Multiple sequence alignment - TraesCS2A01G295000

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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 TraesCS2A01G295000 chr2A 100.000 3897 0 0 1 3897 507602214 507606110 0.000000e+00 7197.0
1 TraesCS2A01G295000 chr2D 92.265 2883 154 21 1073 3896 375256275 375259147 0.000000e+00 4024.0
2 TraesCS2A01G295000 chr2D 92.379 1076 48 16 1 1073 375255193 375256237 0.000000e+00 1502.0
3 TraesCS2A01G295000 chr2B 93.472 1869 69 13 1073 2903 445496526 445498379 0.000000e+00 2726.0
4 TraesCS2A01G295000 chr2B 85.501 1007 104 18 2900 3896 445498880 445499854 0.000000e+00 1013.0
5 TraesCS2A01G295000 chr2B 88.646 458 24 10 1 458 445490416 445490845 2.060000e-147 532.0
6 TraesCS2A01G295000 chr2B 93.617 141 3 5 659 794 445491562 445491701 5.100000e-49 206.0
7 TraesCS2A01G295000 chr2B 83.575 207 26 4 451 656 445491315 445491514 1.850000e-43 187.0
8 TraesCS2A01G295000 chr2B 83.429 175 9 6 908 1073 445496316 445496479 1.130000e-30 145.0
9 TraesCS2A01G295000 chr2B 86.957 115 11 2 804 918 445496188 445496298 4.090000e-25 126.0
10 TraesCS2A01G295000 chr5A 97.119 243 7 0 2113 2355 501850980 501851222 1.010000e-110 411.0
11 TraesCS2A01G295000 chr1A 95.885 243 10 0 2113 2355 540182259 540182017 1.010000e-105 394.0
12 TraesCS2A01G295000 chr1A 82.870 216 23 6 2367 2582 549330359 549330560 8.600000e-42 182.0
13 TraesCS2A01G295000 chr6B 95.455 242 11 0 2114 2355 188499807 188499566 1.700000e-103 387.0
14 TraesCS2A01G295000 chr6B 80.208 192 30 5 3711 3895 642531154 642530964 1.890000e-28 137.0
15 TraesCS2A01G295000 chr6B 89.091 55 6 0 2180 2234 586001070 586001016 6.990000e-08 69.4
16 TraesCS2A01G295000 chr3D 88.288 222 15 6 2367 2588 15994220 15994430 5.000000e-64 255.0
17 TraesCS2A01G295000 chr4D 86.758 219 15 7 2370 2588 196877510 196877306 8.420000e-57 231.0
18 TraesCS2A01G295000 chr1D 85.135 222 22 6 2367 2588 490742977 490742767 2.360000e-52 217.0
19 TraesCS2A01G295000 chr3B 84.018 219 24 4 2370 2588 709286548 709286755 2.370000e-47 200.0
20 TraesCS2A01G295000 chr6A 81.865 193 23 5 2392 2584 29798398 29798218 6.740000e-33 152.0
21 TraesCS2A01G295000 chr6A 87.273 55 7 0 2180 2234 538551920 538551974 3.250000e-06 63.9
22 TraesCS2A01G295000 chr7B 86.614 127 16 1 2934 3060 702455673 702455548 5.250000e-29 139.0
23 TraesCS2A01G295000 chr5B 83.951 81 11 2 2371 2451 457026308 457026230 4.180000e-10 76.8
