Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004699.1 Hibiscus syriacus cultivar Beakdansim tig00010559_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: 104705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1618 original size:105 final size:106
Alignment explanation
Indices: 1504--1954 Score: 672
Period size: 105 Copynumber: 4.3 Consensus size: 106
1494 TCGTGTCTCC
1504 CTATTTCTTCAGGGAGTAGAACT-GAAACAATAATCTTCCTACGGGTCCGCTCTCT-TTTCTTCA
1 CTATTTCTTCAGGGAGTAGAACTCG-AACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
1567 -GGAGTAAGAACCTCG-ACAATAATCTTCCTACGGGTCCGCTCT
65 GGGAGTAAGAA-CTCGAACAATAATCTTCCTACGGGTCCGC-CT
*
1609 CTATTTCTTCA-GGAGTAGAACTCGAAGAATAATCTTCCTACGGGT-CGCTCTCTATTTCTTCAG
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
*
1672 GGAGTAAGAACTCGAACAATAATCTTCCTACGAGTCCGCTCT
66 GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGC-CT
* *
1714 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGACCGCTCTCTTTTTTTCTTC
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTC--TATTTCTTC
*
1779 -GGGACTAAGAACTCGAACAATAATCTTCCTACGGGTCCG-CT
64 AGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCCT
* * *
1820 CTATTTCTTCAGGGAGTAGAACTCAAACAATATTCTTCCTACGGG-CTCTCTCTCTATTTCTTCA
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCTATTTCTTCA
*
1884 GGGAGTAAGAACTCGAACAATAATCTTCCTAC-GGTCCACC-
65 GGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCCT
*
1924 ATATTTCTTCAGGGAGTAGAACTCGAACAAT
1 CTATTTCTTCAGGGAGTAGAACTCGAACAAT
1955 CTTCTGTTGC
Statistics
Matches: 320, Mismatches: 15, Indels: 23
0.89 0.04 0.06
Matches are distributed among these distances:
103 8 0.03
104 85 0.27
105 92 0.29
106 83 0.26
107 7 0.02
108 37 0.12
109 8 0.03
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (106 bp):
CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCCT
Found at i:1703 original size:53 final size:52
Alignment explanation
Indices: 1504--1954 Score: 616
Period size: 53 Copynumber: 8.6 Consensus size: 52
1494 TCGTGTCTCC
1504 CTATTTCTTCAGGGAGTAGAACT-GAAACAATAATCTTCCTACGGGTCCGCTCT
1 CTATTTCTTCAGGGAGTAGAACTCG-AACAATAATCTTCCTACGGGT-CGCTCT
1557 CT-TTTCTTCA-GGAGTAAGAACCTCG-ACAATAATCTTCCTACGGGTCCGCTCT
1 CTATTTCTTCAGGGAGT-AGAA-CTCGAACAATAATCTTCCTACGGGT-CGCTCT
*
1609 CTATTTCTTCA-GGAGTAGAACTCGAAGAATAATCTTCCTACGGGTCGCTCT
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCGCTCT
*
1660 CTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGAGTCCGCTCT
1 CTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGT-CGCTCT
*
1714 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGACCGCTCT
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGG-TCGCTCT
* * *
1767 CTTTTTTTCTTC-GGGACTAAGAACTCGAACAATAATCTTCCTACGGGTC-CGCT
1 C--TATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCGCTCT
* * *
1820 CTATTTCTTCAGGGAGTAGAACTCAAACAATATTCTTCCTACGGGCTCTCTCT
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGG-TCGCTCT
*
1873 CTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTAC-GGTC-CAC-
1 CTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCGCTCT
1923 CATATTTCTTCAGGGAGTAGAACTCGAACAAT
1 C-TATTTCTTCAGGGAGTAGAACTCGAACAAT
1955 CTTCTGTTGC
Statistics
Matches: 364, Mismatches: 17, Indels: 37
0.87 0.04 0.09
Matches are distributed among these distances:
50 15 0.04
51 78 0.21
52 78 0.21
53 104 0.29
54 53 0.15
55 36 0.10
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (52 bp):
CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCGCTCT
Found at i:1888 original size:213 final size:206
Alignment explanation
Indices: 1502--1954 Score: 705
Period size: 213 Copynumber: 2.2 Consensus size: 206
1492 AATCGTGTCT
*
1502 CCCTATTTCTTCAGGGAGTAGAACT-GAAACAATAATCTTCCTACGGGTCCGCTCTCTTTTCTTC
1 CCCTATTTCTTCAGGGAGTAGAACTCG-AACAATAATCTTCCTACGGGACCGCTCTCTTTTCTTC
*
1566 AGGAGTAAGAACCTCGACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGAGTAGAACT
65 AGGACTAAGAACCTCGACAATAATCTTCCTACGGGTCCGC-CTCTATTTCTTCAGGAGTAGAACT
* *
