Multiple sequence alignment - TraesCS4A01G115100

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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 TraesCS4A01G115100 chr4A 100.000 3470 0 0 1 3470 140135872 140132403 0.000000e+00 6408.0
1 TraesCS4A01G115100 chr4B 91.262 1831 102 27 1 1800 411627772 411629575 0.000000e+00 2442.0
2 TraesCS4A01G115100 chr4B 92.052 692 39 8 1987 2676 411629903 411630580 0.000000e+00 959.0
3 TraesCS4A01G115100 chr4B 97.826 46 1 0 1863 1908 42225999 42225954 2.870000e-11 80.5
4 TraesCS4A01G115100 chr4D 95.794 1070 31 6 1618 2683 333266996 333268055 0.000000e+00 1714.0
5 TraesCS4A01G115100 chr4D 98.002 851 12 2 783 1633 333266122 333266967 0.000000e+00 1472.0
6 TraesCS4A01G115100 chr4D 89.744 819 47 5 2686 3470 333268154 333268969 0.000000e+00 1013.0
7 TraesCS4A01G115100 chr4D 91.483 634 47 4 1 629 333130603 333131234 0.000000e+00 865.0
8 TraesCS4A01G115100 chr3B 87.417 151 7 6 1854 2003 448788711 448788850 2.770000e-36 163.0
9 TraesCS4A01G115100 chr3B 92.857 70 4 1 3401 3470 48786594 48786662 2.200000e-17 100.0
10 TraesCS4A01G115100 chr2B 87.413 143 10 3 1862 2004 436958342 436958208 1.290000e-34 158.0
11 TraesCS4A01G115100 chr2B 92.857 56 3 1 1853 1908 457680137 457680083 2.870000e-11 80.5
12 TraesCS4A01G115100 chr6D 87.681 138 8 3 1863 2000 8836356 8836228 6.000000e-33 152.0
13 TraesCS4A01G115100 chr3D 87.500 136 8 3 1864 1999 563835111 563835237 7.760000e-32 148.0
14 TraesCS4A01G115100 chr2D 85.034 147 11 5 1854 1999 513460270 513460406 4.670000e-29 139.0
15 TraesCS4A01G115100 chr2D 92.647 68 4 1 3403 3470 645002458 645002392 2.850000e-16 97.1
16 TraesCS4A01G115100 chr5D 82.840 169 14 7 1855 2010 504792197 504792363 1.680000e-28 137.0
17 TraesCS4A01G115100 chr2A 84.459 148 13 4 1857 2004 498040756 498040619 1.680000e-28 137.0
18 TraesCS4A01G115100 chr7D 86.260 131 9 2 1863 1993 444848234 444848355 2.170000e-27 134.0
19 TraesCS4A01G115100 chr1D 84.921 126 10 2 1863 1988 337361870 337361754 6.080000e-23 119.0
20 TraesCS4A01G115100 chr6A 82.812 128 19 3 1872 1999 32872791 32872915 1.020000e-20 111.0
21 TraesCS4A01G115100 chr1A 80.576 139 15 9 1856 1993 432930381 432930254 2.850000e-16 97.1
22 TraesCS4A01G115100 chr1B 80.147 136 19 6 1860 1993 633041580 633041709 1.030000e-15 95.3
23 TraesCS4A01G115100 chr7B 79.412 136 16 9 1860 1993 307360082 307360207 6.170000e-13 86.1


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 TraesCS4A01G115100 chr4A 140132403 140135872 3469 True 6408.000000 6408 100.000000 1 3470 1 chr4A.!!$R1 3469
