Multiple sequence alignment - TraesCS6D01G288700

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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 TraesCS6D01G288700 chr6D 100.000 4227 0 0 1 4227 399028898 399033124 0.000000e+00 7806.0
1 TraesCS6D01G288700 chr6D 100.000 2578 0 0 4627 7204 399033524 399036101 0.000000e+00 4761.0
2 TraesCS6D01G288700 chr6A 95.570 1580 57 6 2649 4227 545123929 545125496 0.000000e+00 2518.0
3 TraesCS6D01G288700 chr6A 85.598 2576 163 86 20 2492 545120967 545123437 0.000000e+00 2510.0
4 TraesCS6D01G288700 chr6A 93.099 1536 71 21 5675 7204 545126804 545128310 0.000000e+00 2217.0
5 TraesCS6D01G288700 chr6A 96.061 1041 38 2 4627 5664 545125724 545126764 0.000000e+00 1692.0
6 TraesCS6D01G288700 chr6A 89.407 236 24 1 3001 3236 536983033 536983267 5.460000e-76 296.0
7 TraesCS6D01G288700 chr6B 95.992 1547 56 6 2649 4190 597291837 597293382 0.000000e+00 2508.0
8 TraesCS6D01G288700 chr6B 85.099 2067 142 59 403 2398 597289259 597291230 0.000000e+00 1958.0
9 TraesCS6D01G288700 chr6B 95.652 1127 41 7 5689 6815 597294821 597295939 0.000000e+00 1803.0
10 TraesCS6D01G288700 chr6B 93.642 1038 34 10 4627 5659 597293752 597294762 0.000000e+00 1522.0
11 TraesCS6D01G288700 chr6B 94.629 391 18 2 6817 7204 597296108 597296498 2.880000e-168 603.0
12 TraesCS6D01G288700 chr6B 88.050 318 15 6 8 308 597288849 597289160 8.890000e-94 355.0
13 TraesCS6D01G288700 chr6B 90.909 88 4 2 348 435 597289164 597289247 1.640000e-21 115.0
14 TraesCS6D01G288700 chr5A 90.411 365 33 2 3001 3365 259088559 259088921 5.060000e-131 479.0
15 TraesCS6D01G288700 chr5A 87.179 156 20 0 4072 4227 365703376 365703221 2.070000e-40 178.0
16 TraesCS6D01G288700 chr5A 86.538 156 21 0 4072 4227 475225679 475225524 9.610000e-39 172.0
17 TraesCS6D01G288700 chr3B 88.483 356 37 3 3010 3365 546149300 546148949 1.860000e-115 427.0
18 TraesCS6D01G288700 chr3B 82.825 361 43 13 2624 2979 293694091 293693745 9.080000e-79 305.0
19 TraesCS6D01G288700 chr3B 88.506 174 18 2 4049 4221 500525143 500524971 7.320000e-50 209.0
20 TraesCS6D01G288700 chr3B 88.462 156 18 0 4072 4227 804589306 804589461 9.540000e-44 189.0
21 TraesCS6D01G288700 chr2B 88.955 335 34 3 3028 3359 678365843 678366177 1.870000e-110 411.0
22 TraesCS6D01G288700 chr2B 84.071 339 42 6 2643 2981 678365509 678365835 4.190000e-82 316.0
23 TraesCS6D01G288700 chr4B 84.840 376 47 6 2991 3365 342753499 342753133 3.170000e-98 370.0
24 TraesCS6D01G288700 chr4B 83.611 360 43 9 2626 2981 342753825 342753478 2.510000e-84 324.0
25 TraesCS6D01G288700 chr7D 84.412 340 39 11 2643 2981 38912417 38912091 9.020000e-84 322.0
26 TraesCS6D01G288700 chr7B 79.100 311 56 5 3349 3651 681741114 681741423 9.470000e-49 206.0
27 TraesCS6D01G288700 chr1B 87.821 156 19 0 4072 4227 540845343 540845498 4.440000e-42 183.0
28 TraesCS6D01G288700 chr7A 87.179 156 20 0 4072 4227 664001452 664001607 2.070000e-40 178.0
29 TraesCS6D01G288700 chr3A 86.538 156 21 0 4072 4227 636843195 636843040 9.610000e-39 172.0
30 TraesCS6D01G288700 chr3A 90.566 106 9 1 3314 3419 44580124 44580228 9.750000e-29 139.0
31 TraesCS6D01G288700 chr3A 100.000 31 0 0 1585 1615 735405135 735405165 2.810000e-04 58.4
32 TraesCS6D01G288700 chr5B 79.452 219 43 2 5983 6200 357552675 357552892 3.480000e-33 154.0
33 TraesCS6D01G288700 chr1A 81.928 83 9 6 7113 7190 341025025 341025106 1.680000e-06 65.8


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 TraesCS6D01G288700 chr6D 399028898 399036101 7203 False 6283.500000 7806 100.000000 1 7204 2 chr6D.!!$F1 7203
1 TraesCS6D01G288700 chr6A 545120967 545128310 7343 False 2234.250000 2518 92.582000 20 7204 4 chr6A.!!$F2 7184
2 TraesCS6D01G288700 chr6B 597288849 597296498 7649 False 1266.285714 2508 91.996143 8 7204 7 chr6B.!!$F1 7196
3 TraesCS6D01G288700 chr2B 678365509 678366177 668 False 363.500000 411 86.513000 2643 3359 2 chr2B.!!$F1 716
4 TraesCS6D01G288700 chr4B 342753133 342753825 692 True 347.000000 370 84.225500 2626 3365 2 chr4B.!!$R1 739

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
985 1135 0.179097 GTGATCTGAGGAAGGCGGAC 60.179 60.000 0.00 0.00 0.00 4.79 F
1158 1318 0.252284 TCCCTTCCTCTCCCTCACAC 60.252 60.000 0.00 0.00 0.00 3.82 F
2407 2602 0.243907 GAGTTCTGTACGCAGCAGGA 59.756 55.000 0.00 0.00 42.29 3.86 F
3471 4220 0.106769 TTGCTGTTTCAGAGGCACCA 60.107 50.000 0.66 0.00 34.30 4.17 F
3837 4587 0.167908 TCCAGCTGCATTTTTACGCG 59.832 50.000 8.66 3.53 0.00 6.01 F
3843 4593 0.457509 TGCATTTTTACGCGCCCATG 60.458 50.000 5.73 2.82 0.00 3.66 F
4773 5526 0.895100 ACTTTGCATCCGCCACATGT 60.895 50.000 0.00 0.00 37.32 3.21 F