1631 CGAAGAATAATCTTCCTACGGGTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATC
129 CAAACAATAATCTTCCTACGGGTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATC
*
1696 TTCCTACGAGTCCG
194 TTCCTACG-GTCCA
1710 CTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGACCGCTCTCTTTTTTT
1 C-C-CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGACCGCTCTC---TTTT
*
1775 CTTCGGGACTAAGAA-CTCGAACAATAATCTTCCTACGGGTCCG-CTCTATTTCTTCAGGGAGTA
61 CTTCAGGACTAAGAACCTCG-ACAATAATCTTCCTACGGGTCCGCCTCTATTTCTTCA-GGAGTA
* *
1838 GAACTCAAACAATATTCTTCCTACGGGCTCTCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACA
124 GAACTCAAACAATAATCTTCCTACGGG-TCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACA
1903 ATAATCTTCCTACGGTCCA
188 ATAATCTTCCTACGGTCCA
*
1922 CCATATTTCTTCAGGGAGTAGAACTCGAACAAT
1 CCCTATTTCTTCAGGGAGTAGAACTCGAACAAT
1955 CTTCTGTTGC
Statistics
Matches: 227, Mismatches: 9, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
208 1 0.00
209 1 0.00
210 81 0.36
211 15 0.07
212 39 0.17
213 90 0.40
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (206 bp):
CCCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGACCGCTCTCTTTTCTTCA
GGACTAAGAACCTCGACAATAATCTTCCTACGGGTCCGCCTCTATTTCTTCAGGAGTAGAACTCA
AACAATAATCTTCCTACGGGTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTT
CCTACGGTCCA
Found at i:3312 original size:24 final size:24
Alignment explanation
Indices: 3285--3393 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
3275 ATTTGTTTTG
3285 TTTTTTTTTTTTTTTTTTTCATTT
1 TTTTTTTTTTTTTTTTTTTCATTT
3309 TTTTTTTCATTTTTTTTTTTTCATTT
1 TTTTTTT--TTTTTTTTTTTTCATTT
* **
3335 TTTTCATTTTTTCATTTTTTCA-TT
1 TTTT-TTTTTTTTTTTTTTTCATTT
** **
3359 TTTTCATTTTTTCATTTTTCATTT
1 TTTTTTTTTTTTTTTTTTTCATTT
*
3383 TTTTTCTTTTT
1 TTTTTTTTTTT
3394 CATCTTCAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
23 12 0.17
24 24 0.34
25 12 0.17
26 21 0.30
27 2 0.03
ACGTcount: A:0.08, C:0.09, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTTTTTCATTT
Found at i:3321 original size:23 final size:21
Alignment explanation
Indices: 3285--3396 Score: 84
Period size: 23 Copynumber: 5.0 Consensus size: 21
3275 ATTTGTTTTG
3285 TTTTTTTTTTTTTTTTTTTCAT
1 TTTT-TTTTTTTTTTTTTTCAT
3307 TTTTTTTTTCATTTTTTTTT--T
1 TTTTTTTTT--TTTTTTTTTCAT
* **
3328 TTCATTTTTTTCATTTTTTCAT
1 TT-TTTTTTTTTTTTTTTTCAT
*
3350 TTTTTCATTTTTTCATTTTTTCAT
1 TTTTT--TTTTTT-TTTTTTTCAT
*
3374 TTTTCATTTTTTTTCTTTTTCAT
1 TTTT--TTTTTTTTTTTTTTCAT
3397 CTTCAAGCAA
Statistics
Matches: 73, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
20 7 0.10
21 10 0.14
22 13 0.18
23 22 0.30
24 20 0.27
26 1 0.01
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTTTTCAT
Found at i:3335 original size:8 final size:8
Alignment explanation
Indices: 3310--3385 Score: 122
Period size: 8 Copynumber: 9.8 Consensus size: 8
3300 TTTTCATTTT
3310 TTTTTTCA
1 TTTTTTCA
3318 TTTTTT--
1 TTTTTTCA
3324 TTTTTTCA
1 TTTTTTCA
3332 TTTTTTTCA
1 -TTTTTTCA
3341 TTTTTTCA
1 TTTTTTCA
3349 TTTTTTCA
1 TTTTTTCA
3357 TTTTTTCA
1 TTTTTTCA
3365 TTTTTTCA
1 TTTTTTCA
3373 -TTTTTCA
1 TTTTTTCA
3380 TTTTTT
1 TTTTTT
3386 TTCTTTTTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.09
7 7 0.11
8 43 0.67
9 8 0.12
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3337 original size:16 final size:16
Alignment explanation
Indices: 3285--3396 Score: 106
Period size: 16 Copynumber: 7.1 Consensus size: 16
3275 ATTTGTTTTG
*
3285 TTTTTTTTTTTTTT-T
1 TTTTTTTTTTTTTTCA
3300 TTTTCATTTTTTTTTTCA
1 TTTT--TTTTTTTTTTCA
3318 --TTTTTTTTTTTTCA
1 TTTTTTTTTTTTTTCA
*
3332 TTTTTTTCATTTTTTCA
1 TTTTTTT-TTTTTTTCA
**
3349 TTTTTTCATTTTTTCA
1 TTTTTTTTTTTTTTCA
**
3365 -TTTTTTCATTTTTCA
1 TTTTTTTTTTTTTTCA
*
3380 TTTTTTTTCTTTTTCA
1 TTTTTTTTTTTTTTCA
3396 T
1 T
3397 CTTCAAGCAA
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
14 12 0.15
15 16 0.20
16 30 0.37
17 24 0.29
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTTTTTTCA
Found at i:3346 original size:1 final size:1
Alignment explanation
