Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003985.1 Hibiscus syriacus cultivar Beakdansim tig00008667_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: 114454
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2295 original size:21 final size:21
Alignment explanation
Indices: 2269--2310 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2259 ATTTTCTTAT
*
2269 TATTTAGAAAAAACAAA-AATA
1 TATTTACAAAAAA-AAATAATA
2290 TATTTACAAAAAAAAATAATA
1 TATTTACAAAAAAAAATAATA
2311 AAAAGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (21 bp):
TATTTACAAAAAAAAATAATA
Found at i:3758 original size:21 final size:21
Alignment explanation
Indices: 3714--3758 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3704 ACTTAACGTG
* *
3714 TTTAGTACGTAAACTATCAGT
1 TTTAGTACCTAAACTATCAAT
* *
3735 TTTAGTACCTAAATTTTCAAT
1 TTTAGTACCTAAACTATCAAT
3756 TTT
1 TTT
3759 TTTTAAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:5042 original size:21 final size:21
Alignment explanation
Indices: 5018--5060 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5008 TAGGATCGAG
* *
5018 TGATAAAAATTTAATTTAGAT
1 TGATAAAAATATAATTAAGAT
**
5039 TGATTTAAATATAATTAAGAT
1 TGATAAAAATATAATTAAGAT
5060 T
1 T
5061 CTTGATTGAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (21 bp):
TGATAAAAATATAATTAAGAT
Found at i:5494 original size:21 final size:21
Alignment explanation
Indices: 5470--5520 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5460 TTACGTCAGT
*
5470 ATCGTGGACCGTCATGTCAAC
1 ATCGTGAACCGTCATGTCAAC
5491 ATCGTGAACCGTCATGTCAAC
1 ATCGTGAACCGTCATGTCAAC
5512 ATCGTGAAC
1 ATCGTGAAC
5521 GACTACGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
ATCGTGAACCGTCATGTCAAC
Found at i:15013 original size:20 final size:23
Alignment explanation
Indices: 14951--15004 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
14941 TGCACGAATA
14951 AATTAAGGGAGGAATTGAAGAAG
1 AATTAAGGGAGGAATTGAAGAAG
14974 AATTAAGGGAGGAATTGAAGAAG
1 AATTAAGGGAGGAATTGAAGAAG
14997 AATTAAGG
1 AATTAAGG
15005 ATCATGAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (23 bp):
AATTAAGGGAGGAATTGAAGAAG
Found at i:31285 original size:15 final size:15
Alignment explanation
Indices: 31262--31303 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
31252 ATTAAATTAA
31262 TAAATATATATAATAT
1 TAAATATATATAAT-T
* *
31278 T-TATATATTTAATT
1 TAAATATATATAATT
31292 TAAATATATATA
1 TAAATATATATA
31304 TACCCGACCC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATATATAATT
Found at i:32121 original size:20 final size:20
Alignment explanation
Indices: 32096--32140 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
32086 GTCATCCAAT
*
32096 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCAGACCGGA
32116 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
32136 TTTTT
1 TTTTT
32141 TTTCCTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:36875 original size:22 final size:22
Alignment explanation
Indices: 36850--36892 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
36840 GCGGTACAAA
*
36850 CGCGTTCTAGTCGTTTCAAAAT
1 CGCGTTCCAGTCGTTTCAAAAT
36872 CGCGTTCCAGTCGTTTCAAAA
1 CGCGTTCCAGTCGTTTCAAAA
36893 ATCGAGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (22 bp):
CGCGTTCCAGTCGTTTCAAAAT
