Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010932.1 Kokia drynarioides strain JFW-HI SEQ_125900, 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: 176747
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:7243 original size:36 final size:40
Alignment explanation
Indices: 7194--7267 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 40
7184 ACGAATTTAG
*
7194 AATATAAATGTGT-GTTTAAAAATAA-TAT-ATAATAAAT
1 AATATAAACGTGTGGTTTAAAAATAACTATCATAATAAAT
* *
7231 AATA-AAACGTGTGGTTTGAAACTAACTATCATAATAA
1 AATATAAACGTGTGGTTTAAAAATAACTATCATAATAA
7268 CACTTGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 7 0.23
37 14 0.45
38 3 0.10
39 7 0.23
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (40 bp):
AATATAAACGTGTGGTTTAAAAATAACTATCATAATAAAT
Found at i:10939 original size:17 final size:17
Alignment explanation
Indices: 10917--10959 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
10907 AACTTTTAAT
10917 TTTTAAATTTTAATTTA
1 TTTTAAATTTTAATTTA
10934 TTTTAAATTTTAATTTA
1 TTTTAAATTTTAATTTA
*
10951 TTTTGAATT
1 TTTTAAATT
10960 AAAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTAAATTTTAATTTA
Found at i:12794 original size:29 final size:29
Alignment explanation
Indices: 12739--12854 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 29
12729 TCTTGGAGGT
* * *
12739 CCCC-AAACTTCTCCAAAATTATATTTTTGA
1 CCCCGAAACTTC-CAAAAATTA-CTTTTTAA
*
12769 CCCCGAAACTTCCAAAAATTACTTTTTTA
1 CCCCGAAACTTCCAAAAATTACTTTTTAA
*
12798 CCCTCG-AACTTCCAAAAATTCCATTTTTAA
1 CCC-CGAAACTTCCAAAAATTAC-TTTTTAA
*
12828 CCCCAAAACTTCCAAAAATTACTTTTT
1 CCCCGAAACTTCCAAAAATTACTTTTT
12855 TACCTTTGAA
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
29 30 0.40
30 38 0.51
31 7 0.09
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCCGAAACTTCCAAAAATTACTTTTTAA
Found at i:12824 original size:59 final size:59
Alignment explanation
Indices: 12761--13095 Score: 315
Period size: 59 Copynumber: 5.7 Consensus size: 59
12751 CCAAAATTAT
* * **
12761 ATTTTTGACCCCGAAACTTCCAAAAATTACTTTTTTACCCTCGAACTTCCAAAAATTCC
1 ATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCC
** * * * *
12820 ATTTTTAACCCCAAAACTTCCAAAAATTACTTTTTTACCTTTGAACTT-TAAAAATCTCG
1 ATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAT-TCC
* * ** * *
12879 A-TTTTGACCCCTAAACTAT-GGAAAATTACCATTTTACCTTCGAACTTTCAAAAATTCC
1 ATTTTTAACCCCAAAACT-TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCC
*
12937 ATTTTCAACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAA-TATCCAAAAAATTCC
1 ATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACT-TCC-AAAAATTCC
* * * * *
12997 ATTTTTAACCCTAAAACTTTCAAAAATTACCCTTTTACTCC-C-AAATGTCCAAAAATTCT
1 ATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTAC-CCTCGAACT-TCCAAAAATTCC
* * * **
13056 ATTTTTGATCCC-GATTTTCCTAAAAATTACCATTTTACCC
1 ATTTTTAACCCCAAAACTTCC-AAAAATTACCATTTTACCC
13096 CCAGATGTCT
Statistics
Matches: 230, Mismatches: 36, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
58 54 0.23
59 126 0.55
60 48 0.21
61 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (59 bp):
ATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCC
Found at i:12866 original size:29 final size:29
Alignment explanation
Indices: 12775--13026 Score: 127
Period size: 30 Copynumber: 8.6 Consensus size: 29
12765 TTGACCCCGA
*
12775 AACTTCCAAAAATTACTTTTTTACCCTCG
1 AACTTCCAAAAATTACTTTTTTACCCTAG
* * * *
12804 AACTTCCAAAAATTCCATTTTTAACCCCAA
1 AACTTCCAAAAATTAC-TTTTTTACCCTAG
* *
12834 AACTTCCAAAAATTACTTTTTTACCTTTG
1 AACTTCCAAAAATTACTTTTTTACCCTAG
* * *
12863 AACTT-TAAAAATCT-CGATTTTGACCCCTA-
1 AACTTCCAAAAAT-TAC-TTTTTTA-CCCTAG
** ** * *
12892 AACTAT-GGAAAATTACCATTTTACCTTCG
1 AACT-TCCAAAAATTACTTTTTTACCCTAG
* * ** * *
12921 AACTTTCAAAAATTCCATTTTCAACCCCAA
1 AACTTCCAAAAATTAC-TTTTTTACCCTAG
** *
12951 AACTTCCAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTACTTTTTTACCCTAG
* * *
12980 AA-TATCCAAAAAATTCCATTTTTAACCCTAA
1 AACT-TCC-AAAAATTAC-TTTTTTACCCTAG
*
13011 AACTTTCAAAAATTAC
1 AACTTCCAAAAATTAC
13027 CCTTTTACTC
Statistics
Matches: 159, Mismatches: 51, Indels: 25
0.68 0.22 0.11
Matches are distributed among these distances:
28 12 0.08
29 65 0.41
30 69 0.43
31 12 0.08
32 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTACTTTTTTACCCTAG
Found at i:12961 original size:30 final size:29
Alignment explanation
Indices: 12763--13060 Score: 141
Period size: 29 Copynumber: 10.1 Consensus size: 29
12753 AAAATTATAT
* * * *
12763 TTTTGACCCCGAAACTTCCAAAAATTACT
1 TTTTAACCCCAAAACTTCCAAAAATTCCA
* *
12792 TTTTTACCCTC-GAACTTCCAAAAATTCCA
1 TTTTAACCC-CAAAACTTCCAAAAATTCCA
* *
12821 TTTTTAACCCCAAAACTTCCAAAAATTACT
1 -TTTTAACCCCAAAACTTCCAAAAATTCCA
* **** * *
12851 TTTTTACCTTTGAACTT-TAAAAATCTCGA
1 TTTTAACCCCAAAACTTCCAAAAAT-TCCA
* * **
12880 TTTTGACCCCTAAACTAT-GGAAAATTACCA
1 TTTTAACCCCAAAACT-TCCAAAAATT-CCA
* * *
12910 TTTT-ACCTTC-GAACTTTCAAAAATTCCA
1 TTTTAACC-CCAAAACTTCCAAAAATTCCA
12938 TTTTCAACCCCAAAACTTCCAAAAATTACCA
1 TTTT-AACCCCAAAACTTCCAAAAATT-CCA
*
12969 TTTT-ACCCTC-GAA-TATCCAAAAAATTCCA
1 TTTTAACCC-CAAAACT-TCC-AAAAATTCCA
* * *
12998 TTTTTAACCCTAAAACTTTCAAAAATTACCC
1 -TTTTAACCCCAAAACTTCCAAAAATT-CCA
*
13029 TTTT-ACTCCC-AAA-TGTCCAAAAATTCTA
1 TTTTAAC-CCCAAAACT-TCCAAAAATTCCA
13057 TTTT
1 TTTT
13061 TGATCCCGAT
Statistics
Matches: 207, Mismatches: 40, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
28 21 0.10
29 90 0.43
30 78 0.38
31 17 0.08
32 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
TTTTAACCCCAAAACTTCCAAAAATTCCA
Found at i:13061 original size:29 final size:29
Alignment explanation
Indices: 13029--13120 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
13019 AAAATTACCC
13029 TTTTACTCCCAAATGTCCAAAAATTCTAT
1 TTTTACTCCCAAATGTCCAAAAATTCTAT
* * * *
13058 TTTTGA-TCCCGATTTTCCTAAAAATTACCA-
1 TTTT-ACTCCCAAATGTCC-AAAAATT-CTAT
* * * *
13088 TTTTACCCCCAGATGTCTAAAAATTCTGT
1 TTTTACTCCCAAATGTCCAAAAATTCTAT
13117 TTTT
1 TTTT
13121 GATCTCGATT
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
28 1 0.02
29 25 0.54
30 18 0.39
31 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (29 bp):
TTTTACTCCCAAATGTCCAAAAATTCTAT
Found at i:13165 original size:58 final size:59
Alignment explanation
Indices: 13018--13213 Score: 200
Period size: 59 Copynumber: 3.3 Consensus size: 59
13008 TAAAACTTTC
* * * *
13018 AAAAATTACCCTTTTACTCCCAAATGTCCAAAAATTCTATTTTTGATCCCGATTTTCCT
1 AAAAATTACCATTTTACCCCCAGATGTCTAAAAATTCTATTTTTGATCCCGATTTTCCT
