Multiple sequence alignment - TraesCS3D01G231900

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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 TraesCS3D01G231900 chr3D 100.000 7748 0 0 1 7748 318504682 318512429 0.000000e+00 14308.0
1 TraesCS3D01G231900 chr3B 95.764 7105 183 33 1 7082 401287438 401280429 0.000000e+00 11345.0
2 TraesCS3D01G231900 chr3B 95.082 61 3 0 6834 6894 401280642 401280582 6.400000e-16 97.1
3 TraesCS3D01G231900 chr3A 96.395 3190 69 20 2946 6131 408029254 408026107 0.000000e+00 5212.0
4 TraesCS3D01G231900 chr3A 94.758 2976 112 19 1 2950 408034128 408031171 0.000000e+00 4591.0
5 TraesCS3D01G231900 chr3A 95.770 922 29 5 5977 6894 408026115 408025200 0.000000e+00 1478.0
6 TraesCS3D01G231900 chr3A 91.038 212 15 2 6874 7082 408025257 408025047 4.580000e-72 283.0
7 TraesCS3D01G231900 chr3A 94.872 39 2 0 3514 3552 12784338 12784300 2.330000e-05 62.1
8 TraesCS3D01G231900 chr2D 84.239 1307 167 20 4972 6269 382444670 382443394 0.000000e+00 1236.0
9 TraesCS3D01G231900 chr2D 95.082 671 17 7 7079 7748 46864914 46864259 0.000000e+00 1042.0
10 TraesCS3D01G231900 chr2D 94.362 674 34 4 7077 7747 537345779 537345107 0.000000e+00 1031.0
11 TraesCS3D01G231900 chr2D 95.043 585 27 2 7164 7747 123211310 123211893 0.000000e+00 918.0
12 TraesCS3D01G231900 chr2D 84.211 779 87 20 3572 4326 382449323 382448557 0.000000e+00 725.0
13 TraesCS3D01G231900 chr2D 82.055 691 99 16 2663 3348 382449996 382449326 4.060000e-157 566.0
14 TraesCS3D01G231900 chr2D 84.507 284 34 4 4748 5022 382444957 382444675 9.910000e-69 272.0
15 TraesCS3D01G231900 chr2B 84.648 1166 148 23 4972 6123 453231600 453230452 0.000000e+00 1133.0
16 TraesCS3D01G231900 chr2B 95.238 672 29 3 7079 7748 237627178 237626508 0.000000e+00 1061.0
17 TraesCS3D01G231900 chr2B 83.882 577 67 13 3574 4132 453237897 453237329 1.910000e-145 527.0
18 TraesCS3D01G231900 chr2B 81.364 601 95 14 4155 4743 453237215 453236620 2.530000e-129 473.0
19 TraesCS3D01G231900 chr2B 80.103 387 69 8 2971 3353 453238276 453237894 1.650000e-71 281.0
20 TraesCS3D01G231900 chr2B 85.660 265 30 3 4748 5005 453231883 453231620 9.910000e-69 272.0
21 TraesCS3D01G231900 chr2B 94.231 156 9 0 6114 6269 453228580 453228425 1.000000e-58 239.0
22 TraesCS3D01G231900 chr2B 94.828 58 3 0 7690 7747 640505166 640505109 2.980000e-14 91.6
23 TraesCS3D01G231900 chrUn 96.220 582 16 4 7171 7748 17325041 17324462 0.000000e+00 948.0
24 TraesCS3D01G231900 chrUn 95.000 100 4 1 7079 7177 273165694 273165595 1.040000e-33 156.0
25 TraesCS3D01G231900 chr4A 92.250 671 35 8 7079 7747 607469116 607469771 0.000000e+00 935.0
26 TraesCS3D01G231900 chr4A 89.630 405 33 2 7343 7747 714297838 714297443 2.490000e-139 507.0
27 TraesCS3D01G231900 chr2A 83.505 776 93 18 3574 4326 516827524 516826761 0.000000e+00 691.0
