Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012780.1 Kokia drynarioides strain JFW-HI SEQ_127792, 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: 123354
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4663 original size:17 final size:17
Alignment explanation
Indices: 4613--4664 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
4603 AAATTTTATA
*
4613 TTACATATATTAATATAT
1 TTACATATA-TAATATGT
* * * *
4631 TCATAAATAAAATATGT
1 TTACATATATAATATGT
4648 TTACATATATAATATGT
1 TTACATATATAATATGT
4665 ATTTTATTAA
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (17 bp):
TTACATATATAATATGT
Found at i:7841 original size:15 final size:15
Alignment explanation
Indices: 7821--7873 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 15
7811 ATACTACAAA
7821 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
7836 ATATTTATAATTTAAT
1 ATATTTATTA-TTAAT
7852 AAATATTTATTATTAAT
1 --ATATTTATTATTAAT
7869 ATATT
1 ATATT
7874 AATATTGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 14 0.42
16 5 0.15
17 5 0.15
18 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:7937 original size:16 final size:16
Alignment explanation
Indices: 7906--7942 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
7896 TAATGAAGAA
7906 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
7922 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
7938 TATTA
1 TATTA
7943 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:8073 original size:13 final size:13
Alignment explanation
Indices: 8055--8079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8045 TCGAAAATTA
8055 TAATATTTTATAT
1 TAATATTTTATAT
8068 TAATATTTTATA
1 TAATATTTTATA
8080 AATTTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATATTTTATAT
Found at i:18229 original size:38 final size:38
Alignment explanation
Indices: 18147--18256 Score: 136
Period size: 38 Copynumber: 3.0 Consensus size: 38
18137 TCTTTCGAGG
* *
18147 TGTCACTCCATAGAGCCTGTAGAT---CATTTTCATGG
1 TGTCACTCCAAAGAGCCTGTAGATAACCATTTTCATGA
* * *
18182 TGTCGCTCCAAAAAGCATGTAGATAACCATTTTCATGA
1 TGTCACTCCAAAGAGCCTGTAGATAACCATTTTCATGA
* *
18220 TGTCACTCCAAAGAGCCTATAAATAACCATTTTCATG
1 TGTCACTCCAAAGAGCCTGTAGATAACCATTTTCATG
18257 CCTATAGATA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
35 20 0.32
38 42 0.68
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (38 bp):
TGTCACTCCAAAGAGCCTGTAGATAACCATTTTCATGA
Found at i:32184 original size:29 final size:29
Alignment explanation
Indices: 32120--32512 Score: 257
Period size: 29 Copynumber: 13.3 Consensus size: 29
32110 TAGTAATCAA
* **
32120 ATTTTGACCCTCGAACTTTCCAAAAATTTT
1 ATTTTGACCC-CAAACTTTCCAAAAATTAC
* *
32150 ATTTTTGACCCCAAACTTCCCAAAAAATAC
1 A-TTTTGACCCCAAACTTTCCAAAAATTAC
* * *
32180 ATTTTAACCCCAAACTTCCCAAAAATTAT
1 ATTTTGACCCCAAACTTTCCAAAAATTAC
* * *
32209 ATTTTAACCCTTAAACTTTCTAAAAATTAC
1 ATTTTGACCC-CAAACTTTCCAAAAATTAC
* *
32239 ATTTTAACCCTCAAACCTTCTCAAAAATTAC
1 ATTTTGACCC-CAAACTTTC-CAAAAATTAC
* * *
32270 AATTTTGACCCCTAAACTTTGCAATAATTAT
1 -ATTTTGACCCC-AAACTTTCCAAAAATTAC
*
32301 ATTTTGACCCCTAAACTTTCC-AAAATCAC
1 ATTTTGACCCC-AAACTTTCCAAAAATTAC
* ** *
32330 ATTTTTGACCTCGTACTTTTCAAAAATTAC
