Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015152.1 Kokia drynarioides strain JFW-HI SEQ_130196, 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: 54334
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28 AATGATTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:296 original size:29 final size:30
Alignment explanation
Indices: 245--312 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 30
235 AACTTATATA
* *
245 TTTATAATTTTTAAGTGATT-AAAT-TAAATT
1 TTTATCATTTTGAAGTGATTAAAATGT-AA-T
*
275 TTTATCATTTTGAAG-GGTTAAAATGTAAT
1 TTTATCATTTTGAAGTGATTAAAATGTAAT
304 TTTATCATT
1 TTTATCATT
313 ATTAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 13 0.39
30 19 0.58
31 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.51
Consensus pattern (30 bp):
TTTATCATTTTGAAGTGATTAAAATGTAAT
Found at i:1713 original size:20 final size:20
Alignment explanation
Indices: 1688--1727 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1678 CAAAAAATCC
1688 AAGTCAACCATTTGTCATAA
1 AAGTCAACCATTTGTCATAA
*
1708 AAGTCAACTATTTGTCATAA
1 AAGTCAACCATTTGTCATAA
1728 TATAACCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (20 bp):
AAGTCAACCATTTGTCATAA
Found at i:1925 original size:24 final size:24
Alignment explanation
Indices: 1892--1941 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1882 TCTTCCTATT
1892 TAAGGATTGGGAAGGGATTATGAG
1 TAAGGATTGGGAAGGGATTATGAG
* **
1916 TAAGGGTTGGGGTGGGATTATGAG
1 TAAGGATTGGGAAGGGATTATGAG
1940 TA
1 TA
1942 GTTTTAGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (24 bp):
TAAGGATTGGGAAGGGATTATGAG
Found at i:5239 original size:16 final size:19
Alignment explanation
Indices: 5210--5245 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5200 ATAATTTGAC
5210 TTTTAAATTCTAGG-ATTT
1 TTTTAAATTCTAGGTATTT
5228 TTTTAAA-T-TAGGTATTT
1 TTTTAAATTCTAGGTATTT
5245 T
1 T
5246 ATTTTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.24
17 6 0.35
18 7 0.41
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (19 bp):
TTTTAAATTCTAGGTATTT
Found at i:8912 original size:97 final size:96
Alignment explanation
Indices: 8732--8916 Score: 216
Period size: 97 Copynumber: 1.9 Consensus size: 96
8722 GGTAAAATGA
* * ** **
8732 TATTTGATTATCTCGGTTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGTGAAATATTTCAGAATC
1 TATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGACAAATATTTCAGAATC
*
8797 GAAGATAAGGAAACATTGTCTCGATTAAGGG
66 GAAGATAAAGAAACATTGTCTCGATTAAGGG
*
8828 TATTCGATTATTTCGATTTGAAGAAAAAATTGCACCTAGTAAGTTAAGGCACAAAT-TTTC-GAA
1 TATTCGATTATCTCGATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGG-ACAAATATTTCAG-A
*
8891 ACTCGAA-ATAAA-AGAATATTGTCTCG
63 A-TCGAAGATAAAGA-AACATTGTCTCG
8917 GTTTTAAAGT
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
96 22 0.29
97 44 0.59
98 9 0.12
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (96 bp):
TATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGACAAATATTTCAGAATC
GAAGATAAAGAAACATTGTCTCGATTAAGGG
Found at i:9318 original size:58 final size:59
Alignment explanation
Indices: 9198--9484 Score: 343
Period size: 59 Copynumber: 4.9 Consensus size: 59
9188 TAATTTTGAG
* * * * * * *
9198 AGTTTCAAGGTCGAAAATGGAGTTTTTGGACA-TTCGGGGGT--AAATGGTATTTTTGAA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGTTTGAGGGTAAAAATGGAATTTTTGGA
* * *
9255 AGTTTCGGGGT-AAAAATAGAATTTTTGGAAGTTTAAGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
* *
9313 AGTTTCGAGGT-AAAAATGGAACTTTTGGAAGTTTGGGGGTAAAAAT-GAATTTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAA-TTTTTGGA
* * * *
9371 AATTTTGGGGTCAAAAATGGATTTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
* * *
9430 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTT
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTT
9485 CGAACAGTTT
Statistics
Matches: 196, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
55 1 0.01
56 21 0.11
57 12 0.06
58 71 0.36
59 88 0.45
60 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (59 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
