Multiple sequence alignment - TraesCS5A01G537400

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 TraesCS5A01G537400 chr5A 100.000 4498 0 0 1 4498 693851900 693847403 0.000000e+00 8307
1 TraesCS5A01G537400 chr5A 97.074 957 23 4 3544 4498 565281418 565282371 0.000000e+00 1607
2 TraesCS5A01G537400 chr7A 96.382 3483 113 6 1 3481 204200379 204196908 0.000000e+00 5722
3 TraesCS5A01G537400 chr7A 96.862 956 29 1 3544 4498 204196906 204195951 0.000000e+00 1598
4 TraesCS5A01G537400 chr7A 95.000 960 43 5 3544 4498 15516298 15517257 0.000000e+00 1502
5 TraesCS5A01G537400 chr3B 93.221 3496 205 21 1 3478 60579683 60576202 0.000000e+00 5114
6 TraesCS5A01G537400 chr3B 92.187 3507 236 26 1 3479 657798678 657795182 0.000000e+00 4924
7 TraesCS5A01G537400 chr1D 92.669 3492 211 28 1 3481 383341915 383345372 0.000000e+00 4988
8 TraesCS5A01G537400 chr2B 92.154 3505 241 24 1 3479 717665065 717668561 0.000000e+00 4918
9 TraesCS5A01G537400 chr2B 92.204 3502 228 24 1 3479 670336246 670332767 0.000000e+00 4913
10 TraesCS5A01G537400 chr2D 92.940 3357 186 34 1 3344 87965461 87962143 0.000000e+00 4839
11 TraesCS5A01G537400 chr6D 91.667 3504 250 34 1 3481 258016745 258013261 0.000000e+00 4815
12 TraesCS5A01G537400 chr6D 91.690 3502 245 32 1 3481 305369838 305373314 0.000000e+00 4813
13 TraesCS5A01G537400 chr7D 90.899 3505 268 39 1 3481 560760751 560764228 0.000000e+00 4658
14 TraesCS5A01G537400 chr6A 95.099 959 43 4 3544 4498 555099165 555100123 0.000000e+00 1507
15 TraesCS5A01G537400 chr6A 94.995 959 44 4 3544 4498 602792243 602793201 0.000000e+00 1502
16 TraesCS5A01G537400 chr6A 94.473 959 49 4 3544 4498 597462288 597463246 0.000000e+00 1474
17 TraesCS5A01G537400 chr6A 95.068 730 32 4 2754 3481 602791514 602792241 0.000000e+00 1146
18 TraesCS5A01G537400 chr6A 94.384 730 36 4 2754 3481 597461560 597462286 0.000000e+00 1116
19 TraesCS5A01G537400 chr6A 93.690 729 34 4 2754 3481 555098446 555099163 0.000000e+00 1081
20 TraesCS5A01G537400 chr3A 94.069 961 51 6 3544 4498 17908419 17909379 0.000000e+00 1454
21 TraesCS5A01G537400 chr2A 93.431 959 58 5 3544 4498 608575 609532 0.000000e+00 1417
22 TraesCS5A01G537400 chr2A 93.243 962 53 11 3544 4498 30585696 30584740 0.000000e+00 1406
23 TraesCS5A01G537400 chr4B 84.045 796 84 28 2708 3481 75644856 75645630 0.000000e+00 726
24 TraesCS5A01G537400 chr4B 98.462 65 1 0 3482 3546 209217812 209217748 1.020000e-21 115
25 TraesCS5A01G537400 chrUn 98.462 65 1 0 3482 3546 182442155 182442091 1.020000e-21 115
26 TraesCS5A01G537400 chrUn 98.462 65 1 0 3482 3546 222871805 222871741 1.020000e-21 115
27 TraesCS5A01G537400 chr7B 98.462 65 1 0 3482 3546 47133607 47133543 1.020000e-21 115
28 TraesCS5A01G537400 chr7B 98.462 65 1 0 3482 3546 327259613 327259549 1.020000e-21 115
29 TraesCS5A01G537400 chr5B 100.000 62 0 0 3482 3543 130584068 130584129 1.020000e-21 115
