Multiple sequence alignment - TraesCS7A01G096900

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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 TraesCS7A01G096900 chr7A 100.000 5779 0 0 1 5779 59411296 59405518 0.000000e+00 10672.0
1 TraesCS7A01G096900 chr7A 96.970 132 2 2 3082 3213 59408176 59408047 2.710000e-53 220.0
2 TraesCS7A01G096900 chr7A 96.970 132 2 2 3121 3250 59408215 59408084 2.710000e-53 220.0
3 TraesCS7A01G096900 chr7A 94.118 119 6 1 4936 5054 59406303 59406186 4.600000e-41 180.0
4 TraesCS7A01G096900 chr7A 94.118 119 6 1 4994 5111 59406361 59406243 4.600000e-41 180.0
5 TraesCS7A01G096900 chr7A 96.774 93 1 2 3082 3174 59408137 59408047 2.790000e-33 154.0
6 TraesCS7A01G096900 chr7A 96.774 93 1 2 3160 3250 59408215 59408123 2.790000e-33 154.0
7 TraesCS7A01G096900 chr7D 95.278 2986 109 12 2090 5054 55419270 55416296 0.000000e+00 4704.0
8 TraesCS7A01G096900 chr7D 89.663 2283 161 45 2 2231 55421551 55419291 0.000000e+00 2839.0
9 TraesCS7A01G096900 chr7D 89.300 757 58 15 4994 5738 55416413 55415668 0.000000e+00 928.0
10 TraesCS7A01G096900 chr7D 96.970 132 2 2 3121 3250 55418279 55418148 2.710000e-53 220.0
11 TraesCS7A01G096900 chr7D 96.063 127 4 1 3082 3208 55418240 55418115 7.590000e-49 206.0
12 TraesCS7A01G096900 chr7D 96.774 93 1 2 3160 3250 55418279 55418187 2.790000e-33 154.0
13 TraesCS7A01G096900 chr7D 95.455 88 3 1 3082 3169 55418201 55418115 7.810000e-29 139.0
14 TraesCS7A01G096900 chr7D 95.161 62 2 1 4935 4996 55416356 55416296 4.770000e-16 97.1
15 TraesCS7A01G096900 chr7D 96.296 54 0 2 3199 3250 55418279 55418226 2.870000e-13 87.9
16 TraesCS7A01G096900 chr4A 91.160 2285 129 43 950 3208 671936102 671933865 0.000000e+00 3033.0
17 TraesCS7A01G096900 chr4A 94.303 1334 52 13 3741 5054 671933275 671931946 0.000000e+00 2021.0
18 TraesCS7A01G096900 chr4A 97.106 622 18 0 3121 3742 671933990 671933369 0.000000e+00 1050.0
19 TraesCS7A01G096900 chr4A 91.979 374 20 5 4994 5364 671932063 671931697 3.090000e-142 516.0
20 TraesCS7A01G096900 chr4A 90.179 336 23 7 5406 5734 671931703 671931371 4.140000e-116 429.0
21 TraesCS7A01G096900 chr4A 97.959 49 0 1 3082 3130 671933912 671933865 3.710000e-12 84.2
22 TraesCS7A01G096900 chr5D 93.855 179 11 0 4221 4399 377988171 377987993 2.650000e-68 270.0
23 TraesCS7A01G096900 chr5D 93.902 164 10 0 4229 4392 529218327 529218164 1.240000e-61 248.0
24 TraesCS7A01G096900 chr4D 94.444 162 9 0 4229 4390 34661688 34661527 3.460000e-62 250.0
25 TraesCS7A01G096900 chr2B 92.571 175 10 3 4218 4390 608226898 608226725 1.240000e-61 248.0
26 TraesCS7A01G096900 chr2D 92.442 172 12 1 4228 4399 556926932 556927102 1.610000e-60 244.0
27 TraesCS7A01G096900 chr3D 92.442 172 10 3 4235 4404 575678872 575678702 5.790000e-60 243.0
28 TraesCS7A01G096900 chr6B 91.429 175 14 1 4221 4395 633056574 633056401 7.480000e-59 239.0


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 TraesCS7A01G096900 chr7A 59405518 59411296 5778 True 10672.000000 10672 100.000000 1 5779 1 chr7A.!!$R1 5778
1 TraesCS7A01G096900 chr7D 55415668 55421551 5883 True 1041.666667 4704 94.551111 2 5738 9 chr7D.!!$R1 5736
2 TraesCS7A01G096900 chr4A 671931371 671936102 4731 True 1188.866667 3033 93.781000 950 5734 6 chr4A.!!$R1 4784

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
35 36 0.034186 GGCCTCATGGATGTTGGTCA 60.034 55.0 0.00 0.0 34.57 4.02 F
505 509 0.037447 AAGGGCAAGTGAGAAGGAGC 59.963 55.0 0.00 0.0 0.00 4.70 F
850 882 0.106918 ACGAACAAGCCCAGACCAAA 60.107 50.0 0.00 0.0 0.00 3.28 F
1783 1863 0.034767 ACGAGTCCTCCATCGGTACA 60.035 55.0 0.00 0.0 43.12 2.90 F
1886 1972 0.104304 GTGGGATAGGCACGTCGAAT 59.896 55.0 0.00 0.0 0.00 3.34 F
3248 3502 0.899717 GCCATCCTGCTTTGGTTGGA 60.900 55.0 18.59 0.0 45.35 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1404 0.033894 AACGGAACAACCCAACCACT 60.034 50.000 0.00 0.00 34.64 4.00 R
1346 1410 0.531090 CGACTCAACGGAACAACCCA 60.531 55.000 0.00 0.00 34.64 4.51 R
1902 1988 0.670546 TAGCTCGCTCTTGGTGTTGC 60.671 55.000 0.00 0.00 0.00 4.17 R
3383 3637 0.103026 CTTCTGATGGCCGATCGACA 59.897 55.000 18.66 15.57 33.17 4.35 R
3440 3694 2.264455 ACTTCTCTCCTGGTGCAATCT 58.736 47.619 0.00 0.00 0.00 2.40 R
5194 5567 0.042431 AGATGCCACTCCTCACTCCT 59.958 55.000 0.00 0.00 0.00 3.69 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
32 33 1.389609 GCAGGCCTCATGGATGTTGG 61.390 60.000 0.00 0.00 34.57 3.77
34 35 0.257039 AGGCCTCATGGATGTTGGTC 59.743 55.000 0.00 0.00 34.57 4.02
35 36 0.034186 GGCCTCATGGATGTTGGTCA 60.034 55.000 0.00 0.00 34.57 4.02
82 83 6.963322 AGGCCCTATATTTTGAGTGATATCC 58.037 40.000 0.00 0.00 0.00 2.59
84 85 5.817816 GCCCTATATTTTGAGTGATATCCGG 59.182 44.000 0.00 0.00 0.00 5.14
109 110 4.387026 TTGAATTGGAGTTGACCCTCAT 57.613 40.909 0.00 0.00 32.91 2.90
141 142 2.271800 GATGATGGTCTGGTTGTCGAC 58.728 52.381 9.11 9.11 0.00 4.20
144 145 1.272490 GATGGTCTGGTTGTCGACTCA 59.728 52.381 17.92 11.27 0.00 3.41
148 149 2.483188 GGTCTGGTTGTCGACTCACTTT 60.483 50.000 17.92 0.00 0.00 2.66
149 150 3.195661 GTCTGGTTGTCGACTCACTTTT 58.804 45.455 17.92 0.00 0.00 2.27
186 187 5.448654 AGCAAGTTATTGGCCTGATTCATA 58.551 37.500 3.32 0.00 36.88 2.15
