Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006506.1 Kokia drynarioides strain JFW-HI SEQ_121090, 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: 59936
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:8060 original size:16 final size:17
Alignment explanation
Indices: 8022--8061 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
8012 CGAATAAGAG
8022 TTGTTCTATGGTAATAC
1 TTGTTCTATGGTAATAC
8039 TT-TTCT-TGGTAA-AGC
1 TTGTTCTATGGTAATA-C
8054 TTGTTCTA
1 TTGTTCTA
8062 AATAATGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.05
15 9 0.45
16 8 0.40
17 2 0.10
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.50
Consensus pattern (17 bp):
TTGTTCTATGGTAATAC
Found at i:10144 original size:40 final size:40
Alignment explanation
Indices: 10110--10340 Score: 156
Period size: 40 Copynumber: 5.8 Consensus size: 40
10100 ATAACACTGG
* * *
10110 CTCATAGTCTGTTAGGCCGTAGCCCGAATCATAACACCAA
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACCAA
* * * * * * * *
10150 CTCATAACCTGCTAAGCTGTAGCTTGATTCACATCACCGA
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACCAA
* * *
10190 CTCATAGCCTGCTAGGCCGTAGCTCGAGTCATAACACTAG
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACCAA
** * ** * * *
10230 CTCATAGCCTGCTAACCCGTAGCTTGGTTCACATCACCGA
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACCAA
* * * * * * * *
10270 CTCATAGCTTGCTAAGTCGTAGCTTGAATCACATCATCGA
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACCAA
* * * *
10310 CTCATAGCCTGTTAAGCTGTAGCTTGAATCA
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCA
10341 CATTACCGGC
Statistics
Matches: 150, Mismatches: 41, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 150 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (40 bp):
CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACCAA
Found at i:10243 original size:80 final size:80
Alignment explanation
Indices: 10110--10412 Score: 290
Period size: 80 Copynumber: 3.8 Consensus size: 80
10100 ATAACACTGG
* * * * * *
10110 CTCATAGTCTGTTAGGCCGTAGCCCGAATCATAACACCAACTCATAACCTGCTAAGCTGTAGCTT
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACTAGCTCATAGCCTGCTAAGCTGTAGCTT
10175 GATTCACATCACCGA
66 GATTCACATCACCGA
* * *
10190 CTCATAGCCTGCTAGGCCGTAGCTCGAGTCATAACACTAGCTCATAGCCTGCTAACCCGTAGCTT
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACTAGCTCATAGCCTGCTAAGCTGTAGCTT
*
10255 GGTTCACATCACCGA
66 GATTCACATCACCGA
* * * * * * * *
10270 CTCATAGCTTGCTAAGTCGTAGCTTGAATCACATCA-TCGACTCATAGCCTGTTAAGCTGTAGCT
1 CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACTAG-CTCATAGCCTGCTAAGCTGTAGCT
* * *
10334 TGAATCACATTACCGG
65 TGATTCACATCACCGA
* * * * * * *
10350 CTCCA-AGCTTGCTAAGTCGTAGCTTGAAATACATCAC-CT-GCTCAAAGCCTGCTAAGCCGTAG
1 CT-CATAGCCTGCTAGGCCGTAGCTCG-AAT-CATAACACTAGCTCATAGCCTGCTAAGCTGTAG
10412 C
63 C
10413 ATGAAACATA
Statistics
Matches: 187, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
79 2 0.01
80 175 0.94
