Multiple sequence alignment - TraesCS4D01G114100

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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 TraesCS4D01G114100 chr4D 100.000 4945 0 0 1 4945 94872795 94867851 0.000000e+00 9132.0
1 TraesCS4D01G114100 chr4D 84.962 133 18 2 1541 1672 503140660 503140791 3.110000e-27 134.0
2 TraesCS4D01G114100 chr4B 94.247 4102 160 25 881 4945 134376265 134372203 0.000000e+00 6198.0
3 TraesCS4D01G114100 chr4B 82.492 297 31 6 599 883 134376580 134376293 1.780000e-59 241.0
4 TraesCS4D01G114100 chr4B 84.483 116 16 2 1541 1655 648061781 648061895 4.050000e-21 113.0
5 TraesCS4D01G114100 chr4A 92.838 4147 217 41 1 4110 485457844 485461947 0.000000e+00 5939.0
6 TraesCS4D01G114100 chr4A 90.816 294 17 8 4653 4945 485461943 485462227 7.770000e-103 385.0
7 TraesCS4D01G114100 chr7D 79.167 720 116 20 3 694 364412351 364413064 7.500000e-128 468.0
8 TraesCS4D01G114100 chr7D 81.148 488 78 9 14 494 563902364 563901884 3.610000e-101 379.0
9 TraesCS4D01G114100 chr1A 80.581 551 94 11 2 547 301203658 301204200 3.560000e-111 412.0
10 TraesCS4D01G114100 chr2D 80.399 551 97 6 1 546 358039241 358038697 4.610000e-110 409.0
11 TraesCS4D01G114100 chr2D 100.000 29 0 0 660 688 118798635 118798663 2.000000e-03 54.7
12 TraesCS4D01G114100 chrUn 80.224 536 91 11 2 529 126963259 126963787 6.000000e-104 388.0
13 TraesCS4D01G114100 chr6D 79.626 535 93 12 1 529 312761802 312762326 2.170000e-98 370.0
14 TraesCS4D01G114100 chr6D 78.839 534 100 10 1 527 472960280 472959753 1.020000e-91 348.0
15 TraesCS4D01G114100 chr1B 78.637 543 101 13 14 552 404901257 404901788 3.660000e-91 346.0
16 TraesCS4D01G114100 chr5A 94.972 179 8 1 1496 1673 570528226 570528048 3.770000e-71 279.0
17 TraesCS4D01G114100 chr5A 83.846 130 19 2 1544 1672 687366217 687366089 6.720000e-24 122.0
18 TraesCS4D01G114100 chr3D 84.762 105 14 2 1543 1646 530415870 530415973 2.430000e-18 104.0


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 TraesCS4D01G114100 chr4D 94867851 94872795 4944 True 9132.0 9132 100.0000 1 4945 1 chr4D.!!$R1 4944
1 TraesCS4D01G114100 chr4B 134372203 134376580 4377 True 3219.5 6198 88.3695 599 4945 2 chr4B.!!$R1 4346
2 TraesCS4D01G114100 chr4A 485457844 485462227 4383 False 3162.0 5939 91.8270 1 4945 2 chr4A.!!$F1 4944
3 TraesCS4D01G114100 chr7D 364412351 364413064 713 False 468.0 468 79.1670 3 694 1 chr7D.!!$F1 691
4 TraesCS4D01G114100 chr1A 301203658 301204200 542 False 412.0 412 80.5810 2 547 1 chr1A.!!$F1 545
5 TraesCS4D01G114100 chr2D 358038697 358039241 544 True 409.0 409 80.3990 1 546 1 chr2D.!!$R1 545
6 TraesCS4D01G114100 chrUn 126963259 126963787 528 False 388.0 388 80.2240 2 529 1 chrUn.!!$F1 527
7 TraesCS4D01G114100 chr6D 312761802 312762326 524 False 370.0 370 79.6260 1 529 1 chr6D.!!$F1 528
