Multiple sequence alignment - TraesCS7B01G163100

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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 TraesCS7B01G163100 chr7B 100.000 3812 0 0 1 3812 223758869 223755058 0.000000e+00 7040.0
1 TraesCS7B01G163100 chr7B 83.008 359 48 13 529 882 449897690 449898040 2.860000e-81 313.0
2 TraesCS7B01G163100 chr7A 96.978 2614 74 4 946 3558 264859593 264856984 0.000000e+00 4385.0
3 TraesCS7B01G163100 chr7A 86.579 909 87 11 1 905 264927287 264926410 0.000000e+00 970.0
4 TraesCS7B01G163100 chr7A 96.250 240 8 1 3574 3812 264856998 264856759 3.570000e-105 392.0
5 TraesCS7B01G163100 chr7D 95.254 2634 80 12 941 3558 247327375 247324771 0.000000e+00 4130.0
6 TraesCS7B01G163100 chr7D 89.583 240 18 3 3574 3812 247324785 247324552 8.010000e-77 298.0
7 TraesCS7B01G163100 chr7D 81.337 359 57 10 529 883 432743022 432742670 2.240000e-72 283.0
8 TraesCS7B01G163100 chr7D 88.496 226 20 2 1 220 85355933 85356158 6.280000e-68 268.0
9 TraesCS7B01G163100 chr7D 87.892 223 24 2 1 220 85297446 85297668 3.780000e-65 259.0
10 TraesCS7B01G163100 chr7D 84.615 221 29 5 3334 3551 247324632 247324414 8.290000e-52 215.0
11 TraesCS7B01G163100 chr4B 80.830 699 107 20 224 905 458983478 458984166 1.210000e-144 523.0
12 TraesCS7B01G163100 chr2A 79.942 688 89 26 223 905 448297362 448298005 9.650000e-126 460.0
13 TraesCS7B01G163100 chr6A 78.020 687 106 27 224 905 606433010 606432364 1.280000e-104 390.0
14 TraesCS7B01G163100 chr5A 76.562 640 124 23 273 905 666052596 666051976 1.020000e-85 327.0
15 TraesCS7B01G163100 chr5A 89.140 221 23 1 1 221 174344153 174344372 1.350000e-69 274.0
16 TraesCS7B01G163100 chr5B 90.090 222 21 1 1 221 363249038 363249259 1.730000e-73 287.0
17 TraesCS7B01G163100 chr5D 88.688 221 24 1 1 221 315161746 315161965 6.280000e-68 268.0
18 TraesCS7B01G163100 chr5D 80.052 381 54 13 528 905 313153660 313154021 2.920000e-66 263.0
19 TraesCS7B01G163100 chr1D 88.235 221 21 3 1 221 289601465 289601250 3.780000e-65 259.0
20 TraesCS7B01G163100 chr1B 87.892 223 21 6 1 221 384503273 384503491 1.360000e-64 257.0
21 TraesCS7B01G163100 chr3D 86.638 232 25 6 1 231 401479033 401478807 6.320000e-63 252.0
22 TraesCS7B01G163100 chr4A 81.818 319 36 18 525 838 139550136 139550437 8.180000e-62 248.0
23 TraesCS7B01G163100 chr2D 78.855 227 42 5 223 445 484078371 484078147 8.530000e-32 148.0
24 TraesCS7B01G163100 chr4D 80.620 129 20 4 778 905 28559280 28559156 1.130000e-15 95.3
25 TraesCS7B01G163100 chr3A 80.620 129 20 2 778 905 79459780 79459904 1.130000e-15 95.3
26 TraesCS7B01G163100 chr3A 81.667 120 17 2 786 905 432144746 432144860 1.130000e-15 95.3


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 TraesCS7B01G163100 chr7B 223755058 223758869 3811 True 7040.000000 7040 100.000000 1 3812 1 chr7B.!!$R1 3811
