Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014883.1 Kokia drynarioides strain JFW-HI SEQ_129926, 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: 526975
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 171 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:434637 original size:30 final size:30
Alignment explanation
Indices: 434603--434946 Score: 281
Period size: 30 Copynumber: 11.6 Consensus size: 30
434593 CGAGGAATTC
**
434603 GGGGTTAAAATGCCATTTTGGAGAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTA
** *
434633 GGGGTTAAAATACACTTTTGGAGAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTA
* *
434663 -GGGTAAAAATGTAATTTTAGAGAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTA
* * * ** *
434692 AGGGCTAAAATGTAAGTTTAAAGAAATTTA
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTA
* * *
434722 GGGGTTAAAATGTAATTTTAGAAAATTTTTA
1 GGGGTTAAAATGTAATTTTGGAGAA-GTTTA
* * *
434753 -GGGTCAAAATGTGATTTTAG-GAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTA
* * * ** *
434781 AGGGTCAAAATATAATTTTAAAGAAATTTA
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTA
* * *
434811 CGGGTCAAAATATAATTTTGGAGAAGTTT-
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTA
* * *
434840 GGGGTCAAATTGCAATTTTTGGAGAAGTTT-
1 GGGGTTAAAATGTAA-TTTTGGAGAAGTTTA
*
434870 GGGGTTAAAATGTGATTTTGG-GAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAG-AAGTTTA
** *
434900 AAGGTTAAAATATAA-TTTGGAGAAGTTT-
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTA
*
434928 GGGGTTAAAATGTGATTTT
1 GGGGTTAAAATGTAATTTT
434947 TAAAGAAAAT
Statistics
Matches: 258, Mismatches: 47, Indels: 19
0.80 0.15 0.06
Matches are distributed among these distances:
28 16 0.06
29 80 0.31
30 158 0.61
31 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTGGAGAAGTTTA
Found at i:434680 original size:59 final size:58
Alignment explanation
Indices: 434617--434938 Score: 217
Period size: 59 Copynumber: 5.5 Consensus size: 58
434607 TTAAAATGCC
* * *
434617 ATTTTGGAGAAGTTTAGGGGTTAAAATACACTTTTGGAGAAGTTTAGGGTAAAAATGTA
1 ATTTTAGAGAAGTTTAGGGGTTAAAATAGA-TTTTGGAGAAGTTTAGGGTCAAAATGTA
* * * ** * *
434676 ATTTTAGAGAAGTTTAAGGGCTAAAAT-GTAAGTTTAAAGAAATTTAGGGGTTAAAATGTA
1 ATTTTAGAGAAGTTTAGGGGTTAAAATAG--ATTTTGGAGAAGTTTA-GGGTCAAAATGTA
* * * * * *
434736 ATTTTAGAAAATTTTTA-GGGTCAAAATGTGATTTTAG-GAAGTTTAAGGGTCAAAATATA
1 ATTTTAGAGAA-GTTTAGGGGTTAAAAT-AGATTTTGGAGAAGTTT-AGGGTCAAAATGTA
* * * * * * * *
434795 ATTTTAAAGAAATTTACGGGTCAAAATATAATTTTGGAGAAGTTTGGGGTCAAATTGCA
1 ATTTTAGAGAAGTTTAGGGGTTAAAATA-GATTTTGGAGAAGTTTAGGGTCAAAATGTA
* * * * *
434854 ATTTTTGGAGAAGTTT-GGGGTTAAAATGTGATTTTGG-GAAAGTTTAAAGGTTAAAATATA
1 A-TTTTAGAGAAGTTTAGGGGTTAAAAT-AGATTTTGGAG-AAGTTT-AGGGTCAAAATGTA
*
434914 A-TTTGGAGAAGTTT-GGGGTTAAAAT
1 ATTTTAGAGAAGTTTAGGGGTTAAAAT
434939 GTGATTTTTA
Statistics
Matches: 208, Mismatches: 41, Indels: 29
0.75 0.15 0.10
Matches are distributed among these distances:
58 29 0.14
59 110 0.53
60 64 0.31
61 4 0.02
62 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (58 bp):
ATTTTAGAGAAGTTTAGGGGTTAAAATAGATTTTGGAGAAGTTTAGGGTCAAAATGTA
Found at i:434880 original size:89 final size:89
Alignment explanation
Indices: 434604--434946 Score: 343
Period size: 89 Copynumber: 3.9 Consensus size: 89
434594 GAGGAATTCG
** ** * * * *
434604 GGGTTAAAATGCCATTTTGGAGAAGTTTAGGGGTTAAAATACACTTTTGGAGAAGTTTAGGGTAA
1 GGGTTAAAATGTAATTTTAAAGAAATTTAGGGGTTAAAATATAATTTTGGAGAAGTTTAGGGTCA
434669 AAATGTAATTTTAGAGAAGTTTAA
66 AAATGTAATTTTAGAGAAGTTTAA
* * * * * *
434693 GGGCTAAAATGTAAGTTTAAAGAAATTTAGGGGTTAAAATGTAATTTTAGAAAATTTTTAGGGTC
1 GGGTTAAAATGTAATTTTAAAGAAATTTAGGGGTTAAAATATAATTTTGGAGAA-GTTTAGGGTC
*
434758 AAAATGTGATTTTAG-GAAGTTTAA
65 AAAATGTAATTTTAGAGAAGTTTAA
* * * * *
434782 GGGTCAAAATATAATTTTAAAGAAATTTACGGGTCAAAATATAATTTTGGAGAAGTTTGGGGTCA
