Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002581.1 Hibiscus syriacus cultivar Beakdansim tig00005227_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: 123916
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5958 original size:28 final size:28
Alignment explanation
Indices: 5926--6020 Score: 71
Period size: 28 Copynumber: 3.6 Consensus size: 28
5916 TATGCTGTGT
5926 ATTTTTCTGCACTGTTCGAACCAAATCA
1 ATTTTTCTGCACTGTTCGAACCAAATCA
*
5954 ATTTTTTCTG--CTGTTCTG------TTCGA
1 A-TTTTTCTGCACTGTTC-GAACCAAATC-A
* *
5977 ATTTTTCTGCACAGTTCGAACCAAGTCA
1 ATTTTTCTGCACTGTTCGAACCAAATCA
*
6005 GTTTTTCTGCACTGTT
1 ATTTTTCTGCACTGTT
6021 TTTTTCGTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 22
0.65 0.06 0.28
Matches are distributed among these distances:
22 10 0.20
23 3 0.06
24 5 0.10
27 6 0.12
28 17 0.33
29 10 0.20
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (28 bp):
ATTTTTCTGCACTGTTCGAACCAAATCA
Found at i:6101 original size:14 final size:14
Alignment explanation
Indices: 6065--6104 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
6055 GTTCAGAAAA
*
6065 AATAAAATTAATCAG
1 AATAAAATAAAT-AG
6080 AATAAAATAAATAG
1 AATAAAATAAATAG
*
6094 AATGAAATAAA
1 AATAAAATAAA
6105 GTTCGCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (14 bp):
AATAAAATAAATAG
Found at i:6139 original size:11 final size:11
Alignment explanation
Indices: 6112--6153 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
6102 AAAGTTCGCT
6112 AAAAAAAT-AA
1 AAAAAAATAAA
**
6122 ACGAAAATAAA
1 AAAAAAATAAA
6133 AAAAAAATAAA
1 AAAAAAATAAA
6144 AACAAAAATA
1 AA-AAAAATA
6154 TAACGAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 6 0.23
11 13 0.50
12 7 0.27
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:6146 original size:23 final size:21
Alignment explanation
Indices: 6112--6153 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
6102 AAAGTTCGCT
*
6112 AAAAAAATAAACGAAAATAAA
1 AAAAAAATAAACAAAAATAAA
6133 AAAAAAATAAAAACAAAAATA
1 AAAAAAAT--AAACAAAAATA
6154 TAACGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (21 bp):
AAAAAAATAAACAAAAATAAA
Found at i:11762 original size:6 final size:6
Alignment explanation
Indices: 11743--11781 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
11733 AAAATAAAAA
11743 TAATA- TAATA- TAATAG TAATAG TAATAG TAATAG TAATA
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATA
11782 AATATAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (6 bp):
TAATAG
Found at i:11865 original size:23 final size:23
Alignment explanation
Indices: 11815--11865 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
11805 AAGTTGTGGT
* *
11815 TAAAATAAAAAATAAGAATTAAA
1 TAAAAGAAAAAATAAGAAATAAA
*
11838 TAAAAGAAAAAATAATTAAATAAA
1 TAAAAGAAAAAATAA-GAAATAAA
11862 -AAAA
1 TAAAA
11866 TTAAAGAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
TAAAAGAAAAAATAAGAAATAAA
Found at i:12343 original size:12 final size:12
Alignment explanation
Indices: 12328--12357 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12318 AAAAGTATAC
12328 GAAAAATAGAGA
1 GAAAAATAGAGA
*
12340 GAAAACTAGAGA
1 GAAAAATAGAGA
12352 GAAAAA
1 GAAAAA
12358 AGAAGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:12574 original size:76 final size:75
Alignment explanation
Indices: 12464--12611 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
12454 TCTTAAATCC
12464 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAAT-ATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATAAAATGATAAAAATAAT
12528 ATCCTAAAACT
65 ATCCTAAAACT
* * * *
12539 TAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATT
1 TAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAAT
12604 ATCCTAAA
65 ATCCTAAA
12612 TTTGAGTTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 19 0.28
76 48 0.72
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAATA
TCCTAAAACT
Found at i:32992 original size:14 final size:14
Alignment explanation
Indices: 32973--33001 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32963 TTTACTGTTC
32973 ATAAATATGTTTTT
1 ATAAATATGTTTTT
32987 ATAAATATGTTTTT
1 ATAAATATGTTTTT
33001 A
1 A
33002 CCTTAAAATT
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:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATAAATATGTTTTT
Found at i:37642 original size:23 final size:23
Alignment explanation
Indices: 37616--37674 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
37606 CATATAAATG
*
37616 CACCGAAGTGCCACATAGAATTA
1 CACCGTAGTGCCACATAGAATTA
* *
37639 CACCGTAGTGCCGCGTAGAATTA
1 CACCGTAGTGCCACATAGAATTA
37662 CACCGTAGTGCCA
1 CACCGTAGTGCCA
37675 TATAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19
Consensus pattern (23 bp):
CACCGTAGTGCCACATAGAATTA
Found at i:37863 original size:103 final size:103
Alignment explanation
Indices: 37690--37907 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
37680 TAATGTCCAT
*
37690 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
37755 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
37793 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGAGATCAAGTATGTGTCTCACC
*
37857 ATACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
37896 AAGGACCACATA
1 AAGGACCACATA
37908 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 108 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:43672 original size:2 final size:2
Alignment explanation
Indices: 43665--43728 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
43655 TGAATTCAAG
43665 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
43707 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
43729 TTAAATACAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43955 original size:70 final size:72
Alignment explanation
Indices: 43843--43983 Score: 162
Period size: 70 Copynumber: 2.0 Consensus size: 72
43833 TTTATTTTTC
* * *
43843 AATGTTAAGATATATTTAATATATATATATTTATATCTTAAA-TT-CATAAATTTAAAATAAAAA
1 AATGTTAAGATATATTTAATATATATATATTAATATCATAAATTTAAATAAATTTAAAATAAAAA
43906 TATATCT
66 TATATCT
* * * * * *
43913 AATGTTAATATATGTTTCATATATATATCTTAA-ATTCATAAATTTAAAATATATTTTAAATAAA
1 AATGTTAAGATATATTTAATATATATATATTAATA-TCATAAATTT-AAATAAATTTAAAATAAA
43977 AATATAT
64 AATATAT
43984 TTTAAATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
69 1 0.02
70 34 0.59
71 2 0.03
73 21 0.36
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (72 bp):
AATGTTAAGATATATTTAATATATATATATTAATATCATAAATTTAAATAAATTTAAAATAAAAA
TATATCT
Found at i:43965 original size:30 final size:30
Alignment explanation
Indices: 43869--43966 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
43859 TAATATATAT
*
43869 ATATTTATATCTTAAATTCATAAATTTAAA
1 ATATATATATCTTAAATTCATAAATTTAAA
* * * * **
43899 ATAAAAATATATC-TAATGTTAATATATGTT-TC
1 AT--ATATATATCTTAA-ATTCATAAAT-TTAAA
43931 ATATATATATCTTAAATTCATAAATTTAAA
1 ATATATATATCTTAAATTCATAAATTTAAA
43961 ATATAT
1 ATATAT
43967 TTTAAATAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
29 2 0.04
30 23 0.47
31 6 0.12
32 16 0.33
33 2 0.04
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (30 bp):
ATATATATATCTTAAATTCATAAATTTAAA
Found at i:43980 original size:17 final size:17
Alignment explanation
