Multiple sequence alignment - TraesCS1D01G228100

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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 TraesCS1D01G228100 chr1D 100.000 3566 0 0 1 3566 316233499 316237064 0.000000e+00 6586
1 TraesCS1D01G228100 chr1A 94.439 3273 104 28 22 3250 397081292 397084530 0.000000e+00 4964
2 TraesCS1D01G228100 chr1A 96.215 317 12 0 3250 3566 405491415 405491731 1.470000e-143 520
3 TraesCS1D01G228100 chr1A 78.866 194 32 7 1843 2032 236303254 236303066 4.830000e-24 122
4 TraesCS1D01G228100 chr1B 92.325 2723 105 37 22 2706 428605989 428608645 0.000000e+00 3775
5 TraesCS1D01G228100 chr1B 94.326 564 16 3 2703 3250 428615717 428616280 0.000000e+00 850
6 TraesCS1D01G228100 chr5D 97.170 318 7 2 3251 3566 552029045 552028728 1.460000e-148 536
7 TraesCS1D01G228100 chr5D 96.238 319 9 3 3251 3566 78602934 78602616 1.470000e-143 520
8 TraesCS1D01G228100 chr5D 96.226 318 9 3 3251 3566 555413536 555413852 5.280000e-143 518
9 TraesCS1D01G228100 chr5D 83.929 168 21 6 1419 1583 521261160 521260996 4.770000e-34 156
10 TraesCS1D01G228100 chr3D 97.152 316 9 0 3251 3566 388399237 388399552 5.240000e-148 534
11 TraesCS1D01G228100 chr3D 96.855 318 7 2 3251 3566 341939 341623 2.440000e-146 529
12 TraesCS1D01G228100 chr3D 95.988 324 8 4 3246 3566 334129 334450 4.080000e-144 521
13 TraesCS1D01G228100 chr4D 96.541 318 9 1 3251 3566 491381490 491381807 3.150000e-145 525
14 TraesCS1D01G228100 chr4D 78.680 197 34 7 1840 2032 188963040 188963232 1.340000e-24 124
15 TraesCS1D01G228100 chr2D 96.552 319 8 2 3251 3566 617385335 617385017 3.150000e-145 525
16 TraesCS1D01G228100 chr2D 74.185 368 83 11 1674 2032 36535236 36535600 3.710000e-30 143
17 TraesCS1D01G228100 chr2D 78.351 194 34 7 1843 2032 288163029 288162840 6.250000e-23 119
18 TraesCS1D01G228100 chr2A 75.645 349 69 15 1695 2032 40537659 40538002 3.680000e-35 159
19 TraesCS1D01G228100 chr2B 75.000 372 73 16 1674 2032 62546755 62547119 1.710000e-33 154
20 TraesCS1D01G228100 chr5A 83.234 167 24 4 1419 1583 649643113 649642949 2.220000e-32 150
21 TraesCS1D01G228100 chr5B 82.530 166 25 4 1420 1583 657419753 657419590 3.710000e-30 143
22 TraesCS1D01G228100 chr5B 78.974 195 31 8 1843 2032 634280023 634279834 1.340000e-24 124


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 TraesCS1D01G228100 chr1D 316233499 316237064 3565 False 6586 6586 100.000 1 3566 1 chr1D.!!$F1 3565
1 TraesCS1D01G228100 chr1A 397081292 397084530 3238 False 4964 4964 94.439 22 3250 1 chr1A.!!$F1 3228
2 TraesCS1D01G228100 chr1B 428605989 428608645 2656 False 3775 3775 92.325 22 2706 1 chr1B.!!$F1 2684
3 TraesCS1D01G228100 chr1B 428615717 428616280 563 False 850 850 94.326 2703 3250 1 chr1B.!!$F2 547

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
965 999 0.038892 CCGCATTCTGCAAGCAAAGT 60.039 50.0 0.0 0.0 45.36 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2706 2763 0.099436 GCCTATTCTGTTTGGCAGCG 59.901 55.0 0.0 0.0 44.66 5.18 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
20 21 2.804986 TTATGTGATGGCTGCAGGAA 57.195 45.000 17.12 0.00 0.00 3.36
169 182 2.949106 CGCCTGGTGCAGACAAAG 59.051 61.111 0.00 0.00 41.33 2.77
184 198 3.760684 AGACAAAGTGCATTTCATCTCCC 59.239 43.478 0.00 0.00 0.00 4.30
245 259 4.952335 AAGCCTTGTTTAGGATGGATTCAG 59.048 41.667 0.00 0.00 43.46 3.02
246 260 5.281193 AAGCCTTGTTTAGGATGGATTCAGA 60.281 40.000 0.00 0.00 43.46 3.27
290 304 8.477419 AGGTGGAATGTAAGAAGAAAATCAAA 57.523 30.769 0.00 0.00 0.00 2.69
315 329 2.772077 TTGCATTGCAATCAGCCAAT 57.228 40.000 19.77 0.00 43.99 3.16
316 330 3.889520 TTGCATTGCAATCAGCCAATA 57.110 38.095 19.77 0.00 43.99 1.90
333 347 7.046652 CAGCCAATAGAATATAGAGACATGGG 58.953 42.308 0.00 0.00 0.00 4.00
371 385 6.000891 TGCGTTATGATGAAGCATAATTCC 57.999 37.500 4.47 0.00 41.31 3.01
399 413 7.095439 TGCTTATTTTCCATTTTGCCTTTAACG 60.095 33.333 0.00 0.00 0.00 3.18
414 428 4.483311 CTTTAACGGACAGACTACCTGAC 58.517 47.826 0.00 0.00 45.78 3.51