Found at i:9380 original size:30 final size:29
Alignment explanation
Indices: 9211--9484 Score: 310
Period size: 29 Copynumber: 9.4 Consensus size: 29
9201 TTCAAGGTCG
*
9211 AAAATGGAGTTTTTGGACA--TTCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTTC-GGGGTA
* *
9239 -AAATGGTATTTTTGAAAGTTTCGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* **
9267 AAAATAGAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
*
9296 AAAATGGAATTTTTGGAAGTTTCGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* *
9325 AAAATGGAACTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* *
9354 AAAAT-GAATTTTTTGGAAATTTTGGGGTCA
1 AAAATGGAA-TTTTTGGAAGTTTCGGGGT-A
*
9384 AAAATGGATTTTTTGGAAGTTT-GAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
*
9413 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
9443 AAAATGGAATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
*
9472 AAAATGAAATTTT
1 AAAATGGAATTTT
9485 CGAACAGTTT
Statistics
Matches: 211, Mismatches: 24, Indels: 21
0.82 0.09 0.08
Matches are distributed among these distances:
26 1 0.00
27 18 0.09
28 6 0.03
29 137 0.65
30 47 0.22
31 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:10269 original size:7 final size:8
Alignment explanation
Indices: 10252--10277 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
10242 GTGAAAAACC
10252 TTTCTTTT
1 TTTCTTTT
10260 TTTCTTTT
1 TTTCTTTT
10268 TTTCTTTT
1 TTTCTTTT
10276 TT
1 TT
10278 ATTTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTCTTTT
Found at i:11417 original size:36 final size:35
Alignment explanation
Indices: 11353--11450 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 35
11343 TAATTGATTT
* * * * *
11353 TAAATTTAAGTTT-AAAAT-TATTTCAAATTTAGAC
1 TAAATTTAATTTTAAAAATAAATTT-AAATTCAAAA
*
11387 TAAATTTAAATTTTAAAAATGAATTTAAATTCAAAA
1 TAAATTT-AATTTTAAAAATAAATTTAAATTCAAAA
* *
11423 TAAATTTAATTTTAGAAATAAATCTAAA
1 TAAATTTAATTTTAAAAATAAATTTAAA
11451 ACTCATCTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 7 0.13
35 23 0.43
36 19 0.36
37 4 0.08
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (35 bp):
TAAATTTAATTTTAAAAATAAATTTAAATTCAAAA
Found at i:11434 original size:35 final size:34
Alignment explanation
Indices: 11353--11443 Score: 94
Period size: 36 Copynumber: 2.6 Consensus size: 34
11343 TAATTGATTT
* * * * *
11353 TAAATTTAAGTTT-AAAATTATTTCAAATTTAGAC
1 TAAATTTAATTTTAAAAATAATTT-AAATTCAAAA
11387 TAAATTTAAATTTTAAAAATGAATTTAAATTCAAAA
1 TAAATTT-AATTTTAAAAAT-AATTTAAATTCAAAA
*
11423 TAAATTTAATTTTAGAAATAA
1 TAAATTTAATTTTAAAAATAA
11444 ATCTAAAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
34 9 0.19
35 16 0.33
36 19 0.40
37 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (34 bp):
TAAATTTAATTTTAAAAATAATTTAAATTCAAAA
Found at i:29735 original size:37 final size:37
Alignment explanation
Indices: 29685--29759 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
29675 TATAAAATGG
29685 TTACAAAGATTATTTGTCTACATACAAGCAACCACCA
1 TTACAAAGATTATTTGTCTACATACAAGCAACCACCA
29722 TTACAAAGATTATTTGTCTACATACAAGCAACCACCA
1 TTACAAAGATTATTTGTCTACATACAAGCAACCACCA
29759 T
1 T
29760 GAAACCAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (37 bp):
TTACAAAGATTATTTGTCTACATACAAGCAACCACCA
Found at i:29989 original size:5 final size:5
Alignment explanation
Indices: 29979--30010 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
29969 CTGTTTAGAC
29979 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GT
30011 ACATATAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (5 bp):
GTTTT
Found at i:31793 original size:59 final size:58
Alignment explanation
Indices: 31716--32090 Score: 338
Period size: 59 Copynumber: 6.4 Consensus size: 58
31706 GGACACATTA
* * * *
31716 GGGGCAAAATGATTATTTTTGGAAGGTTTGGGTCAAAAAATATGATTTTTAGACATTCG
1 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGTCAAAAAAT-GGATTTTTAGACATTCG
* * * *
31775 GGGGTAAAATGGTAATTTTTGGAA-GTTCGAGGT-TAAAAATGGGATTTTTAGTCATTTG
1 GGGGTAAAATGGTAATTTTTGGAAGGTTTG-GGTCAAAAAAT-GGATTTTTAGACATTCG
* * * *
31833 GGGGTAAAATGGTAATTTTTAGAA-GTTTCGAGGTC-AAAAATGGAGTTTATCGACATTTG