5872 6662 2.557805 GAGTACACGTCCGTCGCA 59.442 61.111 0.00 0.00 44.19 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2598 0.038744 ACAAAGATGCCACCCTCCTG 59.961 55.000 0.00 0.00 0.00 3.86 R
3074 3814 1.272212 GTGTTGATTCCGGCCACAAAT 59.728 47.619 2.24 0.00 0.00 2.32 R
3837 4587 0.391528 AAAAATGGAAGCGCATGGGC 60.392 50.000 26.04 26.04 0.00 5.36 R
4732 5485 1.039233 GCACATACCTGCCAGCCAAT 61.039 55.000 0.00 0.00 0.00 3.16 R
5664 6424 3.945285 TCCTTCGATCCAAAATAAGTGGC 59.055 43.478 0.00 0.00 35.99 5.01 R
5797 6587 4.597507 ACTGAGAACCCAAGGATGAACTTA 59.402 41.667 0.00 0.00 0.00 2.24 R
5913 6703 0.390340 AGCGTGATCGATTGCACTGT 60.390 50.000 17.00 2.86 39.71 3.55 R
6906 7865 0.951040 GAGTTCCACGGGCTCTGTTG 60.951 60.000 0.00 0.00 0.00 3.33 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
73 79 1.215647 CCGCTAGTCGTTTCCTGCT 59.784 57.895 5.97 0.00 36.19 4.24
74 80 0.454600 CCGCTAGTCGTTTCCTGCTA 59.545 55.000 5.97 0.00 36.19 3.49
78 84 3.003482 CGCTAGTCGTTTCCTGCTATAGT 59.997 47.826 0.84 0.00 0.00 2.12
132 138 4.003788 CACGGCGTTCACCCTCCT 62.004 66.667 11.19 0.00 0.00 3.69
214 238 0.240945 CCCTTTCTTCACGCGCAATT 59.759 50.000 5.73 0.00 0.00 2.32
271 295 1.076014 AAAACCCGGGCGAGGAAAT 59.924 52.632 24.08 0.00 0.00 2.17
275 299 2.203070 CCGGGCGAGGAAATGGAG 60.203 66.667 0.00 0.00 0.00 3.86
276 300 2.203070 CGGGCGAGGAAATGGAGG 60.203 66.667 0.00 0.00 0.00 4.30
277 301 2.517166 GGGCGAGGAAATGGAGGC 60.517 66.667 0.00 0.00 0.00 4.70
278 302 2.517166 GGCGAGGAAATGGAGGCC 60.517 66.667 0.00 0.00 0.00 5.19
279 303 2.272146 GCGAGGAAATGGAGGCCA 59.728 61.111 5.01 0.00 38.19 5.36
280 304 1.378514 GCGAGGAAATGGAGGCCAA 60.379 57.895 5.01 0.00 36.95 4.52
281 305 0.965363 GCGAGGAAATGGAGGCCAAA 60.965 55.000 5.01 0.00 36.95 3.28
282 306 1.767759 CGAGGAAATGGAGGCCAAAT 58.232 50.000 5.01 0.00 36.95 2.32
283 307 1.406539 CGAGGAAATGGAGGCCAAATG 59.593 52.381 5.01 0.00 36.95 2.32
284 308 1.137675 GAGGAAATGGAGGCCAAATGC 59.862 52.381 5.01 0.00 36.95 3.56
285 309 0.179103 GGAAATGGAGGCCAAATGCG 60.179 55.000 5.01 0.00 42.61 4.73
286 310 0.817013 GAAATGGAGGCCAAATGCGA 59.183 50.000 5.01 0.00 42.61 5.10
287 311 1.410153 GAAATGGAGGCCAAATGCGAT 59.590 47.619 5.01 0.00 42.61 4.58
288 312 2.363306 AATGGAGGCCAAATGCGATA 57.637 45.000 5.01 0.00 42.61 2.92
289 313 1.901591 ATGGAGGCCAAATGCGATAG 58.098 50.000 5.01 0.00 42.61 2.08
290 314 0.836606 TGGAGGCCAAATGCGATAGA 59.163 50.000 5.01 0.00 42.61 1.98
291 315 1.421268 TGGAGGCCAAATGCGATAGAT 59.579 47.619 5.01 0.00 42.61 1.98
292 316 2.637382 TGGAGGCCAAATGCGATAGATA 59.363 45.455 5.01 0.00 42.61 1.98
293 317 3.072330 TGGAGGCCAAATGCGATAGATAA 59.928 43.478 5.01 0.00 42.61 1.75
294 318 4.263462 TGGAGGCCAAATGCGATAGATAAT 60.263 41.667 5.01 0.00 42.61 1.28
295 319 4.095483 GGAGGCCAAATGCGATAGATAATG 59.905 45.833 5.01 0.00 42.61 1.90
296 320 4.655963 AGGCCAAATGCGATAGATAATGT 58.344 39.130 5.01 0.00 42.61 2.71
304 328 7.984422 AATGCGATAGATAATGTCCAAATCA 57.016 32.000 0.00 0.00 39.76 2.57
309 333 7.674937 GCGATAGATAATGTCCAAATCAATCCG 60.675 40.741 0.00 0.00 39.76 4.18
338 365 6.390048 TCCCAACGGAGTATCTATCTATCT 57.610 41.667 0.00 0.00 45.00 1.98
400 431 1.675552 CAACGGAGAAACCAACCACT 58.324 50.000 0.00 0.00 38.90 4.00
446 477 4.821589 GCCGAGAACGAGCAGGGG 62.822 72.222 0.00 0.00 42.66 4.79
468 533 2.242708 GGGGAGAGAGAAGAGGAGTACA 59.757 54.545 0.00 0.00 0.00 2.90
469 534 3.551846 GGGAGAGAGAAGAGGAGTACAG 58.448 54.545 0.00 0.00 0.00 2.74
470 535 3.201266 GGGAGAGAGAAGAGGAGTACAGA 59.799 52.174 0.00 0.00 0.00 3.41
471 536 4.324719 GGGAGAGAGAAGAGGAGTACAGAA 60.325 50.000 0.00 0.00 0.00 3.02
472 537 4.881850 GGAGAGAGAAGAGGAGTACAGAAG 59.118 50.000 0.00 0.00 0.00 2.85
473 538 4.855340 AGAGAGAAGAGGAGTACAGAAGG 58.145 47.826 0.00 0.00 0.00 3.46
474 539 3.951680 GAGAGAAGAGGAGTACAGAAGGG 59.048 52.174 0.00 0.00 0.00 3.95
475 540 2.429250 GAGAAGAGGAGTACAGAAGGGC 59.571 54.545 0.00 0.00 0.00 5.19
488 553 0.618458 GAAGGGCACAGTGGGATACA 59.382 55.000 0.00 0.00 39.74 2.29
489 554 1.004277 GAAGGGCACAGTGGGATACAA 59.996 52.381 0.00 0.00 39.74 2.41
491 556 0.328258 GGGCACAGTGGGATACAAGT 59.672 55.000 0.00 0.00 39.74 3.16
641 717 1.130054 AACCCAAGGCAGAGCAGAGA 61.130 55.000 0.00 0.00 0.00 3.10
642 718 1.221293 CCCAAGGCAGAGCAGAGAG 59.779 63.158 0.00 0.00 0.00 3.20
643 719 1.449956 CCAAGGCAGAGCAGAGAGC 60.450 63.158 0.00 0.00 46.19 4.09
717 793 4.416738 GCCACCTCCCTCTGCACC 62.417 72.222 0.00 0.00 0.00 5.01
823 946 3.286353 GTCCTGGGAGTGGTACTACTAC 58.714 54.545 13.07 13.07 0.00 2.73
847 973 0.819259 CCATTCCATACCGCCACCAG 60.819 60.000 0.00 0.00 0.00 4.00
952 1086 1.078528 TTTGAGCGAGGGAGGGAGA 59.921 57.895 0.00 0.00 0.00 3.71
972 1107 1.826054 CTCGGGAGGAGCGTGATCT 60.826 63.158 0.00 0.00 35.63 2.75
974 1109 2.121538 CGGGAGGAGCGTGATCTGA 61.122 63.158 0.00 0.00 0.00 3.27
