Multiple sequence alignment - TraesCS2D01G086700

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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 TraesCS2D01G086700 chr2D 100.000 5715 0 0 1001 6715 37261006 37255292 0.000000e+00 10554.0
1 TraesCS2D01G086700 chr2D 100.000 581 0 0 1 581 37262006 37261426 0.000000e+00 1074.0
2 TraesCS2D01G086700 chr2D 100.000 161 0 0 6944 7104 37255063 37254903 1.500000e-76 298.0
3 TraesCS2D01G086700 chr2D 97.143 35 0 1 2546 2579 37259416 37259382 2.770000e-04 58.4
4 TraesCS2D01G086700 chr2D 97.143 35 0 1 2591 2625 37259461 37259428 2.770000e-04 58.4
5 TraesCS2D01G086700 chr2A 95.794 3828 117 24 2591 6404 42160344 42156547 0.000000e+00 6137.0
6 TraesCS2D01G086700 chr2A 92.346 1594 100 12 1001 2579 42161897 42160311 0.000000e+00 2248.0
7 TraesCS2D01G086700 chr2A 88.095 378 23 9 210 580 42162923 42162561 5.090000e-116 429.0
8 TraesCS2D01G086700 chr2A 91.837 147 11 1 7 152 42163209 42163063 3.360000e-48 204.0
9 TraesCS2D01G086700 chr2A 89.441 161 9 3 6944 7104 42156185 42156033 5.620000e-46 196.0
10 TraesCS2D01G086700 chr2A 90.517 116 6 2 6605 6715 42156351 42156236 1.600000e-31 148.0
11 TraesCS2D01G086700 chr2B 93.923 3785 171 32 2664 6435 64995765 64992027 0.000000e+00 5661.0
12 TraesCS2D01G086700 chr2B 89.390 1065 79 16 1548 2579 64996843 64995780 0.000000e+00 1310.0
13 TraesCS2D01G086700 chr2B 89.062 448 28 9 1001 1448 64997111 64996685 2.920000e-148 536.0
14 TraesCS2D01G086700 chr2B 89.153 295 10 7 272 557 64997833 64997552 1.470000e-91 348.0
15 TraesCS2D01G086700 chr2B 89.820 167 6 6 6944 7104 64991490 64991329 3.360000e-48 204.0
16 TraesCS2D01G086700 chr2B 81.538 195 19 7 6530 6715 64991727 64991541 2.070000e-30 145.0
17 TraesCS2D01G086700 chr2B 93.671 79 5 0 4485 4563 64993844 64993766 1.250000e-22 119.0
18 TraesCS2D01G086700 chr2B 97.917 48 0 1 2591 2638 64995813 64995767 1.640000e-11 82.4
19 TraesCS2D01G086700 chr4B 81.921 1770 288 27 2705 4457 414861911 414863665 0.000000e+00 1467.0
20 TraesCS2D01G086700 chr4B 82.517 143 23 2 1096 1237 414859504 414859645 2.690000e-24 124.0
21 TraesCS2D01G086700 chr4D 81.741 1769 292 25 2705 4457 336660261 336662014 0.000000e+00 1448.0
22 TraesCS2D01G086700 chr4D 83.916 143 21 2 1096 1237 336658002 336658143 1.240000e-27 135.0
23 TraesCS2D01G086700 chr4A 81.566 1763 302 22 2705 4455 136757458 136755707 0.000000e+00 1434.0
24 TraesCS2D01G086700 chr4A 83.217 143 22 2 1096 1237 136759708 136759567 5.780000e-26 130.0
25 TraesCS2D01G086700 chr4A 80.916 131 17 2 5689 5811 642917729 642917599 5.870000e-16 97.1
26 TraesCS2D01G086700 chr4A 80.147 136 19 2 5684 5811 658153010 658153145 2.110000e-15 95.3
27 TraesCS2D01G086700 chr5B 74.271 1784 407 46 2705 4459 280462331 280464091 0.000000e+00 704.0
28 TraesCS2D01G086700 chr5D 74.159 1784 410 42 2705 4459 245769754 245771515 0.000000e+00 693.0
29 TraesCS2D01G086700 chr5D 86.364 88 12 0 5687 5774 80206230 80206143 5.870000e-16 97.1
30 TraesCS2D01G086700 chr5A 74.033 1783 414 40 2705 4459 329825628 329827389 0.000000e+00 682.0
31 TraesCS2D01G086700 chr7B 82.353 136 16 2 5684 5811 479759719 479759854 2.090000e-20 111.0
32 TraesCS2D01G086700 chr6B 82.353 136 16 2 5684 5811 52458713 52458848 2.090000e-20 111.0
33 TraesCS2D01G086700 chr3D 86.813 91 12 0 5684 5774 65439289 65439379 1.260000e-17 102.0
34 TraesCS2D01G086700 chr3D 86.813 91 12 0 5684 5774 535486689 535486779 1.260000e-17 102.0


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 TraesCS2D01G086700 chr2D 37254903 37262006 7103 True 2408.560000 10554 98.857200 1 7104 5 chr2D.!!$R1 7103
1 TraesCS2D01G086700 chr2A 42156033 42163209 7176 True 1560.333333 6137 91.338333 7 7104 6 chr2A.!!$R1 7097
2 TraesCS2D01G086700 chr2B 64991329 64997833 6504 True 1050.675000 5661 90.559250 272 7104 8 chr2B.!!$R1 6832
3 TraesCS2D01G086700 chr4B 414859504 414863665 4161 False 795.500000 1467 82.219000 1096 4457 2 chr4B.!!$F1 3361
4 TraesCS2D01G086700 chr4D 336658002 336662014 4012 False 791.500000 1448 82.828500 1096 4457 2 chr4D.!!$F1 3361
5 TraesCS2D01G086700 chr4A 136755707 136759708 4001 True 782.000000 1434 82.391500 1096 4455 2 chr4A.!!$R2 3359
6 TraesCS2D01G086700 chr5B 280462331 280464091 1760 False 704.000000 704 74.271000 2705 4459 1 chr5B.!!$F1 1754
7 TraesCS2D01G086700 chr5D 245769754 245771515 1761 False 693.000000 693 74.159000 2705 4459 1 chr5D.!!$F1 1754
8 TraesCS2D01G086700 chr5A 329825628 329827389 1761 False 682.000000 682 74.033000 2705 4459 1 chr5A.!!$F1 1754

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
383 481 0.528470 ACAACCACAACACGGTTTGG 59.472 50.000 0.00 8.81 44.46 3.28 F
1356 1774 0.250858 CTGCACCAGTGTCCATTCCA 60.251 55.000 0.00 0.00 0.00 3.53 F
1436 1854 0.380378 TTGCGCAAACTCTGGTTGAC 59.620 50.000 22.78 0.00 35.63 3.18 F
2569 4107 0.546122 TGTTGCTGACCACTGACCTT 59.454 50.000 0.00 0.00 0.00 3.50 F
3973 5667 1.003355 CAGAACCGTGCCTGTCCAT 60.003 57.895 0.00 0.00 0.00 3.41 F
4997 6695 0.322816 TTCCTGAAGATGCTGCCACC 60.323 55.000 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 3273 0.261696 ATTGGGGCAATACCACCTCC 59.738 55.000 0.00 0.0 43.75 4.30 R
2473 3786 0.108585 GAACTTGGACAGGTGCTCCA 59.891 55.000 7.70 0.0 35.91 3.86 R
