Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014409.1 Kokia drynarioides strain JFW-HI SEQ_129447, 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: 54640
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:8607 original size:14 final size:14
Alignment explanation
Indices: 8590--8621 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
8580 ATGTTTATTT
8590 TAAATATGATATAA
1 TAAATATGATATAA
*
8604 TAAATATGTTATAA
1 TAAATATGATATAA
8618 TAAA
1 TAAA
8622 GTAAACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (14 bp):
TAAATATGATATAA
Found at i:14025 original size:30 final size:29
Alignment explanation
Indices: 13989--14070 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 29
13979 TTTTTCTTAG
13989 TTTGGTAACTAAACTTTTTTTTGGACTCAA
1 TTTGGTAACTAAACTTTTTTTT-GACTCAA
* * ** *
14019 TTTGGTATCTGAACTTGATTTTTTTTCTTAA
1 TTTGGTAACTAAACTT--TTTTTTGACTCAA
* *
14050 TTTGGTACCTAAGCTTTTTTT
1 TTTGGTAACTAAACTTTTTTT
14071 ATTATTATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
29 5 0.12
30 14 0.33
31 17 0.40
32 6 0.14
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.54
Consensus pattern (29 bp):
TTTGGTAACTAAACTTTTTTTTGACTCAA
Found at i:14404 original size:27 final size:27
Alignment explanation
Indices: 14351--14405 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
14341 GGAAAAGTGT
* * *
14351 AAAATTTTAGTACCAAATTGGATAAAA
1 AAAATTTAAATACCAAATTAGATAAAA
*
14378 AAAATTTAAATACCAAATTA-AGAAAA
1 AAAATTTAAATACCAAATTAGATAAAA
14404 AA
1 AA
14406 TATCAAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAATTTAAATACCAAATTAGATAAAA
Found at i:14423 original size:31 final size:30
Alignment explanation
Indices: 14292--14426 Score: 82
Period size: 31 Copynumber: 4.6 Consensus size: 30
14282 GAACCCCCAA
* * * *
14292 AAGTTTAAGTACTAACTTA-AAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAATATC
* * * * * *
14321 AAGTTTAGGTATCAAATTAAGGAAAAGTGTA
1 AAGTTTAAGTACCAAATT-AGAAAAAATATC
* * *
14352 AAATTTTAGTACCAAATTGGATAAAAA-A--
1 AAGTTTAAGTACCAAATTAGA-AAAAATATC
*
14380 AA-TTTAAATACCAAATTAAGAAAAAATATC
1 AAGTTTAAGTACCAAATT-AGAAAAAATATC
14410 AAGTTTAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
14427 ATTATATTAA
Statistics
Matches: 80, Mismatches: 18, Indels: 14
0.71 0.16 0.12
Matches are distributed among these distances:
27 18 0.22
28 5 0.06
29 14 0.17
30 4 0.05
31 39 0.49
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAGAAAAAATATC
Found at i:15192 original size:19 final size:20
Alignment explanation
Indices: 15164--15214 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
15154 TTAGAAATTA
*
15164 ATTAATTTTTAAG-AATATTT
1 ATTAAATTTTAAGTAAT-TTT
* *
15184 A-TATATTTTTAGTAATTTT
1 ATTAAATTTTAAGTAATTTT
15203 ATTAAATTTTAA
1 ATTAAATTTTAA
15215 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTAAATTTTAAGTAATTTT
Found at i:15211 original size:20 final size:20
Alignment explanation
Indices: 15167--15212 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
15157 GAAATTAATT
15167 AATTTTTAAGAATATTTATA
1 AATTTTTAAGAATATTTATA
*
15187 TATTTTT-AGTAAT-TTTATTA
1 AATTTTTAAG-AATATTTA-TA
15207 AATTTT
1 AATTTT
15213 AATTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
AATTTTTAAGAATATTTATA
Found at i:15440 original size:12 final size:15
Alignment explanation
Indices: 15406--15439 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
15396 GGAAATTTTA
15406 AAAAAAATAATATGT
1 AAAAAAATAATATGT
15421 AAAAAAATAAT-T-T
1 AAAAAAATAATATGT
15434 AAAAAA
1 AAAAAA
15440 TGGGATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 1 0.05
15 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAAAAATAATATGT
Found at i:19162 original size:117 final size:116
Alignment explanation
Indices: 19016--19275 Score: 278
Period size: 117 Copynumber: 2.2 Consensus size: 116
19006 TTTTTGAGGA
* * * * * *
19016 ATTTAGGGATCAAAATTGAAACTTTTGGAAAA-TTTGAAGTTGAAAATGTGATTTTCAAAAAATT
1 ATTTAGGGAT-AAAAATGTAATTTTTGGAAAAGTTT-AAGGTCAAAATGTAATTTT-AAAAAATT
* * ** *
19080 GGGGGC-AAAGTGGTAATTTTTTTATGTTTGA-GGGTAAAATGGTAATTTTTGGAT