196 197 3.244387 GGCCTGATTCATAGTCTTCTCCC 60.244 52.174 0.00 0.00 0.00 4.30
198 199 4.502950 GCCTGATTCATAGTCTTCTCCCTG 60.503 50.000 0.00 0.00 0.00 4.45
200 201 3.389329 TGATTCATAGTCTTCTCCCTGGC 59.611 47.826 0.00 0.00 0.00 4.85
203 204 1.482593 CATAGTCTTCTCCCTGGCGTT 59.517 52.381 0.00 0.00 0.00 4.84
223 224 0.107654 AGAACATGGCGGGTCTTAGC 60.108 55.000 0.00 0.00 0.00 3.09
241 242 4.841441 CAAAGGGCTTGGCTGGTA 57.159 55.556 0.00 0.00 0.00 3.25
260 261 2.254546 ATCGTTGCTCACACTCCAAA 57.745 45.000 0.00 0.00 0.00 3.28
262 263 1.013596 CGTTGCTCACACTCCAAACA 58.986 50.000 0.00 0.00 0.00 2.83
263 264 1.400142 CGTTGCTCACACTCCAAACAA 59.600 47.619 0.00 0.00 0.00 2.83
264 265 2.539547 CGTTGCTCACACTCCAAACAAG 60.540 50.000 0.00 0.00 0.00 3.16
266 267 2.288666 TGCTCACACTCCAAACAAGTC 58.711 47.619 0.00 0.00 0.00 3.01
282 283 0.698818 AGTCCAACTTAGCAAGGGGG 59.301 55.000 0.00 0.00 0.00 5.40
283 284 0.696501 GTCCAACTTAGCAAGGGGGA 59.303 55.000 0.00 0.00 33.97 4.81
284 285 1.285078 GTCCAACTTAGCAAGGGGGAT 59.715 52.381 11.16 0.00 37.24 3.85
303 304 4.323715 GGGATTTTGCCTGAATTCACCAAT 60.324 41.667 3.38 0.00 0.00 3.16
304 305 4.632688 GGATTTTGCCTGAATTCACCAATG 59.367 41.667 3.38 0.00 0.00 2.82
310 311 3.860378 GCCTGAATTCACCAATGCGAAAA 60.860 43.478 3.38 0.00 0.00 2.29
311 312 4.497300 CCTGAATTCACCAATGCGAAAAT 58.503 39.130 3.38 0.00 0.00 1.82
312 313 4.563976 CCTGAATTCACCAATGCGAAAATC 59.436 41.667 3.38 0.00 0.00 2.17
313 314 5.131594 TGAATTCACCAATGCGAAAATCA 57.868 34.783 3.38 0.00 0.00 2.57
314 315 4.922692 TGAATTCACCAATGCGAAAATCAC 59.077 37.500 3.38 0.00 0.00 3.06
315 316 3.998099 TTCACCAATGCGAAAATCACA 57.002 38.095 0.00 0.00 0.00 3.58
317 318 2.030363 TCACCAATGCGAAAATCACACC 60.030 45.455 0.00 0.00 0.00 4.16
318 319 1.272212 ACCAATGCGAAAATCACACCC 59.728 47.619 0.00 0.00 0.00 4.61
320 321 2.598589 CAATGCGAAAATCACACCCAG 58.401 47.619 0.00 0.00 0.00 4.45
321 322 1.909700 ATGCGAAAATCACACCCAGT 58.090 45.000 0.00 0.00 0.00 4.00
355 356 7.859325 ACTCCCACATTTGTATATGTTACAC 57.141 36.000 0.00 0.00 36.64 2.90
358 359 8.815565 TCCCACATTTGTATATGTTACACATT 57.184 30.769 0.00 0.00 39.88 2.71
359 360 9.907229 TCCCACATTTGTATATGTTACACATTA 57.093 29.630 0.00 0.00 39.88 1.90
367 368 7.368059 TGTATATGTTACACATTAGGCGAGAG 58.632 38.462 0.00 0.00 39.88 3.20
400 401 1.202806 ACATGTGGAGGCATATTCGGG 60.203 52.381 0.00 0.00 0.00 5.14
406 407 1.545651 GGAGGCATATTCGGGGGAAAG 60.546 57.143 0.00 0.00 0.00 2.62
412 413 3.005791 GCATATTCGGGGGAAAGGAATTG 59.994 47.826 0.00 0.00 32.92 2.32
413 414 2.159179 ATTCGGGGGAAAGGAATTGG 57.841 50.000 0.00 0.00 0.00 3.16
414 415 0.040499 TTCGGGGGAAAGGAATTGGG 59.960 55.000 0.00 0.00 0.00 4.12
434 435 8.036148 ATTGGGCTCTCAATACCAAATTGTGG 62.036 42.308 0.00 0.00 45.18 4.17
475 476 2.552155 GGACCAAACCACACAGATAGCA 60.552 50.000 0.00 0.00 0.00 3.49
479 480 4.202419 ACCAAACCACACAGATAGCAGTTA 60.202 41.667 0.00 0.00 0.00 2.24
491 492 2.704808 GCAGTTAGCAGGCAAGGGC 61.705 63.158 0.00 0.00 44.79 5.19
493 494 0.895100 CAGTTAGCAGGCAAGGGCAA 60.895 55.000 0.00 0.00 43.71 4.52
502 503 1.246737 GGCAAGGGCAAGTGAGAAGG 61.247 60.000 0.00 0.00 43.71 3.46
505 509 0.037447 AAGGGCAAGTGAGAAGGAGC 59.963 55.000 0.00 0.00 0.00 4.70
509 513 1.675415 GGCAAGTGAGAAGGAGCAGAG 60.675 57.143 0.00 0.00 0.00 3.35
512 516 3.805108 GCAAGTGAGAAGGAGCAGAGAAA 60.805 47.826 0.00 0.00 0.00 2.52
528 532 5.555017 CAGAGAAAAAGATGAGGAACAGGA 58.445 41.667 0.00 0.00 0.00 3.86
529 533 5.642919 CAGAGAAAAAGATGAGGAACAGGAG 59.357 44.000 0.00 0.00 0.00 3.69
530 534 4.331108 AGAAAAAGATGAGGAACAGGAGC 58.669 43.478 0.00 0.00 0.00 4.70
531 535 3.795688 AAAAGATGAGGAACAGGAGCA 57.204 42.857 0.00 0.00 0.00 4.26
532 536 3.347077 AAAGATGAGGAACAGGAGCAG 57.653 47.619 0.00 0.00 0.00 4.24
533 537 1.202330 AGATGAGGAACAGGAGCAGG 58.798 55.000 0.00 0.00 0.00 4.85
534 538 0.179936 GATGAGGAACAGGAGCAGGG 59.820 60.000 0.00 0.00 0.00 4.45
535 539 1.277580 ATGAGGAACAGGAGCAGGGG 61.278 60.000 0.00 0.00 0.00 4.79
536 540 1.613630 GAGGAACAGGAGCAGGGGA 60.614 63.158 0.00 0.00 0.00 4.81
537 541 1.904990 GAGGAACAGGAGCAGGGGAC 61.905 65.000 0.00 0.00 0.00 4.46
538 542 2.266055 GAACAGGAGCAGGGGACG 59.734 66.667 0.00 0.00 0.00 4.79
539 543 2.526873 AACAGGAGCAGGGGACGT 60.527 61.111 0.00 0.00 0.00 4.34
551 555 3.498397 GCAGGGGACGTTGAATATACATG 59.502 47.826 0.00 0.00 0.00 3.21
555 559 5.820947 AGGGGACGTTGAATATACATGTTTC 59.179 40.000 2.30 2.36 0.00 2.78
575 602 4.454948 TGGCACAACCAGTCGAAG 57.545 55.556 0.00 0.00 46.36 3.79
577 604 0.249868 TGGCACAACCAGTCGAAGAG 60.250 55.000 0.00 0.00 46.36 2.85
580 607 2.417719 GCACAACCAGTCGAAGAGAAT 58.582 47.619 0.00 0.00 36.95 2.40
589 618 6.464222 ACCAGTCGAAGAGAATTTTGTCATA 58.536 36.000 0.00 0.00 36.95 2.15
600 629 6.860080 AGAATTTTGTCATACCATGAGCAAG 58.140 36.000 0.00 0.00 40.53 4.01
606 635 4.103627 TGTCATACCATGAGCAAGGATCAT 59.896 41.667 0.00 0.00 39.36 2.45
625 654 6.818644 GGATCATACCACATATGTACACCATC 59.181 42.308 8.32 6.24 41.44 3.51
635 664 6.828785 ACATATGTACACCATCTCTTTTTCCC 59.171 38.462 6.56 0.00 34.86 3.97
676 707 3.412386 ACGAAGTCTTTGGAAAGGATGG 58.588 45.455 4.81 0.00 29.74 3.51
677 708 3.072476 ACGAAGTCTTTGGAAAGGATGGA 59.928 43.478 4.81 0.00 29.74 3.41
678 709 4.072131 CGAAGTCTTTGGAAAGGATGGAA 58.928 43.478 0.00 0.00 33.26 3.53
