Multiple sequence alignment - TraesCS4B01G331000

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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 TraesCS4B01G331000 chr4B 100.000 3710 0 0 1 3710 621708323 621704614 0.000000e+00 6852
1 TraesCS4B01G331000 chr4B 99.071 1507 12 2 3 1507 75186566 75188072 0.000000e+00 2704
2 TraesCS4B01G331000 chr4B 96.020 201 8 0 3510 3710 600914633 600914833 9.930000e-86 327
3 TraesCS4B01G331000 chr4B 95.522 201 9 0 3510 3710 13376717 13376917 4.620000e-84 322
4 TraesCS4B01G331000 chr3B 99.203 1505 12 0 3 1507 644837614 644839118 0.000000e+00 2713
5 TraesCS4B01G331000 chr3B 96.552 203 6 1 3508 3710 16145015 16144814 5.940000e-88 335
6 TraesCS4B01G331000 chr3B 96.020 201 8 0 3510 3710 511619483 511619283 9.930000e-86 327
7 TraesCS4B01G331000 chr5A 99.073 1510 14 0 3 1512 511968105 511969614 0.000000e+00 2712
8 TraesCS4B01G331000 chr5A 93.019 1633 80 15 1650 3263 667303315 667301698 0.000000e+00 2353
9 TraesCS4B01G331000 chr5A 97.015 201 6 0 3510 3710 504234494 504234694 4.590000e-89 339
10 TraesCS4B01G331000 chr5B 99.137 1507 11 2 3 1507 430676229 430674723 0.000000e+00 2710
11 TraesCS4B01G331000 chr5B 96.517 201 7 0 3510 3710 559156630 559156430 2.140000e-87 333
12 TraesCS4B01G331000 chr4A 99.137 1506 12 1 3 1507 38387008 38385503 0.000000e+00 2708
13 TraesCS4B01G331000 chr3A 99.136 1505 13 0 3 1507 44736966 44738470 0.000000e+00 2708
14 TraesCS4B01G331000 chr1A 99.071 1507 12 2 3 1507 366258927 366260433 0.000000e+00 2704
15 TraesCS4B01G331000 chr7A 99.070 1505 13 1 3 1507 704318495 704319998 0.000000e+00 2700
16 TraesCS4B01G331000 chr6B 98.876 1512 14 3 3 1512 184907527 184909037 0.000000e+00 2695
17 TraesCS4B01G331000 chr6B 96.020 201 8 0 3510 3710 649863432 649863232 9.930000e-86 327
18 TraesCS4B01G331000 chr4D 93.063 1283 58 17 1650 2927 486930591 486929335 0.000000e+00 1847
19 TraesCS4B01G331000 chr4D 93.289 149 10 0 1507 1655 486930771 486930623 1.730000e-53 220
20 TraesCS4B01G331000 chr2B 96.098 205 8 0 3506 3710 373297159 373296955 5.940000e-88 335
21 TraesCS4B01G331000 chrUn 95.122 205 10 0 3506 3710 47933070 47932866 1.290000e-84 324


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 TraesCS4B01G331000 chr4B 621704614 621708323 3709 True 6852.0 6852 100.000 1 3710 1 chr4B.!!$R1 3709
1 TraesCS4B01G331000 chr4B 75186566 75188072 1506 False 2704.0 2704 99.071 3 1507 1 chr4B.!!$F2 1504
2 TraesCS4B01G331000 chr3B 644837614 644839118 1504 False 2713.0 2713 99.203 3 1507 1 chr3B.!!$F1 1504
3 TraesCS4B01G331000 chr5A 511968105 511969614 1509 False 2712.0 2712 99.073 3 1512 1 chr5A.!!$F2 1509
4 TraesCS4B01G331000 chr5A 667301698 667303315 1617 True 2353.0 2353 93.019 1650 3263 1 chr5A.!!$R1 1613
5 TraesCS4B01G331000 chr5B 430674723 430676229 1506 True 2710.0 2710 99.137 3 1507 1 chr5B.!!$R1 1504
6 TraesCS4B01G331000 chr4A 38385503 38387008 1505 True 2708.0 2708 99.137 3 1507 1 chr4A.!!$R1 1504
7 TraesCS4B01G331000 chr3A 44736966 44738470 1504 False 2708.0 2708 99.136 3 1507 1 chr3A.!!$F1 1504
8 TraesCS4B01G331000 chr1A 366258927 366260433 1506 False 2704.0 2704 99.071 3 1507 1 chr1A.!!$F1 1504
9 TraesCS4B01G331000 chr7A 704318495 704319998 1503 False 2700.0 2700 99.070 3 1507 1 chr7A.!!$F1 1504
10 TraesCS4B01G331000 chr6B 184907527 184909037 1510 False 2695.0 2695 98.876 3 1512 1 chr6B.!!$F1 1509
11 TraesCS4B01G331000 chr4D 486929335 486930771 1436 True 1033.5 1847 93.176 1507 2927 2 chr4D.!!$R1 1420

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
1228 1231 2.102588 CGATCGGTTCCCCACTTTAGAT 59.897 50.0 7.38 0.0 0.00 1.98 F
2420 2463 1.101331 GCATTTGCTCCTCTTCTGGG 58.899 55.0 0.00 0.0 38.21 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2700 2743 0.179145 TGCTAAGCCGCTACTCGAAC 60.179 55.0 0.00 0.0 41.67 3.95 R
3349 3410 0.040692 CATTCGGCCATCGCATCAAG 60.041 55.0 2.24 0.0 39.05 3.02 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
1228 1231 2.102588 CGATCGGTTCCCCACTTTAGAT 59.897 50.000 7.38 0.00 0.00 1.98
1533 1538 4.836825 TCTTCTCACTTATCCAAGCCAAG 58.163 43.478 0.00 0.00 34.94 3.61
1541 1546 4.534103 ACTTATCCAAGCCAAGTTCTCTCT 59.466 41.667 0.00 0.00 34.94 3.10
1549 1554 6.183360 CCAAGCCAAGTTCTCTCTATCAATTG 60.183 42.308 0.00 0.00 0.00 2.32
1560 1565 5.253330 TCTCTATCAATTGTCCCAAACCAC 58.747 41.667 5.13 0.00 0.00 4.16
1565 1570 1.643310 ATTGTCCCAAACCACCCATG 58.357 50.000 0.00 0.00 0.00 3.66
1592 1597 5.244851 ACATCACGAGCTCCTCATATATTGT 59.755 40.000 8.47 0.00 0.00 2.71
1595 1600 5.985530 TCACGAGCTCCTCATATATTGTTTG 59.014 40.000 8.47 0.00 0.00 2.93
1600 1605 7.307042 CGAGCTCCTCATATATTGTTTGTTCTG 60.307 40.741 8.47 0.00 0.00 3.02
1635 1640 8.862325 ATCAAAGACTGGATTGTACATAAACA 57.138 30.769 0.00 0.00 0.00 2.83
1692 1734 5.823045 CCACACTTTCTCTTTACACTTTCCT 59.177 40.000 0.00 0.00 0.00 3.36
1764 1807 6.806668 TGGAATTCCACCTTTTCTTTCTTT 57.193 33.333 23.63 0.00 42.01 2.52
1775 1818 7.495606 CACCTTTTCTTTCTTTAAATGCCTTGT 59.504 33.333 0.00 0.00 0.00 3.16
2152 2195 3.768468 GACTCTTGTCGGTAAGGAGAG 57.232 52.381 0.00 0.00 39.69 3.20
2167 2210 4.833478 AGGAGAGCATGAACACAGTTAT 57.167 40.909 0.00 0.00 0.00 1.89
2168 2211 4.764172 AGGAGAGCATGAACACAGTTATC 58.236 43.478 0.00 0.00 0.00 1.75
