Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012077.1 Kokia drynarioides strain JFW-HI SEQ_127075, 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: 98252
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 98 characters in sequence are not A, C, G, or T
Found at i:356 original size:30 final size:29
Alignment explanation
Indices: 316--461 Score: 88
Period size: 27 Copynumber: 4.9 Consensus size: 29
306 AAAAAAAATT
*
316 AGTACCAAATTAGGAAAAATGCCAAGTTCA
1 AGTACAAAATTAGGAAAAATG-CAAGTTCA
* *
346 AGTACAAAATT-GGATCCAAAA--AAAGTTTA
1 AGTACAAAATTAGGA---AAAATGCAAGTTCA
* *
375 GGTACCAAATTAGGAAAAAGTGTCAAGTTCA
1 AGTACAAAATTAGGAAAAA-TG-CAAGTTCA
* * *
406 AGTACAAAATTGGGTCAAAA---AAGTTTA
1 AGTACAAAATTAGG-AAAAATGCAAGTTCA
*
433 AGTACCAAATTAGGAAAAAGTGTCAAGTT
1 AGTACAAAATTAGGAAAAA-TG-CAAGTT
462 TAGATACCAA
Statistics
Matches: 87, Mismatches: 15, Indels: 27
0.67 0.12 0.21
Matches are distributed among these distances:
26 4 0.05
27 22 0.25
29 18 0.21
30 13 0.15
31 22 0.25
32 8 0.09
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (29 bp):
AGTACAAAATTAGGAAAAATGCAAGTTCA
Found at i:448 original size:58 final size:60
Alignment explanation
Indices: 316--461 Score: 244
Period size: 58 Copynumber: 2.5 Consensus size: 60
306 AAAAAAAATT
*
316 AGTACCAAATTAGGAAAAA-TGCCAAGTTCAAGTACAAAATTGGATCCAAAAAAAGTTTA
1 AGTACCAAATTAGGAAAAAGTGTCAAGTTCAAGTACAAAATTGGATCCAAAAAAAGTTTA
* *
375 GGTACCAAATTAGGAAAAAGTGTCAAGTTCAAGTACAAAATTGGGT-C-AAAAAAGTTTA
1 AGTACCAAATTAGGAAAAAGTGTCAAGTTCAAGTACAAAATTGGATCCAAAAAAAGTTTA
433 AGTACCAAATTAGGAAAAAGTGTCAAGTT
1 AGTACCAAATTAGGAAAAAGTGTCAAGTT
462 TAGATACCAA
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
58 39 0.48
59 19 0.23
60 24 0.29
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (60 bp):
AGTACCAAATTAGGAAAAAGTGTCAAGTTCAAGTACAAAATTGGATCCAAAAAAAGTTTA
Found at i:470 original size:31 final size:31
Alignment explanation
Indices: 368--473 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
358 GATCCAAAAA
*
368 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
* * * *
399 AAGTTCAAGTACAAAATTGGGTCAAAA-----
1 AAGTTTAAGTACCAAATTAGG-AAAAAGTGTC
426 AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
457 AAGTTT-AGATACCAAAT
1 AAGTTTAAG-TACCAAAT
474 GTTATATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
26 4 0.07
27 18 0.31
30 2 0.03
31 31 0.53
32 4 0.07
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.25
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
Found at i:1466 original size:54 final size:54
Alignment explanation
Indices: 1397--1507 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
1387 TCTCTCACGG
*
1397 TTTAAGATTGTGGGTCAAAATCTAAACCATAATTGAATCCCTTCTCTCTTGCGA
1 TTTAAGATTGTGGGTCAAAATCTAAACCATAATTGAATCCCTACTCTCTTGCGA
1451 TTTAAGATTGTGGGTCAAAATCTAAACCATAATTGAATCCCTACTCTCTTGCGA
1 TTTAAGATTGTGGGTCAAAATCTAAACCATAATTGAATCCCTACTCTCTTGCGA
1505 TTT
1 TTT
1508 TTTCATCAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (54 bp):
TTTAAGATTGTGGGTCAAAATCTAAACCATAATTGAATCCCTACTCTCTTGCGA
Found at i:10856 original size:18 final size:18
Alignment explanation
Indices: 10825--10860 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
10815 ATCATGAAAA
10825 TTAATATTTAATTTGAAT
1 TTAATATTTAATTTGAAT
10843 TTAA-ATTTAGATTTGAAT
1 TTAATATTTA-ATTTGAAT
10861 GATAATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
TTAATATTTAATTTGAAT
Found at i:15769 original size:14 final size:14
