Multiple sequence alignment - TraesCS1D01G196800

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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 TraesCS1D01G196800 chr1D 100.000 3510 0 0 1 3510 276748242 276751751 0.000000e+00 6482.0
1 TraesCS1D01G196800 chr1D 88.706 487 54 1 1055 1541 276719347 276719832 8.390000e-166 593.0
2 TraesCS1D01G196800 chr1D 83.235 340 42 12 720 1057 276536823 276537149 7.370000e-77 298.0
3 TraesCS1D01G196800 chr1A 97.911 1484 27 3 789 2270 348848492 348849973 0.000000e+00 2566.0
4 TraesCS1D01G196800 chr1A 91.584 606 40 6 2273 2872 348850080 348850680 0.000000e+00 826.0
5 TraesCS1D01G196800 chr1A 85.928 334 27 6 2868 3200 348850720 348851034 4.340000e-89 339.0
6 TraesCS1D01G196800 chr1A 88.550 131 11 4 576 704 348848333 348848461 4.690000e-34 156.0
7 TraesCS1D01G196800 chr1A 85.849 106 3 1 3240 3333 239106789 239106894 6.200000e-18 102.0
8 TraesCS1D01G196800 chr1B 92.243 1792 94 17 1417 3200 375859021 375860775 0.000000e+00 2497.0
9 TraesCS1D01G196800 chr1B 94.077 574 30 3 860 1430 375856714 375857286 0.000000e+00 869.0
10 TraesCS1D01G196800 chr1B 88.235 102 9 3 3275 3373 624018068 624017967 6.150000e-23 119.0
11 TraesCS1D01G196800 chr5A 96.226 530 17 2 2 530 13415037 13415564 0.000000e+00 865.0
12 TraesCS1D01G196800 chrUn 96.038 530 18 2 2 530 377699500 377700027 0.000000e+00 859.0
13 TraesCS1D01G196800 chrUn 85.465 172 12 3 3212 3372 89019940 89019771 2.170000e-37 167.0
14 TraesCS1D01G196800 chrUn 82.424 165 16 8 3213 3365 31720044 31720207 7.910000e-27 132.0
15 TraesCS1D01G196800 chrUn 94.737 76 4 0 3414 3489 89019392 89019317 6.150000e-23 119.0
16 TraesCS1D01G196800 chr3B 95.849 530 19 2 2 530 769883333 769883860 0.000000e+00 854.0
17 TraesCS1D01G196800 chr3B 86.715 414 41 9 5 408 74199527 74199118 6.910000e-122 448.0
18 TraesCS1D01G196800 chr3B 83.540 322 24 6 3217 3510 807316143 807315823 1.240000e-69 274.0
19 TraesCS1D01G196800 chr3B 82.353 136 24 0 2345 2480 20544887 20545022 6.150000e-23 119.0
20 TraesCS1D01G196800 chr7B 87.709 537 52 9 5 531 707755705 707756237 6.440000e-172 614.0
21 TraesCS1D01G196800 chr7B 85.267 543 61 9 7 541 279852328 279851797 3.080000e-150 542.0
22 TraesCS1D01G196800 chr4B 86.157 549 59 10 5 541 111992281 111991738 8.450000e-161 577.0
23 TraesCS1D01G196800 chr4B 81.061 132 23 2 1022 1152 110252294 110252424 1.720000e-18 104.0
24 TraesCS1D01G196800 chr7A 95.965 347 11 2 2 347 483811779 483812123 8.510000e-156 560.0
25 TraesCS1D01G196800 chr7A 94.286 210 11 1 322 530 483812128 483812337 1.570000e-83 320.0
26 TraesCS1D01G196800 chr7A 91.111 90 8 0 436 525 309673695 309673606 4.760000e-24 122.0
27 TraesCS1D01G196800 chr2B 85.036 548 57 13 5 541 53575723 53575190 5.160000e-148 534.0
28 TraesCS1D01G196800 chr2B 84.756 164 23 2 3211 3373 139404683 139404521 2.800000e-36 163.0
29 TraesCS1D01G196800 chr3A 85.219 548 48 10 1 541 410124632 410124111 1.850000e-147 532.0