8 TraesCS4D01G114100 chr6D 472959753 472960280 527 True 348.0 348 78.8390 1 527 1 chr6D.!!$R1 526
9 TraesCS4D01G114100 chr1B 404901257 404901788 531 False 346.0 346 78.6370 14 552 1 chr1B.!!$F1 538

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
688 729 0.179073 CGGTGTTGGAGATGCCCTAG 60.179 60.0 0.00 0.00 34.97 3.02 F
1638 1726 0.449388 GATTTTCCAGCTCGCAGGTG 59.551 55.0 7.97 7.97 42.96 4.00 F
2355 2443 0.456221 ACTACAAGCTCGATCGTGGG 59.544 55.0 15.94 7.95 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1981 0.241213 CGAACTGGACGCTCTTGAGA 59.759 55.0 1.30 0.0 0.00 3.27 R
2872 2963 0.970937 TGTTGTAGCCGGAGAGGGAG 60.971 60.0 5.05 0.0 41.48 4.30 R
4303 4403 0.988145 TGGAATAGCCTCCACCCAGG 60.988 60.0 0.00 0.0 40.71 4.45 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
63 67 0.734942 GCGCAATGTGCTTTCATGCT 60.735 50.000 12.00 0.00 42.25 3.79
99 104 2.027377 CACTTGCTGTCAGAAGATCCCT 60.027 50.000 3.32 0.00 0.00 4.20
109 116 1.047801 GAAGATCCCTCTCTGCTCCC 58.952 60.000 0.00 0.00 0.00 4.30
195 203 1.111116 CCCCGCCATCCTTCGTACTA 61.111 60.000 0.00 0.00 0.00 1.82
230 240 2.415168 TGGCGTTCGAAAATAAGCTCAG 59.585 45.455 0.00 0.00 0.00 3.35
238 248 6.169419 TCGAAAATAAGCTCAGTGACATTG 57.831 37.500 0.00 0.00 0.00 2.82
266 276 2.340809 CTAACGGGCGTGGTGACA 59.659 61.111 0.00 0.00 38.70 3.58
329 340 3.295800 GGACGTGTCCTAGGTGGG 58.704 66.667 9.08 0.00 46.16 4.61
336 347 4.753662 TCCTAGGTGGGCGACGCT 62.754 66.667 20.77 1.22 36.20 5.07
361 372 4.250305 AAGGCGAGTGGGTGCGTT 62.250 61.111 0.00 0.00 34.66 4.84
366 377 1.374125 CGAGTGGGTGCGTTGATGA 60.374 57.895 0.00 0.00 0.00 2.92
440 454 1.758514 GTCGGAGGAGGAGGATGCA 60.759 63.158 0.00 0.00 0.00 3.96
460 476 5.464030 GCAGATGCAAAATAAGGGATGAT 57.536 39.130 0.00 0.00 41.59 2.45
532 550 2.877300 GCGGGTGTCGGAGTCCTATATA 60.877 54.545 7.77 0.00 39.69 0.86
539 557 5.416326 GTGTCGGAGTCCTATATATCTGCTT 59.584 44.000 7.77 0.00 0.00 3.91
547 565 4.710375 TCCTATATATCTGCTTTCCGGACC 59.290 45.833 1.83 0.00 0.00 4.46
551 588 1.627297 ATCTGCTTTCCGGACCCCTC 61.627 60.000 1.83 0.00 0.00 4.30
564 601 1.897802 GACCCCTCTGTCTCCGTTTTA 59.102 52.381 0.00 0.00 32.39 1.52
574 611 5.987347 TCTGTCTCCGTTTTACGAGAAAAAT 59.013 36.000 0.05 0.00 46.05 1.82
575 612 5.981174 TGTCTCCGTTTTACGAGAAAAATG 58.019 37.500 0.05 0.00 46.05 2.32
576 613 4.844522 GTCTCCGTTTTACGAGAAAAATGC 59.155 41.667 0.05 0.00 46.05 3.56
577 614 3.801293 TCCGTTTTACGAGAAAAATGCG 58.199 40.909 0.05 0.00 46.05 4.73
578 615 3.248125 TCCGTTTTACGAGAAAAATGCGT 59.752 39.130 0.05 0.00 46.05 5.24
579 616 3.596562 CCGTTTTACGAGAAAAATGCGTC 59.403 43.478 0.05 0.00 46.05 5.19
580 617 4.451557 CGTTTTACGAGAAAAATGCGTCT 58.548 39.130 0.00 0.00 46.05 4.18
581 618 4.314708 CGTTTTACGAGAAAAATGCGTCTG 59.685 41.667 0.00 0.00 46.05 3.51
583 620 2.163818 ACGAGAAAAATGCGTCTGGA 57.836 45.000 0.00 0.00 31.98 3.86
