Multiple sequence alignment - TraesCS2D01G038900

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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 TraesCS2D01G038900 chr2D 100.000 3942 0 0 1 3942 14271005 14267064 0.000000e+00 7280
1 TraesCS2D01G038900 chr2A 93.754 1745 65 14 796 2526 16561763 16560049 0.000000e+00 2579
2 TraesCS2D01G038900 chr2A 94.860 642 26 4 2533 3171 16560007 16559370 0.000000e+00 996
3 TraesCS2D01G038900 chr2A 86.957 759 50 21 3213 3938 16559365 16558623 0.000000e+00 808
4 TraesCS2D01G038900 chr2A 83.634 831 71 32 1 802 16562822 16562028 0.000000e+00 721
5 TraesCS2D01G038900 chr2A 88.715 319 24 4 1463 1781 772533780 772533474 2.870000e-101 379
6 TraesCS2D01G038900 chr2B 92.238 1430 87 17 2532 3940 26108973 26107547 0.000000e+00 2004
7 TraesCS2D01G038900 chr2B 86.289 919 85 20 1 882 26111553 26110639 0.000000e+00 961
8 TraesCS2D01G038900 chr2B 91.298 678 34 9 1354 2012 26110167 26109496 0.000000e+00 902
9 TraesCS2D01G038900 chr2B 90.309 485 44 2 2052 2534 26109493 26109010 2.000000e-177 632
10 TraesCS2D01G038900 chr2B 83.200 625 75 19 2061 2665 20559959 20560573 2.680000e-151 545
11 TraesCS2D01G038900 chr3D 83.968 761 73 18 3213 3934 593344129 593344879 0.000000e+00 684
12 TraesCS2D01G038900 chr3D 84.058 345 18 7 2777 3113 593343763 593344078 8.280000e-77 298
13 TraesCS2D01G038900 chr1B 83.360 625 74 19 2061 2665 545084787 545084173 5.760000e-153 551
14 TraesCS2D01G038900 chr3B 89.101 367 38 2 3496 3862 796538103 796538467 4.640000e-124 455
15 TraesCS2D01G038900 chr5D 91.250 320 16 7 1463 1782 448349338 448349645 3.640000e-115 425
16 TraesCS2D01G038900 chr5D 90.596 319 18 1 1463 1781 235714838 235714532 2.830000e-111 412
17 TraesCS2D01G038900 chr5A 90.881 318 16 4 1464 1781 630721581 630721885 7.880000e-112 414
18 TraesCS2D01G038900 chr5A 89.655 319 22 1 1463 1781 639277079 639276772 2.850000e-106 396
19 TraesCS2D01G038900 chr6D 90.282 319 19 4 1463 1781 53540921 53540615 1.320000e-109 407
20 TraesCS2D01G038900 chr4A 90.282 319 19 1 1463 1781 366765650 366765956 1.320000e-109 407
21 TraesCS2D01G038900 chr4A 89.969 319 20 4 1463 1781 33006537 33006843 6.140000e-108 401
22 TraesCS2D01G038900 chr4A 89.969 319 19 1 1463 1781 411835380 411835075 2.210000e-107 399
23 TraesCS2D01G038900 chr7A 88.715 319 24 1 1463 1781 24784413 24784107 2.870000e-101 379


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 TraesCS2D01G038900 chr2D 14267064 14271005 3941 True 7280.00 7280 100.00000 1 3942 1 chr2D.!!$R1 3941
1 TraesCS2D01G038900 chr2A 16558623 16562822 4199 True 1276.00 2579 89.80125 1 3938 4 chr2A.!!$R2 3937
2 TraesCS2D01G038900 chr2B 26107547 26111553 4006 True 1124.75 2004 90.03350 1 3940 4 chr2B.!!$R1 3939
3 TraesCS2D01G038900 chr2B 20559959 20560573 614 False 545.00 545 83.20000 2061 2665 1 chr2B.!!$F1 604
