Multiple sequence alignment - TraesCS3A01G081300

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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 TraesCS3A01G081300 chr3A 100.000 2604 0 0 1 2604 52557372 52554769 0.000000e+00 4809
1 TraesCS3A01G081300 chr3A 91.542 201 11 6 2298 2493 594949921 594949722 3.300000e-69 272
2 TraesCS3A01G081300 chr3B 86.480 2145 165 68 1 2070 64507588 64509682 0.000000e+00 2239
3 TraesCS3A01G081300 chr3B 89.765 850 61 17 910 1749 64416685 64415852 0.000000e+00 1064
4 TraesCS3A01G081300 chr3B 83.442 308 26 10 2298 2604 554585828 554585545 1.990000e-66 263
5 TraesCS3A01G081300 chr3B 88.532 218 18 7 1817 2032 64415047 64414835 9.250000e-65 257
6 TraesCS3A01G081300 chr3B 95.455 132 3 1 2097 2225 64510042 64510173 9.440000e-50 207
7 TraesCS3A01G081300 chr3B 93.333 135 5 2 2097 2228 64596685 64596818 2.040000e-46 196
8 TraesCS3A01G081300 chr3B 95.413 109 5 0 806 914 64422293 64422185 9.580000e-40 174
9 TraesCS3A01G081300 chr3B 90.000 140 3 2 2097 2225 64414486 64414347 1.240000e-38 171
10 TraesCS3A01G081300 chr3D 86.282 1108 86 35 562 1651 40787468 40786409 0.000000e+00 1144
11 TraesCS3A01G081300 chr3D 94.527 402 22 0 49 450 40787985 40787584 2.850000e-174 621
12 TraesCS3A01G081300 chr3D 94.521 73 4 0 477 549 40787583 40787511 2.120000e-21 113
13 TraesCS3A01G081300 chr5A 92.834 307 19 2 2298 2604 15115208 15115511 2.380000e-120 442
14 TraesCS3A01G081300 chr1B 89.610 308 25 4 2298 2604 577960818 577961119 4.070000e-103 385
15 TraesCS3A01G081300 chr1B 87.838 222 21 5 2298 2514 10536368 10536148 3.330000e-64 255
16 TraesCS3A01G081300 chr2D 86.364 308 20 10 2298 2604 181314959 181315245 1.500000e-82 316
17 TraesCS3A01G081300 chr1D 85.714 308 22 10 2298 2604 487098579 487098293 3.260000e-79 305
18 TraesCS3A01G081300 chr6A 86.909 275 27 8 2298 2569 94186992 94186724 1.510000e-77 300
19 TraesCS3A01G081300 chr7A 84.740 308 25 10 2298 2604 180345505 180345791 3.280000e-74 289
20 TraesCS3A01G081300 chr2A 90.686 204 13 6 2298 2496 52201609 52201407 1.540000e-67 267


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 TraesCS3A01G081300 chr3A 52554769 52557372 2603 True 4809.000000 4809 100.000000 1 2604 1 chr3A.!!$R1 2603
1 TraesCS3A01G081300 chr3B 64507588 64510173 2585 False 1223.000000 2239 90.967500 1 2225 2 chr3B.!!$F2 2224
2 TraesCS3A01G081300 chr3B 64414347 64416685 2338 True 497.333333 1064 89.432333 910 2225 3 chr3B.!!$R3 1315
3 TraesCS3A01G081300 chr3D 40786409 40787985 1576 True 626.000000 1144 91.776667 49 1651 3 chr3D.!!$R1 1602

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
455 469 0.111253 CCTGGCTGTATGGGGATTCC 59.889 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 3637 0.166814 GTGGTGCAGCGAAAGACATC 59.833 55.0 11.91 0.0 0.0 3.06 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
35 36 2.978156 ACCAATCAACCTCCACACAT 57.022 45.000 0.00 0.00 0.00 3.21
37 38 2.108075 ACCAATCAACCTCCACACATGA 59.892 45.455 0.00 0.00 0.00 3.07
39 40 3.057315 CCAATCAACCTCCACACATGAAC 60.057 47.826 0.00 0.00 0.00 3.18
70 71 6.981722 AGTTAACATGCTAGGAAAAAGTTGG 58.018 36.000 8.61 0.00 0.00 3.77
75 76 5.183904 ACATGCTAGGAAAAAGTTGGATGAC 59.816 40.000 0.00 0.00 0.00 3.06
82 83 6.314917 AGGAAAAAGTTGGATGACTTGGTAT 58.685 36.000 0.00 0.00 39.68 2.73
164 165 1.066430 TGACCGATGACTAAGCAACCC 60.066 52.381 0.00 0.00 0.00 4.11
165 166 0.252197 ACCGATGACTAAGCAACCCC 59.748 55.000 0.00 0.00 0.00 4.95
291 305 1.066645 AGTATTTCCCGACCGTGTTCC 60.067 52.381 0.00 0.00 0.00 3.62
292 306 0.975135 TATTTCCCGACCGTGTTCCA 59.025 50.000 0.00 0.00 0.00 3.53
312 326 5.790593 TCCAAGTGTTACTACCTCATTGTC 58.209 41.667 0.00 0.00 0.00 3.18
346 360 4.737054 AGAAGTCTTTGTGTTTGCACTTG 58.263 39.130 0.00 0.00 45.44 3.16
363 377 4.022849 GCACTTGAACAATCCTTGTAAGCT 60.023 41.667 0.00 0.00 44.59 3.74
384 398 4.274459 GCTATTTCTTGATGGTACTGCCTG 59.726 45.833 0.00 0.00 38.35 4.85
450 464 1.905215 CTCTATCCTGGCTGTATGGGG 59.095 57.143 0.00 0.00 0.00 4.96
455 469 0.111253 CCTGGCTGTATGGGGATTCC 59.889 60.000 0.00 0.00 0.00 3.01
469 483 1.395608 GGATTCCGAATTTGCGACGAA 59.604 47.619 0.00 0.00 0.00 3.85
508 522 4.695217 TCGTTCATTATTTTCTGGTGGC 57.305 40.909 0.00 0.00 0.00 5.01
509 523 4.075682 TCGTTCATTATTTTCTGGTGGCA 58.924 39.130 0.00 0.00 0.00 4.92
528 542 4.344865 TTCCTGTTCGGGGCAGCC 62.345 66.667 1.26 1.26 32.93 4.85
557 575 5.423610 ACTCTCATCATAGTTAGTTGCCAGT 59.576 40.000 0.00 0.00 0.00 4.00
558 576 5.664457 TCTCATCATAGTTAGTTGCCAGTG 58.336 41.667 0.00 0.00 0.00 3.66
559 577 4.191544 TCATCATAGTTAGTTGCCAGTGC 58.808 43.478 0.00 0.00 38.26 4.40
600 648 8.519526 CAGTAGGTTTCTTATTGGTTGCAATAA 58.480 33.333 0.59 1.59 36.14 1.40
601 649 9.084533 AGTAGGTTTCTTATTGGTTGCAATAAA 57.915 29.630 0.59 0.19 36.81 1.40
607 655 9.912634 TTTCTTATTGGTTGCAATAAAGAGAAG 57.087 29.630 0.59 6.21 36.81 2.85