1 GGGGTAAAATGGTAATTTTTGGAAGGTTT-G-GGTCAAAAAATGGA-TTTTTAGACATTCG
* * * *
31892 GGGGTAAAATGGTAATTTTTGGTAGGTTTGGG-GACAAAAATGGAGTTTTTGGACATCCG
1 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGTCA-AAAAATGGA-TTTTTAGACATTCG
* * * * *
31951 GGGGTAAAATGGTAATTTTTGAAAGTTTTGGGTCAAAAAA-AGAATTTTAAACATTCG
1 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGTCAAAAAATGGATTTTTAGACATTCG
* * **
32008 GGGGTAAAAT-GTAATTTTTGGAAGTTTTAGGGTC-AAAAATGGAATTTTTGGA-AGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAGGTTT-GGGTCAAAAAATGG-ATTTTTAGACA-TTCG
*
32066 GGGATAAAAATGG-AATTTTTGGAAG
1 GGGGT-AAAATGGTAATTTTTGGAAG
32091 TTCAAGGGTA
Statistics
Matches: 264, Mismatches: 38, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
56 22 0.08
57 27 0.10
58 69 0.26
59 140 0.53
60 6 0.02
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGTCAAAAAATGGATTTTTAGACATTCG
Found at i:31969 original size:29 final size:29
Alignment explanation
Indices: 31760--31971 Score: 130
Period size: 29 Copynumber: 7.2 Consensus size: 29
31750 AAAAAATATG
*
31760 ATTTTTAGACATTCGGGGGTAAAATGGTA
1 ATTTTTGGACATTCGGGGGTAAAATGGTA
* * *
31789 ATTTTTGGA-AGTTCGAGGTTAAAAATGG-G
1 ATTTTTGGACA-TTCGGGGGT-AAAATGGTA
* * *
31818 ATTTTTAGTCATTTGGGGGTAAAATGGTA
1 ATTTTTGGACATTCGGGGGTAAAATGGTA
* *
31847 ATTTTTAGA-AGTTTC-GAGGTCAAAAATGG-A
1 ATTTTTGGACA--TTCGGGGGT--AAAATGGTA
* * * *
31877 GTTTATCGACATTTGGGGGTAAAATGGTA
1 ATTTTTGGACATTCGGGGGTAAAATGGTA
** * **
31906 ATTTTTGGTAGGTTTGGGGACAAAAATGG-A
1 ATTTTTGG-ACATTCGGGG-GTAAAATGGTA
* *
31936 GTTTTTGGACATCCGGGGGTAAAATGGTA
1 ATTTTTGGACATTCGGGGGTAAAATGGTA
31965 ATTTTTG
1 ATTTTTG
31972 AAAGTTTTGG
Statistics
Matches: 136, Mismatches: 33, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
28 23 0.17
29 61 0.45
30 37 0.27
31 15 0.11
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.36
Consensus pattern (29 bp):
ATTTTTGGACATTCGGGGGTAAAATGGTA
Found at i:31988 original size:29 final size:27
Alignment explanation
Indices: 31952--32322 Score: 103
Period size: 29 Copynumber: 12.9 Consensus size: 27
31942 GGACATCCGG
*
31952 GGGTAAAATGGTAATTTTTGAAAGTTTT
1 GGGTAAAATGG-AATTTTTGAAAGTTTA
** * **
31980 GGGTCAAAAAAAGAA-TTTT-AAACATTCGG
1 GGGT--AAAATGGAATTTTTGAAA-GTT-TA
* *
32009 GGGTAAAATGTAATTTTTGGAAGTTTTA
1 GGGTAAAATGGAATTTTTGAAAG-TTTA
*
32037 GGGTCAAAAATGGAATTTTTGGAAGTTTA
1 GGGT--AAAATGGAATTTTTGAAAGTTTA
* *
32066 GGGATAAAAATGGAATTTTTGGAAGTTCAA
1 GGG-T-AAAATGGAATTTTTGAAAGTT-TA
* * *
32096 GGGTAAAAATGTAATTTTTGGAAAG-ATC
1 GGGT-AAAATGGAATTTTT-GAAAGTTTA
* *
32124 GGGATCAAAAATGG-ATTTTTGGAAG-TCA
1 GGG-T--AAAATGGAATTTTTGAAAGTTTA
* *
32152 GGGGTAAAAATGTAATTTTTGGAAAGATT-
1 -GGGT-AAAATGGAATTTTT-GAAAGTTTA
* * *
32181 GAGATCAAAAATGG-ATTTTTGGAAGTTCA
1 G-GGT--AAAATGGAATTTTTGAAAGTTTA
* * **
32210 GGGTAAAATGGTAAAATTTGGAAAAATT-
1 GGGTAAAATGG--AATTTTTGAAAGTTTA
* *
32238 GGAGTAAAAAATGGAATTTTT-AAACATTCAA
1 GG-GT--AAAATGGAATTTTTGAAA-GTT-TA
* *
32269 GGGTAAAATGGTAATTTTTGGAAGTTTC
1 GGGTAAAATGG-AATTTTTGAAAGTTTA
* *
32297 GAGGTCAAAAATAGAATTTTGGAAAG
1 G-GGT--AAAATGGAATTTTTGAAAG
32323 GGTCAAAATA
Statistics
Matches: 258, Mismatches: 50, Indels: 68
0.69 0.13 0.18
Matches are distributed among these distances:
26 7 0.03
27 16 0.06
28 53 0.21
29 106 0.41
30 61 0.24
31 15 0.06
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (27 bp):
GGGTAAAATGGAATTTTTGAAAGTTTA
Found at i:32113 original size:58 final size:59
Alignment explanation
Indices: 32013--32320 Score: 309
Period size: 57 Copynumber: 5.3 Consensus size: 59
32003 ATTCGGGGGT
* ** * *
32013 AAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGG-AAGTTTAGGGAT-A
1 AAAATGGAATTTTTGGAAGTTCAAGGGT-AAAAATGTAATTTTTGGAAAGATT-GGGATCA
*
32072 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAAGATCGGGATCA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAAGATTGGGATCA
* *
32131 AAAATGG-ATTTTTGGAAG-TCAGGGGTAAAAATGTAATTTTTGGAAAGATTGAGATCA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAAGATTGGGATCA
** * *
32188 AAAATGG-ATTTTTGGAAGTTC-AGGGT-AAAATGGTAAAATTTGGAAAAATT-GGAGTAA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAAT-GTAATTTTTGGAAAGATTGGGA-TCA
* * *
32245 AAAATGGAATTTTT-AAACATTCAAGGGT-AAAATGGTAATTTTTGG-AAGTTTCGAGG-TCA
1 AAAATGGAATTTTTGGAA-GTTCAAGGGTAAAAAT-GTAATTTTTGGAAAGATT-G-GGATCA
*
32304 AAAATAGAA-TTTTGGAA
1 AAAATGGAATTTTTGGAA
32321 AGGGTCAAAA
Statistics
Matches: 213, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
56 7 0.03
57 84 0.39
58 51 0.24
59 69 0.32
61 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAAGATTGGGATCA
Found at i:32199 original size:28 final size:29
Alignment explanation
Indices: 32035--32204 Score: 133
Period size: 29 Copynumber: 5.9 Consensus size: 29
32025 TTGGAAGTTT
*
32035 TAGGG-TCAAAAATGGAATTTTTGG-AAGTT
1 TAGGGATCAAAAATGG-ATTTTTGGAAAG-A
*
32064 TAGGGAT-AAAAATGGAATTTTTGG-AAGT
1 TAGGGATCAAAAATGG-ATTTTTGGAAAGA
*
32092 TCAAGGG-T-AAAAATGTAATTTTTGGAAAGA
1 T--AGGGATCAAAAATG-GATTTTTGGAAAGA
*
32122 TCGGGATCAAAAATGGATTTTTGG-AAG-
1 TAGGGATCAAAAATGGATTTTTGGAAAGA
* *
32149 TCAGGGGT-AAAAATGTAATTTTTGGAAAGA
1 T-AGGGATCAAAAATG-GATTTTTGGAAAGA
* *
32179 TTGAGATCAAAAATGGATTTTTGGAA
1 TAGGGATCAAAAATGGATTTTTGGAA
32205 GTTCAGGGTA
Statistics
Matches: 118, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
27 8 0.07
28 20 0.17
29 66 0.56
30 24 0.20
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (29 bp):
TAGGGATCAAAAATGGATTTTTGGAAAGA
Found at i:33941 original size:19 final size:19
Alignment explanation
Indices: 33917--33956 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
33907 CTGTGGCAGT
33917 TGGTGGCAGTGCAAGTTGC
1 TGGTGGCAGTGCAAGTTGC
*
33936 TGGTGGCATTGCAAGTTGC
1 TGGTGGCAGTGCAAGTTGC
33955 TG
1 TG
33957 ATGGTGCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.40, T:0.30
Consensus pattern (19 bp):
TGGTGGCAGTGCAAGTTGC
Found at i:34162 original size:17 final size:17
Alignment explanation
Indices: 34142--34212 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
34132 TTTTAATTTT
* *
34142 ATTTTAATTTTAAATAA
1 ATTTAAATTTCAAATAA
*
34159 ATTTAAATTTCAAGTAA
1 ATTTAAATTTCAAATAA
* * *
34176 ATTCAAA-CTCAAAATGA
1 ATTTAAATTTC-AAATAA
* *
34193 ATTTGAATTTAAAATAA
1 ATTTAAATTTCAAATAA
34210 ATT
1 ATT
34213 CAAACTTATT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
16 2 0.05
17 37 0.93
18 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTCAAATAA
Found at i:34202 original size:34 final size:34
Alignment explanation
Indices: 34153--34218 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
34143 TTTTAATTTT
* *
34153 AAATAAATTTAAATTTCAAGTAAATTCAAACTCA
1 AAATAAATTTAAATTTAAAATAAATTCAAACTCA
* *
34187 AAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAATAAATTTAAATTTAAAATAAATTCAAACT
34219 TATTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (34 bp):
AAATAAATTTAAATTTAAAATAAATTCAAACTCA
Found at i:36682 original size:580 final size:584
Alignment explanation
Indices: 35649--37697 Score: 2485
Period size: 580 Copynumber: 3.5 Consensus size: 584
35639 TTTACTAAGG
* * * * *
35649 AAAGAAAAA-GGGGATGCAACTGGATTCAGTGTATAGC-TTTTTCTTTTGGTTTGGCGCGAGTTT
1 AAAGAAAAAGGGGGACGCGACTGGATTCAGTGTTTAGCATTTTCCTTTTTGTTTGGCGCGAGTTT
* *
35712 TATTTGGCTTTTGCCTTTGCCCTTACTCTGTCTCAGGTGTGAGTGTCTGAGATGGATCTACATGG
66 TATTTGGCTTTTGCCTTTGCCCTTACTTTGACTCAGGTGTGAGTGTCTGAGATGGATCTACATGG
*
35777 GTATTTTCAATTTTCTTTTAGGCTTTTTCATGTATTTGTTGGATTTTTAGA-GGATCATATCTAC
131 GTATTTTCAATTTTCTTCTAGGCTTTTTCATGTATTTGTTGGATTTTTAGATGG-TCATA-CTAC
* *
35841 ATATCCATGTATGCATTGGATGTGGATGTAAGGGGTACTTTAAGAAATATGAAGAGTTAGAACAA
194 -TAT--A--TATGCATTGGATGTGGATGTAAGGGGCACTTTAAG-AATAT-AAAAGTTAGAACAA
** *
35906 CATAACCTTTTACCAATGACCATGTTTCTAAAAAATTT-ATTTCCAAATCATCTGGTTTGGATTT
252 CATAACCTTTTACCCCTGACCATGTTTCTAATAAATTTAATTT-CAAATCATCTGGTTTGGATTT
* * *
35970 TTGAGGACTGATTGGAAAGTAAACTCCCCAAAATAGAAGATTTG-AGCTATCATATTATTTATTT
316 TCGAGGACTGATTGGAACGTAAACTCCCCAAAATAGAAGTTTTGAAG-TATCAT-TTATTTATTT
* * * * *
36034 ATTTCCATCCCCTTAGGCTTTTTATTTTCTTCAATTGATGGAGTATTTTCACAAATGAAATGCAA
379 ATTTCCATCGCCTTAGGTTTTTTATTTTCTTCAATTGATTGAATATTTTCACATATGAAATGCAA
