Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003565.1 Hibiscus syriacus cultivar Beakdansim tig00007527_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: 73628
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:650 original size:23 final size:23
Alignment explanation
Indices: 621--665 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
611 AATTTGATCT
621 TGGTCAATACCCGGACTTTGATA
1 TGGTCAATACCCGGACTTTGATA
* *
644 TGGTCAATACTCGGATTTTGAT
1 TGGTCAATACCCGGACTTTGAT
666 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGGTCAATACCCGGACTTTGATA
Found at i:855 original size:12 final size:12
Alignment explanation
Indices: 832--866 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
822 ATATAATCCT
832 AAGAAG-AAAAG
1 AAGAAGAAAAAG
843 AAGAAGAAAAAG
1 AAGAAGAAAAAG
855 AAGAAGAAAAAG
1 AAGAAGAAAAAG
867 TCCCCGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:3173 original size:32 final size:32
Alignment explanation
Indices: 3115--3221 Score: 132
Period size: 32 Copynumber: 3.4 Consensus size: 32
3105 GGAAATTACT
3115 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACG-GAGA
*
3148 ATCGCAATGCGAAATG-AAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACG-GAGA
*
3179 TTTCGC-ATGCGAAATGAAAATCGCAACGG-GA
1 -ATCGCAATGCGAAATGAAAATCGCAACGGAGA
*
3210 ATCGCAAAGCGA
1 ATCGCAATGCGA
3222 TAGTACTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
30 4 0.06
31 17 0.27
32 27 0.42
33 16 0.25
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGGAGA
Found at i:3347 original size:14 final size:14
Alignment explanation
Indices: 3328--3364 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3318 CATCAATTAA
3328 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3342 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3356 ACAAATCAA
1 ACAAATCAA
3365 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4727 original size:21 final size:20
Alignment explanation
Indices: 4694--4753 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
4684 TGTGAATCGG
*
4694 CTCTTGAATGATGGGAGGGAC
1 CTCTTGAACGATGGGAGGG-C
* **
4715 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGATGGGAG-GGC
4736 CTCTTGAACG-TGGGAGGG
1 CTCTTGAACGATGGGAGGG
4754 GACTCTCGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 2 0.06
20 4 0.13
21 23 0.74
22 2 0.06
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGATGGGAGGGC
Found at i:4778 original size:41 final size:42
Alignment explanation
Indices: 4733--4891 Score: 148
Period size: 41 Copynumber: 3.9 Consensus size: 42
4723 CGATGACAGT
*
4733 GGCCTCTTGAACG-TGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATGGGAGGGGACTCTCGAGGAATGATAGG
* * * * *
4774 GGCCTCTTCAACGAT---AGTGGACTCTTGAGGGATGACAGT
1 GGCCTCTTCAACGATGGGAGGGGACTCTCGAGGAATGATAGG
* * * *
4813 GGTCTCTTGAACGGTGGGA-GGGACTCTCGAGGAATAATAGG
1 GGCCTCTTCAACGATGGGAGGGGACTCTCGAGGAATGATAGG
* * * * *
4854 GGCCTATTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATGGGAGGGGACTCTCGAGGAATGA
4892 CAGGTGAGTC
Statistics
Matches: 89, Mismatches: 24, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
39 31 0.35
41 42 0.47
42 16 0.18
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATGGGAGGGGACTCTCGAGGAATGATAGG
Found at i:4853 original size:80 final size:81
Alignment explanation
Indices: 4724--4894 Score: 274
Period size: 80 Copynumber: 2.1 Consensus size: 81
4714 CCTCTTCAAC
* *
4724 GATGACAGTGGCCTCTTGAACGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
1 GATGACAGTGGCCTCTTGAACGTGGGAGGGGACTCTCGAGGAATAATAGGGGCCTATTCAACGAT
4789 -AGTGGACTCTTGAGG
66 GAGTGGACTCTTGAGG
*
4804 GATGACAGTGGTCTCTTGAACGGTGGGA-GGGACTCTCGAGGAATAATAGGGGCCTATTCAACGA
1 GATGACAGTGGCCTCTTGAAC-GTGGGAGGGGACTCTCGAGGAATAATAGGGGCCTATTCAACGA
4868 TAGGAGTGGACTCTTGAGG
65 T--GAGTGGACTCTTGAGG
4887 GATGACAG
1 GATGACAG
4895 GTGAGTCGGG
Statistics
Matches: 84, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
80 55 0.65
81 6 0.07
83 23 0.27
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (81 bp):
GATGACAGTGGCCTCTTGAACGTGGGAGGGGACTCTCGAGGAATAATAGGGGCCTATTCAACGAT
GAGTGGACTCTTGAGG
Found at i:5233 original size:92 final size:86
Alignment explanation
Indices: 5121--5293 Score: 256
Period size: 92 Copynumber: 1.9 Consensus size: 86
5111 CTTTCAACCA
*
5121 AAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGG
1 AAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGCAGAATTGG
5186 CAGCAACCGAATAAATTTACTTCACC
62 CAGC-ACCGAATAAATTTACTTCACC
* * *
5212 AAAGATAAAACAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGTATTTGCAG
1 AAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAATTGGCAG
5277 CACCGAATAAATTTACT
