Multiple sequence alignment - TraesCS2D01G077700

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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 TraesCS2D01G077700 chr2D 100.000 4592 0 0 1 4592 33227465 33232056 0.000000e+00 8480.0
1 TraesCS2D01G077700 chr2D 95.103 3962 142 21 1 3950 33306921 33310842 0.000000e+00 6194.0
2 TraesCS2D01G077700 chr2D 86.803 2061 248 15 795 2841 33364968 33367018 0.000000e+00 2278.0
3 TraesCS2D01G077700 chr2D 82.546 2011 310 22 856 2843 442441823 442439831 0.000000e+00 1731.0
4 TraesCS2D01G077700 chr2D 87.482 1414 156 14 541 1940 33561859 33563265 0.000000e+00 1611.0
5 TraesCS2D01G077700 chr2D 87.412 1414 157 15 541 1940 33575659 33577065 0.000000e+00 1605.0
6 TraesCS2D01G077700 chr2D 82.369 1072 153 19 2843 3898 33577074 33578125 0.000000e+00 900.0
7 TraesCS2D01G077700 chr2D 83.069 1010 150 13 2843 3840 33563274 33564274 0.000000e+00 898.0
8 TraesCS2D01G077700 chr2D 88.281 256 27 3 4025 4279 33310967 33311220 2.080000e-78 303.0
9 TraesCS2D01G077700 chr2D 82.109 313 42 8 6 305 33561488 33561799 5.900000e-64 255.0
10 TraesCS2D01G077700 chr2D 82.109 313 42 8 6 305 33575288 33575599 5.900000e-64 255.0
11 TraesCS2D01G077700 chr2B 95.023 3978 163 18 1 3957 55177006 55180969 0.000000e+00 6216.0
12 TraesCS2D01G077700 chr2B 83.225 2003 308 17 856 2843 521978242 521976253 0.000000e+00 1812.0
13 TraesCS2D01G077700 chr2B 82.407 972 140 22 2843 3792 55691824 55692786 0.000000e+00 819.0
14 TraesCS2D01G077700 chr2B 83.238 525 60 16 4086 4592 55181103 55181617 1.510000e-124 457.0
15 TraesCS2D01G077700 chr2A 93.810 3619 180 19 1 3594 36383283 36386882 0.000000e+00 5402.0
16 TraesCS2D01G077700 chr2A 83.248 1952 295 20 895 2829 585927846 585925910 0.000000e+00 1764.0
17 TraesCS2D01G077700 chr2A 86.475 902 97 11 541 1427 36408576 36409467 0.000000e+00 966.0
18 TraesCS2D01G077700 chr2A 82.875 800 71 34 3652 4420 36386881 36387645 0.000000e+00 658.0
19 TraesCS2D01G077700 chr2A 79.670 546 69 19 6 538 36407999 36408515 5.650000e-94 355.0
20 TraesCS2D01G077700 chr2A 91.176 68 6 0 3948 4015 36387208 36387275 4.890000e-15 93.5
21 TraesCS2D01G077700 chr6D 86.763 695 92 0 2146 2840 131705472 131704778 0.000000e+00 774.0
22 TraesCS2D01G077700 chr6D 82.857 735 117 5 2846 3574 131704619 131703888 0.000000e+00 651.0
23 TraesCS2D01G077700 chr6A 86.619 695 93 0 2146 2840 170521990 170521296 0.000000e+00 769.0
24 TraesCS2D01G077700 chr6A 82.449 735 120 5 2846 3574 170521137 170520406 6.480000e-178 634.0
25 TraesCS2D01G077700 chr6B 82.473 736 118 6 2846 3574 229279188 229278457 6.480000e-178 634.0
