Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009283.1 Hibiscus syriacus cultivar Beakdansim tig00112970_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: 94935
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4466 original size:15 final size:15
Alignment explanation
Indices: 4448--4477 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4438 CCACGGTGCT
4448 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
4463 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
4478 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:4949 original size:36 final size:37
Alignment explanation
Indices: 4901--4975 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
4891 ATAGCAAAAG
*
4901 AAATCGTCTTTATTCGAA-TTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
4937 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
4974 AA
1 AA
4976 TCCCGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (37 bp):
AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
Found at i:6001 original size:9 final size:9
Alignment explanation
Indices: 5987--6011 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5977 GTCGTCCCTC
5987 TTAAATTTT
1 TTAAATTTT
5996 TTAAATTTT
1 TTAAATTTT
6005 TTAAATT
1 TTAAATT
6012 CATATGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTAAATTTT
Found at i:9949 original size:21 final size:21
Alignment explanation
Indices: 9925--10011 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
9915 TCACCGATCG
* *
9925 TTATTATATTGATATTATAAT
1 TTATAATATTGATATGATAAT
* * * *
9946 TTATAGTGTTGATGTGATGAT
1 TTATAATATTGATATGATAAT
* *
9967 TTAAAATATTGATACGATAAT
1 TTATAATATTGATATGATAAT
* *
9988 TTATAATATTGATGTGATAGT
1 TTATAATATTGATATGATAAT
10009 TTA
1 TTA
10012 GGAAGATAAT
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.48
Consensus pattern (21 bp):
TTATAATATTGATATGATAAT
Found at i:23767 original size:14 final size:14
Alignment explanation
Indices: 23745--23818 Score: 130
Period size: 14 Copynumber: 5.3 Consensus size: 14
23735 CGTTCGTGAA
23745 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
23759 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
23773 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
23787 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
23801 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
23815 CGTT
1 CGTT
23819 TATGTTCATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 56 1.00
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:23785 original size:28 final size:28
Alignment explanation
Indices: 23745--23819 Score: 150
Period size: 28 Copynumber: 2.7 Consensus size: 28
23735 CGTTCGTGAA
23745 CGTTCGGTTATGTTCGTTTGGTTATGTT
1 CGTTCGGTTATGTTCGTTTGGTTATGTT
23773 CGTTCGGTTATGTTCGTTTGGTTATGTT
1 CGTTCGGTTATGTTCGTTTGGTTATGTT
23801 CGTTCGGTTATGTTCGTTT
1 CGTTCGGTTATGTTCGTTT
23820 ATGTTCATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (28 bp):
CGTTCGGTTATGTTCGTTTGGTTATGTT
Found at i:24717 original size:23 final size:23
Alignment explanation
Indices: 24687--24751 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
24677 TGGGGCAATG
24687 TCGAGCTTGAATCAAGCTCAAAA
1 TCGAGCTTGAATCAAGCTCAAAA
24710 TCGAGCTTGAATCAAGCTCAAAA
1 TCGAGCTTGAATCAAGCTCAAAA
* * *
24733 TAGAGCTTCAATCGAGCTC
1 TCGAGCTTGAATCAAGCTC
24752 GAGTCTCGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (23 bp):
TCGAGCTTGAATCAAGCTCAAAA
Found at i:25002 original size:16 final size:16
Alignment explanation
Indices: 24981--25019 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
24971 GGGTCTCCAA
24981 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
24997 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
25013 CGTTTAT
1 CGTTTAT
25020 TTATTAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:34479 original size:44 final size:44
Alignment explanation