28 TraesCS3D01G231900 chr2A 84.839 653 77 17 5638 6282 516745024 516744386 8.480000e-179 638.0
29 TraesCS3D01G231900 chr2A 83.038 678 92 15 4972 5643 516746979 516746319 1.860000e-165 593.0
30 TraesCS3D01G231900 chr2A 79.828 699 112 20 2663 3353 516828198 516827521 4.200000e-132 483.0
31 TraesCS3D01G231900 chr2A 83.099 284 38 4 4748 5022 516747266 516746984 4.640000e-62 250.0
32 TraesCS3D01G231900 chr5B 93.307 254 12 2 7494 7747 496417559 496417807 3.410000e-98 370.0
33 TraesCS3D01G231900 chr5B 90.995 211 16 2 7539 7747 679039873 679040082 1.650000e-71 281.0


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 TraesCS3D01G231900 chr3D 318504682 318512429 7747 False 14308.000000 14308 100.000000 1 7748 1 chr3D.!!$F1 7747
1 TraesCS3D01G231900 chr3B 401280429 401287438 7009 True 11345.000000 11345 95.764000 1 7082 1 chr3B.!!$R1 7081
2 TraesCS3D01G231900 chr3A 408025047 408034128 9081 True 2891.000000 5212 94.490250 1 7082 4 chr3A.!!$R2 7081
3 TraesCS3D01G231900 chr2D 46864259 46864914 655 True 1042.000000 1042 95.082000 7079 7748 1 chr2D.!!$R1 669
4 TraesCS3D01G231900 chr2D 537345107 537345779 672 True 1031.000000 1031 94.362000 7077 7747 1 chr2D.!!$R2 670
5 TraesCS3D01G231900 chr2D 123211310 123211893 583 False 918.000000 918 95.043000 7164 7747 1 chr2D.!!$F1 583
6 TraesCS3D01G231900 chr2D 382443394 382449996 6602 True 699.750000 1236 83.753000 2663 6269 4 chr2D.!!$R3 3606
7 TraesCS3D01G231900 chr2B 237626508 237627178 670 True 1061.000000 1061 95.238000 7079 7748 1 chr2B.!!$R1 669
8 TraesCS3D01G231900 chr2B 453228425 453231883 3458 True 548.000000 1133 88.179667 4748 6269 3 chr2B.!!$R3 1521
9 TraesCS3D01G231900 chr2B 453236620 453238276 1656 True 427.000000 527 81.783000 2971 4743 3 chr2B.!!$R4 1772
10 TraesCS3D01G231900 chrUn 17324462 17325041 579 True 948.000000 948 96.220000 7171 7748 1 chrUn.!!$R1 577
11 TraesCS3D01G231900 chr4A 607469116 607469771 655 False 935.000000 935 92.250000 7079 7747 1 chr4A.!!$F1 668
12 TraesCS3D01G231900 chr2A 516826761 516828198 1437 True 587.000000 691 81.666500 2663 4326 2 chr2A.!!$R2 1663
13 TraesCS3D01G231900 chr2A 516744386 516747266 2880 True 493.666667 638 83.658667 4748 6282 3 chr2A.!!$R1 1534

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
575 591 0.881159 CTTACGTGGCGGTGGTTTGA 60.881 55.000 0.00 0.00 0.00 2.69 F
1510 1541 1.678101 GCTTGTGCACTTTCCTCTGTT 59.322 47.619 19.41 0.00 39.41 3.16 F
1791 1827 0.035152 TTAGTGCCACCATCTGCCAG 60.035 55.000 0.00 0.00 0.00 4.85 F
2160 2197 0.381089 CTTTGCTCAGCCTGCATAGC 59.619 55.000 0.00 8.32 40.34 2.97 F
3009 4972 1.686428 GGATGGGAAGGAGAAAAGCCC 60.686 57.143 0.00 0.00 39.29 5.19 F
3326 5290 2.213499 GTGTACTGCTATGTCCATGCC 58.787 52.381 0.00 0.00 0.00 4.40 F
4110 6117 2.501316 GGGGGCTTTGCAATAATTCACT 59.499 45.455 0.00 0.00 0.00 3.41 F
4424 6527 0.469705 TGGGGTGCTGTTTCTGCAAT 60.470 50.000 3.17 0.00 39.78 3.56 F
