Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017184.1 Corchorus olitorius cultivar O-4 contig17217, 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: 40091
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1651 original size:37 final size:36
Alignment explanation
Indices: 1601--1672 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
1591 ATGTCATCAT
*
1601 GTTGACTGAGTCAAACTGCCACATCATCCTGTTGACC
1 GTTGACAGAGTCAAACTGCCACATCATCC-GTTGACC
* *
1638 GTTGACAGAGTCAACCTGCCACGTCATCCGTTGAC
1 GTTGACAGAGTCAAACTGCCACATCATCCGTTGAC
1673 AAGACAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.25
Consensus pattern (36 bp):
GTTGACAGAGTCAAACTGCCACATCATCCGTTGACC
Found at i:1685 original size:28 final size:29
Alignment explanation
Indices: 1636--1694 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
1626 ATCCTGTTGA
*
1636 CCGTTGACAGAGTCAACCTGCCACGTCAT
1 CCGTTGACAGAGACAACCTGCCACGTCAT
*
1665 CCGTTGACA-AGACAACCTGCCATGTCAT
1 CCGTTGACAGAGACAACCTGCCACGTCAT
1693 CC
1 CC
1695 TACTACGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (29 bp):
CCGTTGACAGAGACAACCTGCCACGTCAT
Found at i:1767 original size:13 final size:14
Alignment explanation
Indices: 1751--1781 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1741 ACTTTGACCA
1751 TTGAC-TTTGATAG
1 TTGACTTTTGATAG
1764 TTGACTTTTGATAG
1 TTGACTTTTGATAG
1778 TTGA
1 TTGA
1782 TCGTTGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (14 bp):
TTGACTTTTGATAG
Found at i:1947 original size:18 final size:18
Alignment explanation
Indices: 1924--2008 Score: 80
Period size: 18 Copynumber: 5.1 Consensus size: 18
1914 TATTTTATGT
1924 CTGTTTGACCTCTTGGTC
1 CTGTTTGACCTCTTGGTC
1942 CTGTTTGACC-CTTTGGTC
1 CTGTTTGACCTC-TTGGTC
1960 CTGTTT----TC-T-G-C
1 CTGTTTGACCTCTTGGTC
*
1971 CTGTTCGACCTCTTGGTC
1 CTGTTTGACCTCTTGGTC
1989 CTGTTTGACCT-TTCGGTC
1 CTGTTTGACCTCTT-GGTC
2007 CT
1 CT
2009 ATTTTATGCA
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
11 6 0.11
12 1 0.02
13 1 0.02
15 3 0.05
16 1 0.02
17 4 0.07
18 39 0.71
ACGTcount: A:0.05, C:0.29, G:0.21, T:0.45
Consensus pattern (18 bp):
CTGTTTGACCTCTTGGTC
Found at i:1975 original size:47 final size:47
Alignment explanation
Indices: 1896--2085 Score: 251
Period size: 47 Copynumber: 4.0 Consensus size: 47
1886 GAGGTTTTCT
*
1896 CTGTTTGACCTTTC-GTCCTATTTTATGTCTGTTTGACCTCTTGGTC
1 CTGTTTGACCTTTCGGTCCTATTTTATGCCTGTTTGACCTCTTGGTC
* * *
1942 CTGTTTGACCCTTT-GGTCCTGTTTTCTGCCTGTTCGACCTCTTGGTC
1 CTGTTTGA-CCTTTCGGTCCTATTTTATGCCTGTTTGACCTCTTGGTC
* *
1989 CTGTTTGACCTTTCGGTCCTATTTTATGCATGTTTTGACCCCTTGGTC
1 CTGTTTGACCTTTCGGTCCTATTTTATGCCTG-TTTGACCTCTTGGTC
* * *
2037 CTGTTTGACCTTTCGGTCCTGTTTTCTGCCTGATTGACCT-TTCGGTC
1 CTGTTTGACCTTTCGGTCCTATTTTATGCCTGTTTGACCTCTT-GGTC
2084 CT
1 CT
2086 CTTTTTTAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
46 15 0.12
47 68 0.54
48 42 0.34
ACGTcount: A:0.07, C:0.27, G:0.19, T:0.46
Consensus pattern (47 bp):
CTGTTTGACCTTTCGGTCCTATTTTATGCCTGTTTGACCTCTTGGTC
Found at i:2045 original size:18 final size:18
Alignment explanation
Indices: 2022--2060 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2012 TTATGCATGT
2022 TTTGACCCCTT-GGTCCTG
1 TTTGA-CCCTTCGGTCCTG
*
2040 TTTGACCTTTCGGTCCTG
1 TTTGACCCTTCGGTCCTG
2058 TTT
1 TTT
2061 TCTGCCTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.05, C:0.28, G:0.21, T:0.46
Consensus pattern (18 bp):
TTTGACCCTTCGGTCCTG
Found at i:2057 original size:95 final size:93