* * *
13077 AAAAATTACCATTTTACCCCCAGATGTCTAAAAATTCTGTTTTTGATCTCGATTTT-TT
1 AAAAATTACCATTTTACCCCCAGATGTCTAAAAATTCTATTTTTGATCCCGATTTTCCT
* * *** * * * * *
13135 AAAAGTTACCGTTTTACCCTTGGGTGTCTAAAAATT-TCATTTTTAACCCCGAACTTTCCC
1 AAAAATTACCATTTTACCCCCAGATGTCTAAAAATTCT-ATTTTTGATCCCG-ATTTTCCT
13195 AAAAA-TACCATTTTACCCC
1 AAAAATTACCATTTTACCCC
13214 TAAAGTCCAA
Statistics
Matches: 111, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
57 1 0.01
58 40 0.36
59 66 0.59
60 4 0.04
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCAGATGTCTAAAAATTCTATTTTTGATCCCGATTTTCCT
Found at i:14010 original size:15 final size:16
Alignment explanation
Indices: 13980--14010 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13970 GACCTACATG
13980 TTTTCAAAACGTTTTT
1 TTTTCAAAACGTTTTT
*
13996 TTTTTAAAACGTTTT
1 TTTTCAAAACGTTTT
14011 GTGGTGATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTTCAAAACGTTTTT
Found at i:17061 original size:30 final size:30
Alignment explanation
Indices: 17027--17091 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
17017 AAATGATAAC
17027 TTTTTAAAAAAATCGAGATCAAAAATAGAA
1 TTTTTAAAAAAATCGAGATCAAAAATAGAA
** * * *
17057 TTTTTATGAAAATCGGGATCAAAATTGGAA
1 TTTTTAAAAAAATCGAGATCAAAAATAGAA
17087 TTTTT
1 TTTTT
17092 GGACATTTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (30 bp):
TTTTTAAAAAAATCGAGATCAAAAATAGAA
Found at i:17145 original size:59 final size:59
Alignment explanation
Indices: 17077--17395 Score: 296
Period size: 59 Copynumber: 5.4 Consensus size: 59
17067 AATCGGGATC
* * * **
17077 AAAATTGGAATTTTTGGACA-TTTGGGGGTAAAAGGGTAATTTTTAAAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGA-AGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTT
* *
17136 AAAAATGGAATTTTTTGG-ACTTTCGAGGGAAAAATGGTAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGAA-TTTTTGGAAGTTT-GAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTT
* *
17196 AAAAATGAAATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTT-GAGAGTTTCG-GAG-T
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGA-AGTTTCGAG-GTT
* * * * * * *
17254 CAAAATCGGGATTTTTGAAAGTTCGAAGGTAAAAAT-GTAA-TTTTGGAAGTTTCAAGGTC
1 AAAAAT-GGAATTTTTGGAAGTTTGAGGGT-AAAATGGTAATTTTTGGAAGTTTCGAGGTT
* * * *
17313 AAAAATGGAATTTTTGGAAGTTTCAGGGTAAAAT-GTAATTTTTAGAAGTTTC-AAGTC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTT
** *
17370 AAAAATATAATTTTGGAGAAGTTTGA
1 AAAAATGGAATTTTTG-GAAGTTTGA
17396 AGACCTCCAA
Statistics
Matches: 216, Mismatches: 31, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
57 26 0.12
58 59 0.27
59 75 0.35
60 56 0.26
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTT
Found at i:17148 original size:30 final size:29
Alignment explanation
Indices: 17077--17364 Score: 227
Period size: 30 Copynumber: 9.8 Consensus size: 29
17067 AATCGGGATC
* * *
17077 AAAATTGGAATTTTTGGACA-TTTGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTCGAGGT
* **
17106 -AAAAGGGTAATTTTTAAAAGTTTCGAGGTT
1 AAAAATGG-AATTTTTGGAAGTTTCGAGG-T
* *
17136 AAAAATGGAATTTTTTGG-ACTTTCGAGGG
1 AAAAATGGAA-TTTTTGGAAGTTTCGAGGT
17165 AAAAATGGTAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGG-AATTTTTGGAAGTTTCGAGG-T
* * *
17196 AAAAATGAAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
17225 -AAAATGGTAATTTTT-GAGAGTTTCG-GAGT
1 AAAAATGG-AATTTTTGGA-AGTTTCGAG-GT
* * *
17254 CAAAATCGGGATTTTTGAAAG-TTCGAAGGT
1 AAAAAT-GGAATTTTTGGAAGTTTCG-AGGT
* *
17284 AAAAATGTAA-TTTTGGAAGTTTCAAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
17312 CAAAAATGGAATTTTTGGAAGTTTC-AGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGA-GGT
* *
17342 -AAAATGTAATTTTTAGAAGTTTC
1 AAAAATGGAATTTTTGGAAGTTTC
17365 AAGTCAAAAA
Statistics
Matches: 211, Mismatches: 28, Indels: 41
0.75 0.10 0.15
Matches are distributed among these distances:
28 48 0.23
29 64 0.30
30 77 0.36
31 22 0.10
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGT
Found at i:17375 original size:29 final size:28
Alignment explanation
Indices: 17112--17393 Score: 153
Period size: 30 Copynumber: 9.6 Consensus size: 28
17102 GGGTAAAAGG
** *
17112 GTAATTTTTAAAAGTTTCGAGGTTAAAAAT
1 GTAATTTTTGGAAGTTTC-AAG-TAAAAAT
* * * *
17142 GGAATTTTTTGG-ACTTTCGAGGGAAAAAT
1 GTAA-TTTTTGGAAGTTTC-AAGTAAAAAT
*
17171 GGTAATTTTTGGAAGTTTCGAGGTTAAAAAT
1 -GTAATTTTTGGAAGTTTC-AAG-TAAAAAT
* ***
17202 GAAATTTTTGGAAGTTTGGGGGT-AAAAT
1 GTAATTTTTGGAAGTTT-CAAGTAAAAAT
* *
17230 GGTAATTTTT-GAGAGTTTCGGAGTCAAAAT
1 -GTAATTTTTGGA-AGTTTC-AAGTAAAAAT
** *
17260 CGGGATTTTTGAAAG-TTCGAAGGTAAAAAT
1 -GTAATTTTTGGAAGTTTC-AA-GTAAAAAT
17290 GTAA-TTTTGGAAGTTTCAAGGTCAAAAAT
1 GTAATTTTTGGAAGTTTCAA-GT-AAAAAT
* *
17319 GGAATTTTTGGAAGTTTCAGGGT-AAAAT
1 GTAATTTTTGGAAGTTTCA-AGTAAAAAT
*
17347 GTAATTTTTAGAAGTTTCAAGTCAAAAAT
1 GTAATTTTTGGAAGTTTCAAGT-AAAAAT
* *
17376 ATAATTTTGGAGAAGTTT
1 GTAATTTTTG-GAAGTTT
17394 GAAGACCTCC
Statistics
Matches: 203, Mismatches: 31, Indels: 36
0.75 0.11 0.13
Matches are distributed among these distances:
27 2 0.01
28 42 0.21
29 61 0.30
30 86 0.42
31 12 0.06
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (28 bp):
GTAATTTTTGGAAGTTTCAAGTAAAAAT
Found at i:17393 original size:30 final size:28
Alignment explanation
Indices: 17284--17386 Score: 120
Period size: 28 Copynumber: 3.6 Consensus size: 28
17274 GTTCGAAGGT
17284 AAAAATGTAATTTTGGAAGTTTCAAGGTC
1 AAAAATGTAATTTTGGAAGTTTCAA-GTC
* *
17313 AAAAATGGAATTTTTGGAAGTTTCAGGGT-
1 AAAAATGTAA-TTTTGGAAGTTTCA-AGTC
*
17342 -AAAATGTAATTTTTAGAAGTTTCAAGTC
1 AAAAATGTAA-TTTTGGAAGTTTCAAGTC
*
17370 AAAAATATAATTTTGGA
1 AAAAATGTAATTTTGGA
17387 GAAGTTTGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
27 2 0.03
28 28 0.44
29 17 0.27
30 16 0.25
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (28 bp):
AAAAATGTAATTTTGGAAGTTTCAAGTC
Found at i:19183 original size:17 final size:17
Alignment explanation
Indices: 19163--19239 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
19153 AATAATTTTT
*
19163 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
19180 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* * ** *
19197 AATTCAACACGAATTTA
1 AATTTAAAATAAATTCA
19214 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
19231 AATTTAAAA
1 AATTTAAAA
19240 ATTAAAAGTT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:19191 original size:34 final size:34
Alignment explanation
Indices: 19153--19239 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 34
19143 TTTTAATATT