30 TraesCS5A01G537400 chr1B 98.462 65 1 0 3482 3546 339035634 339035570 1.020000e-21 115
31 TraesCS5A01G537400 chr1B 100.000 62 0 0 3482 3543 583574287 583574348 1.020000e-21 115
32 TraesCS5A01G537400 chr1B 100.000 62 0 0 3482 3543 619178228 619178289 1.020000e-21 115


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 TraesCS5A01G537400 chr5A 693847403 693851900 4497 True 8307 8307 100.0000 1 4498 1 chr5A.!!$R1 4497
1 TraesCS5A01G537400 chr5A 565281418 565282371 953 False 1607 1607 97.0740 3544 4498 1 chr5A.!!$F1 954
2 TraesCS5A01G537400 chr7A 204195951 204200379 4428 True 3660 5722 96.6220 1 4498 2 chr7A.!!$R1 4497
3 TraesCS5A01G537400 chr7A 15516298 15517257 959 False 1502 1502 95.0000 3544 4498 1 chr7A.!!$F1 954
4 TraesCS5A01G537400 chr3B 60576202 60579683 3481 True 5114 5114 93.2210 1 3478 1 chr3B.!!$R1 3477
5 TraesCS5A01G537400 chr3B 657795182 657798678 3496 True 4924 4924 92.1870 1 3479 1 chr3B.!!$R2 3478
6 TraesCS5A01G537400 chr1D 383341915 383345372 3457 False 4988 4988 92.6690 1 3481 1 chr1D.!!$F1 3480
7 TraesCS5A01G537400 chr2B 717665065 717668561 3496 False 4918 4918 92.1540 1 3479 1 chr2B.!!$F1 3478
8 TraesCS5A01G537400 chr2B 670332767 670336246 3479 True 4913 4913 92.2040 1 3479 1 chr2B.!!$R1 3478
9 TraesCS5A01G537400 chr2D 87962143 87965461 3318 True 4839 4839 92.9400 1 3344 1 chr2D.!!$R1 3343
10 TraesCS5A01G537400 chr6D 258013261 258016745 3484 True 4815 4815 91.6670 1 3481 1 chr6D.!!$R1 3480
11 TraesCS5A01G537400 chr6D 305369838 305373314 3476 False 4813 4813 91.6900 1 3481 1 chr6D.!!$F1 3480
12 TraesCS5A01G537400 chr7D 560760751 560764228 3477 False 4658 4658 90.8990 1 3481 1 chr7D.!!$F1 3480
13 TraesCS5A01G537400 chr6A 602791514 602793201 1687 False 1324 1502 95.0315 2754 4498 2 chr6A.!!$F3 1744
14 TraesCS5A01G537400 chr6A 597461560 597463246 1686 False 1295 1474 94.4285 2754 4498 2 chr6A.!!$F2 1744
15 TraesCS5A01G537400 chr6A 555098446 555100123 1677 False 1294 1507 94.3945 2754 4498 2 chr6A.!!$F1 1744
16 TraesCS5A01G537400 chr3A 17908419 17909379 960 False 1454 1454 94.0690 3544 4498 1 chr3A.!!$F1 954
17 TraesCS5A01G537400 chr2A 608575 609532 957 False 1417 1417 93.4310 3544 4498 1 chr2A.!!$F1 954
18 TraesCS5A01G537400 chr2A 30584740 30585696 956 True 1406 1406 93.2430 3544 4498 1 chr2A.!!$R1 954
19 TraesCS5A01G537400 chr4B 75644856 75645630 774 False 726 726 84.0450 2708 3481 1 chr4B.!!$F1 773

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
941 948 0.534877 AGCACATGAAACCACAGCGA 60.535 50.000 0.0 0.0 0.00 4.93 F
1284 1291 1.160137 CAGTAGAAGCAACTGGCCAC 58.840 55.000 0.0 0.0 46.50 5.01 F
1403 1410 1.401552 TGTGAGTGAGCTGTTTGCAAC 59.598 47.619 0.0 0.0 45.94 4.17 F
3219 3339 0.905357 AGAGCATTACGCCAGTTCCT 59.095 50.000 0.0 0.0 44.04 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 1922 0.109532 TGCTTCGGGTTTGGACATGA 59.890 50.000 0.0 0.0 0.00 3.07 R
2129 2142 0.598065 CACACTAAGCCAAGTTGCCC 59.402 55.000 0.0 0.0 0.00 5.36 R
