Multiple sequence alignment - TraesCS6D01G035600

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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 TraesCS6D01G035600 chr6D 100.000 3530 0 0 1 3530 14617702 14621231 0.000000e+00 6519
1 TraesCS6D01G035600 chr6D 85.449 1615 221 6 933 2547 14626045 14624445 0.000000e+00 1668
2 TraesCS6D01G035600 chr6D 86.671 1493 199 0 1039 2531 14656557 14655065 0.000000e+00 1655
3 TraesCS6D01G035600 chr6D 85.570 1587 217 11 1039 2619 14680743 14679163 0.000000e+00 1652
4 TraesCS6D01G035600 chr6B 92.124 3517 170 35 1 3485 26590098 26593539 0.000000e+00 4861
5 TraesCS6D01G035600 chr6B 85.269 1636 224 9 933 2564 26597837 26596215 0.000000e+00 1670
6 TraesCS6D01G035600 chr6B 85.417 1584 216 13 1043 2619 26645599 26644024 0.000000e+00 1631
7 TraesCS6D01G035600 chr6A 90.724 2598 182 32 666 3215 15782991 15780405 0.000000e+00 3408
8 TraesCS6D01G035600 chr6A 85.785 1625 213 11 1001 2619 15727844 15729456 0.000000e+00 1705
9 TraesCS6D01G035600 chr6A 86.200 1529 204 6 1040 2564 15766016 15767541 0.000000e+00 1648
10 TraesCS6D01G035600 chr6A 92.089 632 42 3 8 631 15783618 15782987 0.000000e+00 883
11 TraesCS6D01G035600 chr7A 88.272 162 17 2 3368 3528 10359488 10359648 3.600000e-45 193
12 TraesCS6D01G035600 chr3B 87.349 166 18 3 3365 3529 585835053 585835216 1.670000e-43 187
13 TraesCS6D01G035600 chr4D 87.662 154 19 0 3371 3524 504197228 504197075 2.800000e-41 180
14 TraesCS6D01G035600 chr4D 85.714 161 21 2 3371 3530 500550282 500550123 6.060000e-38 169
15 TraesCS6D01G035600 chr5D 86.792 159 17 4 3373 3529 551089271 551089427 1.300000e-39 174
16 TraesCS6D01G035600 chr2A 86.250 160 20 2 3371 3529 735925972 735925814 4.680000e-39 172
17 TraesCS6D01G035600 chr1A 86.250 160 19 3 3371 3529 53671063 53670906 1.680000e-38 171
18 TraesCS6D01G035600 chr7D 85.276 163 22 2 3368 3529 600879079 600879240 2.180000e-37 167


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 TraesCS6D01G035600 chr6D 14617702 14621231 3529 False 6519.0 6519 100.0000 1 3530 1 chr6D.!!$F1 3529
1 TraesCS6D01G035600 chr6D 14624445 14626045 1600 True 1668.0 1668 85.4490 933 2547 1 chr6D.!!$R1 1614
2 TraesCS6D01G035600 chr6D 14655065 14656557 1492 True 1655.0 1655 86.6710 1039 2531 1 chr6D.!!$R2 1492
