Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003100.1 Hibiscus syriacus cultivar Beakdansim tig00006473_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: 74965
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Found at i:8067 original size:6 final size:6
Alignment explanation
Indices: 8056--8139 Score: 75
Period size: 6 Copynumber: 14.0 Consensus size: 6
8046 CCTAAAAATG
* * * *
8056 GAAAAA GAAAAA -AGAAAA GAAAGA GAAAAG GAAAAG GAAAAG GAAAAA
1 GAAAAA GAAAAA GA-AAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
*
8104 GGAAAAA GGAAAAA GGAAAA G-AAAA GAAAAA -AAAAA
1 -GAAAAA -GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
8140 AAATGAGAGG
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
5 11 0.16
6 44 0.64
7 14 0.20
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:8962 original size:36 final size:33
Alignment explanation
Indices: 8884--8962 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 33
8874 AATCAAGGAG
*
8884 AAAAAAAGAGGAGGTCTCGAACGAAACAGAAAA
1 AAAAAAAGAGGAGGTCTCGAACCAAACAGAAAA
*
8917 AAAACAAGAGGAGGAAT-TCGAAACCAAACA-AAAA
1 AAAAAAAGAGGAGG--TCTCG-AACCAAACAGAAAA
8951 AAGGAAAAAGAG
1 AA--AAAAAGAG
8963 AGTGAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 13 0.34
34 9 0.24
35 9 0.24
36 7 0.18
ACGTcount: A:0.61, C:0.11, G:0.23, T:0.05
Consensus pattern (33 bp):
AAAAAAAGAGGAGGTCTCGAACCAAACAGAAAA
Found at i:9882 original size:2 final size:2
Alignment explanation
Indices: 9875--9933 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
9865 GATTGCTTCT
9875 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
9917 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
9934 TGATATTGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21341 original size:18 final size:18
Alignment explanation
Indices: 21313--21362 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
21303 CTTAAAAGTG
* *
21313 AATTCGTTACAATTTGTGT
1 AATT-GTTACAATGTATGT
21332 AATTGTTACAATGTATGT
1 AATTGTTACAATGTATGT
21350 AATTGTTACAATG
1 AATTGTTACAATG
21363 AACGAATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (18 bp):
AATTGTTACAATGTATGT
Found at i:21975 original size:33 final size:33
Alignment explanation
Indices: 21938--22004 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
21928 AAGGGACTTG
21938 ACTCAAACTTGAAAATCAATCCACTAATGACTA
1 ACTCAAACTTGAAAATCAATCCACTAATGACTA
21971 ACTCAAACTTGAAAATCAATCCACTAATGACTA
1 ACTCAAACTTGAAAATCAATCCACTAATGACTA
22004 A
1 A
22005 AAATTTTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (33 bp):
ACTCAAACTTGAAAATCAATCCACTAATGACTA
Found at i:22362 original size:2 final size:2
Alignment explanation
Indices: 22314--22344 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22304 AATTTAAATT
22314 TA TA 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 TA TA T
22345 TAATATTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27093 original size:17 final size:17
Alignment explanation
Indices: 27071--27111 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
27061 TATATGAAAA
*
27071 TAAAAGAAATAGTACAG
1 TAAAAGAAACAGTACAG
* *
27088 TAAAAGTAACATTACAG
1 TAAAAGAAACAGTACAG
27105 TAAAAGA
1 TAAAAGA
27112 TACAATACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (17 bp):
TAAAAGAAACAGTACAG
Found at i:27120 original size:17 final size:17
Alignment explanation
Indices: 27083--27130 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
27073 AAAGAAATAG
*
27083 TACAGTAAAAG-TAACAT
1 TACAGTAAAAGAT-ACAA
27100 TACAGTAAAAGATACAA
1 TACAGTAAAAGATACAA
* *
27117 TACAATAAGAGATA
1 TACAGTAAAAGATA
27131 TAGTACAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.21
Consensus pattern (17 bp):
TACAGTAAAAGATACAA
