Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002926.1 Hibiscus syriacus cultivar Beakdansim tig00006047_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: 54673
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:7229 original size:20 final size:20
Alignment explanation
Indices: 7204--7333 Score: 111
Period size: 20 Copynumber: 6.4 Consensus size: 20
7194 GGAAAATCAT
7204 AATGCGATACTGACTATCGC
1 AATGCGATACTGACTATCGC
*
7224 AATGCGATACTTACTATCGC
1 AATGCGATACTGACTATCGC
* *
7244 AATGCGATAAT-ACAAAATCGC
1 AATGCGATACTGAC--TATCGC
* * *
7265 AACGAGATACTGACTTTCGC
1 AATGCGATACTGACTATCGC
* * *
7285 AACGCGATTCTGACTTTCGC
1 AATGCGATACTGACTATCGC
* *
7305 AACGCGATAAT-ACATAATCGC
1 AATGCGATACTGAC-T-ATCGC
7326 AATGCGAT
1 AATGCGAT
7334 TTTCAAAGCG
Statistics
Matches: 91, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 61 0.67
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
AATGCGATACTGACTATCGC
Found at i:7261 original size:61 final size:61
Alignment explanation
Indices: 7204--7333 Score: 179
Period size: 61 Copynumber: 2.1 Consensus size: 61
7194 GGAAAATCAT
* * *
7204 AATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAAATCGC
1 AATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGC
* * * * * *
7265 AACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATAATCGC
1 AATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGC
7326 AATGCGAT
1 AATGCGAT
7334 TTTCAAAGCG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGC
Found at i:7855 original size:20 final size:20
Alignment explanation
Indices: 7801--7859 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
7791 GCGATTCTCT
**
7801 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
7821 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
7841 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
7860 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:8047 original size:25 final size:24
Alignment explanation
Indices: 7993--8047 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
7983 TTATTTTTAT
* *
7993 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
8017 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
8043 TGTTT
1 TGTTT
8048 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:9192 original size:17 final size:18
Alignment explanation
Indices: 9155--9198 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
9145 TCCACTTTGG
*
9155 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCGACCA
*
9173 GAGCTATCACCTC-ACCA
1 GAGCCATCACCTCGACCA
9190 GAGCCATCA
1 GAGCCATCA
9199 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.27, C:0.43, G:0.16, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCGACCA
Found at i:9699 original size:20 final size:20
Alignment explanation
Indices: 9674--9719 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
9664 TAGTTTACTT
9674 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
9694 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
9714 TCGCAA
1 TCGCAA
9720 TGCGAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:9734 original size:18 final size:18
Alignment explanation
Indices: 9713--9793 Score: 91
Period size: 18 Copynumber: 4.7 Consensus size: 18
9703 GGAAATGGCT
9713 ATCGCAATGCGAATGAAA
1 ATCGCAATGCGAATGAAA
*
9731 ATCGCAA--CG-A-CAAA
1 ATCGCAATGCGAATGAAA
9745 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCG-AATGAAA
*
9763 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCG-AATGAAA
9782 ATCGCAATGCGA
1 ATCGCAATGCGA
9794 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 4 0.08
18 26 0.49
19 12 0.23
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAATGAAA
Found at i:9785 original size:37 final size:38
Alignment explanation
Indices: 9693--9793 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 38
9683 GAAAATGACT
***
9693 ATCGCAACGCGGAAATGGCTATCGCAATGCG-AATGAAA
1 ATCGCAACGC-GAAATGAAAATCGCAATGCGAAATGAAA
*
9731 ATCGCAA--CG--A-CAAAATCGCAATGCGAAATG-AA
1 ATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAA
9763 ATCGCAACGCGAAATGAAAATCGCAATGCGA
1 ATCGCAACGCGAAATGAAAATCGCAATGCGA
9794 TTTGTGTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
32 20 0.38
33 5 0.10
34 2 0.04
35 1 0.02
36 2 0.04
37 15 0.29
38 7 0.13
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.14
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAA
Found at i:9824 original size:14 final size:14
Alignment explanation
Indices: 9805--9895 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
9795 TTGTGTTTCG
9805 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
9819 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
9835 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
9851 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