618 666 9.448438 TTGCAATAAAGAGAAGATAAGTTGCTA 57.552 29.630 0.00 0.00 39.88 3.49
645 693 9.883142 AAAAACAATGGTAGATTTCTCAAACAA 57.117 25.926 0.00 0.00 0.00 2.83
658 706 9.617975 GATTTCTCAAACAAAAACTGGAGATAG 57.382 33.333 0.00 0.00 32.08 2.08
659 707 7.510549 TTCTCAAACAAAAACTGGAGATAGG 57.489 36.000 0.00 0.00 32.08 2.57
665 713 5.316987 ACAAAAACTGGAGATAGGAACAGG 58.683 41.667 0.00 0.00 35.34 4.00
676 724 0.193574 AGGAACAGGGGTCAGAAGGA 59.806 55.000 0.00 0.00 0.00 3.36
863 918 1.006813 ATGGCCCCACTGTTATCCAA 58.993 50.000 0.00 0.00 0.00 3.53
882 937 2.945008 CAAACAGGACACACTCACACAT 59.055 45.455 0.00 0.00 0.00 3.21
906 961 3.407424 TGGCAGTATATAAGCAGGCAG 57.593 47.619 9.78 0.00 0.00 4.85
994 1063 6.496565 AGATAGACAGGATCAGATTAACCAGG 59.503 42.308 0.00 0.00 0.00 4.45
1184 1260 1.991264 CGTCTCGTACGTTCTCTCTCA 59.009 52.381 16.05 0.00 46.72 3.27
1186 1262 2.094099 GTCTCGTACGTTCTCTCTCACC 59.906 54.545 16.05 0.00 0.00 4.02
1197 1273 0.252284 TCTCTCACCCCTCCTTGGTC 60.252 60.000 0.00 0.00 32.46 4.02
1213 1299 1.002430 TGGTCAGTCACTGATTGAGCC 59.998 52.381 23.40 17.55 43.01 4.70
1220 1306 0.035725 CACTGATTGAGCCTGAGCCA 60.036 55.000 0.00 0.00 41.25 4.75
1260 1348 1.280710 TCTGGTGGTTGCCATATCGTT 59.719 47.619 0.00 0.00 37.96 3.85
1433 1524 1.224965 GAGTACCTAGCCTACGACGG 58.775 60.000 0.00 0.00 0.00 4.79
1455 1546 2.506444 CCAAAAACGTAACCCTGCCTA 58.494 47.619 0.00 0.00 0.00 3.93
1458 1549 3.428413 AAAACGTAACCCTGCCTACAT 57.572 42.857 0.00 0.00 0.00 2.29
1459 1550 2.396590 AACGTAACCCTGCCTACATG 57.603 50.000 0.00 0.00 0.00 3.21
1470 1561 7.995052 ACCCTGCCTACATGATCATATTATA 57.005 36.000 8.15 0.00 0.00 0.98
1471 1562 8.572884 ACCCTGCCTACATGATCATATTATAT 57.427 34.615 8.15 0.00 0.00 0.86
1472 1563 9.674705 ACCCTGCCTACATGATCATATTATATA 57.325 33.333 8.15 0.00 0.00 0.86
1484 1575 9.657419 TGATCATATTATATAGTTGTGGCACTG 57.343 33.333 19.83 3.79 0.00 3.66
1497 1596 0.250295 GGCACTGCACCTGTCACTAA 60.250 55.000 2.82 0.00 0.00 2.24
1498 1597 1.611673 GGCACTGCACCTGTCACTAAT 60.612 52.381 2.82 0.00 0.00 1.73
1501 1600 3.125316 GCACTGCACCTGTCACTAATAAC 59.875 47.826 0.00 0.00 0.00 1.89
1502 1601 4.569943 CACTGCACCTGTCACTAATAACT 58.430 43.478 0.00 0.00 0.00 2.24
1509 1608 6.872020 GCACCTGTCACTAATAACTGAAACTA 59.128 38.462 0.00 0.00 0.00 2.24
1522 1624 4.579869 ACTGAAACTATGTGTGGATGGAC 58.420 43.478 0.00 0.00 0.00 4.02
1609 1711 2.433436 CAAACCACCAAGTAGCTACCC 58.567 52.381 20.31 0.00 0.00 3.69
1671 1781 0.318784 GCAGGGGTCGATCGATGTAC 60.319 60.000 22.50 8.68 0.00 2.90
1720 1836 1.611977 TGCTACGCTGTCTGTACTGTT 59.388 47.619 0.00 0.00 0.00 3.16
1743 1859 3.563508 TGCACATAAACGAAATGCAGTG 58.436 40.909 0.00 0.00 41.18 3.66
1776 1892 7.437267 TCGTTCGTCTTAAATTCTTATGATCCC 59.563 37.037 0.00 0.00 0.00 3.85
1786 1902 6.581388 ATTCTTATGATCCCTCTGTTCCAA 57.419 37.500 0.00 0.00 0.00 3.53
1889 2741 3.125316 GTGAGATAGTTGAGGCGGTTTTG 59.875 47.826 0.00 0.00 0.00 2.44
1892 2744 4.003648 AGATAGTTGAGGCGGTTTTGAAG 58.996 43.478 0.00 0.00 0.00 3.02
1962 2815 3.200593 CCGGTCGATCGAGTCCGT 61.201 66.667 32.38 0.00 41.17 4.69
1963 2816 1.884464 CCGGTCGATCGAGTCCGTA 60.884 63.158 32.38 6.39 41.17 4.02
2014 2867 9.091220 GTCCATCCTATTCTACCTACAAATACT 57.909 37.037 0.00 0.00 0.00 2.12
2055 2909 1.829222 CTTCCTGCCCAGCAAATCAAT 59.171 47.619 0.00 0.00 38.41 2.57
2063 2917 3.666274 CCCAGCAAATCAATCAAGCAAA 58.334 40.909 0.00 0.00 0.00 3.68
2095 2982 1.478137 AACTAGAACGCGATCGATGC 58.522 50.000 21.57 4.26 39.41 3.91
2141 3336 0.899720 TACAAGCTCAAGTACCCGGG 59.100 55.000 22.25 22.25 0.00 5.73
2206 3404 0.102663 GCAGTACGGCTTCTACTCCC 59.897 60.000 10.99 0.00 0.00 4.30
2214 3412 1.517257 CTTCTACTCCCAGTGCGCG 60.517 63.158 0.00 0.00 0.00 6.86
2262 3460 2.585247 GGCACGTCCCGAGCATAC 60.585 66.667 8.21 0.00 44.45 2.39
2263 3461 2.183300 GCACGTCCCGAGCATACA 59.817 61.111 1.28 0.00 42.44 2.29
2264 3462 1.447140 GCACGTCCCGAGCATACAA 60.447 57.895 1.28 0.00 42.44 2.41
2265 3463 1.421410 GCACGTCCCGAGCATACAAG 61.421 60.000 1.28 0.00 42.44 3.16
2266 3464 1.153628 ACGTCCCGAGCATACAAGC 60.154 57.895 0.00 0.00 0.00 4.01
2275 3473 2.990066 AGCATACAAGCTCAGGTACC 57.010 50.000 2.73 2.73 42.18 3.34
2276 3474 1.486726 AGCATACAAGCTCAGGTACCC 59.513 52.381 8.74 0.00 42.18 3.69
2277 3475 1.806623 GCATACAAGCTCAGGTACCCG 60.807 57.143 8.74 0.00 0.00 5.28
2278 3476 1.120530 ATACAAGCTCAGGTACCCGG 58.879 55.000 8.74 0.85 0.00 5.73
2279 3477 0.040058 TACAAGCTCAGGTACCCGGA 59.960 55.000 8.74 5.96 0.00 5.14
2280 3478 1.258445 ACAAGCTCAGGTACCCGGAG 61.258 60.000 21.37 21.37 46.09 4.63
2281 3479 0.970937 CAAGCTCAGGTACCCGGAGA 60.971 60.000 27.12 12.81 46.21 3.71
2282 3480 0.684805 AAGCTCAGGTACCCGGAGAG 60.685 60.000 27.12 20.46 46.21 3.20
2283 3481 2.128507 GCTCAGGTACCCGGAGAGG 61.129 68.421 27.12 9.17 46.21 3.69
2284 3482 2.043248 TCAGGTACCCGGAGAGGC 60.043 66.667 8.74 0.00 39.21 4.70
