Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007503.1 Hibiscus syriacus cultivar Beakdansim tig00020806_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: 69742
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2963 original size:15 final size:15
Alignment explanation
Indices: 2928--2956 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2918 GTGCTTCAAC
2928 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
2942 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
2957 CTTTTTGAGT
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:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:7488 original size:19 final size:20
Alignment explanation
Indices: 7464--7514 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
7454 CGGCCAAGAG
* *
7464 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
7483 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
7503 CATGTATTTTCA
1 CATGTATTTTCA
7515 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:7900 original size:22 final size:21
Alignment explanation
Indices: 7867--7910 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
7857 CACAATCTCC
* *
7867 ACTTTATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
7888 ACTTCATCTATCAAGACCATCA
1 ACTTCATC-ATCAACACCATCA
7910 A
1 A
7911 TTCCGTAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.39, C:0.30, G:0.02, T:0.30
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:8463 original size:15 final size:15
Alignment explanation
Indices: 8435--8471 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
8425 TCCATTTCAA
*
8435 TTCTTATCATTTCCT
1 TTCTTCTCATTTCCT
8450 TTCTTCTCATTTCCT
1 TTCTTCTCATTTCCT
8465 TTCTTCT
1 TTCTTCT
8472 TCCATTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.30, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCTTCTCATTTCCT
Found at i:8513 original size:15 final size:14
Alignment explanation
Indices: 8435--8513 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 14
8425 TCCATTTCAA
8435 TTCTTATCATTTCCT
1 TTCTTATCATTT-CT
*
8450 TTCTTCTCATTTCCT
1 TTCTTATCATTT-CT
*
8465 TTCTTCTTCCATTTCT
1 TTCTT-AT-CATTTCT
*
8481 TAT-TTAT-ATTTCC
1 T-TCTTATCATTTCT
*
8494 ATCTTAATCATTTCT
1 TTCTT-ATCATTTCT
8509 TTCTT
1 TTCTT
8514 TAATTTTTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
12 1 0.02
13 7 0.14
14 2 0.04
15 29 0.57
16 6 0.12
17 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (14 bp):
TTCTTATCATTTCT
Found at i:8698 original size:6 final size:6
Alignment explanation
Indices: 8687--8721 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
8677 CAAAAGCAAC
*
8687 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAA
8722 GACTCCTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:8708 original size:13 final size:12
Alignment explanation
Indices: 8684--8721 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
8674 CAACAAAAGC
8684 AACAAAAAGAAA
1 AACAAAAAGAAA
*
8696 AAGAAAGAAGAAA
1 AACAAA-AAGAAA
8709 AACAAAAAGAAA
1 AACAAAAAGAAA
8721 A
1 A
8722 GACTCCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:10592 original size:15 final size:15
Alignment explanation
Indices: 10581--10609 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10571 ACTCAAAAAG
10581 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
10596 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
10610 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:16414 original size:16 final size:16
Alignment explanation
Indices: 16380--16428 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
16370 GTAAGTTATC
* * *
16380 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
16396 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
16412 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
16429 CTTTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:29499 original size:19 final size:19
Alignment explanation