Alignment explanation
Indices: 15750--15779 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15740 CATTTATTTG
*
15750 TTTAAATAAAATTA
1 TTTAAAAAAAATTA
15764 TTTAAAAAAAATTA
1 TTTAAAAAAAATTA
15778 TT
1 TT
15780 ACGTTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAAAAAAAATTA
Found at i:15834 original size:24 final size:25
Alignment explanation
Indices: 15783--15835 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
15773 AATTATTACG
**
15783 TTTAAATAAAATTATTGTTTATTTA
1 TTTAAATAAAATTATTGGATATTTA
15808 TTTAAATAAAATTA-TGGATATTTA
1 TTTAAATAAAATTATTGGATATTTA
15832 TTTA
1 TTTA
15836 TAAATTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (25 bp):
TTTAAATAAAATTATTGGATATTTA
Found at i:31332 original size:29 final size:26
Alignment explanation
Indices: 31293--31348 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
31283 AAATATTGTT
31293 AAATATATAAAACTAAATTTATACAATTA
1 AAATATATAAAA-TAAA-TTAT-CAATTA
* *
31322 AAATATTTAAAATAGATTATCAATTA
1 AAATATATAAAATAAATTATCAATTA
31348 A
1 A
31349 GATCTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 4 0.16
28 3 0.12
29 11 0.44
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (26 bp):
AAATATATAAAATAAATTATCAATTA
Found at i:32305 original size:31 final size:31
Alignment explanation
Indices: 32270--32328 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
32260 TCTTTATTAT
*
32270 TTATACATTAT-TTGTTTATTTTATTTATAGA
1 TTATAAATTATATTGTTT-TTTTATTTATAGA
*
32301 TTATAAATTTTATTGTTTTTTTATTTAT
1 TTATAAATTATATTGTTTTTTTATTTAT
32329 TTTATAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (31 bp):
TTATAAATTATATTGTTTTTTTATTTATAGA
Found at i:36136 original size:17 final size:17
Alignment explanation
Indices: 36114--36149 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
36104 AATAAAAATA
*
36114 AATAAATATAGATAGAT
1 AATAAATATAAATAGAT
36131 AATAAATATAAATAGAT
1 AATAAATATAAATAGAT
36148 AA
1 AA
36150 GAAACATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (17 bp):
AATAAATATAAATAGAT
Found at i:36158 original size:17 final size:17
Alignment explanation
Indices: 36125--36158 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
36115 ATAAATATAG
* *
36125 ATAGATAATAAATATAA
1 ATAGATAAGAAACATAA
36142 ATAGATAAGAAACATAA
1 ATAGATAAGAAACATAA
36159 TACCTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.24
Consensus pattern (17 bp):
ATAGATAAGAAACATAA
Found at i:46036 original size:32 final size:30
Alignment explanation
Indices: 45978--46060 Score: 76
Period size: 32 Copynumber: 2.6 Consensus size: 30
45968 AATTTTTTAA
* *
45978 TTTTTAAAATTAAAAAATATATAAAAATTG
1 TTTTTAAAAATAAAAAATATAAAAAAATTG
* *
46008 TTTTTAAAAAATATAAAATTATAAAAAAATAATA
1 TTTTT-AAAAATA-AAAAATATAAAAAAAT--TG
**
46042 TTTTTAAATTTAAAAAATA
1 TTTTTAAAAATAAAAAATA
46061 ATTAAATGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
30 5 0.12
31 6 0.14
32 20 0.48
33 5 0.12
34 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
TTTTTAAAAATAAAAAATATAAAAAAATTG
Found at i:46293 original size:17 final size:17
Alignment explanation
Indices: 46254--46285 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46244 AAATTAGAGA
46254 GCCAAATAAATCATTAT
1 GCCAAATAAATCATTAT
46271 GCCAAATAAAT-ATTA
1 GCCAAATAAATCATTA
46286 ATAGCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (17 bp):
GCCAAATAAATCATTAT
Found at i:48650 original size:21 final size:20
Alignment explanation