3 TraesCS6D01G035600 chr6D 14679163 14680743 1580 True 1652.0 1652 85.5700 1039 2619 1 chr6D.!!$R3 1580
4 TraesCS6D01G035600 chr6B 26590098 26593539 3441 False 4861.0 4861 92.1240 1 3485 1 chr6B.!!$F1 3484
5 TraesCS6D01G035600 chr6B 26596215 26597837 1622 True 1670.0 1670 85.2690 933 2564 1 chr6B.!!$R1 1631
6 TraesCS6D01G035600 chr6B 26644024 26645599 1575 True 1631.0 1631 85.4170 1043 2619 1 chr6B.!!$R2 1576
7 TraesCS6D01G035600 chr6A 15780405 15783618 3213 True 2145.5 3408 91.4065 8 3215 2 chr6A.!!$R1 3207
8 TraesCS6D01G035600 chr6A 15727844 15729456 1612 False 1705.0 1705 85.7850 1001 2619 1 chr6A.!!$F1 1618
9 TraesCS6D01G035600 chr6A 15766016 15767541 1525 False 1648.0 1648 86.2000 1040 2564 1 chr6A.!!$F2 1524

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
917 942 1.303309 CGATCCCAGATCCAAAGCAC 58.697 55.0 0.00 0.0 0.0 4.40 F
2103 2148 0.685785 TCCTCTTCTCCATCTGCGCT 60.686 55.0 9.73 0.0 0.0 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 2300 2.063979 CCCATGTACTCGAGCCCCA 61.064 63.158 13.61 7.05 0.00 4.96 R
3504 3571 0.106708 AAGCACTGGAGCGAGTCAAA 59.893 50.000 0.00 0.00 40.15 2.69 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
121 122 7.598759 ACCTCCGAATTCAACTATATACACT 57.401 36.000 6.22 0.00 0.00 3.55
132 133 1.311859 ATATACACTCGGACGGCGAA 58.688 50.000 16.62 0.00 0.00 4.70
240 242 6.155827 TGAATTTCGTAAAAATCTGCTTGGG 58.844 36.000 0.00 0.00 0.00 4.12
291 298 4.096833 CCATGTGAACAGTATCCCACATTG 59.903 45.833 0.00 0.00 44.88 2.82
295 302 6.716284 TGTGAACAGTATCCCACATTGATTA 58.284 36.000 0.00 0.00 34.96 1.75
631 643 8.792633 CCAAAACAGGAGTGATTAATCAACTAA 58.207 33.333 19.55 0.00 38.75 2.24
664 676 5.263872 TCCCTCCCTTAATTGCTTTGTTA 57.736 39.130 0.00 0.00 0.00 2.41
681 693 6.454186 GCTTTGTTAAACATGAATGATTCCGC 60.454 38.462 0.00 0.00 0.00 5.54
704 718 2.355716 GGGTGCAATGCAGGACTAGTTA 60.356 50.000 8.73 0.00 40.08 2.24
796 814 6.775708 TGGTTAACCTATAGCTGTGAAACTT 58.224 36.000 24.78 0.00 35.43 2.66
894 919 2.178912 GCGCCTGGCTATAAATACCA 57.821 50.000 17.92 0.00 39.11 3.25
917 942 1.303309 CGATCCCAGATCCAAAGCAC 58.697 55.000 0.00 0.00 0.00 4.40
918 943 1.407299 CGATCCCAGATCCAAAGCACA 60.407 52.381 0.00 0.00 0.00 4.57
930 975 4.211125 TCCAAAGCACAAACACCATCTAA 58.789 39.130 0.00 0.00 0.00 2.10
1278 1323 2.948979 CGTGTCTGGCTCTATCTTCTCT 59.051 50.000 0.00 0.00 0.00 3.10