468 482 0.603569 CGAGGAAGGTACAGCACAGT 59.396 55.000 0.00 0.00 0.00 3.55
481 495 3.887110 ACAGCACAGTACAGTACAGTACA 59.113 43.478 25.01 0.00 45.25 2.90
482 496 4.523173 ACAGCACAGTACAGTACAGTACAT 59.477 41.667 25.01 13.32 45.25 2.29
483 497 5.708697 ACAGCACAGTACAGTACAGTACATA 59.291 40.000 25.01 2.40 45.25 2.29
571 588 1.867166 TTTGTTGGTGCATGCATGTG 58.133 45.000 25.64 5.68 0.00 3.21
677 708 5.083122 TGCTTTTGGGATTAATGAGTTCCA 58.917 37.500 0.00 0.00 0.00 3.53
681 712 7.607607 GCTTTTGGGATTAATGAGTTCCAAAAT 59.392 33.333 10.54 0.00 46.41 1.82
835 869 2.750637 TCCGAGACAGCGACCTCC 60.751 66.667 0.00 0.00 0.00 4.30
895 929 7.347485 AGCCTATATAATATGTCCCCCACTTAC 59.653 40.741 0.00 0.00 0.00 2.34
932 966 0.659427 CGCCATCATCACGCTCAAAT 59.341 50.000 0.00 0.00 0.00 2.32
965 999 0.038892 CCGCATTCTGCAAGCAAAGT 60.039 50.000 0.00 0.00 45.36 2.66
968 1002 2.670229 CGCATTCTGCAAGCAAAGTGAT 60.670 45.455 0.00 0.00 45.36 3.06
1149 1188 0.106619 TCCTCTACGGGGAAGAGCTC 60.107 60.000 5.27 5.27 39.36 4.09
1268 1310 3.689897 CGATCGATCGCAGAATTAACC 57.310 47.619 32.34 0.00 43.58 2.85
1378 1421 0.772124 AAGAAGAGGTGGCAGGGGAA 60.772 55.000 0.00 0.00 0.00 3.97
1397 1440 3.118454 CTGGCGTTCGCGGTGAAT 61.118 61.111 6.13 0.00 39.21 2.57
1628 1671 6.920569 TCTTTTCTATTCTTCCGCCATTAC 57.079 37.500 0.00 0.00 0.00 1.89
1651 1700 3.444388 CGGACTCCTCTGCTAAACTAACT 59.556 47.826 0.00 0.00 0.00 2.24
1652 1701 4.639310 CGGACTCCTCTGCTAAACTAACTA 59.361 45.833 0.00 0.00 0.00 2.24
1653 1702 5.125097 CGGACTCCTCTGCTAAACTAACTAA 59.875 44.000 0.00 0.00 0.00 2.24
1654 1703 6.331845 GGACTCCTCTGCTAAACTAACTAAC 58.668 44.000 0.00 0.00 0.00 2.34
1659 1708 6.377712 TCCTCTGCTAAACTAACTAACCTCTC 59.622 42.308 0.00 0.00 0.00 3.20
1660 1709 6.378848 CCTCTGCTAAACTAACTAACCTCTCT 59.621 42.308 0.00 0.00 0.00 3.10
2332 2381 3.630148 GCGTGATGCGGGTGATCG 61.630 66.667 0.00 0.00 41.69 3.69
2385 2434 1.009389 CGCTCACCTTCCTCAACGTC 61.009 60.000 0.00 0.00 0.00 4.34
2394 2443 1.956170 CCTCAACGTCACGCAGCTT 60.956 57.895 0.00 0.00 0.00 3.74
2624 2675 8.197988 CTTGTAATAACCATGACAAGTACTCC 57.802 38.462 12.32 0.00 44.18 3.85
2625 2676 7.490657 TGTAATAACCATGACAAGTACTCCT 57.509 36.000 0.00 0.00 0.00 3.69
2626 2677 8.598202 TGTAATAACCATGACAAGTACTCCTA 57.402 34.615 0.00 0.00 0.00 2.94
2706 2763 6.487103 CGTTTTGATTCCATAGCCTTAAGAC 58.513 40.000 3.36 0.00 0.00 3.01
2890 2947 1.328680 CACGTCTGGCATGCTTGTATC 59.671 52.381 18.92 0.00 0.00 2.24
3012 3076 5.048364 ACAGACTGCGTCTATCTCATAATCC 60.048 44.000 1.25 0.00 41.37 3.01
3250 3329 3.526931 ACTATGGTGGTCTCGTCATTG 57.473 47.619 0.00 0.00 0.00 2.82
3251 3330 3.096852 ACTATGGTGGTCTCGTCATTGA 58.903 45.455 0.00 0.00 0.00 2.57
3252 3331 2.680312 ATGGTGGTCTCGTCATTGAG 57.320 50.000 0.00 0.00 37.33 3.02
3253 3332 1.338107 TGGTGGTCTCGTCATTGAGT 58.662 50.000 0.00 0.00 37.28 3.41
3254 3333 1.000843 TGGTGGTCTCGTCATTGAGTG 59.999 52.381 0.00 0.00 37.28 3.51
3255 3334 1.000955 GGTGGTCTCGTCATTGAGTGT 59.999 52.381 0.00 0.00 37.28 3.55
3256 3335 2.548067 GGTGGTCTCGTCATTGAGTGTT 60.548 50.000 0.00 0.00 37.28 3.32
3257 3336 3.131396 GTGGTCTCGTCATTGAGTGTTT 58.869 45.455 0.00 0.00 37.28 2.83
3258 3337 3.059597 GTGGTCTCGTCATTGAGTGTTTG 60.060 47.826 0.00 0.00 37.28 2.93
3259 3338 3.181470 TGGTCTCGTCATTGAGTGTTTGA 60.181 43.478 0.00 0.00 37.28 2.69
3260 3339 3.184581 GGTCTCGTCATTGAGTGTTTGAC 59.815 47.826 0.00 0.00 37.28 3.18
3261 3340 3.802139 GTCTCGTCATTGAGTGTTTGACA 59.198 43.478 0.00 0.00 39.75 3.58
3262 3341 4.270084 GTCTCGTCATTGAGTGTTTGACAA 59.730 41.667 0.00 0.00 39.75 3.18
3263 3342 4.873259 TCTCGTCATTGAGTGTTTGACAAA 59.127 37.500 0.00 0.00 39.75 2.83
3264 3343 5.352846 TCTCGTCATTGAGTGTTTGACAAAA 59.647 36.000 1.27 0.00 39.75 2.44
3265 3344 5.944013 TCGTCATTGAGTGTTTGACAAAAA 58.056 33.333 1.27 0.00 39.75 1.94
3286 3365 4.462508 AACTACTAGTTTAGGGGTTCGC 57.537 45.455 0.00 0.00 34.11 4.70
3287 3366 2.424956 ACTACTAGTTTAGGGGTTCGCG 59.575 50.000 0.00 0.00 0.00 5.87
3288 3367 1.260544 ACTAGTTTAGGGGTTCGCGT 58.739 50.000 5.77 0.00 0.00 6.01
