Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168077.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_325, 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: 34568
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2047 original size:19 final size:20
Alignment explanation
Indices: 2019--2064 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2009 TCCGGTGAAC
*
2019 TTCCGACGAA-ATTTCCAGA
1 TTCCGGCGAATATTTCCAGA
*
2038 TTCCGGCGAATTTTTCCAGA
1 TTCCGGCGAATATTTCCAGA
*
2058 ATCCGGC
1 TTCCGGC
2065 ACCGGTGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (20 bp):
TTCCGGCGAATATTTCCAGA
Found at i:2293 original size:5 final size:5
Alignment explanation
Indices: 2285--2310 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2275 AGCCCTTTCT
2285 GAGCC GAGCC GAGCC GAGCC GAGCC G
1 GAGCC GAGCC GAGCC GAGCC GAGCC G
2311 TTCTTCCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.42, T:0.00
Consensus pattern (5 bp):
GAGCC
Found at i:2322 original size:14 final size:15
Alignment explanation
Indices: 2303--2344 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
2293 CCGAGCCGAG
2303 CCGAGCCGTTCTTC-
1 CCGAGCCGTTCTTCT
2317 CCGAGCCG--CTTCT
1 CCGAGCCGTTCTTCT
2330 CCGAGCCGTT-TTCT
1 CCGAGCCGTTCTTCT
2344 C
1 C
2345 TTCCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 13 0.52
ACGTcount: A:0.07, C:0.43, G:0.21, T:0.29
Consensus pattern (15 bp):
CCGAGCCGTTCTTCT
Found at i:2335 original size:13 final size:14
Alignment explanation
Indices: 2303--2339 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2293 CCGAGCCGAG
2303 CCGAGCCGTTCTTC
1 CCGAGCCGTTCTTC
2317 CCGAGCCG--CTTC
1 CCGAGCCGTTCTTC
2329 TCCGAGCCGTT
1 -CCGAGCCGTT
2340 TTCTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.08, C:0.43, G:0.24, T:0.24
Consensus pattern (14 bp):
CCGAGCCGTTCTTC
Found at i:2408 original size:9 final size:10
Alignment explanation
Indices: 2393--2419 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2383 GCTCCGGGTT
2393 TTTTTTTGAA
1 TTTTTTTGAA
2403 TTTTTTTGAA
1 TTTTTTTGAA
2413 TTTTTTT
1 TTTTTTT
2420 TTATTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:2425 original size:10 final size:10
Alignment explanation
Indices: 2391--2455 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
2381 CCGCTCCGGG
2391 TTTTTTTTTGAA
1 TTTTTTTTT--A
**
2403 TTTTTTTGAA
1 TTTTTTTTTA
2413 TTTTTTTTTA
1 TTTTTTTTTA
**
2423 TTTTCATTTA
1 TTTTTTTTTA
2433 TTTGTTTTTT-
1 TTT-TTTTTTA
*
2443 TATTTTTTTA
1 TTTTTTTTTA
2453 TTT
1 TTT
2456 ATTAGATTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
9 6 0.15
10 24 0.59
11 4 0.10
12 7 0.17
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:2440 original size:24 final size:24
Alignment explanation
Indices: 2413--2458 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2403 TTTTTTTGAA
2413 TTTTTTT-TTATTTTCATTTATTTG
1 TTTTTTTATT-TTTTCATTTATTTG
*
2437 TTTTTTTATTTTTTTATTTATT
1 TTTTTTTATTTTTTCATTTATT
2459 AGATTAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (24 bp):
TTTTTTTATTTTTTCATTTATTTG
Found at i:2661 original size:58 final size:58
Alignment explanation
Indices: 2575--3100 Score: 664
Period size: 58 Copynumber: 8.9 Consensus size: 58
2565 AAGAAAATCA
* *
2575 AAATTTTCAAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATTTCCAAAAAAG-GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
* * *
2634 AAATTTTCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAAT
1 AAATTTCCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
** *
2692 CAAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 --AAATTTCC-AAAAAAGGAT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
* * *
2755 AAATTTTCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAAT
1 AAATTTCCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
** * *
2813 CAAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAAAT
1 --AAATTTCC-AAAAAAGGAT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT-TAAAAAT
* * *
2877 AAAATTTCAAAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 -AAATTTCCAAAAAAGG-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
* *
2937 AAGTTTCCAAAAAATG--TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATTTCCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
*
2993 AAATTTCCAAAAAA--ATGTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATTTCCAAAAAAGGAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
** *
3050 AAATTTCCAAAAAAATATTTTCTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAATTTCCAAAAAAGGATTTT-TGAGGAAAAGTTGAAAGTATCAATTTTCC
3101 CTACACAAAA
Statistics
Matches: 414, Mismatches: 35, Indels: 36
0.85 0.07 0.07
Matches are distributed among these distances:
56 52 0.13
57 53 0.13
58 75 0.18
59 64 0.15