1 TraesCS7B01G163100 chr7A 264856759 264859593 2834 True 2388.500000 4385 96.614000 946 3812 2 chr7A.!!$R2 2866
2 TraesCS7B01G163100 chr7A 264926410 264927287 877 True 970.000000 970 86.579000 1 905 1 chr7A.!!$R1 904
3 TraesCS7B01G163100 chr7D 247324414 247327375 2961 True 1547.666667 4130 89.817333 941 3812 3 chr7D.!!$R2 2871
4 TraesCS7B01G163100 chr4B 458983478 458984166 688 False 523.000000 523 80.830000 224 905 1 chr4B.!!$F1 681
5 TraesCS7B01G163100 chr2A 448297362 448298005 643 False 460.000000 460 79.942000 223 905 1 chr2A.!!$F1 682
6 TraesCS7B01G163100 chr6A 606432364 606433010 646 True 390.000000 390 78.020000 224 905 1 chr6A.!!$R1 681
7 TraesCS7B01G163100 chr5A 666051976 666052596 620 True 327.000000 327 76.562000 273 905 1 chr5A.!!$R1 632

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
119 120 0.243907 TTGCGTGAGTCTCCTACTGC 59.756 55.0 0.00 0.00 39.07 4.40 F
599 646 0.318441 CGCCAAACCTCTCAGTGAGA 59.682 55.0 21.46 21.46 45.39 3.27 F
624 671 0.321387 CTGCAGCTCATGGTCACACT 60.321 55.0 0.00 0.00 0.00 3.55 F
1044 1100 0.683504 GCGTCCAGGAGGAGAACCTA 60.684 60.0 13.68 0.00 46.92 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 1910 1.066858 CGACCAGCACCTGAATACACT 60.067 52.381 0.00 0.0 32.44 3.55 R
1916 1972 1.547675 CCACCTTTGGCCTTGCTCTAA 60.548 52.381 3.32 0.0 35.56 2.10 R
2616 2672 1.429463 CTCGAACCTTTTGGACTCCG 58.571 55.000 0.00 0.0 44.07 4.63 R
2838 2894 2.752354 CCAACCTTGAGAACAACACACA 59.248 45.455 0.00 0.0 32.27 3.72 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
25 26 5.935206 TCATTGCAATTAACGAGTACAAGGA 59.065 36.000 9.83 0.00 0.00 3.36
33 34 1.899814 ACGAGTACAAGGAGATTGGCA 59.100 47.619 0.00 0.00 43.68 4.92
85 86 2.558265 TTTGTGTGTGTGTGCATGTC 57.442 45.000 0.00 0.00 0.00 3.06
87 88 0.393537 TGTGTGTGTGTGCATGTCCA 60.394 50.000 0.00 0.00 0.00 4.02
88 89 0.308684 GTGTGTGTGTGCATGTCCAG 59.691 55.000 0.00 0.00 0.00 3.86
93 94 1.002468 GTGTGTGCATGTCCAGTTGAC 60.002 52.381 0.00 0.00 44.72 3.18
103 104 2.182014 GTCCAGTTGACGTTTGTTTGC 58.818 47.619 0.00 0.00 33.49 3.68
119 120 0.243907 TTGCGTGAGTCTCCTACTGC 59.756 55.000 0.00 0.00 39.07 4.40
127 128 5.527951 CGTGAGTCTCCTACTGCTTAGATAA 59.472 44.000 0.00 0.00 39.07 1.75
141 142 8.161425 ACTGCTTAGATAAACCTTGGTTCTTAA 58.839 33.333 5.43 2.77 0.00 1.85
142 143 8.331730 TGCTTAGATAAACCTTGGTTCTTAAC 57.668 34.615 5.43 0.00 0.00 2.01
143 144 8.161425 TGCTTAGATAAACCTTGGTTCTTAACT 58.839 33.333 5.43 3.08 0.00 2.24
144 145 8.451748 GCTTAGATAAACCTTGGTTCTTAACTG 58.548 37.037 5.43 0.00 0.00 3.16
186 187 6.282568 ACTATACTACATCACCCTTCCTCT 57.717 41.667 0.00 0.00 0.00 3.69
215 216 4.755266 AATCCTAACGCCTATCACAAGT 57.245 40.909 0.00 0.00 0.00 3.16
238 239 0.944386 AGTGTCGCACAATGTCCAAC 59.056 50.000 11.58 0.00 36.74 3.77