1 TraesCS4A01G115100 chr4B 411627772 411630580 2808 False 1700.500000 2442 91.657000 1 2676 2 chr4B.!!$F1 2675
2 TraesCS4A01G115100 chr4D 333266122 333268969 2847 False 1399.666667 1714 94.513333 783 3470 3 chr4D.!!$F2 2687
3 TraesCS4A01G115100 chr4D 333130603 333131234 631 False 865.000000 865 91.483000 1 629 1 chr4D.!!$F1 628

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
370 379 0.394352 GGCGGATGTCCTCCAACAAT 60.394 55.0 3.20 0.0 45.24 2.71 F
404 413 0.694771 ACTGAGCTCCTTCAATGGCA 59.305 50.0 12.15 0.0 0.00 4.92 F
557 566 0.949105 GCGACATGTTTCACCCGAGT 60.949 55.0 0.00 0.0 0.00 4.18 F
753 765 1.363744 CCTCAATCGACTGTGCTTCC 58.636 55.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 1387 2.557317 TCCATAAAAATCCGGAGCGAC 58.443 47.619 11.34 0.0 0.00 5.19 R
2021 2305 2.998670 GGTAAACGGTCAGGCTAAAGTC 59.001 50.000 0.00 0.0 0.00 3.01 R
2176 2460 4.693095 TGCAGCAATACAACATAACGAGAA 59.307 37.500 0.00 0.0 0.00 2.87 R
2690 3074 3.096852 TGGCCCTACCATGAGTTGA 57.903 52.632 0.00 0.0 46.36 3.18 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
128 134 0.766674 CCCCCATCTCCGATAACCCA 60.767 60.000 0.00 0.00 0.00 4.51
132 138 1.958579 CCATCTCCGATAACCCACGTA 59.041 52.381 0.00 0.00 0.00 3.57
149 155 2.725312 TAGCCTCCGCCTCTTGCAG 61.725 63.158 0.00 0.00 41.33 4.41
174 180 2.554032 CCAACATTGGCGACTTCTTCTT 59.446 45.455 0.00 0.00 42.21 2.52
217 223 7.555914 ACACATTAGCCCAAAGAAAAACAAATT 59.444 29.630 0.00 0.00 0.00 1.82
262 268 2.158769 ACCAAGACAGAGCATCAACACA 60.159 45.455 0.00 0.00 37.82 3.72
271 277 3.353836 ATCAACACACCCGCACGC 61.354 61.111 0.00 0.00 0.00 5.34
301 307 0.404040 AGGGCGAAAATCCTCCAACA 59.596 50.000 0.00 0.00 0.00 3.33
312 318 1.340248 TCCTCCAACAACAGAGACGAC 59.660 52.381 0.00 0.00 31.43 4.34
344 353 1.300971 CCTCCAATGACAGCCACACG 61.301 60.000 0.00 0.00 0.00 4.49
370 379 0.394352 GGCGGATGTCCTCCAACAAT 60.394 55.000 3.20 0.00 45.24 2.71
373 382 2.354821 GCGGATGTCCTCCAACAATAAC 59.645 50.000 0.00 0.00 45.24 1.89
383 392 2.021457 CCAACAATAACGACATCCCCC 58.979 52.381 0.00 0.00 0.00 5.40
384 393 1.668751 CAACAATAACGACATCCCCCG 59.331 52.381 0.00 0.00 0.00 5.73
385 394 1.196911 ACAATAACGACATCCCCCGA 58.803 50.000 0.00 0.00 0.00 5.14
386 395 1.134610 ACAATAACGACATCCCCCGAC 60.135 52.381 0.00 0.00 0.00 4.79
387 396 1.138266 CAATAACGACATCCCCCGACT 59.862 52.381 0.00 0.00 0.00 4.18
404 413 0.694771 ACTGAGCTCCTTCAATGGCA 59.305 50.000 12.15 0.00 0.00 4.92
405 414 1.284198 ACTGAGCTCCTTCAATGGCAT 59.716 47.619 12.15 0.00 0.00 4.40
419 428 1.753930 TGGCATCATCAAGCGACAAT 58.246 45.000 0.00 0.00 0.00 2.71