6271 15004 0.036732 TGGGTAAGCAGCTGAACCTG 59.963 55.000 20.43 0.00 35.93 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1679 0.249741 ACACAAAACGACTAGGCGCT 60.250 50.000 20.33 1.58 33.86 5.92 R
3136 5099 1.129251 CCGCCTGCGCATATGATAAAG 59.871 52.381 12.24 0.00 38.24 1.85 R
3353 5317 4.519540 ACTTCAAATGATTTGGAACGGG 57.480 40.909 17.01 0.33 40.98 5.28 R
4089 6096 2.501316 AGTGAATTATTGCAAAGCCCCC 59.499 45.455 1.71 0.00 0.00 5.40 R
4257 6360 0.179037 GCTGCAGTGATGGCCATCTA 60.179 55.000 38.59 25.38 38.60 1.98 R
4424 6527 3.426787 TTGAAAAGGGAAGCCGTATCA 57.573 42.857 0.00 0.00 0.00 2.15 R
5991 12840 3.274288 CAGAAATAGCACCCCAGTCTTC 58.726 50.000 0.00 0.00 0.00 2.87 R
6375 15108 1.664965 GACGGACGCTCACTGCTTT 60.665 57.895 0.00 0.00 40.11 3.51 R
7562 16303 0.391130 GCACTGCCTTGATCGGTACA 60.391 55.000 0.00 0.00 0.00 2.90 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
25 30 7.446106 TTTATATTCTCCCTGTTAGGAAGCA 57.554 36.000 0.00 0.00 37.67 3.91
117 124 4.976864 AGCCAAAGCCAAATCTTGATTTT 58.023 34.783 5.92 0.00 41.25 1.82
169 176 4.370776 TGAAAGATCTGGAAGGACCCATA 58.629 43.478 0.00 0.00 38.00 2.74
173 180 3.906846 AGATCTGGAAGGACCCATATCAC 59.093 47.826 0.00 0.00 40.35 3.06
191 198 7.362834 CCATATCACACAAATGGTTGTACACAT 60.363 37.037 0.00 0.00 46.47 3.21
303 313 6.539173 TCCTTAGTCTGTTAAGCCAAATCAA 58.461 36.000 0.00 0.00 30.84 2.57
312 322 5.761234 TGTTAAGCCAAATCAACTCGTTAGT 59.239 36.000 0.00 0.00 37.65 2.24
414 425 6.349115 CCTCATATAGTGCAGCAAATTGATCC 60.349 42.308 0.00 0.00 0.00 3.36
419 430 5.726980 AGTGCAGCAAATTGATCCTTTAA 57.273 34.783 0.00 0.00 0.00 1.52
444 455 6.131961 AGCTCCATTGCTAATCCATTTACTT 58.868 36.000 0.00 0.00 42.10 2.24
451 462 9.956720 CATTGCTAATCCATTTACTTTAGGAAG 57.043 33.333 0.00 0.00 36.09 3.46
470 482 4.309933 GAAGCAATGGGAAGGTCAAAAAG 58.690 43.478 0.00 0.00 0.00 2.27
479 491 4.550422 GGAAGGTCAAAAAGCTCAATGAC 58.450 43.478 14.17 14.17 41.06 3.06
545 561 4.202441 CAAGGGTATTTGAGTGGATCAGG 58.798 47.826 0.00 0.00 39.68 3.86
568 584 2.968206 GGAGTCTTACGTGGCGGT 59.032 61.111 0.00 0.00 0.00 5.68
572 588 1.301165 GTCTTACGTGGCGGTGGTT 60.301 57.895 0.00 0.00 0.00 3.67
575 591 0.881159 CTTACGTGGCGGTGGTTTGA 60.881 55.000 0.00 0.00 0.00 2.69
578 594 2.473760 CGTGGCGGTGGTTTGAACA 61.474 57.895 0.00 0.00 0.00 3.18
607 623 2.196997 CTCCCCCAGTTTGCATCCGA 62.197 60.000 0.00 0.00 0.00 4.55
630 646 7.138736 CGATTTGCGGGAATTTAGATAAACAT 58.861 34.615 0.00 0.00 36.03 2.71
637 653 8.028938 GCGGGAATTTAGATAAACATATGCATT 58.971 33.333 3.54 1.02 0.00 3.56
663 679 4.378978 CGAACAAATAAAGGGACGCATTGA 60.379 41.667 0.00 0.00 0.00 2.57
704 726 7.770897 TGATGCCCTTTACTATCTTTCTTCTTC 59.229 37.037 0.00 0.00 0.00 2.87
707 729 7.824779 TGCCCTTTACTATCTTTCTTCTTCTTC 59.175 37.037 0.00 0.00 0.00 2.87
708 730 7.281324 GCCCTTTACTATCTTTCTTCTTCTTCC 59.719 40.741 0.00 0.00 0.00 3.46
