Multiple sequence alignment - TraesCS3D01G439200

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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 TraesCS3D01G439200 chr3D 100.000 6692 0 0 1 6692 549622435 549629126 0.000000e+00 12358
1 TraesCS3D01G439200 chr3D 84.301 2102 217 57 4295 6361 549639709 549641732 0.000000e+00 1949
2 TraesCS3D01G439200 chr3D 83.316 977 123 27 1613 2559 549636310 549637276 0.000000e+00 865
3 TraesCS3D01G439200 chr3D 84.803 737 97 11 3545 4277 549638933 549639658 0.000000e+00 726
4 TraesCS3D01G439200 chr3D 80.513 857 110 26 2648 3498 549638119 549638924 7.420000e-169 604
5 TraesCS3D01G439200 chr3B 94.822 3785 155 15 2151 5909 729205967 729209736 0.000000e+00 5866
6 TraesCS3D01G439200 chr3B 87.185 2185 153 59 1 2152 729203792 729205882 0.000000e+00 2366
7 TraesCS3D01G439200 chr3B 87.000 1600 141 30 4295 5862 729385929 729387493 0.000000e+00 1740
8 TraesCS3D01G439200 chr3B 87.364 736 81 8 3545 4277 729385151 729385877 0.000000e+00 833
9 TraesCS3D01G439200 chr3B 82.321 922 128 23 1616 2513 729382257 729383167 0.000000e+00 767
10 TraesCS3D01G439200 chr3B 80.552 869 103 35 2645 3505 729384342 729385152 5.740000e-170 608
11 TraesCS3D01G439200 chr3B 80.427 562 60 19 5894 6436 729209926 729210456 3.790000e-102 383
12 TraesCS3D01G439200 chr3B 88.210 229 19 5 6465 6692 729210457 729210678 3.980000e-67 267
13 TraesCS3D01G439200 chr3A 95.105 3698 145 19 2516 6185 686836104 686839793 0.000000e+00 5794
14 TraesCS3D01G439200 chr3A 87.976 1971 122 56 1 1916 686833700 686835610 0.000000e+00 2220
15 TraesCS3D01G439200 chr3A 84.864 1949 187 43 4295 6210 686853526 686855399 0.000000e+00 1866
16 TraesCS3D01G439200 chr3A 83.638 984 125 28 1602 2559 686850113 686851086 0.000000e+00 893
17 TraesCS3D01G439200 chr3A 85.889 737 89 11 3545 4277 686852746 686853471 0.000000e+00 771
18 TraesCS3D01G439200 chr3A 92.274 453 20 8 2065 2515 686835617 686836056 4.400000e-176 628
19 TraesCS3D01G439200 chr3A 83.642 593 83 11 2648 3235 686851925 686852508 4.560000e-151 545
20 TraesCS3D01G439200 chr3A 85.288 469 42 11 6232 6692 686839798 686840247 6.120000e-125 459
21 TraesCS3D01G439200 chr3A 90.000 120 10 2 3380 3498 686852619 686852737 3.230000e-33 154
22 TraesCS3D01G439200 chr7D 83.175 315 41 7 6232 6534 113586005 113586319 1.840000e-70 278


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 TraesCS3D01G439200 chr3D 549622435 549629126 6691 False 12358.00 12358 100.00000 1 6692 1 chr3D.!!$F1 6691
1 TraesCS3D01G439200 chr3D 549636310 549641732 5422 False 1036.00 1949 83.23325 1613 6361 4 chr3D.!!$F2 4748
2 TraesCS3D01G439200 chr3B 729203792 729210678 6886 False 2220.50 5866 87.66100 1 6692 4 chr3B.!!$F1 6691
3 TraesCS3D01G439200 chr3B 729382257 729387493 5236 False 987.00 1740 84.30925 1616 5862 4 chr3B.!!$F2 4246
4 TraesCS3D01G439200 chr3A 686833700 686840247 6547 False 2275.25 5794 90.16075 1 6692 4 chr3A.!!$F1 6691
5 TraesCS3D01G439200 chr3A 686850113 686855399 5286 False 845.80 1866 85.60660 1602 6210 5 chr3A.!!$F2 4608

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
711 766 0.109597 CACAAGATTCCCAACTGCGC 60.110 55.0 0.00 0.00 0.00 6.09 F
976 1038 0.331954 AGGCCGGTAAGAGTGAGAGA 59.668 55.0 1.90 0.00 0.00 3.10 F
1253 1318 0.333993 AGCAAGGGAACTGCATCCAT 59.666 50.0 8.58 0.00 42.68 3.41 F
1254 1319 0.743097 GCAAGGGAACTGCATCCATC 59.257 55.0 8.58 0.00 42.68 3.51 F
1777 1857 0.987294 CCTCCTTGGTGTCATGTCCT 59.013 55.0 0.00 0.00 0.00 3.85 F
2887 4160 1.020437 GCATCCCTCTGTTTAGCAGC 58.980 55.0 0.00 0.00 44.66 5.25 F
4585 5910 0.387929 CCAATGGCATCATGACCTGC 59.612 55.0 12.04 12.04 37.66 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2704 3969 1.137872 TGCAAATTGGGCGTTTTGTCT 59.862 42.857 0.0 0.00 35.69 3.41 R
2707 3972 1.261089 CACTGCAAATTGGGCGTTTTG 59.739 47.619 0.0 2.26 36.21 2.44 R
2887 4160 3.770666 AGTGACATGGACGTATCTTTCG 58.229 45.455 0.0 0.00 0.00 3.46 R
2897 4170 4.740934 GCACCCTAAGATAGTGACATGGAC 60.741 50.000 0.0 0.00 33.21 4.02 R
3376 4653 4.965119 AACATTGCTTCGGTTCCTATTC 57.035 40.909 0.0 0.00 0.00 1.75 R
4716 6044 1.139989 ACATCACAAAGACGACAGCG 58.860 50.000 0.0 0.00 44.79 5.18 R
6101 7678 0.110056 GTTCGATGTGCCAAGTGCTG 60.110 55.000 0.0 0.00 42.00 4.41 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
43 51 1.331756 GAATCGCATCGCATGAAAGGT 59.668 47.619 0.00 0.00 0.00 3.50
116 124 2.284798 GAATGGCTGCTCGAGTCGGA 62.285 60.000 15.13 0.00 0.00 4.55
212 220 1.537776 GGTCTGATGGCGAGATGACTG 60.538 57.143 0.00 0.00 0.00 3.51
213 221 1.406898 GTCTGATGGCGAGATGACTGA 59.593 52.381 0.00 0.00 0.00 3.41