584 621 1.798813 ACGAGAAAAATGCGTCTGGAC 59.201 47.619 0.00 0.00 31.98 4.02
586 623 1.128692 GAGAAAAATGCGTCTGGACCG 59.871 52.381 0.00 0.00 0.00 4.79
587 624 0.872388 GAAAAATGCGTCTGGACCGT 59.128 50.000 0.00 0.00 0.00 4.83
588 625 0.872388 AAAAATGCGTCTGGACCGTC 59.128 50.000 0.00 0.00 0.00 4.79
589 626 1.289109 AAAATGCGTCTGGACCGTCG 61.289 55.000 0.00 0.00 0.00 5.12
590 627 2.149803 AAATGCGTCTGGACCGTCGA 62.150 55.000 0.00 0.00 0.00 4.20
591 628 2.814183 AATGCGTCTGGACCGTCGAC 62.814 60.000 5.18 5.18 0.00 4.20
593 630 2.640989 CGTCTGGACCGTCGACAA 59.359 61.111 17.16 0.00 0.00 3.18
594 631 1.728426 CGTCTGGACCGTCGACAAC 60.728 63.158 17.16 5.75 0.00 3.32
595 632 1.372623 GTCTGGACCGTCGACAACC 60.373 63.158 17.16 14.94 0.00 3.77
596 633 2.048503 CTGGACCGTCGACAACCC 60.049 66.667 17.16 12.67 0.00 4.11
597 634 2.838693 TGGACCGTCGACAACCCA 60.839 61.111 17.16 15.11 0.00 4.51
609 648 1.142262 GACAACCCAATATAGGCCCGT 59.858 52.381 0.00 0.00 0.00 5.28
648 687 3.005472 CGTATAGACAACATGACCCGGAT 59.995 47.826 0.73 0.00 0.00 4.18
653 692 3.964688 AGACAACATGACCCGGATGTATA 59.035 43.478 0.73 0.00 32.74 1.47
688 729 0.179073 CGGTGTTGGAGATGCCCTAG 60.179 60.000 0.00 0.00 34.97 3.02
723 764 4.846779 TTGCACATTCCTTAACAGAACC 57.153 40.909 0.00 0.00 0.00 3.62
814 867 3.077359 CGCACAAGAAAGAAAGAGGGAT 58.923 45.455 0.00 0.00 0.00 3.85
822 875 0.990818 AGAAAGAGGGATGGAGGGGC 60.991 60.000 0.00 0.00 0.00 5.80
835 888 3.221771 TGGAGGGGCGATGATTTTTATG 58.778 45.455 0.00 0.00 0.00 1.90
887 970 1.381100 CAGCACTACAACGAACGTACG 59.619 52.381 15.01 15.01 39.31 3.67
890 973 0.951558 ACTACAACGAACGTACGGGT 59.048 50.000 21.06 11.45 37.61 5.28
956 1039 6.377429 CACAAGATAGTAACTGGACTGGACTA 59.623 42.308 0.00 0.00 0.00 2.59
980 1063 6.727824 GCACAAGGCTGGTATATATTACTG 57.272 41.667 0.00 0.00 40.25 2.74
1623 1711 4.856801 ATGCGCGAGGCCGGATTT 62.857 61.111 12.10 0.00 42.61 2.17
1635 1723 1.709147 CCGGATTTTCCAGCTCGCAG 61.709 60.000 0.00 0.00 35.91 5.18
1638 1726 0.449388 GATTTTCCAGCTCGCAGGTG 59.551 55.000 7.97 7.97 42.96 4.00
1720 1808 0.790124 GACGACGACGAGCTCTGTTC 60.790 60.000 15.32 4.54 42.66 3.18
1734 1822 2.235650 CTCTGTTCAGGATTCCAGAGCA 59.764 50.000 12.84 12.84 42.99 4.26
2091 2179 1.002430 AGAAGAGGCGAGCATGTTCAA 59.998 47.619 18.89 0.00 33.40 2.69
2352 2440 3.436496 GCTTAACTACAAGCTCGATCGT 58.564 45.455 15.94 0.00 46.04 3.73
2353 2441 3.240861 GCTTAACTACAAGCTCGATCGTG 59.759 47.826 15.94 14.19 46.04 4.35
2354 2442 2.279582 AACTACAAGCTCGATCGTGG 57.720 50.000 15.94 10.45 0.00 4.94
2355 2443 0.456221 ACTACAAGCTCGATCGTGGG 59.544 55.000 15.94 7.95 0.00 4.61
2356 2444 0.872021 CTACAAGCTCGATCGTGGGC 60.872 60.000 15.94 16.88 0.00 5.36
2394 2482 4.688879 AGTCTTCGATCGTTTAACATTGCA 59.311 37.500 15.94 0.00 0.00 4.08
2521 2609 3.494254 TGGCCCTTGGTCAACGGT 61.494 61.111 0.00 0.00 32.75 4.83
2650 2738 1.807573 GACGAGCAGCAGTACCAGC 60.808 63.158 0.00 0.00 0.00 4.85
