Multiple sequence alignment - TraesCS1A01G307300

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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 TraesCS1A01G307300 chr1A 100.000 4199 0 0 1 4199 498810059 498805861 0.000000e+00 7755.0
1 TraesCS1A01G307300 chr1A 88.707 611 59 7 61 666 579763295 579762690 0.000000e+00 737.0
2 TraesCS1A01G307300 chr1D 94.362 3104 109 27 386 3458 403563532 403560464 0.000000e+00 4702.0
3 TraesCS1A01G307300 chr1D 95.238 231 10 1 3722 3951 403560367 403560137 8.580000e-97 364.0
4 TraesCS1A01G307300 chr1D 90.871 241 14 6 3959 4199 403560044 403559812 2.440000e-82 316.0
5 TraesCS1A01G307300 chr1D 80.176 227 37 6 2759 2980 403561040 403560817 3.360000e-36 163.0
6 TraesCS1A01G307300 chr1D 97.778 45 1 0 3564 3608 403560414 403560370 1.250000e-10 78.7
7 TraesCS1A01G307300 chr1B 93.086 2777 102 35 386 3102 542929409 542926663 0.000000e+00 3982.0
8 TraesCS1A01G307300 chr1B 91.008 645 49 6 2816 3458 542926827 542926190 0.000000e+00 861.0
9 TraesCS1A01G307300 chr1B 90.041 241 16 6 3959 4199 542925708 542925476 5.270000e-79 305.0
10 TraesCS1A01G307300 chr1B 92.090 177 10 2 3780 3956 542926043 542925871 3.240000e-61 246.0
11 TraesCS1A01G307300 chr2D 88.201 678 65 11 1 670 601796756 601796086 0.000000e+00 795.0
12 TraesCS1A01G307300 chr2D 87.255 102 6 4 3599 3700 511922595 511922689 4.440000e-20 110.0
13 TraesCS1A01G307300 chr2D 85.981 107 8 3 3598 3704 172182234 172182135 1.600000e-19 108.0
14 TraesCS1A01G307300 chr4A 87.982 674 67 11 1 666 619021954 619022621 0.000000e+00 784.0
15 TraesCS1A01G307300 chr5B 88.498 626 55 14 52 670 325637096 325637711 0.000000e+00 741.0
16 TraesCS1A01G307300 chr5B 87.903 620 61 9 52 664 624163156 624163768 0.000000e+00 717.0
17 TraesCS1A01G307300 chr5B 87.722 619 62 9 52 663 627763087 627763698 0.000000e+00 710.0
18 TraesCS1A01G307300 chr5B 87.255 102 6 5 3607 3708 218214335 218214241 4.440000e-20 110.0
19 TraesCS1A01G307300 chr3B 88.581 613 56 10 61 666 170069917 170069312 0.000000e+00 732.0
20 TraesCS1A01G307300 chr3B 89.362 94 3 4 3608 3701 66572353 66572267 1.230000e-20 111.0
21 TraesCS1A01G307300 chr4B 87.418 612 64 10 61 666 568680327 568679723 0.000000e+00 691.0
22 TraesCS1A01G307300 chr4B 84.348 115 8 5 3608 3720 616769096 616768990 2.070000e-18 104.0
23 TraesCS1A01G307300 chr6B 86.753 619 68 10 52 663 270177493 270178104 0.000000e+00 676.0
24 TraesCS1A01G307300 chr6B 88.298 94 9 1 3608 3701 637490598 637490507 1.230000e-20 111.0
25 TraesCS1A01G307300 chr7B 86.869 99 9 1 3604 3702 588501275 588501369 1.600000e-19 108.0
26 TraesCS1A01G307300 chr7A 85.981 107 8 3 3598 3704 395309644 395309743 1.600000e-19 108.0
27 TraesCS1A01G307300 chr2A 87.255 102 4 7 3608 3708 590985724 590985631 1.600000e-19 108.0


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 TraesCS1A01G307300 chr1A 498805861 498810059 4198 True 7755.00 7755 100.00000 1 4199 1 chr1A.!!$R1 4198
1 TraesCS1A01G307300 chr1A 579762690 579763295 605 True 737.00 737 88.70700 61 666 1 chr1A.!!$R2 605
2 TraesCS1A01G307300 chr1D 403559812 403563532 3720 True 1124.74 4702 91.68500 386 4199 5 chr1D.!!$R1 3813
3 TraesCS1A01G307300 chr1B 542925476 542929409 3933 True 1348.50 3982 91.55625 386 4199 4 chr1B.!!$R1 3813
4 TraesCS1A01G307300 chr2D 601796086 601796756 670 True 795.00 795 88.20100 1 670 1 chr2D.!!$R2 669
5 TraesCS1A01G307300 chr4A 619021954 619022621 667 False 784.00 784 87.98200 1 666 1 chr4A.!!$F1 665
6 TraesCS1A01G307300 chr5B 325637096 325637711 615 False 741.00 741 88.49800 52 670 1 chr5B.!!$F1 618
7 TraesCS1A01G307300 chr5B 624163156 624163768 612 False 717.00 717 87.90300 52 664 1 chr5B.!!$F2 612
8 TraesCS1A01G307300 chr5B 627763087 627763698 611 False 710.00 710 87.72200 52 663 1 chr5B.!!$F3 611
9 TraesCS1A01G307300 chr3B 170069312 170069917 605 True 732.00 732 88.58100 61 666 1 chr3B.!!$R2 605
10 TraesCS1A01G307300 chr4B 568679723 568680327 604 True 691.00 691 87.41800 61 666 1 chr4B.!!$R1 605
11 TraesCS1A01G307300 chr6B 270177493 270178104 611 False 676.00 676 86.75300 52 663 1 chr6B.!!$F1 611

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
148 151 0.517316 CGCTACAAACTTCACTGGGC 59.483 55.0 0.0 0.0 0.0 5.36 F
1016 1054 0.263172 GAGATGAGTGGAGAGGGGGA 59.737 60.0 0.0 0.0 0.0 4.81 F
1611 1682 0.251474 CATTGGGGGATGGCGATGAT 60.251 55.0 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1099 1137 0.256752 TACCCCTCGTCGATCTGGAA 59.743 55.000 10.70 0.0 0.00 3.53 R
2790 2882 0.636647 TATCTGTCTCTGGCCTCCCA 59.363 55.000 3.32 0.0 39.32 4.37 R
