Multiple sequence alignment - TraesCS5A01G177500

Loading Multiple Alignment...

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 TraesCS5A01G177500 chr5A 100.000 5621 0 0 1 5621 375247135 375252755 0.000000e+00 10381
1 TraesCS5A01G177500 chr5A 94.783 230 5 1 548 777 375242744 375242966 8.960000e-93 351
2 TraesCS5A01G177500 chr5D 96.443 4836 149 18 797 5621 282845116 282849939 0.000000e+00 7956
3 TraesCS5A01G177500 chr5B 96.691 4472 124 16 797 5257 321125571 321130029 0.000000e+00 7417
4 TraesCS5A01G177500 chr5B 76.277 548 99 24 1 540 644606857 644607381 4.320000e-66 263
5 TraesCS5A01G177500 chr7B 89.487 799 52 10 4 778 719899154 719898364 0.000000e+00 981
6 TraesCS5A01G177500 chr7B 90.865 208 10 2 548 755 719911109 719910911 2.580000e-68 270
7 TraesCS5A01G177500 chr7B 75.322 466 86 21 82 540 83106247 83106690 4.440000e-46 196
8 TraesCS5A01G177500 chr6B 84.153 549 85 2 1 548 476594302 476594849 1.070000e-146 531
9 TraesCS5A01G177500 chr7A 83.942 548 84 3 1 548 730244922 730245465 6.450000e-144 521
10 TraesCS5A01G177500 chr1B 83.759 548 89 0 1 548 22085168 22085715 2.320000e-143 520
11 TraesCS5A01G177500 chrUn 92.647 204 15 0 338 541 229271528 229271731 1.530000e-75 294
12 TraesCS5A01G177500 chrUn 92.647 204 15 0 338 541 299755244 299755041 1.530000e-75 294
13 TraesCS5A01G177500 chr3B 75.691 543 98 27 7 540 498433598 498433081 2.020000e-59 241


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 TraesCS5A01G177500 chr5A 375247135 375252755 5620 False 10381 10381 100.000 1 5621 1 chr5A.!!$F2 5620
1 TraesCS5A01G177500 chr5D 282845116 282849939 4823 False 7956 7956 96.443 797 5621 1 chr5D.!!$F1 4824
2 TraesCS5A01G177500 chr5B 321125571 321130029 4458 False 7417 7417 96.691 797 5257 1 chr5B.!!$F1 4460
3 TraesCS5A01G177500 chr5B 644606857 644607381 524 False 263 263 76.277 1 540 1 chr5B.!!$F2 539
4 TraesCS5A01G177500 chr7B 719898364 719899154 790 True 981 981 89.487 4 778 1 chr7B.!!$R1 774
5 TraesCS5A01G177500 chr6B 476594302 476594849 547 False 531 531 84.153 1 548 1 chr6B.!!$F1 547
6 TraesCS5A01G177500 chr7A 730244922 730245465 543 False 521 521 83.942 1 548 1 chr7A.!!$F1 547
7 TraesCS5A01G177500 chr1B 22085168 22085715 547 False 520 520 83.759 1 548 1 chr1B.!!$F1 547
