Multiple sequence alignment - TraesCS6B01G319700

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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 TraesCS6B01G319700 chr6B 100.000 5272 0 0 1 5272 567412299 567407028 0.000000e+00 9736.0
1 TraesCS6B01G319700 chr6D 93.623 5269 209 54 1 5222 379562663 379567851 0.000000e+00 7751.0
2 TraesCS6B01G319700 chr6A 95.453 3475 109 24 1219 4657 521461897 521458436 0.000000e+00 5496.0
3 TraesCS6B01G319700 chr6A 88.448 1134 49 37 13 1113 521463226 521462142 0.000000e+00 1293.0
4 TraesCS6B01G319700 chr6A 90.291 618 33 3 4655 5272 521458321 521457731 0.000000e+00 784.0
5 TraesCS6B01G319700 chr7D 83.436 326 52 2 3948 4272 171306130 171306454 8.580000e-78 302.0
6 TraesCS6B01G319700 chr7B 83.129 326 53 2 3948 4272 137787822 137788146 3.990000e-76 296.0
7 TraesCS6B01G319700 chr7B 95.775 71 2 1 4293 4363 537019942 537019873 4.320000e-21 113.0
8 TraesCS6B01G319700 chrUn 80.606 165 23 6 1960 2124 58727688 58727533 9.270000e-23 119.0
9 TraesCS6B01G319700 chr7A 91.667 84 7 0 2053 2136 174196412 174196495 3.340000e-22 117.0
10 TraesCS6B01G319700 chr5B 95.588 68 2 1 4293 4360 429846986 429847052 2.010000e-19 108.0
11 TraesCS6B01G319700 chr4B 91.549 71 5 1 4293 4363 618860639 618860570 4.350000e-16 97.1
12 TraesCS6B01G319700 chr1B 86.765 68 8 1 4293 4360 30227695 30227761 2.040000e-09 75.0
13 TraesCS6B01G319700 chr1B 100.000 31 0 0 4394 4424 30227765 30227795 2.050000e-04 58.4


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 TraesCS6B01G319700 chr6B 567407028 567412299 5271 True 9736.000000 9736 100.000000 1 5272 1 chr6B.!!$R1 5271
1 TraesCS6B01G319700 chr6D 379562663 379567851 5188 False 7751.000000 7751 93.623000 1 5222 1 chr6D.!!$F1 5221
2 TraesCS6B01G319700 chr6A 521457731 521463226 5495 True 2524.333333 5496 91.397333 13 5272 3 chr6A.!!$R1 5259

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
483 498 0.108329 ACCACTCGATTAACAGCCCG 60.108 55.000 0.00 0.00 0.00 6.13 F
600 620 0.253207 TTTTCTCCCCTCCCTCTCCC 60.253 60.000 0.00 0.00 0.00 4.30 F
1419 1616 0.600255 CGCAGGAAAACCTCGTCACT 60.600 55.000 0.00 0.00 0.00 3.41 F
2188 2407 0.033228 ACTGCTCTGCTCACTGTCAC 59.967 55.000 0.00 0.00 0.00 3.67 F
2294 2516 1.128692 GCCGCAGTACTGTGTCATTTC 59.871 52.381 29.42 8.86 39.31 2.17 F
2778 3003 1.973515 TCATCGAGCTCATAATGGCCT 59.026 47.619 15.40 0.00 0.00 5.19 F
3672 3902 0.037326 ATCACCGTGACTCGCATGTT 60.037 50.000 2.57 0.00 38.35 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1965 0.101040 TGTTGTTGTTCTGCAGCAGC 59.899 50.000 18.43 5.26 39.43 5.25 R
2097 2303 2.577785 GCGACAGATTAGCCGACGC 61.578 63.158 0.00 0.00 38.03 5.19 R