1317 1362 1.222936 CTGCGATCTTCTTGGCCCT 59.777 57.895 0.00 0.00 0.00 5.19
1437 1482 3.760035 GGCTTCTCCCTCGCGACA 61.760 66.667 3.71 0.00 0.00 4.35
1633 1678 1.522569 GCCTACTTCGTGCCAGGAT 59.477 57.895 0.00 0.00 0.00 3.24
1642 1687 1.430632 GTGCCAGGATTGATGCACG 59.569 57.895 0.00 0.00 43.83 5.34
1644 1689 1.307355 TGCCAGGATTGATGCACGTG 61.307 55.000 12.28 12.28 0.00 4.49
1677 1722 2.753043 GTGCTCACCATGGGGCAG 60.753 66.667 23.19 16.29 37.90 4.85
1923 1968 1.213537 CTTCGGCATGGCAAACCTG 59.786 57.895 20.37 1.43 36.63 4.00
2103 2148 0.685785 TCCTCTTCTCCATCTGCGCT 60.686 55.000 9.73 0.00 0.00 5.92
2306 2351 4.320456 CTGCACGCTCCCTGTGGT 62.320 66.667 0.00 0.00 37.80 4.16
2586 2634 5.344933 ACAGTGCGCGTATTATATACACATG 59.655 40.000 8.43 6.76 0.00 3.21
2749 2804 0.323629 ATGTACGTGTCCACTTGGGG 59.676 55.000 0.00 0.00 37.22 4.96
2751 2806 2.886134 TACGTGTCCACTTGGGGCC 61.886 63.158 0.00 0.00 42.20 5.80
2802 2857 6.815089 TGAATCTGTTTTGCCATTGTACTTT 58.185 32.000 0.00 0.00 0.00 2.66
2853 2908 7.327214 ACAAATGTGTAAACAATTGGTGAGTT 58.673 30.769 16.47 0.00 35.72 3.01
2884 2939 8.477419 ACCTTTGAGTGAAATGGAAATAAAGA 57.523 30.769 0.00 0.00 0.00 2.52
2885 2940 9.093458 ACCTTTGAGTGAAATGGAAATAAAGAT 57.907 29.630 0.00 0.00 0.00 2.40
2995 3053 5.055642 TGTCCATGACAGTAGTAAAGACG 57.944 43.478 0.00 0.00 37.67 4.18
3047 3105 6.415798 AAACTGTAAAATGTTTGGTTGCAC 57.584 33.333 0.00 0.00 35.40 4.57
3102 3168 4.437239 CATACTTGAGGTGGATGTCTCAC 58.563 47.826 0.00 0.00 39.43 3.51
3117 3183 6.975772 GGATGTCTCACTGTAAGACTATTCAC 59.024 42.308 12.14 0.00 42.93 3.18
3143 3210 7.059945 CGTACTTGTGCATCTTCAAAATTTCTC 59.940 37.037 0.00 0.00 0.00 2.87
3179 3246 7.007313 AGACATGCAAAACTTTGTTCAAATG 57.993 32.000 0.00 4.18 40.24 2.32
3193 3260 5.350633 TGTTCAAATGTTCCTTGCAGAAAG 58.649 37.500 0.00 0.00 35.47 2.62
3237 3304 6.831769 AGTGTTATCGCAATTAGTTGTCTTG 58.168 36.000 0.00 0.00 37.65 3.02
3288 3355 9.532697 CATTTTGCAAGATAACTGTATTTTTGC 57.467 29.630 1.59 9.70 39.09 3.68
3291 3358 5.109210 GCAAGATAACTGTATTTTTGCCCC 58.891 41.667 6.80 0.00 36.05 5.80
3292 3359 5.105351 GCAAGATAACTGTATTTTTGCCCCT 60.105 40.000 6.80 0.00 36.05 4.79
3293 3360 6.564328 CAAGATAACTGTATTTTTGCCCCTC 58.436 40.000 0.00 0.00 0.00 4.30
3294 3361 4.881850 AGATAACTGTATTTTTGCCCCTCG 59.118 41.667 0.00 0.00 0.00 4.63
