Multiple sequence alignment - TraesCS5A01G290100

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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 TraesCS5A01G290100 chr5A 100.000 3316 0 0 1 3316 496607464 496610779 0.000000e+00 6124.0
1 TraesCS5A01G290100 chr5D 87.557 2427 149 77 941 3302 394827181 394829519 0.000000e+00 2667.0
2 TraesCS5A01G290100 chr5D 85.348 976 50 46 1 917 394826257 394827198 0.000000e+00 924.0
3 TraesCS5A01G290100 chr5B 91.774 1702 73 23 949 2613 474522070 474523741 0.000000e+00 2305.0
4 TraesCS5A01G290100 chr5B 84.940 923 60 34 1 886 474521168 474522048 0.000000e+00 861.0
5 TraesCS5A01G290100 chr5B 86.627 501 41 9 2599 3078 474523796 474524291 6.300000e-147 531.0
6 TraesCS5A01G290100 chr5B 96.667 60 2 0 3110 3169 474524288 474524347 2.100000e-17 100.0
7 TraesCS5A01G290100 chr2B 85.519 366 34 4 1593 1940 98404758 98404394 6.760000e-97 364.0
8 TraesCS5A01G290100 chr1B 96.250 80 3 0 1063 1142 552947874 552947953 7.460000e-27 132.0
9 TraesCS5A01G290100 chr4B 93.506 77 3 2 1068 1142 182233238 182233314 2.700000e-21 113.0
10 TraesCS5A01G290100 chr4A 97.959 49 1 0 1094 1142 95365266 95365218 5.890000e-13 86.1


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 TraesCS5A01G290100 chr5A 496607464 496610779 3315 False 6124.00 6124 100.0000 1 3316 1 chr5A.!!$F1 3315
1 TraesCS5A01G290100 chr5D 394826257 394829519 3262 False 1795.50 2667 86.4525 1 3302 2 chr5D.!!$F1 3301
2 TraesCS5A01G290100 chr5B 474521168 474524347 3179 False 949.25 2305 90.0020 1 3169 4 chr5B.!!$F1 3168

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
23 24 0.031449 TTAACAAAGCCGCTTGCCAC 59.969 50.0 6.34 0.0 42.71 5.01 F
1321 1388 0.179156 GCTGGTGCGAATGGTCAATG 60.179 55.0 0.00 0.0 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1651 0.247736 CTTACTCTGCTTCAGGGCGT 59.752 55.0 0.0 0.0 34.91 5.68 R
3030 3282 0.105593 TGATCAGGAAGCAGATCGCC 59.894 55.0 0.0 0.0 42.72 5.54 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
23 24 0.031449 TTAACAAAGCCGCTTGCCAC 59.969 50.000 6.34 0.00 42.71 5.01
28 29 2.476534 AAAGCCGCTTGCCACATTCG 62.477 55.000 6.34 0.00 42.71 3.34
40 41 0.734889 CACATTCGAATGGGCAGTCC 59.265 55.000 34.69 0.00 40.70 3.85
62 63 3.584052 CTCCTCCTACGTCGCCGG 61.584 72.222 0.00 0.00 38.78 6.13
192 193 1.299620 GCAGCAGCCAACAACAGTG 60.300 57.895 0.00 0.00 33.58 3.66
211 212 3.869272 CTCTCGTTGCCATGCGCC 61.869 66.667 4.18 0.00 36.24 6.53
241 242 2.665052 GTCTCACCCACGAAACGAATAC 59.335 50.000 0.00 0.00 0.00 1.89
242 243 1.997606 CTCACCCACGAAACGAATACC 59.002 52.381 0.00 0.00 0.00 2.73
249 250 0.225489 CGAAACGAATACCTACGCGC 59.775 55.000 5.73 0.00 0.00 6.86
274 278 4.393155 TACACGCAGCAGGGCAGG 62.393 66.667 0.00 0.00 0.00 4.85
293 300 2.433446 CACAGTCCAGCCCAGCTT 59.567 61.111 0.00 0.00 36.40 3.74
433 447 0.612732 AGAGAGCAGCAGCAGAGAGT 60.613 55.000 3.17 0.00 45.49 3.24
434 448 0.458889 GAGAGCAGCAGCAGAGAGTG 60.459 60.000 3.17 0.00 45.49 3.51
435 449 1.448189 GAGCAGCAGCAGAGAGTGG 60.448 63.158 3.17 0.00 45.49 4.00
436 450 2.436292 GCAGCAGCAGAGAGTGGG 60.436 66.667 0.00 0.00 41.58 4.61
437 451 2.952293 GCAGCAGCAGAGAGTGGGA 61.952 63.158 0.00 0.00 41.58 4.37
438 452 1.218585 CAGCAGCAGAGAGTGGGAG 59.781 63.158 0.00 0.00 0.00 4.30
439 453 1.078166 AGCAGCAGAGAGTGGGAGA 59.922 57.895 0.00 0.00 0.00 3.71
440 454 0.971959 AGCAGCAGAGAGTGGGAGAG 60.972 60.000 0.00 0.00 0.00 3.20
466 480 1.152839 GAGAGGGAGAGGTCGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
488 506 2.111878 GATGGCATCCTGACCGGG 59.888 66.667 16.75 0.00 0.00 5.73
514 532 2.436646 CCCTGGGTAAGCGTGCTG 60.437 66.667 3.97 0.00 0.00 4.41
515 533 3.127533 CCTGGGTAAGCGTGCTGC 61.128 66.667 0.00 0.00 46.98 5.25
639 690 3.438017 CTAGCTGGACTGCCGGAGC 62.438 68.421 5.05 3.44 43.76 4.70
685 740 2.094494 CAGACGCACAGATACAGAGGTT 60.094 50.000 0.00 0.00 0.00 3.50
702 760 3.173965 AGGTTGTATACAGAGGCACAGT 58.826 45.455 5.56 0.00 0.00 3.55
703 761 4.350245 AGGTTGTATACAGAGGCACAGTA 58.650 43.478 5.56 0.00 0.00 2.74
704 762 4.402793 AGGTTGTATACAGAGGCACAGTAG 59.597 45.833 5.56 0.00 0.00 2.57
706 764 5.450688 GGTTGTATACAGAGGCACAGTAGAG 60.451 48.000 5.56 0.00 0.00 2.43
709 767 2.889170 ACAGAGGCACAGTAGAGAGA 57.111 50.000 0.00 0.00 0.00 3.10
710 768 2.722094 ACAGAGGCACAGTAGAGAGAG 58.278 52.381 0.00 0.00 0.00 3.20
712 770 2.423185 CAGAGGCACAGTAGAGAGAGTG 59.577 54.545 0.00 0.00 35.19 3.51
713 771 2.041081 AGAGGCACAGTAGAGAGAGTGT 59.959 50.000 0.00 0.00 34.59 3.55
718 776 3.894920 CACAGTAGAGAGAGTGTGTGTG 58.105 50.000 3.68 0.00 43.11 3.82
719 777 3.316588 CACAGTAGAGAGAGTGTGTGTGT 59.683 47.826 3.68 0.00 43.11 3.72
