Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014693.1 Kokia drynarioides strain JFW-HI SEQ_129732, 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: 256866
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 55 characters in sequence are not A, C, G, or T
Found at i:205 original size:18 final size:18
Alignment explanation
Indices: 184--222 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
174 ATTACCACCA
*
184 CCACCTCCTCCTCCATGT
1 CCACCTCCTCCTCCATAT
*
202 CCACCTGCTCCTCCATAT
1 CCACCTCCTCCTCCATAT
220 CCA
1 CCA
223 GCACCGCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.05, T:0.26
Consensus pattern (18 bp):
CCACCTCCTCCTCCATAT
Found at i:205 original size:90 final size:90
Alignment explanation
Indices: 70--242 Score: 229
Period size: 90 Copynumber: 1.9 Consensus size: 90
60 ACTACCGCCG
* * * * *
70 CCTCCGCCACCACCCTTACCTCCTCCTCCACCACCTCCATATCCACCAACTCCTCCATTTCCAGC
1 CCTCCGCCACCACCATTACCACCACCACCACCACCTCCATATCCACCAACTCCTCCATATCCAGC
*
135 TCCACTACCAGCTCCACCCGCACTA
66 ACCACTACCAGCTCCACCCGCACTA
* * * * **
160 CCTCCGCCACGACCATTACCACCACCACCTCCTCCTCCATGTCCACCTGCTCCTCCATATCCAGC
1 CCTCCGCCACCACCATTACCACCACCACCACCACCTCCATATCCACCAACTCCTCCATATCCAGC
*
225 ACCGCTACCAGCTCCACC
66 ACCACTACCAGCTCCACC
243 TCCTTCACCA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.20, C:0.55, G:0.06, T:0.19
Consensus pattern (90 bp):
CCTCCGCCACCACCATTACCACCACCACCACCACCTCCATATCCACCAACTCCTCCATATCCAGC
ACCACTACCAGCTCCACCCGCACTA
Found at i:271 original size:18 final size:18
Alignment explanation
Indices: 231--265 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
221 CAGCACCGCT
*
231 ACCAGCTCCACCTCCTTC
1 ACCAGCTCCACCTCCATC
*
249 ACCAGCTCCACTTCCAT
1 ACCAGCTCCACCTCCAT
266 ATCCAGAAGC
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:0.20, C:0.51, G:0.06, T:0.23
Consensus pattern (18 bp):
ACCAGCTCCACCTCCATC
Found at i:330 original size:18 final size:18
Alignment explanation
Indices: 307--353 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
297 TCCACCACTA
307 CCACCACCACCTCCATGT
1 CCACCACCACCTCCATGT
* * *
325 CCACCAGCACCTCCTTTT
1 CCACCACCACCTCCATGT
*
343 CCAACACCACC
1 CCACCACCACC
354 ACCTTCTCCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.55, G:0.04, T:0.17
Consensus pattern (18 bp):
CCACCACCACCTCCATGT
Found at i:2585 original size:94 final size:94
Alignment explanation
Indices: 2414--2592 Score: 223
Period size: 94 Copynumber: 1.9 Consensus size: 94
2404 TATGGAGCAA
* * * ** * * *
2414 CTTTAAAACTCGTGATCAGTACCCACCCCCTTAATGGGCCTATAGAATGCGGTGGGTTAATTACT
1 CTTTAAAACTCGTGATCAGCACCCACACACTTAATGAACCTATAGAATGCAGAGGATTAATTACT
2479 AGACTCACTCCGGTAGATATCTTGAACAG
66 AGACTCACTCCGGTAGATATCTTGAACAG
* * *
2508 CTTTAAAACTCGTGATCAGCATCCACATACTTAATGAATCTATAGAATGCAGAGGATTAATTACT
1 CTTTAAAACTCGTGATCAGCACCCACACACTTAATGAACCTATAGAATGCAGAGGATTAATTACT
* ***
2573 GGACTTGTTCCGGTAGATAT
66 AGACTCACTCCGGTAGATAT
2593 ATGGAGAAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
94 70 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (94 bp):
CTTTAAAACTCGTGATCAGCACCCACACACTTAATGAACCTATAGAATGCAGAGGATTAATTACT
AGACTCACTCCGGTAGATATCTTGAACAG
Found at i:5545 original size:19 final size:19
Alignment explanation
Indices: 5508--5545 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5498 ATTAAAAATA
*
5508 TTTTTAAAATCATATATAT
1 TTTTTAAAATCATAGATAT
*
5527 TTTTTAAAATTATAGATAT
1 TTTTTAAAATCATAGATAT
5546 CAATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTTAAAATCATAGATAT
Found at i:6787 original size:2 final size:2
Alignment explanation
Indices: 6780--6812 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6770 TAAAACAGAC
6780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6813 AAAACACACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18734 original size:19 final size:19
Alignment explanation
Indices: 18712--18749 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18702 AATTTTATTC
*
18712 AAATTTGTTTATTTAATAT
1 AAATTTATTTATTTAATAT
*
18731 AAATTTATTTTTTTAATAT
1 AAATTTATTTATTTAATAT
18750 GTTTTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
AAATTTATTTATTTAATAT
Found at i:38889 original size:23 final size:23
Alignment explanation
Indices: 38815--38966 Score: 141
Period size: 23 Copynumber: 6.5 Consensus size: 23
38805 ATATACAGAA
* *
38815 TAAACAGAGAGCAC-CAAAGTAC
1 TAAACAGAGAGCACACACAGTGC
*
38837 T-AACAGAGAGCACATA-AGTGC
1 TAAACAGAGAGCACACACAGTGC
38858 TAGGCAACAGAGAGCACACACAGTGC
1 TA---AACAGAGAGCACACACAGTGC
* * *
38884 TAAACAGAGAGTACACAAAGTAC
1 TAAACAGAGAGCACACACAGTGC
* *
38907 TAATCAGAGAGCACACACAATGC
1 TAAACAGAGAGCACACACAGTGC
*
