Multiple sequence alignment - TraesCS3B01G309400

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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 TraesCS3B01G309400 chr3B 100.000 7350 0 0 1 7350 498051672 498059021 0.000000e+00 13573
1 TraesCS3B01G309400 chr3B 80.508 472 67 18 12 468 109069912 109069451 9.130000e-89 339
2 TraesCS3B01G309400 chr3D 94.419 6432 241 53 946 7337 382097786 382104139 0.000000e+00 9780
3 TraesCS3B01G309400 chr3D 90.295 1185 74 15 5732 6912 382497853 382499000 0.000000e+00 1513
4 TraesCS3B01G309400 chr3D 86.510 1023 79 21 1 993 382486483 382487476 0.000000e+00 1070
5 TraesCS3B01G309400 chr3D 88.259 494 32 11 6862 7339 382499000 382499483 1.070000e-157 568
6 TraesCS3B01G309400 chr3D 82.432 444 60 4 472 897 382097217 382097660 9.010000e-99 372
7 TraesCS3B01G309400 chr3D 80.081 492 71 16 1 479 448848348 448848825 2.540000e-89 340
8 TraesCS3B01G309400 chr3D 91.358 162 7 3 5568 5729 382496416 382496570 1.610000e-51 215
9 TraesCS3B01G309400 chr3D 97.468 79 2 0 5504 5582 382495161 382495239 1.290000e-27 135
10 TraesCS3B01G309400 chr3D 82.993 147 17 6 1009 1151 382488478 382488620 7.740000e-25 126
11 TraesCS3B01G309400 chr3A 94.778 4941 161 46 942 5833 505226515 505231407 0.000000e+00 7605
12 TraesCS3B01G309400 chr3A 94.559 1507 56 3 5831 7337 505231488 505232968 0.000000e+00 2305
13 TraesCS3B01G309400 chr2B 86.535 505 43 13 1 483 405670134 405669633 3.900000e-147 532
14 TraesCS3B01G309400 chr2B 85.656 488 52 10 13 483 641272592 641272106 1.420000e-136 497
15 TraesCS3B01G309400 chr2B 82.794 494 64 14 1 483 255326613 255327096 8.820000e-114 422
16 TraesCS3B01G309400 chr2B 81.799 478 76 10 13 481 382879320 382878845 2.490000e-104 390
17 TraesCS3B01G309400 chr5D 86.735 490 43 12 13 481 499599469 499598981 6.530000e-145 525
18 TraesCS3B01G309400 chr4D 86.200 500 43 13 1 477 21790972 21791468 1.090000e-142 518
19 TraesCS3B01G309400 chr5A 84.679 483 58 11 12 482 299635560 299635082 1.120000e-127 468
20 TraesCS3B01G309400 chr7B 82.828 495 66 14 1 481 295877885 295877396 6.820000e-115 425
21 TraesCS3B01G309400 chr1D 80.762 499 71 18 1 482 366650885 366651375 4.190000e-97 366
22 TraesCS3B01G309400 chr1B 80.361 499 73 18 1 482 200319730 200319240 9.070000e-94 355


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 TraesCS3B01G309400 chr3B 498051672 498059021 7349 False 13573.00 13573 100.0000 1 7350 1 chr3B.!!$F1 7349
1 TraesCS3B01G309400 chr3D 382097217 382104139 6922 False 5076.00 9780 88.4255 472 7337 2 chr3D.!!$F2 6865
2 TraesCS3B01G309400 chr3D 382495161 382499483 4322 False 607.75 1513 91.8450 5504 7339 4 chr3D.!!$F4 1835
3 TraesCS3B01G309400 chr3D 382486483 382488620 2137 False 598.00 1070 84.7515 1 1151 2 chr3D.!!$F3 1150
4 TraesCS3B01G309400 chr3A 505226515 505232968 6453 False 4955.00 7605 94.6685 942 7337 2 chr3A.!!$F1 6395