3295 3362 2.871096 ACTGTATTTTTGCCCCTCGA 57.129 45.000 0.00 0.00 0.00 4.04
3296 3363 2.433436 ACTGTATTTTTGCCCCTCGAC 58.567 47.619 0.00 0.00 0.00 4.20
3297 3364 2.039879 ACTGTATTTTTGCCCCTCGACT 59.960 45.455 0.00 0.00 0.00 4.18
3298 3365 3.081804 CTGTATTTTTGCCCCTCGACTT 58.918 45.455 0.00 0.00 0.00 3.01
3299 3366 4.258543 CTGTATTTTTGCCCCTCGACTTA 58.741 43.478 0.00 0.00 0.00 2.24
3300 3367 4.850680 TGTATTTTTGCCCCTCGACTTAT 58.149 39.130 0.00 0.00 0.00 1.73
3332 3399 5.710099 TGTATCTTTTGTCCCTCAACCATTC 59.290 40.000 0.00 0.00 35.61 2.67
3343 3410 1.069513 TCAACCATTCTTCGTCACCGT 59.930 47.619 0.00 0.00 35.01 4.83
3356 3423 2.919229 CGTCACCGTCAACTACCAATAC 59.081 50.000 0.00 0.00 0.00 1.89
3365 3432 6.183360 CCGTCAACTACCAATACTGTCTGATA 60.183 42.308 0.00 0.00 0.00 2.15
3366 3433 6.691818 CGTCAACTACCAATACTGTCTGATAC 59.308 42.308 0.00 0.00 0.00 2.24
3368 3435 8.198109 GTCAACTACCAATACTGTCTGATACAT 58.802 37.037 0.00 0.00 37.50 2.29
3369 3436 8.758829 TCAACTACCAATACTGTCTGATACATT 58.241 33.333 0.00 0.00 37.50 2.71
3375 3442 8.200792 ACCAATACTGTCTGATACATTCTTCTC 58.799 37.037 0.00 0.00 37.50 2.87
3382 3449 7.199078 TGTCTGATACATTCTTCTCTTCATCG 58.801 38.462 0.00 0.00 31.43 3.84
3383 3450 6.640499 GTCTGATACATTCTTCTCTTCATCGG 59.360 42.308 0.00 0.00 0.00 4.18
3385 3452 2.544685 ACATTCTTCTCTTCATCGGCG 58.455 47.619 0.00 0.00 0.00 6.46
3386 3453 1.863454 CATTCTTCTCTTCATCGGCGG 59.137 52.381 7.21 0.00 0.00 6.13
3417 3484 0.747644 TGGTTGCGCTGGTCATATGG 60.748 55.000 9.73 0.00 0.00 2.74
3418 3485 0.463654 GGTTGCGCTGGTCATATGGA 60.464 55.000 9.73 0.00 0.00 3.41
3439 3506 1.079503 CCTTAGCACGGCAACTTCTC 58.920 55.000 0.00 0.00 0.00 2.87
3442 3509 0.530744 TAGCACGGCAACTTCTCGAT 59.469 50.000 0.00 0.00 0.00 3.59
3444 3511 0.179215 GCACGGCAACTTCTCGATTG 60.179 55.000 0.00 0.00 0.00 2.67
3451 3518 4.438336 CGGCAACTTCTCGATTGTCTACTA 60.438 45.833 0.20 0.00 0.00 1.82
3487 3554 2.123854 TCCGATGAGGGAGGGACG 60.124 66.667 0.00 0.00 41.52 4.79
3488 3555 2.123854 CCGATGAGGGAGGGACGA 60.124 66.667 0.00 0.00 35.97 4.20
3489 3556 1.531840 CCGATGAGGGAGGGACGAT 60.532 63.158 0.00 0.00 35.97 3.73
3490 3557 1.662608 CGATGAGGGAGGGACGATG 59.337 63.158 0.00 0.00 0.00 3.84
3491 3558 0.823769 CGATGAGGGAGGGACGATGA 60.824 60.000 0.00 0.00 0.00 2.92
