Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003542.1 Hibiscus syriacus cultivar Beakdansim tig00007470_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: 179575
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:2646 original size:15 final size:15
Alignment explanation
Indices: 2626--2655 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2616 CTTTCTCATA
2626 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
2641 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
2656 TCAGCCTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:3982 original size:29 final size:29
Alignment explanation
Indices: 3939--4021 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
3929 CTCACCTAAC
*
3939 TAAATTGATGTAAGCAATGACATCATTATT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
3969 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
3998 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
4022 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:8841 original size:21 final size:21
Alignment explanation
Indices: 8801--8841 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8791 GGTAGCGTCT
* *
8801 AATATTAATATTTTCGATAAA
1 AATAATAATATTTTAGATAAA
*
8822 AATAATAATATTTTATATAA
1 AATAATAATATTTTAGATAA
8842 TATTTTATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
AATAATAATATTTTAGATAAA
Found at i:8890 original size:14 final size:14
Alignment explanation
Indices: 8871--8903 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
8861 AAAAATATTA
8871 ATATTTTTAATAAT
1 ATATTTTTAATAAT
8885 ATATTTTTAATAAT
1 ATATTTTTAATAAT
8899 ATATT
1 ATATT
8904 AAGACTGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTTTTAATAAT
Found at i:9505 original size:18 final size:18
Alignment explanation
Indices: 9478--9514 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9468 AAAATCGTTC
*
9478 TTTAAAAGTATAATAAAT
1 TTTAAAAGTAAAATAAAT
*
9496 TTTAATAGTAAAATAAAT
1 TTTAAAAGTAAAATAAAT
9514 T
1 T
9515 ATTCAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TTTAAAAGTAAAATAAAT
Found at i:12866 original size:50 final size:51
Alignment explanation
Indices: 12744--12870 Score: 168
Period size: 51 Copynumber: 2.5 Consensus size: 51
12734 TTAGCAGTAA
* **
12744 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGGCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
** *
12795 AGC-ATGCCCCATGCACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTAT
1 AGCGCGGCCCC-TGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
*
12845 AGCGCGGCCCCTGCAGCGCGCTATAC
1 AGCGCGGCCCCTGCACCGCGCTATAC
12871 CTGTATATCT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
50 27 0.42
51 38 0.58
ACGTcount: A:0.17, C:0.35, G:0.31, T:0.17
Consensus pattern (51 bp):
AGCGCGGCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
Found at i:13022 original size:12 final size:10
Alignment explanation
Indices: 12981--13021 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
12971 TTTATCACAC
12981 CAAATTCTCT
1 CAAATTCTCT
12991 CAAATTCTCT
1 CAAATTCTCT
13001 -AAATTTCTCT
1 CAAA-TTCTCT
*
13011 CAAATACTCT
1 CAAATTCTCT
13021 C
1 C
13022 TTTTTAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:13285 original size:111 final size:111
Alignment explanation
Indices: 13145--13366 Score: 349
Period size: 111 Copynumber: 2.0 Consensus size: 111
13135 TGGAAATCAT
* *
13145 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATGTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * *
13210 T-ATTTAGTT-ATTTATTTAATTTCATGATTATTATATTAATAATTAA
66 TAATTT-GTTGATTCATTTAA-TGCATGATTATTAGATTAAGAATTAA
*
13256 ATATCTCGACACTTTGCTGATACGGTAACATGTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATGTTAACGTTTTAATTTAATTTAAATTATTAGTAA
13321 TAATTTGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTTGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
13367 TTTTTGTATT
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