1 A-TTTTGACCCCAAACTTTCCAAAAATTAC
*
32360 ATTTT-ACCCCTAAA-TTTCCAAAAAAT-C
1 ATTTTGACCCC-AAACTTTCCAAAAATTAC
** *
32387 ATATTTTTCCCTCGAACTTT-CAAAAATTACC
1 AT-TTTGACCC-CAAACTTTCCAAAAATTA-C
* * *
32418 ATTTT-ACCCCCAGA-TGTCCAAAAATTAT
1 ATTTTGA-CCCCAAACTTTCCAAAAATTAC
* * * *
32446 TTTTTAACCTCAAATTTTCC-AAAATTACC
1 ATTTTGACCCCAAACTTTCCAAAAATTA-C
* *
32475 ATTTT-ACCCCTGAA-TGTCCAAAAATTAC
1 ATTTTGACCCC-AAACTTTCCAAAAATTAC
*
32503 ATTTTTACCC
1 ATTTTGACCC
32513 TTGAGTTTCC
Statistics
Matches: 290, Mismatches: 51, Indels: 45
0.75 0.13 0.12
Matches are distributed among these distances:
27 3 0.01
28 49 0.17
29 97 0.33
30 96 0.33
31 30 0.10
32 15 0.05
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTTTGACCCCAAACTTTCCAAAAATTAC
Found at i:32412 original size:57 final size:57
Alignment explanation
Indices: 32152--32542 Score: 244
Period size: 57 Copynumber: 6.7 Consensus size: 57
32142 AAAATTTTAT
* * * * *
32152 TTTTGACCC-CAAACTTCCCAAAAAATACATTTTAACCCC-AAACTTCCCAAAAATTATA
1 TTTT-ACCCTCAAACTT-TCAAAAATTACATTTT-ACCCCTAAATTTCCAAAAAATCATA
* * * *
32210 TTTTAACCCTTAAACTTTCTAAAAATTACATTTTAACCCTCAAACCTTCTCAAAAATTACA-A
1 TTTT-ACCCTCAAACTTTC-AAAAATTACATTTTACCCCT-AAA-TTTC-CAAAAAAT-CATA
* * *
32272 TTTTGACCC-CTAAACTTTGCAATAATTATATTTTGACCCCTAAACTTTCC--AAAATCACA
1 TTTT-ACCCTC-AAACTTT-CAAAAATTACATTTT-ACCCCTAAA-TTTCCAAAAAATCATA
**
32331 TTTTTGA-CCTCGTACTTTTCAAAAATTACATTTTACCCCTAAATTTCCAAAAAATCATA
1 -TTTT-ACCCTCAAAC-TTTCAAAAATTACATTTTACCCCTAAATTTCCAAAAAATCATA
* * * * * * *
32390 TTTTTCCCTCGAACTTTCAAAAATTACCATTTTACCCCCAGATGTCC-AAAAATTATT
1 TTTTACCCTCAAACTTTCAAAAATTA-CATTTTACCCCTAAATTTCCAAAAAATCATA
* * * * * *
32447 TTTTAACCTCAAATTTTCCAAAATTACCATTTTACCCCTGAATGTCCAAAAATTACAT-
1 TTTTACCCTCAAACTTTCAAAAATTA-CATTTTACCCCTAAATTTCCAAAAAAT-CATA
** * *
32505 TTTTACCCT-TGAGTTTCCAAAATTACCATTTTACCCCT
1 TTTTACCCTCAAACTTTCAAAAATTA-CATTTTACCCCT
32543 CGAGTGTCCT
Statistics
Matches: 272, Mismatches: 41, Indels: 41
0.77 0.12 0.12
Matches are distributed among these distances:
57 90 0.33
58 65 0.24
59 51 0.19
60 13 0.05
61 5 0.02
62 41 0.15
63 7 0.03
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (57 bp):
TTTTACCCTCAAACTTTCAAAAATTACATTTTACCCCTAAATTTCCAAAAAATCATA
Found at i:32440 original size:28 final size:29
Alignment explanation
Indices: 32407--32600 Score: 139
Period size: 29 Copynumber: 6.7 Consensus size: 29
32397 CTCGAACTTT
32407 CAAAAATTACCATTTTACCCCC-AGATGTC
1 CAAAAATTACCATTTTACCCCCGAG-TGTC
** * ** * *
32436 CAAAAATTA-TTTTTTAACCTCAAATTTTC
1 CAAAAATTACCATTTT-ACCCCCGAGTGTC
* *
32465 C-AAAATTACCATTTTACCCCTGAATGTC
1 CAAAAATTACCATTTTACCCCCGAGTGTC
** *
32493 CAAAAATTA-CATTTTTACCCTTGAGTTTC
1 CAAAAATTACCA-TTTTACCCCCGAGTGTC
32522 C-AAAATTACCATTTTACCCCTCGAGTGTC
1 CAAAAATTACCATTTTACCCC-CGAGTGTC
* * * * *
32551 CTAAATTTATC-TTTCTACCCCCGAATCTC
1 CAAAAATTACCATTT-TACCCCCGAGTGTC
*
32580 TAAAAATTACCATTTTACCCC
1 CAAAAATTACCATTTTACCCC
32601 TGGGCATCCA
Statistics
Matches: 128, Mismatches: 27, Indels: 20
0.73 0.15 0.11
Matches are distributed among these distances:
28 37 0.29
29 74 0.58
30 17 0.13
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCGAGTGTC
Found at i:32542 original size:29 final size:29
Alignment explanation
Indices: 32352--32601 Score: 137
Period size: 29 Copynumber: 8.7 Consensus size: 29
32342 GTACTTTTCA
* *
32352 AAAATTA-CATTTTACCCCT-AAATTTCC
1 AAAATTACCATTTTACCCCTCGAATGTCC
* * ** * *
32379 AAAA-AATCATATTTTTCCCTCGAACTTTCA
1 AAAATTACCAT-TTTACCCCTCGAA-TGTCC
32409 AAAATTACCATTTTACCCC-C-AGATGTCC
1 AAAATTACCATTTTACCCCTCGA-ATGTCC
** * * *
32437 AAAAATTA-TTTTTTA-ACCTCAAATTTTCC
1 -AAAATTACCATTTTACCCCTCGAA-TGTCC
32466 AAAATTACCATTTTACCCCT-GAATGTCC
1 AAAATTACCATTTTACCCCTCGAATGTCC
* * *
32494 AAAAATTA-CATTTTTA-CCCTTGAGTTTCC
1 -AAAATTACCA-TTTTACCCCTCGAATGTCC
*
32523 AAAATTACCATTTTACCCCTCGAGTGTCC
1 AAAATTACCATTTTACCCCTCGAATGTCC
* * * *
32552 TAAATTTATC-TTTCTACCCC-CGAATCTCTA
1 -AAAATTACCATTT-TACCCCTCGAATGTC-C
32582 AAAATTACCATTTTACCCCT
1 AAAATTACCATTTTACCCCT
32602 GGGCATCCAA
Statistics
Matches: 170, Mismatches: 31, Indels: 41
0.70 0.13 0.17
Matches are distributed among these distances:
26 1 0.01
27 9 0.05
28 47 0.28
29 76 0.45
30 33 0.19
31 4 0.02
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTCGAATGTCC
Found at i:32557 original size:57 final size:57
Alignment explanation
Indices: 32347--32601 Score: 211
Period size: 57 Copynumber: 4.4 Consensus size: 57
32337 ACCTCGTACT
* * * *
32347 TTTCAAAAATTA-CATTTTACCCCT-AAATTTCCAAAAAATCATA-TTTTT-CCCTCGAA
1 TTTCAAAAATTACCATTTTACCCCTCGAGTGTCC-AAAAAT--TACTTTTTACCCTAGAA
* *
32403 CTTTCAAAAATTACCATTTTACCCC-C-AGATGTCCAAAAATTATTTTTTAACCTCA-AA
1 -TTTCAAAAATTACCATTTTACCCCTCGAG-TGTCCAAAAATTACTTTTTACCCT-AGAA
* * * *
32460 TTTTCCAAAATTACCATTTTACCCCT-GAATGTCCAAAAATTACATTTTTACCCTTGAG
1 -TTTCAAAAATTACCATTTTACCCCTCGAGTGTCCAAAAATTAC-TTTTTACCCTAGAA
* * * * **
32518 TTTCCAAAATTACCATTTTACCCCTCGAGTGTCCTAAATTTATCTTTCTACCCCCGAA
1 TTTCAAAAATTACCATTTTACCCCTCGAGTGTCCAAAAATTA-CTTTTTACCCTAGAA
*
32576 TCTCTAAAAATTACCATTTTACCCCT
1 TTTC-AAAAATTACCATTTTACCCCT
32602 GGGCATCCAA
Statistics
Matches: 165, Mismatches: 20, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
55 2 0.01
56 5 0.03
57 85 0.52
58 52 0.32
59 21 0.13
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (57 bp):
TTTCAAAAATTACCATTTTACCCCTCGAGTGTCCAAAAATTACTTTTTACCCTAGAA
Found at i:35582 original size:59 final size:57
Alignment explanation
Indices: 35519--35675 Score: 235
Period size: 60 Copynumber: 2.6 Consensus size: 57
35509 ACTAATGTAA
35519 ACATTAAAAAATATTAAA-ATGACTAAATATATAATACTTTATATTATGTAATTTAGAAC
1 ACATTAAAAAA-A-TAAATAT-ACTAAATATATAATACTTTATATTATGTAATTTAGAAC
35578 ACATTAAAAAAAATAAACTTATACTAAATATATAATACTTTATATTATGTAATTTAGAAC
1 ACATT-AAAAAAATAAA--TATACTAAATATATAATACTTTATATTATGTAATTTAGAAC
35638 ACATTAAAAAAATAAACTTATACTAAATATATAATACT
1 ACATTAAAAAAATAAA--TATACTAAATATATAATACT
35676 AATGTAAACA
Statistics
Matches: 94, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
58 4 0.04
59 39 0.41
60 49 0.52
61 2 0.02
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (57 bp):
ACATTAAAAAAATAAATATACTAAATATATAATACTTTATATTATGTAATTTAGAAC
Found at i:35604 original size:60 final size:59
Alignment explanation
Indices: 35540--35675 Score: 263
Period size: 60 Copynumber: 2.3 Consensus size: 59
35530 TATTAAAATG
