 3.53
2145 2278 2.423185 CACAAGTCAAAACTGTGCTCCA 59.577 45.455 0.00 0.00 35.36 3.86
2146 2279 2.423538 ACACAAGTCAAAACTGTGCTCC 59.576 45.455 1.50 0.00 37.72 4.70
2168 2301 4.324402 CGTCTGTGCATTTATTTTCTTGGC 59.676 41.667 0.00 0.00 0.00 4.52
2246 2379 1.461127 GAGGCTGTAGACGCACAAAAG 59.539 52.381 0.00 0.00 0.00 2.27
2252 2385 2.224185 TGAAAAAGAGGCTGTAGACGCA 60.224 45.455 0.00 0.00 0.00 5.24
2254 2387 3.120511 GCTTGAAAAAGAGGCTGTAGACG 60.121 47.826 0.00 0.00 0.00 4.18
2440 2573 6.823286 TTGAATCCTACTGTGGGAATCATA 57.177 37.500 25.53 16.10 40.91 2.15
2608 2741 3.728845 AGAGCAGTGCTTTTCTTTACGA 58.271 40.909 20.80 0.00 39.88 3.43
2623 2756 3.995199 TGTCAGGTGAGTAAAAGAGCAG 58.005 45.455 0.00 0.00 0.00 4.24
2636 2769 3.567164 ACAGCAAAGAATCTTGTCAGGTG 59.433 43.478 0.00 6.05 0.00 4.00
2640 2773 3.953612 ACCAACAGCAAAGAATCTTGTCA 59.046 39.130 0.00 0.00 0.00 3.58
2644 2777 5.111293 CAACAACCAACAGCAAAGAATCTT 58.889 37.500 0.00 0.00 0.00 2.40
2674 2807 9.796120 ACGAACAAAATGTGAAAAAGATAAAGA 57.204 25.926 0.00 0.00 0.00 2.52
2679 2812 8.716909 ACAAAACGAACAAAATGTGAAAAAGAT 58.283 25.926 0.00 0.00 0.00 2.40
2680 2813 8.077836 ACAAAACGAACAAAATGTGAAAAAGA 57.922 26.923 0.00 0.00 0.00 2.52
2681 2814 8.617267 CAACAAAACGAACAAAATGTGAAAAAG 58.383 29.630 0.00 0.00 0.00 2.27
2703 2838 9.911138 CCAATGCATATAATTAAGCATACAACA 57.089 29.630 18.04 0.00 40.78 3.33
2754 2896 5.208890 TGTGCTATCTGTACCCTTATCACT 58.791 41.667 0.00 0.00 0.00 3.41
2756 2898 6.747414 ATTGTGCTATCTGTACCCTTATCA 57.253 37.500 0.00 0.00 0.00 2.15
2761 2903 5.602561 TGACATATTGTGCTATCTGTACCCT 59.397 40.000 0.00 0.00 0.00 4.34
2773 2915 9.713740 TGTTTTTGAAAAATTGACATATTGTGC 57.286 25.926 6.35 0.00 0.00 4.57
2903 3046 6.716628 GGTGCATTTTCCATCTTCCTATCATA 59.283 38.462 0.00 0.00 0.00 2.15
2904 3047 5.537674 GGTGCATTTTCCATCTTCCTATCAT 59.462 40.000 0.00 0.00 0.00 2.45
2914 3057 9.362539 GATCATATTTATGGTGCATTTTCCATC 57.637 33.333 9.68 0.00 42.56 3.51
2967 3110 3.674997 ACTCTTCGGCAGCTTCAAATTA 58.325 40.909 0.00 0.00 0.00 1.40
3010 3153 2.042464 TCCGAGAAGGGGATCAGATTG 58.958 52.381 0.00 0.00 41.52 2.67
3011 3154 2.478872 TCCGAGAAGGGGATCAGATT 57.521 50.000 0.00 0.00 41.52 2.40
3027 3170 3.881795 GCACATTTGCTCAAGATATCCG 58.118 45.455 0.00 0.00 46.17 4.18
3090 3235 4.740695 GTCCGATTCAGATGTACTGTAAGC 59.259 45.833 0.00 0.00 45.86 3.09
3148 3293 2.689983 GGCCTTTGTGGAATCATGTAGG 59.310 50.000 0.00 0.00 38.35 3.18
3209 3360 0.723414 CTACTGTTGCATGTGCCTCG 59.277 55.000 2.07 0.00 41.18 4.63
3239 3391 6.529220 TGTGCCCTTGCTTGTAAAAATTATT 58.471 32.000 0.00 0.00 38.71 1.40
