Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015364.1 Kokia drynarioides strain JFW-HI SEQ_130411, 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: 142054
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 159 characters in sequence are not A, C, G, or T
Found at i:3310 original size:33 final size:34
Alignment explanation
Indices: 3273--3338 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
3263 ACTCTCTCCC
*
3273 TTGACTTTTAA-CTTCCATCTTCATTAATTTTTG
1 TTGACTTTTAACCTTCCATCTTCATTAACTTTTG
3306 TTGACTTTTAACCTTCCATCTTCATTAACTTTT
1 TTGACTTTTAACCTTCCATCTTCATTAACTTTT
3339 CATATTATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (34 bp):
TTGACTTTTAACCTTCCATCTTCATTAACTTTTG
Found at i:15000 original size:126 final size:126
Alignment explanation
Indices: 14722--15108 Score: 478
Period size: 125 Copynumber: 3.1 Consensus size: 126
14712 AAAGTAGATA
* * ** * * *
14722 TTTAGTCAATTAGCTCGATTGGTATGAGTATTGTCCTCAGTGTGAGAGG-TCGTGAGTTTAAGTG
1 TTTAGCCAATCAGCTCGATTGGTATGAGTATTGTTTTCAATGTAAGAGGAT-GTGAGTTTGAGTG
* *
14786 TGTTGAAACTTATTATTTATGGGTT-GGGAGGTCAAAAAGTAGATCTCTCAAGTCGATTGAG
65 TGTTGAAACTCATTATTTATGGGTTGGGGAGGTCAAAAAGTAGATCTTTCAAGTCGATTGAG
* *
14847 TTTAGCCAATCAGTTCGATTGATATGAGTATTGTTTTCAATGTAAGAGGATGTGAGTTTGAGTGT
1 TTTAGCCAATCAGCTCGATTGGTATGAGTATTGTTTTCAATGTAAGAGGATGTGAGTTTGAGTGT
* * * * *
14912 GCTGAAGCGCATTATTTATGAGTTGGGGAGGTCAAAAAGTATG-TCTTTCAACTCGATTGAG
66 GTTGAAACTCATTATTTATGGGTTGGGGAGGTCAAAAAGTA-GATCTTTCAAGTCGATTGAG
* * * * * *
14973 TTTAGTCAATCAACTCGATTGGCATGAGTATTGTTTTCAATGTAAGA-GATGTGAGTTGGAATGC
1 TTTAGCCAATCAGCTCGATTGGTATGAGTATTGTTTTCAATGTAAGAGGATGTGAGTTTGAGTGT
* * * *
15037 GTTGAAATTCATTATTTATGGGATGGTGAGGTCAAAAAGTAGATCTCTT-AAGTCGGTTGAG
66 GTTGAAACTCATTATTTATGGGTTGGGGAGGTCAAAAAGTAGATCT-TTCAAGTCGATTGAG
15098 TTTAGCCAATC
1 TTTAGCCAATC
15109 GGCTTGTCTA
Statistics
Matches: 223, Mismatches: 34, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
124 1 0.00
125 144 0.65
126 77 0.35
127 1 0.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (126 bp):
TTTAGCCAATCAGCTCGATTGGTATGAGTATTGTTTTCAATGTAAGAGGATGTGAGTTTGAGTGT
GTTGAAACTCATTATTTATGGGTTGGGGAGGTCAAAAAGTAGATCTTTCAAGTCGATTGAG
Found at i:16673 original size:3 final size:3
Alignment explanation
Indices: 16665--16690 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16655 CTTCACCTTT
16665 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
16691 GTAGCGACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:22382 original size:12 final size:12
Alignment explanation
Indices: 22365--22409 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
22355 ATAACATTCA
22365 AACAACAAAAAT
1 AACAACAAAAAT
*
22377 AACAACCAAAAT
1 AACAACAAAAAT
*
22389 AGCAACAAAAAT
1 AACAACAAAAAT
*
22401 AACATCAAA
1 AACAACAAA
22410 CAACATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.69, C:0.20, G:0.02, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:22481 original size:18 final size:18
Alignment explanation
Indices: 22450--22484 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22440 CAAAATAGTA
*
22450 AAAAAACACCAAAACAAT
1 AAAAAACACAAAAACAAT
*
22468 AAAAAACATAAAAACAA
1 AAAAAACACAAAAACAA
22485 CAACCAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.17, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAACACAAAAACAAT
Found at i:22493 original size:30 final size:28
Alignment explanation
Indices: 22434--22523 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
22424 ATACGAAAAT
* *
22434 AACAATCAAAATAGTAAAAA-AACACCAA
1 AACAAT-AAAAAAATAAAAACAACACCAA
22462 AACAATAAAAAACATAAAAACAACAACCAA
1 AACAATAAAAAA-ATAAAAACAAC-ACCAA
* *
22492 AACAGTAAAAAAA-AAAAACAGCACCAA
1 AACAATAAAAAAATAAAAACAACACCAA
22519 AACAA
1 AACAA
22524 CAATATAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
27 14 0.26
28 20 0.37
29 4 0.07
30 16 0.30
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.07
Consensus pattern (28 bp):
AACAATAAAAAAATAAAAACAACACCAA
Found at i:22751 original size:15 final size:15
Alignment explanation
Indices: 22733--22765 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
22723 AGGTTTACTC
*
22733 ATTTTTTTTTTTAAT
1 ATTTTATTTTTTAAT
22748 A-TTTATTTTTTAAT
1 ATTTTATTTTTTAAT
22762 ATTT
1 ATTT
22766 AATAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTATTTTTTAAT
Found at i:22758 original size:14 final size:14
Alignment explanation
Indices: 22739--22766 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22729 ACTCATTTTT
22739 TTTTTTAATATTTA
1 TTTTTTAATATTTA
22753 TTTTTTAATATTTA
1 TTTTTTAATATTTA
22767 ATAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:25981 original size:38 final size:38
Alignment explanation
Indices: 25930--26005 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
25920 AAAATGTAGA
25930 ATGATAGAAAGGTAAAAGAGATATTTCTTCTTTCCATT
1 ATGATAGAAAGGTAAAAGAGATATTTCTTCTTTCCATT
25968 ATGATAGAAAGGTAAAAGAGATATTTCTTCTTTCCATT
1 ATGATAGAAAGGTAAAAGAGATATTTCTTCTTTCCATT
26006 CCTGCTTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (38 bp):
ATGATAGAAAGGTAAAAGAGATATTTCTTCTTTCCATT
Found at i:28244 original size:132 final size:132
Alignment explanation
Indices: 28003--28273 Score: 406
Period size: 132 Copynumber: 2.1 Consensus size: 132
27993 AAAATAAATT
* * *
28003 AACA-GGGTGGGGTCCCTGTTAGCCCCCCTTGGCTCCACCATTACAATCAAGAGATGACATGAGT
1 AACAGGGGTGGGGTCCCTGCTAGACCCCCTTGGCTCCACCATTACAACCAAGAGATGACATGAGT
28067 GTCTCGTCTTTGGTGGGATTCGAACCCTGGACCTATACTATATAGATAAATTGTTGAGGCATATG
66 GTCTCGTCTTTGGTGGGATTCGAACCCTGGACCTATACTATATAGATAAATTGTTGAGGCATATG
*
28132 GG
131 AG
* **
28134 AACAGGGGTGGGGTCCCTGCTAGACCCCTTTGGCTCCGTCATTACAACCAAGAGATGA-AGTGAG
1 AACAGGGGTGGGGTCCCTGCTAGACCCCCTTGGCTCCACCATTACAACCAAGAGATGACA-TGAG
* *
28198 TGTCTCGTCTTTGGTGGGATTCGAACCCTTGA-CT-TACGTTATATAGATCAATTGTTGAGGCAT
65 TGTCTCGTCTTTGGTGGGATTCGAACCCTGGACCTATAC--TATATAGATAAATTGTTGAGGCAT
28261 ATGAG
128 ATGAG
28266 AACAGGGG
1 AACAGGGG
28274 CTAATAGAGT
Statistics
Matches: 127, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
130 3 0.02
131 7 0.06
132 117 0.92
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (132 bp):
AACAGGGGTGGGGTCCCTGCTAGACCCCCTTGGCTCCACCATTACAACCAAGAGATGACATGAGT
GTCTCGTCTTTGGTGGGATTCGAACCCTGGACCTATACTATATAGATAAATTGTTGAGGCATATG
AG
Found at i:39986 original size:31 final size:31
Alignment explanation
Indices: 39895--39996 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
39885 TCTAATGATA
* *
39895 TAAAT-AAAAATTTTCGAATAATTCAATAACT
1 TAAATGAAAACTTTT-GAATAGTTCAATAACT
* ** * * *
39926 TATATGAAAACTTTCAAAGAGTTTAATAACC
1 TAAATGAAAACTTTTGAATAGTTCAATAACT
*
39957 TAAATGAAAACTTTTGAATAGTTCCATAACT
1 TAAATGAAAACTTTTGAATAGTTCAATAACT
39988 TAAATGAAA
1 TAAATGAAA