60 27 0.07
61 50 0.12
62 21 0.05
63 67 0.16
64 5 0.01
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (58 bp):
AAATTTCCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
Found at i:2727 original size:121 final size:119
Alignment explanation
Indices: 2567--3100 Score: 775
Period size: 121 Copynumber: 4.5 Consensus size: 119
2557 TTTTAAATAA
* *
2567 GAAAATCAAAATTTTCAAAAAAGATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAA
1 GAAAATCAAAATTTCCAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAA
2631 AATAAATTTTCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTT
65 AATAAATTTTCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTT
2686 GAAAATCAAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAA
1 GAAAATCAAAATTTCC--AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAA
2751 AAATAAATTTTCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTT
64 AAATAAATTTTCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTT
*
2807 GAAAATCAAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCGA
1 GAAAATCAAAATTTCC--AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT-TA
* * *
2872 AAAATAAAATTTCAAAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
63 AAAATAAATTTTC-AAAAAAGG-ATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTT
* * *
2931 GAAAAT--AAGTTTCC--AAAAAATGTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
1 GAAAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
* * *
2991 ATAAATTTCCAAAAAA--ATGTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
66 ATAAATTTTCAAAAAAGGAT-TTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTT
* *
3044 AAAAAT--AAATTTCC-AAAAAAATATTTTCTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 GAAAATCAAAATTTCCAAAAAAAATATTTT-TAGGGAAAAGTTGAAAGTATCAATTTTCC
3101 CTACACAAAA
Statistics
Matches: 386, Mismatches: 19, Indels: 23
0.90 0.04 0.05
Matches are distributed among these distances:
112 1 0.00
113 45 0.12
114 11 0.03
115 6 0.02
116 38 0.10
117 27 0.07
118 12 0.03
119 15 0.04
121 162 0.42
122 21 0.05
123 8 0.02
124 40 0.10
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (119 bp):
GAAAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
ATAAATTTTCAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTACCAATTTTCCTT
Found at i:6819 original size:13 final size:13
Alignment explanation
Indices: 6803--6874 Score: 60
Period size: 13 Copynumber: 5.6 Consensus size: 13
6793 TTTTTATTTG
6803 TTATATTAATAAT
1 TTATATTAATAAT
*
6816 TTATGTTAATAAT
1 TTATATTAATAAT
* *
6829 TAAGA-T-ATAAT
1 TTATATTAATAAT
*
6840 TTATATTAA-AAA
1 TTATATTAATAAT
*
6852 TTATAATTATTAAT
1 TTAT-ATTAATAAT
6866 GTTATATTA
1 -TTATATTA
6875 TTGAATTGAT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
11 8 0.18
12 8 0.18
13 19 0.42
14 6 0.13
15 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (13 bp):
TTATATTAATAAT
Found at i:14008 original size:28 final size:28
Alignment explanation
Indices: 13951--14011 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
13941 TTTAATTCAC
* * *
13951 ATATATATATAAATTAAAATATATATTT
1 ATATATATAAAAATTAAAATATAAAATT
*
13979 ATATTTATAAAAATTAAAA-ATAAAAATT
1 ATATATATAAAAATTAAAATAT-AAAATT
14007 ATATA
1 ATATA
14012 AAAGTAACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATATATAAAAATTAAAATATAAAATT
Found at i:15830 original size:19 final size:19
Alignment explanation
Indices: 15806--15842 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15796 GGTTTACCTT
15806 GTTAAATTTATG-TTTTTGG
1 GTTAAATTT-TGATTTTTGG
15825 GTTAAATTTTGATTTTTG
1 GTTAAATTTTGATTTTTG
15843 AATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (19 bp):
GTTAAATTTTGATTTTTGG
Found at i:16374 original size:35 final size:35
Alignment explanation
Indices: 16334--16404 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
16324 TTGGTTTCAA
*
16334 ACCATGCCACCAATTAAGAATAGTGGTTTTTGTTC
1 ACCATGCCACCAATTAAGAATAGTAGTTTTTGTTC
* ** *
16369 ACCATGCCATCGGTTGAGAATAGTAGTTTTTGTTC
1 ACCATGCCACCAATTAAGAATAGTAGTTTTTGTTC
16404 A
1 A
16405 TCGTACCATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (35 bp):
ACCATGCCACCAATTAAGAATAGTAGTTTTTGTTC
Found at i:21523 original size:18 final size:18
Alignment explanation
Indices: 21496--21539 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
21486 TTTCTCCAAT
*
21496 TTGAATTTCTTGAATCAC
1 TTGAACTTCTTGAATCAC
21514 TTGAACTTCTTGAATCAC
1 TTGAACTTCTTGAATCAC
21532 TTGAACTT
1 TTGAACTT
21540 GTCCTACAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.43
Consensus pattern (18 bp):
TTGAACTTCTTGAATCAC
Found at i:24954 original size:31 final size:31
Alignment explanation
Indices: 24919--24985 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
24909 CTCATTTCTG
24919 TTGGGGAACACCACAGCTT-TGATACCATTTA
