Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014231.1 Kokia drynarioides strain JFW-HI SEQ_129264, 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: 129651
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 62 characters in sequence are not A, C, G, or T
Found at i:10166 original size:64 final size:66
Alignment explanation
Indices: 10093--10228 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 66
10083 TCAATTTCCA
* * *
10093 AATTTCATCAATTGC-A-TCTGAACATATATTACACATACATTTAATTATACATTTTAATTCCAT
1 AATTCCATCAATTGCAAGACTGAACATATATTACACATACATTTAATGATACATTTTAATTCCAT
10156 C
66 C
10157 AATTCCATCAATTGCAAACGGACTGAACATATATTACACATACATTTAATGATACATTTTAATTC
1 AATTCCATCAATTGC-AA--GACTGAACATATATTACACATACATTTAATGATACATTTTAATTC
10222 CATC
63 CATC
10226 AAT
1 AAT
10229 AGCAAACAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
64 14 0.22
66 1 0.02
69 49 0.77
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (66 bp):
AATTCCATCAATTGCAAGACTGAACATATATTACACATACATTTAATGATACATTTTAATTCCAT
C
Found at i:13663 original size:16 final size:16
Alignment explanation
Indices: 13613--13663 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
13603 TATTGAGAAA
13613 AAAATGTAATACAAAAT
1 AAAATGTAATAC-AAAT
*
13630 AAAAT-TAGATA-ATTAT
1 AAAATGTA-ATACA-AAT
13646 AAAATGTAATACAAAT
1 AAAATGTAATACAAAT
13662 AA
1 AA
13664 TGCAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
15 1 0.04
16 16 0.57
17 11 0.39
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (16 bp):
AAAATGTAATACAAAT
Found at i:17056 original size:13 final size:13
Alignment explanation
Indices: 17038--17062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17028 CGGTACTTTT
17038 ATTTCATTCTGAC
1 ATTTCATTCTGAC
17051 ATTTCATTCTGA
1 ATTTCATTCTGA
17063 TTTCAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTTCATTCTGAC
Found at i:20010 original size:168 final size:168
Alignment explanation
Indices: 19731--20206 Score: 731
Period size: 168 Copynumber: 2.8 Consensus size: 168
19721 CGAGGAAGAG
* * *
19731 AGGACAACATCCATCACAACAGATTCAATCATCAGCTCCGCATACTAATTCAGCACAAATGAATA
1 AGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAATGAATA
* * *
19796 ACAATCAGCAGTTGACCAACTCACAGGCTGGATTAGACTTCAATTTTACAGTTCATCCGAATAGT
66 ACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGATCATCCGAATAGT
* * * *
19861 ACATCTTCTAGACCATGTCCAATAACAGGGGTGA-T-A
131 TCATCTTCCAAACCATGTCCAATAACAAGGGTGATTGA
* *
19897 AGTGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGTATACAAATTCAGCACCAATGAG
1 A--GGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAATGAA
* *
19962 TAACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGGTCGTCCGAATA
64 TAACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGATCATCCGAATA
**
20027 GTTCATCTTCCAAACCATGTCCAATGCCAAGGGTGATTGA
129 GTTCATCTTCCAAACCATGTCCAATAACAAGGGTGATTGA
*
20067 AGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCACATACAAATTCAGCACCAATGAATA
1 AGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAATGAATA
* * * *
20132 ACAATCAGCAGTTGACCAGCTCACGGGCTGGCTTAAACTTCGATTTTACAGATCATCCAAATAGT
66 ACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGATCATCCGAATAGT
20197 TCATCTTCCA
131 TCATCTTCCA
20207 GAGCCCAAAC
Statistics
Matches: 282, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
166 1 0.00
168 278 0.99
169 1 0.00
170 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.24
Consensus pattern (168 bp):
AGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAATGAATA
ACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGATCATCCGAATAGT
TCATCTTCCAAACCATGTCCAATAACAAGGGTGATTGA
Found at i:25207 original size:15 final size:15
Alignment explanation
Indices: 25187--25220 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25177 AATGTTAATG
25187 AATAATAAACAAACA
1 AATAATAAACAAACA
* *
25202 AATAATAAATAAATA
1 AATAATAAACAAACA
25217 AATA
1 AATA
25221 CACACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAATAAACAAACA
Found at i:29085 original size:17 final size:17
Alignment explanation
Indices: 29059--29092 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29049 TAAGAAATCT
29059 TAAATTT-AAAATAATA
1 TAAATTTAAAAATAATA
29075 TAAATTTTAAAAATAATA
1 TAAA-TTTAAAAATAATA
29093 ATACGGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 3 0.19
18 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTAAAAATAATA
Found at i:29259 original size:42 final size:42
Alignment explanation
Indices: 29200--29283 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
29190 ATATTAGATT
29200 TATAGCCTGTACTAATATCATACATAGATCCAATCAAAACCC
1 TATAGCCTGTACTAATATCATACATAGATCCAATCAAAACCC
29242 TATAGCCTGTACTAATATCATACATAGATCCAATCAAAACCC
1 TATAGCCTGTACTAATATCATACATAGATCCAATCAAAACCC
29284 AACCTGATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (42 bp):
TATAGCCTGTACTAATATCATACATAGATCCAATCAAAACCC
Found at i:34789 original size:21 final size:22
Alignment explanation
Indices: 34765--34820 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
34755 ATTAGAAATC
34765 ATAAATTATATAA-ATTTTAAA
1 ATAAATTATATAATATTTTAAA
*
34786 ATAAA-TATTAAAATATTTTAAA
1 ATAAATTA-TATAATATTTTAAA
34808 A-AAATATATATAA
1 ATAAAT-TATATAA
34821 CTAAATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 2 0.07
21 12 0.41
22 13 0.45
23 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAATTATATAATATTTTAAA
Found at i:38462 original size:52 final size:52
Alignment explanation
Indices: 38406--38508 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
38396 AGGAAATAAA
*
38406 TTATACTATATGTTTTCTTTATTATATTGCCTTTCTTTGTTTATAAAGGGAC
1 TTATACTATATGTTTTCTTTATTAAATTGCCTTTCTTTGTTTATAAAGGGAC
*
38458 TTATACTATATGTTTTCTTTATTAAATTGTCTTTCTTTGTTTATAAAGGGA
1 TTATACTATATGTTTTCTTTATTAAATTGCCTTTCTTTGTTTATAAAGGGA
38509 TATTATATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (52 bp):
TTATACTATATGTTTTCTTTATTAAATTGCCTTTCTTTGTTTATAAAGGGAC
Found at i:40258 original size:19 final size:19
Alignment explanation
Indices: 40230--40268 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40220 TTATATATTC
*
40230 TTTTAGAATTTTTTAAAAA
1 TTTTAGAATTTTTAAAAAA
*
40249 TTTTATAATTTTTAAAAAA
1 TTTTAGAATTTTTAAAAAA
40268 T
1 T
40269 ATAAAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTTAGAATTTTTAAAAAA
Found at i:40276 original size:18 final size:18
Alignment explanation
Indices: 40239--40277 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40229 CTTTTAGAAT
* * *
40239 TTTTTAAAAATTTTATAA
1 TTTTTAAAAAATATAAAA
40257 TTTTTAAAAAATATAAAA
1 TTTTTAAAAAATATAAAA
40275 TTT
1 TTT
40278 GAAATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTAAAAAATATAAAA
Found at i:40310 original size:19 final size:19
Alignment explanation
Indices: 40283--40323 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
40273 AATTTGAAAT
*
40283 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTAAA
* *
40302 TTTTGAAAATTGTTTTAAA