39997 GCTCTCGAAA
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
31 48 0.87
32 7 0.13
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (31 bp):
TAAATGAAAACTTTTGAATAGTTCAATAACT
Found at i:40013 original size:62 final size:62
Alignment explanation
Indices: 39895--40016 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 62
39885 TCTAATGATA
* * *
39895 TAAATAAAAATTTTCGAATAATTCAATAACTTATATGAAAACTTTCAAAGAGTTTAATAACC
1 TAAATAAAAATTTTCGAATAATTCAATAACTTAAATGAAAACTCTCAAAGAATTTAATAACC
* * * *
39957 TAAATGAAAACTTTT-GAATAGTTCCATAACTTAAATGAAAGCTCTCGAAA-AATTTAATAA
1 TAAAT-AAAAATTTTCGAATAATTCAATAACTTAAATGAAAACTCTC-AAAGAATTTAATAA
40017 TTATTTTGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 40 0.78
63 11 0.22
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (62 bp):
TAAATAAAAATTTTCGAATAATTCAATAACTTAAATGAAAACTCTCAAAGAATTTAATAACC
Found at i:41293 original size:23 final size:26
Alignment explanation
Indices: 41240--41295 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 26
41230 GTTTTTTTAA
41240 TATATTTTCAATTTATTTAAAAATAT
1 TATATTTTCAATTTATTTAAAAATAT
* *
41266 T-TATTTT-AATTT-TTT-AATATCT
1 TATATTTTCAATTTATTTAAAAATAT
41288 TATATTTT
1 TATATTTT
41296 TTAAATTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 6 0.22
23 9 0.33
24 5 0.19
25 6 0.22
26 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
TATATTTTCAATTTATTTAAAAATAT
Found at i:43152 original size:24 final size:24
Alignment explanation
Indices: 43118--43169 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
43108 TTAATTGAGG
*
43118 ATTT-AATATATTCTTTCTTAATT
1 ATTTAAATATATTCGTTCTTAATT
* *
43141 GTTTAAATATATTCGTTCTTCATT
1 ATTTAAATATATTCGTTCTTAATT
43165 ATTTA
1 ATTTA
43170 TTTTTTTGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.58
Consensus pattern (24 bp):
ATTTAAATATATTCGTTCTTAATT
Found at i:43452 original size:19 final size:20
Alignment explanation
Indices: 43412--43457 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
43402 CATGTCATGC
* *
43412 TATTTTTTTGGATATTTATA
1 TATTTTTTTGAAAATTTATA
43432 TATTTTTTTGAAAATTT-TA
1 TATTTTTTTGAAAATTTATA
43451 TAATTTT
1 T-ATTTT
43458 AATATCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (20 bp):
TATTTTTTTGAAAATTTATA
Found at i:46372 original size:20 final size:20
Alignment explanation
Indices: 46353--46389 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
46343 CATTAATTAT
46353 TTTTATTATT-TAATTTTTA
1 TTTTATTATTGTAATTTTTA
46372 TTTTATTATTGTAATTTT
1 TTTTATTATTGTAATTTT
46390 AAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (20 bp):
TTTTATTATTGTAATTTTTA
Found at i:48705 original size:47 final size:47
Alignment explanation
Indices: 48636--48729 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
48626 GACTTCAAAT
48636 TTCATCTAGGATAAATTAGAAAGTATTAACTCCAACCCTACCATGGA
1 TTCATCTAGGATAAATTAGAAAGTATTAACTCCAACCCTACCATGGA
48683 TTCATCTAGGATAAATTAGAAAGTATTAACTCCAACCCTACCATGGA
1 TTCATCTAGGATAAATTAGAAAGTATTAACTCCAACCCTACCATGGA
48730 AAAAAAAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (47 bp):
TTCATCTAGGATAAATTAGAAAGTATTAACTCCAACCCTACCATGGA
Found at i:52029 original size:51 final size:48
Alignment explanation
Indices: 51914--52053 Score: 163
Period size: 48 Copynumber: 2.8 Consensus size: 48
51904 CCATATAGGA
* * * * * *