3377 3589 1.264288 CGGACTGCCTTCAAAACTCAC 59.736 52.381 0.00 0.0 0.00 3.51 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
21 23 4.431416 TTAAAAGGTCTGGCAGAAGTCA 57.569 40.909 20.62 0.00 0.00 3.41
25 27 3.618690 AGGTCTGGCAGAAGTCATAAC 57.381 47.619 20.62 4.36 0.00 1.89
31 33 6.398918 GTCTGGCAGAAGTCATAACTAAGAA 58.601 40.000 20.62 0.00 33.48 2.52
105 108 4.010349 CCAATGAGGTAAACTTCAGTCCC 58.990 47.826 1.35 0.00 35.40 4.46
128 131 7.172019 TCCCATTCTACGAACTAAAAGTTTCAC 59.828 37.037 0.00 0.00 38.80 3.18
143 146 3.311596 AGTTTCACCGCTACAAACTTCAC 59.688 43.478 0.00 0.00 37.09 3.18
148 151 0.517316 CGCTACAAACTTCACTGGGC 59.483 55.000 0.00 0.00 0.00 5.36
150 153 1.266989 GCTACAAACTTCACTGGGCAC 59.733 52.381 0.00 0.00 0.00 5.01
167 170 2.230992 GGCACCATTACAAACATGCAGA 59.769 45.455 0.00 0.00 34.73 4.26
168 171 3.504863 GCACCATTACAAACATGCAGAG 58.495 45.455 0.00 0.00 33.27 3.35
173 176 6.968904 CACCATTACAAACATGCAGAGAATAC 59.031 38.462 0.00 0.00 0.00 1.89
174 177 6.658816 ACCATTACAAACATGCAGAGAATACA 59.341 34.615 0.00 0.00 0.00 2.29
230 233 3.395639 CAAGCAATTGACAGCCACAAAT 58.604 40.909 10.34 0.00 0.00 2.32
235 238 4.232221 CAATTGACAGCCACAAATCAGAC 58.768 43.478 0.00 0.00 0.00 3.51
256 259 6.536582 CAGACATTAACCACCTCATTCTACAG 59.463 42.308 0.00 0.00 0.00 2.74
269 272 5.043903 TCATTCTACAGAAGCTAATCACGC 58.956 41.667 0.00 0.00 37.48 5.34
273 276 3.251479 ACAGAAGCTAATCACGCATCA 57.749 42.857 0.00 0.00 0.00 3.07
275 278 2.286294 CAGAAGCTAATCACGCATCACC 59.714 50.000 0.00 0.00 0.00 4.02
300 303 5.818857 GGAATTAACATAGTCCCAAGCGTAA 59.181 40.000 0.00 0.00 0.00 3.18
305 308 4.752146 ACATAGTCCCAAGCGTAAGTTAC 58.248 43.478 2.72 2.72 41.68 2.50
311 314 2.919229 CCCAAGCGTAAGTTACAGTACG 59.081 50.000 13.33 12.26 44.58 3.67
332 335 1.144936 CCTTCGGATCCAGCAGACC 59.855 63.158 13.41 0.00 0.00 3.85
360 363 0.671781 AGCAGATCAGCCACAACGAC 60.672 55.000 6.46 0.00 34.23 4.34
365 368 3.684305 CAGATCAGCCACAACGACAAATA 59.316 43.478 0.00 0.00 0.00 1.40
374 377 5.460419 GCCACAACGACAAATAAATCAACAA 59.540 36.000 0.00 0.00 0.00 2.83
382 385 9.474920 ACGACAAATAAATCAACAATGACAAAT 57.525 25.926 0.00 0.00 38.69 2.32
518 522 3.503363 GCAGAGCGCACCCATCAC 61.503 66.667 11.47 0.00 41.79 3.06
519 523 2.821366 CAGAGCGCACCCATCACC 60.821 66.667 11.47 0.00 0.00 4.02
520 524 3.321648 AGAGCGCACCCATCACCA 61.322 61.111 11.47 0.00 0.00 4.17
564 570 5.368989 TCTCTCAGAAAAGAGAAAACCACC 58.631 41.667 1.23 0.00 46.76 4.61
565 571 4.127171 TCTCAGAAAAGAGAAAACCACCG 58.873 43.478 0.00 0.00 41.45 4.94
566 572 2.616842 TCAGAAAAGAGAAAACCACCGC 59.383 45.455 0.00 0.00 0.00 5.68
569 575 3.253432 AGAAAAGAGAAAACCACCGCATC 59.747 43.478 0.00 0.00 0.00 3.91
575 593 0.820074 AAAACCACCGCATCAACCGA 60.820 50.000 0.00 0.00 0.00 4.69
590 608 0.608640 ACCGAGGAACGAATCAAGCT 59.391 50.000 0.00 0.00 45.77 3.74
598 616 3.440173 GGAACGAATCAAGCTGAAATGGA 59.560 43.478 0.00 0.00 0.00 3.41
628 646 0.901580 GGCGGGGATCGATTAGGGTA 60.902 60.000 0.00 0.00 42.43 3.69
895 919 3.064958 CAGACTGCTCGGTCGTAAATAGA 59.935 47.826 3.45 0.00 40.76 1.98
1014 1052 0.264359 AGGAGATGAGTGGAGAGGGG 59.736 60.000 0.00 0.00 0.00 4.79
1015 1053 0.762461 GGAGATGAGTGGAGAGGGGG 60.762 65.000 0.00 0.00 0.00 5.40
1016 1054 0.263172 GAGATGAGTGGAGAGGGGGA 59.737 60.000 0.00 0.00 0.00 4.81
1017 1055 0.264359 AGATGAGTGGAGAGGGGGAG 59.736 60.000 0.00 0.00 0.00 4.30
1018 1056 0.762461 GATGAGTGGAGAGGGGGAGG 60.762 65.000 0.00 0.00 0.00 4.30
1019 1057 2.041405 GAGTGGAGAGGGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
1187 1225 4.530161 CCTCAAGGAGAAGAAGAAGAAGGA 59.470 45.833 0.00 0.00 37.39 3.36
1188 1226 5.337491 CCTCAAGGAGAAGAAGAAGAAGGAG 60.337 48.000 0.00 0.00 37.39 3.69
1190 1228 2.837591 AGGAGAAGAAGAAGAAGGAGGC 59.162 50.000 0.00 0.00 0.00 4.70
1191 1229 2.093181 GGAGAAGAAGAAGAAGGAGGCC 60.093 54.545 0.00 0.00 0.00 5.19
1192 1230 1.912731 AGAAGAAGAAGAAGGAGGCCC 59.087 52.381 0.00 0.00 0.00 5.80
1388 1429 2.271497 GGAGGACGAGGACGAGGA 59.729 66.667 0.00 0.00 42.66 3.71
1389 1430 2.114051 GGAGGACGAGGACGAGGAC 61.114 68.421 0.00 0.00 42.66 3.85
1390 1431 2.436292 AGGACGAGGACGAGGACG 60.436 66.667 0.00 0.00 42.66 4.79
1391 1432 3.507009 GGACGAGGACGAGGACGG 61.507 72.222 0.00 0.00 44.46 4.79
1464 1535 1.006102 CCTCAAGGACGTCAACGCT 60.006 57.895 18.91 1.61 44.43 5.07
1557 1628 1.216710 CAACGAGCTCCAGAGGGAC 59.783 63.158 8.47 0.00 38.64 4.46
1563 1634 3.151022 CTCCAGAGGGACGGGCTC 61.151 72.222 0.00 0.00 38.64 4.70
1611 1682 0.251474 CATTGGGGGATGGCGATGAT 60.251 55.000 0.00 0.00 0.00 2.45
