Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 1 of 211
Found at i:3779 original size:123 final size:121
Alignment explanation
Indices: 3611--3855 Score: 365
Period size: 116 Copynumber: 2.0 Consensus size: 121
3601 TTCACACATT
* *
3611 ACAGGTGCTCCAACTTAGTAAAGAGAACCCCAAAATTTTAGGATAGGGAAAATAAATTTTTATTA
1 ACAGATGCTCCAACTTAGTAAAGAGAACCCC-AAATTTTAGGATAGGGAAAAT-AA-----ATGA
3676 TAAAAAAGTAATTATGAAATTAACATAT-AGATGGTATACAGATAAGACA-CACCATTCAAGGG
59 T-AAAAAGTAATTATGAAATTAACATATCAGATGGTATACAGATAAGACACCACCATTCAAGGG
3738 ACAGATGCTCC-ACTTAGT-AAGAGAACCCC-AATTTTAGGATAGGGAAAATAAATGATAAAAAG
1 ACAGATGCTCCAACTTAGTAAAGAGAACCCCAAATTTTAGGATAGGGAAAATAAATGATAAAAAG
3800 TAATTATGAAATTAACATATCAGATGGTATACAGATAAGACACCACCATTCAAGGG
66 TAATTATGAAATTAACATATCAGATGGTATACAGATAAGACACCACCATTCAAGGG
3856 GATCATGAAG
Statistics
Matches: 114, Mismatches: 2, Indels: 13
0.88 0.02 0.10
Matches are distributed among these distances:
116 26 0.23
117 25 0.22
118 13 0.11
122 2 0.02
123 20 0.18
125 11 0.10
126 7 0.06
127 10 0.09
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.24
Consensus pattern (121 bp):
ACAGATGCTCCAACTTAGTAAAGAGAACCCCAAATTTTAGGATAGGGAAAATAAATGATAAAAAG
TAATTATGAAATTAACATATCAGATGGTATACAGATAAGACACCACCATTCAAGGG
Found at i:8131 original size:12 final size:12
Alignment explanation
Indices: 8111--8140 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
8101 GTTCTGCATC
8111 ATCTGCTAGATCA
1 ATCT-CTAGATCA
8124 ATCTCTAGATCA
1 ATCTCTAGATCA
8136 ATCTC
1 ATCTC
8141 ATCTTTGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (12 bp):
ATCTCTAGATCA
Found at i:27566 original size:292 final size:292
Alignment explanation
Indices: 27042--27623 Score: 1164
Period size: 292 Copynumber: 2.0 Consensus size: 292
27032 CCAAACTTTC
27042 TATATTTCCCCCTCTCATTTGATCTACAGATGTTAACTGAGCTTGTTCCTGTATGTTTTAGCTCA
1 TATATTTCCCCCTCTCATTTGATCTACAGATGTTAACTGAGCTTGTTCCTGTATGTTTTAGCTCA
27107 TTAATTGTGTTATGCAAGAAAAGCAGGTTAAAAGGTGAGATGCATGTAAAGACTACTCAAAGCAC
66 TTAATTGTGTTATGCAAGAAAAGCAGGTTAAAAGGTGAGATGCATGTAAAGACTACTCAAAGCAC
27172 GAGATAGTAGCAAAAAGAAAAGGAAAGATAAAAACAAATTGGAAGTTATATCCATCTGCAATAGC
131 GAGATAGTAGCAAAAAGAAAAGGAAAGATAAAAACAAATTGGAAGTTATATCCATCTGCAATAGC
27237 ACAAGGAGTTAGATATAGTTCCCTGGTAAAAACACATTAGCATGTCCTTTCAAATTTGCACATGA
196 ACAAGGAGTTAGATATAGTTCCCTGGTAAAAACACATTAGCATGTCCTTTCAAATTTGCACATGA
27302 TGCATTGGTAGAGAAACCTACATATCGAATTT
261 TGCATTGGTAGAGAAACCTACATATCGAATTT
27334 TATATTTCCCCCTCTCATTTGATCTACAGATGTTAACTGAGCTTGTTCCTGTATGTTTTAGCTCA
1 TATATTTCCCCCTCTCATTTGATCTACAGATGTTAACTGAGCTTGTTCCTGTATGTTTTAGCTCA
27399 TTAATTGTGTTATGCAAGAAAAGCAGGTTAAAAGGTGAGATGCATGTAAAGACTACTCAAAGCAC
66 TTAATTGTGTTATGCAAGAAAAGCAGGTTAAAAGGTGAGATGCATGTAAAGACTACTCAAAGCAC
27464 GAGATAGTAGCAAAAAGAAAAGGAAAGATAAAAACAAATTGGAAGTTATATCCATCTGCAATAGC
131 GAGATAGTAGCAAAAAGAAAAGGAAAGATAAAAACAAATTGGAAGTTATATCCATCTGCAATAGC
27529 ACAAGGAGTTAGATATAGTTCCCTGGTAAAAACACATTAGCATGTCCTTTCAAATTTGCACATGA
196 ACAAGGAGTTAGATATAGTTCCCTGGTAAAAACACATTAGCATGTCCTTTCAAATTTGCACATGA
27594 TGCATTGGTAGAGAAACCTACATATCGAAT
261 TGCATTGGTAGAGAAACCTACATATCGAAT
27624 AAAGCACTGA
Statistics
Matches: 290, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
292 290 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (292 bp):
TATATTTCCCCCTCTCATTTGATCTACAGATGTTAACTGAGCTTGTTCCTGTATGTTTTAGCTCA
TTAATTGTGTTATGCAAGAAAAGCAGGTTAAAAGGTGAGATGCATGTAAAGACTACTCAAAGCAC
GAGATAGTAGCAAAAAGAAAAGGAAAGATAAAAACAAATTGGAAGTTATATCCATCTGCAATAGC
ACAAGGAGTTAGATATAGTTCCCTGGTAAAAACACATTAGCATGTCCTTTCAAATTTGCACATGA
TGCATTGGTAGAGAAACCTACATATCGAATTT
Found at i:29031 original size:25 final size:25
Alignment explanation
Indices: 29003--29053 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
28993 CGCAAATGAA
29003 AGTCAAATAAACTTAAAGCTAGCAG
1 AGTCAAATAAACTTAAAGCTAGCAG
*
29028 AGTCAAATAAGCTTAAAGCTAGCAG
1 AGTCAAATAAACTTAAAGCTAGCAG
29053 A
1 A
29054 AAATAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.20
Consensus pattern (25 bp):
AGTCAAATAAACTTAAAGCTAGCAG
Found at i:31997 original size:16 final size:16
Alignment explanation
Indices: 31976--32008 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31966 AGCTAGTTTG
*
31976 TTTTCTAAGGTGCACC
1 TTTTCTAAGGTCCACC
31992 TTTTCTAAGGTCCACC
1 TTTTCTAAGGTCCACC
32008 T
1 T
32009 AGGTGCAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (16 bp):
TTTTCTAAGGTCCACC
Found at i:33379 original size:159 final size:160
Alignment explanation
Indices: 33085--33386 Score: 597
Period size: 159 Copynumber: 1.9 Consensus size: 160
33075 TGCTCCCCTT
33085 AAATGAAAAATATGACATCAGAATATTCTAATTTATTAGGAAAGTTATATTTAAAGTAATAAAGA
1 AAATGAAAAATATGACATCAGAATATTCTAATTTATTAGGAAAGTTATATTTAAAGTAATAAAGA
33150 AATTTTAAGAAATAAAAAATAGAACCAAATCCCAACAAAATCAGTATCATCCTCTAAAATAAACA
66 AATTTTAAGAAATAAAAAATAGAACCAAATCCCAACAAAATCAGTATCATCCTCTAAAATAAACA
33215 CGACATAATACTTTCTTATTCTAATATGGA
131 CGACATAATACTTTCTTATTCTAATATGGA
33245 AAAT-AAAAATATGACATCAGAATATTCTAATTTATTAGGAAAGTTATATTTAAAGTAATAAAGA
1 AAATGAAAAATATGACATCAGAATATTCTAATTTATTAGGAAAGTTATATTTAAAGTAATAAAGA
33309 AATTTTAAGAAATAAAAAATAGAACCAAATCCCAACAAAATCAGTATCATCCTCTAAAATAAACA
66 AATTTTAAGAAATAAAAAATAGAACCAAATCCCAACAAAATCAGTATCATCCTCTAAAATAAACA
33374 CGACATAATACTT
131 CGACATAATACTT
33387 GTGTTGGGAT
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 138 0.97
160 4 0.03
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (160 bp):
AAATGAAAAATATGACATCAGAATATTCTAATTTATTAGGAAAGTTATATTTAAAGTAATAAAGA
AATTTTAAGAAATAAAAAATAGAACCAAATCCCAACAAAATCAGTATCATCCTCTAAAATAAACA
CGACATAATACTTTCTTATTCTAATATGGA
Found at i:38053 original size:21 final size:21
Alignment explanation
Indices: 38029--38068 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38019 AAAAAAAGCT
38029 AAACCAGACACTAAAACTACC
1 AAACCAGACACTAAAACTACC
* *
38050 AAACCAGGCACTAATACTA
1 AAACCAGACACTAAAACTA
38069 GTGAACCGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.30, G:0.07, T:0.12
Consensus pattern (21 bp):
AAACCAGACACTAAAACTACC
Found at i:46161 original size:30 final size:30
Alignment explanation
Indices: 46127--46186 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
46117 TGTTTACAGA
*
46127 AAGTAAAATTAATTTTACTCAGACATCAGT