Alignment explanation
Indices: 1896--2085 Score: 289
Period size: 95 Copynumber: 2.0 Consensus size: 93
1886 GAGGTTTTCT
*
1896 CTGTTTGACCTTTCGTCCTATTTTATGTCTGTTTGACCTCTTGGTCCTGTTTGACCCTTTGGTCC
1 CTGTTTGACCTTTCGTCCTATTTTATGTCTGTTTGACCCCTTGGTCCTGTTTGACCCTTTGGTCC
1961 TGTTTTCTGCCTG-TTCGACCTCTT-GGTC
66 TGTTTTCTGCCTGATT-GACCT-TTCGGTC
1989 CTGTTTGACCTTTCGGTCCTATTTTATG-CATGTTTTGACCCCTTGGTCCTGTTTGA-CCTTTCG
1 CTGTTTGACCTTTC-GTCCTATTTTATGTC-TG-TTTGACCCCTTGGTCCTGTTTGACCCTTT-G
2052 GTCCTGTTTTCTGCCTGATTGACCTTTCGGTC
62 GTCCTGTTTTCTGCCTGATTGACCTTTCGGTC
2084 CT
1 CT
2086 CTTTTTTAGC
Statistics
Matches: 90, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
93 15 0.17
94 22 0.24
95 51 0.57
96 2 0.02
ACGTcount: A:0.07, C:0.27, G:0.19, T:0.46
Consensus pattern (93 bp):
CTGTTTGACCTTTCGTCCTATTTTATGTCTGTTTGACCCCTTGGTCCTGTTTGACCCTTTGGTCC
TGTTTTCTGCCTGATTGACCTTTCGGTC
Found at i:4399 original size:23 final size:21
Alignment explanation
Indices: 4350--4393 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4340 AAGTAGGAGG
* *
4350 CCATTTTTTTTGCCACATAGA
1 CCATTTTTTTAGCCACACAGA
4371 CCATTTTTTTAGCCACACAGA
1 CCATTTTTTTAGCCACACAGA
4392 CC
1 CC
4394 TAATTTAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.30, G:0.09, T:0.36
Consensus pattern (21 bp):
CCATTTTTTTAGCCACACAGA
Found at i:5568 original size:23 final size:20
Alignment explanation
Indices: 5550--5613 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 20
5540 GGGAAAGAAG
5550 GAGAGGAGAAAAAAAGAAAAA
1 GAGAGGA-AAAAAAAGAAAAA
5571 -AGAAGGAAAAGAAAAAGAAAAA
1 GAG-AGG-AAA-AAAAAGAAAAA
*
5593 AAGAGGAAAAAAAAGAAAAA
1 GAGAGGAAAAAAAAGAAAAA
5613 G
1 G
5614 CCATGTCAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
20 13 0.34
21 8 0.21
22 15 0.39
23 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
GAGAGGAAAAAAAAGAAAAA
Found at i:5574 original size:15 final size:15
Alignment explanation
Indices: 5556--5596 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
5546 GAAGGAGAGG
5556 AGAAAAAAAGAAAAA
1 AGAAAAAAAGAAAAA
*
5571 AGAAGGAAAAG-AAAA
1 AGAA-AAAAAGAAAAA
5586 AGAAAAAAAGA
1 AGAAAAAAAGA
5597 GGAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.23
15 12 0.55
16 5 0.23
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGAAAAA
Found at i:5605 original size:20 final size:20
Alignment explanation
Indices: 5551--5612 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
5541 GGAAAGAAGG
5551 AGAGGAGAAAAAAAG-AAAAA
1 AGAGGA-AAAAAAAGAAAAAA
5571 AGAAGGAAAAGAAAAAGAAAAAA
1 AG-AGG-AAA-AAAAAGAAAAAA
5594 AGAGGAAAAAAAAGAAAAA
1 AGAGGAAAAAAAAGAAAAA
5613 GCCATGTCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 13 0.34
21 8 0.21
22 10 0.26
23 7 0.18
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (20 bp):
AGAGGAAAAAAAAGAAAAAA
Found at i:7086 original size:28 final size:27
Alignment explanation
Indices: 7018--7091 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
7008 AGGGTCACCT
* *
7018 AGGGGCATTTTAGTCATTTGCACGTCC
1 AGGGGCATTTTGGTCATTTGCACGTCA
7045 AGGGGCATTTTGGTCATTTGTACAC-TCA
1 AGGGGCATTTTGGTCATTTG--CACGTCA
*
7073 AGGGGCATTGTGGTCATTT
1 AGGGGCATTTTGGTCATTT
7092 TAAGTTCACA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 19 0.45
28 20 0.48
29 3 0.07
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACGTCA
Found at i:7182 original size:32 final size:32
Alignment explanation
Indices: 7141--7207 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
7131 TCATTTAAAT
*
