Multiple sequence alignment - TraesCS2D01G338900

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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 TraesCS2D01G338900 chr2D 100.000 3329 0 0 1 3329 432082070 432078742 0.000000e+00 6148.0
1 TraesCS2D01G338900 chr2D 90.050 201 17 3 1184 1381 352709646 352709846 1.190000e-64 257.0
2 TraesCS2D01G338900 chr2D 91.160 181 15 1 1187 1366 461078665 461078485 9.230000e-61 244.0
3 TraesCS2D01G338900 chr2D 95.902 122 5 0 1605 1726 461078493 461078372 7.280000e-47 198.0
4 TraesCS2D01G338900 chr2D 94.400 125 7 0 1605 1729 352709821 352709945 3.390000e-45 193.0
5 TraesCS2D01G338900 chr2B 88.963 2392 161 39 550 2870 510898567 510896208 0.000000e+00 2859.0
6 TraesCS2D01G338900 chr2B 89.372 414 35 5 2924 3329 510895825 510895413 2.290000e-141 512.0
7 TraesCS2D01G338900 chr2B 88.839 224 15 6 1 219 510901869 510901651 1.970000e-67 267.0
8 TraesCS2D01G338900 chr2B 89.503 181 14 5 295 471 510898615 510898436 1.200000e-54 224.0
9 TraesCS2D01G338900 chr2B 84.722 72 8 3 2560 2629 13221170 13221240 5.960000e-08 69.4
10 TraesCS2D01G338900 chr2B 88.136 59 4 3 2560 2616 13155717 13155774 2.140000e-07 67.6
11 TraesCS2D01G338900 chr2A 92.812 1906 89 18 619 2509 554414588 554416460 0.000000e+00 2717.0
12 TraesCS2D01G338900 chr2A 84.317 644 84 11 2689 3328 554416621 554417251 6.100000e-172 614.0
13 TraesCS2D01G338900 chr2A 83.333 480 32 19 1 471 554413993 554414433 1.860000e-107 399.0
14 TraesCS2D01G338900 chr6D 92.523 321 24 0 1485 1805 456305687 456305367 8.420000e-126 460.0
15 TraesCS2D01G338900 chr6D 95.690 116 5 0 1912 2027 456305370 456305255 1.580000e-43 187.0
16 TraesCS2D01G338900 chr7D 93.004 243 17 0 1485 1727 171027892 171028134 4.080000e-94 355.0
17 TraesCS2D01G338900 chr7D 95.652 138 6 0 1184 1321 171013669 171013806 4.320000e-54 222.0
18 TraesCS2D01G338900 chr7D 96.850 127 4 0 1320 1446 171027774 171027900 2.600000e-51 213.0
19 TraesCS2D01G338900 chr1D 92.778 180 13 0 1184 1363 307206146 307206325 9.160000e-66 261.0
20 TraesCS2D01G338900 chr1D 94.309 123 7 0 1605 1727 307206321 307206443 4.380000e-44 189.0
21 TraesCS2D01G338900 chr1B 87.437 199 22 3 1189 1384 646571991 646571793 3.340000e-55 226.0
22 TraesCS2D01G338900 chr1B 94.262 122 7 0 1605 1726 646571821 646571700 1.580000e-43 187.0
23 TraesCS2D01G338900 chr1B 89.256 121 12 1 1607 1727 646571586 646571467 2.070000e-32 150.0
24 TraesCS2D01G338900 chr4A 78.667 150 20 5 2552 2689 688451340 688451191 4.570000e-14 89.8


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 TraesCS2D01G338900 chr2D 432078742 432082070 3328 True 6148.000000 6148 100.000000 1 3329 1 chr2D.!!$R1 3328