38930 TAATAACAGAGAGCACGAGAC-GTGC
1 T-A-AACAGAGAGCAC-ACACAGTGC
38955 TAAACAGAGAGC
1 TAAACAGAGAGC
38967 GCGCTAGTGT
Statistics
Matches: 107, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
21 17 0.16
22 2 0.02
23 47 0.44
24 2 0.02
25 29 0.27
26 10 0.09
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
TAAACAGAGAGCACACACAGTGC
Found at i:38894 original size:25 final size:25
Alignment explanation
Indices: 38866--38965 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 25
38856 GCTAGGCAAC
38866 AGAGAGCACACACAGTGCTAAACAG
1 AGAGAGCACACACAGTGCTAAACAG
* *
38891 AGAGTA-CACA-A-AGTACTAATC--
1 AGAG-AGCACACACAGTGCTAAACAG
* *
38912 AGAGAGCACACACAATGCTAATA-AC
1 AGAGAGCACACACAGTGCTAA-ACAG
*
38937 AGAGAGCACGAGAC-GTGCTAAACAG
1 AGAGAGCAC-ACACAGTGCTAAACAG
38962 AGAG
1 AGAG
38966 CGCGCTAGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
20 1 0.02
21 8 0.14
22 1 0.02
23 14 0.24
24 2 0.03
25 28 0.48
26 4 0.07
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (25 bp):
AGAGAGCACACACAGTGCTAAACAG
Found at i:38938 original size:71 final size:69
Alignment explanation
Indices: 38815--38966 Score: 200
Period size: 71 Copynumber: 2.2 Consensus size: 69
38805 ATATACAGAA
* * *
38815 TAAACAGAGAGCACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGCAACAGAGAGCAC-ACAC
1 TAAACAGAGAGCACCAAAGTACTAACAGAGAGCACACAAATGCTAGACAACAGAGAGCACGACAC
38879 AGTGC
66 -GTGC
* *
38884 TAAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAATGCTA-ATAACAGAGAGCACGA
1 TAAACAGAGAGCAC-CAAAGTACTAA-CAGAGAGCACACA-AATGCTAGACAACAGAGAGCACGA
*
38948 GACGTGC
63 CACGTGC
38955 TAAACAGAGAGC
1 TAAACAGAGAGC
38967 GCGCTAGTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
69 13 0.18
70 11 0.15
71 39 0.54
72 9 0.12
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (69 bp):
TAAACAGAGAGCACCAAAGTACTAACAGAGAGCACACAAATGCTAGACAACAGAGAGCACGACAC
GTGC
Found at i:40115 original size:19 final size:19
Alignment explanation
Indices: 40091--40127 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40081 TACTAACCCG
40091 CTTCTATACTTTTCTTTCT
1 CTTCTATACTTTTCTTTCT
40110 CTTCTATACTTTTCTTTC
1 CTTCTATACTTTTCTTTC
40128 AGGAATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (19 bp):
CTTCTATACTTTTCTTTCT
Found at i:42474 original size:29 final size:28
Alignment explanation
Indices: 42442--42504 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
42432 TTTTAATTCG
*
42442 ATTATTATAAATATT-ATTATTAATATAAT
1 ATTATTATAAAT-TTAATTATTAAAAT-AT
42471 ATTA-TATAAATTTAAATTATTAAAATAT
1 ATTATTATAAATTT-AATTATTAAAATAT
42499 ATTATT
1 ATTATT
42505 TTTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 2 0.07
28 13 0.43
29 15 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTATTATAAATTTAATTATTAAAATAT
Found at i:42489 original size:26 final size:29
Alignment explanation
Indices: 42442--42503 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 29
42432 TTTTAATTCG
* *
42442 ATTATTATAAATATTATTATTAATATAAT
1 ATTATTATAAATATTATAATTAATAAAAT
*
42471 ATTA-TATAAAT-TTA-AATTATTAAAAT
1 ATTATTATAAATATTATAATTAATAAAAT
42497 A-TATTAT
1 ATTATTAT
42504 TTTTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 2 0.07
26 13 0.45
27 3 0.10
28 7 0.24
29 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTATTATAAATATTATAATTAATAAAAT
Found at i:50470 original size:5 final size:5
Alignment explanation
Indices: 50460--50491 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
50450 ATCTACTGTC
50460 CCCCG CCCCG CCCCG CCCCG CCCCG CCCCG CC
1 CCCCG CCCCG CCCCG CCCCG CCCCG CCCCG CC
50492 GCCCCCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.81, G:0.19, T:0.00
Consensus pattern (5 bp):
CCCCG
Found at i:52421 original size:21 final size:21
Alignment explanation
Indices: 52388--52428 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52378 AACTTGTTTA
*
52388 GAAATTAACAATATTAAAATT
1 GAAATTAACAATATCAAAATT
52409 GAAATATAA-AATATCAAAAT
1 GAAAT-TAACAATATCAAAAT
52429 AAAAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
GAAATTAACAATATCAAAATT
Found at i:52969 original size:31 final size:31
Alignment explanation
Indices: 52934--52994 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
52924 TACAATGACG
*
52934 TAAATAAAAACTTTCAAATAATTCAATAATT
1 TAAATAAAAACTTTCAAACAATTCAATAATT
* *
52965 TAAATAAAAATTTTCTAACAATTCAATAAT
1 TAAATAAAAACTTTCAAACAATTCAATAAT
52995 CATCTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (31 bp):
TAAATAAAAACTTTCAAACAATTCAATAATT
Found at i:54328 original size:29 final size:29
Alignment explanation
Indices: 54281--54336 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
54271 AGGACTCATT
* *