3289 3368 1.203287 ACTAGTTTAGGGGTTCGCGTC 59.797 52.381 5.77 0.09 0.00 5.19
3290 3369 0.532115 TAGTTTAGGGGTTCGCGTCC 59.468 55.000 5.77 10.33 0.00 4.79
3291 3370 1.742880 GTTTAGGGGTTCGCGTCCC 60.743 63.158 25.59 25.59 43.90 4.46
3292 3371 2.215625 TTTAGGGGTTCGCGTCCCA 61.216 57.895 30.86 16.87 46.26 4.37
3293 3372 2.453379 TTTAGGGGTTCGCGTCCCAC 62.453 60.000 30.86 22.31 46.26 4.61
3296 3375 3.998672 GGGTTCGCGTCCCACAGA 61.999 66.667 27.48 0.00 44.05 3.41
3297 3376 2.029964 GGTTCGCGTCCCACAGAA 59.970 61.111 5.77 0.00 0.00 3.02
3298 3377 2.315386 GGTTCGCGTCCCACAGAAC 61.315 63.158 5.77 0.00 41.40 3.01
3299 3378 1.300697 GTTCGCGTCCCACAGAACT 60.301 57.895 5.77 0.00 39.66 3.01
3300 3379 0.038892 GTTCGCGTCCCACAGAACTA 60.039 55.000 5.77 0.00 39.66 2.24
3301 3380 0.038892 TTCGCGTCCCACAGAACTAC 60.039 55.000 5.77 0.00 0.00 2.73
3302 3381 1.445582 CGCGTCCCACAGAACTACC 60.446 63.158 0.00 0.00 0.00 3.18
3303 3382 1.669440 GCGTCCCACAGAACTACCA 59.331 57.895 0.00 0.00 0.00 3.25
3304 3383 0.669625 GCGTCCCACAGAACTACCAC 60.670 60.000 0.00 0.00 0.00 4.16
3305 3384 0.966920 CGTCCCACAGAACTACCACT 59.033 55.000 0.00 0.00 0.00 4.00
3306 3385 1.343465 CGTCCCACAGAACTACCACTT 59.657 52.381 0.00 0.00 0.00 3.16
3307 3386 2.224209 CGTCCCACAGAACTACCACTTT 60.224 50.000 0.00 0.00 0.00 2.66
3308 3387 3.743269 CGTCCCACAGAACTACCACTTTT 60.743 47.826 0.00 0.00 0.00 2.27
3309 3388 4.204799 GTCCCACAGAACTACCACTTTTT 58.795 43.478 0.00 0.00 0.00 1.94
3330 3409 4.834357 TTAAAAGTGGCCGAAAACTACC 57.166 40.909 0.00 0.00 0.00 3.18
3331 3410 2.351706 AAAGTGGCCGAAAACTACCA 57.648 45.000 0.00 0.00 0.00 3.25
3332 3411 2.351706 AAGTGGCCGAAAACTACCAA 57.648 45.000 0.00 0.00 33.03 3.67
3333 3412 2.351706 AGTGGCCGAAAACTACCAAA 57.648 45.000 0.00 0.00 33.03 3.28
3334 3413 2.657143 AGTGGCCGAAAACTACCAAAA 58.343 42.857 0.00 0.00 33.03 2.44
3335 3414 3.025262 AGTGGCCGAAAACTACCAAAAA 58.975 40.909 0.00 0.00 33.03 1.94
3364 3443 9.673454 GTAAAAACATGACTAAAAACTACCAGG 57.327 33.333 0.00 0.00 0.00 4.45
3365 3444 7.891498 AAAACATGACTAAAAACTACCAGGT 57.109 32.000 0.00 0.00 0.00 4.00
3366 3445 7.891498 AAACATGACTAAAAACTACCAGGTT 57.109 32.000 0.00 0.00 31.24 3.50
3367 3446 6.877611 ACATGACTAAAAACTACCAGGTTG 57.122 37.500 0.00 0.00 0.00 3.77
3368 3447 6.597562 ACATGACTAAAAACTACCAGGTTGA 58.402 36.000 8.17 0.00 0.00 3.18
3369 3448 6.485648 ACATGACTAAAAACTACCAGGTTGAC 59.514 38.462 8.17 0.00 0.00 3.18
3370 3449 6.243216 TGACTAAAAACTACCAGGTTGACT 57.757 37.500 8.17 0.00 0.00 3.41
3384 3463 5.458041 AGGTTGACTGAATGGTGATTTTG 57.542 39.130 0.00 0.00 0.00 2.44
3385 3464 5.139727 AGGTTGACTGAATGGTGATTTTGA 58.860 37.500 0.00 0.00 0.00 2.69
3386 3465 5.010012 AGGTTGACTGAATGGTGATTTTGAC 59.990 40.000 0.00 0.00 0.00 3.18
3387 3466 5.222631 GTTGACTGAATGGTGATTTTGACC 58.777 41.667 0.00 0.00 0.00 4.02
3388 3467 3.501828 TGACTGAATGGTGATTTTGACCG 59.498 43.478 0.00 0.00 36.12 4.79
3389 3468 3.486383 ACTGAATGGTGATTTTGACCGT 58.514 40.909 0.00 0.00 36.12 4.83
3390 3469 3.888930 ACTGAATGGTGATTTTGACCGTT 59.111 39.130 0.00 0.00 43.98 4.44
3391 3470 4.340950 ACTGAATGGTGATTTTGACCGTTT 59.659 37.500 0.00 0.00 41.83 3.60
3392 3471 5.163457 ACTGAATGGTGATTTTGACCGTTTT 60.163 36.000 0.00 0.00 41.83 2.43
3393 3472 6.039941 ACTGAATGGTGATTTTGACCGTTTTA 59.960 34.615 0.00 0.00 41.83 1.52
3394 3473 6.806751 TGAATGGTGATTTTGACCGTTTTAA 58.193 32.000 0.00 0.00 41.83 1.52
3395 3474 6.697892 TGAATGGTGATTTTGACCGTTTTAAC 59.302 34.615 0.00 0.00 41.83 2.01
3396 3475 5.578005 TGGTGATTTTGACCGTTTTAACA 57.422 34.783 0.00 0.00 36.12 2.41
3397 3476 5.583495 TGGTGATTTTGACCGTTTTAACAG 58.417 37.500 0.00 0.00 36.12 3.16
3398 3477 4.443063 GGTGATTTTGACCGTTTTAACAGC 59.557 41.667 0.00 0.00 0.00 4.40
3399 3478 4.145756 GTGATTTTGACCGTTTTAACAGCG 59.854 41.667 0.00 0.00 0.00 5.18
3400 3479 4.035324 TGATTTTGACCGTTTTAACAGCGA 59.965 37.500 0.00 0.00 0.00 4.93
3401 3480 4.555348 TTTTGACCGTTTTAACAGCGAT 57.445 36.364 0.00 0.00 0.00 4.58
3402 3481 4.555348 TTTGACCGTTTTAACAGCGATT 57.445 36.364 0.00 0.00 0.00 3.34
