Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004999.1 Kokia drynarioides strain JFW-HI SEQ_118758, 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: 56623
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6480 original size:17 final size:18
Alignment explanation
Indices: 6460--6498 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6450 AAGTTTCTTA
*
6460 TTTAGATTAGTT-AGAGT
1 TTTAGATTAATTAAGAGT
*
6477 TTTAGTTTAATTAAGAGT
1 TTTAGATTAATTAAGAGT
6495 TTTA
1 TTTA
6499 TTTAGATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (18 bp):
TTTAGATTAATTAAGAGT
Found at i:10943 original size:26 final size:26
Alignment explanation
Indices: 10913--10963 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
10903 CTTAGGAATG
10913 TCGTTACATGAACATGTCCAGAATTA
1 TCGTTACATGAACATGTCCAGAATTA
* *
10939 TCGTTGCATGAACATGTCTAGAATT
1 TCGTTACATGAACATGTCCAGAATT
10964 GCACCCAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (26 bp):
TCGTTACATGAACATGTCCAGAATTA
Found at i:11784 original size:16 final size:16
Alignment explanation
Indices: 11763--11793 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11753 TTGTTGATCC
11763 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
11779 CATTTTATCTTTATT
1 CATTTTACCTTTATT
11794 TTCACATTAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:17822 original size:16 final size:16
Alignment explanation
Indices: 17801--17831 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17791 ATAATGTGAA
17801 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
17817 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
17832 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:19770 original size:29 final size:29
Alignment explanation
Indices: 19624--19872 Score: 175
Period size: 30 Copynumber: 8.4 Consensus size: 29
19614 GGTAAAATCA
*
19624 AAATTTTGGAAAGTATTAGGGGTTAAAATG
1 AAATTTTAGAAAGT-TTAGGGGTTAAAATG
* * * *
19654 TAATTTTCCATAAAGATT-GGGAGTCAAAATG
1 AAATTTT--AGAAAGTTTAGGG-GTTAAAATG
** * * * *
19685 TAGTTTTTAGAAAATTTAAGTGTCAAAATG
1 -AAATTTTAGAAAGTTTAGGGGTTAAAATG
* **
19715 AAATTTTTA-AAAGTTCA-AAGTTAAAAATG
1 AAA-TTTTAGAAAGTTTAGGGGTT-AAAATG
19744 AAATTTTAGAAAGTTTAGGGGTTAAAATG
1 AAATTTTAGAAAGTTTAGGGGTTAAAATG
* * *
19773 ACATTTACAAAAAGTTTAGGGGTTAAAATG
1 AAATTT-TAGAAAGTTTAGGGGTTAAAATG
* * *
19803 ACATTTACAAAAAGTTTAGGGGTTAAAATG
1 AAATTT-TAGAAAGTTTAGGGGTTAAAATG
*
19833 ACATTTTTAGAAAGTTT-GGGGTTAAAAT-
1 A-AATTTTAGAAAGTTTAGGGGTTAAAATG
19861 ATAATTTTAGAA
1 A-AATTTTAGAA
19873 CAAAACAAGG
Statistics
Matches: 176, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
28 17 0.10
29 45 0.26
30 92 0.52
31 14 0.08
32 8 0.05
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (29 bp):
AAATTTTAGAAAGTTTAGGGGTTAAAATG
Found at i:19990 original size:23 final size:23
Alignment explanation
Indices: 19957--20000 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19947 GGACTAAATC
19957 GAAAATGAAATGAAATCAAAAGG
1 GAAAATGAAATGAAATCAAAAGG
* * *
19980 GAAAATTAAATTAAATTAAAA
1 GAAAATGAAATGAAATCAAAA
20001 ATAGTAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.14, T:0.20
