Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001483.1 Hibiscus syriacus cultivar Beakdansim tig00002879_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: 109499
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5749 original size:16 final size:16
Alignment explanation
Indices: 5728--5764 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
5718 TAAGTCGAGG
*
5728 ATGCCGCCAGAAGAGA
1 ATGCCGCCAAAAGAGA
5744 ATGCCGCCAAAAGAGA
1 ATGCCGCCAAAAGAGA
5760 ATGCC
1 ATGCC
5765 TTATTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.27, G:0.27, T:0.08
Consensus pattern (16 bp):
ATGCCGCCAAAAGAGA
Found at i:6969 original size:17 final size:17
Alignment explanation
Indices: 6943--6994 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
6933 ATTGTTCAAG
*
6943 AATAACTTAAAGAAATT
1 AATAATTTAAAGAAATT
**
6960 AATAATTTAAAGTTGATT
1 AATAATTTAAAG-AAATT
*
6978 AATAATTTAAACAAATT
1 AATAATTTAAAGAAATT
6995 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (17 bp):
AATAATTTAAAGAAATT
Found at i:7261 original size:12 final size:12
Alignment explanation
Indices: 7218--7262 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
7208 GATCACCACT
* *
7218 ACCATCACCACC
1 ACCATCATCATC
7230 ACCATCATCATC
1 ACCATCATCATC
*
7242 ACTATCATCATC
1 ACCATCATCATC
*
7254 ACCCTCATC
1 ACCATCATC
7263 TACATGGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (12 bp):
ACCATCATCATC
Found at i:13851 original size:21 final size:21
Alignment explanation
Indices: 13827--13907 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
13817 TTGGTGCAGA
*
13827 GGGAATCGATCCCCCCCATGA-
1 GGGAACCGAT-CCCCCCATGAG
** *
13848 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGA-TCCCCCCATG-AG
*
13871 GGGAACCGATTCCCCCAT-AG
1 GGGAACCGATCCCCCCATGAG
*
13891 GGGAATCGATACCCCCC
1 GGGAACCGAT-CCCCCC
13908 TGGGGTTCTG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
20 10 0.21
21 20 0.43
22 8 0.17
23 9 0.19
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.17
Consensus pattern (21 bp):
GGGAACCGATCCCCCCATGAG
Found at i:16147 original size:13 final size:13
Alignment explanation
Indices: 16129--16172 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
16119 AAAGGGGGAG
16129 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
16142 AA--GTGTGTTTT
1 AAGTGTGTGTTTT
*
16153 ATGTGTGT-TTTT
1 AAGTGTGTGTTTT
16165 AAGTGTGT
1 AAGTGTGT
16173 TTTAAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.37
12 11 0.41
13 6 0.22
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.55
Consensus pattern (13 bp):
AAGTGTGTGTTTT
Found at i:16157 original size:9 final size:11
Alignment explanation
Indices: 16133--16177 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
16123 GGGGAGAAGT
16133 GTGTGTTTTAA
1 GTGTGTTTTAA
*
16144 GTGTGTTTTAT
1 GTGTGTTTTAA
16155 GTGTGTTTTTAA
1 GTGTG-TTTTAA
16167 GTGTGTTTTAA
1 GTGTGTTTTAA
16178 AATGATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.16, C:0.00, G:0.27, T:0.58
Consensus pattern (11 bp):
GTGTGTTTTAA
Found at i:16168 original size:23 final size:24
Alignment explanation
Indices: 16131--16176 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
16121 AGGGGGAGAA
16131 GTGTGTGTTTTAAGTGTGTTTTAT
1 GTGTGTGTTTTAAGTGTGTTTTAT
16155 GTGTGT-TTTTAAGTGTGTTTTA
1 GTGTGTGTTTTAAGTGTGTTTTA
16177 AAATGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.13, C:0.00, G:0.28, T:0.59
Consensus pattern (24 bp):
GTGTGTGTTTTAAGTGTGTTTTAT
Found at i:18378 original size:4 final size:4
