Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012385.1 Kokia drynarioides strain JFW-HI SEQ_127389, 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: 103033
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 136 characters in sequence are not A, C, G, or T
Found at i:3090 original size:4 final size:4
Alignment explanation
Indices: 3081--3135 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
3071 ACAAAATTGC
*
3081 ATGT ATGT ATGT ATGT ATGA ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3129 ATGT ATG
1 ATGT ATG
3136 AATACTTAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:4818 original size:44 final size:44
Alignment explanation
Indices: 4746--4838 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
4736 CAAAATCTAT
*
4746 GAAATACTCCCAAGTGAAAATCAAATATGATATAAATGATTTTA
1 GAAATACTCCCAAGTGAAAATCAAATATGATATAAATGAATTTA
* * *
4790 GAAATCCTCCTAAGT-AAAAGTTAAATATGATATAAATGAATTTA
1 GAAATACTCCCAAGTGAAAA-TCAAATATGATATAAATGAATTTA
*
4834 AAAAT
1 GAAAT
4839 TAATTTTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 4 0.09
44 39 0.91
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (44 bp):
GAAATACTCCCAAGTGAAAATCAAATATGATATAAATGAATTTA
Found at i:4978 original size:28 final size:29
Alignment explanation
Indices: 4903--4966 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
4893 GACTTTCAAA
* * * *
4903 AAATTTAAAAACCAATTTAAAAAAATATT
1 AAATTTAAATATCAAATTAAAAAAATATC
*
4932 AAATTTAAATGTCAAATTAAAAAAATATC
1 AAATTTAAATATCAAATTAAAAAAATATC
4961 AAATTT
1 AAATTT
4967 GAGTATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (29 bp):
AAATTTAAATATCAAATTAAAAAAATATC
Found at i:10067 original size:14 final size:15
Alignment explanation
Indices: 10050--10083 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10040 GATATTTGTA
10050 TTTTAA-TTTGATAT
1 TTTTAATTTTGATAT
*
10064 TTTTAATTTTTATAT
1 TTTTAATTTTGATAT
10079 TTTTA
1 TTTTA
10084 GAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTAATTTTGATAT
Found at i:19251 original size:3 final size:3
Alignment explanation
Indices: 19243--19271 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19233 GATTTTTTGT
19243 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
19272 TTGTTTGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:20357 original size:25 final size:24
Alignment explanation
Indices: 20319--20375 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
20309 TATTTATTTA
* *
20319 TTATTTGTATAAATAATTATAATTAT
1 TTATTTG-A-AAATAAATAAAATTAT
20345 TTGATTTGAAAATAAATAAAATTAT
1 TT-ATTTGAAAATAAATAAAATTAT
20370 TTATTT
1 TTATTT
20376 TTTTAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.14
25 16 0.57
26 3 0.11
27 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (24 bp):
TTATTTGAAAATAAATAAAATTAT
Found at i:21262 original size:17 final size:17
Alignment explanation
Indices: 21242--21274 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21232 TCATATATAA
21242 TTTT-AAGATTGATATTT
1 TTTTCAAGATT-ATATTT
21259 TTTTCAAGATTATATT
1 TTTTCAAGATTATATT
21275 ATTCTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (17 bp):
TTTTCAAGATTATATTT
Found at i:32982 original size:133 final size:133
Alignment explanation
Indices: 32744--33009 Score: 523
Period size: 133 Copynumber: 2.0 Consensus size: 133
32734 AAAAATAGAT
32744 GCCGGAGACTAAATACGGCGTCGGATTCTGATAAACCGTTGGGCGAAGAGAGACTTCTTAACTAA
1 GCCGGAGACTAAATACGGCGTCGGATTCTGATAAACCGTTGGGCGAAGAGAGACTTCTTAACTAA
32809 GTTTTGAAATGGAAGGAGAATGGAGAGCTCGCGCGGCTTGGCTTAGCTTTTTAAAGTTTAAAAGT
66 GTTTTGAAATGGAAGGAGAATGGAGAGCTCGCGCGGCTTGGCTTAGCTTTTTAAAGTTTAAAAGT
32874 GAA
131 GAA
32877 GCCGGAGACTAAATACGGCGTCGGATTCTGATAAACCGTTGGGCGAAGAGAGACTTCTTAACTAA
1 GCCGGAGACTAAATACGGCGTCGGATTCTGATAAACCGTTGGGCGAAGAGAGACTTCTTAACTAA
*