26 TraesCS2D01G077700 chr5A 100.000 35 0 0 1076 1110 582622947 582622981 1.070000e-06 65.8
27 TraesCS2D01G077700 chr5A 81.395 86 9 5 720 804 654097732 654097653 3.840000e-06 63.9
28 TraesCS2D01G077700 chr5A 91.304 46 3 1 759 804 657765145 657765189 1.380000e-05 62.1


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 TraesCS2D01G077700 chr2D 33227465 33232056 4591 False 8480.000000 8480 100.000000 1 4592 1 chr2D.!!$F1 4591
1 TraesCS2D01G077700 chr2D 33306921 33311220 4299 False 3248.500000 6194 91.692000 1 4279 2 chr2D.!!$F3 4278
2 TraesCS2D01G077700 chr2D 33364968 33367018 2050 False 2278.000000 2278 86.803000 795 2841 1 chr2D.!!$F2 2046
3 TraesCS2D01G077700 chr2D 442439831 442441823 1992 True 1731.000000 1731 82.546000 856 2843 1 chr2D.!!$R1 1987
4 TraesCS2D01G077700 chr2D 33561488 33564274 2786 False 921.333333 1611 84.220000 6 3840 3 chr2D.!!$F4 3834
5 TraesCS2D01G077700 chr2D 33575288 33578125 2837 False 920.000000 1605 83.963333 6 3898 3 chr2D.!!$F5 3892
6 TraesCS2D01G077700 chr2B 55177006 55181617 4611 False 3336.500000 6216 89.130500 1 4592 2 chr2B.!!$F2 4591
7 TraesCS2D01G077700 chr2B 521976253 521978242 1989 True 1812.000000 1812 83.225000 856 2843 1 chr2B.!!$R1 1987
8 TraesCS2D01G077700 chr2B 55691824 55692786 962 False 819.000000 819 82.407000 2843 3792 1 chr2B.!!$F1 949
9 TraesCS2D01G077700 chr2A 36383283 36387645 4362 False 2051.166667 5402 89.287000 1 4420 3 chr2A.!!$F1 4419
10 TraesCS2D01G077700 chr2A 585925910 585927846 1936 True 1764.000000 1764 83.248000 895 2829 1 chr2A.!!$R1 1934
11 TraesCS2D01G077700 chr2A 36407999 36409467 1468 False 660.500000 966 83.072500 6 1427 2 chr2A.!!$F2 1421
12 TraesCS2D01G077700 chr6D 131703888 131705472 1584 True 712.500000 774 84.810000 2146 3574 2 chr6D.!!$R1 1428
13 TraesCS2D01G077700 chr6A 170520406 170521990 1584 True 701.500000 769 84.534000 2146 3574 2 chr6A.!!$R1 1428
14 TraesCS2D01G077700 chr6B 229278457 229279188 731 True 634.000000 634 82.473000 2846 3574 1 chr6B.!!$R1 728

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
928 1020 0.453793 TTGTTTGGTGCAGGTTGACG 59.546 50.0 0.0 0.0 0.00 4.35 F
1145 1244 0.385390 AAAACTGTCCGCTGCCAAAG 59.615 50.0 0.0 0.0 0.00 2.77 F
2533 2648 0.321564 CATTGGCTGGAGTTCGGACA 60.322 55.0 0.0 0.0 38.18 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2382 0.681175 CTCAAACTTTGGGGCCCTTG 59.319 55.0 25.93 19.08 0.00 3.61 R
2959 3230 0.106918 TGCCCAGGTTCGAACTTGTT 60.107 50.0 30.91 12.79 34.54 2.83 R
4048 4491 0.249826 CCCACATGGTTTGGTTGTGC 60.250 55.0 0.00 0.00 39.48 4.57 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
