Multiple sequence alignment - TraesCS2D01G367600

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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 TraesCS2D01G367600 chr2D 100.000 3446 0 0 1 3446 472231171 472227726 0.000000e+00 6364.0
1 TraesCS2D01G367600 chr2D 86.819 1047 85 25 1426 2454 472442586 472441575 0.000000e+00 1120.0
2 TraesCS2D01G367600 chr2D 88.433 683 58 11 737 1414 472443918 472443252 0.000000e+00 804.0
3 TraesCS2D01G367600 chr2D 87.928 497 47 4 256 740 472445259 472444764 1.070000e-159 573.0
4 TraesCS2D01G367600 chr2D 82.933 375 58 6 2075 2446 472130409 472130038 1.980000e-87 333.0
5 TraesCS2D01G367600 chr2D 98.077 52 1 0 1 52 296173714 296173765 1.320000e-14 91.6
6 TraesCS2D01G367600 chr2A 87.436 2754 157 58 737 3444 613701036 613698426 0.000000e+00 2994.0
7 TraesCS2D01G367600 chr2A 94.326 705 30 4 46 740 613703628 613702924 0.000000e+00 1072.0
8 TraesCS2D01G367600 chr2A 85.211 852 80 24 1426 2263 613876393 613875574 0.000000e+00 833.0
9 TraesCS2D01G367600 chr2A 88.933 506 43 4 247 740 613878064 613877560 2.270000e-171 612.0
10 TraesCS2D01G367600 chr2A 82.107 693 50 31 737 1412 613877289 613876654 3.050000e-145 525.0
11 TraesCS2D01G367600 chr2A 78.562 737 135 16 1729 2457 613689348 613688627 6.740000e-127 464.0
12 TraesCS2D01G367600 chr2A 81.989 372 63 4 2077 2446 613476663 613476294 2.580000e-81 313.0
13 TraesCS2D01G367600 chr2A 91.324 219 19 0 2253 2471 613874805 613874587 2.010000e-77 300.0
14 TraesCS2D01G367600 chr2A 76.417 441 76 14 1119 1558 613689795 613689382 2.690000e-51 213.0
15 TraesCS2D01G367600 chr2B 94.310 703 31 5 46 740 551534816 551534115 0.000000e+00 1068.0
16 TraesCS2D01G367600 chr2B 90.068 735 66 7 1740 2471 551564953 551564223 0.000000e+00 946.0
17 TraesCS2D01G367600 chr2B 85.815 853 70 22 737 1572 551566029 551565211 0.000000e+00 857.0
18 TraesCS2D01G367600 chr2B 84.951 618 64 17 136 740 551566901 551566300 1.770000e-167 599.0
19 TraesCS2D01G367600 chr2B 82.306 373 64 2 2075 2446 551448884 551448513 4.290000e-84 322.0
20 TraesCS2D01G367600 chr2B 80.287 279 54 1 1124 1402 551399560 551399283 3.480000e-50 209.0
21 TraesCS2D01G367600 chr7A 81.985 272 39 5 1128 1390 68211424 68211694 4.480000e-54 222.0
22 TraesCS2D01G367600 chr7A 78.947 266 52 3 1128 1390 70182815 70183079 9.830000e-41 178.0
23 TraesCS2D01G367600 chr7B 80.147 272 40 9 1130 1390 5942806 5943074 1.260000e-44 191.0
24 TraesCS2D01G367600 chr1D 98.148 54 1 0 1 54 422315929 422315982 1.020000e-15 95.3
25 TraesCS2D01G367600 chr1D 96.364 55 2 0 1 55 13037319 13037373 1.320000e-14 91.6
26 TraesCS2D01G367600 chr1D 96.429 56 1 1 1 55 413538371 413538316 1.320000e-14 91.6
27 TraesCS2D01G367600 chr3B 98.113 53 1 0 1 53 489058841 489058893 3.660000e-15 93.5
28 TraesCS2D01G367600 chrUn 96.364 55 2 0 1 55 36921025 36921079 1.320000e-14 91.6
29 TraesCS2D01G367600 chrUn 96.364 55 2 0 1 55 37006401 37006455 1.320000e-14 91.6
30 TraesCS2D01G367600 chrUn 96.364 55 2 0 1 55 38258622 38258676 1.320000e-14 91.6
31 TraesCS2D01G367600 chrUn 96.364 55 2 0 1 55 196709608 196709554 1.320000e-14 91.6


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 TraesCS2D01G367600 chr2D 472227726 472231171 3445 True 6364.000000 6364 100.000000 1 3446 1 chr2D.!!$R2 3445
1 TraesCS2D01G367600 chr2D 472441575 472445259 3684 True 832.333333 1120 87.726667 256 2454 3 chr2D.!!$R3 2198
2 TraesCS2D01G367600 chr2A 613698426 613703628 5202 True 2033.000000 2994 90.881000 46 3444 2 chr2A.!!$R3 3398
3 TraesCS2D01G367600 chr2A 613874587 613878064 3477 True 567.500000 833 86.893750 247 2471 4 chr2A.!!$R4 2224
4 TraesCS2D01G367600 chr2A 613688627 613689795 1168 True 338.500000 464 77.489500 1119 2457 2 chr2A.!!$R2 1338
5 TraesCS2D01G367600 chr2B 551534115 551534816 701 True 1068.000000 1068 94.310000 46 740 1 chr2B.!!$R3 694
