Multiple sequence alignment - TraesCS1D01G045800

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 TraesCS1D01G045800 chr1D 100.000 3337 0 0 1 3337 25138026 25141362 0.000000e+00 6163.0
1 TraesCS1D01G045800 chr1D 73.178 1070 234 45 1462 2504 72459589 72458546 1.480000e-88 337.0
2 TraesCS1D01G045800 chr1D 77.342 587 116 15 2017 2597 72434542 72433967 6.900000e-87 331.0
3 TraesCS1D01G045800 chr1D 72.923 1071 236 46 1462 2504 72443182 72442138 4.150000e-84 322.0
4 TraesCS1D01G045800 chr1B 89.141 3389 262 48 1 3337 40406196 40409530 0.000000e+00 4122.0
5 TraesCS1D01G045800 chr1B 89.610 2358 160 39 662 2971 40420046 40422366 0.000000e+00 2918.0
6 TraesCS1D01G045800 chr1B 88.383 2195 174 41 1184 3337 40414092 40416246 0.000000e+00 2566.0
7 TraesCS1D01G045800 chr1B 92.110 545 31 5 662 1199 40413323 40413862 0.000000e+00 758.0
8 TraesCS1D01G045800 chr1B 87.894 603 62 6 1 599 40412730 40413325 0.000000e+00 699.0
9 TraesCS1D01G045800 chr1B 87.789 606 61 9 1 599 40419449 40420048 0.000000e+00 697.0
10 TraesCS1D01G045800 chr1B 91.667 108 9 0 3230 3337 40430623 40430730 2.070000e-32 150.0
11 TraesCS1D01G045800 chr1B 86.364 66 4 4 2829 2894 113024514 113024454 2.150000e-07 67.6
12 TraesCS1D01G045800 chr1A 90.726 2782 165 42 589 3310 25806408 25809156 0.000000e+00 3622.0
13 TraesCS1D01G045800 chr1A 77.439 1773 320 53 892 2599 44365658 44363901 0.000000e+00 985.0
14 TraesCS1D01G045800 chr1A 93.103 174 12 0 1 174 25806234 25806407 4.270000e-64 255.0
15 TraesCS1D01G045800 chr1A 97.727 44 1 0 3294 3337 25809170 25809213 3.570000e-10 76.8
16 TraesCS1D01G045800 chr2D 88.205 390 35 9 202 586 637586323 637586706 3.920000e-124 455.0
17 TraesCS1D01G045800 chr7D 87.436 390 41 5 202 586 12158951 12159337 3.060000e-120 442.0
18 TraesCS1D01G045800 chr7D 87.404 389 40 4 202 589 607213999 607214379 3.950000e-119 438.0
19 TraesCS1D01G045800 chr5D 87.277 393 40 5 202 591 507857039 507857424 1.100000e-119 440.0
20 TraesCS1D01G045800 chr5D 87.179 390 41 7 202 589 508274508 508274126 5.110000e-118 435.0
21 TraesCS1D01G045800 chr5D 79.412 102 16 3 1130 1228 44489016 44489115 2.150000e-07 67.6
22 TraesCS1D01G045800 chr6B 86.990 392 42 5 200 586 173576581 173576968 1.840000e-117 433.0
23 TraesCS1D01G045800 chr5A 78.968 504 78 22 2034 2529 451221607 451221124 5.370000e-83 318.0