35540 ACTAAATATATAATACTTTATATTATGTAATTTAGAACACATTAAAAAAAATAAACTTAT
1 ACTAAATATATAATACTTTATATTATGTAATTTAGAACACATT-AAAAAAATAAACTTAT
35600 ACTAAATATATAATACTTTATATTATGTAATTTAGAACACATTAAAAAAATAAACTTAT
1 ACTAAATATATAATACTTTATATTATGTAATTTAGAACACATTAAAAAAATAAACTTAT
35659 ACTAAATATATAATACT
1 ACTAAATATATAATACT
35676 AATGTAAACA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
59 33 0.43
60 43 0.57
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (59 bp):
ACTAAATATATAATACTTTATATTATGTAATTTAGAACACATTAAAAAAATAAACTTAT
Found at i:41986 original size:22 final size:24
Alignment explanation
Indices: 41947--41992 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
41937 AGAAAATAAA
*
41947 AAAACTAAAAAGATAAA-TATTTT
1 AAAACTAAAAAGACAAATTATTTT
*
41970 AAAA-TAAAAATACAAATTATTTT
1 AAAACTAAAAAGACAAATTATTTT
41993 GATCGAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAACTAAAAAGACAAATTATTTT
Found at i:43122 original size:37 final size:35
Alignment explanation
Indices: 42988--43149 Score: 175
Period size: 35 Copynumber: 4.6 Consensus size: 35
42978 AGGCTGACAT
* * * *
42988 TTAACAAA-GTTGGAATAAACTCGTTTAAGACAACC
1 TTAA-AAAGGTTGGGATAGACTCGTCTAAGGCAACC
* *
43023 TTAAAAAGGTTGGGATAGAATCGTCTAAGACAACC
1 TTAAAAAGGTTGGGATAGACTCGTCTAAGGCAACC
* * * *
43058 TTAAAAAGGTCGGGATAGACCTTGTCTAAGGTAACTT
1 TTAAAAAGGTTGGGATAGA-CTCGTCTAAGGCAAC-C
*
43095 TTAAAAAAGGTTAGGATAGACTCGTCTAAGGCAACC
1 TT-AAAAAGGTTGGGATAGACTCGTCTAAGGCAACC
43131 TTAAAAAGGTT-GGATAGAC
1 TTAAAAAGGTTGGGATAGAC
43150 CCGTAAACAG
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
34 11 0.10
35 54 0.50
36 13 0.12
37 15 0.14
38 15 0.14
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (35 bp):
TTAAAAAGGTTGGGATAGACTCGTCTAAGGCAACC
Found at i:43832 original size:2 final size:2
Alignment explanation
Indices: 43825--43865 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
43815 TGTAATTTGG
43825 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
43866 TGTAGTTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:47168 original size:18 final size:18
Alignment explanation
Indices: 47145--47181 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
47135 TTTGTGATCA
47145 AAATTGAAATTGAAAGTG
1 AAATTGAAATTGAAAGTG
*
47163 AAATTGGAATTGAAAGTG
1 AAATTGAAATTGAAAGTG
47181 A
1 A
47182 TATGATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (18 bp):
AAATTGAAATTGAAAGTG
Found at i:50150 original size:16 final size:16
Alignment explanation
Indices: 50125--50169 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
50115 GTGAAAAGAT
*
50125 AATTGGAAAGATGAAA
1 AATTGAAAAGATGAAA
50141 AATTGAAAAGATAGAAA
1 AATTGAAAAGAT-GAAA
*
50158 AA-TAAAAAGATG
1 AATTGAAAAGATG
50170 GGAATAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 1 0.04
16 19 0.73
17 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.18
Consensus pattern (16 bp):
AATTGAAAAGATGAAA
Found at i:55180 original size:11 final size:11
Alignment explanation
Indices: 55166--55216 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
55156 TGTACGTATC
55166 ATACATATCAT
1 ATACATATCAT
*
55177 ATACATGTCAT
1 ATACATATCAT
* *
55188 ATTCATACCAT
1 ATACATATCAT
55199 ATACATATCAT
1 ATACATATCAT
