Multiple sequence alignment - TraesCS1B01G434900

Loading Multiple Alignment...

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 TraesCS1B01G434900 chr1B 100.000 3113 0 0 1 3113 659032697 659035809 0.000000e+00 5749.0
1 TraesCS1B01G434900 chr1B 94.157 1643 48 14 802 2415 659294395 659296018 0.000000e+00 2459.0
2 TraesCS1B01G434900 chr1B 88.725 1898 98 41 554 2420 658968630 658970442 0.000000e+00 2213.0
3 TraesCS1B01G434900 chr1B 92.675 1488 68 19 957 2420 659002555 659004025 0.000000e+00 2106.0
4 TraesCS1B01G434900 chr1B 94.404 1358 29 12 957 2306 659285896 659287214 0.000000e+00 2043.0
5 TraesCS1B01G434900 chr1B 93.750 1216 43 10 1101 2299 659073585 659074784 0.000000e+00 1794.0
6 TraesCS1B01G434900 chr1B 94.291 543 21 3 1 536 659179408 659179947 0.000000e+00 822.0
7 TraesCS1B01G434900 chr1B 94.291 543 21 3 1 536 659282832 659283371 0.000000e+00 822.0
8 TraesCS1B01G434900 chr1B 93.692 539 28 3 957 1493 659182353 659182887 0.000000e+00 802.0
9 TraesCS1B01G434900 chr1B 84.292 643 67 15 1783 2416 659327172 659327789 5.750000e-167 597.0
10 TraesCS1B01G434900 chr1B 83.192 589 60 24 875 1458 659321429 659321983 1.290000e-138 503.0
11 TraesCS1B01G434900 chr1B 83.799 537 43 18 535 1057 659073064 659073570 1.310000e-128 470.0
12 TraesCS1B01G434900 chr1B 88.378 370 34 3 1 361 658967596 658967965 1.330000e-118 436.0
13 TraesCS1B01G434900 chr1B 90.260 308 15 8 58 361 659071926 659072222 3.760000e-104 388.0
14 TraesCS1B01G434900 chr1B 90.909 286 22 4 1 286 659298289 659298570 6.300000e-102 381.0
15 TraesCS1B01G434900 chr1B 84.810 395 26 13 545 919 659285515 659285895 1.760000e-97 366.0
16 TraesCS1B01G434900 chr1B 84.733 393 28 11 545 919 659181974 659182352 6.340000e-97 364.0
17 TraesCS1B01G434900 chr1B 90.226 266 16 5 2155 2420 659190872 659191127 3.850000e-89 339.0
18 TraesCS1B01G434900 chr1B 89.850 266 17 5 2155 2420 659083060 659083315 1.790000e-87 333.0
19 TraesCS1B01G434900 chr1B 92.040 201 12 4 2916 3113 659278517 659278716 2.360000e-71 279.0
20 TraesCS1B01G434900 chr1B 91.542 201 13 4 2916 3113 659174567 659174766 1.100000e-69 274.0
21 TraesCS1B01G434900 chr1B 93.662 142 5 2 301 438 659293475 659293616 3.150000e-50 209.0
22 TraesCS1B01G434900 chr1B 79.767 257 24 8 2613 2846 659174301 659174552 8.930000e-36 161.0
23 TraesCS1B01G434900 chr1B 79.377 257 24 9 2613 2846 659278252 659278502 1.500000e-33 154.0
24 TraesCS1B01G434900 chr1D 86.420 1944 110 55 533 2420 473960653 473962498 0.000000e+00 1986.0