Alignment explanation
Indices: 18369--18518 Score: 101
Period size: 4 Copynumber: 36.8 Consensus size: 4
18359 ATATCCCTTC
* **
18369 AAAT AAAT AAAT AAAT AAATT CGAAA- CAAT AAAAT AAAT TCA- AAAT
1 AAAT AAAT AAAT AAAT AAA-T --AAAT AAAT -AAAT AAAT AAAT AAAT
* ** * *
18415 AAAT AAAT AAAT AAAC AAAT TCA- AAAT AAAT AAAT CCACCAT AAAT AAAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --A-AAT AAAT AAAT
* * **
18465 AAAT TAAT CAAT AAAT AAAT AAAT AAAT AAAT CCA- AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
18512 AAAT AAA
1 AAAT AAA
18519 AATTACTGTC
Statistics
Matches: 112, Mismatches: 23, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
3 5 0.04
4 96 0.86
5 5 0.04
6 1 0.01
7 5 0.04
ACGTcount: A:0.69, C:0.08, G:0.01, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:18422 original size:19 final size:19
Alignment explanation
Indices: 18373--18488 Score: 83
Period size: 19 Copynumber: 5.8 Consensus size: 19
18363 CCCTTCAAAT
*
18373 AAATAAATAAATAAATTCG
1 AAATAAATAAATAAATTCA
*
18392 AAA-CAATAAAATAAATTCA
1 AAATAAAT-AAATAAATTCA
*
18411 AAATAAATAAATAAATAAACA
1 AAATAAATAAATAAAT--TCA
* *
18432 AATTCAAAATAAATAAATCCA
1 AAAT--AAATAAATAAATTCA
** *
18453 CCATAAATAAAAAAATT-A
1 AAATAAATAAATAAATTCA
18471 ATCAATAAATAAATAAAT
1 A--AATAAATAAATAAAT
18489 AAATAAATCC
Statistics
Matches: 75, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
18 4 0.05
19 35 0.47
20 16 0.21
21 8 0.11
23 12 0.16
ACGTcount: A:0.67, C:0.09, G:0.01, T:0.23
Consensus pattern (19 bp):
AAATAAATAAATAAATTCA
Found at i:18438 original size:27 final size:27
Alignment explanation
Indices: 18396--18520 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
18386 AATTCGAAAC
18396 AATAAAATAAATTCAAAATAAATAAATA
1 AATAAAA-AAATTCAAAATAAATAAATA
*
18424 AATAAACAAATTCAAAATAAATAAATCCACCATA
1 AATAAAAAAATTCAAAATAAAT--A---A--ATA
18458 AATAAAAAAATT-AATCAATAAATAAATA
1 AATAAAAAAATTCAA--AATAAATAAATA
* *
18486 AATAAATAAATCCAAAATAAATAAATA
1 AATAAAAAAATTCAAAATAAATAAATA
18513 AATAAAAA
1 AATAAAAA
18521 TTACTGTCGA
Statistics
Matches: 82, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
27 34 0.41
28 19 0.23
29 3 0.04
30 1 0.01
32 1 0.01
33 3 0.04
34 14 0.17
35 7 0.09
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (27 bp):
AATAAAAAAATTCAAAATAAATAAATA
Found at i:18505 original size:19 final size:18
Alignment explanation
Indices: 18373--18521 Score: 82
Period size: 19 Copynumber: 8.2 Consensus size: 18
18363 CCCTTCAAAT
*
18373 AAATAAATAAATAAATTCG
1 AAATAAATAAATAAA-TCA
*
18392 AAA-CAATAAAATAAATTCA
1 AAATAAAT-AAATAAA-TCA
18411 AAATAAATAAATAAAT-A
1 AAATAAATAAATAAATCA
*
18428 AACA-AATTCAAAATAAAT--
1 AA-ATAAAT--AAATAAATCA
*
18446 AAATCCACCATAAATAAA--A
1 AAAT--A-AATAAATAAATCA
* *
18465 AAATTAATCAATAAAT--
1 AAATAAATAAATAAATCA
18481 AAATAAATAAATAAATCCA
1 AAATAAATAAATAAAT-CA
*
18500 AAATAAATAAATAAATAA
1 AAATAAATAAATAAATCA
18518 AAAT
1 AAAT
18522 TACTGTCGAA
Statistics
Matches: 104, Mismatches: 12, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
16 22 0.21
17 7 0.07
18 12 0.12
19 58 0.56
20 4 0.04
21 1 0.01
ACGTcount: A:0.68, C:0.08, G:0.01, T:0.23
Consensus pattern (18 bp):
AAATAAATAAATAAATCA
Found at i:25637 original size:28 final size:28
Alignment explanation
Indices: 25597--25650 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
25587 ATGACTTTCA
25597 ATACAATATACAATGGGCCTTTAAATTG
1 ATACAATATACAATGGGCCTTTAAATTG
25625 ATACAATATACAATGGGCCTTTAAAT
1 ATACAATATACAATGGGCCTTTAAAT
