Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012523.1 Kokia drynarioides strain JFW-HI SEQ_127530, 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: 94342
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:1165 original size:22 final size:22
Alignment explanation
Indices: 1137--1180 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1127 AAAGAATAAT
1137 CATTTAAAGTAGATGAGTTAGA
1 CATTTAAAGTAGATGAGTTAGA
*
1159 CATTTAAAGTAGATGTGTTAGA
1 CATTTAAAGTAGATGAGTTAGA
1181 AGTTACCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (22 bp):
CATTTAAAGTAGATGAGTTAGA
Found at i:3225 original size:20 final size:20
Alignment explanation
Indices: 3200--3253 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3190 AGTCTTCAAG
3200 GTATCGGTAGAAGTGAAGTT
1 GTATCGGTAGAAGTGAAGTT
*
3220 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTGAAGTT
* *
3240 CTACCGGTAGAAGT
1 GTATCGGTAGAAGT
3254 CTCACTGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (20 bp):
GTATCGGTAGAAGTGAAGTT
Found at i:5858 original size:22 final size:23
Alignment explanation
Indices: 5774--5900 Score: 134
Period size: 23 Copynumber: 5.5 Consensus size: 23
5764 AGCACGTTTC
* *
5774 GTGCCCTCTATTCAGCATTGTGT
1 GTGCCCTCTGTTCAGCACTGTGT
*
5797 GTGCCCTCTGTTCAGCATTGTGT
1 GTGCCCTCTGTTCAGCACTGTGT
5820 GTGCCCTCTGTTCAGCACTGTGT
1 GTGCCCTCTGTTCAGCACTGTGT
* * *
5843 GTG-CTTCTGTTTAGCACTTTGT
1 GTGCCCTCTGTTCAGCACTGTGT
* *
5865 GTG-CCTACTGTTGCCAACACT-TAT
1 GTGCCCT-CTGTT--CAGCACTGTGT
5889 GTGCCCTCTGTT
1 GTGCCCTCTGTT
5901 AAGTGCTTCG
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
22 21 0.23
23 52 0.57
24 10 0.11
25 8 0.09
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (23 bp):
GTGCCCTCTGTTCAGCACTGTGT
Found at i:9261 original size:17 final size:16
Alignment explanation
Indices: 9234--9268 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
9224 AAAAATTAAT
*
9234 TAAAAATTAAATAAAA
1 TAAAAATTAAACAAAA
9250 TAAAACATTAAACAAAA
1 TAAAA-ATTAAACAAAA
9267 TA
1 TA
9269 GAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAATTAAACAAAA
Found at i:16080 original size:17 final size:16
Alignment explanation
Indices: 16061--16092 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16051 AAAGTAAAAA
16061 AAAAGGATTAAATTTT
1 AAAAGGATTAAATTTT
16077 AAAAGGATTAAATTTT
1 AAAAGGATTAAATTTT
16093 TTAAAAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
AAAAGGATTAAATTTT
Found at i:17627 original size:20 final size:20
Alignment explanation
Indices: 17604--17645 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
17594 TTTCATTATT
17604 ATATTT-TTAAAAATGTTTAA
1 ATATTTCTTAAAAAT-TTTAA
17624 ATATTTCCTTAAAAATTTTAA
1 ATATTT-CTTAAAAATTTTAA
17645 A
1 A
17646 ATTAGGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTTCTTAAAAATTTTAA
Found at i:18118 original size:29 final size:27
Alignment explanation
Indices: 18053--18120 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
18043 CAGACAGTAT
18053 AATTCAAATAATTATAATTAAAATGAATA
1 AATTCAAAT--TTATAATTAAAATGAATA
* *
18082 ACTACAAATTTATAATTAAAAT-ATATTAA
1 AATTCAAATTTATAATTAAAATGA-A-T-A