2651 2739 2.219325 GACGAGCAGCAGTACCAGCT 62.219 60.000 4.69 4.69 44.62 4.24
2872 2963 0.882042 CTACATCACCGGCAGCATCC 60.882 60.000 0.00 0.00 0.00 3.51
2932 3023 1.431488 CGTCCAAGCCATGTCATCCG 61.431 60.000 0.00 0.00 0.00 4.18
3043 3134 1.578583 ATACCGAAATCGCTTTCCCG 58.421 50.000 6.18 0.00 37.99 5.14
3067 3158 2.710377 TCCATCACGGTTCAATCCAAG 58.290 47.619 0.00 0.00 35.57 3.61
3084 3175 3.343421 GTCACCCAACGGTCACGC 61.343 66.667 0.00 0.00 42.04 5.34
3385 3476 7.038729 GGATCCTACAATGACTTCATCTCCATA 60.039 40.741 3.84 0.00 35.10 2.74
3579 3670 3.663995 ATCAGAGATCGGCATCAAGAG 57.336 47.619 0.00 0.00 0.00 2.85
3604 3695 1.729586 TTGCTAGTGGAAGGGTGAGT 58.270 50.000 0.00 0.00 0.00 3.41
3622 3713 0.038343 GTGGTTGCAATGGCGTTGAT 60.038 50.000 23.09 0.00 45.35 2.57
3719 3810 3.182967 GTCGTCAAGCAGAAGGTCATAG 58.817 50.000 0.00 0.00 0.00 2.23
3821 3912 2.158914 TCCGGTGATGATGAAGGACATG 60.159 50.000 0.00 0.00 39.56 3.21
3834 3925 1.364328 AGGACATGAGGAGGAAGAGGT 59.636 52.381 0.00 0.00 0.00 3.85
4048 4140 5.748402 TCATCTCATGTACAAGAGGCAAAT 58.252 37.500 23.86 10.34 32.76 2.32
4104 4196 3.756434 GCTCTGGCACTGGTACAATTTTA 59.244 43.478 0.00 0.00 36.59 1.52
4106 4198 5.449177 GCTCTGGCACTGGTACAATTTTATC 60.449 44.000 0.00 0.00 36.59 1.75
4107 4199 5.815581 TCTGGCACTGGTACAATTTTATCT 58.184 37.500 0.00 0.00 38.70 1.98
4108 4200 6.245408 TCTGGCACTGGTACAATTTTATCTT 58.755 36.000 0.00 0.00 38.70 2.40
4109 4201 6.719370 TCTGGCACTGGTACAATTTTATCTTT 59.281 34.615 0.00 0.00 38.70 2.52
4137 4229 7.854557 TGTGATTGATTTCATCCAACTAGAG 57.145 36.000 0.00 0.00 0.00 2.43
4151 4243 5.303078 TCCAACTAGAGGCAAGTGAGATATC 59.697 44.000 0.00 0.00 0.00 1.63
4191 4283 1.699083 TCTGAGATCCTGTTGTTGCCA 59.301 47.619 0.00 0.00 0.00 4.92
4202 4294 4.218200 CCTGTTGTTGCCATGTTGAATCTA 59.782 41.667 0.00 0.00 0.00 1.98
4207 4299 2.009051 TGCCATGTTGAATCTAGTGCG 58.991 47.619 0.00 0.00 0.00 5.34
4229 4321 3.079578 TCTACTTCTCGTTGGTCATCGT 58.920 45.455 2.09 0.00 0.00 3.73
4250 4350 1.524002 CCGATGATGGAGTGTGCCT 59.476 57.895 0.00 0.00 0.00 4.75
4253 4353 1.673168 GATGATGGAGTGTGCCTTCC 58.327 55.000 0.00 0.00 32.63 3.46
4254 4354 1.211457 GATGATGGAGTGTGCCTTCCT 59.789 52.381 0.00 0.00 32.63 3.36
4255 4355 0.325933 TGATGGAGTGTGCCTTCCTG 59.674 55.000 0.00 0.00 32.63 3.86
4264 4364 2.296365 TGCCTTCCTGCTCCCTCTG 61.296 63.158 0.00 0.00 0.00 3.35
4298 4398 1.308216 CCCCCATGGTCCTCCTTCT 60.308 63.158 11.73 0.00 34.23 2.85
4299 4399 0.030092 CCCCCATGGTCCTCCTTCTA 60.030 60.000 11.73 0.00 34.23 2.10
4301 4401 0.753262 CCCATGGTCCTCCTTCTACG 59.247 60.000 11.73 0.00 34.23 3.51
4302 4402 0.753262 CCATGGTCCTCCTTCTACGG 59.247 60.000 2.57 0.00 34.23 4.02
4303 4403 0.105039 CATGGTCCTCCTTCTACGGC 59.895 60.000 0.00 0.00 34.23 5.68
4304 4404 1.049289 ATGGTCCTCCTTCTACGGCC 61.049 60.000 0.00 0.00 34.23 6.13
