Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009576.1 Kokia drynarioides strain JFW-HI SEQ_124290, 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: 20252
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:579 original size:24 final size:24
Alignment explanation
Indices: 547--596 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
537 CACCATATAC
*
547 GGAGTTGGATCTTCATTTTCTACT
1 GGAGTTGGATCTTCATTTTCCACT
571 GGAGTTGGATCTTCATTTTCCACT
1 GGAGTTGGATCTTCATTTTCCACT
595 GG
1 GG
597 TTCCACATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (24 bp):
GGAGTTGGATCTTCATTTTCCACT
Found at i:2160 original size:11 final size:11
Alignment explanation
Indices: 2144--2195 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
2134 ATTTGACATG
2144 TTTTTAAATAA
1 TTTTTAAATAA
2155 TTTTTAAATATTA
1 TTTTTAAATA--A
*
2168 TTTTTACAT-A
1 TTTTTAAATAA
2178 TTTTTAAATAA
1 TTTTTAAATAA
2189 CTTTTTA
1 -TTTTTA
2196 TAACATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 9 0.26
11 11 0.31
12 6 0.17
13 9 0.26
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTTAAATAA
Found at i:8573 original size:56 final size:56
Alignment explanation
Indices: 8509--8617 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 56
8499 GTATAAAGAT
* * *
8509 TAAAACTAAAGTTTAATCACTGTCTTATAATATCAAAAACAAAAGAAGCAAGGTAG
1 TAAAACTAAAGCTTAATCACTGCCTTATAATATCAAAAACAAAAAAAGCAAGGTAG
* * *
8565 TAAAACTAAAGCTTGATCATTGCCTTATAATATCAAAAACAAAAAAAGTAAGG
1 TAAAACTAAAGCTTAATCACTGCCTTATAATATCAAAAACAAAAAAAGCAAGG
8618 CAAACCTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (56 bp):
TAAAACTAAAGCTTAATCACTGCCTTATAATATCAAAAACAAAAAAAGCAAGGTAG
Found at i:9038 original size:17 final size:15
Alignment explanation
Indices: 9011--9058 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
9001 CATTATAAAA
9011 ATATAAAAATTAAATT
1 ATAT-AAAATTAAATT
* *
9027 ATGTTAATAATTAAAGT
1 AT-ATAA-AATTAAATT
9044 ATATAAAATTAAATT
1 ATATAAAATTAAATT
9059 TCAAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 8 0.31
16 7 0.27
17 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (15 bp):
ATATAAAATTAAATT
Found at i:9574 original size:6 final size:6
Alignment explanation
Indices: 9563--9633 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
9553 CCCACTTTTC
* * *
9563 TTTAAA TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
*
9609 TTTAAA ATT--A TTCTAAA TTTAAA TT
1 TTTAAA TTTAAA TT-TAAA TTTAAA TT
9634 AAGAGAAGTC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
4 2 0.04
5 10 0.19
6 37 0.71
7 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:9590 original size:17 final size:17
Alignment explanation
Indices: 9570--9612 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
9560 TTCTTTAAAT
9570 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
**
9587 TTAAATTTATTTTAATT
1 TTAAATTTATTTTAAGA
9604 TTAAATTTA
1 TTAAATTTA
9613 AAATTATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:9604 original size:23 final size:22
Alignment explanation
Indices: 9564--9635 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
9554 CCACTTTTCT
*
9564 TTAAATTTAAATTT-ATTTTAAGA
1 TTAAATTT-ATTTTAATTTTAA-A
9587 TTAAATTTATTTTAATTTTAAA
1 TTAAATTTATTTTAATTTTAAA
* * *
9609 TTTAAAATTATTCTAAATTTAAA
1 -TTAAATTTATTTTAATTTTAAA
9632 TTAA
1 TTAA
9636 GAGAAGTCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
22 9 0.21
23 34 0.79
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
TTAAATTTATTTTAATTTTAAA
Found at i:10213 original size:3 final size:3
Alignment explanation