54281 TATATATTTTTTTAATACA-ACATTTCTCG
1 TATATATTATATTAATACACA-ATTTCTCG
*
54310 TATATATTATATTATTACACAATTTCT
1 TATATATTATATTAATACACAATTTCT
54337 TACGAACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.96
30 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (29 bp):
TATATATTATATTAATACACAATTTCTCG
Found at i:67027 original size:2 final size:2
Alignment explanation
Indices: 67020--67048 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
67010 TCTCATAATT
67020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67049 TTCAAACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70738 original size:15 final size:14
Alignment explanation
Indices: 70709--70742 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
70699 AGCCTGAACA
70709 GGTTGGTTGCATTG
1 GGTTGGTTGCATTG
*
70723 GGTTGCGTTGCGTTG
1 GGTTG-GTTGCATTG
70738 GGTTG
1 GGTTG
70743 TGTCACGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.03, C:0.09, G:0.47, T:0.41
Consensus pattern (14 bp):
GGTTGGTTGCATTG
Found at i:78617 original size:26 final size:26
Alignment explanation
Indices: 78588--78641 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
78578 AAAGGTTAAC
78588 ATTTA-ATAGGAATAATTAAAGATATT
1 ATTTATATA-GAATAATTAAAGATATT
* * *
78614 ATTTATTTAGAATAATTGATGATATT
1 ATTTATATAGAATAATTAAAGATATT
78640 AT
1 AT
78642 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (26 bp):
ATTTATATAGAATAATTAAAGATATT
Found at i:84087 original size:30 final size:31
Alignment explanation
Indices: 84016--84092 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
84006 AGATTTTTGA
* *
84016 CATAAATAATACAAAAAAAAAATTTATACAC
1 CATAAATAATATAAAAAAAAAATTAATACAC
*
84047 CAAAATATAATATAAAAAATAAAATTAATA-A-
1 CATAA-ATAATATAAAAAA-AAAATTAATACAC
*
84078 CTTAAATAATATAAA
1 CATAAATAATATAAA
84093 TATATATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 10 0.26
31 7 0.18
32 13 0.33
33 9 0.23
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (31 bp):
CATAAATAATATAAAAAAAAAATTAATACAC
Found at i:87396 original size:28 final size:28
Alignment explanation
Indices: 87322--87389 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
87312 CATTTTTCTG
87322 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATGATTGAAT
87350 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATGATTGAAT
87378 TTGGAATTAATT
1 TTGGAATTAATT
87390 CTGTTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATGATTGAAT
Found at i:87406 original size:28 final size:28
Alignment explanation
Indices: 87322--87407 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 28
87312 CATTTTTCTG
* *
87322 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATAATTAAAT
* *
87350 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATAATTAAAT
**
87378 TTGGAATTAATTCTGTTTA-AATTTAAAT
1 TTGGAATTAATTAAGTTTATAA-TTAAAT
87406 TT
1 TT
87408 ATTTAATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 1 0.02
28 52 0.98
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.49
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATAATTAAAT
Found at i:89971 original size:13 final size:13
Alignment explanation
Indices: 89955--89982 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
89945 TAATTTGTCA
89955 TTTTAAAAAATAT
1 TTTTAAAAAATAT
89968 TTTTAAAAAATAT
1 TTTTAAAAAATAT
89981 TT
1 TT
89983 AATATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:89995 original size:16 final size:17
Alignment explanation
Indices: 89974--90011 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
89964 ATATTTTTAA
89974 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
89990 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
*
90007 CAAAT
1 AAAAT
90012 GAATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:90803 original size:17 final size:17
Alignment explanation
Indices: 90781--90814 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
90771 CCTACAATAA
*
90781 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
90798 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
90815 GAAATTTTTT
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:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:91110 original size:17 final size:19
Alignment explanation
Indices: 91061--91101 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
91051 TAGCAGCATG
*
91061 CAGCAGGGGCAACACACGA
1 CAGCAGGGGCAGCACACGA
91080 CAGCAGGGGCAGCACACGA
1 CAGCAGGGGCAGCACACGA
91099 CAG
1 CAG
91102 ATGGCAGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.32, G:0.34, T:0.00
Consensus pattern (19 bp):
CAGCAGGGGCAGCACACGA
Found at i:97550 original size:14 final size:14
Alignment explanation