24 TraesCS2A01G295000 chr6D 89.091 55 6 0 2180 2234 392619539 392619593 6.990000e-08 69.4


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 TraesCS2A01G295000 chr2A 507602214 507606110 3896 False 7197.000000 7197 100.000000 1 3897 1 chr2A.!!$F1 3896
1 TraesCS2A01G295000 chr2D 375255193 375259147 3954 False 2763.000000 4024 92.322000 1 3896 2 chr2D.!!$F1 3895
2 TraesCS2A01G295000 chr2B 445496188 445499854 3666 False 1002.500000 2726 87.339750 804 3896 4 chr2B.!!$F2 3092
3 TraesCS2A01G295000 chr2B 445490416 445491701 1285 False 308.333333 532 88.612667 1 794 3 chr2B.!!$F1 793

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
427 446 0.033366 GGCGGTGCTTGGTTTGAATT 59.967 50.0 0.00 0.0 0.00 2.17 F
1108 1748 0.672401 GACCGTTGGAATGGAGCGAA 60.672 55.0 4.58 0.0 38.48 4.70 F
2623 3293 0.247460 TCTGCTCGTGATGAGGTTGG 59.753 55.0 3.55 0.0 45.38 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2762 0.250513 GCTTCTCGGACCCAATCACT 59.749 55.000 0.00 0.00 0.0 3.41 R
2673 3352 0.038744 CTCTGAGGCCCAAACACCAT 59.961 55.000 0.00 0.00 0.0 3.55 R
3673 4878 1.152546 TGCATCTAGGGCGCTAGGA 60.153 57.895 30.86 20.33 0.0 2.94 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
235 254 3.118454 GCGCTTCGTGGCTTGCTA 61.118 61.111 0.00 0.00 0.00 3.49
340 359 2.432628 GGTCCAGTTCTGTCGCCG 60.433 66.667 0.00 0.00 0.00 6.46
427 446 0.033366 GGCGGTGCTTGGTTTGAATT 59.967 50.000 0.00 0.00 0.00 2.17
431 450 2.351738 CGGTGCTTGGTTTGAATTCTCC 60.352 50.000 7.05 7.37 0.00 3.71
493 989 5.537300 ACACATCTTCAGTTGTACAGAGT 57.463 39.130 0.00 0.00 0.00 3.24
494 990 5.533482 ACACATCTTCAGTTGTACAGAGTC 58.467 41.667 0.00 0.00 0.00 3.36
495 991 5.303078 ACACATCTTCAGTTGTACAGAGTCT 59.697 40.000 0.00 0.00 0.00 3.24
496 992 5.861251 CACATCTTCAGTTGTACAGAGTCTC 59.139 44.000 0.00 0.00 0.00 3.36
546 1042 0.802494 CTGTACATTCACGGTTGCCC 59.198 55.000 0.00 0.00 0.00 5.36
570 1067 2.125673 CAACCAGCGTACTCCCCG 60.126 66.667 0.00 0.00 0.00 5.73
577 1074 4.077184 CGTACTCCCCGGCTTGCA 62.077 66.667 0.00 0.00 0.00 4.08
637 1134 2.097036 CAGTGTGTATGGACCCGTCTA 58.903 52.381 0.00 0.00 0.00 2.59
658 1207 9.011407 CGTCTATTTCTTTTGTACAGCTAGTAG 57.989 37.037 0.00 0.00 32.19 2.57
659 1208 9.857957 GTCTATTTCTTTTGTACAGCTAGTAGT 57.142 33.333 0.00 0.00 32.19 2.73
704 1254 4.217754 TCGGTGTTTGACTTTTGTATGC 57.782 40.909 0.00 0.00 0.00 3.14