2169 2212 4.223700 AGGAGAGCATGAACACAGTTATCA 59.776 41.667 0.00 0.00 0.00 2.15
2170 2213 4.331168 GGAGAGCATGAACACAGTTATCAC 59.669 45.833 0.00 0.00 0.00 3.06
2206 2249 8.652810 ACATTTCTGGATTCACTTTTCTTTTG 57.347 30.769 0.00 0.00 0.00 2.44
2349 2392 2.703416 TCAATAGAACAGTGGCTGCAG 58.297 47.619 10.11 10.11 34.37 4.41
2420 2463 1.101331 GCATTTGCTCCTCTTCTGGG 58.899 55.000 0.00 0.00 38.21 4.45
2490 2533 4.393062 CAGCAAGTCCTCAATGTTTACGAT 59.607 41.667 0.00 0.00 0.00 3.73
2517 2560 8.749026 AAATACTCTCGAAGAATGAGTACCTA 57.251 34.615 12.18 0.00 43.68 3.08
2556 2599 2.363172 GGCTGACCTCTCCCACCTC 61.363 68.421 0.00 0.00 0.00 3.85
2703 2746 3.567797 GAGCATCCTGGCGCGTTC 61.568 66.667 8.43 0.58 39.27 3.95
2709 2752 2.337749 ATCCTGGCGCGTTCGAGTAG 62.338 60.000 8.43 0.00 38.10 2.57
2715 2758 2.506438 GCGTTCGAGTAGCGGCTT 60.506 61.111 8.26 0.00 41.33 4.35
2716 2759 1.226491 GCGTTCGAGTAGCGGCTTA 60.226 57.895 8.26 0.00 41.33 3.09
2717 2760 1.201098 GCGTTCGAGTAGCGGCTTAG 61.201 60.000 8.26 0.00 41.33 2.18
2718 2761 1.201098 CGTTCGAGTAGCGGCTTAGC 61.201 60.000 8.26 0.00 41.33 3.09
2719 2762 0.179145 GTTCGAGTAGCGGCTTAGCA 60.179 55.000 8.26 0.00 41.33 3.49
2741 2784 3.414700 GGTGGTCGCGAGCAAGTG 61.415 66.667 39.00 0.00 40.82 3.16
2743 2786 2.355837 TGGTCGCGAGCAAGTGTC 60.356 61.111 36.10 9.63 35.69 3.67
2747 2792 3.832171 CGCGAGCAAGTGTCGAGC 61.832 66.667 0.00 0.00 39.92 5.03
2752 2797 3.134401 AGCAAGTGTCGAGCTCATG 57.866 52.632 15.40 0.00 32.05 3.07
2771 2816 3.284323 TGTTGAAGAGCTGTCTACGTC 57.716 47.619 0.00 0.00 30.45 4.34
2831 2879 3.556775 GCTACTTGTGTTGTCGTTTACCA 59.443 43.478 0.00 0.00 0.00 3.25
2839 2887 4.514066 GTGTTGTCGTTTACCAAATCCTCT 59.486 41.667 0.00 0.00 0.00 3.69
2842 2890 4.963373 TGTCGTTTACCAAATCCTCTTCA 58.037 39.130 0.00 0.00 0.00 3.02
2843 2891 5.556915 TGTCGTTTACCAAATCCTCTTCAT 58.443 37.500 0.00 0.00 0.00 2.57
2844 2892 6.001460 TGTCGTTTACCAAATCCTCTTCATT 58.999 36.000 0.00 0.00 0.00 2.57
2846 2894 6.001460 TCGTTTACCAAATCCTCTTCATTGT 58.999 36.000 0.00 0.00 0.00 2.71
2852 2900 5.011023 ACCAAATCCTCTTCATTGTTTGTCC 59.989 40.000 0.00 0.00 0.00 4.02
2889 2937 1.896220 TGAGGCCTGTTTGTGATGTC 58.104 50.000 12.00 0.00 0.00 3.06
2891 2939 1.808945 GAGGCCTGTTTGTGATGTCTG 59.191 52.381 12.00 0.00 0.00 3.51
2943 2993 1.067283 CCTGGTGTGCTCTACTGTCTG 60.067 57.143 0.00 0.00 0.00 3.51
2944 2994 0.318441 TGGTGTGCTCTACTGTCTGC 59.682 55.000 0.00 0.00 0.00 4.26
2952 3002 3.070159 TGCTCTACTGTCTGCTTTTCACT 59.930 43.478 0.00 0.00 0.00 3.41
2953 3003 4.280929 TGCTCTACTGTCTGCTTTTCACTA 59.719 41.667 0.00 0.00 0.00 2.74
2954 3004 5.047021 TGCTCTACTGTCTGCTTTTCACTAT 60.047 40.000 0.00 0.00 0.00 2.12
2955 3005 6.152831 TGCTCTACTGTCTGCTTTTCACTATA 59.847 38.462 0.00 0.00 0.00 1.31
2956 3006 6.474102 GCTCTACTGTCTGCTTTTCACTATAC 59.526 42.308 0.00 0.00 0.00 1.47
3060 3117 9.478768 TGTTGTTGTATTTAGATGTTCTACGAA 57.521 29.630 0.00 0.00 0.00 3.85
3087 3144 4.675146 GCATTCTGGTTGCATATTTCGTGT 60.675 41.667 0.00 0.00 39.90 4.49
3127 3187 6.447084 TGTAAAACATAAAGGAGGGGATCTCT 59.553 38.462 0.00 0.00 42.10 3.10
3166 3227 1.005340 GCTCGAAAGTCAGATGCCTG 58.995 55.000 0.00 0.00 41.74 4.85
3263 3324 3.915437 ACGCTAAAACTTCCCACATTG 57.085 42.857 0.00 0.00 0.00 2.82
3264 3325 3.482436 ACGCTAAAACTTCCCACATTGA 58.518 40.909 0.00 0.00 0.00 2.57
3265 3326 3.252458 ACGCTAAAACTTCCCACATTGAC 59.748 43.478 0.00 0.00 0.00 3.18
3266 3327 3.365969 CGCTAAAACTTCCCACATTGACC 60.366 47.826 0.00 0.00 0.00 4.02
3267 3328 3.826729 GCTAAAACTTCCCACATTGACCT 59.173 43.478 0.00 0.00 0.00 3.85
3268 3329 5.007682 GCTAAAACTTCCCACATTGACCTA 58.992 41.667 0.00 0.00 0.00 3.08
3269 3330 5.652452 GCTAAAACTTCCCACATTGACCTAT 59.348 40.000 0.00 0.00 0.00 2.57
3270 3331 6.152831 GCTAAAACTTCCCACATTGACCTATT 59.847 38.462 0.00 0.00 0.00 1.73
3271 3332 7.338449 GCTAAAACTTCCCACATTGACCTATTA 59.662 37.037 0.00 0.00 0.00 0.98
3272 3333 9.408648 CTAAAACTTCCCACATTGACCTATTAT 57.591 33.333 0.00 0.00 0.00 1.28
3274 3335 8.747538 AAACTTCCCACATTGACCTATTATAC 57.252 34.615 0.00 0.00 0.00 1.47
3275 3336 7.446106 ACTTCCCACATTGACCTATTATACA 57.554 36.000 0.00 0.00 0.00 2.29
3276 3337 7.867921 ACTTCCCACATTGACCTATTATACAA 58.132 34.615 0.00 0.00 0.00 2.41
3277 3338 8.502738 ACTTCCCACATTGACCTATTATACAAT 58.497 33.333 0.00 0.00 34.01 2.71
3308 3369 8.995027 ATAGAGGATAGATAAGCGATGATTCT 57.005 34.615 0.00 0.00 0.00 2.40
3310 3371 8.815565 AGAGGATAGATAAGCGATGATTCTAA 57.184 34.615 0.00 0.00 0.00 2.10
3311 3372 9.249053 AGAGGATAGATAAGCGATGATTCTAAA 57.751 33.333 0.00 0.00 0.00 1.85
3312 3373 9.862371 GAGGATAGATAAGCGATGATTCTAAAA 57.138 33.333 0.00 0.00 0.00 1.52
3313 3374 9.646427 AGGATAGATAAGCGATGATTCTAAAAC 57.354 33.333 0.00 0.00 0.00 2.43
3314 3375 9.424319 GGATAGATAAGCGATGATTCTAAAACA 57.576 33.333 0.00 0.00 0.00 2.83
3318 3379 8.616076 AGATAAGCGATGATTCTAAAACAAAGG 58.384 33.333 0.00 0.00 0.00 3.11
3319 3380 4.986622 AGCGATGATTCTAAAACAAAGGC 58.013 39.130 0.00 0.00 0.00 4.35
3320 3381 4.105486 GCGATGATTCTAAAACAAAGGCC 58.895 43.478 0.00 0.00 0.00 5.19
3321 3382 4.342772 CGATGATTCTAAAACAAAGGCCG 58.657 43.478 0.00 0.00 0.00 6.13
3322 3383 3.569250 TGATTCTAAAACAAAGGCCGC 57.431 42.857 0.00 0.00 0.00 6.53