108 109 2.930040 CAGTATTGTAGCCAACCTGTCG 59.070 50.000 0.00 0.00 32.32 4.35
209 213 7.717568 TGAAGAGAGGTTTAATCGGAATCTAG 58.282 38.462 0.00 0.00 0.00 2.43
284 305 1.523258 CCTGCTGGGATTGCTCTCG 60.523 63.158 0.71 0.00 37.23 4.04
357 378 9.026121 GCCTATGGACTATCTAATGAAGTCTAA 57.974 37.037 0.00 0.00 39.65 2.10
389 410 5.232838 GCATTACATTTTGAGTGCTAATGGC 59.767 40.000 0.00 0.00 42.22 4.40
400 421 4.599041 AGTGCTAATGGCCTTTCATGTTA 58.401 39.130 7.23 0.00 40.92 2.41
747 832 5.207354 TCATCTCTTAGCTGGAGAAGACAT 58.793 41.667 19.96 2.92 42.16 3.06
928 1020 0.453793 TTGTTTGGTGCAGGTTGACG 59.546 50.000 0.00 0.00 0.00 4.35
990 1083 7.174253 GTCTGGAAGTAGTATATCTCACTCCAG 59.826 44.444 7.78 7.78 41.49 3.86
1056 1155 1.167851 CGGGCTCAAATTCTGCAAGA 58.832 50.000 0.00 0.00 44.68 3.02
1145 1244 0.385390 AAAACTGTCCGCTGCCAAAG 59.615 50.000 0.00 0.00 0.00 2.77
1196 1295 2.348411 ACTGACCAACCTGTTCCTTG 57.652 50.000 0.00 0.00 0.00 3.61
1326 1434 5.582950 AGTATCCCAATTGCTATGCCTTA 57.417 39.130 0.00 0.00 0.00 2.69
1343 1451 5.186198 TGCCTTAATAGAGAAAGTTGAGCC 58.814 41.667 0.00 0.00 0.00 4.70
1830 1938 1.312815 GTGCAGCTGAAAGTGAAGGT 58.687 50.000 20.43 0.00 35.30 3.50
2002 2114 0.999712 GGAATCTGAAGGGGTTGGGA 59.000 55.000 0.00 0.00 0.00 4.37
2105 2217 6.393990 CATCTACTGTAGAAGGTATGGATGC 58.606 44.000 20.40 0.00 38.50 3.91
2267 2382 9.783256 ATTTTATGCTCGAATTACAAAGGTAAC 57.217 29.630 0.00 0.00 41.99 2.50
2378 2493 4.561326 GCCTGTTGCTTGTGGACATTTTAT 60.561 41.667 0.00 0.00 36.87 1.40
2455 2570 4.874966 CCTATGAGAAAAGCAGGACAAGAG 59.125 45.833 0.00 0.00 0.00 2.85
2456 2571 2.498167 TGAGAAAAGCAGGACAAGAGC 58.502 47.619 0.00 0.00 0.00 4.09
2533 2648 0.321564 CATTGGCTGGAGTTCGGACA 60.322 55.000 0.00 0.00 38.18 4.02
2726 2841 2.465860 TCACATTGTGTCCCTTACCG 57.534 50.000 16.06 0.00 34.79 4.02
2852 3120 5.376625 TCCAGAAAGCAGTTACACTCAATT 58.623 37.500 0.00 0.00 0.00 2.32
2879 3150 6.018669 GCTGTAGAAGGTACTGATGTTTATGC 60.019 42.308 0.00 0.00 40.86 3.14
2895 3166 7.601073 TGTTTATGCGGAATCTGATGATATC 57.399 36.000 0.00 0.00 31.70 1.63
2943 3214 8.411683 GCTGAATCTGAATTCCATGAATTTACT 58.588 33.333 2.27 0.00 41.56 2.24
2959 3230 8.716646 TGAATTTACTGAAATGAGATCGCTTA 57.283 30.769 0.00 0.00 35.38 3.09
3008 3279 8.759481 TGGGCTCTCTACAATGATATAGATAG 57.241 38.462 0.00 0.00 0.00 2.08
3158 3435 3.254903 GGCTGTGGAATCTTTACGGTTTT 59.745 43.478 0.00 0.00 0.00 2.43
3527 3808 2.949447 TGAAAAAGGAGGCAAGCTTCT 58.051 42.857 0.00 0.00 0.00 2.85
3543 3824 2.877708 GCTTCTAGGCTGTTTGGAGCTT 60.878 50.000 0.00 0.00 39.11 3.74
3695 4045 2.616330 CGTGTTTCATGCTGCCCGT 61.616 57.895 0.00 0.00 0.00 5.28