706 1256 3.974401 CGGTGTTTGACTTTTGTATGCAG 59.026 43.478 0.00 0.00 0.00 4.41
749 1299 1.406069 GGGCACAATCTCATCACTCGT 60.406 52.381 0.00 0.00 0.00 4.18
799 1352 5.869888 GCAATGTGTACTACTCCTATATGGC 59.130 44.000 0.00 0.00 35.26 4.40
802 1355 4.523173 TGTGTACTACTCCTATATGGCAGC 59.477 45.833 0.00 0.00 35.26 5.25
852 1405 4.575885 TCATCGGGAAGAAAAAGGTACTG 58.424 43.478 0.00 0.00 40.86 2.74
853 1406 3.412237 TCGGGAAGAAAAAGGTACTGG 57.588 47.619 0.00 0.00 40.86 4.00
858 1411 5.379187 GGGAAGAAAAAGGTACTGGTACAA 58.621 41.667 12.14 0.00 40.86 2.41
865 1420 4.986054 AAGGTACTGGTACAAATGGTCA 57.014 40.909 12.14 0.00 40.86 4.02
871 1426 6.433093 GGTACTGGTACAAATGGTCAAAAGAT 59.567 38.462 12.14 0.00 38.70 2.40
889 1444 1.626654 ATGAACGCGGCTGAAACGAG 61.627 55.000 12.47 0.00 37.17 4.18
900 1455 4.105486 GGCTGAAACGAGGAAATAAATGC 58.895 43.478 0.00 0.00 0.00 3.56
961 1544 4.899239 GGCTCCCACGCGAGATGG 62.899 72.222 15.93 10.75 36.94 3.51
1008 1591 3.334054 AGGAGAGGCCAGCCCAAC 61.334 66.667 5.01 0.00 40.02 3.77
1015 1598 2.058001 GGCCAGCCCAACCCAATAC 61.058 63.158 0.00 0.00 0.00 1.89
1043 1635 4.238514 GACTCAACGGATAGATACATGCC 58.761 47.826 0.00 0.00 0.00 4.40
1104 1744 1.933853 GATTCGACCGTTGGAATGGAG 59.066 52.381 4.58 0.00 38.48 3.86
1108 1748 0.672401 GACCGTTGGAATGGAGCGAA 60.672 55.000 4.58 0.00 38.48 4.70
1109 1749 0.673644 ACCGTTGGAATGGAGCGAAG 60.674 55.000 4.58 0.00 38.48 3.79
1162 1802 3.297830 AAAACTAAATCCGCAGCAACC 57.702 42.857 0.00 0.00 0.00 3.77
1164 1804 1.062525 CTAAATCCGCAGCAACCGC 59.937 57.895 0.00 0.00 38.99 5.68
1165 1805 1.643868 CTAAATCCGCAGCAACCGCA 61.644 55.000 0.00 0.00 42.27 5.69
1166 1806 1.917782 TAAATCCGCAGCAACCGCAC 61.918 55.000 0.00 0.00 42.27 5.34
1781 2451 3.744719 CGCCCAAGAGGTCGTCGA 61.745 66.667 0.00 0.00 38.26 4.20
1974 2644 4.388499 GGTCGCTCGGAAGCCCAA 62.388 66.667 0.00 0.00 46.34 4.12
2201 2871 2.058675 GTGCTCTACACCACCACCT 58.941 57.895 0.00 0.00 44.02 4.00
2203 2873 0.396435 TGCTCTACACCACCACCTTG 59.604 55.000 0.00 0.00 0.00 3.61
2230 2900 2.087009 CCGCAAGACGTTCGAGGAC 61.087 63.158 0.00 0.00 41.42 3.85
2508 3178 2.040544 GGTTCGTCATGTGCAGGGG 61.041 63.158 0.00 0.00 0.00 4.79
2590 3260 1.373748 GTGCAACGAGAACGGCCTA 60.374 57.895 0.00 0.00 44.46 3.93
2620 3290 0.463204 CCATCTGCTCGTGATGAGGT 59.537 55.000 3.55 0.00 45.38 3.85
2621 3291 1.134580 CCATCTGCTCGTGATGAGGTT 60.135 52.381 3.55 0.00 45.38 3.50
2623 3293 0.247460 TCTGCTCGTGATGAGGTTGG 59.753 55.000 3.55 0.00 45.38 3.77