4305 4405 1.381463 GGTCCTCCTTCTACGGCCT 60.381 63.158 0.00 0.00 0.00 5.19
4306 4406 1.677637 GGTCCTCCTTCTACGGCCTG 61.678 65.000 0.00 0.00 0.00 4.85
4387 4487 4.614673 GCTCGTGCAAGTGGTTTG 57.385 55.556 4.26 0.00 39.88 2.93
4403 4503 2.583143 GTTTGGTTCAAGGCTAGTGGT 58.417 47.619 0.00 0.00 0.00 4.16
4432 4532 0.890542 TTTGCGATGCTTGTGCTCCT 60.891 50.000 0.00 0.00 40.48 3.69
4433 4533 1.579964 TTGCGATGCTTGTGCTCCTG 61.580 55.000 0.00 0.00 40.48 3.86
4440 4540 1.849976 GCTTGTGCTCCTGTCACAGC 61.850 60.000 0.00 0.00 44.18 4.40
4451 4551 0.532640 TGTCACAGCAACATGTCGCT 60.533 50.000 5.18 5.18 39.66 4.93
4464 4564 1.278637 GTCGCTGTTTTGGTGGTCG 59.721 57.895 0.00 0.00 0.00 4.79
4475 4575 0.604243 TGGTGGTCGAATTTGGGTCG 60.604 55.000 0.00 0.00 39.88 4.79
4477 4577 1.232119 GTGGTCGAATTTGGGTCGTT 58.768 50.000 0.00 0.00 39.52 3.85
4514 4614 4.515191 GCTACAAGTTCTTGTTGTGGATGA 59.485 41.667 20.66 2.76 38.33 2.92
4518 4618 5.829924 ACAAGTTCTTGTTGTGGATGATTCT 59.170 36.000 11.75 0.00 36.76 2.40
4544 4644 3.441101 TCCATGCTAGTCTAGGTTGTGT 58.559 45.455 8.97 0.00 0.00 3.72
4547 4647 5.661312 TCCATGCTAGTCTAGGTTGTGTATT 59.339 40.000 8.97 0.00 0.00 1.89
4557 4657 8.643324 AGTCTAGGTTGTGTATTATCATCTTCC 58.357 37.037 0.00 0.00 0.00 3.46
4578 4678 0.736325 CTCGTGGATCGCCGACTTTT 60.736 55.000 0.00 0.00 39.67 2.27
4603 4703 5.221204 GGGTTACTGATCCTAGGTCGTTTAG 60.221 48.000 9.08 3.07 0.00 1.85
4624 4724 5.615925 AGGTTTTCTCAGTTGAGTAGTGT 57.384 39.130 8.85 0.00 42.60 3.55
4625 4725 5.990668 AGGTTTTCTCAGTTGAGTAGTGTT 58.009 37.500 8.85 0.00 42.60 3.32
4657 4757 1.742268 GTCTGCCTCATGCCTTCTTTC 59.258 52.381 0.00 0.00 40.16 2.62
4755 4855 5.514274 TTTCCTGGTTCTGTCAAAATGTC 57.486 39.130 0.00 0.00 0.00 3.06
4758 4858 3.490348 CTGGTTCTGTCAAAATGTCCCT 58.510 45.455 0.00 0.00 0.00 4.20
4759 4859 4.506625 CCTGGTTCTGTCAAAATGTCCCTA 60.507 45.833 0.00 0.00 0.00 3.53
4806 4911 5.874810 TCATTCTAAATTCCGGACAACAGAG 59.125 40.000 1.83 0.00 0.00 3.35
4810 4915 6.761312 TCTAAATTCCGGACAACAGAGTTTA 58.239 36.000 1.83 0.00 0.00 2.01
4814 4943 5.934935 TTCCGGACAACAGAGTTTATTTC 57.065 39.130 1.83 0.00 0.00 2.17
4830 4959 7.848128 AGTTTATTTCCTATCGTCTCCTTGAA 58.152 34.615 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 67 4.508492 CAGCAAGTGCATGAATTGTTTCAA 59.492 37.500 6.00 0.00 45.16 2.69
109 116 0.179056 ATCCACGGGTTTCATAGGCG 60.179 55.000 0.00 0.00 0.00 5.52
230 240 0.872388 GGTGTTCGGTCCAATGTCAC 59.128 55.000 0.00 0.00 0.00 3.67
238 248 1.079612 CCCGTTAGGTGTTCGGTCC 60.080 63.158 0.00 0.00 42.30 4.46
266 276 1.374252 GACGACGTCCATGCTGGTT 60.374 57.895 17.25 0.00 39.03 3.67
297 308 2.919229 CACGTCCGTAGACAATTACACC 59.081 50.000 0.00 0.00 43.73 4.16
329 340 2.240500 CCTTCTATGGCAGCGTCGC 61.241 63.158 9.80 9.80 0.00 5.19
343 354 4.681978 ACGCACCCACTCGCCTTC 62.682 66.667 0.00 0.00 0.00 3.46
