Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014375.1 Kokia drynarioides strain JFW-HI SEQ_129413, 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: 137982
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 91 characters in sequence are not A, C, G, or T
Found at i:3014 original size:18 final size:20
Alignment explanation
Indices: 2982--3020 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2972 AAATTACAAG
2982 AAAATTAAAATAATAT-TTA
1 AAAATTAAAATAATATGTTA
*
3001 AAAATTATAA-AATATGTTA
1 AAAATTAAAATAATATGTTA
3020 A
1 A
3021 GCTGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATTAAAATAATATGTTA
Found at i:7144 original size:15 final size:14
Alignment explanation
Indices: 7109--7148 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
7099 GCTTTTTTAA
*
7109 TTTTTTCTTTTACT
1 TTTTTTCTTTTCCT
*
7123 TTATTTCTTCTTCCT
1 TTTTTTCTT-TTCCT
7138 TTTTTTCTTTT
1 TTTTTTCTTTT
7149 TCCACGTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCTTTTCCT
Found at i:14109 original size:28 final size:28
Alignment explanation
Indices: 14078--14173 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 28
14068 AGGTTTAACG
*
14078 GTTTATAATTTAAGATTTAAGATTTAGA
1 GTTTATAATTTAAAATTTAAGATTTAGA
* *
14106 GTTT-TAGAATAAAAATTTAAGATTTAG-
1 GTTTATA-ATTTAAAATTTAAGATTTAGA
* * * *
14133 GGTTATAA-TTAAAATAGTAATATTTAAA
1 GTTTATAATTTAAAAT-TTAAGATTTAGA
*
14161 GTTTATGATTTAA
1 GTTTATAATTTAA
14174 GATTATTTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
26 6 0.11
27 14 0.26
28 29 0.55
29 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.44
Consensus pattern (28 bp):
GTTTATAATTTAAAATTTAAGATTTAGA
Found at i:15492 original size:24 final size:27
Alignment explanation
Indices: 15465--15513 Score: 68
Period size: 24 Copynumber: 1.9 Consensus size: 27
15455 TTAATTCAAC
15465 TTAATGAA-TTCAAA-CAA-TTTAATT
1 TTAATGAATTTCAAATCAAGTTTAATT
*
15489 TTAATTAATTTCAAATCAAGTTTAA
1 TTAATGAATTTCAAATCAAGTTTAA
15514 AATGTGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 6 0.29
26 3 0.14
27 5 0.24
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (27 bp):
TTAATGAATTTCAAATCAAGTTTAATT
Found at i:16382 original size:18 final size:19
Alignment explanation
Indices: 16342--16382 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
16332 AATATTCATG
* *
16342 TATTTTATTTTTATAATAA
1 TATTTTATTCTTATAAAAA
16361 -ATTTTATTCTTA-AAAAA
1 TATTTTATTCTTATAAAAA
16378 TATTT
1 TATTT
16383 GGATTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTATTCTTATAAAAA
Found at i:18755 original size:2 final size:2
Alignment explanation
Indices: 18748--18780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18738 TAGATATGAA
18748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18781 AATTGCGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21582 original size:218 final size:218
Alignment explanation
Indices: 21204--21645 Score: 794
Period size: 218 Copynumber: 2.0 Consensus size: 218
21194 TACTGTTGCA
*
21204 TTTCTTTTGGAGTTTTGAGGAAAAATCATTTACCAAATGTATCGACAAAACTACTCATACCACAG
1 TTTCTTTTGGAGTTTTGAGGAAAAATCATTTACCAAATATATCGACAAAACTACTCATACCACAG
21269 TGTTTTTATGTCAACTACAACTAGTTTCATGTGACCTGTTTTTAAAAGATTTGTCCTACTCATAT
66 TGTTTTTATGTCAACTACAACTAGTTTCATGTGACCTGTTTTTAAAAGATTTGTCCTACTCATAT
** *
21334 GCCATCTTTGGCTTACTGTCTATACTTTGCAGTTGGAGATTCCAAAACAGTTACTTGATCCAAAT
