Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010847.1 Kokia drynarioides strain JFW-HI SEQ_125814, 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: 168491
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 217 characters in sequence are not A, C, G, or T
Found at i:3297 original size:4 final size:4
Alignment explanation
Indices: 3288--3324 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
3278 TCTCATCCAA
*
3288 AAAT AAAT AAAT AAAT AAAT AAAT AAAA AGAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT
3325 GGATAAGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:6095 original size:29 final size:29
Alignment explanation
Indices: 6043--6113 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
6033 CTAACTCAAG
* *
6043 TTCATATTATTTTTTTTATTTTTAA-AAT
1 TTCATATTATTTTTTTAATATTTAATAAT
6071 TT-ATATTATATTATTTTAATATTTAATAAT
1 TTCATATTAT-TT-TTTTAATATTTAATAAT
6101 TTCATA-TATTTTT
1 TTCATATTATTTTT
6114 ATTTATTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 7 0.19
28 6 0.16
29 13 0.35
30 8 0.22
31 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (29 bp):
TTCATATTATTTTTTTAATATTTAATAAT
Found at i:7352 original size:27 final size:27
Alignment explanation
Indices: 7294--7372 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
7284 ACCAGCCGCT
* * *
7294 TCTTCCTCTGAAGAAGATGAAGAGGCG
1 TCTTCATCTGAGGAAGAAGAAGAGGCG
* *
7321 ACTTCTTCTGAGGAAGAAGAAGAAGG-G
1 TCTTCATCTGAGGAAGAAGAAG-AGGCG
* * *
7348 TCTTCAACTGAGGAGGAAGATGAGG
1 TCTTCATCTGAGGAAGAAGAAGAGG
7373 AAGACCCCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
26 3 0.07
27 36 0.86
28 3 0.07
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (27 bp):
TCTTCATCTGAGGAAGAAGAAGAGGCG
Found at i:9366 original size:41 final size:41
Alignment explanation
Indices: 9235--9366 Score: 99
Period size: 41 Copynumber: 3.1 Consensus size: 41
9225 ACATTGTAGT
9235 TATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACA
1 TATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACA
* * * * * * * **
9276 TATTTCGTTTGAATGTGTAT-GTAT-T-TTCTATTTAGACATTGTAGT
1 TATTT-G---CAATGTCT-TGGT-TGTCTCCTACTGATAC-TTGAACA
9321 TATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACA
1 TATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACA
9362 TATTT
1 TATTT
9367 CGTTTGAATG
Statistics
Matches: 63, Mismatches: 18, Indels: 20
0.62 0.18 0.20
Matches are distributed among these distances:
40 2 0.03
41 23 0.37
42 9 0.14
44 9 0.14
45 18 0.29
46 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (41 bp):
TATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACA
Found at i:9370 original size:86 final size:86
Alignment explanation
Indices: 9225--9396 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
9215 TAATCGTTTC
9225 ACATTGTAGTTATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACATATTTCGTTTGAAT
1 ACATTGTAGTTATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACATATTTCGTTTGAAT
*
9290 GTGTATGTATTTTCTATTTAG
66 GTGTATGTATTTACTATTTAG
9311 ACATTGTAGTTATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACATATTTCGTTTGAAT
1 ACATTGTAGTTATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACATATTTCGTTTGAAT
9376 GTGTATGTATTTACTATTTAG
66 GTGTATGTATTTACTATTTAG
9397 TTAGCTTTCC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (86 bp):
ACATTGTAGTTATTTGCAATGTCTTGGTTGTCTCCTACTGATACTTGAACATATTTCGTTTGAAT
GTGTATGTATTTACTATTTAG
Found at i:13348 original size:18 final size:19
Alignment explanation