111 89 0.87
112 13 0.13
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATGTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTTGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:14893 original size:18 final size:18
Alignment explanation
Indices: 14866--14905 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
14856 CCAGCAGCCA
*
14866 CCGCATCCATATATGATG
1 CCGCAGCCATATATGATG
14884 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
14902 CCGC
1 CCGC
14906 CATCGCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:15255 original size:3 final size:3
Alignment explanation
Indices: 15247--15311 Score: 67
Period size: 3 Copynumber: 21.7 Consensus size: 3
15237 ACCTGTGCAA
* * * * * *
15247 GAC GAC GAC AAC GAC GAT GAT GAC GAC GAC GAC GAC AAC GAC GAT GAT
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
*
15295 GAC GAC GAC GAT GAC GA
1 GAC GAC GAC GAC GAC GA
15312 TGGTGATGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.37, C:0.25, G:0.31, T:0.08
Consensus pattern (3 bp):
GAC
Found at i:15282 original size:27 final size:27
Alignment explanation
Indices: 15247--15305 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
15237 ACCTGTGCAA
15247 GACGACGACAACGACGATGATGACGAC
1 GACGACGACAACGACGATGATGACGAC
15274 GACGACGACAACGACGATGATGACGAC
1 GACGACGACAACGACGATGATGACGAC
15301 GACGA
1 GACGA
15306 TGACGATGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.25, G:0.31, T:0.07
Consensus pattern (27 bp):
GACGACGACAACGACGATGATGACGAC
Found at i:19159 original size:49 final size:51
Alignment explanation
Indices: 19052--19174 Score: 189
Period size: 49 Copynumber: 2.5 Consensus size: 51
19042 TTATACAAAA
19052 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
*
19103 CGCGGTACATGCCCCGCGCTATATAAAATTAT-T-AGGAGTAAAGGTATAG-
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTAT-GT
**
19152 CGCGGTACCTGATCCGCGCTATA
1 CGCGGTACCTGCCCCGCGCTATA
19175 CCCCTACGTG
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
49 34 0.51
50 2 0.03
51 31 0.46
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (51 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
Found at i:19262 original size:50 final size:51
Alignment explanation
Indices: 19186--19311 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 51
19176 CCCTACGTGG
* * * **
19186 CGTATAGCGCGCTGTAGGGGCCGCGCTATA-CCCACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
* *
19236 CGTATAGCGCGGTGCAGGGGGTGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
* *
19287 CGTATAACGCAGTGCAGGGGGCGCG
1 CGTATAGCGCGGTGCAGGGGGCGCG
19312 TTTTACTGCT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 26 0.40
51 39 0.60
ACGTcount: A:0.18, C:0.31, G:0.35, T:0.16
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
Found at i:22141 original size:14 final size:14
Alignment explanation
Indices: 22124--22150 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22114 TAAAAAGTGG
22124 GAAAGAGAGAGAGA
1 GAAAGAGAGAGAGA
22138 GAAAGAGAGAGAG
1 GAAAGAGAGAGAG
22151 TTAACTTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (14 bp):
GAAAGAGAGAGAGA
Found at i:31973 original size:22 final size:21
Alignment explanation
Indices: 31949--31988 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
31939 GAGAAATTGT
31949 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
31970 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
31989 AAATAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:35637 original size:21 final size:21
Alignment explanation
Indices: 35611--35655 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35601 GATTTCTGGG
* *
35611 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
35632 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
35653 CAA
1 CAA
35656 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:37404 original size:23 final size:22