30 TraesCS1D01G196800 chr3A 90.698 86 7 1 3212 3296 63381036 63380951 2.860000e-21 113.0
31 TraesCS1D01G196800 chr6B 86.068 323 20 4 3212 3510 690436071 690435750 1.220000e-84 324.0
32 TraesCS1D01G196800 chr6B 82.540 315 29 10 3212 3510 663172404 663172100 1.620000e-63 254.0
33 TraesCS1D01G196800 chr7D 85.079 315 27 7 3215 3510 534381255 534380942 1.580000e-78 303.0
34 TraesCS1D01G196800 chr3D 85.127 316 19 7 3219 3510 7408548 7408859 7.370000e-77 298.0
35 TraesCS1D01G196800 chr3D 86.505 289 12 4 3248 3510 453981565 453981278 3.430000e-75 292.0
36 TraesCS1D01G196800 chr3D 85.870 92 10 3 3215 3305 8889712 8889623 1.040000e-15 95.3
37 TraesCS1D01G196800 chr4A 92.222 90 7 0 436 525 623992681 623992770 1.020000e-25 128.0
38 TraesCS1D01G196800 chr5B 81.034 174 17 9 3215 3373 700597538 700597710 1.320000e-24 124.0
39 TraesCS1D01G196800 chr5D 82.353 136 16 7 3240 3370 303937671 303937539 1.030000e-20 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G196800 chr1D 276748242 276751751 3509 False 6482.00 6482 100.00000 1 3510 1 chr1D.!!$F3 3509
1 TraesCS1D01G196800 chr1A 348848333 348851034 2701 False 971.75 2566 90.99325 576 3200 4 chr1A.!!$F2 2624
2 TraesCS1D01G196800 chr1B 375856714 375860775 4061 False 1683.00 2497 93.16000 860 3200 2 chr1B.!!$F1 2340
3 TraesCS1D01G196800 chr5A 13415037 13415564 527 False 865.00 865 96.22600 2 530 1 chr5A.!!$F1 528
4 TraesCS1D01G196800 chrUn 377699500 377700027 527 False 859.00 859 96.03800 2 530 1 chrUn.!!$F2 528
5 TraesCS1D01G196800 chr3B 769883333 769883860 527 False 854.00 854 95.84900 2 530 1 chr3B.!!$F2 528
6 TraesCS1D01G196800 chr7B 707755705 707756237 532 False 614.00 614 87.70900 5 531 1 chr7B.!!$F1 526
7 TraesCS1D01G196800 chr7B 279851797 279852328 531 True 542.00 542 85.26700 7 541 1 chr7B.!!$R1 534
8 TraesCS1D01G196800 chr4B 111991738 111992281 543 True 577.00 577 86.15700 5 541 1 chr4B.!!$R1 536
9 TraesCS1D01G196800 chr7A 483811779 483812337 558 False 440.00 560 95.12550 2 530 2 chr7A.!!$F1 528
10 TraesCS1D01G196800 chr2B 53575190 53575723 533 True 534.00 534 85.03600 5 541 1 chr2B.!!$R1 536
11 TraesCS1D01G196800 chr3A 410124111 410124632 521 True 532.00 532 85.21900 1 541 1 chr3A.!!$R2 540

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
710 757 0.610174 CTGCCCTCTGTCTTGCTGTA 59.390 55.0 0.0 0.0 0.00 2.74 F
745 792 0.622665 CACCCAGGATTCAGAGCCTT 59.377 55.0 0.0 0.0 38.99 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 3581 3.196469 TGACAGAGGCAAGAAGGACATAG 59.804 47.826 0.00 0.0 0.00 2.23 R
2526 4430 5.294060 ACCAATTGCAATTGTGACTTCAAAC 59.706 36.000 37.23 0.0 43.24 2.93 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
87 88 7.393216 CCCTAAAACATTTCCCATCAATCAAA 58.607 34.615 0.00 0.00 0.00 2.69
319 330 7.923414 AACTTAGTAATTCGAAGGCATTTCT 57.077 32.000 3.35 0.00 33.97 2.52
326 337 3.634397 TCGAAGGCATTTCTCCTCATT 57.366 42.857 0.00 0.00 33.44 2.57
