Multiple sequence alignment - TraesCS2B01G613800

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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 TraesCS2B01G613800 chr2B 100.000 3966 0 0 1 3966 792992896 792988931 0.000000e+00 7324
1 TraesCS2B01G613800 chr2A 92.188 3597 161 58 1 3571 769220510 769224012 0.000000e+00 4975
2 TraesCS2B01G613800 chr2D 91.768 2867 133 47 744 3565 644093809 644096617 0.000000e+00 3892
3 TraesCS2B01G613800 chr2D 87.753 841 56 22 1 835 644092985 644093784 0.000000e+00 939
4 TraesCS2B01G613800 chr2D 91.731 387 23 6 3561 3945 295803109 295802730 2.710000e-146 529
5 TraesCS2B01G613800 chr2D 91.076 381 28 4 3567 3946 499733721 499734096 9.830000e-141 510
6 TraesCS2B01G613800 chr2D 90.551 381 24 6 3567 3946 640263849 640264218 9.900000e-136 494
7 TraesCS2B01G613800 chr2D 88.743 382 32 8 3567 3946 4177522 4177894 1.300000e-124 457
8 TraesCS2B01G613800 chr3D 90.909 385 26 6 3567 3949 426982490 426982113 3.540000e-140 508
9 TraesCS2B01G613800 chr3D 84.496 129 20 0 2546 2674 484823025 484823153 1.160000e-25 128
10 TraesCS2B01G613800 chr7D 90.231 389 25 8 3567 3951 192985754 192985375 2.750000e-136 496
11 TraesCS2B01G613800 chr7D 89.610 385 30 8 3567 3949 529451161 529450785 7.710000e-132 481
12 TraesCS2B01G613800 chr1B 90.052 382 29 7 3567 3944 474603499 474603123 1.660000e-133 486
13 TraesCS2B01G613800 chr1B 91.736 121 10 0 2847 2967 491982786 491982666 6.820000e-38 169
14 TraesCS2B01G613800 chr1B 86.260 131 16 2 2548 2677 491983007 491982878 1.490000e-29 141
15 TraesCS2B01G613800 chr4B 87.696 382 34 6 3567 3946 347392664 347393034 2.190000e-117 433
16 TraesCS2B01G613800 chr1D 93.388 121 8 0 2847 2967 367429297 367429177 3.150000e-41 180
17 TraesCS2B01G613800 chr1D 82.639 144 25 0 2549 2692 367429517 367429374 1.160000e-25 128
18 TraesCS2B01G613800 chr1A 92.562 121 9 0 2847 2967 466927481 466927361 1.470000e-39 174
19 TraesCS2B01G613800 chr1A 83.217 143 24 0 2550 2692 466927706 466927564 8.940000e-27 132
20 TraesCS2B01G613800 chr3B 86.047 129 18 0 2546 2674 647680718 647680846 5.340000e-29 139
21 TraesCS2B01G613800 chr6B 86.441 118 15 1 2556 2672 538366719 538366836 1.160000e-25 128
22 TraesCS2B01G613800 chr3A 83.721 129 21 0 2546 2674 627864871 627864999 5.380000e-24 122


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 TraesCS2B01G613800 chr2B 792988931 792992896 3965 True 7324.0 7324 100.0000 1 3966 1 chr2B.!!$R1 3965
1 TraesCS2B01G613800 chr2A 769220510 769224012 3502 False 4975.0 4975 92.1880 1 3571 1 chr2A.!!$F1 3570
2 TraesCS2B01G613800 chr2D 644092985 644096617 3632 False 2415.5 3892 89.7605 1 3565 2 chr2D.!!$F4 3564

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
114 115 0.253044 ACTTGAGGCTGTGTGTGTGT 59.747 50.0 0.00 0.0 0.0 3.72 F
928 1046 0.380378 TCACCGTGCTGCTTTTGAAC 59.620 50.0 0.00 0.0 0.0 3.18 F
1266 1385 0.667184 CCCGCAAAGATGTTGTTGCC 60.667 55.0 3.02 0.0 45.9 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1373 1.174712 AAGCGCAGGCAACAACATCT 61.175 50.0 11.47 0.0 43.41 2.90 R
2459 2584 0.170561 CTGAAGTCCGTGGAGTACCG 59.829 60.0 0.00 0.0 39.42 4.02 R
3005 3134 0.312416 CGGGAAGCTCGACATAGAGG 59.688 60.0 0.00 0.0 38.63 3.69 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
62 63 5.543020 AGTTACTCCTGGTTTGTTAGCTAGT 59.457 40.000 0.00 0.00 0.00 2.57
69 70 5.235850 TGGTTTGTTAGCTAGTTGATCCA 57.764 39.130 0.00 0.00 0.00 3.41
80 81 0.391661 GTTGATCCAGGAAGCGCAGA 60.392 55.000 11.47 0.00 0.00 4.26
114 115 0.253044 ACTTGAGGCTGTGTGTGTGT 59.747 50.000 0.00 0.00 0.00 3.72
115 116 0.659427 CTTGAGGCTGTGTGTGTGTG 59.341 55.000 0.00 0.00 0.00 3.82
141 142 5.059833 ACAACTCCTCAGATTCAACTGTTC 58.940 41.667 0.00 0.00 38.79 3.18
183 186 3.492656 GGAAAGAAACCCTGGCTGTTTTC 60.493 47.826 3.15 7.30 36.13 2.29
187 190 2.101640 AACCCTGGCTGTTTTCCATT 57.898 45.000 0.00 0.00 32.37 3.16
188 191 2.101640 ACCCTGGCTGTTTTCCATTT 57.898 45.000 0.00 0.00 32.37 2.32
189 192 3.252554 ACCCTGGCTGTTTTCCATTTA 57.747 42.857 0.00 0.00 32.37 1.40
221 224 0.957395 CAACTGCTGGATCCGTGCTT 60.957 55.000 23.96 12.49 0.00 3.91
222 225 0.957395 AACTGCTGGATCCGTGCTTG 60.957 55.000 23.96 19.29 0.00 4.01
223 226 2.747460 TGCTGGATCCGTGCTTGC 60.747 61.111 23.96 14.05 0.00 4.01
224 227 2.437359 GCTGGATCCGTGCTTGCT 60.437 61.111 18.73 0.00 0.00 3.91
250 253 3.007920 AGAGCTGGGGAGTGCCTG 61.008 66.667 0.00 0.00 0.00 4.85
290 293 2.806244 GAGTCTCCACTCGATCTCTAGC 59.194 54.545 0.00 0.00 39.91 3.42
484 487 2.294449 AGGAACAAGGAGAAAAGGGC 57.706 50.000 0.00 0.00 0.00 5.19
518 521 4.437682 TCAAGGATGCCTGTAATAAGGG 57.562 45.455 0.00 0.00 37.84 3.95
519 522 3.785887 TCAAGGATGCCTGTAATAAGGGT 59.214 43.478 0.00 0.00 37.84 4.34
520 523 3.864789 AGGATGCCTGTAATAAGGGTG 57.135 47.619 0.00 0.00 37.84 4.61
522 525 3.527665 AGGATGCCTGTAATAAGGGTGTT 59.472 43.478 0.00 0.00 37.84 3.32
523 526 4.724798 AGGATGCCTGTAATAAGGGTGTTA 59.275 41.667 0.00 0.00 37.84 2.41
524 527 4.820173 GGATGCCTGTAATAAGGGTGTTAC 59.180 45.833 0.00 0.00 37.84 2.50
578 584 3.243301 GCATCTGGCCATGTTTGTATCTG 60.243 47.826 5.51 0.00 36.11 2.90
599 605 4.055360 TGGTACACAAACGAGAATGACTG 58.945 43.478 0.00 0.00 0.00 3.51
735 741 1.001048 GCATGTGCTTGCAGACAGAAA 60.001 47.619 0.00 0.00 42.31 2.52
760 878 1.398595 GCTGTTAAGCGTGCTTGTTG 58.601 50.000 16.98 5.98 40.27 3.33