Alignment explanation
Indices: 37345--37411 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
37335 TATGGACATC
*
37345 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
37367 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
37389 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
37412 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:40566 original size:21 final size:21
Alignment explanation
Indices: 40540--40584 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40530 GATTTCTGGG
* *
40540 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
40561 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
40582 CAA
1 CAA
40585 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:42337 original size:23 final size:22
Alignment explanation
Indices: 42278--42344 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
42268 TATGGACATC
*
42278 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
42300 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
42322 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
42345 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:43903 original size:23 final size:22
Alignment explanation
Indices: 43875--43956 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
43865 TTGGTGCAGA
43875 GGGAATCAATACCCCACTTAAAG
1 GGGAATCAATACCCC-CTTAAAG
* * *
43898 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCAATACCCCC-TTAAAG
* *
43921 GGGAA-CGAATTCCCCC-TATAG
1 GGGAATC-AATACCCCCTTAAAG
*
43942 GGGAATCGATACCCC
1 GGGAATCAATACCCC
43957 TGGGGGTTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 14 0.29
22 3 0.06
23 31 0.65
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (22 bp):
GGGAATCAATACCCCCTTAAAG
Found at i:45212 original size:22 final size:22
Alignment explanation
Indices: 45184--45245 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
45174 ACTGAATATT
45184 TGTCCCGAATGACCACTGTATA
1 TGTCCCGAATGACCACTGTATA
45206 TGTCCCGAATGACCA----ATA
1 TGTCCCGAATGACCACTGTATA
*
45224 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAATGACCACTGTATA
45246 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 17 0.49
22 18 0.51
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (22 bp):
TGTCCCGAATGACCACTGTATA
Found at i:59856 original size:21 final size:21
Alignment explanation
Indices: 59830--59886 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
59820 CATATGAAAT
59830 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
59851 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
* *
59872 TTATCCCGAATGACC
1 TTGTCCCGAAGGACC
59887 TATGAAACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:61049 original size:12 final size:12
Alignment explanation
Indices: 61032--61057 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61022 AGATGACAAG
61032 TAAAATTCAACT
1 TAAAATTCAACT
61044 TAAAATTCAACT
1 TAAAATTCAACT
61056 TA
1 TA
61058 TCAACTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAAATTCAACT
Found at i:63336 original size:2 final size:2
Alignment explanation
Indices: 63329--63368 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
63319 ACCAATCCAA
* *
63329 AT AT AT AT GT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63369 TGATTAAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63647 original size:27 final size:27
Alignment explanation
Indices: 63600--63653 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
63590 TATGTTATAA
*
63600 ATTATTTTATAATTAATATATAAATAT
1 ATTATTTTATAATTAAAATATAAATAT
* *
63627 ATTATTTATATCA-TAAAATATTAATAT
1 ATTATTT-TATAATTAAAATATAAATAT
63654 TAATATCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTATTTTATAATTAAAATATAAATAT
Found at i:63659 original size:22 final size:22
Alignment explanation
Indices: 63596--63661 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
63586 CATTTATGTT
*
63596 ATAAATTATTTTATAATTAATAT-
1 ATAAA-TATATTAT-ATTAATATC