6 TraesCS2D01G367600 chr2B 551564223 551566901 2678 True 800.666667 946 86.944667 136 2471 3 chr2B.!!$R4 2335

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
967 3518 0.463204 ATCGACCTCTGCCATCACAG 59.537 55.0 0.00 0.0 39.12 3.66 F
2221 5627 0.319297 GTTCTCGGCGTACAAGGTGT 60.319 55.0 6.85 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 6622 0.248907 CGCCGGTATCTCACACGAAT 60.249 55.0 1.9 0.0 0.00 3.34 R
3309 7526 0.472471 TCAAGGGGTGAAGGTGTGTC 59.528 55.0 0.0 0.0 31.51 3.67 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 6.823678 CTACACTAGTGTCAAAAACGTTCT 57.176 37.500 31.11 5.44 43.74 3.01
24 25 7.230466 CTACACTAGTGTCAAAAACGTTCTT 57.770 36.000 31.11 4.99 43.74 2.52
25 26 8.343974 CTACACTAGTGTCAAAAACGTTCTTA 57.656 34.615 31.11 8.36 43.74 2.10
26 27 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
27 28 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
28 29 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
34 35 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
35 36 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
36 37 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
37 38 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
38 39 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
39 40 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
40 41 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
41 42 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
42 43 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
43 44 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
44 45 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
57 58 2.531771 GGAGGGAGTAAGAGATAGGGC 58.468 57.143 0.00 0.00 0.00 5.19
60 61 3.513515 GAGGGAGTAAGAGATAGGGCATG 59.486 52.174 0.00 0.00 0.00 4.06
112 113 6.751888 AGTTTAACTTGTTTTGTCAGATGCAC 59.248 34.615 0.00 0.00 0.00 4.57
145 146 6.165659 TCTTATTTCAGTTTAGCTTCGTGC 57.834 37.500 0.00 0.00 43.29 5.34
162 163 6.458206 GCTTCGTGCTCATTCCAAATAATACA 60.458 38.462 0.00 0.00 38.95 2.29
243 245 4.657039 TCATCCTTCATCATCTCCATGTGA 59.343 41.667 0.00 0.00 0.00 3.58
251 253 7.563888 TCATCATCTCCATGTGATCTTTTTC 57.436 36.000 0.00 0.00 32.98 2.29
323 333 4.034048 TCGTTTTCTTGAGCAGAACTTCAC 59.966 41.667 0.00 0.00 41.56 3.18
574 584 2.548057 GGTTTTGTCAAGAGCGACATGA 59.452 45.455 0.00 0.00 45.03 3.07
686 696 0.916086 TTTGATAGGGATGGCGTGGT 59.084 50.000 0.00 0.00 0.00 4.16
690 700 0.980754 ATAGGGATGGCGTGGTGTCA 60.981 55.000 0.00 0.00 36.02 3.58
821 3340 2.202272 CCGGACGAAGACGACGAC 60.202 66.667 0.00 0.00 42.10 4.34
822 3341 2.570068 CGGACGAAGACGACGACG 60.570 66.667 5.58 5.58 42.10 5.12
823 3342 2.856032 GGACGAAGACGACGACGA 59.144 61.111 15.32 0.00 42.66 4.20
911 3455 3.570550 ACCATAACCGTCTCAGATAGCTC 59.429 47.826 0.00 0.00 0.00 4.09
917 3461 3.329520 ACCGTCTCAGATAGCTCTAGGAT 59.670 47.826 0.00 0.00 0.00 3.24
935 3479 4.886579 AGGATTTTTGGTGTCAAGATTGC 58.113 39.130 0.00 0.00 33.98 3.56
967 3518 0.463204 ATCGACCTCTGCCATCACAG 59.537 55.000 0.00 0.00 39.12 3.66
1024 3580 2.771762 GAGCCATCCTCCCCAGCT 60.772 66.667 0.00 0.00 34.35 4.24
1044 3622 3.395639 CTTGCCAAACACGAGGTTAGTA 58.604 45.455 0.00 0.00 39.29 1.82
1046 3624 3.592059 TGCCAAACACGAGGTTAGTATC 58.408 45.455 0.00 0.00 39.29 2.24
1048 3626 3.369157 GCCAAACACGAGGTTAGTATCCT 60.369 47.826 0.00 0.00 39.29 3.24
1049 3627 4.142093 GCCAAACACGAGGTTAGTATCCTA 60.142 45.833 0.00 0.00 39.29 2.94
1050 3628 5.452917 GCCAAACACGAGGTTAGTATCCTAT 60.453 44.000 0.00 0.00 39.29 2.57
1051 3629 6.239120 GCCAAACACGAGGTTAGTATCCTATA 60.239 42.308 0.00 0.00 39.29 1.31
1053 3631 7.014038 CCAAACACGAGGTTAGTATCCTATACT 59.986 40.741 0.00 5.04 39.29 2.12
1058 3636 9.029243 CACGAGGTTAGTATCCTATACTATACG 57.971 40.741 7.44 11.46 35.20 3.06
1079 3657 0.718343 GCTTAGCAGCTCTTGACGTG 59.282 55.000 0.00 0.00 43.51 4.49
