Multiple sequence alignment - TraesCS7D01G178200

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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 TraesCS7D01G178200 chr7D 100.000 9929 0 0 1 9929 131471897 131461969 0.000000e+00 18336.0
1 TraesCS7D01G178200 chr7D 97.817 733 15 1 1 732 180833412 180834144 0.000000e+00 1264.0
2 TraesCS7D01G178200 chr7D 85.012 407 54 4 1 401 46598429 46598834 3.340000e-109 407.0
3 TraesCS7D01G178200 chr7D 100.000 39 0 0 9087 9125 195654114 195654076 1.380000e-08 73.1
4 TraesCS7D01G178200 chr7D 93.478 46 3 0 9080 9125 428723350 428723305 1.790000e-07 69.4
5 TraesCS7D01G178200 chr7B 94.888 4049 131 40 5851 9859 92317068 92313056 0.000000e+00 6261.0
6 TraesCS7D01G178200 chr7B 96.667 2400 50 16 3507 5898 92319452 92317075 0.000000e+00 3962.0
7 TraesCS7D01G178200 chr7B 90.540 1501 89 22 802 2289 92322544 92321084 0.000000e+00 1936.0
8 TraesCS7D01G178200 chr7B 93.878 637 28 4 2378 3013 92321063 92320437 0.000000e+00 950.0
9 TraesCS7D01G178200 chr7B 97.452 471 10 2 3005 3473 92319922 92319452 0.000000e+00 802.0
10 TraesCS7D01G178200 chr7B 87.079 178 13 3 802 979 92324048 92323881 1.020000e-44 193.0
11 TraesCS7D01G178200 chr7B 91.176 102 7 2 3440 3540 153326836 153326936 4.840000e-28 137.0
12 TraesCS7D01G178200 chr7B 100.000 40 0 0 9087 9126 159549718 159549679 3.850000e-09 75.0
13 TraesCS7D01G178200 chr7A 96.808 2788 58 8 6521 9282 130228357 130225575 0.000000e+00 4626.0
14 TraesCS7D01G178200 chr7A 92.964 1947 104 19 3083 5019 130231901 130229978 0.000000e+00 2806.0
15 TraesCS7D01G178200 chr7A 90.721 1498 94 20 810 2293 130234114 130232648 0.000000e+00 1954.0
16 TraesCS7D01G178200 chr7A 92.039 716 23 12 2245 2935 130232630 130231924 0.000000e+00 976.0
17 TraesCS7D01G178200 chr7A 96.926 553 16 1 5347 5898 130229542 130228990 0.000000e+00 926.0
18 TraesCS7D01G178200 chr7A 93.811 614 31 4 5851 6460 130228983 130228373 0.000000e+00 917.0
19 TraesCS7D01G178200 chr7A 92.254 568 29 5 9316 9875 130225573 130225013 0.000000e+00 791.0
20 TraesCS7D01G178200 chr7A 93.960 298 13 3 5055 5348 130229990 130229694 7.080000e-121 446.0
21 TraesCS7D01G178200 chr7A 93.182 88 5 1 3447 3533 574129409 574129322 2.910000e-25 128.0
22 TraesCS7D01G178200 chr7A 85.294 102 13 2 3528 3628 74150098 74150198 4.910000e-18 104.0
23 TraesCS7D01G178200 chr7A 93.878 49 3 0 2245 2293 130232663 130232615 3.850000e-09 75.0
24 TraesCS7D01G178200 chr4D 84.901 1318 165 20 1860 3170 464860255 464861545 0.000000e+00 1301.0
25 TraesCS7D01G178200 chr4D 84.119 403 59 4 1 401 418386264 418386663 1.560000e-102 385.0
26 TraesCS7D01G178200 chr4D 84.091 88 13 1 3289 3375 51617758 51617671 6.390000e-12 84.2
27 TraesCS7D01G178200 chr4D 97.561 41 1 0 9086 9126 460805806 460805766 4.980000e-08 71.3
28 TraesCS7D01G178200 chr1D 97.015 737 14 3 1 737 364634559 364635287 0.000000e+00 1232.0
29 TraesCS7D01G178200 chr1D 85.539 408 49 7 1 401 366007387 366006983 1.540000e-112 418.0
30 TraesCS7D01G178200 chr1D 84.375 128 15 2 3319 3442 11545407 11545533 4.870000e-23 121.0
31 TraesCS7D01G178200 chr1D 82.979 94 15 1 3296 3388 26971769 26971676 6.390000e-12 84.2
32 TraesCS7D01G178200 chr1D 85.455 55 5 1 3350 3401 77757017 77757071 5.000000e-03 54.7
33 TraesCS7D01G178200 chr2A 85.025 1202 139 24 1989 3185 629631048 629629883 0.000000e+00 1184.0
34 TraesCS7D01G178200 chr2A 84.524 84 10 3 3293 3374 418243649 418243567 8.270000e-11 80.5
35 TraesCS7D01G178200 chr2A 86.667 60 7 1 3558 3616 396713446 396713387 2.310000e-06 65.8
36 TraesCS7D01G178200 chr6A 93.369 739 41 3 1 732 480196546 480197283 0.000000e+00 1086.0
37 TraesCS7D01G178200 chr6A 92.857 98 6 1 3439 3535 548408153 548408056 3.740000e-29 141.0
38 TraesCS7D01G178200 chr5A 84.340 977 109 22 1880 2851 508857395 508856458 0.000000e+00 917.0
39 TraesCS7D01G178200 chr5A 93.478 46 3 0 3528 3573 610234428 610234473 1.790000e-07 69.4
40 TraesCS7D01G178200 chr6B 90.359 612 33 9 114 725 681229997 681230582 0.000000e+00 780.0
41 TraesCS7D01G178200 chr2B 87.859 453 33 8 114 564 174446875 174446443 6.880000e-141 512.0
42 TraesCS7D01G178200 chr2B 93.210 162 11 0 571 732 174433560 174433399 1.290000e-58 239.0
43 TraesCS7D01G178200 chr2B 82.692 104 15 1 3327 3427 131514333 131514436 1.370000e-13 89.8
44 TraesCS7D01G178200 chr1B 82.616 581 65 17 1880 2455 661037200 661037749 1.940000e-131 481.0
45 TraesCS7D01G178200 chr1B 88.393 336 31 5 2518 2852 661037748 661038076 2.010000e-106 398.0
46 TraesCS7D01G178200 chr1B 84.108 409 56 6 1 404 501359063 501359467 4.350000e-103 387.0
47 TraesCS7D01G178200 chr1B 90.551 127 11 1 603 729 29509056 29509181 6.170000e-37 167.0
48 TraesCS7D01G178200 chr1B 85.294 136 14 2 3319 3448 16919462 16919597 1.740000e-27 135.0
49 TraesCS7D01G178200 chr3B 85.990 414 48 5 1 405 251785006 251785418 1.530000e-117 435.0
50 TraesCS7D01G178200 chr3B 85.185 405 49 8 7 403 168276070 168275669 1.200000e-108 405.0
51 TraesCS7D01G178200 chr3B 86.056 251 26 7 489 732 787202538 787202786 2.750000e-65 261.0
52 TraesCS7D01G178200 chr3B 94.186 86 4 1 3447 3531 487224484 487224399 8.090000e-26 130.0
53 TraesCS7D01G178200 chr3B 93.023 86 5 1 3447 3531 423807013 423807098 3.770000e-24 124.0
54 TraesCS7D01G178200 chr3B 89.362 47 4 1 390 436 787202257 787202302 3.870000e-04 58.4