9868 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
9884 CGTTGCGATTTT
1 CGTTGCGATTTT
9896 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:9869 original size:33 final size:33
Alignment explanation
Indices: 9800--9911 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
9790 GCGATTTGTG
*
9800 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
9832 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
9865 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
9898 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
9912 AGCCATTTCC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 26 0.33
33 52 0.67
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:9930 original size:20 final size:19
Alignment explanation
Indices: 9896--9951 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
9886 TTGCGATTTT
*
9896 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
9915 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
9935 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
9952 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:10046 original size:25 final size:25
Alignment explanation
Indices: 9990--10048 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
9980 ATTCTTCTTC
* *
9990 TGGAATGTTTATATATGTTGTCCTT
1 TGGAATGTTTATATAAGTTGTACTT
**
10015 TTAAATGTTTATATAAG-TGTTACTT
1 TGGAATGTTTATATAAGTTG-TACTT
10040 TGGAATGTT
1 TGGAATGTT
10049 ATCTGAGCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.25, C:0.05, G:0.19, T:0.51
Consensus pattern (25 bp):
TGGAATGTTTATATAAGTTGTACTT
Found at i:11971 original size:14 final size:14
Alignment explanation
Indices: 11952--12005 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
11942 GAAACTGACT
11952 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
11966 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
11985 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
11999 ATCGCAA
1 ATCGCAA
12006 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:12060 original size:18 final size:18
Alignment explanation
Indices: 12037--12102 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
12027 CGATTTTCTA
12037 GTTGCGATAGCCATTTTC
1 GTTGCGATAGCCATTTTC
***
12055 GTTGCGATTTTTCA-TTTC
1 GTTGCGA-TAGCCATTTTC
12073 GAATTGCGATAGCCATTTTC
1 G--TTGCGATAGCCATTTTC
12093 GTTGCGATAG
1 GTTGCGATAG
12103 TCAAATGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
18 21 0.55
19 6 0.16
20 11 0.29
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (18 bp):
GTTGCGATAGCCATTTTC
Found at i:12321 original size:20 final size:20
Alignment explanation
Indices: 12296--12345 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
12286 TTGAAGATGA
12296 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
**
12316 TTGCGAAATTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
12336 TTGCGATTTT
1 TTGCGATTTT
12346 GTATTATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:12416 original size:20 final size:21
Alignment explanation
Indices: 12372--12423 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
12362 ATAGTCAGTA
*
12372 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
12393 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
12413 TCGCATTGCGA
1 TCGCATTGCGA
12424 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:12639 original size:12 final size:12
Alignment explanation
Indices: 12620--12653 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12610 CTCTCCGGCG
12620 ACATCCGTTCCT
1 ACATCCGTTCCT
*
12632 ATATCCGTTCCT
1 ACATCCGTTCCT
12644 ACATCC-TTCC
1 ACATCCGTTCC
12654 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:13230 original size:24 final size:24
Alignment explanation
Indices: 13203--13256 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
13193 GTATTCGAAA
*
13203 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
13227 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
13251 TTTGAT
1 TTTGAT
13257 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:13448 original size:12 final size:12
Alignment explanation
Indices: 13431--13455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13421 ATATAATCCT
13431 GAAGAAGAAAAA
1 GAAGAAGAAAAA
13443 GAAGAAGAAAAA
1 GAAGAAGAAAAA
13455 G
1 G
13456 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:15739 original size:39 final size:36
Alignment explanation
Indices: 15696--15843 Score: 145
Period size: 33 Copynumber: 4.3 Consensus size: 36
15686 CTTAATGTCT
*
15696 ATCGCAACGCGGAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAA-GA--ATCGCAATGCGAAATGAAA
*
15735 ATCGCAA--C-GAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
* **
15768 ATCGCAACGC--TAA-TTTCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
*
15801 ATCGCAACGAGG---GAATCGCAATGCGAAATG-AA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