1 TraesCS2D01G338900 chr2B 510895413 510901869 6456 True 965.500000 2859 89.169250 1 3329 4 chr2B.!!$R1 3328
2 TraesCS2D01G338900 chr2A 554413993 554417251 3258 False 1243.333333 2717 86.820667 1 3328 3 chr2A.!!$F1 3327

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
576 3628 0.027063 AAACAACTCGCCAAACGTCG 59.973 50.0 0.0 0.0 44.19 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2459 5579 0.872388 GTTCGCCGAAGTCCAAACAT 59.128 50.0 0.0 0.0 0.0 2.71 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
39 40 1.876156 CGAGAGCTCTGCCTTTGTTTT 59.124 47.619 23.91 0.00 0.00 2.43
74 75 1.166531 GCTGTGCCGTTCCTTTGAGT 61.167 55.000 0.00 0.00 0.00 3.41
75 76 0.588252 CTGTGCCGTTCCTTTGAGTG 59.412 55.000 0.00 0.00 0.00 3.51
78 84 1.072505 GCCGTTCCTTTGAGTGGGA 59.927 57.895 0.00 0.00 0.00 4.37
82 88 2.486548 CCGTTCCTTTGAGTGGGAGAAA 60.487 50.000 0.00 0.00 32.80 2.52
125 131 4.876107 ACATGTTTTATTCCTAGCCTCGTG 59.124 41.667 0.00 0.00 0.00 4.35
179 185 2.642427 CGGTGATTTGACATGGGATGA 58.358 47.619 0.00 0.00 0.00 2.92
182 188 4.272489 GGTGATTTGACATGGGATGAAGA 58.728 43.478 0.00 0.00 0.00 2.87
239 268 2.665649 TACCCATACACACTGAAGCG 57.334 50.000 0.00 0.00 0.00 4.68
253 282 3.506059 AAGCGATCGATGCCCCGAG 62.506 63.158 21.57 0.00 42.21 4.63
257 286 1.666234 GATCGATGCCCCGAGCTTC 60.666 63.158 0.54 1.86 44.23 3.86
260 289 2.423446 GATGCCCCGAGCTTCGAT 59.577 61.111 7.07 0.00 43.74 3.59
261 290 1.666234 GATGCCCCGAGCTTCGATC 60.666 63.158 7.07 0.00 43.74 3.69
262 291 2.093537 GATGCCCCGAGCTTCGATCT 62.094 60.000 7.07 0.00 43.74 2.75
263 292 2.279784 GCCCCGAGCTTCGATCTG 60.280 66.667 7.07 0.00 43.74 2.90
264 293 2.419198 CCCCGAGCTTCGATCTGG 59.581 66.667 7.07 0.00 43.74 3.86
265 294 2.427245 CCCCGAGCTTCGATCTGGT 61.427 63.158 7.07 0.00 43.74 4.00
266 295 1.517832 CCCGAGCTTCGATCTGGTT 59.482 57.895 7.07 0.00 43.74 3.67
267 296 0.807667 CCCGAGCTTCGATCTGGTTG 60.808 60.000 7.07 0.00 43.74 3.77
268 297 0.807667 CCGAGCTTCGATCTGGTTGG 60.808 60.000 7.07 0.00 43.74 3.77
290 319 3.954904 GACCTCTGATTCTACTACAGGCA 59.045 47.826 0.00 0.00 33.19 4.75
370 3360 2.203153 AGCAACTCGCCAACCGTT 60.203 55.556 0.00 0.00 44.04 4.44
377 3367 2.426752 CGCCAACCGTTTTCGCTG 60.427 61.111 0.00 0.00 42.58 5.18
432 3422 1.153628 GGAAGATGCTGCCGTACGT 60.154 57.895 15.21 0.00 0.00 3.57
487 3539 4.141846 ACATTGCGTATCAGGTTGAGAGAT 60.142 41.667 0.00 0.00 0.00 2.75
488 3540 4.471904 TTGCGTATCAGGTTGAGAGATT 57.528 40.909 0.00 0.00 0.00 2.40
502 3554 1.202463 AGAGATTGAGATTCCCACGCG 60.202 52.381 3.53 3.53 0.00 6.01
508 3560 3.254470 TGAGATTCCCACGCGAAAATA 57.746 42.857 15.93 0.00 0.00 1.40
541 3593 0.315568 CTGTACTAGGATCAGCGGCC 59.684 60.000 0.00 0.00 0.00 6.13