55 TraesCS7D01G178200 chr5D 91.150 226 16 1 507 732 4057167 4056946 4.510000e-78 303.0
56 TraesCS7D01G178200 chr5D 95.402 87 3 1 3446 3531 134916580 134916494 4.840000e-28 137.0
57 TraesCS7D01G178200 chr5D 85.000 80 10 2 3296 3374 171013466 171013388 8.270000e-11 80.5
58 TraesCS7D01G178200 chr5D 90.909 44 2 2 3370 3411 539977628 539977585 3.870000e-04 58.4
59 TraesCS7D01G178200 chr6D 95.455 88 3 1 3446 3532 122992105 122992192 1.340000e-28 139.0
60 TraesCS7D01G178200 chr6D 95.745 47 2 0 9079 9125 26738829 26738783 1.070000e-09 76.8
61 TraesCS7D01G178200 chr6D 94.000 50 3 0 9086 9135 418632108 418632059 1.070000e-09 76.8
62 TraesCS7D01G178200 chr6D 90.385 52 2 2 9087 9135 3442605 3442554 2.310000e-06 65.8
63 TraesCS7D01G178200 chr4A 96.341 82 3 0 3453 3534 625404855 625404774 1.740000e-27 135.0
64 TraesCS7D01G178200 chr3D 95.349 86 3 1 3447 3531 326696955 326697040 1.740000e-27 135.0
65 TraesCS7D01G178200 chr1A 84.158 101 15 1 3528 3627 21713120 21713220 8.210000e-16 97.1
66 TraesCS7D01G178200 chr3A 82.857 105 8 6 401 496 718854691 718854794 1.780000e-12 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 TraesCS7D01G178200 chr7D 131461969 131471897 9928 True 18336.000000 18336 100.000000 1 9929 1 chr7D.!!$R1 9928
1 TraesCS7D01G178200 chr7D 180833412 180834144 732 False 1264.000000 1264 97.817000 1 732 1 chr7D.!!$F2 731
2 TraesCS7D01G178200 chr7B 92313056 92324048 10992 True 2350.666667 6261 93.417333 802 9859 6 chr7B.!!$R2 9057
3 TraesCS7D01G178200 chr7A 130225013 130234114 9101 True 1501.888889 4626 93.706778 810 9875 9 chr7A.!!$R2 9065
4 TraesCS7D01G178200 chr4D 464860255 464861545 1290 False 1301.000000 1301 84.901000 1860 3170 1 chr4D.!!$F2 1310
5 TraesCS7D01G178200 chr1D 364634559 364635287 728 False 1232.000000 1232 97.015000 1 737 1 chr1D.!!$F3 736
6 TraesCS7D01G178200 chr2A 629629883 629631048 1165 True 1184.000000 1184 85.025000 1989 3185 1 chr2A.!!$R3 1196
7 TraesCS7D01G178200 chr6A 480196546 480197283 737 False 1086.000000 1086 93.369000 1 732 1 chr6A.!!$F1 731
8 TraesCS7D01G178200 chr5A 508856458 508857395 937 True 917.000000 917 84.340000 1880 2851 1 chr5A.!!$R1 971
9 TraesCS7D01G178200 chr6B 681229997 681230582 585 False 780.000000 780 90.359000 114 725 1 chr6B.!!$F1 611
10 TraesCS7D01G178200 chr1B 661037200 661038076 876 False 439.500000 481 85.504500 1880 2852 2 chr1B.!!$F4 972

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
28 29 0.031314 CCTACAGCTGCATCGACGAT 59.969 55.000 15.27 4.05 0.00 3.73 F
1364 2873 0.250513 GCCCAGGTGAGTAGAACCAG 59.749 60.000 0.00 0.00 40.40 4.00 F
1372 2881 0.610687 GAGTAGAACCAGCAGGCTGT 59.389 55.000 17.16 2.33 42.15 4.40 F
2074 3590 1.003112 ATGGCCGTTTCCGCAAGTA 60.003 52.632 0.00 0.00 0.00 2.24 F
2236 3765 2.027192 GGGTGAGCAAGTCTACAATCCA 60.027 50.000 0.00 0.00 0.00 3.41 F
3946 6105 0.179037 CCGCCATGGACATCATCTGT 60.179 55.000 18.40 0.00 42.00 3.41 F
5039 7203 0.253583 TTGGTGGAGGGATGGGATGA 60.254 55.000 0.00 0.00 0.00 2.92 F
5043 7207 0.343018 TGGAGGGATGGGATGACAGA 59.657 55.000 0.00 0.00 0.00 3.41 F
6519 8901 0.107017 CCAAGCAGACACCCCTATGG 60.107 60.000 0.00 0.00 41.37 2.74 F
6899 9281 2.730183 TGCGTCTTTCACTCAAAACG 57.270 45.000 0.00 0.00 34.41 3.60 F
8497 10884 2.421424 GCATTGAGTCCTCCATGACAAC 59.579 50.000 11.41 0.00 35.46 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 2923 0.037326 AAGGTGCTCGAGAAATGCGA 60.037 50.000 18.75 0.00 36.23 5.10 R
2387 4010 0.673333 TACAGCCATGGCACTCAACG 60.673 55.000 37.18 17.95 44.88 4.10 R
2628 4252 1.462616 TGATGTACATTGGCCAGCAC 58.537 50.000 10.30 3.25 0.00 4.40 R
3500 5653 3.242413 CCGATCCAAAATAAGTGTCGCAG 60.242 47.826 0.00 0.00 0.00 5.18 R
4128 6287 0.327000 ACATCAAGGAGGGGAGGAGG 60.327 60.000 0.00 0.00 0.00 4.30 R
5041 7205 0.108585 AGTGGTGCGATGGTTTGTCT 59.891 50.000 0.00 0.00 0.00 3.41 R
6519 8901 0.320050 GCACTCCAGAGCTATAGGGC 59.680 60.000 1.04 0.00 0.00 5.19 R
6904 9286 5.209818 AGCATGAATGGCTCATTAAATGG 57.790 39.130 0.00 3.52 42.46 3.16 R
8497 10884 3.721035 TCACCGTCTATGATTGCAGATG 58.279 45.455 0.00 0.00 0.00 2.90 R
8898 11306 0.609131 AATCCCCAAGCTTGTCACGG 60.609 55.000 24.35 17.42 0.00 4.94 R
9864 12288 0.319083 TTGCGAGAGAACGGCCTTAA 59.681 50.000 0.00 0.00 0.00 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.104928 CGCCTACAGCTGCATCGA 59.895 61.111 15.27 0.00 40.39 3.59
28 29 0.031314 CCTACAGCTGCATCGACGAT 59.969 55.000 15.27 4.05 0.00 3.73
548 558 1.155042 GCAGCTGAGTTCAGTTCAGG 58.845 55.000 20.43 0.00 45.45 3.86
732 742 3.131400 TGGAAAAACTGTGTAGCCAAACC 59.869 43.478 0.00 0.00 0.00 3.27
733 743 3.383505 GGAAAAACTGTGTAGCCAAACCT 59.616 43.478 0.00 0.00 0.00 3.50
735 745 5.068067 GGAAAAACTGTGTAGCCAAACCTAA 59.932 40.000 0.00 0.00 0.00 2.69
736 746 5.509716 AAAACTGTGTAGCCAAACCTAAC 57.490 39.130 0.00 0.00 0.00 2.34
737 747 4.432980 AACTGTGTAGCCAAACCTAACT 57.567 40.909 0.00 0.00 0.00 2.24
738 748 4.432980 ACTGTGTAGCCAAACCTAACTT 57.567 40.909 0.00 0.00 0.00 2.66
739 749 4.788679 ACTGTGTAGCCAAACCTAACTTT 58.211 39.130 0.00 0.00 0.00 2.66
740 750 5.198207 ACTGTGTAGCCAAACCTAACTTTT 58.802 37.500 0.00 0.00 0.00 2.27
741 751 5.655090 ACTGTGTAGCCAAACCTAACTTTTT 59.345 36.000 0.00 0.00 0.00 1.94
763 773 7.401484 TTTTTGTTGAGACAAGAAACACAAC 57.599 32.000 6.36 0.00 45.80 3.32
764 774 5.957842 TTGTTGAGACAAGAAACACAACT 57.042 34.783 0.00 0.00 40.71 3.16