249 250 0.328258 ATGTCCAACTGCTACCCACC 59.672 55.000 0.00 0.00 0.00 4.61
250 251 1.057275 TGTCCAACTGCTACCCACCA 61.057 55.000 0.00 0.00 0.00 4.17
265 266 1.409521 CCACCAGTGGTTGTTCTTGGA 60.410 52.381 13.62 0.00 45.53 3.53
271 272 0.823356 TGGTTGTTCTTGGAGCTGCC 60.823 55.000 1.53 0.00 37.10 4.85
358 359 2.592796 CGACAATTTCGCACATGTGA 57.407 45.000 29.80 8.82 41.87 3.58
373 382 4.758251 TGACCATGCTCGTGCCCG 62.758 66.667 7.05 0.00 38.71 6.13
428 437 3.199551 TCGGGGTAACGACGATGG 58.800 61.111 0.00 0.00 40.88 3.51
429 438 1.378382 TCGGGGTAACGACGATGGA 60.378 57.895 0.00 0.00 40.88 3.41
431 440 1.378882 CGGGGTAACGACGATGGAGA 61.379 60.000 0.00 0.00 39.61 3.71
432 441 0.384669 GGGGTAACGACGATGGAGAG 59.615 60.000 0.00 0.00 37.60 3.20
433 442 1.386533 GGGTAACGACGATGGAGAGA 58.613 55.000 0.00 0.00 37.60 3.10
434 443 1.334243 GGGTAACGACGATGGAGAGAG 59.666 57.143 0.00 0.00 37.60 3.20
435 444 2.286872 GGTAACGACGATGGAGAGAGA 58.713 52.381 0.00 0.00 0.00 3.10
436 445 2.288458 GGTAACGACGATGGAGAGAGAG 59.712 54.545 0.00 0.00 0.00 3.20
437 446 2.404923 AACGACGATGGAGAGAGAGA 57.595 50.000 0.00 0.00 0.00 3.10
438 447 1.948104 ACGACGATGGAGAGAGAGAG 58.052 55.000 0.00 0.00 0.00 3.20
439 448 1.483004 ACGACGATGGAGAGAGAGAGA 59.517 52.381 0.00 0.00 0.00 3.10
440 449 2.135139 CGACGATGGAGAGAGAGAGAG 58.865 57.143 0.00 0.00 0.00 3.20
441 450 2.223947 CGACGATGGAGAGAGAGAGAGA 60.224 54.545 0.00 0.00 0.00 3.10
442 451 3.393800 GACGATGGAGAGAGAGAGAGAG 58.606 54.545 0.00 0.00 0.00 3.20
443 452 3.038280 ACGATGGAGAGAGAGAGAGAGA 58.962 50.000 0.00 0.00 0.00 3.10
444 453 3.070159 ACGATGGAGAGAGAGAGAGAGAG 59.930 52.174 0.00 0.00 0.00 3.20
445 454 3.321968 CGATGGAGAGAGAGAGAGAGAGA 59.678 52.174 0.00 0.00 0.00 3.10
446 455 4.560311 CGATGGAGAGAGAGAGAGAGAGAG 60.560 54.167 0.00 0.00 0.00 3.20
447 456 3.994317 TGGAGAGAGAGAGAGAGAGAGA 58.006 50.000 0.00 0.00 0.00 3.10
448 457 3.963374 TGGAGAGAGAGAGAGAGAGAGAG 59.037 52.174 0.00 0.00 0.00 3.20
449 458 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
450 459 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
451 460 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
483 514 2.185310 GAGGTGAGTGGGATGGCGTT 62.185 60.000 0.00 0.00 0.00 4.84
490 536 0.394352 GTGGGATGGCGTTCTCCATT 60.394 55.000 0.00 0.00 46.29 3.16
527 573 1.227823 CCCAAGTGGTCGTGCTGAA 60.228 57.895 0.00 0.00 0.00 3.02
599 646 0.318441 CGCCAAACCTCTCAGTGAGA 59.682 55.000 21.46 21.46 45.39 3.27
624 671 0.321387 CTGCAGCTCATGGTCACACT 60.321 55.000 0.00 0.00 0.00 3.55
631 678 1.623311 CTCATGGTCACACTGGTGGTA 59.377 52.381 5.70 0.00 45.32 3.25
674 722 2.170607 ACTGCCAATGGAAGCGTATAGT 59.829 45.455 7.31 0.00 29.34 2.12
678 726 3.248602 GCCAATGGAAGCGTATAGTTCAG 59.751 47.826 2.05 0.00 0.00 3.02
757 812 3.539604 GTCATGCAAGCTTAGGATCTGT 58.460 45.455 0.00 0.00 0.00 3.41