18111 AATTCAAATT
1 AATTCAAATT
18121 CAAAGTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 14 0.44
28 1 0.03
29 16 0.50
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (27 bp):
AATTCAAATTTATAATTAAAATGAATA
Found at i:29101 original size:14 final size:13
Alignment explanation
Indices: 29077--29110 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
29067 TTTATCATTG
29077 ACTTTTTTTTTTT
1 ACTTTTTTTTTTT
29090 ACTTTATTTTTTTT
1 ACTTT-TTTTTTTT
*
29104 AATTTTT
1 ACTTTTT
29111 AAAAGCTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (13 bp):
ACTTTTTTTTTTT
Found at i:29301 original size:21 final size:21
Alignment explanation
Indices: 29275--29315 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29265 AATATTTGAA
*
29275 TTTTTTGGTGAATAATATTTT
1 TTTTTTGATGAATAATATTTT
*
29296 TTTTTTGATGATTAATATTT
1 TTTTTTGATGAATAATATTT
29316 GATGTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.63
Consensus pattern (21 bp):
TTTTTTGATGAATAATATTTT
Found at i:30457 original size:31 final size:31
Alignment explanation
Indices: 30422--30484 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
30412 TTATAAATAA
30422 TATGTTTGAAAAAAAGTAAACAAAATTTATG
1 TATGTTTGAAAAAAAGTAAACAAAATTTATG
30453 TATGTTTGAAAAAAAGTAAACAAAATTTATG
1 TATGTTTGAAAAAAAGTAAACAAAATTTATG
30484 T
1 T
30485 CATTAGGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (31 bp):
TATGTTTGAAAAAAAGTAAACAAAATTTATG
Found at i:33952 original size:15 final size:16
Alignment explanation
Indices: 33932--33964 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
33922 TCTTTTTAAG
33932 ATTATAATA-TTTTAT
1 ATTATAATATTTTTAT
*
33947 ATTATATTATTTTTAT
1 ATTATAATATTTTTAT
33963 AT
1 AT
33965 ATTATGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATAATATTTTTAT
Found at i:58603 original size:28 final size:28
Alignment explanation
Indices: 58544--58603 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
58534 CTTTTATGAG
* *
58544 TTTTGACTATTATTTGATAAAAAATTAT
1 TTTTGACTAATATTTGATAAAAAATTAA
*
58572 TTTTTACTAATATTTG-TAAAAAATATAA
1 TTTTGACTAATATTTGATAAAAAAT-TAA
58600 TTTT
1 TTTT
58604 CAAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (28 bp):
TTTTGACTAATATTTGATAAAAAATTAA
Found at i:59149 original size:19 final size:18
Alignment explanation
Indices: 59125--59173 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
59115 TAAAAATAAA
59125 AAAAATAT-AAAATTATTTT
1 AAAAATATAAAAATTA--TT
59144 AAAAAT-TAAAAATTATT
1 AAAAATATAAAAATTATT
*
59161 AAAAGTATAAAAA
1 AAAAATATAAAAA
59174 AATATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATATAAAAATTATT
Found at i:66105 original size:62 final size:61
Alignment explanation
Indices: 66034--66370 Score: 391
Period size: 62 Copynumber: 5.5 Consensus size: 61
66024 AGAGGTATGG
*
66034 CCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGGGATGTCGGCCATTGCATGG
1 CCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGGG-TGTCGGCCATTGCATGA
* * *
66096 CCAACACCAAAAAAATTTGAAAATTTTTTATCTGAGAAAAAGGGGTGTCGACCATTGTATGA
1 CCAACACCAAAAAAATTTGAAATTTTTTTATCTGAG-AAAAGGGGTGTCGGCCATTGCATGA