24 TraesCS1D01G045800 chr6A 78.519 135 27 2 1091 1224 61814963 61814830 1.650000e-13 87.9
25 TraesCS1D01G045800 chr5B 79.412 102 16 3 1130 1228 43884340 43884439 2.150000e-07 67.6
26 TraesCS1D01G045800 chr5B 79.412 102 16 3 1130 1228 44231417 44231318 2.150000e-07 67.6
27 TraesCS1D01G045800 chr4B 100.000 30 0 0 2647 2676 642083063 642083092 4.650000e-04 56.5


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 TraesCS1D01G045800 chr1D 25138026 25141362 3336 False 6163.000000 6163 100.0000 1 3337 1 chr1D.!!$F1 3336
1 TraesCS1D01G045800 chr1D 72458546 72459589 1043 True 337.000000 337 73.1780 1462 2504 1 chr1D.!!$R3 1042
2 TraesCS1D01G045800 chr1D 72433967 72434542 575 True 331.000000 331 77.3420 2017 2597 1 chr1D.!!$R1 580
3 TraesCS1D01G045800 chr1D 72442138 72443182 1044 True 322.000000 322 72.9230 1462 2504 1 chr1D.!!$R2 1042
4 TraesCS1D01G045800 chr1B 40406196 40422366 16170 False 1960.000000 4122 89.1545 1 3337 6 chr1B.!!$F2 3336
5 TraesCS1D01G045800 chr1A 25806234 25809213 2979 False 1317.933333 3622 93.8520 1 3337 3 chr1A.!!$F1 3336
6 TraesCS1D01G045800 chr1A 44363901 44365658 1757 True 985.000000 985 77.4390 892 2599 1 chr1A.!!$R1 1707

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
212 213 0.037160 TTCATTCAGGCTCAGCTGCA 59.963 50.0 9.47 0.00 34.04 4.41 F
1749 1803 0.032515 TCATCGCTACTCCCTTGGGA 60.033 55.0 8.28 8.28 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2080 1.251251 GAATGGCTCAAGCTTGGTGT 58.749 50.0 25.73 6.19 41.7 4.16 R
2983 9826 0.716108 CATGTTCTTCGTGCGTCCTC 59.284 55.0 0.00 0.00 0.0 3.71 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
27 28 1.660333 CGGCACTCGACAAAGCTTTTC 60.660 52.381 9.53 9.73 42.43 2.29
40 41 7.485913 CGACAAAGCTTTTCATATATGTTTGCT 59.514 33.333 9.53 16.00 0.00 3.91
108 109 1.629043 TCTAGCCAAGTCGGTGTCTT 58.371 50.000 0.00 0.00 36.97 3.01
160 161 4.270808 CGCTTGGCAAAATTGGATATTTCC 59.729 41.667 0.00 0.00 42.94 3.13
185 186 1.033574 GAGTAGGATCCTGGGACACG 58.966 60.000 25.28 0.00 0.00 4.49
190 191 1.224592 GATCCTGGGACACGGCATT 59.775 57.895 0.00 0.00 0.00 3.56
191 192 0.815615 GATCCTGGGACACGGCATTC 60.816 60.000 0.00 0.00 0.00 2.67
194 195 1.002134 CTGGGACACGGCATTCCTT 60.002 57.895 0.00 0.00 31.90 3.36
