Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014948.1 Kokia drynarioides strain JFW-HI SEQ_129991, 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: 76755
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 215 characters in sequence are not A, C, G, or T
Found at i:852 original size:41 final size:41
Alignment explanation
Indices: 790--868 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
780 GCTTATTGTA
*
790 TTTTCAATTTGTTTGTTGTTTTACGAATTGTTTTAATATCG
1 TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATATCG
* * *
831 TTTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATA
1 TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATA
869 ATTTTTAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.20, C:0.04, G:0.13, T:0.63
Consensus pattern (41 bp):
TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATATCG
Found at i:4201 original size:2 final size:2
Alignment explanation
Indices: 4194--4218 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4184 TCATTATTGC
4194 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4219 TTTATGCTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17607 original size:29 final size:29
Alignment explanation
Indices: 17575--17660 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 29
17565 TAGAGTAGAT
17575 AAATGGATCTAGAAGCAGCTTGAGTGTTA
1 AAATGGATCTAGAAGCAGCTTGAGTGTTA
* * ** * *
17604 AAAT---TTTGGAA--AAATAGAGTAGAT-
1 AAATGGATCTAGAAGCAGCTTGAGT-GTTA
17628 AAATGGATCTAGAAGCAGCTTGAGTGTTA
1 AAATGGATCTAGAAGCAGCTTGAGTGTTA
17657 AAAT
1 AAAT
17661 TTTGGAAAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 14
0.59 0.19 0.22
Matches are distributed among these distances:
24 10 0.26
25 2 0.05
26 5 0.13
27 5 0.13
28 2 0.05
29 14 0.37
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (29 bp):
AAATGGATCTAGAAGCAGCTTGAGTGTTA
Found at i:17641 original size:53 final size:53
Alignment explanation
Indices: 17561--17675 Score: 230
Period size: 53 Copynumber: 2.2 Consensus size: 53
17551 ACATGCAAGC
17561 AAAATAGAGTAGATAAATGGATCTAGAAGCAGCTTGAGTGTTAAAATTTTGGA
1 AAAATAGAGTAGATAAATGGATCTAGAAGCAGCTTGAGTGTTAAAATTTTGGA
17614 AAAATAGAGTAGATAAATGGATCTAGAAGCAGCTTGAGTGTTAAAATTTTGGA
1 AAAATAGAGTAGATAAATGGATCTAGAAGCAGCTTGAGTGTTAAAATTTTGGA
17667 AAAATAGAG
1 AAAATAGAG
17676 ATGAGAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.27
Consensus pattern (53 bp):
AAAATAGAGTAGATAAATGGATCTAGAAGCAGCTTGAGTGTTAAAATTTTGGA
Found at i:22146 original size:3 final size:3
Alignment explanation
Indices: 22140--22190 Score: 66
Period size: 3 Copynumber: 16.0 Consensus size: 3
22130 TTTTTTTATT
*
22140 AAG AAG AAG AAG AAG AAG AAG AAG AAG AATA AAG AAAG AAAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG -AAG -AAG AAG AAG
