Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009818.1 Kokia drynarioides strain JFW-HI SEQ_124539, 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: 57751
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:1170 original size:2 final size:2
Alignment explanation
Indices: 1136--1160 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1126 TTTCAAATGC
1136 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1161 GGAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16359 original size:18 final size:18
Alignment explanation
Indices: 16336--16373 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
16326 TATTTTTATA
16336 TAAATATTAATAATAA-AT
1 TAAATATT-ATAATAATAT
16354 TAAATATTATAATAATAT
1 TAAATATTATAATAATAT
16372 TA
1 TA
16374 TAGTATAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATATTATAATAATAT
Found at i:19209 original size:53 final size:51
Alignment explanation
Indices: 18978--19208 Score: 259
Period size: 51 Copynumber: 4.5 Consensus size: 51
18968 CAAAAGGATT
* * * * *
18978 CGATGACTAAGTGCCATCGTGAGTAAATGAATCATTTACGAATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATAAGGATTAAAGGTC
* * *
19029 TGATGACTAAGTGCCATCGTGAGTAAATGAATCCTTTAAGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATAAGGATTAAAGGTC
* * *
19080 CAATGACTAAGTGTCATCTTGAGTAAATGAATCC-ATGATGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTAT-AAGGATTAAAGGTC
* * * *
19131 CGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGGAATAAGAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTATAAGGATTAA-AGGTC
* *
19184 CGATAACTGTA-TGTCATCGTGAGTA
1 CGATGACT-AAGTGTCATCGTGAGTA
19209 TTAAATGAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
50 1 0.01
51 117 0.75
52 10 0.06
53 28 0.18
54 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATAAGGATTAAAGGTC
Found at i:19263 original size:61 final size:61
Alignment explanation
Indices: 19157--19311 Score: 174
Period size: 61 Copynumber: 2.6 Consensus size: 61
19147 TCGTGAGTAT
* * * * * * *
19157 ATGAATTCCTATACGGAATAAGAGGTCCGATAACTGTATGTCATCGTGAGTATTAAATGAA
1 ATGAATTCCTATATGGAACAAGAGGTCTGATGACTATACGACATCGTGAGTATTAAATGAA
*
19218 ATGACTTCCTATATGGAACAAGAGGTCTGATGACTATACGACATCGTGAGTATTAAATGAA
1 ATGAATTCCTATATGGAACAAGAGGTCTGATGACTATACGACATCGTGAGTATTAAATGAA
* *
19279 ACGAGTTCC-A-ATGCGAACAAG-GGTCCT-ATGACT
1 ATGAATTCCTATATG-GAACAAGAGGT-CTGATGACT
19312 TTGTGTCATC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
59 12 0.15
60 10 0.12
61 60 0.73
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (61 bp):
ATGAATTCCTATATGGAACAAGAGGTCTGATGACTATACGACATCGTGAGTATTAAATGAA
Found at i:21274 original size:24 final size:24
Alignment explanation
Indices: 21233--21419 Score: 259
Period size: 24 Copynumber: 7.8 Consensus size: 24
21223 TTAAACTCTA
* * *
21233 TCTGGGCTCATAAAAGCTAACCAC
1 TCTGGGCTCGTAAGAGCTAACCAT
*
21257 TCTAGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
* *
21281 TCTGGGCTCATAAGAACTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
21305 TTTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
** *
21329 TCTGGGCTAATAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
21353 T-TGGGCTTGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
21376 TCTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
21400 TCTGGGCTTGTAAGAGCTAA
1 TCTGGGCTCGTAAGAGCTAA
21420 ATGTTATCTC
Statistics