976 1111 1.739049 GGAGGAGCGTGATCTGAGG 59.261 63.158 0.00 0.00 0.00 3.86
977 1112 0.753479 GGAGGAGCGTGATCTGAGGA 60.753 60.000 0.00 0.00 0.00 3.71
985 1135 0.179097 GTGATCTGAGGAAGGCGGAC 60.179 60.000 0.00 0.00 0.00 4.79
1047 1207 2.370445 CGGGGGACAGAAGCAGGAT 61.370 63.158 0.00 0.00 0.00 3.24
1050 1210 0.842635 GGGGACAGAAGCAGGATGAT 59.157 55.000 0.00 0.00 39.69 2.45
1104 1264 1.000955 GGGGTATCCTACTGCATCACG 59.999 57.143 0.00 0.00 0.00 4.35
1158 1318 0.252284 TCCCTTCCTCTCCCTCACAC 60.252 60.000 0.00 0.00 0.00 3.82
1236 1396 3.317449 CCGTTTCGGGGTTTCTCTT 57.683 52.632 0.00 0.00 44.15 2.85
1237 1397 1.154197 CCGTTTCGGGGTTTCTCTTC 58.846 55.000 0.00 0.00 44.15 2.87
1238 1398 1.270678 CCGTTTCGGGGTTTCTCTTCT 60.271 52.381 0.00 0.00 44.15 2.85
1239 1399 2.067013 CGTTTCGGGGTTTCTCTTCTC 58.933 52.381 0.00 0.00 0.00 2.87
1240 1400 2.067013 GTTTCGGGGTTTCTCTTCTCG 58.933 52.381 0.00 0.00 0.00 4.04
1292 1452 0.527600 CTGCTTGCTGGTCGCGTATA 60.528 55.000 5.77 0.00 43.27 1.47
1478 1639 6.483307 GGATATTCCAAAATAAAAAGCAGGCC 59.517 38.462 0.00 0.00 36.28 5.19
1528 1689 9.931210 GTAGTTTATTAATGCGCTTTAATGAGT 57.069 29.630 34.13 27.80 34.47 3.41
1612 1776 1.073025 TTTGACCCGTGCTGATGCT 59.927 52.632 0.00 0.00 40.48 3.79
1613 1777 0.323302 TTTGACCCGTGCTGATGCTA 59.677 50.000 0.00 0.00 40.48 3.49
1631 1795 4.733850 TGCTAGTACTCGACATTCAACAG 58.266 43.478 0.00 0.00 0.00 3.16
1633 1797 5.031578 GCTAGTACTCGACATTCAACAGAG 58.968 45.833 0.00 0.00 35.28 3.35
1722 1904 2.413453 GACTGGTTTCTGAATCTGCGAC 59.587 50.000 0.00 0.00 0.00 5.19
1737 1919 4.070552 GACCCAGCTTCGCCGTCT 62.071 66.667 0.00 0.00 0.00 4.18
1742 1924 1.511305 CAGCTTCGCCGTCTCCTTA 59.489 57.895 0.00 0.00 0.00 2.69
1794 1977 4.922103 ACTTCGATTCTTACGAGTTTCCAC 59.078 41.667 0.00 0.00 40.72 4.02
1834 2017 7.690952 ATTTGCGATTTTGTAGGGTAGTAAA 57.309 32.000 0.00 0.00 0.00 2.01
1836 2019 6.913873 TGCGATTTTGTAGGGTAGTAAATC 57.086 37.500 0.00 0.00 33.84 2.17
1870 2053 3.355816 TCAACTCACGCGTTGACTT 57.644 47.368 10.22 3.54 45.92 3.01
1875 2058 1.062002 ACTCACGCGTTGACTTGTTTG 59.938 47.619 10.22 0.00 0.00 2.93
1881 2064 2.376032 GCGTTGACTTGTTTGAGCTTC 58.624 47.619 0.00 0.00 0.00 3.86
2041 2224 0.253347 AGGTCCATGTCCACCCATCT 60.253 55.000 6.89 0.00 32.45 2.90
2103 2289 5.301551 GCAGGGGTTTTTCATTTCCATTTTT 59.698 36.000 0.00 0.00 0.00 1.94
2202 2394 3.133464 GCATGGGCGCTGCAGTAA 61.133 61.111 16.64 0.00 39.46 2.24
2276 2468 1.971357 TGGTTCTGAGTCCCTTGTCTC 59.029 52.381 0.00 0.00 0.00 3.36
2324 2518 7.829211 ACATGTAAGGCTGACACTGTAAATAAT 59.171 33.333 6.90 0.00 0.00 1.28
2387 2582 0.462789 ATGCGTACCCTTCCTTACCG 59.537 55.000 0.00 0.00 0.00 4.02
2398 2593 3.119209 CCTTCCTTACCGGAGTTCTGTAC 60.119 52.174 9.46 0.00 44.28 2.90
2403 2598 1.805945 CCGGAGTTCTGTACGCAGC 60.806 63.158 0.00 0.00 42.29 5.25
2407 2602 0.243907 GAGTTCTGTACGCAGCAGGA 59.756 55.000 0.00 0.00 42.29 3.86
2411 2606 2.603473 TGTACGCAGCAGGAGGGT 60.603 61.111 0.00 0.00 36.12 4.34
2416 2611 4.437587 GCAGCAGGAGGGTGGCAT 62.438 66.667 0.00 0.00 45.14 4.40
2417 2612 2.124403 CAGCAGGAGGGTGGCATC 60.124 66.667 0.00 0.00 41.32 3.91
2418 2613 2.285969 AGCAGGAGGGTGGCATCT 60.286 61.111 0.00 0.00 0.00 2.90
2419 2614 1.927527 AGCAGGAGGGTGGCATCTT 60.928 57.895 0.00 0.00 0.00 2.40
2425 2787 2.092323 GGAGGGTGGCATCTTTGTTAC 58.908 52.381 0.00 0.00 0.00 2.50
2449 2811 8.567285 ACTTACAATCCTTTTATGTCTTCCTG 57.433 34.615 0.00 0.00 0.00 3.86
2460 2822 8.924511 TTTTATGTCTTCCTGTCTTGAATTCT 57.075 30.769 7.05 0.00 0.00 2.40
2474 2836 5.882557 TCTTGAATTCTTGCTCATAACTCCC 59.117 40.000 7.05 0.00 0.00 4.30
2477 2839 2.961526 TCTTGCTCATAACTCCCGAC 57.038 50.000 0.00 0.00 0.00 4.79
2481 2843 2.176045 TGCTCATAACTCCCGACTTCA 58.824 47.619 0.00 0.00 0.00 3.02
2499 3233 8.450964 CCGACTTCAAAGACACATAATGTTTAT 58.549 33.333 0.00 0.00 43.56 1.40
2556 3290 6.298361 TGGAGAAATGATGAACAAGAAGTCA 58.702 36.000 0.00 0.00 0.00 3.41
2588 3322 7.210718 TCAGAATATTGATTGGATGATGTGC 57.789 36.000 0.00 0.00 0.00 4.57
2593 3327 4.911514 TTGATTGGATGATGTGCTCATG 57.088 40.909 5.89 0.00 44.83 3.07
2595 3329 4.274978 TGATTGGATGATGTGCTCATGTT 58.725 39.130 5.89 0.00 44.83 2.71
2601 3335 1.962100 TGATGTGCTCATGTTGGCAAA 59.038 42.857 5.89 7.57 40.26 3.68
2603 3337 3.007074 TGATGTGCTCATGTTGGCAAATT 59.993 39.130 5.89 0.00 36.63 1.82
2604 3338 2.756829 TGTGCTCATGTTGGCAAATTG 58.243 42.857 0.00 2.67 40.26 2.32
2605 3339 2.102757 TGTGCTCATGTTGGCAAATTGT 59.897 40.909 0.00 0.00 40.26 2.71
2606 3340 3.320256 TGTGCTCATGTTGGCAAATTGTA 59.680 39.130 0.00 0.00 40.26 2.41
2610 3344 5.996513 TGCTCATGTTGGCAAATTGTATTTT 59.003 32.000 0.00 0.00 35.40 1.82
2612 3346 6.797995 GCTCATGTTGGCAAATTGTATTTTTG 59.202 34.615 0.00 0.00 37.18 2.44