710 732 9.952030 CCTTTACTATCTTTCTTCTTCTTCCTT 57.048 33.333 0.00 0.00 0.00 3.36
787 812 4.348656 CGTCGATTCGAAGTCCTATTTGA 58.651 43.478 10.87 0.00 37.72 2.69
790 815 4.804139 TCGATTCGAAGTCCTATTTGAAGC 59.196 41.667 6.24 0.00 36.31 3.86
792 817 3.973206 TCGAAGTCCTATTTGAAGCCA 57.027 42.857 0.00 0.00 0.00 4.75
1190 1219 3.130693 CCGTTCCTCTCGTAATTCTCCTT 59.869 47.826 0.00 0.00 0.00 3.36
1442 1471 8.935844 TCGCATGTCATAATATAAATTCTCCAC 58.064 33.333 0.00 0.00 0.00 4.02
1510 1541 1.678101 GCTTGTGCACTTTCCTCTGTT 59.322 47.619 19.41 0.00 39.41 3.16
1641 1676 3.462483 TTGTTCGTCCATGTGTGTAGT 57.538 42.857 0.00 0.00 0.00 2.73
1644 1679 1.623163 TCGTCCATGTGTGTAGTGGA 58.377 50.000 0.00 0.00 39.61 4.02
1655 1691 1.355916 GTAGTGGAGCGCCTAGTCG 59.644 63.158 8.34 0.00 34.31 4.18
1662 1698 0.438830 GAGCGCCTAGTCGTTTTGTG 59.561 55.000 2.29 0.00 0.00 3.33
1791 1827 0.035152 TTAGTGCCACCATCTGCCAG 60.035 55.000 0.00 0.00 0.00 4.85
1842 1878 1.852965 CCCAGGGACCCTCATAAACAT 59.147 52.381 11.23 0.00 0.00 2.71
1955 1991 9.113838 TGCTAATCTTTCCTTTCTTGATGTATC 57.886 33.333 0.00 0.00 0.00 2.24
1963 1999 7.257790 TCCTTTCTTGATGTATCTCCTTCAA 57.742 36.000 0.00 0.00 0.00 2.69
1991 2028 5.079689 TCGCTGTTGTTGTATCTATGGAA 57.920 39.130 0.00 0.00 0.00 3.53
2001 2038 8.547481 TGTTGTATCTATGGAACCAGATCTTA 57.453 34.615 0.00 0.00 32.50 2.10
2160 2197 0.381089 CTTTGCTCAGCCTGCATAGC 59.619 55.000 0.00 8.32 40.34 2.97
2193 2230 4.402793 GTGCTTAGTCAAGAGGAGGTCATA 59.597 45.833 0.00 0.00 33.20 2.15
2426 2463 9.757227 TTTGCTAATTTGCTATACTTTTGTTGT 57.243 25.926 12.99 0.00 0.00 3.32
2478 2515 8.148351 TCCATTTTTCTTCGTCGATATATCCTT 58.852 33.333 7.15 0.00 0.00 3.36
2748 2788 5.491982 CTGGGCTCTTAGAAACTACATTGT 58.508 41.667 0.00 0.00 0.00 2.71
2911 2951 6.952935 AAGAACTTCTACATAGCAGTTTCG 57.047 37.500 5.59 0.00 39.33 3.46
2925 2965 3.367025 GCAGTTTCGCTCGTAGTTTGTAT 59.633 43.478 0.00 0.00 0.00 2.29
2962 4925 3.356290 GTTGTGATTACAGGCTGGGATT 58.644 45.455 20.34 0.00 38.23 3.01
3009 4972 1.686428 GGATGGGAAGGAGAAAAGCCC 60.686 57.143 0.00 0.00 39.29 5.19
3034 4997 5.485353 GGGGATGGAAGGAAAGAAAAGAAAT 59.515 40.000 0.00 0.00 0.00 2.17
3225 5188 5.523369 CACTTCCCTGTTGATTTGAAGAAC 58.477 41.667 0.00 0.00 36.72 3.01
3326 5290 2.213499 GTGTACTGCTATGTCCATGCC 58.787 52.381 0.00 0.00 0.00 4.40
3348 5312 5.596772 GCCCCCATGTAACAAACTGTAATAT 59.403 40.000 0.00 0.00 0.00 1.28
3353 5317 7.201875 CCCATGTAACAAACTGTAATATTCCCC 60.202 40.741 0.00 0.00 0.00 4.81
3375 5344 4.262420 CCCCGTTCCAAATCATTTGAAGTT 60.262 41.667 11.98 0.00 43.26 2.66
3376 5345 5.047660 CCCCGTTCCAAATCATTTGAAGTTA 60.048 40.000 11.98 0.00 43.26 2.24
3558 5527 7.921786 TCAAGTAATTTGGAATGGAGTAGTG 57.078 36.000 0.00 0.00 37.39 2.74
4087 6094 9.788889 AAATCTCAGACATATTATTCATCTGCA 57.211 29.630 0.00 0.00 37.34 4.41
4088 6095 9.438228 AATCTCAGACATATTATTCATCTGCAG 57.562 33.333 7.63 7.63 37.34 4.41