51914 ATTCATATGCTCACAATGACTCTGAGTCAACGGACCTTTAATCCATGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTAATCCAAGG
* * *
51962 ATTCGTTTACTCACGATGACACTTAGTCGTCGGACCTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTAATCC---AAGG
52013 ATTCATATACTCACGATGACACTTAGTCATCGGACCCTTTA
1 ATTCATATACTCACGATGACACTTAGTCATCGGA-CCTTTA
52054 GTTTATAGCT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
48 36 0.47
51 34 0.45
52 6 0.08
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (48 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTAATCCAAGG
Found at i:57461 original size:16 final size:18
Alignment explanation
Indices: 57426--57462 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
57416 TGTAGCATAA
57426 AAATAACAAAATAAAGAG
1 AAATAACAAAATAAAGAG
*
57444 AAATAA-AAAA-AAATAG
1 AAATAACAAAATAAAGAG
57460 AAA
1 AAA
57463 ACGAAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (18 bp):
AAATAACAAAATAAAGAG
Found at i:61783 original size:34 final size:34
Alignment explanation
Indices: 61718--61785 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
61708 CCCCTACTTT
* *
61718 TAATTTCAAGACCTTAATCACTATAATTTTTAAA
1 TAATTTCAAGAACTTAATCACCATAATTTTTAAA
*
61752 TAATTTCAAGAACTTAATCTCCAT-ATCTTTTAAA
1 TAATTTCAAGAACTTAATCACCATAAT-TTTTAAA
61786 ATTAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 28 0.93
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.41
Consensus pattern (34 bp):
TAATTTCAAGAACTTAATCACCATAATTTTTAAA
Found at i:72493 original size:107 final size:106
Alignment explanation
Indices: 72263--72530 Score: 261
Period size: 107 Copynumber: 2.5 Consensus size: 106
72253 AACGCTCACC
* * * ** * * * * *
72263 CCATAATTTACTATTGAACTAAATGTCTGAGTATAGCTTGTAGAATTCATTTTTGGATTGGGACA
1 CCATAATTAACCATTGAACTAAATATCCAAATAAAGCTTGTAGAATTCATCTTTGGATAGAGACA
* * **
72328 TATGAACATAAATTGAGCTAAATATTCAGGTTAAACTTGCT
66 CATGAACATAAATTGAGCTAAATATTCAGGTGAAACGAGCT
**** * ** *
72369 CCATAATTTGGTATTGAAC-ATAATGTCCATGTAAAGCTTGTAGAATTCATCTTTGGATAGAGAT
1 CCATAATTAACCATTGAACTA-AATATCCAAATAAAGCTTGTAGAATTCATCTTTGGATAGAGAC
** * *
72433 ACATGAGTATACTATTGAGCTAAATGTTCAGGTGAAACGAGCT
65 ACATGAACATA-AATTGAGCTAAATATTCAGGTGAAACGAGCT
72476 CC-TCAATTAACCATTGAACTAAATATCCAAATAAAGCTTGTAGAATTCATCTTTG
1 CCAT-AATTAACCATTGAACTAAATATCCAAATAAAGCTTGTAGAATTCATCTTTG
72531 AACACAGGTA
Statistics
Matches: 133, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
105 1 0.01
106 61 0.46
107 70 0.53
108 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (106 bp):
CCATAATTAACCATTGAACTAAATATCCAAATAAAGCTTGTAGAATTCATCTTTGGATAGAGACA
CATGAACATAAATTGAGCTAAATATTCAGGTGAAACGAGCT
Found at i:74481 original size:65 final size:65
Alignment explanation
Indices: 74377--74507 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
74367 TTTGAGCCAG
74377 TACGACAACATTAAAACTTGACTTGCAATGTTGATAGAACGGAAAATGCGGTCATTCAACGACTT
1 TACGACAACATTAAAACTTGACTTGCAATGTTGATAGAACGGAAAATGCGGTCATTCAACGACTT
*
74442 TACGACTACATTAAAACTTGACTTGCAATGTTGATAGAACGGAAAATGCGGTCATTCAACGACTT
1 TACGACAACATTAAAACTTGACTTGCAATGTTGATAGAACGGAAAATGCGGTCATTCAACGACTT
74507 T
1 T
74508 GCTTCGTAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (65 bp):
TACGACAACATTAAAACTTGACTTGCAATGTTGATAGAACGGAAAATGCGGTCATTCAACGACTT
Found at i:87878 original size:24 final size:24
Alignment explanation
Indices: 87850--87903 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