679 710 4.702131 CGAAGTCTTTGGAAAGGATGGAAT 59.298 41.667 0.00 0.00 33.26 3.01
710 742 5.984725 TGGTGTAATACATCACTGGTTAGG 58.015 41.667 1.63 0.00 33.64 2.69
742 774 8.671987 TCCCCAAATATGAATGTTTTCCTTTA 57.328 30.769 0.00 0.00 0.00 1.85
760 792 9.651913 TTTCCTTTACAAAATATTCTGAATGCC 57.348 29.630 13.01 0.00 0.00 4.40
796 828 1.480789 AAGAACTGGGCCGTTGTTTT 58.519 45.000 16.44 6.34 27.27 2.43
848 880 1.070786 GACGAACAAGCCCAGACCA 59.929 57.895 0.00 0.00 0.00 4.02
849 881 0.534203 GACGAACAAGCCCAGACCAA 60.534 55.000 0.00 0.00 0.00 3.67
850 882 0.106918 ACGAACAAGCCCAGACCAAA 60.107 50.000 0.00 0.00 0.00 3.28
851 883 0.593128 CGAACAAGCCCAGACCAAAG 59.407 55.000 0.00 0.00 0.00 2.77
861 893 0.865769 CAGACCAAAGACGAAACCGG 59.134 55.000 0.00 0.00 0.00 5.28
864 896 0.877213 ACCAAAGACGAAACCGGTCG 60.877 55.000 8.04 11.49 46.54 4.79
865 897 1.203313 CAAAGACGAAACCGGTCGC 59.797 57.895 8.04 1.23 45.00 5.19
866 898 1.227321 AAAGACGAAACCGGTCGCA 60.227 52.632 8.04 0.00 45.00 5.10
868 900 3.408851 GACGAAACCGGTCGCACC 61.409 66.667 8.04 0.00 45.00 5.01
870 902 2.968156 CGAAACCGGTCGCACCAA 60.968 61.111 8.04 0.00 38.47 3.67
871 903 2.635338 GAAACCGGTCGCACCAAC 59.365 61.111 8.04 0.00 38.47 3.77
872 904 2.124653 AAACCGGTCGCACCAACA 60.125 55.556 8.04 0.00 38.47 3.33
873 905 2.113131 GAAACCGGTCGCACCAACAG 62.113 60.000 8.04 0.00 38.47 3.16
874 906 2.596553 AAACCGGTCGCACCAACAGA 62.597 55.000 8.04 0.00 38.47 3.41
875 907 3.041940 CCGGTCGCACCAACAGAC 61.042 66.667 0.00 0.00 38.47 3.51
920 960 0.397816 CACCTCCACCCAAACCCAAA 60.398 55.000 0.00 0.00 0.00 3.28
921 961 0.397957 ACCTCCACCCAAACCCAAAC 60.398 55.000 0.00 0.00 0.00 2.93
922 962 1.118965 CCTCCACCCAAACCCAAACC 61.119 60.000 0.00 0.00 0.00 3.27
923 963 1.075151 TCCACCCAAACCCAAACCC 60.075 57.895 0.00 0.00 0.00 4.11
924 964 1.383248 CCACCCAAACCCAAACCCA 60.383 57.895 0.00 0.00 0.00 4.51
925 965 0.983378 CCACCCAAACCCAAACCCAA 60.983 55.000 0.00 0.00 0.00 4.12
927 967 0.983905 ACCCAAACCCAAACCCAACC 60.984 55.000 0.00 0.00 0.00 3.77
928 968 1.701031 CCCAAACCCAAACCCAACCC 61.701 60.000 0.00 0.00 0.00 4.11
1060 1117 3.036783 GACAGAGGTACGCGTCGCT 62.037 63.158 18.63 6.72 34.93 4.93
1095 1152 3.400054 GGGTCCCCTCTTCCACGG 61.400 72.222 0.00 0.00 0.00 4.94
1141 1198 1.974236 CGGGGAGGCAAATCTCTAGAT 59.026 52.381 0.00 0.00 36.07 1.98
1176 1236 2.035442 GTGGGTTTCCGCTCTCTGC 61.035 63.158 0.00 0.00 40.31 4.26
1190 1250 0.524392 CTCTGCTTCGTCTGTAGCCG 60.524 60.000 0.00 0.00 37.68 5.52
1253 1317 4.464597 GGGTAATTGGGTTGTAGATTGCAA 59.535 41.667 0.00 0.00 0.00 4.08
1320 1384 5.355071 TGAATCTGTGTGTATTCTGGATTGC 59.645 40.000 0.00 0.00 34.00 3.56
1323 1387 5.419542 TCTGTGTGTATTCTGGATTGCTAC 58.580 41.667 0.00 0.00 0.00 3.58
1339 1403 1.952367 GCTACCAATCTGCCAGTGCTT 60.952 52.381 0.00 0.00 38.71 3.91
1340 1404 2.680805 GCTACCAATCTGCCAGTGCTTA 60.681 50.000 0.00 0.00 38.71 3.09
1346 1410 0.764890 TCTGCCAGTGCTTAGTGGTT 59.235 50.000 3.36 0.00 38.71 3.67
1364 1428 1.332686 GTTGGGTTGTTCCGTTGAGTC 59.667 52.381 0.00 0.00 37.00 3.36
1367 1431 0.857287 GGTTGTTCCGTTGAGTCGAC 59.143 55.000 7.70 7.70 0.00 4.20
1395 1459 2.033194 GCCTGCGGCGAGTTTTAGT 61.033 57.895 12.98 0.00 39.62 2.24
1417 1493 1.671979 CATCCCATACCACACTGCTG 58.328 55.000 0.00 0.00 0.00 4.41
1418 1494 1.065199 CATCCCATACCACACTGCTGT 60.065 52.381 0.00 0.00 0.00 4.40
1447 1523 5.309020 AGGGCATGGCTGATGGTATATATAG 59.691 44.000 19.78 0.00 31.99 1.31
1448 1524 5.072329 GGGCATGGCTGATGGTATATATAGT 59.928 44.000 19.78 0.00 31.99 2.12
1449 1525 6.270000 GGGCATGGCTGATGGTATATATAGTA 59.730 42.308 19.78 0.00 31.99 1.82
1450 1526 7.155328 GGCATGGCTGATGGTATATATAGTAC 58.845 42.308 12.86 0.00 31.99 2.73
1452 1528 8.370940 GCATGGCTGATGGTATATATAGTACAT 58.629 37.037 0.00 0.00 31.99 2.29
1497 1575 1.066573 GGTGTCCTGTGATGTCTGAGG 60.067 57.143 0.00 0.00 0.00 3.86
1524 1602 3.054434 TGTTGACCTGGATGAGTTATGGG 60.054 47.826 0.00 0.00 0.00 4.00
1532 1610 3.843619 TGGATGAGTTATGGGTCTTCACA 59.156 43.478 0.00 0.00 0.00 3.58
1717 1796 3.656651 TTTGATGCTAATCTTCGCACG 57.343 42.857 0.00 0.00 39.21 5.34
1783 1863 0.034767 ACGAGTCCTCCATCGGTACA 60.035 55.000 0.00 0.00 43.12 2.90
1844 1926 3.547468 GCGCGCAACAAGATTTAATCATT 59.453 39.130 29.10 0.00 0.00 2.57
1847 1932 6.558433 GCGCGCAACAAGATTTAATCATTTAG 60.558 38.462 29.10 0.00 0.00 1.85
1886 1972 0.104304 GTGGGATAGGCACGTCGAAT 59.896 55.000 0.00 0.00 0.00 3.34
1890 1976 1.535437 GGATAGGCACGTCGAATTCGT 60.535 52.381 25.93 6.29 42.33 3.85
1902 1988 1.173913 GAATTCGTGTTCCAAGGGGG 58.826 55.000 0.00 0.00 38.37 5.40
1953 2039 4.036734 CCATGGTTGCATATGTGTAAGACC 59.963 45.833 2.57 4.82 30.33 3.85
1956 2042 4.261801 GGTTGCATATGTGTAAGACCTGT 58.738 43.478 4.29 0.00 30.33 4.00
1977 2063 7.507616 ACCTGTGGTCACATTTTTCCTATAAAA 59.492 33.333 4.13 0.00 41.01 1.52
2030 2116 1.086696 CCGCATGGTAACTTCTGGTG 58.913 55.000 0.00 0.00 37.61 4.17
2063 2149 4.112634 ACATGGTTACCACAAATCCTGT 57.887 40.909 6.10 2.07 35.80 4.00
2084 2170 2.167662 CCCTTCGGTACCAATTGCTTT 58.832 47.619 13.54 0.00 0.00 3.51
2098 2184 6.374333 ACCAATTGCTTTATTCGTGTCATAGT 59.626 34.615 0.00 0.00 0.00 2.12
2105 2191 6.384178 TTTATTCGTGTCATAGTGTGTTCG 57.616 37.500 0.00 0.00 0.00 3.95