542 3594 0.106167 TGTACTAGGATCAGCGGCCT 60.106 55.000 0.00 0.00 38.31 5.19
543 3595 1.041437 GTACTAGGATCAGCGGCCTT 58.959 55.000 0.00 0.00 35.73 4.35
547 3599 1.115930 TAGGATCAGCGGCCTTCTCC 61.116 60.000 0.00 0.00 35.73 3.71
562 3614 0.765135 TCTCCCCCTGACGGAAACAA 60.765 55.000 0.00 0.00 0.00 2.83
563 3615 0.605589 CTCCCCCTGACGGAAACAAC 60.606 60.000 0.00 0.00 0.00 3.32
564 3616 1.057851 TCCCCCTGACGGAAACAACT 61.058 55.000 0.00 0.00 0.00 3.16
565 3617 0.605589 CCCCCTGACGGAAACAACTC 60.606 60.000 0.00 0.00 0.00 3.01
566 3618 0.949105 CCCCTGACGGAAACAACTCG 60.949 60.000 0.00 0.00 0.00 4.18
567 3619 1.566018 CCCTGACGGAAACAACTCGC 61.566 60.000 0.00 0.00 0.00 5.03
568 3620 1.566018 CCTGACGGAAACAACTCGCC 61.566 60.000 0.00 0.00 0.00 5.54
569 3621 0.878523 CTGACGGAAACAACTCGCCA 60.879 55.000 0.00 0.00 0.00 5.69
570 3622 0.462225 TGACGGAAACAACTCGCCAA 60.462 50.000 0.00 0.00 0.00 4.52
571 3623 0.658897 GACGGAAACAACTCGCCAAA 59.341 50.000 0.00 0.00 0.00 3.28
572 3624 0.379316 ACGGAAACAACTCGCCAAAC 59.621 50.000 0.00 0.00 0.00 2.93
573 3625 0.656205 CGGAAACAACTCGCCAAACG 60.656 55.000 0.00 0.00 45.62 3.60
574 3626 0.379316 GGAAACAACTCGCCAAACGT 59.621 50.000 0.00 0.00 44.19 3.99
575 3627 1.596220 GGAAACAACTCGCCAAACGTC 60.596 52.381 0.00 0.00 44.19 4.34
576 3628 0.027063 AAACAACTCGCCAAACGTCG 59.973 50.000 0.00 0.00 44.19 5.12
577 3629 2.127758 CAACTCGCCAAACGTCGC 60.128 61.111 0.00 0.00 44.19 5.19
578 3630 3.343421 AACTCGCCAAACGTCGCC 61.343 61.111 0.00 0.00 44.19 5.54
608 3660 1.571460 GCACAGGCTCTGTTCAACG 59.429 57.895 5.24 0.00 42.59 4.10
609 3661 0.880278 GCACAGGCTCTGTTCAACGA 60.880 55.000 5.24 0.00 42.59 3.85
610 3662 1.581934 CACAGGCTCTGTTCAACGAA 58.418 50.000 5.24 0.00 42.59 3.85
611 3663 1.939934 CACAGGCTCTGTTCAACGAAA 59.060 47.619 5.24 0.00 42.59 3.46
612 3664 2.032549 CACAGGCTCTGTTCAACGAAAG 60.033 50.000 5.24 0.00 42.59 2.62
613 3665 2.158957 ACAGGCTCTGTTCAACGAAAGA 60.159 45.455 2.38 0.00 42.59 2.52
614 3666 2.478134 CAGGCTCTGTTCAACGAAAGAG 59.522 50.000 0.00 0.00 39.35 2.85
615 3667 2.365617 AGGCTCTGTTCAACGAAAGAGA 59.634 45.455 7.42 0.00 38.77 3.10
616 3668 3.131396 GGCTCTGTTCAACGAAAGAGAA 58.869 45.455 7.42 0.00 38.77 2.87
617 3669 3.185391 GGCTCTGTTCAACGAAAGAGAAG 59.815 47.826 7.42 0.00 38.77 2.85
647 3701 1.358877 CGCTGTACTGCTGCATTACA 58.641 50.000 25.07 25.07 41.39 2.41
657 3711 1.304052 TGCATTACACCCTGCCACC 60.304 57.895 0.00 0.00 37.59 4.61
678 3732 0.179179 GTGAAAGCGAGATTGCTGCC 60.179 55.000 0.00 0.00 46.60 4.85
810 3883 2.029073 CGACACCTTGCCACGAGT 59.971 61.111 0.00 0.00 0.00 4.18
823 3896 1.209128 CACGAGTTGTCAAAGCGAGT 58.791 50.000 13.36 0.00 0.00 4.18
