Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015333.1 Kokia drynarioides strain JFW-HI SEQ_130380, 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: 503969
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 387 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:342870 original size:24 final size:24
Alignment explanation
Indices: 342843--343282 Score: 378
Period size: 24 Copynumber: 18.3 Consensus size: 24
342833 AAACATTGTA
*
342843 AGCGTAAACGTATATAAGCTGACG
1 AGCGTAAACGTATACAAGCTGACG
* * *
342867 AGCGTAAACGTGTGCAAGCTGACA
1 AGCGTAAACGTATACAAGCTGACG
* * * *
342891 AGTGTAAATGTATATAAGCTAACG
1 AGCGTAAACGTATACAAGCTGACG
*
342915 AGCGTAAACGTATATAAGCTGACG
1 AGCGTAAACGTATACAAGCTGACG
342939 AGCGTAAACGTATACAAGCTGACG
1 AGCGTAAACGTATACAAGCTGACG
*
342963 AGAGTAAACGTATACAAGCTGACG
1 AGCGTAAACGTATACAAGCTGACG
* * *
342987 AGTGTAAACGTATATAAGCTGATG
1 AGCGTAAACGTATACAAGCTGACG
* * *
343011 AGCATAAACGTGTGCAAGCTGACG
1 AGCGTAAACGTATACAAGCTGACG
* * * * *
343035 AGCATAAACGTGTGCAAGCTAACA
1 AGCGTAAACGTATACAAGCTGACG
* * *
343059 AGCGTAAACGTGTGCAA-CTTGACA
1 AGCGTAAACGTATACAAGC-TGACG
* *
343083 AGCGTAAACGTATATAAGCTGGCG
1 AGCGTAAACGTATACAAGCTGACG
* * * * *
343107 AGCATAAACGTGTGCAAGATGACA
1 AGCGTAAACGTATACAAGCTGACG
* * * *
343131 AGAGTAAACGCATATAAGCTGAAG
1 AGCGTAAACGTATACAAGCTGACG
* * *
343155 AGCATAAACGTGTGCAAGCTGACG
1 AGCGTAAACGTATACAAGCTGACG
* * * *
343179 AGCATAAACATGTATAAGCTGACG
1 AGCGTAAACGTATACAAGCTGACG
* * * *
343203 AACATAAACGTGTGCAAGCTGACG
1 AGCGTAAACGTATACAAGCTGACG
* * *
343227 AGTGTAAACGTATATAAGCTAACG
1 AGCGTAAACGTATACAAGCTGACG
* * * *
343251 AGTGTAAACGTGTGCAAGCTGACA
1 AGCGTAAACGTATACAAGCTGACG
*
343275 AGTGTAAA
1 AGCGTAAA
343283 TGCATACACA
Statistics
Matches: 338, Mismatches: 76, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
23 1 0.00
24 336 0.99
25 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (24 bp):
AGCGTAAACGTATACAAGCTGACG
Found at i:342917 original size:48 final size:48
Alignment explanation
Indices: 342843--343282 Score: 513
Period size: 48 Copynumber: 9.2 Consensus size: 48
342833 AAACATTGTA
*
342843 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
* * * * **
342891 AGTGTAAATGTATATAAGCTAACGAGCGTAAACGTATATAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
* * * *
342939 AGCGTAAACGTATACAAGCTGACGAGAGTAAACGTATACAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
* * *
342987 AGTGTAAACGTATATAAGCTGATGAGCATAAACGTGTGCAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
* * ** * * *
343035 AGCATAAACGTGTGCAAGCTAACAAGCGTAAACGTGTGCAA-CTTGACA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGC-TGACG
* * * *
343083 AGCGTAAACGTATATAAGCTGGCGAGCATAAACGTGTGCAAGATGACA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
* * * *
343131 AGAGTAAACGCATATAAGCTGAAGAGCATAAACGTGTGCAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
* * * * *
343179 AGCATAAACATGTATAAGCTGACGAACATAAACGTGTGCAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
* * * *
343227 AGTGTAAACGTATATAAGCTAACGAGTGTAAACGTGTGCAAGCTGACA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
*
343275 AGTGTAAA
1 AGCGTAAA
343283 TGCATACACA
Statistics
Matches: 329, Mismatches: 61, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
47 1 0.00
48 328 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (48 bp):
AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACG
Found at i:342960 original size:72 final size:72
Alignment explanation
Indices: 342843--343282 Score: 416
Period size: 72 Copynumber: 6.1 Consensus size: 72
342833 AAACATTGTA
* * * ** * * *
342843 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACAAGTGTAAATGTATATAA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTATACAAGCTGACGAGCATAAACGTGTACAA
*
342908 GCTAACG
66 GCTGACG
*
342915 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTATACAAGCTGACGAG-AGTAAACGTATACA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTATACAAGCTGACGAGCA-TAAACGTGTACA
