Multiple sequence alignment - TraesCS5A01G364900

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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 TraesCS5A01G364900 chr5A 100.000 6541 0 0 1 6541 565386743 565393283 0.000000e+00 12080.0
1 TraesCS5A01G364900 chr5A 80.469 256 41 9 3518 3771 503618742 503618494 3.110000e-43 187.0
2 TraesCS5A01G364900 chr5B 90.400 3229 172 61 612 3787 545398406 545401549 0.000000e+00 4119.0
3 TraesCS5A01G364900 chr5B 89.509 1649 99 36 4939 6541 545402511 545404131 0.000000e+00 2019.0
4 TraesCS5A01G364900 chr5B 87.692 975 66 26 3829 4800 545401550 545402473 0.000000e+00 1086.0
5 TraesCS5A01G364900 chr5D 90.653 3049 145 66 364 3336 447247702 447244718 0.000000e+00 3923.0
6 TraesCS5A01G364900 chr5D 91.784 1631 70 19 4939 6539 447243216 447241620 0.000000e+00 2211.0
7 TraesCS5A01G364900 chr5D 91.777 754 43 10 4055 4800 447243997 447243255 0.000000e+00 1031.0
8 TraesCS5A01G364900 chr5D 91.990 387 23 4 3365 3746 447244720 447244337 2.680000e-148 536.0
9 TraesCS5A01G364900 chr5D 88.643 361 26 6 1 357 447248087 447247738 6.060000e-115 425.0
10 TraesCS5A01G364900 chr5D 85.630 341 25 9 3825 4161 447244316 447243996 2.920000e-88 337.0
11 TraesCS5A01G364900 chr3A 77.931 435 75 14 3364 3782 387179774 387180203 1.090000e-62 252.0
12 TraesCS5A01G364900 chr3A 84.472 161 23 2 3827 3985 696364225 696364065 2.440000e-34 158.0
13 TraesCS5A01G364900 chr2B 77.252 444 77 15 3365 3788 317239548 317239109 8.480000e-59 239.0
14 TraesCS5A01G364900 chr2D 77.098 441 80 11 3365 3788 423469227 423468791 1.100000e-57 235.0
15 TraesCS5A01G364900 chr2D 76.941 425 64 24 3365 3771 613019161 613019569 1.850000e-50 211.0
16 TraesCS5A01G364900 chr4B 76.037 434 84 11 3365 3782 118190501 118190930 2.390000e-49 207.0
17 TraesCS5A01G364900 chr6D 75.724 449 81 15 3363 3788 451323266 451322823 4.000000e-47 200.0
18 TraesCS5A01G364900 chr6D 75.900 361 66 13 3445 3788 337511341 337510985 1.460000e-36 165.0
19 TraesCS5A01G364900 chr1A 82.090 201 32 4 3827 4024 371693927 371694126 1.130000e-37 169.0
20 TraesCS5A01G364900 chr2A 85.093 161 22 1 3827 3985 553758477 553758317 5.250000e-36 163.0
21 TraesCS5A01G364900 chr2A 84.024 169 25 1 3819 3985 774133263 774133431 1.890000e-35 161.0
22 TraesCS5A01G364900 chr4A 84.568 162 22 2 3827 3985 414407496 414407657 2.440000e-34 158.0
23 TraesCS5A01G364900 chr7D 80.905 199 36 2 3827 4024 270773529 270773726 8.780000e-34 156.0
24 TraesCS5A01G364900 chr4D 80.198 202 34 5 3827 4025 294451587 294451785 5.290000e-31 147.0
25 TraesCS5A01G364900 chr3B 80.097 206 32 5 3827 4023 747151964 747152169 1.900000e-30 145.0
26 TraesCS5A01G364900 chr1B 73.556 450 81 20 3365 3788 32141760 32141323 3.180000e-28 137.0
27 TraesCS5A01G364900 chr7A 86.275 51 7 0 4901 4951 27974882 27974932 1.000000e-03 56.5


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 TraesCS5A01G364900 chr5A 565386743 565393283 6540 False 12080.0 12080 100.000000 1 6541 1 chr5A.!!$F1 6540
1 TraesCS5A01G364900 chr5B 545398406 545404131 5725 False 2408.0 4119 89.200333 612 6541 3 chr5B.!!$F1 5929
2 TraesCS5A01G364900 chr5D 447241620 447248087 6467 True 1410.5 3923 90.079500 1 6539 6 chr5D.!!$R1 6538

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
950 1017 0.174162 GCCGAACGAAACCCTAGCTA 59.826 55.000 0.0 0.0 0.00 3.32 F
1597 1704 0.478072 TCTGGATGGCAGTGTTGGTT 59.522 50.000 0.0 0.0 0.00 3.67 F
1598 1705 0.599558 CTGGATGGCAGTGTTGGTTG 59.400 55.000 0.0 0.0 0.00 3.77 F
3391 3523 0.949105 AAAACAGAGCGCGAACGGAT 60.949 50.000 12.1 0.0 40.57 4.18 F
4004 4146 1.611977 CCGGAAAACCAGAAAGTTCCC 59.388 52.381 0.0 0.0 36.91 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 2551 0.523335 GCAGGAAATTACGCGGCAAG 60.523 55.000 12.47 0.0 0.00 4.01 R
3486 3623 0.320374 TCCGCTCCATGTTCGTTTCT 59.680 50.000 0.00 0.0 0.00 2.52 R
3572 3709 4.846779 TGATTAAGTTTGTTGGTCTGCC 57.153 40.909 0.00 0.0 0.00 4.85 R
4388 4633 0.747255 CCCACACCAGATAGACCTCG 59.253 60.000 0.00 0.0 0.00 4.63 R
5915 6189 0.173481 ATACACGATCACGCTGCTGT 59.827 50.000 0.00 0.0 43.96 4.40 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
27 28 3.188460 ACAAATCTCACGATTTTCCGGTG 59.812 43.478 0.00 0.00 45.18 4.94
40 41 7.148018 ACGATTTTCCGGTGTACTTCTATCTTA 60.148 37.037 0.00 0.00 0.00 2.10
44 45 8.538409 TTTCCGGTGTACTTCTATCTTAAAAC 57.462 34.615 0.00 0.00 0.00 2.43
68 69 7.530010 ACGAAGTCTCACAAATATTTCAATGG 58.470 34.615 0.00 0.00 29.74 3.16
88 89 8.879227 TCAATGGACCATACATGTATCTTGATA 58.121 33.333 15.60 2.12 0.00 2.15
127 132 9.032624 GTATCCCCTATCAGTTAGCTTATGTAA 57.967 37.037 0.00 0.00 0.00 2.41
139 144 2.745152 GCTTATGTAACCGTGCCCAGAT 60.745 50.000 0.00 0.00 0.00 2.90
144 149 0.687920 TAACCGTGCCCAGATCACAA 59.312 50.000 0.00 0.00 34.27 3.33
149 154 1.069022 CGTGCCCAGATCACAAGTTTG 60.069 52.381 0.00 0.00 34.27 2.93