860 3941 2.852075 AAACCGTCCCAGCCAGGA 60.852 61.111 0.00 0.00 41.22 3.86
861 3942 2.895424 AAACCGTCCCAGCCAGGAG 61.895 63.158 0.00 0.00 41.22 3.69
881 3962 0.872021 CGCTCCGTATTGCAGAGTCC 60.872 60.000 2.31 0.00 0.00 3.85
884 3965 1.227263 CCGTATTGCAGAGTCCCGG 60.227 63.158 0.00 0.00 0.00 5.73
908 3989 4.003788 CGTGGCAACCCGGAGAGT 62.004 66.667 0.73 0.00 0.00 3.24
986 4072 0.749091 CCATTCCAATCGAGCAGCCA 60.749 55.000 0.00 0.00 0.00 4.75
1034 4124 2.753043 CCTCTGCATGGCCACCAC 60.753 66.667 8.16 0.00 35.80 4.16
1164 4257 3.462678 GAGGCGTCCTCCTCCACC 61.463 72.222 13.12 0.00 44.36 4.61
1968 5082 4.210304 GGCAACGATCGCTGCGTC 62.210 66.667 30.55 17.99 41.75 5.19
2079 5193 4.717313 GGGGACGGGCTGGTTGTC 62.717 72.222 0.00 0.00 0.00 3.18
2247 5361 4.471726 GACGACGGCGATGACGGT 62.472 66.667 22.49 0.00 39.02 4.83
2344 5458 4.142600 GCTTGTAGTAGGTTGGATTTGCTG 60.143 45.833 0.00 0.00 0.00 4.41
2351 5465 2.094545 AGGTTGGATTTGCTGCGATTTC 60.095 45.455 0.00 0.00 0.00 2.17
2526 5647 2.159517 GCCTGAAACTTATCGGCACAAG 60.160 50.000 0.00 0.00 38.23 3.16
2528 5649 3.502211 CCTGAAACTTATCGGCACAAGTT 59.498 43.478 3.14 3.14 0.00 2.66
2574 5695 4.141801 ACGGGATTGTAAATCTCAATCGGA 60.142 41.667 10.93 0.00 46.78 4.55
2575 5696 4.997395 CGGGATTGTAAATCTCAATCGGAT 59.003 41.667 10.93 0.00 46.78 4.18
2576 5697 5.106948 CGGGATTGTAAATCTCAATCGGATG 60.107 44.000 10.93 0.00 46.78 3.51
2577 5698 5.997746 GGGATTGTAAATCTCAATCGGATGA 59.002 40.000 10.93 0.00 46.78 2.92
2578 5699 6.486657 GGGATTGTAAATCTCAATCGGATGAA 59.513 38.462 10.93 0.00 46.78 2.57
2579 5700 7.355778 GGATTGTAAATCTCAATCGGATGAAC 58.644 38.462 10.93 0.00 46.78 3.18
2580 5701 7.227512 GGATTGTAAATCTCAATCGGATGAACT 59.772 37.037 10.93 0.00 46.78 3.01
2581 5702 7.921786 TTGTAAATCTCAATCGGATGAACTT 57.078 32.000 0.00 0.00 0.00 2.66
2592 5713 4.566004 TCGGATGAACTTAACCAAGTCTG 58.434 43.478 0.00 0.00 44.41 3.51
2611 5732 7.929941 AGTCTGAGTCGATGCTATATTCATA 57.070 36.000 0.00 0.00 0.00 2.15
2620 5741 9.144747 GTCGATGCTATATTCATAAGATGTTGT 57.855 33.333 0.00 0.00 0.00 3.32
2631 5752 5.812127 TCATAAGATGTTGTGTGGAGATTCG 59.188 40.000 0.00 0.00 0.00 3.34
2638 5759 1.601903 TGTGTGGAGATTCGTGCAAAC 59.398 47.619 0.00 0.00 0.00 2.93
2677 5803 5.224888 TCCTTACATGTTACGTCACTTGAC 58.775 41.667 19.16 0.00 41.47 3.18
2679 5805 6.207221 TCCTTACATGTTACGTCACTTGACTA 59.793 38.462 19.16 3.29 42.66 2.59
2693 5831 3.005578 ACTTGACTAAGACTTGGTCGACC 59.994 47.826 28.17 28.17 43.27 4.79
2797 5937 5.762179 AACAAGTCACCTCCATTAGATCA 57.238 39.130 0.00 0.00 0.00 2.92
2798 5938 5.762179 ACAAGTCACCTCCATTAGATCAA 57.238 39.130 0.00 0.00 0.00 2.57
2802 5942 2.434336 TCACCTCCATTAGATCAACCCG 59.566 50.000 0.00 0.00 0.00 5.28