765 775 7.441890 TTTGTTGAGACAAGAAACACAACTA 57.558 32.000 0.00 0.00 45.80 2.24
766 776 7.441890 TTGTTGAGACAAGAAACACAACTAA 57.558 32.000 0.00 0.00 40.71 2.24
767 777 6.837992 TGTTGAGACAAGAAACACAACTAAC 58.162 36.000 0.00 0.00 38.02 2.34
768 778 6.653320 TGTTGAGACAAGAAACACAACTAACT 59.347 34.615 0.00 0.00 38.02 2.24
769 779 6.662414 TGAGACAAGAAACACAACTAACTG 57.338 37.500 0.00 0.00 0.00 3.16
770 780 6.170506 TGAGACAAGAAACACAACTAACTGT 58.829 36.000 0.00 0.00 0.00 3.55
771 781 7.324935 TGAGACAAGAAACACAACTAACTGTA 58.675 34.615 0.00 0.00 0.00 2.74
772 782 7.491372 TGAGACAAGAAACACAACTAACTGTAG 59.509 37.037 0.00 0.00 0.00 2.74
773 783 6.258068 AGACAAGAAACACAACTAACTGTAGC 59.742 38.462 0.00 0.00 0.00 3.58
774 784 5.878116 ACAAGAAACACAACTAACTGTAGCA 59.122 36.000 0.00 0.00 0.00 3.49
775 785 6.542370 ACAAGAAACACAACTAACTGTAGCAT 59.458 34.615 0.00 0.00 0.00 3.79
776 786 7.713507 ACAAGAAACACAACTAACTGTAGCATA 59.286 33.333 0.00 0.00 0.00 3.14
777 787 7.891183 AGAAACACAACTAACTGTAGCATAG 57.109 36.000 0.00 0.00 0.00 2.23
778 788 6.369065 AGAAACACAACTAACTGTAGCATAGC 59.631 38.462 0.00 0.00 0.00 2.97
779 789 5.147330 ACACAACTAACTGTAGCATAGCA 57.853 39.130 0.00 0.00 0.00 3.49
780 790 5.547465 ACACAACTAACTGTAGCATAGCAA 58.453 37.500 0.00 0.00 0.00 3.91
781 791 5.995282 ACACAACTAACTGTAGCATAGCAAA 59.005 36.000 0.00 0.00 0.00 3.68
782 792 6.147821 ACACAACTAACTGTAGCATAGCAAAG 59.852 38.462 0.00 0.00 0.00 2.77
783 793 6.147821 CACAACTAACTGTAGCATAGCAAAGT 59.852 38.462 0.00 0.00 0.00 2.66
784 794 6.710744 ACAACTAACTGTAGCATAGCAAAGTT 59.289 34.615 8.36 8.36 34.18 2.66
785 795 6.727824 ACTAACTGTAGCATAGCAAAGTTG 57.272 37.500 11.63 0.00 32.80 3.16
786 796 6.464222 ACTAACTGTAGCATAGCAAAGTTGA 58.536 36.000 11.63 0.91 32.80 3.18
787 797 5.869753 AACTGTAGCATAGCAAAGTTGAG 57.130 39.130 0.00 0.00 30.65 3.02
788 798 3.686726 ACTGTAGCATAGCAAAGTTGAGC 59.313 43.478 0.00 0.00 0.00 4.26
789 799 3.673902 TGTAGCATAGCAAAGTTGAGCA 58.326 40.909 3.72 0.00 0.00 4.26
790 800 3.436704 TGTAGCATAGCAAAGTTGAGCAC 59.563 43.478 3.72 0.00 0.00 4.40
791 801 1.815003 AGCATAGCAAAGTTGAGCACC 59.185 47.619 3.72 0.00 0.00 5.01
792 802 1.135286 GCATAGCAAAGTTGAGCACCC 60.135 52.381 3.72 0.00 0.00 4.61
793 803 1.131126 CATAGCAAAGTTGAGCACCCG 59.869 52.381 3.72 0.00 0.00 5.28
794 804 1.234615 TAGCAAAGTTGAGCACCCGC 61.235 55.000 3.72 0.00 38.99 6.13
795 805 2.644992 CAAAGTTGAGCACCCGCC 59.355 61.111 0.00 0.00 39.83 6.13
796 806 2.978010 AAAGTTGAGCACCCGCCG 60.978 61.111 0.00 0.00 39.83 6.46
857 867 2.958355 CCACCAAATGACAGAACAAGGT 59.042 45.455 0.00 0.00 0.00 3.50
943 2448 1.324005 CCCTTCTCTCCTCCGTGACC 61.324 65.000 0.00 0.00 0.00 4.02
944 2449 0.612174 CCTTCTCTCCTCCGTGACCA 60.612 60.000 0.00 0.00 0.00 4.02
945 2450 1.257743 CTTCTCTCCTCCGTGACCAA 58.742 55.000 0.00 0.00 0.00 3.67
946 2451 0.966920 TTCTCTCCTCCGTGACCAAC 59.033 55.000 0.00 0.00 0.00 3.77
948 2453 1.889530 CTCTCCTCCGTGACCAACCC 61.890 65.000 0.00 0.00 0.00 4.11
949 2454 2.926242 TCCTCCGTGACCAACCCC 60.926 66.667 0.00 0.00 0.00 4.95
1070 2579 0.876399 TACAAGTACGCAGAGCACGA 59.124 50.000 0.00 0.00 0.00 4.35
1202 2711 4.787280 CCACCCCGCTCCTCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
1203 2712 3.151022 CACCCCGCTCCTCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
1204 2713 4.467107 ACCCCGCTCCTCTCCTCC 62.467 72.222 0.00 0.00 0.00 4.30
1205 2714 4.150454 CCCCGCTCCTCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1238 2747 3.464494 CTAACCCCGTCCCGTCCC 61.464 72.222 0.00 0.00 0.00 4.46
1331 2840 3.470888 CCTCCCCGCCTTCGACAT 61.471 66.667 0.00 0.00 38.10 3.06
1342 2851 3.699955 TTCGACATCGCCGCTCAGG 62.700 63.158 0.00 0.00 44.97 3.86
1360 2869 2.656069 GGCGCCCAGGTGAGTAGAA 61.656 63.158 18.11 0.00 0.00 2.10
1361 2870 1.448013 GCGCCCAGGTGAGTAGAAC 60.448 63.158 0.00 0.00 0.00 3.01
1364 2873 0.250513 GCCCAGGTGAGTAGAACCAG 59.749 60.000 0.00 0.00 40.40 4.00
1366 2875 0.976641 CCAGGTGAGTAGAACCAGCA 59.023 55.000 0.00 0.00 40.40 4.41
1367 2876 1.066573 CCAGGTGAGTAGAACCAGCAG 60.067 57.143 0.00 0.00 40.40 4.24
1372 2881 0.610687 GAGTAGAACCAGCAGGCTGT 59.389 55.000 17.16 2.33 42.15 4.40
1393 2902 2.614013 ACCCGCATCCTCCCCTTT 60.614 61.111 0.00 0.00 0.00 3.11
1431 2940 1.710339 GTCGCATTTCTCGAGCACC 59.290 57.895 7.81 0.00 36.56 5.01
1504 3013 1.066645 GTTGGGTAATCCGGACGAGTT 60.067 52.381 6.12 0.00 38.76 3.01
1677 3186 1.215382 GGTTTCCTGATTTGGCGGC 59.785 57.895 0.00 0.00 0.00 6.53
1713 3222 1.818363 AGAGTCGTCGCCGAGCATA 60.818 57.895 0.00 0.00 45.26 3.14
1839 3348 2.102925 CAGGAAATGCAACCACAGGTTT 59.897 45.455 0.00 0.00 44.33 3.27
1840 3349 2.102925 AGGAAATGCAACCACAGGTTTG 59.897 45.455 0.00 0.00 44.33 2.93
1841 3350 2.158971 GGAAATGCAACCACAGGTTTGT 60.159 45.455 0.00 0.00 44.33 2.83
1892 3401 9.929180 TTAATAGCATACTAGTATTCTTGGCTG 57.071 33.333 24.43 11.44 29.63 4.85
1894 3403 3.430218 GCATACTAGTATTCTTGGCTGCG 59.570 47.826 12.87 0.00 0.00 5.18
1948 3457 6.470235 GTCAAGCATAACTGTGAATTGCATAC 59.530 38.462 0.00 0.00 35.79 2.39
2009 3522 1.826096 GGCTCGGTAGAGACCTTTCTT 59.174 52.381 0.00 0.00 46.89 2.52
2010 3523 3.022406 GGCTCGGTAGAGACCTTTCTTA 58.978 50.000 0.00 0.00 46.89 2.10
2074 3590 1.003112 ATGGCCGTTTCCGCAAGTA 60.003 52.632 0.00 0.00 0.00 2.24
2164 3692 2.744202 CTGTTACATTGCTGGAGACACC 59.256 50.000 0.00 0.00 35.60 4.16
