Multiple sequence alignment - TraesCS3B01G312700

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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 TraesCS3B01G312700 chr3B 100.000 7053 0 0 1 7053 502637702 502644754 0.000000e+00 13025.0
1 TraesCS3B01G312700 chr3B 90.000 440 42 2 1637 2074 793293930 793294369 1.030000e-157 568.0
2 TraesCS3B01G312700 chr3B 89.640 444 40 5 1637 2074 793334364 793334807 1.720000e-155 560.0
3 TraesCS3B01G312700 chr3B 87.826 460 25 7 2254 2689 793334989 793335441 1.750000e-140 510.0
4 TraesCS3B01G312700 chr3B 87.500 464 23 16 2254 2689 793294551 793295007 2.940000e-138 503.0
5 TraesCS3B01G312700 chr3B 92.593 108 8 0 2861 2968 793295022 793295129 9.470000e-34 156.0
6 TraesCS3B01G312700 chr3B 82.692 104 12 5 2908 3010 793335476 793335574 3.500000e-13 87.9
7 TraesCS3B01G312700 chr3B 90.769 65 3 2 2190 2251 793334814 793334878 4.530000e-12 84.2
8 TraesCS3B01G312700 chr3D 96.000 3800 81 22 2807 6593 386435325 386439066 0.000000e+00 6109.0
9 TraesCS3B01G312700 chr3D 93.011 1488 69 14 1 1477 386432343 386433806 0.000000e+00 2139.0
10 TraesCS3B01G312700 chr3D 95.108 1206 46 9 1489 2689 386434133 386435330 0.000000e+00 1888.0
11 TraesCS3B01G312700 chr3D 85.825 388 43 7 6624 7002 24584986 24584602 1.100000e-107 401.0
12 TraesCS3B01G312700 chr3A 96.493 3536 77 16 2807 6336 508163786 508167280 0.000000e+00 5799.0
13 TraesCS3B01G312700 chr3A 93.513 2713 136 18 1 2690 508161097 508163792 0.000000e+00 3999.0
14 TraesCS3B01G312700 chr3A 97.696 434 10 0 6620 7053 17483255 17482822 0.000000e+00 747.0
15 TraesCS3B01G312700 chr3A 94.142 239 8 4 6326 6562 508167373 508167607 6.730000e-95 359.0
16 TraesCS3B01G312700 chr3A 95.370 108 5 0 2695 2802 469050690 469050583 9.410000e-39 172.0
17 TraesCS3B01G312700 chr2A 97.907 430 9 0 6624 7053 746931978 746931549 0.000000e+00 745.0
18 TraesCS3B01G312700 chr2A 97.273 440 9 3 6615 7053 360443291 360442854 0.000000e+00 743.0
19 TraesCS3B01G312700 chr2A 96.313 434 15 1 6619 7051 360444584 360444151 0.000000e+00 712.0
20 TraesCS3B01G312700 chr2D 91.087 460 16 11 2255 2690 582153479 582153021 3.640000e-167 599.0
21 TraesCS3B01G312700 chr2D 91.192 193 8 2 2807 2999 582153027 582152844 3.270000e-63 254.0
22 TraesCS3B01G312700 chr5D 86.817 531 41 11 1729 2251 479386103 479386612 3.690000e-157 566.0
23 TraesCS3B01G312700 chr5D 86.629 531 42 11 1729 2251 371030774 371030265 1.720000e-155 560.0
24 TraesCS3B01G312700 chr5D 83.865 564 58 12 1166 1701 371031330 371030772 2.270000e-139 507.0
25 TraesCS3B01G312700 chr1D 86.792 530 41 12 1729 2250 469879233 469878725 1.330000e-156 564.0
26 TraesCS3B01G312700 chr1D 84.192 563 58 18 1166 1701 469879789 469879231 1.050000e-142 518.0
27 TraesCS3B01G312700 chr1D 93.913 115 2 2 2695 2808 221115235 221115345 1.220000e-37 169.0
28 TraesCS3B01G312700 chr4B 86.038 530 47 7 1729 2251 62873336 62872827 1.730000e-150 544.0
29 TraesCS3B01G312700 chr4B 83.393 560 61 14 1166 1701 62873885 62873334 2.290000e-134 490.0
30 TraesCS3B01G312700 chr6A 86.064 531 43 10 1729 2251 598147479 598146972 6.220000e-150 542.0
31 TraesCS3B01G312700 chr6A 96.875 160 4 1 6624 6783 171802738 171802580 4.190000e-67 267.0
32 TraesCS3B01G312700 chr6A 100.000 140 0 0 6914 7053 171802518 171802379 7.020000e-65 259.0
33 TraesCS3B01G312700 chr6A 92.500 120 6 2 2695 2812 370657919 370657801 1.220000e-37 169.0
34 TraesCS3B01G312700 chr5B 87.826 460 26 7 2254 2689 387887506 387887053 4.880000e-141 512.0
35 TraesCS3B01G312700 chr5B 91.781 219 18 0 2471 2689 81271192 81270974 8.890000e-79 305.0
36 TraesCS3B01G312700 chr5B 92.949 156 9 1 2536 2689 330634530 330634375 7.120000e-55 226.0
37 TraesCS3B01G312700 chr5B 88.083 193 11 2 2807 2999 81270979 81270799 1.190000e-52 219.0
38 TraesCS3B01G312700 chr5B 89.720 107 11 0 2861 2967 330634360 330634254 3.430000e-28 137.0
39 TraesCS3B01G312700 chr6D 84.470 528 44 17 1729 2251 418222116 418221622 2.960000e-133 486.0
40 TraesCS3B01G312700 chr6D 93.043 115 7 1 2695 2809 374815994 374816107 4.380000e-37 167.0
41 TraesCS3B01G312700 chr4A 87.411 421 30 4 2292 2691 359953847 359954265 4.980000e-126 462.0
42 TraesCS3B01G312700 chr4D 86.340 388 43 6 6624 7002 508895590 508895204 1.420000e-111 414.0
43 TraesCS3B01G312700 chr2B 83.333 402 43 10 6624 7002 67420763 67420363 4.050000e-92 350.0
44 TraesCS3B01G312700 chr1A 81.951 410 42 14 6624 7002 453072069 453071661 1.140000e-82 318.0
45 TraesCS3B01G312700 chr7B 91.803 122 6 3 2695 2812 698486769 698486890 4.380000e-37 167.0
46 TraesCS3B01G312700 chr7B 92.920 113 7 1 2695 2807 695503588 695503477 5.660000e-36 163.0
47 TraesCS3B01G312700 chr1B 92.982 114 5 2 2695 2808 174087180 174087290 5.660000e-36 163.0
48 TraesCS3B01G312700 chr7A 92.373 118 2 2 2695 2812 290923846 290923736 2.040000e-35 161.0
49 TraesCS3B01G312700 chr5A 92.982 114 3 4 2695 2808 642536112 642536220 2.040000e-35 161.0