1620 1691 1.345741 GATGGCGATGATGAGGAGGAA 59.654 52.381 0.00 0.00 0.00 3.36
1706 1777 2.266055 GACCGAGGAGCTGTTGGG 59.734 66.667 0.00 0.00 0.00 4.12
1740 1811 2.877168 GGATGATGACAAGCTGGATGAC 59.123 50.000 0.00 0.00 0.00 3.06
1793 1864 1.378646 GGCCCTACCTTGAACCAGC 60.379 63.158 0.00 0.00 34.51 4.85
1800 1871 3.121030 CTTGAACCAGCGCCGGAG 61.121 66.667 18.59 1.55 0.00 4.63
2341 2412 3.463048 AGGAAGATGAATTGCTTGGGT 57.537 42.857 0.00 0.00 0.00 4.51
2358 2429 2.650322 TGGGTTACCTAAAGATTGGGCA 59.350 45.455 0.00 0.00 37.76 5.36
2360 2431 6.647785 TGGGTTACCTAAAGATTGGGCACC 62.648 50.000 0.00 6.10 44.46 5.01
2835 2927 5.622233 GCCAACAAGTGAACAAGAAGAAACT 60.622 40.000 0.00 0.00 0.00 2.66
2990 3202 3.145286 AGTCAAAGAAGAGCAAGAAGGC 58.855 45.455 0.00 0.00 0.00 4.35
3015 3227 0.745845 CTGGCAAGGAATCCAGGTCG 60.746 60.000 0.61 0.00 44.64 4.79
3214 3426 3.806625 ATTGATTTTGGGGATTCAGCG 57.193 42.857 0.00 0.00 0.00 5.18
3269 3481 2.203139 TCTGTGGGTGTTGCCGTG 60.203 61.111 0.00 0.00 38.44 4.94
3348 3560 7.775561 GTCTAATCTTGGAAGTTATGAACCCAT 59.224 37.037 0.00 0.00 36.81 4.00
3375 3587 7.985184 TGTTATCCTAGTAGCAACCTATTTGTG 59.015 37.037 0.00 0.00 37.54 3.33
3377 3589 5.730550 TCCTAGTAGCAACCTATTTGTGTG 58.269 41.667 0.00 0.00 37.54 3.82
3390 3604 6.183360 ACCTATTTGTGTGTGAGTTTTGAAGG 60.183 38.462 0.00 0.00 0.00 3.46
3392 3606 2.441410 TGTGTGTGAGTTTTGAAGGCA 58.559 42.857 0.00 0.00 0.00 4.75
3397 3611 1.264288 GTGAGTTTTGAAGGCAGTCCG 59.736 52.381 0.00 0.00 37.47 4.79
3410 3624 2.602878 GCAGTCCGTTCGTGAAAGATA 58.397 47.619 0.00 0.00 0.00 1.98
3411 3625 3.187700 GCAGTCCGTTCGTGAAAGATAT 58.812 45.455 0.00 0.00 0.00 1.63
3413 3627 4.802039 GCAGTCCGTTCGTGAAAGATATAA 59.198 41.667 0.00 0.00 0.00 0.98
3414 3628 5.462398 GCAGTCCGTTCGTGAAAGATATAAT 59.538 40.000 0.00 0.00 0.00 1.28
3415 3629 6.018994 GCAGTCCGTTCGTGAAAGATATAATT 60.019 38.462 0.00 0.00 0.00 1.40
3416 3630 7.465513 GCAGTCCGTTCGTGAAAGATATAATTT 60.466 37.037 0.00 0.00 0.00 1.82
3417 3631 8.056571 CAGTCCGTTCGTGAAAGATATAATTTC 58.943 37.037 6.11 6.11 37.21 2.17
3420 3634 9.158233 TCCGTTCGTGAAAGATATAATTTCTTT 57.842 29.630 3.75 3.75 44.09 2.52
3452 3666 9.391006 ACTGTTACAGTTTTATTTCTCTTGTGA 57.609 29.630 12.76 0.00 42.59 3.58
3489 3703 4.318332 TCGCTTGTGATTTCTTGATGAGT 58.682 39.130 0.00 0.00 0.00 3.41
3499 3713 7.327032 GTGATTTCTTGATGAGTGGTTTAAAGC 59.673 37.037 10.47 10.47 0.00 3.51
3533 3747 9.941325 ATCTTTCTAAATTATCATCGCATCTCT 57.059 29.630 0.00 0.00 0.00 3.10
3542 3756 9.662947 AATTATCATCGCATCTCTATGATTTGA 57.337 29.630 0.00 0.00 40.11 2.69
3543 3757 6.964741 ATCATCGCATCTCTATGATTTGAC 57.035 37.500 0.00 0.00 37.10 3.18
3544 3758 5.846203 TCATCGCATCTCTATGATTTGACA 58.154 37.500 0.00 0.00 34.84 3.58
3545 3759 5.924825 TCATCGCATCTCTATGATTTGACAG 59.075 40.000 0.00 0.00 34.84 3.51
3546 3760 5.268118 TCGCATCTCTATGATTTGACAGT 57.732 39.130 0.00 0.00 34.84 3.55
3547 3761 5.664457 TCGCATCTCTATGATTTGACAGTT 58.336 37.500 0.00 0.00 34.84 3.16
3548 3762 5.521372 TCGCATCTCTATGATTTGACAGTTG 59.479 40.000 0.00 0.00 34.84 3.16
3549 3763 5.521372 CGCATCTCTATGATTTGACAGTTGA 59.479 40.000 0.00 0.00 34.84 3.18
3550 3764 6.036408 CGCATCTCTATGATTTGACAGTTGAA 59.964 38.462 0.00 0.00 34.84 2.69
3551 3765 7.413328 CGCATCTCTATGATTTGACAGTTGAAA 60.413 37.037 0.00 0.00 34.84 2.69
3552 3766 8.404000 GCATCTCTATGATTTGACAGTTGAAAT 58.596 33.333 0.00 0.00 34.84 2.17
3553 3767 9.932699 CATCTCTATGATTTGACAGTTGAAATC 57.067 33.333 10.24 10.24 38.52 2.17
3555 3769 8.939929 TCTCTATGATTTGACAGTTGAAATCAC 58.060 33.333 17.72 0.12 46.25 3.06
3556 3770 8.620116 TCTATGATTTGACAGTTGAAATCACA 57.380 30.769 17.72 10.08 46.25 3.58
3557 3771 9.234827 TCTATGATTTGACAGTTGAAATCACAT 57.765 29.630 17.72 10.02 46.25 3.21
3560 3774 7.297391 TGATTTGACAGTTGAAATCACATACG 58.703 34.615 13.84 0.00 41.47 3.06
3561 3775 4.661993 TGACAGTTGAAATCACATACGC 57.338 40.909 0.00 0.00 0.00 4.42
3562 3776 3.435327 TGACAGTTGAAATCACATACGCC 59.565 43.478 0.00 0.00 0.00 5.68
3563 3777 2.747446 ACAGTTGAAATCACATACGCCC 59.253 45.455 0.00 0.00 0.00 6.13
3564 3778 3.009723 CAGTTGAAATCACATACGCCCT 58.990 45.455 0.00 0.00 0.00 5.19
3593 3807 5.153950 AGAAAGTACCTGTTCCTCATGAC 57.846 43.478 0.00 0.00 0.00 3.06
3608 3822 5.538433 TCCTCATGACATCGATTACATGGTA 59.462 40.000 26.86 15.93 40.00 3.25
3609 3823 5.635280 CCTCATGACATCGATTACATGGTAC 59.365 44.000 26.86 7.37 40.00 3.34
3611 3825 6.447162 TCATGACATCGATTACATGGTACTC 58.553 40.000 26.86 4.01 40.00 2.59
3612 3826 5.196341 TGACATCGATTACATGGTACTCC 57.804 43.478 0.00 0.00 0.00 3.85