Found at i:27187 original size:38 final size:39
Alignment explanation
Indices: 27113--27189 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 39
27103 AGTAAAAGAT
* * *
27113 ACAATACAATAAGAGATATAGTACAATACAGTATATGAA
1 ACAACACAACAAGAGATATAGTACAATACAGGATATGAA
27152 ACAACACAACAAGAGA-ATAGTACAATA-AGGGATATGAA
1 ACAACACAACAAGAGATATAGTACAATACA-GGATATGAA
27190 TATAGATGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 1 0.03
38 19 0.56
39 14 0.41
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.18
Consensus pattern (39 bp):
ACAACACAACAAGAGATATAGTACAATACAGGATATGAA
Found at i:28010 original size:17 final size:18
Alignment explanation
Indices: 27988--28031 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
27978 CTATAATATG
*
27988 AAAATAAAAGA-AATAGT
1 AAAATAAAAGATAATAAT
*
28005 ACAATAAAA-ATAATAAT
1 AAAATAAAAGATAATAAT
28022 AAAATAAAAG
1 AAAATAAAAG
28032 TAGCATTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (18 bp):
AAAATAAAAGATAATAAT
Found at i:33497 original size:503 final size:502
Alignment explanation
Indices: 32005--33518 Score: 2627
Period size: 508 Copynumber: 3.0 Consensus size: 502
31995 AATAATGTCC
*
32005 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGAATGAGGAGCTTGGTTACGATCTAC
1 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
* *
32070 ACAAGAATCCATAATCACACATACAATATAAATTTTAGTATACTTTCTAACATTTATACAAAATA
66 ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
* *
32135 ATAATGCTCAAAAGTACTATTATTTTCCAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
131 ATAA-ACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
* *
32200 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTTCCGATACCAATTT
195 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
* * * * * *
32265 TAGTATCAATACCATTCTAGCATTTTATTTTTTATTACGATATCGATACCTTCCTCTTGTTACTG
260 CAGTATCAATACCATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCTTGGTATTG
*
32330 ATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTATTCATCCGAATCCTCTA
325 ATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCCGAATCCTCTA
* *
32395 ATTTAAACTTATAGTATCGATAATGTTCTTCTTGTACTGATACCTTTACCAAGATCTTACCTCTT
390 ATTTAACCTTATAGTATCGATAATGTTCTTCCTGTACTGATACCTTTACCAAGATCTTACCTCTT
32460 TTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
455 TTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
* *
32508 AACTATTTGATAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
1 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
*
32573 ACAAGCATCCATAATCATACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
66 ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
32638 AT--ACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATAC
131 ATAAACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATAC
*
32701 TGAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTTC
196 TAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTTC
32766 AGTATCAATACCTTTCTAGCATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCTT
261 AGTATCAATA-----C---CATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCTT
* *
32831 GGTATTGATACCTATACCTCATTATCGTTACTTTTTTAAATCGATATCGATACTGTTCATCCGAA
318 GGTATTGATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCCGAA
* * *
32896 TCCTCTAATTTAACCTTATAGTATCGATAATGATCTTCCTATACTGATACCTTTACCAAGATATT
383 TCCTCTAATTTAACCTTATAGTATCGATAATGTTCTTCCTGTACTGATACCTTTACCAAGATCTT
*
32961 ACCTCTTTTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATGT
448 ACCTCTTTTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
33016 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
1 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
33081 ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