5 TraesCS3B01G309400 chr2B 405669633 405670134 501 True 532.00 532 86.5350 1 483 1 chr2B.!!$R2 482

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
778 823 0.032017 ACCGCCTCCTCCTATGTCTT 60.032 55.000 0.00 0.00 0.0 3.01 F
1538 2675 0.727398 GGTTACGTGGATGCTGCTTC 59.273 55.000 0.00 6.97 0.0 3.86 F
2686 3833 3.190535 ACCCTACAACAAAAGCGCAATAG 59.809 43.478 11.47 0.00 0.0 1.73 F
2841 3990 1.965643 ACCCGTCTAACACAAGCTACA 59.034 47.619 0.00 0.00 0.0 2.74 F
4157 5325 1.278985 TCCGTCTGCAACTTCCATCAT 59.721 47.619 0.00 0.00 0.0 2.45 F
4443 5618 1.737838 TGAATGGTTGCAGTCCGATC 58.262 50.000 5.72 6.69 0.0 3.69 F
5764 9427 1.415659 ACTAGGGATGCATGCAGACTC 59.584 52.381 26.69 20.98 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 2875 1.203994 CAGCTTGCTCCATCCAAAAGG 59.796 52.381 0.00 0.00 0.00 3.11 R
2813 3962 3.167485 TGTGTTAGACGGGTATCCAACT 58.833 45.455 0.00 0.00 0.00 3.16 R
4134 5302 0.468226 TGGAAGTTGCAGACGGACTT 59.532 50.000 0.36 0.36 36.40 3.01 R
4443 5618 1.358152 TCTTCCCCAACAGGTACCAG 58.642 55.000 15.94 9.05 0.00 4.00 R
5296 6485 0.417841 AGGGGAAGGAGAGGCTACAA 59.582 55.000 0.00 0.00 0.00 2.41 R
5809 9474 0.536724 TAGTGGCTGATGCGTGATGT 59.463 50.000 0.00 0.00 40.82 3.06 R
6998 10815 1.141881 CCCCTCCACAAGTCGATCG 59.858 63.158 9.36 9.36 0.00 3.69 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
90 91 5.989168 CCTTGAATACCGTCATAACTATGCA 59.011 40.000 0.00 0.00 33.76 3.96
99 100 6.534079 ACCGTCATAACTATGCACTTTTCTAC 59.466 38.462 0.00 0.00 33.76 2.59
109 110 2.671070 GCACTTTTCTACCAATTGCCCG 60.671 50.000 0.00 0.00 0.00 6.13
116 117 2.167693 TCTACCAATTGCCCGACAGTAG 59.832 50.000 0.00 4.85 0.00 2.57
230 235 7.909641 ACACAAAAATACTTTGCTGCAATTTTC 59.090 29.630 16.77 0.00 30.61 2.29
294 302 7.232534 ACCACTACAAGATTTAATCCTTGCAAA 59.767 33.333 0.00 0.00 42.46 3.68
300 308 8.815912 ACAAGATTTAATCCTTGCAAATAACCT 58.184 29.630 0.00 0.00 42.46 3.50
318 326 1.453155 CTCCAAGGGGATTGACAACG 58.547 55.000 0.00 0.00 43.91 4.10
326 334 1.197721 GGGATTGACAACGCTCTTGTG 59.802 52.381 1.62 0.00 31.96 3.33
361 374 0.529833 TTTTGTGTGTGTGCAGGTGG 59.470 50.000 0.00 0.00 0.00 4.61
381 394 2.937799 GGTGTTCACGAGGTTTTGTGTA 59.062 45.455 0.00 0.00 39.36 2.90
408 435 9.745018 ATTCTTCACCTTGATTCTTAATTGAGA 57.255 29.630 0.00 0.00 0.00 3.27
453 481 2.883026 CATATCCTCTCCTCTTCGGGT 58.117 52.381 0.00 0.00 0.00 5.28
483 511 0.321122 GCAGCTCACAAGTAGCAGGT 60.321 55.000 0.00 0.00 42.62 4.00
496 524 0.179062 AGCAGGTTCCTCATCATCGC 60.179 55.000 0.00 0.00 0.00 4.58
497 525 0.462581 GCAGGTTCCTCATCATCGCA 60.463 55.000 0.00 0.00 0.00 5.10
498 526 1.579698 CAGGTTCCTCATCATCGCAG 58.420 55.000 0.00 0.00 0.00 5.18
499 527 1.134580 CAGGTTCCTCATCATCGCAGT 60.135 52.381 0.00 0.00 0.00 4.40
509 539 0.323816 TCATCGCAGTCTGGACCTCT 60.324 55.000 1.14 0.00 0.00 3.69
535 565 0.178926 TTGTCGAGGGGGTGAGGTTA 60.179 55.000 0.00 0.00 0.00 2.85