2613 3347 7.520292 GCTCATGTTGGCAAATTGTATTTTTGT 60.520 33.333 0.00 0.00 36.63 2.83
2614 3348 8.893219 TCATGTTGGCAAATTGTATTTTTGTA 57.107 26.923 0.00 0.00 36.63 2.41
2616 3350 9.544314 CATGTTGGCAAATTGTATTTTTGTATG 57.456 29.630 0.00 0.00 36.63 2.39
2617 3351 7.579726 TGTTGGCAAATTGTATTTTTGTATGC 58.420 30.769 0.00 0.00 36.63 3.14
2618 3352 7.227314 TGTTGGCAAATTGTATTTTTGTATGCA 59.773 29.630 0.00 0.00 36.63 3.96
2619 3353 7.918536 TGGCAAATTGTATTTTTGTATGCAT 57.081 28.000 3.79 3.79 36.63 3.96
2620 3354 8.332996 TGGCAAATTGTATTTTTGTATGCATT 57.667 26.923 3.54 0.00 36.63 3.56
2621 3355 8.790718 TGGCAAATTGTATTTTTGTATGCATTT 58.209 25.926 3.54 0.00 36.63 2.32
2622 3356 9.276397 GGCAAATTGTATTTTTGTATGCATTTC 57.724 29.630 3.54 0.00 36.63 2.17
2636 3370 7.315142 TGTATGCATTTCTTCAAAGGTTGATC 58.685 34.615 3.54 0.00 39.84 2.92
2637 3371 5.787953 TGCATTTCTTCAAAGGTTGATCA 57.212 34.783 0.00 0.00 39.84 2.92
2639 3373 5.984926 TGCATTTCTTCAAAGGTTGATCAAC 59.015 36.000 27.16 27.16 39.84 3.18
2640 3374 5.984926 GCATTTCTTCAAAGGTTGATCAACA 59.015 36.000 33.42 14.92 42.85 3.33
2641 3375 6.074142 GCATTTCTTCAAAGGTTGATCAACAC 60.074 38.462 33.42 23.92 42.85 3.32
2647 3385 8.106462 TCTTCAAAGGTTGATCAACACCATATA 58.894 33.333 33.42 15.50 42.85 0.86
2693 3432 1.939974 TGCTAGCCTTGCGAAGTATG 58.060 50.000 13.29 0.00 0.00 2.39
3074 3814 4.635765 GCAGTTGTTATCCAGACATTGCTA 59.364 41.667 0.00 0.00 36.18 3.49
3083 3823 2.159198 CCAGACATTGCTATTTGTGGCC 60.159 50.000 0.00 0.00 0.00 5.36
3471 4220 0.106769 TTGCTGTTTCAGAGGCACCA 60.107 50.000 0.66 0.00 34.30 4.17
3475 4224 2.575532 CTGTTTCAGAGGCACCAAAGA 58.424 47.619 0.00 0.00 32.44 2.52
3476 4225 2.291741 CTGTTTCAGAGGCACCAAAGAC 59.708 50.000 0.00 0.00 32.44 3.01
3497 4246 5.471456 AGACAAAAGTGTTCTAGCAGGAATG 59.529 40.000 0.00 0.00 38.41 2.67
3580 4330 0.813210 AGCTGCTCCTTTGATAGCGC 60.813 55.000 0.00 0.00 41.77 5.92
3612 4362 2.027192 TGGACTGTATGAGCTGGGTTTC 60.027 50.000 0.00 0.00 0.00 2.78
3712 4462 4.930963 CACAGGTTGCTAAATGTGTTGAA 58.069 39.130 6.02 0.00 38.54 2.69
3769 4519 2.095768 CGCAATGGTTCGACACAATTCT 60.096 45.455 0.00 0.00 24.35 2.40
3778 4528 5.350365 GGTTCGACACAATTCTTATGCACTA 59.650 40.000 0.00 0.00 0.00 2.74
3782 4532 7.684670 TCGACACAATTCTTATGCACTAAATC 58.315 34.615 0.00 0.00 0.00 2.17
3837 4587 0.167908 TCCAGCTGCATTTTTACGCG 59.832 50.000 8.66 3.53 0.00 6.01
3843 4593 0.457509 TGCATTTTTACGCGCCCATG 60.458 50.000 5.73 2.82 0.00 3.66
3930 4682 5.957771 TGCTGTTCTATTCACTATTCCCT 57.042 39.130 0.00 0.00 0.00 4.20
4089 4841 4.463539 AGATATGCTTGTTCCATTTGCACA 59.536 37.500 0.00 0.00 36.44 4.57
4091 4843 3.472283 TGCTTGTTCCATTTGCACAAT 57.528 38.095 0.00 0.00 30.18 2.71
4092 4844 3.806380 TGCTTGTTCCATTTGCACAATT 58.194 36.364 0.00 0.00 30.18 2.32
4732 5485 2.372264 CCTCTGTACTTAGCCGTGGTA 58.628 52.381 0.00 0.00 0.00 3.25
4773 5526 0.895100 ACTTTGCATCCGCCACATGT 60.895 50.000 0.00 0.00 37.32 3.21
4940 5696 8.548880 TTTATACTTCTACCTAGGAATGCACT 57.451 34.615 17.98 0.00 0.00 4.40
4977 5733 4.048504 TGCATCAACCACTATTCGTATCG 58.951 43.478 0.00 0.00 0.00 2.92
4979 5735 4.923871 GCATCAACCACTATTCGTATCGAT 59.076 41.667 2.16 2.16 35.23 3.59
4983 5739 5.066764 TCAACCACTATTCGTATCGATGTCA 59.933 40.000 8.54 0.00 35.23 3.58
5510 6270 5.971763 ACTTAGCTCTGACCTAGAACAATG 58.028 41.667 0.00 0.00 34.32 2.82
5680 6440 5.813080 AACTACGCCACTTATTTTGGATC 57.187 39.130 0.00 0.00 36.02 3.36
5703 6493 7.265647 TCGAAGGAGTACATATGAGAGAAAG 57.734 40.000 10.38 0.00 0.00 2.62
5797 6587 4.080695 TGCAATCTCAATAGCTTCAGGACT 60.081 41.667 0.00 0.00 0.00 3.85
5872 6662 2.557805 GAGTACACGTCCGTCGCA 59.442 61.111 0.00 0.00 44.19 5.10
5913 6703 1.999048 CGTGCAAGATGGGTACGTAA 58.001 50.000 0.00 0.00 39.11 3.18
5949 6739 3.187227 CACGCTTGCTTTCTATGTGAACT 59.813 43.478 0.00 0.00 33.88 3.01
5951 6741 3.425359 CGCTTGCTTTCTATGTGAACTGG 60.425 47.826 0.00 0.00 33.88 4.00
5952 6742 3.503748 GCTTGCTTTCTATGTGAACTGGT 59.496 43.478 0.00 0.00 33.88 4.00
5972 6762 4.062991 GGTACTGACCGTTTGTTTCATCT 58.937 43.478 0.00 0.00 35.52 2.90
6524 7315 8.472007 ACCTCTAGTAGTTTATCTCATTCTGG 57.528 38.462 0.00 0.00 0.00 3.86
6669 7460 3.936453 TGGATTTGCGGTATGACACTAAC 59.064 43.478 0.00 0.00 0.00 2.34
6690 7481 0.671163 GTAATGTTGTCGGGCGGTGA 60.671 55.000 0.00 0.00 0.00 4.02
6769 7561 7.492524 TGCAGGTATACTCAGACTTGAAATAG 58.507 38.462 2.25 0.00 31.69 1.73
6770 7562 7.124298 TGCAGGTATACTCAGACTTGAAATAGT 59.876 37.037 2.25 0.00 31.69 2.12
6771 7563 7.436673 GCAGGTATACTCAGACTTGAAATAGTG 59.563 40.741 2.25 0.00 31.69 2.74
6772 7564 8.470805 CAGGTATACTCAGACTTGAAATAGTGT 58.529 37.037 2.25 0.00 31.69 3.55
6773 7565 9.696572 AGGTATACTCAGACTTGAAATAGTGTA 57.303 33.333 2.25 0.00 31.69 2.90