2625 3295 0.904649 TGCTCGTGATGAGGTTGGAT 59.095 50.000 3.55 0.00 45.38 3.41
2626 3296 1.278985 TGCTCGTGATGAGGTTGGATT 59.721 47.619 3.55 0.00 45.38 3.01
2627 3297 1.667724 GCTCGTGATGAGGTTGGATTG 59.332 52.381 3.55 0.00 45.38 2.67
2628 3298 2.936993 GCTCGTGATGAGGTTGGATTGT 60.937 50.000 3.55 0.00 45.38 2.71
2673 3352 1.246649 TTGCTTGTCTACCCGTCGTA 58.753 50.000 0.00 0.00 0.00 3.43
2683 3362 0.320946 ACCCGTCGTATGGTGTTTGG 60.321 55.000 0.00 0.00 32.36 3.28
2835 3531 1.544314 GCTTTCAGAAGGGTCACTGCT 60.544 52.381 0.00 0.00 34.41 4.24
2840 3536 5.755409 TTCAGAAGGGTCACTGCTTATTA 57.245 39.130 0.00 0.00 30.27 0.98
2850 3546 5.391523 GGTCACTGCTTATTACATTTTCGCA 60.392 40.000 0.00 0.00 0.00 5.10
2907 4107 6.266323 GTCTTAGATCTGATCACTAAACGCA 58.734 40.000 19.12 0.00 0.00 5.24
2944 4144 2.298661 CCAGAGGTAGGGCCCGTTT 61.299 63.158 18.44 0.39 38.26 3.60
2966 4166 3.192103 AACACTCCGGCTCCCAACC 62.192 63.158 0.00 0.00 0.00 3.77
2988 4188 1.599047 CGGAGCTGAAGTGGTGGAT 59.401 57.895 0.00 0.00 0.00 3.41
2990 4190 1.207089 CGGAGCTGAAGTGGTGGATAA 59.793 52.381 0.00 0.00 0.00 1.75
3000 4200 1.065854 GTGGTGGATAAGAGCAGCACT 60.066 52.381 0.00 0.00 41.23 4.40
3032 4232 2.878743 CGGAGCAGCTATTCTGTCG 58.121 57.895 0.00 0.00 44.66 4.35
3071 4273 1.809209 GCCGAGCAGAGTCAGAAGC 60.809 63.158 0.00 0.00 0.00 3.86
3072 4274 1.588597 CCGAGCAGAGTCAGAAGCA 59.411 57.895 0.00 0.00 0.00 3.91
3091 4293 0.250901 AATCCGTTGCTGAACAGGCT 60.251 50.000 3.99 0.00 31.78 4.58
3092 4294 0.957395 ATCCGTTGCTGAACAGGCTG 60.957 55.000 14.16 14.16 31.78 4.85
3104 4306 5.453339 GCTGAACAGGCTGGTAGTATTATGA 60.453 44.000 20.34 0.00 0.00 2.15
3111 4313 5.366768 AGGCTGGTAGTATTATGAAGCTTCA 59.633 40.000 30.23 30.23 42.14 3.02
3133 4335 6.476378 TCAATAAACTCAAGGAAGGAAGGAG 58.524 40.000 0.00 0.00 0.00 3.69
3204 4406 6.393990 ACATTAAAATTGTGCGCTAATCCAA 58.606 32.000 9.73 4.25 0.00 3.53
3251 4454 2.496470 GGTCGAGTCTGGACTTATGGTT 59.504 50.000 13.88 0.00 42.66 3.67
3252 4455 3.512680 GTCGAGTCTGGACTTATGGTTG 58.487 50.000 7.69 0.00 42.66 3.77
3272 4476 3.778618 TGTCTCTGAGCATTGATCTTCG 58.221 45.455 3.27 0.00 0.00 3.79
3280 4484 5.363101 TGAGCATTGATCTTCGCTTAATCT 58.637 37.500 3.27 0.00 34.12 2.40
3282 4486 4.754114 AGCATTGATCTTCGCTTAATCTCC 59.246 41.667 0.00 0.00 0.00 3.71
3286 4490 5.713792 TGATCTTCGCTTAATCTCCCTAG 57.286 43.478 0.00 0.00 0.00 3.02