87840 TCAAGGCAGC
*
87850 TCGGTTATTAGAGTGTTAAAAGCT
1 TCGGTTAGTAGAGTGTTAAAAGCT
* *
87874 TCGGTTAGTGGAGTGTTACAAGCT
1 TCGGTTAGTAGAGTGTTAAAAGCT
87898 TCGGTT
1 TCGGTT
87904 CATCACTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.37
Consensus pattern (24 bp):
TCGGTTAGTAGAGTGTTAAAAGCT
Found at i:93732 original size:30 final size:30
Alignment explanation
Indices: 93612--93777 Score: 155
Period size: 29 Copynumber: 5.7 Consensus size: 30
93602 CCTTATTTTA
* * * *
93612 TCCAAAAATTTGAATTTGACCAC-GAACTT
1 TCCAAAAATTTGATTTTAACCCCTAAACTT
* * *
93641 T-TAAAAATTTGA-ATTAACCCTTAAA-TT
1 TCCAAAAATTTGATTTTAACCCCTAAACTT
* ** *
93668 CCCAAAAATTCAAGTTTAACCCCTAAAC-T
1 TCCAAAAATTTGATTTTAACCCCTAAACTT
*
93697 TCCAAAAATTTGATTTTGACCCCTAAACTT
1 TCCAAAAATTTGATTTTAACCCCTAAACTT
*
93727 TCC-AAAATTTGATTTTAACCCCTAAATTT
1 TCCAAAAATTTGATTTTAACCCCTAAACTT
* *
93756 TCTAAAATTTTGATTTTAACCC
1 TCCAAAAATTTGATTTTAACCC
93778 TTTTCCTTAT
Statistics
Matches: 110, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
27 7 0.06
28 20 0.18
29 62 0.56
30 21 0.19
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (30 bp):
TCCAAAAATTTGATTTTAACCCCTAAACTT
Found at i:102521 original size:32 final size:32
Alignment explanation
Indices: 102444--102522 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
102434 TATGAAAGAA
*
102444 GTTAATTCTGTAAAGACCGTAAGGGAATAAGG
1 GTTAATTCTGTAAGGACCGTAAGGGAATAAGG
*
102476 GTTAATTCTGTAAGGACTGTAAGGGAATAAGG
1 GTTAATTCTGTAAGGACCGTAAGGGAATAAGG
102508 GTTAATTCTGTAAGG
1 GTTAATTCTGTAAGG
102523 GGTTATCAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (32 bp):
GTTAATTCTGTAAGGACCGTAAGGGAATAAGG
Found at i:115628 original size:32 final size:32
Alignment explanation
Indices: 115592--115655 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
115582 TTGATCCCTG
115592 ATGTTGGCATTTGTCACACAAATTAGTCCTTA
1 ATGTTGGCATTTGTCACACAAATTAGTCCTTA
*
115624 ATGTTGGCATTTGTCACATAAATTAGTCCTTA
1 ATGTTGGCATTTGTCACACAAATTAGTCCTTA
115656 CCATTAACAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (32 bp):
ATGTTGGCATTTGTCACACAAATTAGTCCTTA
Found at i:115810 original size:21 final size:21
Alignment explanation
Indices: 115784--115877 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
115774 AATTTAAAAA
*
115784 AAAATATATTATAAAATTCAG
1 AAAATATATTAAAAAATTCAG
*
115805 AAAATA-ATTTAAAAAGTT---
1 AAAATATA-TTAAAAAATTCAG
*
115823 AAAAT-T-TTAAAAAATTCAC
1 AAAATATATTAAAAAATTCAG
*
115842 AAAATAT-TTAGAAAAATTCAA
1 AAAATATATTA-AAAAATTCAG
115863 AAAATATAGTTAAAA
1 AAAATATA-TTAAAA
115878 TTTTAGAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
16 9 0.15
18 5 0.08
19 5 0.08
20 5 0.08
21 30 0.50
22 3 0.05
23 3 0.05
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAATATATTAAAAAATTCAG
Found at i:115814 original size:36 final size:34
Alignment explanation
Indices: 115759--115857 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
115749 TTAATTGTTT
* *
115759 TAAAATTAAAAAAAAAATTTAAAAAAAAATATATTA
1 TAAAATTCAAAAAATAATTTAAAAAAAAAT-T-TTA
*
115795 TAAAATTCAGAAAATAATTTAAAAAGTTAAAATTTTA
1 TAAAATTCAAAAAATAATTTAAAAA---AAAATTTTA
* * *
115832 AAAAATTCACAAAAT-ATTTAGAAAAA
1 TAAAATTCAAAAAATAATTTAAAAAAA
115858 TTCAAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
33 2 0.04
36 30 0.56
37 16 0.30
38 1 0.02
39 5 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (34 bp):