7141 TGCATTAGAAAAACCCCAAAAAAATCTTAATG
1 TGCATTAGAAAAACCCAAAAAAAATCTTAATG
7173 TGCATTAGAAAAACCCAAAAAAAATCTTAATG
1 TGCATTAGAAAAACCCAAAAAAAATCTTAATG
7205 TGC
1 TGC
7208 GCCTTTGGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.22
Consensus pattern (32 bp):
TGCATTAGAAAAACCCAAAAAAAATCTTAATG
Found at i:12311 original size:132 final size:131
Alignment explanation
Indices: 12069--12322 Score: 411
Period size: 132 Copynumber: 1.9 Consensus size: 131
12059 TTGTTTAAAC
* * * *
12069 TTTTATAGTTTTACTCAACTAAAATCTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
*
12134 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAAAACTTATATATTAGAATTTTTTTTTATAT
66 TTTTATTTTTACCATTTTACTAATTTAATT-AAAAAAACTTATATATTAGAATTTTTTTTTATAT
12199 AT
130 AT
* *
12201 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCTTTATATCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
12266 TTTTATTTTTACCATTTTACTAATTTAATT-AAAAAACTTAGATATATTAGAATTTTT
66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTT--ATATATTAGAATTTTT
12323 AAAATATATT
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
130 9 0.08
132 104 0.92
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (131 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTATATATTAGAATTTTTTTTTATATA
T
Found at i:14546 original size:42 final size:43
Alignment explanation
Indices: 14495--14588 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
14485 AGTGTATTAC
* *
14495 CTAA-ATTCTA-CTCCATCTCTAGGTAATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
14536 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
14581 CTAATATT
1 CTAATATT
14589 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:16757 original size:42 final size:42
Alignment explanation
Indices: 16706--16795 Score: 119
Period size: 45 Copynumber: 2.1 Consensus size: 42
16696 AATGCATTAC
* *
16706 CTAAATTCTA-CTTCATCTCTAGGTAGTTCATCAAAATAAAA
1 CTAAATTCTACCTTCATCTCTAGATAATTCATCAAAATAAAA
*
16747 CTAACATTCTACTCCTTCATCTCTAGATAATTCATCAAAATAAAG
1 CTAA-ATTCTA--CCTTCATCTCTAGATAATTCATCAAAATAAAA
16792 CTAA
1 CTAA
16796 TTTTTTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 4 0.10
42 6 0.14
45 32 0.76
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (42 bp):
CTAAATTCTACCTTCATCTCTAGATAATTCATCAAAATAAAA
Found at i:21187 original size:62 final size:62
Alignment explanation
Indices: 21090--21215 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
21080 CCTCTTCCTT
*
21090 CATAATGTTTAGGTTTAACCCACCATCTCCACCTTCACACACCCTAACCAAATCCAAATATG
1 CATAATGTTTAGGTTTAACCCACCATCTCCACCTTCACACAACCTAACCAAATCCAAATATG
* * *
21152 CATAATGTTTAGGTTTAACCCACCATCTCCGCCTTCACGCAACCTAACCAAATCCGAATATG
1 CATAATGTTTAGGTTTAACCCACCATCTCCACCTTCACACAACCTAACCAAATCCAAATATG
21214 CA
1 CA
21216 AGTTCATTGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.25
Consensus pattern (62 bp):
CATAATGTTTAGGTTTAACCCACCATCTCCACCTTCACACAACCTAACCAAATCCAAATATG
Found at i:24417 original size:37 final size:37
Alignment explanation
Indices: 24360--24440 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
24350 ATGAAAGGTT
* *
24360 ACTAAATTTAAAGGCGAACATATAAGGTTTTAAGTAA
1 ACTATATTTAAAGGCAAACATATAAGGTTTTAAGTAA
24397 ACTATATTTAAAGGCAAACATATAAGGTTTTAAGTAA
1 ACTATATTTAAAGGCAAACATATAAGGTTTTAAGTAA
24434 ACTATAT
1 ACTATAT
24441 AAGTGGGCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.32
Consensus pattern (37 bp):
ACTATATTTAAAGGCAAACATATAAGGTTTTAAGTAA
Found at i:24428 original size:22 final size:22