Indices: 97531--97561 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
97521 CAACAAAATA
97531 GTAGCAAAATAATG
1 GTAGCAAAATAATG
*
97545 GTAGCAAAATAGTG
1 GTAGCAAAATAATG
97559 GTA
1 GTA
97562 AAAAGTGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (14 bp):
GTAGCAAAATAATG
Found at i:99230 original size:15 final size:16
Alignment explanation
Indices: 99209--99249 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
99199 TTCTTTTGTA
99209 ATATATTTCTT-TATT
1 ATATATTTCTTATATT
*
99224 CTATATTT-TTATATT
1 ATATATTTCTTATATT
99239 ATATAATTTCT
1 ATAT-ATTTCT
99250 ATCAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 2 0.10
15 14 0.67
16 4 0.19
17 1 0.05
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATATTTCTTATATT
Found at i:100686 original size:29 final size:31
Alignment explanation
Indices: 100628--100738 Score: 104
Period size: 31 Copynumber: 3.6 Consensus size: 31
100618 ATCTTAAAAT
* **
100628 TATACATG-AACTTTGATTTAATGTACAATTA
1 TATACATGAAACTTTAATTTGGTGT-CAATTA
100659 TATACATG-AACTTTAATTTGGTGT-AATTA
1 TATACATGAAACTTTAATTTGGTGTCAATTA
* * * *
100688 TACACACGAAACTCTAATTATGGT-TCAAATA
1 TATACATGAAACTTTAATT-TGGTGTCAATTA
*
100719 TATACTTGAAACTTTAATTT
1 TATACATGAAACTTTAATTT
100739 TGATTTAATC
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 11 0.17
30 11 0.17
31 44 0.67
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.41
Consensus pattern (31 bp):
TATACATGAAACTTTAATTTGGTGTCAATTA
Found at i:100923 original size:29 final size:30
Alignment explanation
Indices: 100881--100961 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 30
100871 TAATTTGATC
*
100881 AAATCTAAATTTCATGTATAAAATTGCAC-A-
1 AAATC-AAA-TTCATGTATAAAATTACACAAT
* * *
100911 AAATCAAAGTTCATATATATAATTATACAAT
1 AAATCAAA-TTCATGTATAAAATTACACAAT
100942 AAATCATAATTCATGTATAA
1 AAATCA-AATTCATGTATAA
100962 TTTTGATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
29 18 0.44
30 6 0.15
31 15 0.37
32 2 0.05
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATCAAATTCATGTATAAAATTACACAAT
Found at i:106032 original size:21 final size:20
Alignment explanation
Indices: 106008--106049 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
105998 GTAATACATG
* *
106008 ATTATATATTATATTAAAATA
1 ATTAAATATGATA-TAAAATA
106029 ATTAAATATGATATAAAATA
1 ATTAAATATGATATAAAATA
106049 A
1 A
106050 AAGTACGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTAAATATGATATAAAATA
Found at i:123261 original size:13 final size:13
Alignment explanation
Indices: 123243--123268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
123233 AATTCAATAG
123243 GATTAAAGTGAAT
1 GATTAAAGTGAAT
123256 GATTAAAGTGAAT
1 GATTAAAGTGAAT
123269 TACTCTCTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
GATTAAAGTGAAT
Found at i:125104 original size:32 final size:31
Alignment explanation
Indices: 125062--125121 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
125052 GCTTGGTGAC
*
125062 TTAAATAAAAAATTTTAAATAGTTTAATGAT
1 TTAAATAAAAAATTTTAAATAATTTAATGAT
125093 TTAAATGAAAAAATTTTAAATAATTTAAT
1 TTAAAT-AAAAAATTTTAAATAATTTAAT
125122 AATCATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (31 bp):
TTAAATAAAAAATTTTAAATAATTTAATGAT
Found at i:131185 original size:60 final size:60
Alignment explanation
Indices: 131049--131233 Score: 232
Period size: 61 Copynumber: 3.0 Consensus size: 60
131039 AAAAAAAAAA
* * *
131049 TTTGGTATTGGCCATGCAATGATCGACA-CCCCTTTTTGATCTGATAAAAAAAATCAAATTTT
1 TTTGGTGTTGGCCATGCAATG-TCGACACCCCCTTTTTG-TCAGAT-AAAAAATTCAAATTTT
*
131111 TTT-GTGTTGGCCATGCAATGGCTGACACCCCCTTTTT-TCAGATAAAAAATTCAAATTTT
1 TTTGGTGTTGGCCATGCAATGTC-GACACCCCCTTTTTGTCAGATAAAAAATTCAAATTTT
* * * *
131170 TTTGGTGTTGTCCATGCCATAGTCGACACCCCCTTTTTGTCAAATAAAAAATTCGAATTTT
1 TTTGGTGTTGGCCATGCAAT-GTCGACACCCCCTTTTTGTCAGATAAAAAATTCAAATTTT
131231 TTT
1 TTT
131234 ACCAAATAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
59 18 0.17
60 34 0.31
61 45 0.41
62 12 0.11
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (60 bp):
TTTGGTGTTGGCCATGCAATGTCGACACCCCCTTTTTGTCAGATAAAAAATTCAAATTTT
Found at i:131280 original size:61 final size:60
Alignment explanation
Indices: 131215--131437 Score: 226
Period size: 61 Copynumber: 3.7 Consensus size: 60
131205 TTTGTCAAAT
* ** *
131215 AAAAAATTCGAATTTTTTTACCAAATAAAAAAGAGGTGTTGGCCATGGCATGGCTAACACA
1 AAAAAATTCGAATTTTTTTATCTGA-AAAAAAGGGGTGTTGGCCATGGCATGGCTAACACA
* *
131276 AAAAAATTCGAA-TTTTTTATCTGACAAAAAGGGAGTGTCT-GCCATGGCAT-GATCAACACCA
1 AAAAAATTCGAATTTTTTTATCTGAAAAAAAGGG-GTGT-TGGCCATGGCATGGCT-AACA-CA
* * * ** *
131337 AAAAATTTTGAATTTTTTTATCTGAAAAAAAGGGGTGTCGGCCATTACATGGCCAACACAA
