Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000411.1 Hibiscus syriacus cultivar Beakdansim tig00000757_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: 77773
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2007 original size:15 final size:14
Alignment explanation
Indices: 1987--2016 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1977 AAATTATGGA
1987 AAATTTTAAACTTTT
1 AAATTTTAAA-TTTT
2002 AAATTTTAAATTTT
1 AAATTTTAAATTTT
2016 A
1 A
2017 TATCAACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATTTTAAATTTT
Found at i:2010 original size:7 final size:7
Alignment explanation
Indices: 1987--2016 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1977 AAATTATGGA
1987 AAATTTT
1 AAATTTT
1994 AAACTTTT
1 AAA-TTTT
2002 AAATTTT
1 AAATTTT
2009 AAATTTT
1 AAATTTT
2016 A
1 A
2017 TATCAACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (7 bp):
AAATTTT
Found at i:2253 original size:19 final size:19
Alignment explanation
Indices: 2229--2288 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
2219 TTATTTATAA
2229 ATTTTAATAACTCAGTTAT
1 ATTTTAATAACTCAGTTAT
* *
2248 ATTTTAAT---TTA--TAA
1 ATTTTAATAACTCAGTTAT
*
2262 ATTTTATTAACTCAGTTAT
1 ATTTTAATAACTCAGTTAT
2281 ATTTTAAT
1 ATTTTAAT
2289 TTAATTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
14 9 0.30
16 2 0.07
17 2 0.07
19 17 0.57
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTTAATAACTCAGTTAT
Found at i:2258 original size:33 final size:33
Alignment explanation
Indices: 2221--2291 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
2211 GATCTCTATT
2221 ATTTATAAATTTTAATAACTCAGTTATATTTTA
1 ATTTATAAATTTTAATAACTCAGTTATATTTTA
*
2254 ATTTATAAATTTTATTAACTCAGTTATATTTTA
1 ATTTATAAATTTTAATAACTCAGTTATATTTTA
2287 ATTTA
1 ATTTA
2292 ATTTAATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (33 bp):
ATTTATAAATTTTAATAACTCAGTTATATTTTA
Found at i:2820 original size:2 final size:2
Alignment explanation
Indices: 2805--2858 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
2795 CACCATTTTG
*
2805 AT AT AT A- AT TT AT AT AT -T CAT 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
2846 AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT
2859 GAAAAGGGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 3 0.07
2 42 0.91
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:7336 original size:14 final size:14
Alignment explanation
Indices: 7314--7347 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7304 ATGAAAATCC
7314 TAAACCTTAAACCA
1 TAAACCTTAAACCA
* *
7328 TAAATCTTAAACCC
1 TAAACCTTAAACCA
7342 TAAACC
1 TAAACC
7348 CTAACCATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:7338 original size:21 final size:21
Alignment explanation
Indices: 7308--7347 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7298 TTGTTGATGA
*
7308 AAATCCTAAACCTTAAACCAT
1 AAATCCTAAACCCTAAACCAT
*
7329 AAATCTTAAACCCTAAACC
1 AAATCCTAAACCCTAAACC
7348 CTAACCATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATCCTAAACCCTAAACCAT
Found at i:7565 original size:14 final size:13
Alignment explanation
Indices: 7526--7581 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
7516 CAATGGTTAA
7526 GGTTTAGGTTTTAG
1 GGTTTAGG-TTTAG
*
7540 GATTATA-GTTTAG
1 GGTT-TAGGTTTAG
7553 GGTTTAGGATTTAG
1 GGTTTAGG-TTTAG
*
7567 GGTTTTTGGTTTAG
1 GG-TTTAGGTTTAG
7581 G
1 G
7582 ATTTTCATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 2 0.06
13 9 0.26
14 17 0.49
15 7 0.20
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (13 bp):
GGTTTAGGTTTAG
Found at i:7571 original size:21 final size:20
Alignment explanation
Indices: 7525--7585 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
7515 TCAATGGTTA
*
7525 AGGTTTAGGTTTTAGGATTAT
1 AGGTTTAGGGTTTAGGATT-T
7546 A-GTTTAGGGTTTAGGATTT
1 AGGTTTAGGGTTTAGGATTT
**
7565 AGGGTTTTTGGTTTAGGATTT
1 A-GGTTTAGGGTTTAGGATTT