Indices: 13306--13345 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
13296 GAAAAAATTG
13306 AAAA-TCAAATCCAACAAA
1 AAAATTCAAATCCAACAAA
13324 AAAATTCAAATCCAACTAAA
1 AAAATTCAAATCCAAC-AAA
13344 AA
1 AA
13346 TTCTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.65, C:0.20, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAATTCAAATCCAACAAA
Found at i:14099 original size:2 final size:2
Alignment explanation
Indices: 14092--14117 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14082 AACCAAAGGT
14092 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
14118 CTGCTGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:18329 original size:32 final size:33
Alignment explanation
Indices: 18275--18336 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
18265 AAACTTAAGG
* *
18275 TTAATAATATATATTAAAAATAGTA-ATATAAT
1 TTAATAATATAAAATAAAAATAGTATATATAAT
**
18307 TTAATAATATAAAATATTAATAGTATATAT
1 TTAATAATATAAAATAAAAATAGTATATAT
18337 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 21 0.84
33 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (33 bp):
TTAATAATATAAAATAAAAATAGTATATATAAT
Found at i:25327 original size:29 final size:30
Alignment explanation
Indices: 25294--25355 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
25284 GGGATGCTGA
25294 AATTTGAG-TTTTAAATAAGAAGGATGAAT
1 AATTTGAGTTTTTAAATAAGAAGGATGAAT
* *
25323 AATTTGAGTTTTTGAATAAGAAGGATGCAT
1 AATTTGAGTTTTTAAATAAGAAGGATGAAT
25353 AAT
1 AAT
25356 ATATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (30 bp):
AATTTGAGTTTTTAAATAAGAAGGATGAAT
Found at i:38204 original size:23 final size:24
Alignment explanation
Indices: 38178--38228 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38168 ATATGTTGAT
*
38178 ATTTGATTCCTT-AAAAAAATTTA
1 ATTTGATACCTTGAAAAAAATTTA
* *
38201 ATTTGATACCTTGTAAAATATTTA
1 ATTTGATACCTTGAAAAAAATTTA
38225 ATTT
1 ATTT
38229 AAAAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (24 bp):
ATTTGATACCTTGAAAAAAATTTA
Found at i:38670 original size:32 final size:29
Alignment explanation
Indices: 38618--38682 Score: 69
Period size: 32 Copynumber: 2.1 Consensus size: 29
38608 CTAAATTATT
38618 AAATATAAAATTATATTTTAACCCTTCTTAA
1 AAATATAAAATTATATTTTAA-CCTT-TTAA
* *
38649 AAATGATAAAATTTTGA-TTTAATCTTTTAA
1 AAAT-ATAAAATTAT-ATTTTAACCTTTTAA
38679 AAAT
1 AAAT
38683 TATATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
30 8 0.27
31 7 0.23
32 14 0.47
33 1 0.03
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (29 bp):
AAATATAAAATTATATTTTAACCTTTTAA
Found at i:39010 original size:7 final size:7
Alignment explanation
Indices: 38998--39024 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38988 GCTCTTATAT
38998 ATGTCAC
1 ATGTCAC
39005 ATGTCAC
1 ATGTCAC
39012 ATGTCAC
1 ATGTCAC
39019 ATGTCA
1 ATGTCA
39025 TCAGTGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (7 bp):
ATGTCAC
Found at i:50788 original size:59 final size:60
Alignment explanation
Indices: 50711--50849 Score: 187
Period size: 58 Copynumber: 2.4 Consensus size: 60
50701 TTTGAAGTTG
* * **
50711 AAAATGTGA-TTTTG-GAAGTTTTGGGGGAAAAAATGTGATTTTTGGAAGTTTAGGGGC-
1 AAAATGTAATTTTTGAGAAGTTTTAGAAGAAAAAATGTGATTTTTGGAAGTTTAGGGGCA
* * *
50768 AAAATGTAATTTTTGAGAAG-TTTAGAAGTAAAAATGTGATTTTTGGCAGTTTGGGGGCA
1 AAAATGTAATTTTTGAGAAGTTTTAGAAGAAAAAATGTGATTTTTGGAAGTTTAGGGGCA
50827 AAAATGTAATTTTTGAGAAGTTT
1 AAAATGTAATTTTTGAGAAGTTT
50850 GGAGGTCAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 8 0.11
58 37 0.52
59 24 0.34
60 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (60 bp):