216 224 1.134995 TGATGGCGAGATGACTGACAC 60.135 52.381 0.00 0.00 0.00 3.67
316 339 1.300311 TGCAGTGCAAGCATGTTGC 60.300 52.632 17.26 19.66 45.11 4.17
334 357 8.216453 GCATGTTGCTAAAACTTAAAACAGATG 58.784 33.333 0.00 0.00 40.96 2.90
421 456 7.068692 ACAGTTAAATCTGTGTTTATACCGC 57.931 36.000 0.00 0.00 45.40 5.68
441 476 5.122396 ACCGCTTTATTTTCATCTGAGACAC 59.878 40.000 0.00 0.00 0.00 3.67
442 477 5.352569 CCGCTTTATTTTCATCTGAGACACT 59.647 40.000 0.00 0.00 0.00 3.55
446 481 7.439157 TTTATTTTCATCTGAGACACTGTGG 57.561 36.000 13.09 0.00 0.00 4.17
472 511 5.678583 ACTTCATGATGTCCATCTAAGTGG 58.321 41.667 8.37 0.00 40.76 4.00
477 516 3.202818 TGATGTCCATCTAAGTGGCCATT 59.797 43.478 9.72 0.00 37.92 3.16
479 518 3.620488 TGTCCATCTAAGTGGCCATTTC 58.380 45.455 17.86 0.00 39.19 2.17
524 563 7.391275 TCAACATTGAGATGATGCTAGAAAACA 59.609 33.333 0.00 0.00 36.36 2.83
526 565 8.114331 ACATTGAGATGATGCTAGAAAACAAA 57.886 30.769 0.00 0.00 36.73 2.83
527 566 8.746530 ACATTGAGATGATGCTAGAAAACAAAT 58.253 29.630 0.00 0.00 36.73 2.32
529 568 9.798994 ATTGAGATGATGCTAGAAAACAAATTC 57.201 29.630 0.00 0.00 0.00 2.17
530 569 8.571461 TGAGATGATGCTAGAAAACAAATTCT 57.429 30.769 0.00 0.00 42.21 2.40
532 571 9.500864 GAGATGATGCTAGAAAACAAATTCTTC 57.499 33.333 0.00 0.00 40.13 2.87
535 575 7.950512 TGATGCTAGAAAACAAATTCTTCCAA 58.049 30.769 0.00 0.00 40.13 3.53
562 602 5.862323 GTCACGAAGTAAGCAGAGATAAACA 59.138 40.000 0.00 0.00 41.61 2.83
565 605 5.047235 ACGAAGTAAGCAGAGATAAACAGGT 60.047 40.000 0.00 0.00 41.94 4.00
590 630 4.743493 TGAAAGTCTGAAACAAAGTTGGC 58.257 39.130 0.00 0.00 0.00 4.52
591 631 4.219507 TGAAAGTCTGAAACAAAGTTGGCA 59.780 37.500 0.00 0.00 0.00 4.92
592 632 3.782889 AGTCTGAAACAAAGTTGGCAC 57.217 42.857 0.00 0.00 0.00 5.01
593 633 3.356290 AGTCTGAAACAAAGTTGGCACT 58.644 40.909 0.00 0.00 33.11 4.40
594 634 3.763897 AGTCTGAAACAAAGTTGGCACTT 59.236 39.130 0.00 0.00 45.89 3.16
711 766 0.109597 CACAAGATTCCCAACTGCGC 60.110 55.000 0.00 0.00 0.00 6.09
789 844 2.369860 TCACCAGCATTCAGTGAGAAGT 59.630 45.455 0.00 0.00 40.15 3.01
802 857 2.289002 GTGAGAAGTCTGTTGGTTGCAG 59.711 50.000 0.00 0.00 35.43 4.41
803 858 1.265365 GAGAAGTCTGTTGGTTGCAGC 59.735 52.381 0.00 0.00 34.21 5.25
804 859 1.024271 GAAGTCTGTTGGTTGCAGCA 58.976 50.000 2.05 0.00 34.21 4.41
817 876 2.202797 CAGCACGAGGATCCCACG 60.203 66.667 21.91 21.91 42.89 4.94
838 897 0.546507 TCATACCCCAGCACCACAGA 60.547 55.000 0.00 0.00 0.00 3.41
839 898 0.392998 CATACCCCAGCACCACAGAC 60.393 60.000 0.00 0.00 0.00 3.51
840 899 0.840288 ATACCCCAGCACCACAGACA 60.840 55.000 0.00 0.00 0.00 3.41
841 900 1.057275 TACCCCAGCACCACAGACAA 61.057 55.000 0.00 0.00 0.00 3.18
842 901 1.601759 CCCCAGCACCACAGACAAG 60.602 63.158 0.00 0.00 0.00 3.16
843 902 1.149174 CCCAGCACCACAGACAAGT 59.851 57.895 0.00 0.00 0.00 3.16
844 903 0.466189 CCCAGCACCACAGACAAGTT 60.466 55.000 0.00 0.00 0.00 2.66
845 904 0.947244 CCAGCACCACAGACAAGTTC 59.053 55.000 0.00 0.00 0.00 3.01
846 905 0.583438 CAGCACCACAGACAAGTTCG 59.417 55.000 0.00 0.00 0.00 3.95
847 906 0.532862 AGCACCACAGACAAGTTCGG 60.533 55.000 0.00 0.00 0.00 4.30
848 907 0.531974 GCACCACAGACAAGTTCGGA 60.532 55.000 0.00 0.00 0.00 4.55
849 908 1.878102 GCACCACAGACAAGTTCGGAT 60.878 52.381 0.00 0.00 0.00 4.18
851 910 1.691976 ACCACAGACAAGTTCGGATCA 59.308 47.619 0.00 0.00 0.00 2.92
853 912 2.547855 CCACAGACAAGTTCGGATCACA 60.548 50.000 0.00 0.00 0.00 3.58
856 915 3.572682 ACAGACAAGTTCGGATCACAGTA 59.427 43.478 0.00 0.00 0.00 2.74
857 916 4.220821 ACAGACAAGTTCGGATCACAGTAT 59.779 41.667 0.00 0.00 0.00 2.12
858 917 4.800993 CAGACAAGTTCGGATCACAGTATC 59.199 45.833 0.00 0.00 0.00 2.24
859 918 4.462834 AGACAAGTTCGGATCACAGTATCA 59.537 41.667 0.00 0.00 0.00 2.15
860 919 4.495422 ACAAGTTCGGATCACAGTATCAC 58.505 43.478 0.00 0.00 0.00 3.06
861 920 4.021456 ACAAGTTCGGATCACAGTATCACA 60.021 41.667 0.00 0.00 0.00 3.58
862 921 4.111375 AGTTCGGATCACAGTATCACAC 57.889 45.455 0.00 0.00 0.00 3.82
863 922 2.844122 TCGGATCACAGTATCACACG 57.156 50.000 0.00 0.00 0.00 4.49
864 923 1.200483 CGGATCACAGTATCACACGC 58.800 55.000 0.00 0.00 0.00 5.34
865 924 1.200483 GGATCACAGTATCACACGCG 58.800 55.000 3.53 3.53 0.00 6.01
866 925 1.202256 GGATCACAGTATCACACGCGA 60.202 52.381 15.93 0.00 0.00 5.87
869 928 2.258755 TCACAGTATCACACGCGATTG 58.741 47.619 15.93 9.51 0.00 2.67
872 931 1.393196 CAGTATCACACGCGATTGCAA 59.607 47.619 15.93 0.00 42.97 4.08
956 1018 8.967218 CAAGTCATTGTTAAACAATAACACAGG 58.033 33.333 6.19 0.88 46.22 4.00
973 1035 0.684805 AGGAGGCCGGTAAGAGTGAG 60.685 60.000 1.90 0.00 0.00 3.51
