Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012112.1 Kokia drynarioides strain JFW-HI SEQ_127111, 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: 93154
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:245 original size:37 final size:38
Alignment explanation
Indices: 176--254 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 38
166 GTGTCATTAT
** *
176 TTTACTTCGGATAGATTCGATGAGGTATTGGGTACCAC
1 TTTACTTCGGATAGATTCGATGAGACACTGGGTACCAC
* * **
214 TTTACTTCGGCTAGGTT-GATGAGACACTGGGTGTCAC
1 TTTACTTCGGATAGATTCGATGAGACACTGGGTACCAC
251 TTTA
1 TTTA
255 TTGCTTCAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 19 0.56
38 15 0.44
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (38 bp):
TTTACTTCGGATAGATTCGATGAGACACTGGGTACCAC
Found at i:2545 original size:31 final size:31
Alignment explanation
Indices: 2478--2545 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
2468 TAACAGCTCG
* *
2478 GTGATTTAAATAAAAACTTTCGAATAGTTCA
1 GTGATTTAAATAAAAACTTTCAAATAATTCA
* * *
2509 ATGATTTAAATGAAAACTCTT-AAATAATTTA
1 GTGATTTAAATAAAAACT-TTCAAATAATTCA
2540 GTGATT
1 GTGATT
2546 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (31 bp):
GTGATTTAAATAAAAACTTTCAAATAATTCA
Found at i:5472 original size:18 final size:18
Alignment explanation
Indices: 5449--5484 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5439 GTTCTCCAGT
*
5449 TTTGTTGATATATTTCAA
1 TTTGTTGATATAATTCAA
5467 TTTGTTGATATAATTCAA
1 TTTGTTGATATAATTCAA
5485 AACGGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTGTTGATATAATTCAA
Found at i:5829 original size:27 final size:27
Alignment explanation
Indices: 5791--5845 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5781 GAGTTCAGAC
5791 ATCTGTCAAATTACACTGATAATACTG
1 ATCTGTCAAATTACACTGATAATACTG
5818 ATCTGTCAAATTACACTGATAATACTG
1 ATCTGTCAAATTACACTGATAATACTG
5845 A
1 A
5846 GTATCGGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (27 bp):
ATCTGTCAAATTACACTGATAATACTG
Found at i:7215 original size:15 final size:15
Alignment explanation
Indices: 7189--7233 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
7179 TTGAAATTTC
7189 AAAATTTGAAAAATAT
1 AAAA-TTGAAAAATAT
7205 AAAGATT-AAAAATAT
1 AAA-ATTGAAAAATAT
*
7220 CAAATTGAAAAATA
1 AAAATTGAAAAATA
7234 ATGATCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 17 0.65
16 5 0.19
17 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (15 bp):
AAAATTGAAAAATAT
Found at i:7358 original size:22 final size:22
Alignment explanation
Indices: 7331--7374 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7321 TAAAAGTTTA
7331 AAAATTGA-AAAATATAAATATT
1 AAAATTGATAAAATA-AAATATT
7353 AAAATTGATTAAAATAAAATAT
1 AAAATTGA-TAAAATAAAATAT
7375 GATGAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 6 0.30
24 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
AAAATTGATAAAATAAAATATT
Found at i:11471 original size:87 final size:87
Alignment explanation
Indices: 11325--11500 Score: 273
Period size: 87 Copynumber: 2.0 Consensus size: 87
11315 GGGTCAAGTA
* *
11325 CTGGAACTGCAGAAGTGTTGCCTTCATTATCAGGTCTAAGTGGTGATTCTAGTGTTAGTTCCTCA