2673 2898 0.321653 ACCAGAACAGCAATCCCGTC 60.322 55.000 0.00 0.00 0.00 4.79 R
3516 3746 0.390860 ATAGTAGGCCTCTTGCTGCG 59.609 55.000 9.68 0.00 40.92 5.18 R
3672 3902 0.472925 TTCCCCTCACAGCTGTGGTA 60.473 55.000 39.04 24.18 45.65 3.25 R
4058 4288 0.548926 TGGGGAGATACTGGGTGCAA 60.549 55.000 0.00 0.00 0.00 4.08 R
5180 5545 0.390472 CCTGCTCGTTCTGTCCTTCC 60.390 60.000 0.00 0.00 0.00 3.46 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
47 51 2.859165 TGTCACTGGGATTTCACTCC 57.141 50.000 0.00 0.00 34.31 3.85
79 89 7.671819 ACCTAATCTGATCCTCGATTGATTCTA 59.328 37.037 10.51 0.00 32.46 2.10
103 117 1.815613 CCGTAATGCATGGTGACCAAA 59.184 47.619 9.06 0.00 36.95 3.28
111 125 0.251165 ATGGTGACCAAAGGTTCCCG 60.251 55.000 9.06 0.00 36.95 5.14
120 134 2.553466 CCAAAGGTTCCCGTGTCCATTA 60.553 50.000 0.00 0.00 0.00 1.90
126 140 3.261951 CCGTGTCCATTAGCCGCG 61.262 66.667 0.00 0.00 0.00 6.46
128 142 3.573491 GTGTCCATTAGCCGCGCC 61.573 66.667 0.00 0.00 0.00 6.53
129 143 3.781307 TGTCCATTAGCCGCGCCT 61.781 61.111 0.00 0.00 0.00 5.52
130 144 2.967615 GTCCATTAGCCGCGCCTC 60.968 66.667 0.00 0.00 0.00 4.70
182 196 1.488393 CTTCCTCCCTGTCATCTTCCC 59.512 57.143 0.00 0.00 0.00 3.97
263 277 4.742201 CTGACACACGCCTCCCGG 62.742 72.222 0.00 0.00 42.52 5.73
281 295 4.840005 GCTACCTGTCCGGCTGCC 62.840 72.222 9.11 9.11 35.61 4.85
349 363 4.293648 CGCCGTGGTGGTCTGTGA 62.294 66.667 0.00 0.00 41.21 3.58
350 364 2.357517 GCCGTGGTGGTCTGTGAG 60.358 66.667 0.00 0.00 41.21 3.51
351 365 2.867855 GCCGTGGTGGTCTGTGAGA 61.868 63.158 0.00 0.00 41.21 3.27
483 498 0.108329 ACCACTCGATTAACAGCCCG 60.108 55.000 0.00 0.00 0.00 6.13
500 515 2.154462 CCCGCTCTCACTGTTTTTCAT 58.846 47.619 0.00 0.00 0.00 2.57
503 518 4.142816 CCCGCTCTCACTGTTTTTCATAAG 60.143 45.833 0.00 0.00 0.00 1.73
506 521 6.401153 CCGCTCTCACTGTTTTTCATAAGTAC 60.401 42.308 0.00 0.00 0.00 2.73
507 522 6.366332 CGCTCTCACTGTTTTTCATAAGTACT 59.634 38.462 0.00 0.00 0.00 2.73
508 523 7.541091 CGCTCTCACTGTTTTTCATAAGTACTA 59.459 37.037 0.00 0.00 0.00 1.82
509 524 8.865001 GCTCTCACTGTTTTTCATAAGTACTAG 58.135 37.037 0.00 0.00 0.00 2.57
510 525 8.758633 TCTCACTGTTTTTCATAAGTACTAGC 57.241 34.615 0.00 0.00 0.00 3.42
594 614 4.323569 AAGAAGAATTTTCTCCCCTCCC 57.676 45.455 0.00 0.00 36.28 4.30
595 615 3.546840 AGAAGAATTTTCTCCCCTCCCT 58.453 45.455 0.00 0.00 36.28 4.20
597 617 3.228589 AGAATTTTCTCCCCTCCCTCT 57.771 47.619 0.00 0.00 29.94 3.69
598 618 3.119319 AGAATTTTCTCCCCTCCCTCTC 58.881 50.000 0.00 0.00 29.94 3.20
599 619 1.900254 ATTTTCTCCCCTCCCTCTCC 58.100 55.000 0.00 0.00 0.00 3.71
600 620 0.253207 TTTTCTCCCCTCCCTCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
601 621 1.162951 TTTCTCCCCTCCCTCTCCCT 61.163 60.000 0.00 0.00 0.00 4.20