2285 3483 2.042843 CAGGTACCCGGAGAGGCT 60.043 66.667 8.74 0.00 39.21 4.58
2286 3484 2.128507 CAGGTACCCGGAGAGGCTC 61.129 68.421 8.74 6.34 39.21 4.70
2287 3485 2.279408 GGTACCCGGAGAGGCTCT 59.721 66.667 18.80 18.80 39.21 4.09
2288 3486 2.128507 GGTACCCGGAGAGGCTCTG 61.129 68.421 24.21 10.04 39.21 3.35
2293 3491 2.837291 CGGAGAGGCTCTGGGAGG 60.837 72.222 24.21 2.10 33.57 4.30
2294 3492 2.693017 GGAGAGGCTCTGGGAGGA 59.307 66.667 24.21 0.00 0.00 3.71
2295 3493 1.002274 GGAGAGGCTCTGGGAGGAA 59.998 63.158 24.21 0.00 0.00 3.36
2296 3494 1.334384 GGAGAGGCTCTGGGAGGAAC 61.334 65.000 24.21 4.26 0.00 3.62
2297 3495 1.671901 GAGAGGCTCTGGGAGGAACG 61.672 65.000 24.21 0.00 0.00 3.95
2298 3496 1.985116 GAGGCTCTGGGAGGAACGT 60.985 63.158 7.40 0.00 0.00 3.99
2299 3497 1.536662 AGGCTCTGGGAGGAACGTT 60.537 57.895 0.00 0.00 0.00 3.99
2300 3498 0.252103 AGGCTCTGGGAGGAACGTTA 60.252 55.000 0.00 0.00 0.00 3.18
2301 3499 0.175989 GGCTCTGGGAGGAACGTTAG 59.824 60.000 0.00 0.00 0.00 2.34
2302 3500 1.183549 GCTCTGGGAGGAACGTTAGA 58.816 55.000 0.00 0.00 0.00 2.10
2303 3501 1.135053 GCTCTGGGAGGAACGTTAGAC 60.135 57.143 0.00 0.00 0.00 2.59
2304 3502 2.448453 CTCTGGGAGGAACGTTAGACT 58.552 52.381 0.00 0.00 0.00 3.24
2305 3503 2.164624 CTCTGGGAGGAACGTTAGACTG 59.835 54.545 0.00 0.00 0.00 3.51
2306 3504 1.893801 CTGGGAGGAACGTTAGACTGT 59.106 52.381 0.00 0.00 0.00 3.55
2307 3505 3.087031 CTGGGAGGAACGTTAGACTGTA 58.913 50.000 0.00 0.00 0.00 2.74
2308 3506 3.700038 CTGGGAGGAACGTTAGACTGTAT 59.300 47.826 0.00 0.00 0.00 2.29
2309 3507 4.858850 TGGGAGGAACGTTAGACTGTATA 58.141 43.478 0.00 0.00 0.00 1.47
2310 3508 5.452255 TGGGAGGAACGTTAGACTGTATAT 58.548 41.667 0.00 0.00 0.00 0.86
2311 3509 6.604171 TGGGAGGAACGTTAGACTGTATATA 58.396 40.000 0.00 0.00 0.00 0.86
2312 3510 6.488006 TGGGAGGAACGTTAGACTGTATATAC 59.512 42.308 0.00 5.89 0.00 1.47
2313 3511 6.348050 GGGAGGAACGTTAGACTGTATATACG 60.348 46.154 0.00 12.26 35.34 3.06
2314 3512 6.203723 GGAGGAACGTTAGACTGTATATACGT 59.796 42.308 0.00 13.15 43.17 3.57
2315 3513 7.385205 GGAGGAACGTTAGACTGTATATACGTA 59.615 40.741 16.75 0.00 40.82 3.57
2316 3514 8.304202 AGGAACGTTAGACTGTATATACGTAG 57.696 38.462 16.75 3.84 40.82 3.51
2318 3516 8.217778 GGAACGTTAGACTGTATATACGTAGTC 58.782 40.741 18.92 18.92 43.93 2.59
2320 3518 8.879342 ACGTTAGACTGTATATACGTAGTCTT 57.121 34.615 27.75 17.71 45.48 3.01
2321 3519 8.759641 ACGTTAGACTGTATATACGTAGTCTTG 58.240 37.037 27.75 21.99 45.48 3.02
2322 3520 8.759641 CGTTAGACTGTATATACGTAGTCTTGT 58.240 37.037 27.75 14.96 45.48 3.16
2329 3527 9.932699 CTGTATATACGTAGTCTTGTATATGCC 57.067 37.037 18.64 13.02 43.93 4.40
2330 3528 9.676861 TGTATATACGTAGTCTTGTATATGCCT 57.323 33.333 18.64 5.24 43.93 4.75
2333 3531 5.593679 ACGTAGTCTTGTATATGCCTTGT 57.406 39.130 0.00 0.00 29.74 3.16
2334 3532 6.704289 ACGTAGTCTTGTATATGCCTTGTA 57.296 37.500 0.00 0.00 29.74 2.41
2335 3533 7.286215 ACGTAGTCTTGTATATGCCTTGTAT 57.714 36.000 0.00 0.00 29.74 2.29
2336 3534 7.723324 ACGTAGTCTTGTATATGCCTTGTATT 58.277 34.615 0.00 0.00 29.74 1.89
2337 3535 7.652105 ACGTAGTCTTGTATATGCCTTGTATTG 59.348 37.037 0.00 0.00 29.74 1.90
2338 3536 7.652105 CGTAGTCTTGTATATGCCTTGTATTGT 59.348 37.037 0.00 0.00 0.00 2.71
2339 3537 9.976511 GTAGTCTTGTATATGCCTTGTATTGTA 57.023 33.333 0.00 0.00 0.00 2.41
2341 3539 9.712305 AGTCTTGTATATGCCTTGTATTGTATC 57.288 33.333 0.00 0.00 0.00 2.24
2342 3540 9.712305 GTCTTGTATATGCCTTGTATTGTATCT 57.288 33.333 0.00 0.00 0.00 1.98
2343 3541 9.929180 TCTTGTATATGCCTTGTATTGTATCTC 57.071 33.333 0.00 0.00 0.00 2.75
2344 3542 9.935241 CTTGTATATGCCTTGTATTGTATCTCT 57.065 33.333 0.00 0.00 0.00 3.10
2346 3544 9.710900 TGTATATGCCTTGTATTGTATCTCTTG 57.289 33.333 0.00 0.00 0.00 3.02
2347 3545 9.155975 GTATATGCCTTGTATTGTATCTCTTGG 57.844 37.037 0.00 0.00 0.00 3.61
2348 3546 5.435686 TGCCTTGTATTGTATCTCTTGGT 57.564 39.130 0.00 0.00 0.00 3.67
2349 3547 6.553953 TGCCTTGTATTGTATCTCTTGGTA 57.446 37.500 0.00 0.00 0.00 3.25
2350 3548 6.346096 TGCCTTGTATTGTATCTCTTGGTAC 58.654 40.000 0.00 0.00 0.00 3.34
2351 3549 5.462398 GCCTTGTATTGTATCTCTTGGTACG 59.538 44.000 0.00 0.00 0.00 3.67
2352 3550 6.570692 CCTTGTATTGTATCTCTTGGTACGT 58.429 40.000 0.00 0.00 0.00 3.57
2353 3551 6.696148 CCTTGTATTGTATCTCTTGGTACGTC 59.304 42.308 0.00 0.00 0.00 4.34
2354 3552 7.400599 TTGTATTGTATCTCTTGGTACGTCT 57.599 36.000 0.00 0.00 0.00 4.18
2355 3553 8.510243 TTGTATTGTATCTCTTGGTACGTCTA 57.490 34.615 0.00 0.00 0.00 2.59
2356 3554 8.687292 TGTATTGTATCTCTTGGTACGTCTAT 57.313 34.615 0.00 0.00 0.00 1.98
2357 3555 9.783081 TGTATTGTATCTCTTGGTACGTCTATA 57.217 33.333 0.00 0.00 0.00 1.31
2365 3563 9.961264 ATCTCTTGGTACGTCTATATAATGAGA 57.039 33.333 0.00 0.00 0.00 3.27
2366 3564 9.961264 TCTCTTGGTACGTCTATATAATGAGAT 57.039 33.333 0.00 0.00 0.00 2.75
2375 3573 9.727859 ACGTCTATATAATGAGATAGTCACACT 57.272 33.333 0.00 0.00 38.28 3.55