196 197 1.002624 GGGACACGGCATTCCTTCA 60.003 57.895 0.00 0.00 31.90 3.02
197 198 0.394352 GGGACACGGCATTCCTTCAT 60.394 55.000 0.00 0.00 31.90 2.57
198 199 1.463674 GGACACGGCATTCCTTCATT 58.536 50.000 0.00 0.00 0.00 2.57
200 201 2.083774 GACACGGCATTCCTTCATTCA 58.916 47.619 0.00 0.00 0.00 2.57
212 213 0.037160 TTCATTCAGGCTCAGCTGCA 59.963 50.000 9.47 0.00 34.04 4.41
215 216 2.833604 ATTCAGGCTCAGCTGCACCC 62.834 60.000 18.16 13.37 34.04 4.61
297 299 7.665561 TGCGTGCTAGATAATTTTATGCATA 57.334 32.000 1.16 1.16 0.00 3.14
346 348 0.322975 ACAATTGAGCAGCTCTCGGT 59.677 50.000 23.15 12.77 44.86 4.69
347 349 1.550524 ACAATTGAGCAGCTCTCGGTA 59.449 47.619 23.15 0.00 44.86 4.02
348 350 2.028112 ACAATTGAGCAGCTCTCGGTAA 60.028 45.455 23.15 9.16 44.86 2.85
349 351 3.002791 CAATTGAGCAGCTCTCGGTAAA 58.997 45.455 23.15 8.43 44.86 2.01
350 352 2.831685 TTGAGCAGCTCTCGGTAAAA 57.168 45.000 23.15 4.52 44.86 1.52
351 353 2.831685 TGAGCAGCTCTCGGTAAAAA 57.168 45.000 23.15 0.00 44.86 1.94
371 373 4.360951 AAAGACAAAATCGGGGTCTGTA 57.639 40.909 0.00 0.00 40.80 2.74
395 397 3.944422 AAGTTTACTGTTCACGCACTG 57.056 42.857 0.00 0.00 0.00 3.66
398 400 3.308866 AGTTTACTGTTCACGCACTGTTC 59.691 43.478 0.00 0.00 31.81 3.18
400 402 1.290203 ACTGTTCACGCACTGTTCTG 58.710 50.000 0.00 0.00 0.00 3.02
463 465 5.691305 TCAAATGAGTTGAAATTTGAAGCGG 59.309 36.000 8.04 0.00 45.24 5.52
464 466 5.452078 AATGAGTTGAAATTTGAAGCGGA 57.548 34.783 0.00 0.00 0.00 5.54
484 486 5.529791 CGGACCTCACGTATCAAATTATCT 58.470 41.667 0.00 0.00 0.00 1.98
490 492 6.362551 CCTCACGTATCAAATTATCTACCACG 59.637 42.308 0.00 0.00 0.00 4.94
491 493 5.688621 TCACGTATCAAATTATCTACCACGC 59.311 40.000 0.00 0.00 0.00 5.34
495 497 7.064847 ACGTATCAAATTATCTACCACGCAAAA 59.935 33.333 0.00 0.00 0.00 2.44
500 502 7.806014 TCAAATTATCTACCACGCAAAAGTTTC 59.194 33.333 0.00 0.00 0.00 2.78
502 504 8.556213 AATTATCTACCACGCAAAAGTTTCTA 57.444 30.769 0.00 0.00 0.00 2.10
547 551 9.949174 ATTATTTGTTTTGATTTGTTTTCTGGC 57.051 25.926 0.00 0.00 0.00 4.85
548 552 5.809719 TTGTTTTGATTTGTTTTCTGGCC 57.190 34.783 0.00 0.00 0.00 5.36
549 553 3.868077 TGTTTTGATTTGTTTTCTGGCCG 59.132 39.130 0.00 0.00 0.00 6.13
567 571 3.160047 CCGGGAGCAGATGAGCCT 61.160 66.667 0.00 0.00 34.23 4.58
568 572 2.108566 CGGGAGCAGATGAGCCTG 59.891 66.667 0.00 0.00 37.23 4.85