3222 3342 1.134280 CCCAAAGTCATCCAGCGAGAT 60.134 52.381 0.0 0.0 0.00 2.75 R
4464 4608 0.106569 CAGGTATGGGCAGCATCCAA 60.107 55.000 0.0 0.0 37.87 3.53 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
82 83 3.852205 GCAGCGATGATGATGAACAATGG 60.852 47.826 4.02 0.00 0.00 3.16
95 96 7.613585 TGATGAACAATGGATGCTACAATTTT 58.386 30.769 0.00 0.00 0.00 1.82
175 176 3.516981 ATCAGAGACCTTGTGATGACG 57.483 47.619 0.00 0.00 29.59 4.35
449 455 2.593468 CTACCACCACTCCCGCCATG 62.593 65.000 0.00 0.00 0.00 3.66
469 475 7.361201 CGCCATGAAAGAAGATGAAGAAAACTA 60.361 37.037 0.00 0.00 0.00 2.24
576 582 0.955919 GGGGAAAGTCAAGGCAGTCG 60.956 60.000 0.00 0.00 0.00 4.18
625 632 5.048782 CAGTAGCAACAACAGGCAATTTCTA 60.049 40.000 0.00 0.00 0.00 2.10
784 791 4.524316 TTTCATTCCCAATGTCAAGCAG 57.476 40.909 0.00 0.00 39.87 4.24
853 860 4.036734 CAGCTGTTTTTCAGGCAAGTTCTA 59.963 41.667 5.25 0.00 43.78 2.10
941 948 0.534877 AGCACATGAAACCACAGCGA 60.535 50.000 0.00 0.00 0.00 4.93
1149 1156 6.672218 TGGAGATCAAAAGGATACAAGACCTA 59.328 38.462 0.00 0.00 36.00 3.08
1284 1291 1.160137 CAGTAGAAGCAACTGGCCAC 58.840 55.000 0.00 0.00 46.50 5.01
1304 1311 4.006989 CACGGGAACATTCACCATTTCTA 58.993 43.478 0.00 0.00 0.00 2.10
1350 1357 2.779755 TCATGCGTGTTAGTGGGAAT 57.220 45.000 5.68 0.00 0.00 3.01
1403 1410 1.401552 TGTGAGTGAGCTGTTTGCAAC 59.598 47.619 0.00 0.00 45.94 4.17
1566 1573 7.816995 AGTTTCGATCTAGGCATAGATGATTTC 59.183 37.037 24.62 10.34 46.63 2.17
1591 1598 3.313249 CACAAGATCTGCAGACAACACAA 59.687 43.478 20.97 0.00 0.00 3.33
1635 1642 3.242518 CACATTTGCAGAGCATGAGTTG 58.757 45.455 0.00 0.00 38.76 3.16
1678 1687 5.704354 ACCAGCCAATCATCAATATAACCA 58.296 37.500 0.00 0.00 0.00 3.67
1684 1693 6.017109 GCCAATCATCAATATAACCAACGACT 60.017 38.462 0.00 0.00 0.00 4.18
2098 2110 6.795144 TCATGTTATCCAGGCAATTCAAAT 57.205 33.333 0.00 0.00 0.00 2.32
2193 2207 3.732212 TCTCCTTTGATATGACCATGCG 58.268 45.455 0.00 0.00 0.00 4.73
2385 2408 4.780815 TGTAATGGAAGTTGGCATAGAGG 58.219 43.478 0.00 0.00 0.00 3.69
2436 2459 3.989698 AAGCTCGTGATGCCCGTCG 62.990 63.158 0.00 0.00 0.00 5.12
2443 2466 2.267961 GATGCCCGTCGGGTTCTT 59.732 61.111 30.60 13.51 46.51 2.52
2444 2467 1.376812 GATGCCCGTCGGGTTCTTT 60.377 57.895 30.60 11.72 46.51 2.52
2609 2643 2.611971 CCCGGTTCAAGAAGTCGAATCA 60.612 50.000 0.00 0.00 0.00 2.57
2711 2751 6.255453 GCTAAAACTTTTGCTCACACAAATGA 59.745 34.615 9.12 0.00 39.18 2.57
3042 3162 6.867519 TGTTCCCAGTGTTAGAGAATATCA 57.132 37.500 0.00 0.00 0.00 2.15
3141 3261 2.169832 TTCTTGGAGGACGCTCAAAG 57.830 50.000 0.00 0.00 36.09 2.77
3219 3339 0.905357 AGAGCATTACGCCAGTTCCT 59.095 50.000 0.00 0.00 44.04 3.36
3222 3342 1.305219 GCATTACGCCAGTTCCTGCA 61.305 55.000 0.00 0.00 32.04 4.41
3258 3378 3.855159 GGGCTTACCAACATCGACT 57.145 52.632 0.00 0.00 39.85 4.18
3292 3412 9.461312 ACAAAATAATGAGTAAGCATCCACTTA 57.539 29.630 0.00 0.00 0.00 2.24
3415 3548 3.290710 ACTGTGGTGTTTTTGCTCTGAT 58.709 40.909 0.00 0.00 0.00 2.90