Found at i:47551 original size:30 final size:30
Alignment explanation
Indices: 47517--47605 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
47507 TGACCAGAGA
47517 GCTATTTCCATGAAGACATGACAAAACATT
1 GCTATTTCCATGAAGACATGACAAAACATT
***
47547 GCTATTGGTAT-AAG-CA-GAC---AC-TT
1 GCTATTTCCATGAAGACATGACAAAACATT
47570 GCTATTTCCATGAAGACATGACAAAACATT
1 GCTATTTCCATGAAGACATGACAAAACATT
47600 GCTATT
1 GCTATT
47606 GGTATAAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
23 10 0.22
24 5 0.11
25 2 0.04
26 3 0.07
27 3 0.07
28 2 0.04
29 5 0.11
30 16 0.35
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (30 bp):
GCTATTTCCATGAAGACATGACAAAACATT
Found at i:47575 original size:23 final size:23
Alignment explanation
Indices: 47545--47628 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
47535 TGACAAAACA
47545 TTGCTATTGGTATAAGCAGACAC
1 TTGCTATTGGTATAAGCAGACAC
***
47568 TTGCTATTTCCATGAAGACATGACAAAAC
1 TTGCTATTGGTAT-AAG-CA-GAC---AC
47597 ATTGCTATTGGTATAAGCAGACAC
1 -TTGCTATTGGTATAAGCAGACAC
47621 TTGCTATT
1 TTGCTATT
47629 TCCATTCTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
23 18 0.38
24 5 0.10
25 2 0.04
26 3 0.06
27 3 0.06
28 2 0.04
29 5 0.10
30 10 0.21
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (23 bp):
TTGCTATTGGTATAAGCAGACAC
Found at i:47597 original size:53 final size:53
Alignment explanation
Indices: 47517--47633 Score: 234
Period size: 53 Copynumber: 2.2 Consensus size: 53
47507 TGACCAGAGA
47517 GCTATTTCCATGAAGACATGACAAAACATTGCTATTGGTATAAGCAGACACTT
1 GCTATTTCCATGAAGACATGACAAAACATTGCTATTGGTATAAGCAGACACTT
47570 GCTATTTCCATGAAGACATGACAAAACATTGCTATTGGTATAAGCAGACACTT
1 GCTATTTCCATGAAGACATGACAAAACATTGCTATTGGTATAAGCAGACACTT
47623 GCTATTTCCAT
1 GCTATTTCCAT
47634 TCTATTGGAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 64 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (53 bp):
GCTATTTCCATGAAGACATGACAAAACATTGCTATTGGTATAAGCAGACACTT
Found at i:52756 original size:19 final size:19
Alignment explanation
Indices: 52732--52768 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
52722 GAACGCATTT
52732 CATGCACCGATGCACTCTC
1 CATGCACCGATGCACTCTC
*
52751 CATGCATCGATGCACTCT
1 CATGCACCGATGCACTCT
52769 GGATATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
CATGCACCGATGCACTCTC
Found at i:52894 original size:64 final size:65
Alignment explanation
Indices: 52716--52875 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
52706 GAATATATTG
* * * * *
52716 AACATCGAACGCATTTCATGCACCGATGCACTC-TCCATGCATCGATGCACTCTGGA-TA-TTTT
1 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCAC-C-AGACTATTTTT
52778 CAA
63 CAA
52781 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACCAGACTATTTTTC-A
1 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACCAGACTATTTTTCAA
*
52845 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
52876 ACTTGGTGCA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
63 2 0.02
64 35 0.41
65 49 0.57
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACCAGACTATTTTTCAA
Found at i:56695 original size:65 final size:65
Alignment explanation
Indices: 56576--56701 Score: 159
Period size: 65 Copynumber: 1.9 Consensus size: 65
56566 TCGGTATAAT
**
56576 GTTACTTAAAACATTATTTTTTTACCATAAATGTTAATATTAGGTGTTACTTAAAATGTTTAAAT