32942 GTTTTGAAATGGAAGGAGAATGGAGAGCTCGCGCGGCTTGGCTTGGCTTTTTAAAGTTTAAAAGT
66 GTTTTGAAATGGAAGGAGAATGGAGAGCTCGCGCGGCTTGGCTTAGCTTTTTAAAGTTTAAAAGT
33007 GAA
131 GAA
33010 AAAGGTGAGA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 132 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (133 bp):
GCCGGAGACTAAATACGGCGTCGGATTCTGATAAACCGTTGGGCGAAGAGAGACTTCTTAACTAA
GTTTTGAAATGGAAGGAGAATGGAGAGCTCGCGCGGCTTGGCTTAGCTTTTTAAAGTTTAAAAGT
GAA
Found at i:34176 original size:57 final size:54
Alignment explanation
Indices: 34114--34247 Score: 152
Period size: 50 Copynumber: 2.5 Consensus size: 54
34104 ATAATAACAC
34114 AATTTAATAATATAAAATATTTAATATATATATTAAATAAAATTCATGAGTCATTCA
1 AATTTAATAATATAAAATATTTAAT-T-TA-ATTAAATAAAATTCATGAGTCATTCA
* **
34171 AATTT-ATAAAATATAAA-A--T-ATTTAATTCGATAAAATTCATGAGTCATTCA
1 AATTTAATAATATA-AAATATTTAATTTAATTAAATAAAATTCATGAGTCATTCA
*
34221 AATTTATAAAATATAAAATATTTAATT
1 AATTTA-ATAATATAAAATATTTAATT
34248 CGATAAAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
50 29 0.45
51 5 0.08
52 8 0.12
53 2 0.03
54 2 0.03
55 3 0.05
56 8 0.12
57 8 0.12
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (54 bp):
AATTTAATAATATAAAATATTTAATTTAATTAAATAAAATTCATGAGTCATTCA
Found at i:34214 original size:50 final size:50
Alignment explanation
Indices: 34150--34276 Score: 245
Period size: 50 Copynumber: 2.5 Consensus size: 50
34140 TATATATTAA
34150 ATAAAATTCATGAGTCATTCAAATTTATAAAATATAAAATATTTAATTCG
1 ATAAAATTCATGAGTCATTCAAATTTATAAAATATAAAATATTTAATTCG
34200 ATAAAATTCATGAGTCATTCAAATTTATAAAATATAAAATATTTAATTCG
1 ATAAAATTCATGAGTCATTCAAATTTATAAAATATAAAATATTTAATTCG
*
34250 ATAAAATTCATGAGCCATTCAAATTTA
1 ATAAAATTCATGAGTCATTCAAATTTA
34277 ACTCAATTCT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.37
Consensus pattern (50 bp):
ATAAAATTCATGAGTCATTCAAATTTATAAAATATAAAATATTTAATTCG
Found at i:34725 original size:9 final size:10
Alignment explanation
Indices: 34710--34796 Score: 56
Period size: 10 Copynumber: 8.9 Consensus size: 10
34700 ATTTAGATTA
34710 AATTTTTTAT
1 AATTTTTTAT
34720 -A-TTTTTAT
1 AATTTTTTAT
34728 AATTTTTTA-
1 AATTTTTTAT
* **
34737 AATATTAAAT
1 AATTTTTTAT
*
34747 CAAATTTTTAT
1 -AATTTTTTAT
34758 AATTTTTTA-
1 AATTTTTTAT
* **
34767 AATATTAAAT
1 AATTTTTTAT
*
34777 CAAATTTTTAT
1 -AATTTTTTAT
34788 AATTTTTTA
1 AATTTTTTA
34797 AATATTAAAT
Statistics
Matches: 55, Mismatches: 16, Indels: 12
0.66 0.19 0.14
Matches are distributed among these distances:
8 7 0.13
9 14 0.25
10 22 0.40
11 12 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:34756 original size:30 final size:30
Alignment explanation
Indices: 34720--34830 Score: 204
Period size: 30 Copynumber: 3.7 Consensus size: 30
34710 AATTTTTTAT
34720 ATTTTTATAATTTTTTAAATATTAAATCAA
1 ATTTTTATAATTTTTTAAATATTAAATCAA
34750 ATTTTTATAATTTTTTAAATATTAAATCAA
1 ATTTTTATAATTTTTTAAATATTAAATCAA
34780 ATTTTTATAATTTTTTAAATATTAAATCAA
1 ATTTTTATAATTTTTTAAATATTAAATCAA
* *
34810 ATTTTTATCATTTTTAAAATA
1 ATTTTTATAATTTTTTAAATA
34831 CCGAAATATA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTTTTATAATTTTTTAAATATTAAATCAA
Found at i:34830 original size:208 final size:206
Alignment explanation
Indices: 34441--34814 Score: 585
Period size: 208 Copynumber: 1.8 Consensus size: 206
34431 TTGGACCTGG
34441 AATTTCTATATATAAAGGAAATGACAAACAGGACGAATTTATTTTAGGAGGATTTAGATTAAATT
1 AATTTCTATATATAAAGGAAATGACAAACAGGACGAATTTATTTTAGGAGGATTTAGATTAAATT
* *
34506 TTTTATATTTTTATAATTTTTTAAATATTAAATTAAATTTTTATCATTTTTAAAATACCGAAATA
66 TTTTATATTTTTATAATTTTTTAAATATTAAATCAAATTTTTATAATTTTTAAAATACCGAAATA
* ** *
34571 TAATTTTATATTTACTAATTTAAAATTTTTTAAATTTTAAAAGGTTAAAATAAAAAAATTCCCAT
131 TAATTTTATAATTA-T-ATTTAAAATTAATCAAATTTTAAAAGGTTAAAATAAAAAAATTCCCAT
34636 CCGACCCCTGCCA
194 CCGACCCCTGCCA
34649 AATTTCTATATATAAAGGAAATGACAAACAGGACGAATTTATTTTAGGAGGATTTAGATTAAATT