468 477 1.625818 AGTTCCTCGCCAAATCTCACT 59.374 47.619 0.00 0.00 0.00 3.41
473 482 2.366916 CCTCGCCAAATCTCACTATCCT 59.633 50.000 0.00 0.00 0.00 3.24
538 547 3.185188 CCACAACGAAGACATCAACAGAG 59.815 47.826 0.00 0.00 0.00 3.35
557 566 0.949105 GCGACATGTTTCACCCGAGT 60.949 55.000 0.00 0.00 0.00 4.18
623 634 2.635443 GCCCCCACCATTGACAACG 61.635 63.158 0.00 0.00 0.00 4.10
698 710 3.065371 CCTCCAAATATCCAACAAGCGAC 59.935 47.826 0.00 0.00 0.00 5.19
702 714 2.332063 ATATCCAACAAGCGACCTGG 57.668 50.000 0.00 0.00 0.00 4.45
716 728 3.821841 CGACCTGGTTGAAATTAAGCAC 58.178 45.455 8.48 0.00 34.66 4.40
722 734 5.409214 CCTGGTTGAAATTAAGCACCAAATG 59.591 40.000 0.00 0.00 34.66 2.32
746 758 2.028420 TCAATGCCCTCAATCGACTG 57.972 50.000 0.00 0.00 0.00 3.51
753 765 1.363744 CCTCAATCGACTGTGCTTCC 58.636 55.000 0.00 0.00 0.00 3.46
755 767 2.625737 CTCAATCGACTGTGCTTCCAT 58.374 47.619 0.00 0.00 0.00 3.41
780 792 5.187967 CCCGAGGGAGCTTATAGTGATTTAT 59.812 44.000 0.84 0.00 37.50 1.40
781 793 6.380274 CCCGAGGGAGCTTATAGTGATTTATA 59.620 42.308 0.84 0.00 37.50 0.98
863 875 9.820229 TTGCAATTGTATTCTAACTCTTTTACG 57.180 29.630 7.40 0.00 0.00 3.18
864 876 8.995220 TGCAATTGTATTCTAACTCTTTTACGT 58.005 29.630 7.40 0.00 0.00 3.57
897 909 6.069905 ACCACCAACCTTTTCCACTTAAAAAT 60.070 34.615 0.00 0.00 0.00 1.82
1087 1099 1.448540 GCTAGCAAGGCAGCGAAGA 60.449 57.895 10.63 0.00 40.15 2.87
1375 1387 1.743252 GTGAGCCCTTCCTTCGCTG 60.743 63.158 0.00 0.00 31.61 5.18
1391 1403 1.365699 GCTGTCGCTCCGGATTTTTA 58.634 50.000 3.57 0.00 0.00 1.52
1560 1574 7.469043 GCATCATAAATCTTATGGCAGTGTCAA 60.469 37.037 0.00 0.00 0.00 3.18
1637 1697 5.292765 TCTTGCTATGCTAGTACTTGCATC 58.707 41.667 36.75 26.85 46.06 3.91
1660 1720 5.460748 TCGTGGCACAATTATGTACTTATCG 59.539 40.000 19.09 0.00 44.16 2.92
1663 1723 7.327518 CGTGGCACAATTATGTACTTATCGATA 59.672 37.037 19.09 0.00 44.16 2.92
1713 1773 8.462016 GCAAATAGATCTGTAACCTGTTTGATT 58.538 33.333 5.18 0.00 39.66 2.57
1718 1778 5.375417 TCTGTAACCTGTTTGATTGCATG 57.625 39.130 0.00 0.00 0.00 4.06
1766 1826 7.321908 CCAAATGAATGGACACAAACATGATA 58.678 34.615 0.00 0.00 43.54 2.15
1792 1852 8.437575 ACCTCGGATAATCACAAGGTTATAAAT 58.562 33.333 0.00 0.00 33.39 1.40
1908 2192 7.774157 TCCTGTCTTAGATTTGTCTAGATACGT 59.226 37.037 0.00 0.00 0.00 3.57
1909 2193 7.858382 CCTGTCTTAGATTTGTCTAGATACGTG 59.142 40.741 0.00 0.00 0.00 4.49
1910 2194 8.502105 TGTCTTAGATTTGTCTAGATACGTGA 57.498 34.615 0.00 0.00 0.00 4.35
1911 2195 8.396390 TGTCTTAGATTTGTCTAGATACGTGAC 58.604 37.037 0.00 0.00 0.00 3.67
