Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006204.1 Hibiscus syriacus cultivar Beakdansim tig00014770_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: 153925
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1966 original size:3 final size:3
Alignment explanation
Indices: 1954--1996 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
1944 AAAATGTTAG
1954 ATA A-A ATA ATA ATA ATA ATA ATA ATA AT- ATA AT- ATA ATGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
1997 TAAATAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.17
3 27 0.75
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2038 original size:21 final size:22
Alignment explanation
Indices: 2013--2064 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
2003 AATCATAGAG
*
2013 AAAAAAAAAGAAATAA-TAAAT
1 AAAAAAAAAGAAAAAAGTAAAT
* *
2034 CAAAAAAAGGAAAAAAGTAAAT
1 AAAAAAAAAGAAAAAAGTAAAT
2056 AAAAAAAAA
1 AAAAAAAAA
2065 AGGTTTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.10
Consensus pattern (22 bp):
AAAAAAAAAGAAAAAAGTAAAT
Found at i:2062 original size:24 final size:24
Alignment explanation
Indices: 2035--2084 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
2025 ATAATAAATC
2035 AAAAAAAGG-AAAAAAGTAAATAAA
1 AAAAAAAGGTAAAAAA-TAAATAAA
*
2059 AAAAAAAGGTTTAAAAATAAATAAA
1 AAAAAAAGG-TAAAAAATAAATAAA
2084 A
1 A
2085 TTAAAGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 9 0.39
26 5 0.22
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (24 bp):
AAAAAAAGGTAAAAAATAAATAAA
Found at i:3573 original size:32 final size:31
Alignment explanation
Indices: 3530--3605 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
3520 CAATATAGCG
* * *
3530 TATATAATATATAAAAAAATATTTTTTTAAAC
1 TATATATTATATAAAAAAAT-GTTTTTAAAAC
**
3562 TATATATTATATTTAAAAATGTTTTTAAAAC
1 TATATATTATATAAAAAAATGTTTTTAAAAC
3593 TATATATTATATA
1 TATATATTATATA
3606 GTTTTCAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 21 0.55
32 17 0.45
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (31 bp):
TATATATTATATAAAAAAATGTTTTTAAAAC
Found at i:3616 original size:36 final size:36
Alignment explanation
Indices: 3552--3703 Score: 133
Period size: 33 Copynumber: 4.4 Consensus size: 36
3542 AAAAAAATAT
*
3552 TTTTTTAAACTATATA-T-TATA--TTT-AAAAATG
1 TTTTTAAAACTATATATTATATAGTTTTCAAAAATG
3583 TTTTTAAAACTATATATTATATAGTTTTCAAAAATG
1 TTTTTAAAACTATATATTATATAGTTTTCAAAAATG
* * * *
3619 ATTTTAAAA--ATATAATACA-AGTTTTCCAAAAT-
1 TTTTTAAAACTATATATTATATAGTTTTCAAAAATG
* * ** *
3651 TTTTTTAAGCTATATATTATATAAATTTCCAAAATG
1 TTTTTAAAACTATATATTATATAGTTTTCAAAAATG
3687 TTTTTTAAAAACTATAT
1 -TTTTT-AAAACTATAT
3704 TTTCAAAATG
Statistics
Matches: 96, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
31 15 0.16
32 7 0.07
33 16 0.17
34 16 0.17
35 14 0.15
36 15 0.16
37 5 0.05
38 8 0.08
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTTTAAAACTATATATTATATAGTTTTCAAAAATG
Found at i:3704 original size:36 final size:36
Alignment explanation
Indices: 3544--3704 Score: 94
Period size: 36 Copynumber: 4.7 Consensus size: 36
3534 TAATATATAA
* * *
3544 AAAAATATTTTTT-TAAACTATA-TAT-TATATTT-
1 AAAAATGTTTTTTAAAAACTATATTATATAAATTTC
**
3576 AAAAATG-TTTTT-AAAACTATATATTATATAGTTTTC
1 AAAAATGTTTTTTAAAAAC--TATATTATATAAATTTC
* * *
3612 AAAAATG-ATTTTAAAAA-TATA--ATACAAGTTTTC
1 AAAAATGTTTTTTAAAAACTATATTATATAA-ATTTC
* **
3645 CAAAAT-TTTTTTAAGCTA-TATATTATATAAATTTC
1 AAAAATGTTTTTTAA-AAACTATATTATATAAATTTC
*
3680 CAAAATGTTTTTTAAAAACTATATT
1 AAAAATGTTTTTTAAAAACTATATT
3705 TTCAAAATGA
Statistics
Matches: 101, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
31 9 0.09
32 10 0.10
33 20 0.20
34 12 0.12
35 16 0.16
36 30 0.30
37 4 0.04
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
AAAAATGTTTTTTAAAAACTATATTATATAAATTTC
Found at i:11349 original size:13 final size:15
Alignment explanation
Indices: 11321--11356 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
11311 AATATTTTTT
11321 AAATAAAATAATTAA
1 AAATAAAATAATTAA
11336 AAATAAAA-AA-TAA
1 AAATAAAATAATTAA
11349 AAATAAAA
1 AAATAAAA
11357 GATGGTCGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.52
14 2 0.10
15 8 0.38
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAAAATAATTAA
Found at i:13987 original size:28 final size:29
Alignment explanation
Indices: 13952--14034 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
13942 AATTTAAATA
13952 AGTGACTAAAATATAAATTTTGAAAGTTG
1 AGTGACTAAAATATAAATTTTGAAAGTTG
* * * *
13981 A-TGACTAAAGTATAAAATTAGAAAAGTTT
1 AGTGACTAAAATATAAATTTTG-AAAGTTG
*
14010 AGGGACCTAAAATAT-AATTTTGAAA
1 AGTGA-CTAAAATATAAATTTTGAAA
14035 AAATTATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 17 0.40
29 11 0.26
30 7 0.16
31 8 0.19
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.31
Consensus pattern (29 bp):
AGTGACTAAAATATAAATTTTGAAAGTTG
Found at i:17145 original size:20 final size:19
Alignment explanation
Indices: 17114--17155 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
17104 GTTATCTGAA
17114 TTAAATTTAAATT-TGATAT
1 TTAAATTTAAATTATGAT-T
17133 TTAAATATTAAATTATGATT
1 TTAAAT-TTAAATTATGATT
17153 TTA
1 TTA
17156 TGCGATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
TTAAATTTAAATTATGATT
Found at i:38724 original size:29 final size:30
Alignment explanation
Indices: 38692--38749 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
38682 GGGTAGAGCT
38692 AGAAAATTTATTTTGGG-TGTCAAATTTAG
1 AGAAAATTTATTTTGGGTTGTCAAATTTAG
38721 AGAAAATTTATTTTGGGTTGTCAAATTTA
1 AGAAAATTTATTTTGGGTTGTCAAATTTA
38750 AAAATTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (30 bp):
AGAAAATTTATTTTGGGTTGTCAAATTTAG
Found at i:38875 original size:15 final size:15
Alignment explanation
Indices: 38836--38885 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
38826 AATTTCAAAA
*
38836 ATATATTAATTATTT
1 ATATATTAAATATTT
*
38851 ATCT-TTAAATATTT
1 ATATATTAAATATTT
*
38865 TTATATTAAAT-TTAT
1 ATATATTAAATATT-T
38880 ATATAT
1 ATATAT
38886 AAAAAATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATATTAAATATTT
Found at i:39643 original size:31 final size:31
Alignment explanation
Indices: 39605--39672 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
39595 CTTTTTCAGA
39605 GGTCCCCCACCTTTTTAGTTCTCTTCACAGT
1 GGTCCCCCACCTTTTTAGTTCTCTTCACAGT
39636 GGTCCCCCACCTTTTTAGTTCTCTTCACAGT
1 GGTCCCCCACCTTTTTAGTTCTCTTCACAGT
39667 GGTCCC
1 GGTCCC
39673 TCGTTATCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.12, C:0.37, G:0.15, T:0.37
Consensus pattern (31 bp):
GGTCCCCCACCTTTTTAGTTCTCTTCACAGT
Found at i:48252 original size:87 final size:86
Alignment explanation
Indices: 48073--48260 Score: 236
Period size: 87 Copynumber: 2.2 Consensus size: 86
48063 CGATACCAAA
* *
48073 GGTAGTATTGATACTTCCATTACCTTTGGTATCGGTATCTCTTTTGGACCGATACCATTTTTGCA
1 GGTAGTATCGATACTTCCATTACCTTTGGTATCGGTATCTCCTTTGGACCGATACCATTTTTGCA
*
48138 TTATGGAATTTGAGCAATATT
66 TTATAGAATTTGAGCAATATT
* * * *
48159 GGTAGTATCGATACTTCTGA-TACCTTTGGTATCGGTATC-CCTTTGGATATCGGTACTATTTTT
1 GGTAGTATCGATACTTC-CATTACCTTTGGTATCGGTATCTCCTTTGG--ACCGATACCATTTTT
* * *
48222 GTATTCTAGAATTTGAGCAATGTT
63 GCATTATAGAATTTGAGCAATATT
*
48246 GGTAGTATCAATACT
1 GGTAGTATCGATACT
48261 ACCTTGTGAG
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
85 6 0.07
86 35 0.40
87 47 0.53
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.41
Consensus pattern (86 bp):
GGTAGTATCGATACTTCCATTACCTTTGGTATCGGTATCTCCTTTGGACCGATACCATTTTTGCA
TTATAGAATTTGAGCAATATT
Found at i:62120 original size:28 final size:28
Alignment explanation
Indices: 62063--62120 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
62053 AAGTTATTTT
*
62063 AAATAATGAAATAATTATTAAATCTAAA
1 AAATAATGAAATAATTAGTAAATCTAAA
** *
62091 AAATAATGATAATTTTTAGTAAATTTAAA
1 AAATAATGA-AATAATTAGTAAATCTAAA
62120 A
1 A
62121 TTTATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (28 bp):
AAATAATGAAATAATTAGTAAATCTAAA
Found at i:63203 original size:2 final size:2
Alignment explanation
Indices: 63198--63222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63188 AAGGTAAAAT
63198 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
63223 TCGGGTCGGG
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:64260 original size:31 final size:31
Alignment explanation
Indices: 64222--64346 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
64212 TCCGAAAGAC
* * *
64222 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
