Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014420.1 Kokia drynarioides strain JFW-HI SEQ_129458, 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: 412056
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 263 characters in sequence are not A, C, G, or T
Found at i:2589 original size:31 final size:31
Alignment explanation
Indices: 2524--2599 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
2514 ATTTTAATAG
*
2524 TTTAT-ATTTTTATAATGTATTAAATCAAAAT
1 TTTATCATTTTTA-AAAGTATTAAATCAAAAT
* *
2555 TTTATCATTTTTAAAAG-ATTAAAGTGAAACT
1 TTTATCATTTTTAAAAGTATTAAA-TCAAAAT
2586 TTTATCATTTTTAA
1 TTTATCATTTTTAA
2600 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 6 0.15
31 27 0.68
32 7 0.17
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (31 bp):
TTTATCATTTTTAAAAGTATTAAATCAAAAT
Found at i:8983 original size:23 final size:23
Alignment explanation
Indices: 8934--8981 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
8924 GTCACTGTTA
*
8934 TTTATTTATTTTGATGCTTTAAT
1 TTTATTTATTTTGATGCTTCAAT
*
8957 TTTATTTATTTTGATTC-TCAAT
1 TTTATTTATTTTGATGCTTCAAT
8979 TTT
1 TTT
8982 TAAATTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (23 bp):
TTTATTTATTTTGATGCTTCAAT
Found at i:14362 original size:16 final size:18
Alignment explanation
Indices: 14327--14363 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
14317 TTCTTGTTAG
*
14327 AATAAAATACAATGGTAA
1 AATAAAATACAATAGTAA
14345 AATAAAATA-AA-AGTAA
1 AATAAAATACAATAGTAA
14361 AAT
1 AAT
14364 TCATATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.22
Consensus pattern (18 bp):
AATAAAATACAATAGTAA
Found at i:18935 original size:29 final size:29
Alignment explanation
Indices: 18870--18929 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
18860 AACACTTCGA
18870 GGTCAAAAATGAAATCTTTGAAAGTTCAG
1 GGTCAAAAATGAAATCTTTGAAAGTTCAG
* **
18899 GGTCAAAAATGAAATTTTTTTAAGTTCAG
1 GGTCAAAAATGAAATCTTTGAAAGTTCAG
18928 GG
1 GG
18930 GTAAAATGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (29 bp):
GGTCAAAAATGAAATCTTTGAAAGTTCAG
Found at i:18963 original size:29 final size:30
Alignment explanation
Indices: 18931--19187 Score: 142
Period size: 29 Copynumber: 8.7 Consensus size: 30
18921 AGTTCAGGGG
*
18931 TAAAATGGTAA-TTTTGGAAAAATCGAGGT
1 TAAAATGGTAATTTTTGGAAAATTCGAGGT
* *
18960 TAAAAATGG-AATTTTTGG-AAGTTCGAGGG
1 T-AAAATGGTAATTTTTGGAAAATTCGAGGT
* * * *
18989 TAAAATGGTAAATTTTAGAAAGTTCTAGGAT
1 TAAAATGGTAATTTTTGGAAAATTCGAGG-T
* ** * *
19020 CAAAAATGG-AATTTTTGGAAGTTTAG-GGA
1 -TAAAATGGTAATTTTTGGAAAATTCGAGGT
* *
19049 TAAAATGATAATTTTTGGAAAAATCGAGGT
1 TAAAATGGTAATTTTTGGAAAATTCGAGGT
* * * *
19079 CAAAATGG-AATTTTTGG--AAGTCCAGGGG
1 TAAAATGGTAATTTTTGGAAAATTCGA-GGT
*
19107 TAAAATGGTAA-TTTTGAGAAAGTTCG-GGAT
1 TAAAATGGTAATTTTTG-GAAAATTCGAGG-T
* * * *
19137 CAAAAT-ATGAATTTTTGG-AAGTTCGAGGG
1 TAAAATGGT-AATTTTTGGAAAATTCGAGGT
* *
19166 AAAAATGGTAATTTTTAGAAAA
1 TAAAATGGTAATTTTTGGAAAA
19188 ATTTGGGTCA
Statistics
Matches: 170, Mismatches: 39, Indels: 37
0.69 0.16 0.15
Matches are distributed among these distances:
27 5 0.03
28 27 0.16
29 67 0.39
30 45 0.26
31 19 0.11
32 7 0.04
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGAAAATTCGAGGT
Found at i:18965 original size:58 final size:59
Alignment explanation
Indices: 18901--19189 Score: 322
Period size: 58 Copynumber: 4.9 Consensus size: 59
18891 AAGTTCAGGG
* **
18901 TCAAAAATGAAATTTTTTTAAGTTCAGGGGTAAAATGGTAATTTTGGAAAAATCGAGG-
1 TCAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTGGAAAAATCGAGGA
* * ** *
18959 TTAAAAATGGAATTTTTGGAAGTTC-GAGGGTAAAATGGTAAATTTTAGAAAGTTCTAGGA
1 TCAAAAATGGAATTTTTGGAAGTTCAG-GGGTAAAATGGT-AATTTTGGAAAAATCGAGGA
* * *
19019 TCAAAAATGGAATTTTTGGAAGTTTAGGGATAAAATGATAATTTTTGGAAAAATCGAGG-
1 TCAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAATGGTAA-TTTTGGAAAAATCGAGGA
* **
19078 TC-AAAATGGAATTTTTGGAAGTCCAGGGGTAAAATGGTAATTTTGAGAAAGTTCG-GGA
1 TCAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTG-GAAAAATCGAGGA
* *
19136 TCAAAATAT-GAATTTTTGGAAGTTC-GAGGGAAAAATGGTAATTTTTAGAAAAAT
1 TCAAAA-ATGGAATTTTTGGAAGTTCAG-GGGTAAAATGGTAA-TTTTGGAAAAAT
19190 TTGGGTCAAA
Statistics
Matches: 193, Mismatches: 27, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
57 8 0.04
58 77 0.40
59 55 0.28
60 52 0.27
61 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (59 bp):
TCAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTGGAAAAATCGAGGA
Found at i:19274 original size:59 final size:58
Alignment explanation
Indices: 18963--19311 Score: 220
Period size: 59 Copynumber: 6.0 Consensus size: 58
18953 TCGAGGTTAA
* * * *
18963 AAATGGAATTTTTGG-AAG-TTCGAGGGT-AAAATGGTAAATTTTAGAAAGTTCTAGGATC
1 AAATGTAATTTTTGGAAAGTTTAG-GGGTCAAAAT-GTAATTTTTAGAAAGTT-TAGGGTC
* * * ** *
19021 AAAAATGGAATTTTTGG-AAGTTTAGGGAT-AAAATGATAATTTTTGGAAA-AATCGAGGTC
1 --AAATGTAATTTTTGGAAAGTTTAGGGGTCAAAATG-TAATTTTTAGAAAGTTTAG-GGTC
* ** * *
19080 AAAATGGAATTTTTGG-AAGTCCAGGGGT-AAAATGGTAATTTTGAGAAAG-TTCGGGATC
1 -AAATGTAATTTTTGGAAAGTTTAGGGGTCAAAAT-GTAATTTTTAGAAAGTTTAGGG-TC
* * * *
19138 AAAATATGAATTTTTGG-AAG-TTCGAGGG-AAAAATGGTAATTTTTAGAAAAATTT-GGGTC
1 -AAATGT-AATTTTTGGAAAGTTTAG-GGGTCAAAAT-GTAATTTTTAG-AAAGTTTAGGGTC
* * * ** *
19197 AAATGTGATTTTTTGAAAGTTTGGGGGTTGAAATGTAATTTTTAGAAAGTTTAGGGTTG
1 AAATGTAATTTTTGGAAAGTTTAGGGGTCAAAATGTAATTTTTAGAAAGTTTAGGG-TC
* *
19256 AAATGTAATTTTTGGAAAGTTTAGGGGTCAAAATGTAATTTCTAGATAGTTTAGGG
1 AAATGTAATTTTTGGAAAGTTTAGGGGTCAAAATGTAATTTTTAGAAAGTTTAGGG
19312 ACATATTACG
Statistics
Matches: 237, Mismatches: 36, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
57 15 0.06
58 79 0.33
59 95 0.40
60 43 0.18
61 5 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
AAATGTAATTTTTGGAAAGTTTAGGGGTCAAAATGTAATTTTTAGAAAGTTTAGGGTC
Found at i:19276 original size:117 final size:116
Alignment explanation
Indices: 18889--19301 Score: 358
Period size: 118 Copynumber: 3.5 Consensus size: 116
18879 TGAAATCTTT
* * ** * * * *
18889 GAAAGTTCAGGGTCAAAAATGAAATTTTTTTAAGTTCAGGGGTAAAATGGTAA-TTTTGGAAAAA
1 GAAAGTTTAGGGT-AAAAATGTAATTTTTGGAAGTTGAGGGATAAAATGATAATTTTTAGAAAAA
* * * *
18953 TCGAGGTTAAAAATGGAATTTTTGGAAGTTC-GAGGGTAAAATGGTAAATTTTA
65 TCGAGG-TCAAAATGGAATTTTTGAAAGTCCAG-GGGTAAAATGGTAATTTTTA
* * * *
19006 GAAAGTTCTAGGATCAAAAATGGAATTTTTGGAAGTTTAGGGATAAAATGATAATTTTTGGAAAA
1 GAAAGTT-TAGGGT-AAAAATGTAATTTTTGGAAGTTGAGGGATAAAATGATAATTTTTAGAAAA
* *
19071 ATCGAGGTCAAAATGGAATTTTTGGAAGTCCAGGGGTAAAATGGTAATTTTGA
64 ATCGAGGTCAAAATGGAATTTTTGAAAGTCCAGGGGTAAAATGGTAATTTTTA
* *
19124 GAAAG-TTCGGGATCAAAATATG-AATTTTTGGAAGTTCGAGGGA-AAAATGGTAATTTTTAGAA
1 GAAAGTTTAGGG-T-AAAA-ATGTAATTTTTGGAAGTT-GAGGGATAAAATGATAATTTTTAGAA
* * *** *
19186 AAATTTG-GGTC-AAATGTGATTTTTTGAAAGTTTGGGGGTTGAAAT-GTAATTTTTA
62 AAA-TCGAGGTCAAAATG-GAATTTTTGAAAGTCCAGGGG-TAAAATGGTAATTTTTA
** * * *
19241 GAAAGTTTAGGGTTGAAATGTAATTTTTGGAAAGTTTAGGGGTCAAAATG-TAATTTCTAGA
1 GAAAGTTTAGGGTAAAAATGTAATTTTTGG-AAGTTGAGGGAT-AAAATGATAATTTTTAGA
19302 TAGTTTAGGG
Statistics
Matches: 251, Mismatches: 31, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
115 3 0.01
116 23 0.09
117 98 0.39
118 109 0.43
119 18 0.07
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (116 bp):
GAAAGTTTAGGGTAAAAATGTAATTTTTGGAAGTTGAGGGATAAAATGATAATTTTTAGAAAAAT
CGAGGTCAAAATGGAATTTTTGAAAGTCCAGGGGTAAAATGGTAATTTTTA
Found at i:19308 original size:30 final size:30
Alignment explanation
Indices: 19168--19311 Score: 152
Period size: 30 Copynumber: 4.9 Consensus size: 30
19158 TTCGAGGGAA
*
19168 AAATGGTAATTTTTAGAAAAATTT--GGGTC-
1 AAAT-GTAATTTTTAG-AAAGTTTAGGGGTCG
* * * *
19197 AAATGTGATTTTTTGAAAGTTTGGGGGTTG
1 AAATGTAATTTTTAGAAAGTTTAGGGGTCG
*
19227 AAATGTAATTTTTAGAAAGTTTA-GGGTTG
1 AAATGTAATTTTTAGAAAGTTTAGGGGTCG
* *
19256 AAATGTAATTTTTGGAAAGTTTAGGGGTCA
1 AAATGTAATTTTTAGAAAGTTTAGGGGTCG
* *
19286 AAATGTAATTTCTAGATAGTTTAGGG
1 AAATGTAATTTTTAGAAAGTTTAGGG
19312 ACATATTACG
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.06
28 9 0.09
29 36 0.37
30 47 0.48
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.40
Consensus pattern (30 bp):
AAATGTAATTTTTAGAAAGTTTAGGGGTCG
Found at i:20566 original size:19 final size:19