720 778 3.316588 ACAGTAGAGAGAGTGTGTGTGTG 59.683 47.826 0.00 0.00 31.63 3.82
721 779 3.316588 CAGTAGAGAGAGTGTGTGTGTGT 59.683 47.826 0.00 0.00 0.00 3.72
734 792 2.620585 TGTGTGTGTGTGAGAGAGAGAG 59.379 50.000 0.00 0.00 0.00 3.20
839 899 3.032609 GCCACCGCGATCGATCTG 61.033 66.667 21.57 16.35 38.10 2.90
842 902 0.806102 CCACCGCGATCGATCTGTTT 60.806 55.000 21.57 2.51 38.10 2.83
846 906 1.268794 CCGCGATCGATCTGTTTCTCT 60.269 52.381 21.57 0.00 38.10 3.10
852 912 4.606961 GATCGATCTGTTTCTCTGTCTCC 58.393 47.826 18.29 0.00 0.00 3.71
853 913 2.755655 TCGATCTGTTTCTCTGTCTCCC 59.244 50.000 0.00 0.00 0.00 4.30
859 919 2.765250 TTTCTCTGTCTCCCGTGCGC 62.765 60.000 0.00 0.00 0.00 6.09
895 962 4.195334 GGTGGGCGCCATGATCCT 62.195 66.667 30.85 0.00 35.28 3.24
916 983 5.789643 CTATGAAGGAGAAGGAGAAGGAG 57.210 47.826 0.00 0.00 0.00 3.69
917 984 3.835478 TGAAGGAGAAGGAGAAGGAGA 57.165 47.619 0.00 0.00 0.00 3.71
918 985 4.133526 TGAAGGAGAAGGAGAAGGAGAA 57.866 45.455 0.00 0.00 0.00 2.87
919 986 4.093011 TGAAGGAGAAGGAGAAGGAGAAG 58.907 47.826 0.00 0.00 0.00 2.85
920 987 3.114643 AGGAGAAGGAGAAGGAGAAGG 57.885 52.381 0.00 0.00 0.00 3.46
921 988 2.657459 AGGAGAAGGAGAAGGAGAAGGA 59.343 50.000 0.00 0.00 0.00 3.36
922 989 3.031013 GGAGAAGGAGAAGGAGAAGGAG 58.969 54.545 0.00 0.00 0.00 3.69
923 990 3.309556 GGAGAAGGAGAAGGAGAAGGAGA 60.310 52.174 0.00 0.00 0.00 3.71
924 991 4.349365 GAGAAGGAGAAGGAGAAGGAGAA 58.651 47.826 0.00 0.00 0.00 2.87
925 992 4.352893 AGAAGGAGAAGGAGAAGGAGAAG 58.647 47.826 0.00 0.00 0.00 2.85
926 993 3.114643 AGGAGAAGGAGAAGGAGAAGG 57.885 52.381 0.00 0.00 0.00 3.46
927 994 2.657459 AGGAGAAGGAGAAGGAGAAGGA 59.343 50.000 0.00 0.00 0.00 3.36
928 995 3.031013 GGAGAAGGAGAAGGAGAAGGAG 58.969 54.545 0.00 0.00 0.00 3.69
929 996 3.309556 GGAGAAGGAGAAGGAGAAGGAGA 60.310 52.174 0.00 0.00 0.00 3.71
930 997 4.349365 GAGAAGGAGAAGGAGAAGGAGAA 58.651 47.826 0.00 0.00 0.00 2.87
931 998 4.352893 AGAAGGAGAAGGAGAAGGAGAAG 58.647 47.826 0.00 0.00 0.00 2.85
932 999 3.114643 AGGAGAAGGAGAAGGAGAAGG 57.885 52.381 0.00 0.00 0.00 3.46
933 1000 2.657459 AGGAGAAGGAGAAGGAGAAGGA 59.343 50.000 0.00 0.00 0.00 3.36
934 1001 3.031013 GGAGAAGGAGAAGGAGAAGGAG 58.969 54.545 0.00 0.00 0.00 3.69
935 1002 3.309556 GGAGAAGGAGAAGGAGAAGGAGA 60.310 52.174 0.00 0.00 0.00 3.71
936 1003 4.349365 GAGAAGGAGAAGGAGAAGGAGAA 58.651 47.826 0.00 0.00 0.00 2.87
937 1004 4.352893 AGAAGGAGAAGGAGAAGGAGAAG 58.647 47.826 0.00 0.00 0.00 2.85
938 1005 3.114643 AGGAGAAGGAGAAGGAGAAGG 57.885 52.381 0.00 0.00 0.00 3.46
939 1006 2.657459 AGGAGAAGGAGAAGGAGAAGGA 59.343 50.000 0.00 0.00 0.00 3.36
940 1007 3.031013 GGAGAAGGAGAAGGAGAAGGAG 58.969 54.545 0.00 0.00 0.00 3.69
941 1008 3.309556 GGAGAAGGAGAAGGAGAAGGAGA 60.310 52.174 0.00 0.00 0.00 3.71
942 1009 4.349365 GAGAAGGAGAAGGAGAAGGAGAA 58.651 47.826 0.00 0.00 0.00 2.87
943 1010 4.352893 AGAAGGAGAAGGAGAAGGAGAAG 58.647 47.826 0.00 0.00 0.00 2.85
944 1011 3.114643 AGGAGAAGGAGAAGGAGAAGG 57.885 52.381 0.00 0.00 0.00 3.46
945 1012 2.657459 AGGAGAAGGAGAAGGAGAAGGA 59.343 50.000 0.00 0.00 0.00 3.36
946 1013 3.031013 GGAGAAGGAGAAGGAGAAGGAG 58.969 54.545 0.00 0.00 0.00 3.69
947 1014 3.031013 GAGAAGGAGAAGGAGAAGGAGG 58.969 54.545 0.00 0.00 0.00 4.30
957 1024 0.930726 GAGAAGGAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
1265 1332 2.563179 TCGTAAGCTGCTTCTTCTCCTT 59.437 45.455 19.62 0.00 37.18 3.36
1266 1333 2.926838 CGTAAGCTGCTTCTTCTCCTTC 59.073 50.000 19.62 0.00 0.00 3.46
1267 1334 3.367910 CGTAAGCTGCTTCTTCTCCTTCT 60.368 47.826 19.62 0.00 0.00 2.85
1299 1366 0.456312 GCTTGCTTGCTCTGCATGTC 60.456 55.000 0.00 0.00 38.76 3.06
1303 1370 1.714414 CTTGCTCTGCATGTCTCGC 59.286 57.895 0.00 0.00 38.76 5.03
1306 1373 2.172372 GCTCTGCATGTCTCGCTGG 61.172 63.158 0.00 0.00 0.00 4.85
1309 1376 2.743538 TGCATGTCTCGCTGGTGC 60.744 61.111 0.00 0.00 36.39 5.01
1319 1386 3.667087 GCTGGTGCGAATGGTCAA 58.333 55.556 0.00 0.00 0.00 3.18
1320 1387 2.183409 GCTGGTGCGAATGGTCAAT 58.817 52.632 0.00 0.00 0.00 2.57
1321 1388 0.179156 GCTGGTGCGAATGGTCAATG 60.179 55.000 0.00 0.00 0.00 2.82
1322 1389 0.452987 CTGGTGCGAATGGTCAATGG 59.547 55.000 0.00 0.00 0.00 3.16
1323 1390 0.251121 TGGTGCGAATGGTCAATGGT 60.251 50.000 0.00 0.00 0.00 3.55
1326 1393 0.880441 TGCGAATGGTCAATGGTGTG 59.120 50.000 0.00 0.00 0.00 3.82
1333 1400 1.955778 TGGTCAATGGTGTGCTCAAAG 59.044 47.619 0.00 0.00 0.00 2.77
1349 1416 2.682856 TCAAAGCTCAACTGTGTTGGTC 59.317 45.455 10.05 3.54 34.88 4.02
1363 1430 0.806884 TTGGTCGGTGTGTCGTTGAC 60.807 55.000 0.00 0.00 0.00 3.18
1647 1714 5.368989 GAATCTCAATACCACCGGATCTTT 58.631 41.667 9.46 0.00 0.00 2.52