2296 2544 4.595986 AGGGTTAATGTGATGTTGTACCC 58.404 43.478 0.00 0.00 43.42 3.69
2334 2585 6.294787 GGGAATGTGATGTCGTATCTGATACT 60.295 42.308 21.76 6.62 33.59 2.12
2367 2619 8.586744 TCATGGAAATCATTCTTGAATTGAACA 58.413 29.630 0.00 0.00 34.96 3.18
2369 2621 8.991243 TGGAAATCATTCTTGAATTGAACATC 57.009 30.769 0.00 0.00 34.96 3.06
2635 2889 5.049198 TGTCAGAAGTGCAAGAATAAGCAAG 60.049 40.000 0.00 0.00 43.20 4.01
2660 2914 7.826252 AGTCTCCATGGACATATTTATACATGC 59.174 37.037 11.44 0.00 38.57 4.06
2752 3006 6.433404 TGAGACGTACCTTCTGTTTTATCTCT 59.567 38.462 0.00 0.00 32.05 3.10
2753 3007 7.039923 TGAGACGTACCTTCTGTTTTATCTCTT 60.040 37.037 0.00 0.00 32.05 2.85
2754 3008 7.668492 AGACGTACCTTCTGTTTTATCTCTTT 58.332 34.615 0.00 0.00 0.00 2.52
2755 3009 8.800332 AGACGTACCTTCTGTTTTATCTCTTTA 58.200 33.333 0.00 0.00 0.00 1.85
2792 3046 9.889128 TTTCTTTCTCTTTTGATGTGGAAAATT 57.111 25.926 0.00 0.00 0.00 1.82
2896 3150 3.201266 GGTTATCCTGGGTATGTTCCACA 59.799 47.826 0.00 0.00 0.00 4.17
2952 3206 2.100916 GCTCTGCGAGGAGTACCAAATA 59.899 50.000 7.50 0.00 38.94 1.40
2989 3243 6.260870 TGTAAGACAACTTCACTTTTGCAA 57.739 33.333 0.00 0.00 37.53 4.08
3045 3299 5.355596 CCTTTTTGGTTTATCACACAGCAA 58.644 37.500 0.00 0.00 0.00 3.91
3179 3433 3.096092 TGCTTATGGTTTGGATGTTCCC 58.904 45.455 0.00 0.00 35.03 3.97
3207 3461 1.565759 TGAGCCATCCTGCTTATGGTT 59.434 47.619 12.24 7.68 44.87 3.67
3248 3502 0.899717 GCCATCCTGCTTTGGTTGGA 60.900 55.000 18.59 0.00 45.35 3.53
3348 3602 2.423185 TCACTTGGCAAAAGTGTCAGTG 59.577 45.455 23.26 11.27 45.75 3.66
3351 3605 3.258123 ACTTGGCAAAAGTGTCAGTGTTT 59.742 39.130 0.00 0.00 41.33 2.83
3353 3607 2.822561 TGGCAAAAGTGTCAGTGTTTCA 59.177 40.909 0.00 0.00 33.34 2.69
3374 3628 3.680786 GTTGAGCGCCCCAAACCC 61.681 66.667 13.40 0.07 0.00 4.11
3375 3629 4.986708 TTGAGCGCCCCAAACCCC 62.987 66.667 2.29 0.00 0.00 4.95
3383 3637 1.064003 GCCCCAAACCCCTTTTGATT 58.936 50.000 0.00 0.00 46.76 2.57
3440 3694 3.304911 TTTGTTGATGGTCTCCCAACA 57.695 42.857 0.00 0.00 46.04 3.33
3506 3760 8.773645 CAGTATTCTCCGCATCATATTTTTGTA 58.226 33.333 0.00 0.00 0.00 2.41
3962 4312 3.806316 ACGCGTTACCTCATTTTCTTG 57.194 42.857 5.58 0.00 0.00 3.02
3966 4316 4.004982 GCGTTACCTCATTTTCTTGGGTA 58.995 43.478 0.00 0.00 0.00 3.69
4215 4567 8.356533 CATTTGTTGCTTTGATACTTTCACTT 57.643 30.769 0.00 0.00 32.84 3.16
4403 4756 7.490000 ACGGAGGAAGTATATCTTTTAGTGTG 58.510 38.462 0.00 0.00 36.40 3.82
4490 4844 4.795635 TGCAAGTATTGGAAACACATGTGC 60.796 41.667 25.68 9.88 45.87 4.57
4535 4889 6.560253 ACCAAATGTTGTCTCTGTATGTTC 57.440 37.500 0.00 0.00 0.00 3.18
4556 4910 5.966636 TCGCTATTCATGTATCAACACAC 57.033 39.130 0.00 0.00 38.78 3.82
4605 4959 6.775708 AGTAGTATTTGCTGGAACCAACTTA 58.224 36.000 0.00 0.00 0.00 2.24
4618 4972 7.107542 TGGAACCAACTTATAAGAATAAGCGT 58.892 34.615 19.38 2.64 45.80 5.07
4687 5041 1.517475 GCTTCGACGAGAGGAAGGC 60.517 63.158 0.00 0.00 39.96 4.35
4709 5063 0.625849 ACGGCCCATTCCTCAAGATT 59.374 50.000 0.00 0.00 0.00 2.40
4732 5086 2.281208 CGCAAGGTTCCCGTTCCA 60.281 61.111 0.00 0.00 0.00 3.53
4743 5097 2.046314 CGTTCCAACCTCCGCCAT 60.046 61.111 0.00 0.00 0.00 4.40
4757 5111 0.033920 CGCCATCCCATGAAGATCGA 59.966 55.000 0.00 0.00 0.00 3.59
4765 5119 1.064060 CCATGAAGATCGAAAACGCCC 59.936 52.381 0.00 0.00 0.00 6.13
4769 5123 2.232941 TGAAGATCGAAAACGCCCTAGT 59.767 45.455 0.00 0.00 0.00 2.57
4780 5134 1.796190 CGCCCTAGTGCTCGCTGATA 61.796 60.000 0.00 0.00 0.00 2.15
4781 5135 0.605589 GCCCTAGTGCTCGCTGATAT 59.394 55.000 0.00 0.00 0.00 1.63
4843 5214 6.292542 CCATTGTAGATCAGCTATGTTCGTTG 60.293 42.308 0.00 0.00 31.58 4.10
4872 5243 2.535485 TAGCAACCTGTGATGGGCCG 62.535 60.000 0.00 0.00 0.00 6.13
4897 5268 0.469070 AGCTGGAGATTGGCTAGCTG 59.531 55.000 15.72 0.00 46.52 4.24
4908 5279 0.610687 GGCTAGCTGGACAGACTTGT 59.389 55.000 15.72 0.00 41.18 3.16
4926 5297 0.466124 GTCTGATACCCACCTGCCTC 59.534 60.000 0.00 0.00 0.00 4.70
4980 5351 1.102154 TTTTGCGGGTGGATATGCTG 58.898 50.000 0.00 0.00 0.00 4.41
4992 5363 5.359009 GGTGGATATGCTGGAAATGATATGG 59.641 44.000 0.00 0.00 0.00 2.74
5037 5408 1.846007 TTTTTGCGGGTGGATATGCT 58.154 45.000 0.00 0.00 0.00 3.79
5038 5409 2.719531 TTTTGCGGGTGGATATGCTA 57.280 45.000 0.00 0.00 0.00 3.49
5039 5410 2.254546 TTTGCGGGTGGATATGCTAG 57.745 50.000 0.00 0.00 0.00 3.42
5040 5411 1.419381 TTGCGGGTGGATATGCTAGA 58.581 50.000 0.00 0.00 0.00 2.43
5041 5412 1.419381 TGCGGGTGGATATGCTAGAA 58.581 50.000 0.00 0.00 0.00 2.10
5042 5413 1.765904 TGCGGGTGGATATGCTAGAAA 59.234 47.619 0.00 0.00 0.00 2.52
5043 5414 2.371841 TGCGGGTGGATATGCTAGAAAT 59.628 45.455 0.00 0.00 0.00 2.17
5044 5415 2.744202 GCGGGTGGATATGCTAGAAATG 59.256 50.000 0.00 0.00 0.00 2.32
5045 5416 3.557054 GCGGGTGGATATGCTAGAAATGA 60.557 47.826 0.00 0.00 0.00 2.57
5046 5417 4.836825 CGGGTGGATATGCTAGAAATGAT 58.163 43.478 0.00 0.00 0.00 2.45
5047 5418 5.626809 GCGGGTGGATATGCTAGAAATGATA 60.627 44.000 0.00 0.00 0.00 2.15
5048 5419 6.586344 CGGGTGGATATGCTAGAAATGATAT 58.414 40.000 0.00 0.00 0.00 1.63
5049 5420 6.481313 CGGGTGGATATGCTAGAAATGATATG 59.519 42.308 0.00 0.00 0.00 1.78
5050 5421 6.769822 GGGTGGATATGCTAGAAATGATATGG 59.230 42.308 0.00 0.00 0.00 2.74
5051 5422 6.261826 GGTGGATATGCTAGAAATGATATGGC 59.738 42.308 0.00 0.00 0.00 4.40