765 820 5.277058 GCAAGCTTAGGATCTGTAATGAACG 60.277 44.000 0.00 0.00 0.00 3.95
775 830 7.492669 AGGATCTGTAATGAACGAACTTACATG 59.507 37.037 0.00 0.00 35.47 3.21
776 831 7.491372 GGATCTGTAATGAACGAACTTACATGA 59.509 37.037 0.00 0.00 35.47 3.07
827 883 7.778185 AGTTATAGGACTAAACTGACACACT 57.222 36.000 6.29 0.00 32.38 3.55
833 889 5.305644 AGGACTAAACTGACACACTTCAGAT 59.694 40.000 7.12 0.00 45.19 2.90
834 890 6.493802 AGGACTAAACTGACACACTTCAGATA 59.506 38.462 7.12 0.15 45.19 1.98
835 891 6.809196 GGACTAAACTGACACACTTCAGATAG 59.191 42.308 7.12 10.30 45.19 2.08
836 892 7.291411 ACTAAACTGACACACTTCAGATAGT 57.709 36.000 7.12 10.81 45.19 2.12
884 940 9.981114 CAATTTCAAAGTTATAGGACCAAACTT 57.019 29.630 11.72 11.72 43.43 2.66
888 944 9.802039 TTCAAAGTTATAGGACCAAACTTACAT 57.198 29.630 15.80 3.39 41.36 2.29
1044 1100 0.683504 GCGTCCAGGAGGAGAACCTA 60.684 60.000 13.68 0.00 46.92 3.08
1272 1328 4.148825 GCGCACTCCCAGTCGGAT 62.149 66.667 0.30 0.00 41.00 4.18
1455 1511 1.131826 CCAAACCGACGAACGCATC 59.868 57.895 0.00 0.00 41.07 3.91
1470 1526 2.803670 ATCGCGACGACGTTGGTG 60.804 61.111 12.93 11.50 39.18 4.17
1615 1671 1.318886 TGCAGAGGAGCTCTTCGAGG 61.319 60.000 19.04 13.84 38.99 4.63
1854 1910 4.018490 CAACCTGGAATGTGATGATTGGA 58.982 43.478 0.00 0.00 0.00 3.53
1890 1946 2.496817 CGGGCTGTAGAGGCTGTC 59.503 66.667 13.64 0.00 44.48 3.51
1916 1972 6.744175 TCTCTTCAAGATTATGCTGGAGAT 57.256 37.500 0.00 0.00 0.00 2.75
1977 2033 8.548987 CAATCTCTATTGTTGCAGCTGCATGT 62.549 42.308 39.83 26.28 41.23 3.21
2082 2138 2.168496 GCTGCCCTCATTGATATGCAT 58.832 47.619 3.79 3.79 0.00 3.96
2208 2264 1.994779 CGTGGAAAAGATGCAATTGCC 59.005 47.619 26.94 12.98 41.18 4.52
2217 2273 6.799926 AAAGATGCAATTGCCGTTTTTAAT 57.200 29.167 26.94 11.39 41.18 1.40
2455 2511 4.346730 TGAGATGCCAAAGGACATTGAAT 58.653 39.130 0.00 0.00 31.84 2.57
2476 2532 1.266867 ACATGCTGGAATTTGGGGCC 61.267 55.000 0.00 0.00 0.00 5.80
2481 2537 0.926293 CTGGAATTTGGGGCCCTCTA 59.074 55.000 25.93 9.88 0.00 2.43
2490 2546 1.450211 GGGCCCTCTATTAAGCGCA 59.550 57.895 17.04 0.00 38.02 6.09
2616 2672 2.407090 GCAAATGCAAAGAAGTGGGAC 58.593 47.619 0.00 0.00 41.59 4.46
2838 2894 9.956640 AGAATTGAAGATACTCATTTCTCAAGT 57.043 29.630 5.38 0.00 39.87 3.16
2850 2908 5.647658 TCATTTCTCAAGTGTGTGTTGTTCT 59.352 36.000 0.00 0.00 0.00 3.01
2851 2909 5.545658 TTTCTCAAGTGTGTGTTGTTCTC 57.454 39.130 0.00 0.00 0.00 2.87
2852 2910 4.200838 TCTCAAGTGTGTGTTGTTCTCA 57.799 40.909 0.00 0.00 0.00 3.27
2853 2911 4.574892 TCTCAAGTGTGTGTTGTTCTCAA 58.425 39.130 0.00 0.00 0.00 3.02
2981 3039 4.794648 TGCCGTAGCCCATGGTGC 62.795 66.667 11.73 13.78 38.69 5.01
2982 3040 4.794648 GCCGTAGCCCATGGTGCA 62.795 66.667 22.33 9.53 35.49 4.57
2984 3042 2.188829 CCGTAGCCCATGGTGCATG 61.189 63.158 22.33 14.60 41.10 4.06
3004 3062 7.590322 GTGCATGAACAAAGAATAGATATGCTG 59.410 37.037 0.00 0.00 39.17 4.41