2594 4164 1.064758 AGGTCAGTGGTCAGCAACAAA 60.065 47.619 0.00 0.0 0.00 2.83 R
4095 5789 1.407437 CCCAATGTACCTGACTCCAGC 60.407 57.143 0.00 0.0 39.07 4.85 R
5960 7660 1.374252 CGTCGACCACCTTCTTGGG 60.374 63.158 10.58 0.0 41.49 4.12 R
6118 7819 0.253044 TGCGGCAAGGCTTCTTATCT 59.747 50.000 0.00 0.0 0.00 1.98 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
31 32 2.482664 CCATCCATGTCAACCTCTCTCG 60.483 54.545 0.00 0.00 0.00 4.04
40 41 2.158957 TCAACCTCTCTCGTTTGCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
74 76 9.872721 TGTACGTATTTTCTTATGACATAACCA 57.127 29.630 3.68 0.00 0.00 3.67
79 81 6.509418 TTTTCTTATGACATAACCAGTGCC 57.491 37.500 3.68 0.00 0.00 5.01
112 114 2.412870 CACCTGTGCTTACGTGATTGA 58.587 47.619 0.00 0.00 0.00 2.57
113 115 2.157668 CACCTGTGCTTACGTGATTGAC 59.842 50.000 0.00 0.00 0.00 3.18
128 130 4.000325 TGATTGACCCTTGTATTGTCACG 59.000 43.478 0.00 0.00 38.64 4.35
130 132 3.034721 TGACCCTTGTATTGTCACGTC 57.965 47.619 0.00 0.00 34.28 4.34
142 144 2.131972 TGTCACGTCGATCCTTTTGTG 58.868 47.619 0.00 0.00 0.00 3.33
148 150 3.054166 CGTCGATCCTTTTGTGTGTGTA 58.946 45.455 0.00 0.00 0.00 2.90
152 154 4.450757 TCGATCCTTTTGTGTGTGTATGTG 59.549 41.667 0.00 0.00 0.00 3.21
153 155 4.213270 CGATCCTTTTGTGTGTGTATGTGT 59.787 41.667 0.00 0.00 0.00 3.72
154 156 4.891627 TCCTTTTGTGTGTGTATGTGTG 57.108 40.909 0.00 0.00 0.00 3.82
155 157 4.265893 TCCTTTTGTGTGTGTATGTGTGT 58.734 39.130 0.00 0.00 0.00 3.72
156 158 4.095632 TCCTTTTGTGTGTGTATGTGTGTG 59.904 41.667 0.00 0.00 0.00 3.82
157 159 4.142491 CCTTTTGTGTGTGTATGTGTGTGT 60.142 41.667 0.00 0.00 0.00 3.72
158 160 4.348198 TTTGTGTGTGTATGTGTGTGTG 57.652 40.909 0.00 0.00 0.00 3.82
159 161 2.979240 TGTGTGTGTATGTGTGTGTGT 58.021 42.857 0.00 0.00 0.00 3.72
160 162 2.675348 TGTGTGTGTATGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
161 163 2.675844 GTGTGTGTATGTGTGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
170 172 2.881513 TGTGTGTGTGTGTTTCACTGTT 59.118 40.909 1.72 0.00 46.27 3.16
179 181 6.146673 GTGTGTGTTTCACTGTTACCCTATAC 59.853 42.308 1.72 0.00 46.27 1.47
180 182 6.183360 TGTGTGTTTCACTGTTACCCTATACA 60.183 38.462 1.72 0.00 46.27 2.29
187 189 7.837202 TCACTGTTACCCTATACAATTTTCG 57.163 36.000 0.00 0.00 0.00 3.46
189 191 5.587443 ACTGTTACCCTATACAATTTTCGGC 59.413 40.000 0.00 0.00 0.00 5.54
190 192 5.498393 TGTTACCCTATACAATTTTCGGCA 58.502 37.500 0.00 0.00 0.00 5.69
236 330 3.235200 TCAATGGGTTTTCAATCCGGTT 58.765 40.909 0.00 0.00 0.00 4.44
247 341 4.035612 TCAATCCGGTTTCCCACATAAA 57.964 40.909 0.00 0.00 0.00 1.40
262 356 5.256474 CCACATAAACCAGACCAATCTCTT 58.744 41.667 0.00 0.00 30.42 2.85
264 358 6.127897 CCACATAAACCAGACCAATCTCTTTC 60.128 42.308 0.00 0.00 30.42 2.62
265 359 5.946377 ACATAAACCAGACCAATCTCTTTCC 59.054 40.000 0.00 0.00 30.42 3.13
269 363 3.264450 ACCAGACCAATCTCTTTCCGAAT 59.736 43.478 0.00 0.00 30.42 3.34
277 371 3.610786 TCTCTTTCCGAATCGAGATCG 57.389 47.619 14.50 14.50 39.92 3.69
328 426 4.444056 CGGCGACTGATTCAAAAACAAAAT 59.556 37.500 0.00 0.00 0.00 1.82
333 431 7.162385 GCGACTGATTCAAAAACAAAATTTGTG 59.838 33.333 12.50 0.00 44.59 3.33
338 436 8.456471 TGATTCAAAAACAAAATTTGTGCATCA 58.544 25.926 12.50 8.36 44.59 3.07
363 461 9.878599 CAAGTTCGTATTTTGAAATCTTGTACT 57.121 29.630 0.00 0.00 30.69 2.73
369 467 9.537848 CGTATTTTGAAATCTTGTACTACAACC 57.462 33.333 0.00 0.00 33.96 3.77
373 471 7.867305 TTGAAATCTTGTACTACAACCACAA 57.133 32.000 0.00 0.00 33.96 3.33
374 472 7.254227 TGAAATCTTGTACTACAACCACAAC 57.746 36.000 0.00 0.00 33.96 3.32
375 473 6.824196 TGAAATCTTGTACTACAACCACAACA 59.176 34.615 0.00 0.00 33.96 3.33
376 474 6.613755 AATCTTGTACTACAACCACAACAC 57.386 37.500 0.00 0.00 33.96 3.32
377 475 4.114073 TCTTGTACTACAACCACAACACG 58.886 43.478 0.00 0.00 33.96 4.49
379 477 2.168106 TGTACTACAACCACAACACGGT 59.832 45.455 0.00 0.00 38.85 4.83
381 479 2.713877 ACTACAACCACAACACGGTTT 58.286 42.857 0.00 0.00 44.46 3.27
383 481 0.528470 ACAACCACAACACGGTTTGG 59.472 50.000 0.00 8.81 44.46 3.28
384 482 0.528470 CAACCACAACACGGTTTGGT 59.472 50.000 12.90 12.90 44.46 3.67
387 485 1.209990 ACCACAACACGGTTTGGTAGA 59.790 47.619 15.13 0.00 40.69 2.59
388 486 1.600485 CCACAACACGGTTTGGTAGAC 59.400 52.381 3.64 0.00 0.00 2.59
409 507 1.001120 TACATCGGGGAGTGCCAGA 59.999 57.895 5.89 5.89 35.15 3.86
487 591 2.599645 ATTCGCGAGCAGCCAATCCT 62.600 55.000 9.59 0.00 44.76 3.24
1247 1610 1.801512 GGCGCTGAAATTGGTTCGC 60.802 57.895 7.64 6.80 39.30 4.70
1254 1617 2.083774 TGAAATTGGTTCGCCTGCTAG 58.916 47.619 0.00 0.00 39.30 3.42
1322 1740 3.618594 ACATGTCGTGCATACACTGAATC 59.381 43.478 6.97 0.00 45.10 2.52
1334 1752 1.879380 CACTGAATCGTGCTGGGAAAA 59.121 47.619 0.00 0.00 0.00 2.29
1335 1753 1.880027 ACTGAATCGTGCTGGGAAAAC 59.120 47.619 0.00 0.00 0.00 2.43
1356 1774 0.250858 CTGCACCAGTGTCCATTCCA 60.251 55.000 0.00 0.00 0.00 3.53
1364 1782 3.432749 CCAGTGTCCATTCCATGTAGAGG 60.433 52.174 0.00 0.00 0.00 3.69
1394 1812 4.381411 GTCTATGCTATGGGGTCTGTTTC 58.619 47.826 0.00 0.00 0.00 2.78
1397 1815 1.985159 TGCTATGGGGTCTGTTTCTGT 59.015 47.619 0.00 0.00 0.00 3.41
1400 1818 3.307762 GCTATGGGGTCTGTTTCTGTCTT 60.308 47.826 0.00 0.00 0.00 3.01
1414 1832 6.015434 TGTTTCTGTCTTCTATGTAGTGCTGA 60.015 38.462 0.00 0.00 0.00 4.26
1432 1850 2.679837 CTGATATTGCGCAAACTCTGGT 59.320 45.455 28.81 11.35 0.00 4.00