3313 4517 5.335583 CCGTGACAAAATCCTTGATTTGCTA 60.336 40.000 3.03 0.00 40.77 3.49
3322 4526 8.463930 AAATCCTTGATTTGCTATTAATCCGA 57.536 30.769 1.47 0.00 40.24 4.55
3331 4535 6.428083 TTGCTATTAATCCGACCTATTGGA 57.572 37.500 0.00 0.00 43.08 3.53
3354 4558 2.066262 CTGCGTCTTTCGTATGTGGTT 58.934 47.619 0.00 0.00 42.13 3.67
3366 4570 4.328712 TCGTATGTGGTTGATTCAACATCG 59.671 41.667 26.27 19.39 45.11 3.84
3370 4574 4.133820 TGTGGTTGATTCAACATCGAAGT 58.866 39.130 26.27 0.00 45.11 3.01
3373 4577 4.213270 TGGTTGATTCAACATCGAAGTGAC 59.787 41.667 26.27 9.25 45.11 3.67
3379 4583 2.798283 TCAACATCGAAGTGACGAAACC 59.202 45.455 0.00 0.00 45.16 3.27
3381 4585 1.069513 ACATCGAAGTGACGAAACCCA 59.930 47.619 0.00 0.00 45.16 4.51
3403 4607 2.750141 TGCGACCTCTACTTATCCCT 57.250 50.000 0.00 0.00 0.00 4.20
3440 4644 0.837272 TTGCCCTAAGCCTAATCGCT 59.163 50.000 0.00 0.00 42.71 4.93
3441 4645 1.712056 TGCCCTAAGCCTAATCGCTA 58.288 50.000 0.00 0.00 42.71 4.26
3479 4683 0.179004 AAGGGCAATGACGGTGAACA 60.179 50.000 0.00 0.00 0.00 3.18
3558 4763 0.671796 TGAACTCGAGCGACAAAGGA 59.328 50.000 13.61 0.00 0.00 3.36
3582 4787 0.599558 ACGACTTGGCAACGCTACTA 59.400 50.000 9.79 0.00 42.51 1.82
3583 4788 1.000060 ACGACTTGGCAACGCTACTAA 60.000 47.619 9.79 0.00 42.51 2.24
3591 4796 5.270893 TGGCAACGCTACTAATAGAATCA 57.729 39.130 0.00 0.00 42.51 2.57
3642 4847 1.069906 CGTCGCCAAGGTTGAAAAGAG 60.070 52.381 0.00 0.00 0.00 2.85
3699 4911 1.274712 GCCCTAGATGCAGCCTAGAT 58.725 55.000 21.09 0.00 36.58 1.98
3733 4945 7.103641 AGTTTTGGCTATCGAAGTATCTTTGA 58.896 34.615 0.00 2.50 0.00 2.69
3876 5095 4.616181 ATTTATTGCTTGTCGTGCCTAC 57.384 40.909 0.00 0.00 0.00 3.18
3884 5103 0.386476 TGTCGTGCCTACAGTTTCGT 59.614 50.000 0.00 0.00 0.00 3.85
3896 5115 3.670625 ACAGTTTCGTTTATGCCTAGCA 58.329 40.909 0.00 0.00 44.86 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 251 1.659954 CGAGTCAGAGCCGCATAGC 60.660 63.158 0.00 0.00 0.00 2.97
233 252 1.007964 CCGAGTCAGAGCCGCATAG 60.008 63.158 0.00 0.00 0.00 2.23
235 254 2.755876 TCCGAGTCAGAGCCGCAT 60.756 61.111 0.00 0.00 0.00 4.73
324 343 3.112709 GCGGCGACAGAACTGGAC 61.113 66.667 12.98 0.07 34.19 4.02
352 371 2.997897 ACGTCTCCCAGACCCAGC 60.998 66.667 0.00 0.00 42.12 4.85
427 446 1.471829 TTCCTCAAGCACGCAGGAGA 61.472 55.000 10.44 0.00 37.62 3.71
431 450 1.572085 CCTGTTCCTCAAGCACGCAG 61.572 60.000 0.00 0.00 0.00 5.18
493 989 0.106708 ACCAAAGCACGCAAGAGAGA 59.893 50.000 0.00 0.00 43.62 3.10