Indices: 3280--3329 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
3270 CTTTTATTTG
* ** **
3280 TTTTGTTTTTTTTTTTTTTTTTTTCATTTTTTTTTTCATTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3330 CATTTTTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.04, C:0.04, G:0.02, T:0.90
Consensus pattern (1 bp):
T
Found at i:3392 original size:8 final size:8
Alignment explanation
Indices: 3285--3393 Score: 82
Period size: 8 Copynumber: 13.4 Consensus size: 8
3275 ATTTGTTTTG
3285 TTTTT-TT
1 TTTTTCTT
3292 TTTTT-TT
1 TTTTTCTT
3299 TTTTTCATT
1 TTTTTC-TT
3308 TTTTT-TT
1 TTTTTCTT
*
3315 TCATTTTTTT
1 T--TTTTCTT
3325 TTTTTCATT
1 TTTTTC-TT
*
3334 TTTTTCAT
1 TTTTTCTT
*
3342 TTTTTCAT
1 TTTTTCTT
*
3350 TTTTTCAT
1 TTTTTCTT
*
3358 TTTTTCAT
1 TTTTTCTT
*
3366 TTTTTC-A
1 TTTTTCTT
3373 TTTTTCATTT
1 TTTTTC--TT
3383 TTTTTCTT
1 TTTTTCTT
3391 TTT
1 TTT
3394 CATCTTCAAG
Statistics
Matches: 89, Mismatches: 4, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
7 21 0.24
8 40 0.45
9 19 0.21
10 9 0.10
ACGTcount: A:0.08, C:0.09, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:9448 original size:6 final size:6
Alignment explanation
Indices: 9437--9480 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
9427 AATTAAAGCG
***
9437 ATGCAA ATGCAA ATGCAA ATGTGG ATGCAAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGC-AA ATGCAA ATGCAA A
9481 AGGTGTTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:20836 original size:23 final size:23
Alignment explanation
Indices: 20793--20836 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
20783 ATATAATTTA
*
20793 AATAATTTTTTTATATTTTTATT
1 AATAATTTTTTTATACTTTTATT
20816 AATAATTTATTTTAT-CTTTTA
1 AATAATTT-TTTTATACTTTTA
20837 AATGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
AATAATTTTTTTATACTTTTATT
Found at i:21710 original size:26 final size:25
Alignment explanation
Indices: 21683--21784 Score: 78
Period size: 27 Copynumber: 3.8 Consensus size: 25
21673 ATATATCAAC
*
21683 TTTAAGAAATATTTTTTTATATTTACT
1 TTTAA-AAATATTTTTTTATATTTA-A
* *
21710 TATTAAATATATTTTATTATTAATTTAA
1 T-TTAAAAATATTTTTTTA-T-ATTTAA
*
21738 TTTAAAAATATTTTATTTTTATTTAAA
1 TTTAAAAATATTTT-TTTATATTT-AA
* *
21765 TTTAGAAATATATATTTTAT
1 TTTAAAAATAT-TTTTTTAT
21785 TATTATCTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
26 4 0.07
27 41 0.68
28 10 0.17
29 5 0.08
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTAAAAATATTTTTTTATATTTAA
Found at i:21722 original size:17 final size:17
Alignment explanation
Indices: 21700--21732 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21690 AATATTTTTT
21700 TATA-TTTACTTATTAAA
1 TATATTTTA-TTATTAAA
21717 TATATTTTATTATTAA
1 TATATTTTATTATTAA
21733 TTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATTATTAAA
Found at i:21817 original size:31 final size:31
Alignment explanation
Indices: 21714--21847 Score: 134
Period size: 31 Copynumber: 4.4 Consensus size: 31
21704 TTTACTTATT
21714 AAATATATTTTATTATTAATTT-AA-TTT--A
1 AAATATATTTTATTATT-ATTTAAATTTTCAA
* **
21742 AAA-ATATTTTATTTTTATTTAAATTTAGAA
1 AAATATATTTTATTATTATTTAAATTTTCAA
* *
21772 ATATATATTTTATTATTATCTAAATTTTCAA
1 AAATATATTTTATTATTATTTAAATTTTCAA
* *
21803 AAATATATTTTATTAATATTTCAACTTTTCAA
1 AAATATATTTTATTATTATTT-AAATTTTCAA
*
21835 AGTATATATTTTA
1 A-AATATATTTTA
21848 ATTTACTAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
26 4 0.05
27 14 0.16
28 5 0.06
30 3 0.03
31 41 0.47
32 10 0.11
33 10 0.11
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (31 bp):
AAATATATTTTATTATTATTTAAATTTTCAA
Found at i:40622 original size:34 final size:33
Alignment explanation
Indices: 40552--40624 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
40542 GGGTGTGCAG
*
40552 AATTATAATTGCATGCACGTGATTTTGGGAGGC
1 AATTATAATTGCATGCACGTGATTTTGGGAGAC
40585 AATTATAATTGCATGCACGTGATTTTTGGGCA-AC
1 AATTATAATTGCATGCACGTGA-TTTTGGG-AGAC
40619 AATTAT
1 AATTAT
40625 TGGGGTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
33 22 0.59
34 14 0.38