3613 3827 4.038763 TGACATCGATTACATGGTACTCCC 59.961 45.833 0.00 0.00 0.00 4.30
3614 3828 4.223953 ACATCGATTACATGGTACTCCCT 58.776 43.478 0.00 0.00 0.00 4.20
3615 3829 4.281182 ACATCGATTACATGGTACTCCCTC 59.719 45.833 0.00 0.00 0.00 4.30
3617 3831 2.963101 CGATTACATGGTACTCCCTCCA 59.037 50.000 0.00 0.00 38.14 3.86
3618 3832 3.578716 CGATTACATGGTACTCCCTCCAT 59.421 47.826 0.00 0.00 44.15 3.41
3619 3833 4.322049 CGATTACATGGTACTCCCTCCATC 60.322 50.000 0.00 0.00 41.79 3.51
3620 3834 1.807814 ACATGGTACTCCCTCCATCC 58.192 55.000 0.00 0.00 41.79 3.51
3621 3835 1.059913 CATGGTACTCCCTCCATCCC 58.940 60.000 0.00 0.00 41.79 3.85
3622 3836 0.647738 ATGGTACTCCCTCCATCCCA 59.352 55.000 0.00 0.00 39.92 4.37
3623 3837 0.647738 TGGTACTCCCTCCATCCCAT 59.352 55.000 0.00 0.00 0.00 4.00
3624 3838 1.870327 TGGTACTCCCTCCATCCCATA 59.130 52.381 0.00 0.00 0.00 2.74
3625 3839 2.251605 TGGTACTCCCTCCATCCCATAA 59.748 50.000 0.00 0.00 0.00 1.90
3626 3840 3.115962 TGGTACTCCCTCCATCCCATAAT 60.116 47.826 0.00 0.00 0.00 1.28
3627 3841 4.110592 TGGTACTCCCTCCATCCCATAATA 59.889 45.833 0.00 0.00 0.00 0.98
3628 3842 5.222973 TGGTACTCCCTCCATCCCATAATAT 60.223 44.000 0.00 0.00 0.00 1.28
3629 3843 6.009297 TGGTACTCCCTCCATCCCATAATATA 60.009 42.308 0.00 0.00 0.00 0.86
3630 3844 6.555360 GGTACTCCCTCCATCCCATAATATAG 59.445 46.154 0.00 0.00 0.00 1.31
3631 3845 5.542743 ACTCCCTCCATCCCATAATATAGG 58.457 45.833 0.00 0.00 0.00 2.57
3632 3846 5.261181 ACTCCCTCCATCCCATAATATAGGA 59.739 44.000 0.00 0.00 0.00 2.94
3633 3847 5.538877 TCCCTCCATCCCATAATATAGGAC 58.461 45.833 0.00 0.00 30.97 3.85
3634 3848 4.345257 CCCTCCATCCCATAATATAGGACG 59.655 50.000 0.00 0.00 30.97 4.79
3635 3849 4.202264 CCTCCATCCCATAATATAGGACGC 60.202 50.000 0.00 0.00 30.97 5.19
3636 3850 4.620723 TCCATCCCATAATATAGGACGCT 58.379 43.478 0.00 0.00 30.97 5.07
3637 3851 5.030147 TCCATCCCATAATATAGGACGCTT 58.970 41.667 0.00 0.00 30.97 4.68
3638 3852 5.487488 TCCATCCCATAATATAGGACGCTTT 59.513 40.000 0.00 0.00 30.97 3.51
3639 3853 6.012858 TCCATCCCATAATATAGGACGCTTTT 60.013 38.462 0.00 0.00 30.97 2.27
3640 3854 6.659242 CCATCCCATAATATAGGACGCTTTTT 59.341 38.462 0.00 0.00 30.97 1.94
3641 3855 7.362056 CCATCCCATAATATAGGACGCTTTTTG 60.362 40.741 0.00 0.00 30.97 2.44
3642 3856 6.833041 TCCCATAATATAGGACGCTTTTTGA 58.167 36.000 0.00 0.00 0.00 2.69
3643 3857 6.708949 TCCCATAATATAGGACGCTTTTTGAC 59.291 38.462 0.00 0.00 0.00 3.18
3644 3858 6.485313 CCCATAATATAGGACGCTTTTTGACA 59.515 38.462 0.00 0.00 0.00 3.58
3645 3859 7.352739 CCATAATATAGGACGCTTTTTGACAC 58.647 38.462 0.00 0.00 0.00 3.67
3646 3860 7.226720 CCATAATATAGGACGCTTTTTGACACT 59.773 37.037 0.00 0.00 0.00 3.55
3647 3861 8.612619 CATAATATAGGACGCTTTTTGACACTT 58.387 33.333 0.00 0.00 0.00 3.16
3648 3862 7.448748 AATATAGGACGCTTTTTGACACTTT 57.551 32.000 0.00 0.00 0.00 2.66
3649 3863 8.556213 AATATAGGACGCTTTTTGACACTTTA 57.444 30.769 0.00 0.00 0.00 1.85
3650 3864 4.547406 AGGACGCTTTTTGACACTTTAC 57.453 40.909 0.00 0.00 0.00 2.01
3651 3865 3.942748 AGGACGCTTTTTGACACTTTACA 59.057 39.130 0.00 0.00 0.00 2.41
3652 3866 4.033019 GGACGCTTTTTGACACTTTACAC 58.967 43.478 0.00 0.00 0.00 2.90
3653 3867 4.201881 GGACGCTTTTTGACACTTTACACT 60.202 41.667 0.00 0.00 0.00 3.55
3654 3868 5.006941 GGACGCTTTTTGACACTTTACACTA 59.993 40.000 0.00 0.00 0.00 2.74
3655 3869 6.044512 ACGCTTTTTGACACTTTACACTAG 57.955 37.500 0.00 0.00 0.00 2.57
3656 3870 5.583457 ACGCTTTTTGACACTTTACACTAGT 59.417 36.000 0.00 0.00 0.00 2.57
3657 3871 5.901884 CGCTTTTTGACACTTTACACTAGTG 59.098 40.000 21.44 21.44 46.56 2.74
3691 3905 5.623956 AATGTCTTACATTATGGGACGGA 57.376 39.130 3.51 0.00 46.11 4.69
3692 3906 4.665833 TGTCTTACATTATGGGACGGAG 57.334 45.455 0.00 0.00 0.00 4.63
3693 3907 3.386726 TGTCTTACATTATGGGACGGAGG 59.613 47.826 0.00 0.00 0.00 4.30
3694 3908 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3695 3909 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3696 3910 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3697 3911 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3698 3912 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3699 3913 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
3700 3914 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
3701 3915 1.229131 ATGGGACGGAGGGAGTAGTA 58.771 55.000 0.00 0.00 0.00 1.82
3702 3916 1.002069 TGGGACGGAGGGAGTAGTAA 58.998 55.000 0.00 0.00 0.00 2.24
3703 3917 1.341383 TGGGACGGAGGGAGTAGTAAC 60.341 57.143 0.00 0.00 0.00 2.50
3704 3918 1.064091 GGGACGGAGGGAGTAGTAACT 60.064 57.143 0.00 0.00 39.21 2.24