25 TraesCS1B01G434900 chr1D 81.603 886 86 39 875 1729 473879604 473880443 0.000000e+00 662.0
26 TraesCS1B01G434900 chr1D 90.095 525 25 4 2615 3113 473953154 473953677 0.000000e+00 656.0
27 TraesCS1B01G434900 chr1D 83.510 661 64 20 1783 2415 473993105 473993748 2.690000e-160 575.0
28 TraesCS1B01G434900 chr1D 90.566 371 25 2 1 361 473959639 473960009 1.680000e-132 483.0
29 TraesCS1B01G434900 chr1D 80.556 288 37 12 1 282 473878689 473878963 1.460000e-48 204.0
30 TraesCS1B01G434900 chr1D 91.262 103 6 3 437 537 46474792 46474893 1.510000e-28 137.0
31 TraesCS1B01G434900 chr1D 91.346 104 4 5 437 537 454167044 454166943 1.510000e-28 137.0
32 TraesCS1B01G434900 chr1D 81.761 159 21 8 126 282 473990959 473991111 3.260000e-25 126.0
33 TraesCS1B01G434900 chr1D 92.857 42 2 1 398 438 473960154 473960195 3.350000e-05 60.2
34 TraesCS1B01G434900 chr1A 88.842 1192 77 24 535 1710 568265504 568266655 0.000000e+00 1413.0
35 TraesCS1B01G434900 chr1A 88.065 863 66 20 716 1552 568327609 568328460 0.000000e+00 989.0
36 TraesCS1B01G434900 chr1A 93.850 439 24 2 1755 2193 568266926 568267361 0.000000e+00 658.0
37 TraesCS1B01G434900 chr1A 84.891 642 62 15 1785 2416 568399455 568400071 1.590000e-172 616.0
38 TraesCS1B01G434900 chr1A 86.095 525 49 6 2613 3113 568259268 568259792 7.590000e-151 544.0
39 TraesCS1B01G434900 chr1A 84.806 566 54 8 1783 2327 568377871 568378425 9.820000e-150 540.0
40 TraesCS1B01G434900 chr1A 91.328 369 24 2 1 361 568264466 568264834 6.000000e-137 497.0
41 TraesCS1B01G434900 chr1A 91.413 361 28 1 1 361 568326306 568326663 2.790000e-135 492.0
42 TraesCS1B01G434900 chr1A 83.072 573 59 26 877 1444 568393319 568393858 1.300000e-133 486.0
43 TraesCS1B01G434900 chr1A 93.189 323 20 1 1917 2237 568334079 568334401 1.010000e-129 473.0
44 TraesCS1B01G434900 chr1A 90.777 206 14 4 2910 3113 568315961 568316163 1.420000e-68 270.0
45 TraesCS1B01G434900 chr1A 86.740 181 12 5 2243 2420 568267372 568267543 1.140000e-44 191.0
46 TraesCS1B01G434900 chr1A 79.537 259 29 16 15 262 568387397 568387642 2.480000e-36 163.0
47 TraesCS1B01G434900 chr1A 86.713 143 12 4 1589 1729 568122514 568122651 5.380000e-33 152.0
48 TraesCS1B01G434900 chr1A 80.288 208 26 8 1524 1726 568383827 568384024 3.240000e-30 143.0
49 TraesCS1B01G434900 chr5A 90.179 112 6 4 429 536 397512292 397512402 1.160000e-29 141.0
50 TraesCS1B01G434900 chr5A 92.079 101 7 1 437 536 426351481 426351381 1.160000e-29 141.0
51 TraesCS1B01G434900 chr2A 90.090 111 7 3 430 537 9949327 9949218 1.160000e-29 141.0