TAAAATTCAAAAAATAATTTAAAAAAAAATTTTA
Found at i:115866 original size:31 final size:30
Alignment explanation
Indices: 115831--115900 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
115821 TTAAAATTTT
115831 AAAAAATTCACAAAATATTTAGAAAAATTCA
1 AAAAAATTCACAAAAT-TTTAGAAAAATTCA
**** *
115862 AAAAATATAGTTAAAATTTTAGAAAATTTCA
1 AAAAA-ATTCACAAAATTTTAGAAAAATTCA
115893 AAAAAATT
1 AAAAAATT
115901 GAAAATATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.06
31 23 0.72
32 7 0.22
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAAAATTCACAAAATTTTAGAAAAATTCA
Found at i:118306 original size:24 final size:24
Alignment explanation
Indices: 118273--118323 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
118263 ATAAATAATC
* * *
118273 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
118297 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
118321 TTT
1 TTT
118324 GAGTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:123171 original size:28 final size:29
Alignment explanation
Indices: 123129--123184 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
123119 TATTTTATAT
123129 TTTTCATTTTTAAAT-TTTCTTT-AATTTA
1 TTTTCATTTTTAAATATTT-TTTGAATTTA
123157 TTTT-ATTTTTAAAATATTTTTTGAATTT
1 TTTTCATTTTT-AAATATTTTTTGAATTT
123185 TGAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 6 0.24
28 11 0.44
29 8 0.32
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (29 bp):
TTTTCATTTTTAAATATTTTTTGAATTTA
Found at i:123272 original size:21 final size:20
Alignment explanation
Indices: 123226--123273 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
123216 TTAAACAAAG
***
123226 TTTTTTAAAATTATTTTTTT
1 TTTTTTAAAATTATTCACTT
123246 TATTTTTAAAATTTATTCACTT
1 T-TTTTTAAAA-TTATTCACTT
123268 TTTTTT
1 TTTTTT
123274 TTTTTTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTAAAATTATTCACTT
Found at i:123273 original size:22 final size:20
Alignment explanation
Indices: 123226--123274 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
123216 TTAAACAAAG
**
123226 TTTTTTAAAATTATTTTTTT
1 TTTTTTAAAATTATTACTTT
123246 TATTTTTAAAATTTATTCACTTT
1 T-TTTTTAAAA-TTATT-ACTTT
123269 TTTTTT
1 TTTTTT
123275 TTTTTGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 9 0.38
22 10 0.42
23 4 0.17
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTAAAATTATTACTTT
Found at i:124164 original size:89 final size:90
Alignment explanation
Indices: 124000--124166 Score: 202
Period size: 89 Copynumber: 1.9 Consensus size: 90
123990 CTTTAATTGT
*
124000 TTTAAAAAATTCAAAAAAAACTTAAACATTCTTAAAATAAAATTCAAAAAATAATTTAAAAAGTT
1 TTTAAAAAATTCAAAAAAAACTTAAACATTCTTAAAATAAAATACAAAAAATAATTTAAAAAGTT
*
124065 AAAATTTCAAAAAAATCACAAAATA
66 AAAAATTCAAAAAAATCACAAAATA
* * *
124090 TTTAGAAAAATTCAAAAAATATAGTTAAA-ATT-TTAGAA-AAAATGAC-AAAAA-AATTTGAAA
1 TTTA-AAAAATTCAAAAAA-A-ACTTAAACATTCTTAAAATAAAAT-ACAAAAAATAATTTAAAA
124150 A-TATAAAAATTCAAAAA
62 AGT-TAAAAATTCAAAAA
124167 GCAAAAATTG
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
88 1 0.01
89 22 0.33
90 14 0.21
91 20 0.30
92 4 0.06
93 6 0.09
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.28
Consensus pattern (90 bp):
TTTAAAAAATTCAAAAAAAACTTAAACATTCTTAAAATAAAATACAAAAAATAATTTAAAAAGTT
AAAAATTCAAAAAAATCACAAAATA
Found at i:124323 original size:10 final size:10
Alignment explanation