1 AAGTAAAATTAATTTTACTCAGAAATCAGT
46157 AAGTAAAATTAATTTTACTCAGAAATCAGT
1 AAGTAAAATTAATTTTACTCAGAAATCAGT
46187 CGCAATTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (30 bp):
AAGTAAAATTAATTTTACTCAGAAATCAGT
Found at i:50843 original size:25 final size:25
Alignment explanation
Indices: 50790--50848 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
50780 CTTATTTCAT
* * *
50790 TAAATAAA-AAATTTTAAAATATAA
1 TAAATAAATACATTTAAAAACATAA
50814 TAAATCAAATACATTTAAAAACATAA
1 TAAAT-AAATACATTTAAAAACATAA
50840 -AAATAAATA
1 TAAATAAATA
50849 TTAAAACAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.33
25 7 0.23
26 13 0.43
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAATACATTTAAAAACATAA
Found at i:50873 original size:19 final size:20
Alignment explanation
Indices: 50830--50873 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
50820 AAATACATTT
*
50830 AAAAACATAAAAATAAATAT
1 AAAAACATAAAAATAAATAA
* *
50850 TAAAACA-AGAAATAAATAA
1 AAAAACATAAAAATAAATAA
50869 AAAAA
1 AAAAA
50874 TGAAACTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAACATAAAAATAAATAA
Found at i:61658 original size:35 final size:35
Alignment explanation
Indices: 61612--61716 Score: 192
Period size: 35 Copynumber: 3.0 Consensus size: 35
61602 GACGAGCTTG
*
61612 CTGCTTGCGAGCTGCGCAACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
61647 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
*
61682 CTGCTTGCGAGTTGCGCGACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
61717 AGGGCTGAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (35 bp):
CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
Found at i:61715 original size:19 final size:19
Alignment explanation
Indices: 61659--61715 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
61649 GCTTGCGAGC
61659 TGCGCGACTGACTACCGAT
1 TGCGCGACTGACTACCGAT
**
61678 T--GC-ACTG-CTTGCGAGT
1 TGCGCGACTGACTACCGA-T
61694 TGCGCGACTGACTACCGAT
1 TGCGCGACTGACTACCGAT
61713 TGC
1 TGC
61716 AAGGGCTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
15 5 0.17
16 6 0.21
17 2 0.07
18 2 0.07
19 9 0.31
20 5 0.17
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (19 bp):
TGCGCGACTGACTACCGAT
Found at i:61734 original size:33 final size:34
Alignment explanation
Indices: 61630--61734 Score: 115
Period size: 35 Copynumber: 3.1 Consensus size: 34
61620 GAGCTGCGCA
* * *
61630 ACTGACTACCGATTGCACTGCTTGCGAGCTGCGCG
1 ACTGACTACCGATTGCACGGCTT-CGAGTTGAGCG
* *
61665 ACTGACTACCGATTGCACTGCTTGCGAGTTGCGCG
1 ACTGACTACCGATTGCACGGCTT-CGAGTTGAGCG
*
61700 ACTGACTACCGATTGCAAGGGC-T-GAGTTGAGCG
1 ACTGACTACCGATTGC-ACGGCTTCGAGTTGAGCG
61733 AC
1 AC
61735 GGAAAGAGGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
33 11 0.17
35 51 0.78
36 3 0.05
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.23
Consensus pattern (34 bp):
ACTGACTACCGATTGCACGGCTTCGAGTTGAGCG
Found at i:65044 original size:42 final size:42
Alignment explanation
Indices: 64983--65068 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
64973 TAAAGTTTAG
*
64983 GAAGAAATGGAAGTAATCCCTGAAAACTATCGTTTAATTAAT
1 GAAGAAATGGAAGTAATCCCTGAAAACTATCATTTAATTAAT
* *
65025 GAAGAAATGGAAGTTATCCCTGCAAACTATCATTTAATTAAT
1 GAAGAAATGGAAGTAATCCCTGAAAACTATCATTTAATTAAT
65067 GA
1 GA
65069 GCAAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (42 bp):
GAAGAAATGGAAGTAATCCCTGAAAACTATCATTTAATTAAT
Found at i:78906 original size:29 final size:30
Alignment explanation
Indices: 78847--78904 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
78837 TCCGAGCCTT
*
78847 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
78877 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
78905 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:79134 original size:13 final size:13
Alignment explanation
Indices: 79116--79147 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
79106 TTTCCAGCAA
79116 TTATGAATTTATT
1 TTATGAATTTATT
79129 TTATGAATTTATT
1 TTATGAATTTATT
*
79142 TGATGA
1 TTATGA
79148 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:80075 original size:30 final size:32
Alignment explanation
Indices: 80015--80077 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
80005 CACTTATTTT
80015 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
80048 CACCTATGCCGAATGCAACATATATATATA
1 CACCTATGCCGAATGCAACACATAAATATA
80078 CATATCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:80338 original size:41 final size:41
Alignment explanation
Indices: 80293--80489 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
80283 ACCGGCTCTT
*
80293 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
80334 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
80375 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
80416 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
80457 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
80490 TAACGATAAA
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 139 0.94
42 2 0.01
43 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:82040 original size:13 final size:13
Alignment explanation
Indices: 82022--82046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82012 CCATCGAATG
82022 CACACAAAATAAA
1 CACACAAAATAAA
82035 CACACAAAATAA
1 CACACAAAATAA
82047 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:82237 original size:50 final size:50
Alignment explanation
Indices: 82123--82364 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
82113 GGGTTGTTAC
* * * *
82123 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
82179 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
82229 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
82279 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
** *
82329 AGAACATCCCATGTAATACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
82365 TTTGGCATGT
Statistics
Matches: 164, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 28 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 38 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:82307 original size:100 final size:103
Alignment explanation
Indices: 82123--82372 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 103
82113 GGGTTGTTAC
*