1 AATTTCTATATATAAAGGAAATGACAAACAGGACGAATTTATTTTAGGAGGATTTAGATTAAATT
* **
34714 TTTTATATTTTTATAATTTTTTAAATATTAAATCAAATTTTTATAATTTTTTAAATA-TTAAATC
66 TTTTATATTTTTATAATTTTTTAAATATTAAATCAAATTTTTATAATTTTTAAAATACCGAAAT-
34778 A-AATTTTTATAATT-T-TTTAAATATTAAATCAAATTTT
130 ATAA-TTTTATAATTATATTTAAA-ATT-AATCAAATTTT
34815 TATCATTTTT
Statistics
Matches: 153, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
204 6 0.04
205 3 0.02
206 9 0.06
207 6 0.04
208 129 0.84
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (206 bp):
AATTTCTATATATAAAGGAAATGACAAACAGGACGAATTTATTTTAGGAGGATTTAGATTAAATT
TTTTATATTTTTATAATTTTTTAAATATTAAATCAAATTTTTATAATTTTTAAAATACCGAAATA
TAATTTTATAATTATATTTAAAATTAATCAAATTTTAAAAGGTTAAAATAAAAAAATTCCCATCC
GACCCCTGCCA
Found at i:34846 original size:60 final size:59
Alignment explanation
Indices: 34717--34847 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 59
34707 TTAAATTTTT
* * **
34717 TATATTTTTATAATTTTTTAAATATTAAATCAAATTTTTATAATTTTTTAAATATTAAA
1 TATAATTTTATAATTTTTTAAATATTAAATCAAATTTTTATAATTTTTAAAATACGAAA
*
34776 TCA-AATTTTTATAATTTTTTAAATATTAAATCAAATTTTTATCATTTTTAAAATACCGAAA
1 T-ATAA-TTTTATAATTTTTTAAATATTAAATCAAATTTTTATAATTTTTAAAATA-CGAAA
34837 TATAATTTTAT
1 TATAATTTTAT
34848 CTTTACTAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
59 2 0.03
60 55 0.87
61 6 0.10
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.53
Consensus pattern (59 bp):
TATAATTTTATAATTTTTTAAATATTAAATCAAATTTTTATAATTTTTAAAATACGAAA
Found at i:50629 original size:65 final size:65
Alignment explanation
Indices: 50546--50675 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 65
50536 ATTGTTGTTA
*
50546 GTGGATAACGTGAGTTTAAATATATTAAAACGTAATATTTTTTTATTTAAATATTAAAAAAGATT
1 GTGGATAACATGAGTTTAAATATATTAAAACGTAATATTTTTTTATTTAAATATTAAAAAAGATT
* *
50611 GTGGATAATATGAGTTTAAGTATATTAAAACGTAATATTTTTTTATTTAAATATTAAAAAAGATT
1 GTGGATAACATGAGTTTAAATATATTAAAACGTAATATTTTTTTATTTAAATATTAAAAAAGATT
50676 ATGAATAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.42
Consensus pattern (65 bp):
GTGGATAACATGAGTTTAAATATATTAAAACGTAATATTTTTTTATTTAAATATTAAAAAAGATT
Found at i:59616 original size:1 final size:1
Alignment explanation
Indices: 59563--59596 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
59553 TTACAATCAG
59563 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
59597 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:59617 original size:1 final size:1
Alignment explanation
Indices: 59607--59640 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
59597 NNNNNNNNNN
59607 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
59641 TCTTTGGGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:60958 original size:14 final size:14
Alignment explanation
Indices: 60936--60965 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
60926 TAACCATATC
60936 TCTTCTTTTCTTTT
1 TCTTCTTTTCTTTT
*
60950 TCTTTTTTTCTTTT
1 TCTTCTTTTCTTTT
60964 TC
1 TC
60966 ATTTCTTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TCTTCTTTTCTTTT
Found at i:66491 original size:33 final size:34
Alignment explanation
Indices: 66426--66509 Score: 161
Period size: 33 Copynumber: 2.5 Consensus size: 34
66416 TTGGGAATCT
66426 AAGTTGTGCCGTATAATTATTCAAAAAAAAAAAA
1 AAGTTGTGCCGTATAATTATTCAAAAAAAAAAAA
66460 AAGTTGTGCCGTATAATTATTC-AAAAAAAAAAA
1 AAGTTGTGCCGTATAATTATTCAAAAAAAAAAAA
66493 AAGTTGTGCCGTATAAT
1 AAGTTGTGCCGTATAAT
66510 GAGAAACCCT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 28 0.56
34 22 0.44
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (34 bp):
AAGTTGTGCCGTATAATTATTCAAAAAAAAAAAA
Found at i:66962 original size:65 final size:65
Alignment explanation
Indices: 66858--66987 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