4089 6096 7.384477 TCTCAGACATATTATTCATCTGCAGG 58.616 38.462 15.13 0.00 37.34 4.85
4090 6097 6.470278 TCAGACATATTATTCATCTGCAGGG 58.530 40.000 15.13 6.93 37.34 4.45
4091 6098 5.646793 CAGACATATTATTCATCTGCAGGGG 59.353 44.000 15.13 6.54 31.14 4.79
4092 6099 4.927049 ACATATTATTCATCTGCAGGGGG 58.073 43.478 15.13 3.79 0.00 5.40
4109 6116 2.905075 GGGGGCTTTGCAATAATTCAC 58.095 47.619 0.00 0.00 0.00 3.18
4110 6117 2.501316 GGGGGCTTTGCAATAATTCACT 59.499 45.455 0.00 0.00 0.00 3.41
4111 6118 3.430790 GGGGGCTTTGCAATAATTCACTC 60.431 47.826 0.00 0.00 0.00 3.51
4257 6360 3.933861 AAGGTCTTTTGTCTCCACTGT 57.066 42.857 0.00 0.00 0.00 3.55
4424 6527 0.469705 TGGGGTGCTGTTTCTGCAAT 60.470 50.000 3.17 0.00 39.78 3.56
4431 6534 2.419673 TGCTGTTTCTGCAATGATACGG 59.580 45.455 0.00 0.00 35.52 4.02
4565 6684 6.647334 TTGATCTTATTGGTTTGCAGTCAA 57.353 33.333 0.00 0.00 0.00 3.18
4664 6783 3.391296 GCTACATCATCCAGAGGGGTAAA 59.609 47.826 0.00 0.00 38.11 2.01
4685 6804 8.398665 GGTAAACTGCTAAATACCTGAAAGATG 58.601 37.037 0.00 0.00 35.88 2.90
5374 10773 3.536956 TCAGGATTATGGTGTTCGGAC 57.463 47.619 0.00 0.00 0.00 4.79
5750 12452 1.745489 GGAAAGTAGGTGGCTGCCG 60.745 63.158 14.98 0.00 0.00 5.69
5991 12840 0.721718 GAAGATGTTCTTGGGCGTCG 59.278 55.000 0.00 0.00 36.73 5.12
6222 14955 0.823769 CATCTGGCCATGCTGCAGAT 60.824 55.000 20.43 5.31 32.82 2.90
6271 15004 0.036732 TGGGTAAGCAGCTGAACCTG 59.963 55.000 20.43 0.00 35.93 4.00
6283 15016 0.467290 TGAACCTGTTGGAACCTGCC 60.467 55.000 0.00 0.00 37.04 4.85
6375 15108 0.394192 CCAGGAGATATCGCTGGCAA 59.606 55.000 10.64 0.00 0.00 4.52
6448 15181 6.695713 CACTATCGCAGTACAGCTTATTAACA 59.304 38.462 8.72 0.00 34.98 2.41
6452 15185 4.027621 CGCAGTACAGCTTATTAACACTCG 60.028 45.833 8.72 0.00 0.00 4.18
6660 15394 4.087182 CAACCTACCTAGAAGACCTGACA 58.913 47.826 0.00 0.00 0.00 3.58
6738 15475 0.387929 TTGACGACGAGGAGTTTGCT 59.612 50.000 0.00 0.00 0.00 3.91
6842 15579 8.609478 TTGTTTCAAACACTTCGTAAATTCTC 57.391 30.769 1.28 0.00 41.97 2.87
6908 15645 8.021396 GGAGATTGGTTCAACACTTTGTAATAC 58.979 37.037 0.00 0.00 34.02 1.89
6975 15715 1.477700 TCGTGGGGGTGTTCTTATACG 59.522 52.381 0.00 0.00 0.00 3.06
7005 15745 2.154462 CAACCTACAGGCAGTTTGAGG 58.846 52.381 0.00 0.00 39.32 3.86
7047 15787 2.316108 TCACTAATCGCCATAGCCTCA 58.684 47.619 0.00 0.00 34.57 3.86
7291 16031 7.498239 GGATACTATAAAAGAGGTTTGGTCCAC 59.502 40.741 0.00 0.00 0.00 4.02
7295 16036 1.222567 AAGAGGTTTGGTCCACACCT 58.777 50.000 26.79 26.79 45.81 4.00
7388 16129 5.273674 ACGGGATATGATCATCATGCTAG 57.726 43.478 12.53 9.99 37.70 3.42
7402 16143 2.532250 TGCTAGTGTGGAGGATCTGA 57.468 50.000 0.00 0.00 33.73 3.27
7452 16193 4.328118 AAGAAATCCCTCCAGCTGAAAT 57.672 40.909 17.39 0.00 0.00 2.17
7457 16198 1.988107 TCCCTCCAGCTGAAATGTCTT 59.012 47.619 17.39 0.00 0.00 3.01
7458 16199 2.026822 TCCCTCCAGCTGAAATGTCTTC 60.027 50.000 17.39 0.00 0.00 2.87