5052 5423 6.825213 GTGGATATGCTAGAAATGATATGGCA 59.175 38.462 0.00 0.00 0.00 4.92
5053 5424 7.501559 GTGGATATGCTAGAAATGATATGGCAT 59.498 37.037 4.88 4.88 41.03 4.40
5054 5425 8.057011 TGGATATGCTAGAAATGATATGGCATT 58.943 33.333 4.78 0.00 40.04 3.56
5055 5426 8.566260 GGATATGCTAGAAATGATATGGCATTC 58.434 37.037 4.78 4.03 37.50 2.67
5056 5427 5.868043 TGCTAGAAATGATATGGCATTCG 57.132 39.130 4.78 0.00 37.50 3.34
5057 5428 4.154737 TGCTAGAAATGATATGGCATTCGC 59.845 41.667 4.78 0.00 37.50 4.70
5076 5447 2.742372 GTGCTCCCGCGTCACATT 60.742 61.111 4.92 0.00 39.65 2.71
5077 5448 2.031919 TGCTCCCGCGTCACATTT 59.968 55.556 4.92 0.00 39.65 2.32
5078 5449 1.599518 TGCTCCCGCGTCACATTTT 60.600 52.632 4.92 0.00 39.65 1.82
5079 5450 1.169661 TGCTCCCGCGTCACATTTTT 61.170 50.000 4.92 0.00 39.65 1.94
5138 5509 1.972872 ACTGTCTTTGCAACTCCAGG 58.027 50.000 17.76 4.01 0.00 4.45
5158 5530 5.084519 CAGGGGCAGTAGGTAGATACAATA 58.915 45.833 0.00 0.00 0.00 1.90
5194 5567 1.339055 GGTTGCCACTAGTGATGCTGA 60.339 52.381 24.68 9.90 0.00 4.26
5201 5574 2.757314 CACTAGTGATGCTGAGGAGTGA 59.243 50.000 18.45 0.00 33.88 3.41
5202 5575 3.023119 ACTAGTGATGCTGAGGAGTGAG 58.977 50.000 0.00 0.00 0.00 3.51
5203 5576 1.193323 AGTGATGCTGAGGAGTGAGG 58.807 55.000 0.00 0.00 0.00 3.86
5204 5577 1.189752 GTGATGCTGAGGAGTGAGGA 58.810 55.000 0.00 0.00 0.00 3.71
5205 5578 1.136695 GTGATGCTGAGGAGTGAGGAG 59.863 57.143 0.00 0.00 0.00 3.69
5206 5579 1.272928 TGATGCTGAGGAGTGAGGAGT 60.273 52.381 0.00 0.00 0.00 3.85
5207 5580 1.136695 GATGCTGAGGAGTGAGGAGTG 59.863 57.143 0.00 0.00 0.00 3.51
5260 5634 3.558746 CCAGAGTCCAGAGCTGTCAATTT 60.559 47.826 0.00 0.00 0.00 1.82
5304 5678 0.674895 GTTGCTCAGGTTCGCTGGAT 60.675 55.000 0.00 0.00 0.00 3.41
5338 5712 2.743752 CCGTGGAATGTGAGCGCTG 61.744 63.158 18.48 0.00 0.00 5.18
5343 5718 0.391661 GGAATGTGAGCGCTGGAGAA 60.392 55.000 18.48 0.00 0.00 2.87
5354 5729 1.977293 GCTGGAGAAGAAGGCGGGAT 61.977 60.000 0.00 0.00 0.00 3.85
5369 5744 0.179134 GGGATGTCGACGGTGAGAAG 60.179 60.000 11.62 0.00 0.00 2.85
5373 5748 1.286260 GTCGACGGTGAGAAGTGCT 59.714 57.895 0.00 0.00 0.00 4.40
5390 5765 4.450122 TCGCCTGTCGTACGCGTC 62.450 66.667 18.63 6.85 45.85 5.19
5397 5772 4.041917 TCGTACGCGTCCGCCTTT 62.042 61.111 20.01 0.00 39.49 3.11
5525 5901 4.847217 TCGCGAATGTTTTATCGGTTTTTC 59.153 37.500 6.20 0.00 39.38 2.29
5560 5938 1.761449 TCTGTGGCTTGAGTTTGCAA 58.239 45.000 0.00 0.00 0.00 4.08
5591 5972 2.324332 CTGTAGCATCGTCGTCGCCT 62.324 60.000 0.00 0.00 36.96 5.52
5598 5979 1.874345 ATCGTCGTCGCCTCCAAAGT 61.874 55.000 0.00 0.00 36.96 2.66
5600 5981 1.219522 CGTCGTCGCCTCCAAAGTTT 61.220 55.000 0.00 0.00 0.00 2.66
5619 6000 0.175760 TGGACGTCTAGAATGCTGGC 59.824 55.000 16.46 0.00 0.00 4.85
5626 6007 3.003480 GTCTAGAATGCTGGCGTTTTCT 58.997 45.455 0.00 6.11 33.29 2.52
5645 6027 3.184541 TCTAACGGCTCGAGTATTTTGC 58.815 45.455 15.13 0.00 0.00 3.68
5655 6037 5.119125 GCTCGAGTATTTTGCTTGCAAAATT 59.881 36.000 35.36 25.12 42.59 1.82
5681 6063 7.020602 GCAGTCTTTTGATTTTCTCTAGAAGC 58.979 38.462 0.00 0.00 35.21 3.86
5722 6107 7.041508 TGAGCTTTTCTTCTCATCTCACTTTTC 60.042 37.037 0.00 0.00 34.69 2.29
5725 6110 7.802720 GCTTTTCTTCTCATCTCACTTTTCTTC 59.197 37.037 0.00 0.00 0.00 2.87
5727 6112 8.970859 TTTCTTCTCATCTCACTTTTCTTCTT 57.029 30.769 0.00 0.00 0.00 2.52
5728 6113 8.600449 TTCTTCTCATCTCACTTTTCTTCTTC 57.400 34.615 0.00 0.00 0.00 2.87
5734 6119 9.139174 CTCATCTCACTTTTCTTCTTCTCTTAC 57.861 37.037 0.00 0.00 0.00 2.34
5735 6120 8.865090 TCATCTCACTTTTCTTCTTCTCTTACT 58.135 33.333 0.00 0.00 0.00 2.24
5738 6123 8.798402 TCTCACTTTTCTTCTTCTCTTACTAGG 58.202 37.037 0.00 0.00 0.00 3.02
5739 6124 7.379750 TCACTTTTCTTCTTCTCTTACTAGGC 58.620 38.462 0.00 0.00 0.00 3.93
5740 6125 7.233757 TCACTTTTCTTCTTCTCTTACTAGGCT 59.766 37.037 0.00 0.00 0.00 4.58
5741 6126 7.875554 CACTTTTCTTCTTCTCTTACTAGGCTT 59.124 37.037 0.00 0.00 0.00 4.35
5742 6127 8.433599 ACTTTTCTTCTTCTCTTACTAGGCTTT 58.566 33.333 0.00 0.00 0.00 3.51
5743 6128 9.278978 CTTTTCTTCTTCTCTTACTAGGCTTTT 57.721 33.333 0.00 0.00 0.00 2.27
5744 6129 9.628500 TTTTCTTCTTCTCTTACTAGGCTTTTT 57.372 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.465403 CCTGCAGGACGCTAGGCT 61.465 66.667 29.88 0.00 43.06 4.58
21 22 1.733912 CTCACGTGACCAACATCCATG 59.266 52.381 15.76 0.00 0.00 3.66
32 33 2.408050 AGCAACTCAATCTCACGTGAC 58.592 47.619 15.76 0.31 0.00 3.67
34 35 2.663879 GCAAGCAACTCAATCTCACGTG 60.664 50.000 9.94 9.94 0.00 4.49
35 36 1.532868 GCAAGCAACTCAATCTCACGT 59.467 47.619 0.00 0.00 0.00 4.49
82 83 2.423538 GTCAACTCCAATTCAATCCCCG 59.576 50.000 0.00 0.00 0.00 5.73
84 85 2.760650 GGGTCAACTCCAATTCAATCCC 59.239 50.000 0.00 0.00 0.00 3.85
120 121 1.207089 TCGACAACCAGACCATCATCC 59.793 52.381 0.00 0.00 0.00 3.51
141 142 7.626121 TGCTATGCATGATCCTCAAAAGTGAG 61.626 42.308 10.16 0.00 41.64 3.51
144 145 4.529897 TGCTATGCATGATCCTCAAAAGT 58.470 39.130 10.16 0.00 31.71 2.66
148 149 4.160642 ACTTGCTATGCATGATCCTCAA 57.839 40.909 10.16 3.61 38.76 3.02
149 150 3.851458 ACTTGCTATGCATGATCCTCA 57.149 42.857 10.16 0.00 38.76 3.86
162 163 4.854173 TGAATCAGGCCAATAACTTGCTA 58.146 39.130 5.01 0.00 0.00 3.49
165 166 6.769822 AGACTATGAATCAGGCCAATAACTTG 59.230 38.462 5.01 0.00 0.00 3.16