Alignment explanation
Indices: 24366--24429 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
24356 GGTTACTAAA
*
24366 TTTAAAGGCGAACATATAAGGT
1 TTTAAAGGCAAACATATAAGGT
*
24388 TTT-AA-GTAAAC-TAT-A---
1 TTTAAAGGCAAACATATAAGGT
24403 TTTAAAGGCAAACATATAAGGT
1 TTTAAAGGCAAACATATAAGGT
24425 TTTAA
1 TTTAA
24430 GTAAACTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 5 0.16
18 4 0.12
19 4 0.12
20 4 0.12
21 2 0.06
22 8 0.25
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.33
Consensus pattern (22 bp):
TTTAAAGGCAAACATATAAGGT
Found at i:24441 original size:21 final size:20
Alignment explanation
Indices: 24376--24443 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
24366 TTTAAAGGCG
24376 AACATATAAGGTTTTAAGTA
1 AACATATAAGGTTTTAAGTA
* *
24396 AAC-TAT-A--TTTAAAGGCA
1 AACATATAAGGTTTTAA-GTA
24413 AACATATAAGGTTTTAAGTA
1 AACATATAAGGTTTTAAGTA
24433 AACTATATAAG
1 AAC-ATATAAG
24444 TGGGCAAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
16 5 0.13
17 5 0.13
18 4 0.11
19 4 0.11
20 8 0.21
21 12 0.32
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.32
Consensus pattern (20 bp):
AACATATAAGGTTTTAAGTA
Found at i:30698 original size:24 final size:24
Alignment explanation
Indices: 30671--30733 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
30661 TCTCTAATTT
*
30671 TGTTGGGCTTAATGCCTCTGATGC
1 TGTTGGGCTTAATGCCCCTGATGC
*
30695 TGTTGGGTTTAATGCCCCTGATGC
1 TGTTGGGCTTAATGCCCCTGATGC
***
30719 AACTGGGCTTAATGC
1 TGTTGGGCTTAATGC
30734 TCAGCATGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.35
Consensus pattern (24 bp):
TGTTGGGCTTAATGCCCCTGATGC
Found at i:33518 original size:166 final size:165
Alignment explanation
Indices: 33244--33571 Score: 439
Period size: 166 Copynumber: 2.0 Consensus size: 165
33234 TAAAAGTACG
33244 AATAATGAAAAACTTTATGTTTTCCGATTGTACACTTTTTTCAAATATATTTCTAAATTGACATT
1 AATAATGAAAAACTTTATGTTTTCCGATTGTACACTTTTTTCAAATATATTTCTAAATTGACATT
** *
33309 ATTAAAATTTCTTATTTAAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAA
66 ATTAAAATTTAGTA-TTAAAAATTAATTATAAAATTTCAATTTAGACCGAAATATAAGTTTGTAA
33374 AATTGATTTTCATTAATGAACATGCAAATTTCTACT
130 AATTGATTTTCATTAATGAACATGCAAATTTCTACT
** * ***
33410 AATAATGGGAAACTTTATGTTTTCCGATTGTAC-CTTTTTTCTTCAATTATATTTCTAAATTTTT
1 AATAATGAAAAACTTTATGTTTTCCGATTGTACAC--TTTT-TTCAAATATATTTCTAAATTGAC
**
33474 ATTATTAAAATTTAGTA-T-AATTTTATATT-TAAAAATTTCAATTTAGACCGAAATATAAGTTT
63 ATTATTAAAATTTAGTATTAAAAATTA-ATTAT-AAAATTTCAATTTAGACCGAAATATAAGTTT
* * * *
33536 GTCAAATTGGTTTTCGTTGATGAACATGCAAATTTC
126 GTAAAATTGATTTTCATTAATGAACATGCAAATTTC
33572 CTTTACTATT
Statistics
Matches: 142, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
165 7 0.05
166 97 0.68
167 4 0.03
168 34 0.24
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (165 bp):
AATAATGAAAAACTTTATGTTTTCCGATTGTACACTTTTTTCAAATATATTTCTAAATTGACATT
ATTAAAATTTAGTATTAAAAATTAATTATAAAATTTCAATTTAGACCGAAATATAAGTTTGTAAA
ATTGATTTTCATTAATGAACATGCAAATTTCTACT
Found at i:33622 original size:20 final size:20
Alignment explanation
Indices: 33585--33623 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33575 TACTATTATT
33585 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
33605 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
33624 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:33817 original size:22 final size:22
Alignment explanation
Indices: 33789--34021 Score: 127
Period size: 22 Copynumber: 10.5 Consensus size: 22