337 380 7.101700 GCATTTCTCCTCATTCAAGGAAAATT 58.898 34.615 8.83 0.00 44.81 1.82
352 395 6.481954 AGGAAAATTTCACTCATCGTGTAC 57.518 37.500 8.09 0.00 44.16 2.90
422 467 7.829378 AGTGAAAATACATCTCCGTTAACTC 57.171 36.000 3.71 0.00 0.00 3.01
614 660 7.687941 ACAGAAAACAGAGAACAGAAAGAAA 57.312 32.000 0.00 0.00 0.00 2.52
704 751 3.334054 GGGGCTGCCCTCTGTCTT 61.334 66.667 34.99 0.00 44.66 3.01
707 754 2.350514 GCTGCCCTCTGTCTTGCT 59.649 61.111 0.00 0.00 0.00 3.91
708 755 2.039405 GCTGCCCTCTGTCTTGCTG 61.039 63.158 0.00 0.00 0.00 4.41
709 756 1.374190 CTGCCCTCTGTCTTGCTGT 59.626 57.895 0.00 0.00 0.00 4.40
710 757 0.610174 CTGCCCTCTGTCTTGCTGTA 59.390 55.000 0.00 0.00 0.00 2.74
711 758 1.002430 CTGCCCTCTGTCTTGCTGTAA 59.998 52.381 0.00 0.00 0.00 2.41
726 773 0.750850 TGTAAGCGAGACATAGGGGC 59.249 55.000 0.00 0.00 0.00 5.80
727 774 0.750850 GTAAGCGAGACATAGGGGCA 59.249 55.000 0.00 0.00 0.00 5.36
728 775 0.750850 TAAGCGAGACATAGGGGCAC 59.249 55.000 0.00 0.00 0.00 5.01
741 788 4.972875 GGCACCCAGGATTCAGAG 57.027 61.111 0.00 0.00 0.00 3.35
742 789 1.452833 GGCACCCAGGATTCAGAGC 60.453 63.158 0.00 0.00 0.00 4.09
743 790 1.452833 GCACCCAGGATTCAGAGCC 60.453 63.158 0.00 0.00 0.00 4.70
744 791 1.919600 GCACCCAGGATTCAGAGCCT 61.920 60.000 0.00 0.00 44.16 4.58
745 792 0.622665 CACCCAGGATTCAGAGCCTT 59.377 55.000 0.00 0.00 38.99 4.35
746 793 1.005215 CACCCAGGATTCAGAGCCTTT 59.995 52.381 0.00 0.00 38.99 3.11
747 794 2.239654 CACCCAGGATTCAGAGCCTTTA 59.760 50.000 0.00 0.00 38.99 1.85
748 795 2.507471 ACCCAGGATTCAGAGCCTTTAG 59.493 50.000 0.00 0.00 38.99 1.85
749 796 2.570135 CCAGGATTCAGAGCCTTTAGC 58.430 52.381 0.00 0.00 38.99 3.09
779 826 4.329545 GGTTCAGAGCCCACCGCA 62.330 66.667 0.00 0.00 41.38 5.69
780 827 3.050275 GTTCAGAGCCCACCGCAC 61.050 66.667 0.00 0.00 41.38 5.34
781 828 3.555324 TTCAGAGCCCACCGCACA 61.555 61.111 0.00 0.00 41.38 4.57
782 829 2.894257 TTCAGAGCCCACCGCACAT 61.894 57.895 0.00 0.00 41.38 3.21
783 830 2.360350 CAGAGCCCACCGCACATT 60.360 61.111 0.00 0.00 41.38 2.71
784 831 1.973281 CAGAGCCCACCGCACATTT 60.973 57.895 0.00 0.00 41.38 2.32
785 832 1.675641 AGAGCCCACCGCACATTTC 60.676 57.895 0.00 0.00 41.38 2.17
786 833 3.039202 GAGCCCACCGCACATTTCG 62.039 63.158 0.00 0.00 41.38 3.46
948 995 0.870393 GGTCGATATCGCTCGTACCA 59.130 55.000 20.34 0.00 38.05 3.25
952 999 3.072211 TCGATATCGCTCGTACCATCTT 58.928 45.455 20.34 0.00 39.62 2.40
1367 1416 0.875059 CTTCGAGTTTGGGTGCTTCC 59.125 55.000 0.00 0.00 0.00 3.46
1461 3258 4.155826 CGCTGGTATGAAATTTGAGGAACA 59.844 41.667 0.00 0.00 0.00 3.18
1717 3516 4.520111 TGTCAGGTTTGATGAAGAATGGTG 59.480 41.667 0.00 0.00 35.39 4.17
1782 3581 0.543277 TGGGGACTGTGATGATGAGC 59.457 55.000 0.00 0.00 0.00 4.26
2277 4181 7.441890 TTCCATTCAGCGTTACTAAATCAAA 57.558 32.000 0.00 0.00 0.00 2.69
2483 4387 4.223255 AGAGGCTTACCCTTCAACTTAGAC 59.777 45.833 0.00 0.00 46.60 2.59
2526 4430 9.360093 TGTTTTCTAATTACACCAGTTTTTGTG 57.640 29.630 0.00 0.00 38.44 3.33
