Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001761.1 Hibiscus syriacus cultivar Beakdansim tig00003558_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: 73856
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4469 original size:33 final size:31
Alignment explanation
Indices: 4404--4494 Score: 114
Period size: 30 Copynumber: 2.9 Consensus size: 31
4394 CCTCAAGCTT
* *
4404 CTCACCATCATCTTCACTGACTTTAACA-TC
1 CTCACCACCATCTTCACTCACTTTAACATTC
4434 CTCACCACCATCTTCACTCACTTTAACATCTTC
1 CTCACCACCATCTTCACTCACTTTAACA--TTC
* *
4467 CTCACCACTATC-TCACTCACTTCAACAT
1 CTCACCACCATCTTCACTCACTTTAACAT
4495 GTTTCTTCTC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
30 27 0.50
32 14 0.26
33 13 0.24
ACGTcount: A:0.26, C:0.41, G:0.01, T:0.32
Consensus pattern (31 bp):
CTCACCACCATCTTCACTCACTTTAACATTC
Found at i:9947 original size:15 final size:16
Alignment explanation
Indices: 9922--10002 Score: 79
Period size: 15 Copynumber: 5.4 Consensus size: 16
9912 CGAGTTTGCC
9922 TTATT-TACTTTTACT
1 TTATTATACTTTTACT
*
9937 TTATTAT-CTTTT-TT
1 TTATTATACTTTTACT
9951 ATTATT-TACTTTTACT
1 -TTATTATACTTTTACT
9967 TTATTAT-CTTTT--T
1 TTATTATACTTTTACT
9980 ATTATT-TACTTTTACT
1 -TTATTATACTTTTACT
9996 TTATTAT
1 TTATTAT
10003 TTTGTGAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
13 2 0.04
14 12 0.22
15 35 0.65
16 5 0.09
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATACTTTTACT
Found at i:9988 original size:29 final size:30
Alignment explanation
Indices: 9922--10002 Score: 155
Period size: 29 Copynumber: 2.7 Consensus size: 30
9912 CGAGTTTGCC
9922 TTATTTACTTTTACTTTATTATCTTTTTTA
1 TTATTTACTTTTACTTTATTATCTTTTTTA
9952 TTATTTACTTTTACTTTATTATC-TTTTTA
1 TTATTTACTTTTACTTTATTATCTTTTTTA
9981 TTATTTACTTTTACTTTATTAT
1 TTATTTACTTTTACTTTATTAT
10003 TTTGTGAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 28 0.55
30 23 0.45
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (30 bp):
TTATTTACTTTTACTTTATTATCTTTTTTA
Found at i:9991 original size:14 final size:14
Alignment explanation
Indices: 9946--9992 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
9936 TTTATTATCT
9946 TTTTTATTATTTAC
1 TTTTTATTATTTAC
9960 -TTTTACTT-TATTATC
1 TTTTTA-TTAT-TTA-C
9975 TTTTTATTATTTAC
1 TTTTTATTATTTAC
9989 TTTT
1 TTTT
9993 ACTTTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.21
14 10 0.36
15 6 0.21
16 6 0.21
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTATTATTTAC
Found at i:17298 original size:19 final size:19
Alignment explanation
Indices: 17274--17310 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17264 ATGACCAACA
*
17274 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
17293 AAATCGTAACGCGATCTC
1 AAATCGCAACGCGATCTC
17311 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:17692 original size:19 final size:19
Alignment explanation
Indices: 17668--17776 Score: 110
Period size: 19 Copynumber: 5.4 Consensus size: 19
17658 TTATTTTGAA
17668 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
17687 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
17709 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
17731 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* *
17750 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
17769 ATTTTTCA
1 -TTTTTCA
17777 AAATCGCGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
19 44 0.57
20 5 0.06
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:17830 original size:21 final size:21
Alignment explanation
Indices: 17778--17838 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
17768 CATTTTTCAA
*