1669 1736 5.675684 TGTAGATCACAGCTAACCAATGA 57.324 39.130 0.00 0.00 31.89 2.57
1671 1738 6.051074 TGTAGATCACAGCTAACCAATGATG 58.949 40.000 0.00 0.00 30.23 3.07
1672 1739 5.108187 AGATCACAGCTAACCAATGATGT 57.892 39.130 0.00 0.00 32.72 3.06
1673 1740 5.503927 AGATCACAGCTAACCAATGATGTT 58.496 37.500 0.00 0.00 29.85 2.71
1678 1745 2.943033 AGCTAACCAATGATGTTACGGC 59.057 45.455 0.00 0.00 0.00 5.68
2078 2157 2.592308 GAGAGGGCCATGGTGACC 59.408 66.667 14.67 13.47 0.00 4.02
2272 2366 0.107703 GCCACCAAGGATGACGATGA 60.108 55.000 0.00 0.00 41.22 2.92
2273 2367 1.656652 CCACCAAGGATGACGATGAC 58.343 55.000 0.00 0.00 41.22 3.06
2274 2368 1.280982 CACCAAGGATGACGATGACG 58.719 55.000 0.00 0.00 45.75 4.35
2275 2369 1.135112 CACCAAGGATGACGATGACGA 60.135 52.381 0.00 0.00 42.66 4.20
2276 2370 1.757118 ACCAAGGATGACGATGACGAT 59.243 47.619 0.00 0.00 42.66 3.73
2277 2371 2.130395 CCAAGGATGACGATGACGATG 58.870 52.381 0.00 0.00 42.66 3.84
2369 2467 2.808919 TGAAGATGAAGAGGACGAGGT 58.191 47.619 0.00 0.00 0.00 3.85
2370 2468 3.165875 TGAAGATGAAGAGGACGAGGTT 58.834 45.455 0.00 0.00 0.00 3.50
2371 2469 3.193691 TGAAGATGAAGAGGACGAGGTTC 59.806 47.826 0.00 0.00 0.00 3.62
2372 2470 2.808919 AGATGAAGAGGACGAGGTTCA 58.191 47.619 0.00 0.00 33.61 3.18
2373 2471 2.757868 AGATGAAGAGGACGAGGTTCAG 59.242 50.000 0.00 0.00 32.64 3.02
2375 2473 3.150458 TGAAGAGGACGAGGTTCAGTA 57.850 47.619 0.00 0.00 0.00 2.74
2376 2474 3.082548 TGAAGAGGACGAGGTTCAGTAG 58.917 50.000 0.00 0.00 0.00 2.57
2378 2476 1.004979 AGAGGACGAGGTTCAGTAGCT 59.995 52.381 0.00 0.00 37.28 3.32
2388 2497 8.215926 ACGAGGTTCAGTAGCTATATATGATC 57.784 38.462 0.00 0.00 33.94 2.92
2401 2510 8.916062 AGCTATATATGATCAGATCAGTCTTGG 58.084 37.037 18.13 8.50 43.53 3.61
2405 2514 5.954153 ATGATCAGATCAGTCTTGGTTCT 57.046 39.130 18.13 0.00 43.53 3.01
2406 2515 8.718158 ATATGATCAGATCAGTCTTGGTTCTA 57.282 34.615 18.13 2.88 43.53 2.10
2407 2516 6.462552 TGATCAGATCAGTCTTGGTTCTAG 57.537 41.667 9.21 0.00 33.59 2.43
2431 2540 4.178545 AGGGAATTTTGATCGCAAGTTG 57.821 40.909 0.00 0.00 35.04 3.16
2434 2547 3.365820 GGAATTTTGATCGCAAGTTGCTG 59.634 43.478 24.61 17.64 42.25 4.41
2487 2609 2.226674 CCCGCTCTTCCTTTCTTGAAAC 59.773 50.000 0.00 0.00 0.00 2.78
2519 2647 7.227156 GTGGTTTAGATGGAGATGGACATATT 58.773 38.462 0.00 0.00 0.00 1.28
2542 2671 7.899648 TTATGAATATAGCTCCTACTAGGGC 57.100 40.000 2.04 5.09 35.59 5.19
2543 2672 5.538082 TGAATATAGCTCCTACTAGGGCT 57.462 43.478 17.38 17.38 42.15 5.19
2544 2673 5.905088 TGAATATAGCTCCTACTAGGGCTT 58.095 41.667 18.08 11.34 40.65 4.35
2545 2674 5.952947 TGAATATAGCTCCTACTAGGGCTTC 59.047 44.000 18.08 12.32 40.65 3.86
2549 2678 1.414550 GCTCCTACTAGGGCTTCCTTG 59.585 57.143 2.04 0.00 41.96 3.61
2573 2702 3.123157 AGAAGCCATGATCGATCCTTG 57.877 47.619 22.31 18.21 0.00 3.61
2581 2710 1.827344 TGATCGATCCTTGCTGTGTCT 59.173 47.619 22.31 0.00 0.00 3.41
2582 2711 2.200067 GATCGATCCTTGCTGTGTCTG 58.800 52.381 14.76 0.00 0.00 3.51
2583 2712 0.969149 TCGATCCTTGCTGTGTCTGT 59.031 50.000 0.00 0.00 0.00 3.41
2584 2713 1.067565 TCGATCCTTGCTGTGTCTGTC 60.068 52.381 0.00 0.00 0.00 3.51
2588 2717 2.288666 TCCTTGCTGTGTCTGTCAAAC 58.711 47.619 0.00 0.00 0.00 2.93
2618 2819 3.511146 TCATCACCATTTTCTTTGGCTCC 59.489 43.478 0.00 0.00 37.81 4.70
2620 2821 1.067635 CACCATTTTCTTTGGCTCCGG 60.068 52.381 0.00 0.00 37.81 5.14
2625 2830 1.515081 TTTCTTTGGCTCCGGTTACG 58.485 50.000 0.00 0.00 40.55 3.18
2633 2838 1.966493 GCTCCGGTTACGCATGTGTG 61.966 60.000 22.00 4.76 39.22 3.82
2635 2840 0.668096 TCCGGTTACGCATGTGTGTC 60.668 55.000 22.00 13.46 39.74 3.67
2636 2841 1.632046 CCGGTTACGCATGTGTGTCC 61.632 60.000 22.00 19.89 39.74 4.02
2637 2842 1.632046 CGGTTACGCATGTGTGTCCC 61.632 60.000 22.00 15.94 39.74 4.46
2639 2844 0.947180 GTTACGCATGTGTGTCCCGT 60.947 55.000 22.00 9.65 39.74 5.28
2640 2845 0.946700 TTACGCATGTGTGTCCCGTG 60.947 55.000 22.00 0.00 39.74 4.94
2641 2846 2.773397 TACGCATGTGTGTCCCGTGG 62.773 60.000 22.00 0.00 39.74 4.94
2642 2847 2.281484 GCATGTGTGTCCCGTGGT 60.281 61.111 0.00 0.00 0.00 4.16
2643 2848 1.896660 GCATGTGTGTCCCGTGGTT 60.897 57.895 0.00 0.00 0.00 3.67
2644 2849 1.852067 GCATGTGTGTCCCGTGGTTC 61.852 60.000 0.00 0.00 0.00 3.62
2645 2850 1.301401 ATGTGTGTCCCGTGGTTCG 60.301 57.895 0.00 0.00 39.52 3.95
2646 2851 1.750341 ATGTGTGTCCCGTGGTTCGA 61.750 55.000 0.00 0.00 42.86 3.71
2669 2874 1.202302 TCGTTGCTCGATCAGTCCATC 60.202 52.381 0.00 0.00 44.01 3.51
2670 2875 1.576356 GTTGCTCGATCAGTCCATCC 58.424 55.000 0.00 0.00 0.00 3.51
2684 2889 3.464456 AGTCCATCCATCCATTTCCATCA 59.536 43.478 0.00 0.00 0.00 3.07