AAAATGTAATTTTTGAGAAGTTTTAGAAGAAAAAATGTGATTTTTGGAAGTTTAGGGGCA
Found at i:50851 original size:30 final size:30
Alignment explanation
Indices: 50711--50971 Score: 164
Period size: 29 Copynumber: 8.8 Consensus size: 30
50701 TTTGAAGTTG
* *
50711 AAAATGTGA-TTTTG-GAAGTTTTGGGGGAA
1 AAAATGTAATTTTTGAGAAG-TTTGGGGGCA
* *
50740 AAAATGTGATTTTTG-GAAGTTTAGGGGC-
1 AAAATGTAATTTTTGAGAAGTTTGGGGGCA
* ** *
50768 AAAATGTAATTTTTGAGAAGTTTAGAAGTA
1 AAAATGTAATTTTTGAGAAGTTTGGGGGCA
* *
50798 AAAATGTGATTTTTG-GCAGTTTGGGGGCA
1 AAAATGTAATTTTTGAGAAGTTTGGGGGCA
*
50827 AAAATGTAATTTTTGAGAAGTTTGGAGGTC-
1 AAAATGTAATTTTTGAGAAGTTTGG-GGGCA
* * * * *
50857 -AAATGTAATTTTGGAAAAAAAAAATTAGGGGTC-
1 AAAATGTAATTTTTG-----AGAAGTTTGGGGGCA
* ** **
50890 AAAATGTAATTTTGGAGAAGTTAAGGGGTT
1 AAAATGTAATTTTTGAGAAGTTTGGGGGCA
* * *
50920 AAAATGTAATTTTTGATAAGTTT-AGGGTA
1 AAAATGTAATTTTTGAGAAGTTTGGGGGCA
*
50949 AAAATGTAATTTTGGA-AAGTTTG
1 AAAATGTAATTTTTGAGAAGTTTG
50972 AGTTGTCAAA
Statistics
Matches: 189, Mismatches: 30, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
28 20 0.11
29 90 0.48
30 51 0.27
31 3 0.02
33 4 0.02
34 21 0.11
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTGGGGGCA
Found at i:50861 original size:58 final size:58
Alignment explanation
Indices: 50739--50970 Score: 200
Period size: 59 Copynumber: 3.9 Consensus size: 58
50729 TTTTGGGGGA
50739 AAAAATGTGATTTTTGGAAGTTTAGGGGCAAAATGTAATTTTTGAGAAGTTTAGAAGT
1 AAAAATGTGATTTTTGGAAGTTTAGGGGCAAAATGTAATTTTTGAGAAGTTTAGAAGT
* * * *
50797 AAAAATGTGATTTTTGGCAGTTTGGGGGCAAAAATGTAATTTTTGAGAAGTTTGGAGGT
1 AAAAATGTGATTTTTGGAAGTTTAGGGGC-AAAATGTAATTTTTGAGAAGTTTAGAAGT
* * ** * * **
50856 -CAAATGT-AATTTTGGAAAAAAAAAATTAGGGGTCAAAATGTAATTTTGGAGAAGTTAAGGGGT
1 AAAAATGTGATTTTTGG------AAGTTTAGGGG-CAAAATGTAATTTTTGAGAAGTTTAGAAGT
* * * ** *
50919 TAAAATGTAATTTTTGATAAGTTTAGGGTAAAAATGTAATTTTGGA-AAGTTT
1 AAAAATGTGATTTTTG-GAAGTTTAGGGGCAAAATGTAATTTTTGAGAAGTTT
50971 GAGTTGTCAA
Statistics
Matches: 141, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
57 7 0.05
58 38 0.27
59 43 0.30
60 8 0.06
63 32 0.23
64 7 0.05
65 6 0.04
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (58 bp):
AAAAATGTGATTTTTGGAAGTTTAGGGGCAAAATGTAATTTTTGAGAAGTTTAGAAGT
Found at i:52739 original size:23 final size:23
Alignment explanation
Indices: 52711--52755 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52701 TTTTGGACTT
* * *
52711 TTTAAACTAAATTTAAAGTTAAG
1 TTTAAAATAAATTCAAACTTAAG
52734 TTTAAAATAAATTCAAACTTAA
1 TTTAAAATAAATTCAAACTTAA
52756 AATAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (23 bp):
TTTAAAATAAATTCAAACTTAAG
Found at i:52772 original size:17 final size:17
Alignment explanation
Indices: 52735--52772 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
52725 AAAGTTAAGT
*
52735 TTAAAATAAATTCAAAC
1 TTAAAATAAATTCAAAA
*
52752 TTAAAATAAATTTAAAA
1 TTAAAATAAATTCAAAA
52769 TTAA
1 TTAA
52773 CAATTGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAATAAATTCAAAA
Found at i:54233 original size:26 final size:26
Alignment explanation
Indices: 54186--54235 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
54176 TTTTTATGCA
* **
54186 TCATTTTAATTTTTACCCTTTTTTTT
1 TCATTTTAATATTTAAACTTTTTTTT
54212 TCATTTTAATATTTAAA-TTTTTTT
1 TCATTTTAATATTTAAACTTTTTTT
54236 CACTCGGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (26 bp):
TCATTTTAATATTTAAACTTTTTTTT
Found at i:74775 original size:54 final size:54
Alignment explanation
Indices: 74675--74779 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
