Multiple sequence alignment - TraesCS4D01G281900

Loading Multiple Alignment...

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 TraesCS4D01G281900 chr4D 100.000 5467 0 0 1 5467 453047402 453052868 0.000000e+00 10096.0
1 TraesCS4D01G281900 chr4A 89.567 1984 104 47 3460 5402 14165166 14163245 0.000000e+00 2422.0
2 TraesCS4D01G281900 chr4A 87.399 2095 102 44 84 2068 14168928 14166886 0.000000e+00 2257.0
3 TraesCS4D01G281900 chr4A 90.442 565 33 12 2691 3243 14166221 14165666 0.000000e+00 725.0
4 TraesCS4D01G281900 chr4A 86.491 570 26 20 2104 2634 14166776 14166219 3.670000e-161 579.0
5 TraesCS4D01G281900 chr4A 97.727 44 1 0 5424 5467 14163253 14163210 5.870000e-10 76.8
6 TraesCS4D01G281900 chr4B 92.301 1078 45 21 998 2068 566235508 566236554 0.000000e+00 1496.0
7 TraesCS4D01G281900 chr4B 93.619 1003 30 11 3918 4890 566238419 566239417 0.000000e+00 1467.0
8 TraesCS4D01G281900 chr4B 90.000 1140 58 11 2699 3835 566237289 566238375 0.000000e+00 1423.0
9 TraesCS4D01G281900 chr4B 89.293 1018 59 17 1 998 566234488 566235475 0.000000e+00 1230.0
10 TraesCS4D01G281900 chr4B 87.645 518 42 12 4894 5399 566239551 566240058 2.840000e-162 582.0
11 TraesCS4D01G281900 chr4B 84.331 568 29 24 2065 2582 566236591 566237148 8.180000e-138 501.0
12 TraesCS4D01G281900 chr2B 85.375 253 15 12 1143 1391 159849484 159849250 5.470000e-60 243.0
13 TraesCS4D01G281900 chr6B 94.444 36 0 2 1682 1715 708517717 708517682 3.000000e-03 54.7


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 TraesCS4D01G281900 chr4D 453047402 453052868 5466 False 10096.00 10096 100.0000 1 5467 1 chr4D.!!$F1 5466
1 TraesCS4D01G281900 chr4A 14163210 14168928 5718 True 1211.96 2422 90.3252 84 5467 5 chr4A.!!$R1 5383
2 TraesCS4D01G281900 chr4B 566234488 566240058 5570 False 1116.50 1496 89.5315 1 5399 6 chr4B.!!$F1 5398

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
69 71 0.811281 CCTTGGGATTTGGAACGAGC 59.189 55.0 0.00 0.00 0.00 5.03 F
1239 1325 0.179234 TCCCCCGACACGTACGTATA 59.821 55.0 22.34 0.00 0.00 1.47 F
2617 2926 0.095417 GTTCGACAGCTTGGAATCGC 59.905 55.0 0.00 0.00 34.59 4.58 F
2626 2935 0.391130 CTTGGAATCGCCCGAGAACA 60.391 55.0 0.00 0.00 39.60 3.18 F
2639 2948 0.394565 GAGAACACCACCACTGCTCT 59.605 55.0 0.00 0.00 0.00 4.09 F
2829 3149 0.401738 TGAGCAAAGCTAGCCCAACT 59.598 50.0 12.13 4.21 39.88 3.16 F
3890 4542 1.130955 GTTCGCCGAAGTCGTTGTTA 58.869 50.0 0.00 0.00 37.74 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1271 1357 0.027586 CCAAAGCCGCGTACATAAGC 59.972 55.000 4.92 0.0 0.00 3.09 R
2620 2929 0.394565 AGAGCAGTGGTGGTGTTCTC 59.605 55.000 0.00 0.0 30.36 2.87 R
3647 4284 0.181114 TGGATAGCATGTCAGTGCCC 59.819 55.000 0.00 0.0 46.19 5.36 R
3739 4377 0.396060 TGGACACTACACATGCAGCA 59.604 50.000 0.00 0.0 0.00 4.41 R
3740 4378 0.798776 GTGGACACTACACATGCAGC 59.201 55.000 0.00 0.0 38.67 5.25 R
4103 4771 1.376037 CTGGCTGAAGAACCCGGTC 60.376 63.158 0.00 0.0 0.00 4.79 R
5407 6278 0.034198 TGCATTGTCCTCCGTTTCGA 59.966 50.000 0.00 0.0 0.00 3.71 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 1.762370 TGATATGCACACCCTCGACAT 59.238 47.619 0.00 0.00 0.00 3.06
38 39 1.300233 GACATGATCGCTCCCCGTC 60.300 63.158 0.00 0.00 38.35 4.79
56 57 1.224592 CCGTGGAAGGATCCTTGGG 59.775 63.158 31.79 20.87 46.70 4.12
58 59 0.839946 CGTGGAAGGATCCTTGGGAT 59.160 55.000 31.79 7.25 46.28 3.85
65 67 3.388552 AGGATCCTTGGGATTTGGAAC 57.611 47.619 9.02 0.00 43.27 3.62
69 71 0.811281 CCTTGGGATTTGGAACGAGC 59.189 55.000 0.00 0.00 0.00 5.03
100 108 4.088762 CGCCATGTCGTGTGTGCC 62.089 66.667 0.00 0.00 0.00 5.01
181 189 1.741732 CGACCTGAGCAAAGAGATGGG 60.742 57.143 0.00 0.00 0.00 4.00
345 354 1.341209 GCCCGGATTTGATTTCCATCC 59.659 52.381 0.73 0.00 34.18 3.51
406 416 2.712539 CACGCCAAGCAACGAACA 59.287 55.556 0.00 0.00 0.00 3.18
412 422 1.996191 GCCAAGCAACGAACAAACAAA 59.004 42.857 0.00 0.00 0.00 2.83
413 423 2.222707 GCCAAGCAACGAACAAACAAAC 60.223 45.455 0.00 0.00 0.00 2.93
442 454 1.118965 CCCCCTGTTTCCAAACCCAC 61.119 60.000 0.00 0.00 38.11 4.61
679 699 3.901797 CTTCCCCCGCACTCCACAC 62.902 68.421 0.00 0.00 0.00 3.82
692 712 4.662961 CACACCGCGGCTGACTGA 62.663 66.667 28.58 0.00 0.00 3.41
693 713 4.664677 ACACCGCGGCTGACTGAC 62.665 66.667 28.58 0.00 0.00 3.51
697 717 4.662961 CGCGGCTGACTGACCACA 62.663 66.667 0.00 0.00 0.00 4.17
698 718 3.044305 GCGGCTGACTGACCACAC 61.044 66.667 0.00 0.00 0.00 3.82
699 719 2.734723 CGGCTGACTGACCACACG 60.735 66.667 0.00 0.00 0.00 4.49
703 723 1.373497 CTGACTGACCACACGAGCC 60.373 63.158 0.00 0.00 0.00 4.70
706 726 4.742201 CTGACCACACGAGCCGGG 62.742 72.222 2.18 0.00 35.82 5.73
939 985 1.672441 CCTGACACAGAAGCTCAGCTC 60.672 57.143 0.00 0.00 38.25 4.09