Indices: 43958--43991 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43948 TCATAAATTT
43958 AAAATATATTTTAAATA
1 AAAATATATTTTAAATA
43975 AAAATATATTTTAAATA
1 AAAATATATTTTAAATA
43992 TAATTTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATATATTTTAAATA
Found at i:43997 original size:29 final size:30
Alignment explanation
Indices: 43954--44017 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
43944 AAATTCATAA
*
43954 ATTTAAAATATATTTTAA-ATAA-AA-ATAT
1 ATTTTAAATATA-TTTAAGATAAGAATATAT
43982 ATTTTAAATATAATTTAAGATAAGAATATAT
1 ATTTTAAATAT-ATTTAAGATAAGAATATAT
44013 ATTTT
1 ATTTT
44018 TAATGTTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 15 0.48
29 5 0.16
30 2 0.06
31 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
ATTTTAAATATATTTAAGATAAGAATATAT
Found at i:52804 original size:3 final size:3
Alignment explanation
Indices: 52796--52830 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
52786 TACAGGGTTT
52796 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
52831 GCAGCCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:55746 original size:15 final size:16
Alignment explanation
Indices: 55719--55755 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
55709 TTTCAAGCGA
55719 ATGAAGTTTTCCACTGG
1 ATGAAGTTTTCCA-TGG
55736 -TGAAG-TTTCCATGG
1 ATGAAGTTTTCCATGG
55750 ATGAAG
1 ATGAAG
55756 CACAAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 11 0.58
16 5 0.26
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (16 bp):
ATGAAGTTTTCCATGG
Found at i:57794 original size:15 final size:16
Alignment explanation
Indices: 57767--57799 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
57757 GGCCAAGTCG
57767 GAGCAGACCCGAAGCA
1 GAGCAGACCCGAAGCA
57783 GAGCAG-CCCGAAGCA
1 GAGCAGACCCGAAGCA
57798 GA
1 GA
57800 ACAGTTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.30, G:0.33, T:0.00
Consensus pattern (16 bp):
GAGCAGACCCGAAGCA
Found at i:70794 original size:10 final size:10
Alignment explanation
Indices: 70764--70829 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
70754 ATTTTGCTTG
*
70764 AAGAAGAAAT
1 AAGAAGAAAA
*
70774 AA-AAGAGAA
1 AAGAAGAAAA
70783 AAGAAGAAAA
1 AAGAAGAAAA
70793 AATG-AG--AA
1 AA-GAAGAAAA
70801 AAGAAGAAAA
1 AAGAAGAAAA
70811 AATG-AGAAAA
1 AA-GAAGAAAA
70821 AAGAA-AAAA
1 AAGAAGAAAA
70830 TGATGGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
7 1 0.02
8 6 0.13
9 12 0.26
10 25 0.54
11 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:70801 original size:18 final size:18
Alignment explanation
Indices: 70764--70904 Score: 115
Period size: 18 Copynumber: 8.1 Consensus size: 18
70754 ATTTTGCTTG
*
70764 AAGAAGAAATAAAAGAGAA
1 AAGAAGAAA-AAATGAGAA
70783 AAGAAGAAAAAATGAGAA
1 AAGAAGAAAAAATGAGAA
70801 AAGAAGAAAAAATGAGAA
1 AAGAAGAAAAAATGAGAA
70819 AA-AAGAAAAAATGATGGAA
1 AAGAAGAAAAAATGA--GAA
70838 AA-AACGAAAAGAA--A-AA
1 AAGAA-GAAAA-AATGAGAA
70854 AAG-AGAAAAAATG-GAAA
1 AAGAAGAAAAAATGAG-AA
*
70871 AAGGAAG-GAAAA-GAGAA
1 AA-GAAGAAAAAATGAGAA
*
70888 AA-ATGAAAAAA-GAGAA
1 AAGAAGAAAAAATGAGAA
70904 A
1 A
70905 TAAAAGGAGG
Statistics
Matches: 105, Mismatches: 4, Indels: 29
0.76 0.03 0.21
Matches are distributed among these distances:
14 2 0.02
15 7 0.07
16 15 0.14
17 21 0.20
18 34 0.32
19 19 0.18
20 5 0.05
21 2 0.02
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (18 bp):
AAGAAGAAAAAATGAGAA
Found at i:70825 original size:25 final size:24
Alignment explanation
Indices: 70774--70904 Score: 76
Period size: 25 Copynumber: 5.1 Consensus size: 24
70764 AAGAAGAAAT
70774 AAAAG-AGAAAAGAA-GAAAAAATGAG
1 AAAAGAAGAAAA-AATGAAAAAA--AG
70799 AAAAGAAGAAAAAATGAGAAAAAAG