2538 4443 5.221342 ACCAGTTTTTGTGTTTGAAGTCACA 60.221 36.000 2.20 2.20 41.81 3.58
2545 4450 4.814147 TGTGTTTGAAGTCACAATTGCAA 58.186 34.783 5.05 0.00 40.81 4.08
2603 4508 8.421249 ACAGAAACAATCTATGGATGGAAAAA 57.579 30.769 0.00 0.00 36.32 1.94
2716 4621 7.214467 TCACCAAATTGTAAAGATCCTTGTC 57.786 36.000 0.00 0.00 0.00 3.18
2808 4713 9.209048 ACTATTACCACTCCACACTGATTATTA 57.791 33.333 0.00 0.00 0.00 0.98
2821 4726 9.166173 CACACTGATTATTATGTTTCTTCCTCA 57.834 33.333 0.00 0.00 0.00 3.86
2833 4738 8.655935 ATGTTTCTTCCTCATAAAATTCCTGT 57.344 30.769 0.00 0.00 0.00 4.00
2858 4766 5.086058 GTCAGCATGTTTGTGTAAATACCG 58.914 41.667 0.00 0.00 37.40 4.02
2860 4768 5.086058 CAGCATGTTTGTGTAAATACCGAC 58.914 41.667 0.00 0.00 0.00 4.79
3050 5001 3.076621 TGTGCATCCTTTTGACTGCTAG 58.923 45.455 0.00 0.00 35.66 3.42
3080 5031 1.777878 ACATTACCTGGACCCACAACA 59.222 47.619 0.00 0.00 0.00 3.33
3081 5032 2.224769 ACATTACCTGGACCCACAACAG 60.225 50.000 0.00 0.00 0.00 3.16
3082 5033 0.109723 TTACCTGGACCCACAACAGC 59.890 55.000 0.00 0.00 0.00 4.40
3083 5034 1.057275 TACCTGGACCCACAACAGCA 61.057 55.000 0.00 0.00 0.00 4.41
3084 5035 1.152777 CCTGGACCCACAACAGCAA 60.153 57.895 0.00 0.00 0.00 3.91
3085 5036 1.455383 CCTGGACCCACAACAGCAAC 61.455 60.000 0.00 0.00 0.00 4.17
3086 5037 0.751277 CTGGACCCACAACAGCAACA 60.751 55.000 0.00 0.00 0.00 3.33
3087 5038 1.034838 TGGACCCACAACAGCAACAC 61.035 55.000 0.00 0.00 0.00 3.32
3088 5039 0.751643 GGACCCACAACAGCAACACT 60.752 55.000 0.00 0.00 0.00 3.55
3125 5076 1.098050 AATAGGCCTGCAAAAGAGCG 58.902 50.000 17.99 0.00 37.31 5.03
3133 5084 2.413371 CCTGCAAAAGAGCGAGTTAAGC 60.413 50.000 0.00 0.00 37.31 3.09
3147 5099 6.206829 AGCGAGTTAAGCCTTTTTATCAGTTT 59.793 34.615 0.00 0.00 34.64 2.66
3150 5102 8.073768 CGAGTTAAGCCTTTTTATCAGTTTCAA 58.926 33.333 0.00 0.00 0.00 2.69
3184 5137 8.099364 AGTGTCCTTACATGTTCAACAATAAG 57.901 34.615 2.30 14.18 38.08 1.73
3188 5141 9.431887 GTCCTTACATGTTCAACAATAAGTAGA 57.568 33.333 17.53 9.95 32.94 2.59
3209 5162 9.372369 AGTAGATTAAGTTGAATAGTGTCAAGC 57.628 33.333 0.00 0.00 38.17 4.01
3210 5163 7.295952 AGATTAAGTTGAATAGTGTCAAGCG 57.704 36.000 0.00 0.00 38.17 4.68
3211 5164 3.813529 AAGTTGAATAGTGTCAAGCGC 57.186 42.857 0.00 0.00 38.17 5.92
3212 5165 2.076863 AGTTGAATAGTGTCAAGCGCC 58.923 47.619 2.29 0.00 38.17 6.53
3213 5166 1.075542 TTGAATAGTGTCAAGCGCCG 58.924 50.000 2.29 0.00 32.56 6.46
3214 5167 1.348594 GAATAGTGTCAAGCGCCGC 59.651 57.895 2.29 0.00 0.00 6.53
3215 5168 2.348140 GAATAGTGTCAAGCGCCGCG 62.348 60.000 8.83 8.83 0.00 6.46
3216 5169 3.642778 ATAGTGTCAAGCGCCGCGT 62.643 57.895 15.34 0.00 0.00 6.01
3240 5193 3.470888 CGTAGCCCTCCCTGGTGG 61.471 72.222 0.00 0.00 0.00 4.61
3241 5194 3.798511 GTAGCCCTCCCTGGTGGC 61.799 72.222 10.25 10.25 45.70 5.01
3266 5219 1.007154 GGAACCCTAGATCGAGCGC 60.007 63.158 0.00 0.00 0.00 5.92
3267 5220 1.007154 GAACCCTAGATCGAGCGCC 60.007 63.158 2.29 0.00 0.00 6.53