81 6 0.03
82 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (80 bp):
CTCATAGCCTGCTAGGCCGTAGCTCGAATCATAACACTAGCTCATAGCCTGCTAAGCTGTAGCTT
GATTCACATCACCGA
Found at i:10341 original size:40 final size:40
Alignment explanation
Indices: 10135--10426 Score: 245
Period size: 40 Copynumber: 7.3 Consensus size: 40
10125 GCCGTAGCCC
* * * *
10135 GAATCATAACACCAACTCATAACCTGCTAAGCTGTAGCTT
1 GAATCACATCACCGACTCATAGCCTGCTAAGCTGTAGCTT
* * * *
10175 GATTCACATCACCGACTCATAGCCTGCTAGGCCGTAGCTC
1 GAATCACATCACCGACTCATAGCCTGCTAAGCTGTAGCTT
* * * * * *
10215 GAGTCATAACA-CTAGCTCATAGCCTGCTAACCCGTAGCTT
1 GAATCACATCACCGA-CTCATAGCCTGCTAAGCTGTAGCTT
** *
10255 GGTTCACATCACCGACTCATAGCTTGCTAAG-TCGTAGCTT
1 GAATCACATCACCGACTCATAGCCTGCTAAGCT-GTAGCTT
* *
10295 GAATCACATCATCGACTCATAGCCTGTTAAGCTGTAGCTT
1 GAATCACATCACCGACTCATAGCCTGCTAAGCTGTAGCTT
* * *
10335 GAATCACATTACCGGCTCCA-AGCTTGCTAAG-TCGTAGCTT
1 GAATCACATCACCGACT-CATAGCCTGCTAAGCT-GTAGCTT
* * *
10375 GAAAT-ACATCACCTG-CTCAAAGCCTGCTAAGCCGTAGCAT
1 G-AATCACATCACC-GACTCATAGCCTGCTAAGCTGTAGCTT
* *
10415 GAAACATATCAC
1 GAATCACATCAC
10427 ATTAAATTAA
Statistics
Matches: 202, Mismatches: 39, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
39 7 0.03
40 186 0.92
41 9 0.04
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (40 bp):
GAATCACATCACCGACTCATAGCCTGCTAAGCTGTAGCTT
Found at i:10384 original size:120 final size:119
Alignment explanation
Indices: 10126--10426 Score: 275
Period size: 120 Copynumber: 2.5 Consensus size: 119
10116 GTCTGTTAGG
** * * * * *
10126 CCGTAGCCCGAATCATAACACCAACTCATAACCTGCTAAGCTGTAGCTTGATTCACATCACCGAC
1 CCGTAGCTTGAATCACATCACCGACTCATAGCCTGCTAAGC-GTAGCTTGAATCACATCACCGAC
* * * *
10191 TCATAGCCTGCTAGGCCGTAGCTCGAGTCATAACACTAGCTCATAGCCTGCTAAC
65 TCATAGCCTGCTAAGCCGTAGCTCGAATCACAACACCAGCTCATAGCCTGCTAAC
** * *
10246 CCGTAGCTTGGTTCACATCACCGACTCATAGCTTGCTAAGTCGTAGCTTGAATCACATCATCGAC
1 CCGTAGCTTGAATCACATCACCGACTCATAGCCTGCTAAG-CGTAGCTTGAATCACATCACCGAC
* * * ** * * *
10311 TCATAGCCTGTTAAGCTGTAGCTTGAATCACATTACCGGCTCCA-AGCTTGCTAAG
65 TCATAGCCTGCTAAGCCGTAGCTCGAATCACAACACCAGCT-CATAGCCTGCTAAC
* * * * *
10366 TCGTAGCTTGAAAT-ACATCACCTG-CTCAAAGCCTGCTAAGCCGTAGCATGAAACATATCAC
1 CCGTAGCTTG-AATCACATCACC-GACTCATAGCCTGCTAAG-CGTAGCTTGAATCACATCAC
10427 ATTAAATTAA
Statistics
Matches: 144, Mismatches: 33, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
120 139 0.97
121 5 0.03
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (119 bp):
CCGTAGCTTGAATCACATCACCGACTCATAGCCTGCTAAGCGTAGCTTGAATCACATCACCGACT
CATAGCCTGCTAAGCCGTAGCTCGAATCACAACACCAGCTCATAGCCTGCTAAC
Found at i:18398 original size:29 final size:26
Alignment explanation
Indices: 18344--18399 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 26
18334 TAACACAATA
*
18344 AAATAAAATAACATAATCATGGTAAT
1 AAATAAAATAACATAATCATAGTAAT
18370 AAATAAAATAACAATATAATCATAGTAAT
1 AAATAAAATAAC---ATAATCATAGTAAT
18399 A
1 A
18400 GATGACAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.46