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 TraesCS3B01G312700 chr3B 502637702 502644754 7052 False 13025.000000 13025 100.000000 1 7053 1 chr3B.!!$F1 7052
1 TraesCS3B01G312700 chr3B 793293930 793295129 1199 False 409.000000 568 90.031000 1637 2968 3 chr3B.!!$F2 1331
2 TraesCS3B01G312700 chr3B 793334364 793335574 1210 False 310.525000 560 87.731750 1637 3010 4 chr3B.!!$F3 1373
3 TraesCS3B01G312700 chr3D 386432343 386439066 6723 False 3378.666667 6109 94.706333 1 6593 3 chr3D.!!$F1 6592
4 TraesCS3B01G312700 chr3A 508161097 508167607 6510 False 3385.666667 5799 94.716000 1 6562 3 chr3A.!!$F1 6561
5 TraesCS3B01G312700 chr2A 360442854 360444584 1730 True 727.500000 743 96.793000 6615 7053 2 chr2A.!!$R2 438
6 TraesCS3B01G312700 chr2D 582152844 582153479 635 True 426.500000 599 91.139500 2255 2999 2 chr2D.!!$R1 744
7 TraesCS3B01G312700 chr5D 479386103 479386612 509 False 566.000000 566 86.817000 1729 2251 1 chr5D.!!$F1 522
8 TraesCS3B01G312700 chr5D 371030265 371031330 1065 True 533.500000 560 85.247000 1166 2251 2 chr5D.!!$R1 1085
9 TraesCS3B01G312700 chr1D 469878725 469879789 1064 True 541.000000 564 85.492000 1166 2250 2 chr1D.!!$R1 1084
10 TraesCS3B01G312700 chr4B 62872827 62873885 1058 True 517.000000 544 84.715500 1166 2251 2 chr4B.!!$R1 1085
11 TraesCS3B01G312700 chr6A 598146972 598147479 507 True 542.000000 542 86.064000 1729 2251 1 chr6A.!!$R2 522

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 0.034896 GTTTTGAGCGGGACTCTCCA 59.965 55.000 0.00 0.00 46.41 3.86 F
345 346 0.606944 TGGGTGGGCGTATGTGTTTC 60.607 55.000 0.00 0.00 0.00 2.78 F
685 686 0.749649 CCATCTCCCTCAACCTCTCG 59.250 60.000 0.00 0.00 0.00 4.04 F
1292 1315 0.912487 AAGTCCGCCATGTAAGGGGA 60.912 55.000 2.67 2.67 43.81 4.81 F
2704 3251 0.040067 CTTCGACAAACCTTGCCTGC 60.040 55.000 0.00 0.00 0.00 4.85 F
2742 3289 0.033642 TGCGTGTTGTTCGGATGGTA 59.966 50.000 0.00 0.00 0.00 3.25 F
2767 3314 0.107410 TTGACTTTGTGCTCGGTGGT 60.107 50.000 0.00 0.00 0.00 4.16 F
2768 3315 0.107410 TGACTTTGTGCTCGGTGGTT 60.107 50.000 0.00 0.00 0.00 3.67 F
2774 3321 0.179043 TGTGCTCGGTGGTTGCTTTA 60.179 50.000 0.00 0.00 0.00 1.85 F
2775 3322 1.165270 GTGCTCGGTGGTTGCTTTAT 58.835 50.000 0.00 0.00 0.00 1.40 F
2776 3323 1.539827 GTGCTCGGTGGTTGCTTTATT 59.460 47.619 0.00 0.00 0.00 1.40 F
2777 3324 2.030274 GTGCTCGGTGGTTGCTTTATTT 60.030 45.455 0.00 0.00 0.00 1.40 F
4444 4999 3.054802 AGACGGAGAAAAAGATCTGGCAT 60.055 43.478 0.00 0.00 31.74 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1422 1.332195 CCTATCTGATCTCCGCACCA 58.668 55.000 0.00 0.0 0.00 4.17 R
2125 2508 0.998928 ATTCATGTAGCCCCACCACA 59.001 50.000 0.00 0.0 0.00 4.17 R
2297 2794 4.780815 TGGGTATCTCCAGTGCTTTAATG 58.219 43.478 0.00 0.0 38.11 1.90 R
2723 3270 0.033642 TACCATCCGAACAACACGCA 59.966 50.000 0.00 0.0 0.00 5.24 R
3707 4258 0.478507 AGTTTGACAACTGGGGGAGG 59.521 55.000 0.00 0.0 42.05 4.30 R
4169 4724 0.872388 GTTACAGGTTGCAACTCGGG 59.128 55.000 27.64 16.7 0.00 5.14 R
4609 5164 2.772287 CAAGAGTCCACTTCCAACTCC 58.228 52.381 0.00 0.0 40.21 3.85 R
4693 5248 5.358090 TGCAACAAACAATGATGTGACAAT 58.642 33.333 0.00 0.0 40.46 2.71 R
4889 5444 2.356022 CCTGGACATACACAAGCCATCA 60.356 50.000 0.00 0.0 0.00 3.07 R
4894 5449 2.014068 GCTCCCTGGACATACACAAGC 61.014 57.143 0.00 0.0 0.00 4.01 R
4972 5527 1.339291 GAGGATAATTTGCTGGGCTGC 59.661 52.381 0.00 0.0 0.00 5.25 R
5042 5597 8.863872 AGCACAAAATACTTACCAATAGAAGT 57.136 30.769 0.00 0.0 39.25 3.01 R
6597 7270 0.465460 AAGCCACACGAAGAAGCCAA 60.465 50.000 0.00 0.0 0.00 4.52 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
28 29 0.034896 GTTTTGAGCGGGACTCTCCA 59.965 55.000 0.00 0.00 46.41 3.86
70 71 1.202651 CCCCAATCACGGTGATAGTCC 60.203 57.143 22.91 0.00 35.76 3.85
92 93 2.481795 CCATCAATTTGTTCGGATGCCC 60.482 50.000 0.00 0.00 36.64 5.36
184 185 8.387354 CAGAATAGCAAACATGTCACGTTAATA 58.613 33.333 0.00 0.00 0.00 0.98
276 277 7.039434 TGGCCATGTGAACACTGAAATTATAAA 60.039 33.333 0.00 0.00 0.00 1.40
323 324 4.655963 AGCACACTGAAATCATAAGGTGT 58.344 39.130 1.61 1.61 38.24 4.16
345 346 0.606944 TGGGTGGGCGTATGTGTTTC 60.607 55.000 0.00 0.00 0.00 2.78
369 370 1.210538 ATCTGCCATCTCAAGCTCCA 58.789 50.000 0.00 0.00 0.00 3.86
370 371 0.986527 TCTGCCATCTCAAGCTCCAA 59.013 50.000 0.00 0.00 0.00 3.53
391 392 6.021596 CCAACCGAAATTGATTTCTTCTACG 58.978 40.000 12.98 1.80 42.96 3.51
396 397 8.601476 ACCGAAATTGATTTCTTCTACGTATTC 58.399 33.333 12.98 0.00 42.96 1.75
404 405 9.151471 TGATTTCTTCTACGTATTCTTTGGAAG 57.849 33.333 10.60 10.60 34.70 3.46
465 466 4.340894 TCTAATCGCAAATGAGCACAAC 57.659 40.909 0.00 0.00 0.00 3.32
471 472 2.046313 GCAAATGAGCACAACTTCACG 58.954 47.619 0.00 0.00 0.00 4.35
493 494 3.166679 GAGAGGACTAAACCACTGGACT 58.833 50.000 0.71 0.00 31.49 3.85
522 523 2.507407 TGATTAACAGGCAGGGGAAC 57.493 50.000 0.00 0.00 0.00 3.62
685 686 0.749649 CCATCTCCCTCAACCTCTCG 59.250 60.000 0.00 0.00 0.00 4.04
834 844 1.283613 GGTGTGGTGGTGGGAATGATA 59.716 52.381 0.00 0.00 0.00 2.15