131 GCCATCTTTGGCTTACCATCTATACTTTGCAGTTGGAGATTCCAAAACAATTACTTGATCCAAAT
21399 TTGATCAATGCTTGGATGATGCT
196 TTGATCAATGCTTGGATGATGCT
* * *
21422 TTTCTTTTGGAGTTTTGAGGAAAAATCATTTACCAAATATATTGACAAAATTACTCATACTACAG
1 TTTCTTTTGGAGTTTTGAGGAAAAATCATTTACCAAATATATCGACAAAACTACTCATACCACAG
* *
21487 TGTTTTTATGTCAACTGCAACTAGTTTCATGTGACCTGTTTTTATAAGATTTGTCCTACTCATAT
66 TGTTTTTATGTCAACTACAACTAGTTTCATGTGACCTGTTTTTAAAAGATTTGTCCTACTCATAT
21552 GCCATCTTTGGCTTACCATCTATACTTTGCAGTTGGAGATTCCAAAACAATTACTTGATCCAAAT
131 GCCATCTTTGGCTTACCATCTATACTTTGCAGTTGGAGATTCCAAAACAATTACTTGATCCAAAT
*
21617 TTGTTCAATGCTTGGATGATGCT
196 TTGATCAATGCTTGGATGATGCT
21640 TTTCTT
1 TTTCTT
21646 AAATGTTTTG
Statistics
Matches: 214, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 214 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (218 bp):
TTTCTTTTGGAGTTTTGAGGAAAAATCATTTACCAAATATATCGACAAAACTACTCATACCACAG
TGTTTTTATGTCAACTACAACTAGTTTCATGTGACCTGTTTTTAAAAGATTTGTCCTACTCATAT
GCCATCTTTGGCTTACCATCTATACTTTGCAGTTGGAGATTCCAAAACAATTACTTGATCCAAAT
TTGATCAATGCTTGGATGATGCT
Found at i:25339 original size:28 final size:28
Alignment explanation
Indices: 25298--25370 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
25288 TGACTTGACT
25298 TTTCCTTTCATGCTTTTTTTTGGCCAAA
1 TTTCCTTTCATGCTTTTTTTTGGCCAAA
*
25326 TTTCCTTTCGTGCTTTTTTTTGGCCAAA
1 TTTCCTTTCATGCTTTTTTTTGGCCAAA
*
25354 TTTCTTTTCATGCTTTT
1 TTTCCTTTCATGCTTTT
25371 AATCAGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.11, C:0.21, G:0.11, T:0.58
Consensus pattern (28 bp):
TTTCCTTTCATGCTTTTTTTTGGCCAAA
Found at i:42874 original size:23 final size:23
Alignment explanation
Indices: 42825--42876 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
42815 TAACTAACCA
* ** * *
42825 AATTAATTAAAATATTTCTATTT
1 AATTAATTAAAAAAAATCGATTC
42848 AATTAATTAAAAAAAATCGATTC
1 AATTAATTAAAAAAAATCGATTC
42871 AATTAA
1 AATTAA
42877 CGTTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
AATTAATTAAAAAAAATCGATTC
Found at i:49510 original size:21 final size:21
Alignment explanation
Indices: 49484--49525 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49474 ATTTCTAAGT
*
49484 AATTAATATTA-ATTATTTAAA
1 AATTAA-ATTAGATTATATAAA
49505 AATTAAATTAGATTATATAAA
1 AATTAAATTAGATTATATAAA
49526 TTATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AATTAAATTAGATTATATAAA
Found at i:51736 original size:15 final size:16
Alignment explanation
Indices: 51706--51740 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
51696 AAGTTTTATA
*
51706 TAATTTATATATTTTT
1 TAATTTATAAATTTTT
51722 TAATTTA-AAATTTTT
1 TAATTTATAAATTTTT
51737 TAAT
1 TAAT
51741 GGATGCAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTATAAATTTTT
Found at i:54232 original size:24 final size:23
Alignment explanation
Indices: 54179--54226 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
54169 AAATTAAAAA
* * *
54179 AAAAAAAAAAAAAAACTAAATTT
1 AAAAAATACAAAAAACTAAAATT
*
54202 AAAAAATACAAAAAATTAAAATT
1 AAAAAATACAAAAAACTAAAATT
54225 AA
1 AA
54227 CCAAATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (23 bp):
AAAAAATACAAAAAACTAAAATT
Found at i:56600 original size:10 final size:10
Alignment explanation
Indices: 56575--56615 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
56565 CATTTTAAAC
*
