Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014003.1 Kokia drynarioides strain JFW-HI SEQ_129034, 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: 80950
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 91 characters in sequence are not A, C, G, or T
Found at i:5628 original size:23 final size:23
Alignment explanation
Indices: 5602--5655 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5592 TAGCGTAAAT
* * *
5602 CAGTAGGCACACAATGTTCGAAA
1 CAGTAAGCACACAAAGTGCGAAA
*
5625 CAGTAAGCATACAAAGTGCGAAA
1 CAGTAAGCACACAAAGTGCGAAA
5648 CAGTAAGC
1 CAGTAAGC
5656 GCGCTAGCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTGCGAAA
Found at i:8398 original size:40 final size:39
Alignment explanation
Indices: 8320--8398 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
8310 AGTGAAGTTA
* * * * *
8320 CATCGTCAACCAATTTTTTACCCCGAGCTTAGGGCAGAT
1 CATCGTCAACAAATCTCTTACCCCGAGCTAAGGACAGAT
*
8359 CATCGTCAACTAAATCTCTTACCCCTAGCTAAGGACAGAT
1 CATCGTCAAC-AAATCTCTTACCCCGAGCTAAGGACAGAT
8399 TAAAACCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 10 0.30
40 23 0.70
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (39 bp):
CATCGTCAACAAATCTCTTACCCCGAGCTAAGGACAGAT
Found at i:9119 original size:209 final size:209
Alignment explanation
Indices: 8501--9357 Score: 1119
Period size: 210 Copynumber: 4.1 Consensus size: 209
8491 AACAGTGAGG
*
8501 CGATCATCTTCCTGATGAGATACGGAGAAGTAGACCAAATCAATG--A-AA----CAAAGCGAGC
1 CGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGACACAAGGCTCAAAGCGAGC
* *
8559 AAATCTTCGAACCCCGGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
66 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAG
** *
8624 CTTATTGATGAGATACTGAGAAGTGGACTAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGAT
131 CTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGAT
8689 TGAAACAAGCGATA
196 TGAAACAAGCGATA
* * * * * *
8703 CGGTCATCTTCCTAATGAGATATTGAGAAGTAAACCAAATCAATGAAACAAGGCTCAAATCGAGC
1 CGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGACACAAGGCTCAAAGCGAGC
* * *
8768 AAAATCTTTGAACCCCAGCTTCCTGATTAGATACTGAGAAG-AAGGTTGAAGCAATAAAATGGTT
66 -AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAA-GTCGAAGCAATAAAATGGTT
* * *
8832 AGCTTCCTGATGACATACTGAGAAGTGGACCAAATCCATCTTCTTGATGAGATACAGAGAAGCGG
129 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGG
8897 ATTGAAACAAGCGATA
194 ATTGAAACAAGCGATA
*
8913 CGATCATCTTCCTGATGAGATACTGAAAAGTAGACCAAATCAATGACACAAGGCTCAAAGCGAGC
1 CGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGACACAAGGCTCAAAGCGAGC
*
8978 AAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAG
66 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAG
* * * * * *
9043 CTTCCTGATGAGATACTAAGAAATGGACCGAATTCGTCTTCCTGATAAGATACAGAGAAGCGAAT
131 CTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGAT
*
9108 TGAAACAAGCGATG
196 TGAAACAAGCGATA
* * * * * * *
9122 C-AGTCATCTTCCTGATGAGATACTTAGAAGAAGACCAAATCAA--ACTC-ACGCTCGATGTGAG