22188 AAG
1 AAG
22191 TGAACTGACC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 35 0.80
4 9 0.20
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:23094 original size:60 final size:60
Alignment explanation
Indices: 23030--23155 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
23020 GAAAAAATAA
* *
23030 AAAAAAAATGATTTTTTTTA-TGTTGCCCA-TGAATTGGTCGACATCACC-TTTTTATCAT-AT
1 AAAAAAAAT--TTTTTTTTAGTGTTGCCCATTG-ATTGATCAACATCACCTTTTTTATC-TGAT
* * *
23090 AAAAAATATTTTTTTTTAGTGTTGGCCATTGCTTGATCAACATCACCTTTTTTATCTGAT
1 AAAAAAAATTTTTTTTTAGTGTTGCCCATTGATTGATCAACATCACCTTTTTTATCTGAT
23150 AAAAAA
1 AAAAAA
23156 TTCAAATTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
58 9 0.16
59 22 0.39
60 26 0.46
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (60 bp):
AAAAAAAATTTTTTTTTAGTGTTGCCCATTGATTGATCAACATCACCTTTTTTATCTGAT
Found at i:23133 original size:59 final size:58
Alignment explanation
Indices: 23032--23449 Score: 287
Period size: 59 Copynumber: 7.1 Consensus size: 58
23022 AAAAATAAAA
* * * * *
23032 AAAAAATGATTTTTTTTA-TGTTGCCCA-TGAATTGGTCGACATCACCTTTTTATCATAT
1 AAAAAAT-ATTTTTTTTAGTGTTGGCCATTG-CTTGATCGACACCACCTTTTTATCAGAT
* * *
23090 AAAAAATATTTTTTTTTAGTGTTGGCCATTGCTTGATCAACATCACCTTTTTTATCTGAT
1 AAAAAATA-TTTTTTTTAGTGTTGGCCATTGCTTGATCGACACCACC-TTTTTATCAGAT
* * * * *
23150 AAAAAATTCAAATTTTTTT-GTGTTGGTCA-TGCATTGACCGACACTAGCATTTTTTATCAGAT
1 AAAAAA-T--ATTTTTTTTAGTGTTGGCCATTGC-TTGATCGACACCA-C-CTTTTTATCAGAT
* * * * * *
23212 AAAAAATA-TTTTTTTGGTATTGGCCATTGCTTG-GCTACACCAGCATTTTTTTATCAGGT
1 AAAAAATATTTTTTTTAGTGTTGGCCATTGCTTGATCGACACCA-C--CTTTTTATCAGAT
* * * * * * * *
23271 AAAAGATA-TTTTTTTGGTGTTGGTCATTACTTAACCGATACCACTTTTTTATCTA-AT
1 AAAAAATATTTTTTTTAGTGTTGGCCATTGCTTGATCGACACCACCTTTTTATC-AGAT
* * * *
23328 AAAAAATTCAAATTTTTTTAGTGTTGG-TAATGCATTGACCGACACCACCTTTTTATCAGAT
1 AAAAAA-T--ATTTTTTTTAGTGTTGGCCATTGC-TTGATCGACACCACCTTTTTATCAGAT
* ** * *
23389 AAAAAATATTTTTTTTTGTGTTGGTAATTACTTGATCGACACCACCTTTTTATCAAAT
1 AAAAAATATTTTTTTTAGTGTTGGCCATTGCTTGATCGACACCACCTTTTTATCAGAT
23447 AAA
1 AAA
23450 TTTTTTTGTG
Statistics
Matches: 293, Mismatches: 45, Indels: 44
0.77 0.12 0.12
Matches are distributed among these distances:
57 16 0.05
58 76 0.26
59 77 0.26
60 36 0.12
61 62 0.21
62 25 0.09
63 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (58 bp):
AAAAAATATTTTTTTTAGTGTTGGCCATTGCTTGATCGACACCACCTTTTTATCAGAT
Found at i:23203 original size:61 final size:59
Alignment explanation
Indices: 23078--23449 Score: 264
Period size: 58 Copynumber: 6.3 Consensus size: 59
23068 CGACATCACC
* * * * * * * *
23078 TTTTTATCATATAAAAAATATTTTTTTTTAGTGTTGGCCATTGC-TTGATCAACATCACCT
1 TTTTTATCAGATAAAAAATA-ATTTTTTTGGTGTTGGTCA-TGCATTGACCGACACCACAT
* *