168 169 6.995091 AGAAGACTATGAATCAGGCCAATAAC 59.005 38.462 5.01 0.00 0.00 1.89
186 187 1.187087 CTAACGCCAGGGAGAAGACT 58.813 55.000 0.00 0.00 0.00 3.24
196 197 1.705337 CCGCCATGTTCTAACGCCAG 61.705 60.000 0.00 0.00 0.00 4.85
198 199 2.469516 CCCGCCATGTTCTAACGCC 61.470 63.158 0.00 0.00 0.00 5.68
200 201 0.108329 AGACCCGCCATGTTCTAACG 60.108 55.000 0.00 0.00 0.00 3.18
203 204 1.138266 GCTAAGACCCGCCATGTTCTA 59.862 52.381 0.00 0.00 0.00 2.10
240 241 3.064207 GTTTGGAGTGTGAGCAACGATA 58.936 45.455 0.00 0.00 0.00 2.92
241 242 1.873591 GTTTGGAGTGTGAGCAACGAT 59.126 47.619 0.00 0.00 0.00 3.73
260 261 2.489073 CCCCTTGCTAAGTTGGACTTGT 60.489 50.000 3.70 0.00 39.11 3.16
262 263 1.075536 CCCCCTTGCTAAGTTGGACTT 59.924 52.381 0.00 0.00 41.97 3.01
263 264 0.698818 CCCCCTTGCTAAGTTGGACT 59.301 55.000 0.00 0.00 0.00 3.85
264 265 0.696501 TCCCCCTTGCTAAGTTGGAC 59.303 55.000 0.00 0.00 0.00 4.02
266 267 2.532250 AATCCCCCTTGCTAAGTTGG 57.468 50.000 0.00 0.00 0.00 3.77
282 283 4.093850 GCATTGGTGAATTCAGGCAAAATC 59.906 41.667 8.80 0.00 0.00 2.17
283 284 4.004982 GCATTGGTGAATTCAGGCAAAAT 58.995 39.130 8.80 2.22 0.00 1.82
284 285 3.401182 GCATTGGTGAATTCAGGCAAAA 58.599 40.909 8.80 0.00 0.00 2.44
289 290 3.574284 TTTCGCATTGGTGAATTCAGG 57.426 42.857 8.80 0.00 42.66 3.86
290 291 5.061311 GTGATTTTCGCATTGGTGAATTCAG 59.939 40.000 8.80 0.00 42.66 3.02
303 304 3.412722 ACTGGGTGTGATTTTCGCA 57.587 47.368 0.00 0.00 34.04 5.10
313 314 0.321298 GTACATTCGGCACTGGGTGT 60.321 55.000 0.00 0.00 35.75 4.16
314 315 0.036388 AGTACATTCGGCACTGGGTG 60.036 55.000 0.00 0.00 36.51 4.61
315 316 0.249398 GAGTACATTCGGCACTGGGT 59.751 55.000 0.00 0.00 0.00 4.51
317 318 0.462047 GGGAGTACATTCGGCACTGG 60.462 60.000 0.00 0.00 0.00 4.00
318 319 0.249120 TGGGAGTACATTCGGCACTG 59.751 55.000 0.00 0.00 0.00 3.66
320 321 0.036765 TGTGGGAGTACATTCGGCAC 60.037 55.000 0.00 0.00 0.00 5.01
321 322 0.908910 ATGTGGGAGTACATTCGGCA 59.091 50.000 0.00 0.00 38.05 5.69
322 323 2.038387 AATGTGGGAGTACATTCGGC 57.962 50.000 0.00 0.00 45.49 5.54
355 356 2.887783 TCCTCTAAGCTCTCGCCTAATG 59.112 50.000 0.00 0.00 36.60 1.90
358 359 2.299521 GTTCCTCTAAGCTCTCGCCTA 58.700 52.381 0.00 0.00 36.60 3.93
359 360 1.107945 GTTCCTCTAAGCTCTCGCCT 58.892 55.000 0.00 0.00 36.60 5.52
360 361 0.248702 CGTTCCTCTAAGCTCTCGCC 60.249 60.000 0.00 0.00 36.60 5.54
361 362 0.733729 TCGTTCCTCTAAGCTCTCGC 59.266 55.000 0.00 0.00 0.00 5.03
367 368 2.094182 TCCACATGTCGTTCCTCTAAGC 60.094 50.000 0.00 0.00 0.00 3.09
368 369 3.429547 CCTCCACATGTCGTTCCTCTAAG 60.430 52.174 0.00 0.00 0.00 2.18
400 401 1.005924 TGAGAGCCCAATTCCTTTCCC 59.994 52.381 0.00 0.00 0.00 3.97
406 407 3.297134 TGGTATTGAGAGCCCAATTCC 57.703 47.619 10.67 10.67 41.49 3.01
412 413 3.131046 CCACAATTTGGTATTGAGAGCCC 59.869 47.826 0.78 0.00 41.10 5.19
413 414 4.376340 CCACAATTTGGTATTGAGAGCC 57.624 45.455 0.78 0.00 41.10 4.70
434 435 3.440173 TCCTTCTCATCGATTGGTTTTGC 59.560 43.478 0.00 0.00 0.00 3.68
438 439 2.571653 TGGTCCTTCTCATCGATTGGTT 59.428 45.455 0.00 0.00 0.00 3.67
439 440 2.187958 TGGTCCTTCTCATCGATTGGT 58.812 47.619 0.00 0.00 0.00 3.67
441 442 3.375299 GGTTTGGTCCTTCTCATCGATTG 59.625 47.826 0.00 0.00 0.00 2.67
442 443 3.009033 TGGTTTGGTCCTTCTCATCGATT 59.991 43.478 0.00 0.00 0.00 3.34
443 444 2.571653 TGGTTTGGTCCTTCTCATCGAT 59.428 45.455 0.00 0.00 0.00 3.59
444 445 1.974957 TGGTTTGGTCCTTCTCATCGA 59.025 47.619 0.00 0.00 0.00 3.59
446 447 2.814336 GTGTGGTTTGGTCCTTCTCATC 59.186 50.000 0.00 0.00 0.00 2.92
475 476 0.610232 CTTGCCCTTGCCTGCTAACT 60.610 55.000 0.00 0.00 36.33 2.24
479 480 2.599578 CACTTGCCCTTGCCTGCT 60.600 61.111 0.00 0.00 36.33 4.24
491 492 3.674528 TTCTCTGCTCCTTCTCACTTG 57.325 47.619 0.00 0.00 0.00 3.16
493 494 4.346418 TCTTTTTCTCTGCTCCTTCTCACT 59.654 41.667 0.00 0.00 0.00 3.41
502 503 4.999950 TGTTCCTCATCTTTTTCTCTGCTC 59.000 41.667 0.00 0.00 0.00 4.26
505 509 5.555017 TCCTGTTCCTCATCTTTTTCTCTG 58.445 41.667 0.00 0.00 0.00 3.35
509 513 4.074970 TGCTCCTGTTCCTCATCTTTTTC 58.925 43.478 0.00 0.00 0.00 2.29
512 516 2.026449 CCTGCTCCTGTTCCTCATCTTT 60.026 50.000 0.00 0.00 0.00 2.52
528 532 2.769663 TGTATATTCAACGTCCCCTGCT 59.230 45.455 0.00 0.00 0.00 4.24
529 533 3.188159 TGTATATTCAACGTCCCCTGC 57.812 47.619 0.00 0.00 0.00 4.85
530 534 4.703897 ACATGTATATTCAACGTCCCCTG 58.296 43.478 0.00 0.00 0.00 4.45
531 535 5.367945 AACATGTATATTCAACGTCCCCT 57.632 39.130 0.00 0.00 0.00 4.79
532 536 5.820947 AGAAACATGTATATTCAACGTCCCC 59.179 40.000 10.56 0.00 0.00 4.81
533 537 6.920569 AGAAACATGTATATTCAACGTCCC 57.079 37.500 10.56 0.00 0.00 4.46
534 538 7.696453 CCAAAGAAACATGTATATTCAACGTCC 59.304 37.037 10.56 0.00 0.00 4.79
535 539 7.218204 GCCAAAGAAACATGTATATTCAACGTC 59.782 37.037 10.56 0.00 0.00 4.34
536 540 7.027161 GCCAAAGAAACATGTATATTCAACGT 58.973 34.615 10.56 0.00 0.00 3.99
537 541 7.008266 GTGCCAAAGAAACATGTATATTCAACG 59.992 37.037 10.56 0.00 0.00 4.10
538 542 7.812191 TGTGCCAAAGAAACATGTATATTCAAC 59.188 33.333 10.56 0.00 0.00 3.18
539 543 7.890515 TGTGCCAAAGAAACATGTATATTCAA 58.109 30.769 10.56 0.00 0.00 2.69
567 594 6.368791 TGGTATGACAAAATTCTCTTCGACTG 59.631 38.462 0.00 0.00 0.00 3.51
574 601 6.182627 TGCTCATGGTATGACAAAATTCTCT 58.817 36.000 0.00 0.00 35.06 3.10