82123 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
82188 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
82229 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
82291 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* * *
82329 AGAACATCCCATGTAATACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
82373 GTTATTATCA
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.39
101 38 0.29
105 2 0.02
106 39 0.30
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:92937 original size:17 final size:17
Alignment explanation
Indices: 92915--92949 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
92905 CTTTGGGCTG
* *
92915 TGATTTGAATGGGGTTT
1 TGATTTCAATGGGCTTT
92932 TGATTTCAATGGGCTTT
1 TGATTTCAATGGGCTTT
92949 T
1 T
92950 CCGGAACAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.49
Consensus pattern (17 bp):
TGATTTCAATGGGCTTT
Found at i:99872 original size:26 final size:27
Alignment explanation
Indices: 99843--99893 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
99833 GTAATGATTT
* *
99843 AATGTGATTCATTGAT-ATGCATCATG
1 AATGTGATGCATTCATAATGCATCATG
*
99869 AATGTTATGCATTCATAATGCATCA
1 AATGTGATGCATTCATAATGCATCA
99894 AATATTATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (27 bp):
AATGTGATGCATTCATAATGCATCATG
Found at i:102733 original size:18 final size:17
Alignment explanation
Indices: 102687--102735 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
102677 ATGCAACGTG
*
102687 TTATTTTTTAAATAATT
1 TTATTTTTTAAAAAATT
* *
102704 TAATTGTATTAAAAAATT
1 TTATT-TTTTAAAAAATT
102722 ATTATTTTTTAAAA
1 -TTATTTTTTAAAA
102736 GAAAATATGC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTATTTTTTAAAAAATT
Found at i:103886 original size:5 final size:5
Alignment explanation
Indices: 103876--103904 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
103866 AAGGTACTCT
103876 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
103905 TTGGTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:114584 original size:21 final size:21
Alignment explanation
Indices: 114555--114604 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
114545 AGAATAGATT
* *
114555 TAATATTTATTGTTTAAACAA
1 TAATATTTATTGTGTAAAAAA
*
114576 TATTATTTATTGTGTAAAAAA
1 TAATATTTATTGTGTAAAAAA
114597 TAATATTT
1 TAATATTT
114605 TTAAAGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (21 bp):
TAATATTTATTGTGTAAAAAA
Found at i:123128 original size:19 final size:19
Alignment explanation
Indices: 123106--123152 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
123096 AATTTAGAAT
123106 TAATAATATATATTAAAT-A
1 TAATAATATA-ATTAAATAA
*
123125 TAATAATATAATTTAATAA
1 TAATAATATAATTAAATAA
*
123144 TAAAAATAT
1 TAATAATAT
123153 CAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAATATAATTAAATAA
Found at i:123217 original size:25 final size:25
Alignment explanation
Indices: 123188--123235 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
123178 TTATAGATAG
*
123188 TTCAAATCAATTATTACCTAATTCA
1 TTCAAATCAATTATTACCAAATTCA
123213 TTCAAATCAATTATTACCAAATT
1 TTCAAATCAATTATTACCAAATT
123236 TGAATTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (25 bp):
TTCAAATCAATTATTACCAAATTCA
Found at i:130186 original size:19 final size:19
Alignment explanation
Indices: 130162--130198 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
130152 AAACACCTAA
130162 TATTTATTTATTAAGTATT
1 TATTTATTTATTAAGTATT
130181 TATTTATTTATTAAGTAT
1 TATTTATTTATTAAGTAT
130199 GCAAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TATTTATTTATTAAGTATT
Found at i:164733 original size:28 final size:28
Alignment explanation
Indices: 164701--164756 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
164691 CATCATTTTA
*
164701 TGTGTATAATCACACTAAATCAAAATTT
1 TGTGTATAATCACAATAAATCAAAATTT
* *
164729 TGTGTATAATTACAATAAATTAAAATTT
1 TGTGTATAATCACAATAAATCAAAATTT
164757 CATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (28 bp):
TGTGTATAATCACAATAAATCAAAATTT
Found at i:164764 original size:28 final size:28
Alignment explanation
Indices: 164705--164765 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
164695 ATTTTATGTG
* ** *
164705 TATAATCACACTAAATCAAAATTTTGTG
1 TATAATCACAATAAATCAAAATTTCATA
* *
164733 TATAATTACAATAAATTAAAATTTCATA
1 TATAATCACAATAAATCAAAATTTCATA
164761 TATAA
1 TATAA
164766 AATTGTATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (28 bp):
TATAATCACAATAAATCAAAATTTCATA
Found at i:167212 original size:28 final size:29
Alignment explanation
Indices: 167163--167226 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
167153 ATGTCACACC
167163 AATAAATTTAAAAGTGTTAAAAATAGAAG
1 AATAAATTTAAAAGTGTTAAAAATAGAAG
* *
167192 AATAATTTTAAAA-T-TTAAAAAGTAGAGG
1 AATAAATTTAAAAGTGTTAAAAA-TAGAAG
167220 AACTAAA
1 AA-TAAA
167227 ATCCTGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 7 0.23
28 8 0.27
29 15 0.50
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.28
Consensus pattern (29 bp):
AATAAATTTAAAAGTGTTAAAAATAGAAG
Found at i:174163 original size:18 final size:19
Alignment explanation
Indices: 174131--174169 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
174121 TAGTTCTTTT
174131 TTTTCCTATTATATTAGTA
1 TTTTCCTATTATATTAGTA
*
174150 TTTT-CTATTCTATTAGTA
1 TTTTCCTATTATATTAGTA
174168 TT
1 TT
174170 AGATTAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTCCTATTATATTAGTA
Found at i:175290 original size:19 final size:19
Alignment explanation
Indices: 175263--175302 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
175253 CAAATGAAAA
175263 TTAAAAATT-TTTAAATAAT
1 TTAAAAATTATTT-AATAAT
*
175282 TTAATAATTATTTAATAAT
1 TTAAAAATTATTTAATAAT
175301 TT
1 TT
175303 TTTAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAAAATTATTTAATAAT
Found at i:176933 original size:63 final size:62
Alignment explanation
Indices: 176817--176945 Score: 163
Period size: 63 Copynumber: 2.1 Consensus size: 62
176807 TGCACTTAAC
* * *
176817 AAATTGGCATGAATAAATCAATATGTAAATCCCACTTCGACCTGACTTCCAAAAATTATCTTA
1 AAATCGGCATGAAGAAATCAATATGTAAATCCCACTTCGACCTAACTTCC-AAAATTATCTTA
* * *
176880 AAATCGGCATGAAGAAATCAATACT-TAAATCCGACTTTGACAC-AACTTTCAAAATTATCTTA
1 AAATCGGCATGAAGAAATCAATA-TGTAAATCCCACTTCGAC-CTAACTTCCAAAATTATCTTA