23138 TTTTTATCTGATAAAAAATTCAAATTTTTTT-GTGTTGGTCATGCATTGACCGACACTAGCAT
1 TTTTTATCAGATAAAAAA-T--AATTTTTTTGGTGTTGGTCATGCATTGACCGACACCA-CAT
* * * *
23200 TTTTTATCAGATAAAAAAT-ATTTTTTTGGTATTGGCCATTGC-TTG-GCTACACCAGCATT
1 TTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCA-TGCATTGACCGACACCA-CA-T
* * * * *
23259 TTTTTATCAGGTAAAAGAT-ATTTTTTTGGTGTTGGTCAT-TACTTAACCGATACCAC-T
1 TTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCATGCA-TTGACCGACACCACAT
* * *
23316 TTTTTATCTA-ATAAAAAATTCAAATTTTTTTAGTGTTGGTAATGCATTGACCGACACCAC-C
1 TTTTTATC-AGATAAAAAA-T--AATTTTTTTGGTGTTGGTCATGCATTGACCGACACCACAT
* * * * * *
23377 TTTTTATCAGATAAAAAATATTTTTTTTTGTGTTGGTAAT-TACTTGATCGACACCAC-C
1 TTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCATGCA-TTGACCGACACCACAT
*
23435 TTTTTATCAAATAAA
1 TTTTTATCAGATAAA
23450 TTTTTTTGTG
Statistics
Matches: 256, Mismatches: 37, Indels: 40
0.77 0.11 0.12
Matches are distributed among these distances:
57 16 0.06
58 67 0.26
59 49 0.19
60 30 0.12
61 66 0.26
62 27 0.11
63 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (59 bp):
TTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCATGCATTGACCGACACCACAT
Found at i:23319 original size:58 final size:57
Alignment explanation
Indices: 23068--23449 Score: 279
Period size: 61 Copynumber: 6.4 Consensus size: 57
23058 ATGAATTGGT
* * * * * * *
23068 CGACATCACCTTTTTATCATATAAAAAATATTTTTTTTTAGTGTTGGCCATTGCTTGAT
1 CGACACCACTTTTTTATCAGATAAAAAATA--TTTTTTTGGTGTTGGTCATTACTTGAC
* * * *
23127 CAACATCACCTTTTTTATCTGATAAAAAATTCAAATTTTTTT-GTGTTGGTCA-TGCATTGAC
1 CGACACCA-CTTTTTTATCAGATAAAAAA-T---ATTTTTTTGGTGTTGGTCATTAC-TTGAC
* * * * *
23188 CGACACTAGCATTTTTTATCAGATAAAAAATATTTTTTTGGTATTGGCCATTGCTTG-G
1 CGACACCA-C-TTTTTTATCAGATAAAAAATATTTTTTTGGTGTTGGTCATTACTTGAC
* * * *
23246 CTACACCAGCATTTTTTTATCAGGTAAAAGATATTTTTTTGGTGTTGGTCATTACTTAAC
1 CGACACCA-C--TTTTTTATCAGATAAAAAATATTTTTTTGGTGTTGGTCATTACTTGAC
* * * *
23306 CGATACCACTTTTTTATCTA-ATAAAAAATTCAAATTTTTTTAGTGTTGGT-AATGCATTGAC
1 CGACACCACTTTTTTATC-AGATAAAAAA-T---ATTTTTTTGGTGTTGGTCATTAC-TTGAC
* * * *
23367 CGACACCACCTTTTTATCAGATAAAAAATATTTTTTTTTGTGTTGGTAATTACTTGAT
1 CGACACCACTTTTTTATCAGATAAAAAATA-TTTTTTTGGTGTTGGTCATTACTTGAC
* *
23425 CGACACCACCTTTTTATCAAATAAA
1 CGACACCACTTTTTTATCAGATAAA
23450 TTTTTTTGTG
Statistics
Matches: 264, Mismatches: 39, Indels: 41
0.77 0.11 0.12
Matches are distributed among these distances:
57 16 0.06
58 61 0.23
59 62 0.23
60 34 0.13
61 65 0.25
62 25 0.09
64 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (57 bp):
CGACACCACTTTTTTATCAGATAAAAAATATTTTTTTGGTGTTGGTCATTACTTGAC
Found at i:24325 original size:59 final size:58
Alignment explanation
Indices: 24220--24624 Score: 321
Period size: 58 Copynumber: 7.0 Consensus size: 58