64253 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
64284 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
64315 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
64346 C
1 C
64347 CTTCGACCAT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:66763 original size:39 final size:38
Alignment explanation
Indices: 66681--66763 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 38
66671 AACAAGTTAG
* *
66681 AAAATATTTATATATTTTCTTTAAAAAGTTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAGTTGAAAATCAT
* *
66720 -AAAATTTATATATATTTTTTTCACAAAGTTGAAAAT-AT
1 AAAAATTTATATAT-TTTCTTT-AAAAAGTTGAAAATCAT
66758 AAAAAT
1 AAAAAT
66764 GTTTAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
37 10 0.27
38 11 0.30
39 16 0.43
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAGTTGAAAATCAT
Found at i:73595 original size:17 final size:18
Alignment explanation
Indices: 73561--73595 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
73551 CCTTGAAGTC
73561 ATTTCACTATCTTGGGTT
1 ATTTCACTATCTTGGGTT
*
73579 ATTTTACTATC-TGGGTT
1 ATTTCACTATCTTGGGTT
73596 TCTTTCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (18 bp):
ATTTCACTATCTTGGGTT
Found at i:75961 original size:9 final size:9
Alignment explanation
Indices: 75947--75976 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
75937 TACAGTTACT
*
75947 CAGCAGCAG
1 CAGCAGCAA
75956 CAGCAGCAA
1 CAGCAGCAA
75965 CAGCAGCAA
1 CAGCAGCAA
75974 CAG
1 CAG
75977 ATAAAGCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.33, G:0.27, T:0.00
Consensus pattern (9 bp):
CAGCAGCAA
Found at i:78805 original size:4 final size:4
Alignment explanation
Indices: 78796--78825 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
78786 GTGTCATTAC
78796 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
78826 TTCTTTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:91700 original size:6 final size:6
Alignment explanation
Indices: 91689--91717 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
91679 TTCGCCCTTT
91689 AACTTC AACTTC AACTTC AACTTC AACTT
1 AACTTC AACTTC AACTTC AACTTC AACTT
91718 TAAGAAGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
AACTTC
Found at i:92111 original size:6 final size:6
Alignment explanation
Indices: 92100--92125 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
92090 GTGTTTCTGG
92100 TTCCGT TTCCGT TTCCGT TTCCGT TT
1 TTCCGT TTCCGT TTCCGT TTCCGT TT
92126 TGGATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.15, T:0.54
Consensus pattern (6 bp):
TTCCGT
Found at i:93610 original size:31 final size:31
Alignment explanation
Indices: 93575--93648 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
93565 AGAAAGTATA
93575 TGGATCATTTTGGTGATTTTTAAAAATAGTT
1 TGGATCATTTTGGTGATTTTTAAAAATAGTT
*
93606 TGGATCATTTTGGTGATTTTTAAAAATCGTT
1 TGGATCATTTTGGTGATTTTTAAAAATAGTT
93637 TGGATCATTTTG
1 TGGATCATTTTG
93649 ACGACTTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.26, C:0.05, G:0.20, T:0.49
Consensus pattern (31 bp):
TGGATCATTTTGGTGATTTTTAAAAATAGTT
Found at i:96271 original size:2 final size:2
Alignment explanation
Indices: 96264--96292 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
96254 ATGAAAACTG
96264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96293 CAGGAATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96548 original size:21 final size:20
Alignment explanation
Indices: 96524--96587 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
96514 AACTTTGAAA
96524 AAATAGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
*
96545 AAATG-TTT---A-TTT-GA
1 AAATGTTTTCAAAGTTTGGT
96559 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
96580 AAATGTTT
1 AAATGTTT
96588 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 8 0.24
21 9 0.26
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:96561 original size:37 final size:35
Alignment explanation
Indices: 96517--96634 Score: 166
Period size: 35 Copynumber: 3.3 Consensus size: 35
96507 GGTAACTAAC
96517 TTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 TTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