1 GTTACTTAAAACATTATTTTTTTACCATAAATGTTAATATTAGCCGTTACTTAAAAT-TTTAAAT
56641 C
65 C
* * *
56642 GTTACTTAAAATATTA-TTTTTTATCGA-AAATGTTAATATT-GACCGTTATTTAAAATTTTA
1 GTTACTTAAAACATTATTTTTTTA-CCATAAATGTTAATATTAG-CCGTTACTTAAAATTTTA
56702 TTTTTTCTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
64 5 0.09
65 31 0.58
66 17 0.32
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.47
Consensus pattern (65 bp):
GTTACTTAAAACATTATTTTTTTACCATAAATGTTAATATTAGCCGTTACTTAAAATTTTAAATC
Found at i:57654 original size:17 final size:17
Alignment explanation
Indices: 57632--57672 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
57622 ACGGTTGACT
*
57632 GTTGACCGTTGACCTCC
1 GTTGACCGTTGACCGCC
* *
57649 GTTGACTGTTGACCGGC
1 GTTGACCGTTGACCGCC
57666 GTTGACC
1 GTTGACC
57673 AATGTTGACC
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:0.12, C:0.29, G:0.29, T:0.29
Consensus pattern (17 bp):
GTTGACCGTTGACCGCC
Found at i:59970 original size:24 final size:23
Alignment explanation
Indices: 59943--60025 Score: 58
Period size: 24 Copynumber: 3.5 Consensus size: 23
59933 ATTTCCGATT
59943 TGAATTCTGTTCTGACATCTGATC
1 TGAATTCTGTTCTGA-ATCTGATC
* * * *
59967 TGAAATCTATTCTGATTCCTGACC
1 TGAATTCTGTTCTGAAT-CTGATC
* * * *
59991 TGGATTCGGTTATGATATATGATC
1 TGAATTCTGTTCTGA-ATCTGATC
*
60015 TGAATTTTGTT
1 TGAATTCTGTT
60026 TTGTTTTCTG
Statistics
Matches: 42, Mismatches: 15, Indels: 4
0.69 0.25 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.95
25 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (23 bp):
TGAATTCTGTTCTGAATCTGATC
Found at i:61330 original size:101 final size:101
Alignment explanation
Indices: 61212--61408 Score: 394
Period size: 101 Copynumber: 2.0 Consensus size: 101
61202 TCAATGCACG
61212 TTAGGACAGATATAGAATTTTTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAA
1 TTAGGACAGATATAGAATTTTTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAA
61277 ATTTGTAAAATTTTAAGATTAAAAATAAATCGTGCA
66 ATTTGTAAAATTTTAAGATTAAAAATAAATCGTGCA
61313 TTAGGACAGATATAGAATTTTTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAA
1 TTAGGACAGATATAGAATTTTTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAA
61378 ATTTGTAAAATTTTAAGATTAAAAATAAATC
66 ATTTGTAAAATTTTAAGATTAAAAATAAATC
61409 TTCATAAAAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (101 bp):
TTAGGACAGATATAGAATTTTTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAA
ATTTGTAAAATTTTAAGATTAAAAATAAATCGTGCA
Found at i:61442 original size:101 final size:101
Alignment explanation
Indices: 61232--61442 Score: 300
Period size: 101 Copynumber: 2.1 Consensus size: 101
61222 TATAGAATTT
61232 TTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAAATTTGTAAAATTTTAAGATT
1 TTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAAATTTGTAAAATTTTAAGATT
** * * ***
61297 AAAAATAAATCGTGCATTAGGACAGATATAGAATTT
66 AAAAATAAATCGTGCATTAAAAAAGAAATAGAAAAG
61333 TTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAAATTTGTAAAATTTTAAGATT
1 TTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAAATTTGTAAAATTTTAAGATT
* *
61398 AAAAATAAATC-TTCA-TAAAAAATAAATAGATAAAAG
66 AAAAATAAATCGTGCATTAAAAAAGAAATAG--AAAAG
*
61434 TTTGTGTTG
1 TTTATGTTG
61443 AAAATAAATA
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
99 9 0.09
100 3 0.03
101 86 0.88