569 599 4.451150 GGGCCGACGCACAGATGA 62.451 66.667 0.00 0.00 38.75 2.92
598 628 3.151906 GTGAGGCTGACACCCACT 58.848 61.111 0.00 0.00 31.78 4.00
600 630 1.459348 TGAGGCTGACACCCACTGA 60.459 57.895 0.00 0.00 0.00 3.41
718 763 2.360350 ATGGTGTCGCCCTTGCAG 60.360 61.111 0.00 0.00 37.32 4.41
729 774 1.591703 CCTTGCAGTAGGTCTCGCA 59.408 57.895 0.00 0.00 0.00 5.10
778 823 0.032017 ACCGCCTCCTCCTATGTCTT 60.032 55.000 0.00 0.00 0.00 3.01
851 898 1.032014 CCAAGGGCCACATTTATCCG 58.968 55.000 6.18 0.00 0.00 4.18
860 907 4.142271 GGCCACATTTATCCGATTTTGTGA 60.142 41.667 14.74 0.00 37.28 3.58
1063 2186 1.079956 CGAAGCAGAGCAGAGCAGT 60.080 57.895 0.00 0.00 0.00 4.40
1263 2396 4.803426 CAGGTCGAGGAGTGGCGC 62.803 72.222 0.00 0.00 0.00 6.53
1377 2510 2.966732 CGGCCAGGAAGTAAGCCCA 61.967 63.158 2.24 0.00 42.66 5.36
1444 2577 1.152860 CTAGGCTCTGCTCCTCCGA 60.153 63.158 0.00 0.00 35.21 4.55
1472 2605 2.027897 TGTAGTTTCGTGCGGCGT 59.972 55.556 9.37 0.00 42.13 5.68
1526 2660 1.273327 CGGTTGGAGGTTAGGTTACGT 59.727 52.381 0.00 0.00 0.00 3.57
1530 2664 2.823959 TGGAGGTTAGGTTACGTGGAT 58.176 47.619 0.00 0.00 0.00 3.41
1538 2675 0.727398 GGTTACGTGGATGCTGCTTC 59.273 55.000 0.00 6.97 0.00 3.86
1557 2703 4.865925 GCTTCAATTGTGAATGCAATGCTA 59.134 37.500 6.82 0.00 42.85 3.49
1729 2875 3.370061 GCAAACCGTACAGTGAATACCTC 59.630 47.826 0.00 0.00 0.00 3.85
1730 2876 3.881937 AACCGTACAGTGAATACCTCC 57.118 47.619 0.00 0.00 0.00 4.30
2366 3513 6.639632 AACTGCATTGTTCTATCAAACTGT 57.360 33.333 0.00 0.00 0.00 3.55
2526 3673 7.624360 TGAGATGTGTTTCAACAACTACTTT 57.376 32.000 0.00 0.00 41.21 2.66
2545 3692 7.819900 ACTACTTTTCCAGTGCTGAACTAATAG 59.180 37.037 0.02 0.00 36.83 1.73
2686 3833 3.190535 ACCCTACAACAAAAGCGCAATAG 59.809 43.478 11.47 0.00 0.00 1.73
2687 3834 3.427503 CCCTACAACAAAAGCGCAATAGG 60.428 47.826 11.47 8.10 0.00 2.57
2791 3940 6.713762 ATTCAGTGTTTTGATCAAACTGGA 57.286 33.333 26.94 22.79 44.68 3.86
2813 3962 8.815565 TGGAATGCTTCATTTTACCTTGTATA 57.184 30.769 0.00 0.00 33.90 1.47
2841 3990 1.965643 ACCCGTCTAACACAAGCTACA 59.034 47.619 0.00 0.00 0.00 2.74
2842 3991 2.366266 ACCCGTCTAACACAAGCTACAA 59.634 45.455 0.00 0.00 0.00 2.41
2843 3992 2.993899 CCCGTCTAACACAAGCTACAAG 59.006 50.000 0.00 0.00 0.00 3.16
2844 3993 2.412089 CCGTCTAACACAAGCTACAAGC 59.588 50.000 0.00 0.00 42.84 4.01
2845 3994 2.412089 CGTCTAACACAAGCTACAAGCC 59.588 50.000 0.00 0.00 43.77 4.35
2846 3995 3.665190 GTCTAACACAAGCTACAAGCCT 58.335 45.455 0.00 0.00 43.77 4.58
2847 3996 4.617530 CGTCTAACACAAGCTACAAGCCTA 60.618 45.833 0.00 0.00 43.77 3.93
2848 3997 4.626172 GTCTAACACAAGCTACAAGCCTAC 59.374 45.833 0.00 0.00 43.77 3.18
2892 4041 2.631062 ACCTGAGGTTCATCACAACGTA 59.369 45.455 0.00 0.00 27.29 3.57
3014 4169 5.023533 TCTCTTACAAGAACACAAGCAGT 57.976 39.130 0.00 0.00 34.03 4.40
3253 4410 4.142600 CCAAGGTCTGCTTTGTATGCTTAC 60.143 45.833 2.86 2.86 30.74 2.34
