Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015108.1 Kokia drynarioides strain JFW-HI SEQ_130152, 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: 43874
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:4321 original size:58 final size:59
Alignment explanation
Indices: 4247--4399 Score: 143
Period size: 59 Copynumber: 2.6 Consensus size: 59
4237 TTAATATAAT
* * * *
4247 ATTTGGTATCTGAACTTGACA-CTTTTACTTAATTTGATAAT-TAAATCTTTTTT-ACTCA
1 ATTTGATACCTGAACTTGACATCTTTTACCTAATTTGAT-ATCTAAA-CTTTTTTGACCCA
* * *
4305 ATTTGATACCTGAACTTGATATTTTTTTCCTAATTTGATATCTAAACTTTTTTGACCCA
1 ATTTGATACCTGAACTTGACATCTTTTACCTAATTTGATATCTAAACTTTTTTGACCCA
* * * * *
4364 ATTTGGTACTTAAACTTTG-CATTTTTTCCCTAATTT
1 ATTTGATACCTGAAC-TTGACATCTTTTACCTAATTT
4400 AGCACCTAAG
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
58 27 0.34
59 49 0.62
60 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (59 bp):
ATTTGATACCTGAACTTGACATCTTTTACCTAATTTGATATCTAAACTTTTTTGACCCA
Found at i:4367 original size:59 final size:59
Alignment explanation
Indices: 4276--4399 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 59
4266 CACTTTTACT
* * * *
4276 TAATTTGATAATTAAATCTTTTTTACTCAATTTGATACCTGAAC-TTGATATTTTTTTCC
1 TAATTTGATAATTAAATCTTTTTTACCCAATTTGATACCTAAACTTTG-CATTTTTTCCC
* *
4335 TAATTTGAT-ATCTAAA-CTTTTTTGACCCAATTTGGTACTTAAACTTTGCATTTTTTCCC
1 TAATTTGATAAT-TAAATCTTTTTT-ACCCAATTTGATACCTAAACTTTGCATTTTTTCCC
4394 TAATTT
1 TAATTT
4400 AGCACCTAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
58 9 0.16
59 44 0.79
60 3 0.05
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.50
Consensus pattern (59 bp):
TAATTTGATAATTAAATCTTTTTTACCCAATTTGATACCTAAACTTTGCATTTTTTCCC
Found at i:5388 original size:27 final size:29
Alignment explanation
Indices: 5358--5414 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
5348 AAAATTATTA
5358 TTTTAGAAATTTTT-GAATTTT-TAATTT
1 TTTTAGAAATTTTTAGAATTTTATAATTT
* *
5385 TTTTATATATTTTTAGAATTTTATAATTT
1 TTTTAGAAATTTTTAGAATTTTATAATTT
5414 T
1 T
5415 AAAAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 12 0.46
28 7 0.27
29 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (29 bp):
TTTTAGAAATTTTTAGAATTTTATAATTT
Found at i:5422 original size:28 final size:27
Alignment explanation
Indices: 5366--5422 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
5356 TATTTTAGAA
** *
5366 ATTTTTGAATTTTTAATTTTTTTATAT
1 ATTTTTGAATTTTTAATTTTTAAAAAT
5393 ATTTTTAGAATTTTATAA-TTTTAAAAAT
1 ATTTTT-GAATTTT-TAATTTTTAAAAAT
5421 AT
1 AT
5423 AAAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 6 0.24
28 16 0.64
29 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (27 bp):
ATTTTTGAATTTTTAATTTTTAAAAAT
Found at i:6999 original size:87 final size:87
Alignment explanation
Indices: 6830--6999 Score: 252
Period size: 87 Copynumber: 2.0 Consensus size: 87
6820 AAAAAAAACG
** * *
6830 ACAACAATGTGGATAGGGCTGCTGAGAACGACACTGATGTCACTGCAACAGCTGTCCCTAACACC
1 ACAACAACCTGGATAGGGCTGCTGAGAACAACACTGATGTCACCGCAACAGCTGTCCCTAACACC
* *
6895 AACGACCACCACCACCACAACA
66 AACGACCAACACAACCACAACA
*
6917 ACAACAACCTGGATAGGGCTGCTGTGAACAACACTGATGTCACCGCAACAGCTGTCCCTAACACC
