Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012155.1 Kokia drynarioides strain JFW-HI SEQ_127156, 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: 112619
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:851 original size:40 final size:40
Alignment explanation
Indices: 796--1077 Score: 241
Period size: 40 Copynumber: 7.0 Consensus size: 40
786 AAATTACATC
* * *
796 ACCATCCAACCTTTTACCCTAACTAGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTATCCAGAGGGCAGATTGAAG
* * * *
836 ACCATCCAATCTTTTACCTTAACCAGAAGGCATATTGAAG
1 ACCATCCAATCTTTTACCCTATCCAGAGGGCAGATTGAAG
* * *
876 ACCATCCAATCTTTTACCCTATCCACTA-GGCAAATTAAAG
1 ACCATCCAATCTTTTACCCTATCCA-GAGGGCAGATTGAAG
* *
916 TCAACATCCAATCTTTTACCCTATCTAGAGGGCAGATTGAAG
1 --ACCATCCAATCTTTTACCCTATCCAGAGGGCAGATTGAAG
* * * *
958 TCACTATCCAATCTTTTACCCCAT-CAAATGGGCAGATTAAAG
1 --ACCATCCAATCTTTTACCCTATCCAGA-GGGCAGATTGAAG
* * * * *
1000 -CCATCGAACCTTTTA-CCTCAACTAGAGGGTAGATTGAAG
1 ACCATCCAATCTTTTACCCT-ATCCAGAGGGCAGATTGAAG
* * * *
1039 -CCATTCAATCTCTTACCCCATCCAGAGGGTAGATTGAAG
1 ACCATCCAATCTTTTACCCTATCCAGAGGGCAGATTGAAG
1078 TATGAAAGTG
Statistics
Matches: 197, Mismatches: 37, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.01
39 53 0.27
40 72 0.37
41 4 0.02
42 66 0.34
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (40 bp):
ACCATCCAATCTTTTACCCTATCCAGAGGGCAGATTGAAG
Found at i:955 original size:82 final size:79
Alignment explanation
Indices: 837--1062 Score: 240
Period size: 84 Copynumber: 2.8 Consensus size: 79
827 AGATTGAAGA
* * * * * *
837 CCATCCAATCTTTTACCTTAACCAGAAGGCATATTGAAGACCATCCAATCTTTTACCCTATCCAC
1 CCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCCATCCAA
902 TAGGCAAATTAAAG
66 TAGGCAAATTAAAG
* *
916 TCAACATCCAATCTTTTACCCTATCTAGAGGGCAGATTGAAGTCACTATCCAATCTTTTACCCCA
1 -C--CATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAG--ACCATCCAATCTTTTACCCCA
* * *
981 TCAAATGGGCAGATTAAAG
61 TCCAATAGGCAAATTAAAG
* * * * *
1000 CCATCGAACCTTTTA-CCTCAACTAGAGGGTAGATTGAAG-CCATTCAATCTCTTACCCCATCCA
1 CCATCCAATCTTTTACCCT-AACTAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCCATCCA
1063 GAGGGTAGAT
Statistics
Matches: 122, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
78 20 0.16
80 4 0.03
81 30 0.25
82 33 0.27
83 1 0.01
84 34 0.28
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (79 bp):
CCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCCATCCAA
TAGGCAAATTAAAG
Found at i:991 original size:42 final size:42
Alignment explanation
Indices: 878--999 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
868 TATTGAAGAC
* * * *
878 CATCCAATCTTTTACCCTATCCACTAGGCAAATTAAAGTCAA
1 CATCCAATCTTTTACCCTATCAAATGGGCAGATTAAAGTCAA
* *
920 CATCCAATCTTTTACCCTATCTAGA-GGGCAGATTGAAGTC-A
1 CATCCAATCTTTTACCCTATC-AAATGGGCAGATTAAAGTCAA
*
961 CTATCCAATCTTTTACCCCATCAAATGGGCAGATTAAAG
1 C-ATCCAATCTTTTACCCTATCAAATGGGCAGATTAAAG
1000 CCATCGAACC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 4 0.06
42 64 0.94
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (42 bp):
CATCCAATCTTTTACCCTATCAAATGGGCAGATTAAAGTCAA
Found at i:1034 original size:39 final size:39
Alignment explanation
Indices: 991--1073 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
981 TCAAATGGGC
* * *
991 AGATTAAAGCCA-TCGAACCTTTTACCTCAACTAGAGGGT
1 AGATTAAAGCCATTC-AACCTCTTACCCCAACCAGAGGGT
* * *
1030 AGATTGAAGCCATTCAATCTCTTACCCCATCCAGAGGGT
1 AGATTAAAGCCATTCAACCTCTTACCCCAACCAGAGGGT
1069 AGATT
1 AGATT
1074 GAAGTATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (39 bp):
AGATTAAAGCCATTCAACCTCTTACCCCAACCAGAGGGT
Found at i:8837 original size:118 final size:118
Alignment explanation
