Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012892.1 Kokia drynarioides strain JFW-HI SEQ_127906, 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: 47348
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:650 original size:15 final size:15
Alignment explanation
Indices: 618--651 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
608 TGAGTGCCGT
*
618 CACTTTAAGTGCCAC
1 CACTTTAAGTCCCAC
*
633 CACTTTAAGTCCCTC
1 CACTTTAAGTCCCAC
648 CACT
1 CACT
652 AATAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.38, G:0.09, T:0.29
Consensus pattern (15 bp):
CACTTTAAGTCCCAC
Found at i:1550 original size:19 final size:21
Alignment explanation
Indices: 1517--1555 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1507 TTTTTAAATA
*
1517 ATTTTTTTATGAAAT-TTTTG
1 ATTTTTTAATGAAATGTTTTG
1537 ATTTTTTAAT-AAATGTTTT
1 ATTTTTTAATGAAATGTTTT
1556 AAATTCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (21 bp):
ATTTTTTAATGAAATGTTTTG
Found at i:3150 original size:16 final size:15
Alignment explanation
Indices: 3109--3152 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
3099 TTTTTTATAT
3109 TATATAAAAT-TAAA
1 TATATAAAATATAAA
*
3123 TATATGATAATATAAA
1 TATAT-AAAATATAAA
3139 TATTATAAAATATA
1 TA-TATAAAATATA
3153 TTAAGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 13 0.52
17 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TATATAAAATATAAA
Found at i:3616 original size:6 final size:6
Alignment explanation
Indices: 3605--3699 Score: 68
Period size: 6 Copynumber: 15.2 Consensus size: 6
3595 TTATATCCCT
* * * *
3605 AACATA AACATA AACATA AGCATA AATATA ATTA-ATTA AATACA AACATA
1 AACATA AACATA AACATA AACATA AACATA A--ACA-TA AACATA AACATA
* *
3655 AACATA AACATA ATTA-ATTA AATACA AACATA AACATA AACATA A
1 AACATA AACATA A--ACA-TA AACATA AACATA AACATA AACATA A
3700 TTAATTTCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
6 60 0.83
7 4 0.06
8 8 0.11
ACGTcount: A:0.63, C:0.13, G:0.01, T:0.23
Consensus pattern (6 bp):
AACATA
Found at i:3661 original size:32 final size:32
Alignment explanation
Indices: 3616--3705 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
3606 ACATAAACAT
* *
3616 AAACATAAGCATAAATATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
3648 AAACATAAACATAAACATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
3680 AAACATAAACATAAACATAATTAATT
1 AAACATAAACATAAACATAATTAATT
3706 TCAAATTCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.61, C:0.11, G:0.01, T:0.27
Consensus pattern (32 bp):
AAACATAAACATAAACATAATTAATTAAATAC
Found at i:6605 original size:26 final size:27
Alignment explanation
Indices: 6563--6615 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
6553 TAAATTAATT
6563 AAAAAATTTATAAAATAA-ATAGAAAAC
1 AAAAAATTTAT-AAATAACATAGAAAAC
*
6590 AAAAAATATTAT-AATAACATATAAAA
1 AAAAAAT-TTATAAATAACATAGAAAA
6616 ATATAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 5 0.22
27 14 0.61
28 4 0.17
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAAAATTTATAAATAACATAGAAAAC
Found at i:6616 original size:28 final size:27
Alignment explanation
Indices: 6563--6616 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
6553 TAAATTAATT
*
6563 AAAAAATTTATAAAATAAATAGAAAAC
1 AAAAAATTTATAAAACAAATAGAAAAC
*
6590 AAAAAATATTATAATAACATATA-AAAA
1 AAAAAAT-TTATAA-AACAAATAGAAAA
6617 TATAAACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 10 0.43
29 6 0.26
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (27 bp):
AAAAAATTTATAAAACAAATAGAAAAC
Found at i:6717 original size:28 final size:27
Alignment explanation
Indices: 6663--6741 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 27
6653 CATTTAATCA
*
6663 AAAAATAAATTATAACAAACAACATTTT
1 AAAAATAAATTAAAACAAACAACA-TTT
*
6691 AAAAATAAATTAAAATCAACCAA-ATTT
1 AAAAATAAATTAAAA-CAAACAACATTT
* *
6718 AAAATTTAAATTAAATAAAAACAA
1 AAAA-ATAAATTAAA-ACAAACAA
6742 AACCCTAAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.16