342979 AGCTGACG
65 AGCTGACG
* * * * * *
342987 AGTGTAAACGTATATAAGCTGATGAGCATAAACGTGTGCAAGCTGACGAGCATAAACGTGTGCAA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTATACAAGCTGACGAGCATAAACGTGTACAA
* *
343052 GCTAACA
66 GCTGACG
* ** * * * *
343059 AGCGTAAACGTGTGCAA-CTTGACAAGCGTAAACGTATATAAGCTGGCGAGCATAAACGTGTGCA
1 AGCGTAAACGTATATAAGC-TGACGAGCGTAAACGTATACAAGCTGACGAGCATAAACGTGTACA
* *
343123 AGATGACA
65 AGCTGACG
* * * * * * * *
343131 AGAGTAAACGCATATAAGCTGAAGAGCATAAACGTGTGCAAGCTGACGAGCATAAACATGTATAA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTATACAAGCTGACGAGCATAAACGTGTACAA
343196 GCTGACG
66 GCTGACG
* * * ** * * * ** *
343203 AACATAAACGTGTGCAAGCTGACGAGTGTAAACGTATATAAGCTAACGAGTGTAAACGTGTGCAA
1 AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTATACAAGCTGACGAGCATAAACGTGTACAA
*
343268 GCTGACA
66 GCTGACG
*
343275 AGTGTAAA
1 AGCGTAAA
343283 TGCATACACA
Statistics
Matches: 295, Mismatches: 69, Indels: 8
0.79 0.19 0.02
Matches are distributed among these distances:
71 1 0.00
72 292 0.99
73 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (72 bp):
AGCGTAAACGTATATAAGCTGACGAGCGTAAACGTATACAAGCTGACGAGCATAAACGTGTACAA
GCTGACG
Found at i:343305 original size:2 final size:2
Alignment explanation
Indices: 343292--343324 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
343282 ATGCATACAC
*
343292 AT AT AT AA 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 AT AT AT A
343325 CTAAAGGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:343909 original size:40 final size:40
Alignment explanation
Indices: 343865--343953 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
343855 TATGCTTGAG
*
343865 TATCGGTAGTTGTAGTTGTTGCGATAGATGGAATTTCTTA
1 TATCGGTAGTTGTAGTTGTTGCAATAGATGGAATTTCTTA
*
343905 TATCGGTAGTTGTAGTTGTTGCAATAGATGGAATTTCTTG
1 TATCGGTAGTTGTAGTTGTTGCAATAGATGGAATTTCTTA
343945 TATCGGTAG
1 TATCGGTAG
343954 AAGTTTGTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.22, C:0.08, G:0.28, T:0.42
Consensus pattern (40 bp):
TATCGGTAGTTGTAGTTGTTGCAATAGATGGAATTTCTTA
Found at i:347572 original size:21 final size:19
Alignment explanation
Indices: 347534--347580 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
347524 AATCCTTTTT
*
347534 ATTTAATTACTAACCAAAC
1 ATTTAATTACTAACCAAAA
*
347553 ATTTGAATTACTTTACCAAAA
1 ATTT-AATTAC-TAACCAAAA
347574 ATTTAAT
1 ATTTAAT
347581 ATGACGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 9 0.38
21 11 0.46
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTTAATTACTAACCAAAA
Found at i:352494 original size:13 final size:13
Alignment explanation
Indices: 352476--352501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
352466 TTAGGAGAAC
352476 TTAAAGTTTTAGA
1 TTAAAGTTTTAGA
352489 TTAAAGTTTTAGA
1 TTAAAGTTTTAGA
352502 AGCCTGCTTC
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTAAAGTTTTAGA
Found at i:352987 original size:25 final size:25
Alignment explanation
Indices: 352937--352987 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
352927 TATTGCATAT
*
352937 AACTAATACAAATCAGCATTATTCA
1 AACTAATACAAATCAGCATTAATCA
*
352962 AACTAATAACAAATTAGCA-TAATCA
1 AACTAAT-ACAAATCAGCATTAATCA
352987 A
1 A
352988 TGTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.25
Consensus pattern (25 bp):
AACTAATACAAATCAGCATTAATCA
Found at i:357727 original size:20 final size:20
Alignment explanation
Indices: 357702--357746 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
357692 ATAGATTTAA
*
357702 TTAATGCGACAATAGGGGTT
1 TTAATGCGACAATAAGGGTT
357722 TTAATGCGACAATAAGGGTT
1 TTAATGCGACAATAAGGGTT
357742 TTAAT
1 TTAAT
357747 TTGAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (20 bp):
TTAATGCGACAATAAGGGTT
Found at i:358266 original size:13 final size:13
Alignment explanation
Indices: 358249--358287 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
