Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014607.1 Kokia drynarioides strain JFW-HI SEQ_129646, 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: 74927
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:1485 original size:18 final size:18
Alignment explanation
Indices: 1462--1496 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1452 ACCAAAACTT
1462 TATTTTAAATTTT-TTATA
1 TATTTT-AATTTTATTATA
1480 TATTTTAATTTTATTAT
1 TATTTTAATTTTATTAT
1497 GCACATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTAATTTTATTATA
Found at i:1995 original size:21 final size:21
Alignment explanation
Indices: 1969--2008 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1959 ATTATTTATT
1969 ATATGTTATTTTAAA-ACATAA
1 ATATG-TATTTTAAATACATAA
*
1990 ATATGTGTTTTAAATACAT
1 ATATGTATTTTAAATACAT
2009 GCATGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATGTATTTTAAATACATAA
Found at i:2706 original size:16 final size:16
Alignment explanation
Indices: 2685--2715 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2675 TTTTTTTAAA
*
2685 AAATTCATCAAATTAT
1 AAATTCATAAAATTAT
2701 AAATTCATAAAATTA
1 AAATTCATAAAATTA
2716 AATTTTAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTCATAAAATTAT
Found at i:3312 original size:21 final size:21
Alignment explanation
Indices: 3288--3334 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3278 AGGTTTAAAA
*
3288 TTTTAAAATTAGGGTTTAGGT
1 TTTTAAAATTAGAGTTTAGGT
* *
3309 TTTTTAAATTAGAGTTTTGGT
1 TTTTAAAATTAGAGTTTAGGT
*
3330 ATTTA
1 TTTTA
3335 TTTTATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (21 bp):
TTTTAAAATTAGAGTTTAGGT
Found at i:4602 original size:21 final size:21
Alignment explanation
Indices: 4578--4628 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
4568 CAAAGTGAAC
*
4578 CAAATCCAATTGAACCAAGTT
1 CAAACCCAATTGAACCAAGTT
**
4599 CAAACCCAATTGAACCAAGAC
1 CAAACCCAATTGAACCAAGTT
4620 CAAACCCAA
1 CAAACCCAA
4629 ACCAAGTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.31, G:0.08, T:0.14
Consensus pattern (21 bp):
CAAACCCAATTGAACCAAGTT
Found at i:4657 original size:11 final size:11
Alignment explanation
Indices: 4641--4682 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
4631 CAAGTCAAAT
4641 CGTTGACCGAC
1 CGTTGACCGAC
* *
4652 CGTTGATCGAT
1 CGTTGACCGAC
*
4663 CGCTGACCGAC
1 CGTTGACCGAC
4674 CGTTGACCG
1 CGTTGACCG
4683 GCCATTAACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (11 bp):
CGTTGACCGAC
Found at i:5811 original size:14 final size:14
Alignment explanation
Indices: 5788--5821 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5778 AATTTACATC
* *
5788 ATTTTATTATTATT
1 ATTTTGTTATTAAT
5802 ATTTTGTTATTAAT
1 ATTTTGTTATTAAT
5816 ATTTTG
1 ATTTTG
5822 GTTTTGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
ATTTTGTTATTAAT
Found at i:11757 original size:21 final size:21
Alignment explanation
Indices: 11733--11773 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
11723 CCAAAGTGAA
11733 CCAAATCCAATTGAACCAAGT
1 CCAAATCCAATTGAACCAAGT
*
11754 CCAAATCTAATTGAACCAAG
1 CCAAATCCAATTGAACCAAG
11774 ACTAAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.20
Consensus pattern (21 bp):
CCAAATCCAATTGAACCAAGT
Found at i:11812 original size:11 final size:11
Alignment explanation
Indices: 11795--11844 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
11785 ACCAAGTCAA
11795 ACCGTTGATCG
1 ACCGTTGATCG
* *
11806 GCCGTTGACCG
1 ACCGTTGATCG
11817 ACCGTTGATCG
1 ACCGTTGATCG
* *
11828 ATCGTTGACCG
1 ACCGTTGATCG
11839 ACCGTT
1 ACCGTT
11845 AACTGTTGAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (11 bp):
ACCGTTGATCG
Found at i:11823 original size:22 final size:22
Alignment explanation
Indices: 11795--11844 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
11785 ACCAAGTCAA
*
11795 ACCGTTGATCGGCCGTTGACCG
1 ACCGTTGATCGACCGTTGACCG
*
11817 ACCGTTGATCGATCGTTGACCG
1 ACCGTTGATCGACCGTTGACCG
11839 ACCGTT
1 ACCGTT
11845 AACTGTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (22 bp):