3040 3098 3.552132 TGGCGATCCAAGTATAAAGCA 57.448 42.857 0.00 0.00 39.99 3.91
3186 3260 2.353704 GGTAGTCCAAAGCCCAAAATGC 60.354 50.000 0.00 0.00 0.00 3.56
3210 3284 6.128172 GCAACTGTTCATAGAATTGCTACACT 60.128 38.462 8.50 0.00 39.42 3.55
3248 3322 7.824779 AGCTTTCAAATTCGGAAGTAGAACTAT 59.175 33.333 0.00 0.00 0.00 2.12
3384 3458 2.744202 AGCTAGTGCATGACCTTTTTCG 59.256 45.455 0.00 0.00 42.74 3.46
3420 3494 4.378874 GCTTTCCTTCTCTGTTGTATGCAC 60.379 45.833 0.00 0.00 0.00 4.57
3471 3545 0.523519 TCAGCTGTGTGAGAGCTACG 59.476 55.000 14.67 0.00 45.24 3.51
3544 3618 9.206690 ACTTTGATCTCTAGTGATCTTATCCAA 57.793 33.333 26.78 14.71 42.30 3.53
3548 3622 9.599056 TGATCTCTAGTGATCTTATCCAAATCT 57.401 33.333 26.78 0.00 42.30 2.40
3551 3625 9.653516 TCTCTAGTGATCTTATCCAAATCTTCT 57.346 33.333 0.00 0.00 0.00 2.85
3552 3626 9.695526 CTCTAGTGATCTTATCCAAATCTTCTG 57.304 37.037 0.00 0.00 0.00 3.02
3553 3627 9.206690 TCTAGTGATCTTATCCAAATCTTCTGT 57.793 33.333 0.00 0.00 0.00 3.41
3554 3628 9.829507 CTAGTGATCTTATCCAAATCTTCTGTT 57.170 33.333 0.00 0.00 0.00 3.16
3556 3630 9.525826 AGTGATCTTATCCAAATCTTCTGTTTT 57.474 29.630 0.00 0.00 0.00 2.43
3780 3855 1.599518 TGCATGACCTTTTCCGCGT 60.600 52.632 4.92 0.00 0.00 6.01
3781 3856 1.154225 GCATGACCTTTTCCGCGTG 60.154 57.895 4.92 0.00 0.00 5.34
3783 3858 1.599518 ATGACCTTTTCCGCGTGCA 60.600 52.632 4.92 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.967270 GCAAGAGGGTTGCCAATCT 58.033 52.632 0.00 0.00 39.38 2.40
33 34 1.528309 CAACACGGGCAAGAGGGTT 60.528 57.895 0.00 0.00 0.00 4.11
65 66 2.416566 GGACATGCACACACACACAAAA 60.417 45.455 0.00 0.00 0.00 2.44
67 68 0.737804 GGACATGCACACACACACAA 59.262 50.000 0.00 0.00 0.00 3.33
69 70 0.308684 CTGGACATGCACACACACAC 59.691 55.000 0.00 0.00 0.00 3.82
85 86 1.187715 CGCAAACAAACGTCAACTGG 58.812 50.000 0.00 0.00 0.00 4.00
87 88 1.465387 TCACGCAAACAAACGTCAACT 59.535 42.857 0.00 0.00 41.32 3.16
88 89 1.837747 CTCACGCAAACAAACGTCAAC 59.162 47.619 0.00 0.00 41.32 3.18
93 94 1.332904 GGAGACTCACGCAAACAAACG 60.333 52.381 4.53 0.00 0.00 3.60
94 95 1.940613 AGGAGACTCACGCAAACAAAC 59.059 47.619 4.53 0.00 32.90 2.93
103 104 3.271729 TCTAAGCAGTAGGAGACTCACG 58.728 50.000 4.53 0.00 43.67 4.35
119 120 9.720769 TCAGTTAAGAACCAAGGTTTATCTAAG 57.279 33.333 5.87 0.00 38.60 2.18
127 128 5.888982 TCTCTCAGTTAAGAACCAAGGTT 57.111 39.130 3.73 3.73 41.54 3.50
186 187 0.107557 GGCGTTAGGATTTCCCCGAA 60.108 55.000 5.44 0.00 36.42 4.30
215 216 1.428448 GACATTGTGCGACACTGCTA 58.572 50.000 10.54 0.00 32.73 3.49
249 250 1.605710 CAGCTCCAAGAACAACCACTG 59.394 52.381 0.00 0.00 0.00 3.66
250 251 1.972872 CAGCTCCAAGAACAACCACT 58.027 50.000 0.00 0.00 0.00 4.00
260 261 0.108233 GAGAGTGAGGCAGCTCCAAG 60.108 60.000 5.21 0.00 37.29 3.61
265 266 0.541530 TCAGTGAGAGTGAGGCAGCT 60.542 55.000 0.00 0.00 0.00 4.24