** * * *
66158 CCAACACCAAAAAAATTTGAAATTTTTTTATCAAATAAATAGGGGTGTCGACCATTGCATGG
1 CCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAA-AGGGGTGTCGGCCATTGCATGA
* * * * * * *
66220 CCAACACAAAAAAAAATTGAAATTTTTTTATTTGAAAAAAAGAGATGTCGGCCATTGGATGA
1 CCAACACCAAAAAAATTTGAAATTTTTTTATCTG-AGAAAAGGGGTGTCGGCCATTGCATGA
* * * *
66282 CCAACACC-CAAAAATTTG--ATCTTTTTTATCAGATAAATAGGGGTGTCGGTCATTGCATGA
1 CCAACACCAAAAAAATTTGAAAT-TTTTTTATCTGAGAAA-AGGGGTGTCGGCCATTGCATGA
66342 CCAACACC-AAAAAA-TTG-AA-TTTTTTATCT
1 CCAACACCAAAAAAATTTGAAATTTTTTTATCT
66371 AATAAAAAAA
Statistics
Matches: 236, Mismatches: 33, Indels: 16
0.83 0.12 0.06
Matches are distributed among these distances:
58 9 0.04
59 9 0.04
60 41 0.17
61 11 0.05
62 154 0.65
63 12 0.05
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (61 bp):
CCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGGGTGTCGGCCATTGCATGA
Found at i:66167 original size:124 final size:123
Alignment explanation
Indices: 66028--66393 Score: 458
Period size: 124 Copynumber: 3.0 Consensus size: 123
66018 GAGAAAAGAG
* * *
66028 GTATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAA-AGGGGATGTCGGCCATTGC
1 GTATGACCAACACCAAAAAAATTTGAAATTTTTTTATCAGATAAATAGGGG-TGTCGGCCATTGC
* * *
66092 ATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCTGAGAAAAAGGGGTGTCGACCATT
65 ATGGCCAACACCAAAAAAA-TTGAAAATTTTTTATCTGAAAAAAAGAGATGTCGACCATT
* *
66152 GTATGACCAACACCAAAAAAATTTGAAATTTTTTTATCAAATAAATAGGGGTGTCGACCATTGCA
1 GTATGACCAACACCAAAAAAATTTGAAATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCA
* * * *
66217 TGGCCAACACAAAAAAAAATTGAAATTTTTTTATTTGAAAAAAAGAGATGTCGGCCATT
66 TGGCCAACAC-CAAAAAAATTGAAAATTTTTTATCTGAAAAAAAGAGATGTCGACCATT
* * *
66276 GGATGACCAACACC-CAAAAATTTG--ATCTTTTTTATCAGATAAATAGGGGTGTCGGTCATTGC
1 GTATGACCAACACCAAAAAAATTTGAAAT-TTTTTTATCAGATAAATAGGGGTGTCGGCCATTGC
* * * * *
66338 ATGACCAACACC-AAAAAATTG--AATTTTTTATCTAATAAAAAAAAGGTGTCGGCCAT
65 ATGGCCAACACCAAAAAAATTGAAAATTTTTTATCTGA-AAAAAAGAGATGTCGACCAT
66394 GCTAAAATTT
Statistics
Matches: 214, Mismatches: 24, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
118 11 0.05
119 18 0.08
120 9 0.04
121 2 0.01
122 42 0.20
123 9 0.04
124 111 0.52
125 12 0.06
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (123 bp):
GTATGACCAACACCAAAAAAATTTGAAATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCA
TGGCCAACACCAAAAAAATTGAAAATTTTTTATCTGAAAAAAAGAGATGTCGACCATT
Found at i:66994 original size:17 final size:17
Alignment explanation
Indices: 66947--66996 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
66937 AAATTTTAAA
66947 AATATATTTTATATTATTT
1 AATA-ATTTTATA-TATTT
*
66966 -TTAA-TTTA-ATATTT
1 AATAATTTTATATATTT
66980 AATAATTTTATATATTT
1 AATAATTTTATATATTT
66997 TTTCATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 5 0.19
15 4 0.15
16 8 0.31
17 7 0.27
18 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATAATTTTATATATTT
Found at i:67838 original size:57 final size:57
Alignment explanation
Indices: 67775--67888 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
67765 ACAAATATAG