52 TraesCS1B01G434900 chr5B 90.741 108 3 7 434 536 386533363 386533468 1.510000e-28 137.0
53 TraesCS1B01G434900 chr4D 91.176 102 8 1 437 537 480505087 480505188 1.510000e-28 137.0


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 TraesCS1B01G434900 chr1B 659032697 659035809 3112 False 5749.000000 5749 100.000000 1 3113 1 chr1B.!!$F2 3112
1 TraesCS1B01G434900 chr1B 659002555 659004025 1470 False 2106.000000 2106 92.675000 957 2420 1 chr1B.!!$F1 1463
2 TraesCS1B01G434900 chr1B 658967596 658970442 2846 False 1324.500000 2213 88.551500 1 2420 2 chr1B.!!$F7 2419
3 TraesCS1B01G434900 chr1B 659282832 659287214 4382 False 1077.000000 2043 91.168333 1 2306 3 chr1B.!!$F12 2305
4 TraesCS1B01G434900 chr1B 659293475 659298570 5095 False 1016.333333 2459 92.909333 1 2415 3 chr1B.!!$F13 2414
5 TraesCS1B01G434900 chr1B 659071926 659074784 2858 False 884.000000 1794 89.269667 58 2299 3 chr1B.!!$F8 2241
6 TraesCS1B01G434900 chr1B 659179408 659182887 3479 False 662.666667 822 90.905333 1 1493 3 chr1B.!!$F10 1492
7 TraesCS1B01G434900 chr1B 659327172 659327789 617 False 597.000000 597 84.292000 1783 2416 1 chr1B.!!$F6 633
8 TraesCS1B01G434900 chr1B 659321429 659321983 554 False 503.000000 503 83.192000 875 1458 1 chr1B.!!$F5 583
9 TraesCS1B01G434900 chr1D 473959639 473962498 2859 False 843.066667 1986 89.947667 1 2420 3 chr1D.!!$F4 2419
10 TraesCS1B01G434900 chr1D 473953154 473953677 523 False 656.000000 656 90.095000 2615 3113 1 chr1D.!!$F2 498
11 TraesCS1B01G434900 chr1D 473878689 473880443 1754 False 433.000000 662 81.079500 1 1729 2 chr1D.!!$F3 1728
12 TraesCS1B01G434900 chr1D 473990959 473993748 2789 False 350.500000 575 82.635500 126 2415 2 chr1D.!!$F5 2289
13 TraesCS1B01G434900 chr1A 568326306 568328460 2154 False 740.500000 989 89.739000 1 1552 2 chr1A.!!$F9 1551
14 TraesCS1B01G434900 chr1A 568264466 568267543 3077 False 689.750000 1413 90.190000 1 2420 4 chr1A.!!$F8 2419
15 TraesCS1B01G434900 chr1A 568399455 568400071 616 False 616.000000 616 84.891000 1785 2416 1 chr1A.!!$F7 631
16 TraesCS1B01G434900 chr1A 568259268 568259792 524 False 544.000000 544 86.095000 2613 3113 1 chr1A.!!$F2 500
17 TraesCS1B01G434900 chr1A 568377871 568378425 554 False 540.000000 540 84.806000 1783 2327 1 chr1A.!!$F5 544
18 TraesCS1B01G434900 chr1A 568393319 568393858 539 False 486.000000 486 83.072000 877 1444 1 chr1A.!!$F6 567

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