Indices: 8692--8930 Score: 478
Period size: 118 Copynumber: 2.0 Consensus size: 118
8682 TGACAATATC
8692 AACAATCCTCGAAATTCACCCTTTTAATGTCAAGACATTGGTGATTAATTTCGTTTTCGAATTTC
1 AACAATCCTCGAAATTCACCCTTTTAATGTCAAGACATTGGTGATTAATTTCGTTTTCGAATTTC
8757 ATTGCCCACTTGCTCAACTTGATGAAACCAAAAAAGTTTTTTTATCAATAAAA
66 ATTGCCCACTTGCTCAACTTGATGAAACCAAAAAAGTTTTTTTATCAATAAAA
8810 AACAATCCTCGAAATTCACCCTTTTAATGTCAAGACATTGGTGATTAATTTCGTTTTCGAATTTC
1 AACAATCCTCGAAATTCACCCTTTTAATGTCAAGACATTGGTGATTAATTTCGTTTTCGAATTTC
8875 ATTGCCCACTTGCTCAACTTGATGAAACCAAAAAAGTTTTTTTATCAATAAAA
66 ATTGCCCACTTGCTCAACTTGATGAAACCAAAAAAGTTTTTTTATCAATAAAA
8928 AAC
1 AAC
8931 CAGCGTTTTC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (118 bp):
AACAATCCTCGAAATTCACCCTTTTAATGTCAAGACATTGGTGATTAATTTCGTTTTCGAATTTC
ATTGCCCACTTGCTCAACTTGATGAAACCAAAAAAGTTTTTTTATCAATAAAA
Found at i:11009 original size:29 final size:28
Alignment explanation
Indices: 10970--11368 Score: 276
Period size: 30 Copynumber: 13.9 Consensus size: 28
10960 GAAGGTCCCT
10970 AACTATCCAAAAATTACCATTTTACCCTCG
1 AACT-TCCAAAAATTACCATTTTACCC-CG
* *
11000 AACTTCCAAAAA-TCCCATTTTTGACCCCT
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
11029 AACCTTCCAAAAATTACCATTTTACCCCTG
1 AA-CTTCCAAAAATTACCATTTTACCCC-G
* **
11059 AACTTCCAAAAA-TCCCATTTTTCACCCAAA
1 AACTTCCAAAAATTACCA-TTTT-ACCC-CG
*
11089 AACTTCTAAAAATTACCATTTTACCCCG
1 AACTTCCAAAAATTACCATTTTACCCCG
11117 AACTTCCAAAAA-T--C------CCCCG
1 AACTTCCAAAAATTACCATTTTACCCCG
* *
11136 AACTTTCAAAAATCT--CATTTTTTGACCCCAA
1 AACTTCCAAAAAT-TACCA--TTTT-ACCCC-G
* *
11167 AACTTCCTAAAATTACCATTTTACCCCCCA
1 AACTTCCAAAAATTACCATTTTA--CCCCG
*
11197 AACTTCCAAAAA-TCCCATTTTAACCCCG
1 AACTTCCAAAAATTACCATTTT-ACCCCG
*
11225 AACCTTCCAAAAATTACCATTTTACCCCCA
1 AA-CTTCCAAAAATTACCATTTTA-CCCCG
*
11255 AACTTCC-AAAA-TCCCATTTTTGACCCCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
* *
11283 AAACTTCCAAAAAAAATACCATTTTACCCCA
1 -AACTTCC--AAAAATTACCATTTTACCCCG
11314 AACTTCCAAAAA-T-CTCATTTTTGACCCCG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCCG
11343 ACACTTCCAAAAAATTACCATTTTAC
1 A-ACTTCC-AAAAATTACCATTTTAC
11369 TCTCGGATGT
Statistics
Matches: 300, Mismatches: 26, Indels: 86
0.73 0.06 0.21
Matches are distributed among these distances:
19 16 0.05
21 2 0.01
25 1 0.00
26 1 0.00
27 8 0.03
28 46 0.15
29 77 0.26
30 94 0.31
31 37 0.12
32 13 0.04
33 5 0.02
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.29
Consensus pattern (28 bp):
AACTTCCAAAAATTACCATTTTACCCCG
Found at i:11038 original size:30 final size:28
Alignment explanation
Indices: 10970--11368 Score: 288
Period size: 29 Copynumber: 13.8 Consensus size: 28
10960 GAAGGTCCCT
10970 AACTATCCAAAAATTACCATTTTACCCTCG-
1 AACT-TCCAAAAA-TACCATTTTACCC-CGA
* *
11000 AACTTCCAAAAATCCCATTTTTGACCCCTA
1 AACTTCCAAAAATACCA-TTTT-ACCCCGA
*
11030 ACCTTCCAAAAATTACCATTTTACCCCTG-
1 AACTTCCAAAAA-TACCATTTTACCCC-GA
* **
11059 AACTTCCAAAAATCCCATTTTTCACCCAAA
1 AACTTCCAAAAATACCA-TTTT-ACCCCGA
*
11089 AACTTCTAAAAATTACCATTTTACCCCG-
1 AACTTCCAAAAA-TACCATTTTACCCCGA
11117 AACTTCCAAAAAT--C------CCCCG-
1 AACTTCCAAAAATACCATTTTACCCCGA
* ** *
11136 AACTTTCAAAAATCTCATTTTTTGACCCCAA
1 AACTTCCAAAAATACCA--TTTT-ACCCCGA
* *
11167 AACTTCCTAAAATTACCATTTTACCCCCCA
1 AACTTCC-AAAAATACCATTTTA-CCCCGA
*
11197 AACTTCCAAAAATCCCATTTTAACCCCGA
1 AACTTCCAAAAATACCATTTT-ACCCCGA
* *
11226 ACCTTCCAAAAATTACCATTTTACCCCCA
1 AACTTCCAAAAA-TACCATTTTACCCCGA
*
11255 AACTTCC-AAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAAATACCA-TTTT-ACCCCGA
11284 AACTTCCAAAAAAAATACCATTTTACCCC-A
1 AACTTCC---AAAAATACCATTTTACCCCGA
11314 AACTTCCAAAAAT-CTCATTTTTGACCCCGA
1 AACTTCCAAAAATAC-CA-TTTT-ACCCCGA
*