1 ACAACAACCTGGATAGGGCTGCTGAGAACAACACTGATGTCACCGCAACAGCTGTCCCTAACACC
*
6982 AACG-GCAACAGCAACCAC
66 AACGACCAACA-CAACCAC
7000 CCTGTTGAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 4 0.05
87 70 0.95
ACGTcount: A:0.34, C:0.34, G:0.19, T:0.14
Consensus pattern (87 bp):
ACAACAACCTGGATAGGGCTGCTGAGAACAACACTGATGTCACCGCAACAGCTGTCCCTAACACC
AACGACCAACACAACCACAACA
Found at i:9700 original size:6 final size:6
Alignment explanation
Indices: 9689--9717 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9679 TTGAAGGGTC
9689 AATTGT AATTGT AATTGT AATTGT AATTG
1 AATTGT AATTGT AATTGT AATTGT AATTG
9718 AGTAGGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
AATTGT
Found at i:10985 original size:21 final size:20
Alignment explanation
Indices: 10960--10998 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
10950 CAAAAACCAG
10960 TTATTAAATAGAAGTAATAAA
1 TTATTAAATAGAA-TAATAAA
*
10981 TTATTAAATATAATAATA
1 TTATTAAATAGAATAATA
10999 TTTTTGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTATTAAATAGAATAATAAA
Found at i:12119 original size:40 final size:40
Alignment explanation
Indices: 12060--12161 Score: 168
Period size: 40 Copynumber: 2.5 Consensus size: 40
12050 CTGCAACATT
*
12060 TATATAAATAGTCTAAAATTTGGTACCAACATAATAAAAC
1 TATATAAATAGTCTGAAATTTGGTACCAACATAATAAAAC
*
12100 TATGTAAATAGTCTGAAATTTGGTACCAACATAATAAAAC
1 TATATAAATAGTCTGAAATTTGGTACCAACATAATAAAAC
*
12140 TATATAAAATAGTTTGAAATTT
1 TATAT-AAATAGTCTGAAATTT
12162 TTATTTTTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 42 0.74
41 15 0.26
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (40 bp):
TATATAAATAGTCTGAAATTTGGTACCAACATAATAAAAC
Found at i:12829 original size:15 final size:15
Alignment explanation
Indices: 12806--12840 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12796 CTAAGGTTCA
12806 ACCACTCAAAACACT
1 ACCACTCAAAACACT
* *
12821 ACCAGTCAAAACATT
1 ACCACTCAAAACACT
12836 ACCAC
1 ACCAC
12841 CAACAATGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.46, C:0.37, G:0.03, T:0.14
Consensus pattern (15 bp):
ACCACTCAAAACACT
Found at i:17234 original size:21 final size:21
Alignment explanation
Indices: 17196--17235 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17186 CGTATTTTAT
***
17196 ATAAAAATTATTTTAAAAAGA
1 ATAAAAATTATGAAAAAAAGA
17217 ATAAAAATTATGAAAAAAA
1 ATAAAAATTATGAAAAAAA
17236 ATCTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
ATAAAAATTATGAAAAAAAGA
Found at i:19597 original size:3 final size:3
Alignment explanation
Indices: 19591--19661 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
19581 CCACCACCTC
* * *
19591 CAA CAA CAA CAA CAA CCA CAA CAA CAA CAA CAA CAA CCA CAA CAG CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* *
19639 CAA CAA CAA AAA CAA CAG CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CA
19662 TGGATAGGGC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.62, C:0.35, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:24899 original size:23 final size:22
Alignment explanation
Indices: 24872--24918 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
24862 CGTTTTGATT
*
24872 TTTTTTAAAAATTCTTAACAAAAA
1 TTTTTAAAAAATT-TTAA-AAAAA
