Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015234.1 Kokia drynarioides strain JFW-HI SEQ_130279, 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: 325792
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:232596 original size:172 final size:172
Alignment explanation
Indices: 232307--232675 Score: 585
Period size: 172 Copynumber: 2.1 Consensus size: 172
232297 AATTTGATCT
*
232307 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTTAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
* * * * * * *
232372 CAAGAAGATGGAGTTTGAAGTTTCACTCACATTGAGCTTCACTTCGTTGAATTGGTTTACTTTTT
66 CAAGAAGATGAAGTTTGAAGTTTCACTCACATTGAGCTTCACTCCATTGAATTGATATACTTCTC
*
232437 TGTACCTCATCAGGAGGATGACCGCACCACTTGTTTTAATCC
131 TGTACCTCATCAGGAAGATGACCGCACCACTTGTTTTAATCC
* * *
232479 ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTGTCCCACTTCTCCGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
* *
232544 CAGGAAGATGAAGTTTGAAGTTTCACTCACATTGAGCTTTACTCCATTGAATTGATATACTTCTC
66 CAAGAAGATGAAGTTTGAAGTTTCACTCACATTGAGCTTCACTCCATTGAATTGATATACTTCTC
* *
232609 TGTACCTCATCAGGAAGATGATCGCATCACTTGTTTTAATCC
131 TGTACCTCATCAGGAAGATGACCGCACCACTTGTTTTAATCC
*
232651 ACTTCTCTGTATCTCATCAAGAAGA
1 ACTTCTCTGTATCTCATCAGGAAGA
232676 CGGATTTGGT
Statistics
Matches: 180, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
172 180 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (172 bp):
ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
CAAGAAGATGAAGTTTGAAGTTTCACTCACATTGAGCTTCACTCCATTGAATTGATATACTTCTC
TGTACCTCATCAGGAAGATGACCGCACCACTTGTTTTAATCC
Found at i:232770 original size:86 final size:86
Alignment explanation
Indices: 232601--232760 Score: 216
Period size: 86 Copynumber: 1.9 Consensus size: 86
232591 TGAATTGATA
* * * *
232601 TACTTCTCTGTACCTCATCAGGAAGATGATCGCATCACTTGTTTTAATCCACTTCTCTGTATCTC
1 TACTTCTCTATACCTCATCAGGAAGATGACCGCATCACTTGTTTTAACCCACTTCTATGTATCTC
232666 ATCAAGAAGACGGATTTGGTC
66 ATCAAGAAGACGGATTTGGTC
* * * *
232687 TACTTCTCTATATCTCATCAGGAAGATGACCTCTTTA-TTGCTTTT-ACCCACTTCTATGTATCT
1 TACTTCTCTATACCTCATCAGGAAGATGACCGCATCACTTG-TTTTAACCCACTTCTATGTATCT
*
232750 CATCAGGAAGA
65 CATCAAGAAGA
232761 TGTAGTTTGG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 29 0.45
86 35 0.55
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (86 bp):
TACTTCTCTATACCTCATCAGGAAGATGACCGCATCACTTGTTTTAACCCACTTCTATGTATCTC
ATCAAGAAGACGGATTTGGTC
Found at i:237128 original size:12 final size:12
Alignment explanation
Indices: 237111--237141 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
237101 AAGAATAAGC
237111 AATTTAAGTTAG
1 AATTTAAGTTAG
237123 AATTTAAGTTAG
1 AATTTAAGTTAG
237135 AATTTAA
1 AATTTAA
237142 CCAGACTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (12 bp):
AATTTAAGTTAG
Found at i:240043 original size:23 final size:22
Alignment explanation
Indices: 240011--240143 Score: 108
Period size: 23 Copynumber: 5.9 Consensus size: 22
240001 GCTGGGGAAA
*
240011 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
240033 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
240056 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
* * *
240079 CAGTAGGCACAGGA-GGTGCGAAA
1 CAGTAGGCACA-CACAGTGC-AAT
* *
240102 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAGGCACAC-ACAGTGC-AAT
*
240125 CAGTAAGCACACACAGTGC
1 CAGTAGGCACACACAGTGC