569 573 2.509916 GGGAGCAGATGAGCCTGG 59.490 66.667 0.00 0.00 34.82 4.45
650 654 1.341852 ACGTGTAGCACATGTGTACCA 59.658 47.619 26.01 16.49 45.78 3.25
763 782 3.830744 TCCGTAAATCCATGATCCGTT 57.169 42.857 0.00 0.00 0.00 4.44
773 792 3.193479 TCCATGATCCGTTCTATGATCGG 59.807 47.826 9.91 9.91 43.68 4.18
798 824 1.794714 ACTAGGATTCGGCCACAGAT 58.205 50.000 2.24 0.00 0.00 2.90
803 829 1.217882 GATTCGGCCACAGATTACGG 58.782 55.000 2.24 0.00 0.00 4.02
823 849 1.135199 GTTCGGAGGCGTACATCTCAA 60.135 52.381 12.61 0.10 0.00 3.02
969 1010 1.130561 GTGCCTGCGACCAATAAGAAC 59.869 52.381 0.00 0.00 0.00 3.01
999 1040 1.228154 AGTTCCCACGGCCAAGAAC 60.228 57.895 2.24 9.71 39.09 3.01
1120 1167 0.467384 CAGCCTTCCCGATGACATCT 59.533 55.000 13.45 0.00 0.00 2.90
1230 1277 2.351322 CTCGATCTCGACGCCACG 60.351 66.667 0.00 0.00 44.22 4.94
1236 1283 2.613739 ATCTCGACGCCACGGACATG 62.614 60.000 0.00 0.00 0.00 3.21
1255 1302 6.095440 GGACATGTGCTCCAACAAATATAAGT 59.905 38.462 10.51 0.00 32.81 2.24
1282 1329 2.122167 GTCGTCTCCGGCATCCTCT 61.122 63.158 0.00 0.00 38.92 3.69
1296 1343 1.127567 TCCTCTGTGACCACCTTGGG 61.128 60.000 0.00 0.00 43.37 4.12
1369 1416 6.398655 AAGGGTATATCATGGATGATGCTT 57.601 37.500 11.66 1.03 46.34 3.91
1386 1433 1.003839 TTGGATCGAGCGCTGGTTT 60.004 52.632 18.48 5.91 0.00 3.27
1388 1435 2.517450 GGATCGAGCGCTGGTTTCG 61.517 63.158 18.48 12.96 35.76 3.46
1446 1493 1.583495 GCTTCCGGCTGTTGGGTAAC 61.583 60.000 0.00 0.00 38.06 2.50
1509 1560 2.571757 CGCTTGGCACCGACTCTA 59.428 61.111 0.82 0.00 0.00 2.43
1520 1571 0.389948 CCGACTCTAGTTGTGGCCAC 60.390 60.000 29.67 29.67 0.00 5.01
1522 1573 1.066858 CGACTCTAGTTGTGGCCACAT 60.067 52.381 37.97 26.57 41.52 3.21
1564 1618 1.808945 GTGAGATTGCACCTTGTCTGG 59.191 52.381 0.00 0.00 32.68 3.86
1584 1638 1.289244 ATTTTCCCCTCCTCCGGCAT 61.289 55.000 0.00 0.00 0.00 4.40
1621 1675 4.516195 GCGTCTCGGAGGAAGCCC 62.516 72.222 4.96 0.00 35.33 5.19
1684 1738 3.885724 TTCTGCAGGATATTCGTGACA 57.114 42.857 15.13 0.00 34.44 3.58
1742 1796 2.362397 TCATCTGGTTCATCGCTACTCC 59.638 50.000 0.00 0.00 0.00 3.85
1749 1803 0.032515 TCATCGCTACTCCCTTGGGA 60.033 55.000 8.28 8.28 0.00 4.37
1804 1858 4.871513 CCTTGAAAGGCTACTTTTTCCAC 58.128 43.478 0.00 0.00 46.51 4.02
1821 1875 1.471676 CCACGCTTAGATGGTGAGACC 60.472 57.143 0.00 0.00 39.22 3.85