2384 3582 8.954950 AATGAGATAGTCACACTCCATTTAAG 57.045 34.615 0.00 0.00 38.28 1.85
2385 3583 6.878317 TGAGATAGTCACACTCCATTTAAGG 58.122 40.000 0.00 0.00 0.00 2.69
2386 3584 6.440647 TGAGATAGTCACACTCCATTTAAGGT 59.559 38.462 0.00 0.00 0.00 3.50
2387 3585 6.644347 AGATAGTCACACTCCATTTAAGGTG 58.356 40.000 0.00 0.00 35.99 4.00
2388 3586 4.706842 AGTCACACTCCATTTAAGGTGT 57.293 40.909 0.00 0.00 42.60 4.16
2389 3587 4.642429 AGTCACACTCCATTTAAGGTGTC 58.358 43.478 0.00 0.00 40.34 3.67
2390 3588 3.432252 GTCACACTCCATTTAAGGTGTCG 59.568 47.826 0.00 0.00 40.34 4.35
2391 3589 3.322541 TCACACTCCATTTAAGGTGTCGA 59.677 43.478 0.00 0.00 40.34 4.20
2392 3590 3.679980 CACACTCCATTTAAGGTGTCGAG 59.320 47.826 0.00 0.00 40.34 4.04
2393 3591 2.673368 CACTCCATTTAAGGTGTCGAGC 59.327 50.000 0.00 0.00 33.37 5.03
2394 3592 2.280628 CTCCATTTAAGGTGTCGAGCC 58.719 52.381 0.00 0.00 0.00 4.70
2395 3593 1.626321 TCCATTTAAGGTGTCGAGCCA 59.374 47.619 8.46 0.00 0.00 4.75
2396 3594 2.009774 CCATTTAAGGTGTCGAGCCAG 58.990 52.381 8.46 0.00 0.00 4.85
2397 3595 2.615493 CCATTTAAGGTGTCGAGCCAGT 60.615 50.000 8.46 0.00 0.00 4.00
2398 3596 2.922740 TTTAAGGTGTCGAGCCAGTT 57.077 45.000 8.46 0.00 0.00 3.16
2399 3597 2.922740 TTAAGGTGTCGAGCCAGTTT 57.077 45.000 8.46 0.00 0.00 2.66
2400 3598 2.450609 TAAGGTGTCGAGCCAGTTTC 57.549 50.000 8.46 0.00 0.00 2.78
2401 3599 0.250338 AAGGTGTCGAGCCAGTTTCC 60.250 55.000 8.46 0.00 0.00 3.13
2402 3600 1.671379 GGTGTCGAGCCAGTTTCCC 60.671 63.158 1.39 0.00 0.00 3.97
2403 3601 1.070786 GTGTCGAGCCAGTTTCCCA 59.929 57.895 0.00 0.00 0.00 4.37
2404 3602 0.534203 GTGTCGAGCCAGTTTCCCAA 60.534 55.000 0.00 0.00 0.00 4.12
2405 3603 0.181587 TGTCGAGCCAGTTTCCCAAA 59.818 50.000 0.00 0.00 0.00 3.28
2406 3604 0.591659 GTCGAGCCAGTTTCCCAAAC 59.408 55.000 0.00 0.00 41.69 2.93
2407 3605 0.536460 TCGAGCCAGTTTCCCAAACC 60.536 55.000 0.00 0.00 42.34 3.27
2408 3606 1.524008 CGAGCCAGTTTCCCAAACCC 61.524 60.000 0.00 0.00 42.34 4.11
2409 3607 0.178961 GAGCCAGTTTCCCAAACCCT 60.179 55.000 0.00 0.00 42.34 4.34
2410 3608 1.074889 GAGCCAGTTTCCCAAACCCTA 59.925 52.381 0.00 0.00 42.34 3.53
2411 3609 1.716503 AGCCAGTTTCCCAAACCCTAT 59.283 47.619 0.00 0.00 42.34 2.57
2412 3610 2.923629 AGCCAGTTTCCCAAACCCTATA 59.076 45.455 0.00 0.00 42.34 1.31
2413 3611 3.531814 AGCCAGTTTCCCAAACCCTATAT 59.468 43.478 0.00 0.00 42.34 0.86
2414 3612 4.016572 AGCCAGTTTCCCAAACCCTATATT 60.017 41.667 0.00 0.00 42.34 1.28
2415 3613 4.714802 GCCAGTTTCCCAAACCCTATATTT 59.285 41.667 0.00 0.00 42.34 1.40
2416 3614 5.188948 GCCAGTTTCCCAAACCCTATATTTT 59.811 40.000 0.00 0.00 42.34 1.82
2417 3615 6.381707 GCCAGTTTCCCAAACCCTATATTTTA 59.618 38.462 0.00 0.00 42.34 1.52
2418 3616 7.632028 GCCAGTTTCCCAAACCCTATATTTTAC 60.632 40.741 0.00 0.00 42.34 2.01
2419 3617 7.397761 CCAGTTTCCCAAACCCTATATTTTACA 59.602 37.037 0.00 0.00 42.34 2.41
2420 3618 8.977412 CAGTTTCCCAAACCCTATATTTTACAT 58.023 33.333 0.00 0.00 42.34 2.29
2421 3619 8.977412 AGTTTCCCAAACCCTATATTTTACATG 58.023 33.333 0.00 0.00 42.34 3.21
2422 3620 7.906199 TTCCCAAACCCTATATTTTACATGG 57.094 36.000 0.00 0.00 0.00 3.66
2423 3621 6.987557 TCCCAAACCCTATATTTTACATGGT 58.012 36.000 0.00 0.00 0.00 3.55
2424 3622 8.115490 TCCCAAACCCTATATTTTACATGGTA 57.885 34.615 0.00 0.00 0.00 3.25
2425 3623 8.738592 TCCCAAACCCTATATTTTACATGGTAT 58.261 33.333 0.00 0.00 0.00 2.73
2426 3624 9.020731 CCCAAACCCTATATTTTACATGGTATC 57.979 37.037 0.00 0.00 0.00 2.24
2427 3625 9.581289 CCAAACCCTATATTTTACATGGTATCA 57.419 33.333 0.00 0.00 0.00 2.15
2439 3637 8.706492 TTTACATGGTATCAGTTTAGGTTACG 57.294 34.615 0.00 0.00 0.00 3.18
2440 3638 6.534475 ACATGGTATCAGTTTAGGTTACGA 57.466 37.500 0.00 0.00 0.00 3.43
2441 3639 7.120923 ACATGGTATCAGTTTAGGTTACGAT 57.879 36.000 0.00 0.00 0.00 3.73
2442 3640 6.984474 ACATGGTATCAGTTTAGGTTACGATG 59.016 38.462 0.00 0.00 36.02 3.84
2443 3641 6.534475 TGGTATCAGTTTAGGTTACGATGT 57.466 37.500 0.00 0.00 0.00 3.06
2444 3642 6.567050 TGGTATCAGTTTAGGTTACGATGTC 58.433 40.000 0.00 0.00 0.00 3.06
2445 3643 6.379133 TGGTATCAGTTTAGGTTACGATGTCT 59.621 38.462 0.00 0.00 0.00 3.41
2446 3644 7.093640 TGGTATCAGTTTAGGTTACGATGTCTT 60.094 37.037 0.00 0.00 0.00 3.01
2447 3645 7.763071 GGTATCAGTTTAGGTTACGATGTCTTT 59.237 37.037 0.00 0.00 0.00 2.52
2448 3646 7.829378 ATCAGTTTAGGTTACGATGTCTTTC 57.171 36.000 0.00 0.00 0.00 2.62
2449 3647 5.860182 TCAGTTTAGGTTACGATGTCTTTCG 59.140 40.000 0.00 0.00 44.56 3.46
2450 3648 4.624452 AGTTTAGGTTACGATGTCTTTCGC 59.376 41.667 0.00 0.00 42.82 4.70
2451 3649 4.445452 TTAGGTTACGATGTCTTTCGCT 57.555 40.909 0.00 0.00 42.82 4.93
2452 3650 2.607187 AGGTTACGATGTCTTTCGCTG 58.393 47.619 0.00 0.00 42.82 5.18
2453 3651 1.060698 GGTTACGATGTCTTTCGCTGC 59.939 52.381 0.00 0.00 42.82 5.25
2454 3652 1.724623 GTTACGATGTCTTTCGCTGCA 59.275 47.619 0.00 0.00 42.82 4.41