3492 3559 0.676736 GATGAGGGAGGGACGATGAC 59.323 60.000 0.00 0.00 0.00 3.06
3493 3560 0.032117 ATGAGGGAGGGACGATGACA 60.032 55.000 0.00 0.00 0.00 3.58
3494 3561 0.684479 TGAGGGAGGGACGATGACAG 60.684 60.000 0.00 0.00 0.00 3.51
3495 3562 2.022240 GAGGGAGGGACGATGACAGC 62.022 65.000 0.00 0.00 0.00 4.40
3496 3563 2.105128 GGAGGGACGATGACAGCG 59.895 66.667 12.26 12.26 0.00 5.18
3497 3564 2.105128 GAGGGACGATGACAGCGG 59.895 66.667 18.40 0.00 0.00 5.52
3498 3565 4.148825 AGGGACGATGACAGCGGC 62.149 66.667 18.40 15.16 35.64 6.53
3500 3567 4.796231 GGACGATGACAGCGGCGT 62.796 66.667 18.40 6.60 37.74 5.68
3501 3568 3.545481 GACGATGACAGCGGCGTG 61.545 66.667 18.40 8.36 37.07 5.34
3511 3578 4.090057 GCGGCGTGCCTTTGACTC 62.090 66.667 9.37 0.00 37.76 3.36
3512 3579 3.777925 CGGCGTGCCTTTGACTCG 61.778 66.667 9.55 0.00 0.00 4.18
3513 3580 4.090057 GGCGTGCCTTTGACTCGC 62.090 66.667 2.98 0.00 46.16 5.03
3514 3581 3.044305 GCGTGCCTTTGACTCGCT 61.044 61.111 0.00 0.00 44.21 4.93
3515 3582 3.016474 GCGTGCCTTTGACTCGCTC 62.016 63.158 0.00 0.00 44.21 5.03
3516 3583 2.383527 CGTGCCTTTGACTCGCTCC 61.384 63.158 0.00 0.00 0.00 4.70
3517 3584 1.301716 GTGCCTTTGACTCGCTCCA 60.302 57.895 0.00 0.00 0.00 3.86
3518 3585 1.004560 TGCCTTTGACTCGCTCCAG 60.005 57.895 0.00 0.00 0.00 3.86
3519 3586 1.004440 GCCTTTGACTCGCTCCAGT 60.004 57.895 0.00 0.00 0.00 4.00
3520 3587 1.294659 GCCTTTGACTCGCTCCAGTG 61.295 60.000 0.00 0.00 0.00 3.66
3521 3588 1.294659 CCTTTGACTCGCTCCAGTGC 61.295 60.000 0.00 0.00 0.00 4.40
3522 3589 0.320247 CTTTGACTCGCTCCAGTGCT 60.320 55.000 0.00 0.00 0.00 4.40
3523 3590 0.106708 TTTGACTCGCTCCAGTGCTT 59.893 50.000 0.00 0.00 0.00 3.91
3524 3591 0.966179 TTGACTCGCTCCAGTGCTTA 59.034 50.000 0.00 0.00 0.00 3.09
3525 3592 1.186200 TGACTCGCTCCAGTGCTTAT 58.814 50.000 0.00 0.00 0.00 1.73
3526 3593 2.375146 TGACTCGCTCCAGTGCTTATA 58.625 47.619 0.00 0.00 0.00 0.98
3527 3594 2.359214 TGACTCGCTCCAGTGCTTATAG 59.641 50.000 0.00 0.00 0.00 1.31
3528 3595 2.359531 GACTCGCTCCAGTGCTTATAGT 59.640 50.000 0.00 0.00 0.00 2.12
3529 3596 2.761208 ACTCGCTCCAGTGCTTATAGTT 59.239 45.455 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.134610 ACGGCCAAATACTTACCTCGG 60.135 52.381 2.24 0.00 0.00 4.63
103 104 6.581542 CCGTCCGAGTGTATATAGTTGAATTC 59.418 42.308 0.00 0.00 0.00 2.17