66848 TTTACAATAT
*
66858 TTGGATTTACATTTCAATTCATCTATAATTTTAATTATAAAAGTTTATACAAAATTAATTTGTCG
1 TTGGATTTACAGTTCAATTCATCTATAATTTTAATTATAAAAGTTTATACAAAATTAATTTGTCG
66923 TTGGATTTACAGTTCAATTCATCTATAATTTTAATTATAAAAGTTTATACAAAATTAATTTGTCG
1 TTGGATTTACAGTTCAATTCATCTATAATTTTAATTATAAAAGTTTATACAAAATTAATTTGTCG
66988 AAAATTTATA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.45
Consensus pattern (65 bp):
TTGGATTTACAGTTCAATTCATCTATAATTTTAATTATAAAAGTTTATACAAAATTAATTTGTCG
Found at i:68618 original size:96 final size:96
Alignment explanation
Indices: 68444--68635 Score: 264
Period size: 96 Copynumber: 2.0 Consensus size: 96
68434 TTTTGGGGAA
** **
68444 AAGGATATTCGATTATTTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTTA
1 AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTTA
*
68509 GAATCGAAGATAAAGA-AACATTGCCTCGATT
66 GAATCGAAGATAAA-ATAACATTACCTCGATT
* *
68540 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTT
1 AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTTA
*
68604 GAAACTCGAA-ATAAAATAATATTACCTCGATT
66 G-AA-TCGAAGATAAAATAACATTACCTCGATT
68636 TTAAAGTCTT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 7 0.08
96 73 0.86
97 5 0.06
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (96 bp):
AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTTA
GAATCGAAGATAAAATAACATTACCTCGATT
Found at i:68931 original size:30 final size:29
Alignment explanation
Indices: 68897--68987 Score: 101
Period size: 30 Copynumber: 3.1 Consensus size: 29
68887 TTTGGGAAAG
* *
68897 TTCGAGGTTAAAAGATGGAATTTTTAGACA
1 TTCGAGGTTAAAA-ATAGAATTTTTGGACA
* **
68927 TTCGAGGGTAAAAAATAGAATTTTTGGAGT
1 TTCGA-GGTTAAAAATAGAATTTTTGGACA
* *
68957 TTCGAGGTTGAAAATAGAGTTTTTGGACA
1 TTCGAGGTTAAAAATAGAATTTTTGGACA
68986 TT
1 TT
68988 TGGGGGTAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 21 0.42
30 22 0.44
31 7 0.14
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
TTCGAGGTTAAAAATAGAATTTTTGGACA
Found at i:69040 original size:30 final size:29
Alignment explanation
Indices: 68871--69312 Score: 296
Period size: 29 Copynumber: 15.0 Consensus size: 29
68861 TGGATACCTG
*
68871 GGGGT-AAAATGGTAATTTTGGGAAAG-TTC
1 GGGGTAAAAATGG-AATTTTTGG-AAGTTTC
* *
68900 GAGGTTAAAAGATGGAATTTTTAGACA--TTC
1 G-GGGTAAAA-ATGGAATTTTTGGA-AGTTTC
*
68930 GAGGGTAAAAAATAGAATTTTTGG-AGTTTC
1 G-GGGT-AAAAATGGAATTTTTGGAAGTTTC
* * * * *
68960 GAGGTTGAAAATAGAGTTTTTGGACA-TTTG
1 G-GGGTAAAAATGGAATTTTTGGA-AGTTTC
* * * * *
68990 GGGGTAGAATTGTAATTTTTGAAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
*
69019 GGGGTCAAAAATGGAAATTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
* * * *
69048 GGATGCAGAAA-GAGAATTTTTGGAAGTTTA
1 GG-GGTAAAAATG-GAATTTTTGGAAGTTTC
* *
69078 GAGGTCAAAAATGGAGTTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
69107 GAGGGTAAAAATGGAATTTTTGGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
* * **
69137 GGGATAAAAATGGGATTTTTTTAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
*
69166 GGGGTTGAAAATGGAATTTTTGGAAG-TTC
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTC
* *
69195 GAGGATAAAAAT-GAGATTTTTTGAAGTTTC
1 G-GGGTAAAAATGGA-ATTTTTGGAAGTTTC
* * * *
69225 AGGGGTAAAAACGAAATTTTTGGAAATTTT
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
69255 GGGGTCGAAAATGAAATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
* *
69284 GGGGTAAAAATGTAATTTTCGGATAGTTT
1 GGGGTAAAAATGGAATTTTTGGA-AGTTT
69313 AGGGATCTCT
Statistics
Matches: 323, Mismatches: 63, Indels: 53
0.74 0.14 0.12
Matches are distributed among these distances:
28 20 0.06
29 142 0.44
30 138 0.43
31 19 0.06
32 4 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTC
Found at i:69117 original size:88 final size:90
Alignment explanation
Indices: 68911--69312 Score: 325