1912 2196 8.396390 GTCTTAGATTTGTCTAGATACGTGACA 58.604 37.037 0.00 0.00 38.71 3.58
1913 2197 9.121658 TCTTAGATTTGTCTAGATACGTGACAT 57.878 33.333 6.51 0.00 39.92 3.06
2106 2390 5.187772 TGAGCTATTCTGAAAAGGCAGTAGA 59.812 40.000 12.51 0.00 37.20 2.59
2128 2412 7.617041 AGATACTGAAAAGGCAGTCATTTAC 57.383 36.000 0.00 0.00 45.54 2.01
2358 2644 4.631813 GCGTCCTTCATATCTTCAACTTGT 59.368 41.667 0.00 0.00 0.00 3.16
2391 2677 6.952773 AGGTGTATGTGCTTCTTTTGTTTA 57.047 33.333 0.00 0.00 0.00 2.01
2664 2952 8.095169 TGAAGAAGGTAGAATTTTAGGAGTGAC 58.905 37.037 0.00 0.00 0.00 3.67
2683 2971 5.645497 AGTGACTAATTGCTTGATCTTGACC 59.355 40.000 0.00 0.00 0.00 4.02
2684 2972 4.631377 TGACTAATTGCTTGATCTTGACCG 59.369 41.667 0.00 0.00 0.00 4.79
2690 3074 3.411446 TGCTTGATCTTGACCGTGAAAT 58.589 40.909 0.00 0.00 0.00 2.17
2734 3118 5.570320 TCTTTTGCAGCTTATAGGACCTTT 58.430 37.500 0.00 0.00 0.00 3.11
2748 3132 7.790782 ATAGGACCTTTTTGCCAAATTAAGA 57.209 32.000 0.00 0.00 0.00 2.10
2807 3191 5.806734 GCTTAACTTATTTCCACCCTCACCT 60.807 44.000 0.00 0.00 0.00 4.00
2930 3335 2.047274 CACCTGTACCCAGCCACG 60.047 66.667 0.00 0.00 37.38 4.94
2931 3336 3.319198 ACCTGTACCCAGCCACGG 61.319 66.667 0.00 0.00 37.38 4.94
2941 3346 1.622607 CCAGCCACGGACCCTTGATA 61.623 60.000 0.00 0.00 0.00 2.15
2974 3380 1.927895 ATCGATTCGTTCTGTCTGGC 58.072 50.000 5.89 0.00 0.00 4.85
2985 3391 0.034059 CTGTCTGGCGAACAAGGAGT 59.966 55.000 0.00 0.00 0.00 3.85
2987 3393 0.033504 GTCTGGCGAACAAGGAGTGA 59.966 55.000 0.00 0.00 0.00 3.41
2988 3394 0.756294 TCTGGCGAACAAGGAGTGAA 59.244 50.000 0.00 0.00 0.00 3.18
2999 3405 3.898123 ACAAGGAGTGAACTCTTCAGCTA 59.102 43.478 10.17 0.00 41.01 3.32
3040 3446 1.208293 CCTCTGCTTGTCCCTTACCTC 59.792 57.143 0.00 0.00 0.00 3.85
3064 3470 1.682684 CACCCGTCCCTCTAGTGCT 60.683 63.158 0.00 0.00 0.00 4.40
3067 3473 0.757188 CCCGTCCCTCTAGTGCTGAT 60.757 60.000 0.00 0.00 0.00 2.90
3073 3479 3.891977 GTCCCTCTAGTGCTGATGACATA 59.108 47.826 0.00 0.00 0.00 2.29
3077 3483 4.320129 CCTCTAGTGCTGATGACATAGACG 60.320 50.000 0.00 0.00 0.00 4.18
3144 3550 2.175322 GCACTCAGCGCTTGAAGC 59.825 61.111 7.50 7.20 34.81 3.86
3146 3552 1.786582 CACTCAGCGCTTGAAGCTC 59.213 57.895 15.92 7.41 44.06 4.09
3153 3559 2.821810 GCTTGAAGCTCCGCCTCC 60.822 66.667 10.44 0.00 38.45 4.30
3223 3629 1.153804 GTCGGAAAGCTCCTCGTCC 60.154 63.158 0.00 0.00 39.93 4.79
3303 3721 3.749064 TCGTGTGCGAGCTCTCCC 61.749 66.667 12.85 0.00 42.81 4.30
3325 3743 2.203983 TCCAGCCAGCTTCCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
3418 3836 7.941790 TCTGATTGTAGACATAGAGATGTAGCT 59.058 37.037 0.00 0.00 46.64 3.32