25651 CGTTTCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (28 bp):
ATACAATATACAATGGGCCTTTAAATTG
Found at i:28946 original size:20 final size:20
Alignment explanation
Indices: 28923--29021 Score: 62
Period size: 20 Copynumber: 5.0 Consensus size: 20
28913 TTACTCTGAT
28923 AATATAAAAAATAAATTTTA
1 AATATAAAAAATAAATTTTA
**
28943 AATATAATGAATATAATATTTA
1 AATATAAAAAATA-AAT-TTTA
*
28965 AA-AT-AATAATAAA-TTTA
1 AATATAAAAAATAAATTTTA
* ** *
28982 ATATTTTTAAAATAAATTTAA
1 A-ATATAAAAAATAAATTTTA
* *
29003 AAT-TTAAAAATTAATTTTA
1 AATATAAAAAATAAATTTTA
29022 TCGAAACTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
17 5 0.08
18 1 0.02
19 16 0.26
20 25 0.40
21 9 0.15
22 6 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (20 bp):
AATATAAAAAATAAATTTTA
Found at i:28983 original size:24 final size:24
Alignment explanation
Indices: 28937--29011 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
28927 TAAAAAATAA
* * *
28937 ATTTTAAAT-ATAATGAATATAAT
1 ATTTAAAATAATAATAAATTTAAT
28960 ATTTAAAATAATAATAAATTTAAT
1 ATTTAAAATAATAATAAATTTAAT
* *
28984 ATTT---TTAA-AATAAATTTAAA
1 ATTTAAAATAATAATAAATTTAAT
29004 ATTTAAAA
1 ATTTAAAA
29012 ATTAATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 15 0.36
21 3 0.07
23 8 0.19
24 16 0.38
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
ATTTAAAATAATAATAAATTTAAT
Found at i:28990 original size:26 final size:25
Alignment explanation
Indices: 28926--28996 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 25
28916 CTCTGATAAT
28926 ATAA-AAA-ATAA-ATTTT-AAAT-
1 ATAATAAATATAATATTTTAAAATA
*
28946 ATAATGAATATAATA-TTTAAAATA
1 ATAATAAATATAATATTTTAAAATA
*
28970 ATAATAAATTTAATATTTTTAAAATA
1 ATAATAAATATAATA-TTTTAAAATA
28996 A
1 A
28997 ATTTAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.10
21 2 0.05
22 7 0.17
23 5 0.12
24 13 0.32
26 10 0.24
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (25 bp):
ATAATAAATATAATATTTTAAAATA
Found at i:29018 original size:19 final size:20
Alignment explanation
Indices: 28972--29019 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
28962 TTAAAATAAT
* *
28972 AATAAATTTAATATTTTTAA
1 AATAAATTTAATAATTTAAA
28992 AATAAATTTAA-AATTTAAA
1 AATAAATTTAATAATTTAAA
*
29011 AATTAATTT
1 AATAAATTT
29020 TATCGAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAAATTTAATAATTTAAA
Found at i:29511 original size:2 final size:2
Alignment explanation
Indices: 29506--29535 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29496 TTTTTTAGAA
29506 AT 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
29536 TTAACGCAAA
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):
AT
Found at i:38184 original size:21 final size:21
Alignment explanation
Indices: 38158--38197 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38148 CCCCCTTTGA
*
38158 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
38179 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
38198 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:42674 original size:17 final size:18
Alignment explanation
Indices: 42647--42686 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
42637 AATTATCAAA
42647 AAAATAATAAATTTTAAT
1 AAAATAATAAATTTTAAT
*
42665 AAAA-AATAAATTTTATT
1 AAAATAATAAATTTTAAT
42682 AAAAT
1 AAAAT
42687 TCGTCATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATAAATTTTAAT
Found at i:43893 original size:23 final size:23
Alignment explanation
Indices: 43850--43908 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
43840 AAACTACGCA