1 CGA-TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGACACAAGGCTCAAAGCGAG
*
9183 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
65 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTA
* * * * * * * * *
9248 ACTTCATGATGAGATAC-GAAAAAGTGAATCAAATCCGTCTTCTTGATGAAACACAGAGAAGTGG
130 GCTTCCTGATGAGATACTG-AGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGG
** * *
9312 ATCAAAACAAGTGATG
194 ATTGAAACAAGCGATA
* * * *
9328 TGGTCAACTTCCTGATGAGATACTAAGAAG
1 CGATCATCTTCCTGATGAGATACTGAGAAG
9358 AAGGTCAAGT
Statistics
Matches: 572, Mismatches: 70, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
202 40 0.07
204 1 0.00
205 2 0.00
206 159 0.28
207 3 0.01
208 1 0.00
209 175 0.31
210 191 0.33
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (209 bp):
CGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGACACAAGGCTCAAAGCGAGC
AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAG
CTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAAGCGATA
Found at i:9704 original size:6 final size:6
Alignment explanation
Indices: 9693--9788 Score: 76
Period size: 6 Copynumber: 16.7 Consensus size: 6
9683 AGCCCAACAG
* * * *
9693 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGTTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * * *
9738 ACTTAA AATTTA AATTT- -ATTATA AATTTA AGTTTA AATTTA ATTTTA
1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA
9785 AATT
1 AATT
9789 AATGTCCAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
4 3 0.04
5 12 0.17
6 51 0.74
7 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:9738 original size:34 final size:34
Alignment explanation
Indices: 9693--9772 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
9683 AGCCCAACAG
* *
9693 AATTTAAATTTATTTTAAAA-TTAAATTTATTTTA
1 AATTTAAATTTA-CTTAAAATTTAAATTTATTATA
*
9727 AGTTTAAATTTACTTAAAATTTAAATTTATTATA
1 AATTTAAATTTACTTAAAATTTAAATTTATTATA
*
9761 AATTTAAGTTTA
1 AATTTAAATTTA
9773 AATTTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 6 0.15
34 34 0.85
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
AATTTAAATTTACTTAAAATTTAAATTTATTATA
Found at i:9781 original size:17 final size:17
Alignment explanation
Indices: 9693--9788 Score: 95
Period size: 17 Copynumber: 5.6 Consensus size: 17
9683 AGCCCAACAG
*
9693 AATTTAAATTTATTTTA
1 AATTTAAATTTAATTTA
* *
9710 AAATTAAATTTATTTTA
1 AATTTAAATTTAATTTA
* * *
9727 AGTTTAAATTTACTTAA
1 AATTTAAATTTAATTTA
9744 AATTTAAATTT-ATTATA
1 AATTTAAATTTAATT-TA
*
9761 AATTTAAGTTTAAATTTA
1 AATTTAAATTT-AATTTA
*
9779 ATTTTAAATT
1 AATTTAAATT
9789 AATGTCCAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
16 2 0.03
17 50 0.77
18 10 0.15
19 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTAATTTA
Found at i:10425 original size:3 final size:3
Alignment explanation
Indices: 10417--10462 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
10407 CCATTACCAT
* * *