1126 3704 2.995283 TGCAAGAATCTCATCCACTGG 58.005 47.619 0.00 0.00 0.00 4.00
1133 3711 1.133181 TCTCATCCACTGGGGTTGCA 61.133 55.000 1.98 0.00 36.48 4.08
1319 3899 2.105128 CTGGAGATCACGGACGCC 59.895 66.667 0.00 0.00 0.00 5.68
1386 3966 4.479619 CAAGCTAAACATTCTGGCAAGTC 58.520 43.478 0.00 0.00 0.00 3.01
1434 4693 0.387929 GTATACCACGGCTGCTAGCA 59.612 55.000 18.22 18.22 44.75 3.49
1637 4905 2.661176 ATACTCCTGGAGGAACCCAA 57.339 50.000 26.56 4.55 44.91 4.12
1657 4925 1.285078 ACCAAGAACCAAGGATAGGCC 59.715 52.381 0.00 0.00 0.00 5.19
1704 4980 7.138736 ACTTGATTGGTTCATTCGTTAAAGTG 58.861 34.615 0.00 0.00 33.34 3.16
1884 5277 1.271656 GTGCAGACCAACTACTACGGT 59.728 52.381 0.00 0.00 35.12 4.83
1887 5280 2.751806 GCAGACCAACTACTACGGTACT 59.248 50.000 0.00 0.00 31.63 2.73
1935 5328 0.396435 TGCTTCAAGCTTCCTCCGAA 59.604 50.000 11.57 0.00 42.97 4.30
1991 5384 5.270794 ACTGCTAAGGGTAAGTAAGCTAGT 58.729 41.667 0.00 0.00 34.28 2.57
1992 5385 6.430007 ACTGCTAAGGGTAAGTAAGCTAGTA 58.570 40.000 0.00 0.00 34.28 1.82
2039 5445 3.674997 AGCTAACCCAGTACAACATGTG 58.325 45.455 0.00 0.00 0.00 3.21
2070 5476 4.626604 CCGTGTCAATTTTTGCAGCATATT 59.373 37.500 0.00 0.00 0.00 1.28
2130 5536 3.488423 CTGACACAGGGGAGGCTT 58.512 61.111 0.00 0.00 0.00 4.35
2187 5593 1.522355 CGGCTCGTTGGAGATGCAT 60.522 57.895 0.00 0.00 43.27 3.96
2221 5627 0.319297 GTTCTCGGCGTACAAGGTGT 60.319 55.000 6.85 0.00 0.00 4.16
2275 6461 2.681778 CGAGGAGGCACCCTGAGT 60.682 66.667 3.07 0.00 40.05 3.41
2286 6472 2.034879 CCCTGAGTTGCGCGTCAAT 61.035 57.895 16.68 8.05 36.99 2.57
2502 6688 2.831597 GTGCCGTACACTGGGTTAC 58.168 57.895 0.00 0.00 46.41 2.50
2543 6729 2.159240 ACGTGCTAGATTGAGATTGCGA 60.159 45.455 0.00 0.00 0.00 5.10
2544 6730 2.860136 CGTGCTAGATTGAGATTGCGAA 59.140 45.455 0.00 0.00 0.00 4.70
2545 6731 3.492383 CGTGCTAGATTGAGATTGCGAAT 59.508 43.478 0.00 0.00 0.00 3.34
2546 6732 4.681483 CGTGCTAGATTGAGATTGCGAATA 59.319 41.667 0.00 0.00 0.00 1.75
2547 6733 5.175673 CGTGCTAGATTGAGATTGCGAATAA 59.824 40.000 0.00 0.00 0.00 1.40
2548 6734 6.588552 GTGCTAGATTGAGATTGCGAATAAG 58.411 40.000 0.00 0.00 0.00 1.73
2549 6735 6.422100 GTGCTAGATTGAGATTGCGAATAAGA 59.578 38.462 0.00 0.00 0.00 2.10
2550 6736 7.117523 GTGCTAGATTGAGATTGCGAATAAGAT 59.882 37.037 0.00 0.00 0.00 2.40
2551 6737 7.117379 TGCTAGATTGAGATTGCGAATAAGATG 59.883 37.037 0.00 0.00 0.00 2.90
2552 6738 7.117523 GCTAGATTGAGATTGCGAATAAGATGT 59.882 37.037 0.00 0.00 0.00 3.06
2553 6739 7.187244 AGATTGAGATTGCGAATAAGATGTG 57.813 36.000 0.00 0.00 0.00 3.21
2554 6740 6.765036 AGATTGAGATTGCGAATAAGATGTGT 59.235 34.615 0.00 0.00 0.00 3.72
2555 6741 5.973651 TGAGATTGCGAATAAGATGTGTC 57.026 39.130 0.00 0.00 0.00 3.67
2556 6742 5.664457 TGAGATTGCGAATAAGATGTGTCT 58.336 37.500 0.00 0.00 35.82 3.41
2557 6743 6.108687 TGAGATTGCGAATAAGATGTGTCTT 58.891 36.000 0.00 0.00 46.22 3.01
2558 6744 6.595326 TGAGATTGCGAATAAGATGTGTCTTT 59.405 34.615 0.00 0.00 41.92 2.52
2559 6745 7.119699 TGAGATTGCGAATAAGATGTGTCTTTT 59.880 33.333 0.00 0.00 41.92 2.27
2560 6746 7.467623 AGATTGCGAATAAGATGTGTCTTTTC 58.532 34.615 0.00 1.16 41.92 2.29
2561 6747 6.801539 TTGCGAATAAGATGTGTCTTTTCT 57.198 33.333 0.00 0.00 41.92 2.52
2562 6748 6.801539 TGCGAATAAGATGTGTCTTTTCTT 57.198 33.333 0.00 0.00 41.92 2.52
2563 6749 7.202016 TGCGAATAAGATGTGTCTTTTCTTT 57.798 32.000 0.00 0.00 41.92 2.52
2564 6750 7.648142 TGCGAATAAGATGTGTCTTTTCTTTT 58.352 30.769 0.00 0.00 41.92 2.27
2565 6751 8.779303 TGCGAATAAGATGTGTCTTTTCTTTTA 58.221 29.630 0.00 0.00 41.92 1.52
2566 6752 9.267096 GCGAATAAGATGTGTCTTTTCTTTTAG 57.733 33.333 0.00 0.00 41.92 1.85
2567 6753 9.760660 CGAATAAGATGTGTCTTTTCTTTTAGG 57.239 33.333 0.00 0.00 41.92 2.69
2569 6755 9.807921 AATAAGATGTGTCTTTTCTTTTAGGGA 57.192 29.630 0.00 0.00 41.92 4.20
2609 6795 4.340097 TCACAAGAAACAGACTACCGAGAA 59.660 41.667 0.00 0.00 0.00 2.87