240144 TGAACATAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
22 17 0.18
23 75 0.81
24 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.26, T:0.11
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:240149 original size:23 final size:21
Alignment explanation
Indices: 239983--240149 Score: 86
Period size: 23 Copynumber: 7.2 Consensus size: 21
239973 CGAAGTACTT
239983 AACAGTAAGCACACAAGTGCTGGGG
1 AACAGTAAGCACACAAGTGC----G
240008 AAACAGTAAGCACACACAGTGC-
1 -AACAGTAAGCACACA-AGTGCG
*
240030 AATCCAGTAGGCACACACAGTGC-
1 AA--CAGTAAGCACACA-AGTGCG
* * * *
240053 AATCAGTAGGCGCACATAGCGCA
1 AA-CAGTAAGCACACA-AGTGCG
* * *
240076 AATCAGTAGGCACAGGAGGTGCG
1 AA-CAGTAAGCACA-CAAGTGCG
240099 AAACAGTAAGCACACGAAGTGCG
1 -AACAGTAAGCACAC-AAGTGCG
240122 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACA-AGTGC-G
240146 AACA
1 AACA
240150 TAAAGCGCGC
Statistics
Matches: 119, Mismatches: 13, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.02
22 17 0.14
23 76 0.64
24 4 0.03
26 15 0.13
27 5 0.04
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.11
Consensus pattern (21 bp):
AACAGTAAGCACACAAGTGCG
Found at i:240256 original size:24 final size:26
Alignment explanation
Indices: 240218--240265 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
240208 TCTACATGGG
240218 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
240244 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
240266 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:249740 original size:22 final size:22
Alignment explanation
Indices: 249715--249784 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
249705 TAATTTGGAA
*
249715 TTTAATTTTAAAAGTTTAGGTT
1 TTTAATTTTAAAAGTTTAGGAT
*** ** *
249737 TTTAGCATTATGA-TTTAGGGT
1 TTTAATTTTAAAAGTTTAGGAT
249758 TTTAATATTT-AAAGTTTAGGAT
1 TTTAAT-TTTAAAAGTTTAGGAT
249780 TTTAA
1 TTTAA
249785 AATTTTATAA
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
21 12 0.35
22 22 0.65
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.51
Consensus pattern (22 bp):
TTTAATTTTAAAAGTTTAGGAT
Found at i:250547 original size:17 final size:17
Alignment explanation
Indices: 250525--250602 Score: 68
Period size: 17 Copynumber: 4.5 Consensus size: 17
250515 CAACAAAGAT
**
250525 TTAAATTTATTTTAAAA
1 TTAAATTTATCATAAAA
**
250542 TTAAATTTATCATAAGT
1 TTAAATTTATCATAAAA
*
250559 TTAAATTTA-CTTAAAA
1 TTAAATTTATCATAAAA
* *
250575 TTTAAATTTATTATAAAT
1 -TTAAATTTATCATAAAA
250593 TTAAAATTTA
1 TT-AAATTTA
250603 AATCTATTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
16 4 0.08
17 33 0.69
18 11 0.23
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (17 bp):
TTAAATTTATCATAAAA
Found at i:250567 original size:34 final size:34
Alignment explanation
Indices: 250523--250602 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 34
250513 CCCAACAAAG
*
250523 ATTTAAATTTATTTTAAAA-TTAAATTTATCATAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATCATAA
* *
250557 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATCATAA
250591 ATTTAAAATTTA
1 ATTT-AAATTTA
250603 AATCTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 6 0.15
34 27 0.68
35 7 0.17
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATCATAA
Found at i:250597 original size:24 final size:23
Alignment explanation
Indices: 250569--250615 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
250559 TTAAATTTAC
*