29 14 0.54
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (26 bp):
AAATAAAATAACATAATCATAGTAAT
Found at i:19583 original size:45 final size:45
Alignment explanation
Indices: 19521--20016 Score: 539
Period size: 45 Copynumber: 11.0 Consensus size: 45
19511 AGATTAGATT
* * *
19521 TGGTGACTTCAATCTGCCCCTTTAGATTAAGGGTAAAAGATTGGA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
* * *
19566 TGATTGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGATTGGA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
* * * *
19611 TGGTGGCATCAATCTGCCCCTTTGGATTAGAGGTAAAAGATTGGA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
* * * *
19656 TGGTTGCTTCAATTTGTCCCTCTAGATTAGGGGTAAAAGACTGGA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
* * * *
19701 TGGTGGCTTCAATTTGTCCCTCTAGATTAGGGGTAAAAGACTAGA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
* * * * **
19746 TGGTGGCTTTAATTTTCCCCTCTAGATTAGGGGTAAAAGACTATA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
* * * *
19791 TGGTGACTTCAATCTGCCCCTTTGGATTAAGGGTAAAAGATTGGA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
* * * * ** *
19836 TGGTTGC-TCAATTTG-CCCTTCTGGATTAGAGACAAAAGACTAGA
1 TGGTGGCTTCAATCTGCCCCTT-TAGATTAGGGGTAAAAGACTGGA
* * * *
19880 TGGTGGCTTCAATCTACCCCTCTAAATTAGGGGTAAAAGATTGGA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
* * * *
19925 TGGTGGCTTAAATCTG-CCTTTCTAGATTAGGGGTAAAATACTAGA
1 TGGTGGCTTCAATCTGCCCCTT-TAGATTAGGGGTAAAAGACTGGA
* * *
19970 TGGTGGTTTCAATCTACCCCTCTAGATTAGGGGTAAAAGACTGGA
1 TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
20015 TG
1 TG
20017 TGATGACTTC
Statistics
Matches: 378, Mismatches: 68, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
43 5 0.01
44 33 0.09
45 333 0.88
46 7 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (45 bp):
TGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGACTGGA
Found at i:20123 original size:49 final size:49
Alignment explanation
Indices: 20031--20349 Score: 172
Period size: 49 Copynumber: 6.6 Consensus size: 49
20021 GACTTCGTTT
* * * * *** * *
20031 AATCTTTCTCTCTCTGTTTTTAGGGTGTAAGATTTTCCATTACAAATTC
1 AATCTTTCCCTCTTTGATTTTAGGGTGTTAGATCCACCGTTACGAATTC
* * *
20080 AATCTTTCCCTCTTTGATTTTAGGGTGTTAGATCTACCGTTAC-AGTTTT
1 AATCTTTCCCTCTTTGATTTTAGGGTGTTAGATCCACCGTTACGA-ATTC
* * * * *
20129 AATCTATCCCTCTTTGGTTTTAGGATGTTAGGTCCACCGTTACGGCA-TC
1 AATCTTTCCCTCTTTGATTTTAGGGTGTTAGATCCACCGTTAC-GAATTC
* * * ** * * ** ** *
20178 AACCTATCCCTATTCAATTTTAAGGTGTAAGATCCATTGTTGTGACTTC
1 AATCTTTCCCTCTTTGATTTTAGGGTGTTAGATCCACCGTTACGAATTC
* ** * * **
20227 GATCTTTCCCTCTTAAATTTTAAGGTGTTAGGTCTGCCG--AC---TTC
1 AATCTTTCCCTCTTTGATTTTAGGGTGTTAGATCCACCGTTACGAATTC
* * * *
20271 AA-CTTATCCCTCTTT-AGTTTAAGGTGTAAGATCCACCGTTACGACTTC
1 AATCTT-TCCCTCTTTGATTTTAGGGTGTTAGATCCACCGTTACGAATTC
20319 AATCTTTCCCTCTTT-AGTTTTAGGGTGTTAG
1 AATCTTTCCCTCTTTGA-TTTTAGGGTGTTAG
20350 TTCCGCCATT
Statistics
Matches: 203, Mismatches: 55, Indels: 24