66 ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
33146 ATAACACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
131 ATAA-ACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
33211 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
195 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
*
33276 CAGTATCAATACCATTCTAGTATTTCATTTTTGATTACGGTATCGATACCTTCCTCTTGGTATTG
260 CAGTATCAATACCATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCTTGGTATTG
* *
33341 ATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCTGAATACTCTA
325 ATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCCGAATCCTCTA
* *
33406 ATTTAACCTTATAGTATCGGTAATGTTCTTCCTGTACTGATACATTTACCAAGATCTTACCTCTT
390 ATTTAACCTTATAGTATCGATAATGTTCTTCCTGTACTGATACCTTTACCAAGATCTTACCTCTT
* *
33471 TTACTTCGAGTTTTAAGTAAATTCCACCTAAATCTCTTACTCTTATCT
455 TTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
33519 CCAACCATAT
Statistics
Matches: 957, Mismatches: 43, Indels: 22
0.94 0.04 0.02
Matches are distributed among these distances:
500 130 0.14
503 344 0.36
505 1 0.00
506 1 0.00
508 346 0.36
511 135 0.14
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (502 bp):
AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
ATAAACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATAC
TAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTTC
AGTATCAATACCATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCTTGGTATTGA
TACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCCGAATCCTCTAA
TTTAACCTTATAGTATCGATAATGTTCTTCCTGTACTGATACCTTTACCAAGATCTTACCTCTTT
TACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
Found at i:33750 original size:25 final size:23
Alignment explanation
Indices: 33722--33767 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
33712 TCAATAACTG
33722 ACCATATTTCATCAAATCACTAAAA
1 ACCAT-TTT-ATCAAATCACTAAAA
* *
33747 ACCATTTTATTAAATCTCTAA
1 ACCATTTTATCAAATCACTAA
33768 TAAATCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (23 bp):
ACCATTTTATCAAATCACTAAAA
Found at i:46021 original size:6 final size:6
Alignment explanation
Indices: 46019--46096 Score: 86
Period size: 6 Copynumber: 12.8 Consensus size: 6
46009 GGAAAAAGAA
* * * *
46019 AAAAAG AAAAAG AAAGAG AAAAGG AAAAGG AAAAGG AAAAAGG AAAAAGG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAAA-G
*
46069 AAAAAG GAAAAG -AAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
46097 AAATGAGAGG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
5 5 0.08
6 47 0.72
7 13 0.20
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:46040 original size:12 final size:11
Alignment explanation
Indices: 46020--46099 Score: 72
Period size: 11 Copynumber: 6.8 Consensus size: 11
46010 GAAAAAGAAA
46020 AAAAGAAAAAG
1 AAAAGAAAAAG
*
46031 AAAGAGAAAAGG
1 AAA-AGAAAAAG
*
46043 AAAAGGAAAAGG
1 AAAA-GAAAAAG
46055 AAAAAGGAAAAAGG
1 -AAAA-GAAAAA-G
*
46069 AAAAAGGAAAAG
1 -AAAAGAAAAAG
46081 AAAAGAAAAAG
1 AAAAGAAAAAG
46092 AAAA-AAAA
1 AAAAGAAAA
46100 TGAGAGGTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
10 4 0.07
11 18 0.30
12 18 0.30
13 15 0.25
14 6 0.10
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:46058 original size:44 final size:45
Alignment explanation
Indices: 46003--46096 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 45
45993 TATTACGCCT
*
46003 AAAAATGGAAAAAGAAAAAAAGAAAAA-GAAAGAGAAAAGGAAAAG
1 AAAAATGGAAAAAGAAAAAAAGAAAAAGGAAA-AGAAAAGAAAAAG
* * *
46048 GAAAA-GGAAAAAGGAAAAAGGAAAAAGGAAAAGAAAAGAAAAAG
1 AAAAATGGAAAAAGAAAAAAAGAAAAAGGAAAAGAAAAGAAAAAG
46092 AAAAA
1 AAAAA
46097 AAATGAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 35 0.81
45 8 0.19
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (45 bp):