65 CACCGAATAAATTTACT
5294 AAGCAATCTA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
87 16 0.21
88 24 0.31
91 10 0.13
92 27 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (86 bp):
AAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAATTGGCAGC
ACCGAATAAATTTACTTCACC
Found at i:7034 original size:19 final size:19
Alignment explanation
Indices: 6970--7120 Score: 141
Period size: 19 Copynumber: 8.1 Consensus size: 19
6960 TCTTTTGGTT
* *
6970 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
* * *
6989 GATAATGAGAATCACAATGC
1 GA-AATGAAAATCGCAACGC
** *
7009 GGAAATGACTATTGCAACGC
1 -GAAATGAAAATCGCAACGC
**
7029 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
7046 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
7062 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
7081 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
7100 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
7119 GA
1 GA
7121 TTTTGGTTTC
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 69 0.62
20 26 0.23
21 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:7078 original size:52 final size:53
Alignment explanation
Indices: 6995--7098 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 53
6985 ATGAGATAAT
* ** * **
6995 GAGAATCACAATGCGGAAATGACTATTGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCACAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGA
*
7048 GAGAATCGCAACGC-GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCACAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACG
7099 CGAAATGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 32 0.73
53 12 0.27
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.13
Consensus pattern (53 bp):
GAGAATCACAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:7138 original size:19 final size:19
Alignment explanation
Indices: 7116--7163 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
7106 AAAATCGCAA
*
7116 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
7135 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
7155 TGCGATTTT
1 TGCGATTTT
7164 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:7742 original size:20 final size:20
Alignment explanation
Indices: 7717--7770 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
7707 GATTTTGTAT
7717 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
7737 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
7757 TATCGCATTGCGAT
1 TATCGCATTGCGAT
7771 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:9393 original size:2 final size:2
Alignment explanation
Indices: 9386--9417 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9376 TTCATTAATA
9386 AT AT AT AT AT A- AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9418 TTGCAGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9404 original size:13 final size:13
Alignment explanation
Indices: 9381--9417 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
9371 ATAGATTCAT
9381 TAATAATATATATA
1 TAAT-ATATATATA
9395 TAATATATATATA
1 TAATATATATATA
9408 TAATATATAT
1 TAATATATAT
9418 TTGCAGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATATATATA
Found at i:9417 original size:11 final size:11
Alignment explanation
Indices: 9383--9416 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9373 AGATTCATTA
9383 ATAATATATAT
1 ATAATATATAT
9394 ATAATATATAT
1 ATAATATATAT
9405 AT-ATA-ATAT
1 ATAATATATAT
9414 ATA
1 ATA
9417 TTTGCAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 3 0.14
11 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATATAT
Found at i:24902 original size:30 final size:31
Alignment explanation
Indices: 24841--24903 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
24831 TATAATGTAT
* * *
24841 TTTTGTCAAAGTAAGTGCTTAAAATTATTTA
1 TTTTATCAAAATAAGTACTTAAAATTATTTA
24872 TTTTATCAAAATAAGTAC-TAAAA-TACTTTA
1 TTTTATCAAAATAAGTACTTAAAATTA-TTTA
24902 TT
1 TT
24904 ACTAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.07
30 11 0.39
31 15 0.54
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTTATCAAAATAAGTACTTAAAATTATTTA
Found at i:25051 original size:29 final size:30
Alignment explanation
Indices: 25002--25071 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
24992 ATACTTAAAT
* *
25002 TAAAT-ATTTTAAATACATATTTTGACTAA
1 TAAATAATTTTAAATACATATTCTGAATAA
*
25031 -AAATAATTTTAAGTA-ATTATTCTGAATAA
1 TAAATAATTTTAAATACA-TATTCTGAATAA
*
25060 TCAATAATTTTA
1 TAAATAATTTTA
25072 GACATACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 5 0.15
29 19 0.56
30 10 0.29
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (30 bp):
TAAATAATTTTAAATACATATTCTGAATAA