352 363 0.251121 AACCATCATCAACGCACCCA 60.251 50.000 0.00 0.00 0.00 4.51
361 372 0.107703 GACCTCCGCAACCATCATCA 60.108 55.000 0.00 0.00 0.00 3.07
440 454 6.723052 CCCTTATCATCCCTTATTTTGCATCT 59.277 38.462 0.00 0.00 0.00 2.90
456 470 3.138283 TCTTTCAATCCGGCCCTTATCAT 59.862 43.478 0.00 0.00 0.00 2.45
457 471 2.507886 TCTTTCAATCCGGCCCTTATCA 59.492 45.455 0.00 0.00 0.00 2.15
460 476 3.443145 TTTCTTTCAATCCGGCCCTTA 57.557 42.857 0.00 0.00 0.00 2.69
512 529 1.906990 ATATAGGACTCCGACACCCG 58.093 55.000 0.00 0.00 38.18 5.28
532 550 1.616628 AGGGGTCCGGAAAGCAGAT 60.617 57.895 5.23 0.00 0.00 2.90
539 557 1.305046 GAGACAGAGGGGTCCGGAA 60.305 63.158 5.23 0.00 38.59 4.30
547 565 1.542915 TCGTAAAACGGAGACAGAGGG 59.457 52.381 0.00 0.00 42.81 4.30
551 588 5.646467 TTTTTCTCGTAAAACGGAGACAG 57.354 39.130 0.00 0.00 42.81 3.51
564 601 1.798813 GTCCAGACGCATTTTTCTCGT 59.201 47.619 0.00 0.00 39.33 4.18
574 611 4.034258 GTCGACGGTCCAGACGCA 62.034 66.667 0.00 0.00 34.00 5.24
575 612 3.547249 TTGTCGACGGTCCAGACGC 62.547 63.158 11.62 0.00 37.69 5.19
576 613 1.728426 GTTGTCGACGGTCCAGACG 60.728 63.158 11.62 0.00 37.69 4.18
577 614 1.372623 GGTTGTCGACGGTCCAGAC 60.373 63.158 11.62 5.94 35.61 3.51
578 615 2.567497 GGGTTGTCGACGGTCCAGA 61.567 63.158 19.67 0.00 0.00 3.86
579 616 2.048503 GGGTTGTCGACGGTCCAG 60.049 66.667 19.67 0.00 0.00 3.86
580 617 1.760479 ATTGGGTTGTCGACGGTCCA 61.760 55.000 19.67 18.04 0.00 4.02
581 618 0.247185 TATTGGGTTGTCGACGGTCC 59.753 55.000 11.62 12.37 0.00 4.46
583 620 2.101917 CCTATATTGGGTTGTCGACGGT 59.898 50.000 11.62 0.00 0.00 4.83
584 621 2.750948 CCTATATTGGGTTGTCGACGG 58.249 52.381 11.62 0.00 0.00 4.79
586 623 2.490991 GGCCTATATTGGGTTGTCGAC 58.509 52.381 9.11 9.11 0.00 4.20
587 624 1.418637 GGGCCTATATTGGGTTGTCGA 59.581 52.381 0.84 0.00 0.00 4.20
588 625 1.876416 CGGGCCTATATTGGGTTGTCG 60.876 57.143 0.84 0.00 0.00 4.35
589 626 1.142262 ACGGGCCTATATTGGGTTGTC 59.858 52.381 0.84 0.00 0.00 3.18
590 627 1.133915 CACGGGCCTATATTGGGTTGT 60.134 52.381 0.84 0.00 0.00 3.32
591 628 1.133915 ACACGGGCCTATATTGGGTTG 60.134 52.381 0.84 0.00 0.00 3.77
593 630 1.133915 CAACACGGGCCTATATTGGGT 60.134 52.381 0.84 0.00 0.00 4.51
594 631 1.604604 CAACACGGGCCTATATTGGG 58.395 55.000 0.84 0.00 0.00 4.12
595 632 1.142060 TCCAACACGGGCCTATATTGG 59.858 52.381 17.99 17.99 38.35 3.16
596 633 2.631160 TCCAACACGGGCCTATATTG 57.369 50.000 0.84 2.96 34.36 1.90
597 634 2.708861 TCATCCAACACGGGCCTATATT 59.291 45.455 0.84 0.00 34.36 1.28
629 668 2.771943 ACATCCGGGTCATGTTGTCTAT 59.228 45.455 0.00 0.00 29.75 1.98
630 669 2.184533 ACATCCGGGTCATGTTGTCTA 58.815 47.619 0.00 0.00 29.75 2.59
648 687 3.487376 CGACTCTTAAACGCCCGTATACA 60.487 47.826 3.32 0.00 0.00 2.29
653 692 1.080298 CCGACTCTTAAACGCCCGT 60.080 57.895 0.00 0.00 0.00 5.28
688 729 4.086547 GCAAAGCATGTGGGGGCC 62.087 66.667 0.00 0.00 0.00 5.80