24210 GAAAATTTGA
* * ** *
24220 ATTTTTTATCAGATAAAAAAGGCGGTGTCTTCCAA-GCAATGGCCAACACCAAAAAAAT
1 ATTTTTTATCTGATAAAAAAGGTGGTGTCGACCAATGC-ATGACCAACACCAAAAAAAT
* *
24278 ATTTTTTATCTGATAAAAAATGCTGGTGTCGACCAATGCATGACCAACACAAAAAAAATT
1 ATTTTTTATCTGATAAAAAA-GGTGGTGTCGACCAATGCATGACCAACACCAAAAAAA-T
* * **
24338 AAAATTTTTTATCAGATAAAAAAGGTGGTGTGGACCAA-GCAATGACCAACACC-AAAATTT
1 ---ATTTTTTATCTGATAAAAAAGGTGGTGTCGACCAATGC-ATGACCAACACCAAAAAAAT
* * * *
24398 TTTTTTTATCTGAT-AAAAAGGTGGTGTCAACCAATGCATGGCCAACACTAAAAAAAT
1 ATTTTTTATCTGATAAAAAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAAT
** * * *
24455 ATTTTTTATCAAATAAAAAAGGTGATGTCGACCAATGCATGATCGACACC---AAAAT
1 ATTTTTTATCTGATAAAAAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAAT
* * * * *
24510 -TGTTTTTATTTGAT-AAAAAGGTGATGCCGGCCAA-GCATTGGCCAACACC-AAAAAAT
1 AT-TTTTTATCTGATAAAAAAGGTGGTGTCGACCAATGCA-TGACCAACACCAAAAAAAT
* * ** ** **
24566 -TTTATTTTTTTGATAAAAAAATACTGGTGTCGGTCAATGCATGACCAACATAAAAAAAA
1 ATTT-TTTATCTGAT-AAAAAA-GGTGGTGTCGACCAATGCATGACCAACACCAAAAAAA
24625 ATTGTCTGAC
Statistics
Matches: 280, Mismatches: 47, Indels: 38
0.77 0.13 0.10
Matches are distributed among these distances:
53 3 0.01
54 27 0.10
55 16 0.06
56 43 0.15
57 30 0.11
58 53 0.19
59 46 0.16
60 13 0.05
61 6 0.02
62 24 0.09
63 19 0.07
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (58 bp):
ATTTTTTATCTGATAAAAAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAAT
Found at i:24516 original size:114 final size:115
Alignment explanation
Indices: 24183--24575 Score: 382
Period size: 121 Copynumber: 3.4 Consensus size: 115
24173 GGAAAGTTGA
* * * * * * * *
24183 TGTCGACCAATACATGGCTAACGCCAAGAAAATTTGAATTTTTTATCAGATAAAAAAGGCGGTGT
1 TGTCGACCAATGCATGGCCAAC-ACAAAAAAAATT-AATTTTTTATCAAATAAAAAAGGTGATGT
** * * * *
24248 CTTCCAAGCAATGGCCAACACCAAAAAAATATTTTTTATCTGATAAAAAATGCTGG
64 CGACCAAGCAATGACCAACACC--AAAATTGTTTTTTATCTGAT-AAAAA-GGTGG
* * *
24304 TGTCGACCAATGCATGACCAACACAAAAAAAATTAAAATTTTTTATCAGATAAAAAAGGTGGTGT
1 TGTCGACCAATGCATGGCCAACACAAAAAAAATT--AATTTTTTATCAAATAAAAAAGGTGATGT
* *
24369 GGACCAAGCAATGACCAACACCAAAATTTTTTTTTTATCTGATAAAAAGGTGG
64 CGACCAAGCAATGACCAACACCAAAA-TTGTTTTTTATCTGATAAAAAGGTGG
* *
24422 TGTCAACCAATGCATGGCCAACACTAAAAAAA-T-ATTTTTTATCAAATAAAAAAGGTGATGTCG
1 TGTCGACCAATGCATGGCCAACACAAAAAAAATTAATTTTTTATCAAATAAAAAAGGTGATGTCG
* * * *
24485 ACCAATGC-ATGATCGACACCAAAATTG-TTTTTATTTGATAAAAAGGTGA
66 ACCAA-GCAATGACCAACACCAAAATTGTTTTTTATCTGATAAAAAGGTGG
* * * * *
24534 TGCCGGCCAA-GCATTGGCCAACACCAAAAAATTTTATTTTTT
1 TGTCGACCAATGCA-TGGCCAACACAAAAAAAATTAATTTTTT
24576 TGATAAAAAA
Statistics
Matches: 235, Mismatches: 31, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
111 3 0.01
112 43 0.18
113 3 0.01
114 53 0.23
115 2 0.01