35 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (33 bp):
AATTATAATTGCATGCACGTGATTTTGGGAGAC
Found at i:40745 original size:4 final size:4
Alignment explanation
Indices: 40736--40884 Score: 204
Period size: 4 Copynumber: 39.0 Consensus size: 4
40726 AAGGACAAGA
40736 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG G-AG GAAG GAAG
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG
* * * *
40783 GAAG GAAG GAAG G-AG GAGG GAAG GAAG G-AG GAGG GAAG GAAT GAGG
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG
*
40829 GAAG GAAG GAAG GAAG GGAG GAAG GAA- GAAG GAA- GAAG GAA- GAAG
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG
40874 GAA- GAAG GAAG
1 GAAG GAAG GAAG
40885 AAAAATCATA
Statistics
Matches: 128, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
3 21 0.16
4 107 0.84
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.01
Consensus pattern (4 bp):
GAAG
Found at i:42103 original size:37 final size:37
Alignment explanation
Indices: 42062--42140 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
42052 ATTAAAATAA
* * ** *
42062 AAATAAACATATATAAGTGTTCAAGTACAAATAGTTC
1 AAATAAACAGATACAAACGTTCAAGTACAAATAATTC
* *
42099 AAATAGACAGATACAAACGTTTAAGTACAAATAATTC
1 AAATAAACAGATACAAACGTTCAAGTACAAATAATTC
42136 AAATA
1 AAATA
42141 TCAAAATATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (37 bp):
AAATAAACAGATACAAACGTTCAAGTACAAATAATTC
Found at i:48552 original size:16 final size:16
Alignment explanation
Indices: 48531--48563 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
48521 GACCGATGGT
48531 TGAGTATCGATACTCA
1 TGAGTATCGATACTCA
*
48547 TGAGTATCGATTCTCA
1 TGAGTATCGATACTCA
48563 T
1 T
48564 TTAAACAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (16 bp):
TGAGTATCGATACTCA
Found at i:55280 original size:15 final size:16
Alignment explanation
Indices: 55260--55295 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
55250 TTATATTTGA
55260 ATAA-TTGAATCGAAT
1 ATAATTTGAATCGAAT
55275 ATAATTTTGAATCGAAT
1 ATAA-TTTGAATCGAAT
55292 ATAA
1 ATAA
55296 AATCTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
17 15 0.79
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (16 bp):
ATAATTTGAATCGAAT
Found at i:58226 original size:31 final size:31
Alignment explanation
Indices: 58190--58330 Score: 246
Period size: 31 Copynumber: 4.5 Consensus size: 31
58180 ATTCAACATC
*
58190 CAAGTGACCAAAATTTAATAAAACAATAATG
1 CAAGTGACCAAAACTTAATAAAACAATAATG
*
58221 TAAGTGACCAAAACTTAATAAAACAATAATG
1 CAAGTGACCAAAACTTAATAAAACAATAATG
*
58252 CAAGTGATCAAAACTTAATAAAACAATAATG
1 CAAGTGACCAAAACTTAATAAAACAATAATG
*
58283 TAAGTGACCAAAACTTAATAAAACAATAATG
1 CAAGTGACCAAAACTTAATAAAACAATAATG
58314 CAAGTGACCAAAACTTA
1 CAAGTGACCAAAACTTA
58331 TGTTTTATGA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 103 1.00
ACGTcount: A:0.54, C:0.14, G:0.10, T:0.22
Consensus pattern (31 bp):
CAAGTGACCAAAACTTAATAAAACAATAATG
Found at i:59403 original size:23 final size:24
Alignment explanation
Indices: 59353--59406 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
59343 ATTTAAATCT
* * *
59353 TAAAATATTAATTGAGTTCTATTA
1 TAAAATATTAATTAAATTCTACTA
59377 -AAAATATTAATTAAATT-TACTA
1 TAAAATATTAATTAAATTCTACTA
59399 TAAAATAT
1 TAAAATAT
59407 CTATATTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
TAAAATATTAATTAAATTCTACTA
Found at i:60143 original size:13 final size:14
Alignment explanation
Indices: 60115--60147 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
60105 TAAGTATAAA
60115 TATAATTTAAATTT
1 TATAATTTAAATTT
*
60129 TATATTTTAAA-TT
1 TATAATTTAAATTT
60142 TATAAT
1 TATAAT
60148 ATAACGTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATAATTTAAATTT
Found at i:60772 original size:27 final size:27
Alignment explanation
Indices: 60739--60818 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
60729 ATTTGCTCGG
60739 CGCTTTTTGCGGCGTTTTTCCTATCGA
1 CGCTTTTTGCGGCGTTTTTCCTATCGA
* *
60766 CGTTTTTTGCGGCGTTTTTTCTATCGA
1 CGCTTTTTGCGGCGTTTTTCCTATCGA
*