ACCGTTGATCGACCGTTGACCG
Found at i:12959 original size:14 final size:14
Alignment explanation
Indices: 12936--12969 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12926 AATTTACATC
* *
12936 ATTTTATTATTATT
1 ATTTTGTTATTAAT
12950 ATTTTGTTATTAAT
1 ATTTTGTTATTAAT
12964 ATTTTG
1 ATTTTG
12970 GTTTTGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
ATTTTGTTATTAAT
Found at i:15561 original size:25 final size:25
Alignment explanation
Indices: 15533--15583 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
15523 TCTTGTATAT
*
15533 TTTAATTTTGAATAGGGTATTCAAC
1 TTTAATTTTAAATAGGGTATTCAAC
15558 TTTAATTTTAAATAGGGTATTCAAC
1 TTTAATTTTAAATAGGGTATTCAAC
15583 T
1 T
15584 GTCTCTGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (25 bp):
TTTAATTTTAAATAGGGTATTCAAC
Found at i:16299 original size:26 final size:25
Alignment explanation
Indices: 16247--16300 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
16237 ACAACAAGAT
***
16247 AAATAAACAAAAAAATTAAATGCTA
1 AAATAAACAAAAAAATTAAACAATA
*
16272 AAATAAACAAACAAATATAAACAATA
1 AAATAAACAAAAAAAT-TAAACAATA
16298 AAA
1 AAA
16301 ATAATTGGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (25 bp):
AAATAAACAAAAAAATTAAACAATA
Found at i:16354 original size:15 final size:15
Alignment explanation
Indices: 16320--16361 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16310 ATTAGGCATG
*
16320 AAAATAAAT-GACAA
1 AAAATAAATAAACAA
16334 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
16350 AAAATCAATAAA
1 AAAATAAATAAA
16362 TTAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:17156 original size:44 final size:43
Alignment explanation
Indices: 17090--17311 Score: 166
Period size: 43 Copynumber: 5.2 Consensus size: 43
17080 GGTGTTGTAA
* * *
17090 CTTCAATCTGCCCCTCTAGATTAGTAGTAAGAGATTGAATGATGG
1 CTTCAATTTG-CCCTCTAGATTAG-AGTAAAAGATTGAATGGTGG
* * * *
17135 CTTCAGTTTGCCCTCTGGATTAG-GATAAAAGATTGGATGGTTG
1 CTTCAATTTGCCCTCTAGATTAGAG-TAAAAGATTGAATGGTGG
* * * * *
17178 CTTCAATCTGCCTTCTAGATTAGGGTAAAAGATTAAATGGGTGA
1 CTTCAATTTGCCCTCTAGATTAGAGTAAAAGATTGAAT-GGTGG
* * * * *
17222 CTTCAATTTGCCCTTTGGATAAGGGTAAAAGATTTG-ATAGTGG
1 CTTCAATTTGCCCTCTAGATTAGAGTAAAAGA-TTGAATGGTGG
* * * * *
17265 CTTCAATCTGTCCTTTGGATTAGGGTAAAAGATT--A-GGTGG
1 CTTCAATTTGCCCTCTAGATTAGAGTAAAAGATTGAATGGTGG
17305 CTTCAAT
1 CTTCAAT
17312 CTACCCCATG
Statistics
Matches: 146, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
40 11 0.08
41 1 0.01
42 3 0.02
43 76 0.52
44 45 0.31
45 10 0.07
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.34
Consensus pattern (43 bp):
CTTCAATTTGCCCTCTAGATTAGAGTAAAAGATTGAATGGTGG
Found at i:17182 original size:43 final size:43
Alignment explanation
Indices: 17090--17910 Score: 353
Period size: 42 Copynumber: 19.9 Consensus size: 43
17080 GGTGTTGTAA
* * * *
17090 CTTCAATCTGCCCCTCTAGATTAGTAGTAAGAGATTGAATGATGG
1 CTTCAATCTG-CCCTCTGGATTAG-GGTAAAAGATTGAATGGTGG
* * * * *
17135 CTTCAGTTTGCCCTCTGGATTAGGATAAAAGATTGGATGGTTG
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
* * * *
17178 CTTCAATCTGCCTTCTAGATTAGGGTAAAAGATTAAATGGGTGA
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAAT-GGTGG
* * * *
17222 CTTCAATTTGCCCTTTGGATAAGGGTAAAAGATTTG-ATAGTGG
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGA-TTGAATGGTGG
* *
17265 CTTCAATCTGTCCTTTGGATTAGGGTAAAAGATT--A-GGTGG
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
* * * *
17305 CTTCAATCTACCC-CATGG--TAGAGGTAAGAGATTGGATGGTGT
1 CTTCAATCTGCCCTC-TGGATTAG-GGTAAAAGATTGAATGGTGG
* * *
17347 TTTCAATCTGCCCTCCGG-TTAGGGTAAAAGATTG---GATGG
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
* * * * * *
17386 CTTCAATTTGCCC-CGTGG--TCGAGGTAAAATATTGGATAGTGT
1 CTTCAATCTGCCCTC-TGGATTAG-GGTAAAAGATTGAATGGTGG
* * *
17428 CTTCAATCTGCTCTCTTG-TTAGGGTAAAAGATTGGATGGT--
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
** * *
17468 -TTCAATCTGCCC-CATGG-TCGGGGTAAAAGATTG---GATGA
1 CTTCAATCTGCCCTC-TGGATTAGGGTAAAAGATTGAATGGTGG
