Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014601.1 Kokia drynarioides strain JFW-HI SEQ_129640, 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: 86514
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 95 characters in sequence are not A, C, G, or T
Found at i:832 original size:18 final size:17
Alignment explanation
Indices: 794--904 Score: 107
Period size: 18 Copynumber: 6.4 Consensus size: 17
784 CTTTACTTAT
* *
794 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
811 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
829 TTTAAACTT-AAATCAAA
1 TTTAAATTTAAAAT-AAA
*
846 TTTAAATTCAAAATAAA
1 TTTAAATTTAAAATAAA
* *
863 TTTAAAATTTTAAACAAA
1 TTT-AAATTTAAAATAAA
*
881 TTTAATTTTTAAAATAAA
1 TTTAA-ATTTAAAATAAA
*
899 CTTAAA
1 TTTAAA
905 GAGAGTTTGG
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.05
17 27 0.36
18 45 0.59
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:833 original size:35 final size:35
Alignment explanation
Indices: 794--904 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 35
784 CTTTACTTAT
* *
794 TTTAAATTTATAATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTATAATAAATTTAAATTTCAAAATAAA
*
829 TTTAAACTTA-AATCAAATTTAAA-TTCAAAATAAA
1 TTTAAATTTATAAT-AAATTTAAATTTCAAAATAAA
* * *
863 TTTAAAATTT-TAAACAAATTTAATTTTTAAAATAAA
1 TTT-AAATTTAT-AATAAATTTAAATTTCAAAATAAA
*
899 CTTAAA
1 TTTAAA
905 GAGAGTTTGG
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
34 16 0.25
35 33 0.52
36 14 0.22
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (35 bp):
TTTAAATTTATAATAAATTTAAATTTCAAAATAAA
Found at i:7675 original size:30 final size:29
Alignment explanation
Indices: 7626--7958 Score: 185
Period size: 30 Copynumber: 11.1 Consensus size: 29
7616 TGGATGTTCG
7626 GGGGT-AAAATAGTAATTTTGGAGAAGTTTA
1 GGGGTCAAAATA-T-ATTTTGGAGAAGTTTA
7656 GGGGTCAAAATATACTTTTGGAGAAGTTTA
1 GGGGTCAAAATATA-TTTTGGAGAAGTTTA
* *
7686 GGGATCAAAATATAATTTTAGAGAAGTTTA
1 GGGGTCAAAATAT-ATTTTGGAGAAGTTTA
* ** *
7716 GGGGTCAAAATGTATTTTTAAGAAATTTA
1 GGGGTCAAAATATATTTTGGAGAAGTTTA
* *
7745 GAGGGTCAAAATATGATTTTTGAGAAATTTA
1 G-GGGTCAAAATAT-ATTTTGGAGAAGTTTA
* * * ** *
7776 AGGGTTAAAATGTGATTTTTAAGAAG-TTC
1 GGGGTCAAAATAT-ATTTTGGAGAAGTTTA
* *
7805 GAGGGTTAAAATGTAATGTTTGTGA-AA-TTTA
1 G-GGGTCAAAATAT-AT-TTTG-GAGAAGTTTA
* * * *
7836 AGGGTTAAAATGTGATTTTTGAGAAGTTTA
1 GGGGTCAAAATAT-ATTTTGGAGAAGTTTA
* * *
7866 AGGGTCAAAATGTAATTTT-TATGAAGTTTA
1 GGGGTCAAAATAT-ATTTTGGA-GAAGTTTA
* * * *
7896 AGGGTTAAAATGTAATTTT-TACGAAGTTTA
1 GGGGTCAAAATAT-ATTTTGGA-GAAGTTTA
* * **
7926 AGGGTCAAAATGTGATTTTTAAGAAGTTT-
1 GGGGTCAAAATAT-ATTTTGGAGAAGTTTA
7955 GGGG
1 GGGG
7959 ACCTTTTGAG
Statistics
Matches: 258, Mismatches: 32, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
28 2 0.01
29 26 0.10
30 199 0.77
31 30 0.12
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
GGGGTCAAAATATATTTTGGAGAAGTTTA
Found at i:7702 original size:60 final size:58
Alignment explanation
Indices: 7627--7954 Score: 295