768 886 0.951040 GCGTGCTTGTTGTAGGAGCT 60.951 55.000 0.00 0.00 37.32 4.09
769 887 1.671850 GCGTGCTTGTTGTAGGAGCTA 60.672 52.381 0.00 0.00 37.32 3.32
770 888 1.993370 CGTGCTTGTTGTAGGAGCTAC 59.007 52.381 0.00 0.00 37.32 3.58
771 889 2.352814 CGTGCTTGTTGTAGGAGCTACT 60.353 50.000 2.64 2.64 37.78 2.57
849 967 3.803186 AATCTATGGCATGCCTTAGCT 57.197 42.857 37.36 30.74 41.14 3.32
850 968 3.803186 ATCTATGGCATGCCTTAGCTT 57.197 42.857 37.36 28.48 41.14 3.74
860 978 4.096984 GCATGCCTTAGCTTGTTCTGTAAT 59.903 41.667 6.36 0.00 44.06 1.89
861 979 5.575957 CATGCCTTAGCTTGTTCTGTAATG 58.424 41.667 0.00 0.00 38.89 1.90
862 980 4.651778 TGCCTTAGCTTGTTCTGTAATGT 58.348 39.130 0.00 0.00 40.80 2.71
863 981 5.070001 TGCCTTAGCTTGTTCTGTAATGTT 58.930 37.500 0.00 0.00 40.80 2.71
864 982 5.181245 TGCCTTAGCTTGTTCTGTAATGTTC 59.819 40.000 0.00 0.00 40.80 3.18
865 983 5.181245 GCCTTAGCTTGTTCTGTAATGTTCA 59.819 40.000 0.00 0.00 35.50 3.18
866 984 6.293955 GCCTTAGCTTGTTCTGTAATGTTCAA 60.294 38.462 0.00 0.00 35.50 2.69
867 985 7.575720 GCCTTAGCTTGTTCTGTAATGTTCAAT 60.576 37.037 0.00 0.00 35.50 2.57
900 1018 4.771590 TGCCTTTGAGCTTATTTCACAG 57.228 40.909 0.00 0.00 0.00 3.66
928 1046 0.380378 TCACCGTGCTGCTTTTGAAC 59.620 50.000 0.00 0.00 0.00 3.18
956 1075 2.358003 ACTCTTGCTGCTGTCGCC 60.358 61.111 0.00 0.00 34.43 5.54
957 1076 2.047465 CTCTTGCTGCTGTCGCCT 60.047 61.111 0.00 0.00 34.43 5.52
958 1077 2.357881 TCTTGCTGCTGTCGCCTG 60.358 61.111 0.00 0.00 34.43 4.85
991 1110 2.749621 GGTTACTCAGGGTTTGCATCAG 59.250 50.000 0.00 0.00 0.00 2.90
1041 1160 1.861575 CGCGATTTAAGGGAGAGCTTC 59.138 52.381 0.00 0.00 0.00 3.86
1245 1364 1.577328 AAGACGACAGCAATTGGCCG 61.577 55.000 7.72 0.00 46.50 6.13
1254 1373 2.598985 AATTGGCCGTCCCGCAAA 60.599 55.556 0.00 0.00 35.87 3.68
1266 1385 0.667184 CCCGCAAAGATGTTGTTGCC 60.667 55.000 3.02 0.00 45.90 4.52
1287 1406 0.790814 GCGCTTCTGTCTGTACAACC 59.209 55.000 0.00 0.00 34.49 3.77
1296 1415 3.579335 GTCTGTACAACCTGGAGAGAC 57.421 52.381 0.00 0.84 43.15 3.36
1311 1430 4.164796 TGGAGAGACATGTGCAAGGATATT 59.835 41.667 1.15 0.00 0.00 1.28
1382 1501 2.084546 GCAGGTAACCACACCATTCTC 58.915 52.381 0.00 0.00 41.40 2.87
1385 1504 2.572104 AGGTAACCACACCATTCTCTCC 59.428 50.000 0.00 0.00 41.40 3.71
1388 1507 1.221840 CCACACCATTCTCTCCCGG 59.778 63.158 0.00 0.00 0.00 5.73
1401 1520 7.012421 CCATTCTCTCCCGGTTAATAAGAAAAG 59.988 40.741 0.00 0.00 0.00 2.27
1406 1525 5.633117 TCCCGGTTAATAAGAAAAGTTGGT 58.367 37.500 0.00 0.00 0.00 3.67
1453 1575 6.093633 GGCCCTGTATTTAATTAAGCTATCCG 59.906 42.308 0.00 0.00 0.00 4.18
1578 1700 3.381272 TCAAAAGGGACAAGTCAAAGCTG 59.619 43.478 2.29 0.00 0.00 4.24
1620 1742 5.642491 GTCCCTTACTTCTGGTATGTTTGTC 59.358 44.000 0.00 0.00 0.00 3.18
1628 1750 6.942576 ACTTCTGGTATGTTTGTCTAATTGCT 59.057 34.615 0.00 0.00 0.00 3.91
1641 1763 2.574006 AATTGCTCTGCACTTCTCCA 57.426 45.000 0.00 0.00 38.71 3.86
1661 1783 5.698104 TCCATTGTGCTCCTAATCATCATT 58.302 37.500 0.00 0.00 0.00 2.57
1762 1885 5.153950 AGCCTTCAGTAACCTCAGTAAAG 57.846 43.478 0.00 0.00 0.00 1.85
1791 1914 6.670695 GGGATGCCCTGTTTTATTCATAAT 57.329 37.500 0.00 0.00 41.34 1.28
1823 1948 8.741603 TTTGCTACAGAGGTTTAAGTAGTTTT 57.258 30.769 0.00 0.00 37.02 2.43
1848 1973 8.777865 TGTTTTAATATGGTCAGAAGTCAGAG 57.222 34.615 0.00 0.00 0.00 3.35
1850 1975 6.544928 TTAATATGGTCAGAAGTCAGAGCA 57.455 37.500 7.86 7.86 42.46 4.26
1853 1978 2.838736 TGGTCAGAAGTCAGAGCAAAC 58.161 47.619 3.45 0.00 37.03 2.93
1882 2007 2.991190 CACACTGAGCATTTTGATTGCC 59.009 45.455 0.00 0.00 41.06 4.52
1884 2009 4.081406 ACACTGAGCATTTTGATTGCCTA 58.919 39.130 0.00 0.00 41.06 3.93
2048 2173 3.399330 ACATACCCTTTGACAACAGTCG 58.601 45.455 0.00 0.00 35.00 4.18
2126 2251 4.832248 TCTAACAGACAACATGGATGGTC 58.168 43.478 0.00 0.00 0.00 4.02
2251 2376 1.275421 CCTCCAGGAAAGTCTCCCCC 61.275 65.000 0.00 0.00 46.81 5.40
2380 2505 2.043248 ACATCGGCGGTAGACCCT 60.043 61.111 7.21 0.00 0.00 4.34
2383 2508 1.152525 ATCGGCGGTAGACCCTGAT 60.153 57.895 7.21 5.95 31.63 2.90
2459 2584 3.670377 GCACCACCGCAAGTTCCC 61.670 66.667 0.00 0.00 0.00 3.97
2487 2612 2.033141 GGACTTCAGCAGCTGCCA 59.967 61.111 34.39 19.42 43.38 4.92
2527 2652 1.567357 GGCCTCTGAGAGAAGAAGGT 58.433 55.000 11.82 0.00 0.00 3.50
2768 2893 3.465403 AGCCTACCTCTGCTGCCG 61.465 66.667 0.00 0.00 36.23 5.69
2770 2895 4.537433 CCTACCTCTGCTGCCGCC 62.537 72.222 0.00 0.00 34.43 6.13
2824 2949 2.812609 TCGTCGTCCTCGTCCTCG 60.813 66.667 0.00 0.00 38.33 4.63
2979 3108 6.310467 GCGTGTGAATAAACAGATTCTCAGTA 59.690 38.462 2.14 0.00 39.01 2.74
3004 3133 0.037326 TCAGCGGTCATTCAGTGTCC 60.037 55.000 0.00 0.00 33.31 4.02
3005 3134 1.021390 CAGCGGTCATTCAGTGTCCC 61.021 60.000 0.00 0.00 33.08 4.46
3010 3139 2.467880 GGTCATTCAGTGTCCCCTCTA 58.532 52.381 0.00 0.00 30.78 2.43
3011 3140 3.041946 GGTCATTCAGTGTCCCCTCTAT 58.958 50.000 0.00 0.00 30.78 1.98
3053 3190 1.203313 GGAACAAACGAGCGAACGG 59.797 57.895 0.00 0.00 37.61 4.44
3086 3223 4.612932 GCAGGACTAAATTTCTCTGCAG 57.387 45.455 20.28 7.63 44.68 4.41
3087 3224 3.181502 GCAGGACTAAATTTCTCTGCAGC 60.182 47.826 9.47 6.50 44.68 5.25
3088 3225 4.005650 CAGGACTAAATTTCTCTGCAGCA 58.994 43.478 9.47 0.00 0.00 4.41
3089 3226 4.639310 CAGGACTAAATTTCTCTGCAGCAT 59.361 41.667 9.47 0.00 0.00 3.79
3090 3227 5.819379 CAGGACTAAATTTCTCTGCAGCATA 59.181 40.000 9.47 0.00 0.00 3.14