974 1036 0.683504 GGAGGCCGGTAAGAGTGAGA 60.684 60.000 1.90 0.00 0.00 3.27
975 1037 0.741915 GAGGCCGGTAAGAGTGAGAG 59.258 60.000 1.90 0.00 0.00 3.20
976 1038 0.331954 AGGCCGGTAAGAGTGAGAGA 59.668 55.000 1.90 0.00 0.00 3.10
995 1057 5.630121 AGAGAGAGATCATCATCGTACCTT 58.370 41.667 0.00 0.00 33.75 3.50
996 1058 5.473162 AGAGAGAGATCATCATCGTACCTTG 59.527 44.000 0.00 0.00 33.75 3.61
1209 1274 1.746220 CTCTTCCTCGGTTCGACAGAT 59.254 52.381 0.00 0.00 0.00 2.90
1227 1292 9.521503 TCGACAGATATCTTCATTTTCTTACAG 57.478 33.333 1.33 0.00 0.00 2.74
1228 1293 9.307121 CGACAGATATCTTCATTTTCTTACAGT 57.693 33.333 1.33 0.00 0.00 3.55
1251 1316 2.128771 TAAGCAAGGGAACTGCATCC 57.871 50.000 0.00 0.00 42.68 3.51
1253 1318 0.333993 AGCAAGGGAACTGCATCCAT 59.666 50.000 8.58 0.00 42.68 3.41
1254 1319 0.743097 GCAAGGGAACTGCATCCATC 59.257 55.000 8.58 0.00 42.68 3.51
1275 1344 3.967326 TCTCGATTCCTGTTATGATGGGT 59.033 43.478 0.00 0.00 0.00 4.51
1276 1345 5.144832 TCTCGATTCCTGTTATGATGGGTA 58.855 41.667 0.00 0.00 0.00 3.69
1277 1346 5.010719 TCTCGATTCCTGTTATGATGGGTAC 59.989 44.000 0.00 0.00 0.00 3.34
1278 1347 4.899457 TCGATTCCTGTTATGATGGGTACT 59.101 41.667 0.00 0.00 0.00 2.73
1280 1349 5.696724 CGATTCCTGTTATGATGGGTACTTC 59.303 44.000 0.00 0.00 0.00 3.01
1281 1350 5.367945 TTCCTGTTATGATGGGTACTTCC 57.632 43.478 0.00 0.00 0.00 3.46
1282 1351 4.631234 TCCTGTTATGATGGGTACTTCCT 58.369 43.478 0.00 0.00 36.25 3.36
1283 1352 4.654262 TCCTGTTATGATGGGTACTTCCTC 59.346 45.833 0.00 0.00 36.25 3.71
1284 1353 4.656112 CCTGTTATGATGGGTACTTCCTCT 59.344 45.833 0.00 0.00 36.25 3.69
1285 1354 5.453903 CCTGTTATGATGGGTACTTCCTCTG 60.454 48.000 0.00 0.00 36.25 3.35
1287 1356 5.487488 TGTTATGATGGGTACTTCCTCTGTT 59.513 40.000 0.00 0.00 36.25 3.16
1288 1357 4.762289 ATGATGGGTACTTCCTCTGTTC 57.238 45.455 0.00 0.00 36.25 3.18
1289 1358 2.838202 TGATGGGTACTTCCTCTGTTCC 59.162 50.000 0.00 0.00 36.25 3.62
1290 1359 2.715763 TGGGTACTTCCTCTGTTCCT 57.284 50.000 0.00 0.00 36.25 3.36
1291 1360 2.537143 TGGGTACTTCCTCTGTTCCTC 58.463 52.381 0.00 0.00 36.25 3.71
1292 1361 2.158219 TGGGTACTTCCTCTGTTCCTCA 60.158 50.000 0.00 0.00 36.25 3.86
1293 1362 3.108376 GGGTACTTCCTCTGTTCCTCAT 58.892 50.000 0.00 0.00 36.25 2.90
1294 1363 4.264668 TGGGTACTTCCTCTGTTCCTCATA 60.265 45.833 0.00 0.00 36.25 2.15
1295 1364 4.715297 GGGTACTTCCTCTGTTCCTCATAA 59.285 45.833 0.00 0.00 36.25 1.90
1299 1368 6.187727 ACTTCCTCTGTTCCTCATAAAACA 57.812 37.500 0.00 0.00 34.41 2.83
1308 1377 6.634805 TGTTCCTCATAAAACAGCAAACAAA 58.365 32.000 0.00 0.00 31.97 2.83
1311 1380 8.611757 GTTCCTCATAAAACAGCAAACAAAAAT 58.388 29.630 0.00 0.00 0.00 1.82
1314 1384 8.610896 CCTCATAAAACAGCAAACAAAAATTCA 58.389 29.630 0.00 0.00 0.00 2.57
1396 1466 7.094334 GGAAGGCTGCTAAAAGTAACTAATGTT 60.094 37.037 0.00 0.00 39.98 2.71
1463 1537 5.416952 AGCAACTAAACATATCAGCTGCTTT 59.583 36.000 9.47 3.91 38.27 3.51
1568 1643 8.562892 ACAACTAAGCATATTAATAAGCTGCTG 58.437 33.333 22.20 17.97 42.05 4.41
1586 1661 3.265791 GCTGTCCTTGAGGTGAATGTAG 58.734 50.000 0.00 0.00 36.34 2.74
1777 1857 0.987294 CCTCCTTGGTGTCATGTCCT 59.013 55.000 0.00 0.00 0.00 3.85
1782 1862 3.843619 TCCTTGGTGTCATGTCCTTGATA 59.156 43.478 0.00 0.00 0.00 2.15
1874 1954 5.465724 GCGATGGTAAGTAAATACCTTCCAG 59.534 44.000 11.53 3.40 44.72 3.86
2000 2096 1.605710 CGAATGGCCATAGGAGCAAAG 59.394 52.381 21.15 0.00 0.00 2.77
2001 2097 1.339291 GAATGGCCATAGGAGCAAAGC 59.661 52.381 21.15 0.00 0.00 3.51
2070 2174 7.547370 GCATAGGTTTAGACAGCATCTTATAGG 59.453 40.741 0.00 0.00 39.04 2.57
2128 2234 6.729187 GCATTAAGCACTTAGGTCCATAAAG 58.271 40.000 0.00 0.00 44.79 1.85
2231 2426 7.581213 TGTCTTATGAATTCACAACCTTTGT 57.419 32.000 11.07 0.00 46.75 2.83
2487 2682 6.058183 GCTAACTCCATGTATTTCAGGTGAT 58.942 40.000 0.00 0.00 0.00 3.06
2582 3842 6.096141 TGTGGACACTTGAACAAATAATGTGT 59.904 34.615 3.91 8.48 42.99 3.72
2626 3886 4.424061 TGAACACATGCTCATGCTAAAC 57.576 40.909 9.58 0.31 42.39 2.01
2628 3888 4.460034 TGAACACATGCTCATGCTAAACAT 59.540 37.500 9.58 0.00 42.39 2.71
2630 3890 6.150809 TGAACACATGCTCATGCTAAACATTA 59.849 34.615 9.58 0.00 42.39 1.90
2631 3891 6.704289 ACACATGCTCATGCTAAACATTAT 57.296 33.333 9.58 0.00 42.39 1.28
2633 3893 8.224389 ACACATGCTCATGCTAAACATTATTA 57.776 30.769 9.58 0.00 42.39 0.98
2704 3969 7.510549 AAAGCAACTTATTGTTCTGCTAGAA 57.489 32.000 0.00 0.00 40.63 2.10
2707 3972 6.370166 AGCAACTTATTGTTCTGCTAGAAGAC 59.630 38.462 0.00 0.00 39.98 3.01
2766 4032 6.324819 GCATGATTGCTTTCAGCTTAACTAA 58.675 36.000 0.00 0.00 45.77 2.24
2767 4033 6.252228 GCATGATTGCTTTCAGCTTAACTAAC 59.748 38.462 0.00 0.00 45.77 2.34