2610 6796 5.047847 CACAAGAAACAGACTACCGAGAAA 58.952 41.667 0.00 0.00 0.00 2.52
2613 6799 5.272283 AGAAACAGACTACCGAGAAAACA 57.728 39.130 0.00 0.00 0.00 2.83
2615 6801 4.395959 AACAGACTACCGAGAAAACACA 57.604 40.909 0.00 0.00 0.00 3.72
2620 6806 3.714391 ACTACCGAGAAAACACACTCAC 58.286 45.455 0.00 0.00 33.86 3.51
2650 6836 4.080863 AGGCTACCGAAAAATCATGAGAGT 60.081 41.667 0.09 0.00 0.00 3.24
2651 6837 5.128827 AGGCTACCGAAAAATCATGAGAGTA 59.871 40.000 0.09 0.00 0.00 2.59
2736 6926 4.737765 GCTTCAACAGTTTGATAAACGCAA 59.262 37.500 0.00 0.00 45.88 4.85
2749 6939 0.392998 AACGCAATAGTGGGAGCCTG 60.393 55.000 14.55 0.00 40.06 4.85
2768 6958 4.522789 GCCTGTTGGACCAGAAAGAAATTA 59.477 41.667 0.00 0.00 34.23 1.40
2774 6964 6.603940 TGGACCAGAAAGAAATTAAATGGG 57.396 37.500 0.00 0.00 0.00 4.00
2776 6966 5.187772 GGACCAGAAAGAAATTAAATGGGCT 59.812 40.000 0.00 0.00 34.65 5.19
2777 6967 6.379988 GGACCAGAAAGAAATTAAATGGGCTA 59.620 38.462 0.00 0.00 34.65 3.93
2778 6968 7.410120 ACCAGAAAGAAATTAAATGGGCTAG 57.590 36.000 0.00 0.00 0.00 3.42
2779 6969 6.127338 ACCAGAAAGAAATTAAATGGGCTAGC 60.127 38.462 6.04 6.04 0.00 3.42
2780 6970 6.276091 CAGAAAGAAATTAAATGGGCTAGCC 58.724 40.000 26.55 26.55 0.00 3.93
2807 7007 1.697982 GCCCACTGGTACCCTATTAGG 59.302 57.143 10.07 2.43 34.30 2.69
2813 7013 2.572104 CTGGTACCCTATTAGGCCATCC 59.428 54.545 10.07 4.77 32.73 3.51
2815 7015 2.305052 GGTACCCTATTAGGCCATCCAC 59.695 54.545 5.01 0.00 32.73 4.02
2823 7023 3.492102 TTAGGCCATCCACATAGCTTC 57.508 47.619 5.01 0.00 33.74 3.86
2824 7024 1.516110 AGGCCATCCACATAGCTTCT 58.484 50.000 5.01 0.00 33.74 2.85
2825 7025 1.849039 AGGCCATCCACATAGCTTCTT 59.151 47.619 5.01 0.00 33.74 2.52
2826 7026 2.158696 AGGCCATCCACATAGCTTCTTC 60.159 50.000 5.01 0.00 33.74 2.87
2827 7027 2.158696 GGCCATCCACATAGCTTCTTCT 60.159 50.000 0.00 0.00 0.00 2.85
2828 7028 3.071602 GGCCATCCACATAGCTTCTTCTA 59.928 47.826 0.00 0.00 0.00 2.10
2829 7029 4.444876 GGCCATCCACATAGCTTCTTCTAA 60.445 45.833 0.00 0.00 0.00 2.10
2830 7030 5.126067 GCCATCCACATAGCTTCTTCTAAA 58.874 41.667 0.00 0.00 0.00 1.85
2831 7031 5.590259 GCCATCCACATAGCTTCTTCTAAAA 59.410 40.000 0.00 0.00 0.00 1.52
2832 7032 6.095440 GCCATCCACATAGCTTCTTCTAAAAA 59.905 38.462 0.00 0.00 0.00 1.94
2851 7051 2.834638 AAAAGGCCATCCACATAGCT 57.165 45.000 5.01 0.00 33.74 3.32
2852 7052 2.834638 AAAGGCCATCCACATAGCTT 57.165 45.000 5.01 0.00 33.74 3.74
2853 7053 2.355010 AAGGCCATCCACATAGCTTC 57.645 50.000 5.01 0.00 33.74 3.86
2854 7054 1.516110 AGGCCATCCACATAGCTTCT 58.484 50.000 5.01 0.00 33.74 2.85
2855 7055 1.419387 AGGCCATCCACATAGCTTCTC 59.581 52.381 5.01 0.00 33.74 2.87
2856 7056 1.141657 GGCCATCCACATAGCTTCTCA 59.858 52.381 0.00 0.00 0.00 3.27
2867 7067 1.224039 GCTTCTCATGCAGGGAGCT 59.776 57.895 12.16 0.00 45.94 4.09
2892 7092 3.542742 GCGTCGCAGCGTACTTCC 61.543 66.667 15.93 0.29 0.00 3.46
2903 7103 2.672651 TACTTCCACCGCCGTCGA 60.673 61.111 0.00 0.00 38.10 4.20
2904 7104 2.693762 TACTTCCACCGCCGTCGAG 61.694 63.158 0.00 0.00 38.10 4.04
2905 7105 3.744719 CTTCCACCGCCGTCGAGA 61.745 66.667 0.00 0.00 38.10 4.04
2957 7157 3.003173 CTTCCTCCTCGCACCCCA 61.003 66.667 0.00 0.00 0.00 4.96
3003 7203 1.142748 CCCTACCTCGCAGCTTCTG 59.857 63.158 0.00 0.00 34.12 3.02
3021 7221 4.821589 CCTCCTTCGCCTCACCGC 62.822 72.222 0.00 0.00 0.00 5.68
3048 7248 2.802816 CAATCAAGAATCGACGATCCCC 59.197 50.000 11.42 3.94 0.00 4.81
3080 7280 2.240612 GACGCGATTGGCAGGTCAAC 62.241 60.000 15.93 0.00 43.84 3.18
3081 7281 2.324330 CGCGATTGGCAGGTCAACA 61.324 57.895 0.00 0.00 43.84 3.33
3109 7309 0.535102 AACCCTGACACTTGCTTCGG 60.535 55.000 0.00 0.00 0.00 4.30
3121 7321 0.615331 TGCTTCGGGATCTGCTCTTT 59.385 50.000 0.00 0.00 0.00 2.52
3217 7417 5.601313 TCCCACTTACTCCCACATAATCTAC 59.399 44.000 0.00 0.00 0.00 2.59
3232 7432 6.600032 ACATAATCTACGCTAGTCTAGATGGG 59.400 42.308 11.27 1.00 28.95 4.00