* * * * * *
17506 CTTCAATTTACCC-CATGG-TT-GGGATAAGAGATTGGATGATGT
1 CTTCAATCTGCCCTC-TGGATTAGGG-TAAAAGATTGAATGGTGG
* * ** * * *
17548 TTTCAATTTGCCCTCT-TTTTAGGGTAAAATATTG---GATGA
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
* * * *
17587 CTTCAATCTGTCCC-ATGG-TTGGGGTAAAAGATTGGATGGTGT
1 CTTCAATCTG-CCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
* * * * *
17629 TTTTAATCTGCCCTCT-TATTAGAGTAAAAGATTG---GATGG
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
* * * *
17668 CTTCAATCTGCCC-CATGG-TT-GAGGTAAGAGATTGGATGATGT
1 CTTCAATCTGCCCTC-TGGATTAG-GGTAAAAGATTGAATGGTGG
* * *
17710 CTTCAATCTACCCTCTTG-TTAGGGTAAAAGATTGAA---TGA
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
* * * * * *
17749 CTTCAATCTACCC-CATGG-TTGGGGTAAGATATTGGATGGTGT
1 CTTCAATCTGCCCTC-TGGATTAGGGTAAAAGATTGAATGGTGG
* * *
17791 CTTCAATCTGCCCTCTTG-TTAGAGTAAAAGATTG---GATGG
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
* * * * *
17830 CTTCAATTTTCCC-CATGG-TTGGGGTAAGAGATT-AGATGGTGT
1 CTTCAATCTGCCCTC-TGGATTAGGGTAAAAGATTGA-ATGGTGG
* * *
17872 CTTCAATCTGCCCTCTTG-TTAGAGTAAAAGATTGGATGG
1 CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGG
17911 CTTGAATATG
Statistics
Matches: 595, Mismatches: 127, Indels: 111
0.71 0.15 0.13
Matches are distributed among these distances:
36 2 0.00
38 14 0.02
39 202 0.34
40 21 0.04
41 5 0.01
42 205 0.34
43 92 0.15
44 44 0.07
45 10 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (43 bp):
CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGAATGGTGG
Found at i:17232 original size:87 final size:87
Alignment explanation
Indices: 17090--17460 Score: 274
Period size: 81 Copynumber: 4.4 Consensus size: 87
17080 GGTGTTGTAA
* * * * * *
17090 CTTCAATCTGCCCCTCTAGATTAGTAGTAAGAGATTGAATGATGGCTTCAGTTTGCCCTCTGGAT
1 CTTCAATCTGCCCTTCTAGATTAG-GGTAAAAGATTAAATGATGACTTCAATTTGCCCTCTGGAT
* * *
17155 TAGGATAAAAGATTGGATGGTTG
65 AAGGATAAAAGATTGGATAGTGG
* *
17178 CTTCAATCTG-CCTTCTAGATTAGGGTAAAAGATTAAATGGGTGACTTCAATTTGCCCTTTGGAT
1 CTTCAATCTGCCCTTCTAGATTAGGGTAAAAGATTAAAT-GATGACTTCAATTTGCCCTCTGGAT
* *
17242 AAGGGTAAAAGATTTGATAGTGG
65 AAGGATAAAAGATTGGATAGTGG
* * * * * *
17265 CTTCAATCTGTCCTT-TGGATTAGGGTAAAAGATT--A-GGTGGCTTCAATCTACCC-CATGG-T
1 CTTCAATCTGCCCTTCTAGATTAGGGTAAAAGATTAAATGATGACTTCAATTTGCCCTC-TGGAT
* * *
17324 AGAGG-TAAGAGATTGGATGGTGT
65 A-AGGATAAAAGATTGGATAGTGG
* * * * *
17347 TTTCAATCTGCCC-TC-CGGTTAGGGTAAAAGATT---GGATGGCTTCAATTTGCCC-CGTGG-T
1 CTTCAATCTGCCCTTCTAGATTAGGGTAAAAGATTAAATGATGACTTCAATTTGCCCTC-TGGAT
* * *
17405 CGAGG-TAAAATATTGGATAGTGT
65 -AAGGATAAAAGATTGGATAGTGG
* *
17428 CTTCAATCTGCTC-TCTTG-TTAGGGTAAAAGATT
1 CTTCAATCTGCCCTTCTAGATTAGGGTAAAAGATT
17461 GGATGGTTTC
Statistics
Matches: 238, Mismatches: 37, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
81 83 0.35
82 28 0.12
83 21 0.09
85 1 0.00
86 12 0.05
87 79 0.33
88 14 0.06
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.33
Consensus pattern (87 bp):
CTTCAATCTGCCCTTCTAGATTAGGGTAAAAGATTAAATGATGACTTCAATTTGCCCTCTGGATA
AGGATAAAAGATTGGATAGTGG
Found at i:17387 original size:81 final size:81
Alignment explanation
Indices: 17160--17989 Score: 360
Period size: 81 Copynumber: 10.2 Consensus size: 81
17150 TGGATTAGGA
* * * *
17160 TAAAAGATTGGATGGT-TGCTTCAATCTGCCTTCTAGATTAGGGTAAAAGATTAAATGGGTGACT
1 TAAAAGATTGGATGGTGT-CTTCAATCTGCCCTCT-GGTTAGGGTAAAAGA-T---TGGATGGCT
* ** *
17224 TCAATTTGCCCTTTGGAT-AAGGG
60 TCAATCTGCCCCATGG-TCGA-GG
* * * * *
17247 TAAAAGATTTGATAGTGGCTTCAATCTGTCCTTTGGATTAGGGTAAAAGATTAGG-TGGCTTCAA
1 TAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTGG-TTAGGGTAAAAGATT-GGATGGCTTCAA
* *
17311 TCTACCCCATGGTAGAGG
64 TCTGCCCCATGGTCGAGG
* * * *
17329 TAAGAGATTGGATGGTGTTTTCAATCTGCCCTCCGGTTAGGGTAAAAGATTGGATGGCTTCAATT
1 TAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATC
*
17394 TGCCCCGTGGTCGAGG
66 TGCCCCATGGTCGAGG
* * * * *
17410 TAAAATATTGGATAGTGTCTTCAATCTGCTCTCTTGTTAGGGTAAAAGATTGGATGGTTTCAATC
