Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 352 of 352
Found at i:112897175 original size:12 final size:12
Alignment explanation
Indices: 112897127--112897185 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
112897117 AAATTGTTAT
*
112897127 TATATGATATTA
1 TATATTATATTA
112897139 T-TATTATA-T-
1 TATATTATATTA
*
112897148 TATAGTATA-T-
1 TATATTATATTA
112897158 TATATTATATTA
1 TATATTATATTA
112897170 TATATTATATTA
1 TATATTATATTA
112897182 TATA
1 TATA
112897186 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 1 0.02
10 16 0.39
11 7 0.17
12 17 0.41
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATTATATTA
Found at i:112898301 original size:15 final size:15
Alignment explanation
Indices: 112898281--112898337 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
112898271 CGATGAATTT
112898281 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
112898296 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
112898311 ATTGAATTTATATTG
1 ATTGAATTTATATTG
112898326 ATTGAA-TTATAT
1 ATTGAATTTATAT
112898338 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:112898740 original size:23 final size:23
Alignment explanation
Indices: 112898710--112898795 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 23
112898700 GCTTTATCGA
*
112898710 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTCATGTGTCGTATT
* *
112898733 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTCATGTGTCGTATT
* *
112898754 TCAGGCA-TCTCGTGTATCGT-TT
1 TCAGGCACT-TCATGTGTCGTATT
*
112898776 T-AGGCACTTTATGTGTCGTA
1 TCAGGCACTTCATGTGTCGTA
112898796 CTCTGATCAG
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
21 30 0.60
22 2 0.04
23 18 0.36
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACTTCATGTGTCGTATT
Found at i:112899278 original size:28 final size:29
Alignment explanation
Indices: 112899247--112899302 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
112899237 TATTATTATT
*
112899247 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
112899275 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
112899303 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:112900638 original size:18 final size:18
Alignment explanation
Indices: 112900615--112900657 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
112900605 ATGTGAGGTA
112900615 AGTATTAATATTAGTATT
1 AGTATTAATATTAGTATT
*
112900633 AGTATTATTATTAGTATT
1 AGTATTAATATTAGTATT
*
112900651 ATTATTA
1 AGTATTA
112900658 TGAGTGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTATTAATATTAGTATT
Found at i:112900658 original size:6 final size:6
Alignment explanation
Indices: 112900615--112900657 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
112900605 ATGTGAGGTA
* * *
112900615 AGTATT AATATT AGTATT AGTATT ATTATT AGTATT ATTATT A
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT A
112900658 TGAGTGGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:112900842 original size:24 final size:27
Alignment explanation
Indices: 112900810--112900869 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
112900800 CGGATTAATT
112900810 ATTG-ATTGAAAG-GTG-GAAA-AATG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
**
112900833 ATTGAATTGAAAGTGTGAGAAAGTGTG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
112900860 ATTGAATTGA
1 ATTGAATTGA
112900870 GAATATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.13
24 8 0.26
25 3 0.10
26 4 0.13
27 12 0.39
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (27 bp):
ATTGAATTGAAAGTGTGAGAAAGAATG
Found at i:112901072 original size:37 final size:39
Alignment explanation
Indices: 112901013--112901108 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
112901003 CGGATAGATT
* * * *
112901013 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
112901050 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
112901089 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
112901109 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:112905041 original size:22 final size:23
Alignment explanation
Indices: 112905016--112905061 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
