Multiple sequence alignment - TraesCS2A01G304300

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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 TraesCS2A01G304300 chr2A 100.000 4663 0 0 1 4663 522843991 522839329 0.000000e+00 8612.0
1 TraesCS2A01G304300 chr2A 79.921 254 35 12 936 1177 769191319 769191070 6.200000e-39 172.0
2 TraesCS2A01G304300 chr2D 95.874 1551 41 11 2724 4266 386582643 386581108 0.000000e+00 2488.0
3 TraesCS2A01G304300 chr2D 91.138 1591 85 27 1 1565 386585281 386583721 0.000000e+00 2106.0
4 TraesCS2A01G304300 chr2D 96.739 1012 23 5 1562 2563 386583652 386582641 0.000000e+00 1677.0
5 TraesCS2A01G304300 chr2D 97.619 168 4 0 2562 2729 516708476 516708309 5.900000e-74 289.0
6 TraesCS2A01G304300 chr2D 97.076 171 4 1 2563 2732 475088339 475088509 2.120000e-73 287.0
7 TraesCS2A01G304300 chr2D 96.364 165 6 0 2562 2726 196347492 196347328 5.950000e-69 272.0
8 TraesCS2A01G304300 chr2B 96.653 1494 33 2 2724 4216 457681859 457680382 0.000000e+00 2466.0
9 TraesCS2A01G304300 chr2B 98.237 964 17 0 1600 2563 457682820 457681857 0.000000e+00 1687.0
10 TraesCS2A01G304300 chr2B 88.404 871 62 13 725 1565 457683754 457682893 0.000000e+00 1013.0
11 TraesCS2A01G304300 chr2B 89.884 692 49 15 1 679 457684435 457683752 0.000000e+00 870.0
12 TraesCS2A01G304300 chr3D 94.000 350 21 0 4262 4611 564677046 564677395 8.880000e-147 531.0
13 TraesCS2A01G304300 chr3D 92.857 350 25 0 4262 4611 439819520 439819869 4.160000e-140 508.0
14 TraesCS2A01G304300 chr3D 95.122 41 0 2 688 727 569467555 569467516 3.900000e-06 63.9
15 TraesCS2A01G304300 chr1D 93.143 350 24 0 4262 4611 347792330 347791981 8.950000e-142 514.0
16 TraesCS2A01G304300 chr1A 93.123 349 24 0 4263 4611 585692586 585692934 3.220000e-141 512.0
17 TraesCS2A01G304300 chrUn 93.103 348 24 0 4264 4611 321126107 321126454 1.160000e-140 510.0
18 TraesCS2A01G304300 chrUn 93.103 348 24 0 4264 4611 321129425 321129772 1.160000e-140 510.0
19 TraesCS2A01G304300 chrUn 93.103 348 24 0 4264 4611 336388302 336387955 1.160000e-140 510.0
20 TraesCS2A01G304300 chrUn 98.214 56 1 0 4608 4663 28776845 28776900 1.070000e-16 99.0
21 TraesCS2A01G304300 chrUn 98.214 56 1 0 4608 4663 97152868 97152923 1.070000e-16 99.0
22 TraesCS2A01G304300 chrUn 98.214 56 1 0 4608 4663 97168659 97168714 1.070000e-16 99.0
23 TraesCS2A01G304300 chrUn 98.214 56 1 0 4608 4663 101300252 101300197 1.070000e-16 99.0
24 TraesCS2A01G304300 chrUn 98.214 56 1 0 4608 4663 321126501 321126556 1.070000e-16 99.0
25 TraesCS2A01G304300 chrUn 98.214 56 1 0 4608 4663 321129819 321129874 1.070000e-16 99.0
26 TraesCS2A01G304300 chrUn 84.783 92 13 1 1590 1680 479229945 479230036 1.790000e-14 91.6
27 TraesCS2A01G304300 chr6D 92.857 350 24 1 4262 4611 412730752 412730404 1.500000e-139 507.0
28 TraesCS2A01G304300 chr6D 95.000 180 7 2 2553 2730 32865159 32865338 9.880000e-72 281.0
29 TraesCS2A01G304300 chr6D 100.000 28 0 0 703 730 309950098 309950071 8.000000e-03 52.8
30 TraesCS2A01G304300 chr5D 91.899 358 29 0 4254 4611 437083251 437082894 6.970000e-138 501.0
31 TraesCS2A01G304300 chr7D 85.572 402 29 13 4262 4663 2575049 2575421 1.220000e-105 394.0
32 TraesCS2A01G304300 chr7D 94.086 186 9 2 2543 2727 517575216 517575400 9.880000e-72 281.0
33 TraesCS2A01G304300 chr7D 94.872 39 2 0 689 727 569401916 569401878 1.400000e-05 62.1
34 TraesCS2A01G304300 chr5A 97.619 168 4 0 2562 2729 651496822 651496989 5.900000e-74 289.0
35 TraesCS2A01G304300 chr6A 95.480 177 7 1 2562 2737 24072060 24071884 9.880000e-72 281.0
36 TraesCS2A01G304300 chr5B 93.085 188 13 0 2547 2734 575061143 575061330 4.600000e-70 276.0
37 TraesCS2A01G304300 chr3A 92.632 190 10 4 2559 2746 362899679 362899866 2.140000e-68 270.0
38 TraesCS2A01G304300 chr3A 93.651 63 3 1 4601 4663 8856086 8856025 4.970000e-15 93.5
39 TraesCS2A01G304300 chr7A 81.224 245 36 7 936 1174 409248044 409248284 6.160000e-44 189.0
40 TraesCS2A01G304300 chr7A 93.651 63 3 1 4601 4663 163630934 163630995 4.970000e-15 93.5
41 TraesCS2A01G304300 chr4D 84.783 92 13 1 1590 1680 371139990 371140081 1.790000e-14 91.6
42 TraesCS2A01G304300 chr4B 84.783 92 13 1 1590 1680 456385585 456385676 1.790000e-14 91.6