152 157 2.229792 GCCCAGATCACAAGTTTGTCA 58.770 47.619 0.00 0.00 39.91 3.58
180 185 5.413833 ACCACTATCGTAGGGTTCATATACG 59.586 44.000 0.00 0.00 42.70 3.06
197 202 1.173913 ACGCCTCCATTAACAAAGCC 58.826 50.000 0.00 0.00 0.00 4.35
198 203 0.455815 CGCCTCCATTAACAAAGCCC 59.544 55.000 0.00 0.00 0.00 5.19
199 204 0.455815 GCCTCCATTAACAAAGCCCG 59.544 55.000 0.00 0.00 0.00 6.13
204 209 3.020984 TCCATTAACAAAGCCCGATTCC 58.979 45.455 0.00 0.00 0.00 3.01
216 221 2.277084 CCCGATTCCTAAAGAACCACG 58.723 52.381 0.00 0.00 37.29 4.94
246 251 5.022122 TCACCATTGCCTTATTCCAATCAA 58.978 37.500 0.00 0.00 29.71 2.57
282 287 3.664107 TGCACTATGAAGAGGTTGTCAC 58.336 45.455 0.00 0.00 0.00 3.67
283 288 3.003480 GCACTATGAAGAGGTTGTCACC 58.997 50.000 0.00 0.00 44.67 4.02
291 296 2.725641 GGTTGTCACCAAACCGCC 59.274 61.111 0.00 0.00 43.61 6.13
292 297 1.826487 GGTTGTCACCAAACCGCCT 60.826 57.895 0.00 0.00 43.61 5.52
293 298 1.652563 GTTGTCACCAAACCGCCTC 59.347 57.895 0.00 0.00 30.94 4.70
294 299 1.527380 TTGTCACCAAACCGCCTCC 60.527 57.895 0.00 0.00 0.00 4.30
295 300 3.047877 GTCACCAAACCGCCTCCG 61.048 66.667 0.00 0.00 0.00 4.63
296 301 3.235481 TCACCAAACCGCCTCCGA 61.235 61.111 0.00 0.00 36.29 4.55
297 302 2.281208 CACCAAACCGCCTCCGAA 60.281 61.111 0.00 0.00 36.29 4.30
298 303 2.281276 ACCAAACCGCCTCCGAAC 60.281 61.111 0.00 0.00 36.29 3.95
302 307 3.837570 AAACCGCCTCCGAACCACC 62.838 63.158 0.00 0.00 36.29 4.61
317 322 1.780919 ACCACCTCTTTAGCTGGGTTT 59.219 47.619 0.00 0.00 0.00 3.27
323 328 3.691609 CCTCTTTAGCTGGGTTTCATGAC 59.308 47.826 0.00 0.00 0.00 3.06
357 362 1.069204 CAATCAGAGCGCTAGGGCTAA 59.931 52.381 31.75 20.73 44.93 3.09
358 363 1.414158 ATCAGAGCGCTAGGGCTAAA 58.586 50.000 31.75 20.40 44.93 1.85
359 364 1.191535 TCAGAGCGCTAGGGCTAAAA 58.808 50.000 31.75 17.69 44.93 1.52
361 366 0.178301 AGAGCGCTAGGGCTAAAACC 59.822 55.000 31.75 19.59 44.93 3.27
362 367 0.178301 GAGCGCTAGGGCTAAAACCT 59.822 55.000 31.75 10.64 44.93 3.50
391 425 2.397597 TCTTGGGTGGATCATCGATCA 58.602 47.619 0.00 0.00 40.50 2.92
392 426 2.974794 TCTTGGGTGGATCATCGATCAT 59.025 45.455 0.00 0.00 40.50 2.45
398 432 4.453819 GGGTGGATCATCGATCATTTCTTC 59.546 45.833 0.00 0.00 40.50 2.87
401 435 6.073331 GGTGGATCATCGATCATTTCTTCTTC 60.073 42.308 0.00 0.00 40.50 2.87
414 448 7.290842 TCATTTCTTCTTCAAAGACGAATTCG 58.709 34.615 25.64 25.64 41.18 3.34
425 459 1.708027 CGAATTCGTCCGCACCTTC 59.292 57.895 19.67 0.00 34.11 3.46
429 463 2.558554 ATTCGTCCGCACCTTCCTCG 62.559 60.000 0.00 0.00 0.00 4.63
436 470 4.454948 CACCTTCCTCGTGCACAA 57.545 55.556 18.64 0.00 0.00 3.33
441 475 1.532868 CCTTCCTCGTGCACAAGAAAG 59.467 52.381 18.64 7.30 0.00 2.62
443 477 0.179059 TCCTCGTGCACAAGAAAGCA 60.179 50.000 18.64 0.00 38.65 3.91
444 478 0.236711 CCTCGTGCACAAGAAAGCAG 59.763 55.000 18.64 0.00 42.14 4.24
467 501 2.640316 AGAAGTTGGGCTCGTTTCTT 57.360 45.000 0.00 0.00 0.00 2.52
471 505 0.591659 GTTGGGCTCGTTTCTTCCAC 59.408 55.000 0.00 0.00 0.00 4.02
476 510 0.955919 GCTCGTTTCTTCCACCCCTG 60.956 60.000 0.00 0.00 0.00 4.45
482 516 2.757099 CTTCCACCCCTGCCATGC 60.757 66.667 0.00 0.00 0.00 4.06
491 525 2.117156 CCTGCCATGCTTCCTTCGG 61.117 63.158 0.00 0.00 0.00 4.30
496 530 3.518003 ATGCTTCCTTCGGCATGC 58.482 55.556 9.90 9.90 45.81 4.06
501 535 3.643595 TTCCTTCGGCATGCAGGGG 62.644 63.158 21.36 19.71 0.00 4.79
550 584 1.802337 GAACCCAAAACGCCTCACCC 61.802 60.000 0.00 0.00 0.00 4.61
551 585 2.203422 CCCAAAACGCCTCACCCA 60.203 61.111 0.00 0.00 0.00 4.51
560 594 3.174987 CCTCACCCACCACCACCA 61.175 66.667 0.00 0.00 0.00 4.17
561 595 2.113139 CTCACCCACCACCACCAC 59.887 66.667 0.00 0.00 0.00 4.16
562 596 3.491598 CTCACCCACCACCACCACC 62.492 68.421 0.00 0.00 0.00 4.61
707 764 3.124686 GGGCAGACCGCAAAACAA 58.875 55.556 0.00 0.00 45.17 2.83
710 767 0.594796 GGCAGACCGCAAAACAACTG 60.595 55.000 0.00 0.00 45.17 3.16
911 978 4.890306 GCCTCCTCCCCTCCCTCC 62.890 77.778 0.00 0.00 0.00 4.30
912 979 3.039526 CCTCCTCCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
913 980 2.652113 CCTCCTCCCCTCCCTCCTT 61.652 68.421 0.00 0.00 0.00 3.36
917 984 1.398234 CTCCCCTCCCTCCTTCCTT 59.602 63.158 0.00 0.00 0.00 3.36
920 987 2.066999 CCCTCCCTCCTTCCTTCCG 61.067 68.421 0.00 0.00 0.00 4.30
950 1017 0.174162 GCCGAACGAAACCCTAGCTA 59.826 55.000 0.00 0.00 0.00 3.32
951 1018 1.918595 CCGAACGAAACCCTAGCTAC 58.081 55.000 0.00 0.00 0.00 3.58
1208 1307 4.427661 GTGCGCGCACTCTCTCCT 62.428 66.667 46.82 0.00 43.12 3.69
1209 1308 4.121669 TGCGCGCACTCTCTCCTC 62.122 66.667 33.09 0.00 0.00 3.71
1210 1309 4.863925 GCGCGCACTCTCTCCTCC 62.864 72.222 29.10 0.00 0.00 4.30
1211 1310 3.137459 CGCGCACTCTCTCCTCCT 61.137 66.667 8.75 0.00 0.00 3.69
1212 1311 2.804856 GCGCACTCTCTCCTCCTC 59.195 66.667 0.30 0.00 0.00 3.71
1213 1312 2.781158 GCGCACTCTCTCCTCCTCC 61.781 68.421 0.30 0.00 0.00 4.30
1214 1313 2.124693 CGCACTCTCTCCTCCTCCC 61.125 68.421 0.00 0.00 0.00 4.30