1436 1854 0.380378 TTGCGCAAACTCTGGTTGAC 59.620 50.000 22.78 0.00 35.63 3.18
1477 1895 7.744087 TTAGTTTGTTGCAATGACATACTCT 57.256 32.000 14.00 3.85 39.15 3.24
1492 1910 9.650539 ATGACATACTCTGCATATACTGAATTC 57.349 33.333 0.00 0.00 0.00 2.17
1504 1922 9.224267 GCATATACTGAATTCCAATGACATACT 57.776 33.333 2.27 0.00 0.00 2.12
1528 1969 6.389906 TGCATATACTGATCTGGTTGATACG 58.610 40.000 4.49 0.00 35.14 3.06
1589 2030 3.962718 CAAATACTGAATTGCCCTGGGAT 59.037 43.478 19.27 0.00 0.00 3.85
1600 2041 4.753516 TGCCCTGGGATATTATGTATCG 57.246 45.455 19.27 0.00 0.00 2.92
1623 2064 5.994054 CGATGTCCATTCCATGTAGAGATTT 59.006 40.000 0.00 0.00 0.00 2.17
1700 2141 4.017407 ACTCTGGTAGATACTGGTCTGGAA 60.017 45.833 0.00 0.00 0.00 3.53
1807 2258 2.286885 GGAACCTGGGGATGGGGA 60.287 66.667 0.00 0.00 0.00 4.81
1844 2295 9.952188 GTGCCTTTTCTGTCTATATAAATTTCC 57.048 33.333 0.00 0.00 0.00 3.13
1845 2296 9.693739 TGCCTTTTCTGTCTATATAAATTTCCA 57.306 29.630 0.00 0.00 0.00 3.53
1888 2349 6.770746 ACCACGTTACTGTATTCTAGATGT 57.229 37.500 0.00 0.00 0.00 3.06
1965 3266 5.873712 TGGTCTACGTGTTTGTTTTTGTCTA 59.126 36.000 0.00 0.00 0.00 2.59
1971 3272 9.872757 CTACGTGTTTGTTTTTGTCTATTGTAT 57.127 29.630 0.00 0.00 0.00 2.29
1972 3273 8.555166 ACGTGTTTGTTTTTGTCTATTGTATG 57.445 30.769 0.00 0.00 0.00 2.39
1979 3280 6.432783 TGTTTTTGTCTATTGTATGGAGGTGG 59.567 38.462 0.00 0.00 0.00 4.61
2027 3331 6.387465 ACTGATCTGAAATTGCTGAATGTTG 58.613 36.000 6.60 0.00 0.00 3.33
2038 3342 1.201414 CTGAATGTTGTTAACCCGCCC 59.799 52.381 2.48 0.00 0.00 6.13
2066 3376 4.460263 GGCATGTAATGGTCCATAACAGA 58.540 43.478 4.33 0.00 46.86 3.41
2067 3377 4.516698 GGCATGTAATGGTCCATAACAGAG 59.483 45.833 4.33 0.00 46.86 3.35
2084 3394 3.942829 CAGAGAAACTGGGTATTGCTGA 58.057 45.455 0.00 0.00 42.39 4.26
2122 3432 4.642445 TTGATCAGCAATGCGAATGAAT 57.358 36.364 0.00 0.00 0.00 2.57
2136 3446 1.733387 ATGAATCCTGGGGATGGGGC 61.733 60.000 0.00 0.00 42.27 5.80
2148 3458 3.150903 ATGGGGCCAGTGCTTGTGT 62.151 57.895 4.39 0.00 37.74 3.72
2217 3530 5.102953 TCAGCTGGTTCTGCAACTAATAT 57.897 39.130 15.13 0.00 34.19 1.28
2238 3551 5.571784 ATGCCACATTTCTCATGTGTTAG 57.428 39.130 12.72 1.10 45.74 2.34
2258 3571 8.732531 GTGTTAGGCCTGTTGTATTAAACATAA 58.267 33.333 17.99 0.00 39.25 1.90
2473 3786 3.129638 GCTCTGACAGAGGAACTAACGAT 59.870 47.826 29.26 0.00 42.54 3.73
2513 3827 5.006896 TCCAGGTTTGTCTCTAGTCCTTA 57.993 43.478 0.00 0.00 0.00 2.69
2566 4104 3.119495 ACTTTTTGTTGCTGACCACTGAC 60.119 43.478 0.00 0.00 0.00 3.51
2567 4105 1.388547 TTTGTTGCTGACCACTGACC 58.611 50.000 0.00 0.00 0.00 4.02
2569 4107 0.546122 TGTTGCTGACCACTGACCTT 59.454 50.000 0.00 0.00 0.00 3.50
2570 4108 1.765904 TGTTGCTGACCACTGACCTTA 59.234 47.619 0.00 0.00 0.00 2.69
2573 4111 3.788227 TGCTGACCACTGACCTTATTT 57.212 42.857 0.00 0.00 0.00 1.40
2574 4112 3.411446 TGCTGACCACTGACCTTATTTG 58.589 45.455 0.00 0.00 0.00 2.32
2576 4114 4.041075 TGCTGACCACTGACCTTATTTGTA 59.959 41.667 0.00 0.00 0.00 2.41
2579 4117 4.286032 TGACCACTGACCTTATTTGTAGCT 59.714 41.667 0.00 0.00 0.00 3.32
2581 4119 6.014070 TGACCACTGACCTTATTTGTAGCTTA 60.014 38.462 0.00 0.00 0.00 3.09
2582 4120 6.171213 ACCACTGACCTTATTTGTAGCTTAC 58.829 40.000 0.00 0.00 0.00 2.34
2585 4155 6.092259 CACTGACCTTATTTGTAGCTTACCAC 59.908 42.308 0.00 0.00 0.00 4.16
2588 4158 6.014070 TGACCTTATTTGTAGCTTACCACTGA 60.014 38.462 0.00 0.00 0.00 3.41
2589 4159 6.171213 ACCTTATTTGTAGCTTACCACTGAC 58.829 40.000 0.00 0.00 0.00 3.51
2594 4164 6.368779 TTTGTAGCTTACCACTGACCTTAT 57.631 37.500 0.00 0.00 0.00 1.73
2598 4168 5.242795 AGCTTACCACTGACCTTATTTGT 57.757 39.130 0.00 0.00 0.00 2.83
2600 4170 5.473504 AGCTTACCACTGACCTTATTTGTTG 59.526 40.000 0.00 0.00 0.00 3.33
2601 4171 5.699097 TTACCACTGACCTTATTTGTTGC 57.301 39.130 0.00 0.00 0.00 4.17
2604 4174 3.820467 CCACTGACCTTATTTGTTGCTGA 59.180 43.478 0.00 0.00 0.00 4.26
2606 4176 3.821033 ACTGACCTTATTTGTTGCTGACC 59.179 43.478 0.00 0.00 0.00 4.02
2608 4178 3.568007 TGACCTTATTTGTTGCTGACCAC 59.432 43.478 0.00 0.00 0.00 4.16
2652 4222 5.255687 TGCATACACCACTTCAGATTTCAT 58.744 37.500 0.00 0.00 0.00 2.57
2654 4224 6.316140 TGCATACACCACTTCAGATTTCATAC 59.684 38.462 0.00 0.00 0.00 2.39
2657 4227 5.869579 ACACCACTTCAGATTTCATACACT 58.130 37.500 0.00 0.00 0.00 3.55
2658 4228 6.299141 ACACCACTTCAGATTTCATACACTT 58.701 36.000 0.00 0.00 0.00 3.16
2659 4229 6.428159 ACACCACTTCAGATTTCATACACTTC 59.572 38.462 0.00 0.00 0.00 3.01
2689 4259 7.386059 TGCTTTGATATGACTGTCTAACTTGA 58.614 34.615 9.51 0.00 0.00 3.02
2809 4479 6.992063 TCCTTTATCAAATCTGAAGTCTGC 57.008 37.500 0.00 0.00 34.49 4.26
3454 5124 3.584834 GATGTTTGGTGGTATTGTTGGC 58.415 45.455 0.00 0.00 0.00 4.52
3550 5222 8.154203 TCTTCTTTGTTCTTATGGTCACACATA 58.846 33.333 0.00 0.00 32.39 2.29
3934 5628 2.146342 CTGCTAATGCTATCAACCCCG 58.854 52.381 0.00 0.00 40.48 5.73
3973 5667 1.003355 CAGAACCGTGCCTGTCCAT 60.003 57.895 0.00 0.00 0.00 3.41
4095 5789 2.613977 CCTGTACTTCCAGAAGCCACTG 60.614 54.545 7.32 9.17 41.99 3.66
4552 6246 3.119352 GGATTTTAAGCTGCTGACTTGGG 60.119 47.826 1.35 0.00 0.00 4.12
4640 6334 7.093289 TGCTAGGCTCTCAACTAGATTTTAAGT 60.093 37.037 0.00 0.00 39.16 2.24
4653 6347 9.425577 ACTAGATTTTAAGTTGCTCACTTAGTC 57.574 33.333 0.00 8.59 46.61 2.59
4913 6611 7.823745 TTTGGCTCAAGTTAAAATCTCTCTT 57.176 32.000 0.00 0.00 0.00 2.85