7586 TCATCAACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 17 0.49
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (20 bp):
AGGTTTAGGGTTTAGGATTT
Found at i:7878 original size:7 final size:7
Alignment explanation
Indices: 7830--7881 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
7820 TTGAAAATCT
*
7830 TAAACCT
1 TAAACCC
7837 TAAACCC
1 TAAACCC
7844 TAAACCC
1 TAAACCC
7851 TTAAA--C
1 -TAAACCC
*
7857 TATAATCC
1 TA-AACCC
7865 TAAACCC
1 TAAACCC
7872 TAAACCC
1 TAAACCC
7879 TAA
1 TAA
7882 TTATTGATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 2 0.05
6 3 0.08
7 27 0.69
8 7 0.18
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:9235 original size:23 final size:23
Alignment explanation
Indices: 9197--9259 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
9187 CAACTCATAT
9197 AAATGCACCG-AGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
9219 AATTGCACCTAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
9242 AAATGGACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
9260 TATAAGATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 8 0.24
23 25 0.76
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:10247 original size:20 final size:22
Alignment explanation
Indices: 10222--10279 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
10212 TTCCCCTTGA
10222 AGTGCATCGATGCATTC-TA-C
1 AGTGCATCGATGCATTCTTAGC
10242 AGTGCATCGATGCATTCTTTAGC
1 AGTGCATCGATGCATTC-TTAGC
10265 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
10280 CCCCTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 2 0.06
23 2 0.06
24 13 0.38
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAGC
Found at i:11220 original size:23 final size:23
Alignment explanation
Indices: 11193--11247 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
11183 TATATACACT
*
11193 GAAGTGCCACGTAGAATTGCACC
1 GAAGTGCCACGTAGAAATGCACC
*
11216 TAAGTGCCACGTAGAAATGCACC
1 GAAGTGCCACGTAGAAATGCACC
11239 GAAGTGCCA
1 GAAGTGCCA
11248 TATAAGATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.16
Consensus pattern (23 bp):
GAAGTGCCACGTAGAAATGCACC
Found at i:12263 original size:24 final size:20
Alignment explanation
Indices: 12206--12243 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12196 TTCCCATTGA
12206 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
12226 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
12244 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:12338 original size:64 final size:62
Alignment explanation
Indices: 12251--12411 Score: 214
Period size: 64 Copynumber: 2.5 Consensus size: 62
12241 TCTTTAACAT
* * *
12251 GTGCATTGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGG
* * * * *
12314 GATGCATCGATGCACTCCTTATGCATTGATGCACTACTTGCATTCGATGTTTCCATTTTAAGGG
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGG
12378 GTGCATCGATGCACTTCCTATGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
12412 CTAAACAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 29 0.35
64 55 0.65
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGG
Found at i:17286 original size:14 final size:14
Alignment explanation
Indices: 17269--17296 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17259 ATCATTAAAA
17269 AATTATATAACTAT
1 AATTATATAACTAT
17283 AATTATATAACTAT
1 AATTATATAACTAT
17297 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:23342 original size:20 final size:20
Alignment explanation
Indices: 23319--23360 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
23309 TCAACCGTTG
23319 CTATTGAGCCACAACCTTCA
1 CTATTGAGCCACAACCTTCA
23339 CTATTGAGCCACAACCTTCA
1 CTATTGAGCCACAACCTTCA
23359 CT
1 CT
23361 TCTGCTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.36, G:0.10, T:0.26
Consensus pattern (20 bp):
CTATTGAGCCACAACCTTCA
Found at i:23894 original size:24 final size:24