3403 3482 3.799137 TGACCGTTTTAACAGCGATTC 57.201 42.857 0.00 0.00 0.00 2.52
3404 3483 3.395639 TGACCGTTTTAACAGCGATTCT 58.604 40.909 0.00 0.00 0.00 2.40
3406 3485 3.395639 ACCGTTTTAACAGCGATTCTGA 58.604 40.909 0.00 0.00 45.72 3.27
3407 3486 3.185797 ACCGTTTTAACAGCGATTCTGAC 59.814 43.478 0.00 0.00 45.72 3.51
3408 3487 3.395671 CGTTTTAACAGCGATTCTGACG 58.604 45.455 0.00 0.00 45.72 4.35
3409 3488 3.121126 CGTTTTAACAGCGATTCTGACGT 60.121 43.478 0.00 0.00 45.72 4.34
3410 3489 4.141680 GTTTTAACAGCGATTCTGACGTG 58.858 43.478 0.00 0.00 45.72 4.49
3411 3490 3.291809 TTAACAGCGATTCTGACGTGA 57.708 42.857 0.00 0.00 45.72 4.35
3412 3491 1.702886 AACAGCGATTCTGACGTGAG 58.297 50.000 0.00 0.00 45.72 3.51
3423 3502 2.111043 ACGTGAGTGGCCCACTTG 59.889 61.111 19.36 13.46 45.44 3.16
3424 3503 3.357079 CGTGAGTGGCCCACTTGC 61.357 66.667 19.36 12.71 45.44 4.01
3450 3529 3.845259 CGGCCCGCCTAAGTGCTA 61.845 66.667 3.84 0.00 0.00 3.49
3451 3530 2.587889 GGCCCGCCTAAGTGCTAA 59.412 61.111 0.00 0.00 0.00 3.09
3452 3531 1.818363 GGCCCGCCTAAGTGCTAAC 60.818 63.158 0.00 0.00 0.00 2.34
3453 3532 2.171725 GCCCGCCTAAGTGCTAACG 61.172 63.158 0.00 0.00 0.00 3.18
3454 3533 1.520787 CCCGCCTAAGTGCTAACGG 60.521 63.158 0.00 0.00 40.30 4.44
3455 3534 2.171725 CCGCCTAAGTGCTAACGGC 61.172 63.158 0.00 0.00 42.22 5.68
3456 3535 3.395669 GCCTAAGTGCTAACGGCG 58.604 61.111 4.80 4.80 45.43 6.46
3482 3561 4.493747 GCCGTTAGAGCCGCTCGT 62.494 66.667 14.71 6.21 35.36 4.18
3483 3562 2.278013 CCGTTAGAGCCGCTCGTC 60.278 66.667 14.71 8.28 35.36 4.20
3484 3563 2.648102 CGTTAGAGCCGCTCGTCG 60.648 66.667 14.71 15.41 35.36 5.12
3495 3574 4.778415 CTCGTCGGTCGCACCTGG 62.778 72.222 0.00 0.00 35.66 4.45
3502 3581 4.736896 GTCGCACCTGGTCGGGAC 62.737 72.222 21.23 21.23 37.83 4.46
3513 3592 3.754766 GTCGGGACCAGGTCATAAC 57.245 57.895 21.75 11.24 33.68 1.89
3514 3593 0.177373 GTCGGGACCAGGTCATAACC 59.823 60.000 21.75 11.82 46.87 2.85
3522 3601 4.534401 GGTCATAACCTGGCCGAC 57.466 61.111 0.00 0.00 40.55 4.79
3523 3602 1.153229 GGTCATAACCTGGCCGACC 60.153 63.158 7.82 7.82 40.55 4.79
3524 3603 1.520787 GTCATAACCTGGCCGACCG 60.521 63.158 0.00 0.00 39.70 4.79
3525 3604 2.203015 CATAACCTGGCCGACCGG 60.203 66.667 0.00 0.00 42.66 5.28
3546 3625 4.459089 GCTCGTCCCCACCAGCTC 62.459 72.222 0.00 0.00 0.00 4.09
3547 3626 2.681778 CTCGTCCCCACCAGCTCT 60.682 66.667 0.00 0.00 0.00 4.09
3548 3627 2.680352 TCGTCCCCACCAGCTCTC 60.680 66.667 0.00 0.00 0.00 3.20
3549 3628 2.681778 CGTCCCCACCAGCTCTCT 60.682 66.667 0.00 0.00 0.00 3.10
3550 3629 2.716017 CGTCCCCACCAGCTCTCTC 61.716 68.421 0.00 0.00 0.00 3.20
3551 3630 1.610673 GTCCCCACCAGCTCTCTCA 60.611 63.158 0.00 0.00 0.00 3.27
3552 3631 1.610673 TCCCCACCAGCTCTCTCAC 60.611 63.158 0.00 0.00 0.00 3.51
3553 3632 1.611851 CCCCACCAGCTCTCTCACT 60.612 63.158 0.00 0.00 0.00 3.41
3554 3633 1.612395 CCCCACCAGCTCTCTCACTC 61.612 65.000 0.00 0.00 0.00 3.51
3555 3634 0.614415 CCCACCAGCTCTCTCACTCT 60.614 60.000 0.00 0.00 0.00 3.24
3556 3635 0.817013 CCACCAGCTCTCTCACTCTC 59.183 60.000 0.00 0.00 0.00 3.20
3557 3636 0.817013 CACCAGCTCTCTCACTCTCC 59.183 60.000 0.00 0.00 0.00 3.71
3558 3637 0.324275 ACCAGCTCTCTCACTCTCCC 60.324 60.000 0.00 0.00 0.00 4.30
3559 3638 1.042559 CCAGCTCTCTCACTCTCCCC 61.043 65.000 0.00 0.00 0.00 4.81
3560 3639 1.042559 CAGCTCTCTCACTCTCCCCC 61.043 65.000 0.00 0.00 0.00 5.40
3561 3640 2.124693 GCTCTCTCACTCTCCCCCG 61.125 68.421 0.00 0.00 0.00 5.73
3562 3641 1.610327 CTCTCTCACTCTCCCCCGA 59.390 63.158 0.00 0.00 0.00 5.14
3563 3642 0.465460 CTCTCTCACTCTCCCCCGAG 60.465 65.000 0.00 0.00 37.48 4.63
3564 3643 2.043852 TCTCACTCTCCCCCGAGC 60.044 66.667 0.00 0.00 35.94 5.03
3565 3644 2.043450 CTCACTCTCCCCCGAGCT 60.043 66.667 0.00 0.00 35.94 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.220110 CTTCCTGCAGCCATCACATAAT 58.780 45.455 8.66 0.00 0.00 1.28
1 2 2.646930 CTTCCTGCAGCCATCACATAA 58.353 47.619 8.66 0.00 0.00 1.90
2 3 1.748244 GCTTCCTGCAGCCATCACATA 60.748 52.381 8.66 0.00 42.31 2.29
3 4 1.035932 GCTTCCTGCAGCCATCACAT 61.036 55.000 8.66 0.00 42.31 3.21