1 AAAAAATTCGAATTTTTTTATCTGAAAAAAAGGGGTGTTGGCCATGGCATGGCTAACAC-A
*
131398 AAAAAATT-GAA-TTTTTTATCTGACAAAAAGGGG-G-TGGCCA
1 AAAAAATTCGAATTTTTTTATCTGAAAAAAAGGGGTGTTGGCCA
131438 ACACTAAAAA
Statistics
Matches: 137, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
57 5 0.04
58 1 0.01
59 30 0.22
60 31 0.23
61 49 0.36
62 21 0.15
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (60 bp):
AAAAAATTCGAATTTTTTTATCTGAAAAAAAGGGGTGTTGGCCATGGCATGGCTAACACA
Found at i:131320 original size:60 final size:58
Alignment explanation
Indices: 131242--131437 Score: 227
Period size: 61 Copynumber: 3.3 Consensus size: 58
131232 TTACCAAATA
* *
131242 AAAAAGAGGTGTTGGCCATGGCATGGCTAACACAAAAAAATTCGAATTTTTTATCTGAC
1 AAAAAGGGGTGTCGGCCATGGCATGGCTAACACAAAAAAATT-GAATTTTTTATCTGAC
* * * *
131301 AAAAAGGGAGTGTCTGCCATGGCAT-GATCAACACCAAAAAATTTTGAATTTTTTTATCTGAA
1 AAAAAGGG-GTGTCGGCCATGGCATGGCT-AACA-CAAAAAA-ATTGAA-TTTTTTATCTGAC
** *
131363 AAAAAGGGGTGTCGGCCATTACATGGCCAACACAAAAAAAATTGAATTTTTTATCTGAC
1 AAAAAGGGGTGTCGGCCATGGCATGGCTAACAC-AAAAAAATTGAATTTTTTATCTGAC
131422 AAAAAGGGG-GT-GGCCA
1 AAAAAGGGGTGTCGGCCA
131438 ACACTAAAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
57 5 0.04
58 2 0.02
59 30 0.26
60 24 0.21
61 33 0.28
62 23 0.20
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (58 bp):
AAAAAGGGGTGTCGGCCATGGCATGGCTAACACAAAAAAATTGAATTTTTTATCTGAC
Found at i:135476 original size:16 final size:17
Alignment explanation
Indices: 135448--135479 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
135438 AAATGTACTT
135448 AAATTATATTAAAATAA
1 AAATTATATTAAAATAA
135465 AAATTA-ATTAAAATA
1 AAATTATATTAAAATA
135480 TGCACATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTATATTAAAATAA
Found at i:137429 original size:4 final size:4
Alignment explanation
Indices: 137422--137452 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
137412 AACATGCATG
137422 CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CAT
137453 CAATGGCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:145044 original size:2 final size:2
Alignment explanation
Indices: 145037--145064 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
145027 TTATAATTTA
145037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
145065 TGATGTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:147949 original size:11 final size:11
Alignment explanation
Indices: 147935--147970 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
147925 TTGTTGTTTT
147935 TTTCATTATTA
1 TTTCATTATTA
147946 TTTCATTATTA
1 TTTCATTATTA
147957 TGTT-ATTATTA
1 T-TTCATTATTA
147968 TTT
1 TTT
147971 TATTTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTCATTATTA
Found at i:147973 original size:11 final size:11
Alignment explanation
Indices: 147934--147974 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
147924 TTTGTTGTTT
147934 TTTTCATTATTA
1 TTTT-ATTATTA
*
147946 TTTCATTATTA
1 TTTTATTATTA
*
147957 TGTTATTATTA
1 TTTTATTATTA
147968 TTTTATT
1 TTTTATT
147975 TGTTATTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 22 0.88
12 3 0.12
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:148652 original size:27 final size:27
Alignment explanation
Indices: 148590--148652 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
148580 GTTTTTTTTA
* ** *
148590 TAAAATTAATTAGTTACATAAATGATT
1 TAAAATTTATTAAATACATAAATGATC
***
148617 TATTTTTTATTAAATACATAAATGATC
1 TAAAATTTATTAAATACATAAATGATC
148644 TAAAATTTA
1 TAAAATTTA
148653 CAGTGAAAGT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (27 bp):
TAAAATTTATTAAATACATAAATGATC
Found at i:171986 original size:23 final size:23
Alignment explanation
Indices: 171951--172080 Score: 124
Period size: 23 Copynumber: 5.7 Consensus size: 23
171941 AAAAGAGTAC
*
171951 CAAAGTACT-AACAGAGAGCACA
1 CAAAGTGCTAAACAGAGAGCACA
* **
171973 CACAGTGCTAAACAGAGAGTTCA
1 CAAAGTGCTAAACAGAGAGCACA
*
171996 CAAAGTACTAATA-AGAGAGCACA
1 CAAAGTGCTAA-ACAGAGAGCACA
172019 CAAAGTGCTAATA-AGAGAGCACA
1 CAAAGTGCTAA-ACAGAGAGCACA
* * *
172042 CAAAGTGCTGATCAGAGGGCACGA
1 CAAAGTGCTAAACAGAGAGCAC-A
*
172066 -AACGTGCTAAACAGA
1 CAAAGTGCTAAACAGA
172081 AAGCGCGCTA
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
22 7 0.08
23 80 0.90
24 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (23 bp):
CAAAGTGCTAAACAGAGAGCACA
Found at i:172019 original size:46 final size:46
Alignment explanation
Indices: 171951--172080 Score: 149
Period size: 46 Copynumber: 2.8 Consensus size: 46
171941 AAAAGAGTAC
**
171951 CAAAGTACTAA-CAGAGAGCACACACAGTGCTAAACAGAGAGTTCA
1 CAAAGTACTAATCAGAGAGCACACACAGTGCTAAACAGAGAGCACA
* *