Indices: 34430--34518 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
34420 GTCGGACTTT
*
34430 TAAAATTCTAGTTGACGAAAAAATATTATCAATAAATAAGATTA
1 TAAAATTCTAGTTGACGAAAAAAGATTATCAATAAATAAGATTA
* *
34474 TAAAATTCTAGTTGACGAAAATAGATTATCAATAGATAAGATTA
1 TAAAATTCTAGTTGACGAAAAAAGATTATCAATAAATAAGATTA
34518 T
1 T
34519 TAACAGATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (44 bp):
TAAAATTCTAGTTGACGAAAAAAGATTATCAATAAATAAGATTA
Found at i:36253 original size:20 final size:20
Alignment explanation
Indices: 36207--36280 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 20
36197 AACATTAAAT
* *
36207 TTATCAAA-ATTTATATTAA
1 TTATCAAATAATTATTTTAA
*
36226 ATAT-AAATAATTATTTTAA
1 TTATCAAATAATTATTTTAA
36245 TTATCAAAT-ATT-TTTTAAA
1 TTATCAAATAATTATTTT-AA
*
36264 TTAATCAAATTATTATT
1 TT-ATCAAATAATTATT
36281 AAATGTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
18 7 0.16
19 22 0.49
20 11 0.24
21 3 0.07
22 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATCAAATAATTATTTTAA
Found at i:36254 original size:58 final size:54
Alignment explanation
Indices: 36174--36328 Score: 156
Period size: 52 Copynumber: 2.8 Consensus size: 54
36164 ATTTTTTTAA
36174 ATTATTCAAATTATTATAAAATAAACATTAAATTTATCAAAATTTA-TATTAAAT
1 ATTATT-AAATTATTATAAAATAAACATTAAATTTATCAAAATTTATTATTAAAT
* * * * * *
36228 ATAAAT-AATTATTTTAATTATCAAATATTTTTTAAATTAATC-AAA-TTATTATTAAAT
1 ATTATTAAATTATTATAA-AAT-AAACA----TTAAATTTATCAAAATTTATTATTAAAT
*
36285 GTTATTAAATTATTATAAAATAAACATTAAATTTATCAAAATTT
1 ATTATTAAATTATTATAAAATAAACATTAAATTTATCAAAATTT
36329 CATAGTTGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
52 20 0.26
53 5 0.06
54 10 0.13
56 7 0.09
57 16 0.21
58 20 0.26
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.45
Consensus pattern (54 bp):
ATTATTAAATTATTATAAAATAAACATTAAATTTATCAAAATTTATTATTAAAT
Found at i:39323 original size:31 final size:30
Alignment explanation
Indices: 39265--39355 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 30
39255 AGCAATATTT
39265 AAACTATTATATCATTCTAAATTAATCCTC
1 AAACTATTATATCATTCTAAATTAATCCTC
*
39295 AAACTATTATGT-ATTCTATATATTAATCCTC
1 AAACTATTATATCATTCTA-A-ATTAATCCTC
* **
39326 AAACTATCATTATCATTCTATTTTAATCCT
1 AAACTATTA-TATCATTCTAAATTAATCCT
39356 TCTACTGATG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 6 0.12
30 12 0.23
31 26 0.50
32 2 0.04
33 6 0.12
ACGTcount: A:0.36, C:0.19, G:0.01, T:0.44
Consensus pattern (30 bp):
AAACTATTATATCATTCTAAATTAATCCTC
Found at i:47685 original size:13 final size:15
Alignment explanation
Indices: 47653--47686 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
47643 CATCTCGAAA
47653 AGAGTTAATACTTAT
1 AGAGTTAATACTTAT
47668 AGAGTTAATA-TT-T
1 AGAGTTAATACTTAT
47681 AGAGTT
1 AGAGTT
47687 GAATTCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 2 0.11
15 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (15 bp):
AGAGTTAATACTTAT
Found at i:47766 original size:118 final size:118
Alignment explanation
Indices: 47554--47776 Score: 351
Period size: 118 Copynumber: 1.9 Consensus size: 118
47544 ATGATATATT
*
47554 TTAATATTCAGAGTTGATTTCTCTAAGATTTTGAGTCGAAGATCTCGTATGAAATATTTTAATTT
1 TTAATATTCAGAGTTGAATTCTCTAAGATTTTGAGTCGAAGATCTCGTATGAAATATTTTAATTT
*
47619 TCAAAATCAACTATGATGCCAAAACATCTCGAAAAGAGTTAATACTTATAGAG
66 TCAAAATCAACTATAATGCCAAAACATCTCGAAAAGAGTTAATACTTATAGAG
*
47672 TTAATATTTAGAGTTGAATTCGT-TAAGATTTTGAGTCGAAGATCT-GATATGAAATATTTTAAT
1 TTAATATTCAGAGTTGAATTC-TCTAAGATTTTGAGTCGAAGATCTCG-TATGAAATATTTTAAT
* * * *
47735 TTTCAAAATCAATTCTAATGTCAAAATATCTCGAAAAGAGTT
64 TTTCAAAATCAACTATAATGCCAAAACATCTCGAAAAGAGTT
47777 TTAATAAGAA
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
117 1 0.01
118 94 0.98
119 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (118 bp):
TTAATATTCAGAGTTGAATTCTCTAAGATTTTGAGTCGAAGATCTCGTATGAAATATTTTAATTT
TCAAAATCAACTATAATGCCAAAACATCTCGAAAAGAGTTAATACTTATAGAG