1 GGGTTAAAATGTAATTTTAAAGAAATTTAGGGGTTAAAATATAATTTTGGAGAAGTTTAGGGTCA
* * * *
434847 AATTGCAATTTTTGGAGAAGTTT-G
66 AAATGTAA-TTTTAGAGAAGTTTAA
* ** ** * *
434871 GGGTTAAAATGTGATTTT-GGGAAAGTTTAAAGGTTAAAATATAA-TTTGGAGAAGTTTGGGGTT
1 GGGTTAAAATGTAATTTTAAAGAAA-TTTAGGGGTTAAAATATAATTTTGGAGAAGTTTAGGGTC
*
434934 AAAATGTGATTTT
65 AAAATGTAATTTT
434947 TAAAGAAAAT
Statistics
Matches: 207, Mismatches: 43, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
87 4 0.02
88 42 0.20
89 132 0.64
90 29 0.14
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (89 bp):
GGGTTAAAATGTAATTTTAAAGAAATTTAGGGGTTAAAATATAATTTTGGAGAAGTTTAGGGTCA
AAATGTAATTTTAGAGAAGTTTAA
Found at i:436206 original size:24 final size:23
Alignment explanation
Indices: 436141--436206 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 23
436131 ATTTTGCTTC
436141 TTTTGTATTGATTTCGAATCTGA
1 TTTTGTATTGATTTCGAATCTGA
* *
436164 TCTCT-TA-TGTATTTTGAATCACT-A
1 T-TTTGTATTG-ATTTCGAAT--CTGA
436188 TTTTGTATTGATTTCGAAT
1 TTTTGTATTGATTTCGAAT
436207 GCCAGAAGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 14 0.42
25 4 0.12
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.53
Consensus pattern (23 bp):
TTTTGTATTGATTTCGAATCTGA
Found at i:437149 original size:39 final size:39
Alignment explanation
Indices: 437088--437503 Score: 247
Period size: 39 Copynumber: 10.7 Consensus size: 39
437078 GATGGTTGCA
* * *
437088 ATCTACCCCTGGCTCGGTGTAAGAGATTGGCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * **
437127 ACCTGCCCCAAGCTCAGGGTAAGAGA-T--CAAATGACTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGA-TG
* * *
437164 CAATCTGCCCCAGGCTCGAGGTAAGAGATTGACTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * *
437205 ATCTGCCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * *
437244 ATCTACCTCAGGCTCGAGGTAAGAAATGAATGGCTG--CA--
1 ATCTGCCCCAGGCTCGGGGTAAG--A-GATTGGCTGATGATG
*** * *
437282 ATCTGCCCCAGGCTCGGGGTAAGAGATACACTAATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * * **
437321 ACCTGCCCCAAGCTCGGGGTAAGAGATCGGATGGCT-ACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCT-GATGATG
* * * * *
437360 ATCTGCCACAGGCTCAGGGTAAGAGATTAGTTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * * **
437399 ATCTACCCCAGGCTCGGGGTAAAAGATCGGATGGCT-ACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCT-GATGATG
* * * * * *
437438 ATCTGTCCTAGGCTCAGGGTAAGAGATTGACTAATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
*
437477 ATCTGCCCCAAGCTCGGGGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
437504 CCGACGGTTA
Statistics
Matches: 273, Mismatches: 87, Indels: 34
0.69 0.22 0.09
Matches are distributed among these distances:
35 4 0.01
36 6 0.02
37 2 0.01
38 24 0.09
39 219 0.80
40 4 0.01
41 3 0.01
42 11 0.04
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
Found at i:437256 original size:78 final size:78
Alignment explanation
Indices: 437088--437503 Score: 325
Period size: 78 Copynumber: 5.3 Consensus size: 78
437078 GATGGTTGCA
* * * * * *
437088 ATCTACCCCTGGCTCGGTGTAAGAGATTGGCTGAT-GATGACCTGCCCCAAGCTCAGGGTAAGAG
1 ATCTACCCCAGGCTCGGGGTAAGAGATT-GCGGATGGCTGATCTGCCCCAGGCTCAGGGTAAGAG
* ** **
437152 ATCAAATGACT-GCA
65 ATTAGCTGA-TGGTG
* * * * *
437166 ATCTGCCCCAGGCTCGAGGTAAGAGATTGACTGATGG-TGATCTGCCCTAGGCTCGGGGTAAGAG
1 ATCTACCCCAGGCTCGGGGTAAGAGATTG-CGGATGGCTGATCTGCCCCAGGCTCAGGGTAAGAG
437230 ATTAGCTGATGGTG
65 ATTAGCTGATGGTG
* * * * *
437244 ATCTACCTCAGGCTCGAGGTAAGA-AAT--GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGA
1 ATCTACCCCAGGCTCGGGGTAAGAGATTGCGGATGGCTG--ATCTGCCCCAGGCTCAGGGTAAGA
* *
437306 GA-TACACTAATGGTG
64 GATTA-GCTGATGGTG
* * * * *
437321 ACCTGCCCCAAGCTCGGGGTAAGAGA-T-CGGATGGCTACAATCTGCCACAGGCTCAGGGTAAGA
1 ATCTACCCCAGGCTCGGGGTAAGAGATTGCGGATGGCT--GATCTGCCCCAGGCTCAGGGTAAGA
*
437384 GATTAGTTGATGGTG