271 272 2.411904 GCAAAGGTCAGTGAGAGTGAG 58.588 52.381 0.00 0.00 0.00 3.51
304 305 0.620556 ATGGAGGAGTGCGTGGAAAT 59.379 50.000 0.00 0.00 0.00 2.17
373 382 0.028902 GGTCGTGCAGGTTGTTGTTC 59.971 55.000 6.26 0.00 0.00 3.18
428 437 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
429 438 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
431 440 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
432 441 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
433 442 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
434 443 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
435 444 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
436 445 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
437 446 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
438 447 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
439 448 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
440 449 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
441 450 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
442 451 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
443 452 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
444 453 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
445 454 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
446 455 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
447 456 3.708631 CACCTCTCTCTCTCTCTCTCTCT 59.291 52.174 0.00 0.00 0.00 3.10
448 457 3.706594 TCACCTCTCTCTCTCTCTCTCTC 59.293 52.174 0.00 0.00 0.00 3.20
449 458 3.708631 CTCACCTCTCTCTCTCTCTCTCT 59.291 52.174 0.00 0.00 0.00 3.10
450 459 3.452627 ACTCACCTCTCTCTCTCTCTCTC 59.547 52.174 0.00 0.00 0.00 3.20
451 460 3.198635 CACTCACCTCTCTCTCTCTCTCT 59.801 52.174 0.00 0.00 0.00 3.10
490 536 6.099706 TTGGGACATCTTGAGCCAATCTCA 62.100 45.833 0.00 0.00 44.66 3.27
507 553 1.961277 CAGCACGACCACTTGGGAC 60.961 63.158 0.00 0.00 41.15 4.46
624 671 3.329889 CCTGCAGGCCTACCACCA 61.330 66.667 22.33 0.00 39.06 4.17
704 754 4.895961 TGATGCATTTTTCAAATGAGCCA 58.104 34.783 12.43 2.83 0.00 4.75
757 812 9.004717 TCCAAAATCATGTAAGTTCGTTCATTA 57.995 29.630 0.00 0.00 0.00 1.90
765 820 9.914923 GTTTTTGTTCCAAAATCATGTAAGTTC 57.085 29.630 3.24 0.00 0.00 3.01
775 830 8.686397 AAAATTGCAGTTTTTGTTCCAAAATC 57.314 26.923 13.60 3.37 0.00 2.17
907 963 4.076394 ACCGCTTTATGCAGTCCTAAAAA 58.924 39.130 0.00 0.00 43.06 1.94
908 964 3.681593 ACCGCTTTATGCAGTCCTAAAA 58.318 40.909 0.00 0.00 43.06 1.52
909 965 3.343941 ACCGCTTTATGCAGTCCTAAA 57.656 42.857 0.00 0.00 43.06 1.85
910 966 3.735820 CGTACCGCTTTATGCAGTCCTAA 60.736 47.826 0.00 0.00 43.06 2.69
911 967 2.223641 CGTACCGCTTTATGCAGTCCTA 60.224 50.000 0.00 0.00 43.06 2.94
912 968 1.470979 CGTACCGCTTTATGCAGTCCT 60.471 52.381 0.00 0.00 43.06 3.85
913 969 0.928229 CGTACCGCTTTATGCAGTCC 59.072 55.000 0.00 0.00 43.06 3.85