Period size: 88 Copynumber: 4.5 Consensus size: 90
68901 AGGTTAAAAG
* * *
68911 ATGGAATTTTTAGACA-TTCGAGGGTAAAAAATAGAATTTTTGG-AGTTTCGAGGTTGAAAATA-
1 ATGGAATTTTTGGA-AGTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTC-AGGATGAAAA-AC
* *
68973 GAG--TTTTTGGACA-TTTGGGGGTAG-AA
62 GAGAATTTTTGGA-AGTTTAGGGGTCGAAA
* * * * * *
68999 TTGTAATTTTTGAAAGTTTTG-GGGTCAAAAATGGAAATTTTGGAAG-TTC-GGATGCAGAAA-G
1 ATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTCAGGATG-AAAAACG
* *
69060 AGAATTTTTGGAAGTTTAGAGGTCAAAA
63 AGAATTTTTGGAAGTTTAGGGGTCGAAA
* * * *
69088 ATGGAGTTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGAT-AAAAATG-GG
1 ATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAGGATGAAAAACGAGA
** * *
69151 ATTTTTTTAAGTTTCGGGGTTGAAA
66 ATTTTTGGAAGTTTAGGGGTCGAAA
* * *
69176 ATGGAATTTTTGGAAGTTCGAGGATAAAAAT-GAGATTTTTTGAAGTTTCAGG-GGTAAAAACGA
1 ATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGA-ATTTTTGGAAGTTTCAGGATG-AAAAACGA
* *
69239 -AATTTTTGGAAATTTTGGGGTCGAAA
64 GAATTTTTGGAAGTTTAGGGGTCGAAA
* * *
69265 ATGAAATTTTTGGAAGTTCG-GGGTAAAAATGTAATTTTCGGATAGTTT
1 ATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA-AGTTT
69313 AGGGATCTCT
Statistics
Matches: 251, Mismatches: 45, Indels: 35
0.76 0.14 0.11
Matches are distributed among these distances:
86 8 0.03
87 7 0.03
88 154 0.61
89 78 0.31
90 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (90 bp):
ATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAGGATGAAAAACGAGA
ATTTTTGGAAGTTTAGGGGTCGAAA
Found at i:69124 original size:59 final size:58
Alignment explanation
Indices: 68871--69312 Score: 312
Period size: 59 Copynumber: 7.5 Consensus size: 58
68861 TGGATACCTG
* * * *
68871 GGGGT-AAAATGGTAATTTTGGGAAAG-TTCGAGGTTAAAAGATGGAATTTTTAGACA-TTC
1 GGGGTAAAAATGG-AATTTTTGG-AAGTTTCGAGGTCAAAA-ATGGAGTTTTTGGA-AGTTC
* ** * * *
68930 GAGGGTAAAAAATAGAATTTTTGG-AGTTTCGAGGTTGAAAATAGAGTTTTTGGACATTTG
1 G-GGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAGTTTTTGGA-AGTTC
* * * * * * **
68990 GGGGTAGAATTGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAAATTTTGGAAGTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGTTC
* * * *
69048 GGATGCAGAAA-GAGAATTTTTGGAAGTTTAGAGGTCAAAAATGGAGTTTTTGGAAGTTC
1 GG-GGTAAAAATG-GAATTTTTGGAAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGTTC
**
69107 GAGGGTAAAAATGGAATTTTTGGAAGTTTCG-GGAT-AAAAATGG-GATTTTTTTAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGG-TCAAAAATGGAG-TTTTTGGAAG-TTC
* *
69166 GGGGTTGAAAATGGAATTTTTGGAAG-TTCGAGGAT-AAAAAT-GAGATTTTTTGAAGTTTC
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTCGAGG-TCAAAAATGGAG-TTTTTGGAAG-TTC
* * * * * * * *
69225 AGGGGTAAAAACGAAATTTTTGGAAATTTTGGGGTCGAAAATGAAATTTTTGGAAGTTC
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGTTC
* *
69284 GGGGTAAAAATGTAATTTTCGGATAGTTT
1 GGGGTAAAAATGGAATTTTTGGA-AGTTT
69313 AGGGATCTCT
Statistics
Matches: 310, Mismatches: 52, Indels: 42
0.77 0.13 0.10
Matches are distributed among these distances:
57 1 0.00
58 64 0.21
59 186 0.60
60 44 0.14
61 9 0.03
62 6 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (58 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGTTC
Found at i:70253 original size:3 final size:3
Alignment explanation
Indices: 70245--70312 Score: 57
Period size: 3 Copynumber: 22.0 Consensus size: 3
70235 CGTTTCTTTT
* * * **
70245 TTA TTA TTA TTA TTAA TTA ATA ATA TTA TTA TTA -AA ACA GTTA TTTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA
70292 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
70313 ATGCTATCAG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 1 0.02
3 47 0.85
4 7 0.13
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:70310 original size:22 final size:22
Alignment explanation