4 TraesCS2D01G038900 chr3D 593343763 593344879 1116 False 491.00 684 84.01300 2777 3934 2 chr3D.!!$F1 1157
5 TraesCS2D01G038900 chr1B 545084173 545084787 614 True 551.00 551 83.36000 2061 2665 1 chr1B.!!$R1 604

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
605 656 0.043334 CTCTCCTTCCTCCCTCCCAA 59.957 60.0 0.0 0.0 0.00 4.12 F
643 713 0.174617 GTCTTCCTCTCGCCTTCCTG 59.825 60.0 0.0 0.0 0.00 3.86 F
677 770 0.393944 CCTAACCTCCCCCGCTTTTC 60.394 60.0 0.0 0.0 0.00 2.29 F
2247 2652 0.248134 CTGTTCCGACGATCTCCGAC 60.248 60.0 0.0 0.0 41.76 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 1809 0.319900 ACGACGATGAGCAGCTTGTT 60.320 50.000 0.0 0.0 0.00 2.83 R
2054 2459 0.524862 CAGGCAAGGAATGTGTGCTC 59.475 55.000 0.0 0.0 38.36 4.26 R
2467 2874 1.421268 TGCAAAGAGAAGCAAGGAGGA 59.579 47.619 0.0 0.0 37.90 3.71 R
3493 4004 0.317479 CCGGTTCTCAGGAAGTTCGT 59.683 55.000 0.0 0.0 31.46 3.85 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
34 35 7.214381 AGTTATTTATGTCCTACAATAGCGCA 58.786 34.615 11.47 0.00 0.00 6.09
75 76 3.517901 TCCGACAAGATAAACCACATCCT 59.482 43.478 0.00 0.00 0.00 3.24
76 77 3.623060 CCGACAAGATAAACCACATCCTG 59.377 47.826 0.00 0.00 0.00 3.86
95 96 4.458989 TCCTGCATGGTGTATTTCACTTTC 59.541 41.667 0.00 0.00 45.50 2.62
96 97 4.380867 CCTGCATGGTGTATTTCACTTTCC 60.381 45.833 0.00 0.00 45.50 3.13
110 111 3.394274 TCACTTTCCCCACATTTCTCTCA 59.606 43.478 0.00 0.00 0.00 3.27
185 186 1.078848 GATCCTCAAGCGGCACTGT 60.079 57.895 1.45 0.00 0.00 3.55
189 190 1.301244 CTCAAGCGGCACTGTGAGT 60.301 57.895 12.86 0.00 32.95 3.41
227 243 1.528309 AACCACCCCAAACGCAGAG 60.528 57.895 0.00 0.00 0.00 3.35
228 244 3.365265 CCACCCCAAACGCAGAGC 61.365 66.667 0.00 0.00 0.00 4.09
229 245 3.365265 CACCCCAAACGCAGAGCC 61.365 66.667 0.00 0.00 0.00 4.70
230 246 4.660938 ACCCCAAACGCAGAGCCC 62.661 66.667 0.00 0.00 0.00 5.19
231 247 4.659172 CCCCAAACGCAGAGCCCA 62.659 66.667 0.00 0.00 0.00 5.36
232 248 2.361610 CCCAAACGCAGAGCCCAT 60.362 61.111 0.00 0.00 0.00 4.00
233 249 2.703798 CCCAAACGCAGAGCCCATG 61.704 63.158 0.00 0.00 0.00 3.66
234 250 1.973281 CCAAACGCAGAGCCCATGT 60.973 57.895 0.00 0.00 0.00 3.21
235 251 1.526575 CCAAACGCAGAGCCCATGTT 61.527 55.000 0.00 0.00 0.00 2.71
236 252 0.109597 CAAACGCAGAGCCCATGTTC 60.110 55.000 0.00 0.00 0.00 3.18
237 253 0.537143 AAACGCAGAGCCCATGTTCA 60.537 50.000 0.00 0.00 0.00 3.18
238 254 1.237285 AACGCAGAGCCCATGTTCAC 61.237 55.000 0.00 0.00 0.00 3.18
239 255 1.376424 CGCAGAGCCCATGTTCACT 60.376 57.895 0.00 0.00 0.00 3.41
240 256 1.642037 CGCAGAGCCCATGTTCACTG 61.642 60.000 0.00 0.00 0.00 3.66
241 257 0.321919 GCAGAGCCCATGTTCACTGA 60.322 55.000 11.20 0.00 0.00 3.41
255 271 1.412710 TCACTGACTTTGTCGAGGCTT 59.587 47.619 0.00 0.00 34.95 4.35
260 276 2.101750 TGACTTTGTCGAGGCTTGTGTA 59.898 45.455 0.77 0.00 34.95 2.90
302 319 1.810030 GGCAACTCGACCACGGATC 60.810 63.158 0.00 0.00 40.21 3.36