11344 CACTTCCAAAAAATTACCATTTTAC
1 AACTTCC-AAAAA-TACCATTTTAC
11369 TCTCGGATGT
Statistics
Matches: 299, Mismatches: 32, Indels: 76
0.73 0.08 0.19
Matches are distributed among these distances:
19 17 0.06
21 1 0.00
25 1 0.00
26 1 0.00
27 13 0.04
28 31 0.10
29 96 0.32
30 88 0.29
31 28 0.09
32 14 0.05
33 9 0.03
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.29
Consensus pattern (28 bp):
AACTTCCAAAAATACCATTTTACCCCGA
Found at i:11062 original size:59 final size:58
Alignment explanation
Indices: 10966--11132 Score: 248
Period size: 59 Copynumber: 2.8 Consensus size: 58
10956 CCCCGAAGGT
*
10966 CCCTAACTATCCAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAACT-TCCAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTCAC
11025 CCCTAACCTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTCAC
1 CCCTAA-CTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTCAC
** *
11084 CCAAAAACTTCTAAAAATTACCATTTTACCCC-GAACTTCCAAAAATCCC
1 CC-CTAACTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCC
11133 CCGAACTTTC
Statistics
Matches: 101, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
58 17 0.17
59 76 0.75
60 8 0.08
ACGTcount: A:0.35, C:0.34, G:0.02, T:0.29
Consensus pattern (58 bp):
CCCTAACTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTCAC
Found at i:11136 original size:19 final size:19
Alignment explanation
Indices: 11112--11149 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11102 TACCATTTTA
11112 CCCCGAACTTCCAAAAATC
1 CCCCGAACTTCCAAAAATC
*
11131 CCCCGAACTTTCAAAAATC
1 CCCCGAACTTCCAAAAATC
11150 TCATTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.18
Consensus pattern (19 bp):
CCCCGAACTTCCAAAAATC
Found at i:11186 original size:78 final size:78
Alignment explanation
Indices: 11053--11212 Score: 225
Period size: 78 Copynumber: 2.0 Consensus size: 78
11043 TACCATTTTA
* *
11053 CCCCTGAACTTCCAAAAATCCCATTTTTCACCCAAAAACTTCTAAAAATTACCATTTTA-CCCCG
1 CCCCCGAACTTCCAAAAATCCCATTTTTCACCCAAAAACTTCTAAAAATTACCATTTTACCCCCA
11117 AACTTCCAAAAAT
66 AACTTCCAAAAAT
* * * *
11130 CCCCCGAACTTTCAAAAATCTCATTTTTTGACCCCAAAACTTCCT-AAAATTACCATTTTACCCC
1 CCCCCGAACTTCCAAAAATCCCA-TTTTTCACCCAAAAACTT-CTAAAAATTACCATTTTA-CCC
11194 CCAAACTTCCAAAAAT
63 CCAAACTTCCAAAAAT
11210 CCC
1 CCC
11213 ATTTTAACCC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
77 20 0.27
78 31 0.42
79 2 0.03
80 20 0.27
ACGTcount: A:0.36, C:0.34, G:0.03, T:0.28
Consensus pattern (78 bp):
CCCCCGAACTTCCAAAAATCCCATTTTTCACCCAAAAACTTCTAAAAATTACCATTTTACCCCCA
AACTTCCAAAAAT
Found at i:11186 original size:137 final size:136
Alignment explanation
Indices: 10998--11269 Score: 386
Period size: 137 Copynumber: 2.0 Consensus size: 136
10988 ATTTTACCCT
* * **
10998 CGAACTTCCAAAAATCCCATTTTTGACCCCTAACCTTCCAAAAATTACCATTTTA-CCCCTGAAC
1 CGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCCAAAC
* * *
11062 TTCCAAAAATCCCATTTTTCACCCAAAAACTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAA
66 TTCCAAAAATCCCA-TTTTAACCCAAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTCC-A
11126 AAATCCCC
129 AAATCCCC
* * *
11134 CGAACTTTCAAAAATCTCATTTTTTGACCCCAAAACTTCCTAAAATTACCATTTTACCCCCCAAA
1 CGAACTTCCAAAAATCCCA-TTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCCAAA
** *
11199 CTTCCAAAAATCCCATTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAA
65 CTTCCAAAAATCCCATTTTAACCCAAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAA
11264 AATCCC
130 AATCCC
11270 ATTTTTGACC
Statistics
Matches: 120, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
136 17 0.14
137 71 0.59
138 32 0.27
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.28
Consensus pattern (136 bp):
CGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCCAAAC
TTCCAAAAATCCCATTTTAACCCAAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAA
ATCCCC
Found at i:11247 original size:59 final size:60
Alignment explanation
Indices: 11130--11368 Score: 326
Period size: 59 Copynumber: 4.0 Consensus size: 60
11120 TTCCAAAAAT
* * * * *
11130 CCCCCGAACTTTCAAAAATCTCATTTTTTGACCCCAAAACTTCC-TAAAATTACCATTTTA
1 CCCCCAAACTTCCAAAAATCCCA-TTTTTGACCCCGAAACTTCCAAAAAATTACCATTTTA
* *
11190 CCCCCCAAACTTCCAAAAATCCCA-TTTTAACCCCGAACCTTCC-AAAAATTACCATTTTA
1 -CCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAAATTACCATTTTA
*
11249 CCCCCAAACTTCC-AAAATCCCATTTTTGACCCCGAAACTTCCAAAAAAAATACCATTTTA
1 CCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCC-AAAAAATTACCATTTTA
* *
11309 -CCCCAAACTTCCAAAAATCTCATTTTTGACCCCGACACTTCCAAAAAATTACCATTTTA
1 CCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAAATTACCATTTTA
11368 C
1 C
11369 TCTCGGATGT
Statistics
Matches: 160, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
57 9 0.06
58 30 0.19
59 59 0.37
60 42 0.26
61 20 0.12
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.28
Consensus pattern (60 bp):
CCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAAATTACCATTTTA
Found at i:14703 original size:15 final size:15
Alignment explanation
Indices: 14685--14716 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14675 TCTTGATAAA
*
14685 TTAAAAAATTAAGTG
1 TTAAAAAATTAAATG
14700 TTAAAAAATTAAATG
1 TTAAAAAATTAAATG
14715 TT
1 TT
14717 GAATTTTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (15 bp):
TTAAAAAATTAAATG
Found at i:16444 original size:16 final size:15
Alignment explanation
Indices: 16399--16447 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
16389 TGTTTTTGGG
16399 TTTGGTTTAAAATTT
1 TTTGGTTTAAAATTT
* ** *
16414 TTTTGTTCGAGATTT
1 TTTGGTTTAAAATTT
16429 TTTGAGTTTAAAATTT
1 TTTG-GTTTAAAATTT
16445 TTT
1 TTT
16448 TTTTGGATTT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.61
Consensus pattern (15 bp):
TTTGGTTTAAAATTT
Found at i:21081 original size:15 final size:15
Alignment explanation
Indices: 21061--21099 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
21051 GCACATCAAA
*
21061 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
21076 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
21090 CAAGAATTAA
1 CAAGAATTAA
21100 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:22357 original size:21 final size:22
Alignment explanation
Indices: 22331--22411 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 22
22321 CAAAGAGTAC
22331 CAAAGTACTAACAGAGAGCACA
1 CAAAGTACTAACAGAGAGCACA
*
22353 -TAAGTACTGGGCAACAGAGAGCACA
1 CAAAGTACT----AACAGAGAGCACA
*
22378 CAAAGTGCTAATCAGAGAGCACA
1 CAAAGTACTAA-CAGAGAGCACA
* *
22401 CACAGTGCTAA
1 CAAAGTACTAA
22412 TAACAGAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.14
22 2 0.04
23 21 0.43
25 13 0.27
26 6 0.12
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (22 bp):
CAAAGTACTAACAGAGAGCACA
Found at i:22393 original size:23 final size:24
Alignment explanation
Indices: 22366--22445 Score: 94
Period size: 23 Copynumber: 3.4 Consensus size: 24
22356 GTACTGGGCA
22366 ACAGAGAGCACACAAAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAAT
*
22390 -CAGAGAGCACACACAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAAT
* *
22413 AACAGAGAGCACGA-GATGTGCTAA-
1 -ACAGAGAGCAC-ACAAAGTGCTAAT
22437 ACAGAGAGC
1 ACAGAGAGC
22446 GCGCTAGTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
23 31 0.63
25 17 0.35
26 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.11
Consensus pattern (24 bp):
ACAGAGAGCACACAAAGTGCTAAT