* * *
19153 AATAATTTTTAATTCAAAATAAATTCAAATTTAA
1 AATAAATTTAAATTCAAAACAAATTCAAATTTAA
* * *
19187 AATAAATTTAAATTCAACACGAATTTAAATTTAA
1 AATAAATTTAAATTCAAAACAAATTCAAATTTAA
* *
19221 AATAAATTCAAATTTAAAA
1 AATAAATTTAAATTCAAAA
19240 ATTAAAAGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (34 bp):
AATAAATTTAAATTCAAAACAAATTCAAATTTAA
Found at i:26670 original size:16 final size:18
Alignment explanation
Indices: 26635--26684 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
26625 AATTAGATTA
*
26635 TATATTTTTATGATATAATT
1 TATATATTTAT-A-ATAATT
26655 TAT-TATTT-TAATAATT
1 TATATATTTATAATAATT
26671 TATATATTTATAAT
1 TATATATTTATAAT
26685 TTTTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 5 0.19
19 4 0.15
20 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATATATTTATAATAATT
Found at i:26691 original size:15 final size:15
Alignment explanation
Indices: 26648--26691 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
26638 ATTTTTATGA
26648 TATAATTTATTAT-TT
1 TATAATTT-TTATATT
*
26663 TAATAATTTATATATT
1 T-ATAATTTTTATATT
26679 TATAATTTTTATA
1 TATAATTTTTATA
26692 AAATTAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATAATTTTTATATT
Found at i:26712 original size:31 final size:33
Alignment explanation
Indices: 26677--26746 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
26667 AATTTATATA
* *
26677 TTTATAATTTT-TATAAAATTAAATCA-AATTT
1 TTTATAATTTTAAAAAAAATTAAATCATAATTT
* *
26708 TTTATCATTTTAAAAAAAATTAAATTATAATTT
1 TTTATAATTTTAAAAAAAATTAAATCATAATTT
26741 TATTAT
1 T-TTAT
26747 TATTAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 10 0.31
32 12 0.38
33 6 0.19
34 4 0.12
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTATAATTTTAAAAAAAATTAAATCATAATTT
Found at i:26765 original size:16 final size:16
Alignment explanation
Indices: 26746--26796 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
26736 AATTTTATTA
26746 TTATTAAATTAAAATT
1 TTATTAAATTAAAATT
*
26762 TTA-TAAATTATAAAAT
1 TTATTAAATTA-AAATT
*
26778 AT-TTAAATTAAAATT
1 TTATTAAATTAAAATT
26793 TTAT
1 TTAT
26797 CATTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATTAAATTAAAATT
Found at i:26775 original size:22 final size:22
Alignment explanation
Indices: 26726--26777 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
26716 TTTAAAAAAA
* *
26726 ATTAAATTATAATTTTATTATT
1 ATTAAATTAAAATTTTATAATT
26748 ATTAAATTAAAATTTTATAAATT
1 ATTAAATTAAAATTTTAT-AATT
*
26771 ATAAAAT
1 ATTAAAT
26778 ATTTAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAAATTAAAATTTTATAATT
Found at i:27188 original size:27 final size:26
Alignment explanation
Indices: 27132--27194 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
27122 TTTTCTATCG
27132 TTTCTCTTCCTGGGTTTGGTCAAGATTT
1 TTTCT-TTCCTGGGTTTGGTCAAGA-TT
*
27160 TTTCTTTTCTGGGTTTGGCTTCAAG-TT
1 TTTCTTTCCTGGGTTTGG--TCAAGATT
*
27187 TTCCTTTC
1 TTTCTTTC
27195 GTGCTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 20 0.67
28 5 0.17
29 5 0.17
ACGTcount: A:0.08, C:0.19, G:0.19, T:0.54
Consensus pattern (26 bp):
TTTCTTTCCTGGGTTTGGTCAAGATT
Found at i:38793 original size:159 final size:159
Alignment explanation
Indices: 38570--39277 Score: 1172
Period size: 159 Copynumber: 4.5 Consensus size: 159
38560 GCTTCACAAT
38570 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
1 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
* * *
38635 GGGCGAAGCCAATGATAGAAATGGCTTCAGTTTCTGCATTTCTTACTTTTTAGATTAAAAAATGA
66 GGGCGAAGCCAATGAGAGAAATGGTTTCAGTTTCTGCATTTCTTACTTTTTAGATTAAAAGATGA
* *
38700 ATAACGAGGTAATTATCAAGACTTTCAAC
131 ATAACGAGGTAATTGTCAAGACTTGCAAC
* *
38729 GTGGTTTCGTGGTGTAGTTGGTTATAACGTCAGTCTAACACACTGAAGTTCTCCGGTTCGAGTCC
1 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
*
38794 GGGCGAAGCCAATGAGAGAAATAGTTTCAGTTTCTGCATTTCTTAC-TTTTAGATTAAAAGATGA
66 GGGCGAAGCCAATGAGAGAAATGGTTTCAGTTTCTGCATTTCTTACTTTTTAGATTAAAAGATGA
*
38858 ATAACGAGGTAATTGTCAGGACTTGCAAC
131 ATAACGAGGTAATTGTCAAGACTTGCAAC
38887 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
1 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
* *
38952 GGGCGAAGCCAATGAGAGAAATGGTTTCAGTTTCTGCATTTCTTACATTTTAAATTAAAAGATGA
66 GGGCGAAGCCAATGAGAGAAATGGTTTCAGTTTCTGCATTTCTTACTTTTTAGATTAAAAGATGA
*
39017 ATAACGAGGTAATTGTCAGGACTTGCAAC
131 ATAACGAGGTAATTGTCAAGACTTGCAAC
*
39046 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTTC
1 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
* * *
39111 GGGTGAAGCCAATGAGAGAAATGGTTTTAGTTTCTGCATTTCTTACTTTTTAGATTAAAATATGA
66 GGGCGAAGCCAATGAGAGAAATGGTTTCAGTTTCTGCATTTCTTACTTTTTAGATTAAAAGATGA
* *
39176 ATAATGAGGTAATTGTCAAGACTTGCAAT
131 ATAACGAGGTAATTGTCAAGACTTGCAAC
* * * * *
39205 GTGATTTC---GTGTAGTTGGTTATCACGTCAGTCTAACACGCCGAAAGTCTTCGGTTCGAGTCC
1 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
*
39267 GGGCAAAGCCA
66 GGGCGAAGCCA
39278 TTTGTAGGCA
Statistics
Matches: 518, Mismatches: 30, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
156 58 0.11
158 151 0.29
159 309 0.60
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (159 bp):
GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
GGGCGAAGCCAATGAGAGAAATGGTTTCAGTTTCTGCATTTCTTACTTTTTAGATTAAAAGATGA
ATAACGAGGTAATTGTCAAGACTTGCAAC
Found at i:38940 original size:317 final size:318
Alignment explanation
Indices: 38570--39277 Score: 1172
Period size: 317 Copynumber: 2.2 Consensus size: 318
38560 GCTTCACAAT
38570 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
1 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
* * *
38635 GGGCGAAGCCAATGATAGAAATGGCTTCAGTTTCTGCATTTCTTACTTTTTAGATTAAAAAATGA
66 GGGCGAAGCCAATGAGAGAAATGGCTTCAGTTTCTGCATTTCTTACATTTTAAATTAAAAAATGA
*
38700 ATAACGAGGTAATTATCAAGACTTTCAACGTGGTTTCGTGGTGTAGTTGGTTATAACGTCAGTCT
131 ATAACGAGGTAATTATCAAGACTTGCAACGTGGTTTCGTGGTGTAGTTGGTTATAACGTCAGTCT
*
38765 AACACACTGAAGTTCTCCGGTTCGAGTCCGGGCGAAGCCAATGAGAGAAATAGTTTCAGTTTCTG
196 AACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGAAGCCAATGAGAGAAATAGTTTCAGTTTCTG
*
38830 CATTTCTTAC-TTTTAGATTAAAAGATGAATAACGAGGTAATTGTCAGGACTTGCAAC
261 CATTTCTTACTTTTTAGATTAAAAGATGAATAACGAGGTAATTGTCAAGACTTGCAAC
38887 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
1 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
* *
38952 GGGCGAAGCCAATGAGAGAAATGGTTTCAGTTTCTGCATTTCTTACATTTTAAATTAAAAGATGA
66 GGGCGAAGCCAATGAGAGAAATGGCTTCAGTTTCTGCATTTCTTACATTTTAAATTAAAAAATGA
* * *