2812 5952 1.728490 GATCAACCCGAAGCCATGGC 61.728 60.000 30.12 30.12 42.33 4.40
2883 6023 4.083862 GCCTCGTTCGCTTCCCCT 62.084 66.667 0.00 0.00 0.00 4.79
2886 6026 1.592223 CTCGTTCGCTTCCCCTTCT 59.408 57.895 0.00 0.00 0.00 2.85
2948 6417 1.470285 GCACGGAAGCGTAGGATACAA 60.470 52.381 0.00 0.00 43.24 2.41
2954 6423 3.869832 GGAAGCGTAGGATACAAAAGTCC 59.130 47.826 0.00 0.00 43.24 3.85
2959 6428 3.449737 CGTAGGATACAAAAGTCCTGGGA 59.550 47.826 4.25 0.00 44.39 4.37
2995 6464 2.803593 ATTTGGGTCCAATGGCCGCT 62.804 55.000 3.00 0.00 35.70 5.52
3017 6486 1.678627 AGCTATGCTCTAGTGTGTCGG 59.321 52.381 0.00 0.00 30.62 4.79
3031 6500 2.606519 TCGGGGTTGCTAGGCTGT 60.607 61.111 0.00 0.00 0.00 4.40
3039 6508 1.234615 TTGCTAGGCTGTTTGGCGAC 61.235 55.000 0.00 0.00 46.88 5.19
3045 6514 2.590575 CTGTTTGGCGACCGTGGT 60.591 61.111 0.00 0.00 0.00 4.16
3066 6536 0.189822 GAGGAGATGCCCCTACCTCT 59.810 60.000 0.00 0.00 42.41 3.69
3106 6576 4.154015 CAGTGAATATCGTTGGACAAAGCA 59.846 41.667 0.00 0.00 0.00 3.91
3108 6578 3.438781 TGAATATCGTTGGACAAAGCACC 59.561 43.478 0.00 0.00 0.00 5.01
3110 6580 1.234615 ATCGTTGGACAAAGCACCCG 61.235 55.000 0.00 0.00 0.00 5.28
3115 6585 0.179004 TGGACAAAGCACCCGAATGT 60.179 50.000 0.00 0.00 0.00 2.71
3170 6641 0.366871 CGCAAAGGTGACGATTCTCG 59.633 55.000 0.00 0.00 46.93 4.04
3182 6654 0.179108 GATTCTCGTCCTTGACCGGG 60.179 60.000 6.32 0.00 0.00 5.73
3274 6747 3.206211 AATGGTTTGTGGCGCGGTG 62.206 57.895 8.83 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.159028 AGAGCTCTCGGCCATAAAGTTC 60.159 50.000 11.45 1.78 43.05 3.01
39 40 4.261741 GGCACAGCTTCATCTGAAAAGAAA 60.262 41.667 7.19 0.00 37.51 2.52
51 52 0.465460 AAAGGAACGGCACAGCTTCA 60.465 50.000 0.00 0.00 0.00 3.02
82 88 0.886490 CACGGTGCAGCCTCTCTTTT 60.886 55.000 10.90 0.00 34.25 2.27
86 92 2.433318 GTCACGGTGCAGCCTCTC 60.433 66.667 10.90 0.00 34.25 3.20
125 131 1.449778 GACGTTTCTGCCTAGCCCC 60.450 63.158 0.00 0.00 0.00 5.80
189 195 2.039084 ACTCGATGAAAGTCCTGCCTTT 59.961 45.455 0.00 0.00 37.37 3.11
190 196 1.625818 ACTCGATGAAAGTCCTGCCTT 59.374 47.619 0.00 0.00 0.00 4.35
197 226 1.462541 GCGTTGCACTCGATGAAAGTC 60.463 52.381 13.52 0.00 0.00 3.01
198 227 0.512952 GCGTTGCACTCGATGAAAGT 59.487 50.000 13.52 0.00 0.00 2.66
202 231 1.724623 GTAAAGCGTTGCACTCGATGA 59.275 47.619 13.52 0.00 0.00 2.92
239 268 1.666234 GAAGCTCGGGGCATCGATC 60.666 63.158 1.17 0.00 44.79 3.69
253 282 0.250513 AGGTCCAACCAGATCGAAGC 59.749 55.000 0.00 0.00 41.95 3.86
257 286 1.186200 TCAGAGGTCCAACCAGATCG 58.814 55.000 0.00 0.00 41.95 3.69
258 287 3.454082 AGAATCAGAGGTCCAACCAGATC 59.546 47.826 0.00 0.00 41.95 2.75
259 288 3.458831 AGAATCAGAGGTCCAACCAGAT 58.541 45.455 0.00 0.00 41.95 2.90