1236 1322 3.058160 CTCCCCCGACACGTACGT 61.058 66.667 16.72 16.72 0.00 3.57
1237 1323 1.745115 CTCCCCCGACACGTACGTA 60.745 63.158 22.34 1.40 0.00 3.57
1238 1324 1.077787 TCCCCCGACACGTACGTAT 60.078 57.895 22.34 10.64 0.00 3.06
1239 1325 0.179234 TCCCCCGACACGTACGTATA 59.821 55.000 22.34 0.00 0.00 1.47
1240 1326 0.307760 CCCCCGACACGTACGTATAC 59.692 60.000 22.34 13.70 0.00 1.47
1244 1330 3.067106 CCCGACACGTACGTATACCTAT 58.933 50.000 22.34 0.50 0.00 2.57
1247 1333 3.473367 GACACGTACGTATACCTATGCG 58.527 50.000 22.34 7.05 45.30 4.73
1252 1338 3.117589 CGTATACCTATGCGTGCCC 57.882 57.895 0.00 0.00 37.10 5.36
1253 1339 0.601558 CGTATACCTATGCGTGCCCT 59.398 55.000 0.00 0.00 37.10 5.19
1267 1353 1.379576 GCCCTCTTCCATGCTTGCT 60.380 57.895 0.00 0.00 0.00 3.91
1270 1356 1.475682 CCCTCTTCCATGCTTGCTTTC 59.524 52.381 0.00 0.00 0.00 2.62
1271 1357 1.131883 CCTCTTCCATGCTTGCTTTCG 59.868 52.381 0.00 0.00 0.00 3.46
1274 1360 0.961019 TTCCATGCTTGCTTTCGCTT 59.039 45.000 0.00 0.00 36.97 4.68
1275 1361 1.819928 TCCATGCTTGCTTTCGCTTA 58.180 45.000 0.00 0.00 36.97 3.09
1276 1362 2.368439 TCCATGCTTGCTTTCGCTTAT 58.632 42.857 0.00 0.00 36.97 1.73
1277 1363 2.097954 TCCATGCTTGCTTTCGCTTATG 59.902 45.455 0.00 0.00 36.97 1.90
1278 1364 2.159338 CCATGCTTGCTTTCGCTTATGT 60.159 45.455 0.00 0.00 36.97 2.29
1279 1365 3.065233 CCATGCTTGCTTTCGCTTATGTA 59.935 43.478 0.00 0.00 36.97 2.29
1291 1379 0.655733 CTTATGTACGCGGCTTTGGG 59.344 55.000 12.47 0.00 0.00 4.12
1297 1390 3.977244 CGCGGCTTTGGGTTTGCT 61.977 61.111 0.00 0.00 0.00 3.91
1300 1393 1.221466 GCGGCTTTGGGTTTGCTTTC 61.221 55.000 0.00 0.00 0.00 2.62
1318 1414 1.220529 TCGCTTATGTATGCTGCTGC 58.779 50.000 8.89 8.89 40.20 5.25
1710 1833 4.891168 TCCATCCATTCATTCATTCACCTG 59.109 41.667 0.00 0.00 0.00 4.00
1951 2090 3.789756 CGTCGTGTTTACTGCCACTATAG 59.210 47.826 0.00 0.00 0.00 1.31
1996 2144 4.351938 CGTCCCCACGCGTCTTCA 62.352 66.667 9.86 0.00 39.69 3.02
2005 2153 1.597663 CACGCGTCTTCAACCTTTTCT 59.402 47.619 9.86 0.00 0.00 2.52
2184 2407 5.118664 GGAAGAATCTTTGTTAAAAAGCGGC 59.881 40.000 0.00 0.00 0.00 6.53
2253 2489 3.517901 ACAGTTGTTATCTTGGGATCCGA 59.482 43.478 5.45 0.00 33.71 4.55
2320 2564 0.242017 GGCCGCCATTATTGATGCTC 59.758 55.000 3.91 0.00 34.25 4.26
2321 2565 1.242076 GCCGCCATTATTGATGCTCT 58.758 50.000 0.00 0.00 34.25 4.09
2322 2566 1.198637 GCCGCCATTATTGATGCTCTC 59.801 52.381 0.00 0.00 34.25 3.20
2323 2567 1.808945 CCGCCATTATTGATGCTCTCC 59.191 52.381 0.00 0.00 34.25 3.71
2324 2568 2.551721 CCGCCATTATTGATGCTCTCCT 60.552 50.000 0.00 0.00 34.25 3.69
2331 2575 1.210538 TTGATGCTCTCCTCCATGCT 58.789 50.000 0.00 0.00 0.00 3.79
2335 2579 1.210538 TGCTCTCCTCCATGCTTCAT 58.789 50.000 0.00 0.00 0.00 2.57
2466 2749 3.696051 TGCCCTCATCTTTGATAAAGTGC 59.304 43.478 1.70 0.00 39.52 4.40
2467 2750 3.696051 GCCCTCATCTTTGATAAAGTGCA 59.304 43.478 1.70 0.00 39.52 4.57
2468 2751 4.340381 GCCCTCATCTTTGATAAAGTGCAT 59.660 41.667 0.00 0.00 39.52 3.96
2469 2752 5.735354 GCCCTCATCTTTGATAAAGTGCATG 60.735 44.000 0.00 0.00 39.52 4.06
2582 2868 1.832366 TCCCAAATCGAACCACGGATA 59.168 47.619 0.00 0.00 42.82 2.59
2617 2926 0.095417 GTTCGACAGCTTGGAATCGC 59.905 55.000 0.00 0.00 34.59 4.58
2620 2929 2.436646 ACAGCTTGGAATCGCCCG 60.437 61.111 0.00 0.00 34.97 6.13
2621 2930 2.125147 CAGCTTGGAATCGCCCGA 60.125 61.111 0.00 0.00 34.97 5.14
2622 2931 2.176273 CAGCTTGGAATCGCCCGAG 61.176 63.158 0.00 0.00 40.10 4.63
2623 2932 2.186903 GCTTGGAATCGCCCGAGA 59.813 61.111 9.02 0.00 39.60 4.04
2625 2934 1.706287 GCTTGGAATCGCCCGAGAAC 61.706 60.000 9.02 0.00 39.60 3.01
2626 2935 0.391130 CTTGGAATCGCCCGAGAACA 60.391 55.000 0.00 0.00 39.60 3.18
2627 2936 0.672401 TTGGAATCGCCCGAGAACAC 60.672 55.000 0.00 0.00 34.97 3.32
2629 2938 1.079405 GAATCGCCCGAGAACACCA 60.079 57.895 0.00 0.00 0.00 4.17
2630 2939 1.359459 GAATCGCCCGAGAACACCAC 61.359 60.000 0.00 0.00 0.00 4.16
2632 2941 4.308458 CGCCCGAGAACACCACCA 62.308 66.667 0.00 0.00 0.00 4.17
2633 2942 2.668550 GCCCGAGAACACCACCAC 60.669 66.667 0.00 0.00 0.00 4.16
2634 2943 3.148084 CCCGAGAACACCACCACT 58.852 61.111 0.00 0.00 0.00 4.00
2635 2944 1.301716 CCCGAGAACACCACCACTG 60.302 63.158 0.00 0.00 0.00 3.66
2636 2945 1.961277 CCGAGAACACCACCACTGC 60.961 63.158 0.00 0.00 0.00 4.40
2638 2947 0.946221 CGAGAACACCACCACTGCTC 60.946 60.000 0.00 0.00 0.00 4.26
2639 2948 0.394565 GAGAACACCACCACTGCTCT 59.605 55.000 0.00 0.00 0.00 4.09
2641 2950 2.037251 GAGAACACCACCACTGCTCTTA 59.963 50.000 0.00 0.00 0.00 2.10
2642 2951 2.639839 AGAACACCACCACTGCTCTTAT 59.360 45.455 0.00 0.00 0.00 1.73
2643 2952 3.073062 AGAACACCACCACTGCTCTTATT 59.927 43.478 0.00 0.00 0.00 1.40
2644 2953 3.059352 ACACCACCACTGCTCTTATTC 57.941 47.619 0.00 0.00 0.00 1.75