64 GATTAGCTGATGGTG
* * * *
437399 ATCTACCCCAGGCTCGGGGTAAAAGA-T-CGGATGGCTACAATCTGTCCTAGGCTCAGGGTAAGA
1 ATCTACCCCAGGCTCGGGGTAAGAGATTGCGGATGGCT--GATCTGCCCCAGGCTCAGGGTAAGA
*
437462 GATT-GACTAATGGTG
64 GATTAG-CTGATGGTG
* *
437477 ATCTGCCCCAAGCTCGGGGTAAGAGAT
1 ATCTACCCCAGGCTCGGGGTAAGAGAT
437504 CCGACGGTTA
Statistics
Matches: 279, Mismatches: 45, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
74 4 0.01
75 2 0.01
76 2 0.01
77 58 0.21
78 210 0.75
79 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (78 bp):
ATCTACCCCAGGCTCGGGGTAAGAGATTGCGGATGGCTGATCTGCCCCAGGCTCAGGGTAAGAGA
TTAGCTGATGGTG
Found at i:437308 original size:116 final size:117
Alignment explanation
Indices: 437094--437347 Score: 325
Period size: 116 Copynumber: 2.2 Consensus size: 117
437084 TGCAATCTAC
* * * *
437094 CCCT-GGCTCGGTGTAAGAGATTGGCTGATGATGACCTGCCCCAAGCTCAGGGTAAGAGATCAAA
1 CCCTAGGCTCGGGGTAAGAGATTAGCTGATGATGACCTACCCCAAGCTCAGGGTAAGAAATCAAA
** * *
437158 TGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATCTG
66 TGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATACACTAATGGTGACCTG
* * * * *
437210 CCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTACCTCAGGCTC-GAGGTAAGAAAT-GA
1 CCCTAGGCTCGGGGTAAGAGATTAGCTGATGATGACCTACCCCAAGCTCAG-GGTAAGAAATCAA
* *
437273 ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATACACTAATGGTGACCTG
65 ATGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATACACTAATGGTGACCTG
* *
437326 CCCCAAGCTCGGGGTAAGAGAT
1 CCCTAGGCTCGGGGTAAGAGAT
437348 CGGATGGCTA
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
116 73 0.61
117 46 0.39
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (117 bp):
CCCTAGGCTCGGGGTAAGAGATTAGCTGATGATGACCTACCCCAAGCTCAGGGTAAGAAATCAAA
TGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATACACTAATGGTGACCTG
Found at i:437372 original size:116 final size:115
Alignment explanation
Indices: 437138--437383 Score: 291
Period size: 116 Copynumber: 2.1 Consensus size: 115
437128 CCTGCCCCAA
* * ** *
437138 GCTCAGGGTAAGAGATCAAATGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGACTGATGG
1 GCTCAGGGTAAGAAAT-GAATGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATACACTAATGG
* * * * * *
437203 TGATCTGCCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTACCTCAG
65 TGACCTGCCCCAAGCTCGGGGTAAGAGATTA-CGGATGGTAATCTACCACAG
* *
437255 GCTC-GAGGTAAGAAATGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATACACTAATGG
1 GCTCAG-GGTAAGAAATGAATGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATACACTAATGG
*
437319 TGACCTGCCCCAAGCTCGGGGTAAGAGA-T-CGGATGGCTACAATCTGCCACAG
65 TGACCTGCCCCAAGCTCGGGGTAAGAGATTACGGATGG-T--AATCTACCACAG
437371 GCTCAGGGTAAGA
1 GCTCAGGGTAAGA
437384 GATTAGTTGA
Statistics
Matches: 110, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
113 6 0.05
114 1 0.01
115 1 0.01
116 88 0.80
117 14 0.13
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (115 bp):
GCTCAGGGTAAGAAATGAATGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATACACTAATGGT
GACCTGCCCCAAGCTCGGGGTAAGAGATTACGGATGGTAATCTACCACAG
Found at i:437461 original size:194 final size:194
Alignment explanation
Indices: 437079--437503 Score: 465
Period size: 194 Copynumber: 2.2 Consensus size: 194
437069 AAGACGTTGG
* * * *** *
437079 ATGGTTGCAATCTACCCCTGGCTCGGTGTAAGAGATTGGCTGATGATGACCTGCCCCAAGCTCAG
1 ATGG-TGCAATCTGCCCCAGGCTCGGGGTAAGAGATACACTAATGATGACCTGCCCCAAGCTCAG
* *
437144 GGTAAGAGATCAAATGACTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATCT
65 GGTAAGAGATCAAATGACTACAATCTGCCACAGGCTCGAGGTAAGAGATTGACTGATGGTGATCT
* * * * *
437209 GCCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTACCTCAGGCTCGAGGTAAGA-AATG-
130 ACCCCAGGCTCGGGGTAAAAGATTA-CGGATGGTAATCTACCTCAGGCTCGAGGTAAGAGAATGA
437272 A
194 A
* *
437273 ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATACACTAATGGTGACCTGCCCCAAGCTCGG