2177 3705 2.758423 GGAGACACCGGCCAATTAATTT 59.242 45.455 0.00 0.00 0.00 1.82
2236 3765 2.027192 GGGTGAGCAAGTCTACAATCCA 60.027 50.000 0.00 0.00 0.00 3.41
2248 3778 8.999431 CAAGTCTACAATCCAAGTTTAAGCTTA 58.001 33.333 0.86 0.86 0.00 3.09
2249 3779 9.740710 AAGTCTACAATCCAAGTTTAAGCTTAT 57.259 29.630 7.08 0.00 0.00 1.73
2304 3900 5.964958 ACTTCTTTAAAGCAGCAGCATAA 57.035 34.783 13.87 0.00 45.49 1.90
2314 3913 3.765511 AGCAGCAGCATAATTTTGAGGAA 59.234 39.130 3.17 0.00 45.49 3.36
2317 3916 5.583457 GCAGCAGCATAATTTTGAGGAATTT 59.417 36.000 0.00 0.00 41.58 1.82
2330 3953 7.672983 TTTGAGGAATTTAGTGAGACACATC 57.327 36.000 4.75 0.00 36.74 3.06
2360 3983 6.985188 TTGCAGACTCCTTAACATACAATC 57.015 37.500 0.00 0.00 0.00 2.67
2387 4010 6.929606 TCTCCTTGTTACTTCTTACAAAGAGC 59.070 38.462 0.00 0.00 40.30 4.09
2554 4177 8.933653 TCCATTTCCCTTCTTTTTAATCAAAGT 58.066 29.630 0.74 0.00 35.56 2.66
2631 4255 4.782019 TGACAATGGTTTTATCCTGTGC 57.218 40.909 0.00 0.00 0.00 4.57
2744 4368 3.748083 AGTTTTGCTCTTCATGCAGAGA 58.252 40.909 24.25 8.21 42.81 3.10
2810 4434 9.096160 GATAGCATAACCTGTCATGATTATCAG 57.904 37.037 0.00 0.99 0.00 2.90
3081 5229 6.065374 TCCCAGCTTAAAAGTGATGTGTTTA 58.935 36.000 0.00 0.00 0.00 2.01
3301 5450 2.905415 TAAGTCGAACTACCCCTCCA 57.095 50.000 0.00 0.00 0.00 3.86
3473 5626 3.555956 CCTCCGATCCAAAATAAGTGTCG 59.444 47.826 0.00 0.00 0.00 4.35
3486 5639 6.854496 AATAAGTGTCGCAGTTTTGAACTA 57.146 33.333 5.46 0.00 40.46 2.24
3487 5640 6.854496 ATAAGTGTCGCAGTTTTGAACTAA 57.146 33.333 5.46 0.00 40.46 2.24
3488 5641 4.531659 AGTGTCGCAGTTTTGAACTAAC 57.468 40.909 0.00 0.00 40.46 2.34
3489 5642 3.311596 AGTGTCGCAGTTTTGAACTAACC 59.688 43.478 0.00 0.00 40.46 2.85
3490 5643 2.614983 TGTCGCAGTTTTGAACTAACCC 59.385 45.455 0.00 0.00 40.46 4.11
3491 5644 2.614983 GTCGCAGTTTTGAACTAACCCA 59.385 45.455 0.00 0.00 40.46 4.51
3492 5645 2.875933 TCGCAGTTTTGAACTAACCCAG 59.124 45.455 0.00 0.00 40.46 4.45
3493 5646 2.616842 CGCAGTTTTGAACTAACCCAGT 59.383 45.455 0.00 0.00 40.46 4.00
3546 5699 9.137459 CGGAGGGAGTATTATAGATGTTGATAT 57.863 37.037 0.00 0.00 0.00 1.63
3672 5827 7.820872 GCTGTGGAAAGTAGTAATGGTAGTTTA 59.179 37.037 0.00 0.00 0.00 2.01
3946 6105 0.179037 CCGCCATGGACATCATCTGT 60.179 55.000 18.40 0.00 42.00 3.41
4117 6276 1.277557 CCACTAGAAGGTGCTCAAGCT 59.722 52.381 0.00 0.00 42.66 3.74
4123 6282 3.334054 GGTGCTCAAGCTCCCCCT 61.334 66.667 11.22 0.00 46.01 4.79
4128 6287 4.760220 TCAAGCTCCCCCTCCCCC 62.760 72.222 0.00 0.00 0.00 5.40
4160 6319 5.246981 TCCTTGATGTTTTCCAGATCAGT 57.753 39.130 0.00 0.00 0.00 3.41
4243 6402 7.672983 TTGCATCTAGAGTTTCTTTTACCAG 57.327 36.000 0.00 0.00 0.00 4.00
4476 6636 7.687941 AAGTGTTCCTGTCAAATACTATTGG 57.312 36.000 0.00 0.00 29.29 3.16
4548 6709 1.131883 GTGGAGTGCAGCATGTTGATC 59.868 52.381 14.38 7.43 39.31 2.92
4625 6786 7.389330 CCAGGTACTAATGTTTGTAATGACACA 59.611 37.037 0.00 0.00 36.02 3.72
4806 6967 8.301002 TCAAAGTTTTGCATTTAGTATGTACCC 58.699 33.333 0.00 0.00 38.05 3.69
4916 7077 4.074259 CAGTCTCCATCATGACCACAAAA 58.926 43.478 0.00 0.00 34.02 2.44
4917 7078 4.520111 CAGTCTCCATCATGACCACAAAAA 59.480 41.667 0.00 0.00 34.02 1.94
4918 7079 4.520492 AGTCTCCATCATGACCACAAAAAC 59.480 41.667 0.00 0.00 34.02 2.43
5039 7203 0.253583 TTGGTGGAGGGATGGGATGA 60.254 55.000 0.00 0.00 0.00 2.92
5040 7204 0.988145 TGGTGGAGGGATGGGATGAC 60.988 60.000 0.00 0.00 0.00 3.06
5041 7205 0.988145 GGTGGAGGGATGGGATGACA 60.988 60.000 0.00 0.00 0.00 3.58
5042 7206 0.471617 GTGGAGGGATGGGATGACAG 59.528 60.000 0.00 0.00 0.00 3.51
5043 7207 0.343018 TGGAGGGATGGGATGACAGA 59.657 55.000 0.00 0.00 0.00 3.41
5063 7227 1.167851 CAAACCATCGCACCACTCAT 58.832 50.000 0.00 0.00 0.00 2.90
5177 7341 9.762933 ACTAAGTGACAAACAAATGCAATAAAT 57.237 25.926 0.00 0.00 0.00 1.40
5266 7430 1.576356 GAGACGATGGCATGAGAACC 58.424 55.000 3.81 0.00 0.00 3.62
5594 7913 9.515020 TTGTTTTTCATTTGAAAGTAGCACTAG 57.485 29.630 5.92 0.00 43.90 2.57
5827 8146 4.650734 TGATCACAACTGGCTTGACATTA 58.349 39.130 0.00 0.00 33.59 1.90
6106 8483 4.691860 AGGAACTTCAAAATGCTCATCG 57.308 40.909 0.00 0.00 27.25 3.84
6117 8494 3.302968 GCTCATCGCAAGCACTTTC 57.697 52.632 0.00 0.00 39.61 2.62
6144 8521 9.249053 GACTCCCTCATGTATATGAATTCTCTA 57.751 37.037 7.05 0.00 42.48 2.43
6189 8566 2.893489 AGTCCAGGCCTCATTTCAAAAC 59.107 45.455 0.00 0.00 0.00 2.43
6212 8589 2.919666 GTGTGCAATATGGACGCTTT 57.080 45.000 8.09 0.00 44.24 3.51
6237 8614 2.495270 ACTCTCATGCTCCTGTACAGTG 59.505 50.000 21.18 12.41 0.00 3.66
6254 8631 1.508632 GTGGACACACGCTGTAATGT 58.491 50.000 0.00 0.00 37.94 2.71
6296 8673 0.947244 GGACTGCAAGGATTATGCCG 59.053 55.000 0.00 0.00 43.16 5.69
6403 8780 3.225177 AGCATCCCTTGGATCAGATTG 57.775 47.619 0.00 0.00 40.98 2.67
6411 8788 6.496743 TCCCTTGGATCAGATTGATTTCTTT 58.503 36.000 0.00 0.00 37.20 2.52
6435 8812 2.569853 TCGGTTTTGATGCCCTTCTCTA 59.430 45.455 0.00 0.00 0.00 2.43
6442 8822 7.503902 GGTTTTGATGCCCTTCTCTATAAGATT 59.496 37.037 0.00 0.00 32.82 2.40
6486 8868 8.539770 ACACAACAATAATCATCGATCTATCC 57.460 34.615 0.00 0.00 0.00 2.59
6489 8871 6.874278 ACAATAATCATCGATCTATCCCCA 57.126 37.500 0.00 0.00 0.00 4.96
6492 8874 4.815533 AATCATCGATCTATCCCCACTG 57.184 45.455 0.00 0.00 0.00 3.66
6515 8897 0.768221 TCTTCCAAGCAGACACCCCT 60.768 55.000 0.00 0.00 0.00 4.79
6516 8898 0.984230 CTTCCAAGCAGACACCCCTA 59.016 55.000 0.00 0.00 0.00 3.53