3292 7509 4.772886 ATGGATTAACAGTCCCACCTAC 57.227 45.455 0.00 0.00 34.76 3.18
3309 7526 5.295950 CACCTACAGCCTGATTCTTCATAG 58.704 45.833 0.00 0.00 0.00 2.23
3317 7534 4.383552 GCCTGATTCTTCATAGACACACCT 60.384 45.833 0.00 0.00 0.00 4.00
3318 7535 5.738909 CCTGATTCTTCATAGACACACCTT 58.261 41.667 0.00 0.00 0.00 3.50
3320 7537 6.358974 TGATTCTTCATAGACACACCTTCA 57.641 37.500 0.00 0.00 0.00 3.02
3336 7553 2.827921 CCTTCACCCCTTGAATTTCAGG 59.172 50.000 1.69 1.69 43.54 3.86
3344 7561 2.490718 CCTTGAATTTCAGGGGGTGTGA 60.491 50.000 17.56 0.00 39.69 3.58
3345 7562 2.286365 TGAATTTCAGGGGGTGTGAC 57.714 50.000 0.00 0.00 0.00 3.67
3361 7578 4.003648 GTGTGACCCCTTACTCTGATTTG 58.996 47.826 0.00 0.00 0.00 2.32
3366 7583 5.163141 TGACCCCTTACTCTGATTTGTTTCA 60.163 40.000 0.00 0.00 0.00 2.69
3367 7584 5.701224 ACCCCTTACTCTGATTTGTTTCAA 58.299 37.500 0.00 0.00 0.00 2.69
3390 7607 7.281774 TCAATCAGATGATTCCAACTAAGCTTC 59.718 37.037 0.00 0.00 42.41 3.86
3418 7635 4.609691 AAAGTTCGTAAATATGTGCCCG 57.390 40.909 0.00 0.00 0.00 6.13
3421 7638 2.674357 GTTCGTAAATATGTGCCCGTGT 59.326 45.455 0.00 0.00 0.00 4.49
3429 7646 1.444119 ATGTGCCCGTGTGTGTGTTC 61.444 55.000 0.00 0.00 0.00 3.18
3430 7647 2.892914 TGCCCGTGTGTGTGTTCG 60.893 61.111 0.00 0.00 0.00 3.95
3444 7661 2.286950 TGTGTTCGCTTGTCATTGCTTC 60.287 45.455 0.00 0.00 0.00 3.86
3445 7662 1.946081 TGTTCGCTTGTCATTGCTTCA 59.054 42.857 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
1 2 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
8 9 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
9 10 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
10 11 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
11 12 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
12 13 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
13 14 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
14 15 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
15 16 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
16 17 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
17 18 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
18 19 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
19 20 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
20 21 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
21 22 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
22 23 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
23 24 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
24 25 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
25 26 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
26 27 4.106825 TCTTACTCCCTCCGTCCCATAATA 59.893 45.833 0.00 0.00 0.00 0.98
27 28 3.116862 TCTTACTCCCTCCGTCCCATAAT 60.117 47.826 0.00 0.00 0.00 1.28
28 29 2.245546 TCTTACTCCCTCCGTCCCATAA 59.754 50.000 0.00 0.00 0.00 1.90
29 30 1.854939 TCTTACTCCCTCCGTCCCATA 59.145 52.381 0.00 0.00 0.00 2.74
30 31 0.635009 TCTTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
31 32 0.033405 CTCTTACTCCCTCCGTCCCA 60.033 60.000 0.00 0.00 0.00 4.37
32 33 0.258194 TCTCTTACTCCCTCCGTCCC 59.742 60.000 0.00 0.00 0.00 4.46
33 34 2.368311 ATCTCTTACTCCCTCCGTCC 57.632 55.000 0.00 0.00 0.00 4.79
34 35 3.414269 CCTATCTCTTACTCCCTCCGTC 58.586 54.545 0.00 0.00 0.00 4.79
35 36 2.108601 CCCTATCTCTTACTCCCTCCGT 59.891 54.545 0.00 0.00 0.00 4.69
36 37 2.797786 CCCTATCTCTTACTCCCTCCG 58.202 57.143 0.00 0.00 0.00 4.63
37 38 2.158295 TGCCCTATCTCTTACTCCCTCC 60.158 54.545 0.00 0.00 0.00 4.30
38 39 3.246416 TGCCCTATCTCTTACTCCCTC 57.754 52.381 0.00 0.00 0.00 4.30
39 40 3.515562 CATGCCCTATCTCTTACTCCCT 58.484 50.000 0.00 0.00 0.00 4.20
40 41 2.027653 GCATGCCCTATCTCTTACTCCC 60.028 54.545 6.36 0.00 0.00 4.30
41 42 2.027653 GGCATGCCCTATCTCTTACTCC 60.028 54.545 27.24 0.00 0.00 3.85
42 43 2.903135 AGGCATGCCCTATCTCTTACTC 59.097 50.000 33.14 2.70 44.08 2.59