39017 ATAACGAGGTAATTGTCAGGACTTGCAACGTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCT
131 ATAACGAGGTAATTATCAAGACTTGCAACGTGGTTTCGTGGTGTAGTTGGTTATAACGTCAGTCT
* * * *
39082 AACACACTGAAGGTCTCCGGTTCGAGTTCGGGTGAAGCCAATGAGAGAAATGGTTTTAGTTTCTG
196 AACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGAAGCCAATGAGAGAAATAGTTTCAGTTTCTG
* * *
39147 CATTTCTTACTTTTTAGATTAAAATATGAATAATGAGGTAATTGTCAAGACTTGCAAT
261 CATTTCTTACTTTTTAGATTAAAAGATGAATAACGAGGTAATTGTCAAGACTTGCAAC
* * * * *
39205 GTGATTTC---GTGTAGTTGGTTATCACGTCAGTCTAACACGCCGAAAGTCTTCGGTTCGAGTCC
1 GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
*
39267 GGGCAAAGCCA
66 GGGCGAAGCCA
39278 TTTGTAGGCA
Statistics
Matches: 366, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
315 60 0.16
317 256 0.70
318 50 0.14
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (318 bp):
GTGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCC
GGGCGAAGCCAATGAGAGAAATGGCTTCAGTTTCTGCATTTCTTACATTTTAAATTAAAAAATGA
ATAACGAGGTAATTATCAAGACTTGCAACGTGGTTTCGTGGTGTAGTTGGTTATAACGTCAGTCT
AACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGAAGCCAATGAGAGAAATAGTTTCAGTTTCTG
CATTTCTTACTTTTTAGATTAAAAGATGAATAACGAGGTAATTGTCAAGACTTGCAAC
Found at i:40946 original size:13 final size:14
Alignment explanation
Indices: 40905--40951 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 14
40895 CCATGTCAAC
*
40905 AAAAAATAAAGTTAA
1 AAAAAATAAA-TTTA
40920 AACATAAATAAATTTA
1 AA-A-AAATAAATTTA
40936 AAAAAAT-AATTTA
1 AAAAAATAAATTTA
40949 AAA
1 AAA
40952 CACCATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 9 0.31
14 4 0.14
15 3 0.10
16 6 0.21
17 7 0.24
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (14 bp):
AAAAAATAAATTTA
Found at i:41461 original size:23 final size:23
Alignment explanation
Indices: 41397--41464 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
41387 GTTTATGGTT
* ** *
41397 GTCGAATTTGGAGATTTTAAGTT
1 GTCGAATTTGGGGATTTTGGGTG
*
41420 GTTGAATTTGGGGATTTTGGGTG
1 GTCGAATTTGGGGATTTTGGGTG
41443 GTCGAATTTGGGGATTTTGGGT
1 GTCGAATTTGGGGATTTTGGGT
41465 AAGAGTTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.03, G:0.37, T:0.43
Consensus pattern (23 bp):
GTCGAATTTGGGGATTTTGGGTG
Found at i:41867 original size:25 final size:25
Alignment explanation
Indices: 41839--41921 Score: 60
Period size: 27 Copynumber: 3.2 Consensus size: 25
41829 ATAAAAACTC
41839 AAAATAAAAAATTCATTTGCTTGAT
1 AAAATAAAAAATTCATTTGCTTGAT
* ** * *
41864 AAAA-CAAATTTCCTCATCTGGTTTGAAT
1 AAAATAAAAAAT--TCAT-TTGCTTG-AT
*
41892 CAAAATAAAAAACTCATTTGCTTGAT
1 -AAAATAAAAAATTCATTTGCTTGAT
41918 AAAA
1 AAAA
41922 CCCAAACTGG
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
24 4 0.10
25 8 0.20
26 6 0.15
27 10 0.24
28 6 0.15
29 4 0.10
30 3 0.07
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (25 bp):
AAAATAAAAAATTCATTTGCTTGAT
Found at i:51589 original size:16 final size:17
Alignment explanation
Indices: 51543--51581 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
51533 TTTTTATATG
*
51543 ATAATATAATATTAAAAT
1 ATAATATAA-AATAAAAT
51561 ATAATATAAAATAAAAT
1 ATAATATAAAATAAAAT
51578 -TAAT
1 ATAAT
51582 TGAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATATAAAATAAAAT
Found at i:54588 original size:21 final size:21
Alignment explanation
Indices: 54541--54617 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
54531 ACTAGTGCAG
**
54541 ACTTCTATTGATACAAGTGA-T
1 ACTTCTACCGATACAAGT-ACT
*
54562 AGTTCTACCGATACAAGTTACT
1 ACTTCTACCGATACAAG-TACT
* * *
54584 -CTTCTACTGAAACAAGTATT
1 ACTTCTACCGATACAAGTACT
54604 ACTTCTACCGATAC
1 ACTTCTACCGATAC
54618 TAAAAACTCC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.07
21 39 0.89
22 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTACT
Found at i:55370 original size:53 final size:53
Alignment explanation
Indices: 55290--55533 Score: 348
Period size: 53 Copynumber: 4.6 Consensus size: 53
55280 TTCACATTTG
* * * *
55290 ATAACTCACAATGACACCGAGTCATCGGACCTTTAATCCGTAATAAGATTCGT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* *
55343 ATAACTCACGATAACACAGAGTCATCGGACCCTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * *
55396 ATAACACATGATGACATAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * * *
55449 ATAACTCACGATGACACAAAGTCATTGGACCTTTAATCTGTGATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
*
55502 ATAACTCACGATGACAC--AGTCATCGGTCCTTT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTT
55534 TTTTGCATTT
Statistics
Matches: 171, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
51 13 0.08
53 158 0.92
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
Found at i:58423 original size:34 final size:32
Alignment explanation
Indices: 58382--58448 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 32
58372 TTATACTATA
*
58382 AAATATTTATTATTAATATATTAATAATTGTAAT
1 AAATATTTATTATTAAAATATTAAT-ATTG-AAT
58416 AAATATTTATTATTAAAATATTAATATTGAAT
1 AAATATTTATTATTAAAATATTAATATTGAAT
58448 A
1 A
58449 TTTTCAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 4 0.12
33 4 0.12
34 24 0.75
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (32 bp):
AAATATTTATTATTAAAATATTAATATTGAAT
Found at i:58436 original size:15 final size:15
Alignment explanation
Indices: 58380--58437 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
58370 CTTTATACTA
58380 TAAAATATTTATTAT
1 TAAAATATTTATTAT
* *
58395 TAATATATTAATAATTGT
1 TAAAATATT--T-ATTAT
*
58413 AATAAATATTTATTAT
1 TA-AAATATTTATTAT
58429 TAAAATATT
1 TAAAATATT
58438 AATATTGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 15 0.45
16 5 0.15
17 2 0.06
18 5 0.15
19 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TAAAATATTTATTAT
Found at i:58501 original size:16 final size:16
Alignment explanation
Indices: 58470--58506 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
58460 ATGTGAAGAA
58470 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
58486 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
58502 TATTA
1 TATTA
58507 AAATAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:69589 original size:19 final size:20
Alignment explanation
Indices: 69539--69589 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
69529 GTTTTCAAAT
*
69539 AATCAAAATTAATTTTAAAT
1 AATCAAAATTAATTTTAAAA
*
69559 GAT-AAAATTTAA-TTTAAAA
1 AATCAAAA-TTAATTTTAAAA
*
69578 AATCAAAGTTAA
1 AATCAAAATTAA
69590 ATGTCATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
AATCAAAATTAATTTTAAAA
Found at i:73378 original size:4 final size:4