358239 TACTATTTGT
358249 ATTTTT-TATTTA
1 ATTTTTATATTTA
358261 ATTTTTATATTTA
1 ATTTTTATATTTA
358274 ATTTTTATATTTA
1 ATTTTTATATTTA
358287 A
1 A
358288 AATTTTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTATATTTA
Found at i:364782 original size:111 final size:111
Alignment explanation
Indices: 364535--364783 Score: 275
Period size: 111 Copynumber: 2.2 Consensus size: 111
364525 CTTCGAAATC
* * * * * * *
364535 TTTTCATGTTTGAAGTAACTATTTCATGCTTTAAGTAATTCTTTTATGTACTATAAATTATTTTC
1 TTTTTATGTTTTAAGTAATTATTTCATACTTTAAGTAATTCTTTCATGTACCATAAATTAATTTC
* * *
364600 CTAGAACTTTTTCATATTTTACGAATTATTTAATATCCTAAAAATA
66 CTAGAACTCTTTCATATTTTACGAATTACTTAATATCCTAAAAACA
** * *
364646 TTTTTATGTTTTAAAAAATTATTTCATATTTTAAGTAATTCTTTCATGTACCGTAAATTAATTTC
1 TTTTTATGTTTTAAGTAATTATTTCATACTTTAAGTAATTCTTTCATGTACCATAAATTAATTTC
* ** * ** *
364711 CTAGAACTCTTTCATGTTTTTTGAATTACTTAATTTTTTATAAAC-
66 CTAGAACTCTTTCATATTTTACGAATTACTTAATATCCTAAAAACA
* *
364756 CTTTTATTGTTTTAAGTAATTCTTTCAT
1 TTTTTA-TGTTTTAAGTAATTATTTCAT
364784 TTATTATGAA
Statistics
Matches: 112, Mismatches: 25, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
110 5 0.04
111 107 0.96
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (111 bp):
TTTTTATGTTTTAAGTAATTATTTCATACTTTAAGTAATTCTTTCATGTACCATAAATTAATTTC
CTAGAACTCTTTCATATTTTACGAATTACTTAATATCCTAAAAACA
Found at i:364972 original size:20 final size:20
Alignment explanation
Indices: 364921--364972 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
364911 CTTAGAATCG
364921 TTTCATGTTTTAATTAACTT
1 TTTCATGTTTTAATTAACTT
** * *
364941 TTTCCGGATTTAATTCA-TT
1 TTTCATGTTTTAATTAACTT
364960 CTTTCATGTTTTA
1 -TTTCATGTTTTA
364973 TAAATTATGT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTCATGTTTTAATTAACTT
Found at i:366641 original size:17 final size:16
Alignment explanation
Indices: 366602--366643 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
366592 AATATGTAAC
366602 AAAT-TTATAAAAAAA
1 AAATGTTATAAAAAAA
*
366617 AAATTGTTATAAAAAACT
1 AAA-TGTTATAAAAAA-A
366635 AAATGTTAT
1 AAATGTTAT
366644 TTGGTTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 3 0.13
16 1 0.04
17 16 0.70
18 3 0.13
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (16 bp):
AAATGTTATAAAAAAA
Found at i:367173 original size:6 final size:6
Alignment explanation
Indices: 367160--367197 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
367150 GCATCCCCGC
* *
367160 TAAAAA TGAAAA TGAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
367198 TTCAATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:367626 original size:29 final size:29
Alignment explanation
Indices: 367568--367632 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
367558 TAATTTTTAT
*
367568 AAAAAATAAAAATATATATTTAAAATTAGA
1 AAAAAATAAAAATATATA-TGAAAATTAGA
367598 AAAAAATATAAAATATATA-G-AAATATAGA
1 AAAAAATA-AAAATATATATGAAAAT-TAGA
367627 AAAAAA
1 AAAAAA
367633 AATTATAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.12
29 10 0.31
30 8 0.25
31 10 0.31
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.25
Consensus pattern (29 bp):
AAAAAATAAAAATATATATGAAAATTAGA
Found at i:367915 original size:19 final size:19
Alignment explanation
Indices: 367893--368032 Score: 84
Period size: 19 Copynumber: 7.7 Consensus size: 19
367883 TTATGCATTA
*
367893 TATATATTTTTATGATTTT
1 TATATATTTTTATAATTTT
* * * *
367912 TATAAAATTTTACATTTTT
1 TATATATTTTTATAATTTT
*
367931 TATA-ATTTTTTTACCA-TTT
1 TATATATTTTTATA--ATTTT
*
367950 T-T-TATTTTTAAAATTTT
1 TATATATTTTTATAATTTT
**
367967 TA-ATATTTTTATTAAAATT
1 TATATATTTTTA-TAATTTT
367986 TA-ATAATTTTTATAATTTT
1 TATAT-ATTTTTATAATTTT
*
368005 TAT-TGTTTTT-T-ATTTT
1 TATATATTTTTATAATTTT
368021 T-TATATTTTTAT
1 TATATATTTTTAT
368033 CAAAGTCATA
Statistics
Matches: 92, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
15 1 0.01
16 13 0.14
17 6 0.07
18 27 0.29
