Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005139.1 Hibiscus syriacus cultivar Beakdansim tig00011575_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: 80266
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:746 original size:17 final size:17
Alignment explanation
Indices: 724--781 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
714 CTTGGCTTGC
724 TTTCTTTT-TGAATTCTT
1 TTTCTTTTCTG-ATTCTT
*
741 TTTCTTTTCT-TTTCTT
1 TTTCTTTTCTGATTCTT
757 TCTTCTTTTCTGATT-TT
1 T-TTCTTTTCTGATTCTT
*
774 TCTCTTTT
1 TTTCTTTT
782 GAATTTCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 12 0.34
17 20 0.57
18 3 0.09
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTCTTTTCTGATTCTT
Found at i:1480 original size:19 final size:20
Alignment explanation
Indices: 1439--1489 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1429 GAAACCCCTT
*
1439 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1459 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1478 TGAAGATACATG
1 TGAAAATACATG
1490 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4874 original size:5 final size:5
Alignment explanation
Indices: 4843--4867 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4833 TCTTTTTGAA
4843 TTCTT TTCTT TTCTT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT
4868 CTTTTCTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTCTT
Found at i:5598 original size:19 final size:20
Alignment explanation
Indices: 5557--5607 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5547 GAAACCCCTT
*
5557 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5577 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5596 TGAAGATACATG
1 TGAAAATACATG
5608 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:9739 original size:19 final size:20
Alignment explanation
Indices: 9698--9748 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
9688 GAAACCCCTT
*
9698 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
9718 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
9737 TGAAGATACATG
1 TGAAAATACATG
9749 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:14810 original size:12 final size:13
Alignment explanation
Indices: 14779--14811 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
14769 TTAGCCAAAA
14779 TTGAAAAGGTATG
1 TTGAAAAGGTATG
14792 TTGAAAAGGTATG
1 TTGAAAAGGTATG
14805 -TGAAAAG
1 TTGAAAAG
14812 TGTTTAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TTGAAAAGGTATG
Found at i:16852 original size:15 final size:15
Alignment explanation
Indices: 16841--16869 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16831 ACTCAAAAAG
16841 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
16856 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
16870 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:23971 original size:14 final size:14
Alignment explanation
Indices: 23952--23988 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
23942 TAAGATACTA
23952 TTTCCATCACCATC
1 TTTCCATCACCATC
23966 TTTCCATCACCATC
1 TTTCCATCACCATC
*
23980 ATT-CATCAC
1 TTTCCATCAC
23989 TTTCACGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:25906 original size:22 final size:21
Alignment explanation
Indices: 25880--25923 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
25870 GGCTGCAGAA
*
25880 TTGATGGTCTTGATGGATGAAG
1 TTGATGATCTTGAT-GATGAAG
*
25902 TTGATGATGTTGATGATGAAG
1 TTGATGATCTTGATGATGAAG
25923 T
1 T
25924 GGAGATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.25, C:0.02, G:0.34, T:0.39
Consensus pattern (21 bp):
TTGATGATCTTGATGATGAAG
Found at i:30945 original size:23 final size:23
Alignment explanation
Indices: 30900--30945 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
30890 TTATACCTAT
*
30900 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
30923 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
30946 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:32734 original size:33 final size:33
Alignment explanation
Indices: 32655--32758 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
32645 ATACAATCTG
* *
32655 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
32691 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
32724 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
32757 TC
1 TC
32759 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:34571 original size:36 final size:36
Alignment explanation
Indices: 34519--34666 Score: 228
Period size: 36 Copynumber: 4.2 Consensus size: 36
34509 GATACTATTT
* *
34519 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
34555 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
34591 TCATCACCATTGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* *
34627 T-ATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