63619 ATAAATATATTAT-TT-ATATC
1 ATAAATATATTATATTAATATC
63639 ATAAA-ATATTAATATTAATATC
1 ATAAATATATT-ATATTAATATC
63661 A
1 A
63662 ATATTTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 9 0.24
20 9 0.24
21 2 0.05
22 13 0.34
23 5 0.13
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAATATATTATATTAATATC
Found at i:64006 original size:68 final size:68
Alignment explanation
Indices: 63920--64048 Score: 213
Period size: 68 Copynumber: 1.9 Consensus size: 68
63910 ACATATCATC
63920 TTATTGATCGAATAAAACAATTAAAAATATTATAACGTGAAAATTAAAAATAATAATAATAGGGT
1 TTATTGATCGAATAAAACAATTAAAAATATTATAACGTGAAAATTAAAAATAATAATAATAGGGT
63985 AAA
66 AAA
* * ** *
63988 TTATTGGTCGAATGAAACAATTAAAAATATTATATTGTGAAAATTAATAATAATAATAATA
1 TTATTGATCGAATAAAACAATTAAAAATATTATAACGTGAAAATTAAAAATAATAATAATA
64049 ATAATAATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (68 bp):
TTATTGATCGAATAAAACAATTAAAAATATTATAACGTGAAAATTAAAAATAATAATAATAGGGT
AAA
Found at i:64040 original size:3 final size:3
Alignment explanation
Indices: 64032--64058 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
64022 TTGTGAAAAT
64032 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
64059 ATAGGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:69895 original size:2 final size:2
Alignment explanation
Indices: 69888--69912 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
69878 GCATGTTTAG
69888 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
69913 CGCTGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71711 original size:186 final size:186
Alignment explanation
Indices: 71440--71831 Score: 662
Period size: 186 Copynumber: 2.1 Consensus size: 186
71430 TTTTTCAATT
* * *
71440 TATATAA-AAATTAAATATTTTATAATTAAAAAAAGCAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTAAAAAAAGCAGTTTACAATTAATTTAAATAATATATA
71504 ATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
71569 TTGGATATTAAATTATTAATTGGGTTTTAAATTGTTTGGGCTGAGCTCATATGTTA
131 TTGGATATTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCTCATATGTTA
* * *
71625 TATATAATATATTTAATATTTTTTAATTCTAAAAAA-TAGTTTACAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATT-AAAAAAAGCAGTTTACAATTAATTTAAATAATATAT
*
71689 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
65 AATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
* *
71754 ATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCTCATATGTTA
130 ATTGGATATTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCTCATATGTTA
*
71811 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
71832 AAAATTTTAA
Statistics
Matches: 194, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
185 7 0.04
186 181 0.93
187 6 0.03
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTAAAAAAAGCAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGGATATTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCTCATATGTTA
Found at i:74174 original size:12 final size:12
Alignment explanation
Indices: 74157--74184 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
74147 AAATATAATA
74157 AATTATAAATTT
1 AATTATAAATTT
74169 AATTATAAATTT
1 AATTATAAATTT
74181 AATT
1 AATT
74185 TCTTAACGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTATAAATTT
Found at i:78380 original size:35 final size:34
Alignment explanation
Indices: 78295--78381 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
78285 AATATAATTT
*
78295 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
78329 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
78367 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
78382 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:80722 original size:17 final size:18
Alignment explanation
Indices: 80679--80719 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
80669 GAATTATATT
80679 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