3337 4494 2.136298 TTGTGTGTTTCCAGGCTTCA 57.864 45.000 0.00 0.00 0.00 3.02
3529 4692 8.427276 TCTCATAAATCATCATAGTGCAGAAGT 58.573 33.333 0.00 0.00 0.00 3.01
3615 4778 4.933400 TGGTAGTCGAAAAATAGCACCTTC 59.067 41.667 0.00 0.00 0.00 3.46
3619 4782 2.415168 TCGAAAAATAGCACCTTCGCAG 59.585 45.455 0.00 0.00 40.27 5.18
3765 4929 7.899648 AATGTAGTGCTCCTTACAGTATACT 57.100 36.000 0.00 0.00 0.00 2.12
3839 5006 4.158579 TGACATCATTCTTGCGAGAGTAGT 59.841 41.667 3.32 1.34 32.44 2.73
3840 5007 5.078411 ACATCATTCTTGCGAGAGTAGTT 57.922 39.130 3.32 0.00 32.44 2.24
3841 5008 4.867047 ACATCATTCTTGCGAGAGTAGTTG 59.133 41.667 3.32 6.38 32.44 3.16
3929 5096 8.980481 TGAATCAGGGGTAAATATTCTTCTTC 57.020 34.615 0.00 0.00 0.00 2.87
4018 5186 6.660521 TCATTTGGTCATCAAGATTGCTTACT 59.339 34.615 0.00 0.00 36.62 2.24
4019 5187 5.885230 TTGGTCATCAAGATTGCTTACTG 57.115 39.130 0.00 0.00 31.81 2.74
4044 5212 7.393796 TGGACACCAAAGTTTTTCTGTACTTTA 59.606 33.333 0.00 0.00 41.34 1.85
4134 5302 8.986847 CAGGTTTTATTTTATGCATGTCAAACA 58.013 29.630 10.16 0.00 0.00 2.83
4157 5325 1.278985 TCCGTCTGCAACTTCCATCAT 59.721 47.619 0.00 0.00 0.00 2.45
4345 5520 5.242393 TGTTAGTCCTAGTGTAAAAGCTCGT 59.758 40.000 0.00 0.00 0.00 4.18
4392 5567 2.223479 ACCTTTGTGCTTTTACACTGCG 60.223 45.455 0.00 0.00 41.30 5.18
4443 5618 1.737838 TGAATGGTTGCAGTCCGATC 58.262 50.000 5.72 6.69 0.00 3.69
4544 5719 6.369629 TGGTGGAAGAAAGTGGAAGAAATTA 58.630 36.000 0.00 0.00 0.00 1.40
4559 5734 6.151312 GGAAGAAATTAGGAGGGTGAGAAAAC 59.849 42.308 0.00 0.00 0.00 2.43
4980 6169 6.590068 ACATAGTATTTGCAGAGCTGATTCT 58.410 36.000 0.85 0.00 0.00 2.40
5226 6415 8.772705 GGTTTATGCATTTTGATTTGTTCTGAA 58.227 29.630 3.54 0.00 0.00 3.02
5296 6485 2.203788 TGACTCGCTCCCTGGGTT 60.204 61.111 13.56 0.00 0.00 4.11
5325 6515 2.581354 CTTCCCCTCTCACCGCAG 59.419 66.667 0.00 0.00 0.00 5.18
5343 6535 5.825679 ACCGCAGTTTGAATTAATATAGCCA 59.174 36.000 0.00 0.00 0.00 4.75
5345 6537 6.803320 CCGCAGTTTGAATTAATATAGCCATG 59.197 38.462 0.00 0.00 0.00 3.66
5364 6556 4.201910 CCATGGGTAACGAATTCATGTCAC 60.202 45.833 2.85 0.00 34.94 3.67
5376 6568 5.845985 ATTCATGTCACTCAACTTGTACG 57.154 39.130 0.00 0.00 0.00 3.67
5410 6602 2.583441 CGACAACCCAGAGAGGCCA 61.583 63.158 5.01 0.00 35.39 5.36
5492 6684 7.031372 CACTTTTGCATGCTTGAATAGTACAT 58.969 34.615 20.33 0.00 0.00 2.29
5756 9419 5.830799 TGATCATTGTACTAGGGATGCAT 57.169 39.130 0.00 0.00 0.00 3.96
5763 9426 1.504912 ACTAGGGATGCATGCAGACT 58.495 50.000 26.69 23.11 0.00 3.24
5764 9427 1.415659 ACTAGGGATGCATGCAGACTC 59.584 52.381 26.69 20.98 0.00 3.36
5809 9474 7.175990 GTCCACCAAAGAAATTAATACAGTCCA 59.824 37.037 0.00 0.00 0.00 4.02
5854 9606 9.565213 AAAGTAGTATGTACGTGCTTTAGTTAG 57.435 33.333 11.13 0.00 30.76 2.34
6103 9855 4.202346 GGGAAAGCTTCTGAGATAGCAGAT 60.202 45.833 15.43 4.80 43.84 2.90
6104 9856 5.367302 GGAAAGCTTCTGAGATAGCAGATT 58.633 41.667 15.43 9.26 43.84 2.40