1 TAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATC
*
17475 TGCCCCATGGTCGGGG
66 TGCCCCATGGTCGAGG
* * * * *
17491 TAAAAGATTGGA---TGACTTCAATTTACCC-CATGGTT-GGGATAAGAGATTGGATGATGTTTT
1 TAAAAGATTGGATGGTGTCTTCAATCTGCCCTC-TGGTTAGGG-TAAAAGATTGGATG--G-CTT
* * ** *
17551 CAATTTGCCCTCTTTTTAG-GG
61 CAATCTGCCC-CATGGTCGAGG
* * * * * *
17572 TAAAATATTGGA---TGACTTCAATCTGTCCC-ATGGTTGGGGTAAAAGATTGGATGGTGTTTTT
1 TAAAAGATTGGATGGTGTCTTCAATCTG-CCCTCTGGTTAGGGTAAAAGATTGGAT-G-G-CTTC
* ** *
17633 AATCTGCCCTCTTATTAGA-G
62 AATCTGCCC-CATGGTCGAGG
*
17653 TAAAAGATTGGAT-G-G-CTTCAATCTGCCC-CATGGTT-GAGGTAAGAGATTGGATGATGTCTT
1 TAAAAGATTGGATGGTGTCTTCAATCTGCCCTC-TGGTTAG-GGTAAAAGATTGGATG--G-CTT
* * * *
17713 CAATCTACCCTCTTGTTAG-GG
61 CAATCTGCCC-CATGGTCGAGG
* * * * * *
17734 TAAAAGATT-GA--ATGACTTCAATCTACCC-CATGGTTGGGGTAAGATATTGGATGGTGTCTTC
1 TAAAAGATTGGATGGTGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGAT-G-G-CTTC
* * *
17795 AATCTGCCCTCTTGTTAGA-G
62 AATCTGCCC-CATGGTCGAGG
* * * * *
17815 TAAAAGATTGGAT-G-G-CTTCAATTTTCCC-CATGGTTGGGGTAAGAGATTAGATGGTGTCTTC
1 TAAAAGATTGGATGGTGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGAT-G-G-CTTC
* * *
17876 AATCTGCCCTCTTGTTAGA-G
62 AATCTGCCC-CATGGTCGAGG
* * * * *
17896 TAAAAGATTGGAT-G-G-CTTGAATATGCTCC-ATGGTTGGGGTAAGAGATTGGATGGTATCTTC
1 TAAAAGATTGGATGGTGTCTTCAATCTGC-CCTCTGGTTAGGGTAAAAGATTGGATGG---CTTC
* * *
17957 AATCTACCCCATGATTGAGG
62 AATCTGCCCCATGGTCGAGG
*
17977 TAAGAGATTGGAT
1 TAAAAGATTGGAT
17990 AGATGATGTA
Statistics
Matches: 629, Mismatches: 82, Indels: 70
0.81 0.10 0.09
Matches are distributed among these distances:
77 4 0.01
78 29 0.05
79 1 0.00
80 18 0.03
81 465 0.74
82 50 0.08
83 18 0.03
84 2 0.00
86 2 0.00
87 40 0.06
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (81 bp):
TAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATC
TGCCCCATGGTCGAGG
Found at i:17520 original size:201 final size:201
Alignment explanation
Indices: 17287--17748 Score: 579
Period size: 201 Copynumber: 2.3 Consensus size: 201
17277 CTTTGGATTA
* *
17287 GGGTAAAAGATTAGG-TGGCTTCAATCTACCCCATGGTAGAGG-TAAGAGATTGGATGGTGTTTT
1 GGGTAAAAGATT-GGATGACTTCAATCTACCCCATGGTAG-GGATAAGAGATTGGATGATGTTTT
* * *
17350 CAATCTGCCCTCCGGTTAGGGTAAAAGATTGGATGGCTTCAATTTGCCCCGTGGTCGAGGTAAAA
64 CAATCTGCCCTCCGGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGAGGTAAAA
* * * * *
17415 TATTGGATAGTGTCTTCAATCTGCTCTCTTGTTAGGGTAAAAGATTGGATGGTTTCAATCTGCCC
129 GATTGGATAGTGTCTTCAATCTGCCCTCTTATTAGAGTAAAAGATTGGATGGCTTCAATCTGCCC
17480 CATGGTCG
194 CATGGTCG
* *
17488 GGGTAAAAGATTGGATGACTTCAATTTACCCCATGGTTGGGATAAGAGATTGGATGATGTTTTCA
1 GGGTAAAAGATTGGATGACTTCAATCTACCCCATGGTAGGGATAAGAGATTGGATGATGTTTTCA
* *** * * * *
17553 ATTTGCCCTCTTTTTAGGGTAAAATATTGGATGACTTCAATCTGTCCCATGGTTGGGGTAAAAGA
66 ATCTGCCCTCCGGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGAGGTAAAAGA
* * *
17618 TTGGATGGTGTTTTTAATCTGCCCTCTTATTAGAGTAAAAGATTGGATGGCTTCAATCTGCCCCA
131 TTGGATAGTGTCTTCAATCTGCCCTCTTATTAGAGTAAAAGATTGGATGGCTTCAATCTGCCCCA
*
17683 TGGTTG
196 TGGTCG
* * * * * *
17689 AGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCTTGTTAGGG-TAAAAGATTGAATGA
1 GGGTAAAAGATTGGATGA---CTTCAATCTACCC-CATGGTAGGGATAAGAGATTGGATGA
17749 CTTCAATCTA
Statistics
Matches: 223, Mismatches: 32, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
200 4 0.02
201 187 0.84
204 25 0.11
205 7 0.03
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (201 bp):
GGGTAAAAGATTGGATGACTTCAATCTACCCCATGGTAGGGATAAGAGATTGGATGATGTTTTCA
ATCTGCCCTCCGGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGAGGTAAAAGA
TTGGATAGTGTCTTCAATCTGCCCTCTTATTAGAGTAAAAGATTGGATGGCTTCAATCTGCCCCA
TGGTCG
Found at i:17555 original size:162 final size:161
Alignment explanation
Indices: 17243--17989 Score: 652
Period size: 162 Copynumber: 4.6 Consensus size: 161
17233 CCTTTGGATA
* * * * *
17243 AGGGTAAAAGATTTGATAGTGGCTTCAATCTG-TCCTTTGGATTAGGGTAAAAGATTAGG-TGGC
1 AGGGTAAAAGATTGGATAGTGACTTCAATCTGCTCC-ATGG-TTGGGGTAAAAGATT-GGATGGT