3091 3228 5.819901 AGGACTAAATTTCTCTGCAGCATAC 59.180 40.000 9.47 0.00 0.00 2.39
3092 3229 5.586243 GGACTAAATTTCTCTGCAGCATACA 59.414 40.000 9.47 0.00 0.00 2.29
3093 3230 6.238320 GGACTAAATTTCTCTGCAGCATACAG 60.238 42.308 9.47 0.15 36.44 2.74
3094 3231 4.367386 AAATTTCTCTGCAGCATACAGC 57.633 40.909 9.47 0.00 46.19 4.40
3297 3464 3.282021 CTGGGACTGGTATGAAATGTGG 58.718 50.000 0.00 0.00 0.00 4.17
3298 3465 2.916269 TGGGACTGGTATGAAATGTGGA 59.084 45.455 0.00 0.00 0.00 4.02
3299 3466 3.527253 TGGGACTGGTATGAAATGTGGAT 59.473 43.478 0.00 0.00 0.00 3.41
3300 3467 4.017591 TGGGACTGGTATGAAATGTGGATT 60.018 41.667 0.00 0.00 0.00 3.01
3374 3544 2.630580 GAGTTGTCCTGGTCTCTCAGTT 59.369 50.000 0.00 0.00 33.14 3.16
3376 3546 3.134458 GTTGTCCTGGTCTCTCAGTTTG 58.866 50.000 0.00 0.00 33.14 2.93
3387 3557 3.266772 TCTCTCAGTTTGGGGCATTGTAT 59.733 43.478 0.00 0.00 0.00 2.29
3399 3575 1.683011 GCATTGTATCTGGTGGGTGCT 60.683 52.381 0.00 0.00 0.00 4.40
3403 3579 0.462759 GTATCTGGTGGGTGCTCAGC 60.463 60.000 0.00 0.00 35.87 4.26
3410 3586 3.640407 GGGTGCTCAGCCCAGACA 61.640 66.667 6.84 0.00 45.40 3.41
3411 3587 2.046507 GGTGCTCAGCCCAGACAG 60.047 66.667 0.00 0.00 0.00 3.51
3412 3588 2.745492 GTGCTCAGCCCAGACAGC 60.745 66.667 0.00 0.00 0.00 4.40
3413 3589 3.243816 TGCTCAGCCCAGACAGCA 61.244 61.111 0.00 0.00 39.58 4.41
3414 3590 2.271497 GCTCAGCCCAGACAGCAT 59.729 61.111 0.00 0.00 0.00 3.79
3424 3600 3.069586 GCCCAGACAGCATACATGTACTA 59.930 47.826 7.96 0.00 0.00 1.82
3434 3610 8.750298 ACAGCATACATGTACTAGAAGTTACTT 58.250 33.333 7.96 0.00 0.00 2.24
3435 3611 9.025020 CAGCATACATGTACTAGAAGTTACTTG 57.975 37.037 7.96 0.00 0.00 3.16
3436 3612 8.967918 AGCATACATGTACTAGAAGTTACTTGA 58.032 33.333 7.96 0.00 0.00 3.02
3502 3680 1.454276 CAGTTGATTTGCTTGCTTGCG 59.546 47.619 0.00 0.00 35.36 4.85
3518 3696 2.896854 CGTGGTGTGCTGCACTGT 60.897 61.111 30.43 0.00 46.86 3.55
3528 3706 2.349886 GTGCTGCACTGTATCTGCTAAC 59.650 50.000 24.68 0.00 35.53 2.34
3565 3743 9.884465 CACTGCCATTATATTAGCTTAAAAGAC 57.116 33.333 0.00 0.00 0.00 3.01
3566 3744 8.774586 ACTGCCATTATATTAGCTTAAAAGACG 58.225 33.333 0.00 0.00 0.00 4.18
3567 3745 8.896320 TGCCATTATATTAGCTTAAAAGACGA 57.104 30.769 0.00 0.00 0.00 4.20
3568 3746 9.332502 TGCCATTATATTAGCTTAAAAGACGAA 57.667 29.630 0.00 0.00 0.00 3.85
3584 3762 2.475200 CGAAAATCAATTCGGCTCCC 57.525 50.000 1.72 0.00 46.32 4.30
3595 3773 3.451894 GGCTCCCGGGTGCAAATG 61.452 66.667 39.91 16.27 36.47 2.32
3596 3774 4.133796 GCTCCCGGGTGCAAATGC 62.134 66.667 36.48 18.75 42.50 3.56
3608 3786 4.397010 AAATGCACCCGGGGCCAT 62.397 61.111 27.92 22.78 0.00 4.40
3609 3787 3.922116 AAATGCACCCGGGGCCATT 62.922 57.895 27.92 26.90 32.10 3.16
3610 3788 3.922116 AATGCACCCGGGGCCATTT 62.922 57.895 27.92 15.06 28.23 2.32
3611 3789 3.922116 ATGCACCCGGGGCCATTTT 62.922 57.895 27.92 3.31 0.00 1.82
3612 3790 3.318384 GCACCCGGGGCCATTTTT 61.318 61.111 27.92 0.00 0.00 1.94
3613 3791 2.661997 CACCCGGGGCCATTTTTG 59.338 61.111 27.92 7.34 0.00 2.44
3614 3792 1.910772 CACCCGGGGCCATTTTTGA 60.911 57.895 27.92 0.00 0.00 2.69
3615 3793 1.152226 ACCCGGGGCCATTTTTGAA 60.152 52.632 27.92 0.00 0.00 2.69
3616 3794 0.764752 ACCCGGGGCCATTTTTGAAA 60.765 50.000 27.92 0.00 0.00 2.69
3617 3795 0.398318 CCCGGGGCCATTTTTGAAAA 59.602 50.000 14.71 0.00 0.00 2.29
3618 3796 1.202818 CCCGGGGCCATTTTTGAAAAA 60.203 47.619 14.71 5.47 0.00 1.94
3689 3867 3.483808 TCACTACAAATGTGACCTGCA 57.516 42.857 0.00 0.00 39.23 4.41
3690 3868 3.814625 TCACTACAAATGTGACCTGCAA 58.185 40.909 0.00 0.00 39.23 4.08
3691 3869 4.203226 TCACTACAAATGTGACCTGCAAA 58.797 39.130 0.00 0.00 39.23 3.68
3692 3870 4.826733 TCACTACAAATGTGACCTGCAAAT 59.173 37.500 0.00 0.00 39.23 2.32
3693 3871 5.301551 TCACTACAAATGTGACCTGCAAATT 59.698 36.000 0.00 0.00 39.23 1.82
3694 3872 5.984926 CACTACAAATGTGACCTGCAAATTT 59.015 36.000 0.00 0.00 43.61 1.82
3695 3873 6.479660 CACTACAAATGTGACCTGCAAATTTT 59.520 34.615 0.00 0.00 40.71 1.82
3696 3874 5.738118 ACAAATGTGACCTGCAAATTTTG 57.262 34.783 4.72 4.72 40.71 2.44
3697 3875 5.426504 ACAAATGTGACCTGCAAATTTTGA 58.573 33.333 13.26 0.00 40.71 2.69
3698 3876 5.524646 ACAAATGTGACCTGCAAATTTTGAG 59.475 36.000 13.26 7.30 40.71 3.02
3699 3877 5.534207 AATGTGACCTGCAAATTTTGAGA 57.466 34.783 13.26 0.00 29.96 3.27
3700 3878 4.305989 TGTGACCTGCAAATTTTGAGAC 57.694 40.909 13.26 2.42 0.00 3.36
3701 3879 3.698539 TGTGACCTGCAAATTTTGAGACA 59.301 39.130 13.26 4.73 0.00 3.41
3702 3880 4.159321 TGTGACCTGCAAATTTTGAGACAA 59.841 37.500 13.26 0.00 0.00 3.18
3703 3881 5.108517 GTGACCTGCAAATTTTGAGACAAA 58.891 37.500 13.26 0.00 0.00 2.83
3704 3882 5.580297 GTGACCTGCAAATTTTGAGACAAAA 59.420 36.000 13.26 11.14 0.00 2.44
3705 3883 6.091986 GTGACCTGCAAATTTTGAGACAAAAA 59.908 34.615 13.26 0.00 33.76 1.94
3706 3884 6.822676 TGACCTGCAAATTTTGAGACAAAAAT 59.177 30.769 13.26 3.31 40.60 1.82
3707 3885 7.018635 ACCTGCAAATTTTGAGACAAAAATG 57.981 32.000 13.26 14.07 39.20 2.32
3708 3886 6.598850 ACCTGCAAATTTTGAGACAAAAATGT 59.401 30.769 13.26 0.00 39.20 2.71
3709 3887 7.121020 ACCTGCAAATTTTGAGACAAAAATGTT 59.879 29.630 13.26 6.11 39.20 2.71
3710 3888 8.610896 CCTGCAAATTTTGAGACAAAAATGTTA 58.389 29.630 13.26 8.32 39.20 2.41
3711 3889 9.985318 CTGCAAATTTTGAGACAAAAATGTTAA 57.015 25.926 13.26 6.19 39.20 2.01
3726 3904 5.783100 AATGTTAATCATTTTGGCTTGCG 57.217 34.783 0.00 0.00 43.33 4.85