28 29 0.67
29 7 0.16
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAATAAATTAAAACAAACAACATTT
Found at i:6893 original size:20 final size:21
Alignment explanation
Indices: 6868--6912 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
6858 TGCCGTCGAT
6868 TTTCCTTCC-TTCTTT-TTCTC
1 TTTCCTTCCTTTCTTTCTT-TC
6888 TTTCCTTCCTTTCTTTCTTTC
1 TTTCCTTCCTTTCTTTCTTTC
6909 TTTC
1 TTTC
6913 TTTCTTCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.39
21 12 0.52
22 2 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTCCTTCCTTTCTTTCTTTC
Found at i:6894 original size:16 final size:17
Alignment explanation
Indices: 6873--6920 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
6863 TCGATTTTCC
6873 TTCCTTCTTT-TTCTCT
1 TTCCTTCTTTCTTCTCT
6889 TTCCTTCCTTTCTT-TCT
1 TTCCTT-CTTTCTTCTCT
*
6906 TTCTTTCTTTCTTCT
1 TTCCTTCTTTCTTCT
6921 GCTGGTTGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 13 0.46
17 13 0.46
18 2 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCCTTCTTTCTTCTCT
Found at i:6903 original size:4 final size:4
Alignment explanation
Indices: 6877--6918 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
6867 TTTTCCTTCC
*
6877 TTCT TT-T TCTCT TTCCT TCCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT T-TCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT T
6919 CTGCTGGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 2 0.06
4 26 0.79
5 5 0.15
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:7448 original size:20 final size:21
Alignment explanation
Indices: 7409--7446 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
7399 TCTCTCGTAT
7409 TTTTTCATTTAATCAATTTGA
1 TTTTTCATTTAATCAATTTGA
7430 TTTTT-ATTT-ATCAATTT
1 TTTTTCATTTAATCAATTT
7447 TGTGTCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (21 bp):
TTTTTCATTTAATCAATTTGA
Found at i:7767 original size:16 final size:16
Alignment explanation
Indices: 7748--7798 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
7738 TGACAAGAAC
7748 CTTTTGTGTATTTACA
1 CTTTTGTGTATTTACA
*
7764 CTTTTG-GTCCTTT-CA
1 CTTTTGTGT-ATTTACA
* *
7779 CTTTTTTGAATTTACA
1 CTTTTGTGTATTTACA
7795 CTTT
1 CTTT
7799 AACCACTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.16, C:0.18, G:0.10, T:0.57
Consensus pattern (16 bp):
CTTTTGTGTATTTACA
Found at i:9916 original size:16 final size:16
Alignment explanation
Indices: 9895--9930 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
9885 ATTTGAATTC
9895 GAAAAAATTAAAATCT
1 GAAAAAATTAAAATCT
*
9911 GAAAAAATTCAAATCT
1 GAAAAAATTAAAATCT
9927 -AAAA
1 GAAAA
9931 GGATCGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.22
Consensus pattern (16 bp):
GAAAAAATTAAAATCT
Found at i:31847 original size:17 final size:17
Alignment explanation
Indices: 31816--31896 Score: 117
Period size: 17 Copynumber: 4.8 Consensus size: 17
31806 TAGCCTATTG
*
31816 AAATTTGAATTTATTTT
1 AAATTTAAATTTATTTT
* *
31833 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
*
31850 AAATTTAAATTTATTTG
1 AAATTTAAATTTATTTT
*
31867 AAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
31884 AAATTTAAATTTA
1 AAATTTAAATTTA
31897 AAATATCCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:31872 original size:7 final size:6
Alignment explanation
Indices: 31816--31898 Score: 61
Period size: 6 Copynumber: 14.5 Consensus size: 6
31806 TAGCCTATTG
* * * * *
31816 AAATTT GAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
31862 --ATTT GAAATTT AAATTT --ATTAT AAATTT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAATTT AAA
31899 ATATCCAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
4 7 0.11
5 9 0.15
6 38 0.62
7 7 0.11
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:32129 original size:13 final size:13
Alignment explanation
Indices: 32111--32135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32101 CAATCTCATG
32111 ACCATCTTCAACC
1 ACCATCTTCAACC
32124 ACCATCTTCAAC