Matches: 143, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
23 20 0.14
24 123 0.86
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACCAT
Found at i:21383 original size:71 final size:72
Alignment explanation
Indices: 21233--21419 Score: 259
Period size: 71 Copynumber: 2.6 Consensus size: 72
21223 TTAAACTCTA
* * * * *
21233 TCTGGGCTCATAAAAGCTAACCACTCTAGGCTCGTAAGAGCTAACCATTCTGGGCTCATAAGAAC
1 TCTGGGCTCGTAAGAGCTAACCATTCTGGGCTAGTAAGAGCTAACCATTCTGGGCTCATAAGAAC
21298 TAACCAT
66 TAACCAT
* * * ** *
21305 TTTGGGCTCGTAAGAGCTAACCATTCTGGGCTAATAAGAGCTAATCATT-TGGGCTTGTAAGAGC
1 TCTGGGCTCGTAAGAGCTAACCATTCTGGGCTAGTAAGAGCTAACCATTCTGGGCTCATAAGAAC
21369 TAACCAT
66 TAACCAT
*
21376 TCTGGGCTCGTAAGAGCTAACCATTCTGGGCTTGTAAGAGCTAA
1 TCTGGGCTCGTAAGAGCTAACCATTCTGGGCTAGTAAGAGCTAA
21420 ATGTTATCTC
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 60 0.59
72 41 0.41
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (72 bp):
TCTGGGCTCGTAAGAGCTAACCATTCTGGGCTAGTAAGAGCTAACCATTCTGGGCTCATAAGAAC
TAACCAT
Found at i:40678 original size:19 final size:20
Alignment explanation
Indices: 40646--40688 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
40636 TTTCTCTGCT
40646 TGTT-CTCTATTTTCTATTC-
1 TGTTACTCTATTTTCT-TTCA
40665 TGTTACTCTA-TTTCTTTCA
1 TGTTACTCTATTTTCTTTCA
40684 TGTTA
1 TGTTA
40689 TCAGTCGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.14, C:0.19, G:0.07, T:0.60
Consensus pattern (20 bp):
TGTTACTCTATTTTCTTTCA
Found at i:42362 original size:97 final size:97
Alignment explanation
Indices: 42195--42388 Score: 280
Period size: 97 Copynumber: 2.0 Consensus size: 97
42185 AACCTTGAAA
* * *
42195 AAGGGTATTCGATTATTCCGGTTTAAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCAGTTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* * *
42260 AAACCCGAAGTACAGGAATATTGCCTCAATTT
66 AAACCCGAAATAAAGGAATATTACCTCAATTT
* * **
42292 AAGGGTATTTGATTATCCCAGTTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCATGAATTTTCA
1 AAGGGTATTCGATTATCCCAGTTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
42357 GAACCCGAAATAAAGGAATATTACCTCGATTT
66 AAACCCGAAATAAAGGAATATTACCTCAATTT
42389 TAAATATTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 85 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCAGTTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAACCCGAAATAAAGGAATATTACCTCAATTT
Found at i:42873 original size:30 final size:30
Alignment explanation
Indices: 42732--42977 Score: 179
Period size: 29 Copynumber: 8.4 Consensus size: 30
42722 AAAGTCAAAC
* * * * *
42732 TTTTGGAAAATTTAAAGTTGAAAGTGTGATT
1 TTTTGGAAAGTTTAAGGGTAAAAATGTGA-T
* *
42763 TTTTGG-AAGTTTGAGGGT-AAAATG-GTAA
1 TTTTGGAAAGTTTAAGGGTAAAAATGTG-AT
* * *
42791 TTTTGG-ATG-TTCAGGGACAAAAATGTGA-
1 TTTTGGAAAGTTTAAGGG-TAAAAATGTGAT
* ** * *
42819 ATTTGGAAA-TTCGAGGGCAAAAATGTGCT
1 TTTTGGAAAGTTTAAGGGTAAAAATGTGAT
42848 TTTTGGAAAGTTTAAGGGTAAAAATGTGAT
1 TTTTGGAAAGTTTAAGGGTAAAAATGTGAT
*
42878 TTTT-GAAAGTTTAAGGGTGAAAATG-GAAT
1 TTTTGGAAAGTTTAAGGGTAAAAATGTG-AT
* *
42907 TTTTGGAAAGTTTAA-GGTCAAAATGTAAT
1 TTTTGGAAAGTTTAAGGGTAAAAATGTGAT
* ** * *
42936 TTTTGGAAATTTTGGGGGTCAAAATGTAAT
1 TTTTGGAAAGTTTAAGGGTAAAAATGTGAT
42966 TTTTGGAAAGTT
1 TTTTGGAAAGTT
42978 CAAAGTTTAG
Statistics
Matches: 177, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
27 6 0.03
28 25 0.14
29 76 0.43
30 64 0.36
31 6 0.03