3727 3905 2.992543 TGTTAATCATTTTGGCTTGCGC 59.007 40.909 0.00 0.00 0.00 6.09
3728 3906 2.992543 GTTAATCATTTTGGCTTGCGCA 59.007 40.909 5.66 5.66 38.10 6.09
3729 3907 2.166821 AATCATTTTGGCTTGCGCAA 57.833 40.000 23.48 23.48 38.10 4.85
3730 3908 2.166821 ATCATTTTGGCTTGCGCAAA 57.833 40.000 25.01 8.49 38.10 3.68
3731 3909 1.945387 TCATTTTGGCTTGCGCAAAA 58.055 40.000 25.01 15.30 37.28 2.44
3754 3932 8.791327 AAAAAGACAAATCAAAGACCAAATGT 57.209 26.923 0.00 0.00 0.00 2.71
3755 3933 8.424274 AAAAGACAAATCAAAGACCAAATGTC 57.576 30.769 0.00 0.00 44.82 3.06
3769 3947 7.977789 GACCAAATGTCACCCAAAATTTATT 57.022 32.000 0.00 0.00 43.85 1.40
3770 3948 8.389779 GACCAAATGTCACCCAAAATTTATTT 57.610 30.769 0.00 0.00 43.85 1.40
3771 3949 9.495572 GACCAAATGTCACCCAAAATTTATTTA 57.504 29.630 0.00 0.00 43.85 1.40
3778 3956 8.713271 TGTCACCCAAAATTTATTTATTTTCGC 58.287 29.630 0.00 0.00 35.98 4.70
3779 3957 8.172484 GTCACCCAAAATTTATTTATTTTCGCC 58.828 33.333 0.00 0.00 35.98 5.54
3780 3958 7.063544 TCACCCAAAATTTATTTATTTTCGCCG 59.936 33.333 0.00 0.00 35.98 6.46
3781 3959 7.063544 CACCCAAAATTTATTTATTTTCGCCGA 59.936 33.333 0.00 0.00 35.98 5.54
3782 3960 7.063662 ACCCAAAATTTATTTATTTTCGCCGAC 59.936 33.333 0.00 0.00 35.98 4.79
3783 3961 7.108005 CCAAAATTTATTTATTTTCGCCGACG 58.892 34.615 0.00 0.00 35.98 5.12
3784 3962 6.799786 AAATTTATTTATTTTCGCCGACGG 57.200 33.333 10.29 10.29 40.63 4.79
3785 3963 5.738118 ATTTATTTATTTTCGCCGACGGA 57.262 34.783 20.50 0.00 40.63 4.69
3786 3964 5.542616 TTTATTTATTTTCGCCGACGGAA 57.457 34.783 20.50 2.60 40.63 4.30
3787 3965 2.878906 TTTATTTTCGCCGACGGAAC 57.121 45.000 20.50 0.00 36.21 3.62
3788 3966 1.793258 TTATTTTCGCCGACGGAACA 58.207 45.000 20.50 0.00 36.21 3.18
3789 3967 1.070038 TATTTTCGCCGACGGAACAC 58.930 50.000 20.50 0.00 36.21 3.32
3790 3968 1.571215 ATTTTCGCCGACGGAACACC 61.571 55.000 20.50 0.00 36.21 4.16
3800 3978 4.681978 GGAACACCGCTGCTCCGT 62.682 66.667 0.00 0.00 0.00 4.69
3801 3979 2.665185 GAACACCGCTGCTCCGTT 60.665 61.111 0.00 0.00 0.00 4.44
3802 3980 2.665185 AACACCGCTGCTCCGTTC 60.665 61.111 0.00 0.00 0.00 3.95
3803 3981 4.681978 ACACCGCTGCTCCGTTCC 62.682 66.667 0.00 0.00 0.00 3.62
3809 3987 4.717629 CTGCTCCGTTCCGCGTGA 62.718 66.667 4.92 0.00 39.32 4.35
3810 3988 4.287781 TGCTCCGTTCCGCGTGAA 62.288 61.111 4.92 5.58 39.32 3.18
3811 3989 2.813908 GCTCCGTTCCGCGTGAAT 60.814 61.111 4.92 0.00 39.32 2.57
3812 3990 2.388232 GCTCCGTTCCGCGTGAATT 61.388 57.895 4.92 0.00 39.32 2.17
3813 3991 1.908066 GCTCCGTTCCGCGTGAATTT 61.908 55.000 4.92 0.00 39.32 1.82
3814 3992 0.515564 CTCCGTTCCGCGTGAATTTT 59.484 50.000 4.92 0.00 39.32 1.82
3815 3993 0.236187 TCCGTTCCGCGTGAATTTTG 59.764 50.000 4.92 1.03 39.32 2.44
3816 3994 0.040781 CCGTTCCGCGTGAATTTTGT 60.041 50.000 4.92 0.00 39.32 2.83
3817 3995 1.314581 CGTTCCGCGTGAATTTTGTC 58.685 50.000 4.92 0.00 34.90 3.18
3818 3996 1.333347 CGTTCCGCGTGAATTTTGTCA 60.333 47.619 4.92 0.00 34.90 3.58
3819 3997 2.722071 GTTCCGCGTGAATTTTGTCAA 58.278 42.857 4.92 0.00 34.90 3.18
3820 3998 2.679355 TCCGCGTGAATTTTGTCAAG 57.321 45.000 4.92 0.00 0.00 3.02
3821 3999 1.052287 CCGCGTGAATTTTGTCAAGC 58.948 50.000 4.92 3.45 45.85 4.01
3827 4005 5.640218 CGTGAATTTTGTCAAGCATGTTT 57.360 34.783 0.00 0.00 0.00 2.83
3828 4006 5.425398 CGTGAATTTTGTCAAGCATGTTTG 58.575 37.500 15.50 15.50 0.00 2.93
3829 4007 5.005586 CGTGAATTTTGTCAAGCATGTTTGT 59.994 36.000 20.01 0.95 0.00 2.83
3830 4008 6.186785 GTGAATTTTGTCAAGCATGTTTGTG 58.813 36.000 20.01 0.00 0.00 3.33
3831 4009 6.035866 GTGAATTTTGTCAAGCATGTTTGTGA 59.964 34.615 20.01 6.97 0.00 3.58
3832 4010 5.971895 ATTTTGTCAAGCATGTTTGTGAC 57.028 34.783 20.01 13.44 40.64 3.67
3833 4011 4.446994 TTTGTCAAGCATGTTTGTGACA 57.553 36.364 20.01 15.66 46.42 3.58
3834 4012 3.419264 TGTCAAGCATGTTTGTGACAC 57.581 42.857 20.01 12.23 44.02 3.67
3835 4013 2.098934 TGTCAAGCATGTTTGTGACACC 59.901 45.455 20.01 5.42 44.02 4.16
3836 4014 2.098934 GTCAAGCATGTTTGTGACACCA 59.901 45.455 20.01 0.00 42.04 4.17
3837 4015 2.757314 TCAAGCATGTTTGTGACACCAA 59.243 40.909 20.01 0.00 42.04 3.67
3838 4016 2.859538 CAAGCATGTTTGTGACACCAAC 59.140 45.455 13.64 14.09 42.04 3.77
3839 4017 2.098614 AGCATGTTTGTGACACCAACA 58.901 42.857 22.98 22.98 42.04 3.33
3840 4018 2.694628 AGCATGTTTGTGACACCAACAT 59.305 40.909 24.87 24.87 42.04 2.71
3841 4019 2.796031 GCATGTTTGTGACACCAACATG 59.204 45.455 37.31 37.31 42.04 3.21
3842 4020 3.490590 GCATGTTTGTGACACCAACATGA 60.491 43.478 41.47 20.26 42.04 3.07
3843 4021 4.796946 GCATGTTTGTGACACCAACATGAT 60.797 41.667 41.47 22.51 42.04 2.45
3844 4022 4.566545 TGTTTGTGACACCAACATGATC 57.433 40.909 18.49 0.00 32.00 2.92
3845 4023 3.950395 TGTTTGTGACACCAACATGATCA 59.050 39.130 18.49 0.00 32.00 2.92
3846 4024 4.583907 TGTTTGTGACACCAACATGATCAT 59.416 37.500 18.49 1.18 32.00 2.45
3847 4025 5.156355 GTTTGTGACACCAACATGATCATC 58.844 41.667 15.65 0.00 0.00 2.92
3848 4026 4.290711 TGTGACACCAACATGATCATCT 57.709 40.909 4.86 0.00 0.00 2.90
3849 4027 5.419239 TGTGACACCAACATGATCATCTA 57.581 39.130 4.86 0.00 0.00 1.98
3850 4028 5.178061 TGTGACACCAACATGATCATCTAC 58.822 41.667 4.86 0.00 0.00 2.59
3851 4029 5.178061 GTGACACCAACATGATCATCTACA 58.822 41.667 4.86 0.00 0.00 2.74
3852 4030 5.292834 GTGACACCAACATGATCATCTACAG 59.707 44.000 4.86 0.00 0.00 2.74