1 ACCATCTTCAAC
32136 ATCCACTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (13 bp):
ACCATCTTCAACC
Found at i:33713 original size:29 final size:28
Alignment explanation
Indices: 33663--34043 Score: 323
Period size: 29 Copynumber: 13.0 Consensus size: 28
33653 GAAGGTCCCT
*
33663 AAACTATCCAAAAATTCCATTTTTACTCCC
1 AAACT-TCCAAAAATCCCATTTTTAC-CCC
* * *
33693 GAACTTTCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTT-ACC-CC
*
33723 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATCCCATTTTTACCC-C
* *
33752 GAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATCCCATTTTT-ACCC-C
*
33782 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTA-CCCC
*
33811 AAACTTCCAAAAATCCCATTTTCAACCCC
1 AAACTTCCAAAAATCCCATTTT-TACCCC
** * *
33840 AAAACTTCTTACAATTCCATTTTTACCCC
1 -AAACTTCCAAAAATCCCATTTTTACCCC
* *
33869 TAAACTTCCAAAAATCCCATTTTAACCCT
1 -AAACTTCCAAAAATCCCATTTTTACCCC
* *
33898 AAAATTCCAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATCCCATTTTTACCCC
* * * * *
33926 TGAACTTCTAAAAATCTCATTTTCGACCCTA
1 -AAACTTCCAAAAATCCCATTTT-TACCC-C
* *
33957 AAACTTCTAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATCCCATTTTTACCCC
* * * *
33985 TTAACTTCCAAAAA-CACCTTTTTTGATACCT
1 -AAACTTCCAAAAATC-CCATTTTT-A-CCCC
* *
34016 AAATTTCCAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATCCCATTTTTACCCC
34044 CCAAATGTCT
Statistics
Matches: 280, Mismatches: 56, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
28 27 0.10
29 134 0.48
30 117 0.42
31 2 0.01
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (28 bp):
AAACTTCCAAAAATCCCATTTTTACCCC
Found at i:33734 original size:30 final size:29
Alignment explanation
Indices: 33663--34068 Score: 356
Period size: 30 Copynumber: 13.8 Consensus size: 29
33653 GAAGGTCCCT
33663 AAACTATCCAAAAATTCCATTTTTACTCCCG
1 AAACT-TCCAAAAATTCCATTTTTAC-CCCG
* * *
33694 -AACTTTCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
33723 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
* **
33753 -AACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
*
33782 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* * *
33811 AAACTTCCAAAAATCCCATTTTCAACCCCA
1 AAACTTCCAAAAATTCCATTTT-TACCCCG
** * *
33841 AAACTTCTTACAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* * *
33870 AAACTTCCAAAAATCCCA-TTTTAACCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCG
*
33898 AAAATTCCAAAAATTCCATTTTTACCCCTG
1 AAACTTCCAAAAATTCCATTTTTACCCC-G
* * **
33928 -AACTTCTAAAAA-TCTCATTTTCGACCCTA
1 AAACTTCCAAAAATTC-CATTTT-TACCCCG
* *
33957 AAACTTCTAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* ** * ** *
33986 TAACTTCCAAAAACACCTTTTTTGATACCT
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
34016 AAATTTCCAAAAATTCCATTTTTACCCCCC
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
*
34046 AAA-TGTCTAAAAATTCCATTTTT
1 AAACT-TCCAAAAATTCCATTTTT
34069 TTAAACCACG
Statistics
Matches: 306, Mismatches: 54, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
28 27 0.09
29 135 0.44
30 142 0.46
31 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:33763 original size:59 final size:58
Alignment explanation
Indices: 33663--34043 Score: 450
Period size: 59 Copynumber: 6.5 Consensus size: 58
33653 GAAGGTCCCT
* * *
33663 AAACTATCCAAAAATTCCATTTTTACTCCC-GAACTTTCAAAAATCCCATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTAC-CCCTGAACTTCCAAAAATCCCATTTTTAACC-CA
33723 AAACTTCCAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCT-GAACTTCCAAAAATCCCATTTTTAACCC-A
** *
33782 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTCAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAA-CCCA
** * *
33841 AAACTTCTTACAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCA-TTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCC-A
* * **
33899 AAA-TTCCAAAAATTCCATTTTTACCCCTGAACTTCTAAAAATCTCATTTTCGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCC-A
* * * *