3425 3843 9.757227 GTAGACATAGAGATGTAGCTGATTTTT 57.243 33.333 0.00 0.00 46.64 1.94
3429 3847 8.671921 ACATAGAGATGTAGCTGATTTTTGTTG 58.328 33.333 0.00 0.00 44.77 3.33
3430 3848 8.886719 CATAGAGATGTAGCTGATTTTTGTTGA 58.113 33.333 0.00 0.00 0.00 3.18
3431 3849 7.138692 AGAGATGTAGCTGATTTTTGTTGAC 57.861 36.000 0.00 0.00 0.00 3.18
3432 3850 6.712095 AGAGATGTAGCTGATTTTTGTTGACA 59.288 34.615 0.00 0.00 0.00 3.58
3433 3851 6.906659 AGATGTAGCTGATTTTTGTTGACAG 58.093 36.000 0.00 0.00 0.00 3.51
3454 3872 5.130477 ACAGTTCTTCAGGTTTCAGGAAGTA 59.870 40.000 0.00 0.00 39.19 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.375773 TGCTTTGTATAGCTTATGCATGGA 58.624 37.500 10.16 0.00 41.76 3.41
40 41 7.482654 TTGCTACTGCTTTGTATAGCTTATG 57.517 36.000 0.00 0.00 41.76 1.90
97 100 0.972883 GATGGGGGAAGAGAGGATCG 59.027 60.000 0.00 0.00 42.67 3.69
98 101 2.256306 GAGATGGGGGAAGAGAGGATC 58.744 57.143 0.00 0.00 0.00 3.36
174 180 3.157881 TGTGTTGTTGTTGTGAGGGAAA 58.842 40.909 0.00 0.00 0.00 3.13
262 268 2.972505 CTTCTGTTGCGTGCGGGT 60.973 61.111 0.00 0.00 0.00 5.28
271 277 1.227999 TTTCGCCCTCGCTTCTGTTG 61.228 55.000 0.00 0.00 35.26 3.33
301 307 1.203563 CGTCGTCGTCGTCTCTGTT 59.796 57.895 3.67 0.00 38.33 3.16
334 343 2.979676 CCATGTGCGTGTGGCTGT 60.980 61.111 0.00 0.00 44.05 4.40
344 353 3.211963 GGACATCCGCCCATGTGC 61.212 66.667 0.00 0.00 37.11 4.57
370 379 0.323633 TCAGTCGGGGGATGTCGTTA 60.324 55.000 0.00 0.00 0.00 3.18
373 382 2.808315 CTCAGTCGGGGGATGTCG 59.192 66.667 0.00 0.00 0.00 4.35
383 392 1.649664 CCATTGAAGGAGCTCAGTCG 58.350 55.000 17.19 0.00 0.00 4.18
384 393 1.339438 TGCCATTGAAGGAGCTCAGTC 60.339 52.381 17.19 12.25 0.00 3.51
385 394 0.694771 TGCCATTGAAGGAGCTCAGT 59.305 50.000 17.19 1.37 0.00 3.41
386 395 1.948145 GATGCCATTGAAGGAGCTCAG 59.052 52.381 17.19 0.00 0.00 3.35
387 396 1.282738 TGATGCCATTGAAGGAGCTCA 59.717 47.619 17.19 0.00 0.00 4.26
404 413 5.468072 GTCATCCTTATTGTCGCTTGATGAT 59.532 40.000 0.00 0.00 39.24 2.45
405 414 4.811024 GTCATCCTTATTGTCGCTTGATGA 59.189 41.667 0.00 0.00 35.92 2.92
419 428 2.447408 TACGGGAGCAGTCATCCTTA 57.553 50.000 0.00 0.00 37.01 2.69
468 477 1.897423 CACTGGTGGTGCGAGGATA 59.103 57.895 0.00 0.00 39.22 2.59
538 547 0.949105 ACTCGGGTGAAACATGTCGC 60.949 55.000 0.00 0.00 39.98 5.19
623 634 1.439679 GATGGGTCGTGTGGAACTTC 58.560 55.000 0.00 0.00 38.04 3.01
634 645 1.002659 TGTTGGTAAGTGGATGGGTCG 59.997 52.381 0.00 0.00 0.00 4.79
698 710 4.599047 TTGGTGCTTAATTTCAACCAGG 57.401 40.909 0.00 0.00 0.00 4.45
702 714 7.489574 TTTCCATTTGGTGCTTAATTTCAAC 57.510 32.000 0.00 0.00 36.34 3.18