6517 8899 1.561542 CTTCCAAGCAGACACCCCTAT 59.438 52.381 0.00 0.00 0.00 2.57
6518 8900 0.911769 TCCAAGCAGACACCCCTATG 59.088 55.000 0.00 0.00 0.00 2.23
6519 8901 0.107017 CCAAGCAGACACCCCTATGG 60.107 60.000 0.00 0.00 41.37 2.74
6747 9129 5.835113 GCCTTATGCTAAAATCAAGACCA 57.165 39.130 0.00 0.00 36.87 4.02
6751 9133 7.013274 GCCTTATGCTAAAATCAAGACCATGTA 59.987 37.037 0.00 0.00 36.87 2.29
6899 9281 2.730183 TGCGTCTTTCACTCAAAACG 57.270 45.000 0.00 0.00 34.41 3.60
6904 9286 4.511734 CGTCTTTCACTCAAAACGGTTAC 58.488 43.478 0.00 0.00 30.92 2.50
7049 9431 8.840321 ACTAATCCAAAAGGACAATATGATTCG 58.160 33.333 0.00 0.00 0.00 3.34
7276 9658 6.961554 GTCTTTAACACTGCATATTAGCACAC 59.038 38.462 0.00 0.00 40.11 3.82
7911 10294 7.530010 AGACAAGTACATGTGTTTCATTATGC 58.470 34.615 8.74 0.00 34.09 3.14
7967 10350 3.667960 GCAAGTGCTATTTTGTCAGGTCG 60.668 47.826 0.00 0.00 38.21 4.79
7985 10368 3.184581 GGTCGTGTATAATAAGCAGCTGC 59.815 47.826 31.53 31.53 42.49 5.25
8364 10748 8.122472 TCTTTTCCCCTTTCAGATATGTTTTC 57.878 34.615 0.00 0.00 0.00 2.29
8378 10762 8.557864 CAGATATGTTTTCTGATTCACATCTCC 58.442 37.037 0.00 0.00 42.63 3.71
8497 10884 2.421424 GCATTGAGTCCTCCATGACAAC 59.579 50.000 11.41 0.00 35.46 3.32
8525 10912 4.516698 GCAATCATAGACGGTGATGGAAAT 59.483 41.667 0.00 0.00 36.49 2.17
8824 11213 5.705609 AGAAATGCATCGTTGTAACCTTT 57.294 34.783 0.00 0.00 0.00 3.11
8898 11306 9.723601 ATAGATATCAAAGAGGAGCAGAAAATC 57.276 33.333 5.32 0.00 0.00 2.17
9198 11613 1.953559 TTGTCAGTGAGTGGTTGAGC 58.046 50.000 0.00 0.00 0.00 4.26
9435 11851 6.346838 GCAGTTTTGTCAGATATGCCAAAAAC 60.347 38.462 10.51 11.98 38.20 2.43
9533 11950 3.133901 TGGCTCGTGAAATCAGGCTATTA 59.866 43.478 0.00 0.00 0.00 0.98
9538 11955 5.972935 TCGTGAAATCAGGCTATTACTTCA 58.027 37.500 0.00 0.00 0.00 3.02
9539 11956 6.582636 TCGTGAAATCAGGCTATTACTTCAT 58.417 36.000 0.00 0.00 0.00 2.57
9572 11993 9.314501 GTCAATCTCGTTTGTTCTTACATAAAC 57.685 33.333 0.00 0.00 33.44 2.01
9666 12087 5.107133 GGTAGCGCTGACTCTTGTAATTAA 58.893 41.667 22.90 0.00 0.00 1.40
9669 12090 3.370978 GCGCTGACTCTTGTAATTAAGCA 59.629 43.478 0.00 0.00 0.00 3.91
9837 12261 4.279922 TGTCAGACAACGACTAGAATGGAA 59.720 41.667 0.00 0.00 34.37 3.53
9849 12273 5.934781 ACTAGAATGGAATCTGGACAATCC 58.065 41.667 0.00 0.00 36.96 3.01
9852 12276 6.776887 AGAATGGAATCTGGACAATCCTAT 57.223 37.500 0.00 0.00 37.46 2.57
9864 12288 9.218525 TCTGGACAATCCTATTTTCTAGAATCT 57.781 33.333 5.89 0.00 37.46 2.40
9875 12299 6.980051 TTTTCTAGAATCTTAAGGCCGTTC 57.020 37.500 5.89 3.20 0.00 3.95
9876 12300 5.934402 TTCTAGAATCTTAAGGCCGTTCT 57.066 39.130 0.00 9.78 33.96 3.01
9877 12301 5.517322 TCTAGAATCTTAAGGCCGTTCTC 57.483 43.478 0.00 0.00 32.02 2.87
9878 12302 5.202004 TCTAGAATCTTAAGGCCGTTCTCT 58.798 41.667 0.00 0.00 32.02 3.10
9879 12303 4.394439 AGAATCTTAAGGCCGTTCTCTC 57.606 45.455 0.00 0.00 0.00 3.20
9880 12304 2.873133 ATCTTAAGGCCGTTCTCTCG 57.127 50.000 0.00 0.00 0.00 4.04
9881 12305 0.172803 TCTTAAGGCCGTTCTCTCGC 59.827 55.000 0.00 0.00 0.00 5.03
9882 12306 0.108804 CTTAAGGCCGTTCTCTCGCA 60.109 55.000 0.00 0.00 0.00 5.10
9883 12307 0.319083 TTAAGGCCGTTCTCTCGCAA 59.681 50.000 0.00 0.00 0.00 4.85
9884 12308 0.319083 TAAGGCCGTTCTCTCGCAAA 59.681 50.000 0.00 0.00 0.00 3.68
9885 12309 0.534203 AAGGCCGTTCTCTCGCAAAA 60.534 50.000 0.00 0.00 0.00 2.44
9886 12310 0.534203 AGGCCGTTCTCTCGCAAAAA 60.534 50.000 0.00 0.00 0.00 1.94
9887 12311 0.385598 GGCCGTTCTCTCGCAAAAAC 60.386 55.000 0.00 0.00 0.00 2.43
9888 12312 0.306533 GCCGTTCTCTCGCAAAAACA 59.693 50.000 0.00 0.00 0.00 2.83
9889 12313 1.268335 GCCGTTCTCTCGCAAAAACAA 60.268 47.619 0.00 0.00 0.00 2.83
9890 12314 2.793237 GCCGTTCTCTCGCAAAAACAAA 60.793 45.455 0.00 0.00 0.00 2.83
9891 12315 3.430931 CCGTTCTCTCGCAAAAACAAAA 58.569 40.909 0.00 0.00 0.00 2.44
9892 12316 3.482110 CCGTTCTCTCGCAAAAACAAAAG 59.518 43.478 0.00 0.00 0.00 2.27
9893 12317 4.339429 CGTTCTCTCGCAAAAACAAAAGA 58.661 39.130 0.00 0.00 0.00 2.52
9894 12318 4.970003 CGTTCTCTCGCAAAAACAAAAGAT 59.030 37.500 0.00 0.00 0.00 2.40
9895 12319 5.108630 CGTTCTCTCGCAAAAACAAAAGATG 60.109 40.000 0.00 0.00 0.00 2.90
9896 12320 5.749596 TCTCTCGCAAAAACAAAAGATGA 57.250 34.783 0.00 0.00 0.00 2.92
9897 12321 6.130298 TCTCTCGCAAAAACAAAAGATGAA 57.870 33.333 0.00 0.00 0.00 2.57
9898 12322 6.559810 TCTCTCGCAAAAACAAAAGATGAAA 58.440 32.000 0.00 0.00 0.00 2.69
9899 12323 7.032580 TCTCTCGCAAAAACAAAAGATGAAAA 58.967 30.769 0.00 0.00 0.00 2.29
9900 12324 7.543868 TCTCTCGCAAAAACAAAAGATGAAAAA 59.456 29.630 0.00 0.00 0.00 1.94
9901 12325 7.674564 TCTCGCAAAAACAAAAGATGAAAAAG 58.325 30.769 0.00 0.00 0.00 2.27
9902 12326 7.543868 TCTCGCAAAAACAAAAGATGAAAAAGA 59.456 29.630 0.00 0.00 0.00 2.52
9903 12327 8.023050 TCGCAAAAACAAAAGATGAAAAAGAA 57.977 26.923 0.00 0.00 0.00 2.52
9904 12328 8.499162 TCGCAAAAACAAAAGATGAAAAAGAAA 58.501 25.926 0.00 0.00 0.00 2.52
9905 12329 9.111702 CGCAAAAACAAAAGATGAAAAAGAAAA 57.888 25.926 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.431766 CGGACCTTTATCCTTCCAATCGT 60.432 47.826 0.00 0.00 36.52 3.73
28 29 1.064979 GCCGGACCTTTATCCTTCCAA 60.065 52.381 5.05 0.00 36.52 3.53
548 558 4.928661 AACTGTTGCATTCATCGTCTAC 57.071 40.909 0.00 0.00 0.00 2.59
704 714 4.142026 GGCTACACAGTTTTTCCAAAACCT 60.142 41.667 8.20 0.00 0.00 3.50