604 624 3.039526 CCCCTCCCTCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
657 677 3.955101 CCTACTCCGGCGAGCGAG 61.955 72.222 9.30 9.50 40.03 5.03
658 678 4.615834 CTACTCCGGCGAGCGAGC 62.616 72.222 9.30 0.00 40.03 5.03
704 728 4.512914 GCATGTCTGCCCCCTCCC 62.513 72.222 0.00 0.00 42.88 4.30
705 729 2.693864 CATGTCTGCCCCCTCCCT 60.694 66.667 0.00 0.00 0.00 4.20
1083 1132 3.706373 GCCAACGGCCTCCTCTCA 61.706 66.667 0.00 0.00 44.06 3.27
1101 1150 1.002315 TCACCCAAGGGCGTAAACTAC 59.998 52.381 4.70 0.00 39.32 2.73
1153 1202 5.780958 AGAGCCCTACTGGTTATTCTTTT 57.219 39.130 0.00 0.00 36.04 2.27
1155 1204 5.014228 AGAGCCCTACTGGTTATTCTTTTGT 59.986 40.000 0.00 0.00 36.04 2.83
1157 1206 4.765339 GCCCTACTGGTTATTCTTTTGTGT 59.235 41.667 0.00 0.00 36.04 3.72
1158 1207 5.106277 GCCCTACTGGTTATTCTTTTGTGTC 60.106 44.000 0.00 0.00 36.04 3.67
1171 1220 4.391830 TCTTTTGTGTCTCTGTGTGTGTTC 59.608 41.667 0.00 0.00 0.00 3.18
1216 1374 0.649993 CGCCACCTTGTTTTGTTTGC 59.350 50.000 0.00 0.00 0.00 3.68
1238 1428 4.800471 GCACTCTTCTTCCTTTGTTTGTTG 59.200 41.667 0.00 0.00 0.00 3.33
1242 1432 4.097892 TCTTCTTCCTTTGTTTGTTGCTCC 59.902 41.667 0.00 0.00 0.00 4.70
1401 1598 1.448540 GACCATGGTCACCTGCTCG 60.449 63.158 35.21 0.00 44.02 5.03
1419 1616 0.600255 CGCAGGAAAACCTCGTCACT 60.600 55.000 0.00 0.00 0.00 3.41
1445 1642 1.136336 GTAAGTTTTCTGTCGCGGCTG 60.136 52.381 13.81 12.70 0.00 4.85
1477 1674 4.665451 TCCATCACACACCAATCATTTCT 58.335 39.130 0.00 0.00 0.00 2.52
1486 1683 2.095059 ACCAATCATTTCTGTCGCAAGC 60.095 45.455 0.00 0.00 37.18 4.01
1534 1734 7.999679 TGTCATCTCTCTGTTTCAATTTGTTT 58.000 30.769 0.00 0.00 0.00 2.83
1537 1737 8.137437 TCATCTCTCTGTTTCAATTTGTTTTCC 58.863 33.333 0.00 0.00 0.00 3.13
1621 1821 6.102663 CCAATCTCGAGATAGTGTGAGTTTT 58.897 40.000 27.52 6.03 33.73 2.43
1646 1846 2.767394 TGCCATCATTAGCCTTGCAAAT 59.233 40.909 0.00 0.00 0.00 2.32
1656 1856 1.069049 GCCTTGCAAATCACCACTGTT 59.931 47.619 0.00 0.00 0.00 3.16
1660 1860 3.883830 TGCAAATCACCACTGTTTGTT 57.116 38.095 0.00 0.00 35.75 2.83
1670 1870 4.994217 CACCACTGTTTGTTTGTTCCTTTT 59.006 37.500 0.00 0.00 0.00 2.27
1671 1871 5.468409 CACCACTGTTTGTTTGTTCCTTTTT 59.532 36.000 0.00 0.00 0.00 1.94
1672 1872 5.699001 ACCACTGTTTGTTTGTTCCTTTTTC 59.301 36.000 0.00 0.00 0.00 2.29
1673 1873 5.931724 CCACTGTTTGTTTGTTCCTTTTTCT 59.068 36.000 0.00 0.00 0.00 2.52
1714 1914 3.161866 GGGAGTATGTTTCTTTTGGGCA 58.838 45.455 0.00 0.00 0.00 5.36
1753 1955 3.585289 ACCTTTTCTTCTCCCTCTTCTCC 59.415 47.826 0.00 0.00 0.00 3.71
1859 2061 1.622811 CTCTCCAGCAACCACTTCTCT 59.377 52.381 0.00 0.00 0.00 3.10
1949 2151 2.998279 GCCACTGCCAGCCATGAAC 61.998 63.158 0.00 0.00 0.00 3.18
1952 2154 1.028330 CACTGCCAGCCATGAACGAT 61.028 55.000 0.00 0.00 0.00 3.73