112905006 CAACTAAATT
112905016 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
112905038 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
112905061 A
1 A
112905062 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:112905067 original size:23 final size:23
Alignment explanation
Indices: 112905023--112905067 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
112905013 ATTAATTCAA
*
112905023 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
112905046 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
112905068 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:112908102 original size:7 final size:7
Alignment explanation
Indices: 112908090--112908114 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
112908080 GATCGTATTA
112908090 GCATGCT
1 GCATGCT
112908097 GCATGCT
1 GCATGCT
112908104 GCATGCT
1 GCATGCT
112908111 GCAT
1 GCAT
112908115 ACTTCATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
GCATGCT
Found at i:112913924 original size:12 final size:12
Alignment explanation
Indices: 112913907--112913933 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
112913897 TAATATAACA
112913907 TAACATAACATG
1 TAACATAACATG
112913919 TAACATAACATG
1 TAACATAACATG
112913931 TAA
1 TAA
112913934 TGTGGTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (12 bp):
TAACATAACATG
Found at i:112914016 original size:25 final size:25
Alignment explanation
Indices: 112913974--112914042 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
112913964 AAACCCTCAC
112913974 TAAATATATTTGTA-TAAATAA-AACA
1 TAAATATATTTGTATTAAA-AATAA-A
* *
112913999 TAAATA-ATTTTTATTAAAAATAAT
1 TAAATATATTTGTATTAAAAATAAA
112914023 TAAATATATTTGTATTAAAA
1 TAAATATATTTGTATTAAAA
112914043 CGCTCAGGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
24 14 0.37
25 24 0.63
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (25 bp):
TAAATATATTTGTATTAAAAATAAA
Found at i:112921259 original size:20 final size:19
Alignment explanation
Indices: 112921230--112921274 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
112921220 ATTTTAAATC
*
112921230 TAAACTCAAA-TCTGAACTT
1 TAAACTCAAACTC-GAACCT
112921249 TAAATCTCAAACTCGAACCT
1 TAAA-CTCAAACTCGAACCT
112921269 TAAACT
1 TAAACT
112921275 TTAAATCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 15 0.65
21 2 0.09
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.29
Consensus pattern (19 bp):
TAAACTCAAACTCGAACCT
Found at i:112922133 original size:18 final size:17
Alignment explanation
Indices: 112922110--112922159 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
112922100 TTAAATATTC
*
112922110 TTAATTAAATTA-ATAAT
1 TTAATTAAAATATA-AAT
112922127 TTAAATTAAAATATAAAT
1 TT-AATTAAAATATAAAT
*
112922145 TTAATTAAAAAATAA
1 TTAATTAAAATATAA
112922160 GACCAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 14 0.48
18 14 0.48
19 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAATTAAAATATAAAT
Found at i:112950446 original size:3 final size:3
Alignment explanation
Indices: 112950440--112950479 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
112950430 ATGATTCAAC
112950440 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
112950480 GAAGTCAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:112953097 original size:13 final size:13
Alignment explanation
Indices: 112953079--112953113 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
112953069 GATGACCAAA
112953079 AAATTATTTTATG
1 AAATTATTTTATG
*
112953092 AAATTATGTTATG
1 AAATTATTTTATG
112953105 AAATTATTT
1 AAATTATTT
112953114 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
AAATTATTTTATG
Found at i:112962907 original size:3 final size:3
Alignment explanation
Indices: 112962899--112962929 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
112962889 AAAAGTGGGG
112962899 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
112962930 TAGCTTCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:112986406 original size:22 final size:22
Alignment explanation
Indices: 112986381--112986426 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
