Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005699.1 Hibiscus syriacus cultivar Beakdansim tig00013329_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63463
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:6499 original size:44 final size:46
Alignment explanation
Indices: 6428--6530 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 46
6418 ATTTATTTTC
* *
6428 GTTTTTTTTTCGAATAAATGCATGCGAACTAGGTATCATGCGGTTAG
1 GTTTATTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAG
*
6475 GTTTATTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAG
1 GTTTATTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAG
*
6519 GATTTCTTTTTG
1 G-TTTATTTTTG
6531 TGGATAACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 27 0.53
45 11 0.22
46 4 0.08
47 9 0.18
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (46 bp):
GTTTATTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAG
Found at i:16239 original size:8 final size:8
Alignment explanation
Indices: 16227--16300 Score: 55
Period size: 7 Copynumber: 9.1 Consensus size: 8
16217 AAAAACGAAA
16227 AAAAAAATG
1 AAAAAAA-G
16236 AAAAAAAG
1 AAAAAAAG
16244 -AAAAAA-
1 AAAAAAAG
* *
16250 AAGAAGAG
1 AAAAAAAG
16258 AAAAAAATGG
1 AAAAAAA--G
16268 AAAAAAA-
1 AAAAAAAG
*
16275 ATAAAAAG
1 AAAAAAAG
*
16283 AGAAAAATG
1 A-AAAAAAG
16292 AAAAAAAG
1 AAAAAAAG
16300 A
1 A
16301 GAAATAAAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
7 16 0.31
8 14 0.27
9 13 0.25
10 8 0.16
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:16239 original size:41 final size:39
Alignment explanation
Indices: 16194--16293 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 39
16184 AGAAAAGAAG
* *
16194 GAAAAAGAAAAAATGATGATGGAAAAAACGAAAAAAAAAAT
1 GAAAAAGAAAAAATGAAGA-GAAAAAAACG-AAAAAAAAAT
* * *
16235 GAAAAAAAGAAAAAAAAGAAGAGAAAAAAATGGAAAAAAAAT
1 G--AAAAAG-AAAAAATGAAGAGAAAAAAACGAAAAAAAAAT
16277 -AAAAAGAGAAAAATGAA
1 GAAAAAGA-AAAAATGAA
16294 AAAAAGAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
38 1 0.02
39 14 0.29
41 1 0.02
42 9 0.18
43 14 0.29
44 10 0.20
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.07
Consensus pattern (39 bp):
GAAAAAGAAAAAATGAAGAGAAAAAAACGAAAAAAAAAT
Found at i:16272 original size:25 final size:24
Alignment explanation
Indices: 16224--16304 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 24
16214 GGAAAAAACG
*
16224 AAAAAAA-AAATGAAAAAAA-G-A
1 AAAAAAAGAAAAGAAAAAAATGAA
*
16245 AAAAAAAGAAGAGAAAAAAATGGAA
1 AAAAAAAGAAAAGAAAAAAAT-GAA
*
16270 AAAAAATA-AAAAGAGAAAAATGAA
1 AAAAAA-AGAAAAGAAAAAAATGAA
*
16294 AAAAAGAGAAA
1 AAAAAAAGAAA
16305 TAAAAGGAGG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.14
22 10 0.20
23 1 0.02
24 12 0.24
25 18 0.37
26 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (24 bp):
AAAAAAAGAAAAGAAAAAAATGAA
Found at i:17682 original size:51 final size:51
Alignment explanation
Indices: 17620--18140 Score: 589
Period size: 51 Copynumber: 10.0 Consensus size: 51
17610 GAAGCAAATT
* *
17620 AGTTCGTTGAAGATTGAGTCCTATAATCTCTGAAGGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
17671 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
17722 AGTTCG-TGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
17772 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* * *
17823 AGTTTGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
17874 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
** ** * * * * *
17925 AGTTTATTGAAGAACGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACC
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* * * * * * *
17976 CGTT-TTATGAAGATTGTTCGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACC
1 AGTTCGT-TGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* * * * * *
18031 CGTT-TTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 AGTTCGT-TGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* * * * * *
18086 CGTTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGGATAGGGAGCGGAC
1 AG-TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
18141 CCGTTTTATG