2693 2898 8.143673 TCCATCCATTTCCATCAATTTTAACA 57.856 30.769 0.00 0.00 0.00 2.41
2703 2908 6.016693 TCCATCAATTTTAACAGCGTCAGAAA 60.017 34.615 0.00 0.00 0.00 2.52
2740 2947 0.179062 CTTGAGGGCTTCTGATCCGG 60.179 60.000 0.00 0.00 0.00 5.14
2743 2950 2.034048 GAGGGCTTCTGATCCGGTCC 62.034 65.000 0.00 0.00 0.00 4.46
2758 2965 1.090052 GGTCCGATCGAAAAGCCAGG 61.090 60.000 18.66 0.00 0.00 4.45
2782 2989 1.577468 TACAACCGCACTGACACAAG 58.423 50.000 0.00 0.00 0.00 3.16
2787 2994 0.602638 CCGCACTGACACAAGGCTAA 60.603 55.000 0.00 0.00 0.00 3.09
2794 3001 1.338674 TGACACAAGGCTAACCGATGG 60.339 52.381 0.00 0.00 42.76 3.51
2807 3014 1.003580 ACCGATGGGATATGTGATGGC 59.996 52.381 0.00 0.00 36.97 4.40
2812 3019 1.355381 TGGGATATGTGATGGCCCATC 59.645 52.381 17.13 17.13 43.57 3.51
2820 3027 1.228367 GATGGCCCATCGCTGGATT 60.228 57.895 8.21 0.00 46.37 3.01
2839 3061 3.409851 TTCTGCAGCGCATCAATTAAG 57.590 42.857 11.47 0.00 38.13 1.85
2857 3079 3.775314 CAGCCGTGCAATGCATTG 58.225 55.556 30.92 30.92 41.91 2.82
2870 3102 3.413522 GCATTGCTGCTTTGACTCC 57.586 52.632 0.16 0.00 45.32 3.85
2872 3104 0.877071 CATTGCTGCTTTGACTCCGT 59.123 50.000 0.00 0.00 0.00 4.69
2919 3155 3.197790 CAAGCACGCATCCGAGGG 61.198 66.667 0.00 0.00 38.29 4.30
2920 3156 3.390521 AAGCACGCATCCGAGGGA 61.391 61.111 0.00 0.00 38.29 4.20
2921 3157 3.376935 AAGCACGCATCCGAGGGAG 62.377 63.158 0.00 0.00 34.05 4.30
2922 3158 3.838271 GCACGCATCCGAGGGAGA 61.838 66.667 0.00 0.00 34.05 3.71
2923 3159 2.105128 CACGCATCCGAGGGAGAC 59.895 66.667 0.00 0.00 34.05 3.36
2953 3189 2.859273 ATCGGGCCGAGTGAAAGCAG 62.859 60.000 33.82 0.00 39.91 4.24
2963 3203 3.849953 GAAAGCAGCGGCCGTACG 61.850 66.667 28.70 16.39 42.56 3.67
2964 3204 4.675029 AAAGCAGCGGCCGTACGT 62.675 61.111 28.70 11.87 42.56 3.57
2965 3205 3.285523 AAAGCAGCGGCCGTACGTA 62.286 57.895 28.70 0.00 42.56 3.57
2966 3206 3.976902 AAGCAGCGGCCGTACGTAC 62.977 63.158 28.70 15.90 42.56 3.67
2980 3220 3.802377 CGTACTCGTCGACATCCTC 57.198 57.895 17.16 1.86 0.00 3.71
3030 3282 3.131155 TTGCTGGTGCTTGGCAAG 58.869 55.556 22.75 22.75 41.47 4.01
3036 3288 2.486966 GTGCTTGGCAAGGCGATC 59.513 61.111 27.25 11.60 41.47 3.69
3048 3300 0.392336 AGGCGATCTGCTTCCTGATC 59.608 55.000 8.94 0.00 45.43 2.92
3057 3309 1.094073 GCTTCCTGATCATGCACGCT 61.094 55.000 0.00 0.00 0.00 5.07
3078 3330 1.478288 GGAGGCATTCATGGAAGGAGG 60.478 57.143 0.00 0.00 0.00 4.30
3084 3336 0.619255 TTCATGGAAGGAGGCGGGTA 60.619 55.000 0.00 0.00 0.00 3.69
3086 3338 2.432300 ATGGAAGGAGGCGGGTACG 61.432 63.158 0.00 0.00 44.63 3.67
3101 3353 2.386501 GTACGCTACCACAGATCTCG 57.613 55.000 0.00 0.00 0.00 4.04
3102 3354 0.661552 TACGCTACCACAGATCTCGC 59.338 55.000 0.00 0.00 0.00 5.03
3103 3355 1.313091 ACGCTACCACAGATCTCGCA 61.313 55.000 0.00 0.00 0.00 5.10
3104 3356 0.867753 CGCTACCACAGATCTCGCAC 60.868 60.000 0.00 0.00 0.00 5.34
3105 3357 0.867753 GCTACCACAGATCTCGCACG 60.868 60.000 0.00 0.00 0.00 5.34
3106 3358 0.867753 CTACCACAGATCTCGCACGC 60.868 60.000 0.00 0.00 0.00 5.34
3107 3359 1.313091 TACCACAGATCTCGCACGCT 61.313 55.000 0.00 0.00 0.00 5.07
3108 3360 2.163390 CCACAGATCTCGCACGCTG 61.163 63.158 0.00 0.00 34.65 5.18
3181 3433 0.803768 CATGACGCCACGGAGAGAAG 60.804 60.000 0.00 0.00 0.00 2.85
3186 3438 0.734253 CGCCACGGAGAGAAGAAGTG 60.734 60.000 0.00 0.00 0.00 3.16
3193 3445 1.611936 GGAGAGAAGAAGTGGGGTTGC 60.612 57.143 0.00 0.00 0.00 4.17
3215 3467 4.740822 ATGGCAAGGCACGGGGTC 62.741 66.667 0.00 0.00 0.00 4.46
3246 3498 2.291043 GGCCGTGAAGGAAGAGGGA 61.291 63.158 0.00 0.00 45.00 4.20
3258 3510 0.393267 AAGAGGGACGACGAGAGAGG 60.393 60.000 0.00 0.00 0.00 3.69
3260 3512 3.519930 GGGACGACGAGAGAGGGC 61.520 72.222 0.00 0.00 0.00 5.19
3261 3513 2.438795 GGACGACGAGAGAGGGCT 60.439 66.667 0.00 0.00 0.00 5.19
3262 3514 2.766400 GGACGACGAGAGAGGGCTG 61.766 68.421 0.00 0.00 0.00 4.85
3268 3526 2.279069 CGAGAGAGGGCTGTGTGGT 61.279 63.158 0.00 0.00 0.00 4.16
3293 3551 4.494811 CGCCTCACGCATACAGAA 57.505 55.556 0.00 0.00 37.30 3.02
3302 3560 2.069273 ACGCATACAGAAACACAGAGC 58.931 47.619 0.00 0.00 0.00 4.09
3303 3561 2.068519 CGCATACAGAAACACAGAGCA 58.931 47.619 0.00 0.00 0.00 4.26
3304 3562 2.093310 CGCATACAGAAACACAGAGCAG 59.907 50.000 0.00 0.00 0.00 4.24
3305 3563 3.329386 GCATACAGAAACACAGAGCAGA 58.671 45.455 0.00 0.00 0.00 4.26
3306 3564 3.370366 GCATACAGAAACACAGAGCAGAG 59.630 47.826 0.00 0.00 0.00 3.35
3307 3565 4.814147 CATACAGAAACACAGAGCAGAGA 58.186 43.478 0.00 0.00 0.00 3.10
3308 3566 3.104843 ACAGAAACACAGAGCAGAGAC 57.895 47.619 0.00 0.00 0.00 3.36
3309 3567 2.432146 ACAGAAACACAGAGCAGAGACA 59.568 45.455 0.00 0.00 0.00 3.41
