Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003763.1 Hibiscus syriacus cultivar Beakdansim tig00008062_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: 63332
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5246 original size:15 final size:15
Alignment explanation
Indices: 5226--5268 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5216 TTATTTTGGT
5226 TTATTTATTTAT-TTA
1 TTATTT-TTTATATTA
5241 TTA-TTTTTACTATTA
1 TTATTTTTTA-TATTA
5256 TTATTTTTTATAT
1 TTATTTTTTATAT
5269 CTTAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.16
14 3 0.12
15 12 0.48
16 6 0.24
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTTTTATATTA
Found at i:6824 original size:16 final size:17
Alignment explanation
Indices: 6803--6860 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 17
6793 AAAGTCAACA
6803 GTCAACGGTC-GGTCGG
1 GTCAACGGTCGGGTCGG
6819 GTCAACGGTCGGGTCGGGTGG
1 GTCAACGGTCGGGTC----GG
6840 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
6857 GTCA
1 GTCA
6861 GACCGGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 10 0.27
17 10 0.27
21 17 0.46
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:6829 original size:12 final size:12
Alignment explanation
Indices: 6812--6854 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
6802 AGTCAACGGT
6812 CGGTCGGGTCAA
1 CGGTCGGGTCAA
6824 CGGTCGGGTC--
1 CGGTCGGGTCAA
*
6834 GGGT-GGGTCAA
1 CGGTCGGGTCAA
6845 CGGTCGGGTC
1 CGGTCGGGTC
6855 GGGTCAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (12 bp):
CGGTCGGGTCAA
Found at i:6857 original size:21 final size:22
Alignment explanation
Indices: 6809--6859 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
6799 AACAGTCAAC
6809 GGTC-GGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
6830 GGTCGGGT-GGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
6851 GGTCGGGTC
1 GGTCGGGTC
6860 AGACCGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.08, C:0.22, G:0.51, T:0.20
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:6874 original size:9 final size:9
Alignment explanation
Indices: 6856--6934 Score: 77
Period size: 9 Copynumber: 8.3 Consensus size: 9
6846 GGTCGGGTCG
*
6856 GGTCAGACC
1 GGTCAAACC
6865 GGTCAAACC
1 GGTCAAACC
*
6874 GGTTCGAACC
1 GG-TCAAACC
*
6884 GGTTGAAACC
1 GG-TCAAACC
6894 GGTCAAACC
1 GGTCAAACC
6903 GGTCAGAACC
1 GGTCA-AACC
*
6913 GGTTGAAACC
1 GG-TCAAACC
*
6923 GGTTAAACC
1 GGTCAAACC
6932 GGT
1 GGT
6935 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
9 30 0.50
10 28 0.47
11 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:6884 original size:19 final size:19
Alignment explanation
Indices: 6862--6935 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
6852 GTCGGGTCAG
6862 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCGA
* *
6881 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCGA
6900 ACCGGTCAGAACCGGTT-GAA
1 ACCGGTCA-AACCGGTTCG-A
*
6920 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
6936 TCCAGCAGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.04
19 27 0.59
20 17 0.37
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:6885 original size:10 final size:9
Alignment explanation
Indices: 6870--6935 Score: 60
Period size: 10 Copynumber: 6.9 Consensus size: 9
6860 AGACCGGTCA
6870 AACCGGTTCG
1 AACCGGTT-G
6880 AACCGGTTG
1 AACCGGTTG
**
6889 AAACCGGTCA
1 -AACCGGTTG
*
6899 AACCGGTCAG
1 AACCGGT-TG
6909 AACCGGTTG
1 AACCGGTTG
*
6918 AAACCGGTTA
1 -AACCGGTTG
6928 AACCGGTT
1 AACCGGTT
6936 TCCAGCAGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
9 17 0.36
10 30 0.64
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (9 bp):
AACCGGTTG
Found at i:6896 original size:29 final size:30