60793 CGCTTTTTGCGGCGTTTTTCTTATCG
1 CGCTTTTTGCGGCGTTTTTCCTATCG
60819 CCGCAAGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.06, C:0.23, G:0.23, T:0.49
Consensus pattern (27 bp):
CGCTTTTTGCGGCGTTTTTCCTATCGA
Found at i:61037 original size:36 final size:37
Alignment explanation
Indices: 60997--61067 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
60987 CAATATTAAA
* *
60997 AAAAAAAT-TCTCACTTCTTCTCTGTTTCATAGTATT
1 AAAAAAATCACTCACTTCTTCTCTATTTCATAGTATT
*
61033 AAAAAAATCACTCATTTCTTCTCTATTTCATAGTA
1 AAAAAAATCACTCACTTCTTCTCTATTTCATAGTA
61068 GCACTACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 8 0.26
37 23 0.74
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (37 bp):
AAAAAAATCACTCACTTCTTCTCTATTTCATAGTATT
Found at i:61037 original size:37 final size:38
Alignment explanation
Indices: 60977--61067 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 38
60967 AATCACTCAA
* * *
60977 CTCTGTTTCACAATATTAAAAAAAAAAT-TCTCACTTCTT
1 CTCTGTTTCATAGTATT--AAAAAAAATCACTCACTTCTT
*
61016 CTCTGTTTCATAGTATT-AAAAAAATCACTCATTTCTT
1 CTCTGTTTCATAGTATTAAAAAAAATCACTCACTTCTT
*
61053 CTCTATTTCATAGTA
1 CTCTGTTTCATAGTA
61068 GCACTACAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 8 0.17
37 23 0.50
39 15 0.33
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (38 bp):
CTCTGTTTCATAGTATTAAAAAAAATCACTCACTTCTT
Found at i:61523 original size:28 final size:28
Alignment explanation
Indices: 61492--61549 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
61482 TATATCATTT
*
61492 AGGTGGTAAATTCTACCATATATCAACG
1 AGGTGGCAAATTCTACCATATATCAACG
61520 AGGTGGCAAATTCTACCATATATCAACG
1 AGGTGGCAAATTCTACCATATATCAACG
61548 AG
1 AG
61550 ACGGTATAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (28 bp):
AGGTGGCAAATTCTACCATATATCAACG
Found at i:62339 original size:20 final size:20
Alignment explanation
Indices: 62314--62363 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
62304 ACTTTTGAAC
62314 AATTTAAAATTAAATAATTT
1 AATTTAAAATTAAATAATTT
62334 AATTTAAAATTAAATAATTT
1 AATTTAAAATTAAATAATTT
62354 AATTTAAAAT
1 AATTTAAAAT
62364 ATTTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTAAAATTAAATAATTT
Found at i:62562 original size:14 final size:15
Alignment explanation
Indices: 62543--62571 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62533 GACAGTTGGC
62543 CTGTTTCCCA-TCTT
1 CTGTTTCCCACTCTT
62557 CTGTTTCCCACTCTT
1 CTGTTTCCCACTCTT
62572 TTGAAGGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.38, G:0.07, T:0.48
Consensus pattern (15 bp):
CTGTTTCCCACTCTT
Found at i:62714 original size:59 final size:57
Alignment explanation
Indices: 62650--62813 Score: 161
Period size: 60 Copynumber: 2.7 Consensus size: 57
62640 TCATCATACG
*
62650 TCCTTAATCTATGACTTTATTTTAAATTAGTCCCTAAATTTTTAAAAAATTCAATAT-CA
1 TCCTTAAT-TATGA-TTTATTTTAAATTAGTCCCTAAACTTTTAAAAAATTC-ATATCCA
* * *
62709 TCCTTAAATTATGATTATCATTTTAAATTAG-CCCTCAAACTTTTAAATATTTCATTTCCA
1 TCCTT-AATTATGATT-T-ATTTTAAATTAGTCCCT-AAACTTTTAAAAAATTCATATCCA
* **
62769 TCCCTAAATTATGAATCTTATACTAAATTAGTCCCTAAACTTTTA
1 T-CCTTAATTATG-AT-TTATTTTAAATTAGTCCCTAAACTTTTA
62814 GATCTTTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
58 2 0.02
59 18 0.20
60 58 0.65
61 10 0.11
62 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (57 bp):
TCCTTAATTATGATTTATTTTAAATTAGTCCCTAAACTTTTAAAAAATTCATATCCA
Found at i:62733 original size:60 final size:60
Alignment explanation
Indices: 62668--62813 Score: 170
Period size: 60 Copynumber: 2.4 Consensus size: 60
62658 CTATGACTTT
* * *
62668 ATTTTAAATTAGTCCCTAAATTTTTAAAAAATTCAATAT-CATCCTTAAATTATGATTATC
1 ATTTTAAATTAGTCCCTAAACTTTTAAAAAATTC-ATATCCATCCCTAAATTATGAATATC
* * * * *
62728 ATTTTAAATTAG-CCCTCAAACTTTTAAATATTTCATTTCCATCCCTAAATTATGAATCTT
1 ATTTTAAATTAGTCCCT-AAACTTTTAAAAAATTCATATCCATCCCTAAATTATGAATATC
**
62788 ATACTAAATTAGTCCCTAAACTTTTA
1 ATTTTAAATTAGTCCCTAAACTTTTA
62814 GATCTTTCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 7 0.10
60 62 0.85
61 4 0.05