260 289 2.907892 AGAATCAGAGGTCCAACCAGA 58.092 47.619 0.00 0.00 41.95 3.86
261 290 3.772025 AGTAGAATCAGAGGTCCAACCAG 59.228 47.826 0.00 0.00 41.95 4.00
262 291 3.791320 AGTAGAATCAGAGGTCCAACCA 58.209 45.455 0.00 0.00 41.95 3.67
263 292 4.710375 TGTAGTAGAATCAGAGGTCCAACC 59.290 45.833 0.00 0.00 38.99 3.77
264 293 5.163499 CCTGTAGTAGAATCAGAGGTCCAAC 60.163 48.000 0.00 0.00 0.00 3.77
265 294 4.956700 CCTGTAGTAGAATCAGAGGTCCAA 59.043 45.833 0.00 0.00 0.00 3.53
266 295 4.537751 CCTGTAGTAGAATCAGAGGTCCA 58.462 47.826 0.00 0.00 0.00 4.02
267 296 3.319689 GCCTGTAGTAGAATCAGAGGTCC 59.680 52.174 0.00 0.00 0.00 4.46
268 297 3.954904 TGCCTGTAGTAGAATCAGAGGTC 59.045 47.826 0.00 0.00 0.00 3.85
290 319 3.609853 ACATTCCTGATACGCAATGTGT 58.390 40.909 4.41 4.41 37.92 3.72
311 3299 3.044156 AGCTGATTCTGGCTTCATCCTA 58.956 45.455 0.00 0.00 34.96 2.94
487 3539 1.885560 TTTTCGCGTGGGAATCTCAA 58.114 45.000 5.77 0.00 0.00 3.02
488 3540 2.107950 ATTTTCGCGTGGGAATCTCA 57.892 45.000 5.77 0.00 0.00 3.27
526 3578 0.397816 AGAAGGCCGCTGATCCTAGT 60.398 55.000 0.00 0.00 31.24 2.57
541 3593 0.036294 GTTTCCGTCAGGGGGAGAAG 60.036 60.000 0.00 0.00 38.33 2.85
542 3594 0.765135 TGTTTCCGTCAGGGGGAGAA 60.765 55.000 0.00 0.00 38.33 2.87
543 3595 0.765135 TTGTTTCCGTCAGGGGGAGA 60.765 55.000 0.00 0.00 38.33 3.71
547 3599 0.949105 CGAGTTGTTTCCGTCAGGGG 60.949 60.000 0.00 0.00 38.33 4.79
590 3642 0.880278 TCGTTGAACAGAGCCTGTGC 60.880 55.000 8.37 7.36 44.62 4.57
591 3643 1.581934 TTCGTTGAACAGAGCCTGTG 58.418 50.000 8.37 0.00 44.62 3.66
593 3645 2.478134 CTCTTTCGTTGAACAGAGCCTG 59.522 50.000 0.00 1.16 37.52 4.85
594 3646 2.365617 TCTCTTTCGTTGAACAGAGCCT 59.634 45.455 6.35 0.00 32.42 4.58
595 3647 2.755650 TCTCTTTCGTTGAACAGAGCC 58.244 47.619 6.35 0.00 32.42 4.70
596 3648 3.363477 GCTTCTCTTTCGTTGAACAGAGC 60.363 47.826 6.35 0.00 32.42 4.09
597 3649 3.121194 CGCTTCTCTTTCGTTGAACAGAG 60.121 47.826 5.15 5.15 33.00 3.35
598 3650 2.794910 CGCTTCTCTTTCGTTGAACAGA 59.205 45.455 0.00 0.00 0.00 3.41
599 3651 2.794910 TCGCTTCTCTTTCGTTGAACAG 59.205 45.455 0.00 0.00 0.00 3.16
600 3652 2.816689 TCGCTTCTCTTTCGTTGAACA 58.183 42.857 0.00 0.00 0.00 3.18
601 3653 3.854286 TTCGCTTCTCTTTCGTTGAAC 57.146 42.857 0.00 0.00 0.00 3.18
602 3654 4.116961 TCTTTCGCTTCTCTTTCGTTGAA 58.883 39.130 0.00 0.00 0.00 2.69
603 3655 3.713288 TCTTTCGCTTCTCTTTCGTTGA 58.287 40.909 0.00 0.00 0.00 3.18
604 3656 4.389645 CATCTTTCGCTTCTCTTTCGTTG 58.610 43.478 0.00 0.00 0.00 4.10
605 3657 3.120511 GCATCTTTCGCTTCTCTTTCGTT 60.121 43.478 0.00 0.00 0.00 3.85
606 3658 2.413453 GCATCTTTCGCTTCTCTTTCGT 59.587 45.455 0.00 0.00 0.00 3.85