8 TraesCS5A01G177500 chr3B 498433081 498433598 517 True 241 241 75.691 7 540 1 chr3B.!!$R1 533

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
923 951 0.443869 CTTTGTCGCTCCATTCGTGG 59.556 55.0 0.00 0.0 0.00 4.94 F
1641 1669 0.617535 TTCTCGGGATGCAAGAGGGA 60.618 55.0 8.60 0.0 33.16 4.20 F
3290 3325 0.539051 ATCACAGCTGAGGCACCTAC 59.461 55.0 23.35 0.0 41.70 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 1818 0.535102 AACCCTCGCACCAACTGAAG 60.535 55.0 0.00 0.0 0.00 3.02 R
3341 3376 1.363744 AAAAGAGCAGATCCGCGAAG 58.636 50.0 8.23 0.0 36.85 3.79 R
5011 5050 0.316204 CAAACTACAGGGACGGTCGT 59.684 55.0 1.43 0.0 38.12 4.34 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
161 162 2.031420 CGAGTAGTTGTTGTCGTCCAGA 60.031 50.000 0.00 0.00 0.00 3.86
245 246 1.003442 CACCTGGATGGGAGGAGGA 59.997 63.158 0.00 0.00 41.11 3.71
488 489 4.189188 CGGAGCGGACGTCGGAAT 62.189 66.667 25.40 13.30 39.69 3.01
572 599 5.580691 CAGAGTGTTTAAATACATGCGGAGA 59.419 40.000 16.24 0.00 0.00 3.71
573 600 5.812642 AGAGTGTTTAAATACATGCGGAGAG 59.187 40.000 16.24 0.00 0.00 3.20
605 632 9.923143 CCCGATAAGATCAGTTACAACAATATA 57.077 33.333 0.00 0.00 0.00 0.86
613 640 8.858003 ATCAGTTACAACAATATAGTGACTCG 57.142 34.615 7.27 0.00 30.84 4.18
614 641 7.823665 TCAGTTACAACAATATAGTGACTCGT 58.176 34.615 7.27 1.18 30.84 4.18
615 642 7.753580 TCAGTTACAACAATATAGTGACTCGTG 59.246 37.037 7.27 0.08 30.84 4.35
616 643 7.753580 CAGTTACAACAATATAGTGACTCGTGA 59.246 37.037 7.27 0.00 30.84 4.35
637 664 1.038130 AGAAGGAGGGGATCACGACG 61.038 60.000 0.00 0.00 0.00 5.12
697 724 4.933064 CTCCCGAGCGATCCGTGC 62.933 72.222 0.00 0.00 0.00 5.34
778 805 2.198827 CCCAGTGGCAGATGTGTTTA 57.801 50.000 2.61 0.00 0.00 2.01
779 806 1.812571 CCCAGTGGCAGATGTGTTTAC 59.187 52.381 2.61 0.00 0.00 2.01
780 807 2.503331 CCAGTGGCAGATGTGTTTACA 58.497 47.619 0.00 0.00 41.89 2.41
781 808 2.485426 CCAGTGGCAGATGTGTTTACAG 59.515 50.000 0.00 0.00 40.79 2.74
782 809 3.141398 CAGTGGCAGATGTGTTTACAGT 58.859 45.455 0.00 0.00 40.79 3.55
783 810 3.187227 CAGTGGCAGATGTGTTTACAGTC 59.813 47.826 0.00 0.00 40.79 3.51
784 811 2.484264 GTGGCAGATGTGTTTACAGTCC 59.516 50.000 0.00 0.00 40.79 3.85
785 812 1.732259 GGCAGATGTGTTTACAGTCCG 59.268 52.381 0.00 0.00 40.79 4.79
786 813 2.611971 GGCAGATGTGTTTACAGTCCGA 60.612 50.000 0.00 0.00 40.79 4.55