74665 TCTTAATCAA
** *
74675 AAGCAAAGCATGGTTCGAAACTGCCGATAATAAAAAAGGATTAAATTGTTATTT
1 AAGCAAAGCATGGTTCGAAACTGCAAATAATAAAAAAGGATAAAATTGTTATTT
* * *
74729 AAGCAAAGCATGGTTGGACACTGCAAATAAATAAAAAATGA-AAAATTGTTA
1 AAGCAAAGCATGGTTCGAAACTGCAAAT-AATAAAAAAGGATAAAATTGTTA
74780 ATTTTTTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
54 33 0.75
55 11 0.25
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (54 bp):
AAGCAAAGCATGGTTCGAAACTGCAAATAATAAAAAAGGATAAAATTGTTATTT
Found at i:75436 original size:23 final size:23
Alignment explanation
Indices: 75410--75466 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
75400 CTTTAAATTT
*
75410 ATTTTAAAATTAAATTTGTTTAA
1 ATTTTAAAATTAAATTTATTTAA
* * *
75433 ATTTT-AATTTTAATTTATTTTA
1 ATTTTAAAATTAAATTTATTTAA
*
75455 AGTTTAAAATTA
1 ATTTTAAAATTA
75467 TTTTCAAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTTTAAAATTAAATTTATTTAA
Found at i:75439 original size:17 final size:17
Alignment explanation
Indices: 75401--75442 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
75391 TCAAACTCCC
*
75401 TTTAAATTTATTTTAAA
1 TTTAAATTTAGTTTAAA
*
75418 ATTAAATTT-GTTTAAA
1 TTTAAATTTAGTTTAAA
*
75434 TTTTAATTT
1 TTTAAATTT
75443 TAATTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTAAATTTAGTTTAAA
Found at i:75465 original size:18 final size:19
Alignment explanation
Indices: 75444--75483 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
75434 TTTTAATTTT
*
75444 AATTTATTTT-AAGTTTAA
1 AATTTATTTTCAAATTTAA
75462 AA-TTATTTTCAAATTTAA
1 AATTTATTTTCAAATTTAA
75480 AATT
1 AATT
75484 ATCATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 7 0.37
18 11 0.58
19 1 0.05
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
AATTTATTTTCAAATTTAA
Found at i:75484 original size:18 final size:17
Alignment explanation
Indices: 75433--75499 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
75423 ATTTGTTTAA
* *
75433 ATTTT-AATTTTAATTT
1 ATTTTAAATTTAAAATT
*
75449 ATTTTAAGTTTAAAATT
1 ATTTTAAATTTAAAATT
75466 ATTTTCAAATTTAAAATT
1 ATTTT-AAATTTAAAATT
**
75484 ATCATAAATTTAAAAT
1 ATTTTAAATTTAAAAT
75500 AAATAAAGCT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
16 5 0.12
17 24 0.56
18 14 0.33
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (17 bp):
ATTTTAAATTTAAAATT
Found at i:77367 original size:29 final size:29
Alignment explanation
Indices: 77324--77705 Score: 279
Period size: 29 Copynumber: 13.0 Consensus size: 29
77314 AAAGGTCCCT
77324 AAACTGTCCAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* **
77354 AAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
77384 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * * *
77413 GAACTTTCAAAAATCCCATTCTTGACCTCA
1 AAACTTCCAAAAATTCCATT-TTTACCCCC
*
77443 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * ** * * *
77472 GAATTTCTGAAAA-TCTCATTTTTGATCTCG
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCC
* * * **
77502 AAACTTCCAAAAAATACGTTTTTACCCTT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * * *
77531 GAACTTTCGAAAATCCCAATTTTGACCCCG
1 AAACTTCCAAAAATTCC-ATTTTTACCCCC
*
77561 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
77590 GAACTTTCGAAAA-TCTCATTTTTGACCCCA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCC
*
77620 AAACTTCCAAAAA-TACATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
77648 AAACTTCCAAAAA-TCTCATTTTTAACCTC
1 AAACTTCCAAAAATTC-CATTTTTACCCCC
* * *
77677 GAATTTCCCAAAATTACCA-TTTTACCCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCCC
77706 TGGTATCCGA
Statistics
Matches: 269, Mismatches: 72, Indels: 23
0.74 0.20 0.06
Matches are distributed among these distances:
28 23 0.09
29 135 0.50
30 109 0.41
31 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:77418 original size:59 final size:59
Alignment explanation
Indices: 77320--77670 Score: 404
Period size: 59 Copynumber: 6.0 Consensus size: 59
77310 CCCTAAAGGT
* *
77320 CCCT-AAACTGTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* *
77379 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCCATTCTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* ** *
77438 -CCTCAAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCTGAAAATCTCATTTTTGA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * * * * * * *
77497 -TCTCGAAACTTCCAAAAAATACGTTTTTACCCTTGAACTTTCGAAAATCCCAATTTTGA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
** * * *
77556 CCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCGAAAATCTCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * * *
77615 CCCCAAAACTTCCAAAAA-TACATTTTTACCCCCAAACTTCCAAAAATCTCATTTTT
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTT
77671 AACCTCGAAT
Statistics
Matches: 254, Mismatches: 35, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
58 36 0.14
59 212 0.83
60 6 0.02
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (59 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:86647 original size:187 final size:189
Alignment explanation
Indices: 86294--86649 Score: 494
Period size: 186 Copynumber: 1.9 Consensus size: 189
86284 ATCATTAGAC
* * *
86294 AAAATAATTAATAAGAGGAAGGCCAAAAAGAAATTAGGTTGAATTAAATTGAATTACACATTATT
1 AAAATAATTAATAAAAGGAAGG-CAAAAAGAAATTAGCTTGAATTAAATTGAATTACACATTACT
* *
86359 TCCCTACTAAAATGTGTTTCATTTTATATGCAAAATTCACCTTCGACGTGACAACTTCATCTTTC
65 TCCCTACTAAAATGTGTTTCATTTTATATGCAAAATTCACCTTCGACGTGACAACCTCATATTTC
86424 TAGACCTAATTTTTTTTAAAAAATTACTAAATTTTGTTTCTATTTGAATCATTGGATGAT
130 TAGACCTAATTTTTTTTAAAAAATTACTAAATTTTGTTTCTATTTGAATCATTGGATGAT
*
86484 AAAATAATTAATAAAAGGAAGAG-AAATA-AAA-TAGCTTGAATTAAATTGAATTACACATT-CT
1 AAAATAATTAATAAAAGGAAG-GCAAAAAGAAATTAGCTTGAATTAAATTGAATTACACATTACT
* * * *
86545 TGCCTGCTAAAATGTGTTTCATTTTATATGCAAAATTCACCTTTGATGTGAC-ACCTCAATATTT
65 TCCCTACTAAAATGTGTTTCATTTTATATGCAAAATTCACCTTCGACGTGACAACCTC-ATATTT
*
86609 CTAGA-C-AACCTATTTTTTTAAAAACCTT-CTAAATTTTGTTT
129 CTAGACCTAA--T-TTTTTTTAAAAA-ATTACTAAATTTTGTTT
86650 TTTGCTTCCA
Statistics
Matches: 149, Mismatches: 11, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
184 2 0.01
185 5 0.03
186 60 0.40
187 52 0.35
188 5 0.03
189 4 0.03
190 20 0.13
191 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (189 bp):
AAAATAATTAATAAAAGGAAGGCAAAAAGAAATTAGCTTGAATTAAATTGAATTACACATTACTT
CCCTACTAAAATGTGTTTCATTTTATATGCAAAATTCACCTTCGACGTGACAACCTCATATTTCT
AGACCTAATTTTTTTTAAAAAATTACTAAATTTTGTTTCTATTTGAATCATTGGATGAT
Found at i:87339 original size:15 final size:15
Alignment explanation
Indices: 87318--87366 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
87308 TTTAAAAATA
87318 AAAAAATAGAATTTT
1 AAAAAATAGAATTTT
*
87333 TAAAAAT--AA-TTT
1 AAAAAATAGAATTTT
87345 AAAAAATAGAATTTT
1 AAAAAATAGAATTTT
*
87360 CAAAAAT
1 AAAAAAT
87367 TATAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 9 0.32
13 2 0.07
14 2 0.07
15 15 0.54
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
AAAAAATAGAATTTT
Found at i:87374 original size:26 final size:26
Alignment explanation