2455 3653 1.346365 TACGATGTCTTTCGCTGCAC 58.654 50.000 0.00 0.00 42.82 4.57
2456 3654 1.291877 ACGATGTCTTTCGCTGCACC 61.292 55.000 0.00 0.00 42.82 5.01
2457 3655 1.291184 CGATGTCTTTCGCTGCACCA 61.291 55.000 0.00 0.00 31.60 4.17
2458 3656 0.166814 GATGTCTTTCGCTGCACCAC 59.833 55.000 0.00 0.00 0.00 4.16
2459 3657 1.237285 ATGTCTTTCGCTGCACCACC 61.237 55.000 0.00 0.00 0.00 4.61
2460 3658 1.598130 GTCTTTCGCTGCACCACCT 60.598 57.895 0.00 0.00 0.00 4.00
2461 3659 1.301716 TCTTTCGCTGCACCACCTC 60.302 57.895 0.00 0.00 0.00 3.85
2462 3660 2.281484 TTTCGCTGCACCACCTCC 60.281 61.111 0.00 0.00 0.00 4.30
2463 3661 3.113514 TTTCGCTGCACCACCTCCA 62.114 57.895 0.00 0.00 0.00 3.86
2464 3662 3.535629 TTCGCTGCACCACCTCCAG 62.536 63.158 0.00 0.00 0.00 3.86
2530 3728 4.845580 CTGCTGCACCGGCCCTAG 62.846 72.222 0.00 0.00 40.13 3.02
2541 3739 2.336809 GCCCTAGCCTCGATGTCG 59.663 66.667 0.00 0.00 41.45 4.35
2542 3740 2.336809 CCCTAGCCTCGATGTCGC 59.663 66.667 0.00 0.00 39.60 5.19
2543 3741 2.336809 CCTAGCCTCGATGTCGCC 59.663 66.667 0.00 0.00 39.60 5.54
2544 3742 2.336809 CTAGCCTCGATGTCGCCC 59.663 66.667 0.00 0.00 39.60 6.13
2545 3743 2.123854 TAGCCTCGATGTCGCCCT 60.124 61.111 0.00 0.00 39.60 5.19
2546 3744 1.739338 CTAGCCTCGATGTCGCCCTT 61.739 60.000 0.00 0.00 39.60 3.95
2547 3745 1.735376 TAGCCTCGATGTCGCCCTTC 61.735 60.000 0.00 0.00 39.60 3.46
2548 3746 2.107141 CCTCGATGTCGCCCTTCC 59.893 66.667 0.00 0.00 39.60 3.46
2549 3747 2.427245 CCTCGATGTCGCCCTTCCT 61.427 63.158 0.00 0.00 39.60 3.36
2550 3748 1.227089 CTCGATGTCGCCCTTCCTG 60.227 63.158 0.00 0.00 39.60 3.86
2551 3749 2.202932 CGATGTCGCCCTTCCTGG 60.203 66.667 0.00 0.00 0.00 4.45
2560 3758 3.787001 CCTTCCTGGCCTCCCGAC 61.787 72.222 3.32 0.00 0.00 4.79
2561 3759 3.787001 CTTCCTGGCCTCCCGACC 61.787 72.222 3.32 0.00 0.00 4.79
2562 3760 4.649705 TTCCTGGCCTCCCGACCA 62.650 66.667 3.32 0.00 0.00 4.02
2565 3763 3.775654 CTGGCCTCCCGACCACTC 61.776 72.222 3.32 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.033299 GTGTGTTCATGTGTGGAGGTTG 59.967 50.000 0.00 0.00 0.00 3.77
35 36 6.649141 CCTAGCATGTTAACTTAGTGTGTTCA 59.351 38.462 7.22 0.00 0.00 3.18
37 38 6.765403 TCCTAGCATGTTAACTTAGTGTGTT 58.235 36.000 7.22 0.00 0.00 3.32
39 40 7.667043 TTTCCTAGCATGTTAACTTAGTGTG 57.333 36.000 7.22 0.00 0.00 3.82
70 71 5.163652 GGCAAACCAACTATACCAAGTCATC 60.164 44.000 0.00 0.00 35.26 2.92
75 76 2.758423 GGGGCAAACCAACTATACCAAG 59.242 50.000 0.00 0.00 42.91 3.61
82 83 2.463047 AACAAGGGGCAAACCAACTA 57.537 45.000 0.00 0.00 42.91 2.24
285 299 4.952460 TGAGGTAGTAACACTTGGAACAC 58.048 43.478 0.00 0.00 39.29 3.32
291 305 7.387673 TCATTGACAATGAGGTAGTAACACTTG 59.612 37.037 23.89 0.00 42.69 3.16
292 306 7.450074 TCATTGACAATGAGGTAGTAACACTT 58.550 34.615 23.89 0.00 42.69 3.16
312 326 4.391216 ACAAAGACTTCTCTCGCATCATTG 59.609 41.667 0.00 0.00 0.00 2.82
363 377 5.435686 ACAGGCAGTACCATCAAGAAATA 57.564 39.130 0.00 0.00 43.14 1.40
384 398 5.059404 ACATTGCACAGCTTAACCATAAC 57.941 39.130 0.00 0.00 0.00 1.89
450 464 2.093783 AGTTCGTCGCAAATTCGGAATC 59.906 45.455 3.28 0.00 0.00 2.52
455 469 2.570468 TTCAGTTCGTCGCAAATTCG 57.430 45.000 0.00 0.00 0.00 3.34
469 483 2.362397 ACGATATGCACGGAGATTCAGT 59.638 45.455 0.00 0.00 34.93 3.41
509 523 2.750350 CTGCCCCGAACAGGAACT 59.250 61.111 0.00 0.00 45.00 3.01
528 542 7.383572 GGCAACTAACTATGATGAGAGTACATG 59.616 40.741 0.00 0.00 0.00 3.21
557 575 5.072193 ACCTACTGGTGAATGATGATATGCA 59.928 40.000 0.00 0.00 46.51 3.96
558 576 5.555017 ACCTACTGGTGAATGATGATATGC 58.445 41.667 0.00 0.00 46.51 3.14
645 693 3.267031 CCCCTGTTCCTATCTCCAGTTTT 59.733 47.826 0.00 0.00 0.00 2.43
658 706 0.615850 CTCCTTCTGACCCCTGTTCC 59.384 60.000 0.00 0.00 0.00 3.62
659 707 1.276705 GTCTCCTTCTGACCCCTGTTC 59.723 57.143 0.00 0.00 0.00 3.18
665 713 2.745968 AGAGATGTCTCCTTCTGACCC 58.254 52.381 6.41 0.00 43.88 4.46
676 724 7.044798 GCACAGGATAAGTAAAAGAGATGTCT 58.955 38.462 0.00 0.00 32.81 3.41
731 783 3.817647 CAGGCTTCATACTTATCTTGCCC 59.182 47.826 0.00 0.00 39.90 5.36
831 886 2.191641 GCCATGTGCTCTCCTCCC 59.808 66.667 0.00 0.00 36.87 4.30
863 918 2.485479 GGATGTGTGAGTGTGTCCTGTT 60.485 50.000 0.00 0.00 0.00 3.16
870 925 0.806868 GCCATGGATGTGTGAGTGTG 59.193 55.000 18.40 0.00 0.00 3.82
871 926 0.401356 TGCCATGGATGTGTGAGTGT 59.599 50.000 18.40 0.00 0.00 3.55
872 927 1.092348 CTGCCATGGATGTGTGAGTG 58.908 55.000 18.40 0.00 0.00 3.51
873 928 0.694771 ACTGCCATGGATGTGTGAGT 59.305 50.000 18.40 1.76 0.00 3.41
874 929 2.696989 TACTGCCATGGATGTGTGAG 57.303 50.000 18.40 1.12 0.00 3.51
875 930 4.980339 ATATACTGCCATGGATGTGTGA 57.020 40.909 18.40 3.48 0.00 3.58
876 931 5.122869 GCTTATATACTGCCATGGATGTGTG 59.877 44.000 18.40 0.17 0.00 3.82
877 932 5.221904 TGCTTATATACTGCCATGGATGTGT 60.222 40.000 18.40 13.42 0.00 3.72
882 937 3.307691 GCCTGCTTATATACTGCCATGGA 60.308 47.826 18.40 0.00 0.00 3.41