*
55210 ATTCATA
1 ATACATA
55217 AGCAGATGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (11 bp):
ATACATATCAT
Found at i:55187 original size:20 final size:20
Alignment explanation
Indices: 55145--55210 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
55135 ACCCCAAACA
* * *
55145 CATACACATCATGTACGTAT
1 CATACATATCATATACATAT
*
55165 CATACATATCATATACATGT
1 CATACATATCATATACATAT
*
55185 CATATTCATACCATATACATAT
1 CATA--CATATCATATACATAT
55207 CATA
1 CATA
55211 TTCATAAGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 20 0.53
22 18 0.47
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (20 bp):
CATACATATCATATACATAT
Found at i:55199 original size:22 final size:22
Alignment explanation
Indices: 55162--55216 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
55152 ATCATGTACG
*
55162 TATCATA--CATATCATATACA
1 TATCATATTCATACCATATACA
*
55182 TGTCATATTCATACCATATACA
1 TATCATATTCATACCATATACA
55204 TATCATATTCATA
1 TATCATATTCATA
55217 AGCAGATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 6 0.20
22 24 0.80
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (22 bp):
TATCATATTCATACCATATACA
Found at i:57464 original size:29 final size:30
Alignment explanation
Indices: 57411--57480 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
57401 ATCCCAAAAT
57411 TATATATGAACTATGGTTTAATGTGCAATTG
1 TATATATGAACTATGGTTT-ATGTGCAATTG
* * *
57442 TATACATGAACTTTGGTTT-TGTGCAATTT
1 TATATATGAACTATGGTTTATGTGCAATTG
57471 TATATATGAA
1 TATATATGAA
57481 ATTTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.44
Consensus pattern (30 bp):
TATATATGAACTATGGTTTATGTGCAATTG
Found at i:57491 original size:29 final size:29
Alignment explanation
Indices: 57432--57491 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
57422 TATGGTTTAA
* **
57432 TGTGCAATTGTATACATGAACTTTGGTTT
1 TGTGCAATTGTATACATGAAATTTGAATT
* * *
57461 TGTGCAATTTTATATATGAAATTTTAATT
1 TGTGCAATTGTATACATGAAATTTGAATT
57490 TG
1 TG
57492 ATCCAATTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (29 bp):
TGTGCAATTGTATACATGAAATTTGAATT
Found at i:69186 original size:13 final size:14
Alignment explanation
Indices: 69168--69198 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
69158 TTATAGTTAG
69168 AAAATGTTTTTC-A
1 AAAATGTTTTTCGA
69181 AAAATGTTTTTCGA
1 AAAATGTTTTTCGA
69195 AAAA
1 AAAA
69199 AAAATGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (14 bp):
AAAATGTTTTTCGA
Found at i:70155 original size:28 final size:30
Alignment explanation
Indices: 70112--70215 Score: 95
Period size: 33 Copynumber: 3.4 Consensus size: 30
70102 ATCATATATA
*
70112 AAAATTTTAAAAAATTAAATATAATA-A-AT
1 AAAA-TTTAAATAATTAAATATAATATACAT
*
70141 AAAATTTAAATAATTTAATATAATAGTACAT
1 AAAATTTAAATAATTAAATATAATA-TACAT
* * *
70172 AAAATATTTAGATAATTAAAAATAATCATATAT
1 -AAA-ATTTAAATAATTAAATATAAT-ATACAT
*
70205 AAAATATAAAT
1 AAAATTTAAAT
70216 TAATCTATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
28 19 0.31
29 4 0.07
30 1 0.02
31 8 0.13
32 6 0.10
33 22 0.36
34 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTTAAATAATTAAATATAATATACAT
Found at i:76668 original size:61 final size:61
Alignment explanation