2768 4034 6.875948 TGATTGCTTTCAGCTTAACTAACA 57.124 33.333 0.00 0.00 42.97 2.41
2769 4035 7.270757 TGATTGCTTTCAGCTTAACTAACAA 57.729 32.000 0.00 0.00 42.97 2.83
2770 4036 7.711846 TGATTGCTTTCAGCTTAACTAACAAA 58.288 30.769 0.00 0.00 42.97 2.83
2771 4037 7.862372 TGATTGCTTTCAGCTTAACTAACAAAG 59.138 33.333 0.00 0.00 42.97 2.77
2856 4129 5.240713 AGTCGTTAACTCAAGGTATACCG 57.759 43.478 16.31 4.68 35.40 4.02
2887 4160 1.020437 GCATCCCTCTGTTTAGCAGC 58.980 55.000 0.00 0.00 44.66 5.25
2893 4166 2.612972 CCCTCTGTTTAGCAGCGAAAGA 60.613 50.000 0.20 0.00 44.66 2.52
2897 4170 3.857665 TCTGTTTAGCAGCGAAAGATACG 59.142 43.478 0.20 0.00 44.66 3.06
3376 4653 7.871973 TGAAAATGGATATTGTGTCTTTTGTGG 59.128 33.333 0.00 0.00 0.00 4.17
3525 4803 1.564348 TGGCTGGAGAGGGAATAAACC 59.436 52.381 0.00 0.00 0.00 3.27
3836 5119 6.666678 AGGATCAGCTAAGAAATGGAATGAA 58.333 36.000 0.00 0.00 0.00 2.57
3846 5129 7.486407 AAGAAATGGAATGAATTAGGCACTT 57.514 32.000 0.00 0.00 41.75 3.16
4153 5437 6.291648 TGGCAATGCATATGGTAAGAAAAA 57.708 33.333 7.79 0.00 0.00 1.94
4269 5553 4.739716 CCTTACACAACTGTTTCATGCAAC 59.260 41.667 0.84 0.84 0.00 4.17
4280 5564 7.196331 ACTGTTTCATGCAACTTCTCTTAAAC 58.804 34.615 9.63 1.29 0.00 2.01
4337 5660 4.154737 TGCACTGAAGTTGCTCATAACATC 59.845 41.667 0.00 0.00 33.02 3.06
4342 5665 6.128090 ACTGAAGTTGCTCATAACATCATGTG 60.128 38.462 0.00 0.00 37.56 3.21
4380 5703 2.271800 CCAGATTGTCGGCAAGTAGTC 58.728 52.381 9.01 0.10 38.10 2.59
4529 5852 7.754851 AATGTCTGCATAGCATGATCAATTA 57.245 32.000 0.00 0.00 38.13 1.40
4584 5909 2.061509 TCCAATGGCATCATGACCTG 57.938 50.000 0.00 0.00 33.18 4.00
4585 5910 0.387929 CCAATGGCATCATGACCTGC 59.612 55.000 12.04 12.04 37.66 4.85
5401 6729 2.105477 GGAGATGCAATGGAGCCTTCTA 59.895 50.000 0.00 0.00 0.00 2.10
5541 6869 3.782523 TCCATCTGCTGGGAGAAACTAAT 59.217 43.478 0.00 0.00 45.98 1.73
5958 7530 2.364002 GTTTGGCCAACTCTTTGCCTTA 59.636 45.455 20.35 0.00 32.87 2.69
5961 7534 2.562298 TGGCCAACTCTTTGCCTTATTG 59.438 45.455 0.61 0.00 32.87 1.90
6033 7607 5.069383 ACCTACCGGCAAAAGTTAAACAAAT 59.931 36.000 0.00 0.00 0.00 2.32
6064 7638 2.738314 TGACTTGTGTGCATTCATCTCG 59.262 45.455 0.00 0.00 0.00 4.04
6071 7645 4.216042 TGTGTGCATTCATCTCGAATTGTT 59.784 37.500 0.00 0.00 41.83 2.83
6074 7649 6.968904 GTGTGCATTCATCTCGAATTGTTTAT 59.031 34.615 0.00 0.00 41.83 1.40
6075 7650 7.485913 GTGTGCATTCATCTCGAATTGTTTATT 59.514 33.333 0.00 0.00 41.83 1.40
6101 7678 3.011119 TGTTACGAATTGTATGTGGCCC 58.989 45.455 0.00 0.00 31.81 5.80
6117 7694 2.693762 CCCAGCACTTGGCACATCG 61.694 63.158 0.00 0.00 46.32 3.84
6123 7700 2.325082 ACTTGGCACATCGAACGCC 61.325 57.895 14.36 14.36 46.43 5.68
6135 7712 4.202161 ACATCGAACGCCTCTATTTCTGAT 60.202 41.667 0.00 0.00 0.00 2.90
6168 7745 5.049267 GCAGATTTGCCAAACATGACAAAAT 60.049 36.000 0.00 0.00 44.74 1.82
6185 7762 7.370383 TGACAAAATGAGGAAGAACTAATTGC 58.630 34.615 0.00 0.00 0.00 3.56
6206 7792 2.604914 CGCATTTGAGCTACTGTACCAG 59.395 50.000 0.00 0.00 37.52 4.00
6207 7793 3.676049 CGCATTTGAGCTACTGTACCAGA 60.676 47.826 0.00 0.00 35.18 3.86
6208 7794 3.619038 GCATTTGAGCTACTGTACCAGAC 59.381 47.826 0.00 0.00 35.18 3.51
6209 7795 4.621747 GCATTTGAGCTACTGTACCAGACT 60.622 45.833 0.00 0.00 35.18 3.24
6210 7796 5.394224 GCATTTGAGCTACTGTACCAGACTA 60.394 44.000 0.00 0.00 35.18 2.59
6211 7797 5.640189 TTTGAGCTACTGTACCAGACTAC 57.360 43.478 0.00 0.00 35.18 2.73
6212 7798 3.618351 TGAGCTACTGTACCAGACTACC 58.382 50.000 0.00 0.00 35.18 3.18
6213 7799 3.009805 TGAGCTACTGTACCAGACTACCA 59.990 47.826 0.00 0.00 35.18 3.25
6214 7800 3.622630 AGCTACTGTACCAGACTACCAG 58.377 50.000 0.00 0.00 35.18 4.00
6215 7801 3.010361 AGCTACTGTACCAGACTACCAGT 59.990 47.826 0.00 0.00 35.18 4.00
6216 7802 4.226846 AGCTACTGTACCAGACTACCAGTA 59.773 45.833 0.00 0.00 35.18 2.74
6217 7803 5.104024 AGCTACTGTACCAGACTACCAGTAT 60.104 44.000 0.00 0.00 35.18 2.12
6218 7804 5.239087 GCTACTGTACCAGACTACCAGTATC 59.761 48.000 0.00 0.00 35.18 2.24
6219 7805 4.534797 ACTGTACCAGACTACCAGTATCC 58.465 47.826 0.00 0.00 35.18 2.59
6220 7806 4.230041 ACTGTACCAGACTACCAGTATCCT 59.770 45.833 0.00 0.00 35.18 3.24
6221 7807 4.533815 TGTACCAGACTACCAGTATCCTG 58.466 47.826 0.00 0.00 38.50 3.86
6222 7808 3.759815 ACCAGACTACCAGTATCCTGT 57.240 47.619 0.00 0.00 36.95 4.00
6223 7809 4.875578 ACCAGACTACCAGTATCCTGTA 57.124 45.455 0.00 0.00 36.95 2.74
6224 7810 5.405063 ACCAGACTACCAGTATCCTGTAT 57.595 43.478 0.00 0.00 36.95 2.29
6225 7811 5.386924 ACCAGACTACCAGTATCCTGTATC 58.613 45.833 0.00 0.00 36.95 2.24
6226 7812 4.767928 CCAGACTACCAGTATCCTGTATCC 59.232 50.000 0.00 0.00 36.95 2.59