1 TTTTAAAAATTATTTTAAA
40321 TTT
1 TTT
40324 ATTTTTGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:41915 original size:7 final size:7
Alignment explanation
Indices: 41904--41944 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
41894 AGCTATTCGG
*
41904 GGTTCAG
1 GGTTCAA
*
41911 GGTTCAG
1 GGTTCAA
41918 GGTTCAA
1 GGTTCAA
41925 GGTTCAA
1 GGTTCAA
41932 GGTTCAA
1 GGTTCAA
41939 GGTTCA
1 GGTTCA
41945 CCCTTGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.22, C:0.15, G:0.34, T:0.29
Consensus pattern (7 bp):
GGTTCAA
Found at i:50495 original size:7 final size:7
Alignment explanation
Indices: 50479--50516 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
50469 GCTTCAAAAC
50479 AATT-CA
1 AATTCCA
50485 AATTCCA
1 AATTCCA
50492 AATTCCA
1 AATTCCA
50499 AATTCCA
1 AATTCCA
50506 AATTCCA
1 AATTCCA
50513 AATT
1 AATT
50517 AACGTCTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTCCA
Found at i:55544 original size:19 final size:19
Alignment explanation
Indices: 55508--55553 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 19
55498 CATTATATTC
55508 TAATATATCATATGTTAAAT
1 TAATATATCATATGTT-AAT
55528 ATAATATAT-ATAT-TTAAT
1 -TAATATATCATATGTTAAT
55546 TAATATAT
1 TAATATAT
55554 GTAATTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 2 0.08
20 4 0.16
21 8 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATATATCATATGTTAAT
Found at i:62656 original size:13 final size:13
Alignment explanation
Indices: 62640--62673 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
62630 ATATGATATA
62640 AAAATATTGGTTC
1 AAAATATTGGTTC
*
62653 AAAATAGTGGTTC
1 AAAATATTGGTTC
62666 AAAATATT
1 AAAATATT
62674 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (13 bp):
AAAATATTGGTTC
Found at i:65315 original size:30 final size:30
Alignment explanation
Indices: 65276--65332 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
65266 TTTTACAAAT
65276 AATTAATATTA-AT-TACTTACAAATATTTAA
1 AATTAATATTATATATA-TTA-AAATATTTAA
*
65306 AATTTATATTATATATATTAAAATATT
1 AATTAATATTATATATATTAAAATATT
65333 AATAATGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 17 0.71
31 5 0.21
32 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTAATATTATATATATTAAAATATTTAA
Found at i:66333 original size:107 final size:108
Alignment explanation
Indices: 66211--66420 Score: 280
Period size: 110 Copynumber: 1.9 Consensus size: 108
66201 TCTGTGTTTT
* *
66211 TTGGTATGGTATTTGATCTT-ATATAGTCTCACTTATGAATC-TGTTTTTTTCGATTCGATGTGT
1 TTGGTATGGTATTTGAT-TTCATATACTCTCACTTATCAATCTTGTTTTTTTCGATTCGATGTGT
* *
66274 TGGTGCAGTGGTTCAAGTTTGAATTTTTAATCAAGTTTACACTC
65 TGGTGCAGTGATTCAAGCTTGAATTTTTAATCAAGTTTACACTC
* * * ** *
66318 TTGGTATGGTATTTGATTTCATATTCTCTCGCTTATCAATCTTTTTTTTTTTTTTATTCTATGTG
1 TTGGTATGGTATTTGATTTCATATACTCTCACTTATCAATC--TTGTTTTTTTCGATTCGATGTG
*
66383 TTGGTGTAGTGATTCAAGCTTGAATTTTTAATCAAGTT
64 TTGGTGCAGTGATTCAAGCTTGAATTTTTAATCAAGTT
66421 AACATTTTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
106 2 0.02
107 34 0.39
110 52 0.59
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.50
Consensus pattern (108 bp):
TTGGTATGGTATTTGATTTCATATACTCTCACTTATCAATCTTGTTTTTTTCGATTCGATGTGTT
GGTGCAGTGATTCAAGCTTGAATTTTTAATCAAGTTTACACTC
Found at i:72927 original size:38 final size:38
Alignment explanation
Indices: 72884--72960 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
72874 CCACATTAAA
72884 TATTGGTGGATCTGATCATTTTCATAACTTCACATTGT
1 TATTGGTGGATCTGATCATTTTCATAACTTCACATTGT