43 TraesCS2A01G304300 chr4A 83.673 98 15 1 1590 1686 92736412 92736315 1.790000e-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 TraesCS2A01G304300 chr2A 522839329 522843991 4662 True 8612.000000 8612 100.000000 1 4663 1 chr2A.!!$R1 4662
1 TraesCS2A01G304300 chr2D 386581108 386585281 4173 True 2090.333333 2488 94.583667 1 4266 3 chr2D.!!$R3 4265
2 TraesCS2A01G304300 chr2B 457680382 457684435 4053 True 1509.000000 2466 93.294500 1 4216 4 chr2B.!!$R1 4215
3 TraesCS2A01G304300 chrUn 321126107 321129874 3767 False 304.500000 510 95.658500 4264 4663 4 chrUn.!!$F5 399

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
24 25 0.689055 AGCTGACTGCATGGACTTCA 59.311 50.0 7.11 0.0 45.94 3.02 F
1239 1276 0.251209 TGCTACTCGACCTCACACCT 60.251 55.0 0.00 0.0 0.00 4.00 F
1510 1578 0.243365 GGACAATGAAATGGCACGCA 59.757 50.0 0.00 0.0 0.00 5.24 F
2575 2725 1.192428 ACATGTACTCCCTCCGTTCC 58.808 55.0 0.00 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1458 0.386113 CGCCCTAACCTGCTAGAGTC 59.614 60.000 0.0 0.0 0.0 3.36 R
2710 2860 2.177734 GTTTCTACTCCCTCCGTTCCT 58.822 52.381 0.0 0.0 0.0 3.36 R
2711 2861 2.177734 AGTTTCTACTCCCTCCGTTCC 58.822 52.381 0.0 0.0 0.0 3.62 R
4571 8047 0.112412 ATCAGGTTTTTGGGGAGCGT 59.888 50.000 0.0 0.0 0.0 5.07 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 0.689055 AGCTGACTGCATGGACTTCA 59.311 50.000 7.11 0.00 45.94 3.02
90 91 3.253188 CGGTCATCTTCCAGCAAAAGAAA 59.747 43.478 0.42 0.00 36.41 2.52
91 92 4.614535 CGGTCATCTTCCAGCAAAAGAAAG 60.615 45.833 0.42 0.00 36.41 2.62
266 273 3.702330 GTTTCTTTACGGCACTGCTTTT 58.298 40.909 0.00 0.00 0.00 2.27
332 339 1.747355 CCCTGCAGTGTGATCCAATTC 59.253 52.381 13.81 0.00 0.00 2.17
466 479 6.320418 TCAAATCATGTCTGATGGATTCTTGG 59.680 38.462 0.00 0.00 41.34 3.61
554 569 3.057806 GTGTTTGTGTGGTGGTATAAGCC 60.058 47.826 0.00 0.00 0.00 4.35
557 572 1.982226 TGTGTGGTGGTATAAGCCTGT 59.018 47.619 0.00 0.00 0.00 4.00
674 694 4.999950 AGTGAGGTAAAACATGAGAGCTTG 59.000 41.667 0.00 0.00 0.00 4.01
678 698 4.288626 AGGTAAAACATGAGAGCTTGGGTA 59.711 41.667 0.00 0.00 0.00 3.69
679 699 5.044846 AGGTAAAACATGAGAGCTTGGGTAT 60.045 40.000 0.00 0.00 0.00 2.73
680 700 5.652452 GGTAAAACATGAGAGCTTGGGTATT 59.348 40.000 0.00 0.00 0.00 1.89
681 701 6.826741 GGTAAAACATGAGAGCTTGGGTATTA 59.173 38.462 0.00 0.00 0.00 0.98
682 702 6.759497 AAAACATGAGAGCTTGGGTATTAC 57.241 37.500 0.00 0.00 0.00 1.89
683 703 5.435686 AACATGAGAGCTTGGGTATTACA 57.564 39.130 0.00 0.00 0.00 2.41
684 704 5.028549 ACATGAGAGCTTGGGTATTACAG 57.971 43.478 0.00 0.00 0.00 2.74
685 705 4.471386 ACATGAGAGCTTGGGTATTACAGT 59.529 41.667 0.00 0.00 0.00 3.55
686 706 5.045578 ACATGAGAGCTTGGGTATTACAGTT 60.046 40.000 0.00 0.00 0.00 3.16
687 707 6.156256 ACATGAGAGCTTGGGTATTACAGTTA 59.844 38.462 0.00 0.00 0.00 2.24
694 714 9.694137 GAGCTTGGGTATTACAGTTATACTAAG 57.306 37.037 9.11 12.91 32.38 2.18
695 715 8.148999 AGCTTGGGTATTACAGTTATACTAAGC 58.851 37.037 25.14 25.14 41.79 3.09
701 721 3.454371 ACAGTTATACTAAGCCTGCGG 57.546 47.619 0.00 0.00 0.00 5.69
733 753 4.890988 TGGATTGGAGGGAGTAGATGTTA 58.109 43.478 0.00 0.00 0.00 2.41
849 874 3.573598 TCATCAAATGCGAATTTGCGTT 58.426 36.364 22.05 17.82 45.62 4.84
889 914 6.286240 AGAAGGGGCATAAATGAACTTTTC 57.714 37.500 0.00 0.00 0.00 2.29
921 946 2.356535 CCCCTTCTTCCATCAAGACAGG 60.357 54.545 0.00 0.00 41.13 4.00
953 978 2.597510 GGCACCAGAACCACACCC 60.598 66.667 0.00 0.00 0.00 4.61
954 979 2.597510 GCACCAGAACCACACCCC 60.598 66.667 0.00 0.00 0.00 4.95
1014 1039 4.492160 GCGATGGCGACGACTCCA 62.492 66.667 0.65 0.00 40.82 3.86
1229 1266 1.380524 GAGGTACTGCTGCTACTCGA 58.619 55.000 0.00 0.00 41.55 4.04
1239 1276 0.251209 TGCTACTCGACCTCACACCT 60.251 55.000 0.00 0.00 0.00 4.00
1240 1277 1.003928 TGCTACTCGACCTCACACCTA 59.996 52.381 0.00 0.00 0.00 3.08
1241 1278 2.089980 GCTACTCGACCTCACACCTAA 58.910 52.381 0.00 0.00 0.00 2.69
1242 1279 2.159407 GCTACTCGACCTCACACCTAAC 60.159 54.545 0.00 0.00 0.00 2.34
1243 1280 2.289592 ACTCGACCTCACACCTAACT 57.710 50.000 0.00 0.00 0.00 2.24
1244 1281 1.887198 ACTCGACCTCACACCTAACTG 59.113 52.381 0.00 0.00 0.00 3.16
1245 1282 2.160205 CTCGACCTCACACCTAACTGA 58.840 52.381 0.00 0.00 0.00 3.41
1246 1283 1.884579 TCGACCTCACACCTAACTGAC 59.115 52.381 0.00 0.00 0.00 3.51