63 AGGGGCTAAAATGGTAA-TTTTGGATGTTAGAGGGGTAAAATGGTAA-TTTTGGAT
* *** *
19134 GTTTAGGGAT-AAAATGGTAATTTTTGGAAAAGTTTAAGGTCAAAATGTAATTTTTGGATATTAG
1 ATTTAGGGATAAAAAT-GTAATTTTTGGAAAAGTTTAAGGTCAAAATGTAATTTTAAAAAATTAG
19198 GGGCTAAAATGGTAATTTTGGATGTTAGAGGGGTAAAATGGTAATTTTGGAT
65 GGGCTAAAATGGTAATTTTGGATGTTAGAGGGGTAAAATGGTAATTTTGGAT
19250 ATTTGAGGG-TAAAAATGTAATTTTTG
1 ATTT-AGGGATAAAAATGTAATTTTTG
19276 AGAAGTTCGA
Statistics
Matches: 119, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
116 46 0.39
117 61 0.51
118 12 0.10
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.38
Consensus pattern (116 bp):
ATTTAGGGATAAAAATGTAATTTTTGGAAAAGTTTAAGGTCAAAATGTAATTTTAAAAAATTAGG
GGCTAAAATGGTAATTTTGGATGTTAGAGGGGTAAAATGGTAATTTTGGAT
Found at i:19184 original size:88 final size:86
Alignment explanation
Indices: 19114--19275 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 86
19104 TGTTTGAGGG
* *
19114 TAAAATGGTAATTTTTGGATGTT-TAGGGATAAAATGGTAATTTTTGGAAAAGTTT-AAGGTCAA
1 TAAAATGGTAA-TTTTGGATGTTAGAGGGATAAAATGGTAA-TTTTGG-AAA-TTTGAAGGTAAA
19177 AATGTAATTTTTGGATATTAGGGGC
62 AATGTAATTTTTGGATATTAGGGGC
* * *
19202 TAAAATGGTAATTTTGGATGTTAGAGGGGTAAAATGGTAATTTTGGATATTTGAGGGTAAAAATG
1 TAAAATGGTAATTTTGGATGTTAGAGGGATAAAATGGTAATTTTGGAAATTTGAAGGTAAAAATG
19267 TAATTTTTG
66 TAATTTTTG
19276 AGAAGTTCGA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
85 3 0.04
86 21 0.31
87 17 0.25
88 26 0.39
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.39
Consensus pattern (86 bp):
TAAAATGGTAATTTTGGATGTTAGAGGGATAAAATGGTAATTTTGGAAATTTGAAGGTAAAAATG
TAATTTTTGGATATTAGGGGC
Found at i:19452 original size:31 final size:30
Alignment explanation
Indices: 19109--19533 Score: 262
Period size: 29 Copynumber: 14.4 Consensus size: 30
19099 TTTTATGTTT
*
19109 GAGGGT-AAAATGGTAATTTTTG-GATGTT-
1 GAGGGTAAAAAT-GTAATTTTTGAGAAGTTC
* *
19137 TAGGG-ATAAAATGGTAATTTTTGGAAAAGTT-
1 GAGGGTA-AAAAT-GTAATTTTT-GAGAAGTTC
* * * *
19168 TAAGGTCAAAATGTAATTTTTG-GATA-TTA
1 GAGGGTAAAAATGTAATTTTTGAGA-AGTTC
* *
19197 G-GGGCT-AAAATGGTAA-TTTTG-GATGTTA
1 GAGGG-TAAAAAT-GTAATTTTTGAGAAGTTC
*
19225 GAGGGGT-AAAATGGTAA-TTTTG-GATA-TTT
1 GA-GGGTAAAAAT-GTAATTTTTGAGA-AGTTC
19254 GAGGGTAAAAATGTAATTTTTGAGAAGTTC
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTC
* * *
19284 GAGAGTAAAAATGTGATTTTTTGAGATGTTC
1 GAGGGTAAAAATGT-AATTTTTGAGAAGTTC
* * *
19315 GAGGGTGAAAATGTGATTTTTG-GAAGTTT
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTC
* * *
19344 GGGGGTAAAAATGTGATTTTTG-GAAGTTT
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTC
* * *
19373 GGGGGTCAAAATGTGATTTTTG-GAAGTTC
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTC
* * *
19402 G-GGAGTAAAATTTTAATTTTTGAGAAATTC
1 GAGG-GTAAAAATGTAATTTTTGAGAAGTTC
* * *
19432 GAGGGTAAAACATATAATTTTGGAGAAATT-
1 GAGGGTAAAA-ATGTAATTTTTGAGAAGTTC
* * *
19462 TAGGGGTGAAAATGTAATTTTTGAGAAGTTT
1 GA-GGGTAAAAATGTAATTTTTGAGAAGTTC
* * * *
19493 TAGGGTAAAAATATAA-TTTGGAGAAATTC
1 GAGGGTAAAAATGTAATTTTTGAGAAGTTC
19522 GAGGGTAAAAAT
1 GAGGGTAAAAAT
19534 ATATTTGAGG
Statistics
Matches: 329, Mismatches: 44, Indels: 47
0.78 0.10 0.11
Matches are distributed among these distances:
28 35 0.11
29 150 0.46
30 78 0.24
31 66 0.20
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (30 bp):
GAGGGTAAAAATGTAATTTTTGAGAAGTTC
Found at i:19482 original size:90 final size:89
Alignment explanation
Indices: 19346--19536 Score: 226
Period size: 90 Copynumber: 2.1 Consensus size: 89
19336 GGAAGTTTGG
* * * * * * *
19346 GGGTAAAAATGTGATTTTTG-GAAGTTTGGGGGTCAAAATGTGATTTTTG-GAAG-TTCGGGAGT
1 GGGTAAAAATATAATTTTGGAGAAATTTAGGGGTCAAAATGTAATTTTTGAGAAGTTTCAGG-GT
* * *
19408 AAAATTTTAATTTTTGAGAAATTCGA
65 AAAAATATAA-TTTGGAGAAATTCGA
* *
19434 GGGTAAAACATATAATTTTGGAGAAATTTAGGGGTGAAAATGTAATTTTTGAGAAGTTTTAGGGT
1 GGGTAAAA-ATATAATTTTGGAGAAATTTAGGGGTCAAAATGTAATTTTTGAGAAGTTTCAGGGT
19499 AAAAATATAATTTGGAGAAATTCGA
65 AAAAATATAATTTGGAGAAATTCGA
19524 GGGTAAAAATATA
1 GGGTAAAAATATA
19537 TTTGAGGGTA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
88 8 0.09