Period size: 60 Copynumber: 5.5 Consensus size: 58
7617 GGATGTTCGG
* * * **
7627 GGGT-AAAATAGTAATTTTGGAGAAGTTTAGGGGTCAAAATATACTTTTGGAGAAGTTTA
1 GGGTCAAAATA-TAATTTTGGAGAAGTTTAAGGGTTAAAATGTA-TTTTTAAGAAGTTTA
* * * *
7686 GGGATCAAAATATAATTTTAGAGAAGTTTAGGGGTCAAAATGTATTTTTAAGAAATTTAGA
1 GGG-TCAAAATATAATTTTGGAGAAGTTTAAGGGTTAAAATGTATTTTTAAGAAGTTT--A
* * * *
7747 GGGTCAAAATATGATTTTTGAGAAATTTAAGGGTTAAAATGTGATTTTTAAGAAGTTCGA
1 GGGTCAAAATATAATTTTGGAGAAGTTTAAGGGTTAAAATGT-ATTTTTAAGAAGTT-TA
* * *
7807 GGGTTAAAATGTAATGTTTGTGA-AA-TTTAAGGGTTAAAATGTGATTTTTGAGAAGTTTAA
1 GGGTCAAAATATAAT-TTTG-GAGAAGTTTAAGGGTTAAAATGT-ATTTTTAAGAAGTTT-A
* * *
7867 GGGTCAAAATGTAATTTT-TATGAAGTTTAAGGGTTAAAATGTAATTTTTACGAAGTTTAA
1 GGGTCAAAATATAATTTTGGA-GAAGTTTAAGGGTTAAAATGT-ATTTTTAAGAAGTTT-A
* * **
7927 GGGTCAAAATGTGATTTTTAAGAAGTTT
1 GGGTCAAAATATAATTTTGGAGAAGTTT
7955 GGGGACCTTT
Statistics
Matches: 231, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
57 1 0.00
59 19 0.08
60 180 0.78
61 29 0.13
62 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (58 bp):
GGGTCAAAATATAATTTTGGAGAAGTTTAAGGGTTAAAATGTATTTTTAAGAAGTTTA
Found at i:7752 original size:90 final size:89
Alignment explanation
Indices: 7625--7954 Score: 353
Period size: 90 Copynumber: 3.7 Consensus size: 89
7615 TTGGATGTTC
* ** * * *
7625 GGGGGTAAAATAGTAATTTTGGAGAAGTTTAGGGGTCAAAATAT-ACTTTTGGAGAAGTTT-AGG
1 GGGGTTAAAAT-GTAATTTTTAAGAAATTTAAGGGTCAAAATATGA-TTTTTGAGAAGTTTAAGG
*
7688 GATCAAAATATAATTTTAGAGAAGTTTA
64 G-TCAAAATGTAATTTTA-AGAAGTTTA
* *
7716 GGGGTCAAAATGT-ATTTTTAAGAAATTTAGAGGGTCAAAATATGATTTTTGAGAAATTTAAGGG
1 GGGGTTAAAATGTAATTTTTAAGAAATTTA-AGGGTCAAAATATGATTTTTGAGAAGTTTAAGGG
* * *
7780 TTAAAATGTGATTTTTAAGAAG-TTC
65 TCAAAATGT-AATTTTAAGAAGTTTA
* ** * *
7805 GAGGGTTAAAATGTAATGTTTGTGAAATTTAAGGGTTAAAATGTGATTTTTGAGAAGTTTAAGGG
1 G-GGGTTAAAATGTAATTTTTAAGAAATTTAAGGGTCAAAATATGATTTTTGAGAAGTTTAAGGG
*
7870 TCAAAATGTAATTTTTATGAAGTTTA
65 TCAAAATGTAA-TTTTAAGAAGTTTA
* * * * *
7896 AGGGTTAAAATGTAATTTTTACGAAGTTTAAGGGTCAAAATGTGATTTTTAAGAAGTTT
1 GGGGTTAAAATGTAATTTTTAAGAAATTTAAGGGTCAAAATATGATTTTTGAGAAGTTT
7955 GGGGACCTTT
Statistics
Matches: 201, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
89 17 0.08
90 149 0.74
91 35 0.17
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (89 bp):
GGGGTTAAAATGTAATTTTTAAGAAATTTAAGGGTCAAAATATGATTTTTGAGAAGTTTAAGGGT
CAAAATGTAATTTTAAGAAGTTTA
Found at i:9049 original size:12 final size:12
Alignment explanation
Indices: 9023--9075 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
9013 TTTCATTTCT
9023 TATTATT-TT-A
1 TATTATTATTAA
9033 T-TTATTATTAA
1 TATTATTATTAA
9044 TATTATTATTAA
1 TATTATTATTAA
9056 TATTA-TATTTAA
1 TATTATTA-TTAA
9068 TATGTATT
1 TAT-TATT
9076 TACTGCTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.14
10 3 0.08
11 4 0.11
12 22 0.59
13 2 0.05
14 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:9769 original size:2 final size:2
Alignment explanation
Indices: 9756--9793 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