Alignment explanation
Indices: 23862--23910 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
23852 TTTTTTTCTC
23862 TAGGTTTTTGTTTGAGGCAATAAA
1 TAGGTTTTTGTTTGAGGCAATAAA
23886 TAGGTTTTTGTTTGAGGCAATAAA
1 TAGGTTTTTGTTTGAGGCAATAAA
23910 T
1 T
23911 TGAAGGTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (24 bp):
TAGGTTTTTGTTTGAGGCAATAAA
Found at i:35973 original size:10 final size:10
Alignment explanation
Indices: 35958--36025 Score: 67
Period size: 10 Copynumber: 7.1 Consensus size: 10
35948 CTGGTTTTTA
35958 ACCGGTTCTG
1 ACCGGTTCTG
35968 ACCGGTT-TG
1 ACCGGTTCTG
35977 ACCGGTT-TCG
1 ACCGGTTCT-G
35987 ACCGGTTC-G
1 ACCGGTTCTG
35996 AACCGGTT-TG
1 -ACCGGTTCTG
36006 ACCGG-TCTG
1 ACCGGTTCTG
36015 AACCGG-TCTG
1 -ACCGGTTCTG
36025 A
1 A
36026 ACCAGTCTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.02
9 19 0.37
10 32 0.62
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:35982 original size:19 final size:20
Alignment explanation
Indices: 35938--36021 Score: 86
Period size: 19 Copynumber: 4.3 Consensus size: 20
35928 GCTGCTGGAA
* * * *
35938 ACCGGTTTAACTGGTTTTTA
1 ACCGGTTTGACCGGTTCTGA
35958 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
35977 ACCGGTTTCGACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
35997 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
36016 ACCGGT
1 ACCGGT
36022 CTGAACCAGT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
18 3 0.05
19 30 0.54
20 16 0.29
21 7 0.12
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:36019 original size:29 final size:30
Alignment explanation
Indices: 35957--36025 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
35947 ACTGGTTTTT
*
35957 AACCGGTTCTGACCGGTTTGACCGGTTTCG
1 AACCGGTTCTGACCGGTTTGACCGGTCTCG
35987 -ACCGGTTC-GAACCGGTTTGACCGGTCT-G
1 AACCGGTTCTG-ACCGGTTTGACCGGTCTCG
36015 AACCGG-TCTGA
1 AACCGGTTCTGA
36026 ACCAGTCTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
28 5 0.14
29 30 0.86
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (30 bp):
AACCGGTTCTGACCGGTTTGACCGGTCTCG
Found at i:36026 original size:10 final size:10
Alignment explanation
Indices: 35957--36035 Score: 60
Period size: 10 Copynumber: 8.1 Consensus size: 10
35947 ACTGGTTTTT
35957 AACCGGTTCTG
1 AACCGG-TCTG
*
35968 -ACCGGTTTG
1 AACCGGTCTG
*
35977 -ACCGGTTTCG
1 AACCGGTCT-G
35987 -ACCGGT-TCG
1 AACCGGTCT-G
*
35996 AACCGGTTTG
1 AACCGGTCTG
36006 -ACCGGTCTG
1 AACCGGTCTG
36015 AACCGGTCTG
1 AACCGGTCTG
*
36025 AACCAGTCTG
1 AACCGGTCTG
36035 A
1 A
36036 CCCGACCGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
9 22 0.36
10 38 0.62
11 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (10 bp):
AACCGGTCTG
Found at i:36027 original size:29 final size:30
Alignment explanation
Indices: 35957--36037 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
35947 ACTGGTTTTT
*
35957 AACCGGTTCTG-ACCGGTTTGACCGGTTTCG
1 AACCGG-TCTGAACCGGTTTGACCGGTCTCG
35987 -ACCGGT-TCGAACCGGTTTGACCGGTCT-G
1 AACCGGTCT-GAACCGGTTTGACCGGTCTCG
* *
36015 AACCGGTCTGAACCAGTCTGACC
1 AACCGGTCTGAACCGGTTTGACC
36038 CGACCGTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 1 0.02
28 3 0.07
29 39 0.89
30 1 0.02
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (30 bp):
AACCGGTCTGAACCGGTTTGACCGGTCTCG
Found at i:54945 original size:6 final size:6
Alignment explanation
Indices: 54934--54962 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54924 ATTTATTAGA
54934 CTAATC CTAATC CTAATC CTAATC CTAAT
1 CTAATC CTAATC CTAATC CTAATC CTAAT
54963 ATTATTTAAT
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):
CTAATC
Found at i:56398 original size:82 final size:81
Alignment explanation
Indices: 56251--56407 Score: 260
Period size: 82 Copynumber: 1.9 Consensus size: 81
56241 AATAATTTAT
* * *
56251 GGTGATTATAAGATAATGTTTATTTGGAATTTTTTAATCTATTGACAATACATATTTAACAAACC