947 3629 0.320247 CCACAGCCACAGAGAGACAC 60.32 60.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 5433 0.179018 ACCTGTGGAGTCCAAACTGC 60.179 55.0 15.09 1.01 43.66 4.4 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
24 28 3.062639 GCTTGCCAGCATTGGGTT 58.937 55.556 4.63 0.00 46.49 4.11
38 42 1.368374 TGGGTTAGAGGGGTTTCAGG 58.632 55.000 0.00 0.00 0.00 3.86
59 63 5.032170 AGGAAACTAATGGAAATGGGCATT 58.968 37.500 0.00 0.00 40.61 3.56
104 114 1.302033 ACCTTGGCAGCTCTGTTCG 60.302 57.895 0.00 0.00 0.00 3.95
119 132 1.816835 TGTTCGGAAGAGCACGTATCT 59.183 47.619 0.00 0.00 46.64 1.98
133 146 2.510382 ACGTATCTTCCTCCTCCTCTCA 59.490 50.000 0.00 0.00 0.00 3.27
172 185 1.094073 ATTGGCTGATCTGCACGCTC 61.094 55.000 23.84 8.55 34.04 5.03
364 573 7.965718 TGAATTTGGAATCATGGAGAAGTTTT 58.034 30.769 0.00 0.00 0.00 2.43
552 3044 3.496160 GGAACAAGCTAGGGTCAGAACAA 60.496 47.826 5.79 0.00 0.00 2.83
624 3138 3.902218 TGCAGCTTAGCCAGGAAATTAT 58.098 40.909 0.00 0.00 0.00 1.28
649 3164 9.844257 ATGTCAAACAATTATTCAAGGGAAAAA 57.156 25.926 0.00 0.00 36.43 1.94
650 3165 9.323985 TGTCAAACAATTATTCAAGGGAAAAAG 57.676 29.630 0.00 0.00 36.43 2.27
651 3166 9.541143 GTCAAACAATTATTCAAGGGAAAAAGA 57.459 29.630 0.00 0.00 36.43 2.52
695 3238 9.829507 AATCAAATTGTCTTTTACATCAAACCA 57.170 25.926 0.00 0.00 38.10 3.67
702 3245 6.039616 GTCTTTTACATCAAACCAAAGCACA 58.960 36.000 0.00 0.00 0.00 4.57
725 3283 1.201343 GCTACGACGGATTCAAGAGC 58.799 55.000 0.00 0.00 0.00 4.09
815 3462 1.081242 GCAGTGTGCAAATGGACCG 60.081 57.895 2.51 0.00 44.26 4.79
889 3560 7.867909 TGATAATGATACTAGCTCAGAAAACCG 59.132 37.037 0.00 0.00 0.00 4.44
910 3592 3.506067 CGGCAAAACCTTATTGTCCTCTT 59.494 43.478 0.00 0.00 35.61 2.85
945 3627 1.294780 CCCACAGCCACAGAGAGAC 59.705 63.158 0.00 0.00 0.00 3.36
947 3629 0.320247 CCACAGCCACAGAGAGACAC 60.320 60.000 0.00 0.00 0.00 3.67
950 3643 0.394192 CAGCCACAGAGAGACACCAA 59.606 55.000 0.00 0.00 0.00 3.67
1097 3809 7.140048 AGAAAGTAGTGTTCTTAGTTCGAGTG 58.860 38.462 0.00 0.00 31.10 3.51
1673 4515 3.372566 CCTGGCCCAATTTATCAGTGGTA 60.373 47.826 0.00 0.00 0.00 3.25
1699 4548 5.673337 TCTTAGCACAATCAGACAAACAC 57.327 39.130 0.00 0.00 0.00 3.32
1760 4948 2.366533 TCTGGTGGTCTAGCTAGAACG 58.633 52.381 29.06 17.30 42.93 3.95
1877 5075 1.618837 TGTAAGCTCCAGTGGACAGTC 59.381 52.381 8.12 0.00 0.00 3.51
2153 5392 5.779922 TGTAAGAAGTTGTACCTGTAGCAG 58.220 41.667 0.00 0.00 0.00 4.24
2157 5396 6.415206 AGAAGTTGTACCTGTAGCAGTTTA 57.585 37.500 0.00 0.00 0.00 2.01
2193 5433 0.527565 GTTTAGCTGGCCACCATGTG 59.472 55.000 0.00 0.00 30.82 3.21
2244 5501 1.081892 CCGAATCCTTGTCACTGCTG 58.918 55.000 0.00 0.00 0.00 4.41