Found at i:51209 original size:2 final size:2
Alignment explanation
Indices: 51202--51232 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51192 ACTAAGTTTC
51202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51233 AAACAATGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55772 original size:74 final size:75
Alignment explanation
Indices: 55651--55792 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 75
55641 AATGTCATAG
* * *
55651 CTTTGACATTTGTGTCAAGCTTTGCTTTATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGA-A
1 CTTTGACATTTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGACA
55715 AATTTTATAC
66 AATTTTATAC
* * * *
55725 CTTTGGCATTTGTATCAAGCTCTGGTATATTTCTTCTTGTCATGCAGAGACTTTGGTTTAAGACA
1 CTTTGACATTTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGACA
55790 AAT
66 AAT
55793 CTAAAGCTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
74 56 0.93
75 4 0.07
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42
Consensus pattern (75 bp):
CTTTGACATTTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGACA
AATTTTATAC
Found at i:56699 original size:30 final size:31
Alignment explanation
Indices: 56632--56716 Score: 127
Period size: 33 Copynumber: 2.7 Consensus size: 31
56622 GAGTTAAATC
*
56632 AAATATAAATTTTAGAAATGTTTGTACCAAAAA
1 AAATGTAAATTTTAGAAATGTTTGTACC--AAA
56665 AAATGTAAATTTTAGAAATGTTTGTACC-AA
1 AAATGTAAATTTTAGAAATGTTTGTACCAAA
*
56695 AAATGAAAATTTTAGAAATGTT
1 AAATGTAAATTTTAGAAATGTT
56717 ATGGAATAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
30 23 0.46
33 27 0.54
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (31 bp):
AAATGTAAATTTTAGAAATGTTTGTACCAAA
Found at i:61418 original size:18 final size:19
Alignment explanation
Indices: 61377--61419 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
61367 AAAATGTTCT
* *
61377 TAAATTTATATATTTTTTG
1 TAAATTTATATATTATTTA
61396 T-AATTTAT-TATTATTTA
1 TAAATTTATATATTATTTA
61413 TAAATTT
1 TAAATTT
61420 TAAACTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 12 0.57
19 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TAAATTTATATATTATTTA
Found at i:61522 original size:18 final size:18
Alignment explanation
Indices: 61487--61528 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
61477 CATATATTTT
*
61487 TATAAAAAAATCTATAAC
1 TATAAAAAAATCAATAAC
61505 TATAAAAAAAT-AACTAAC
1 TATAAAAAAATCAA-TAAC
*
61523 TCTAAA
1 TATAAA
61529 TTATACATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (18 bp):
TATAAAAAAATCAATAAC
Found at i:61651 original size:24 final size:24
Alignment explanation
Indices: 61624--61716 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
61614 TTATACTATC
61624 ACCAATAATTCGTTTTTTTATTAA
1 ACCAATAATTCGTTTTTTTATTAA
61648 ACCAATAATTCAGCAATAATTCCTTTTTTTATTAA
1 ACCAATAATTC-G---T--TT--TTTT---ATTAA
61683 ACCAATAATTCGTTTTTTTATTAA
1 ACCAATAATTCGTTTTTTTATTAA
61707 ACCAATAATT
1 ACCAATAATT
61717 AGTTAGTTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 22
0.73 0.00 0.28
Matches are distributed among these distances:
24 26 0.45
25 1 0.02
27 4 0.07
28 1 0.02
29 2 0.03
30 2 0.03
31 1 0.02
32 4 0.07
34 1 0.02
35 16 0.28
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.45
Consensus pattern (24 bp):
ACCAATAATTCGTTTTTTTATTAA
Found at i:61675 original size:35 final size:35
Alignment explanation
Indices: 61626--61693 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
61616 ATACTATCAC
*
61626 CAATAATTCGTTTTTTTATTAAACCAATAATTCAG
1 CAATAATTCCTTTTTTTATTAAACCAATAATTCAG
61661 CAATAATTCCTTTTTTTATTAAACCAATAATTC
1 CAATAATTCCTTTTTTTATTAAACCAATAATTC
61694 GTTTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (35 bp):
CAATAATTCCTTTTTTTATTAAACCAATAATTCAG
Found at i:61726 original size:24 final size:24
Alignment explanation
Indices: 61675--61726 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
61665 AATTCCTTTT
* **