3310 3568 2.799412 CAGAAACACAGAGCAGAGACAC 59.201 50.000 0.00 0.00 0.00 3.67
3311 3569 2.697751 AGAAACACAGAGCAGAGACACT 59.302 45.455 0.00 0.00 0.00 3.55
3312 3570 3.891977 AGAAACACAGAGCAGAGACACTA 59.108 43.478 0.00 0.00 0.00 2.74
3313 3571 3.651803 AACACAGAGCAGAGACACTAC 57.348 47.619 0.00 0.00 0.00 2.73
3314 3572 2.870175 ACACAGAGCAGAGACACTACT 58.130 47.619 0.00 0.00 0.00 2.57
3315 3573 2.556189 ACACAGAGCAGAGACACTACTG 59.444 50.000 0.00 0.00 37.22 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.019673 CTGGACTGCCCATTCGAATG 58.980 55.000 27.66 27.66 45.57 2.67
28 29 0.107459 GAGGACTGGACTGCCCATTC 60.107 60.000 0.00 0.00 45.57 2.67
40 41 1.716826 GCGACGTAGGAGGAGGACTG 61.717 65.000 0.00 0.00 0.00 3.51
41 42 1.451747 GCGACGTAGGAGGAGGACT 60.452 63.158 0.00 0.00 0.00 3.85
42 43 2.479750 GGCGACGTAGGAGGAGGAC 61.480 68.421 0.00 0.00 0.00 3.85
43 44 2.124403 GGCGACGTAGGAGGAGGA 60.124 66.667 0.00 0.00 0.00 3.71
127 128 3.071206 GCCCTCTCGCTCTGGTGA 61.071 66.667 0.00 0.00 0.00 4.02
129 130 3.991924 ATGGCCCTCTCGCTCTGGT 62.992 63.158 0.00 0.00 0.00 4.00
174 175 1.299620 CACTGTTGTTGGCTGCTGC 60.300 57.895 7.10 7.10 38.76 5.25
175 176 0.029834 GACACTGTTGTTGGCTGCTG 59.970 55.000 0.00 0.00 35.47 4.41
176 177 0.107017 AGACACTGTTGTTGGCTGCT 60.107 50.000 0.00 0.00 35.47 4.24
182 183 2.285834 GCAACGAGAGACACTGTTGTTG 60.286 50.000 18.44 18.44 45.86 3.33
183 184 1.933853 GCAACGAGAGACACTGTTGTT 59.066 47.619 12.78 0.00 38.54 2.83
184 185 1.571919 GCAACGAGAGACACTGTTGT 58.428 50.000 12.78 0.00 38.54 3.32
192 193 3.084579 CGCATGGCAACGAGAGAC 58.915 61.111 7.43 0.00 42.51 3.36
222 223 1.997606 GGTATTCGTTTCGTGGGTGAG 59.002 52.381 0.00 0.00 0.00 3.51
288 292 4.659172 TGGCACGGGGGAAAGCTG 62.659 66.667 0.00 0.00 0.00 4.24
293 300 2.283532 CCATTTGGCACGGGGGAA 60.284 61.111 0.00 0.00 0.00 3.97
433 447 1.230650 TCTCCCTCTCCCTCTCCCA 60.231 63.158 0.00 0.00 0.00 4.37
434 448 1.541672 CTCTCCCTCTCCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
435 449 1.541672 CCTCTCCCTCTCCCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
436 450 0.996762 TCCCTCTCCCTCTCCCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
437 451 0.998945 CTCCCTCTCCCTCTCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
438 452 0.996762 TCTCCCTCTCCCTCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
439 453 0.998945 CTCTCCCTCTCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
440 454 1.541672 CTCTCCCTCTCCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
602 620 1.646447 AGGGGTAGAGTGGATCAGTGA 59.354 52.381 0.00 0.00 0.00 3.41
685 740 5.104485 TCTCTCTACTGTGCCTCTGTATACA 60.104 44.000 5.25 5.25 31.82 2.29
702 760 3.066760 CACACACACACACACTCTCTCTA 59.933 47.826 0.00 0.00 0.00 2.43
703 761 2.103373 ACACACACACACACTCTCTCT 58.897 47.619 0.00 0.00 0.00 3.10
704 762 2.159240 TCACACACACACACACTCTCTC 60.159 50.000 0.00 0.00 0.00 3.20
706 764 2.159240 TCTCACACACACACACACTCTC 60.159 50.000 0.00 0.00 0.00 3.20
709 767 1.824852 TCTCTCACACACACACACACT 59.175 47.619 0.00 0.00 0.00 3.55
710 768 2.159240 TCTCTCTCACACACACACACAC 60.159 50.000 0.00 0.00 0.00 3.82
712 770 2.359214 TCTCTCTCTCACACACACACAC 59.641 50.000 0.00 0.00 0.00 3.82
713 771 2.620585 CTCTCTCTCTCACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
714 772 2.881513 TCTCTCTCTCTCACACACACAC 59.118 50.000 0.00 0.00 0.00 3.82
715 773 3.145286 CTCTCTCTCTCTCACACACACA 58.855 50.000 0.00 0.00 0.00 3.72
716 774 2.487762 CCTCTCTCTCTCTCACACACAC 59.512 54.545 0.00 0.00 0.00 3.82
717 775 2.107378 ACCTCTCTCTCTCTCACACACA 59.893 50.000 0.00 0.00 0.00 3.72
718 776 2.747446 GACCTCTCTCTCTCTCACACAC 59.253 54.545 0.00 0.00 0.00 3.82
719 777 2.642311 AGACCTCTCTCTCTCTCACACA 59.358 50.000 0.00 0.00 0.00 3.72
720 778 3.009723 CAGACCTCTCTCTCTCTCACAC 58.990 54.545 0.00 0.00 0.00 3.82
721 779 2.642311 ACAGACCTCTCTCTCTCTCACA 59.358 50.000 0.00 0.00 0.00 3.58
749 809 2.233186 GGGTAGGCGAGAGTGTTTAAGT 59.767 50.000 0.00 0.00 0.00 2.24
780 840 0.692756 GAGAAGAAGGGAGGAGGGGG 60.693 65.000 0.00 0.00 0.00 5.40
785 845 0.033011 CGAGGGAGAAGAAGGGAGGA 60.033 60.000 0.00 0.00 0.00 3.71
792 852 1.002087 GTTCTTGGCGAGGGAGAAGAA 59.998 52.381 0.97 0.00 33.15 2.52
828 888 2.786578 GACAGAGAAACAGATCGATCGC 59.213 50.000 19.33 8.18 0.00 4.58
839 899 1.009389 CGCACGGGAGACAGAGAAAC 61.009 60.000 0.00 0.00 0.00 2.78
842 902 3.749064 GCGCACGGGAGACAGAGA 61.749 66.667 0.30 0.00 0.00 3.10
895 962 5.473849 TCTCCTTCTCCTTCTCCTTCATA 57.526 43.478 0.00 0.00 0.00 2.15
903 970 4.352893 CTTCTCCTTCTCCTTCTCCTTCT 58.647 47.826 0.00 0.00 0.00 2.85
904 971 3.450817 CCTTCTCCTTCTCCTTCTCCTTC 59.549 52.174 0.00 0.00 0.00 3.46