311 328 2.044832 GACCACGGATCGTCGATCGT 62.045 60.000 24.87 22.07 39.72 3.73
340 357 3.311103 ACTTATTAGCTGTGGAGGGGGTA 60.311 47.826 0.00 0.00 0.00 3.69
344 361 2.784984 CTGTGGAGGGGGTAGGGA 59.215 66.667 0.00 0.00 0.00 4.20
345 362 1.383248 CTGTGGAGGGGGTAGGGAG 60.383 68.421 0.00 0.00 0.00 4.30
348 373 2.333462 TGGAGGGGGTAGGGAGAGG 61.333 68.421 0.00 0.00 0.00 3.69
352 377 0.343726 AGGGGGTAGGGAGAGGAAAG 59.656 60.000 0.00 0.00 0.00 2.62
364 389 4.220163 GGGAGAGGAAAGAACTTAACGAGA 59.780 45.833 0.00 0.00 0.00 4.04
375 400 5.875359 AGAACTTAACGAGAGCTAAAATGGG 59.125 40.000 0.00 0.00 0.00 4.00
379 404 6.884836 ACTTAACGAGAGCTAAAATGGGAAAT 59.115 34.615 0.00 0.00 0.00 2.17
481 525 0.609131 AACGGTCCCAGCATTTCAGG 60.609 55.000 0.00 0.00 0.00 3.86
486 530 1.198094 TCCCAGCATTTCAGGGTCGA 61.198 55.000 0.00 0.00 41.91 4.20
494 539 3.365969 GCATTTCAGGGTCGACGAAATTT 60.366 43.478 20.44 6.12 37.28 1.82
549 594 6.659242 ACACTTGCTTGTTATATTTACAGCCT 59.341 34.615 0.00 0.00 0.00 4.58
550 595 6.968904 CACTTGCTTGTTATATTTACAGCCTG 59.031 38.462 0.00 0.00 0.00 4.85
551 596 6.659242 ACTTGCTTGTTATATTTACAGCCTGT 59.341 34.615 1.54 1.54 0.00 4.00
552 597 6.435430 TGCTTGTTATATTTACAGCCTGTG 57.565 37.500 7.83 0.00 0.00 3.66
555 600 6.458342 GCTTGTTATATTTACAGCCTGTGTCC 60.458 42.308 7.83 0.00 40.94 4.02
594 645 4.205287 CTGCTGCAGCTCTCCTTC 57.795 61.111 36.61 8.49 42.66 3.46
595 646 1.449956 CTGCTGCAGCTCTCCTTCC 60.450 63.158 36.61 7.74 42.66 3.46
599 650 1.970352 CTGCAGCTCTCCTTCCTCCC 61.970 65.000 0.00 0.00 0.00 4.30
600 651 1.688884 GCAGCTCTCCTTCCTCCCT 60.689 63.158 0.00 0.00 0.00 4.20
601 652 1.685355 GCAGCTCTCCTTCCTCCCTC 61.685 65.000 0.00 0.00 0.00 4.30
604 655 1.706575 CTCTCCTTCCTCCCTCCCA 59.293 63.158 0.00 0.00 0.00 4.37
605 656 0.043334 CTCTCCTTCCTCCCTCCCAA 59.957 60.000 0.00 0.00 0.00 4.12
608 659 0.327576 TCCTTCCTCCCTCCCAATCC 60.328 60.000 0.00 0.00 0.00 3.01
609 660 0.624500 CCTTCCTCCCTCCCAATCCA 60.625 60.000 0.00 0.00 0.00 3.41
610 661 1.527457 CTTCCTCCCTCCCAATCCAT 58.473 55.000 0.00 0.00 0.00 3.41
614 684 0.402566 CTCCCTCCCAATCCATCCCT 60.403 60.000 0.00 0.00 0.00 4.20
643 713 0.174617 GTCTTCCTCTCGCCTTCCTG 59.825 60.000 0.00 0.00 0.00 3.86
650 726 4.441695 TCGCCTTCCTGCTGCTCG 62.442 66.667 0.00 0.00 0.00 5.03
674 767 3.408853 GCCTAACCTCCCCCGCTT 61.409 66.667 0.00 0.00 0.00 4.68
675 768 2.980177 GCCTAACCTCCCCCGCTTT 61.980 63.158 0.00 0.00 0.00 3.51
676 769 1.689412 CCTAACCTCCCCCGCTTTT 59.311 57.895 0.00 0.00 0.00 2.27
677 770 0.393944 CCTAACCTCCCCCGCTTTTC 60.394 60.000 0.00 0.00 0.00 2.29
678 771 0.618981 CTAACCTCCCCCGCTTTTCT 59.381 55.000 0.00 0.00 0.00 2.52
679 772 0.616891 TAACCTCCCCCGCTTTTCTC 59.383 55.000 0.00 0.00 0.00 2.87
680 773 2.138453 AACCTCCCCCGCTTTTCTCC 62.138 60.000 0.00 0.00 0.00 3.71
681 774 2.272471 CTCCCCCGCTTTTCTCCC 59.728 66.667 0.00 0.00 0.00 4.30
