Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002919.1 Kokia drynarioides strain JFW-HI SEQ_115356, 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: 53846
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 74 characters in sequence are not A, C, G, or T
Found at i:944 original size:30 final size:31
Alignment explanation
Indices: 888--945 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
878 ACGGAAAAGC
888 ACTATTTTGTCACATTTTTAAAAGTTGAGAG
1 ACTATTTTGTCACATTTTTAAAAGTTGAGAG
*
919 ACTATTTTGTCACA-TTTTCAAAGTTGA
1 ACTATTTTGTCACATTTTTAAAAGTTGA
946 TGGACTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (31 bp):
ACTATTTTGTCACATTTTTAAAAGTTGAGAG
Found at i:2574 original size:26 final size:25
Alignment explanation
Indices: 2545--2622 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
2535 TTTTCTATAA
2545 TAATATAAAAAAATTTAAAATTTAAG
1 TAATATAAAAAAA-TTAAAATTTAAG
* *
2571 TAATATGTATAAAATTAAAATTTAAG
1 TAATAT-AAAAAAATTAAAATTTAAG
*
2597 TAATATGTATAAAAATTAAAATTTAA
1 TAATA--TAAAAAAATTAAAATTTAA
2623 AAATGGATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 23 0.52
27 20 0.45
28 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (25 bp):
TAATATAAAAAAATTAAAATTTAAG
Found at i:2611 original size:27 final size:27
Alignment explanation
Indices: 2553--2622 Score: 124
Period size: 26 Copynumber: 2.6 Consensus size: 27
2543 AATAATATAA
2553 AAAAATTTAAAATTTAAGTAATATGTAT
1 AAAAA-TTAAAATTTAAGTAATATGTAT
2581 -AAAATTAAAATTTAAGTAATATGTAT
1 AAAAATTAAAATTTAAGTAATATGTAT
2607 AAAAATTAAAATTTAA
1 AAAAATTAAAATTTAA
2623 AAATGGATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.54
27 19 0.46
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (27 bp):
AAAAATTAAAATTTAAGTAATATGTAT
Found at i:4350 original size:6 final size:6
Alignment explanation
Indices: 4339--4371 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4329 TTCACTGTTT
*
4339 TTCTCC TTCTCC TTCTCC TTCTCC TTCTTC TTC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTC
4372 CTTTTTTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
TTCTCC
Found at i:14772 original size:22 final size:23
Alignment explanation
Indices: 14747--14804 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
14737 CATAAGGCAG
*
14747 AAGCGTGCCACAATGTAGA-GAA
1 AAGCGTGCCACAAGGTAGAGGAA
*
14769 AAGCGTACCACAAGGTAGAGGAA
1 AAGCGTGCCACAAGGTAGAGGAA
*
14792 AAGTGTGCCACAA
1 AAGCGTGCCACAA
14805 AAACAGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (23 bp):
AAGCGTGCCACAAGGTAGAGGAA
Found at i:16821 original size:27 final size:27
Alignment explanation
Indices: 16763--16832 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
16753 GATATTTTGG
*
16763 AGATATT-TTTTATTAATTAATTAGTT
1 AGATATTATTTTATTAATTAATTACTT
* **
16789 AAATATTATTTTATTAATTTTTTACTT
1 AGATATTATTTTATTAATTAATTACTT
16816 AGATATTTATTATTATT
1 AGATA-TTATT-TTATT
16833 TTATTTAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.17
27 20 0.56
28 5 0.14
29 5 0.14
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (27 bp):
AGATATTATTTTATTAATTAATTACTT
Found at i:16824 original size:23 final size:23
Alignment explanation
Indices: 16798--16841 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
16788 TAAATATTAT
16798 TTTATTAATT-TTTTACTTAGATA
1 TTTATT-ATTATTTTACTTAGATA
*
16821 TTTATTATTATTTTATTTAGA