1215 1314 1.760480 GCACTCTCTCCTCCTCCCC 60.760 68.421 0.00 0.00 0.00 4.81
1216 1315 1.075600 CACTCTCTCCTCCTCCCCC 60.076 68.421 0.00 0.00 0.00 5.40
1232 1331 1.236708 CCCCCTCTCTTCTCCTCCTA 58.763 60.000 0.00 0.00 0.00 2.94
1246 1345 4.046489 TCTCCTCCTATTAGCCATGGATCT 59.954 45.833 18.40 6.51 0.00 2.75
1252 1351 1.699054 TTAGCCATGGATCTGCGCCT 61.699 55.000 18.40 2.36 0.00 5.52
1481 1587 4.478371 GGGGAAGGTAACCGCGGG 62.478 72.222 31.76 11.88 37.17 6.13
1482 1588 4.478371 GGGAAGGTAACCGCGGGG 62.478 72.222 31.76 18.33 40.11 5.73
1503 1609 3.119352 GGGCTTGCTTATTTTCTCCACTG 60.119 47.826 0.00 0.00 0.00 3.66
1512 1618 4.590850 ATTTTCTCCACTGTGGCTTTTC 57.409 40.909 22.02 0.00 37.47 2.29
1523 1630 4.058817 CTGTGGCTTTTCGTTTCTCTACT 58.941 43.478 0.00 0.00 0.00 2.57
1525 1632 5.603596 TGTGGCTTTTCGTTTCTCTACTAA 58.396 37.500 0.00 0.00 0.00 2.24
1530 1637 9.275398 TGGCTTTTCGTTTCTCTACTAATAAAA 57.725 29.630 0.00 0.00 0.00 1.52
1595 1702 1.843368 AATCTGGATGGCAGTGTTGG 58.157 50.000 0.00 0.00 0.00 3.77
1596 1703 0.700564 ATCTGGATGGCAGTGTTGGT 59.299 50.000 0.00 0.00 0.00 3.67
1597 1704 0.478072 TCTGGATGGCAGTGTTGGTT 59.522 50.000 0.00 0.00 0.00 3.67
1598 1705 0.599558 CTGGATGGCAGTGTTGGTTG 59.400 55.000 0.00 0.00 0.00 3.77
1609 1716 3.088532 AGTGTTGGTTGCTTCTGTTGAA 58.911 40.909 0.00 0.00 0.00 2.69
1621 1729 5.978919 TGCTTCTGTTGAATAGTTTTGCTTG 59.021 36.000 0.00 0.00 0.00 4.01
1625 1733 7.275888 TCTGTTGAATAGTTTTGCTTGTGAT 57.724 32.000 0.00 0.00 0.00 3.06
1732 1840 2.154462 CATCAGCAAACGAAAGACCCT 58.846 47.619 0.00 0.00 0.00 4.34
1739 1848 4.814294 CGAAAGACCCTCCGCCCG 62.814 72.222 0.00 0.00 0.00 6.13
1758 1867 2.358957 CGAGAGTTCAATTGGGCATGA 58.641 47.619 5.42 0.00 0.00 3.07
1848 1957 6.000840 TGTTGTTTCTGTCCAATAGCATGTA 58.999 36.000 0.00 0.00 0.00 2.29
1868 1978 9.716507 GCATGTAGTTTAACCTTTACATACATG 57.283 33.333 18.59 18.59 46.04 3.21
1931 2054 8.272866 GCATGTTGTTTAACCTTTACATTTGAC 58.727 33.333 0.00 0.00 35.92 3.18
1980 2103 6.128227 GCGTTCAAATATAGTGGTGTTTGGTA 60.128 38.462 0.00 0.00 32.91 3.25
2013 2136 5.028549 TGAAATTTTTGTTAGCTTGGCCA 57.971 34.783 0.00 0.00 0.00 5.36
2042 2165 3.242576 TGCATTTATGTATCGTTGTGGCG 60.243 43.478 0.00 0.00 0.00 5.69
2094 2217 2.616960 CTGTGGTGTAATTAGCAGCGA 58.383 47.619 10.52 0.00 37.18 4.93
2366 2491 1.284982 CTCAGCGAAACACCAGACCG 61.285 60.000 0.00 0.00 0.00 4.79
2418 2543 7.395206 GCTTAAACTTGTAGGGGATTCCTTAAA 59.605 37.037 2.01 0.00 45.47 1.52
2419 2544 9.304335 CTTAAACTTGTAGGGGATTCCTTAAAA 57.696 33.333 2.01 0.00 45.47 1.52
2426 2551 4.344978 AGGGGATTCCTTAAAAGCTGAAC 58.655 43.478 2.01 0.00 45.47 3.18
2433 2558 2.319472 CTTAAAAGCTGAACTTGCCGC 58.681 47.619 0.00 0.00 39.09 6.53
2464 2589 4.158394 CCTGCATAGCATGTTGTTAACCTT 59.842 41.667 2.48 0.00 38.13 3.50
2597 2722 1.068948 TGTAAGTAAGGGCCTGCCAA 58.931 50.000 6.92 0.00 37.98 4.52
2660 2785 2.106338 TGTTCCACATGCAGAGGAAGAA 59.894 45.455 15.24 6.66 45.82 2.52
3088 3220 8.662781 TGCTAATTTACTTCAGACATCATACC 57.337 34.615 0.00 0.00 0.00 2.73
3264 3396 4.263068 GGTACTGCAGGATATGGCTATGTT 60.263 45.833 19.93 0.00 0.00 2.71
3354 3486 6.578919 GTGCTAGCTTTTTGTTTGAGACATAC 59.421 38.462 17.23 0.00 38.26 2.39
3356 3488 7.040478 TGCTAGCTTTTTGTTTGAGACATACAT 60.040 33.333 17.23 0.00 38.26 2.29
3383 3515 2.024176 TAGGGATGAAAACAGAGCGC 57.976 50.000 0.00 0.00 0.00 5.92
3384 3516 1.021390 AGGGATGAAAACAGAGCGCG 61.021 55.000 0.00 0.00 0.00 6.86
3391 3523 0.949105 AAAACAGAGCGCGAACGGAT 60.949 50.000 12.10 0.00 40.57 4.18
3409 3541 2.301346 GATGGAATTGGGTGCTACCAG 58.699 52.381 7.49 0.00 42.47 4.00
3457 3593 6.151817 GGAAGCAGAAATGAATACAGAAACCT 59.848 38.462 0.00 0.00 0.00 3.50
3463 3600 9.748708 CAGAAATGAATACAGAAACCTCAAAAA 57.251 29.630 0.00 0.00 0.00 1.94
3572 3709 8.611757 CCCTTGAACCATAAAGAAAAACAAAAG 58.388 33.333 0.00 0.00 0.00 2.27
3576 3713 7.279758 TGAACCATAAAGAAAAACAAAAGGCAG 59.720 33.333 0.00 0.00 0.00 4.85
3595 3732 4.982295 GGCAGACCAACAAACTTAATCAAC 59.018 41.667 0.00 0.00 35.26 3.18
3600 3737 7.220683 CAGACCAACAAACTTAATCAACTGTTG 59.779 37.037 14.24 14.24 41.96 3.33
3697 3834 9.128404 CATAGGGTCTAGTTAAGTATGTGTGTA 57.872 37.037 0.00 0.00 0.00 2.90
3712 3849 4.659115 TGTGTGTAGTAGTAGAAGCCAGA 58.341 43.478 0.00 0.00 0.00 3.86
3747 3884 4.741185 CCATTTTGTCACTGTCATTGTGTG 59.259 41.667 0.00 0.00 36.83 3.82
3761 3898 3.753294 TTGTGTGTTGTTTGGTGGTTT 57.247 38.095 0.00 0.00 0.00 3.27
3762 3899 3.753294 TGTGTGTTGTTTGGTGGTTTT 57.247 38.095 0.00 0.00 0.00 2.43
3772 3909 3.810310 TTGGTGGTTTTGCTACAAAGG 57.190 42.857 0.00 0.00 0.00 3.11
3883 4020 5.134202 GGAAAGATCCATTTCCGTGTTTT 57.866 39.130 9.92 0.00 46.43 2.43
3953 4092 8.914328 AAAATTCCATTTTTGCTTCTGTTTTG 57.086 26.923 0.00 0.00 39.28 2.44
3954 4093 5.482686 TTCCATTTTTGCTTCTGTTTTGC 57.517 34.783 0.00 0.00 0.00 3.68