682 775 2.204090 TCCCCCGCTTTTCTCCCT 60.204 61.111 0.00 0.00 0.00 4.20
683 776 2.258748 CTCCCCCGCTTTTCTCCCTC 62.259 65.000 0.00 0.00 0.00 4.30
684 777 2.301738 CCCCCGCTTTTCTCCCTCT 61.302 63.158 0.00 0.00 0.00 3.69
685 778 1.222113 CCCCGCTTTTCTCCCTCTC 59.778 63.158 0.00 0.00 0.00 3.20
686 779 1.222113 CCCGCTTTTCTCCCTCTCC 59.778 63.158 0.00 0.00 0.00 3.71
687 780 1.222113 CCGCTTTTCTCCCTCTCCC 59.778 63.158 0.00 0.00 0.00 4.30
751 849 2.442643 CCATTCCATTGGCCGCCT 60.443 61.111 11.61 0.00 0.00 5.52
886 1265 2.513897 CGGAATCGGCCCAACTCC 60.514 66.667 0.00 0.00 0.00 3.85
912 1291 1.996070 GCTTTCTTATCCCCCGCCCT 61.996 60.000 0.00 0.00 0.00 5.19
977 1361 0.536460 GCCGGTTTCTTGGTCTTGGA 60.536 55.000 1.90 0.00 0.00 3.53
978 1362 1.975660 CCGGTTTCTTGGTCTTGGAA 58.024 50.000 0.00 0.00 0.00 3.53
1155 1541 3.408099 CTCCTCCTCCTCGCCGAGA 62.408 68.421 17.19 0.68 30.97 4.04
1189 1575 1.339055 CGCACCCATTCCTCTTCTTCA 60.339 52.381 0.00 0.00 0.00 3.02
1272 1658 2.041405 CTCCTCTCCCACCTCCCC 60.041 72.222 0.00 0.00 0.00 4.81
1329 1715 2.596851 CCACCTCACCCACCTCCAG 61.597 68.421 0.00 0.00 0.00 3.86
1332 1718 2.667418 CTCACCCACCTCCAGCAG 59.333 66.667 0.00 0.00 0.00 4.24
1335 1721 3.644606 ACCCACCTCCAGCAGCAG 61.645 66.667 0.00 0.00 0.00 4.24
1337 1723 4.340246 CCACCTCCAGCAGCAGCA 62.340 66.667 3.17 0.00 45.49 4.41
1347 1733 2.281970 CAGCAGCAGCAGGACCAA 60.282 61.111 3.17 0.00 45.49 3.67
1383 1769 0.757188 AGCAGCAGTACCTAGCCGAT 60.757 55.000 0.00 0.00 0.00 4.18
1389 1775 0.465824 AGTACCTAGCCGATGACGCT 60.466 55.000 0.00 0.00 38.29 5.07
1434 1835 1.010935 ACAAGCTGCTCATCGTCGTG 61.011 55.000 1.00 0.00 0.00 4.35
1781 2182 2.503061 CCTCCGCCAGATCAGGTG 59.497 66.667 10.62 10.62 38.90 4.00
1798 2201 2.451294 GCCCCATCTCCCCCATCT 60.451 66.667 0.00 0.00 0.00 2.90
1847 2250 2.032894 ACGAAATGTGCAGTCTTTGACG 60.033 45.455 0.00 0.00 37.67 4.35
1859 2262 8.840867 GTGCAGTCTTTGACGAATTTTTATTAG 58.159 33.333 0.00 0.00 37.67 1.73
1862 2265 9.250986 CAGTCTTTGACGAATTTTTATTAGTCG 57.749 33.333 0.00 0.00 38.46 4.18
1881 2284 3.794028 GTCGTCTCAAGAATCAAGATCCG 59.206 47.826 0.00 0.00 0.00 4.18
1939 2342 4.097589 AGCAAAATTTGGCATCTAGAGCTC 59.902 41.667 19.63 5.27 0.00 4.09
1963 2367 7.267128 TCAAATATCAAAACTTCATCCATGGC 58.733 34.615 6.96 0.00 0.00 4.40
1984 2388 4.162812 GCGTTGCTATCCGAATTGAAAAA 58.837 39.130 0.00 0.00 0.00 1.94
2018 2423 4.668576 ACAAGATTCGTTAGTGCACATG 57.331 40.909 21.04 4.71 0.00 3.21
2023 2428 7.119116 ACAAGATTCGTTAGTGCACATGATTTA 59.881 33.333 21.04 0.00 0.00 1.40
2048 2453 1.276989 CCAGGTTGCCATTGATGCTTT 59.723 47.619 0.00 0.00 0.00 3.51
2054 2459 4.739716 GGTTGCCATTGATGCTTTAATACG 59.260 41.667 0.00 0.00 0.00 3.06
2247 2652 0.248134 CTGTTCCGACGATCTCCGAC 60.248 60.000 0.00 0.00 41.76 4.79
2327 2732 1.075482 ACACAAGTGGGGATGCCAG 59.925 57.895 5.30 0.00 34.19 4.85
2597 3053 7.589954 CGTGGAAATTCGAAAGATAACAAAAGT 59.410 33.333 0.00 0.00 41.60 2.66