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAGTTTAAGGGTAAAAATGTGAT
Found at i:42910 original size:59 final size:59
Alignment explanation
Indices: 42847--42977 Score: 183
Period size: 59 Copynumber: 2.2 Consensus size: 59
42837 AAAAATGTGC
* *
42847 TTTTTGGAAAGTTTAAGGGTAAAAATGTGATTTTT-GAAAGTTTAAGGGTGAAAATGGAA
1 TTTTTGGAAAGTTTAA-GGTAAAAATGTAATTTTTGGAAAGTTTAAGGGTCAAAATGGAA
* * ** *
42906 TTTTTGGAAAGTTTAAGGTCAAAATGTAATTTTTGGAAATTTTGGGGGTCAAAATGTAA
1 TTTTTGGAAAGTTTAAGGTAAAAATGTAATTTTTGGAAAGTTTAAGGGTCAAAATGGAA
42965 TTTTTGGAAAGTT
1 TTTTTGGAAAGTT
42978 CAAAGTTTAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
58 16 0.25
59 48 0.75
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (59 bp):
TTTTTGGAAAGTTTAAGGTAAAAATGTAATTTTTGGAAAGTTTAAGGGTCAAAATGGAA
Found at i:42968 original size:29 final size:30
Alignment explanation
Indices: 42838--43055 Score: 201
Period size: 29 Copynumber: 7.2 Consensus size: 30
42828 TTCGAGGGCA
** *
42838 AAAATGTGCTTTTTGGAAAGTTTAAGGGTA
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTC
* *
42868 AAAATGTGATTTTT-GAAAGTTTAAGGGTG
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTC
*
42897 AAAATGGAATTTTTGGAAAGTTTAA-GGTC
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTC
* **
42926 AAAATGTAATTTTTGGAAATTTTGGGGGTC
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTC
*
42956 AAAATGTAATTTTTGGAAAGTTCAAAGTTTAGGGGTC
1 AAAATGTAATTTTT-G---G---AAAGTTTAAGGGTC
*** *
42993 -AAATGTAATTTTTGGAAAGTTCGGGGGTA
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTC
* *
43022 AAAATATAATTTTTGGAAAG-TTAAGGATC
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTC
43051 AAAAT
1 AAAAT
43056 TTGATTATTG
Statistics
Matches: 158, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
29 70 0.44
30 59 0.37
31 1 0.01
32 1 0.01
34 1 0.01
35 1 0.01
36 13 0.08
37 12 0.08
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTAAGGGTC
Found at i:42997 original size:66 final size:66
Alignment explanation
Indices: 42913--43043 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
42903 GAATTTTTGG
* * * *
42913 AAAGTTTAAGGTCAAAATGTAATTTTTGGAAATTTTGGGGGTCAAAATGTAATTTTTGGAAAGTT
1 AAAGTTTAAGGTCAAAATGTAATTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGTT
42978 C
66 C
*
42979 AAAGTTTAGGGGTC-AAATGTAATTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGT
1 AAAGTTTA-AGGTCAAAATGTAATTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGT
43043 T
65 T
43044 AAGGATCAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 55 0.93
67 4 0.07
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (66 bp):
AAAGTTTAAGGTCAAAATGTAATTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGTT
C
Found at i:43054 original size:95 final size:96
Alignment explanation
Indices: 42883--43074 Score: 217
Period size: 95 Copynumber: 2.0 Consensus size: 96
42873 GTGATTTTTG
* * * *
42883 AAAGTTTAAGGGTGAAAATGGAATTTTTGGAAAGTTTAAGGTCAAAATGTAATTTTTGGAAATTT
1 AAAGTTTAAGGGTGAAAATGGAATTTTTGGAAAGTTGAAGGTAAAAATATAATTTTTGGAAATGT
** * *
42948 TGGGGGTCAAAATGTAATTTTTGGAAAGTTC
66 TAAGGATCAAAATGTAATTATTGGAAAGTTC
* * * **
42979 AAAGTTTAGGGGT-CAAATGTAATTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAA-G
1 AAAGTTTAAGGGTGAAAATGGAATTTTTGGAAAGTT-GAAGGTAAAAATATAATTTTTGGAAATG
* * *
43042 TTAAGGATCAAAATTTGATTATTGGATAGTTC
65 TTAAGGATCAAAATGTAATTATTGGAAAGTTC
43074 A
1 A
43075 GGGATTTCTG