3268 5221 2.734756 GAACCCTAGATCGAGCGCCG 62.735 65.000 2.29 8.02 40.25 6.46
3269 5222 4.708968 CCCTAGATCGAGCGCCGC 62.709 72.222 2.29 0.00 38.37 6.53
3270 5223 4.708968 CCTAGATCGAGCGCCGCC 62.709 72.222 4.98 0.00 38.37 6.13
3364 5317 2.108976 GCGATTCGGCTGGATCCA 59.891 61.111 15.27 15.27 0.00 3.41
3365 5318 2.247437 GCGATTCGGCTGGATCCAC 61.247 63.158 11.44 8.06 0.00 4.02
3366 5319 1.595382 CGATTCGGCTGGATCCACC 60.595 63.158 11.44 15.95 39.54 4.61
3367 5320 1.227973 GATTCGGCTGGATCCACCC 60.228 63.158 15.36 15.36 38.00 4.61
3368 5321 2.682582 GATTCGGCTGGATCCACCCC 62.683 65.000 18.83 16.41 38.00 4.95
3385 5338 4.900704 CCCCCGGGCATGATGTGG 62.901 72.222 17.73 3.94 0.00 4.17
3386 5339 4.127744 CCCCGGGCATGATGTGGT 62.128 66.667 17.73 0.00 0.00 4.16
3387 5340 2.829914 CCCGGGCATGATGTGGTG 60.830 66.667 8.08 0.00 0.00 4.17
3388 5341 3.520862 CCGGGCATGATGTGGTGC 61.521 66.667 0.00 0.00 40.55 5.01
3392 5345 4.197498 GCATGATGTGGTGCCGGC 62.197 66.667 22.73 22.73 35.35 6.13
3393 5346 2.438975 CATGATGTGGTGCCGGCT 60.439 61.111 29.70 5.42 0.00 5.52
3394 5347 2.124570 ATGATGTGGTGCCGGCTC 60.125 61.111 29.70 24.78 0.00 4.70
3395 5348 3.704231 ATGATGTGGTGCCGGCTCC 62.704 63.158 35.31 35.31 0.00 4.70
3396 5349 4.101448 GATGTGGTGCCGGCTCCT 62.101 66.667 39.01 24.94 0.00 3.69
3397 5350 4.101448 ATGTGGTGCCGGCTCCTC 62.101 66.667 39.01 35.63 0.00 3.71
3487 5440 4.404098 CCGCCCTACCACCACCAC 62.404 72.222 0.00 0.00 0.00 4.16
3488 5441 4.404098 CGCCCTACCACCACCACC 62.404 72.222 0.00 0.00 0.00 4.61
3489 5442 2.933834 GCCCTACCACCACCACCT 60.934 66.667 0.00 0.00 0.00 4.00
3490 5443 2.967946 GCCCTACCACCACCACCTC 61.968 68.421 0.00 0.00 0.00 3.85
3491 5444 2.656069 CCCTACCACCACCACCTCG 61.656 68.421 0.00 0.00 0.00 4.63
3492 5445 2.264794 CTACCACCACCACCTCGC 59.735 66.667 0.00 0.00 0.00 5.03
3493 5446 3.642778 CTACCACCACCACCTCGCG 62.643 68.421 0.00 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 5.716979 TCTTTATAGGTGAGTCCCTATGCT 58.283 41.667 21.48 7.19 45.42 3.79
209 219 7.886629 ATGCAAGGTACTACAATGATGAATT 57.113 32.000 0.00 0.00 38.49 2.17
319 330 6.777091 TGAGTGAAATTTTCCTTGAATGAGGA 59.223 34.615 6.68 0.00 43.99 3.71
420 464 7.035004 TGTTCTGATTTGTGTTCCTTTTTGAG 58.965 34.615 0.00 0.00 0.00 3.02
422 467 7.593875 TTGTTCTGATTTGTGTTCCTTTTTG 57.406 32.000 0.00 0.00 0.00 2.44
573 619 8.401709 TGTTTTCTGTTTTCTGTTTTGCTTTTT 58.598 25.926 0.00 0.00 0.00 1.94
574 620 7.924940 TGTTTTCTGTTTTCTGTTTTGCTTTT 58.075 26.923 0.00 0.00 0.00 2.27
575 621 7.440856 TCTGTTTTCTGTTTTCTGTTTTGCTTT 59.559 29.630 0.00 0.00 0.00 3.51
576 622 6.928492 TCTGTTTTCTGTTTTCTGTTTTGCTT 59.072 30.769 0.00 0.00 0.00 3.91
577 623 6.454795 TCTGTTTTCTGTTTTCTGTTTTGCT 58.545 32.000 0.00 0.00 0.00 3.91
578 624 6.586082 TCTCTGTTTTCTGTTTTCTGTTTTGC 59.414 34.615 0.00 0.00 0.00 3.68
579 625 8.427774 GTTCTCTGTTTTCTGTTTTCTGTTTTG 58.572 33.333 0.00 0.00 0.00 2.44