1 ATGG-TGCAATCTGCCCCAGGCTCGGGGTAAGAGATACACTAATGATGACCTGCCCCAAGCTCAG
** * *
437338 GGTAAGAGATCGGATGGCTACAATCTGCCACAGGCTC-AGGGTAAGAGATT-AGTTGATGGTGAT
65 GGTAAGAGATCAAATGACTACAATCTGCCACAGGCTCGA-GGTAAGAGATTGA-CTGATGGTGAT
*
437401 CTACCCCAGGCTCGGGGTAAAAGA-T-CGGATGGCTACAATCTGTCCT-AGGCTC-AGGGTAAGA
128 CTACCCCAGGCTCGGGGTAAAAGATTACGGATGG-T--AATCT-ACCTCAGGCTCGA-GGTAAGA
*
437462 GATTGACTA
188 GAATGA--A
*
437471 ATGGTG--ATCTGCCCCAAGCTCGGGGTAAGAGAT
1 ATGGTGCAATCTGCCCCAGGCTCGGGGTAAGAGAT
437504 CCGACGGTTA
Statistics
Matches: 196, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
191 6 0.03
192 1 0.01
193 4 0.02
194 146 0.74
195 32 0.16
197 2 0.01
198 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (194 bp):
ATGGTGCAATCTGCCCCAGGCTCGGGGTAAGAGATACACTAATGATGACCTGCCCCAAGCTCAGG
GTAAGAGATCAAATGACTACAATCTGCCACAGGCTCGAGGTAAGAGATTGACTGATGGTGATCTA
CCCCAGGCTCGGGGTAAAAGATTACGGATGGTAATCTACCTCAGGCTCGAGGTAAGAGAATGAA
Found at i:437502 original size:156 final size:155
Alignment explanation
Indices: 437205--437504 Score: 451
Period size: 156 Copynumber: 1.9 Consensus size: 155
437195 ACTGATGGTG
* *
437205 ATCTGCCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTACCTCAGGCTCGAGGTAAGAAA
1 ATCTGCCCTAGGCTCAGGGTAAGAGATTAGCTGATGGTGATCTACCCCAGGCTCGAGGTAAGAAA
* *
437270 TGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATACACTAATGGTGACCTGCCCCAAGCT
66 TGAATGGCTACAATCTGCCCCAGGCTCAGGGTAAGAGATACACTAATGGTGACCTGCCCCAAGCT
437335 CGGGGTAAGAGATCGGATGGCTACA
131 CGGGGTAAGAGATCGGATGGCTACA
* *
437360 ATCTGCCAC-AGGCTCAGGGTAAGAGATTAGTTGATGGTGATCTACCCCAGGCTCGGGGTAA-AA
1 ATCTGCC-CTAGGCTCAGGGTAAGAGATTAGCTGATGGTGATCTACCCCAGGCTCGAGGTAAGAA
* * * ** *
437423 GATCGGATGGCTACAATCTGTCCTAGGCTCAGGGTAAGAGATTGACTAATGGTGATCTGCCCCAA
65 -AT-GAATGGCTACAATCTGCCCCAGGCTCAGGGTAAGAGATACACTAATGGTGACCTGCCCCAA
437488 GCTCGGGGTAAGAGATC
128 GCTCGGGGTAAGAGATC
437505 CGACGGTTAT
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
154 2 0.02
155 57 0.44
156 71 0.55
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22
Consensus pattern (155 bp):
ATCTGCCCTAGGCTCAGGGTAAGAGATTAGCTGATGGTGATCTACCCCAGGCTCGAGGTAAGAAA
TGAATGGCTACAATCTGCCCCAGGCTCAGGGTAAGAGATACACTAATGGTGACCTGCCCCAAGCT
CGGGGTAAGAGATCGGATGGCTACA
Found at i:437523 original size:78 final size:78
Alignment explanation
Indices: 437166--437504 Score: 375
Period size: 78 Copynumber: 4.4 Consensus size: 78
437156 AATGACTGCA
* * * * *
437166 ATCTGCCCCAGGCTCGAGGTAAGAGATTGACTGATGG-T--GATCTGCCCTAGGCTCGGGGTAAG
1 ATCTGCCCCAGGCTCGGGGTAAGAGA-T--CGGATGGCTACAATCTGCCCCAGGCTCAGGGTAAG
*
437228 AGATTAGCTGATGGTG
63 AGATTAGCTAATGGTG
* * * * * * *
437244 ATCTACCTCAGGCTCGAGGTAAGAAAT-GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGGCTACAATCTGCCCCAGGCTCAGGGTAAGAGA
*
437308 -TACACTAATGGTG
66 TTA-GCTAATGGTG
* * *
437321 ACCTGCCCCAAGCTCGGGGTAAGAGATCGGATGGCTACAATCTGCCACAGGCTCAGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGGCTACAATCTGCCCCAGGCTCAGGGTAAGAGA
* *
437386 TTAGTTGATGGTG
66 TTAGCTAATGGTG
* * * *
437399 ATCTACCCCAGGCTCGGGGTAAAAGATCGGATGGCTACAATCTGTCCTAGGCTCAGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGGCTACAATCTGCCCCAGGCTCAGGGTAAGAGA
437464 TT-GACTAATGGTG
66 TTAG-CTAATGGTG
*
437477 ATCTGCCCCAAGCTCGGGGTAAGAGATC
1 ATCTGCCCCAGGCTCGGGGTAAGAGATC
437505 CGACGGTTAT
Statistics
Matches: 220, Mismatches: 34, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
74 4 0.02
75 1 0.00
76 2 0.01
77 56 0.25
78 155 0.70
79 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22
Consensus pattern (78 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGGCTACAATCTGCCCCAGGCTCAGGGTAAGAGA
TTAGCTAATGGTG
Found at i:449220 original size:30 final size:29
Alignment explanation
Indices: 449166--449490 Score: 309