56575 ATATTTTTTT
1 ATATTTTTAT
56585 AGTATTTTTAT
1 A-TATTTTTAT
56596 ATATTTTTA-
1 ATATTTTTAT
56605 AT-TTTTTAT
1 ATATTTTTAT
56614 AT
1 AT
56616 TATTATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.21
9 4 0.14
10 9 0.32
11 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:56619 original size:19 final size:20
Alignment explanation
Indices: 56575--56619 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
56565 CATTTTAAAC
*
56575 ATATT-TTTTTAGTATTTTT
1 ATATTATTTTTAATATTTTT
56594 ATA-TATTTTTAAT-TTTTT
1 ATATTATTTTTAATATTTTT
56612 ATATTATT
1 ATATTATT
56620 ATTGTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
ATATTATTTTTAATATTTTT
Found at i:60532 original size:17 final size:18
Alignment explanation
Indices: 60510--60543 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60500 ATAATTGTAA
60510 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
60527 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
60544 CATAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:60803 original size:30 final size:31
Alignment explanation
Indices: 60769--60832 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
60759 ATGATGAAAT
*
60769 AAATATTAA-AATTTATTTAAGTATAAATTA
1 AAATATTAATAATTTATTTAAATATAAATTA
*
60799 AAATATTAATAATTTATTTAAATGTAAATTA
1 AAATATTAATAATTTATTTAAATATAAATTA
60830 AAA
1 AAA
60833 GGTACGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (31 bp):
AAATATTAATAATTTATTTAAATATAAATTA
Found at i:66463 original size:30 final size:29
Alignment explanation
Indices: 66422--66478 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
66412 AGTATTAAGT
66422 TAAAATTATAAAAATCAAGATTAAATTGA
1 TAAAATTATAAAAATCAAGATTAAATTGA
* * *
66451 TAAAATATATAAATATCGATATTAAATT
1 TAAAAT-TATAAAAATCAAGATTAAATT
66479 TATTATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (29 bp):
TAAAATTATAAAAATCAAGATTAAATTGA
Found at i:72085 original size:13 final size:13
Alignment explanation
Indices: 72051--72088 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
72041 TAAAATAAAA
72051 ATATATCTTTTATT
1 ATATAT-TTTTATT
72065 AT-TATTTTTATT
1 ATATATTTTTATT
72077 ATATATTTTTAT
1 ATATATTTTTAT
72089 CAAATAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 12 0.52
14 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATATTTTTATT
Found at i:74317 original size:13 final size:13
Alignment explanation
Indices: 74299--74323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74289 TTTTTTTAAT
74299 TTTAGGGAAATTA
1 TTTAGGGAAATTA
74312 TTTAGGGAAATT
1 TTTAGGGAAATT
74324 TTAAATTAAA
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (13 bp):
TTTAGGGAAATTA
Found at i:81506 original size:12 final size:11
Alignment explanation
Indices: 81483--81541 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
81473 CAATAATAAT
*
81483 AAAATAATAAC
1 AAAATAACAAC
81494 AAATATAACAAC
1 AAA-ATAACAAC
**
81506 AAAATAACAGT
1 AAAATAACAAC
*
81517 AAAATAACATC
1 AAAATAACAAC
*
81528 AAAATAACAGC
1 AAAATAACAAC
81539 AAA
1 AAA
81542 CAACAGTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 31 0.76
12 10 0.24
ACGTcount: A:0.68, C:0.14, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAATAACAAC
Found at i:82870 original size:20 final size:21
Alignment explanation
Indices: 82837--82882 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