121 122 1.077645 CGGTAAAATTCGCCGTCCGA 61.078 55.000 0.00 0.00 45.77 4.55
132 133 4.638865 GTGAATTCCACCTAGCGGTAAAAT 59.361 41.667 2.27 0.00 43.24 1.82
180 182 7.750229 AATTTGAGTTAGATTTGAGTCTGCA 57.250 32.000 0.00 0.00 0.00 4.41
291 298 3.695816 GCCTTCTTGATTTGGCGTAATC 58.304 45.455 5.49 5.49 35.79 1.75
390 400 0.743097 GCTCATTGACTTGGATGCCC 59.257 55.000 0.00 0.00 0.00 5.36
395 405 0.674581 CCAGCGCTCATTGACTTGGA 60.675 55.000 7.13 0.00 0.00 3.53
563 575 1.478510 GGAGAGCGTTGAATCTGGAGA 59.521 52.381 0.00 0.00 0.00 3.71
612 624 8.140112 AGTGAGTTAGTTGATTAATCACTCCT 57.860 34.615 17.76 15.00 41.39 3.69
664 676 2.428171 CCCTGCGGAATCATTCATGTTT 59.572 45.455 0.00 0.00 0.00 2.83
681 693 0.035152 TAGTCCTGCATTGCACCCTG 60.035 55.000 7.38 0.00 33.79 4.45
704 718 1.332997 GCTAGCAGCGCAGATTCAATT 59.667 47.619 11.47 0.00 0.00 2.32
796 814 4.646945 ACTCGATTCCTGAAGATTCTAGCA 59.353 41.667 0.00 0.00 0.00 3.49
881 905 2.443887 TCGGCGTGGTATTTATAGCC 57.556 50.000 6.85 0.00 41.03 3.93
883 907 3.056393 TGGGATCGGCGTGGTATTTATAG 60.056 47.826 6.85 0.00 0.00 1.31
894 919 1.622607 TTTGGATCTGGGATCGGCGT 61.623 55.000 6.85 0.00 0.00 5.68
917 942 3.076621 TGCTGCTCTTAGATGGTGTTTG 58.923 45.455 0.00 0.00 0.00 2.93
918 943 3.341823 CTGCTGCTCTTAGATGGTGTTT 58.658 45.455 0.00 0.00 0.00 2.83
930 975 2.282040 GGTGGTTGCTGCTGCTCT 60.282 61.111 17.00 0.00 40.48 4.09
1032 1077 3.921767 CTTGCTCGCAGCCTCGTCA 62.922 63.158 5.82 0.00 41.51 4.35
1335 1380 1.064783 CGCTGCGAGCATGACTAGA 59.935 57.895 18.66 0.00 42.58 2.43
1437 1482 2.143122 CAGTACTGGCACGACACAAAT 58.857 47.619 15.49 0.00 0.00 2.32
1593 1638 2.130821 TACGCCATGCCACAAAGGGA 62.131 55.000 0.00 0.00 44.34 4.20
1633 1678 0.959867 CCCATCACCACGTGCATCAA 60.960 55.000 10.91 0.00 32.98 2.57
1642 1687 2.439156 GAGCAGGCCCATCACCAC 60.439 66.667 0.00 0.00 0.00 4.16
1644 1689 4.101448 ACGAGCAGGCCCATCACC 62.101 66.667 0.00 0.00 0.00 4.02
1923 1968 4.256180 CCCATGGGCCTAGCGACC 62.256 72.222 20.41 0.00 0.00 4.79
2122 2167 2.356125 CGAAGGGGATGACACCAAAGAT 60.356 50.000 0.00 0.00 43.15 2.40
2255 2300 2.063979 CCCATGTACTCGAGCCCCA 61.064 63.158 13.61 7.05 0.00 4.96
2586 2634 3.924686 CGGATTTCAGGCGTATATACACC 59.075 47.826 11.37 11.37 0.00 4.16
2634 2689 9.537852 TCACTACCCATATATACTTACGGAAAT 57.462 33.333 0.00 0.00 0.00 2.17