Alignment explanation
Indices: 20542--20581 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
20532 TGGAAAGGTG
20542 CTTGGAAAATTAGGGTTTC
1 CTTGGAAAATTAGGGTTTC
20561 CTTGGAAAATTAGGGTTTC
1 CTTGGAAAATTAGGGTTTC
20580 CT
1 CT
20582 AATTTCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (19 bp):
CTTGGAAAATTAGGGTTTC
Found at i:20973 original size:20 final size:20
Alignment explanation
Indices: 20948--20987 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20938 AAACTCAGAG
20948 TAAAGTTGTTTCTTCAATGC
1 TAAAGTTGTTTCTTCAATGC
20968 TAAAGTTGTTTCTTCAATGC
1 TAAAGTTGTTTCTTCAATGC
20988 AATATTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
TAAAGTTGTTTCTTCAATGC
Found at i:22127 original size:14 final size:14
Alignment explanation
Indices: 22108--22137 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22098 TTTTTAAAAA
22108 AATTTAAATAACTT
1 AATTTAAATAACTT
*
22122 AATTTAATTAACTT
1 AATTTAAATAACTT
22136 AA
1 AA
22138 AATTTGAAAA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTAAATAACTT
Found at i:23963 original size:2 final size:2
Alignment explanation
Indices: 23956--24001 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
23946 TTGTCATTGG
23956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23998 AT AT
1 AT AT
24002 TTATGATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28206 original size:30 final size:29
Alignment explanation
Indices: 28124--28206 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
28114 CATAAATCCT
* *
28124 TTTACTTTTCATAAATTTAAATTTTAGTCCC
1 TTTATTTTTCAT--ATTTAAAATTTAGTCCC
*
28155 TATATTTTT-AT-TTTGACAAATTTAGTCCC
1 TTTATTTTTCATATTT-A-AAATTTAGTCCC
28184 TTTATTTTTCATATTTCAAAATT
1 TTTATTTTTCATATTT-AAAATT
28207 CAGGTACATT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.07
28 1 0.02
29 19 0.44
30 9 0.21
31 11 0.26
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTATTTTTCATATTTAAAATTTAGTCCC
Found at i:31482 original size:28 final size:28
Alignment explanation
Indices: 31429--31483 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
31419 ATTGATTAAT
* * **
31429 TATAAATATATGTATTTTTTTGGTTGAA
1 TATAAACATATGTATTTATTACGTTGAA
31457 TATAAACATATGTATTTATTACGTTGA
1 TATAAACATATGTATTTATTACGTTGA
31484 CAATTTGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (28 bp):
TATAAACATATGTATTTATTACGTTGAA
Found at i:38774 original size:12 final size:12
Alignment explanation
Indices: 38759--38816 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
38749 ATAATAGCAA
38759 AACAA-AAACAAC
1 AACAACAAA-AAC
*
38771 AACAACAAAAAT
1 AACAACAAAAAC
*
38783 AGCAACAAAAAC
1 AACAACAAAAAC
*
38795 AACAACAAAAAT
1 AACAACAAAAAC
*
38807 AGCAACAAAA
1 AACAACAAAA
38817 TTAACAGCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
12 36 0.92
13 3 0.08
ACGTcount: A:0.72, C:0.21, G:0.03, T:0.03
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:38800 original size:24 final size:24
Alignment explanation
Indices: 38768--38840 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
38758 AAACAAAAAC
38768 AACAACAACAAAAATAGCAACAAA
1 AACAACAACAAAAATAGCAACAAA
38792 AACAACAACAAAAATAGCAACAAA
1 AACAACAACAAAAATAGCAACAAA
** * *
38816 ATTAACAGCAAAAATAGCATCAAA
1 AACAACAACAAAAATAGCAACAAA
38840 A
1 A
38841 CAATAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.67, C:0.19, G:0.05, T:0.08
Consensus pattern (24 bp):
AACAACAACAAAAATAGCAACAAA
Found at i:38839 original size:12 final size:12
Alignment explanation
Indices: 38773--38840 Score: 82
Period size: 12 Copynumber: 5.7 Consensus size: 12
38763 AAAACAACAA
38773 CAACAAAAATAG
1 CAACAAAAATAG
* *
38785 CAACAAAAACAA
1 CAACAAAAATAG
38797 CAACAAAAATAG
1 CAACAAAAATAG
* *
38809 CAACAAAATTAA
1 CAACAAAAATAG
*
38821 CAGCAAAAATAG
1 CAACAAAAATAG
*
38833 CATCAAAA
1 CAACAAAA
38841 CAATAAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.66, C:0.19, G:0.06, T:0.09
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:45707 original size:205 final size:205
Alignment explanation
Indices: 45355--45764 Score: 820
Period size: 205 Copynumber: 2.0 Consensus size: 205
45345 TGAGGGGGTA
45355 GAGGAGAAGTGTGTTCTTTGTTTATTATTTTGGCTTGTTGTACAATCACTAATAATAATACGCGT
1 GAGGAGAAGTGTGTTCTTTGTTTATTATTTTGGCTTGTTGTACAATCACTAATAATAATACGCGT
45420 TGTTTTGTCGGCTTCTGCTTTTGGAAGTTTGAGGAGGTAAGTCGAAAAATTCAAACCAAAGAAAG
66 TGTTTTGTCGGCTTCTGCTTTTGGAAGTTTGAGGAGGTAAGTCGAAAAATTCAAACCAAAGAAAG
45485 AACTGAAATTTATGGATGACTGCAAAGGTATTAGCCACCAAGTAATTTAATGTAATCAGACCAAA
131 AACTGAAATTTATGGATGACTGCAAAGGTATTAGCCACCAAGTAATTTAATGTAATCAGACCAAA
45550 TCCTCACATT
196 TCCTCACATT
45560 GAGGAGAAGTGTGTTCTTTGTTTATTATTTTGGCTTGTTGTACAATCACTAATAATAATACGCGT
1 GAGGAGAAGTGTGTTCTTTGTTTATTATTTTGGCTTGTTGTACAATCACTAATAATAATACGCGT
45625 TGTTTTGTCGGCTTCTGCTTTTGGAAGTTTGAGGAGGTAAGTCGAAAAATTCAAACCAAAGAAAG
66 TGTTTTGTCGGCTTCTGCTTTTGGAAGTTTGAGGAGGTAAGTCGAAAAATTCAAACCAAAGAAAG
45690 AACTGAAATTTATGGATGACTGCAAAGGTATTAGCCACCAAGTAATTTAATGTAATCAGACCAAA
131 AACTGAAATTTATGGATGACTGCAAAGGTATTAGCCACCAAGTAATTTAATGTAATCAGACCAAA
45755 TCCTCACATT
196 TCCTCACATT
45765 CACACTAAGC
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 205 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (205 bp):
GAGGAGAAGTGTGTTCTTTGTTTATTATTTTGGCTTGTTGTACAATCACTAATAATAATACGCGT
TGTTTTGTCGGCTTCTGCTTTTGGAAGTTTGAGGAGGTAAGTCGAAAAATTCAAACCAAAGAAAG
AACTGAAATTTATGGATGACTGCAAAGGTATTAGCCACCAAGTAATTTAATGTAATCAGACCAAA
TCCTCACATT
Found at i:51960 original size:24 final size:24
Alignment explanation
Indices: 51932--51982 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
51922 AGAAACAATC
*
51932 TTTCAGCTAAACTCTGTTTAATTG
1 TTTCAACTAAACTCTGTTTAATTG
* *
51956 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAACTAAACTCTGTTTAATTG
51980 TTT
1 TTT
51983 GAGTCAAACT
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:0.24, C:0.14, G:0.10, T:0.53
Consensus pattern (24 bp):
TTTCAACTAAACTCTGTTTAATTG
Found at i:51991 original size:24 final size:24
Alignment explanation
Indices: 51940--51994 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
51930 TCTTTCAGCT
*
51940 AAACTCTGTTTAATTGTTTCAATT
1 AAACTCTGTTTAATTGTTTCAATC
* * *
51964 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTAATTGTTTCAATC
51988 AAACTCT
1 AAACTCT
51995 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (24 bp):
AAACTCTGTTTAATTGTTTCAATC
Found at i:52089 original size:13 final size:13
Alignment explanation
Indices: 52071--52095 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52061 ACCTTAGAAA
52071 ATACACCCATTAG
1 ATACACCCATTAG
52084 ATACACCCATTA
1 ATACACCCATTA
52096 AAGTTTAGAA
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:0.32, G:0.04, T:0.24
Consensus pattern (13 bp):
ATACACCCATTAG
Found at i:54330 original size:5 final size:5
Alignment explanation
Indices: 54320--54345 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
54310 ACATTAACAG
54320 CTAAC CTAAC CTAAC CTAAC CTAAC C
1 CTAAC CTAAC CTAAC CTAAC CTAAC C
54346 AAATACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.19
Consensus pattern (5 bp):
CTAAC
Found at i:56895 original size:18 final size:19
Alignment explanation
Indices: 56861--56903 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
56851 AATTACCAAA
*
56861 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
56880 AAAATTCAAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
56898 AAAAAT
1 AAAAAT
56904 ACCAAATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:61019 original size:21 final size:21
Alignment explanation
Indices: 60993--61036 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
60983 ACTTGACTTT
*
60993 TCATAGTCGACAGTACATCCC
1 TCATAGTCGACAATACATCCC
*
61014 TCATAGTCGATAATACATCCC
1 TCATAGTCGACAATACATCCC
61035 TC
1 TC
61037 GAATGACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (21 bp):
TCATAGTCGACAATACATCCC
Found at i:67056 original size:217 final size:217
Alignment explanation
Indices: 66681--67112 Score: 767
Period size: 217 Copynumber: 2.0 Consensus size: 217
66671 TTTTTATGAT
* * *
66681 AAAATATTGAAAAAATTGAAGATATATAACAACAATTAAATTGAAACGAAACAGTGTGGGATGGA
1 AAAATATTGAAAAAATTAAAGATATATAACAACAATTAAATTGAAACGAAACAGTGTGAGATGAA