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
95 46 0.58
96 33 0.42
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (96 bp):
AAAGTTTAAGGGTGAAAATGGAATTTTTGGAAAGTTGAAGGTAAAAATATAATTTTTGGAAATGT
TAAGGATCAAAATGTAATTATTGGAAAGTTC
Found at i:44818 original size:28 final size:28
Alignment explanation
Indices: 44741--44860 Score: 82
Period size: 28 Copynumber: 4.2 Consensus size: 28
44731 AAGTGTGATT
* * *
44741 TTTTGGAAGTTCGAGGGTAAAACG-GTAA
1 TTTTGGAAATTCGAGGGAAAAATGTG-AA
** * *
44769 TTTTGGATGTTCAAGGAAAAAATGTGAA
1 TTTTGGAAATTCGAGGGAAAAATGTGAA
**
44797 TTTTGGAAATTCGAGGGCAAAAATGTGCT
1 TTTTGGAAATTCGAGGG-AAAAATGTGAA
* *
44826 TTTTGGAAAGTT-TAGGGGTAAAAATGTGAT
1 TTTTGGAAA-TTCGA-GGG-AAAAATGTGAA
44856 TTTTG
1 TTTTG
44861 AAAGTTTAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
28 34 0.46
29 20 0.27
30 20 0.27
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (28 bp):
TTTTGGAAATTCGAGGGAAAAATGTGAA
Found at i:44851 original size:30 final size:30
Alignment explanation
Indices: 44786--45055 Score: 167
Period size: 29 Copynumber: 8.9 Consensus size: 30
44776 TGTTCAAGGA
* * *
44786 AAAAATGTGAATTTTGGAAA--TTCGAGGGC
1 AAAAATGTGATTTTTGGAAAGTTTAG-GGGT
*
44815 AAAAATGTGCTTTTTGGAAAGTTTAGGGGT
1 AAAAATGTGATTTTTGGAAAGTTTAGGGGT
*
44845 AAAAATGTGATTTTT-GAAAGTTTAAGGGT
1 AAAAATGTGATTTTTGGAAAGTTTAGGGGT
* *
44874 GAAAATG-GAATTTTTGGAAAGTTTA-AGGT
1 AAAAATGTG-ATTTTTGGAAAGTTTAGGGGT
* * * * *
44903 CAAAATGTAATTTTTAGAAATTTTGGGGGT
1 AAAAATGTGATTTTTGGAAAGTTTAGGGGT
* *
44933 CAAAATGTAATTTTTGGAAAGTTCAAAGTTTAGGGGT
1 AAAAATGTGATTTTT-G---G---AAAGTTTAGGGGT
* * * **
44970 -CAAATATAATTTTTGGAAAGTTCGGGGGT
1 AAAAATGTGATTTTTGGAAAGTTTAGGGGT
* * *
44999 AAAAATATAATTTTTGGAAAGTTT-GGGAT
1 AAAAATGTGATTTTTGGAAAGTTTAGGGGT
* * * * *
45028 CAAAATTTGATTATTGGATAGTTCAGGG
1 AAAAATGTGATTTTTGGAAAGTTTAGGG
45056 ATCTTCTGGG
Statistics
Matches: 196, Mismatches: 30, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
28 1 0.01
29 98 0.50
30 68 0.35
31 3 0.02
32 1 0.01
34 1 0.01
35 1 0.01
36 12 0.06
37 11 0.06
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAAATGTGATTTTTGGAAAGTTTAGGGGT
Found at i:44980 original size:66 final size:66
Alignment explanation
Indices: 44891--45021 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
44881 GAATTTTTGG
* * * * *
44891 AAAGTTTAAGGTCAAAATGTAATTTTTAGAAATTTTGGGGGTCAAAATGTAATTTTTGGAAAGTT
1 AAAGTTTAAGGTCAAAATATAATTTTTAGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGTT
44956 C
66 C
* *
44957 AAAGTTTAGGGGTC-AAATATAATTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGT
1 AAAGTTTA-AGGTCAAAATATAATTTTTAGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGT
45021 T
65 T
45022 TGGGATCAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (66 bp):
AAAGTTTAAGGTCAAAATATAATTTTTAGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGTT
C
Found at i:45022 original size:59 final size:59
Alignment explanation
Indices: 44740--45031 Score: 195
Period size: 59 Copynumber: 4.9 Consensus size: 59
44730 AAAGTGTGAT
** * * * ***
44740 TTTTTGG-AAGTTCGAGGGTAAAACGGTAA-TTTTGG-ATGTTCAAGGAAAAAATGTGAA
1 TTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTCAAATGT-AA
* ** * *
44797 -TTTTGGAAA-TTCGAGGGCAAAAATGTGCTTTTTGGAAAGTTTAGGGGTAAAAATGTGA
1 TTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGT-CAAATGTAA
** * * *
44855 TTTTT-GAAAGTTTAAGGGTGAAAATGGAATTTTTGGAAAGTTTA-AGGTCAAAATGTAA