2616 3074 7.439056 ACAAAAGTTGTCAATGGAGCAAAATAG 59.561 33.333 0.00 0.00 40.56 1.73
2665 3125 5.010516 CCATCTAACAACATGGTGGTCAAAA 59.989 40.000 16.70 0.00 35.67 2.44
2666 3126 6.295236 CCATCTAACAACATGGTGGTCAAAAT 60.295 38.462 16.70 0.00 35.67 1.82
2717 3181 4.774200 AGCTTTGTTTGGATCTTATTGGCT 59.226 37.500 0.00 0.00 0.00 4.75
2721 3185 5.772825 TGTTTGGATCTTATTGGCTATGC 57.227 39.130 0.00 0.00 0.00 3.14
3017 3482 4.323257 GGTTTACTTTTCGATCCCCTCTCA 60.323 45.833 0.00 0.00 0.00 3.27
3041 3510 0.389556 CTCTGCTTTCGCTCTCTGCA 60.390 55.000 0.00 0.00 43.06 4.41
3056 3525 1.134310 TCTGCATCTGGATTGCGATGT 60.134 47.619 0.00 0.00 39.30 3.06
3117 3592 3.564644 ACTTGACGCTAGCGAGTATACAT 59.435 43.478 41.33 18.27 42.83 2.29
3120 3595 2.225963 GACGCTAGCGAGTATACATGGT 59.774 50.000 41.33 16.11 42.83 3.55
3124 3599 3.736252 GCTAGCGAGTATACATGGTTGTG 59.264 47.826 5.50 0.00 36.53 3.33
3125 3600 3.179443 AGCGAGTATACATGGTTGTGG 57.821 47.619 5.50 0.00 36.53 4.17
3166 3642 7.391554 TCCTGTCTCTTTATTCCAGTGAATTTG 59.608 37.037 0.00 0.00 41.44 2.32
3206 3682 1.078497 TGTGCAATGGTAGGGCTCG 60.078 57.895 0.00 0.00 0.00 5.03
3208 3684 2.297895 TGCAATGGTAGGGCTCGGT 61.298 57.895 0.00 0.00 0.00 4.69
3209 3685 1.819632 GCAATGGTAGGGCTCGGTG 60.820 63.158 0.00 0.00 0.00 4.94
3312 3795 3.044305 AGCGCGCTTTCAGTCACC 61.044 61.111 31.32 0.00 0.00 4.02
3365 3853 3.472652 TCACGCAACACTAGATTGGTTT 58.527 40.909 0.00 0.00 0.00 3.27
3529 4052 3.153919 ACCGGACTATGCATTTGTTTGT 58.846 40.909 9.46 1.32 0.00 2.83
3536 4059 7.090173 GGACTATGCATTTGTTTGTGTACATT 58.910 34.615 3.54 0.00 0.00 2.71
3537 4060 7.062138 GGACTATGCATTTGTTTGTGTACATTG 59.938 37.037 3.54 0.00 0.00 2.82
3539 4062 4.691175 TGCATTTGTTTGTGTACATTGCT 58.309 34.783 0.00 0.00 37.90 3.91
3562 4085 1.463674 ATCGCTTTCGCCTTGGAATT 58.536 45.000 0.00 0.00 35.26 2.17
3596 4133 3.441572 CCCAGCCTCTGAATAAGTTTGTG 59.558 47.826 0.00 0.00 32.44 3.33
3686 4223 6.015519 TGCTTTGTTTCAGGCATTTACATAGT 60.016 34.615 0.00 0.00 0.00 2.12
3881 4424 5.833082 TGCCGTGTAAATGTAAATGTTGTT 58.167 33.333 0.00 0.00 0.00 2.83
3940 4484 9.683069 CCAAAAGGTGAAATATATATGCAAGAC 57.317 33.333 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.823356 AGGTGAAACAATGGCGTGCT 60.823 50.000 0.00 0.00 39.98 4.40
95 96 2.431954 AGCATGAGAGAAATGTGGGG 57.568 50.000 0.00 0.00 0.00 4.96
96 97 2.353889 CGAAGCATGAGAGAAATGTGGG 59.646 50.000 0.00 0.00 0.00 4.61
185 186 1.227527 CGAGCCACCACAACACTCA 60.228 57.895 0.00 0.00 0.00 3.41
189 190 1.234821 GAAATCGAGCCACCACAACA 58.765 50.000 0.00 0.00 0.00 3.33
194 195 0.109532 TGGTTGAAATCGAGCCACCA 59.890 50.000 5.04 5.04 0.00 4.17
195 196 0.521735 GTGGTTGAAATCGAGCCACC 59.478 55.000 0.00 5.37 42.58 4.61
227 243 1.956477 ACAAAGTCAGTGAACATGGGC 59.044 47.619 0.00 0.00 0.00 5.36
228 244 2.224079 CGACAAAGTCAGTGAACATGGG 59.776 50.000 0.00 0.00 32.09 4.00