*
66746 AATAGGTGCATCCAACATTAATGAAAATGATAGTAAATTTCAAAATTATGCATCCAATTATAAAA
66 AATAGATGCATCCAACATTAATGAAAATGATAGTAAATTTCAAAATTATGCATCCAATTATAAAA
*
66811 CGGTAATTAATTTAACAATATCCACCCTACCTCACCCATTTACATGTATATATCATGGCAACTCA
131 CGGCAATTAATTTAACAATATCCACCCTACCTCACCCATTTACATGTATATATCATGGCAACTCA
66876 TATCCAAATCCATCGAGTTGAA
196 TATCCAAATCCATCGAGTTGAA
* *
66898 AAAATATTGAAAAAATTAAAGATATATAACAACAATTAAATTGGAACGGAACAGTGTGAGATGAA
1 AAAATATTGAAAAAATTAAAGATATATAACAACAATTAAATTGAAACGAAACAGTGTGAGATGAA
* *
66963 AAT-GAATGCATCCAACCTTAATGAAAATGATAGTAAATTTCAAAATTATTCATCCAATTATAAA
66 AATAG-ATGCATCCAACATTAATGAAAATGATAGTAAATTTCAAAATTATGCATCCAATTATAAA
67027 ACGGCAATTAATTTAACAATATCCACCCTACCTCACCCATTTACATGTATATATCATGGCAACTC
130 ACGGCAATTAATTTAACAATATCCACCCTACCTCACCCATTTACATGTATATATCATGGCAACTC
67092 ATATCCAAATCCATCGAGTTG
195 ATATCCAAATCCATCGAGTTG
67113 CCCTGCTGGA
Statistics
Matches: 205, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
216 1 0.00
217 204 1.00
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.28
Consensus pattern (217 bp):
AAAATATTGAAAAAATTAAAGATATATAACAACAATTAAATTGAAACGAAACAGTGTGAGATGAA
AATAGATGCATCCAACATTAATGAAAATGATAGTAAATTTCAAAATTATGCATCCAATTATAAAA
CGGCAATTAATTTAACAATATCCACCCTACCTCACCCATTTACATGTATATATCATGGCAACTCA
TATCCAAATCCATCGAGTTGAA
Found at i:76142 original size:21 final size:21
Alignment explanation
Indices: 76112--76152 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
76102 CGAATTTGAT
76112 TAAATAATTTCTT-GAAAAATC
1 TAAATAATTT-TTGGAAAAATC
*
76133 TAAATGATTTTTGGAAAAAT
1 TAAATAATTTTTGGAAAAAT
76153 TAATTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (21 bp):
TAAATAATTTTTGGAAAAATC
Found at i:81084 original size:20 final size:20
Alignment explanation
Indices: 81023--81089 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
81013 TTGGTGCTTT
*
81023 TTTTTTTACTGTTTTAGTTG
1 TTTTTTTACTGTTTTTGTTG
*
81043 CTGTTTTTTGCT-TTTTTG-TG
1 -T-TTTTTTACTGTTTTTGTTG
81063 TTTTTTTACTGTTTTTGTTG
1 TTTTTTTACTGTTTTTGTTG
81083 TTATTTT
1 TT-TTTT
81090 CATGTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 8 0.21
19 7 0.18
20 6 0.15
21 10 0.26
22 8 0.21
ACGTcount: A:0.06, C:0.06, G:0.15, T:0.73
Consensus pattern (20 bp):
TTTTTTTACTGTTTTTGTTG
Found at i:81089 original size:12 final size:12
Alignment explanation
Indices: 81074--81195 Score: 86
Period size: 12 Copynumber: 9.9 Consensus size: 12
81064 TTTTTTACTG
81074 TTTTTGTTGTTA
1 TTTTTGTTGTTA
** *
81086 -TTTTCATGTTG
1 TTTTTGTTGTTA
*
81097 TTTTTGCTGTTA
1 TTTTTGTTGTTA
* *
81109 TTTTTGTTGCTG
1 TTTTTGTTGTTA
* *
81121 TTTTTATTGCTA
1 TTTTTGTTGTTA
81133 TTTTTGTTGTT-
1 TTTTTGTTGTTA
81144 TTTTATGTTTGCTGTTA
1 TTTT-TG--T--TGTTA
* *
81161 TTTTTGCTGTTG
1 TTTTTGTTGTTA
*
81173 TTTTGGTTGTTA
1 TTTTTGTTGTTA
81185 TTTTTGTTGTT
1 TTTTTGTTGTT
81196 TGGATGTTAT
Statistics
Matches: 84, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
11 12 0.14
12 61 0.73
14 1 0.01
16 6 0.07
17 4 0.05
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:81098 original size:23 final size:21
Alignment explanation
Indices: 81047--81146 Score: 80
Period size: 23 Copynumber: 4.7 Consensus size: 21
81037 TAGTTGCTGT
*
81047 TTTTTGCT-TTTTTG-TGTT-
1 TTTTTGTTGTTTTTGTTGTTA
**
81065 TTTTTACTGTTTTTGTTGTTA
1 TTTTTGTTGTTTTTGTTGTTA
*
81086 TTTTCATGTTGTTTTTGCTGTTA
1 TTTT--TGTTGTTTTTGTTGTTA
* *
81109 TTTTTGTTGCTGTTTTTATTGCTA
1 TTTTTG-T--TGTTTTTGTTGTTA
81133 TTTTTGTTGTTTTT
1 TTTTTGTTGTTTTT
81147 TATGTTTGCT
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.10
19 6 0.09
20 4 0.06
21 13 0.19
22 1 0.01
23 19 0.28
24 17 0.25
ACGTcount: A:0.06, C:0.06, G:0.16, T:0.72
Consensus pattern (21 bp):
TTTTTGTTGTTTTTGTTGTTA
Found at i:81210 original size:21 final size:22
Alignment explanation
Indices: 81156--81210 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
81146 TTATGTTTGC
*
81156 TGTTATTTTTGCTGTTGTTTTGGT
1 TGTTATTTTT--TGTTGTTTTGGA
81180 TGTTA-TTTTTGTTG-TTTGGA
1 TGTTATTTTTTGTTGTTTTGGA
81200 TGTTATTTTTT
1 TGTTATTTTTT
81211 TATGCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.34
21 10 0.34
23 4 0.14
24 5 0.17
ACGTcount: A:0.07, C:0.02, G:0.22, T:0.69
Consensus pattern (22 bp):
TGTTATTTTTTGTTGTTTTGGA
Found at i:82091 original size:20 final size:19
Alignment explanation
Indices: 82057--82095 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
82047 ATTCCTGATT
82057 AAGTGTATGGTAATGGTAAA
1 AAGTGTATGGTAAT-GTAAA
82077 AAGTGTATTGG-AATGTAAA
1 AAGTGTA-TGGTAATGTAAA
82096 GAATATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 10 0.56
21 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (19 bp):
AAGTGTATGGTAATGTAAA
Found at i:83408 original size:24 final size:25
Alignment explanation
Indices: 83368--83414 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
83358 TAATAATACT
83368 TCTAAACATCTTATCTAT-ATCTTG
1 TCTAAACATCTTATCTATGATCTTG
*
83392 TCTAAACGTTCTT-TCTATGATCT
1 TCTAAAC-ATCTTATCTATGATCT
83415 GTATGCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (25 bp):
TCTAAACATCTTATCTATGATCTTG
Found at i:91333 original size:31 final size:31
Alignment explanation
Indices: 91291--91353 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
91281 TGGAAATTTT
* * *
91291 ACAAAATTAAAATGC-AGGGACCAAATTGATA
1 ACAAAAATAAAATACAAGGG-CCAAAATGATA
91322 ACAAAAATAAAATACAAGGGCCAAAATGATA
1 ACAAAAATAAAATACAAGGGCCAAAATGATA
91353 A
1 A
91354 AAGTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.57, C:0.13, G:0.14, T:0.16
Consensus pattern (31 bp):
ACAAAAATAAAATACAAGGGCCAAAATGATA
Found at i:96669 original size:2 final size:2
Alignment explanation
Indices: 96662--96686 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
96652 ATAATGAGAT
96662 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
96687 GGATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105157 original size:67 final size:67
Alignment explanation
Indices: 105049--105183 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
105039 TCCATATTCT
105049 ATAAAAATTAGAACAAATGGCCAAGAAGGAAAAACCCAATCTTCTAAAAGGGTAAGAAACTTTAA
1 ATAAAAATTAGAACAAATGGCCAAGAAGGAAAAACCCAATCTTCTAAAAGGGTAAGAAACTTTAA
105114 TA
66 TA
*
105116 ATAAAAATTAGATCAAATGGCCAAGAAGGAAAAACCCAATCTTCTAAAAGGGTAAGAAACTTTAA
1 ATAAAAATTAGAACAAATGGCCAAGAAGGAAAAACCCAATCTTCTAAAAGGGTAAGAAACTTTAA
105181 TA
66 TA
105183 A
1 A
105184 AGCAATGAAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.20
Consensus pattern (67 bp):
ATAAAAATTAGAACAAATGGCCAAGAAGGAAAAACCCAATCTTCTAAAAGGGTAAGAAACTTTAA
TA
Found at i:114053 original size:31 final size:31
Alignment explanation
Indices: 113981--114058 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
113971 GTAATATACC
* *
113981 ATTTGATACTTATA-TTTGGCTTCAATGTTCA
1 ATTTGATACCTA-AGTTTGGCTTCAATATTCA
114012 ATTT-AGTACCTAAGTTTGGCTTCAATATTCA
1 ATTTGA-TACCTAAGTTTGGCTTCAATATTCA
114043 ATTTGATACCTGAAGT
1 ATTTGATACCT-AAGT
114059 AAACATATCA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 2 0.05
31 34 0.83
32 5 0.12
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (31 bp):
ATTTGATACCTAAGTTTGGCTTCAATATTCA
Found at i:122269 original size:19 final size:18
Alignment explanation
Indices: 122242--122293 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
122232 ATATAATTGA
122242 TTATTTAATATTGTAATT
1 TTATTTAATATTGTAATT
*
122260 TTATTTTAATATT-AAATT
1 TTA-TTTAATATTGTAATT
**
122278 TTAAGTAATATTGTAA
1 TTATTTAATATTGTAA
122294 AATATTATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.25
18 12 0.43
19 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTATTTAATATTGTAATT
Found at i:122377 original size:21 final size:23
Alignment explanation
Indices: 122353--122403 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
122343 ACAATTTATA
122353 AATATTTT-ATGATATAA-CATG
1 AATATTTTAATGATATAATCATG
* *
122374 AATATTTTAATTATATAATTATG
1 AATATTTTAATGATATAATCATG
122397 AATATTT
1 AATATTT
122404 ATTTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 8 0.31
22 8 0.31
23 10 0.38
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (23 bp):
AATATTTTAATGATATAATCATG
Found at i:122401 original size:23 final size:22
Alignment explanation