3323 3384 2.095466 TGATTCTAAAACAAAGGCCGCG 60.095 45.455 0.00 0.00 0.00 6.46
3324 3385 1.310904 TTCTAAAACAAAGGCCGCGT 58.689 45.000 4.92 0.00 0.00 6.01
3325 3386 1.310904 TCTAAAACAAAGGCCGCGTT 58.689 45.000 4.92 0.00 0.00 4.84
3326 3387 1.677052 TCTAAAACAAAGGCCGCGTTT 59.323 42.857 4.92 12.66 34.42 3.60
3327 3388 1.784283 CTAAAACAAAGGCCGCGTTTG 59.216 47.619 28.32 28.32 42.53 2.93
3328 3389 1.425267 AAAACAAAGGCCGCGTTTGC 61.425 50.000 29.34 8.73 41.17 3.68
3329 3390 2.564553 AAACAAAGGCCGCGTTTGCA 62.565 50.000 29.34 0.00 41.17 4.08
3330 3391 3.029735 CAAAGGCCGCGTTTGCAC 61.030 61.111 21.74 0.00 42.97 4.57
3331 3392 3.216292 AAAGGCCGCGTTTGCACT 61.216 55.556 10.15 0.00 42.97 4.40
3332 3393 2.781158 AAAGGCCGCGTTTGCACTT 61.781 52.632 10.15 4.71 42.97 3.16
3333 3394 1.448922 AAAGGCCGCGTTTGCACTTA 61.449 50.000 10.15 0.00 42.97 2.24
3334 3395 1.852067 AAGGCCGCGTTTGCACTTAG 61.852 55.000 4.92 0.00 42.97 2.18
3335 3396 2.613506 GGCCGCGTTTGCACTTAGT 61.614 57.895 4.92 0.00 42.97 2.24
3336 3397 1.440353 GCCGCGTTTGCACTTAGTG 60.440 57.895 8.18 8.18 42.97 2.74
3349 3410 4.928661 CACTTAGTGCAGTTGTATCACC 57.071 45.455 0.00 0.00 0.00 4.02
3350 3411 4.569943 CACTTAGTGCAGTTGTATCACCT 58.430 43.478 0.00 0.00 0.00 4.00
3351 3412 4.997395 CACTTAGTGCAGTTGTATCACCTT 59.003 41.667 0.00 0.00 0.00 3.50
3352 3413 4.997395 ACTTAGTGCAGTTGTATCACCTTG 59.003 41.667 0.00 0.00 0.00 3.61
3353 3414 3.769739 AGTGCAGTTGTATCACCTTGA 57.230 42.857 0.00 0.00 0.00 3.02
3354 3415 4.292186 AGTGCAGTTGTATCACCTTGAT 57.708 40.909 0.00 0.00 40.72 2.57
3355 3416 4.005650 AGTGCAGTTGTATCACCTTGATG 58.994 43.478 0.00 0.00 37.70 3.07
3356 3417 2.749076 TGCAGTTGTATCACCTTGATGC 59.251 45.455 0.00 0.00 37.70 3.91
3357 3418 2.223112 GCAGTTGTATCACCTTGATGCG 60.223 50.000 0.00 0.00 41.50 4.73
3358 3419 3.261580 CAGTTGTATCACCTTGATGCGA 58.738 45.455 0.00 0.00 41.50 5.10
3359 3420 3.873361 CAGTTGTATCACCTTGATGCGAT 59.127 43.478 0.00 0.00 41.50 4.58
3360 3421 3.873361 AGTTGTATCACCTTGATGCGATG 59.127 43.478 0.00 0.00 41.50 3.84
3361 3422 2.837498 TGTATCACCTTGATGCGATGG 58.163 47.619 0.00 0.00 41.50 3.51
3362 3423 1.532868 GTATCACCTTGATGCGATGGC 59.467 52.381 0.00 0.00 37.70 4.40
3363 3424 0.820891 ATCACCTTGATGCGATGGCC 60.821 55.000 0.00 0.00 35.43 5.36
3364 3425 2.514592 ACCTTGATGCGATGGCCG 60.515 61.111 0.00 0.00 38.85 6.13
3365 3426 2.203056 CCTTGATGCGATGGCCGA 60.203 61.111 0.00 0.00 41.76 5.54
3366 3427 1.819208 CCTTGATGCGATGGCCGAA 60.819 57.895 0.00 0.00 41.76 4.30
3367 3428 1.168407 CCTTGATGCGATGGCCGAAT 61.168 55.000 0.00 0.00 39.80 3.34
3368 3429 0.040692 CTTGATGCGATGGCCGAATG 60.041 55.000 0.00 0.00 36.46 2.67
3369 3430 0.463474 TTGATGCGATGGCCGAATGA 60.463 50.000 0.00 0.00 36.46 2.57
3370 3431 0.463474 TGATGCGATGGCCGAATGAA 60.463 50.000 0.00 0.00 36.46 2.57
3371 3432 0.662619 GATGCGATGGCCGAATGAAA 59.337 50.000 0.00 0.00 36.46 2.69
3372 3433 1.267806 GATGCGATGGCCGAATGAAAT 59.732 47.619 0.00 0.00 36.46 2.17
3373 3434 1.102154 TGCGATGGCCGAATGAAATT 58.898 45.000 0.00 0.00 41.76 1.82
3374 3435 1.476085 TGCGATGGCCGAATGAAATTT 59.524 42.857 0.00 0.00 41.76 1.82
3375 3436 2.094286 TGCGATGGCCGAATGAAATTTT 60.094 40.909 0.00 0.00 41.76 1.82
3376 3437 3.129462 TGCGATGGCCGAATGAAATTTTA 59.871 39.130 0.00 0.00 41.76 1.52
3377 3438 4.202101 TGCGATGGCCGAATGAAATTTTAT 60.202 37.500 0.00 0.00 41.76 1.40
3378 3439 4.382754 GCGATGGCCGAATGAAATTTTATC 59.617 41.667 0.00 0.00 36.07 1.75
3379 3440 4.917415 CGATGGCCGAATGAAATTTTATCC 59.083 41.667 0.00 0.00 36.07 2.59
3380 3441 5.507149 CGATGGCCGAATGAAATTTTATCCA 60.507 40.000 0.00 4.28 36.07 3.41
3381 3442 5.667539 TGGCCGAATGAAATTTTATCCAA 57.332 34.783 0.00 0.00 36.07 3.53
3382 3443 6.042638 TGGCCGAATGAAATTTTATCCAAA 57.957 33.333 0.00 0.00 36.07 3.28
3383 3444 6.467677 TGGCCGAATGAAATTTTATCCAAAA 58.532 32.000 0.00 0.00 36.07 2.44
3384 3445 6.936900 TGGCCGAATGAAATTTTATCCAAAAA 59.063 30.769 0.00 0.00 36.07 1.94
3410 3471 9.490379 AAAGACGATTCTAAAAGATTGTACTGT 57.510 29.630 0.00 0.00 0.00 3.55
3437 3498 5.468540 AAAAACTGTAAAGGCCTGGATTC 57.531 39.130 5.69 0.00 0.00 2.52
3438 3499 2.808906 ACTGTAAAGGCCTGGATTCC 57.191 50.000 5.69 0.00 0.00 3.01
3439 3500 1.992557 ACTGTAAAGGCCTGGATTCCA 59.007 47.619 5.69 5.05 0.00 3.53
3440 3501 2.582636 ACTGTAAAGGCCTGGATTCCAT 59.417 45.455 5.69 0.00 30.82 3.41
3441 3502 2.954318 CTGTAAAGGCCTGGATTCCATG 59.046 50.000 5.69 4.62 30.82 3.66
3442 3503 2.310538 GTAAAGGCCTGGATTCCATGG 58.689 52.381 5.69 4.97 30.82 3.66
3443 3504 0.712380 AAAGGCCTGGATTCCATGGT 59.288 50.000 5.69 0.00 30.82 3.55
3444 3505 1.607225 AAGGCCTGGATTCCATGGTA 58.393 50.000 5.69 1.50 30.82 3.25
3445 3506 0.846693 AGGCCTGGATTCCATGGTAC 59.153 55.000 12.58 4.41 30.82 3.34
3446 3507 0.178990 GGCCTGGATTCCATGGTACC 60.179 60.000 12.58 13.71 30.82 3.34
3447 3508 0.550914 GCCTGGATTCCATGGTACCA 59.449 55.000 18.99 18.99 30.82 3.25
3448 3509 1.750682 GCCTGGATTCCATGGTACCAC 60.751 57.143 19.09 2.64 30.82 4.16
3449 3510 1.846439 CCTGGATTCCATGGTACCACT 59.154 52.381 19.09 3.70 30.82 4.00
3450 3511 3.045634 CCTGGATTCCATGGTACCACTA 58.954 50.000 19.09 2.22 30.82 2.74
3451 3512 3.652869 CCTGGATTCCATGGTACCACTAT 59.347 47.826 19.09 8.14 30.82 2.12
3452 3513 4.844085 CCTGGATTCCATGGTACCACTATA 59.156 45.833 19.09 3.76 30.82 1.31