10417 TTA TTA TTA TCA CTA TTA TCA TTA TTA TTA TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10463 TAAGGTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:11725 original size:30 final size:28
Alignment explanation
Indices: 11689--11991 Score: 178
Period size: 30 Copynumber: 10.2 Consensus size: 28
11679 CCTTGAAGGT
11689 CCCTAAACTGTCTATAAATTATATTTTTAC
1 CCCTAAACT-TCTA-AAATTATATTTTTAC
11719 CCCTAAACTTCTCTAAAATTATATATTTTA-
1 CCCTAAAC-T-TCTAAAATTATAT-TTTTAC
* *
11749 CCCTAAACTTTTTAAAATTACATTTTTAC
1 CCCTAAAC-TTCTAAAATTATATTTTTAC
* *
11778 CCTTAAAACTTCCCAAAATTATATTTTTAC
1 CCCT-AAACTT-CTAAAATTATATTTTTAC
* * ** *
11808 CCTTAAACTTCCAAAAATTCCATTTTAAC
1 CCCTAAACTT-CTAAAATTATATTTTTAC
* * * *
11837 CCCGAGACTTCCCAAAATTACATTTTTAC
1 CCCTAAACTT-CTAAAATTATATTTTTAC
* * **
11866 CCCCAAACTTCCAAAAATTCCATTTTTAAC
1 CCCTAAACTT-CTAAAATTATATTTTT-AC
* * *
11896 CCCGAAACTTTTAAAAATTACATTTTTTA-
1 CCCTAAACTTCT-AAAATTATA-TTTTTAC
* * **
11925 CCCTCGAACTTCCAAAAATTCCATTTTTGAC
1 CCCT-AAACTT-CTAAAATTATATTTTT-AC
* * * *
11956 CCCAAAACTTTTAAAAATTACAATTTTAC
1 CCCTAAACTTCT-AAAATTATATTTTTAC
11985 CCCTAAA
1 CCCTAAA
11992 TGTCCAAAAA
Statistics
Matches: 223, Mismatches: 37, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.02
29 99 0.44
30 101 0.45
31 18 0.08
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (28 bp):
CCCTAAACTTCTAAAATTATATTTTTAC
Found at i:11784 original size:29 final size:29
Alignment explanation
Indices: 11689--12012 Score: 285
Period size: 29 Copynumber: 11.0 Consensus size: 29
11679 CCTTGAAGGT
* * *
11689 CCCTAAACTGTCTATAAATTATATTTTTAC
1 CCCTAAACT-TCCAAAAATTACATTTTTAC
* *
11719 CCCTAAACTTCTCTAAAATTATATATTTTA-
1 CCCTAAACTTC-CAAAAATTACAT-TTTTAC
***
11749 CCCTAAACTTTTTAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * *
11778 CCTTAAAACTTCCCAAAATTATATTTTTAC
1 CCCT-AAACTTCCAAAAATTACATTTTTAC
* * *
11808 CCTTAAACTTCCAAAAATTCCATTTTAAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * *
11837 CCCGAGACTTCCCAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* *
11866 CCCCAAACTTCCAAAAATTCCATTTTTAAC
1 CCCTAAACTTCCAAAAATTACATTTTT-AC
* **
11896 CCCGAAACTTTTAAAAATTACATTTTTTA-
1 CCCTAAACTTCCAAAAATTACA-TTTTTAC
* *
11925 CCCTCGAACTTCCAAAAATTCCATTTTTGAC
1 CCCT-AAACTTCCAAAAATTACATTTTT-AC
* ** *
11956 CCCAAAACTTTTAAAAATTACAATTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
*
11985 CCCTAAA-TGTCCAAAAATTCCATTTTTA
1 CCCTAAACT-TCCAAAAATTACATTTTTA
12013 TCTCGATTTT
Statistics
Matches: 239, Mismatches: 45, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
28 6 0.03
29 113 0.47
30 107 0.45
31 13 0.05
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:11796 original size:59 final size:56
Alignment explanation
Indices: 11689--11957 Score: 196
Period size: 59 Copynumber: 4.6 Consensus size: 56
11679 CCTTGAAGGT
* * *
11689 CCCTAAACTGTCTATAAATTATATTTTTACCCCTAAACTTCTCTAAAATTATATATTTTA
1 CCCTAAACTTTCTA-AAATTACATTTTTA-CCCTAAACTTC-CCAAAATTATAT-TTTTA
*
11749 CCCTAAACTTTTTAAAATTACATTTTTACCCTTAAAACTTCCCAAAATTATATTTTTA