Indices: 122348--122403 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
122338 GTATTACAAT
*
122348 TTATAAATATTTTATGATATAA
1 TTATGAATATTTTATGATATAA
* *
122370 -CATGAATATTTTAATTATATAA
1 TTATGAATATTTT-ATGATATAA
122392 TTATGAATATTT
1 TTATGAATATTT
122404 ATTTAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 10 0.36
22 8 0.29
23 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTATGAATATTTTATGATATAA
Found at i:122404 original size:22 final size:21
Alignment explanation
Indices: 122348--122415 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
122338 GTATTACAAT
* *
122348 TTATAAATATTTTATGATATAA
1 TTATGAATA-TTTATTATATAA
*
122370 -CATGAATATTTTAATTATATAA
1 TTATGAATA-TTT-ATTATATAA
122392 TTATGAATATTTATT-TA-AA
1 TTATGAATATTTATTATATAA
122411 TTATG
1 TTATG
122416 TTTAGCTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.17
20 2 0.05
21 13 0.32
22 11 0.28
23 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (21 bp):
TTATGAATATTTATTATATAA
Found at i:145018 original size:31 final size:31
Alignment explanation
Indices: 144983--145118 Score: 120
Period size: 31 Copynumber: 4.5 Consensus size: 31
144973 TTAATAAAAC
*
144983 ATTTGGTACTTGAACTTGACACTTTTTCTTA
1 ATTTGGTACTTAAACTTGACACTTTTTCTTA
* *** ** *
145014 ATTTGGTAC-TAAAATT-TTTCTTGGTC-CA
1 ATTTGGTACTTAAACTTGACACTTTTTCTTA
* * *
145042 ATTTGGTACTCAAACTTGACATTTTTTCCTA
1 ATTTGGTACTTAAACTTGACACTTTTTCTTA
*
145073 ATTTGGTACCTAAACTTGACAC-TTTT-TTA
1 ATTTGGTACTTAAACTTGACACTTTTTCTTA
*
145102 AGTTGGTACTTAAACTT
1 ATTTGGTACTTAAACTT
145119 TTTGGGATCT
Statistics
Matches: 79, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
28 10 0.13
29 27 0.34
30 13 0.16
31 29 0.37
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACACTTTTTCTTA
Found at i:145147 original size:57 final size:58
Alignment explanation
Indices: 145070--145180 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 58
145060 ACATTTTTTC
* *
145070 CTAATTTGGTACCTAAACTTGACACTTTTT-TAAGTTGGTACTTAAACTTTTTGGGAT
1 CTAATTTGATACCTAAACTTGACACTTTTTCTAAGTTGGTACCTAAACTTTTTGGGAT
* * * * *
145127 CTAATTTGATACTTGAACTTGACTCTTTTTCCTAATTTGGTACCTAATCTTTTT
1 CTAATTTGATACCTAAACTTGACACTTTTT-CTAAGTTGGTACCTAAACTTTTT
145181 TTAATATTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 26 0.58
59 19 0.42
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (58 bp):
CTAATTTGATACCTAAACTTGACACTTTTTCTAAGTTGGTACCTAAACTTTTTGGGAT
Found at i:145156 original size:88 final size:90
Alignment explanation
Indices: 144983--145173 Score: 246
Period size: 88 Copynumber: 2.1 Consensus size: 90
144973 TTAATAAAAC
* * * * * *
144983 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACTAAAATTTTTCTTGGTCCAATTTGG
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGTACTAAAACTTTTCTGGGTCCAATTTGA
145048 TACTCAAACTTGACATTTTTTCCTA
66 TACTCAAACTTGACATTTTTTCCTA
* *
145073 ATTTGGTACCTAAACTTGACAC-TTTT-TTAAGTTGGTACTTAAACTTTT-TGGGATCTAATTTG
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGTACTAAAACTTTTCTGGG-TCCAATTTG
**
145135 ATACTTGAACTTGAC-TCTTTTTCCTA
65 ATACTCAAACTTGACAT-TTTTTCCTA
145161 ATTTGGTACCTAA
1 ATTTGGTACCTAA
145174 TCTTTTTTTA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
87 4 0.04
88 61 0.69
89 4 0.04
90 20 0.22
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (90 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGTACTAAAACTTTTCTGGGTCCAATTTGA
TACTCAAACTTGACATTTTTTCCTA
Found at i:145476 original size:26 final size:26
Alignment explanation
Indices: 145438--145489 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
145428 AAAAAGTATC
*
145438 AAGTTCAATTACCAAATT-GGATAAAA
1 AAGTTCAAGTACCAAATTAGGA-AAAA
* *
145464 AAGTTTAAGTACCGAATTAGGAAAAA
1 AAGTTCAAGTACCAAATTAGGAAAAA
145490 TTATCAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (26 bp):
AAGTTCAAGTACCAAATTAGGAAAAA
Found at i:156598 original size:15 final size:15
Alignment explanation
Indices: 156578--156606 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
156568 CAAATTGACC
156578 AAAATACTATGAAAA
1 AAAATACTATGAAAA
156593 AAAATACTATGAAA
1 AAAATACTATGAAA
156607 TACCTTTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAATACTATGAAAA
Found at i:169138 original size:29 final size:29
Alignment explanation
Indices: 169110--169183 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
169100 GGATTGAAAT
169110 TAAATTATAATTTTTATAA-TAGTAAAAA
1 TAAATTATAATTTTTATAATTAGTAAAAA
* * * **
169138 TATAGTTTTTATTTTTATAATTTTTAAAAAA
1 TA-AATTATAATTTTTATAATTAGT-AAAAA
169169 TAAATTA-AATTTTTA
1 TAAATTATAATTTTTA
169184 ATATTTTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
28 2 0.06
29 21 0.60
30 5 0.14
31 7 0.20
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
TAAATTATAATTTTTATAATTAGTAAAAA
Found at i:176827 original size:2 final size:2
Alignment explanation
Indices: 176814--176843 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
176804 CACTTAACTG
*
176814 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176844 GGTCATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:192154 original size:23 final size:23
Alignment explanation
Indices: 192122--192168 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
192112 TCAATGAAAG
192122 AAATAGAAAATCATA-AGTTATAA
1 AAATAGAAAATCATATA-TTATAA
* *
192145 AAATATAAAATTATATATTATAA
1 AAATAGAAAATCATATATTATAA
192168 A
1 A
192169 TTAAAATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATAGAAAATCATATATTATAA
Found at i:192571 original size:5 final size:5
Alignment explanation
Indices: 192561--192587 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
192551 ATTTTTTAAA
192561 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
192588 CACTCACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:197173 original size:29 final size:30
Alignment explanation
Indices: 197140--197200 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
197130 TTAATTTTAT
* *
197140 AAATTAT-ATTTTACTCTTTAAAAATGATA
1 AAATTATGATTTAACTCTGTAAAAATGATA
* * *
197169 AAATTTTGATTTAATTCTGTAAAAATTATA
1 AAATTATGATTTAACTCTGTAAAAATGATA
197199 AA
1 AA
197201 GACATAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
AAATTATGATTTAACTCTGTAAAAATGATA
Found at i:206657 original size:22 final size:22
Alignment explanation
Indices: 206631--206672 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
206621 AAGCTTTGAT
206631 TTTAAAATTAGATTTAAATTAA
1 TTTAAAATTAGATTTAAATTAA
* **
206653 TTTAAATTTATTTTTAAATT
1 TTTAAAATTAGATTTAAATT
206673 TAAATTTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTAAAATTAGATTTAAATTAA
Found at i:206662 original size:6 final size:6
Alignment explanation
Indices: 206631--206701 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
206621 AAGCTTTGAT
* * **
206631 TTTAAA ATTAGA TTTAAA -TT-AA TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
206677 TTTATCTT TTTAAA TTTAAA TTTAA
1 TTTA--AA TTTAAA TTTAAA TTTAA
206702 TCAAATTTGA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
4 2 0.04
5 4 0.08
6 39 0.80
8 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:206688 original size:20 final size:18
Alignment explanation
Indices: 206651--206700 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 18
206641 GATTTAAATT
206651 AATTTAAATTTATTTTTA
1 AATTTAAATTTATTTTTA
206669 AATTTAAATTTATCTTTTTA
1 AATTTAAATTTA--TTTTTA
206689 AATTTAAATTTA
1 AATTTAAATTTA
206701 ATCAAATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.40
20 18 0.60
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTAAATTTATTTTTA
Found at i:207477 original size:13 final size:13
Alignment explanation
Indices: 207452--207503 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 13
207442 TTAGTCATAA
207452 TAATAAT-AATAT
1 TAATAATAAATAT
*
207464 TGATAATAAATAT
1 TAATAATAAATAT
**
207477 TAATAAT-AACGT
1 TAATAATAAATAT
207489 TAATAATAAATAT
1 TAATAATAAATAT
207502 TA
1 TA
207504 GCAATGAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 16 0.50
13 16 0.50
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (13 bp):
TAATAATAAATAT
Found at i:207494 original size:25 final size:25
Alignment explanation
Indices: 207452--207503 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