2252 5516 0.250467 TTGTCACTGCTGCCTTCCTC 60.250 55.000 0.00 0.00 0.00 3.71
2253 5517 1.376553 GTCACTGCTGCCTTCCTCC 60.377 63.158 0.00 0.00 0.00 4.30
2254 5518 1.537397 TCACTGCTGCCTTCCTCCT 60.537 57.895 0.00 0.00 0.00 3.69
2255 5519 1.130054 TCACTGCTGCCTTCCTCCTT 61.130 55.000 0.00 0.00 0.00 3.36
2256 5520 0.676151 CACTGCTGCCTTCCTCCTTC 60.676 60.000 0.00 0.00 0.00 3.46
2257 5521 1.077858 CTGCTGCCTTCCTCCTTCC 60.078 63.158 0.00 0.00 0.00 3.46
2258 5522 1.539869 TGCTGCCTTCCTCCTTCCT 60.540 57.895 0.00 0.00 0.00 3.36
2304 5568 5.339695 TGTTAAAGAACCACAGGAAGAACCT 60.340 40.000 0.00 0.00 41.47 3.50
2305 5569 6.126710 TGTTAAAGAACCACAGGAAGAACCTA 60.127 38.462 0.00 0.00 39.93 3.08
2306 5570 7.583809 TGTTAAAGAACCACAGGAAGAACCTAA 60.584 37.037 0.00 0.00 39.93 2.69
2369 5637 8.791327 TCACTGTTAAGCATCATTGAATCTAA 57.209 30.769 0.00 0.00 0.00 2.10
2385 5653 2.749600 TCTAAGGTGGTATTACGGCCA 58.250 47.619 2.24 0.00 0.00 5.36
2422 5849 4.277672 CAGTCCTTGAGATTGGCCATATTG 59.722 45.833 6.09 0.00 0.00 1.90
2436 5863 4.501400 GGCCATATTGTTTCCAGCCATAAC 60.501 45.833 0.00 0.00 38.79 1.89
2440 5867 6.925165 CCATATTGTTTCCAGCCATAACAATC 59.075 38.462 13.71 0.00 44.72 2.67
2446 5873 3.346315 TCCAGCCATAACAATCACACTG 58.654 45.455 0.00 0.00 0.00 3.66
2454 5881 6.183360 GCCATAACAATCACACTGTTCTCTAC 60.183 42.308 0.00 0.00 38.05 2.59
2461 5888 7.438459 ACAATCACACTGTTCTCTACAAGTAAC 59.562 37.037 0.00 0.00 36.02 2.50
2470 5897 6.015688 TGTTCTCTACAAGTAACAGTACAGGG 60.016 42.308 0.00 0.00 32.64 4.45
2476 5903 5.365619 ACAAGTAACAGTACAGGGTGAAAG 58.634 41.667 0.00 0.00 32.12 2.62
2489 5916 5.221244 ACAGGGTGAAAGTAAACTTCATTGC 60.221 40.000 0.00 0.00 34.61 3.56
2503 5930 3.153369 TCATTGCTAACAAGGCAGGAA 57.847 42.857 0.00 0.00 39.69 3.36
2519 5946 6.116126 AGGCAGGAAAAGTACATCAAGATAC 58.884 40.000 0.00 0.00 0.00 2.24
2521 5948 6.037610 GGCAGGAAAAGTACATCAAGATACAG 59.962 42.308 0.00 0.00 0.00 2.74
2523 5950 5.812642 AGGAAAAGTACATCAAGATACAGCG 59.187 40.000 0.00 0.00 0.00 5.18
2526 5953 7.306866 GGAAAAGTACATCAAGATACAGCGATC 60.307 40.741 0.00 0.00 0.00 3.69
2527 5954 5.774498 AGTACATCAAGATACAGCGATCA 57.226 39.130 0.00 0.00 0.00 2.92
2528 5955 6.149129 AGTACATCAAGATACAGCGATCAA 57.851 37.500 0.00 0.00 0.00 2.57
2529 5956 6.212235 AGTACATCAAGATACAGCGATCAAG 58.788 40.000 0.00 0.00 0.00 3.02
2530 5957 5.268118 ACATCAAGATACAGCGATCAAGA 57.732 39.130 0.00 0.00 0.00 3.02
2531 5958 5.851720 ACATCAAGATACAGCGATCAAGAT 58.148 37.500 0.00 0.00 0.00 2.40
2535 5962 6.805713 TCAAGATACAGCGATCAAGATAACA 58.194 36.000 0.00 0.00 0.00 2.41