1836 1890 5.362717 TGGTGAGACCATTCGAGTACATAAT 59.637 40.000 0.00 0.00 44.79 1.28
1875 1929 3.503099 GGGCCTTTGTCACCCCTA 58.497 61.111 0.84 0.00 37.70 3.53
1876 1930 1.001269 GGGCCTTTGTCACCCCTAC 60.001 63.158 0.84 0.00 37.70 3.18
1904 1958 6.015856 TCCAAAATCGAGATTGCAAACCTAAA 60.016 34.615 1.71 0.00 0.00 1.85
1947 2012 6.599244 CACCCTTATTGTCTCTTGCATTAAGA 59.401 38.462 0.00 0.00 43.01 2.10
1964 2040 8.476447 TGCATTAAGAAAATCCTGCATAATTGA 58.524 29.630 0.00 0.00 34.92 2.57
1975 2051 8.929260 ATCCTGCATAATTGATTCTAATGTCA 57.071 30.769 0.00 0.00 0.00 3.58
2000 2088 3.773418 TTTTAGGGAACGATCACACCA 57.227 42.857 0.00 0.00 0.00 4.17
2032 2120 4.450757 CCATTCGATATGCACCGTGAATAA 59.549 41.667 3.18 0.00 0.00 1.40
2064 2152 3.105959 AGTTTGCTGGCCCTGATTTAT 57.894 42.857 0.00 0.00 0.00 1.40
2084 2172 4.955811 ATATGCGGTTCTCAATGTCCTA 57.044 40.909 0.00 0.00 0.00 2.94
2247 2354 1.653151 GCAGTGGGACGAATCCTTAC 58.347 55.000 0.00 0.00 45.46 2.34
2273 2380 4.036380 GCAGAGATGATCAACATGCATCAA 59.964 41.667 20.84 0.00 40.57 2.57
2347 2454 7.116075 ACTGGTGTTGAATAATTATGTAGGCA 58.884 34.615 0.00 0.00 0.00 4.75
2429 2536 9.082313 AGAAATCAAATTTGGAGTGTCTAATGT 57.918 29.630 17.90 0.00 31.47 2.71
2458 2565 4.384056 CAACGATAGGAAATGGATGAGCT 58.616 43.478 0.00 0.00 43.77 4.09
2580 9405 5.072741 ACAAGTGACTTACCAATTGCTGAT 58.927 37.500 0.00 0.00 43.46 2.90
2583 9408 4.018960 AGTGACTTACCAATTGCTGATCCT 60.019 41.667 0.00 0.00 0.00 3.24
2642 9467 0.027063 ACGTGGCGTTTCGTTTTCTG 59.973 50.000 0.00 0.00 36.35 3.02
2778 9620 1.130561 GGCTAGTTCCAATCAACGTGC 59.869 52.381 0.00 0.00 0.00 5.34
2946 9789 1.618837 CTCCCTCGTCTTCAACTCCAA 59.381 52.381 0.00 0.00 0.00 3.53
2974 9817 6.473397 GAGAAACTCGATGTTGTTCTCAAT 57.527 37.500 16.32 0.00 40.03 2.57
2983 9826 2.099062 GTTCTCAATGCTGCGCCG 59.901 61.111 4.18 0.00 0.00 6.46
3053 9899 0.238289 AATGGTGCTTTCGTTGCTCG 59.762 50.000 0.00 0.00 41.41 5.03
3182 10030 2.097791 GCACCTTGTAACCGTTTGTCAA 59.902 45.455 0.00 0.00 0.00 3.18
3219 10067 3.721706 CTGGTCTCAGGCCCACCC 61.722 72.222 0.00 0.00 37.36 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.297701 GTTCTTTTCCACAGGCACTCA 58.702 47.619 0.00 0.00 34.60 3.41
91 92 1.200716 CGTAAGACACCGACTTGGCTA 59.799 52.381 0.00 0.00 40.89 3.93
160 161 2.158652 TCCCAGGATCCTACTCACTACG 60.159 54.545 15.67 0.00 0.00 3.51