945 959 2.362077 GCTTTTCACTTTCAGGCCTTCA 59.638 45.455 0.00 0.00 0.00 3.02
1054 1077 2.570706 GAGACAGAGCTCGCAGCA 59.429 61.111 8.37 0.00 45.56 4.41
1292 1315 0.912487 AAGTCCGCCATGTAAGGGGA 60.912 55.000 2.67 2.67 43.81 4.81
1322 1345 6.321690 ACTCACGCTCCATATTAGTACTTCTT 59.678 38.462 0.00 0.00 0.00 2.52
1362 1385 2.203294 GCGGTGTTTGGGAGTGGT 60.203 61.111 0.00 0.00 0.00 4.16
1377 1400 3.292159 GGTGGGTTTGGGTGCGAC 61.292 66.667 0.00 0.00 0.00 5.19
1391 1414 1.219124 GCGACAGATGGGCTTCAGA 59.781 57.895 0.00 0.00 0.00 3.27
1439 1474 0.952497 TTGCTTGGCTTCTGCTCGAG 60.952 55.000 8.45 8.45 39.59 4.04
1464 1499 7.778853 AGATTGGAAGCTCACTGATAAATTCAT 59.221 33.333 0.00 0.00 32.72 2.57
1481 1516 6.445451 AATTCATCTATGTAGCAGATGGGT 57.555 37.500 11.34 0.30 46.23 4.51
1486 1521 1.885049 ATGTAGCAGATGGGTGGAGT 58.115 50.000 0.00 0.00 0.00 3.85
1507 1857 3.848272 AATTGCTTGATTGTGGTACCG 57.152 42.857 7.57 0.00 0.00 4.02
1512 1862 3.823873 TGCTTGATTGTGGTACCGAAATT 59.176 39.130 7.57 0.00 0.00 1.82
1533 1883 9.631452 GAAATTTTTGCTCATAGAAGCTTAGTT 57.369 29.630 0.00 0.00 42.94 2.24
1549 1899 4.459337 GCTTAGTTCTGCCAATTAGGTGTT 59.541 41.667 0.00 0.00 40.61 3.32
1558 1929 9.502091 TTCTGCCAATTAGGTGTTGTATATATC 57.498 33.333 0.00 0.00 40.61 1.63
1566 1937 6.233905 AGGTGTTGTATATATCAGTGTGCA 57.766 37.500 0.00 0.00 0.00 4.57
1860 2243 0.971959 GGATGGTTCATGGGCTTGCA 60.972 55.000 0.00 0.00 0.00 4.08
2064 2447 9.528018 CTGTTTAAGGCTTTATTTCAAACTTCA 57.472 29.630 17.26 2.72 0.00 3.02
2125 2508 3.824443 ACCGCTTTACCAAACTGCTTAAT 59.176 39.130 0.00 0.00 0.00 1.40
2161 2545 6.484288 ACATGAATAAACCTCTCAATCCACA 58.516 36.000 0.00 0.00 0.00 4.17
2297 2794 7.969536 ATGCAAGTAGTATTGGTCATACATC 57.030 36.000 0.00 0.00 40.49 3.06
2328 2825 3.209410 CTGGAGATACCCATTTGCAGAC 58.791 50.000 0.00 0.00 37.01 3.51
2690 3237 8.323567 ACCATTTTAGGGTTATAAGAACTTCGA 58.676 33.333 0.00 0.00 34.10 3.71
2691 3238 8.610035 CCATTTTAGGGTTATAAGAACTTCGAC 58.390 37.037 0.00 0.00 0.00 4.20
2692 3239 9.158233 CATTTTAGGGTTATAAGAACTTCGACA 57.842 33.333 0.00 0.00 0.00 4.35
2693 3240 9.729281 ATTTTAGGGTTATAAGAACTTCGACAA 57.271 29.630 0.00 0.00 0.00 3.18
2694 3241 9.558396 TTTTAGGGTTATAAGAACTTCGACAAA 57.442 29.630 0.00 0.00 0.00 2.83
2695 3242 8.538409 TTAGGGTTATAAGAACTTCGACAAAC 57.462 34.615 0.00 0.00 0.00 2.93
2696 3243 5.936372 AGGGTTATAAGAACTTCGACAAACC 59.064 40.000 9.13 9.13 34.46 3.27
2697 3244 5.936372 GGGTTATAAGAACTTCGACAAACCT 59.064 40.000 13.92 0.00 35.35 3.50
2698 3245 6.429078 GGGTTATAAGAACTTCGACAAACCTT 59.571 38.462 13.92 0.00 35.35 3.50
2699 3246 7.295930 GGTTATAAGAACTTCGACAAACCTTG 58.704 38.462 9.88 0.00 32.87 3.61
2700 3247 3.692791 AAGAACTTCGACAAACCTTGC 57.307 42.857 0.00 0.00 0.00 4.01
2701 3248 1.947456 AGAACTTCGACAAACCTTGCC 59.053 47.619 0.00 0.00 0.00 4.52
2702 3249 1.947456 GAACTTCGACAAACCTTGCCT 59.053 47.619 0.00 0.00 0.00 4.75
2703 3250 1.308998 ACTTCGACAAACCTTGCCTG 58.691 50.000 0.00 0.00 0.00 4.85
2704 3251 0.040067 CTTCGACAAACCTTGCCTGC 60.040 55.000 0.00 0.00 0.00 4.85
2705 3252 1.781025 TTCGACAAACCTTGCCTGCG 61.781 55.000 0.00 0.00 0.00 5.18
2706 3253 2.644992 GACAAACCTTGCCTGCGG 59.355 61.111 0.00 0.00 0.00 5.69
2707 3254 2.123897 ACAAACCTTGCCTGCGGT 60.124 55.556 0.00 0.00 34.27 5.68
2708 3255 2.336088 CAAACCTTGCCTGCGGTG 59.664 61.111 0.00 0.00 32.86 4.94
2709 3256 2.912025 AAACCTTGCCTGCGGTGG 60.912 61.111 0.00 0.00 32.86 4.61
2718 3265 4.312231 CTGCGGTGGCGTTGTGTG 62.312 66.667 0.00 0.00 44.10 3.82
2720 3267 4.605967 GCGGTGGCGTTGTGTGTG 62.606 66.667 0.00 0.00 0.00 3.82
2721 3268 3.199190 CGGTGGCGTTGTGTGTGT 61.199 61.111 0.00 0.00 0.00 3.72
2722 3269 2.407210 GGTGGCGTTGTGTGTGTG 59.593 61.111 0.00 0.00 0.00 3.82
2723 3270 2.403378 GGTGGCGTTGTGTGTGTGT 61.403 57.895 0.00 0.00 0.00 3.72
2724 3271 1.226267 GTGGCGTTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2725 3272 2.277884 GGCGTTGTGTGTGTGTGC 60.278 61.111 0.00 0.00 0.00 4.57
2726 3273 2.647481 GCGTTGTGTGTGTGTGCG 60.647 61.111 0.00 0.00 0.00 5.34
2727 3274 2.781957 CGTTGTGTGTGTGTGCGT 59.218 55.556 0.00 0.00 0.00 5.24
2728 3275 1.579879 CGTTGTGTGTGTGTGCGTG 60.580 57.895 0.00 0.00 0.00 5.34
2729 3276 1.499949 GTTGTGTGTGTGTGCGTGT 59.500 52.632 0.00 0.00 0.00 4.49
2730 3277 0.109964 GTTGTGTGTGTGTGCGTGTT 60.110 50.000 0.00 0.00 0.00 3.32
2731 3278 0.110010 TTGTGTGTGTGTGCGTGTTG 60.110 50.000 0.00 0.00 0.00 3.33
2732 3279 1.231296 TGTGTGTGTGTGCGTGTTGT 61.231 50.000 0.00 0.00 0.00 3.32
2733 3280 0.109964 GTGTGTGTGTGCGTGTTGTT 60.110 50.000 0.00 0.00 0.00 2.83
2734 3281 0.167033 TGTGTGTGTGCGTGTTGTTC 59.833 50.000 0.00 0.00 0.00 3.18
2735 3282 0.855670 GTGTGTGTGCGTGTTGTTCG 60.856 55.000 0.00 0.00 0.00 3.95
2736 3283 1.297304 GTGTGTGCGTGTTGTTCGG 60.297 57.895 0.00 0.00 0.00 4.30
2737 3284 1.448013 TGTGTGCGTGTTGTTCGGA 60.448 52.632 0.00 0.00 0.00 4.55
2738 3285 0.812014 TGTGTGCGTGTTGTTCGGAT 60.812 50.000 0.00 0.00 0.00 4.18
2739 3286 0.384230 GTGTGCGTGTTGTTCGGATG 60.384 55.000 0.00 0.00 0.00 3.51