3481 3614 3.501445 GCTGAGGATATTCCAAGCATCAC 59.499 47.826 13.39 0.00 43.73 3.06
3482 3615 4.746089 GCTGAGGATATTCCAAGCATCACT 60.746 45.833 13.39 0.00 43.73 3.41
3483 3616 4.965814 TGAGGATATTCCAAGCATCACTC 58.034 43.478 0.00 0.00 39.61 3.51
3484 3617 4.657504 TGAGGATATTCCAAGCATCACTCT 59.342 41.667 0.00 0.00 39.61 3.24
3485 3618 4.970711 AGGATATTCCAAGCATCACTCTG 58.029 43.478 0.00 0.00 39.61 3.35
3486 3619 3.501445 GGATATTCCAAGCATCACTCTGC 59.499 47.826 0.00 0.00 38.27 4.26
3487 3620 6.928582 AGGATATTCCAAGCATCACTCTGCT 61.929 44.000 0.00 0.00 43.75 4.24
3488 3621 8.643385 AGGATATTCCAAGCATCACTCTGCTC 62.643 46.154 0.00 0.00 43.44 4.26
3493 3626 3.254629 GCATCACTCTGCTCCCAAA 57.745 52.632 0.00 0.00 39.12 3.28
3494 3627 0.807496 GCATCACTCTGCTCCCAAAC 59.193 55.000 0.00 0.00 39.12 2.93
3495 3628 1.612726 GCATCACTCTGCTCCCAAACT 60.613 52.381 0.00 0.00 39.12 2.66
3496 3629 2.355108 GCATCACTCTGCTCCCAAACTA 60.355 50.000 0.00 0.00 39.12 2.24
3497 3630 3.869912 GCATCACTCTGCTCCCAAACTAA 60.870 47.826 0.00 0.00 39.12 2.24
3498 3631 4.326826 CATCACTCTGCTCCCAAACTAAA 58.673 43.478 0.00 0.00 0.00 1.85
3499 3632 4.008074 TCACTCTGCTCCCAAACTAAAG 57.992 45.455 0.00 0.00 0.00 1.85
3500 3633 3.646162 TCACTCTGCTCCCAAACTAAAGA 59.354 43.478 0.00 0.00 0.00 2.52
3501 3634 3.999663 CACTCTGCTCCCAAACTAAAGAG 59.000 47.826 0.00 0.00 36.58 2.85
3502 3635 3.904339 ACTCTGCTCCCAAACTAAAGAGA 59.096 43.478 3.93 0.00 34.97 3.10
3503 3636 4.348168 ACTCTGCTCCCAAACTAAAGAGAA 59.652 41.667 3.93 0.00 34.97 2.87
3504 3637 5.163195 ACTCTGCTCCCAAACTAAAGAGAAA 60.163 40.000 3.93 0.00 34.97 2.52
3505 3638 5.308825 TCTGCTCCCAAACTAAAGAGAAAG 58.691 41.667 0.00 0.00 0.00 2.62
3506 3639 4.398319 TGCTCCCAAACTAAAGAGAAAGG 58.602 43.478 0.00 0.00 0.00 3.11
3507 3640 4.104102 TGCTCCCAAACTAAAGAGAAAGGA 59.896 41.667 0.00 0.00 0.00 3.36
3508 3641 5.070685 GCTCCCAAACTAAAGAGAAAGGAA 58.929 41.667 0.00 0.00 0.00 3.36
3509 3642 5.535030 GCTCCCAAACTAAAGAGAAAGGAAA 59.465 40.000 0.00 0.00 0.00 3.13
3510 3643 6.294231 GCTCCCAAACTAAAGAGAAAGGAAAG 60.294 42.308 0.00 0.00 0.00 2.62
3511 3644 6.068670 TCCCAAACTAAAGAGAAAGGAAAGG 58.931 40.000 0.00 0.00 0.00 3.11
3512 3645 6.068670 CCCAAACTAAAGAGAAAGGAAAGGA 58.931 40.000 0.00 0.00 0.00 3.36
3513 3646 6.207614 CCCAAACTAAAGAGAAAGGAAAGGAG 59.792 42.308 0.00 0.00 0.00 3.69
3514 3647 6.998673 CCAAACTAAAGAGAAAGGAAAGGAGA 59.001 38.462 0.00 0.00 0.00 3.71
3515 3648 7.041030 CCAAACTAAAGAGAAAGGAAAGGAGAC 60.041 40.741 0.00 0.00 0.00 3.36
3517 3650 6.764379 ACTAAAGAGAAAGGAAAGGAGACTG 58.236 40.000 0.00 0.00 42.68 3.51
3518 3651 5.896073 AAAGAGAAAGGAAAGGAGACTGA 57.104 39.130 0.00 0.00 42.68 3.41
3519 3652 6.446909 AAAGAGAAAGGAAAGGAGACTGAT 57.553 37.500 0.00 0.00 42.68 2.90
3520 3653 5.675684 AGAGAAAGGAAAGGAGACTGATC 57.324 43.478 0.00 0.00 42.68 2.92
3521 3654 5.341169 AGAGAAAGGAAAGGAGACTGATCT 58.659 41.667 0.00 0.00 42.68 2.75