19 38 0.41
20 7 0.08
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (19 bp):
TATATATTTTTATAATTTT
Found at i:368007 original size:9 final size:9
Alignment explanation
Indices: 367893--368032 Score: 83
Period size: 9 Copynumber: 15.3 Consensus size: 9
367883 TTATGCATTA
367893 TATATATTTT
1 TATA-ATTTT
*
367903 TATGATTTT
1 TATAATTTT
*
367912 TATAAAATTT
1 TAT-AATTTT
* *
367922 TACATTTTT
1 TATAATTTT
367931 TATAATTTT
1 TATAATTTT
*
367940 TTTACCATTTT
1 TATA--ATTTT
367951 T-T-ATTTT
1 TATAATTTT
*
367958 TAAAATTTT
1 TATAATTTT
367967 TA-ATATTTT
1 TATA-ATTTT
*
367976 TATTAAAATTT
1 TA-T-AATTTT
*
367987 AATAATTTT
1 TATAATTTT
367996 TATAATTTT
1 TATAATTTT
**
368005 TATTGTTTT
1 TATAATTTT
*
368014 T-TATTTTT
1 TATAATTTT
368022 TAT-ATTTT
1 TATAATTTT
368030 TAT
1 TAT
368033 CAAAGTCATA
Statistics
Matches: 101, Mismatches: 19, Indels: 22
0.71 0.13 0.15
Matches are distributed among these distances:
7 6 0.06
8 14 0.14
9 58 0.57
10 11 0.11
11 11 0.11
12 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (9 bp):
TATAATTTT
Found at i:368015 original size:64 final size:63
Alignment explanation
Indices: 367898--368031 Score: 157
Period size: 65 Copynumber: 2.1 Consensus size: 63
367888 CATTATATAT
* *
367898 ATTTTT-ATGATTTTTATAAAATTTTACATTTTTTATAATTTTTTTACCATTTTTTATTTTTAAA
1 ATTTTTAATGATTTTTATAAAATTTAACAATTTTTATAATTTTTTTA-C-TTTTTTATTTTTAAA
* * * *
367962 ATTTTTAAT-ATTTTTATTAAAATTTAATAATTTTTATAATTTTTATT-GTTTTTTATTTTTTAT
1 ATTTTTAATGATTTTTA-TAAAATTTAACAATTTTTATAATTTTT-TTACTTTTTTATTTTTAAA
368025 ATTTTTA
1 ATTTTTA
368032 TCAAAGTCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
63 20 0.33
64 13 0.21
65 26 0.43
66 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (63 bp):
ATTTTTAATGATTTTTATAAAATTTAACAATTTTTATAATTTTTTTACTTTTTTATTTTTAAA
Found at i:368111 original size:13 final size:14
Alignment explanation
Indices: 368093--368134 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
368083 AAAAATTATG
368093 AACAGTTAATT-TT
1 AACAGTTAATTGTT
*
368106 AACAGTCAATTGTT
1 AACAGTTAATTGTT
*
368120 AA-AGTTAACTGTT
1 AACAGTTAATTGTT
368133 AA
1 AA
368135 AATTAATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (14 bp):
AACAGTTAATTGTT
Found at i:368779 original size:17 final size:16
Alignment explanation
Indices: 368753--368791 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
368743 TCAAAATTAA
368753 TATTTTTTAAAATATT
1 TATTTTTTAAAATATT
*
368769 TATTCTTTTAAAATTTT
1 TATT-TTTTAAAATATT
368786 TATTTT
1 TATTTT
368792 AAATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTTTAAAATATT
Found at i:371769 original size:22 final size:23
Alignment explanation
Indices: 371738--371792 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
371728 TATTATTTTT
*
371738 TATTTTTTTATATAT-ATATTTA
1 TATTATTTTATATATAATATTTA
*
371760 TATTATTTTAT-TTTAATATTTA
1 TATTATTTTATATATAATATTTA
*
371782 -ATAATTTTATA
1 TATTATTTTATA
371793 CATTTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTATTTTATATATAATATTTA
Found at i:372562 original size:32 final size:32
Alignment explanation
Indices: 372515--372585 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
372505 ATTTTTAAAA
* * *
372515 AAAATAATAATTTTAGTCAAAATAAAATTAAG
1 AAAATAACAAATTTAGTCAAAACAAAATTAAG
*
372547 AAAATAACAAATTTAGTCAAAACAAAATTAAT
1 AAAATAACAAATTTAGTCAAAACAAAATTAAG
372579 AAAATAA
1 AAAATAA
372586 GTAAATAGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (32 bp):
AAAATAACAAATTTAGTCAAAACAAAATTAAG
Found at i:374036 original size:15 final size:15
Alignment explanation
Indices: 374018--374049 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
374008 ATATTAAAAA
374018 TTTAACAATTAATTT
1 TTTAACAATTAATTT
*
374033 TTTAACACTTAATTT
1 TTTAACAATTAATTT
374048 TT
1 TT
374050 CAATTGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAACAATTAATTT
Found at i:374993 original size:17 final size:18
Alignment explanation