1247 1284 1.067776 CGACCTCACACCTAACTGACC 60.068 57.143 0.00 0.00 0.00 4.02
1257 1294 5.011329 CACACCTAACTGACCCTGTTACTTA 59.989 44.000 0.00 0.00 0.00 2.24
1259 1296 4.529769 ACCTAACTGACCCTGTTACTTACC 59.470 45.833 0.00 0.00 0.00 2.85
1307 1353 2.821546 TGAGTTGTTTCGACTGTCCAG 58.178 47.619 1.55 0.00 0.00 3.86
1308 1354 2.167693 TGAGTTGTTTCGACTGTCCAGT 59.832 45.455 0.00 0.00 45.84 4.00
1309 1355 3.382227 TGAGTTGTTTCGACTGTCCAGTA 59.618 43.478 1.55 0.00 42.66 2.74
1316 1362 1.132453 TCGACTGTCCAGTATGCGAAG 59.868 52.381 1.55 0.00 42.66 3.79
1325 1371 1.863454 CAGTATGCGAAGTGAGATGCC 59.137 52.381 0.00 0.00 0.00 4.40
1339 1385 3.451556 ATGCCGCTGTGGATCTCGG 62.452 63.158 12.29 0.00 42.00 4.63
1354 1400 2.126888 CGGCAATTGCGCGAGTTT 60.127 55.556 26.88 0.00 43.26 2.66
1356 1402 1.274798 CGGCAATTGCGCGAGTTTTT 61.275 50.000 26.88 0.00 43.26 1.94
1412 1458 2.047061 TCATTACCGGGATCTCTTGGG 58.953 52.381 6.32 0.00 0.00 4.12
1430 1498 0.753867 GGACTCTAGCAGGTTAGGGC 59.246 60.000 0.00 0.00 0.00 5.19
1435 1503 0.386113 CTAGCAGGTTAGGGCGAGAC 59.614 60.000 0.00 0.00 35.13 3.36
1444 1512 0.813184 TAGGGCGAGACCGTACAAAG 59.187 55.000 0.00 0.00 40.62 2.77
1486 1554 7.116519 GGATTCTTATGTAGCGACCTAAATGTC 59.883 40.741 0.00 0.00 0.00 3.06
1510 1578 0.243365 GGACAATGAAATGGCACGCA 59.757 50.000 0.00 0.00 0.00 5.24
1550 1618 7.040473 AGGTAGATTACTATGTGGAAGAACG 57.960 40.000 0.00 0.00 0.00 3.95
1613 1753 2.367241 GGCTAGAGATTCCTTGACCCTC 59.633 54.545 0.00 0.00 0.00 4.30
1652 1792 6.913170 TGGCAAGATTTGTAAAGAGAATGTC 58.087 36.000 0.00 0.00 0.00 3.06
1895 2043 8.833231 TTGTAGGACTTAAGACTGAGAAAATG 57.167 34.615 10.09 0.00 0.00 2.32
1932 2080 3.714487 AAGCTGCACCGGTGTTGGT 62.714 57.895 33.92 27.03 45.21 3.67
2217 2365 2.028112 TGCGCCTGATGTTTCTACTCTT 60.028 45.455 4.18 0.00 0.00 2.85
2295 2443 1.611519 TCATCGGTTTTGGGGTCAAC 58.388 50.000 0.00 0.00 31.78 3.18
2482 2630 7.547227 CCCATTTGAAGGTAATTGTTAGGAAG 58.453 38.462 0.00 0.00 0.00 3.46
2563 2713 8.542497 TGAGTGGTAATTTGACTAACATGTAC 57.458 34.615 0.00 0.00 0.00 2.90
2564 2714 8.372459 TGAGTGGTAATTTGACTAACATGTACT 58.628 33.333 0.00 0.00 0.00 2.73
2565 2715 8.773404 AGTGGTAATTTGACTAACATGTACTC 57.227 34.615 0.00 0.00 0.00 2.59
2566 2716 7.822822 AGTGGTAATTTGACTAACATGTACTCC 59.177 37.037 0.00 0.00 0.00 3.85
2567 2717 7.065443 GTGGTAATTTGACTAACATGTACTCCC 59.935 40.741 0.00 0.00 0.00 4.30
2568 2718 7.037873 TGGTAATTTGACTAACATGTACTCCCT 60.038 37.037 0.00 0.00 0.00 4.20
2569 2719 7.494952 GGTAATTTGACTAACATGTACTCCCTC 59.505 40.741 0.00 0.00 0.00 4.30
2570 2720 5.416271 TTTGACTAACATGTACTCCCTCC 57.584 43.478 0.00 0.00 0.00 4.30
2571 2721 3.021695 TGACTAACATGTACTCCCTCCG 58.978 50.000 0.00 0.00 0.00 4.63
2572 2722 3.022406 GACTAACATGTACTCCCTCCGT 58.978 50.000 0.00 0.00 0.00 4.69
2573 2723 3.438183 ACTAACATGTACTCCCTCCGTT 58.562 45.455 0.00 0.00 0.00 4.44
2574 2724 3.446516 ACTAACATGTACTCCCTCCGTTC 59.553 47.826 0.00 0.00 0.00 3.95
2575 2725 1.192428 ACATGTACTCCCTCCGTTCC 58.808 55.000 0.00 0.00 0.00 3.62
2576 2726 1.273098 ACATGTACTCCCTCCGTTCCT 60.273 52.381 0.00 0.00 0.00 3.36
2577 2727 2.024655 ACATGTACTCCCTCCGTTCCTA 60.025 50.000 0.00 0.00 0.00 2.94
2578 2728 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2579 2729 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2580 2730 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2581 2731 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2582 2732 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2583 2733 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
2584 2734 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2585 2735 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2586 2736 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2587 2737 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2588 2738 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2589 2739 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2590 2740 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2591 2741 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2592 2742 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2609 2759 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2610 2760 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