711 723 4.004982 GCATTGATTTCCATTTGGTGCTT 58.995 39.130 0.00 0.00 36.34 3.91
716 728 3.198200 TGAGGGCATTGATTTCCATTTGG 59.802 43.478 0.00 0.00 0.00 3.28
722 734 2.951642 TCGATTGAGGGCATTGATTTCC 59.048 45.455 0.00 0.00 0.00 3.13
746 758 2.190578 CCCTCGGGATGGAAGCAC 59.809 66.667 0.00 0.00 37.50 4.40
753 765 2.232452 CACTATAAGCTCCCTCGGGATG 59.768 54.545 4.90 1.45 44.24 3.51
755 767 1.497716 TCACTATAAGCTCCCTCGGGA 59.502 52.381 4.32 4.32 42.90 5.14
897 909 2.137523 GCGAGACGTGGAAAGGTTTAA 58.862 47.619 0.00 0.00 0.00 1.52
974 986 0.329596 CTGGGGTTTCAGGGGAAGAG 59.670 60.000 0.00 0.00 33.82 2.85
975 987 1.789576 GCTGGGGTTTCAGGGGAAGA 61.790 60.000 0.00 0.00 35.43 2.87
977 989 1.368268 AAGCTGGGGTTTCAGGGGAA 61.368 55.000 0.00 0.00 35.43 3.97
1375 1387 2.557317 TCCATAAAAATCCGGAGCGAC 58.443 47.619 11.34 0.00 0.00 5.19
1391 1403 4.042684 GGCTCCTTCTATTCCAGATTCCAT 59.957 45.833 0.00 0.00 31.77 3.41
1531 1545 5.475909 ACTGCCATAAGATTTATGATGCAGG 59.524 40.000 25.92 16.57 40.87 4.85
1637 1697 5.460748 TCGATAAGTACATAATTGTGCCACG 59.539 40.000 1.57 0.37 39.07 4.94
1660 1720 6.511767 CGGTTCCAGTTTCATGCAACTATATC 60.512 42.308 10.49 3.04 35.10 1.63
1663 1723 3.440173 CGGTTCCAGTTTCATGCAACTAT 59.560 43.478 10.49 0.00 35.10 2.12
1718 1778 7.885297 TGGCTATTAATCAATTTACATGCTCC 58.115 34.615 0.00 0.00 0.00 4.70
1766 1826 5.888982 ATAACCTTGTGATTATCCGAGGT 57.111 39.130 13.43 13.43 39.08 3.85
1792 1852 7.173562 ACATGTAGCGAATACTTGTTACCAAAA 59.826 33.333 0.00 0.00 45.58 2.44
1909 2193 7.192148 ACATGACTAGATACAGACGTATGTC 57.808 40.000 20.67 6.50 45.86 3.06
1910 2194 7.569639 AACATGACTAGATACAGACGTATGT 57.430 36.000 20.85 20.85 38.48 2.29
1911 2195 8.858003 AAAACATGACTAGATACAGACGTATG 57.142 34.615 8.99 8.99 38.48 2.39
1913 2197 9.170734 ACTAAAACATGACTAGATACAGACGTA 57.829 33.333 0.00 0.00 0.00 3.57
1914 2198 7.968956 CACTAAAACATGACTAGATACAGACGT 59.031 37.037 0.00 0.00 0.00 4.34
1915 2199 7.968956 ACACTAAAACATGACTAGATACAGACG 59.031 37.037 0.00 0.00 0.00 4.18
1916 2200 9.640963 AACACTAAAACATGACTAGATACAGAC 57.359 33.333 0.00 0.00 0.00 3.51
1951 2235 9.256228 TCTTGTCTTAGGTTTGTCTAGATACAT 57.744 33.333 0.00 0.00 0.00 2.29
1959 2243 7.201911 CCCAAAATTCTTGTCTTAGGTTTGTCT 60.202 37.037 0.00 0.00 0.00 3.41
2021 2305 2.998670 GGTAAACGGTCAGGCTAAAGTC 59.001 50.000 0.00 0.00 0.00 3.01
2117 2401 8.901016 ACTTCTGCAAGTACAGTAAATGACTGC 61.901 40.741 0.00 0.00 46.04 4.40
2128 2412 5.741388 AACTGAAACTTCTGCAAGTACAG 57.259 39.130 16.91 16.91 42.45 2.74
2169 2453 7.413000 GCAATACAACATAACGAGAAGACATGT 60.413 37.037 0.00 0.00 32.23 3.21