250569 TTAAAATTTAAATTTATTATAAAT
1 TTAAAATTTAAATCTATT-TAAAT
250593 TTAAAATTTAAATCTATTTAAAT
1 TTAAAATTTAAATCTATTTAAAT
250616 CAAGTCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAAATTTAAATCTATTTAAAT
Found at i:252394 original size:58 final size:58
Alignment explanation
Indices: 252299--252494 Score: 195
Period size: 58 Copynumber: 3.4 Consensus size: 58
252289 GAGGTCCGAA
* *
252299 AACTTCTAAAAATACCATTTTTGACCCCAAAACTTCCAAAAATT-CCATTTTTACCCTCG
1 AACTTCCAAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTACCA-TTTTACCCTCG
* *
252358 AACTTCCAAAAATTCCATTTTGACCCTAAAACTTCCAAAAATTACCATTTTGCCCTCG
1 AACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCG
* * * * * *
252416 AA-TGTCCAAAAACTCCATTTTCAACCTCGAAAC-TCTC-AAAATTACCCTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTT-GACCCCAAAACTTC-CAAAAATTACCATTTTACCCTCG
* *
252474 GA-TGTCTAAAAATTCCATTTT
1 AACT-TCCAAAAATTCCATTTT
252495 TAACTCCGAA
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
57 1 0.01
58 91 0.77
59 26 0.22
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCG
Found at i:252409 original size:30 final size:29
Alignment explanation
Indices: 252297--252436 Score: 158
Period size: 29 Copynumber: 4.8 Consensus size: 29
252287 AGGAGGTCCG
* * *
252297 AAAACTTCTAAAAATACCATTTTTGACCCC
1 AAAACTTCCAAAAATTCCA-TTTTGACCCT
*
252327 AAAACTTCCAAAAATTCCATTTTTACCCT
1 AAAACTTCCAAAAATTCCATTTTGACCCT
**
252356 CGAACTTCCAAAAATTCCATTTTGACCCT
1 AAAACTTCCAAAAATTCCATTTTGACCCT
252385 AAAACTTCCAAAAATTACCATTTTG-CCCT
1 AAAACTTCCAAAAATT-CCATTTTGACCCT
** *
252414 CGAA-TGTCCAAAAACTCCATTTT
1 AAAACT-TCCAAAAATTCCATTTT
252437 CAACCTCGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.08
29 63 0.66
30 25 0.26
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAACTTCCAAAAATTCCATTTTGACCCT
Found at i:252423 original size:29 final size:27
Alignment explanation
Indices: 252332--252494 Score: 130
Period size: 29 Copynumber: 5.7 Consensus size: 27
252322 ACCCCAAAAC
252332 TTCCAAAAATTCCATTTTTACCCTCGAA
1 TTCCAAAAATTCCA-TTTTACCCTCGAA
**
252360 CTTCCAAAAATTCCATTTTGACCCTAAAA
1 -TTCCAAAAATTCCATTTT-ACCCTCGAA
*
252389 CTTCCAAAAATTACCATTTTGCCCTCGAA
1 -TTCCAAAAATT-CCATTTTACCCTCGAA
* *
252418 TGTCCAAAAACTCCATTTTCAACCTCGAAA
1 T-TCCAAAAATTCCATTTT-ACCCTCG-AA
* * * *
252448 CTCTC-AAAATTACCCTTTTACCCCCGGA
1 TTC-CAAAAATT-CCATTTTACCCTCGAA
*
252476 TGTCTAAAAATTCCATTTT
1 T-TCCAAAAATTCCATTTT
252495 TAACTCCGAA
Statistics
Matches: 108, Mismatches: 17, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
28 19 0.18
29 73 0.68
30 16 0.15
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (27 bp):
TTCCAAAAATTCCATTTTACCCTCGAA
Found at i:256284 original size:2 final size:2
Alignment explanation
Indices: 256277--256304 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
256267 GACCTTCGTC
256277 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
256305 TCCTTCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:262997 original size:21 final size:19
Alignment explanation
Indices: 262967--263007 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
262957 CTACTATTTT
262967 GTCAACATGTTGTTTTTATAA
1 GTCAACATG-T-TTTTTATAA
*
262988 GTCAAGATGTTTTTTATAA
1 GTCAACATGTTTTTTATAA
263007 G
1 G
263008 AATCATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (19 bp):
GTCAACATGTTTTTTATAA
Found at i:264751 original size:12 final size:12