1 CTGGAACTGCAGAAGTGTTCCCTTCATTATCAGGTCCAAGTGGTGATTCTAGTGTTAGTTCCTCA
* *
11390 ATATTATCTAATAGAGTGACCC
66 AGAATATCTAATAGAGTGACCC
*
11412 CTGGAACTGCAGAAGTGTTCCCTTCATTATCAGTTCCAAGTGGTGATTCT-GATGTTAGTTCCTC
1 CTGGAACTGCAGAAGTGTTCCCTTCATTATCAGGTCCAAGTGGTGATTCTAG-TGTTAGTTCCTC
**
11476 TGGAATATCTAATAGAGTGACCC
65 AAGAATATCTAATAGAGTGACCC
11499 CT
1 CT
11501 AATCAGTTGG
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 1 0.01
87 80 0.99
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (87 bp):
CTGGAACTGCAGAAGTGTTCCCTTCATTATCAGGTCCAAGTGGTGATTCTAGTGTTAGTTCCTCA
AGAATATCTAATAGAGTGACCC
Found at i:25441 original size:16 final size:17
Alignment explanation
Indices: 25405--25442 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
25395 GATCTTATGC
* *
25405 TTTGCGGAGAAAGAGAT
1 TTTGCGGAGAAAAAGAA
25422 TTTG-GGAGAAAAAGAA
1 TTTGCGGAGAAAAAGAA
25438 TTTGC
1 TTTGC
25443 CGAGGAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (17 bp):
TTTGCGGAGAAAAAGAA
Found at i:33204 original size:32 final size:32
Alignment explanation
Indices: 33163--33228 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
33153 ATATTAAAAA
33163 TAGAATGGATACTTATATATCGAGTTGTACTC
1 TAGAATGGATACTTATATATCGAGTTGTACTC
33195 TAGAATGGATACTTATATATCGAGTTGTACTC
1 TAGAATGGATACTTATATATCGAGTTGTACTC
33227 TA
1 TA
33229 ATAGATAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (32 bp):
TAGAATGGATACTTATATATCGAGTTGTACTC
Found at i:35196 original size:94 final size:91
Alignment explanation
Indices: 35038--35215 Score: 239
Period size: 94 Copynumber: 1.9 Consensus size: 91
35028 ATACACATAT
* * *
35038 ACACATGTATATATATGAGAAACCTGTTGAAGTTGCATCATTTCACCGATTTCTCTTCATTTGAG
1 ACACATGTATATATATGAGAAAACTGTTGAAGTCGCATCATTTCACCAATTTCTCTTCATTTGAG
*
35103 ACTCTGCAGACTGATATTTCTCTCTC
66 ACTATGCAGACTGATATTTCTCTCTC
* ** *
35129 ACACATGTATATATTTATGAGAAAACTGTTTTAAGTCGCATCATTTCTTCAATTTGTCTTCATTT
1 ACACATGTATATA--TATGAGAAAACTG-TTGAAGTCGCATCATTTCACCAATTTCTCTTCATTT
**
35194 GAGACTATGCAGGTTGATATTT
63 GAGACTATGCAGACTGATATTT
35216 TCTGCCCCTG
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
91 13 0.18
93 12 0.16
94 49 0.66
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (91 bp):
ACACATGTATATATATGAGAAAACTGTTGAAGTCGCATCATTTCACCAATTTCTCTTCATTTGAG
ACTATGCAGACTGATATTTCTCTCTC
Found at i:42383 original size:23 final size:23
Alignment explanation
Indices: 42356--42401 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
42346 AATTTGACAT
42356 TATTTTTTATTTTTTTAAATATA
1 TATTTTTTATTTTTTTAAATATA
42379 TATTTTTTATTTTTTTAAATATA
1 TATTTTTTATTTTTTTAAATATA
42402 CTGGTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTTTTATTTTTTTAAATATA
Found at i:53813 original size:23 final size:23
Alignment explanation
Indices: 53787--53830 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53777 GAATTGAAAA
*
53787 TATTGAAATTCGAACTTTAAATG
1 TATTAAAATTCGAACTTTAAATG
*
53810 TATTAAAATTCGAATTTTAAA
1 TATTAAAATTCGAACTTTAAA
53831 AGAAACCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (23 bp):
TATTAAAATTCGAACTTTAAATG
Found at i:55748 original size:4 final size:4
Alignment explanation