67775 ATGCACATCAGATTACAAAATTAAATCCTATCTCCATTCGCTATACACCATCTCCGA
1 ATGCACATCAGATTACAAAATTAAATCCTATCTCCATTCGCTATACACCATCTCCGA
*
67832 ATGCACATCAGATTACAAAATTAAATCTTATCTCCATTCGCTATACACCATCTCCGA
1 ATGCACATCAGATTACAAAATTAAATCCTATCTCCATTCGCTATACACCATCTCCGA
67889 CCATCTTTAC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.29
Consensus pattern (57 bp):
ATGCACATCAGATTACAAAATTAAATCCTATCTCCATTCGCTATACACCATCTCCGA
Found at i:68152 original size:13 final size:13
Alignment explanation
Indices: 68134--68159 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68124 AGATATGTGT
68134 ACGACATACATGC
1 ACGACATACATGC
68147 ACGACATACATGC
1 ACGACATACATGC
68160 TTTACACATC
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:0.38, C:0.31, G:0.15, T:0.15
Consensus pattern (13 bp):
ACGACATACATGC
Found at i:71988 original size:21 final size:21
Alignment explanation
Indices: 71964--72016 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
71954 AAGAGAGGCA
*
71964 ACTATCGATACAAGTCATGAT
1 ACTACCGATACAAGTCATGAT
71985 ACTACCGATACAAGTCATGAT
1 ACTACCGATACAAGTCATGAT
72006 ACTACCGATAC
1 ACTACCGATAC
72017 TAAAAACTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (21 bp):
ACTACCGATACAAGTCATGAT
Found at i:72744 original size:24 final size:24
Alignment explanation
Indices: 72717--72762 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
72707 CACAGACAAA
72717 TTAGCCCACACGAGCCCAGAATGG
1 TTAGCCCACACGAGCCCAGAATGG
* **
72741 TTAGCTCTTACGAGCCCAGAAT
1 TTAGCCCACACGAGCCCAGAAT
72763 CAAAATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (24 bp):
TTAGCCCACACGAGCCCAGAATGG
Found at i:72815 original size:27 final size:27
Alignment explanation
Indices: 72744--72820 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
72734 AGAATGGTTA
* * *
72744 GCTCTTACGAGCCCAGAATCAAAATAAT
1 GCTCTTTCGAG-CCAGAATCAGAATAAC
* * *
72772 GCTCTTTCAAACTAGAATCAGAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
72799 GCTCTTTCGAGCCAGAATCAGA
1 GCTCTTTCGAGCCAGAATCAGA
72821 TTACTCCTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 32 0.80
28 8 0.20
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (27 bp):
GCTCTTTCGAGCCAGAATCAGAATAAC
Found at i:74421 original size:54 final size:53
Alignment explanation
Indices: 74349--74457 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 53
74339 ATAAAAATAT
74349 TTACCGCCTTAATTTTAGAAACAAGGTCTCGATACCTCATTTTCTAAAATCAC
1 TTACCGCCTTAATTTTAGAAACAAGGTCTCGATACCTCATTTTCTAAAATCAC
*
74402 TTACGGCCTTTAATTTTAGAAACAAGGTCTCGATACCTCATTTTCTAAAATCAC
1 TTACCGCC-TTAATTTTAGAAACAAGGTCTCGATACCTCATTTTCTAAAATCAC
74456 TT
1 TT
74458 GACTTTTGAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 7 0.13
54 47 0.87
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (53 bp):
TTACCGCCTTAATTTTAGAAACAAGGTCTCGATACCTCATTTTCTAAAATCAC
Found at i:77221 original size:29 final size:31
Alignment explanation
Indices: 77188--77250 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
77178 TTTATAATTG
77188 AATTTG-GCATCAACCTTT-AAAAAAAGTCA
1 AATTTGAGCATCAACCTTTCAAAAAAAGTCA
** * *
77217 AATTTGATTATTAACCTTTCAAAAAGAGTCA