2720 2775 3.071312 TGGACACGTACATAAACACCCTT 59.929 43.478 0.00 0.00 0.00 3.95
2749 2804 3.504520 TCATTTAACTTTGGAACCGAGGC 59.495 43.478 0.00 0.00 0.00 4.70
2751 2806 6.067263 TGTTCATTTAACTTTGGAACCGAG 57.933 37.500 0.00 0.00 38.99 4.63
2853 2908 7.889873 TTCCATTTCACTCAAAGGTCTTTAA 57.110 32.000 0.00 0.00 0.00 1.52
2951 3009 8.406297 GGACATGTTCTTGACTAGTTTCTTTTT 58.594 33.333 0.00 0.00 0.00 1.94
2952 3010 7.556275 TGGACATGTTCTTGACTAGTTTCTTTT 59.444 33.333 5.55 0.00 0.00 2.27
2995 3053 8.557869 AGTATGTACTAAATCATTTCGTCGAC 57.442 34.615 5.18 5.18 34.13 4.20
3087 3153 3.764434 TCTTACAGTGAGACATCCACCTC 59.236 47.826 0.00 0.00 35.23 3.85
3102 3168 6.033619 GCACAAGTACGTGAATAGTCTTACAG 59.966 42.308 16.00 0.00 39.34 2.74
3117 3183 6.857964 AGAAATTTTGAAGATGCACAAGTACG 59.142 34.615 0.00 0.00 0.00 3.67
3143 3210 5.947503 TTTGCATGTCTTCAAACTTTTCG 57.052 34.783 0.00 0.00 0.00 3.46
3179 3246 5.444663 AAGTTGATCTTTCTGCAAGGAAC 57.555 39.130 0.00 0.00 31.57 3.62
3221 3288 6.195868 TGTACAAACAAGACAACTAATTGCG 58.804 36.000 0.00 0.00 34.03 4.85
3263 3330 8.720562 GGCAAAAATACAGTTATCTTGCAAAAT 58.279 29.630 0.00 0.00 39.48 1.82
3277 3344 2.711542 AGTCGAGGGGCAAAAATACAG 58.288 47.619 0.00 0.00 0.00 2.74
3288 3355 4.205587 ACACTACACTATAAGTCGAGGGG 58.794 47.826 0.00 0.00 0.00 4.79
3292 3359 9.999009 CAAAAGATACACTACACTATAAGTCGA 57.001 33.333 0.00 0.00 0.00 4.20
3293 3360 9.784680 ACAAAAGATACACTACACTATAAGTCG 57.215 33.333 0.00 0.00 0.00 4.18
3296 3363 9.530633 GGGACAAAAGATACACTACACTATAAG 57.469 37.037 0.00 0.00 0.00 1.73
3297 3364 9.263446 AGGGACAAAAGATACACTACACTATAA 57.737 33.333 0.00 0.00 0.00 0.98
3298 3365 8.834004 AGGGACAAAAGATACACTACACTATA 57.166 34.615 0.00 0.00 0.00 1.31
3299 3366 7.399191 TGAGGGACAAAAGATACACTACACTAT 59.601 37.037 0.00 0.00 0.00 2.12
3300 3367 6.722590 TGAGGGACAAAAGATACACTACACTA 59.277 38.462 0.00 0.00 0.00 2.74
3343 3410 7.712204 TGTATCAGACAGTATTGGTAGTTGA 57.288 36.000 0.00 0.00 32.86 3.18
3356 3423 7.379262 CGATGAAGAGAAGAATGTATCAGACAG 59.621 40.741 0.00 0.00 42.79 3.51
3365 3432 2.544685 CGCCGATGAAGAGAAGAATGT 58.455 47.619 0.00 0.00 0.00 2.71
3366 3433 1.863454 CCGCCGATGAAGAGAAGAATG 59.137 52.381 0.00 0.00 0.00 2.67
3368 3435 0.460284 GCCGCCGATGAAGAGAAGAA 60.460 55.000 0.00 0.00 0.00 2.52
3369 3436 1.141881 GCCGCCGATGAAGAGAAGA 59.858 57.895 0.00 0.00 0.00 2.87