**
36099 TTG-AACAGACTCCAATTTGATGAAGCAACCCTGAATGCAAAATGGGGGAAGGGGAAGATAAGGA
444 TTGAAACAGACTCCAGCTTGATGAAGCAA-CCTGAATGCAAAATGGGGGAAGGGGAAGATAAGGA
*
36163 ACTTAAAGGTATTTCTTGAATTCTGTAGTCATCTTCTTTTCCTTTTCTATTTACTAAGGAAATAT
508 ACTCAAAGGTATTTCTTGAATTCTGTAGTCATCTTCTTTTCCTTTTCTATTTACTAAGGAAATAT
36228 AAGATGGTCCAA
573 AAGATGGTCCAA
* * * *
36240 AAAGAAAAAGGGGGATGTGATTGGATTCAGTGTTTAGC-TTTTCCTTTTTGTTTGGCACGAGTTT
1 AAAGAAAAAGGGGGACGCGACTGGATTCAGTGTTTAGCATTTTCCTTTTTGTTTGGCGCGAGTTT
* * *
36304 TATTTGGCTTTTGCCTTTGCCCTTACTTTGACTTAGGTGTGAGTGTCTGAGATGGATCAACATAG
66 TATTTGGCTTTTGCCTTTGCCCTTACTTTGACTCAGGTGTGAGTGTCTGAGATGGATCTACATGG
36369 GTATTTTCAATTTTCTTCTAGGCTTTTTCATGTATTTGTTGGATGTTTTAGATGGTCATA-T-CT
131 GTATTTTCAATTTTCTTCTAGGCTTTTTCATGTATTTGTTGGAT-TTTTAGATGGTCATACTACT
36432 ATAT-T-CATTGGATGTGGATGTAAGGGGCACTTTAAG-ATATAAAGAGTTAGAACAACATAACC
195 ATATATGCATTGGATGTGGATGTAAGGGGCACTTTAAGAATATAAA-AGTTAGAACAACATAACC
36494 TTTTA-CCCTGACCATGTTTCTAATAAATTTAATTTCAAATCATCTGGTTTGGATTTTCGAGGAC
259 TTTTACCCCTGACCATGTTTCTAATAAATTTAATTTCAAATCATCTGGTTTGGATTTTCGAGGAC
** * *
36558 TGATCAGAACCTAAACTCCCCGAAATAGAAGTTTTGAAGTATCATGTTATTTATTTATTTCCATC
324 TGATTGGAACGTAAACTCCCCAAAATAGAAGTTTTGAAGTATCAT-TTATTTATTTATTTCCATC
* *
36623 GCTTTAGGTTTTTTATTTTCTTCAATTGATTGAATATTTTCACATACGAAATGCAATTGAAACAG
388 GCCTTAGGTTTTTTATTTTCTTCAATTGATTGAATATTTTCACATATGAAATGCAATTGAAACAG
*
36688 ACTCCAGCTTGATGAAGCAACCTGAATGCAACATGGGGGAAGGGGAAGATAAGGAACTCAAAGGT
453 ACTCCAGCTTGATGAAGCAACCTGAATGCAAAATGGGGGAAGGGGAAGATAAGGAACTCAAAGGT
*
36753 ATTTCTTGAATTCTGTAGTCATCTTCTTTT-CTTTTTTATTTACTAAGGAAATATAAGATGGTCC
518 ATTTCTTGAATTCTGTAGTCATCTTCTTTTCCTTTTCTATTTACTAAGGAAATATAAGATGGTCC
36817 AA
583 AA
* * *
36819 AAATATAAAGGGGGACACGACTGGATTCAGTGTTTAGCATTTT-CTTTTT-TTATGGCGCGAGTT
1 AAAGAAAAAGGGGGACGCGACTGGATTCAGTGTTTAGCATTTTCCTTTTTGTT-TGGCGCGAGTT
* *
36882 TCATTTGGCTTTTGCCTTTGCCCTTACTTTGACTCAGGTGTGAGTGTCTGAGATGGATCGACATG
65 TTATTTGGCTTTTGCCTTTGCCCTTACTTTGACTCAGGTGTGAGTGTCTGAGATGGATCTACATG
* * * * * * * * *
36947 GGTA--TT--A-TTT-GT-T-GGATGTTT-A-G-A--TGCT-CATATCTACAT-ATCCATA-TA-
130 GGTATTTTCAATTTTCTTCTAGGCTTTTTCATGTATTTGTTGGATTTTTAGATGGT-CATACTAC
** * * * * * *
36995 TGCAT-TGGATGTGGATGT--A---AGGGGCAC-TTTAAGGAATATGAAAAGTTAGAACATAACC
194 TATATATGCAT-TGGATGTGGATGTAAGGG-GCACTTTAAGAATAT-AAAAGTTAG-----AA-C
37053 TTTTATCACATAACCTTTTATCCCTGACCATGACCATGTTTCTAATAAATTTAATTTCAAATCAT
250 ----A--ACATAACCTTTTA--CC---CC-TGACCATGTTTCTAATAAATTTAATTTCAAATCAT
* * *
37118 CTGCTTTGGATTTTGGAGGACTGATTGGAACGTAAACTCCCCAAAATAGAAGTTTTGAATTATCA
303 CTGGTTTGGATTTTCGAGGACTGATTGGAACGTAAACTCCCCAAAATAGAAGTTTTGAAGTATCA
*
37183 --TA-TTATTTATTTCCATCGCCTTAGGTTTTCTATTTTCTTCAATTGATTGAATATTTTCACAT
368 TTTATTTATTTATTTCCATCGCCTTAGGTTTTTTATTTTCTTCAATTGATTGAATATTTTCACAT
*
37245 ATGAAATGCAATTGAAACAGACTCCAGCTTGATGAAGCAACCTGAATGCAACAA-GGGAGAAGGG
433 ATGAAATGCAATTGAAACAGACTCCAGCTTGATGAAGCAACCTGAATGCAA-AATGGGGGAAGGG
37309 GAAGATAAGGAACTCAAAGGTATTTCTTGAATTCTGTAGTCATCTTCTTTTCTTTTCTTTTTCTA
497 GAAGATAAGGAACTCAAAGGTATTTCTTGAATTCTGTAGTCATCTTCTTTTC----C-TTTTCTA
*
37374 TTTACTAAGGAAATATAGGATGGTCCAA
557 TTTACTAAGGAAATATAAGATGGTCCAA
* * * *
37402 AAAGAAAAAGGGGGACGCGATTGGATTCAATGTTTAGCTTTTTCTTTTTGCTTTTTGTTTGGGGC
1 AAAGAAAAAGGGGGACGCGACTGGATTCAGTGTTTAGCATTTTC------CTTTTTGTTTGGCGC
* * *
37467 AAGTTTTATTTGGCTTTTGCCTTTACCCTTTACCCTTACGTTGACTCAGGTGTGAGTGTTTGAGA
60 GAGTTTTATTTGGCTTTTGCCTTTGCCC-TTA--C-T---TTGACTCAGGTGTGAGTGTCTGAGA
* ** *
37532 TGGATCTACATGGTTATTTTCAATTTTCTTCTAGGCTTTTTCATGTATTTGTCAGATTTTTAGAG
118 TGGATCTACATGGGTATTTTCAATTTTCTTCTAGGCTTTTTCATGTATTTGTTGGATTTTTAGAT
* *
37597 GGTCATATCTACTATCCTTATATGCATTGGATGTGGATGTAAGAGGCACTTTAAGAAATATGAAA
183 GGTCATA-CTACTA----TATATGCATTGGATGTGGATGTAAGGGGCACTTTAAG-AATATAAAA
*
37662 GTTAGAACAACATAACCTTTTACCCCTGATCATGTT
242 GTTAGAACAACATAACCTTTTACCCCTGACCATGTT
37698 AAGTTTCTTG
Statistics
Matches: 1256, Mismatches: 115, Indels: 160
0.82 0.08 0.10
Matches are distributed among these distances:
561 8 0.01
562 11 0.01
563 4 0.00
564 15 0.01
565 4 0.00
566 10 0.01
567 2 0.00
568 2 0.00
569 1 0.00
570 1 0.00
571 6 0.00