43 44 2.636893 CAGGCATGCCCTATCTCTTACT 59.363 50.000 33.14 7.02 44.09 2.24
44 45 2.370189 ACAGGCATGCCCTATCTCTTAC 59.630 50.000 33.14 3.40 44.09 2.34
60 61 4.558538 AAGATCATTTATGCGAACAGGC 57.441 40.909 0.00 0.00 0.00 4.85
112 113 8.555361 GCTAAACTGAAATAAGATCCTGCTTAG 58.445 37.037 0.00 0.00 34.16 2.18
243 245 4.764308 GCTTTCTGACAGGGAGAAAAAGAT 59.236 41.667 13.44 0.00 38.62 2.40
251 253 1.805869 CTGTGCTTTCTGACAGGGAG 58.194 55.000 1.81 2.34 36.69 4.30
301 311 4.274865 GTGAAGTTCTGCTCAAGAAAACG 58.725 43.478 4.17 0.00 46.51 3.60
323 333 2.072298 CCTTCTTCAGTTCTTCGCTGG 58.928 52.381 0.00 0.00 34.89 4.85
574 584 0.036732 AACACTCCCATGTGCATCGT 59.963 50.000 0.00 0.00 41.30 3.73
656 666 4.871871 TCCCTATCAAAATAAGCACCCA 57.128 40.909 0.00 0.00 0.00 4.51
690 700 5.178623 CCATTACACGTACAGTCACACAAAT 59.821 40.000 0.00 0.00 0.00 2.32
776 3295 7.040892 ACAAACATCGAGCATGATTTATAGCAT 60.041 33.333 0.00 0.00 36.21 3.79
780 3299 6.429624 GCACAAACATCGAGCATGATTTATA 58.570 36.000 0.00 0.00 36.21 0.98
781 3300 5.276270 GCACAAACATCGAGCATGATTTAT 58.724 37.500 0.00 0.00 36.21 1.40
852 3378 5.362430 AGGAAGGAGAGCAAGACACTTATAG 59.638 44.000 0.00 0.00 0.00 1.31
911 3455 6.095377 GCAATCTTGACACCAAAAATCCTAG 58.905 40.000 0.00 0.00 0.00 3.02
917 3461 3.243367 CCTCGCAATCTTGACACCAAAAA 60.243 43.478 0.00 0.00 0.00 1.94
985 3536 2.672651 CATGAGGTTGGGCGCACA 60.673 61.111 9.15 9.15 0.00 4.57
1024 3580 2.335316 ACTAACCTCGTGTTTGGCAA 57.665 45.000 0.00 0.00 38.42 4.52
1044 3622 4.880120 TGCTAAGCGCGTATAGTATAGGAT 59.120 41.667 8.43 0.48 43.27 3.24
1046 3624 4.589252 CTGCTAAGCGCGTATAGTATAGG 58.411 47.826 8.43 5.64 43.27 2.57
1048 3626 4.012319 GCTGCTAAGCGCGTATAGTATA 57.988 45.455 8.43 1.76 43.27 1.47
1049 3627 2.864968 GCTGCTAAGCGCGTATAGTAT 58.135 47.619 8.43 0.00 43.27 2.12
1050 3628 2.327081 GCTGCTAAGCGCGTATAGTA 57.673 50.000 8.43 9.29 43.27 1.82
1051 3629 3.180984 GCTGCTAAGCGCGTATAGT 57.819 52.632 8.43 0.00 43.27 2.12
1097 3675 6.072508 TGGATGAGATTCTTGCAAGTTGTAAC 60.073 38.462 25.19 13.83 0.00 2.50
1100 3678 4.217118 GTGGATGAGATTCTTGCAAGTTGT 59.783 41.667 25.19 13.07 0.00 3.32
1110 3688 2.240667 CAACCCCAGTGGATGAGATTCT 59.759 50.000 11.95 0.00 39.20 2.40
1133 3711 4.353437 GTGACGACGGCGACCCTT 62.353 66.667 22.49 0.00 41.64 3.95
1371 3951 3.632145 ACGAAAAGACTTGCCAGAATGTT 59.368 39.130 0.00 0.00 0.00 2.71
1415 3996 0.387929 TGCTAGCAGCCGTGGTATAC 59.612 55.000 14.93 0.00 41.51 1.47
1434 4693 1.615392 GTGCTTCAAACCTTGGATGCT 59.385 47.619 0.00 0.00 35.79 3.79
1586 4854 8.205297 GCAGTAACAAATTACAAAAACGCTAAG 58.795 33.333 0.44 0.00 42.83 2.18
1589 4857 6.270064 AGCAGTAACAAATTACAAAAACGCT 58.730 32.000 0.44 0.00 42.83 5.07
1637 4905 1.285078 GGCCTATCCTTGGTTCTTGGT 59.715 52.381 0.00 0.00 0.00 3.67
1657 4925 2.249557 AATTGCTCGCTGCGCTTGAG 62.250 55.000 18.65 13.99 46.63 3.02
1671 4939 7.116233 ACGAATGAACCAATCAAGTAAAATTGC 59.884 33.333 0.00 0.00 42.54 3.56
1704 4980 3.378013 AAAAAGTCGCGCCGATTTC 57.622 47.368 0.00 0.00 34.94 2.17
1726 5002 3.066203 GTCTGGTGTGTCCGAACAATTTT 59.934 43.478 0.00 0.00 37.08 1.82
1794 5187 3.648067 ACTCAACTCTCTGGTGGAAATCA 59.352 43.478 0.00 0.00 33.29 2.57
1884 5277 4.344102 AGGGCTTCGATTACATGCTTAGTA 59.656 41.667 0.00 0.00 0.00 1.82
1887 5280 3.466836 CAGGGCTTCGATTACATGCTTA 58.533 45.455 0.00 0.00 0.00 3.09
1935 5328 4.345854 AGGAGACGTTCACTATTCTTCCT 58.654 43.478 0.00 0.00 0.00 3.36
2018 5412 3.326588 TCACATGTTGTACTGGGTTAGCT 59.673 43.478 0.00 0.00 0.00 3.32
2039 5445 4.485163 CAAAAATTGACACGGAATCCCTC 58.515 43.478 0.00 0.00 0.00 4.30
2070 5476 2.583441 CCTCACCTCCTCGTTGCCA 61.583 63.158 0.00 0.00 0.00 4.92
2142 5548 3.610242 CGAAGTCCTTGATGAACTTCTCG 59.390 47.826 11.41 0.00 44.24 4.04
2173 5579 0.392863 CACCCATGCATCTCCAACGA 60.393 55.000 0.00 0.00 0.00 3.85
2221 5627 2.361104 GTTCATGGCGGCCTTGGA 60.361 61.111 28.28 20.97 30.78 3.53