2626 2776 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2627 2777 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2628 2778 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2629 2779 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
2630 2780 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2631 2781 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
2632 2782 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
2633 2783 9.339850 GACTACCACATACGGATGTATATAGAT 57.660 37.037 22.62 12.37 44.82 1.98
2667 2817 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
2668 2818 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
2669 2819 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
2670 2820 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
2671 2821 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2672 2822 9.031360 GTAGATTCACTCATTTTGCTTCGTATA 57.969 33.333 0.00 0.00 0.00 1.47
2673 2823 8.668510 AGATTCACTCATTTTGCTTCGTATAT 57.331 30.769 0.00 0.00 0.00 0.86
2674 2824 9.764363 AGATTCACTCATTTTGCTTCGTATATA 57.236 29.630 0.00 0.00 0.00 0.86
2676 2826 8.942338 TTCACTCATTTTGCTTCGTATATAGT 57.058 30.769 0.00 0.00 0.00 2.12
2677 2827 8.575565 TCACTCATTTTGCTTCGTATATAGTC 57.424 34.615 0.00 0.00 0.00 2.59
2678 2828 7.378728 TCACTCATTTTGCTTCGTATATAGTCG 59.621 37.037 0.00 0.00 0.00 4.18
2679 2829 6.144080 ACTCATTTTGCTTCGTATATAGTCGC 59.856 38.462 0.00 0.00 0.00 5.19
2680 2830 6.213677 TCATTTTGCTTCGTATATAGTCGCT 58.786 36.000 0.00 0.00 0.00 4.93
2681 2831 6.700081 TCATTTTGCTTCGTATATAGTCGCTT 59.300 34.615 0.00 0.00 0.00 4.68
2682 2832 5.883328 TTTGCTTCGTATATAGTCGCTTG 57.117 39.130 0.00 0.00 0.00 4.01
2683 2833 4.563337 TGCTTCGTATATAGTCGCTTGT 57.437 40.909 0.00 0.00 0.00 3.16
2684 2834 4.928601 TGCTTCGTATATAGTCGCTTGTT 58.071 39.130 0.00 0.00 0.00 2.83
2685 2835 4.738252 TGCTTCGTATATAGTCGCTTGTTG 59.262 41.667 0.00 0.00 0.00 3.33
2686 2836 4.974275 GCTTCGTATATAGTCGCTTGTTGA 59.026 41.667 0.00 0.00 0.00 3.18
2687 2837 5.457799 GCTTCGTATATAGTCGCTTGTTGAA 59.542 40.000 0.00 0.00 0.00 2.69
2688 2838 6.020121 GCTTCGTATATAGTCGCTTGTTGAAA 60.020 38.462 0.00 0.00 0.00 2.69
2689 2839 7.306632 GCTTCGTATATAGTCGCTTGTTGAAAT 60.307 37.037 0.00 0.00 0.00 2.17
2690 2840 7.997107 TCGTATATAGTCGCTTGTTGAAATT 57.003 32.000 0.00 0.00 0.00 1.82
2691 2841 8.415192 TCGTATATAGTCGCTTGTTGAAATTT 57.585 30.769 0.00 0.00 0.00 1.82
2692 2842 8.537223 TCGTATATAGTCGCTTGTTGAAATTTC 58.463 33.333 11.41 11.41 0.00 2.17
2693 2843 8.540492 CGTATATAGTCGCTTGTTGAAATTTCT 58.460 33.333 18.64 0.00 0.00 2.52
2696 2846 9.817809 ATATAGTCGCTTGTTGAAATTTCTAGA 57.182 29.630 18.64 7.52 0.00 2.43
2697 2847 6.861065 AGTCGCTTGTTGAAATTTCTAGAA 57.139 33.333 18.64 14.37 0.00 2.10
2698 2848 7.259290 AGTCGCTTGTTGAAATTTCTAGAAA 57.741 32.000 19.83 19.83 34.46 2.52
2699 2849 7.355778 AGTCGCTTGTTGAAATTTCTAGAAAG 58.644 34.615 21.75 16.46 33.32 2.62
2700 2850 7.226720 AGTCGCTTGTTGAAATTTCTAGAAAGA 59.773 33.333 21.75 13.82 33.32 2.52
2701 2851 7.321509 GTCGCTTGTTGAAATTTCTAGAAAGAC 59.678 37.037 21.75 19.48 33.32 3.01
2702 2852 7.011950 TCGCTTGTTGAAATTTCTAGAAAGACA 59.988 33.333 21.75 17.21 33.32 3.41
2703 2853 7.643764 CGCTTGTTGAAATTTCTAGAAAGACAA 59.356 33.333 21.75 20.91 33.32 3.18
2704 2854 9.301153 GCTTGTTGAAATTTCTAGAAAGACAAA 57.699 29.630 21.75 11.66 33.32 2.83
2717 2867 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2718 2868 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2719 2869 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2720 2870 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2721 2871 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2722 2872 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2723 2873 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2724 2874 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2725 2875 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2808 2959 2.240493 ACACAGGACGTTTCTTGGAG 57.760 50.000 0.00 0.00 33.06 3.86
2937 3088 5.927115 GGATGACTCGGATGTAAATTCTACC 59.073 44.000 0.00 0.00 0.00 3.18
3156 3307 0.464554 GTTCCAGCTACCAGCATCCC 60.465 60.000 0.38 0.00 45.56 3.85
3379 3531 3.554324 TCAGCATCCGTTTTATAGTTCGC 59.446 43.478 0.00 0.00 0.00 4.70