1962 2165 6.111382 CCAGCCATGAACGATTGATAGATAT 58.889 40.000 0.00 0.00 0.00 1.63
2149 2355 4.193826 TGTGAGTATCCTCTGCTTGTTC 57.806 45.455 0.00 0.00 38.61 3.18
2188 2407 0.033228 ACTGCTCTGCTCACTGTCAC 59.967 55.000 0.00 0.00 0.00 3.67
2234 2453 6.014669 GGATCTGTCCTACAATAATCTGAGCT 60.015 42.308 0.00 0.00 41.60 4.09
2294 2516 1.128692 GCCGCAGTACTGTGTCATTTC 59.871 52.381 29.42 8.86 39.31 2.17
2313 2535 7.805071 GTCATTTCATCTTTGACCAAAGTACTG 59.195 37.037 18.57 14.83 45.88 2.74
2486 2710 4.202111 GCCTGAATAACACACAAGGTTTGT 60.202 41.667 0.00 0.00 46.75 2.83
2673 2898 2.205022 TCAGCATCCTTTTCCCAGTG 57.795 50.000 0.00 0.00 0.00 3.66
2778 3003 1.973515 TCATCGAGCTCATAATGGCCT 59.026 47.619 15.40 0.00 0.00 5.19
2813 3039 5.304686 ACTTGGTGGAATCAGTTACTGAA 57.695 39.130 19.42 0.00 44.04 3.02
2957 3183 4.882842 AGGCGGTTTTGGAAATGTTTAT 57.117 36.364 0.00 0.00 0.00 1.40
3289 3518 9.401058 CAGATATAAGTTGGTCTTGAAGGATTT 57.599 33.333 0.00 0.00 37.56 2.17
3290 3519 9.981460 AGATATAAGTTGGTCTTGAAGGATTTT 57.019 29.630 0.00 0.00 37.56 1.82
3342 3571 3.372822 TGCTCGTTCGAAACTTCAACTTT 59.627 39.130 0.00 0.00 0.00 2.66
3438 3668 5.184479 ACAAAGAATCCCACATGACAAGATG 59.816 40.000 0.00 0.00 0.00 2.90
3439 3669 3.285484 AGAATCCCACATGACAAGATGC 58.715 45.455 0.00 0.00 0.00 3.91
3672 3902 0.037326 ATCACCGTGACTCGCATGTT 60.037 50.000 2.57 0.00 38.35 2.71
3708 3938 1.614317 GGAACTGTAGGCCACATTGCT 60.614 52.381 5.01 0.00 36.29 3.91
3866 4096 5.674525 TGACTGGGTAAGATCATTGTCATC 58.325 41.667 0.00 0.00 0.00 2.92
3867 4097 5.189539 TGACTGGGTAAGATCATTGTCATCA 59.810 40.000 0.00 0.00 0.00 3.07
3868 4098 6.126681 TGACTGGGTAAGATCATTGTCATCAT 60.127 38.462 0.00 0.00 0.00 2.45
4077 4307 0.548926 TTGCACCCAGTATCTCCCCA 60.549 55.000 0.00 0.00 0.00 4.96
4121 4351 0.614697 TGGTCAGGATGCTCGAAGGA 60.615 55.000 0.00 0.00 34.76 3.36
4196 4426 1.228154 GGTGCCCGACTTCACCTTT 60.228 57.895 4.31 0.00 46.90 3.11
4226 4456 0.322636 ACTCCGACCTGACAGACGAT 60.323 55.000 18.49 5.91 0.00 3.73
4229 4459 0.526211 CCGACCTGACAGACGATTCA 59.474 55.000 18.49 0.00 0.00 2.57
4259 4489 0.604780 TGCAAGCAGTTGAGCTCTCC 60.605 55.000 16.19 5.16 45.89 3.71
4265 4495 1.228894 AGTTGAGCTCTCCGGACCA 60.229 57.895 16.19 0.00 0.00 4.02
4274 4504 2.029470 GCTCTCCGGACCAAGATGATAG 60.029 54.545 0.00 0.00 0.00 2.08
4288 4518 3.314913 AGATGATAGCACGACAGAGAGTG 59.685 47.826 0.00 0.00 41.01 3.51
4294 4524 1.667467 GCACGACAGAGAGTGGAAGAC 60.667 57.143 0.00 0.00 38.68 3.01
4335 4565 1.673477 CAGCAGGACCTGTACAGCA 59.327 57.895 22.58 0.00 33.43 4.41
4521 4751 6.371548 TGGTACAATAAAGATGACAGAGCAAC 59.628 38.462 0.00 0.00 31.92 4.17
4694 5059 6.142958 GCAAATCTTTGTCAAGAAAGTAGTGC 59.857 38.462 4.71 4.72 42.53 4.40