2537 5964 7.436376 TCAAGATACAGCGATCAAGATAACAAG 59.564 37.037 0.00 0.00 0.00 3.16
2538 5965 6.219473 AGATACAGCGATCAAGATAACAAGG 58.781 40.000 0.00 0.00 0.00 3.61
2539 5966 4.471904 ACAGCGATCAAGATAACAAGGA 57.528 40.909 0.00 0.00 0.00 3.36
2557 5994 3.950397 AGGAAAGACACACAAGTCACAA 58.050 40.909 0.00 0.00 40.98 3.33
2565 6002 3.947196 ACACACAAGTCACAATGTCACAT 59.053 39.130 0.00 0.00 0.00 3.21
2566 6003 4.201940 ACACACAAGTCACAATGTCACATG 60.202 41.667 0.00 0.00 0.00 3.21
2567 6004 4.035441 CACACAAGTCACAATGTCACATGA 59.965 41.667 0.00 0.00 0.00 3.07
2568 6005 4.823442 ACACAAGTCACAATGTCACATGAT 59.177 37.500 0.00 0.00 0.00 2.45
2569 6006 5.151389 CACAAGTCACAATGTCACATGATG 58.849 41.667 0.00 0.00 0.00 3.07
2578 6015 7.771826 TCACAATGTCACATGATGATACTTCAT 59.228 33.333 0.00 0.00 45.39 2.57
2585 6022 9.499479 GTCACATGATGATACTTCATTAATCCT 57.501 33.333 0.00 0.00 42.73 3.24
2688 6508 7.682787 ACTATCATGAGTAGAACCAATCCTT 57.317 36.000 15.02 0.00 0.00 3.36
2709 6529 6.044871 TCCTTTTCTTCCTTCTCCTCTTGATT 59.955 38.462 0.00 0.00 0.00 2.57
2808 6652 0.389948 AAAACTCCACCGAGCTAGCG 60.390 55.000 9.55 0.00 40.03 4.26
2823 6667 2.675317 GCTAGCGTCTTCATTGTGGTCT 60.675 50.000 0.00 0.00 0.00 3.85
2894 6738 5.105392 TGGAGTCAAGTTGTTGCTTCAAAAT 60.105 36.000 2.11 0.00 33.23 1.82
2955 6814 7.659390 ACAAGAAGAGAAGTTCTAACATGGAAG 59.341 37.037 5.09 0.00 35.65 3.46
2958 6817 3.942115 GAGAAGTTCTAACATGGAAGGGC 59.058 47.826 5.09 0.00 0.00 5.19
3022 7745 2.761767 TCATCATTGCCCACCTTCATTG 59.238 45.455 0.00 0.00 0.00 2.82
3024 7747 2.170166 TCATTGCCCACCTTCATTGTC 58.830 47.619 0.00 0.00 0.00 3.18
3026 7749 2.307496 TTGCCCACCTTCATTGTCAT 57.693 45.000 0.00 0.00 0.00 3.06
3081 8014 7.659799 GGAAAAGTTGGTAATTACAAAAGGCAT 59.340 33.333 17.16 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 42 5.976458 TCAATGCCCATTTCCATTAGTTTC 58.024 37.500 0.00 0.00 30.96 2.78
54 58 4.161333 CAAAAACGTCTCATCTCAATGCC 58.839 43.478 0.00 0.00 32.58 4.40
59 63 3.485463 ACCCAAAAACGTCTCATCTCA 57.515 42.857 0.00 0.00 0.00 3.27
119 132 1.623557 CCCACATGAGAGGAGGAGGAA 60.624 57.143 0.00 0.00 0.00 3.36
172 185 0.653636 GTCGGCAGAGAGTCTCGTAG 59.346 60.000 14.47 9.75 35.36 3.51
364 573 5.587043 CACCAAGGTTGTAGTGTTCAACTTA 59.413 40.000 8.34 0.00 42.97 2.24
490 726 3.340253 GGCGTGCGTTTGTACCGT 61.340 61.111 0.00 0.00 0.00 4.83
596 3104 1.198637 CTGGCTAAGCTGCAACTCAAC 59.801 52.381 1.02 0.00 34.04 3.18
602 3110 2.220653 ATTTCCTGGCTAAGCTGCAA 57.779 45.000 1.02 0.00 34.04 4.08
624 3138 9.323985 CTTTTTCCCTTGAATAATTGTTTGACA 57.676 29.630 0.00 0.00 0.00 3.58