0.72 0.20 0.09
Matches are distributed among these distances:
43 21 0.10
44 12 0.06
45 2 0.01
48 17 0.08
49 151 0.74
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (49 bp):
AATCTTTCCCTCTTTGATTTTAGGGTGTTAGATCCACCGTTACGAATTC
Found at i:23007 original size:16 final size:15
Alignment explanation
Indices: 22988--23041 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
22978 ATTCTCCTTA
22988 TTTTTTTTCCTCTTTC
1 TTTTTTTTCCT-TTTC
*
23004 TTTTTTCTCTCTTTTTC
1 TTTTTT-T-TCCTTTTC
*
23021 TTTTTCTTTTCTTTTC
1 TTTTT-TTTCCTTTTC
23037 TTTTT
1 TTTTT
23042 GCTAGTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 17 0.53
17 11 0.34
18 4 0.12
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCCTTTTC
Found at i:23008 original size:17 final size:16
Alignment explanation
Indices: 22988--23041 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
22978 ATTCTCCTTA
22988 TTTTTTTTCCTCTTTCT
1 TTTTTTTTCCT-TTTCT
* *
23005 TTTTTCTCTCTTTTTCT
1 TTTTT-TTTCCTTTTCT
23022 TTTTCTTTT-CTTTTCT
1 TTTT-TTTTCCTTTTCT
23038 TTTT
1 TTTT
23042 GCTAGTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 10 0.32
17 16 0.52
18 5 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCCTTTTCT
Found at i:23093 original size:47 final size:48
Alignment explanation
Indices: 23031--23126 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 48
23021 TTTTTCTTTT
23031 CTTTTCTTTTTGCTAGTTTGAG-CTGCCATTTCAAGTTTTCAACTCAAA
1 CTTTTCTTTTTGCTAGTTTGAGTC-GCCATTTCAAGTTTTCAACTCAAA
* *
23079 CTTTT-TTTTTGCTAGTTTGAGTCGCCCTTTCAGGTTTTCAACTCAAA
1 CTTTTCTTTTTGCTAGTTTGAGTCGCCATTTCAAGTTTTCAACTCAAA
23126 C
1 C
23127 CCTCTGTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 39 0.87
48 6 0.13
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.46
Consensus pattern (48 bp):
CTTTTCTTTTTGCTAGTTTGAGTCGCCATTTCAAGTTTTCAACTCAAA
Found at i:30781 original size:24 final size:24
Alignment explanation
Indices: 30706--30782 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
30696 CTCTATCTGG
30706 GCTAACCATTCTAGGCTTGTAAGA
1 GCTAACCATTCTAGGCTTGTAAGA
*
30730 GATAACCATTCTAGGCTTGTAAGA
1 GCTAACCATTCTAGGCTTGTAAGA
* *
30754 GCTAATCATTCTGGGCTTGTATAG-
1 GCTAACCATTCTAGGCTTGTA-AGA
30778 GCTAA
1 GCTAA
30783 ATGTTGTCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 46 0.96
25 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (24 bp):
GCTAACCATTCTAGGCTTGTAAGA
Found at i:34702 original size:24 final size:24
Alignment explanation
Indices: 34632--34690 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
34622 ATTTTGGGCT
* *
34632 CATTCTAGGCTCGCAAGAGCTAAC
1 CATTCTGGGCTCGTAAGAGCTAAC
*
34656 CATTCTGGGCTCGTAAGAGCTAAT
1 CATTCTGGGCTCGTAAGAGCTAAC
34680 CATTCTGGGCT
1 CATTCTGGGCT
34691 TGTGTGGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (24 bp):
CATTCTGGGCTCGTAAGAGCTAAC
Found at i:37503 original size:29 final size:31
Alignment explanation
Indices: 37444--37504 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