1 CCCTAAACTTTCTAAAATTACATTTTTACCC-T-AAACTTCCCAAAATTATATTTTTA
* * * * * * *
11807 CCCTTAAACTTCCAAAAATTCCATTTTAACCCCGAGACTTCCCAAAATTACATTTTTA
1 CCC-TAAACTTTCTAAAATTACATTTTTA-CCCTAAACTTCCCAAAATTATATTTTTA
* * * * * *** *
11865 CCCCCAAACTTCCAAAAATTCCATTTTTAACCCCGAAACTTTTAAAAATTACATTTTTTA
1 -CCCTAAACTTTCTAAAATTACATTTTT-A-CCCTAAACTTCCCAAAATTATA-TTTTTA
* * * *
11925 CCCTCGAACTTCCAAAAATTCCATTTTTGACCC
1 CCCT-AAACTTTCTAAAATTACATTTTT-ACCC
11958 CAAAACTTTT
Statistics
Matches: 180, Mismatches: 21, Indels: 17
0.83 0.10 0.08
Matches are distributed among these distances:
58 55 0.31
59 74 0.41
60 51 0.28
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.38
Consensus pattern (56 bp):
CCCTAAACTTTCTAAAATTACATTTTTACCCTAAACTTCCCAAAATTATATTTTTA
Found at i:22235 original size:114 final size:114
Alignment explanation
Indices: 22034--22270 Score: 429
Period size: 114 Copynumber: 2.1 Consensus size: 114
22024 AAGTATACTT
* * *
22034 GTATCGGTAGAATCCTTTGCCCAAAGTGACCGTTGGAGTCGTTGTACTGGTAGATCCAACCTTGT
1 GTATCGGTAGAATCCTTTGCCCAAAGTGACCGTTGGAATCGTTGTACCGATAGATCCAACCTTGT
*
22099 ATCGGTATAACTCTGAGGGTTTCATTTGGTATCGGTAGAACCCATCAGA
66 ATCGGTATAACTCTGAGAGTTTCATTTGGTATCGGTAGAACCCATCAGA
*
22148 GTATCGGTAGAATCCTTTTCCCAAAGTGACCGTTGGAATCGTTGTACCGATAGATCCAACCTTGT
1 GTATCGGTAGAATCCTTTGCCCAAAGTGACCGTTGGAATCGTTGTACCGATAGATCCAACCTTGT
22213 ATCGGTATAACTCTGAGAGTTTCATTTGGTATCGGTAGAACCCATCAGA
66 ATCGGTATAACTCTGAGAGTTTCATTTGGTATCGGTAGAACCCATCAGA
22262 GTATCGGTA
1 GTATCGGTA
22271 AAAGTGCAGG
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 118 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (114 bp):
GTATCGGTAGAATCCTTTGCCCAAAGTGACCGTTGGAATCGTTGTACCGATAGATCCAACCTTGT
ATCGGTATAACTCTGAGAGTTTCATTTGGTATCGGTAGAACCCATCAGA
Found at i:22802 original size:21 final size:20
Alignment explanation
Indices: 22756--22803 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
22746 CATATTTAAT
**
22756 TAATTAGAATATTTACCTTA
1 TAATTAGAATATTTAAATTA
*
22776 TCAATTAGAATTTTTAAATTCA
1 T-AATTAGAATATTTAAATT-A
22798 TAATTA
1 TAATTA
22804 TTTACTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
TAATTAGAATATTTAAATTA
Found at i:31507 original size:247 final size:247
Alignment explanation
Indices: 31162--32035 Score: 1553
Period size: 247 Copynumber: 3.6 Consensus size: 247
31152 TAGGGTTCTT
* *
31162 CTTTTCTTAAAAGCCCA-TTCATTTT-AAATATTAATTTTTT-TTCTTATTTATATGAACCATAT
1 CTTTT-TTAAAAG-TCAGTTCATTTTAAAATGTTAATTTTTTATTCTTATTTATATGAACCATAT
*
31224 TATAAATTATAAAAAATTTAAAAATTAAATATTTATGTTATTTTATATTTATTTTCTATTAATAT
64 TATAAATTATAAAAAATTTAAAAATTAAACATTTATGTTATTTTATATTTATTTTCTATTAATAT
* *
31289 TTTTCAAACGTTTCAAATTTCGTAATAAAATTTTTAGGGTTCCCCCAATTATATAAACAAATTGA
129 TTTTCAAACGTTTCAAATTTCGTAACAAAATTTTTAGGGTTCCCCCAATTATATAAACACATTGA
*
31354 AAAAAGGTTTAATTTCTATTCCAAAATTAAACTTTCTCTTTATTCTAAGCGTTG
194 AAAAAGGTTTAATTTCTATTCCAAAATTGAACTTTCTCTTTATTCTAAGCGTTG
*
31408 TTTTTTTAAAAGTCAGTTCATTTTAAAATGTTAATTTTTTATTCTTATTTATATGAACCATATTA
