Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002636.1 Hibiscus syriacus cultivar Beakdansim tig00005374_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: 58234
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2561 original size:27 final size:27
Alignment explanation
Indices: 2531--2600 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
2521 ATTTAGTTTA
2531 TTAAATATATTTTATTACTAACTTAAT
1 TTAAATATATTTTATTACTAACTTAAT
* * **
2558 TTAAAAATA-TTTATTATTATTTTAAT
1 TTAAATATATTTTATTACTAACTTAAT
*
2584 TAAAAGTATATTTTATT
1 TTAAA-TATATTTTATT
2601 CTTATCTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 18 0.51
27 11 0.31
28 6 0.17
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (27 bp):
TTAAATATATTTTATTACTAACTTAAT
Found at i:2693 original size:29 final size:28
Alignment explanation
Indices: 2650--2722 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
2640 TTTCAAAGTA
* *
2650 TATATTTTATATTAATTTACTAATATAT
1 TATATTTTATTTTAAGTTACTAATATAT
* *
2678 TATATTATTATTTTAAGTTATTGATATAT
1 TATATT-TTATTTTAAGTTACTAATATAT
2707 T-TATTCTTATCTTTAA
1 TATATT-TTAT-TTTAA
2723 CTTCAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 14 0.37
29 24 0.63
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (28 bp):
TATATTTTATTTTAAGTTACTAATATAT
Found at i:2767 original size:21 final size:21
Alignment explanation
Indices: 2727--2785 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
2717 CTTTAACTTC
2727 AAAATA-TTTTAACA-TAAAAT
1 AAAATATTTTTAA-ATTAAAAT
*
2747 -ATATATTTTTATAATTAAAAT
1 AAAATATTTTTA-AATTAAAAT
2768 AAAATATTTTTAAATTAA
1 AAAATATTTTTAAATTAA
2786 GTTAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 13 0.39
22 10 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATATTTTTAAATTAAAAT
Found at i:2800 original size:27 final size:24
Alignment explanation
Indices: 2747--2823 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 24
2737 AACATAAAAT
*
2747 ATATATTTTTATAATTAA-AATAAA
1 ATATA-TTTAATAATTAATAATAAA
*
2771 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATATTT-AA-TAA-TTAATAATAAA
2798 ATATATTTAATAATTAAT-ATAAA
1 ATATATTTAATAATTAATAATAAA
2821 ATA
1 ATA
2824 CTTCTTTCCC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 11 0.24
24 10 0.22
25 6 0.13
26 6 0.13
27 13 0.28
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
ATATATTTAATAATTAATAATAAA
Found at i:4786 original size:28 final size:28
Alignment explanation
Indices: 4721--4786 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
4711 AATCGTATAA
*
4721 AATCATAAA-ATAATATTTAAACCATTT
1 AATCATAAATATAATATATAAACCATTT
* * *
4748 ATAACAT-AATATTATATATAAACTATTT
1 A-ATCATAAATATAATATATAAACCATTT
4776 AATCATAAATA
1 AATCATAAATA
4787 CGAACTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (28 bp):
AATCATAAATATAATATATAAACCATTT
Found at i:5264 original size:21 final size:21
Alignment explanation
Indices: 5240--5281 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5230 TTCGTATATA
5240 TTTCAGA-ACTTTTCATTTCAT
1 TTTCAGATACTTTTC-TTTCAT
*
5261 TTTCATATACTTTTCTTTCAT
1 TTTCAGATACTTTTCTTTCAT
5282 ATTCTGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTCAGATACTTTTCTTTCAT
Found at i:5984 original size:21 final size:21
Alignment explanation
Indices: 5959--6075 Score: 61
Period size: 21 Copynumber: 5.8 Consensus size: 21
5949 TGCTATATAA
5959 ATGTCCCGAAAGACCACATAT
1 ATGTCCCGAAAGACCACATAT
* *
5980 ATGTCCTG--GGACCAC--AT
1 ATGTCCCGAAAGACCACATAT
* *
5997 ATGTTCC-AAAGGACCAAATAT
1 ATGTCCCGAAA-GACCACATAT
* * *
6018 A-GTCCAAGAAGGACCTCATAT
1 ATGTCC-CGAAAGACCACATAT
* *
6039 ATGTTCC-AAAGGATCACA-AT
1 ATGTCCCGAAA-GACCACATAT
*
6059 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAAGACCAC
6076 GTAGAACCCT
Statistics
Matches: 67, Mismatches: 19, Indels: 21
0.63 0.18 0.20
Matches are distributed among these distances:
17 7 0.10
19 11 0.16
20 18 0.27
21 26 0.39