80696 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
80714 ATTAAA
1 AGTAAA
80720 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:80780 original size:10 final size:10
Alignment explanation
Indices: 80761--80791 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
80751 CTTAAACAGA
*
80761 GAGAGTATTT
1 GAGAGAATTT
80771 GAGAGAATTT
1 GAGAGAATTT
80781 GAGAGAATTT
1 GAGAGAATTT
80791 G
1 G
80792 GTGTGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:82785 original size:26 final size:26
Alignment explanation
Indices: 82754--82803 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
82744 ATTCCCCATC
*
82754 TTCTTTTTATTCACTTTTCTTCTTCT
1 TTCTTTCTATTCACTTTTCTTCTTCT
*
82780 TTCTTTCTCTTCACTTTTCTTCTT
1 TTCTTTCTATTCACTTTTCTTCTT
82804 TTCTTCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (26 bp):
TTCTTTCTATTCACTTTTCTTCTTCT
Found at i:82816 original size:23 final size:25
Alignment explanation
Indices: 82754--82816 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
82744 ATTCCCCATC
*
82754 TTCTTTTTATTCACTTTTCTTCTTCT
1 TTCTTCTTA-TCACTTTTCTTCTTCT
82780 TTCTTTCTCT-TCACTTTTCTTC-T-T
1 TTC-TTCT-TATCACTTTTCTTCTTCT
82804 TTCTTCTTATCAC
1 TTCTTCTTATCAC
82817 ACACGTTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
22 1 0.03
23 8 0.24
24 4 0.12
25 1 0.03
26 15 0.45
27 3 0.09
28 1 0.03
ACGTcount: A:0.08, C:0.27, G:0.00, T:0.65
Consensus pattern (25 bp):
TTCTTCTTATCACTTTTCTTCTTCT
Found at i:85774 original size:17 final size:17
Alignment explanation
Indices: 85752--85787 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
85742 TCACATGCAC
85752 TCTCGTTTGGTTTTTGT
1 TCTCGTTTGGTTTTTGT
85769 TCTCGTTTGGTTTTTGT
1 TCTCGTTTGGTTTTTGT
85786 TC
1 TC
85788 ATCAGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.14, G:0.22, T:0.64
Consensus pattern (17 bp):
TCTCGTTTGGTTTTTGT
Found at i:87137 original size:35 final size:35
Alignment explanation
Indices: 87096--87166 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
87086 AGTTCAAAAC
*
87096 TCCAAAACACTTCAATTATATTCTAAACCCCAAAT
1 TCCAAAACACTTAAATTATATTCTAAACCCCAAAT
* * * *
87131 TCCAAAATACTTAAATTATATTTTAAATCCTAAAT
1 TCCAAAACACTTAAATTATATTCTAAACCCCAAAT
87166 T
1 T
87167 GAAGTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
TCCAAAACACTTAAATTATATTCTAAACCCCAAAT
Found at i:88051 original size:118 final size:116
Alignment explanation
Indices: 87717--88064 Score: 385
Period size: 123 Copynumber: 2.9 Consensus size: 116
87707 TTATAGTTAG
* *
87717 TATTTTAAATTTTTAGTGTTTTTAATGTTTAATAAGTAAATAACTATTATGCCATAACTATTTAT
1 TATTTTAAATGTTTAGTATTTTTAATGTTTAATAAGTAAATAACTATTATGCCATAACTATTTAT
*** * * * * * *
87782 T-AAACTTTTAATTTTATTTTTTTAAATTTATACTTAATTTACACGTTAAAGA
66 TGAAAAAATT-ATTTTATATTTTTAAA-TTATACTAAATTAAAAAGTGAAAGA
* * *
87834 TGTTTTAAATGTTTAGTATTTTTTTTTACTATGTTTAATAAGTAAAGAACTATTATGTCATAACT
1 TATTTTAAATGTTTAGTA----TTTTTA--ATGTTTAATAAGTAAATAACTATTATGCCATAACT
*
87899 ATTTATTG-AAAAATTATCTTTATATTTTTAAAATTATACAAAATTAAAAAGTGAAAGA
60 ATTTATTGAAAAAATTAT-TTTATATTTTT-AAATTATACTAAATTAAAAAGTGAAAGA
* * * *
87957 TATTTTAAATGTTTAGTATATTATAATGTTTGATAAGTATATAACTATTGTGCCATAACTATTTA
1 TATTTTAAATGTTTAGTAT-TTTTAATGTTTAATAAGTAAATAACTATTATGCCATAACTATTTA
**
88022 TTGAAAAAATTGATTTTATATCCTTAAATTATACTAAATTAAA
65 TTGAAAAAATT-ATTTTATATTTTTAAATTATACTAAATTAAA
88065 TTATACTTAG
Statistics
Matches: 194, Mismatches: 25, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
117 15 0.08
118 55 0.28
119 17 0.09
120 6 0.03
121 6 0.03
122 2 0.01
123 90 0.46
124 3 0.02
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (116 bp):
TATTTTAAATGTTTAGTATTTTTAATGTTTAATAAGTAAATAACTATTATGCCATAACTATTTAT
TGAAAAAATTATTTTATATTTTTAAATTATACTAAATTAAAAAGTGAAAGA
Found at i:88803 original size:13 final size:13
Alignment explanation
Indices: 88785--88812 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
88775 CTTGGTTTTG
88785 AATTGTTTTTGAA
1 AATTGTTTTTGAA
88798 AATTGTTTTTGAA