7514 16255 1.028330 ATGCAGCCAATCTCACCACG 61.028 55.000 0.00 0.00 0.00 4.94
7653 16397 3.387699 TGTGGATGGATCTTATTCAGCGA 59.612 43.478 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.173782 TGACCCTTTGTGTTGCTTCCTA 59.826 45.455 0.00 0.00 0.00 2.94
19 20 1.067060 GTGACCCTTTGTGTTGCTTCC 59.933 52.381 0.00 0.00 0.00 3.46
25 30 2.291282 TGAACAGGTGACCCTTTGTGTT 60.291 45.455 5.96 5.96 39.89 3.32
77 83 9.726817 GCTTTGGCTAATTTGGCATAATGCAAC 62.727 40.741 16.20 0.52 42.07 4.17
117 124 7.175990 ACGTATGGAAAGCTAAAATTCCTTTGA 59.824 33.333 14.50 0.00 44.43 2.69
169 176 7.611467 AGATATGTGTACAACCATTTGTGTGAT 59.389 33.333 0.00 0.00 45.91 3.06
173 180 8.726068 TGTTAGATATGTGTACAACCATTTGTG 58.274 33.333 0.00 0.00 45.91 3.33
273 283 6.827727 TGGCTTAACAGACTAAGGATAATCC 58.172 40.000 0.00 0.00 36.58 3.01
303 313 5.419471 AGAAGATGGCTTTCTACTAACGAGT 59.581 40.000 0.00 0.00 35.51 4.18
352 362 9.712305 TCAAGCTATATTAGTAAGAGAAATGGC 57.288 33.333 0.00 0.00 0.00 4.40
414 425 6.455360 TGGATTAGCAATGGAGCTTTAAAG 57.545 37.500 11.02 11.02 43.70 1.85
419 430 6.131961 AGTAAATGGATTAGCAATGGAGCTT 58.868 36.000 0.00 0.00 43.70 3.74
444 455 2.647299 TGACCTTCCCATTGCTTCCTAA 59.353 45.455 0.00 0.00 0.00 2.69
451 462 2.037641 AGCTTTTTGACCTTCCCATTGC 59.962 45.455 0.00 0.00 0.00 3.56
470 482 4.232221 CAGGTGTTCAAATGTCATTGAGC 58.768 43.478 0.00 2.58 40.21 4.26
479 491 1.608590 ACGAAGGCAGGTGTTCAAATG 59.391 47.619 0.00 0.00 0.00 2.32
545 561 0.109412 CCACGTAAGACTCCGACACC 60.109 60.000 0.00 0.00 43.62 4.16
568 584 0.173708 GTTTGCGGGTGTTCAAACCA 59.826 50.000 6.58 0.00 43.58 3.67
572 588 1.104577 GGAGGTTTGCGGGTGTTCAA 61.105 55.000 0.00 0.00 0.00 2.69
575 591 2.203437 GGGAGGTTTGCGGGTGTT 60.203 61.111 0.00 0.00 0.00 3.32
607 623 9.912634 CATATGTTTATCTAAATTCCCGCAAAT 57.087 29.630 0.00 0.00 0.00 2.32
621 637 7.552458 TGTTCGTGAATGCATATGTTTATCT 57.448 32.000 0.00 0.00 0.00 1.98
630 646 6.375736 TCCCTTTATTTGTTCGTGAATGCATA 59.624 34.615 0.00 0.00 0.00 3.14
637 653 2.481185 GCGTCCCTTTATTTGTTCGTGA 59.519 45.455 0.00 0.00 0.00 4.35
663 679 3.627577 GGGCATCATCGTAGTTTGTCATT 59.372 43.478 0.00 0.00 0.00 2.57
734 759 3.792515 GTAGCCCCTCCTACCAGATAAT 58.207 50.000 0.00 0.00 33.24 1.28
930 958 4.613394 GCTGCTTCTGCTTCTTCTTCTTTC 60.613 45.833 0.00 0.00 40.48 2.62
935 964 1.532523 GGCTGCTTCTGCTTCTTCTT 58.467 50.000 0.00 0.00 40.48 2.52
936 965 0.322366 GGGCTGCTTCTGCTTCTTCT 60.322 55.000 0.00 0.00 40.48 2.85
937 966 0.607489 TGGGCTGCTTCTGCTTCTTC 60.607 55.000 0.00 0.00 40.48 2.87
938 967 0.892814 GTGGGCTGCTTCTGCTTCTT 60.893 55.000 0.00 0.00 40.48 2.52
939 968 1.303155 GTGGGCTGCTTCTGCTTCT 60.303 57.895 0.00 0.00 40.48 2.85
940 969 2.684843 CGTGGGCTGCTTCTGCTTC 61.685 63.158 0.00 0.00 40.48 3.86
941 970 2.670934 CGTGGGCTGCTTCTGCTT 60.671 61.111 0.00 0.00 40.48 3.91
942 971 2.680974 TTTCGTGGGCTGCTTCTGCT 62.681 55.000 0.00 0.00 40.48 4.24