33957 AAACTTCTAAAAATTCCATTTTTACCCCTTAACTTCCAAAAA-CACCTTTTTTGATA-CCT
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATC-CCATTTTT-A-ACCCA
*
34016 AAATTTCCAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
34044 CCAAATGTCT
Statistics
Matches: 281, Mismatches: 29, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
57 43 0.15
58 23 0.08
59 201 0.72
60 13 0.05
61 1 0.00
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCA
Found at i:45310 original size:27 final size:27
Alignment explanation
Indices: 45267--45326 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
45257 AATTTTCAAC
*
45267 TAATGATTGTTTTCTTTGATCCTCTTTT
1 TAAT-ATTGTTTCCTTTGATCCTCTTTT
45295 TAATATTGTTTCCTTTGATCCTCTTTT
1 TAATATTGTTTCCTTTGATCCTCTTTT
45322 TAATA
1 TAATA
45327 GAATTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.18, C:0.15, G:0.08, T:0.58
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCCTCTTTT
Found at i:45970 original size:44 final size:44
Alignment explanation
Indices: 45900--46016 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
45890 CTTTGAACCC
*
45900 TAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAGGT
1 TAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAGGT
* *
45944 TAGCTTCTTGATGAGACACTGGGAAGCAGGTCGAAGCAATAAACGGT
1 TAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT--A-GGT
* * *
45991 TAGTTTCCTGATGAGATATTGAGAAG
1 TAGCTTCCTGATGAGACACTGAGAAG
46017 TGAACCAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 37 0.60
46 1 0.02
47 24 0.39
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.25
Consensus pattern (44 bp):
TAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAGGT
Found at i:46241 original size:204 final size:199
Alignment explanation
Indices: 45945--46310 Score: 477
Period size: 204 Copynumber: 1.8 Consensus size: 199
45935 GCAATAGGTT
* * * *
45945 AGCTTCTTGATGAGACACTGGGAAGCAGGTCGAAGCAATAAACGGTTAGTTTCCTGATGAGATAT
1 AGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAAATAT
* * * * * *
46010 TGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAA-CAAAAGACAC
66 CGAGAAGTAAACCAAATTCATCTTCCTGATGAAACACAGAGAAGCAGA-TCAAAGC--AAG--AC
46074 GGTCATCTTCCTAATGAAATACTGAGAAGAAGACCAAATCCAAACCCACGCGCGATGAACGAATC
126 GGTCATCTTCCTAATGAAATACTGAGAAGAAGACCAAATCCAAACCCACGCGCGATGAACGAATC
46139 TTCGAACCC
191 TTCGAACCC
* * *
46148 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAAATA
1 AGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT-AAACGGTTAGCTTCCTGATGAAATA
** **
46213 -CGAGGAAGTAAACCAAAATT-ATCTTCCTGATGAAACACAGAGAAGTGGATCAAAGCAAGGTGG
65 TCGA-GAAGTAAACC-AAATTCATCTTCCTGATGAAACACAGAGAAGCAGATCAAAGCAAGACGG
*
46276 TCATCTTCCTAATGAAATACTGAGAAGAAGGCCAA
128 TCATCTTCCTAATGAAATACTGAGAAGAAGACCAA
46311 GTCAACAAAA
Statistics
Matches: 141, Mismatches: 18, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
200 36 0.26
202 3 0.02
203 41 0.29
204 56 0.40
205 5 0.04
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (199 bp):
AGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAAATAT
CGAGAAGTAAACCAAATTCATCTTCCTGATGAAACACAGAGAAGCAGATCAAAGCAAGACGGTCA
TCTTCCTAATGAAATACTGAGAAGAAGACCAAATCCAAACCCACGCGCGATGAACGAATCTTCGA
ACCC
Found at i:46652 original size:17 final size:17
Alignment explanation
Indices: 46618--46667 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
46608 TCTTGGCCTA
* *
46618 TTGAAATTTGAATTTAT
1 TTGAAAATTAAATTTAT
* *
46635 TTTAAAATTAAGTTTAT
1 TTGAAAATTAAATTTAT
*
46652 TTGAAATTTAAATTTA
1 TTGAAAATTAAATTTA
46668 AAATATCCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (17 bp):
TTGAAAATTAAATTTAT
Found at i:46900 original size:13 final size:13
Alignment explanation
Indices: 46882--46906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46872 CAATCTCATG
46882 ACCATCTTCAACC
1 ACCATCTTCAACC
46895 ACCATCTTCAAC
1 ACCATCTTCAAC
46907 ATCCACTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (13 bp):
ACCATCTTCAACC
Done.