Alignment explanation
Indices: 73371--73395 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
73361 CAAGAAAGAA
73371 AAAC AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC A
73396 CCAAATATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:74427 original size:2 final size:2
Alignment explanation
Indices: 74409--74445 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
74399 GTGAGCTTGG
* *
74409 GA GA GA AA GA GA AA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
74446 GGACAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:75502 original size:19 final size:19
Alignment explanation
Indices: 75456--75493 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
75446 TTTAAAAGCT
75456 AAAAAAAAAGCTTAACAAA
1 AAAAAAAAAGCTTAACAAA
*
75475 AAAAAAAAAGGTTAA-AAA
1 AAAAAAAAAGCTTAACAAA
75493 A
1 A
75494 GACAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAGCTTAACAAA
Found at i:77474 original size:20 final size:20
Alignment explanation
Indices: 77426--77476 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
77416 TTCGATTCAA
77426 TTAAATAAAT-TACTAAAAAT
1 TTAAA-AAATATACTAAAAAT
* *
77446 TTATAAAAATATATTAAAATT
1 TTA-AAAAATATACTAAAAAT
77467 TTAAAAAATA
1 TTAAAAAATA
77477 GAAAAAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAAAATATACTAAAAAT
Found at i:84405 original size:69 final size:68
Alignment explanation
Indices: 84301--85157 Score: 347
Period size: 69 Copynumber: 12.4 Consensus size: 68
84291 TCAACACAAA
* * * * * * *
84301 AGCGAGAGAAAAACTCCCAACTGTTATGTTAAGGTTCGTAATGGAAAAGCCATAACCTCCAACAT
1 AGCGAGAGCAAAGCTCCTAACTATCATATTAAGGTTCGTAA-GGAAAAGCCATAACCTCCAACAC
84366 AGTT
65 AGTT
* * * * *
84370 AGCGAGAGCAAAGCTCCTAACTATCACATTAAGGTTC-TCAAACGAAGAGCCGTAACCTACAACA
1 AGCGAGAGCAAAGCTCCTAACTATCATATTAAGGTTCGT--AAGGAAAAGCCATAACCTCCAACA
84434 CAGTT
64 CAGTT
* * * * * * ** **
84439 AGCGAGAGTAAAACT--TACAGTTGTTATATTAAGGTTCGT-AGGCAAAGAGTCGCAACCTTTAA
1 AGCGAGAGCAAAGCTCCTA-A-CTATCATATTAAGGTTCGTAAGG-AAA-AGCCATAACCTCCAA
84501 CACAGTT
62 CACAGTT
* * * * * * * * *
84508 AGCGAGAGTAAAGCTCCTAGCTGTCATATTAAGGTTTGTAGACGAAGAGCTACAACCTTCAACAC
1 AGCGAGAGCAAAGCTCCTAACTATCATATTAAGGTTCGTA-AGGAAAAGCCATAACCTCCAACAC
84573 AGTT
65 AGTT
* * *
84577 AGCGAGAGAAAAGCT-CTCAATTATCATATTAAGG-T-GTAAGAGAAAAGCCATAATCTCCAACA
1 AGCGAGAGCAAAGCTCCT-AACTATCATATTAAGGTTCGTAAG-GAAAAGCCATAACCTCCAACA
*
84639 CAATT
64 CAGTT
* * * * ** * * ** *
84644 AGTGAGAGCAAAGCTCCCAGA-TGTTATATTAAGGTTCCCAAGCGAAGATCCGCAACCTCCAGCA
1 AGCGAGAGCAAAGCTCCTA-ACTATCATATTAAGGTTCGTAAG-GAAAAGCCATAACCTCCAACA
*
84708 CAATT
64 CAGTT
* * * * * * * * *
84713 AGCGAGAGCAAAACTCCCAGCTGTTATATTAAGGTTC--ACAGTCGAAGAGTCGTAACCTTCAAC
1 AGCGAGAGCAAAGCTCCTAACTATCATATTAAGGTTCGTA-AG--GAAAAGCCATAACCTCCAAC
*
84776 ATAGTT
63 ACAGTT
* * * * * * * * * *
84782 AGAGAGAGCAAAGCT-CTCAATTGTCACATTAAGATTC-TCAAGCGAAGAGTCGTAACTTACAAC
1 AGCGAGAGCAAAGCTCCT-AACTATCATATTAAGGTTCGT-AAG-GAAAAGCCATAACCTCCAAC
84845 ACAGTT
63 ACAGTT
* ** * * * * * ***
84851 AGTGAGAGCAAAGCTCAC-AGTTGTCATATTAAGGTTCATAGACGAAGATCTGCAACCTCCAACA
1 AGCGAGAGCAAAGCTC-CTAACTATCATATTAAGGTTCGTA-AGGAAAAGCCATAACCTCCAACA
84915 CACGGTT
64 CA--GTT
* * * ** * * * * * **
84922 AGAGAGAGCAAAGCTCCCAGCCGTCACATTAAGGTTC-TCAAGCGAAGAGTCTTAACTTTTAACA
1 AGCGAGAGCAAAGCTCCTAACTATCATATTAAGGTTCGT-AAG-GAAAAGCCATAACCTCCAACA
84986 CAGTT
64 CAGTT
* ** * * ** * * * *
84991 AGCGAGAGCAAAGCTCCCAGTTGTCATATTAAGGTTCGCAGACAAAAAGTCGTAATCTCCAACAG
1 AGCGAGAGCAAAGCTCCTAACTATCATATTAAGGTTCGTA-AGGAAAAGCCATAACCTCCAACAC
*
85056 AGTC
65 AGTT
* * * * * * * ** *
85060 AGTGAGAGCAAAGCTCCCAACTGTTATATTAAGGTTCATAGGTGAAGAGCCGCAACCTCTAACAC
1 AGCGAGAGCAAAGCTCCTAACTATCATATTAAGGTTCGTAAG-GAAAAGCCATAACCTCCAACAC
85125 AGTT
65 AGTT
* *
85129 AGCGAGAGCAAAAGCTCCCAACTAGCATA
1 AGCGAGAGC-AAAGCTCCTAACTATCATA
85158 CTAGAACTGA
Statistics
Matches: 612, Mismatches: 140, Indels: 71
0.74 0.17 0.09
Matches are distributed among these distances:
66 1 0.00
67 53 0.09
68 13 0.02
69 460 0.75
70 29 0.05
71 56 0.09
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (68 bp):
AGCGAGAGCAAAGCTCCTAACTATCATATTAAGGTTCGTAAGGAAAAGCCATAACCTCCAACACA
GTT
Found at i:84508 original size:138 final size:138
Alignment explanation
Indices: 84260--85148 Score: 762
Period size: 138 Copynumber: 6.4 Consensus size: 138
84250 TTTTTCTCAT
* * ** * **
84260 ATTAAGGTTCACAAGCGAAGAGCTGCAACCTTCAACACA-AAAGCGAGAGAAAAACTCCCAACTG
1 ATTAAGGTTCTCAAGCGAAGAGCCGCAACCTTCAACACAGTTAGCGAGAGCAAAACTCCCAGTTG
* * * * * *
84324 TTATGTTAAGGTTCGTAATGG-AAA-AGCCATAACCTCCAACATAGTTAGCGAGAGCAAAGCTCC
66 TCATATTAAGGTTCGT-A-GGCAAAGAGTCGTAACCTCCAACACAGTTAGAGAGAGCAAAGCTCC
* *
84387 TAACTATCAC
129 CAACTGTCAC
* * * * **
84397 ATTAAGGTTCTCAAACGAAGAGCCGTAACCTACAACACAGTTAGCGAGAGTAAAACTTACAGTTG
1 ATTAAGGTTCTCAAGCGAAGAGCCGCAACCTTCAACACAGTTAGCGAGAGCAAAACTCCCAGTTG
* * ** * * *
84462 TTATATTAAGGTTCGTAGGCAAAGAGTCGCAACCTTTAACACAGTTAGCGAGAGTAAAGCTCCTA
66 TCATATTAAGGTTCGTAGGCAAAGAGTCGTAACCTCCAACACAGTTAGAGAGAGCAAAGCTCCCA
* *
84527 GCTGTCAT
131 ACTGTCAC
** ** * *
84535 ATTAAGGTT-TGTAGACGAAGAGCTACAACCTTCAACACAGTTAGCGAGAG-AAAAGCTCTCAAT
1 ATTAAGGTTCTCAAG-CGAAGAGCCGCAACCTTCAACACAGTTAGCGAGAGCAAAA-CTCCCAGT
* * * * * *
84598 TATCATATTAAGG-T-GTAAGAG-AAA-AGCCATAATCTCCAACACAATTAGTGAGAGCAAAGCT
64 TGTCATATTAAGGTTCGT-AG-GCAAAGAGTCGTAACCTCCAACACAGTTAGAGAGAGCAAAGCT
* *
84659 CCCAGA-TGTTAT
127 CCCA-ACTGTCAC
* * * * * *
84671 ATTAAGGTTCCCAAGCGAAGATCCGCAACCTCCAGCACAATTAGCGAGAGCAAAACTCCCAGCTG
1 ATTAAGGTTCTCAAGCGAAGAGCCGCAACCTTCAACACAGTTAGCGAGAGCAAAACTCCCAGTTG
* ** * * * * *
84736 TTATATTAAGGTTCACAGTCGAAGAGTCGTAACCTTCAACATAGTTAGAGAGAGCAAAGCTCTCA
66 TCATATTAAGGTTCGTAGGCAAAGAGTCGTAACCTCCAACACAGTTAGAGAGAGCAAAGCTCCCA
*
84801 ATTGTCAC
131 ACTGTCAC
* * * * * *
84809 ATTAAGATTCTCAAGCGAAGAGTCGTAA-CTTACAACACAGTTAGTGAGAGCAAAGCTCACAGTT
1 ATTAAGGTTCTCAAGCGAAGAGCCGCAACCTT-CAACACAGTTAGCGAGAGCAAAACTCCCAGTT
* * * *
84873 GTCATATTAAGGTTCATAGACGAAGA-TCTGCAACCTCCAACACACGGTTAGAGAGAGCAAAGCT
65 GTCATATTAAGGTTCGTAGGCAAAGAGTC-GTAACCTCCAACACA--GTTAGAGAGAGCAAAGCT
* *
84937 CCCAGCCGTCAC
127 CCCAACTGTCAC
* ** * * *
84949 ATTAAGGTTCTCAAGCGAAGAGTCTTAACTTTTAACACAGTTAGCGAGAGCAAAGCTCCCAGTTG
1 ATTAAGGTTCTCAAGCGAAGAGCCGCAACCTTCAACACAGTTAGCGAGAGCAAAACTCCCAGTTG
* * * * * * *
85014 TCATATTAAGGTTCGCAGACAAAAAGTCGTAATCTCCAACAGAGTCAGTGAGAGCAAAGCTCCCA
66 TCATATTAAGGTTCGTAGGCAAAGAGTCGTAACCTCCAACACAGTTAGAGAGAGCAAAGCTCCCA
* *
85079 ACTGTTAT
131 ACTGTCAC
* *