17778 AATCGCGTTGCGAATCT-TAC
1 AATCGCGTTGCGAATCTGGAC
* *
17798 AATCGTGTTGCGAATCTGGAT
1 AATCGCGTTGCGAATCTGGAC
* *
17819 ATTCGCGTTGCGAATTTGGA
1 AATCGCGTTGCGAATCTGGA
17839 AACTGAGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (21 bp):
AATCGCGTTGCGAATCTGGAC
Found at i:20087 original size:64 final size:64
Alignment explanation
Indices: 19982--20109 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
19972 CCATGTCAGC
*
19982 CCCCATCAGCGGCATCATTGAGATAACCCAACCTACTCTGGTTAATCCGTTCCAAAACCTCTTT
1 CCCCATCAGCGGCATCATTGAGATAACCCAACCTACCCTGGTTAATCCGTTCCAAAACCTCTTT
*
20046 CCCCATCAGCGGCATCATTGAGATAACCCAACCTACCCTGGTTAATCCGTTCCACAACCTCTTT
1 CCCCATCAGCGGCATCATTGAGATAACCCAACCTACCCTGGTTAATCCGTTCCAAAACCTCTTT
20110 TGATGTCATT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.26, C:0.36, G:0.12, T:0.26
Consensus pattern (64 bp):
CCCCATCAGCGGCATCATTGAGATAACCCAACCTACCCTGGTTAATCCGTTCCAAAACCTCTTT
Found at i:20793 original size:16 final size:16
Alignment explanation
Indices: 20768--20800 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20758 GTTACCATTT
*
20768 GTGAAGAAGAAGAAAA
1 GTGAAAAAGAAGAAAA
20784 GTGAAAAAGAAGAAAA
1 GTGAAAAAGAAGAAAA
20800 G
1 G
20801 AAGAAGAAGA
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:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (16 bp):
GTGAAAAAGAAGAAAA
Found at i:24010 original size:20 final size:20
Alignment explanation
Indices: 23985--24025 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
23975 TGTTCTTAAT
23985 ATCATCGTTATAGGACGCCA
1 ATCATCGTTATAGGACGCCA
*
24005 ATCATCGTTATAGGATGCCA
1 ATCATCGTTATAGGACGCCA
24025 A
1 A
24026 AAGTCATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCATCGTTATAGGACGCCA
Found at i:26598 original size:23 final size:25
Alignment explanation
Indices: 26572--26622 Score: 79
Period size: 23 Copynumber: 2.1 Consensus size: 25
26562 ATAATTATGA
26572 TTTTGTGTCAC-GTTTTTC-TTTTC
1 TTTTGTGTCACTGTTTTTCGTTTTC
*
26595 TTTTGTGTCACTTTTTTTCGTTTTC
1 TTTTGTGTCACTGTTTTTCGTTTTC
26620 TTT
1 TTT
26623 CTCGATCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 6 0.24
25 8 0.32
ACGTcount: A:0.04, C:0.16, G:0.12, T:0.69
Consensus pattern (25 bp):
TTTTGTGTCACTGTTTTTCGTTTTC
Found at i:27123 original size:12 final size:12
Alignment explanation
Indices: 27106--27132 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27096 AAAAACAAGC
27106 ATAAATACATAT
1 ATAAATACATAT
27118 ATAAATACATAT
1 ATAAATACATAT
27130 ATA
1 ATA
27133 TACGCATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAATACATAT
Found at i:28537 original size:18 final size:18
Alignment explanation
Indices: 28514--28548 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
28504 AGAATCACTT
28514 GGTATAAATAACATACTC
1 GGTATAAATAACATACTC
28532 GGTATAAATAACATACT
1 GGTATAAATAACATACT
28549 TCAAGGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
GGTATAAATAACATACTC
Found at i:30995 original size:2 final size:2
Alignment explanation
Indices: 30988--31072 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
30978 AGAATTTGAT
30988 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31072 T
1 T
31073 TATTATAATT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32830 original size:28 final size:30
Alignment explanation
Indices: 32765--32830 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
32755 AATTAACAAC
*
32765 CGGTGGTTTGATTGAATCAATTAAATAGTT
1 CGGTGGTCTGATTGAATCAATTAAATAGTT
* * *
32795 AGGTGGTCT-ATTGATTCAATTGAA-AGTT
1 CGGTGGTCTGATTGAATCAATTAAATAGTT
32823 CGGTGGTC
1 CGGTGGTC
32831 ACATTAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 11 0.35