1 AATTGTTTTTGAA
88811 AA
1 AA
88813 GTGCAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
AATTGTTTTTGAA
Found at i:91224 original size:24 final size:24
Alignment explanation
Indices: 91180--91226 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
91170 GTGCTGAAAG
91180 TACGCAAATGTACTAATACAAAAA
1 TACGCAAATGTACTAATACAAAAA
*
91204 TACGACAAATGTATTAA-ACAAAA
1 TACG-CAAATGTACTAATACAAAA
91227 TCGATTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (24 bp):
TACGCAAATGTACTAATACAAAAA
Found at i:92743 original size:19 final size:20
Alignment explanation
Indices: 92719--92764 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
92709 CAAAATAACC
* *
92719 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCCAACAT
92738 CAATTTCAACACTCCAACAT
1 CAATTTCAACACTCCAACAT
*
92758 AAATTTC
1 CAATTTC
92765 TAGCATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (20 bp):
CAATTTCAACACTCCAACAT
Found at i:99523 original size:3 final size:3
Alignment explanation
Indices: 99515--99552 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
99505 ATCAGAAACA
99515 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
99553 AAATAAACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:101687 original size:25 final size:25
Alignment explanation
Indices: 101659--101707 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
101649 GGACATGGGA
101659 AATCACGGGGTGAGCAGAGAGATGC
1 AATCACGGGGTGAGCAGAGAGATGC
*
101684 AATCACGGGGTGAGTAGAGAGATG
1 AATCACGGGGTGAGCAGAGAGATG
101708 TTGTTGCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.41, T:0.14
Consensus pattern (25 bp):
AATCACGGGGTGAGCAGAGAGATGC
Found at i:105286 original size:13 final size:13
Alignment explanation
Indices: 105268--105292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105258 TTTACTACTA
105268 AATAATTATTAAT
1 AATAATTATTAAT
105281 AATAATTATTAA
1 AATAATTATTAA
105293 ATCATTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATTATTAAT
Found at i:105293 original size:24 final size:24
Alignment explanation
Indices: 105266--105312 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
105256 TTTTTACTAC
105266 TAAATAATTATTAATAATAATTAT
1 TAAATAATTATTAATAATAATTAT
* * *
105290 TAAATCATTATTAGTAATTATTA
1 TAAATAATTATTAATAATAATTA
105313 CAATTTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TAAATAATTATTAATAATAATTAT
Found at i:105345 original size:24 final size:24
Alignment explanation
Indices: 105263--105346 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
105253 GGTTTTTTAC
* *
105263 TACTAAATAATTA-TTAATAATAAT
1 TACTAAATCATTATTTAA-AATTAT
* *
105287 TATTAAATCATTA-TTAGTAATTAT
1 TACTAAATCATTATTTA-AAATTAT
* *
105311 TAC-AATTTCATTATTTCAAATTAT
1 TACTAA-ATCATTATTTAAAATTAT
105335 TACTAAATCATT
1 TACTAAATCATT
105347 TGTATTAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
23 2 0.04
24 41 0.87
25 4 0.09
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (24 bp):
TACTAAATCATTATTTAAAATTAT
Found at i:105420 original size:24 final size:24
Alignment explanation
Indices: 105292--105421 Score: 78
Period size: 24 Copynumber: 5.5 Consensus size: 24
105282 ATAATTATTA
*
105292 AATCATTATTAGT-AATTATTAC-
1 AATCATTATTAGTAAATCATTACT
*
105314 AATTTCATTATT--TCAAATTATTACT
1 AA--TCATTATTAGT-AAATCATTACT
*
105339 AAATCATT-TGTATTAAATCATTA--
1 -AATCATTAT-TAGTAAATCATTACT
* * * *
105362 AAT-ATTAATAATAAAACATTATT
1 AATCATTATTAGTAAATCATTACT
105385 AGTATCATTATTAGTAAATCATTACT
1 A--ATCATTATTAGTAAATCATTACT
105411 AATCATTATTA
1 AATCATTATTA
105422 AATCATGTCA
Statistics
Matches: 85, Mismatches: 8, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
21 14 0.16
22 6 0.07
23 2 0.02
24 33 0.39
25 10 0.12
26 20 0.24
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (24 bp):
AATCATTATTAGTAAATCATTACT
Found at i:105432 original size:26 final size:26
Alignment explanation
Indices: 105402--105460 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