Consensus pattern (23 bp):
GAAAATGAAATGAAATCAAAAGG
Found at i:21544 original size:25 final size:25
Alignment explanation
Indices: 21503--21550 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21493 GCTTCAATCC
*
21503 GCCCCATGATCATGGTAAAAGATCT
1 GCCCCATGATCAGGGTAAAAGATCT
* *
21528 GCCCCATGATCGGGGTAAGAGAT
1 GCCCCATGATCAGGGTAAAAGAT
21551 TGTTGTGTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (25 bp):
GCCCCATGATCAGGGTAAAAGATCT
Found at i:21584 original size:40 final size:39
Alignment explanation
Indices: 21524--21861 Score: 219
Period size: 40 Copynumber: 8.7 Consensus size: 39
21514 ATGGTAAAAG
* **
21524 ATCTGCCCCATGATCGGGGTAAGAGATTGTTGTGTCTTCA
1 ATCTGCCCTATGATTAGGGTAAGAGATTG-TGTGTCTTCA
* *
21564 ATATGCCCTTTGATTAGGGTAAGAGATTG-GATG-CTTCA
1 ATCTGCCCTATGATTAGGGTAAGAGATTGTG-TGTCTTCA
* * * * *
21602 ATCTACCCCATAATTGGGGTATGAGATTGGTGTGTCTTCA
1 ATCTGCCCTATGATTAGGGTAAGAGATT-GTGTGTCTTCA
* * * *
21642 ATCTGCCCTCTAATTAGGATAAAAGATTG-GATG-CTTCA
1 ATCTGCCCTATGATTAGGGTAAGAGATTGTG-TGTCTTCA
* * ** *
21680 ATCTACCCCATGATCGGGGTAAGAGATTGGTATGTCTTCA
1 ATCTGCCCTATGATTAGGGTAAGAGATT-GTGTGTCTTCA
* * * *
21720 ATCTGCCCTCTAATTAGGGCAAAAGATTG-GATG-CTTCA
1 ATCTGCCCTATGATTAGGGTAAGAGATTGTG-TGTCTTCA
* ** *
21758 ATCT-ACCTCATGATCGGGGTAAGAGATTGGTTTGTCTTCA
1 ATCTGCCCT-ATGATTAGGGTAAGAGATT-GTGTGTCTTCA
* * *
21798 ATCTGCCTTCTGATTAAGGTAAGAGATTG-GATG-CTTCA
1 ATCTGCCCTATGATTAGGGTAAGAGATTGTG-TGTCTTCA
* * *
21836 ATTTGTCCC-ATGATCAGGGCAAGAGA
1 ATCTG-CCCTATGATTAGGGTAAGAGA
21862 CTAGATGGCT
Statistics
Matches: 224, Mismatches: 58, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
37 3 0.01
38 97 0.43
39 22 0.10
40 100 0.45
41 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (39 bp):
ATCTGCCCTATGATTAGGGTAAGAGATTGTGTGTCTTCA
Found at i:21658 original size:78 final size:78
Alignment explanation
Indices: 21524--22160 Score: 470
Period size: 78 Copynumber: 7.9 Consensus size: 78
21514 ATGGTAAAAG
* * * * * *
21524 ATCTGCCCCATGATCGGGGTAAGAGATTGTTGTGTCTTCAATATGCCCTTTGATTAGGGTAAGAG
1 ATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGGTAAAAG
21589 ATTGGATGCTTCA
66 ATTGGATGCTTCA
* * * *
21602 ATCTACCCCATAATTGGGGTATGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGATAAAAG
1 ATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGGTAAAAG
21667 ATTGGATGCTTCA
66 ATTGGATGCTTCA
* *
21680 ATCTACCCCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTGCCCTCTAATTAGGGCAAAAG
1 ATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGGTAAAAG
21745 ATTGGATGCTTCA
66 ATTGGATGCTTCA
* * * * * *
21758 ATCTACCTCATGATCGGGGTAAGAGATTGGTTTGTCTTCAATCTGCCTTCTGATTAAGGTAAGAG
1 ATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGGTAAAAG
21823 ATTGGATGCTTCA
66 ATTGGATGCTTCA
* ** * * * * * * *
21836 ATTTGTCCCATGATCAGGGCAAGAGACTAGATG-G-CTTCAATCTACCGATCTTGATTTAGAGGT
1 ATCTACCCCATGATCGGGGTAAGAGA-TTGGTGTGTCTTCAATCTGCC-CTC-T-AATTAG-GGT
21899 AAAAGATTGGATGATCTTCA
61 AAAAGATTGGATG--CTTCA
* * * * * * *
21919 ATCTGCCCCTCTTGACTTAGGGGTAAAAGATTAG-ATG---T--A-C--CCCTCTTGACTTAGGG
1 ATCT-ACCC-CATGA--TCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTC-T-AATTA-GG