3955 4094 4.511527 TCCATTTTTGCTTCTGTTTTGCA 58.488 34.783 0.00 0.00 34.69 4.08
3956 4095 4.940046 TCCATTTTTGCTTCTGTTTTGCAA 59.060 33.333 0.00 0.00 43.69 4.08
3985 4127 4.703093 TGTTTCCATTTCCGTATTTCCTCC 59.297 41.667 0.00 0.00 0.00 4.30
3986 4128 3.188159 TCCATTTCCGTATTTCCTCCG 57.812 47.619 0.00 0.00 0.00 4.63
4002 4144 2.552743 CCTCCGGAAAACCAGAAAGTTC 59.447 50.000 5.23 0.00 0.00 3.01
4004 4146 1.611977 CCGGAAAACCAGAAAGTTCCC 59.388 52.381 0.00 0.00 36.91 3.97
4091 4235 8.428063 AGGAAATCAGAGAACAATATGGACTAG 58.572 37.037 0.00 0.00 0.00 2.57
4141 4285 9.958234 GGAGGAATTTAAGCAAGATTTTATCTC 57.042 33.333 0.00 0.00 39.08 2.75
4215 4457 6.463995 TTTTATGTGATGGGGTATTTCTGC 57.536 37.500 0.00 0.00 0.00 4.26
4231 4473 3.781341 TCTGCGTTGACGTTTTGTATC 57.219 42.857 5.36 0.00 42.22 2.24
4388 4633 1.799548 GCTACTCAACCAGCTACGAGC 60.800 57.143 0.00 0.00 42.84 5.03
4446 4691 6.490381 GTCAATGGTATTTATTCCCTTCCCTC 59.510 42.308 0.00 0.00 0.00 4.30
4448 4693 5.646692 TGGTATTTATTCCCTTCCCTCTG 57.353 43.478 0.00 0.00 0.00 3.35
4489 4734 6.016777 GTGACCTGGGAATATGTTTGATCATC 60.017 42.308 0.00 0.00 0.00 2.92
4550 4795 1.450360 AGGAGGAAAGAAGGTTGGCT 58.550 50.000 0.00 0.00 0.00 4.75
4661 4907 4.364817 CGGCACCCGTAGAACAAA 57.635 55.556 0.00 0.00 42.73 2.83
4662 4908 2.619362 CGGCACCCGTAGAACAAAA 58.381 52.632 0.00 0.00 42.73 2.44
4663 4909 1.161843 CGGCACCCGTAGAACAAAAT 58.838 50.000 0.00 0.00 42.73 1.82
4664 4910 2.348660 CGGCACCCGTAGAACAAAATA 58.651 47.619 0.00 0.00 42.73 1.40
4669 4915 6.592607 CGGCACCCGTAGAACAAAATATATAT 59.407 38.462 0.00 0.00 42.73 0.86
4741 4987 5.521906 TGTATTCCTTCAGTAGCTAGCTG 57.478 43.478 27.68 11.86 35.43 4.24
4742 4988 2.969628 TTCCTTCAGTAGCTAGCTGC 57.030 50.000 27.68 25.63 43.29 5.25
4743 4989 1.852633 TCCTTCAGTAGCTAGCTGCA 58.147 50.000 30.79 11.81 45.94 4.41
4747 4993 3.320541 CCTTCAGTAGCTAGCTGCATACT 59.679 47.826 30.79 21.29 45.94 2.12
4772 5021 5.001232 TCCTCCGTTTGAAAATACTTGGAG 58.999 41.667 0.00 0.00 41.08 3.86
4794 5043 4.220163 AGGTTCTAGGTTTGTCCTAAGTCG 59.780 45.833 0.00 0.00 46.81 4.18
4802 5060 4.995487 GGTTTGTCCTAAGTCGAACATCTT 59.005 41.667 0.00 0.00 29.79 2.40
4821 5079 8.553459 ACATCTTTATGTTTGACCAAGTCTAG 57.447 34.615 0.00 0.00 44.07 2.43
4823 5081 8.877779 CATCTTTATGTTTGACCAAGTCTAGAG 58.122 37.037 0.00 0.00 33.15 2.43
4825 5083 8.647796 TCTTTATGTTTGACCAAGTCTAGAGAA 58.352 33.333 0.00 0.00 33.15 2.87
4826 5084 9.273016 CTTTATGTTTGACCAAGTCTAGAGAAA 57.727 33.333 0.00 0.00 33.15 2.52
4828 5086 9.621629 TTATGTTTGACCAAGTCTAGAGAAAAA 57.378 29.630 0.00 0.00 33.15 1.94
4829 5087 8.697507 ATGTTTGACCAAGTCTAGAGAAAAAT 57.302 30.769 0.00 0.00 33.15 1.82
4830 5088 9.793259 ATGTTTGACCAAGTCTAGAGAAAAATA 57.207 29.630 0.00 0.00 33.15 1.40
4831 5089 9.793259 TGTTTGACCAAGTCTAGAGAAAAATAT 57.207 29.630 0.00 0.00 33.15 1.28
4859 5117 9.643693 TCAACGTATACATCGACTATAGTATGA 57.356 33.333 18.45 13.98 0.00 2.15
4928 5186 9.533253 AGACTTGGTCAAATTTAAAGATGTTTG 57.467 29.630 0.00 5.89 34.60 2.93
4929 5187 9.528018 GACTTGGTCAAATTTAAAGATGTTTGA 57.472 29.630 9.56 9.56 38.01 2.69
4966 5225 6.040391 CCCAGAACTTTGAGTATTTGGAAACA 59.960 38.462 6.88 0.00 39.83 2.83
4972 5231 6.209391 ACTTTGAGTATTTGGAAACAGATGGG 59.791 38.462 0.00 0.00 44.54 4.00
5175 5434 2.749621 GGTGCTAATGACTTGAGGGTTG 59.250 50.000 0.00 0.00 0.00 3.77
5400 5664 6.769822 TCATAAAGAGGAAATTCTCATGCTCC 59.230 38.462 0.00 0.00 34.88 4.70
5438 5702 9.064706 CCAAGTTGCAGAGATCAAATCTAATAT 57.935 33.333 0.00 0.00 40.38 1.28
5651 5916 1.296832 TGATCCTGGATCCCCCTGTTA 59.703 52.381 28.99 9.24 38.20 2.41
5657 5922 3.140895 CCTGGATCCCCCTGTTATTGATT 59.859 47.826 9.90 0.00 35.38 2.57
5714 5979 2.051334 TTGTGTTGGTCTGACTTGGG 57.949 50.000 7.85 0.00 0.00 4.12
5727 5992 4.937620 TCTGACTTGGGAGATTTTGATTCG 59.062 41.667 0.00 0.00 0.00 3.34
5798 6069 5.584649 AGAAGTCATTTGTTCTGTTGTCGAA 59.415 36.000 0.00 0.00 31.63 3.71
5860 6133 6.372659 TGAGGATGAAATTAGCAGTGTCTTTC 59.627 38.462 0.00 0.00 0.00 2.62
5871 6144 2.047061 AGTGTCTTTCCACCAGCTGTA 58.953 47.619 13.81 0.00 35.93 2.74
5902 6176 5.429681 AGTACCATATGTTGTTAGCACCA 57.570 39.130 1.24 0.00 0.00 4.17
5904 6178 6.423182 AGTACCATATGTTGTTAGCACCATT 58.577 36.000 1.24 0.00 30.29 3.16
5915 6189 6.842437 TGTTAGCACCATTATTTTGCCTTA 57.158 33.333 0.00 0.00 36.91 2.69
5917 6191 6.209589 TGTTAGCACCATTATTTTGCCTTACA 59.790 34.615 0.00 0.00 36.91 2.41
5939 6213 2.473816 CAGCGTGATCGTGTATCCATT 58.526 47.619 0.00 0.00 39.49 3.16
5941 6215 2.159099 AGCGTGATCGTGTATCCATTGT 60.159 45.455 0.00 0.00 39.49 2.71
5971 6246 3.684305 GCAAAAGAGGTGTTGCTTGTTTT 59.316 39.130 1.26 0.00 45.34 2.43
5996 6285 1.673168 ATGCAATTCTTCTCTCCGGC 58.327 50.000 0.00 0.00 0.00 6.13
6004 6293 1.004394 TCTTCTCTCCGGCACTACTCA 59.996 52.381 0.00 0.00 0.00 3.41
6091 6380 1.593469 GAACTAATCTCGCGCCCTTTC 59.407 52.381 0.00 0.00 0.00 2.62