176942 AAAT
1 AAAT
176946 TTGTAGACCG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
62 16 0.28
63 40 0.69
64 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.29
Consensus pattern (62 bp):
AAATCGGCATGAAGAAATCAATATGTAAATCCCACTTCGACCTAACTTCCAAAATTATCTTA
Found at i:186498 original size:18 final size:19
Alignment explanation
Indices: 186477--186514 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
186467 TAATTTTTCT
*
186477 AAAATTTTAAATAT-ATTA
1 AAAATGTTAAATATAATTA
*
186495 AAAATGTTAAGTATAATTA
1 AAAATGTTAAATATAATTA
186514 A
1 A
186515 TTTTAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATGTTAAATATAATTA
Found at i:186537 original size:23 final size:26
Alignment explanation
Indices: 186483--186542 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 26
186473 TTCTAAAATT
186483 TTAAATATATTAAAAATGTTAAGTATAA
1 TTAAAT-T-TTAAAAATGTTAAGTATAA
* *
186511 TT-AATTTTAAAAGT-TTAA-TATAT
1 TTAAATTTTAAAAATGTTAAGTATAA
186534 TTAAATTTT
1 TTAAATTTT
186543 TAATATACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 6 0.21
24 10 0.34
25 7 0.24
26 1 0.03
27 3 0.10
28 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (26 bp):
TTAAATTTTAAAAATGTTAAGTATAA
Found at i:186538 original size:17 final size:17
Alignment explanation
Indices: 186516--186554 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
186506 TATAATTAAT
186516 TTTAAAAGTTTAATATA
1 TTTAAAAGTTTAATATA
**
186533 TTTAAATTTTTAATATA
1 TTTAAAAGTTTAATATA
*
186550 CTTAA
1 TTTAA
186555 TACATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTAAAAGTTTAATATA
Found at i:186617 original size:18 final size:18
Alignment explanation
Indices: 186594--186635 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
186584 AAATTTTCTT
* *
186594 AATATATTTAAAATTTTA
1 AATATATTAAAAATGTTA
186612 AATATATTAAAAATGTTA
1 AATATATTAAAAATGTTA
*
186630 AGTATA
1 AATATA
186636 ACTAATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
AATATATTAAAAATGTTA
Found at i:186657 original size:41 final size:41
Alignment explanation
Indices: 186476--186660 Score: 119
Period size: 41 Copynumber: 4.4 Consensus size: 41
186466 TTAATTTTTC
*
186476 TAAAATTTTAAATATATTAAAAATGTTAAGTATAATTAATTT
1 TAAAATTTT-AATATATTAAAAATGTTAAGTATAACTAATTT
* * * * * *
186518 TAAAAGTTTAATATATTTAAATTTTTAATATACTTAATACATATTTT
1 TAAAATTTTAATATATTAAAAATGTTAA-GTA--T-A-AC-TAATTT
* * * * ** **
186565 TAATATTTAAAGACAAAAAAAAT-TT-TCT-TAA-T-ATATT
1 TAAAATTTTAATATATTAAAAATGTTAAGTATAACTAAT-TT
186602 TAAAATTTTAAATATATTAAAAATGTTAAGTATAACTAATTT
1 TAAAATTTT-AATATATTAAAAATGTTAAGTATAACTAATTT
186644 TAAAATTTTAATATATT
1 TAAAATTTTAATATATT
186661 CAATATATAT
Statistics
Matches: 103, Mismatches: 27, Indels: 27
0.66 0.17 0.17
Matches are distributed among these distances:
36 1 0.01
37 10 0.10
38 10 0.10
39 3 0.03
40 2 0.02
41 28 0.27
42 22 0.21
43 2 0.02
44 2 0.02
45 1 0.01
46 3 0.03
47 19 0.18
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (41 bp):
TAAAATTTTAATATATTAAAAATGTTAAGTATAACTAATTT
Found at i:186681 original size:13 final size:13
Alignment explanation
Indices: 186665--186692 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
186655 TATATTCAAT
186665 ATATATTTTAAAA
1 ATATATTTTAAAA
186678 ATATATTTTAAAA
1 ATATATTTTAAAA
186691 AT
1 AT
186693 TTAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATTTTAAAA
Found at i:186682 original size:15 final size:14
Alignment explanation
Indices: 186662--186690 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
186652 TAATATATTC
186662 AATATATATTTTAA
1 AATATATATTTTAA
186676 AA-ATATATTTTAA
1 AATATATATTTTAA
186689 AA
1 AA
186691 ATTTAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.87
14 2 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATATATTTTAA
Found at i:186758 original size:17 final size:17
Alignment explanation
Indices: 186735--186803 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
186725 GAGAGAAGAT
*
186735 TTTTTAATATATTTAAAA
1 TTTTAAATATA-TTAAAA
* *
186753 TTTTAAAAATTTTACAAA
1 TTTTAAATATATTA-AAA
**
186771 AATTAAATATATTAAAA
1 TTTTAAATATATTAAAA
*
186788 TTTTAAATATGTTAAA
1 TTTTAAATATATTAAA
186804 GAAAATGTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
17 19 0.47
18 21 0.52
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTTAAATATATTAAAA
Found at i:186809 original size:36 final size:36
Alignment explanation
Indices: 186740--186809 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
186730 AAGATTTTTT
* *
186740 AATATATTTAAAATTTTAAAAATTTTACAAAAATTA
1 AATATATTTAAAATTTTAAAAATGTTAAAAAAATTA
*
186776 AATATA-TTAAAATTTTAAATATGTTAAAGAAAAT
1 AATATATTTAAAATTTTAAAAATGTTAAA-AAAAT
186810 GTTGAGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (36 bp):
AATATATTTAAAATTTTAAAAATGTTAAAAAAATTA
Found at i:186881 original size:17 final size:17
Alignment explanation
Indices: 186826--186888 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
186816 TATAACCGAT
*
186826 TTAAAATTTTTAATATA
1 TTAAAATTTTAAATATA
*
186843 CTTAATATATTTAAATATA
1 -TTAAAAT-TTTAAATATA
* *
186862 TTAAAATTTTGAACATA
1 TTAAAATTTTAAATATA
186879 TTAAAATTTT
1 TTAAAATTTT
186889 TTTAAGTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
17 18 0.46
18 12 0.31
19 9 0.23
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (17 bp):
TTAAAATTTTAAATATA
Found at i:188601 original size:32 final size:32
Alignment explanation
Indices: 188552--188613 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
188542 GGCATAAATG
*
188552 TATATATATTATAAATATTTAAAGTTAAAAAA
1 TATATATATTATAAATATTAAAAGTTAAAAAA
188584 TATATAATATTAT-AATATTAAAAGTTAAAA
1 TATAT-ATATTATAAATATTAAAAGTTAAAA
188614 GTTTAAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (32 bp):
TATATATATTATAAATATTAAAAGTTAAAAAA
Found at i:189199 original size:36 final size:36
Alignment explanation
Indices: 189154--189257 Score: 199
Period size: 36 Copynumber: 2.9 Consensus size: 36
189144 GAGATATTAA
*
189154 ATGAGATTGAATTGTGTTGTATTGATGAATTTACAT
1 ATGAAATTGAATTGTGTTGTATTGATGAATTTACAT
189190 ATGAAATTGAATTGTGTTGTATTGATGAATTTACAT
1 ATGAAATTGAATTGTGTTGTATTGATGAATTTACAT
189226 ATGAAATTGAATTGTGTTGTATTGATGAATTT
1 ATGAAATTGAATTGTGTTGTATTGATGAATTT