21975 GTAAAAGATTGGATGGTCTTCA
59 GTAAAAGATTGGAT-G-CTTCA
* * * * * * * *
21997 ATCTGCCCATCTTGACTTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTGCCCTTTTTGACTTA
1 ATCTACCC--CATGA--TCGGGGTAAGAGATT-GGT-GTGTCTTCAATCTGCCC--TCT-AATTA
*
22062 GGGGTAAAAGATTGGATGCTTCG
57 -GGGTAAAAGATTGGATGCTTCA
* * * * *
22085 ATTTTCCCCATGGTCGGGGTATA-AGATTGGTGTGTCTTCAATTTGCCCCTCTTGATTTAAGGGT
1 ATCTACCCCATGATCGGGGTA-AGAGATTGGTGTGTCTTCAATCTG-CCCTC-T-AATT-AGGGT
22149 AAAAGATTGGAT
61 AAAAGATTGGAT
22161 AATCTTCAAT
Statistics
Matches: 459, Mismatches: 68, Indels: 60
0.78 0.12 0.10
Matches are distributed among these distances:
77 14 0.03
78 291 0.63
79 8 0.02
80 3 0.01
81 19 0.04
82 34 0.07
83 14 0.03
84 16 0.03
85 5 0.01
86 6 0.01
87 10 0.02
88 10 0.02
89 4 0.01
90 24 0.05
91 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (78 bp):
ATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGGTAAAAG
ATTGGATGCTTCA
Found at i:21860 original size:38 final size:37
Alignment explanation
Indices: 21524--21878 Score: 237
Period size: 38 Copynumber: 9.1 Consensus size: 37
21514 ATGGTAAAAG
*
21524 ATCTGCCCCATGATCGGGGTAAGAGATTGTTG-TGTCTTCA
1 ATCTG-CCCATGATCAGGGTAAGAGATTG--GATG-CTTCA
* * *
21564 ATATGCCCTTTGATTAGGGTAAGAGATTGGATGCTTCA
1 ATCTGCCC-ATGATCAGGGTAAGAGATTGGATGCTTCA
* * ** * *
21602 ATCTACCCCATAATTGGGGTATGAGATTGGTGTGTCTTCA
1 ATCT-GCCCATGATCAGGGTAAGAGATTGG-ATG-CTTCA
* * * * *
21642 ATCTGCCCTCTAATTAGGATAAAAGATTGGATGCTTCA
1 ATCTGCCC-ATGATCAGGGTAAGAGATTGGATGCTTCA
* *
21680 ATCTACCCCATGATCGGGGTAAGAGATTGGTATGTCTTCA
1 ATCT-GCCCATGATCAGGGTAAGAGATTGG-ATG-CTTCA
* * * * *
21720 ATCTGCCCTCTAATTAGGGCAAAAGATTGGATGCTTCA
1 ATCTGCCC-ATGATCAGGGTAAGAGATTGGATGCTTCA
* * *
21758 ATCTACCTCATGATCGGGGTAAGAGATTGGTTTGTCTTCA
1 ATCTGCC-CATGATCAGGGTAAGAGATTGG-ATG-CTTCA
* *
21798 ATCTGCCTTC-TGATTAAGGTAAGAGATTGGATGCTTCA
1 ATCTGCC--CATGATCAGGGTAAGAGATTGGATGCTTCA
* * * *
21836 ATTTGTCCCATGATCAGGGCAAGAGACTAGATGGCTTCA
1 ATCTG-CCCATGATCAGGGTAAGAGATTGGAT-GCTTCA
21875 ATCT
1 ATCT
21879 ACCGATCTTG
Statistics
Matches: 246, Mismatches: 52, Indels: 35
0.74 0.16 0.11
Matches are distributed among these distances:
37 1 0.00
38 102 0.41
39 43 0.17
40 98 0.40
41 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (37 bp):
ATCTGCCCATGATCAGGGTAAGAGATTGGATGCTTCA
Found at i:21933 original size:44 final size:44
Alignment explanation
Indices: 21870--22287 Score: 384
Period size: 44 Copynumber: 9.8 Consensus size: 44
21860 GACTAGATGG
* ** * *
21870 CTTCAATCTACCGATCTTGATTTAGAGGTAAAAGATTGGATGAT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
21914 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATT--A-GAT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
* *
21955 -GT--A----CCCCTCTTGACTTAGGGGTAAAAGATTGGATGGT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
* * *
21992 CTTCAATCTGCCCATCTTGACTTAGGGGTAAAAGATTAGATGGT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
* *
22036 GGCTTCAATCTGCCCTTTTTGACTTAGGGGTAAAAGATTGGATG--
1 --CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
* ** * * * * *