3853 4031 5.046376 TGACACCAACATGATCATCTACAGT 60.046 40.000 4.86 0.00 0.00 3.55
3854 4032 5.809001 ACACCAACATGATCATCTACAGTT 58.191 37.500 4.86 3.87 0.00 3.16
3855 4033 6.240894 ACACCAACATGATCATCTACAGTTT 58.759 36.000 4.86 0.00 0.00 2.66
3856 4034 6.716628 ACACCAACATGATCATCTACAGTTTT 59.283 34.615 4.86 0.00 0.00 2.43
3857 4035 7.231317 ACACCAACATGATCATCTACAGTTTTT 59.769 33.333 4.86 0.00 0.00 1.94
3909 4087 2.483014 TTTGGGGTACTGTTCATCCG 57.517 50.000 0.00 0.00 0.00 4.18
3910 4088 0.616371 TTGGGGTACTGTTCATCCGG 59.384 55.000 0.00 0.00 0.00 5.14
3911 4089 1.268992 TGGGGTACTGTTCATCCGGG 61.269 60.000 0.00 0.00 0.00 5.73
3912 4090 1.269703 GGGGTACTGTTCATCCGGGT 61.270 60.000 0.00 0.00 0.00 5.28
3913 4091 0.107848 GGGTACTGTTCATCCGGGTG 60.108 60.000 8.97 8.97 0.00 4.61
3914 4092 0.743345 GGTACTGTTCATCCGGGTGC 60.743 60.000 10.80 0.00 0.00 5.01
3915 4093 0.036765 GTACTGTTCATCCGGGTGCA 60.037 55.000 10.80 1.76 0.00 4.57
3916 4094 0.687920 TACTGTTCATCCGGGTGCAA 59.312 50.000 10.80 2.38 0.00 4.08
3917 4095 0.179004 ACTGTTCATCCGGGTGCAAA 60.179 50.000 10.80 0.00 0.00 3.68
3918 4096 1.176527 CTGTTCATCCGGGTGCAAAT 58.823 50.000 10.80 0.00 0.00 2.32
3919 4097 0.887247 TGTTCATCCGGGTGCAAATG 59.113 50.000 10.80 0.24 0.00 2.32
3920 4098 0.458370 GTTCATCCGGGTGCAAATGC 60.458 55.000 10.80 0.00 42.50 3.56
3930 4108 4.133796 GCAAATGCACCCGGGAGC 62.134 66.667 33.35 33.35 41.59 4.70
3931 4109 3.451894 CAAATGCACCCGGGAGCC 61.452 66.667 35.77 20.40 0.00 4.70
3932 4110 3.978193 AAATGCACCCGGGAGCCA 61.978 61.111 35.77 24.84 0.00 4.75
3933 4111 3.521765 AAATGCACCCGGGAGCCAA 62.522 57.895 35.77 21.62 0.00 4.52
3934 4112 3.521765 AATGCACCCGGGAGCCAAA 62.522 57.895 35.77 20.89 0.00 3.28
3935 4113 3.521765 ATGCACCCGGGAGCCAAAA 62.522 57.895 35.77 20.52 0.00 2.44
3936 4114 3.680786 GCACCCGGGAGCCAAAAC 61.681 66.667 30.60 3.28 0.00 2.43
3937 4115 3.361977 CACCCGGGAGCCAAAACG 61.362 66.667 32.02 0.00 0.00 3.60
3941 4119 3.431725 CGGGAGCCAAAACGCCTC 61.432 66.667 0.00 0.00 0.00 4.70
3942 4120 3.062466 GGGAGCCAAAACGCCTCC 61.062 66.667 0.00 0.00 0.00 4.30
3943 4121 3.062466 GGAGCCAAAACGCCTCCC 61.062 66.667 0.00 0.00 0.00 4.30
3944 4122 3.062466 GAGCCAAAACGCCTCCCC 61.062 66.667 0.00 0.00 0.00 4.81
3945 4123 4.678743 AGCCAAAACGCCTCCCCC 62.679 66.667 0.00 0.00 0.00 5.40
3946 4124 4.678743 GCCAAAACGCCTCCCCCT 62.679 66.667 0.00 0.00 0.00 4.79
3957 4135 2.894765 CGCCTCCCCCTTAAAAGAAAAA 59.105 45.455 0.00 0.00 0.00 1.94
3958 4136 3.513912 CGCCTCCCCCTTAAAAGAAAAAT 59.486 43.478 0.00 0.00 0.00 1.82
3959 4137 4.707934 CGCCTCCCCCTTAAAAGAAAAATA 59.292 41.667 0.00 0.00 0.00 1.40
3960 4138 5.393787 CGCCTCCCCCTTAAAAGAAAAATAC 60.394 44.000 0.00 0.00 0.00 1.89
3961 4139 5.720041 GCCTCCCCCTTAAAAGAAAAATACT 59.280 40.000 0.00 0.00 0.00 2.12
3962 4140 6.893554 GCCTCCCCCTTAAAAGAAAAATACTA 59.106 38.462 0.00 0.00 0.00 1.82
3963 4141 7.147949 GCCTCCCCCTTAAAAGAAAAATACTAC 60.148 40.741 0.00 0.00 0.00 2.73
3964 4142 8.114102 CCTCCCCCTTAAAAGAAAAATACTACT 58.886 37.037 0.00 0.00 0.00 2.57
3965 4143 9.175312 CTCCCCCTTAAAAGAAAAATACTACTC 57.825 37.037 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.636206 CCTGGATCAACTAGCTAACAAACC 59.364 45.833 0.00 0.00 0.00 3.27
62 63 0.324614 TTCTGCGCTTCCTGGATCAA 59.675 50.000 9.73 0.00 0.00 2.57
114 115 5.528690 CAGTTGAATCTGAGGAGTTGTTTCA 59.471 40.000 0.00 0.00 37.61 2.69
115 116 5.529060 ACAGTTGAATCTGAGGAGTTGTTTC 59.471 40.000 0.65 0.00 38.63 2.78
141 142 1.457823 TTCACCAAAGGCTGCTGCAG 61.458 55.000 24.80 24.80 41.91 4.41
183 186 6.684686 CAGTTGGCATCTGGATAATAAATGG 58.315 40.000 16.17 0.00 0.00 3.16
187 190 6.210442 CCAGCAGTTGGCATCTGGATAATAA 61.210 44.000 23.14 0.00 46.80 1.40
188 191 4.747623 CCAGCAGTTGGCATCTGGATAATA 60.748 45.833 23.14 0.00 46.80 0.98
189 192 4.001845 CCAGCAGTTGGCATCTGGATAAT 61.002 47.826 23.14 0.00 46.80 1.28
281 284 2.685388 GGGTGCCTTTTTGCTAGAGATC 59.315 50.000 0.00 0.00 0.00 2.75
484 487 4.201990 GGCATCCTTGATCAGCAAAACTAG 60.202 45.833 6.27 0.00 35.74 2.57
518 521 0.385098 GCGAAAGGCCAACGTAACAC 60.385 55.000 5.01 0.00 34.80 3.32
519 522 1.943293 GCGAAAGGCCAACGTAACA 59.057 52.632 5.01 0.00 34.80 2.41
520 523 4.832767 GCGAAAGGCCAACGTAAC 57.167 55.556 5.01 0.00 34.80 2.50
578 584 4.304110 TCAGTCATTCTCGTTTGTGTACC 58.696 43.478 0.00 0.00 0.00 3.34
599 605 3.679389 ACAGTGGACCAATCAGTTGATC 58.321 45.455 0.00 0.00 37.53 2.92
640 646 2.969821 AACCATGCCCACTTGACTAA 57.030 45.000 0.00 0.00 0.00 2.24
726 732 1.858091 ACAGCGACTGTTTCTGTCTG 58.142 50.000 6.67 0.00 42.59 3.51
758 876 4.030913 AGCATGGTAAGTAGCTCCTACAA 58.969 43.478 0.00 0.00 39.22 2.41
760 878 3.385111 ACAGCATGGTAAGTAGCTCCTAC 59.615 47.826 0.00 0.00 43.62 3.18
768 886 1.273886 TCGCACACAGCATGGTAAGTA 59.726 47.619 0.00 0.00 46.13 2.24
769 887 0.034756 TCGCACACAGCATGGTAAGT 59.965 50.000 0.00 0.00 46.13 2.24
770 888 1.372582 ATCGCACACAGCATGGTAAG 58.627 50.000 0.00 0.00 46.13 2.34
771 889 2.276201 GTATCGCACACAGCATGGTAA 58.724 47.619 0.00 0.00 46.13 2.85
793 911 2.100252 TCCTATCTAGCGACAAAACCGG 59.900 50.000 0.00 0.00 0.00 5.28
860 978 4.463539 AGGCATGCTATGAACAATTGAACA 59.536 37.500 18.92 11.65 0.00 3.18
861 979 5.002464 AGGCATGCTATGAACAATTGAAC 57.998 39.130 18.92 6.09 0.00 3.18
862 980 5.664294 AAGGCATGCTATGAACAATTGAA 57.336 34.783 18.92 0.00 0.00 2.69
863 981 5.185442 TCAAAGGCATGCTATGAACAATTGA 59.815 36.000 18.92 11.06 0.00 2.57