914 970 1.917273 TCGTACCGCTTTATGCAGTC 58.083 50.000 0.00 0.00 43.06 3.51
915 971 2.596904 ATCGTACCGCTTTATGCAGT 57.403 45.000 0.00 0.00 43.06 4.40
916 972 3.183775 GGTAATCGTACCGCTTTATGCAG 59.816 47.826 0.00 0.00 40.59 4.41
917 973 3.125316 GGTAATCGTACCGCTTTATGCA 58.875 45.455 0.00 0.00 40.59 3.96
918 974 3.783111 GGTAATCGTACCGCTTTATGC 57.217 47.619 0.00 0.00 40.59 3.14
928 984 3.187022 GTGTGTGTTTGGGGTAATCGTAC 59.813 47.826 0.00 0.00 0.00 3.67
929 985 3.071312 AGTGTGTGTTTGGGGTAATCGTA 59.929 43.478 0.00 0.00 0.00 3.43
930 986 2.158726 AGTGTGTGTTTGGGGTAATCGT 60.159 45.455 0.00 0.00 0.00 3.73
931 987 2.500229 AGTGTGTGTTTGGGGTAATCG 58.500 47.619 0.00 0.00 0.00 3.34
932 988 4.822896 TGTAAGTGTGTGTTTGGGGTAATC 59.177 41.667 0.00 0.00 0.00 1.75
933 989 4.794334 TGTAAGTGTGTGTTTGGGGTAAT 58.206 39.130 0.00 0.00 0.00 1.89
934 990 4.232188 TGTAAGTGTGTGTTTGGGGTAA 57.768 40.909 0.00 0.00 0.00 2.85
935 991 3.928005 TGTAAGTGTGTGTTTGGGGTA 57.072 42.857 0.00 0.00 0.00 3.69
936 992 2.810870 TGTAAGTGTGTGTTTGGGGT 57.189 45.000 0.00 0.00 0.00 4.95
937 993 4.500716 GGATTTGTAAGTGTGTGTTTGGGG 60.501 45.833 0.00 0.00 0.00 4.96
938 994 4.340950 AGGATTTGTAAGTGTGTGTTTGGG 59.659 41.667 0.00 0.00 0.00 4.12
939 995 5.067153 TCAGGATTTGTAAGTGTGTGTTTGG 59.933 40.000 0.00 0.00 0.00 3.28
1023 1079 2.035155 TTCTCCTCCTGGACGCGA 59.965 61.111 15.93 0.00 37.46 5.87
1030 1086 1.746220 CACGAGTAGGTTCTCCTCCTG 59.254 57.143 0.00 0.00 43.94 3.86
1123 1179 2.665185 GACGAAGCTGTTGCGGGT 60.665 61.111 0.00 0.00 45.42 5.28
1455 1511 4.986587 TCCACCAACGTCGTCGCG 62.987 66.667 0.00 0.00 41.18 5.87
1615 1671 2.586357 GTTCCTCTCCGGCATCGC 60.586 66.667 0.00 0.00 34.56 4.58
1854 1910 1.066858 CGACCAGCACCTGAATACACT 60.067 52.381 0.00 0.00 32.44 3.55
1880 1936 3.283259 TGAAGAGATCGACAGCCTCTA 57.717 47.619 8.33 0.00 36.36 2.43
1890 1946 5.536260 TCCAGCATAATCTTGAAGAGATCG 58.464 41.667 0.00 0.00 44.41 3.69
1916 1972 1.547675 CCACCTTTGGCCTTGCTCTAA 60.548 52.381 3.32 0.00 35.56 2.10
1977 2033 2.281208 GGTAACCCACACTGCGCA 60.281 61.111 10.98 10.98 0.00 6.09
2082 2138 7.338449 GCCCTTTCTATATTACCACACTTTGAA 59.662 37.037 0.00 0.00 0.00 2.69
2208 2264 7.305935 CCATTGTCACACAACTCATTAAAAACG 60.306 37.037 0.00 0.00 41.40 3.60
2217 2273 2.346766 AGCCATTGTCACACAACTCA 57.653 45.000 0.00 0.00 41.40 3.41
2455 2511 1.559368 CCCCAAATTCCAGCATGTGA 58.441 50.000 0.00 0.00 0.00 3.58
2476 2532 4.021894 AGTCCTACATGCGCTTAATAGAGG 60.022 45.833 9.73 6.43 0.00 3.69
2481 2537 5.163447 TGAGTAAGTCCTACATGCGCTTAAT 60.163 40.000 9.73 0.00 32.37 1.40
2490 2546 6.440647 TCTCCACATTTGAGTAAGTCCTACAT 59.559 38.462 0.00 0.00 32.37 2.29
2616 2672 1.429463 CTCGAACCTTTTGGACTCCG 58.571 55.000 0.00 0.00 44.07 4.63
2838 2894 2.752354 CCAACCTTGAGAACAACACACA 59.248 45.455 0.00 0.00 32.27 3.72