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (101 bp):
TTTATGTTGGGTTAAATTTTTTAAATTTTAGGGAATCAAATTTAAATTTGTAAAATTTTAAGATT
AAAAATAAATCGTGCATTAAAAAAGAAATAGAAAAG
Found at i:61706 original size:51 final size:51
Alignment explanation
Indices: 61646--61743 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
61636 TATGAGATAA
*
61646 TATTTAAATAAAATCTTTAGTCATTTGATATTAAATATTTATATTTTATAT
1 TATTTAAATAAAATCTTTAATCATTTGATATTAAATATTTATATTTTATAT
*
61697 TATTTAAATATAATCTTTAATCATTTGATATTAAATATTTATATTTT
1 TATTTAAATAAAATCTTTAATCATTTGATATTAAATATTTATATTTT
61744 TTATATTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (51 bp):
TATTTAAATAAAATCTTTAATCATTTGATATTAAATATTTATATTTTATAT
Found at i:61734 original size:27 final size:27
Alignment explanation
Indices: 61649--61734 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
61639 GAGATAATAT
* *
61649 TTAAATAAAATCTTTAGTCATTTGATA
1 TTAAATATAATCTTTAATCATTTGATA
* * *
61676 TTAAATATTTATATTTTAT-A-TT-AT-
1 TTAAATA-TAATCTTTAATCATTTGATA
61700 TTAAATATAATCTTTAATCATTTGATA
1 TTAAATATAATCTTTAATCATTTGATA
61727 TTAAATAT
1 TTAAATAT
61735 TTATATTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
23 8 0.17
24 8 0.17
25 4 0.09
26 4 0.09
27 16 0.35
28 6 0.13
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (27 bp):
TTAAATATAATCTTTAATCATTTGATA
Found at i:61749 original size:22 final size:24
Alignment explanation
Indices: 61720--61775 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
61710 TCTTTAATCA
*
61720 TTTGATATTAA-ATAT-TTATATT
1 TTTGATATTAACAAATATTATATT
*
61742 TTTTATATTAATCAAATATTATATT
1 TTTGATATTAA-CAAATATTATATT
61767 TTTGATATT
1 TTTGATATT
61776 CCTAATACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.36
24 3 0.11
25 15 0.54
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTGATATTAACAAATATTATATT
Found at i:72798 original size:42 final size:42
Alignment explanation
Indices: 72736--72820 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
72726 CCTTATTAGC
* *
72736 AGATGATATTCCATCGGCCCTACCAGCCATAAGATTCGTCCT
1 AGATGATATTCCATCAGCCCTACAAGCCATAAGATTCGTCCT
72778 AGATGATATTCCATCAGCCCTACAAGCCATAAGATTCGTCCT
1 AGATGATATTCCATCAGCCCTACAAGCCATAAGATTCGTCCT
72820 A
1 A
72821 TTGATTGAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (42 bp):
AGATGATATTCCATCAGCCCTACAAGCCATAAGATTCGTCCT
Found at i:74231 original size:36 final size:36
Alignment explanation
Indices: 74191--74364 Score: 237
Period size: 36 Copynumber: 4.9 Consensus size: 36
74181 CTTCGTATTC
* **
74191 CTCCTCCTCCTCCGGCTCATACTCTTCTTCTTCCTT
1 CTCCTCCTCCACCACCTCATACTCTTCTTCTTCCTT
* *
74227 CTCCTCCT---CCACCTCATACTCTTATACTTCCTT
1 CTCCTCCTCCACCACCTCATACTCTTCTTCTTCCTT
*
74260 TTCCTCCTCCACCACCTCATACTCTTCTTCTTCCTT
1 CTCCTCCTCCACCACCTCATACTCTTCTTCTTCCTT
74296 CTCCTCCTCCACCACCTCATACTCTTCTTCTTCCTT
1 CTCCTCCTCCACCACCTCATACTCTTCTTCTTCCTT
* * * *
74332 CTCCACCTCCTCCACCTCATATTCTTCATCTTC
1 CTCCTCCTCCACCACCTCATACTCTTCTTCTTC
74365 TTCCTCATCA
Statistics
Matches: 123, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
33 28 0.23
36 95 0.77
ACGTcount: A:0.11, C:0.48, G:0.01, T:0.40
Consensus pattern (36 bp):
CTCCTCCTCCACCACCTCATACTCTTCTTCTTCCTT
Found at i:74381 original size:30 final size:30
Alignment explanation
Indices: 74347--74403 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