6100 6389 1.005156 GCGCCCTTTCAATTTGCCA 60.005 52.632 0.00 0.00 0.00 4.92
6106 6395 3.189080 GCCCTTTCAATTTGCCACAAATC 59.811 43.478 6.05 0.00 0.00 2.17
6177 6471 2.396601 CTTGCGTGCATGAACACATTT 58.603 42.857 10.93 0.00 40.73 2.32
6185 6479 5.331458 CGTGCATGAACACATTTTACAACAC 60.331 40.000 4.29 0.00 40.73 3.32
6186 6480 5.046529 TGCATGAACACATTTTACAACACC 58.953 37.500 0.00 0.00 0.00 4.16
6245 6539 2.827921 GTTGAGTGGATCCCAAGCAAAT 59.172 45.455 9.90 0.00 34.18 2.32
6267 6561 1.995542 AGGAGGAAAAAGGAGCCATGA 59.004 47.619 0.00 0.00 0.00 3.07
6268 6562 2.379907 AGGAGGAAAAAGGAGCCATGAA 59.620 45.455 0.00 0.00 0.00 2.57
6269 6563 2.757314 GGAGGAAAAAGGAGCCATGAAG 59.243 50.000 0.00 0.00 0.00 3.02
6270 6564 3.425659 GAGGAAAAAGGAGCCATGAAGT 58.574 45.455 0.00 0.00 0.00 3.01
6271 6565 3.425659 AGGAAAAAGGAGCCATGAAGTC 58.574 45.455 0.00 0.00 0.00 3.01
6272 6566 2.162408 GGAAAAAGGAGCCATGAAGTCG 59.838 50.000 0.00 0.00 0.00 4.18
6273 6567 1.826385 AAAAGGAGCCATGAAGTCGG 58.174 50.000 0.00 0.00 0.00 4.79
6280 6574 1.900351 CCATGAAGTCGGCTGGAGA 59.100 57.895 0.00 0.00 0.00 3.71
6281 6575 0.250234 CCATGAAGTCGGCTGGAGAA 59.750 55.000 0.00 0.00 0.00 2.87
6284 6578 1.219393 GAAGTCGGCTGGAGAAGGG 59.781 63.158 0.00 0.00 0.00 3.95
6285 6579 1.229209 AAGTCGGCTGGAGAAGGGA 60.229 57.895 0.00 0.00 0.00 4.20
6380 6681 2.364972 AGAACCTCAAACCCACCAAG 57.635 50.000 0.00 0.00 0.00 3.61
6426 6739 1.338337 CCTCTGCCTCAGTGTATACCG 59.662 57.143 0.00 0.00 32.61 4.02
6441 6754 5.865552 GTGTATACCGAACACTAAAGCTCAA 59.134 40.000 0.00 0.00 43.13 3.02
6477 6790 3.049708 TCACTTCACTGGATTCTGCTG 57.950 47.619 0.00 0.00 0.00 4.41
6536 6849 3.578688 CTTTAACCTTTGCACAGCCATC 58.421 45.455 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.965824 ATTGAAATATTTGTGAGACTTCGTTTT 57.034 25.926 5.17 0.00 0.00 2.43
44 45 7.693951 GTCCATTGAAATATTTGTGAGACTTCG 59.306 37.037 5.17 0.00 0.00 3.79
59 60 8.853126 CAAGATACATGTATGGTCCATTGAAAT 58.147 33.333 22.93 2.57 0.00 2.17
60 61 8.052141 TCAAGATACATGTATGGTCCATTGAAA 58.948 33.333 22.93 0.00 0.00 2.69
68 69 9.155975 GGTTCATATCAAGATACATGTATGGTC 57.844 37.037 22.93 9.80 0.00 4.02
127 132 1.003355 CTTGTGATCTGGGCACGGT 60.003 57.895 0.00 0.00 39.07 4.83
139 144 3.013921 GTGGTCCTTGACAAACTTGTGA 58.986 45.455 0.00 0.00 42.43 3.58
144 149 3.926616 CGATAGTGGTCCTTGACAAACT 58.073 45.455 6.92 6.92 35.91 2.66
180 185 0.455815 CGGGCTTTGTTAATGGAGGC 59.544 55.000 0.00 0.00 0.00 4.70
197 202 2.093869 TCCGTGGTTCTTTAGGAATCGG 60.094 50.000 10.12 10.12 41.63 4.18
198 203 2.928116 GTCCGTGGTTCTTTAGGAATCG 59.072 50.000 0.00 0.00 37.85 3.34
199 204 3.683340 GTGTCCGTGGTTCTTTAGGAATC 59.317 47.826 0.00 0.00 36.24 2.52
204 209 3.432252 GTGATGTGTCCGTGGTTCTTTAG 59.568 47.826 0.00 0.00 0.00 1.85
216 221 1.549203 AAGGCAATGGTGATGTGTCC 58.451 50.000 0.00 0.00 0.00 4.02
246 251 3.402628 AGTGCAGTTCGGATGTTTAGT 57.597 42.857 0.00 0.00 0.00 2.24
282 287 3.053896 GGTTCGGAGGCGGTTTGG 61.054 66.667 0.00 0.00 0.00 3.28
283 288 2.281208 TGGTTCGGAGGCGGTTTG 60.281 61.111 0.00 0.00 0.00 2.93
287 292 4.452733 GAGGTGGTTCGGAGGCGG 62.453 72.222 0.00 0.00 0.00 6.13
288 293 2.450479 AAAGAGGTGGTTCGGAGGCG 62.450 60.000 0.00 0.00 0.00 5.52
289 294 0.611714 TAAAGAGGTGGTTCGGAGGC 59.388 55.000 0.00 0.00 0.00 4.70
290 295 1.405661 GCTAAAGAGGTGGTTCGGAGG 60.406 57.143 0.00 0.00 0.00 4.30
291 296 1.550976 AGCTAAAGAGGTGGTTCGGAG 59.449 52.381 0.00 0.00 30.28 4.63
292 297 1.275291 CAGCTAAAGAGGTGGTTCGGA 59.725 52.381 0.00 0.00 45.66 4.55
293 298 1.726853 CAGCTAAAGAGGTGGTTCGG 58.273 55.000 0.00 0.00 45.66 4.30
302 307 3.372206 CGTCATGAAACCCAGCTAAAGAG 59.628 47.826 0.00 0.00 0.00 2.85
323 328 0.381445 TGATTGCGGGCATGAAATCG 59.619 50.000 0.00 0.00 32.78 3.34
351 356 1.924731 AGGCAAAGAGGTTTTAGCCC 58.075 50.000 0.00 0.00 42.97 5.19
357 362 2.319844 CCCAAGAAGGCAAAGAGGTTT 58.680 47.619 0.00 0.00 35.39 3.27
358 363 1.217942 ACCCAAGAAGGCAAAGAGGTT 59.782 47.619 0.00 0.00 35.39 3.50
359 364 0.853530 ACCCAAGAAGGCAAAGAGGT 59.146 50.000 0.00 0.00 35.39 3.85
361 366 1.202927 TCCACCCAAGAAGGCAAAGAG 60.203 52.381 0.00 0.00 35.39 2.85
362 367 0.850100 TCCACCCAAGAAGGCAAAGA 59.150 50.000 0.00 0.00 35.39 2.52
414 448 2.432628 CACGAGGAAGGTGCGGAC 60.433 66.667 0.00 0.00 0.00 4.79
425 459 0.236711 CTGCTTTCTTGTGCACGAGG 59.763 55.000 29.69 17.16 35.20 4.63
429 463 2.549754 TCTAAGCTGCTTTCTTGTGCAC 59.450 45.455 21.29 10.75 35.20 4.57
432 466 5.210715 CAACTTCTAAGCTGCTTTCTTGTG 58.789 41.667 21.29 8.47 0.00 3.33
434 468 4.320788 CCCAACTTCTAAGCTGCTTTCTTG 60.321 45.833 21.29 13.32 0.00 3.02
436 470 3.416156 CCCAACTTCTAAGCTGCTTTCT 58.584 45.455 21.29 0.00 0.00 2.52
441 475 1.090728 GAGCCCAACTTCTAAGCTGC 58.909 55.000 0.00 0.00 32.97 5.25
443 477 0.977395 ACGAGCCCAACTTCTAAGCT 59.023 50.000 0.00 0.00 36.25 3.74
444 478 1.809684 AACGAGCCCAACTTCTAAGC 58.190 50.000 0.00 0.00 0.00 3.09