1 TTTATTATTATTTTACTTAGA
16842 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
TTTATTATTATTTTACTTAGATA
Found at i:25263 original size:101 final size:103
Alignment explanation
Indices: 25068--25281 Score: 272
Period size: 106 Copynumber: 2.1 Consensus size: 103
25058 TACAGCCTAC
* *
25068 CAGGATGATGCCACTTCCATAATGATATGATCAAGCATCTCAATCACAAAAGAAAAAAAAACATA
1 CAGGATTATGCCACTCCCATAATGATATGATCAAGCATCTCAAT-AC-AAAGAAAAAAAAACATA
* *
25133 TGTGATGGATGTTAGATATCAATTACTCTACAAATGAACTG
64 TGAGATGGATGTTAGACATCAATTACTCTA-AAATGAACTG
* * ** * *
25174 CAGGATTATGTCACTCCCATAATGATATGATCAAGCATCTCAAT-C-ATG-ATGAAGAGCATATG
1 CAGGATTATGCCACTCCCATAATGATATGATCAAGCATCTCAATACAAAGAAAAAAAAACATATG
*
25236 AGATGGATGTTAGACATCAATTCCTCTAAAATGAACTG
66 AGATGGATGTTAGACATCAATTACTCTAAAATGAACTG
*
25274 CAGCATTA
1 CAGGATTA
25282 CAATATTATC
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
100 17 0.18
101 35 0.36
102 2 0.02
104 1 0.01
106 41 0.43
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (103 bp):
CAGGATTATGCCACTCCCATAATGATATGATCAAGCATCTCAATACAAAGAAAAAAAAACATATG
AGATGGATGTTAGACATCAATTACTCTAAAATGAACTG
Found at i:26888 original size:24 final size:24
Alignment explanation
Indices: 26856--26906 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
26846 GTTAAATTCA
26856 AGAAAGGACTAAGAGGTGAAACAT
1 AGAAAGGACTAAGAGGTGAAACAT
26880 AGAAAGGACTAAGAGGTGAAACAT
1 AGAAAGGACTAAGAGGTGAAACAT
26904 AGA
1 AGA
26907 TTTAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.29, T:0.12
Consensus pattern (24 bp):
AGAAAGGACTAAGAGGTGAAACAT
Found at i:27516 original size:6 final size:6
Alignment explanation
Indices: 27505--27538 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
27495 CCATCGCCTC
*
27505 CTCCGT CTCCGT CTCCGT CTCCGT CTCCGC CTCC
1 CTCCGT CTCCGT CTCCGT CTCCGT CTCCGT CTCC
27539 ACATCCATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.56, G:0.15, T:0.29
Consensus pattern (6 bp):
CTCCGT
Found at i:32609 original size:22 final size:20
Alignment explanation
Indices: 32584--32628 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
32574 ATAATTACTT
32584 ATATTAATTACACAAAATAAAA
1 ATATTAATTA-A-AAAATAAAA
* *
32606 ATATTTATTAAATAATAAAA
1 ATATTAATTAAAAAATAAAA
32626 ATA
1 ATA
32629 ATTATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 9 0.43
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATTAATTAAAAAATAAAA
Found at i:43177 original size:2 final size:2
Alignment explanation
Indices: 43170--43199 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43160 ATTTAGTATC
43170 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
43200 TAATTTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43853 original size:17 final size:18
Alignment explanation
Indices: 43822--43855 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43812 GGAAAAAGTA
*
43822 ATTACAAAAATATGAAAG
1 ATTACAAAAAGATGAAAG
43840 ATTA-AAAAAGATGAAA
1 ATTACAAAAAGATGAAA
43856 AGTTAAAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.21
Consensus pattern (18 bp):
ATTACAAAAAGATGAAAG
Found at i:45202 original size:97 final size:97
Alignment explanation
Indices: 45017--45210 Score: 248
Period size: 97 Copynumber: 2.0 Consensus size: 97
45007 AACTTTGGAA
* *
45017 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTAGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATAGCACCTAGTAAGTTAAAGCACAAATTTTCA