85087 ATTAAGGTTCAT-AGGTGAAGAGCCGCAACC-TCTAACACAGTTAGCGAGAGCAAAAGCTCCCA
1 ATTAAGGTTC-TCAAGCGAAGAGCCGCAACCTTC-AACACAGTTAGCGAGAGCAAAA-CTCCCA
85149 ACTAGCATAC
Statistics
Matches: 604, Mismatches: 124, Indels: 46
0.78 0.16 0.06
Matches are distributed among these distances:
136 94 0.16
137 67 0.11
138 317 0.52
139 7 0.01
140 115 0.19
141 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (138 bp):
ATTAAGGTTCTCAAGCGAAGAGCCGCAACCTTCAACACAGTTAGCGAGAGCAAAACTCCCAGTTG
TCATATTAAGGTTCGTAGGCAAAGAGTCGTAACCTCCAACACAGTTAGAGAGAGCAAAGCTCCCA
ACTGTCAC
Found at i:84746 original size:274 final size:273
Alignment explanation
Indices: 84256--85145 Score: 855
Period size: 274 Copynumber: 3.2 Consensus size: 273
84246 AGCATTTTTC
* * ** * *
84256 TCATATTAAGGTTCACAAGCGAAGAGCTGCAACCTTCAACACA-AAAGCGAGAGAAAAACTCCCA
1 TCATATTAAGGTTTA-TAGCGAAGAGCTGCAACCTTCAACACAGTTAGCGAGAGAAAAGCTCACA
* * * * *
84320 ACTGTTATGTTAAGGTTCGTAATG-GAAAAGCCATAACCTCCAACATAGTTAGCGAGAGCAAAGC
65 ATTGTCATATTAAGG-T-GTAA-GAGAAAAGCCATAACCTCCAACACAGTTAGAGAGAGCAAAGC
* * * * *
84384 TCCTA-ACTATCACATTAAGGTTCTCAAACGAAGAGCCGTAACCTACAACACAGTTAGCGAGAGT
127 TCCCAGA-TGTCACATTAAGGTTCTCAAGCGAAGATCCGTAACCTACAACACAGTTAGCGAGAGC
** * * * * *
84448 AAAACTTACAGTTGTTATATTAAGGTTCGTAGGCAAAGAGTCGCAACCTTTAACACAGTTAGCGA
191 AAAACTCCCAGTTGTTATATTAAGGTTCGCAGACAAAGAGTCGTAACCTTCAACACAGTTAGAGA
* *
84513 GAGTAAAGCTCCTAGCTG
256 GAGCAAAGCTCCTAACTG
* * *
84531 TCATATTAAGGTTTGTAGACGAAGAGCTACAACCTTCAACACAGTTAGCGAGAGAAAAGCTCTCA
1 TCATATTAAGGTTTATAG-CGAAGAGCTGCAACCTTCAACACAGTTAGCGAGAGAAAAGCTCACA
* * * *
84596 ATTATCATATTAAGGTGTAAGAGAAAAGCCATAATCTCCAACACAATTAGTGAGAGCAAAGCTCC
65 ATTGTCATATTAAGGTGTAAGAGAAAAGCCATAACCTCCAACACAGTTAGAGAGAGCAAAGCTCC
* * * * * * *
84661 CAGATGTTATATTAAGGTTCCCAAGCGAAGATCCGCAACCTCCAGCACAATTAGCGAGAGCAAAA
130 CAGATGTCACATTAAGGTTCTCAAGCGAAGATCCGTAACCTACAACACAGTTAGCGAGAGCAAAA
* * * * *
84726 CTCCCAGCTGTTATATTAAGGTTCACAGTCGAAGAGTCGTAACCTTCAACATAGTTAGAGAGAGC
195 CTCCCAGTTGTTATATTAAGGTTCGCAGACAAAGAGTCGTAACCTTCAACACAGTTAGAGAGAGC
*
84791 AAAGCT-CTCAATTG
260 AAAGCTCCT-AACTG
* * * * *
84805 TCACATTAAGATTCTCA-AGCGAAGAG-TCGTAA-CTTACAACACAGTTAGTGAGAGCAAAGCTC
1 TCATATTAAGGTT-T-ATAGCGAAGAGCT-GCAACCTT-CAACACAGTTAGCGAGAGAAAAGCTC
* * * ***
84867 ACAGTTGTCATATTAAGGT-TCATAGACGAAGATCTGCAACCTCCAACACACGGTTAGAGAGAGC
62 ACAATTGTCATATTAAGGTGT-A-AGA-GAAAAGCCATAACCTCCAACACA--GTTAGAGAGAGC
** * * **
84931 AAAGCTCCCAGCCGTCACATTAAGGTTCTCAAGCGAAGAGT-CTTAACTTTTAACACAGTTAGCG
122 AAAGCTCCCAGATGTCACATTAAGGTTCTCAAGCGAAGA-TCCGTAACCTACAACACAGTTAGCG
* * * * * * *
84995 AGAGCAAAGCTCCCAGTTGTCATATTAAGGTTCGCAGACAAAAAGTCGTAATCTCCAACAGAGTC
186 AGAGCAAAACTCCCAGTTGTTATATTAAGGTTCGCAGACAAAGAGTCGTAACCTTCAACACAGTT
* *
85060 AGTGAGAGCAAAGCTCCCAACTG
251 AGAGAGAGCAAAGCTCCTAACTG
* * * *
85083 TTATATTAAGGTTCATAGGTGAAGAGCCGCAACC-TCTAACACAGTTAGCGAGAGCAAAAGCTC
1 TCATATTAAGGTTTATA-GCGAAGAGCTGCAACCTTC-AACACAGTTAGCGAGAG-AAAAGCTC
85146 CCAACTAGCA
Statistics
Matches: 498, Mismatches: 95, Indels: 40
0.79 0.15 0.06
Matches are distributed among these distances:
273 8 0.02
274 219 0.44
275 44 0.09
276 46 0.09
277 2 0.00
278 169 0.34
279 10 0.02
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (273 bp):
TCATATTAAGGTTTATAGCGAAGAGCTGCAACCTTCAACACAGTTAGCGAGAGAAAAGCTCACAA
TTGTCATATTAAGGTGTAAGAGAAAAGCCATAACCTCCAACACAGTTAGAGAGAGCAAAGCTCCC
AGATGTCACATTAAGGTTCTCAAGCGAAGATCCGTAACCTACAACACAGTTAGCGAGAGCAAAAC
TCCCAGTTGTTATATTAAGGTTCGCAGACAAAGAGTCGTAACCTTCAACACAGTTAGAGAGAGCA
AAGCTCCTAACTG
Found at i:85268 original size:55 final size:55
Alignment explanation
Indices: 85200--85503 Score: 259
Period size: 58 Copynumber: 5.4 Consensus size: 55
85190 GATATTCCTC
* * * *
85200 AAAATTTTTTAAGTACAAAATAGCTCGTGGATTCACATCCCAACTTATTATTAAT
1 AAAATTTTCTAAGTACAAAATAGCTCGTGGATTTATATCCCAACTTATTATTAAG
** * *
85255 AAAATTTTCTAAGTACAAAATAGCTCGCAGATTTATATCCCAACCTATTACTAAG
1 AAAATTTTCTAAGTACAAAATAGCTCGTGGATTTATATCCCAACTTATTATTAAG
* * * *
85310 AAAATTTTCTAAGTATC-AAATAGCTCATGGATTTACATCTCGACTTATTATTATTAAG
1 AAAATTTTCTAAGTA-CAAAATAGCTCGTGGATTTATATCCCAAC---TTATTATTAAG
* ** *** * *
85368 AAAATTTTGTAAGTATGAAATAGCTCACAGATTTATATCCGAGCTTATTATCTTTAAG
1 AAAATTTTCTAAGTACAAAATAGCTCGTGGATTTATATCCCAACTTATTA---TTAAG
* * * * * * *
85426 AAAATTTTATATGTACGAAATAACTCGTGGATTCATATCCCAGCTTGTTATTTTGAAG
1 AAAATTTTCTAAGTACAAAATAGCTCGTGGATTTATATCCCAACTTATTA--TT-AAG
*
85484 AAAATTTTCCAAGTACAAAA
1 AAAATTTTCTAAGTACAAAA
85504 CAACTCATAG
Statistics
Matches: 200, Mismatches: 40, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
55 89 0.44
56 1 0.00
57 3 0.01
58 107 0.54
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (55 bp):
AAAATTTTCTAAGTACAAAATAGCTCGTGGATTTATATCCCAACTTATTATTAAG
Found at i:85406 original size:113 final size:110
Alignment explanation
Indices: 85200--85503 Score: 313
Period size: 113 Copynumber: 2.7 Consensus size: 110
85190 GATATTCCTC
* * *
85200 AAAATTTTTTAAGTACAAAATAGCTCGTGGATTCACATCCCAACTTATTATTAATAAAATTTTCT
1 AAAATTTTCTAAGTACAAAATAGCTCATGGATTCACATCCCAACTTATTATTAAGAAAATTTTCT
*
85265 AAGTACAAAATAGCTCGCAGATTTATATCCCAACCTATTACTAAG
66 AAGTACAAAATAGCTCACAGATTTATATCCCAACCTATTACTAAG
* * *
85310 AAAATTTTCTAAGTATC-AAATAGCTCATGGATTTACATCTCGACTTATTATTATTAAGAAAATT
1 AAAATTTTCTAAGTA-CAAAATAGCTCATGGATTCACATCCCAAC---TTATTATTAAGAAAATT
* ** * * *
85374 TTGTAAGTATGAAATAGCTCACAGATTTATATCCGAGCTTATTATCTTTAAG
62 TTCTAAGTACAAAATAGCTCACAGATTTATATCCCAACCTATTA-C--TAAG
* * * * * * * *
85426 AAAATTTTATATGTACGAAATAACTCGTGGATTCATATCCCAGCTTGTTATTTTGAAGAAAATTT
1 AAAATTTTCTAAGTACAAAATAGCTCATGGATTCACATCCCAACTTATTA--TT-AAGAAAATTT
*
85491 TCCAAGTACAAAA
63 TCTAAGTACAAAA
85504 CAACTCATAG
Statistics
Matches: 156, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
110 37 0.24
111 1 0.01
113 58 0.37
114 1 0.01
115 3 0.02
116 56 0.36
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (110 bp):
AAAATTTTCTAAGTACAAAATAGCTCATGGATTCACATCCCAACTTATTATTAAGAAAATTTTCT
AAGTACAAAATAGCTCACAGATTTATATCCCAACCTATTACTAAG
Found at i:85498 original size:116 final size:111
Alignment explanation
Indices: 85200--85503 Score: 335
Period size: 116 Copynumber: 2.7 Consensus size: 111
85190 GATATTCCTC
* * *
85200 AAAATTTTTTAAGTACAAAATAGCTCGTGGATTCACATCCCAACTTATTA--TTAATAAAATTTT
1 AAAATTTTATAAGTAC-AAATAGCTCGTGGATTCACATCCCAGCTTATTATTTTAAGAAAATTTT
*
85263 CTAAGTACAAAATAGCTCGCAGATTTATATCCCAACCTATTACTAAG
65 CTAAGTACAAAATAGCTCACAGATTTATATCCCAACCTATTACTAAG
* * * *