787 814 2.668457 GCAGATGTGTTTACAGTCCGAG 59.332 50.000 0.00 0.00 40.79 4.63
788 815 3.861131 GCAGATGTGTTTACAGTCCGAGT 60.861 47.826 0.00 0.00 40.79 4.18
789 816 3.675225 CAGATGTGTTTACAGTCCGAGTG 59.325 47.826 1.39 1.39 40.79 3.51
790 817 3.572682 AGATGTGTTTACAGTCCGAGTGA 59.427 43.478 10.31 0.00 40.79 3.41
791 818 4.220821 AGATGTGTTTACAGTCCGAGTGAT 59.779 41.667 10.31 0.00 40.79 3.06
792 819 4.330944 TGTGTTTACAGTCCGAGTGATT 57.669 40.909 10.31 0.00 31.91 2.57
793 820 4.699637 TGTGTTTACAGTCCGAGTGATTT 58.300 39.130 10.31 0.00 31.91 2.17
794 821 4.748102 TGTGTTTACAGTCCGAGTGATTTC 59.252 41.667 10.31 0.00 31.91 2.17
795 822 3.985279 TGTTTACAGTCCGAGTGATTTCG 59.015 43.478 10.31 0.00 40.18 3.46
835 863 0.608035 TAAGGCGCCCCACAAGAAAG 60.608 55.000 26.15 0.00 0.00 2.62
923 951 0.443869 CTTTGTCGCTCCATTCGTGG 59.556 55.000 0.00 0.00 0.00 4.94
946 974 3.413300 ACCACCACCACACCCGTT 61.413 61.111 0.00 0.00 0.00 4.44
1227 1255 2.359967 CGACTTCCTCCACCCCTCC 61.360 68.421 0.00 0.00 0.00 4.30
1264 1292 3.522731 CGCCCTGGTCTCTCCTCG 61.523 72.222 0.00 0.00 37.07 4.63
1266 1294 3.151022 CCCTGGTCTCTCCTCGCC 61.151 72.222 0.00 0.00 37.07 5.54
1635 1663 0.984230 AGGAAGTTCTCGGGATGCAA 59.016 50.000 2.25 0.00 0.00 4.08
1641 1669 0.617535 TTCTCGGGATGCAAGAGGGA 60.618 55.000 8.60 0.00 33.16 4.20
1855 1883 3.191791 TGCCAGTGATGACATTGTTGATG 59.808 43.478 0.00 0.00 41.71 3.07
1926 1954 1.209128 GCGAGGACGATACAATGGTG 58.791 55.000 0.00 0.00 42.66 4.17
1998 2026 3.751175 GTGCTAATGAACAGTGCTTACCA 59.249 43.478 0.00 0.00 0.00 3.25
2004 2032 3.664107 TGAACAGTGCTTACCAGTCATC 58.336 45.455 0.00 0.00 0.00 2.92
2209 2242 7.225011 TGGTTTGTTGTACTATCCACAATACA 58.775 34.615 0.00 0.00 38.13 2.29
2210 2243 7.389330 TGGTTTGTTGTACTATCCACAATACAG 59.611 37.037 0.00 0.00 38.13 2.74
2248 2281 7.587629 TCTGTTGATTCAAATGCTAAGAACAG 58.412 34.615 0.00 0.00 39.28 3.16
2264 2298 7.334421 GCTAAGAACAGTCTCCATGTAAATTGA 59.666 37.037 0.00 0.00 30.70 2.57
2381 2415 7.459234 AGGTATGCTTAGTTTACTTTTGGACT 58.541 34.615 0.00 0.00 0.00 3.85
2806 2841 5.250543 TCCCTCTGTTCTTAAATCCATGTCA 59.749 40.000 0.00 0.00 0.00 3.58
2865 2900 4.248859 CTGTTACTTCTCATCCCACACAG 58.751 47.826 0.00 0.00 0.00 3.66
2933 2968 9.990888 GACGAATCTAATAGTACTAATTTTGCG 57.009 33.333 6.70 8.38 0.00 4.85