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.42
Consensus pattern (60 bp):
ATTTTAAATTAGTCCCTAAACTTTTAAAAAATTCATATCCATCCCTAAATTATGAATATC
Found at i:63917 original size:13 final size:13
Alignment explanation
Indices: 63876--63924 Score: 73
Period size: 13 Copynumber: 3.7 Consensus size: 13
63866 TTTATTTTTA
63876 AATAATTAAAA-T
1 AATAATTAAAAGT
63888 AAATAATTAAAAGT
1 -AATAATTAAAAGT
63902 AATAATTAAAAGT
1 AATAATTAAAAGT
63915 AATAAATTAA
1 AAT-AATTAA
63925 TTTTTAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 27 0.79
14 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (13 bp):
AATAATTAAAAGT
Found at i:65735 original size:16 final size:16
Alignment explanation
Indices: 65714--65772 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
65704 CATTTAATAA
*
65714 ATAAACGAACACGAAC
1 ATAAACAAACACGAAC
65730 ATAAACAAACACGAAC
1 ATAAACAAACACGAAC
**
65746 ATAAATGAACACGAAC
1 ATAAACAAACACGAAC
65762 ATAAACAAACA
1 ATAAACAAACA
65773 GAAACGTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.61, C:0.22, G:0.08, T:0.08
Consensus pattern (16 bp):
ATAAACAAACACGAAC
Found at i:66871 original size:14 final size:14
Alignment explanation
Indices: 66854--66895 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
66844 GATTGGGTTA
* *
66854 AACATAAATGAATG
1 AACATAAACGAACG
66868 AACATAAACGAACG
1 AACATAAACGAACG
*
66882 AACATAACCGAACG
1 AACATAAACGAACG
66896 TTCACGAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.55, C:0.19, G:0.14, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:69705 original size:31 final size:31
Alignment explanation
Indices: 69667--69749 Score: 148
Period size: 31 Copynumber: 2.7 Consensus size: 31
69657 ATTTTAAAAT
69667 ATTAATAATTTAAGTACTAAAACAGATTAAA
1 ATTAATAATTTAAGTACTAAAACAGATTAAA
* *
69698 ATTAATAATTTAAGTAATAAAACATATTAAA
1 ATTAATAATTTAAGTACTAAAACAGATTAAA
69729 ATTAATAATTTAAGTACTAAA
1 ATTAATAATTTAAGTACTAAA
69750 CACGTCATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (31 bp):
ATTAATAATTTAAGTACTAAAACAGATTAAA
Found at i:70858 original size:23 final size:23
Alignment explanation
Indices: 70822--70886 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
70812 GCGAACATTA
* * *
70822 AAAGTATATATTCGTAAATGTT-
1 AAAGAATATGTTCGTAAACGTTG
* *
70844 AAATAATCATGTTCGCAAACGTTG
1 AAAGAAT-ATGTTCGTAAACGTTG
*
70868 AACGAATATGTTCGTAAAC
1 AAAGAATATGTTCGTAAAC
70887 ACAAAACGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
22 5 0.15
23 23 0.70
24 5 0.15
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (23 bp):
AAAGAATATGTTCGTAAACGTTG
Found at i:70882 original size:46 final size:46
Alignment explanation
Indices: 70795--70885 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
70785 TTAAATTAAC
* * *
70795 GTTAACTAAACATGTTCGCGAACATTAAAAGTATATATTCGTAAAT
1 GTTAAATAAACATGTTCGCAAACATTAAAAGAATATATTCGTAAAT
* * * * *
70841 GTTAAATAATCATGTTCGCAAACGTTGAACGAATATGTTCGTAAA
1 GTTAAATAAACATGTTCGCAAACATTAAAAGAATATATTCGTAAA
70886 CACAAAACGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (46 bp):
GTTAAATAAACATGTTCGCAAACATTAAAAGAATATATTCGTAAAT
Found at i:71047 original size:2 final size:2
Alignment explanation
Indices: 71040--71081 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
71030 AGTAACTTTG
71040 AT AT AT AT AT AT 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 AT AT AT AT AT AT
71082 TAAATCAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73513 original size:35 final size:35
Alignment explanation
Indices: 73443--73513 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
73433 GTTAAAAATT
* * *
73443 ATATTAATATACTAAATTAAAAGTATGACCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGACCCATAA
* * *
73478 ATATTAATAAACTAAATTAGAAGCAGGGCCTATAA
1 ATATTAATAAACTAAATTAAAAGCAGGACCCATAA
73513 A
1 A
73514 CTTATTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGCAGGACCCATAA
Found at i:79943 original size:24 final size:24
Alignment explanation
Indices: 79914--79961 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
79904 GGCAGGAATG