4916 6614 7.875971 TGGCTCAAGTTAAAATCTCTCTTTTC 58.124 34.615 0.00 0.00 31.15 2.29
4918 6616 8.572185 GGCTCAAGTTAAAATCTCTCTTTTCTT 58.428 33.333 0.00 0.00 31.15 2.52
4919 6617 9.958234 GCTCAAGTTAAAATCTCTCTTTTCTTT 57.042 29.630 0.00 0.00 31.15 2.52
4997 6695 0.322816 TTCCTGAAGATGCTGCCACC 60.323 55.000 0.00 0.00 0.00 4.61
5148 6846 3.201930 TGCTATACCTGAATGGGCAAAGA 59.798 43.478 0.00 0.00 41.11 2.52
5150 6848 4.036852 GCTATACCTGAATGGGCAAAGAAC 59.963 45.833 0.00 0.00 41.11 3.01
5175 6873 4.657436 AGTAAGCTGGCTGATGTAGTAC 57.343 45.455 0.00 0.00 0.00 2.73
5183 6881 5.521906 TGGCTGATGTAGTACAGAAGATC 57.478 43.478 15.74 6.56 36.38 2.75
5184 6882 4.956075 TGGCTGATGTAGTACAGAAGATCA 59.044 41.667 15.74 10.14 36.38 2.92
5185 6883 5.600069 TGGCTGATGTAGTACAGAAGATCAT 59.400 40.000 15.74 0.00 36.38 2.45
5368 7066 8.581253 AAACCTATCCAATTTGAGAAGGTAAG 57.419 34.615 13.65 0.00 34.93 2.34
5371 7069 8.832735 ACCTATCCAATTTGAGAAGGTAAGTAA 58.167 33.333 12.30 0.00 34.49 2.24
5372 7070 9.853177 CCTATCCAATTTGAGAAGGTAAGTAAT 57.147 33.333 0.00 0.00 0.00 1.89
5375 7073 8.348285 TCCAATTTGAGAAGGTAAGTAATTGG 57.652 34.615 14.43 14.43 45.92 3.16
5407 7107 4.773323 GCATCAGCAAGTCCTAAGTTTT 57.227 40.909 0.00 0.00 41.58 2.43
5412 7112 7.651704 GCATCAGCAAGTCCTAAGTTTTAAAAA 59.348 33.333 1.31 0.00 41.58 1.94
5436 7136 5.954296 ATGTTCAGAAATCTTCACAGGTG 57.046 39.130 0.00 0.00 0.00 4.00
5437 7137 4.780815 TGTTCAGAAATCTTCACAGGTGT 58.219 39.130 0.00 0.00 0.00 4.16
5440 7140 6.183360 TGTTCAGAAATCTTCACAGGTGTTTC 60.183 38.462 0.00 2.81 0.00 2.78
5442 7142 6.826668 TCAGAAATCTTCACAGGTGTTTCTA 58.173 36.000 12.51 3.68 35.01 2.10
5457 7157 7.174946 CAGGTGTTTCTAATCCACATTACAACT 59.825 37.037 0.00 0.00 28.61 3.16
5481 7181 8.531982 ACTCTTATGTACTCTTCAGCATGTAAA 58.468 33.333 0.00 0.00 37.40 2.01
5482 7182 9.539825 CTCTTATGTACTCTTCAGCATGTAAAT 57.460 33.333 0.00 0.00 37.40 1.40
5496 7196 4.746611 GCATGTAAATAATGCCTTGGCTTC 59.253 41.667 13.18 0.00 43.78 3.86
5497 7197 5.452356 GCATGTAAATAATGCCTTGGCTTCT 60.452 40.000 13.18 0.13 43.78 2.85
5545 7245 4.917385 TCCACATGGATTTAATATCCGGG 58.083 43.478 0.00 0.00 39.78 5.73
5563 7263 2.202285 TTAGCAAACATGCGCGCG 60.202 55.556 28.44 28.44 40.27 6.86
5638 7338 2.031516 GATCATCCCAGCCATCGCG 61.032 63.158 0.00 0.00 41.18 5.87
5731 7431 2.423577 GAGGACTACCGCAACACATTT 58.576 47.619 0.00 0.00 41.83 2.32
5740 7440 1.130955 GCAACACATTTGCGAACCTG 58.869 50.000 0.00 0.00 35.58 4.00
5758 7458 3.011517 GCCCTGCCCCTCTTCTCA 61.012 66.667 0.00 0.00 0.00 3.27
5938 7638 3.304659 CCCTGCTGTACAACAACATGTTC 60.305 47.826 8.48 0.00 38.77 3.18
5954 7654 3.158537 TTCGCGAGGCACAAGGACA 62.159 57.895 9.59 0.00 0.00 4.02
5960 7660 3.368571 GGCACAAGGACAGGCTGC 61.369 66.667 15.89 7.42 0.00 5.25
5978 7678 1.374252 CCCAAGAAGGTGGTCGACG 60.374 63.158 9.92 0.00 36.90 5.12
6007 7707 2.978010 GTGGGCAAGGTGGACGTG 60.978 66.667 0.00 0.00 0.00 4.49
6146 7847 1.805254 CCTTGCCGCATCTCCAAAG 59.195 57.895 0.00 0.00 0.00 2.77
6211 7921 0.444260 TCGCGCTGATAGCTCTATCG 59.556 55.000 5.56 7.87 43.64 2.92
6226 7936 4.760715 GCTCTATCGTGGTCACCTAAGATA 59.239 45.833 0.00 1.05 0.00 1.98
6228 7938 6.403855 GCTCTATCGTGGTCACCTAAGATATC 60.404 46.154 0.00 0.00 0.00 1.63
6234 7944 4.525100 GTGGTCACCTAAGATATCCTCTCC 59.475 50.000 0.00 0.00 31.03 3.71
6276 7986 0.800683 TTATCTGCTCGTTGGTCGCG 60.801 55.000 0.00 0.00 39.67 5.87
6282 7992 1.736645 CTCGTTGGTCGCGGTCAAT 60.737 57.895 6.13 0.00 39.67 2.57
6300 8016 4.938226 GTCAATTAGTTGGAGTTGGAGGAG 59.062 45.833 0.00 0.00 35.99 3.69
6405 8123 5.488262 TTGTCATCTTTCATCTCCAGTGA 57.512 39.130 0.00 0.00 0.00 3.41
6406 8124 5.082251 TGTCATCTTTCATCTCCAGTGAG 57.918 43.478 0.00 0.00 40.17 3.51
6422 8140 0.884514 TGAGCTCACTCGGTCTTCTG 59.115 55.000 13.74 0.00 46.69 3.02
6423 8141 0.885196 GAGCTCACTCGGTCTTCTGT 59.115 55.000 9.40 0.00 32.04 3.41
6429 8147 2.293677 TCACTCGGTCTTCTGTCTGAAC 59.706 50.000 0.00 0.00 0.00 3.18
6441 8159 2.540101 CTGTCTGAACCTGTGACGTTTC 59.460 50.000 0.00 0.00 33.81 2.78
6445 8163 1.483004 TGAACCTGTGACGTTTCTCCA 59.517 47.619 0.00 0.00 0.00 3.86
6446 8164 2.104111 TGAACCTGTGACGTTTCTCCAT 59.896 45.455 0.00 0.00 0.00 3.41
6447 8165 2.169832 ACCTGTGACGTTTCTCCATG 57.830 50.000 0.00 0.00 0.00 3.66
6448 8166 1.691976 ACCTGTGACGTTTCTCCATGA 59.308 47.619 0.00 0.00 0.00 3.07
6449 8167 2.289072 ACCTGTGACGTTTCTCCATGAG 60.289 50.000 0.00 0.00 0.00 2.90
6450 8168 2.341257 CTGTGACGTTTCTCCATGAGG 58.659 52.381 0.00 0.00 0.00 3.86
6451 8169 1.967779 TGTGACGTTTCTCCATGAGGA 59.032 47.619 0.00 0.00 43.21 3.71
6452 8170 2.567169 TGTGACGTTTCTCCATGAGGAT 59.433 45.455 0.00 0.00 44.70 3.24
6453 8171 3.007940 TGTGACGTTTCTCCATGAGGATT 59.992 43.478 0.00 0.00 44.70 3.01
6454 8172 4.003648 GTGACGTTTCTCCATGAGGATTT 58.996 43.478 0.00 0.00 44.70 2.17
6455 8173 4.455877 GTGACGTTTCTCCATGAGGATTTT 59.544 41.667 0.00 0.00 44.70 1.82
6456 8174 4.695455 TGACGTTTCTCCATGAGGATTTTC 59.305 41.667 0.00 0.00 44.70 2.29
6457 8175 3.684788 ACGTTTCTCCATGAGGATTTTCG 59.315 43.478 0.00 0.00 44.70 3.46
6462 8180 3.070159 TCTCCATGAGGATTTTCGCCTAG 59.930 47.826 0.00 0.00 44.70 3.02
6464 8182 3.454447 TCCATGAGGATTTTCGCCTAGAA 59.546 43.478 0.00 0.00 39.61 2.10
6465 8183 4.103153 TCCATGAGGATTTTCGCCTAGAAT 59.897 41.667 0.00 0.00 39.61 2.40