3522 3655 5.784906 AGAGAAAGGAAAGGAGACTGATCTT 59.215 40.000 0.00 0.00 42.68 2.40
3523 3656 5.803552 AGAAAGGAAAGGAGACTGATCTTG 58.196 41.667 0.00 0.00 42.68 3.02
3524 3657 5.545723 AGAAAGGAAAGGAGACTGATCTTGA 59.454 40.000 0.00 0.00 42.68 3.02
3525 3658 4.817318 AGGAAAGGAGACTGATCTTGAC 57.183 45.455 0.00 0.00 42.68 3.18
3526 3659 3.194542 AGGAAAGGAGACTGATCTTGACG 59.805 47.826 0.00 0.00 42.68 4.35
3527 3660 3.056465 GGAAAGGAGACTGATCTTGACGT 60.056 47.826 0.00 0.00 42.68 4.34
3528 3661 3.859411 AAGGAGACTGATCTTGACGTC 57.141 47.619 9.11 9.11 42.68 4.34
3529 3662 1.740585 AGGAGACTGATCTTGACGTCG 59.259 52.381 11.62 0.00 41.13 5.12
3530 3663 1.202200 GGAGACTGATCTTGACGTCGG 60.202 57.143 11.62 6.54 34.34 4.79
3531 3664 1.469308 GAGACTGATCTTGACGTCGGT 59.531 52.381 11.62 0.00 34.34 4.69
3532 3665 1.200252 AGACTGATCTTGACGTCGGTG 59.800 52.381 11.62 3.51 34.24 4.94
3533 3666 0.959553 ACTGATCTTGACGTCGGTGT 59.040 50.000 11.62 0.00 32.91 4.16
3534 3667 1.068472 ACTGATCTTGACGTCGGTGTC 60.068 52.381 11.62 7.40 39.37 3.67
3535 3668 0.109919 TGATCTTGACGTCGGTGTCG 60.110 55.000 11.62 0.00 41.87 4.35
3536 3669 0.797249 GATCTTGACGTCGGTGTCGG 60.797 60.000 11.62 0.00 41.87 4.79
3537 3670 1.521450 ATCTTGACGTCGGTGTCGGT 61.521 55.000 11.62 0.00 41.87 4.69
3538 3671 1.299620 CTTGACGTCGGTGTCGGTT 60.300 57.895 11.62 0.00 41.87 4.44
3539 3672 0.872881 CTTGACGTCGGTGTCGGTTT 60.873 55.000 11.62 0.00 41.87 3.27
3540 3673 0.459934 TTGACGTCGGTGTCGGTTTT 60.460 50.000 11.62 0.00 41.87 2.43
3541 3674 0.459934 TGACGTCGGTGTCGGTTTTT 60.460 50.000 11.62 0.00 41.87 1.94
3542 3675 0.230515 GACGTCGGTGTCGGTTTTTC 59.769 55.000 0.00 0.00 36.95 2.29
3698 3835 4.799564 TTGCTCTTTTGTGAACTTTGGT 57.200 36.364 0.00 0.00 0.00 3.67
3701 3838 5.189928 TGCTCTTTTGTGAACTTTGGTCTA 58.810 37.500 0.00 0.00 0.00 2.59
3708 3845 0.689055 GAACTTTGGTCTACCGGGGT 59.311 55.000 6.32 0.00 39.43 4.95
3955 4097 1.547820 TCAAAGCACACAACAGGCAAA 59.452 42.857 0.00 0.00 0.00 3.68
4020 4162 2.038557 AGTCAGCCACAAGAAACCGTAT 59.961 45.455 0.00 0.00 0.00 3.06
4027 4169 4.510340 GCCACAAGAAACCGTATACCATAG 59.490 45.833 0.00 0.00 0.00 2.23
4111 4254 5.478407 TCGACACATCTTTTCAGCAATCTA 58.522 37.500 0.00 0.00 0.00 1.98
4148 4291 2.361104 GCCAATCTGGTCGGGCAA 60.361 61.111 0.00 0.00 45.70 4.52
4160 4303 0.250945 TCGGGCAACTTGCACCATTA 60.251 50.000 15.61 1.30 45.87 1.90
4216 4359 3.908643 TCTCTTCAGATGCAGCTCAAT 57.091 42.857 0.00 0.00 0.00 2.57
4220 4363 1.100510 TCAGATGCAGCTCAATTGCC 58.899 50.000 0.00 0.00 40.81 4.52
4242 4385 6.760770 TGCCGATTGAATTCTTTTTGACTTTT 59.239 30.769 7.05 0.00 0.00 2.27
4379 4523 2.740981 GCATGTAGAGATGCCATACTGC 59.259 50.000 0.22 0.00 42.57 4.40
4464 4608 5.871396 TCTTCTTGTGTAGTTGAAGACCT 57.129 39.130 0.00 0.00 39.64 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.135603 CGCTGCTTGCATTTTCAGCTA 60.136 47.619 20.12 4.67 46.95 3.32
95 96 5.940617 TCTGTCCCTCTTCTTTTCAATCAA 58.059 37.500 0.00 0.00 0.00 2.57
