Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003990.1 Hibiscus syriacus cultivar Beakdansim tig00008682_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: 76814
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:2568 original size:16 final size:16
Alignment explanation
Indices: 2547--2588 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2537 AAAATGCATG
2547 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
* *
2563 AAAAAAGAAGAAAAAT
1 AAAAAATAAAAAAAAT
2579 -AAAAATAAAA
1 AAAAAATAAAA
2589 TGGTTAGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:5733 original size:4 final size:4
Alignment explanation
Indices: 5724--5884 Score: 299
Period size: 4 Copynumber: 40.8 Consensus size: 4
5714 AGCCTATTGT
5724 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
5772 CATA CATA CATA CATA CATA TATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5820 CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5866 CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CAT
5885 TTACATAGGT
Statistics
Matches: 153, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
2 2 0.01
4 151 0.99
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:5990 original size:25 final size:25
Alignment explanation
Indices: 5962--6011 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5952 TTTAACACCA
5962 TATCACTACATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
*
5987 TATCACTATATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
6012 ACCCCTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (25 bp):
TATCACTACATGTTTATGCTTCAGT
Found at i:8150 original size:3 final size:3
Alignment explanation
Indices: 8138--8193 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
8128 TTATTATTAT
* * * *
8138 TAA TAA -AA TAA TAA TTA TTA TAA TAA TAA TAA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
8185 AAA TAA TAA
1 TAA TAA TAA
8194 AAAAGAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:8156 original size:18 final size:18
Alignment explanation
Indices: 8133--8184 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
8123 TATTATTATT
8133 ATTATTAATAA-AATAATA
1 ATTATT-ATAATAATAATA
8151 ATTATTATAATAATAATA
1 ATTATTATAATAATAATA
8169 ATTATTATAATAATAA
1 ATTATTATAATAATAA
8185 AAATAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.12
18 29 0.88
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATTATAATAATAATA
Found at i:10672 original size:27 final size:21
Alignment explanation
Indices: 10614--10665 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
10604 AGACTCAGGT
10614 TGCTTCTCAGGCAGGAACAGC
1 TGCTTCTCAGGCAGGAACAGC
10635 TGCTTCTCAGGCAGGAACAGC
1 TGCTTCTCAGGCAGGAACAGC
10656 TGCTTCTCAG
1 TGCTTCTCAG
10666 TCCCAGGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.23
Consensus pattern (21 bp):
TGCTTCTCAGGCAGGAACAGC
Found at i:24488 original size:2 final size:2
Alignment explanation
Indices: 24483--24508 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24473 AACTCTTCAT
24483 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
24509 CAAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26813 original size:21 final size:20
Alignment explanation
Indices: 26772--26816 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
26762 AAATAAAAAT
*
26772 TATTTTTTTTACAAAGTTAA
1 TATTTTTTTTACAAAGATAA
26792 TATTTGTTATTTA-AAAGATAA
1 TATTT-TT-TTTACAAAGATAA
26813 TATT
1 TATT
26817 AATTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (20 bp):
TATTTTTTTTACAAAGATAA
Found at i:31939 original size:23 final size:23
Alignment explanation
Indices: 31905--31954 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
31895 ATTTATTCTA
31905 TATACCAAAAGATATGTAGATTT
1 TATACCAAAAGATATGTAGATTT
*
31928 TATACCAGAAGATATGTAGATTT
1 TATACCAAAAGATATGTAGATTT
31951 TATA
1 TATA
31955 TTCCTGGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (23 bp):
TATACCAAAAGATATGTAGATTT
Found at i:33038 original size:3 final size:3
Alignment explanation
Indices: 33030--33066 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
33020 GAAATACAAA
* *
33030 TGC TGC TGC GGC TGC TGC TAC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