9746 GGGCTCCAAC
* *
9756 AT AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9794 TAACATCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10880 original size:29 final size:29
Alignment explanation
Indices: 10848--11020 Score: 176
Period size: 29 Copynumber: 6.0 Consensus size: 29
10838 AATTCGAATT
* *
10848 TAAAAATGGAATTTTTAGACA-TTCCGGGA
1 TAAAAATGGAATTTTTAGA-AGTTTCGGGG
* * *
10877 TAAAAGTGTAATTTTGAG-AGTTTCGGGG
1 TAAAAATGGAATTTTTAGAAGTTTCGGGG
*
10905 TCAAAAATGAAATTTTTAGAAG-TTCGAGGG
1 T-AAAAATGGAATTTTTAGAAGTTTCG-GGG
*
10935 TAAAAATGGAATTTTTAGAAGTTTTGGGG
1 TAAAAATGGAATTTTTAGAAGTTTCGGGG
* *
10964 TCAAAAATGGAATTTTTGGAAG-CTCGGGGG
1 T-AAAAATGGAATTTTTAGAAGTTTC-GGGG
*
10994 T-AAAATGGAATTTTTGGAAGTTTCGGG
1 TAAAAATGGAATTTTTAGAAGTTTCGGG
11021 ACCTCCTGGG
Statistics
Matches: 122, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.01
28 29 0.24
29 59 0.48
30 33 0.27
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.33
Consensus pattern (29 bp):
TAAAAATGGAATTTTTAGAAGTTTCGGGG
Found at i:10978 original size:59 final size:58
Alignment explanation
Indices: 10849--11020 Score: 206
Period size: 58 Copynumber: 2.9 Consensus size: 58
10839 ATTCGAATTT
* * * *
10849 AAAAATGGAATTTTTAGACA-TTCCGGGATAAAAGTGTAATTTTGAG-AGTTTCGGGGTC
1 AAAAATGGAATTTTTAGA-AGTT-CGGGGTAAAAATGGAATTTTTAGAAGTTTCGGGGTC
* *
10907 AAAAATGAAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTAGAAGTTCG-GGGTAAAAATGGAATTTTTAGAAGTTTCGGGGTC
* * *
10966 AAAAATGGAATTTTTGGAAGCTCGGGGGT-AAAATGGAATTTTTGGAAGTTTCGGG
1 AAAAATGGAATTTTTAGAAGTTC-GGGGTAAAAATGGAATTTTTAGAAGTTTCGGG
11021 ACCTCCTGGG
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
57 3 0.03
58 60 0.61
59 35 0.35
60 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAAATGGAATTTTTAGAAGTTCGGGGTAAAAATGGAATTTTTAGAAGTTTCGGGGTC
Found at i:12851 original size:17 final size:18
Alignment explanation
Indices: 12829--12871 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12819 TTTTTAATTT
*
12829 ATTTTAAATTT-ATAATA
1 ATTTTAAATTTGAAAATA
12846 ATTTTAAATTTGAAAATA
1 ATTTTAAATTTGAAAATA
*
12864 AATTTAAA
1 ATTTTAAA
12872 CTTAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTTAAATTTGAAAATA
Found at i:12899 original size:17 final size:17
Alignment explanation
Indices: 12831--12888 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
12821 TTTAATTTAT
* *
12831 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
12848 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
12866 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
12883 TTTAAA
1 TTTAAA
12889 ATAAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:12900 original size:11 final size:11
Alignment explanation
Indices: 12868--12901 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12858 AAAATAAATT
* *
12868 TAAACTTAAAT
1 TAAATTTAAAA
12879 TAAATTTAAAA
1 TAAATTTAAAA
12890 TAAATTTAAAA
1 TAAATTTAAAA
12901 T
1 T
12902 GAGTTTGGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:15178 original size:22 final size:22
