Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000723.1 Hibiscus syriacus cultivar Beakdansim tig00001402_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: 72574
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:6778 original size:23 final size:23
Alignment explanation
Indices: 6730--6781 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
6720 AGGTGTCAAA
* *
6730 TAGATTTGTCCCGAAGGACCATG
1 TAGAATTGTCCCGAAGGACCACG
* *
6753 TAGAATTGTTCCGAAGGACCGCG
1 TAGAATTGTCCCGAAGGACCACG
6776 TAGAAT
1 TAGAAT
6782 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCACG
Found at i:12834 original size:41 final size:41
Alignment explanation
Indices: 12786--12909 Score: 239
Period size: 41 Copynumber: 3.0 Consensus size: 41
12776 TTATCTCCAC
12786 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
1 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
12827 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
1 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
*
12868 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCTAGGTA
1 AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
12909 A
1 A
12910 TGAATTGTAG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (41 bp):
AGACTCCAAGGAGTTTATCTGGTTTTGGAATCCTCCAGGTA
Found at i:16889 original size:2 final size:2
Alignment explanation
Indices: 16877--16914 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
16867 ATCTTATGTT
* *
16877 CA CA CA GA CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
16915 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.47, G:0.05, T:0.00
Consensus pattern (2 bp):
CA
Found at i:16919 original size:2 final size:2
Alignment explanation
Indices: 16914--16941 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16904 ACACACACAC
16914 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
16942 CAATGATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21265 original size:23 final size:23
Alignment explanation
Indices: 21239--21328 Score: 99
Period size: 23 Copynumber: 3.9 Consensus size: 23
21229 CACCACAGCT
*
21239 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
21262 CGTAGAATTGCACCGTAGTACCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
21285 CGTAGAATTGTACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
21308 CGTAGAAATACACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
21329 TATATAAGGT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:29952 original size:22 final size:22
Alignment explanation
Indices: 29935--30023 Score: 160
Period size: 22 Copynumber: 4.0 Consensus size: 22
29925 CTCGTATAAA
29935 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
29957 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
29979 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
30001 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
30023 T
1 T
30024 ATGTCCATAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:29988 original size:13 final size:13
Alignment explanation
Indices: 29948--30010 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
29938 ACCGAAGTGC
29948 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
29961 CC---GAAGTGC-
1 CCGTAGAATTGCA
29970 CCGTAGAATTGCA
1 CCGTAGAATTGCA
29983 CCGTAG---TGC-
1 CCGTAGAATTGCA
29992 CCGTAGAATTGCA
1 CCGTAGAATTGCA
30005 CCGTAG
1 CCGTAG
30011 TGCCCGTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 8 0.20
10 9 0.22
12 9 0.22
13 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:52080 original size:21 final size:21
Alignment explanation
Indices: 52052--52099 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
52042 AAATTCGCGT
*
52052 TGCG-ATTACGTAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
*
52072 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
52093 TGCGAAT
1 TGCGAAT
52100 CTGACTATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
TGCGAATTACGAAAATCGCAA
Found at i:52687 original size:19 final size:20
Alignment explanation
Indices: 52645--52699 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
52635 TAGTTTCGAG
52645 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
**
52665 AATGACTATCGCAACGC-GA
1 AATGAAAATCGCAACGCGGA
52684 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
52700 AGATAATCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:52810 original size:20 final size:19
Alignment explanation
Indices: 52742--52818 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 19
52732 GCGATTCTCT
52742 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
52761 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
*
52781 CGTTGCGATTTTCATTATCT
1 CGTTGCGATTTTCATT-TCG
52801 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
52819 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 17 0.33
20 33 0.65
21 1 0.02
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:54693 original size:94 final size:93
Alignment explanation
Indices: 54502--54877 Score: 634
Period size: 94 Copynumber: 4.1 Consensus size: 93
54492 TAGATTACTT
* *
54502 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
54563 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
54592 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
54657 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
54686 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
54751 ATTTATCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
54780 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
54845 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
54873 AGTAA
1 AGTAA
54878 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
90 35 0.13
92 3 0.01
93 28 0.10
94 208 0.76
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:55038 original size:19 final size:19
Alignment explanation
Indices: 54976--55041 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
54966 TATCTTTTGG
*
54976 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTTA
*
54995 TTTCGCGTTACGA----T-
1 TTTCGCGTTGCGATTTTTA
* *
55009 TCTCTCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTTTTA
55028 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
55042 AGTGATTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
14 10 0.29
18 1 0.03
19 24 0.69
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTTA
Found at i:55542 original size:21 final size:21
Alignment explanation