74337 CCTCCTCCAC
*
74347 CTCATATTCTTCATCTTCTTCCTCATCAAT
1 CTCATAATCTTCATCTTCTTCCTCATCAAT
** *
74377 CTCATAATCTTTGTCTTCTTCTTCATC
1 CTCATAATCTTCATCTTCTTCCTCATC
74404 CGATACACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.18, C:0.32, G:0.02, T:0.49
Consensus pattern (30 bp):
CTCATAATCTTCATCTTCTTCCTCATCAAT
Found at i:75989 original size:22 final size:21
Alignment explanation
Indices: 75964--76008 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
75954 ACACTACCAA
* *
75964 TTATTTTCTTATTCTTTTTAAT
1 TTATTATCTTATT-TTTGTAAT
75986 TTATTATCTTATTTTTGTAAT
1 TTATTATCTTATTTTTGTAAT
76007 TT
1 TT
76009 TCCTTAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTATCTTATTTTTGTAAT
Found at i:78451 original size:26 final size:26
Alignment explanation
Indices: 78422--78485 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
78412 ATTGCCTGAG
78422 CTCTCAAACTCTCTTAAATTCTCAAA
1 CTCTCAAACTCTCTTAAATTCTCAAA
78448 CTCTCAAACTCTCTTAAATTCTCAAA
1 CTCTCAAACTCTCTTAAATTCTCAAA
*
78474 CTCTCTAACTCT
1 CTCTCAAACTCT
78486 GAAACTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (26 bp):
CTCTCAAACTCTCTTAAATTCTCAAA
Found at i:78452 original size:8 final size:8
Alignment explanation
Indices: 78422--78529 Score: 90
Period size: 8 Copynumber: 13.0 Consensus size: 8
78412 ATTGCCTGAG
78422 CTCTCAAA
1 CTCTCAAA
78430 CTCTCTTAAA
1 CTCTC--AAA
*
78440 TTCTCAAA
1 CTCTCAAA
78448 CTCTCAAA
1 CTCTCAAA
78456 CTCTCTTAAA
1 CTCTC--AAA
*
78466 TTCTCAAA
1 CTCTCAAA
*
78474 CTCTCTAA
1 CTCTCAAA
*
78482 CTCTGAAA
1 CTCTCAAA
* *
78490 CTATTAAA
1 CTCTCAAA
*
78498 CTCTGAAA
1 CTCTCAAA
*
78506 CTTTCAAA
1 CTCTCAAA
*
78514 CTCTTAAA
1 CTCTCAAA
*
78522 TTCTCAAA
1 CTCTCAAA
78530 ATGGCTCTTA
Statistics
Matches: 79, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
8 65 0.82
10 14 0.18
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (8 bp):
CTCTCAAA
Found at i:79104 original size:60 final size:60
Alignment explanation
Indices: 79025--79164 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 60
79015 TTCATCTGGT
* * *
79025 AACTTCTTTGACGTCAATATGGATATGCCTTATAGTTCC-AGGGAGAGAAATTCGTTTGCC
1 AACTTCTTTGACCTCAATATGGATATGCCTTACAGTTCCAAGGG-GAGAAATTCATTTGCC
* * * * *
79085 AACTTCTTTGACCTTAATATGGATATGTCTTCCAGTTCCAAGGGGAGACATTCATTTTCC
1 AACTTCTTTGACCTCAATATGGATATGCCTTACAGTTCCAAGGGGAGAAATTCATTTGCC
*
79145 AACTTCTTCGACCTCAATAT
1 AACTTCTTTGACCTCAATAT
79165 AAAGATGTCT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
60 65 0.94
61 4 0.06
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (60 bp):
AACTTCTTTGACCTCAATATGGATATGCCTTACAGTTCCAAGGGGAGAAATTCATTTGCC
Found at i:79173 original size:60 final size:60
Alignment explanation
Indices: 79058--79176 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
79048 TATGCCTTAT
* * * ** *
79058 AGTTCCAGGGAGAGAAATTCGTTTGCCAACTTCTTTGACCTTAATATGGATATGTCTTCC
1 AGTTCCAGGGAGAGAAATTCATTTGCCAACTTCTTCGACCTCAATATAAAGATGTCTTCC
* *
79118 AGTTCCAAGGG-GAGACATTCATTTTCCAACTTCTTCGACCTCAATATAAAGATGTCTTC
1 AGTTCC-AGGGAGAGAAATTCATTTGCCAACTTCTTCGACCTCAATATAAAGATGTCTTC
79177 GACACAACAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
60 46 0.92
61 4 0.08
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (60 bp):
AGTTCCAGGGAGAGAAATTCATTTGCCAACTTCTTCGACCTCAATATAAAGATGTCTTCC