2176 2460 4.693095 TGCAGCAATACAACATAACGAGAA 59.307 37.500 0.00 0.00 0.00 2.87
2358 2644 6.714810 AGAAGCACATACACCTTTTACATGAA 59.285 34.615 0.00 0.00 0.00 2.57
2391 2677 9.103861 CCTAAAACAAAACAACATGTTACCAAT 57.896 29.630 11.53 0.00 40.14 3.16
2657 2945 5.877012 TCAAGATCAAGCAATTAGTCACTCC 59.123 40.000 0.00 0.00 0.00 3.85
2664 2952 4.631377 TCACGGTCAAGATCAAGCAATTAG 59.369 41.667 0.00 0.00 0.00 1.73
2683 2971 3.623060 CCCTACCATGAGTTGATTTCACG 59.377 47.826 0.00 0.00 0.00 4.35
2684 2972 3.378427 GCCCTACCATGAGTTGATTTCAC 59.622 47.826 0.00 0.00 0.00 3.18
2690 3074 3.096852 TGGCCCTACCATGAGTTGA 57.903 52.632 0.00 0.00 46.36 3.18
2734 3118 8.553459 TTGTTCTTTTGTCTTAATTTGGCAAA 57.447 26.923 16.01 16.01 0.00 3.68
2748 3132 7.095816 CCAAAACGAGTTCTTTTGTTCTTTTGT 60.096 33.333 7.23 0.00 37.04 2.83
2807 3191 4.706476 CCAGCTTATTTCCATTGTGAAGGA 59.294 41.667 0.00 0.00 0.00 3.36
2922 3327 1.622607 TATCAAGGGTCCGTGGCTGG 61.623 60.000 3.29 0.00 0.00 4.85
2974 3380 3.717707 TGAAGAGTTCACTCCTTGTTCG 58.282 45.455 3.20 0.00 43.88 3.95
2985 3391 2.567615 GGAACCCTAGCTGAAGAGTTCA 59.432 50.000 11.61 0.00 36.25 3.18
3028 3434 2.288025 GGGTGCGAGGTAAGGGACA 61.288 63.158 0.00 0.00 0.00 4.02
3058 3464 3.551846 TCCGTCTATGTCATCAGCACTA 58.448 45.455 0.00 0.00 0.00 2.74
3064 3470 2.073252 AGCCTCCGTCTATGTCATCA 57.927 50.000 0.00 0.00 0.00 3.07
3067 3473 1.319541 GCTAGCCTCCGTCTATGTCA 58.680 55.000 2.29 0.00 0.00 3.58
3073 3479 3.742248 GAGGGGCTAGCCTCCGTCT 62.742 68.421 30.65 19.34 37.26 4.18
3170 3576 3.312718 GGCATGGCTTTGGTGGCA 61.313 61.111 12.86 0.00 46.31 4.92
3277 3695 2.261361 CGCACACGAGGGTCATCA 59.739 61.111 0.00 0.00 43.93 3.07
3303 3721 4.785453 GAAGCTGGCTGGACGGGG 62.785 72.222 0.00 0.00 0.00 5.73
3306 3724 2.125350 GAGGAAGCTGGCTGGACG 60.125 66.667 0.00 0.00 0.00 4.79
3325 3743 4.622695 GCTCAATGGACAACTAGAGAGCTT 60.623 45.833 0.00 0.00 42.77 3.74
3418 3836 6.152661 ACCTGAAGAACTGTCAACAAAAATCA 59.847 34.615 0.00 0.00 0.00 2.57
3425 3843 4.584874 TGAAACCTGAAGAACTGTCAACA 58.415 39.130 0.00 0.00 0.00 3.33
3429 3847 4.073293 TCCTGAAACCTGAAGAACTGTC 57.927 45.455 0.00 0.00 0.00 3.51
3430 3848 4.080299 ACTTCCTGAAACCTGAAGAACTGT 60.080 41.667 5.57 0.00 39.01 3.55
3431 3849 4.455606 ACTTCCTGAAACCTGAAGAACTG 58.544 43.478 5.57 0.00 39.01 3.16
3432 3850 4.779993 ACTTCCTGAAACCTGAAGAACT 57.220 40.909 5.57 0.00 39.01 3.01
3433 3851 7.332182 CACTATACTTCCTGAAACCTGAAGAAC 59.668 40.741 5.57 0.00 39.01 3.01


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

AutoCloner maintained by Alex Coulton.