6781 7573 6.258727 CAGACTTGAAATAGTGTATTGCGGAT 59.741 38.462 0.00 0.00 0.00 4.18
6815 7607 7.199541 AGTTCTGAATGTTTCTTCTGACATG 57.800 36.000 0.00 0.00 36.65 3.21
6818 7610 6.466812 TCTGAATGTTTCTTCTGACATGCTA 58.533 36.000 0.00 0.00 36.65 3.49
6820 7612 5.997129 TGAATGTTTCTTCTGACATGCTACA 59.003 36.000 0.00 0.00 36.65 2.74
6821 7613 6.486320 TGAATGTTTCTTCTGACATGCTACAA 59.514 34.615 0.00 0.00 36.65 2.41
6823 7615 5.122519 TGTTTCTTCTGACATGCTACAACA 58.877 37.500 0.00 0.00 0.00 3.33
6824 7616 5.764686 TGTTTCTTCTGACATGCTACAACAT 59.235 36.000 0.00 0.00 0.00 2.71
6906 7865 1.613925 TGGATACTGCGAGCTGATACC 59.386 52.381 8.91 8.44 37.61 2.73
6907 7866 1.613925 GGATACTGCGAGCTGATACCA 59.386 52.381 8.91 0.00 0.00 3.25
7078 8038 0.729116 CCACTAGAGGCAAACATGCG 59.271 55.000 0.00 0.00 35.24 4.73
7079 8039 0.729116 CACTAGAGGCAAACATGCGG 59.271 55.000 0.00 0.00 35.24 5.69
7081 8041 2.040213 CTAGAGGCAAACATGCGGCG 62.040 60.000 0.51 0.51 35.24 6.46
7107 8067 1.962547 CGTCGCACTGTTTTTCATTCG 59.037 47.619 0.00 0.00 0.00 3.34
7150 8112 4.628074 TCTAGCAGATTATTACGGTTGGC 58.372 43.478 0.00 0.00 0.00 4.52
7157 8119 1.080298 TATTACGGTTGGCTGTTGCG 58.920 50.000 0.00 0.00 40.82 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.800655 GCTCCTACTCGACTCGTACGA 60.801 57.143 18.41 18.41 38.11 3.43
3 4 0.576328 GCTCCTACTCGACTCGTACG 59.424 60.000 9.53 9.53 0.00 3.67
4 5 1.327156 GTGCTCCTACTCGACTCGTAC 59.673 57.143 0.00 0.00 0.00 3.67
5 6 1.649664 GTGCTCCTACTCGACTCGTA 58.350 55.000 0.00 0.00 0.00 3.43
6 7 1.025647 GGTGCTCCTACTCGACTCGT 61.026 60.000 0.00 0.00 0.00 4.18
7 8 0.745128 AGGTGCTCCTACTCGACTCG 60.745 60.000 5.27 0.00 43.12 4.18
8 9 1.018910 GAGGTGCTCCTACTCGACTC 58.981 60.000 7.45 0.00 45.24 3.36
9 10 0.394625 GGAGGTGCTCCTACTCGACT 60.395 60.000 9.95 0.00 46.41 4.18
10 11 2.108568 GGAGGTGCTCCTACTCGAC 58.891 63.158 9.95 0.00 46.41 4.20
11 12 4.659986 GGAGGTGCTCCTACTCGA 57.340 61.111 9.95 0.00 46.41 4.04
73 79 2.419574 GCCTGTTTTGGGCGAGACTATA 60.420 50.000 0.00 0.00 40.19 1.31
74 80 1.679032 GCCTGTTTTGGGCGAGACTAT 60.679 52.381 0.00 0.00 40.19 2.12
121 127 2.515854 GAGGGAAAAAGGAGGGTGAAC 58.484 52.381 0.00 0.00 0.00 3.18
132 138 0.616891 GGGGAGCTACGAGGGAAAAA 59.383 55.000 0.00 0.00 0.00 1.94
271 295 0.836606 TCTATCGCATTTGGCCTCCA 59.163 50.000 3.32 0.00 40.31 3.86
275 299 4.142600 GGACATTATCTATCGCATTTGGCC 60.143 45.833 0.00 0.00 40.31 5.36
276 300 4.455533 TGGACATTATCTATCGCATTTGGC 59.544 41.667 0.00 0.00 39.90 4.52
277 301 6.558771 TTGGACATTATCTATCGCATTTGG 57.441 37.500 0.00 0.00 0.00 3.28
278 302 8.291740 TGATTTGGACATTATCTATCGCATTTG 58.708 33.333 0.00 0.00 0.00 2.32
279 303 8.394971 TGATTTGGACATTATCTATCGCATTT 57.605 30.769 0.00 0.00 0.00 2.32
280 304 7.984422 TGATTTGGACATTATCTATCGCATT 57.016 32.000 0.00 0.00 0.00 3.56
281 305 7.984422 TTGATTTGGACATTATCTATCGCAT 57.016 32.000 0.00 0.00 0.00 4.73
282 306 7.119699 GGATTGATTTGGACATTATCTATCGCA 59.880 37.037 0.00 0.00 33.93 5.10
283 307 7.467623 GGATTGATTTGGACATTATCTATCGC 58.532 38.462 0.00 0.00 33.93 4.58
284 308 7.331934 ACGGATTGATTTGGACATTATCTATCG 59.668 37.037 0.00 0.00 33.93 2.92
285 309 8.553459 ACGGATTGATTTGGACATTATCTATC 57.447 34.615 0.00 0.00 33.03 2.08
286 310 8.378565 AGACGGATTGATTTGGACATTATCTAT 58.621 33.333 0.00 0.00 0.00 1.98
287 311 7.735917 AGACGGATTGATTTGGACATTATCTA 58.264 34.615 0.00 0.00 0.00 1.98
288 312 6.595682 AGACGGATTGATTTGGACATTATCT 58.404 36.000 0.00 0.00 0.00 1.98
289 313 6.867662 AGACGGATTGATTTGGACATTATC 57.132 37.500 0.00 0.00 0.00 1.75
290 314 7.509546 AGTAGACGGATTGATTTGGACATTAT 58.490 34.615 0.00 0.00 0.00 1.28
291 315 6.884832 AGTAGACGGATTGATTTGGACATTA 58.115 36.000 0.00 0.00 0.00 1.90
292 316 5.745227 AGTAGACGGATTGATTTGGACATT 58.255 37.500 0.00 0.00 0.00 2.71
293 317 5.359194 AGTAGACGGATTGATTTGGACAT 57.641 39.130 0.00 0.00 0.00 3.06
294 318 4.382685 GGAGTAGACGGATTGATTTGGACA 60.383 45.833 0.00 0.00 0.00 4.02
295 319 4.120589 GGAGTAGACGGATTGATTTGGAC 58.879 47.826 0.00 0.00 0.00 4.02
296 320 3.134081 GGGAGTAGACGGATTGATTTGGA 59.866 47.826 0.00 0.00 0.00 3.53
337 364 4.764940 CGTGTTTTTGGAGTTTACGGTAG 58.235 43.478 0.00 0.00 0.00 3.18
338 365 3.002144 GCGTGTTTTTGGAGTTTACGGTA 59.998 43.478 0.00 0.00 0.00 4.02
390 417 2.508526 GATGCTTCTGAGTGGTTGGTT 58.491 47.619 0.00 0.00 0.00 3.67
391 418 1.609061 CGATGCTTCTGAGTGGTTGGT 60.609 52.381 0.00 0.00 0.00 3.67
392 419 1.081892 CGATGCTTCTGAGTGGTTGG 58.918 55.000 0.00 0.00 0.00 3.77
393 420 0.445436 GCGATGCTTCTGAGTGGTTG 59.555 55.000 0.00 0.00 0.00 3.77
400 431 4.161295 CGGGGGCGATGCTTCTGA 62.161 66.667 0.00 0.00 0.00 3.27
446 477 0.634465 ACTCCTCTTCTCTCTCCCCC 59.366 60.000 0.00 0.00 0.00 5.40