6227 7813 5.458362 CCAGACTACCAGTATCCTGTATCCT 60.458 48.000 0.00 0.00 36.95 3.24
6228 7814 5.708230 CAGACTACCAGTATCCTGTATCCTC 59.292 48.000 0.00 0.00 36.95 3.71
6229 7815 5.000570 ACTACCAGTATCCTGTATCCTCC 57.999 47.826 0.00 0.00 36.95 4.30
6230 7816 4.670727 ACTACCAGTATCCTGTATCCTCCT 59.329 45.833 0.00 0.00 36.95 3.69
6231 7817 5.856160 ACTACCAGTATCCTGTATCCTCCTA 59.144 44.000 0.00 0.00 36.95 2.94
6234 7820 4.011023 CAGTATCCTGTATCCTCCTACCG 58.989 52.174 0.00 0.00 33.80 4.02
6237 7823 2.133520 TCCTGTATCCTCCTACCGACT 58.866 52.381 0.00 0.00 0.00 4.18
6255 7841 6.460781 ACCGACTGTGTGATTGTAAGAAATA 58.539 36.000 0.00 0.00 0.00 1.40
6256 7842 7.103641 ACCGACTGTGTGATTGTAAGAAATAT 58.896 34.615 0.00 0.00 0.00 1.28
6258 7844 8.540492 CCGACTGTGTGATTGTAAGAAATATAC 58.460 37.037 0.00 0.00 0.00 1.47
6259 7845 9.083080 CGACTGTGTGATTGTAAGAAATATACA 57.917 33.333 0.00 0.00 0.00 2.29
6292 7879 8.530311 AGTGTGGATTAAATAAATGTGCATCAA 58.470 29.630 0.00 0.00 0.00 2.57
6303 7890 5.524971 AATGTGCATCAATTATGACCAGG 57.475 39.130 0.00 0.00 38.69 4.45
6308 7902 5.009911 GTGCATCAATTATGACCAGGCATTA 59.990 40.000 0.00 0.00 38.69 1.90
6317 7911 4.842531 TGACCAGGCATTATCTTCTCAA 57.157 40.909 0.00 0.00 0.00 3.02
6325 7919 6.805271 CAGGCATTATCTTCTCAACAAACAAG 59.195 38.462 0.00 0.00 0.00 3.16
6424 8020 3.734463 TCGGATTTGTGCACAGAACTAA 58.266 40.909 20.59 11.54 0.00 2.24
6431 8027 2.729360 TGTGCACAGAACTAATTCGACG 59.271 45.455 17.42 0.00 40.04 5.12
6438 8034 4.863131 ACAGAACTAATTCGACGTGAATCC 59.137 41.667 11.80 0.00 46.65 3.01
6447 8043 2.093181 TCGACGTGAATCCATCCCAAAT 60.093 45.455 0.00 0.00 0.00 2.32
6498 8097 2.947652 AGGCATTCCATCAAACATCTCG 59.052 45.455 0.00 0.00 33.74 4.04
6499 8098 2.033801 GGCATTCCATCAAACATCTCGG 59.966 50.000 0.00 0.00 0.00 4.63
6511 8110 0.933097 CATCTCGGAGGCATTTGTCG 59.067 55.000 4.96 0.00 0.00 4.35
6513 8112 1.448540 CTCGGAGGCATTTGTCGCT 60.449 57.895 0.00 0.00 0.00 4.93
6514 8113 1.699656 CTCGGAGGCATTTGTCGCTG 61.700 60.000 0.00 0.00 0.00 5.18
6541 8145 3.473093 AATACTGCGAGATCGTATCCG 57.527 47.619 3.94 0.00 42.22 4.18
6552 8156 4.270834 AGATCGTATCCGTACCTATGCAT 58.729 43.478 3.79 3.79 35.01 3.96
6557 8161 3.685139 ATCCGTACCTATGCATTCCAG 57.315 47.619 3.54 0.00 0.00 3.86
6578 8182 1.303236 CACCTGGGCGAATCCACAA 60.303 57.895 0.00 0.00 36.21 3.33
6622 8226 4.643387 ACTTGCCACCAGTCCGCC 62.643 66.667 0.00 0.00 0.00 6.13
6624 8228 4.947147 TTGCCACCAGTCCGCCAC 62.947 66.667 0.00 0.00 0.00 5.01
6627 8231 4.394712 CCACCAGTCCGCCACTCC 62.395 72.222 0.00 0.00 30.26 3.85
6628 8232 3.625897 CACCAGTCCGCCACTCCA 61.626 66.667 0.00 0.00 30.26 3.86
6630 8234 2.224159 ACCAGTCCGCCACTCCATT 61.224 57.895 0.00 0.00 30.26 3.16
6632 8236 1.296392 CAGTCCGCCACTCCATTCA 59.704 57.895 0.00 0.00 30.26 2.57
6633 8237 0.107508 CAGTCCGCCACTCCATTCAT 60.108 55.000 0.00 0.00 30.26 2.57
6634 8238 0.179000 AGTCCGCCACTCCATTCATC 59.821 55.000 0.00 0.00 0.00 2.92
6635 8239 0.815615 GTCCGCCACTCCATTCATCC 60.816 60.000 0.00 0.00 0.00 3.51
6636 8240 0.982852 TCCGCCACTCCATTCATCCT 60.983 55.000 0.00 0.00 0.00 3.24
6638 8242 0.107508 CGCCACTCCATTCATCCTGT 60.108 55.000 0.00 0.00 0.00 4.00
6639 8243 1.679944 CGCCACTCCATTCATCCTGTT 60.680 52.381 0.00 0.00 0.00 3.16
6640 8244 2.419990 CGCCACTCCATTCATCCTGTTA 60.420 50.000 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 51 1.301874 CGCCCGGTGGTTTCAACTA 60.302 57.895 0.00 0.00 0.00 2.24
129 137 0.729140 CAGCCAAAACGATTGACCGC 60.729 55.000 7.17 3.32 0.00 5.68
130 138 0.729140 GCAGCCAAAACGATTGACCG 60.729 55.000 7.17 0.00 0.00 4.79
139 147 0.670239 CCCAAATCGGCAGCCAAAAC 60.670 55.000 13.30 0.00 0.00 2.43
421 456 7.173907 ACCACAGTGTCTCAGATGAAAATAAAG 59.826 37.037 0.00 0.00 0.00 1.85
441 476 4.578871 TGGACATCATGAAGTAACCACAG 58.421 43.478 3.08 0.00 0.00 3.66
442 477 4.632327 TGGACATCATGAAGTAACCACA 57.368 40.909 3.08 0.00 0.00 4.17
446 481 7.225538 CCACTTAGATGGACATCATGAAGTAAC 59.774 40.741 18.49 1.20 43.02 2.50
472 511 6.775594 ATGGTTAGAAAGTTAGGAAATGGC 57.224 37.500 0.00 0.00 0.00 4.40
524 563 6.391227 ACTTCGTGACAATTGGAAGAATTT 57.609 33.333 21.65 6.54 38.48 1.82
526 565 6.348540 GCTTACTTCGTGACAATTGGAAGAAT 60.349 38.462 21.65 8.80 38.48 2.40
527 566 5.049680 GCTTACTTCGTGACAATTGGAAGAA 60.050 40.000 21.65 14.69 38.48 2.52
529 568 4.213270 TGCTTACTTCGTGACAATTGGAAG 59.787 41.667 10.83 14.14 41.20 3.46
530 569 4.130857 TGCTTACTTCGTGACAATTGGAA 58.869 39.130 10.83 2.71 0.00 3.53
532 571 3.745975 TCTGCTTACTTCGTGACAATTGG 59.254 43.478 10.83 0.00 0.00 3.16
535 575 4.521130 TCTCTGCTTACTTCGTGACAAT 57.479 40.909 0.00 0.00 0.00 2.71