3453 3514 5.488919 CCTGGATTCCATGGTACCACTATAT 59.511 44.000 19.09 8.90 30.82 0.86
3454 3515 6.012508 CCTGGATTCCATGGTACCACTATATT 60.013 42.308 19.09 0.00 30.82 1.28
3455 3516 7.182026 CCTGGATTCCATGGTACCACTATATTA 59.818 40.741 19.09 0.00 30.82 0.98
3456 3517 8.146053 TGGATTCCATGGTACCACTATATTAG 57.854 38.462 19.09 0.00 0.00 1.73
3457 3518 7.737607 TGGATTCCATGGTACCACTATATTAGT 59.262 37.037 19.09 0.00 40.28 2.24
3472 3533 8.327941 ACTATATTAGTGTTATGGCATTGCTG 57.672 34.615 4.78 0.00 37.69 4.41
3473 3534 4.924305 ATTAGTGTTATGGCATTGCTGG 57.076 40.909 4.78 0.00 0.00 4.85
3474 3535 2.220653 AGTGTTATGGCATTGCTGGT 57.779 45.000 4.78 0.00 0.00 4.00
3475 3536 2.094675 AGTGTTATGGCATTGCTGGTC 58.905 47.619 4.78 0.00 0.00 4.02
3476 3537 1.818060 GTGTTATGGCATTGCTGGTCA 59.182 47.619 4.78 0.00 0.00 4.02
3477 3538 2.230992 GTGTTATGGCATTGCTGGTCAA 59.769 45.455 4.78 0.00 39.32 3.18
3478 3539 2.492881 TGTTATGGCATTGCTGGTCAAG 59.507 45.455 4.78 0.00 38.22 3.02
3487 3548 2.282462 CTGGTCAAGCACCCACCC 60.282 66.667 0.00 0.00 46.18 4.61
3488 3549 3.099841 TGGTCAAGCACCCACCCA 61.100 61.111 0.00 0.00 46.18 4.51
3489 3550 2.597510 GGTCAAGCACCCACCCAC 60.598 66.667 0.00 0.00 39.69 4.61
3490 3551 2.597510 GTCAAGCACCCACCCACC 60.598 66.667 0.00 0.00 0.00 4.61
3491 3552 3.897122 TCAAGCACCCACCCACCC 61.897 66.667 0.00 0.00 0.00 4.61
3492 3553 4.994756 CAAGCACCCACCCACCCC 62.995 72.222 0.00 0.00 0.00 4.95
3496 3557 3.966543 CACCCACCCACCCCTGTC 61.967 72.222 0.00 0.00 0.00 3.51
3500 3561 3.650950 CACCCACCCCTGTCCCTG 61.651 72.222 0.00 0.00 0.00 4.45
3508 3569 3.775654 CCTGTCCCTGCGGTCCTC 61.776 72.222 0.00 0.00 0.00 3.71
3509 3570 2.997315 CTGTCCCTGCGGTCCTCA 60.997 66.667 0.00 0.00 0.00 3.86
3510 3571 2.997315 TGTCCCTGCGGTCCTCAG 60.997 66.667 1.51 1.51 0.00 3.35
3515 3576 4.020617 CTGCGGTCCTCAGGCCAA 62.021 66.667 5.01 0.00 0.00 4.52
3516 3577 4.329545 TGCGGTCCTCAGGCCAAC 62.330 66.667 5.01 0.00 0.00 3.77
3517 3578 4.021925 GCGGTCCTCAGGCCAACT 62.022 66.667 5.01 0.00 0.00 3.16
3518 3579 2.266055 CGGTCCTCAGGCCAACTC 59.734 66.667 5.01 0.00 0.00 3.01
3519 3580 2.671682 GGTCCTCAGGCCAACTCC 59.328 66.667 5.01 0.00 0.00 3.85
3520 3581 2.224159 GGTCCTCAGGCCAACTCCA 61.224 63.158 5.01 0.00 0.00 3.86
3521 3582 1.003233 GTCCTCAGGCCAACTCCAC 60.003 63.158 5.01 0.00 0.00 4.02
3522 3583 2.224159 TCCTCAGGCCAACTCCACC 61.224 63.158 5.01 0.00 0.00 4.61
3523 3584 2.046892 CTCAGGCCAACTCCACCG 60.047 66.667 5.01 0.00 0.00 4.94
3524 3585 4.329545 TCAGGCCAACTCCACCGC 62.330 66.667 5.01 0.00 0.00 5.68
3548 3609 4.181010 CCATCCTGTCCGGCCCTG 62.181 72.222 0.00 0.00 0.00 4.45
3549 3610 3.402681 CATCCTGTCCGGCCCTGT 61.403 66.667 0.00 0.00 0.00 4.00
3550 3611 3.083997 ATCCTGTCCGGCCCTGTC 61.084 66.667 0.00 0.00 0.00 3.51
3559 3620 3.961414 GGCCCTGTCCGTTTGGGA 61.961 66.667 0.91 0.00 43.47 4.37
3574 3635 2.080654 TGGGACAAAAGGGACAAAGG 57.919 50.000 0.00 0.00 31.92 3.11
3575 3636 1.571457 TGGGACAAAAGGGACAAAGGA 59.429 47.619 0.00 0.00 31.92 3.36
3576 3637 2.239400 GGGACAAAAGGGACAAAGGAG 58.761 52.381 0.00 0.00 0.00 3.69
3577 3638 2.239400 GGACAAAAGGGACAAAGGAGG 58.761 52.381 0.00 0.00 0.00 4.30
3578 3639 1.613925 GACAAAAGGGACAAAGGAGGC 59.386 52.381 0.00 0.00 0.00 4.70
3579 3640 0.598065 CAAAAGGGACAAAGGAGGCG 59.402 55.000 0.00 0.00 0.00 5.52
3580 3641 0.539669 AAAAGGGACAAAGGAGGCGG 60.540 55.000 0.00 0.00 0.00 6.13
3581 3642 3.569200 AAGGGACAAAGGAGGCGGC 62.569 63.158 0.00 0.00 0.00 6.53
3584 3645 4.344865 GACAAAGGAGGCGGCCCA 62.345 66.667 17.02 0.00 0.00 5.36
3585 3646 4.351054 ACAAAGGAGGCGGCCCAG 62.351 66.667 17.02 1.90 0.00 4.45
3612 3673 4.176752 GCCCGGACCCATCCTGTC 62.177 72.222 0.73 0.00 43.73 3.51
3616 3677 3.400188 GGACCCATCCTGTCCGTT 58.600 61.111 0.00 0.00 42.63 4.44
3617 3678 1.683441 GGACCCATCCTGTCCGTTT 59.317 57.895 0.00 0.00 42.63 3.60
3618 3679 0.037734 GGACCCATCCTGTCCGTTTT 59.962 55.000 0.00 0.00 42.63 2.43
3619 3680 1.165270 GACCCATCCTGTCCGTTTTG 58.835 55.000 0.00 0.00 0.00 2.44
3620 3681 0.476771 ACCCATCCTGTCCGTTTTGT 59.523 50.000 0.00 0.00 0.00 2.83
3621 3682 0.881118 CCCATCCTGTCCGTTTTGTG 59.119 55.000 0.00 0.00 0.00 3.33
3622 3683 1.604604 CCATCCTGTCCGTTTTGTGT 58.395 50.000 0.00 0.00 0.00 3.72
3623 3684 1.535462 CCATCCTGTCCGTTTTGTGTC 59.465 52.381 0.00 0.00 0.00 3.67
3624 3685 1.535462 CATCCTGTCCGTTTTGTGTCC 59.465 52.381 0.00 0.00 0.00 4.02
3625 3686 0.531090 TCCTGTCCGTTTTGTGTCCG 60.531 55.000 0.00 0.00 0.00 4.79
3626 3687 0.531090 CCTGTCCGTTTTGTGTCCGA 60.531 55.000 0.00 0.00 0.00 4.55
3627 3688 0.859232 CTGTCCGTTTTGTGTCCGAG 59.141 55.000 0.00 0.00 0.00 4.63
3628 3689 1.155424 TGTCCGTTTTGTGTCCGAGC 61.155 55.000 0.00 0.00 0.00 5.03
3629 3690 1.595929 TCCGTTTTGTGTCCGAGCC 60.596 57.895 0.00 0.00 0.00 4.70
3630 3691 2.549282 CGTTTTGTGTCCGAGCCG 59.451 61.111 0.00 0.00 0.00 5.52
3631 3692 1.952133 CGTTTTGTGTCCGAGCCGA 60.952 57.895 0.00 0.00 0.00 5.54
3632 3693 1.568025 GTTTTGTGTCCGAGCCGAC 59.432 57.895 0.00 0.00 0.00 4.79
3633 3694 1.595929 TTTTGTGTCCGAGCCGACC 60.596 57.895 0.00 0.00 31.35 4.79
3634 3695 2.999739 TTTTGTGTCCGAGCCGACCC 63.000 60.000 0.00 0.00 31.35 4.46
3636 3697 3.771160 GTGTCCGAGCCGACCCAT 61.771 66.667 0.00 0.00 31.35 4.00