* * * * * *
17306 TTCAATCTACCCCATGGTAGAGGTAAGAGATTGGATGGTGTTTTCAATCTGCCCTC-CGGTTAGG
63 TTCAATCTGCCCCATGGTTGGGGTAAAAGATTGGAT-G-G-CTTCAATCTGCCC-CATGGTT-GG
* * * *
17370 GTAAAAGATTGGATG--G-CTTCAATTTGCCC-CGTGGT
123 GTAAGAGATTGGATGATGTCTTCAATCTGCCCTCTTGTT
* * * * *
17405 CGAGGTAAAATATTGGATAGTGTCTTCAATCTGCTCTC-TTGTTAGGGTAAAAGATTGGATGGTT
1 AG-GGTAAAAGATTGGATAGTGACTTCAATCTGCTC-CATGGTTGGGGTAAAAGATTGGATGGTT
* * * *
17469 TCAATCTGCCCCATGGTCGGGGTAAAAGATTGGATGACTTCAATTTACCCCATGGTTGGGATAAG
64 TCAATCTGCCCCATGGTTGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTTGGG-TAAG
* * *
17534 AGATTGGATGATGTTTTCAATTTGCCCTCTTTTT
128 AGATTGGATGATGTCTTCAATCTGCCCTCTTGTT
*
17568 AGGGTAAAATATTGG--A-TGACTTCAATCTG-TCCCATGGTTGGGGTAAAAGATTGGATGGTGT
1 AGGGTAAAAGATTGGATAGTGACTTCAATCTGCT-CCATGGTTGGGGTAAAAGATTGGAT-G-G-
* ** * *
17629 TTTTAATCTGCCCTC-TTATTAGAGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTTGAGGT
62 TTTCAATCTGCCC-CATGGTTGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTTG-GGT
*
17693 AAGAGATTGGATGATGTCTTCAATCTACCCTCTTGTT
125 AAGAGATTGGATGATGTCTTCAATCTGCCCTCTTGTT
* * * *
17730 AGGGTAAAAGATT-GA-A-TGACTTCAATCTACCCCATGGTTGGGGTAAGATATTGGATGGTGTC
1 AGGGTAAAAGATTGGATAGTGACTTCAATCTGCTCCATGGTTGGGGTAAAAGATTGGAT-G-GT-
* * * * *
17792 TTCAATCTGCCCTC-TTGTTAGAGTAAAAGATTGGATGGCTTCAATTTTCCCCATGGTTGGGGTA
63 TTCAATCTGCCC-CATGGTTGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTT-GGGTA
* *
17856 AGAGATTAGATGGTGTCTTCAATCTGCCCTCTTGTT
126 AGAGATTGGATGATGTCTTCAATCTGCCCTCTTGTT
* * * *
17892 AGAGTAAAAGATTGGAT-G-G-CTTGAATATGCTCCATGGTTGGGGTAAGAGATTGGATGGTATC
1 AGGGTAAAAGATTGGATAGTGACTTCAATCTGCTCCATGGTTGGGGTAAAAGATTGGATGG--T-
* * * *
17954 TTCAATCTACCCCATGATTGAGGTAAGAGATTGGAT
63 TTCAATCTGCCCCATGGTTGGGGTAAAAGATTGGAT
17990 AGATGATGTA
Statistics
Matches: 496, Mismatches: 62, Indels: 54
0.81 0.10 0.09
Matches are distributed among these distances:
158 6 0.01
159 60 0.12
160 3 0.01
161 9 0.02
162 375 0.76
163 40 0.08
164 2 0.00
165 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (161 bp):
AGGGTAAAAGATTGGATAGTGACTTCAATCTGCTCCATGGTTGGGGTAAAAGATTGGATGGTTTC
AATCTGCCCCATGGTTGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTTGGGTAAGAGA
TTGGATGATGTCTTCAATCTGCCCTCTTGTT
Found at i:17763 original size:243 final size:243
Alignment explanation
Indices: 17488--17965 Score: 733
Period size: 243 Copynumber: 2.0 Consensus size: 243
17478 CCCATGGTCG
* * *
17488 GGGTAAAAGATTGGATGACTTCAATTTACCCCATGGTTGGGATAAGAGATTGGATGATGTTTTCA
1 GGGTAAAAGATTGAATGACTTCAATCTACCCCATGGTTGGGATAAGAGATTGGATGATGTCTTCA
* * * *
17553 ATTTGCCCTCTTTTTAGGGTAAAATATTGGATGACTTCAATCTGT-CCCATGGTTGGGGTAAAAG
66 ATCTGCCCTCTTGTTAGAGTAAAAGATTGGATGACTTCAAT-TGTCCCCATGGTTGGGGTAAAAG
* * * *
17617 ATTGGATGGTGTTTTTAATCTGCCCTCTTATTAGAGTAAAAGATTGGATGGCTTCAATCTGCCCC
130 ATTAGATGGTGTCTTCAATCTGCCCTCTTATTAGAGTAAAAGATTGGATGGCTTCAATATGCCCC
*
17682 ATGGTTGAGGTAAGAGATTGGATGATGTCTTCAATCTACCCTCTTGTTA
195 ATGGTTGAGGTAAGAGATTGGATGATATCTTCAATCTACCCTCTTGTTA
* * *
17731 GGGTAAAAGATTGAATGACTTCAATCTACCCCATGGTTGGGGTAAGATATTGGATGGTGTCTTCA
1 GGGTAAAAGATTGAATGACTTCAATCTACCCCATGGTTGGGATAAGAGATTGGATGATGTCTTCA
* * *
17796 ATCTGCCCTCTTGTTAGAGTAAAAGATTGGATGGCTTCAATTTTCCCCATGGTTGGGGTAAGAGA
66 ATCTGCCCTCTTGTTAGAGTAAAAGATTGGATGACTTCAATTGTCCCCATGGTTGGGGTAAAAGA
* * *
17861 TTAGATGGTGTCTTCAATCTGCCCTCTTGTTAGAGTAAAAGATTGGATGGCTTGAATATGCTCCA
131 TTAGATGGTGTCTTCAATCTGCCCTCTTATTAGAGTAAAAGATTGGATGGCTTCAATATGCCCCA
* *
17926 TGGTTGGGGTAAGAGATTGGATGGTATCTTCAATCTACCC
196 TGGTTGAGGTAAGAGATTGGATGATATCTTCAATCTACCC
17966 CATGATTGAG
Statistics
Matches: 211, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
242 2 0.01
243 209 0.99
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (243 bp):
GGGTAAAAGATTGAATGACTTCAATCTACCCCATGGTTGGGATAAGAGATTGGATGATGTCTTCA
ATCTGCCCTCTTGTTAGAGTAAAAGATTGGATGACTTCAATTGTCCCCATGGTTGGGGTAAAAGA
TTAGATGGTGTCTTCAATCTGCCCTCTTATTAGAGTAAAAGATTGGATGGCTTCAATATGCCCCA