3705 3919 2.173569 GGGACGGAGGGAGTAGTAACTA 59.826 54.545 0.00 0.00 35.56 2.24
3706 3920 3.372025 GGGACGGAGGGAGTAGTAACTAA 60.372 52.174 0.00 0.00 35.56 2.24
3709 3923 5.704978 GGACGGAGGGAGTAGTAACTAATAG 59.295 48.000 0.00 0.00 35.56 1.73
3713 3927 6.208994 CGGAGGGAGTAGTAACTAATAGCAAT 59.791 42.308 0.00 0.00 35.56 3.56
3766 3981 9.979578 TCTTGTTAGTTTCATGCATAAACAAAT 57.020 25.926 22.46 12.00 38.92 2.32
3778 3993 5.305644 TGCATAAACAAATACCCCACTGTTT 59.694 36.000 4.63 4.63 42.83 2.83
3859 4074 7.752239 CCTTCTGTGCAGTCTAAAATGTAATTG 59.248 37.037 0.00 0.00 36.10 2.32
3960 4175 3.751479 AAAAATGGGTTCTGTTCAGGC 57.249 42.857 0.00 0.00 0.00 4.85
3962 4177 1.620822 AATGGGTTCTGTTCAGGCAC 58.379 50.000 0.00 0.00 0.00 5.01
4003 4378 2.720915 GGCTGAAGAAGAAAGCTCCAT 58.279 47.619 0.00 0.00 37.12 3.41
4004 4379 2.682352 GGCTGAAGAAGAAAGCTCCATC 59.318 50.000 0.00 0.00 37.12 3.51
4005 4380 3.341823 GCTGAAGAAGAAAGCTCCATCA 58.658 45.455 0.00 0.00 34.05 3.07
4006 4381 3.755378 GCTGAAGAAGAAAGCTCCATCAA 59.245 43.478 0.00 0.00 34.05 2.57
4017 4392 9.638176 AAGAAAGCTCCATCAATCAATAATAGT 57.362 29.630 0.00 0.00 0.00 2.12
4021 4396 6.946583 AGCTCCATCAATCAATAATAGTGCAT 59.053 34.615 0.00 0.00 0.00 3.96
4023 4398 7.094506 GCTCCATCAATCAATAATAGTGCATGA 60.095 37.037 0.00 0.00 0.00 3.07
4024 4399 8.331730 TCCATCAATCAATAATAGTGCATGAG 57.668 34.615 0.00 0.00 0.00 2.90
4035 4410 6.428385 AATAGTGCATGAGAAAGCAGTAAC 57.572 37.500 0.00 0.00 46.27 2.50
4144 4519 5.008415 CACAATTAGCATCTCCTCAACCATC 59.992 44.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 13 5.582665 CCACTTCTTAGTTATGACTTCTGCC 59.417 44.000 0.00 0.00 37.33 4.85
12 14 5.064071 GCCACTTCTTAGTTATGACTTCTGC 59.936 44.000 0.00 0.00 37.33 4.26
21 23 7.331791 CCTAGAACAAGCCACTTCTTAGTTAT 58.668 38.462 0.00 0.00 30.26 1.89
25 27 4.508662 CCCTAGAACAAGCCACTTCTTAG 58.491 47.826 0.00 0.00 0.00 2.18
31 33 1.296715 CGCCCTAGAACAAGCCACT 59.703 57.895 0.00 0.00 0.00 4.00
105 108 7.007697 CGGTGAAACTTTTAGTTCGTAGAATG 58.992 38.462 0.00 0.00 37.47 2.67
128 131 1.156736 CCCAGTGAAGTTTGTAGCGG 58.843 55.000 0.00 0.00 0.00 5.52
143 146 2.674747 GCATGTTTGTAATGGTGCCCAG 60.675 50.000 0.00 0.00 36.75 4.45
148 151 5.375417 TTCTCTGCATGTTTGTAATGGTG 57.625 39.130 0.00 0.00 0.00 4.17
150 153 7.087409 TGTATTCTCTGCATGTTTGTAATGG 57.913 36.000 0.00 0.00 0.00 3.16
158 161 9.265901 GAACTGTATATGTATTCTCTGCATGTT 57.734 33.333 0.00 0.00 32.00 2.71
161 164 7.601886 GCTGAACTGTATATGTATTCTCTGCAT 59.398 37.037 0.00 0.00 34.29 3.96
168 171 9.372369 GGGATAAGCTGAACTGTATATGTATTC 57.628 37.037 0.00 0.00 0.00 1.75
173 176 6.524734 TGTGGGATAAGCTGAACTGTATATG 58.475 40.000 0.00 0.00 0.00 1.78
174 177 6.747414 TGTGGGATAAGCTGAACTGTATAT 57.253 37.500 0.00 0.00 0.00 0.86
177 180 4.901197 TTGTGGGATAAGCTGAACTGTA 57.099 40.909 0.00 0.00 0.00 2.74
193 196 4.764679 TGCTTGCTGTACTTATTTGTGG 57.235 40.909 0.00 0.00 0.00 4.17
230 233 5.762179 AGAATGAGGTGGTTAATGTCTGA 57.238 39.130 0.00 0.00 0.00 3.27
235 238 6.037610 GCTTCTGTAGAATGAGGTGGTTAATG 59.962 42.308 0.00 0.00 33.01 1.90
256 259 1.258982 CGGTGATGCGTGATTAGCTTC 59.741 52.381 0.00 0.00 38.68 3.86
269 272 4.755123 GGGACTATGTTAATTCCGGTGATG 59.245 45.833 0.00 0.00 0.00 3.07
273 276 4.777463 CTTGGGACTATGTTAATTCCGGT 58.223 43.478 0.00 0.00 0.00 5.28
275 278 3.247648 CGCTTGGGACTATGTTAATTCCG 59.752 47.826 0.00 0.00 0.00 4.30
300 303 3.875369 ATCCGAAGGGTCGTACTGTAACT 60.875 47.826 0.00 0.00 28.78 2.24
305 308 0.384669 GGATCCGAAGGGTCGTACTG 59.615 60.000 0.00 0.00 28.78 2.74
311 314 1.144936 CTGCTGGATCCGAAGGGTC 59.855 63.158 7.39 0.00 28.78 4.46
332 335 2.093288 TGGCTGATCTGCTAGTTCCTTG 60.093 50.000 21.99 0.00 0.00 3.61
374 377 6.332635 TCCAAGGGTATGGATCTATTTGTCAT 59.667 38.462 0.00 0.00 44.52 3.06
518 522 5.673337 TCTTCTCACTGTTTTTCGATTGG 57.327 39.130 0.00 0.00 0.00 3.16
519 523 7.117523 AGAGATCTTCTCACTGTTTTTCGATTG 59.882 37.037 0.00 0.00 45.73 2.67
520 524 7.158021 AGAGATCTTCTCACTGTTTTTCGATT 58.842 34.615 0.00 0.00 45.73 3.34
552 558 1.880027 GTTGATGCGGTGGTTTTCTCT 59.120 47.619 0.00 0.00 0.00 3.10
553 559 1.068541 GGTTGATGCGGTGGTTTTCTC 60.069 52.381 0.00 0.00 0.00 2.87
555 561 0.386731 CGGTTGATGCGGTGGTTTTC 60.387 55.000 0.00 0.00 0.00 2.29
556 562 0.820074 TCGGTTGATGCGGTGGTTTT 60.820 50.000 0.00 0.00 0.00 2.43
558 564 1.671054 CTCGGTTGATGCGGTGGTT 60.671 57.895 0.00 0.00 0.00 3.67
561 567 1.375396 TTCCTCGGTTGATGCGGTG 60.375 57.895 0.00 0.00 0.00 4.94
564 570 1.011968 TTCGTTCCTCGGTTGATGCG 61.012 55.000 0.00 0.00 40.32 4.73
565 571 1.327764 GATTCGTTCCTCGGTTGATGC 59.672 52.381 0.00 0.00 40.32 3.91