Period size: 30 Copynumber: 10.9 Consensus size: 29
449156 GAAAAAGAAG
* *
449166 TTTTGGGGAA-TTTAGGGTTGAAATGCT-A
1 TTTTGGAGAAGTTTAGGGTTAAAATG-TAA
*
449194 TTTTGGAGAAGTTTAGGGGTTAAAATGCAA
1 TTTTGGAGAAGTTTA-GGGTTAAAATGTAA
*
449224 TTTTGGAGAAGTTTAAGGGTTTAAATGTAA
1 TTTTGGAGAAGTTT-AGGGTTAAAATGTAA
* * *
449254 GTTTAGAGAAATTTAGGGGTTAAAATGTAA
1 TTTTGGAGAAGTTTA-GGGTTAAAATGTAA
* * *
449284 TTTTAGGA-AAGTTTTAAGGTCAAAAATGTGA
1 TTTT-GGAGAAG-TTTAGGGT-TAAAATGTAA
449315 TTTTAGG-GAAGTTTAAGGGTTAAAATGTAA
1 TTTT-GGAGAAGTTT-AGGGTTAAAATGTAA
* *
449345 TTTTGAAGAAGTTTAAAGGTTAAAATGTAA
1 TTTTGGAGAAGTTT-AGGGTTAAAATGTAA
*
449375 TTTTGGAGAAGTTTAGGGTTAAAATGTATT
1 TTTTGGAGAAGTTTAGGGTTAAAATGTA-A
* * *
449405 TTTTAGAGAAGTTTAGGGTCAAAATGTGA
1 TTTTGGAGAAGTTTAGGGTTAAAATGTAA
*
449434 TTTTAGGA-AAGTTTAAGGGTTAAAATATAA
1 TTTT-GGAGAAGTTT-AGGGTTAAAATGTAA
* *
449464 TTTTGGAAAAGATTTGGGGGTTAAAAT
1 TTTTGGAGAAG-TTT-AGGGTTAAAAT
449491 ATTATTTTTT
Statistics
Matches: 248, Mismatches: 33, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
28 9 0.04
29 32 0.13
30 165 0.67
31 42 0.17
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (29 bp):
TTTTGGAGAAGTTTAGGGTTAAAATGTAA
Found at i:449409 original size:121 final size:119
Alignment explanation
Indices: 449193--449468 Score: 378
Period size: 121 Copynumber: 2.3 Consensus size: 119
449183 TTGAAATGCT
* * * * *
449193 ATTTT-GGAGAAGTTTAGGGGTTAAAATGCAATTTTGGAGAAGTTTAAGGGTTTAAATGTAAGTT
1 ATTTTAGG-GAAGTTTAAGGGTTAAAATGTAATTTTGAAGAAGTTTAAAGGTTAAAATGTAAGTT
449257 TAGAGAAATTTAGGGGTTAAAATGTAATTTTAG-GAAAGTTTTAAGGTCAAAAATGTG
65 TAGAGAAATTTAGGGGTTAAAATGTAATTTTAGAG-AAG-TTTAAGGTC-AAAATGTG
*
449314 ATTTTAGGGAAGTTTAAGGGTTAAAATGTAATTTTGAAGAAGTTTAAAGGTTAAAATGTAATTTT
1 ATTTTAGGGAAGTTTAAGGGTTAAAATGTAATTTTGAAGAAGTTTAAAGGTTAAAATGTAAGTTT
* * * *
449379 GGAGAAGTTTA-GGGTTAAAATGTATTTTTTAGAGAAGTTTAGGGTCAAAATGTG
66 AGAGAAATTTAGGGGTTAAAATGTA-ATTTTAGAGAAGTTTAAGGTCAAAATGTG
* *
449433 ATTTTAGGAAAGTTTAAGGGTTAAAATATAATTTTG
1 ATTTTAGGGAAGTTTAAGGGTTAAAATGTAATTTTG
449469 GAAAAGATTT
Statistics
Matches: 140, Mismatches: 12, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
119 42 0.30
120 21 0.15
121 74 0.53
122 3 0.02
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (119 bp):
ATTTTAGGGAAGTTTAAGGGTTAAAATGTAATTTTGAAGAAGTTTAAAGGTTAAAATGTAAGTTT
AGAGAAATTTAGGGGTTAAAATGTAATTTTAGAGAAGTTTAAGGTCAAAATGTG
Found at i:449793 original size:29 final size:29
Alignment explanation
Indices: 449761--449825 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
449751 AAAATGAAAT
*
449761 AAAATTAATAGGCAATTTTAAAATTAATA
1 AAAAATAATAGGCAATTTTAAAATTAATA
*
449790 AAAAATACTAGGCAATTTTAAAATTAATA
1 AAAAATAATAGGCAATTTTAAAATTAATA
449819 AAAAATA
1 AAAAATA
449826 CAAAAAGGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAAATAATAGGCAATTTTAAAATTAATA
Found at i:449826 original size:29 final size:29
Alignment explanation
Indices: 449769--449826 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
449759 ATAAAATTAA
449769 TAGGCAATTTTAAAATTAATAAAAAATAC
1 TAGGCAATTTTAAAATTAATAAAAAATAC
449798 TAGGCAATTTTAAAATTAATAAAAAATAC
1 TAGGCAATTTTAAAATTAATAAAAAATAC
449827 AAAAAGGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
TAGGCAATTTTAAAATTAATAAAAAATAC
Found at i:458180 original size:28 final size:28
Alignment explanation
Indices: 458148--458204 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
458138 TGTTATCTGC
458148 TTGATGTTTCTGAAACTAGACTCAATTA
1 TTGATGTTTCTGAAACTAGACTCAATTA
458176 TTGATGTTTCTGAAACTAGACTCAATTA
1 TTGATGTTTCTGAAACTAGACTCAATTA
458204 T
1 T
458205 CTTTTTATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (28 bp):
TTGATGTTTCTGAAACTAGACTCAATTA
Found at i:463917 original size:22 final size:21
Alignment explanation
Indices: 463877--463947 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 21
463867 ATATCAATAT