Indices: 124310--124353 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
124300 ATTTTTTTCC
*
124310 TTTTTTAAAA
1 TTTTTGAAAA
124320 TTTTTGAAAA
1 TTTTTGAAAA
*
124330 TTTTT-AACTA
1 TTTTTGAA-AA
124340 TTTTTGAAAA
1 TTTTTGAAAA
124350 TTTT
1 TTTT
124354 CTTTAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.07
10 25 0.86
11 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (10 bp):
TTTTTGAAAA
Found at i:124333 original size:20 final size:21
Alignment explanation
Indices: 124310--124353 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
124300 ATTTTTTTCC
124310 TTTTTTAA-AATTTTTGAAAA
1 TTTTTTAACAATTTTTGAAAA
*
124330 -TTTTTAACTATTTTTGAAAA
1 TTTTTTAACAATTTTTGAAAA
124350 TTTT
1 TTTT
124354 CTTTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTTTAACAATTTTTGAAAA
Found at i:124362 original size:30 final size:28
Alignment explanation
Indices: 124328--124402 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 28
124318 AATTTTTGAA
124328 AATTTTTAACTATTTTTGAAAAT-TTTCTTT
1 AATTTTT-A-TATTTTT-AAAATATTTCTTT
* *
124358 AATTTATTTTTATTTTTAAAATATTTTTTT
1 AA-TT-TTTATATTTTTAAAATATTTCTTT
124388 AATTTTTTATATTTT
1 AA-TTTTTATATTTT
124403 CAATTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 14 0.36
30 20 0.51
31 2 0.05
32 3 0.08
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (28 bp):
AATTTTTATATTTTTAAAATATTTCTTT
Found at i:124388 original size:25 final size:24
Alignment explanation
Indices: 124360--124419 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 24
124350 TTTTCTTTAA
124360 TTTATTTTTAT-TTTTAAAATATTTT
1 TTTATTTTTATATTTT-AAAT-TTTT
*
124385 TTTAATTTTTTATATTTTCAATTTTT
1 TTT-A-TTTTTATATTTTAAATTTTT
*
124411 TTAATTTTT
1 TTTATTTTT
124420 GAAATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 5 0.17
25 4 0.13
26 7 0.23
27 10 0.33
28 4 0.13
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTATTTTTATATTTTAAATTTTT
Found at i:126624 original size:24 final size:24
Alignment explanation
Indices: 126591--126641 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
126581 ATAAATAATC
* * *
126591 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
126615 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
126639 TTT
1 TTT
126642 GAGTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:128551 original size:12 final size:13
Alignment explanation
Indices: 128524--128556 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
128514 TTTTGAACTA
*
128524 ATAATTGTATATT
1 ATAATTATATATT
128537 ATAATTATA-ATT
1 ATAATTATATATT
128549 ATAATTAT
1 ATAATTAT
128557 CACAACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
ATAATTATATATT
Found at i:128667 original size:17 final size:18
Alignment explanation
Indices: 128645--128678 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
128635 ACAATTGTAA
*
128645 TTTAAATTC-TAATTATT
1 TTTAAATACATAATTATT
128662 TTTAAATACATAATTAT
1 TTTAAATACATAATTAT
128679 CAAAACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATACATAATTATT
Found at i:132859 original size:28 final size:28
Alignment explanation
Indices: 132827--132913 Score: 156
Period size: 28 Copynumber: 3.1 Consensus size: 28
132817 CATCACGTGC
132827 CCATCTGAAATTTGTTCATACTACGGGA
1 CCATCTGAAATTTGTTCATACTACGGGA
132855 CCATCTGAAATTTGTTCATACTACGGGA
1 CCATCTGAAATTTGTTCATACTACGGGA
* *
132883 CCATCTGAAATTTGTTAATACTACAGGA
