Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008265.1 Hibiscus syriacus cultivar Beakdansim tig00110919_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: 111834
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3008 original size:32 final size:32
Alignment explanation
Indices: 2952--3034 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
2942 TGATGTTTAT
* *
2952 GGCGTGAT-ATGGTG-TGGAATATGGTGATATA
1 GGCGTGATAATGGTGATGGACTATGGTGAT-GA
2983 GGC-TGATAATGGTGATGGACTATGGTGATGA
1 GGCGTGATAATGGTGATGGACTATGGTGATGA
3014 GGCGTGATAATGGTGATGGAC
1 GGCGTGATAATGGTGATGGAC
3035 ATATTGTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
30 4 0.09
31 13 0.28
32 30 0.64
ACGTcount: A:0.25, C:0.06, G:0.40, T:0.29
Consensus pattern (32 bp):
GGCGTGATAATGGTGATGGACTATGGTGATGA
Found at i:7295 original size:33 final size:35
Alignment explanation
Indices: 7245--7360 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 35
7235 ATGATTAATG
* * *
7245 GTGATGAATGGTAATGGA-A-GGATGATGTTATTGGC
1 GTGAT-AATGGTGATGGATATGG-TGATGATATAGGC
7280 GTGAT-ATGGTGATGGAATATGGTGATGATATAGGC
1 GTGATAATGGTGATGG-ATATGGTGATGATATAGGC
7315 GTGATAATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATGGTGATGGA-TATGGTGATGATATAGGC
7351 GTGATAATGG
1 GTGATAATGG
7361 ATGGACAGAT
Statistics
Matches: 73, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
33 9 0.12
34 1 0.01
35 23 0.32
36 40 0.55
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.31
Consensus pattern (35 bp):
GTGATAATGGTGATGGATATGGTGATGATATAGGC
Found at i:7301 original size:13 final size:12
Alignment explanation
Indices: 7282--7346 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
7272 TTATTGGCGT
7282 GATATGGTGATG
1 GATATGGTGATG
7294 GAATATGGTGAT-
1 G-ATATGGTGATG
*
7306 GATATAGGCG-T-
1 GATAT-GGTGATG
7317 GATAATGGTGATG
1 GAT-ATGGTGATG
7330 GACTATGGTGAT-
1 GA-TATGGTGATG
7342 GATAT
1 GATAT
7347 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:7337 original size:36 final size:36
Alignment explanation
Indices: 7267--7360 Score: 154
Period size: 36 Copynumber: 2.6 Consensus size: 36
7257 AATGGAAGGA
* *
7267 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
7302 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
7338 TGATGATATAGGCGTGATAATGG
1 TGATGATATAGGCGTGATAATGG
7361 ATGGACAGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 16 0.29
36 39 0.71
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:9225 original size:24 final size:21
Alignment explanation
Indices: 9190--9232 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
9180 GGTTCATTCT
*
9190 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
9213 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
9233 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:10473 original size:21 final size:23
Alignment explanation
Indices: 10426--10476 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
10416 TTATTTTCCT
10426 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTT-AA
10450 TTTCTTCTTTT-GAGTGCTTT-A
1 TTTCTTCTTTTCGAGTGCTTTAA
10471 TTTCTT
1 TTTCTT
10477 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.26
23 9 0.33
24 11 0.41
ACGTcount: A:0.10, C:0.18, G:0.12, T:0.61
Consensus pattern (23 bp):
TTTCTTCTTTTCGAGTGCTTTAA
Found at i:13011 original size:19 final size:19
Alignment explanation
Indices: 12972--13013 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12962 AGCATTTATC
*
12972 TTCATTAAAATTATGTATT
1 TTCATTAAAAGTATGTATT
* *
12991 TTCATTAAAAGTCTGTGTT
1 TTCATTAAAAGTATGTATT
13010 TTCA
1 TTCA
13014 AAGGGGTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (19 bp):
TTCATTAAAAGTATGTATT
Found at i:13843 original size:13 final size:13
Alignment explanation
Indices: 13820--13851 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
13810 CAAAAGCAAC
13820 AAAAG-AGAAAAA
1 AAAAGAAGAAAAA
13832 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
13845 AAAAGAA
1 AAAAGAA
13852 AAGAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAA
Found at i:13845 original size:15 final size:15
Alignment explanation
Indices: 13825--13859 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
13815 GCAACAAAAG
13825 AGAAAAAAAAAG--A
1 AGAAAAAAAAAGAAA
13838 AGAAAAAAAAAGAAA
1 AGAAAAAAAAAGAAA
13853 AGAAAAA
1 AGAAAAA
13860 GACTCCTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
15 8 0.40
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAGAAA
Found at i:13858 original size:13 final size:12
Alignment explanation
Indices: 13820--13859 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
13810 CAAAAGCAAC
*
13820 AAAAGAGAAAAA
1 AAAAGAAAAAAA
13832 AAAAGAAGAAAAA
1 AAAAGAA-AAAAA
13845 AAAAGAAAAGAAA
1 AAAAGAAAA-AAA
13858 AA
1 AA
13860 GACTCCTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:29637 original size:34 final size:34
Alignment explanation
Indices: 29583--29685 Score: 104
Period size: 34 Copynumber: 3.0 Consensus size: 34
29573 ATACAATCTG
*
29583 TCCATCACCATTATCACGCC-ATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T-T