Alignment explanation
Indices: 15135--15185 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
15125 TTATATTAAG
*
15135 ATTTGTTA-TTTGAATTTGATTT
1 ATTT-TTATTTTGAATTTAATTT
15157 -TTTTTATTTTGAAATTTAATTT
1 ATTTTTATTTTG-AATTTAATTT
15179 ATTTTTA
1 ATTTTTA
15186 CTTAATTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 7 0.28
22 9 0.36
23 6 0.24
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (22 bp):
ATTTTTATTTTGAATTTAATTT
Found at i:15194 original size:27 final size:28
Alignment explanation
Indices: 15142--15194 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
15132 AAGATTTGTT
* *
15142 ATTTGAATTTGATTTTTTTTATTTTGAA
1 ATTTGAATTTGATTTTTCTTAATTTGAA
15170 ATTT-AATTT-ATTTTTACTTAATTTG
1 ATTTGAATTTGATTTTT-CTTAATTTG
15195 GTACTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 6 0.27
27 12 0.55
28 4 0.18
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (28 bp):
ATTTGAATTTGATTTTTCTTAATTTGAA
Found at i:15260 original size:29 final size:28
Alignment explanation
Indices: 15220--15325 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 28
15210 ACTTTTTTCT
15220 AATTTGGTACCTAAACTTTTTTTGGACTC
1 AATTTGGTACCTAAACTTTTTTT-GACTC
* ** *
15249 AATTTGGTACCTGAACTTGGCATTTTTTCCCC
1 AATTTGGTACCTAAACTT----TTTTTGACTC
* * *
15281 TAATTTGGTACCTAAGCTTTTTTTAGATTT
1 -AATTTGGTACCTAAACTTTTTTT-GACTC
15311 AATTTGGTACCTAAA
1 AATTTGGTACCTAAA
15326 TTTATTAAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
29 36 0.61
32 2 0.03
33 21 0.36
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (28 bp):
AATTTGGTACCTAAACTTTTTTTGACTC
Found at i:15315 original size:62 final size:60
Alignment explanation
Indices: 15185--15322 Score: 188
Period size: 62 Copynumber: 2.3 Consensus size: 60
15175 ATTTATTTTT
* *
15185 ACTTAATTTGGTACTTGAACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTTGG
1 ACTTAATTTGGTACCTGAACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTTAG
* * *
15245 ACTCAATTTGGTACCTGAACTTGGCA-TTTTTTCCCCTAATTTGGTACCTAAGCTTTTTTTAG
1 ACTTAATTTGGTACCTGAACTTGACACTTTTTT---CTAATTTGGTACCTAAACTTTTTTTAG
*
15307 ATTTAATTTGGTACCT
1 ACTTAATTTGGTACCT
15323 AAATTTATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 6 0.09
60 23 0.34
62 39 0.57
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.46
Consensus pattern (60 bp):
ACTTAATTTGGTACCTGAACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTTAG
Found at i:16946 original size:8 final size:8
Alignment explanation
Indices: 16933--16963 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
16923 TGATCTATAG
16933 TTATGAAT
1 TTATGAAT
16941 TTATGAAT
1 TTATGAAT
16949 TTATGAAT
1 TTATGAAT
16957 TT-TGAAT
1 TTATGAAT
16964 ATAGTTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (8 bp):
TTATGAAT
Found at i:17023 original size:92 final size:91
Alignment explanation
Indices: 16866--17047 Score: 346
Period size: 92 Copynumber: 2.0 Consensus size: 91
16856 CATTGATTGA
16866 TTGAATATAGTTATCTAGAATCTAGAGTGTAGTTTTGTGAATTCGATTTATGAATTTTGATCTAT