1 GGTGATTATAAGATAATATTTATTTAGAATTTTTTAATCTATTGACAATACATATTCAACAAACC
56316 TAATTATTTGAATTAG
66 TAATTATTTGAATTAG
*
56332 GGTGATTATAAGATAATATTTATTTAGAATTTTCTTAATCTATTGATAATACATATTCAACAAAC
1 GGTGATTATAAGATAATATTTATTTAGAATTTT-TTAATCTATTGACAATACATATTCAACAAAC
*
56397 CTAATTGTTTG
65 CTAATTATTTG
56408 GAGTCAACAC
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 31 0.44
82 39 0.56
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.43
Consensus pattern (81 bp):
GGTGATTATAAGATAATATTTATTTAGAATTTTTTAATCTATTGACAATACATATTCAACAAACC
TAATTATTTGAATTAG
Found at i:60674 original size:60 final size:60
Alignment explanation
Indices: 60546--60676 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 60
60536 AATTAAACCT
* * * *
60546 GATAAGTTTAGTCTCTTTTAATTAGGTGCCTAGTTTATTAAATTAGATAATAGTTCAGCC
1 GATAAGTTTAGTCTCTTTCAATTAGGTGCCTACTTTATTAAATAAGATAATAGATCAGCC
* * *
60606 TA-ATAGTTTAG-CTTCTTTCAATTAGGTGCTTACTTTATT-AATAAGTTAAT-GATCAAGCAC
1 GATA-AGTTTAGTC-TCTTTCAATTAGGTGCCTACTTTATTAAATAAGATAATAGATC-AGC-C
60666 GATAAGTTTAG
1 GATAAGTTTAG
60677 GTGCTTTTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
58 3 0.05
59 14 0.24
60 40 0.69
61 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (60 bp):
GATAAGTTTAGTCTCTTTCAATTAGGTGCCTACTTTATTAAATAAGATAATAGATCAGCC
Found at i:61768 original size:19 final size:19
Alignment explanation
Indices: 61746--61790 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
61736 TTGTATTGCC
*
61746 ATTAATT-TTTAATTTATTG
1 ATTAATTATTT-ATTTATTA
*
61765 ATTAATTATTTTTTTATTA
1 ATTAATTATTTATTTATTA
61784 ATTAATT
1 ATTAATT
61791 CAAATCGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTAATTATTTATTTATTA
Found at i:64449 original size:78 final size:81
Alignment explanation
Indices: 64296--64462 Score: 243
Period size: 78 Copynumber: 2.1 Consensus size: 81
64286 ACATCTCGTG
*
64296 TTACGAAAACTAATTTCTGTATTTCACATTAAAGTCCTTATGAATCCAACAATAAATAACAACTC
1 TTACAAAAACTAATTTCTGTATTTCACATTAAAGTCCTTATGAATCC-ACAATAAATAACAACTC
64361 AAGCCTAGTTATATTGT
65 AAGCCTAGTTATATTGT
* * *
64378 TTACAAAAACTGATTTGTGTATTTCACA-TAAAGTCCTTATGAAT-C-CAAT-AATGAACAATTC
1 TTACAAAAACTAATTTCTGTATTTCACATTAAAGTCCTTATGAATCCACAATAAAT-AACAACTC
*
64439 ATGCCTAGTTATATTGT
65 AAGCCTAGTTATATTGT
64456 TTACAAA
1 TTACAAA
64463 GTAATAAAAT
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
77 3 0.04
78 34 0.43
80 1 0.01
81 16 0.20
82 25 0.32
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (81 bp):
TTACAAAAACTAATTTCTGTATTTCACATTAAAGTCCTTATGAATCCACAATAAATAACAACTCA
AGCCTAGTTATATTGT
Found at i:66934 original size:2 final size:2
Alignment explanation
Indices: 66929--66993 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
66919 TAATTTTTTA
66929 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
66971 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
66994 CGTGACACAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70224 original size:46 final size:46
Alignment explanation
Indices: 70161--70248 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
70151 AAGTATATCA
* *
70161 CTGCCATTAAGACAGTAATGGGACGAGGACATGGCTAACAATCACT
1 CTGCCATTAAGACAGTAACGAGACGAGGACATGGCTAACAATCACT
* * * * *
70207 CTGCCGTTAAGATAGTAACGAGATGATGACATGGCTAGCAAT
1 CTGCCATTAAGACAGTAACGAGACGAGGACATGGCTAACAAT
70249 TAATGACGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 35 1.00
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGCCATTAAGACAGTAACGAGACGAGGACATGGCTAACAATCACT
Found at i:75953 original size:31 final size:31
Alignment explanation
Indices: 75917--75977 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
75907 ACCAACTCTT
75917 TTGATTGTTGCTTTTGATCAAACGTCACCGA
1 TTGATTGTTGCTTTTGATCAAACGTCACCGA
75948 TTGATTGTTGCTTTTGATCAAACGTCACCG
1 TTGATTGTTGCTTTTGATCAAACGTCACCG
75978 GTCTACATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (31 bp):
TTGATTGTTGCTTTTGATCAAACGTCACCGA
Done.