22080 CTTCGAT-TTTCCC-CATG--GTCGGGGTATAAGATTGG-TGTGT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATG-AT
* * * *
22120 CTTCAATTTGCCCCTCTTGATTTAAGGGTAAAAGATTGGATAAT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
* * * * *
22164 CTTCAATATACCCCTCTTGACTCAAGGGTAAAAGATTGGATGTT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
* * * *
22208 CTTCAATCTACCCCTCTTGACTCAGGGGTAAAAGATTGAATGTT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
*
22252 CTTCAATCTGCCCCTCTTGACTTAAGGGTAAAAGAT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGAT
22288 AGGAAGGTAA
Statistics
Matches: 310, Mismatches: 44, Indels: 40
0.79 0.11 0.10
Matches are distributed among these distances:
34 27 0.09
36 1 0.00
37 4 0.01
38 17 0.05
40 10 0.03
41 10 0.03
42 10 0.03
44 191 0.62
45 1 0.00
46 39 0.13
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (44 bp):
CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGAT
Found at i:21967 original size:34 final size:34
Alignment explanation
Indices: 21924--21989 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
21914 CTTCAATCTG
21924 CCCCTCTTGACTTAGGGGTAAAAGATTAGATGTA
1 CCCCTCTTGACTTAGGGGTAAAAGATTAGATGTA
*
21958 CCCCTCTTGACTTAGGGGTAAAAGATTGGATG
1 CCCCTCTTGACTTAGGGGTAAAAGATTAGATG
21990 GTCTTCAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (34 bp):
CCCCTCTTGACTTAGGGGTAAAAGATTAGATGTA
Found at i:22732 original size:24 final size:24
Alignment explanation
Indices: 22700--22751 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
22690 AAATGAGTCA
22700 AATGCTCCTAACTAGATGCGCATG
1 AATGCTCCTAACTAGATGCGCATG
* *
22724 AATGCTCCTAACTAGATGGGTATG
1 AATGCTCCTAACTAGATGCGCATG
22748 AATG
1 AATG
22752 ATGAATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (24 bp):
AATGCTCCTAACTAGATGCGCATG
Found at i:23464 original size:17 final size:18
Alignment explanation
Indices: 23442--23494 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
23432 CAACCTCTCA
23442 TTTTCTTTCTTTTTCTT-
1 TTTTCTTTCTTTTTCTTC
23459 TTTTCTTTTCTTTTTCTCTTCC
1 TTTTC-TTTC-TTTT-TCTT-C
23481 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
23495 TGGGTGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 5 0.16
18 4 0.13
19 5 0.16
20 8 0.26
21 4 0.13
22 5 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCTTTCTTTTTCTTC
Found at i:24475 original size:6 final size:7
Alignment explanation
Indices: 24458--24491 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
24448 TCTTGACTCT
*
24458 TTTTTTC
1 TTTTTTA
24465 TTTTTTA
1 TTTTTTA
24472 TTTTTTA
1 TTTTTTA
24479 TTTTTTA
1 TTTTTTA
24486 TTTTTT
1 TTTTTT
24492 GTTTGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:24490 original size:75 final size:75
Alignment explanation
Indices: 24353--24492 Score: 187
Period size: 75 Copynumber: 1.9 Consensus size: 75
24343 GATTTTCAAG
* * *
24353 ATGCCCTTTGCAGGTTTTCATCTTGACTTTTTTCTTTCTTTCCTTCTTTTTCTTTTTTTTTTTTT
1 ATGCCCTTTACAGGTTTTCATCTTGACTCTTTTCTTTCTTTCCTTCTTTTTATTTTTTTTTTTTT
24418 GGGTTTTAAT
66 GGGTTTTAAT
* * *
24428 ATGCCCTTTAC-GAGTTTTCATCTTGACTCTTTT-TTTCTTT-TTTATTTTTTATTTTTTATTTT
1 ATGCCCTTTACAG-GTTTTCATCTTGACTCTTTTCTTTCTTTCCTT-CTTTTTATTTTTTTTTTT