Indices: 48624--48667 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
48614 TTGTGTTACA
48624 TTAATAATTTCATCTTAAATT
1 TTAATAATTTCAT-TTAAATT
* * *
48645 TTAATATTTTTATTTGAATT
1 TTAATAATTTCATTTAAATT
48665 TTA
1 TTA
48668 TTTTTTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
TTAATAATTTCATTTAAATT
Found at i:50477 original size:24 final size:24
Alignment explanation
Indices: 50450--50502 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
50440 TTTAACATAC
*
50450 ATGAACTACTTTACCC-TTTTTTTG
1 ATGAA-TACTTTACCCATTTTTTTA
*
50474 ATGAATACTTTGCCCATTTTTTTA
1 ATGAATACTTTACCCATTTTTTTA
50498 ATGAA
1 ATGAA
50503 AAGAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.47
Consensus pattern (24 bp):
ATGAATACTTTACCCATTTTTTTA
Found at i:50493 original size:23 final size:24
Alignment explanation
Indices: 50450--50495 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
50440 TTTAACATAC
*
50450 ATGAACTACTTTACCCTTTTTTTG
1 ATGAACTACTTTACCCATTTTTTG
*
50474 ATGAA-TACTTTGCCCATTTTTT
1 ATGAACTACTTTACCCATTTTTT
50496 TAATGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.50
Consensus pattern (24 bp):
ATGAACTACTTTACCCATTTTTTG
Found at i:50633 original size:21 final size:21
Alignment explanation
Indices: 50587--50634 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
50577 GAATTTAAAG
* *
50587 TTTTTATTACGTAAAATTCAA
1 TTTTTATTACGGAAAATACAA
*
50608 ATTTTATGTACGGAAAA-ACAA
1 TTTTTAT-TACGGAAAATACAA
50629 TTTTTA
1 TTTTTA
50635 AAAAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (21 bp):
TTTTTATTACGGAAAATACAA
Found at i:56628 original size:43 final size:43
Alignment explanation
Indices: 56564--56658 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 43
56554 ACGGTGGTCG
*
56564 AGGCTTTAGCATGTTTAAAAGCGATTTCTTTTACGGCAAATTT
1 AGGCTTTAGCATGTTTAAAAGCGATTTCTTTTACGGCAAATCT
* *
56607 AGGCTTTAGCATGTTTGAAAGCGATTTCTTTTGCGGCAAATCT
1 AGGCTTTAGCATGTTTAAAAGCGATTTCTTTTACGGCAAATCT
*
56650 AAGCTTTAG
1 AGGCTTTAG
56659 AGATGTGGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (43 bp):
AGGCTTTAGCATGTTTAAAAGCGATTTCTTTTACGGCAAATCT
Found at i:57326 original size:29 final size:30
Alignment explanation
Indices: 57293--57366 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
57283 ATTTCAAAAG
* * *
57293 AAATTCATGTGTATAATTACAC-CAAATTA
1 AAATTCATGTATAAAATTACACACAAATCA
* *
57322 AAATTCATATATAAAATTACACATTAAATCA
1 AAATTCATGTATAAAATTACACA-CAAATCA
57353 AAATTCATGTATAA
1 AAATTCATGTATAA
57367 TTTTGATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
31 18 0.49
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (30 bp):
AAATTCATGTATAAAATTACACACAAATCA
Found at i:64460 original size:87 final size:90
Alignment explanation
Indices: 64356--64528 Score: 230
Period size: 87 Copynumber: 2.0 Consensus size: 90
64346 TAATGGTACC
*
64356 TAAACTATTCTTCGTTACTCAAAATGACACCTAAATTATA-CATTTTTTTC-TCGAGTTGGTACC
1 TAAACTATTCTTCGTTACTCAAAATGACACCTAAACTATACCATTTTTTTCTTCGAGTTGGTACC
64419 TAAA-T-TTTTTTAGATCACAACTTG
66 TAAATTATTTTTTA-ATCACAACTTG
* * ** * *
64443 TAAACTATAT-TTTGTTACTCAAAGTGGTAGCTAAACTATACCTTTTTTTTCTTCGAGTTGGTAC
1 TAAACTAT-TCTTCGTTACTCAAAATGACACCTAAACTATACCATTTTTTTCTTCGAGTTGGTAC
64507 CTAAATTATTTTTTAATCACAA
65 CTAAATTATTTTTTAATCACAA
64529 GTGGTACTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
87 32 0.43
88 10 0.14
89 17 0.23
90 8 0.11
91 7 0.09
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43
Consensus pattern (90 bp):