22 5 0.07
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
ATGTCCCGAAAGACCACATAT
Found at i:6010 original size:19 final size:19
Alignment explanation
Indices: 5988--6075 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
5978 ATATGTCCTG
5988 GGACCACATATGTTCCAAA
1 GGACCACATATGTTCCAAA
*
6007 GGACCAAATATAG-TCCAAGAA
1 GGACCACATAT-GTTCC-A-AA
*
6028 GGACCTCATATATGTTCCAAA
1 GGA-C-CACATATGTTCCAAA
* * *
6049 GGATCACAATATGTCCCGAA
1 GGACCAC-ATATGTTCCAAA
6069 GGACCAC
1 GGACCAC
6076 GTAGAACCCT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
19 15 0.27
20 18 0.33
21 10 0.18
22 3 0.05
23 9 0.16
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (19 bp):
GGACCACATATGTTCCAAA
Found at i:6046 original size:42 final size:41
Alignment explanation
Indices: 5995--6073 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
5985 CTGGGACCAC
5995 ATATGTTCCAAAGGACCA-AATATAGTCCAAGAAGGACCTCAT
1 ATATGTTCCAAAGGACCACAATAT-GTCC-AGAAGGACCTCAT
* *
6037 ATATGTTCCAAAGGATCACAATATGTCCCGAAGGACC
1 ATATGTTCCAAAGGACCACAATATGTCCAGAAGGACC
6074 ACGTAGAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
41 8 0.24
42 21 0.62
43 5 0.15
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
ATATGTTCCAAAGGACCACAATATGTCCAGAAGGACCTCAT
Found at i:6676 original size:20 final size:20
Alignment explanation
Indices: 6647--6684 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6637 TTTCAAAGGG
*
6647 ATGCACCGATGCATCAATCC
1 ATGCACCGATGCACCAATCC
*
6667 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
6685 GAATAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:6787 original size:65 final size:62
Alignment explanation
Indices: 6695--6852 Score: 203
Period size: 65 Copynumber: 2.5 Consensus size: 62
6685 GAATAAATTG
* *
6695 AACATCGAATGCATTGATGCATCGATGCACATA-CCATGCATCGATACACTCAGGAT-TTAATGA
1 AACATCGAATGCATTGATGCATCGATGCACA-AGCCATGCATAGATACACTCAAGATATT--T-A
6758 A
62 A
* *
6759 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATAGATGCACTCAAGCTATTTAA
1 AACATCGAATGCA-TTGATGCATCGATGCACAAGCCATGCATAGATACACTCAAGATATTTAA
*
6822 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTGATGCATCGATGCAC
6853 CGATGCAATA
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
63 31 0.36
64 15 0.18
65 37 0.44
66 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (62 bp):
AACATCGAATGCATTGATGCATCGATGCACAAGCCATGCATAGATACACTCAAGATATTTAA
Found at i:12626 original size:21 final size:22
Alignment explanation
Indices: 12580--12632 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
12570 ACACCTAACA
* * *
12580 GTGCATCGATATATCCTTGAAT
1 GTGCATCGATATAACCATGAAG
12602 GTGCATCGATA-AACCATGAAG
1 GTGCATCGATATAACCATGAAG
*
12623 GTGCACCGAT
1 GTGCATCGAT
12633 GCACTCCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (22 bp):
GTGCATCGATATAACCATGAAG
Found at i:12649 original size:23 final size:23
Alignment explanation
Indices: 12580--12659 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
12570 ACACCTAACA
**
12580 GTGCATCGATATA-TCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
** * *
12602 GTGCATCGAT--AAACCATGAAG
1 GTGCATCGATGCACTCCTTGAAT
*
12623 GTGCACCGATGCACTCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
12646 GTGCATCGATGCAC
1 GTGCATCGATGCAC
12660 AAGGCCATCC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
22 10 0.22
23 20 0.43
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:16002 original size:20 final size:20
Alignment explanation
Indices: 15981--16107 Score: 121
Period size: 20 Copynumber: 6.3 Consensus size: 20
15971 AAATCACAAT
*
15981 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
16001 GCGATACTTACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
16021 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* *
16042 GAGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
16062 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* * *