Indices: 70244--70311 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
70234 TCGTTTCTTT
*
70244 TTTATTATTATTATTAATTAATA
1 TTTATTATTATTATT-ATTATTA
* * **
70267 -ATATTATTATTA-AAACAGTTA
1 TTTATTATTATTATTATTA-TTA
70288 TTTATTATTATTATTATTATTA
1 TTTATTATTATTATTATTATTA
70310 TT
1 TT
70312 AATGCTATCA
Statistics
Matches: 33, Mismatches: 9, Indels: 7
0.67 0.18 0.14
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 27 0.82
23 2 0.06
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (22 bp):
TTTATTATTATTATTATTATTA
Found at i:71029 original size:6 final size:6
Alignment explanation
Indices: 71012--71093 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
71002 ATTTAAATAG
* *
71012 ATTTAA ATTTTAA ATTTATA A--TAA ATTTAA ATTT-A A-GTAC ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
71058 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
71094 CTTGTTGGGC
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
4 3 0.05
5 13 0.23
6 33 0.58
7 8 0.14
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:71040 original size:17 final size:17
Alignment explanation
Indices: 71015--71093 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
71005 TAAATAGATT
*
71015 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
*
71033 TAAATTTAAATTT-AAG
1 TAAATTTAAATTTAAAA
* *
71049 TACATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
71066 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
71083 TAAATTTAAAT
1 TAAATTTAAAT
71094 CTTGTTGGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
16 12 0.24
17 35 0.69
18 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:72203 original size:20 final size:20
Alignment explanation
Indices: 72175--72212 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
72165 GATAAAAAAT
*
72175 TATAATATTTTTTTAATAAA
1 TATAATATTTTTATAATAAA
*
72195 TATATTATTTTTATAATA
1 TATAATATTTTTATAATA
72213 TATAGCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATAATATTTTTATAATAAA
Found at i:73225 original size:22 final size:21
Alignment explanation
Indices: 73176--73288 Score: 76
Period size: 21 Copynumber: 5.4 Consensus size: 21
73166 AAGAATAATA
*
73176 AATAAATAAAATACATAAAAC
1 AATAAATAAAATAAATAAAAC
73197 AATAAATAAAATTAAATAAAAGC
1 AATAAATAAAA-TAAATAAAA-C
* * *
73220 GA-AAATGTAAAT-AACAAAA-
1 AATAAAT-AAAATAAATAAAAC
* *
73239 AATGAATAATCGATAAATAAATA-
1 AATAAATAA--AATAAATAAA-AC
73262 AATAAAT--AATAAATAAAAC
1 AATAAATAAAATAAATAAAAC
73281 AATAAATA
1 AATAAATA
73289 TATGAAATGC
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
18 1 0.01
19 18 0.25
20 3 0.04
21 19 0.27
22 18 0.25
23 12 0.17
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.21
Consensus pattern (21 bp):
AATAAATAAAATAAATAAAAC
Found at i:73229 original size:72 final size:72
Alignment explanation
Indices: 73127--73279 Score: 179
Period size: 72 Copynumber: 2.1 Consensus size: 72
73117 TATCAATGAG
* * * *
73127 TAAATAAAATTAAATGAAGGTAAAATTGTAAATAGC-ATAAA-GAATAATAAATAAATAAAATAC
1 TAAATAAAATTAAATAAAGGTAAAATTGTAAATAACAAAAAATGAATAATAAATAAAT-AAATAA
73190 ATAAAACAA
65 AT-AAACAA
**
73199 TAAATAAAATTAAATAAAAGCG-AAAA-TGTAAATAACAAAAAATGAATAATCGATAAATAAATA
1 TAAATAAAATTAAAT-AAAG-GTAAAATTGTAAATAACAAAAAATGAATAATAAATAAATAAATA
*
73262 AATAAATAA
64 AATAAACAA
73271 TAAATAAAA
1 TAAATAAAA
73280 CAATAAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
72 38 0.54
73 18 0.26
74 14 0.20
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (72 bp):
TAAATAAAATTAAATAAAGGTAAAATTGTAAATAACAAAAAATGAATAATAAATAAATAAATAAA
TAAACAA
Found at i:73260 original size:4 final size:4
Alignment explanation
Indices: 73251--73288 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
73241 TGAATAATCG
73251 ATAA ATAA ATAA ATAA AT-A ATAA ATAA A-ACA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATA
73289 TATGAAATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 4 0.13
4 26 0.84
5 1 0.03
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:73284 original size:15 final size:15
Alignment explanation
Indices: 73169--73288 Score: 54
Period size: 14 Copynumber: 8.0 Consensus size: 15
73159 TAGCATAAAG
73169 AATAATAAATAAATAA
1 AATAATAAATAAAT-A
73185 AATACATAAA-ACAATA
1 AATA-ATAAATA-AATA
*
73201 AATAA-AATTAAATA
1 AATAATAAATAAATA
** **
73215 AA-AGCGAAA-ATGTA
1 AATA-ATAAATAAATA
* *
73229 AATAACAAA-AAATG
1 AATAATAAATAAATA
**
73243 AATAATCGATAAATA
1 AATAATAAATAAATA
73258 AATAAATAAAT-AATA
1 AAT-AATAAATAAATA
*
73273 AATAAAACAATAAATA
1 AATAATA-AATAAATA
73289 TATGAAATGC
Statistics
Matches: 77, Mismatches: 17, Indels: 20
0.68 0.15 0.18
Matches are distributed among these distances:
13 1 0.01
14 27 0.35
15 22 0.29
16 19 0.25
17 8 0.10
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (15 bp):
AATAATAAATAAATA
Found at i:73562 original size:13 final size:13
Alignment explanation
Indices: 73489--73562 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 13
73479 ACAACTAGAT
73489 AAATAAACAAAATAA
1 AAATAAAC--AATAA
73504 ATAATAAA-AATAA
1 A-AATAAACAATAA
***
73517 AAATTAAATGCT-A
1 AAA-TAAACAATAA
73530 AAATAAACAAATAA
1 AAATAAAC-AATAA
*
73544 ATATAAACAATAA
1 AAATAAACAATAA
73557 AAATAA
1 AAATAA
73563 TTGAGATTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
12 6 0.13
13 25 0.53
14 9 0.19
15 1 0.02
16 6 0.13
ACGTcount: A:0.73, C:0.05, G:0.01, T:0.20
Consensus pattern (13 bp):
AAATAAACAATAA
Found at i:83176 original size:86 final size:85
Alignment explanation
Indices: 83031--83196 Score: 287
Period size: 86 Copynumber: 1.9 Consensus size: 85
83021 GTACTATTCA
*
83031 TTCAATTATAAAGTAAATTTGATTTACTGAAATAAAATATTTAGCTGATTAATAATTTTAGATAT
1 TTCAATTATAAAATAAATTTGATTTACTGAAATAAAATATTTAGCTGATTAATAATTTTAGATAT
83096 TAAAAAAAATTCGAAGATAGG
66 T-AAAAAAATTCGAAGATAGG
* *
83117 TTCAATTATAAAATAAATTTGATTTACTGAAATTAAATATTTAGTTGATTAATAATTTTAGATAT
1 TTCAATTATAAAATAAATTTGATTTACTGAAATAAAATATTTAGCTGATTAATAATTTTAGATAT
*
83182 TAAAAAAGTTCGAAG
66 TAAAAAAATTCGAAG
83197 TATTCTATCA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 13 0.17
86 63 0.83
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (85 bp):
TTCAATTATAAAATAAATTTGATTTACTGAAATAAAATATTTAGCTGATTAATAATTTTAGATAT
TAAAAAAATTCGAAGATAGG
Found at i:86160 original size:27 final size:26
Alignment explanation
Indices: 86108--86166 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
86098 ATATTTGGAG
86108 ATATTTTTTATTAATTAATTAATTAA
1 ATATTTTTTATTAATTAATTAATTAA
* *
86134 ATATTATTTTATTAA-TATTTTACTTAA
1 ATATT-TTTTATTAATTA-ATTAATTAA
86161 ATATTT
1 ATATTT
86167 ATCATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
ATATTTTTTATTAATTAATTAATTAA
Found at i:96040 original size:6 final size:7
Alignment explanation
Indices: 96013--96037 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
96003 ATAGAACCCT
96013 AAAAAGA
1 AAAAAGA
96020 AAAAAGA
1 AAAAAGA
96027 AAAAAGA
1 AAAAAGA
96034 AAAA
1 AAAA
96038 GAAGCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:98082 original size:13 final size:13
Alignment explanation
Indices: 98066--98095 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
98056 AAAAGTTGTT
98066 ATAAAAAATAAAA
1 ATAAAAAATAAAA
*
98079 ATAAAATATAAAA
1 ATAAAAAATAAAA
98092 ATAA
1 ATAA
98096 TCAATTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:102205 original size:21 final size:21
Alignment explanation
Indices: 102181--102235 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 21
102171 GGACCAACGA
*
102181 AAAATGAAGGAAA-AATGAAAG
1 AAAA-GAAGGAAAGAAAGAAAG
102202 AAAA-AAGAGAAAGAAAGAAAG
1 AAAAGAAG-GAAAGAAAGAAAG
102223 AAAGAAGAAGGAA
1 -AA-AAGAAGGAA