112986371 AATTTTTTTT
112986381 TTGTCATAATTATATATATATA
1 TTGTCATAATTATATATATATA
112986403 TTGTCATAATTATATATATATA
1 TTGTCATAATTATATATATATA
112986425 TT
1 TT
112986427 ATTTTCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
TTGTCATAATTATATATATATA
Found at i:113000088 original size:17 final size:19
Alignment explanation
Indices: 113000052--113000091 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
113000042 ATACCCATCA
113000052 ATACCCATCATTACATTTTT
1 ATACCCATCA-TACATTTTT
113000072 ATACCCATCA-A-ATTTTT
1 ATACCCATCATACATTTTT
113000089 ATA
1 ATA
113000092 TAACCAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
20 10 0.50
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (19 bp):
ATACCCATCATACATTTTT
Found at i:113001501 original size:6 final size:6
Alignment explanation
Indices: 113001490--113001521 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
113001480 GATGGCGTGG
*
113001490 TTTGCT TTTGCT TTTGCT TTTGCT TTAGCT TT
1 TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TT
113001522 ACCTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.16, G:0.16, T:0.66
Consensus pattern (6 bp):
TTTGCT
Found at i:113001965 original size:6 final size:6
Alignment explanation
Indices: 113001954--113001988 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
113001944 GCAGAGCAGG
*
113001954 TGCCCC TGCCCC TGCCCC TGCCCC TGCCGC TGCCC
1 TGCCCC TGCCCC TGCCCC TGCCCC TGCCCC TGCCC
113001989 TCCCTCTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.63, G:0.20, T:0.17
Consensus pattern (6 bp):
TGCCCC
Found at i:113002098 original size:14 final size:14
Alignment explanation
Indices: 113002076--113002112 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
113002066 ATGCTACCCC
113002076 TTCTCTCTTTATCT
1 TTCTCTCTTTATCT
* *
113002090 TTTTCTCTTTTTCT
1 TTCTCTCTTTATCT
113002104 TTCTCTCTT
1 TTCTCTCTT
113002113 GCTTTCCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTCTCTTTATCT
Found at i:113003354 original size:9 final size:9
Alignment explanation
Indices: 113003342--113003372 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
113003332 CAACCACCAC
*
113003342 CGGCGGCGG
1 CGGCGGCAG
113003351 CGGCGGCAG
1 CGGCGGCAG
113003360 CGGCGGCAG
1 CGGCGGCAG
113003369 CGGC
1 CGGC
113003373 TATGAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.06, C:0.35, G:0.58, T:0.00
Consensus pattern (9 bp):
CGGCGGCAG
Found at i:113004380 original size:15 final size:15
Alignment explanation
Indices: 113004360--113004391 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
113004350 AAAGCTTTTT
113004360 TTGTTGTTGTTGCTA
1 TTGTTGTTGTTGCTA
113004375 TTGTTGTTGTTGCTA
1 TTGTTGTTGTTGCTA
113004390 TT
1 TT
113004392 CTATGTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.25, T:0.62
Consensus pattern (15 bp):
TTGTTGTTGTTGCTA
Found at i:113005591 original size:56 final size:56
Alignment explanation
Indices: 113005524--113005637 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
113005514 AAAATATATA
113005524 AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
1 AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
113005580 AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
1 AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
113005636 AA
1 AA
113005638 ATTACTCCGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (56 bp):
AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
Found at i:113010372 original size:49 final size:49
Alignment explanation
Indices: 113010300--113010400 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
113010290 AGCTAACAAC
113010300 AATGCTCGAGCACTTGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
1 AATGCTCGAGCACTTGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
113010349 AATGCTCGAGCA-TTCGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
1 AATGCTCGAGCACTT-GTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
113010398 AAT
1 AAT
113010401 CTCCAATAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 2 0.04
49 49 0.96
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (49 bp):
AATGCTCGAGCACTTGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
Found at i:113011246 original size:12 final size:13
Alignment explanation
Indices: 113011229--113011260 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
113011219 AAGAATTATG
113011229 ATAATTATAA-TT
1 ATAATTATAATTT
113011241 ATAATT-TAATTT
1 ATAATTATAATTT
113011253 ATAATTAT
1 ATAATTAT
113011261 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 14 0.78
13 1 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAATTATAATTT
Found at i:113011267 original size:18 final size:18
Alignment explanation
Indices: 113011233--113011267 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
113011223 ATTATGATAA
*
113011233 TTATAATTATAATTTAAT
1 TTATAATTATAAGTTAAT
*
113011251 TTATAATTATTAGTTAA
1 TTATAATTATAAGTTAA
113011268 AAATTATTTT
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATAATTATAAGTTAAT
Found at i:113023854 original size:19 final size:19
Alignment explanation
Indices: 113023832--113023868 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
113023822 ACTTATTTAT
*
113023832 ATATAAAATATTATTAAAC
1 ATATAAAACATTATTAAAC
*
113023851 ATATGAAACATTATTAAA
1 ATATAAAACATTATTAAA
113023869 AAACTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATAAAACATTATTAAAC
Found at i:113030437 original size:20 final size:20
Alignment explanation
Indices: 113030412--113030452 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
113030402 AATCAAGTTG
*
113030412 TAATATTTATAGTGTTACAA
1 TAATATTTATAATGTTACAA
113030432 TAATATTTATAATGTTACAA
1 TAATATTTATAATGTTACAA
113030452 T
1 T
113030453 GAAACATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (20 bp):
TAATATTTATAATGTTACAA
Found at i:113031736 original size:31 final size:31
Alignment explanation
Indices: 113031701--113031766 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
113031691 CAAAATGGTC
* *
113031701 ATTGAATTATTCAAAAATTTTCATTTAAGTT
1 ATTGAACTATTCAAAAATTTTCATTTAAGTA
** * *
113031732 ATTGAACTATTTGAAAGTTTTTATTTAAGTA
1 ATTGAACTATTCAAAAATTTTCATTTAAGTA
113031763 ATTG
1 ATTG
113031767 GTTTGTTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (31 bp):
ATTGAACTATTCAAAAATTTTCATTTAAGTA
Found at i:113049007 original size:17 final size:17
Alignment explanation
Indices: 113048985--113049018 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
113048975 ACCTTCAGGT
113048985 TCTTGCTCCTCAACTAA
1 TCTTGCTCCTCAACTAA
*
113049002 TCTTGCTTCTCAACTAA
1 TCTTGCTCCTCAACTAA
113049019 CTGAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTTGCTCCTCAACTAA
Found at i:113057992 original size:73 final size:75
Alignment explanation
Indices: 113057915--113058055 Score: 214
Period size: 75 Copynumber: 1.9 Consensus size: 75
113057905 TAAAAATTAT
* * * * *
113057915 AAATATTGGTAGGTTAATTTTACTATTATGC-CA-AAAAAAATCACATCAACATGATTTAACTTA
1 AAATATTGGCAGGTGAATTTTACTATTATACTAAGAAAAAAATCACATCAACATGATTTAACATA
113057978 TAAAATATGC
66 TAAAATATGC
*
113057988 AAATATTGGCAGGTGAATTTTACTATTATACTAAGAAAAAAATCACGTCAACATGATTTAACATA
1 AAATATTGGCAGGTGAATTTTACTATTATACTAAGAAAAAAATCACATCAACATGATTTAACATA
113058053 TAA
66 TAA
113058056 GTGACTCGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 28 0.47
74 1 0.02
75 31 0.52
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (75 bp):
AAATATTGGCAGGTGAATTTTACTATTATACTAAGAAAAAAATCACATCAACATGATTTAACATA
TAAAATATGC
Found at i:113085281 original size:78 final size:78
Alignment explanation
Indices: 113085152--113085304 Score: 234
Period size: 78 Copynumber: 2.0 Consensus size: 78
113085142 ATATTCTACT
* * *
113085152 ATTAAACCGTGATCCCTTGATCTCACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATCACC
1 ATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATCACC
*
113085217 ATGGAGTTTGACC
66 ATGGACTTTGACC
* * * *
113085230 ATTAAACCCTGATCGCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATCACC
1 ATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATCACC
113085295 ATGGACTTTG
66 ATGGACTTTG
113085305 TGTACCAGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (78 bp):
ATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATCACC
ATGGACTTTGACC