4760 5125 5.597806 ACTTGATGGCAAATATCTGCATTG 58.402 37.500 2.94 0.00 44.52 2.82
4763 5128 6.020971 TGATGGCAAATATCTGCATTGATC 57.979 37.500 2.94 0.00 44.52 2.92
4817 5182 3.484065 GCAGCAAACAAAAGAACAAGCAC 60.484 43.478 0.00 0.00 0.00 4.40
4829 5194 0.098025 ACAAGCACGAAACAACCACG 59.902 50.000 0.00 0.00 0.00 4.94
4890 5255 1.198408 AGCATTGTCAGTGATGTTGCG 59.802 47.619 14.55 0.00 33.99 4.85
4896 5261 1.798223 GTCAGTGATGTTGCGCTGTTA 59.202 47.619 9.73 0.00 44.55 2.41
4905 5270 2.044135 GTTGCGCTGTTAACTTCTTGC 58.956 47.619 9.73 4.79 0.00 4.01
4909 5274 2.351738 GCGCTGTTAACTTCTTGCCAAT 60.352 45.455 7.22 0.00 0.00 3.16
4915 5280 4.761739 TGTTAACTTCTTGCCAATCTCCAG 59.238 41.667 7.22 0.00 0.00 3.86
5026 5391 6.942532 TCATATAGCTGGAATTTTGTGGAC 57.057 37.500 0.00 0.00 0.00 4.02
5151 5516 1.203523 CTAGAGAAGAGCAGCACGGTT 59.796 52.381 0.00 0.00 0.00 4.44
5167 5532 2.038557 ACGGTTACTTTCAGACAGGCAT 59.961 45.455 0.00 0.00 0.00 4.40
5219 5584 2.203728 ACACGCTCCACCCTGGTA 60.204 61.111 0.00 0.00 39.03 3.25
5220 5585 2.264794 CACGCTCCACCCTGGTAC 59.735 66.667 0.00 0.00 39.03 3.34
5223 5588 1.125711 ACGCTCCACCCTGGTACTTT 61.126 55.000 0.00 0.00 39.03 2.66
5231 5596 0.624254 CCCTGGTACTTTCCCCCTTC 59.376 60.000 0.00 0.00 0.00 3.46
5232 5597 0.624254 CCTGGTACTTTCCCCCTTCC 59.376 60.000 0.00 0.00 0.00 3.46
5247 5612 2.110011 CCCTTCCTTTTTCTCCCTTCCA 59.890 50.000 0.00 0.00 0.00 3.53
5260 5625 2.576191 TCCCTTCCATTTCCAATCGACT 59.424 45.455 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.502211 ACAAGGAAGATAAACACAAGGCG 59.498 43.478 0.00 0.00 0.00 5.52
11 12 6.293626 CCAGTGACAAGGAAGATAAACACAAG 60.294 42.308 0.00 0.00 0.00 3.16
47 51 6.406692 TCGAGGATCAGATTAGGTAAAAGG 57.593 41.667 0.00 0.00 33.17 3.11
79 89 2.288666 GTCACCATGCATTACGGATGT 58.711 47.619 8.47 0.00 41.66 3.06
111 125 3.573491 GGCGCGGCTAATGGACAC 61.573 66.667 27.05 0.00 0.00 3.67
128 142 2.045536 GGCCTGCCTGAAGTGGAG 60.046 66.667 0.00 0.00 0.00 3.86
129 143 4.020617 CGGCCTGCCTGAAGTGGA 62.021 66.667 6.60 0.00 0.00 4.02
157 171 4.475135 GACAGGGAGGAAGCGCCC 62.475 72.222 2.29 0.00 45.04 6.13
263 277 4.840005 GCAGCCGGACAGGTAGCC 62.840 72.222 5.05 0.00 43.70 3.93
287 301 0.978907 AGCAAAAGAATTGCCCAGGG 59.021 50.000 0.00 0.00 45.98 4.45
288 302 1.942586 GCAGCAAAAGAATTGCCCAGG 60.943 52.381 9.37 0.00 45.98 4.45
289 303 1.270412 TGCAGCAAAAGAATTGCCCAG 60.270 47.619 9.37 2.30 45.98 4.45
290 304 0.757512 TGCAGCAAAAGAATTGCCCA 59.242 45.000 9.37 5.07 45.98 5.36
291 305 1.802365 CTTGCAGCAAAAGAATTGCCC 59.198 47.619 9.65 2.68 45.98 5.36
292 306 2.758009 TCTTGCAGCAAAAGAATTGCC 58.242 42.857 9.65 0.00 45.98 4.52
337 351 0.752658 CACAGTCTCACAGACCACCA 59.247 55.000 0.00 0.00 46.18 4.17