Indices: 374954--374997 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
374944 TTAATTAAAA
*
374954 AAATATAATTTTATATAT
1 AAATATGATTTTATATAT
*
374972 AAATATGATTTTAT-TTT
1 AAATATGATTTTATATAT
374989 AAATATGAT
1 AAATATGAT
374998 AATAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
AAATATGATTTTATATAT
Found at i:376193 original size:26 final size:27
Alignment explanation
Indices: 376159--376219 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
376149 AATAATAATA
376159 ATAATTATAATAA-AAAAATTATTAAAGT
1 ATAA-TATAATAATAAAAATT-TTAAAGT
* *
376187 A-AATATAATAATTATAATTTTAAAGT
1 ATAATATAATAATAAAAATTTTAAAGT
376213 ATAATAT
1 ATAATAT
376220 TTATTGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 16 0.55
27 12 0.41
28 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (27 bp):
ATAATATAATAATAAAAATTTTAAAGT
Found at i:377997 original size:3 final size:3
Alignment explanation
Indices: 377989--378018 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
377979 AAGATTGAAC
377989 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
378019 AATTGAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:382439 original size:33 final size:33
Alignment explanation
Indices: 382402--382469 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
382392 CCCGTATTGT
382402 CGTAAACATGTAATTGTTTTCTATTTAATTGAA
1 CGTAAACATGTAATTGTTTTCTATTTAATTGAA
382435 CGTAAACATGTAATTGTTTTCTATTTAATTGAA
1 CGTAAACATGTAATTGTTTTCTATTTAATTGAA
382468 CG
1 CG
382470 ATGAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (33 bp):
CGTAAACATGTAATTGTTTTCTATTTAATTGAA
Found at i:386089 original size:22 final size:21
Alignment explanation
Indices: 386045--386086 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
386035 TCTTTGTAAT
*
386045 TTAGGTTTAGTGTTTTCTTTC
1 TTAGGTTTAGTATTTTCTTTC
386066 TTAGGCTTTAGTTATTTTCTT
1 TTAGG-TTTAG-TATTTTCTT
386087 CTTTTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (21 bp):
TTAGGTTTAGTATTTTCTTTC
Found at i:395203 original size:15 final size:16
Alignment explanation
Indices: 395174--395203 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
395164 TTCTTATTTA
395174 TTTTATTATATTTTTC
1 TTTTATTATATTTTTC
395190 TTTTATTA-ATTTTT
1 TTTTATTATATTTTT
395204 ATTTATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTATATTTTTC
Found at i:408935 original size:73 final size:73
Alignment explanation
Indices: 408816--408964 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
408806 TTCCATCGGC
408816 ATGACAAGTCGATAGAGATTGCTTATCGCTAGATGTCACAATCTAAATCGGTTTGGGGAAAAGGT
1 ATGACAAGTCGATAGAGATTGCTTATCGCTAGATGTCACAATCTAAATCGGTTTGGGGAAAAGGT
408881 GTTCATAT
66 GTTCATAT
408889 ATGACAAGTCGATAGAGATTGCTTATCGCTAGATGTCACAATCTAAATCGGTTTGGGGAAAAGGT
1 ATGACAAGTCGATAGAGATTGCTTATCGCTAGATGTCACAATCTAAATCGGTTTGGGGAAAAGGT
408954 GTTCATAT
66 GTTCATAT
408962 ATG
1 ATG
408965 GGCAATACCA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (73 bp):
ATGACAAGTCGATAGAGATTGCTTATCGCTAGATGTCACAATCTAAATCGGTTTGGGGAAAAGGT
GTTCATAT
Found at i:424014 original size:42 final size:40
Alignment explanation
Indices: 423956--424041 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 40
423946 CGATAGATCA
*
423956 TAAGTATAAGTTGTGTATCAGCGAAGCTACTCACA-AGAGCT
1 TAAGTATAACTTGTGTATCAGCGAAGCT-CTC-CAGAGAGCT
423997 TAAGTGATAACTTGTGTATCAGCGAAGCTCTCCATGAGAGCT
1 TAAGT-ATAACTTGTGTATCAGCGAAGCTCTCCA-GAGAGCT
424039 TAA
1 TAA
424042 ATGTTTGTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
40 2 0.05
41 8 0.20
42 31 0.76
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (40 bp):
TAAGTATAACTTGTGTATCAGCGAAGCTCTCCAGAGAGCT
Found at i:456422 original size:22 final size:25
Alignment explanation
Indices: 456376--456426 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 25
456366 TACAATATAT
*
456376 AAATATTAATAAATTAATAAATTCA
1 AAATATTAATAAATTAAAAAATTCA
456401 AAATA-TAA-AAA-TAAAAAATTCA
1 AAATATTAATAAATTAAAAAATTCA