6469 8187 6.194796 TGAGGATTTTCGCCTAGAATTTTG 57.805 37.500 0.00 0.00 38.86 2.44
6489 8207 3.715628 GCGGATGCACCTTCAAATATT 57.284 42.857 0.00 0.00 42.15 1.28
6491 8209 3.798337 GCGGATGCACCTTCAAATATTTG 59.202 43.478 20.13 20.13 42.15 2.32
6499 8219 5.644644 CACCTTCAAATATTTGAGCCAGAC 58.355 41.667 25.58 0.00 46.68 3.51
6531 8251 2.615869 CTCAAAGAGGTGAGCTAGTGC 58.384 52.381 0.00 0.00 38.74 4.40
6532 8252 1.970640 TCAAAGAGGTGAGCTAGTGCA 59.029 47.619 0.00 0.00 42.74 4.57
6533 8253 2.028658 TCAAAGAGGTGAGCTAGTGCAG 60.029 50.000 0.00 0.00 42.74 4.41
6534 8254 0.901124 AAGAGGTGAGCTAGTGCAGG 59.099 55.000 0.00 0.00 42.74 4.85
6535 8255 0.040351 AGAGGTGAGCTAGTGCAGGA 59.960 55.000 0.00 0.00 42.74 3.86
6536 8256 0.459489 GAGGTGAGCTAGTGCAGGAG 59.541 60.000 0.00 0.00 42.74 3.69
6537 8257 0.252012 AGGTGAGCTAGTGCAGGAGT 60.252 55.000 0.00 0.00 42.74 3.85
6538 8258 1.006043 AGGTGAGCTAGTGCAGGAGTA 59.994 52.381 0.00 0.00 42.74 2.59
6539 8259 1.135333 GGTGAGCTAGTGCAGGAGTAC 59.865 57.143 0.00 0.00 42.74 2.73
6541 8261 2.098443 GTGAGCTAGTGCAGGAGTACTC 59.902 54.545 14.87 14.87 41.21 2.59
6551 8541 2.158986 GCAGGAGTACTCACTGCATCAT 60.159 50.000 36.10 8.20 45.06 2.45
6578 8568 9.463443 GTCACCTGATATTATATTTTTGTTGGC 57.537 33.333 0.00 0.00 0.00 4.52
6579 8569 9.194972 TCACCTGATATTATATTTTTGTTGGCA 57.805 29.630 0.00 0.00 0.00 4.92
6580 8570 9.248291 CACCTGATATTATATTTTTGTTGGCAC 57.752 33.333 0.00 0.00 0.00 5.01
6581 8571 8.134895 ACCTGATATTATATTTTTGTTGGCACG 58.865 33.333 0.00 0.00 0.00 5.34
6582 8572 8.349245 CCTGATATTATATTTTTGTTGGCACGA 58.651 33.333 0.00 0.00 0.00 4.35
6583 8573 9.729023 CTGATATTATATTTTTGTTGGCACGAA 57.271 29.630 0.00 0.00 0.00 3.85
6584 8574 9.509855 TGATATTATATTTTTGTTGGCACGAAC 57.490 29.630 0.00 0.00 0.00 3.95
6587 8577 5.968528 ATATTTTTGTTGGCACGAACCTA 57.031 34.783 0.00 0.00 0.00 3.08
6588 8578 3.701532 TTTTTGTTGGCACGAACCTAG 57.298 42.857 0.00 0.00 0.00 3.02
6590 8580 0.759959 TTGTTGGCACGAACCTAGGA 59.240 50.000 17.98 0.00 0.00 2.94
6591 8581 0.034337 TGTTGGCACGAACCTAGGAC 59.966 55.000 17.98 8.20 0.00 3.85
6592 8582 0.320697 GTTGGCACGAACCTAGGACT 59.679 55.000 17.98 1.01 0.00 3.85
6593 8583 1.547372 GTTGGCACGAACCTAGGACTA 59.453 52.381 17.98 0.00 0.00 2.59
6594 8584 1.927487 TGGCACGAACCTAGGACTAA 58.073 50.000 17.98 0.00 0.00 2.24
6595 8585 2.250031 TGGCACGAACCTAGGACTAAA 58.750 47.619 17.98 0.00 0.00 1.85
6597 8587 3.259902 GGCACGAACCTAGGACTAAAAG 58.740 50.000 17.98 1.86 0.00 2.27
6598 8588 3.306571 GGCACGAACCTAGGACTAAAAGT 60.307 47.826 17.98 2.51 0.00 2.66
6599 8589 4.082026 GGCACGAACCTAGGACTAAAAGTA 60.082 45.833 17.98 0.00 0.00 2.24
6600 8590 5.394993 GGCACGAACCTAGGACTAAAAGTAT 60.395 44.000 17.98 0.00 0.00 2.12
6602 8592 6.592994 GCACGAACCTAGGACTAAAAGTATTT 59.407 38.462 17.98 0.00 42.41 1.40
7001 9000 1.359848 CGGCATGTGAGTCTTGGTAC 58.640 55.000 0.00 0.00 0.00 3.34
7004 9005 3.735208 CGGCATGTGAGTCTTGGTACTAG 60.735 52.174 0.00 0.00 0.00 2.57
7009 9010 7.042335 GCATGTGAGTCTTGGTACTAGTTTAT 58.958 38.462 0.00 0.00 0.00 1.40
7010 9011 7.549488 GCATGTGAGTCTTGGTACTAGTTTATT 59.451 37.037 0.00 0.00 0.00 1.40
7035 9036 8.722342 TTTTGCGATTAAAGAACAATACTGTC 57.278 30.769 0.00 0.00 33.45 3.51
7074 9078 0.545309 TGCTCTGCTTCTGGGGTAGT 60.545 55.000 0.00 0.00 0.00 2.73
7075 9079 1.273041 TGCTCTGCTTCTGGGGTAGTA 60.273 52.381 0.00 0.00 0.00 1.82
7076 9080 1.137282 GCTCTGCTTCTGGGGTAGTAC 59.863 57.143 0.00 0.00 0.00 2.73
7077 9081 2.741145 CTCTGCTTCTGGGGTAGTACT 58.259 52.381 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.624777 AGGTTGACATGGATGGACAATC 58.375 45.455 0.00 0.00 33.53 2.67
5 6 3.267812 AGAGGTTGACATGGATGGACAAT 59.732 43.478 0.00 0.00 33.53 2.71
13 14 1.924731 ACGAGAGAGGTTGACATGGA 58.075 50.000 0.00 0.00 0.00 3.41
31 32 2.869233 ACATGACACCACAAGCAAAC 57.131 45.000 0.00 0.00 0.00 2.93
40 41 8.035984 TCATAAGAAAATACGTACATGACACCA 58.964 33.333 0.00 0.00 0.00 4.17
74 76 0.613260 TGGTTAAGAGATGCGGCACT 59.387 50.000 4.03 4.66 0.00 4.40
79 81 2.002586 CACAGGTGGTTAAGAGATGCG 58.997 52.381 0.00 0.00 0.00 4.73
112 114 1.614903 TCGACGTGACAATACAAGGGT 59.385 47.619 0.00 0.00 0.00 4.34
113 115 2.357327 TCGACGTGACAATACAAGGG 57.643 50.000 0.00 0.00 0.00 3.95
128 130 4.451096 ACATACACACACAAAAGGATCGAC 59.549 41.667 0.00 0.00 0.00 4.20
130 132 4.213270 ACACATACACACACAAAAGGATCG 59.787 41.667 0.00 0.00 0.00 3.69
142 144 4.142795 TGAAACACACACACACATACACAC 60.143 41.667 0.00 0.00 0.00 3.82
157 159 6.422344 TGTATAGGGTAACAGTGAAACACA 57.578 37.500 0.00 0.00 41.43 3.72
158 160 7.916914 ATTGTATAGGGTAACAGTGAAACAC 57.083 36.000 0.00 0.00 41.43 3.32
159 161 8.927675 AAATTGTATAGGGTAACAGTGAAACA 57.072 30.769 0.00 0.00 41.43 2.83
160 162 9.836076 GAAAATTGTATAGGGTAACAGTGAAAC 57.164 33.333 0.00 0.00 39.74 2.78
161 163 8.723311 CGAAAATTGTATAGGGTAACAGTGAAA 58.277 33.333 0.00 0.00 39.74 2.69
170 172 4.121317 CGTGCCGAAAATTGTATAGGGTA 58.879 43.478 0.00 0.00 0.00 3.69
179 181 1.535462 AGAGAACCGTGCCGAAAATTG 59.465 47.619 0.00 0.00 0.00 2.32
180 182 1.892209 AGAGAACCGTGCCGAAAATT 58.108 45.000 0.00 0.00 0.00 1.82
187 189 5.616488 TTATTTACAAAGAGAACCGTGCC 57.384 39.130 0.00 0.00 0.00 5.01
189 191 6.961576 TGGTTTATTTACAAAGAGAACCGTG 58.038 36.000 0.00 0.00 38.25 4.94
190 192 7.571080 TTGGTTTATTTACAAAGAGAACCGT 57.429 32.000 0.00 0.00 38.25 4.83