89 14 0.16
90 47 0.54
91 14 0.16
92 4 0.05
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.35
Consensus pattern (89 bp):
GGGTAAAAATATAATTTTGGAGAAATTTAGGGGTCAAAATGTAATTTTTGAGAAGTTTCAGGGTA
AAAATATAATTTGGAGAAATTCGA
Found at i:19517 original size:29 final size:29
Alignment explanation
Indices: 19406--19536 Score: 111
Period size: 30 Copynumber: 4.4 Consensus size: 29
19396 AAGTTCGGGA
* * * **
19406 GTAAAATTTTAATTTTTGAGAAATTCGAGG
1 GTAAAAATATAATTTTGGAG-AATTTTAGG
*
19436 GTAAAACATATAATTTTGGAGAAATTTAGGG
1 GTAAAA-ATATAATTTTGGAGAATTTTA-GG
* * *
19467 GTGAAAATGTAATTTTTGAGAAGTTTTAGG
1 GTAAAAATATAATTTTGGAGAA-TTTTAGG
**
19497 GTAAAAATATAA-TTTGGAGAAATTCGAGG
1 GTAAAAATATAATTTTGGAG-AATTTTAGG
19526 GTAAAAATATA
1 GTAAAAATATA
19537 TTTGAGGGTA
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
29 22 0.27
30 38 0.46
31 22 0.27
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (29 bp):
GTAAAAATATAATTTTGGAGAATTTTAGG
Found at i:19558 original size:19 final size:19
Alignment explanation
Indices: 19517--19558 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
19507 AATTTGGAGA
*
19517 AATTCGAGGGTAAAAATAT
1 AATTTGAGGGTAAAAATAT
19536 -ATTTGAGGGTAAAAATAT
1 AATTTGAGGGTAAAAATAT
19554 AATTT
1 AATTT
19559 TGGAGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.33
Consensus pattern (19 bp):
AATTTGAGGGTAAAAATAT
Found at i:21770 original size:39 final size:39
Alignment explanation
Indices: 21724--22313 Score: 231
Period size: 39 Copynumber: 15.2 Consensus size: 39
21714 TACCCCATGA
* * *
21724 TCGGGGTAAGAGATTGGCTGATAATGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
* ** * ** *
21763 TCGGGGTAAAAGATCAAATGACT-GCAATCTGCCCTAGGC
1 TCGGGGTAAGAGATTGACTGA-TAGTGATCTGCCCCAGGC
** * *
21802 TCGAGGGTAAGAGATTGGTTGATGGTGATCTGGCCCAAGTTNAGGC
1 TCG-GGGTAAGAGATTGACTGATAGTGATCT-GCCC-----CAGGC
* * * * ** * *
21848 TCGGGGTAAAAGATTGAATGGTTGCAATTTGCCTCAGGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
* * * *
21887 TCGAGGTAAGAGATTGACTGATGGTGATCTGCCTCAAGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
* * * * * **
21926 TTGGGGTAAGACATCGAATGGCTA-CAATCTGCCCCCAGGC
1 TCGGGGTAAGAGATTGACT-GATAGTGATCTG-CCCCAGGC
* * *
21966 TTGGGGTAAGAGATTGATTGGT--TGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
* ** *
22003 TCGGGGT-A-AGATTGAATGACT-GCAATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGACTGA-TAGTGATCTGCCCCAGGC
* * * *
22040 TTGGGGTAAGAAATTGGCTGATGGTGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
* * ** * *
22079 TCGGGGTAAGAGATCGAATGACT-GCAACCTGCCCTAGGC
1 TCGGGGTAAGAGATTGACTGA-TAGTGATCTGCCCCAGGC
*** * *
22118 TTAAGGTAAGAGATTGACTGGT--TGATCTGCCCAAGGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
** * *
22155 TTAGGGTAAGAGATTGACTGGT--TGATCTGTCCCAGGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
* * * * *
22192 TCGAGGTAAGATCGAATGGCT-ACA---ATCTGCCTCAGGC
1 TCGGGGTAAGA--GATTGACTGATAGTGATCTGCCCCAGGC
**** * * * **
22229 TCAACATAAGAGATTGGCTGATGGTGATCTGTCTTAGGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
* * * * **
22268 TCGGGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
22307 TCGGGGT
1 TCGGGGT
22314 GAAAGATCGA
Statistics
Matches: 407, Mismatches: 120, Indels: 48
0.71 0.21 0.08
Matches are distributed among these distances:
35 16 0.04
36 3 0.01
37 104 0.26
38 8 0.02
39 199 0.49
40 44 0.11
41 4 0.01
44 3 0.01
45 19 0.05
46 7 0.02
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGACTGATAGTGATCTGCCCCAGGC
Found at i:21887 original size:85 final size:83
Alignment explanation
Indices: 21761--22152 Score: 267
Period size: 78 Copynumber: 5.0 Consensus size: 83
21751 TCTGCCCCAA
**
21761 GCTCGGGGTAAAAGATCAAATGACTGCAATCTGCCCTAGGCTCGAGGGTAAGAGATTGGTTGATG
1 GCTCGGGGTAAAAGATCAAATGACTGCAATCTGCCCTAGGCTCGA-GGTAAGAGATTGACTGATG
21826 GTGATCTGGCCCAAGTTNAG
65 GTGATCTGGCCCAAGTT-AG
** ** *
21846 GCTCGGGGTAAAAGATTGAATGGTTGCAATTTG-CCTCAGGCTCGAGGTAAGAGATTGACTGATG
1 GCTCGGGGTAAAAGATCAAATGACTGCAATCTGCCCT-AGGCTCGAGGTAAGAGATTGACTGATG
21910 GTGATCT-GCCTC-A---A-
65 GTGATCTGGCC-CAAGTTAG