4 5 1.676635 GCTTCCTGCAGCCATCACA 60.677 57.895 8.66 0.00 42.31 3.58
5 6 3.194719 GCTTCCTGCAGCCATCAC 58.805 61.111 8.66 0.00 42.31 3.06
14 15 0.607489 TGGAAAGAGCTGCTTCCTGC 60.607 55.000 19.42 5.63 43.25 4.85
15 16 1.451067 CTGGAAAGAGCTGCTTCCTG 58.549 55.000 19.42 16.16 35.24 3.86
16 17 0.322366 GCTGGAAAGAGCTGCTTCCT 60.322 55.000 19.42 3.01 35.24 3.36
17 18 2.178856 GCTGGAAAGAGCTGCTTCC 58.821 57.895 14.15 14.15 35.24 3.46
169 182 3.350833 AGAACAGGGAGATGAAATGCAC 58.649 45.455 0.00 0.00 0.00 4.57
245 259 3.181491 CCTCTGAGAAGAATCTGACGGTC 60.181 52.174 6.17 0.00 35.54 4.79
246 260 2.757868 CCTCTGAGAAGAATCTGACGGT 59.242 50.000 6.17 0.00 35.54 4.83
315 329 8.958060 AGTTTAGCCCATGTCTCTATATTCTA 57.042 34.615 0.00 0.00 0.00 2.10
316 330 7.732593 AGAGTTTAGCCCATGTCTCTATATTCT 59.267 37.037 0.00 0.00 31.73 2.40
333 347 7.925703 TCATAACGCATAGTAAGAGTTTAGC 57.074 36.000 0.00 0.00 31.53 3.09
371 385 4.835678 AGGCAAAATGGAAAATAAGCAGG 58.164 39.130 0.00 0.00 0.00 4.85
399 413 2.028930 CCAACTGTCAGGTAGTCTGTCC 60.029 54.545 4.53 0.00 43.76 4.02
414 428 2.879103 ACAGGAACCCATACCAACTG 57.121 50.000 0.00 0.00 0.00 3.16
481 495 6.373774 GCTGCTGATCTGCACCTATTTATTAT 59.626 38.462 21.87 0.00 38.12 1.28
482 496 5.702670 GCTGCTGATCTGCACCTATTTATTA 59.297 40.000 21.87 0.00 38.12 0.98
483 497 4.518211 GCTGCTGATCTGCACCTATTTATT 59.482 41.667 21.87 0.00 38.12 1.40
677 708 6.819649 CACATGTTCAGCCCATTAATCATTTT 59.180 34.615 0.00 0.00 0.00 1.82
681 712 4.598022 TCACATGTTCAGCCCATTAATCA 58.402 39.130 0.00 0.00 0.00 2.57
835 869 1.806542 CCATGAGTTCTTCACCGTTGG 59.193 52.381 0.00 0.00 38.99 3.77
1174 1213 1.227853 GGTGTGCCCAGTTTCGACT 60.228 57.895 0.00 0.00 0.00 4.18
1180 1219 2.426023 GTCGAGGTGTGCCCAGTT 59.574 61.111 0.00 0.00 34.66 3.16
1182 1221 3.916392 GACGTCGAGGTGTGCCCAG 62.916 68.421 16.63 0.00 34.66 4.45
1184 1223 3.916392 CTGACGTCGAGGTGTGCCC 62.916 68.421 16.63 1.05 34.57 5.36
1285 1327 6.237313 TCGATCAGTACGTCCATAGTATTG 57.763 41.667 0.00 0.00 34.44 1.90
1289 1331 4.643463 AGATCGATCAGTACGTCCATAGT 58.357 43.478 26.47 0.00 0.00 2.12
1323 1365 3.480133 CTCCACCCCCGATCCACC 61.480 72.222 0.00 0.00 0.00 4.61
1397 1440 1.740664 CTCGTCCTCGTCCTCGTCA 60.741 63.158 0.00 0.00 38.33 4.35
1598 1641 4.513318 CGGAAGAATAGAAAAGATGGGAGC 59.487 45.833 0.00 0.00 0.00 4.70
1628 1671 1.187087 AGTTTAGCAGAGGAGTCCGG 58.813 55.000 2.76 0.00 0.00 5.14
1651 1700 3.189618 CATGCATGCAGAGAGAGGTTA 57.810 47.619 26.69 0.00 0.00 2.85
1652 1701 2.039818 CATGCATGCAGAGAGAGGTT 57.960 50.000 26.69 2.26 0.00 3.50
1653 1702 3.782632 CATGCATGCAGAGAGAGGT 57.217 52.632 26.69 3.09 0.00 3.85
1711 1760 1.353103 CGAACATCATCCGCTTGCC 59.647 57.895 0.00 0.00 0.00 4.52
1712 1761 0.247814 CACGAACATCATCCGCTTGC 60.248 55.000 0.00 0.00 0.00 4.01
2004 2053 1.978580 AGGTAGGTGTTGAAGACCAGG 59.021 52.381 14.33 0.00 35.76 4.45
2332 2381 3.607661 GCCGTCGAGGATCTCCCC 61.608 72.222 6.70 0.00 45.00 4.81
2373 2422 1.891060 GCTGCGTGACGTTGAGGAAG 61.891 60.000 6.91 0.00 0.00 3.46
2385 2434 0.447801 GGTACATGGAAAGCTGCGTG 59.552 55.000 0.00 0.00 36.07 5.34
2589 2640 8.789762 GTCATGGTTATTACAAGTTTACAACCT 58.210 33.333 0.00 0.00 35.93 3.50
2590 2641 8.569641 TGTCATGGTTATTACAAGTTTACAACC 58.430 33.333 0.00 0.00 35.58 3.77
2591 2642 9.953697 TTGTCATGGTTATTACAAGTTTACAAC 57.046 29.630 0.00 0.00 29.55 3.32
2599 2650 8.041323 AGGAGTACTTGTCATGGTTATTACAAG 58.959 37.037 16.84 16.84 46.56 3.16
2604 2655 9.656323 TCTATAGGAGTACTTGTCATGGTTATT 57.344 33.333 0.00 0.00 0.00 1.40
2621 2672 2.356330 CGGGAGGCCTACTCTATAGGAG 60.356 59.091 16.60 0.00 45.83 3.69
2622 2673 1.634459 CGGGAGGCCTACTCTATAGGA 59.366 57.143 16.60 0.00 45.83 2.94
2623 2674 1.634459 TCGGGAGGCCTACTCTATAGG 59.366 57.143 16.60 0.00 45.83 2.57
2624 2675 2.306512 ACTCGGGAGGCCTACTCTATAG 59.693 54.545 16.60 7.89 45.83 1.31
2625 2676 2.346529 ACTCGGGAGGCCTACTCTATA 58.653 52.381 16.60 0.00 45.83 1.31
2626 2677 1.150872 ACTCGGGAGGCCTACTCTAT 58.849 55.000 16.60 0.00 45.83 1.98