1 AATTTGAGCATCAACCTTTCAAAAAAAGTCA
77248 AAT
1 AAT
77251 ACGGATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.21
30 9 0.32
31 13 0.46
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (31 bp):
AATTTGAGCATCAACCTTTCAAAAAAAGTCA
Found at i:77344 original size:21 final size:21
Alignment explanation
Indices: 77318--77357 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
77308 TTCTATGCTA
77318 TTTTTTCTGAACT-TTGAATAG
1 TTTTTTCTGAA-TGTTGAATAG
*
77339 TTTTTTTTGAATGTTGAAT
1 TTTTTTCTGAATGTTGAAT
77358 TTGTATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (21 bp):
TTTTTTCTGAATGTTGAATAG
Found at i:78802 original size:22 final size:22
Alignment explanation
Indices: 78780--78820 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
78770 TTTTTACATA
78780 AATGATACA-AAAAATAATAAT
1 AATGATACACAAAAATAATAAT
* *
78801 AATTATCCACAAAAATAATA
1 AATGATACACAAAAATAATA
78821 CACTCCCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (22 bp):
AATGATACACAAAAATAATAAT
Found at i:86164 original size:86 final size:86
Alignment explanation
Indices: 86019--86192 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 86
86009 ACTCAAACAT
86019 ATCACGTTTATCATTATTATCAACATAGCATGATTAGCTTTTGTCCGAATAAATATGAAGTGTAG
1 ATCACGTTTATCATTATTATCAACATAGCATGATTAGCTTTTGTCCGAATAAATATGAAGTGTAG
86084 AAACAAACTATTATAATACAA
66 AAACAAACTATTATAATACAA
*
86105 ATCACGTTTATCATTATTATCAACATAGCATGATTAGCTTTTGTCTGAATAAATATGAAGTGTAG
1 ATCACGTTTATCATTATTATCAACATAGCATGATTAGCTTTTGTCCGAATAAATATGAAGTGTAG
86170 AAACAAACTATTATAATACAA
66 AAACAAACTATTATAATACAA
86191 AT
1 AT
86193 GCACTAAGGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (86 bp):
ATCACGTTTATCATTATTATCAACATAGCATGATTAGCTTTTGTCCGAATAAATATGAAGTGTAG
AAACAAACTATTATAATACAA
Found at i:88792 original size:31 final size:30
Alignment explanation
Indices: 88757--88841 Score: 75
Period size: 31 Copynumber: 2.7 Consensus size: 30
88747 TATATATGAA
88757 TTTTAATTTGATGTAATTATACACGTGAAAC
1 TTTTAATTTGAT-TAATTATACACGTGAAAC
* * * *
88788 TTTT-ATTGTGGTTCAAATATATACTTGAAAC
1 TTTTAATT-TGATT-AATTATACACGTGAAAC
88819 -TTTAATTTTGATTTAATTATACA
1 TTTTAA-TTTGA-TTAATTATACA
88842 TATTTAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
30 7 0.17
31 31 0.74
32 4 0.10
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (30 bp):
TTTTAATTTGATTAATTATACACGTGAAAC
Found at i:89924 original size:19 final size:19
Alignment explanation
Indices: 89892--89934 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
89882 ATTCAAGACT
* * *
89892 AATTTGAAACAAATCGGAA
1 AATTTAAAAAAAATCAGAA
*
89911 AATTTAAAAAAAATTAGAA
1 AATTTAAAAAAAATCAGAA
89930 AATTT
1 AATTT
89935 GGTGAAACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (19 bp):
AATTTAAAAAAAATCAGAA
Found at i:91916 original size:21 final size:21
Alignment explanation
Indices: 91892--91932 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
91882 TTATAATTTA
*
91892 TAAAACCGATGCTTATGTTTC
1 TAAAACCGATACTTATGTTTC
* *
91913 TAAAATCGATATTTATGTTT
1 TAAAACCGATACTTATGTTT
91933 GCTATTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
TAAAACCGATACTTATGTTTC
Done.