864 982 5.412640 TCAAAGGCATGCTATGAACAATTG 58.587 37.500 18.92 3.24 0.00 2.32
865 983 5.657474 CTCAAAGGCATGCTATGAACAATT 58.343 37.500 18.92 0.00 0.00 2.32
866 984 4.441079 GCTCAAAGGCATGCTATGAACAAT 60.441 41.667 18.92 0.00 0.00 2.71
867 985 3.119388 GCTCAAAGGCATGCTATGAACAA 60.119 43.478 18.92 0.00 0.00 2.83
900 1018 1.299541 CAGCACGGTGATCAATACCC 58.700 55.000 13.29 0.00 34.66 3.69
956 1075 1.965930 TAACCAACCGCAGCAGCAG 60.966 57.895 0.82 0.00 42.27 4.24
957 1076 2.112087 TAACCAACCGCAGCAGCA 59.888 55.556 0.82 0.00 42.27 4.41
958 1077 1.912371 GAGTAACCAACCGCAGCAGC 61.912 60.000 0.00 0.00 37.42 5.25
1041 1160 2.325082 CCGCCTTGACAGGTTTCCG 61.325 63.158 0.00 0.00 43.18 4.30
1108 1227 2.286294 CAGATTCAAGCGATTTCCCTCG 59.714 50.000 0.00 0.00 41.54 4.63
1245 1364 1.930371 GCAACAACATCTTTGCGGGAC 60.930 52.381 0.00 0.00 38.86 4.46
1254 1373 1.174712 AAGCGCAGGCAACAACATCT 61.175 50.000 11.47 0.00 43.41 2.90
1266 1385 1.457303 GTTGTACAGACAGAAGCGCAG 59.543 52.381 11.47 0.00 36.76 5.18
1287 1406 1.277273 TCCTTGCACATGTCTCTCCAG 59.723 52.381 0.00 0.00 0.00 3.86
1296 1415 4.201657 TCCTCACAATATCCTTGCACATG 58.798 43.478 0.00 0.00 0.00 3.21
1382 1501 5.708697 ACCAACTTTTCTTATTAACCGGGAG 59.291 40.000 6.32 0.00 0.00 4.30
1385 1504 7.337436 TGGATACCAACTTTTCTTATTAACCGG 59.663 37.037 0.00 0.00 0.00 5.28
1401 1520 9.561069 AGACTGATAAACAATATGGATACCAAC 57.439 33.333 0.00 0.00 36.95 3.77
1406 1525 7.168219 GGCCAGACTGATAAACAATATGGATA 58.832 38.462 3.32 0.00 0.00 2.59
1419 1538 6.763715 ATTAAATACAGGGCCAGACTGATA 57.236 37.500 13.73 4.06 39.24 2.15
1453 1575 9.705290 AAATATCACATCCCAAGTAACAAAAAC 57.295 29.630 0.00 0.00 0.00 2.43
1463 1585 8.525290 AAGGTAAGAAAATATCACATCCCAAG 57.475 34.615 0.00 0.00 0.00 3.61
1493 1615 7.424803 CACATGAGAAATTGAACCAAGTGTTA 58.575 34.615 0.00 0.00 37.29 2.41
1494 1616 6.275335 CACATGAGAAATTGAACCAAGTGTT 58.725 36.000 0.00 0.00 40.81 3.32
1495 1617 5.737063 GCACATGAGAAATTGAACCAAGTGT 60.737 40.000 0.00 0.00 31.54 3.55
1620 1742 3.603532 TGGAGAAGTGCAGAGCAATTAG 58.396 45.455 4.59 0.00 46.68 1.73
1746 1869 6.014840 TCCCTACAACTTTACTGAGGTTACTG 60.015 42.308 0.00 0.00 0.00 2.74
1823 1948 7.334421 GCTCTGACTTCTGACCATATTAAAACA 59.666 37.037 0.00 0.00 0.00 2.83
1848 1973 1.939934 TCAGTGTGCTGTGTAGTTTGC 59.060 47.619 0.00 0.00 43.05 3.68
1850 1975 2.213499 GCTCAGTGTGCTGTGTAGTTT 58.787 47.619 9.90 0.00 43.05 2.66
1853 1978 2.090400 ATGCTCAGTGTGCTGTGTAG 57.910 50.000 17.38 0.00 43.05 2.74
1882 2007 2.681344 TCATCAAGCACAGCTGCAATAG 59.319 45.455 15.27 1.30 46.97 1.73
1884 2009 1.541379 TCATCAAGCACAGCTGCAAT 58.459 45.000 15.27 0.00 46.97 3.56
2048 2173 1.633945 AGTGACAATGGGGTAAGGGAC 59.366 52.381 0.00 0.00 0.00 4.46
2180 2305 4.832248 CAGAGTTTACTGGCATTGTAGGA 58.168 43.478 0.00 0.00 34.64 2.94
2251 2376 1.961277 AGTCGCCGCTGGAACTTTG 60.961 57.895 0.00 0.00 0.00 2.77
2419 2544 1.996798 AGGATTCCTCGAATAGCCGA 58.003 50.000 0.00 0.00 31.89 5.54
2459 2584 0.170561 CTGAAGTCCGTGGAGTACCG 59.829 60.000 0.00 0.00 39.42 4.02
2487 2612 0.473117 TCCCCCAAACTCGGAGAAGT 60.473 55.000 12.86 0.00 34.09 3.01
2527 2652 3.427425 CCCGCATTTTCGTCGCCA 61.427 61.111 0.00 0.00 0.00 5.69
2824 2949 4.295119 ACCGTGTCGTGGTGGCTC 62.295 66.667 0.00 0.00 38.60 4.70
2979 3108 2.079158 CTGAATGACCGCTGATGTTGT 58.921 47.619 0.00 0.00 0.00 3.32
3004 3133 0.676736 GGGAAGCTCGACATAGAGGG 59.323 60.000 0.00 0.00 38.63 4.30
3005 3134 0.312416 CGGGAAGCTCGACATAGAGG 59.688 60.000 0.00 0.00 38.63 3.69
3068 3205 5.586243 TGTATGCTGCAGAGAAATTTAGTCC 59.414 40.000 20.43 0.00 0.00 3.85
3071 3208 5.508872 GCTGTATGCTGCAGAGAAATTTAG 58.491 41.667 20.43 5.65 39.07 1.85
3086 3223 3.334691 TGAACCAACAGTAGCTGTATGC 58.665 45.455 0.00 0.00 44.62 3.14
3097 3234 2.618709 GGGACTGAAACTGAACCAACAG 59.381 50.000 0.00 0.00 42.78 3.16
3129 3266 7.931948 CCTACCTATTGATAACACCTTTACCAG 59.068 40.741 0.00 0.00 0.00 4.00
3130 3267 7.147444 CCCTACCTATTGATAACACCTTTACCA 60.147 40.741 0.00 0.00 0.00 3.25
3138 3295 6.497259 TCATCTCCCCTACCTATTGATAACAC 59.503 42.308 0.00 0.00 0.00 3.32
3141 3298 7.180946 CACATCATCTCCCCTACCTATTGATAA 59.819 40.741 0.00 0.00 0.00 1.75
3297 3464 5.645497 ACCTTGCAACTCAACATCTCTAATC 59.355 40.000 0.00 0.00 0.00 1.75
3298 3465 5.564550 ACCTTGCAACTCAACATCTCTAAT 58.435 37.500 0.00 0.00 0.00 1.73
3299 3466 4.973168 ACCTTGCAACTCAACATCTCTAA 58.027 39.130 0.00 0.00 0.00 2.10
3300 3467 4.623932 ACCTTGCAACTCAACATCTCTA 57.376 40.909 0.00 0.00 0.00 2.43
3374 3544 1.341877 CCACCAGATACAATGCCCCAA 60.342 52.381 0.00 0.00 0.00 4.12
3376 3546 0.468029 CCCACCAGATACAATGCCCC 60.468 60.000 0.00 0.00 0.00 5.80
3387 3557 3.640407 GGCTGAGCACCCACCAGA 61.640 66.667 6.82 0.00 0.00 3.86
3399 3575 1.134310 CATGTATGCTGTCTGGGCTGA 60.134 52.381 0.00 0.00 0.00 4.26
3403 3579 3.827008 AGTACATGTATGCTGTCTGGG 57.173 47.619 9.18 0.00 0.00 4.45
3405 3581 6.800543 ACTTCTAGTACATGTATGCTGTCTG 58.199 40.000 9.18 0.00 0.00 3.51
3406 3582 7.411486 AACTTCTAGTACATGTATGCTGTCT 57.589 36.000 9.18 2.85 0.00 3.41
3407 3583 8.407064 AGTAACTTCTAGTACATGTATGCTGTC 58.593 37.037 9.18 0.00 0.00 3.51
3409 3585 9.025020 CAAGTAACTTCTAGTACATGTATGCTG 57.975 37.037 9.18 0.80 0.00 4.41
3410 3586 8.967918 TCAAGTAACTTCTAGTACATGTATGCT 58.032 33.333 9.18 5.06 0.00 3.79
3411 3587 9.239002 CTCAAGTAACTTCTAGTACATGTATGC 57.761 37.037 9.18 0.00 0.00 3.14