29618 TCCATCACCATATCACGCCAATAACATCATCCTT
1 TCCATCACCATATCACGCCAATAACATCATCCTT
* * * *
29652 TCCATTACCATTTCATCACCATTAA-ATCATCCTT
1 TCCATCACCATATCA-CGCCAATAACATCATCCTT
29686 CATTCATCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 32 0.53
35 26 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (34 bp):
TCCATCACCATATCACGCCAATAACATCATCCTT
Found at i:32538 original size:19 final size:20
Alignment explanation
Indices: 32514--32556 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
32504 AGCATTTATC
*
32514 TTCATTAAAA-TTATGTATT
1 TTCATTAAAAGTCATGTATT
*
32533 TTCATTAAAAGTCATGTGTT
1 TTCATTAAAAGTCATGTATT
32553 TTCA
1 TTCA
32557 ACCTTAACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAGTCATGTATT
Found at i:32910 original size:13 final size:13
Alignment explanation
Indices: 32892--32917 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32882 ACTATCTGTT
32892 CATCACCATTTTC
1 CATCACCATTTTC
32905 CATCACCATTTTC
1 CATCACCATTTTC
32918 ACGCCTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:35517 original size:19 final size:20
Alignment explanation
Indices: 35475--35526 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
35465 GAAACCCCTT
*
35475 TGAAAATACATGATTTTTTTA
1 TGAAAATACATGA-TTTTTAA
35496 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
35515 TGAATATACATG
1 TGAAAATACATG
35527 CTCTTGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:36476 original size:30 final size:31
Alignment explanation
Indices: 36436--36495 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
36426 ACATGCTGCC
**
36436 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
36467 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
36496 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:44380 original size:20 final size:20
Alignment explanation
Indices: 44352--44395 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
44342 GCCATCTCTC
*
44352 TTTCATTTATT-TCTATTTCA
1 TTTCATTTATTATATA-TTCA
*
44372 TTTCCTTTATTATATATTCA
1 TTTCATTTATTATATATTCA
44392 TTTC
1 TTTC
44396 TTAAGACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTTATTATATATTCA
Found at i:52662 original size:30 final size:31
Alignment explanation
Indices: 52622--52681 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
52612 ACATGCTGCC
**
52622 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
52653 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
52682 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:56774 original size:19 final size:20
Alignment explanation
Indices: 56735--56774 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
56725 GAATAATAAT
56735 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
56755 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
56774 A
1 A
56775 ATAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:57228 original size:19 final size:20
Alignment explanation
Indices: 57187--57237 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
57177 GAAACCCCTT
*
57187 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
57207 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
57226 TGAAGATACATG
1 TGAAAATACATG
57238 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:58175 original size:30 final size:31
Alignment explanation
Indices: 58136--58195 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
58126 ACATGCTTCC
**
58136 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
58167 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
58196 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:58865 original size:35 final size:34
Alignment explanation
Indices: 58819--58893 Score: 123
Period size: 35 Copynumber: 2.2 Consensus size: 34
58809 TACTATCAAT
*
58819 TCATCACCATCTTCCATCACCATTGCACTCCTATA
1 TCATCACCATCTTCCATCACCATT-CACACCTATA
*
58854 TCATCACCATCTTCTATCACCATTCACACCTATA
1 TCATCACCATCTTCCATCACCATTCACACCTATA
58888 TCATCA
1 TCATCA
58894 TCATTCCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 15 0.39
35 23 0.61
ACGTcount: A:0.28, C:0.39, G:0.01, T:0.32
Consensus pattern (34 bp):
TCATCACCATCTTCCATCACCATTCACACCTATA
Found at i:61115 original size:36 final size:36
Alignment explanation
Indices: 61063--61167 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
61053 GATACAATCT
*
61063 GTCCATCACCATTATCACGCCTATATCATCACCGTA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
61099 GTCCGTCACCATTATCACGCCTATATCATCACCATT
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
61135 TTCCATCACCA-TATCACACCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
61168 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 20 0.32
36 42 0.68
ACGTcount: A:0.29, C:0.36, G:0.06, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:61562 original size:15 final size:14
Alignment explanation
Indices: 61542--61580 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
61532 CAACAACAAA
61542 AAAACAAGAAAGAAG
1 AAAACAA-AAAGAAG
61557 AAAAC-AAAAG-AG
1 AAAACAAAAAGAAG
61569 AAAACAAAAAGA
1 AAAACAAAAAGA
61581 CTCCTACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.32