24490 TTG
64 TTG
24493 TTTGTTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 2 0.04
74 26 0.46
75 29 0.51
ACGTcount: A:0.10, C:0.16, G:0.09, T:0.65
Consensus pattern (75 bp):
ATGCCCTTTACAGGTTTTCATCTTGACTCTTTTCTTTCTTTCCTTCTTTTTATTTTTTTTTTTTT
GGGTTTTAAT
Found at i:30947 original size:30 final size:30
Alignment explanation
Indices: 30878--31110 Score: 213
Period size: 30 Copynumber: 7.8 Consensus size: 30
30868 GGAAAAATGG
* * * **
30878 GGGT-AAAATCAAAATTTTGGAAAGTTTTT
1 GGGTCAAAATGAAATTTTTAGAAAGTTTAA
* *
30907 GGGTTTAAAATGTAATTTTTAGAAAGTTTAA
1 GGG-TCAAAATGAAATTTTTAGAAAGTTTAA
*
30938 GGGTCAAAATGAAATTTTTAGAAAGTTTAG
1 GGGTCAAAATGAAATTTTTAGAAAGTTTAA
* *
30968 GGGTCAAAAAAGAAATTTATAGAAAGTTT-A
1 GGGTC-AAAATGAAATTTTTAGAAAGTTTAA
* *
30998 GGGATCAAAAT-AACATTTCTAAAAAGTTTAA
1 GGG-TCAAAATGAA-ATTTTTAGAAAGTTTAA
* * * *
31029 TGGTTAAAATGACATTTTTAGAAAGTTTAG
1 GGGTCAAAATGAAATTTTTAGAAAGTTTAA
* * * *
31059 GGGTCAAAATGACATTTTCAAAAAGTTTGA
1 GGGTCAAAATGAAATTTTTAGAAAGTTTAA
*
31089 GGGTCAAAATGTAA-TTTTAGAA
1 GGGTCAAAATGAAATTTTTAGAA
31111 CAAAACAAGG
Statistics
Matches: 166, Mismatches: 31, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
29 11 0.07
30 106 0.64
31 49 0.30
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATGAAATTTTTAGAAAGTTTAA
Found at i:30962 original size:61 final size:60
Alignment explanation
Indices: 30898--31110 Score: 213
Period size: 61 Copynumber: 3.5 Consensus size: 60
30888 AAAATTTTGG
* *
30898 AAAGTTTTTGGGTTTAAAATGTAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTAG
1 AAAGTTTATGGG-TTAAAATGTAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTAA
* * * * * *
30959 AAAGTTTAGGGGTCAAAAAAGAAATTTATAGAAAGTTT-AGGGATCAAAAT-AACATTTCTAA
1 AAAGTTTATGGGT-TAAAATGTAATTTTTAGAAAGTTTAAGGG-TCAAAATGAA-ATTTTTAA
* * *
31020 AAAGTTTAAT-GGTTAAAATG-ACATTTTTAGAAAGTTTAGGGGTCAAAATGACATTTTCAA
1 AAAGTTT-ATGGGTTAAAATGTA-ATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTAA
*
31080 AAAGTTTGA-GGGTCAAAATGTAA-TTTTAGAA
1 AAAGTTT-ATGGGTTAAAATGTAATTTTTAGAA
31111 CAAAACAAGG
Statistics
Matches: 125, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
59 9 0.07
60 57 0.46
61 58 0.46
62 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
AAAGTTTATGGGTTAAAATGTAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTAA
Found at i:31008 original size:91 final size:90
Alignment explanation
Indices: 30913--31110 Score: 251
Period size: 91 Copynumber: 2.2 Consensus size: 90
30903 TTTTGGGTTT
30913 AAAATGTAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTAGAAAGTTTAGGGGTCAAAAA
1 AAAATGTAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTAGAAAGTTTAGGGGTC-AAAA
*
30978 AGAAATTTAT-AGAAAGTTT-AGGGATC
65 AGAAATTT-TCAAAAAGTTTGAGGG-TC
* * * * * *
31004 AAAAT-AACATTTCTAAAAAGTTTAATGGTTAAAATGACATTTTTAGAAAGTTTAGGGGTCAAAA
1 AAAATGTA-ATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTAGAAAGTTTAGGGGTCAAAA
* *
31068 TGACATTTTCAAAAAGTTTGAGGGTC
65 AGAAATTTTCAAAAAGTTTGAGGGTC
31094 AAAATGTAA-TTTTAGAA
1 AAAATGTAATTTTTAGAA
31111 CAAAACAAGG
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
89 7 0.08
90 27 0.30