2645 2954 2.290323 ACACCACCACTGCTCTTATTCC 60.290 50.000 0.00 0.00 0.00 3.01
2646 2955 1.282157 ACCACCACTGCTCTTATTCCC 59.718 52.381 0.00 0.00 0.00 3.97
2648 2957 2.092212 CCACCACTGCTCTTATTCCCAT 60.092 50.000 0.00 0.00 0.00 4.00
2649 2958 3.624777 CACCACTGCTCTTATTCCCATT 58.375 45.455 0.00 0.00 0.00 3.16
2650 2959 3.629398 CACCACTGCTCTTATTCCCATTC 59.371 47.826 0.00 0.00 0.00 2.67
2651 2960 3.525199 ACCACTGCTCTTATTCCCATTCT 59.475 43.478 0.00 0.00 0.00 2.40
2652 2961 4.133078 CCACTGCTCTTATTCCCATTCTC 58.867 47.826 0.00 0.00 0.00 2.87
2654 2963 5.070981 CCACTGCTCTTATTCCCATTCTCTA 59.929 44.000 0.00 0.00 0.00 2.43
2656 2965 6.041409 CACTGCTCTTATTCCCATTCTCTAGA 59.959 42.308 0.00 0.00 0.00 2.43
2657 2966 6.267471 ACTGCTCTTATTCCCATTCTCTAGAG 59.733 42.308 13.98 13.98 0.00 2.43
2659 2968 6.041409 TGCTCTTATTCCCATTCTCTAGAGTG 59.959 42.308 19.21 11.07 32.51 3.51
2660 2969 6.041523 GCTCTTATTCCCATTCTCTAGAGTGT 59.958 42.308 19.21 6.72 32.51 3.55
2661 2970 7.353414 TCTTATTCCCATTCTCTAGAGTGTG 57.647 40.000 19.21 17.10 30.84 3.82
2662 2971 6.897966 TCTTATTCCCATTCTCTAGAGTGTGT 59.102 38.462 19.21 6.47 30.84 3.72
2664 2973 6.723298 ATTCCCATTCTCTAGAGTGTGTAG 57.277 41.667 19.21 11.90 30.84 2.74
2665 2974 5.452341 TCCCATTCTCTAGAGTGTGTAGA 57.548 43.478 19.21 13.60 30.84 2.59
2666 2975 5.441500 TCCCATTCTCTAGAGTGTGTAGAG 58.558 45.833 19.21 2.42 43.41 2.43
2693 3013 6.320418 AGAACGATATACATACCACAGACACA 59.680 38.462 0.00 0.00 0.00 3.72
2694 3014 6.073327 ACGATATACATACCACAGACACAG 57.927 41.667 0.00 0.00 0.00 3.66
2695 3015 5.826208 ACGATATACATACCACAGACACAGA 59.174 40.000 0.00 0.00 0.00 3.41
2696 3016 6.143496 CGATATACATACCACAGACACAGAC 58.857 44.000 0.00 0.00 0.00 3.51
2697 3017 6.238648 CGATATACATACCACAGACACAGACA 60.239 42.308 0.00 0.00 0.00 3.41
2829 3149 0.401738 TGAGCAAAGCTAGCCCAACT 59.598 50.000 12.13 4.21 39.88 3.16
2833 3153 2.159382 GCAAAGCTAGCCCAACTAACA 58.841 47.619 12.13 0.00 0.00 2.41
2841 3161 3.059352 AGCCCAACTAACACTAGCAAG 57.941 47.619 0.00 0.00 0.00 4.01
2845 3165 4.322499 GCCCAACTAACACTAGCAAGTAGA 60.322 45.833 0.00 0.00 33.48 2.59
2850 3176 7.309012 CCAACTAACACTAGCAAGTAGACAGTA 60.309 40.741 0.00 0.00 33.48 2.74
2851 3177 7.380431 ACTAACACTAGCAAGTAGACAGTAG 57.620 40.000 0.00 0.00 33.48 2.57
2852 3178 6.941436 ACTAACACTAGCAAGTAGACAGTAGT 59.059 38.462 0.00 0.00 33.48 2.73
2862 3188 9.726438 AGCAAGTAGACAGTAGTAAAATTTGAT 57.274 29.630 0.00 0.00 0.00 2.57
2893 3219 3.492383 CACGATCTGATTCCCGAAATCTG 59.508 47.826 10.54 10.03 43.61 2.90
2894 3220 3.133003 ACGATCTGATTCCCGAAATCTGT 59.867 43.478 10.54 3.67 43.61 3.41
3107 3437 3.344515 GGCCAGTTTCGGTCTAGAAAAT 58.655 45.455 0.00 0.00 41.18 1.82
3218 3588 7.047891 TCAAGACTAGAGAAAGTTTCAGCAAA 58.952 34.615 17.65 2.01 0.00 3.68
3269 3642 3.391296 AGTGTGGCCTACTTGAAGAAAGA 59.609 43.478 3.32 0.00 39.38 2.52
3276 3649 4.082354 GCCTACTTGAAGAAAGAGTACGGA 60.082 45.833 0.00 0.00 39.38 4.69
3277 3650 5.566230 GCCTACTTGAAGAAAGAGTACGGAA 60.566 44.000 0.00 0.00 39.38 4.30
3278 3651 6.094061 CCTACTTGAAGAAAGAGTACGGAAG 58.906 44.000 0.00 0.00 39.38 3.46
3279 3652 5.786264 ACTTGAAGAAAGAGTACGGAAGA 57.214 39.130 0.00 0.00 39.38 2.87
3280 3653 6.347859 ACTTGAAGAAAGAGTACGGAAGAT 57.652 37.500 0.00 0.00 39.38 2.40
3281 3654 6.159988 ACTTGAAGAAAGAGTACGGAAGATG 58.840 40.000 0.00 0.00 39.38 2.90
3282 3655 4.495422 TGAAGAAAGAGTACGGAAGATGC 58.505 43.478 0.00 0.00 0.00 3.91
3283 3656 4.021456 TGAAGAAAGAGTACGGAAGATGCA 60.021 41.667 0.00 0.00 0.00 3.96
3284 3657 3.851098 AGAAAGAGTACGGAAGATGCAC 58.149 45.455 0.00 0.00 0.00 4.57
3285 3658 3.258372 AGAAAGAGTACGGAAGATGCACA 59.742 43.478 0.00 0.00 0.00 4.57
3286 3659 2.656560 AGAGTACGGAAGATGCACAC 57.343 50.000 0.00 0.00 0.00 3.82
3287 3660 1.893137 AGAGTACGGAAGATGCACACA 59.107 47.619 0.00 0.00 0.00 3.72
3288 3661 2.299013 AGAGTACGGAAGATGCACACAA 59.701 45.455 0.00 0.00 0.00 3.33
3289 3662 3.055819 AGAGTACGGAAGATGCACACAAT 60.056 43.478 0.00 0.00 0.00 2.71
3290 3663 4.159693 AGAGTACGGAAGATGCACACAATA 59.840 41.667 0.00 0.00 0.00 1.90
3291 3664 5.023533 AGTACGGAAGATGCACACAATAT 57.976 39.130 0.00 0.00 0.00 1.28
3292 3665 6.040504 AGAGTACGGAAGATGCACACAATATA 59.959 38.462 0.00 0.00 0.00 0.86
3293 3666 6.759272 AGTACGGAAGATGCACACAATATAT 58.241 36.000 0.00 0.00 0.00 0.86
3372 3766 2.744202 GGGGCACTGCATTTCTATATCG 59.256 50.000 2.82 0.00 0.00 2.92
3385 3779 2.027469 TCTATATCGGCAGCGTCCTCTA 60.027 50.000 0.00 0.00 0.00 2.43
3466 4103 7.012232 TGACACAACACGGATTATATACTCGTA 59.988 37.037 4.56 0.00 32.56 3.43
3467 4104 7.134815 ACACAACACGGATTATATACTCGTAC 58.865 38.462 4.56 0.00 32.56 3.67
3502 4139 3.194542 CCAGCCCCTCTAGAATATTCTCG 59.805 52.174 21.17 15.22 38.70 4.04
3590 4227 6.126568 TGGAGTAAATGGCGTAAAAATAGC 57.873 37.500 0.00 0.00 0.00 2.97