1 TTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTC-AAATGTAA
* * * * * *
44913 TTTTTAGAAATTTTGGGGGTCAAAATGTAATTTTTGGAAAGTTCAAAGTTTAGGGGTCAAATATA
1 TTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTT-G---G---AAAGTTTAGGGGTCAAATGTA
44978 A
59 A
* * *
44979 TTTTTGGAAAGTTCGGGGGTAAAAATATAATTTTTGGAAAGTTT-GGGATCAAA
1 TTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTCAAA
45032 ATTTGATTAT
Statistics
Matches: 185, Mismatches: 34, Indels: 31
0.74 0.14 0.12
Matches are distributed among these distances:
56 20 0.11
57 8 0.04
58 35 0.19
59 69 0.37
60 1 0.01
62 1 0.01
63 1 0.01
65 1 0.01
66 45 0.24
67 4 0.02
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (59 bp):
TTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTCAAATGTAA
Found at i:46801 original size:17 final size:17
Alignment explanation
Indices: 46779--46898 Score: 117
Period size: 17 Copynumber: 7.3 Consensus size: 17
46769 AATTTCGGAC
*
46779 TTAAATTTAAAATAATT
1 TTAAATTTAAAATAAAT
46796 TTAAATTTAAAAATAAAT
1 TTAAATTT-AAAATAAAT
* *
46814 TTAAACTTAAATTAAAT
1 TTAAATTTAAAATAAAT
46831 TTAAA-TT----TAAAT
1 TTAAATTTAAAATAAAT
** *
46843 TTAAA-ACAAATTTAAAT
1 TTAAATTTAAA-ATAAAT
*
46860 TTAAATTTAAAACAAAT
1 TTAAATTTAAAATAAAT
46877 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
46894 TTAAA
1 TTAAA
46899 AGAGTGAGTT
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
12 10 0.12
16 2 0.02
17 56 0.65
18 18 0.21
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:46804 original size:6 final size:6
Alignment explanation
Indices: 46779--46898 Score: 115
Period size: 6 Copynumber: 20.8 Consensus size: 6
46769 AATTTCGGAC
* * * * *
46779 TTAAAT TTAAA- ATAATT TTAAAT TTAAAA ATAAAT TTAAAC TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
**
46825 TTAAAT TTAAAT TTAAAT TTAAA- ACAAAT TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** *
46871 ACAAAT TTAAAT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
46899 AGAGTGAGTT
Statistics
Matches: 90, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
5 18 0.20
6 72 0.80
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:46813 original size:29 final size:28
Alignment explanation
Indices: 46780--46864 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
46770 ATTTCGGACT
46780 TAAATTTAAAATAATTTTAAATTTAAAAA
1 TAAATTTAAAATAA-TTTAAATTTAAAAA
* * **
46809 TAAATTTAAACTTAAATTAAATTTAAATT
1 TAAATTTAAA-ATAATTTAAATTTAAAAA
*
46838 TAAATTTAAAACAAATTTAAATTTAAA
1 TAAATTTAAAA-TAATTTAAATTTAAA
46865 TTTAAAACAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 44 0.94
30 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAATTTAAAATAATTTAAATTTAAAAA
Found at i:46828 original size:23 final size:23
Alignment explanation
Indices: 46827--46892 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
46817 AACTTAAATT
*
46827 AAATTTAAATTTAAATTTAAAAC
1 AAATTTAAATTTAAATTAAAAAC
*
46850 AAATTTAAATTTAAATTTAAAAC
1 AAATTTAAATTTAAATTAAAAAC
*
46873 AAATTTAAATTTAAAATAAA
1 AAATTTAAATTTAAATTAAA
46893 TTTAAAAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTAAATTTAAATTAAAAAC
Found at i:56935 original size:2 final size:2
Alignment explanation
Indices: 56928--56954 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56918 TTATTAACTA
56928 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
56955 AGAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.