3015 3050 5.996513 GCAGACATCATCTATTTCCTCATGT 59.003 40.000 0.00 0.00 35.15 3.21
3016 3051 6.485984 GCAGACATCATCTATTTCCTCATGTT 59.514 38.462 0.00 0.00 35.15 2.71
3074 3109 4.464069 AGTCTATTGAGTGGCAGAGTTC 57.536 45.455 0.00 0.00 0.00 3.01
3290 3325 0.539051 ATCACAGCTGAGGCACCTAC 59.461 55.000 23.35 0.00 41.70 3.18
3291 3326 0.831711 TCACAGCTGAGGCACCTACA 60.832 55.000 23.35 0.00 41.70 2.74
3341 3376 8.788325 TCCTGGAAAGCTTTAGTTATTTCTAC 57.212 34.615 12.68 0.00 33.25 2.59
3346 3381 7.903946 GGAAAGCTTTAGTTATTTCTACTTCGC 59.096 37.037 12.68 0.00 33.25 4.70
3363 3398 3.179443 TCGCGGATCTGCTCTTTTATT 57.821 42.857 23.71 0.00 0.00 1.40
3439 3474 2.541556 GAGGTAAACGAGCATGACCTC 58.458 52.381 10.69 10.69 46.89 3.85
3613 3648 3.599343 TGACAATCCTGACATGTGCTAC 58.401 45.455 1.15 0.00 0.00 3.58
3724 3759 6.406177 CCAGGCAATTGCATTTCTACAGTAAT 60.406 38.462 30.32 0.00 44.36 1.89
3968 4003 7.263100 TGATGGAGGTATTTCGATCATTTTG 57.737 36.000 0.00 0.00 37.38 2.44
4003 4038 9.244292 ACTCAATAGTAGAATCTGTGACAGTTA 57.756 33.333 12.93 0.00 32.84 2.24
4080 4115 8.789825 AGCTAAATTGATATTGCCAGATCTAG 57.210 34.615 0.00 0.00 0.00 2.43
4151 4187 1.176527 AGATGGTCAAAATGCCACCG 58.823 50.000 0.00 0.00 37.62 4.94
4344 4380 5.086104 AGATGGTGCGTTCTTGTACTTAT 57.914 39.130 0.00 0.00 0.00 1.73
4345 4381 4.870426 AGATGGTGCGTTCTTGTACTTATG 59.130 41.667 0.00 0.00 0.00 1.90
4552 4590 8.850156 AGAAGTTCCCAAATATCCATTAATTCG 58.150 33.333 0.00 0.00 0.00 3.34
4867 4905 6.258068 GGTTACCTCAATCTGTAGCATTACAC 59.742 42.308 0.00 0.00 34.91 2.90
4964 5003 5.751243 ATTAGCAAACAACAGTCGTTTCT 57.249 34.783 0.00 0.00 34.40 2.52
4968 5007 4.621034 AGCAAACAACAGTCGTTTCTTTTG 59.379 37.500 0.00 0.00 34.40 2.44
5104 5143 3.005554 CCTACCTTGTGCTCACTTGATG 58.994 50.000 1.47 0.00 0.00 3.07
5118 5157 9.023962 TGCTCACTTGATGTCCTATTTAATTTT 57.976 29.630 0.00 0.00 0.00 1.82
5167 5207 5.177326 TGTGCTGCATATCAAAAATTTCCC 58.823 37.500 5.27 0.00 0.00 3.97
5200 5240 6.815089 TCTTCATCTTCAATAAGCCTCTCTC 58.185 40.000 0.00 0.00 32.36 3.20
5208 5248 6.426646 TCAATAAGCCTCTCTCTAATTCCC 57.573 41.667 0.00 0.00 0.00 3.97
5224 5264 1.210204 TCCCTTGCCCTTGAGCATCT 61.210 55.000 0.00 0.00 43.64 2.90
5258 5298 5.659463 TCACCTTCCTCATTTTTGTGTTTG 58.341 37.500 0.00 0.00 0.00 2.93
5297 5337 5.971763 TGAAATCACTAGCTTCTCTTCTCC 58.028 41.667 0.00 0.00 0.00 3.71