82827 TAATTAGGTT
* *
82837 TAAAAATAATAAATCAAAGTG
1 TAAAAATAAAAAATCAAAGAG
82858 TAAAAA-AAAAAATCAAAGAG
1 TAAAAATAAAAAATCAAAGAG
82878 TAAAA
1 TAAAA
82883 GCTTCATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (21 bp):
TAAAAATAAAAAATCAAAGAG
Found at i:87044 original size:32 final size:32
Alignment explanation
Indices: 87003--87226 Score: 362
Period size: 32 Copynumber: 7.1 Consensus size: 32
86993 ACTCCGCCAC
* *
87003 CACATCTTTATCGAAACGGCTTCAAGTTAAAA
1 CACATCTTTATCGAAACGGTTTCAATTTAAAA
*
87035 CACATCTTTATCGAAACAGTTTCAATTTAAAA
1 CACATCTTTATCGAAACGGTTTCAATTTAAAA
87067 CACATCTTTATCGAAACGGTTTCAATTTAAAA
1 CACATCTTTATCGAAACGGTTTCAATTTAAAA
* *
87099 CACATCTTTATCGAAACGGCTTCAAGTTAAAA
1 CACATCTTTATCGAAACGGTTTCAATTTAAAA
*
87131 CACATCTTTATTGAAACGGTTTCAATTT-AAA
1 CACATCTTTATCGAAACGGTTTCAATTTAAAA
*
87162 CACATTTTTATCGAAACGGTTTCAATTT-AAA
1 CACATCTTTATCGAAACGGTTTCAATTTAAAA
*
87193 CACATTTTTATCGAAACGGTTTCAATTTAAAA
1 CACATCTTTATCGAAACGGTTTCAATTTAAAA
87225 CA
1 CA
87227 TAGTCTTATA
Statistics
Matches: 180, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
31 60 0.33
32 120 0.67
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (32 bp):
CACATCTTTATCGAAACGGTTTCAATTTAAAA
Found at i:87273 original size:58 final size:58
Alignment explanation
Indices: 87193--87449 Score: 399
Period size: 58 Copynumber: 4.4 Consensus size: 58
87183 TCAATTTAAA
* *
87193 CACATTTTTATCGAAACGGTTTCAATTTAAAACATAGTCTTATAGTGATCTCCGCCAC
1 CACATCTTTATCGAAACGGTTTCAATTTAAAACATAGTCTCATAGTGATCTCCGCCAC
* * * *
87251 CACATCTTTATTGAAACAGTTTCAATTTAAAAAATTA-TCTCATAGTGATCTCCGCTAC
1 CACATCTTTATCGAAACGGTTTCAATTTAAAACA-TAGTCTCATAGTGATCTCCGCCAC
* *
87309 CACATCTTTATCAAAATGGTTTCAATTTAAAACATAGTCTCATAGTGATCTCCGCCAC
1 CACATCTTTATCGAAACGGTTTCAATTTAAAACATAGTCTCATAGTGATCTCCGCCAC
* *
87367 CACATCTTTATCGAAAAGGTTTCAATTTAAAACATAGTCTCATAGTGATCTCCACCAC
1 CACATCTTTATCGAAACGGTTTCAATTTAAAACATAGTCTCATAGTGATCTCCGCCAC
*
87425 CACATCTTTATCGAAATGGTTTCAA
1 CACATCTTTATCGAAACGGTTTCAA
87450 CCAGATGACA
Statistics
Matches: 181, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
57 2 0.01
58 177 0.98
59 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.34
Consensus pattern (58 bp):
CACATCTTTATCGAAACGGTTTCAATTTAAAACATAGTCTCATAGTGATCTCCGCCAC
Found at i:88718 original size:35 final size:35
Alignment explanation
Indices: 88679--88748 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
88669 ACAACCCACT
88679 AAGGAAAATAGGAAATGGGAAAGAAAGGAGAAGAG
1 AAGGAAAATAGGAAATGGGAAAGAAAGGAGAAGAG
88714 AAGGAAAATAGGAAATGGGAAAGAAAGGAGAAGAG
1 AAGGAAAATAGGAAATGGGAAAGAAAGGAGAAGAG
88749 GAATCGGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.06
Consensus pattern (35 bp):
AAGGAAAATAGGAAATGGGAAAGAAAGGAGAAGAG
Found at i:88739 original size:19 final size:19
Alignment explanation
Indices: 88682--88739 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
88672 ACCCACTAAG
88682 GAAAATAGGAAATGGGAAA
1 GAAAATAGGAAATGGGAAA
* *
88701 G--AA-AGGAGAA-GAGAAG
1 GAAAATAGGA-AATGGGAAA
88717 GAAAATAGGAAATGGGAAA
1 GAAAATAGGAAATGGGAAA
88736 GAAA
1 GAAA
88740 GGAGAAGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 9 0.30
17 4 0.13
18 4 0.13
19 13 0.43
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (19 bp):
GAAAATAGGAAATGGGAAA