* * * * * * * * *
21924 GCTTGGGGTAAGACATCGAATGGCTACAATCTGCCCCCAGGCTTGGGGTAAGAGATTGA-T--TG
1 GCTCGGGGTAAAAGATCAAATGACTGCAATCTG-CCCTAGGCTCGAGGTAAGAGATTGACTGATG
*
21986 GTTGATCT-GCCC----CAG
65 G-TGATCTGGCCCAAGTTAG
** * * * * * *
22001 GCTCGGGGT--AAGATTGAATGACTGCAATCTGCCCCAAGCTTGGGGTAAGAAATTGGCTGATGG
1 GCTCGGGGTAAAAGATCAAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGACTGATGG
*
22064 TGATCT-GCCC----CAG
66 TGATCTGGCCCAAGTTAG
* * * ** *
22077 GCTCGGGGTAAGAGATCGAATGACTGCAACCTGCCCTAGGCTTAAGGTAAGAGATTGACTG--GT
1 GCTCGGGGTAAAAGATCAAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGACTGATGG
22140 TGATCT-GCCCAAG
66 TGATCTGGCCCAAG
22153 GCTTAGGGTA
Statistics
Matches: 256, Mismatches: 36, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
74 22 0.09
75 18 0.07
76 38 0.15
77 20 0.08
78 68 0.27
79 20 0.08
80 2 0.01
83 4 0.02
84 28 0.11
85 36 0.14
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (83 bp):
GCTCGGGGTAAAAGATCAAATGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGACTGATGG
TGATCTGGCCCAAGTTAG
Found at i:22191 original size:189 final size:190
Alignment explanation
Indices: 21952--22307 Score: 498
Period size: 189 Copynumber: 1.9 Consensus size: 190
21942 AATGGCTACA
* * * * *
21952 ATCTGCCCCCAGGCTTGGGGTAAGAGATTGATTGGTTGATCTGCCCCAGGCTCGGGGTAAGATTG
1 ATCTGCCCCAAGGCTTAGGGTAAGAGATTGACTGGTTGATCTGCCCCAGGCTCGAGGTAAGATCG
* *****
22017 AATGACTGCAATCTGCCCCAAGCTTGGGGTAAGAAATTGGCTGATGGTGATCTGCCCCAGGCTCG
66 AATGACTACAATCTGCCCCAAGCTCAACATAAGAAATTGGCTGATGGTGATCTGCCCCAGGCTCG
*
22082 GGGTAAGAGATCGAATGACTGCAACCTGCCCTAGGCTTAAGGTAAGAGATTGACTGGTTG
131 GGGTAAGAGATCGAATGACTGCAACCTGCCCCAGGCTTAAGGTAAGAGATTGACTGGTTG
*
22142 ATCTG-CCCAAGGCTTAGGGTAAGAGATTGACTGGTTGATCTGTCCCAGGCTCGAGGTAAGATCG
1 ATCTGCCCCAAGGCTTAGGGTAAGAGATTGACTGGTTGATCTGCCCCAGGCTCGAGGTAAGATCG
* * * * * **
22206 AATGGCTACAATCTGCCTCAGGCTCAACATAAGAGATTGGCTGATGGTGATCTGTCTTAGGCTCG
66 AATGACTACAATCTGCCCCAAGCTCAACATAAGAAATTGGCTGATGGTGATCTGCCCCAGGCTCG
** *
22271 GGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCT
131 GGGTAAGAGATCGAATGACTGCAACCTGCCCCAGGCT
22308 CGGGGTGAAA
Statistics
Matches: 143, Mismatches: 23, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
189 138 0.97
190 5 0.03
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.25
Consensus pattern (190 bp):
ATCTGCCCCAAGGCTTAGGGTAAGAGATTGACTGGTTGATCTGCCCCAGGCTCGAGGTAAGATCG
AATGACTACAATCTGCCCCAAGCTCAACATAAGAAATTGGCTGATGGTGATCTGCCCCAGGCTCG
GGGTAAGAGATCGAATGACTGCAACCTGCCCCAGGCTTAAGGTAAGAGATTGACTGGTTG
Found at i:22325 original size:39 final size:39
Alignment explanation
Indices: 21844--22313 Score: 303
Period size: 39 Copynumber: 12.3 Consensus size: 39
21834 GCCCAAGTTN
* * *
21844 AGGCTCGGGGTAAAAGATTGAATGGTTGCAATTTGCCTC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
* * * * ** *
21883 AGGCTCGAGGTAAGAGATTGACTGATGGTGATCTGCCTC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
* * * * * *
21922 AAGCTTGGGGTAAGACATCGAATGGCTACAATCTGCCCCC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTG-CCCC
* *
21962 AGGCTTGGGGTAAGAGATTGATTGGTTG--ATCTGCCCC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
**
21999 AGGCTCGGGGT-A-AGATTGAATGACTGCAATCTGCCCC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
* * * ** * * **
22036 AAGCTTGGGGTAAGAAATTGGCTGATGGTGATCTGCCCC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
* ** * *
22075 AGGCTCGGGGTAAGAGATCGAATGACTGCAACCTGCCCT
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
*** * *
22114 AGGCTTAAGGTAAGAGATTGACTGGTTG--ATCTGCCCA
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
** * *
22151 AGGCTTAGGGTAAGAGATTGACTGGTTG--ATCTGTCCC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
* * * * *
22188 AGGCTCGAGGT-A-AGATCGAATGGCTACAATCTGCCTC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
**** ** * * ** * **
22225 AGGCTCAACATAAGAGATTGGCTGATGGTGATCTGTCTT
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
*
22264 AGGCTCGGGGTAAGAGATCGAATGGTTGCAATCTGCCCC
1 AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