943 972 2.260869 TTTCGTGGGCTGCTTCTGC 61.261 57.895 0.00 0.00 40.20 4.26
984 1013 0.382515 CCATCTCCCGTCTCGTCTTC 59.617 60.000 0.00 0.00 0.00 2.87
1190 1219 1.573829 GCACGAAATCGCAACCCTCA 61.574 55.000 2.15 0.00 44.43 3.86
1510 1541 4.058721 CCATCTCGGTTGATATGTGTGA 57.941 45.455 0.00 0.00 29.19 3.58
1641 1676 0.669318 CAAAACGACTAGGCGCTCCA 60.669 55.000 20.33 0.00 33.74 3.86
1644 1679 0.249741 ACACAAAACGACTAGGCGCT 60.250 50.000 20.33 1.58 33.86 5.92
1655 1691 7.308049 GGTCTATCCAGAAAGAGAACACAAAAC 60.308 40.741 0.00 0.00 35.97 2.43
1791 1827 1.557371 AGTTCCTAGAGCCAAAGGAGC 59.443 52.381 4.98 4.98 42.74 4.70
1842 1878 4.209307 TGTAACCCTCGCATGTTATTCA 57.791 40.909 0.00 0.00 30.35 2.57
1963 1999 7.171508 CCATAGATACAACAACAGCGATTATGT 59.828 37.037 0.00 0.00 0.00 2.29
1991 2028 6.222038 ACATAATGTCGTGTAAGATCTGGT 57.778 37.500 0.00 0.00 0.00 4.00
2160 2197 0.737715 GACTAAGCACCAGTGAGGCG 60.738 60.000 0.99 0.00 43.14 5.52
2426 2463 5.884322 AGCTGCAGAAATATGGATCCATTA 58.116 37.500 31.70 17.56 37.82 1.90
2478 2515 7.078249 TGCCTTATAGCAATAGAAGAATCCA 57.922 36.000 0.00 0.00 40.56 3.41
2748 2788 4.811969 TTCAACCGCAGACTAAGGAATA 57.188 40.909 2.72 0.00 0.00 1.75
2962 4925 4.406972 AGCTTCAGGCACATAATCAGAGTA 59.593 41.667 0.00 0.00 44.79 2.59
3009 4972 2.507407 TTTCTTTCCTTCCATCCCCG 57.493 50.000 0.00 0.00 0.00 5.73
3136 5099 1.129251 CCGCCTGCGCATATGATAAAG 59.871 52.381 12.24 0.00 38.24 1.85
3225 5188 5.177142 CAGAAGACATCGAATGCCAGATAAG 59.823 44.000 0.00 0.00 0.00 1.73
3326 5290 7.201875 GGGAATATTACAGTTTGTTACATGGGG 60.202 40.741 0.00 0.00 0.00 4.96
3353 5317 4.519540 ACTTCAAATGATTTGGAACGGG 57.480 40.909 17.01 0.33 40.98 5.28
4089 6096 2.501316 AGTGAATTATTGCAAAGCCCCC 59.499 45.455 1.71 0.00 0.00 5.40
4090 6097 3.195396 TGAGTGAATTATTGCAAAGCCCC 59.805 43.478 1.71 0.00 0.00 5.80
4091 6098 4.082026 ACTGAGTGAATTATTGCAAAGCCC 60.082 41.667 1.71 0.00 0.00 5.19
4092 6099 4.860907 CACTGAGTGAATTATTGCAAAGCC 59.139 41.667 6.79 0.00 35.23 4.35
4093 6100 5.570589 GTCACTGAGTGAATTATTGCAAAGC 59.429 40.000 18.01 0.00 44.49 3.51
4094 6101 6.088824 GGTCACTGAGTGAATTATTGCAAAG 58.911 40.000 18.01 0.00 44.49 2.77
4095 6102 5.534278 TGGTCACTGAGTGAATTATTGCAAA 59.466 36.000 18.01 0.00 44.49 3.68
4096 6103 5.069318 TGGTCACTGAGTGAATTATTGCAA 58.931 37.500 18.01 0.00 44.49 4.08
4097 6104 4.650734 TGGTCACTGAGTGAATTATTGCA 58.349 39.130 18.01 0.00 44.49 4.08
4098 6105 5.412594 TCTTGGTCACTGAGTGAATTATTGC 59.587 40.000 18.01 2.64 44.49 3.56
4099 6106 7.439157 TTCTTGGTCACTGAGTGAATTATTG 57.561 36.000 18.01 6.11 44.49 1.90
4100 6107 8.641498 ATTTCTTGGTCACTGAGTGAATTATT 57.359 30.769 18.01 0.00 44.49 1.40
4101 6108 8.641498 AATTTCTTGGTCACTGAGTGAATTAT 57.359 30.769 18.01 1.85 44.49 1.28
4102 6109 8.463930 AAATTTCTTGGTCACTGAGTGAATTA 57.536 30.769 18.01 3.74 44.49 1.40
4103 6110 6.966534 AATTTCTTGGTCACTGAGTGAATT 57.033 33.333 18.01 8.61 44.49 2.17