3431 3583 0.247736 CGAAGGTGGAGGGTTCAGAG 59.752 60.000 0.00 0.00 0.00 3.35
4097 4255 5.125257 TGTTTTGTCAACTCTTCAGCAATGA 59.875 36.000 0.00 0.00 0.00 2.57
4186 4344 8.231161 GCAAGATCAGTCATCAATGAATAGATG 58.769 37.037 0.00 0.00 42.25 2.90
4205 4363 2.596346 TGTGTACTCCCTCCGTAAACA 58.404 47.619 0.00 0.00 33.79 2.83
4210 4368 5.578336 GTGTACTCCCTCCGTAAACAAATAC 59.422 44.000 0.00 0.00 0.00 1.89
4216 4374 4.035208 CCCTCCGTAAACAAATACATGAGC 59.965 45.833 0.00 0.00 0.00 4.26
4217 4375 4.634004 CCTCCGTAAACAAATACATGAGCA 59.366 41.667 0.00 0.00 0.00 4.26
4218 4376 5.296780 CCTCCGTAAACAAATACATGAGCAT 59.703 40.000 0.00 0.00 0.00 3.79
4219 4377 6.481976 CCTCCGTAAACAAATACATGAGCATA 59.518 38.462 0.00 0.00 0.00 3.14
4220 4378 7.241663 TCCGTAAACAAATACATGAGCATAC 57.758 36.000 0.00 0.00 0.00 2.39
4221 4379 7.045416 TCCGTAAACAAATACATGAGCATACT 58.955 34.615 0.00 0.00 0.00 2.12
4222 4380 7.223971 TCCGTAAACAAATACATGAGCATACTC 59.776 37.037 0.00 0.00 43.76 2.59
4223 4381 7.345192 CGTAAACAAATACATGAGCATACTCC 58.655 38.462 0.00 0.00 42.74 3.85
4224 4382 7.224753 CGTAAACAAATACATGAGCATACTCCT 59.775 37.037 0.00 0.00 42.74 3.69
4225 4383 9.542462 GTAAACAAATACATGAGCATACTCCTA 57.458 33.333 0.00 0.00 42.74 2.94
4227 4385 9.632638 AAACAAATACATGAGCATACTCCTATT 57.367 29.630 0.00 0.00 42.74 1.73
4228 4386 9.632638 AACAAATACATGAGCATACTCCTATTT 57.367 29.630 0.00 0.00 42.74 1.40
4229 4387 9.060347 ACAAATACATGAGCATACTCCTATTTG 57.940 33.333 16.97 16.97 42.01 2.32
4235 4393 7.224753 ACATGAGCATACTCCTATTTGTTTACG 59.775 37.037 0.00 0.00 42.74 3.18
4240 4398 6.684613 GCATACTCCTATTTGTTTACGGAGGA 60.685 42.308 8.33 0.00 44.27 3.71
4271 4429 6.916360 AACATCCATGTACTTGTTGGAAAT 57.084 33.333 7.86 0.15 42.53 2.17
4333 7809 9.717892 CATATGATAAATCATGACAGCAATAGC 57.282 33.333 14.37 0.00 46.34 2.97
4336 7812 6.993902 TGATAAATCATGACAGCAATAGCAGA 59.006 34.615 0.00 0.00 45.49 4.26
4429 7905 8.812513 ATGAATTCTACCATGATCTCAAACAA 57.187 30.769 7.05 0.00 0.00 2.83
4450 7926 7.348080 ACAAGAAGGATAGAATCACATACGA 57.652 36.000 0.00 0.00 0.00 3.43
4475 7951 4.357947 GGAGCAGCACCGACGACA 62.358 66.667 0.00 0.00 0.00 4.35
4480 7956 1.565156 GCAGCACCGACGACATTGAA 61.565 55.000 0.00 0.00 0.00 2.69
4532 8008 0.601558 CGAGGTCGGGAAAGAAGTCA 59.398 55.000 0.00 0.00 35.37 3.41
4571 8047 4.476410 CCAGCAGTCGCGCGAGTA 62.476 66.667 36.92 13.33 45.49 2.59
4627 8153 3.012959 ACAGGAGGGATGGAGAAGACTTA 59.987 47.826 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.982130 CTTACGGCTCCCAGCACT 59.018 61.111 0.00 0.00 44.75 4.40
73 74 3.504375 AGGCTTTCTTTTGCTGGAAGAT 58.496 40.909 0.00 0.00 34.07 2.40
266 273 8.726988 GTTCAAGCCACTTGTATTATTAACAGA 58.273 33.333 7.18 0.00 41.66 3.41
332 339 1.600413 GCCAAGAGGAACGCAAACAAG 60.600 52.381 0.00 0.00 36.89 3.16
423 430 5.384063 TTTGAGCAATTTTCGCCAGATTA 57.616 34.783 0.00 0.00 0.00 1.75
424 431 3.940209 TTGAGCAATTTTCGCCAGATT 57.060 38.095 0.00 0.00 0.00 2.40
554 569 2.993899 CAAGTACCAAGCCGAAGTACAG 59.006 50.000 0.00 0.00 39.04 2.74
557 572 3.656559 GAACAAGTACCAAGCCGAAGTA 58.343 45.455 0.00 0.00 0.00 2.24
639 659 7.708998 TGTTTTACCTCACTTACCAATTGAAC 58.291 34.615 7.12 0.00 0.00 3.18
674 694 6.872547 GCAGGCTTAGTATAACTGTAATACCC 59.127 42.308 0.00 0.00 31.41 3.69
678 698 5.539048 CCGCAGGCTTAGTATAACTGTAAT 58.461 41.667 0.00 0.00 46.14 1.89
679 699 4.940463 CCGCAGGCTTAGTATAACTGTAA 58.060 43.478 0.00 0.00 46.14 2.41
680 700 4.579454 CCGCAGGCTTAGTATAACTGTA 57.421 45.455 0.00 0.00 46.14 2.74
681 701 3.454371 CCGCAGGCTTAGTATAACTGT 57.546 47.619 0.00 0.00 46.14 3.55
701 721 5.129320 ACTCCCTCCAATCCAAATTAATTGC 59.871 40.000 0.39 0.00 37.73 3.56
709 729 4.111577 ACATCTACTCCCTCCAATCCAAA 58.888 43.478 0.00 0.00 0.00 3.28
733 753 2.050168 CGCTGCAACGCCAAATGT 60.050 55.556 0.00 0.00 0.00 2.71
849 874 5.456763 CCCCTTCTTCTTCTGAAAAAGAGGA 60.457 44.000 14.90 2.11 39.14 3.71
889 914 2.625883 GGAAGAAGGGGTTTATTGGGGG 60.626 54.545 0.00 0.00 0.00 5.40
921 946 3.050275 GCCCACGGAACTGTCTGC 61.050 66.667 0.00 0.00 32.86 4.26
950 975 2.580601 CGTCTGAACGGGAAGGGGT 61.581 63.158 0.00 0.00 45.21 4.95
1206 1243 1.756950 TAGCAGCAGTACCTCGGGG 60.757 63.158 0.00 0.00 38.88 5.73
1229 1266 1.132817 AGGGTCAGTTAGGTGTGAGGT 60.133 52.381 0.00 0.00 0.00 3.85