72922 TATTGGTGGATCTGATCATTTTCATAACTTCACATTGT
1 TATTGGTGGATCTGATCATTTTCATAACTTCACATTGT
72960 T
1 T
72961 TGCCATGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (38 bp):
TATTGGTGGATCTGATCATTTTCATAACTTCACATTGT
Found at i:80026 original size:31 final size:30
Alignment explanation
Indices: 79972--80049 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
79962 ATACTTAACA
**
79972 TATATTTTTTAGAATATTTTTTTGAAAATTT
1 TATATTTTTTA-AATATAATTTTGAAAATTT
**
80003 TATATTTTTTAAATATAAATTTTGAATTTTT
1 TATATTTTTTAAATAT-AATTTTGAAAATTT
80034 TATAATTATTTTAAAT
1 TAT-ATT-TTTTAAAT
80050 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.12
31 24 0.60
32 3 0.08
33 8 0.20
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (30 bp):
TATATTTTTTAAATATAATTTTGAAAATTT
Found at i:80044 original size:20 final size:19
Alignment explanation
Indices: 80021--80095 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
80011 TTAAATATAA
80021 ATTTTGAATTTTTTATAATT
1 ATTTTGAA-TTTTTATAATT
* *
80041 ATTTT-AAATTTTAAAATTT
1 ATTTTGAATTTTTATAA-TT
*
80060 ATTTTGAAATTTTAATAATT
1 ATTTTG-AATTTTTATAATT
*
80080 ATTTTGTAGTTTTTAT
1 ATTTTG-AATTTTTAT
80096 TGTGAAAGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
18 7 0.16
19 9 0.20
20 20 0.45
21 8 0.18
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
ATTTTGAATTTTTATAATT
Found at i:81951 original size:28 final size:24
Alignment explanation
Indices: 81891--81976 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 24
81881 TTCAACATAA
* * *
81891 TAATATAA-AATTCAATTTATTAT
1 TAATATAATATTTTAATTTAATAT
81914 T-ATAT-ATATTTTTAAAATTTAATAT
1 TAATATAATA-TTTT--AATTTAATAT
*
81939 TAATATAATTATTTTCATTTAATAT
1 TAATATAA-TATTTTAATTTAATAT
*
81964 TAATATAAAATTT
1 TAATATAATATTT
81977 AAAGTTATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
21 1 0.02
22 5 0.10
23 3 0.06
24 4 0.08
25 27 0.53
26 4 0.08
27 5 0.10
28 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATATAATATTTTAATTTAATAT
Found at i:93300 original size:11 final size:12
Alignment explanation
Indices: 93278--93306 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
93268 TTAAAAATAT
93278 AATATATTTTAA
1 AATATATTTTAA
93290 AATAT-TTTTAA
1 AATATATTTTAA
93301 AATATA
1 AATATA
93307 AAATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATATTTTAA
Found at i:93314 original size:29 final size:30
Alignment explanation
Indices: 93247--93314 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
93237 CAAATGATTT
93247 TAAAATTA--TTAAAATTATTTTTTAAAAA
1 TAAAATTATTTTAAAATTATTTTTTAAAAA
*
93275 TATAATATATTTTAAAA-TA-TTTTTAAAATA
1 TAAAAT-TATTTTAAAATTATTTTTTAAAA-A
93305 TAAAATTATT
1 TAAAATTATT
93315 AAATAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
28 5 0.15
29 15 0.44
30 8 0.24
31 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAAATTATTTTAAAATTATTTTTTAAAAA
Found at i:93714 original size:16 final size:15
Alignment explanation
Indices: 93693--93758 Score: 54
Period size: 16 Copynumber: 4.7 Consensus size: 15
93683 TAAAATTGTT
93693 TTTTTAAAATATAAAA
1 TTTTTAAAATAT-AAA
*
93709 TTTTT-AAA-ATCAA
1 TTTTTAAAATATAAA
93722 --TTTAAAAT-T-AA
1 TTTTTAAAATATAAA
93733 TTTTTAAAATATAAAA
1 TTTTTAAAATAT-AAA
*
93749 TTATTAAAAT
1 TTTTTAAAAT
93759 CATCATCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
11 5 0.12
12 4 0.10
13 10 0.24
14 3 0.07
15 3 0.07
16 16 0.39
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTTAAAATATAAA
Found at i:93747 original size:20 final size:19
Alignment explanation
Indices: 93693--93753 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
93683 TAAAATTGTT
93693 TTTTTAAAATATAAAATT-
1 TTTTTAAAATATAAAATTA
** *
93711 TTTAAAATCAATTTAAAATTAA
1 TTTTTAA--AATATAAAATT-A
93733 TTTTTAAAATATAAAATTA
1 TTTTTAAAATATAAAATTA
93752 TT
1 TT
93754 AAAATCATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 5 0.15
19 3 0.09
20 20 0.61
22 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTTTAAAATATAAAATTA
Found at i:103646 original size:18 final size:18
Alignment explanation
Indices: 103625--103663 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
103615 TTTTTGAAAA
103625 TATAAATTTTAGAATTTT
1 TATAAATTTTAGAATTTT
*
103643 TATAAATTTTGGAATTTT
1 TATAAATTTTAGAATTTT
103661 TAT
1 TAT
103664 CGAGAGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (18 bp):
TATAAATTTTAGAATTTT
Found at i:109537 original size:17 final size:17
Alignment explanation
Indices: 109515--109564 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
109505 TGTGTAAATT
109515 TAATATTTTAATTTTTA
1 TAATATTTTAATTTTTA
109532 TAATATCTTTAATTAGTTTA
1 TAATAT-TTTAATT--TTTA
109552 -AATA-TTTAATTTT
1 TAATATTTTAATTTT
109565 AATTAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
17 13 0.43
18 7 0.23
19 4 0.13
20 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATATTTTAATTTTTA
Found at i:109688 original size:15 final size:15
Alignment explanation
Indices: 109668--109698 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109658 AAATATTAAG
109668 ATTATTTTATTTTTT
1 ATTATTTTATTTTTT
109683 ATTATTTTATTTTTT
1 ATTATTTTATTTTTT
109698 A
1 A
109699 AAATGTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTATTTTATTTTTT
Found at i:116979 original size:60 final size:59
Alignment explanation
Indices: 116850--116988 Score: 147
Period size: 59 Copynumber: 2.3 Consensus size: 59
116840 ATATTTAAAT
* *
116850 TTGAT-ATTTTTTTTAATTTTGGTACCTAAACTTTTTTGGATCAATTTGGTACCTGAAC
1 TTGATAATTTTTTTTAATTTTGGCACCTAAACTTTTTTGGACCAATTTGGTACCTGAAC
* * * * * ** *
116908 TTGATACTTTTTCTTAATTTTGGCATCTAAATTTTTTTGGACCCGATTTGGTATTTTAAC
1 TTGATAATTTTTTTTAATTTTGGCACCTAAACTTTTTTGGA-CCAATTTGGTACCTGAAC
116968 TTAGA-AATTTTTTTCTAATTT
1 TT-GATAATTTTTTT-TAATTT
116989 GACACTTAAG
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
58 5 0.08
59 30 0.46
60 22 0.34
61 8 0.12
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (59 bp):
TTGATAATTTTTTTTAATTTTGGCACCTAAACTTTTTTGGACCAATTTGGTACCTGAAC
Found at i:117264 original size:30 final size:31
Alignment explanation
Indices: 117228--117287 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
117218 GGATCTCAAA
*
117228 AAGTTTA-AGTATCAACTTA-AAAAAAGTGTT
1 AAGTTTAGA-TATCAAATTAGAAAAAAGTGTT
*
117258 AAGTTTAGATATCAAATTAGGAAAAAGTGT
1 AAGTTTAGATATCAAATTAGAAAAAAGTGT
117288 CAAAATTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.32
Consensus pattern (31 bp):
AAGTTTAGATATCAAATTAGAAAAAAGTGTT
Found at i:118932 original size:13 final size:13
Alignment explanation
Indices: 118916--118941 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
118906 TCTAAAATCT
118916 TTTTATAAAAAAA
1 TTTTATAAAAAAA
118929 TTTTATAAAAAAA
1 TTTTATAAAAAAA
118942 AACAAACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTTATAAAAAAA
Found at i:122833 original size:43 final size:44
Alignment explanation
Indices: 122772--122939 Score: 175
Period size: 43 Copynumber: 3.9 Consensus size: 44