2307 6493 1.293924 CCATGCTCATGTCGGTCTTC 58.706 55.000 8.81 0.00 37.11 2.87
2359 6545 2.132996 CCACCTTGGCCAAGTTGCA 61.133 57.895 37.09 8.62 36.72 4.08
2436 6622 0.248907 CGCCGGTATCTCACACGAAT 60.249 55.000 1.90 0.00 0.00 3.34
2488 6674 0.606604 AGCCAGTAACCCAGTGTACG 59.393 55.000 0.00 0.00 0.00 3.67
2490 6676 0.981183 CCAGCCAGTAACCCAGTGTA 59.019 55.000 0.00 0.00 0.00 2.90
2502 6688 2.496899 AAGGTAACACATCCAGCCAG 57.503 50.000 0.00 0.00 41.41 4.85
2543 6729 9.807921 TCCCTAAAAGAAAAGACACATCTTATT 57.192 29.630 0.00 0.00 44.82 1.40
2544 6730 9.807921 TTCCCTAAAAGAAAAGACACATCTTAT 57.192 29.630 0.00 0.00 44.82 1.73
2545 6731 9.635404 TTTCCCTAAAAGAAAAGACACATCTTA 57.365 29.630 0.00 0.00 44.82 2.10
2547 6733 8.712228 ATTTCCCTAAAAGAAAAGACACATCT 57.288 30.769 0.00 0.00 36.83 2.90
2550 6736 9.635404 TCTTATTTCCCTAAAAGAAAAGACACA 57.365 29.630 0.00 0.00 36.83 3.72
2557 6743 9.581289 TGACACATCTTATTTCCCTAAAAGAAA 57.419 29.630 0.00 0.00 37.61 2.52
2558 6744 9.753674 ATGACACATCTTATTTCCCTAAAAGAA 57.246 29.630 0.00 0.00 0.00 2.52
2559 6745 9.396022 GATGACACATCTTATTTCCCTAAAAGA 57.604 33.333 0.00 0.00 0.00 2.52
2560 6746 9.401058 AGATGACACATCTTATTTCCCTAAAAG 57.599 33.333 8.23 0.00 0.00 2.27
2561 6747 9.396022 GAGATGACACATCTTATTTCCCTAAAA 57.604 33.333 14.13 0.00 0.00 1.52
2562 6748 8.548025 TGAGATGACACATCTTATTTCCCTAAA 58.452 33.333 14.13 0.00 0.00 1.85
2563 6749 7.987458 GTGAGATGACACATCTTATTTCCCTAA 59.013 37.037 14.13 0.00 40.11 2.69
2564 6750 7.125659 TGTGAGATGACACATCTTATTTCCCTA 59.874 37.037 14.13 0.00 44.29 3.53
2565 6751 6.070021 TGTGAGATGACACATCTTATTTCCCT 60.070 38.462 14.13 0.00 44.29 4.20
2566 6752 6.115446 TGTGAGATGACACATCTTATTTCCC 58.885 40.000 14.13 2.66 44.29 3.97
2629 6815 6.926272 AGATACTCTCATGATTTTTCGGTAGC 59.074 38.462 0.00 0.00 0.00 3.58
2650 6836 5.037385 CGAGAATGAGAACGCTTTGAGATA 58.963 41.667 0.00 0.00 0.00 1.98
2651 6837 3.862267 CGAGAATGAGAACGCTTTGAGAT 59.138 43.478 0.00 0.00 0.00 2.75
2659 6845 9.910511 TTATTATTTTTACGAGAATGAGAACGC 57.089 29.630 0.00 0.00 0.00 4.84
2706 6895 9.463443 GTTTATCAAACTGTTGAAGCATACTTT 57.537 29.630 0.00 0.00 46.66 2.66
2719 6908 5.106317 CCCACTATTGCGTTTATCAAACTGT 60.106 40.000 0.80 0.00 39.23 3.55
2726 6915 2.548480 GGCTCCCACTATTGCGTTTATC 59.452 50.000 0.00 0.00 0.00 1.75
2727 6916 2.172717 AGGCTCCCACTATTGCGTTTAT 59.827 45.455 0.00 0.00 0.00 1.40
2728 6917 1.557832 AGGCTCCCACTATTGCGTTTA 59.442 47.619 0.00 0.00 0.00 2.01
2729 6918 0.328258 AGGCTCCCACTATTGCGTTT 59.672 50.000 0.00 0.00 0.00 3.60
2736 6926 0.912486 GTCCAACAGGCTCCCACTAT 59.088 55.000 0.00 0.00 0.00 2.12
2749 6939 6.873605 CCCATTTAATTTCTTTCTGGTCCAAC 59.126 38.462 0.00 0.00 0.00 3.77
2774 6964 1.152943 GTGGGCTAAAGGGGCTAGC 60.153 63.158 6.04 6.04 40.93 3.42
2776 6966 1.279025 CCAGTGGGCTAAAGGGGCTA 61.279 60.000 0.00 0.00 0.00 3.93
2777 6967 2.616458 CCAGTGGGCTAAAGGGGCT 61.616 63.158 0.00 0.00 0.00 5.19
2778 6968 1.568118 TACCAGTGGGCTAAAGGGGC 61.568 60.000 15.21 0.00 37.90 5.80
2779 6969 0.255033 GTACCAGTGGGCTAAAGGGG 59.745 60.000 15.21 0.00 37.90 4.79
2780 6970 0.255033 GGTACCAGTGGGCTAAAGGG 59.745 60.000 15.21 0.00 37.90 3.95
2781 6971 3.875865 GGTACCAGTGGGCTAAAGG 57.124 57.895 15.21 0.00 37.90 3.11
2807 7007 3.205784 AGAAGAAGCTATGTGGATGGC 57.794 47.619 0.00 0.00 36.33 4.40
2831 7031 3.105959 AGCTATGTGGATGGCCTTTTT 57.894 42.857 3.32 0.00 36.75 1.94
2832 7032 2.834638 AGCTATGTGGATGGCCTTTT 57.165 45.000 3.32 0.00 36.75 2.27
2833 7033 2.243221 AGAAGCTATGTGGATGGCCTTT 59.757 45.455 3.32 0.00 36.75 3.11
2834 7034 1.849039 AGAAGCTATGTGGATGGCCTT 59.151 47.619 3.32 0.00 36.75 4.35
2835 7035 1.419387 GAGAAGCTATGTGGATGGCCT 59.581 52.381 3.32 0.00 36.75 5.19
2836 7036 1.141657 TGAGAAGCTATGTGGATGGCC 59.858 52.381 0.00 0.00 36.75 5.36
2837 7037 2.627515 TGAGAAGCTATGTGGATGGC 57.372 50.000 0.00 0.00 36.33 4.40