Indices: 76573--76690 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
76563 TTAAGAGTTA
76573 ATGATAGAACTAGAACTGTTCTATAATTTTATTTTATACTTTTCAGTTTATAACCACGATG
1 ATGATAGAACTAGAACTGTTCTATAATTTTATTTTATACTTTTCAGTTTATAACCACGATG
*
76634 ATGATAGAACTAGAACTGTTTTATAATTTTATTTTATACTTTTCAGTTTATAACCAC
1 ATGATAGAACTAGAACTGTTCTATAATTTTATTTTATACTTTTCAGTTTATAACCAC
76691 AATGGTGCTG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (61 bp):
ATGATAGAACTAGAACTGTTCTATAATTTTATTTTATACTTTTCAGTTTATAACCACGATG
Found at i:78616 original size:6 final size:6
Alignment explanation
Indices: 78601--78631 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
78591 ACATTATATC
78601 AATT-T AATTCT AATTCT AATTCT AATTCT AA
1 AATTCT AATTCT AATTCT AATTCT AATTCT AA
78632 ATAATGTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTCT
Found at i:81706 original size:31 final size:30
Alignment explanation
Indices: 81667--81748 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
81657 GGTATCAAAT
* *
81667 ATTCATATTTTCATTATCATACCTTGTAATC
1 ATTCATATTTACA-TATCATACCATGTAATC
* **
81698 ATTTATATTCGCATATTCATACCATGTAATC
1 ATTCATATTTACATA-TCATACCATGTAATC
*
81729 ATTCAAATTTACATATCATA
1 ATTCATATTTACATATCATA
81749 ACCTATAATG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 7 0.17
31 35 0.83
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.44
Consensus pattern (30 bp):
ATTCATATTTACATATCATACCATGTAATC
Found at i:83952 original size:20 final size:19
Alignment explanation
Indices: 83928--83986 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
83918 AGCAAAAATC
83928 AAAAGTATCGATACCCTTA
1 AAAAGTATCGATACCCTTA
*
83947 ACAAAGTATCAATA-CCTTGCA
1 A-AAAGTATCGATACCCTT--A
*
83968 AAAATTATCGATACCCTTA
1 AAAAGTATCGATACCCTTA
83987 CTTGGTATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 6 0.18
20 21 0.64
21 6 0.18
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.27
Consensus pattern (19 bp):
AAAAGTATCGATACCCTTA
Found at i:88318 original size:23 final size:21
Alignment explanation
Indices: 88254--88321 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
88244 TACAAAATGA
*
88254 ATCTCTAAGA-TTACAATCAA
1 ATCTCTAAGATTTACAATCAT
88274 ATCTCTAAGATTATA-AGGATCAT
1 ATCTCTAAGATT-TACA--ATCAT
88297 ATCTTCTAAGATTTACATATCAT
1 ATC-TCTAAGATTTACA-ATCAT
88320 AT
1 AT
88322 ATAGGATTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 10 0.25
21 2 0.05
22 2 0.05
23 16 0.40
24 10 0.25
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (21 bp):
ATCTCTAAGATTTACAATCAT
Found at i:93374 original size:24 final size:23
Alignment explanation
Indices: 93343--93389 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
93333 AAAATGAATC
93343 TCTAAGATTATAAGGATCATATCT
1 TCTAAGATT-TAAGGATCATATCT
* *
93367 TCTAAGATTTACGTATCATATCT
1 TCTAAGATTTAAGGATCATATCT
93390 AGGATTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (23 bp):
TCTAAGATTTAAGGATCATATCT
Found at i:103268 original size:25 final size:25
Alignment explanation
Indices: 103239--103308 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
103229 CAAATTAATT
* *
103239 AATTTAATTAACCTAATTTAATAAC
1 AATTTAATCAACCCAATTTAATAAC
* *
103264 AATTTAACCAACCCAATTTTATAAC