1 TTGAATATAGTTATCTAGAATCTAGAGTGTAGTTTTGTGAATTCGATTTATGAATTTTGATCTAT
*
16931 AGTTATGAATTTATGAATTTATGAATT
66 AGTTATGAATCTATGAATTT-TGAATT
16958 TTGAATATAGTTATCTAGAATCTAGAGTGTAGTTTTGTGAATTCGATTTATGAATTTTGATCTAT
1 TTGAATATAGTTATCTAGAATCTAGAGTGTAGTTTTGTGAATTCGATTTATGAATTTTGATCTAT
17023 AGTTATGAATCTATGAATTTTGAAT
66 AGTTATGAATCTATGAATTTTGAAT
17048 ATAGTTACCT
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
91 5 0.06
92 84 0.94
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (91 bp):
TTGAATATAGTTATCTAGAATCTAGAGTGTAGTTTTGTGAATTCGATTTATGAATTTTGATCTAT
AGTTATGAATCTATGAATTTTGAATT
Found at i:21964 original size:14 final size:14
Alignment explanation
Indices: 21940--21980 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
21930 TCCATATATT
21940 TTATGTTTAAATAA
1 TTATGTTTAAATAA
* * *
21954 TTTTTTTTAAAGAA
1 TTATGTTTAAATAA
21968 TTATGTTTAAATA
1 TTATGTTTAAATA
21981 TTTACTTCAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (14 bp):
TTATGTTTAAATAA
Found at i:25768 original size:21 final size:21
Alignment explanation
Indices: 25742--25791 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
25732 AATTATGTAT
* *
25742 TTTGGATTTATAAATTTTATG
1 TTTGGATTTATAAACTTTATA
*
25763 TTTGGATTTCTAAACTTTATA
1 TTTGGATTTATAAACTTTATA
25784 TTTGGATT
1 TTTGGATT
25792 ATGTTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.04, G:0.14, T:0.56
Consensus pattern (21 bp):
TTTGGATTTATAAACTTTATA
Found at i:26874 original size:17 final size:17
Alignment explanation
Indices: 26850--26888 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
26840 ATGTCAGGTC
*
26850 AATA-ATTTTGTCTAAA
1 AATATATTTTGTCAAAA
*
26866 AATATATTTTTTCAAAA
1 AATATATTTTGTCAAAA
26883 AATATA
1 AATATA
26889 AATAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (17 bp):
AATATATTTTGTCAAAA
Found at i:26899 original size:16 final size:16
Alignment explanation
Indices: 26880--26912 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26870 TATTTTTTCA
26880 AAAAAT-ATAAATAATT
1 AAAAATAATAAA-AATT
26896 AAAAATAATAAAAATT
1 AAAAATAATAAAAATT
26912 A
1 A
26913 CATATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATAATAAAAATT
Found at i:27777 original size:23 final size:24
Alignment explanation
Indices: 27751--27795 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
27741 CAAATTCCAT
*
27751 GTTTTTATAATTTA-TATTTTTTA
1 GTTTATATAATTTATTATTTTTTA
27774 GTTTATATAATTTATTATTTTT
1 GTTTATATAATTTATTATTTTT
27796 AATAACCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
GTTTATATAATTTATTATTTTTTA
Found at i:27934 original size:18 final size:18
Alignment explanation
Indices: 27902--27937 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27892 GCACTTCAAT
**
27902 ATTTTAAAATTTTTTTAA
1 ATTTTAAAAGATTTTTAA
27920 ATTTTAAAAGATTTTTAA
1 ATTTTAAAAGATTTTTAA
27938 TGATTTTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTTAAAAGATTTTTAA
Found at i:28943 original size:4 final size:4
Alignment explanation
Indices: 28928--28963 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