Found at i:81606 original size:18 final size:18
Alignment explanation
Indices: 81583--81633 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
81573 ATAAAGAAAA
81583 AATAAATGAAAATATTAC
1 AATAAATGAAAATATTAC
* *
81601 AATAAATTAAAATATTAT
1 AATAAATGAAAATATTAC
81619 AATAAATGAAAATAT
1 AATAAATGAAAATAT
81634 CATCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
AATAAATGAAAATATTAC
Found at i:81773 original size:15 final size:16
Alignment explanation
Indices: 81742--81784 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
81732 CACTCTCATT
81742 ATCATCGTCATTTGATC
1 ATCATCGTCA-TTGATC
*
81759 GTCATCGTC-TTGATC
1 ATCATCGTCATTGATC
81774 ATCATCGTCAT
1 ATCATCGTCAT
81785 CATCATCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 14 0.61
16 1 0.04
17 8 0.35
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (16 bp):
ATCATCGTCATTGATC
Found at i:83685 original size:14 final size:14
Alignment explanation
Indices: 83666--83693 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
83656 AAAAAATATT
83666 TAAATAAATTCTAA
1 TAAATAAATTCTAA
83680 TAAATAAATTCTAA
1 TAAATAAATTCTAA
83694 CAATTTAAAT
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:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATAAATTCTAA
Found at i:84375 original size:63 final size:62
Alignment explanation
Indices: 84280--84405 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 62
84270 TTAAAAAATT
* *
84280 ATATAATAAATTTAGGGGATTAAATTATAAAATATTAAATAATATTAAATTTGACCATAAAA
1 ATATAATAAATTTAGGGGATTAAAATATAAAATATTAAAGAATATTAAATTTGACCATAAAA
* *
84342 ATATAATAAATTTAAGGGTATTAAAATATAAAATTTTAAAGAATATTAAATTTGACCATAAAA
1 ATATAATAAATTT-AGGGGATTAAAATATAAAATATTAAAGAATATTAAATTTGACCATAAAA
84405 A
1 A
84406 ATGCAACGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
62 13 0.22
63 46 0.78
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (62 bp):
ATATAATAAATTTAGGGGATTAAAATATAAAATATTAAAGAATATTAAATTTGACCATAAAA
Found at i:93991 original size:297 final size:293
Alignment explanation
Indices: 93426--94008 Score: 918
Period size: 297 Copynumber: 2.0 Consensus size: 293
93416 GAACAAAGAT
* * *
93426 AGTGTAGAAATTAAAGAGCCTAAAGACCAGGTTCATTGTCCTACATTTTTTACTTAAAGCTTGCT
1 AGTGTAGAAATGAAAGAACCTAAAGACCAGGTTCATTGTCCTACATTTTTAACTTAAAGCTTGCT
* *
93491 TATAGTTGATCATTTATTTTGTACAAACACCGTTTCGCTTGTATATCACTTTTCAACCGTTTCCA
66 TATAGTTGATCATTTATTTTGTACAAACAACGTTTCGCTCGTATATCACTTTTCAACCGTTTCCA
* * *
93556 GATAGCTAGTCTTAAAGCAGCCTCTGCCACAGTGGAAAAGGAAGGAGAACCCGAGCAAGTGCAAG
131 GATAGCTAGTCTTAAAGCAGCCTCAGCCACAGCGAAAAAGGAAGGAGAACCCGAGCAAGTGCAAG
* ** *
93621 AGAGTCAATCCATACCAACTTGCCCAGGAATGAAAACACCGAGATTTGAAACATCCTCTTCTCTT
196 AGAGTCAATCCATACCAACTAGCCCAGGAACAAAAACACCGAGATTTGAAACATCCCCTTCTCTT
93686 CCACAATGCCAAAGTCCCAGTGATCAATCCAGC
261 CCACAATGCCAAAGTCCCAGTGATCAATCCAGC
*
93719 AGTGTGGAAATGAAAGAACCTAAAGACCAGGTTTCTTCATTGTCCTACATTTTTAACTTAAAGCT
1 AGTGTAGAAATGAAAGAACCTAAAGACCAGG----TTCATTGTCCTACATTTTTAACTTAAAGCT
* * *
93784 TGCTTATATTTGCTCATTTATTTTGTACAAACATAC-TTTCGCTCGTATATCTCTTTTCAACCGT
62 TGCTTATAGTTGATCATTTATTTTGTACAAACA-ACGTTTCGCTCGTATATCACTTTTCAACCGT
** *
93848 TTCCAGATAGCTAGTCTTAAAGCAGCCTCAGCTGCAGCGAAAAAGGAAGGAGAGCCCGAGCAAGT
126 TTCCAGATAGCTAGTCTTAAAGCAGCCTCAGCCACAGCGAAAAAGGAAGGAGAACCCGAGCAAGT