24896 TTTTTAAAAAATTTTAAAAAAA
1 TTTTTAAAAAATTTTAAAAAAA
24918 T
1 T
24919 CTTAAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 4 0.18
24 12 0.55
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTTAAAAAATTTTAAAAAAA
Found at i:24907 original size:11 final size:11
Alignment explanation
Indices: 24878--24923 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
24868 GATTTTTTTT
24878 AAAAATTCTTAA
1 AAAAATT-TTAA
*
24890 CAAAAATTTTTA
1 -AAAAATTTTAA
24902 AAAAATTTTAA
1 AAAAATTTTAA
*
24913 AAAAATCTTAA
1 AAAAATTTTAA
24924 GATAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 20 0.67
12 3 0.10
13 7 0.23
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:25959 original size:20 final size:20
Alignment explanation
Indices: 25922--25959 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25912 TTTATATTGT
*
25922 TGTTTTGGTGCATTTTTTAC
1 TGTTTTGGTGCATGTTTTAC
25942 TGTTTTGGTTG-ATGTTTT
1 TGTTTTGG-TGCATGTTTT
25960 TAAGTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.08, C:0.05, G:0.24, T:0.63
Consensus pattern (20 bp):
TGTTTTGGTGCATGTTTTAC
Found at i:25992 original size:12 final size:11
Alignment explanation
Indices: 25977--26101 Score: 51
Period size: 12 Copynumber: 10.9 Consensus size: 11
25967 TTTTTTATTG
25977 TTTTGATTGTTA
1 TTTTG-TTGTTA
*
25989 TTTTCG-TGTAA
1 TTTT-GTTGTTA
*
26000 TTTTTGCTGTTA
1 -TTTTGTTGTTA
*
26012 TTTTTGTTGTTG
1 -TTTTGTTGTTA
*
26024 TTTTATTGTTA
1 TTTTGTTGTTA
26035 -TTT-TTGTTA
1 TTTTGTTGTTA
*
26044 TTTT-TAATGTTG
1 TTTTGT--TGTTA
**
26056 TTTTACTGTTA
1 TTTTGTTGTTA
* *
26067 TTTTTGTTGCTG
1 -TTTTGTTGTTA
*
26079 TTTTGGTTTTTA
1 TTTT-GTTGTTA
26091 TTTTTGTTGTT
1 -TTTTGTTGTT
26102 TGGATGTTAT
Statistics
Matches: 86, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
9 6 0.07
10 7 0.08
11 22 0.26
12 46 0.53
13 5 0.06
ACGTcount: A:0.10, C:0.03, G:0.17, T:0.70
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:26003 original size:23 final size:25
Alignment explanation
Indices: 25977--26038 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 25
25967 TTTTTTATTG
25977 TTTTGATTGTTATTTTCG-TGTAAT
1 TTTTGATTGTTATTTTCGTTGTAAT
* *
26001 TTTTG-CTGTTATTTTTGTTGT--T
1 TTTTGATTGTTATTTTCGTTGTAAT
26023 GTTTT-ATTGTTATTTT
1 -TTTTGATTGTTATTTT
26039 TGTTATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 1 0.03
23 23 0.72
24 8 0.25
ACGTcount: A:0.11, C:0.03, G:0.16, T:0.69
Consensus pattern (25 bp):
TTTTGATTGTTATTTTCGTTGTAAT
Found at i:26031 original size:55 final size:55
Alignment explanation
Indices: 25963--26082 Score: 140
Period size: 55 Copynumber: 2.2 Consensus size: 55
25953 ATGTTTTTAA
** *
25963 GTTGTT-TTTTATTGTT-TTGATTGTTA-TTTTCGTGTAAT-TTTTGCTGTTATTTTT
1 GTTGTTGTTTTATTGTTATT-ATTGTTATTTTTAATGT--TGTTTTACTGTTATTTTT
*
26017 GTTGTTGTTTTATTGTTATTTTTGTTATTTTTAATGTTGTTTTACTGTTATTTTT
1 GTTGTTGTTTTATTGTTATTATTGTTATTTTTAATGTTGTTTTACTGTTATTTTT
*
26072 GTTGCTGTTTT
1 GTTGTTGTTTT
26083 GGTTTTTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
54 7 0.12
55 41 0.72
56 9 0.16
ACGTcount: A:0.11, C:0.03, G:0.17, T:0.69
Consensus pattern (55 bp):
GTTGTTGTTTTATTGTTATTATTGTTATTTTTAATGTTGTTTTACTGTTATTTTT
Found at i:26043 original size:32 final size:32