43850 TTTAA-TA-TTTAAATTATTA-T
1 TTTAATTATTTTAAATTATTATT
43870 TTTAATATATTTTAATATTA-TATT
1 TTTAAT-TATTTTAA-ATTATTATT
43894 TTTAATTATTTTAAA
1 TTTAATTATTTTAAA
43909 ATCATACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.15
22 3 0.09
23 15 0.44
24 11 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTAATTATTTTAAATTATTATT
Found at i:50709 original size:30 final size:29
Alignment explanation
Indices: 50673--50736 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
50663 CTTAAAATAT
*
50673 TTTTTTTGTCAAAATAAATACCTAAAGTTA
1 TTTTTTTATCAAAATAAATACCTAAAG-TA
**
50703 TTTTTTTATCAAAATAGGTACCTAAAGTA
1 TTTTTTTATCAAAATAAATACCTAAAGTA
50732 TTTTT
1 TTTTT
50737 AAGGCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTTTTTATCAAAATAAATACCTAAAGTA
Found at i:52529 original size:32 final size:32
Alignment explanation
Indices: 52465--52529 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
52455 GTGAATGAGC
* *
52465 TTCTGCTTTTGCTTGTATATTTTATAAGGAGT
1 TTCTGCTTTTGCTTATATATTTTATAACGAGT
* *
52497 TTCTGCTTTTGCTTATGTATTTTATATCGAGT
1 TTCTGCTTTTGCTTATATATTTTATAACGAGT
52529 T
1 T
52530 GTCAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (32 bp):
TTCTGCTTTTGCTTATATATTTTATAACGAGT
Found at i:55936 original size:13 final size:13
Alignment explanation
Indices: 55918--55943 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55908 GTTCACATTG
55918 ATTGACATGAACT
1 ATTGACATGAACT
55931 ATTGACATGAACT
1 ATTGACATGAACT
55944 GGGTAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATTGACATGAACT
Found at i:57261 original size:19 final size:20
Alignment explanation
Indices: 57237--57328 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
57227 AAATGACCAA
57237 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACGCGATCTC
* *
57256 CAAATTCGTAACGCGAACTC
1 CAAATTCGCAACGCGATCTC
* ***
57276 CAATTTCGCAACATAAGT-TC
1 CAAATTCGCAACGCGA-TCTC
*
57296 CAAAATCGCAACGCGATCTTC
1 CAAATTCGCAACGCGATC-TC
57317 CAAATTCGCAAC
1 CAAATTCGCAAC
57329 ACAAATAGGT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 18 0.33
20 24 0.44
21 13 0.24
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACGCGATCTC
Found at i:57350 original size:20 final size:20
Alignment explanation
Indices: 57325--57371 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
57315 TCCAAATTCG
57325 CAACACAAATAGGTAAATCC
1 CAACACAAATAGGTAAATCC
* * *
57345 CAACACGAATATGTAAATCG
1 CAACACAAATAGGTAAATCC
57365 CAACACA
1 CAACACA
57372 GAAGTCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.15
Consensus pattern (20 bp):
CAACACAAATAGGTAAATCC
Found at i:57573 original size:20 final size:20
Alignment explanation
Indices: 57548--57619 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
57538 GGAGAATTCG
57548 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* **
57568 CGTTGCGATTTACCTATTCG
1 CGTTGCGATTTACATATTAT
* * *
57588 CATTGTGAATTACATATTAT
1 CGTTGCGATTTACATATTAT
57608 CGTTGCGATTTA
1 CGTTGCGATTTA
57620 ACTATTCGCA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:57601 original size:40 final size:40
Alignment explanation
Indices: 57543--57635 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
57533 AATTTGGAGA
* * * *
57543 ATTCGCGTTGCGATTTACATATTATCGTTGCGATTTACCT
1 ATTCGCATTGTGAATTACATATTATCGTTGCGATTTAACT
57583 ATTCGCATTGTGAATTACATATTATCGTTGCGATTTAACT
1 ATTCGCATTGTGAATTACATATTATCGTTGCGATTTAACT
57623 ATTCGCATTGTGA
1 ATTCGCATTGTGA
57636 TTTAACTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (40 bp):