22303 AGGCTCGGGGT
1 AGGCTCGGGGT
22314 GAAAGATCGA
Statistics
Matches: 321, Mismatches: 101, Indels: 18
0.73 0.23 0.04
Matches are distributed among these distances:
35 21 0.07
36 2 0.01
37 96 0.30
38 7 0.02
39 170 0.53
40 25 0.08
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (39 bp):
AGGCTCGGGGTAAGAGATTGAATGGTTGCAATCTGCCCC
Found at i:34316 original size:29 final size:29
Alignment explanation
Indices: 34284--34503 Score: 168
Period size: 28 Copynumber: 7.7 Consensus size: 29
34274 CGAAAATTTA
*
34284 GGGGTAAAGTGGTAATTTTTGGATGTTTG
1 GGGGTAAAATGGTAATTTTTGGATGTTTG
* *
34313 GGGGCAAAATGATAA-TTTTGGATGTTTG
1 GGGGTAAAATGGTAATTTTTGGATGTTTG
* * *
34341 GGGGTAAAATAGTAATTTTTGAAAAAGTTT-
1 GGGGTAAAATGGTAATTTTTG--GATGTTTG
* * * * *
34371 GGGGT--CATTGTAATTTTGGGATATTCG
1 GGGGTAAAATGGTAATTTTTGGATGTTTG
* *
34398 GGGGTAAAATGGTAA-TTTTAGATGTTAAG
1 GGGGTAAAATGGTAATTTTTGGATGTT-TG
* * **
34427 GGGG-AAAATGATAATTTTTGGATATTCA
1 GGGGTAAAATGGTAATTTTTGGATGTTTG
* *
34455 GGGGAAAAAT-GTAATTTTTGAGAAGTTTG
1 GGGGTAAAATGGTAATTTTTG-GATGTTTG
*
34484 AGGGTAAAAT-GTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
34504 AGAAATTCGA
Statistics
Matches: 148, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
26 3 0.02
27 5 0.03
28 66 0.45
29 64 0.43
30 5 0.03
31 5 0.03
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGATGTTTG
Found at i:34345 original size:57 final size:57
Alignment explanation
Indices: 34284--34521 Score: 211
Period size: 57 Copynumber: 4.2 Consensus size: 57
34274 CGAAAATTTA
* * * *
34284 GGGGTAAAGTGGTAATTTTTG-GATGTTTGGGGGCAAAATGATAATTTTGGATGTTTG
1 GGGGTAAAATGGTAATTTTTGAGAAGTTTGGGGGCAAAATG-TAATTTTGGATATTCG
* * * *
34341 GGGGTAAAATAGTAATTTTTGAAAAAGTTTGGGGTC--ATTGTAATTTTGGGATATTCG
1 GGGGTAAAATGGTAATTTTTG-AGAAGTTTGGGGGCAAAATGTAATTTT-GGATATTCG
* * *
34398 GGGGTAAAATGGTAA-TTTT-AGATGTTAAGGGGG-AAAATGATAATTTTTGGATATTCA
1 GGGGTAAAATGGTAATTTTTGAGAAGTT-TGGGGGCAAAATG-TAA-TTTTGGATATTCG
* * * *
34455 GGGGAAAAAT-GTAATTTTTGAGAAGTTTGAGGGTAAAATGTAATTTTTGAGAAATTCG
1 GGGGTAAAATGGTAATTTTTGAGAAGTTTGGGGGCAAAATGTAA-TTTTG-GATATTCG
*
34513 AGGGTAAAA
1 GGGGTAAAA
34522 AATATGATTT
Statistics
Matches: 146, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
54 5 0.03
55 4 0.03
56 18 0.12
57 80 0.55
58 29 0.20
59 10 0.07
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGAGAAGTTTGGGGGCAAAATGTAATTTTGGATATTCG
Found at i:34504 original size:29 final size:29
Alignment explanation
Indices: 34285--34651 Score: 181
Period size: 29 Copynumber: 12.7 Consensus size: 29
34275 GAAAATTTAG
* * *
34285 GGGTAAAGTGGTAATTTTTG-GATGTTTGG
1 GGGTAAAAT-GTAATTTTTGAGAAGTTTGA
* * *
34314 GGGCAAAATGATAA-TTTTG-GATGTTTGG
1 GGGTAAAATG-TAATTTTTGAGAAGTTTGA
*
34342 GGGTAAAATAGTAATTTTTGAAAAAGTTTG-
1 GGGTAAAAT-GTAATTTTTG-AGAAGTTTGA
* * * * *
34372 GGGT-CATTGTAA-TTTTGGGATA-TTCGG
1 GGGTAAAATGTAATTTTTGAGA-AGTTTGA
* *
34399 GGGTAAAATGGTAA-TTTT-AGATG-TTAA
1 GGGTAAAAT-GTAATTTTTGAGAAGTTTGA
* *
34426 GGGGGAAAATGATAATTTTTG-G-A-TATTCA
1 -GGGTAAAATG-TAATTTTTGAGAAGT-TTGA
*
34455 GGGGAAAAATGTAATTTTTGAGAAGTTTGA
1 -GGGTAAAATGTAATTTTTGAGAAGTTTGA
* *
34485 GGGTAAAATGTAATTTTTGAGAAATTCGA
1 GGGTAAAATGTAATTTTTGAGAAGTTTGA
* * * *
34514 GGGTAAAAAATATGATTTTTGAGAAATTCGA
1 GGGT--AAAATGTAATTTTTGAGAAGTTTGA
* *
34545 GGGTGAAAATGTATTTTTTGAGAAGTTAG-
1 GGGT-AAAATGTAATTTTTGAGAAGTTTGA
* * * *
34574 GGGTAATAATATAATTTTAGAGAAATATGA
1 GGGTAA-AATGTAATTTTTGAGAAGTTTGA
* * *
34604 GGGTAAAAATATAA--TTTGAGAAATTTAA
1 GGGT-AAAATGTAATTTTTGAGAAGTTTGA
*
34632 GGGTGAAAATATAATTTTTG
1 GGGT-AAAATGTAATTTTTG
34652 GAAAATTCGG
Statistics
Matches: 269, Mismatches: 43, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
26 4 0.01
27 12 0.04
28 80 0.30
29 95 0.35
30 42 0.16
31 36 0.13
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGTAAAATGTAATTTTTGAGAAGTTTGA
Found at i:34563 original size:30 final size:29
Alignment explanation
Indices: 34431--34660 Score: 195
Period size: 29 Copynumber: 7.8 Consensus size: 29
34421 GTTAAGGGGG
* *
34431 AAAATGATAATTTTTG-GATATTC-AGGGGA