5365 5406 2.023673 TCATGCCGTGATTGATTTCCC 58.976 47.619 0.00 0.00 0.00 3.97
5397 5438 1.841663 GCACCTAGGTTGTGTGTGCG 61.842 60.000 13.15 0.00 42.29 5.34
5405 5446 0.109964 GTTGTGTGTGCGTGTGTGTT 60.110 50.000 0.00 0.00 0.00 3.32
5449 5490 9.918630 AAACTCTGTCTGATCCAAATTAAATTG 57.081 29.630 0.00 0.00 0.00 2.32
5532 5573 9.860650 ATGTACAATTATTTCTATACCAGGCAA 57.139 29.630 0.00 0.00 0.00 4.52
5578 5619 2.348411 AAGTGTCACCTTGGACTTGG 57.652 50.000 0.00 0.00 38.61 3.61
5580 5621 2.057922 AGTGTCACCTTGGACTTGGAT 58.942 47.619 0.00 0.00 38.61 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 1.912043 CTCATCCCCTTCAAGGTGAGT 59.088 52.381 12.54 0.00 31.93 3.41
166 167 1.488393 GGTCTCTCATCCCCTTCAAGG 59.512 57.143 0.00 0.00 34.30 3.61
235 236 2.683465 GCCATTGCTCCTCCTCCCA 61.683 63.158 0.00 0.00 33.53 4.37
488 489 2.125552 CACGCTTCCGCCATGAGA 60.126 61.111 0.00 0.00 38.22 3.27
572 599 3.912248 ACTGATCTTATCGGGTGTACCT 58.088 45.455 0.44 0.00 40.02 3.08
573 600 4.667519 AACTGATCTTATCGGGTGTACC 57.332 45.455 0.00 0.00 40.02 3.34
605 632 2.432444 CTCCTTCTCTCACGAGTCACT 58.568 52.381 0.00 0.00 38.45 3.41
610 637 0.033991 TCCCCTCCTTCTCTCACGAG 60.034 60.000 0.00 0.00 38.67 4.18
611 638 0.631753 ATCCCCTCCTTCTCTCACGA 59.368 55.000 0.00 0.00 0.00 4.35
612 639 1.036707 GATCCCCTCCTTCTCTCACG 58.963 60.000 0.00 0.00 0.00 4.35
613 640 1.760029 GTGATCCCCTCCTTCTCTCAC 59.240 57.143 0.00 0.00 0.00 3.51
614 641 1.686428 CGTGATCCCCTCCTTCTCTCA 60.686 57.143 0.00 0.00 0.00 3.27
615 642 1.036707 CGTGATCCCCTCCTTCTCTC 58.963 60.000 0.00 0.00 0.00 3.20
616 643 0.631753 TCGTGATCCCCTCCTTCTCT 59.368 55.000 0.00 0.00 0.00 3.10
626 653 1.227263 CCATCCACGTCGTGATCCC 60.227 63.158 26.53 0.00 35.23 3.85
637 664 2.125106 GCCCACGACTCCATCCAC 60.125 66.667 0.00 0.00 0.00 4.02
709 736 3.453679 AGAGCGCTCGGGAAGGAC 61.454 66.667 30.39 5.23 34.09 3.85
778 805 0.603569 AGCGAAATCACTCGGACTGT 59.396 50.000 0.00 0.00 39.27 3.55
779 806 2.561733 TAGCGAAATCACTCGGACTG 57.438 50.000 0.00 0.00 39.27 3.51
780 807 3.448686 CAATAGCGAAATCACTCGGACT 58.551 45.455 0.00 0.00 39.27 3.85
781 808 2.033662 GCAATAGCGAAATCACTCGGAC 60.034 50.000 0.00 0.00 39.27 4.79
782 809 2.201732 GCAATAGCGAAATCACTCGGA 58.798 47.619 0.00 0.00 39.27 4.55
783 810 2.652662 GCAATAGCGAAATCACTCGG 57.347 50.000 0.00 0.00 39.27 4.63