ATTCGCATTGTGAATTACATATTATCGTTGCGATTTAACT
Found at i:57637 original size:20 final size:20
Alignment explanation
Indices: 57574--57652 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
57564 TTATCGTTGC
*
57574 GATTTACCTATTCGCATTGT
1 GATTTAACTATTCGCATTGT
* ** * *
57594 GAATT-ACATATTATCGTTGC
1 GATTTAAC-TATTCGCATTGT
57614 GATTTAACTATTCGCATTGT
1 GATTTAACTATTCGCATTGT
*
57634 GATTTAACTATTCACATTG
1 GATTTAACTATTCGCATTG
57653 CGAATTTGAC
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.93
21 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
GATTTAACTATTCGCATTGT
Found at i:57729 original size:20 final size:21
Alignment explanation
Indices: 57682--57732 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
57672 GCGAATTTTG
*
57682 TTTTCGCAACACGATTCTTCA
1 TTTTCGCAACACGAATCTTCA
***
57703 AAATCGCAACACGAAT-TTCA
1 TTTTCGCAACACGAATCTTCA
57723 TTTTCGCAAC
1 TTTTCGCAAC
57733 GCTAATTACC
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (21 bp):
TTTTCGCAACACGAATCTTCA
Found at i:57971 original size:105 final size:105
Alignment explanation
Indices: 57824--58035 Score: 363
Period size: 105 Copynumber: 2.0 Consensus size: 105
57814 AAAATCGCAA
57824 TGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCATTGCGAAATTCGAGTTG
1 TGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCATTGCGAAATTCGAGTTG
57889 CAAATTTGGAGAATTCGAGTAT-CGATTTACATATTATCGT
66 CAAATTTGGAGAATTCGAGT-TGCGATTTACATATTATCGT
* *
57929 TGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTG
1 TGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCATTGCGAAATTCGAGTTG
* * *
57994 CAAATTTGGAGAATTTGCGTTGTGATTTACATATTATCGT
66 CAAATTTGGAGAATTCGAGTTGCGATTTACATATTATCGT
58034 TG
1 TG
58036 TGATTTACCT
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
104 1 0.01
105 100 0.99
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (105 bp):
TGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCATTGCGAAATTCGAGTTG
CAAATTTGGAGAATTCGAGTTGCGATTTACATATTATCGT
Found at i:58036 original size:20 final size:20
Alignment explanation
Indices: 58010--58058 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
58000 TGGAGAATTT
58010 GCGTTGTGATTTACATATTA
1 GCGTTGTGATTTACATATTA
* * *
58030 TCGTTGTGATTTACCTATTC
1 GCGTTGTGATTTACATATTA
58050 GCGTTGTGA
1 GCGTTGTGA
58059 ATTTGACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.45
Consensus pattern (20 bp):
GCGTTGTGATTTACATATTA
Found at i:74750 original size:24 final size:24
Alignment explanation
Indices: 74723--74777 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
74713 CTGCATGTAC
*
74723 TCTCACACACCCACTTAACAGTAA
1 TCTCACACACCCACTTAACAGCAA
*
74747 TCTCACACACTCACTTAACAGCAA
1 TCTCACACACCCACTTAACAGCAA
*
74771 CCTCACA
1 TCTCACA
74778 TATTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.40, G:0.04, T:0.20
Consensus pattern (24 bp):
TCTCACACACCCACTTAACAGCAA
Found at i:74967 original size:28 final size:28
Alignment explanation
Indices: 74873--74976 Score: 97
Period size: 28 Copynumber: 3.6 Consensus size: 28
74863 TATTTTCATT
*
74873 TAAGTACCTAAAGTATTTTTAGCTCAAAA
1 TAAGTACTTAAAGTATTTTTAG-TCAAAA
* *
74902 TAACTA-TATAAAGTTATATTTTAGTTAAAA
1 TAAGTACT-TAAAG-TAT-TTTTAGTCAAAA
74932 T-AGATACTTAAAGTA-TTTTATGTCAAAA
1 TAAG-TACTTAAAGTATTTTTA-GTCAAAA
*
74960 TAAGTACTTAAACTATT
1 TAAGTACTTAAAGTATT
74977 CAAACATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
27 5 0.08
28 17 0.28
29 16 0.26
30 16 0.26
31 7 0.11
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (28 bp):