Alignment explanation
Indices: 264736--264766 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
264726 ACAAGGCGGG
264736 AAGAAGAAGAAC
1 AAGAAGAAGAAC
264748 AAGAAGAAGAAC
1 AAGAAGAAGAAC
264760 AAGAAGA
1 AAGAAGA
264767 TTCAATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAC
Found at i:271956 original size:26 final size:25
Alignment explanation
Indices: 271908--271956 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
271898 TTCAACCGTG
*
271908 ACAGAATATGATTATTCAAGCCCTT
1 ACAGAATATGATCATTCAAGCCCTT
* *
271933 ACAGAATATAGCTCATTCGAGCCC
1 ACAGAATAT-GATCATTCAAGCCC
271957 AGAACAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (25 bp):
ACAGAATATGATCATTCAAGCCCTT
Found at i:272727 original size:31 final size:31
Alignment explanation
Indices: 272689--272762 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
272679 AAAAAGCAGC
*** *
272689 AGGTACTTTGTACTGGTGTCTAAAAAGTATT
1 AGGTACTTTGTACCAATGCCTAAAAAGTATT
* *
272720 AGTTACTTTGTACCAATGCCTACAAAGTATT
1 AGGTACTTTGTACCAATGCCTAAAAAGTATT
272751 AGGTACTTTGTA
1 AGGTACTTTGTA
272763 TTTGTGTTGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (31 bp):
AGGTACTTTGTACCAATGCCTAAAAAGTATT
Found at i:293772 original size:18 final size:17
Alignment explanation
Indices: 293745--293778 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
293735 AAATATAAAA
293745 TATTAATAAATATTTAC
1 TATTAATAAATATTTAC
293762 TATTAAATAAATATTTA
1 TATT-AATAAATATTTA
293779 GAATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAATAAATATTTAC
Found at i:294189 original size:24 final size:25
Alignment explanation
Indices: 294144--294191 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
294134 TATCTATGTG
* * *
294144 TATTTATATTTTTTTATTTTTAAAT
1 TATTTACATTTTTCTATGTTTAAAT
294169 TATTTACATTTTTCTA-GTTTAAA
1 TATTTACATTTTTCTATGTTTAAA
294192 CTTAAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (25 bp):
TATTTACATTTTTCTATGTTTAAAT
Found at i:296289 original size:24 final size:24
Alignment explanation
Indices: 296257--296305 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
296247 TTAGTCAAAA
296257 TAACTTTTTATTATTTTATAATTT
1 TAACTTTTTATTATTTTATAATTT
296281 TAACTTTTTATTATTTTATAATTT
1 TAACTTTTTATTATTTTATAATTT
296305 T
1 T
296306 TTGCATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TAACTTTTTATTATTTTATAATTT
Found at i:296899 original size:23 final size:24
Alignment explanation
Indices: 296868--296921 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
296858 AATGTATTAT
*
296868 ATATATTT-AAAAATTATATAAAA
1 ATATTTTTAAAAAATTATATAAAA
296891 ATATTTTTAAAAAATTATATAAAA
1 ATATTTTTAAAAAATTATATAAAA
296915 ATATTTT
1 ATATTTT
296922 AATATAAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATTTTTAAAAAATTATATAAAA
Found at i:302044 original size:17 final size:16
Alignment explanation
Indices: 302015--302048 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
302005 AACTAATTTA
302015 TTTTAATTTATTTGAT
1 TTTTAATTTATTTGAT
*
302031 TTTTTATTTAATTTGAT
1 TTTTAATTT-ATTTGAT
302048 T
1 T
302049 CTCAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTAATTTATTTGAT
Found at i:303956 original size:18 final size:16
Alignment explanation
Indices: 303928--303968 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
303918 TCACATCAGC
303928 AAAAA-AAATTAAAGTT
1 AAAAATAAATTAAA-TT
303944 AAAACATAAATTAAATT
1 AAAA-ATAAATTAAATT