96553 ATTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 -TTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
96588 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 -TTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
96625 GTTGAAAAAT
1 TTTGAAAAAT
96635 GATAATGGGA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.45
36 15 0.20
37 26 0.35
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (35 bp):
TTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:101160 original size:21 final size:21
Alignment explanation
Indices: 101136--101196 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
101126 AACTTTGAAA
101136 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
101157 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
101171 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
101192 AAATG
1 AAATG
101197 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:101227 original size:37 final size:37
Alignment explanation
Indices: 101128--101246 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
101118 TGGTAACCAA
101128 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
101165 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
101200 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
101237 -GTTGAAAAAT
1 CTTTGAAAAAT
101247 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:114022 original size:2 final size:2
Alignment explanation
Indices: 114015--114039 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
114005 GATCAATGCA
114015 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
114040 AATCAGCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:119397 original size:21 final size:21
Alignment explanation
Indices: 119367--119467 Score: 75
Period size: 21 Copynumber: 4.8 Consensus size: 21
119357 GATTTACATA
*
119367 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
119388 TTCGCGTTGCGATTTATTCCAA-
1 TTCGCGTTGCGA--TAGTCCAAG
* * *
119410 -ACTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
119430 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
119453 TT--CGTTGCGATAGTC
1 TTCGCGTTGCGATAGTC
119468 TAAAATCGCA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
19 10 0.16
21 37 0.60
23 15 0.24
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:119424 original size:42 final size:42
Alignment explanation
Indices: 119373--119467 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
119363 CATATTCGCA
119373 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAACTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAACTCG
* *
119415 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAACTCG
119457 TTGCGATAGTC
1 TTGCGATAGTC
119468 TAAAATCGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAACTCG
Found at i:119571 original size:6 final size:6
Alignment explanation
Indices: 119560--119586 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
119550 GACACGTATT
119560 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
119587 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:119703 original size:6 final size:6
Alignment explanation
Indices: 119692--119754 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
119682 CGTCTCGTTG
** *
119692 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTATT GGTAGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
* *
119740 GGTAGT GGTAGT GGT
1 GGTCGT GGTCGT GGT
119755 AATGGTAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.06, C:0.10, G:0.49, T:0.35
Consensus pattern (6 bp):
GGTCGT
Found at i:119763 original size:6 final size:6
Alignment explanation
Indices: 119696--119761 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
119686 TCGTTGGGTC
* * * * * *
119696 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTA TTGGTA GTGGTA
1 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA
*
119744 GTGGTA GTGGTA ATGGTA
1 GTGGTA GTGGTA GTGGTA
119762 ATACGTGTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.11, C:0.08, G:0.47, T:0.35
Consensus pattern (6 bp):
GTGGTA
Found at i:119991 original size:22 final size:23
Alignment explanation
Indices: 119939--119993 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