448 479 3.201266 TCTGTACTCCTCTTCTCTCTCCC 59.799 52.174 0.00 0.00 0.00 4.30
449 480 4.497291 TCTGTACTCCTCTTCTCTCTCC 57.503 50.000 0.00 0.00 0.00 3.71
468 533 0.912486 GTATCCCACTGTGCCCTTCT 59.088 55.000 1.29 0.00 0.00 2.85
469 534 0.618458 TGTATCCCACTGTGCCCTTC 59.382 55.000 1.29 0.00 0.00 3.46
470 535 1.004745 CTTGTATCCCACTGTGCCCTT 59.995 52.381 1.29 0.00 0.00 3.95
471 536 0.620556 CTTGTATCCCACTGTGCCCT 59.379 55.000 1.29 0.00 0.00 5.19
472 537 0.328258 ACTTGTATCCCACTGTGCCC 59.672 55.000 1.29 0.00 0.00 5.36
473 538 2.906354 CTACTTGTATCCCACTGTGCC 58.094 52.381 1.29 0.00 0.00 5.01
474 539 2.093447 AGCTACTTGTATCCCACTGTGC 60.093 50.000 1.29 0.00 0.00 4.57
475 540 3.895232 AGCTACTTGTATCCCACTGTG 57.105 47.619 0.00 0.00 0.00 3.66
488 553 2.959707 CGAATCTCCCCTGTAGCTACTT 59.040 50.000 23.84 7.85 0.00 2.24
489 554 2.588620 CGAATCTCCCCTGTAGCTACT 58.411 52.381 23.84 0.68 0.00 2.57
491 556 1.329256 GCGAATCTCCCCTGTAGCTA 58.671 55.000 0.00 0.00 0.00 3.32
547 619 1.068287 CAAAACCGCATTTACGCCCG 61.068 55.000 0.00 0.00 0.00 6.13
609 681 4.308458 GGGTTTGGTTTGCGGGGC 62.308 66.667 0.00 0.00 0.00 5.80
618 694 1.531602 GCTCTGCCTTGGGTTTGGT 60.532 57.895 0.00 0.00 0.00 3.67
641 717 1.979693 GTCGTCACCCTCTCTGGCT 60.980 63.158 0.00 0.00 0.00 4.75
642 718 2.574399 GTCGTCACCCTCTCTGGC 59.426 66.667 0.00 0.00 0.00 4.85
643 719 2.878429 CGTCGTCACCCTCTCTGG 59.122 66.667 0.00 0.00 0.00 3.86
644 720 2.179517 GCGTCGTCACCCTCTCTG 59.820 66.667 0.00 0.00 0.00 3.35
645 721 3.432588 CGCGTCGTCACCCTCTCT 61.433 66.667 0.00 0.00 0.00 3.10
646 722 4.477975 CCGCGTCGTCACCCTCTC 62.478 72.222 4.92 0.00 0.00 3.20
823 946 0.609131 GGCGGTATGGAATGGGATGG 60.609 60.000 0.00 0.00 0.00 3.51
824 947 0.110295 TGGCGGTATGGAATGGGATG 59.890 55.000 0.00 0.00 0.00 3.51
825 948 0.110486 GTGGCGGTATGGAATGGGAT 59.890 55.000 0.00 0.00 0.00 3.85
826 949 1.529796 GTGGCGGTATGGAATGGGA 59.470 57.895 0.00 0.00 0.00 4.37
827 950 1.528309 GGTGGCGGTATGGAATGGG 60.528 63.158 0.00 0.00 0.00 4.00
832 955 2.665089 CCACTGGTGGCGGTATGGA 61.665 63.158 6.84 0.00 44.73 3.41
847 973 2.813908 CGGTACAGCGGCTTCCAC 60.814 66.667 0.00 0.00 0.00 4.02
911 1045 4.424566 GCCACAATGCAGCCCGTG 62.425 66.667 0.00 0.00 0.00 4.94
912 1046 4.666253 AGCCACAATGCAGCCCGT 62.666 61.111 0.00 0.00 0.00 5.28
913 1047 3.818787 GAGCCACAATGCAGCCCG 61.819 66.667 0.00 0.00 0.00 6.13
914 1048 2.362120 AGAGCCACAATGCAGCCC 60.362 61.111 0.00 0.00 0.00 5.19
915 1049 2.707849 CCAGAGCCACAATGCAGCC 61.708 63.158 0.00 0.00 0.00 4.85
916 1050 1.530013 AACCAGAGCCACAATGCAGC 61.530 55.000 0.00 0.00 0.00 5.25
917 1051 0.963962 AAACCAGAGCCACAATGCAG 59.036 50.000 0.00 0.00 0.00 4.41
918 1052 0.675083 CAAACCAGAGCCACAATGCA 59.325 50.000 0.00 0.00 0.00 3.96
965 1100 1.227089 CCGCCTTCCTCAGATCACG 60.227 63.158 0.00 0.00 0.00 4.35
966 1101 0.179097 GTCCGCCTTCCTCAGATCAC 60.179 60.000 0.00 0.00 0.00 3.06
967 1102 1.667154 CGTCCGCCTTCCTCAGATCA 61.667 60.000 0.00 0.00 0.00 2.92
970 1105 3.068691 CCGTCCGCCTTCCTCAGA 61.069 66.667 0.00 0.00 0.00 3.27
972 1107 4.689549 TCCCGTCCGCCTTCCTCA 62.690 66.667 0.00 0.00 0.00 3.86
1068 1228 4.785453 CCGGGCAGCTGGTCCTTC 62.785 72.222 17.12 0.00 39.98 3.46
1089 1249 1.683917 GGACTCGTGATGCAGTAGGAT 59.316 52.381 0.00 0.00 0.00 3.24
1158 1318 4.814294 CGGACGAAAGGGGGAGCG 62.814 72.222 0.00 0.00 0.00 5.03
1167 1327 4.705519 GGCGACGGACGGACGAAA 62.706 66.667 14.94 0.00 42.83 3.46
1235 1395 1.074248 GAAAACCCAGCCCCGAGAA 59.926 57.895 0.00 0.00 0.00 2.87
1236 1396 2.754375 GAAAACCCAGCCCCGAGA 59.246 61.111 0.00 0.00 0.00 4.04
1237 1397 2.361230 GGAAAACCCAGCCCCGAG 60.361 66.667 0.00 0.00 34.14 4.63
1238 1398 4.338710 CGGAAAACCCAGCCCCGA 62.339 66.667 0.00 0.00 42.49 5.14
1285 1445 1.588082 CGGCAAAGTTCGTTATACGCG 60.588 52.381 3.53 3.53 42.21 6.01
1286 1446 1.391144 ACGGCAAAGTTCGTTATACGC 59.609 47.619 0.00 0.00 42.21 4.42
1289 1449 3.068560 AGCAACGGCAAAGTTCGTTATA 58.931 40.909 1.08 0.00 46.05 0.98
1478 1639 1.483316 GGAACAAAACGGAAAAGGCG 58.517 50.000 0.00 0.00 0.00 5.52
1528 1689 1.133915 GGAGGATATTCAACGGGGCAA 60.134 52.381 0.00 0.00 0.00 4.52
1565 1729 4.796290 GCAGCGGCATCAGTTATTAGTAGA 60.796 45.833 3.18 0.00 40.72 2.59
1566 1730 3.430218 GCAGCGGCATCAGTTATTAGTAG 59.570 47.826 3.18 0.00 40.72 2.57
1567 1731 3.390135 GCAGCGGCATCAGTTATTAGTA 58.610 45.455 3.18 0.00 40.72 1.82
1568 1732 2.213499 GCAGCGGCATCAGTTATTAGT 58.787 47.619 3.18 0.00 40.72 2.24
1569 1733 2.957576 GCAGCGGCATCAGTTATTAG 57.042 50.000 3.18 0.00 40.72 1.73
1583 1747 1.007387 GGGTCAAACCTTTGCAGCG 60.007 57.895 0.00 0.00 38.64 5.18
1612 1776 6.127980 CCTTCTCTGTTGAATGTCGAGTACTA 60.128 42.308 0.00 0.00 0.00 1.82
1613 1777 5.336055 CCTTCTCTGTTGAATGTCGAGTACT 60.336 44.000 0.00 0.00 0.00 2.73