34661 ACATCA
1 TCATCA
34667 TCCTTCCATT
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
34 12 0.12
35 22 0.21
36 70 0.67
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:34574 original size:13 final size:11
Alignment explanation
Indices: 34519--34652 Score: 69
Period size: 13 Copynumber: 11.3 Consensus size: 11
34509 GATACTATTT
34519 TCATCACCATAA
1 TCATCACCAT-A
*
34531 TCCATCTCCATTA
1 T-CATCACCA-TA
*
34544 TCA-CGCCTATA
1 TCATCACC-ATA
34555 TCATCACCATA
1 TCATCACCATA
34566 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
34580 TCA-CGCCTATA
1 TCATCACC-ATA
*
34591 TCATCACCATTG
1 TCATCACCA-TA
34603 TCCATCACCATTA
1 T-CATCACCA-TA
*
34616 TCA-CGCCTATA
1 TCATCACC-ATA
34627 T-ATCACCATA
1 TCATCACCATA
34637 TTCCATCACCATA
1 -T-CATCACCATA
34650 TCA
1 TCA
34653 CGCCAATAAC
Statistics
Matches: 97, Mismatches: 9, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
10 4 0.04
11 32 0.33
12 20 0.21
13 38 0.39
14 3 0.03
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:35052 original size:76 final size:76
Alignment explanation
Indices: 34926--35077 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
34916 GTAGCATTTG
34926 GTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTGGTTA
1 GTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTGGTTA
34991 GCCTCACATCA
66 GCCTCACATCA
35002 GTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTGGTTA
1 GTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTGGTTA
35067 GCCTCACATCA
66 GCCTCACATCA
35078 CGTACCTTTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (76 bp):
GTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTGGTTA
GCCTCACATCA
Found at i:36291 original size:8 final size:8
Alignment explanation
Indices: 36280--36304 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
36270 TAGAAAAATC
36280 AGAAAAGA
1 AGAAAAGA
36288 AGAAAAGA
1 AGAAAAGA
36296 AGAAAAGA
1 AGAAAAGA
36304 A
1 A
36305 AAGAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:39243 original size:23 final size:23
Alignment explanation
Indices: 39198--39243 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39188 TTATACCTAT
*
39198 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
39221 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
39244 TTATACCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:44081 original size:24 final size:21
Alignment explanation
Indices: 44047--44089 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
44037 TGCACAAGAT
*
44047 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
44069 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
44090 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:48584 original size:13 final size:13
Alignment explanation
Indices: 48566--48591 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48556 GGAAGTAATG
48566 CCACAAGGACCAA
1 CCACAAGGACCAA
48579 CCACAAGGACCAA
1 CCACAAGGACCAA
48592 TAACTCGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.38, G:0.15, T:0.00
Consensus pattern (13 bp):
CCACAAGGACCAA
Found at i:49929 original size:33 final size:33
Alignment explanation
Indices: 49850--49929 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 33
49840 ATACAATCTG
* *
49850 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCA-TATCACGCCAATAGCATCACC--AT
49886 TCCATCACCATATCACGCCAATAGCATCATCC-T
1 TCCATCACCATATCACGCCAATAGCATCA-CCAT
*
49919 TCCATTACCAT
1 TCCATCACCAT
49930 TTCATCACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 11 0.28
35 17 0.43
36 12 0.30
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.29
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAGCATCACCAT
Found at i:55603 original size:33 final size:33
Alignment explanation
Indices: 55559--55627 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
55549 CATCACCATA
*
55559 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
55592 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
55625 TTC
1 TTC
55628 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:56495 original size:36 final size:36
Alignment explanation
Indices: 56422--56597 Score: 300
Period size: 36 Copynumber: 4.9 Consensus size: 36
56412 ATTTATAAGT
* *
56422 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* **
56457 TGGTGATGATATAGGCATGATAATGGTGATGGGTTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
56493 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
56529 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
56565 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
56598 TAGATTGTAT
Statistics
Matches: 133, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 19 0.14
36 114 0.86
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:56520 original size:23 final size:23
Alignment explanation