3279 3432 5.815581 ACATTTTCTTAGCCATGGTGAGTA 58.184 37.500 14.67 0.20 0.00 2.59
3320 3473 1.738099 CACTACTCCGGCACTGCAC 60.738 63.158 2.82 0.00 0.00 4.57
3321 3474 2.656646 CACTACTCCGGCACTGCA 59.343 61.111 2.82 0.00 0.00 4.41
3402 3557 0.896940 ACGCCTGTACGAGGAAGGAA 60.897 55.000 13.57 0.00 46.33 3.36
3416 3574 2.345244 CTGACCTGAGCAACGCCT 59.655 61.111 0.00 0.00 0.00 5.52
3470 3628 2.194056 CAGCCGCCATGATCCCTT 59.806 61.111 0.00 0.00 0.00 3.95
3563 3721 2.026641 CATTGCTCCGTCATTCCCATT 58.973 47.619 0.00 0.00 0.00 3.16
3585 3743 0.616111 GAGAAGGAGAGACCCAGCCA 60.616 60.000 0.00 0.00 40.05 4.75
3621 3779 1.692762 GGAGAAGGAGATACCCAGCCA 60.693 57.143 0.00 0.00 40.05 4.75
3662 3820 1.915983 GCTCCCTCCCCTTGTTAGG 59.084 63.158 0.00 0.00 41.60 2.69
3702 3863 1.144057 CTCGTTTCATCCCTCCCGG 59.856 63.158 0.00 0.00 0.00 5.73
3715 3876 0.320697 CGGTCTCCCCTTTTCTCGTT 59.679 55.000 0.00 0.00 0.00 3.85
3726 3887 4.862823 CCCCTCTCCCGGTCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
3727 3888 3.089419 ATCCCCTCTCCCGGTCTCC 62.089 68.421 0.00 0.00 0.00 3.71
3728 3889 1.532078 GATCCCCTCTCCCGGTCTC 60.532 68.421 0.00 0.00 0.00 3.36
3729 3890 2.609920 GATCCCCTCTCCCGGTCT 59.390 66.667 0.00 0.00 0.00 3.85
3730 3891 2.913060 CGATCCCCTCTCCCGGTC 60.913 72.222 0.00 0.00 0.00 4.79
3733 3894 3.610669 CTGCGATCCCCTCTCCCG 61.611 72.222 0.00 0.00 0.00 5.14
3881 4043 1.446445 CACCCGCCGAAACGTATCA 60.446 57.895 0.00 0.00 0.00 2.15
4074 4238 7.992608 AGTGAATGCCAATACAGTGACAATATA 59.007 33.333 0.00 0.00 0.00 0.86
4081 4245 3.609853 GGAGTGAATGCCAATACAGTGA 58.390 45.455 0.00 0.00 0.00 3.41
4264 4428 6.349300 AGTAATCACAGTCACAAGTCAAACT 58.651 36.000 0.00 0.00 0.00 2.66
4293 4457 4.468153 AGATCCAGTCTAAGTGAAAGGACC 59.532 45.833 0.00 0.00 34.69 4.46
4352 4516 4.261238 CCTGGCGAATAGATATACTAGGCG 60.261 50.000 0.00 0.00 35.88 5.52
4368 4532 3.292492 TCAGAATAGTAGACCTGGCGA 57.708 47.619 0.00 0.00 0.00 5.54
4369 4533 4.038042 TGAATCAGAATAGTAGACCTGGCG 59.962 45.833 0.00 0.00 0.00 5.69
4372 4536 7.158021 GGGAATGAATCAGAATAGTAGACCTG 58.842 42.308 0.00 0.00 0.00 4.00
4417 4611 9.685276 TTGTTATGCAGCTGGCTATAATAATAT 57.315 29.630 17.12 0.00 45.15 1.28
4418 4612 8.946085 GTTGTTATGCAGCTGGCTATAATAATA 58.054 33.333 17.12 4.17 45.15 0.98
4419 4613 7.667219 AGTTGTTATGCAGCTGGCTATAATAAT 59.333 33.333 17.12 0.00 45.15 1.28
4420 4614 6.998074 AGTTGTTATGCAGCTGGCTATAATAA 59.002 34.615 17.12 13.73 45.15 1.40
4421 4615 6.533730 AGTTGTTATGCAGCTGGCTATAATA 58.466 36.000 17.12 9.62 45.15 0.98
4422 4616 5.380043 AGTTGTTATGCAGCTGGCTATAAT 58.620 37.500 17.12 0.47 45.15 1.28