2706 2763 0.099436 GCCTATTCTGTTTGGCAGCG 59.901 55.000 0.00 0.00 44.66 5.18
2917 2974 5.741388 AGGTCGAATTAAGTACGTACGAT 57.259 39.130 24.41 14.84 0.00 3.73
2934 2991 9.932207 CTCAGTATATATAGAGGGTATAGGTCG 57.068 40.741 0.00 0.00 0.00 4.79
3012 3076 2.974935 TTTCGACGAACGGTGTGGGG 62.975 60.000 10.38 0.00 42.82 4.96
3237 3316 3.130633 CAAACACTCAATGACGAGACCA 58.869 45.455 0.00 0.00 36.47 4.02
3262 3341 5.702670 GCGAACCCCTAAACTAGTAGTTTTT 59.297 40.000 28.44 18.15 45.38 1.94
3263 3342 5.240891 GCGAACCCCTAAACTAGTAGTTTT 58.759 41.667 28.44 13.09 45.38 2.43
3265 3344 3.119352 CGCGAACCCCTAAACTAGTAGTT 60.119 47.826 9.85 9.85 40.80 2.24
3266 3345 2.424956 CGCGAACCCCTAAACTAGTAGT 59.575 50.000 0.00 0.00 0.00 2.73
3267 3346 2.424956 ACGCGAACCCCTAAACTAGTAG 59.575 50.000 15.93 0.00 0.00 2.57
3268 3347 2.423538 GACGCGAACCCCTAAACTAGTA 59.576 50.000 15.93 0.00 0.00 1.82
3269 3348 1.203287 GACGCGAACCCCTAAACTAGT 59.797 52.381 15.93 0.00 0.00 2.57
3270 3349 1.470458 GGACGCGAACCCCTAAACTAG 60.470 57.143 15.93 0.00 0.00 2.57
3271 3350 0.532115 GGACGCGAACCCCTAAACTA 59.468 55.000 15.93 0.00 0.00 2.24
3272 3351 1.294459 GGACGCGAACCCCTAAACT 59.706 57.895 15.93 0.00 0.00 2.66
3273 3352 1.742880 GGGACGCGAACCCCTAAAC 60.743 63.158 26.60 8.35 41.38 2.01
3274 3353 2.215625 TGGGACGCGAACCCCTAAA 61.216 57.895 30.83 17.20 46.21 1.85
3275 3354 2.604079 TGGGACGCGAACCCCTAA 60.604 61.111 30.83 17.47 46.21 2.69
3276 3355 3.384532 GTGGGACGCGAACCCCTA 61.385 66.667 30.83 18.03 46.21 3.53
3279 3358 3.524648 TTCTGTGGGACGCGAACCC 62.525 63.158 28.81 28.81 45.01 4.11
3280 3359 2.029964 TTCTGTGGGACGCGAACC 59.970 61.111 15.93 15.44 45.01 3.62
3281 3360 0.038892 TAGTTCTGTGGGACGCGAAC 60.039 55.000 15.93 3.65 45.26 3.95
3282 3361 0.038892 GTAGTTCTGTGGGACGCGAA 60.039 55.000 15.93 0.00 45.01 4.70
3283 3362 1.582968 GTAGTTCTGTGGGACGCGA 59.417 57.895 15.93 0.00 45.01 5.87
3284 3363 1.445582 GGTAGTTCTGTGGGACGCG 60.446 63.158 3.53 3.53 45.01 6.01
3285 3364 0.669625 GTGGTAGTTCTGTGGGACGC 60.670 60.000 0.00 0.00 40.62 5.19
3286 3365 0.966920 AGTGGTAGTTCTGTGGGACG 59.033 55.000 0.00 0.00 0.00 4.79
3287 3366 3.487120 AAAGTGGTAGTTCTGTGGGAC 57.513 47.619 0.00 0.00 0.00 4.46
3288 3367 4.513406 AAAAAGTGGTAGTTCTGTGGGA 57.487 40.909 0.00 0.00 0.00 4.37
3306 3385 6.041511 GGTAGTTTTCGGCCACTTTTAAAAA 58.958 36.000 2.24 0.00 0.00 1.94
3307 3386 5.126707 TGGTAGTTTTCGGCCACTTTTAAAA 59.873 36.000 2.24 0.00 0.00 1.52
3308 3387 4.643784 TGGTAGTTTTCGGCCACTTTTAAA 59.356 37.500 2.24 0.00 0.00 1.52
3309 3388 4.205587 TGGTAGTTTTCGGCCACTTTTAA 58.794 39.130 2.24 0.00 0.00 1.52
3310 3389 3.818180 TGGTAGTTTTCGGCCACTTTTA 58.182 40.909 2.24 0.00 0.00 1.52
3311 3390 2.657143 TGGTAGTTTTCGGCCACTTTT 58.343 42.857 2.24 0.00 0.00 2.27
3312 3391 2.351706 TGGTAGTTTTCGGCCACTTT 57.648 45.000 2.24 0.00 0.00 2.66
3313 3392 2.351706 TTGGTAGTTTTCGGCCACTT 57.648 45.000 2.24 0.00 0.00 3.16
3314 3393 2.351706 TTTGGTAGTTTTCGGCCACT 57.648 45.000 2.24 0.08 0.00 4.00
3315 3394 3.439895 TTTTTGGTAGTTTTCGGCCAC 57.560 42.857 2.24 0.00 0.00 5.01
3338 3417 9.673454 CCTGGTAGTTTTTAGTCATGTTTTTAC 57.327 33.333 0.00 0.00 0.00 2.01
3339 3418 9.411189 ACCTGGTAGTTTTTAGTCATGTTTTTA 57.589 29.630 0.00 0.00 0.00 1.52
3340 3419 8.301252 ACCTGGTAGTTTTTAGTCATGTTTTT 57.699 30.769 0.00 0.00 0.00 1.94
3341 3420 7.891498 ACCTGGTAGTTTTTAGTCATGTTTT 57.109 32.000 0.00 0.00 0.00 2.43
3342 3421 7.558444 TCAACCTGGTAGTTTTTAGTCATGTTT 59.442 33.333 0.00 0.00 0.00 2.83
3343 3422 7.012989 GTCAACCTGGTAGTTTTTAGTCATGTT 59.987 37.037 0.00 0.00 0.00 2.71
3344 3423 6.485648 GTCAACCTGGTAGTTTTTAGTCATGT 59.514 38.462 0.00 0.00 0.00 3.21
3345 3424 6.710744 AGTCAACCTGGTAGTTTTTAGTCATG 59.289 38.462 0.00 0.00 0.00 3.07
3346 3425 6.710744 CAGTCAACCTGGTAGTTTTTAGTCAT 59.289 38.462 0.00 0.00 37.54 3.06
3347 3426 6.053005 CAGTCAACCTGGTAGTTTTTAGTCA 58.947 40.000 0.00 0.00 37.54 3.41
3348 3427 6.285990 TCAGTCAACCTGGTAGTTTTTAGTC 58.714 40.000 0.00 0.00 41.83 2.59
3349 3428 6.243216 TCAGTCAACCTGGTAGTTTTTAGT 57.757 37.500 0.00 0.00 41.83 2.24