906 961 1.135139 TCTGACGATCAGGCTAAGCAC 59.865 52.381 12.89 0.00 44.39 4.40
994 1063 1.890979 CGGTGGCCTGCATCATCTC 60.891 63.158 3.32 0.00 0.00 2.75
1184 1260 1.128188 GTGACTGACCAAGGAGGGGT 61.128 60.000 0.00 0.00 43.89 4.95
1186 1262 0.322975 CAGTGACTGACCAAGGAGGG 59.677 60.000 6.79 0.00 43.89 4.30
1197 1273 2.619147 CTCAGGCTCAATCAGTGACTG 58.381 52.381 6.18 6.18 46.05 3.51
1213 1299 2.028420 TGATGATCGGTTTGGCTCAG 57.972 50.000 0.00 0.00 0.00 3.35
1220 1306 2.715749 TGGCAGATGATGATCGGTTT 57.284 45.000 0.00 0.00 33.34 3.27
1332 1420 3.792053 CTCCGGGTACATCTGCGCC 62.792 68.421 4.18 0.00 0.00 6.53
1433 1524 0.319211 GCAGGGTTACGTTTTTGGCC 60.319 55.000 0.00 0.00 0.00 5.36
1458 1549 9.657419 CAGTGCCACAACTATATAATATGATCA 57.343 33.333 0.00 0.00 0.00 2.92
1459 1550 8.607459 GCAGTGCCACAACTATATAATATGATC 58.393 37.037 2.85 0.00 0.00 2.92
1470 1561 0.401738 AGGTGCAGTGCCACAACTAT 59.598 50.000 13.72 0.00 37.46 2.12
1471 1562 0.534877 CAGGTGCAGTGCCACAACTA 60.535 55.000 13.72 0.00 37.46 2.24
1472 1563 1.825191 CAGGTGCAGTGCCACAACT 60.825 57.895 13.72 0.00 37.46 3.16
1473 1564 2.063541 GACAGGTGCAGTGCCACAAC 62.064 60.000 13.72 3.46 37.46 3.32
1474 1565 1.823470 GACAGGTGCAGTGCCACAA 60.823 57.895 13.72 0.00 37.46 3.33
1478 1569 0.250295 TTAGTGACAGGTGCAGTGCC 60.250 55.000 13.72 3.70 0.00 5.01
1484 1575 5.701290 AGTTTCAGTTATTAGTGACAGGTGC 59.299 40.000 0.00 0.00 33.49 5.01
1497 1596 6.823689 GTCCATCCACACATAGTTTCAGTTAT 59.176 38.462 0.00 0.00 0.00 1.89
1498 1597 6.170506 GTCCATCCACACATAGTTTCAGTTA 58.829 40.000 0.00 0.00 0.00 2.24
1501 1600 3.618594 CGTCCATCCACACATAGTTTCAG 59.381 47.826 0.00 0.00 0.00 3.02
1502 1601 3.595173 CGTCCATCCACACATAGTTTCA 58.405 45.455 0.00 0.00 0.00 2.69
1509 1608 0.464373 GCATCCGTCCATCCACACAT 60.464 55.000 0.00 0.00 0.00 3.21
1522 1624 2.438434 GGGAACACCCTGCATCCG 60.438 66.667 0.00 0.00 40.49 4.18
1609 1711 2.200067 GATGTACTGCTGCTGCTAGTG 58.800 52.381 21.84 11.59 40.48 2.74
1615 1717 2.320745 TGATGGATGTACTGCTGCTG 57.679 50.000 4.89 4.89 0.00 4.41
1671 1781 9.961265 ATGTTCTTGCTTATTATTCACATGATG 57.039 29.630 0.00 0.00 0.00 3.07
1720 1836 4.443725 CACTGCATTTCGTTTATGTGCAAA 59.556 37.500 0.00 0.00 44.20 3.68
1924 2776 8.678593 ACCGGGATTATTATCTCTTTTCTTTC 57.321 34.615 6.32 0.00 0.00 2.62
2034 2887 1.252904 TGATTTGCTGGGCAGGAAGC 61.253 55.000 0.00 0.00 40.61 3.86
2036 2889 1.826720 GATTGATTTGCTGGGCAGGAA 59.173 47.619 0.00 0.00 40.61 3.36
2063 2917 4.083802 GCGTTCTAGTTTGATTCTGCACTT 60.084 41.667 0.00 0.00 0.00 3.16
2070 2924 3.789756 TCGATCGCGTTCTAGTTTGATTC 59.210 43.478 11.09 0.00 38.98 2.52
2073 2927 2.905959 TCGATCGCGTTCTAGTTTGA 57.094 45.000 11.09 1.44 38.98 2.69
2075 2929 1.852895 GCATCGATCGCGTTCTAGTTT 59.147 47.619 11.09 0.00 38.98 2.66
2077 2931 0.663688 AGCATCGATCGCGTTCTAGT 59.336 50.000 11.09 0.00 38.98 2.57
2270 3468 2.128507 CAGAGCCTCTCCGGGTACC 61.129 68.421 2.17 2.17 45.40 3.34
2271 3469 2.128507 CCAGAGCCTCTCCGGGTAC 61.129 68.421 0.00 0.00 45.40 3.34
2272 3470 2.279073 CCAGAGCCTCTCCGGGTA 59.721 66.667 0.00 0.00 45.40 3.69
2274 3472 4.465446 TCCCAGAGCCTCTCCGGG 62.465 72.222 10.30 10.30 46.68 5.73
2275 3473 2.837291 CTCCCAGAGCCTCTCCGG 60.837 72.222 0.00 0.00 0.00 5.14
2276 3474 2.837291 CCTCCCAGAGCCTCTCCG 60.837 72.222 0.00 0.00 0.00 4.63
2277 3475 1.002274 TTCCTCCCAGAGCCTCTCC 59.998 63.158 0.00 0.00 0.00 3.71
2278 3476 1.671901 CGTTCCTCCCAGAGCCTCTC 61.672 65.000 0.00 0.00 0.00 3.20
2279 3477 1.684049 CGTTCCTCCCAGAGCCTCT 60.684 63.158 0.00 0.00 0.00 3.69
2280 3478 1.545706 AACGTTCCTCCCAGAGCCTC 61.546 60.000 0.00 0.00 0.00 4.70
2281 3479 0.252103 TAACGTTCCTCCCAGAGCCT 60.252 55.000 2.82 0.00 0.00 4.58
2282 3480 0.175989 CTAACGTTCCTCCCAGAGCC 59.824 60.000 2.82 0.00 0.00 4.70
2283 3481 1.135053 GTCTAACGTTCCTCCCAGAGC 60.135 57.143 2.82 0.00 0.00 4.09
2284 3482 2.164624 CAGTCTAACGTTCCTCCCAGAG 59.835 54.545 2.82 0.00 0.00 3.35
2285 3483 2.168496 CAGTCTAACGTTCCTCCCAGA 58.832 52.381 2.82 0.00 0.00 3.86
2286 3484 1.893801 ACAGTCTAACGTTCCTCCCAG 59.106 52.381 2.82 0.00 0.00 4.45
2287 3485 2.005370 ACAGTCTAACGTTCCTCCCA 57.995 50.000 2.82 0.00 0.00 4.37
2288 3486 6.348050 CGTATATACAGTCTAACGTTCCTCCC 60.348 46.154 2.82 0.00 0.00 4.30
2289 3487 6.203723 ACGTATATACAGTCTAACGTTCCTCC 59.796 42.308 2.82 0.00 40.31 4.30
2290 3488 7.183580 ACGTATATACAGTCTAACGTTCCTC 57.816 40.000 2.82 0.00 40.31 3.71
2291 3489 7.928706 ACTACGTATATACAGTCTAACGTTCCT 59.071 37.037 2.82 0.00 42.78 3.36
2292 3490 8.077836 ACTACGTATATACAGTCTAACGTTCC 57.922 38.462 2.82 0.00 42.78 3.62
2293 3491 8.973378 AGACTACGTATATACAGTCTAACGTTC 58.027 37.037 24.21 9.38 44.49 3.95
2294 3492 8.879342 AGACTACGTATATACAGTCTAACGTT 57.121 34.615 24.21 5.88 44.49 3.99
2295 3493 8.759641 CAAGACTACGTATATACAGTCTAACGT 58.240 37.037 25.08 15.34 45.33 3.99
2296 3494 8.759641 ACAAGACTACGTATATACAGTCTAACG 58.240 37.037 25.08 20.23 45.33 3.18