814 841 0.178987 TTCTTGTGGGGCGCCTTAAA 60.179 50.000 28.56 14.60 0.00 1.52
816 843 0.608035 CTTTCTTGTGGGGCGCCTTA 60.608 55.000 28.56 13.14 0.00 2.69
817 844 1.903404 CTTTCTTGTGGGGCGCCTT 60.903 57.895 28.56 0.00 0.00 4.35
818 845 1.774894 TACTTTCTTGTGGGGCGCCT 61.775 55.000 28.56 3.67 0.00 5.52
820 847 0.240145 GTTACTTTCTTGTGGGGCGC 59.760 55.000 0.00 0.00 0.00 6.53
821 848 0.879090 GGTTACTTTCTTGTGGGGCG 59.121 55.000 0.00 0.00 0.00 6.13
822 849 1.886542 CTGGTTACTTTCTTGTGGGGC 59.113 52.381 0.00 0.00 0.00 5.80
923 951 1.822186 GTGTGGTGGTGGTGGTGAC 60.822 63.158 0.00 0.00 0.00 3.67
946 974 2.777400 TGTGGGGTTTCCGGGGAA 60.777 61.111 0.00 0.00 38.76 3.97
1635 1663 0.267356 CCTCCTTCCTCCATCCCTCT 59.733 60.000 0.00 0.00 0.00 3.69
1641 1669 2.041265 ACCGCCTCCTTCCTCCAT 59.959 61.111 0.00 0.00 0.00 3.41
1777 1805 6.559810 CACCAACTGAAGTCACACAAAATTA 58.440 36.000 0.00 0.00 0.00 1.40
1790 1818 0.535102 AACCCTCGCACCAACTGAAG 60.535 55.000 0.00 0.00 0.00 3.02
1926 1954 4.697756 TGGTACACTGCTGCGGGC 62.698 66.667 13.87 0.00 42.22 6.13
1998 2026 2.825223 TCTGAGGTGGACATGATGACT 58.175 47.619 0.00 0.00 0.00 3.41
2004 2032 0.914644 ACCCATCTGAGGTGGACATG 59.085 55.000 14.67 0.00 39.12 3.21
2209 2242 8.058667 TGAATCAACAGATAAATTGTGCATCT 57.941 30.769 0.00 0.00 0.00 2.90
2210 2243 8.692110 TTGAATCAACAGATAAATTGTGCATC 57.308 30.769 0.00 0.00 0.00 3.91
2275 2309 5.350504 TCTGCAATGGTTTCAAAAGGAAA 57.649 34.783 0.00 0.00 43.07 3.13
2288 2322 5.624159 TGGGAAGAATAGTATCTGCAATGG 58.376 41.667 0.00 0.00 0.00 3.16
2290 2324 5.767168 GCTTGGGAAGAATAGTATCTGCAAT 59.233 40.000 0.00 0.00 0.00 3.56
2381 2415 3.506810 CAAACGAGGAAAAAGCACAACA 58.493 40.909 0.00 0.00 0.00 3.33
2738 2773 2.478200 GGCTCGAGGACTAAAGACTTCG 60.478 54.545 15.58 7.45 39.63 3.79
2781 2816 5.501156 ACATGGATTTAAGAACAGAGGGAC 58.499 41.667 0.00 0.00 0.00 4.46
2786 2821 8.634335 TGAAATGACATGGATTTAAGAACAGA 57.366 30.769 0.00 0.00 0.00 3.41
2806 2841 4.246712 AGAGATTGCCCATGTCTGAAAT 57.753 40.909 0.00 0.00 34.15 2.17
3015 3050 5.499004 AACCTGCTGAAGATTACTACCAA 57.501 39.130 0.00 0.00 0.00 3.67
3016 3051 6.614694 TTAACCTGCTGAAGATTACTACCA 57.385 37.500 0.00 0.00 0.00 3.25
3106 3141 4.629200 CAGACTGAGGTTGATGCTCTTAAC 59.371 45.833 0.00 0.00 0.00 2.01
3210 3245 8.637099 TGTGTCAATAATTTCCTCAATGTTTGA 58.363 29.630 0.00 0.00 38.17 2.69