Alignment explanation
Indices: 26007--26074 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
25997 TAATTTTTGC
** *
26007 TGTTATTTTTGTTGTTGTTTTATTGTTATTTT
1 TGTTATTTTTAATGTTGTTTTACTGTTATTTT
26039 TGTTATTTTTAATGTTGTTTTACTGTTATTTT
1 TGTTATTTTTAATGTTGTTTTACTGTTATTTT
26071 TGTT
1 TGTT
26075 GCTGTTTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.01, G:0.15, T:0.72
Consensus pattern (32 bp):
TGTTATTTTTAATGTTGTTTTACTGTTATTTT
Found at i:26080 original size:23 final size:23
Alignment explanation
Indices: 26039--26082 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
26029 TTGTTATTTT
*
26039 TGTTATTTTTAATGTTGTTTTAC
1 TGTTATTTTTAATGCTGTTTTAC
**
26062 TGTTATTTTTGTTGCTGTTTT
1 TGTTATTTTTAATGCTGTTTT
26083 GGTTTTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (23 bp):
TGTTATTTTTAATGCTGTTTTAC
Found at i:26109 original size:55 final size:55
Alignment explanation
Indices: 26001--26114 Score: 140
Period size: 55 Copynumber: 2.1 Consensus size: 55
25991 TTCGTGTAAT
* * * * *
26001 TTTTGCTGTTATTTTTGTTGTTGTTTTATTGTTATTTTTGTTATTTTTAATGTTG
1 TTTTACTGTTATTTTTGTTGCTGTTTTATTGTTATTTTTGTTAGTTTGAATGTTA
* * *
26056 TTTTACTGTTATTTTTGTTGCTGTTTTGGTTTTTATTTTTGTT-GTTTGGATGTTA
1 TTTTACTGTTATTTTTGTTGCTGTTTT-ATTGTTATTTTTGTTAGTTTGAATGTTA
26111 TTTT
1 TTTT
26115 TTATGTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
55 37 0.74
56 13 0.26
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.70
Consensus pattern (55 bp):
TTTTACTGTTATTTTTGTTGCTGTTTTATTGTTATTTTTGTTAGTTTGAATGTTA
Found at i:26318 original size:49 final size:47
Alignment explanation
Indices: 26225--26319 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 47
26215 TATCTTAATA
* * *
26225 TAATTTTTTAATGTATTTTAAATTTATTTATTTTTTAATGTTTGTTT
1 TAATTTTTTAATGTATTTGAAATTTATATATTTTTTAATATTTGTTT
*
26272 TAATGTTTTTAAGTGTATTTGATATATTATATATTTTTTAA-ATTTGTT
1 TAAT-TTTTTAA-TGTATTTGAAAT-TTATATATTTTTTAATATTTGTT
26320 GTATGTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 4 0.10
48 7 0.17
49 16 0.39
50 14 0.34
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.64
Consensus pattern (47 bp):
TAATTTTTTAATGTATTTGAAATTTATATATTTTTTAATATTTGTTT
Found at i:26641 original size:10 final size:10
Alignment explanation
Indices: 26595--26641 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
26585 ATTTTAATGA
26595 TTTAAATTTT
1 TTTAAATTTT
*
26605 TTTTAA-TTT
1 TTTAAATTTT
26614 TTTAGAATTATT
1 TTTA-AATT-TT
*
26626 ATTAAATTTT
1 TTTAAATTTT
26636 TTTAAA
1 TTTAAA
26642 AAAAATCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 6 0.20
10 14 0.47
11 5 0.17
12 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTAAATTTT
Found at i:35778 original size:5 final size:6
Alignment explanation
Indices: 35750--35778 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35740 TGTAATTATC
35750 TTAAAT TTAAAT TTAAAT TTAAA- TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
35779 AATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:35918 original size:21 final size:21
Alignment explanation
Indices: 35880--35937 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
35870 AAAATCTAAT
* *
35880 GATAACAA-ATTTAAATATTAA