Indices: 87314--87374 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
87304 TTTATTTAAA
*
87314 AATAAAAAAATAGAATTTTTAAAAAT
1 AATAAAAAAATAGAATTTTCAAAAAT
*
87340 AATTTAAAAAATAGAATTTTCAAAAAT
1 AA-TAAAAAAATAGAATTTTCAAAAAT
*
87367 TATAAAAA
1 AATAAAAA
87375 TACTATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (26 bp):
AATAAAAAAATAGAATTTTCAAAAAT
Found at i:87838 original size:10 final size:10
Alignment explanation
Indices: 87823--87859 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
87813 AAATATTTTT
87823 TATTTTTTCA
1 TATTTTTTCA
87833 TA-TTTTTCA
1 TATTTTTTCA
87842 TAATTTTTTCA
1 T-ATTTTTTCA
87853 -ATTTTTT
1 TATTTTTT
87860 TAATTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 15 0.60
10 3 0.12
11 7 0.28
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTTTCA
Found at i:87849 original size:20 final size:18
Alignment explanation
Indices: 87824--87867 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
87814 AATATTTTTT
87824 ATTTTTTCATATTTTTCATA
1 ATTTTTTCA-ATTTTT-ATA
*
87844 ATTTTTTCAATTTTTTTA
1 ATTTTTTCAATTTTTATA
87862 ATTTTT
1 ATTTTT
87868 GAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 9 0.39
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTTCAATTTTTATA
Found at i:88585 original size:28 final size:27
Alignment explanation
Indices: 88533--88597 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
88523 TTTTTCTAAG
* *
88533 TTTATATTTTTCAAATTTAGTTTTTTT
1 TTTATATTTTTAAAATTTAGATTTTTT
*
88560 ATTTTTATTTTTAAAAATTTA-ATTTTTT
1 -TTTATATTTTT-AAAATTTAGATTTTTT
88588 TTTATATTTT
1 TTTATATTTT
88598 AAATTTTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 9 0.28
28 16 0.50
29 7 0.22
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTATATTTTTAAAATTTAGATTTTTT
Found at i:90138 original size:22 final size:22
Alignment explanation
Indices: 90113--90162 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
90103 TAATAATAAT
*
90113 ATAATAGTAAAATGACAGTAAA
1 ATAATAGTAAAATGACAGCAAA
* * * *
90135 ATAACATTTAAATGGCAGCAAA
1 ATAATAGTAAAATGACAGCAAA
90157 ATAATA
1 ATAATA
90163 ATAGGAAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (22 bp):
ATAATAGTAAAATGACAGCAAA
Found at i:92208 original size:21 final size:21
Alignment explanation
Indices: 92182--92224 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
92172 ATACATCAAT
92182 TAGAGTGTAGAACTCCTAACA
1 TAGAGTGTAGAACTCCTAACA
*
92203 TAGAGTTTAGAACTCCTAACA
1 TAGAGTGTAGAACTCCTAACA
92224 T
1 T
92225 GTTTGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (21 bp):
TAGAGTGTAGAACTCCTAACA
Found at i:92980 original size:129 final size:128
Alignment explanation
Indices: 92841--93075 Score: 380
Period size: 129 Copynumber: 1.8 Consensus size: 128
92831 AAATTTTAAT
*
92841 TTTTAATAGCCTATATCTTCATGATTTTTAAAGAATTAAATCAAATTTTTATTATTTTTACGAGG
1 TTTTAATAGCCTATATCTTCATGATTTTTAAAGAATTAAATCAAATTATTATTATTTTTACGAGG
* *
92906 CAAAATGTAATTTTATTTTTACTAATTTTAAAATTTTCAAATGACCTAAATGGATAATTTTCCA
66 CAAAATGTAATTTTATCTTTACTAA-TTTAAAATTTTAAAATGACCTAAATGGATAATTTTCCA
* * * * *
92970 TTTTAATAGCCTATATTTTTATGATTTTTAAAGAATTAAATTAAATTATTATTATTTTTATGGGG
1 TTTTAATAGCCTATATCTTCATGATTTTTAAAGAATTAAATCAAATTATTATTATTTTTACGAGG
*
93035 TAAAATGTAATTTTATCTTTACTAATTTAAAATTTTAAAAT
66 CAAAATGTAATTTTATCTTTACTAATTTAAAATTTTAAAAT
93076 TTTTAAATGA
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
128 15 0.15
129 82 0.85
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (128 bp):
TTTTAATAGCCTATATCTTCATGATTTTTAAAGAATTAAATCAAATTATTATTATTTTTACGAGG
CAAAATGTAATTTTATCTTTACTAATTTAAAATTTTAAAATGACCTAAATGGATAATTTTCCA