102236 GAAGGAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 3 0.11
20 4 0.14
21 11 0.39
22 2 0.07
23 5 0.18
24 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (21 bp):
AAAAGAAGGAAAGAAAGAAAG
Found at i:102237 original size:18 final size:17
Alignment explanation
Indices: 102197--102256 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 17
102187 AAGGAAAAAT
102197 GAAAGAAAAAAGAGAAA
1 GAAAGAAAAAAGAGAAA
*
102214 GAAAGAAAGAA-AG-AA
1 GAAAGAAAAAAGAGAAA
* * * *
102229 GAAGGAAGAAGGAGAAT
1 GAAAGAAAAAAGAGAAA
102246 GAAA-AAAAAAG
1 GAAAGAAAAAAG
102257 GTAATGTGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
15 9 0.28
16 9 0.28
17 14 0.44
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (17 bp):
GAAAGAAAAAAGAGAAA
Found at i:102457 original size:12 final size:12
Alignment explanation
Indices: 102439--102524 Score: 56
Period size: 12 Copynumber: 7.1 Consensus size: 12
102429 TTTAAAATAT
102439 TTTAATTTGTTA
1 TTTAATTTGTTA
*
102451 GTTAATTTGATTA
1 TTTAATTTG-TTA
102464 TTTTAATTT-TT-
1 -TTTAATTTGTTA
*
102475 TTGT--TTTCTTTAA
1 TT-TAATTT-GTT-A
102488 TTTAATTT-TTA
1 TTTAATTTGTTA
*
102499 ATTAATTTGTTA
1 TTTAATTTGTTA
102511 TTTAATGTTGTTA
1 TTTAAT-TTGTTA
102524 T
1 T
102525 AGTTGATGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
9 3 0.05
10 2 0.03
11 11 0.19
12 21 0.36
13 12 0.20
14 10 0.17
ACGTcount: A:0.24, C:0.01, G:0.08, T:0.66
Consensus pattern (12 bp):
TTTAATTTGTTA
Found at i:102513 original size:23 final size:22
Alignment explanation
Indices: 102439--102516 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
102429 TTTAAAATAT
102439 TTTAATTTGTTAGTTAATTTGATTA
1 TTTAATTT-TTA-TTAATTTG-TTA
** *
102464 TTTTAATTTTT-TTGTTTTCTTTAA
1 -TTTAATTTTTATTAATTT-GTT-A
102488 TTTAATTTTTAATTAATTTGTTA
1 TTTAATTTTT-ATTAATTTGTTA
102511 TTTAAT
1 TTTAAT
102517 GTTGTTATAG
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
23 24 0.57
24 3 0.07
25 7 0.17
26 8 0.19
ACGTcount: A:0.26, C:0.01, G:0.06, T:0.67
Consensus pattern (22 bp):
TTTAATTTTTATTAATTTGTTA
Found at i:102933 original size:30 final size:30
Alignment explanation
Indices: 102897--102995 Score: 114
Period size: 30 Copynumber: 3.3 Consensus size: 30
102887 TAAACTTAGC
102897 TAATTAATTACCAAAATATAATATAAAAAA
1 TAATTAATTACCAAAATATAATATAAAAAA
* ** **
102927 TAATTAATTATCAAAATA-ATATATCCATCA
1 TAATTAATTACCAAAATATA-ATATAAAAAA
102957 T-ATT-ATTGACCAAAATATAATATAAAAAA
1 TAATTAATT-ACCAAAATATAATATAAAAAA
102986 TAATTAATTA
1 TAATTAATTA
102996 TGAAAATAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
28 3 0.06
29 19 0.35
30 29 0.54
31 3 0.06
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (30 bp):
TAATTAATTACCAAAATATAATATAAAAAA
Found at i:102942 original size:16 final size:16
Alignment explanation
Indices: 102897--102946 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
102887 TAAACTTAGC
*
102897 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
102913 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
102927 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
102943 TAAT
1 TAAT
102947 ATATCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:102969 original size:59 final size:59
Alignment explanation
Indices: 102906--103031 Score: 216
Period size: 59 Copynumber: 2.1 Consensus size: 59
102896 CTAATTAATT
*
102906 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATATCCATCATATTATTG
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATACCCATCATATTATTG
* * *
102965 ACCAAAATATAATATAAAAAATAATTAATTATGAAAATAATATCCCCATCATATTATTT
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATACCCATCATATTATTG
103024 ACCAAAAT
1 ACCAAAAT
103032 GG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.33
Consensus pattern (59 bp):
ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATACCCATCATATTATTG
Done.