16082 GCAATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
16102 GTGATA
1 GCGATA
16108 ATACATAATC
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.02
20 73 0.81
21 13 0.14
22 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:16017 original size:61 final size:60
Alignment explanation
Indices: 15952--16087 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 60
15942 GAATAAGTAA
** * * * *
15952 ATCGCAACGCGAATTGGGAAAATCACAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATT-ACAAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACT
* * * *
16013 ATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATACTGACT
1 ATCGCAACGCGA-ATTACAAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACT
*
16074 TTCGCAACGC-AATT
1 ATCGCAACGCGAATT
16088 CTGACTTTCG
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
59 2 0.03
60 1 0.02
61 56 0.92
62 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (60 bp):
ATCGCAACGCGAATTACAAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACT
Found at i:16655 original size:20 final size:20
Alignment explanation
Indices: 16601--16659 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
16591 GCGATTCTCT
**
16601 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
16621 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
16641 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
16660 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:16848 original size:25 final size:24
Alignment explanation
Indices: 16794--16848 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
16784 TGTTTATTAT
* *
16794 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
16818 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
16844 TGTTT
1 TGTTT
16849 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:17996 original size:18 final size:18
Alignment explanation
Indices: 17975--18019 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
17965 TCCACTTCGG
*
17975 GAGCCATCACCTCACCCA
1 GAGCTATCACCTCACCCA
17993 GAGCTATCACCTCACCCA
1 GAGCTATCACCTCACCCA
18011 GAGCTATCA
1 GAGCTATCA
18020 TCTGATCGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.42, G:0.13, T:0.16
Consensus pattern (18 bp):
GAGCTATCACCTCACCCA
Found at i:18549 original size:19 final size:20
Alignment explanation
Indices: 18506--18550 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18496 CGTAACACGA
18506 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
18526 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
18545 AAATGA
1 AAATGA
18551 AAATCGCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:18556 original size:19 final size:19
Alignment explanation
Indices: 18534--18592 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
18524 AGAAATGGCT
18534 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
18553 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
18567 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
18586 ATCGCAA
1 ATCGCAA
18593 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:18569 original size:14 final size:14
Alignment explanation
Indices: 18550--18608 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
18540 ATGCGAAATG
18550 AAAATCGCAATGAC
1 AAAATCGCAATGAC
*
18564 AAAATCGCAATGCGAAATG
1 AAAATCGCAAT--G--A-C
*
18583 AAAATCGCAACGAC
1 AAAATCGCAATGAC
18597 AAAATCGCAATG
1 AAAATCGCAATG
18609 CGATTTGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 22 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAATGAC
Found at i:18576 original size:33 final size:33
Alignment explanation
Indices: 18534--18611 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
18524 AGAAATGGCT
*
18534 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
18567 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
18600 ATCGCAATGCGA
1 ATCGCAATGCGA