33067 AAACTGAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.32, G:0.32, T:0.32
Consensus pattern (3 bp):
TGC
Found at i:34752 original size:124 final size:124
Alignment explanation
Indices: 34550--34797 Score: 487
Period size: 124 Copynumber: 2.0 Consensus size: 124
34540 AAGTTTCAAC
34550 ATTATATTTCGAGTTCGAGTTGAACTTGATAATTTTTAGCTCGTGAGTTTGAGTCGAGTTGAGCT
1 ATTATATTTCGAGTTCGAGTTGAACTTGATAATTTTTAGCTCGTGAGTTTGAGTCGAGTTGAGCT
34615 TACTTTTAAAGTTTTCAAGTTCGAGTCGAGATCAGTAATACTCGAGTTCGCTTGGCTCG
66 TACTTTTAAAGTTTTCAAGTTCGAGTCGAGATCAGTAATACTCGAGTTCGCTTGGCTCG
34674 ATTATATTTCGAGTTCGAGTTGAACTTGATAATTTTTAGCTCGTGAGTTTGAGTCGAGTTGAGCT
1 ATTATATTTCGAGTTCGAGTTGAACTTGATAATTTTTAGCTCGTGAGTTTGAGTCGAGTTGAGCT
*
34739 TACTTTTAAAGTTTTCAAGTTCGAGTTGAGATCAGTAATACTCGAGTTCGCTTGGCTCG
66 TACTTTTAAAGTTTTCAAGTTCGAGTCGAGATCAGTAATACTCGAGTTCGCTTGGCTCG
34798 TTTAACAAAC
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.39
Consensus pattern (124 bp):
ATTATATTTCGAGTTCGAGTTGAACTTGATAATTTTTAGCTCGTGAGTTTGAGTCGAGTTGAGCT
TACTTTTAAAGTTTTCAAGTTCGAGTCGAGATCAGTAATACTCGAGTTCGCTTGGCTCG
Found at i:43369 original size:22 final size:21
Alignment explanation
Indices: 43340--43388 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
43330 TTTAATTAAA
43340 TAATTTAA-TTATTTTATAATT
1 TAATTTAACTT-TTTTATAATT
*
43361 TAATATTAACTTTTTTATTATTT
1 TAAT-TTAACTTTTTTA-TAATT
43384 TAATT
1 TAATT
43389 CATCCTTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 10 0.42
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TAATTTAACTTTTTTATAATT
Found at i:45769 original size:18 final size:18
Alignment explanation
Indices: 45745--45784 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45735 TTGTAGCCCT
45745 TATTATAT-A-ATGCATA
1 TATTATATAATATGCATA
*
45761 TATTATATAATATGTATA
1 TATTATATAATATGCATA
45779 TATTAT
1 TATTAT
45785 TTACATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (18 bp):
TATTATATAATATGCATA
Found at i:46891 original size:4 final size:4
Alignment explanation
Indices: 46884--46978 Score: 60
Period size: 4 Copynumber: 24.5 Consensus size: 4
46874 TCTCTTTCTT
* * *
46884 TTTA TTTA TCT- TTTA -TTA TTTT TTTA TTT- TTTA TTTCC TTTA --TA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA
* *
46928 TTTA TTTTA TTTC TTTA TTTC TTTA TTCT- TGTT- TTTA TTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA TTTA TTTA TTTA TTTA
46977 TT
1 TT
46979 ATATATATAT
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
2 2 0.03
3 10 0.14
4 50 0.70
5 9 0.13
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:46924 original size:28 final size:27
Alignment explanation
Indices: 46884--46975 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 27
46874 TCTCTTTCTT
*
46884 TTTATTTATCT-TTTATTATTTTTTTA
1 TTTATTTATTTCTTTATTATTTTTTTA
46910 TTT-TTTATTTCCTTTA-TATTTATTTTA
1 TTTATTTATTT-CTTTATTATTT-TTTTA
* *
46937 TTTCTTTATTTCTTTATTCTTGTTTTTA
1 TTTATTTATTTCTTTATTATT-TTTTTA
46965 TTTATTTATTT
1 TTTATTTATTT
46976 ATTATATATA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
25 6 0.11
26 8 0.14
27 17 0.30
28 25 0.44
29 1 0.02
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (27 bp):
TTTATTTATTTCTTTATTATTTTTTTA
Found at i:46985 original size:2 final size:2
Alignment explanation
Indices: 46978--47020 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
46968 ATTTATTTAT
46978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47020 T
1 T
47021 TTTCTTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50961 original size:2 final size:2
Alignment explanation
Indices: 50954--50979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50944 AATTAATTAT
50954 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
50980 ACACTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55416 original size:31 final size:31
Alignment explanation
Indices: 55381--55468 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 31
55371 TTTAGTTACA
* *
55381 TGACACATGA-CACATTATCATTTTAATGGCG
1 TGACACAT-ACCACATCATCATTTTAATGACG
* *
55412 TGACACATACCACATCATTATTTTGAATGATG
1 TGACACATACCACATCATCATTTT-AATGACG
* *
55444 TGACATATATCACATCATCATTTTA
1 TGACACATACCACATCATCATTTTA
55469 GATAATATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.02
31 21 0.44
32 26 0.54