37434 ATTAATAACA
*
37444 AAATAAAATAAAATAACATAATCATGGTAAT
1 AAATAAAATAAAATAACATAATCATAGTAAT
*
37475 AAATAAAAT-AAA-AATATAATCATAGTAAT
1 AAATAAAATAAAATAACATAATCATAGTAAT
37504 A
1 A
37505 GATGGCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.57
30 3 0.11
31 9 0.32
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (31 bp):
AAATAAAATAAAATAACATAATCATAGTAAT
Found at i:40578 original size:14 final size:14
Alignment explanation
Indices: 40559--40590 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
40549 TTGACCAATC
*
40559 TGACCCATTGACTT
1 TGACCCATTAACTT
40573 TGACCCATTAACTT
1 TGACCCATTAACTT
40587 TGAC
1 TGAC
40591 TGTTGACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.34
Consensus pattern (14 bp):
TGACCCATTAACTT
Found at i:46172 original size:2 final size:2
Alignment explanation
Indices: 46118--46154 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
46108 AATAAGCCAA
46118 AT AT AT AT AT AT AT AT CA- 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 AT A
46155 AGCCAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:46191 original size:43 final size:42
Alignment explanation
Indices: 46094--46198 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 42
46084 AAAAAAAATA
46094 ATAATA-AT-AATA-ATA-ATAAGCCAAATATATATATATAT
1 ATAATATATAAATATATATATAAGCCAAATATATATATATAT
*
46132 ATCAATATATATATATATATATAAGCCAAATATATATATAT-T
1 AT-AATATATAAATATATATATAAGCCAAATATATATATATAT
* *
46174 AGTATATGTATAAATATAGATATAA
1 A-TA-ATATATAAATATATATATAA
46199 AAGTTGTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
38 2 0.04
39 4 0.07
40 2 0.04
41 3 0.05
42 6 0.11
43 39 0.70
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (42 bp):
ATAATATATAAATATATATATAAGCCAAATATATATATATAT
Found at i:47491 original size:21 final size:21
Alignment explanation
Indices: 47465--47510 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
47455 TTTATTCTAC
*
47465 CGGTAGAAGTCATGGT-TGTAT
1 CGGTAGAAGTCA-GGTAGGTAT
47486 CGGTAGAAGTCAGGTAGGTAT
1 CGGTAGAAGTCAGGTAGGTAT
47507 CGGT
1 CGGT
47511 CGTTTGTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.24, C:0.11, G:0.37, T:0.28
Consensus pattern (21 bp):
CGGTAGAAGTCAGGTAGGTAT
Found at i:48458 original size:40 final size:41
Alignment explanation
Indices: 48396--48611 Score: 156
Period size: 40 Copynumber: 5.4 Consensus size: 41
48386 ATAACACTGG
* *
48396 CTCATAGCCCGCT-AGGCTATAGCCCGAATCATAACACC-A
1 CTCATAGCCTGCTAAGGCTATAGCCCGAATCAGAACACCGA
* * * * *
48435 GTTCATAGCCTGCTAAGTC-ATAGCTCGACTCAGATCACCGA
1 -CTCATAGCCTGCTAAGGCTATAGCCCGAATCAGAACACCGA
** * *
48476 CTCATAGCCTGCTAA-GCTATAGCTTGAATCACATCACCGA
1 CTCATAGCCTGCTAAGGCTATAGCCCGAATCAGAACACCGA
* * ** * * *
48516 CTCATTGCCTGCTAA-GCTGTAGCTTGAATCACATCACCGG
1 CTCATAGCCTGCTAAGGCTATAGCCCGAATCAGAACACCGA
* ** * * *
48556 CTCATAGCCTGCTAA-GCTGTAGCTTGAATCACATCACCAA
1 CTCATAGCCTGCTAAGGCTATAGCCCGAATCAGAACACCGA
*
48596 CTCAAAGCCTGCTAAG
1 CTCATAGCCTGCTAAG
48612 CCGTAGCTTG
Statistics