2850 2908 5.420421 TGATGAAAGAAACAACCAACCTTGA 59.580 36.000 0.00 0.00 0.00 3.02
2851 2909 5.659463 TGATGAAAGAAACAACCAACCTTG 58.341 37.500 0.00 0.00 0.00 3.61
2852 2910 5.930837 TGATGAAAGAAACAACCAACCTT 57.069 34.783 0.00 0.00 0.00 3.50
2853 2911 5.930837 TTGATGAAAGAAACAACCAACCT 57.069 34.783 0.00 0.00 0.00 3.50
2894 2952 7.375053 TCAGTCCAGAATTTTAAAATTTCCCG 58.625 34.615 23.44 13.61 38.64 5.14
2981 3039 7.082602 GGCAGCATATCTATTCTTTGTTCATG 58.917 38.462 0.00 0.00 0.00 3.07
2982 3040 6.208204 GGGCAGCATATCTATTCTTTGTTCAT 59.792 38.462 0.00 0.00 0.00 2.57
2984 3042 5.532406 TGGGCAGCATATCTATTCTTTGTTC 59.468 40.000 0.00 0.00 0.00 3.18
3040 3098 4.639078 AATTTAAATTTGGCAGCCACCT 57.361 36.364 15.89 0.33 30.78 4.00
3186 3260 7.095060 ACAGTGTAGCAATTCTATGAACAGTTG 60.095 37.037 0.00 0.00 0.00 3.16
3210 3284 3.586470 TTGAAAGCTCCAACCCTTACA 57.414 42.857 0.00 0.00 0.00 2.41
3221 3295 6.147985 AGTTCTACTTCCGAATTTGAAAGCTC 59.852 38.462 0.00 0.00 0.00 4.09
3248 3322 9.547753 GAGAATATGTGCTCATAAGACCTTTTA 57.452 33.333 12.17 0.00 39.55 1.52
3293 3367 2.636830 CCACCACATGGCTTCTAAGAG 58.363 52.381 0.00 0.00 43.24 2.85
3322 3396 3.475566 ACACTTGCACTACACATGTCT 57.524 42.857 0.00 0.00 0.00 3.41
3384 3458 1.202698 AGGAAAGCCTCATATCGCACC 60.203 52.381 0.00 0.00 42.19 5.01
3420 3494 0.040067 GCAAGGACCAAGAGCAAACG 60.040 55.000 0.00 0.00 0.00 3.60
3559 3633 7.100409 ACCAGAAGATTTTTCCGTTTCAAAAA 58.900 30.769 0.00 0.00 37.18 1.94
3560 3634 6.635755 ACCAGAAGATTTTTCCGTTTCAAAA 58.364 32.000 0.00 0.00 0.00 2.44
3561 3635 6.215495 ACCAGAAGATTTTTCCGTTTCAAA 57.785 33.333 0.00 0.00 0.00 2.69
3562 3636 5.845391 ACCAGAAGATTTTTCCGTTTCAA 57.155 34.783 0.00 0.00 0.00 2.69
3563 3637 5.845391 AACCAGAAGATTTTTCCGTTTCA 57.155 34.783 0.00 0.00 0.00 2.69
3564 3638 7.919091 AGTAAAACCAGAAGATTTTTCCGTTTC 59.081 33.333 4.31 0.00 30.80 2.78
3565 3639 7.778083 AGTAAAACCAGAAGATTTTTCCGTTT 58.222 30.769 0.00 0.00 30.80 3.60
3566 3640 7.342769 AGTAAAACCAGAAGATTTTTCCGTT 57.657 32.000 0.00 0.00 30.80 4.44
3567 3641 6.954487 AGTAAAACCAGAAGATTTTTCCGT 57.046 33.333 0.00 0.00 30.80 4.69
3568 3642 7.918562 TGAAAGTAAAACCAGAAGATTTTTCCG 59.081 33.333 0.00 0.00 30.80 4.30
3569 3643 9.594478 TTGAAAGTAAAACCAGAAGATTTTTCC 57.406 29.630 0.00 0.00 30.80 3.13
3571 3645 9.599866 CCTTGAAAGTAAAACCAGAAGATTTTT 57.400 29.630 0.00 0.00 30.80 1.94
3572 3646 8.977412 TCCTTGAAAGTAAAACCAGAAGATTTT 58.023 29.630 0.00 0.00 32.85 1.82
3573 3647 8.533569 TCCTTGAAAGTAAAACCAGAAGATTT 57.466 30.769 0.00 0.00 0.00 2.17
3780 3855 2.796483 AAAGCCTCATACCGCGTGCA 62.796 55.000 4.92 0.00 0.00 4.57
3781 3856 2.036764 GAAAGCCTCATACCGCGTGC 62.037 60.000 4.92 0.00 0.00 5.34
3783 3858 1.153429 GGAAAGCCTCATACCGCGT 60.153 57.895 4.92 0.00 0.00 6.01


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

AutoCloner maintained by Alex Coulton.