Found at i:94873 original size:17 final size:17
Alignment explanation
Indices: 94853--94897 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
94843 AATAATTTCC
*
94853 TTTTGAAAAAATA-AAA
1 TTTTTAAAAAATAGAAA
*
94869 TTTTTTAAAAAATAGATA
1 -TTTTTAAAAAATAGAAA
94887 TTTTTAAAAAA
1 TTTTTAAAAAA
94898 AGGACACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
TTTTTAAAAAATAGAAA
Found at i:94898 original size:18 final size:17
Alignment explanation
Indices: 94853--94898 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
94843 AATAATTTCC
*
94853 TTTTGAAAAAATAAAAT
1 TTTTAAAAAAATAAAAT
* *
94870 TTTTTAAAAAATAGATAT
1 TTTTAAAAAAATA-AAAT
94888 TTTTAAAAAAA
1 TTTTAAAAAAA
94899 GGACACTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAAATAAAAT
Found at i:98316 original size:32 final size:32
Alignment explanation
Indices: 98280--98346 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
98270 CTTAAGAATT
*
98280 TGAGGTATTTTAGTTGTTTAAGAATGCCACTG
1 TGAGGTATTTTAGTCGTTTAAGAATGCCACTG
98312 TGAGGTATTTTAGTCGTTTAAGAATGCCACTG
1 TGAGGTATTTTAGTCGTTTAAGAATGCCACTG
98344 TGA
1 TGA
98347 CTTCCTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (32 bp):
TGAGGTATTTTAGTCGTTTAAGAATGCCACTG
Found at i:101177 original size:91 final size:91
Alignment explanation
Indices: 101022--101235 Score: 376
Period size: 91 Copynumber: 2.4 Consensus size: 91
101012 TCGTAAATCA
*
101022 AAACCCTAAACCCGATCAATATTTTAAGCAACCCCATCAATGGAAAGTACTAGTTATCATAGTTC
1 AAACCCTAAACCCAATCAATATTTTAAGCAACCCCATCAATGGAAAGTACTAGTTATCATAGTTC
*
101087 TACAAACCCTAGATCTATTAGAGCAT
66 TACAAACCCTAGAACTATTAGAGCAT
101113 AAACCCTAAACCCAATCAATATTTTAAGCAACCCCATCAATGGAAAGTACTAGTTATCATAGTTC
1 AAACCCTAAACCCAATCAATATTTTAAGCAACCCCATCAATGGAAAGTACTAGTTATCATAGTTC
* *
101178 TACAATCCCTAGAACTATTAGGGCAT
66 TACAAACCCTAGAACTATTAGAGCAT
101204 AAACCCTAAACCCAA-CAAATATTTTAAGCAAC
1 AAACCCTAAACCCAATC-AATATTTTAAGCAAC
101236 ATCACTCATA
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
90 1 0.01
91 117 0.99
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (91 bp):
AAACCCTAAACCCAATCAATATTTTAAGCAACCCCATCAATGGAAAGTACTAGTTATCATAGTTC
TACAAACCCTAGAACTATTAGAGCAT
Found at i:102824 original size:21 final size:23
Alignment explanation
Indices: 102789--102832 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
102779 TATTTTTAAA
102789 AATATTTATATTAATTTTAATTT
1 AATATTTATATTAATTTTAATTT
*
102812 AATATTTA-A-TAATTTTCATTT
1 AATATTTATATTAATTTTAATTT
102833 TATTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 1 0.05
23 8 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AATATTTATATTAATTTTAATTT
Found at i:107771 original size:236 final size:233
Alignment explanation
Indices: 107297--108005 Score: 686
Period size: 236 Copynumber: 3.0 Consensus size: 233
107287 TATGGAATAG
* * * * * *
107297 AACAATCTACACACACATAAATAAGGAAC-CCATTCCAATTTT-CAGTACCAAATATCTGAG-TT
1 AACAAACTACACGCATATAAATAAGGAACACCATTTCAATTTTCCA-TATCAAATATCCGAGTTT
** * * *
107359 TATAGTGCCAACAAAAGGTTGAAGGAGAGAATCCGTTTCTTGCAGGC-TTTC-GCTAACAAGTGC
65 TATAGTG-CAA-AAAAACTTGAAGGAGAGAATCAGTTTTTTGCAGTCATTTCTG--AACAAGTGC
* * * * *
107422 AACAAACTGGATGGGCATTTCCCAA-CTACTTAATGAAGAACTTCAGCATATGCCTTAAATGCAT
126 AACAAACTGGATGGACAATT--CAAGCTACTTAATTAAGAACTTCAGCAGATGCCTTAAGT-C-T
* * *
107486 GATACCCCATCTTATGCGTTACTTAAGCAATAAATA-TTCTTTACAGC