572 2 0.00
573 1 0.00
574 16 0.01
575 1 0.00
577 171 0.14
578 5 0.00
579 148 0.12
580 238 0.19
581 149 0.12
582 1 0.00
583 100 0.08
584 1 0.00
585 1 0.00
587 1 0.00
589 3 0.00
590 37 0.03
591 15 0.01
592 150 0.12
593 13 0.01
594 3 0.00
597 38 0.03
599 2 0.00
601 1 0.00
602 3 0.00
603 1 0.00
604 1 0.00
605 15 0.01
606 3 0.00
607 1 0.00
608 1 0.00
609 2 0.00
610 2 0.00
611 23 0.02
612 1 0.00
613 3 0.00
614 1 0.00
617 1 0.00
618 11 0.01
619 4 0.00
620 1 0.00
622 1 0.00
623 15 0.01
624 5 0.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (584 bp):
AAAGAAAAAGGGGGACGCGACTGGATTCAGTGTTTAGCATTTTCCTTTTTGTTTGGCGCGAGTTT
TATTTGGCTTTTGCCTTTGCCCTTACTTTGACTCAGGTGTGAGTGTCTGAGATGGATCTACATGG
GTATTTTCAATTTTCTTCTAGGCTTTTTCATGTATTTGTTGGATTTTTAGATGGTCATACTACTA
TATATGCATTGGATGTGGATGTAAGGGGCACTTTAAGAATATAAAAGTTAGAACAACATAACCTT
TTACCCCTGACCATGTTTCTAATAAATTTAATTTCAAATCATCTGGTTTGGATTTTCGAGGACTG
ATTGGAACGTAAACTCCCCAAAATAGAAGTTTTGAAGTATCATTTATTTATTTATTTCCATCGCC
TTAGGTTTTTTATTTTCTTCAATTGATTGAATATTTTCACATATGAAATGCAATTGAAACAGACT
CCAGCTTGATGAAGCAACCTGAATGCAAAATGGGGGAAGGGGAAGATAAGGAACTCAAAGGTATT
TCTTGAATTCTGTAGTCATCTTCTTTTCCTTTTCTATTTACTAAGGAAATATAAGATGGTCCAA
Found at i:37065 original size:15 final size:15
Alignment explanation
Indices: 37045--37074 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37035 AAAAGTTAGA
37045 ACATAACCTTTTATC
1 ACATAACCTTTTATC
37060 ACATAACCTTTTATC
1 ACATAACCTTTTATC
37075 CCTGACCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (15 bp):
ACATAACCTTTTATC
Found at i:37875 original size:13 final size:13
Alignment explanation
Indices: 37857--37884 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
37847 CTGCTTTCAG
37857 CTTTCAAGTGGAA
1 CTTTCAAGTGGAA
37870 CTTTCAAGTGGAA
1 CTTTCAAGTGGAA
37883 CT
1 CT
37885 ATGTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (13 bp):
CTTTCAAGTGGAA
Found at i:38286 original size:21 final size:21
Alignment explanation
Indices: 38262--38305 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
38252 TCCATATGCA
38262 GAAATACATTTCTTTTGAGCT
1 GAAATACATTTCTTTTGAGCT
38283 GAAATACATTTCTTTTGAGCT
1 GAAATACATTTCTTTTGAGCT
38304 GA
1 GA
38306 CCCTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (21 bp):
GAAATACATTTCTTTTGAGCT
Found at i:39248 original size:2 final size:2
Alignment explanation
Indices: 39241--39271 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
39231 CAGGGATTTT
39241 TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39272 CTGTCAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:39472 original size:246 final size:246
Alignment explanation
Indices: 39020--39505 Score: 877
Period size: 246 Copynumber: 2.0 Consensus size: 246
39010 CTTAACCCAA
*
39020 TTGTGCTGTCAAGGGTGTACTCTATAACCCGTATGTGCATGTTTTGGTATCTCTCTATCATACAC
1 TTGTGCTGTCAAGGGTGCACTCTATAACCCGTATGTGCATGTTTTGGTATCTCTCTATCATACAC
* * *
39085 ACGCGCGCACACAATTATGATAATAGAATCTAAAAAGTGATCCTTTTTGTTGATCAATATGGATA
66 ACACACGCACACAATTATGATAATAGAATCTAAAAAGTGATCCCTTTTGTTGATCAATAT-GATA
39150 TTTTTGTTGTTGTTGAGGAGGAGAGTTTGATAAAAGTACAATGATTGAAATTGACTTGAGGGTTA
130 TTTTTGTTGTTGTTGAGGAGGAGAGTTTGATAAAAGTACAATGATTGAAATTGACTTGAGGGTTA
39215 AATTCACCCATAGCTGCAGGGATTTTTGTGTGTGTGTGTGTGTGTGTGTGTG
195 AATTCACCCATAGCTGCAGGGATTTTTGTGTGTGTGTGTGTGTGTGTGTGTG
*
39267 TTGTGCTGTCAAGGGTGCACTCTATAACCCGTATGTGCTTGTTTTGGTATCTCTCTCTATCATAC
1 TTGTGCTGTCAAGGGTGCACTCTATAACCCGTATGTGCATGTTTTGGTA--TCTCTCTATCATAC
39332 ACACACACGCACACAATTATGATAATAGAATCTAAAAAGTGATCCCTTTTGTTGATCAAT-T-AT
64 ACACACACGCACACAATTATGATAATAGAATCTAAAAAGTGATCCCTTTTGTTGATCAATATGAT
*
39395 ATTTTTGTTGTTGTTGAGGAGGAGAGTTTGATAAAAGTTCAATGATTGAAATTGACTTGAGGGTT
129 ATTTTTGTTGTTGTTGAGGAGGAGAGTTTGATAAAAGTACAATGATTGAAATTGACTTGAGGGTT
39460 AAATTCACCCATAGCTGCAGGGATTTTTGTGTGTGTGTGTGTGTGT
194 AAATTCACCCATAGCTGCAGGGATTTTTGTGTGTGTGTGTGTGTGT
39506 TTTCATTAGA
Statistics
Matches: 231, Mismatches: 6, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
246 112 0.48
247 47 0.20
248 1 0.00
249 71 0.31
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (246 bp):