3637 3698 3.000819 TGTCCGAGCCGACCCATT 61.001 61.111 0.00 0.00 31.35 3.16
3638 3699 2.267961 GTCCGAGCCGACCCATTT 59.732 61.111 0.00 0.00 0.00 2.32
3639 3700 1.814169 GTCCGAGCCGACCCATTTC 60.814 63.158 0.00 0.00 0.00 2.17
3640 3701 2.890474 CCGAGCCGACCCATTTCG 60.890 66.667 0.00 0.00 38.80 3.46
3641 3702 2.183300 CGAGCCGACCCATTTCGA 59.817 61.111 0.00 0.00 41.78 3.71
3642 3703 1.878522 CGAGCCGACCCATTTCGAG 60.879 63.158 0.00 0.00 41.78 4.04
3643 3704 2.125106 AGCCGACCCATTTCGAGC 60.125 61.111 0.00 0.00 41.78 5.03
3644 3705 3.564027 GCCGACCCATTTCGAGCG 61.564 66.667 0.00 0.00 41.78 5.03
3645 3706 3.564027 CCGACCCATTTCGAGCGC 61.564 66.667 0.00 0.00 41.78 5.92
3646 3707 2.813474 CGACCCATTTCGAGCGCA 60.813 61.111 11.47 0.00 41.78 6.09
3647 3708 2.387445 CGACCCATTTCGAGCGCAA 61.387 57.895 11.47 0.00 41.78 4.85
3648 3709 1.873165 GACCCATTTCGAGCGCAAA 59.127 52.632 11.47 1.09 0.00 3.68
3649 3710 0.454452 GACCCATTTCGAGCGCAAAC 60.454 55.000 11.47 0.00 0.00 2.93
3650 3711 0.889186 ACCCATTTCGAGCGCAAACT 60.889 50.000 11.47 0.00 0.00 2.66
3651 3712 0.240945 CCCATTTCGAGCGCAAACTT 59.759 50.000 11.47 0.00 0.00 2.66
3652 3713 1.330306 CCATTTCGAGCGCAAACTTG 58.670 50.000 11.47 0.00 0.00 3.16
3661 3722 4.279043 GCAAACTTGCGCCGGGTT 62.279 61.111 4.18 4.28 45.11 4.11
3662 3723 2.415426 CAAACTTGCGCCGGGTTT 59.585 55.556 4.18 10.66 34.10 3.27
3663 3724 1.948635 CAAACTTGCGCCGGGTTTG 60.949 57.895 24.29 24.29 42.01 2.93
3664 3725 3.145422 AAACTTGCGCCGGGTTTGG 62.145 57.895 17.28 0.00 32.84 3.28
3683 3744 4.690719 TCGCGGCGGACACCAAAT 62.691 61.111 23.46 0.00 0.00 2.32
3684 3745 4.459331 CGCGGCGGACACCAAATG 62.459 66.667 15.84 0.00 0.00 2.32
3685 3746 4.114997 GCGGCGGACACCAAATGG 62.115 66.667 9.78 0.00 42.17 3.16
3686 3747 2.359354 CGGCGGACACCAAATGGA 60.359 61.111 6.42 0.00 38.94 3.41
3687 3748 2.686816 CGGCGGACACCAAATGGAC 61.687 63.158 6.42 0.00 38.94 4.02
3688 3749 2.686816 GGCGGACACCAAATGGACG 61.687 63.158 6.42 6.38 38.94 4.79
3689 3750 2.867472 CGGACACCAAATGGACGC 59.133 61.111 6.42 0.00 38.94 5.19
3690 3751 2.867472 GGACACCAAATGGACGCG 59.133 61.111 3.53 3.53 38.94 6.01
3691 3752 2.175811 GACACCAAATGGACGCGC 59.824 61.111 5.73 0.00 38.94 6.86
3692 3753 3.645157 GACACCAAATGGACGCGCG 62.645 63.158 30.96 30.96 38.94 6.86
3696 3757 4.520846 CAAATGGACGCGCGCCTC 62.521 66.667 32.36 23.38 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1549 1554 1.118356 TTGCATGGGTGGTTTGGGAC 61.118 55.000 0.00 0.00 0.00 4.46
1560 1565 1.028330 AGCTCGTGATGTTGCATGGG 61.028 55.000 0.00 0.00 0.00 4.00
1565 1570 0.390340 TGAGGAGCTCGTGATGTTGC 60.390 55.000 14.78 0.00 32.35 4.17
1592 1597 8.612619 GTCTTTGATTACTTGACTCAGAACAAA 58.387 33.333 0.00 0.00 0.00 2.83
1595 1600 7.095439 CCAGTCTTTGATTACTTGACTCAGAAC 60.095 40.741 0.00 0.00 36.05 3.01
1600 1605 7.389053 ACAATCCAGTCTTTGATTACTTGACTC 59.611 37.037 0.00 0.00 36.05 3.36
1635 1640 7.528996 TCTTGCCTGCAAAATATATAGCATT 57.471 32.000 6.00 0.00 36.28 3.56
1764 1807 5.480073 AGCAGGTTTCAATACAAGGCATTTA 59.520 36.000 0.00 0.00 0.00 1.40
1769 1812 2.558359 ACAGCAGGTTTCAATACAAGGC 59.442 45.455 0.00 0.00 0.00 4.35
1775 1818 3.500448 TGGTGACAGCAGGTTTCAATA 57.500 42.857 2.50 0.00 35.01 1.90
1986 2029 2.169789 CCGCAGCCTGATGAACTCG 61.170 63.158 0.00 0.00 0.00 4.18
2152 2195 7.182761 GTGATAAGTGATAACTGTGTTCATGC 58.817 38.462 0.00 0.00 0.00 4.06
2167 2210 6.693466 TCCAGAAATGTAACGTGATAAGTGA 58.307 36.000 0.00 0.00 0.00 3.41
2168 2211 6.961359 TCCAGAAATGTAACGTGATAAGTG 57.039 37.500 0.00 0.00 0.00 3.16
2169 2212 7.822334 TGAATCCAGAAATGTAACGTGATAAGT 59.178 33.333 0.00 0.00 0.00 2.24
2170 2213 8.116753 GTGAATCCAGAAATGTAACGTGATAAG 58.883 37.037 0.00 0.00 0.00 1.73
2205 2248 0.468226 ACGTTGCCTTTCAGTCCTCA 59.532 50.000 0.00 0.00 0.00 3.86
2206 2249 0.868406 CACGTTGCCTTTCAGTCCTC 59.132 55.000 0.00 0.00 0.00 3.71
2349 2392 1.153389 GAAGCTCTGAGCCTCTGCC 60.153 63.158 25.09 5.57 43.77 4.85
2420 2463 1.133976 CCATGTGGTCCTGAGGGATTC 60.134 57.143 0.00 0.00 44.33 2.52
2490 2533 7.339721 AGGTACTCATTCTTCGAGAGTATTTCA 59.660 37.037 12.85 0.00 44.09 2.69
2517 2560 4.606071 GTGAACTCATCGCCAGCT 57.394 55.556 0.00 0.00 32.15 4.24
2556 2599 0.806102 CAATGTACTGCGAGTCCGGG 60.806 60.000 0.00 0.00 36.06 5.73
2697 2740 2.908088 TAAGCCGCTACTCGAACGCG 62.908 60.000 3.53 3.53 45.86 6.01
2700 2743 0.179145 TGCTAAGCCGCTACTCGAAC 60.179 55.000 0.00 0.00 41.67 3.95
2703 2746 1.589196 GGTGCTAAGCCGCTACTCG 60.589 63.158 0.00 0.00 38.08 4.18
2709 2752 2.359975 ACCAAGGTGCTAAGCCGC 60.360 61.111 0.00 0.00 0.00 6.53
2730 2773 3.832171 GCTCGACACTTGCTCGCG 61.832 66.667 0.00 0.00 0.00 5.87
2747 2792 3.856521 CGTAGACAGCTCTTCAACATGAG 59.143 47.826 0.00 0.00 0.00 2.90
2752 2797 3.562567 AGACGTAGACAGCTCTTCAAC 57.437 47.619 0.00 0.00 0.00 3.18
2771 2816 8.864069 AGAACACATGAAAGTAAGATCGATAG 57.136 34.615 0.00 0.00 0.00 2.08
2831 2879 5.835280 ACAGGACAAACAATGAAGAGGATTT 59.165 36.000 0.00 0.00 0.00 2.17
2839 2887 4.019858 TGGTTCACAGGACAAACAATGAA 58.980 39.130 0.00 0.00 0.00 2.57
2889 2937 0.726827 AACGGCGCAATGTACATCAG 59.273 50.000 10.83 6.36 0.00 2.90
2891 2939 3.392769 TTAAACGGCGCAATGTACATC 57.607 42.857 10.83 0.00 0.00 3.06
2943 2993 9.774742 CTTTCTGTTAATGGTATAGTGAAAAGC 57.225 33.333 0.00 0.00 0.00 3.51