1239 1276 5.011329 CAGTGGTAAGTAACAGGGTCAGTTA 59.989 44.000 0.00 0.00 0.00 2.24
1240 1277 3.971971 AGTGGTAAGTAACAGGGTCAGTT 59.028 43.478 0.00 0.00 0.00 3.16
1241 1278 3.323979 CAGTGGTAAGTAACAGGGTCAGT 59.676 47.826 0.00 0.00 0.00 3.41
1242 1279 3.864921 GCAGTGGTAAGTAACAGGGTCAG 60.865 52.174 0.00 0.00 0.00 3.51
1243 1280 2.038033 GCAGTGGTAAGTAACAGGGTCA 59.962 50.000 0.00 0.00 0.00 4.02
1244 1281 2.302157 AGCAGTGGTAAGTAACAGGGTC 59.698 50.000 0.00 0.00 0.00 4.46
1245 1282 2.302157 GAGCAGTGGTAAGTAACAGGGT 59.698 50.000 0.00 0.00 0.00 4.34
1246 1283 2.354805 GGAGCAGTGGTAAGTAACAGGG 60.355 54.545 0.00 0.00 0.00 4.45
1247 1284 2.354805 GGGAGCAGTGGTAAGTAACAGG 60.355 54.545 0.00 0.00 0.00 4.00
1257 1294 2.681778 CCTCTCGGGAGCAGTGGT 60.682 66.667 6.84 0.00 38.21 4.16
1259 1296 2.279069 ACACCTCTCGGGAGCAGTG 61.279 63.158 17.18 17.18 37.58 3.66
1274 1320 3.542712 ACAACTCAATTCGCATCACAC 57.457 42.857 0.00 0.00 0.00 3.82
1279 1325 3.498397 AGTCGAAACAACTCAATTCGCAT 59.502 39.130 2.52 0.00 44.04 4.73
1307 1353 0.855349 CGGCATCTCACTTCGCATAC 59.145 55.000 0.00 0.00 0.00 2.39
1308 1354 0.875908 GCGGCATCTCACTTCGCATA 60.876 55.000 0.00 0.00 44.87 3.14
1309 1355 2.176273 GCGGCATCTCACTTCGCAT 61.176 57.895 0.00 0.00 44.87 4.73
1316 1362 1.153289 ATCCACAGCGGCATCTCAC 60.153 57.895 1.45 0.00 33.14 3.51
1325 1371 1.091771 AATTGCCGAGATCCACAGCG 61.092 55.000 0.00 0.00 0.00 5.18
1354 1400 7.086685 ACTCTCAATTACCCTACTTCCAAAA 57.913 36.000 0.00 0.00 0.00 2.44
1356 1402 6.697641 AACTCTCAATTACCCTACTTCCAA 57.302 37.500 0.00 0.00 0.00 3.53
1362 1408 5.334724 TCCGAAACTCTCAATTACCCTAC 57.665 43.478 0.00 0.00 0.00 3.18
1367 1413 3.863424 TGCGATCCGAAACTCTCAATTAC 59.137 43.478 0.00 0.00 0.00 1.89
1372 1418 1.272490 ACTTGCGATCCGAAACTCTCA 59.728 47.619 0.00 0.00 0.00 3.27
1376 1422 2.386661 ATGACTTGCGATCCGAAACT 57.613 45.000 0.00 0.00 0.00 2.66
1412 1458 0.386113 CGCCCTAACCTGCTAGAGTC 59.614 60.000 0.00 0.00 0.00 3.36
1430 1498 4.985044 AATTTCACTTTGTACGGTCTCG 57.015 40.909 0.00 0.00 43.02 4.04
1466 1534 6.533723 CACTTGACATTTAGGTCGCTACATAA 59.466 38.462 0.00 0.00 40.72 1.90
1471 1539 3.512329 TCCACTTGACATTTAGGTCGCTA 59.488 43.478 0.00 0.00 40.72 4.26
1472 1540 2.301870 TCCACTTGACATTTAGGTCGCT 59.698 45.455 0.00 0.00 40.72 4.93
1486 1554 3.319755 GTGCCATTTCATTGTCCACTTG 58.680 45.455 0.00 0.00 0.00 3.16
1495 1563 0.896923 ATGGTGCGTGCCATTTCATT 59.103 45.000 7.00 0.00 46.33 2.57
1504 1572 0.523072 ATTGAAGTGATGGTGCGTGC 59.477 50.000 0.00 0.00 0.00 5.34
1510 1578 9.614792 GTAATCTACCTTAATTGAAGTGATGGT 57.385 33.333 0.00 0.00 32.74 3.55
1550 1618 1.402325 GGGCGTGCTACAACAATTTCC 60.402 52.381 0.00 0.00 0.00 3.13
1613 1753 2.957491 TGCCAAACTTTGTCCAACAG 57.043 45.000 0.88 0.00 0.00 3.16
1652 1792 2.290514 TGGAATCTTGCCAACTCTCCAG 60.291 50.000 0.00 0.00 31.13 3.86
1832 1980 6.575162 AGTTCCCTGCTTTTATAACAGTTG 57.425 37.500 0.00 0.00 0.00 3.16
1932 2080 4.248908 TGGGCTCACTCAATCCCA 57.751 55.556 0.00 0.00 45.87 4.37
2217 2365 3.055891 TCTTGATTGCAGAATCCGACTCA 60.056 43.478 0.00 0.00 37.74 3.41
2295 2443 5.467735 TCCATATTCAGCAATCAATGACTCG 59.532 40.000 0.00 0.00 0.00 4.18
2482 2630 9.301897 AGACATAAGGAGGGAATAAAATAATGC 57.698 33.333 0.00 0.00 0.00 3.56
2563 2713 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2564 2714 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2565 2715 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2566 2716 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2583 2733 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
2584 2734 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
2588 2738 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2589 2739 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2590 2740 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2591 2741 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2592 2742 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2593 2743 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2594 2744 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
2595 2745 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
2596 2746 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