185 186 1.680207 GAGCCTGAATGAAGGAATGCC 59.320 52.381 0.00 0.00 40.02 4.40
190 191 1.065636 CAGCTGAGCCTGAATGAAGGA 60.066 52.381 8.42 0.00 40.02 3.36
191 192 1.380524 CAGCTGAGCCTGAATGAAGG 58.619 55.000 8.42 0.00 40.63 3.46
194 195 0.675837 GTGCAGCTGAGCCTGAATGA 60.676 55.000 20.43 0.00 34.77 2.57
196 197 1.378250 GGTGCAGCTGAGCCTGAAT 60.378 57.895 20.43 0.00 34.77 2.57
197 198 2.033141 GGTGCAGCTGAGCCTGAA 59.967 61.111 20.43 0.00 34.77 3.02
198 199 4.025858 GGGTGCAGCTGAGCCTGA 62.026 66.667 20.43 0.00 34.77 3.86
212 213 2.589442 TTTTTCGTCAGCGCGGGT 60.589 55.556 8.83 0.00 38.14 5.28
275 277 8.721478 ACCTTATGCATAAAATTATCTAGCACG 58.279 33.333 19.32 3.58 32.92 5.34
297 299 5.066913 AGTTGAAATTTGGAGAGGACCTT 57.933 39.130 0.00 0.00 0.00 3.50
330 332 3.334583 TTTTACCGAGAGCTGCTCAAT 57.665 42.857 29.49 11.74 44.15 2.57
348 350 3.958147 ACAGACCCCGATTTTGTCTTTTT 59.042 39.130 0.00 0.00 37.25 1.94
349 351 3.562182 ACAGACCCCGATTTTGTCTTTT 58.438 40.909 0.00 0.00 37.25 2.27
350 352 3.223674 ACAGACCCCGATTTTGTCTTT 57.776 42.857 0.00 0.00 37.25 2.52
351 353 2.951229 ACAGACCCCGATTTTGTCTT 57.049 45.000 0.00 0.00 37.25 3.01
352 354 4.360951 TTTACAGACCCCGATTTTGTCT 57.639 40.909 0.00 0.00 39.86 3.41
353 355 5.441709 TTTTTACAGACCCCGATTTTGTC 57.558 39.130 0.00 0.00 0.00 3.18
380 382 2.100087 TCAGAACAGTGCGTGAACAGTA 59.900 45.455 0.00 0.00 0.00 2.74
389 391 0.670546 AATCGGGTCAGAACAGTGCG 60.671 55.000 0.00 0.00 0.00 5.34
395 397 4.830826 AAAAGACAAATCGGGTCAGAAC 57.169 40.909 0.00 0.00 37.74 3.01
463 465 7.381678 GTGGTAGATAATTTGATACGTGAGGTC 59.618 40.741 0.00 0.00 0.00 3.85
464 466 7.208080 GTGGTAGATAATTTGATACGTGAGGT 58.792 38.462 0.00 0.00 0.00 3.85
484 486 4.339872 TCCTAGAAACTTTTGCGTGGTA 57.660 40.909 0.00 0.00 0.00 3.25
522 526 8.401709 GGCCAGAAAACAAATCAAAACAAATAA 58.598 29.630 0.00 0.00 0.00 1.40
533 537 0.732538 CGGCGGCCAGAAAACAAATC 60.733 55.000 20.71 0.00 0.00 2.17
549 553 4.925861 GGCTCATCTGCTCCCGGC 62.926 72.222 0.00 0.00 42.22 6.13
567 571 0.608035 GAAATCCAACTCGGTGCCCA 60.608 55.000 0.00 0.00 35.57 5.36
568 572 1.313091 GGAAATCCAACTCGGTGCCC 61.313 60.000 0.00 0.00 35.57 5.36
569 573 1.644786 CGGAAATCCAACTCGGTGCC 61.645 60.000 0.00 0.00 35.57 5.01
650 654 4.163839 GCCTAGCTAGGATCATGGATTCAT 59.836 45.833 38.74 0.00 46.63 2.57