6174 9926 9.836864 ATAGCATATGTAGAACATTTCACAAGA 57.163 29.630 4.29 0.00 39.88 3.02
6177 9929 8.454106 GCATATGTAGAACATTTCACAAGAACT 58.546 33.333 4.29 0.00 39.88 3.01
6180 9932 7.402811 TGTAGAACATTTCACAAGAACTACG 57.597 36.000 0.00 0.00 33.99 3.51
6181 9933 5.924475 AGAACATTTCACAAGAACTACGG 57.076 39.130 0.00 0.00 32.39 4.02
6182 9934 4.755123 AGAACATTTCACAAGAACTACGGG 59.245 41.667 0.00 0.00 32.39 5.28
6183 9935 4.081322 ACATTTCACAAGAACTACGGGT 57.919 40.909 0.00 0.00 32.39 5.28
6184 9936 3.813166 ACATTTCACAAGAACTACGGGTG 59.187 43.478 0.00 0.00 32.39 4.61
6303 10055 5.245977 CCTTTTGTTCCTGGTTGTTATGGAT 59.754 40.000 0.00 0.00 0.00 3.41
6575 10327 1.194781 ACAGATTGCCAGGACTCGGT 61.195 55.000 0.00 0.00 0.00 4.69
6686 10438 6.581171 AATCTGCGAGATTTCTTTTCCTTT 57.419 33.333 5.80 0.00 41.90 3.11
6901 10653 4.202305 GCAGAGCCTAGTTACCAAGATGAT 60.202 45.833 0.00 0.00 0.00 2.45
6931 10733 5.968676 AGCAAGGGGTTATAACTATGACA 57.031 39.130 15.05 0.00 0.00 3.58
6932 10734 6.321821 AGCAAGGGGTTATAACTATGACAA 57.678 37.500 15.05 0.00 0.00 3.18
7024 10841 3.108376 GACTTGTGGAGGGGAGATAAGT 58.892 50.000 0.00 0.00 0.00 2.24
7205 11022 3.584848 AGGACATGTTACCTCAAGCTCTT 59.415 43.478 0.00 0.00 0.00 2.85
7206 11023 3.686726 GGACATGTTACCTCAAGCTCTTG 59.313 47.826 0.00 3.32 41.71 3.02
7327 11144 0.605319 TGAGTTTTGGCTAGTGGGCG 60.605 55.000 0.00 0.00 44.11 6.13
7339 11156 3.305813 GCTAGTGGGCGTATGCAAGTATA 60.306 47.826 9.59 0.00 45.35 1.47
7340 11157 3.107642 AGTGGGCGTATGCAAGTATAC 57.892 47.619 9.59 0.00 45.35 1.47
7341 11158 2.432874 AGTGGGCGTATGCAAGTATACA 59.567 45.455 9.59 0.00 45.35 2.29
7342 11159 2.542595 GTGGGCGTATGCAAGTATACAC 59.457 50.000 9.59 2.52 45.35 2.90
7343 11160 1.790623 GGGCGTATGCAAGTATACACG 59.209 52.381 9.59 6.25 45.35 4.49
7344 11161 2.544277 GGGCGTATGCAAGTATACACGA 60.544 50.000 9.59 0.00 45.35 4.35
7345 11162 2.470257 GGCGTATGCAAGTATACACGAC 59.530 50.000 9.59 8.03 45.35 4.34
7346 11163 3.110358 GCGTATGCAAGTATACACGACA 58.890 45.455 13.47 3.50 42.15 4.35
7347 11164 3.179795 GCGTATGCAAGTATACACGACAG 59.820 47.826 13.47 0.00 42.15 3.51
7348 11165 4.594136 CGTATGCAAGTATACACGACAGA 58.406 43.478 5.50 0.00 34.02 3.41
7349 11166 4.436847 CGTATGCAAGTATACACGACAGAC 59.563 45.833 5.50 4.60 34.02 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.824759 ACCGACTCCTGCCTGAATAC 59.175 55.000 0.00 0.00 0.00 1.89
7 8 1.112113 GACCGACTCCTGCCTGAATA 58.888 55.000 0.00 0.00 0.00 1.75
75 76 6.018994 GGTAGAAAAGTGCATAGTTATGACGG 60.019 42.308 3.38 0.00 35.75 4.79
90 91 2.817844 GTCGGGCAATTGGTAGAAAAGT 59.182 45.455 7.72 0.00 0.00 2.66
99 100 1.821216 AACTACTGTCGGGCAATTGG 58.179 50.000 7.72 0.00 0.00 3.16
109 110 2.105993 AGTGGGGGAACAAACTACTGTC 59.894 50.000 0.00 0.00 0.00 3.51
116 117 1.544246 GCATACAGTGGGGGAACAAAC 59.456 52.381 0.00 0.00 0.00 2.93
171 172 3.876255 AAGGTAGACCCGGGGCCAA 62.876 63.158 27.30 9.43 38.74 4.52