189258 TAATTGTTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (36 bp):
ATGAAATTGAATTGTGTTGTATTGATGAATTTACAT
Found at i:189482 original size:24 final size:23
Alignment explanation
Indices: 189455--189501 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
189445 ATTGAAATAG
189455 ATTGATTTAGTATGTGA-TGAATTT
1 ATTGATTTA-TAT-TGATTGAATTT
189479 ATTGATTTATATTGATTGAATTT
1 ATTGATTTATATTGATTGAATTT
189502 GTATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.14
23 10 0.45
24 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (23 bp):
ATTGATTTATATTGATTGAATTT
Found at i:189701 original size:41 final size:40
Alignment explanation
Indices: 189656--189787 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 40
189646 CGACTTCGAG
189656 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
* *
189696 TTCGATGAGGCACTGGGTG-CTAA--T-TTACTTCGGTTTAA
1 -TCGATGAGACACTGGGTGTC-AATTTATTACTTCGGATTAA
* ** *
189734 CCGATGAGACACTATGTGTCAATTTATTACTTCGAATT-A
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
*
189773 TCTGATGAGGCACTG
1 TC-GATGAGACACTG
189788 CATGCCAAAC
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
37 16 0.22
38 14 0.19
39 4 0.05
40 21 0.28
41 19 0.26
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
Found at i:189758 original size:37 final size:38
Alignment explanation
Indices: 189657--189759 Score: 111
Period size: 37 Copynumber: 2.7 Consensus size: 38
189647 GACTTCGAGT
*
189657 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAA--T-TTACTTCGGATTAATC
* *
189698 CGATGAGGCACTGGGTG-CTAATTTACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTC-AATTTACTTCGGATTAATC
**
189735 CGATGAGACACTATGTGTCAATTTA
1 CGATGAGACACTGGGTGTCAATTTA
189760 TTACTTCGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
37 20 0.37
38 14 0.26
39 1 0.02
40 1 0.02
41 18 0.33
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAATTTACTTCGGATTAATC
Found at i:190614 original size:31 final size:31
Alignment explanation
Indices: 190578--190652 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
190568 TTTTGTGTTG
*
190578 CTTATTGTTAAAGATTGTAAGGAATGGTAAA
1 CTTATTGTTAAAGATTGCAAGGAATGGTAAA
* * *
190609 CTTATTGTTCAAGCTTGCAGGGAATGGTAAA
1 CTTATTGTTAAAGATTGCAAGGAATGGTAAA
*
190640 CTTCTTGTTAAAG
1 CTTATTGTTAAAG
190653 TTTTTACTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (31 bp):
CTTATTGTTAAAGATTGCAAGGAATGGTAAA
Found at i:209099 original size:31 final size:31
Alignment explanation
Indices: 209064--209133 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
209054 CTACAAAATG
209064 GTTATTGAACCATTCGAAAATTTTCATTTAA
1 GTTATTGAACCATTCGAAAATTTTCATTTAA
* *
209095 GTTATTGAACTATTCGAAAATTTTTATTTAA
1 GTTATTGAACCATTCGAAAATTTTCATTTAA
209126 GTTATTGA
1 GTTATTGA
209134 GTTGTTAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (31 bp):
GTTATTGAACCATTCGAAAATTTTCATTTAA
Found at i:226983 original size:172 final size:171
Alignment explanation
Indices: 226681--226989 Score: 469
Period size: 172 Copynumber: 1.8 Consensus size: 171
226671 AATGTCATTG
* * *
226681 ACAATACATGACATAAAATCAAATAATTCTTGTACTGAAATAAATACTAAATCGTAAAACATCCA
1 ACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCGTAAAACAACCA
*
226746 ACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAACTATGGAACTCAAACCCAAGATAACTGC
66 ACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTGC
226811 AGACATGGAGGAGAAACATGAACACAACATGTATGCCACTA
131 AGACATGGAGGAGAAACATGAACACAACATGTATGCCACTA
* * * * *
226852 ACAATACATGACAATACAATCAAAGAATGTC-TGTACTGAAATAAAGACTAAATCTTCAGATAAC
1 ACAATACATGAC-ATAAAATCAAAGAAT-TCTTGTACTGAAATAAAGACTAAATCGTAAAACAAC
** *
226916 CAACTGTCTTTCGATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCC-AGATAAC
64 CAACCATCTTTCGATT-TCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAAC
226980 TGCAGACATG
128 TGCAGACATG
226990 TCATAGAAAC
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
171 12 0.10
172 71 0.58
173 40 0.33
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (171 bp):
ACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCGTAAAACAACCA
ACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTGC
AGACATGGAGGAGAAACATGAACACAACATGTATGCCACTA
Found at i:227218 original size:148 final size:147
Alignment explanation
Indices: 226862--227278 Score: 534
Period size: 148 Copynumber: 2.8 Consensus size: 147
226852 ACAATACATG
* * **
226862 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTAAATCTTCAGATAACCAACTGTCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTGAATCTTCACATAACCAACCATCTTT
* * *
226927 CGATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAGACATGTC
66 CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAAACACGTC
*
226992 ATAGAAACACGCCACCA
131 ATACAAACACGCCACCA
* * *
227009 ACAACACAATCAAAGAACGTCTGTACTGAAATAAAGACTGTATCTTCACATAACCAACCATCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTGAATCTTCACATAACCAACCATCTTT
* * * *
227074 CGGTTATCTCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCATATCA-TAG-AAACACGA
66 CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACT-GCAAACACG-
* * * *
227137 ATACA-ACATATATGCCACTA
129 -T-CATACAAACACGCCACCA
* * * * * *
227157 ACAATACAATCAAAGAATGTCCGTACTGAATTGAAGACTGCATCTTCACATAACCACCCATCTCT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTGAATCTTCACATAACCAACCATCTTT
* *
227222 CGATTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCTAACCCAGATAACTGCA
66 CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCA
227279 GACAACTGAG
Statistics
Matches: 231, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
146 6 0.03
147 106 0.46
148 115 0.50
149 4 0.02
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (147 bp):
ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTGAATCTTCACATAACCAACCATCTTT
CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAAACACGTC
ATACAAACACGCCACCA
Found at i:227548 original size:164 final size:163
Alignment explanation
Indices: 227321--227741 Score: 553
Period size: 164 Copynumber: 2.6 Consensus size: 163
227311 CACATGAATA
* * *
227321 ATGCCACCAACAATACATGACAATAAAATCAAAGAATGCCCATACTGCAATAAAGACTAAATCTT
1 ATGCCACCAACAATACACGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* ** * *