338 352 1.040646 TCACAGTCTCACAGACCACC 58.959 55.000 0.00 0.00 46.18 4.61
339 353 1.409064 TGTCACAGTCTCACAGACCAC 59.591 52.381 0.00 0.00 46.18 4.16
340 354 1.683385 CTGTCACAGTCTCACAGACCA 59.317 52.381 0.00 0.00 46.18 4.02
341 355 1.683917 ACTGTCACAGTCTCACAGACC 59.316 52.381 3.98 0.00 46.18 3.85
464 478 0.108329 CGGGCTGTTAATCGAGTGGT 60.108 55.000 0.00 0.00 0.00 4.16
483 498 7.659652 AGTACTTATGAAAAACAGTGAGAGC 57.340 36.000 0.00 0.00 0.00 4.09
507 522 4.285003 TGAAAACCCAAGCTAGTACTGCTA 59.715 41.667 16.73 0.00 40.22 3.49
508 523 3.072476 TGAAAACCCAAGCTAGTACTGCT 59.928 43.478 5.39 9.69 43.32 4.24
509 524 3.188667 GTGAAAACCCAAGCTAGTACTGC 59.811 47.826 5.39 7.40 0.00 4.40
510 525 4.213482 GTGTGAAAACCCAAGCTAGTACTG 59.787 45.833 5.39 0.00 0.00 2.74
594 614 0.972983 TCGGAGCAAAGGAGGGAGAG 60.973 60.000 0.00 0.00 0.00 3.20
595 615 0.325671 ATCGGAGCAAAGGAGGGAGA 60.326 55.000 0.00 0.00 0.00 3.71
597 617 2.103153 ATATCGGAGCAAAGGAGGGA 57.897 50.000 0.00 0.00 0.00 4.20
598 618 2.104792 TCAATATCGGAGCAAAGGAGGG 59.895 50.000 0.00 0.00 0.00 4.30
599 619 3.397482 CTCAATATCGGAGCAAAGGAGG 58.603 50.000 0.00 0.00 0.00 4.30
600 620 3.181461 ACCTCAATATCGGAGCAAAGGAG 60.181 47.826 0.00 0.00 0.00 3.69
601 621 2.771943 ACCTCAATATCGGAGCAAAGGA 59.228 45.455 0.00 0.00 0.00 3.36
604 624 2.158813 GGGACCTCAATATCGGAGCAAA 60.159 50.000 0.00 0.00 0.00 3.68
703 727 0.991920 TACAAAAGCAGGGGAGGAGG 59.008 55.000 0.00 0.00 0.00 4.30
704 728 1.340114 GGTACAAAAGCAGGGGAGGAG 60.340 57.143 0.00 0.00 0.00 3.69
705 729 0.696501 GGTACAAAAGCAGGGGAGGA 59.303 55.000 0.00 0.00 0.00 3.71
966 1008 3.898123 GGCTCTCTCTCTCTCTCTCTCTA 59.102 52.174 0.00 0.00 0.00 2.43
1023 1069 1.457455 GAGGAGGAGGAGCAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
1083 1132 0.037046 CGTAGTTTACGCCCTTGGGT 60.037 55.000 7.61 0.00 45.81 4.51
1113 1162 6.894103 AGGGCTCTTGATTTGAGAACATTAAT 59.106 34.615 0.00 0.00 33.68 1.40
1153 1202 2.760650 AGAGAACACACACAGAGACACA 59.239 45.455 0.00 0.00 0.00 3.72
1155 1204 4.183865 CAAAGAGAACACACACAGAGACA 58.816 43.478 0.00 0.00 0.00 3.41
1157 1206 3.197766 ACCAAAGAGAACACACACAGAGA 59.802 43.478 0.00 0.00 0.00 3.10
1158 1207 3.535561 ACCAAAGAGAACACACACAGAG 58.464 45.455 0.00 0.00 0.00 3.35
1171 1220 3.253188 TCCGATGCAAGAAAACCAAAGAG 59.747 43.478 0.00 0.00 0.00 2.85
1216 1374 4.800471 GCAACAAACAAAGGAAGAAGAGTG 59.200 41.667 0.00 0.00 0.00 3.51
1238 1428 4.996434 ACACACCAGCGCAGGAGC 62.996 66.667 27.14 0.00 37.42 4.70
1242 1432 2.588596 TGTCACACACCAGCGCAG 60.589 61.111 11.47 0.00 0.00 5.18
1419 1616 2.489971 CGACAGAAAACTTACAGGCCA 58.510 47.619 5.01 0.00 0.00 5.36
1445 1642 1.064758 TGTGTGATGGAACCATAGCCC 60.065 52.381 6.31 0.00 36.70 5.19