18612 TTTGTGTTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:18641 original size:13 final size:13
Alignment explanation
Indices: 18623--18679 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 13
18613 TTGTGTTTCG
18623 CGTTGCGATTTTT
1 CGTTGCGATTTTT
18636 CGTTGCGATTTCATTT
1 CGTTGCGA-TT--TTT
18652 CGCATTGCGATTTTGT
1 CG--TTGCGATTTT-T
18668 CGTTGCGATTTT
1 CGTTGCGATTTT
18680 CATTTAGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 8 0.21
14 12 0.32
15 2 0.05
16 8 0.21
17 2 0.05
18 6 0.16
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.49
Consensus pattern (13 bp):
CGTTGCGATTTTT
Found at i:18690 original size:33 final size:31
Alignment explanation
Indices: 18625--18695 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 31
18615 GTGTTTCGCG
*
18625 TTGCGATTTTTCGTTGCGATTTCATTTCGCA
1 TTGCGATTTTTCGTTGCGATTTCATTTAGCA
18656 TTGCGATTTTGTCGTTGCGATTTTCATTTAGCA
1 TTGCGATTTT-TCGTTGCGA-TTTCATTTAGCA
18689 TTGCGAT
1 TTGCGAT
18696 AGCAATTTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 10 0.27
32 9 0.24
33 18 0.49
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (31 bp):
TTGCGATTTTTCGTTGCGATTTCATTTAGCA
Found at i:18714 original size:20 final size:20
Alignment explanation
Indices: 18689--18735 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
18679 TCATTTAGCA
18689 TTGCGATAG-CAATTTCCGCG
1 TTGCGATAGTC-ATTTCCGCG
*
18709 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTCCGCG
18729 TTGCGAT
1 TTGCGAT
18736 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:20621 original size:14 final size:14
Alignment explanation
Indices: 20602--20637 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20592 ATTGTTTAAT
20602 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
20616 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
20630 TGATTTGT
1 TGATTTGT
20638 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:20783 original size:14 final size:14
Alignment explanation
Indices: 20764--20817 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
20754 GAAACTGACT
*
20764 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
20778 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
20797 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
20811 ATCGCAA
1 ATCGCAA
20818 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:20801 original size:19 final size:17
Alignment explanation
Indices: 20777--20822 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
20767 GCAACGAGAG
20777 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
20796 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
20810 AATCGCAATGCGA
1 AATCGCAATGCGA
20823 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:20871 original size:20 final size:20
Alignment explanation
Indices: 20841--20917 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
20831 TCGCATTGCG
*
20841 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
20861 ATTTTTGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
**
20881 ATTTTCGCGTTATGATA-CC
1 ATTTTCGCGTTGCGATAGCC
20900 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
20918 TCAAATGAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
19 17 0.35
20 32 0.65
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:21279 original size:20 final size:20
Alignment explanation
Indices: 21249--21321 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
21239 GATTCTGTAT
*
21249 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
21269 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
21289 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
21309 TATCGCGTTGCGA
1 TATCGCGTTGCGA
21322 TTTTGTATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:21335 original size:21 final size:20
Alignment explanation
Indices: 21307--21366 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
21297 TGCGAAAGTC
*
21307 AGTATCGCGTTGCGATTTTGT