Indices: 55727--55764 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
55717 TCCCCCATTG
* *
55727 GTAT GTAT GCAT GCAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
55765 TGACTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:57375 original size:14 final size:14
Alignment explanation
Indices: 57356--57388 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
57346 ACTAAAAAAT
57356 AAAATTTA-AGTACC
1 AAAATTTAGA-TACC
57370 AAAATTTAGATACC
1 AAAATTTAGATACC
57384 AAAAT
1 AAAAT
57389 AGTAAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (14 bp):
AAAATTTAGATACC
Found at i:60548 original size:4 final size:4
Alignment explanation
Indices: 60539--60565 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
60529 CGGTTTCAAT
60539 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
60566 TGGAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:62653 original size:33 final size:32
Alignment explanation
Indices: 62604--62667 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
62594 TAAAATCTTA
62604 TAGAATATTAGATATAAAATAAAAAAAATAAT
1 TAGAATATTAGATATAAAATAAAAAAAATAAT
* *
62636 TAGAATATTA-ATTTATAAAATTAGAAAAATAA
1 TAGAATATTAGA--TATAAAATAAAAAAAATAA
62668 GTAAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.04
32 10 0.36
33 17 0.61
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (32 bp):
TAGAATATTAGATATAAAATAAAAAAAATAAT
Found at i:70204 original size:21 final size:21
Alignment explanation
Indices: 70180--70221 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
70170 AGGTGGTGGA
*
70180 AGAGGTGGTCGTGGAGGAGGC
1 AGAGGTGGTCGTAGAGGAGGC
*
70201 AGAGGTGGTGGTAGAGGAGGC
1 AGAGGTGGTCGTAGAGGAGGC
70222 GGTCGTGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.57, T:0.14
Consensus pattern (21 bp):
AGAGGTGGTCGTAGAGGAGGC
Found at i:71635 original size:29 final size:29
Alignment explanation
Indices: 71598--71655 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
71588 AAAACCCTGA
71598 AACAAAATCACCATTTTTGAACAATCCTC
1 AACAAAATCACCATTTTTGAACAATCCTC
*
71627 AACACAATCACCATTTTTGAACAATCCTC
1 AACAAAATCACCATTTTTGAACAATCCTC
71656 TCTTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.29, G:0.03, T:0.28
Consensus pattern (29 bp):
AACAAAATCACCATTTTTGAACAATCCTC
Found at i:79109 original size:60 final size:60
Alignment explanation
Indices: 79041--79160 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
79031 TATTCTAAAG
79041 AAGGAACCTTTTAAAGAAAGATTTTACCTTTGTTCTCTAGGAGCTTTTTGCTATTCATGC
1 AAGGAACCTTTTAAAGAAAGATTTTACCTTTGTTCTCTAGGAGCTTTTTGCTATTCATGC
79101 AAGGAACCTTTTAAAGAAAGATTTTACCTTTGTTCTCTAGGAGCTTTTTGCTATTCATGC
1 AAGGAACCTTTTAAAGAAAGATTTTACCTTTGTTCTCTAGGAGCTTTTTGCTATTCATGC
79161 CATTGATGCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (60 bp):
AAGGAACCTTTTAAAGAAAGATTTTACCTTTGTTCTCTAGGAGCTTTTTGCTATTCATGC
Found at i:85332 original size:6 final size:6
Alignment explanation
Indices: 85321--85379 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
85311 AAGCTTATAT
85321 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC
85369 AGTGAC AGTGA
1 AGTGAC AGTGA
85380 ACTAGAGCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.34, C:0.15, G:0.34, T:0.17