* *
79914 TGTTAAAAGTCTAAATTGGTAGCT
1 TGTTAAAAGTCCAAATTGGCAGCT
79938 TGTTAAAAGTCCAAATTGGCAGCT
1 TGTTAAAAGTCCAAATTGGCAGCT
79962 GCAAATTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (24 bp):
TGTTAAAAGTCCAAATTGGCAGCT
Found at i:82046 original size:22 final size:22
Alignment explanation
Indices: 82018--82061 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
82008 TCAACACGCC
82018 AAATTCTAGAGGCAAAAGTGTT
1 AAATTCTAGAGGCAAAAGTGTT
82040 AAATTCTAGAGGCAAAAGTGTT
1 AAATTCTAGAGGCAAAAGTGTT
82062 CTAGAATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (22 bp):
AAATTCTAGAGGCAAAAGTGTT
Found at i:90914 original size:258 final size:261
Alignment explanation
Indices: 90443--90923 Score: 655
Period size: 258 Copynumber: 1.9 Consensus size: 261
90433 TTTAATCAGC
* * *
90443 TCGATATCCCACATTGTCTTTTCATCCGAGAAGCTTCTTTGTTCTTTCTCTCTCTCTCTAGGCTC
1 TCGATATCCCACATTATCTTTTCATCCAAGAAGCTTCTTTGTTC-TTCTCTCTCTCTCTAGACTC
* *
90508 ATTAACCGAATTTCCTCTCTCAACAACCCAGCCTCAATCAGGAGCCTCCTCAGTCACGCTTCCAT
65 ATTAACCGAATTTCCTCTCACAACAACCCAGCCTCAATCAGGAGCCTCCTCAATCACGCTTCCAT
* * * *
90573 GATCAACCCATCATCCAAATTCGGCCTTAGGGTGTTGTCATTAATCCTCCCCAACCTCCGAATCT
130 GATCAACCCATCATCCAAATTCAGCCTTAGGGTGTTGTCATTAATCCTCCCCAACCACCAAACCT
* *
90638 CGTATCCTAGCGTAAATACAGACTCCATTATTTTTATGAATTATTCTAATGTTACTAATTTGTAT
195 CGTAGCCTAGCATAAATACAGACTCCATTATTTTTATGAATTATTCTAATGTTACTAATTTGTAT
90703 CT
260 CT
*
90705 TCGATCTCCCACATTATCTTTTCATCCAAGAAGCTTCTTTGTTC-T-T-TCTCTCTCTAGACTCA
1 TCGATATCCCACATTATCTTTTCATCCAAGAAGCTTCTTTGTTCTTCTCTCTCTCTCTAGACTCA
* * * * * *
90767 TTAACTGAATTTCCTCTCACAACAACTCAGCCTCAGTCGGGAGCCTCCTCAATCGCTCTTCCAT-
66 TTAACCGAATTTCCTCTCACAACAACCCAGCCTCAATCAGGAGCCTCCTCAATCACGCTTCCATG
** * * * * *
90831 AGTCAGTCCATCCTCTAAATTCAGCCTTGGGGTGTTGTCATTAATCCTCCCTAGCCACCAAACCT
131 A-TCAACCCATCATCCAAATTCAGCCTTAGGGTGTTGTCATTAATCCTCCCCAACCACCAAACCT
* * * *
90896 CGTAGGCTGGTATAAATACAGGCTCCAT
195 CGTAGCCTAGCATAAATACAGACTCCAT
90924 CATATTGAAG
Statistics
Matches: 189, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
257 1 0.01
258 145 0.77
259 1 0.01
260 1 0.01
262 41 0.22
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (261 bp):
TCGATATCCCACATTATCTTTTCATCCAAGAAGCTTCTTTGTTCTTCTCTCTCTCTCTAGACTCA
TTAACCGAATTTCCTCTCACAACAACCCAGCCTCAATCAGGAGCCTCCTCAATCACGCTTCCATG
ATCAACCCATCATCCAAATTCAGCCTTAGGGTGTTGTCATTAATCCTCCCCAACCACCAAACCTC
GTAGCCTAGCATAAATACAGACTCCATTATTTTTATGAATTATTCTAATGTTACTAATTTGTATC
T
Found at i:95295 original size:31 final size:31
Alignment explanation
Indices: 95260--95320 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
95250 TTATGGTTAC
95260 TTATGTTA-CTATTTTATTAAGTTTAGATCAT
1 TTATGTTATC-ATTTTATTAAGTTTAGATCAT
* *
95291 TTATGTTATCGTTTTATTAAGTTTTGATCA
1 TTATGTTATCATTTTATTAAGTTTAGATCA
95321 CTTAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (31 bp):
TTATGTTATCATTTTATTAAGTTTAGATCAT
Found at i:99413 original size:65 final size:63
Alignment explanation
Indices: 99344--99464 Score: 154
Period size: 65 Copynumber: 1.9 Consensus size: 63
99334 GGGAAGACTT
*
99344 AGTGCATCGGTACACTAGG-GGTGCATCGATGCATAAAATACATTCAATGTTTCAAATAAGCCTG
1 AGTGCATCGATACA-T-GGCGGTGCATCGATGCATAAAATACATTCAATG-TTCAAATAAGCCTG
99408 G
63 G
* * * *
99409 AGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAAT
1 AGTGCATCGATACATGG-CGGTGCATCGATGCATAAAATACATTCAATGTTCAAAT
99465 TATTTAGGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
63 2 0.04
64 8 0.16
65 39 0.80
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATACATGGCGGTGCATCGATGCATAAAATACATTCAATGTTCAAATAAGCCTGG
Found at i:99496 original size:64 final size:65
Alignment explanation
Indices: 99364--99519 Score: 183
Period size: 64 Copynumber: 2.4 Consensus size: 65
99354 TACACTAGGG
* * *
99364 GTGCATCGATGCATAAAATACATTCAATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGCTCT
* **
99429 GTGCATCGATGCATAAAATGCATTCGATG-TTCAAATTA-TTTAGGAGTGCATCGATGCATGC-C
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCT-GGAGTGCATCGATGCATGCTC