303961 AAAAATAA
1 AAAAATAA
303969 TAAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 7 0.30
18 8 0.35
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAATAAATTAAATT
Found at i:310574 original size:3 final size:3
Alignment explanation
Indices: 310566--310609 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
310556 GACTTTAGGA
310566 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
310610 ATGCTCGTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:316913 original size:57 final size:58
Alignment explanation
Indices: 316826--316937 Score: 183
Period size: 57 Copynumber: 1.9 Consensus size: 58
316816 TTTGTACCTA
* *
316826 AACTTGATATTTTTTTAATTTGGTACCTAAA-TTTTTTT-GACCCAATTTGGTACTTG
1 AACTTGACATTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCAATTTGGTACTTG
316882 AACTTGACACTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCAATTTGGTAC
1 AACTTGACA-TTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCAATTTGGTAC
316938 CTAAACTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
56 8 0.16
57 21 0.41
58 7 0.14
59 15 0.29
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (58 bp):
AACTTGACATTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCAATTTGGTACTTG
Found at i:316938 original size:29 final size:30
Alignment explanation
Indices: 316899--316972 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
316889 CACTTTTCTT
*
316899 AATTTGGTACCTAAAC-TTTTTTTGGACCC
1 AATTTGGTACCTAAACTTTTTTTTAGACCC
**
316928 AATTTGGTACCTAAACTTTTTTTTAGATTC
1 AATTTGGTACCTAAACTTTTTTTTAGACCC
316958 AATTTGGTACCTAAA
1 AATTTGGTACCTAAA
316973 ATTATGCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (30 bp):
AATTTGGTACCTAAACTTTTTTTTAGACCC
Found at i:316962 original size:59 final size:55
Alignment explanation
Indices: 316814--316972 Score: 160
Period size: 59 Copynumber: 2.8 Consensus size: 55
316804 TTAATATAAT
* *
316814 ATTTTGTACCTAAACTTGATA-TTTTTTTAATTTGGTACCTAAATTTTTTTGACCCA
1 ATTTGGTACCTAAACTT-A-ACTTTTATTAATTTGGTACCTAAATTTTTTTGACCCA
* * *
316870 ATTTGGTACTTGAACTTGACACTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTAAACTT-A-ACTTTTATTAATTTGGTACCTAAA-TTTTTTT-GACCCA
**
316929 ATTTGGTACCTAAACTT-TTTTTTAGATTCAATTTGGTACCTAAA
1 ATTTGGTACCTAAACTTAACTTTT--ATT-AATTTGGTACCTAAA
316973 ATTATGCAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
56 21 0.24
57 21 0.24
58 9 0.10
59 36 0.41
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (55 bp):
ATTTGGTACCTAAACTTAACTTTTATTAATTTGGTACCTAAATTTTTTTGACCCA
Found at i:317207 original size:29 final size:29
Alignment explanation
Indices: 317155--317240 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 29
317145 GGACCCCAAA
* * * *
317155 AAGTTTACGTATCAACTTA-AAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAA-TGGC
317184 AAGTTTAAGTACCAAATTAGAAAAAAATGGC
1 AAGTTTAAGTACCAAATTAG--AAAAATGGC
*
317215 AAGTTTGAGTACCAAATTAGACAAAA
1 AAGTTTAAGTACCAAATTAGA-AAAA
317241 AAAAACTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 17 0.35
30 4 0.08
31 22 0.46
32 5 0.10
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.26
Consensus pattern (29 bp):
AAGTTTAAGTACCAAATTAGAAAAATGGC
Found at i:317241 original size:32 final size:32
Alignment explanation
Indices: 317173--317242 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
317163 GTATCAACTT
*
317173 AAAAAAGTGTCAAGTTTAAGTACCAAATTAGA