3621 4258 2.162608 CGTGAGAGACTCTGTACTTGGG 59.837 54.545 10.44 0.00 0.00 4.12
3647 4284 2.257286 CTGATGGTCCAAAAGCGCCG 62.257 60.000 2.29 0.00 0.00 6.46
3648 4285 3.051392 GATGGTCCAAAAGCGCCGG 62.051 63.158 2.29 0.00 0.00 6.13
3694 4332 2.811307 TTGCCAAGCAAGCAGAGTT 58.189 47.368 0.00 0.00 43.99 3.01
3695 4333 1.979855 TTGCCAAGCAAGCAGAGTTA 58.020 45.000 0.00 0.00 43.99 2.24
3696 4334 2.205022 TGCCAAGCAAGCAGAGTTAT 57.795 45.000 0.00 0.00 34.76 1.89
3697 4335 2.086869 TGCCAAGCAAGCAGAGTTATC 58.913 47.619 0.00 0.00 34.76 1.75
3730 4368 5.762179 ACTTCACTGACATCCCATTTCTA 57.238 39.130 0.00 0.00 0.00 2.10
3731 4369 5.738909 ACTTCACTGACATCCCATTTCTAG 58.261 41.667 0.00 0.00 0.00 2.43
3732 4370 4.142609 TCACTGACATCCCATTTCTAGC 57.857 45.455 0.00 0.00 0.00 3.42
3733 4371 3.519107 TCACTGACATCCCATTTCTAGCA 59.481 43.478 0.00 0.00 0.00 3.49
3734 4372 4.164796 TCACTGACATCCCATTTCTAGCAT 59.835 41.667 0.00 0.00 0.00 3.79
3735 4373 4.275196 CACTGACATCCCATTTCTAGCATG 59.725 45.833 0.00 0.00 0.00 4.06
3736 4374 4.080129 ACTGACATCCCATTTCTAGCATGT 60.080 41.667 0.00 0.00 0.00 3.21
3737 4375 4.454678 TGACATCCCATTTCTAGCATGTC 58.545 43.478 0.00 0.00 40.29 3.06
3738 4376 4.080413 TGACATCCCATTTCTAGCATGTCA 60.080 41.667 8.17 8.17 44.86 3.58
3739 4377 5.057843 ACATCCCATTTCTAGCATGTCAT 57.942 39.130 0.00 0.00 0.00 3.06
3740 4378 4.825634 ACATCCCATTTCTAGCATGTCATG 59.174 41.667 8.56 8.56 0.00 3.07
3752 4390 3.334272 CATGTCATGCTGCATGTGTAG 57.666 47.619 34.14 21.83 41.98 2.74
3753 4391 2.477845 TGTCATGCTGCATGTGTAGT 57.522 45.000 34.14 3.11 41.98 2.73
3778 4430 4.160439 TCCACATGTAGAACTAGAAGCAGG 59.840 45.833 0.00 0.00 0.00 4.85
3808 4460 2.135139 TGCAGTAGCTCACAGTTTTCG 58.865 47.619 0.00 0.00 42.74 3.46
3821 4473 3.566742 ACAGTTTTCGGTGTGGTAATTCC 59.433 43.478 0.00 0.00 0.00 3.01
3852 4504 3.955471 ACATCGGTTCCAATGTTCAGAT 58.045 40.909 0.00 0.00 32.24 2.90
3857 4509 3.372206 CGGTTCCAATGTTCAGATGACTC 59.628 47.826 0.00 0.00 0.00 3.36
3890 4542 1.130955 GTTCGCCGAAGTCGTTGTTA 58.869 50.000 0.00 0.00 37.74 2.41
3899 4551 4.530388 CGAAGTCGTTGTTAGTGTGACTA 58.470 43.478 0.00 0.00 38.87 2.59
3909 4561 8.385111 CGTTGTTAGTGTGACTAAAGAAAGAAA 58.615 33.333 0.00 0.00 41.80 2.52
4166 4834 4.803426 GACTCGCAGCTCACCCGG 62.803 72.222 0.00 0.00 0.00 5.73
4516 5201 4.393062 TGTAACACGTAGTAGTCCAGTAGC 59.607 45.833 0.00 0.00 41.61 3.58
4517 5202 3.063510 ACACGTAGTAGTCCAGTAGCA 57.936 47.619 0.00 0.00 41.61 3.49
4649 5336 9.232473 AGAAAGAAAAACTCACAGTTTCTAAGT 57.768 29.630 2.19 0.00 46.78 2.24
4655 5342 4.561105 ACTCACAGTTTCTAAGTAGCTGC 58.439 43.478 0.00 0.00 0.00 5.25
4656 5343 3.926616 TCACAGTTTCTAAGTAGCTGCC 58.073 45.455 0.00 0.00 0.00 4.85
4657 5344 3.578716 TCACAGTTTCTAAGTAGCTGCCT 59.421 43.478 0.00 0.00 0.00 4.75
4667 5379 5.932303 TCTAAGTAGCTGCCTGTAAAAACTG 59.068 40.000 0.00 0.00 0.00 3.16
4771 5483 5.620206 TCTGCAAGAAAGATTCAAGGTACA 58.380 37.500 0.00 0.00 42.31 2.90
4818 5530 8.190784 ACAGTTTTGTTTGGTTCTCTTATTCTG 58.809 33.333 0.00 0.00 32.28 3.02
4909 5762 1.270625 TGACCTACGCTTGGTTCCTTG 60.271 52.381 0.00 0.00 38.03 3.61
4916 5769 2.282180 TTGGTTCCTTGCGGCCTC 60.282 61.111 0.00 0.00 0.00 4.70
4951 5804 2.291465 TCTGCATGAGAAGTTGTGCAAC 59.709 45.455 6.94 6.94 45.77 4.17
4972 5825 8.465201 TGCAACAATATTATTGTTACATCAGCA 58.535 29.630 26.38 25.20 40.30 4.41
5013 5866 0.749454 GGAATCAGCAGAACGGCCAT 60.749 55.000 2.24 0.00 0.00 4.40
5021 5874 2.440247 GAACGGCCATTCCCCTGG 60.440 66.667 0.00 0.00 39.45 4.45
5075 5928 2.831685 ACTTTGACAGTGTCCGCATA 57.168 45.000 20.43 0.00 32.83 3.14
5092 5945 3.181461 CGCATACCCTCTTTCTCCTTGAT 60.181 47.826 0.00 0.00 0.00 2.57
5093 5946 4.133078 GCATACCCTCTTTCTCCTTGATG 58.867 47.826 0.00 0.00 0.00 3.07
5094 5947 4.141620 GCATACCCTCTTTCTCCTTGATGA 60.142 45.833 0.00 0.00 0.00 2.92
5095 5948 5.455899 GCATACCCTCTTTCTCCTTGATGAT 60.456 44.000 0.00 0.00 0.00 2.45
5108 5961 8.661752 TCTCCTTGATGATGATGATAGTACAT 57.338 34.615 0.00 0.00 0.00 2.29
5109 5962 9.097946 TCTCCTTGATGATGATGATAGTACATT 57.902 33.333 0.00 0.00 0.00 2.71
5310 6170 4.117661 ACGCCGGCTCGTCTTCTC 62.118 66.667 26.68 0.00 38.44 2.87
5311 6171 4.856607 CGCCGGCTCGTCTTCTCC 62.857 72.222 26.68 0.00 0.00 3.71
5312 6172 3.453679 GCCGGCTCGTCTTCTCCT 61.454 66.667 22.15 0.00 0.00 3.69
5313 6173 3.007973 GCCGGCTCGTCTTCTCCTT 62.008 63.158 22.15 0.00 0.00 3.36
5314 6174 1.139947 CCGGCTCGTCTTCTCCTTC 59.860 63.158 0.00 0.00 0.00 3.46
5315 6175 1.316706 CCGGCTCGTCTTCTCCTTCT 61.317 60.000 0.00 0.00 0.00 2.85
5316 6176 0.099791 CGGCTCGTCTTCTCCTTCTC 59.900 60.000 0.00 0.00 0.00 2.87
5325 6185 4.142469 CGTCTTCTCCTTCTCCTTCTTCTC 60.142 50.000 0.00 0.00 0.00 2.87