AAAAATGGAAAAAGAAAAAAAGAAAAAGGAAAAGAAAAGAAAAAG
Found at i:46921 original size:36 final size:33
Alignment explanation
Indices: 46842--46921 Score: 83
Period size: 36 Copynumber: 2.3 Consensus size: 33
46832 AATCAAGGAG
*
46842 AAAAAAAGAGGAGGTCTCGAACGAAACAGAAAA
1 AAAAAAAGAGGAGGTCTCGAACCAAACAGAAAA
46875 AAAAACAAGAGGAGGAAT-TCGAAACCAAACA-AAAA
1 AAAAA-AAGAGGAGG--TCTCG-AACCAAACAGAAAA
46910 AAGGAAAAAGAG
1 AA--AAAAAGAG
46922 AGTGAAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
33 5 0.12
34 9 0.22
35 9 0.22
36 14 0.35
37 3 0.08
ACGTcount: A:0.61, C:0.11, G:0.23, T:0.05
Consensus pattern (33 bp):
AAAAAAAGAGGAGGTCTCGAACCAAACAGAAAA
Found at i:47842 original size:2 final size:2
Alignment explanation
Indices: 47835--47893 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
47825 ATTGCTTCTT
47835 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
47877 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
47894 TGATATTGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59294 original size:18 final size:18
Alignment explanation
Indices: 59266--59315 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
59256 CTTAAAAGTG
* *
59266 AATTCGTTACAATTTGTGT
1 AATT-GTTACAATGTATGT
59285 AATTGTTACAATGTATGT
1 AATTGTTACAATGTATGT
59303 AATTGTTACAATG
1 AATTGTTACAATG
59316 AACGAATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (18 bp):
AATTGTTACAATGTATGT
Found at i:59927 original size:33 final size:33
Alignment explanation
Indices: 59890--59956 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
59880 AAGGGACTTG
59890 ACTCAAACTTGAAAATCAATCCACTAATGACTA
1 ACTCAAACTTGAAAATCAATCCACTAATGACTA
59923 ACTCAAACTTGAAAATCAATCCACTAATGACTA
1 ACTCAAACTTGAAAATCAATCCACTAATGACTA
59956 A
1 A
59957 AAATTTTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (33 bp):
ACTCAAACTTGAAAATCAATCCACTAATGACTA
Found at i:60312 original size:2 final size:2
Alignment explanation
Indices: 60262--60300 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
60252 AATTTAAATT
60262 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
60301 TTCTTAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65030 original size:17 final size:17
Alignment explanation
Indices: 65008--65048 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
64998 TATATGAAAA
*
65008 TAAAAGAAATAGTACAG
1 TAAAAGAAACAGTACAG
* *
65025 TAAAAGTAACATTACAG
1 TAAAAGAAACAGTACAG
65042 TAAAAGA
1 TAAAAGA
65049 TACAATACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (17 bp):
TAAAAGAAACAGTACAG
Found at i:65057 original size:17 final size:17
Alignment explanation
Indices: 65020--65067 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
65010 AAAGAAATAG
*
65020 TACAGTAAAAG-TAACAT
1 TACAGTAAAAGAT-ACAA
65037 TACAGTAAAAGATACAA
1 TACAGTAAAAGATACAA
* *
65054 TACAATAAGAGATA
1 TACAGTAAAAGATA
65068 TAGTACAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.21
Consensus pattern (17 bp):
TACAGTAAAAGATACAA
Found at i:65124 original size:38 final size:39
Alignment explanation
Indices: 65050--65126 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 39
65040 AGTAAAAGAT
* * *
65050 ACAATACAATAAGAGATATAGTACAATACAGTATATGAA
1 ACAACACAACAAGAGATATAGTACAATACAGGATATGAA
65089 ACAACACAACAAGAGA-ATAGTACAATA-AGGGATATGAA
1 ACAACACAACAAGAGATATAGTACAATACA-GGATATGAA
65127 TATAGATGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 1 0.03
38 19 0.56
39 14 0.41
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.18
Consensus pattern (39 bp):
ACAACACAACAAGAGATATAGTACAATACAGGATATGAA
Found at i:65947 original size:17 final size:18
Alignment explanation
Indices: 65925--65968 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
65915 CTATAATATG
*