566 572 2.616960 TGATTCGTTCCTCGGTTGATG 58.383 47.619 0.00 0.00 40.32 3.07
569 575 1.128692 GCTTGATTCGTTCCTCGGTTG 59.871 52.381 0.00 0.00 40.32 3.77
575 593 3.441572 CCATTTCAGCTTGATTCGTTCCT 59.558 43.478 0.00 0.00 0.00 3.36
590 608 1.745115 CGCCGCTCCTTCCATTTCA 60.745 57.895 0.00 0.00 0.00 2.69
676 700 4.506255 CATCCGCACCCCCTTCCC 62.506 72.222 0.00 0.00 0.00 3.97
920 944 2.959372 TGGAGACACACCGCGTAG 59.041 61.111 4.92 0.00 33.40 3.51
1014 1052 2.040359 CTCTTCCCCTCCCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
1015 1053 2.040359 CCTCTTCCCCTCCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
1016 1054 2.543637 TCCTCTTCCCCTCCCCCT 60.544 66.667 0.00 0.00 0.00 4.79
1017 1055 2.040359 CTCCTCTTCCCCTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
1018 1056 2.040359 CCTCCTCTTCCCCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
1019 1057 2.040359 CCCTCCTCTTCCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
1099 1137 0.256752 TACCCCTCGTCGATCTGGAA 59.743 55.000 10.70 0.00 0.00 3.53
1161 1199 0.898320 TCTTCTTCTCCTTGAGGCGG 59.102 55.000 0.00 0.00 34.44 6.13
1206 1244 2.048784 TCGTCGTCCTCGTCGTCT 60.049 61.111 7.05 0.00 45.27 4.18
1440 1511 0.601558 TGACGTCCTTGAGGTACAGC 59.398 55.000 14.12 0.00 36.34 4.40
1557 1628 3.393360 AGGAACTCCTTGAGCCCG 58.607 61.111 0.00 0.00 46.09 6.13
1611 1682 3.517100 CCTTGAACAGATCTTCCTCCTCA 59.483 47.826 0.00 0.00 0.00 3.86
1620 1691 1.002430 TGCTTCGCCTTGAACAGATCT 59.998 47.619 0.00 0.00 31.87 2.75
1706 1777 3.193479 GTCATCATCCCCAAAAACCTCAC 59.807 47.826 0.00 0.00 0.00 3.51
1793 1864 2.881352 GCGAGAACTTCTCCGGCG 60.881 66.667 12.37 0.00 40.34 6.46
2341 2412 3.589735 TCAGGTGCCCAATCTTTAGGTAA 59.410 43.478 0.00 0.00 0.00 2.85
2358 2429 4.470304 GTAGACCCTTCTTTACCATCAGGT 59.530 45.833 0.00 0.00 41.60 4.00
2360 2431 5.665459 CAGTAGACCCTTCTTTACCATCAG 58.335 45.833 0.00 0.00 32.75 2.90
2517 2609 2.502947 CAGATCTCCAATGGTGTCCTCA 59.497 50.000 0.00 0.00 0.00 3.86
2583 2675 3.566322 GCAGTATCTCATACGTCTCCAGT 59.434 47.826 0.00 0.00 40.64 4.00
2790 2882 0.636647 TATCTGTCTCTGGCCTCCCA 59.363 55.000 3.32 0.00 39.32 4.37
2835 2927 3.490439 TTTGACTCTGTCTTGCCATCA 57.510 42.857 0.00 0.00 33.15 3.07
2908 3000 2.224621 TGACTTCCTCTGCCTTTTCAGG 60.225 50.000 0.00 0.00 44.28 3.86
2990 3202 3.203618 CTGGATTCCTTGCCAGTCTTGG 61.204 54.545 3.95 0.00 45.21 3.61
3015 3227 2.112190 CCAGAACTAGGGTCTTCCTCC 58.888 57.143 0.00 0.00 44.06 4.30
3269 3481 2.867647 GCTCCAAGCAAATGTTTCCACC 60.868 50.000 0.00 0.00 41.89 4.61
3329 3541 5.982890 ACAATGGGTTCATAACTTCCAAG 57.017 39.130 0.00 0.00 32.44 3.61
3331 3543 6.605594 GGATAACAATGGGTTCATAACTTCCA 59.394 38.462 0.00 0.00 40.96 3.53
3348 3560 8.545472 ACAAATAGGTTGCTACTAGGATAACAA 58.455 33.333 0.00 0.00 41.31 2.83
3375 3587 2.033424 GGACTGCCTTCAAAACTCACAC 59.967 50.000 0.00 0.00 0.00 3.82
3377 3589 1.264288 CGGACTGCCTTCAAAACTCAC 59.736 52.381 0.00 0.00 0.00 3.51
3390 3604 1.429463 ATCTTTCACGAACGGACTGC 58.571 50.000 0.00 0.00 0.00 4.40
3392 3606 7.980099 AGAAATTATATCTTTCACGAACGGACT 59.020 33.333 11.29 0.00 35.51 3.85
3434 3648 9.125026 ACTGAACATCACAAGAGAAATAAAACT 57.875 29.630 0.00 0.00 0.00 2.66
3435 3649 9.736023 AACTGAACATCACAAGAGAAATAAAAC 57.264 29.630 0.00 0.00 0.00 2.43
3442 3656 9.950680 GAAATAAAACTGAACATCACAAGAGAA 57.049 29.630 0.00 0.00 0.00 2.87
3443 3657 8.282592 CGAAATAAAACTGAACATCACAAGAGA 58.717 33.333 0.00 0.00 0.00 3.10
3444 3658 7.059945 GCGAAATAAAACTGAACATCACAAGAG 59.940 37.037 0.00 0.00 0.00 2.85
3445 3659 6.855914 GCGAAATAAAACTGAACATCACAAGA 59.144 34.615 0.00 0.00 0.00 3.02
3446 3660 6.857964 AGCGAAATAAAACTGAACATCACAAG 59.142 34.615 0.00 0.00 0.00 3.16
3447 3661 6.734137 AGCGAAATAAAACTGAACATCACAA 58.266 32.000 0.00 0.00 0.00 3.33
3448 3662 6.312399 AGCGAAATAAAACTGAACATCACA 57.688 33.333 0.00 0.00 0.00 3.58
3449 3663 6.636850 ACAAGCGAAATAAAACTGAACATCAC 59.363 34.615 0.00 0.00 0.00 3.06
3450 3664 6.636447 CACAAGCGAAATAAAACTGAACATCA 59.364 34.615 0.00 0.00 0.00 3.07
3451 3665 6.855914 TCACAAGCGAAATAAAACTGAACATC 59.144 34.615 0.00 0.00 0.00 3.06
3452 3666 6.734137 TCACAAGCGAAATAAAACTGAACAT 58.266 32.000 0.00 0.00 0.00 2.71
3453 3667 6.125327 TCACAAGCGAAATAAAACTGAACA 57.875 33.333 0.00 0.00 0.00 3.18
3454 3668 7.623268 AATCACAAGCGAAATAAAACTGAAC 57.377 32.000 0.00 0.00 0.00 3.18
3455 3669 8.134895 AGAAATCACAAGCGAAATAAAACTGAA 58.865 29.630 0.00 0.00 0.00 3.02
3456 3670 7.648142 AGAAATCACAAGCGAAATAAAACTGA 58.352 30.769 0.00 0.00 0.00 3.41
3457 3671 7.858052 AGAAATCACAAGCGAAATAAAACTG 57.142 32.000 0.00 0.00 0.00 3.16