Found at i:24851 original size:33 final size:34
Alignment explanation
Indices: 24785--24875 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 34
24775 GTTGGTCAAA
* *
24785 AAAGTCAA-CGGTCAACGATCAAAGTTAACGGTC
1 AAAGTCAATGGGTCAAAGATCAAAGTTAACGGTC
*
24818 AAGGTCAATGGGTCAAAG-TCAACAGTTAA-GGTC
1 AAAGTCAATGGGTCAAAGATCAA-AGTTAACGGTC
*
24851 AAAGTCAAT-AGTCAACA-ATCAAAGT
1 AAAGTCAATGGGTCAA-AGATCAAAGT
24876 CAATAGGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
32 8 0.16
33 28 0.57
34 13 0.27
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.20
Consensus pattern (34 bp):
AAAGTCAATGGGTCAAAGATCAAAGTTAACGGTC
Found at i:24877 original size:26 final size:25
Alignment explanation
Indices: 24829--24878 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
24819 AGGTCAATGG
* * *
24829 GTCAAAGTCAACAGTTAAGGTCAAA
1 GTCAAAGTCAACAATCAAAGTCAAA
24854 GTCAATAGTCAACAATCAAAGTCAA
1 GTCAA-AGTCAACAATCAAAGTCAA
24879 TAGGTTAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (25 bp):
GTCAAAGTCAACAATCAAAGTCAAA
Found at i:28625 original size:11 final size:11
Alignment explanation
Indices: 28602--28632 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28592 GGTTTTTGTT
28602 TTTCTTTTA-A
1 TTTCTTTTAGA
28612 TTTCTTTTAGA
1 TTTCTTTTAGA
28623 TTTCTTTTAG
1 TTTCTTTTAG
28633 GACGTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (11 bp):
TTTCTTTTAGA
Found at i:29316 original size:14 final size:14
Alignment explanation
Indices: 29271--29316 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
29261 ATTGTTCTTG
29271 ATTTTTTATTCTAA
1 ATTTTTTATTCTAA
* ** *
29285 ATTGTGAATTCTCA
1 ATTTTTTATTCTAA
29299 ATTTTTTATTCTAA
1 ATTTTTTATTCTAA
29313 ATTT
1 ATTT
29317 CCAATTCCAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (14 bp):
ATTTTTTATTCTAA
Found at i:29322 original size:28 final size:27
Alignment explanation
Indices: 29271--29333 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
29261 ATTGTTCTTG
*
29271 ATTTTTTATTCTAAATTGTGAATTCTCA
1 ATTTTTTATTCTAAATTGTCAATTC-CA
29299 ATTTTTTATTCTAAATT-TCCAATTCCA
1 ATTTTTTATTCTAAATTGT-CAATTCCA
*
29326 TTTTTTTA
1 ATTTTTTA
29334 AAAAAATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 10 0.31
28 22 0.69
ACGTcount: A:0.27, C:0.13, G:0.03, T:0.57
Consensus pattern (27 bp):
ATTTTTTATTCTAAATTGTCAATTCCA
Found at i:31507 original size:52 final size:52
Alignment explanation
Indices: 31411--31515 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
31401 TTACAAATGG
* * *
31411 TAAGAAAGTATTATTTAATTATTTAATTTTAATCCGTTAATTATTATGATGT
1 TAAGAAAATATTATTAAATTATTTAATTTTAATCAGTTAATTATTATGATGT
* *
31463 TAAGAAAATATTATTAAATTATTTAATTTTAAAT-AGTTAGTTATTATGTTGT
1 TAAGAAAATATTATTAAATTATTTAATTTT-AATCAGTTAATTATTATGATGT
31515 T
1 T
31516 GAGATTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 44 0.94
53 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (52 bp):
TAAGAAAATATTATTAAATTATTTAATTTTAATCAGTTAATTATTATGATGT
Found at i:44520 original size:27 final size:28
Alignment explanation
Indices: 44481--44542 Score: 108
Period size: 27 Copynumber: 2.2 Consensus size: 28
44471 CACCTTGAAG
44481 TTTTTTCGGGTTAAGAGATGTTTGGGGA
1 TTTTTTCGGGTTAAGAGATGTTTGGGGA
44509 TTTTTT-GGGTTAAGAGATGTTTGGGGA
1 TTTTTTCGGGTTAAGAGATGTTTGGGGA
*
44536 TTCTTTC
1 TTTTTTC
44543 ATCTATTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 26 0.81
28 6 0.19
ACGTcount: A:0.16, C:0.05, G:0.32, T:0.47
Consensus pattern (28 bp):
TTTTTTCGGGTTAAGAGATGTTTGGGGA
Found at i:45319 original size:21 final size:21
Alignment explanation
Indices: 45295--45344 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
45285 TTTTCCCAAT
45295 TTTCCCTCCTAAACCAAAATA