2303 3501 9.932699 GGCATATACAAGACTACGTATATACAG 57.067 37.037 13.22 6.23 38.59 2.74
2304 3502 9.676861 AGGCATATACAAGACTACGTATATACA 57.323 33.333 13.22 0.00 38.59 2.29
2307 3505 9.021807 ACAAGGCATATACAAGACTACGTATAT 57.978 33.333 0.00 9.93 40.35 0.86
2308 3506 8.400184 ACAAGGCATATACAAGACTACGTATA 57.600 34.615 0.00 6.98 35.59 1.47
2309 3507 7.286215 ACAAGGCATATACAAGACTACGTAT 57.714 36.000 0.00 3.65 33.08 3.06
2310 3508 6.704289 ACAAGGCATATACAAGACTACGTA 57.296 37.500 0.00 0.00 0.00 3.57
2311 3509 5.593679 ACAAGGCATATACAAGACTACGT 57.406 39.130 0.00 0.00 0.00 3.57
2312 3510 7.652105 ACAATACAAGGCATATACAAGACTACG 59.348 37.037 0.00 0.00 0.00 3.51
2313 3511 8.888579 ACAATACAAGGCATATACAAGACTAC 57.111 34.615 0.00 0.00 0.00 2.73
2315 3513 9.712305 GATACAATACAAGGCATATACAAGACT 57.288 33.333 0.00 0.00 0.00 3.24
2316 3514 9.712305 AGATACAATACAAGGCATATACAAGAC 57.288 33.333 0.00 0.00 0.00 3.01
2317 3515 9.929180 GAGATACAATACAAGGCATATACAAGA 57.071 33.333 0.00 0.00 0.00 3.02
2318 3516 9.935241 AGAGATACAATACAAGGCATATACAAG 57.065 33.333 0.00 0.00 0.00 3.16
2320 3518 9.710900 CAAGAGATACAATACAAGGCATATACA 57.289 33.333 0.00 0.00 0.00 2.29
2321 3519 9.155975 CCAAGAGATACAATACAAGGCATATAC 57.844 37.037 0.00 0.00 0.00 1.47
2322 3520 8.880244 ACCAAGAGATACAATACAAGGCATATA 58.120 33.333 0.00 0.00 0.00 0.86
2323 3521 7.749666 ACCAAGAGATACAATACAAGGCATAT 58.250 34.615 0.00 0.00 0.00 1.78
2324 3522 7.136822 ACCAAGAGATACAATACAAGGCATA 57.863 36.000 0.00 0.00 0.00 3.14
2325 3523 6.006275 ACCAAGAGATACAATACAAGGCAT 57.994 37.500 0.00 0.00 0.00 4.40
2326 3524 5.435686 ACCAAGAGATACAATACAAGGCA 57.564 39.130 0.00 0.00 0.00 4.75
2327 3525 5.462398 CGTACCAAGAGATACAATACAAGGC 59.538 44.000 0.00 0.00 0.00 4.35
2328 3526 6.570692 ACGTACCAAGAGATACAATACAAGG 58.429 40.000 0.00 0.00 0.00 3.61
2329 3527 7.481642 AGACGTACCAAGAGATACAATACAAG 58.518 38.462 0.00 0.00 0.00 3.16
2330 3528 7.400599 AGACGTACCAAGAGATACAATACAA 57.599 36.000 0.00 0.00 0.00 2.41
2331 3529 8.687292 ATAGACGTACCAAGAGATACAATACA 57.313 34.615 0.00 0.00 0.00 2.29
2339 3537 9.961264 TCTCATTATATAGACGTACCAAGAGAT 57.039 33.333 0.00 0.00 0.00 2.75
2340 3538 9.961264 ATCTCATTATATAGACGTACCAAGAGA 57.039 33.333 0.00 0.00 0.00 3.10
2349 3547 9.727859 AGTGTGACTATCTCATTATATAGACGT 57.272 33.333 0.00 0.00 31.44 4.34
2359 3557 7.989741 CCTTAAATGGAGTGTGACTATCTCATT 59.010 37.037 0.00 0.00 0.00 2.57
2360 3558 7.126421 ACCTTAAATGGAGTGTGACTATCTCAT 59.874 37.037 0.00 0.00 0.00 2.90
2361 3559 6.440647 ACCTTAAATGGAGTGTGACTATCTCA 59.559 38.462 0.00 0.00 0.00 3.27
2362 3560 6.758886 CACCTTAAATGGAGTGTGACTATCTC 59.241 42.308 0.00 0.00 0.00 2.75
2363 3561 6.213600 ACACCTTAAATGGAGTGTGACTATCT 59.786 38.462 0.00 0.00 41.69 1.98
2364 3562 6.407202 ACACCTTAAATGGAGTGTGACTATC 58.593 40.000 0.00 0.00 41.69 2.08
2365 3563 6.374417 ACACCTTAAATGGAGTGTGACTAT 57.626 37.500 0.00 0.00 41.69 2.12
2366 3564 5.566032 CGACACCTTAAATGGAGTGTGACTA 60.566 44.000 0.00 0.00 43.22 2.59
2367 3565 4.642429 GACACCTTAAATGGAGTGTGACT 58.358 43.478 0.00 0.00 43.22 3.41
2368 3566 3.432252 CGACACCTTAAATGGAGTGTGAC 59.568 47.826 0.00 0.00 43.22 3.67
2369 3567 3.322541 TCGACACCTTAAATGGAGTGTGA 59.677 43.478 0.00 0.00 43.22 3.58
2370 3568 3.659786 TCGACACCTTAAATGGAGTGTG 58.340 45.455 0.00 0.00 43.22 3.82
2371 3569 3.864921 GCTCGACACCTTAAATGGAGTGT 60.865 47.826 0.00 0.00 45.72 3.55
2372 3570 2.673368 GCTCGACACCTTAAATGGAGTG 59.327 50.000 0.00 0.00 36.30 3.51
2373 3571 2.354805 GGCTCGACACCTTAAATGGAGT 60.355 50.000 0.00 0.00 33.71 3.85
2374 3572 2.280628 GGCTCGACACCTTAAATGGAG 58.719 52.381 0.00 0.00 0.00 3.86
2375 3573 1.626321 TGGCTCGACACCTTAAATGGA 59.374 47.619 1.65 0.00 0.00 3.41
2376 3574 2.009774 CTGGCTCGACACCTTAAATGG 58.990 52.381 1.65 0.00 0.00 3.16
2377 3575 2.699954 ACTGGCTCGACACCTTAAATG 58.300 47.619 1.65 0.00 0.00 2.32
2378 3576 3.418684 AACTGGCTCGACACCTTAAAT 57.581 42.857 1.65 0.00 0.00 1.40
2379 3577 2.922740 AACTGGCTCGACACCTTAAA 57.077 45.000 1.65 0.00 0.00 1.52
2380 3578 2.549349 GGAAACTGGCTCGACACCTTAA 60.549 50.000 1.65 0.00 0.00 1.85
2381 3579 1.001633 GGAAACTGGCTCGACACCTTA 59.998 52.381 1.65 0.00 0.00 2.69
2382 3580 0.250338 GGAAACTGGCTCGACACCTT 60.250 55.000 1.65 0.00 0.00 3.50
2383 3581 1.371558 GGAAACTGGCTCGACACCT 59.628 57.895 1.65 0.00 0.00 4.00
2384 3582 1.671379 GGGAAACTGGCTCGACACC 60.671 63.158 0.00 0.00 0.00 4.16
2385 3583 0.534203 TTGGGAAACTGGCTCGACAC 60.534 55.000 0.00 0.00 0.00 3.67
2386 3584 0.181587 TTTGGGAAACTGGCTCGACA 59.818 50.000 0.00 0.00 0.00 4.35
2387 3585 0.591659 GTTTGGGAAACTGGCTCGAC 59.408 55.000 0.00 0.00 38.35 4.20
2388 3586 0.536460 GGTTTGGGAAACTGGCTCGA 60.536 55.000 0.00 0.00 41.14 4.04
2389 3587 1.524008 GGGTTTGGGAAACTGGCTCG 61.524 60.000 0.00 0.00 41.14 5.03
2390 3588 0.178961 AGGGTTTGGGAAACTGGCTC 60.179 55.000 0.00 0.00 41.14 4.70