Found at i:98644 original size:15 final size:14
Alignment explanation
Indices: 98618--98647 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
98608 TACATTAGAG
98618 TAGTATTATATATT
1 TAGTATTATATATT
98632 TAGTATATATATATT
1 TAGTAT-TATATATT
98647 T
1 T
98648 TTTAATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TAGTATTATATATT
Found at i:98702 original size:15 final size:16
Alignment explanation
Indices: 98665--98703 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
98655 TTTTTAAATT
98665 ATATTAT-ATATAAAA
1 ATATTATAATATAAAA
*
98680 ATAATATAATAT-AAA
1 ATATTATAATATAAAA
98695 ATATTATAA
1 ATATTATAA
98704 ACTTAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATTATAATATAAAA
Found at i:102302 original size:26 final size:26
Alignment explanation
Indices: 102266--102317 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
102256 TCTCAAAATT
*
102266 GCTTGTGTGCTAATTTGGAAGATTAA
1 GCTTGTGTGCTAATGTGGAAGATTAA
*
102292 GCTTGTGTGCTAATGTGGAATATTAA
1 GCTTGTGTGCTAATGTGGAAGATTAA
102318 AACTCAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (26 bp):
GCTTGTGTGCTAATGTGGAAGATTAA
Found at i:111809 original size:16 final size:16
Alignment explanation
Indices: 111780--111812 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
111770 GATTTTTTTT
111780 ATTGTATTATATAATA
1 ATTGTATTATATAATA
111796 ATTGT-TTATAATAATA
1 ATTGTATTAT-ATAATA
111812 A
1 A
111813 CATGTGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
ATTGTATTATATAATA
Found at i:117565 original size:12 final size:12
Alignment explanation
Indices: 117543--117567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
117533 TCATTTTTGC
117543 TCCTTTTTTTTT
1 TCCTTTTTTTTT
117555 TCCTTTTTTTTT
1 TCCTTTTTTTTT
117567 T
1 T
117568 TAAATTTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCCTTTTTTTTT
Found at i:118535 original size:25 final size:25
Alignment explanation
Indices: 118502--118550 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
118492 CTCATGAACT
118502 TTTTTTTTTTAATAATCTTATTATC
1 TTTTTTTTTTAATAATCTTATTATC
*
118527 TTTTTTTTTTAATAATTTTATTAT
1 TTTTTTTTTTAATAATCTTATTAT
118551 AGGTTCTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTTTTTTTAATAATCTTATTATC
Found at i:132880 original size:17 final size:17
Alignment explanation
Indices: 132860--132895 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
132850 AAATCAAATT
* *
132860 TATTTATTTTAATTAAA
1 TATTAATTTTAAATAAA
132877 TATTAATTTTAAATAAA
1 TATTAATTTTAAATAAA
132894 TA
1 TA
132896 ATGAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTAATTTTAAATAAA
Found at i:137940 original size:23 final size:22
Alignment explanation
Indices: 137901--137948 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
137891 AAAATAACAA
*
137901 AAACAAATAATAAAAACCTTAAG
1 AAACAAATAATAAAAA-CTGAAG
*
137924 AAACAAATAA-ATTAAACTGAAG
1 AAACAAATAATA-AAAACTGAAG
137946 AAA
1 AAA
137949 TTGACTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.10, G:0.06, T:0.17
Consensus pattern (22 bp):
AAACAAATAATAAAAACTGAAG
Found at i:140364 original size:24 final size:24
Alignment explanation
Indices: 140337--140387 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
140327 AAGAGGTCTG
*
140337 CGAATTGGAGAACGGCTCCGCCTA
1 CGAATTGGAGAACGGCTACGCCTA
* *
140361 CGAATTGGAGAAGGGCTACGTCTA
1 CGAATTGGAGAACGGCTACGCCTA
140385 CGA
1 CGA
140388 TTGAAGGGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (24 bp):
CGAATTGGAGAACGGCTACGCCTA
Found at i:144964 original size:31 final size:31