1 TTTCCCTCCTAAACCAAAATA
*
45316 TTTCCCTCCTAAACCGAAATA
1 TTTCCCTCCTAAACCAAAATA
45337 TTTCCCTC
1 TTTCCCTC
45345 TTTCTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (21 bp):
TTTCCCTCCTAAACCAAAATA
Found at i:48747 original size:31 final size:31
Alignment explanation
Indices: 48712--48779 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
48702 TTAACAACTG
* *
48712 AGTGACTTGAATAAAAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTTCGAATAGTTC
* *
48743 AGTGACTTAAATGAAAACTTTCGAATAGTTT
1 AGTGACTTAAATAAAAACTTTCGAATAGTTC
48774 AGTGAC
1 AGTGAC
48780 CAAATTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTCGAATAGTTC
Found at i:72025 original size:2 final size:2
Alignment explanation
Indices: 72018--72045 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
72008 TCACTCAAAA
72018 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
72046 TTTGTGTTCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:72887 original size:15 final size:17
Alignment explanation
Indices: 72867--72902 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
72857 AAACTCATCC
72867 AAAAAAAAAA-AGA-AG
1 AAAAAAAAAAGAGAGAG
72882 AAAAAAAAAAGAGAGAG
1 AAAAAAAAAAGAGAGAG
72899 AAAA
1 AAAA
72903 GAGAGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAGAGAG
Found at i:73290 original size:30 final size:31
Alignment explanation
Indices: 73250--73310 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
73240 TTACCTAGTG
*
73250 GGTCCATAAAC-TTTCCAGAAATCATATTTT
1 GGTCCATAAACTTTTCCAAAAATCATATTTT
* *
73280 GGTCCCTAAACTTTTCCAAAAATTATATTTT
1 GGTCCATAAACTTTTCCAAAAATCATATTTT
73311 TACCCTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (31 bp):
GGTCCATAAACTTTTCCAAAAATCATATTTT
Found at i:73479 original size:119 final size:117
Alignment explanation
Indices: 73268--73801 Score: 471
Period size: 119 Copynumber: 4.6 Consensus size: 117
73258 AACTTTCCAG
* * * *
73268 AAATCATATTTTGGTCCCTAAACTTTTCCAAAAATTATATTTTTACCCTCAAACTTTTTCAAAAT
1 AAATCACATTTTGATCCCTAAACTTTTCC-AAAATTACATTTTGACCCTCAAACTTTTTCAAAAT
*
73333 TACATTTTTATTCCAACATTTCAAAAATCACATTTTTACCTCCAAAA-TTTTCTA
65 TACATTTTTATTCCAACATTTCAAAAATCACATTTTGACC-CCAAAATTTTTC-A
*
73387 AAATCACATTTTGATCCCTAAACTTTTCCGAAAATTACATTTTGACCCTCGAACTTTTTCAAAAT
1 AAATCACATTTTGATCCCTAAACTTTTCC-AAAATTACATTTTGACCCTCAAACTTTTTCAAAAT
* *
73452 TACATTTTTATTCCAACATTTCAAAAATCACATTTTGACCCTAAACTTTTTCA
65 TACATTTTTATTCCAACATTTCAAAAATCACATTTTGACCCCAAAATTTTTCA
* * * * * *
73505 AAATCACATTTTGA-CCTTAAACTTTTCCAAAATCACATTTTGA-CC-CAAAGTTTTCCAGAATC
1 AAATCACATTTTGATCCCTAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTTTTCAAAATT
* * * * * * * * **
73567 ACAATTTGA-CCCTTAAC-TTTCCTAAAATTATATTTTGATCCC-AAACTTCCCA
66 ACATTTTTATTCC--AACATTT-CAAAAATCACATTTTGACCCCAAAATTTTTCA
* * * * * *
73619 AAATCACATTTTTA-CCCTCAAAATTTTCCAAAATTACATTTTAACTCTTAAACTTTTCCAAAAT
1 AAATCACATTTTGATCCCT-AAACTTTTCCAAAATTACATTTTGACCCTCAAACTTTTTCAAAAT
* * ** * * * * *
73683 CACATTTTGACCCCTATAC-TTTCCCAAAATCACATTTTGGCCCCCAACTTTTCCA
65 TACATTTTTATTCC-A-ACATTT-CAAAAATCACATTTTGACCCCAAAATTTTTCA
* * * * * *
73738 AAACCATATTTTGA-CCCTAAACTTTCCCAAAACTACATTTTTA-CCTTAAAC-TTTTCTAAAAT
1 AAATCACATTTTGATCCCTAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTTTTC-AAAAT
73800 TA
65 TA
73802 TGTTTTAACC
Statistics
Matches: 348, Mismatches: 56, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
113 2 0.01
114 44 0.13
115 43 0.12
116 19 0.05
117 50 0.14
118 65 0.19
119 125 0.36
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (117 bp):
AAATCACATTTTGATCCCTAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTTTTCAAAATT
ACATTTTTATTCCAACATTTCAAAAATCACATTTTGACCCCAAAATTTTTCA