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (31 bp):
TGACACATACCACATCATCATTTTAATGACG
Found at i:55510 original size:13 final size:13
Alignment explanation
Indices: 55492--55530 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
55482 ATGTCATGTC
55492 ATCACTTTAAATG
1 ATCACTTTAAATG
55505 ATCACTTTATTAAATG
1 ATCAC--T-TTAAATG
55521 ATCACTTTAA
1 ATCACTTTAA
55531 GATTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 9 0.39
14 1 0.04
15 1 0.04
16 12 0.52
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (13 bp):
ATCACTTTAAATG
Found at i:55519 original size:16 final size:16
Alignment explanation
Indices: 55498--55529 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55488 TGTCATCACT
55498 TTAAATGATCACTTTA
1 TTAAATGATCACTTTA
55514 TTAAATGATCACTTTA
1 TTAAATGATCACTTTA
55530 AGATTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
TTAAATGATCACTTTA
Found at i:55934 original size:14 final size:14
Alignment explanation
Indices: 55907--55944 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
55897 TTTACATTTG
*
55907 TTTATATTCGTTCA
1 TTTATATTCATTCA
*
55921 TTTATGTTCATTCA
1 TTTATATTCATTCA
55935 TTTATATTCA
1 TTTATATTCA
55945 GCCCAATCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (14 bp):
TTTATATTCATTCA
Found at i:56029 original size:17 final size:17
Alignment explanation
Indices: 56009--56043 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
55999 ACTCAATAAT
56009 ATTTTAAAACCCAAATA
1 ATTTTAAAACCCAAATA
56026 ATTTTAAAACCCAAATA
1 ATTTTAAAACCCAAATA
56043 A
1 A
56044 AAAAATACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTTTAAAACCCAAATA
Found at i:56385 original size:4 final size:4
Alignment explanation
Indices: 56376--56407 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
56366 CAATATATTG
56376 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
56408 GTAACACCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:57731 original size:96 final size:96
Alignment explanation
Indices: 57558--57754 Score: 247
Period size: 96 Copynumber: 2.1 Consensus size: 96
57548 TTCAAGTAAT
* * * *
57558 AACCAGTATATTTCATGATCCATAAATCAAGAACAATCATATTTTTTCGTGAAGACAAGAAACCA
1 AACCAGTAGATTCCATGATCCATAAATCAAGAACAATCATATTTTTACGTGAAAACAAGAAACCA
* * *
57623 AATAACACATTTCTAGTAATC-ATGGTTCATA
66 AAGAACACATTTCAAGTAA-CAATAGTTCATA
* *
57654 AACCAGTAGATTCCATGATCCATAAATTAAGAACGATCATA-TTTTACAGTGAAAAC-AGATAAC
1 AACCAGTAGATTCCATGATCCATAAATCAAGAACAATCATATTTTTAC-GTGAAAACAAGA-AAC
* *
57717 CAGAGAACATATTTCAAGTAACAATAGTTCATA
64 CAAAGAACACATTTCAAGTAACAATAGTTCATA
57750 AACCA
1 AACCA
57755 ATAAATCAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
95 9 0.10
96 78 0.90
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (96 bp):
AACCAGTAGATTCCATGATCCATAAATCAAGAACAATCATATTTTTACGTGAAAACAAGAAACCA
AAGAACACATTTCAAGTAACAATAGTTCATA
Found at i:59760 original size:64 final size:63
Alignment explanation
Indices: 59646--59783 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 63
59636 TTCCCTTGAA
* *
59646 GTGCATCGATGCACTACTCATGCATCGATACACAATTCACCTTTGGTGTTT-TCA-TTTTAAGGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAATTCA-CTTCGATGTTTCT-ATTTTTAA-GG
59709 G
63 G
* * * *
59710 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCA-TTCGATGTTTCTATTTTTAATGG
1 GTGCATCGATGCACTACTCATGCATCGATACAC-AATT-CACTTCGATGTTTCTATTTTTAAGGG
59774 GTGCATCGAT
1 GTGCATCGAT
59784 ACACATTGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
64 51 0.80
65 11 0.17
66 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (63 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAATTCACTTCGATGTTTCTATTTTTAAGGG
Found at i:60452 original size:20 final size:20
Alignment explanation
Indices: 60397--60443 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
60387 AGAATACAAA
60397 ATTTTACTTATCAATTGACC
1 ATTTTACTTATCAATTGACC
60417 ATTTTACTTATCAATTGACC
1 ATTTTACTTATCAATTGACC
60437 ATTTTAC
1 ATTTTAC
60444 CCTTTAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (20 bp):
ATTTTACTTATCAATTGACC
Found at i:63069 original size:27 final size:28
Alignment explanation
Indices: 63018--63083 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
63008 TTAATCAGTT
* * *
63018 AATTATATATATATATATCAGTT-AACGA