2740 3287 1.206578 GTGCGTGTTGTTCGGATGG 59.793 57.895 0.00 0.00 0.00 3.51
2741 3288 1.227704 TGCGTGTTGTTCGGATGGT 60.228 52.632 0.00 0.00 0.00 3.55
2742 3289 0.033642 TGCGTGTTGTTCGGATGGTA 59.966 50.000 0.00 0.00 0.00 3.25
2743 3290 0.441145 GCGTGTTGTTCGGATGGTAC 59.559 55.000 0.00 0.00 0.00 3.34
2744 3291 1.073177 CGTGTTGTTCGGATGGTACC 58.927 55.000 4.43 4.43 0.00 3.34
2745 3292 1.337447 CGTGTTGTTCGGATGGTACCT 60.337 52.381 14.36 0.00 0.00 3.08
2746 3293 2.774687 GTGTTGTTCGGATGGTACCTT 58.225 47.619 14.36 6.75 0.00 3.50
2747 3294 2.482721 GTGTTGTTCGGATGGTACCTTG 59.517 50.000 14.36 0.12 0.00 3.61
2748 3295 2.105134 TGTTGTTCGGATGGTACCTTGT 59.895 45.455 14.36 0.00 0.00 3.16
2749 3296 3.143728 GTTGTTCGGATGGTACCTTGTT 58.856 45.455 14.36 0.00 0.00 2.83
2750 3297 2.773487 TGTTCGGATGGTACCTTGTTG 58.227 47.619 14.36 0.00 0.00 3.33
2751 3298 2.369203 TGTTCGGATGGTACCTTGTTGA 59.631 45.455 14.36 1.96 0.00 3.18
2752 3299 2.740447 GTTCGGATGGTACCTTGTTGAC 59.260 50.000 14.36 2.06 0.00 3.18
2753 3300 2.253610 TCGGATGGTACCTTGTTGACT 58.746 47.619 14.36 0.00 0.00 3.41
2754 3301 2.635915 TCGGATGGTACCTTGTTGACTT 59.364 45.455 14.36 0.00 0.00 3.01
2755 3302 3.071892 TCGGATGGTACCTTGTTGACTTT 59.928 43.478 14.36 0.00 0.00 2.66
2756 3303 3.188460 CGGATGGTACCTTGTTGACTTTG 59.812 47.826 14.36 0.00 0.00 2.77
2757 3304 4.142038 GGATGGTACCTTGTTGACTTTGT 58.858 43.478 14.36 0.00 0.00 2.83
2758 3305 4.023193 GGATGGTACCTTGTTGACTTTGTG 60.023 45.833 14.36 0.00 0.00 3.33
2759 3306 2.685897 TGGTACCTTGTTGACTTTGTGC 59.314 45.455 14.36 0.00 0.00 4.57
2760 3307 2.949644 GGTACCTTGTTGACTTTGTGCT 59.050 45.455 4.06 0.00 0.00 4.40
2761 3308 3.003378 GGTACCTTGTTGACTTTGTGCTC 59.997 47.826 4.06 0.00 0.00 4.26
2762 3309 1.670811 ACCTTGTTGACTTTGTGCTCG 59.329 47.619 0.00 0.00 0.00 5.03
2763 3310 1.002468 CCTTGTTGACTTTGTGCTCGG 60.002 52.381 0.00 0.00 0.00 4.63
2764 3311 1.670811 CTTGTTGACTTTGTGCTCGGT 59.329 47.619 0.00 0.00 0.00 4.69
2765 3312 1.013596 TGTTGACTTTGTGCTCGGTG 58.986 50.000 0.00 0.00 0.00 4.94
2766 3313 0.307760 GTTGACTTTGTGCTCGGTGG 59.692 55.000 0.00 0.00 0.00 4.61
2767 3314 0.107410 TTGACTTTGTGCTCGGTGGT 60.107 50.000 0.00 0.00 0.00 4.16
2768 3315 0.107410 TGACTTTGTGCTCGGTGGTT 60.107 50.000 0.00 0.00 0.00 3.67
2769 3316 0.307760 GACTTTGTGCTCGGTGGTTG 59.692 55.000 0.00 0.00 0.00 3.77
2770 3317 1.008538 CTTTGTGCTCGGTGGTTGC 60.009 57.895 0.00 0.00 0.00 4.17
2771 3318 1.447317 CTTTGTGCTCGGTGGTTGCT 61.447 55.000 0.00 0.00 0.00 3.91
2772 3319 1.034838 TTTGTGCTCGGTGGTTGCTT 61.035 50.000 0.00 0.00 0.00 3.91
2773 3320 1.034838 TTGTGCTCGGTGGTTGCTTT 61.035 50.000 0.00 0.00 0.00 3.51
2774 3321 0.179043 TGTGCTCGGTGGTTGCTTTA 60.179 50.000 0.00 0.00 0.00 1.85
2775 3322 1.165270 GTGCTCGGTGGTTGCTTTAT 58.835 50.000 0.00 0.00 0.00 1.40
2776 3323 1.539827 GTGCTCGGTGGTTGCTTTATT 59.460 47.619 0.00 0.00 0.00 1.40
2777 3324 2.030274 GTGCTCGGTGGTTGCTTTATTT 60.030 45.455 0.00 0.00 0.00 1.40
2778 3325 3.189702 GTGCTCGGTGGTTGCTTTATTTA 59.810 43.478 0.00 0.00 0.00 1.40
2779 3326 4.013728 TGCTCGGTGGTTGCTTTATTTAT 58.986 39.130 0.00 0.00 0.00 1.40
2780 3327 5.065474 GTGCTCGGTGGTTGCTTTATTTATA 59.935 40.000 0.00 0.00 0.00 0.98
2781 3328 5.648526 TGCTCGGTGGTTGCTTTATTTATAA 59.351 36.000 0.00 0.00 0.00 0.98
2782 3329 6.151312 TGCTCGGTGGTTGCTTTATTTATAAA 59.849 34.615 0.00 0.00 0.00 1.40
2792 3339 5.427036 CTTTATTTATAAAGCGGGGCGAA 57.573 39.130 8.78 0.00 41.69 4.70
2793 3340 5.823353 CTTTATTTATAAAGCGGGGCGAAA 58.177 37.500 8.78 0.00 41.69 3.46
2794 3341 3.982576 ATTTATAAAGCGGGGCGAAAG 57.017 42.857 3.94 0.00 0.00 2.62
2809 3356 3.891056 CGAAAGCCTTTTTCGGTAACT 57.109 42.857 12.72 0.00 45.17 2.24
2810 3357 4.219143 CGAAAGCCTTTTTCGGTAACTT 57.781 40.909 12.72 0.00 45.17 2.66
2811 3358 4.216731 CGAAAGCCTTTTTCGGTAACTTC 58.783 43.478 12.72 0.00 45.17 3.01
2812 3359 3.891056 AAGCCTTTTTCGGTAACTTCG 57.109 42.857 0.00 0.00 0.00 3.79
2873 3420 7.864108 TGGTATTTGTCTATTTGATGACCTG 57.136 36.000 0.00 0.00 32.67 4.00
2975 3522 8.027524 TGGAAGTTCAGAGATAGCATTAATCT 57.972 34.615 5.01 0.00 36.40 2.40
3370 3918 4.927267 TTCCATACCAAGTTCCATCTGT 57.073 40.909 0.00 0.00 0.00 3.41
3476 4024 6.092259 GCAATATCGGTGAGTTTCTTGTAGTT 59.908 38.462 0.00 0.00 0.00 2.24
3477 4025 7.674240 GCAATATCGGTGAGTTTCTTGTAGTTC 60.674 40.741 0.00 0.00 0.00 3.01
3478 4026 4.931661 TCGGTGAGTTTCTTGTAGTTCT 57.068 40.909 0.00 0.00 0.00 3.01
3802 4353 6.462207 CGTTTCTAAGGATGGTCTCTGATGAT 60.462 42.308 0.00 0.00 0.00 2.45
3803 4354 7.278875 GTTTCTAAGGATGGTCTCTGATGATT 58.721 38.462 0.00 0.00 0.00 2.57
3804 4355 7.443302 TTCTAAGGATGGTCTCTGATGATTT 57.557 36.000 0.00 0.00 0.00 2.17
3805 4356 7.443302 TCTAAGGATGGTCTCTGATGATTTT 57.557 36.000 0.00 0.00 0.00 1.82
3806 4357 7.865820 TCTAAGGATGGTCTCTGATGATTTTT 58.134 34.615 0.00 0.00 0.00 1.94
3989 4544 7.092979 ACCCCTCCTACTACTTTATTCAGTTTC 60.093 40.741 0.00 0.00 0.00 2.78
4202 4757 4.585879 ACCTGTAACAACTGAAACTGTGT 58.414 39.130 0.00 0.00 0.00 3.72