3712 4062 2.027561 CCCGTAGTTCTCCATGTTCCAA 60.028 50.000 0.00 0.00 0.00 3.53
3800 4161 4.142293 TGACATTTGTTGCAGCTGTTGTTA 60.142 37.500 16.64 2.75 0.00 2.41
3801 4162 4.947645 ACATTTGTTGCAGCTGTTGTTAT 58.052 34.783 16.64 0.00 0.00 1.89
3802 4163 5.358922 ACATTTGTTGCAGCTGTTGTTATT 58.641 33.333 16.64 0.00 0.00 1.40
3856 4217 4.398673 ACTCTTCCTTCGCTCGTAGTTTAT 59.601 41.667 0.00 0.00 0.00 1.40
3911 4276 0.268869 TGGATGGGATCTGCCTACCT 59.731 55.000 0.00 0.00 36.66 3.08
3923 4288 3.135712 TCTGCCTACCTCAACTTGTTTGA 59.864 43.478 0.00 0.00 42.26 2.69
3959 4396 3.097877 TGTTGTTGTTGTTGTTGTGCA 57.902 38.095 0.00 0.00 0.00 4.57
3999 4442 3.181479 GGCTCATTGTGCATGTCATTGAT 60.181 43.478 12.33 0.66 34.06 2.57
4028 4471 6.889301 AAACAATTCATGTGTGAGATCACT 57.111 33.333 13.74 0.00 46.55 3.41
4029 4472 7.984422 AAACAATTCATGTGTGAGATCACTA 57.016 32.000 13.74 4.14 46.55 2.74
4030 4473 8.571461 AAACAATTCATGTGTGAGATCACTAT 57.429 30.769 13.74 6.11 46.55 2.12
4031 4474 8.571461 AACAATTCATGTGTGAGATCACTATT 57.429 30.769 13.74 2.69 46.55 1.73
4032 4475 7.982224 ACAATTCATGTGTGAGATCACTATTG 58.018 34.615 13.74 13.51 46.55 1.90
4033 4476 7.825761 ACAATTCATGTGTGAGATCACTATTGA 59.174 33.333 13.74 10.22 46.55 2.57
4042 4485 6.155827 GTGAGATCACTATTGATGGAGTAGC 58.844 44.000 5.72 0.00 42.95 3.58
4048 4491 3.389329 ACTATTGATGGAGTAGCACCCTG 59.611 47.826 0.00 0.00 0.00 4.45
4083 4527 6.287525 CCATGTGGGTTTTTCATTTTACTGT 58.712 36.000 0.00 0.00 0.00 3.55
4084 4528 7.437748 CCATGTGGGTTTTTCATTTTACTGTA 58.562 34.615 0.00 0.00 0.00 2.74
4173 4618 4.287766 AGAATCTGGGAAACACTGGTAC 57.712 45.455 0.00 0.00 0.00 3.34
4217 4662 7.315247 TGGTGAGGAAAAATATTATGTGTCG 57.685 36.000 0.00 0.00 0.00 4.35
4263 4708 5.536161 TCTTTTGTTTTGCCTAGCAGAGAAT 59.464 36.000 0.00 0.00 40.61 2.40
4264 4709 5.376854 TTTGTTTTGCCTAGCAGAGAATC 57.623 39.130 0.00 0.00 40.61 2.52
4299 4768 3.575256 TGAGCCTGCAAATGTTGAATTCT 59.425 39.130 7.05 0.00 0.00 2.40
4300 4769 3.921677 AGCCTGCAAATGTTGAATTCTG 58.078 40.909 7.05 0.00 0.00 3.02
4311 4780 5.034852 TGTTGAATTCTGAGGACTGTGAA 57.965 39.130 7.05 0.00 0.00 3.18
4312 4781 5.624159 TGTTGAATTCTGAGGACTGTGAAT 58.376 37.500 7.05 0.00 0.00 2.57
4313 4782 5.702670 TGTTGAATTCTGAGGACTGTGAATC 59.297 40.000 7.05 0.00 0.00 2.52
4314 4783 5.752036 TGAATTCTGAGGACTGTGAATCT 57.248 39.130 7.05 0.00 0.00 2.40
4315 4784 5.485620 TGAATTCTGAGGACTGTGAATCTG 58.514 41.667 7.05 0.00 0.00 2.90
4316 4785 5.012458 TGAATTCTGAGGACTGTGAATCTGT 59.988 40.000 7.05 0.00 0.00 3.41
4317 4786 3.949842 TCTGAGGACTGTGAATCTGTG 57.050 47.619 0.00 0.00 0.00 3.66