456423 AAAT
1 AAAT
456427 TTTTTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 14 0.56
23 3 0.12
24 3 0.12
25 5 0.20
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
AAATATTAATAAATTAAAAAATTCA
Found at i:457365 original size:41 final size:41
Alignment explanation
Indices: 457300--457394 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
457290 GAATTTTATT
* * * *
457300 TTAATAAGAATTCTAGTCATCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCCAATCACCCAATTCTAACAATCTCCACC
457341 TTAACAAGAATTCCAATCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCCAATCACCCAATTCTAACAATCTCCACC
*
457382 TTGACAAGAATTC
1 TTAACAAGAATTC
457395 TCTACGAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.28
Consensus pattern (41 bp):
TTAACAAGAATTCCAATCACCCAATTCTAACAATCTCCACC
Found at i:459784 original size:17 final size:18
Alignment explanation
Indices: 459746--459784 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
459736 CTTTACTTTT
* *
459746 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
459764 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
459781 ATTT
1 ATTT
459785 AGTCACCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:461277 original size:21 final size:21
Alignment explanation
Indices: 461251--461293 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
461241 TGGTACAAAG
461251 TCCAAGCAGTGTGGATATGAT
1 TCCAAGCAGTGTGGATATGAT
461272 TCCAAGCAGTGTGGATATGAT
1 TCCAAGCAGTGTGGATATGAT
461293 T
1 T
461294 GAATCCACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (21 bp):
TCCAAGCAGTGTGGATATGAT
Found at i:463191 original size:18 final size:18
Alignment explanation
Indices: 463168--463208 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
463158 AGGAATAGCG
463168 ATACTGGCTCGCTTGAGC
1 ATACTGGCTCGCTTGAGC
*
463186 ATACTGGCTCGTTTGAGC
1 ATACTGGCTCGCTTGAGC
463204 ATACT
1 ATACT
463209 AGCTTATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (18 bp):
ATACTGGCTCGCTTGAGC
Found at i:463232 original size:19 final size:19
Alignment explanation
Indices: 463200--463297 Score: 85
Period size: 19 Copynumber: 5.2 Consensus size: 19
463190 TGGCTCGTTT
*
463200 GAGC-ATACTAGCTTATAA
1 GAGCGATACTGGCTTATAA
*
463218 GAGCGATACTGGCTTGTAA
1 GAGCGATACTGGCTTATAA
* **
463237 GAGCAATA-TCGGCTCGTAA
1 GAGCGATACT-GGCTTATAA
*
463256 GGGCGATACTGGCTCT-TAA
1 GAGCGATACTGGCT-TATAA
* *
463275 GAGCGATGCTGGCTCATAA
1 GAGCGATACTGGCTTATAA
463294 GAGC
1 GAGC
463298 AATTTACTGT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
18 5 0.08
19 59 0.91
20 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (19 bp):
GAGCGATACTGGCTTATAA
Found at i:463289 original size:38 final size:38
Alignment explanation
Indices: 463214--463297 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
463204 ATACTAGCTT
463214 ATAAGAGCGATACTGGCTTGTAAGAGCAATATCGGCTC
1 ATAAGAGCGATACTGGCTTGTAAGAGCAATATCGGCTC
* * * *
463252 GTAAGGGCGATACTGGCTCT-TAAGAGCGAT-GCTGGCTC
1 ATAAGAGCGATACTGGCT-TGTAAGAGCAATATC-GGCTC
463290 ATAAGAGC
1 ATAAGAGC
463298 AATTTACTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
37 1 0.03
38 36 0.95
39 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (38 bp):
ATAAGAGCGATACTGGCTTGTAAGAGCAATATCGGCTC
Found at i:464926 original size:20 final size:20
Alignment explanation
Indices: 464901--464956 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
464891 TTGGCCTAGG
*
464901 ACTTCTACCGATAGAACTTC
1 ACTTCTACCGATACAACTTC
* *
464921 ACTTCTACCTATACAATTTC
1 ACTTCTACCGATACAACTTC
*
464941 AGTTCTACCGATACAA
1 ACTTCTACCGATACAA
464957 GTATGCTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (20 bp):
ACTTCTACCGATACAACTTC
Found at i:465510 original size:59 final size:59
Alignment explanation
Indices: 465418--465531 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 59
465408 TTATACAAAT
* *
465418 CTAGTGGATTTGGAAAAATCTTTAGTTGTGGAAAGCTAAGGTAGTGAAGTAGGCAACCA