229 245 3.130633 TCGACAAAGTCAGTGAACATGG 58.869 45.455 0.00 0.00 32.09 3.66
230 246 3.185188 CCTCGACAAAGTCAGTGAACATG 59.815 47.826 0.00 0.00 32.09 3.21
231 247 3.393800 CCTCGACAAAGTCAGTGAACAT 58.606 45.455 0.00 0.00 32.09 2.71
232 248 2.821546 CCTCGACAAAGTCAGTGAACA 58.178 47.619 0.00 0.00 32.09 3.18
233 249 1.527311 GCCTCGACAAAGTCAGTGAAC 59.473 52.381 0.00 0.00 32.09 3.18
234 250 1.412710 AGCCTCGACAAAGTCAGTGAA 59.587 47.619 0.00 0.00 32.09 3.18
235 251 1.040646 AGCCTCGACAAAGTCAGTGA 58.959 50.000 0.00 0.00 32.09 3.41
236 252 1.528586 CAAGCCTCGACAAAGTCAGTG 59.471 52.381 0.00 0.00 32.09 3.66
237 253 1.139058 ACAAGCCTCGACAAAGTCAGT 59.861 47.619 0.00 0.00 32.09 3.41
238 254 1.528586 CACAAGCCTCGACAAAGTCAG 59.471 52.381 0.00 0.00 32.09 3.51
239 255 1.134521 ACACAAGCCTCGACAAAGTCA 60.135 47.619 0.00 0.00 32.09 3.41
240 256 1.583054 ACACAAGCCTCGACAAAGTC 58.417 50.000 0.00 0.00 0.00 3.01
241 257 2.364324 TCTACACAAGCCTCGACAAAGT 59.636 45.455 0.00 0.00 0.00 2.66
311 328 3.512329 TCCACAGCTAATAAGTTCGACCA 59.488 43.478 0.00 0.00 0.00 4.02
328 345 1.865045 TCTCCCTACCCCCTCCACA 60.865 63.158 0.00 0.00 0.00 4.17
340 357 4.158015 TCGTTAAGTTCTTTCCTCTCCCT 58.842 43.478 0.00 0.00 0.00 4.20
344 361 4.525100 AGCTCTCGTTAAGTTCTTTCCTCT 59.475 41.667 0.00 0.00 0.00 3.69
345 362 4.811908 AGCTCTCGTTAAGTTCTTTCCTC 58.188 43.478 0.00 0.00 0.00 3.71
348 373 7.958025 CCATTTTAGCTCTCGTTAAGTTCTTTC 59.042 37.037 0.00 0.00 0.00 2.62
352 377 5.873164 TCCCATTTTAGCTCTCGTTAAGTTC 59.127 40.000 0.00 0.00 0.00 3.01
419 445 2.274437 GCCGGCAGTAACTTTACTACC 58.726 52.381 24.80 7.99 41.82 3.18
439 465 1.076332 CGTTTTCTACCGGAGCTTGG 58.924 55.000 9.46 4.50 0.00 3.61
549 594 3.681417 CGATATATCTACGGACGGACACA 59.319 47.826 10.93 0.00 0.00 3.72
550 595 3.928992 TCGATATATCTACGGACGGACAC 59.071 47.826 10.93 0.00 0.00 3.67
551 596 4.179298 CTCGATATATCTACGGACGGACA 58.821 47.826 10.93 0.00 0.00 4.02
552 597 3.001127 GCTCGATATATCTACGGACGGAC 59.999 52.174 10.93 0.00 0.00 4.79
555 600 3.544440 GCAGCTCGATATATCTACGGACG 60.544 52.174 10.93 0.00 0.00 4.79
581 632 1.992277 GGGAGGAAGGAGAGCTGCA 60.992 63.158 1.02 0.00 0.00 4.41
593 644 0.401979 GGATGGATTGGGAGGGAGGA 60.402 60.000 0.00 0.00 0.00 3.71
594 645 1.430369 GGGATGGATTGGGAGGGAGG 61.430 65.000 0.00 0.00 0.00 4.30
595 646 0.402566 AGGGATGGATTGGGAGGGAG 60.403 60.000 0.00 0.00 0.00 4.30
599 650 1.072159 GCGAGGGATGGATTGGGAG 59.928 63.158 0.00 0.00 0.00 4.30
600 651 2.452064 GGCGAGGGATGGATTGGGA 61.452 63.158 0.00 0.00 0.00 4.37
601 652 2.113986 GGCGAGGGATGGATTGGG 59.886 66.667 0.00 0.00 0.00 4.12
604 655 4.609018 CGCGGCGAGGGATGGATT 62.609 66.667 19.16 0.00 34.27 3.01
671 764 1.222113 CCGGGAGAGGGAGAAAAGC 59.778 63.158 0.00 0.00 0.00 3.51
672 765 0.537653 GACCGGGAGAGGGAGAAAAG 59.462 60.000 6.32 0.00 35.02 2.27
673 766 0.908180 GGACCGGGAGAGGGAGAAAA 60.908 60.000 6.32 0.00 35.02 2.29