Indices: 55518--55584 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
55508 TCATTCCTCG
55518 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
55539 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
55560 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
55581 AGAG
1 AGAG
55585 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:55542 original size:42 final size:42
Alignment explanation
Indices: 55491--55584 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
55481 CCACTCTTAT
* *
55491 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
55533 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
55575 CATTCAAGAG
1 CGTTCAAGAG
55585 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:56898 original size:14 final size:14
Alignment explanation
Indices: 56879--56914 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
56869 ATTGTTTAAT
56879 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
56893 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
56907 TGATTTGT
1 TGATTTGT
56915 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:57043 original size:19 final size:18
Alignment explanation
Indices: 57021--57152 Score: 92
Period size: 19 Copynumber: 7.7 Consensus size: 18
57011 AAAAATGACT
57021 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
57040 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
57054 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
57073 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
57087 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
57106 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
57120 ATCGCAACGCGAAACT-AAA
1 ATCGCAA-GCGAAA-TGAAA
57139 ATCGCAAAGCGAAA
1 ATCGC-AAGCGAAA
57153 CTAAATTCGC
Statistics
Matches: 91, Mismatches: 5, Indels: 34
0.70 0.04 0.26
Matches are distributed among these distances:
14 30 0.33
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 41 0.45
20 2 0.02
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:57058 original size:14 final size:14
Alignment explanation
Indices: 57039--57093 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
57029 GCGAAATGAA
57039 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
57053 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
57072 AATCGCAACGAGAG
1 AATCGCAACGAGAG
57086 AATCGCAA
1 AATCGCAA
57094 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:57066 original size:33 final size:33
Alignment explanation
Indices: 57021--57145 Score: 198
Period size: 33 Copynumber: 3.8 Consensus size: 33
57011 AAAAATGACT
*
57021 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
57054 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
57087 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
57120 ATCGCAACGCGAAACT-AAAATCGCAA
1 ATCGCAACGCGAAA-TGAAAATCGCAA
57146 AGCGAAACTA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:57169 original size:19 final size:19
Alignment explanation
Indices: 57086--57162 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
57076 GCAACGAGAG
*
57086 AATCGCAATGCGAAA-TGAA
1 AATCGCAAAGCGAAACT-AA
57105 AATCGC-AA-CG--AC-AA
1 AATCGCAAAGCGAAACTAA
*
57119 AATCGCAACGCGAAACTAA
1 AATCGCAAAGCGAAACTAA
57138 AATCGCAAAGCGAAACTAA
1 AATCGCAAAGCGAAACTAA
*
57157 ATTCGC
1 AATCGC
57163 GTTGCGATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.17
15 2 0.04
16 2 0.04
17 2 0.04
18 3 0.06
19 31 0.65
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (19 bp):
AATCGCAAAGCGAAACTAA
Found at i:57180 original size:19 final size:19
Alignment explanation
Indices: 57158--57308 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
57148 CGAAACTAAA
57158 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
57177 TTCGCTTTGCGA-TTT--T
1 TTCGCGTTGCGATTTTCAT
*
57193 GT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
57210 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
57225 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
57243 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
57258 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
57276 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
57295 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
57309 AGACATTAAG
Statistics
Matches: 98, Mismatches: 18, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 24 0.24
15 3 0.03
16 8 0.08
17 8 0.08
18 3 0.03
19 42 0.43
20 10 0.10
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:57204 original size:33 final size:33
Alignment explanation
Indices: 57162--57288 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
57152 ACTAAATTCG
* * *
57162 CGTTGCGATTTTCATTTCGCTTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
57195 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
57228 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
57261 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
57289 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:57307 original size:20 final size:20
Alignment explanation
Indices: 57261--57354 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
57251 GCGATTCTCT
**
57261 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
57280 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
57300 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
57319 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
57341 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
57355 AATGATTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:59849 original size:24 final size:24
Alignment explanation
Indices: 59815--59868 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
59805 CTGAAACATC
*
59815 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
59839 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
59863 ATCAAA
1 ATCAAA
59869 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:60625 original size:20 final size:20
Alignment explanation
Indices: 60604--60708 Score: 165
Period size: 20 Copynumber: 5.2 Consensus size: 20
60594 TGTATTATCT
* *
60604 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
*
60624 CGTTGCGAAAGTCAAAATCG
1 CGTTGCGAAAGTCAGAATCG
60644 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
60664 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
60684 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
60704 CGTTG
1 CGTTG
60709 TAATTTTGTA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:60753 original size:20 final size:20