3385 3452 3.605664 AACCAAACAGCAGCCGCC 61.606 61.111 0.00 0.00 39.83 6.13
3386 3453 2.355009 CAACCAAACAGCAGCCGC 60.355 61.111 0.00 0.00 38.99 6.53
3390 3457 1.659335 CAGCGCAACCAAACAGCAG 60.659 57.895 11.47 0.00 0.00 4.24
3399 3466 0.463654 TCCATATGACCAGCGCAACC 60.464 55.000 11.47 0.00 0.00 3.77
3401 3468 0.815213 GCTCCATATGACCAGCGCAA 60.815 55.000 11.47 0.00 0.00 4.85
3442 3509 5.009210 GGGCAAACATTGTTGTAGTAGACAA 59.991 40.000 2.13 2.49 46.03 3.18
3444 3511 4.378046 CGGGCAAACATTGTTGTAGTAGAC 60.378 45.833 2.13 0.00 34.06 2.59
3451 3518 1.336755 GAGTCGGGCAAACATTGTTGT 59.663 47.619 2.13 0.00 37.82 3.32
3488 3555 4.704833 AAGGCACGCCGCTGTCAT 62.705 61.111 1.61 0.00 41.91 3.06
3489 3556 4.927782 AAAGGCACGCCGCTGTCA 62.928 61.111 1.61 0.00 41.91 3.58
3490 3557 4.389576 CAAAGGCACGCCGCTGTC 62.390 66.667 1.61 0.00 41.91 3.51
3491 3558 4.927782 TCAAAGGCACGCCGCTGT 62.928 61.111 1.61 0.00 41.91 4.40
3492 3559 4.389576 GTCAAAGGCACGCCGCTG 62.390 66.667 1.61 4.33 41.91 5.18
3493 3560 4.626081 AGTCAAAGGCACGCCGCT 62.626 61.111 1.61 0.00 41.91 5.52
3494 3561 4.090057 GAGTCAAAGGCACGCCGC 62.090 66.667 1.61 0.00 41.95 6.53
3495 3562 3.777925 CGAGTCAAAGGCACGCCG 61.778 66.667 1.61 0.00 41.95 6.46
3496 3563 4.090057 GCGAGTCAAAGGCACGCC 62.090 66.667 0.00 0.00 42.79 5.68
3498 3565 2.383527 GGAGCGAGTCAAAGGCACG 61.384 63.158 0.00 0.00 0.00 5.34
3499 3566 1.294659 CTGGAGCGAGTCAAAGGCAC 61.295 60.000 0.00 0.00 0.00 5.01
3500 3567 1.004560 CTGGAGCGAGTCAAAGGCA 60.005 57.895 0.00 0.00 0.00 4.75
3501 3568 1.004440 ACTGGAGCGAGTCAAAGGC 60.004 57.895 0.00 0.00 0.00 4.35
3502 3569 1.294659 GCACTGGAGCGAGTCAAAGG 61.295 60.000 0.00 0.00 0.00 3.11
3503 3570 0.320247 AGCACTGGAGCGAGTCAAAG 60.320 55.000 0.00 0.00 40.15 2.77
3504 3571 0.106708 AAGCACTGGAGCGAGTCAAA 59.893 50.000 0.00 0.00 40.15 2.69
3505 3572 0.966179 TAAGCACTGGAGCGAGTCAA 59.034 50.000 0.00 0.00 40.15 3.18
3506 3573 1.186200 ATAAGCACTGGAGCGAGTCA 58.814 50.000 0.00 0.00 40.15 3.41
3507 3574 2.359531 ACTATAAGCACTGGAGCGAGTC 59.640 50.000 0.00 0.00 40.15 3.36
3508 3575 2.379972 ACTATAAGCACTGGAGCGAGT 58.620 47.619 0.00 0.00 40.15 4.18
3509 3576 3.444703 AACTATAAGCACTGGAGCGAG 57.555 47.619 0.00 0.00 40.15 5.03


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

AutoCloner maintained by Alex Coulton.