814 867 3.221771 CATAAAAATCATCGCCCCTCCA 58.778 45.455 0.00 0.00 0.00 3.86
822 875 6.974677 ATTAGCGTTGCATAAAAATCATCG 57.025 33.333 0.00 0.00 0.00 3.84
835 888 6.900299 GTGTTAAGATGTCTAATTAGCGTTGC 59.100 38.462 7.67 0.00 0.00 4.17
887 970 8.512138 GCATGGATATTGTAAGTTATTGTACCC 58.488 37.037 0.00 0.00 0.00 3.69
976 1059 5.594725 TGGTCTGTGTTAATTTTTGGCAGTA 59.405 36.000 0.00 0.00 0.00 2.74
978 1061 4.942852 TGGTCTGTGTTAATTTTTGGCAG 58.057 39.130 0.00 0.00 0.00 4.85
979 1062 5.112686 GTTGGTCTGTGTTAATTTTTGGCA 58.887 37.500 0.00 0.00 0.00 4.92
980 1063 4.509970 GGTTGGTCTGTGTTAATTTTTGGC 59.490 41.667 0.00 0.00 0.00 4.52
1158 1246 4.101448 GCCTGCCTCACCACGGAT 62.101 66.667 0.00 0.00 0.00 4.18
1281 1369 3.992641 TGGGAGTGGGAGCGGAGA 61.993 66.667 0.00 0.00 0.00 3.71
1623 1711 1.004560 CTTCACCTGCGAGCTGGAA 60.005 57.895 24.46 10.52 38.26 3.53
1635 1723 0.313043 TCTCGACGTTGTCCTTCACC 59.687 55.000 1.96 0.00 0.00 4.02
1638 1726 1.699343 CCTTCTCGACGTTGTCCTTC 58.301 55.000 1.96 0.00 0.00 3.46
1691 1779 0.455464 CGTCGTCGTCATGTTAGCCA 60.455 55.000 0.00 0.00 0.00 4.75
1720 1808 2.005451 CGACTTTGCTCTGGAATCCTG 58.995 52.381 0.00 0.00 0.00 3.86
1893 1981 0.241213 CGAACTGGACGCTCTTGAGA 59.759 55.000 1.30 0.00 0.00 3.27
2091 2179 0.539901 AGTACTGTGAGTGTCCGCCT 60.540 55.000 0.00 0.00 0.00 5.52
2349 2437 3.755628 GTAGCCACGAGCCCACGA 61.756 66.667 0.00 0.00 45.47 4.35
2350 2438 3.296709 AAGTAGCCACGAGCCCACG 62.297 63.158 0.00 0.00 45.47 4.94
2351 2439 1.448013 GAAGTAGCCACGAGCCCAC 60.448 63.158 0.00 0.00 45.47 4.61
2352 2440 2.978824 GAAGTAGCCACGAGCCCA 59.021 61.111 0.00 0.00 45.47 5.36
2353 2441 2.202756 CGAAGTAGCCACGAGCCC 60.203 66.667 0.00 0.00 45.47 5.19
2354 2442 1.226717 CTCGAAGTAGCCACGAGCC 60.227 63.158 0.00 0.00 44.67 4.70
2355 2443 4.386245 CTCGAAGTAGCCACGAGC 57.614 61.111 0.00 0.00 44.67 5.03
2432 2520 5.411361 ACGAACGAAAATCAATCAATCAGGA 59.589 36.000 0.14 0.00 0.00 3.86
2650 2738 2.348666 GCATGTACGTACCTGCTGAAAG 59.651 50.000 34.57 11.79 42.23 2.62
2651 2739 2.289133 TGCATGTACGTACCTGCTGAAA 60.289 45.455 37.98 24.72 44.63 2.69
2872 2963 0.970937 TGTTGTAGCCGGAGAGGGAG 60.971 60.000 5.05 0.00 41.48 4.30
2998 3089 2.196749 CACCGAGGAAGATCACGAATG 58.803 52.381 0.00 0.00 0.00 2.67
3043 3134 2.618709 GGATTGAACCGTGATGGATTCC 59.381 50.000 0.00 0.00 42.00 3.01
3589 3680 1.697432 CAACCACTCACCCTTCCACTA 59.303 52.381 0.00 0.00 0.00 2.74
3604 3695 1.539157 TATCAACGCCATTGCAACCA 58.461 45.000 0.00 0.00 38.29 3.67
3622 3713 2.364972 TGGCATCCTCGAGACTGATA 57.635 50.000 15.71 0.89 0.00 2.15
3719 3810 4.070552 ACTGTCTTCCTCGCCGCC 62.071 66.667 0.00 0.00 0.00 6.13
3821 3912 5.245075 CACTATCCAATACCTCTTCCTCCTC 59.755 48.000 0.00 0.00 0.00 3.71
3834 3925 5.241728 CAGATCTCCACGTCACTATCCAATA 59.758 44.000 0.00 0.00 0.00 1.90
4048 4140 9.693739 AAAGACCAAACACCAATATACATATGA 57.306 29.630 10.38 0.00 0.00 2.15