Alignment explanation
Indices: 6862--6935 Score: 125
Period size: 29 Copynumber: 2.5 Consensus size: 30
6852 GTCGGGTCAG
6862 ACCGGTCAAACCGGTTC-GAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAA
6891 ACCGGTCAAACCGG-TCAGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAA
*
6920 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
6936 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 2 0.05
29 39 0.93
30 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (30 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAA
Found at i:10490 original size:20 final size:21
Alignment explanation
Indices: 10464--10514 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
10454 AGGGCAGAGT
*
10464 TTGAAGCTGTGAATAACGAAC
1 TTGAAGCTGAGAATAACGAAC
* * *
10485 -TGAAGCAGAGGATAAGGAAC
1 TTGAAGCTGAGAATAACGAAC
10505 TTGAAGCTGA
1 TTGAAGCTGA
10515 ACATTATCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (21 bp):
TTGAAGCTGAGAATAACGAAC
Found at i:18369 original size:7 final size:7
Alignment explanation
Indices: 18357--18389 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
18347 GTCCTAAGTT
18357 GAAAAAA
1 GAAAAAA
18364 GAAAAAA
1 GAAAAAA
18371 G-AAAAA
1 GAAAAAA
18377 GAAAAAGA
1 GAAAAA-A
18385 GAAAA
1 GAAAA
18390 CATTTAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 12 0.50
8 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:18377 original size:13 final size:14
Alignment explanation
Indices: 18359--18389 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
18349 CCTAAGTTGA
18359 AAAAAGAAAAA-AG
1 AAAAAGAAAAAGAG
18372 AAAAAGAAAAAGAG
1 AAAAAGAAAAAGAG
18386 AAAA
1 AAAA
18390 CATTTAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAG
Found at i:18439 original size:6 final size:6
Alignment explanation
Indices: 18428--18478 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 6
18418 CCTAAATTGA
18428 AAAAAG AAAAAG AAAAGAG AAAAAGAG AAAAAG AACAAA- AGAAAAG AAAAA
1 AAAAAG AAAAAG AAAA-AG -AAAA-AG AAAAAG AA-AAAG A-AAAAG AAAAA
18479 TAAGGTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 22 0.55
7 11 0.28
8 7 0.17
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:18451 original size:21 final size:22
Alignment explanation
Indices: 18427--18472 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
18417 CCCTAAATTG
*
18427 AAAAAAGAAAAAGAA-AAGAGA
1 AAAAAAGAAAAAGAACAAAAGA
*
18448 AAAAGAGAAAAAGAACAAAAGA
1 AAAAAAGAAAAAGAACAAAAGA
18470 AAA
1 AAA
18473 GAAAAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAGAACAAAAGA
Found at i:18473 original size:21 final size:20
Alignment explanation
Indices: 18426--18478 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
18416 TCCCTAAATT
* *
18426 GAAAAAAGAAAAAGAAAAGA
1 GAAAAGAGAAAAAGAAAAAA
18446 GAAAAAGAGAAAAAGAACAAAA
1 G-AAAAGAGAAAAAGAA-AAAA
18468 GAAAAGA-AAAA
1 GAAAAGAGAAAA
18479 TAAGGTGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 20 0.69
22 4 0.14
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
GAAAAGAGAAAAAGAAAAAA
Found at i:19778 original size:106 final size:105
Alignment explanation
Indices: 19582--19890 Score: 474
Period size: 106 Copynumber: 2.9 Consensus size: 105
19572 ACGAAGGGGC
* *
19582 TTCCTAATTTCAGAGCCAATTTCAACTTCACGACGAAAGATATTGGACCCCAGACAACACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACGACG-AAGATATTGGACCCAAGACAACACAAGCT
*
19647 CAACTTCACGACGAATGGGCGGCTGACTGTCAACAAACAAT
65 CAACTTCACGACGAAGGGGCGGCTGACTGTCAACAAACAAT
* *
19688 TTCCCAATTTCATAGCCAATTTCAACTTCACAACGAAGCATATTGGACCCAAGACAACACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAAG-ATATTGGACCCAAGACAACACAAGCT
* * *
19753 CAACTTCACGATGAAGGGGCAGCTGATTGTCAACAAACAAT
65 CAACTTCACGACGAAGGGGCGGCTGACTGTCAACAAACAAT