739 749 7.206687 AGTTGTGTTTCTTGTCTCAACAAAAA 58.793 30.769 0.00 0.00 44.53 1.94
740 750 6.744112 AGTTGTGTTTCTTGTCTCAACAAAA 58.256 32.000 0.00 0.00 44.53 2.44
741 751 6.325919 AGTTGTGTTTCTTGTCTCAACAAA 57.674 33.333 0.00 0.00 44.53 2.83
742 752 5.957842 AGTTGTGTTTCTTGTCTCAACAA 57.042 34.783 0.00 0.00 43.06 2.83
743 753 6.653320 AGTTAGTTGTGTTTCTTGTCTCAACA 59.347 34.615 0.00 0.00 39.17 3.33
744 754 6.961554 CAGTTAGTTGTGTTTCTTGTCTCAAC 59.038 38.462 0.00 0.00 37.91 3.18
745 755 6.653320 ACAGTTAGTTGTGTTTCTTGTCTCAA 59.347 34.615 0.00 0.00 0.00 3.02
746 756 6.170506 ACAGTTAGTTGTGTTTCTTGTCTCA 58.829 36.000 0.00 0.00 0.00 3.27
747 757 6.663944 ACAGTTAGTTGTGTTTCTTGTCTC 57.336 37.500 0.00 0.00 0.00 3.36
748 758 6.258068 GCTACAGTTAGTTGTGTTTCTTGTCT 59.742 38.462 0.00 0.00 32.56 3.41
749 759 6.036735 TGCTACAGTTAGTTGTGTTTCTTGTC 59.963 38.462 0.00 0.00 32.56 3.18
750 760 5.878116 TGCTACAGTTAGTTGTGTTTCTTGT 59.122 36.000 0.00 0.00 32.56 3.16
751 761 6.358118 TGCTACAGTTAGTTGTGTTTCTTG 57.642 37.500 0.00 0.00 32.56 3.02
752 762 7.095187 GCTATGCTACAGTTAGTTGTGTTTCTT 60.095 37.037 0.00 0.00 32.56 2.52
753 763 6.369065 GCTATGCTACAGTTAGTTGTGTTTCT 59.631 38.462 0.00 0.00 32.56 2.52
754 764 6.147164 TGCTATGCTACAGTTAGTTGTGTTTC 59.853 38.462 0.00 0.00 32.56 2.78
755 765 5.995282 TGCTATGCTACAGTTAGTTGTGTTT 59.005 36.000 0.00 0.00 32.56 2.83
756 766 5.547465 TGCTATGCTACAGTTAGTTGTGTT 58.453 37.500 0.00 0.00 32.56 3.32
757 767 5.147330 TGCTATGCTACAGTTAGTTGTGT 57.853 39.130 0.00 0.00 32.56 3.72
758 768 6.147821 ACTTTGCTATGCTACAGTTAGTTGTG 59.852 38.462 0.00 0.00 32.56 3.33
759 769 6.231211 ACTTTGCTATGCTACAGTTAGTTGT 58.769 36.000 0.00 0.00 35.09 3.32
760 770 6.727824 ACTTTGCTATGCTACAGTTAGTTG 57.272 37.500 0.00 0.00 0.00 3.16
761 771 6.934645 TCAACTTTGCTATGCTACAGTTAGTT 59.065 34.615 0.00 0.00 0.00 2.24
762 772 6.464222 TCAACTTTGCTATGCTACAGTTAGT 58.536 36.000 0.00 0.00 0.00 2.24
763 773 6.456181 GCTCAACTTTGCTATGCTACAGTTAG 60.456 42.308 0.00 0.00 0.00 2.34
764 774 5.351465 GCTCAACTTTGCTATGCTACAGTTA 59.649 40.000 0.00 0.00 0.00 2.24
765 775 4.154918 GCTCAACTTTGCTATGCTACAGTT 59.845 41.667 0.00 0.00 0.00 3.16
766 776 3.686726 GCTCAACTTTGCTATGCTACAGT 59.313 43.478 0.00 0.00 0.00 3.55
767 777 3.686241 TGCTCAACTTTGCTATGCTACAG 59.314 43.478 0.00 0.00 0.00 2.74
768 778 3.436704 GTGCTCAACTTTGCTATGCTACA 59.563 43.478 0.00 0.00 0.00 2.74
769 779 3.181506 GGTGCTCAACTTTGCTATGCTAC 60.182 47.826 0.00 0.00 0.00 3.58
770 780 3.009723 GGTGCTCAACTTTGCTATGCTA 58.990 45.455 0.00 0.00 0.00 3.49
771 781 1.815003 GGTGCTCAACTTTGCTATGCT 59.185 47.619 0.00 0.00 0.00 3.79
772 782 1.135286 GGGTGCTCAACTTTGCTATGC 60.135 52.381 0.00 0.00 0.00 3.14
773 783 1.131126 CGGGTGCTCAACTTTGCTATG 59.869 52.381 0.00 0.00 0.00 2.23
774 784 1.453155 CGGGTGCTCAACTTTGCTAT 58.547 50.000 0.00 0.00 0.00 2.97
775 785 1.234615 GCGGGTGCTCAACTTTGCTA 61.235 55.000 0.00 0.00 38.39 3.49
776 786 2.555547 GCGGGTGCTCAACTTTGCT 61.556 57.895 0.00 0.00 38.39 3.91
777 787 2.050077 GCGGGTGCTCAACTTTGC 60.050 61.111 0.00 0.00 38.39 3.68
778 788 2.644992 GGCGGGTGCTCAACTTTG 59.355 61.111 0.00 0.00 42.25 2.77
779 789 2.978010 CGGCGGGTGCTCAACTTT 60.978 61.111 0.00 0.00 42.25 2.66
791 801 3.869272 GAGATTGCACTGCGGCGG 61.869 66.667 9.78 7.39 36.28 6.13
792 802 3.869272 GGAGATTGCACTGCGGCG 61.869 66.667 0.51 0.51 36.28 6.46
793 803 2.437359 AGGAGATTGCACTGCGGC 60.437 61.111 0.00 0.00 33.57 6.53
794 804 1.078918 TGAGGAGATTGCACTGCGG 60.079 57.895 0.00 0.00 33.57 5.69
795 805 1.364626 GGTGAGGAGATTGCACTGCG 61.365 60.000 0.00 0.00 33.57 5.18
796 806 1.028868 GGGTGAGGAGATTGCACTGC 61.029 60.000 0.00 0.00 33.25 4.40
797 807 0.742281 CGGGTGAGGAGATTGCACTG 60.742 60.000 0.00 0.00 33.25 3.66
798 808 1.194781 ACGGGTGAGGAGATTGCACT 61.195 55.000 0.00 0.00 33.25 4.40
799 809 1.021390 CACGGGTGAGGAGATTGCAC 61.021 60.000 0.00 0.00 0.00 4.57
800 810 1.191489 TCACGGGTGAGGAGATTGCA 61.191 55.000 0.00 0.00 34.14 4.08
806 816 1.889530 GAGGGTTCACGGGTGAGGAG 61.890 65.000 1.37 0.00 41.13 3.69
857 867 1.076549 GTGATGGGCTTTGGGGACA 59.923 57.895 0.00 0.00 39.83 4.02
890 2394 0.726118 GCGCTGCTCGGTTCTTTTTC 60.726 55.000 0.00 0.00 38.94 2.29
920 2425 0.033894 ACGGAGGAGAGAAGGGAGAC 60.034 60.000 0.00 0.00 0.00 3.36
955 2460 3.402095 GAAACGGCTAGGAGGGGGC 62.402 68.421 0.00 0.00 0.00 5.80
957 2462 2.499685 CGAAACGGCTAGGAGGGG 59.500 66.667 0.00 0.00 0.00 4.79
958 2463 2.202892 GCGAAACGGCTAGGAGGG 60.203 66.667 0.00 0.00 0.00 4.30
959 2464 2.582498 CGCGAAACGGCTAGGAGG 60.582 66.667 0.00 0.00 38.44 4.30
960 2465 3.255379 GCGCGAAACGGCTAGGAG 61.255 66.667 12.10 0.00 43.93 3.69
1202 2711 1.229853 GGTTTGGGGAGGAGGAGGA 60.230 63.158 0.00 0.00 0.00 3.71
1203 2712 2.309504 GGGTTTGGGGAGGAGGAGG 61.310 68.421 0.00 0.00 0.00 4.30
1204 2713 0.044244 TAGGGTTTGGGGAGGAGGAG 59.956 60.000 0.00 0.00 0.00 3.69
1205 2714 0.499147 TTAGGGTTTGGGGAGGAGGA 59.501 55.000 0.00 0.00 0.00 3.71
1342 2851 2.656069 TTCTACTCACCTGGGCGCC 61.656 63.158 21.18 21.18 0.00 6.53
1352 2861 0.610174 CAGCCTGCTGGTTCTACTCA 59.390 55.000 11.31 0.00 40.17 3.41
1396 2905 2.264813 CGACGATAGAAGCGGGAAAAA 58.735 47.619 0.00 0.00 41.38 1.94
1397 2906 1.917273 CGACGATAGAAGCGGGAAAA 58.083 50.000 0.00 0.00 41.38 2.29
1398 2907 0.526954 GCGACGATAGAAGCGGGAAA 60.527 55.000 0.00 0.00 41.38 3.13
1399 2908 1.065273 GCGACGATAGAAGCGGGAA 59.935 57.895 0.00 0.00 41.38 3.97