207442 TTAGTCATAA
* *
207452 TAATAATAATATTGATAATAAATAT
1 TAATAATAACATTAATAATAAATAT
*
207477 TAATAATAACGTTAATAATAAATAT
1 TAATAATAACATTAATAATAAATAT
207502 TA
1 TA
207504 GCAATGAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
TAATAATAACATTAATAATAAATAT
Found at i:207549 original size:9 final size:9
Alignment explanation
Indices: 207535--207577 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
207525 TATTAACAGA
207535 AATATTAAT
1 AATATTAAT
*
207544 AATATTAGTAAA
1 AATA-T--TAAT
207556 AATATTAAT
1 AATATTAAT
207565 AATATTAAT
1 AATATTAAT
207574 AATA
1 AATA
207578 AAAAATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 20 0.69
10 1 0.03
11 1 0.03
12 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
AATATTAAT
Found at i:207558 original size:21 final size:21
Alignment explanation
Indices: 207516--207572 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
207506 AATGAATGGC
*
207516 ATTAATAAGTATTAACAGAAAT
1 ATTAATAA-TATTAACAAAAAT
**
207538 ATTAATAATATTAGTAAAAAT
1 ATTAATAATATTAACAAAAAT
207559 ATTAATAATATTAA
1 ATTAATAATATTAA
207573 TAATAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (21 bp):
ATTAATAATATTAACAAAAAT
Found at i:207917 original size:24 final size:24
Alignment explanation
Indices: 207857--207915 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
207847 TAAAAGTATA
* *
207857 AAAAAGGGAAAAGGATTTTCAAAG
1 AAAAAGGGAAAAGCATTTTAAAAG
**
207881 AAAAATCGAAAAGCA-TTTAAAAG
1 AAAAAGGGAAAAGCATTTTAAAAG
207904 AAAAAGGGAAAA
1 AAAAAGGGAAAA
207916 AGAAAAGGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.61, C:0.05, G:0.20, T:0.14
Consensus pattern (24 bp):
AAAAAGGGAAAAGCATTTTAAAAG
Found at i:208768 original size:29 final size:29
Alignment explanation
Indices: 208712--208906 Score: 118
Period size: 29 Copynumber: 6.7 Consensus size: 29
208702 CCCTAAACTA
* *
208712 TCCAAAAATT-CCATTTTGACCC-CGAAAC
1 TCCAAAAATTATCATTTTTACCCTC-AAAC
208740 TCACAAAAATTAT-ATTTTTACCCTCAAAC
1 TC-CAAAAATTATCATTTTTACCCTCAAAC
*** * *
208769 TTTTAAAATTTTCATTTTTTGACCCTAAAAC
1 TCCAAAAATTATCA-TTTTT-ACCCTCAAAC
208800 TTCCAAAAATT-TCATTTTTACCCTCAAACC
1 -TCCAAAAATTATCATTTTTACCCTCAAA-C
* * *
208830 TCTAAAAATT-CCATTTTTGACCCTAAAAC
1 TCCAAAAATTATCATTTTT-ACCCTCAAAC
* * ***
208859 TTTC-AAAATTATCA-TTTTACCCCCTAGTG
1 -TCCAAAAATTATCATTTTTACCCTC-AAAC
208888 TCCAAAAATT-TCATTTTTA
1 TCCAAAAATTATCATTTTTA
208907 TCCCGATTTT
Statistics
Matches: 130, Mismatches: 23, Indels: 27
0.72 0.13 0.15
Matches are distributed among these distances:
28 18 0.14
29 70 0.54
30 23 0.18
31 12 0.09
32 7 0.05
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
TCCAAAAATTATCATTTTTACCCTCAAAC
Found at i:208874 original size:59 final size:60
Alignment explanation
Indices: 208715--208880 Score: 207
Period size: 60 Copynumber: 2.8 Consensus size: 60
208705 TAAACTATCC
** * * *
208715 AAAAATTCCA-TTTTGACCCCGAAACTCACAAAAATTAT-ATTTTTACCCTCAAACTTTT
1 AAAAATTCCATTTTTGACCCTAAAACTTACAAAAATTATCATTTTTACCCTCAAACCTCT
* * *
208773 AAAATTTTCATTTTTTGACCCTAAAACTTCCAAAAATT-TCATTTTTACCCTCAAACCTCT
1 AAAAATTCCA-TTTTTGACCCTAAAACTTACAAAAATTATCATTTTTACCCTCAAACCTCT
*
208833 AAAAATTCCATTTTTGACCCTAAAACTTTC-AAAATTATCA-TTTTACCC
1 AAAAATTCCATTTTTGACCCTAAAACTTACAAAAATTATCATTTTTACCC
208881 CCTAGTGTCC
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
58 22 0.24
59 23 0.25
60 48 0.52
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (60 bp):
AAAAATTCCATTTTTGACCCTAAAACTTACAAAAATTATCATTTTTACCCTCAAACCTCT
Found at i:209038 original size:28 final size:28
Alignment explanation
Indices: 208977--209037 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
208967 CCAAAATTTC
*
208977 CCAAATTTACCATTTTGCCCCCGAGAAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
*
209005 CCAAAATTACCATTTTGCCCCCG-GTAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
209032 CCAAAA
1 CCAAAA
209038 AGTCTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.31, C:0.33, G:0.10, T:0.26
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGAAT
Found at i:214895 original size:14 final size:16
Alignment explanation
Indices: 214864--214907 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
214854 ATAATCGTTT
214864 TATAACATTTA-AATAA
1 TATAACATTTATAAT-A
*
214880 TATAAAATTTATAATA
1 TATAACATTTATAATA
214896 TATAACATTTAT
1 TATAACATTTAT
214908 CAAAAAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAACATTTATAATA
Found at i:222303 original size:21 final size:21
Alignment explanation
Indices: 222258--222311 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
222248 TTGGAGTTTG
222258 TTGTATTGGTAGTAGTATGAA
1 TTGTATTGGTAGTAGTATGAA
* *
222279 TTGTTTTGGTAGTAGTCAT-AC
1 TTGTATTGGTAGTAGT-ATGAA
*
222300 TTGTATCGGTAG
1 TTGTATTGGTAG
222312 AACCATTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (21 bp):
TTGTATTGGTAGTAGTATGAA
Found at i:226442 original size:2 final size:2
Alignment explanation
Indices: 226435--226483 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
226425 CCTAATCTAA
*
226435 AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
226477 AT AT AT A
1 AT AT AT A
226484 ATAGATCAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:229657 original size:20 final size:21
Alignment explanation
Indices: 229632--229678 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
229622 AAAAAAATTA
229632 TTGTTTT-CCCTATTTTGTTG
1 TTGTTTTGCCCTATTTTGTTG
*
229652 TTGTTTTGTCCTATTTTGTTG
1 TTGTTTTGCCCTATTTTGTTG
*
229673 TCGTTT
1 TTGTTT
229679 CATAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.04, C:0.13, G:0.17, T:0.66
Consensus pattern (21 bp):
TTGTTTTGCCCTATTTTGTTG
Found at i:235138 original size:18 final size:18
Alignment explanation
Indices: 235110--235156 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
235100 ATAATCTAGT
*
235110 AATATATAAAATAAAA-AA
1 AATATA-AAAAAAAAACAA
*
235128 TATATAAAAAAAAAACAA
1 AATATAAAAAAAAAACAA
235146 AATAATAAAAA
1 AAT-ATAAAAA
235157 CCTTTTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 9 0.38
19 7 0.29
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (18 bp):
AATATAAAAAAAAAACAA
Found at i:235139 original size:14 final size:16
Alignment explanation
Indices: 235110--235142 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
235100 ATAATCTAGT
235110 AATATATAAAATAAAA
1 AATATATAAAATAAAA
235126 AATATATAAAA-AAAA
1 AATATATAAAATAAAA
235141 AA
1 AA
235143 CAAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AATATATAAAATAAAA
Found at i:237580 original size:18 final size:19
Alignment explanation
Indices: 237546--237582 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
237536 TAATGTTCAA
*
237546 TTTAATGTTTGAATTTAGT
1 TTTAATATTTGAATTTAGT
237565 TTTAATATTT-AATTTAGT
1 TTTAATATTTGAATTTAGT
237583 GATCAGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (19 bp):
TTTAATATTTGAATTTAGT
Found at i:251185 original size:2 final size:2
Alignment explanation
Indices: 251178--251213 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
251168 CATTGGCTCC
*
251178 TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
251214 GCTTTTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:261958 original size:20 final size:20
Alignment explanation
Indices: 261933--261989 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
261923 TGGACAATGG
261933 CTGGTATTGCTCGATGCTCC
1 CTGGTATTGCTCGATGCTCC
* *
261953 CTGGTACTGCTCGATGCTTC
1 CTGGTATTGCTCGATGCTCC
* * *
261973 CTGATGTTGTTCGATGC
1 CTGGTATTGCTCGATGC
261990 ATGTTGGTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.37
Consensus pattern (20 bp):
CTGGTATTGCTCGATGCTCC
Found at i:269913 original size:2 final size:2
Alignment explanation
Indices: 269906--269949 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
269896 ATGTCAAATG
269906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
269948 TA
1 TA
269950 ACGAAATAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:270319 original size:2 final size:2
Alignment explanation
Indices: 270312--270343 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
270302 TAAATAAATA
270312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