Indices: 10205--10329 Score: 58
Period size: 3 Copynumber: 40.7 Consensus size: 3
10195 ATGAATTAAA
** * *
10205 AAT AAT AAT AAT TTT AAT AAT AAC AAT AAT AGT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * * * ** **
10251 ATT TAT AA- AAT -CT AAT AAAT ACT TTT GCT AAT AAT AAAT ACATT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT A-A-T AAT
*
10298 AAT AAT AAT AAT AAT AA- ATAT AAT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
10330 AAAAAAGAAA
Statistics
Matches: 90, Mismatches: 23, Indels: 18
0.69 0.18 0.14
Matches are distributed among these distances:
2 4 0.04
3 72 0.80
4 12 0.13
5 2 0.02
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:11403 original size:30 final size:29
Alignment explanation
Indices: 11367--11457 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 29
11357 CCCTAAAGGT
11367 CCCTAAACTATCCAAAAATTACATTTTTAC
1 CCCTAAACT-TCCAAAAATTACATTTTTAC
* *
11397 CCCTAAACTTCTAAAAATTCCATTTTTA-
1 CCCTAAACTTCCAAAAATTACATTTTTAC
**
11425 CCCTAATTTCTCCAAAAATTAC-TATTTTAC
1 CCCTAAACT-TCCAAAAATTACAT-TTTTAC
11455 CCC
1 CCC
11458 CGAATGTCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
28 8 0.15
29 32 0.62
30 12 0.23
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:11441 original size:28 final size:29
Alignment explanation
Indices: 11367--11480 Score: 101
Period size: 29 Copynumber: 3.9 Consensus size: 29
11357 CCCTAAAGGT
*
11367 CCCTAAACTATCCAAAAATTACATTTTTAC
1 CCCTAAACT-TCTAAAAATTACATTTTTAC
*
11397 CCCTAAACTTCTAAAAATTCCATTTTTA-
1 CCCTAAACTTCTAAAAATTACATTTTTAC
*
11425 CCCT-AATTTCTCCAAAAATTAC-TATTTTAC
1 CCCTAAACTTCT--AAAAATTACAT-TTTTAC
** *
11455 CCCCGAA-TGTCTAAAAATTCCATTTT
1 CCCTAAACT-TCTAAAAATTACATTTT
11481 AAACCTTGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
27 6 0.08
28 5 0.07
29 41 0.58
30 14 0.20
31 5 0.07
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTCTAAAAATTACATTTTTAC
Found at i:16627 original size:22 final size:23
Alignment explanation
Indices: 16602--16645 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16592 ATTCAATGAA
* *
16602 AAAAAGA-AGCAAAAGAAAAAAG
1 AAAAAGAGAGAAAAACAAAAAAG
16624 AAAAAGAGAGAAAAACAAAAAA
1 AAAAAGAGAGAAAAACAAAAAA
16646 AGAGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.80, C:0.05, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAGAGAGAAAAACAAAAAAG
Found at i:16637 original size:16 final size:15
Alignment explanation
Indices: 16615--16663 Score: 71
Period size: 17 Copynumber: 3.1 Consensus size: 15
16605 AAGAAGCAAA
16615 AGAAAAAAGAAAAAGAG
1 AGAAAAAA-AAAAA-AG
16632 AGAAAAACAAAAAAAG
1 AGAAAAA-AAAAAAAG
16648 AGAAAAAAAAAAAAG
1 AGAAAAAAAAAAAAG
16663 A
1 A
16664 AAAGGAGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.29
16 9 0.29
17 12 0.39
18 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAAAG
Found at i:17760 original size:99 final size:99
Alignment explanation
Indices: 17625--18774 Score: 1300
Period size: 99 Copynumber: 11.8 Consensus size: 99
17615 AGCACGAAGA
* *
17625 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAAGGAAATGTT
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
* *
17690 TAAGTCACAACGACGAACCTAATACCTCAGAGAC
66 TAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
*
17724 ATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
17789 TAAGTCGCAACGANCGAACCTAGTACCTCAGAGAC
66 TAAGTCGCAACGA-CGAACCTAGTACCTCAGAGAC
* ** *
17824 ATGAAGGGAAAGATCTAAGCCGCAACGACGGATTTAGTACCGCAAAGATACAAAAGGGAAAGGTC
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
* *
17889 TAAGTTGCAACAACGAACCTAGTACCTCAGAGAC