TGGTTGAGGTAAGAGATTGGATGATATCTTCAATCTACCCTCTTGTTA
Found at i:18401 original size:49 final size:49
Alignment explanation
Indices: 18213--18613 Score: 145
Period size: 49 Copynumber: 8.3 Consensus size: 49
18203 CCCTTTTCAG
* ** **
18213 TTTTAAGGTGTTAGATCTACCATTGTGGCTTTAAATCTATCTGTCTTCAA
1 TTTTAAGGTGTTAGATCTATCATTGTGGC-TTAAATCTATCCCTCTTTGA
* * * * * * *
18263 TTTTAGGGTGTTAGGT-TCGTCGTTATGGCTTCAACCTATCCCT-TTTCGA
1 TTTTAAGGTGTTAGATCT-ATCATTGTGGCTTAAATCTATCCCTCTTT-GA
* * * * *
18312 CTTTAAGGTG---GATC--TCATTGCT-GCTTAAATATTTCTCTCTTTGG
1 TTTTAAGGTGTTAGATCTATCATTG-TGGCTTAAATCTATCCCTCTTTGA
* * *
18356 TTTTAGGGTGTTAGATCTATCATTGTGGCTTCAATCTATCCCTCTTCGA
1 TTTTAAGGTGTTAGATCTATCATTGTGGCTTAAATCTATCCCTCTTTGA
** * * * * *
18405 TTTTAA-G-GTTAG-TC-CGCTGTTGCGGCTTCAACCAATCCCT-TTTCGA
1 TTTTAAGGTGTTAGATCTATC-ATTGTGGCTTAAATCTATCCCTCTTT-GA
* * * * *
18451 TTTTAAGGTGTAAGA--T-TCGTTGTTGCGACTTAAAATCTTTCTCTCTTCGA
1 TTTTAAGGTGTTAGATCTATCATTG-TG-G-CTT-AAATCTATCCCTCTTTGA
* * * * * **
18501 TTTT-AGGTTTTAGGT-TCACCATTGTGGCTTCAACCTATCCCTCTTCAA
1 TTTTAAGGTGTTAGATCT-ATCATTGTGGCTTAAATCTATCCCTCTTTGA
* * * *** * * *
18549 TTTTAAGGTGTAAGACCTGTCATTGCAACTTTAATCTTTCCCTCTTCGA
1 TTTTAAGGTGTTAGATCTATCATTGTGGCTTAAATCTATCCCTCTTTGA
18598 TTTTAAGGTGTTAGAT
1 TTTTAAGGTGTTAGAT
18614 TCGCCGTTAC
Statistics
Matches: 251, Mismatches: 73, Indels: 55
0.66 0.19 0.15
Matches are distributed among these distances:
44 24 0.10
45 7 0.03
46 34 0.14
47 12 0.05
48 26 0.10
49 103 0.41
50 37 0.15
51 4 0.02
52 4 0.02
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (49 bp):
TTTTAAGGTGTTAGATCTATCATTGTGGCTTAAATCTATCCCTCTTTGA
Found at i:18545 original size:144 final size:139
Alignment explanation
Indices: 18213--18557 Score: 356
Period size: 144 Copynumber: 2.4 Consensus size: 139
18203 CCCTTTTCAG
* * * ** *
18213 TTTTAAGGTGTTAGATCTACCATTGTGGCTTTAAATCTATCTGTCTTCAATTTTAGGGTGTTAGG
1 TTTTAGGGTGTTAGATCTACCATTGTGGC-TTCAACCTATCCCTCTTCAATTTTA-AG-GTTA-G
* ** *
18278 TTCG-TCGTTATGGCTTCAACCTATCCCTTTTCGACTTTAAGGTGGATCTCATTGCTGCTTAAAT
62 TCCGCT-GTTGCGGCTTCAACCAATCCCTTTTCGACTTTAAGGTGGATCTCATTGCTGCTTAAAT
* *
18342 ATTTCTCTCTTTGG
126 ATTTCTCTCTTCGA
* * *
18356 TTTTAGGGTGTTAGATCTATCATTGTGGCTTCAATCTATCCCTCTTCGATTTTAAGGTTAGTCCG
1 TTTTAGGGTGTTAGATCTACCATTGTGGCTTCAACCTATCCCTCTTCAATTTTAAGGTTAGTCCG
* * *
18421 CTGTTGCGGCTTCAACCAATCCCTTTTCGATTTTAAGGTGTAAGAT-TCGTTGTTGCGACTTAAA
66 CTGTTGCGGCTTCAACCAATCCCTTTTCGACTTTAAGGTG---GATCTCATTGCT--G-CTT-AA
*
18485 ATCTTTCTCTCTTCGA
124 ATATTTCTCTCTTCGA
* *
18501 TTTTA-GGTTTTAGGT-TCACCATTGTGGCTTCAACCTATCCCTCTTCAATTTTAAGGT
1 TTTTAGGGTGTTAGATCT-ACCATTGTGGCTTCAACCTATCCCTCTTCAATTTTAAGGT
18558 GTAAGACCTG
Statistics
Matches: 171, Mismatches: 22, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
139 38 0.22
140 5 0.03
141 7 0.04
142 24 0.14
143 29 0.17
144 48 0.28
145 20 0.12
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (139 bp):
TTTTAGGGTGTTAGATCTACCATTGTGGCTTCAACCTATCCCTCTTCAATTTTAAGGTTAGTCCG
CTGTTGCGGCTTCAACCAATCCCTTTTCGACTTTAAGGTGGATCTCATTGCTGCTTAAATATTTC
TCTCTTCGA
Found at i:18629 original size:98 final size:98
Alignment explanation
Indices: 18388--18636 Score: 265
Period size: 98 Copynumber: 2.6 Consensus size: 98
18378 TTGTGGCTTC
* * * * * *
18388 AATCTATCCCTCTTCGATTTTAA-G-GTTAGTCCGCTGTTGCGGCTTCAACCAATCCCTTTTCGA
1 AATCTTTCCCTCTTCGATTTTAAGGTGTTAGTTCGCCGTTGCGGCTTCAACCTATCCCTCTTCAA
* ** *
18451 TTTTAAGGTGTAAGATTCGTTGTTGCGACTTAA
66 TTTTAAGGTGTAAGACTCGTCATTGCAACTTAA
* * * * *
18484 AATCTTTCTCTCTTCGATTTT-AGGTTTTAGGTTCACCATTGTGGCTTCAACCTATCCCTCTTCA
1 AATCTTTCCCTCTTCGATTTTAAGGTGTTA-GTTCGCCGTTGCGGCTTCAACCTATCCCTCTTCA
*
18548 ATTTTAAGGTGTAAGAC-CTGTCATTGCAACTT-T
65 ATTTTAAGGTGTAAGACTC-GTCATTGCAACTTAA
* * *
18581 AATCTTTCCCTCTTCGATTTTAAGGTGTTAGATTCGCCGTTACAGCTTCAATCTAT
1 AATCTTTCCCTCTTCGATTTTAAGGTGTTAG-TTCGCCGTTGCGGCTTCAACCTAT
18637 TTTCTTCGGT
Statistics
Matches: 123, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
95 1 0.01
96 20 0.16
97 25 0.20
98 77 0.63