575 602 6.441093 TGCTCATGGTATGACAAAATTCTC 57.559 37.500 0.00 0.00 35.06 2.87
577 604 6.038356 CCTTGCTCATGGTATGACAAAATTC 58.962 40.000 0.00 0.00 35.06 2.17
580 607 4.661222 TCCTTGCTCATGGTATGACAAAA 58.339 39.130 0.00 0.00 35.06 2.44
589 618 2.779430 TGGTATGATCCTTGCTCATGGT 59.221 45.455 0.00 0.00 35.12 3.55
600 629 6.109156 TGGTGTACATATGTGGTATGATCC 57.891 41.667 18.81 9.36 42.34 3.36
606 635 7.432148 AAAGAGATGGTGTACATATGTGGTA 57.568 36.000 18.81 1.69 40.72 3.25
625 654 9.810545 TTTATGTGTTGTAAAAGGGAAAAAGAG 57.189 29.630 0.00 0.00 0.00 2.85
635 664 9.925268 ACTTCGTACTTTTATGTGTTGTAAAAG 57.075 29.630 13.75 13.75 46.77 2.27
686 717 6.411376 CCTAACCAGTGATGTATTACACCAA 58.589 40.000 0.00 0.00 37.69 3.67
742 774 4.677779 GCGTGGGCATTCAGAATATTTTGT 60.678 41.667 5.93 0.00 39.62 2.83
848 880 1.227321 TGCGACCGGTTTCGTCTTT 60.227 52.632 9.42 0.00 41.26 2.52
849 881 1.952635 GTGCGACCGGTTTCGTCTT 60.953 57.895 9.42 0.00 41.26 3.01
850 882 2.355481 GTGCGACCGGTTTCGTCT 60.355 61.111 9.42 0.00 41.26 4.18
851 883 3.408851 GGTGCGACCGGTTTCGTC 61.409 66.667 9.42 5.88 41.26 4.20
861 893 1.222115 GGACTGTCTGTTGGTGCGAC 61.222 60.000 7.85 0.00 0.00 5.19
864 896 0.886490 CCTGGACTGTCTGTTGGTGC 60.886 60.000 7.85 0.00 0.00 5.01
865 897 0.250467 CCCTGGACTGTCTGTTGGTG 60.250 60.000 7.85 0.00 0.00 4.17
866 898 2.056906 GCCCTGGACTGTCTGTTGGT 62.057 60.000 7.85 0.00 0.00 3.67
868 900 0.321122 GAGCCCTGGACTGTCTGTTG 60.321 60.000 7.85 0.00 0.00 3.33
870 902 1.915769 GGAGCCCTGGACTGTCTGT 60.916 63.158 7.85 0.00 0.00 3.41
871 903 2.664081 GGGAGCCCTGGACTGTCTG 61.664 68.421 7.85 1.42 0.00 3.51
872 904 2.284995 GGGAGCCCTGGACTGTCT 60.285 66.667 7.85 0.00 0.00 3.41
873 905 3.403558 GGGGAGCCCTGGACTGTC 61.404 72.222 5.38 0.00 41.34 3.51
897 929 3.909651 TTTGGGTGGAGGTGGGGC 61.910 66.667 0.00 0.00 0.00 5.80
898 930 2.117423 GTTTGGGTGGAGGTGGGG 59.883 66.667 0.00 0.00 0.00 4.96
1087 1144 2.141535 GAGAATCGATCCCGTGGAAG 57.858 55.000 0.00 0.00 34.34 3.46
1141 1198 3.727258 CACCCCCTTCGCCCATCA 61.727 66.667 0.00 0.00 0.00 3.07
1190 1250 0.250081 CCCTAGGAATCTTCAGCGGC 60.250 60.000 11.48 0.00 0.00 6.53
1253 1317 1.757764 GCAACAAAGGTTCCCCTCCTT 60.758 52.381 0.00 0.00 45.84 3.36
1320 1384 2.119801 AAGCACTGGCAGATTGGTAG 57.880 50.000 23.66 2.87 44.61 3.18
1323 1387 1.741706 CACTAAGCACTGGCAGATTGG 59.258 52.381 23.66 15.93 44.61 3.16
1339 1403 0.838608 ACGGAACAACCCAACCACTA 59.161 50.000 0.00 0.00 34.64 2.74
1340 1404 0.033894 AACGGAACAACCCAACCACT 60.034 50.000 0.00 0.00 34.64 4.00
1346 1410 0.531090 CGACTCAACGGAACAACCCA 60.531 55.000 0.00 0.00 34.64 4.51
1364 1428 1.534175 CCGCAGGCTAGAAACTAGTCG 60.534 57.143 0.00 0.00 46.14 4.18
1395 1459 1.140852 GCAGTGTGGTATGGGATGCTA 59.859 52.381 0.00 0.00 0.00 3.49
1497 1575 3.214328 ACTCATCCAGGTCAACACAAAC 58.786 45.455 0.00 0.00 0.00 2.93
1524 1602 4.390297 GTGGATTACTCTTGCTGTGAAGAC 59.610 45.833 0.00 0.00 0.00 3.01
1532 1610 1.134670 GCTCCGTGGATTACTCTTGCT 60.135 52.381 0.00 0.00 0.00 3.91
1717 1796 0.739561 CGGAGCTACCACTACAGACC 59.260 60.000 0.00 0.00 38.90 3.85
1768 1848 4.272748 GCTAAAAATGTACCGATGGAGGAC 59.727 45.833 0.00 0.00 34.73 3.85
1776 1856 7.675962 ACATAGTTTGCTAAAAATGTACCGA 57.324 32.000 7.33 0.00 31.32 4.69
1886 1972 2.114411 GCCCCCTTGGAACACGAA 59.886 61.111 0.00 0.00 39.29 3.85
1890 1976 1.456705 GTGTTGCCCCCTTGGAACA 60.457 57.895 0.00 0.00 35.39 3.18
1902 1988 0.670546 TAGCTCGCTCTTGGTGTTGC 60.671 55.000 0.00 0.00 0.00 4.17
1953 2039 9.927668 AATTTTATAGGAAAAATGTGACCACAG 57.072 29.630 8.87 0.00 45.48 3.66
1977 2063 8.675705 AACGAATTTCCAAATTTCCTGAAAAT 57.324 26.923 9.74 3.97 38.64 1.82
2030 2116 6.183360 TGTGGTAACCATGTTTACTGGAAAAC 60.183 38.462 12.26 3.93 39.35 2.43
2084 2170 5.050644 ACGAACACACTATGACACGAATA 57.949 39.130 0.00 0.00 0.00 1.75
2098 2184 4.153835 ACTTAAAACCGAACAACGAACACA 59.846 37.500 0.00 0.00 45.77 3.72
2105 2191 3.904234 GCGATCACTTAAAACCGAACAAC 59.096 43.478 0.00 0.00 0.00 3.32
2334 2585 7.118060 TCAAGAATGATTTCCATGACCACATA 58.882 34.615 0.00 0.00 35.24 2.29
2490 2742 9.736023 GGAGTGCTTCCAAAATTACAATTATAG 57.264 33.333 3.32 0.00 46.01 1.31
2635 2889 7.826252 AGCATGTATAAATATGTCCATGGAGAC 59.174 37.037 16.81 5.54 37.28 3.36
2660 2914 7.678947 ACAACTTCCTACATTCATCTTTCAG 57.321 36.000 0.00 0.00 0.00 3.02
2712 2966 3.684788 ACGTCTCATCAAAACAGGCATAC 59.315 43.478 0.00 0.00 0.00 2.39
2792 3046 8.098286 AGGCATTTATAATGCGGTATAAGTGTA 58.902 33.333 15.75 0.26 45.41 2.90
3034 3288 5.697633 GGATCAAAACAATTTGCTGTGTGAT 59.302 36.000 0.00 0.00 44.52 3.06
3045 3299 5.144100 TGGTACCTGTGGATCAAAACAATT 58.856 37.500 14.36 0.00 0.00 2.32
3187 3441 1.216064 ACCATAAGCAGGATGGCTCA 58.784 50.000 10.54 0.00 46.76 4.26
3248 3502 2.993264 GCTGGCAGTGCACCCAAT 60.993 61.111 18.61 0.00 0.00 3.16
3309 3563 5.975693 AGTGAAGAACTTCTCTGGACTAG 57.024 43.478 15.25 0.00 40.58 2.57
3348 3602 0.238553 GGGCGCTCAACTTCTGAAAC 59.761 55.000 7.64 0.00 32.17 2.78
3351 3605 2.050836 TTGGGGCGCTCAACTTCTGA 62.051 55.000 10.74 0.00 0.00 3.27
3353 3607 1.150536 TTTGGGGCGCTCAACTTCT 59.849 52.632 10.74 0.00 0.00 2.85
3374 3628 1.064060 GGCCGATCGACAATCAAAAGG 59.936 52.381 18.66 0.00 33.65 3.11
3375 3629 1.737236 TGGCCGATCGACAATCAAAAG 59.263 47.619 18.66 0.00 33.65 2.27