4318 4787 3.500343 TCTGAGGACTGTGAATCTGTGA 58.500 45.455 0.00 0.00 0.00 3.58
4325 4794 4.629200 GGACTGTGAATCTGTGATGTCTTC 59.371 45.833 0.00 0.00 0.00 2.87
4332 4801 3.934457 TCTGTGATGTCTTCGCACTTA 57.066 42.857 0.00 0.00 39.90 2.24
4376 4845 5.986501 TCTCTAGGTTCTGTTTCTCCTTC 57.013 43.478 0.00 0.00 0.00 3.46
4378 4847 2.171341 AGGTTCTGTTTCTCCTTCGC 57.829 50.000 0.00 0.00 0.00 4.70
4424 4893 2.095819 TGTGTTACAATGCTGTCATGCG 60.096 45.455 0.00 0.00 36.96 4.73
4425 4894 1.135717 TGTTACAATGCTGTCATGCGC 60.136 47.619 0.00 0.00 36.96 6.09
4451 4920 3.424703 AGAAAATTAAGCTCAGCAGGCA 58.575 40.909 0.00 0.00 0.00 4.75
4454 4923 4.813750 AAATTAAGCTCAGCAGGCAATT 57.186 36.364 0.00 0.00 0.00 2.32
4464 4933 1.143183 CAGGCAATTGAGGCATGGC 59.857 57.895 12.14 12.14 39.22 4.40
4473 4942 1.246056 TGAGGCATGGCTGTGCTTTC 61.246 55.000 28.55 10.98 44.45 2.62
4474 4943 2.180017 GGCATGGCTGTGCTTTCG 59.820 61.111 12.86 0.00 44.45 3.46
4477 4946 0.455633 GCATGGCTGTGCTTTCGAAG 60.456 55.000 0.00 0.00 41.82 3.79
4508 4977 8.786826 TCTTATTAACTTCACTTATGGTGGTG 57.213 34.615 0.00 0.00 45.38 4.17
4509 4978 5.897377 ATTAACTTCACTTATGGTGGTGC 57.103 39.130 0.00 0.00 45.38 5.01
4510 4979 3.508845 AACTTCACTTATGGTGGTGCT 57.491 42.857 0.00 0.00 45.38 4.40
4511 4980 3.508845 ACTTCACTTATGGTGGTGCTT 57.491 42.857 0.00 0.00 45.38 3.91
4512 4981 4.634012 ACTTCACTTATGGTGGTGCTTA 57.366 40.909 0.00 0.00 45.38 3.09
4513 4982 4.324267 ACTTCACTTATGGTGGTGCTTAC 58.676 43.478 0.00 0.00 45.38 2.34
4515 4984 1.396996 CACTTATGGTGGTGCTTACGC 59.603 52.381 0.00 0.00 41.90 4.42
4516 4985 1.002659 ACTTATGGTGGTGCTTACGCA 59.997 47.619 0.00 0.00 45.60 5.24
4517 4986 4.482113 CACTTATGGTGGTGCTTACGCAT 61.482 47.826 0.00 0.00 41.76 4.73
4518 4987 5.924869 CACTTATGGTGGTGCTTACGCATT 61.925 45.833 0.00 0.00 41.76 3.56
4519 4988 7.332951 CACTTATGGTGGTGCTTACGCATTT 62.333 44.000 0.00 0.00 41.76 2.32
4520 4989 8.710277 CACTTATGGTGGTGCTTACGCATTTT 62.710 42.308 0.00 0.00 41.76 1.82
4541 5010 4.376225 TTTTACGGGGTCCAAGAAAGAT 57.624 40.909 0.00 0.00 0.00 2.40
4543 5012 4.476628 TTACGGGGTCCAAGAAAGATAC 57.523 45.455 0.00 0.00 0.00 2.24
4545 5014 2.640826 ACGGGGTCCAAGAAAGATACAA 59.359 45.455 0.00 0.00 0.00 2.41
4555 5024 5.355350 CCAAGAAAGATACAACATGGTCCTC 59.645 44.000 0.00 0.00 0.00 3.71
4565 5034 4.461119 TGGTCCTCCACAGCTAGG 57.539 61.111 0.00 0.00 39.03 3.02
4569 5038 1.481363 GGTCCTCCACAGCTAGGTTAC 59.519 57.143 0.18 0.65 34.30 2.50
4577 5046 3.195610 CCACAGCTAGGTTACTGTCATGA 59.804 47.826 0.00 0.00 45.15 3.07
4578 5047 4.141846 CCACAGCTAGGTTACTGTCATGAT 60.142 45.833 0.00 0.00 45.15 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.104566 AGTTGGTAAATTGTACTATGTGCCTTA 58.895 33.333 13.94 2.35 0.00 2.69