1 GATAATAATATTTATAT-TTAA
*
35901 GATAAATAATATTTATATTTAT
1 GAT-AATAATATTTATATTTAA
*
35923 GATAATATTATTTAT
1 GATAATAATATTTAT
35938 TTTTGGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 14 0.45
22 10 0.32
23 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (21 bp):
GATAATAATATTTATATTTAA
Found at i:37513 original size:9 final size:9
Alignment explanation
Indices: 37484--37547 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
37474 AGAATTTTTT
37484 TTATAAAAA
1 TTATAAAAA
*
37493 TCGTAGAAAAA
1 T--TATAAAAA
37504 TTATAAAAA
1 TTATAAAAA
*
37513 TT-TCAAAATT
1 TTAT-AAAA-A
37523 TTATAAAAA
1 TTATAAAAA
*
37532 TCAT-AAAA
1 TTATAAAAA
37540 TTATAAAA
1 TTATAAAA
37548 TACATAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
8 8 0.19
9 20 0.47
10 6 0.14
11 9 0.21
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:37522 original size:17 final size:17
Alignment explanation
Indices: 37500--37556 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
37490 AAATCGTAGA
37500 AAAATTATAAAAATTTCA-
1 AAAATTATAAAAA--TCAT
*
37518 AAATTTTATAAAAATCAT
1 AAA-ATTATAAAAATCAT
37536 AAAATTAT-AAAATACAT
1 AAAATTATAAAAAT-CAT
37553 AAAA
1 AAAA
37557 ACATTTTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 5 0.15
17 14 0.41
18 6 0.18
19 9 0.26
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAAATCAT
Found at i:37539 original size:19 final size:19
Alignment explanation
Indices: 37482--37541 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
37472 ATAGAATTTT
*
37482 TTTTATAAAAATCGTAGAAA
1 TTTTATAAAAATCATA-AAA
** *
37502 AATTATAAAAAT-TTCAAAA
1 TTTTATAAAAATCAT-AAAA
37521 TTTTATAAAAATCATAAAA
1 TTTTATAAAAATCATAAAA
37540 TT
1 TT
37542 ATAAAATACA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTTATAAAAATCATAAAA
Found at i:37635 original size:36 final size:37
Alignment explanation
Indices: 37582--37658 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
37572 ACTTTAATCA
*
37582 TTAACTGTTCAAATTAAACGATCTCT-AGTTTTTTAG
1 TTAACTGTTCAAATTAAACGATCCCTAAGTTTTTTAG
*
37618 TTAACTGTT-AAAGTTAAACGATCCCTAATTTTTTTAG
1 TTAACTGTTCAAA-TTAAACGATCCCTAAGTTTTTTAG
37655 TTAA
1 TTAA
37659 AATCATAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 3 0.08
36 21 0.57
37 13 0.35
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (37 bp):
TTAACTGTTCAAATTAAACGATCCCTAAGTTTTTTAG
Found at i:39783 original size:24 final size:25
Alignment explanation
Indices: 39755--39806 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
39745 TTATATTGTC
* * *
39755 AAATTATAATTGAAATTA-AATAAA
1 AAATTAGAAATGAAATTATAAAAAA
*
39779 AAATTCGAAATGAAATTATAAAAAA
1 AAATTAGAAATGAAATTATAAAAAA
39804 AAA
1 AAA
39807 AAAAAAGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (25 bp):
AAATTAGAAATGAAATTATAAAAAA
Found at i:40336 original size:25 final size:25
Alignment explanation
Indices: 40304--40355 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40294 ATTAATATTG
40304 TTTTCCATTAAAAATATTCTTAATA
1 TTTTCCATTAAAAATATTCTTAATA
40329 TTTTCCATTAAAAATATTCTTAATA
1 TTTTCCATTAAAAATATTCTTAATA
40354 TT
1 TT
40356 AAAGTCTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTCCATTAAAAATATTCTTAATA
Done.