270344 GAATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:271324 original size:8 final size:8
Alignment explanation
Indices: 271311--271341 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
271301 GCTTTTAAAA
271311 AAAGAAAT
1 AAAGAAAT
271319 AAAGAAAT
1 AAAGAAAT
271327 AAAGAAAT
1 AAAGAAAT
271335 AAAGAAA
1 AAAGAAA
271342 AATGCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (8 bp):
AAAGAAAT
Found at i:276667 original size:20 final size:20
Alignment explanation
Indices: 276637--276676 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
276627 CACAGATTAA
276637 AAAAGGAAAAAGAATAGAAAG
1 AAAAGGAAAAAGAA-AGAAAG
276658 AAAA-GAAAAAGAAAGAAAG
1 AAAAGGAAAAAGAAAGAAAG
276677 GGCAACAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (20 bp):
AAAAGGAAAAAGAAAGAAAG
Found at i:282542 original size:22 final size:22
Alignment explanation
Indices: 282500--282542 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
282490 ATTTTTATAC
* *
282500 TTTAATTTTATGTTCTAATTTT
1 TTTAATATTATGTTATAATTTT
*
282522 TTTAATATTATGTTATGATTT
1 TTTAATATTATGTTATAATTT
282543 AAATTACCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (22 bp):
TTTAATATTATGTTATAATTTT
Found at i:282603 original size:250 final size:250
Alignment explanation
Indices: 282162--282765 Score: 1073
Period size: 250 Copynumber: 2.4 Consensus size: 250
282152 ATAATAGTAA
282162 CATTTTCATCAAATTGATATTAAAATAAAATCATCAAATTATGATTTTCGCTTATATATTATATA
1 CATTTTCATCAAATTGATATTAAAATAAAATCATCAAATTATGATTTTCGCTTATATATTATATA
*
282227 ATTTGACCACTGAATTTTTATACTTTAATTTTATGTTCTAATATTTTTAATATTATATTCTGATT
66 ATTTGACCACTGAATTTTTATACTTTAATTTTATGTTCTAATATTTTTAATATTATATTATGATT
* * *
282292 TAAATTATCAATATGATTAATATTTGTAAAGAAACCCTACATTAGCTTCAATATTCGTAAAAAAA
131 TAAATTACCAATATGATTAATATTTGTAAAGAAACCCCACACTAGCTTCAATATTCGTAAAAAAA
* *
282357 TTATTTTTCTGAATGATCTTCTATTTATACAATTTTTTAAAGGATATAATTTTAT
196 TTATTTTTCTAAATGATCTTCTATTTATACAATTTTTTAAAGGATACAATTTTAT
*
282412 CATTTTCATCAAATTTATATTAAAATAAAATCATCAAATTATGATTTTCGCTTATATATTATATA
1 CATTTTCATCAAATTGATATTAAAATAAAATCATCAAATTATGATTTTCGCTTATATATTATATA
* *
282477 ATTTGACCACTGAATTTTTATACTTTAATTTTATGTTCTAATTTTTTTAATATTATGTTATGATT
66 ATTTGACCACTGAATTTTTATACTTTAATTTTATGTTCTAATATTTTTAATATTATATTATGATT
* *
282542 TAAATTACCACTATGATTAATATTTGTAAAGAAACCCCACACTAGCTTCAATATTCGTAAAAAAG
131 TAAATTACCAATATGATTAATATTTGTAAAGAAACCCCACACTAGCTTCAATATTCGTAAAAAAA
*
282607 TTGTTTTTCTAAATGATCTTCTATTTATACAATTTTTTAAAGGATACAATTTTAT
196 TTATTTTTCTAAATGATCTTCTATTTATACAATTTTTTAAAGGATACAATTTTAT
* *
282662 CATTTTCATCAAATTGATATTAAAATAAAATCATCAAATTATGGTTTTTGCTTATATATTATATA
1 CATTTTCATCAAATTGATATTAAAATAAAATCATCAAATTATGATTTTCGCTTATATATTATATA
*
282727 ATTTGCCCACTGAATTTTTATACTTTAATTTTATGTTCT
66 ATTTGACCACTGAATTTTTATACTTTAATTTTATGTTCT
282766 GATTAAATTA
Statistics
Matches: 338, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
250 338 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (250 bp):
CATTTTCATCAAATTGATATTAAAATAAAATCATCAAATTATGATTTTCGCTTATATATTATATA
ATTTGACCACTGAATTTTTATACTTTAATTTTATGTTCTAATATTTTTAATATTATATTATGATT
TAAATTACCAATATGATTAATATTTGTAAAGAAACCCCACACTAGCTTCAATATTCGTAAAAAAA
TTATTTTTCTAAATGATCTTCTATTTATACAATTTTTTAAAGGATACAATTTTAT
Found at i:287485 original size:68 final size:68
Alignment explanation
Indices: 287376--287509 Score: 196
Period size: 68 Copynumber: 2.0 Consensus size: 68
287366 TCTAATATAA
* * * * *
287376 TCTTTTTCTTCGAAACAATTTCAAATTATCTCAACATTTTTGGGATATTTGTGGGCACTGCCCTC
1 TCTTTTCCTTCGAAACAATTTCAAATCATCTCAACACTTTTGGGACATCTGTGGGCACTGCCCTC
287441 AAT
66 AAT
* * *
287444 TCTTTTCCTTCGAAACAATTTCAAATCATTTTAAGACTTTTGGGACATCTGTGGGCACTGCCCTC
1 TCTTTTCCTTCGAAACAATTTCAAATCATCTCAACACTTTTGGGACATCTGTGGGCACTGCCCTC
287509 A
66 A
287510 TATCACAAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (68 bp):
TCTTTTCCTTCGAAACAATTTCAAATCATCTCAACACTTTTGGGACATCTGTGGGCACTGCCCTC
AAT
Found at i:291630 original size:29 final size:30
Alignment explanation
Indices: 291561--291634 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
291551 ATAAATATCA
*
291561 AATTTATATATGAACTTTGATTCAATATGC
1 AATTTATACATGAACTTTGATTCAATATGC
* *
291591 AATTTAATACATGAACTTTGATT-GA-GTGC
1 AATTT-ATACATGAACTTTGATTCAATATGC
291620 AATTATATACATGAA
1 AATT-TATACATGAA
291635 ACTCGAATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.41
30 7 0.18
31 16 0.41
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (30 bp):
AATTTATACATGAACTTTGATTCAATATGC
Found at i:295079 original size:3 final size:3
Alignment explanation
Indices: 295071--295095 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
295061 CAAAAGGGTT
295071 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
295096 TCTTTCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:300617 original size:29 final size:28
Alignment explanation
Indices: 300571--300851 Score: 124
Period size: 29 Copynumber: 9.6 Consensus size: 28
300561 ACTCGAGGGT
300571 AAAATGGTAATTTTGGAAAAATAGGGTCA
1 AAAATGG-AATTTTGGAAAAATAGGGTCA
*
300600 AAAATGGAATTTTAGG-AAGATCGAGGGT--
1 AAAATGGAATTTT-GGAAAAAT--AGGGTCA
**
300628 AAAATGGTAATTTTTGGTGAAATAGAGGTCA
1 AAAATGG-AA-TTTTGGAAAAATAG-GGTCA
** * ***
300659 AAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGAAAAATAGGGTCA
** * *
300687 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AA-TTTTGGAAAAAT-AGGGTCA
* ** * *
300718 AAATTGGAATTTTGGAAAGTTTGGG-CGT
1 AAAATGGAATTTTGGAAAAATAGGGTC-A
* * * *
300746 AAAATGTAATTTTTGGTAAAATTGAGATC-
1 AAAATGGAA-TTTTGGAAAAATAG-GGTCA
* *
300775 AAAATGGAATTTTGGAAAACTCGGGGGT-A
1 AAAATGGAATTTTGGAAAAAT--AGGGTCA
* * *
300804 AAAATGTTATTTTTGGAAAAATAGAGGTTA
1 AAAATG-GAATTTTGGAAAAATAG-GGTCA
300834 AAAATGGAATTTTGGAAA
1 AAAATGGAATTTTGGAAA
300852 GTTTAGAGGT
Statistics
Matches: 186, Mismatches: 44, Indels: 44
0.68 0.16 0.16
Matches are distributed among these distances:
28 49 0.26
29 75 0.40
30 45 0.24
31 17 0.09
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAAATAGGGTCA
Found at i:300687 original size:59 final size:58
Alignment explanation
Indices: 300567--300875 Score: 347
Period size: 59 Copynumber: 5.3 Consensus size: 58
300557 AGACACTCGA
* * * *
300567 GGGTAAAATGGTAA-TTTTGGAAAAATAG-GGTCAAAAATGGAATTTTAGG-AAGATCGA
1 GGGTAAAAT-GTAATTTTTGGTAAAATAGAGGTCAAAAATGGAATTTT-GGAAAGTTTGG
*
300624 GGGTAAAATGGTAATTTTTGGTGAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAAT-GTAATTTTTGGTAAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTGG
* * * * *
300683 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATTGGAATTTTGGAAAGTTTGG
1 GGGTAAAAT-GTAATTTTTGGTAAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTGG
* * * ** *
300742 GCGTAAAATGTAATTTTTGGTAAAATTGAGATC-AAAATGGAATTTTGGAAAACTCGG
1 GGGTAAAATGTAATTTTTGGTAAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTGG
* * * *
300799 GGGTAAAAATGTTATTTTTGGAAAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GGGT-AAAATGTAATTTTTGGTAAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTGG
*
300858 AGGTAAAAATGTAATTTT
1 GGGT-AAAATGTAATTTT
300876 CAAAAAGTTT
Statistics
Matches: 216, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
57 37 0.17
58 57 0.26
59 122 0.56
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTTGGTAAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTGG
Found at i:300702 original size:30 final size:29
Alignment explanation
Indices: 300659--300927 Score: 119
Period size: 30 Copynumber: 9.2 Consensus size: 29
300649 ATAGAGGTCA
300659 AAAATGG-AATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGGAAAGTTTGGGGGT
* *
300687 AAAATGGTAATTTTTGGTGAAA--TCGGGGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTTGGGGGT
*
300717 AAAATTGG-AATTTTGGAAAGTTTGGGCGT
1 AAAA-TGGTAATTTTGGAAAGTTTGGGGGT
* * *
300746 AAAAT-GTAATTTTTGGTAAA-ATT-GAGAT
1 AAAATGGTAA-TTTTGG-AAAGTTTGGGGGT
** *
300774 CAAAATGG-AATTTTGGAAAACTCGGGGGT
1 -AAAATGGTAATTTTGGAAAGTTTGGGGGT
* * ** * * *
300803 AAAAATGTTATTTTTGGAAAAATAGAGGTT
1 -AAAATGGTAATTTTGGAAAGTTTGGGGGT
* *
300833 AAAAATGG-AATTTTGGAAAGTTTAGAGGT
1 -AAAATGGTAATTTTGGAAAGTTTGGGGGT
** *
300862 AAAAAT-GTAATTTTCAAAAAGTTTAGGGGTT
1 -AAAATGGTAATTTT-GGAAAGTTT-GGGGGT