2391 3589 1.154430 TAGGGTTTGGGAAACTGGCT 58.846 50.000 0.00 0.00 41.14 4.75
2392 3590 2.231716 ATAGGGTTTGGGAAACTGGC 57.768 50.000 0.00 0.00 41.14 4.85
2393 3591 6.867519 AAAATATAGGGTTTGGGAAACTGG 57.132 37.500 0.00 0.00 41.14 4.00
2394 3592 8.356000 TGTAAAATATAGGGTTTGGGAAACTG 57.644 34.615 0.00 0.00 41.14 3.16
2395 3593 8.977412 CATGTAAAATATAGGGTTTGGGAAACT 58.023 33.333 0.00 0.00 41.14 2.66
2396 3594 8.201464 CCATGTAAAATATAGGGTTTGGGAAAC 58.799 37.037 0.00 0.00 40.65 2.78
2397 3595 7.901861 ACCATGTAAAATATAGGGTTTGGGAAA 59.098 33.333 0.00 0.00 29.37 3.13
2398 3596 7.423341 ACCATGTAAAATATAGGGTTTGGGAA 58.577 34.615 0.00 0.00 29.37 3.97
2399 3597 6.987557 ACCATGTAAAATATAGGGTTTGGGA 58.012 36.000 0.00 0.00 29.37 4.37
2400 3598 8.950007 ATACCATGTAAAATATAGGGTTTGGG 57.050 34.615 0.00 0.00 35.56 4.12
2401 3599 9.581289 TGATACCATGTAAAATATAGGGTTTGG 57.419 33.333 0.00 0.00 35.56 3.28
2413 3611 9.153721 CGTAACCTAAACTGATACCATGTAAAA 57.846 33.333 0.00 0.00 0.00 1.52
2414 3612 8.530311 TCGTAACCTAAACTGATACCATGTAAA 58.470 33.333 0.00 0.00 0.00 2.01
2415 3613 8.065473 TCGTAACCTAAACTGATACCATGTAA 57.935 34.615 0.00 0.00 0.00 2.41
2416 3614 7.643569 TCGTAACCTAAACTGATACCATGTA 57.356 36.000 0.00 0.00 0.00 2.29
2417 3615 6.534475 TCGTAACCTAAACTGATACCATGT 57.466 37.500 0.00 0.00 0.00 3.21
2418 3616 6.984474 ACATCGTAACCTAAACTGATACCATG 59.016 38.462 0.00 0.00 0.00 3.66
2419 3617 7.069578 AGACATCGTAACCTAAACTGATACCAT 59.930 37.037 0.00 0.00 0.00 3.55
2420 3618 6.379133 AGACATCGTAACCTAAACTGATACCA 59.621 38.462 0.00 0.00 0.00 3.25
2421 3619 6.803642 AGACATCGTAACCTAAACTGATACC 58.196 40.000 0.00 0.00 0.00 2.73
2422 3620 8.699283 AAAGACATCGTAACCTAAACTGATAC 57.301 34.615 0.00 0.00 0.00 2.24
2423 3621 7.699391 CGAAAGACATCGTAACCTAAACTGATA 59.301 37.037 0.00 0.00 38.01 2.15
2424 3622 6.530534 CGAAAGACATCGTAACCTAAACTGAT 59.469 38.462 0.00 0.00 38.01 2.90
2425 3623 5.860182 CGAAAGACATCGTAACCTAAACTGA 59.140 40.000 0.00 0.00 38.01 3.41
2426 3624 5.444218 GCGAAAGACATCGTAACCTAAACTG 60.444 44.000 0.00 0.00 44.49 3.16
2427 3625 4.624452 GCGAAAGACATCGTAACCTAAACT 59.376 41.667 0.00 0.00 44.49 2.66
2428 3626 4.624452 AGCGAAAGACATCGTAACCTAAAC 59.376 41.667 0.00 0.00 44.49 2.01
2429 3627 4.624024 CAGCGAAAGACATCGTAACCTAAA 59.376 41.667 0.00 0.00 44.49 1.85
2430 3628 4.171005 CAGCGAAAGACATCGTAACCTAA 58.829 43.478 0.00 0.00 44.49 2.69
2431 3629 3.766151 CAGCGAAAGACATCGTAACCTA 58.234 45.455 0.00 0.00 44.49 3.08
2432 3630 2.607187 CAGCGAAAGACATCGTAACCT 58.393 47.619 0.00 0.00 44.49 3.50
2433 3631 1.060698 GCAGCGAAAGACATCGTAACC 59.939 52.381 0.00 0.00 44.49 2.85
2434 3632 1.724623 TGCAGCGAAAGACATCGTAAC 59.275 47.619 0.00 0.00 44.49 2.50
2435 3633 1.724623 GTGCAGCGAAAGACATCGTAA 59.275 47.619 0.00 0.00 44.49 3.18
2436 3634 1.346365 GTGCAGCGAAAGACATCGTA 58.654 50.000 0.00 0.00 44.49 3.43
2437 3635 1.291877 GGTGCAGCGAAAGACATCGT 61.292 55.000 0.00 0.00 44.49 3.73
2438 3636 1.291184 TGGTGCAGCGAAAGACATCG 61.291 55.000 11.91 0.00 45.41 3.84
2439 3637 0.166814 GTGGTGCAGCGAAAGACATC 59.833 55.000 11.91 0.00 0.00 3.06
2440 3638 1.237285 GGTGGTGCAGCGAAAGACAT 61.237 55.000 11.91 0.00 0.00 3.06
2441 3639 1.891919 GGTGGTGCAGCGAAAGACA 60.892 57.895 11.91 0.00 0.00 3.41
2442 3640 1.569479 GAGGTGGTGCAGCGAAAGAC 61.569 60.000 11.91 2.97 36.92 3.01
2443 3641 1.301716 GAGGTGGTGCAGCGAAAGA 60.302 57.895 11.91 0.00 36.92 2.52
2444 3642 2.328099 GGAGGTGGTGCAGCGAAAG 61.328 63.158 11.91 0.00 36.92 2.62
2445 3643 2.281484 GGAGGTGGTGCAGCGAAA 60.281 61.111 11.91 0.00 36.92 3.46
2446 3644 3.535629 CTGGAGGTGGTGCAGCGAA 62.536 63.158 11.91 0.00 37.86 4.70
2447 3645 4.007644 CTGGAGGTGGTGCAGCGA 62.008 66.667 11.91 0.00 37.86 4.93
2513 3711 4.845580 CTAGGGCCGGTGCAGCAG 62.846 72.222 17.33 5.61 40.13 4.24
2524 3722 2.336809 CGACATCGAGGCTAGGGC 59.663 66.667 0.00 0.00 43.02 5.19
2525 3723 2.336809 GCGACATCGAGGCTAGGG 59.663 66.667 5.26 0.00 43.02 3.53
2526 3724 2.336809 GGCGACATCGAGGCTAGG 59.663 66.667 5.26 0.00 43.02 3.02
2527 3725 1.739338 AAGGGCGACATCGAGGCTAG 61.739 60.000 5.26 0.00 43.02 3.42
2528 3726 1.735376 GAAGGGCGACATCGAGGCTA 61.735 60.000 5.26 0.00 43.02 3.93
2529 3727 3.077556 AAGGGCGACATCGAGGCT 61.078 61.111 5.26 0.00 43.02 4.58
2530 3728 2.586357 GAAGGGCGACATCGAGGC 60.586 66.667 5.26 0.00 43.02 4.70
2531 3729 2.107141 GGAAGGGCGACATCGAGG 59.893 66.667 5.26 0.00 43.02 4.63
2532 3730 1.227089 CAGGAAGGGCGACATCGAG 60.227 63.158 5.26 0.00 43.02 4.04
2533 3731 2.721167 CCAGGAAGGGCGACATCGA 61.721 63.158 5.26 0.00 43.02 3.59
2534 3732 2.202932 CCAGGAAGGGCGACATCG 60.203 66.667 0.00 0.00 43.27 3.84
2535 3733 2.514824 GCCAGGAAGGGCGACATC 60.515 66.667 0.00 0.00 45.40 3.06
2543 3741 3.787001 GTCGGGAGGCCAGGAAGG 61.787 72.222 5.01 0.00 41.84 3.46


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

AutoCloner maintained by Alex Coulton.