Found at i:73760 original size:29 final size:29
Alignment explanation
Indices: 73256--73799 Score: 442
Period size: 30 Copynumber: 18.6 Consensus size: 29
73246 AGTGGGTCCA
* *
73256 TAAAC-TTTCCAGAAATCATATTTTGGTCCC
1 TAAACTTTTCCA-AAATCACATTTT-GACCC
* * *
73286 TAAACTTTTCCAAAAATTATATTTTTACCC
1 TAAACTTTTCC-AAAATCACATTTTGACCC
* * * *
73316 TCAAACTTTTTCAAAATTACATTTTTATTCC
1 T-AAACTTTTCCAAAATCACATTTTGA-CCC
* * *
73347 --AACATTTCAAAAATCACATTTTTACCTC
1 TAAACTTTTCCAAAATCACATTTTGACC-C
* * *
73375 CAAAATTTTCTAAAATCACATTTTGATCCC
1 TAAACTTTTCCAAAATCACATTTTGA-CCC
*
73405 TAAACTTTTCCGAAAATTACATTTTGACCC
1 TAAACTTTTCC-AAAATCACATTTTGACCC
* * * * *
73435 TCGAACTTTTTCAAAATTACATTTTTATTCC
1 T-AAACTTTTCCAAAATCACATTTTGA-CCC
* *
73466 --AACATTTCAAAAATCACATTTTGACCC
1 TAAACTTTTCCAAAATCACATTTTGACCC
* *
73493 TAAACTTTTTCAAAATCACATTTTGACCT
1 TAAACTTTTCCAAAATCACATTTTGACCC
73522 TAAACTTTTCCAAAATCACATTTTGACCC
1 TAAACTTTTCCAAAATCACATTTTGACCC
* * *
73551 -AAAGTTTTCCAGAATCACAATTTGACCC
1 TAAACTTTTCCAAAATCACATTTTGACCC
* * *
73579 TTAAC-TTTCCTAAAATTATATTTTGATCCC
1 TAAACTTTTCC-AAAATCACATTTTGA-CCC
* *
73609 -AAAC-TTCCCAAAATCACATTTTTACCC
1 TAAACTTTTCCAAAATCACATTTTGACCC
* * * *
73636 TCAAAATTTTCCAAAATTACATTTTAACTCT
1 T-AAACTTTTCCAAAATCACATTTTGAC-CC
73667 TAAACTTTTCCAAAATCACATTTTGACCCC
1 TAAACTTTTCCAAAATCACATTTTGA-CCC
* * *
73697 TATACTTTCCCAAAATCACATTTTGGCCC
1 TAAACTTTTCCAAAATCACATTTTGACCC
** * *
73726 CCAACTTTTCCAAAACCATATTTTGACCC
1 TAAACTTTTCCAAAATCACATTTTGACCC
* * *
73755 TAAACTTTCCCAAAA-CTACATTTTTACCT
1 TAAACTTTTCCAAAATC-ACATTTTGACCC
*
73784 TAAACTTTTCTAAAAT
1 TAAACTTTTCCAAAAT
73800 TATGTTTTAA
Statistics
Matches: 415, Mismatches: 76, Indels: 46
0.77 0.14 0.09
Matches are distributed among these distances:
27 6 0.01
28 83 0.20
29 132 0.32
30 137 0.33
31 56 0.13
32 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAACTTTTCCAAAATCACATTTTGACCC
Found at i:73777 original size:58 final size:57
Alignment explanation
Indices: 73257--73799 Score: 384
Period size: 58 Copynumber: 9.3 Consensus size: 57
73247 GTGGGTCCAT
* * * * *
73257 AAAC-TTTCCAGAAATCATATTTTGGTCCCTAAACTTTTCCAAAAATTATATTTTTACCCTC
1 AAACTTTTCCA-AAATCACATTTT-GACCCTAAAC-TTTCCCAAAA-TACATTTTGACCC-C
* * * * * *
73318 AAACTTTTTCAAAATTACATTTTTATTCC--AACATTT-CAAAAATCACATTTTTACCTCC
1 AAACTTTTCCAAAATCACATTTTGA-CCCTAAAC-TTTCCCAAAAT-ACATTTTGACC-CC
* * *
73376 AAAATTTTCTAAAATCACATTTTGATCCCTAAACTTTTCCGAAAATTACATTTTGACCCTC
1 AAACTTTTCCAAAATCACATTTTGA-CCCTAAAC-TTTCCCAAAA-TACATTTTGACCC-C
* * * * * * *
73437 GAACTTTTTCAAAATTACATTTTTATTCC--AACATTT-CAAAAATCACATTTTGACCCT
1 AAACTTTTCCAAAATCACATTTTGA-CCCTAAAC-TTTCCCAAAAT-ACATTTTGACCCC
* * *
73494 AAACTTTTTCAAAATCACATTTTGACCTTAAACTTTTCCAAAATCACATTTTGA-CCC
1 AAACTTTTCCAAAATCACATTTTGACCCTAAACTTTCCCAAAAT-ACATTTTGACCCC
* * * * * * *
73551 AAAGTTTTCCAGAATCACAATTTGACCCTTAACTTTCCTAAAATTATATTTTGATCCC
1 AAACTTTTCCAAAATCACATTTTGACCCTAAACTTTCCCAAAA-TACATTTTGACCCC
* * * * * **
73609 AAAC-TTCCCAAAATCACATTTTTACCCTCAAAATTTTCCAAAATTACATTTTAACTCTT
1 AAACTTTTCCAAAATCACATTTTGACCCT-AAACTTTCCCAAAA-TACATTTTGAC-CCC
* *
73668 AAACTTTTCCAAAATCACATTTTGACCCCTATACTTTCCCAAAATCACATTTTGGCCCC
1 AAACTTTTCCAAAATCACATTTTGA-CCCTAAACTTTCCCAAAAT-ACATTTTGACCCC
* * * * **
73727 CAACTTTTCCAAAACCATATTTTGACCCTAAACTTTCCCAAAACTACATTTTTACCTT
1 AAACTTTTCCAAAATCACATTTTGACCCTAAACTTTCCCAAAA-TACATTTTGACCCC
*
73785 AAACTTTTCTAAAAT
1 AAACTTTTCCAAAAT
73800 TATGTTTTAA
Statistics
Matches: 384, Mismatches: 77, Indels: 45
0.76 0.15 0.09
Matches are distributed among these distances:
56 1 0.00
57 92 0.24
58 140 0.36
59 43 0.11
60 44 0.11
61 58 0.15
62 6 0.02
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (57 bp):