Matches: 153, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.01
40 148 0.97
41 4 0.03
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (41 bp):
CTCATAGCCTGCTAAGGCTATAGCCCGAATCAGAACACCGA
Found at i:48529 original size:80 final size:79
Alignment explanation
Indices: 48394--48712 Score: 325
Period size: 80 Copynumber: 4.0 Consensus size: 79
48384 CAATAACACT
* * ** * * * * *
48394 GGCTCATAGCCCGCTAGGCTATAGCCCGAATCATAACACC-AGTTCATAGCCTGCTAAGTCATAG
1 GGCTCATAGCCTGCTAAGCTATAGCTTGAATCACATCACCGA-CTCAAAGCCTGCTAAG-CGTAG
* * *
48458 CTCGACTCAGATCACC
64 CTTGAATCACATCACC
* **
48474 GACTCATAGCCTGCTAAGCTATAGCTTGAATCACATCACCGACTCATTGCCTGCTAAGCTGTAGC
1 GGCTCATAGCCTGCTAAGCTATAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGC-GTAGC
48539 TTGAATCACATCACC
65 TTGAATCACATCACC
* *
48554 GGCTCATAGCCTGCTAAGCTGTAGCTTGAATCACATCACCAACTCAAAGCCTGCTAAGCCGTAGC
1 GGCTCATAGCCTGCTAAGCTATAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAG-CGTAGC
* *
48619 TTGAAACACATCACT
65 TTGAATCACATCACC
* * ** * * * *
48634 GGCTCAAAGCCTGCTAACCCGTAGCTTGAAACACATCACTGGCTCAAAGCCTGCTAACCCGTAGC
1 GGCTCATAGCCTGCTAAGCTATAGCTTGAATCACATCACCGACTCAAAGCCTGCTAA-GCGTAGC
* *
48699 TTGAAACATATCAC
65 TTGAATCACATCAC
48713 ATTAAATTAA
Statistics
Matches: 206, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.00
80 203 0.99
81 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (79 bp):
GGCTCATAGCCTGCTAAGCTATAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGCGTAGCT
TGAATCACATCACC
Found at i:48612 original size:40 final size:40
Alignment explanation
Indices: 48441--48712 Score: 312
Period size: 40 Copynumber: 6.8 Consensus size: 40
48431 ACCAGTTCAT
* * * * *
48441 AGCCTGCTAAG-TCATAGCTCGACTCAGATCACCGACTCAT
1 AGCCTGCTAAGCT-GTAGCTTGAATCACATCACCGACTCAA
* *
48481 AGCCTGCTAAGCTATAGCTTGAATCACATCACCGACTCAT
1 AGCCTGCTAAGCTGTAGCTTGAATCACATCACCGACTCAA
* * *
48521 TGCCTGCTAAGCTGTAGCTTGAATCACATCACCGGCTCAT
1 AGCCTGCTAAGCTGTAGCTTGAATCACATCACCGACTCAA
*
48561 AGCCTGCTAAGCTGTAGCTTGAATCACATCACCAACTCAA
1 AGCCTGCTAAGCTGTAGCTTGAATCACATCACCGACTCAA
* * * *
48601 AGCCTGCTAAGCCGTAGCTTGAAACACATCACTGGCTCAA
1 AGCCTGCTAAGCTGTAGCTTGAATCACATCACCGACTCAA
* * * * *
48641 AGCCTGCTAACCCGTAGCTTGAAACACATCACTGGCTCAA
1 AGCCTGCTAAGCTGTAGCTTGAATCACATCACCGACTCAA
* * * *
48681 AGCCTGCTAACCCGTAGCTTGAAACATATCAC
1 AGCCTGCTAAGCTGTAGCTTGAATCACATCAC
48713 ATTAAATTAA
Statistics
Matches: 214, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 213 1.00
41 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (40 bp):
AGCCTGCTAAGCTGTAGCTTGAATCACATCACCGACTCAA
Found at i:50655 original size:18 final size:18
Alignment explanation
Indices: 50632--50672 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
50622 TAAAAATCCC
*
50632 AATTTGGGTAATTCGGGT
1 AATTTGGGTAATTCGGAT
*
50650 AATTTGGTTAATTCGGAT
1 AATTTGGGTAATTCGGAT
50668 AATTT
1 AATTT
50673 TTATACTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (18 bp):
AATTTGGGTAATTCGGAT
Done.