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (98 bp):
AATCTTTCCCTCTTCGATTTTAAGGTGTTAGTTCGCCGTTGCGGCTTCAACCTATCCCTCTTCAA
TTTTAAGGTGTAAGACTCGTCATTGCAACTTAA
Found at i:18634 original size:49 final size:49
Alignment explanation
Indices: 18383--18669 Score: 210
Period size: 49 Copynumber: 5.9 Consensus size: 49
18373 TATCATTGTG
* * *
18383 GCTTCAATCTATCCCTCTTCGATTTTAA-G-GTTAG-TCCGCTGTTGCG
1 GCTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAGATTCGCCGTTGCA
* * * * **
18429 GCTTCAACCAATCCCTTTTCGATTTTAAGGTGTAAGATTCGTTGTTGC-
1 GCTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAGATTCGCCGTTGCA
* * * * * * * **
18477 GACTTAAAATCTTTCTCTCTTCGATTTT-AGGTTTTAGGTTCACCATTGTG
1 G-CTT-CAATCTATCCCTCTTCGATTTTAAGGTGTTAGATTCGCCGTTGCA
* * * * * *
18527 GCTTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGA-CCTGTCATTGCA
1 GCTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAGATTC-GCCGTTGCA
* * * *
18576 ACTTTAATCTTTCCCTCTTCGATTTTAAGGTGTTAGATTCGCCGTTACA
1 GCTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAGATTCGCCGTTGCA
** * *
18625 GCTTCAATCTAT-TTTCTTCGGTTTTAAGGTGTTAGGTTCGCCGTT
1 GCTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAGATTCGCCGTT
18670 ACGAGTTTCA
Statistics
Matches: 182, Mismatches: 50, Indels: 16
0.73 0.20 0.06
Matches are distributed among these distances:
46 25 0.14
47 1 0.01
48 52 0.29
49 86 0.47
50 18 0.10
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.41
Consensus pattern (49 bp):
GCTTCAATCTATCCCTCTTCGATTTTAAGGTGTTAGATTCGCCGTTGCA
Found at i:19765 original size:14 final size:12
Alignment explanation
Indices: 19755--19789 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
19745 CCTTTTTTCC
19755 TTTTTCTTTTTT
1 TTTTTCTTTTTT
19767 TTTTTCTCTTTTT
1 TTTTTCT-TTTTT
*
19780 TTTTCCTTTT
1 TTTTTCTTTT
19790 CNNNNNNNNN
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:19782 original size:31 final size:31
Alignment explanation
Indices: 19730--19789 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
19720 GACCCCTAAT
19730 TTTTTTGTTTTTCCTCCTTTTTTCCTTTTTC
1 TTTTTTGTTTTTCCTCCTTTTTTCCTTTTTC
**
19761 TTTTTT-TTTTTCTCTTTTTTTTTCCTTTT
1 TTTTTTGTTTTTC-CTCCTTTTTTCCTTTT
19790 CNNNNNNNNN
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (31 bp):
TTTTTTGTTTTTCCTCCTTTTTTCCTTTTTC
Found at i:21992 original size:4 final size:4
Alignment explanation
Indices: 21983--22019 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
21973 TAATAAATTG
21983 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
22020 GACTCATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:44879 original size:24 final size:27
Alignment explanation
Indices: 44831--44879 Score: 77
Period size: 24 Copynumber: 1.9 Consensus size: 27
44821 ACTAATCTTC
44831 ATTTAATAAGAATTATAAAAATATAAT
1 ATTTAATAAGAATTATAAAAATATAAT
44858 ATTTAAT-A-AATTA-AAAAATATA
1 ATTTAATAAGAATTATAAAAATATA
44880 TAAAATCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 5 0.23
26 1 0.05
27 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
ATTTAATAAGAATTATAAAAATATAAT
Found at i:49830 original size:52 final size:52
Alignment explanation
Indices: 49755--49864 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 52
49745 AATGGTCGTG
* *
49755 AAATGGAGAAATAGGAAACATTTGGAAATGATTATGATTTTCTCAAAAAATGA
1 AAATGGAGAAATAGGAAACATTTGGAAATGAATATGAGTTTCTC-AAAAATGA
* * * *
49808 AAATGGA-AAATTGGAATCATTTGGAAATGAATATGGGTTTCTCCAAAATGA
1 AAATGGAGAAATAGGAAACATTTGGAAATGAATATGAGTTTCTCAAAAATGA
49859 AAATGG
1 AAATGG
49865 CTTGAAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 13 0.25
52 31 0.61
53 7 0.14
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (52 bp):
AAATGGAGAAATAGGAAACATTTGGAAATGAATATGAGTTTCTCAAAAATGA
Found at i:50447 original size:14 final size:15
Alignment explanation
Indices: 50423--50452 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
50413 GAGTTGTTTG
50423 AAAGCATAAAAATAA
1 AAAGCATAAAAATAA
50438 AAAG-ATAAAAATAA
1 AAAGCATAAAAATAA