4249 4804 3.181497 CGAGTATTTTTGACTGGCATGGG 60.181 47.826 0.00 0.00 0.00 4.00
4376 4931 4.804108 TCTTGGGTGTTTTGCAAATATCG 58.196 39.130 13.65 0.00 0.00 2.92
4444 4999 3.054802 AGACGGAGAAAAAGATCTGGCAT 60.055 43.478 0.00 0.00 31.74 4.40
4585 5140 6.522054 AGACGATTTTAGAGTCCAAAGTTGA 58.478 36.000 1.68 0.00 35.65 3.18
4889 5444 6.228995 CACATGTTCTGCTCCATATATGACT 58.771 40.000 14.54 0.00 0.00 3.41
4894 5449 5.672421 TCTGCTCCATATATGACTGATGG 57.328 43.478 14.54 0.00 41.36 3.51
4972 5527 7.182761 GGTCTGATGAACAATCTAAACAATCG 58.817 38.462 0.00 0.00 36.15 3.34
5489 6050 9.155975 CATACTAGTGTCTAGTGCTTTGATTTT 57.844 33.333 16.60 0.00 0.00 1.82
5490 6051 9.726438 ATACTAGTGTCTAGTGCTTTGATTTTT 57.274 29.630 16.60 0.00 0.00 1.94
5541 6102 5.117355 TGTCACCGTTTTGTGTGTTTTTA 57.883 34.783 0.00 0.00 37.51 1.52
5543 6104 6.157211 TGTCACCGTTTTGTGTGTTTTTATT 58.843 32.000 0.00 0.00 37.51 1.40
5544 6105 6.308282 TGTCACCGTTTTGTGTGTTTTTATTC 59.692 34.615 0.00 0.00 37.51 1.75
5597 6160 5.963176 TGATTTTATGAAGCAGAGCAACA 57.037 34.783 0.00 0.00 0.00 3.33
5809 6372 5.779922 TGAAACTACGTCTACTGCTGAAAT 58.220 37.500 0.00 0.00 0.00 2.17
6008 6571 0.319211 TCCGCTCTACAACGTTGTGG 60.319 55.000 37.43 34.63 42.31 4.17
6089 6652 6.719370 CCTTTACAGTCTCAGATAGCTAGGAT 59.281 42.308 0.00 0.00 0.00 3.24
6244 6807 2.551938 GGTGAGAGGCTGAGCTCTTTTT 60.552 50.000 16.19 0.00 32.44 1.94
6262 6825 1.275666 TTGTCACATGTCTCGGGGAT 58.724 50.000 0.00 0.00 0.00 3.85
6263 6826 0.536724 TGTCACATGTCTCGGGGATG 59.463 55.000 0.00 0.00 0.00 3.51
6288 6851 5.297527 TGTTATTGATAGCATTGCTGACTGG 59.702 40.000 21.31 0.00 40.10 4.00
6291 6854 1.945394 GATAGCATTGCTGACTGGTGG 59.055 52.381 21.31 0.00 40.10 4.61
6317 6880 5.010933 AGACATTCTCTTCCTAACTCGTGA 58.989 41.667 0.00 0.00 0.00 4.35
6326 6889 1.067060 CCTAACTCGTGATCGGCATCA 59.933 52.381 0.00 0.00 36.62 3.07
6327 6890 2.481276 CCTAACTCGTGATCGGCATCAA 60.481 50.000 1.98 0.00 40.90 2.57
6375 7040 2.965671 AGCTATGTGCCATATGCCTT 57.034 45.000 0.00 0.00 44.23 4.35
6425 7092 5.976534 GGCAATGCAAATATATGTTTCGTGA 59.023 36.000 7.79 0.00 0.00 4.35
6427 7094 6.471841 GCAATGCAAATATATGTTTCGTGACA 59.528 34.615 0.00 0.00 0.00 3.58
6562 7235 8.816894 TCAACTCTGAATAGTAAGAATCAACCT 58.183 33.333 0.00 0.00 0.00 3.50
6588 7261 0.322322 TGAAACCGTCCAAGGCGTAT 59.678 50.000 3.12 0.00 33.69 3.06
6593 7266 2.125269 GTCCAAGGCGTATGCGGT 60.125 61.111 5.09 0.00 44.10 5.68
6594 7267 2.125310 TCCAAGGCGTATGCGGTG 60.125 61.111 5.09 1.23 44.10 4.94
6595 7268 3.202001 CCAAGGCGTATGCGGTGG 61.202 66.667 11.81 11.81 44.10 4.61
6596 7269 3.202001 CAAGGCGTATGCGGTGGG 61.202 66.667 5.09 0.00 44.10 4.61
6597 7270 3.712907 AAGGCGTATGCGGTGGGT 61.713 61.111 5.09 0.00 44.10 4.51
6598 7271 3.262448 AAGGCGTATGCGGTGGGTT 62.262 57.895 5.09 0.00 44.10 4.11
6599 7272 3.505184 GGCGTATGCGGTGGGTTG 61.505 66.667 5.09 0.00 44.10 3.77
6600 7273 3.505184 GCGTATGCGGTGGGTTGG 61.505 66.667 5.09 0.00 38.78 3.77
6601 7274 3.505184 CGTATGCGGTGGGTTGGC 61.505 66.667 0.00 0.00 0.00 4.52
6602 7275 2.045340 GTATGCGGTGGGTTGGCT 60.045 61.111 0.00 0.00 0.00 4.75
6603 7276 1.677633 GTATGCGGTGGGTTGGCTT 60.678 57.895 0.00 0.00 0.00 4.35
6604 7277 1.377987 TATGCGGTGGGTTGGCTTC 60.378 57.895 0.00 0.00 0.00 3.86
6605 7278 1.847798 TATGCGGTGGGTTGGCTTCT 61.848 55.000 0.00 0.00 0.00 2.85
6606 7279 2.597510 GCGGTGGGTTGGCTTCTT 60.598 61.111 0.00 0.00 0.00 2.52
6607 7280 2.626780 GCGGTGGGTTGGCTTCTTC 61.627 63.158 0.00 0.00 0.00 2.87
6608 7281 2.325082 CGGTGGGTTGGCTTCTTCG 61.325 63.158 0.00 0.00 0.00 3.79
6609 7282 1.228154 GGTGGGTTGGCTTCTTCGT 60.228 57.895 0.00 0.00 0.00 3.85
6610 7283 1.515521 GGTGGGTTGGCTTCTTCGTG 61.516 60.000 0.00 0.00 0.00 4.35
6611 7284 0.818040 GTGGGTTGGCTTCTTCGTGT 60.818 55.000 0.00 0.00 0.00 4.49
6612 7285 0.817634 TGGGTTGGCTTCTTCGTGTG 60.818 55.000 0.00 0.00 0.00 3.82
6613 7286 1.515521 GGGTTGGCTTCTTCGTGTGG 61.516 60.000 0.00 0.00 0.00 4.17
6614 7287 1.282875 GTTGGCTTCTTCGTGTGGC 59.717 57.895 0.00 0.00 0.00 5.01
6615 7288 1.148273 TTGGCTTCTTCGTGTGGCT 59.852 52.632 0.00 0.00 0.00 4.75
6616 7289 0.465460 TTGGCTTCTTCGTGTGGCTT 60.465 50.000 0.00 0.00 0.00 4.35
6617 7290 1.165907 TGGCTTCTTCGTGTGGCTTG 61.166 55.000 0.00 0.00 0.00 4.01
6618 7291 1.576421 GCTTCTTCGTGTGGCTTGG 59.424 57.895 0.00 0.00 0.00 3.61
6619 7292 1.576421 CTTCTTCGTGTGGCTTGGC 59.424 57.895 0.00 0.00 0.00 4.52
6765 7438 1.468127 TCGTACGCGTAGGATTCACAA 59.532 47.619 31.33 12.77 39.49 3.33
6789 7462 2.203788 AGGCTCAGGGTTCGACCA 60.204 61.111 6.41 0.00 41.02 4.02
6831 7504 2.840651 AGTAGGAAGCACACATAAGCCT 59.159 45.455 0.00 0.00 0.00 4.58
6880 7553 3.490759 GGAGCACCGCACACATCG 61.491 66.667 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.485066 GACTATCACCGTGATTGGGGT 59.515 52.381 18.97 12.44 38.26 4.95
70 71 2.481795 GGCATCCGAACAAATTGATGGG 60.482 50.000 0.00 0.00 36.09 4.00
184 185 0.813184 CGCATGTTTCTTGCCTGGAT 59.187 50.000 0.00 0.00 36.75 3.41