294 302 3.197983 TGTCAATCCCCTTGGAGGTTAT 58.802 45.455 0.00 0.00 46.08 1.89
338 348 2.032799 ACCTGCACACACACAAAATACG 59.967 45.455 0.00 0.00 0.00 3.06
346 359 1.312371 AACACCACCTGCACACACAC 61.312 55.000 0.00 0.00 0.00 3.82
361 374 4.603231 TTACACAAAACCTCGTGAACAC 57.397 40.909 0.00 0.00 36.91 3.32
408 435 9.409918 TGCAGTACAGTAGAGATAAGTATTTCT 57.590 33.333 0.00 0.00 32.62 2.52
427 454 4.083003 CGAAGAGGAGAGGATATGCAGTAC 60.083 50.000 0.00 0.00 0.00 2.73
436 463 3.399952 TTTACCCGAAGAGGAGAGGAT 57.600 47.619 0.00 0.00 45.00 3.24
453 481 1.271108 TGTGAGCTGCGTTGGGATTTA 60.271 47.619 0.00 0.00 0.00 1.40
483 511 1.137675 CCAGACTGCGATGATGAGGAA 59.862 52.381 0.00 0.00 0.00 3.36
496 524 4.282195 ACAAAGACTAAGAGGTCCAGACTG 59.718 45.833 0.00 0.00 36.95 3.51
497 525 4.484912 ACAAAGACTAAGAGGTCCAGACT 58.515 43.478 0.00 0.00 36.95 3.24
498 526 4.616373 CGACAAAGACTAAGAGGTCCAGAC 60.616 50.000 0.00 0.00 36.95 3.51
499 527 3.506455 CGACAAAGACTAAGAGGTCCAGA 59.494 47.826 0.00 0.00 36.95 3.86
509 539 1.621814 CACCCCCTCGACAAAGACTAA 59.378 52.381 0.00 0.00 0.00 2.24
535 565 0.541863 CCCTCGCCAACCTCTACAAT 59.458 55.000 0.00 0.00 0.00 2.71
569 599 0.818445 AGCCTCACCGTATCGATCGT 60.818 55.000 15.94 5.23 0.00 3.73
598 628 2.843545 GGGAGTTGGTGGCCTTCA 59.156 61.111 3.32 0.00 0.00 3.02
600 630 3.966543 CCGGGAGTTGGTGGCCTT 61.967 66.667 3.32 0.00 0.00 4.35
622 652 2.922503 TGCGGCCTCAACCTCAGA 60.923 61.111 0.00 0.00 0.00 3.27
661 691 0.337773 TCCTCCTGCTCCATCTCACT 59.662 55.000 0.00 0.00 0.00 3.41
718 763 4.796225 GCACTCTGCGAGACCTAC 57.204 61.111 11.64 0.00 31.71 3.18
729 774 1.672356 GGCAACATGTCCGCACTCT 60.672 57.895 18.72 0.00 0.00 3.24
778 823 0.324460 GAAGAGAACGGGGGAGGAGA 60.324 60.000 0.00 0.00 0.00 3.71
963 1094 1.904287 CGGGTTGGGTTTTGAGATGA 58.096 50.000 0.00 0.00 0.00 2.92
1036 2159 1.997928 GCTCTGCTTCGGATTTGGCC 61.998 60.000 0.00 0.00 0.00 5.36
1063 2186 4.947147 GGTGTTGCTCCCGGTGCA 62.947 66.667 14.27 14.27 38.80 4.57
1291 2424 3.362797 TTGAGACGGAGAGCGCGT 61.363 61.111 8.43 0.00 0.00 6.01
1363 2496 1.077429 GGGCTGGGCTTACTTCCTG 60.077 63.158 0.00 0.00 0.00 3.86
1395 2528 3.555324 TCGAACAGCACAGGGGCA 61.555 61.111 0.00 0.00 35.83 5.36
1444 2577 3.180980 CACGAAACTACACGAACACGAAT 59.819 43.478 0.00 0.00 0.00 3.34
1472 2605 2.449518 TGTGCCCCAAGGTCCTCA 60.450 61.111 0.00 0.00 34.57 3.86
1526 2660 2.516906 TCACAATTGAAGCAGCATCCA 58.483 42.857 13.59 0.00 0.00 3.41
1530 2664 2.036089 TGCATTCACAATTGAAGCAGCA 59.964 40.909 13.59 13.12 45.07 4.41
1538 2675 5.886992 TCTCTAGCATTGCATTCACAATTG 58.113 37.500 11.91 3.24 38.19 2.32
1557 2703 2.831333 CACAACTGAAGCACACTCTCT 58.169 47.619 0.00 0.00 0.00 3.10
1729 2875 1.203994 CAGCTTGCTCCATCCAAAAGG 59.796 52.381 0.00 0.00 0.00 3.11
1730 2876 1.203994 CCAGCTTGCTCCATCCAAAAG 59.796 52.381 0.00 0.00 0.00 2.27
1871 3017 4.708909 TGGCATTGGCTTATTGAACATGTA 59.291 37.500 11.84 0.00 40.87 2.29