3290 3325 6.159299 AGGAGAATGACATCTCATACAGTG 57.841 41.667 13.45 0.00 46.24 3.66
3291 3326 5.896106 TGAGGAGAATGACATCTCATACAGT 59.104 40.000 13.45 0.00 46.24 3.55
3341 3376 1.363744 AAAAGAGCAGATCCGCGAAG 58.636 50.000 8.23 0.00 36.85 3.79
3346 3381 6.128172 ACACTTTCAATAAAAGAGCAGATCCG 60.128 38.462 4.64 0.00 46.18 4.18
3385 3420 6.292596 GCTGCTTTCTCCTAGTTTCGATATTG 60.293 42.308 0.00 0.00 0.00 1.90
3613 3648 3.318839 TCAGTTGAATCTTTGCCCACTTG 59.681 43.478 0.00 0.00 0.00 3.16
3968 4003 9.571810 CAGATTCTACTATTGAGTATCTGATGC 57.428 37.037 11.65 0.00 43.28 3.91
4003 4038 4.994217 CGATGGCCAAACCTAAAAATGTTT 59.006 37.500 10.96 0.00 40.22 2.83
4070 4105 6.624352 TTTGTATTTGATGCTAGATCTGGC 57.376 37.500 23.11 23.11 37.60 4.85
4143 4179 3.286694 ATGGCTTCCACGGTGGCAT 62.287 57.895 22.42 15.93 41.18 4.40
4151 4187 2.927553 GACATTGACATGGCTTCCAC 57.072 50.000 0.00 0.00 35.19 4.02
4344 4380 9.088512 GAAACAAAACATTTACAATACCACACA 57.911 29.630 0.00 0.00 0.00 3.72
4345 4381 9.308318 AGAAACAAAACATTTACAATACCACAC 57.692 29.630 0.00 0.00 0.00 3.82
4552 4590 4.145052 AGATCCCCACTTCAAGTTCAAAC 58.855 43.478 0.00 0.00 0.00 2.93
4964 5003 5.110814 TGAAAGTGAGGTCCTCTTCAAAA 57.889 39.130 19.82 0.00 31.70 2.44
4968 5007 3.815962 GGTTTGAAAGTGAGGTCCTCTTC 59.184 47.826 19.82 14.84 0.00 2.87
5011 5050 0.316204 CAAACTACAGGGACGGTCGT 59.684 55.000 1.43 0.00 38.12 4.34
5167 5207 5.656213 ATTGAAGATGAAGAAAAGGGCAG 57.344 39.130 0.00 0.00 0.00 4.85
5200 5240 2.027385 GCTCAAGGGCAAGGGAATTAG 58.973 52.381 0.00 0.00 0.00 1.73
5208 5248 1.948145 GATGAGATGCTCAAGGGCAAG 59.052 52.381 0.00 0.00 44.04 4.01
5224 5264 0.548031 GGAAGGTGAGGCCATGATGA 59.452 55.000 5.01 0.00 40.61 2.92
5258 5298 5.293324 GTGATTTCAGTTTTGGGGTTTGAAC 59.707 40.000 0.00 0.00 0.00 3.18
5297 5337 0.176219 ATGGCCAAATGGAATGCACG 59.824 50.000 10.96 0.00 37.39 5.34
5365 5406 3.513515 ACCTAGGTGCAAGAAGAAGAGAG 59.486 47.826 15.42 0.00 0.00 3.20
5397 5438 4.386049 CGAGTATTGGAGAGAAACACACAC 59.614 45.833 0.00 0.00 0.00 3.82
5405 5446 4.094476 AGTTTCCCGAGTATTGGAGAGAA 58.906 43.478 0.00 0.00 45.05 2.87
5465 5506 6.564328 GGCTAAACCTAAAAATGATCCACTG 58.436 40.000 0.00 0.00 34.51 3.66


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

AutoCloner maintained by Alex Coulton.