5327 6187 3.835478 TCTCCTTCTCCTTCTTCTCCA 57.165 47.619 0.00 0.00 0.00 3.86
5329 6200 3.169099 CTCCTTCTCCTTCTTCTCCACA 58.831 50.000 0.00 0.00 0.00 4.17
5332 6203 0.891373 TCTCCTTCTTCTCCACAGCG 59.109 55.000 0.00 0.00 0.00 5.18
5379 6250 2.519013 GAATCTGGCTGGTTTTGTCCT 58.481 47.619 0.00 0.00 0.00 3.85
5399 6270 1.591703 CTCCTTGGACGCTGCACTA 59.408 57.895 0.00 0.00 0.00 2.74
5400 6271 0.037326 CTCCTTGGACGCTGCACTAA 60.037 55.000 0.00 0.00 0.00 2.24
5401 6272 0.613260 TCCTTGGACGCTGCACTAAT 59.387 50.000 0.00 0.00 0.00 1.73
5402 6273 1.003118 TCCTTGGACGCTGCACTAATT 59.997 47.619 0.00 0.00 0.00 1.40
5403 6274 1.812571 CCTTGGACGCTGCACTAATTT 59.187 47.619 0.00 0.00 0.00 1.82
5404 6275 2.228822 CCTTGGACGCTGCACTAATTTT 59.771 45.455 0.00 0.00 0.00 1.82
5405 6276 3.305335 CCTTGGACGCTGCACTAATTTTT 60.305 43.478 0.00 0.00 0.00 1.94
5424 6295 3.889196 TTTTCGAAACGGAGGACAATG 57.111 42.857 10.79 0.00 0.00 2.82
5425 6296 1.153353 TTCGAAACGGAGGACAATGC 58.847 50.000 0.00 0.00 0.00 3.56
5426 6297 0.034198 TCGAAACGGAGGACAATGCA 59.966 50.000 0.00 0.00 0.00 3.96
5427 6298 0.165944 CGAAACGGAGGACAATGCAC 59.834 55.000 0.00 0.00 0.00 4.57
5428 6299 1.523758 GAAACGGAGGACAATGCACT 58.476 50.000 0.00 0.00 0.00 4.40
5429 6300 2.695359 GAAACGGAGGACAATGCACTA 58.305 47.619 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.762370 TCATGTCGAGGGTGTGCATAT 59.238 47.619 0.00 0.00 0.00 1.78
8 9 0.543277 ATCATGTCGAGGGTGTGCAT 59.457 50.000 0.00 0.00 0.00 3.96
10 11 2.682893 GATCATGTCGAGGGTGTGC 58.317 57.895 0.00 0.00 0.00 4.57
34 35 1.614241 AAGGATCCTTCCACGGACGG 61.614 60.000 21.89 2.14 45.30 4.79
35 36 0.460284 CAAGGATCCTTCCACGGACG 60.460 60.000 24.67 6.91 45.30 4.79
38 39 1.224592 CCCAAGGATCCTTCCACGG 59.775 63.158 24.67 20.76 45.30 4.94
56 57 2.761195 GCCCGGCTCGTTCCAAATC 61.761 63.158 0.71 0.00 0.00 2.17
58 59 4.257654 TGCCCGGCTCGTTCCAAA 62.258 61.111 11.61 0.00 0.00 3.28
181 189 0.461961 CCCAAGATCTCTCACCGTCC 59.538 60.000 0.00 0.00 0.00 4.79
208 216 2.202987 CTCGCCATCAGTCCCTGC 60.203 66.667 0.00 0.00 0.00 4.85
210 218 3.474570 GCCTCGCCATCAGTCCCT 61.475 66.667 0.00 0.00 0.00 4.20
362 371 2.756207 TGTCGACTCATTCATTCCCGTA 59.244 45.455 17.92 0.00 0.00 4.02
365 374 1.927174 CGTGTCGACTCATTCATTCCC 59.073 52.381 17.92 0.00 0.00 3.97
406 416 1.134640 GGGGTTTCCGCTTGTTTGTTT 60.135 47.619 0.00 0.00 33.42 2.83
442 454 2.310538 GTTGGATATGGGCTTCCCTTG 58.689 52.381 3.27 0.00 45.70 3.61
454 466 2.591715 GCTGCGCCCGTTGGATAT 60.592 61.111 4.18 0.00 0.00 1.63
682 702 2.734723 CGTGTGGTCAGTCAGCCG 60.735 66.667 0.00 0.00 0.00 5.52
684 704 2.024319 GCTCGTGTGGTCAGTCAGC 61.024 63.158 0.00 0.00 0.00 4.26
687 707 2.430921 CGGCTCGTGTGGTCAGTC 60.431 66.667 0.00 0.00 0.00 3.51
688 708 3.991051 CCGGCTCGTGTGGTCAGT 61.991 66.667 0.00 0.00 0.00 3.41
689 709 4.742201 CCCGGCTCGTGTGGTCAG 62.742 72.222 0.00 0.00 0.00 3.51
691 711 4.736896 GACCCGGCTCGTGTGGTC 62.737 72.222 0.00 7.05 40.40 4.02
957 1003 1.515020 CTCTCCCTGTCGCTTCTGG 59.485 63.158 0.00 0.00 0.00 3.86
1167 1253 3.213402 GCGAGGACGGAGAGGAGG 61.213 72.222 0.00 0.00 40.15 4.30
1236 1322 2.304221 AGAGGGCACGCATAGGTATA 57.696 50.000 0.00 0.00 0.00 1.47
1237 1323 1.344763 GAAGAGGGCACGCATAGGTAT 59.655 52.381 0.00 0.00 0.00 2.73
1238 1324 0.750850 GAAGAGGGCACGCATAGGTA 59.249 55.000 0.00 0.00 0.00 3.08
1239 1325 1.522569 GAAGAGGGCACGCATAGGT 59.477 57.895 0.00 0.00 0.00 3.08
1240 1326 1.227674 GGAAGAGGGCACGCATAGG 60.228 63.158 0.00 0.00 0.00 2.57
1244 1330 2.046023 CATGGAAGAGGGCACGCA 60.046 61.111 0.00 0.00 0.00 5.24
1247 1333 1.941999 GCAAGCATGGAAGAGGGCAC 61.942 60.000 0.00 0.00 0.00 5.01
1250 1336 1.475682 GAAAGCAAGCATGGAAGAGGG 59.524 52.381 0.00 0.00 0.00 4.30
1252 1338 2.539346 CGAAAGCAAGCATGGAAGAG 57.461 50.000 0.00 0.00 0.00 2.85
1271 1357 0.027586 CCAAAGCCGCGTACATAAGC 59.972 55.000 4.92 0.00 0.00 3.09
1274 1360 0.036199 AACCCAAAGCCGCGTACATA 60.036 50.000 4.92 0.00 0.00 2.29
1275 1361 0.891904 AAACCCAAAGCCGCGTACAT 60.892 50.000 4.92 0.00 0.00 2.29
1276 1362 1.526455 AAACCCAAAGCCGCGTACA 60.526 52.632 4.92 0.00 0.00 2.90
1277 1363 1.081708 CAAACCCAAAGCCGCGTAC 60.082 57.895 4.92 0.00 0.00 3.67
1278 1364 2.910345 GCAAACCCAAAGCCGCGTA 61.910 57.895 4.92 0.00 0.00 4.42
1279 1365 4.279043 GCAAACCCAAAGCCGCGT 62.279 61.111 4.92 0.00 0.00 6.01
1297 1390 2.032054 GCAGCAGCATACATAAGCGAAA 59.968 45.455 0.00 0.00 41.58 3.46
1300 1393 1.070108 CAGCAGCAGCATACATAAGCG 60.070 52.381 3.17 0.00 45.49 4.68
1335 1431 0.248336 TTATGTACTGCGCCGACGAG 60.248 55.000 4.18 0.00 43.93 4.18
1723 1846 2.743928 CTGTGGAGCGGTGGAAGC 60.744 66.667 0.00 0.00 0.00 3.86
1725 1848 2.741092 GACTGTGGAGCGGTGGAA 59.259 61.111 0.00 0.00 36.69 3.53
1817 1949 1.909302 GTGGAAAGATGGAGGAGGACA 59.091 52.381 0.00 0.00 0.00 4.02