122762 AAACGCCACT
* *
122772 ATGATTTTTAGCGGCGCTTTTAC-CACAAGCACCGCTAAAGAAC
1 ATGATCTTTAGCGGCGCTTTTACTCACAAACACCGCTAAAGAAC
* *
122815 ATGATCTTTACCGGCGC-TTTCCTCACAAACACCGCTAAAGAAC
1 ATGATCTTTAGCGGCGCTTTTACTCACAAACACCGCTAAAGAAC
* * * * *
122858 ATGATCTTTAGCGGCTC-TTT-CGTTACAAACGCCACTAAAAAAC
1 ATGATCTTTAGCGGCGCTTTTAC-TCACAAACACCGCTAAAGAAC
* * * *
122901 ATGGTCTTTAGCAGTGCTTTT-CTCACAAACGCCGCTAAA
1 ATGATCTTTAGCGGCGCTTTTACTCACAAACACCGCTAAA
122940 ATTAACAGAT
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
42 5 0.05
43 97 0.92
44 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (44 bp):
ATGATCTTTAGCGGCGCTTTTACTCACAAACACCGCTAAAGAAC
Found at i:122990 original size:15 final size:15
Alignment explanation
Indices: 122970--122998 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
122960 TTATCTTGTA
122970 AATTCAAATCCAACT
1 AATTCAAATCCAACT
122985 AATTCAAATCCAAC
1 AATTCAAATCCAAC
122999 CAATATCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTCAAATCCAACT
Found at i:124401 original size:30 final size:32
Alignment explanation
Indices: 124345--124404 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
124335 TGTTTGTATG
*
124345 AAATTGAAGAAAGAGGGAGGAAGGAGAAAGACC
1 AAATTGAAGAAAGAAGGA-GAAGGAGAAAGACC
124378 AAATTGAAGAAA-AAGGA-AAGGAGAAAG
1 AAATTGAAGAAAGAAGGAGAAGGAGAAAG
124405 CTAAGGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
32 4 0.15
33 12 0.46
ACGTcount: A:0.57, C:0.03, G:0.33, T:0.07
Consensus pattern (32 bp):
AAATTGAAGAAAGAAGGAGAAGGAGAAAGACC
Found at i:127399 original size:43 final size:43
Alignment explanation
Indices: 127192--127412 Score: 187
Period size: 43 Copynumber: 5.2 Consensus size: 43
127182 ATTAAAGCGT
* * * * * *
127192 CGCTAAAAAATATGATCTTTAGTGGCGCATTTATCACAAACTC
1 CGCTAAAAAACATGGTCTTTAGCGGCGCTTTTCTCACAAACAC
* * *
127235 CGCTAAAGAACATGGTCTTTAGCGGCTCTTTTAC-CACAAGCAC
1 CGCTAAAAAACATGGTCTTTAGCGGCGCTTTT-CTCACAAACAC
* ** * *
127278 CGCTAAAGAACATGGTCTTTAGCAACGCTTTCCTCACAAATAC
1 CGCTAAAAAACATGGTCTTTAGCGGCGCTTTTCTCACAAACAC
* * * *
127321 CGCTAGAAAA-A-GGATCTTTAGCGGCACTTTCCTCACAAACGC
1 CGCTAAAAAACATGG-TCTTTAGCGGCGCTTTTCTCACAAACAC
* * * * *
127363 CGCTAAAAAATATGGTTTTTAGCAGTGCTTTTCTCACAAACGC
1 CGCTAAAAAACATGGTCTTTAGCGGCGCTTTTCTCACAAACAC
*
127406 CGTTAAA
1 CGCTAAA
127413 GTTAACAGAT
Statistics
Matches: 144, Mismatches: 29, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
41 2 0.01
42 34 0.24
43 106 0.74
44 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (43 bp):
CGCTAAAAAACATGGTCTTTAGCGGCGCTTTTCTCACAAACAC
Found at i:129241 original size:20 final size:20
Alignment explanation
Indices: 129216--129261 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
129206 AGAAAGGAAG
129216 GAAGAAGGAGAGGAAAGAAA
1 GAAGAAGGAGAGGAAAGAAA
*
129236 GAAGAAGGAGAGGATAGAAA
1 GAAGAAGGAGAGGAAAGAAA
129256 GAAGAA
1 GAAGAA
129262 TGAAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (20 bp):
GAAGAAGGAGAGGAAAGAAA
Found at i:129249 original size:25 final size:24
Alignment explanation
Indices: 129204--129258 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
129194 GAAAGAAAAT
129204 AAAGAAAGGAAGGAAGAAGGAGAGG
1 AAAGAAAGGAAGGAAGAAGGAGA-G
*
129229 AAAGAAA-GAA-GAAGGAGAGGATAG
1 AAAGAAAGGAAGGAA-GA-AGGAGAG
129253 AAAGAA
1 AAAGAA
129259 GAATGAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.11
24 12 0.44
25 12 0.44
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (24 bp):
AAAGAAAGGAAGGAAGAAGGAGAG
Done.