607 3659 2.222908 GGCATCTTTCGCTTCTCTTTCG 60.223 50.000 0.00 0.00 0.00 3.46
608 3660 2.222908 CGGCATCTTTCGCTTCTCTTTC 60.223 50.000 0.00 0.00 0.00 2.62
609 3661 1.734465 CGGCATCTTTCGCTTCTCTTT 59.266 47.619 0.00 0.00 0.00 2.52
610 3662 1.363744 CGGCATCTTTCGCTTCTCTT 58.636 50.000 0.00 0.00 0.00 2.85
611 3663 3.056628 CGGCATCTTTCGCTTCTCT 57.943 52.632 0.00 0.00 0.00 3.10
647 3701 3.491598 CTTTCACCGGTGGCAGGGT 62.492 63.158 33.40 4.39 36.87 4.34
657 3711 0.095935 CAGCAATCTCGCTTTCACCG 59.904 55.000 0.00 0.00 41.38 4.94
678 3732 2.621998 GCATCAACCTGGGATCAATCAG 59.378 50.000 0.00 0.00 0.00 2.90
784 3857 2.995574 AAGGTGTCGGGGACTCGG 60.996 66.667 0.00 0.00 33.15 4.63
785 3858 2.261671 CAAGGTGTCGGGGACTCG 59.738 66.667 0.00 0.00 33.15 4.18
786 3859 2.047179 GCAAGGTGTCGGGGACTC 60.047 66.667 0.00 0.00 33.15 3.36
787 3860 3.637273 GGCAAGGTGTCGGGGACT 61.637 66.667 0.00 0.00 33.15 3.85
788 3861 3.948719 TGGCAAGGTGTCGGGGAC 61.949 66.667 0.00 0.00 0.00 4.46
789 3862 3.948719 GTGGCAAGGTGTCGGGGA 61.949 66.667 0.00 0.00 0.00 4.81
810 3883 1.864711 GCACAGTACTCGCTTTGACAA 59.135 47.619 6.56 0.00 0.00 3.18
843 3916 2.852075 TCCTGGCTGGGACGGTTT 60.852 61.111 10.79 0.00 36.83 3.27
860 3941 1.227089 CTCTGCAATACGGAGCGCT 60.227 57.895 11.27 11.27 44.72 5.92
861 3942 3.313750 CTCTGCAATACGGAGCGC 58.686 61.111 0.00 0.00 44.72 5.92
999 4085 2.109126 GCGCGGGAGAAGCTTCATT 61.109 57.895 27.57 8.66 33.33 2.57
1164 4257 2.131067 GGAGAGCGAAGGGAGGGAG 61.131 68.421 0.00 0.00 0.00 4.30
1321 4435 2.741092 GGTGCAGAGGTCGTGGAA 59.259 61.111 0.00 0.00 0.00 3.53
1539 4653 3.006728 TTGGACGGGAGCGGGAAT 61.007 61.111 0.00 0.00 0.00 3.01
1837 4951 0.944386 TTCTTGCTCTGTCGTTTGGC 59.056 50.000 0.00 0.00 0.00 4.52
1928 5042 3.665675 GAGTACAGCACCTGCCCCG 62.666 68.421 0.00 0.00 43.38 5.73
2217 5331 1.979693 GTCGTCTCCTCCCTGCAGT 60.980 63.158 13.81 0.00 0.00 4.40
2247 5361 2.285368 ACCCTCCATTCCTCGCCA 60.285 61.111 0.00 0.00 0.00 5.69
2322 5436 4.142600 GCAGCAAATCCAACCTACTACAAG 60.143 45.833 0.00 0.00 0.00 3.16
2344 5458 2.223377 ACTTTCCAACGTCAGAAATCGC 59.777 45.455 11.92 0.00 31.89 4.58
2351 5465 3.757745 AAACACACTTTCCAACGTCAG 57.242 42.857 0.00 0.00 0.00 3.51
2459 5579 0.872388 GTTCGCCGAAGTCCAAACAT 59.128 50.000 0.00 0.00 0.00 2.71
2461 5581 0.942252 AAGTTCGCCGAAGTCCAAAC 59.058 50.000 7.76 0.00 0.00 2.93
2501 5622 1.287425 CCGATAAGTTTCAGGCGACC 58.713 55.000 0.00 0.00 0.00 4.79
2526 5647 5.359009 GGGGTAAATGGCTAAAAGAGGTAAC 59.641 44.000 0.00 0.00 0.00 2.50
2528 5649 4.540906 TGGGGTAAATGGCTAAAAGAGGTA 59.459 41.667 0.00 0.00 0.00 3.08
2574 5695 5.010719 TCGACTCAGACTTGGTTAAGTTCAT 59.989 40.000 0.00 0.00 46.79 2.57
2575 5696 4.340097 TCGACTCAGACTTGGTTAAGTTCA 59.660 41.667 0.00 0.00 46.79 3.18