TAAGTACTTAAAGTATTTTTAGTCAAAA
Found at i:75112 original size:30 final size:27
Alignment explanation
Indices: 75072--75130 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 27
75062 TTTAGGTATC
75072 TATTTCGACCAAAAATATACTTTAAGTACT
1 TATTTCGACCAAAAA-ATACTTT--GTACT
* *
75102 TATTTTGACCAAACAATACTTTGTACT
1 TATTTCGACCAAAAAATACTTTGTACT
75129 TA
1 TA
75131 AATGAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
29 7 0.26
30 13 0.48
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (27 bp):
TATTTCGACCAAAAAATACTTTGTACT
Found at i:78878 original size:20 final size:20
Alignment explanation
Indices: 78855--78892 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
78845 ATTATTATTT
78855 TATTAA-TATAATTAAAATAA
1 TATTAATTA-AATTAAAATAA
78875 TATTAATTAAATTAAAAT
1 TATTAATTAAATTAAAAT
78893 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTAATTAAATTAAAATAA
Found at i:85927 original size:43 final size:44
Alignment explanation
Indices: 85849--85963 Score: 115
Period size: 43 Copynumber: 2.6 Consensus size: 44
85839 CGATGTTATT
* ***
85849 TTCTCGTATTATGATCGTGTTTTTGCCGTCATCGTCATCG-CTG
1 TTCTCGTATTATGATCGTGTTCTTGTTATCATCGTCATCGTCTG
** * * *
85892 TTCTCGTATTATGATCGTGTTCTTGTTATTGTCGTCGTCGTTTTT
1 TTCTCGTATTATGATCGTGTTCTTGTTATCATCGTCATCG-TCTG
* *
85937 TTCTTGTATTATGATCGTGTTGTTGTT
1 TTCTCGTATTATGATCGTGTTCTTGTT
85964 GTTTTGCTTG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 33 0.56
45 26 0.44
ACGTcount: A:0.10, C:0.17, G:0.21, T:0.52
Consensus pattern (44 bp):
TTCTCGTATTATGATCGTGTTCTTGTTATCATCGTCATCGTCTG
Found at i:87421 original size:37 final size:37
Alignment explanation
Indices: 87345--87421 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
87335 TTTTTATATT
*
87345 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
87382 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
87419 TTT
1 TTT
87422 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:89209 original size:135 final size:135
Alignment explanation
Indices: 88959--89227 Score: 376
Period size: 135 Copynumber: 2.0 Consensus size: 135
88949 GATCAGCATG
*
88959 TGTTCGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAATCAGCCGCTGCT
1 TGTTCGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAGCCGCTGCT
* * ** *
89024 CTTTTTTTAGACTCAAAGCCTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCT
66 CGTTTTTCAGAAGCAAAGCCTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCA
89089 CTTCA
131 CTTCA
* * * * * * * **
89094 TGTTTGATACTGAAGATGTTCAAGACGGCAAGAGATGGTCCTCTCAGCCACAACCATCTTCTGCT
1 TGTTCGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAGCCGCTGCT
* * *
89159 CGTTTTTCAGAAGCGAAGCCTTTGTATAGAACTTCATCATATCCCTAGCAGCAACCAGATCCTCA
66 CGTTTTTCAGAAGCAAAGCCTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCA
89224 CTTC
131 CTTC
89228 TGAAGGGAAC
Statistics
Matches: 116, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
135 116 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (135 bp):
TGTTCGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAGCCGCTGCT
CGTTTTTCAGAAGCAAAGCCTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCA
CTTCA
Found at i:95980 original size:22 final size:21
Alignment explanation
Indices: 95955--96014 Score: 50
Period size: 22 Copynumber: 2.7 Consensus size: 21
95945 ATAAAATATG
95955 CAAAGGAAAAAAAACGAAAATA
1 CAAAGGAAAAAAAA-GAAAATA
*
95977 CAAA-TAAAGAAAGAAGAAAATA
1 CAAAGGAAA-AAA-AAGAAAATA
*
95999 TAAATGGATAAAAAAA
1 CAAA-GGA-AAAAAAA