1400 2909 1.452953 ATGCGACGATAGAAGCGGGA 61.453 55.000 0.00 0.00 42.75 5.14
1401 2910 0.597637 AATGCGACGATAGAAGCGGG 60.598 55.000 0.00 0.00 42.75 6.13
1402 2911 1.190323 GAAATGCGACGATAGAAGCGG 59.810 52.381 0.00 0.00 42.75 5.52
1413 2922 0.737715 AGGTGCTCGAGAAATGCGAC 60.738 55.000 18.75 2.45 33.71 5.19
1414 2923 0.037326 AAGGTGCTCGAGAAATGCGA 60.037 50.000 18.75 0.00 36.23 5.10
1677 3186 4.232221 ACTCTGCAAAAATGAAAGCATCG 58.768 39.130 0.00 0.00 36.28 3.84
1713 3222 1.492993 GCTTCACCCTCACCTTCCCT 61.493 60.000 0.00 0.00 0.00 4.20
1832 3341 3.384146 TGCATCACAATTCACAAACCTGT 59.616 39.130 0.00 0.00 35.63 4.00
1838 3347 5.598769 TGAAACATGCATCACAATTCACAA 58.401 33.333 0.00 0.00 29.62 3.33
1839 3348 5.197682 TGAAACATGCATCACAATTCACA 57.802 34.783 0.00 0.00 29.62 3.58
1840 3349 4.624024 CCTGAAACATGCATCACAATTCAC 59.376 41.667 0.00 0.00 30.75 3.18
1841 3350 4.322123 CCCTGAAACATGCATCACAATTCA 60.322 41.667 0.00 2.86 32.14 2.57
1842 3351 4.178540 CCCTGAAACATGCATCACAATTC 58.821 43.478 0.00 0.00 0.00 2.17
1843 3352 3.618019 GCCCTGAAACATGCATCACAATT 60.618 43.478 0.00 0.00 0.00 2.32
1844 3353 2.093869 GCCCTGAAACATGCATCACAAT 60.094 45.455 0.00 0.00 0.00 2.71
1885 3394 1.638467 GCTCGAATACGCAGCCAAG 59.362 57.895 0.00 0.00 37.01 3.61
1892 3401 1.160329 ATGCAAGGGCTCGAATACGC 61.160 55.000 0.00 0.00 41.91 4.42
1894 3403 5.120830 CACTAATATGCAAGGGCTCGAATAC 59.879 44.000 0.00 0.00 41.91 1.89
1968 3481 5.476599 AGCCATGCTAGTAAGTAGATCAGAG 59.523 44.000 0.00 0.00 36.99 3.35
1970 3483 5.618863 CGAGCCATGCTAGTAAGTAGATCAG 60.619 48.000 0.00 0.00 39.88 2.90
1980 3493 2.105993 TCTCTACCGAGCCATGCTAGTA 59.894 50.000 0.00 0.00 39.88 1.82
1985 3498 1.068250 GGTCTCTACCGAGCCATGC 59.932 63.158 0.00 0.00 35.62 4.06
2164 3692 5.520376 AGAAGATGGAAATTAATTGGCCG 57.480 39.130 0.39 0.00 0.00 6.13
2229 3758 6.948309 ACAGGATAAGCTTAAACTTGGATTGT 59.052 34.615 20.95 10.72 0.00 2.71
2236 3765 9.692749 GCTTTTAAACAGGATAAGCTTAAACTT 57.307 29.630 10.85 1.73 38.47 2.66
2248 3778 4.342092 ACACTGCAAGCTTTTAAACAGGAT 59.658 37.500 0.00 0.00 37.60 3.24
2249 3779 3.699038 ACACTGCAAGCTTTTAAACAGGA 59.301 39.130 0.00 0.00 37.60 3.86
2304 3900 8.641498 ATGTGTCTCACTAAATTCCTCAAAAT 57.359 30.769 1.72 0.00 35.11 1.82
2314 3913 6.805016 ATCTCTGGATGTGTCTCACTAAAT 57.195 37.500 1.72 0.00 35.11 1.40
2317 3916 4.142071 GCAATCTCTGGATGTGTCTCACTA 60.142 45.833 1.72 0.00 35.11 2.74
2330 3953 4.187694 GTTAAGGAGTCTGCAATCTCTGG 58.812 47.826 14.60 0.00 0.00 3.86
2360 3983 8.833231 TCTTTGTAAGAAGTAACAAGGAGATG 57.167 34.615 0.00 0.00 36.95 2.90
2387 4010 0.673333 TACAGCCATGGCACTCAACG 60.673 55.000 37.18 17.95 44.88 4.10
2460 4083 1.783365 TCTAGCTCAGGATAGCAGGGA 59.217 52.381 0.00 0.00 45.30 4.20
2462 4085 2.170166 CCTCTAGCTCAGGATAGCAGG 58.830 57.143 5.81 0.00 45.30 4.85
2554 4177 9.554395 TGTTTCTCACTAATGAAATCACACTAA 57.446 29.630 0.00 0.00 35.13 2.24
2628 4252 1.462616 TGATGTACATTGGCCAGCAC 58.537 50.000 10.30 3.25 0.00 4.40
2631 4255 5.766670 ACAATAGATGATGTACATTGGCCAG 59.233 40.000 10.30 0.00 39.56 4.85
2744 4368 5.127682 AGAAGCACTTTGACAACCTTTTGAT 59.872 36.000 0.00 0.00 36.48 2.57
2810 4434 6.401047 GCACGCTTTCTTGGATTTTTATTTCC 60.401 38.462 0.00 0.00 0.00 3.13
2960 4584 6.564709 TCAAGATCATCAAAACACAAGGAG 57.435 37.500 0.00 0.00 0.00 3.69
2961 4585 6.957920 TTCAAGATCATCAAAACACAAGGA 57.042 33.333 0.00 0.00 0.00 3.36
3013 5160 4.762289 ACTTATCTGGTAAAGCTCCTGG 57.238 45.455 0.00 0.00 0.00 4.45
3473 5626 4.649088 AACTGGGTTAGTTCAAAACTGC 57.351 40.909 2.65 0.00 46.55 4.40
3491 5644 5.751243 AATAAGTGTCGCAGTTTTGAACT 57.249 34.783 5.46 0.00 44.06 3.01
3492 5645 6.291585 CCAAAATAAGTGTCGCAGTTTTGAAC 60.292 38.462 16.09 0.00 38.26 3.18
3493 5646 5.746245 CCAAAATAAGTGTCGCAGTTTTGAA 59.254 36.000 16.09 0.00 38.26 2.69
3495 5648 5.277825 TCCAAAATAAGTGTCGCAGTTTTG 58.722 37.500 5.46 11.07 36.70 2.44
3496 5649 5.508200 TCCAAAATAAGTGTCGCAGTTTT 57.492 34.783 5.46 0.00 0.00 2.43
3498 5651 4.142902 CGATCCAAAATAAGTGTCGCAGTT 60.143 41.667 5.48 5.48 0.00 3.16
3499 5652 3.370978 CGATCCAAAATAAGTGTCGCAGT 59.629 43.478 0.00 0.00 0.00 4.40
3500 5653 3.242413 CCGATCCAAAATAAGTGTCGCAG 60.242 47.826 0.00 0.00 0.00 5.18
3503 5656 3.555956 CCTCCGATCCAAAATAAGTGTCG 59.444 47.826 0.00 0.00 0.00 4.35
3504 5657 3.877508 CCCTCCGATCCAAAATAAGTGTC 59.122 47.826 0.00 0.00 0.00 3.67
4128 6287 0.327000 ACATCAAGGAGGGGAGGAGG 60.327 60.000 0.00 0.00 0.00 4.30
4129 6288 1.589414 AACATCAAGGAGGGGAGGAG 58.411 55.000 0.00 0.00 0.00 3.69
4130 6289 2.059756 AAACATCAAGGAGGGGAGGA 57.940 50.000 0.00 0.00 0.00 3.71
4455 6615 5.565509 TGCCAATAGTATTTGACAGGAACA 58.434 37.500 0.00 0.00 0.00 3.18
4472 6632 8.938801 TGTATCATGGATAGTTAAATGCCAAT 57.061 30.769 3.91 0.00 31.53 3.16
4488 6649 9.590451 AGCAACTGAAATTTAAATGTATCATGG 57.410 29.630 0.39 0.45 0.00 3.66
4548 6709 2.290641 CACGAACCTTTGTTCCAGAAGG 59.709 50.000 0.00 0.80 46.67 3.46
4806 6967 9.219603 TGAAATATGGAAGTACTTTGTCTCTTG 57.780 33.333 10.02 0.00 0.00 3.02
4916 7077 7.337942 CCTTGTTATTCTATCTCAAAGCCTGTT 59.662 37.037 0.00 0.00 0.00 3.16
4917 7078 6.825721 CCTTGTTATTCTATCTCAAAGCCTGT 59.174 38.462 0.00 0.00 0.00 4.00
4918 7079 6.238593 GCCTTGTTATTCTATCTCAAAGCCTG 60.239 42.308 0.00 0.00 0.00 4.85
5039 7203 0.179032 TGGTGCGATGGTTTGTCTGT 60.179 50.000 0.00 0.00 0.00 3.41