584 630 7.076842 TCTGTTCTCTGTTTTCTGTTTTCTG 57.923 36.000 0.00 0.00 0.00 3.02
585 631 7.687941 TTCTGTTCTCTGTTTTCTGTTTTCT 57.312 32.000 0.00 0.00 0.00 2.52
591 637 8.970691 TTTTTCTTTCTGTTCTCTGTTTTCTG 57.029 30.769 0.00 0.00 0.00 3.02
614 660 5.047021 GCTCCAGCCTCCTTTTTCTAATTTT 60.047 40.000 0.00 0.00 34.31 1.82
618 664 2.644798 AGCTCCAGCCTCCTTTTTCTAA 59.355 45.455 0.00 0.00 43.38 2.10
619 665 2.269940 AGCTCCAGCCTCCTTTTTCTA 58.730 47.619 0.00 0.00 43.38 2.10
656 703 3.816367 GAGCTCTACATGGGCCGCC 62.816 68.421 6.43 0.00 0.00 6.13
688 735 2.045536 CAAGACAGAGGGCAGCCC 60.046 66.667 24.90 24.90 45.90 5.19
696 743 2.095008 TCTCGCTTACAGCAAGACAGAG 60.095 50.000 0.00 0.00 42.58 3.35
704 751 1.409064 CCCTATGTCTCGCTTACAGCA 59.591 52.381 0.00 0.00 42.58 4.41
707 754 0.750850 GCCCCTATGTCTCGCTTACA 59.249 55.000 0.00 0.00 0.00 2.41
708 755 0.750850 TGCCCCTATGTCTCGCTTAC 59.249 55.000 0.00 0.00 0.00 2.34
709 756 0.750850 GTGCCCCTATGTCTCGCTTA 59.249 55.000 0.00 0.00 0.00 3.09
710 757 1.522569 GTGCCCCTATGTCTCGCTT 59.477 57.895 0.00 0.00 0.00 4.68
711 758 2.435693 GGTGCCCCTATGTCTCGCT 61.436 63.158 0.00 0.00 0.00 4.93
713 760 2.032860 CTGGGTGCCCCTATGTCTCG 62.033 65.000 11.10 0.00 45.70 4.04
714 761 1.700042 CCTGGGTGCCCCTATGTCTC 61.700 65.000 11.10 0.00 45.70 3.36
715 762 1.694169 CCTGGGTGCCCCTATGTCT 60.694 63.158 11.10 0.00 45.70 3.41
716 763 1.062488 ATCCTGGGTGCCCCTATGTC 61.062 60.000 11.10 0.00 45.70 3.06
717 764 0.627469 AATCCTGGGTGCCCCTATGT 60.627 55.000 11.10 0.00 45.70 2.29
719 766 0.328450 TGAATCCTGGGTGCCCCTAT 60.328 55.000 11.10 1.08 45.70 2.57
720 767 0.988145 CTGAATCCTGGGTGCCCCTA 60.988 60.000 11.10 0.00 45.70 3.53
721 768 2.204291 TGAATCCTGGGTGCCCCT 60.204 61.111 11.10 0.00 45.70 4.79
722 769 2.276309 CTCTGAATCCTGGGTGCCCC 62.276 65.000 4.59 3.42 45.71 5.80
723 770 1.225704 CTCTGAATCCTGGGTGCCC 59.774 63.158 0.00 0.00 0.00 5.36
724 771 1.452833 GCTCTGAATCCTGGGTGCC 60.453 63.158 0.00 0.00 0.00 5.01
726 773 0.622665 AAGGCTCTGAATCCTGGGTG 59.377 55.000 0.00 0.00 32.00 4.61
727 774 1.376649 AAAGGCTCTGAATCCTGGGT 58.623 50.000 0.00 0.00 32.00 4.51
728 775 2.747799 GCTAAAGGCTCTGAATCCTGGG 60.748 54.545 0.00 0.00 38.06 4.45
729 776 2.570135 GCTAAAGGCTCTGAATCCTGG 58.430 52.381 0.00 0.00 38.06 4.45
762 809 4.329545 TGCGGTGGGCTCTGAACC 62.330 66.667 0.00 0.00 44.05 3.62
763 810 3.050275 GTGCGGTGGGCTCTGAAC 61.050 66.667 0.00 0.00 44.05 3.18
764 811 2.410322 AATGTGCGGTGGGCTCTGAA 62.410 55.000 0.00 0.00 44.05 3.02
765 812 2.410322 AAATGTGCGGTGGGCTCTGA 62.410 55.000 0.00 0.00 44.05 3.27
766 813 1.926511 GAAATGTGCGGTGGGCTCTG 61.927 60.000 0.00 0.00 44.05 3.35
767 814 1.675641 GAAATGTGCGGTGGGCTCT 60.676 57.895 0.00 0.00 44.05 4.09
768 815 2.877691 GAAATGTGCGGTGGGCTC 59.122 61.111 0.00 0.00 44.05 4.70
769 816 3.055719 CGAAATGTGCGGTGGGCT 61.056 61.111 0.00 0.00 44.05 5.19
770 817 4.114997 CCGAAATGTGCGGTGGGC 62.115 66.667 0.00 0.00 43.66 5.36