19 20 5.935789 GCTCCACAGTTGGTAAATTGTACTA 59.064 40.000 0.00 0.00 44.35 1.82
27 28 6.322712 ACAATTAAAGCTCCACAGTTGGTAAA 59.677 34.615 0.00 0.00 44.35 2.01
86 87 3.368013 CGACAGGTTGGCTACAATACTGA 60.368 47.826 16.49 0.00 42.29 3.41
108 109 1.346722 TGTTTCGAGGAGGAACCCTTC 59.653 52.381 0.00 0.00 40.05 3.46
276 297 2.037121 TGTTGAACTGATCCGAGAGCAA 59.963 45.455 0.00 0.00 0.00 3.91
357 378 6.073657 GCACTCAAAATGTAATGCATGTGTTT 60.074 34.615 0.00 0.00 37.96 2.83
389 410 5.003804 AGCCACTGTTACTAACATGAAAGG 58.996 41.667 0.00 2.63 41.26 3.11
400 421 9.686683 ATCTCATAATTTTTAGCCACTGTTACT 57.313 29.630 0.00 0.00 0.00 2.24
539 618 5.164620 TGTCCTCTCTAAATGACATGCAA 57.835 39.130 0.00 0.00 33.09 4.08
756 841 7.995488 AGTTGGAAGAGAGAGAAATGAGAAAAA 59.005 33.333 0.00 0.00 0.00 1.94
757 842 7.512992 AGTTGGAAGAGAGAGAAATGAGAAAA 58.487 34.615 0.00 0.00 0.00 2.29
758 843 7.072263 AGTTGGAAGAGAGAGAAATGAGAAA 57.928 36.000 0.00 0.00 0.00 2.52
848 937 6.959361 TCTAAAACAGAAGAACAGCATGAAC 58.041 36.000 0.00 0.00 39.69 3.18
849 938 7.566760 TTCTAAAACAGAAGAACAGCATGAA 57.433 32.000 0.00 0.00 38.39 2.57
850 939 7.229306 ACATTCTAAAACAGAAGAACAGCATGA 59.771 33.333 0.00 0.00 46.37 3.07
904 996 0.172352 ACCTGCACCAAACAAACACG 59.828 50.000 0.00 0.00 0.00 4.49
928 1020 6.224584 AGCAGTAGACCAAAGAAAGTAACTC 58.775 40.000 0.00 0.00 0.00 3.01
990 1083 4.696479 ATGGAGATTCATGGTGGTAGTC 57.304 45.455 0.00 0.00 0.00 2.59
1056 1155 1.115467 TGGTCCAAAATGTTTGCGGT 58.885 45.000 0.00 0.00 0.00 5.68
1145 1244 2.288186 GCTATAAAGGCCTTCGAGCAAC 59.712 50.000 28.42 11.51 0.00 4.17
1326 1434 3.769844 TCTCCGGCTCAACTTTCTCTATT 59.230 43.478 0.00 0.00 0.00 1.73
1343 1451 4.928601 TGTCCGTACTTCATTATTCTCCG 58.071 43.478 0.00 0.00 0.00 4.63
1451 1559 8.620416 TGTAAATCATAATACCATCAGTGTTGC 58.380 33.333 0.00 0.00 31.47 4.17
1454 1562 9.330063 CAGTGTAAATCATAATACCATCAGTGT 57.670 33.333 0.00 0.00 0.00 3.55
1830 1938 3.298686 TCGAGAGCTCCTTCTGGAATA 57.701 47.619 10.93 0.00 42.66 1.75
2002 2114 1.676746 CATGTAGCATGCTGCCTCTT 58.323 50.000 30.42 10.75 46.52 2.85
2105 2217 1.998315 CGTGGTCAGATTCTTCAGCAG 59.002 52.381 0.00 0.00 0.00 4.24
2267 2382 0.681175 CTCAAACTTTGGGGCCCTTG 59.319 55.000 25.93 19.08 0.00 3.61
2455 2570 7.159322 TCTTAGGATATATCTCAAACGAGGC 57.841 40.000 12.42 0.00 0.00 4.70
2456 2571 9.632807 CTTTCTTAGGATATATCTCAAACGAGG 57.367 37.037 12.42 0.00 0.00 4.63
2533 2648 7.933215 ACTTAAAGTCTGTGTGGTTTTTAGT 57.067 32.000 0.00 0.00 0.00 2.24
2726 2841 0.991920 TTCAGTCCCCTCCATCCAAC 59.008 55.000 0.00 0.00 0.00 3.77