4423 4617 4.780815 AGTTGTTATGCAGCTGGCTATAA 58.219 39.130 17.12 10.93 45.15 0.98
4424 4618 4.422073 AGTTGTTATGCAGCTGGCTATA 57.578 40.909 17.12 6.13 45.15 1.31
4462 4656 4.764679 ACTGATCAAGCGTGCATAAAAA 57.235 36.364 0.00 0.00 0.00 1.94
4463 4657 6.435430 AATACTGATCAAGCGTGCATAAAA 57.565 33.333 0.00 0.00 0.00 1.52
4470 4664 5.536554 ACAGAAAATACTGATCAAGCGTG 57.463 39.130 0.00 0.00 40.63 5.34
4755 4951 9.429359 GTATCGATTGATGAGTAATTTGGATCT 57.571 33.333 1.71 0.00 35.99 2.75
4759 4955 6.936900 AGGGTATCGATTGATGAGTAATTTGG 59.063 38.462 1.71 0.00 35.99 3.28
4873 5069 6.072286 AGTCAATGACAGAATCAATGTTGGTC 60.072 38.462 16.38 0.00 41.93 4.02
4888 5084 0.764271 TCACCAGCCAGTCAATGACA 59.236 50.000 16.38 0.00 34.60 3.58
4903 5099 4.130118 TCTTCTTCTTTGAGTGCTTCACC 58.870 43.478 0.00 0.00 34.94 4.02
4984 5182 2.420058 ACAGCCCCAATGCTAAGTAC 57.580 50.000 0.00 0.00 40.32 2.73
5188 5392 2.229543 TGCACAAAACCATGCAGAGATC 59.770 45.455 0.00 0.00 46.63 2.75
5213 5418 5.122239 TCAACATTTCATCAGATTGACCGAC 59.878 40.000 0.00 0.00 0.00 4.79
5276 5484 4.743705 TTAAGGAACCCAACCCATGTTA 57.256 40.909 0.00 0.00 32.09 2.41
5340 5552 7.886629 ATACTGCCTGTATGATGTTTCAAAT 57.113 32.000 0.00 0.00 40.12 2.32
5359 5571 8.450578 TGCAAGGACTCCAAATTTATATACTG 57.549 34.615 0.00 0.00 0.00 2.74
5361 5573 7.809806 GCATGCAAGGACTCCAAATTTATATAC 59.190 37.037 14.21 0.00 0.00 1.47
5362 5574 7.725397 AGCATGCAAGGACTCCAAATTTATATA 59.275 33.333 21.98 0.00 0.00 0.86
5363 5575 6.552350 AGCATGCAAGGACTCCAAATTTATAT 59.448 34.615 21.98 0.00 0.00 0.86
5403 5615 7.297391 GTTTTCACAGCACAAAATGTTTCTTT 58.703 30.769 0.00 0.00 0.00 2.52
5544 5757 4.082081 TGAATGATGGGAAAATGTCAGCAC 60.082 41.667 0.00 0.00 29.43 4.40
5655 5878 4.497291 AATTGCAATCAAAGATGCCCAT 57.503 36.364 13.38 0.00 41.87 4.00
5701 5924 1.529010 TGGCCAAGTGGTCAGCTTG 60.529 57.895 0.61 0.00 46.36 4.01
5702 5925 2.926250 TGGCCAAGTGGTCAGCTT 59.074 55.556 0.61 0.00 46.36 3.74
5707 5930 0.890683 CCAGATTTGGCCAAGTGGTC 59.109 55.000 25.27 18.87 41.09 4.02
5708 5931 0.542702 CCCAGATTTGGCCAAGTGGT 60.543 55.000 28.55 15.37 43.58 4.16
5709 5932 1.891722 GCCCAGATTTGGCCAAGTGG 61.892 60.000 26.09 26.09 43.58 4.00
5710 5933 1.593265 GCCCAGATTTGGCCAAGTG 59.407 57.895 19.46 16.56 43.58 3.16
5711 5934 4.118584 GCCCAGATTTGGCCAAGT 57.881 55.556 19.48 16.87 43.58 3.16
5717 5940 2.133281 TGACAGATGCCCAGATTTGG 57.867 50.000 0.00 0.00 44.60 3.28
5718 5941 4.021719 AGTTTTGACAGATGCCCAGATTTG 60.022 41.667 0.00 0.00 0.00 2.32
5719 5942 4.154942 AGTTTTGACAGATGCCCAGATTT 58.845 39.130 0.00 0.00 0.00 2.17