304 305 5.882000 TGAATGTGAAGACCATATCCAAGTG 59.118 40.000 0.00 0.00 0.00 3.16
469 475 5.768662 CAGATGGCTCCAATATGAAACTGAT 59.231 40.000 0.00 0.00 0.00 2.90
604 611 6.398234 TTTAGAAATTGCCTGTTGTTGCTA 57.602 33.333 0.00 0.00 0.00 3.49
625 632 5.065235 CCCATGAATTGCCTCTTTTGTTTT 58.935 37.500 0.00 0.00 0.00 2.43
784 791 3.213206 TGCCAGAATATGTGATCCACC 57.787 47.619 0.00 0.00 32.73 4.61
853 860 2.197465 GGGGTCCAGTGTTTCCTCTAT 58.803 52.381 0.00 0.00 0.00 1.98
928 935 1.454201 TGTGTTTCGCTGTGGTTTCA 58.546 45.000 0.00 0.00 0.00 2.69
941 948 3.926058 AGTCACCTAGTGGTTGTGTTT 57.074 42.857 0.00 0.00 46.05 2.83
992 999 3.070476 TGGCTGACTGCATCACATTTA 57.930 42.857 6.65 0.00 45.15 1.40
1149 1156 1.004745 CCCATGGTTACAGCTTCAGGT 59.995 52.381 11.73 0.00 0.00 4.00
1284 1291 4.881273 TCATAGAAATGGTGAATGTTCCCG 59.119 41.667 0.00 0.00 33.61 5.14
1304 1311 0.753262 GTACCGCTCCTCCACATCAT 59.247 55.000 0.00 0.00 0.00 2.45
1350 1357 6.816134 TTGATTTCTAGTGCATTGCTTGTA 57.184 33.333 10.49 0.00 0.00 2.41
1403 1410 3.412981 TGTTGTTTGGATCAACACACG 57.587 42.857 7.28 0.00 46.35 4.49
1529 1536 2.158667 AGATCGAAACTTGGTGTTGGGT 60.159 45.455 0.00 0.00 39.13 4.51
1566 1573 2.174363 TGTCTGCAGATCTTGTGTGG 57.826 50.000 21.47 0.00 0.00 4.17
1591 1598 2.942804 TGACCCAACATGTTGATGTGT 58.057 42.857 34.76 24.88 42.30 3.72
1635 1642 4.224370 TGGTTATGTACTGGGAGTTCCTTC 59.776 45.833 0.00 0.00 36.20 3.46
1678 1687 7.327975 TCAACATCCAACAGATAATAGTCGTT 58.672 34.615 0.00 0.00 32.37 3.85
1684 1693 6.422333 TGCCTTCAACATCCAACAGATAATA 58.578 36.000 0.00 0.00 32.37 0.98
1698 1707 3.270027 CGGTTCATCTATGCCTTCAACA 58.730 45.455 0.00 0.00 0.00 3.33
1913 1922 0.109532 TGCTTCGGGTTTGGACATGA 59.890 50.000 0.00 0.00 0.00 3.07
2098 2110 9.767684 CTATAAATCGATTGCTTGTAAACACAA 57.232 29.630 12.25 0.00 0.00 3.33
2116 2128 5.562890 GCCAAGTTGCCCGATTCTATAAATC 60.563 44.000 0.00 0.00 0.00 2.17
2129 2142 0.598065 CACACTAAGCCAAGTTGCCC 59.402 55.000 0.00 0.00 0.00 5.36
2193 2207 1.963515 ACTCAGGAAAAACACATGGGC 59.036 47.619 0.00 0.00 0.00 5.36
2378 2401 7.065563 GGCAAGTTCATCATTATAGCCTCTATG 59.934 40.741 0.00 0.00 36.72 2.23
2385 2408 4.580167 TGGTGGCAAGTTCATCATTATAGC 59.420 41.667 0.00 0.00 0.00 2.97
2436 2459 4.295857 TGCGTTTTCTTACAAAGAACCC 57.704 40.909 1.67 0.00 46.53 4.11
2443 2466 4.739195 AGTTGCTTTGCGTTTTCTTACAA 58.261 34.783 0.00 0.00 0.00 2.41
2444 2467 4.364415 AGTTGCTTTGCGTTTTCTTACA 57.636 36.364 0.00 0.00 0.00 2.41
2457 2480 8.899771 ACACAAAACTACACTATTAGTTGCTTT 58.100 29.630 0.00 0.00 40.69 3.51
2554 2588 5.474189 CCTTGCCATTCAATTCCATGTTTTT 59.526 36.000 0.00 0.00 33.57 1.94
2609 2643 2.370849 ACCATGTCTTTACGGTCCAAGT 59.629 45.455 0.00 0.00 0.00 3.16
2952 3059 7.661536 ACAATACTAGAAGCTGGATGTAAGA 57.338 36.000 0.00 0.00 0.00 2.10
3075 3195 6.025280 CCCTTATGTTCACGTTAAAAATCCG 58.975 40.000 0.00 0.00 0.00 4.18
3141 3261 3.492313 CGCAAACATCTAAAGCCTTGTC 58.508 45.455 0.00 0.00 0.00 3.18