29 13 0.42
30 7 0.23
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.38
Consensus pattern (30 bp):
CGGTGGTCTGATTGAATCAATTAAATAGTT
Found at i:33471 original size:21 final size:21
Alignment explanation
Indices: 33442--33511 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
33432 GAATGAAATG
*
33442 TGGAATGTCTAGTAAGGTGAT
1 TGGACTGTCTAGTAAGGTGAT
33463 TGGACTGTC---TAAGGTGAT
1 TGGACTGTCTAGTAAGGTGAT
*
33481 TGGACTCTCTAGTAAGGTGAT
1 TGGACTGTCTAGTAAGGTGAT
33502 TGGACTGTCT
1 TGGACTGTCT
33512 TCAATTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
18 17 0.40
21 26 0.60
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.34
Consensus pattern (21 bp):
TGGACTGTCTAGTAAGGTGAT
Found at i:33477 original size:18 final size:18
Alignment explanation
Indices: 33454--33511 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
33444 GAATGTCTAG
33454 TAAGGTGATTGGACTGTC
1 TAAGGTGATTGGACTGTC
*
33472 TAAGGTGATTGGACTCTC
1 TAAGGTGATTGGACTGTC
33490 TAGTAAGGTGATTGGACTGTC
1 ---TAAGGTGATTGGACTGTC
33511 T
1 T
33512 TCAATTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 18 0.51
21 17 0.49
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.34
Consensus pattern (18 bp):
TAAGGTGATTGGACTGTC
Found at i:35740 original size:32 final size:31
Alignment explanation
Indices: 35702--35778 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
35692 CGGGGTTGTG
* *
35702 GGGCCTACCTAAGAACACATCTTAGGGCCGTA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
35734 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
35765 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
35779 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:36705 original size:29 final size:29
Alignment explanation
Indices: 36668--36860 Score: 269
Period size: 29 Copynumber: 6.7 Consensus size: 29
36658 CATATTCGAA
* * *
36668 AATTACAAAAATATCATCATTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
* **
36697 AATTACAAAAATATCATTGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
36726 AATTACCAAAATATCACCGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
** *
36755 AATTACCAAAATATCACTATTTTAAAAAC
1 AATTACCAAAATATCACCGTTTTAAAAAT
36784 AATTACCAAAATATCACCGTTTTAAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
* *
36813 AATTACCAAAATATCACCTTTTTCAAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
* *
36842 ATTTACTAAAATATCACCG
1 AATTACCAAAATATCACCG
36861 GGTCGGGTCG
Statistics
Matches: 148, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 148 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATATCACCGTTTTAAAAAT
Found at i:36910 original size:18 final size:17
Alignment explanation
Indices: 36859--36906 Score: 87
Period size: 18 Copynumber: 2.8 Consensus size: 17
36849 AAAATATCAC
36859 CGGGTCGGGTCGGTCAA
1 CGGGTCGGGTCGGTCAA
36876 CGGGTCGGGTCAGGTCAA
1 CGGGTCGGGTC-GGTCAA
36894 CGGGTCGGGTCGG
1 CGGGTCGGGTCGG
36907 GTCAGACCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTCGGTCAA
Found at i:43202 original size:32 final size:31
Alignment explanation
Indices: 43164--43240 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
43154 CGGAGCCATG
* *
43164 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** **
43196 GGGCCTACCCGAGAATGATCTCAGGGCCACA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
43227 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
43241 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:44175 original size:29 final size:29
Alignment explanation
Indices: 44143--44421 Score: 318
Period size: 29 Copynumber: 9.7 Consensus size: 29
44133 AATTTTTTTT
*