227386 CACACATCCATCTGACTTTCAATCAGTCAAACTAAAATACTACAGAACACAAACCTGAGACA-AA
66 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAATACTACAGAACAAAAACCCGAGACACAA
* **
227450 CAG-CGACTTGTCGGAG-GAACATGAACACAACATAT
131 CAGAC-ACAT-T-GGAGAG-ACACCAACACAACATAT
* * *
227485 ATGCCACCAACAATACACAACAATAAAATCAAGGAATGCCTATACTACAATAAAGATTAAATCTT
1 ATGCCACCAACAATACACGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* *
227550 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAGTACTACAGAACAAAAACCCGAGACAGCC
66 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAATACTACAGAACAAAAACCCGAGACA-CA
**
227615 ACAGACACATTGGAGAGACACCAACATGACATAT
130 ACAGACACATTGGAGAGACACCAACACAACATAT
* *
227649 ATGTCACCAACAATACACGACAATAAAATCAAAGAAAGCCTATACTACAATAAAGACTAAAT-TT
1 ATGCCACCAACAATACACGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* * *
227713 CCATATATACAACCAACTTTCAATCAGTC
66 -CACACATCCAACCAACTTTCAATCAGTC
227742 GGAGGAACAT
Statistics
Matches: 226, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
163 2 0.01
164 214 0.95
165 2 0.01
166 7 0.03
167 1 0.00
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19
Consensus pattern (163 bp):
ATGCCACCAACAATACACGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
CACACATCCAACCAACTTTCAATCAGTCAAACTAAAATACTACAGAACAAAAACCCGAGACACAA
CAGACACATTGGAGAGACACCAACACAACATAT
Found at i:236622 original size:12 final size:11
Alignment explanation
Indices: 236591--236615 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
236581 AGTGAATCTA
236591 GGGAATTTTTT
1 GGGAATTTTTT
236602 GGGAATTTTTT
1 GGGAATTTTTT
236613 GGG
1 GGG
236616 GTATTTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (11 bp):
GGGAATTTTTT
Found at i:236693 original size:14 final size:14
Alignment explanation
Indices: 236674--236700 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
236664 CTTTATGAGG
236674 GTCAAATTTTATGT
1 GTCAAATTTTATGT
236688 GTCAAATTTTATG
1 GTCAAATTTTATG
236701 GAATATGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (14 bp):
GTCAAATTTTATGT
Found at i:238132 original size:15 final size:16
Alignment explanation
Indices: 238105--238139 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
238095 AATTGGGCTG
*
238105 GAAAAATACGAAACAA
1 GAAAAATACGAAAAAA
238121 GAAAAATA-GAAAAAA
1 GAAAAATACGAAAAAA
238136 GAAA
1 GAAA
238140 TTTTTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (16 bp):
GAAAAATACGAAAAAA
Found at i:244182 original size:268 final size:268
Alignment explanation
Indices: 243417--244217 Score: 1194
Period size: 259 Copynumber: 3.0 Consensus size: 268
243407 TGGTTGTCAT
* * *
243417 CCCACTTCGGTAAAATCCGGGATTGCGTATGCTCTTTACATTCAAGTCAGCTTTAAGTTGGATTC
1 CCCACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCGAGTCAGCTTTAAGTTGGA-TC
*
243482 C-GTTATATTGTTGTTGTTGTTGTTGTTATTGCATGTTCGAGTTTATCAC-ATGATAGGCTATTA
65 CTGTTATA------TTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACAAT-ATAGGCTATTA
*
243545 TATTATCTGCATATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCT
123 TATTATCTGCCTATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCT
* *
243610 TTGTTGTAGTTTTCAGGGGATAAGCCTGCTCATTTGGAGGAACTCAGGTTGCAACCGGTTGATCC
188 TTGTTGTAGTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCC
*
243675 AAATGATGTAAGGAAA
253 AAATGATGTAAGGAAG
* * * *
243691 CCTACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACGTTCGAGTCAGCATTAAGTTGGATTC
1 CCCACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCGAGTCAGCTTTAAGTTGGATCC
**
243756 TG-TA-A----TA---TTGTTATTGCATGTTCGAGTTTATCACACGATAGGCTATTATATTATCT
66 TGTTATATTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACAATATAGGCTATTATATTATCT
* *
243812 GCCTATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCGAAGTTCTCCCCCTTTGTTGTA
131 GCCTATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGTA
243877 GTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATG
196 GTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATG
243942 TAAGGAAG
261 TAAGGAAG
* ** * *
243950 CCCACATTGGTTAAATTTGGGATTGCGTATGCTCTTTACATTTGAGTCAGTTTTAAGTTGGATCC
1 CCCACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCGAGTCAGCTTTAAGTTGGATCC
* *
244015 TGTTATATTGTTATTGTTGTTATTGCATGTTTGAGTTTATCACAATATAGGCGATTATATTATCT
66 TGTTATATTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACAATATAGGCTATTATATTATCT
* *
244080 ACCTATGGAGGTCTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCC-TTATTGT
131 GCCTATGGAGGT-TTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGT
**
244144 AGTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCTGAATGAT
195 AGTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGAT
244209 GTAAGGAAG
260 GTAAGGAAG
244218 GACCAAAAAT
Statistics
Matches: 480, Mismatches: 35, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
259 236 0.49
260 2 0.00
261 1 0.00
262 1 0.00
265 2 0.00
268 134 0.28
269 42 0.09
272 1 0.00
273 4 0.01
274 57 0.12
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (268 bp):
CCCACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCGAGTCAGCTTTAAGTTGGATCC
TGTTATATTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACAATATAGGCTATTATATTATCT
GCCTATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGTA
GTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATG
TAAGGAAG
Found at i:258577 original size:67 final size:67
Alignment explanation
Indices: 258469--258598 Score: 260
Period size: 67 Copynumber: 1.9 Consensus size: 67
258459 CATTCACAGC
258469 CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAATA
1 CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAATA
258534 TT
66 TT
258536 CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAA
1 CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAA
258599 ATGAATATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (67 bp):
CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAATA
TT
Found at i:261313 original size:21 final size:21
Alignment explanation
Indices: 261272--261313 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
261262 ATATTTTTTA
*
261272 TAAAAATTAAAATAATCATTT
1 TAAAAATTAAAATAATAATTT
261293 TAAAAAGTTAAAAT-ATAATTT
1 TAAAAA-TTAAAATAATAATTT
261314 AATAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAAATTAAAATAATAATTT
Found at i:263967 original size:12 final size:12
Alignment explanation
Indices: 263952--263978 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
263942 ACAATTAGAA
263952 TTCTCTATTAAT
1 TTCTCTATTAAT
263964 TTCTCTATTAAT
1 TTCTCTATTAAT
263976 TTC
1 TTC
263979 AAGTTGACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (12 bp):
TTCTCTATTAAT
Found at i:265886 original size:192 final size:194
Alignment explanation
Indices: 265547--265998 Score: 515
Period size: 193 Copynumber: 2.3 Consensus size: 194
265537 TTATAATTCC
* ** * *
265547 CAAAGATGAAAAAAAAATCAGTTTAATCCTTTTAAAATTCTAAAAT-A-AA-TATATAAAA-ATA
1 CAAAGAT--AAAAAAATTCAGTTTAATCCCCTTAAAATTCGAAAATAACAAGCATATAAAAGAT-
** * * *
265608 AAATTTTACTTTTGACCCCTTAAAATTTTCATAATATACTTTTGGCCCCTCAAAAGGCAAATTAT
63 AAA--CCACTTTTGACCCATTAAAAGTTTCATAATATACTTTTAGCCCCTCAAAAGGCAAATTAT
* ** *
265673 CAATTTAGTCCCTTGAAGTTTTTAATATTATATTTTAATTT-AATAGTAAAAATACACTTTGACC
126 CAATTTAGTCCCTTGAAGTTTTTAAAATTATAAGTTAATTTAAATAGTAAAAATACACTTTGACA
265737 TCCA
191 TCCA
* * * * *
265741 TAGAGATGAAAAATTTCAGTTTAATCCCCTTAAAATTCGAAAATAACAAGCATGTACAAAGATAA
1 CAAAGATAAAAAAATTCAGTTTAATCCCCTTAAAATTCGAAAATAACAAGCATATA-AAAGATAA
* * * * *
265806 ACCACTTTTGACCCATT-AAAGTTTCATAATTTATTTTTAG-CCC-CAAAAGGGGAAATTGTCAT
65 ACCACTTTTGACCCATTAAAAGTTTCATAATATACTTTTAGCCCCTCAAAA-GGCAAATTATCAA
* * *
265868 TTTAGTCCCTTTAAGTTTTTAAAATTATAAGTTAATTTAAATGGTAAAAATACACTTTGGCATCC
129 TTTAGTCCCTTGAAGTTTTTAAAATTATAAGTTAATTTAAATAGTAAAAATACACTTTGACATCC
*
265933 C
194 A
* *
265934 CAAAGATAAAAAAATTCAGTTTAATCCCTTTAAAATTCTAAAATAACAAGCATATAAAAGATAAA
1 CAAAGATAAAAAAATTCAGTTTAATCCCCTTAAAATTCGAAAATAACAAGCATATAAAAGATAAA
265999 ATTATACTTT
Statistics
Matches: 216, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
191 5 0.02
192 87 0.40
193 92 0.43
194 20 0.09
195 4 0.02
196 6 0.03
197 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (194 bp):
CAAAGATAAAAAAATTCAGTTTAATCCCCTTAAAATTCGAAAATAACAAGCATATAAAAGATAAA
CCACTTTTGACCCATTAAAAGTTTCATAATATACTTTTAGCCCCTCAAAAGGCAAATTATCAATT
TAGTCCCTTGAAGTTTTTAAAATTATAAGTTAATTTAAATAGTAAAAATACACTTTGACATCCA
Found at i:269043 original size:31 final size:31
Alignment explanation
Indices: 269006--269082 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
268996 TAAGTTTACA
*
269006 TTTTAATTTAAGTTACTAAATTATTCGAAAG
1 TTTTAATTTAAGTCACTAAATTATTCGAAAG
*
269037 TTTTAATTGAAGTCACTAAATTATTCGAAAG
1 TTTTAATTTAAGTCACTAAATTATTCGAAAG
*
269068 TTTTTATTTAAGTCA
1 TTTTAATTTAAGTCA
269083 TCAGGCTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (31 bp):
TTTTAATTTAAGTCACTAAATTATTCGAAAG
Found at i:270728 original size:30 final size:30
Alignment explanation
Indices: 270689--270745 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
270679 TTTTATAAAT
*
270689 AATTAATATTT-ATTTATTTAAAATATTTAA
1 AATTAATATTTCATATA-TTAAAATATTTAA
*
270719 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
270746 AACAACAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:272007 original size:5 final size:5
Alignment explanation
Indices: 271997--272030 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
271987 TTACTTACTG
271997 TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
272031 TTACAAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:294377 original size:5 final size:5
Alignment explanation
Indices: 294369--294400 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
294359 AAAAATAAAA
294369 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
294401 CGATAGTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:295312 original size:42 final size:40
Alignment explanation
Indices: 295254--295388 Score: 128
Period size: 42 Copynumber: 3.2 Consensus size: 40
295244 TAGATGTTAC
*
295254 TTAGTATTATTGTTAGTAAAAAACTAGTATTATTATTATGG
1 TTAGTATTATTTTTAGTAAAAAACTA-TATTATTATTATGG
** * *
295295 TTAGTTATTATTTTTAGTAAAACCCTA-ATTATTATTGTTAG
1 TTAG-TATTATTTTTAGTAAAAAACTATATTATTATT-ATGG
* * *
295336 TTAGTATTATTTTGAGTATAAAACTATTATTATTGTTATTGTG
1 TTAGTATTATTTTTAGTAAAAAACTA-TATTATTATTA-TG-G
295379 TTAGTTATTA
1 TTAG-TATTA
295389 GGGTTAGTGG
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
40 27 0.36
41 10 0.13
42 28 0.37
43 5 0.07
44 5 0.07
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.51
Consensus pattern (40 bp):
TTAGTATTATTTTTAGTAAAAAACTATATTATTATTATGG
Found at i:296116 original size:51 final size:51
Alignment explanation
Indices: 296041--296144 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
296031 TTGATGTGGT
296041 TGGTGGTGAAGAAGAAGGTGGTAGCGATCATTGGGATGAAGAGGTCGATAG
1 TGGTGGTGAAGAAGAAGGTGGTAGCGATCATTGGGATGAAGAGGTCGATAG
296092 TGGTGGTGAAGAAGAAGGTGGTAGCGATCATTGGGATGAAGAGGTCGATAG
1 TGGTGGTGAAGAAGAAGGTGGTAGCGATCATTGGGATGAAGAGGTCGATAG
296143 TG
1 TG
296145 ACGTTGATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.29, C:0.06, G:0.43, T:0.22
Consensus pattern (51 bp):
TGGTGGTGAAGAAGAAGGTGGTAGCGATCATTGGGATGAAGAGGTCGATAG
Found at i:296132 original size:27 final size:27
Alignment explanation
Indices: 296051--296133 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
296041 TGGTGGTGAA
296051 GAAGAAGGTGGTAGCGATCATTGGGAT
1 GAAGAAGGTGGTAGCGATCATTGGGAT
* ** *
296078 GAAG-AGGTCGATA--G-T-GGTGGTGAA
1 GAAGAAGGT-GGTAGCGATCATTGG-GAT
296102 GAAGAAGGTGGTAGCGATCATTGGGAT
1 GAAGAAGGTGGTAGCGATCATTGGGAT
296129 GAAGA
1 GAAGA
296134 GGTCGATAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
23 3 0.07
24 10 0.24
25 5 0.12
26 5 0.12
27 15 0.37
28 3 0.07
ACGTcount: A:0.31, C:0.06, G:0.42, T:0.20
Consensus pattern (27 bp):
GAAGAAGGTGGTAGCGATCATTGGGAT
Found at i:301979 original size:9 final size:9
Alignment explanation
Indices: 301965--302004 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
301955 GTTAAACGAA
301965 TCGAGTTAT
1 TCGAGTTAT
301974 TCGAGTTAT
1 TCGAGTTAT
*
301983 TCGAGTTAA
1 TCGAGTTAT
301992 TCGAGTTAT
1 TCGAGTTAT
302001 TCGA
1 TCGA
302005 ATCAACTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:302335 original size:30 final size:31
Alignment explanation
Indices: 302301--302360 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
302291 AAACCTTTTA
*
302301 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