28918 CACCAAACCA
28928 TAAT TAAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT T-AAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
28964 GCTGTCTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:30165 original size:28 final size:27
Alignment explanation
Indices: 30106--30165 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
30096 TAAAATAAAA
*
30106 TTTAAATATTAAATAATTTATTGTATG
1 TTTAAATATTAAATAATTCATTGTATG
*
30133 ATTAAATA-TAAATAATTACATATGTATG
1 TTTAAATATTAAATAATT-CAT-TGTATG
30161 TTTAA
1 TTTAA
30166 TAAATATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.32
27 9 0.32
28 10 0.36
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (27 bp):
TTTAAATATTAAATAATTCATTGTATG
Found at i:35001 original size:3 final size:3
Alignment explanation
Indices: 34993--35019 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34983 TACAAAGTTA
34993 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
35020 CTGTTGTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42778 original size:3 final size:3
Alignment explanation
Indices: 42770--42801 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42760 ATCCTTTTGG
42770 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42802 CAAAGCGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:45922 original size:20 final size:21
Alignment explanation
Indices: 45884--45922 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
45874 TCAGTTCAGC
* *
45884 TTGTAAAGATTGAACTTGCTG
1 TTGTAAAGACTGAAATTGCTG
45905 TTGTAAAG-CTGAAATTGC
1 TTGTAAAGACTGAAATTGC
45923 ACCCATGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (21 bp):
TTGTAAAGACTGAAATTGCTG
Found at i:56209 original size:21 final size:20
Alignment explanation
Indices: 56183--56221 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
56173 TTAGTTTTTT
56183 TAAATAAAATATAACATTAAA
1 TAAATAAAATATAA-ATTAAA
*
56204 TAAATAAAATTTAAATTA
1 TAAATAAAATATAAATTA
56222 CGTGAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATAAAATATAAATTAAA
Found at i:76482 original size:16 final size:15
Alignment explanation
Indices: 76461--76495 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
76451 AAAATAACTT
*
76461 AAAAAGTTTAAAAATA
1 AAAAAGTAT-AAAATA
76477 AAAAAGTATAAAATA
1 AAAAAGTATAAAATA
76492 AAAA
1 AAAA
76496 TTAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (15 bp):
AAAAAGTATAAAATA
Found at i:76775 original size:33 final size:33
Alignment explanation
Indices: 76738--76835 Score: 112
Period size: 33 Copynumber: 2.9 Consensus size: 33
76728 AATTTATGAC
*
76738 AAATTTCAATTTATATAATATTTTTATTTTTTA
1 AAATTTCAATTTATATAATATTTTAATTTTTTA
*
76771 AAATTTAAATTTATAT-AT-TTTATAATTTTTTA
1 AAATTTCAATTTATATAATATTT-TAATTTTTTA
*
76803 AAATTTTCAATTTTTATATAA-ATTTTAAATTTT
1 AAA-TTTCAA--TTTATATAATATTTTAATTTTT
76836 ATATAATCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 3 0.05
32 14 0.25
33 20 0.36
35 14 0.25
36 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (33 bp):