4104 6111 6.966534 AAATTTCTTGGTCACTGAGTGAAT 57.033 33.333 18.01 2.21 44.49 2.57
4105 6112 6.773976 AAAATTTCTTGGTCACTGAGTGAA 57.226 33.333 18.01 0.00 44.49 3.18
4106 6113 7.873719 TTAAAATTTCTTGGTCACTGAGTGA 57.126 32.000 11.93 11.93 40.50 3.41
4107 6114 9.612620 GTATTAAAATTTCTTGGTCACTGAGTG 57.387 33.333 6.18 6.18 34.45 3.51
4108 6115 9.574516 AGTATTAAAATTTCTTGGTCACTGAGT 57.425 29.630 0.00 0.00 0.00 3.41
4110 6117 9.567776 TGAGTATTAAAATTTCTTGGTCACTGA 57.432 29.630 0.00 0.00 0.00 3.41
4257 6360 0.179037 GCTGCAGTGATGGCCATCTA 60.179 55.000 38.59 25.38 38.60 1.98
4424 6527 3.426787 TTGAAAAGGGAAGCCGTATCA 57.573 42.857 0.00 0.00 0.00 2.15
4431 6534 5.885912 TCTGGTATACATTGAAAAGGGAAGC 59.114 40.000 5.01 0.00 0.00 3.86
4565 6684 5.674052 AGTGCTACTGTTTCATCAGAGAT 57.326 39.130 0.65 0.00 38.63 2.75
4643 6762 4.656112 AGTTTACCCCTCTGGATGATGTAG 59.344 45.833 0.00 0.00 38.00 2.74
4664 6783 6.820656 CAGTCATCTTTCAGGTATTTAGCAGT 59.179 38.462 0.00 0.00 0.00 4.40
5374 10773 6.183360 ACAACCACTGTCAACAATTGTTAGAG 60.183 38.462 22.87 18.92 35.83 2.43
5991 12840 3.274288 CAGAAATAGCACCCCAGTCTTC 58.726 50.000 0.00 0.00 0.00 2.87
6222 14955 7.604164 GGATGATTTAACAGTCTTGTGAAGAGA 59.396 37.037 0.00 0.00 38.41 3.10
6271 15004 3.306019 CCTTTTACATGGCAGGTTCCAAC 60.306 47.826 11.12 0.00 39.96 3.77
6283 15016 3.433306 TCCTCACCCACCTTTTACATG 57.567 47.619 0.00 0.00 0.00 3.21
6375 15108 1.664965 GACGGACGCTCACTGCTTT 60.665 57.895 0.00 0.00 40.11 3.51
6448 15181 0.395311 TCGAGGAATAGCCCACGAGT 60.395 55.000 0.00 0.00 39.70 4.18
6452 15185 0.249657 CTGCTCGAGGAATAGCCCAC 60.250 60.000 15.58 0.00 37.37 4.61
6660 15394 0.904865 TCATCAACTCCGTCAGGCCT 60.905 55.000 0.00 0.00 37.47 5.19
6684 15418 2.219458 TCGACTCGAGAATAATCCGCT 58.781 47.619 21.68 0.00 0.00 5.52
6738 15475 9.891828 GTTTTTGTCATATAAAGTCACATGTCA 57.108 29.630 0.00 0.00 0.00 3.58
6842 15579 4.216257 ACAAAGTGTTGAATCAATCTCCGG 59.784 41.667 0.00 0.00 38.20 5.14
6908 15645 5.896432 CGAATCAATGTCCGAAGAATTTACG 59.104 40.000 0.00 0.00 0.00 3.18
6960 15697 6.094193 AGCTAATACGTATAAGAACACCCC 57.906 41.667 8.83 0.00 0.00 4.95
6975 15715 5.163437 ACTGCCTGTAGGTTGTAGCTAATAC 60.163 44.000 0.00 0.00 37.57 1.89
6991 15731 0.536006 GCTGACCTCAAACTGCCTGT 60.536 55.000 0.00 0.00 0.00 4.00
7005 15745 0.811616 CACTATCCTTGGCGGCTGAC 60.812 60.000 11.43 0.00 0.00 3.51
7274 16014 2.384828 GGTGTGGACCAAACCTCTTTT 58.615 47.619 24.86 0.00 42.59 2.27
7291 16031 4.228912 CACAACTTGCTCCTTTTAGGTG 57.771 45.455 0.00 0.00 36.53 4.00
7388 16129 4.437239 CACAAGTATCAGATCCTCCACAC 58.563 47.826 0.00 0.00 0.00 3.82
7402 16143 7.308770 CCATGCGATAATTCATTCCACAAGTAT 60.309 37.037 0.00 0.00 0.00 2.12
7514 16255 5.049129 CGATTTCCCTCTGATAATTTGCTCC 60.049 44.000 0.00 0.00 0.00 4.70
7562 16303 0.391130 GCACTGCCTTGATCGGTACA 60.391 55.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.