1477 1674 2.020720 TCAAAAGGAAAGCTTGCGACA 58.979 42.857 0.00 0.00 0.00 4.35
1486 1683 6.267699 ACAAAGGGTTAGGATCAAAAGGAAAG 59.732 38.462 0.00 0.00 0.00 2.62
1621 1821 2.658285 CAAGGCTAATGATGGCAGGAA 58.342 47.619 0.00 0.00 34.13 3.36
1646 1846 3.426615 AGGAACAAACAAACAGTGGTGA 58.573 40.909 3.31 0.00 0.00 4.02
1670 1870 8.754080 TCCCATGTGTTCTAAAAAGAAAAAGAA 58.246 29.630 0.00 0.00 0.00 2.52
1671 1871 8.299990 TCCCATGTGTTCTAAAAAGAAAAAGA 57.700 30.769 0.00 0.00 0.00 2.52
1672 1872 8.197439 ACTCCCATGTGTTCTAAAAAGAAAAAG 58.803 33.333 0.00 0.00 0.00 2.27
1673 1873 8.073467 ACTCCCATGTGTTCTAAAAAGAAAAA 57.927 30.769 0.00 0.00 0.00 1.94
1683 1883 6.620877 AGAAACATACTCCCATGTGTTCTA 57.379 37.500 0.00 0.00 39.10 2.10
1753 1955 1.853114 CTGCAGCAGCCTGTGAACAG 61.853 60.000 10.14 3.35 41.26 3.16
1763 1965 0.101040 TGTTGTTGTTCTGCAGCAGC 59.899 50.000 18.43 5.26 39.43 5.25
1949 2151 8.930760 GGAAACCTTCAGAATATCTATCAATCG 58.069 37.037 0.00 0.00 0.00 3.34
2097 2303 2.577785 GCGACAGATTAGCCGACGC 61.578 63.158 0.00 0.00 38.03 5.19
2149 2355 4.065088 AGTACACAACCACATAACAGCAG 58.935 43.478 0.00 0.00 0.00 4.24
2188 2407 3.285484 CCTGAGAATTGGGAAGTCCATG 58.715 50.000 0.00 0.00 46.52 3.66
2294 2516 6.964131 TGGAGACAGTACTTTGGTCAAAGATG 60.964 42.308 24.80 20.51 42.18 2.90
2486 2710 3.356290 TGGATGAGATCGACTGACTGAA 58.644 45.455 0.00 0.00 0.00 3.02
2669 2894 0.798776 GAACAGCAATCCCGTCACTG 59.201 55.000 0.00 0.00 0.00 3.66
2673 2898 0.321653 ACCAGAACAGCAATCCCGTC 60.322 55.000 0.00 0.00 0.00 4.79
2761 2986 1.413118 TCAGGCCATTATGAGCTCGA 58.587 50.000 5.01 0.00 0.00 4.04
2778 3003 4.211125 TCCACCAAGTTAAACAAGCATCA 58.789 39.130 0.00 0.00 0.00 3.07
2813 3039 3.243267 GGTCTGCAAAATAACCAACACGT 60.243 43.478 0.00 0.00 0.00 4.49
2903 3129 2.175878 TCTTGCTGCTGAAGTTCTCC 57.824 50.000 4.17 0.00 0.00 3.71
3128 3354 8.448068 TTCCATTGGACATGTATGGATAGATA 57.552 34.615 23.37 10.27 45.26 1.98
3357 3586 7.376435 TGTGAGAATCGAATGCAAATCTTTA 57.624 32.000 0.00 0.00 38.61 1.85
3516 3746 0.390860 ATAGTAGGCCTCTTGCTGCG 59.609 55.000 9.68 0.00 40.92 5.18
3672 3902 0.472925 TTCCCCTCACAGCTGTGGTA 60.473 55.000 39.04 24.18 45.65 3.25
3866 4096 3.811497 CCACACTGTGCCATATGAGTATG 59.189 47.826 7.90 0.00 37.93 2.39
3867 4097 3.455910 ACCACACTGTGCCATATGAGTAT 59.544 43.478 7.90 0.00 31.34 2.12
3868 4098 2.837591 ACCACACTGTGCCATATGAGTA 59.162 45.455 7.90 0.00 31.34 2.59
4058 4288 0.548926 TGGGGAGATACTGGGTGCAA 60.549 55.000 0.00 0.00 0.00 4.08
4077 4307 1.478510 CGACATCTTAGGCCTGTGACT 59.521 52.381 17.99 2.14 0.00 3.41
4196 4426 2.992689 TCGGAGTAGCAACGCCCA 60.993 61.111 0.00 0.00 42.21 5.36
4259 4489 1.067060 TCGTGCTATCATCTTGGTCCG 59.933 52.381 0.00 0.00 0.00 4.79