AAACTTTTCCAAAATCACATTTTGACCCTAAACTTTCCCAAAATACATTTTGACCCC
Found at i:81261 original size:17 final size:17
Alignment explanation
Indices: 81239--81277 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
81229 CTCTACCTTG
* *
81239 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
*
81256 ACAAGAACTCTCAATGA
1 ACAAGAACTCTCAACGA
81273 ACAAG
1 ACAAG
81278 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:91115 original size:20 final size:21
Alignment explanation
Indices: 91069--91171 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 21
91059 AGTTTGAAAC
* *
91069 AATTTTAAAATCAAGTTAAAAT
1 AATTTTAAACT-AAGTCAAAAT
* *
91091 TATTTTAAAC-ATGTCAAAAT
1 AATTTTAAACTAAGTCAAAAT
*
91111 AA-TTTGAACTAAGTCAAAAT
1 AATTTTAAACTAAGTCAAAAT
* * *
91131 CATTTT-AAC-AATTAAAAAT
1 AATTTTAAACTAAGTCAAAAT
91150 -ATTTCTCAAAC-AAGTCAAAAT
1 AATTT-T-AAACTAAGTCAAAAT
91171 A
1 A
91172 GCTCTAGGCT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
18 4 0.06
19 15 0.24
20 22 0.35
21 14 0.22
22 8 0.13
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (21 bp):
AATTTTAAACTAAGTCAAAAT
Found at i:92946 original size:21 final size:21
Alignment explanation
Indices: 92921--92979 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
92911 ACAATGTAGA
92921 CTTCTATCGATACAAGTGACAG
1 CTTCTATCGATACAAGTGAC-G
*
92943 -TTCTATCGATACAAGAGACG
1 CTTCTATCGATACAAGTGACG
* *
92963 CTTCTACCGAAACAAGT
1 CTTCTATCGATACAAGT
92980 TATACTTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (21 bp):
CTTCTATCGATACAAGTGACG
Found at i:94691 original size:24 final size:24
Alignment explanation
Indices: 94664--94738 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
94654 CCAGACAAAA
* *
94664 TTAGCTCTCACGAGCTCAGGATGG
1 TTAGCTCTTACGAGCTCAGAATGG
*
94688 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCTCAGAATGG
* *
94712 TTAGCTCTTACGACCTTAGAATGG
1 TTAGCTCTTACGAGCTCAGAATGG
94736 TTA
1 TTA
94739 ACTAGTATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (24 bp):
TTAGCTCTTACGAGCTCAGAATGG
Found at i:96414 original size:18 final size:18
Alignment explanation
Indices: 96393--96428 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
96383 ACAGCTGTAC
96393 AAAGAAATAATCAAGAAT
1 AAAGAAATAATCAAGAAT
96411 AAAGAAATAATCAAGAAT
1 AAAGAAATAATCAAGAAT
96429 GGAGGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (18 bp):
AAAGAAATAATCAAGAAT
Found at i:104150 original size:21 final size:21
Alignment explanation
Indices: 104113--104153 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
104103 TTTTTAGTAC
*
104113 CGGTAGAAGCTTGACTTGTTT
1 CGGTAGAAGCTTCACTTGTTT
104134 CGGTAGAAG-TTACACTTGTT
1 CGGTAGAAGCTT-CACTTGTT
104154 CCAATAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.37
Consensus pattern (21 bp):
CGGTAGAAGCTTCACTTGTTT
Found at i:105172 original size:18 final size:16
Alignment explanation
Indices: 105141--105184 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
105131 AGGTTTAGAT
*
105141 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
105158 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
105172 TTAAAAATTTATT
1 TTAAAAATTTATT
105185 ATCATCCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:107064 original size:30 final size:31
Alignment explanation
Indices: 107002--107065 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
106992 AAAATGGTCG
*
107002 TTGAATTATTCTAAAGCTTTTATTTAAATCA
1 TTGAATTATTCTAAAGCTTTCATTTAAATCA
*
107033 TTGAATTATT-TGAAAG-TTTCATTTAATTCA
1 TTGAATTATTCT-AAAGCTTTCATTTAAATCA
107063 TTG
1 TTG
107066 GGCTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (31 bp):
TTGAATTATTCTAAAGCTTTCATTTAAATCA
Done.