Statistics
Matches: 432, Mismatches: 30, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
50 51 0.12
51 246 0.57
55 89 0.21
56 45 0.10
57 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (51 bp):
AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
Found at i:18266 original size:55 final size:55
Alignment explanation
Indices: 17787--18227 Score: 502
Period size: 55 Copynumber: 8.2 Consensus size: 55
17777 GTTGAAGATT
* * * * **
17787 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTTGT-TGAAGA---TT-
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTT-TATGAAGATTGTTC
* * * ** *
17838 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACAAGTTCGT-TGAAGA---TT-
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTT-TTATGAAGATTGTTC
* * * * ** *
17889 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTTATTGAAGA----AC
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTA-TGAAGATTGTTC
17940 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
17995 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* * *
18050 GAGTTCTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTT-ATGAAGATTGTTC
18106 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
*
18161 GAGTTCTATACTCCCTGAACGGATAGGTAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
18216 GAG-TCTTATACT
1 GAGTTC-TATACT
18228 TCTTGAAGGA
Statistics
Matches: 356, Mismatches: 21, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
49 1 0.00
50 1 0.00
51 127 0.36
52 4 0.01
54 4 0.01
55 168 0.47
56 49 0.14
57 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (55 bp):
GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
Found at i:22437 original size:15 final size:15
Alignment explanation
Indices: 22417--22469 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
22407 TTGGGTAAAC
22417 CCATAAATCCAAATT
1 CCATAAATCCAAATT
* *
22432 CCATAAAAT-TATAATC
1 CCAT-AAATCCA-AATT
22448 CCATAAATCCAAATT
1 CCATAAATCCAAATT
22463 CCATAAA
1 CCATAAA
22470 ATTATAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (15 bp):
CCATAAATCCAAATT
Found at i:22451 original size:16 final size:16
Alignment explanation
Indices: 22432--22488 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
22422 AATCCAAATT
22432 CCATAAAATTATAATC
1 CCATAAAATTATAATC
* *
22448 CCAT-AAATCCA-AATT
1 CCATAAAAT-TATAATC
*
22463 CCATAAAATTATAAAC
1 CCATAAAATTATAATC
22479 CCATAAAATT
1 CCATAAAATT
22489 CAGTCCAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (16 bp):
CCATAAAATTATAATC
Found at i:22452 original size:31 final size:31
Alignment explanation
Indices: 22412--22485 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
22402 AAACATTGGG
22412 TAAACCCATAAATCCAAATTCCATAAAATTA
1 TAAACCCATAAATCCAAATTCCATAAAATTA
*
22443 TAATCCCATAAATCCAAATTCCATAAAATTA
1 TAAACCCATAAATCCAAATTCCATAAAATTA
22474 TAAACCCATAAA
1 TAAACCCATAAA
22486 ATTCAGTCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (31 bp):
TAAACCCATAAATCCAAATTCCATAAAATTA
Found at i:36888 original size:21 final size:22
Alignment explanation
Indices: 36839--36898 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
36829 ATTTAAAGTT
* *
36839 ATAAAATTTTAATTATTTGTTA
1 ATAATATTTTAATTATTTATTA
*
36861 ATAATATTTTTATT-TTTATTA
1 ATAATATTTTAATTATTTATTA
* **
36882 TTAATATAATAATTATT
1 ATAATATTTTAATTATT
36899 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATAATATTTTAATTATTTATTA
Found at i:37712 original size:16 final size:18
Alignment explanation
Indices: 37668--37714 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
37658 TATTTATGAG
37668 GGAATTGGAATCTGTTAA
1 GGAATTGGAATCTGTTAA
*
37686 GGAATTAGAATCTG-TAA
1 GGAATTGGAATCTGTTAA
37703 -GAATTGGAATCT
1 GGAATTGGAATCT
37715 AATTACATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 13 0.48
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (18 bp):
GGAATTGGAATCTGTTAA
Found at i:38375 original size:37 final size:38
Alignment explanation
Indices: 38291--38379 Score: 155
Period size: 38 Copynumber: 2.4 Consensus size: 38
38281 TCTACACCCG