1 AAAAGAAGAAAAAATGA-AAAAAAG
* *
70824 AAAAAATGATGGAAAAAACGAAAAGAAA-
1 --AAAA-GA-AGAAAAAATGAAAA-AAAG
70852 AAAAG-AGAAAAAATGGAAAAAGGAAGG
1 AAAAGAAGAAAAAAT-GAAAAA--AA-G
70879 AAAAG-AG-AAAAATGAAAAAAGAG
1 AAAAGAAGAAAAAATGAAAAAA-AG
70902 AAA
1 AAA
70905 TAAAAGGAGG
Statistics
Matches: 88, Mismatches: 4, Indels: 30
0.72 0.03 0.25
Matches are distributed among these distances:
23 13 0.15
24 6 0.07
25 18 0.20
26 18 0.20
27 16 0.18
28 5 0.06
29 12 0.14
ACGTcount: A:0.73, C:0.01, G:0.22, T:0.05
Consensus pattern (24 bp):
AAAAGAAGAAAAAATGAAAAAAAG
Found at i:70832 original size:35 final size:34
Alignment explanation
Indices: 70764--70904 Score: 123
Period size: 35 Copynumber: 4.0 Consensus size: 34
70754 ATTTTGCTTG
70764 AAGAAGAAATAAAAGAGAAAAGAAGAAAAAATGAGAA
1 AAGAAG-AA-AAAAGAGAAAA-AAGAAAAAATGAGAA
70801 AAGAAGAAAAAATGAGAAAAAAGAAAAAATGATGGAA
1 AAGAAGAAAAAA-GAGAAAAAAGAAAAAATGA--GAA
*
70838 AA-AACGAAAAGAA-A-AAAAGAGAAAAAATG-GAAA
1 AAGAA-GAAAA-AAGAGAAAAAAGAAAAAATGAG-AA
* *
70871 AAGGAAG-GAAAAGAGAAAAATGAAAAAA-GAGAA
1 AA-GAAGAAAAAAGAGAAAAAAGAAAAAATGAGAA
70904 A
1 A
70905 TAAAAGGAGG
Statistics
Matches: 89, Mismatches: 4, Indels: 26
0.75 0.03 0.22
Matches are distributed among these distances:
32 3 0.03
33 11 0.12
34 13 0.15
35 32 0.36
36 12 0.13
37 16 0.18
38 2 0.02
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (34 bp):
AAGAAGAAAAAAGAGAAAAAAGAAAAAATGAGAA
Found at i:70860 original size:42 final size:42
Alignment explanation
Indices: 70804--70904 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 42
70794 ATGAGAAAAG
* * *
70804 AAGAAAAAATGAGAAAAAA-GAAAAAATGATGGAAAAAACGAA
1 AAGAAAAAAAGAGAAAAAATGAAAAAAGGAAGGAAAAAA-GAA
* *
70846 AAGAAAAAAAGAGAAAAAATGGAAAAAGGAAGGAAAAGAGAA
1 AAGAAAAAAAGAGAAAAAATGAAAAAAGGAAGGAAAAAAGAA
70888 AA-ATGAAAAAAGAGAAA
1 AAGA--AAAAAAGAGAAA
70905 TAAAAGGAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 1 0.02
42 23 0.45
43 27 0.53
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (42 bp):
AAGAAAAAAAGAGAAAAAATGAAAAAAGGAAGGAAAAAAGAA
Found at i:72288 original size:51 final size:50
Alignment explanation
Indices: 72228--72444 Score: 229
Period size: 51 Copynumber: 4.2 Consensus size: 50
72218 AATTAGTTCG
* *
72228 TTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTT
1 TTGAAGATTGAGTCCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTT
* *
72278 GTTGAAGATTGAGTCCTATACT-CTTGAATGAATAGGGAGCGGACAAGTTT
1 -TTGAAGATTGAGTCCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTT
** * * **
72328 ATTGAAGAACGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTT
1 -TTGAAGATTGAGTCCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTT
* * **
72379 TATGAAGATTGTTCGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTT
1 T-TGAAGA---TT-GAGTCCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTT
72434 TATGAAGATTG
1 T-TGAAGATTG
72445 TTCGAGTTCT
Statistics
Matches: 146, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
50 44 0.30
51 51 0.35
52 2 0.01
55 49 0.34
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (50 bp):
TTGAAGATTGAGTCCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTT
Found at i:72333 original size:50 final size:49
Alignment explanation
Indices: 72228--72499 Score: 202
Period size: 55 Copynumber: 5.2 Consensus size: 49
72218 AATTAGTTCG
72228 TTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTT
1 TTGAAGATTGAGTCCTATACTCT-TGAAAGAATAGGGAGCGGACAAGTTT
*
72278 GTTGAAGATTGAGTCCTATACTCTTGAATGAATAGGGAGCGGACAAGTTT
1 -TTGAAGATTGAGTCCTATACTCTTGAAAGAATAGGGAGCGGACAAGTTT