96015 ATACACATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
21 3 0.10
22 17 0.57
23 4 0.13
24 4 0.13
25 2 0.07
ACGTcount: A:0.72, C:0.05, G:0.13, T:0.10
Consensus pattern (21 bp):
CAAAGGAAAAAAAAGAAAATA
Found at i:96017 original size:19 final size:19
Alignment explanation
Indices: 95993--96040 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
95983 AAGAAAGAAG
*
95993 AAAATATAAATGGATAAAA-
1 AAAATATAAAT-AATAAAAT
* *
96012 AAAATACACATAATAAAAT
1 AAAATATAAATAATAAAAT
96031 AAAATATAAA
1 AAAATATAAA
96041 ACAATGAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAATATAAATAATAAAAT
Found at i:96140 original size:14 final size:14
Alignment explanation
Indices: 96123--96149 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
96113 AAAAATAGTA
96123 ATGAAATAATAATG
1 ATGAAATAATAATG
96137 ATGAAATAATAAT
1 ATGAAATAATAAT
96150 AAAATATATA
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:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
ATGAAATAATAATG
Found at i:96276 original size:22 final size:20
Alignment explanation
Indices: 96243--96299 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
96233 ACATATACGT
96243 ATATAATA-ATAAAAAATATA
1 ATATAATAGATAAAAAA-ATA
*
96263 ATATAATAGCATAAATAAATA
1 ATATAATAG-ATAAAAAAATA
96284 ATAATAATAG-TAAAAA
1 AT-ATAATAGATAAAAA
96300 GTAAAAGGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 13 0.41
21 5 0.16
22 14 0.44
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (20 bp):
ATATAATAGATAAAAAAATA
Found at i:98564 original size:105 final size:105
Alignment explanation
Indices: 98235--98904 Score: 1288
Period size: 105 Copynumber: 6.4 Consensus size: 105
98225 GTATTGTTCC
98235 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
98300 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
98340 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
98404 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
98444 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
98509 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
98549 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
98614 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
98654 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
98719 CAGCGGTCCCTTCGTCGCGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
98759 GAGTCCAATATCCTTCGTTGTGAAATTGAATTTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
98824 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
98864 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
98905 GTAAAACCTG
Statistics
Matches: 554, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
104 103 0.19
105 451 0.81
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:99725 original size:14 final size:13
Alignment explanation
Indices: 99715--99761 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
99705 CGTTTTTCTC
99715 TTTTTGTTTTTTTG
1 TTTTTG-TTTTTTG
99729 TTTTTG-TTTTTG
1 TTTTTGTTTTTTG
99741 TTTTTG-TTTTTG
1 TTTTTGTTTTTTG
99753 TTTTT-TTTT
1 TTTTTGTTTT
99762 CGACTTAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 26 0.81
14 6 0.19
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:99732 original size:6 final size:6
Alignment explanation
Indices: 99723--99761 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
99713 TCTTTTTGTT
99723 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT- TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
99762 CGACTTAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTTG
Done.