494 990 1.728971 CTACCAAAGCACGCAAGAGAG 59.271 52.381 0.00 0.00 43.62 3.20
495 991 1.608025 CCTACCAAAGCACGCAAGAGA 60.608 52.381 0.00 0.00 43.62 3.10
496 992 0.798776 CCTACCAAAGCACGCAAGAG 59.201 55.000 0.00 0.00 43.62 2.85
577 1074 1.765230 TGGTTTTGTTTAGCACGGGT 58.235 45.000 0.00 0.00 0.00 5.28
658 1207 7.745022 TTTGCACAATGATACTACGTACTAC 57.255 36.000 0.00 0.00 0.00 2.73
659 1208 7.377662 CGATTTGCACAATGATACTACGTACTA 59.622 37.037 0.00 0.00 0.00 1.82
660 1209 6.198403 CGATTTGCACAATGATACTACGTACT 59.802 38.462 0.00 0.00 0.00 2.73
661 1210 6.344800 CGATTTGCACAATGATACTACGTAC 58.655 40.000 0.00 0.00 0.00 3.67
662 1211 5.460748 CCGATTTGCACAATGATACTACGTA 59.539 40.000 0.00 0.00 0.00 3.57
663 1212 4.270084 CCGATTTGCACAATGATACTACGT 59.730 41.667 0.00 0.00 0.00 3.57
664 1213 4.270084 ACCGATTTGCACAATGATACTACG 59.730 41.667 0.00 0.00 0.00 3.51
706 1256 5.450550 CCCCAAAGAAAGAGTGAAGTGAAAC 60.451 44.000 0.00 0.00 0.00 2.78
799 1352 8.723942 ATAATTTTACTTCTGGAGTACTGCTG 57.276 34.615 15.92 14.91 40.51 4.41
833 1386 2.707257 ACCAGTACCTTTTTCTTCCCGA 59.293 45.455 0.00 0.00 0.00 5.14
852 1405 5.856455 CGTTCATCTTTTGACCATTTGTACC 59.144 40.000 0.00 0.00 32.84 3.34
853 1406 5.342259 GCGTTCATCTTTTGACCATTTGTAC 59.658 40.000 0.00 0.00 32.84 2.90
858 1411 2.095263 CCGCGTTCATCTTTTGACCATT 60.095 45.455 4.92 0.00 32.84 3.16
865 1420 1.234821 TTCAGCCGCGTTCATCTTTT 58.765 45.000 4.92 0.00 0.00 2.27
871 1426 2.279584 TCGTTTCAGCCGCGTTCA 60.280 55.556 4.92 0.00 0.00 3.18
961 1544 2.236146 GGGTTGGGTTCCCATTTCATTC 59.764 50.000 11.65 0.00 44.05 2.67
1008 1591 0.739462 TTGAGTCGCGCAGTATTGGG 60.739 55.000 8.75 0.00 40.04 4.12
1015 1598 1.202973 CTATCCGTTGAGTCGCGCAG 61.203 60.000 8.75 0.00 0.00 5.18
1153 1793 4.962122 GTGTGTGCGGTTGCTGCG 62.962 66.667 0.00 0.00 43.34 5.18
1162 1802 2.053116 GTCAAGTGCGTGTGTGCG 60.053 61.111 0.00 0.00 37.81 5.34
1164 1804 1.272715 GTCGTCAAGTGCGTGTGTG 59.727 57.895 0.00 0.00 0.00 3.82
1165 1805 1.881252 GGTCGTCAAGTGCGTGTGT 60.881 57.895 0.00 0.00 0.00 3.72
1166 1806 2.927618 CGGTCGTCAAGTGCGTGTG 61.928 63.158 0.00 0.00 0.00 3.82
1167 1807 2.657296 CGGTCGTCAAGTGCGTGT 60.657 61.111 0.00 0.00 0.00 4.49
1420 2090 2.558286 GGAGACGACGTGGTCCACA 61.558 63.158 24.70 0.00 37.66 4.17
1423 2093 2.675772 AGGGAGACGACGTGGTCC 60.676 66.667 24.70 16.44 37.66 4.46
1781 2451 2.049433 CGTGTTCCTCCGCTTCGT 60.049 61.111 0.00 0.00 0.00 3.85