905 972 3.078305 TCCTTCTCCTTCTCCTTCTCCTT 59.922 47.826 0.00 0.00 0.00 3.36
906 973 2.657459 TCCTTCTCCTTCTCCTTCTCCT 59.343 50.000 0.00 0.00 0.00 3.69
907 974 3.031013 CTCCTTCTCCTTCTCCTTCTCC 58.969 54.545 0.00 0.00 0.00 3.71
908 975 3.976015 TCTCCTTCTCCTTCTCCTTCTC 58.024 50.000 0.00 0.00 0.00 2.87
909 976 4.352893 CTTCTCCTTCTCCTTCTCCTTCT 58.647 47.826 0.00 0.00 0.00 2.85
910 977 3.450817 CCTTCTCCTTCTCCTTCTCCTTC 59.549 52.174 0.00 0.00 0.00 3.46
911 978 3.078305 TCCTTCTCCTTCTCCTTCTCCTT 59.922 47.826 0.00 0.00 0.00 3.36
912 979 2.657459 TCCTTCTCCTTCTCCTTCTCCT 59.343 50.000 0.00 0.00 0.00 3.69
913 980 3.031013 CTCCTTCTCCTTCTCCTTCTCC 58.969 54.545 0.00 0.00 0.00 3.71
914 981 3.976015 TCTCCTTCTCCTTCTCCTTCTC 58.024 50.000 0.00 0.00 0.00 2.87
915 982 4.352893 CTTCTCCTTCTCCTTCTCCTTCT 58.647 47.826 0.00 0.00 0.00 2.85
916 983 3.450817 CCTTCTCCTTCTCCTTCTCCTTC 59.549 52.174 0.00 0.00 0.00 3.46
917 984 3.078305 TCCTTCTCCTTCTCCTTCTCCTT 59.922 47.826 0.00 0.00 0.00 3.36
918 985 2.657459 TCCTTCTCCTTCTCCTTCTCCT 59.343 50.000 0.00 0.00 0.00 3.69
919 986 3.031013 CTCCTTCTCCTTCTCCTTCTCC 58.969 54.545 0.00 0.00 0.00 3.71
920 987 3.976015 TCTCCTTCTCCTTCTCCTTCTC 58.024 50.000 0.00 0.00 0.00 2.87
921 988 4.352893 CTTCTCCTTCTCCTTCTCCTTCT 58.647 47.826 0.00 0.00 0.00 2.85
922 989 3.450817 CCTTCTCCTTCTCCTTCTCCTTC 59.549 52.174 0.00 0.00 0.00 3.46
923 990 3.078305 TCCTTCTCCTTCTCCTTCTCCTT 59.922 47.826 0.00 0.00 0.00 3.36
924 991 2.657459 TCCTTCTCCTTCTCCTTCTCCT 59.343 50.000 0.00 0.00 0.00 3.69
925 992 3.031013 CTCCTTCTCCTTCTCCTTCTCC 58.969 54.545 0.00 0.00 0.00 3.71
926 993 3.031013 CCTCCTTCTCCTTCTCCTTCTC 58.969 54.545 0.00 0.00 0.00 2.87
927 994 2.657459 TCCTCCTTCTCCTTCTCCTTCT 59.343 50.000 0.00 0.00 0.00 2.85
928 995 3.031013 CTCCTCCTTCTCCTTCTCCTTC 58.969 54.545 0.00 0.00 0.00 3.46
929 996 2.292851 CCTCCTCCTTCTCCTTCTCCTT 60.293 54.545 0.00 0.00 0.00 3.36
930 997 1.290732 CCTCCTCCTTCTCCTTCTCCT 59.709 57.143 0.00 0.00 0.00 3.69
931 998 1.289530 TCCTCCTCCTTCTCCTTCTCC 59.710 57.143 0.00 0.00 0.00 3.71
932 999 2.666317 CTCCTCCTCCTTCTCCTTCTC 58.334 57.143 0.00 0.00 0.00 2.87
933 1000 1.290732 CCTCCTCCTCCTTCTCCTTCT 59.709 57.143 0.00 0.00 0.00 2.85
934 1001 1.289530 TCCTCCTCCTCCTTCTCCTTC 59.710 57.143 0.00 0.00 0.00 3.46
935 1002 1.290732 CTCCTCCTCCTCCTTCTCCTT 59.709 57.143 0.00 0.00 0.00 3.36
936 1003 0.933700 CTCCTCCTCCTCCTTCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
937 1004 0.105709 CCTCCTCCTCCTCCTTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
938 1005 0.930726 TCCTCCTCCTCCTCCTTCTC 59.069 60.000 0.00 0.00 0.00 2.87
939 1006 0.933700 CTCCTCCTCCTCCTCCTTCT 59.066 60.000 0.00 0.00 0.00 2.85
940 1007 0.930726 TCTCCTCCTCCTCCTCCTTC 59.069 60.000 0.00 0.00 0.00 3.46
941 1008 0.933700 CTCTCCTCCTCCTCCTCCTT 59.066 60.000 0.00 0.00 0.00 3.36
942 1009 0.998945 CCTCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
943 1010 1.541672 CCTCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
944 1011 1.541672 CCCTCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
945 1012 2.018086 CCCCTCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
946 1013 1.376249 ATCCCCTCTCCTCCTCCTCC 61.376 65.000 0.00 0.00 0.00 4.30
947 1014 1.357761 CTATCCCCTCTCCTCCTCCTC 59.642 61.905 0.00 0.00 0.00 3.71
957 1024 2.085934 AGCCACCTATCTATCCCCTCT 58.914 52.381 0.00 0.00 0.00 3.69
1265 1332 1.754621 AAGCGCATCGAGGAGGAGA 60.755 57.895 11.47 0.00 0.00 3.71
1266 1333 1.591059 CAAGCGCATCGAGGAGGAG 60.591 63.158 11.47 0.00 0.00 3.69
1267 1334 2.496341 CAAGCGCATCGAGGAGGA 59.504 61.111 11.47 0.00 0.00 3.71
1303 1370 0.452987 CCATTGACCATTCGCACCAG 59.547 55.000 0.00 0.00 0.00 4.00
1306 1373 0.881118 ACACCATTGACCATTCGCAC 59.119 50.000 0.00 0.00 0.00 5.34
1309 1376 1.131126 GAGCACACCATTGACCATTCG 59.869 52.381 0.00 0.00 0.00 3.34
1310 1377 2.161855 TGAGCACACCATTGACCATTC 58.838 47.619 0.00 0.00 0.00 2.67
1311 1378 2.291209 TGAGCACACCATTGACCATT 57.709 45.000 0.00 0.00 0.00 3.16
1312 1379 2.291209 TTGAGCACACCATTGACCAT 57.709 45.000 0.00 0.00 0.00 3.55
1313 1380 1.955778 CTTTGAGCACACCATTGACCA 59.044 47.619 0.00 0.00 0.00 4.02
1314 1381 1.336240 GCTTTGAGCACACCATTGACC 60.336 52.381 0.00 0.00 41.89 4.02
1317 1384 1.610038 TGAGCTTTGAGCACACCATTG 59.390 47.619 2.47 0.00 45.56 2.82
1318 1385 1.985473 TGAGCTTTGAGCACACCATT 58.015 45.000 2.47 0.00 45.56 3.16
1319 1386 1.610522 GTTGAGCTTTGAGCACACCAT 59.389 47.619 2.47 0.00 45.56 3.55
1320 1387 1.024271 GTTGAGCTTTGAGCACACCA 58.976 50.000 2.47 0.00 45.56 4.17