1 AGTATCGCATTGCGATTTT-T
* **
21328 ATTATCGCATTGCGATAGTT
1 AGTATCGCATTGCGATTTTT
21348 AGTATCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
21367 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
AGTATCGCATTGCGATTTTT
Found at i:21365 original size:41 final size:41
Alignment explanation
Indices: 21229--21366 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
21219 AACTTTGAAA
* * *
21229 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** *
21270 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
* * * *
21310 ATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTTAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
21351 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
21367 CCCAATTCGC
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.40
41 45 0.56
42 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:21382 original size:41 final size:41
Alignment explanation
Indices: 21229--21384 Score: 118
Period size: 41 Copynumber: 3.8 Consensus size: 41
21219 AACTTTGAAA
* ** * * * *
21229 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *** * *
21270 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* ** * * *
21310 ATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTTAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
21351 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
21385 TTACTTATTC
Statistics
Matches: 92, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
40 33 0.36
41 57 0.62
42 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Found at i:27078 original size:21 final size:21
Alignment explanation
Indices: 27054--27144 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
27044 TGACTCGTAT
27054 GACCACATATATGTTCCAAAG
1 GACCACATATATGTTCCAAAG
*
27075 GACCAAATATATG-TCCAAGAAG
1 GACCACATATATGTTCC-A-AAG
**
27097 GACTTCATATATGTTCCAAAG
1 GACCACATATATGTTCCAAAG
* * *
27118 GATCACATATATGTCCCGAAG
1 GACCACATATATGTTCCAAAG
27139 GACCAC
1 GACCAC
27145 GTAGAACCCT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 3 0.05
21 37 0.65
22 14 0.25
23 3 0.05
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (21 bp):
GACCACATATATGTTCCAAAG
Found at i:27113 original size:43 final size:42
Alignment explanation
Indices: 27059--27141 Score: 130
Period size: 43 Copynumber: 2.0 Consensus size: 42
27049 CGTATGACCA
27059 CATATATGTTCCAAAGGACCAAATATATGTCCAAGAAGGACTT
1 CATATATGTTCCAAAGGACCAAATATATGTCC-AGAAGGACTT
* * *
27102 CATATATGTTCCAAAGGATCACATATATGTCCCGAAGGAC
1 CATATATGTTCCAAAGGACCAAATATATGTCCAGAAGGAC
27142 CACGTAGAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 7 0.19
43 30 0.81
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (42 bp):
CATATATGTTCCAAAGGACCAAATATATGTCCAGAAGGACTT
Found at i:32395 original size:31 final size:31
Alignment explanation
Indices: 32342--32416 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
32332 CAACGAAGTG
*** *
32342 ATCATTTTGTTACAATTTGATAATATTAGTA
1 ATCATTTTGTTACAAACCGATAACATTAGTA
*
32373 ATCATTTTGTTACAAACCGATAACATTAGTG
1 ATCATTTTGTTACAAACCGATAACATTAGTA
* *
32404 ATCAATCTGTTAC
1 ATCATTTTGTTAC
32417 TTTTGAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (31 bp):
ATCATTTTGTTACAAACCGATAACATTAGTA
Found at i:34017 original size:2 final size:2
Alignment explanation
Indices: 34010--34129 Score: 226
Period size: 2 Copynumber: 61.0 Consensus size: 2
34000 ACACATTGTG
34010 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
34052 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34092 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
34130 TGTGTTTGAT
Statistics
Matches: 116, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
1 2 0.02
2 114 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34667 original size:2 final size:2
Alignment explanation
Indices: 34660--34701 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