65925 AAAATAAAAGA-AATAGT
1 AAAATAAAAGATAATAAT
*
65942 ACAATAAAA-ATAATAAT
1 AAAATAAAAGATAATAAT
65959 AAAATAAAAG
1 AAAATAAAAG
65969 TAGCATTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (18 bp):
AAAATAAAAGATAATAAT
Found at i:69943 original size:45 final size:45
Alignment explanation
Indices: 69848--70011 Score: 242
Period size: 45 Copynumber: 3.7 Consensus size: 45
69838 GATAAACATG
* *
69848 AAAATAAGCTTACGAGCTTATCGAAT-AATGATAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
69892 AAAATAAGCTTATGAGCTTATGGAGTAAATGGTAAGTATATTAGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
69937 AAAATAAGCTTACGGGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
69982 AGAATAAGCTTACGAGCTTATAGG-ATAAAT
1 AAAATAAGCTTACGAGCTTAT-GGAATAAAT
70012 AATAAGAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
44 23 0.21
45 82 0.77
46 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:72863 original size:15 final size:15
Alignment explanation
Indices: 72857--72923 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 15
72847 AAAATAATAT
72857 AAGAAAAAACAAAAA
1 AAGAAAAAACAAAAA
*
72872 AAGAAAAAAAAAGAAAA
1 AAG-AAAAAACA-AAAA
*
72889 AAGAAAATGAAGAAAAA
1 AAGAAAA--AACAAAAA
*
72906 ATAGAAAAAAGAAAAA
1 A-AGAAAAAACAAAAA
72922 AA
1 AA
72924 AAATGATGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
15 4 0.09
16 20 0.44
17 12 0.27
18 9 0.20
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (15 bp):
AAGAAAAAACAAAAA
Found at i:72878 original size:7 final size:7
Alignment explanation
Indices: 72857--72926 Score: 58
Period size: 7 Copynumber: 10.0 Consensus size: 7
72847 AAAATAATAT
72857 AAGAAAA
1 AAGAAAA
*
72864 AA-CAAA
1 AAGAAAA
*
72870 AA-AAGA
1 AAGAAAA
72876 AA-AAAA
1 AAGAAAA
72882 AAGAAAA
1 AAGAAAA
72889 AAGAAAA
1 AAGAAAA
72896 TGAAGAAAAA
1 --AAG-AAAA
72906 ATAGAAAA
1 A-AGAAAA
72914 AAGAAAA
1 AAGAAAA
72921 AA-AAAA
1 AAGAAAA
72927 TGATGAGATG
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
6 18 0.33
7 21 0.39
8 6 0.11
9 5 0.09
10 4 0.07
ACGTcount: A:0.84, C:0.01, G:0.11, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:72879 original size:9 final size:9
Alignment explanation
Indices: 72867--72926 Score: 61
Period size: 9 Copynumber: 6.8 Consensus size: 9
72857 AAGAAAAAAC
72867 AAAAAAAGA
1 AAAAAAAGA
72876 AAAAAAA-A
1 AAAAAAAGA
*
72884 GAAAAAAGA
1 AAAAAAAGA
**
72893 AAATGAAGA
1 AAAAAAAGA
*
72902 AAAAATAGA
1 AAAAAAAGA
72911 AAAAAGAA-A
1 AAAAA-AAGA
72920 AAAAAAA
1 AAAAAAA
72927 TGATGAGATG
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
8 9 0.22
9 31 0.76
10 1 0.02
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:72885 original size:25 final size:24
Alignment explanation
Indices: 72857--72923 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 24
72847 AAAATAATAT
*
72857 AAGAAAAAACAAAAAAAGAAAAAAA
1 AAGAAAAAAGAAAAAAAG-AAAAAA
*
72882 AAGAAAAAAGAAAATGAAGAAAAAA
1 AAGAAAAAAGAAAA-AAAGAAAAAA
*
72907 TAGAAAAAAGAAAAAAA
1 AAGAAAAAAGAAAAAAA
72924 AAATGATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 2 0.05
25 32 0.86
26 3 0.08
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAGAAAAAAAGAAAAAA
Found at i:72893 original size:32 final size:35
Alignment explanation
Indices: 72857--72926 Score: 92
Period size: 36 Copynumber: 2.1 Consensus size: 35
72847 AAAATAATAT
*
72857 AAGAAAA-AACAAAAAA-AGAAAAAA-AAAGAAAA
1 AAGAAAAGAACAAAAAATAGAAAAAAGAAAAAAAA
*
72889 AAGAAAATGAAGAAAAAATAGAAAAAAGAAAAAAAA
1 AAGAAAA-GAACAAAAAATAGAAAAAAGAAAAAAAA
72925 AA
1 AA
72927 TGATGAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 7 0.22
34 8 0.25
35 8 0.25
36 9 0.28
ACGTcount: A:0.84, C:0.01, G:0.11, T:0.03
Consensus pattern (35 bp):
AAGAAAAGAACAAAAAATAGAAAAAAGAAAAAAAA
Done.