50452 A
1 A
50453 GTAAGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAGCATAAAAATAA
Found at i:51791 original size:23 final size:23
Alignment explanation
Indices: 51761--51805 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
51751 GTAATTTGTG
51761 GTATGAGAATAACATAAAAGATC
1 GTATGAGAATAACATAAAAGATC
* *
51784 GTATGAGAATAGCATATAAGAT
1 GTATGAGAATAACATAAAAGAT
51806 TGTTTGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (23 bp):
GTATGAGAATAACATAAAAGATC
Found at i:53539 original size:33 final size:34
Alignment explanation
Indices: 53471--53539 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
53461 AATACTTATG
* * *
53471 TACCAAATTTTAAAAAAAAAATATCAAATCTAAA
1 TACCAAATTTTAAAAAAAAAACATCAAAACCAAA
53505 TACCAAA-TTTAAAAAAAAAACAT-AAACACCAAA
1 TACCAAATTTTAAAAAAAAAACATCAAA-ACCAAA
53538 TA
1 TA
53540 AAAAAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 3 0.10
33 21 0.68
34 7 0.23
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (34 bp):
TACCAAATTTTAAAAAAAAAACATCAAAACCAAA
Found at i:54132 original size:28 final size:29
Alignment explanation
Indices: 54083--54138 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
54073 CTTATATTGG
* *
54083 ATAAATATAATTATTATGTATA-CAATAT
1 ATAAATATAATAATGATGTATATCAATAT
54111 ATAAATATAA-AATGATGTTATATCAATA
1 ATAAATATAATAATGATG-TATATCAATA
54139 ATTGTGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 14 0.58
29 5 0.21
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (29 bp):
ATAAATATAATAATGATGTATATCAATAT
Found at i:54775 original size:45 final size:45
Alignment explanation
Indices: 54711--54802 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
54701 AAACTCCAAC
*
54711 GAAGTTGGCATATCCACATCATGTCTGACACTAAAAATGTTAACT
1 GAAGTTGGCATATCCACATCATGTCTGACACTAAAAATGTGAACT
** *
54756 GAAGTTGGCATATCCACATCATGTCTGACTTTAGAAATGTGAACT
1 GAAGTTGGCATATCCACATCATGTCTGACACTAAAAATGTGAACT
54801 GA
1 GA
54803 CTTTATTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (45 bp):
GAAGTTGGCATATCCACATCATGTCTGACACTAAAAATGTGAACT
Found at i:55532 original size:17 final size:17
Alignment explanation
Indices: 55510--55543 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55500 AAAAAAATAC
*
55510 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
55527 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
55544 TCCTGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:56076 original size:33 final size:33
Alignment explanation
Indices: 56005--56077 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
55995 TAAAATTTTA
* ***
56005 AAAAAATATTTTTGAATATTAAAAATTTGAAAT
1 AAAAAATATTTTTAAATATTAAAAATGACAAAT
* *
56038 AAAAAATATTTTTAAATTTTTAAAATGACAAATT
1 AAAAAATATTTTTAAATATTAAAAATGACAAA-T
56072 AAAAAA
1 AAAAAA
56078 AATAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (33 bp):
AAAAAATATTTTTAAATATTAAAAATGACAAAT
Found at i:59208 original size:31 final size:30
Alignment explanation
Indices: 59092--59209 Score: 87
Period size: 30 Copynumber: 3.9 Consensus size: 30
59082 TTAAATTATA
** *
59092 GTTAAAATATTATTTTTATTTTTAAAAAAAT
1 GTTAAAATATT-TTTAAAATTTTAAAAAAAT
* * *
59123 -TTAATAATAATTTTAAAAATCTAAAAAAAT
1 GTTAA-AATATTTTTAAAATTTTAAAAAAAT
* ** * *
59153 CTTAAAATAGATAT-AAATTATTAAAAATTAT
1 GTTAAAATATTTTTAAAATT-TTAAAAA-AAT
59184 GTTAAAATATTTTTAAAATTTTAAAA
1 GTTAAAATATTTTTAAAATTTTAAAA
59210 TATATAGGTA
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
29 4 0.06
30 30 0.45
31 27 0.41
32 5 0.08
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.43
Consensus pattern (30 bp):
GTTAAAATATTTTTAAAATTTTAAAAAAAT
Found at i:71242 original size:17 final size:18
Alignment explanation
Indices: 71220--71263 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
71210 TAGTTAAATT
71220 TAAAAATTTA-AAAAAAA
1 TAAAAATTTAGAAAAAAA
*
71237 TAAAAATTAAGAAAAAAA
1 TAAAAATTTAGAAAAAAA
*
71255 TAATAATTT
1 TAAAAATTT
71264 CATACGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
TAAAAATTTAGAAAAAAA
Done.