5720 5943 3.771216 AGTTTTGACAGATGCCCAGATT 58.229 40.909 0.00 0.00 0.00 2.40
5721 5944 3.446442 AGTTTTGACAGATGCCCAGAT 57.554 42.857 0.00 0.00 0.00 2.90
5722 5945 2.957402 AGTTTTGACAGATGCCCAGA 57.043 45.000 0.00 0.00 0.00 3.86
5763 5986 6.648879 TTTGAGGTGATTTTCCTTCGAATT 57.351 33.333 0.00 0.00 35.20 2.17
5764 5987 6.490040 TCTTTTGAGGTGATTTTCCTTCGAAT 59.510 34.615 0.00 0.00 35.20 3.34
5765 5988 5.825679 TCTTTTGAGGTGATTTTCCTTCGAA 59.174 36.000 0.00 0.00 35.20 3.71
5766 5989 5.373222 TCTTTTGAGGTGATTTTCCTTCGA 58.627 37.500 0.00 0.00 35.20 3.71
5767 5990 5.689383 TCTTTTGAGGTGATTTTCCTTCG 57.311 39.130 0.00 0.00 35.20 3.79
5768 5991 7.327032 CGATTTCTTTTGAGGTGATTTTCCTTC 59.673 37.037 0.00 0.00 35.20 3.46
5769 5992 7.014230 TCGATTTCTTTTGAGGTGATTTTCCTT 59.986 33.333 0.00 0.00 35.20 3.36
5770 5993 6.490040 TCGATTTCTTTTGAGGTGATTTTCCT 59.510 34.615 0.00 0.00 38.09 3.36
5771 5994 6.677913 TCGATTTCTTTTGAGGTGATTTTCC 58.322 36.000 0.00 0.00 0.00 3.13
5772 5995 7.327032 CCTTCGATTTCTTTTGAGGTGATTTTC 59.673 37.037 0.00 0.00 0.00 2.29
5773 5996 7.014230 TCCTTCGATTTCTTTTGAGGTGATTTT 59.986 33.333 0.00 0.00 0.00 1.82
5774 5997 6.490040 TCCTTCGATTTCTTTTGAGGTGATTT 59.510 34.615 0.00 0.00 0.00 2.17
5775 5998 6.003950 TCCTTCGATTTCTTTTGAGGTGATT 58.996 36.000 0.00 0.00 0.00 2.57
5776 5999 5.560724 TCCTTCGATTTCTTTTGAGGTGAT 58.439 37.500 0.00 0.00 0.00 3.06
5777 6000 4.968259 TCCTTCGATTTCTTTTGAGGTGA 58.032 39.130 0.00 0.00 0.00 4.02
5778 6001 5.689383 TTCCTTCGATTTCTTTTGAGGTG 57.311 39.130 0.00 0.00 0.00 4.00
5779 6002 6.239036 CCTTTTCCTTCGATTTCTTTTGAGGT 60.239 38.462 0.00 0.00 0.00 3.85
5780 6003 6.016276 TCCTTTTCCTTCGATTTCTTTTGAGG 60.016 38.462 0.00 0.00 0.00 3.86
5781 6004 6.970484 TCCTTTTCCTTCGATTTCTTTTGAG 58.030 36.000 0.00 0.00 0.00 3.02
5782 6005 6.952773 TCCTTTTCCTTCGATTTCTTTTGA 57.047 33.333 0.00 0.00 0.00 2.69
5783 6006 8.593492 ATTTCCTTTTCCTTCGATTTCTTTTG 57.407 30.769 0.00 0.00 0.00 2.44
5784 6007 9.613428 AAATTTCCTTTTCCTTCGATTTCTTTT 57.387 25.926 0.00 0.00 0.00 2.27
5785 6008 9.261180 GAAATTTCCTTTTCCTTCGATTTCTTT 57.739 29.630 6.95 0.00 32.42 2.52
5786 6009 8.642432 AGAAATTTCCTTTTCCTTCGATTTCTT 58.358 29.630 14.61 0.00 38.65 2.52
5787 6010 8.183104 AGAAATTTCCTTTTCCTTCGATTTCT 57.817 30.769 14.61 0.00 37.61 2.52
5788 6011 8.818141 AAGAAATTTCCTTTTCCTTCGATTTC 57.182 30.769 14.61 0.00 36.47 2.17
5791 6014 9.045223 CAAAAAGAAATTTCCTTTTCCTTCGAT 57.955 29.630 19.86 6.43 41.42 3.59


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

AutoCloner maintained by Alex Coulton.