777 824 4.036804 TGCGGTGCCGAAATGTGC 62.037 61.111 15.45 0.00 42.83 4.57
778 825 2.126888 GTGCGGTGCCGAAATGTG 60.127 61.111 15.45 0.00 42.83 3.21
779 826 1.523154 AATGTGCGGTGCCGAAATGT 61.523 50.000 15.45 0.00 42.83 2.71
780 827 0.388391 AAATGTGCGGTGCCGAAATG 60.388 50.000 15.45 0.00 42.83 2.32
781 828 0.109319 GAAATGTGCGGTGCCGAAAT 60.109 50.000 15.45 1.30 42.83 2.17
782 829 1.284408 GAAATGTGCGGTGCCGAAA 59.716 52.632 15.45 0.00 42.83 3.46
783 830 2.950673 GAAATGTGCGGTGCCGAA 59.049 55.556 15.45 0.00 42.83 4.30
784 831 3.418913 CGAAATGTGCGGTGCCGA 61.419 61.111 15.45 0.00 42.83 5.54
785 832 4.459331 CCGAAATGTGCGGTGCCG 62.459 66.667 6.22 6.22 43.66 5.69
804 851 4.039357 CGTGGAGTCGAGTGCGGT 62.039 66.667 7.30 0.00 38.28 5.68
805 852 4.778415 CCGTGGAGTCGAGTGCGG 62.778 72.222 7.30 9.70 38.28 5.69
836 883 4.849329 GGGTGCTCGTCGGCGTAG 62.849 72.222 10.18 6.92 39.49 3.51
948 995 1.497309 TTGGGGTTGGAGCCGAAGAT 61.497 55.000 0.00 0.00 36.39 2.40
952 999 4.344865 GCTTGGGGTTGGAGCCGA 62.345 66.667 0.00 0.00 36.39 5.54
1367 1416 0.109873 AGACGCCGACTGTAAACTCG 60.110 55.000 0.00 0.00 0.00 4.18
1461 3258 4.500375 GGCAGCTTGAAAAATTCAGAGTGT 60.500 41.667 0.00 0.00 41.38 3.55
1782 3581 3.196469 TGACAGAGGCAAGAAGGACATAG 59.804 47.826 0.00 0.00 0.00 2.23
2163 3963 7.902920 ACCATCTAATGTGGCAAAGATTAAT 57.097 32.000 0.00 0.00 40.49 1.40
2291 4195 8.616799 AGAGGATTAAATTCTACTTGAGGTCT 57.383 34.615 0.00 0.00 0.00 3.85
2526 4430 5.294060 ACCAATTGCAATTGTGACTTCAAAC 59.706 36.000 37.23 0.00 43.24 2.93
2538 4443 7.095102 GCTAAGTGAAATCAACCAATTGCAATT 60.095 33.333 18.99 18.99 36.64 2.32
2603 4508 5.726980 TTTCTTGGATTGTAGCTTGCATT 57.273 34.783 0.00 0.00 0.00 3.56
2607 4512 7.869429 AGAATTGTTTTCTTGGATTGTAGCTTG 59.131 33.333 0.00 0.00 0.00 4.01
2738 4643 6.206634 ACATCGTTCTGTTGGTTGTCAATATT 59.793 34.615 0.00 0.00 37.73 1.28
2808 4713 8.655935 ACAGGAATTTTATGAGGAAGAAACAT 57.344 30.769 0.00 0.00 0.00 2.71
2821 4726 7.944729 AACATGCTGACTACAGGAATTTTAT 57.055 32.000 0.00 0.00 46.58 1.40
2829 4734 3.141398 ACACAAACATGCTGACTACAGG 58.859 45.455 2.54 0.00 43.62 4.00
2833 4738 6.091577 CGGTATTTACACAAACATGCTGACTA 59.908 38.462 2.54 0.00 0.00 2.59
2858 4766 7.845066 AAACTAATTGATACCTTCTTCCGTC 57.155 36.000 0.00 0.00 0.00 4.79
2860 4768 9.032420 GTCTAAACTAATTGATACCTTCTTCCG 57.968 37.037 0.00 0.00 0.00 4.30
3050 5001 2.092646 TCCAGGTAATGTATGGTGGCAC 60.093 50.000 9.70 9.70 35.51 5.01
3086 5037 1.024271 AACATTCGCTGTTGTGCAGT 58.976 45.000 2.86 0.00 46.37 4.40
3087 5038 3.851620 AACATTCGCTGTTGTGCAG 57.148 47.368 2.86 0.00 46.37 4.41
3094 5045 3.206150 CAGGCCTATTAACATTCGCTGT 58.794 45.455 3.98 0.00 40.84 4.40
3095 5046 2.031682 GCAGGCCTATTAACATTCGCTG 60.032 50.000 3.98 0.00 0.00 5.18
3096 5047 2.222027 GCAGGCCTATTAACATTCGCT 58.778 47.619 3.98 0.00 0.00 4.93
3125 5076 9.914131 ATTGAAACTGATAAAAAGGCTTAACTC 57.086 29.630 0.00 0.00 0.00 3.01
3156 5108 4.819630 TGTTGAACATGTAAGGACACTTCC 59.180 41.667 0.00 0.00 43.22 3.46