2838 7038 2.812591 GCATGAGAAGCTATGTGGATGG 59.187 50.000 0.00 0.00 0.00 3.51
2839 7039 3.473625 TGCATGAGAAGCTATGTGGATG 58.526 45.455 0.00 0.00 0.00 3.51
2840 7040 3.496337 CCTGCATGAGAAGCTATGTGGAT 60.496 47.826 0.00 0.00 0.00 3.41
2841 7041 2.158856 CCTGCATGAGAAGCTATGTGGA 60.159 50.000 0.00 0.00 0.00 4.02
2842 7042 2.219458 CCTGCATGAGAAGCTATGTGG 58.781 52.381 0.00 0.00 0.00 4.17
2843 7043 2.158856 TCCCTGCATGAGAAGCTATGTG 60.159 50.000 0.00 0.00 0.00 3.21
2844 7044 2.104451 CTCCCTGCATGAGAAGCTATGT 59.896 50.000 7.45 0.00 31.26 2.29
2845 7045 2.768698 CTCCCTGCATGAGAAGCTATG 58.231 52.381 7.45 0.00 31.26 2.23
2846 7046 1.072015 GCTCCCTGCATGAGAAGCTAT 59.928 52.381 15.50 0.00 42.31 2.97
2847 7047 0.467384 GCTCCCTGCATGAGAAGCTA 59.533 55.000 15.50 0.00 42.31 3.32
2848 7048 1.224039 GCTCCCTGCATGAGAAGCT 59.776 57.895 15.50 0.00 42.31 3.74
2849 7049 1.096386 CAGCTCCCTGCATGAGAAGC 61.096 60.000 15.50 9.40 45.94 3.86
2850 7050 0.540454 TCAGCTCCCTGCATGAGAAG 59.460 55.000 15.50 7.92 45.94 2.85
2851 7051 0.540454 CTCAGCTCCCTGCATGAGAA 59.460 55.000 15.50 1.96 43.29 2.87
2852 7052 1.335882 CCTCAGCTCCCTGCATGAGA 61.336 60.000 13.13 0.00 43.29 3.27
2853 7053 1.146485 CCTCAGCTCCCTGCATGAG 59.854 63.158 0.00 5.87 45.94 2.90
2854 7054 2.372890 CCCTCAGCTCCCTGCATGA 61.373 63.158 0.00 0.00 45.94 3.07
2855 7055 2.192443 CCCTCAGCTCCCTGCATG 59.808 66.667 0.00 0.00 45.94 4.06
2856 7056 3.806667 GCCCTCAGCTCCCTGCAT 61.807 66.667 0.00 0.00 45.94 3.96
2878 7078 2.260434 GGTGGAAGTACGCTGCGA 59.740 61.111 30.47 9.65 0.00 5.10
2892 7092 2.949678 CGATTCTCGACGGCGGTG 60.950 66.667 12.58 4.17 43.74 4.94
2928 7128 1.743252 GAGGAAGAAGCAGCCGTGG 60.743 63.158 0.00 0.00 0.00 4.94
2933 7133 1.813337 GCGAGGAGGAAGAAGCAGC 60.813 63.158 0.00 0.00 0.00 5.25
2938 7138 2.291043 GGGGTGCGAGGAGGAAGAA 61.291 63.158 0.00 0.00 0.00 2.52
2957 7157 4.070552 GTGCGAGCCGGAAGAGGT 62.071 66.667 5.05 0.00 0.00 3.85
3003 7203 4.821589 CGGTGAGGCGAAGGAGGC 62.822 72.222 0.00 0.00 0.00 4.70
3007 7207 3.883744 AACAGCGGTGAGGCGAAGG 62.884 63.158 23.44 0.00 38.18 3.46
3010 7210 4.373116 GGAACAGCGGTGAGGCGA 62.373 66.667 23.44 0.00 38.18 5.54
3021 7221 3.926527 TCGTCGATTCTTGATTGGAACAG 59.073 43.478 0.00 0.00 42.39 3.16
3057 7257 4.812476 CTGCCAATCGCGTCCGGA 62.812 66.667 5.77 0.00 42.08 5.14
3070 7270 3.368571 GGCTGCTGTTGACCTGCC 61.369 66.667 0.00 0.00 38.58 4.85
3080 7280 3.970410 TCAGGGTTGGGGCTGCTG 61.970 66.667 0.00 0.00 0.00 4.41
3081 7281 3.971702 GTCAGGGTTGGGGCTGCT 61.972 66.667 0.00 0.00 0.00 4.24
3109 7309 4.641989 TGCCTCAATTTAAAGAGCAGATCC 59.358 41.667 0.00 0.00 0.00 3.36
3121 7321 6.309357 AGATGCTTATGGATGCCTCAATTTA 58.691 36.000 0.00 0.00 0.00 1.40
3189 7389 1.080498 TGTGGGAGTAAGTGGGATCCT 59.920 52.381 12.58 0.00 32.18 3.24
3217 7417 2.554893 GGAAGTCCCATCTAGACTAGCG 59.445 54.545 4.47 0.00 43.77 4.26
3292 7509 4.569966 GTGTGTCTATGAAGAATCAGGCTG 59.430 45.833 8.58 8.58 39.39 4.85
3309 7526 0.472471 TCAAGGGGTGAAGGTGTGTC 59.528 55.000 0.00 0.00 31.51 3.67
3318 7535 1.077005 CCCCTGAAATTCAAGGGGTGA 59.923 52.381 27.33 0.00 43.09 4.02
3344 7561 5.319043 TGAAACAAATCAGAGTAAGGGGT 57.681 39.130 0.00 0.00 0.00 4.95
3345 7562 6.434028 TGATTGAAACAAATCAGAGTAAGGGG 59.566 38.462 0.00 0.00 40.72 4.79
3361 7578 7.699812 GCTTAGTTGGAATCATCTGATTGAAAC 59.300 37.037 10.04 12.52 44.14 2.78
3366 7583 6.545298 GGAAGCTTAGTTGGAATCATCTGATT 59.455 38.462 0.00 5.13 46.54 2.57
3367 7584 6.060788 GGAAGCTTAGTTGGAATCATCTGAT 58.939 40.000 0.00 0.00 36.07 2.90
3377 7594 6.779860 ACTTTAATGAGGAAGCTTAGTTGGA 58.220 36.000 0.00 0.00 0.00 3.53
3390 7607 7.855904 GGCACATATTTACGAACTTTAATGAGG 59.144 37.037 0.00 0.00 0.00 3.86
3418 7635 0.724549 TGACAAGCGAACACACACAC 59.275 50.000 0.00 0.00 0.00 3.82
3421 7638 1.268488 GCAATGACAAGCGAACACACA 60.268 47.619 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.