AAATTTCAATTTATATAATATTTTAATTTTTTA
Found at i:76782 original size:22 final size:22
Alignment explanation
Indices: 76757--76798 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
76747 TTTATATAAT
* *
76757 ATTTTTATTTTTTAAAATTTAA
1 ATTTATATATTTTAAAATTTAA
*
76779 ATTTATATATTTTATAATTT
1 ATTTATATATTTTAAAATTT
76799 TTTAAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTATATATTTTAAAATTTAA
Found at i:76827 original size:19 final size:18
Alignment explanation
Indices: 76747--76841 Score: 78
Period size: 18 Copynumber: 5.5 Consensus size: 18
76737 CAAATTTCAA
*
76747 TTTATATAATATTTTTATT
1 TTTATATAA-ATTTTAATT
*
76766 TTT-TA-AAA-TTTAA-A
1 TTTATATAAATTTTAATT
*
76780 TTTATAT-ATTTTATAATT
1 TTTATATAAATTT-TAATT
76798 TTT-TA-AAATTTTCAATT
1 TTTATATAAATTTT-AATT
*
76815 TTTATATAAATTTTAAAT
1 TTTATATAAATTTTAATT
76833 TTTATATAA
1 TTTATATAA
76842 TCTATTGGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
14 3 0.05
15 7 0.11
16 4 0.07
17 18 0.30
18 19 0.31
19 10 0.16
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATATAAATTTTAATT
Found at i:85043 original size:20 final size:20
Alignment explanation
Indices: 85018--85087 Score: 95
Period size: 20 Copynumber: 3.4 Consensus size: 20
85008 ATATATTTAT
85018 AATTTTTAAAAATTAAATTA
1 AATTTTTAAAAATTAAATTA
* *
85038 AATTTTTAAAAAATATATTTA
1 AATTTTTAAAAATTA-AATTA
*
85059 TAATTTTTAAAAATTAAATAA
1 -AATTTTTAAAAATTAAATTA
85080 AATTTTTA
1 AATTTTTA
85088 TTTTTTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
20 22 0.51
21 7 0.16
22 14 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTTTAAAAATTAAATTA
Found at i:85055 original size:42 final size:42
Alignment explanation
Indices: 85008--85087 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
84998 TTAATAATTT
*
85008 ATATATTTATAATTTTTAAAAATTAAATTAAATTTTTAAAAA
1 ATATATTTATAATTTTTAAAAATTAAATAAAATTTTTAAAAA
85050 ATATATTTATAATTTTTAAAAATTAAATAAAATTTTTA
1 ATATATTTATAATTTTTAAAAATTAAATAAAATTTTTA
85088 TTTTTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
ATATATTTATAATTTTTAAAAATTAAATAAAATTTTTAAAAA
Found at i:85063 original size:22 final size:22
Alignment explanation
Indices: 85008--85071 Score: 96
Period size: 20 Copynumber: 3.0 Consensus size: 22
84998 TTAATAATTT
85008 ATATATTTATAATTTTTAAAAA
1 ATATATTTATAATTTTTAAAAA
* *
85030 TTA-AATTA-AATTTTTAAAAA
1 ATATATTTATAATTTTTAAAAA
85050 ATATATTTATAATTTTTAAAAA
1 ATATATTTATAATTTTTAAAAA
85072 TTAAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.39
21 8 0.22
22 14 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATATTTATAATTTTTAAAAA
Found at i:85076 original size:29 final size:29
Alignment explanation
Indices: 85043--85099 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
85033 AATTAAATTT
85043 TTAAA-AAATATATTTATAATTTTTAAAAA
1 TTAAATAAA-ATATTTATAATTTTTAAAAA
* **
85072 TTAAATAAAATTTTTATTTTTTTTAAAA
1 TTAAATAAAATATTTATAATTTTTAAAA
85100 GCATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTAAATAAAATATTTATAATTTTTAAAAA
Done.