1 AAAAT-ATAATTTTTGAGAAATTCGA-GGGT
* * *
34460 AAAATGTAATTTTTGAGAAGTTTGAGGGT
1 AAAATATAATTTTTGAGAAATTCGAGGGT
*
34489 AAAATGTAATTTTTGAGAAATTCGAGGGT
1 AAAATATAATTTTTGAGAAATTCGAGGGT
*
34518 AAAAAATATGATTTTTGAGAAATTCGAGGGT
1 --AAAATATAATTTTTGAGAAATTCGAGGGT
* * * *
34549 GAAAATGTATTTTTTGAGAAGTTAG-GGGT
1 -AAAATATAATTTTTGAGAAATTCGAGGGT
*
34578 AATAATATAATTTTAGAGAAATAT-GAGGGT
1 AA-AATATAATTTTTGAGAAAT-TCGAGGGT
**
34608 AAAAATATAA--TTTGAGAAATTTAAGGGT
1 -AAAATATAATTTTTGAGAAATTCGAGGGT
34636 GAAAATATAATTTTTG-GAAAATTCG
1 -AAAATATAATTTTTGAG-AAATTCG
34661 GGGACCTTTT
Statistics
Matches: 165, Mismatches: 24, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.01
28 34 0.21
29 60 0.36
30 41 0.25
31 29 0.18
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (29 bp):
AAAATATAATTTTTGAGAAATTCGAGGGT
Found at i:37443 original size:51 final size:50
Alignment explanation
Indices: 37383--37561 Score: 216
Period size: 51 Copynumber: 3.5 Consensus size: 50
37373 TCATATACCT
* * * *
37383 ACGACGACACTGAGTCATCAGACCTTTAATTTGTCA-TGGATTCATTTACTC
1 ACGATGACACT-AGTCATCAGACCTTTAATTCGT-AGAGGATTCGTTTACTC
* * ** * *
37434 ACAATGACACTAATCATTGGACCTTTAATCCGTAGAGGATTTGTTTACTC
1 ACGATGACACTAGTCATCAGACCTTTAATTCGTAGAGGATTCGTTTACTC
*
37484 ACGATGACACTTAGTCATCGGACCTTTAATTCGTAGAGGATTCGTTTACTC
1 ACGATGACAC-TAGTCATCAGACCTTTAATTCGTAGAGGATTCGTTTACTC
37535 ACGATGACACCTAGTCATCAGACCTTT
1 ACGATGACA-CTAGTCATCAGACCTTT
37562 CATTTATAGC
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 38 0.35
51 69 0.63
52 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (50 bp):
ACGATGACACTAGTCATCAGACCTTTAATTCGTAGAGGATTCGTTTACTC
Found at i:38547 original size:18 final size:18
Alignment explanation
Indices: 38524--38564 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
38514 TTGGTATAAA
38524 AATTACTTAAATTAACCG
1 AATTACTTAAATTAACCG
* *
38542 AATTACTTGAATTAATCG
1 AATTACTTAAATTAACCG
38560 AATTA
1 AATTA
38565 GTCGAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (18 bp):
AATTACTTAAATTAACCG
Found at i:38571 original size:18 final size:18
Alignment explanation
Indices: 38533--38573 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38523 AAATTACTTA
*
38533 AATTAACCGAATTACTTG
1 AATTAACCGAATTACTCG
* *
38551 AATTAATCGAATTAGTCG
1 AATTAACCGAATTACTCG
38569 AATTA
1 AATTA
38574 CCCAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (18 bp):
AATTAACCGAATTACTCG
Found at i:48334 original size:80 final size:79
Alignment explanation
Indices: 48201--48359 Score: 291
Period size: 80 Copynumber: 2.0 Consensus size: 79
48191 CGATCGTGCA
*
48201 TGGGTGTTTCGTATAAGCACGATTTGGGGCACGGCTGTGTGACCCCTGTTTCGCTGAAATTTCAA
1 TGGGTGTTTCGTATAAGCACGATTTGGGGCACAGCTGTGTGACCCCTGTTTCGCTGAAATTTCAA
48266 AGTTTTGAGCGATG
66 AGTTTTGAGCGATG
*
48280 NTGGGTGTTTCGTATAAGCACGGTTTGGGGCACAGCTGTGTGACCCCTGTTTCGCTGAAATTTCA
1 -TGGGTGTTTCGTATAAGCACGATTTGGGGCACAGCTGTGTGACCCCTGTTTCGCTGAAATTTCA
48345 AAGTTTTGAGCGATG
65 AAGTTTTGAGCGATG
48360 ATTCGGTTGC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (79 bp):
TGGGTGTTTCGTATAAGCACGATTTGGGGCACAGCTGTGTGACCCCTGTTTCGCTGAAATTTCAA
AGTTTTGAGCGATG
Found at i:48415 original size:14 final size:14
Alignment explanation
Indices: 48392--48429 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
48382 CCCTTGCATG
48392 TGAT-AATGATAAA
1 TGATGAATGATAAA
48405 TGATGAATGATAAA
1 TGATGAATGATAAA
48419 TCGAATGAATG
1 T-G-ATGAATG
48430 TGTTGTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 10 0.45
15 1 0.05
16 7 0.32
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (14 bp):
TGATGAATGATAAA
Found at i:52984 original size:81 final size:81
Alignment explanation
Indices: 52892--53638 Score: 889
Period size: 81 Copynumber: 9.2 Consensus size: 81
52882 CTTGATTAGG
* * * * * * * *
52892 GGTAAAAGATTGGATGGTGTTTTAAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
52957 TTTGCCCCATGGTCGA
66 TCTGCCCCATGGTCGA
* * *
52973 GGTAAGAGATTGAATGGTGTCTTCAATCTGCCTTCTGGTTAGGGTAAAAGATTGGATGACTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
53038 TCTGCCCCATGGTCGG