13 9 0.41
14 1 0.05
15 5 0.23
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAGAAG
Found at i:61636 original size:14 final size:15
Alignment explanation
Indices: 61602--61648 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
61592 AATTTGGAGT
61602 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
61617 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
61631 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
61648 G
1 G
61649 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:64533 original size:13 final size:11
Alignment explanation
Indices: 64492--64576 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
64482 ACAATATGTC
64492 CATCACCATTAT
1 CATCACCA-TAT
*
64504 CA-CGCCTATAT
1 CATCACC-ATAT
64515 CATCACCATAGT
1 CATCACCATA-T
64527 CCATCACCATTAT
1 -CATCACCA-TAT
*
64540 CA-CGCCTATAT
1 CATCACC-ATAT
64551 CATCACCATATT
1 CATCACCATA-T
64563 CCATCACCATAT
1 -CATCACCATAT
64575 CA
1 CA
64577 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:64536 original size:36 final size:36
Alignment explanation
Indices: 64489--64593 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
64479 GATACAATAT
64489 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
64525 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
64561 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
64594 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:76021 original size:33 final size:33
Alignment explanation
Indices: 75978--76045 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
75968 ATACAATCTG
*
75978 TCCATCACCATATCA-CGCCAATAACATCATCCT
1 TCCATCACCATATCATCACCAATAA-ATCATCCT
* * *
76011 TCCATTACCATTTCATCACCATTAAATCATCCT
1 TCCATCACCATATCATCACCAATAAATCATCCT
76044 TC
1 TC
76046 ATTCATCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.37, G:0.01, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCATCACCAATAAATCATCCT
Found at i:79938 original size:19 final size:20
Alignment explanation
Indices: 79914--79964 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
79904 CGGCCAAGAG
* *
79914 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
79933 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
79953 CATGTATTTTCA
1 CATGTATTTTCA
79965 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:84105 original size:19 final size:20
Alignment explanation
Indices: 84081--84131 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
84071 CGGCCAAGAG
* *
84081 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
84100 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
84120 CATGTATTTTCA
1 CATGTATTTTCA
84132 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:88044 original size:19 final size:20
Alignment explanation
Indices: 88022--88072 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
88012 TCATCCTTAG
* *
88022 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
88041 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
88061 CATGTATTTTCA
1 CATGTATTTTCA
88073 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:88752 original size:5 final size:5
Alignment explanation
Indices: 88744--88768 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
88734 ATCAGAAAAG
88744 AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA
88769 TTCAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:92138 original size:19 final size:20
Alignment explanation
Indices: 92114--92164 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
92104 CGGCCAAGAG
* *
92114 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
92133 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
92153 CATGTATTTTCA
1 CATGTATTTTCA
92165 AGGGGTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:93094 original size:13 final size:13
Alignment explanation
Indices: 93076--93142 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
93066 TTGAAGTGAA
**
93076 GGTGATGGACTAT
1 GGTGATGGAAGAT
93089 GGTGATGGAAGAT
1 GGTGATGGAAGAT
** *
93102 GGTGATGTTATA-
1 GGTGATGGAAGAT
*
93114 GGTG-T-GAAAAT
1 GGTGATGGAAGAT
93125 GGTGATGGAAGAT
1 GGTGATGGAAGAT
93138 GGTGA
1 GGTGA
93143 AGTTTAGGTA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
10 2 0.05
11 5 0.12
12 5 0.12
13 30 0.71
ACGTcount: A:0.28, C:0.01, G:0.42, T:0.28
Consensus pattern (13 bp):
GGTGATGGAAGAT
Found at i:93509 original size:19 final size:19
Alignment explanation
Indices: 93485--93534 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
93475 GAAACCCCTT
93485 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
93504 TGAAAATTCATGATTTTAA
1 TGAAAATACATGATTTTAA
*
93523 TGAAGATACATG
1 TGAAAATACATG
93535 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:111578 original size:15 final size:16
Alignment explanation
Indices: 111555--111586 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
111545 CTTGATGAAC
111555 TCAAGCTAGTTAGCTT
1 TCAAGCTAGTTAGCTT
111571 TCAA-CTAGTTAGCTT
1 TCAAGCTAGTTAGCTT
111586 T
1 T
111587 GGTCTTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (16 bp):
TCAAGCTAGTTAGCTT
Done.