TAAACTATTCTTCGTTACTCAAAATGACACCTAAACTATACCATTTTTTTCTTCGAGTTGGTACC
TAAATTATTTTTTAATCACAACTTG
Found at i:69307 original size:31 final size:31
Alignment explanation
Indices: 69243--69308 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
69233 ACGGCTGGTA
* * **
69243 ACCAAAAAAGAAAAATTCAAATATTTGGGTG
1 ACCAAAAAAGAAAAAGTCAAATAGTTGAATG
*
69274 ACCAAAGAAGAAAAAGTCAAATAGTTGAATG
1 ACCAAAAAAGAAAAAGTCAAATAGTTGAATG
69305 ACCA
1 ACCA
69309 TTTTGTAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.53, C:0.12, G:0.17, T:0.18
Consensus pattern (31 bp):
ACCAAAAAAGAAAAAGTCAAATAGTTGAATG
Found at i:69754 original size:14 final size:15
Alignment explanation
Indices: 69729--69757 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
69719 AAATTTGAAT
69729 AATATAAAAATTAAA
1 AATATAAAAATTAAA
69744 AATAT-AAAATTAAA
1 AATATAAAAATTAAA
69758 GTACATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATATAAAAATTAAA
Found at i:85460 original size:17 final size:17
Alignment explanation
Indices: 85438--85472 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
85428 TTATTTTAGT
*
85438 TTAATTAATTAATTAAA
1 TTAATTAATTAAATAAA
*
85455 TTAATTGATTAAATAAA
1 TTAATTAATTAAATAAA
85472 T
1 T
85473 AATATTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAATTAATTAAATAAA
Found at i:88264 original size:32 final size:32
Alignment explanation
Indices: 88223--88286 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
88213 GGTAACCCAA
88223 ATGTTAGAACCCATTTAAGTGACCCATACCCT
1 ATGTTAGAACCCATTTAAGTGACCCATACCCT
88255 ATGTTAGAACCCATTTAAGTGACCCATACCCT
1 ATGTTAGAACCCATTTAAGTGACCCATACCCT
88287 TGACCCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (32 bp):
ATGTTAGAACCCATTTAAGTGACCCATACCCT
Found at i:88378 original size:37 final size:38
Alignment explanation
Indices: 88327--88402 Score: 118
Period size: 37 Copynumber: 2.0 Consensus size: 38
88317 GTTAACCTGA
88327 AACCATGACCCGAACCCGATCGACCCGACCCATTGATC
1 AACCATGACCCGAACCCGATCGACCCGACCCATTGATC
* * *
88365 AACCA-GACTCGAACCCGATTGACCCGACCCGTTGATC
1 AACCATGACCCGAACCCGATCGACCCGACCCATTGATC
88402 A
1 A
88403 TTGACAGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 30 0.86
38 5 0.14
ACGTcount: A:0.29, C:0.39, G:0.17, T:0.14
Consensus pattern (38 bp):
AACCATGACCCGAACCCGATCGACCCGACCCATTGATC
Found at i:89945 original size:22 final size:21
Alignment explanation
Indices: 89915--89960 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
89905 TTAGAAAATA
89915 AAATATTTATAATTTAATAATT
1 AAATATTTATAATTT-ATAATT
* * *
89937 AAATTTTTATTATTTTTAATT
1 AAATATTTATAATTTATAATT
89958 AAA
1 AAA
89961 AATAATTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATTTATAATTTATAATT
Found at i:91027 original size:4 final size:4
Alignment explanation
Indices: 91020--91089 Score: 52
Period size: 4 Copynumber: 17.2 Consensus size: 4
91010 AAACAAACGG
* * * * *
91020 GAAA GAAA GAAA GAAAA GAAA GAAA GGAA GGAA GGAA GAAG GAGAG GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
* *
91070 GAAA G-GA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA G
91090 GTAATGTGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
3 2 0.04
4 45 0.82
5 8 0.15
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:91039 original size:13 final size:13
Alignment explanation
Indices: 91021--91045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
91011 AACAAACGGG
91021 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
91034 AAAGAAAGAAAG