85310 AAAATTTTCTAAGTATCAAATAGCTCATGGATTTACATCTC-GACTTATTATTATTAAGAAAATT
1 AAAATTTTATAAGTA-CAAATAGCTCGTGGATTCACATCCCAG-CTTATTATT-TTAAGAAAATT
* ** * * *
85374 TTGTAAGTATGAAATAGCTCACAGATTTATATCCGAGCTTATTATCTTTAAG
63 TTCTAAGTACAAAATAGCTCACAGATTTATATCCCAACCTATTA-C--TAAG
* * * *
85426 AAAATTTTATATGTACGAAATAACTCGTGGATTCATATCCCAGCTTGTTATTTTGAAGAAAATTT
1 AAAATTTTATAAGTAC-AAATAGCTCGTGGATTCACATCCCAGCTTATTATTTT-AAGAAAATTT
*
85491 TCCAAGTACAAAA
64 TCTAAGTACAAAA
85504 CAACTCATAG
Statistics
Matches: 158, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
110 42 0.27
111 1 0.01
113 47 0.30
114 1 0.01
115 3 0.02
116 63 0.40
117 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (111 bp):
AAAATTTTATAAGTACAAATAGCTCGTGGATTCACATCCCAGCTTATTATTTTAAGAAAATTTTC
TAAGTACAAAATAGCTCACAGATTTATATCCCAACCTATTACTAAG
Found at i:85509 original size:58 final size:58
Alignment explanation
Indices: 85391--85567 Score: 155
Period size: 58 Copynumber: 3.1 Consensus size: 58
85381 TATGAAATAG
* * * * ** * * *
85391 CTCACAGATTTATATCCGAGCTTATTATCTTT-AAGAAAATTTTATATGTACGAAATAA
1 CTCATAGATTCATATCCCAGCTTGTTAT-TTTGAAGAAAATTTTCCAAGTACAAAACAA
* *
85449 CTCGTGGATTCATATCCCAGCTTGTTATTTTGAAGAAAATTTTCCAAGTACAAAACAA
1 CTCATAGATTCATATCCCAGCTTGTTATTTTGAAGAAAATTTTCCAAGTACAAAACAA
* * * * *
85507 CTCATAGACTCACACTCTCAGCTTGTTATTTTG--G-AAATTTTCCTAACTATAAAACAA
1 CTCATAGATTCATA-TCCCAGCTTGTTATTTTGAAGAAAATTTTCC-AAGTACAAAACAA
85564 CTCA
1 CTCA
85568 CATGCGTAGT
Statistics
Matches: 98, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
56 9 0.09
57 19 0.19
58 53 0.54
59 17 0.17
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (58 bp):
CTCATAGATTCATATCCCAGCTTGTTATTTTGAAGAAAATTTTCCAAGTACAAAACAA
Found at i:87154 original size:13 final size:14
Alignment explanation
Indices: 87129--87157 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
87119 GCTCAAAGTA
87129 GAAAATGAAGGTAT
1 GAAAATGAAGGTAT
87143 GAAAAT-AAGGTAT
1 GAAAATGAAGGTAT
87156 GA
1 GA
87158 GATTCTCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (14 bp):
GAAAATGAAGGTAT
Found at i:100043 original size:2 final size:2
Alignment explanation
Indices: 100036--100072 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
100026 AGAAATAACT
100036 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
100073 TACTAGGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:103306 original size:42 final size:42
Alignment explanation
Indices: 103236--103315 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
103226 TGTAGGGATT
** *
103236 TATACTTTAGGTTTTCTTTAGGATTAGGTTATAATTTTTATA
1 TATACTTTAGGTTTTCTTTAAAACTAGGTTATAATTTTTATA
*
103278 TATACTTTAGG-TTTCTTTTAAAACTAGGTTTTAATTTT
1 TATACTTTAGGTTTTC-TTTAAAACTAGGTTATAATTTT
103316 CTTTATTAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.12
42 29 0.88
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.55
Consensus pattern (42 bp):
TATACTTTAGGTTTTCTTTAAAACTAGGTTATAATTTTTATA
Found at i:110680 original size:22 final size:22
Alignment explanation
Indices: 110652--110699 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
110642 AATAATAAAA
*
110652 TTCTCTCTGCTTTGTAGA-ACGT
1 TTCTCTCTACTTTGTA-ACACGT
110674 TTCTCTCTACTTTGTAACACGT
1 TTCTCTCTACTTTGTAACACGT
110696 TTCT
1 TTCT
110700 AGGTTTGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.48
Consensus pattern (22 bp):
TTCTCTCTACTTTGTAACACGT
Found at i:114444 original size:21 final size:22
Alignment explanation
Indices: 114418--114466 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
114408 ACTTTTCCAT
114418 TTTTTA-ATAAATGACCCAATA
1 TTTTTACATAAATGACCCAATA
*
114439 TTTTTACATAAATGACCTAATA
1 TTTTTACATAAATGACCCAATA
*
114461 TGTTTA
1 TTTTTA
114467 TGCTTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (22 bp):
TTTTTACATAAATGACCCAATA
Found at i:115290 original size:20 final size:20
Alignment explanation
Indices: 115265--115302 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
115255 TTGTTATTTT
*
115265 TTAAAAGTTGAGTGACTAAA
1 TTAAAACTTGAGTGACTAAA
115285 TTAAAACTTGAGTGACTA
1 TTAAAACTTGAGTGACTA
115303 TTTAGTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (20 bp):
TTAAAACTTGAGTGACTAAA
Found at i:115493 original size:23 final size:24
Alignment explanation
Indices: 115448--115493 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
115438 GCCATCCATT
* *
115448 AAAATAGAAAAGAAATTGTAGAAA
1 AAAATAGAAAAGAAATCGGAGAAA
115472 AAAATAGAAAAGAAA-CGGAGAA
1 AAAATAGAAAAGAAATCGGAGAA
115494 TTGGCTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.11
Consensus pattern (24 bp):
AAAATAGAAAAGAAATCGGAGAAA
Found at i:125975 original size:79 final size:78
Alignment explanation
Indices: 125833--126046 Score: 216
Period size: 79 Copynumber: 2.7 Consensus size: 78
125823 CAATAGAAAT
* * * * ** * * **
125833 CGAATAAATTATATTGAACGACAAGAATAAATCCTGAAACA-AATTTATTTTAATTTATTTCTGT
1 CGAATAAATTCTGTTAAATGACAAGAATAAATCCCAAAACAGAA-TTA-TTCAATTAACATCTGT
*
125897 TTGGATACA-AAAAC
64 TTGGAAACATAAAAC
* * *
125911 TCGAATAAATTCTGTTAAATGGCAAGAATAAAATCCTAAAACAGAATTGTTCAATTAACATCTGT
1 -CGAATAAATTCTGTTAAATGACAAGAAT-AAATCCCAAAACAGAATTATTCAATTAACATCTGT
125976 TTGGAAACATAAAAC
64 TTGGAAACATAAAAC
* * * *
125991 CGAATAAATTCTTTTGAATGACAGGAATAAATCCCAAAATAGAATTATTCAATTAA
1 CGAATAAATTCTGTTAAATGACAAGAATAAATCCCAAAACAGAATTATTCAATTAA
126047 TTTTTGTTTA
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
78 25 0.22
79 67 0.59
80 19 0.17
81 2 0.02
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (78 bp):
CGAATAAATTCTGTTAAATGACAAGAATAAATCCCAAAACAGAATTATTCAATTAACATCTGTTT
GGAAACATAAAAC
Found at i:127741 original size:14 final size:14
Alignment explanation
Indices: 127722--127750 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
127712 GATTTAATTT
127722 ACTTAATTAATCTA
1 ACTTAATTAATCTA
127736 ACTTAATTAATCTA
1 ACTTAATTAATCTA
127750 A
1 A
127751 TCATGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTTAATTAATCTA
Found at i:128558 original size:21 final size:19
Alignment explanation
Indices: 128525--128563 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
128515 TTGTAAACTA
128525 TAACTACTTACAAACTAAT
1 TAACTACTTACAAACTAAT
128544 TAACTATCTTTACAAACTAA
1 TAACTA-C-TTACAAACTAA
128564 CAACTAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (19 bp):
TAACTACTTACAAACTAAT
Found at i:129175 original size:16 final size:16
Alignment explanation
Indices: 129154--129186 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
129144 AAAGCAATCT