1631 1795 5.032863 CGACAATCATGCAAATTCCTTCTC 58.967 41.667 0.00 0.00 0.00 2.87
1633 1797 4.107622 CCGACAATCATGCAAATTCCTTC 58.892 43.478 0.00 0.00 0.00 3.46
1737 1919 1.961394 ACGCTGACACAAGTCTAAGGA 59.039 47.619 0.00 0.00 45.20 3.36
1742 1924 1.137086 AGTTGACGCTGACACAAGTCT 59.863 47.619 0.00 0.00 45.20 3.24
1749 1931 1.269569 ACAATCGAGTTGACGCTGACA 60.270 47.619 12.53 0.00 40.37 3.58
1794 1977 4.211164 TCGCAAATATAGCACCAGATTTCG 59.789 41.667 1.62 0.00 0.00 3.46
1834 2017 8.680903 GTGAGTTGATATGAAACCAAAGATGAT 58.319 33.333 0.00 0.00 0.00 2.45
1836 2019 6.963242 CGTGAGTTGATATGAAACCAAAGATG 59.037 38.462 0.00 0.00 0.00 2.90
1870 2053 1.522806 ACGCGGTGAAGCTCAAACA 60.523 52.632 12.47 0.00 34.40 2.83
1875 2058 4.077188 GTGCACGCGGTGAAGCTC 62.077 66.667 12.47 3.63 35.23 4.09
2041 2224 3.380954 TCAATGCAGCTGAAAGTGACAAA 59.619 39.130 20.43 0.00 35.30 2.83
2103 2289 5.159273 TGCATGATAACACACAAGGTAGA 57.841 39.130 0.00 0.00 0.00 2.59
2232 2424 4.499183 ACAAGAATTCGCTCTCCTACAAG 58.501 43.478 0.00 0.00 0.00 3.16
2239 2431 4.214332 AGAACCAAACAAGAATTCGCTCTC 59.786 41.667 0.00 0.00 0.00 3.20
2276 2468 2.996621 GGATTTGACTCGGTTCAGACAG 59.003 50.000 0.00 0.00 0.00 3.51
2324 2518 9.739276 ATTAGGATAACAAAAGTGTGATTCTCA 57.261 29.630 0.00 0.00 34.30 3.27
2383 2578 2.945510 TGCGTACAGAACTCCGGTA 58.054 52.632 0.00 0.00 0.00 4.02
2403 2598 0.038744 ACAAAGATGCCACCCTCCTG 59.961 55.000 0.00 0.00 0.00 3.86
2407 2602 3.525800 AAGTAACAAAGATGCCACCCT 57.474 42.857 0.00 0.00 0.00 4.34
2425 2787 8.567285 ACAGGAAGACATAAAAGGATTGTAAG 57.433 34.615 0.00 0.00 0.00 2.34
2449 2811 6.183360 GGGAGTTATGAGCAAGAATTCAAGAC 60.183 42.308 8.44 0.00 0.00 3.01
2460 2822 2.565391 TGAAGTCGGGAGTTATGAGCAA 59.435 45.455 0.00 0.00 0.00 3.91
2499 3233 7.147915 GCATTCAACCTTACAAATTCTCCCATA 60.148 37.037 0.00 0.00 0.00 2.74
2507 3241 5.010922 TGCAGAGCATTCAACCTTACAAATT 59.989 36.000 0.00 0.00 31.71 1.82
2509 3243 3.888323 TGCAGAGCATTCAACCTTACAAA 59.112 39.130 0.00 0.00 31.71 2.83
2562 3296 7.808381 GCACATCATCCAATCAATATTCTGAAG 59.192 37.037 0.00 0.00 0.00 3.02
2576 3310 2.756207 CCAACATGAGCACATCATCCAA 59.244 45.455 0.00 0.00 46.01 3.53
2588 3322 7.863666 ACAAAAATACAATTTGCCAACATGAG 58.136 30.769 0.00 0.00 40.58 2.90
2593 3327 7.579726 TGCATACAAAAATACAATTTGCCAAC 58.420 30.769 0.00 0.00 40.58 3.77
2595 3329 7.918536 ATGCATACAAAAATACAATTTGCCA 57.081 28.000 0.00 0.00 40.58 4.92
2605 3339 9.995003 ACCTTTGAAGAAATGCATACAAAAATA 57.005 25.926 0.00 0.00 0.00 1.40
2606 3340 8.907222 ACCTTTGAAGAAATGCATACAAAAAT 57.093 26.923 0.00 0.00 0.00 1.82
2610 3344 7.048629 TCAACCTTTGAAGAAATGCATACAA 57.951 32.000 0.00 0.00 36.59 2.41
2612 3346 7.315142 TGATCAACCTTTGAAGAAATGCATAC 58.685 34.615 0.00 0.00 43.95 2.39
2613 3347 7.465353 TGATCAACCTTTGAAGAAATGCATA 57.535 32.000 0.00 0.00 43.95 3.14
2614 3348 6.349243 TGATCAACCTTTGAAGAAATGCAT 57.651 33.333 0.00 0.00 43.95 3.96
2616 3350 5.984926 TGTTGATCAACCTTTGAAGAAATGC 59.015 36.000 30.66 5.51 43.95 3.56
2617 3351 6.421801 GGTGTTGATCAACCTTTGAAGAAATG 59.578 38.462 30.66 0.00 43.95 2.32
2618 3352 6.098124 TGGTGTTGATCAACCTTTGAAGAAAT 59.902 34.615 30.66 0.00 43.95 2.17
2619 3353 5.420421 TGGTGTTGATCAACCTTTGAAGAAA 59.580 36.000 30.66 9.56 43.95 2.52
2620 3354 4.952957 TGGTGTTGATCAACCTTTGAAGAA 59.047 37.500 30.66 10.25 43.95 2.52
2621 3355 4.531854 TGGTGTTGATCAACCTTTGAAGA 58.468 39.130 30.66 10.92 43.95 2.87
2622 3356 4.916983 TGGTGTTGATCAACCTTTGAAG 57.083 40.909 30.66 0.00 43.95 3.02
2623 3357 8.821686 ATATATGGTGTTGATCAACCTTTGAA 57.178 30.769 30.66 15.22 43.95 2.69
2624 3358 8.821686 AATATATGGTGTTGATCAACCTTTGA 57.178 30.769 30.66 16.48 45.01 2.69
2636 3370 9.814899 TTAATGGAAGCAAAATATATGGTGTTG 57.185 29.630 0.00 0.00 0.00 3.33
2637 3371 9.816354 GTTAATGGAAGCAAAATATATGGTGTT 57.184 29.630 0.00 0.00 0.00 3.32
2647 3385 9.783081 AAAAGATGAAGTTAATGGAAGCAAAAT 57.217 25.926 0.00 0.00 0.00 1.82
2693 3432 7.600752 AGCGAAATTATCCTGCTTTCTATAGAC 59.399 37.037 0.67 0.00 30.27 2.59
2767 3507 6.159988 ACTAAGTTTCTCACTGAGCACATAC 58.840 40.000 0.62 0.00 37.49 2.39
3004 3744 5.702622 ACACAATTAGTCATCAATCGACG 57.297 39.130 0.00 0.00 38.46 5.12
3074 3814 1.272212 GTGTTGATTCCGGCCACAAAT 59.728 47.619 2.24 0.00 0.00 2.32
3083 3823 3.056107 TCTGTAGAAGGGTGTTGATTCCG 60.056 47.826 0.00 0.00 0.00 4.30
3242 3991 6.433093 GGAAAAGATTACTGGGAAGCAAGTAA 59.567 38.462 0.00 0.00 41.70 2.24
3471 4220 5.437060 TCCTGCTAGAACACTTTTGTCTTT 58.563 37.500 0.00 0.00 33.55 2.52
3475 4224 4.520492 CCATTCCTGCTAGAACACTTTTGT 59.480 41.667 0.00 0.00 37.67 2.83
3476 4225 4.616835 GCCATTCCTGCTAGAACACTTTTG 60.617 45.833 0.00 0.00 0.00 2.44
3497 4246 3.188460 TGAGATTGAAAGTTAAGCACGCC 59.812 43.478 0.00 0.00 0.00 5.68