TTGTGCTGTCAAGGGTGCACTCTATAACCCGTATGTGCATGTTTTGGTATCTCTCTATCATACAC
ACACACGCACACAATTATGATAATAGAATCTAAAAAGTGATCCCTTTTGTTGATCAATATGATAT
TTTTGTTGTTGTTGAGGAGGAGAGTTTGATAAAAGTACAATGATTGAAATTGACTTGAGGGTTAA
ATTCACCCATAGCTGCAGGGATTTTTGTGTGTGTGTGTGTGTGTGTGTGTG
Found at i:40055 original size:21 final size:21
Alignment explanation
Indices: 40029--40092 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
40019 CTGCAGCGAC
40029 TCCTGCAGATACGAGGGTTAT
1 TCCTGCAGATACGAGGGTTAT
* *
40050 TCCTGCAGAAACGAGGGTTTT
1 TCCTGCAGATACGAGGGTTAT
40071 TCCTGCAGATACGAGGGTTAT
1 TCCTGCAGATACGAGGGTTAT
40092 T
1 T
40093 ATGGGTTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
TCCTGCAGATACGAGGGTTAT
Found at i:40524 original size:27 final size:27
Alignment explanation
Indices: 40494--40583 Score: 74
Period size: 29 Copynumber: 3.2 Consensus size: 27
40484 TATAGGTTGT
40494 TGTAGGCCTTACATCTATTGATTTAGG
1 TGTAGGCCTTACATCTATTGATTTAGG
** * * * *
40521 TGTAGTTTCTTGCATACTTTTTATAGGTT-GT
1 TGTAG-GCCTTACAT-CTATTGAT---TTAGG
40552 TGTAGGCCTTACATCTATTGATTTAGG
1 TGTAGGCCTTACATCTATTGATTTAGG
40579 TGTAG
1 TGTAG
40584 TTTCTTGCAT
Statistics
Matches: 45, Mismatches: 12, Indels: 12
0.65 0.17 0.17
Matches are distributed among these distances:
26 2 0.04
27 11 0.24
28 6 0.13
29 12 0.27
30 6 0.13
31 6 0.13
32 2 0.04
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.46
Consensus pattern (27 bp):
TGTAGGCCTTACATCTATTGATTTAGG
Found at i:40567 original size:58 final size:58
Alignment explanation
Indices: 40477--40593 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
40467 TTCATCTTAT
40477 TACTTTTTATAGGTTGTTGTAGGCCTTACATCTATTGATTTAGGTGTAGTTTCTTGCA
1 TACTTTTTATAGGTTGTTGTAGGCCTTACATCTATTGATTTAGGTGTAGTTTCTTGCA
40535 TACTTTTTATAGGTTGTTGTAGGCCTTACATCTATTGATTTAGGTGTAGTTTCTTGCA
1 TACTTTTTATAGGTTGTTGTAGGCCTTACATCTATTGATTTAGGTGTAGTTTCTTGCA
40593 T
1 T
40594 TTCTCATGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.49
Consensus pattern (58 bp):
TACTTTTTATAGGTTGTTGTAGGCCTTACATCTATTGATTTAGGTGTAGTTTCTTGCA
Found at i:43366 original size:38 final size:38
Alignment explanation
Indices: 43326--43410 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
43316 CAACAAATTT
* * *
43326 AAAAAATATATAATATATCAAATACACTTAAAA-ACATTA
1 AAAAAATAT-TAAAAAAT-AAATAAACTTAAAATACATTA
*
43365 AAACAAATATTAAAAAATAAATAAATTTAAAATACATTA
1 AAA-AAATATTAAAAAATAAATAAACTTAAAATACATTA
43404 AAAAAAT
1 AAAAAAT
43411 TTATATTAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 16 0.40
39 18 0.45
40 6 0.15
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (38 bp):
AAAAAATATTAAAAAATAAATAAACTTAAAATACATTA
Found at i:43553 original size:12 final size:12
Alignment explanation
Indices: 43536--43638 Score: 52
Period size: 12 Copynumber: 8.8 Consensus size: 12
43526 ATAACATCCA
43536 AACAACAAAAAT
1 AACAACAAAAAT
* *
43548 AACAACCAAAAC
1 AACAACAAAAAT
* *
43560 AGCAACAAGAAT
1 AACAACAAAAAT
* *
43572 AACAGC-AAAAC
1 AACAACAAAAAT
**
43583 AA-AA-TTAAA-
1 AACAACAAAAAT
43592 AACAACAAAAAT
1 AACAACAAAAAT
**
43604 AGTAACAAAAAT
1 AACAACAAAAAT
* * *
43616 AACATCAAAGAC
1 AACAACAAAAAT
43628 AACAACGAAAA
1 AACAAC-AAAA
43639 CTATAAAAAA
Statistics
Matches: 63, Mismatches: 23, Indels: 9
0.66 0.24 0.09
Matches are distributed among these distances:
9 2 0.03
10 6 0.10
11 8 0.13
12 44 0.70
13 3 0.05
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:43572 original size:24 final size:23
Alignment explanation
Indices: 43538--43583 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
43528 AACATCCAAA
43538 CAACAAAAATAACAACCAAAACAG
1 CAACAAAAATAAC-ACCAAAACAG
* *
43562 CAACAAGAATAACAGCAAAACA
1 CAACAAAAATAACACCAAAACA
43584 AAATTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.65, C:0.24, G:0.07, T:0.04
Consensus pattern (23 bp):
CAACAAAAATAACACCAAAACAG
Found at i:43575 original size:44 final size:44
Alignment explanation
Indices: 43522--43683 Score: 136
Period size: 44 Copynumber: 3.7 Consensus size: 44
43512 AAAACGCATA
* *
43522 AAAAATAACATCCAAACAACAA-AAATAACAACCAAAACAGCAAC
1 AAAAATAACATCAAAACAACAATAAA-AACAACAAAAACAGCAAC