91 57 0.63
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (90 bp):
AAAATGTAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTAGAAAGTTTAGGGGTCAAAAA
GAAATTTTCAAAAAGTTTGAGGGTC
Found at i:32797 original size:82 final size:82
Alignment explanation
Indices: 32694--32847 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 82
32684 ATATGATAGA
* * *
32694 TTAAATATTATTAAATATTAATTATCATTTAATTAATATTATAGTTATATATTAATTAAAATTAA
1 TTAAATATTATTAAATATTAATTATCATTTAATTAATATTACAATTATATATCAATTAAAATTAA
32759 AATTTACTGAAGTATCG
66 AATTTACTGAAGTATCG
* * *
32776 TTAAATATTATTTTAA-ATTAATTATCATTTAATTAGTGTTACAATTATATATCAATTAAAATTA
1 TTAAATATTA-TTAAATATTAATTATCATTTAATTAATATTACAATTATATATCAATTAAAATTA
*
32840 AGATTTAC
65 AAATTTAC
32848 CATCATAAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
82 60 0.94
83 4 0.06
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (82 bp):
TTAAATATTATTAAATATTAATTATCATTTAATTAATATTACAATTATATATCAATTAAAATTAA
AATTTACTGAAGTATCG
Found at i:33315 original size:13 final size:12
Alignment explanation
Indices: 33292--33322 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
33282 GAGATTTAAG
33292 GTTTAAGTTTGA
1 GTTTAAGTTTGA
33304 GTTTAGAGTTTGA
1 GTTTA-AGTTTGA
33317 GTTTAA
1 GTTTAA
33323 TGTTCAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (12 bp):
GTTTAAGTTTGA
Found at i:33436 original size:7 final size:7
Alignment explanation
Indices: 33424--33449 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
33414 GCGATATGAA
33424 TTTAAAG
1 TTTAAAG
33431 TTTAAAG
1 TTTAAAG
33438 TTTAAAG
1 TTTAAAG
33445 TTTAA
1 TTTAA
33450 GAATTTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (7 bp):
TTTAAAG
Found at i:48629 original size:21 final size:20
Alignment explanation
Indices: 48598--48693 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 20
48588 TGGAACTTAT
*
48598 TGTATCAGTAGAAGGGTAGGA
1 TGTATCGGTAGAA-GGTAGGA
* * *
48619 TGTATTGGTAG-AGCTCAGAGT
1 TGTATCGGTAGAAGGT-AG-GA
* ***
48640 TGTATCGGTAGAAGTTTTTA
1 TGTATCGGTAGAAGGTAGGA
48660 TTGTATCGGTAGAAGGGTAGGA
1 -TGTATCGGTAGAA-GGTAGGA
*
48682 TGTATTGGTAGA
1 TGTATCGGTAGA
48694 GCTCAGACCG
Statistics
Matches: 55, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
19 2 0.04
20 3 0.05
21 44 0.80
22 6 0.11
ACGTcount: A:0.27, C:0.05, G:0.34, T:0.33
Consensus pattern (20 bp):
TGTATCGGTAGAAGGTAGGA
Found at i:52046 original size:14 final size:14
Alignment explanation
Indices: 52027--52055 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52017 TACTAAGAAG
52027 AAGTCAGGCGGTTA
1 AAGTCAGGCGGTTA
52041 AAGTCAGGCGGTTA
1 AAGTCAGGCGGTTA
52055 A
1 A
52056 CCTTGCGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (14 bp):
AAGTCAGGCGGTTA
Found at i:55743 original size:15 final size:15
Alignment explanation
Indices: 55719--55751 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
55709 AGGAAGACAT
55719 AAAGTAA-TTTTAGG
1 AAAGTAATTTTTAGG
55733 AAAGTTAATTTTTAGG
1 AAAG-TAATTTTTAGG
55749 AAA
1 AAA
55752 CTAGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 3 0.18
16 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (15 bp):
AAAGTAATTTTTAGG
Done.