171996 CAAAGTACTAATAAGAGAGCACACAAAGTGCTAATA-AGAGAGCACA
1 CAAAGTACTAATCAGAGAGCACACACAGTGCTAA-ACAGAGAGCACA
* * * *
172042 CAAAGTGCTGATCAGAGGGCACGAAAC-GTGCTAAACAGA
1 CAAAGTACTAATCAGAGAGCAC-ACACAGTGCTAAACAGA
172081 AAGCGCGCTA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
45 12 0.17
46 56 0.79
47 3 0.04
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (46 bp):
CAAAGTACTAATCAGAGAGCACACACAGTGCTAAACAGAGAGCACA
Found at i:178602 original size:6 final size:7
Alignment explanation
Indices: 178576--178601 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
178566 TGGAAAGGGA
178576 TTTTTTC
1 TTTTTTC
178583 TTTTTTC
1 TTTTTTC
178590 TTTTTTC
1 TTTTTTC
178597 TTTTT
1 TTTTT
178602 CCAACATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:183013 original size:18 final size:19
Alignment explanation
Indices: 182980--183015 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
182970 AAAAAATTCA
*
182980 AAATATTTTTTAAAATTTG
1 AAATATTTTATAAAATTTG
182999 AAATA-TTTATAAAATTT
1 AAATATTTTATAAAATTT
183016 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AAATATTTTATAAAATTTG
Found at i:183088 original size:31 final size:30
Alignment explanation
Indices: 183016--183093 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 30
183006 TATAAAATTT
*
183016 ATATTTTTAAAAATATATACAAATTAAATAA
1 ATATTTTTAAAAA-ATATACAAATGAAATAA
* *
183047 A-ATTTCTAAAAAATATATAAA-GAAAGTTAA
1 ATATTTTTAAAAAATATACAAATGAAA--TAA
183077 ATATTTTTAAAATAATA
1 ATATTTTTAAAA-AATA
183094 ATTTTGAGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 3 0.08
29 8 0.21
30 14 0.36
31 10 0.26
32 4 0.10
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (30 bp):
ATATTTTTAAAAAATATACAAATGAAATAA
Found at i:190020 original size:118 final size:118
Alignment explanation
Indices: 189806--190038 Score: 385
Period size: 118 Copynumber: 2.0 Consensus size: 118
189796 AAAAGAAGGG
* *
189806 TAAGTAGAGCCTTTGATTGGTGTAAGCGGTGTGATTTTAATTGTCCAGTTGCTTAAATGAAAACT
1 TAAGGAGAGCCTTTGATTGGTGTAAGCGGTGTGATTTTAATTGTCCAGTTACTTAAATGAAAACT
* * * *
189871 TTTGAATAGTTTGATTTGCAGATTCACGACGCTTAAAAGTTTTATGAAGATTT
66 TTTGAATAATTTGATTTACAAATTCACGACGCTCAAAAGTTTTATGAAGATTT
*
189924 TAAGGAGAGCTTTTGATTGGTGTAAGCGGTGTGATTTTAATTGTCCAGTTACTTAAATGAAAACT
1 TAAGGAGAGCCTTTGATTGGTGTAAGCGGTGTGATTTTAATTGTCCAGTTACTTAAATGAAAACT
**
189989 TTTGAATAATTTGATTTACAAATTCGTGACGCTCAAAAGTTTTATGAAGA
66 TTTGAATAATTTGATTTACAAATTCACGACGCTCAAAAGTTTTATGAAGA
190039 CAAAGCTAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 106 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (118 bp):
TAAGGAGAGCCTTTGATTGGTGTAAGCGGTGTGATTTTAATTGTCCAGTTACTTAAATGAAAACT
TTTGAATAATTTGATTTACAAATTCACGACGCTCAAAAGTTTTATGAAGATTT
Found at i:197756 original size:18 final size:18
Alignment explanation
Indices: 197733--197777 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
197723 ATATATTTAC
197733 AAATAATATTTT-AAATAA
1 AAATAATATTTTAAAAT-A
*
197751 AAATAA-ATATTAAAATA
1 AAATAATATTTTAAAATA
197768 AAATAATATT
1 AAATAATATT
197778 GAAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAATATTTTAAAATA
Found at i:197770 original size:17 final size:17
Alignment explanation
Indices: 197733--197782 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
197723 ATATATTTAC
*
197733 AAATAATATTTTAAATAA
1 AAATAATA-TTAAAATAA
197751 AAATAAATATTAAAAT-A
1 AAAT-AATATTAAAATAA
*
197768 AAATAATATTGAAAT
1 AAATAATATTAAAAT
197783 TTAAAAAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 10 0.34
17 5 0.17
18 10 0.34
19 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAATAATATTAAAATAA
Found at i:200533 original size:89 final size:92
Alignment explanation
Indices: 200406--200587 Score: 316
Period size: 90 Copynumber: 2.0 Consensus size: 92
200396 ATACAATTCC
*
200406 TTAAAAGAAAATATACAATACAATTAAAAATATTGATGTA-TTTTTTAAAATAAACTATTTATCA
1 TTAAAAGAAAATATACAATACAACTAAAAATATTGATGTATTTTTTTAAAATAAACTATTTATCA
*
200470 TCATCTAACCTTCCATTTTATATAACT
66 TCACCTAACCTTCCATTTTATATAACT
*
200497 TTAAAA-AATATATACAATACAACT-AAAATATTGATGTATTTTTTTAAAATAAACTATTTATCA
1 TTAAAAGAAAATATACAATACAACTAAAAATATTGATGTATTTTTTTAAAATAAACTATTTATCA
200560 TCACCTAACCTTCCATTTTATATAACT
66 TCACCTAACCTTCCATTTTATATAACT
200587 T
1 T
200588 CATTAAAAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
89 14 0.16
90 67 0.77
91 6 0.07
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (92 bp):
TTAAAAGAAAATATACAATACAACTAAAAATATTGATGTATTTTTTTAAAATAAACTATTTATCA
TCACCTAACCTTCCATTTTATATAACT
Found at i:201056 original size:26 final size:26
Alignment explanation
Indices: 201001--201058 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
200991 AATTTAAAAT
* * *