3580 4330 4.832248 TCATACAGTCCAAAGCCAACTAG 58.168 43.478 0.00 0.00 0.00 2.57
3612 4362 1.688735 TGCTCAGATCTTACCGATGGG 59.311 52.381 0.00 0.00 40.11 4.00
3673 4423 5.336744 ACCTGTGTATTTGTTGTTCAAACG 58.663 37.500 0.00 0.00 46.77 3.60
3712 4462 2.957402 TCAGTTCAGGCAGACCAATT 57.043 45.000 0.00 0.00 39.06 2.32
3778 4528 9.607988 CTGGGTAACAAAAGGTTAAAAAGATTT 57.392 29.630 0.00 0.00 43.30 2.17
3782 4532 6.342111 TGCTGGGTAACAAAAGGTTAAAAAG 58.658 36.000 0.00 0.00 43.30 2.27
3837 4587 0.391528 AAAAATGGAAGCGCATGGGC 60.392 50.000 26.04 26.04 0.00 5.36
3930 4682 5.299949 CAGATATGCATACAGCCACACTAA 58.700 41.667 8.99 0.00 44.83 2.24
4019 4771 2.084546 GCACCACCAATTAGTCCAGAC 58.915 52.381 0.00 0.00 0.00 3.51
4089 4841 6.854496 TCGTGTTACTAAACAGCAAGAATT 57.146 33.333 0.00 0.00 46.06 2.17
4091 4843 6.259167 ACATTCGTGTTACTAAACAGCAAGAA 59.741 34.615 0.00 0.00 46.06 2.52
4092 4844 5.756347 ACATTCGTGTTACTAAACAGCAAGA 59.244 36.000 0.00 0.00 46.06 3.02
4633 5386 8.741841 AGACTACAAACATAGAAGTTAGGAGAC 58.258 37.037 0.00 0.00 0.00 3.36
4732 5485 1.039233 GCACATACCTGCCAGCCAAT 61.039 55.000 0.00 0.00 0.00 3.16
4784 5537 6.429078 TGAGTTCAAAGTTGGAGATTGATCTG 59.571 38.462 0.00 0.00 37.25 2.90
4865 5618 7.895429 AGAAGATCCATTTCCAGTTCCAAATAA 59.105 33.333 0.00 0.00 0.00 1.40
4977 5733 4.579454 AGCATAATGGTTGCATGACATC 57.421 40.909 0.00 0.00 42.62 3.06
4979 5735 4.018490 AGAAGCATAATGGTTGCATGACA 58.982 39.130 0.00 0.00 42.62 3.58
4983 5739 4.186159 GCAAAGAAGCATAATGGTTGCAT 58.814 39.130 0.00 0.00 42.62 3.96
5415 6175 8.681806 TGCTAAGCATTATAAGCAACATTACAA 58.318 29.630 8.84 0.00 41.74 2.41
5422 6182 8.958043 GTTATTGTGCTAAGCATTATAAGCAAC 58.042 33.333 0.00 0.00 45.81 4.17
5660 6420 4.116961 TCGATCCAAAATAAGTGGCGTAG 58.883 43.478 0.00 0.00 35.99 3.51
5664 6424 3.945285 TCCTTCGATCCAAAATAAGTGGC 59.055 43.478 0.00 0.00 35.99 5.01
5667 6427 6.942976 TGTACTCCTTCGATCCAAAATAAGT 58.057 36.000 0.00 0.00 0.00 2.24
5668 6428 9.712305 ATATGTACTCCTTCGATCCAAAATAAG 57.288 33.333 0.00 0.00 0.00 1.73
5669 6429 9.489084 CATATGTACTCCTTCGATCCAAAATAA 57.511 33.333 0.00 0.00 0.00 1.40
5670 6430 8.866093 TCATATGTACTCCTTCGATCCAAAATA 58.134 33.333 1.90 0.00 0.00 1.40
5671 6431 7.735917 TCATATGTACTCCTTCGATCCAAAAT 58.264 34.615 1.90 0.00 0.00 1.82
5672 6432 7.069455 TCTCATATGTACTCCTTCGATCCAAAA 59.931 37.037 1.90 0.00 0.00 2.44
5675 6435 5.631119 TCTCATATGTACTCCTTCGATCCA 58.369 41.667 1.90 0.00 0.00 3.41
5676 6436 5.941058 TCTCTCATATGTACTCCTTCGATCC 59.059 44.000 1.90 0.00 0.00 3.36
5677 6437 7.441890 TTCTCTCATATGTACTCCTTCGATC 57.558 40.000 1.90 0.00 0.00 3.69
5680 6440 7.265647 TCTTTCTCTCATATGTACTCCTTCG 57.734 40.000 1.90 0.00 0.00 3.79
5703 6493 7.498570 ACCAGAGCTTCTATCAGAATTCAAATC 59.501 37.037 8.44 0.00 33.13 2.17
5797 6587 4.597507 ACTGAGAACCCAAGGATGAACTTA 59.402 41.667 0.00 0.00 0.00 2.24
5872 6662 0.907704 TGTGTACAGGGCCGAATCCT 60.908 55.000 0.00 0.00 34.39 3.24
5913 6703 0.390340 AGCGTGATCGATTGCACTGT 60.390 50.000 17.00 2.86 39.71 3.55
5951 6741 5.668558 AAGATGAAACAAACGGTCAGTAC 57.331 39.130 0.00 0.00 0.00 2.73
5952 6742 6.987992 AGTTAAGATGAAACAAACGGTCAGTA 59.012 34.615 0.00 0.00 0.00 2.74
6137 6927 0.827925 ACTCCTCGCTCCTTGTGTCA 60.828 55.000 0.00 0.00 0.00 3.58
6633 7424 4.319046 CGCAAATCCACTGATACATAGCAC 60.319 45.833 0.00 0.00 0.00 4.40
6669 7460 0.672401 ACCGCCCGACAACATTACTG 60.672 55.000 0.00 0.00 0.00 2.74
6690 7481 2.264813 CATAACGACCGACATTCCGTT 58.735 47.619 0.00 0.00 45.50 4.44
6756 7548 5.580691 TCCGCAATACACTATTTCAAGTCTG 59.419 40.000 0.00 0.00 0.00 3.51
6769 7561 7.834068 ACTTCATATATCATCCGCAATACAC 57.166 36.000 0.00 0.00 0.00 2.90
6770 7562 8.314021 AGAACTTCATATATCATCCGCAATACA 58.686 33.333 0.00 0.00 0.00 2.29
6771 7563 8.598924 CAGAACTTCATATATCATCCGCAATAC 58.401 37.037 0.00 0.00 0.00 1.89
6772 7564 8.531146 TCAGAACTTCATATATCATCCGCAATA 58.469 33.333 0.00 0.00 0.00 1.90
6773 7565 7.389232 TCAGAACTTCATATATCATCCGCAAT 58.611 34.615 0.00 0.00 0.00 3.56
6776 7568 7.332926 ACATTCAGAACTTCATATATCATCCGC 59.667 37.037 0.00 0.00 0.00 5.54
6820 7612 6.805713 AGAAGAAACGACATGGAAAAATGTT 58.194 32.000 0.00 0.00 40.87 2.71
6821 7613 6.391227 AGAAGAAACGACATGGAAAAATGT 57.609 33.333 0.00 0.00 43.47 2.71
6885 7844 2.035961 GGTATCAGCTCGCAGTATCCAA 59.964 50.000 0.00 0.00 0.00 3.53
6906 7865 0.951040 GAGTTCCACGGGCTCTGTTG 60.951 60.000 0.00 0.00 0.00 3.33
6907 7866 1.122019 AGAGTTCCACGGGCTCTGTT 61.122 55.000 9.32 0.00 38.09 3.16
7107 8067 8.231161 GCTAGAGAAAAGAGTTAATCCACAAAC 58.769 37.037 0.00 0.00 0.00 2.93
7150 8112 7.688372 ACATAGATAAAATCAGAACGCAACAG 58.312 34.615 0.00 0.00 0.00 3.16
7157 8119 7.917505 CCAAGCCAACATAGATAAAATCAGAAC 59.082 37.037 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.