2954 3004 9.793259 AGATCAAGTTTCTTTCTGTTAATGGTA 57.207 29.630 0.00 0.00 0.00 3.25
2955 3005 8.697507 AGATCAAGTTTCTTTCTGTTAATGGT 57.302 30.769 0.00 0.00 0.00 3.55
2956 3006 9.971922 AAAGATCAAGTTTCTTTCTGTTAATGG 57.028 29.630 0.00 0.00 38.71 3.16
3012 3069 7.801716 ACATTTGCAAACTAGAACTAACAGA 57.198 32.000 15.41 0.00 0.00 3.41
3014 3071 7.767261 ACAACATTTGCAAACTAGAACTAACA 58.233 30.769 15.41 0.00 0.00 2.41
3024 3081 9.762933 ATCTAAATACAACAACATTTGCAAACT 57.237 25.926 15.41 0.00 0.00 2.66
3048 3105 5.446473 CCAGAATGCAAGTTCGTAGAACATC 60.446 44.000 14.31 4.51 36.54 3.06
3057 3114 1.689959 GCAACCAGAATGCAAGTTCG 58.310 50.000 0.00 0.00 43.29 3.95
3095 3152 9.196139 CCCCTCCTTTATGTTTTACAATATCAA 57.804 33.333 0.00 0.00 0.00 2.57
3105 3162 7.350921 TGATAGAGATCCCCTCCTTTATGTTTT 59.649 37.037 0.00 0.00 42.97 2.43
3114 3171 5.480710 TCAAATTGATAGAGATCCCCTCCT 58.519 41.667 0.00 0.00 42.97 3.69
3115 3172 5.802821 GCTCAAATTGATAGAGATCCCCTCC 60.803 48.000 0.00 0.00 42.97 4.30
3127 3187 3.446799 GCAAATGCGGCTCAAATTGATA 58.553 40.909 0.00 0.00 31.21 2.15
3282 3343 9.420118 AGAATCATCGCTTATCTATCCTCTATT 57.580 33.333 0.00 0.00 0.00 1.73
3283 3344 8.995027 AGAATCATCGCTTATCTATCCTCTAT 57.005 34.615 0.00 0.00 0.00 1.98
3284 3345 9.907229 TTAGAATCATCGCTTATCTATCCTCTA 57.093 33.333 0.00 0.00 0.00 2.43
3285 3346 8.815565 TTAGAATCATCGCTTATCTATCCTCT 57.184 34.615 0.00 0.00 0.00 3.69
3286 3347 9.862371 TTTTAGAATCATCGCTTATCTATCCTC 57.138 33.333 0.00 0.00 0.00 3.71
3287 3348 9.646427 GTTTTAGAATCATCGCTTATCTATCCT 57.354 33.333 0.00 0.00 0.00 3.24
3288 3349 9.424319 TGTTTTAGAATCATCGCTTATCTATCC 57.576 33.333 0.00 0.00 0.00 2.59
3292 3353 8.616076 CCTTTGTTTTAGAATCATCGCTTATCT 58.384 33.333 0.00 0.00 0.00 1.98
3293 3354 7.377131 GCCTTTGTTTTAGAATCATCGCTTATC 59.623 37.037 0.00 0.00 0.00 1.75
3294 3355 7.196331 GCCTTTGTTTTAGAATCATCGCTTAT 58.804 34.615 0.00 0.00 0.00 1.73
3295 3356 6.404293 GGCCTTTGTTTTAGAATCATCGCTTA 60.404 38.462 0.00 0.00 0.00 3.09
3296 3357 5.402398 GCCTTTGTTTTAGAATCATCGCTT 58.598 37.500 0.00 0.00 0.00 4.68
3297 3358 4.142381 GGCCTTTGTTTTAGAATCATCGCT 60.142 41.667 0.00 0.00 0.00 4.93
3298 3359 4.105486 GGCCTTTGTTTTAGAATCATCGC 58.895 43.478 0.00 0.00 0.00 4.58
3299 3360 4.342772 CGGCCTTTGTTTTAGAATCATCG 58.657 43.478 0.00 0.00 0.00 3.84
3300 3361 4.105486 GCGGCCTTTGTTTTAGAATCATC 58.895 43.478 0.00 0.00 0.00 2.92
3301 3362 3.427503 CGCGGCCTTTGTTTTAGAATCAT 60.428 43.478 0.00 0.00 0.00 2.45
3302 3363 2.095466 CGCGGCCTTTGTTTTAGAATCA 60.095 45.455 0.00 0.00 0.00 2.57
3303 3364 2.095415 ACGCGGCCTTTGTTTTAGAATC 60.095 45.455 12.47 0.00 0.00 2.52
3304 3365 1.883926 ACGCGGCCTTTGTTTTAGAAT 59.116 42.857 12.47 0.00 0.00 2.40
3305 3366 1.310904 ACGCGGCCTTTGTTTTAGAA 58.689 45.000 12.47 0.00 0.00 2.10
3306 3367 1.310904 AACGCGGCCTTTGTTTTAGA 58.689 45.000 12.47 0.00 0.00 2.10
3307 3368 1.784283 CAAACGCGGCCTTTGTTTTAG 59.216 47.619 12.47 2.13 33.80 1.85
3308 3369 1.841450 CAAACGCGGCCTTTGTTTTA 58.159 45.000 12.47 0.00 33.80 1.52
3309 3370 1.425267 GCAAACGCGGCCTTTGTTTT 61.425 50.000 20.28 2.45 33.80 2.43
3310 3371 1.880796 GCAAACGCGGCCTTTGTTT 60.881 52.632 20.28 12.68 36.31 2.83
3311 3372 2.279186 GCAAACGCGGCCTTTGTT 60.279 55.556 20.28 7.82 32.18 2.83
3312 3373 3.522731 TGCAAACGCGGCCTTTGT 61.523 55.556 20.28 2.11 32.18 2.83
3313 3374 2.952291 AAGTGCAAACGCGGCCTTTG 62.952 55.000 12.47 16.74 0.00 2.77
3314 3375 1.448922 TAAGTGCAAACGCGGCCTTT 61.449 50.000 12.47 0.00 0.00 3.11
3315 3376 1.852067 CTAAGTGCAAACGCGGCCTT 61.852 55.000 12.47 11.98 0.00 4.35
3316 3377 2.281208 TAAGTGCAAACGCGGCCT 60.281 55.556 12.47 1.01 0.00 5.19
3317 3378 2.175811 CTAAGTGCAAACGCGGCC 59.824 61.111 12.47 0.00 0.00 6.13
3318 3379 1.440353 CACTAAGTGCAAACGCGGC 60.440 57.895 12.47 4.68 0.00 6.53
3319 3380 4.818417 CACTAAGTGCAAACGCGG 57.182 55.556 12.47 0.00 0.00 6.46
3328 3389 4.569943 AGGTGATACAACTGCACTAAGTG 58.430 43.478 0.00 0.00 36.51 3.16
3329 3390 4.891992 AGGTGATACAACTGCACTAAGT 57.108 40.909 0.00 0.00 26.22 2.24
3330 3391 5.237815 TCAAGGTGATACAACTGCACTAAG 58.762 41.667 0.00 0.00 28.79 2.18
3331 3392 5.222079 TCAAGGTGATACAACTGCACTAA 57.778 39.130 0.00 0.00 28.79 2.24
3332 3393 4.882842 TCAAGGTGATACAACTGCACTA 57.117 40.909 0.00 0.00 28.79 2.74
3333 3394 3.769739 TCAAGGTGATACAACTGCACT 57.230 42.857 0.00 0.00 28.79 4.40
3334 3395 3.426695 GCATCAAGGTGATACAACTGCAC 60.427 47.826 0.00 0.00 34.28 4.57
3335 3396 2.749076 GCATCAAGGTGATACAACTGCA 59.251 45.455 0.00 0.00 34.28 4.41
3336 3397 2.223112 CGCATCAAGGTGATACAACTGC 60.223 50.000 0.00 0.00 34.28 4.40
3337 3398 3.261580 TCGCATCAAGGTGATACAACTG 58.738 45.455 0.00 0.00 34.28 3.16
3338 3399 3.610040 TCGCATCAAGGTGATACAACT 57.390 42.857 0.00 0.00 34.28 3.16
3339 3400 3.002656 CCATCGCATCAAGGTGATACAAC 59.997 47.826 0.00 0.00 34.28 3.32
3340 3401 3.205338 CCATCGCATCAAGGTGATACAA 58.795 45.455 0.00 0.00 34.28 2.41
3341 3402 2.837498 CCATCGCATCAAGGTGATACA 58.163 47.619 0.00 0.00 34.28 2.29
3342 3403 1.532868 GCCATCGCATCAAGGTGATAC 59.467 52.381 0.00 0.00 34.28 2.24
3343 3404 1.543208 GGCCATCGCATCAAGGTGATA 60.543 52.381 0.00 0.00 34.28 2.15
3344 3405 0.820891 GGCCATCGCATCAAGGTGAT 60.821 55.000 0.00 0.00 37.65 3.06