1818 1950 1.210722 GGTGGAAAGATGGAGGAGGAC 59.789 57.143 0.00 0.00 0.00 3.85
1996 2144 2.159014 GCAACGGGGAAAAGAAAAGGTT 60.159 45.455 0.00 0.00 0.00 3.50
2005 2153 2.491022 CGGGTTGCAACGGGGAAAA 61.491 57.895 22.67 0.00 0.00 2.29
2068 2217 0.394762 AGTACGTCCTATGTGCCGGA 60.395 55.000 5.05 0.00 0.00 5.14
2117 2340 5.365605 ACCGATTACATGGTGGATCTTTCTA 59.634 40.000 0.00 0.00 37.02 2.10
2320 2564 2.038295 GGGAGTATGAAGCATGGAGGAG 59.962 54.545 0.00 0.00 0.00 3.69
2321 2565 2.050144 GGGAGTATGAAGCATGGAGGA 58.950 52.381 0.00 0.00 0.00 3.71
2322 2566 1.770658 TGGGAGTATGAAGCATGGAGG 59.229 52.381 0.00 0.00 0.00 4.30
2323 2567 2.809665 GCTGGGAGTATGAAGCATGGAG 60.810 54.545 0.00 0.00 35.69 3.86
2324 2568 1.141657 GCTGGGAGTATGAAGCATGGA 59.858 52.381 0.00 0.00 35.69 3.41
2331 2575 3.266772 AGGAAATGTGCTGGGAGTATGAA 59.733 43.478 0.00 0.00 0.00 2.57
2335 2579 3.181434 ACAAAGGAAATGTGCTGGGAGTA 60.181 43.478 0.00 0.00 0.00 2.59
2466 2749 0.465097 GACATCTCCCAGTGGGCATG 60.465 60.000 27.07 27.07 43.94 4.06
2467 2750 0.622738 AGACATCTCCCAGTGGGCAT 60.623 55.000 24.75 14.69 43.94 4.40
2468 2751 1.229625 AGACATCTCCCAGTGGGCA 60.230 57.895 24.75 12.85 43.94 5.36
2469 2752 1.222936 CAGACATCTCCCAGTGGGC 59.777 63.158 24.75 8.31 43.94 5.36
2485 2768 1.934525 GAGCTCACACATGCTGATCAG 59.065 52.381 18.84 18.84 39.91 2.90
2549 2835 5.601662 TCGATTTGGGAGTTGCTAAGATAG 58.398 41.667 0.00 0.00 0.00 2.08
2617 2926 1.301716 CAGTGGTGGTGTTCTCGGG 60.302 63.158 0.00 0.00 0.00 5.14
2620 2929 0.394565 AGAGCAGTGGTGGTGTTCTC 59.605 55.000 0.00 0.00 30.36 2.87
2621 2930 0.839946 AAGAGCAGTGGTGGTGTTCT 59.160 50.000 0.00 0.00 32.50 3.01
2622 2931 2.543777 TAAGAGCAGTGGTGGTGTTC 57.456 50.000 0.00 0.00 38.51 3.18
2623 2932 3.412386 GAATAAGAGCAGTGGTGGTGTT 58.588 45.455 0.00 0.00 40.49 3.32
2625 2934 2.359900 GGAATAAGAGCAGTGGTGGTG 58.640 52.381 0.00 0.00 33.41 4.17
2626 2935 1.282157 GGGAATAAGAGCAGTGGTGGT 59.718 52.381 0.00 0.00 37.01 4.16
2627 2936 1.281867 TGGGAATAAGAGCAGTGGTGG 59.718 52.381 0.00 0.00 0.00 4.61
2629 2938 3.525199 AGAATGGGAATAAGAGCAGTGGT 59.475 43.478 0.00 0.00 0.00 4.16
2630 2939 4.133078 GAGAATGGGAATAAGAGCAGTGG 58.867 47.826 0.00 0.00 0.00 4.00
2632 2941 6.139671 TCTAGAGAATGGGAATAAGAGCAGT 58.860 40.000 0.00 0.00 0.00 4.40
2633 2942 6.267471 ACTCTAGAGAATGGGAATAAGAGCAG 59.733 42.308 26.57 0.00 34.02 4.24
2634 2943 6.041409 CACTCTAGAGAATGGGAATAAGAGCA 59.959 42.308 26.57 0.00 34.02 4.26
2635 2944 6.041523 ACACTCTAGAGAATGGGAATAAGAGC 59.958 42.308 26.57 0.00 34.02 4.09
2636 2945 7.069331 ACACACTCTAGAGAATGGGAATAAGAG 59.931 40.741 26.57 0.00 36.23 2.85
2638 2947 7.118496 ACACACTCTAGAGAATGGGAATAAG 57.882 40.000 26.57 5.03 0.00 1.73
2639 2948 8.059461 TCTACACACTCTAGAGAATGGGAATAA 58.941 37.037 26.57 4.64 0.00 1.40
2641 2950 6.436027 TCTACACACTCTAGAGAATGGGAAT 58.564 40.000 26.57 9.64 0.00 3.01
2642 2951 5.827756 TCTACACACTCTAGAGAATGGGAA 58.172 41.667 26.57 11.57 0.00 3.97
2643 2952 5.044772 ACTCTACACACTCTAGAGAATGGGA 60.045 44.000 26.57 19.86 39.75 4.37
2644 2953 5.197451 ACTCTACACACTCTAGAGAATGGG 58.803 45.833 26.57 17.75 39.75 4.00
2645 2954 7.276658 TCTACTCTACACACTCTAGAGAATGG 58.723 42.308 26.57 13.90 39.75 3.16
2646 2955 8.609176 GTTCTACTCTACACACTCTAGAGAATG 58.391 40.741 26.57 22.54 39.75 2.67
2648 2957 6.812656 CGTTCTACTCTACACACTCTAGAGAA 59.187 42.308 26.57 2.55 39.75 2.87
2649 2958 6.152492 TCGTTCTACTCTACACACTCTAGAGA 59.848 42.308 26.57 2.18 39.75 3.10
2650 2959 6.331845 TCGTTCTACTCTACACACTCTAGAG 58.668 44.000 18.49 18.49 42.10 2.43
2651 2960 6.278172 TCGTTCTACTCTACACACTCTAGA 57.722 41.667 0.00 0.00 0.00 2.43
2652 2961 8.821147 ATATCGTTCTACTCTACACACTCTAG 57.179 38.462 0.00 0.00 0.00 2.43
2654 2963 8.202811 TGTATATCGTTCTACTCTACACACTCT 58.797 37.037 0.00 0.00 0.00 3.24
2656 2965 8.905660 ATGTATATCGTTCTACTCTACACACT 57.094 34.615 0.00 0.00 0.00 3.55
2659 2968 9.212641 TGGTATGTATATCGTTCTACTCTACAC 57.787 37.037 0.00 0.00 0.00 2.90
2660 2969 9.212641 GTGGTATGTATATCGTTCTACTCTACA 57.787 37.037 0.00 0.00 0.00 2.74
2661 2970 9.212641 TGTGGTATGTATATCGTTCTACTCTAC 57.787 37.037 0.00 0.00 0.00 2.59
2662 2971 9.433153 CTGTGGTATGTATATCGTTCTACTCTA 57.567 37.037 0.00 0.00 0.00 2.43
2664 2973 8.229137 GTCTGTGGTATGTATATCGTTCTACTC 58.771 40.741 0.00 0.00 0.00 2.59
2665 2974 7.718314 TGTCTGTGGTATGTATATCGTTCTACT 59.282 37.037 0.00 0.00 0.00 2.57
2666 2975 7.802251 GTGTCTGTGGTATGTATATCGTTCTAC 59.198 40.741 0.00 0.00 0.00 2.59
2829 3149 8.853077 TTACTACTGTCTACTTGCTAGTGTTA 57.147 34.615 11.27 0.00 35.78 2.41
2841 3161 9.151471 TCAGCATCAAATTTTACTACTGTCTAC 57.849 33.333 0.00 0.00 0.00 2.59
2845 3165 8.396272 ACTTCAGCATCAAATTTTACTACTGT 57.604 30.769 0.00 0.00 0.00 3.55