276 277 1.271840 TAGCCCGCCACTTCAATCCT 61.272 55.000 0.00 0.00 0.00 3.24
284 285 1.296715 CTGAAACTAGCCCGCCACT 59.703 57.895 0.00 0.00 0.00 4.00
323 324 1.223211 CACATACGCCCACCCATGA 59.777 57.895 0.00 0.00 0.00 3.07
345 346 4.172505 GAGCTTGAGATGGCAGATATACG 58.827 47.826 0.00 0.00 0.00 3.06
433 434 4.782019 TTGCGATTAGAAACAAAGCCAT 57.218 36.364 0.00 0.00 0.00 4.40
447 448 3.004629 TGAAGTTGTGCTCATTTGCGATT 59.995 39.130 0.00 0.00 35.36 3.34
465 466 2.561419 TGGTTTAGTCCTCTCCGTGAAG 59.439 50.000 0.00 0.00 0.00 3.02
471 472 2.234168 GTCCAGTGGTTTAGTCCTCTCC 59.766 54.545 9.54 0.00 0.00 3.71
493 494 6.491062 CCCTGCCTGTTAATCATGATTTCATA 59.509 38.462 25.26 10.60 34.26 2.15
522 523 4.085876 CAAGTCCTTGGGCCAGTG 57.914 61.111 6.23 3.77 36.95 3.66
812 822 2.150719 ATTCCCACCACCACACCGA 61.151 57.895 0.00 0.00 0.00 4.69
945 959 5.765182 AGAAATTCGATGCCGATAAAGGAAT 59.235 36.000 0.00 0.00 45.10 3.01
1280 1303 1.486726 GAGTGAGGTCCCCTTACATGG 59.513 57.143 7.79 0.00 41.78 3.66
1292 1315 1.781786 ATATGGAGCGTGAGTGAGGT 58.218 50.000 0.00 0.00 0.00 3.85
1299 1322 6.710597 AAGAAGTACTAATATGGAGCGTGA 57.289 37.500 0.00 0.00 0.00 4.35
1322 1345 4.570772 CGAACAGCAGGCTATTAGCTAAAA 59.429 41.667 10.85 0.00 41.99 1.52
1362 1385 2.063015 ATCTGTCGCACCCAAACCCA 62.063 55.000 0.00 0.00 0.00 4.51
1391 1414 2.129555 ATCTCCGCACCAACCAAGCT 62.130 55.000 0.00 0.00 0.00 3.74
1399 1422 1.332195 CCTATCTGATCTCCGCACCA 58.668 55.000 0.00 0.00 0.00 4.17
1439 1474 7.325660 TGAATTTATCAGTGAGCTTCCAATC 57.674 36.000 0.00 0.00 33.04 2.67
1464 1499 3.234353 CTCCACCCATCTGCTACATAGA 58.766 50.000 0.00 0.00 0.00 1.98
1481 1516 4.406456 ACCACAATCAAGCAATTACTCCA 58.594 39.130 0.00 0.00 0.00 3.86
1486 1521 4.580868 TCGGTACCACAATCAAGCAATTA 58.419 39.130 13.54 0.00 0.00 1.40
1507 1857 9.631452 AACTAAGCTTCTATGAGCAAAAATTTC 57.369 29.630 0.00 0.00 45.12 2.17
1512 1862 6.128172 GCAGAACTAAGCTTCTATGAGCAAAA 60.128 38.462 0.00 0.00 45.12 2.44
1533 1883 8.655901 TGATATATACAACACCTAATTGGCAGA 58.344 33.333 0.00 0.00 40.22 4.26
1558 1929 6.129009 GCTTGTGAAAATTAGAATGCACACTG 60.129 38.462 0.00 0.00 36.16 3.66
1593 1964 4.034975 GCAAGTGGAGAACATCATAGAAGC 59.965 45.833 0.00 0.00 0.00 3.86
1594 1965 5.426504 AGCAAGTGGAGAACATCATAGAAG 58.573 41.667 0.00 0.00 0.00 2.85
1595 1966 5.426689 AGCAAGTGGAGAACATCATAGAA 57.573 39.130 0.00 0.00 0.00 2.10
1596 1967 5.426689 AAGCAAGTGGAGAACATCATAGA 57.573 39.130 0.00 0.00 0.00 1.98
1647 2022 1.525923 CCACAGCTCTAGCCTGCAT 59.474 57.895 9.36 0.00 43.38 3.96
1681 2056 4.003648 CTCAGCCCTTTCGTCAAATACTT 58.996 43.478 0.00 0.00 0.00 2.24
1860 2243 2.095059 GTCAAGCGTTTCATCCAGCAAT 60.095 45.455 0.00 0.00 0.00 3.56
2064 2447 7.040201 TGTTTTTCATATCAGCAAAGAAGAGCT 60.040 33.333 0.00 0.00 42.94 4.09
2125 2508 0.998928 ATTCATGTAGCCCCACCACA 59.001 50.000 0.00 0.00 0.00 4.17
2297 2794 4.780815 TGGGTATCTCCAGTGCTTTAATG 58.219 43.478 0.00 0.00 38.11 1.90
2701 3248 4.312231 CACACAACGCCACCGCAG 62.312 66.667 0.00 0.00 38.22 5.18
2703 3250 4.605967 CACACACAACGCCACCGC 62.606 66.667 0.00 0.00 38.22 5.68
2704 3251 3.199190 ACACACACAACGCCACCG 61.199 61.111 0.00 0.00 41.14 4.94
2705 3252 2.403378 ACACACACACAACGCCACC 61.403 57.895 0.00 0.00 0.00 4.61
2706 3253 1.226267 CACACACACACAACGCCAC 60.226 57.895 0.00 0.00 0.00 5.01
2707 3254 3.045277 GCACACACACACAACGCCA 62.045 57.895 0.00 0.00 0.00 5.69
2708 3255 2.277884 GCACACACACACAACGCC 60.278 61.111 0.00 0.00 0.00 5.68
2709 3256 2.647481 CGCACACACACACAACGC 60.647 61.111 0.00 0.00 0.00 4.84
2710 3257 1.579879 CACGCACACACACACAACG 60.580 57.895 0.00 0.00 0.00 4.10
2711 3258 0.109964 AACACGCACACACACACAAC 60.110 50.000 0.00 0.00 0.00 3.32
2712 3259 0.110010 CAACACGCACACACACACAA 60.110 50.000 0.00 0.00 0.00 3.33
2713 3260 1.231296 ACAACACGCACACACACACA 61.231 50.000 0.00 0.00 0.00 3.72
2714 3261 0.109964 AACAACACGCACACACACAC 60.110 50.000 0.00 0.00 0.00 3.82
2715 3262 0.167033 GAACAACACGCACACACACA 59.833 50.000 0.00 0.00 0.00 3.72
2716 3263 0.855670 CGAACAACACGCACACACAC 60.856 55.000 0.00 0.00 0.00 3.82
2717 3264 1.421877 CGAACAACACGCACACACA 59.578 52.632 0.00 0.00 0.00 3.72
2718 3265 1.297304 CCGAACAACACGCACACAC 60.297 57.895 0.00 0.00 0.00 3.82
2719 3266 0.812014 ATCCGAACAACACGCACACA 60.812 50.000 0.00 0.00 0.00 3.72
2720 3267 0.384230 CATCCGAACAACACGCACAC 60.384 55.000 0.00 0.00 0.00 3.82
2721 3268 1.502990 CCATCCGAACAACACGCACA 61.503 55.000 0.00 0.00 0.00 4.57
2722 3269 1.206578 CCATCCGAACAACACGCAC 59.793 57.895 0.00 0.00 0.00 5.34
2723 3270 0.033642 TACCATCCGAACAACACGCA 59.966 50.000 0.00 0.00 0.00 5.24
2724 3271 0.441145 GTACCATCCGAACAACACGC 59.559 55.000 0.00 0.00 0.00 5.34
2725 3272 1.073177 GGTACCATCCGAACAACACG 58.927 55.000 7.15 0.00 0.00 4.49
2726 3273 2.467566 AGGTACCATCCGAACAACAC 57.532 50.000 15.94 0.00 0.00 3.32
2727 3274 2.105134 ACAAGGTACCATCCGAACAACA 59.895 45.455 15.94 0.00 0.00 3.33
2728 3275 2.774687 ACAAGGTACCATCCGAACAAC 58.225 47.619 15.94 0.00 0.00 3.32