66 TAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
* * * ** * *
17923 ATGAAAGGAAAGATCTAAGTCGTAACGGTTGATCTAGTACCACAAAGATAC---------A----
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
* **
17975 -AAGTCGCAATGATAAACCTAGTACCTCAGAGAC
66 TAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
* * * * *
18008 ATGAAGGGAAAGATCTAAGCCACAACGACGGATCAAGTACAGAAAAAAAGATACAAAAGGGAAAG
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCG---CAAAGATACAAAAGGGAAAG
*
18073 GTTTAAGTCGTAACGACGAACCTAGTACCTCAGAGAC
63 GTTTAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
* * *
18110 ATGAAGGGAAAGATCTAAGCCGCAACGACTGATCCAGTATCGCAAAGATACAAAAGGGAAAGGTT
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
*
18175 TAAGTCGCAATGACGAACCTAGTACCTCAGAGAC
66 TAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
*
18209 ATGAAGGGAAAGATCTAAGCCGTAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
* *
18274 TAAGTCGTAACGACGAACCTAGTACCTCATAGAC
66 TAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
* * *
18308 ATGAAGGGAAAGGTTTAAGCCGCAACGGCGGATCCAGTACCTCAAAGATACAAAAGGGAAAGGTT
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
*
18373 TAAGTCGCAACGACGAACCTAATACCTCAGAGAC
66 TAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
* * * * * * *
18407 ATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGACAC-GAAGGGAAAGGTT
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
* * * *
18471 TAAGTCGGAATGGCGAACCGT-GTACCACAGAGAC
66 TAAGTCGCAACGACGAACC-TAGTACCTCAGAGAC
* * * * * *
18505 ATGAAGGGAAAGATTTAAGTCGCAACGGTGAATCCAGTACCGCGAAGATA-TAAAGGGAAAGGTT
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
* * ** * *
18569 CAAGTTGCAACGGTGAACTTAGTACCGCAGAGAC
66 TAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
* * * * * *** * *
18603 ATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCCAATACCTTGAAGATA-TAAAGGGAAAGATT
1 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
* * * * *
18667 TAAGCCGCAACGGCGAATCTAGTACCGC-GAAGAT
66 TAAGTCGCAACGACGAACCTAGTACCTCAG-AGAC
* * * * * * * * *
18701 ATAAAGGGAAAGGTTTGAA-TCGCAACGGCGAATCTAGTACCTCAAAG--ACATGAAGGGAAAGA
1 ATGAAGGGAAAGATCT-AAGCCGCAACGGCGGATCCAGTACCGCAAAGATACA-AAAGGGAAAGG
*
18763 TTTAAGCCGCAA
64 TTTAAGTCGCAA
18775 TGACAAATCC
Statistics
Matches: 917, Mismatches: 109, Indels: 51
0.85 0.10 0.05
Matches are distributed among these distances:
85 60 0.07
88 8 0.01
90 1 0.00
96 1 0.00
97 3 0.00
98 263 0.29
99 424 0.46
100 91 0.10
102 66 0.07
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (99 bp):
ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTT
TAAGTCGCAACGACGAACCTAGTACCTCAGAGAC
Found at i:18137 original size:49 final size:49
Alignment explanation
Indices: 18064--18985 Score: 639
Period size: 49 Copynumber: 18.8 Consensus size: 49
18054 AAAGATACAA
* * * *
18064 AAGGGAAAGGTTTAAGTCGTAACGACGAACCTAGTACCTCAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * ** * *
18113 AAGGGAAAGATCTAAGCCGCAACGACTGATCC-AGTATCGCAAAGATACA-A
1 AAGGGAAAGATTTAAGCCGCAACGGC-GAACCTAGTA-C-CTCAGAGACATG
* * * *
18163 AAGGGAAAGGTTTAAGTCGCAATGACGAACCTAGTACCTCAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * * * *
18212 AAGGGAAAGATCTAAGCCGTAACGGCGGATCC-AGTACCGCAAAGATACA-A
1 AAGGGAAAGATTTAAGCCGCAACGGC-GAACCTAGTACCTC--AGAGACATG
* * * * *
18262 AAGGGAAAGGTTTAAGTCGTAACGACGAACCTAGTACCTCATAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * *
18311 AAGGGAAAGGTTTAAGCCGCAACGGCGGATCC-AGTACCTCAAAGATACA-A
1 AAGGGAAAGATTTAAGCCGCAACGGC-GAACCTAGTACCTC--AGAGACATG
* * * *