562 602 6.415573 ACTTTGTTTCAGACTTTCAGTACCT 58.584 36.000 0.00 0.00 0.00 3.08
565 605 6.404293 GCCAACTTTGTTTCAGACTTTCAGTA 60.404 38.462 0.00 0.00 0.00 2.74
573 613 3.782889 AGTGCCAACTTTGTTTCAGAC 57.217 42.857 0.00 0.00 30.14 3.51
574 614 4.201871 CGTAAGTGCCAACTTTGTTTCAGA 60.202 41.667 0.00 0.00 44.47 3.27
575 615 4.035017 CGTAAGTGCCAACTTTGTTTCAG 58.965 43.478 0.00 0.00 44.47 3.02
576 616 3.732471 GCGTAAGTGCCAACTTTGTTTCA 60.732 43.478 0.00 0.00 44.47 2.69
577 617 2.787129 GCGTAAGTGCCAACTTTGTTTC 59.213 45.455 0.00 0.00 44.47 2.78
578 618 2.425668 AGCGTAAGTGCCAACTTTGTTT 59.574 40.909 0.00 0.00 44.47 2.83
579 619 2.021457 AGCGTAAGTGCCAACTTTGTT 58.979 42.857 0.00 0.00 44.47 2.83
580 620 1.602377 GAGCGTAAGTGCCAACTTTGT 59.398 47.619 0.00 0.00 44.47 2.83
581 621 1.601903 TGAGCGTAAGTGCCAACTTTG 59.398 47.619 0.00 0.00 44.47 2.77
582 622 1.602377 GTGAGCGTAAGTGCCAACTTT 59.398 47.619 0.00 0.00 44.47 2.66
584 624 0.105964 TGTGAGCGTAAGTGCCAACT 59.894 50.000 0.00 0.00 38.71 3.16
585 625 0.941542 TTGTGAGCGTAAGTGCCAAC 59.058 50.000 0.00 0.00 41.68 3.77
586 626 1.225855 CTTGTGAGCGTAAGTGCCAA 58.774 50.000 0.00 0.00 41.68 4.52
587 627 0.105964 ACTTGTGAGCGTAAGTGCCA 59.894 50.000 0.00 0.00 35.91 4.92
588 628 0.790814 GACTTGTGAGCGTAAGTGCC 59.209 55.000 0.00 0.00 37.27 5.01
589 629 1.192534 GTGACTTGTGAGCGTAAGTGC 59.807 52.381 0.00 0.00 37.27 4.40
590 630 2.469826 TGTGACTTGTGAGCGTAAGTG 58.530 47.619 0.00 0.00 37.27 3.16
591 631 2.545952 CCTGTGACTTGTGAGCGTAAGT 60.546 50.000 0.00 0.00 39.67 2.24
592 632 2.061773 CCTGTGACTTGTGAGCGTAAG 58.938 52.381 0.00 0.00 43.44 2.34
593 633 1.411246 ACCTGTGACTTGTGAGCGTAA 59.589 47.619 0.00 0.00 0.00 3.18
594 634 1.037493 ACCTGTGACTTGTGAGCGTA 58.963 50.000 0.00 0.00 0.00 4.42
789 844 1.153269 TCGTGCTGCAACCAACAGA 60.153 52.632 2.77 0.00 37.32 3.41
817 876 0.037590 TGTGGTGCTGGGGTATGAAC 59.962 55.000 0.00 0.00 0.00 3.18
838 897 4.021456 TGTGATACTGTGATCCGAACTTGT 60.021 41.667 0.00 0.00 0.00 3.16
839 898 4.327357 GTGTGATACTGTGATCCGAACTTG 59.673 45.833 0.00 0.00 0.00 3.16
840 899 4.495422 GTGTGATACTGTGATCCGAACTT 58.505 43.478 0.00 0.00 0.00 2.66
841 900 3.427638 CGTGTGATACTGTGATCCGAACT 60.428 47.826 0.00 0.00 0.00 3.01
842 901 2.852413 CGTGTGATACTGTGATCCGAAC 59.148 50.000 0.00 0.00 0.00 3.95
843 902 2.734175 GCGTGTGATACTGTGATCCGAA 60.734 50.000 0.00 0.00 0.00 4.30
844 903 1.202256 GCGTGTGATACTGTGATCCGA 60.202 52.381 0.00 0.00 0.00 4.55
845 904 1.200483 GCGTGTGATACTGTGATCCG 58.800 55.000 0.00 0.00 0.00 4.18
846 905 1.200483 CGCGTGTGATACTGTGATCC 58.800 55.000 0.00 0.00 0.00 3.36
847 906 2.188837 TCGCGTGTGATACTGTGATC 57.811 50.000 5.77 0.00 0.00 2.92
848 907 2.860136 CAATCGCGTGTGATACTGTGAT 59.140 45.455 5.77 0.00 35.84 3.06
849 908 2.258755 CAATCGCGTGTGATACTGTGA 58.741 47.619 5.77 0.00 0.00 3.58
851 910 0.999406 GCAATCGCGTGTGATACTGT 59.001 50.000 5.77 0.00 0.00 3.55
853 912 1.720805 TTGCAATCGCGTGTGATACT 58.279 45.000 5.77 0.00 42.97 2.12
856 915 1.155889 TCTTTGCAATCGCGTGTGAT 58.844 45.000 5.77 0.00 42.97 3.06
857 916 0.940833 TTCTTTGCAATCGCGTGTGA 59.059 45.000 5.77 0.00 42.97 3.58
858 917 1.752753 TTTCTTTGCAATCGCGTGTG 58.247 45.000 5.77 6.72 42.97 3.82
859 918 2.223479 ACTTTTCTTTGCAATCGCGTGT 60.223 40.909 5.77 0.00 42.97 4.49
860 919 2.384382 ACTTTTCTTTGCAATCGCGTG 58.616 42.857 5.77 0.00 42.97 5.34
861 920 2.774439 ACTTTTCTTTGCAATCGCGT 57.226 40.000 5.77 0.00 42.97 6.01
862 921 3.056319 CGTTACTTTTCTTTGCAATCGCG 59.944 43.478 0.00 0.00 42.97 5.87
863 922 4.215965 TCGTTACTTTTCTTTGCAATCGC 58.784 39.130 0.00 0.00 39.24 4.58
864 923 5.115021 GGTTCGTTACTTTTCTTTGCAATCG 59.885 40.000 0.00 0.00 0.00 3.34
865 924 6.142320 CAGGTTCGTTACTTTTCTTTGCAATC 59.858 38.462 0.00 0.00 0.00 2.67
866 925 5.977129 CAGGTTCGTTACTTTTCTTTGCAAT 59.023 36.000 0.00 0.00 0.00 3.56
869 928 4.916870 ACAGGTTCGTTACTTTTCTTTGC 58.083 39.130 0.00 0.00 0.00 3.68
872 931 5.644636 TGACAACAGGTTCGTTACTTTTCTT 59.355 36.000 0.00 0.00 0.00 2.52
956 1018 0.741915 CTCTCACTCTTACCGGCCTC 59.258 60.000 0.00 0.00 0.00 4.70
973 1035 5.471797 TCAAGGTACGATGATGATCTCTCTC 59.528 44.000 0.00 0.00 0.00 3.20
974 1036 5.240623 GTCAAGGTACGATGATGATCTCTCT 59.759 44.000 2.97 0.00 32.35 3.10
975 1037 5.457140 GTCAAGGTACGATGATGATCTCTC 58.543 45.833 2.97 0.00 32.35 3.20
976 1038 4.023622 CGTCAAGGTACGATGATGATCTCT 60.024 45.833 11.38 0.00 45.68 3.10
1017 1079 2.125952 GCTCCATTGCCGTTTGCC 60.126 61.111 0.00 0.00 40.16 4.52
1018 1080 1.444895 CAGCTCCATTGCCGTTTGC 60.445 57.895 0.00 0.00 41.77 3.68
1095 1160 1.682257 GAACCTCTGCAGCCTCCTT 59.318 57.895 9.47 0.00 0.00 3.36