Indices: 29472--29510 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29462 CCTTGCTGCC
*
29472 ATGTATGAAGGCATGAGCT
1 ATGTATGAAGGCATAAGCT
*
29491 ATGTTTGAAGGCATAAGCT
1 ATGTATGAAGGCATAAGCT
29510 A
1 A
29511 ATTATATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (19 bp):
ATGTATGAAGGCATAAGCT
Found at i:31361 original size:21 final size:22
Alignment explanation
Indices: 31301--31369 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 22
31291 ATCTCTATCC
31301 CTTCTTTATT-TCATTTCATTT
1 CTTCTTTATTATCATTTCATTT
31322 CTTATCTTTATTATTTCATTT-A-TT
1 C-T-TCTTTATTA--TCATTTCATTT
31346 CTTCTTTATTAATCATCTTCATTT
1 CTTCTTTATT-ATCAT-TTCATTT
31370 TCTTATCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
21 5 0.13
22 11 0.28
23 11 0.28
24 5 0.13
25 1 0.03
26 6 0.15
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (22 bp):
CTTCTTTATTATCATTTCATTT
Found at i:31378 original size:27 final size:24
Alignment explanation
Indices: 31303--31379 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 24
31293 CTCTATCCCT
31303 TCTTTATT-TCATTTCATTTCTTA
1 TCTTTATTATCATTTCATTTCTTA
31326 TCTTTATTATTTCATTT-A-TTC-T-
1 TCTTTATTA--TCATTTCATTTCTTA
31348 TCTTTATTAATCATCTTCATTTTCTTA
1 TCTTTATT-ATCAT-TTCA-TTTCTTA
31375 TCTTT
1 TCTTT
31380 GTTGCAGTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
21 4 0.09
22 10 0.23
23 11 0.25
24 3 0.07
25 4 0.09
26 7 0.16
27 5 0.11
ACGTcount: A:0.18, C:0.17, G:0.00, T:0.65
Consensus pattern (24 bp):
TCTTTATTATCATTTCATTTCTTA
Found at i:31963 original size:24 final size:21
Alignment explanation
Indices: 31929--31971 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
31919 TGCACAAGAT
*
31929 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
31951 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
31972 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:33541 original size:13 final size:11
Alignment explanation
Indices: 33500--33584 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
33490 ACAATCTATC
33500 CATCACCATTAT
1 CATCACCA-TAT
*
33512 CA-CGCCTATAT
1 CATCACC-ATAT
33523 CATCACCATAGT
1 CATCACCATA-T
33535 CCATCACCATTAT
1 -CATCACCA-TAT
*
33548 CA-CGCCTATAT
1 CATCACC-ATAT
33559 CATCACCATATT
1 CATCACCATA-T
33571 CCATCACCATAT
1 -CATCACCATAT
33583 CA
1 CA
33585 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:33545 original size:36 final size:36
Alignment explanation
Indices: 33498--33598 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
33488 ATACAATCTA
33498 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
33534 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
33570 TCCATCACCA-TATCACGCCAATAACATCA
1 TCCATCACCATTATCACGCCTATATCATCA
33599 TCCTTCCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 17 0.27
36 45 0.73
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.27
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:33613 original size:33 final size:34
Alignment explanation
Indices: 33498--33614 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 34
33488 ATACAATCTA
* *
33498 TCCATCACCATTATCACGCCTATATCATCACCAT
1 TCCATCACCATTATCACGCCAATAACATCACCAT
* *
33532 AGTCCATCACCATTATCACGCCTATATCATCACCATAT
1 --TCCATCACCATTATCACGCCAATAACATCACC--AT
33570 TCCATCACCA-TATCACGCCAATAACATCATCC-T
1 TCCATCACCATTATCACGCCAATAACATCA-CCAT
*
33603 TCCATTACCATT
1 TCCATCACCATT
33615 TCATCACCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 10 0.14
34 1 0.01
35 17 0.23
36 44 0.59
38 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCACCAT
Found at i:33632 original size:33 final size:33
Alignment explanation
Indices: 33498--33637 Score: 88
Period size: 36 Copynumber: 4.1 Consensus size: 33
33488 ATACAATCTA
* * *
33498 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACACCAATAACATCATCC-T
* * *
33532 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACACCAATAACATCATCC---T
*
33570 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACACCAATAACATCATCCT
* * *
33603 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CACCAATAACATCATCCT
33636 TC
1 TC
33638 ATTCATCAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.07
35 17 0.18
36 44 0.47
38 2 0.02
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACACCAATAACATCATCCT
Found at i:34017 original size:24 final size:24
Alignment explanation
Indices: 33977--34023 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
33967 AAAGTTCTAC
33977 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
34002 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
34024 CTCCTACAAC
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:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:37948 original size:13 final size:11
Alignment explanation
Indices: 37907--37991 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
37897 ACAATCTATC
37907 CATCACCATTAT
1 CATCACCA-TAT
*
37919 CA-CGCCTATAT
1 CATCACC-ATAT
37930 CATCACCATAGT
1 CATCACCATA-T
37942 CCATCACCATTAT
1 -CATCACCA-TAT
*
37955 CA-CGCCTATAT
1 CATCACC-ATAT
37966 CATCACCATATT
1 CATCACCATA-T
37978 CCATCACCATAT
1 -CATCACCATAT
37990 CA
1 CA
37992 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:37952 original size:36 final size:36
Alignment explanation
Indices: 37905--38005 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
37895 ATACAATCTA
37905 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
37941 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
37977 TCCATCACCA-TATCACGCCAATAACATCA
1 TCCATCACCATTATCACGCCTATATCATCA
38006 TCCTTCCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 17 0.27
36 45 0.73
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.27
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:38020 original size:33 final size:34
Alignment explanation
Indices: 37905--38021 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 34
37895 ATACAATCTA
* *
37905 TCCATCACCATTATCACGCCTATATCATCACCAT
1 TCCATCACCATTATCACGCCAATAACATCACCAT
* *
37939 AGTCCATCACCATTATCACGCCTATATCATCACCATAT
1 --TCCATCACCATTATCACGCCAATAACATCACC--AT
37977 TCCATCACCA-TATCACGCCAATAACATCATCC-T
1 TCCATCACCATTATCACGCCAATAACATCA-CCAT
*
38010 TCCATTACCATT
1 TCCATCACCATT
38022 TCATCACCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 10 0.14
34 1 0.01
35 17 0.23
36 44 0.59
38 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCACCAT
Found at i:38039 original size:33 final size:33
Alignment explanation
Indices: 37905--38044 Score: 88
Period size: 36 Copynumber: 4.1 Consensus size: 33
37895 ATACAATCTA
* * *
37905 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACACCAATAACATCATCC-T
* * *
37939 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACACCAATAACATCATCC---T
*
37977 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACACCAATAACATCATCCT
* * *
38010 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CACCAATAACATCATCCT
38043 TC
1 TC
38045 ATTCATCAAC
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.07
35 17 0.18
36 44 0.47
38 2 0.02
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACACCAATAACATCATCCT
Found at i:40133 original size:1 final size:1
Alignment explanation
Indices: 40129--40191 Score: 72
Period size: 1 Copynumber: 63.0 Consensus size: 1
40119 AAATTTTGGC
* * * * * *
40129 TTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40192 AAAAAAATAG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:40143 original size:11 final size:11
Alignment explanation
Indices: 40129--40191 Score: 85
Period size: 11 Copynumber: 5.7 Consensus size: 11
40119 AAATTTTGGC
40129 TTTTTTTGTTT-
1 TTTTTTT-TTTG
40140 TTTTTTGTTTTG
1 TTTTTT-TTTTG
40152 TTTTTTTTTTG
1 TTTTTTTTTTG
*
40163 TTTTTTTTGT-
1 TTTTTTTTTTG
40173 TTTTTTTTTTG
1 TTTTTTTTTTG
40184 TTTTTTTT
1 TTTTTTTT
40192 AAAAAAATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
10 9 0.19
11 31 0.66
12 7 0.15
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:40150 original size:25 final size:23