Consensus pattern (6 bp):
AGTGAC
Found at i:86319 original size:48 final size:48
Alignment explanation
Indices: 86259--86532 Score: 188
Period size: 48 Copynumber: 5.5 Consensus size: 48
86249 TAATAATGTC
* **
86259 GCATTAGAACAAGGAAGAACAAAGCTGATTGTGTCCCAACATCAGAAG
1 GCATTAGCACAAGGAAGAACAAAGCAAATTGTGTCCCAACATCAGAAG
* *
86307 GCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGACAACATCAGAAG
1 GCATTAGCACAAGGAAGAACAAAGCAAATTGTGT-CC-----CAACATCAGAAG
* * * * * * * * * *
86361 GCATCAGCACAAAGAAGAACAAGGCACATTTTATACAAACACCAAAAG
1 GCATTAGCACAAGGAAGAACAAAGCAAATTGTGTCCCAACATCAGAAG
* *
86409 GCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGACAACATCAGAAG
1 GCATTAGCACAAGGAAGAACAAAGCAAATTGTGT-CC-----CAACATCAGAAG
* * * * * * * * * * *
86463 GCATCAGCACAAAGAATAACAAGGCACATTTTATACAAACACCAAAAG
1 GCATTAGCACAAGGAAGAACAAAGCAAATTGTGTCCCAACATCAGAAG
86511 GCATTAGCACAAGGAAGAACAA
1 GCATTAGCACAAGGAAGAACAA
86533 GGTTCATTGT
Statistics
Matches: 170, Mismatches: 44, Indels: 24
0.71 0.18 0.10
Matches are distributed among these distances:
48 93 0.55
49 3 0.02
53 2 0.01
54 72 0.42
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (48 bp):
GCATTAGCACAAGGAAGAACAAAGCAAATTGTGTCCCAACATCAGAAG
Found at i:86357 original size:54 final size:54
Alignment explanation
Indices: 86295--86484 Score: 225
Period size: 54 Copynumber: 3.6 Consensus size: 54
86285 GATTGTGTCC
* *
86295 CAACATCAGAAGGCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGA
1 CAACATCAGAAGGCATCAGCACAAAGAAGAACAAAACCAATTGTGTGCCAATGA
**
86349 CAACATCAGAAGGCATCAGCACAAAGAAGAAC-AAGGCACATT-T-T----AT-A
1 CAACATCAGAAGGCATCAGCACAAAGAAGAACAAAACCA-ATTGTGTGCCAATGA
* * * *
86396 CAAACACCAAAAGGCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGA
1 C-AACATCAGAAGGCATCAGCACAAAGAAGAACAAAACCAATTGTGTGCCAATGA
*
86451 CAACATCAGAAGGCATCAGCACAAAGAATAACAA
1 CAACATCAGAAGGCATCAGCACAAAGAAGAACAA
86485 GGCACATTTT
Statistics
Matches: 111, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
47 2 0.02
48 32 0.29
49 5 0.05
50 1 0.01
52 1 0.01
53 5 0.05
54 63 0.57
55 2 0.02
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (54 bp):
CAACATCAGAAGGCATCAGCACAAAGAAGAACAAAACCAATTGTGTGCCAATGA
Found at i:86545 original size:102 final size:102
Alignment explanation
Indices: 86304--86532 Score: 449
Period size: 102 Copynumber: 2.2 Consensus size: 102
86294 CCAACATCAG
86304 AAGGCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGACAACATCAGAAGGCATCAGC
1 AAGGCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGACAACATCAGAAGGCATCAGC
86369 ACAAAGAAGAACAAGGCACATTTTATACAAACACCAA
66 ACAAAGAAGAACAAGGCACATTTTATACAAACACCAA
86406 AAGGCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGACAACATCAGAAGGCATCAGC
1 AAGGCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGACAACATCAGAAGGCATCAGC
*
86471 ACAAAGAATAACAAGGCACATTTTATACAAACACCAA
66 ACAAAGAAGAACAAGGCACATTTTATACAAACACCAA
86508 AAGGCATTAGCACAAGGAAGAACAA
1 AAGGCATTAGCACAAGGAAGAACAA
86533 GGTTCATTGT
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 126 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.14