3222 3342 1.134280 CCCAAAGTCATCCAGCGAGAT 60.134 52.381 0.00 0.00 0.00 2.75
3258 3378 9.823647 TGCTTACTCATTATTTTGTTTTGGAAA 57.176 25.926 0.00 0.00 0.00 3.13
3415 3548 0.605319 CTCCCAACCGTTTGCTAGCA 60.605 55.000 14.93 14.93 0.00 3.49
3481 3614 4.543590 TCTCTTTAGTTTGGGAGCAGAG 57.456 45.455 0.00 0.00 0.00 3.35
3482 3615 4.974645 TTCTCTTTAGTTTGGGAGCAGA 57.025 40.909 0.00 0.00 0.00 4.26
3483 3616 4.457257 CCTTTCTCTTTAGTTTGGGAGCAG 59.543 45.833 0.00 0.00 0.00 4.24
3484 3617 4.104102 TCCTTTCTCTTTAGTTTGGGAGCA 59.896 41.667 0.00 0.00 0.00 4.26
3485 3618 4.652822 TCCTTTCTCTTTAGTTTGGGAGC 58.347 43.478 0.00 0.00 0.00 4.70
3486 3619 6.207614 CCTTTCCTTTCTCTTTAGTTTGGGAG 59.792 42.308 0.00 0.00 0.00 4.30
3487 3620 6.068670 CCTTTCCTTTCTCTTTAGTTTGGGA 58.931 40.000 0.00 0.00 0.00 4.37
3488 3621 6.068670 TCCTTTCCTTTCTCTTTAGTTTGGG 58.931 40.000 0.00 0.00 0.00 4.12
3489 3622 6.998673 TCTCCTTTCCTTTCTCTTTAGTTTGG 59.001 38.462 0.00 0.00 0.00 3.28
3490 3623 7.717436 AGTCTCCTTTCCTTTCTCTTTAGTTTG 59.283 37.037 0.00 0.00 0.00 2.93
3491 3624 7.717436 CAGTCTCCTTTCCTTTCTCTTTAGTTT 59.283 37.037 0.00 0.00 0.00 2.66
3492 3625 7.071321 TCAGTCTCCTTTCCTTTCTCTTTAGTT 59.929 37.037 0.00 0.00 0.00 2.24
3493 3626 6.555360 TCAGTCTCCTTTCCTTTCTCTTTAGT 59.445 38.462 0.00 0.00 0.00 2.24
3494 3627 6.998802 TCAGTCTCCTTTCCTTTCTCTTTAG 58.001 40.000 0.00 0.00 0.00 1.85
3495 3628 6.996180 TCAGTCTCCTTTCCTTTCTCTTTA 57.004 37.500 0.00 0.00 0.00 1.85
3496 3629 5.896073 TCAGTCTCCTTTCCTTTCTCTTT 57.104 39.130 0.00 0.00 0.00 2.52
3497 3630 5.784906 AGATCAGTCTCCTTTCCTTTCTCTT 59.215 40.000 0.00 0.00 0.00 2.85
3498 3631 5.341169 AGATCAGTCTCCTTTCCTTTCTCT 58.659 41.667 0.00 0.00 0.00 3.10
3499 3632 5.675684 AGATCAGTCTCCTTTCCTTTCTC 57.324 43.478 0.00 0.00 0.00 2.87
3500 3633 5.545723 TCAAGATCAGTCTCCTTTCCTTTCT 59.454 40.000 0.00 0.00 32.15 2.52
3501 3634 5.641636 GTCAAGATCAGTCTCCTTTCCTTTC 59.358 44.000 0.00 0.00 32.15 2.62
3502 3635 5.555966 GTCAAGATCAGTCTCCTTTCCTTT 58.444 41.667 0.00 0.00 32.15 3.11
3503 3636 4.322349 CGTCAAGATCAGTCTCCTTTCCTT 60.322 45.833 0.00 0.00 32.15 3.36
3504 3637 3.194542 CGTCAAGATCAGTCTCCTTTCCT 59.805 47.826 0.00 0.00 32.15 3.36
3505 3638 3.056465 ACGTCAAGATCAGTCTCCTTTCC 60.056 47.826 0.00 0.00 32.15 3.13
3506 3639 4.170256 GACGTCAAGATCAGTCTCCTTTC 58.830 47.826 11.55 0.00 32.15 2.62
3507 3640 3.366476 CGACGTCAAGATCAGTCTCCTTT 60.366 47.826 17.16 0.00 32.15 3.11
3508 3641 2.162608 CGACGTCAAGATCAGTCTCCTT 59.837 50.000 17.16 0.00 32.15 3.36
3509 3642 1.740585 CGACGTCAAGATCAGTCTCCT 59.259 52.381 17.16 0.00 32.15 3.69
3510 3643 1.202200 CCGACGTCAAGATCAGTCTCC 60.202 57.143 17.16 0.00 32.15 3.71
3511 3644 1.469308 ACCGACGTCAAGATCAGTCTC 59.531 52.381 17.16 0.00 32.15 3.36
3512 3645 1.200252 CACCGACGTCAAGATCAGTCT 59.800 52.381 17.16 0.00 35.82 3.24
3513 3646 1.068472 ACACCGACGTCAAGATCAGTC 60.068 52.381 17.16 0.00 0.00 3.51