119929 AACCCTCTAT
*
119939 ATATTATTTTTTTCAATTAAATCA
1 ATATT-TTTTTTTCAATAAAATCA
* *
119963 ATGTTTTTTTTTGAATAAAAT-A
1 ATATTTTTTTTTCAATAAAATCA
119985 ATATTTTTT
1 ATATTTTTT
119994 ATTATTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.33
23 14 0.52
24 4 0.15
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
ATATTTTTTTTTCAATAAAATCA
Found at i:131405 original size:21 final size:21
Alignment explanation
Indices: 131381--131455 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 21
131371 CCCAGGGGGT
131381 ATCGATTCCCTAAAGGAGGGA
1 ATCGATTCCCTAAAGGAGGGA
*
131402 ATCGGTTCCCATTCAAAGG-GGGA
1 ATCGATTCCC--T-AAAGGAGGGA
* * * *
131425 ATCGGTTCCCT-TATGAGGGT
1 ATCGATTCCCTAAAGGAGGGA
131445 ATCGATTCCCT
1 ATCGATTCCCT
131456 TTGCCAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 10 0.22
23 15 0.33
24 5 0.11
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (21 bp):
ATCGATTCCCTAAAGGAGGGA
Found at i:137286 original size:20 final size:19
Alignment explanation
Indices: 137227--137275 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
137217 TTGAACAGTG
137227 GGGGGGAATCGATACCCCT
1 GGGGGGAATCGATACCCCT
137246 GGGGGGAATCGATACCCCT
1 GGGGGGAATCGATACCCCT
137265 GGGGGGAATCG
1 GGGGGGAATCG
137276 GTTACCTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.43, T:0.14
Consensus pattern (19 bp):
GGGGGGAATCGATACCCCT
Found at i:140705 original size:22 final size:21
Alignment explanation
Indices: 140663--140702 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
140653 GAGTTTATTT
*
140663 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
140684 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
140703 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:140866 original size:15 final size:15
Alignment explanation
Indices: 140846--140882 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
140836 TTCTTGTTCC
140846 TCTTCATTGGAACTT
1 TCTTCATTGGAACTT
140861 TCTTCATTGGAACTT
1 TCTTCATTGGAACTT
140876 TCTTCAT
1 TCTTCAT
140883 CGCTCCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (15 bp):
TCTTCATTGGAACTT
Found at i:146287 original size:23 final size:21
Alignment explanation
Indices: 146261--146322 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 21
146251 GGAATTATTA
146261 TGTCTTTATGACATGTTTATCTC
1 TGTCTTT-TGACA-GTTTATCTC
*
146284 TGTCTTTGTGACACGTTTATCTT
1 TGTCTTT-TGACA-GTTTATCTC
146307 TGTCTTTTGACAGTTT
1 TGTCTTTTGACAGTTT
146323 TCGATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 27 0.75
ACGTcount: A:0.15, C:0.16, G:0.16, T:0.53
Consensus pattern (21 bp):
TGTCTTTTGACAGTTTATCTC
Found at i:148082 original size:20 final size:20
Alignment explanation
Indices: 148057--148097 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
148047 GTGCTGCCTT
148057 TCTGAAAGACTATCACCCTC
1 TCTGAAAGACTATCACCCTC
148077 TCTGAAAGACTATCACCCTC
1 TCTGAAAGACTATCACCCTC
148097 T
1 T
148098 ACAAGTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.27
Consensus pattern (20 bp):
TCTGAAAGACTATCACCCTC
Found at i:149639 original size:13 final size:14
Alignment explanation
Indices: 149621--149655 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
149611 ACCACTGAGT
149621 TTGACTTTGACT-A
1 TTGACTTTGACTCA
149634 TTGACTTTGACTCA
1 TTGACTTTGACTCA
149648 TTGACTTT
1 TTGACTTT
149656 TTCTGAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (14 bp):
TTGACTTTGACTCA
Found at i:150402 original size:23 final size:23
Alignment explanation
Indices: 150375--150434 Score: 106
Period size: 22 Copynumber: 2.7 Consensus size: 23
150365 ATTAAAACCT
150375 TATTTTTTATTAAATAAAAGTAA
1 TATTTTTTATTAAATAAAAGTAA
150398 TA-TTTTTATTAAATAAAAGTAA
1 TATTTTTTATTAAATAAAAGTAA
150420 TATTTTTTA-TAAATA
1 TATTTTTTATTAAATA
150435 TATTATTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 28 0.78
23 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (23 bp):
TATTTTTTATTAAATAAAAGTAA
Found at i:152647 original size:2 final size:2
Alignment explanation
Indices: 152642--152675 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
152632 TTTTTCTTGC
152642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
152676 AAAAATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.