15833 ATCGCAACGCG
1 ATCGCAACGCG
15844 AATTAATTTC
Statistics
Matches: 94, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
32 12 0.13
33 68 0.72
34 1 0.01
35 2 0.02
36 3 0.03
37 1 0.01
39 7 0.07
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.16
Consensus pattern (36 bp):
ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
Found at i:15758 original size:33 final size:33
Alignment explanation
Indices: 15716--15841 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
15706 GGAAATTACT
15716 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
15749 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
15781 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
15815 ATCGCAATGCGAAATG-AAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
15842 CGAATTAATT
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
32 12 0.14
33 71 0.85
34 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:15823 original size:66 final size:65
Alignment explanation
Indices: 15717--15847 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 65
15707 GAAATTACTA
*
15717 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-AAATCGCAACGCGAAT
15782 T
65 T
*
15783 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
15848 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 16 0.25
66 47 0.75
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (65 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
Found at i:15893 original size:19 final size:19
Alignment explanation
Indices: 15849--15915 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
15839 ACGCGAATTA
15849 ATTTCGCGTTGCGATTCTC
1 ATTTCGCGTTGCGATTCTC
*
15868 ---T--CGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTC
15882 ATTTCGCGTTGCGATTCTC
1 ATTTCGCGTTGCGATTCTC
*
15901 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
15916 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 12 0.30
16 1 0.03
17 1 0.03
19 26 0.65
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTCTC
Found at i:16041 original size:14 final size:14
Alignment explanation
Indices: 16022--16058 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
16012 CATCAATTAA
16022 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
16036 ACAAATCACCTTTT
1 ACAAATCAACTTTT
16050 ACAAATCAA
1 ACAAATCAA
16059 TTAAACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:17464 original size:21 final size:21
Alignment explanation
Indices: 17398--17464 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
17388 GTGAATCGGG
*
17398 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
17418 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
17440 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
17461 CTCT
1 CTCT
17465 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:17483 original size:42 final size:41
Alignment explanation
Indices: 17398--17520 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
17388 GTGAATCGGG
* * * *
17398 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
17440 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
17482 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
17521 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:19656 original size:20 final size:19
Alignment explanation
Indices: 19611--19789 Score: 117
Period size: 19 Copynumber: 9.8 Consensus size: 19
19601 TCTTTTGGTT
19611 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
19630 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
19651 GAAATGACTATCGTAACGA
1 GAAATGAAAATCGCAACGA
* *
19670 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
** * *
19684 GAAATGACTATCGCGATGA
1 GAAATGAAAATCGCAACGA
* *
19703 G--A-G--AATCGCGACGC
1 GAAATGAAAATCGCAACGA
* *
19717 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGA
*
19736 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
19755 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
19774 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
19790 TGCGATTTTG
Statistics
Matches: 129, Mismatches: 19, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
14 17 0.13
16 4 0.03
17 4 0.03
19 74 0.57
20 28 0.22
21 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:19693 original size:33 final size:33
Alignment explanation
Indices: 19636--19723 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
19626 ACGAGATAAT
*
19636 GAGAATCGCAACGCGGAAATGACTATCGTAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* * *
19670 GAGAATCGCAATGCGAAATGACTATCGCGATGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
*
19703 GAGAATCGCGACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
19724 AAATCACAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 35 0.73
34 13 0.27
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.15