2852 3120 5.483685 AACATCAGTACCTTCTACAGCAA 57.516 39.130 0.00 0.00 0.00 3.91
2895 3166 4.430007 CACATTCAAATTCTGCCTGGATG 58.570 43.478 0.00 0.00 0.00 3.51
2943 3214 6.401047 CGAACTTGTTAAGCGATCTCATTTCA 60.401 38.462 0.00 0.00 0.00 2.69
2959 3230 0.106918 TGCCCAGGTTCGAACTTGTT 60.107 50.000 30.91 12.79 34.54 2.83
3158 3435 7.047891 AGTCTTAATAGCATCATTTTCACCGA 58.952 34.615 0.00 0.00 0.00 4.69
3199 3476 8.144478 TCTACTACATACAGGATGAGAAAATGC 58.856 37.037 0.00 0.00 39.69 3.56
3527 3808 2.356125 GGATCAAGCTCCAAACAGCCTA 60.356 50.000 0.00 0.00 40.65 3.93
3543 3824 0.250234 CTGGCACCGAGAAAGGATCA 59.750 55.000 0.00 0.00 34.73 2.92
3695 4045 6.065976 ACATCATTGGAACATGGAGAACTA 57.934 37.500 0.00 0.00 39.30 2.24
3712 4062 8.284945 AGTAAACAAGCACATCATAACATCAT 57.715 30.769 0.00 0.00 0.00 2.45
3761 4122 6.069963 ACAAATGTCAGGCCTCTAACTAGATT 60.070 38.462 0.00 0.00 0.00 2.40
3802 4163 9.589111 GTTCAATAACCAGACCAAAAGTAAAAA 57.411 29.630 0.00 0.00 0.00 1.94
3817 4178 5.071788 AGGAAGAGTGTCAGTTCAATAACCA 59.928 40.000 0.00 0.00 36.15 3.67
3911 4276 5.437060 AGCCTTTAGTCTCAAACAAGTTGA 58.563 37.500 10.54 0.00 44.20 3.18
3923 4288 5.185056 ACAACAACAACAAAGCCTTTAGTCT 59.815 36.000 0.00 0.00 0.00 3.24
3959 4396 4.281435 TGAGCCACACAAAAATGATGATGT 59.719 37.500 0.00 0.00 0.00 3.06
3999 4442 5.825151 TCTCACACATGAATTGTTTGTACCA 59.175 36.000 0.00 0.00 37.32 3.25
4018 4461 6.155827 GCTACTCCATCAATAGTGATCTCAC 58.844 44.000 1.94 2.01 42.88 3.51
4019 4462 5.835280 TGCTACTCCATCAATAGTGATCTCA 59.165 40.000 1.94 0.00 42.88 3.27
4020 4463 6.155827 GTGCTACTCCATCAATAGTGATCTC 58.844 44.000 1.94 0.00 42.88 2.75
4021 4464 5.011533 GGTGCTACTCCATCAATAGTGATCT 59.988 44.000 1.94 0.00 42.88 2.75
4022 4465 5.233988 GGTGCTACTCCATCAATAGTGATC 58.766 45.833 1.94 0.00 42.88 2.92
4023 4466 4.040952 GGGTGCTACTCCATCAATAGTGAT 59.959 45.833 0.00 0.00 45.80 3.06
4024 4467 3.388024 GGGTGCTACTCCATCAATAGTGA 59.612 47.826 0.00 0.00 38.41 3.41
4025 4468 3.389329 AGGGTGCTACTCCATCAATAGTG 59.611 47.826 0.00 0.00 0.00 2.74
4026 4469 3.389329 CAGGGTGCTACTCCATCAATAGT 59.611 47.826 0.00 0.00 0.00 2.12
4027 4470 3.805108 GCAGGGTGCTACTCCATCAATAG 60.805 52.174 0.00 0.00 40.96 1.73
4028 4471 2.104792 GCAGGGTGCTACTCCATCAATA 59.895 50.000 0.00 0.00 40.96 1.90
4029 4472 1.133976 GCAGGGTGCTACTCCATCAAT 60.134 52.381 0.00 0.00 40.96 2.57
4030 4473 0.253044 GCAGGGTGCTACTCCATCAA 59.747 55.000 0.00 0.00 40.96 2.57
4031 4474 0.909133 TGCAGGGTGCTACTCCATCA 60.909 55.000 0.00 0.00 45.31 3.07
4032 4475 0.462759 GTGCAGGGTGCTACTCCATC 60.463 60.000 0.00 0.00 45.31 3.51