728 739 8.455682 TGGATTTACGGATTCACTATTTTGTTC 58.544 33.333 0.00 0.00 0.00 3.18
763 782 7.927092 CGAATCCTAGTAGTATCCGATCATAGA 59.073 40.741 0.00 0.00 0.00 1.98
773 792 3.825014 TGTGGCCGAATCCTAGTAGTATC 59.175 47.826 0.00 0.00 0.00 2.24
798 824 1.240641 TGTACGCCTCCGAACCGTAA 61.241 55.000 0.00 0.00 38.90 3.18
803 829 0.454600 TGAGATGTACGCCTCCGAAC 59.545 55.000 10.59 0.00 38.29 3.95
823 849 1.406887 CCAACGCTACCATGGCTAACT 60.407 52.381 13.04 0.00 0.00 2.24
955 996 1.062148 GGCTTCGTTCTTATTGGTCGC 59.938 52.381 0.00 0.00 0.00 5.19
969 1010 2.815647 GGAACTGCCTCGGCTTCG 60.816 66.667 9.65 0.66 42.51 3.79
999 1040 1.453379 CCTCTTGGCTGCCCTCATG 60.453 63.158 17.53 0.00 0.00 3.07
1052 1099 2.025359 GAGATCGCGTGCCCTTTTCG 62.025 60.000 5.77 0.00 0.00 3.46
1120 1167 1.492176 GAGGGAGATGATGGCCTCAAA 59.508 52.381 3.32 0.00 37.44 2.69
1206 1253 2.203084 TCGAGATCGAGAGGCGCT 60.203 61.111 7.64 0.00 44.22 5.92
1218 1265 3.060000 ATGTCCGTGGCGTCGAGA 61.060 61.111 0.00 0.00 0.00 4.04
1230 1277 4.989279 ATATTTGTTGGAGCACATGTCC 57.011 40.909 0.00 0.00 34.31 4.02
1236 1283 5.309323 TGCACTTATATTTGTTGGAGCAC 57.691 39.130 0.00 0.00 0.00 4.40
1282 1329 4.263572 CGGCCCAAGGTGGTCACA 62.264 66.667 0.00 0.00 35.17 3.58
1355 1402 2.369532 TCGATCCAAGCATCATCCATGA 59.630 45.455 0.00 0.00 41.70 3.07
1358 1405 1.541889 GCTCGATCCAAGCATCATCCA 60.542 52.381 9.33 0.00 39.61 3.41
1362 1409 1.884464 GCGCTCGATCCAAGCATCA 60.884 57.895 13.49 0.00 39.81 3.07
1369 1416 1.447838 GAAACCAGCGCTCGATCCA 60.448 57.895 7.13 0.00 0.00 3.41
1446 1493 2.022129 GTTCCTGGACACGTCTGCG 61.022 63.158 0.00 0.00 44.93 5.18
1509 1560 4.079446 CCGAATGTGGCCACAACT 57.921 55.556 40.48 29.95 45.41 3.16
1520 1571 2.513065 GAACCTGCACACGCCGAATG 62.513 60.000 0.00 0.00 37.32 2.67
1522 1573 2.970324 GAACCTGCACACGCCGAA 60.970 61.111 0.00 0.00 37.32 4.30
1606 1660 2.896443 CAGGGCTTCCTCCGAGAC 59.104 66.667 0.00 0.00 39.29 3.36
1656 1710 5.163195 ACGAATATCCTGCAGAAATAGGGTT 60.163 40.000 17.39 4.45 0.00 4.11
1684 1738 1.736032 GCTAACACGAAGGCAGTCGAT 60.736 52.381 16.16 5.82 43.86 3.59
1742 1796 5.535753 AAACAATTCTTGTCTTCCCAAGG 57.464 39.130 0.00 0.00 44.59 3.61
1749 1803 7.228706 ACGTCCTCAATAAACAATTCTTGTCTT 59.771 33.333 0.00 0.00 44.59 3.01
1821 1875 3.059884 AGGCGCATTATGTACTCGAATG 58.940 45.455 10.83 9.33 34.37 2.67