3464 3678 6.072286 ACTCATCAAGAAATCACAAGCGAAAT 60.072 34.615 0.00 0.00 0.00 2.17
3489 3703 8.189119 AGAAAGATAACCATTGCTTTAAACCA 57.811 30.769 0.00 0.00 31.30 3.67
3520 3734 6.461640 TGTCAAATCATAGAGATGCGATGAT 58.538 36.000 0.00 0.00 46.95 2.45
3534 3748 7.964559 CGTATGTGATTTCAACTGTCAAATCAT 59.035 33.333 21.39 13.84 45.93 2.45
3535 3749 7.297391 CGTATGTGATTTCAACTGTCAAATCA 58.703 34.615 17.47 17.47 43.54 2.57
3536 3750 6.249260 GCGTATGTGATTTCAACTGTCAAATC 59.751 38.462 14.06 14.06 38.83 2.17
3537 3751 6.086222 GCGTATGTGATTTCAACTGTCAAAT 58.914 36.000 0.00 0.00 0.00 2.32
3538 3752 5.448438 GCGTATGTGATTTCAACTGTCAAA 58.552 37.500 0.00 0.00 0.00 2.69
3539 3753 4.083537 GGCGTATGTGATTTCAACTGTCAA 60.084 41.667 0.00 0.00 0.00 3.18
3540 3754 3.435327 GGCGTATGTGATTTCAACTGTCA 59.565 43.478 0.00 0.00 0.00 3.58
3541 3755 3.181510 GGGCGTATGTGATTTCAACTGTC 60.182 47.826 0.00 0.00 0.00 3.51
3542 3756 2.747446 GGGCGTATGTGATTTCAACTGT 59.253 45.455 0.00 0.00 0.00 3.55
3543 3757 3.009723 AGGGCGTATGTGATTTCAACTG 58.990 45.455 0.00 0.00 0.00 3.16
3544 3758 3.350219 AGGGCGTATGTGATTTCAACT 57.650 42.857 0.00 0.00 0.00 3.16
3545 3759 4.189231 ACTAGGGCGTATGTGATTTCAAC 58.811 43.478 0.00 0.00 0.00 3.18
3546 3760 4.481368 ACTAGGGCGTATGTGATTTCAA 57.519 40.909 0.00 0.00 0.00 2.69
3547 3761 4.647853 ACTACTAGGGCGTATGTGATTTCA 59.352 41.667 0.00 0.00 0.00 2.69
3548 3762 5.197682 ACTACTAGGGCGTATGTGATTTC 57.802 43.478 0.00 0.00 0.00 2.17
3549 3763 6.066690 TCTACTACTAGGGCGTATGTGATTT 58.933 40.000 0.00 0.00 0.00 2.17
3550 3764 5.628130 TCTACTACTAGGGCGTATGTGATT 58.372 41.667 0.00 0.00 0.00 2.57
3551 3765 5.238624 TCTACTACTAGGGCGTATGTGAT 57.761 43.478 0.00 0.00 0.00 3.06
3552 3766 4.694760 TCTACTACTAGGGCGTATGTGA 57.305 45.455 0.00 0.00 0.00 3.58
3553 3767 5.298777 ACTTTCTACTACTAGGGCGTATGTG 59.701 44.000 0.00 0.00 0.00 3.21
3554 3768 5.444176 ACTTTCTACTACTAGGGCGTATGT 58.556 41.667 0.00 0.00 0.00 2.29
3555 3769 6.072783 GGTACTTTCTACTACTAGGGCGTATG 60.073 46.154 0.00 0.00 0.00 2.39
3556 3770 6.000840 GGTACTTTCTACTACTAGGGCGTAT 58.999 44.000 0.00 0.00 0.00 3.06
3557 3771 5.131142 AGGTACTTTCTACTACTAGGGCGTA 59.869 44.000 0.00 0.00 27.25 4.42
3558 3772 4.080072 AGGTACTTTCTACTACTAGGGCGT 60.080 45.833 0.00 0.00 27.25 5.68
3559 3773 4.275443 CAGGTACTTTCTACTACTAGGGCG 59.725 50.000 0.00 0.00 34.60 6.13
3560 3774 5.199723 ACAGGTACTTTCTACTACTAGGGC 58.800 45.833 0.00 0.00 34.60 5.19
3561 3775 6.320926 GGAACAGGTACTTTCTACTACTAGGG 59.679 46.154 0.00 0.00 34.60 3.53
3562 3776 7.118060 AGGAACAGGTACTTTCTACTACTAGG 58.882 42.308 0.00 0.00 34.60 3.02
3563 3777 7.828223 TGAGGAACAGGTACTTTCTACTACTAG 59.172 40.741 0.00 0.00 34.60 2.57
3564 3778 7.693132 TGAGGAACAGGTACTTTCTACTACTA 58.307 38.462 0.00 0.00 34.60 1.82
3593 3807 4.322049 GGAGGGAGTACCATGTAATCGATG 60.322 50.000 0.00 0.00 43.89 3.84
3608 3822 5.261181 TCCTATATTATGGGATGGAGGGAGT 59.739 44.000 4.74 0.00 34.71 3.85
3609 3823 5.604650 GTCCTATATTATGGGATGGAGGGAG 59.395 48.000 11.49 0.00 42.23 4.30
3611 3825 4.345257 CGTCCTATATTATGGGATGGAGGG 59.655 50.000 16.73 0.50 42.23 4.30
3612 3826 4.202264 GCGTCCTATATTATGGGATGGAGG 60.202 50.000 22.69 11.91 44.50 4.30
3613 3827 4.651503 AGCGTCCTATATTATGGGATGGAG 59.348 45.833 22.69 12.08 44.50 3.86
3614 3828 4.620723 AGCGTCCTATATTATGGGATGGA 58.379 43.478 22.69 5.65 44.50 3.41
3615 3829 5.359194 AAGCGTCCTATATTATGGGATGG 57.641 43.478 22.69 14.37 44.50 3.51
3617 3831 7.390718 GTCAAAAAGCGTCCTATATTATGGGAT 59.609 37.037 11.49 0.00 42.23 3.85
3618 3832 6.708949 GTCAAAAAGCGTCCTATATTATGGGA 59.291 38.462 4.74 4.74 37.61 4.37
3619 3833 6.485313 TGTCAAAAAGCGTCCTATATTATGGG 59.515 38.462 0.00 0.00 0.00 4.00
3620 3834 7.226720 AGTGTCAAAAAGCGTCCTATATTATGG 59.773 37.037 0.00 0.00 0.00 2.74
3621 3835 8.142994 AGTGTCAAAAAGCGTCCTATATTATG 57.857 34.615 0.00 0.00 0.00 1.90
3622 3836 8.732746 AAGTGTCAAAAAGCGTCCTATATTAT 57.267 30.769 0.00 0.00 0.00 1.28
3623 3837 8.556213 AAAGTGTCAAAAAGCGTCCTATATTA 57.444 30.769 0.00 0.00 0.00 0.98
3624 3838 7.448748 AAAGTGTCAAAAAGCGTCCTATATT 57.551 32.000 0.00 0.00 0.00 1.28
3625 3839 7.604927 TGTAAAGTGTCAAAAAGCGTCCTATAT 59.395 33.333 0.00 0.00 0.00 0.86
3626 3840 6.930164 TGTAAAGTGTCAAAAAGCGTCCTATA 59.070 34.615 0.00 0.00 0.00 1.31
3627 3841 5.761234 TGTAAAGTGTCAAAAAGCGTCCTAT 59.239 36.000 0.00 0.00 0.00 2.57
3628 3842 5.006941 GTGTAAAGTGTCAAAAAGCGTCCTA 59.993 40.000 0.00 0.00 0.00 2.94
3629 3843 3.942748 TGTAAAGTGTCAAAAAGCGTCCT 59.057 39.130 0.00 0.00 0.00 3.85
3630 3844 4.033019 GTGTAAAGTGTCAAAAAGCGTCC 58.967 43.478 0.00 0.00 0.00 4.79