467 501 3.267233 AAGCATGGCAGGGGTGGA 61.267 61.111 0.00 0.00 0.00 4.02
471 505 1.755783 GAAGGAAGCATGGCAGGGG 60.756 63.158 0.00 0.00 0.00 4.79
501 535 0.597898 GCTCGCCGTTAGAGGGAATC 60.598 60.000 2.10 0.00 36.31 2.52
510 544 4.764336 CGGACGTGCTCGCCGTTA 62.764 66.667 25.21 0.00 44.68 3.18
527 561 1.228459 AGGCGTTTTGGGTTCCCTC 60.228 57.895 9.43 0.00 0.00 4.30
550 584 2.912025 GCTTGGGTGGTGGTGGTG 60.912 66.667 0.00 0.00 0.00 4.17
551 585 4.579384 CGCTTGGGTGGTGGTGGT 62.579 66.667 0.00 0.00 0.00 4.16
560 594 0.110486 ATCAAACTCCACGCTTGGGT 59.890 50.000 9.71 3.51 44.11 4.51
561 595 0.804989 GATCAAACTCCACGCTTGGG 59.195 55.000 9.71 2.85 44.11 4.12
562 596 0.804989 GGATCAAACTCCACGCTTGG 59.195 55.000 1.99 1.99 45.56 3.61
707 764 3.966543 CGGCCCCTTGGGTTCAGT 61.967 66.667 0.00 0.00 46.51 3.41
710 767 4.986708 TTGCGGCCCCTTGGGTTC 62.987 66.667 0.00 0.00 46.51 3.62
747 804 4.101448 CACGGGCTCCCTTGGGAG 62.101 72.222 26.93 26.93 38.88 4.30
903 970 2.736826 GCGGAAGGAAGGAGGGAGG 61.737 68.421 0.00 0.00 0.00 4.30
905 972 2.687566 GGCGGAAGGAAGGAGGGA 60.688 66.667 0.00 0.00 0.00 4.20
906 973 4.162690 CGGCGGAAGGAAGGAGGG 62.163 72.222 0.00 0.00 0.00 4.30
907 974 4.840005 GCGGCGGAAGGAAGGAGG 62.840 72.222 9.78 0.00 0.00 4.30
993 1092 3.757248 CTTCTTCCCCATCCCCGCG 62.757 68.421 0.00 0.00 0.00 6.46
1197 1296 1.760480 GGGGAGGAGGAGAGAGTGC 60.760 68.421 0.00 0.00 0.00 4.40
1199 1298 3.446050 GGGGGAGGAGGAGAGAGT 58.554 66.667 0.00 0.00 0.00 3.24
1213 1312 1.236708 TAGGAGGAGAAGAGAGGGGG 58.763 60.000 0.00 0.00 0.00 5.40
1214 1313 3.628832 AATAGGAGGAGAAGAGAGGGG 57.371 52.381 0.00 0.00 0.00 4.79
1215 1314 4.086457 GCTAATAGGAGGAGAAGAGAGGG 58.914 52.174 0.00 0.00 0.00 4.30
1216 1315 4.086457 GGCTAATAGGAGGAGAAGAGAGG 58.914 52.174 0.00 0.00 0.00 3.69
1217 1316 4.735369 TGGCTAATAGGAGGAGAAGAGAG 58.265 47.826 0.00 0.00 0.00 3.20
1218 1317 4.816048 TGGCTAATAGGAGGAGAAGAGA 57.184 45.455 0.00 0.00 0.00 3.10
1219 1318 4.222588 CCATGGCTAATAGGAGGAGAAGAG 59.777 50.000 0.00 0.00 0.00 2.85
1220 1319 4.140686 TCCATGGCTAATAGGAGGAGAAGA 60.141 45.833 6.96 0.00 0.00 2.87
1223 1322 3.923273 TCCATGGCTAATAGGAGGAGA 57.077 47.619 6.96 0.00 0.00 3.71
1232 1331 0.607489 GGCGCAGATCCATGGCTAAT 60.607 55.000 10.83 0.00 0.00 1.73
1289 1391 0.530650 CACGGATCCAATCGAGGGTG 60.531 60.000 13.41 5.17 0.00 4.61
1292 1394 1.595382 GGCACGGATCCAATCGAGG 60.595 63.158 13.41 0.00 0.00 4.63
1481 1587 3.092301 AGTGGAGAAAATAAGCAAGCCC 58.908 45.455 0.00 0.00 0.00 5.19
1482 1588 3.507622 ACAGTGGAGAAAATAAGCAAGCC 59.492 43.478 0.00 0.00 0.00 4.35
1503 1609 6.723131 ATTAGTAGAGAAACGAAAAGCCAC 57.277 37.500 0.00 0.00 0.00 5.01
1530 1637 7.800092 AGCAAATACTCTGGTCTATGAAGAAT 58.200 34.615 0.00 0.00 32.16 2.40
1549 1656 6.037610 CAGCGGAGAAAATAACTAGAGCAAAT 59.962 38.462 0.00 0.00 0.00 2.32
1595 1702 5.979517 AGCAAAACTATTCAACAGAAGCAAC 59.020 36.000 0.00 0.00 0.00 4.17
1596 1703 6.147864 AGCAAAACTATTCAACAGAAGCAA 57.852 33.333 0.00 0.00 0.00 3.91
1597 1704 5.772825 AGCAAAACTATTCAACAGAAGCA 57.227 34.783 0.00 0.00 0.00 3.91
1598 1705 5.979517 ACAAGCAAAACTATTCAACAGAAGC 59.020 36.000 0.00 0.00 0.00 3.86
1609 1716 4.142093 GGCCATCATCACAAGCAAAACTAT 60.142 41.667 0.00 0.00 0.00 2.12
1621 1729 0.029834 GCGTGATTGGCCATCATCAC 59.970 55.000 29.34 29.34 44.11 3.06
1732 1840 0.391130 CAATTGAACTCTCGGGCGGA 60.391 55.000 0.00 0.00 0.00 5.54
1739 1848 6.645790 AATATCATGCCCAATTGAACTCTC 57.354 37.500 7.12 0.00 0.00 3.20
1758 1867 5.895534 ACAACATGCCATTGGAGAGAAATAT 59.104 36.000 6.95 0.00 0.00 1.28
1848 1957 8.700439 ACCAACATGTATGTAAAGGTTAAACT 57.300 30.769 0.00 0.00 40.80 2.66
1868 1978 4.584327 AACAAGGCAAGTTCATACCAAC 57.416 40.909 0.00 0.00 0.00 3.77
1870 1980 6.719370 AGAAATAACAAGGCAAGTTCATACCA 59.281 34.615 0.00 0.00 0.00 3.25
1915 2038 4.216687 CCGCCTTGTCAAATGTAAAGGTTA 59.783 41.667 14.16 0.00 41.11 2.85
1952 2075 9.378977 CCAAACACCACTATATTTGAACGCAGT 62.379 40.741 0.00 0.00 34.62 4.40
1958 2081 8.735315 CATGTACCAAACACCACTATATTTGAA 58.265 33.333 0.00 0.00 42.09 2.69
2011 2134 4.597079 GATACATAAATGCACACCGTTGG 58.403 43.478 0.00 0.00 0.00 3.77
2013 2136 3.936453 ACGATACATAAATGCACACCGTT 59.064 39.130 0.00 0.00 0.00 4.44
2094 2217 2.933834 GGTGGTGGGCTACTGGGT 60.934 66.667 0.00 0.00 0.00 4.51
2185 2308 1.532505 GCGATGTGTGTGCATGGATTC 60.533 52.381 0.00 0.00 0.00 2.52
2276 2401 6.149474 TGAGAAAGGTAGCTATTTCACTTTGC 59.851 38.462 17.81 1.40 37.78 3.68
2308 2433 1.298859 GGATGGTCTTGCGTGTGGTC 61.299 60.000 0.00 0.00 0.00 4.02
2418 2543 0.882927 TTACGCGGCAAGTTCAGCTT 60.883 50.000 12.47 0.00 38.08 3.74
2419 2544 0.673644 ATTACGCGGCAAGTTCAGCT 60.674 50.000 12.47 0.00 0.00 4.24
2426 2551 0.523335 GCAGGAAATTACGCGGCAAG 60.523 55.000 12.47 0.00 0.00 4.01
2433 2558 4.818534 ACATGCTATGCAGGAAATTACG 57.181 40.909 11.13 0.00 43.36 3.18
2472 2597 8.107095 TGGTAAGTTCAGCAGTTAAGGAATATT 58.893 33.333 0.00 0.00 0.00 1.28