4265 4495 3.951037 ACTCTCTGTCGTGCTATCATCTT 59.049 43.478 0.00 0.00 0.00 2.40
4274 4504 0.598562 TCTTCCACTCTCTGTCGTGC 59.401 55.000 0.00 0.00 0.00 5.34
4288 4518 4.583871 ACTGATGATGTTTCCTGTCTTCC 58.416 43.478 0.00 0.00 0.00 3.46
4335 4565 5.649831 TGTTTGCCATTTTAAGCAGGTTTTT 59.350 32.000 0.00 0.00 40.73 1.94
4381 4611 3.188048 CACTTCCTGACAGAAAGCATCAC 59.812 47.826 3.32 0.00 0.00 3.06
4388 4618 1.768275 TGCTCCACTTCCTGACAGAAA 59.232 47.619 3.32 0.00 0.00 2.52
4494 4724 6.595326 TGCTCTGTCATCTTTATTGTACCAAG 59.405 38.462 0.00 0.00 0.00 3.61
4540 4770 1.773541 AAGGGGGAAAGAGGACCAAT 58.226 50.000 0.00 0.00 0.00 3.16
4549 4779 6.238621 GCAACAATTTTACAAAAGGGGGAAAG 60.239 38.462 0.00 0.00 0.00 2.62
4617 4865 4.819630 AGACTAGAGTTTGGAGCTCTATCG 59.180 45.833 14.64 0.00 42.54 2.92
4716 5081 7.121611 TCAAGTTATGATGTCAGTTGCATTGAT 59.878 33.333 4.91 0.00 31.50 2.57
4750 5115 9.140874 TCTTTTCTAGAGAGATCAATGCAGATA 57.859 33.333 0.00 0.00 0.00 1.98
4760 5125 7.715657 TGCAGATCTTCTTTTCTAGAGAGATC 58.284 38.462 16.31 16.31 41.59 2.75
4763 5128 7.490840 TGATGCAGATCTTCTTTTCTAGAGAG 58.509 38.462 0.00 0.00 33.51 3.20
4817 5182 1.127701 CATTTGCCGTGGTTGTTTCG 58.872 50.000 0.00 0.00 0.00 3.46
4829 5194 1.772836 AGAGCCTCATTCCATTTGCC 58.227 50.000 0.00 0.00 0.00 4.52
4890 5255 4.379918 GGAGATTGGCAAGAAGTTAACAGC 60.380 45.833 8.61 3.69 0.00 4.40
4896 5261 3.328931 TCTCTGGAGATTGGCAAGAAGTT 59.671 43.478 5.96 0.00 31.41 2.66
4909 5274 2.045524 GCTGGGATGAATCTCTGGAGA 58.954 52.381 2.63 2.63 42.37 3.71
4915 5280 2.883386 GTCCAATGCTGGGATGAATCTC 59.117 50.000 0.00 0.00 43.71 2.75
4919 5284 0.703488 TGGTCCAATGCTGGGATGAA 59.297 50.000 0.00 0.00 43.71 2.57
4923 5288 3.565307 GAAATATGGTCCAATGCTGGGA 58.435 45.455 0.00 0.00 43.71 4.37
5026 5391 3.697045 TCTGGTAACACAAACCAAACCTG 59.303 43.478 0.00 0.00 46.14 4.00
5067 5432 8.177119 ACACATCAAATAAAAACTGGAAGCTA 57.823 30.769 0.00 0.00 37.60 3.32
5151 5516 5.237815 CACTACAATGCCTGTCTGAAAGTA 58.762 41.667 0.00 0.00 39.64 2.24
5167 5532 1.180456 TCCTTCCGACGGCACTACAA 61.180 55.000 9.66 0.00 0.00 2.41
5176 5541 0.454620 CTCGTTCTGTCCTTCCGACG 60.455 60.000 0.00 0.00 45.23 5.12
5180 5545 0.390472 CCTGCTCGTTCTGTCCTTCC 60.390 60.000 0.00 0.00 0.00 3.46
5219 5584 3.438078 GGAGAAAAAGGAAGGGGGAAAGT 60.438 47.826 0.00 0.00 0.00 2.66
5220 5585 3.165875 GGAGAAAAAGGAAGGGGGAAAG 58.834 50.000 0.00 0.00 0.00 2.62
5223 5588 1.081481 GGGAGAAAAAGGAAGGGGGA 58.919 55.000 0.00 0.00 0.00 4.81
5231 5596 4.159557 TGGAAATGGAAGGGAGAAAAAGG 58.840 43.478 0.00 0.00 0.00 3.11
5232 5597 5.806654 TTGGAAATGGAAGGGAGAAAAAG 57.193 39.130 0.00 0.00 0.00 2.27
5247 5612 2.787473 TGCCTCAGTCGATTGGAAAT 57.213 45.000 8.17 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.