3345 3406 1.451927 GGCCATCGCATCAAGGTGA 60.452 57.895 0.00 0.00 36.38 4.02
3346 3407 2.827051 CGGCCATCGCATCAAGGTG 61.827 63.158 2.24 0.00 36.38 4.00
3347 3408 2.514592 CGGCCATCGCATCAAGGT 60.515 61.111 2.24 0.00 36.38 3.50
3348 3409 1.168407 ATTCGGCCATCGCATCAAGG 61.168 55.000 2.24 0.00 39.05 3.61
3349 3410 0.040692 CATTCGGCCATCGCATCAAG 60.041 55.000 2.24 0.00 39.05 3.02
3350 3411 0.463474 TCATTCGGCCATCGCATCAA 60.463 50.000 2.24 0.00 39.05 2.57
3351 3412 0.463474 TTCATTCGGCCATCGCATCA 60.463 50.000 2.24 0.00 39.05 3.07
3352 3413 0.662619 TTTCATTCGGCCATCGCATC 59.337 50.000 2.24 0.00 39.05 3.91
3353 3414 1.321474 ATTTCATTCGGCCATCGCAT 58.679 45.000 2.24 0.00 39.05 4.73
3354 3415 1.102154 AATTTCATTCGGCCATCGCA 58.898 45.000 2.24 0.00 39.05 5.10
3355 3416 2.208326 AAATTTCATTCGGCCATCGC 57.792 45.000 2.24 0.00 39.05 4.58
3356 3417 4.917415 GGATAAAATTTCATTCGGCCATCG 59.083 41.667 2.24 0.00 40.90 3.84
3357 3418 5.841810 TGGATAAAATTTCATTCGGCCATC 58.158 37.500 2.24 0.00 0.00 3.51
3358 3419 5.867903 TGGATAAAATTTCATTCGGCCAT 57.132 34.783 2.24 0.00 0.00 4.40
3359 3420 5.667539 TTGGATAAAATTTCATTCGGCCA 57.332 34.783 2.24 0.00 0.00 5.36
3360 3421 6.976636 TTTTGGATAAAATTTCATTCGGCC 57.023 33.333 0.00 0.00 31.13 6.13
3384 3445 9.490379 ACAGTACAATCTTTTAGAATCGTCTTT 57.510 29.630 0.00 0.00 35.12 2.52
3415 3476 4.283467 GGAATCCAGGCCTTTACAGTTTTT 59.717 41.667 0.00 0.00 0.00 1.94
3416 3477 3.832490 GGAATCCAGGCCTTTACAGTTTT 59.168 43.478 0.00 0.00 0.00 2.43
3417 3478 3.181423 TGGAATCCAGGCCTTTACAGTTT 60.181 43.478 0.00 0.00 0.00 2.66
3418 3479 2.378547 TGGAATCCAGGCCTTTACAGTT 59.621 45.455 0.00 0.00 0.00 3.16
3419 3480 1.992557 TGGAATCCAGGCCTTTACAGT 59.007 47.619 0.00 0.00 0.00 3.55
3420 3481 2.806945 TGGAATCCAGGCCTTTACAG 57.193 50.000 0.00 0.00 0.00 2.74
3421 3482 2.358090 CCATGGAATCCAGGCCTTTACA 60.358 50.000 5.56 1.76 36.75 2.41
3422 3483 2.310538 CCATGGAATCCAGGCCTTTAC 58.689 52.381 5.56 0.00 36.75 2.01
3423 3484 1.929494 ACCATGGAATCCAGGCCTTTA 59.071 47.619 21.47 0.00 36.75 1.85
3424 3485 0.712380 ACCATGGAATCCAGGCCTTT 59.288 50.000 21.47 0.00 36.75 3.11
3425 3486 1.215423 GTACCATGGAATCCAGGCCTT 59.785 52.381 21.47 0.00 36.75 4.35
3426 3487 0.846693 GTACCATGGAATCCAGGCCT 59.153 55.000 21.47 0.00 36.75 5.19
3427 3488 0.178990 GGTACCATGGAATCCAGGCC 60.179 60.000 21.47 0.65 36.75 5.19
3428 3489 0.550914 TGGTACCATGGAATCCAGGC 59.449 55.000 21.47 0.00 36.75 4.85
3429 3490 1.846439 AGTGGTACCATGGAATCCAGG 59.154 52.381 21.47 7.69 36.75 4.45
3430 3491 4.982241 ATAGTGGTACCATGGAATCCAG 57.018 45.455 21.47 0.00 36.75 3.86
3431 3492 7.737607 ACTAATATAGTGGTACCATGGAATCCA 59.262 37.037 21.47 19.31 37.69 3.41
3432 3493 8.147244 ACTAATATAGTGGTACCATGGAATCC 57.853 38.462 21.47 16.96 37.69 3.01
3447 3508 7.391554 CCAGCAATGCCATAACACTAATATAGT 59.608 37.037 0.00 0.00 40.28 2.12
3448 3509 7.391554 ACCAGCAATGCCATAACACTAATATAG 59.608 37.037 0.00 0.00 0.00 1.31
3449 3510 7.230747 ACCAGCAATGCCATAACACTAATATA 58.769 34.615 0.00 0.00 0.00 0.86
3450 3511 6.070656 ACCAGCAATGCCATAACACTAATAT 58.929 36.000 0.00 0.00 0.00 1.28
3451 3512 5.445069 ACCAGCAATGCCATAACACTAATA 58.555 37.500 0.00 0.00 0.00 0.98
3452 3513 4.280819 ACCAGCAATGCCATAACACTAAT 58.719 39.130 0.00 0.00 0.00 1.73
3453 3514 3.694072 GACCAGCAATGCCATAACACTAA 59.306 43.478 0.00 0.00 0.00 2.24
3454 3515 3.278574 GACCAGCAATGCCATAACACTA 58.721 45.455 0.00 0.00 0.00 2.74
3455 3516 2.094675 GACCAGCAATGCCATAACACT 58.905 47.619 0.00 0.00 0.00 3.55
3456 3517 1.818060 TGACCAGCAATGCCATAACAC 59.182 47.619 0.00 0.00 0.00 3.32
3457 3518 2.212812 TGACCAGCAATGCCATAACA 57.787 45.000 0.00 0.00 0.00 2.41
3458 3519 3.155093 CTTGACCAGCAATGCCATAAC 57.845 47.619 0.00 0.00 35.59 1.89
3472 3533 2.597510 GTGGGTGGGTGCTTGACC 60.598 66.667 0.00 0.00 45.28 4.02
3473 3534 2.597510 GGTGGGTGGGTGCTTGAC 60.598 66.667 0.00 0.00 0.00 3.18
3474 3535 3.897122 GGGTGGGTGGGTGCTTGA 61.897 66.667 0.00 0.00 0.00 3.02
3475 3536 4.994756 GGGGTGGGTGGGTGCTTG 62.995 72.222 0.00 0.00 0.00 4.01
3479 3540 3.966543 GACAGGGGTGGGTGGGTG 61.967 72.222 0.00 0.00 0.00 4.61
3483 3544 3.650950 CAGGGACAGGGGTGGGTG 61.651 72.222 0.00 0.00 0.00 4.61
3498 3559 4.020617 TTGGCCTGAGGACCGCAG 62.021 66.667 17.68 17.68 0.00 5.18
3499 3560 4.329545 GTTGGCCTGAGGACCGCA 62.330 66.667 0.00 0.00 0.00 5.69
3500 3561 3.959991 GAGTTGGCCTGAGGACCGC 62.960 68.421 0.00 0.00 0.00 5.68
3501 3562 2.266055 GAGTTGGCCTGAGGACCG 59.734 66.667 0.00 0.00 0.00 4.79
3502 3563 2.224159 TGGAGTTGGCCTGAGGACC 61.224 63.158 0.00 3.08 0.00 4.46
3503 3564 1.003233 GTGGAGTTGGCCTGAGGAC 60.003 63.158 0.65 0.00 0.00 3.85
3504 3565 2.224159 GGTGGAGTTGGCCTGAGGA 61.224 63.158 0.65 0.00 0.00 3.71
3505 3566 2.352805 GGTGGAGTTGGCCTGAGG 59.647 66.667 3.32 0.00 0.00 3.86
3506 3567 2.046892 CGGTGGAGTTGGCCTGAG 60.047 66.667 3.32 0.00 0.00 3.35
3507 3568 4.329545 GCGGTGGAGTTGGCCTGA 62.330 66.667 3.32 0.00 0.00 3.86
3531 3592 4.181010 CAGGGCCGGACAGGATGG 62.181 72.222 11.00 0.00 45.00 3.51
3532 3593 3.391665 GACAGGGCCGGACAGGATG 62.392 68.421 11.00 4.29 45.00 3.51
3533 3594 3.083997 GACAGGGCCGGACAGGAT 61.084 66.667 11.00 0.00 45.00 3.24
3542 3603 3.961414 TCCCAAACGGACAGGGCC 61.961 66.667 0.00 0.00 42.52 5.80