* * *
19794 TTTCCAATTTCAGAGCCAATTTCAACTTCACGATGAAGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAA-GATATTGGACCCAAGACAACACAAGCT
* *
19859 CAACTTCACAACGAAGGAGCGGCTGACTGTCA
65 CAACTTCACGACGAAGGGGCGGCTGACTGTCA
19891 GTTTCATTCA
Statistics
Matches: 183, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
105 3 0.02
106 179 0.98
107 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
TTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAAGATATTGGACCCAAGACAACACAAGCTC
AACTTCACGACGAAGGGGCGGCTGACTGTCAACAAACAAT
Found at i:19969 original size:95 final size:95
Alignment explanation
Indices: 19802--19985 Score: 260
Period size: 95 Copynumber: 1.9 Consensus size: 95
19792 ATTTTCCAAT
* * *
19802 TTCAGAGCCAATTTCAACTTCACGATGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
19867 CAACGAAGGAGCGGCTGACTGTCAGTTTCA
66 CAACGAAGGAGCGGCTGACTGTCAGTTTCA
* ** * * **
19897 TTCAGAGTCAATTTTTACTTCACAACGAAGGATATTAGACTCGATACAGTACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* *
19962 CAGCGAAGGTGCGGCTGACTGTCA
66 CAACGAAGGAGCGGCTGACTGTCA
19986 ACAAACAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
95 77 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (95 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGAGCGGCTGACTGTCAGTTTCA
Found at i:22035 original size:4 final size:4
Alignment explanation
Indices: 22026--22102 Score: 50
Period size: 4 Copynumber: 18.8 Consensus size: 4
22016 TTATTTTTGG
* * * *
22026 TTTA TTTA TTTA TTTA TTT- TTACTA TTATT TTTA TTT- TTTA TATC TTAA
1 TTTA TTTA TTTA TTTA TTTA TT--TA TT-TA TTTA TTTA TTTA TTTA TTTA
* *
22075 TTTA TATA TATA TATTA TTTA TTTA TTT
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTT
22103 GTATTTTGTT
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
3 5 0.09
4 43 0.75
5 7 0.12
6 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:22451 original size:2 final size:2
Alignment explanation
Indices: 22444--22470 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22434 GATAACTTAT
22444 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
22471 TCTTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22640 original size:15 final size:15
Alignment explanation
Indices: 22576--22648 Score: 60
Period size: 15 Copynumber: 4.7 Consensus size: 15
22566 CTCTATGTTC
*
22576 TTATATTTTTTTC-CT
1 TTAT-TTTTTTTCATT
22591 TTATTTATTTTTTCATT
1 TTA-TT-TTTTTTCATT
* *
22608 TTATTTTCTGTT-AAT
1 TTATTTT-TTTTCATT
22623 TTATTTTTTTTCATT
1 TTATTTTTTTTCATT
22638 TTATTTGTTTT
1 TTATTT-TTTT
22649 ACTTATGCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.06
15 23 0.49
16 17 0.36
17 4 0.09
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (15 bp):
TTATTTTTTTTCATT
Found at i:26800 original size:14 final size:14
Alignment explanation
Indices: 26763--26801 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
26753 TAATCTTTTG
26763 TTTTCACAAATTTA
1 TTTTCACAAATTTA
*
26777 -TTTCAAAAATTTA
1 TTTTCACAAATTTA
26790 TTTTCACAAATT
1 TTTTCACAAATT
26802 ATCATAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTTCACAAATTTA
Found at i:28304 original size:19 final size:20
Alignment explanation
Indices: 28276--28323 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
28266 TTAGTTAAGT
*
28276 TTTAATATATAATTA-AAAA
1 TTTAAAATATAATTACAAAA
* *
28295 TTTAAAATATTATTACAATA
1 TTTAAAATATAATTACAAAA
*
28315 TTAAAAATA
1 TTTAAAATA
28324 AGATTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAAATATAATTACAAAA
Found at i:31508 original size:27 final size:27
Alignment explanation
Indices: 31477--31534 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
31467 TGGGATTGCT
*
31477 TCGTCTCCACCTTTGCTGCAGTACCCC
1 TCGTCTCCACCTTTGCTGCAGCACCCC