44143 AAATAATTACCAAAATATCATTGTTTTAA
1 AAATAATTACCAAAATATCACTGTTTTAA
* * *
44172 AAATAATTATCAGAATATCATTGTTTTAA
1 AAATAATTACCAAAATATCACTGTTTTAA
* *
44201 AAA-AATCACCAAAATATCA-TATTTTAA
1 AAATAATTACCAAAATATCACTGTTTTAA
* *
44228 AAATAATTACTAAAATATCACCGTTTTAA
1 AAATAATTACCAAAATATCACTGTTTTAA
*
44257 AAATAATTACCAAAATATCACT-ATTTAA
1 AAATAATTACCAAAATATCACTGTTTTAA
** *
44285 AAA-AATTACTGAAATATCACCGTTTTAA
1 AAATAATTACCAAAATATCACTGTTTTAA
**
44313 AACATAATTACCAAAATATCACCATTTTAA
1 AA-ATAATTACCAAAATATCACTGTTTTAA
44343 AAATAATTACCAAAATATCA-TCGTTTTAA
1 AAATAATTACCAAAATATCACT-GTTTTAA
* * *
44372 AAATAATTTCTAAAATATCACAT-TTTTCA
1 AAATAATTACCAAAATATCAC-TGTTTTAA
* *
44401 AAATATTTACTAAAATATCAC
1 AAATAATTACCAAAATATCAC
44422 CAGGTCGGGT
Statistics
Matches: 215, Mismatches: 27, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
27 25 0.12
28 42 0.20
29 123 0.57
30 24 0.11
31 1 0.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATAATTACCAAAATATCACTGTTTTAA
Found at i:44200 original size:56 final size:56
Alignment explanation
Indices: 44138--44422 Score: 317
Period size: 57 Copynumber: 5.0 Consensus size: 56
44128 AAATCAATTT
* * * * **
44138 TTTTTAAATAATTACCAAAATATCATTGTTTTAAAAATAATTATCAGAATATCATTG
1 TTTTAAAATAATTACCAAAATATCACTATTTTAAAAATAATTA-CAAAATATCACCG
* *
44195 TTTTAAAAAAATCACCAAAATATCA-TATTTTAAAAATAATTACTAAAATATCACCG
1 TTTTAAAATAATTACCAAAATATCACTATTTTAAAAATAATTAC-AAAATATCACCG
*
44251 TTTTAAAAATAATTACCAAAATATCACTA-TTTAAAAA-AATTACTGAAATATCACCG
1 TTTT-AAAATAATTACCAAAATATCACTATTTTAAAAATAATTAC-AAAATATCACCG
* *
44307 TTTTAAAACATAATTACCAAAATATCACCATTTTAAAAATAATTACCAAAATATCATCG
1 TTTT-AAA-ATAATTACCAAAATATCACTATTTTAAAAATAATTA-CAAAATATCACCG
* * * *
44366 TTTTAAAAATAATTTCTAAAATATCAC-ATTTTTCAAAATATTTACTAAAATATCACC
1 TTTT-AAAATAATTACCAAAATATCACTA-TTTTAAAAATAATTAC-AAAATATCACC
44423 AGGTCGGGTC
Statistics
Matches: 201, Mismatches: 18, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
55 1 0.00
56 55 0.27
57 71 0.35
58 50 0.25
59 23 0.11
60 1 0.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (56 bp):
TTTTAAAATAATTACCAAAATATCACTATTTTAAAAATAATTACAAAATATCACCG
Found at i:44220 original size:57 final size:57
Alignment explanation
Indices: 44143--44422 Score: 345
Period size: 56 Copynumber: 4.9 Consensus size: 57
44133 AATTTTTTTT
* * * **
44143 AAATAATTACCAAAATATCATTGTTTTAAAAATAATTATCAGAATATCATTGTTTTAA
1 AAATAATTACCAAAATATCACTATTTTAAAAATAATTA-CAAAATATCACCGTTTTAA
*
44201 AAA-AATCACCAAAATATCA-TATTTTAAAAATAATTACTAAAATATCACCGTTTTAA
1 AAATAATTACCAAAATATCACTATTTTAAAAATAATTAC-AAAATATCACCGTTTTAA
*
44257 AAATAATTACCAAAATATCACTA-TTTAAAAA-AATTACTGAAATATCACCGTTTTAA
1 AAATAATTACCAAAATATCACTATTTTAAAAATAATTAC-AAAATATCACCGTTTTAA
* *
44313 AACATAATTACCAAAATATCACCATTTTAAAAATAATTACCAAAATATCATCGTTTTAA
1 AA-ATAATTACCAAAATATCACTATTTTAAAAATAATTA-CAAAATATCACCGTTTTAA
* * * *
44372 AAATAATTTCTAAAATATCAC-ATTTTTCAAAATATTTACTAAAATATCACC
1 AAATAATTACCAAAATATCACTA-TTTTAAAAATAATTAC-AAAATATCACC
44423 AGGTCGGGTC
Statistics
Matches: 198, Mismatches: 15, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
55 1 0.01
56 60 0.30
57 60 0.30
58 53 0.27
59 23 0.12
60 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (57 bp):
AAATAATTACCAAAATATCACTATTTTAAAAATAATTACAAAATATCACCGTTTTAA
Found at i:44344 original size:86 final size:84
Alignment explanation
Indices: 44143--44423 Score: 321
Period size: 85 Copynumber: 3.3 Consensus size: 84
44133 AATTTTTTTT
*** * * * *
44143 AAATAATTACCAAAATATCATTGTTTTAAAAATAATTATCAGAATATCATTGTTTTAAAAAAATC
1 AAATAATTACCAAAATATCACCATTTTAAAAATAATTACCAAAATATCA--CTTTTAAAAAAATT
* *
44208 ACCAAAATATCA-TATTTTAA