61675 TTTATTAAACCAATAATTCGTTTT
1 TTTATTAAACCAATAATTAGTTAG
61699 TTTATTAAACCAATAATTAGTTAG
1 TTTATTAAACCAATAATTAGTTAG
61723 TTTA
1 TTTA
61727 ATAGAATGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (24 bp):
TTTATTAAACCAATAATTAGTTAG
Found at i:69334 original size:10 final size:10
Alignment explanation
Indices: 69319--69402 Score: 60
Period size: 10 Copynumber: 7.8 Consensus size: 10
69309 ACGAGCTATG
69319 CGAGGGCATC
1 CGAGGGCATC
*
69329 CGAGGGCAAC
1 CGAGGGCATC
*
69339 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
69352 CGAGGGAATC
1 CGAGGGCATC
*
69362 CGAGGGCAAC
1 CGAGGGCATC
*
69372 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
69385 CGAGGGAATC
1 CGAGGGCATC
69395 CGAGGGCA
1 CGAGGGCA
69403 ACCCGAGCGA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
10 36 0.64
11 4 0.07
12 6 0.11
13 10 0.18
ACGTcount: A:0.26, C:0.25, G:0.40, T:0.08
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:69347 original size:33 final size:33
Alignment explanation
Indices: 69295--69413 Score: 193
Period size: 33 Copynumber: 3.6 Consensus size: 33
69285 GACCATCCGA
* * * *
69295 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
69328 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
69361 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
69394 CCGAGGGCAACCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
69414 GGTAGGTCGC
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 72 0.89
34 9 0.11
ACGTcount: A:0.26, C:0.28, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:69526 original size:10 final size:10
Alignment explanation
Indices: 69484--69580 Score: 68
Period size: 10 Copynumber: 9.1 Consensus size: 10
69474 CCCTCGCTCG
*
69484 CTCGGATTCC
1 CTCGGATGCC
*
69494 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
69506 GCTCGGTTGCC
1 -CTCGGATGCC
69517 CTCGGATGCC
1 CTCGGATGCC
*
69527 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
69539 GTTCGGATGGC
1 -CTCGGATGCC
*
69550 CTCGGATGCT
1 CTCGGATGCC
*
69560 CTCGGATGGC
1 CTCGGATGCC
69570 CTCGGATGCC
1 CTCGGATGCC
69580 C
1 C
69581 AGCGTGTTGG
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
10 46 0.70
11 5 0.08
12 5 0.08
13 10 0.15
ACGTcount: A:0.10, C:0.36, G:0.29, T:0.25
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:69529 original size:33 final size:33
Alignment explanation
Indices: 69484--69563 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
69474 CCCTCGCTCG
* *
69484 CTCGGATTCCCTCGCATAGCTCGCTCGGTTGCC
1 CTCGGATGCCCTCGCATAGCTCGCTCGGATGCC
* *
69517 CTCGGATGCCCTCGCATAGCTCGTTCGGATGGC
1 CTCGGATGCCCTCGCATAGCTCGCTCGGATGCC
*
69550 CTCGGATGCTCTCG
1 CTCGGATGCCCTCG
69564 GATGGCCTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.10, C:0.36, G:0.28, T:0.26
Consensus pattern (33 bp):
CTCGGATGCCCTCGCATAGCTCGCTCGGATGCC
Found at i:69566 original size:20 final size:20
Alignment explanation
Indices: 69507--69578 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
69497 GCATAGCTCG
* * *
69507 CTCGGTTGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
*
69527 CTCGCATAGCTCGTTCGGATGGC
1 CTCGGAT-GCTC--TCGGATGGC
69550 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
69570 CTCGGATGC
1 CTCGGATGC
69579 CCAGCGTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 23 0.52
21 3 0.07
22 4 0.09
23 14 0.32
ACGTcount: A:0.10, C:0.33, G:0.32, T:0.25
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:69659 original size:30 final size:30
Alignment explanation
Indices: 69625--69697 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
69615 CTGCATGGAT
* *
69625 TGCATGGTGACCTACCTAGGTCGTTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
**
69655 TGCATGGCGACCT-GGTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
69684 TGCATGGCGACCTA
1 TGCATGGCGACCTA
69698 TATGGGGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 26 0.68
30 12 0.32