187 GATACCCCTTCTTATGTGTTACTTAAGCAATAAA-AGTTCTTTGCAGC
* * *
107533 AACAAACTACATGCATATAAATAAGGAACACCGTTTCAATTTTCCATATAAAATATCCGAGTTTT
1 AACAAACTACACGCATATAAATAAGGAACACCATTTCAATTTTCCATATCAAATATCCGAGTTTT
* * * *
107598 ATAGTGCAAAAAAACTTGAAGGAAAGAATTAGTTTTTTGCAGTCACTTCTGAACAAATGCAACAA
66 ATAGTGCAAAAAAACTTGAAGGAGAGAATCAGTTTTTTGCAGTCATTTCTGAACAAGTGCAACAA
* **
107663 ACTGGATGGACAATTGCAAGATACTTAATTAA-AACCTTCAGCAGACACCTTAACGTCTGATACC
131 ACTGGATGGACAATT-CAAGCTACTTAATTAAGAA-CTTCAGCAGATGCCTTAA-GTCTGATACC
* *
107727 TCTTCTTTTGTGTTACTTAAGCAATAAAACGTTCTTTGCAGC
193 CCTTCTTATGTGTTACTTAAGCAATAAAA-GTTCTTTGCAGC
* * * * *
107769 AACAAACTAGACGCATATAAACAAGGAATCA-AATTTCAA-TTTCCACATCAAATACCCGAGTTT
1 AACAAACTACACGCATATAAATAAGGAA-CACCATTTCAATTTTCCATATCAAATATCCGAGTTT
** **** * ** *
107832 TATAAAGGTCGAAGAC-TGAAGGAGAGAATCAGTCATTTGCAATCATTTCCT-AACAAGTGCAAC
65 TATAGTGCAAAAAAACTTGAAGGAGAGAATCAGTTTTTTGCAGTCATTT-CTGAACAAGTGCAAC
* * * * *
107895 AAACTGGATGGACAAATCCAGCTACTTAATTAAGAAATTCAGCAGATGTCTTAATGTGTGATACC
129 AAACTGGATGGACAATTCAAGCTACTTAATTAAGAACTTCAGCAGATGCCTTAA-GTCTGATACC
* * * *
107960 CCTTCTAATGTGTTACTTAAGCATTACATGTTCTTTGCAGC
193 CCTTCTTATGTGTTACTTAAGCAATAAAAGTTCTTTGCAGC
108001 AACAA
1 AACAA
108006 GCTCTAGAAT
Statistics
Matches: 391, Mismatches: 69, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
232 17 0.04
233 60 0.15
234 56 0.14
235 68 0.17
236 146 0.37
237 32 0.08
238 12 0.03
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (233 bp):
AACAAACTACACGCATATAAATAAGGAACACCATTTCAATTTTCCATATCAAATATCCGAGTTTT
ATAGTGCAAAAAAACTTGAAGGAGAGAATCAGTTTTTTGCAGTCATTTCTGAACAAGTGCAACAA
ACTGGATGGACAATTCAAGCTACTTAATTAAGAACTTCAGCAGATGCCTTAAGTCTGATACCCCT
TCTTATGTGTTACTTAAGCAATAAAAGTTCTTTGCAGC
Found at i:112794 original size:2 final size:2
Alignment explanation
Indices: 112781--112812 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
112771 AATCTATTAC
*
112781 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112813 GAGAGAGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:130664 original size:31 final size:30
Alignment explanation
Indices: 130608--130667 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
130598 TAAAATTGTA
*
130608 ATTTTTAAGGGATTAAATTAAAATTTTATC
1 ATTTTTAAGGGATTAAAGTAAAATTTTATC
**
130638 ATTTTTAAGGGAGTTAAAGTGTAATTTTAT
1 ATTTTTAAGGGA-TTAAAGTAAAATTTTAT
130668 TTTTATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (30 bp):
ATTTTTAAGGGATTAAAGTAAAATTTTATC
Found at i:135724 original size:24 final size:24
Alignment explanation
Indices: 135691--135737 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
135681 TTAATTATAA
*
135691 ATTTTTAAATATGAATATAAAAAC
1 ATTTTCAAATATGAATATAAAAAC
* *
135715 ATTTTCAAATTTTAATATAAAAA
1 ATTTTCAAATATGAATATAAAAA
135738 AGAGATTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTTTCAAATATGAATATAAAAAC
Found at i:135940 original size:26 final size:25
Alignment explanation
Indices: 135887--135950 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
135877 TGAAGAGGTT
* * * *
135887 TTATTTTCAATATAACTTTTACTCA
1 TTATTTTAAATTTAAATTTTACTAA
135912 TTATTTTAAATTTAAATTTATACTAA
1 TTATTTTAAATTTAAATTT-TACTAA
*
135938 TTATTTTTAATTT
1 TTATTTTAAATTT
135951 TATGTCTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (25 bp):
TTATTTTAAATTTAAATTTTACTAA
Done.