3514 3647 0.959553 ACACCGACGTCAAGATCAGT 59.040 50.000 17.16 0.83 0.00 3.41
3515 3648 1.618861 GACACCGACGTCAAGATCAG 58.381 55.000 17.16 0.00 35.88 2.90
3516 3649 0.109919 CGACACCGACGTCAAGATCA 60.110 55.000 17.16 0.00 38.22 2.92
3517 3650 0.797249 CCGACACCGACGTCAAGATC 60.797 60.000 17.16 6.59 38.22 2.75
3518 3651 1.211969 CCGACACCGACGTCAAGAT 59.788 57.895 17.16 0.00 38.22 2.40
3519 3652 1.727511 AACCGACACCGACGTCAAGA 61.728 55.000 17.16 0.00 38.22 3.02
3520 3653 0.872881 AAACCGACACCGACGTCAAG 60.873 55.000 17.16 8.75 38.22 3.02
3521 3654 0.459934 AAAACCGACACCGACGTCAA 60.460 50.000 17.16 0.00 38.22 3.18
3522 3655 0.459934 AAAAACCGACACCGACGTCA 60.460 50.000 17.16 0.00 38.22 4.35
3523 3656 0.230515 GAAAAACCGACACCGACGTC 59.769 55.000 5.18 5.18 38.22 4.34
3524 3657 1.481819 CGAAAAACCGACACCGACGT 61.482 55.000 0.00 0.00 38.22 4.34
3525 3658 1.199859 CGAAAAACCGACACCGACG 59.800 57.895 0.00 0.00 38.22 5.12
3526 3659 0.929615 TTCGAAAAACCGACACCGAC 59.070 50.000 0.00 0.00 38.39 4.79
3527 3660 1.327156 GTTTCGAAAAACCGACACCGA 59.673 47.619 13.10 0.00 39.10 4.69
3528 3661 1.062294 TGTTTCGAAAAACCGACACCG 59.938 47.619 13.10 0.00 43.44 4.94
3529 3662 2.828874 TGTTTCGAAAAACCGACACC 57.171 45.000 13.10 0.00 43.44 4.16
3530 3663 4.794246 TCAATTGTTTCGAAAAACCGACAC 59.206 37.500 13.10 0.00 43.44 3.67
3531 3664 4.794246 GTCAATTGTTTCGAAAAACCGACA 59.206 37.500 13.10 2.81 43.44 4.35
3532 3665 5.032220 AGTCAATTGTTTCGAAAAACCGAC 58.968 37.500 13.10 14.62 43.44 4.79
3533 3666 5.238006 AGTCAATTGTTTCGAAAAACCGA 57.762 34.783 13.10 0.53 43.44 4.69
3534 3667 6.469595 TGTTAGTCAATTGTTTCGAAAAACCG 59.530 34.615 13.10 0.87 43.44 4.44
3535 3668 7.512426 CGTGTTAGTCAATTGTTTCGAAAAACC 60.512 37.037 13.10 0.75 43.44 3.27
3536 3669 7.007636 ACGTGTTAGTCAATTGTTTCGAAAAAC 59.992 33.333 13.10 10.32 44.18 2.43
3537 3670 7.007546 CACGTGTTAGTCAATTGTTTCGAAAAA 59.992 33.333 13.10 3.93 0.00 1.94
3538 3671 6.466413 CACGTGTTAGTCAATTGTTTCGAAAA 59.534 34.615 13.10 0.00 0.00 2.29
3539 3672 5.960683 CACGTGTTAGTCAATTGTTTCGAAA 59.039 36.000 6.47 6.47 0.00 3.46
3540 3673 5.494618 CACGTGTTAGTCAATTGTTTCGAA 58.505 37.500 7.58 0.00 0.00 3.71
3541 3674 4.025563 CCACGTGTTAGTCAATTGTTTCGA 60.026 41.667 15.65 0.00 0.00 3.71
3542 3675 4.208355 CCACGTGTTAGTCAATTGTTTCG 58.792 43.478 15.65 5.17 0.00 3.46
3701 3838 3.007323 GGCAACTCCTACCCCGGT 61.007 66.667 0.00 0.00 0.00 5.28
3955 4097 6.719370 TGAGTTGCCTGGTTATAAGTTTTGAT 59.281 34.615 0.00 0.00 0.00 2.57
4131 4274 2.361104 TTGCCCGACCAGATTGGC 60.361 61.111 0.00 0.00 42.67 4.52
4216 4359 5.841810 AGTCAAAAAGAATTCAATCGGCAA 58.158 33.333 8.44 0.00 0.00 4.52
4220 4363 8.579682 AGGAAAAGTCAAAAAGAATTCAATCG 57.420 30.769 8.44 0.00 32.53 3.34
4242 4385 5.396213 CCAAAATCAACAACAAAAGGGAGGA 60.396 40.000 0.00 0.00 0.00 3.71
4464 4608 0.106569 CAGGTATGGGCAGCATCCAA 60.107 55.000 0.00 0.00 37.87 3.53


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

AutoCloner maintained by Alex Coulton.