** * * * * **
72328 ATTGAAGAACGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTT
1 -TTGAAGATTGAGTCCTATACT-CTTGAAAGAATAGGGAGCGGACAAGTTT
* * * * **
72379 TATGAAGATTGTTCGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTT
1 T-TGAAGA---TT-GAGTCCTATACT-CTTGAAAGAATAGGGAGCGGACAAGTTT
* * * **
72434 TATGAAGATTGTTCGAGTTCTTATACTCCTTGAAAGAAAAGGGAGCAGACCCGTTAT
1 T-TGAAGA---TT-GAG-TCCTATACT-CTTGAAAGAATAGGGAGCGGACAAGTT-T
72491 TTGAAGATT
1 TTGAAGATT
72500 TTTCAAGTAT
Statistics
Matches: 194, Mismatches: 19, Indels: 14
0.85 0.08 0.06
Matches are distributed among these distances:
50 44 0.23
51 52 0.27
53 2 0.01
55 58 0.30
56 36 0.19
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (49 bp):
TTGAAGATTGAGTCCTATACTCTTGAAAGAATAGGGAGCGGACAAGTTT
Found at i:72485 original size:56 final size:55
Alignment explanation
Indices: 72337--72499 Score: 256
Period size: 55 Copynumber: 2.9 Consensus size: 55
72327 TATTGAAGAA
72337 CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTT
1 CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTT
72392 CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTT
1 CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTT
* * * * *
72447 CGAGTTCTTATACTCCTTGAAAGAAAAGGGAGCAGACCCGTTATT-TGAAGATT
1 CGAGTTC-TATACTCCCTGAACGGATAGGGAGCGGACCCGTT-TTATGAAGATT
72500 TTTCAAGTAT
Statistics
Matches: 101, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
55 62 0.61
56 37 0.37
57 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (55 bp):
CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTT
Found at i:72698 original size:15 final size:16
Alignment explanation
Indices: 72671--72703 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
72661 GGCCAAGTCG
72671 GAGCAGACCCGAAGCA
1 GAGCAGACCCGAAGCA
72687 GAGCAG-CCCGAAGCA
1 GAGCAGACCCGAAGCA
72702 GA
1 GA
72704 ACAGTTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.30, G:0.33, T:0.00
Consensus pattern (16 bp):
GAGCAGACCCGAAGCA
Found at i:84052 original size:26 final size:26
Alignment explanation
Indices: 84023--84080 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
84013 TTATTAATTA
* *
84023 TGCATGATTTTTATTCACACTGATTT
1 TGCATGATATTTACTCACACTGATTT
** *
84049 TGCATGATATTTACTCATGCTGGTTT
1 TGCATGATATTTACTCACACTGATTT
84075 TGCATG
1 TGCATG
84081 TAATACTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (26 bp):
TGCATGATATTTACTCACACTGATTT
Found at i:84370 original size:26 final size:26
Alignment explanation
Indices: 84298--84375 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
84288 TGTACACCAT
** * *
84298 ATATTTACTCGTATTGATTATGCATG
1 ATATTTACTCACACTGATTTTGCATG
*
84324 ATATTTATTCACACTGATTTTGCATG
1 ATATTTACTCACACTGATTTTGCATG
** *
84350 ATATTTACTCATGCTGGTTTTGCATG
1 ATATTTACTCACACTGATTTTGCATG
84376 TACTACTCAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.46
Consensus pattern (26 bp):
ATATTTACTCACACTGATTTTGCATG
Found at i:95274 original size:18 final size:18
Alignment explanation
Indices: 95251--95285 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
95241 TTTTCAAATT
*
95251 TTTATTTCATTACTTTCC
1 TTTATTTAATTACTTTCC
*
95269 TTTATTTAATTTCTTTC
1 TTTATTTAATTACTTTC
95286 AACTCTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATTTAATTACTTTCC
Found at i:98185 original size:40 final size:40
Alignment explanation
Indices: 98139--98272 Score: 141
Period size: 40 Copynumber: 3.4 Consensus size: 40
98129 GCGATCGATA
98139 ATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAG
1 ATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAG
* ** * * *
98179 ATTCGCAATGCGAT-TTTGGACTATCGC-AATGC-G-ATCGATA