674 767 1.305887 GGACCGGGAGAGGGAGAAA 60.306 63.158 6.32 0.00 35.02 2.52
675 768 2.363361 GGACCGGGAGAGGGAGAA 59.637 66.667 6.32 0.00 35.02 2.87
676 769 2.944954 TGGACCGGGAGAGGGAGA 60.945 66.667 6.32 0.00 35.02 3.71
677 770 2.760385 GTGGACCGGGAGAGGGAG 60.760 72.222 6.32 0.00 35.02 4.30
678 771 4.753662 CGTGGACCGGGAGAGGGA 62.754 72.222 6.32 0.00 35.02 4.20
838 1217 3.992641 AAAGGGAAAGGGGGCGGG 61.993 66.667 0.00 0.00 0.00 6.13
839 1218 2.679996 CAAAGGGAAAGGGGGCGG 60.680 66.667 0.00 0.00 0.00 6.13
840 1219 1.977009 GTCAAAGGGAAAGGGGGCG 60.977 63.158 0.00 0.00 0.00 6.13
841 1220 0.612174 GAGTCAAAGGGAAAGGGGGC 60.612 60.000 0.00 0.00 0.00 5.80
842 1221 0.039764 GGAGTCAAAGGGAAAGGGGG 59.960 60.000 0.00 0.00 0.00 5.40
843 1222 0.039764 GGGAGTCAAAGGGAAAGGGG 59.960 60.000 0.00 0.00 0.00 4.79
844 1223 0.322546 CGGGAGTCAAAGGGAAAGGG 60.323 60.000 0.00 0.00 0.00 3.95
883 1262 1.070914 GATAAGAAAGCGGGGAGGGAG 59.929 57.143 0.00 0.00 0.00 4.30
884 1263 1.129058 GATAAGAAAGCGGGGAGGGA 58.871 55.000 0.00 0.00 0.00 4.20
885 1264 0.108774 GGATAAGAAAGCGGGGAGGG 59.891 60.000 0.00 0.00 0.00 4.30
886 1265 0.108774 GGGATAAGAAAGCGGGGAGG 59.891 60.000 0.00 0.00 0.00 4.30
977 1361 0.107654 CGCCTCCGAATTCCTTCCTT 60.108 55.000 0.00 0.00 36.29 3.36
978 1362 1.522569 CGCCTCCGAATTCCTTCCT 59.477 57.895 0.00 0.00 36.29 3.36
1133 1519 2.520741 GCGAGGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
1134 1520 2.520741 GGCGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1135 1521 4.507916 CGGCGAGGAGGAGGAGGA 62.508 72.222 0.00 0.00 0.00 3.71
1136 1522 4.507916 TCGGCGAGGAGGAGGAGG 62.508 72.222 4.99 0.00 0.00 4.30
1137 1523 2.895426 TTCTCGGCGAGGAGGAGGAG 62.895 65.000 33.93 8.85 34.74 3.69
1138 1524 2.494777 TTTCTCGGCGAGGAGGAGGA 62.495 60.000 33.93 12.73 34.74 3.71
1165 1551 2.438434 GAGGAATGGGTGCGGGTG 60.438 66.667 0.00 0.00 0.00 4.61
1176 1562 0.253327 GGCGGGTGAAGAAGAGGAAT 59.747 55.000 0.00 0.00 0.00 3.01
1272 1658 3.330720 GGGAGGGTGTGGTGGAGG 61.331 72.222 0.00 0.00 0.00 4.30
1291 1677 2.371259 GGGAGGAGGAGGAGTTGGC 61.371 68.421 0.00 0.00 0.00 4.52
1294 1680 2.788589 GGGGGAGGAGGAGGAGTT 59.211 66.667 0.00 0.00 0.00 3.01
1316 1702 3.640407 GCTGCTGGAGGTGGGTGA 61.640 66.667 0.00 0.00 0.00 4.02
1332 1718 3.368571 GGTTGGTCCTGCTGCTGC 61.369 66.667 8.89 8.89 40.20 5.25
1335 1721 2.036256 ATGGGTTGGTCCTGCTGC 59.964 61.111 0.00 0.00 36.25 5.25
1337 1723 1.380302 GTCATGGGTTGGTCCTGCT 59.620 57.895 0.00 0.00 36.25 4.24
1347 1733 3.259314 TGCTGCTGGGTCATGGGT 61.259 61.111 0.00 0.00 0.00 4.51
1409 1804 1.580845 GATGAGCAGCTTGTTGGCGT 61.581 55.000 0.00 0.00 37.29 5.68
1410 1805 1.136147 GATGAGCAGCTTGTTGGCG 59.864 57.895 0.00 0.00 37.29 5.69
1412 1807 0.445436 GACGATGAGCAGCTTGTTGG 59.555 55.000 0.00 0.00 0.00 3.77
1414 1809 0.319900 ACGACGATGAGCAGCTTGTT 60.320 50.000 0.00 0.00 0.00 2.83
1781 2182 2.451294 AGATGGGGGAGATGGGGC 60.451 66.667 0.00 0.00 0.00 5.80