3549 3610 0.551879 TCCCTTTTGTCCCAAACGGA 59.448 50.000 12.31 7.06 38.83 4.69
3550 3611 0.671796 GTCCCTTTTGTCCCAAACGG 59.328 55.000 5.50 5.50 0.00 4.44
3551 3612 1.394618 TGTCCCTTTTGTCCCAAACG 58.605 50.000 0.00 0.00 0.00 3.60
3552 3613 3.431626 CCTTTGTCCCTTTTGTCCCAAAC 60.432 47.826 0.00 0.00 0.00 2.93
3553 3614 2.769095 CCTTTGTCCCTTTTGTCCCAAA 59.231 45.455 0.00 0.00 0.00 3.28
3554 3615 2.023888 TCCTTTGTCCCTTTTGTCCCAA 60.024 45.455 0.00 0.00 0.00 4.12
3555 3616 1.571457 TCCTTTGTCCCTTTTGTCCCA 59.429 47.619 0.00 0.00 0.00 4.37
3556 3617 2.239400 CTCCTTTGTCCCTTTTGTCCC 58.761 52.381 0.00 0.00 0.00 4.46
3557 3618 2.239400 CCTCCTTTGTCCCTTTTGTCC 58.761 52.381 0.00 0.00 0.00 4.02
3558 3619 1.613925 GCCTCCTTTGTCCCTTTTGTC 59.386 52.381 0.00 0.00 0.00 3.18
3559 3620 1.704641 GCCTCCTTTGTCCCTTTTGT 58.295 50.000 0.00 0.00 0.00 2.83
3560 3621 0.598065 CGCCTCCTTTGTCCCTTTTG 59.402 55.000 0.00 0.00 0.00 2.44
3561 3622 0.539669 CCGCCTCCTTTGTCCCTTTT 60.540 55.000 0.00 0.00 0.00 2.27
3562 3623 1.074951 CCGCCTCCTTTGTCCCTTT 59.925 57.895 0.00 0.00 0.00 3.11
3563 3624 2.757077 CCGCCTCCTTTGTCCCTT 59.243 61.111 0.00 0.00 0.00 3.95
3564 3625 4.035102 GCCGCCTCCTTTGTCCCT 62.035 66.667 0.00 0.00 0.00 4.20
3567 3628 4.344865 TGGGCCGCCTCCTTTGTC 62.345 66.667 9.86 0.00 0.00 3.18
3568 3629 4.351054 CTGGGCCGCCTCCTTTGT 62.351 66.667 9.86 0.00 0.00 2.83
3600 3661 1.165270 CAAAACGGACAGGATGGGTC 58.835 55.000 0.00 0.00 43.62 4.46
3601 3662 0.476771 ACAAAACGGACAGGATGGGT 59.523 50.000 0.00 0.00 43.62 4.51
3602 3663 0.881118 CACAAAACGGACAGGATGGG 59.119 55.000 0.00 0.00 43.62 4.00
3603 3664 1.535462 GACACAAAACGGACAGGATGG 59.465 52.381 0.00 0.00 43.62 3.51
3604 3665 1.535462 GGACACAAAACGGACAGGATG 59.465 52.381 0.00 0.00 46.00 3.51
3605 3666 1.876416 CGGACACAAAACGGACAGGAT 60.876 52.381 0.00 0.00 0.00 3.24
3606 3667 0.531090 CGGACACAAAACGGACAGGA 60.531 55.000 0.00 0.00 0.00 3.86
3607 3668 0.531090 TCGGACACAAAACGGACAGG 60.531 55.000 0.00 0.00 0.00 4.00
3608 3669 0.859232 CTCGGACACAAAACGGACAG 59.141 55.000 0.00 0.00 0.00 3.51
3609 3670 1.155424 GCTCGGACACAAAACGGACA 61.155 55.000 0.00 0.00 0.00 4.02
3610 3671 1.568025 GCTCGGACACAAAACGGAC 59.432 57.895 0.00 0.00 0.00 4.79
3611 3672 1.595929 GGCTCGGACACAAAACGGA 60.596 57.895 0.00 0.00 0.00 4.69
3612 3673 2.943653 GGCTCGGACACAAAACGG 59.056 61.111 0.00 0.00 0.00 4.44
3613 3674 1.952133 TCGGCTCGGACACAAAACG 60.952 57.895 0.00 0.00 0.00 3.60
3614 3675 1.568025 GTCGGCTCGGACACAAAAC 59.432 57.895 3.18 0.00 36.91 2.43
3615 3676 1.595929 GGTCGGCTCGGACACAAAA 60.596 57.895 9.30 0.00 38.70 2.44
3616 3677 2.029964 GGTCGGCTCGGACACAAA 59.970 61.111 9.30 0.00 38.70 2.83
3617 3678 3.998672 GGGTCGGCTCGGACACAA 61.999 66.667 9.30 0.00 40.14 3.33
3619 3680 2.798148 AAATGGGTCGGCTCGGACAC 62.798 60.000 9.30 6.43 40.81 3.67
3620 3681 2.515996 GAAATGGGTCGGCTCGGACA 62.516 60.000 9.30 0.00 38.70 4.02
3621 3682 1.814169 GAAATGGGTCGGCTCGGAC 60.814 63.158 0.00 0.00 36.18 4.79
3622 3683 2.582436 GAAATGGGTCGGCTCGGA 59.418 61.111 0.00 0.00 0.00 4.55
3623 3684 2.890474 CGAAATGGGTCGGCTCGG 60.890 66.667 0.00 0.00 37.37 4.63
3624 3685 1.878522 CTCGAAATGGGTCGGCTCG 60.879 63.158 0.00 0.00 41.43 5.03
3625 3686 2.174319 GCTCGAAATGGGTCGGCTC 61.174 63.158 0.00 0.00 41.43 4.70
3626 3687 2.125106 GCTCGAAATGGGTCGGCT 60.125 61.111 0.00 0.00 41.43 5.52
3627 3688 3.564027 CGCTCGAAATGGGTCGGC 61.564 66.667 0.00 0.00 41.43 5.54
3628 3689 3.564027 GCGCTCGAAATGGGTCGG 61.564 66.667 0.00 0.00 41.43 4.79
3629 3690 1.906994 TTTGCGCTCGAAATGGGTCG 61.907 55.000 9.73 0.00 42.48 4.79
3630 3691 0.454452 GTTTGCGCTCGAAATGGGTC 60.454 55.000 9.73 0.00 0.00 4.46
3631 3692 0.889186 AGTTTGCGCTCGAAATGGGT 60.889 50.000 9.73 0.00 0.00 4.51
3632 3693 0.240945 AAGTTTGCGCTCGAAATGGG 59.759 50.000 9.73 0.00 0.00 4.00
3633 3694 1.330306 CAAGTTTGCGCTCGAAATGG 58.670 50.000 9.73 0.00 0.00 3.16
3634 3695 0.704551 GCAAGTTTGCGCTCGAAATG 59.295 50.000 9.73 1.98 45.11 2.32
3635 3696 3.092081 GCAAGTTTGCGCTCGAAAT 57.908 47.368 9.73 0.00 45.11 2.17
3636 3697 4.607024 GCAAGTTTGCGCTCGAAA 57.393 50.000 9.73 0.00 45.11 3.46
3645 3706 1.948635 CAAACCCGGCGCAAGTTTG 60.949 57.895 24.85 24.85 42.93 2.93
3646 3707 2.415426 CAAACCCGGCGCAAGTTT 59.585 55.556 10.83 12.71 41.68 2.66
3647 3708 3.601685 CCAAACCCGGCGCAAGTT 61.602 61.111 10.83 6.41 41.68 2.66
3666 3727 4.690719 ATTTGGTGTCCGCCGCGA 62.691 61.111 15.93 0.00 0.00 5.87
3667 3728 4.459331 CATTTGGTGTCCGCCGCG 62.459 66.667 5.59 5.59 0.00 6.46
3668 3729 4.114997 CCATTTGGTGTCCGCCGC 62.115 66.667 0.00 0.00 0.00 6.53
3669 3730 2.359354 TCCATTTGGTGTCCGCCG 60.359 61.111 0.00 0.00 36.34 6.46
3670 3731 2.686816 CGTCCATTTGGTGTCCGCC 61.687 63.158 0.00 0.00 36.34 6.13
3671 3732 2.867472 CGTCCATTTGGTGTCCGC 59.133 61.111 0.00 0.00 36.34 5.54
3672 3733 2.867472 GCGTCCATTTGGTGTCCG 59.133 61.111 0.00 0.00 36.34 4.79
3673 3734 2.867472 CGCGTCCATTTGGTGTCC 59.133 61.111 0.00 0.00 36.34 4.02
3674 3735 2.175811 GCGCGTCCATTTGGTGTC 59.824 61.111 8.43 0.00 36.34 3.67
3675 3736 3.722295 CGCGCGTCCATTTGGTGT 61.722 61.111 24.19 0.00 36.34 4.16
3679 3740 4.520846 GAGGCGCGCGTCCATTTG 62.521 66.667 36.43 8.02 0.00 2.32


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

AutoCloner maintained by Alex Coulton.