201001 AAAATATACAAAAATTATATATTTTT
1 AAAATATACAAAAATTATAAATTATA
201027 AAAATATA-AAGAAATTATAAATTATA
1 AAAATATACAA-AAATTATAAATTATA
201053 AAAATA
1 AAAATA
201059 CATGTATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
AAAATATACAAAAATTATAAATTATA
Found at i:201451 original size:16 final size:14
Alignment explanation
Indices: 201430--201463 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
201420 GTGTGTTTAA
201430 ATTTAATTATGATTAT
1 ATTTAATTAT-A-TAT
201446 ATTTAATTATATAT
1 ATTTAATTATATAT
201460 ATTT
1 ATTT
201464 GAAGATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 1 0.06
16 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
ATTTAATTATATAT
Found at i:203610 original size:28 final size:29
Alignment explanation
Indices: 203578--203639 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
203568 GAGACTGTCC
* * *
203578 ATATTATTTCTATTT-TTTTTTAATATTT
1 ATATTATTTCAATTTAATATTTAATATTT
203606 ATATTATTTCAATTTAATATTTAATATTT
1 ATATTATTTCAATTTAATATTTAATATTT
*
203635 TTATT
1 ATATT
203640 TATTGAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (29 bp):
ATATTATTTCAATTTAATATTTAATATTT
Found at i:203613 original size:22 final size:20
Alignment explanation
Indices: 203588--203641 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
203578 ATATTATTTC
*
203588 TATTTTTTTTTAATATTT-A
1 TATTTTTATTTAATATTTAA
203607 TATTATTTCAATTTAATATTTAA
1 TATT-TTT--ATTTAATATTTAA
203630 TATTTTTATTTA
1 TATTTTTATTTA
203642 TTGAAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 4 0.13
20 8 0.27
22 13 0.43
23 5 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTTATTTAATATTTAA
Found at i:212270 original size:22 final size:23
Alignment explanation
Indices: 212225--212273 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
212215 TGCTTTTTTT
* **
212225 TTTTTTTAATTGTTTTGTTGCTA
1 TTTTTTTAATTGTTTTCTCACTA
212248 TTTTTTT-ATTGTTTTCTCACTA
1 TTTTTTTAATTGTTTTCTCACTA
212270 TTTT
1 TTTT
212274 GCTACCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.71
Consensus pattern (23 bp):
TTTTTTTAATTGTTTTCTCACTA
Found at i:213994 original size:94 final size:94
Alignment explanation
Indices: 213797--213983 Score: 220
Period size: 94 Copynumber: 2.0 Consensus size: 94
213787 AAATTAAAAG
* *
213797 AAATTAAAAACATAAAATGATTTTACTATAAATACTAAAGTAATTTTCTTTAAAACCCGGGACTT
1 AAATTAAAAACATAAAATGATTTTACTATAAATACTAAAGCAACTTTCTTTAAAACCCGGGACTT
* * **
213862 TCCTTACACTGAAAAAAATAATTATAAAC
66 TCCTTACACTAAAAAAAAAAAACATAAAC
* * * *
213891 AAATTAAAAATATAAAATGATTTTACTATGAATACTCGAA-CAACTTTCTTTAAAA-CCGGAGGC
1 AAATTAAAAACATAAAATGATTTTACTATAAATACT-AAAGCAACTTTCTTTAAAACCCGG-GAC
213954 TTTCCTCTTAC-C-AAAAAAAAAAAACATAAA
64 TTT-C-CTTACACTAAAAAAAAAAAACATAAA
213984 AATTCTAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
93 4 0.05
94 66 0.84
95 4 0.05
96 5 0.06
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (94 bp):
AAATTAAAAACATAAAATGATTTTACTATAAATACTAAAGCAACTTTCTTTAAAACCCGGGACTT
TCCTTACACTAAAAAAAAAAAACATAAAC
Found at i:219057 original size:45 final size:45
Alignment explanation
Indices: 218765--219336 Score: 403
Period size: 45 Copynumber: 13.2 Consensus size: 45
218755 GAAGGCAAAC
** * *
218765 AAAGAGATTGCCTCGACAGTGAATAGCTCAGCTGAGAAGATGAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* ** * * *
218810 AACGAGATGGTCATGACAGTAAATAGCTCCA-CTGAGGAGATGAA-
1 AAAGAGACAGCCTTGACAGTAAATAGCT-CAGCTGAGAAGATGAAG
* * *
218854 AAGAGAGACA-ACTT--CAATAAAGAGCTCAG-TGGAGAAGATGAAG
1 AA-AGAGACAGCCTTGACAGTAAATAGCTCAGCT-GAGAAGATGAAG
* *
218897 AAAGA-A-A-CATT---ATTAAATAGCTCAGCTGAGAAGATGAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * *
218936 AAAGA-A-A--CAT--CATTAAATAGCTCAGCTGAGCAGATG-AG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * * *
218974 ACAAGAGACAG-C-T-ACAGAAAATGGTTCAGCTGAAAAGATGAAG
1 A-AAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * * *
219017 AAAGAGACAGCCTTCACAGTAAATATCTCAGCTAAGAAGATGAAC
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* *
219062 AAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
** ** * *
219107 AAAGAGATGGCCAGGACAGTCAATAGCTCAGCCGAGAAGATG-AG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* *
219151 ACAAGAGACAG-C-T-ACAGTAAATGGTTCAGCTGAGAAGATGAAG
1 A-AAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * * * * *
219194 AAAGAGACGGCCTTGACGGTAAAGAGCTCGAAC-GAGAAGGTAAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTC-AGCTGAGAAGATGAAG
* * * * *
219239 AAAGAAACAGCCTTGACAGTAAATAACTCGGCTGAGAAGGTTAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * *
219284 AAAGAGATC-G-C-TGCAACAGTGAATGGCTCAGCTGAGAAGATGAAA
1 AAAGAGA-CAGCCTTG--ACAGTAAATAGCTCAGCTGAGAAGATGAAG