3161 5114 9.214957 CTACTTATTGTTGAACATGTAAGGACA 57.785 33.333 23.13 13.43 40.72 4.02
3162 5115 9.431887 TCTACTTATTGTTGAACATGTAAGGAC 57.568 33.333 23.13 0.00 34.10 3.85
3184 5137 8.321716 CGCTTGACACTATTCAACTTAATCTAC 58.678 37.037 0.00 0.00 32.02 2.59
3188 5141 5.163754 GGCGCTTGACACTATTCAACTTAAT 60.164 40.000 7.64 0.00 32.02 1.40
3222 5175 4.162690 CACCAGGGAGGGCTACGC 62.163 72.222 0.00 0.00 43.89 4.42
3223 5176 3.470888 CCACCAGGGAGGGCTACG 61.471 72.222 0.00 0.00 43.89 3.51
3224 5177 3.798511 GCCACCAGGGAGGGCTAC 61.799 72.222 15.29 0.00 44.32 3.58
3246 5199 1.807495 CGCTCGATCTAGGGTTCCCC 61.807 65.000 4.02 0.00 45.90 4.81
3247 5200 1.660917 CGCTCGATCTAGGGTTCCC 59.339 63.158 0.00 0.00 0.00 3.97
3248 5201 1.007154 GCGCTCGATCTAGGGTTCC 60.007 63.158 12.11 0.00 0.00 3.62
3249 5202 1.007154 GGCGCTCGATCTAGGGTTC 60.007 63.158 7.64 3.05 0.00 3.62
3250 5203 2.846652 CGGCGCTCGATCTAGGGTT 61.847 63.158 7.64 0.00 42.43 4.11
3251 5204 3.288290 CGGCGCTCGATCTAGGGT 61.288 66.667 7.64 0.00 42.43 4.34
3252 5205 4.708968 GCGGCGCTCGATCTAGGG 62.709 72.222 26.86 6.92 42.43 3.53
3253 5206 4.708968 GGCGGCGCTCGATCTAGG 62.709 72.222 32.30 0.00 42.43 3.02
3344 5297 4.256180 ATCCAGCCGAATCGCCCC 62.256 66.667 0.00 0.00 0.00 5.80
3345 5298 2.666526 GATCCAGCCGAATCGCCC 60.667 66.667 0.00 0.00 0.00 6.13
3346 5299 2.666526 GGATCCAGCCGAATCGCC 60.667 66.667 6.95 0.00 0.00 5.54
3347 5300 2.108976 TGGATCCAGCCGAATCGC 59.891 61.111 11.44 0.00 0.00 4.58
3348 5301 1.595382 GGTGGATCCAGCCGAATCG 60.595 63.158 29.98 0.00 38.38 3.34
3349 5302 4.464262 GGTGGATCCAGCCGAATC 57.536 61.111 29.98 10.05 38.38 2.52
3368 5321 4.900704 CCACATCATGCCCGGGGG 62.901 72.222 25.28 8.38 38.57 5.40
3369 5322 4.127744 ACCACATCATGCCCGGGG 62.128 66.667 25.28 9.31 0.00 5.73
3370 5323 2.829914 CACCACATCATGCCCGGG 60.830 66.667 19.09 19.09 0.00 5.73
3371 5324 3.520862 GCACCACATCATGCCCGG 61.521 66.667 0.00 0.00 35.73 5.73
3375 5328 4.197498 GCCGGCACCACATCATGC 62.197 66.667 24.80 0.00 41.29 4.06
3376 5329 2.438975 AGCCGGCACCACATCATG 60.439 61.111 31.54 0.00 0.00 3.07
3377 5330 2.124570 GAGCCGGCACCACATCAT 60.125 61.111 31.54 3.33 0.00 2.45
3378 5331 4.408821 GGAGCCGGCACCACATCA 62.409 66.667 34.66 0.00 0.00 3.07
3379 5332 4.101448 AGGAGCCGGCACCACATC 62.101 66.667 39.03 22.41 0.00 3.06
3380 5333 4.101448 GAGGAGCCGGCACCACAT 62.101 66.667 39.03 22.86 0.00 3.21
3470 5423 4.404098 GTGGTGGTGGTAGGGCGG 62.404 72.222 0.00 0.00 0.00 6.13
3471 5424 4.404098 GGTGGTGGTGGTAGGGCG 62.404 72.222 0.00 0.00 0.00 6.13
3472 5425 2.933834 AGGTGGTGGTGGTAGGGC 60.934 66.667 0.00 0.00 0.00 5.19
3473 5426 2.656069 CGAGGTGGTGGTGGTAGGG 61.656 68.421 0.00 0.00 0.00 3.53
3474 5427 2.978824 CGAGGTGGTGGTGGTAGG 59.021 66.667 0.00 0.00 0.00 3.18
3475 5428 2.264794 GCGAGGTGGTGGTGGTAG 59.735 66.667 0.00 0.00 0.00 3.18
3476 5429 3.687102 CGCGAGGTGGTGGTGGTA 61.687 66.667 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.