1 CTTTTTTAAAAGTCAGTTCATTTTAAAATGTTAATTTTTTATTCTTATTTATATGAACCATATTA
31473 TAAATTATAAAAAATTTAAAAATTAAACATTTATGTTATTTTATATTTATTTTCTATTAATATTT
66 TAAATTATAAAAAATTTAAAAATTAAACATTTATGTTATTTTATATTTATTTTCTATTAATATTT
* *
31538 TTCAAACGTTTCAAATTTCGTAACAAAATTTTTAGGGTTTCTCCAATTATATAAACACATTGAAA
131 TTCAAACGTTTCAAATTTCGTAACAAAATTTTTAGGGTTCCCCCAATTATATAAACACATTGAAA
* *
31603 AAAGATTTAATTTCTATTCCAAAATTGAACTTTCTTTTTATTCTAAGCGTTG
196 AAAGGTTTAATTTCTATTCCAAAATTGAACTTTCTCTTTATTCTAAGCGTTG
31655 CTTTTTTAAAAGTCAGTTCATTTTAAAATGTTAATTTTTTATTCTTATTTATATGAACCATATTA
1 CTTTTTTAAAAGTCAGTTCATTTTAAAATGTTAATTTTTTATTCTTATTTATATGAACCATATTA
31720 TAAATTATAAAAAATTTAAAAATTAAACATTTATGTTATTTTATATTTATTTTCTATTAATATTT
66 TAAATTATAAAAAATTTAAAAATTAAACATTTATGTTATTTTATATTTATTTTCTATTAATATTT
31785 TTCAAACGTTTCAAATTTCGTAACAAAATTTTTAGGGTTCCCCCAATTATATAAACACATTGAAA
131 TTCAAACGTTTCAAATTTCGTAACAAAATTTTTAGGGTTCCCCCAATTATATAAACACATTGAAA
31850 AAAGGTTTAATTTCTATTCCAAAATTGAACTTTCTCTTTATTCTAAGCGTTG
196 AAAGGTTTAATTTCTATTCCAAAATTGAACTTTCTCTTTATTCTAAGCGTTG
* **
31902 CTTTTTTAAAAGTCAGTTCATTTTAAAATGTTAATTTTTTATTCTTATTTATAGGAGTCATATTA
1 CTTTTTTAAAAGTCAGTTCATTTTAAAATGTTAATTTTTTATTCTTATTTATATGAACCATATTA
*
31967 TAAATTAT--AAAATTTAGAAATTAAACATTTATGTTA-TTTATATTTATTTTCTATTAATATTT
66 TAAATTATAAAAAATTTAAAAATTAAACATTTATGTTATTTTATATTTATTTTCTATTAATATTT
32029 TTCAAAC
131 TTCAAAC
32036 ATAAAAAATT
Statistics
Matches: 605, Mismatches: 20, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
244 35 0.06
245 42 0.07
246 18 0.03
247 510 0.84
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.47
Consensus pattern (247 bp):
CTTTTTTAAAAGTCAGTTCATTTTAAAATGTTAATTTTTTATTCTTATTTATATGAACCATATTA
TAAATTATAAAAAATTTAAAAATTAAACATTTATGTTATTTTATATTTATTTTCTATTAATATTT
TTCAAACGTTTCAAATTTCGTAACAAAATTTTTAGGGTTCCCCCAATTATATAAACACATTGAAA
AAAGGTTTAATTTCTATTCCAAAATTGAACTTTCTCTTTATTCTAAGCGTTG
Found at i:33246 original size:6 final size:6
Alignment explanation
Indices: 33235--33261 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
33225 CCGATCCAGA
33235 TTCCGG TTCCGG TTCCGG TTCCGG TTC
1 TTCCGG TTCCGG TTCCGG TTCCGG TTC
33262 TGAAATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.30, T:0.37
Consensus pattern (6 bp):
TTCCGG
Found at i:40423 original size:20 final size:20
Alignment explanation
Indices: 40386--40423 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40376 CTCGAATTAG
*
40386 AATCTCTAAAAATCAGCTGT
1 AATCTCTAAAAATAAGCTGT
*
40406 AATCTCTAAAGATAAGCT
1 AATCTCTAAAAATAAGCT
40424 ATTCAATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (20 bp):
AATCTCTAAAAATAAGCTGT
Found at i:42701 original size:233 final size:234
Alignment explanation
Indices: 42312--42779 Score: 769
Period size: 233 Copynumber: 2.0 Consensus size: 234
42302 ACAGAACAAG
*
42312 GTGTTATCTCTTCATTTTTAATAATCTCCCCTGAAGAGATGGTTGTGATGAAGAAAAGTAGGGCT
1 GTGTCATCTCTTCATTTTTAATAATCTCCCCTGAAGAGATGGTTGTGATGAAGAAAAGTAGGGCT