2576 5697 4.868067 TCGACTCAGACTTGGTTAAGTTC 58.132 43.478 0.00 0.00 46.79 3.01
2577 5698 4.931661 TCGACTCAGACTTGGTTAAGTT 57.068 40.909 0.00 0.00 46.79 2.66
2579 5700 3.614616 GCATCGACTCAGACTTGGTTAAG 59.385 47.826 0.00 0.00 39.86 1.85
2580 5701 3.258372 AGCATCGACTCAGACTTGGTTAA 59.742 43.478 0.00 0.00 0.00 2.01
2581 5702 2.826128 AGCATCGACTCAGACTTGGTTA 59.174 45.455 0.00 0.00 0.00 2.85
2592 5713 9.579768 AACATCTTATGAATATAGCATCGACTC 57.420 33.333 0.00 0.00 0.00 3.36
2611 5732 3.748048 CACGAATCTCCACACAACATCTT 59.252 43.478 0.00 0.00 0.00 2.40
2620 5741 2.254546 AGTTTGCACGAATCTCCACA 57.745 45.000 0.00 0.00 0.00 4.17
2655 5776 5.511088 GTCAAGTGACGTAACATGTAAGG 57.489 43.478 5.68 0.00 35.12 2.69
2677 5803 2.082231 TCTCGGTCGACCAAGTCTTAG 58.918 52.381 32.80 14.79 35.14 2.18
2679 5805 0.597072 GTCTCGGTCGACCAAGTCTT 59.403 55.000 32.80 0.00 35.14 3.01
2693 5831 2.969628 AAGAATGTGGCTAGGTCTCG 57.030 50.000 0.00 0.00 0.00 4.04
2696 5834 4.489306 AGGTAAAGAATGTGGCTAGGTC 57.511 45.455 0.00 0.00 0.00 3.85
2812 5952 4.785453 GGGGCCGCACAAGGAGAG 62.785 72.222 16.21 0.00 0.00 3.20
2827 5967 1.753470 CTCCTGATAGCCTGCTGGG 59.247 63.158 12.06 1.66 38.36 4.45
2833 5973 3.373830 GGATATGAGCTCCTGATAGCCT 58.626 50.000 15.93 0.00 43.86 4.58
2841 5981 0.470833 ACAGCCGGATATGAGCTCCT 60.471 55.000 12.15 3.56 33.70 3.69
2871 6011 1.078356 GGGAGAAGGGGAAGCGAAC 60.078 63.158 0.00 0.00 0.00 3.95
2873 6013 1.229529 AAGGGAGAAGGGGAAGCGA 60.230 57.895 0.00 0.00 0.00 4.93
2933 6402 4.567159 CAGGACTTTTGTATCCTACGCTTC 59.433 45.833 0.00 0.00 43.84 3.86
2954 6423 1.966451 GACGCCAAACCTGTCCCAG 60.966 63.158 0.00 0.00 0.00 4.45
3017 6486 1.877576 GCCAAACAGCCTAGCAACCC 61.878 60.000 0.00 0.00 0.00 4.11
3031 6500 3.818121 CTCCACCACGGTCGCCAAA 62.818 63.158 0.00 0.00 35.57 3.28
3039 6508 2.187946 GCATCTCCTCCACCACGG 59.812 66.667 0.00 0.00 0.00 4.94
3045 6514 1.074471 GGTAGGGGCATCTCCTCCA 60.074 63.158 0.00 0.00 35.19 3.86
3106 6576 3.264845 AAGGCCCCACATTCGGGT 61.265 61.111 0.00 0.00 45.80 5.28
3108 6578 2.440247 GGAAGGCCCCACATTCGG 60.440 66.667 0.00 0.00 0.00 4.30
3110 6580 1.141858 CTAGAGGAAGGCCCCACATTC 59.858 57.143 0.00 0.00 34.66 2.67
3115 6585 0.617820 GACACTAGAGGAAGGCCCCA 60.618 60.000 0.00 0.00 34.66 4.96
3170 6641 0.175989 GATCACTCCCGGTCAAGGAC 59.824 60.000 0.00 0.00 0.00 3.85
3182 6654 1.341531 CCGGTATGACCCTGATCACTC 59.658 57.143 0.00 0.00 33.75 3.51
3274 6747 2.513666 TGCCGCCATGATCGAACC 60.514 61.111 8.56 0.00 0.00 3.62
3303 6776 2.596046 ACGCCACCCGATTGCAAA 60.596 55.556 1.71 0.00 41.02 3.68


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

AutoCloner maintained by Alex Coulton.