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:19728 original size:19 final size:19
Alignment explanation
Indices: 19706--19794 Score: 151
Period size: 19 Copynumber: 4.7 Consensus size: 19
19696 GCGATGAGAG
*
19706 AATCGCGACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
19725 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
19744 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
19763 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
19782 AATCGCAATGCGA
1 AATCGCAACGCGA
19795 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:19817 original size:19 final size:19
Alignment explanation
Indices: 19790--19833 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
19780 AAAATCGCAA
**
19790 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
19808 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
19827 TGCGATT
1 TGCGATT
19834 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:20487 original size:20 final size:20
Alignment explanation
Indices: 20376--20489 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
20366 CGCTATGTAA
* *
20376 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
20396 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
20416 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
* * *
20437 ATCGCATTGCAATTGTAAGT
1 ATCGCATTGCGATAGTCAGT
20457 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
20477 ATCGCATTGCGAT
1 ATCGCATTGCGAT
20490 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 4 0.05
20 61 0.78
21 11 0.14
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:23402 original size:208 final size:208
Alignment explanation
Indices: 23044--23456 Score: 817
Period size: 208 Copynumber: 2.0 Consensus size: 208
23034 AAACATTTTG
23044 ATACCTATGGATCACCTTATTGTCCTCCCAGAGCAGGTGCATGGACTTATGCCTTTCAAATCATA
1 ATACCTATGGATCACCTTATTGTCCTCCCAGAGCAGGTGCATGGACTTATGCCTTTCAAATCATA
*
23109 TATCAGGTATGTCCTAGATTTTGCTTATCTGATTCCTGGTTTCTCTTCTGTGTTCCAATGGTAGC
66 TATCAGGCATGTCCTAGATTTTGCTTATCTGATTCCTGGTTTCTCTTCTGTGTTCCAATGGTAGC
23174 CAACTTCGTTATATTTCGTGTATTCGGTAGCAGTTATTATATAGTTTAGATACATAGATGAAGTC
131 CAACTTCGTTATATTTCGTGTATTCGGTAGCAGTTATTATATAGTTTAGATACATAGATGAAGTC
23239 ATCGTGATTTTAC
196 ATCGTGATTTTAC
23252 ATACCTATGGATCACCTTATTGTCCTCCCAGAGCAGGTGCATGGACTTATGCCTTTCAAATCATA
1 ATACCTATGGATCACCTTATTGTCCTCCCAGAGCAGGTGCATGGACTTATGCCTTTCAAATCATA
23317 TATCAGGCATGTCCTAGATTTTGCTTATCTGATTCCTGGTTTCTCTTCTGTGTTCCAATGGTAGC
66 TATCAGGCATGTCCTAGATTTTGCTTATCTGATTCCTGGTTTCTCTTCTGTGTTCCAATGGTAGC
23382 CAACTTCGTTATATTTCGTGTATTCGGTAGCAGTTATTATATAGTTTAGATACATAGATGAAGTC
131 CAACTTCGTTATATTTCGTGTATTCGGTAGCAGTTATTATATAGTTTAGATACATAGATGAAGTC
23447 ATCGTGATTT
196 ATCGTGATTT
23457 GCCTAATGAT
Statistics
Matches: 204, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
208 204 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (208 bp):
ATACCTATGGATCACCTTATTGTCCTCCCAGAGCAGGTGCATGGACTTATGCCTTTCAAATCATA
TATCAGGCATGTCCTAGATTTTGCTTATCTGATTCCTGGTTTCTCTTCTGTGTTCCAATGGTAGC
CAACTTCGTTATATTTCGTGTATTCGGTAGCAGTTATTATATAGTTTAGATACATAGATGAAGTC
ATCGTGATTTTAC
Found at i:25464 original size:60 final size:60
Alignment explanation
Indices: 25354--25516 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 60
25344 GAAATTTTCA
* * * * * ** *
25354 AAAAGTTTAGGGGCTAATTTAAAATGAAGGTC-TTATTTTGGGATGGAATTGCAATGTTC
1 AAAAGTTTAGAGACTAATTTAGAATGAAGATCATAATTTAAGGATGAAATTGCAATGTTC
* * * * * *
25413 AAAAGTTT-GAGAATTAGTTTAGAATGACGATCATAGTTTAAGGATGAAATTGGAATGTTT
1 AAAAGTTTAGAG-ACTAATTTAGAATGAAGATCATAATTTAAGGATGAAATTGCAATGTTC
*
25473 AAAAGTTTAGAGACTAATTTAGAATGAAGATCATAATTTGAGGA
1 AAAAGTTTAGAGACTAATTTAGAATGAAGATCATAATTTAAGGA
25517 CATGGGATAC
Statistics
Matches: 82, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
58 2 0.02
59 22 0.27
60 55 0.67
61 3 0.04
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (60 bp):
AAAAGTTTAGAGACTAATTTAGAATGAAGATCATAATTTAAGGATGAAATTGCAATGTTC
Found at i:27419 original size:12 final size:12
Alignment explanation
Indices: 27386--27425 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
27376 GTCAAAGAAA
*
27386 GTCAACGGTCACG
1 GTCAACGGTC-GG
27399 GTCAACGGTCGG
1 GTCAACGGTCGG
*
27411 GTCAGCGGTCGG
1 GTCAACGGTCGG
27423 GTC
1 GTC
27426 GGGTCAGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.15, C:0.28, G:0.40, T:0.17
Consensus pattern (12 bp):
GTCAACGGTCGG
Found at i:34719 original size:6 final size:7
Alignment explanation
Indices: 34697--34732 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
34687 GTCAAAGGAA
34697 GTCAACG
1 GTCAACG
34704 GTCAACG
1 GTCAACG
34711 GTC-ACG
1 GTCAACG
34717 GTCAACG
1 GTCAACG
34724 GTC-ACG
1 GTCAACG
34730 GTC
1 GTC
34733 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:34719 original size:13 final size:13