196 198 9.369904 CCCATTGATTGGTTTATTTACAAAGAG 57.630 33.333 0.00 0.00 44.83 2.85
221 315 2.736144 GGGAAACCGGATTGAAAACC 57.264 50.000 9.46 0.00 43.64 3.27
236 330 3.885976 TTGGTCTGGTTTATGTGGGAA 57.114 42.857 0.00 0.00 0.00 3.97
247 341 2.257207 TCGGAAAGAGATTGGTCTGGT 58.743 47.619 0.00 0.00 33.97 4.00
253 347 4.046938 TCTCGATTCGGAAAGAGATTGG 57.953 45.455 18.93 2.51 35.13 3.16
293 387 3.476419 TCGCCGGGGGAAGGAATC 61.476 66.667 19.63 0.00 0.00 2.52
294 388 3.793888 GTCGCCGGGGGAAGGAAT 61.794 66.667 19.63 0.00 0.00 3.01
308 403 7.162385 GCACAAATTTTGTTTTTGAATCAGTCG 59.838 33.333 12.02 0.00 43.23 4.18
312 407 8.456471 TGATGCACAAATTTTGTTTTTGAATCA 58.544 25.926 12.02 12.81 43.23 2.57
328 426 6.499172 TCAAAATACGAACTTGATGCACAAA 58.501 32.000 0.00 0.00 38.08 2.83
333 431 8.368126 CAAGATTTCAAAATACGAACTTGATGC 58.632 33.333 0.00 0.00 31.86 3.91
369 467 2.281517 TGTCTACCAAACCGTGTTGTG 58.718 47.619 0.00 0.00 0.00 3.33
373 471 2.694628 TGTACTGTCTACCAAACCGTGT 59.305 45.455 0.00 0.00 0.00 4.49
374 472 3.374220 TGTACTGTCTACCAAACCGTG 57.626 47.619 0.00 0.00 0.00 4.94
375 473 3.366679 CGATGTACTGTCTACCAAACCGT 60.367 47.826 0.00 0.00 0.00 4.83
376 474 3.176708 CGATGTACTGTCTACCAAACCG 58.823 50.000 0.00 0.00 0.00 4.44
377 475 3.518590 CCGATGTACTGTCTACCAAACC 58.481 50.000 0.00 0.00 0.00 3.27
379 477 2.498481 CCCCGATGTACTGTCTACCAAA 59.502 50.000 0.00 0.00 0.00 3.28
380 478 2.104967 CCCCGATGTACTGTCTACCAA 58.895 52.381 0.00 0.00 0.00 3.67
381 479 1.285667 TCCCCGATGTACTGTCTACCA 59.714 52.381 0.00 0.00 0.00 3.25
383 481 2.358267 CACTCCCCGATGTACTGTCTAC 59.642 54.545 0.00 0.00 0.00 2.59
384 482 2.651455 CACTCCCCGATGTACTGTCTA 58.349 52.381 0.00 0.00 0.00 2.59
387 485 1.614241 GGCACTCCCCGATGTACTGT 61.614 60.000 0.00 0.00 0.00 3.55
388 486 1.144057 GGCACTCCCCGATGTACTG 59.856 63.158 0.00 0.00 0.00 2.74
409 507 0.252197 ATTTCGAAACCCGGCTAGCT 59.748 50.000 13.81 0.00 39.14 3.32
1122 1484 1.152922 AGGTCCTCGTCGATCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
1247 1610 2.022240 GCGGAGAAGGGACTAGCAGG 62.022 65.000 0.00 0.00 38.49 4.85
1254 1617 4.475135 GGCAGGCGGAGAAGGGAC 62.475 72.222 0.00 0.00 0.00 4.46
1294 1712 2.677337 TGTATGCACGACATGTCATTGG 59.323 45.455 24.93 11.35 40.06 3.16
1322 1740 1.165907 TGCAGAGTTTTCCCAGCACG 61.166 55.000 0.00 0.00 0.00 5.34
1334 1752 3.970332 TGGACACTGGTGCAGAGT 58.030 55.556 0.17 0.00 40.73 3.24
1356 1774 4.100189 GCATAGACCAGTCAACCTCTACAT 59.900 45.833 0.00 0.00 0.00 2.29
1364 1782 3.495100 CCCCATAGCATAGACCAGTCAAC 60.495 52.174 0.00 0.00 0.00 3.18
1394 1812 7.116090 GCAATATCAGCACTACATAGAAGACAG 59.884 40.741 0.00 0.00 0.00 3.51
1397 1815 6.152379 CGCAATATCAGCACTACATAGAAGA 58.848 40.000 0.00 0.00 0.00 2.87
1400 1818 4.237724 GCGCAATATCAGCACTACATAGA 58.762 43.478 0.30 0.00 0.00 1.98
1414 1832 3.081061 TCAACCAGAGTTTGCGCAATAT 58.919 40.909 25.64 15.67 32.45 1.28
1432 1850 9.739276 AACTAAATAATTCCAGATCAGTGTCAA 57.261 29.630 0.00 0.00 0.00 3.18
1477 1895 9.002600 GTATGTCATTGGAATTCAGTATATGCA 57.997 33.333 7.93 0.00 0.00 3.96
1492 1910 8.039538 AGATCAGTATATGCAGTATGTCATTGG 58.960 37.037 0.00 0.00 39.31 3.16
1504 1922 6.015434 ACGTATCAACCAGATCAGTATATGCA 60.015 38.462 0.00 0.00 38.19 3.96
1559 2000 5.163519 GGGCAATTCAGTATTTGCAGTATGT 60.164 40.000 9.54 0.00 39.31 2.29
1569 2010 3.979501 ATCCCAGGGCAATTCAGTATT 57.020 42.857 0.00 0.00 0.00 1.89
1589 2030 8.947055 CATGGAATGGACATCGATACATAATA 57.053 34.615 0.00 0.00 41.79 0.98
1623 2064 1.078823 ACAGACCCCATAGACCAGTCA 59.921 52.381 0.00 0.00 0.00 3.41
1700 2141 1.461897 CGGTTAAAAACGTCCAGCGAT 59.538 47.619 0.00 0.00 44.77 4.58
1807 2258 2.961062 AGAAAAGGCACAAGCACTCATT 59.039 40.909 0.00 0.00 44.61 2.57
1844 2295 6.200097 GTGGTAAGCCTTTTGTGTAAACATTG 59.800 38.462 0.00 0.00 35.27 2.82
1845 2296 6.277605 GTGGTAAGCCTTTTGTGTAAACATT 58.722 36.000 0.00 0.00 35.27 2.71
1853 2304 3.562557 AGTAACGTGGTAAGCCTTTTGTG 59.437 43.478 0.00 0.00 35.27 3.33
1888 2349 7.176690 GGTGAAGAATTTTCCAGGACAATTCTA 59.823 37.037 31.22 20.23 43.67 2.10
1940 3241 5.181622 AGACAAAAACAAACACGTAGACCAA 59.818 36.000 0.00 0.00 0.00 3.67
1948 3249 7.858382 TCCATACAATAGACAAAAACAAACACG 59.142 33.333 0.00 0.00 0.00 4.49
1950 3251 8.356657 CCTCCATACAATAGACAAAAACAAACA 58.643 33.333 0.00 0.00 0.00 2.83
1965 3266 3.436470 GGGCAATACCACCTCCATACAAT 60.436 47.826 0.00 0.00 42.05 2.71
1971 3272 1.143329 TTGGGGCAATACCACCTCCA 61.143 55.000 0.00 0.00 43.75 3.86
1972 3273 0.261696 ATTGGGGCAATACCACCTCC 59.738 55.000 0.00 0.00 43.75 4.30
1979 3280 3.391296 TCTCTACCAGATTGGGGCAATAC 59.609 47.826 0.00 0.00 43.37 1.89
2027 3331 1.974875 CCCAACAGGGCGGGTTAAC 60.975 63.158 0.00 0.00 37.70 2.01
2038 3342 1.750778 GGACCATTACATGCCCAACAG 59.249 52.381 0.00 0.00 0.00 3.16
2066 3376 3.445096 GCATTCAGCAATACCCAGTTTCT 59.555 43.478 0.00 0.00 44.79 2.52
2067 3377 3.774066 GCATTCAGCAATACCCAGTTTC 58.226 45.455 0.00 0.00 44.79 2.78
2084 3394 7.147794 TGCTGATCAATAAATCAAAGGAGCATT 60.148 33.333 0.00 0.00 35.32 3.56
2136 3446 2.261345 CACAAACAACACAAGCACTGG 58.739 47.619 0.00 0.00 0.00 4.00
2148 3458 4.762289 AAAAATGGGTAGCCACAAACAA 57.238 36.364 17.60 0.00 0.00 2.83
2196 3509 4.497006 GCATATTAGTTGCAGAACCAGCTG 60.497 45.833 6.78 6.78 39.90 4.24
2200 3513 3.694072 GTGGCATATTAGTTGCAGAACCA 59.306 43.478 0.00 0.00 41.95 3.67