695 3238 2.094390 TCCGTCGTAGCTAATGTGCTTT 60.094 45.455 0.00 0.00 43.74 3.51
702 3245 4.793353 GCTCTTGAATCCGTCGTAGCTAAT 60.793 45.833 0.00 0.00 0.00 1.73
803 3450 0.316841 GCCTTTTCGGTCCATTTGCA 59.683 50.000 0.00 0.00 34.25 4.08
815 3462 5.406477 CCTGTTTGAGCAATTAAGCCTTTTC 59.594 40.000 0.00 0.00 34.23 2.29
868 3515 4.740934 GCCGGTTTTCTGAGCTAGTATCAT 60.741 45.833 1.90 0.00 0.00 2.45
889 3560 4.767409 AGAAGAGGACAATAAGGTTTTGCC 59.233 41.667 0.00 0.00 37.58 4.52
910 3592 1.777878 TGGGTTAAAAGGTGGCTGAGA 59.222 47.619 0.00 0.00 0.00 3.27
945 3627 4.641645 TGGGAGCGTGCCTTGGTG 62.642 66.667 0.00 0.00 0.00 4.17
1097 3809 3.616956 TCAGGTGAGATGTGATGTTCC 57.383 47.619 0.00 0.00 0.00 3.62
1169 3895 1.072331 TGTTCTCCTTCTTGCTCCACC 59.928 52.381 0.00 0.00 0.00 4.61
1588 4423 1.426621 GTGCCAGTCGTCATGCATG 59.573 57.895 21.07 21.07 35.96 4.06
1589 4424 1.746615 GGTGCCAGTCGTCATGCAT 60.747 57.895 0.00 0.00 35.96 3.96
1673 4515 8.454106 GTGTTTGTCTGATTGTGCTAAGATTAT 58.546 33.333 0.00 0.00 0.00 1.28
1699 4548 6.015095 AGCTTTTTCTTTGGAAGTAGGGAATG 60.015 38.462 0.00 0.00 32.61 2.67
1760 4948 6.670077 ACTCAAACAGAAGAGACTTGTTTC 57.330 37.500 0.91 0.00 35.83 2.78
1877 5075 9.046296 AGAGATCTAGTTTGTACAACTTTGTTG 57.954 33.333 8.07 8.66 42.35 3.33
2071 5303 1.374252 CGACTTGGTTCCACGGGAG 60.374 63.158 0.00 0.00 31.21 4.30
2193 5433 0.179018 ACCTGTGGAGTCCAAACTGC 60.179 55.000 15.09 1.01 43.66 4.40
2244 5501 3.519913 TCTCTTTTAGGAAGGAGGAAGGC 59.480 47.826 0.00 0.00 38.95 4.35
2252 5516 8.151596 AGTTTAGTGAACTCTCTTTTAGGAAGG 58.848 37.037 0.00 0.00 45.40 3.46
2304 5568 9.154847 CAGATGTCGATTATTCTGGCATTATTA 57.845 33.333 0.00 0.00 33.54 0.98
2305 5569 7.879677 TCAGATGTCGATTATTCTGGCATTATT 59.120 33.333 13.42 0.00 36.95 1.40
2306 5570 7.389232 TCAGATGTCGATTATTCTGGCATTAT 58.611 34.615 13.42 0.00 36.95 1.28
2369 5637 2.037144 CTACTGGCCGTAATACCACCT 58.963 52.381 0.00 0.00 0.00 4.00
2385 5653 6.495181 TCTCAAGGACTGTTCTTGATTCTACT 59.505 38.462 27.14 0.00 46.24 2.57
2422 5849 4.218417 AGTGTGATTGTTATGGCTGGAAAC 59.782 41.667 0.00 0.00 0.00 2.78
2436 5863 7.438160 TGTTACTTGTAGAGAACAGTGTGATTG 59.562 37.037 0.00 0.00 39.87 2.67
2440 5867 6.755461 CTGTTACTTGTAGAGAACAGTGTG 57.245 41.667 0.00 0.00 42.40 3.82
2446 5873 6.015603 ACCCTGTACTGTTACTTGTAGAGAAC 60.016 42.308 11.96 0.00 33.55 3.01
2454 5881 5.365619 ACTTTCACCCTGTACTGTTACTTG 58.634 41.667 0.00 0.00 0.00 3.16
2461 5888 6.053005 TGAAGTTTACTTTCACCCTGTACTG 58.947 40.000 0.00 0.00 36.11 2.74