2850 3176 6.204688 TCGTGACTTCAGCATCAAATTTTACT 59.795 34.615 0.00 0.00 0.00 2.24
2851 3177 6.370593 TCGTGACTTCAGCATCAAATTTTAC 58.629 36.000 0.00 0.00 0.00 2.01
2852 3178 6.552859 TCGTGACTTCAGCATCAAATTTTA 57.447 33.333 0.00 0.00 0.00 1.52
2859 3185 2.493278 TCAGATCGTGACTTCAGCATCA 59.507 45.455 0.00 0.00 0.00 3.07
2862 3188 3.515630 GAATCAGATCGTGACTTCAGCA 58.484 45.455 0.00 0.00 38.28 4.41
3269 3642 2.831685 TTGTGTGCATCTTCCGTACT 57.168 45.000 0.00 0.00 0.00 2.73
3276 3649 7.935755 AGCTTCTGTATATATTGTGTGCATCTT 59.064 33.333 0.00 0.00 0.00 2.40
3277 3650 7.387122 CAGCTTCTGTATATATTGTGTGCATCT 59.613 37.037 0.00 0.00 0.00 2.90
3278 3651 7.172190 ACAGCTTCTGTATATATTGTGTGCATC 59.828 37.037 0.00 0.00 43.46 3.91
3279 3652 6.994496 ACAGCTTCTGTATATATTGTGTGCAT 59.006 34.615 0.00 0.00 43.46 3.96
3280 3653 6.348498 ACAGCTTCTGTATATATTGTGTGCA 58.652 36.000 0.00 0.00 43.46 4.57
3281 3654 6.851222 ACAGCTTCTGTATATATTGTGTGC 57.149 37.500 0.00 0.00 43.46 4.57
3282 3655 8.491152 GCTAACAGCTTCTGTATATATTGTGTG 58.509 37.037 0.00 0.00 44.62 3.82
3283 3656 8.594881 GCTAACAGCTTCTGTATATATTGTGT 57.405 34.615 0.00 0.00 44.62 3.72
3313 3704 8.892723 CAATTGTACAATCTTTGCTCCACTATA 58.107 33.333 21.02 0.00 0.00 1.31
3372 3766 1.395826 ATGGAGTAGAGGACGCTGCC 61.396 60.000 0.00 0.00 0.00 4.85
3385 3779 6.893583 AGAGCATAGTTTATTGTCATGGAGT 58.106 36.000 0.00 0.00 0.00 3.85
3451 3849 6.536582 TCTGGTAGCGTACGAGTATATAATCC 59.463 42.308 21.65 6.37 36.15 3.01
3466 4103 2.973899 CTGGCAGTCTGGTAGCGT 59.026 61.111 6.28 0.00 0.00 5.07
3467 4104 2.510238 GCTGGCAGTCTGGTAGCG 60.510 66.667 17.16 0.00 0.00 4.26
3590 4227 3.192422 AGAGTCTCTCACGTGGATTTCTG 59.808 47.826 17.00 0.34 32.06 3.02
3621 4258 4.176271 GCTTTTGGACCATCAGTTTATGC 58.824 43.478 0.00 0.00 0.00 3.14
3647 4284 0.181114 TGGATAGCATGTCAGTGCCC 59.819 55.000 0.00 0.00 46.19 5.36
3648 4285 2.267174 ATGGATAGCATGTCAGTGCC 57.733 50.000 0.00 0.00 46.19 5.01
3694 4332 8.525290 TGTCAGTGAAGTTGATCAGATAGATA 57.475 34.615 0.00 0.00 37.00 1.98
3695 4333 7.415592 TGTCAGTGAAGTTGATCAGATAGAT 57.584 36.000 0.00 0.00 40.48 1.98
3696 4334 6.840780 TGTCAGTGAAGTTGATCAGATAGA 57.159 37.500 0.00 0.00 0.00 1.98
3697 4335 6.700960 GGATGTCAGTGAAGTTGATCAGATAG 59.299 42.308 0.00 0.00 0.00 2.08
3733 4371 2.681344 CACTACACATGCAGCATGACAT 59.319 45.455 36.91 23.73 43.81 3.06
3734 4372 2.078392 CACTACACATGCAGCATGACA 58.922 47.619 36.91 20.97 43.81 3.58
3735 4373 2.079158 ACACTACACATGCAGCATGAC 58.921 47.619 36.91 0.00 43.81 3.06
3736 4374 2.349590 GACACTACACATGCAGCATGA 58.650 47.619 36.91 17.31 43.81 3.07
3737 4375 1.399440 GGACACTACACATGCAGCATG 59.601 52.381 30.34 30.34 46.18 4.06
3738 4376 1.003464 TGGACACTACACATGCAGCAT 59.997 47.619 0.52 0.52 0.00 3.79
3739 4377 0.396060 TGGACACTACACATGCAGCA 59.604 50.000 0.00 0.00 0.00 4.41
3740 4378 0.798776 GTGGACACTACACATGCAGC 59.201 55.000 0.00 0.00 38.67 5.25
3741 4379 2.168326 TGTGGACACTACACATGCAG 57.832 50.000 3.91 0.00 43.35 4.41
3747 4385 5.135508 AGTTCTACATGTGGACACTACAC 57.864 43.478 11.95 6.39 39.26 2.90
3748 4386 6.243148 TCTAGTTCTACATGTGGACACTACA 58.757 40.000 11.95 8.03 0.00 2.74
3749 4387 6.754702 TCTAGTTCTACATGTGGACACTAC 57.245 41.667 11.95 7.49 0.00 2.73
3750 4388 6.127703 GCTTCTAGTTCTACATGTGGACACTA 60.128 42.308 21.37 21.37 0.00 2.74
3751 4389 5.336849 GCTTCTAGTTCTACATGTGGACACT 60.337 44.000 21.41 21.41 0.00 3.55
3752 4390 4.865365 GCTTCTAGTTCTACATGTGGACAC 59.135 45.833 11.95 12.64 0.00 3.67
3753 4391 4.526650 TGCTTCTAGTTCTACATGTGGACA 59.473 41.667 11.95 1.18 0.00 4.02
3808 4460 7.662897 TGTAATTTTCAAGGAATTACCACACC 58.337 34.615 13.89 0.00 43.96 4.16
3821 4473 7.090173 ACATTGGAACCGATGTAATTTTCAAG 58.910 34.615 21.10 0.00 46.07 3.02
3864 4516 1.891060 GACTTCGGCGAACAGTGCAG 61.891 60.000 19.83 9.69 0.00 4.41
3866 4518 2.853914 GACTTCGGCGAACAGTGC 59.146 61.111 19.83 6.80 0.00 4.40
3909 4561 6.548251 TGCATGGACAAGATCAACATCAATAT 59.452 34.615 0.00 0.00 0.00 1.28
3913 4565 3.441222 GTGCATGGACAAGATCAACATCA 59.559 43.478 13.07 0.00 0.00 3.07
3914 4566 3.441222 TGTGCATGGACAAGATCAACATC 59.559 43.478 18.56 0.00 0.00 3.06
4103 4771 1.376037 CTGGCTGAAGAACCCGGTC 60.376 63.158 0.00 0.00 0.00 4.79
4106 4774 3.121030 CGCTGGCTGAAGAACCCG 61.121 66.667 0.00 0.00 0.00 5.28
4469 5137 2.097007 CCTGCGTACGATCGAGTAGTAC 60.097 54.545 24.34 12.19 36.08 2.73
4470 5138 2.130395 CCTGCGTACGATCGAGTAGTA 58.870 52.381 24.34 8.49 0.00 1.82
4516 5201 5.170625 CACACCGACGAAACTAAACAAAATG 59.829 40.000 0.00 0.00 0.00 2.32
4517 5202 5.163733 ACACACCGACGAAACTAAACAAAAT 60.164 36.000 0.00 0.00 0.00 1.82
4649 5336 4.277423 GGTTTCAGTTTTTACAGGCAGCTA 59.723 41.667 0.00 0.00 0.00 3.32
4651 5338 3.068165 AGGTTTCAGTTTTTACAGGCAGC 59.932 43.478 0.00 0.00 0.00 5.25