1321 1388 1.002033 CAGTTGAGCTTTGAGCACACC 60.002 52.381 2.47 0.00 45.56 4.16
1322 1389 1.672881 ACAGTTGAGCTTTGAGCACAC 59.327 47.619 2.47 0.00 45.56 3.82
1323 1390 1.672363 CACAGTTGAGCTTTGAGCACA 59.328 47.619 2.47 0.00 45.56 4.57
1326 1393 2.542411 CCAACACAGTTGAGCTTTGAGC 60.542 50.000 11.19 0.00 42.84 4.26
1333 1400 0.814010 ACCGACCAACACAGTTGAGC 60.814 55.000 11.19 2.48 0.00 4.26
1584 1651 0.247736 CTTACTCTGCTTCAGGGCGT 59.752 55.000 0.00 0.00 34.91 5.68
1624 1691 4.608948 AGATCCGGTGGTATTGAGATTC 57.391 45.455 0.00 0.00 0.00 2.52
1647 1714 5.675684 TCATTGGTTAGCTGTGATCTACA 57.324 39.130 0.00 0.00 37.78 2.74
1669 1736 1.450312 GCAGCAGGAGCCGTAACAT 60.450 57.895 0.00 0.00 43.56 2.71
1671 1738 2.047274 TGCAGCAGGAGCCGTAAC 60.047 61.111 0.00 0.00 43.56 2.50
1672 1739 2.265739 CTGCAGCAGGAGCCGTAA 59.734 61.111 15.35 0.00 43.56 3.18
1673 1740 2.997315 ACTGCAGCAGGAGCCGTA 60.997 61.111 26.38 0.00 43.56 4.02
1828 1904 1.753649 TCGGAGCAGAGGAAGAAGATG 59.246 52.381 0.00 0.00 0.00 2.90
1829 1905 2.151502 TCGGAGCAGAGGAAGAAGAT 57.848 50.000 0.00 0.00 0.00 2.40
1830 1906 1.546476 GTTCGGAGCAGAGGAAGAAGA 59.454 52.381 0.00 0.00 0.00 2.87
2078 2157 1.471684 GGCATTGCCTCTTCTCTGTTG 59.528 52.381 20.66 0.00 46.69 3.33
2272 2366 0.665369 GTTGTCGTTCCGGTCATCGT 60.665 55.000 0.00 0.00 37.11 3.73
2273 2367 1.349259 GGTTGTCGTTCCGGTCATCG 61.349 60.000 0.00 2.62 38.88 3.84
2274 2368 1.017701 GGGTTGTCGTTCCGGTCATC 61.018 60.000 0.00 0.00 0.00 2.92
2275 2369 1.004200 GGGTTGTCGTTCCGGTCAT 60.004 57.895 0.00 0.00 0.00 3.06
2276 2370 2.422591 GGGTTGTCGTTCCGGTCA 59.577 61.111 0.00 0.00 0.00 4.02
2277 2371 2.735857 CGGGTTGTCGTTCCGGTC 60.736 66.667 0.00 0.00 40.07 4.79
2287 2381 4.954970 CAGGTGCTGCCGGGTTGT 62.955 66.667 2.18 0.00 43.70 3.32
2361 2459 6.598457 TCATATATAGCTACTGAACCTCGTCC 59.402 42.308 0.00 0.00 0.00 4.79
2375 2473 8.916062 CCAAGACTGATCTGATCATATATAGCT 58.084 37.037 19.84 7.67 38.85 3.32
2376 2474 8.694540 ACCAAGACTGATCTGATCATATATAGC 58.305 37.037 19.84 5.82 38.85 2.97
2388 2497 5.395103 CCTTCCTAGAACCAAGACTGATCTG 60.395 48.000 0.00 0.00 34.48 2.90
2399 2508 5.592587 TCAAAATTCCCTTCCTAGAACCA 57.407 39.130 0.00 0.00 0.00 3.67
2401 2510 5.220873 GCGATCAAAATTCCCTTCCTAGAAC 60.221 44.000 0.00 0.00 0.00 3.01
2403 2512 4.080582 TGCGATCAAAATTCCCTTCCTAGA 60.081 41.667 0.00 0.00 0.00 2.43
2404 2513 4.199310 TGCGATCAAAATTCCCTTCCTAG 58.801 43.478 0.00 0.00 0.00 3.02
2405 2514 4.229304 TGCGATCAAAATTCCCTTCCTA 57.771 40.909 0.00 0.00 0.00 2.94
2406 2515 3.085952 TGCGATCAAAATTCCCTTCCT 57.914 42.857 0.00 0.00 0.00 3.36
2407 2516 3.193479 ACTTGCGATCAAAATTCCCTTCC 59.807 43.478 0.00 0.00 0.00 3.46
2431 2540 4.058817 ACTTACACAAGCTTAGACACAGC 58.941 43.478 0.00 0.00 34.94 4.40
2434 2547 4.448060 GGTCACTTACACAAGCTTAGACAC 59.552 45.833 0.00 0.00 34.94 3.67
2487 2609 1.760613 TCCATCTAAACCACCTAGCGG 59.239 52.381 0.00 0.00 0.00 5.52
2519 2647 7.227355 AGCCCTAGTAGGAGCTATATTCATA 57.773 40.000 23.22 0.00 39.20 2.15
2533 2662 4.794334 TCTACTCAAGGAAGCCCTAGTAG 58.206 47.826 12.16 12.16 45.13 2.57
2534 2663 4.875578 TCTACTCAAGGAAGCCCTAGTA 57.124 45.455 0.00 0.00 43.48 1.82
2535 2664 3.759815 TCTACTCAAGGAAGCCCTAGT 57.240 47.619 0.00 0.00 43.48 2.57
2536 2665 4.664150 CTTCTACTCAAGGAAGCCCTAG 57.336 50.000 0.00 0.00 43.48 3.02
2542 2671 4.478206 TCATGGCTTCTACTCAAGGAAG 57.522 45.455 0.00 0.00 41.08 3.46
2543 2672 4.442052 CGATCATGGCTTCTACTCAAGGAA 60.442 45.833 0.00 0.00 0.00 3.36
2544 2673 3.068732 CGATCATGGCTTCTACTCAAGGA 59.931 47.826 0.00 0.00 0.00 3.36
2545 2674 3.068732 TCGATCATGGCTTCTACTCAAGG 59.931 47.826 0.00 0.00 0.00 3.61
2549 2678 3.509575 AGGATCGATCATGGCTTCTACTC 59.490 47.826 25.93 4.71 0.00 2.59
2581 2710 3.329386 GTGATGAGCTAGCTGTTTGACA 58.671 45.455 24.99 13.21 0.00 3.58
2582 2711 2.675348 GGTGATGAGCTAGCTGTTTGAC 59.325 50.000 24.99 10.36 0.00 3.18
2583 2712 2.302733 TGGTGATGAGCTAGCTGTTTGA 59.697 45.455 24.99 0.39 0.00 2.69
2584 2713 2.703416 TGGTGATGAGCTAGCTGTTTG 58.297 47.619 24.99 0.00 0.00 2.93
2588 2717 4.197750 AGAAAATGGTGATGAGCTAGCTG 58.802 43.478 24.99 0.00 0.00 4.24
2618 2819 1.632046 GGGACACACATGCGTAACCG 61.632 60.000 0.00 0.00 37.07 4.44
2620 2821 0.947180 ACGGGACACACATGCGTAAC 60.947 55.000 0.00 0.00 0.00 2.50
2625 2830 1.852067 GAACCACGGGACACACATGC 61.852 60.000 0.00 0.00 0.00 4.06
2633 2838 1.731969 CGAACTCGAACCACGGGAC 60.732 63.158 0.00 0.00 46.62 4.46
2636 2841 1.850640 CAACGAACTCGAACCACGG 59.149 57.895 6.05 0.00 43.02 4.94
2637 2842 1.200839 GCAACGAACTCGAACCACG 59.799 57.895 6.05 0.00 43.02 4.94
2639 2844 2.895039 GAGCAACGAACTCGAACCA 58.105 52.632 6.05 0.00 43.02 3.67