Consensus pattern (102 bp):
AAGGCATTAGCACAAGGAAGAACAAAACCAATTGTGTGCCAATGACAACATCAGAAGGCATCAGC
ACAAAGAAGAACAAGGCACATTTTATACAAACACCAA
Found at i:87209 original size:69 final size:69
Alignment explanation
Indices: 87070--87230 Score: 178
Period size: 69 Copynumber: 2.3 Consensus size: 69
87060 AAGGATCTAG
* * * * * * * *
87070 TGCTACCATAAGATTTATACGAGTCTCTTGATTATTCTAATCTCTTTAAGCTGCTCGAAGCTAAT
1 TGCTACCATTAGATTGATATGAGTCTCTTGATTATTCTAATATCCTTAAACTACTCGAAACTAAT
*
87135 CTGA
66 ATGA
* * ** *
87139 TGCTACCATTAGATTGATATGAGTCTTTTGATTCTTCTAATATCCTTAAACTACTTTAAATTAAT
1 TGCTACCATTAGATTGATATGAGTCTCTTGATTATTCTAATATCCTTAAACTACTCGAAACTAAT
87204 ATGA
66 ATGA
*
87208 TGCTACTATTAGATTGATTATGA
1 TGCTACCATTAGATTGA-TATGA
87231 ACGAAATTTA
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
69 71 0.93
70 5 0.07
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (69 bp):
TGCTACCATTAGATTGATATGAGTCTCTTGATTATTCTAATATCCTTAAACTACTCGAAACTAAT
ATGA
Found at i:89388 original size:69 final size:69
Alignment explanation
Indices: 89276--89405 Score: 188
Period size: 69 Copynumber: 1.9 Consensus size: 69
89266 AATCCGATGT
* * * * * *
89276 TACCATCATATTCATATGAGTCTCTTGATTCTTTTAATTTCCTTAAGCTACCTGAAGCTAATCCA
1 TACCATCAGATTCATACGAGTCTCTTGATTATTCTAATCTCCTTAAACTACCTGAAGCTAATCCA
89341 GTGC
66 GTGC
* *
89345 TACCATCAGATTGATACGAGTCTCTTGATTATTCTAATCTCCTTAAACTACTTGAAGCTAA
1 TACCATCAGATTCATACGAGTCTCTTGATTATTCTAATCTCCTTAAACTACCTGAAGCTAA
89406 CTTTACTTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (69 bp):
TACCATCAGATTCATACGAGTCTCTTGATTATTCTAATCTCCTTAAACTACCTGAAGCTAATCCA
GTGC
Found at i:92481 original size:23 final size:23
Alignment explanation
Indices: 92408--92581 Score: 140
Period size: 23 Copynumber: 7.5 Consensus size: 23
92398 TATACGGAAC
* *
92408 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
92430 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
92451 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
92477 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
92500 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * * *
92523 AATCAAAGAGCACACACAGTGTT
1 AAACAGAGAGCACACAAAGTGCT
* *
92546 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
92571 AAACAGAGAGC
1 AAACAGAGAGC
92582 GCGCTAGTGT
Statistics
Matches: 122, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
21 17 0.14
23 69 0.57
24 2 0.02
25 27 0.22
26 7 0.06
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:92533 original size:69 final size:67
Alignment explanation
Indices: 92408--92557 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 67
92398 TATACGGAAC
* *
92408 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAAAGAGCACACACAG
92473 TGCT-
63 TGCTA
92477 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAAAGAGCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAAAGAGCACACACA
*
92541 GTGTTA
62 GTGCTA
92547 ATAACAGAGAG
1 A-AACAGAGAG
92558 CACGAGACGT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 31 0.43
70 12 0.17
71 20 0.28
72 7 0.10
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAAAGAGCACACACAGTGC
TA
Done.