33779 TGTCTCTGTG
33789 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
33811 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
33834 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
33855 TGGTTATCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
33878 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
33899 AGGTTATCAAAATTTTAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
33921 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* ** *
33943 TCAGGTTATTAAAATTTTTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* ** *
33967 AGGTTATTGAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
33989 TGGTTATCACAATTTTAT-AGAA
1 TGGTTATCAAAATTTCATAAG-A
*
34011 AGGTTATCAAA
1 TGGTTATCAAA
34022 TAGATTATCA
Statistics
Matches: 159, Mismatches: 41, Indels: 22
0.72 0.18 0.10
Matches are distributed among these distances:
20 1 0.01
21 5 0.03
22 131 0.82
23 4 0.03
24 18 0.11
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:33892 original size:66 final size:68
Alignment explanation
Indices: 33786--34833 Score: 369
Period size: 66 Copynumber: 16.3 Consensus size: 68
33776 TCTTGTCTCT
* * * *
33786 GTGTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCC
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
33849 ATA
66 ATA
33852 GTGTGGTTATCAAAATTTCATATGGA-A-GTTATCAAAATTTCATG-GGAAGGTTATCAAAATTT
1 GTGTGGTTATCAAAATTTCATA-GGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
*
33914 TATA
65 CATA
* * * * **
33918 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTT-TTTAGGAAGGTTATTGAAATTT
1 GTGTGGTTATCAAAATTTCATAGGAT-AGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
33982 CATA
65 CATA
* * * * *
33986 GTGTGGTTATCACAATTTTATA-GAAAGGTTATC--AA----AT-A-G-A--TTATCAGAATATC
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
34039 ATA
66 ATA
* * * * * *
34042 GCGAGGTTAT-AAGAATTTTATAGTG-T-GGTTAACAAAATTTCATAAGG-AGGTTA-CTAATAT
1 GTGTGGTTATCAA-AATTTCATAG-GATAGGTTATCAAAATTTCATGAGGAAGGTTATC-AAAAT
34102 TTCATA
63 TTCATA
* * * * * * *
34108 G-GAAGTTTATCAAAATTTCATAGTG-T-GGTTATTAAAATTT-TTTAGTG-TGGTTATCAAATT
1 GTG-TGGTTATCAAAATTTCATAG-GATAGGTTATCAAAATTTCATGAG-GAAGGTTATCAAAAT
34168 TTCATA
63 TTCATA
* * *** * * *
34174 -TGAAGGTTAT-AAAAGTCTTAATTTCATAAGGAGTACCAAAATTTGAT-A-GAAGGTTATC-AA
1 GTG-TGGTTATCAAAA-T-TTCATAGGAT-AGG-TTATCAAAATTTCATGAGGAAGGTTATCAAA
*
34234 ATCTCATA
61 ATTTCATA
* * * * * * *
34242 GAGTGATTATCGAAATTTCATAGAGATCGAATTATCAAAATTT-AT-AAGAAGATTATCAAAATT
1 GTGTGGTTATCAAAATTTCATAG-GATAG-GTTATCAAAATTTCATGAGGAAGGTTATCAAAATT
34305 TCATA
64 TCATA
* * * * ** *
34310 GTGTTGTTATCAAAATTTCAAAGCG--AGGTTATCAAAATTAT-ATAATGAA-AATATCAAACTT
1 GTGTGGTTATCAAAATTTCATAG-GATAGGTTATCAAAATT-TCATGAGGAAGGTTATCAAAATT
34371 TCATA
64 TCATA
* * * * * * *
34376 GAGGGGTCAACAAAATTTTATA-GATAGATTATCAAAATTTTAT-A--AAGGTTAT-AAAATTTT
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAA-TTT
*
34436 CAAA
65 CATA
* * ** * *
34440 ATGTGATTGCCGAAATTTCATA-G-T-GG---T----ATTT-ATGGGGAA-GTTATCAAAATTTC
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
34493 ATA
66 ATA
* * * * * *
34496 GTATGGTTA-CCAAA--T--TAGGA-AGGTTATTAAACTTTTACT-ATGG-A-GTAATCAAAATT
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCA-TGA-GGAAGGTTATCAAAATT
34552 TCAT-
64 TCATA
* * * ** *
34556 G-GAGGATATCAAAATTTCATATGA-AGGTTATCAAAATTTCAT-AGTTTA-GTTTTCAAAATTT
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAG-GAAGGTTATCAAAATTT