Alignment explanation
Indices: 40129--40191 Score: 92
Period size: 25 Copynumber: 2.7 Consensus size: 23
40119 AAATTTTGGC
40129 TTTTTTTGTTTTTTTTTGTTTTG
1 TTTTTTTGTTTTTTTTTGTTTTG
*
40152 TTTTTTTTTTGTTTTTTTTGTTTT-
1 -TTTTTTTGT-TTTTTTTTGTTTTG
40176 TTTTTTTGTTTTTTTT
1 TTTTTTTGTTTTTTTT
40192 AAAAAAATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 13 0.36
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (23 bp):
TTTTTTTGTTTTTTTTTGTTTTG
Found at i:40155 original size:21 final size:19
Alignment explanation
Indices: 40131--40190 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 19
40121 ATTTTGGCTT
40131 TTTTTGTTTTTTTTTGTTTTG
1 TTTTT-TTTTTTTTT-TTTTG
40152 TTTTTTTTTTGTTTTTTTTG
1 TTTTTTTTTT-TTTTTTTTG
40172 TTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTT-TTTTTTT
40191 TAAAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.03
20 27 0.73
21 9 0.24
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTTTG
Found at i:45415 original size:19 final size:21
Alignment explanation
Indices: 45376--45416 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
45366 GGATAATAAT
45376 ATAAGTAATGAAAAAGAAATA
1 ATAAGTAATGAAAAAGAAATA
*
45397 ATAAG-AATG-AAATGAAATA
1 ATAAGTAATGAAAAAGAAATA
45416 A
1 A
45417 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (21 bp):
ATAAGTAATGAAAAAGAAATA
Found at i:51179 original size:21 final size:19
Alignment explanation
Indices: 51155--51208 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
51145 ATTCTTTTTC
51155 TTTTCTTTTCTTCTTT-TCT
1 TTTTCTTTTCTT-TTTGTCT
*
51174 GATTTTCTCTTCTTTTTGTCT
1 --TTTTCTTTTCTTTTTGTCT
51195 TTTTC-TTTCTTTTT
1 TTTTCTTTTCTTTTT
51209 ACACTCCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 8 0.27
19 5 0.17
20 3 0.10
21 14 0.47
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTGTCT
Found at i:51197 original size:18 final size:16
Alignment explanation
Indices: 51160--51208 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
51150 TTTTCTTTTC
51160 TTTTCTTCTTTTCTGAT
1 TTTTCTTCTTTT-TGAT
*
51177 TTTCTCTTCTTTTTGTCT
1 TTT-TCTTCTTTTTG-AT
51195 TTTTCTTTCTTTTT
1 TTTTC-TTCTTTTT
51209 ACACTCCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTCTTCTTTTTGAT
Found at i:51932 original size:19 final size:20
Alignment explanation
Indices: 51894--51936 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
51884 GAAACCCCTT
*
51894 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
51914 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
51933 TGAA
1 TGAA
51937 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:53207 original size:23 final size:23
Alignment explanation
Indices: 53181--53232 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
53171 TAGGGAGTTA
53181 TAGCTTGATGAACTCAAGCTAGT
1 TAGCTTGATGAACTCAAGCTAGT
53204 TAGCTTGATGAACTCAAGCTAGT
1 TAGCTTGATGAACTCAAGCTAGT
53227 TAGCTT
1 TAGCTT
53233 TGGTCTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (23 bp):
TAGCTTGATGAACTCAAGCTAGT
Found at i:65938 original size:21 final size:22
Alignment explanation
Indices: 65878--65938 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
65868 ATTTATATCC
65878 CTTCTTTATT-TCATTTCATTT
1 CTTCTTTATTATCATTTCATTT
65899 CTTATCTTTATTATTTCATTT-A-TT
1 C-T-TCTTTATTA--TCATTTCATTT
65923 CTTCTTTATTAATCAT
1 CTTCTTTATT-ATCAT
65939 CTTCCTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
21 5 0.15
22 9 0.26
23 10 0.29
24 3 0.09
25 1 0.03
26 6 0.18
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (22 bp):
CTTCTTTATTATCATTTCATTT
Found at i:68891 original size:16 final size:16
Alignment explanation
Indices: 68870--68901 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
68860 TAGTTAGCTC
68870 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
68886 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
68902 TGGTAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Done.