1 AAAAAAGTGGCAAGTTTAAGTACCAAATTAGA
*
317205 AAAAAA-TGGCAAGTTTGAGTACCAAATTAGA
1 AAAAAAGTGGCAAGTTTAAGTACCAAATTAGA
317236 CAAAAAA
1 -AAAAAA
317243 AAACTTTAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.21
Consensus pattern (32 bp):
AAAAAAGTGGCAAGTTTAAGTACCAAATTAGA
Found at i:321022 original size:15 final size:15
Alignment explanation
Indices: 321002--321040 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
320992 TCTGTTAAAG
321002 TAATTTTATTTTTAT
1 TAATTTTATTTTTAT
*
321017 TAATTTAAATTTTTAT
1 TAATTT-TATTTTTAT
*
321033 AAATTTTA
1 TAATTTTA
321041 AAAGAGTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTATTTTTAT
Found at i:323233 original size:26 final size:26
Alignment explanation
Indices: 323196--323248 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
323186 TAGAAGTAAC
* *
323196 TTTTTTTAAATTAATTATGTAAATAA
1 TTTTTTTAAATTAAATATGAAAATAA
*
323222 TTTTTTTTAATTAAATATGAAAATAA
1 TTTTTTTAAATTAAATATGAAAATAA
323248 T
1 T
323249 CTAAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTTTTAAATTAAATATGAAAATAA
Found at i:323399 original size:10 final size:11
Alignment explanation
Indices: 323370--323402 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
323360 ATATCTGTAT
*
323370 AAATATTATAA
1 AAATATTAAAA
323381 AAATATTAAAA
1 AAATATTAAAA
323392 AAAT-TTAAAA
1 AAATATTAAAA
323402 A
1 A
323403 TAAAAGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATATTAAAA
Found at i:323666 original size:17 final size:16
Alignment explanation
Indices: 323646--323699 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
323636 AAATAATATT
323646 TTTAAATTAGAAATAAA
1 TTTAAATTA-AAATAAA
* *
323663 TTTAAA--ATAATAAT
1 TTTAAATTAAAATAAA
323677 TTTAAATTAAAAATAAA
1 TTTAAATT-AAAATAAA
323694 TTTAAA
1 TTTAAA
323700 ATTTAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 11 0.37
15 1 0.03
17 18 0.60
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TTTAAATTAAAATAAA
Found at i:323672 original size:31 final size:31
Alignment explanation
Indices: 323634--323701 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
323624 TTTTCTTCAC
* *
323634 TAAAATAATATTTTTAAATTAGAAATAAATT
1 TAAAATAATAATTTTAAATTAAAAATAAATT
323665 TAAAATAATAATTTTAAATTAAAAATAAATT
1 TAAAATAATAATTTTAAATTAAAAATAAATT
323696 TAAAAT
1 TAAAAT
323702 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
TAAAATAATAATTTTAAATTAAAAATAAATT
Found at i:323684 original size:20 final size:20
Alignment explanation
Indices: 323659--323712 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
323649 AAATTAGAAA
323659 TAAATTTAAAATAATAATTT
1 TAAATTTAAAATAATAATTT
*
323679 TAAATTAAAAAT-A-AATTT
1 TAAATTTAAAATAATAATTT
*
323697 AAAATTTAAAA-AATAA
1 TAAATTTAAAATAATAA
323713 ATAATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 15 0.52
19 3 0.10
20 11 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATTTAAAATAATAATTT
Found at i:323713 original size:20 final size:20
Alignment explanation
Indices: 323660--323714 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
323650 AATTAGAAAT
*
323660 AAATTTAAAATAAT-AATTTT
1 AAATTTAAAA-AATAAATTTA
323680 AAA-TT-AAAAATAAATTTA
1 AAATTTAAAAAATAAATTTA
323698 AAATTTAAAAAATAAAT
1 AAATTTAAAAAATAAAT
323715 AATAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 3 0.10
18 11 0.35
19 4 0.13
20 13 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTAAAAAATAAATTTA
Done.