34650 TTAAGAGCGG
34660 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
34702 TAATAACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36287 original size:14 final size:15
Alignment explanation
Indices: 36255--36294 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
36245 AATATTTTGA
*
36255 TAAAAATTAAAATAT
1 TAAAAATTAAAATAG
36270 TAAAAATTAAAAT-G
1 TAAAAATTAAAATAG
*
36284 TAAAAAATAAA
1 TAAAAATTAAA
36295 TGAAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
TAAAAATTAAAATAG
Found at i:36531 original size:216 final size:218
Alignment explanation
Indices: 36131--36564 Score: 574
Period size: 216 Copynumber: 2.0 Consensus size: 218
36121 TTTACATGTC
* * * * *
36131 ATGTCATCACTTTTGAGTGACGTGACATATATCATATTATTAATTAAATACATGTGATAATATTA
1 ATGTCATCACTTTTGAGTGACGAGACATATATCATATAATTAATTAAACACATATGAAAATATTA
* * *
36196 CGTCAGTAATATGTTGATCATTAATTAATTAATAATAAATTAAAAAAATAATATTTTGATAAAAA
66 CATCAGTAACATGTTGATCATTAATTAATCAATAATAAATTAAAAAAATAATATTTTGATAAAAA
*
36261 TTAAAATATTAAAAATTAAAATGTAAAAAATAAATGAAAATGAAAATAATTATTTATATAAATCT
131 TTAAAATATTAAAAATTAAAATGTAAAAAATAAATGAAAATAAAAATAATTATTTATATAAATCT
*
36326 TATCATTATGTCCAAAAT-AATT
196 TATCATTATGACCAAAATCAATT
* *
36348 ATGTCATCACTTTTTGAGTGAC-AGACATGTATCATATAATTAATTAAACATATAT-AAAATATT
1 ATGTCATCAC-TTTTGAGTGACGAGACATATATCATATAATTAATTAAACACATATGAAAATATT
* * *** **
36411 ATATCAGTAACATGTTGATCGTTAATTAATCAATAATTTTTTTTAAAAATAATATTTTGATTAAA
65 ACATCAGTAACATGTTGATCATTAATTAATCAATAATAAATTAAAAAAATAATATTTTGA-TAAA
* * * *
36476 AATTTAAAATATTAAAAGTTAAAATGTAAAAAGTAAAT-AAAA-AAAAACT-ATTATTTATGTAG
129 AA-TTAAAATATTAAAAATTAAAATGTAAAAAATAAATGAAAATAAAAA-TAATTATTTATATAA
*
36538 ATCTTATCATTCTGACCAAAATCAATT
192 ATCTTATCATTATGACCAAAATCAATT
36565 GAGTTGAGTC
Statistics
Matches: 188, Mismatches: 24, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
216 92 0.49
217 52 0.28
218 44 0.23
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (218 bp):
ATGTCATCACTTTTGAGTGACGAGACATATATCATATAATTAATTAAACACATATGAAAATATTA
CATCAGTAACATGTTGATCATTAATTAATCAATAATAAATTAAAAAAATAATATTTTGATAAAAA
TTAAAATATTAAAAATTAAAATGTAAAAAATAAATGAAAATAAAAATAATTATTTATATAAATCT
TATCATTATGACCAAAATCAATT
Found at i:42768 original size:65 final size:65
Alignment explanation
Indices: 42697--42824 Score: 177
Period size: 65 Copynumber: 2.0 Consensus size: 65
42687 CATTAATTGC
** *
42697 ATTCGATGTTTCAAAAAAGCCTGGAGTGCATCGATGCATG-ATATGTTCATCGGTACACAAAATC
1 ATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGCAT-TGTGCATCGGTACACAAAATC
42761 A
65 A
* ** *
42762 ATTCGATGTTTCAAAACATTCAAGAGTGCATCGATGCATGCCTTGTGCATCGGTACACAAAAT
1 ATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGCATTGTGCATCGGTACACAAAAT
42825 GCACTCGGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 54 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (65 bp):
ATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGCATTGTGCATCGGTACACAAAATCA
Found at i:52755 original size:31 final size:32
Alignment explanation
Indices: 52701--52790 Score: 112
Period size: 31 Copynumber: 2.8 Consensus size: 32
52691 AACAATAAAA
*
52701 AAAATAAAAAGTTAGTATGTTAGTAAGAACAA-
1 AAAAT-AAAAGTTAGAATGTTAGTAAGAACAAT
**
52733 ATAAATAAAA-TTAGAATGTTAGTTCGAACAAT
1 A-AAATAAAAGTTAGAATGTTAGTAAGAACAAT
*
52765 AAAATAAAAGTTAGAATGCTAGTAAG
1 AAAATAAAAGTTAGAATGTTAGTAAG
52791 TTAGTGATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
31 26 0.53
32 19 0.39
33 4 0.08
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (32 bp):
AAAATAAAAGTTAGAATGTTAGTAAGAACAAT
Found at i:57235 original size:15 final size:15
Alignment explanation
Indices: 57215--57245 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57205 ACATTTATGT
57215 TTCAGTTCTATGAAA
1 TTCAGTTCTATGAAA
57230 TTCAGTTCTATGAAA
1 TTCAGTTCTATGAAA
57245 T
1 T
57246 CTTCCGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TTCAGTTCTATGAAA
Done.