1 TTGGGGAACACCACAG-TTCTGATACCATTTA
*
24950 TTGGGGAACACCACAGTTCTGATACCATTTG
1 TTGGGGAACACCACAGTTCTGATACCATTTA
24981 TTGGG
1 TTGGG
24986 CTAAAAGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (31 bp):
TTGGGGAACACCACAGTTCTGATACCATTTA
Found at i:25556 original size:52 final size:52
Alignment explanation
Indices: 25470--25574 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
25460 TATAACCATA
* *
25470 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * * *
25522 CAAACTTACCTATTAAGAATCCCTTTCCTTTTAGAATTTTTCTCTTGCAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
25574 C
1 C
25575 TTCTTGTCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.38
Consensus pattern (52 bp):
CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:25630 original size:11 final size:11
Alignment explanation
Indices: 25599--25630 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
25589 GCAATATCTG
*
25599 ACAAATCTCAA
1 ACAAATCTCTA
25610 ACAAATCTCTA
1 ACAAATCTCTA
25621 ACAAATCTCT
1 ACAAATCTCT
25631 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:25901 original size:24 final size:24
Alignment explanation
Indices: 25874--25970 Score: 95
Period size: 25 Copynumber: 4.0 Consensus size: 24
25864 CATGCACTTC
*
25874 TCACATCTCGAACTTTCAGCTCTT
1 TCACATCTCGAACCTTCAGCTCTT
* *
25898 TCACATATCGAACCTTCGGCTCTT
1 TCACATCTCGAACCTTCAGCTCTT
* * *
25922 TCCACATCTTGAATCTTCAACTCTT
1 T-CACATCTCGAACCTTCAGCTCTT
** *
25947 CTCATGTTTCGAACCTTCAGCTCT
1 -TCACATCTCGAACCTTCAGCTCT
25971 GATACCACTT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
24 22 0.39
25 34 0.60
26 1 0.02
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.37
Consensus pattern (24 bp):
TCACATCTCGAACCTTCAGCTCTT
Found at i:26556 original size:52 final size:52
Alignment explanation
Indices: 26470--26574 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
26460 TATAACCATA
* *
26470 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * *
26522 CAAACTTACCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
26574 C
1 C
26575 TTCTTGTCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.37
Consensus pattern (52 bp):
CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:26630 original size:11 final size:11
Alignment explanation
Indices: 26599--26630 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
26589 GCAATATCTG
*
26599 ACAAATCTCAA
1 ACAAATCTCTA
26610 ACAAATCTCTA
1 ACAAATCTCTA
26621 ACAAATCTCT
1 ACAAATCTCT
26631 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:28427 original size:16 final size:14
Alignment explanation
Indices: 28390--28438 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
28380 AATTTGATTT
28390 AACAAAAAA-AA-A
1 AACAAAAAATAATA
*
28402 AA-AGAAAATAACTA
1 AACAAAAAATAA-TA
28416 TAACAAAAAATAATA
1 -AACAAAAAATAATA
28431 AACAAAAA
1 AACAAAAA
28439 GAATCTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 5 0.17
12 4 0.13
14 9 0.30
15 4 0.13
16 8 0.27
ACGTcount: A:0.80, C:0.08, G:0.02, T:0.10
Consensus pattern (14 bp):
AACAAAAAATAATA
Found at i:28437 original size:13 final size:16
Alignment explanation
Indices: 28406--28438 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
28396 AAAAAAAAAG
28406 AAAATAACTATAACAA
1 AAAATAACTATAACAA
28422 AAAATAA-TA-AACAA
1 AAAATAACTATAACAA
28436 AAA
1 AAA
28439 GAATCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAATAACTATAACAA
Found at i:29248 original size:16 final size:16
Alignment explanation
Indices: 29229--29262 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29219 CTCAGATAAT
* *
29229 ATTAAACTTTTGCAAA
1 ATTAAACGTTTGAAAA
29245 ATTAAACGTTTGAAAA
1 ATTAAACGTTTGAAAA
29261 AT
1 AT
29263 CATGTACCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (16 bp):
ATTAAACGTTTGAAAA
Found at i:29619 original size:30 final size:29
Alignment explanation
Indices: 29551--29637 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
29541 CTCTAAATCT
* *
29551 TCTA-TTTCAAATCAATTGAACCTTTGAATA
1 TCTATTTTC-AATCAATT-AAACTTTTAATA
* *
29581 TATTTTTTCAATCAATTAAACTTTTACATA
1 TCTATTTTCAATCAATTAAACTTTTA-ATA
*
29611 TCTATTTTCATTCAATTAAACTCTTTA
1 TCTATTTTCAATCAATTAAACT-TTTA
29638 TTGGATGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.15
30 32 0.68
31 8 0.17
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.47
Consensus pattern (29 bp):
TCTATTTTCAATCAATTAAACTTTTAATA
Found at i:34323 original size:20 final size:20
Alignment explanation
Indices: 34286--34324 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34276 TTTTTGTAGT
* *
34286 TTTTTTTTTCTATATTTTCA
1 TTTTTATTTATATATTTTCA
*
34306 TTTTTATTTATATTTTTTC
1 TTTTTATTTATATATTTTC
34325 TCTTTTCTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTATTTATATATTTTCA
Done.