1 CTAGTGGATTTGGAAAAACCTTTAGTTGTGGAAAACTAAGGTAGTGAAGTAGGCAACCA
465477 CTAGTGGATTTGGAAAAACCTTTAGTTGTGGAAAACTAAGGTAGTGAAGTAGGCA
1 CTAGTGGATTTGGAAAAACCTTTAGTTGTGGAAAACTAAGGTAGTGAAGTAGGCA
465532 TTTGGGATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (59 bp):
CTAGTGGATTTGGAAAAACCTTTAGTTGTGGAAAACTAAGGTAGTGAAGTAGGCAACCA
Found at i:472227 original size:23 final size:23
Alignment explanation
Indices: 472201--472274 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
472191 GAATGAATTA
472201 GATTAATGATTATTCAATATTTT
1 GATTAATGATTATTCAATATTTT
* * **
472224 GATT-ATG-TGAATCAAAATATAAT
1 GATTAATGATTATTC--AATATTTT
472247 G-TTAAATGATTATTCAATATTTT
1 GATT-AATGATTATTCAATATTTT
472270 GATTA
1 GATTA
472275 TGCAAATCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 19 0.51
24 5 0.14
25 4 0.11
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (23 bp):
GATTAATGATTATTCAATATTTT
Found at i:472258 original size:46 final size:46
Alignment explanation
Indices: 472205--472297 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
472195 GAATTAGATT
**
472205 AATGATTATTCAATATTTTGATTATGTGAATCAAAATATAATGTTA
1 AATGATTATTCAATATTTTGATTATGCAAATCAAAATATAATGTTA
472251 AATGATTATTCAATATTTTGATTATGCAAATCAAAATATAATGTTA
1 AATGATTATTCAATATTTTGATTATGCAAATCAAAATATAATGTTA
472297 A
1 A
472298 GTAAATGGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (46 bp):
AATGATTATTCAATATTTTGATTATGCAAATCAAAATATAATGTTA
Found at i:475734 original size:49 final size:50
Alignment explanation
Indices: 475662--475760 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 50
475652 TTTGTATATA
*
475662 ACTACACTTCTTCTATTCAACATTGATTAGAATAAGGTTGTTT-AACCTT
1 ACTACACTTCATCTATTCAACATTGATTAGAATAAGGTTGTTTCAACCTT
** * *
475711 ACTACACTTCATCTATTTGACATTGATTAGAATAATGTTTTTTCAACCTT
1 ACTACACTTCATCTATTCAACATTGATTAGAATAAGGTTGTTTCAACCTT
475761 TAAATAGATG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 38 0.86
50 6 0.14
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (50 bp):
ACTACACTTCATCTATTCAACATTGATTAGAATAAGGTTGTTTCAACCTT
Found at i:484501 original size:11 final size:12
Alignment explanation
Indices: 484469--484501 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
484459 TGAGATGATT
*
484469 TTATTAAATAAA
1 TTATTAAAAAAA
484481 TTATTAAAAAAA
1 TTATTAAAAAAA
484493 TTA-TAAAAA
1 TTATTAAAAA
484502 TTTCATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTATTAAAAAAA
Found at i:485386 original size:2 final size:2
Alignment explanation
Indices: 485379--485413 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
485369 CAAGTAAAAC
* *
485379 AT AT AT AT CT AC 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 AT AT AT AT A
485414 CAAACTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:485394 original size:12 final size:12
Alignment explanation
Indices: 485377--485415 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
485367 CCCAAGTAAA
*
485377 ACATATATATCT
1 ACATATATATAT
485389 ACATATATATAT
1 ACATATATATAT
*
485401 ATATATATATAT
1 ACATATATATAT
485413 ACA
1 ACA
485416 AACTACATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
ACATATATATAT
Found at i:487721 original size:2 final size:2
Alignment explanation
Indices: 487714--487744 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
487704 ATCATCATAA
487714 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
487745 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:488946 original size:24 final size:24
Alignment explanation
Indices: 488906--488954 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
488896 TCCCACTCCA
488906 TCTCACCTCCTTATTTCTCC-TTT
1 TCTCACCTCCTTATTTCTCCATTT
*
488929 TCTCACCTTCCTTTTTTCTCCATTT
1 TCTCACC-TCCTTATTTCTCCATTT
488954 T
1 T
488955 TAGGAGATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.30
24 12 0.52
25 4 0.17
ACGTcount: A:0.08, C:0.37, G:0.00, T:0.55
Consensus pattern (24 bp):
TCTCACCTCCTTATTTCTCCATTT