463877 TAATATAATTTTATTTAATTTTTA
1 TAATA-AATTTTA--TAATTTTTA
463901 TAA-AAATTATTTATAATTTTTA
1 TAATAAA-T-TTTATAATTTTTA
* *
463923 TAATACATTTTATAATTTTAA
1 TAATAAATTTTATAATTTTTA
463944 TAAT
1 TAAT
463948 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 16 0.38
22 15 0.36
23 4 0.10
24 7 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATAAATTTTATAATTTTTA
Found at i:463922 original size:9 final size:9
Alignment explanation
Indices: 463880--463950 Score: 52
Period size: 9 Copynumber: 7.0 Consensus size: 9
463870 TCAATATTAA
463880 TATAATTTT
1 TATAATTTT
*
463889 ATTTAATTTT
1 -TATAATTTT
463899 TATAAAAATTATT
1 TAT---AATT-TT
463912 TATAATTTT
1 TATAATTTT
463921 TATAATACATTT
1 TATAAT---TTT
463933 TATAATTTT
1 TATAATTTT
*
463942 AATAATTTT
1 TATAATTTT
463951 AAAAATATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
9 21 0.41
10 12 0.24
12 13 0.25
13 5 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (9 bp):
TATAATTTT
Found at i:463934 original size:21 final size:23
Alignment explanation
Indices: 463892--463947 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 23
463882 TAATTTTATT
463892 TAATTTTTATAA-AAATTATTTA
1 TAATTTTTATAATAAATTATTTA
*
463914 TAATTTTTATAATACA-T-TTTA
1 TAATTTTTATAATAAATTATTTA
*
463935 TAATTTTAATAAT
1 TAATTTTTATAAT
463948 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 16 0.52
22 13 0.42
23 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATTTTTATAATAAATTATTTA
Found at i:465685 original size:21 final size:21
Alignment explanation
Indices: 465659--465704 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
465649 CTAACTTCTT
*
465659 TGTTGCGACATACAGGGGTTA
1 TGTTGCGACATACAGGGGCTA
*
465680 TGTTGCGACATACATGGGCTA
1 TGTTGCGACATACAGGGGCTA
465701 TGTT
1 TGTT
465705 CCAGCAACGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
TGTTGCGACATACAGGGGCTA
Found at i:466140 original size:139 final size:139
Alignment explanation
Indices: 465890--466173 Score: 559
Period size: 139 Copynumber: 2.0 Consensus size: 139
465880 AAAATGGTTG
*
465890 GCCAAGGCTATAAATAAGGCATTTAGCACTAGGTTTAAACACACCATTTACTAGCTTTTAGTTTT
1 GCCAATGCTATAAATAAGGCATTTAGCACTAGGTTTAAACACACCATTTACTAGCTTTTAGTTTT
465955 TACTTTGTATTTTCATTTTAGAAACAAGATTGTAGAACTTGCATAAGCGTTCGAGGAATTTTTCT
66 TACTTTGTATTTTCATTTTAGAAACAAGATTGTAGAACTTGCATAAGCGTTCGAGGAATTTTTCT
466020 CGACAGATT
131 CGACAGATT
466029 GCCAATGCTATAAATAAGGCATTTAGCACTAGGTTTAAACACACCATTTACTAGCTTTTAGTTTT
1 GCCAATGCTATAAATAAGGCATTTAGCACTAGGTTTAAACACACCATTTACTAGCTTTTAGTTTT
466094 TACTTTGTATTTTCATTTTAGAAACAAGATTGTAGAACTTGCATAAGCGTTCGAGGAATTTTTCT
66 TACTTTGTATTTTCATTTTAGAAACAAGATTGTAGAACTTGCATAAGCGTTCGAGGAATTTTTCT
466159 CGACAGATT
131 CGACAGATT
466168 GCCAAT
1 GCCAAT
466174 ACAATTAAAG
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 144 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (139 bp):
GCCAATGCTATAAATAAGGCATTTAGCACTAGGTTTAAACACACCATTTACTAGCTTTTAGTTTT
TACTTTGTATTTTCATTTTAGAAACAAGATTGTAGAACTTGCATAAGCGTTCGAGGAATTTTTCT
CGACAGATT
Found at i:466350 original size:36 final size:36
Alignment explanation
Indices: 466303--466373 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
466293 AAGTATGATT
466303 TTTTAAATGTTGATTAATAGATATTTCTCATTTCGG
1 TTTTAAATGTTGATTAATAGATATTTCTCATTTCGG
466339 TTTTAAATGTTGATTAATAGATATTTCTCATTTCG
1 TTTTAAATGTTGATTAATAGATATTTCTCATTTCG
466374 AATCAACTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (36 bp):
TTTTAAATGTTGATTAATAGATATTTCTCATTTCGG
Found at i:476071 original size:172 final size:172
Alignment explanation
Indices: 475762--476103 Score: 535
Period size: 172 Copynumber: 2.0 Consensus size: 172
475752 GGATTCTCAA
*
475762 TATCACTAGGAAAAGTGCCTGGTGATCTTATACTCAAATTAGAAGCCAACTGTCCTAGTTGGGTT
1 TATCACTAGGAAAAGTGCCTGGTGATCTTATACTCAAATTAGAAGCCAACTGTCCTAGTTAGGTT
* * * * *