99491 TT
65 -T
* * * *
99493 GTGCAGCGGTACACAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
99520 AATTCAATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 50 0.63
65 27 0.34
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGCTCT
Found at i:99526 original size:64 final size:64
Alignment explanation
Indices: 99407--99532 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
99397 AAATAAGCCT
* * * * **
99407 GGAGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTA
1 GGAGTGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTTA
* *
99471 GGAGTGCATCGATGCATGC-CTTGTGCAGCGGTACACAAAATGCATTCGAAATTCAATTTATT
1 GGAGTGCATCGATGCATGCTC-TGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATT
99533 CAAGGGCGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 1 0.02
64 52 0.98
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
GGAGTGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTTA
Found at i:99544 original size:64 final size:64
Alignment explanation
Indices: 99407--99551 Score: 150
Period size: 64 Copynumber: 2.3 Consensus size: 64
99397 AAATAAGCCT
* * * * * ** *
99407 GGAGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTA
1 GGAGCGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTAA
* * *
99471 GGAGTGCATCGATGCATGC-CTTGTGCAGCGGTACACAAAATGCATTCGAAATTCAATTTATTCA
1 GGAGCGCATCGATGCATGCTC-TGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATT-A
99535 A
64 A
*
99536 GG-GCGCATCAATGCAT
1 GGAGCGCATCGATGCAT
99552 TATATAGTGC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 64 0.94
65 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (64 bp):
GGAGCGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTAA
Found at i:101064 original size:21 final size:21
Alignment explanation
Indices: 101038--101078 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
101028 ATTAGCGATG
*
101038 GTTTCCGAATTGATGAAAATA
1 GTTTCCAAATTGATGAAAATA
101059 GTTTCCAAATTGATGAAAAT
1 GTTTCCAAATTGATGAAAAT
101079 GACTTCTCCT
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:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
GTTTCCAAATTGATGAAAATA
Found at i:102122 original size:20 final size:21
Alignment explanation
Indices: 102093--102150 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
102083 CAAACCTGAT
*
102093 GAGTGTATCGATGCACAGT-A
1 GAGTGCATCGATGCACAGTAA
*
102113 GAGTGCATCGATGCACATTCAA
1 GAGTGCATCGATGCACAGT-AA
*
102135 GAGTGCATCGGTGCAC
1 GAGTGCATCGATGCAC
102151 CTTCAAGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 17 0.52
22 16 0.48
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (21 bp):
GAGTGCATCGATGCACAGTAA
Found at i:102140 original size:22 final size:22
Alignment explanation
Indices: 102093--102194 Score: 104
Period size: 22 Copynumber: 4.7 Consensus size: 22
102083 CAAACCTGAT
* *
102093 GAGTGTATCGATGCACAGT--A
1 GAGTGCATCGATGCACATTCAA
102113 GAGTGCATCGATGCACATTCAA
1 GAGTGCATCGATGCACATTCAA
* *
102135 GAGTGCATCGGTGCACCTTCAA
1 GAGTGCATCGATGCACATTCAA
* *
102157 G-GTGTATCGATGCATATTCAA
1 GAGTGCATCGATGCACATTCAA
102178 -AGGATGCATCGATGCAC
1 GA-G-TGCATCGATGCAC
102195 TGTCTAGTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.25
21 16 0.24
22 23 0.34
23 11 0.16
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (22 bp):
GAGTGCATCGATGCACATTCAA
Found at i:102176 original size:43 final size:43
Alignment explanation
Indices: 102099--102214 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
102089 TGATGAGTGT
* * *
102099 ATCGATGCACAGT-AGAGTGCATCGATGCACATTC-AA-GAGTGC
1 ATCGATGCACTGTCA-AGTGTATCGATGCATATTCAAAGGA-TGC
*
102141 ATCGGTGCACCT-TCAAGGTGTATCGATGCATATTCAAAGGATGC
1 ATCGATGCA-CTGTCAA-GTGTATCGATGCATATTCAAAGGATGC
*
102185 ATCGATGCACTGTCTAGTGTATCGATGCAT
1 ATCGATGCACTGTCAAGTGTATCGATGCAT
102215 TATGCACTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
42 10 0.16
43 34 0.55
44 16 0.26
45 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (43 bp):
ATCGATGCACTGTCAAGTGTATCGATGCATATTCAAAGGATGC
Done.