3414 3590 8.242053 GCACTCAAGTAACTTCTAGTACATGTA 58.758 37.037 0.08 0.08 0.00 2.29
3424 3600 3.643792 AGTCCAGCACTCAAGTAACTTCT 59.356 43.478 0.00 0.00 0.00 2.85
3434 3610 1.001293 GTCACATCAGTCCAGCACTCA 59.999 52.381 0.00 0.00 30.26 3.41
3435 3611 1.674221 GGTCACATCAGTCCAGCACTC 60.674 57.143 0.00 0.00 30.26 3.51
3436 3612 0.322975 GGTCACATCAGTCCAGCACT 59.677 55.000 0.00 0.00 34.67 4.40
3518 3696 1.385528 TCGCCGACTGTTAGCAGATA 58.614 50.000 14.09 0.00 45.28 1.98
3528 3706 2.887568 GGCAGTGATCGCCGACTG 60.888 66.667 1.76 4.61 40.35 3.51
3552 3730 9.325150 CGAATTGATTTTCGTCTTTTAAGCTAA 57.675 29.630 0.00 0.00 42.63 3.09
3565 3743 2.475200 GGGAGCCGAATTGATTTTCG 57.525 50.000 0.00 0.00 46.14 3.46
3578 3756 3.451894 CATTTGCACCCGGGAGCC 61.452 66.667 35.77 20.40 0.00 4.70
3579 3757 4.133796 GCATTTGCACCCGGGAGC 62.134 66.667 33.35 33.35 41.59 4.70
3591 3769 3.922116 AATGGCCCCGGGTGCATTT 62.922 57.895 28.24 19.72 0.00 2.32
3592 3770 3.922116 AAATGGCCCCGGGTGCATT 62.922 57.895 28.24 22.21 0.00 3.56
3593 3771 3.922116 AAAATGGCCCCGGGTGCAT 62.922 57.895 28.24 18.90 0.00 3.96
3594 3772 4.629958 AAAATGGCCCCGGGTGCA 62.630 61.111 28.24 17.80 0.00 4.57
3595 3773 3.318384 AAAAATGGCCCCGGGTGC 61.318 61.111 21.85 21.86 0.00 5.01
3596 3774 1.476007 TTCAAAAATGGCCCCGGGTG 61.476 55.000 21.85 12.44 0.00 4.61
3597 3775 0.764752 TTTCAAAAATGGCCCCGGGT 60.765 50.000 21.85 0.00 0.00 5.28
3598 3776 0.398318 TTTTCAAAAATGGCCCCGGG 59.602 50.000 15.80 15.80 0.00 5.73
3599 3777 2.262423 TTTTTCAAAAATGGCCCCGG 57.738 45.000 0.00 0.00 0.00 5.73
3669 3847 3.483808 TGCAGGTCACATTTGTAGTGA 57.516 42.857 0.00 0.00 43.23 3.41
3670 3848 4.566545 TTTGCAGGTCACATTTGTAGTG 57.433 40.909 0.00 0.00 38.32 2.74
3671 3849 5.789643 AATTTGCAGGTCACATTTGTAGT 57.210 34.783 0.00 0.00 0.00 2.73
3672 3850 6.700960 TCAAAATTTGCAGGTCACATTTGTAG 59.299 34.615 0.00 0.00 35.79 2.74
3673 3851 6.577103 TCAAAATTTGCAGGTCACATTTGTA 58.423 32.000 0.00 0.00 35.79 2.41
3674 3852 5.426504 TCAAAATTTGCAGGTCACATTTGT 58.573 33.333 0.00 0.00 35.79 2.83
3675 3853 5.754406 TCTCAAAATTTGCAGGTCACATTTG 59.246 36.000 0.00 0.00 35.79 2.32
3676 3854 5.754890 GTCTCAAAATTTGCAGGTCACATTT 59.245 36.000 0.00 0.00 36.82 2.32
3677 3855 5.163426 TGTCTCAAAATTTGCAGGTCACATT 60.163 36.000 0.00 0.00 0.00 2.71
3678 3856 4.341806 TGTCTCAAAATTTGCAGGTCACAT 59.658 37.500 0.00 0.00 0.00 3.21
3679 3857 3.698539 TGTCTCAAAATTTGCAGGTCACA 59.301 39.130 0.00 0.00 0.00 3.58
3680 3858 4.305989 TGTCTCAAAATTTGCAGGTCAC 57.694 40.909 0.00 0.00 0.00 3.67
3681 3859 4.998671 TTGTCTCAAAATTTGCAGGTCA 57.001 36.364 0.00 1.91 0.00 4.02
3682 3860 6.660887 TTTTTGTCTCAAAATTTGCAGGTC 57.339 33.333 0.00 0.00 0.00 3.85
3683 3861 6.598850 ACATTTTTGTCTCAAAATTTGCAGGT 59.401 30.769 0.00 0.09 0.00 4.00
3684 3862 7.018635 ACATTTTTGTCTCAAAATTTGCAGG 57.981 32.000 0.00 0.00 0.00 4.85
3685 3863 9.985318 TTAACATTTTTGTCTCAAAATTTGCAG 57.015 25.926 0.00 0.44 0.00 4.41
3729 3907 8.791327 ACATTTGGTCTTTGATTTGTCTTTTT 57.209 26.923 0.00 0.00 0.00 1.94
3730 3908 8.424274 GACATTTGGTCTTTGATTTGTCTTTT 57.576 30.769 0.00 0.00 43.46 2.27
3752 3930 8.713271 GCGAAAATAAATAAATTTTGGGTGACA 58.287 29.630 0.00 0.00 38.77 3.58
3753 3931 8.172484 GGCGAAAATAAATAAATTTTGGGTGAC 58.828 33.333 0.00 0.00 38.77 3.67
3754 3932 7.063544 CGGCGAAAATAAATAAATTTTGGGTGA 59.936 33.333 0.00 0.00 38.77 4.02
3755 3933 7.063544 TCGGCGAAAATAAATAAATTTTGGGTG 59.936 33.333 7.35 0.00 38.77 4.61
3756 3934 7.063662 GTCGGCGAAAATAAATAAATTTTGGGT 59.936 33.333 12.92 0.00 38.77 4.51
3757 3935 7.395645 GTCGGCGAAAATAAATAAATTTTGGG 58.604 34.615 12.92 0.00 38.77 4.12
3758 3936 7.108005 CGTCGGCGAAAATAAATAAATTTTGG 58.892 34.615 12.92 0.52 38.77 3.28
3759 3937 7.008447 TCCGTCGGCGAAAATAAATAAATTTTG 59.992 33.333 12.93 0.00 38.77 2.44
3760 3938 7.028361 TCCGTCGGCGAAAATAAATAAATTTT 58.972 30.769 12.93 0.00 40.79 1.82
3761 3939 6.553524 TCCGTCGGCGAAAATAAATAAATTT 58.446 32.000 12.93 0.00 41.33 1.82
3762 3940 6.121613 TCCGTCGGCGAAAATAAATAAATT 57.878 33.333 12.93 0.00 41.33 1.82
3763 3941 5.738118 TCCGTCGGCGAAAATAAATAAAT 57.262 34.783 12.93 0.00 41.33 1.40
3764 3942 5.106791 TGTTCCGTCGGCGAAAATAAATAAA 60.107 36.000 12.93 0.00 41.33 1.40
3765 3943 4.391216 TGTTCCGTCGGCGAAAATAAATAA 59.609 37.500 12.93 0.00 41.33 1.40
3766 3944 3.931468 TGTTCCGTCGGCGAAAATAAATA 59.069 39.130 12.93 0.00 41.33 1.40
3767 3945 2.743126 TGTTCCGTCGGCGAAAATAAAT 59.257 40.909 12.93 0.00 41.33 1.40
3768 3946 2.096318 GTGTTCCGTCGGCGAAAATAAA 60.096 45.455 12.93 0.00 41.33 1.40
3769 3947 1.460359 GTGTTCCGTCGGCGAAAATAA 59.540 47.619 12.93 0.65 41.33 1.40
3770 3948 1.070038 GTGTTCCGTCGGCGAAAATA 58.930 50.000 12.93 0.00 41.33 1.40
3771 3949 1.571215 GGTGTTCCGTCGGCGAAAAT 61.571 55.000 12.93 0.00 41.33 1.82
3772 3950 2.246042 GGTGTTCCGTCGGCGAAAA 61.246 57.895 12.93 1.11 41.33 2.29
3773 3951 2.662527 GGTGTTCCGTCGGCGAAA 60.663 61.111 12.93 0.00 41.33 3.46
3784 3962 2.665185 AACGGAGCAGCGGTGTTC 60.665 61.111 21.41 21.41 33.28 3.18
3785 3963 2.665185 GAACGGAGCAGCGGTGTT 60.665 61.111 17.07 10.65 0.00 3.32
3786 3964 4.681978 GGAACGGAGCAGCGGTGT 62.682 66.667 17.07 2.78 0.00 4.16
3799 3977 2.392933 TGACAAAATTCACGCGGAAC 57.607 45.000 12.47 0.00 38.60 3.62
3800 3978 2.856720 GCTTGACAAAATTCACGCGGAA 60.857 45.455 12.47 11.89 40.46 4.30