475827 TCCAATGCACGGATAGAAGAAGAATTACCTTGATCAATTACTTTAGTTCGCGTAATTTGCTTTCA
66 TCCAATGCACGAATAGAAGAAGAATTACCTTGATAAATTACTTCAGTTCGCGTAATATGCTCTCA
* *
475892 TGTCAGTGCTTCAAGAGTAGCCATAGGATCTGATCTTTGTAG
131 CGTCAGTGCTTCAAGAGCAGCCATAGGATCTGATCTTTGTAG
* *
475934 TATCACTAGG-AAAGCTGCCTGGTGATCTTGTACTCAAATTAGAAGCCAATTGTCCTAGTTAGGT
1 TATCACTAGGAAAAG-TGCCTGGTGATCTTATACTCAAATTAGAAGCCAACTGTCCTAGTTAGGT
* *
475998 TTCCAATGCATGAATAGAAGAAGAATTACCTTGGA-AAATTACTTCAGTTCGTGTAATATGCTCT
65 TTCCAATGCACGAATAGAAGAAGAATTACCTT-GATAAATTACTTCAGTTCGCGTAATATGCTCT
*
476062 CGCGTCAGTGCTTCAAGAGCAGCCATAGGATCTGATCTTTGT
129 CACGTCAGTGCTTCAAGAGCAGCCATAGGATCTGATCTTTGT
476104 TGAGAAAACT
Statistics
Matches: 155, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
171 4 0.03
172 149 0.96
173 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (172 bp):
TATCACTAGGAAAAGTGCCTGGTGATCTTATACTCAAATTAGAAGCCAACTGTCCTAGTTAGGTT
TCCAATGCACGAATAGAAGAAGAATTACCTTGATAAATTACTTCAGTTCGCGTAATATGCTCTCA
CGTCAGTGCTTCAAGAGCAGCCATAGGATCTGATCTTTGTAG
Found at i:476301 original size:14 final size:15
Alignment explanation
Indices: 476272--476301 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
476262 ATTATTGTTG
476272 TAACTCCCTTGTCTA
1 TAACTCCCTTGTCTA
476287 TAACTCCCTTG-CTA
1 TAACTCCCTTGTCTA
476301 T
1 T
476302 GAGGAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (15 bp):
TAACTCCCTTGTCTA
Found at i:514543 original size:19 final size:17
Alignment explanation
Indices: 514508--514559 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
514498 GGGTGTTAAG
*
514508 GAAGAGGAGGAAGAAGA
1 GAAGAGGAAGAAGAAGA
514525 GAAGAGAGAAGAAGCAAGA
1 GAAGAG-GAAGAAG-AAGA
* *
514544 GAAAAAGAA-AAGAAGA
1 GAAGAGGAAGAAGAAGA
514560 AGAATTTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
18 9 0.30
19 8 0.27
ACGTcount: A:0.62, C:0.02, G:0.37, T:0.00
Consensus pattern (17 bp):
GAAGAGGAAGAAGAAGA
Found at i:517034 original size:597 final size:597
Alignment explanation
Indices: 515871--517042 Score: 1808
Period size: 597 Copynumber: 2.0 Consensus size: 597
515861 TTTGGGGGTG
* *
515871 TGATATCATTAGAAATAACCATTAAATTCTCCCTAATTAGAGTATAAGTTGTTCCCTTTGTATCA
1 TGATAGCATTAGAAATAACCATTAAATTCTCCCTAATTAAAGTATAAGTTGTTCCCTTTGTATCA
* * *
515936 TATTTAGCATACATTTTCAGCATTTTATACTTAGTAATTGCATTTTCTAAGTCAGTATTGTATGG
66 TATTTAACATACATTTTCAACATTTTATACTTAATAATTGCATTTTCTAAGTCAGTATTGTATGG
* * *
516001 TCTTATTTTCTTTCATTTGATCCCATTAGTGCTACTAATGTCGCTACGTTTAGTATCAGTTTTTG
131 TCATATTTTCTTTCATTTGATCCCATTAGTGCTACTAATGTCACTACATTTAGTATCAGTTTTTG
* *
516066 CGTCTAAAGATGTCAGCGCAGGAATCCATCTTAAAAGATCGAAGCAGGAAAGCATTCAGAGCTGT
196 CGTCTAAAGATGTCAGCGCAGGAATCCATCTTAAAAGATCAAAGCAAGAAAGCATTCAGAGCTGT
* * *
516131 AGCCACAAGTTCGATATAGAACTATGCCTAAATATGTCACCGCATGAATACTTCTAGATTACAAT
261 AGCCACAAGTTCGATATAAAACTACGCCTAAATATGTCACCGCATGAATACTTCCAGATTACAAT
* * ** * *
516196 AGGGACTTTAAGCTACTAACATATCCAGAAGCTCCAGTGCATGAAAATGTCAAGTTATCGCAGTG
326 AGGGAATTTAAGCTACTAACATATCCAGAAGCACCAGCACATGAAAATGTCAAGTTATCACAGCG
** *
516261 AATAAAAATATAAATTTGCGTCCGGTAATGTCGCGACAACCTGCAACTTCCTAATGCATAAACCA
391 AATAAAAATATAAATTTGCACCCAGTAATGTCGCGACAACCTGCAACTTCCTAATGCATAAACCA
* * * *
516326 GATCTGCGTGAGTATACAGCTGGAGTAACTAACTTGTACTGCTGCAAGGAAGTTAGATCTGAGAA
456 GATATGCGTGAGTATACAGATGGAGTAACTAACATGTACAGCTGCAAGGAAGTTAGATCTGAGAA
*
516391 AAGGAGGATACCTATACTGGCTAGCAATCACAAATAAAGGGGAGAGAGAGAAAATGAAAAAAGAG
521 AAGGAGGATACCTATACTGGCTAGCAATCACAAATAAAGCGGAGAGAGAGAAAATGAAAAAAGAG
516456 GAGGAAGTTCGT
586 GAGGAAGTTCGT
* *
516468 TGATAGCATTAGAAATGACCATTAAATTCTCCCTAATTAAAGTATAATTTGTTCCCTTTGTATCA
1 TGATAGCATTAGAAATAACCATTAAATTCTCCCTAATTAAAGTATAAGTTGTTCCCTTTGTATCA
516533 TATTTAACATACATTTTCAACATTTTATACTTAATAATTGCATTTTCTAAGTCAGTATTGTATGG
66 TATTTAACATACATTTTCAACATTTTATACTTAATAATTGCATTTTCTAAGTCAGTATTGTATGG
* *
516598 TCATATTTTCTTTCATTTGATCCCATTTGTGCTACTAATGTCACTGCATTTAGTATCAGTTTTTG