* * * *
43566 AAGAATAACAGCAAAACAA-AATTAAAAACAACAAAAATAGTAAC
1 AAAAATAACATCAAAACAACAA-TAAAAACAACAAAAACAGCAAC
** *
43610 AAAAATAACATCAAAGACAACAACGAAAACTATA-AAAAACAAC-AC
1 AAAAATAACATCAAA-ACAACAATAAAAAC-A-ACAAAAACAGCAAC
* * *
43655 AAAAACAGCAT-AAAACAACAATCAAAACA
1 AAAAATAACATCAAAACAACAATAAAAACA
43684 GTAAAAAAAT
Statistics
Matches: 95, Mismatches: 17, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
42 1 0.01
43 14 0.15
44 47 0.49
45 23 0.24
46 9 0.09
47 1 0.01
ACGTcount: A:0.67, C:0.20, G:0.04, T:0.09
Consensus pattern (44 bp):
AAAAATAACATCAAAACAACAATAAAAACAACAAAAACAGCAAC
Found at i:43691 original size:22 final size:22
Alignment explanation
Indices: 43626--43691 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
43616 AACATCAAAG
*
43626 ACAACAACGAAAACTA-TAAAAA
1 ACAACAACAAAAAC-AGTAAAAA
* *
43648 ACAAC-ACAAAAACAGCATAAA
1 ACAACAACAAAAACAGTAAAAA
43669 ACAACAATC-AAAACAGTAAAAA
1 ACAACAA-CAAAAACAGTAAAAA
43691 A
1 A
43692 ATAGCACCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 1 0.03
21 16 0.44
22 18 0.50
23 1 0.03
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.08
Consensus pattern (22 bp):
ACAACAACAAAAACAGTAAAAA
Found at i:45901 original size:20 final size:20
Alignment explanation
Indices: 45865--45902 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45855 AACATAATCT
*
45865 TAAACATTAAATCTAAAATA
1 TAAACATTAAATATAAAATA
45885 TAAACA-TATAATATAAAA
1 TAAACATTA-AATATAAAA
45903 ATTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAACATTAAATATAAAATA
Found at i:50539 original size:17 final size:17
Alignment explanation
Indices: 50517--50561 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 17
50507 GTCCTGCAAC
50517 ATAAAGTATCGATACCT
1 ATAAAGTATCGATACCT
50534 ATAAAGTGGGTATCGATACCT
1 ATAAA----GTATCGATACCT
50555 ATAAAGT
1 ATAAAGT
50562 GGGTATCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 7 0.29
21 17 0.71
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (17 bp):
ATAAAGTATCGATACCT
Found at i:50548 original size:21 final size:21
Alignment explanation
Indices: 50522--50572 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
50512 GCAACATAAA
50522 GTATCGATACCTATAAAGTGG
1 GTATCGATACCTATAAAGTGG
50543 GTATCGATACCTATAAAGTGG
1 GTATCGATACCTATAAAGTGG
50564 GTATCGATA
1 GTATCGATA
50573 TTTTTTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (21 bp):
GTATCGATACCTATAAAGTGG
Found at i:50786 original size:40 final size:39
Alignment explanation
Indices: 50718--50813 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 39
50708 TTTTGAAAGA
* *
50718 GGGTATCGATATAATTCAAAGATAATCGATA-C-TCAGTTGT
1 GGGTATCGATAT-TTTCAAAGATAATCGATACCTTAAG-T-T
50758 GGGTATCGATATTTTCAAA-ATATTATCGATACCTTAAGTT
1 GGGTATCGATATTTTCAAAGATA--ATCGATACCTTAAGTT
50798 GGGTATCGATATTTTC
1 GGGTATCGATATTTTC
50814 TCAAAGTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
38 3 0.06
39 6 0.12
40 36 0.72
41 2 0.04
42 3 0.06
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (39 bp):
GGGTATCGATATTTTCAAAGATAATCGATACCTTAAGTT
Found at i:50908 original size:40 final size:40
Alignment explanation
Indices: 50864--50961 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
50854 TATTAAAAGA
50864 GGGTATCGATATTTTTCAAATATTATCGATA-CTTAAATAT
1 GGGTATCGATATTTTTCAAATATTATCGATACCTTAAA-AT
* **
50904 GGGTA-CTGATATTTTCCAAATATTATCGATACCTTTGAAT
1 GGGTATC-GATATTTTTCAAATATTATCGATACCTTAAAAT
*
50944 GAGTATCGATATTTTTCA
1 GGGTATCGATATTTTTCA
50962 GACGTTTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.02
40 44 0.88
41 5 0.10
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (40 bp):
GGGTATCGATATTTTTCAAATATTATCGATACCTTAAAAT
Found at i:53308 original size:20 final size:20
Alignment explanation
Indices: 53283--53331 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
53273 ATGCACATGA
53283 GTATCGATATTTTTAAGA-AG
1 GTATCGATATTTTTAA-ACAG
*
53303 GTATCGATATTTTTAAACTG
1 GTATCGATATTTTTAAACAG
53323 GTATCGATA
1 GTATCGATA
53332 CCAAATCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
GTATCGATATTTTTAAACAG
Done.