*
93913 GCAAGAGAGTCAATCCGTACCAACTAGCCCAGGAACAAAAACACCGAG-TCTTGAAACATCCCCT
191 GCAAGAGAGTCAATCCATACCAACTAGCCCAGGAACAAAAACACCGAGAT-TTGAAACATCCCCT
93977 TCTCTTCCACAATGCCAAAGTCCCAGTGATCA
255 TCTCTTCCACAATGCCAAAGTCCCAGTGATCA
94009 GTCTAGAAGT
Statistics
Matches: 264, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
293 28 0.11
296 1 0.00
297 234 0.89
298 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (293 bp):
AGTGTAGAAATGAAAGAACCTAAAGACCAGGTTCATTGTCCTACATTTTTAACTTAAAGCTTGCT
TATAGTTGATCATTTATTTTGTACAAACAACGTTTCGCTCGTATATCACTTTTCAACCGTTTCCA
GATAGCTAGTCTTAAAGCAGCCTCAGCCACAGCGAAAAAGGAAGGAGAACCCGAGCAAGTGCAAG
AGAGTCAATCCATACCAACTAGCCCAGGAACAAAAACACCGAGATTTGAAACATCCCCTTCTCTT
CCACAATGCCAAAGTCCCAGTGATCAATCCAGC
Found at i:94346 original size:24 final size:24
Alignment explanation
Indices: 94314--94545 Score: 154
Period size: 24 Copynumber: 9.7 Consensus size: 24
94304 GATTCAGGAC
* *
94314 TCTTCAACCGCATCTAGGAATGAG
1 TCTTCAACCCCATCTACGAATGAG
** *
94338 TCTTCAACCCCATCTTGGACTGAG
1 TCTTCAACCCCATCTACGAATGAG
*
94362 TCTTCAACCCCATC-ACCGACTGAG
1 TCTTCAACCCCATCTA-CGAATGAG
* * *
94386 ACTTCAACCCCATCT-CCAGCTGAG
1 TCTTCAACCCCATCTACGA-ATGAG
* *
94410 ACTTCAACCCCATCTCCG-ATCGAG
1 TCTTCAACCCCATCTACGAAT-GAG
** * *
94434 TCTTCAACTGCATCT-CCAACCGAG
1 TCTTCAACCCCATCTACGAA-TGAG
* * * *
94458 ACTTCAACCACATCTCCG-ATCAAG
1 TCTTCAACCCCATCTACGAAT-GAG
*
94482 TCTTCAACCCCATCT-CTGACTGAG
1 TCTTCAACCCCATCTAC-GAATGAG
94506 TCTTCAACCCCATCT-CGGAATGAG
1 TCTTCAACCCCATCTAC-GAATGAG
* *
94530 TCTCCAACCTCATCTA
1 TCTTCAACCCCATCTA
94546 ATAAAAGTCC
Statistics
Matches: 168, Mismatches: 28, Indels: 23
0.77 0.13 0.11
Matches are distributed among these distances:
23 5 0.03
24 160 0.95
25 3 0.02
ACGTcount: A:0.25, C:0.37, G:0.13, T:0.25
Consensus pattern (24 bp):
TCTTCAACCCCATCTACGAATGAG
Found at i:94391 original size:48 final size:48
Alignment explanation
Indices: 94335--94544 Score: 212
Period size: 48 Copynumber: 4.4 Consensus size: 48
94325 ATCTAGGAAT
* * *
94335 GAGTCTTCAACCCCATCTTGGACTGAGTCTTCAACCCCATCACCGA-C
1 GAGTCTTCAACCCCATCTTCGACTGAGACTTCAACCCCATCTCCGATC
* *
94382 TGAGACTTCAACCCCATC-TCCAGCTGAGACTTCAACCCCATCTCCGATC
1 -GAGTCTTCAACCCCATCTTCGA-CTGAGACTTCAACCCCATCTCCGATC
** * * * *
94431 GAGTCTTCAACTGCATCTCCAACCGAGACTTCAACCACATCTCCGATC
1 GAGTCTTCAACCCCATCTTCGACTGAGACTTCAACCCCATCTCCGATC
* * *
94479 AAGTCTTCAACCCCATC-TCTGACTGAGTCTTCAACCCCATCTCGGAAT-
1 GAGTCTTCAACCCCATCTTC-GACTGAGACTTCAACCCCATCTCCG-ATC
* *
94527 GAGTCTCCAACCTCATCT
1 GAGTCTTCAACCCCATCT
94545 AATAAAAGTC
Statistics
Matches: 132, Mismatches: 24, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
47 3 0.02
48 124 0.94
49 5 0.04
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.24
Consensus pattern (48 bp):
GAGTCTTCAACCCCATCTTCGACTGAGACTTCAACCCCATCTCCGATC
Found at i:94435 original size:72 final size:71
Alignment explanation
Indices: 94315--94519 Score: 232
Period size: 72 Copynumber: 2.8 Consensus size: 71
94305 ATTCAGGACT
* ** ** *
94315 CTTCAACCGCATCTAGGAATGAGTCTTCAACCCCATCTTGGACTGAGTCTTCAACCCCATCACCG
1 CTTCAACCACATCTCCG-ATGAGTCTTCAACCCCATCTCCGACTGAGTCTTCAACCCCATCACCA
*
94380 ACTGAGA
65 ACCGAGA
* * * ** *
94387 CTTCAACCCCATCTCCAGCTGAGACTTCAACCCCATCTCCGA-TCGAGTCTTCAACTGCATCTCC