31504 TCGTCTCCACCTTTGCTGCAGCACCCC
1 TCGTCTCCACCTTTGCTGCAGCACCCC
31531 TCGT
1 TCGT
31535 TCCCATCGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.10, C:0.45, G:0.16, T:0.29
Consensus pattern (27 bp):
TCGTCTCCACCTTTGCTGCAGCACCCC
Found at i:32476 original size:34 final size:34
Alignment explanation
Indices: 32437--32506 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
32427 TCAGTAACAT
*
32437 AAATGAATATTTATTTAAACGTGAGTGGTATTTG
1 AAATGAATATTTATTTAAACGTGAATGGTATTTG
32471 AAATGAATATTTATTTAAACGTGAATGGTATTTG
1 AAATGAATATTTATTTAAACGTGAATGGTATTTG
32505 AA
1 AA
32507 GTAAAACCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.40
Consensus pattern (34 bp):
AAATGAATATTTATTTAAACGTGAATGGTATTTG
Found at i:32502 original size:17 final size:17
Alignment explanation
Indices: 32448--32503 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
32438 AATGAATATT
*
32448 TATTTAAACGTGAGTGG
1 TATTTAAACGTGAATGG
**
32465 TATTTGAAA--TGAATATT
1 TATTT-AAACGTGAAT-GG
32482 TATTTAAACGTGAATGG
1 TATTTAAACGTGAATGG
32499 TATTT
1 TATTT
32504 GAAGTAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 7 0.23
17 15 0.50
18 8 0.27
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.43
Consensus pattern (17 bp):
TATTTAAACGTGAATGG
Found at i:32519 original size:34 final size:34
Alignment explanation
Indices: 32437--32520 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
32427 TCAGTAACAT
* * *
32437 AAATGAATATTTATTTAAACGTGAGTGGTATTTG
1 AAATGAAAACTTATTTAAACGTGAATGGTATTTG
* *
32471 AAATGAATATTTATTTAAACGTGAATGGTATTTG
1 AAATGAAAACTTATTTAAACGTGAATGGTATTTG
*
32505 AAGT-AAAACCTTATTT
1 AAATGAAAA-CTTATTT
32521 TAATTTAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 3 0.07
34 42 0.93
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (34 bp):
AAATGAAAACTTATTTAAACGTGAATGGTATTTG
Found at i:43813 original size:43 final size:43
Alignment explanation
Indices: 43750--43862 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
43740 TCAACAAAGT
* * * *
43750 GCATTTATATGAAAATTGACTATATGTAGTTTTTTAAGATAGG
1 GCATTTCTATGAAAAATGACTATATGTAGGTTTTTAAGAGAGG
*
43793 GCATTTCTATGAAAAATGACTATATGTAGGTTTTTAAGAGAGT
1 GCATTTCTATGAAAAATGACTATATGTAGGTTTTTAAGAGAGG
* * *
43836 GAATTTAC-ATGAAAAATAAATATATGT
1 GCATTT-CTATGAAAAATGACTATATGT
43863 CTTCCACAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 60 0.98
44 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (43 bp):
GCATTTCTATGAAAAATGACTATATGTAGGTTTTTAAGAGAGG
Found at i:44284 original size:41 final size:41
Alignment explanation
Indices: 44235--44315 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
44225 CAACACACCC
44235 ACTATAAAGAACCTAGGATATACCACTCACACTACACCAAT
1 ACTATAAAGAACCTAGGATATACCACTCACACTACACCAAT
44276 ACTATAAAGAACCTAGGATATACCACTCACACTACACCAA
1 ACTATAAAGAACCTAGGATATACCACTCACACTACACCAA
44316 CACTTTTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.44, C:0.30, G:0.07, T:0.19
Consensus pattern (41 bp):
ACTATAAAGAACCTAGGATATACCACTCACACTACACCAAT
Found at i:51492 original size:2 final size:2
Alignment explanation
Indices: 51487--51541 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
51477 TTGAAACAAT
51487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51529 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
51542 TATGTATGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51804 original size:2 final size:2
Alignment explanation
Indices: 51797--51914 Score: 88
Period size: 2 Copynumber: 60.5 Consensus size: 2
51787 CTTATAATTA
51797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
51837 AT -T AT A- AGT AT AT AC AT AT GT GT GT AT AT AT AT -T A- AT ACT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