Alignment explanation
Indices: 144914--144972 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
144904 CTTAACAATC
144914 CAGTCACTCAAATAAAAACTTTTAAATAGTT
1 CAGTCACTCAAATAAAAACTTTTAAATAGTT
* * * *
144945 CAGTGACTTAAATGAAAACTTTTGAATA
1 CAGTCACTCAAATAAAAACTTTTAAATA
144973 ATTAAATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (31 bp):
CAGTCACTCAAATAAAAACTTTTAAATAGTT
Found at i:151177 original size:29 final size:30
Alignment explanation
Indices: 151135--151193 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
151125 TATAGTTTAA
* *
151135 TGTGCAATTGTATATATG-AATTTTGATTT
1 TGTGCAATTATATACATGAAATTTTGATTT
*
151164 TGTGCGATTATATACATGAAATTTTGATTT
1 TGTGCAATTATATACATGAAATTTTGATTT
151194 GATCCAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (30 bp):
TGTGCAATTATATACATGAAATTTTGATTT
Found at i:151204 original size:30 final size:29
Alignment explanation
Indices: 151139--151204 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
151129 GTTTAATGTG
* * *
151139 CAATTGTATATATGAATTTTGATTTTGTG
1 CAATTATATACATGAATTTTGATTTTGTC
*
151168 CGATTATATACATGAAATTTTGA-TTTGATC
1 CAATTATATACATG-AATTTTGATTTTG-TC
151198 CAATTAT
1 CAATTAT
151205 TGTAAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (29 bp):
CAATTATATACATGAATTTTGATTTTGTC
Found at i:152740 original size:17 final size:17
Alignment explanation
Indices: 152727--152769 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
152717 CTTTTAATTT
152727 TTTTATAATTTTAAAAA
1 TTTTATAATTTTAAAAA
152744 TTTTATAATTTTAAAAA
1 TTTTATAATTTTAAAAA
152761 TTTTA-AATT
1 TTTTATAATT
152770 AATATATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATAATTTTAAAAA
Found at i:152762 original size:9 final size:9
Alignment explanation
Indices: 152733--152767 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
152723 ATTTTTTTAT
152733 AATTTTAAA
1 AATTTTAAA
*
152742 AATTTT-AT
1 AATTTTAAA
152750 AATTTTAAA
1 AATTTTAAA
152759 AATTTTAAA
1 AATTTTAAA
152768 TTAATATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTTTAAA
Found at i:155801 original size:11 final size:11
Alignment explanation
Indices: 155785--155824 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
155775 TTATTTTATT
155785 TAAAAATAATA
1 TAAAAATAATA
155796 TAAAAA-AAT-
1 TAAAAATAATA
155805 TAAAAATAATA
1 TAAAAATAATA
155816 TAAAAATAA
1 TAAAAATAA
155825 AGATACTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.22
10 6 0.22
11 15 0.56
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:155809 original size:20 final size:20
Alignment explanation
Indices: 155784--155821 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
155774 ATTATTTTAT
155784 TTAAAAATAATATAAAAAAA
1 TTAAAAATAATATAAAAAAA
155804 TTAAAAATAATATAAAAA
1 TTAAAAATAATATAAAAA
155822 TAAAGATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAAAAATAATATAAAAAAA
Found at i:163385 original size:51 final size:51
Alignment explanation
Indices: 163328--163434 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 51
163318 ATAAAGAAAA
163328 TTTTCAATACTAACAAACTTATTTCT-AAACTAAAAACAATTAATTTGTATC
1 TTTTCAATACTAACAAACTTATTTCTAAAACTAAAAACAATTAATTTGTA-C
* ** **
163379 TTTTCAATACTTACAATTTTATTTCTAAAAACTAAAAGTAATTAATTTGTAC
1 TTTTCAATACTAACAAACTTATTTCT-AAAACTAAAAACAATTAATTTGTAC
163431 TTTT
1 TTTT
163435 ATCTACCATC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 23 0.47
52 5 0.10
53 21 0.43
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (51 bp):
TTTTCAATACTAACAAACTTATTTCTAAAACTAAAAACAATTAATTTGTAC
Done.