18361 AAGGGAAAGGTTTAAGTCGCAACGACGAACCTAATACCTCAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * *
18410 AAGGGAAAGATTTAAGCCGCAACGGTGAATCC-AGTACCAC-GAAGACACG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTCAG-AGACATG
* * * * *
18459 AAGGGAAAGGTTTAAGTCGGAATGGCGAACCGT-GTACCACAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACC-TAGTACCTCAGAGACATG
* * * * *
18508 AAGGGAAAGATTTAAGTCGCAACGGTGAATCC-AGTACCGC-GAAGATATA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTCAG-AGACATG
* * ** * * *
18557 AAGGGAAAGGTTCAAGTTGCAACGGTGAACTTAGTACCGCAGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * * * *
18606 AAGGGAAAGATTTAAGCCGTAACGGTGAATCC-AATACCT-TGAAGATATA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTCAG-AGACATG
* * * *
18655 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCGC-GAAGATATA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAG-AGACATG
* * * *
18704 AAGGGAAAGGTTTGAA-TCGCAACGGCGAATCTAGTACCTCAAAGACATG
1 AAGGGAAAGATTT-AAGCCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * * * **
18753 AAGGGAAAGATTTAAGCCGCAATGACAAATCC-AATACCAC-GAAGACAAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTCAG-AGACATG
* * * * *
18802 AAGGGAAAGGTTTAAGTCGCAACGGCAAAGCTAGTACCTCA-AAAGCATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAGAGA-CATG
* *
18851 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCATGA-AGACA-A
1 AAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACC-TCAGAGACATG
* * * ** * * *
18899 AAGGAAAAGGTTTAAGTCGCAGTGGTGAACCTTA-CACCTCAAAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAACC-TAGTACCTCAGAGACATG
*
18948 AAGGGAAATATTTAAGCCGCAACGGCGAATCC-AGTACC
1 AAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACC
18986 ACGAAGGAAC
Statistics
Matches: 685, Mismatches: 143, Indels: 90
0.75 0.16 0.10
Matches are distributed among these distances:
47 4 0.01
48 62 0.09
49 485 0.71
50 116 0.17
51 18 0.03
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTCAGAGACATG
Found at i:18579 original size:147 final size:145
Alignment explanation
Indices: 18163--19018 Score: 708
Period size: 147 Copynumber: 5.8 Consensus size: 145
18153 AAAGATACAA
* * * * * *
18163 AAGGGAAAGGTTTAAGTCGCAATGACGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAG
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAACC-AATACCACAGAGACATAAAGGGAAAGATTTAAG
* * * * * *
18228 CCGTAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTTTAAGTCGTAACGACGAA-C
65 CCGCAACGGCGAATCCAGTACCGCGAAGATA-TAAAGGGAAAGGTTTAAGTCGCAACGGCGAATC
*
18292 CTAGTACCTCATAGACATG
129 C-AGTACCACA-AGACATG
* * * * * *
18311 AAGGGAAAGGTTTAAGCCGCAACGGCGGATCCAGTACCTCAAAGATACA-AAAGGGAAAGGTTTA
1 AAGGGAAAGGTTTAAGCCGCAATGGC-GAACCAATA-C-CACAGAGACATAAAGGGAAAGATTTA
* * * * * * * * *
18375 AGTCGCAACGACGAA-CCTAATACCTC-AGAGACATGAAGGGAAAGATTTAAGCCGCAACGGTGA
63 AGCCGCAACGGCGAATCC-AGTACCGCGA-AGATATAAAGGGAAAGGTTTAAGTCGCAACGGCGA
*
18438 ATCCAGTACCACGAAGACACG
126 ATCCAGTACCAC-AAGACATG
* * ** *
18459 AAGGGAAAGGTTTAAGTCGGAATGGCGAACCGTGTACCACAGAGACATGAAGGGAAAGATTTAAG
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAACC-AATACCACAGAGACATAAAGGGAAAGATTTAAG
* * * * *
18524 TCGCAACGGTGAATCCAGTACCGCGAAGATATAAAGGGAAAGGTTCAAGTTGCAACGGTGAA-CT
65 CCGCAACGGCGAATCCAGTACCGCGAAGATATAAAGGGAAAGGTTTAAGTCGCAACGGCGAATC-
* *
18588 TAGTACCGCAGAGACATG
129 CAGTACCACA-AGACATG
* * * * ** *
18606 AAGGGAAAGATTTAAGCCGTAACGGTGAATCCAATACC-TTGAAGATATAAAGGGAAAGATTTAA
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAA-CCAATACCACAG-AGACATAAAGGGAAAGATTTAA