51877 TT AT AT AT A- AGT GT AT AT ACT AT AT AT AT CT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT A
51915 ATTATAAAGT
Statistics
Matches: 95, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
1 7 0.07
2 84 0.88
3 4 0.04
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51920 original size:10 final size:9
Alignment explanation
Indices: 51789--51965 Score: 72
Period size: 8 Copynumber: 20.0 Consensus size: 9
51779 ACATTACACT
51789 TATA-ATTA
1 TATATATTA
51797 -ATATA-TA
1 TATATATTA
51804 TATATA-TA
1 TATATATTA
51812 TATATA-TA
1 TATATATTA
51820 TATATA-TA
1 TATATATTA
51828 TATATATTA
1 TATATATTA
*
51837 -AT-TATAA
1 TATATATTA
*
51844 GTATATA-CA
1 -TATATATTA
* *
51853 TATGTGTGTA
1 TATATAT-TA
51863 TATATATTA
1 TATATATTA
51872 -ATACT-TTA
1 TATA-TATTA
* *
51880 TATATAAGTG
1 TATAT-ATTA
*
51890 TATATACTA
1 TATATATTA
51899 TATATATCTA
1 TATATAT-TA
51909 TATATAATTA
1 TATAT-ATTA
* *
51919 TAAAGTATAA
1 TATA-TATTA
*
51929 TATA-AGTA
1 TATATATTA
* *
51937 TATACATAA
1 TATATATTA
*
51946 GTATATATGTG
1 -TATATAT-TA
51957 TATATATTA
1 TATATATTA
51966 ATAACATACA
Statistics
Matches: 128, Mismatches: 23, Indels: 35
0.69 0.12 0.19
Matches are distributed among these distances:
7 9 0.07
8 49 0.38
9 22 0.17
10 45 0.35
11 3 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (9 bp):
TATATATTA
Found at i:52751 original size:19 final size:19
Alignment explanation
Indices: 52719--52760 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52709 TATTGTCAAT
*
52719 TCAAAATCTCACAATTTCA
1 TCAAAATCTCACAATTACA
* *
52738 TCAAAGTCTTACAATTACA
1 TCAAAATCTCACAATTACA
52757 TCAA
1 TCAA
52761 TTGTAACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (19 bp):
TCAAAATCTCACAATTACA
Found at i:53891 original size:31 final size:31
Alignment explanation
Indices: 53855--53928 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
53845 GTATTACCTA
* *
53855 AATGCAACATGAACGTATTGTACATTATCTG
1 AATGCAACATGAACATATTATACATTATCTG
* *
53886 AATGC-ACACTG-ACATATTATGCATTATTTG
1 AATGCAACA-TGAACATATTATACATTATCTG
53916 AATGCAAACATGA
1 AATGC-AACATGA
53929 CTAGCATCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
30 23 0.66
31 9 0.26
32 3 0.09
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (31 bp):
AATGCAACATGAACATATTATACATTATCTG
Found at i:57920 original size:19 final size:20
Alignment explanation
Indices: 57896--57935 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
57886 AATTTAATCG
*
57896 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
57915 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
57935 A
1 A
57936 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:62026 original size:22 final size:23
Alignment explanation
Indices: 61994--62036 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
61984 AATGTTTTGT
61994 TCTTTCAAATA-GAAAAATAATA
1 TCTTTCAAATATGAAAAATAATA
* *
62016 TCTTTCGAATATGAATAATAA
1 TCTTTCAAATATGAAAAATAA
62037 CTTTTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (23 bp):
TCTTTCAAATATGAAAAATAATA
Found at i:62916 original size:73 final size:73
Alignment explanation
Indices: 62797--62942 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
62787 AAGTGAACAA
* * *
62797 TATGGTGAAGACTTTTTATGCATAATTTTAATGTTTCTAAATTTTAATGTATTTTGTTGTTAAGT
1 TATGGTGAAGACTGTTTATGCATAACTTTAATGTTTCTAAATTTTAATGTATTCTGTTGTTAAGT
62862 ATTAATTT
66 ATTAATTT
62870 TATGGTGAAGACTGTTTATGCATAACTTTAATGTTTCTAAATTTTAATGTATTCTGTTGTTAAGT
1 TATGGTGAAGACTGTTTATGCATAACTTTAATGTTTCTAAATTTTAATGTATTCTGTTGTTAAGT
62935 ATTAATTT
66 ATTAATTT
62943 ATGCATAACT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.51
Consensus pattern (73 bp):
TATGGTGAAGACTGTTTATGCATAACTTTAATGTTTCTAAATTTTAATGTATTCTGTTGTTAAGT
ATTAATTT
Done.