34617 CATAA
65 CAT-A
* * * * * *
34622 GAG-GGTTATCAAAATTTCATA-G-TATGTAGATCAAAATTTCAT-AGGGAGATTAACAAAATTT
1 GTGTGGTTATCAAAATTTCATAGGATAGGT-TATCAAAATTTCATGAGGAAGGTTATCAAAATTT
34683 CATA
65 CATA
* * ** * * * *
34687 ATGAGGTTATCAAAAAATCATA-GAGAGGTTATC-AAACTT--T---GTA-GTTATCAAGATTTC
1 GTGTGGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
34744 ATAA
66 AT-A
* * * * * *
34748 G-GAGGTTATCAAAATTTTATAAGG--AGGTTTATTAAAATTTTAT-AGCAAGGTTATCATAATT
1 GTGTGGTTATCAAAATTTCAT-AGGATAGG-TTATCAAAATTTCATGAGGAAGGTTATCAAAATT
34809 TCATA
64 TCATA
*
34814 GTGTGATTATCAAAATTTCA
1 GTGTGGTTATCAAAATTTCA
34834 GAGTGTGATT
Statistics
Matches: 740, Mismatches: 152, Indels: 179
0.69 0.14 0.17
Matches are distributed among these distances:
51 2 0.00
52 1 0.00
53 3 0.00
54 2 0.00
55 9 0.01
56 52 0.07
57 6 0.01
58 4 0.01
59 6 0.01
60 41 0.06
61 26 0.04
62 14 0.02
63 10 0.01
64 62 0.08
65 39 0.05
66 269 0.36
67 75 0.10
68 95 0.13
69 13 0.02
70 10 0.01
71 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (68 bp):
GTGTGGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
ATA
Found at i:34014 original size:44 final size:45
Alignment explanation
Indices: 33790--34831 Score: 261
Period size: 44 Copynumber: 23.8 Consensus size: 45
33780 GTCTCTGTGT
* * * *
33790 GGTTATCAAAATTTCATA-AGATGGTTATTATAATTTCATGAGG-A
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTAT-AGGAA
* *
33834 GGTTATCAAAATTCCATAGTG-TGGTTATCAAAATTTCATATGGAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATA-GGAA
* * *
33879 -GTTATCAAAATTTCAT-GGGAAGGTTATCAAAATTTTATAGTG-T
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAG-GAA
* * *
33922 GGTTACCAAAATTTCATAG-GATCAGGTTATTAAAATTTTTTAGGAA
1 GGTTATCAAAATTTCATAGTGAT--GGTTATCAAAATTTTATAGGAA
** * *
33968 GGTTATTGAAATTTCATAGTG-TGGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAGGAA
* * *
34012 GGTTATC--AA----ATA--GA---TTATCAGAATATCATAGCG-A
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAG-GAA
* * *
34046 GGTTAT-AAGAATTTTATAGTG-TGGTTAACAAAATTTCATAAGG-A
1 GGTTATCAA-AATTTCATAGTGATGGTTATCAAAATTTTAT-AGGAA
* * * * *
34090 GGTTA-CTAATATTTCATAG-GAAGTTTATCAAAATTTCATAGTG-T
1 GGTTATC-AAAATTTCATAGTGATGGTTATCAAAATTTTATAG-GAA
* ** *
34134 GGTTATTAAAATTTTTTAGTG-TGGTTATC-AAATTTTCATATGAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTT-ATAGGAA
* * * * * *
34178 GGTTAT-AAAAGTCTTAAT-TTCATAAGGAGTACCAAAATTTGATA-GAA
1 GGTTATCAAAA-T-TTCATAGTGAT--GG-TTATCAAAATTTTATAGGAA
* * * * * *
34225 GGTTATC-AAATCTCATAGAG-TGATTATCGAAATTTCATAGAGATC
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAG-GA-A
* * * * * *
34270 GAATTATCAAAATTT-ATA-AGAAGATTATCAAAATTTCATAGTG-T
1 G-GTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAG-GAA
* * * * *
34314 TGTTATCAAAATTTCAAAGCGA-GGTTATCAAAATTATATAATGAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTAT-AGGAA
** * * * * *
34359 -AATATCAAACTTTCATAGAG-GGGTCAACAAAATTTTATA-GATA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAGGA-A
* * *
34402 GATTATCAAAATTT--TA-TAAAGGTTAT-AAAATTTTCA-A--AA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTT-ATAGGAA
** * * * *
34441 TGTGATTGCCGAAATTTCATAGTGGTATTTATGGGGAAGTTATCAAAATTTCATAGTAT
1 -G-G-TTATCAAAATTTCATAGT-G-----AT---G--GTTATCAAAATTTTATAGGAA
* * * *
34500 GGTTA-CCAAA--T--TAG-GAAGGTTATTAAACTTTTACTATGG-A
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTA-TA-GGAA
* * * *
34540 -GTAATCAAAATTTCAT-G-GA-GGATATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAGGAA
* * * * * *
34581 GGTTATCAAAATTTCATAGT-TTAGTTTTCAAAATTTCATAAGAG
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAGGAA
* * *
34625 GGTTATCAAAATTTCATAGT-AT-GTAGATCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGATGGT-TATCAAAATTTTATAGGAA
* * * ** *
34669 GATTAACAAAATTTCATAATGA-GGTTATCAAAAAATCATA-GAGA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAGGA-A
* * *
34713 GGTTATC-AAACTT--T-GT-A--GTTATCAAGATTTCATAAGG-A
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTAT-AGGAA
* * *
34751 GGTTATCAAAATTTTATAAG-GA-GGTTTATTAAAATTTTATAGCAA
1 GGTTATCAAAATTTCAT-AGTGATGG-TTATCAAAATTTTATAGGAA
* *
34796 GGTTATCATAATTTCATAGTG-TGATTATCAAAATTT
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTT
34832 CAGAGTGTGA
Statistics
Matches: 739, Mismatches: 151, Indels: 216
0.67 0.14 0.20
Matches are distributed among these distances:
34 21 0.03
36 3 0.00
38 24 0.03
39 23 0.03
40 14 0.02
41 16 0.02
42 61 0.08
43 47 0.06
44 349 0.47
45 57 0.08
46 62 0.08
47 20 0.03
48 6 0.01
49 7 0.01
51 4 0.01
53 1 0.00
54 1 0.00
55 4 0.01
56 8 0.01
57 9 0.01
58 1 0.00
59 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTTATAGGAA
Found at i:34071 original size:22 final size:21
Alignment explanation
Indices: 34037--34187 Score: 92
Period size: 22 Copynumber: 6.9 Consensus size: 21
34027 TATCAGAATA
* *
34037 TCATAGCGAGGTTATAAGAATT
1 TCATAGTGTGGTTATAA-AATT
* *
34059 TTATAGTGTGGTTAACAAAATT
1 TCATAGTGTGGTT-ATAAAATT
* *
34081 TCATAAG-GAGGTTACTAATATT
1 TCAT-AGTGTGGTTA-TAAAATT
* *
34103 TCATAG-GAAGTTTATCAAAATT
1 TCATAGTG-TGGTTAT-AAAATT
34125 TCATAGTGTGGTTATTAAAATT
1 TCATAGTGTGGTTA-TAAAATT
** *
34147 TTTTAGTGTGGTTATCAAATTT
1 TCATAGTGTGGTTAT-AAAATT
*
34169 TCATA-TGAAGGTTATAAAA
1 TCATAGTG-TGGTTATAAAA
34188 GTCTTAATTT
Statistics
Matches: 101, Mismatches: 19, Indels: 19
0.73 0.14 0.14
Matches are distributed among these distances:
21 11 0.11
22 83 0.82
23 7 0.07
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (21 bp):
TCATAGTGTGGTTATAAAATT
Found at i:34164 original size:144 final size:144
Alignment explanation
Indices: 33899--34166 Score: 360
Period size: 144 Copynumber: 1.8 Consensus size: 144
33889 TTTCATGGGA
* * **
33899 AGGTTATCAAAATTTTATAGTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTTTTA
1 AGGTTATCAAAATTTTATAGTGTGGTTAACAAAATTTCATAGGA--AGGTTACTAAAATTTCATA
** *
33964 GGAAGGTTATTGAAATTTCATAGTGTGGTTATCACAATTTTATAGAAAGGTTATCAAATAGATTA
64 GGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATAGAAAGGTTATCAAATAGATTA
34029 TCAGAATATCATAGCG
129 TCAGAATATCATAGCG
*
34045 AGGTTAT-AAGAATTTTATAGTGTGGTTAACAAAATTTCATAAGG-AGGTTACTAATATTTCATA
1 AGGTTATCAA-AATTTTATAGTGTGGTTAACAAAATTTCAT-AGGAAGGTTACTAAAATTTCATA
* * * ***
34108 GGAAGTTTATCAAAATTTCATAGTGTGGTTATTAAAATTTTTTAGTGTGGTTATCAAAT
64 GGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATAGAAAGGTTATCAAAT
34167 TTTCATATGA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
144 65 0.61
145 2 0.02
146 36 0.34
147 3 0.03
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (144 bp):
AGGTTATCAAAATTTTATAGTGTGGTTAACAAAATTTCATAGGAAGGTTACTAAAATTTCATAGG
AAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATAGAAAGGTTATCAAATAGATTATC
AGAATATCATAGCG
Found at i:34262 original size:22 final size:23
Alignment explanation
Indices: 34210--34415 Score: 114
Period size: 22 Copynumber: 9.3 Consensus size: 23
34200 TAAGGAGTAC
* *