64 ACTAAAATATCACAATTTTAA
* *
44228 AAATAATTACTAAAATATCACCGTTTTAAAAATAATTACCAAAATATCACTATTTAAAAAAATTA
1 AAATAATTACCAAAATATCACCATTTTAAAAATAATTACCAAAATATCACT-TTTAAAAAAATTA
* **
44293 CTGAAATATCACCGTTTTAA
65 CTAAAATATCACAATTTTAA
44313 AACATAATTACCAAAATATCACCATTTTAAAAATAATTACCAAAATATCATCGTTTTAAAAATAA
1 AA-ATAATTACCAAAATATCACCATTTTAAAAATAATTACCAAAATATCA-C-TTTTAAAAA-AA
* * *
44378 TTTCTAAAATATCACATTTTTCA
62 TTACTAAAATATCACAATTTTAA
* *
44401 AAATATTTACTAAAATATCACCA
1 AAATAATTACCAAAATATCACCA
44424 GGTCGGGTCG
Statistics
Matches: 170, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
83 1 0.01
84 21 0.12
85 52 0.31
86 45 0.26
87 28 0.16
88 23 0.14
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (84 bp):
AAATAATTACCAAAATATCACCATTTTAAAAATAATTACCAAAATATCACTTTTAAAAAAATTAC
TAAAATATCACAATTTTAA
Found at i:44458 original size:18 final size:18
Alignment explanation
Indices: 44424--44469 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
44414 AATATCACCA
*
44424 GGTCGGGTC-GATCAACG
1 GGTCGGGTCAGGTCAACG
*
44441 GGTCTGGTCAGGTCAACG
1 GGTCGGGTCAGGTCAACG
44459 GGTCGGGTCAG
1 GGTCGGGTCAG
44470 ACCGATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.15, C:0.22, G:0.43, T:0.20
Consensus pattern (18 bp):
GGTCGGGTCAGGTCAACG
Found at i:47365 original size:49 final size:51
Alignment explanation
Indices: 47251--47379 Score: 190
Period size: 49 Copynumber: 2.5 Consensus size: 51
47241 CTATTTAAAC
* **
47251 GACACCAATCATATTCATGAATCTAAAACAGCACAGCAGGGTATGATATGAT
1 GACACCAATCATATTCATGAATCTAAAACA-CACAACAGGAAATGATATGAT
*
47303 GACACCAACCATATTCATGAATCTAAAACA-A-AACAGGAAATGATATGAT
1 GACACCAATCATATTCATGAATCTAAAACACACAACAGGAAATGATATGAT
*
47352 GACATCAATCATATTCATGAATCTAAAA
1 GACACCAATCATATTCATGAATCTAAAA
47380 AATGAAGATA
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
49 41 0.58
50 1 0.01
52 29 0.41
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (51 bp):
GACACCAATCATATTCATGAATCTAAAACACACAACAGGAAATGATATGAT
Found at i:52786 original size:2 final size:2
Alignment explanation
Indices: 52779--52803 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52769 ATCCCTCAAC
52779 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
52804 CAATTAGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55006 original size:44 final size:44
Alignment explanation
Indices: 54958--55060 Score: 206
Period size: 44 Copynumber: 2.3 Consensus size: 44
54948 TCAAACACTA
54958 AAATATATTTTTATTTGTAAATTTAAATATTTTTATTAAAATAT
1 AAATATATTTTTATTTGTAAATTTAAATATTTTTATTAAAATAT
55002 AAATATATTTTTATTTGTAAATTTAAATATTTTTATTAAAATAT
1 AAATATATTTTTATTTGTAAATTTAAATATTTTTATTAAAATAT
55046 AAATATATTTTTATT
1 AAATATATTTTTATT
55061 AAAATATAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (44 bp):
AAATATATTTTTATTTGTAAATTTAAATATTTTTATTAAAATAT
Found at i:55053 original size:22 final size:22
Alignment explanation
Indices: 54958--55075 Score: 136
Period size: 22 Copynumber: 5.4 Consensus size: 22
54948 TCAAACACTA
*
54958 AAATATATTTTTATTTGTAAAT-T
1 AAATATATTTTTA-TT-AAAATAT
*
54981 TAA-ATATTTTTATTAAAATAT
1 AAATATATTTTTATTAAAATAT
*
55002 AAATATATTTTTATTTGTAAAT-T
1 AAATATATTTTTA-TT-AAAATAT
*
55025 TAA-ATATTTTTATTAAAATAT
1 AAATATATTTTTATTAAAATAT
55046 AAATATATTTTTATTAAAATAT
1 AAATATATTTTTATTAAAATAT
55068 AAATATAT
1 AAATATAT
55076 GAAAAATATA
Statistics
Matches: 82, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.10
21 10 0.12
22 53 0.65
23 7 0.09
24 4 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AAATATATTTTTATTAAAATAT
Found at i:55084 original size:11 final size:11
Alignment explanation