3631 3845 4.905269 AGTGTAAAGTGTCAAAAAGCGTC 58.095 39.130 0.00 0.00 0.00 5.19
3632 3846 4.957759 AGTGTAAAGTGTCAAAAAGCGT 57.042 36.364 0.00 0.00 0.00 5.07
3633 3847 5.901884 CACTAGTGTAAAGTGTCAAAAAGCG 59.098 40.000 15.06 0.00 39.61 4.68
3666 3880 6.887545 TCCGTCCCATAATGTAAGACATTTTT 59.112 34.615 9.92 0.00 45.80 1.94
3667 3881 6.419791 TCCGTCCCATAATGTAAGACATTTT 58.580 36.000 9.92 0.33 45.80 1.82
3668 3882 5.996644 TCCGTCCCATAATGTAAGACATTT 58.003 37.500 9.92 0.00 45.80 2.32
3670 3884 4.040461 CCTCCGTCCCATAATGTAAGACAT 59.960 45.833 0.00 0.00 41.31 3.06
3671 3885 3.386726 CCTCCGTCCCATAATGTAAGACA 59.613 47.826 0.00 0.00 0.00 3.41
3672 3886 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3673 3887 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3674 3888 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3675 3889 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3676 3890 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3677 3891 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3678 3892 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3679 3893 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3680 3894 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3681 3895 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3682 3896 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
3683 3897 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3684 3898 1.064091 AGTTACTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
3685 3899 2.433662 AGTTACTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
3686 3900 5.181056 GCTATTAGTTACTACTCCCTCCGTC 59.819 48.000 0.00 0.00 35.78 4.79
3687 3901 5.069318 GCTATTAGTTACTACTCCCTCCGT 58.931 45.833 0.00 0.00 35.78 4.69
3688 3902 5.068636 TGCTATTAGTTACTACTCCCTCCG 58.931 45.833 0.00 0.00 35.78 4.63
3689 3903 6.973460 TTGCTATTAGTTACTACTCCCTCC 57.027 41.667 0.00 0.00 35.78 4.30
3706 3920 9.686683 AGGAAACAAAGAGTGTATTATTGCTAT 57.313 29.630 0.00 0.00 40.60 2.97
3709 3923 8.296713 TCAAGGAAACAAAGAGTGTATTATTGC 58.703 33.333 0.00 0.00 40.60 3.56
3713 3927 6.995686 TGCTCAAGGAAACAAAGAGTGTATTA 59.004 34.615 0.00 0.00 40.60 0.98
3717 3931 3.620488 TGCTCAAGGAAACAAAGAGTGT 58.380 40.909 0.00 0.00 44.64 3.55
3720 3934 5.702349 AGATTGCTCAAGGAAACAAAGAG 57.298 39.130 0.00 0.00 0.00 2.85
3766 3981 4.148838 CAAATGGAGAAAACAGTGGGGTA 58.851 43.478 0.00 0.00 0.00 3.69
3778 3993 7.592938 CAATGCTGTACTAAACAAATGGAGAA 58.407 34.615 0.00 0.00 37.74 2.87
3814 4029 3.092301 AGGCAATTCCTAAAAGCAGTCC 58.908 45.455 0.00 0.00 45.41 3.85
3859 4074 9.339850 TCTATCTGACTTGGTATTACAGTACTC 57.660 37.037 0.00 0.00 0.00 2.59
3869 4084 9.821240 AGTTGATCTATCTATCTGACTTGGTAT 57.179 33.333 0.00 0.00 0.00 2.73
3890 4105 2.016318 CTGTGTCCACTTTGCAGTTGA 58.984 47.619 0.00 0.00 0.00 3.18
3946 4161 1.620822 ATTGTGCCTGAACAGAACCC 58.379 50.000 3.19 0.00 0.00 4.11
3960 4175 3.062639 GGTGAACACGAGAGCATATTGTG 59.937 47.826 0.00 2.60 37.94 3.33
3962 4177 2.282555 CGGTGAACACGAGAGCATATTG 59.717 50.000 0.00 0.00 0.00 1.90
3973 4348 0.878523 TTCTTCAGCCGGTGAACACG 60.879 55.000 8.95 0.78 40.45 4.49
4003 4378 8.347771 GCTTTCTCATGCACTATTATTGATTGA 58.652 33.333 0.00 0.00 0.00 2.57
4004 4379 8.132995 TGCTTTCTCATGCACTATTATTGATTG 58.867 33.333 0.00 0.00 33.94 2.67
4005 4380 8.229253 TGCTTTCTCATGCACTATTATTGATT 57.771 30.769 0.00 0.00 33.94 2.57
4006 4381 7.501559 ACTGCTTTCTCATGCACTATTATTGAT 59.498 33.333 0.00 0.00 35.20 2.57
4016 4391 3.077359 AGGTTACTGCTTTCTCATGCAC 58.923 45.455 0.00 0.00 35.20 4.57
4017 4392 3.423539 AGGTTACTGCTTTCTCATGCA 57.576 42.857 0.00 0.00 37.63 3.96
4021 4396 4.591498 TGGTTCTAGGTTACTGCTTTCTCA 59.409 41.667 0.00 0.00 0.00 3.27
4023 4398 5.071923 ACTTGGTTCTAGGTTACTGCTTTCT 59.928 40.000 0.00 0.00 0.00 2.52
4024 4399 5.306394 ACTTGGTTCTAGGTTACTGCTTTC 58.694 41.667 0.00 0.00 0.00 2.62
4027 4402 4.021016 CAGACTTGGTTCTAGGTTACTGCT 60.021 45.833 0.00 0.00 0.00 4.24
4035 4410 1.208293 GAGGCCAGACTTGGTTCTAGG 59.792 57.143 5.01 0.00 46.80 3.02
4105 4480 0.753867 TTGTGTTGACCTGGTCGCTA 59.246 50.000 21.15 7.41 34.95 4.26
4106 4481 0.108585 ATTGTGTTGACCTGGTCGCT 59.891 50.000 21.15 0.00 34.95 4.93
4107 4482 0.951558 AATTGTGTTGACCTGGTCGC 59.048 50.000 21.15 16.40 34.95 5.19
4108 4483 2.159627 GCTAATTGTGTTGACCTGGTCG 59.840 50.000 21.15 4.71 34.95 4.79
4109 4484 3.146066 TGCTAATTGTGTTGACCTGGTC 58.854 45.455 19.96 19.96 0.00 4.02
4144 4519 2.381725 TGACAAGAGCAGAGCAGATG 57.618 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.