1 CCATCTGAAATTTGTTCATACTACGGGA
132911 CCA
1 CCA
132914 AGTGATTAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (28 bp):
CCATCTGAAATTTGTTCATACTACGGGA
Found at i:136081 original size:7 final size:7
Alignment explanation
Indices: 136065--136127 Score: 69
Period size: 7 Copynumber: 9.3 Consensus size: 7
136055 TTCGAAAAAA
136065 TCAACAG
1 TCAACAG
*
136072 TCAACGG
1 TCAACAG
136079 TCAAC-G
1 TCAACAG
136085 ATCAA-AG
1 -TCAACAG
136092 TCAACAG
1 TCAACAG
*
136099 TCAACAA
1 TCAACAG
136106 TCAA-AG
1 TCAACAG
*
136112 TCAACGG
1 TCAACAG
136119 TCAACAG
1 TCAACAG
136126 TC
1 TC
136128 GGTCAATGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
6 10 0.21
7 37 0.79
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (7 bp):
TCAACAG
Found at i:136095 original size:20 final size:20
Alignment explanation
Indices: 136063--136124 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
136053 TTTTCGAAAA
136063 AATCAACAGTCAACGGTCAAC
1 AATCAA-AGTCAACGGTCAAC
* *
136084 GATCAAAGTCAACAGTCAAC
1 AATCAAAGTCAACGGTCAAC
136104 AATCAAAGTCAACGGTCAAC
1 AATCAAAGTCAACGGTCAAC
136124 A
1 A
136125 GTCGGTCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 32 0.86
21 5 0.14
ACGTcount: A:0.45, C:0.26, G:0.15, T:0.15
Consensus pattern (20 bp):
AATCAAAGTCAACGGTCAAC
Found at i:136109 original size:27 final size:27
Alignment explanation
Indices: 136065--136127 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
136055 TTCGAAAAAA
** *
136065 TCAACAGTCAACGGTCAACGATCAA-AG
1 TCAACAGTCAACAATCAAAG-TCAACAG
*
136092 TCAACAGTCAACAATCAAAGTCAACGG
1 TCAACAGTCAACAATCAAAGTCAACAG
136119 TCAACAGTC
1 TCAACAGTC
136128 GGTCAATGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (27 bp):
TCAACAGTCAACAATCAAAGTCAACAG
Found at i:139381 original size:17 final size:18
Alignment explanation
Indices: 139359--139392 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
139349 AAAATTGTAA
*
139359 TTTAAATTC-TAATTATT
1 TTTAAATACATAATTATT
139376 TTTAAATACATAATTAT
1 TTTAAATACATAATTAT
139393 CACAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATACATAATTATT
Found at i:139437 original size:45 final size:44
Alignment explanation
Indices: 139360--139450 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
139350 AAATTGTAAT
*
139360 TTAAATTCTAATTATTTTTAAATACATAATTATCACAACTTCTA
1 TTAAATTATAATTATTTTTAAATACATAATTATCACAACTTCTA
* * *
139404 TTAAATTATAATTATTTTTTAAATATATAATTATCATAACTTTTA
1 TTAAATTATAATTA-TTTTTAAATACATAATTATCACAACTTCTA
139449 TT
1 TT
139451 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 13 0.31
45 29 0.69
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.51
Consensus pattern (44 bp):
TTAAATTATAATTATTTTTAAATACATAATTATCACAACTTCTA
Found at i:139447 original size:25 final size:25
Alignment explanation
Indices: 139374--139447 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
139364 ATTCTAATTA
* *
139374 TTTTTAAATACATAATTATCACAAC
1 TTTTTAAATATATAATTATCATAAC
139399 TTCTATTAAAT-TATAA-T-T-AT---
1 TT-T-TTAAATATATAATTATCATAAC
139419 TTTTTAAATATATAATTATCATAAC
1 TTTTTAAATATATAATTATCATAAC
139444 TTTT
1 TTTT
139448 ATTTTATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
18 6 0.16
19 6 0.16
20 3 0.08
21 1 0.03
22 2 0.05
23 1 0.03
24 1 0.03
25 7 0.18
26 5 0.13
27 6 0.16
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTTAAATATATAATTATCATAAC
Done.