Alignment explanation
Indices: 34701--34732 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
34691 AAGGAAGTCA
34701 ACGGTCAACGGTC
1 ACGGTCAACGGTC
34714 ACGGTCAACGGTC
1 ACGGTCAACGGTC
34727 ACGGTC
1 ACGGTC
34733 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.16
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:34757 original size:9 final size:9
Alignment explanation
Indices: 34745--34797 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
34735 GTCGGGTCTG
34745 ACCGGTCAA
1 ACCGGTCAA
*
34754 ACCGGTTCAG
1 ACCGG-TCAA
*
34764 ACCGGTCGA
1 ACCGGTCAA
*
34773 ACCGGTCGGA
1 ACCGGTC-AA
34783 ACCGGTCAA
1 ACCGGTCAA
34792 ACCGGT
1 ACCGGT
34798 TTTCCAGCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 21 0.55
10 17 0.45
ACGTcount: A:0.25, C:0.32, G:0.30, T:0.13
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:34766 original size:19 final size:19
Alignment explanation
Indices: 34744--34798 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
34734 GGTCGGGTCT
34744 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
* *
34763 GACCGGTCGAACCGG-TCG
1 GACCGGTCAAACCGGTTCA
34781 GAACCGGTCAAACCGGTT
1 G-ACCGGTCAAACCGGTT
34799 TTCCAGCAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.10
19 27 0.87
20 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.15
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:37747 original size:19 final size:22
Alignment explanation
Indices: 37713--37752 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
37703 CTTTAAAAAA
37713 TATAATATTATAAAT-ATATTT
1 TATAATATTATAAATAATATTT
37734 TATAAT-TT-TAAATAATATT
1 TATAATATTATAAATAATATT
37753 CATTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAATATTATAAATAATATTT
Found at i:43693 original size:2 final size:2
Alignment explanation
Indices: 43686--43725 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
43676 AACAAAATGA
43686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43726 ATTTAGAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48995 original size:42 final size:42
Alignment explanation
Indices: 48878--48997 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
48868 TTTCCCCGAA
* *
48878 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
48920 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
48962 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
48998 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:49226 original size:23 final size:23
Alignment explanation
Indices: 49183--49315 Score: 71
Period size: 24 Copynumber: 5.7 Consensus size: 23
49173 TAATTATTAA
* *
49183 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
49204 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
*
49227 -ATATTT-TAATATTATATAA-AAT
1 AATATTTATAATA--ATATAATATT
* * *
49249 AATCAATTAT-ATTATATTAATATA
1 AAT-ATTTATAATAATA-TAATATT
** * *
49273 AGATATTATATTTTATTATAATAAT
1 A-ATATT-TATAATAATATAATATT
49298 ATATATTTATAATAATAT
1 A-ATATTTATAATAATAT
49316 TTATATATTT
Statistics
Matches: 83, Mismatches: 17, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
21 16 0.19
22 15 0.18
23 15 0.18
24 17 0.20
25 17 0.20
26 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:49236 original size:21 final size:23
Alignment explanation
Indices: 49177--49244 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
49167 AAATATTAAT
* *
49177 TATTAAAATATTTAA-AATATATT
1 TATTAATAT-TTTAATAATATATA
49200 TATTAATATTTATAATAATATA-A
1 TATTAATATTT-TAATAATATATA
*
49223 TATT-ATATTTTAATATTATATA
1 TATTAATATTTTAATAATATATA
49245 AAATAATCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.23
22 9 0.23
23 15 0.38
24 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAATATTTTAATAATATATA
Found at i:49250 original size:33 final size:31
Alignment explanation
Indices: 49202--49261 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
49192 AATATATTTA
49202 TTAATATTTATAATAAT-ATAATATTATATT
1 TTAATATTTATAATAATAATAATATTATATT
*
49232 TTAATATTATATAA-AATAATCA-ATTATATT
1 TTAATATT-TATAATAATAATAATATTATATT
49262 ATATTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
TTAATATTTATAATAATAATAATATTATATT
Found at i:49269 original size:33 final size:30
Alignment explanation
Indices: 49192--49271 Score: 85
Period size: 33 Copynumber: 2.6 Consensus size: 30
49182 AAATATTTAA
49192 AATATATT-TATTAATATTTATAATAATAT
1 AATATATTATATTAATATTTATAATAATAT
*
49221 AATAT-TATATTTTAATATTATATAA-AATAAT
1 AATATAT-TATATTAATATT-TATAATAAT-AT
49252 CAATTATATTATATTAATAT
1 -AA-TATATTATATTAATAT
49272 AAGATATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
28 1 0.02
29 6 0.14
30 12 0.29
31 7 0.17
32 2 0.05
33 13 0.31
34 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (30 bp):
AATATATTATATTAATATTTATAATAATAT
Found at i:49271 original size:28 final size:28