2597 2747 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
2598 2748 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
2599 2749 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
2600 2750 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
2601 2751 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2602 2752 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2603 2753 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2604 2754 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2605 2755 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2606 2756 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2607 2757 8.728337 TCTATATACATCCGTATGTGGTAGTC 57.272 38.462 3.56 0.00 45.99 2.59
2644 2794 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
2645 2795 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
2646 2796 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2647 2797 9.764363 ATATACGAAGCAAAATGAGTGAATCTA 57.236 29.630 0.00 0.00 0.00 1.98
2648 2798 6.992063 ATACGAAGCAAAATGAGTGAATCT 57.008 33.333 0.00 0.00 0.00 2.40
2650 2800 9.547753 ACTATATACGAAGCAAAATGAGTGAAT 57.452 29.630 0.00 0.00 0.00 2.57
2651 2801 8.942338 ACTATATACGAAGCAAAATGAGTGAA 57.058 30.769 0.00 0.00 0.00 3.18
2652 2802 7.378728 CGACTATATACGAAGCAAAATGAGTGA 59.621 37.037 0.00 0.00 0.00 3.41
2653 2803 7.494130 CGACTATATACGAAGCAAAATGAGTG 58.506 38.462 0.00 0.00 0.00 3.51
2654 2804 6.144080 GCGACTATATACGAAGCAAAATGAGT 59.856 38.462 0.00 0.00 0.00 3.41
2655 2805 6.363626 AGCGACTATATACGAAGCAAAATGAG 59.636 38.462 0.00 0.00 0.00 2.90
2656 2806 6.213677 AGCGACTATATACGAAGCAAAATGA 58.786 36.000 0.00 0.00 0.00 2.57
2657 2807 6.453643 AGCGACTATATACGAAGCAAAATG 57.546 37.500 0.00 0.00 0.00 2.32
2658 2808 6.479001 ACAAGCGACTATATACGAAGCAAAAT 59.521 34.615 0.00 0.00 0.00 1.82
2659 2809 5.808540 ACAAGCGACTATATACGAAGCAAAA 59.191 36.000 0.00 0.00 0.00 2.44
2660 2810 5.345702 ACAAGCGACTATATACGAAGCAAA 58.654 37.500 0.00 0.00 0.00 3.68
2661 2811 4.928601 ACAAGCGACTATATACGAAGCAA 58.071 39.130 0.00 0.00 0.00 3.91
2662 2812 4.563337 ACAAGCGACTATATACGAAGCA 57.437 40.909 0.00 0.00 0.00 3.91
2663 2813 4.974275 TCAACAAGCGACTATATACGAAGC 59.026 41.667 0.00 0.00 0.00 3.86
2664 2814 7.445900 TTTCAACAAGCGACTATATACGAAG 57.554 36.000 0.00 0.00 0.00 3.79
2665 2815 7.997107 ATTTCAACAAGCGACTATATACGAA 57.003 32.000 0.00 0.00 0.00 3.85
2666 2816 7.997107 AATTTCAACAAGCGACTATATACGA 57.003 32.000 0.00 0.00 0.00 3.43
2667 2817 8.540492 AGAAATTTCAACAAGCGACTATATACG 58.460 33.333 19.99 0.00 0.00 3.06
2670 2820 9.817809 TCTAGAAATTTCAACAAGCGACTATAT 57.182 29.630 19.99 0.00 0.00 0.86
2671 2821 9.647797 TTCTAGAAATTTCAACAAGCGACTATA 57.352 29.630 19.99 0.00 0.00 1.31
2672 2822 8.547967 TTCTAGAAATTTCAACAAGCGACTAT 57.452 30.769 19.99 0.00 0.00 2.12
2673 2823 7.956420 TTCTAGAAATTTCAACAAGCGACTA 57.044 32.000 19.99 0.00 0.00 2.59
2674 2824 6.861065 TTCTAGAAATTTCAACAAGCGACT 57.139 33.333 19.99 0.00 0.00 4.18
2675 2825 7.321509 GTCTTTCTAGAAATTTCAACAAGCGAC 59.678 37.037 18.02 12.64 30.65 5.19
2676 2826 7.011950 TGTCTTTCTAGAAATTTCAACAAGCGA 59.988 33.333 18.02 5.04 30.65 4.93
2677 2827 7.132213 TGTCTTTCTAGAAATTTCAACAAGCG 58.868 34.615 18.02 2.79 30.65 4.68
2678 2828 8.856490 TTGTCTTTCTAGAAATTTCAACAAGC 57.144 30.769 18.02 11.53 30.65 4.01
2691 2841 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2692 2842 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2693 2843 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2694 2844 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2695 2845 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2696 2846 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2697 2847 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2698 2848 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2699 2849 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2700 2850 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2701 2851 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2702 2852 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2703 2853 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