117 1 0.00
118 33 0.14
119 9 0.04
120 23 0.10
121 65 0.28
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (115 bp):
TGTCGACCAATGCATGGCCAACACAAAAAAAATTAATTTTTTATCAAATAAAAAAGGTGATGTCG
ACCAAGCAATGACCAACACCAAAATTGTTTTTTATCTGATAAAAAGGTGG
Found at i:24586 original size:112 final size:113
Alignment explanation
Indices: 24220--24564 Score: 329
Period size: 114 Copynumber: 3.0 Consensus size: 113
24210 GAAAATTTGA
* * * ** * *
24220 ATTTTTTATCAGATAAAAAAGGCGGTGTCTTCCAAGCAATGGCCAACACCAAAAAAATAT-TTTT
1 ATTTTTTATCAAATAAAAAAGGTGATGTCGACCAAGCAATGACCAACACC---AAAATTTGTTTT
* * * * * *
24284 TATCTGATAAAAAATGCTGGTGTCGACCAATGCATGACCAACACAAAAAAAATT
63 TATCTGAT-AAAAA-GGTGATGCCAACCAATGCATGGCCAACACCAAAAAAA-T
* * * *
24338 AAAATTTTTTATCAGATAAAAAAGGTGGTGTGGACCAAGCAATGACCAACACCAAAATTTTTTTT
1 ---ATTTTTTATCAAATAAAAAAGGTGATGTCGACCAAGCAATGACCAACACCAAAA-TTTGTTT
* * *
24403 TTATCTGATAAAAAGGTGGTGTCAACCAATGCATGGCCAACACTAAAAAAAT
62 TTATCTGATAAAAAGGTGATGCCAACCAATGCATGGCCAACACCAAAAAAAT
* *
24455 ATTTTTTATCAAATAAAAAAGGTGATGTCGACCAATGC-ATGATCGACACCAAAA-TTGTTTTTA
1 ATTTTTTATCAAATAAAAAAGGTGATGTCGACCAA-GCAATGACCAACACCAAAATTTGTTTTTA
* **
24518 TTTGATAAAAAGGTGATGCCGGCCAA-GCATTGGCCAACACCAAAAAA
65 TCTGATAAAAAGGTGATGCCAACCAATGCA-TGGCCAACACCAAAAAA
24565 TTTTATTTTT
Statistics
Matches: 198, Mismatches: 22, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
111 3 0.02
112 45 0.23
114 46 0.23
115 2 0.01
117 1 0.01
118 37 0.19
119 7 0.04
120 12 0.06
121 45 0.23
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (113 bp):
ATTTTTTATCAAATAAAAAAGGTGATGTCGACCAAGCAATGACCAACACCAAAATTTGTTTTTAT
CTGATAAAAAGGTGATGCCAACCAATGCATGGCCAACACCAAAAAAAT
Found at i:24971 original size:6 final size:6
Alignment explanation
Indices: 24960--24984 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24950 CATTCGCCTG
24960 CCTCAC CCTCAC CCTCAC CCTCAC C
1 CCTCAC CCTCAC CCTCAC CCTCAC C
24985 ATTGAAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCTCAC
Found at i:32427 original size:22 final size:22
Alignment explanation
Indices: 32400--32443 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
32390 TTCTGAAATT
* *
32400 ATTATGGTAGAAAGATATTTGA
1 ATTATGATAAAAAGATATTTGA
32422 ATTATGATAAAAAGATATTTGA
1 ATTATGATAAAAAGATATTTGA
32444 GTCTAGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (22 bp):
ATTATGATAAAAAGATATTTGA
Found at i:32724 original size:22 final size:22
Alignment explanation
Indices: 32696--32760 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
32686 TTTCGTGCCC
32696 TCTGTTCAGCACTGTGTGTGCT
1 TCTGTTCAGCACTGTGTGTGCT
32718 TCTGTTCAGCACTGTGTGTGCT
1 TCTGTTCAGCACTGTGTGTGCT
32740 TCTGTTCAGCACTGTGTGTGC
1 TCTGTTCAGCACTGTGTGTGC
32761 CTATTGTTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.28, T:0.40