** *
300893 AAAA-AATAATTTTGGAGAAGTTTAGGGGTT
1 AAAATGGTAATTTTGGA-AAGTTT-GGGGGT
300923 AAAAT
1 AAAAT
300928 ATAGTTTTTG
Statistics
Matches: 183, Mismatches: 37, Indels: 39
0.71 0.14 0.15
Matches are distributed among these distances:
27 8 0.04
28 21 0.11
29 65 0.36
30 78 0.43
31 7 0.04
32 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTTGGGGGT
Found at i:300851 original size:116 final size:114
Alignment explanation
Indices: 300561--300875 Score: 364
Period size: 116 Copynumber: 2.7 Consensus size: 114
300551 AATTCTAGAC
* * * * * *
300561 ACTCGAGGGTAAAATGGTAATTTTGGAAAAATAGGGTCAAAAATGGAATTTTAGG-AAGATCGAG
1 ACTCGGGGGTAAAATGTTATTTTTGGAAAAATAGGGTTAAAAATGGAATTTT-GGAAAGTTTG-G
* *
300625 GGTAAAATGGTAATTTTTGGTGAAATAGAGGTCAAAAATGGAATTTTGGAAA
64 GGTAAAAT-GTAATTTTTGGTAAAATAGAGATCAAAAATGGAATTTTGGAAA
** * * ** * *
300677 GTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATTGGAATTTTGGAAAGTTTGG
1 ACTCGGGGGTAAAAT-GTTATTTTTGGAAAAAT-AGGGTTAAAAATGGAATTTTGGAAAGTTTGG
*
300742 GCGTAAAATGTAATTTTTGGTAAAATTGAGATC-AAAATGGAATTTTGGAAA
64 G-GTAAAATGTAATTTTTGGTAAAATAGAGATCAAAAATGGAATTTTGGAAA
300793 ACTCGGGGGTAAAAATGTTATTTTTGGAAAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 ACTCGGGGGT-AAAATGTTATTTTTGGAAAAATAG-GGTTAAAAATGGAATTTTGGAAAGTTT-G
*
300858 AGGTAAAAATGTAATTTT
63 GGGT-AAAATGTAATTTT
300876 CAAAAAGTTT
Statistics
Matches: 165, Mismatches: 26, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
115 1 0.01
116 78 0.47
117 57 0.35
118 29 0.18
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (114 bp):
ACTCGGGGGTAAAATGTTATTTTTGGAAAAATAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGG
TAAAATGTAATTTTTGGTAAAATAGAGATCAAAAATGGAATTTTGGAAA
Found at i:300864 original size:29 final size:29
Alignment explanation
Indices: 300658--300927 Score: 139
Period size: 29 Copynumber: 9.2 Consensus size: 29
300648 AATAGAGGTC
*
300658 AAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGT
*
300687 -AAAATGGTAATTTTTGGTGAAA---TCGGGGTT
1 AAAAATGG-AA-TTTT-G-GAAAGTTTAGGGG-T
*
300717 AAAATTGGAATTTTGGAAAGTTT-GGGCGT
1 AAAAATGGAATTTTGGAAAGTTTAGGG-GT
* * * *
300746 -AAAATGTAATTTTTGGTAAA-ATT-GAGAT
1 AAAAATGGAA-TTTTGG-AAAGTTTAGGGGT
* ** **
300774 CAAAATGGAATTTTGGAAAACTCGGGGGT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGT
* * ** *
300803 AAAAATGTTATTTTTGGAAA-AATAGAGGTT
1 AAAAATG-GAATTTTGGAAAGTTTAG-GGGT
*
300833 AAAAATGGAATTTTGGAAAGTTTAGAGGT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGT
* **
300862 AAAAATGTAATTTTCAAAAAGTTTAGGGGTT
1 AAAAATGGAATTTT-GGAAAGTTTAGGGG-T
300893 AAAAAAT--AATTTTGGAGAAGTTTAGGGGT
1 -AAAAATGGAATTTTGGA-AAGTTTAGGGGT
*
300922 TAAAAT
1 AAAAAT
300928 ATAGTTTTTG
Statistics
Matches: 186, Mismatches: 33, Indels: 45
0.70 0.12 0.17
Matches are distributed among these distances:
27 7 0.04
28 28 0.15
29 70 0.38
30 63 0.34
31 8 0.04
32 10 0.05
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:300938 original size:31 final size:29
Alignment explanation
Indices: 300841--300947 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 29
300831 TTAAAAATGG
* *
300841 AATTTTGGAAAGTTTAGAGG-TAAAAATGT
1 AATTTTGGAAAGTTTAGGGGTTAAAAA-AT
**
300870 AATTTTCAAAAAGTTTAGGGGTTAAAAAAT
1 AATTTT-GGAAAGTTTAGGGGTTAAAAAAT
*
300900 AATTTTGGAGAAGTTTAGGGGTTAAAATAT
1 AATTTTGGA-AAGTTTAGGGGTTAAAAAAT
* *
300930 AGTTTTTGGATAGTTTAG
1 A-ATTTTGGAAAGTTTAG
300948 AGACCTTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 7 0.11
30 45 0.69
31 13 0.20
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.37
Consensus pattern (29 bp):
AATTTTGGAAAGTTTAGGGGTTAAAAAAT
Found at i:302798 original size:17 final size:17
Alignment explanation
Indices: 302757--302836 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
302747 GTATTGGGAC
*
302757 ATAATTTTAAATTTGAAA
1 ATAAATTTAAATTTG-AA
*
302775 ATAAATTTAAACTTGAA
1 ATAAATTTAAATTTGAA
* *
302792 TTAAATTTAAATTTAAA
1 ATAAATTTAAATTTGAA
*
302809 ATAAATTTAAATTTAAA
1 ATAAATTTAAATTTGAA
*
302826 ACAAATTTAAA
1 ATAAATTTAAA
302837 ATAAACTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
17 42 0.76
18 13 0.24
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (17 bp):
ATAAATTTAAATTTGAA
Found at i:302801 original size:6 final size:6
Alignment explanation
Indices: 302762--302825 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
302752 GGGACATAAT
* * *
302762 TTTAAA TTTGAAA -ATAAA TTTAAA CTTGAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
302809 -ATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
302826 ACAAATTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
5 11 0.23
6 33 0.70
7 3 0.06
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:302804 original size:11 final size:11
Alignment explanation
Indices: 302763--302821 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
302753 GGACATAATT
302763 TTAAATTTGAAA
1 TTAAATTT-AAA
*
302775 ATAAATTTAAA
1 TTAAATTTAAA
*
302786 CTTGAA-TTAAA
1 -TTAAATTTAAA
302797 TTTAAATTTAAA
1 -TTAAATTTAAA
*
302809 ATAAATTTAAA
1 TTAAATTTAAA
302820 TT
1 TT
302822 TAAAACAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 23 0.61
12 15 0.39
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:311168 original size:51 final size:51
Alignment explanation
Indices: 311039--311229 Score: 199
Period size: 51 Copynumber: 3.7 Consensus size: 51
311029 TTTCATTTAA
* ** ** *
311039 TACTCACGATAACA-TATAGTCATCGGACCTCTTGTTCTGTATAGGAATTC-TT
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * * * *
311091 ATACTCAAGATGACTCTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 -TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
311143 TACTCACGATGACACTTAGAT-ATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAG-TCATCGGACCTTTAATCCATAAAGGATTCATT
311194 TACTCACGATGACACTTAGTCATCGGACCCTTTAAT
1 TACTCACGATGACACTTAGTCATCGGA-CCTTTAAT
311230 TTATAGCTCA
Statistics
Matches: 116, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
50 1 0.01
51 72 0.62
52 18 0.16
53 24 0.21
54 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:316700 original size:18 final size:16
Alignment explanation
Indices: 316673--316720 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
316663 TGGCCCCTCA
*
316673 AGAATGGAGAGAATAGTG
1 AGAATTGAGAGAATA--G
**
316691 AGAATTGAGAGTTTAG
1 AGAATTGAGAGAATAG
316707 AGAATTGAGAGAAT
1 AGAATTGAGAGAAT
316721 TGGATTTAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 13 0.52
18 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (16 bp):
AGAATTGAGAGAATAG
Found at i:316717 original size:9 final size:9
Alignment explanation
Indices: 316673--316722 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
316663 TGGCCCCTCA
*
316673 AGAATGGAG
1 AGAATTGAG
* *
316682 AGAATAGTG
1 AGAATTGAG
316691 AGAATTGAG
1 AGAATTGAG
*
316700 AG--TTTAG
1 AGAATTGAG
316707 AGAATTGAG
1 AGAATTGAG
316716 AGAATTG
1 AGAATTG
316723 GATTTAAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.18
9 27 0.82
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.24
Consensus pattern (9 bp):
AGAATTGAG
Found at i:317992 original size:30 final size:30
Alignment explanation
Indices: 317958--318035 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
317948 AAGAAACAAC
317958 TTTAAAAAATAAATATGTTATATAAATAT-T
1 TTTAAAAAATAAATATGTTATATAAAT-TCT
* *
317988 TTTAAAATATATATAT-TCTATATAAATTCT
1 TTTAAAAAATAAATATGT-TATATAAATTCT
318018 TTTAAAAAATAAA-ATGTT
1 TTTAAAAAATAAATATGTT
318036 GTTTCAACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.12
30 36 0.88
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTAAAAAATAAATATGTTATATAAATTCT
Found at i:321206 original size:3 final size:3
Alignment explanation
Indices: 321200--321234 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
321190 ATGGAGCATT
*
321200 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGA AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
321235 AAGTGGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:324740 original size:19 final size:20
Alignment explanation
Indices: 324716--324755 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
324706 AATTTAAAAA
324716 TATAAAT-TTTGAAATTTTT