1 ATTCGCAACGCGATCTCCGG--TATCGCAAAT-CAGTTTCCA-G
98219 ATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAG
1 ATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAG
*
98259 ATTCGCAATGCGAT
1 ATTCGCAACGCGAT
98273 TTTGGACTAT
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
39 13 0.18
40 47 0.64
41 13 0.18
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
ATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAG
Found at i:98254 original size:80 final size:80
Alignment explanation
Indices: 98121--98292 Score: 344
Period size: 80 Copynumber: 2.1 Consensus size: 80
98111 GACCAACTAA
98121 ATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCA
1 ATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCA
98186 ATGCGATTTTGGACT
66 ATGCGATTTTGGACT
98201 ATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCA
1 ATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCA
98266 ATGCGATTTTGGACT
66 ATGCGATTTTGGACT
98281 ATCGCAATGCGA
1 ATCGCAATGCGA
98293 ACTTGGACTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 92 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (80 bp):
ATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCA
ATGCGATTTTGGACT
Found at i:98287 original size:21 final size:21
Alignment explanation
Indices: 98261--98479 Score: 141
Period size: 21 Copynumber: 10.8 Consensus size: 21
98251 GTTTCCAGAT
*
98261 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAATTTGGACTA
*
98282 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAATTTGGACTA
* * *
98303 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAATTTGGACTA
* * * *
98323 TCGCAATGCGATAGTAGAAGT-
1 TCGCAATGCGA-ATTTGGACTA
*
98344 TCGCAA---GAAGTTGGACTA
1 TCGCAATGCGAATTTGGACTA
* * *
98362 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAATTTGGACTA
* * * *
98382 TCGCAATACGAATATGTA-AA
1 TCGCAATGCGAATTTGGACTA
* **
98402 TCGCAATGCG-ATAGTCAACTA
1 TCGCAATGCGAAT-TTGGACTA
*
98423 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAATTTGGACTA
* *
98444 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAATTTGGACTA
*
98465 TCGCATTGCG-ATTTG
1 TCGCAATGCGAATTTG
98480 TATATTCGTA
Statistics
Matches: 157, Mismatches: 32, Indels: 19
0.75 0.15 0.09
Matches are distributed among these distances:
17 6 0.04
18 8 0.05
19 2 0.01
20 46 0.29
21 94 0.60
22 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGACTA
Found at i:98327 original size:20 final size:20
Alignment explanation
Indices: 98302--98434 Score: 111
Period size: 20 Copynumber: 6.7 Consensus size: 20
98292 AACTTGGACT
98302 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
98322 ATCGCAATGCG-ATA-GTAGA
1 ATCGCAATGCGAATATGTA-A
* *
98341 AGTTCGCAA---GAAGT-TGGACT
1 A--TCGCAATGCGAA-TATGTA-A
98361 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
98381 ATCGCAATACGAATATGTAA
1 ATCGCAATGCGAATATGTAA
98401 ATCGCAATGCG-ATA-GTCAA
1 ATCGCAATGCGAATATGT-AA
98420 CTATCGCAATGCGAA
1 --ATCGCAATGCGAA
98435 CTTGGACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 26
0.74 0.06 0.21
Matches are distributed among these distances:
18 12 0.13
19 11 0.12
20 45 0.49
21 23 0.25
22 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:98401 original size:79 final size:81
Alignment explanation
Indices: 98274--98469 Score: 256
Period size: 79 Copynumber: 2.4 Consensus size: 81
98264 CAATGCGATT
* *
98274 TTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTA
1 TTGGACTATCGCAATGCGAACTTGGACAATCGCAATACGAATATGTAAATCGCAATGCGATAGT-
* * *
98339 GAAGT-TCGCAA-GAAG
65 CAACTATCGCAACGAAC
*
98354 TTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATACGAATATGTAAATCGCAATGCGATAGT