3350 3429 7.308589 CCATTCAGTCAACCTGGTAGTTTTTAG 60.309 40.741 0.00 0.00 41.83 1.85
3351 3430 6.488683 CCATTCAGTCAACCTGGTAGTTTTTA 59.511 38.462 0.00 0.00 41.83 1.52
3352 3431 5.301805 CCATTCAGTCAACCTGGTAGTTTTT 59.698 40.000 0.00 0.00 41.83 1.94
3353 3432 4.827284 CCATTCAGTCAACCTGGTAGTTTT 59.173 41.667 0.00 0.00 41.83 2.43
3354 3433 4.141251 ACCATTCAGTCAACCTGGTAGTTT 60.141 41.667 0.00 0.00 41.83 2.66
3355 3434 3.394606 ACCATTCAGTCAACCTGGTAGTT 59.605 43.478 0.00 0.00 41.83 2.24
3356 3435 2.979678 ACCATTCAGTCAACCTGGTAGT 59.020 45.455 0.00 0.00 41.83 2.73
3357 3436 3.007940 TCACCATTCAGTCAACCTGGTAG 59.992 47.826 0.00 0.00 41.83 3.18
3358 3437 2.976185 TCACCATTCAGTCAACCTGGTA 59.024 45.455 0.00 0.00 41.83 3.25
3359 3438 1.774254 TCACCATTCAGTCAACCTGGT 59.226 47.619 0.00 0.00 41.83 4.00
3360 3439 2.566833 TCACCATTCAGTCAACCTGG 57.433 50.000 0.00 0.00 41.83 4.45
3361 3440 5.009911 TCAAAATCACCATTCAGTCAACCTG 59.990 40.000 0.00 0.00 42.97 4.00
3362 3441 5.010012 GTCAAAATCACCATTCAGTCAACCT 59.990 40.000 0.00 0.00 0.00 3.50
3363 3442 5.222631 GTCAAAATCACCATTCAGTCAACC 58.777 41.667 0.00 0.00 0.00 3.77
3364 3443 5.222631 GGTCAAAATCACCATTCAGTCAAC 58.777 41.667 0.00 0.00 33.63 3.18
3365 3444 4.023279 CGGTCAAAATCACCATTCAGTCAA 60.023 41.667 0.00 0.00 32.89 3.18
3366 3445 3.501828 CGGTCAAAATCACCATTCAGTCA 59.498 43.478 0.00 0.00 32.89 3.41
3367 3446 3.502211 ACGGTCAAAATCACCATTCAGTC 59.498 43.478 0.00 0.00 32.89 3.51
3368 3447 3.486383 ACGGTCAAAATCACCATTCAGT 58.514 40.909 0.00 0.00 32.89 3.41
3369 3448 4.503741 AACGGTCAAAATCACCATTCAG 57.496 40.909 0.00 0.00 32.89 3.02
3370 3449 4.927978 AAACGGTCAAAATCACCATTCA 57.072 36.364 0.00 0.00 32.89 2.57
3371 3450 6.697892 TGTTAAAACGGTCAAAATCACCATTC 59.302 34.615 0.00 0.00 32.89 2.67
3372 3451 6.574350 TGTTAAAACGGTCAAAATCACCATT 58.426 32.000 0.00 0.00 32.89 3.16
3373 3452 6.150396 TGTTAAAACGGTCAAAATCACCAT 57.850 33.333 0.00 0.00 32.89 3.55
3374 3453 5.578005 TGTTAAAACGGTCAAAATCACCA 57.422 34.783 0.00 0.00 32.89 4.17
3375 3454 4.443063 GCTGTTAAAACGGTCAAAATCACC 59.557 41.667 3.75 0.00 37.60 4.02
3376 3455 4.145756 CGCTGTTAAAACGGTCAAAATCAC 59.854 41.667 3.75 0.00 37.60 3.06
3377 3456 4.035324 TCGCTGTTAAAACGGTCAAAATCA 59.965 37.500 3.75 0.00 37.60 2.57
3378 3457 4.529446 TCGCTGTTAAAACGGTCAAAATC 58.471 39.130 3.75 0.00 37.60 2.17
3379 3458 4.555348 TCGCTGTTAAAACGGTCAAAAT 57.445 36.364 3.75 0.00 37.60 1.82
3380 3459 4.555348 ATCGCTGTTAAAACGGTCAAAA 57.445 36.364 3.75 0.00 37.60 2.44
3381 3460 4.273969 AGAATCGCTGTTAAAACGGTCAAA 59.726 37.500 3.75 0.00 37.60 2.69
3382 3461 3.810941 AGAATCGCTGTTAAAACGGTCAA 59.189 39.130 3.75 0.00 37.60 3.18
3383 3462 3.185594 CAGAATCGCTGTTAAAACGGTCA 59.814 43.478 3.75 0.00 39.85 4.02
3384 3463 3.430895 TCAGAATCGCTGTTAAAACGGTC 59.569 43.478 3.75 0.00 45.14 4.79
3385 3464 3.185797 GTCAGAATCGCTGTTAAAACGGT 59.814 43.478 3.75 0.00 45.14 4.83
3386 3465 3.720920 CGTCAGAATCGCTGTTAAAACGG 60.721 47.826 0.00 0.00 45.14 4.44
3387 3466 3.121126 ACGTCAGAATCGCTGTTAAAACG 60.121 43.478 0.00 0.00 45.14 3.60
3388 3467 4.084745 TCACGTCAGAATCGCTGTTAAAAC 60.085 41.667 0.00 0.00 45.14 2.43
3389 3468 4.052608 TCACGTCAGAATCGCTGTTAAAA 58.947 39.130 0.00 0.00 45.14 1.52
3390 3469 3.644823 TCACGTCAGAATCGCTGTTAAA 58.355 40.909 0.00 0.00 45.14 1.52
3391 3470 3.242518 CTCACGTCAGAATCGCTGTTAA 58.757 45.455 0.00 0.00 45.14 2.01
3392 3471 2.228103 ACTCACGTCAGAATCGCTGTTA 59.772 45.455 0.00 0.00 45.14 2.41
3393 3472 1.000163 ACTCACGTCAGAATCGCTGTT 60.000 47.619 0.00 0.00 45.14 3.16
3394 3473 0.598562 ACTCACGTCAGAATCGCTGT 59.401 50.000 0.00 0.00 45.14 4.40
3395 3474 0.987715 CACTCACGTCAGAATCGCTG 59.012 55.000 0.00 0.00 46.31 5.18
3396 3475 0.109086 CCACTCACGTCAGAATCGCT 60.109 55.000 0.00 0.00 0.00 4.93
3397 3476 1.687494 GCCACTCACGTCAGAATCGC 61.687 60.000 0.00 0.00 0.00 4.58
3398 3477 1.078759 GGCCACTCACGTCAGAATCG 61.079 60.000 0.00 0.00 0.00 3.34
3399 3478 0.741221 GGGCCACTCACGTCAGAATC 60.741 60.000 4.39 0.00 0.00 2.52