42377 TATACTCACGAAATGTTACATCCATACTTACATAATACTTTCCAGATGGTGGATGATAACATTTG
66 TATACTCACGAAATGTTACATCCATACTTA-AT-ATACTTTCCAGATGGTGGATGATAACATTTG
* * *
42442 TAACCCATCTGTGTGGGAGAGTATCCAATGAAAACATATTTGTCTGCTCGAGGATCCAGTTTGCT
129 TAACCCATCTGTGTAGGAGAGTATCCAATGAAAACACATTTGTCTGCTCGAGGATCCAATTTGCT
*
42507 CCCATGTCGAAGATGGACGAAGCAAACACAACCAAAAACCA
194 CCCATGTCGAAGATAGACGAAGCAAACACAACCAAAAACCA
*
42548 GTGTCATCTTTTCATTTTTAATAATCTCCTCCTGAAGAGATGGTTGTGATGAAGAAAAGTAGGGC
1 GTGTCATCTCTTCATTTTTAATAATCTCC-CCTGAAGAGATGGTTGTGATGAAGAAAAGTAGGGC
* * * * **
42613 TTATACTTACGAAATGTTACGTCCGTACTT-AT-TTCTTTTTAGATGGTGGATGATAACATTTGT
65 TTATACTCACGAAATGTTACATCCATACTTAATATACTTTCCAGATGGTGGATGATAACATTTGT
* *
42676 AACCCTTCTGTGTAGGAGAGTATCCAATGAAAACACATTTGTCTGCTCGAGGTTCCAATTTGCTC
130 AACCCATCTGTGTAGGAGAGTATCCAATGAAAACACATTTGTCTGCTCGAGGATCCAATTTGCTC
42741 CCATGTCGAAGATAGACGAAGCAAACACAACCAAAAACC
195 CCATGTCGAAGATAGACGAAGCAAACACAACCAAAAACC
42780 TTAATGAAAC
Statistics
Matches: 217, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
233 126 0.58
235 2 0.01
236 27 0.12
237 62 0.29
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (234 bp):
GTGTCATCTCTTCATTTTTAATAATCTCCCCTGAAGAGATGGTTGTGATGAAGAAAAGTAGGGCT
TATACTCACGAAATGTTACATCCATACTTAATATACTTTCCAGATGGTGGATGATAACATTTGTA
ACCCATCTGTGTAGGAGAGTATCCAATGAAAACACATTTGTCTGCTCGAGGATCCAATTTGCTCC
CATGTCGAAGATAGACGAAGCAAACACAACCAAAAACCA
Found at i:55041 original size:17 final size:17
Alignment explanation
Indices: 55019--55052 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55009 ATGTTCCACA
55019 GTTGATTTTCATCTGTT
1 GTTGATTTTCATCTGTT
*
55036 GTTGATTTTCATTTGTT
1 GTTGATTTTCATCTGTT
55053 TTATGAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.62
Consensus pattern (17 bp):
GTTGATTTTCATCTGTT
Found at i:62950 original size:26 final size:27
Alignment explanation
Indices: 62920--62971 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
62910 TTCATAACAA
*
62920 TTAAATTTTGAA-TTTTAAAATCCATT
1 TTAAATCTTGAATTTTTAAAATCCATT
62946 TTAAATCTTGAATTTTTTAAAATCCA
1 TTAAATCTTGAA-TTTTTAAAATCCA
62972 AGATTGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.48
28 12 0.52
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (27 bp):
TTAAATCTTGAATTTTTAAAATCCATT
Found at i:74378 original size:80 final size:80
Alignment explanation
Indices: 74245--74404 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
74235 CACAACATTA
74245 TTCGATTAATGGAGTTGTACAATCTGGAAACACTAGAGAAAGTAACATATGGTAATAGGAGGACA
1 TTCGATTAATGGAGTTGTACAATCTGGAAACACTAGAGAAAGTAACATATGGTAATAGGAGGACA
74310 AAGCATGCGAGTAAG
66 AAGCATGCGAGTAAG
74325 TTCGATTAATGGAGTTGTACAATCTGGAAACACTAGAGAAAGTAACATATGGTAATAGGAGGACA
1 TTCGATTAATGGAGTTGTACAATCTGGAAACACTAGAGAAAGTAACATATGGTAATAGGAGGACA
74390 AAGCATGCGAGTAAG
66 AAGCATGCGAGTAAG
74405 ATTACTTAGT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (80 bp):
TTCGATTAATGGAGTTGTACAATCTGGAAACACTAGAGAAAGTAACATATGGTAATAGGAGGACA
AAGCATGCGAGTAAG
Done.