2536 2661 4.700213 AGGTTCAGCGCTTACATGTAATTT 59.300 37.500 18.35 2.68 0.00 1.82
2537 2662 4.261801 AGGTTCAGCGCTTACATGTAATT 58.738 39.130 18.35 3.01 0.00 1.40
2597 2722 7.070821 ACGACATAGTATTGGAGGGAAATAACT 59.929 37.037 0.00 0.00 0.00 2.24
3264 3396 8.532186 AAATCAACATACCATGGTTATTAGCA 57.468 30.769 25.38 2.58 36.00 3.49
3360 3492 5.479306 GCGCTCTGTTTTCATCCCTATATA 58.521 41.667 0.00 0.00 0.00 0.86
3383 3515 0.732571 CACCCAATTCCATCCGTTCG 59.267 55.000 0.00 0.00 0.00 3.95
3384 3516 0.455815 GCACCCAATTCCATCCGTTC 59.544 55.000 0.00 0.00 0.00 3.95
3391 3523 1.367346 TCTGGTAGCACCCAATTCCA 58.633 50.000 0.00 0.00 37.50 3.53
3463 3600 9.739276 TTCTGGTAGTATCTGTTTCAAATTCAT 57.261 29.630 0.00 0.00 0.00 2.57
3464 3601 9.567776 TTTCTGGTAGTATCTGTTTCAAATTCA 57.432 29.630 0.00 0.00 0.00 2.57
3465 3602 9.827411 GTTTCTGGTAGTATCTGTTTCAAATTC 57.173 33.333 0.00 0.00 0.00 2.17
3467 3604 7.876068 TCGTTTCTGGTAGTATCTGTTTCAAAT 59.124 33.333 0.00 0.00 0.00 2.32
3486 3623 0.320374 TCCGCTCCATGTTCGTTTCT 59.680 50.000 0.00 0.00 0.00 2.52
3572 3709 4.846779 TGATTAAGTTTGTTGGTCTGCC 57.153 40.909 0.00 0.00 0.00 4.85
3576 3713 7.254852 TCAACAGTTGATTAAGTTTGTTGGTC 58.745 34.615 12.24 0.00 43.23 4.02
3595 3732 8.649841 CATATTGTTTTGTAGCCATTTCAACAG 58.350 33.333 0.00 0.00 0.00 3.16
3671 3808 8.008513 ACACACATACTTAACTAGACCCTATG 57.991 38.462 0.00 0.00 0.00 2.23
3697 3834 3.245300 TGTGAGGTCTGGCTTCTACTACT 60.245 47.826 0.00 0.00 0.00 2.57
3712 3849 1.269012 CAAAATGGCCCATGTGAGGT 58.731 50.000 0.00 0.00 0.00 3.85
3747 3884 3.851098 TGTAGCAAAACCACCAAACAAC 58.149 40.909 0.00 0.00 0.00 3.32
3761 3898 2.683742 GCCTATGGCTCCTTTGTAGCAA 60.684 50.000 0.73 0.00 46.69 3.91
3762 3899 1.134098 GCCTATGGCTCCTTTGTAGCA 60.134 52.381 0.73 0.00 46.69 3.49
3883 4020 2.702592 ACGGTGGTTTCAGACAGAAA 57.297 45.000 0.00 0.00 43.71 2.52
3940 4079 4.626604 CAGAAACTTGCAAAACAGAAGCAA 59.373 37.500 0.00 0.00 45.07 3.91
3942 4081 4.176271 ACAGAAACTTGCAAAACAGAAGC 58.824 39.130 0.00 0.00 0.00 3.86
3943 4082 6.183360 GGAAACAGAAACTTGCAAAACAGAAG 60.183 38.462 0.00 0.00 0.00 2.85
3944 4083 5.637387 GGAAACAGAAACTTGCAAAACAGAA 59.363 36.000 0.00 0.00 0.00 3.02
3945 4084 5.167845 GGAAACAGAAACTTGCAAAACAGA 58.832 37.500 0.00 0.00 0.00 3.41
3946 4085 4.928615 TGGAAACAGAAACTTGCAAAACAG 59.071 37.500 0.00 0.00 35.01 3.16
3947 4086 4.887748 TGGAAACAGAAACTTGCAAAACA 58.112 34.783 0.00 0.00 35.01 2.83
3985 4127 1.265905 CGGGAACTTTCTGGTTTTCCG 59.734 52.381 0.00 0.00 44.36 4.30
3986 4128 1.000607 GCGGGAACTTTCTGGTTTTCC 60.001 52.381 0.00 0.00 37.40 3.13
3994 4136 3.888930 TGAAAATGAAGCGGGAACTTTCT 59.111 39.130 0.00 0.00 0.00 2.52
4002 4144 1.767759 AGGGATGAAAATGAAGCGGG 58.232 50.000 0.00 0.00 0.00 6.13
4004 4146 6.808008 ATATGTAGGGATGAAAATGAAGCG 57.192 37.500 0.00 0.00 0.00 4.68
4115 4259 9.958234 GAGATAAAATCTTGCTTAAATTCCTCC 57.042 33.333 0.00 0.00 40.38 4.30
4180 4422 9.685276 CCCCATCACATAAAATGAGCTATATAA 57.315 33.333 0.00 0.00 0.00 0.98
4181 4423 8.835734 ACCCCATCACATAAAATGAGCTATATA 58.164 33.333 0.00 0.00 0.00 0.86
4202 4444 1.816074 GTCAACGCAGAAATACCCCA 58.184 50.000 0.00 0.00 0.00 4.96
4215 4457 4.625742 AGATGGAGATACAAAACGTCAACG 59.374 41.667 0.12 0.12 46.33 4.10
4231 4473 8.618702 AGAGCAAACATAAATATCAGATGGAG 57.381 34.615 0.00 0.00 0.00 3.86
4388 4633 0.747255 CCCACACCAGATAGACCTCG 59.253 60.000 0.00 0.00 0.00 4.63
4446 4691 4.932200 GGTCACCTGTAAGAATGAGAACAG 59.068 45.833 0.00 0.00 34.07 3.16
4448 4693 4.932200 CAGGTCACCTGTAAGAATGAGAAC 59.068 45.833 16.65 0.00 45.82 3.01
4477 4722 7.114754 ACACTTGTATCTGGATGATCAAACAT 58.885 34.615 0.00 0.00 36.65 2.71
4519 4764 8.560903 ACCTTCTTTCCTCCTACATAAATCAAT 58.439 33.333 0.00 0.00 0.00 2.57
4550 4795 1.990424 CACCTGGTACATGGGCAGA 59.010 57.895 0.00 0.00 38.20 4.26
4574 4819 4.262894 CCAGAACTTACCTGGCTAGTTTCA 60.263 45.833 13.31 0.00 43.93 2.69
4633 4879 2.672996 GGTGCCGCACTCCAATGT 60.673 61.111 22.41 0.00 34.40 2.71
4669 4915 9.071276 ACATTTATTTCTCTCTTTCAAAGCTCA 57.929 29.630 0.00 0.00 0.00 4.26
4717 4963 6.520272 CAGCTAGCTACTGAAGGAATACATT 58.480 40.000 18.86 0.00 37.32 2.71
4735 4981 2.101582 ACGGAGGAAAGTATGCAGCTAG 59.898 50.000 0.00 0.00 0.00 3.42
4737 4983 0.905357 ACGGAGGAAAGTATGCAGCT 59.095 50.000 0.00 0.00 0.00 4.24
4741 4987 4.759516 TTTCAAACGGAGGAAAGTATGC 57.240 40.909 0.00 0.00 0.00 3.14
4742 4988 8.040716 AGTATTTTCAAACGGAGGAAAGTATG 57.959 34.615 0.00 0.00 34.77 2.39
4743 4989 8.512138 CAAGTATTTTCAAACGGAGGAAAGTAT 58.488 33.333 0.00 0.00 34.77 2.12
4747 4993 5.828859 TCCAAGTATTTTCAAACGGAGGAAA 59.171 36.000 0.00 0.00 0.00 3.13
4802 5060 9.621629 TTTTTCTCTAGACTTGGTCAAACATAA 57.378 29.630 0.00 0.00 34.60 1.90
4833 5091 9.643693 TCATACTATAGTCGATGTATACGTTGA 57.356 33.333 9.12 10.51 0.00 3.18
4902 5160 9.533253 CAAACATCTTTAAATTTGACCAAGTCT 57.467 29.630 0.00 0.00 34.62 3.24