Found at i:113088907 original size:30 final size:30
Alignment explanation
Indices: 113088871--113088938 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
113088861 TGAGATAGCA
113088871 GAAGTATTAGGTAAGGTTGGCATTTGAAGG
1 GAAGTATTAGGTAAGGTTGGCATTTGAAGG
113088901 GAAGTATTAGGTAAGGTTGGCATTTGAAGG
1 GAAGTATTAGGTAAGGTTGGCATTTGAAGG
113088931 GAAGTATT
1 GAAGTATT
113088939 TTCATGTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (30 bp):
GAAGTATTAGGTAAGGTTGGCATTTGAAGG
Found at i:113089450 original size:47 final size:47
Alignment explanation
Indices: 113089397--113089492 Score: 140
Period size: 47 Copynumber: 2.0 Consensus size: 47
113089387 GACCTAACGT
*
113089397 ACAAAGCTTGATTAGGTGAG-CTGAATCAGATAGAGATATTGTATGTA
1 ACAAAGCTTGATTAGGTG-GTCTGAATCAGATAAAGATATTGTATGTA
* * *
113089444 ACAAAGCTTGATTAGGTGGTTTGAATCCGGTAAAGATATTGTATGTA
1 ACAAAGCTTGATTAGGTGGTCTGAATCAGATAAAGATATTGTATGTA
113089491 AC
1 AC
113089493 TGTATTGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 1 0.02
47 43 0.98
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.31
Consensus pattern (47 bp):
ACAAAGCTTGATTAGGTGGTCTGAATCAGATAAAGATATTGTATGTA
Found at i:113095199 original size:16 final size:16
Alignment explanation
Indices: 113095178--113095214 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
113095168 TACTCAGGTT
113095178 CCACAAATTTACTATG
1 CCACAAATTTACTATG
113095194 CCACAAATTTACTATG
1 CCACAAATTTACTATG
113095210 CCACA
1 CCACA
113095215 CTAAAAGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (16 bp):
CCACAAATTTACTATG
Found at i:113095401 original size:259 final size:263
Alignment explanation
Indices: 113094929--113095457 Score: 960
Period size: 259 Copynumber: 2.0 Consensus size: 263
113094919 TACTCAGGTT
113094929 CCACAAATTTACTATGCCACACTAAAAGGGGTTCAGGAAATCTATAATTGTTAAAAGTATTGTTG
1 CCACAAATTTACTATGCCACACTAAAAGGGGTTCAGGAAATCTATAATTGTTAAAAGTATTGTTG
113094994 TGAATCACTAAAATTTTCCCATTGAGGAAAAAAAGAAGAAGAAGGATTCGGATATCATCCGTCTA
66 TGAATCACTAAAATTTTCCCATTGAGG-AAAAAAGAAG-AGAAGGATTCGGATATCATCCGTCTA
*
113095059 AATATTCCTTTTCTTAATTGAGGGGAACTGCATTCCTTACTTTATTATCTTCATTTCCTTTTGCA
129 AATATTCCATTTCTTAATTGAGGGGAACTGCATTCCTTACTTTATTATCTTCATTTCCTTTTGCA
113095124 TATTTCTGAGATGCTCAATCCTTCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTA
194 TATTTCTGAGATGCTCAATCCTTCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTA
113095189 CTATG
259 CTATG
113095194 CCACAAATTTACTATGCCACACTAAAAGGGGTTCAGGAAATCTATAATTGTTAAAAGTATTGTTG
1 CCACAAATTTACTATGCCACACTAAAAGGGGTTCAGGAAATCTATAATTGTTAAAAGTATTGTTG
113095259 TGAATCACTAAAATTTTCCCATTGAGG-AAAAA-AAG-G-AGGATTCGGATATCATCCGTCTAAA
66 TGAATCACTAAAATTTTCCCATTGAGGAAAAAAGAAGAGAAGGATTCGGATATCATCCGTCTAAA
** *
113095320 TATTCCATTTCTTAATTGAGGGGAACTGTGTGT-GTTACTTTATTATCTTCATTTCCTTTTGCAT
131 TATTCCATTTCTTAATTGAGGGGAACTGCAT-TCCTTACTTTATTATCTTCATTTCCTTTTGCAT
113095384 ATTTCTGAGATGCTCAATCCTTCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTAC
195 ATTTCTGAGATGCTCAATCCTTCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTAC
113095449 TATG
260 TATG
113095453 CCACA
1 CCACA
113095458 CTAAAAGGGG
Statistics
Matches: 259, Mismatches: 4, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
259 157 0.61
260 2 0.01
262 3 0.01
263 5 0.02
265 92 0.36
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (263 bp):
CCACAAATTTACTATGCCACACTAAAAGGGGTTCAGGAAATCTATAATTGTTAAAAGTATTGTTG
TGAATCACTAAAATTTTCCCATTGAGGAAAAAAGAAGAGAAGGATTCGGATATCATCCGTCTAAA
TATTCCATTTCTTAATTGAGGGGAACTGCATTCCTTACTTTATTATCTTCATTTCCTTTTGCATA
TTTCTGAGATGCTCAATCCTTCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTACT
ATG
Found at i:113098762 original size:14 final size:14
Alignment explanation
Indices: 113098722--113098764 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 14
113098712 TTGGGGTTTT
113098722 TAAAAAATTATATATA
1 TAAAAAATT-TA-ATA
113098738 TAAAAAA--TAATA
1 TAAAAAATTTAATA
113098750 TAAAAAATTTAATA
1 TAAAAAATTTAATA
113098764 T
1 T
113098765 GCATGGGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 2 0.08
14 6 0.24
16 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAAAATTTAATA
Done.