129154 TCCAATTAATCTTTGA
1 TCCAATTAATCTTTGA
129170 TCCAATTAATCTTTGA
1 TCCAATTAATCTTTGA
129186 T
1 T
129187 AAACTATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (16 bp):
TCCAATTAATCTTTGA
Found at i:135127 original size:9 final size:9
Alignment explanation
Indices: 135113--135142 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
135103 TATATTCAAT
135113 TTTTAAATA
1 TTTTAAATA
135122 TTTTAAATTA
1 TTTTAAA-TA
135132 TTTTAAATA
1 TTTTAAATA
135141 TT
1 TT
135143 CAATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTAAATA
Found at i:135154 original size:19 final size:20
Alignment explanation
Indices: 135111--135155 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
135101 TATATATTCA
*
135111 ATTTTTAAATATTTTAAATT
1 ATTTTTAAATATTTCAAATT
*
135131 A-TTTTAAATA-TTCAATTT
1 ATTTTTAAATATTTCAAATT
135149 ATTTTTA
1 ATTTTTA
135156 TGAATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 14 0.64
20 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTAAATATTTCAAATT
Found at i:142645 original size:21 final size:22
Alignment explanation
Indices: 142621--142665 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
142611 TTTATTACTA
142621 TAAAAT-AATATTTTACTTTTT
1 TAAAATAAATATTTTACTTTTT
* *
142642 TAAATTAAATATTTTAGTTTTT
1 TAAAATAAATATTTTACTTTTT
142664 TA
1 TA
142666 GATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TAAAATAAATATTTTACTTTTT
Found at i:142846 original size:15 final size:15
Alignment explanation
Indices: 142826--142876 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
142816 TTGTCTCAAA
142826 TTACATTTTAATTAC
1 TTACATTTTAATTAC
* *
142841 TTACATTTGAAATA-
1 TTACATTTTAATTAC
*
142855 TTACATTTTAATCAC
1 TTACATTTTAATTAC
142870 TTACATT
1 TTACATT
142877 ATCATGTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (15 bp):
TTACATTTTAATTAC
Found at i:143065 original size:17 final size:18
Alignment explanation
Indices: 143043--143083 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 18
143033 TATGTTTTTC
143043 TTTCCTTTTCTTCCC-AT
1 TTTCCTTTTCTTCCCAAT
143060 TTTCC--TTCTTCCCAAT
1 TTTCCTTTTCTTCCCAAT
143076 TTT-CTTTT
1 TTTCCTTTT
143084 TTTTTNNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTCCTTTTCTTCCCAAT
Found at i:145239 original size:18 final size:17
Alignment explanation
Indices: 145211--145244 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
145201 CATTCCATAT
*
145211 ATTTATTATTTTTTATC
1 ATTTATTATTTGTTATC
145228 ATTTATTTATTTGTTAT
1 ATTTA-TTATTTGTTAT
145245 TTTTTATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTATTATTTGTTATC
Found at i:145263 original size:25 final size:24
Alignment explanation
Indices: 145210--145268 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
145200 GCATTCCATA
*
145210 TATTTATTATTTTTTATCATTTATT
1 TATTT-TTATTTTTTATCATTTATG
145235 TATTTGTTATTTTTTATGC-TATT-TG
1 TATTT-TTATTTTTTAT-CAT-TTATG
145260 TATTTTTAT
1 TATTTTTAT
145269 CTTCATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.13
25 23 0.77
26 3 0.10
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.71
Consensus pattern (24 bp):
TATTTTTATTTTTTATCATTTATG
Found at i:145303 original size:16 final size:17
Alignment explanation
Indices: 145260--145311 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
145250 ATGCTATTTG
145260 TATTTTTATCTTCATTTAA
1 TATTTTTA--TTCATTTAA
*
145279 TTTTATTTATTCA-TTAA
1 TATT-TTTATTCATTTAA
*
145296 TATTTTTATTTATTTA
1 TATTTTTATTCATTTA
145312 TATGTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.25
17 10 0.36
18 4 0.14
19 3 0.11
20 4 0.14
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTTATTCATTTAA
Found at i:150004 original size:62 final size:59
Alignment explanation
Indices: 149932--150048 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
149922 TTTTATTATC
* * *
149932 TTAATATTAAAATTAATTTAATGTTTATTTTGTAGATAAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAAATTAATCTAATATTTA-TTT-T-GATAAATATTATATTAATTTAATAAGAT
* *
149994 TTAATATTAAATTTAATCTAATATTTATTTTGATAAGTATTATATTAATTTAATA
1 TTAATATTAAAATTAATCTAATATTTATTTTGATAAATATTATATTAATTTAATA
150049 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.44
60 1 0.02
61 3 0.06
62 24 0.48
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (59 bp):
TTAATATTAAAATTAATCTAATATTTATTTTGATAAATATTATATTAATTTAATAAGAT
Found at i:151591 original size:36 final size:36
Alignment explanation
Indices: 151544--151615 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
151534 GTGCCTGAGC
151544 TTAACATAGTTAAAGGATTTCGTTGGGCTCCTAAGA
1 TTAACATAGTTAAAGGATTTCGTTGGGCTCCTAAGA
151580 TTAACATAGTTAAAGGATTTCGTTGGGCTCCTAAGA
1 TTAACATAGTTAAAGGATTTCGTTGGGCTCCTAAGA
151616 CATTCTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (36 bp):
TTAACATAGTTAAAGGATTTCGTTGGGCTCCTAAGA
Found at i:172454 original size:22 final size:21
Alignment explanation
Indices: 172426--172466 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
172416 TAAATGGATA
172426 TTTAACTTTTCATCTCTCTTCC
1 TTTAACTTTTCATCT-TCTTCC
172448 TTTAACTTTTCATCTTCTT
1 TTTAACTTTTCATCTTCTT
172467 TAATTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAACTTTTCATCTTCTTCC
Found at i:172469 original size:17 final size:17
Alignment explanation
Indices: 172442--172489 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
172432 TTTTCATCTC
172442 TCTTCCTTTAACTTTTCA
1 TCTT-CTTTAACTTTTCA
*
172460 TCTTCTTTAATTTTTCA
1 TCTTCTTTAACTTTTCA
*
172477 TATTCTTGTAACT
1 TCTTCTT-TAACT
172490 AATTTTTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.58
Consensus pattern (17 bp):
TCTTCTTTAACTTTTCA
Found at i:172760 original size:21 final size:20
Alignment explanation
Indices: 172736--172779 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
172726 TTTTATCATG
* *
172736 ATGTTCATCATTATTGTTCTT
1 ATGTTCATAATT-GTGTTCTT
*
172757 ATGTTTATAATTGTGTTCTT
1 ATGTTCATAATTGTGTTCTT
172777 ATG
1 ATG
172780 ATTTTACAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (20 bp):
ATGTTCATAATTGTGTTCTT
Found at i:174092 original size:10 final size:10
Alignment explanation
Indices: 174059--174099 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
174049 TTATATTATG
174059 TTTTAAACTAT
1 TTTTAAA-TAT
*
174070 TTATAAATA-
1 TTTTAAATAT
174079 TTTTAAATAT
1 TTTTAAATAT
174089 TTTTAAA-AT
1 TTTTAAATAT
174098 TT
1 TT
174100 ATGTGACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 12 0.44
10 9 0.33
11 6 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAATAT
Done.