Alignment explanation
Indices: 60599--60752 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
60589 GATTCTGTAT
* *
60599 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
60619 AATCTCGTTGCGAAAGTCAA
1 TATCGCGTTGCGAAAGTCAG
*
60639 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
60659 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
60679 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
60699 TATCGCGTTG-TAATTTTGT-AT
1 TATCGCGTTGCGAA---AGTCAG
*
60720 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
60740 TATCGCATTGCGA
1 TATCGCGTTGCGA
60753 TTTTCCAAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.03
20 97 0.84
21 11 0.10
22 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:60786 original size:20 final size:21
Alignment explanation
Indices: 60742--60793 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
60732 ATAGTCAGTA
*
60742 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
60763 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
60783 TCGCATTGCGA
1 TCGCATTGCGA
60794 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:60835 original size:21 final size:22
Alignment explanation
Indices: 60783--60835 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
60773 ATTTACTTAT
*
60783 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGAAAAA
**
60804 TCGCAACGCGAAATT-GAAAAA
1 TCGCATTGCGAAATTGGAAAAA
60825 TCGCATTGCGA
1 TCGCATTGCGA
60836 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:65675 original size:2 final size:2
Alignment explanation
Indices: 65668--65707 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
65658 TCAAAGAAGG
65668 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
65708 TTTCTTTGTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:66095 original size:14 final size:14
Alignment explanation
Indices: 66076--66102 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
66066 TTAGGGGTTT
66076 ATCTGTTATTCATG
1 ATCTGTTATTCATG
66090 ATCTGTTATTCAT
1 ATCTGTTATTCAT
66103 ATATACGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (14 bp):
ATCTGTTATTCATG
Found at i:66386 original size:13 final size:13
Alignment explanation
Indices: 66359--66397 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
66349 TTTATTTTTA
*
66359 TTTAA-TTTAATT
1 TTTAATTTTAAAT
*
66371 TTTATTTTTAAAT
1 TTTAATTTTAAAT
66384 TTTAATTTTAAAT
1 TTTAATTTTAAAT
66397 T
1 T
66398 ATAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTAATTTTAAAT
Found at i:67546 original size:21 final size:20
Alignment explanation
Indices: 67504--67546 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
67494 ATTATTTAAT
*
67504 AATTATATGTAAAATGTTTC
1 AATTATATGTAAAATGTATC
67524 AATTATAATGTAAGAAT-TATC
1 AATTAT-ATGTAA-AATGTATC
67545 AA
1 AA
67547 ATGTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 11 0.55
22 3 0.15
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (20 bp):
AATTATATGTAAAATGTATC
Found at i:68032 original size:22 final size:22
Alignment explanation
Indices: 68005--68051 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
67995 ATTTAAAAAA
*
68005 ATTATAACTAAT-AATATTAATT
1 ATTAT-ACTAATAAATATTAAAT
*
68027 ATTATATTAATAAATATTAAAT
1 ATTATACTAATAAATATTAAAT
68049 ATT
1 ATT
68052 TTATGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTATACTAATAAATATTAAAT
Found at i:70986 original size:8 final size:8
Alignment explanation
Indices: 70973--71010 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
70963 CTCATTTTCA
70973 GAGAATTT
1 GAGAATTT
70981 GAGAATTT
1 GAGAATTT
*
70989 -AGAGTTT
1 GAGAATTT
*
70996 GGGAATTT
1 GAGAATTT
71004 GAGAATT
1 GAGAATT
71011 GAAAGATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:71314 original size:125 final size:125
Alignment explanation
Indices: 71082--71447 Score: 548
Period size: 125 Copynumber: 2.9 Consensus size: 125
71072 ATAATCGGAG
* *
71082 TACTATTTACATGAAGGCGTGTTCCC--GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
71145 TCATTGCCCTATTATGTCACTCATATCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTA-TAT
*
71206 TCACTATTCACATGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTA-TTCGTCAGAG-A-ATGTT
1 T-ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTT
71268 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGGACACTAGATATATCAGTACCTATAT
65 ATCATTGCCCTATTATGTCACTCATGTCCCTC-GGGGACACTAGATATATCAGTACCTATAT
* *** * *
71330 TTCTCAGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGT
1 TACT-A-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
71395 TATCATTGCCCTA-T-TGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
64 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
71448 AATCAGGTAA
Statistics
Matches: 222, Mismatches: 11, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
123 2 0.01
124 42 0.19
125 108 0.49
126 35 0.16
127 18 0.08
128 17 0.08
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (125 bp):
TACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATAT
Found at i:71826 original size:17 final size:18
Alignment explanation
Indices: 71800--71833 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
71790 ATAATTATAT
*
71800 AAATATTATTTA-ATAAA
1 AAATAATATTTACATAAA
71817 AAATAATATTTACATAA
1 AAATAATATTTACATAA
71834 TATATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATATTTACATAAA
Found at i:71843 original size:29 final size:34
Alignment explanation
Indices: 71780--71856 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 34
71770 AAATTAATTC
*
71780 TAAATAAATAATAATTATATAAATATTATTT-A-A
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
*
71813 TAAAAAATAATATTTACAT-AATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
71844 TAAAAAATAATAA
1 TAAAAAATAATAA
71857 ACTATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 2 0.05
30 3 0.08
31 17 0.44
32 13 0.33
33 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:71847 original size:31 final size:32
Alignment explanation
Indices: 71780--71856 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
71770 AAATTAATTC
* *
71780 TAAATAAATAATAATTATATAAATATTATTTAA
1 TAAA-AAATAATAATTACATAAATATTATATAA
*
71813 TAAAAAATAATATTTACATAATATATTA-AT-A
1 TAAAAAATAATAATTACATAA-ATATTATATAA
71844 TAAAAAATAATAA
1 TAAAAAATAATAA
71857 ACTATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 13 0.33
32 16 0.41
33 10 0.26
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATATAA
Done.