1 CTTCAACCACATCTCC-GATGAGTCTTCAACCCCATCTCCGACT-GAGTCTTCAACCCCATCACC
94451 AACCGAGA
64 AACCGAGA
* *
94459 CTTCAACCACATCTCCGATCAAGTCTTCAACCCCATCTCTGACTGAGTCTTCAACCCCATC
1 CTTCAACCACATCTCCGAT-GAGTCTTCAACCCCATCTCCGACTGAGTCTTCAACCCCATC
94520 TCGGAATGAG
Statistics
Matches: 110, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
71 3 0.03
72 105 0.95
73 2 0.02
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.24
Consensus pattern (71 bp):
CTTCAACCACATCTCCGATGAGTCTTCAACCCCATCTCCGACTGAGTCTTCAACCCCATCACCAA
CCGAGA
Found at i:94520 original size:72 final size:72
Alignment explanation
Indices: 94336--94521 Score: 234
Period size: 72 Copynumber: 2.6 Consensus size: 72
94326 TCTAGGAATG
* * * *
94336 AGTCTTCAACCCCATCT-TGGACTGAGTCTTCAACCCCATCACCGACTGAGACTTCAACCCCATC
1 AGTCTTCAACCCCATCTCT-GACTGAGTCTTCAACCCCATCTCCAACCGAGACTTCAACCACATC
*
94400 TCCAGCTG
65 TCCAGCTA
* * **
94408 AGACTTCAACCCCATCTCCGA-TCGAGTCTTCAACTGCATCTCCAACCGAGACTTCAACCACATC
1 AGTCTTCAACCCCATCTCTGACT-GAGTCTTCAACCCCATCTCCAACCGAGACTTCAACCACATC
*
94472 TCC-GATCA
65 TCCAGCT-A
94480 AGTCTTCAACCCCATCTCTGACTGAGTCTTCAACCCCATCTC
1 AGTCTTCAACCCCATCTCTGACTGAGTCTTCAACCCCATCTC
94522 GGAATGAGTC
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
71 3 0.03
72 92 0.96
73 1 0.01
ACGTcount: A:0.25, C:0.39, G:0.12, T:0.24
Consensus pattern (72 bp):
AGTCTTCAACCCCATCTCTGACTGAGTCTTCAACCCCATCTCCAACCGAGACTTCAACCACATCT
CCAGCTA
Found at i:94538 original size:72 final size:71
Alignment explanation
Indices: 94336--94544 Score: 217
Period size: 72 Copynumber: 2.9 Consensus size: 71
94326 TCTAGGAATG
* * *
94336 AGTCTTCAACCCCATCT-TGGACTGAGTCTTCAACCCCATCACCGACTGAGACTTCAACCCCATC
1 AGTCTTCAACCCCATCTCT-GACTGAGTCTTCAACCCCATC-TCGAATGAGACTTCAACCACATC
*
94400 TCCAGCTG
64 TCCAGCTA
* * ** * *
94408 AGACTTCAACCCCATCTCCGA-TCGAGTCTTCAACTGCATCTCCAACCGAGACTTCAACCACATC
1 AGTCTTCAACCCCATCTCTGACT-GAGTCTTCAACCCCATCTCGAA-TGAGACTTCAACCACATC
*
94472 TCC-GATCA
64 TCCAGCT-A
* * *
94480 AGTCTTCAACCCCATCTCTGACTGAGTCTTCAACCCCATCTCGGAATGAGTCTCCAACCTCATCT
1 AGTCTTCAACCCCATCTCTGACTGAGTCTTCAACCCCATCTC-GAATGAGACTTCAACCACATCT
94545 AATAAAAGTC
Statistics
Matches: 111, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
71 5 0.05
72 103 0.93
73 3 0.03
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.24
Consensus pattern (71 bp):
AGTCTTCAACCCCATCTCTGACTGAGTCTTCAACCCCATCTCGAATGAGACTTCAACCACATCTC
CAGCTA
Found at i:96102 original size:14 final size:14
Alignment explanation
Indices: 96085--96113 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
96075 AAGGTGTAGT
96085 ACTAAAATGAAACA
1 ACTAAAATGAAACA
96099 ACTAAAATGAAACA
1 ACTAAAATGAAACA
96113 A
1 A
96114 AAATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
ACTAAAATGAAACA
Found at i:96785 original size:30 final size:31
Alignment explanation
Indices: 96731--96805 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 31
96721 AGGGTAAAAT
96731 TTTGATAAATTTAATAATCATTTTATAATAA
1 TTTGATAAATTTAATAATCATTTTATAATAA
*
96762 TTTGATAAAATTTAAT-A-CATTTTATAATAG
1 TTTGAT-AAATTTAATAATCATTTTATAATAA
96792 TTTGATAAATTTAA
1 TTTGATAAATTTAA
96806 AAATTATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 8 0.19
30 18 0.43
31 7 0.17
32 9 0.21
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTGATAAATTTAATAATCATTTTATAATAA
Done.