3801 3979 1.334599 GCTTGACAAAATTCACGCGGA 60.335 47.619 12.47 1.33 31.87 5.54
3802 3980 1.052287 GCTTGACAAAATTCACGCGG 58.948 50.000 12.47 0.00 31.87 6.46
3803 3981 1.752753 TGCTTGACAAAATTCACGCG 58.247 45.000 3.53 3.53 42.27 6.01
3804 3982 3.052036 ACATGCTTGACAAAATTCACGC 58.948 40.909 6.60 0.00 40.34 5.34
3805 3983 5.005586 ACAAACATGCTTGACAAAATTCACG 59.994 36.000 15.55 0.00 0.00 4.35
3806 3984 6.035866 TCACAAACATGCTTGACAAAATTCAC 59.964 34.615 15.55 0.00 0.00 3.18
3807 3985 6.035866 GTCACAAACATGCTTGACAAAATTCA 59.964 34.615 15.55 0.00 38.60 2.57
3808 3986 6.035866 TGTCACAAACATGCTTGACAAAATTC 59.964 34.615 15.55 0.00 44.09 2.17
3809 3987 5.873712 TGTCACAAACATGCTTGACAAAATT 59.126 32.000 15.55 0.00 44.09 1.82
3810 3988 5.417811 TGTCACAAACATGCTTGACAAAAT 58.582 33.333 15.55 0.00 44.09 1.82
3811 3989 4.814147 TGTCACAAACATGCTTGACAAAA 58.186 34.783 15.55 0.00 44.09 2.44
3812 3990 4.446994 TGTCACAAACATGCTTGACAAA 57.553 36.364 15.55 0.00 44.09 2.83
3814 3992 2.098934 GGTGTCACAAACATGCTTGACA 59.901 45.455 15.55 13.90 44.68 3.58
3815 3993 2.098934 TGGTGTCACAAACATGCTTGAC 59.901 45.455 15.55 11.68 40.80 3.18
3816 3994 2.373224 TGGTGTCACAAACATGCTTGA 58.627 42.857 15.55 0.00 40.80 3.02
3817 3995 2.859538 GTTGGTGTCACAAACATGCTTG 59.140 45.455 16.95 7.30 40.80 4.01
3818 3996 2.495270 TGTTGGTGTCACAAACATGCTT 59.505 40.909 20.01 0.00 40.80 3.91
3819 3997 2.098614 TGTTGGTGTCACAAACATGCT 58.901 42.857 20.01 0.00 40.80 3.79
3820 3998 2.575694 TGTTGGTGTCACAAACATGC 57.424 45.000 20.01 0.00 40.80 4.06
3821 3999 4.304537 TCATGTTGGTGTCACAAACATG 57.695 40.909 38.63 38.63 40.80 3.21
3822 4000 4.583907 TGATCATGTTGGTGTCACAAACAT 59.416 37.500 26.61 26.61 40.80 2.71
3823 4001 3.950395 TGATCATGTTGGTGTCACAAACA 59.050 39.130 24.75 24.75 34.78 2.83
3824 4002 4.566545 TGATCATGTTGGTGTCACAAAC 57.433 40.909 15.30 15.30 31.17 2.93
3825 4003 5.072055 AGATGATCATGTTGGTGTCACAAA 58.928 37.500 14.30 0.00 31.17 2.83
3826 4004 4.654915 AGATGATCATGTTGGTGTCACAA 58.345 39.130 14.30 0.00 0.00 3.33
3827 4005 4.290711 AGATGATCATGTTGGTGTCACA 57.709 40.909 14.30 0.00 0.00 3.58
3828 4006 5.178061 TGTAGATGATCATGTTGGTGTCAC 58.822 41.667 14.30 2.86 0.00 3.67
3829 4007 5.046376 ACTGTAGATGATCATGTTGGTGTCA 60.046 40.000 14.30 2.46 0.00 3.58
3830 4008 5.423015 ACTGTAGATGATCATGTTGGTGTC 58.577 41.667 14.30 0.00 0.00 3.67
3831 4009 5.426689 ACTGTAGATGATCATGTTGGTGT 57.573 39.130 14.30 4.06 0.00 4.16
3832 4010 6.748333 AAACTGTAGATGATCATGTTGGTG 57.252 37.500 14.30 3.45 0.00 4.17
3833 4011 7.765695 AAAAACTGTAGATGATCATGTTGGT 57.234 32.000 14.30 6.12 0.00 3.67
3888 4066 3.150767 CGGATGAACAGTACCCCAAAAA 58.849 45.455 0.00 0.00 0.00 1.94
3889 4067 2.553466 CCGGATGAACAGTACCCCAAAA 60.553 50.000 0.00 0.00 0.00 2.44
3890 4068 1.003812 CCGGATGAACAGTACCCCAAA 59.996 52.381 0.00 0.00 0.00 3.28
3891 4069 0.616371 CCGGATGAACAGTACCCCAA 59.384 55.000 0.00 0.00 0.00 4.12
3892 4070 1.268992 CCCGGATGAACAGTACCCCA 61.269 60.000 0.73 0.00 0.00 4.96
3893 4071 1.269703 ACCCGGATGAACAGTACCCC 61.270 60.000 0.73 0.00 0.00 4.95
3894 4072 0.107848 CACCCGGATGAACAGTACCC 60.108 60.000 0.73 0.00 0.00 3.69
3895 4073 0.743345 GCACCCGGATGAACAGTACC 60.743 60.000 0.00 0.00 0.00 3.34
3896 4074 0.036765 TGCACCCGGATGAACAGTAC 60.037 55.000 0.00 0.00 0.00 2.73
3897 4075 0.687920 TTGCACCCGGATGAACAGTA 59.312 50.000 0.00 0.00 0.00 2.74
3898 4076 0.179004 TTTGCACCCGGATGAACAGT 60.179 50.000 0.00 0.00 0.00 3.55
3899 4077 1.135315 CATTTGCACCCGGATGAACAG 60.135 52.381 0.00 0.00 0.00 3.16
3900 4078 0.887247 CATTTGCACCCGGATGAACA 59.113 50.000 0.00 0.00 0.00 3.18
3901 4079 0.458370 GCATTTGCACCCGGATGAAC 60.458 55.000 0.00 0.00 41.59 3.18
3902 4080 1.889454 GCATTTGCACCCGGATGAA 59.111 52.632 0.00 0.00 41.59 2.57
3903 4081 3.602103 GCATTTGCACCCGGATGA 58.398 55.556 0.00 0.00 41.59 2.92
3913 4091 4.133796 GCTCCCGGGTGCATTTGC 62.134 66.667 36.48 18.75 42.50 3.68
3914 4092 3.451894 GGCTCCCGGGTGCATTTG 61.452 66.667 39.91 16.27 36.47 2.32
3915 4093 3.521765 TTGGCTCCCGGGTGCATTT 62.522 57.895 39.91 0.00 36.47 2.32
3916 4094 3.521765 TTTGGCTCCCGGGTGCATT 62.522 57.895 39.91 0.00 36.47 3.56
3917 4095 3.521765 TTTTGGCTCCCGGGTGCAT 62.522 57.895 39.91 0.00 36.47 3.96
3918 4096 4.211330 TTTTGGCTCCCGGGTGCA 62.211 61.111 39.91 26.58 36.47 4.57
3919 4097 3.680786 GTTTTGGCTCCCGGGTGC 61.681 66.667 34.54 34.54 0.00 5.01
3920 4098 3.361977 CGTTTTGGCTCCCGGGTG 61.362 66.667 22.86 20.53 0.00 4.61
3929 4107 2.774687 TAAGGGGGAGGCGTTTTGGC 62.775 60.000 0.00 0.00 45.27 4.52
3930 4108 0.251430 TTAAGGGGGAGGCGTTTTGG 60.251 55.000 0.00 0.00 0.00 3.28
3931 4109 1.623163 TTTAAGGGGGAGGCGTTTTG 58.377 50.000 0.00 0.00 0.00 2.44
3932 4110 2.158430 TCTTTTAAGGGGGAGGCGTTTT 60.158 45.455 0.00 0.00 0.00 2.43
3933 4111 1.426215 TCTTTTAAGGGGGAGGCGTTT 59.574 47.619 0.00 0.00 0.00 3.60
3934 4112 1.069775 TCTTTTAAGGGGGAGGCGTT 58.930 50.000 0.00 0.00 0.00 4.84
3935 4113 1.069775 TTCTTTTAAGGGGGAGGCGT 58.930 50.000 0.00 0.00 0.00 5.68
3936 4114 2.209690 TTTCTTTTAAGGGGGAGGCG 57.790 50.000 0.00 0.00 0.00 5.52
3937 4115 5.720041 AGTATTTTTCTTTTAAGGGGGAGGC 59.280 40.000 0.00 0.00 0.00 4.70
3938 4116 8.114102 AGTAGTATTTTTCTTTTAAGGGGGAGG 58.886 37.037 0.00 0.00 0.00 4.30
3939 4117 9.175312 GAGTAGTATTTTTCTTTTAAGGGGGAG 57.825 37.037 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.