1 TTGGACTATCGCAATGCGAACT-TGGACAATCGCAATACGAATATGTAAATCGCAATGCGATAGT
98417 CAACTATCGCAATGCGAAC
65 CAACTATCGCAA--CGAAC
* *
98436 TTGGACTATCGCAATGCGAACTTCGACTATCGCA
1 TTGGACTATCGCAATGCGAACTTGGACAATCGCA
98470 TTGCGATTTG
Statistics
Matches: 100, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
78 3 0.03
79 42 0.42
80 23 0.23
82 25 0.25
83 7 0.07
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (81 bp):
TTGGACTATCGCAATGCGAACTTGGACAATCGCAATACGAATATGTAAATCGCAATGCGATAGTC
AACTATCGCAACGAAC
Found at i:98542 original size:42 final size:42
Alignment explanation
Indices: 98399--98584 Score: 130
Period size: 42 Copynumber: 4.5 Consensus size: 42
98389 ACGAATATGT
* * * * *
98399 AAATCGCAATGCGATAGTCAACTATCGCAATGCGA-ACTTGGA
1 AAATCGCATTGCGATAGTCGACTATCGCATTGCGATA-GTCGA
** * * *
98441 CTATCGCAATGCGA-ACTTCGACTATCGCATTGCGAT--TTGTA
1 AAATCGCATTGCGATA-GTCGACTATCGCATTGCGATAGTCG-A
* * * * * *
98482 TATTCGTATTGTGATAGTCGAAGT-TCGCTTTGCGATAGTCGA
1 AAATCGCATTGCGATAGTCG-ACTATCGCATTGCGATAGTCGA
** *
98524 AGCTCGCATTGCGATAGTCGACTATCGCATTGCGATAGTCTA
1 AAATCGCATTGCGATAGTCGACTATCGCATTGCGATAGTCGA
98566 AAATCGCATTGCGATAGTC
1 AAATCGCATTGCGATAGTC
98585 CAAAATCACA
Statistics
Matches: 110, Mismatches: 26, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
40 2 0.02
41 26 0.24
42 80 0.73
43 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (42 bp):
AAATCGCATTGCGATAGTCGACTATCGCATTGCGATAGTCGA
Found at i:98589 original size:21 final size:21
Alignment explanation
Indices: 98489--98591 Score: 116
Period size: 21 Copynumber: 4.9 Consensus size: 21
98479 GTATATTCGT
* **
98489 ATTGTGATAGTCGAAGTTCGC
1 ATTGCGATAGTCGAAAATCGC
* **
98510 TTTGCGATAGTCGAAGCTCGC
1 ATTGCGATAGTCGAAAATCGC
**
98531 ATTGCGATAGTCGACTATCGC
1 ATTGCGATAGTCGAAAATCGC
*
98552 ATTGCGATAGTCTAAAATCGC
1 ATTGCGATAGTCGAAAATCGC
*
98573 ATTGCGATAGTCCAAAATC
1 ATTGCGATAGTCGAAAATC
98592 ACAACGACTG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (21 bp):
ATTGCGATAGTCGAAAATCGC
Found at i:106312 original size:16 final size:16
Alignment explanation
Indices: 106288--106321 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
106278 TATCGCCGAC
*
106288 CAAATTTTACTATTCA
1 CAAAATTTACTATTCA
106304 CAAAATTTACTATTCA
1 CAAAATTTACTATTCA
106320 CA
1 CA
106322 TGAATCGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (16 bp):
CAAAATTTACTATTCA
Found at i:119129 original size:87 final size:87
Alignment explanation
Indices: 118983--119157 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
118973 ATTTAATACA
118983 TAGTTTCTTCTATATTTTTTTTAGAAGGAAGGATGAGTGGTTGCCATACATGGATCTCGGAGCCT
1 TAGTTTCTTCTATATTTTTTTTAGAAGGAAGGATGAGTGGTTGCCATACATGGATCTCGGAGCCT
*
119048 AATTTTAGGATTAAAACGTTGT
66 AATGTTAGGATTAAAACGTTGT
119070 TAGTTTCTTCTATATTTTTTTTAGAAGGAAGGATGAGTGGTTGCCATACATGGATCTCGGAGCCT
1 TAGTTTCTTCTATATTTTTTTTAGAAGGAAGGATGAGTGGTTGCCATACATGGATCTCGGAGCCT
119135 AATGTTAGGATTAAAACGTTGT
66 AATGTTAGGATTAAAACGTTGT
119157 T
1 T
119158 GTAAACTTTA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.39
Consensus pattern (87 bp):
TAGTTTCTTCTATATTTTTTTTAGAAGGAAGGATGAGTGGTTGCCATACATGGATCTCGGAGCCT
AATGTTAGGATTAAAACGTTGT
Found at i:119616 original size:26 final size:26
Alignment explanation
Indices: 119563--119612 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
119553 CATATTCGTA
* * *
119563 TTTTTTTATATCTAATTGATCAATAT
1 TTTTTTTAGATCTAAGTGATAAATAT
119589 TTTTTTTAGATCT-AGTGATAAATA
1 TTTTTTTAGATCTAAGTGATAAATA
119613 ATTTGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (26 bp):
TTTTTTTAGATCTAAGTGATAAATAT
Done.