1227 1292 5.412904 GGATGCAGTTCCCTTGCTTATATAC 59.587 44.000 0.00 0.00 42.02 1.47
1228 1293 5.073008 TGGATGCAGTTCCCTTGCTTATATA 59.927 40.000 3.88 0.00 42.02 0.86
1232 1297 1.354031 TGGATGCAGTTCCCTTGCTTA 59.646 47.619 3.88 0.00 42.02 3.09
1251 1316 4.934001 CCCATCATAACAGGAATCGAGATG 59.066 45.833 0.00 0.00 33.32 2.90
1253 1318 3.967326 ACCCATCATAACAGGAATCGAGA 59.033 43.478 0.00 0.00 0.00 4.04
1254 1319 4.342862 ACCCATCATAACAGGAATCGAG 57.657 45.455 0.00 0.00 0.00 4.04
1275 1344 7.311092 TGTTTTATGAGGAACAGAGGAAGTA 57.689 36.000 0.00 0.00 32.43 2.24
1276 1345 6.187727 TGTTTTATGAGGAACAGAGGAAGT 57.812 37.500 0.00 0.00 32.43 3.01
1284 1353 5.843673 TGTTTGCTGTTTTATGAGGAACA 57.156 34.783 0.00 0.00 34.80 3.18
1285 1354 7.532682 TTTTGTTTGCTGTTTTATGAGGAAC 57.467 32.000 0.00 0.00 0.00 3.62
1287 1356 8.729805 AATTTTTGTTTGCTGTTTTATGAGGA 57.270 26.923 0.00 0.00 0.00 3.71
1288 1357 8.610896 TGAATTTTTGTTTGCTGTTTTATGAGG 58.389 29.630 0.00 0.00 0.00 3.86
1289 1358 9.424659 GTGAATTTTTGTTTGCTGTTTTATGAG 57.575 29.630 0.00 0.00 0.00 2.90
1290 1359 8.939929 TGTGAATTTTTGTTTGCTGTTTTATGA 58.060 25.926 0.00 0.00 0.00 2.15
1291 1360 9.552114 TTGTGAATTTTTGTTTGCTGTTTTATG 57.448 25.926 0.00 0.00 0.00 1.90
1293 1362 9.604626 CTTTGTGAATTTTTGTTTGCTGTTTTA 57.395 25.926 0.00 0.00 0.00 1.52
1294 1363 8.348507 TCTTTGTGAATTTTTGTTTGCTGTTTT 58.651 25.926 0.00 0.00 0.00 2.43
1295 1364 7.869800 TCTTTGTGAATTTTTGTTTGCTGTTT 58.130 26.923 0.00 0.00 0.00 2.83
1299 1368 8.321650 TCTTTCTTTGTGAATTTTTGTTTGCT 57.678 26.923 0.00 0.00 34.24 3.91
1308 1377 9.956720 CAGACTGTTATCTTTCTTTGTGAATTT 57.043 29.630 0.00 0.00 34.24 1.82
1311 1380 6.542005 TGCAGACTGTTATCTTTCTTTGTGAA 59.458 34.615 3.99 0.00 0.00 3.18
1314 1384 6.058183 AGTGCAGACTGTTATCTTTCTTTGT 58.942 36.000 3.99 0.00 0.00 2.83
1463 1537 5.192176 TGGTTATGCAAACTCATGATGCTA 58.808 37.500 18.06 7.55 40.66 3.49
1475 1549 4.192317 GTTGGGTTGTTTGGTTATGCAAA 58.808 39.130 0.00 0.00 0.00 3.68
1511 1585 7.814264 ATGCAAGCTTATAAGATGCTAAAGT 57.186 32.000 28.74 15.66 39.57 2.66
1568 1643 6.183360 GCAAATACTACATTCACCTCAAGGAC 60.183 42.308 2.30 0.00 38.94 3.85
1586 1661 8.524870 AACAAAATCAGTCAGATTGCAAATAC 57.475 30.769 1.71 0.00 46.09 1.89
1782 1862 9.440761 AATGGAAGGAGAAGTACAGTATAGATT 57.559 33.333 0.00 0.00 0.00 2.40
1794 1874 8.910944 CAATATTTCATCAATGGAAGGAGAAGT 58.089 33.333 0.00 0.00 0.00 3.01
1874 1954 8.025445 ACATGCAATTTCTGTCAAGAAGATAAC 58.975 33.333 0.00 0.00 43.27 1.89
1970 2052 5.012664 TCCTATGGCCATTCGCTTCTTTATA 59.987 40.000 26.37 0.00 37.74 0.98
1974 2056 1.490490 TCCTATGGCCATTCGCTTCTT 59.510 47.619 26.37 0.00 37.74 2.52
2019 2120 5.539955 AGTGGGATTGTGGGAATATTTATGC 59.460 40.000 0.00 0.00 0.00 3.14
2119 2225 7.877612 ACATGTTTTGGATTTTCCTTTATGGAC 59.122 33.333 0.00 0.00 46.14 4.02
2128 2234 9.353999 GTACTTATCACATGTTTTGGATTTTCC 57.646 33.333 0.00 0.00 36.96 3.13
2231 2426 1.904287 AAGTGCAAATGTTCCGCCTA 58.096 45.000 0.00 0.00 0.00 3.93
2487 2682 7.628234 AGATGAGCTTAAGAAAGAAAGGATGA 58.372 34.615 6.67 0.00 34.37 2.92
2686 3951 8.560374 GTTTTGTCTTCTAGCAGAACAATAAGT 58.440 33.333 0.00 0.00 32.26 2.24
2704 3969 1.137872 TGCAAATTGGGCGTTTTGTCT 59.862 42.857 0.00 0.00 35.69 3.41
2707 3972 1.261089 CACTGCAAATTGGGCGTTTTG 59.739 47.619 0.00 2.26 36.21 2.44
2856 4129 4.019501 ACAGAGGGATGCATCCTAATGATC 60.020 45.833 37.94 25.68 46.35 2.92
2887 4160 3.770666 AGTGACATGGACGTATCTTTCG 58.229 45.455 0.00 0.00 0.00 3.46
2893 4166 5.477291 CCCTAAGATAGTGACATGGACGTAT 59.523 44.000 0.00 0.00 0.00 3.06
2897 4170 4.740934 GCACCCTAAGATAGTGACATGGAC 60.741 50.000 0.00 0.00 33.21 4.02
3376 4653 4.965119 AACATTGCTTCGGTTCCTATTC 57.035 40.909 0.00 0.00 0.00 1.75
4269 5553 6.516718 TGAGGTGAAGACTGTTTAAGAGAAG 58.483 40.000 0.00 0.00 0.00 2.85
4337 5660 4.037208 GGCAAATAGATGAGGGAACACATG 59.963 45.833 0.00 0.00 41.98 3.21
4342 5665 3.117888 TCTGGGCAAATAGATGAGGGAAC 60.118 47.826 0.00 0.00 0.00 3.62
4350 5673 3.480470 CCGACAATCTGGGCAAATAGAT 58.520 45.455 0.00 0.00 35.25 1.98
4380 5703 7.306051 GCAATATAGCATATTAGCGAGTAACGG 60.306 40.741 0.00 0.00 42.83 4.44
4541 5864 7.093771 GGAATTTGGAAGAATGTACCAATCTGT 60.094 37.037 0.00 0.00 42.14 3.41
4551 5874 4.286549 TGCCATTGGAATTTGGAAGAATGT 59.713 37.500 6.95 0.00 34.81 2.71
4693 6021 8.424133 AGCGATACCTGCATATATGATGATTAA 58.576 33.333 17.10 0.00 33.85 1.40
4716 6044 1.139989 ACATCACAAAGACGACAGCG 58.860 50.000 0.00 0.00 44.79 5.18
4837 6165 6.806751 TGTAGAATGCTGAGGATAAGTACAC 58.193 40.000 0.00 0.00 0.00 2.90
5401 6729 5.535333 CAACCTTGCATCTTGAACTTCAAT 58.465 37.500 4.65 0.00 35.59 2.57