4132 4224 6.647334 TGAAGATATCTCACTTGCCTCTAG 57.353 41.667 5.51 0.00 0.00 2.43
4137 4229 7.172361 GGATAGTTTGAAGATATCTCACTTGCC 59.828 40.741 5.51 7.30 0.00 4.52
4151 4243 7.227711 TCTCAGACGATCTAGGATAGTTTGAAG 59.772 40.741 12.24 8.53 40.38 3.02
4191 4283 5.584253 AGTAGACGCACTAGATTCAACAT 57.416 39.130 0.00 0.00 0.00 2.71
4202 4294 1.068472 CCAACGAGAAGTAGACGCACT 60.068 52.381 0.00 0.00 0.00 4.40
4207 4299 3.119919 ACGATGACCAACGAGAAGTAGAC 60.120 47.826 6.68 0.00 0.00 2.59
4229 4321 1.971505 GCACACTCCATCATCGGGGA 61.972 60.000 0.00 0.00 0.00 4.81
4264 4364 3.443588 GGTGAACAGCCACAACCC 58.556 61.111 0.00 0.00 38.74 4.11
4296 4396 2.363795 CTCCACCCAGGCCGTAGA 60.364 66.667 0.00 0.00 37.29 2.59
4303 4403 0.988145 TGGAATAGCCTCCACCCAGG 60.988 60.000 0.00 0.00 40.71 4.45
4304 4404 2.620234 TGGAATAGCCTCCACCCAG 58.380 57.895 0.00 0.00 40.71 4.45
4305 4405 4.931292 TGGAATAGCCTCCACCCA 57.069 55.556 0.00 0.00 40.71 4.51
4387 4487 4.489306 AATCTACCACTAGCCTTGAACC 57.511 45.455 0.00 0.00 0.00 3.62
4403 4503 6.718388 CACAAGCATCGCAAAGATAAATCTA 58.282 36.000 0.00 0.00 37.52 1.98
4432 4532 1.941072 GCGACATGTTGCTGTGACA 59.059 52.632 27.68 0.00 37.03 3.58
4433 4533 4.826600 GCGACATGTTGCTGTGAC 57.173 55.556 27.68 0.77 37.03 3.67
4440 4540 2.118683 CACCAAAACAGCGACATGTTG 58.881 47.619 8.88 8.88 42.49 3.33
4451 4551 2.101582 CCCAAATTCGACCACCAAAACA 59.898 45.455 0.00 0.00 0.00 2.83
4464 4564 4.387559 GCCACATTAAAACGACCCAAATTC 59.612 41.667 0.00 0.00 0.00 2.17
4475 4575 2.745281 TGTAGCCGAGCCACATTAAAAC 59.255 45.455 0.00 0.00 0.00 2.43
4477 4577 2.772077 TGTAGCCGAGCCACATTAAA 57.228 45.000 0.00 0.00 0.00 1.52
4514 4614 6.328672 ACCTAGACTAGCATGGAATCAAGAAT 59.671 38.462 3.76 0.00 0.00 2.40
4518 4618 5.189736 ACAACCTAGACTAGCATGGAATCAA 59.810 40.000 3.76 0.00 0.00 2.57
4557 4657 2.543687 AAGTCGGCGATCCACGAGTG 62.544 60.000 14.79 0.00 45.77 3.51
4569 4669 1.886886 TCAGTAACCCAAAAGTCGGC 58.113 50.000 0.00 0.00 0.00 5.54
4570 4670 3.007635 GGATCAGTAACCCAAAAGTCGG 58.992 50.000 0.00 0.00 0.00 4.79
4578 4678 2.024655 ACGACCTAGGATCAGTAACCCA 60.025 50.000 17.98 0.00 0.00 4.51
4603 4703 5.504173 GCAACACTACTCAACTGAGAAAACC 60.504 44.000 13.61 0.00 44.74 3.27
4624 4724 1.580942 GCAGACATCGCCAAAGCAA 59.419 52.632 0.00 0.00 39.83 3.91
4625 4725 3.266964 GCAGACATCGCCAAAGCA 58.733 55.556 0.00 0.00 39.83 3.91
4648 4748 6.690194 AGATGATACAACATGAAAGAAGGC 57.310 37.500 0.00 0.00 0.00 4.35
4709 4809 1.291877 GCTCGCTTGCTTCTCCGAAA 61.292 55.000 0.00 0.00 0.00 3.46
4793 4898 4.041198 AGGAAATAAACTCTGTTGTCCGGA 59.959 41.667 0.00 0.00 0.00 5.14
4806 4911 8.664211 ATTCAAGGAGACGATAGGAAATAAAC 57.336 34.615 0.00 0.00 43.77 2.01
4810 4915 8.581253 AAAAATTCAAGGAGACGATAGGAAAT 57.419 30.769 0.00 0.00 43.77 2.17


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

AutoCloner maintained by Alex Coulton.