1 TATAAATATTTGAAATTTTT
*
324735 TATAAATATTTTAAATTTTT
1 TATAAATATTTGAAATTTTT
324755 T
1 T
324756 GAAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TATAAATATTTGAAATTTTT
Found at i:324761 original size:20 final size:22
Alignment explanation
Indices: 324721--324769 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
324711 AAAAATATAA
324721 ATTTTGAAATTTTTTATAAA-T
1 ATTTTGAAATTTTTTATAAATT
324742 ATTTT-AAATTTTTTGA-AAATT
1 ATTTTGAAATTTTTT-ATAAATT
324763 ATTTTGA
1 ATTTTGA
324770 TTGTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 12 0.48
21 12 0.48
22 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
ATTTTGAAATTTTTTATAAATT
Found at i:330054 original size:23 final size:22
Alignment explanation
Indices: 330016--330078 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 22
330006 AATATGAACG
*
330016 TTTA-ATTTAATGATATTTTAT
1 TTTATATTTAATAATATTTTAT
330037 TTTATATTATAATAATATTTT-T
1 TTTATATT-TAATAATATTTTAT
**
330059 AAT-TATTTAATAATATTTTA
1 TTTATATTTAATAATATTTTA
330079 AGGTTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 12 0.33
21 8 0.22
22 5 0.14
23 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTATATTTAATAATATTTTAT
Found at i:336847 original size:18 final size:18
Alignment explanation
Indices: 336821--336859 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
336811 TTTATTTTGT
*
336821 TTTTGCATAATTTATTTA
1 TTTTCCATAATTTATTTA
*
336839 TTTTCCATAATTTTTTTA
1 TTTTCCATAATTTATTTA
336857 TTT
1 TTT
336860 AATTTAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTCCATAATTTATTTA
Found at i:336963 original size:2 final size:2
Alignment explanation
Indices: 336956--336997 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
336946 TTCGAGATAC
*
336956 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
336998 TAAATACAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:338347 original size:111 final size:110
Alignment explanation
Indices: 338194--338417 Score: 385
Period size: 111 Copynumber: 2.0 Consensus size: 110
338184 GGTGTTCATA
*
338194 TTGGATATTCTTTGCTTAATAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAATAATGA
1 TTGGATATTCATTGCTTAATAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAATAATGA
* *
338259 AAAGTGATTATTGTTCTTTTTTCTTCTTCAAGCTTTCAAGATATT
66 AAAATAATTATTGTTCTTTTTTCTTCTTCAAGCTTTCAAGATATT
*
338304 TTGGATATTCATTGCTTAATTAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAGTAATG
1 TTGGATATTCATTGCTTAA-TAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAATAATG
* *
338369 AAAAATAATTGTTGTTCTTTTTTCTTCTTCAAGCTTTTAAGATATT
65 AAAAATAATTATTGTTCTTTTTTCTTCTTCAAGCTTTCAAGATATT
338415 TTG
1 TTG
338418 ATTATATTTG
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 18 0.17
111 89 0.83
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (110 bp):
TTGGATATTCATTGCTTAATAGATGGTTCTGTATTGAATATTAATAATGGCTCCTACAATAATGA
AAAATAATTATTGTTCTTTTTTCTTCTTCAAGCTTTCAAGATATT
Found at i:359036 original size:7 final size:7
Alignment explanation
Indices: 359024--359049 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
359014 CAGAATTAGA
359024 AAAAGGG
1 AAAAGGG
359031 AAAAGGG
1 AAAAGGG
359038 AAAAGGG
1 AAAAGGG
359045 AAAAG
1 AAAAG
359050 ATGACACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (7 bp):
AAAAGGG
Found at i:373018 original size:23 final size:24
Alignment explanation
Indices: 372991--373035 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
372981 AATAGATTTC
*
372991 AAAG-TTAATCTACTTCAAATATG
1 AAAGTTTAATCTACTACAAATATG
373014 AAAGTTTAATCTACTACAAATA
1 AAAGTTTAATCTACTACAAATA
373036 AAATTGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (24 bp):
AAAGTTTAATCTACTACAAATATG
Found at i:375159 original size:3 final size:3
Alignment explanation
Indices: 375151--375181 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
375141 TTCCTTTCTT
375151 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
375182 CTTTCTGACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:376406 original size:23 final size:22
Alignment explanation
Indices: 376375--376425 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
376365 TCACCAATAA
*
376375 GCACAGAAATGCTTAAACAGTAG
1 GCACTGAAATG-TTAAACAGTAG
* *
376398 GCACTGAAATGTTGAGCAGTAG
1 GCACTGAAATGTTAAACAGTAG
*
376420 ACACTG
1 GCACTG
376426 TCCATGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (22 bp):
GCACTGAAATGTTAAACAGTAG
Found at i:378549 original size:8 final size:8
Alignment explanation
Indices: 378532--378564 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
378522 AAAATAATAG
378532 AAAA-AAA
1 AAAAGAAA
378539 AAAAGAAA
1 AAAAGAAA
378547 AAAAGAAAA
1 AAAAG-AAA
378556 AAAAGAAA
1 AAAAGAAA
378564 A
1 A
378565 CAAAATCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.17
8 12 0.50
9 8 0.33
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:378549 original size:9 final size:9
Alignment explanation
Indices: 378535--378569 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
378525 ATAATAGAAA
378535 AAAAAAAAG
1 AAAAAAAAG
378544 -AAAAAAAG
1 AAAAAAAAG
378552 AAAAAAAAG
1 AAAAAAAAG
378561 AAAACAAAA
1 AAAA-AAAA
378570 TCCAGCACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 12 0.50
10 4 0.17
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:380080 original size:15 final size:16
Alignment explanation
Indices: 380052--380089 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
380042 AAGGACAAAA
*
380052 AGAAATTCCTTTACTT
1 AGAAATTCCTTTACAT
*
380068 AGAATTTCC-TTACAT
1 AGAAATTCCTTTACAT
380083 AGAAATT
1 AGAAATT
380090 AAAAAAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (16 bp):
AGAAATTCCTTTACAT
Found at i:380324 original size:5 final size:5
Alignment explanation
Indices: 380314--380344 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
380304 AAGAAAAAGG
380314 AGACT AGACT AGACT AGACT AGACT AGACT A
1 AGACT AGACT AGACT AGACT AGACT AGACT A
380345 AGGTCAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
AGACT
Found at i:393864 original size:23 final size:23
Alignment explanation
Indices: 393807--393874 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
393797 TTAGTGAGAG
*
393807 CATTCTGGCACTTCGATGCAATT
1 CATTCTGGCACTTCGGTGCAATT
** *
393830 CATTCTAACACTTTGGTGCAATT
1 CATTCTGGCACTTCGGTGCAATT
* *
393853 CATTTTGGCACTTCGGTACAAT
1 CATTCTGGCACTTCGGTGCAAT
393875 GTATATTGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (23 bp):
CATTCTGGCACTTCGGTGCAATT
Found at i:396199 original size:2 final size:2
Alignment explanation
Indices: 396192--396221 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
396182 AATAAAAATA
396192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
396222 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:400454 original size:14 final size:14
Alignment explanation
Indices: 400435--400462 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
400425 TTTCCTCTTT
400435 TTCTTTTTCCTTCC
1 TTCTTTTTCCTTCC
400449 TTCTTTTTCCTTCC
1 TTCTTTTTCCTTCC
400463 CATTTTCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTCTTTTTCCTTCC
Found at i:406259 original size:14 final size:15
Alignment explanation
Indices: 406240--406268 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
406230 CTTTTTGTTT
406240 TTCCTTCCC-TTTTC
1 TTCCTTCCCATTTTC
406254 TTCCTTCCCATTTTC
1 TTCCTTCCCATTTTC
406269 GTTTGAGCTC
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:0.03, C:0.41, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCCTTCCCATTTTC
Found at i:407706 original size:3 final size:3
Alignment explanation
Indices: 407692--407722 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
407682 AATTAATGTG
*
407692 GGT GGG GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
407723 ATCAGACCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.71, T:0.29
Consensus pattern (3 bp):
GGT
Found at i:412031 original size:2 final size:2
Alignment explanation
Indices: 412024--412056 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
412014 ATTTTAATGG
412024 AT AT AT 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 AT AT AT A
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.