1798 2201 4.941609 GGCTGAATCTGAAGGCGA 57.058 55.556 0.00 0.00 0.00 5.54
1859 2262 3.794028 CGGATCTTGATTCTTGAGACGAC 59.206 47.826 0.00 0.00 0.00 4.34
1862 2265 5.004922 ACTCGGATCTTGATTCTTGAGAC 57.995 43.478 0.00 0.00 0.00 3.36
1881 2284 4.708726 AAGCAAGCATACATTGGAACTC 57.291 40.909 0.00 0.00 0.00 3.01
1939 2342 6.199531 CGCCATGGATGAAGTTTTGATATTTG 59.800 38.462 18.40 0.00 0.00 2.32
1963 2367 6.869421 AATTTTTCAATTCGGATAGCAACG 57.131 33.333 0.00 0.00 0.00 4.10
1984 2388 7.440523 AACGAATCTTGTAAGAAAGCAGAAT 57.559 32.000 0.00 0.00 38.77 2.40
2048 2453 3.621268 GCAAGGAATGTGTGCTCGTATTA 59.379 43.478 0.00 0.00 35.36 0.98
2054 2459 0.524862 CAGGCAAGGAATGTGTGCTC 59.475 55.000 0.00 0.00 38.36 4.26
2327 2732 3.015327 ACATGAAATCTCTGGAGCTTGC 58.985 45.455 0.00 0.00 0.00 4.01
2467 2874 1.421268 TGCAAAGAGAAGCAAGGAGGA 59.579 47.619 0.00 0.00 37.90 3.71
2529 2945 3.356290 GTTAGGACAGGACAAATGCCAT 58.644 45.455 0.00 0.00 0.00 4.40
2597 3053 5.538053 TGTTCCTATTTTGCTCCATTGACAA 59.462 36.000 0.00 0.00 0.00 3.18
2635 3095 4.883585 CACCATGTTGTTAGATGGCTACAT 59.116 41.667 0.00 0.00 46.55 2.29
2721 3185 4.277476 TGTTAATACCCCATGCAGAAAGG 58.723 43.478 0.00 0.00 0.00 3.11
2722 3186 4.202050 GCTGTTAATACCCCATGCAGAAAG 60.202 45.833 0.00 0.00 0.00 2.62
3041 3510 3.827008 ACTACACATCGCAATCCAGAT 57.173 42.857 0.00 0.00 0.00 2.90
3117 3592 2.642154 ACATAACCGAACCACAACCA 57.358 45.000 0.00 0.00 0.00 3.67
3120 3595 3.315749 GGACAAACATAACCGAACCACAA 59.684 43.478 0.00 0.00 0.00 3.33
3124 3599 3.143728 ACAGGACAAACATAACCGAACC 58.856 45.455 0.00 0.00 0.00 3.62
3125 3600 4.062991 AGACAGGACAAACATAACCGAAC 58.937 43.478 0.00 0.00 0.00 3.95
3166 3642 3.251004 ACTTTCTGCAATTTCGTGGAGAC 59.749 43.478 0.00 0.00 44.56 3.36
3206 3682 5.065218 CAGATGCCAACTAATCTAACACACC 59.935 44.000 0.00 0.00 31.87 4.16
3208 3684 6.048732 TCAGATGCCAACTAATCTAACACA 57.951 37.500 0.00 0.00 31.87 3.72
3209 3685 7.066284 ACAATCAGATGCCAACTAATCTAACAC 59.934 37.037 0.00 0.00 31.87 3.32
3298 3781 2.551270 CACGGTGACTGAAAGCGC 59.449 61.111 0.74 0.00 42.03 5.92
3299 3782 1.771073 TTGCACGGTGACTGAAAGCG 61.771 55.000 13.29 4.85 43.79 4.68
3493 4004 0.317479 CCGGTTCTCAGGAAGTTCGT 59.683 55.000 0.00 0.00 31.46 3.85
3504 4015 3.270877 ACAAATGCATAGTCCGGTTCTC 58.729 45.455 0.00 0.00 0.00 2.87
3576 4102 3.119708 GGCACAAACTTATTCAGAGGCTG 60.120 47.826 0.00 0.00 0.00 4.85
3596 4133 2.437200 TGCATTGCAACAACTAAGGC 57.563 45.000 9.33 0.00 34.76 4.35
3637 4174 4.427312 CAGCAATTGGGTTCAGATAAAGC 58.573 43.478 7.72 0.00 0.00 3.51
3686 4223 2.517959 CCAATCTTCAAGGCTCAACCA 58.482 47.619 0.00 0.00 43.14 3.67
3793 4336 2.787601 TCTCAAAAGTCGTACTGCGT 57.212 45.000 0.00 0.00 42.13 5.24
3881 4424 6.676950 ACTCAACAAATGAATACAAATCGCA 58.323 32.000 0.00 0.00 37.67 5.10


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

AutoCloner maintained by Alex Coulton.