3383 3637 0.103026 CTTCTGATGGCCGATCGACA 59.897 55.000 18.66 15.57 33.17 4.35
3440 3694 2.264455 ACTTCTCTCCTGGTGCAATCT 58.736 47.619 0.00 0.00 0.00 2.40
3506 3760 5.954150 AGGTTGCAAATGGAACTAATGAGAT 59.046 36.000 15.81 0.00 44.36 2.75
3837 4186 4.157472 AGAGCCTTAGGTACTCAAACGTAC 59.843 45.833 0.00 0.00 41.75 3.67
3840 4189 3.870633 AGAGCCTTAGGTACTCAAACG 57.129 47.619 0.00 0.00 41.75 3.60
3962 4312 8.398665 CAGAAGTAGCTATTTGTTCATTTACCC 58.601 37.037 6.18 0.00 0.00 3.69
3966 4316 7.693969 AGCAGAAGTAGCTATTTGTTCATTT 57.306 32.000 6.18 0.00 41.32 2.32
4215 4567 8.716674 AACGGAGGTAGTATGAAGGAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
4490 4844 8.994429 TGGTTTTGCATATTAAATGTGTAAGG 57.006 30.769 0.00 0.00 29.10 2.69
4507 4861 4.432712 ACAGAGACAACATTTGGTTTTGC 58.567 39.130 0.00 0.00 37.72 3.68
4535 4889 4.751172 CGTGTGTTGATACATGAATAGCG 58.249 43.478 0.00 0.00 39.39 4.26
4579 4933 6.068670 AGTTGGTTCCAGCAAATACTACTTT 58.931 36.000 8.28 0.00 37.34 2.66
4594 4948 7.549615 ACGCTTATTCTTATAAGTTGGTTCC 57.450 36.000 12.19 0.00 43.38 3.62
4605 4959 3.883489 GGCCCAGAAACGCTTATTCTTAT 59.117 43.478 0.00 0.00 34.99 1.73
4618 4972 2.281484 GTCTGTGCGGCCCAGAAA 60.281 61.111 16.68 0.00 40.44 2.52
4687 5041 3.323758 TTGAGGAATGGGCCGTCGG 62.324 63.158 6.99 6.99 0.00 4.79
4703 5057 3.365364 GGAACCTTGCGAACTGAATCTTG 60.365 47.826 0.00 0.00 0.00 3.02
4732 5086 1.570857 TTCATGGGATGGCGGAGGTT 61.571 55.000 0.00 0.00 0.00 3.50
4757 5111 2.033194 GCGAGCACTAGGGCGTTTT 61.033 57.895 12.24 0.00 39.27 2.43
4765 5119 1.203523 GGGGATATCAGCGAGCACTAG 59.796 57.143 4.83 0.00 0.00 2.57
4769 5123 3.471620 GGGGGATATCAGCGAGCA 58.528 61.111 4.83 0.00 0.00 4.26
4843 5214 1.550976 ACAGGTTGCTACTACAGGCTC 59.449 52.381 0.00 0.00 0.00 4.70
4872 5243 0.807496 GCCAATCTCCAGCTGACAAC 59.193 55.000 17.39 0.00 0.00 3.32
4908 5279 0.691078 GGAGGCAGGTGGGTATCAGA 60.691 60.000 0.00 0.00 0.00 3.27
4964 5335 1.631071 TTCCAGCATATCCACCCGCA 61.631 55.000 0.00 0.00 0.00 5.69
4992 5363 4.160635 CGGGAACACGGCGAATGC 62.161 66.667 16.62 3.91 41.71 3.56
5033 5404 5.163683 GCGAATGCCATATCATTTCTAGCAT 60.164 40.000 0.00 0.00 40.98 3.79
5034 5405 4.154737 GCGAATGCCATATCATTTCTAGCA 59.845 41.667 0.00 0.00 36.85 3.49
5035 5406 4.656041 GCGAATGCCATATCATTTCTAGC 58.344 43.478 0.00 0.00 36.85 3.42
5076 5447 4.155709 TCCAACATATCCACCTGCAAAAA 58.844 39.130 0.00 0.00 0.00 1.94
5077 5448 3.772387 TCCAACATATCCACCTGCAAAA 58.228 40.909 0.00 0.00 0.00 2.44
5078 5449 3.448093 TCCAACATATCCACCTGCAAA 57.552 42.857 0.00 0.00 0.00 3.68
5079 5450 3.448093 TTCCAACATATCCACCTGCAA 57.552 42.857 0.00 0.00 0.00 4.08
5080 5451 3.448093 TTTCCAACATATCCACCTGCA 57.552 42.857 0.00 0.00 0.00 4.41
5081 5452 3.068590 CCATTTCCAACATATCCACCTGC 59.931 47.826 0.00 0.00 0.00 4.85
5082 5453 4.280819 ACCATTTCCAACATATCCACCTG 58.719 43.478 0.00 0.00 0.00 4.00
5083 5454 4.608170 ACCATTTCCAACATATCCACCT 57.392 40.909 0.00 0.00 0.00 4.00
5084 5455 5.278957 GCATACCATTTCCAACATATCCACC 60.279 44.000 0.00 0.00 0.00 4.61
5085 5456 5.301551 TGCATACCATTTCCAACATATCCAC 59.698 40.000 0.00 0.00 0.00 4.02
5086 5457 5.453158 TGCATACCATTTCCAACATATCCA 58.547 37.500 0.00 0.00 0.00 3.41
5087 5458 6.594788 ATGCATACCATTTCCAACATATCC 57.405 37.500 0.00 0.00 0.00 2.59
5088 5459 9.410556 GTTTATGCATACCATTTCCAACATATC 57.589 33.333 5.74 0.00 35.34 1.63
5089 5460 9.146586 AGTTTATGCATACCATTTCCAACATAT 57.853 29.630 5.74 0.00 35.34 1.78
5090 5461 8.412456 CAGTTTATGCATACCATTTCCAACATA 58.588 33.333 5.74 0.00 35.34 2.29
5138 5509 6.437793 AGACATATTGTATCTACCTACTGCCC 59.562 42.308 0.00 0.00 0.00 5.36
5158 5530 2.107204 GCAACCCCAGGATATCAGACAT 59.893 50.000 4.83 0.00 0.00 3.06
5194 5567 0.042431 AGATGCCACTCCTCACTCCT 59.958 55.000 0.00 0.00 0.00 3.69
5207 5580 2.203209 CCCCGGCTACAAGATGCC 60.203 66.667 0.00 0.00 45.25 4.40
5260 5634 2.111999 CTCTTGCGGTTCCTGTCCCA 62.112 60.000 0.00 0.00 0.00 4.37
5304 5678 0.103208 ACGGCAAAATCAACGGCAAA 59.897 45.000 0.00 0.00 0.00 3.68
5338 5712 0.179070 GACATCCCGCCTTCTTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
5343 5718 2.893398 GTCGACATCCCGCCTTCT 59.107 61.111 11.55 0.00 0.00 2.85
5354 5729 1.007734 GCACTTCTCACCGTCGACA 60.008 57.895 17.16 0.00 0.00 4.35
5369 5744 2.874780 CGTACGACAGGCGAGCAC 60.875 66.667 10.44 0.00 44.57 4.40
5525 5901 4.033358 GCCACAGATAAAGATGAAGACACG 59.967 45.833 0.00 0.00 0.00 4.49
5560 5938 1.924731 TGCTACAGCCTACAGACACT 58.075 50.000 0.00 0.00 41.18 3.55
5598 5979 2.935238 GCCAGCATTCTAGACGTCCAAA 60.935 50.000 13.01 4.58 0.00 3.28
5600 5981 0.175760 GCCAGCATTCTAGACGTCCA 59.824 55.000 13.01 0.00 0.00 4.02
5602 5983 0.179134 ACGCCAGCATTCTAGACGTC 60.179 55.000 7.70 7.70 0.00 4.34
5626 6007 3.241067 AGCAAAATACTCGAGCCGTTA 57.759 42.857 13.61 0.00 0.00 3.18
5655 6037 7.308229 GCTTCTAGAGAAAATCAAAAGACTGCA 60.308 37.037 0.00 0.00 33.07 4.41
5664 6046 9.950496 AAGTATCAAGCTTCTAGAGAAAATCAA 57.050 29.630 0.00 0.00 33.07 2.57
5665 6047 9.593134 GAAGTATCAAGCTTCTAGAGAAAATCA 57.407 33.333 0.00 0.00 39.25 2.57
5681 6063 8.266392 AGAAAAGCTCATCAAGAAGTATCAAG 57.734 34.615 0.00 0.00 0.00 3.02
5712 6097 8.798402 CCTAGTAAGAGAAGAAGAAAAGTGAGA 58.202 37.037 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.