105392 TTATTAGTAA
*
105402 ATCATTACT-AATCATTATTAAATCAT
1 ATCATTACTAAATCATTA-AAAATCAT
*
105428 GTCATTACTAAATCATTAAAAATCAT
1 ATCATTACTAAATCATTAAAAATCAT
105454 ATCATTA
1 ATCATTA
105461 AATTAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (26 bp):
ATCATTACTAAATCATTAAAAATCAT
Found at i:105434 original size:16 final size:16
Alignment explanation
Indices: 105413--105443 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
105403 TCATTACTAA
*
105413 TCATTATTAAATCATG
1 TCATTACTAAATCATG
105429 TCATTACTAAATCAT
1 TCATTACTAAATCAT
105444 TAAAAATCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (16 bp):
TCATTACTAAATCATG
Found at i:105489 original size:14 final size:14
Alignment explanation
Indices: 105360--105408 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
105350 ATTAAATCAT
* *
105360 TAAAT-ATTAATAA
1 TAAATCATTATTAG
*
105373 TAAAACATTATTAG
1 TAAATCATTATTAG
105387 T--ATCATTATTAG
1 TAAATCATTATTAG
105399 TAAATCATTA
1 TAAATCATTA
105409 CTAATCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 11 0.38
13 4 0.14
14 14 0.48
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (14 bp):
TAAATCATTATTAG
Found at i:107271 original size:84 final size:84
Alignment explanation
Indices: 107094--107275 Score: 274
Period size: 84 Copynumber: 2.2 Consensus size: 84
107084 TTTTGCTTCT
* * *
107094 TTTTATGCTGTTTTGTGTTCTGTTTTCGATGGATAATTGCCCATTATCACATGCATTATTACCCT
1 TTTTATGTTGTTTTGTGTTCTGTTTTAGAAGGATAATTGCCCATTATCACATGCATTATTACCCT
** * *
107159 TTCTTTTTTTTTTGCTTTG
66 TTCTTTTACTTTTCCTTTA
* *
107178 TTTTATGTTGTTTTGTGTTCTGTTTTAGAAGGATTATTGTCCATTATCACATGCATTATTACCCT
1 TTTTATGTTGTTTTGTGTTCTGTTTTAGAAGGATAATTGCCCATTATCACATGCATTATTACCCT
107243 TTCTTTTACTTTTCCTTTA
66 TTCTTTTACTTTTCCTTTA
*
107262 TTTTGTGTTGTTTT
1 TTTTATGTTGTTTT
107276 ATGGGACCAA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.15, C:0.15, G:0.14, T:0.57
Consensus pattern (84 bp):
TTTTATGTTGTTTTGTGTTCTGTTTTAGAAGGATAATTGCCCATTATCACATGCATTATTACCCT
TTCTTTTACTTTTCCTTTA
Found at i:109940 original size:30 final size:30
Alignment explanation
Indices: 109899--109962 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
109889 TGCATGCAAA
* * *
109899 TTCTGCTAAAGACGTCGATAGATCCATGTT
1 TTCTACTAAAGACGCCGATAGATCCAAGTT
109929 TTCTACTAAAGACGCCGATAGATCCAAGTT
1 TTCTACTAAAGACGCCGATAGATCCAAGTT
109959 TTCT
1 TTCT
109963 GTGTAAATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (30 bp):
TTCTACTAAAGACGCCGATAGATCCAAGTT
Found at i:115044 original size:18 final size:18
Alignment explanation
Indices: 114997--115049 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
114987 TTAGTCATTT
*
114997 CAAAAAATTCAGCCACTG
1 CAAAAAATTCGGCCACTG
* * * *
115015 CAGATAACTCGGTCACTG
1 CAAAAAATTCGGCCACTG
115033 CAAAAAATTCGGCCACT
1 CAAAAAATTCGGCCACT
115050 TCAATCTGTA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.19
Consensus pattern (18 bp):
CAAAAAATTCGGCCACTG
Found at i:120081 original size:16 final size:17
Alignment explanation
Indices: 120050--120082 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
120040 TTTACCTCAA
*
120050 AAACATCATCATTCCAC
1 AAACATCATCAGTCCAC
120067 AAACA-CATCAGTCCAC
1 AAACATCATCAGTCCAC
120083 CAGCAGACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.36, G:0.03, T:0.18
Consensus pattern (17 bp):
AAACATCATCAGTCCAC
Found at i:127169 original size:28 final size:29
Alignment explanation
Indices: 127138--127202 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
127128 GTAAATAGAG
* *
127138 TTAGATTTACTGTAA-ATAACAAAGTAGT
1 TTAGATATACTGTAACATAACAAAGTAAT
* * *
127166 TTAGATATCCTGTAACTTAACTAAGTAAT
1 TTAGATATACTGTAACATAACAAAGTAAT
127195 TTAGATAT
1 TTAGATAT
127203 CCTATAACTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (29 bp):
TTAGATATACTGTAACATAACAAAGTAAT
Found at i:127219 original size:31 final size:31
Alignment explanation