1 AAAGAAAGAAAG
91046 GAAGGAAGGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:91090 original size:29 final size:31
Alignment explanation
Indices: 91019--91090 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
91009 CAAACAAACG
*
91019 GGAAAGAAAGAAA-GAAAAGAAAGAAAGGAA
1 GGAAGGAAAGAAAGGAAAAGAAAGAAAGGAA
* *
91049 GGAAGG-AAG-AAGGAGAGGAAAGAAAGG-A
1 GGAAGGAAAGAAAGGAAAAGAAAGAAAGGAA
91077 -GAAGGAAAGAAAGG
1 GGAAGGAAAGAAAGG
91091 TAATGTGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 5 0.14
28 6 0.17
29 20 0.56
30 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (31 bp):
GGAAGGAAAGAAAGGAAAAGAAAGAAAGGAA
Found at i:94202 original size:28 final size:28
Alignment explanation
Indices: 94133--94204 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
94123 CCCTCCTTAA
94133 TCAA-TCTAATGG-TTACGATTTAGAGTT
1 TCAAGTCT-ATGGTTTACGATTTAGAGTT
94160 TCAAGTCTA-GTGTTTACGATTTA-AGGTT
1 TCAAGTCTATG-GTTTACGATTTAGA-GTT
*
94188 TCAAGTTTATGGTTTAC
1 TCAAGTCTATGGTTTAC
94205 AGTTTAGGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
26 1 0.03
27 7 0.18
28 30 0.77
29 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.43
Consensus pattern (28 bp):
TCAAGTCTATGGTTTACGATTTAGAGTT
Found at i:94210 original size:28 final size:27
Alignment explanation
Indices: 94145--94215 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
94135 AATCTAATGG
94145 TTACGATTTAGAGTTTCAAGTCTAGTGT
1 TTACGATTTAG-GTTTCAAGTCTAGTGT
*
94173 TTACGATTTAAGGTTTCAAGTTTA-TGGT
1 TTACGATTT-AGGTTTCAAGTCTAGT-GT
94201 TTAC-AGTTTAGGTTT
1 TTACGA-TTTAGGTTT
94216 TAGGGTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 8 0.21
28 29 0.74
29 2 0.05
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTACGATTTAGGTTTCAAGTCTAGTGT
Found at i:94546 original size:45 final size:45
Alignment explanation
Indices: 94482--94618 Score: 188
Period size: 45 Copynumber: 3.0 Consensus size: 45
94472 GGGAGGAATA
* *
94482 GAGTATTGCGGTAGCTCGTCAAACTCAGCTTGATATCCTT-CTCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGCTTGATATCCTTGC-CTT
*
94527 GAGTATTGCGGTGGCTCGTCAAATTGAGGC-TGATATCCTTGCCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGA-GCTTGATATCCTTGCCTT
* * *
94572 AAGTATTGCGGTGGCTCGTCAAACTGAGGTTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGCTTGATATCCTTGCCTT
94617 GA
1 GA
94619 TGAGCTATGC
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
44 1 0.01
45 77 0.95
46 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTGAGCTTGATATCCTTGCCTT
Found at i:96568 original size:16 final size:16
Alignment explanation
Indices: 96547--96596 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
96537 TGATGGGGAT
96547 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
96563 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
96578 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
96593 ATTA
1 ATTA
96597 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:97490 original size:24 final size:21
Alignment explanation
Indices: 97463--97517 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
97453 TTCCCCTTTC
97463 TTCTCTTTCTTCCTTCTTCTTTAT
1 TTCT-TTTCTT-CTT-TTCTTTAT
97487 TTCTTTCTCTT-TTTTCTTTAT
1 TTCTTT-TCTTCTTTTCTTTAT
97508 TT-TTTTCTTC
1 TTCTTTTCTTC
97518 AATTTTCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.14
20 3 0.10
21 10 0.34
22 2 0.07
23 2 0.07
24 8 0.28
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCTTTTCTTCTTTTCTTTAT
Done.