2059 2729 2.896443 CCTTCCTCCGACAGCTCC 59.104 66.667 0.00 0.00 0.00 4.70
2092 2762 0.250513 GCTTCTCGGACCCAATCACT 59.749 55.000 0.00 0.00 0.00 3.41
2250 2920 3.822192 CGTCGTGGGCCTCGATCA 61.822 66.667 30.40 8.81 39.45 2.92
2620 3290 6.037786 TGTAACACCAAACAAACAATCCAA 57.962 33.333 0.00 0.00 0.00 3.53
2621 3291 5.661056 TGTAACACCAAACAAACAATCCA 57.339 34.783 0.00 0.00 0.00 3.41
2623 3293 6.018343 CCCAATGTAACACCAAACAAACAATC 60.018 38.462 0.00 0.00 0.00 2.67
2625 3295 5.178797 CCCAATGTAACACCAAACAAACAA 58.821 37.500 0.00 0.00 0.00 2.83
2626 3296 4.223032 ACCCAATGTAACACCAAACAAACA 59.777 37.500 0.00 0.00 0.00 2.83
2627 3297 4.760878 ACCCAATGTAACACCAAACAAAC 58.239 39.130 0.00 0.00 0.00 2.93
2628 3298 5.046591 TCAACCCAATGTAACACCAAACAAA 60.047 36.000 0.00 0.00 0.00 2.83
2673 3352 0.038744 CTCTGAGGCCCAAACACCAT 59.961 55.000 0.00 0.00 0.00 3.55
2918 4118 1.912043 GCCCTACCTCTGGATGCATAT 59.088 52.381 0.00 0.00 0.00 1.78
2944 4144 3.319198 GGAGCCGGAGTGTTCCCA 61.319 66.667 5.05 0.00 40.67 4.37
2988 4188 7.362662 CAAAAATTAACTGAGTGCTGCTCTTA 58.637 34.615 5.62 0.80 44.41 2.10
2990 4190 5.766222 CAAAAATTAACTGAGTGCTGCTCT 58.234 37.500 3.55 3.55 44.41 4.09
3000 4200 3.611530 GCTGCTCCGCAAAAATTAACTGA 60.612 43.478 0.00 0.00 38.41 3.41
3006 4206 3.445096 AGAATAGCTGCTCCGCAAAAATT 59.555 39.130 4.91 0.00 38.41 1.82
3023 4223 3.450817 TGGAAATGAGGAGCGACAGAATA 59.549 43.478 0.00 0.00 0.00 1.75
3032 4232 0.449388 CAACGCTGGAAATGAGGAGC 59.551 55.000 0.00 0.00 0.00 4.70
3055 4255 1.925847 GATTGCTTCTGACTCTGCTCG 59.074 52.381 0.00 0.00 0.00 5.03
3058 4258 1.005340 CGGATTGCTTCTGACTCTGC 58.995 55.000 0.00 0.00 31.81 4.26
3060 4260 2.693069 CAACGGATTGCTTCTGACTCT 58.307 47.619 3.46 0.00 34.56 3.24
3071 4273 0.109597 GCCTGTTCAGCAACGGATTG 60.110 55.000 0.00 0.00 40.95 2.67
3072 4274 0.250901 AGCCTGTTCAGCAACGGATT 60.251 50.000 0.00 0.00 40.95 3.01
3082 4284 6.553953 TTCATAATACTACCAGCCTGTTCA 57.446 37.500 0.00 0.00 0.00 3.18
3104 4306 6.306987 TCCTTCCTTGAGTTTATTGAAGCTT 58.693 36.000 0.00 0.00 0.00 3.74
3111 4313 6.241645 CACTCCTTCCTTCCTTGAGTTTATT 58.758 40.000 0.00 0.00 34.21 1.40
3119 4321 2.158608 ACAACCACTCCTTCCTTCCTTG 60.159 50.000 0.00 0.00 0.00 3.61
3120 4322 2.136026 ACAACCACTCCTTCCTTCCTT 58.864 47.619 0.00 0.00 0.00 3.36
3133 4335 7.648142 TCTTCTCATTAAACATCAACAACCAC 58.352 34.615 0.00 0.00 0.00 4.16