2729 3276 3.142951 CAACAAGGTACCATCCGAACAA 58.857 45.455 15.94 0.00 0.00 2.83
2730 3277 2.369203 TCAACAAGGTACCATCCGAACA 59.631 45.455 15.94 0.00 0.00 3.18
2731 3278 2.740447 GTCAACAAGGTACCATCCGAAC 59.260 50.000 15.94 1.68 0.00 3.95
2732 3279 2.635915 AGTCAACAAGGTACCATCCGAA 59.364 45.455 15.94 0.00 0.00 4.30
2733 3280 2.253610 AGTCAACAAGGTACCATCCGA 58.746 47.619 15.94 0.60 0.00 4.55
2734 3281 2.762535 AGTCAACAAGGTACCATCCG 57.237 50.000 15.94 1.33 0.00 4.18
2735 3282 4.023193 CACAAAGTCAACAAGGTACCATCC 60.023 45.833 15.94 0.00 0.00 3.51
2736 3283 4.556699 GCACAAAGTCAACAAGGTACCATC 60.557 45.833 15.94 0.00 0.00 3.51
2737 3284 3.317993 GCACAAAGTCAACAAGGTACCAT 59.682 43.478 15.94 0.00 0.00 3.55
2738 3285 2.685897 GCACAAAGTCAACAAGGTACCA 59.314 45.455 15.94 0.00 0.00 3.25
2739 3286 2.949644 AGCACAAAGTCAACAAGGTACC 59.050 45.455 2.73 2.73 0.00 3.34
2740 3287 3.303132 CGAGCACAAAGTCAACAAGGTAC 60.303 47.826 0.00 0.00 0.00 3.34
2741 3288 2.869801 CGAGCACAAAGTCAACAAGGTA 59.130 45.455 0.00 0.00 0.00 3.08
2742 3289 1.670811 CGAGCACAAAGTCAACAAGGT 59.329 47.619 0.00 0.00 0.00 3.50
2743 3290 1.002468 CCGAGCACAAAGTCAACAAGG 60.002 52.381 0.00 0.00 0.00 3.61
2744 3291 1.670811 ACCGAGCACAAAGTCAACAAG 59.329 47.619 0.00 0.00 0.00 3.16
2745 3292 1.400142 CACCGAGCACAAAGTCAACAA 59.600 47.619 0.00 0.00 0.00 2.83
2746 3293 1.013596 CACCGAGCACAAAGTCAACA 58.986 50.000 0.00 0.00 0.00 3.33
2747 3294 0.307760 CCACCGAGCACAAAGTCAAC 59.692 55.000 0.00 0.00 0.00 3.18
2748 3295 0.107410 ACCACCGAGCACAAAGTCAA 60.107 50.000 0.00 0.00 0.00 3.18
2749 3296 0.107410 AACCACCGAGCACAAAGTCA 60.107 50.000 0.00 0.00 0.00 3.41
2750 3297 0.307760 CAACCACCGAGCACAAAGTC 59.692 55.000 0.00 0.00 0.00 3.01
2751 3298 1.724582 GCAACCACCGAGCACAAAGT 61.725 55.000 0.00 0.00 0.00 2.66
2752 3299 1.008538 GCAACCACCGAGCACAAAG 60.009 57.895 0.00 0.00 0.00 2.77
2753 3300 1.034838 AAGCAACCACCGAGCACAAA 61.035 50.000 0.00 0.00 0.00 2.83
2754 3301 1.034838 AAAGCAACCACCGAGCACAA 61.035 50.000 0.00 0.00 0.00 3.33
2755 3302 0.179043 TAAAGCAACCACCGAGCACA 60.179 50.000 0.00 0.00 0.00 4.57
2756 3303 1.165270 ATAAAGCAACCACCGAGCAC 58.835 50.000 0.00 0.00 0.00 4.40
2757 3304 1.904287 AATAAAGCAACCACCGAGCA 58.096 45.000 0.00 0.00 0.00 4.26
2758 3305 4.632538 ATAAATAAAGCAACCACCGAGC 57.367 40.909 0.00 0.00 0.00 5.03
2771 3318 5.733937 GCTTTCGCCCCGCTTTATAAATAAA 60.734 40.000 0.00 0.00 0.00 1.40
2772 3319 4.261280 GCTTTCGCCCCGCTTTATAAATAA 60.261 41.667 0.00 0.00 0.00 1.40
2773 3320 3.251487 GCTTTCGCCCCGCTTTATAAATA 59.749 43.478 0.00 0.00 0.00 1.40
2774 3321 2.034179 GCTTTCGCCCCGCTTTATAAAT 59.966 45.455 0.00 0.00 0.00 1.40
2775 3322 1.402613 GCTTTCGCCCCGCTTTATAAA 59.597 47.619 0.00 0.00 0.00 1.40
2776 3323 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.000 0.00 0.00 0.00 0.98
2777 3324 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
2778 3325 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
2788 3335 2.031420 AGTTACCGAAAAAGGCTTTCGC 60.031 45.455 13.76 7.41 46.89 4.70
2790 3337 4.216731 CGAAGTTACCGAAAAAGGCTTTC 58.783 43.478 13.76 0.41 33.69 2.62
2791 3338 3.004002 CCGAAGTTACCGAAAAAGGCTTT 59.996 43.478 6.68 6.68 33.69 3.51
2792 3339 2.551032 CCGAAGTTACCGAAAAAGGCTT 59.449 45.455 0.00 0.00 33.69 4.35
2793 3340 2.148768 CCGAAGTTACCGAAAAAGGCT 58.851 47.619 0.00 0.00 33.69 4.58
2794 3341 2.145536 TCCGAAGTTACCGAAAAAGGC 58.854 47.619 0.00 0.00 33.69 4.35
2795 3342 3.656559 TCTCCGAAGTTACCGAAAAAGG 58.343 45.455 0.00 0.00 37.30 3.11
2796 3343 6.534079 ACATATCTCCGAAGTTACCGAAAAAG 59.466 38.462 0.00 0.00 0.00 2.27
2797 3344 6.400568 ACATATCTCCGAAGTTACCGAAAAA 58.599 36.000 0.00 0.00 0.00 1.94
2798 3345 5.969423 ACATATCTCCGAAGTTACCGAAAA 58.031 37.500 0.00 0.00 0.00 2.29
2799 3346 5.587388 ACATATCTCCGAAGTTACCGAAA 57.413 39.130 0.00 0.00 0.00 3.46
2800 3347 5.587388 AACATATCTCCGAAGTTACCGAA 57.413 39.130 0.00 0.00 0.00 4.30
2801 3348 5.587388 AAACATATCTCCGAAGTTACCGA 57.413 39.130 0.00 0.00 0.00 4.69
2802 3349 7.941795 ATAAAACATATCTCCGAAGTTACCG 57.058 36.000 0.00 0.00 0.00 4.02
2873 3420 7.497249 AGGCTTCTTGAGTTATATGAACACATC 59.503 37.037 0.00 0.00 0.00 3.06
2990 3538 6.507900 AGATAAACATGACACGGTAGATCAG 58.492 40.000 0.00 0.00 0.00 2.90
3224 3772 5.107065 CCTGATTGACAACTTAGAACGGTTC 60.107 44.000 12.91 12.91 0.00 3.62
3338 3886 9.239551 GGAACTTGGTATGGAAATAGTAGTTTT 57.760 33.333 0.00 0.00 0.00 2.43
3339 3887 8.387813 TGGAACTTGGTATGGAAATAGTAGTTT 58.612 33.333 0.00 0.00 0.00 2.66
3340 3888 7.924541 TGGAACTTGGTATGGAAATAGTAGTT 58.075 34.615 0.00 0.00 0.00 2.24
3341 3889 7.504926 TGGAACTTGGTATGGAAATAGTAGT 57.495 36.000 0.00 0.00 0.00 2.73
3342 3890 8.432805 AGATGGAACTTGGTATGGAAATAGTAG 58.567 37.037 0.00 0.00 0.00 2.57
3370 3918 9.739276 ATTTTCAATGGAGTAACAGACATTAGA 57.261 29.630 0.00 0.00 32.71 2.10
3519 4070 1.557832 ACGAGGCTGGCAACCTAAATA 59.442 47.619 9.93 0.00 37.77 1.40
3706 4257 0.539669 GTTTGACAACTGGGGGAGGG 60.540 60.000 0.00 0.00 0.00 4.30