*
18670 GCCGCAACGGCGAATCTAGTACCGCGAAGATATAAAGGGAAAGGTTTGAA-TCGCAACGGCGAAT
64 GCCGCAACGGCGAATCCAGTACCGCGAAGATATAAAGGGAAAGGTTT-AAGTCGCAACGGCGAAT
* *
18734 CTAGTACCTCAAAGACATG
128 CCAGTACCAC-AAGACATG
* * * * *
18753 AAGGGAAAGATTTAAGCCGCAATGACAAATCCAATACCAC-GAAGACAAAAAGGGAAAGGTTTAA
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAA-CCAATACCACAG-AGACATAAAGGGAAAGATTTAA
* * * * * * * * * *
18817 GTCGCAACGGCAAAGCTAGTACCTC-AAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAAT
64 GCCGCAACGGCGAATCCAGTACCGCGAAGA-TATAAAGGGAAAGGTTTAAGTCGCAACGGCGAAT
* *
18881 CCAGTACCATGAAGACA-A
128 CCAGTACCA-CAAGACATG
* * * * * * * * * *
18899 AAGGAAAAGGTTTAAGTCGCAGTGGTGAACCTTACACCTCAAAGACATGAAGGGAAATATTTAAG
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAACC-AATACCACAGAGACATAAAGGGAAAGATTTAAG
* *
18964 CCGCAACGGCGAATCCAGTACCACGAAGGA-ACAAAGGGAAAGGTTTAAGTCGCAA
65 CCGCAACGGCGAATCCAGTACCGCGAA-GATATAAAGGGAAAGGTTTAAGTCGCAA
19019 TGACAAACCT
Statistics
Matches: 569, Mismatches: 113, Indels: 54
0.77 0.15 0.07
Matches are distributed among these distances:
145 2 0.00
146 102 0.18
147 314 0.55
148 103 0.18
149 41 0.07
150 7 0.01
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (145 bp):
AAGGGAAAGGTTTAAGCCGCAATGGCGAACCAATACCACAGAGACATAAAGGGAAAGATTTAAGC
CGCAACGGCGAATCCAGTACCGCGAAGATATAAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCA
GTACCACAAGACATG
Found at i:18966 original size:195 final size:196
Alignment explanation
Indices: 18655--19018 Score: 529
Period size: 195 Copynumber: 1.9 Consensus size: 196
18645 TGAAGATATA
* * * *
18655 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCGCGAAGATATAAAGGGAAAGGTTTGAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGAAAAGGTTTGAA
* * *
18720 TCGCAACGGCGAATCTAGTACCTCAAAGACATGAAGGGAAAGATTTAAGCCGCAATGACAAATCC
66 TCGCAACGGCGAACCTAGCACCTCAAAGACATGAAGGGAAAGATTTAAGCCGCAACGACAAATCC
18785 AATACCACGAA-GACAAAAAGGGAAAGGTTTAAGTCGCAACGGCAAAGCTAGTACCTCAAAAGCA
131 AATACCACGAAGGA-AAAAAGGGAAAGGTTTAAGTCGCAACGGCAAAGCTAGTACCTCAAAAGCA
18849 TG
195 TG
*
18851 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAGACA-AAAGGAAAAGGTTT-AA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGAAAAGGTTTGAA
** * * * *
18914 GTCGCAGTGGTGAACCTTA-CACCTCAAAGACATGAAGGGAAATATTTAAGCCGCAACGGCGAAT
66 -TCGCAACGGCGAACC-TAGCACCTCAAAGACATGAAGGGAAAGATTTAAGCCGCAACGACAAAT
* *
18978 CCAGTACCACGAAGGAACAAAGGGAAAGGTTTAAGTCGCAA
129 CCAATACCACGAAGGAAAAAAGGGAAAGGTTTAAGTCGCAA
19019 TGACAAACCT
Statistics
Matches: 149, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
194 2 0.01
195 100 0.67
196 47 0.32
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (196 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGAAAAGGTTTGAA
TCGCAACGGCGAACCTAGCACCTCAAAGACATGAAGGGAAAGATTTAAGCCGCAACGACAAATCC
AATACCACGAAGGAAAAAAGGGAAAGGTTTAAGTCGCAACGGCAAAGCTAGTACCTCAAAAGCAT
G
Found at i:19705 original size:17 final size:17
Alignment explanation
Indices: 19678--19776 Score: 146
Period size: 17 Copynumber: 5.8 Consensus size: 17
19668 TCCACTTTTC
19678 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
19695 TTTAAGA-TTAAATTTAT
1 TTTAA-ATTTAAATTTAT
*
19712 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTAT
*
19729 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTAT
*
19746 TTTAAATTTAAAATTAT
1 TTTAAATTTAAATTTAT
*
19763 TCTAAATTTAAATT
1 TTTAAATTTAAATT
19777 AAGAGAAGTC
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
16 1 0.01
17 73 0.97
18 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Done.