1 AATTTAATCAACCCAATTTAATAAC
*
103289 ATTTTAATCAACCCAATTTA
1 AATTTAATCAACCCAATTTA
103309 TGAAATAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (25 bp):
AATTTAATCAACCCAATTTAATAAC
Found at i:106914 original size:18 final size:19
Alignment explanation
Indices: 106882--106917 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
106872 GAAACATAAA
*
106882 CAAATAAAATTAAAAATAG
1 CAAATAAAATGAAAAATAG
106901 CAAA-AAAATGAAAAATA
1 CAAATAAAATGAAAAATA
106918 AAATTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (19 bp):
CAAATAAAATGAAAAATAG
Found at i:109731 original size:80 final size:80
Alignment explanation
Indices: 109598--109757 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
109588 ACTTGTTACA
* *
109598 CTCATTTTCAACAATTGGGATTCCACCTTTCTTCGATACACACTGTACCAGACTTACCCATGAAC
1 CTCATTTTCAACAATCGGGATTCCACCTTTCTTCGATACACACTGTACCAGACTTAACCATGAAC
109663 TATCTTAGAGGGGGT
66 TATCTTAGAGGGGGT
109678 CTCATTTTCAACAATCGGGATTCCACCTTTCTTCGATACACACTGTACCAGACTTAACCATGAAC
1 CTCATTTTCAACAATCGGGATTCCACCTTTCTTCGATACACACTGTACCAGACTTAACCATGAAC
109743 TATCTTAGAGGGGGT
66 TATCTTAGAGGGGGT
109758 AAATAATTCC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (80 bp):
CTCATTTTCAACAATCGGGATTCCACCTTTCTTCGATACACACTGTACCAGACTTAACCATGAAC
TATCTTAGAGGGGGT
Found at i:111029 original size:20 final size:20
Alignment explanation
Indices: 111006--111075 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
110996 ATTACCCTTG
111006 TCATATAACTAATGAAGTAA
1 TCATATAACTAATGAAGTAA
* * * * *
111026 TCATTTAACCGGATTGAAATTA
1 TCATATAA-C-TAATGAAGTAA
111048 T-ATATAACTAATGAAGTAA
1 TCATATAACTAATGAAGTAA
*
111067 TCATTTAAC
1 TCATATAAC
111076 CGGATTGAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 8 0.22
20 14 0.39
21 6 0.17
22 8 0.22
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (20 bp):
TCATATAACTAATGAAGTAA
Found at i:111053 original size:41 final size:41
Alignment explanation
Indices: 111008--111089 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
110998 TACCCTTGTC
111008 ATATAACTAATGAAGTAATCATTTAACCGGATTGAAATTAT
1 ATATAACTAATGAAGTAATCATTTAACCGGATTGAAATTAT
111049 ATATAACTAATGAAGTAATCATTTAACCGGATTGAAATTAT
1 ATATAACTAATGAAGTAATCATTTAACCGGATTGAAATTAT
111090 GATTAATGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (41 bp):
ATATAACTAATGAAGTAATCATTTAACCGGATTGAAATTAT
Found at i:118200 original size:24 final size:24
Alignment explanation
Indices: 118143--118200 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
118133 AACTTATATA
*
118143 TATATATTAGAAATTTTATAATTTT
1 TATATA-TATAAATTTTATAATTTT
* * *
118168 TAAAAATATAAATTTTGTAATTTT
1 TATATATATAAATTTTATAATTTT
118192 TATATATAT
1 TATATATAT
118201 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
TATATATATAAATTTTATAATTTT
Found at i:118697 original size:23 final size:23
Alignment explanation
Indices: 118651--118697 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
118641 CATGTAAAAT
*
118651 AATTTTAAAAAATAAAAGAGGAA
1 AATTTTAAAAAATAAAAGAAGAA
118674 AATTTTAAAAATATAAAA-AAGAA
1 AATTTTAAAAA-ATAAAAGAAGAA
118697 A
1 A
118698 GAAATTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (23 bp):
AATTTTAAAAAATAAAAGAAGAA
Done.