2238 3551 7.222611 CAGCATTTATGTTTAATACAACAGGCC 59.777 37.037 0.00 0.00 40.01 5.19
2473 3786 0.108585 GAACTTGGACAGGTGCTCCA 59.891 55.000 7.70 0.00 35.91 3.86
2513 3827 6.048509 GTGGAAAACAATGGATTTTGACAGT 58.951 36.000 0.00 0.00 29.44 3.55
2566 4104 5.585047 GGTCAGTGGTAAGCTACAAATAAGG 59.415 44.000 0.00 0.00 0.00 2.69
2567 4105 6.407202 AGGTCAGTGGTAAGCTACAAATAAG 58.593 40.000 0.00 0.00 0.00 1.73
2569 4107 6.368779 AAGGTCAGTGGTAAGCTACAAATA 57.631 37.500 0.00 0.00 0.00 1.40
2570 4108 4.910458 AGGTCAGTGGTAAGCTACAAAT 57.090 40.909 0.00 0.00 0.00 2.32
2573 4111 6.170506 CAAATAAGGTCAGTGGTAAGCTACA 58.829 40.000 0.00 0.00 0.00 2.74
2574 4112 6.171213 ACAAATAAGGTCAGTGGTAAGCTAC 58.829 40.000 0.00 0.00 0.00 3.58
2576 4114 5.242795 ACAAATAAGGTCAGTGGTAAGCT 57.757 39.130 0.00 0.00 0.00 3.74
2579 4117 5.240623 CAGCAACAAATAAGGTCAGTGGTAA 59.759 40.000 0.00 0.00 0.00 2.85
2581 4119 3.569701 CAGCAACAAATAAGGTCAGTGGT 59.430 43.478 0.00 0.00 0.00 4.16
2582 4120 3.820467 TCAGCAACAAATAAGGTCAGTGG 59.180 43.478 0.00 0.00 0.00 4.00
2585 4155 3.820467 TGGTCAGCAACAAATAAGGTCAG 59.180 43.478 0.00 0.00 0.00 3.51
2588 4158 3.569701 CAGTGGTCAGCAACAAATAAGGT 59.430 43.478 0.00 0.00 0.00 3.50
2589 4159 3.820467 TCAGTGGTCAGCAACAAATAAGG 59.180 43.478 0.00 0.00 0.00 2.69
2594 4164 1.064758 AGGTCAGTGGTCAGCAACAAA 60.065 47.619 0.00 0.00 0.00 2.83
2598 4168 3.788227 AATAAGGTCAGTGGTCAGCAA 57.212 42.857 0.00 0.00 0.00 3.91
2600 4170 3.412386 ACAAATAAGGTCAGTGGTCAGC 58.588 45.455 0.00 0.00 0.00 4.26
2601 4171 4.631813 GCTACAAATAAGGTCAGTGGTCAG 59.368 45.833 0.00 0.00 0.00 3.51
2604 4174 3.587506 AGGCTACAAATAAGGTCAGTGGT 59.412 43.478 0.00 0.00 0.00 4.16
2606 4176 3.375299 GCAGGCTACAAATAAGGTCAGTG 59.625 47.826 0.00 0.00 0.00 3.66
2608 4178 3.624861 CAGCAGGCTACAAATAAGGTCAG 59.375 47.826 0.00 0.00 0.00 3.51
2657 4227 4.754618 ACAGTCATATCAAAGCAACACGAA 59.245 37.500 0.00 0.00 0.00 3.85
2658 4228 4.314961 ACAGTCATATCAAAGCAACACGA 58.685 39.130 0.00 0.00 0.00 4.35
2659 4229 4.389992 AGACAGTCATATCAAAGCAACACG 59.610 41.667 2.66 0.00 0.00 4.49
2689 4259 3.102204 AGCCTGCCATGAAAATAAGCTT 58.898 40.909 3.48 3.48 0.00 3.74
2809 4479 1.892209 AGACACTACCAAAAAGGCCG 58.108 50.000 0.00 0.00 43.14 6.13
3454 5124 2.689983 ACAAGCCTTCACAACTTCTTGG 59.310 45.455 0.00 0.00 36.26 3.61
3550 5222 6.950619 AGTTGGAGCTTAATCAGAAAAGGATT 59.049 34.615 0.00 0.00 38.46 3.01
3920 5614 1.645402 AAGGCCGGGGTTGATAGCAT 61.645 55.000 2.18 0.00 0.00 3.79
3934 5628 3.080319 GGAGAGCATCAATATGAAGGCC 58.920 50.000 0.00 0.00 37.82 5.19
3973 5667 5.596772 TGTCATGGAAGACATTCTCGGTATA 59.403 40.000 0.00 0.00 43.18 1.47
4095 5789 1.407437 CCCAATGTACCTGACTCCAGC 60.407 57.143 0.00 0.00 39.07 4.85
4640 6334 6.997239 TTATCTAGACGACTAAGTGAGCAA 57.003 37.500 0.00 0.00 0.00 3.91
4645 6339 9.388346 GTGATGAATTATCTAGACGACTAAGTG 57.612 37.037 0.00 0.00 36.71 3.16
4997 6695 2.636830 CAGAAAGGAGCACCCATACTG 58.363 52.381 0.00 0.00 37.41 2.74
5148 6846 3.261897 ACATCAGCCAGCTTACTAGTGTT 59.738 43.478 5.39 0.00 0.00 3.32
5150 6848 3.533606 ACATCAGCCAGCTTACTAGTG 57.466 47.619 5.39 0.00 0.00 2.74
5175 6873 7.652727 TCGAATGTAGGAACTATGATCTTCTG 58.347 38.462 0.00 0.00 45.60 3.02
5183 6881 4.322080 TGGCTCGAATGTAGGAACTATG 57.678 45.455 0.00 0.00 45.60 2.23
5184 6882 5.353394 TTTGGCTCGAATGTAGGAACTAT 57.647 39.130 0.00 0.00 45.60 2.12
5185 6883 4.755411 CTTTGGCTCGAATGTAGGAACTA 58.245 43.478 0.00 0.00 41.75 2.24
5333 7031 8.093927 TCAAATTGGATAGGTTTCATTTGGAAC 58.906 33.333 0.00 0.00 34.56 3.62
5368 7066 6.421801 GCTGATGCAATATTTGGACCAATTAC 59.578 38.462 7.99 0.00 39.41 1.89
5371 7069 4.952460 GCTGATGCAATATTTGGACCAAT 58.048 39.130 7.99 1.22 39.41 3.16
5372 7070 4.389890 GCTGATGCAATATTTGGACCAA 57.610 40.909 1.69 1.69 39.41 3.67
5412 7112 6.322201 ACACCTGTGAAGATTTCTGAACATTT 59.678 34.615 3.94 0.00 0.00 2.32
5413 7113 5.829924 ACACCTGTGAAGATTTCTGAACATT 59.170 36.000 3.94 0.00 0.00 2.71
5414 7114 5.380043 ACACCTGTGAAGATTTCTGAACAT 58.620 37.500 3.94 0.00 0.00 2.71
5421 7121 7.174946 TGGATTAGAAACACCTGTGAAGATTTC 59.825 37.037 3.94 3.98 0.00 2.17
5426 7126 5.063204 TGTGGATTAGAAACACCTGTGAAG 58.937 41.667 3.94 0.00 34.33 3.02
5427 7127 5.042463 TGTGGATTAGAAACACCTGTGAA 57.958 39.130 3.94 0.00 34.33 3.18
5433 7133 7.390718 AGAGTTGTAATGTGGATTAGAAACACC 59.609 37.037 0.00 0.00 31.13 4.16
5442 7142 9.601217 GAGTACATAAGAGTTGTAATGTGGATT 57.399 33.333 0.00 0.00 34.54 3.01
5461 7161 8.562892 GCATTATTTACATGCTGAAGAGTACAT 58.437 33.333 0.00 0.00 43.26 2.29
5481 7181 3.973425 ACAAGAGAAGCCAAGGCATTAT 58.027 40.909 14.40 2.21 44.88 1.28
5482 7182 3.439857 ACAAGAGAAGCCAAGGCATTA 57.560 42.857 14.40 0.00 44.88 1.90
5492 7192 4.808364 GTCATCATCCTGTACAAGAGAAGC 59.192 45.833 0.00 0.00 0.00 3.86
5493 7193 5.809562 GTGTCATCATCCTGTACAAGAGAAG 59.190 44.000 0.00 0.00 0.00 2.85
5496 7196 4.081476 TGGTGTCATCATCCTGTACAAGAG 60.081 45.833 0.00 0.00 0.00 2.85
5497 7197 3.837731 TGGTGTCATCATCCTGTACAAGA 59.162 43.478 0.00 0.00 0.00 3.02
5563 7263 2.102252 CTCTGGGATGCTGTAGTTCCTC 59.898 54.545 0.00 0.00 0.00 3.71
5938 7638 3.114616 CTGTCCTTGTGCCTCGCG 61.115 66.667 0.00 0.00 0.00 5.87
5954 7654 2.437897 CACCTTCTTGGGCAGCCT 59.562 61.111 12.43 0.00 41.11 4.58
5960 7660 1.374252 CGTCGACCACCTTCTTGGG 60.374 63.158 10.58 0.00 41.49 4.12