2669 2874 7.011669 GCTGTTAAAATTGATGGAAATGGATGG 59.988 37.037 0.00 0.00 0.00 3.51
2670 2875 7.254185 CGCTGTTAAAATTGATGGAAATGGATG 60.254 37.037 0.00 0.00 0.00 3.51
2684 2889 5.508200 TGGTTTCTGACGCTGTTAAAATT 57.492 34.783 0.00 0.00 0.00 1.82
2693 2898 1.968493 TCCTACTTGGTTTCTGACGCT 59.032 47.619 0.00 0.00 37.07 5.07
2703 2908 6.156429 CCCTCAAGTTTATACTCCTACTTGGT 59.844 42.308 12.31 0.00 44.63 3.67
2740 2947 1.090052 CCCTGGCTTTTCGATCGGAC 61.090 60.000 16.41 1.01 0.00 4.79
2743 2950 2.472909 GGCCCTGGCTTTTCGATCG 61.473 63.158 9.36 9.36 41.60 3.69
2758 2965 1.376683 TCAGTGCGGTTGTATGGCC 60.377 57.895 0.00 0.00 0.00 5.36
2782 2989 2.301870 TCACATATCCCATCGGTTAGCC 59.698 50.000 0.00 0.00 0.00 3.93
2787 2994 1.003580 GCCATCACATATCCCATCGGT 59.996 52.381 0.00 0.00 0.00 4.69
2794 3001 1.742761 CGATGGGCCATCACATATCC 58.257 55.000 37.95 15.93 40.54 2.59
2807 3014 1.153107 TGCAGAATCCAGCGATGGG 60.153 57.895 21.53 3.94 0.00 4.00
2814 3021 1.093496 TGATGCGCTGCAGAATCCAG 61.093 55.000 20.43 1.63 43.65 3.86
2820 3027 1.064505 GCTTAATTGATGCGCTGCAGA 59.935 47.619 20.43 0.00 43.65 4.26
2839 3061 2.125832 AATGCATTGCACGGCTGC 60.126 55.556 14.66 6.57 43.04 5.25
2850 3072 1.203994 GGAGTCAAAGCAGCAATGCAT 59.796 47.619 8.35 0.00 37.25 3.96
2854 3076 1.537202 GAACGGAGTCAAAGCAGCAAT 59.463 47.619 0.00 0.00 45.00 3.56
2856 3078 0.179059 TGAACGGAGTCAAAGCAGCA 60.179 50.000 0.00 0.00 45.00 4.41
2857 3079 0.235926 GTGAACGGAGTCAAAGCAGC 59.764 55.000 0.00 0.00 45.00 5.25
2858 3080 0.508641 CGTGAACGGAGTCAAAGCAG 59.491 55.000 0.00 0.00 45.00 4.24
2919 3155 1.273300 CGATCGGTCGTCTCGTCTC 59.727 63.158 10.62 0.00 42.78 3.36
2920 3156 2.172372 CCGATCGGTCGTCTCGTCT 61.172 63.158 26.35 0.00 46.25 4.18
2921 3157 2.323790 CCGATCGGTCGTCTCGTC 59.676 66.667 26.35 0.00 46.25 4.20
2922 3158 3.200593 CCCGATCGGTCGTCTCGT 61.201 66.667 31.22 0.00 46.25 4.18
2923 3159 4.609247 GCCCGATCGGTCGTCTCG 62.609 72.222 31.22 15.83 46.25 4.04
2939 3175 3.793144 CCGCTGCTTTCACTCGGC 61.793 66.667 0.00 0.00 33.36 5.54
2963 3203 2.612672 TGATGAGGATGTCGACGAGTAC 59.387 50.000 11.62 0.00 0.00 2.73
2964 3204 2.872858 CTGATGAGGATGTCGACGAGTA 59.127 50.000 11.62 0.00 0.00 2.59
2965 3205 1.673400 CTGATGAGGATGTCGACGAGT 59.327 52.381 11.62 0.00 0.00 4.18
2966 3206 1.001924 CCTGATGAGGATGTCGACGAG 60.002 57.143 11.62 0.00 42.93 4.18
2980 3220 2.860628 GCGCGCGTAACTCCTGATG 61.861 63.158 32.35 0.00 0.00 3.07
3030 3282 0.105593 TGATCAGGAAGCAGATCGCC 59.894 55.000 0.00 0.00 42.72 5.54
3036 3288 0.656259 CGTGCATGATCAGGAAGCAG 59.344 55.000 12.39 4.85 35.66 4.24
3057 3309 1.213678 CTCCTTCCATGAATGCCTCCA 59.786 52.381 0.00 0.00 0.00 3.86
3084 3336 1.313091 TGCGAGATCTGTGGTAGCGT 61.313 55.000 0.00 0.00 0.00 5.07
3086 3338 0.867753 CGTGCGAGATCTGTGGTAGC 60.868 60.000 0.00 0.00 0.00 3.58
3087 3339 0.867753 GCGTGCGAGATCTGTGGTAG 60.868 60.000 0.00 0.00 0.00 3.18
3088 3340 1.138883 GCGTGCGAGATCTGTGGTA 59.861 57.895 0.00 0.00 0.00 3.25
3089 3341 2.125912 GCGTGCGAGATCTGTGGT 60.126 61.111 0.00 0.00 0.00 4.16
3090 3342 2.163390 CAGCGTGCGAGATCTGTGG 61.163 63.158 0.00 0.00 0.00 4.17
3091 3343 2.163390 CCAGCGTGCGAGATCTGTG 61.163 63.158 0.00 0.00 0.00 3.66
3092 3344 2.182791 CCAGCGTGCGAGATCTGT 59.817 61.111 0.00 0.00 0.00 3.41
3093 3345 2.584418 CCCAGCGTGCGAGATCTG 60.584 66.667 0.00 0.00 0.00 2.90
3094 3346 2.755876 TCCCAGCGTGCGAGATCT 60.756 61.111 0.00 0.00 0.00 2.75
3095 3347 2.279120 CTCCCAGCGTGCGAGATC 60.279 66.667 0.00 0.00 0.00 2.75
3096 3348 4.521062 GCTCCCAGCGTGCGAGAT 62.521 66.667 0.00 0.00 0.00 2.75
3101 3353 3.984193 ATGAAGGCTCCCAGCGTGC 62.984 63.158 0.00 0.00 43.62 5.34
3102 3354 2.110967 CATGAAGGCTCCCAGCGTG 61.111 63.158 0.00 0.00 43.62 5.34
3103 3355 2.270205 CATGAAGGCTCCCAGCGT 59.730 61.111 0.00 0.00 43.62 5.07
3104 3356 2.515523 CCATGAAGGCTCCCAGCG 60.516 66.667 0.00 0.00 43.62 5.18
3181 3433 1.607467 ATGGCAGCAACCCCACTTC 60.607 57.895 0.00 0.00 33.17 3.01
3232 3484 0.109226 CGTCGTCCCTCTTCCTTCAC 60.109 60.000 0.00 0.00 0.00 3.18
3246 3498 2.034376 ACAGCCCTCTCTCGTCGT 59.966 61.111 0.00 0.00 0.00 4.34
3258 3510 2.186826 GTGACCACACCACACAGCC 61.187 63.158 0.00 0.00 40.74 4.85
3260 3512 2.534019 GCGTGACCACACCACACAG 61.534 63.158 0.00 0.00 43.34 3.66
3261 3513 2.512745 GCGTGACCACACCACACA 60.513 61.111 0.00 0.00 43.34 3.72
3262 3514 3.276846 GGCGTGACCACACCACAC 61.277 66.667 2.57 0.00 43.34 3.82
3268 3526 4.961511 GCGTGAGGCGTGACCACA 62.962 66.667 0.85 0.00 43.14 4.17
3293 3551 3.005261 CAGTAGTGTCTCTGCTCTGTGTT 59.995 47.826 0.00 0.00 37.01 3.32


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

AutoCloner maintained by Alex Coulton.