Indices: 56492--56595 Score: 74
Period size: 23 Copynumber: 4.4 Consensus size: 23
56482 GTGATGGGTT
56492 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
*
56515 ATGGTGATGGACTAT-GGTGATGAT-
1 ATGGTGAT-GA-TATAGGCG-TGATA
* *
56539 ATAGGCG-TGATA-ATG-GTGATGGA
1 AT-GGTGATGATATAGGCGTGAT--A
56562 CTATGGTGATGATATAGGCGTGATA
1 --ATGGTGATGATATAGGCGTGATA
56587 ATGGTGATG
1 ATGGTGATG
56596 GATAGATTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 26
0.67 0.05 0.28
Matches are distributed among these distances:
20 4 0.06
21 1 0.02
22 3 0.05
23 19 0.30
24 11 0.17
25 18 0.29
26 2 0.03
27 5 0.08
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:56533 original size:13 final size:12
Alignment explanation
Indices: 56440--56599 Score: 83
Period size: 11 Copynumber: 13.3 Consensus size: 12
56430 ATATAGGCGT
56440 GATATGGTGATG
1 GATATGGTGATG
56452 GAATATGGTGAT-
1 G-ATATGGTGATG
*
56464 GATATAGG-CAT-
1 GATAT-GGTGATG
56475 GATAATGGTGATGG
1 GAT-ATGGTGAT-G
*
56489 GTTATGGTGAT-
1 GATATGGTGATG
*
56500 GATATAGGCG-T-
1 GATAT-GGTGATG
56511 GATAATGGTGATG
1 GAT-ATGGTGATG
56524 GACTATGGTGAT-
1 GA-TATGGTGATG
*
56536 GATATAGGCG-T-
1 GATAT-GGTGATG
56547 GATAATGGTGATG
1 GAT-ATGGTGATG
56560 GACTATGGTGAT-
1 GA-TATGGTGATG
*
56572 GATATAGGCG-T-
1 GATAT-GGTGATG
56583 GATAATGGTGATG
1 GAT-ATGGTGATG
56596 GATA
1 GATA
56600 GATTGTATCT
Statistics
Matches: 118, Mismatches: 10, Indels: 40
0.70 0.06 0.24
Matches are distributed among these distances:
11 42 0.36
12 31 0.26
13 41 0.35
14 4 0.03
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:61393 original size:15 final size:15
Alignment explanation
Indices: 61382--61410 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61372 ACTCAAAAAG
61382 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
61397 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
61411 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:62933 original size:24 final size:25
Alignment explanation
Indices: 62906--62953 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
62896 GTCTATTTTT
* * *
62906 GATGAGGAACCTGAA-ACAATGCAA
1 GATGAAGAAACTGAAGAAAATGCAA
62930 GATGAAGAAACTGAAGAAAATGCA
1 GATGAAGAAACTGAAGAAAATGCA
62954 GATCATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (25 bp):
GATGAAGAAACTGAAGAAAATGCAA
Found at i:69886 original size:35 final size:36
Alignment explanation
Indices: 69838--69906 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
69828 ATTTATAAGT
*
69838 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATAATATAGGCGTGAAAATGGTAATGGAATA
** *
69873 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAA
1 TGGTGATAATATAGGCGTGAAAATGGTAATGGAA
69907 GGTGGTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 17 0.59
36 12 0.41
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGAAAATGGTAATGGAATA
Found at i:72154 original size:21 final size:22
Alignment explanation
Indices: 72116--72156 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
72106 TGAATAATAA
72116 AGAAAGGAATAAAGATGGAATT
1 AGAAAGGAATAAAGATGGAATT
72138 AGAAA-GAATAGAA-ATGGAA
1 AGAAAGGAATA-AAGATGGAA
72157 AGGAATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.15
Consensus pattern (22 bp):
AGAAAGGAATAAAGATGGAATT
Found at i:72349 original size:35 final size:36
Alignment explanation
Indices: 72301--72384 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
72291 ATTTATAAGT
* * *
72301 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
* * *
72336 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
72372 TGGTGATGA-ATAG
1 TGGTGATGATATAG
72385 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
Found at i:76265 original size:24 final size:24
Alignment explanation
Indices: 76233--76279 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
76223 AATGTAGGAG
76233 TCTTTTTCTT-TT-CTCTTTTGTTT
1 TCTTTTTCTTGTTGCT-TTTTGTTT
76256 TCTTCTTTCTTGTTGCTTTTTGTT
1 TCTT-TTTCTTGTTGCTTTTTGTT
76280 GTAGCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (24 bp):
TCTTTTTCTTGTTGCTTTTTGTTT
Found at i:76703 original size:35 final size:36
Alignment explanation
Indices: 76655--76738 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
76645 ATTTATAAGT
* * *
76655 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
* * *
76690 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
76726 TGGTGATGA-ATAG
1 TGGTGATGATATAG
76739 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
Found at i:78734 original size:14 final size:14
Alignment explanation
Indices: 78715--78742 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
78705 TAAGATACTA
78715 TTTCCATCACCATC
1 TTTCCATCACCATC
78729 TTTCCATCACCATC
1 TTTCCATCACCATC
78743 ATTCATCTCT
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:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Done.