Found at i:26005 original size:24 final size:24
Alignment explanation
Indices: 25978--26042 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
25968 GAGAAAGTGA
*
25978 AAGAGGAAGAAGTGGAAAAAGAGG
1 AAGAGAAAGAAGTGGAAAAAGAGG
**
26002 AAGAGAAAGAAGTGGAGGAAGAGG
1 AAGAGAAAGAAGTGGAAAAAGAGG
*
26026 AAG-GAAAAGAAGAGGAA
1 AAGAG-AAAGAAGTGGAA
26043 GAGGAAGAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (24 bp):
AAGAGAAAGAAGTGGAAAAAGAGG
Found at i:26015 original size:39 final size:38
Alignment explanation
Indices: 25956--26052 Score: 90
Period size: 39 Copynumber: 2.5 Consensus size: 38
25946 AGTTGACGAG
* *
25956 AAAGAGG-AG-GAAGAGAAAGTGAAAGAGGAAGAAGTGGAA
1 AAAGAGGAAGAGAA-AG-AAGTGAAAGAAGAAGAAG-GAAA
* * *
25995 AAAGAGGAAGAGAAAGAAGTGGAGGAAGAGGAAGGAAA
1 AAAGAGGAAGAGAAAGAAGTGAAAGAAGAAGAAGGAAA
*
26033 AGAAGAGGAAGAGGAAGAAG
1 A-AAGAGGAAGAGAAAGAAG
26053 ACAGCGGAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
38 4 0.08
39 38 0.78
40 4 0.08
41 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (38 bp):
AAAGAGGAAGAGAAAGAAGTGAAAGAAGAAGAAGGAAA
Found at i:27979 original size:2 final size:2
Alignment explanation
Indices: 27972--27998 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27962 TTTTGCTCCT
27972 TA 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 TA T
27999 CTTTTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33433 original size:125 final size:127
Alignment explanation
Indices: 33206--33448 Score: 373
Period size: 125 Copynumber: 1.9 Consensus size: 127
33196 TGCTGATGTA
* * *
33206 GCATGTACATGTGTGATGTCACATCATCATTTTTAAAAATATTAATTAATAATAAATAATTATTT
1 GCATGTACACGTGTGATGCCACATCAACATTTTTAAAAATATTAATTAATAATAAATAATTATTT
*
33271 TTTACTAAATTAATAACAACCAATCAGATACTGCCACGTGGCACATGAATTTTGTTGATGCG
66 TTTACTAAATTAATAACAACCAATCAGATACTACCACGTGGCACATGAATTTTGTTGATGCG
* * *
33333 GCATGTAGACGTGTGATGCCACATCAACATTTTT-TAAA-ATTAATTAATAATAAGTAATTATTT
1 GCATGTACACGTGTGATGCCACATCAACATTTTTAAAAATATTAATTAATAATAAATAATTATTT
* * * *
33396 TTTATTAAATTAATAACAACCAATCATATGCTACCACGTGTCACATGAATTTT
66 TTTACTAAATTAATAACAACCAATCAGATACTACCACGTGGCACATGAATTTT
33449 TTATTAAATT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
125 72 0.69
126 3 0.03
127 30 0.29
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (127 bp):
GCATGTACACGTGTGATGCCACATCAACATTTTTAAAAATATTAATTAATAATAAATAATTATTT
TTTACTAAATTAATAACAACCAATCAGATACTACCACGTGGCACATGAATTTTGTTGATGCG
Found at i:33623 original size:17 final size:18
Alignment explanation
Indices: 33598--33635 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
33588 TTAAATTTAT
*
33598 ATTTAAAATTT-TAATTA
1 ATTTAAAATTTATAACTA
*
33615 ATTTTAAATTTATAACTA
1 ATTTAAAATTTATAACTA
33633 ATT
1 ATT
33636 AATATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAAATTTATAACTA
Found at i:34287 original size:34 final size:30
Alignment explanation
Indices: 34249--34317 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
34239 TTGATATAAC
34249 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
34283 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
34312 AATTTA
1 AATTTA
34318 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:34328 original size:29 final size:30
Alignment explanation
Indices: 34258--34317 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
34248 CAATTTAAGG
34258 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
34289 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
34318 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:34539 original size:20 final size:21
Alignment explanation
Indices: 34496--34591 Score: 142
Period size: 20 Copynumber: 4.7 Consensus size: 21
34486 ATGCATTTAG
* *
34496 TGCATGGATGCATCCTTTCCA
1 TGCATCGATGCATCCTTGCCA
34517 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
34537 TGCATCCATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
34558 TGCATCGATGCAT-CTTGCCA
1 TGCATCGATGCATCCTTGCCA
*
34578 TGCATCCATGCATC
1 TGCATCGATGCATC
34592 AAGGCTGCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
20 37 0.54
21 31 0.46
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:34548 original size:41 final size:41
Alignment explanation
Indices: 34503--34591 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
34493 TAGTGCATGG
*
34503 ATGCATCCTTTCCATGCATCGATGCATCCTGCCATGCATCC
1 ATGCATCCTTGCCATGCATCGATGCATCCTGCCATGCATCC
*
34544 ATGCATCCTTGCCATGCATCGATGCATCTTGCCATGCATCC
1 ATGCATCCTTGCCATGCATCGATGCATCCTGCCATGCATCC
34585 ATGCATC
1 ATGCATC
34592 AAGGCTGCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (41 bp):
ATGCATCCTTGCCATGCATCGATGCATCCTGCCATGCATCC
Found at i:34995 original size:34 final size:32