4655 5342 7.067008 TCTCAAGAAGGTTTCAGTTTTTACAGG 59.933 37.037 0.00 0.00 0.00 4.00
4656 5343 7.985476 TCTCAAGAAGGTTTCAGTTTTTACAG 58.015 34.615 0.00 0.00 0.00 2.74
4657 5344 7.931578 TCTCAAGAAGGTTTCAGTTTTTACA 57.068 32.000 0.00 0.00 0.00 2.41
4667 5379 5.555966 AGGAGTTCATCTCAAGAAGGTTTC 58.444 41.667 0.00 0.00 44.40 2.78
4818 5530 2.159379 GGCAGCAGTACATTAACAAGGC 60.159 50.000 0.00 0.00 0.00 4.35
4916 5769 1.817099 GCAGATCAGCGACCAAGGG 60.817 63.158 0.00 0.00 0.00 3.95
4951 5804 7.806487 CCTGCTGCTGATGTAACAATAATATTG 59.194 37.037 11.14 11.14 0.00 1.90
4964 5817 1.298993 CCTCACCTGCTGCTGATGT 59.701 57.895 8.20 0.00 0.00 3.06
4972 5825 0.764369 TGGAACTCACCTCACCTGCT 60.764 55.000 0.00 0.00 0.00 4.24
5013 5866 0.854218 TTGTTAACAGCCCAGGGGAA 59.146 50.000 7.91 0.00 37.50 3.97
5021 5874 2.351350 CCAACCATCGTTGTTAACAGCC 60.351 50.000 15.74 7.01 46.71 4.85
5075 5928 4.107072 TCATCATCAAGGAGAAAGAGGGT 58.893 43.478 0.00 0.00 0.00 4.34
5092 5945 5.863935 GCGTGCTAATGTACTATCATCATCA 59.136 40.000 0.00 0.00 0.00 3.07
5093 5946 5.003872 CGCGTGCTAATGTACTATCATCATC 59.996 44.000 0.00 0.00 0.00 2.92
5094 5947 4.859245 CGCGTGCTAATGTACTATCATCAT 59.141 41.667 0.00 0.00 0.00 2.45
5095 5948 4.226761 CGCGTGCTAATGTACTATCATCA 58.773 43.478 0.00 0.00 0.00 3.07
5108 5961 2.028337 TGCAGTGACGCGTGCTAA 59.972 55.556 20.70 3.68 40.54 3.09
5109 5962 2.733218 GTGCAGTGACGCGTGCTA 60.733 61.111 20.70 0.00 40.54 3.49
5302 6162 3.761752 AGAAGAAGGAGAAGGAGAAGACG 59.238 47.826 0.00 0.00 0.00 4.18
5303 6163 4.159693 GGAGAAGAAGGAGAAGGAGAAGAC 59.840 50.000 0.00 0.00 0.00 3.01
5304 6164 4.202727 TGGAGAAGAAGGAGAAGGAGAAGA 60.203 45.833 0.00 0.00 0.00 2.87
5307 6167 3.181417 TGTGGAGAAGAAGGAGAAGGAGA 60.181 47.826 0.00 0.00 0.00 3.71
5308 6168 3.169099 TGTGGAGAAGAAGGAGAAGGAG 58.831 50.000 0.00 0.00 0.00 3.69
5310 6170 2.354604 GCTGTGGAGAAGAAGGAGAAGG 60.355 54.545 0.00 0.00 0.00 3.46
5311 6171 2.673610 CGCTGTGGAGAAGAAGGAGAAG 60.674 54.545 0.00 0.00 0.00 2.85
5312 6172 1.273606 CGCTGTGGAGAAGAAGGAGAA 59.726 52.381 0.00 0.00 0.00 2.87
5313 6173 0.891373 CGCTGTGGAGAAGAAGGAGA 59.109 55.000 0.00 0.00 0.00 3.71
5314 6174 0.605589 ACGCTGTGGAGAAGAAGGAG 59.394 55.000 0.00 0.00 0.00 3.69
5315 6175 0.603569 GACGCTGTGGAGAAGAAGGA 59.396 55.000 0.00 0.00 0.00 3.36
5316 6176 0.734253 CGACGCTGTGGAGAAGAAGG 60.734 60.000 0.00 0.00 0.00 3.46
5352 6223 3.207669 CAGCCAGATTCCGCAGCC 61.208 66.667 0.00 0.00 0.00 4.85
5379 6250 3.939939 TGCAGCGTCCAAGGAGCA 61.940 61.111 11.34 5.31 0.00 4.26
5403 6274 3.549221 GCATTGTCCTCCGTTTCGAAAAA 60.549 43.478 13.10 0.79 0.00 1.94
5404 6275 2.031508 GCATTGTCCTCCGTTTCGAAAA 60.032 45.455 13.10 0.00 0.00 2.29
5405 6276 1.533731 GCATTGTCCTCCGTTTCGAAA 59.466 47.619 6.47 6.47 0.00 3.46
5406 6277 1.153353 GCATTGTCCTCCGTTTCGAA 58.847 50.000 0.00 0.00 0.00 3.71
5407 6278 0.034198 TGCATTGTCCTCCGTTTCGA 59.966 50.000 0.00 0.00 0.00 3.71
5408 6279 0.165944 GTGCATTGTCCTCCGTTTCG 59.834 55.000 0.00 0.00 0.00 3.46
5409 6280 1.523758 AGTGCATTGTCCTCCGTTTC 58.476 50.000 0.00 0.00 0.00 2.78
5410 6281 2.851263 TAGTGCATTGTCCTCCGTTT 57.149 45.000 0.00 0.00 0.00 3.60
5411 6282 2.851263 TTAGTGCATTGTCCTCCGTT 57.149 45.000 0.00 0.00 0.00 4.44
5412 6283 2.632377 CATTAGTGCATTGTCCTCCGT 58.368 47.619 0.00 0.00 0.00 4.69
5413 6284 1.942657 CCATTAGTGCATTGTCCTCCG 59.057 52.381 0.00 0.00 0.00 4.63
5414 6285 3.281727 TCCATTAGTGCATTGTCCTCC 57.718 47.619 0.00 0.00 0.00 4.30
5415 6286 4.702131 AGTTTCCATTAGTGCATTGTCCTC 59.298 41.667 0.00 0.00 0.00 3.71
5416 6287 4.666512 AGTTTCCATTAGTGCATTGTCCT 58.333 39.130 0.00 0.00 0.00 3.85
5417 6288 4.437390 CGAGTTTCCATTAGTGCATTGTCC 60.437 45.833 0.00 0.00 0.00 4.02
5418 6289 4.651994 CGAGTTTCCATTAGTGCATTGTC 58.348 43.478 0.00 0.00 0.00 3.18
5419 6290 3.119849 GCGAGTTTCCATTAGTGCATTGT 60.120 43.478 0.00 0.00 0.00 2.71
5420 6291 3.429085 GCGAGTTTCCATTAGTGCATTG 58.571 45.455 0.00 0.00 0.00 2.82
5421 6292 2.095853 CGCGAGTTTCCATTAGTGCATT 59.904 45.455 0.00 0.00 0.00 3.56
5422 6293 1.665679 CGCGAGTTTCCATTAGTGCAT 59.334 47.619 0.00 0.00 0.00 3.96
5423 6294 1.075542 CGCGAGTTTCCATTAGTGCA 58.924 50.000 0.00 0.00 0.00 4.57
5424 6295 1.355971 TCGCGAGTTTCCATTAGTGC 58.644 50.000 3.71 0.00 0.00 4.40
5425 6296 3.301835 CGAATCGCGAGTTTCCATTAGTG 60.302 47.826 16.66 0.00 44.57 2.74
5426 6297 2.858344 CGAATCGCGAGTTTCCATTAGT 59.142 45.455 16.66 0.00 44.57 2.24
5427 6298 2.218759 CCGAATCGCGAGTTTCCATTAG 59.781 50.000 16.66 2.10 44.57 1.73
5428 6299 2.159212 TCCGAATCGCGAGTTTCCATTA 60.159 45.455 16.66 0.00 44.57 1.90
5429 6300 1.006832 CCGAATCGCGAGTTTCCATT 58.993 50.000 16.66 0.85 44.57 3.16


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

AutoCloner maintained by Alex Coulton.