Alignment explanation
Indices: 49195--49300 Score: 78
Period size: 28 Copynumber: 3.8 Consensus size: 28
49185 TATTTAAAAT
*
49195 ATATT-TATTAATATT--TATAATAATATA
1 ATATTATATT-ATATTAATATAA-AATATC
49222 ATATTATATTTTAATATT-ATATAAAATAATC
1 ATATTATA--TT-ATATTAATATAAAAT-ATC
* *
49253 A-ATTATATTATATTAATATAAGATATT
1 ATATTATATTATATTAATATAAAATATC
* *
49280 ATATTTTATTATAATAATATA
1 ATATTATATTATATTAATATA
49301 TATTTATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
27 13 0.19
28 29 0.43
30 17 0.25
31 8 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATATTATATTATATTAATATAAAATATC
Found at i:49302 original size:20 final size:21
Alignment explanation
Indices: 49270--49325 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
49260 TTATATTAAT
* *
49270 ATAAGATAT-TATATTTTATT
1 ATAATATATATATATTTTATA
49290 ATAATA-ATATATA-TTTATA
1 ATAATATATATATATTTTATA
*
49309 ATAATATTTATATATTT
1 ATAATATATATATATTT
49326 CAATAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 13 0.43
20 15 0.50
21 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATATATATATATTTTATA
Found at i:49338 original size:20 final size:20
Alignment explanation
Indices: 49297--49336 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
49287 ATTATAATAA
*
49297 TATATATTTATAATAATATT
1 TATATATTTACAATAATATT
49317 TATATATTT-CAATAATATT
1 TATATATTTACAATAATATT
49336 T
1 T
49337 TAGTAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATTTACAATAATATT
Found at i:49576 original size:20 final size:20
Alignment explanation
Indices: 49498--49567 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
49488 TTTCCAGATG
*
49498 TTTTTCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
49518 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
49538 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
49558 TTTTCCAGAA
1 TTTTCCAGAA
49568 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:49576 original size:40 final size:40
Alignment explanation
Indices: 49498--49576 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
49488 TTTCCAGATG
* **
49498 TTTTTCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
49538 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
49577 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:49586 original size:15 final size:15
Alignment explanation
Indices: 49550--49631 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
49540 TTACAGAAAT
**
49550 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
49565 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
49579 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
*
49594 GTAATTCAAATTCTA
1 GTAATTCAAATTCCA
49609 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
49624 GTAATTCA
1 GTAATTCA
49632 TTTTCTGGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 12 0.21
15 44 0.79
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:49600 original size:30 final size:30
Alignment explanation
Indices: 49550--49631 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
49540 TTACAGAAAT
49550 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* *
49579 GTAATTCATTTTTCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
49609 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
49632 TTTTCTGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 15 0.32
30 32 0.68
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:50780 original size:2 final size:2
Alignment explanation
Indices: 50773--50800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50763 AGGGTAAACC
50773 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
50801 GATCGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51387 original size:2 final size:2
Alignment explanation
Indices: 51380--51428 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
51370 GTAATTTATC
51380 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
51422 AT AT AT A
1 AT AT AT A
51429 AAAGCCGTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52070 original size:18 final size:17
Alignment explanation
Indices: 52043--52084 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
52033 TTTAAACTAA
52043 TTTTTATCAAAATTTCAT
1 TTTTTATC-AAATTTCAT
*
52061 TTTTTTTCAAATTTCAT
1 TTTTTATCAAATTTCAT
52078 TTTTTAT
1 TTTTTAT
52085 TATCAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTATCAAATTTCAT
Found at i:52736 original size:27 final size:27
Alignment explanation
Indices: 52706--52763 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
52696 AATTGTTCAA
* *
52706 CTTCAGCATTCAATCATACTCTGGATT
1 CTTCAACATTCAATAATACTCTGGATT
*
52733 CTTCAACATTCAATAATAGTCTGGATT
1 CTTCAACATTCAATAATACTCTGGATT
52760 CTTC
1 CTTC
52764 TTGATAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (27 bp):
CTTCAACATTCAATAATACTCTGGATT
Done.