4033 4476 1.200760 TGTGCAGGGTGCTACTCCAT 61.201 55.000 0.00 0.00 45.31 3.41
4042 4485 1.326213 TGGTTTGGTTGTGCAGGGTG 61.326 55.000 0.00 0.00 0.00 4.61
4048 4491 0.249826 CCCACATGGTTTGGTTGTGC 60.250 55.000 0.00 0.00 39.48 4.57
4078 4522 8.918202 AACTTGGAGAAAATGTGATTACAGTA 57.082 30.769 0.00 0.00 40.79 2.74
4079 4523 7.721399 AGAACTTGGAGAAAATGTGATTACAGT 59.279 33.333 0.00 0.00 40.79 3.55
4080 4524 8.103948 AGAACTTGGAGAAAATGTGATTACAG 57.896 34.615 0.00 0.00 40.79 2.74
4081 4525 8.463930 AAGAACTTGGAGAAAATGTGATTACA 57.536 30.769 0.00 0.00 41.89 2.41
4083 4527 8.690203 TGAAGAACTTGGAGAAAATGTGATTA 57.310 30.769 0.00 0.00 0.00 1.75
4084 4528 7.587037 TGAAGAACTTGGAGAAAATGTGATT 57.413 32.000 0.00 0.00 0.00 2.57
4173 4618 4.099573 ACCAGGTTTATCGTACTCATGAGG 59.900 45.833 26.08 9.26 0.00 3.86
4235 4680 3.951037 TGCTAGGCAAAACAAAAGAGTGA 59.049 39.130 0.00 0.00 34.76 3.41
4244 4689 4.005650 CAGATTCTCTGCTAGGCAAAACA 58.994 43.478 0.00 0.00 37.72 2.83
4263 4708 1.625315 AGGCTCACAACAGCATACAGA 59.375 47.619 0.00 0.00 41.65 3.41
4264 4709 1.736126 CAGGCTCACAACAGCATACAG 59.264 52.381 0.00 0.00 41.65 2.74
4299 4768 3.580022 ACATCACAGATTCACAGTCCTCA 59.420 43.478 0.00 0.00 0.00 3.86
4300 4769 4.081752 AGACATCACAGATTCACAGTCCTC 60.082 45.833 0.00 0.00 0.00 3.71
4311 4780 3.325293 AAGTGCGAAGACATCACAGAT 57.675 42.857 0.00 0.00 33.44 2.90
4312 4781 2.820059 AAGTGCGAAGACATCACAGA 57.180 45.000 0.00 0.00 33.44 3.41
4313 4782 4.990543 TTTAAGTGCGAAGACATCACAG 57.009 40.909 0.00 0.00 33.44 3.66
4314 4783 5.743026 TTTTTAAGTGCGAAGACATCACA 57.257 34.783 0.00 0.00 33.44 3.58
4342 4811 9.508642 AACAGAACCTAGAGAATTAGAAAAAGG 57.491 33.333 0.00 0.00 0.00 3.11
4424 4893 3.174375 CTGAGCTTAATTTTCTTGCCGC 58.826 45.455 0.00 0.00 0.00 6.53
4425 4894 3.174375 GCTGAGCTTAATTTTCTTGCCG 58.826 45.455 0.00 0.00 0.00 5.69
4451 4920 1.895238 GCACAGCCATGCCTCAATT 59.105 52.632 0.00 0.00 39.86 2.32
4473 4942 8.190888 AGTGAAGTTAATAAGATTCAGCTTCG 57.809 34.615 2.02 0.00 35.29 3.79
4519 4988 4.167652 TCTTTCTTGGACCCCGTAAAAA 57.832 40.909 0.00 0.00 0.00 1.94
4520 4989 3.860968 TCTTTCTTGGACCCCGTAAAA 57.139 42.857 0.00 0.00 0.00 1.52
4521 4990 4.286549 TGTATCTTTCTTGGACCCCGTAAA 59.713 41.667 0.00 0.00 0.00 2.01
4555 5024 3.195610 TCATGACAGTAACCTAGCTGTGG 59.804 47.826 5.58 0.42 44.89 4.17
4564 5033 3.627395 TGTCCCATCATGACAGTAACC 57.373 47.619 0.00 0.00 37.80 2.85
4565 5034 3.941483 CCTTGTCCCATCATGACAGTAAC 59.059 47.826 0.00 0.00 43.14 2.50
4569 5038 1.561076 TCCCTTGTCCCATCATGACAG 59.439 52.381 0.00 0.00 43.14 3.51


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

AutoCloner maintained by Alex Coulton.