5541 6869 1.530419 ATTTTGCTCCGCCACCACA 60.530 52.632 0.00 0.00 0.00 4.17
5885 7244 8.758633 ACTGCTAACAAACACTTATACAGTAG 57.241 34.615 0.00 0.00 33.20 2.57
5961 7534 9.612620 CACATACTAAGATTTTGAGTTTTCCAC 57.387 33.333 0.00 0.00 0.00 4.02
6033 7607 9.225436 TGAATGCACACAAGTCATACTTTATTA 57.775 29.630 0.00 0.00 36.03 0.98
6049 7623 4.346734 ACAATTCGAGATGAATGCACAC 57.653 40.909 6.54 0.00 46.65 3.82
6053 7627 9.502145 TGTTAATAAACAATTCGAGATGAATGC 57.498 29.630 6.54 0.00 41.91 3.56
6074 7649 7.244898 GCCACATACAATTCGTAACATGTTAA 58.755 34.615 19.63 7.29 32.59 2.01
6075 7650 6.183360 GGCCACATACAATTCGTAACATGTTA 60.183 38.462 14.35 14.35 32.59 2.41
6101 7678 0.110056 GTTCGATGTGCCAAGTGCTG 60.110 55.000 0.00 0.00 42.00 4.41
6114 7691 4.302455 CATCAGAAATAGAGGCGTTCGAT 58.698 43.478 0.00 0.00 0.00 3.59
6117 7694 3.198068 TGCATCAGAAATAGAGGCGTTC 58.802 45.455 0.00 0.00 45.00 3.95
6123 7700 3.003482 GCTGCCTTGCATCAGAAATAGAG 59.997 47.826 13.29 0.00 38.13 2.43
6135 7712 1.290955 GCAAATCTGCTGCCTTGCA 59.709 52.632 18.19 0.00 45.74 4.08
6168 7745 3.052455 TGCGCAATTAGTTCTTCCTCA 57.948 42.857 8.16 0.00 0.00 3.86
6185 7762 2.616960 TGGTACAGTAGCTCAAATGCG 58.383 47.619 11.06 0.00 38.13 4.73
6214 7800 4.009002 GTCGGTAGGAGGATACAGGATAC 58.991 52.174 0.00 0.00 41.41 2.24
6215 7801 3.915073 AGTCGGTAGGAGGATACAGGATA 59.085 47.826 0.00 0.00 41.41 2.59
6216 7802 2.717515 AGTCGGTAGGAGGATACAGGAT 59.282 50.000 0.00 0.00 41.41 3.24
6217 7803 2.133520 AGTCGGTAGGAGGATACAGGA 58.866 52.381 0.00 0.00 41.41 3.86
6218 7804 2.231529 CAGTCGGTAGGAGGATACAGG 58.768 57.143 0.00 0.00 41.41 4.00
6219 7805 2.619177 CACAGTCGGTAGGAGGATACAG 59.381 54.545 0.00 0.00 41.41 2.74
6220 7806 2.025605 ACACAGTCGGTAGGAGGATACA 60.026 50.000 0.00 0.00 41.41 2.29
6221 7807 2.358267 CACACAGTCGGTAGGAGGATAC 59.642 54.545 0.00 0.00 0.00 2.24
6222 7808 2.240414 TCACACAGTCGGTAGGAGGATA 59.760 50.000 0.00 0.00 0.00 2.59
6223 7809 1.005569 TCACACAGTCGGTAGGAGGAT 59.994 52.381 0.00 0.00 0.00 3.24
6224 7810 0.402887 TCACACAGTCGGTAGGAGGA 59.597 55.000 0.00 0.00 0.00 3.71
6225 7811 1.475403 ATCACACAGTCGGTAGGAGG 58.525 55.000 0.00 0.00 0.00 4.30
6226 7812 2.231478 ACAATCACACAGTCGGTAGGAG 59.769 50.000 0.00 0.00 0.00 3.69
6227 7813 2.244695 ACAATCACACAGTCGGTAGGA 58.755 47.619 0.00 0.00 0.00 2.94
6228 7814 2.743636 ACAATCACACAGTCGGTAGG 57.256 50.000 0.00 0.00 0.00 3.18
6229 7815 5.055642 TCTTACAATCACACAGTCGGTAG 57.944 43.478 0.00 0.00 0.00 3.18
6230 7816 5.456548 TTCTTACAATCACACAGTCGGTA 57.543 39.130 0.00 0.00 0.00 4.02
6231 7817 4.330944 TTCTTACAATCACACAGTCGGT 57.669 40.909 0.00 0.00 0.00 4.69
6237 7823 7.282224 GGCCTGTATATTTCTTACAATCACACA 59.718 37.037 0.00 0.00 0.00 3.72
6255 7841 1.298953 ATCCACACTTGGGCCTGTAT 58.701 50.000 4.53 0.00 44.11 2.29
6256 7842 1.072266 AATCCACACTTGGGCCTGTA 58.928 50.000 4.53 0.00 44.11 2.74
6258 7844 2.214376 TTAATCCACACTTGGGCCTG 57.786 50.000 4.53 0.00 44.11 4.85
6259 7845 2.990740 TTTAATCCACACTTGGGCCT 57.009 45.000 4.53 0.00 44.11 5.19
6279 7866 6.461370 GCCTGGTCATAATTGATGCACATTTA 60.461 38.462 0.00 0.00 35.29 1.40
6292 7879 7.083062 TGAGAAGATAATGCCTGGTCATAAT 57.917 36.000 0.00 0.00 0.00 1.28
6297 7884 4.517285 TGTTGAGAAGATAATGCCTGGTC 58.483 43.478 0.00 0.00 0.00 4.02
6299 7886 5.183713 TGTTTGTTGAGAAGATAATGCCTGG 59.816 40.000 0.00 0.00 0.00 4.45
6303 7890 7.362662 TGACTTGTTTGTTGAGAAGATAATGC 58.637 34.615 0.00 0.00 0.00 3.56
6351 7946 1.649664 CTGCTGATTTCGGACCTCAG 58.350 55.000 10.28 10.28 39.50 3.35
6431 8027 2.893489 GGGCTATTTGGGATGGATTCAC 59.107 50.000 0.00 0.00 0.00 3.18
6438 8034 1.949525 CTTCGTGGGCTATTTGGGATG 59.050 52.381 0.00 0.00 0.00 3.51
6462 8058 3.787001 CCTGCCGGGACCTCTTCC 61.787 72.222 2.18 0.00 45.00 3.46
6498 8097 0.960364 TTCCAGCGACAAATGCCTCC 60.960 55.000 0.00 0.00 0.00 4.30
6499 8098 0.449388 CTTCCAGCGACAAATGCCTC 59.551 55.000 0.00 0.00 0.00 4.70
6541 8145 3.467803 GTGGACTGGAATGCATAGGTAC 58.532 50.000 0.00 0.00 0.00 3.34
6557 8161 2.124695 GGATTCGCCCAGGTGGAC 60.125 66.667 0.00 0.00 37.39 4.02
6578 8182 2.421775 CAGCGATCGGTCTCTATATGCT 59.578 50.000 18.38 0.00 0.00 3.79
6622 8226 3.249320 CGCATAACAGGATGAATGGAGTG 59.751 47.826 0.00 0.00 39.69 3.51
6624 8228 3.732212 TCGCATAACAGGATGAATGGAG 58.268 45.455 0.00 0.00 39.69 3.86
6626 8230 6.748333 ATTATCGCATAACAGGATGAATGG 57.252 37.500 0.00 0.00 39.69 3.16
6627 8231 6.957635 CGAATTATCGCATAACAGGATGAATG 59.042 38.462 0.00 0.00 42.96 2.67
6628 8232 7.065216 CGAATTATCGCATAACAGGATGAAT 57.935 36.000 0.00 0.00 42.96 2.57


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

AutoCloner maintained by Alex Coulton.