4903 5161 9.528018 TCAAACATCTTTAAATTTGACCAAGTC 57.472 29.630 9.56 0.00 36.42 3.01
4915 5173 9.974980 GTTTCCCATAAGTCAAACATCTTTAAA 57.025 29.630 0.00 0.00 0.00 1.52
4916 5174 8.581578 GGTTTCCCATAAGTCAAACATCTTTAA 58.418 33.333 0.00 0.00 31.52 1.52
4917 5175 7.177744 GGGTTTCCCATAAGTCAAACATCTTTA 59.822 37.037 0.00 0.00 44.65 1.85
4918 5176 6.014584 GGGTTTCCCATAAGTCAAACATCTTT 60.015 38.462 0.00 0.00 44.65 2.52
4919 5177 5.480422 GGGTTTCCCATAAGTCAAACATCTT 59.520 40.000 0.00 0.00 44.65 2.40
4920 5178 5.016831 GGGTTTCCCATAAGTCAAACATCT 58.983 41.667 0.00 0.00 44.65 2.90
4921 5179 5.324784 GGGTTTCCCATAAGTCAAACATC 57.675 43.478 0.00 0.00 44.65 3.06
4935 5193 2.945456 ACTCAAAGTTCTGGGTTTCCC 58.055 47.619 0.00 0.00 45.71 3.97
4936 5194 6.447162 CAAATACTCAAAGTTCTGGGTTTCC 58.553 40.000 0.00 0.00 30.79 3.13
4937 5195 6.264518 TCCAAATACTCAAAGTTCTGGGTTTC 59.735 38.462 0.00 0.00 30.79 2.78
4943 5201 7.930217 TCTGTTTCCAAATACTCAAAGTTCTG 58.070 34.615 0.00 0.00 0.00 3.02
4951 5209 5.014123 ACTCCCATCTGTTTCCAAATACTCA 59.986 40.000 0.00 0.00 0.00 3.41
4952 5210 5.501156 ACTCCCATCTGTTTCCAAATACTC 58.499 41.667 0.00 0.00 0.00 2.59
4966 5225 3.933886 ACCATCTCACATACTCCCATCT 58.066 45.455 0.00 0.00 0.00 2.90
5013 5272 4.371624 ACACCAAGGAGATGTCATGAAA 57.628 40.909 0.00 0.00 0.00 2.69
5056 5315 1.233950 TGCGCGAAATCAGCAGGAAA 61.234 50.000 12.10 0.00 35.81 3.13
5057 5316 1.670730 TGCGCGAAATCAGCAGGAA 60.671 52.632 12.10 0.00 35.81 3.36
5247 5511 4.147322 CCGCACGTGGTGAATCGC 62.147 66.667 18.88 0.00 35.23 4.58
5438 5702 5.890424 AGTTTCGAAACAAAGAAAGGTGA 57.110 34.783 35.29 0.00 41.30 4.02
5454 5718 4.776743 CTCATCTGTCCACAAAAGTTTCG 58.223 43.478 0.00 0.00 0.00 3.46
5556 5820 3.482786 GCATCAAGCTGTTTACTGAACG 58.517 45.455 0.00 0.00 41.29 3.95
5657 5922 8.512956 CAGTAGCTCAAGTCACTAACTAAGTAA 58.487 37.037 0.00 0.00 37.17 2.24
5674 5939 3.751479 TCTTTCAACTGCAGTAGCTCA 57.249 42.857 22.01 2.60 42.74 4.26
5789 6060 2.785713 TCGTCAGTCATTCGACAACA 57.214 45.000 0.00 0.00 45.23 3.33
5798 6069 7.751768 TGAAGATACTCATATCGTCAGTCAT 57.248 36.000 8.32 0.00 45.59 3.06
5878 6151 6.342906 TGGTGCTAACAACATATGGTACTAC 58.657 40.000 7.80 0.00 39.04 2.73
5902 6176 3.443681 ACGCTGCTGTAAGGCAAAATAAT 59.556 39.130 0.00 0.00 41.94 1.28
5904 6178 2.161410 CACGCTGCTGTAAGGCAAAATA 59.839 45.455 0.00 0.00 41.94 1.40
5915 6189 0.173481 ATACACGATCACGCTGCTGT 59.827 50.000 0.00 0.00 43.96 4.40
5917 6191 0.249073 GGATACACGATCACGCTGCT 60.249 55.000 0.00 0.00 43.96 4.24
5939 6213 3.699038 ACACCTCTTTTGCTTTGCTAACA 59.301 39.130 0.00 0.00 0.00 2.41
5941 6215 4.681744 CAACACCTCTTTTGCTTTGCTAA 58.318 39.130 0.00 0.00 0.00 3.09
5971 6246 4.333649 CGGAGAGAAGAATTGCATTTGCTA 59.666 41.667 3.94 0.00 42.66 3.49
5996 6285 9.495572 AAAGGTAAAGAGAAAAGATGAGTAGTG 57.504 33.333 0.00 0.00 0.00 2.74
6004 6293 6.565999 CGTTGCGAAAGGTAAAGAGAAAAGAT 60.566 38.462 0.00 0.00 0.00 2.40
6091 6380 6.480981 AGAAAGTTCAGATTTGTGGCAAATTG 59.519 34.615 8.27 8.59 0.00 2.32
6100 6389 6.489361 AGCATTCTCAGAAAGTTCAGATTTGT 59.511 34.615 0.00 0.00 0.00 2.83
6106 6395 6.252441 CGTACTAGCATTCTCAGAAAGTTCAG 59.748 42.308 0.00 0.00 0.00 3.02
6177 6471 2.877786 CAGCATCTGTGTGGTGTTGTAA 59.122 45.455 6.77 0.00 41.41 2.41
6185 6479 1.534163 CACAAGTCAGCATCTGTGTGG 59.466 52.381 7.67 0.00 32.61 4.17
6186 6480 2.032290 CACACAAGTCAGCATCTGTGTG 60.032 50.000 16.91 16.91 46.74 3.82
6245 6539 1.444933 TGGCTCCTTTTTCCTCCTCA 58.555 50.000 0.00 0.00 0.00 3.86
6267 6561 1.229209 TCCCTTCTCCAGCCGACTT 60.229 57.895 0.00 0.00 0.00 3.01
6268 6562 1.684049 CTCCCTTCTCCAGCCGACT 60.684 63.158 0.00 0.00 0.00 4.18
6269 6563 2.726351 CCTCCCTTCTCCAGCCGAC 61.726 68.421 0.00 0.00 0.00 4.79
6270 6564 2.364317 CCTCCCTTCTCCAGCCGA 60.364 66.667 0.00 0.00 0.00 5.54
6271 6565 2.364317 TCCTCCCTTCTCCAGCCG 60.364 66.667 0.00 0.00 0.00 5.52
6272 6566 2.069430 CCTCCTCCCTTCTCCAGCC 61.069 68.421 0.00 0.00 0.00 4.85
6273 6567 0.399806 ATCCTCCTCCCTTCTCCAGC 60.400 60.000 0.00 0.00 0.00 4.85
6274 6568 1.715785 GATCCTCCTCCCTTCTCCAG 58.284 60.000 0.00 0.00 0.00 3.86
6275 6569 0.266152 GGATCCTCCTCCCTTCTCCA 59.734 60.000 3.84 0.00 32.53 3.86
6276 6570 0.565674 AGGATCCTCCTCCCTTCTCC 59.434 60.000 9.02 0.00 45.66 3.71
6297 6591 0.254178 GCTGCCCAGAGAGAAATGGA 59.746 55.000 0.00 0.00 39.02 3.41
6300 6594 0.394080 GCTGCTGCCCAGAGAGAAAT 60.394 55.000 3.85 0.00 44.64 2.17
6301 6595 1.002868 GCTGCTGCCCAGAGAGAAA 60.003 57.895 3.85 0.00 44.64 2.52
6380 6681 3.644738 AGGCATGGAAATGATTGGATTCC 59.355 43.478 0.00 0.00 42.39 3.01
6426 6739 3.371285 GGGACGATTGAGCTTTAGTGTTC 59.629 47.826 0.00 0.00 0.00 3.18
6441 6754 4.466370 TGAAGTGAAATAGTGAGGGACGAT 59.534 41.667 0.00 0.00 0.00 3.73
6477 6790 1.353076 GCAAATGCAGCAAAGCTACC 58.647 50.000 0.00 0.00 36.40 3.18


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

AutoCloner maintained by Alex Coulton.