Indices: 55068--55093 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55058 ATTAAAATAT
55068 AAATATATGAA
1 AAATATATGAA
55079 AAATATATGAA
1 AAATATATGAA
55090 AAAT
1 AAAT
55094 GTAATATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (11 bp):
AAATATATGAA
Found at i:59670 original size:32 final size:32
Alignment explanation
Indices: 59634--59701 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
59624 TCGGGTAGGA
* * *
59634 GTCGGGTGGAGGATATATATTTTTTAGGTCAG
1 GTCGGATGGAGGATATAAAATTTTTAGGTCAG
* *
59666 GTCGGATGTAGGATATAAAATTTTTAGGTCGG
1 GTCGGATGGAGGATATAAAATTTTTAGGTCAG
59698 GTCG
1 GTCG
59702 AGTTTGGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.24, C:0.07, G:0.34, T:0.35
Consensus pattern (32 bp):
GTCGGATGGAGGATATAAAATTTTTAGGTCAG
Found at i:66309 original size:23 final size:23
Alignment explanation
Indices: 66265--66309 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
66255 TTAATTAGAT
*
66265 TTTAAAATATTAATGAGTTTAAG
1 TTTAAAATATTAATAAGTTTAAG
*
66288 TTTAAAAT-TTATTAAGTCTTAA
1 TTTAAAATATTAATAAGT-TTAA
66310 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (23 bp):
TTTAAAATATTAATAAGTTTAAG
Found at i:69696 original size:29 final size:29
Alignment explanation
Indices: 69634--69768 Score: 126
Period size: 29 Copynumber: 4.5 Consensus size: 29
69624 AACCCAACCA
* * **
69634 TAGGTCGCCAAGCACTCCAAGCGACCTAC
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
*
69663 AAGGTCGCCATGCACTCCCAGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
* * * *
69692 TAGGTCGCCAAGCAATCCCGGCGACCAAGATGG
1 TAGGTCGCCATGCACTCCCAGCGACC----TTG
* * *
69725 TAGGTCGCCATGTACGCCCAGCGACCTTA
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
69754 TAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
69769 GCCGGCGTCC
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
29 61 0.73
33 23 0.27
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTTG
Found at i:70429 original size:21 final size:21
Alignment explanation
Indices: 70404--70447 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
70394 AATTTAGTTA
70404 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
70425 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
70446 AT
1 AT
70448 ATTATATTAA
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:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:73812 original size:60 final size:59
Alignment explanation
Indices: 73670--73856 Score: 296
Period size: 60 Copynumber: 3.2 Consensus size: 59
73660 TGATTTGATG
*
73670 GTAATGA-TAGTAATAATGAAATTATTATTAATATTTAATGA-TTGAT-TAATGATTTA
1 GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATAATGATTTA
*
73726 GT-ATGATTAGT-ATAATGAAATCATTATTAATTTTTAATGATTTGATAATAATGATTTA
1 GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGAT-ATAATGATTTA
73784 GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTA
1 GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATA-TAATGATTTA
73843 GTAATGATTAGTAA
1 GTAATGATTAGTAA
Statistics
Matches: 121, Mismatches: 3, Indels: 11
0.90 0.02 0.08
Matches are distributed among these distances:
55 31 0.26
56 11 0.09
58 12 0.10
59 27 0.22
60 40 0.33
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (59 bp):
GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATAATGATTTA
Found at i:73844 original size:10 final size:10
Alignment explanation
Indices: 73831--73856 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
73821 AATGATTTGA
73831 TAGTAATGAT
1 TAGTAATGAT
73841 TAGTAATGAT
1 TAGTAATGAT
73851 TAGTAA
1 TAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (10 bp):
TAGTAATGAT
Done.