3400 3479 1.296715 GGGCCACTCACGTCAGAAT 59.703 57.895 4.39 0.00 0.00 2.40
3401 3480 2.137528 TGGGCCACTCACGTCAGAA 61.138 57.895 0.00 0.00 0.00 3.02
3402 3481 2.523168 TGGGCCACTCACGTCAGA 60.523 61.111 0.00 0.00 0.00 3.27
3403 3482 2.357517 GTGGGCCACTCACGTCAG 60.358 66.667 29.22 0.00 0.00 3.51
3404 3483 2.439960 AAGTGGGCCACTCACGTCA 61.440 57.895 37.60 0.00 44.62 4.35
3405 3484 1.961277 CAAGTGGGCCACTCACGTC 60.961 63.158 37.60 9.99 44.62 4.34
3406 3485 2.111043 CAAGTGGGCCACTCACGT 59.889 61.111 37.60 20.86 44.62 4.49
3407 3486 3.357079 GCAAGTGGGCCACTCACG 61.357 66.667 37.60 27.89 44.62 4.35
3433 3512 3.379865 TTAGCACTTAGGCGGGCCG 62.380 63.158 24.35 24.35 41.95 6.13
3434 3513 1.818363 GTTAGCACTTAGGCGGGCC 60.818 63.158 0.18 0.18 39.27 5.80
3435 3514 2.171725 CGTTAGCACTTAGGCGGGC 61.172 63.158 0.00 0.00 39.27 6.13
3436 3515 1.520787 CCGTTAGCACTTAGGCGGG 60.521 63.158 0.00 0.00 39.27 6.13
3437 3516 2.171725 GCCGTTAGCACTTAGGCGG 61.172 63.158 0.00 0.00 42.97 6.13
3438 3517 3.395669 GCCGTTAGCACTTAGGCG 58.604 61.111 0.00 0.00 42.97 5.52
3439 3518 2.810012 GCGCCGTTAGCACTTAGGC 61.810 63.158 0.00 0.00 44.04 3.93
3440 3519 2.514013 CGCGCCGTTAGCACTTAGG 61.514 63.158 0.00 0.00 44.04 2.69
3441 3520 2.995482 CGCGCCGTTAGCACTTAG 59.005 61.111 0.00 0.00 44.04 2.18
3442 3521 3.183323 GCGCGCCGTTAGCACTTA 61.183 61.111 23.24 0.00 44.04 2.24
3463 3542 4.893601 GAGCGGCTCTAACGGCCC 62.894 72.222 22.32 0.00 46.24 5.80
3465 3544 4.493747 ACGAGCGGCTCTAACGGC 62.494 66.667 25.96 0.42 36.23 5.68
3466 3545 2.278013 GACGAGCGGCTCTAACGG 60.278 66.667 25.96 13.44 0.00 4.44
3467 3546 2.648102 CGACGAGCGGCTCTAACG 60.648 66.667 25.96 22.04 36.03 3.18
3478 3557 4.778415 CCAGGTGCGACCGACGAG 62.778 72.222 0.00 0.00 44.90 4.18
3485 3564 4.736896 GTCCCGACCAGGTGCGAC 62.737 72.222 0.00 0.00 38.74 5.19
3494 3573 3.182860 GGTTATGACCTGGTCCCGACC 62.183 61.905 23.42 21.34 43.19 4.79
3495 3574 0.177373 GGTTATGACCTGGTCCCGAC 59.823 60.000 23.42 17.09 42.99 4.79
3496 3575 2.599216 GGTTATGACCTGGTCCCGA 58.401 57.895 23.42 6.09 42.99 5.14
3505 3584 1.153229 GGTCGGCCAGGTTATGACC 60.153 63.158 0.00 5.68 46.92 4.02
3506 3585 1.520787 CGGTCGGCCAGGTTATGAC 60.521 63.158 6.96 0.00 34.09 3.06
3507 3586 2.727392 CCGGTCGGCCAGGTTATGA 61.727 63.158 6.96 0.00 34.09 2.15
3508 3587 2.203015 CCGGTCGGCCAGGTTATG 60.203 66.667 6.96 0.00 34.09 1.90
3509 3588 3.476419 CCCGGTCGGCCAGGTTAT 61.476 66.667 6.96 0.00 34.09 1.89
3529 3608 4.459089 GAGCTGGTGGGGACGAGC 62.459 72.222 0.00 0.00 40.95 5.03
3530 3609 2.681778 AGAGCTGGTGGGGACGAG 60.682 66.667 0.00 0.00 0.00 4.18
3531 3610 2.680352 GAGAGCTGGTGGGGACGA 60.680 66.667 0.00 0.00 0.00 4.20
3532 3611 2.681778 AGAGAGCTGGTGGGGACG 60.682 66.667 0.00 0.00 0.00 4.79
3533 3612 1.610673 TGAGAGAGCTGGTGGGGAC 60.611 63.158 0.00 0.00 0.00 4.46
3534 3613 1.610673 GTGAGAGAGCTGGTGGGGA 60.611 63.158 0.00 0.00 0.00 4.81
3535 3614 1.611851 AGTGAGAGAGCTGGTGGGG 60.612 63.158 0.00 0.00 0.00 4.96
3536 3615 0.614415 AGAGTGAGAGAGCTGGTGGG 60.614 60.000 0.00 0.00 0.00 4.61
3537 3616 0.817013 GAGAGTGAGAGAGCTGGTGG 59.183 60.000 0.00 0.00 0.00 4.61
3538 3617 0.817013 GGAGAGTGAGAGAGCTGGTG 59.183 60.000 0.00 0.00 0.00 4.17
3539 3618 0.324275 GGGAGAGTGAGAGAGCTGGT 60.324 60.000 0.00 0.00 0.00 4.00
3540 3619 1.042559 GGGGAGAGTGAGAGAGCTGG 61.043 65.000 0.00 0.00 0.00 4.85
3541 3620 1.042559 GGGGGAGAGTGAGAGAGCTG 61.043 65.000 0.00 0.00 0.00 4.24
3542 3621 1.309688 GGGGGAGAGTGAGAGAGCT 59.690 63.158 0.00 0.00 0.00 4.09
3543 3622 2.124693 CGGGGGAGAGTGAGAGAGC 61.125 68.421 0.00 0.00 0.00 4.09
3544 3623 0.465460 CTCGGGGGAGAGTGAGAGAG 60.465 65.000 0.00 0.00 33.75 3.20
3545 3624 1.610327 CTCGGGGGAGAGTGAGAGA 59.390 63.158 0.00 0.00 33.75 3.10
3546 3625 2.124693 GCTCGGGGGAGAGTGAGAG 61.125 68.421 0.00 0.00 40.26 3.20
3547 3626 2.043852 GCTCGGGGGAGAGTGAGA 60.044 66.667 0.00 0.00 40.26 3.27
3548 3627 2.043450 AGCTCGGGGGAGAGTGAG 60.043 66.667 0.00 0.00 40.26 3.51


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

AutoCloner maintained by Alex Coulton.