5040 7204 0.238289 GTGGTGCGATGGTTTGTCTG 59.762 55.000 0.00 0.00 0.00 3.51
5041 7205 0.108585 AGTGGTGCGATGGTTTGTCT 59.891 50.000 0.00 0.00 0.00 3.41
5042 7206 0.517316 GAGTGGTGCGATGGTTTGTC 59.483 55.000 0.00 0.00 0.00 3.18
5043 7207 0.179032 TGAGTGGTGCGATGGTTTGT 60.179 50.000 0.00 0.00 0.00 2.83
5266 7430 6.088217 CACACTCGTAAATAGACTGTGAGTTG 59.912 42.308 0.00 0.00 35.73 3.16
5362 7681 6.855914 CAGTGAAACACCAATACACATTACAC 59.144 38.462 0.00 0.00 41.43 2.90
5563 7882 6.401955 ACTTTCAAATGAAAAACAACACCG 57.598 33.333 9.63 0.00 42.72 4.94
5594 7913 8.878769 TCAAAAGAAAATTGCTACCAAGAAAAC 58.121 29.630 0.00 0.00 33.80 2.43
6037 8411 4.838665 ACAGTGCAAAAATTTTGACACG 57.161 36.364 25.03 22.54 34.25 4.49
6106 8483 0.603975 AGGGAGTCGAAAGTGCTTGC 60.604 55.000 0.00 0.00 0.00 4.01
6117 8494 6.929625 AGAATTCATATACATGAGGGAGTCG 58.070 40.000 8.44 0.00 42.11 4.18
6189 8566 1.016627 CGTCCATATTGCACACAGGG 58.983 55.000 0.00 0.00 0.00 4.45
6212 8589 2.836636 ACAGGAGCATGAGAGTAGGA 57.163 50.000 0.00 0.00 0.00 2.94
6237 8614 0.796312 CCACATTACAGCGTGTGTCC 59.204 55.000 4.99 0.00 43.14 4.02
6245 8622 2.482326 GCTGACCCCACATTACAGC 58.518 57.895 0.00 0.00 44.88 4.40
6254 8631 0.840617 TGTTTGTACTGCTGACCCCA 59.159 50.000 0.00 0.00 0.00 4.96
6296 8673 1.672356 ACAAGCGATCCTGGTGTGC 60.672 57.895 0.00 0.00 0.00 4.57
6370 8747 5.653769 CCAAGGGATGCTTTCTCAAGATAAA 59.346 40.000 0.00 0.00 30.57 1.40
6411 8788 2.962421 AGAAGGGCATCAAAACCGAAAA 59.038 40.909 0.00 0.00 0.00 2.29
6429 8806 8.727100 TCATAGGCCAAGAATCTTATAGAGAA 57.273 34.615 5.01 0.00 38.06 2.87
6435 8812 8.055181 TCTTGTTTCATAGGCCAAGAATCTTAT 58.945 33.333 5.01 0.00 40.07 1.73
6442 8822 4.072131 GTGTCTTGTTTCATAGGCCAAGA 58.928 43.478 5.01 0.00 40.57 3.02
6486 8868 1.001641 CTTGGAAGAGGGCAGTGGG 60.002 63.158 0.00 0.00 0.00 4.61
6489 8871 1.377994 CTGCTTGGAAGAGGGCAGT 59.622 57.895 0.00 0.00 44.69 4.40
6492 8874 0.957888 GTGTCTGCTTGGAAGAGGGC 60.958 60.000 0.00 0.00 0.00 5.19
6515 8897 2.383683 ACTCCAGAGCTATAGGGCCATA 59.616 50.000 6.18 0.43 0.00 2.74
6516 8898 1.150986 ACTCCAGAGCTATAGGGCCAT 59.849 52.381 6.18 0.00 0.00 4.40
6517 8899 0.563173 ACTCCAGAGCTATAGGGCCA 59.437 55.000 6.18 0.00 0.00 5.36
6518 8900 0.972883 CACTCCAGAGCTATAGGGCC 59.027 60.000 0.00 0.00 0.00 5.80
6519 8901 0.320050 GCACTCCAGAGCTATAGGGC 59.680 60.000 1.04 0.00 0.00 5.19
6602 8984 5.221382 GCAAATGCATATTGTCTGGGAGATT 60.221 40.000 17.25 0.00 41.59 2.40
6738 9120 6.845908 AGAGGCATAAATACATGGTCTTGAT 58.154 36.000 0.00 0.00 0.00 2.57
6739 9121 6.252599 AGAGGCATAAATACATGGTCTTGA 57.747 37.500 0.00 0.00 0.00 3.02
6787 9169 8.360390 TCGCATACTATTAATGAGAATGTCAGT 58.640 33.333 0.00 0.00 39.07 3.41
6899 9281 6.463995 TGAATGGCTCATTAAATGGTAACC 57.536 37.500 1.06 0.00 33.90 2.85
6904 9286 5.209818 AGCATGAATGGCTCATTAAATGG 57.790 39.130 0.00 3.52 42.46 3.16
7049 9431 7.751732 TGATGTTAAGTGCAGTACATTCATTC 58.248 34.615 10.55 1.12 31.76 2.67
7358 9740 6.200854 GGAAAGTGTTTCAAAAGGTTATGCAG 59.799 38.462 0.00 0.00 41.43 4.41
7577 9959 5.065090 GCCATTTTCCATATTTCCAAACAGC 59.935 40.000 0.00 0.00 0.00 4.40
7967 10350 7.701924 TGAAAATTGCAGCTGCTTATTATACAC 59.298 33.333 36.61 21.89 42.66 2.90
8364 10748 4.102838 AGAATGAGGGGAGATGTGAATCAG 59.897 45.833 0.00 0.00 0.00 2.90
8378 10762 8.970859 AAAATATAGAACTGTGAGAATGAGGG 57.029 34.615 0.00 0.00 0.00 4.30
8497 10884 3.721035 TCACCGTCTATGATTGCAGATG 58.279 45.455 0.00 0.00 0.00 2.90
8525 10912 3.507162 TGGAAATTGGAGTTCAGAGCA 57.493 42.857 0.00 0.00 0.00 4.26
8824 11213 6.069673 ACATTGGGAACACTCCACATAATCTA 60.070 38.462 0.00 0.00 44.51 1.98
8898 11306 0.609131 AATCCCCAAGCTTGTCACGG 60.609 55.000 24.35 17.42 0.00 4.94
9179 11594 1.486310 AGCTCAACCACTCACTGACAA 59.514 47.619 0.00 0.00 0.00 3.18
9215 11630 4.993905 ACTTTGTTCTTTTAGCTTGCGTT 58.006 34.783 0.00 0.00 0.00 4.84
9435 11851 6.914215 GTGGTAAGCAATCATCATTACATGTG 59.086 38.462 9.11 0.00 31.25 3.21
9449 11865 3.776969 TCCTCATCAGAGTGGTAAGCAAT 59.223 43.478 0.00 0.00 40.40 3.56
9533 11950 8.393366 CAAACGAGATTGACATTGATATGAAGT 58.607 33.333 0.00 0.00 35.65 3.01
9538 11955 8.498054 AGAACAAACGAGATTGACATTGATAT 57.502 30.769 0.00 0.00 34.38 1.63
9539 11956 7.905604 AGAACAAACGAGATTGACATTGATA 57.094 32.000 0.00 0.00 34.38 2.15
9572 11993 4.452455 ACATCTTCAAACTTTAGCACTCCG 59.548 41.667 0.00 0.00 0.00 4.63
9615 12036 8.603242 ATTGTTAGAGATTTACAAGACAACGT 57.397 30.769 0.00 0.00 35.48 3.99
9788 12212 6.462500 CATAGATCCAGCAGCAAGTAGTAAT 58.538 40.000 0.00 0.00 0.00 1.89
9799 12223 2.364647 TCTGACAGCATAGATCCAGCAG 59.635 50.000 0.00 0.00 0.00 4.24
9800 12224 2.102084 GTCTGACAGCATAGATCCAGCA 59.898 50.000 2.24 0.00 0.00 4.41
9849 12273 8.664211 AACGGCCTTAAGATTCTAGAAAATAG 57.336 34.615 9.71 3.33 0.00 1.73
9852 12276 6.708285 AGAACGGCCTTAAGATTCTAGAAAA 58.292 36.000 9.71 0.00 0.00 2.29
9864 12288 0.319083 TTGCGAGAGAACGGCCTTAA 59.681 50.000 0.00 0.00 0.00 1.85
9875 12299 6.810888 TTTCATCTTTTGTTTTTGCGAGAG 57.189 33.333 0.00 0.00 0.00 3.20
9876 12300 7.543868 TCTTTTTCATCTTTTGTTTTTGCGAGA 59.456 29.630 0.00 0.00 0.00 4.04
9877 12301 7.674564 TCTTTTTCATCTTTTGTTTTTGCGAG 58.325 30.769 0.00 0.00 0.00 5.03
9878 12302 7.588143 TCTTTTTCATCTTTTGTTTTTGCGA 57.412 28.000 0.00 0.00 0.00 5.10
9879 12303 8.652592 TTTCTTTTTCATCTTTTGTTTTTGCG 57.347 26.923 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.