3707 4258 0.478507 AGTTTGACAACTGGGGGAGG 59.521 55.000 0.00 0.00 42.05 4.30
3708 4259 2.364972 AAGTTTGACAACTGGGGGAG 57.635 50.000 0.00 0.00 42.89 4.30
3709 4260 3.396276 TCATAAGTTTGACAACTGGGGGA 59.604 43.478 0.00 0.00 42.89 4.81
3710 4261 3.761897 TCATAAGTTTGACAACTGGGGG 58.238 45.455 0.00 0.00 42.89 5.40
3711 4262 4.218417 CCTTCATAAGTTTGACAACTGGGG 59.782 45.833 0.00 0.00 42.89 4.96
3712 4263 4.827284 ACCTTCATAAGTTTGACAACTGGG 59.173 41.667 0.00 0.00 42.89 4.45
3713 4264 5.278463 CCACCTTCATAAGTTTGACAACTGG 60.278 44.000 0.00 0.00 42.89 4.00
3714 4265 5.278463 CCCACCTTCATAAGTTTGACAACTG 60.278 44.000 0.00 0.00 42.89 3.16
3989 4544 6.535150 CACACATACACACTGTAATAGAAGGG 59.465 42.308 0.00 0.00 36.31 3.95
4169 4724 0.872388 GTTACAGGTTGCAACTCGGG 59.128 55.000 27.64 16.70 0.00 5.14
4202 4757 2.880443 ACTACCCGAGGTTGTGAAGTA 58.120 47.619 8.78 0.00 39.88 2.24
4376 4931 8.844690 CAGTTTCGCAGAAATTAAGAGATTTTC 58.155 33.333 6.93 0.00 45.90 2.29
4444 4999 6.493115 ACATATCATCAAACAAAACAGTCCCA 59.507 34.615 0.00 0.00 0.00 4.37
4533 5088 5.674525 TGCAACCATGAAATAACAAAACCA 58.325 33.333 0.00 0.00 0.00 3.67
4609 5164 2.772287 CAAGAGTCCACTTCCAACTCC 58.228 52.381 0.00 0.00 40.21 3.85
4676 5231 6.767423 TGTGACAATACATTACATATGCAGCT 59.233 34.615 1.58 0.00 0.00 4.24
4679 5234 8.674263 TGATGTGACAATACATTACATATGCA 57.326 30.769 1.58 0.00 41.15 3.96
4693 5248 5.358090 TGCAACAAACAATGATGTGACAAT 58.642 33.333 0.00 0.00 40.46 2.71
4889 5444 2.356022 CCTGGACATACACAAGCCATCA 60.356 50.000 0.00 0.00 0.00 3.07
4894 5449 2.014068 GCTCCCTGGACATACACAAGC 61.014 57.143 0.00 0.00 0.00 4.01
4972 5527 1.339291 GAGGATAATTTGCTGGGCTGC 59.661 52.381 0.00 0.00 0.00 5.25
5042 5597 8.863872 AGCACAAAATACTTACCAATAGAAGT 57.136 30.769 0.00 0.00 39.25 3.01
5079 5638 7.657336 CACACTGGTACCACAAGATAATTTTT 58.343 34.615 11.60 0.00 0.00 1.94
5255 5814 7.428020 CAACTCATCACAATTCCAAAAGAGAA 58.572 34.615 0.00 0.00 0.00 2.87
5259 5818 5.232463 CCCAACTCATCACAATTCCAAAAG 58.768 41.667 0.00 0.00 0.00 2.27
5262 5821 3.164268 CCCCAACTCATCACAATTCCAA 58.836 45.455 0.00 0.00 0.00 3.53
5263 5822 2.109834 ACCCCAACTCATCACAATTCCA 59.890 45.455 0.00 0.00 0.00 3.53
5489 6050 3.650942 AGATCAGACCCAACACCTTGTAA 59.349 43.478 0.00 0.00 0.00 2.41
5490 6051 3.248024 AGATCAGACCCAACACCTTGTA 58.752 45.455 0.00 0.00 0.00 2.41
5541 6102 6.596309 TCGCATAATCCACTATCAGAGAAT 57.404 37.500 0.00 0.00 0.00 2.40
5543 6104 5.770162 TCTTCGCATAATCCACTATCAGAGA 59.230 40.000 0.00 0.00 0.00 3.10
5544 6105 6.018589 TCTTCGCATAATCCACTATCAGAG 57.981 41.667 0.00 0.00 0.00 3.35
5597 6160 2.224670 TGTGGAACAGCGGACCTATTTT 60.225 45.455 0.00 0.00 45.67 1.82
5809 6372 3.000819 CCCTCCGGCACCTGTGTA 61.001 66.667 0.00 0.00 0.00 2.90
5827 6390 3.747852 TCCAGGTTTATCCCTCAATCCT 58.252 45.455 0.00 0.00 36.75 3.24
6008 6571 3.224269 AGGCCTCCTCGTATTTCTCTAC 58.776 50.000 0.00 0.00 0.00 2.59
6089 6652 4.094830 AGCCATGCAATATCACAGATCA 57.905 40.909 0.00 0.00 0.00 2.92
6244 6807 0.536724 CATCCCCGAGACATGTGACA 59.463 55.000 1.15 0.00 0.00 3.58
6262 6825 5.882000 AGTCAGCAATGCTATCAATAACACA 59.118 36.000 7.70 0.00 36.40 3.72
6263 6826 6.197276 CAGTCAGCAATGCTATCAATAACAC 58.803 40.000 7.70 0.00 36.40 3.32
6317 6880 4.497300 CATTTGAAGGTTTTGATGCCGAT 58.503 39.130 0.00 0.00 0.00 4.18
6326 6889 3.620821 CCAACGTTGCATTTGAAGGTTTT 59.379 39.130 22.93 0.00 30.93 2.43
6327 6890 3.118956 TCCAACGTTGCATTTGAAGGTTT 60.119 39.130 22.93 0.00 30.93 3.27
6375 7040 3.020984 TGTGAGTATATCCAGTCGCACA 58.979 45.455 0.00 0.00 38.00 4.57
6425 7092 8.106247 AGAATTTAACATTGTACGGAACATGT 57.894 30.769 0.00 0.00 38.10 3.21
6562 7235 2.685897 CCTTGGACGGTTTCAAAGTTCA 59.314 45.455 0.00 0.00 33.70 3.18
6588 7261 3.429372 AAGAAGCCAACCCACCGCA 62.429 57.895 0.00 0.00 0.00 5.69
6593 7266 0.817634 CACACGAAGAAGCCAACCCA 60.818 55.000 0.00 0.00 0.00 4.51
6594 7267 1.515521 CCACACGAAGAAGCCAACCC 61.516 60.000 0.00 0.00 0.00 4.11
6595 7268 1.949257 CCACACGAAGAAGCCAACC 59.051 57.895 0.00 0.00 0.00 3.77
6596 7269 1.166531 AGCCACACGAAGAAGCCAAC 61.167 55.000 0.00 0.00 0.00 3.77
6597 7270 0.465460 AAGCCACACGAAGAAGCCAA 60.465 50.000 0.00 0.00 0.00 4.52
6598 7271 1.148273 AAGCCACACGAAGAAGCCA 59.852 52.632 0.00 0.00 0.00 4.75
6599 7272 1.576421 CAAGCCACACGAAGAAGCC 59.424 57.895 0.00 0.00 0.00 4.35
6600 7273 1.576421 CCAAGCCACACGAAGAAGC 59.424 57.895 0.00 0.00 0.00 3.86
6601 7274 1.576421 GCCAAGCCACACGAAGAAG 59.424 57.895 0.00 0.00 0.00 2.85
6602 7275 3.744559 GCCAAGCCACACGAAGAA 58.255 55.556 0.00 0.00 0.00 2.52
6620 7293 2.743928 GAAGCTCCGCCAGTGGTG 60.744 66.667 16.24 16.24 0.00 4.17
6621 7294 4.379243 CGAAGCTCCGCCAGTGGT 62.379 66.667 11.74 0.00 0.00 4.16
6734 7407 2.176055 CGTACGACTCTGCTGCGT 59.824 61.111 10.44 0.00 41.58 5.24
6765 7438 2.527951 GAACCCTGAGCCTGCATCGT 62.528 60.000 0.00 0.00 0.00 3.73
6789 7462 2.052690 ACTATGAGGCCGCAGTCGT 61.053 57.895 16.31 8.71 0.00 4.34


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

AutoCloner maintained by Alex Coulton.