1966 3113 8.377799 AGAATTCCCTTTCATTGCAAAACTTAT 58.622 29.630 1.71 0.00 0.00 1.73
1979 3126 6.806668 AAAAAGGTCAAGAATTCCCTTTCA 57.193 33.333 20.21 0.00 42.47 2.69
2114 3261 9.947433 AATATCAACATGGACAAATTCAACATT 57.053 25.926 0.00 0.00 0.00 2.71
2366 3513 5.404466 AAAGCCAAAGCACTTGCAATATA 57.596 34.783 0.00 0.00 45.16 0.86
2686 3833 6.484308 ACAACCAACTACATACTACACAAACC 59.516 38.462 0.00 0.00 0.00 3.27
2687 3834 7.225145 TCACAACCAACTACATACTACACAAAC 59.775 37.037 0.00 0.00 0.00 2.93
2776 3925 6.159299 TGAAGCATTCCAGTTTGATCAAAA 57.841 33.333 22.07 7.19 46.93 2.44
2813 3962 3.167485 TGTGTTAGACGGGTATCCAACT 58.833 45.455 0.00 0.00 0.00 3.16
2841 3990 3.710209 AGATCTTGCAGTTGTAGGCTT 57.290 42.857 0.00 0.00 0.00 4.35
2842 3991 3.710209 AAGATCTTGCAGTTGTAGGCT 57.290 42.857 7.30 0.00 0.00 4.58
2843 3992 3.503748 ACAAAGATCTTGCAGTTGTAGGC 59.496 43.478 9.17 0.00 30.88 3.93
2844 3993 4.516698 ACACAAAGATCTTGCAGTTGTAGG 59.483 41.667 9.17 1.42 31.44 3.18
2845 3994 5.237127 TCACACAAAGATCTTGCAGTTGTAG 59.763 40.000 9.17 5.78 31.44 2.74
2846 3995 5.122519 TCACACAAAGATCTTGCAGTTGTA 58.877 37.500 9.17 0.00 31.44 2.41
2847 3996 3.947196 TCACACAAAGATCTTGCAGTTGT 59.053 39.130 9.17 6.32 32.78 3.32
2848 3997 4.556942 TCACACAAAGATCTTGCAGTTG 57.443 40.909 9.17 5.63 0.00 3.16
2892 4041 9.386122 AGGGAGTACTTCATATTGTCTGATTAT 57.614 33.333 2.92 0.00 0.00 1.28
3014 4169 9.926158 AAATAGTCAAACATGAACATTATGCAA 57.074 25.926 0.00 0.00 0.00 4.08
3253 4410 4.520492 AGGAACACCAAAACAGAGCATAAG 59.480 41.667 0.00 0.00 0.00 1.73
3337 4494 5.763204 ACGGACATGAGACTGTACAAAAATT 59.237 36.000 0.00 0.00 29.82 1.82
3540 4703 7.498900 TGTCTATTTGTGAAGTGAACTGTCATT 59.501 33.333 0.00 0.00 35.80 2.57
3619 4782 6.203723 GCAGGTTATTCATATCAGTCCTGAAC 59.796 42.308 11.33 0.00 43.58 3.18
3765 4929 5.339008 ACGAGCACCAGTATTCTTAATCA 57.661 39.130 0.00 0.00 0.00 2.57
3839 5006 6.239217 AGGTCTAGTCATCATTACATGCAA 57.761 37.500 0.00 0.00 0.00 4.08
3840 5007 5.876651 AGGTCTAGTCATCATTACATGCA 57.123 39.130 0.00 0.00 0.00 3.96
3841 5008 7.928706 ACTTAAGGTCTAGTCATCATTACATGC 59.071 37.037 7.53 0.00 0.00 4.06
3871 5038 6.488769 TGAACCCTTCAAGTGTAGAAGTTA 57.511 37.500 0.00 0.00 40.62 2.24
3890 5057 4.232221 CCTGATTCAACAGTGCATTGAAC 58.768 43.478 16.98 10.44 46.05 3.18
3995 5163 6.127535 CCAGTAAGCAATCTTGATGACCAAAT 60.128 38.462 0.00 0.00 33.76 2.32
4018 5186 5.258051 AGTACAGAAAAACTTTGGTGTCCA 58.742 37.500 0.00 0.00 0.00 4.02
4019 5187 5.830000 AGTACAGAAAAACTTTGGTGTCC 57.170 39.130 0.00 0.00 0.00 4.02
4044 5212 7.761249 GGCAATGCTAGAACTAACAATTTTGAT 59.239 33.333 4.82 0.00 0.00 2.57
4068 5236 8.197439 ACTAAAAATATGGAACTAATGCTTGGC 58.803 33.333 0.00 0.00 0.00 4.52
4134 5302 0.468226 TGGAAGTTGCAGACGGACTT 59.532 50.000 0.36 0.36 36.40 3.01
4392 5567 4.771590 TGTTGAGATCAATGCAAGGAAC 57.228 40.909 0.00 0.00 38.24 3.62