219329 AAAGAGAC
1 AAAGAGAC
219337 CACTGTGGCT
Statistics
Matches: 422, Mismatches: 79, Indels: 53
0.76 0.14 0.10
Matches are distributed among these distances:
38 4 0.01
39 59 0.14
40 5 0.01
41 6 0.01
42 84 0.20
43 12 0.03
44 13 0.03
45 234 0.55
46 5 0.01
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.16
Consensus pattern (45 bp):
AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
Found at i:219058 original size:87 final size:87
Alignment explanation
Indices: 218949--219222 Score: 336
Period size: 87 Copynumber: 3.1 Consensus size: 87
218939 GAAACATCAT
* *
218949 TAAATAGCTCAGCTGAGCAGATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATG
1 TAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAGAAGATG
* *
219014 AAGAAAGAGACAGCCTTCACAG
66 AAGAAAGAGACGGCCTTGACAG
* * ***
219036 TAAATATCTCAGCTAAGAAGATGA-ACAAAGAGACAGCCTTGACA-ATAAATAACTCAGCTGAGA
1 TAAATAGCTCAGCTGAGAAGATGAGAC-AAGAGACAG-C-T-ACAGA-AAATGGTTCAGCTGAGA
* **
219099 AGATGAAGAAAGAGATGGCCAGGACAG
61 AGATGAAGAAAGAGACGGCCTTGACAG
* * *
219126 TCAATAGCTCAGCCGAGAAGATGAGACAAGAGACAGCTACAGTAAATGGTTCAGCTGAGAAGATG
1 TAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAGAAGATG
*
219191 AAGAAAGAGACGGCCTTGACGG
66 AAGAAAGAGACGGCCTTGACAG
*
219213 TAAAGAGCTC
1 TAAATAGCTC
219223 GAACGAGAAG
Statistics
Matches: 154, Mismatches: 26, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
86 2 0.01
87 78 0.51
88 2 0.01
89 3 0.02
90 67 0.44
91 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.15
Consensus pattern (87 bp):
TAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAGAAGATG
AAGAAAGAGACGGCCTTGACAG
Found at i:219251 original size:177 final size:176
Alignment explanation
Indices: 218910--219336 Score: 508
Period size: 177 Copynumber: 2.4 Consensus size: 176
218900 GAAACATTAT
* * * * * *
218910 TAAATAGCTCAGCTGAGAAGATGAAGAAAGA-A----ACATCATTAAATAGCTCAGCTGAGCAGA
1 TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATCGCGCAACAGTCAATAGCTCAGCTGAGAAGA
218970 TGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTCACA
66 TGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTCACA
* * * * *
219035 GTAAATATCTCAGCTAAGAAGATGAACAAAGAGACAGCCTTGACAA
131 GTAAAGAGCTCAACTAAGAAGATAAACAAAGAAACAGCCTTGACAA
* *
219081 TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGC-CAGGACAGTCAATAGCTCAGCCGAGAA
1 TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATCGCGCA--ACAGTCAATAGCTCAGCTGAGAA
* * * *
219145 GATGAGACAAGAGACAGCTACAGTAAATGGTTCAGCTGAGAAGATGAAGAAAGAGACGGCCTTGA
64 GATGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTCA
* * * * *
219210 CGGTAAAGAGCTCGAAC-GAGAAGGTAAAGAAAGAAACAGCCTTGACAG
129 CAGTAAAGAGCTC-AACTAAGAAGATAAACAAAGAAACAGCCTTGACAA
* * * * *
219258 TAAATAACTCGGCTGAGAAGGTTAAGAAAGAGATCGCTGCAACAGTGAATGGCTCAGCTGAGAAG
1 TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATCGC-GCAACAGTCAATAGCTCAGCTGAGAAG
* *
219323 ATGAAAAAAGAGAC
65 ATGAGACAAGAGAC
219337 CACTGTGGCT
Statistics
Matches: 217, Mismatches: 29, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
171 30 0.14
172 1 0.00
175 2 0.01
177 180 0.83
178 2 0.01
179 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.26, T:0.15
Consensus pattern (176 bp):
TAAATAACTCAGCTGAGAAGATGAAGAAAGAGATCGCGCAACAGTCAATAGCTCAGCTGAGAAGA
TGAGACAAGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTCACA
GTAAAGAGCTCAACTAAGAAGATAAACAAAGAAACAGCCTTGACAA
Found at i:220418 original size:26 final size:26
Alignment explanation
Indices: 220382--220433 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
220372 CAAAATAATA
220382 ATCGTTGTGATAAATTGTTTCATTTC
1 ATCGTTGTGATAAATTGTTTCATTTC
220408 ATCGTTGTGATAAATTGTTTCATTTC
1 ATCGTTGTGATAAATTGTTTCATTTC
220434 GTTTGTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (26 bp):
ATCGTTGTGATAAATTGTTTCATTTC
Found at i:237915 original size:24 final size:25
Alignment explanation
Indices: 237888--237935 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
237878 AGTCTATTTA
*
237888 ATTTAGTAT-TTGGATTTTTTATGG
1 ATTTAGCATGTTGGATTTTTTATGG
*
237912 ATTTAGCATGGTTTGATTTTTTAT
1 ATTTAGCAT-GTTGGATTTTTTAT
237936 TTTTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.58
Consensus pattern (25 bp):
ATTTAGCATGTTGGATTTTTTATGG
Found at i:246396 original size:19 final size:20
Alignment explanation
Indices: 246364--246401 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
246354 ATATTTATTA
246364 AAAATAATTAATTAAAAGTT
1 AAAATAATTAATTAAAAGTT
*
246384 AAAA-AATTTATTAAAAGT
1 AAAATAATTAATTAAAAGT
246402 ACCTCCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATAATTAATTAAAAGTT
Done.