131 TCATATTTTCTTTCATTTGATCCCATTAGTGCTACTAATGTCACTACATTTAGTATCAGTTTTTG
* * ** *
516663 CGTCTAAAGATGTCAGTGTAGGAATCCATCTTAAAAGATCAAAGCAAGAAAGTGTTTAGAGCTGT
196 CGTCTAAAGATGTCAGCGCAGGAATCCATCTTAAAAGATCAAAGCAAGAAAGCATTCAGAGCTGT
* * *
516728 AGCCACAAGTTCGATATAAAACTGCGCCTAAATATGTCATCGCATGAATACTTCCAGATTGCAAT
261 AGCCACAAGTTCGATATAAAACTACGCCTAAATATGTCACCGCATGAATACTTCCAGATTACAAT
* * * *
516793 AGGGAATTTATGCTGCTAACATATCCAGAAGCACCAGCACATGAAAATGTCAAGTTGTCACGGCG
326 AGGGAATTTAAGCTACTAACATATCCAGAAGCACCAGCACATGAAAATGTCAAGTTATCACAGCG
* *
516858 AATAAAAATATAAATTTGCACCCAGTAATGTTGCGACAACCTGCAACTTCCTAATGCATAAATCA
391 AATAAAAATATAAATTTGCACCCAGTAATGTCGCGACAACCTGCAACTTCCTAATGCATAAACCA
* * * *
516923 GTTATGCGTGAGTGTACA-ATAGGAGTAACTAACATGTACAGTTGCAAGGAAGTTAGATTTGAGA
456 GATATGCGTGAGTATACAGAT-GGAGTAACTAACATGTACAGCTGCAAGGAAGTTAGATCTGAGA
* * * * * * *
516987 AAAGGAGGATACTTGTACTTGCTAGTGAA-GATAAATAGAGCGGAGAGAGAGAAAAT
520 AAAGGAGGATACCTATACTGGCTAG-CAATCACAAATAAAGCGGAGAGAGAGAAAAT
517043 CATCATCAAG
Statistics
Matches: 517, Mismatches: 56, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
596 1 0.00
597 514 0.99
598 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (597 bp):
TGATAGCATTAGAAATAACCATTAAATTCTCCCTAATTAAAGTATAAGTTGTTCCCTTTGTATCA
TATTTAACATACATTTTCAACATTTTATACTTAATAATTGCATTTTCTAAGTCAGTATTGTATGG
TCATATTTTCTTTCATTTGATCCCATTAGTGCTACTAATGTCACTACATTTAGTATCAGTTTTTG
CGTCTAAAGATGTCAGCGCAGGAATCCATCTTAAAAGATCAAAGCAAGAAAGCATTCAGAGCTGT
AGCCACAAGTTCGATATAAAACTACGCCTAAATATGTCACCGCATGAATACTTCCAGATTACAAT
AGGGAATTTAAGCTACTAACATATCCAGAAGCACCAGCACATGAAAATGTCAAGTTATCACAGCG
AATAAAAATATAAATTTGCACCCAGTAATGTCGCGACAACCTGCAACTTCCTAATGCATAAACCA
GATATGCGTGAGTATACAGATGGAGTAACTAACATGTACAGCTGCAAGGAAGTTAGATCTGAGAA
AAGGAGGATACCTATACTGGCTAGCAATCACAAATAAAGCGGAGAGAGAGAAAATGAAAAAAGAG
GAGGAAGTTCGT
Found at i:523650 original size:21 final size:20
Alignment explanation
Indices: 523626--523664 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
523616 ATATTTAAAC
*
523626 AATGGGCAACAATTCAAAGTA
1 AATGGCCAACAATT-AAAGTA
*
523647 AATGGCCAACGATTAAAG
1 AATGGCCAACAATTAAAG
523665 CACTACCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (20 bp):
AATGGCCAACAATTAAAGTA
Found at i:526224 original size:17 final size:17
Alignment explanation
Indices: 526202--526264 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
526192 TTGGAAATTG
*
526202 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
526219 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
* *
526236 AATTTAAGTTTATTATA
1 AATTTAAATTTATTTTA
*
526253 AAATTAAATTTA
1 AATTTAAATTTA
526265 GAAAAGTCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:526319 original size:15 final size:15
Alignment explanation
Indices: 526301--526368 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
526291 AAACAAAAGT
526301 CCCAATTACAAATGG
1 CCCAATTACAAATGG
*
526316 CCCAAATAACAAATGG
1 CCC-AATTACAAATGG
* * *
526332 -CCAGTTATAGATGG
1 CCCAATTACAAATGG
*
526346 CCCAAATACAAATGG
1 CCCAATTACAAATGG
*
526361 TCCAATTA
1 CCCAATTA
526369 TAAAGTGCCC
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
14 8 0.20
15 21 0.52
16 11 0.28
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.21
Consensus pattern (15 bp):
CCCAATTACAAATGG
Found at i:526347 original size:30 final size:30
Alignment explanation
Indices: 526302--526370 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
526292 AACAAAAGTC
* *
526302 CCAATTACAAATGGCCCAAATAACAAATGG-
1 CCAATTATAGATGGCCCAAAT-ACAAATGGT
*
526332 CCAGTTATAGATGGCCCAAATACAAATGGT
1 CCAATTATAGATGGCCCAAATACAAATGGT
526362 CCAATTATA
1 CCAATTATA
526371 AAGTGCCCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 8 0.24
30 26 0.76
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (30 bp):
CCAATTATAGATGGCCCAAATACAAATGGT
Done.