Indices: 127154--127245 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
127144 TTACTGTAAA
* *
127154 TAACAAAGTAGTTTAGATATCCTGTAA--CT
1 TAACTAAGTAGTTTAGATATCCTATAACTCT
*
127183 TAACTAAGTAATTTAGATATCCTATAACTCT
1 TAACTAAGTAGTTTAGATATCCTATAACTCT
*
127214 TAACTAAGCAGTTTAGATATCCTATAACTCT
1 TAACTAAGTAGTTTAGATATCCTATAACTCT
127245 T
1 T
127246 TATCTCTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 24 0.43
31 32 0.57
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (31 bp):
TAACTAAGTAGTTTAGATATCCTATAACTCT
Found at i:133707 original size:86 final size:86
Alignment explanation
Indices: 133562--133728 Score: 334
Period size: 86 Copynumber: 1.9 Consensus size: 86
133552 ACTGCTTGCT
133562 AAGATTCACTATATAAACAAAAAAATGAACTTAAACAATCTAATGCTGGTAAACAAACTAATATT
1 AAGATTCACTATATAAACAAAAAAATGAACTTAAACAATCTAATGCTGGTAAACAAACTAATATT
133627 AATAGCATTTATCAAAAAAAA
66 AATAGCATTTATCAAAAAAAA
133648 AAGATTCACTATATAAACAAAAAAATGAACTTAAACAATCTAATGCTGGTAAACAAACTAATATT
1 AAGATTCACTATATAAACAAAAAAATGAACTTAAACAATCTAATGCTGGTAAACAAACTAATATT
133713 AATAGCATTTATCAAA
66 AATAGCATTTATCAAA
133729 TATCGAATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.26
Consensus pattern (86 bp):
AAGATTCACTATATAAACAAAAAAATGAACTTAAACAATCTAATGCTGGTAAACAAACTAATATT
AATAGCATTTATCAAAAAAAA
Found at i:136927 original size:15 final size:15
Alignment explanation
Indices: 136907--136951 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
136897 CCAGAGGTAA
136907 TTGTTGAACCTACTC
1 TTGTTGAACCTACTC
*
136922 TTGTTGACCCTACTC
1 TTGTTGAACCTACTC
* *
136937 TTGCTAAACCTACTC
1 TTGTTGAACCTACTC
136952 CCAATAATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.20, C:0.31, G:0.11, T:0.38
Consensus pattern (15 bp):
TTGTTGAACCTACTC
Found at i:163933 original size:33 final size:33
Alignment explanation
Indices: 163891--163954 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
163881 GGTGTTAATA
*
163891 GGCTTTAAGGTTCTTGGAGATTCATGGATTTAT
1 GGCTTTAAGGTTCTTGGAGATTCATAGATTTAT
163924 GGCTTTAAGGTTCTTGGAGATTCATAGATTT
1 GGCTTTAAGGTTCTTGGAGATTCATAGATTT
163955 TATGAGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (33 bp):
GGCTTTAAGGTTCTTGGAGATTCATAGATTTAT
Found at i:167368 original size:21 final size:21
Alignment explanation
Indices: 167339--167379 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
167329 ACCATCCACA
167339 CTTAGAAGTATTACCTGACTG
1 CTTAGAAGTATTACCTGACTG
*
167360 CTTATAAGTATTACCTGACT
1 CTTAGAAGTATTACCTGACT
167380 ACCAATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (21 bp):
CTTAGAAGTATTACCTGACTG
Found at i:167387 original size:21 final size:21
Alignment explanation
Indices: 167344--167387 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
167334 CCACACTTAG
* **
167344 AAGTATTACCTGACTGCTTAT
1 AAGTATTACCTGACTACCAAT
167365 AAGTATTACCTGACTACCAAT
1 AAGTATTACCTGACTACCAAT
167386 AA
1 AA
167388 CTCCGCATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.32
Consensus pattern (21 bp):
AAGTATTACCTGACTACCAAT
Found at i:168376 original size:21 final size:21
Alignment explanation
Indices: 168350--168404 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
168340 TGTTTTATAC
168350 GAGTAAGATCAATCACTTTGG
1 GAGTAAGATCAATCACTTTGG
168371 GAGTAAGATCAATCACTTTGG
1 GAGTAAGATCAATCACTTTGG
* *
168392 GAATAAGAACAAT
1 GAGTAAGATCAAT
168405 AATAGTCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (21 bp):
GAGTAAGATCAATCACTTTGG
Found at i:176076 original size:37 final size:38
Alignment explanation
Indices: 175996--176076 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
175986 AACAAGCTGG
* *
175996 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
176035 -AAAATTTATATAATTTT-TTTACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
176071 AAAAAT
1 AAAAAT
176077 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 2 0.05
37 27 0.73
38 8 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Done.