38291 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
38329 AACCCGACCCGA-CTCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGACCT-GACCCGAATATCACACTTAAAAA
38366 AACCCGACCCGACC
1 AACCCGACCCGACC
38380 CGAACAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
37 18 0.37
38 31 0.63
ACGTcount: A:0.37, C:0.40, G:0.11, T:0.11
Consensus pattern (38 bp):
AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
Found at i:38615 original size:32 final size:33
Alignment explanation
Indices: 38551--38627 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 33
38541 CTAAACCCAA
38551 ACCCGACCCGAATATCACACTTAAAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
38584 ATCCGACCCGAATATCACACTT-AAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
38616 ACCCGACCCGAA
1 ACCCGACCCGAA
38628 CAAAATAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 21 0.50
33 21 0.50
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.12
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:38744 original size:239 final size:240
Alignment explanation
Indices: 38306--38836 Score: 798
Period size: 239 Copynumber: 2.2 Consensus size: 240
38296 GACCCGACCT
*
38306 GACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCC
1 GACCCGAATATCACACTTAAAAAAACCCGA----TC-CGACCCGAATATCACACTTAAAAAACCC
* *
38371 GACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCTATGAATTAGAAATCCGACCCGAC
61 GACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGAACATATGAATTAGAAATCCGA--C-AC
* **
38436 TCGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGGTCC
123 TCGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGACCC
* * *
38501 GAATTATATATATTTTTGGGTCGGTACGGTTTTTTTCATCCTAAACCCAAACCC
188 GAATTATATATATTTTCGGGTCGGT-CGGTTTTTTTAACCCTAAACCCAAACCC
38555 GACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGAATATCACACTTAAAAAACCCGACCC
1 GACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGAATATCACACTTAAAAAACCCGACCC
*
38620 GACCCGAACAAAATAAAGTTTCATCCGACCCGAATATATGAATTAGAAATCCGA-AC-CGACCCA
66 GACCCGAACAAAATAAAGTTTCATCCGACCCGAACATATGAATTAGAAATCCGACACTCGACCCA
38683 AAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGACCCGAATTATA
131 AAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGACCCGAATTATA
* *
38748 TATATTTTCGGGTCGGTCTGTTTTTTTAACCCTAAACCTAAACCC
196 TATATTTTCGGGTCGGTCGGTTTTTTTAACCCTAAACCCAAACCC
*
38793 GACCCGACCCAAATATCACACTT-AAAAAATCCGATCCGACCCGA
1 GACCCG-----AATATCACACTTAAAAAAACCCGATCCGACCCGA
38837 CCAAAATAAA
Statistics
Matches: 264, Mismatches: 13, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
238 30 0.11
239 85 0.32
240 2 0.01
242 20 0.08
243 12 0.05
244 84 0.32
245 1 0.00
249 30 0.11
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.23
Consensus pattern (240 bp):
GACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGAATATCACACTTAAAAAACCCGACCC
GACCCGAACAAAATAAAGTTTCATCCGACCCGAACATATGAATTAGAAATCCGACACTCGACCCA
AAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGACCCGAATTATA
TATATTTTCGGGTCGGTCGGTTTTTTTAACCCTAAACCCAAACCC
Found at i:38790 original size:244 final size:240
Alignment explanation
Indices: 38297--38836 Score: 782
Period size: 244 Copynumber: 2.2 Consensus size: 240
38287 CCCGAACCCG
* * *
38297 ACCCGACCTGACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTT
1 ACCCAACCCGACCCGAATATCACACTTAAAAAAACCCGA----TC-CGACCCGAATATCACACTT
* *
38362 AAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCTATGAATTAGAAATC
61 AAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGAACATATGAATTAGAAATC
*
38427 CGACCCGACTCGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCTG
126 CGA--C-ACTCGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTG
** * *
38492 ACCCGGTCCGAATTATATATATTTTTGGGTCGGTACGGTTTTTTTCATCCTAA
188 ACCCGACCCGAATTATATATATTTTCGGGTCGGTACGGTTTTTTTCAACCTAA
38545 ACCCAAACCCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGAATATCACACTTAAAA
1 ACCC-AACCCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGAATATCACACTTAAAA
*
38610 AACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGAATATATGAATTAGAAATCCGA-
65 AACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGAACATATGAATTAGAAATCCGAC
38674 AC-CGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGAC
130 ACTCGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGAC
*
38738 CCGAATTATATATATTTTCGGGTCGGT-CTGTTTTTTTAACCCTAAACCTAA
195 CCGAATTATATATATTTTCGGGTCGGTACGGTTTTTTT----C--AACCTAA
* * *
38789 ACCCGACCCGACCCAAATATCACACTT-AAAAAATCCGATCCGACCCGA
1 ACCCAACCCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGA
38837 CCAAAATAAA
Statistics
Matches: 270, Mismatches: 15, Indels: 20
0.89 0.05 0.07
Matches are distributed among these distances:
238 9 0.03
239 85 0.31
240 2 0.01
242 21 0.08
243 21 0.08
244 94 0.35
245 1 0.00
248 4 0.01
249 33 0.12
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (240 bp):
ACCCAACCCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGAATATCACACTTAAAAA
ACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGAACATATGAATTAGAAATCCGACA
CTCGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGACC
CGAATTATATATATTTTCGGGTCGGTACGGTTTTTTTCAACCTAA
Found at i:43003 original size:22 final size:21
Alignment explanation
Indices: 42955--43016 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
42945 CCATAACCCC
* * *
42955 AAGGGGGTATCGATTCCCCTA
1 AAGGGGGAATCGGTTCCCTTA
*
42976 AGGGGGGAATCGGTTCCCTTCA
1 AAGGGGGAATCGGTTCCCTT-A
42998 AAGGGGGAATCGGTTCCCT
1 AAGGGGGAATCGGTTCCCT
43017 CATGAGATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23
Consensus pattern (21 bp):
AAGGGGGAATCGGTTCCCTTA
Found at i:50259 original size:30 final size:30
Alignment explanation
Indices: 50181--50262 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
50171 TTTGTAATAA
* *
50181 AATTAGAATTGCGAGATCAAATAAACTTTT
1 AATTAAAATTGAGAGATCAAATAAACTTTT
* *
50211 AATTAAAACT-ACAGGATCAAATAAACTTTT
1 AATTAAAATTGAGA-GATCAAATAAACTTTT
* *
50241 AATTACAATTGTGAGATCAAAT
1 AATTAAAATTGAGAGATCAAAT
50263 GAATTATTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 1 0.02
30 40 0.95
31 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (30 bp):
AATTAAAATTGAGAGATCAAATAAACTTTT
Found at i:52427 original size:9 final size:10
Alignment explanation
Indices: 52401--52448 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
52391 CTTATTTCTG
52401 ATTTTATAAT
1 ATTTTATAAT
52411 ACTTTTATAAT
1 A-TTTTATAAT
*
52422 -TTTTATATT
1 ATTTTATAAT
*
52431 ATTTTATTAT
1 ATTTTATAAT
*
52441 AATTTATA
1 ATTTTATA
52449 TTTGTTTCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 8 0.26
10 14 0.45
11 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:53236 original size:21 final size:21
Alignment explanation
Indices: 53210--53252 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
53200 TATTCTTCAT
53210 AACATAAGAGAGAGATAGAGA
1 AACATAAGAGAGAGATAGAGA
53231 AACATAAGAGAGAGATAGAGA
1 AACATAAGAGAGAGATAGAGA
53252 A
1 A
53253 CAAGGGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.05, G:0.28, T:0.09
Consensus pattern (21 bp):
AACATAAGAGAGAGATAGAGA
Found at i:57775 original size:74 final size:74
Alignment explanation
Indices: 57654--57801 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
57644 CTTAGGAGCT
57654 CATGAGTAAATGCAAATCTTTTCCCTAAACATTTTTAAGAATGAAACCGTTTGCTGTTGCAGAGG
1 CATGAGTAAATGCAAATCTTTTCCCTAAACATTTTTAAGAATGAAACCGTTTGCTGTTGCAGAGG
57719 TCTGGAAGA
66 TCTGGAAGA
57728 CATGAGTAAATGCAAATCTTTTCCCTAAACATTTTTAAGAATGAAACCGTTTGCTGTTGCAGAGG
1 CATGAGTAAATGCAAATCTTTTCCCTAAACATTTTTAAGAATGAAACCGTTTGCTGTTGCAGAGG
57793 TCTGGAAGA
66 TCTGGAAGA
57802 GTTGATGAAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (74 bp):
CATGAGTAAATGCAAATCTTTTCCCTAAACATTTTTAAGAATGAAACCGTTTGCTGTTGCAGAGG
TCTGGAAGA
Found at i:63238 original size:14 final size:14
Alignment explanation
Indices: 63217--63256 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
63207 GGTTTTTGGT
63217 TAAGTGTTATGTAA
1 TAAGTGTTATGTAA
* *
63231 TCAGTGTTATGTAT
1 TAAGTGTTATGTAA
63245 TAAGTGTTATGT
1 TAAGTGTTATGT
63257 TGTAAGCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (14 bp):
TAAGTGTTATGTAA
Done.