2704 2854 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2705 2855 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2706 2856 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2707 2857 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2708 2858 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
2709 2859 3.011032 AGTTTCTACTCCCTCCGTTCCTA 59.989 47.826 0.00 0.00 0.00 2.94
2710 2860 2.177734 GTTTCTACTCCCTCCGTTCCT 58.822 52.381 0.00 0.00 0.00 3.36
2711 2861 2.177734 AGTTTCTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 0.00 3.62
2712 2862 3.957591 AAGTTTCTACTCCCTCCGTTC 57.042 47.619 0.00 0.00 31.99 3.95
2713 2863 4.701651 AAAAGTTTCTACTCCCTCCGTT 57.298 40.909 0.00 0.00 31.99 4.44
2714 2864 4.701651 AAAAAGTTTCTACTCCCTCCGT 57.298 40.909 0.00 0.00 31.99 4.69
2715 2865 8.959705 ATATTAAAAAGTTTCTACTCCCTCCG 57.040 34.615 0.00 0.00 31.99 4.63
2808 2959 3.438360 CAGCGATTGCCTTACAAAATCC 58.562 45.455 0.00 0.00 42.86 3.01
2922 3073 4.137543 CCAGCTGGGTAGAATTTACATCC 58.862 47.826 26.14 0.00 0.00 3.51
2937 3088 5.011023 AGACCTCAAAATTTTTACCAGCTGG 59.989 40.000 31.60 31.60 42.17 4.85
3366 3518 4.092383 ACACGACATGGCGAACTATAAAAC 59.908 41.667 31.27 0.00 34.83 2.43
3379 3531 6.533819 TTTTTAGTCAGTTACACGACATGG 57.466 37.500 0.00 0.00 34.48 3.66
3431 3583 3.314541 TGGTCGCCTTCTTCTAACTTC 57.685 47.619 0.00 0.00 0.00 3.01
3566 3718 9.357652 GCAACAACAAACATGAGAATGTATAAT 57.642 29.630 0.00 0.00 33.81 1.28
3765 3920 1.268032 GGCGAATATCACAAGCAACCG 60.268 52.381 0.00 0.00 0.00 4.44
3779 3934 1.714794 CTGACAGAGAAACGGCGAAT 58.285 50.000 16.62 0.07 0.00 3.34
4097 4255 9.427821 AACCTGATACTGTAATACTCATCTTCT 57.572 33.333 0.00 0.00 0.00 2.85
4186 4344 3.665745 TTGTTTACGGAGGGAGTACAC 57.334 47.619 0.00 0.00 0.00 2.90
4205 4363 9.632638 AACAAATAGGAGTATGCTCATGTATTT 57.367 29.630 13.14 13.75 43.37 1.40
4210 4368 7.307396 CCGTAAACAAATAGGAGTATGCTCATG 60.307 40.741 13.14 5.85 43.37 3.07
4216 4374 6.812998 TCCTCCGTAAACAAATAGGAGTATG 58.187 40.000 8.71 0.00 45.12 2.39
4217 4375 7.125356 ACTTCCTCCGTAAACAAATAGGAGTAT 59.875 37.037 8.71 0.00 45.12 2.12
4218 4376 6.438425 ACTTCCTCCGTAAACAAATAGGAGTA 59.562 38.462 8.71 0.00 45.12 2.59
4219 4377 5.247792 ACTTCCTCCGTAAACAAATAGGAGT 59.752 40.000 8.71 0.00 45.12 3.85
4220 4378 5.731591 ACTTCCTCCGTAAACAAATAGGAG 58.268 41.667 3.02 3.02 45.90 3.69
4221 4379 5.750352 ACTTCCTCCGTAAACAAATAGGA 57.250 39.130 0.00 0.00 0.00 2.94
4222 4380 9.603921 TTAATACTTCCTCCGTAAACAAATAGG 57.396 33.333 0.00 0.00 0.00 2.57
4225 4383 9.287373 TGTTTAATACTTCCTCCGTAAACAAAT 57.713 29.630 4.74 0.00 38.07 2.32
4226 4384 8.674263 TGTTTAATACTTCCTCCGTAAACAAA 57.326 30.769 4.74 0.00 38.07 2.83
4227 4385 8.851541 ATGTTTAATACTTCCTCCGTAAACAA 57.148 30.769 9.94 0.00 41.87 2.83
4228 4386 7.550196 GGATGTTTAATACTTCCTCCGTAAACA 59.450 37.037 8.69 8.69 44.07 2.83
4229 4387 7.550196 TGGATGTTTAATACTTCCTCCGTAAAC 59.450 37.037 16.39 0.00 46.35 2.01
4235 4393 8.211629 AGTACATGGATGTTTAATACTTCCTCC 58.788 37.037 16.39 0.00 46.35 4.30
4309 7785 8.851541 TGCTATTGCTGTCATGATTTATCATA 57.148 30.769 0.00 0.00 41.66 2.15
4311 7787 6.993902 TCTGCTATTGCTGTCATGATTTATCA 59.006 34.615 0.00 0.00 39.62 2.15
4325 7801 9.790344 ATGATTAGTTTAATCTCTGCTATTGCT 57.210 29.630 0.00 0.00 43.79 3.91
4332 7808 8.186821 AGTTTGCATGATTAGTTTAATCTCTGC 58.813 33.333 18.98 18.98 44.88 4.26
4336 7812 9.177608 TGCTAGTTTGCATGATTAGTTTAATCT 57.822 29.630 0.00 0.00 40.38 2.40
4403 7879 9.904198 TTGTTTGAGATCATGGTAGAATTCATA 57.096 29.630 8.44 0.00 0.00 2.15
4417 7893 8.542926 TGATTCTATCCTTCTTGTTTGAGATCA 58.457 33.333 0.00 0.00 0.00 2.92
4424 7900 8.258007 TCGTATGTGATTCTATCCTTCTTGTTT 58.742 33.333 0.00 0.00 0.00 2.83
4429 7905 6.015095 TGCATCGTATGTGATTCTATCCTTCT 60.015 38.462 0.00 0.00 0.00 2.85
4473 7949 2.618241 ACATGTGCGACAACTTCAATGT 59.382 40.909 0.00 0.00 0.00 2.71
4475 7951 2.096268 CGACATGTGCGACAACTTCAAT 60.096 45.455 1.15 0.00 0.00 2.57
4480 7956 1.275471 CGACGACATGTGCGACAACT 61.275 55.000 19.74 2.30 0.00 3.16
4489 7965 0.741326 CCTCATCCTCGACGACATGT 59.259 55.000 0.00 0.00 0.00 3.21
4523 7999 2.163818 TCGCCAACGATGACTTCTTT 57.836 45.000 0.00 0.00 45.12 2.52
4571 8047 0.112412 ATCAGGTTTTTGGGGAGCGT 59.888 50.000 0.00 0.00 0.00 5.07
4627 8153 2.751436 ATCATTGCGCCGCCAAGT 60.751 55.556 6.63 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.