* * *
45082 GAATCAGAGATAAAGGAACATTGCTTCGATTT
66 AAATCAGAAATAAAGGAACATTGCCTCGATTT
* * * * * *
45114 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGTACTTAGTAAGTTAAAGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATAGCACCTAGTAAGTTAAAGCACAAATTTTCA
*
45179 AAACTC-GAAATAGAA-GAATATTGCCTCGATTT
66 AAA-TCAGAAATA-AAGGAACATTGCCTCGATTT
45211 TAAAGTTTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
97 79 0.95
98 4 0.05
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATAGCACCTAGTAAGTTAAAGCACAAATTTTCA
AAATCAGAAATAAAGGAACATTGCCTCGATTT
Found at i:45505 original size:29 final size:28
Alignment explanation
Indices: 45469--45768 Score: 181
Period size: 29 Copynumber: 10.3 Consensus size: 28
45459 GGTCACTCGA
*
45469 GGGGCAAAATGGTAATTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTGGAAAGTTC
*
45497 GGGGTCAAAAATAG-AATTTTTGG-AAGTTC
1 GGGGT--AAAATGGTAA-TTTTGGAAAGTTC
* * *
45526 GGGGTCAAATGATAATTTTTGGAAA-ATC
1 GGGGTAAAATGGTAA-TTTTGGAAAGTTC
* *
45554 GGGGTACAAAT-GAAATCTTTGGAAAAATT-
1 GGGGTA-AAATGGTAAT-TTTGG-AAAGTTC
**
45583 GAGGGTAAAATGGTAATTTTTTGGAAAAATC
1 G-GGGTAAAATGGTAA--TTTTGGAAAGTTC
*
45614 GAGGTACAAATGG-AATCTTTGG-AAGTTC
1 GGGGTA-AAATGGTAAT-TTTGGAAAGTTC
45642 AGGGGTAAAATGGTAATTTTTTGGAAA--TC
1 -GGGGTAAAATGGTAA--TTTTGGAAAGTTC
* *
45671 AGGGTTAAAAATGG-AATTTTGGAAAGTTTA
1 -GGGGT-AAAATGGTAATTTTGGAAAG-TTC
* *
45701 GGTGTAAAATGGTAATTTTTGGAAAGATTA
1 GGGGTAAAATGGTAA-TTTTGGAAAG-TTC
* *
45731 GGGTTAAAAATGG-AATTTTGGAAAGTTTA
1 GGGGT-AAAATGGTAATTTTGGAAAG-TTC
45760 GGGGTAAAA
1 GGGGTAAAA
45769 AATGTATTTT
Statistics
Matches: 219, Mismatches: 25, Indels: 56
0.73 0.08 0.19
Matches are distributed among these distances:
27 14 0.06
28 49 0.22
29 70 0.32
30 63 0.29
31 22 0.10
32 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTC
Found at i:45651 original size:59 final size:58
Alignment explanation
Indices: 45468--45836 Score: 307
Period size: 59 Copynumber: 6.3 Consensus size: 58
45458 TGGTCACTCG
* ** * *
45468 AGGGGCAAAATGGTAA-TTTTGGAAAGTTCGGGGTCAAAAATAGAATTTTTGG-AAGTTC
1 AGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGT-AAAAATGGAA-TTTTGGAAAGTTC
* * * * * * *
45526 -GGGGTCAAATGATAATTTTTGG-AAAATCGGGGTACAAATGAAATCTTTGGAAAAATTG
1 AGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAATGGAAT-TTTGG-AAAGTTC
*
45584 A-GGGTAAAATGGTAATTTTTTGGAAAAATCGAGGTACAAATGGAATCTTTGG-AAGTTC
1 AGGGGTAAAATGGTAA-TTTTTGGAAAAATCGAGGTAAAAATGGAAT-TTTGGAAAGTTC
*
45642 AGGGGTAAAATGGTAATTTTTTGG--AAATC-AGGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAA-TTTTTGGAAAAATCGA-GG-TAAAAATGGAATTTTGGAAAGTTC
* * * *
45700 AGGTGTAAAATGGTAATTTTTGGAAAGAT-TAGGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGAAAAATCGA-GG-TAAAAATGGAATTTTGGAAAGTTC
* *
45759 AGGGGTAAAAAAT-GT-ATTTTTGGAAAAAT-TAGTGTCAAAAATGGAATTTCGGAAAGTTC
1 AGGGGT--AAAATGGTAATTTTTGGAAAAATCGAG-GT-AAAAATGGAATTTTGGAAAGTTC
**
45818 AATGGTAAAAT-GTAATTTT
1 AGGGGTAAAATGGTAATTTT
45837 CAAAAGGTTT
Statistics
Matches: 266, Mismatches: 26, Indels: 38
0.81 0.08 0.12
Matches are distributed among these distances:
55 1 0.00
56 13 0.05
57 47 0.18
58 65 0.24
59 107 0.40
60 28 0.11
61 5 0.02
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.32
Consensus pattern (58 bp):
AGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAATGGAATTTTGGAAAGTTC
Found at i:45670 original size:117 final size:115
Alignment explanation
Indices: 45474--45785 Score: 334
Period size: 117 Copynumber: 2.7 Consensus size: 115
45464 CTCGAGGGGC
* * * *
45474 AAAATGGTAA-TTTTGGAAAGTTCGGGGTCAAAAATAGAATTTTTGGAAGTTC-GGGGTCAAATG
1 AAAATGGTAATTTTTGGAAAGATCGAGGT-AAAAATGGAA-TTTTGGAAGTTCAGGGGTAAAATG
*
45537 ATAATTTTTGGAAAATC-GGGGTACAAATGAAATCTTTGGAAAAATTGAGG-GT
64 ATAATTTTTGGAAAATCAGGGGTAAAAATGAAAT-TTTGG-AAAATTGAGGTGT
* *
45589 AAAATGGTAATTTTTTGGAAAAATCGAGGTACAAATGGAATCTTTGGAAGTTCAGGGGTAAAATG
1 AAAATGGTAA-TTTTTGGAAAGATCGAGGTAAAAATGGAAT-TTTGGAAGTTCAGGGGTAAAATG
* * * * *
45654 GTAATTTTTTGG-AAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGTGT
64 ATAA-TTTTTGGAAAATCAGGGGTAAAAATGAAATTTTGGAAAATTGAGGTGT
* *
45706 AAAATGGTAATTTTTGGAAAGAT-TAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAA
1 AAAATGGTAATTTTTGGAAAGATCGA-GG-TAAAAATGGAATTTTGG-AAGTTCAGGGGT--AAA
45770 ATG-T-ATTTTTGGAAAA
61 ATGATAATTTTTGGAAAA
45786 ATTAGTGTCA
Statistics
Matches: 168, Mismatches: 16, Indels: 24
0.81 0.08 0.12
Matches are distributed among these distances:
115 12 0.07
116 53 0.32
117 76 0.45
118 21 0.12
119 6 0.04
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (115 bp):
AAAATGGTAATTTTTGGAAAGATCGAGGTAAAAATGGAATTTTGGAAGTTCAGGGGTAAAATGAT
AATTTTTGGAAAATCAGGGGTAAAAATGAAATTTTGGAAAATTGAGGTGT
Found at i:45769 original size:29 final size:29
Alignment explanation
Indices: 45616--45880 Score: 177
Period size: 30 Copynumber: 9.0 Consensus size: 29
45606 GAAAAATCGA
* *
45616 GGTACAAATGGAATCTTTGG-AAGTTCAGG
1 GGTAAAAATGGAAT-TTTGGAAAGTTTAGG
*
45645 GGT-AAAATGGTAATTTTTTGGAAA--TCAGG
1 GGTAAAAATGG-AA--TTTTGGAAAGTTTAGG
*
45674 GTTAAAAATGGAATTTTGGAAAGTTTAGG
1 GGTAAAAATGGAATTTTGGAAAGTTTAGG
* *
45703 TGT-AAAATGGTAATTTTTGGAAAGATTAGG
1 GGTAAAAATGG-AA-TTTTGGAAAGTTTAGG
*
45733 GTTAAAAATGGAATTTTGGAAAGTTTAGG
1 GGTAAAAATGGAATTTTGGAAAGTTTAGG
* * **
45762 GGTAAAAAATGTATTTTTGGAAAAATTA-G
1 GGT-AAAAATGGAATTTTGGAAAGTTTAGG
* * * **
45791 TGTCAAAAATGGAATTTCGGAAAGTTCAAT
1 GGT-AAAAATGGAATTTTGGAAAGTTTAGG
* **
45821 GGT-AAAATGTAATTTTCAAAAGGTTT-GG
1 GGTAAAAATGGAATTTTGGAAA-GTTTAGG
* * *
45849 GGTCTAAAATGAAATTTTAGAAAAGTTTAGG
1 GGT-AAAAATGGAATTTT-GGAAAGTTTAGG
45880 G
1 G
45881 ATCAAAAGAT
Statistics
Matches: 186, Mismatches: 33, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
27 9 0.05
28 30 0.16
29 62 0.33
30 68 0.37
31 17 0.09
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
GGTAAAAATGGAATTTTGGAAAGTTTAGG
Found at i:47053 original size:13 final size:12
Alignment explanation
Indices: 47017--47057 Score: 50
Period size: 10 Copynumber: 3.5 Consensus size: 12
47007 TTCCCTTTTT
47017 TTATTAATAATA
1 TTATTAATAATA
*
47029 CTATT--TAATA
1 TTATTAATAATA
47039 TTATTAATAATTA
1 TTATTAATAA-TA
47052 TTATTA
1 TTATTA
47058 GTTCTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 9 0.38
12 7 0.29
13 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATTAATAATA
Found at i:47087 original size:22 final size:21
Alignment explanation
Indices: 47016--47089 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
47006 TTTCCCTTTT
* *
47016 TTTATTAATAA-TACTATTTAA
1 TTTATTTATAATTATTA-TTAA
* *
47037 TATTATTAATAATTATTATTAG
1 T-TTATTTATAATTATTATTAA
*
47059 TTCTATTTATTATTATTATTAA
1 TT-TATTTATAATTATTATTAA
47081 TGTTATTTA
1 T-TTATTTA