6110 7810 4.792704 GCAAGGCTTCTTATCTCTCTCGAG 60.793 50.000 5.93 5.93 38.67 4.04
6115 7816 2.478831 CGGCAAGGCTTCTTATCTCTC 58.521 52.381 0.00 0.00 0.00 3.20
6116 7817 1.474143 GCGGCAAGGCTTCTTATCTCT 60.474 52.381 0.00 0.00 0.00 3.10
6117 7818 0.940833 GCGGCAAGGCTTCTTATCTC 59.059 55.000 0.00 0.00 0.00 2.75
6118 7819 0.253044 TGCGGCAAGGCTTCTTATCT 59.747 50.000 0.00 0.00 0.00 1.98
6146 7847 2.233007 CTTTCGCGAGCCAACAGAGC 62.233 60.000 9.59 0.00 0.00 4.09
6211 7921 4.525100 GGAGAGGATATCTTAGGTGACCAC 59.475 50.000 3.63 0.00 38.84 4.16
6226 7936 4.227197 CCAGTATACCACAAGGAGAGGAT 58.773 47.826 0.00 0.00 38.69 3.24
6228 7938 3.375699 ACCAGTATACCACAAGGAGAGG 58.624 50.000 0.00 0.00 38.69 3.69
6234 7944 4.710375 ACTGTAGGACCAGTATACCACAAG 59.290 45.833 0.00 0.00 43.71 3.16
6276 7986 4.010349 CCTCCAACTCCAACTAATTGACC 58.990 47.826 0.00 0.00 38.15 4.02
6282 7992 3.583228 TCACTCCTCCAACTCCAACTAA 58.417 45.455 0.00 0.00 0.00 2.24
6300 8016 2.210116 ACCGATGTGTCTGTTGTTCAC 58.790 47.619 0.00 0.00 0.00 3.18
6371 8087 5.526846 TGAAAGATGACAATGCGCACATATA 59.473 36.000 14.90 0.00 34.62 0.86
6372 8088 4.336153 TGAAAGATGACAATGCGCACATAT 59.664 37.500 14.90 6.07 34.62 1.78
6405 8123 0.885196 GACAGAAGACCGAGTGAGCT 59.115 55.000 0.00 0.00 0.00 4.09
6406 8124 0.885196 AGACAGAAGACCGAGTGAGC 59.115 55.000 0.00 0.00 0.00 4.26
6422 8140 2.795470 GAGAAACGTCACAGGTTCAGAC 59.205 50.000 0.00 0.00 40.14 3.51
6423 8141 2.223971 GGAGAAACGTCACAGGTTCAGA 60.224 50.000 0.00 0.00 40.14 3.27
6429 8147 2.341257 CTCATGGAGAAACGTCACAGG 58.659 52.381 0.00 0.00 0.00 4.00
6441 8159 2.338577 AGGCGAAAATCCTCATGGAG 57.661 50.000 0.00 0.00 46.91 3.86
6445 8163 6.681368 GCAAAATTCTAGGCGAAAATCCTCAT 60.681 38.462 0.00 0.00 34.79 2.90
6446 8164 5.393027 GCAAAATTCTAGGCGAAAATCCTCA 60.393 40.000 0.00 0.00 34.79 3.86
6447 8165 5.037385 GCAAAATTCTAGGCGAAAATCCTC 58.963 41.667 0.00 0.00 34.79 3.71
6448 8166 4.998788 GCAAAATTCTAGGCGAAAATCCT 58.001 39.130 0.00 0.00 34.79 3.24
6457 8175 2.125461 GCATCCGCAAAATTCTAGGC 57.875 50.000 0.00 0.00 38.36 3.93
6465 8183 8.949339 CAAATATTTGAAGGTGCATCCGCAAAA 61.949 37.037 21.35 10.14 44.83 2.44
6469 8187 3.715628 AATATTTGAAGGTGCATCCGC 57.284 42.857 0.00 0.00 41.99 5.54
6471 8189 5.045872 GCTCAAATATTTGAAGGTGCATCC 58.954 41.667 26.57 7.61 45.61 3.51
6479 8197 9.565213 CTAAAAGTCTGGCTCAAATATTTGAAG 57.435 33.333 26.57 21.48 45.61 3.02
6482 8200 8.902040 GACTAAAAGTCTGGCTCAAATATTTG 57.098 34.615 20.13 20.13 41.88 2.32
6499 8219 4.453819 CACCTCTTTGAGCCAGACTAAAAG 59.546 45.833 0.00 0.00 45.27 2.27
6525 8245 2.159310 GCAGTGAGTACTCCTGCACTAG 60.159 54.545 36.10 22.33 45.12 2.57
6527 8247 0.605589 GCAGTGAGTACTCCTGCACT 59.394 55.000 36.10 25.34 45.12 4.40
6528 8248 3.129792 GCAGTGAGTACTCCTGCAC 57.870 57.895 36.10 24.01 45.12 4.57
6531 8251 3.118847 ACATGATGCAGTGAGTACTCCTG 60.119 47.826 25.29 25.29 34.07 3.86
6532 8252 3.102972 ACATGATGCAGTGAGTACTCCT 58.897 45.455 20.11 13.32 34.07 3.69
6533 8253 3.118992 TGACATGATGCAGTGAGTACTCC 60.119 47.826 20.11 11.29 34.07 3.85
6534 8254 3.862267 GTGACATGATGCAGTGAGTACTC 59.138 47.826 16.32 16.32 34.07 2.59
6535 8255 3.368843 GGTGACATGATGCAGTGAGTACT 60.369 47.826 0.00 0.00 37.75 2.73
6536 8256 2.932614 GGTGACATGATGCAGTGAGTAC 59.067 50.000 0.00 0.00 0.00 2.73
6537 8257 2.833943 AGGTGACATGATGCAGTGAGTA 59.166 45.455 0.00 0.00 0.00 2.59
6538 8258 1.627329 AGGTGACATGATGCAGTGAGT 59.373 47.619 0.00 0.00 0.00 3.41
6539 8259 2.007608 CAGGTGACATGATGCAGTGAG 58.992 52.381 0.00 0.00 0.00 3.51
6541 8261 2.103537 TCAGGTGACATGATGCAGTG 57.896 50.000 0.00 0.00 0.00 3.66
6577 8567 3.922910 ACTTTTAGTCCTAGGTTCGTGC 58.077 45.455 9.08 0.00 0.00 5.34
6578 8568 8.543862 AAAATACTTTTAGTCCTAGGTTCGTG 57.456 34.615 9.08 0.00 0.00 4.35
6587 8577 8.537858 ACGACAGGATAAAATACTTTTAGTCCT 58.462 33.333 12.54 12.54 40.14 3.85
6588 8578 8.713737 ACGACAGGATAAAATACTTTTAGTCC 57.286 34.615 0.00 10.01 38.40 3.85
6590 8580 9.148104 GTGACGACAGGATAAAATACTTTTAGT 57.852 33.333 0.00 0.00 38.40 2.24
6591 8581 8.601476 GGTGACGACAGGATAAAATACTTTTAG 58.399 37.037 0.00 0.00 38.40 1.85
6592 8582 8.483307 GGTGACGACAGGATAAAATACTTTTA 57.517 34.615 0.00 0.00 39.24 1.52
6593 8583 7.373778 GGTGACGACAGGATAAAATACTTTT 57.626 36.000 0.00 0.00 36.67 2.27
6594 8584 6.980051 GGTGACGACAGGATAAAATACTTT 57.020 37.500 0.00 0.00 0.00 2.66
6612 8602 0.599204 TCTTGCCTCGTTTCGGTGAC 60.599 55.000 0.00 0.00 0.00 3.67
6613 8603 0.320374 ATCTTGCCTCGTTTCGGTGA 59.680 50.000 0.00 0.00 0.00 4.02
6658 8648 4.033702 GTGGATTAACTTAAGTACTGGCGC 59.966 45.833 8.92 0.00 0.00 6.53
6662 8652 9.630098 TTAACGAGTGGATTAACTTAAGTACTG 57.370 33.333 8.92 5.48 0.00 2.74
7009 9010 9.176181 GACAGTATTGTTCTTTAATCGCAAAAA 57.824 29.630 0.00 0.00 37.76 1.94
7010 9011 7.532546 CGACAGTATTGTTCTTTAATCGCAAAA 59.467 33.333 0.00 0.00 37.76 2.44
7026 9027 2.854777 GTGACTAGCAGCGACAGTATTG 59.145 50.000 0.00 0.00 0.00 1.90
7035 9036 1.080772 TTGACCGTGACTAGCAGCG 60.081 57.895 0.00 0.00 0.00 5.18
7074 9078 4.657039 GGTTTACATGGATGGGAGGTAGTA 59.343 45.833 0.00 0.00 0.00 1.82
7075 9079 3.458487 GGTTTACATGGATGGGAGGTAGT 59.542 47.826 0.00 0.00 0.00 2.73
7076 9080 3.458118 TGGTTTACATGGATGGGAGGTAG 59.542 47.826 0.00 0.00 0.00 3.18
7077 9081 3.465832 TGGTTTACATGGATGGGAGGTA 58.534 45.455 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.