1836 1890 3.876914 CCAATATCTTCAGTTTAGGCGCA 59.123 43.478 10.83 0.00 0.00 6.09
1874 1928 6.567687 TTGCAATCTCGATTTTGGAAAGTA 57.432 33.333 10.57 0.00 31.44 2.24
1875 1929 5.452078 TTGCAATCTCGATTTTGGAAAGT 57.548 34.783 10.57 0.00 31.44 2.66
1876 1930 5.119125 GGTTTGCAATCTCGATTTTGGAAAG 59.881 40.000 20.03 0.37 41.66 2.62
1995 2080 1.251251 GAATGGCTCAAGCTTGGTGT 58.749 50.000 25.73 6.19 41.70 4.16
2000 2088 2.551459 GCATATCGAATGGCTCAAGCTT 59.449 45.455 0.00 0.00 41.70 3.74
2032 2120 2.298163 CCAGCAAACTTGAGAGCCAAAT 59.702 45.455 0.00 0.00 33.76 2.32
2064 2152 3.490249 CGTAGGACATTGAGAACCGCATA 60.490 47.826 0.00 0.00 0.00 3.14
2084 2172 3.570212 AAGCAGGGGAAGCACCGT 61.570 61.111 0.00 0.00 40.11 4.83
2196 2290 8.283291 GGCACAACAGATATATGTTAAAGTAGC 58.717 37.037 15.01 13.49 41.41 3.58
2247 2354 2.290916 GCATGTTGATCATCTCTGCCTG 59.709 50.000 15.39 1.57 34.09 4.85
2273 2380 5.668135 TGATTGGATTCAGGGGTTCATAT 57.332 39.130 0.00 0.00 0.00 1.78
2319 2426 9.832445 CCTACATAATTATTCAACACCAGTACT 57.168 33.333 0.00 0.00 0.00 2.73
2340 2447 4.442893 CCAATATCTTCCTCGTTGCCTACA 60.443 45.833 0.00 0.00 0.00 2.74
2347 2454 3.378427 GCAAAGCCAATATCTTCCTCGTT 59.622 43.478 0.00 0.00 0.00 3.85
2380 2487 6.695278 TCTTTTACCACTTTCGCATTCAAAAG 59.305 34.615 0.00 0.00 38.24 2.27
2429 2536 3.631686 CCATTTCCTATCGTTGCCAATCA 59.368 43.478 0.00 0.00 0.00 2.57
2458 2565 3.444034 ACTTCTAGCAGCGTGACTTGATA 59.556 43.478 0.00 0.00 0.00 2.15
2580 9405 4.685924 AGTTAAAACGACAGTCGAAAGGA 58.314 39.130 29.53 9.20 43.74 3.36
2583 9408 5.023286 GCAAAGTTAAAACGACAGTCGAAA 58.977 37.500 29.53 13.94 43.74 3.46
2642 9467 7.214467 TCAATTTTACTGTTCACAAGGATCC 57.786 36.000 2.48 2.48 0.00 3.36
2757 9599 1.737793 CACGTTGATTGGAACTAGCCC 59.262 52.381 0.00 0.00 0.00 5.19
2827 9669 9.847706 GAAAAAGAAAGGATAATTCAGTCTTCC 57.152 33.333 0.00 0.00 0.00 3.46
2983 9826 0.716108 CATGTTCTTCGTGCGTCCTC 59.284 55.000 0.00 0.00 0.00 3.71
3053 9899 6.651225 CCAAGGTAGCCTTAATTATAGCAGAC 59.349 42.308 9.24 6.80 42.67 3.51
3110 9956 7.766283 AGAAAAAGAGGTGAAAAAGAGTTCAG 58.234 34.615 0.00 0.00 38.17 3.02
3163 10011 6.263617 ACATTATTGACAAACGGTTACAAGGT 59.736 34.615 10.00 0.00 0.00 3.50
3182 10030 3.693085 CAGGCTGAAGTGCTGAACATTAT 59.307 43.478 9.42 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.