3174 4376 6.111768 AGCGCACAATTTTAATGTCTCTAG 57.888 37.500 11.47 0.00 0.00 2.43
3191 4393 1.095807 GGAGGGTTGGATTAGCGCAC 61.096 60.000 11.47 0.00 0.00 5.34
3204 4406 5.399052 AAAATGATGATGATCTGGAGGGT 57.601 39.130 0.00 0.00 0.00 4.34
3251 4454 3.778618 CGAAGATCAATGCTCAGAGACA 58.221 45.455 0.00 0.00 0.00 3.41
3252 4455 2.539274 GCGAAGATCAATGCTCAGAGAC 59.461 50.000 0.00 0.00 0.00 3.36
3272 4476 2.036089 CACGGGACTAGGGAGATTAAGC 59.964 54.545 0.00 0.00 0.00 3.09
3280 4484 1.719529 TTTTGTCACGGGACTAGGGA 58.280 50.000 20.37 0.00 44.61 4.20
3282 4486 2.236395 AGGATTTTGTCACGGGACTAGG 59.764 50.000 20.37 0.00 44.61 3.02
3286 4490 2.500229 TCAAGGATTTTGTCACGGGAC 58.500 47.619 11.93 11.93 44.57 4.46
3313 4517 4.041691 CAGGGTCCAATAGGTCGGATTAAT 59.958 45.833 0.00 0.00 32.83 1.40
3322 4526 1.905512 GACGCAGGGTCCAATAGGT 59.094 57.895 6.33 0.00 39.90 3.08
3331 4535 0.606604 ACATACGAAAGACGCAGGGT 59.393 50.000 0.00 0.00 46.94 4.34
3354 4558 3.908213 TCGTCACTTCGATGTTGAATCA 58.092 40.909 0.39 0.00 34.85 2.57
3366 4570 2.661594 GCATTTGGGTTTCGTCACTTC 58.338 47.619 0.00 0.00 0.00 3.01
3370 4574 0.589223 GTCGCATTTGGGTTTCGTCA 59.411 50.000 0.00 0.00 0.00 4.35
3373 4577 0.168128 GAGGTCGCATTTGGGTTTCG 59.832 55.000 0.00 0.00 0.00 3.46
3379 4583 4.058817 GGATAAGTAGAGGTCGCATTTGG 58.941 47.826 0.00 0.00 0.00 3.28
3381 4585 3.967987 AGGGATAAGTAGAGGTCGCATTT 59.032 43.478 0.00 0.00 0.00 2.32
3403 4607 1.699634 CAAGAGTGGAAGAAGGGGACA 59.300 52.381 0.00 0.00 0.00 4.02
3455 4659 2.046285 CCGTCATTGCCCTTCACCC 61.046 63.158 0.00 0.00 0.00 4.61
3456 4660 1.303317 ACCGTCATTGCCCTTCACC 60.303 57.895 0.00 0.00 0.00 4.02
3531 4736 1.499502 GCTCGAGTTCAAGCTTGGC 59.500 57.895 25.73 18.14 35.60 4.52
3582 4787 3.318275 TCGCCTAGAACGCTGATTCTATT 59.682 43.478 0.00 0.00 39.79 1.73
3583 4788 2.885266 TCGCCTAGAACGCTGATTCTAT 59.115 45.455 0.00 0.00 39.79 1.98
3591 4796 1.446272 GTTGCTCGCCTAGAACGCT 60.446 57.895 0.00 0.00 0.00 5.07
3673 4878 1.152546 TGCATCTAGGGCGCTAGGA 60.153 57.895 30.86 20.33 0.00 2.94
3699 4911 9.826574 ACTTCGATAGCCAAAACTATATTTACA 57.173 29.630 0.00 0.00 32.95 2.41
3789 5001 4.946772 TGGGCGAGATTTCAATGACAATAA 59.053 37.500 0.00 0.00 0.00 1.40
3795 5007 3.130869 CCAAATGGGCGAGATTTCAATGA 59.869 43.478 0.00 0.00 0.00 2.57
3858 5077 2.028476 ACTGTAGGCACGACAAGCAATA 60.028 45.455 0.00 0.00 44.60 1.90


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

AutoCloner maintained by Alex Coulton.