4443 5618 1.358152 TCTTCCCCAACAGGTACCAG 58.642 55.000 15.94 9.05 0.00 4.00
4544 5719 5.600669 AATTTAGGTTTTCTCACCCTCCT 57.399 39.130 0.00 0.00 37.58 3.69
4559 5734 7.586300 CGCAAAAGATGTACGGAATAATTTAGG 59.414 37.037 0.00 0.00 0.00 2.69
4682 5864 7.546667 GTGTTGTATCTTGAAATGATGCCAAAT 59.453 33.333 0.00 0.00 33.23 2.32
5043 6232 9.394477 CGACATCTATCGTCAATAAACAGAATA 57.606 33.333 0.00 0.00 37.33 1.75
5146 6335 7.755582 AGAAAATAACACAAAAGCAGAACAC 57.244 32.000 0.00 0.00 0.00 3.32
5226 6415 2.344950 CTGCAAAGCGTCAGAGATCTT 58.655 47.619 0.00 0.00 32.26 2.40
5296 6485 0.417841 AGGGGAAGGAGAGGCTACAA 59.582 55.000 0.00 0.00 0.00 2.41
5325 6515 9.908152 GTTACCCATGGCTATATTAATTCAAAC 57.092 33.333 6.09 0.00 0.00 2.93
5343 6535 4.843728 AGTGACATGAATTCGTTACCCAT 58.156 39.130 0.00 0.00 0.00 4.00
5345 6537 4.250464 TGAGTGACATGAATTCGTTACCC 58.750 43.478 0.00 0.00 0.00 3.69
5364 6556 1.071605 GCTGGAGCGTACAAGTTGAG 58.928 55.000 10.54 1.74 0.00 3.02
5410 6602 6.941436 AGACTGAGAGAAGATTTTTGCATTCT 59.059 34.615 0.00 0.00 34.78 2.40
5492 6684 0.978907 TCATGTTCTGGCTGAGCAGA 59.021 50.000 15.34 4.58 39.21 4.26
5763 9426 3.535629 GATGCGGATGATGCGGGGA 62.536 63.158 8.71 0.00 34.24 4.81
5764 9427 3.052082 GATGCGGATGATGCGGGG 61.052 66.667 8.71 0.00 34.24 5.73
5809 9474 0.536724 TAGTGGCTGATGCGTGATGT 59.463 50.000 0.00 0.00 40.82 3.06
5854 9606 1.275291 TCCGTCCACTGGAGATTGAAC 59.725 52.381 0.00 0.00 29.39 3.18
6103 9855 0.834612 AGACGTTGTTGAGGGTGGAA 59.165 50.000 0.00 0.00 0.00 3.53
6104 9856 1.342174 GTAGACGTTGTTGAGGGTGGA 59.658 52.381 0.00 0.00 0.00 4.02
6351 10103 6.640518 TGTAAAGTTGTCCAGAGATGGTATC 58.359 40.000 0.00 0.00 0.00 2.24
6575 10327 4.584325 AGACAGCAAAGAAAGCAAATACCA 59.416 37.500 0.00 0.00 0.00 3.25
6684 10436 6.259167 GGTTCATTACATACCATCGTGCTAAA 59.741 38.462 0.00 0.00 32.12 1.85
6686 10438 5.163395 TGGTTCATTACATACCATCGTGCTA 60.163 40.000 0.00 0.00 37.04 3.49
6850 10602 1.548269 GAAATTTTGGTCCCCATCGCA 59.452 47.619 0.00 0.00 31.53 5.10
6853 10605 3.519107 ACATGGAAATTTTGGTCCCCATC 59.481 43.478 0.00 0.00 32.57 3.51
6855 10607 2.983296 ACATGGAAATTTTGGTCCCCA 58.017 42.857 0.00 0.00 32.48 4.96
6901 10653 7.266905 AGTTATAACCCCTTGCTTTCTAAGA 57.733 36.000 12.05 0.00 0.00 2.10
6931 10733 5.127031 AGGTATTGCTGTCTGTTGTTGTTTT 59.873 36.000 0.00 0.00 0.00 2.43
6932 10734 4.644685 AGGTATTGCTGTCTGTTGTTGTTT 59.355 37.500 0.00 0.00 0.00 2.83
6998 10815 1.141881 CCCCTCCACAAGTCGATCG 59.858 63.158 9.36 9.36 0.00 3.69
7024 10841 4.353777 AGAGTACTAGGAATGCCTGTCAA 58.646 43.478 0.88 0.00 46.45 3.18
7205 11022 6.351033 CCCTTCAACTACAGCTCTTATGTACA 60.351 42.308 0.00 0.00 32.02 2.90
7206 11023 6.043411 CCCTTCAACTACAGCTCTTATGTAC 58.957 44.000 0.00 0.00 32.02 2.90
7327 11144 5.868177 GTCTGTCGTGTATACTTGCATAC 57.132 43.478 4.17 0.00 32.91 2.39


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

AutoCloner maintained by Alex Coulton.