47090 AAGAAATTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.05
22 37 0.84
23 5 0.11
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTATTTATAATTATTATTAA
Found at i:47814 original size:17 final size:17
Alignment explanation
Indices: 47746--47840 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
47736 TGGATTTTTT
* *
47746 AATTTGAAATAAATTCGA
1 AATTTAAAATAAATT-TA
*
47764 ATTTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* * * *
47781 AACTCAAAGTAAGTTTA
1 AATTTAAAATAAATTTA
47798 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* * *
47815 AATTTAAAAGAAAATAA
1 AATTTAAAATAAATTTA
47832 AATTTAAAA
1 AATTTAAAA
47841 ACAATTCACA
Statistics
Matches: 62, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
17 49 0.79
18 13 0.21
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:48774 original size:26 final size:26
Alignment explanation
Indices: 48721--48771 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
48711 AATAAGTTAT
* *
48721 CTTATTTAAATATATAATTTTATTAA
1 CTTATTTAAATATATAAATTAATTAA
48747 CTTATTTAAATATA-AAATTAATTAA
1 CTTATTTAAATATATAAATTAATTAA
48772 ACTCTATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (26 bp):
CTTATTTAAATATATAAATTAATTAA
Found at i:49592 original size:16 final size:17
Alignment explanation
Indices: 49571--49603 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
49561 ATGATTAAAA
*
49571 TTATTTTATAA-AATAT
1 TTATTTCATAATAATAT
49587 TTATTTCATAATAATAT
1 TTATTTCATAATAATAT
49604 AATGATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTCATAATAATAT
Found at i:50554 original size:13 final size:13
Alignment explanation
Indices: 50536--50561 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50526 TTTTATTCAT
50536 AAGAAAAAAAAAA
1 AAGAAAAAAAAAA
50549 AAGAAAAAAAAAA
1 AAGAAAAAAAAAA
50562 GGAATAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAAA
Found at i:51023 original size:24 final size:24
Alignment explanation
Indices: 50996--51074 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
50986 CAAAGAACAT
*
50996 AAAAGGAAAAAAATTAAATTGCTC
1 AAAACGAAAAAAATTAAATTGCTC
*
51020 AAAACGAAAAAAA--GAA---CAT-
1 AAAACGAAAAAAATTAAATTGC-TC
*
51039 AAAAGGAAAAAAATTAAATTGCTC
1 AAAACGAAAAAAATTAAATTGCTC
51063 AAAACGAAAAAA
1 AAAACGAAAAAA
51075 TTATAAGGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
19 13 0.30
20 1 0.02
21 2 0.05
22 2 0.05
23 1 0.02
24 24 0.56
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.14
Consensus pattern (24 bp):
AAAACGAAAAAAATTAAATTGCTC
Found at i:51034 original size:43 final size:43
Alignment explanation
Indices: 50987--51074 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
50977 AGAAAAGTTC
50987 AAAGAACATAAAAGGAAAAAAATTAAATTGCTCAAAACGAAAA
1 AAAGAACATAAAAGGAAAAAAATTAAATTGCTCAAAACGAAAA
51030 AAAGAACATAAAAGGAAAAAAATTAAATTGCTCAAAACGAAAA
1 AAAGAACATAAAAGGAAAAAAATTAAATTGCTCAAAACGAAAA
51073 AA
1 AA
51075 TTATAAGGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.14
Consensus pattern (43 bp):
AAAGAACATAAAAGGAAAAAAATTAAATTGCTCAAAACGAAAA
Found at i:51400 original size:4 final size:4
Alignment explanation
Indices: 51391--51421 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
51381 AATTGAAGCA
51391 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
51422 ATACATGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Done.