Alignment explanation
Indices: 34956--35025 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
34946 TTTTGTAAAG
* *
34956 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
34990 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
35022 GGGA
1 GGGA
35026 GTTGTAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:36548 original size:18 final size:18
Alignment explanation
Indices: 36513--36551 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
36503 ATGATCATTA
**
36513 AATTTATTAAAATTTTAT
1 AATTTATTAAAACCTTAT
*
36531 AATTTATTATAACCTTAT
1 AATTTATTAAAACCTTAT
36549 AAT
1 AAT
36552 AATCATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTATTAAAACCTTAT
Found at i:40133 original size:14 final size:14
Alignment explanation
Indices: 40113--40166 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
40103 TTCGGTTATG
*
40113 TTCGTTTATGTTCG
1 TTCGTTTATGTTCA
*
40127 TTTGTTTATGTTCA
1 TTCGTTTATGTTCA
40141 TTCGTTTATGTTCA
1 TTCGTTTATGTTCA
*
40155 TTCATTTATGTT
1 TTCGTTTATGTT
40167 TAACCCAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.13, C:0.11, G:0.15, T:0.61
Consensus pattern (14 bp):
TTCGTTTATGTTCA
Found at i:40604 original size:16 final size:16
Alignment explanation
Indices: 40583--40633 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
40573 GTCTCCAACG
*
40583 TTTATGTTCTTGTTCA
1 TTTATGTTCGTGTTCA
*
40599 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
40615 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
40629 TTTAT
1 TTTAT
40634 TAAATGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 25 0.78
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.63
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:45485 original size:2 final size:2
Alignment explanation
Indices: 45478--45517 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
45468 ATTGATTAAT
45478 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
45518 AAGATGGGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45616 original size:2 final size:2
Alignment explanation
Indices: 45609--45658 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
45599 ATCACGATTC
45609 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
45651 AT AT AT AT
1 AT AT AT AT
45659 GAGCTGACGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59396 original size:5 final size:5
Alignment explanation
Indices: 59386--59416 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
59376 CGGCAAAGAG
59386 AGCTT AGCTT AGCTT AGCTT AGCTT AGCTT A
1 AGCTT AGCTT AGCTT AGCTT AGCTT AGCTT A
59417 ACTGAGACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
AGCTT
Found at i:60166 original size:30 final size:30
Alignment explanation
Indices: 60130--60193 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
60120 GTAACACATG
* * *
60130 ACTTGATTGTTACCATCGATTAATTGAGTC
1 ACTTGATTGTTACAATCAATTAATAGAGTC
*
60160 ACTTGATTGTTACAATCAATTAATAGAGTT
1 ACTTGATTGTTACAATCAATTAATAGAGTC
60190 ACTT
1 ACTT
60194 AATAGTAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (30 bp):
ACTTGATTGTTACAATCAATTAATAGAGTC
Found at i:60515 original size:15 final size:16
Alignment explanation
Indices: 60484--60517 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
60474 TGTATCTTTT
*
60484 TAAATTAATTGATTAA
1 TAAATTAAATGATTAA
60500 TAAATTAAAT-ATTAA
1 TAAATTAAATGATTAA
60515 TAA
1 TAA
60518 TTTATCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TAAATTAAATGATTAA
Found at i:65847 original size:2 final size:2
Alignment explanation
Indices: 65840--65902 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
65830 TATTCACTCA
65840 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
65882 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
65903 ACTTGACTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66108 original size:38 final size:38
Alignment explanation
Indices: 66047--66122 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
66037 GAAAAATGAT
* * *
66047 AATTTTAGGGTTGAATTATATATTTAATCACCTAACTG
1 AATTTTAGGGGTGAAATACATATTTAATCACCTAACTG
66085 AATTTTAGGGGTGAAATACATATTTAATCACCTAACTG
1 AATTTTAGGGGTGAAATACATATTTAATCACCTAACTG
66123 TTCGAAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (38 bp):
AATTTTAGGGGTGAAATACATATTTAATCACCTAACTG
Found at i:72235 original size:19 final size:19
Alignment explanation
Indices: 72211--72248 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
72201 TGAACTGGTT
72211 TGACCCGTTAACTTTGACC
1 TGACCCGTTAACTTTGACC
*
72230 TGACCCGTTGACTTTGACC
1 TGACCCGTTAACTTTGACC
72249 AGAGTTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (19 bp):
TGACCCGTTAACTTTGACC
Done.