ACGTcount: A:0.14, C:0.25, G:0.38, T:0.23
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGCTGGGCG
Found at i:70393 original size:17 final size:17
Alignment explanation
Indices: 70373--70406 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
70363 ATATATACAT
* *
70373 AAAATATAAGAATATTA
1 AAAATAAAAGAAAATTA
70390 AAAATAAAAGAAAATTA
1 AAAATAAAAGAAAATTA
70407 CTATTTTCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAATAAAAGAAAATTA
Found at i:75694 original size:60 final size:60
Alignment explanation
Indices: 75566--75680 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
75556 ACCATATGTC
** * * *
75566 CCCAAACTATAACTCTCATTTTAAATAGGTCCTTAAACTTTTAAATATTCTAATTTAATT
1 CCCAAACTATGGCTTTCATTCTAAATAGGTCATTAAACTTTTAAATATTCTAATTTAATT
75626 CCCAAACTATGGCTTTCATTCTAAATTA-GTCATTAAACTTTTGAAA-ATTCTAATT
1 CCCAAACTATGGCTTTCATTCTAAA-TAGGTCATTAAACTTTT-AAATATTCTAATT
75681 ACATCCCTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 43 0.90
61 5 0.10
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (60 bp):
CCCAAACTATGGCTTTCATTCTAAATAGGTCATTAAACTTTTAAATATTCTAATTTAATT
Found at i:79132 original size:21 final size:21
Alignment explanation
Indices: 79108--79151 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
79098 CCGTTGATGA
* *
79108 AACTAAAACTTTTAATTAAGC
1 AACTAAAACATGTAATTAAGC
*
79129 AACTAAAACATGTCATTAAGC
1 AACTAAAACATGTAATTAAGC
79150 AA
1 AA
79152 ATAGCAAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (21 bp):
AACTAAAACATGTAATTAAGC
Found at i:81343 original size:16 final size:16
Alignment explanation
Indices: 81322--81363 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
81312 TAATATCATT
81322 AGTGAAAAAAGAGCTC
1 AGTGAAAAAAGAGCTC
81338 AGTGAAAAAAGAGCTC
1 AGTGAAAAAAGAGCTC
81354 AGTGAAAAAA
1 AGTGAAAAAA
81364 AACTCAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.24, T:0.12
Consensus pattern (16 bp):
AGTGAAAAAAGAGCTC
Found at i:87109 original size:16 final size:14
Alignment explanation
Indices: 87074--87107 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
87064 TATGACATTT
87074 TATAT-TTTGTTAA
1 TATATATTTGTTAA
87087 TATATATTTGTTAA
1 TATATATTTGTTAA
87101 TATATAT
1 TATATAT
87108 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (14 bp):
TATATATTTGTTAA
Found at i:88760 original size:13 final size:13
Alignment explanation
Indices: 88742--88766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88732 TTCTCCAGAA
88742 CTTCTTCTTCCTT
1 CTTCTTCTTCCTT
88755 CTTCTTCTTCCT
1 CTTCTTCTTCCT
88767 CTCCTCCCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
CTTCTTCTTCCTT
Found at i:90910 original size:18 final size:18
Alignment explanation
Indices: 90887--90959 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
90877 GTTCTTAAAG
90887 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
90905 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
90924 CAGTGGTCTTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
90943 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
90960 ATATTCAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:90938 original size:38 final size:38
Alignment explanation
Indices: 90887--90961 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
90877 GTTCTTAAAG
*
90887 AGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATC
* *
90925 AGTGGTCTTTCGGGACATAGTGGTCCTTCGGGACAAT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAAT
90962 ATTCAATGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATC
Found at i:91558 original size:12 final size:12
Alignment explanation
Indices: 91541--91566 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
91531 CGTAGGTTAC
91541 AGAAGCGATAAG
1 AGAAGCGATAAG
91553 AGAAGCGATAAG
1 AGAAGCGATAAG
91565 AG
1 AG
91567 CAAAACAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.35, T:0.08
Consensus pattern (12 bp):
AGAAGCGATAAG
Done.