2463 5890 7.360361 CAATGAAGTTTACTTTCACCCTGTAC 58.640 38.462 0.00 0.00 36.11 2.90
2464 5891 6.016610 GCAATGAAGTTTACTTTCACCCTGTA 60.017 38.462 0.00 0.00 36.11 2.74
2470 5897 8.850454 TTGTTAGCAATGAAGTTTACTTTCAC 57.150 30.769 0.00 0.00 36.11 3.18
2476 5903 5.768317 TGCCTTGTTAGCAATGAAGTTTAC 58.232 37.500 0.00 0.00 37.28 2.01
2489 5916 5.705441 TGATGTACTTTTCCTGCCTTGTTAG 59.295 40.000 0.00 0.00 0.00 2.34
2503 5930 6.573434 TGATCGCTGTATCTTGATGTACTTT 58.427 36.000 0.00 0.00 0.00 2.66
2519 5946 5.582269 TCTTTCCTTGTTATCTTGATCGCTG 59.418 40.000 0.00 0.00 0.00 5.18
2521 5948 5.351465 TGTCTTTCCTTGTTATCTTGATCGC 59.649 40.000 0.00 0.00 0.00 4.58
2523 5950 7.173218 TGTGTGTCTTTCCTTGTTATCTTGATC 59.827 37.037 0.00 0.00 0.00 2.92
2526 5953 6.618287 TGTGTGTCTTTCCTTGTTATCTTG 57.382 37.500 0.00 0.00 0.00 3.02
2527 5954 6.828785 ACTTGTGTGTCTTTCCTTGTTATCTT 59.171 34.615 0.00 0.00 0.00 2.40
2528 5955 6.357367 ACTTGTGTGTCTTTCCTTGTTATCT 58.643 36.000 0.00 0.00 0.00 1.98
2529 5956 6.260050 TGACTTGTGTGTCTTTCCTTGTTATC 59.740 38.462 0.00 0.00 37.79 1.75
2530 5957 6.038271 GTGACTTGTGTGTCTTTCCTTGTTAT 59.962 38.462 0.00 0.00 37.79 1.89
2531 5958 5.353123 GTGACTTGTGTGTCTTTCCTTGTTA 59.647 40.000 0.00 0.00 37.79 2.41
2535 5962 3.950397 TGTGACTTGTGTGTCTTTCCTT 58.050 40.909 0.00 0.00 37.79 3.36
2537 5964 4.096382 ACATTGTGACTTGTGTGTCTTTCC 59.904 41.667 0.00 0.00 37.79 3.13
2538 5965 5.163764 TGACATTGTGACTTGTGTGTCTTTC 60.164 40.000 0.00 0.00 37.46 2.62
2539 5966 4.699735 TGACATTGTGACTTGTGTGTCTTT 59.300 37.500 0.00 0.00 37.46 2.52
2565 6002 6.840527 TGCCAGGATTAATGAAGTATCATCA 58.159 36.000 0.00 0.00 45.60 3.07
2566 6003 6.128063 GCTGCCAGGATTAATGAAGTATCATC 60.128 42.308 0.00 0.00 45.60 2.92
2568 6005 5.065914 GCTGCCAGGATTAATGAAGTATCA 58.934 41.667 0.00 0.00 40.57 2.15
2569 6006 5.065914 TGCTGCCAGGATTAATGAAGTATC 58.934 41.667 0.00 0.00 0.00 2.24
2671 6491 6.044404 AGGAAGAAAAGGATTGGTTCTACTCA 59.956 38.462 0.00 0.00 31.41 3.41
2688 6508 9.494055 TCTATAATCAAGAGGAGAAGGAAGAAA 57.506 33.333 0.00 0.00 0.00 2.52
2808 6652 3.988379 TTGCAAGACCACAATGAAGAC 57.012 42.857 0.00 0.00 0.00 3.01
2823 6667 6.208402 TGCAGACTAAACCTATTCATTTGCAA 59.792 34.615 0.00 0.00 34.20 4.08
2894 6738 7.236847 TCAGGAGATGGAGTAAAAGTAAAAGGA 59.763 37.037 0.00 0.00 0.00 3.36
2955 6814 8.837389 CCATGTTAGAACTACTAATAAAAGCCC 58.163 37.037 0.00 0.00 42.11 5.19
3081 8014 7.094377 GGCAAAACCTATTTATGTCAGAAGTGA 60.094 37.037 0.00 0.00 34.51 3.41


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

AutoCloner maintained by Alex Coulton.