Consensus pattern (22 bp):
TCTGTTCAGCACTGTGTGTGCT
Found at i:39597 original size:20 final size:19
Alignment explanation
Indices: 39572--39623 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
39562 ATGAAAGTAA
*
39572 TAAAATATACATA-ATATAAT
1 TAAAATATAAATATA-AT-AT
39592 TAAAATATAAATATAATAT
1 TAAAATATAAATATAATAT
39611 TAAAATA-AAATAT
1 TAAAATATAAATAT
39624 TTATTTAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 6 0.20
19 9 0.30
20 14 0.47
21 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATATAAATATAATAT
Found at i:54510 original size:16 final size:16
Alignment explanation
Indices: 54452--54511 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
54442 ATTGCTTTTA
54452 AGAAA-TATTTTTGAG
1 AGAAAGTATTTTTGAG
* * *
54467 ATAAAAGTATTCTT-AA
1 A-GAAAGTATTTTTGAG
* *
54483 ATAAATTATTTTTGAG
1 AGAAAGTATTTTTGAG
54499 AGAAAGTATTTTT
1 AGAAAGTATTTTT
54512 CTCAAACCAA
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
15 10 0.30
16 17 0.52
17 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (16 bp):
AGAAAGTATTTTTGAG
Found at i:66756 original size:3 final size:3
Alignment explanation
Indices: 66748--66776 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
66738 TAAAAGAAAT
66748 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
66777 AATACAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:69573 original size:6 final size:6
Alignment explanation
Indices: 69558--69590 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
69548 CTTACTTGCT
*
69558 CAACAA CAACAC CAACAC CAACAC CAACAC CAA
1 CAACAC CAACAC CAACAC CAACAC CAACAC CAA
69591 ATGATGATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (6 bp):
CAACAC
Found at i:72236 original size:4 final size:4
Alignment explanation
Indices: 72227--72283 Score: 62
Period size: 4 Copynumber: 14.2 Consensus size: 4
72217 AAATAAACGG
* * *
72227 GAAA GAAA GAAA GAAA TAAA GAAA GAAA GAGAG GAAA GAAA G-AA GAAT
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA
*
72275 GAGA GAAA G
1 GAAA GAAA G
72284 GTAATGTGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
3 3 0.07
4 37 0.86
5 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.04
Consensus pattern (4 bp):
GAAA
Found at i:72272 original size:20 final size:20
Alignment explanation
Indices: 72227--72283 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
72217 AAATAAACGG
* *
72227 GAAAGAAAGAAAGAAATAAA
1 GAAAGAAAGAGAGAAAGAAA
72247 GAAAGAAAGAGAGGAAAGAAA
1 GAAAGAAAGAGA-GAAAGAAA
*
72268 G-AAGAATGAGAGAAAG
1 GAAAGAAAGAGAGAAAG
72284 GTAATGTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.15
20 20 0.61
21 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.04
Consensus pattern (20 bp):
GAAAGAAAGAGAGAAAGAAA
Done.