34210 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
34231 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
34252 CGAAATTTCATAGAGATCGAATTAT
1 CAAAATTTCATAGAGAT-G-ATTAT
*
34277 CAAAATTT-ATA-AGAAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
34298 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
34320 CAAAATTTCAAAGCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
34342 CAAAATTAT-ATA-ATGA-AAATAT
1 CAAAATT-TCATAGA-GATGATTAT
* * * * *
34364 CAAACTTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* *
34386 CAAAATTTTATAGATA-GATTAT
1 CAAAATTTCATAGAGATGATTAT
34408 CAAAATTT
1 CAAAATTT
34416 TATAAAGGTT
Statistics
Matches: 141, Mismatches: 29, Indels: 29
0.71 0.15 0.15
Matches are distributed among these distances:
20 10 0.07
21 22 0.16
22 85 0.60
23 8 0.06
24 4 0.03
25 12 0.09
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:34590 original size:22 final size:22
Alignment explanation
Indices: 34543--34968 Score: 167
Period size: 22 Copynumber: 19.6 Consensus size: 22
34533 CTATGGAGTA
* *
34543 ATCAAAATTTC--ATGGAGGAT
1 ATCAAAATTTCATATGAAGGTT
34563 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
34585 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
34607 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
34629 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
34651 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
34673 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
**
34695 ATCAAAAAATCATA-GAGAGGTT
1 ATCAAAATTTCATATGA-AGGTT
* *
34717 ATC-AAA---C-TTTGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
34733 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
34755 ATCAAAATTTTATAAGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* *
34778 ATTAAAATTTTATA-GCAAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
34800 ATCATAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
34822 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
34844 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * *
34866 -TTAAAATTTTCATAACG-TGGTT
1 ATCAAAA-TTTCAT-ATGAAGGTT
* * * *
34888 ATCAATATATCATATGGAGGTA
1 ATCAAAATTTCATATGAAGGTT
* * *
34910 ATCAACATCTCATA-GTATTGGTT
1 ATCAAAATTTCATATG-A-AGGTT
34933 ATCAAAATTTCAT-TCGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
34955 ATCAAAATTTCATA
1 ATCAAAATTTCATA
34969 GTGAGGTCTT
Statistics
Matches: 310, Mismatches: 61, Indels: 67
0.71 0.14 0.15
Matches are distributed among these distances:
16 6 0.02
17 4 0.01
18 2 0.01
20 15 0.05
21 18 0.06
22 215 0.69
23 47 0.15
24 2 0.01
25 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:34959 original size:45 final size:45
Alignment explanation
Indices: 34883--34970 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
34873 TTTCATAACG
* * *
34883 TGGTTATCAATATATCATATGGAGGTAATCAACATCTCATAGTAT
1 TGGTTATCAAAATATCATATGGAAGTAATCAAAATCTCATAGTAT
* * *
34928 TGGTTATCAAAATTTCAT-TCGGAAGTTATCAAAATTTCATAGT
1 TGGTTATCAAAATATCATAT-GGAAGTAATCAAAATCTCATAGT
34971 GAGGTCTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTAATCAAAATCTCATAGTAT
Found at i:38828 original size:13 final size:13
Alignment explanation
Indices: 38810--38834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38800 TTTGCCAAAA
38810 AATAATTTTAAGC
1 AATAATTTTAAGC
38823 AATAATTTTAAG
1 AATAATTTTAAG
38835 GTGGTAAAAA
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:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AATAATTTTAAGC
Done.