1 AATTA-ATATATATATATAAATTAAACAA
*
63046 AATTAATATATTTATATAAATTAAACAA
1 AATTAATATATATATATAAATTAAACAA
63074 AACTTAATAT
1 AA-TTAATAT
63084 TTAGATGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 14 0.44
28 11 0.34
29 7 0.22
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (28 bp):
AATTAATATATATATATAAATTAAACAA
Found at i:63266 original size:2 final size:2
Alignment explanation
Indices: 63261--63290 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
63251 AAATTCTAAT
63261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63291 ATTATTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64018 original size:46 final size:43
Alignment explanation
Indices: 63937--64021 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
63927 TTAGTAGAGT
*
63937 GTTATTTAAAATATTATTTTTATCAAAAATATTAATATCGGAC
1 GTTATTTAAAATATTATTTTTACCAAAAATATTAATATCGGAC
* *
63980 GTTATTTAAAATAATATTTTTTTACCAAAAAATGTTAATATC
1 GTTATTTAAAAT-AT-TATTTTTACC-AAAAATATTAATATC
64022 AAAAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 12 0.33
44 2 0.06
45 8 0.22
46 14 0.39
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (43 bp):
GTTATTTAAAATATTATTTTTACCAAAAATATTAATATCGGAC
Found at i:64082 original size:21 final size:21
Alignment explanation
Indices: 64022--64082 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
64012 TGTTAATATC
* *
64022 AAAAATATTATTTTAAGTAGC
1 AAAAATAATATTTTAAGTAGA
* * **
64043 GAAATTAATATTTCCAGTAGA
1 AAAAATAATATTTTAAGTAGA
*
64064 AAAAATAACATTTTAAGTA
1 AAAAATAATATTTTAAGTA
64083 TCGCTCTACC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (21 bp):
AAAAATAATATTTTAAGTAGA
Found at i:64512 original size:14 final size:14
Alignment explanation
Indices: 64495--64526 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
64485 CTTAAAAAAC
*
64495 AAAATTTAATTTTT
1 AAAATCTAATTTTT
64509 AAAATCTAATTTTT
1 AAAATCTAATTTTT
64523 AAAA
1 AAAA
64527 GATTTCGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAATCTAATTTTT
Found at i:65644 original size:17 final size:18
Alignment explanation
Indices: 65622--65668 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
65612 TTATATGCAA
65622 CATAATACAAA-ATATTT
1 CATAATACAAATATATTT
65639 CATAATATCAACATATATTT
1 CATAATA-CAA-ATATATTT
*
65659 TAT-ATACAAA
1 CATAATACAAA
65669 CAACATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.31
18 6 0.23
19 4 0.15
20 8 0.31
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (18 bp):
CATAATACAAATATATTT
Found at i:67429 original size:5 final size:5
Alignment explanation
Indices: 67416--67467 Score: 50
Period size: 6 Copynumber: 9.4 Consensus size: 5
67406 TCTGCCACAG
*
67416 AAATA AAATT AAATAA AAATAA AAATAA AAATAA AAATA AAATAA AAATA
1 AAATA AAATA AAAT-A AAAT-A AAAT-A AAAT-A AAATA AAAT-A AAATA
67466 AA
1 AA
67468 TGATGATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 16 0.37
6 27 0.63
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:67445 original size:11 final size:11
Alignment explanation
Indices: 67416--67467 Score: 70
Period size: 11 Copynumber: 4.6 Consensus size: 11
67406 TCTGCCACAG
*
67416 AAATAAAAT-T
1 AAATAAAATAA
67426 AAATAAAAATAA
1 AAAT-AAAATAA
67438 AAATAAAAATAA
1 AAAT-AAAATAA
67450 AAATAAAATAA
1 AAATAAAATAA
67461 AAATAAA
1 AAATAAA
67468 TGATGATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
10 4 0.10
11 19 0.49
12 16 0.41
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:67451 original size:17 final size:17
Alignment explanation
Indices: 67416--67467 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
67406 TCTGCCACAG
*
67416 AAATAAAAT-TAAATAA
1 AAATAAAATAAAAATAA
67432 AAATAAAAATAAAAATAA
1 AAAT-AAAATAAAAATAA
67450 AAATAAAATAAAAATAA
1 AAATAAAATAAAAATAA
67467 A
1 A
67468 TGATGATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 4 0.12
17 19 0.58
18 10 0.30
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATAAAATAAAAATAA
Found at i:67487 original size:6 final size:6
Alignment explanation
Indices: 67426--67467 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
67416 AAATAAAATT
67426 AAATAA AAATAA AAATAA AAATAA AAAT-A AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
67468 TGATGATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Done.