66 TCTGCCCCATGGTCGA
* *
53054 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTAGCTAGGGTAAAAGATTGGATGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
53119 TCTGCCCTATGGTC-A
66 TCTGCCCCATGGTCGA
* * * * *
53134 GGGTAAGAGATT-GAGTGGTGTCTTCAATTTTCCCTCTGGTTATGATAAAAGATTGAATGGCTTC
1 -GGTAAGAGATTGGA-TGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTC
53198 AATCTGCCCCATGGTC-A
64 AATCTGCCCCATGGTCGA
**
53215 GGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATAACTTCA
1 -GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
* * * *
53280 ATTTGCCCCATGATTGG
65 ATCTGCCCCATGGTCGA
* * * *
53297 GGTAAGAGATTGAATGATGTCTTCAATCTACCCTCTGGTTAGGGTAAAAGATTGGTTGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
53362 TCTGCCTCATGGTC-A
66 TCTGCCCCATGGTCGA
* ** * *
53377 GGGTAAGA-ATTTGAAT-GTGTCTTCAATCTGCCCTCTTATTAGGGTAAAAGATTAGATGGTTTC
1 -GGTAAGAGA-TTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTC
* * *
53440 AATCTGCCCCTTGGTTGG
64 AATCTGCCCCATGGTCGA
* * *
53458 GGTAAGAGATTGGATGGTGTCTTCAATCTGCTCTCTGATTAGGGTAAAAGATTGGATGGCTTTAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
** *
53523 TCTATCCTATGGTC-A
66 TCTGCCCCATGGTCGA
* * * * * *
53538 GAGTAAGAGATTAGATAGTGTCTTCAATATGCTCTCTGGTTAGGGTAAAAGATTTGATGGGTTCA
1 G-GTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
*
53603 ATCTGTCCCATGGTCTG-
65 ATCTGCCCCATGGTC-GA
*
53620 GGTAAGAGATTTGATGGTG
1 GGTAAGAGATTGGATGGTG
53639 ATGTAATTTC
Statistics
Matches: 570, Mismatches: 84, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
80 69 0.12
81 498 0.87
82 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (81 bp):
GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
TCTGCCCCATGGTCGA
Found at i:53344 original size:243 final size:243
Alignment explanation
Indices: 52891--53638 Score: 978
Period size: 243 Copynumber: 3.1 Consensus size: 243
52881 TCTTGATTAG
* * * *
52891 GGGTAAAAGATTGGA-TGGTGTTTTAAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
* * *
52955 AATTTGCCCCATGGTCGAGGTAAGAGATTGAATGGTGTCTTCAATCTGCCTTCTGGTTAGGGTAA
66 AATCTGCCCCATGGTCG-GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
* *
53020 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGGTGTCTTCAATCTGC
130 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGC
* *
53085 CCTCTAGCTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
195 CCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
* * * *
53134 GGGTAAGAGA-TTGAGTGGTGTCTTCAATTTTCCCTCTGGTTATGATAAAAGATTGAATGGCTTC
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
53198 AATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
66 AATCTGCCCCATGGTC-GGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
* * * * *
53263 AAGATTGGATAACTTCAATTTGCCCCATGATTGGGGTAAGAGATTGAATGATGTCTTCAATCTAC
130 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGC
*
53328 CCTCTGGTTAGGGTAAAAGATTGGTTGGCTTCAATCTG-CCTCATGGTCA
195 CCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCT-ATGGTCA
* * *
53377 GGGTAAGA-ATTTGAAT-GTGTCTTCAATCTGCCCTCTTA-TTAGGGTAAAAGATT-AGATGGTT
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTC-TAGTTAGGGTAAAAGATTGA-ATGGTT
* * * *
53438 TCAATCTGCCCCTTGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCTCTCTGATTAGGGT
64 TCAATCTGCCCCATGG-TCGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGT
* * ** * * *
53503 AAAAGATTGGATGGCTTTAATCTATCCTATGGTCAGAGTAAGAGATT-AGAT-AGTGTCTTCAAT
128 AAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGA-ATGA-TGTCTTCAAT
* * * * *
53566 ATGCTCTCTGGTTAGGGTAAAAGATTTGATGGGTTCAATCTGTCCC-ATGGTCT
191 CTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTG-CCCTATGGTCA
53619 GGGTAAGAGATTTGA-TGGTG
1 GGGTAAGAGATTTGAGTGGTG
53639 ATGTAATTTC
Statistics
Matches: 442, Mismatches: 50, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
241 3 0.01
242 200 0.45
243 236 0.53
244 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (243 bp):
GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
AATCTGCCCCATGGTCGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
AGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGCC
CTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
Found at i:53968 original size:93 final size:92
Alignment explanation
Indices: 53747--54354 Score: 357
Period size: 93 Copynumber: 6.4 Consensus size: 92
53737 GGTTTTGAAA
* * * * *** *
53747 CTTCACTCCATTCCACTTTAACCTTAGGGACATTAAGATCTGCTT-TTGGCTTTAATCTGA-CCT
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTACTCATTTTAATCCGATCC-
* * * *
53810 ACAGCAACTTC-AGTGGTATAGGATCTAGTG
63 ACTGTAACTTCAAG-GATATAGGATCTGGTG
** *** * *
53840 CTTCACTCCATTCTGCTGTAACCTCAAACACATTGAGATTCATTACTCATTTTAATCCAATTCAC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTC-TTACTCATTTTAATCCGATCCAC
53905 TGTAACTTCAAGGATATAGGATCTGGTG
65 TGTAACTTCAAGGATATAGGATCTGGTG
* *** * **
53933 CTTCACTCCATTCCACTGTAACCTCAGGGATATTGAGATCTGCTT-CGTTGCTTTAATTCGGCCC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTAC-TCATTTTAATCCGATCC
* * * * *
53997 ATTATAACTT-ATGGGTATAGGATTTGGTATTG
63 ACTGTAACTTCAAGGATATAGGATCTGG---TG
* * * * *
54029 TAACTTCTCTCCATTCCACTGTAACCTTAGGGACATTGAGATCCGTACTCATTTTAATCCAATCC
1 ---CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTCTTACTCATTTTAATCCGATCC
* * *
54094 ATTGCAACTTCAAAGATATAGGATCTGGTG
63 ACTGTAACTTCAAGGATATAGGATCTGGTG
* * * ** ** * *
54124 CTTCACTCTATTCCACTGTAGCCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAATCTGACCCA
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTACTCATTTTAATCCGATCCA
** * * * *
54189 CTACAAC-TCTGAGG-TATGGGATTTGATATTGTAA
64 CTGTAACTTC-AAGGATATAGGATCTG-----GT-G
* * * * * * *
54223 CTTCTCTCCATTCCACTATAACCTTAGAGACATTAAGATTCGTTACTCATTTTGATTCGATCCAC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTC-TTACTCATTTTAATCCGATCCAC
* * *
54288 TGTAACTTTAGGGATATAGGATTTGGTG
65 TGTAACTTCAAGGATATAGGATCTGGTG
* *
54316 CTTCACTCCATTCCATTGTAATCTCAGGGACATTGAGAT
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT
54355 CTGCTTCATT
Statistics
Matches: 381, Mismatches: 107, Indels: 54
0.70 0.20 0.10
Matches are distributed among these distances:
91 1 0.00
92 37 0.10
93 154 0.40
94 47 0.12
95 3 0.01
96 2 0.01
97 21 0.06
98 38 0.10
99 78 0.20
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (92 bp):
CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTCTTACTCATTTTAATCCGATCCACT
GTAACTTCAAGGATATAGGATCTGGTG
Found at i:54067 original size:192 final size:193
Alignment explanation
Indices: 53869--54403 Score: 695
Period size: 191 Copynumber: 2.8 Consensus size: 193
53859 AACCTCAAAC
*
53869 ACATTGAGATTCATTACTCATTTTAATCCAATTCACTGTAACTTCAAGGATATAGGATCTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * *
53934 TTCACTCCATTCCACTGTAACCTCAGGGATATTGAGATCTGCTTCGTTGCTTTAATTC-GGCCCA
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
* * * * *
53998 TTATAACTTATG-GGTATAGGATTTGGTATTGTAACTTCTCTCCATTCCACTGTAACCTTAGGG
131 CTACAAC-TATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
** * * *
54061 ACATTGAGA-TCCGTACTCATTTTAATCCAATCCATTGCAACTTCAAAGATATAGGATCTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * * *
54125 TTCACTCTATTCCACTGTAGCCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAA-TCTGACCCA
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
* *
54189 CTACAACTCTGAGGTATGGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
131 CTACAACTATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
* * * * * * * *
54252 ACATTAAGATTCGTTACTCATTTTGATTCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * * *
54317 TTCACTCCATTCCATTGTAATCTCAGGGACATTGAGATCTGCTTCATTGTTTTAA-TCTG-CTTC
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGAC-CC
* * *
54380 ACTTCAACTTTGAGGTATAAGATT
130 ACTACAACTATGAGGTATAGGATT
54404 CACCATTACA
Statistics
Matches: 295, Mismatches: 44, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
190 5 0.02
191 164 0.56
192 126 0.43
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (193 bp):
ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
CTACAACTATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
Done.