Found at i:489057 original size:30 final size:30
Alignment explanation
Indices: 489021--489082 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
489011 TGGTTTTTGA
489021 GTAAGATTTCTTTTTATTTTCTACTTTATG
1 GTAAGATTTCTTTTTATTTTCTACTTTATG
489051 GTAAGATTTCTTTTTATTTTCTACTTTATG
1 GTAAGATTTCTTTTTATTTTCTACTTTATG
489081 GT
1 GT
489083 GACTTGATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.10, G:0.11, T:0.60
Consensus pattern (30 bp):
GTAAGATTTCTTTTTATTTTCTACTTTATG
Found at i:490274 original size:25 final size:25
Alignment explanation
Indices: 490237--490336 Score: 71
Period size: 25 Copynumber: 4.0 Consensus size: 25
490227 TCAAGTCTTC
* *
490237 TAGAATTTAGCTCA-ATGAGCCTAGA
1 TAGAATATAGCTCATACGAG-CTAGA
*
490262 TAGAATATCGCTCATACGAGCTAGA
1 TAGAATATAGCTCATACGAGCTAGA
* * * *
490287 CAGAAT-TACGCTCTTGCAAGCTAGA
1 TAGAATATA-GCTCATACGAGCTAGA
* *
490312 TAGAAT-TACGCTCTTATGAGCTAGA
1 TAGAATATA-GCTCATACGAGCTAGA
490337 CAAAATTATG
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
24 1 0.02
25 56 0.92
26 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (25 bp):
TAGAATATAGCTCATACGAGCTAGA
Found at i:490343 original size:25 final size:25
Alignment explanation
Indices: 490270--490392 Score: 140
Period size: 25 Copynumber: 5.0 Consensus size: 25
490260 GATAGAATAT
* * *
490270 CGCTCATACGAGCTAGACAGAATTA
1 CGCTCTTATGAGCTAGACAAAATTA
*** * *
490295 CGCTCTTGCAAGCTAGATAGAATTA
1 CGCTCTTATGAGCTAGACAAAATTA
490320 CGCTCTTATGAGCTAGACAAAATTA
1 CGCTCTTATGAGCTAGACAAAATTA
* *
490345 TGCTCTTATGAGCCAGAC-AAATTA
1 CGCTCTTATGAGCTAGACAAAATTA
*
490369 CGCTCTTATGAGCTAGACATAATT
1 CGCTCTTATGAGCTAGACAAAATT
490393 TCACTTTTAC
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 22 0.27
25 61 0.73
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (25 bp):
CGCTCTTATGAGCTAGACAAAATTA
Found at i:490384 original size:49 final size:50
Alignment explanation
Indices: 490270--490426 Score: 154
Period size: 50 Copynumber: 3.2 Consensus size: 50
490260 GATAGAATAT
* * * * * *
490270 CGCTCATACGAGCTAGACAGAATTACGCTCTTGCAAGCTAGATAGAATTA
1 CGCTCTTATGAGCTAGACAAAATTACGCTCTTACAAGCCAGACAGAATTA
* **
490320 CGCTCTTATGAGCTAGACAAAATTATGCTCTTATGAGCCAGACA-AATTA
1 CGCTCTTATGAGCTAGACAAAATTACGCTCTTACAAGCCAGACAGAATTA
* * * * * * *
490369 CGCTCTTATGAGCTAGACATAATTTCACTTTTACGAGCCAAACAGAATTT
1 CGCTCTTATGAGCTAGACAAAATTACGCTCTTACAAGCCAGACAGAATTA
*
490419 TGCTCTTA
1 CGCTCTTA
490427 CGAGTCATAT
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
49 42 0.48
50 46 0.52
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (50 bp):
CGCTCTTATGAGCTAGACAAAATTACGCTCTTACAAGCCAGACAGAATTA
Found at i:490427 original size:25 final size:25
Alignment explanation
Indices: 490321--490460 Score: 111
Period size: 25 Copynumber: 5.6 Consensus size: 25
490311 ATAGAATTAC
* * *
490321 GCTCTTATGAGCTAGACAAAATTAT
1 GCTCTTATGAGCCAGACAGAATTTT
**
490346 GCTCTTATGAGCCAGACA-AATTAC
1 GCTCTTATGAGCCAGACAGAATTTT
* * *
490370 GCTCTTATGAGCTAGACATAATTTC
1 GCTCTTATGAGCCAGACAGAATTTT
* * * *
490395 ACTTTTACGAGCCAAACAGAATTTT
1 GCTCTTATGAGCCAGACAGAATTTT
* * * *
490420 GCTCTTACGAGTCATATAGAATTTT
1 GCTCTTATGAGCCAGACAGAATTTT
* *
490445 GCTTTTATGAGTCAGA
1 GCTCTTATGAGCCAGA
490461 TTCAGAATAT
Statistics
Matches: 95, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
24 22 0.23
25 73 0.77
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (25 bp):
GCTCTTATGAGCCAGACAGAATTTT
Found at i:503951 original size:16 final size:16
Alignment explanation
Indices: 503911--503948 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
503901 ACTTATAAAA
503911 AAAAAAG-AAAGTGAT
1 AAAAAAGAAAAGTGAT
503926 AAAGAAAGAAAAGTTGAT
1 AAA-AAAGAAAAG-TGAT
503944 AAAAA
1 AAAAA
503949 GAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.15
16 4 0.20
17 6 0.30
18 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.13
Consensus pattern (16 bp):
AAAAAAGAAAAGTGAT
Done.