302331 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
302361 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:303995 original size:293 final size:294
Alignment explanation
Indices: 303365--304539 Score: 1383
Period size: 293 Copynumber: 3.9 Consensus size: 294
303355 TGCCATTTAT
303365 TCGTATTATTTTTCTCGAATTTTATTA-TTTTAAATAAAAATATATTATTTTCGTATTTTATTAT
1 TCGTATTA-TTTTCTCGAATTTTATTACTTTT-AATAAAAATATATTATTTTCGTATTTTATTAT
* * * * * * *
303429 TTTACATTATTTTAGTAAATTATGTTTG---CA-GTGTATTAATTATTTCT--TTTTTCTAAAAA
64 TTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTT-T--AAA
* * *
303488 AAAGTTAGTAAAAAAC-CTTATTTCGGCCATTTGTTCGTATTTTTTTC-CCGAATTTTATTACTT
126 AAATTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAC-T
* * * * * * * * *
303551 TCAATAAAAATAT-ATTATTTCTGTATTTTTAAAAATTATTTC-TGAATTTTATTACTTTCA-AT
190 T---TAAAAATATCATAATTTC--TAATTTT-ATAATT-TTACAT-TATTTCAGTACATT-ATGT
* * * * *
303613 AT-AAATTT-TTAAAAATTTAGTGTAAAAAAACCCTTATTTCTGTCCTTTGC
246 TTGAAATTTATT---AATTTAGTGTATAAAAACCTTTATTCCTGCCCTTTGC
* *
303663 TCGTATAATTTTCCCGAATTTTATTACTTTTAATAAAAATATATTATTTTCGTATTTTATTATTT
1 TCGTATTATTTTCTCGAATTTTATTACTTTTAATAAAAATATATTATTTTCGTATTTTATTATTT
* *
303728 TATATTATTTCAGTACATTTTTTTTGAAATATTTGTATTCATTATTTCTGAATTTTTAAAAAATT
66 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATT
* *
303793 TAGTAAAAGACTCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
131 TAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
*
303858 ATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTAAT
196 ATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAATTTATTAAT
303923 TTAGTGT-TAAAAACCTTTATTCCTGCCCTTTGC
261 TTAGTGTATAAAAACCTTTATTCCTGCCCTTTGC
* * *
303956 TCGTATTATTTTCTCAAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATATTATTATTT
1 TCGTATTATTTTCTCGAATTTTATTACTTTTAATAAAAATATATTATTTTCGTATTTTATTATTT
* *
304021 TATATTATTTCAGTATATTTTGTTTGAAATATTTGTATTCATTATTTCTGAATTTTTAAAAAATT
66 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATT
* * *
304086 TAGTAAAATACTCTTACTTCGGCCCTTTGTTCATA-TTTTTTCTCCGCATTTTATTACTTTAAAA
131 TAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTT-AAA
* *
304150 AATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTAAAATTTATTAA
195 AATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAATTTATTAA
* *
304215 TTTAGTGTATTTTTTAAATTAATTTAGTGTAAAAAAAATCTTTATTCCTGCCCTTTAC
260 TTTAGTG-----------------TA---T---AAAAACCTTTATTCCTGCCCTTTGC
304273 TCGTATTATTTTCTCGAATTTTATTACTTTTAATAAAAATATATTATTTTCGTATTTTATTATTT
1 TCGTATTATTTTCTCGAATTTTATTACTTTTAATAAAAATATATTATTTTCGTATTTTATTATTT
* * *
304338 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTAAAAAAAAT
66 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATT
*
304403 TAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
131 TAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
* * * * * *
304468 ATACCGTAATTTTTAATTTTATTATTTTACATTGTTTTAGTACATTATGTTTGAAATTTATTAAT
196 ATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAATTTATTAAT
304533 TTAGTGT
261 TTAGTGT
304540 GTTTTTTAAA
Statistics
Matches: 775, Mismatches: 62, Indels: 78
0.85 0.07 0.09
Matches are distributed among these distances:
292 25 0.03
293 252 0.33
294 11 0.01
295 14 0.02
296 12 0.02
297 80 0.10
298 20 0.03
299 7 0.01
300 19 0.02
301 46 0.06
302 14 0.02
303 4 0.01
310 1 0.00
314 1 0.00
317 244 0.31
318 25 0.03
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (294 bp):
TCGTATTATTTTCTCGAATTTTATTACTTTTAATAAAAATATATTATTTTCGTATTTTATTATTT
TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATT
TAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
ATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAATTTATTAAT
TTAGTGTATAAAAACCTTTATTCCTGCCCTTTGC
Found at i:304141 original size:160 final size:158
Alignment explanation
Indices: 303947--304524 Score: 578
Period size: 157 Copynumber: 3.7 Consensus size: 158
303937 CTTTATTCCT
* *
303947 GCCCTTTGCTCGTATTATTTTCTCAAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATA
1 GCCCTTTGCTCGTATTATTTTCTCGAATTTTATTACTTT-AATAAAAATATATTATTTTCGTATT
*
304012 TTATTATTTTATATTATTTCAGTATATTTTGTTTGAAATATTTGTATTCATTATTTCTGAATTTT
65 TTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATT-ATTATTTCTGAATTTT
*
304077 TAAAAAATTTAGTAAAATACTCTTACTTCG
129 TAAAAAATTTAGTAAAAAACTCTTACTTCG
* * * *
304107 GCCCTTTGTTCATATT-TTTTCTCCGCATTTTATTACTTT-A-AAAAATATCA-TAATTTC-TAA
1 GCCCTTTGCTCGTATTATTTTCT-CGAATTTTATTACTTTAATAAAAATAT-ATTATTTTCGT-A
* * * * * *
304167 TTTTATAATTTTACATTATTTCAGTGCATTATGTTT-AAA-A-TT-TATTA--ATTTAGTGTATT
63 TTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTATTT-CTG-AAT
* * *
304226 TTTTAAATTAATTTAGTGTAAAAAAAATCTTTA-TTCCT
126 TTTTAAA-AAATTTA--GT-AAAAAACTC-TTACTT-CG
*
304264 GCCCTTTACTCGTATTATTTTCTCGAATTTTATTACTTTTAATAAAAATATATTATTTTCGTATT
1 GCCCTTTGCTCGTATTATTTTCTCGAATTTTATTAC-TTTAATAAAAATATATTATTTTCGTATT
*
304329 TTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTT
65 TTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATT-ATTATTTCTGAATTTT
* * *
304394 AAAAAAAATTAGTAAAACACTCTTACTTCG
129 TAAAAAATTTAGTAAAAAACTCTTACTTCG
* * * * ** *
304424 GCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAC-TT--TAAAAATACCGTAATTTT--TAA
1 GCCCTTTGCTCGTATTATTTTCT-CGAATTTTATTACTTTAATAAAAATA-TATTATTTTCGT-A
* * * *
304484 TTTTATTATTTTACATTGTTTTAGTACATTATGTTTGAAAT
63 TTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAAT
304525 TTATTAATTT
Statistics
Matches: 343, Mismatches: 47, Indels: 59
0.76 0.10 0.13
Matches are distributed among these distances:
150 4 0.01
151 2 0.01
152 10 0.03
153 10 0.03
154 2 0.01
155 3 0.01
156 14 0.04
157 120 0.35
158 17 0.05
159 10 0.03
160 98 0.29
161 25 0.07
162 3 0.01
163 2 0.01
164 9 0.03
165 9 0.03
166 1 0.00
167 4 0.01
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.52
Consensus pattern (158 bp):
GCCCTTTGCTCGTATTATTTTCTCGAATTTTATTACTTTAATAAAAATATATTATTTTCGTATTT
TATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTATTTCTGAATTTTTA
AAAAATTTAGTAAAAAACTCTTACTTCG
Found at i:304516 original size:317 final size:315
Alignment explanation
Indices: 303917--304550 Score: 1027
Period size: 317 Copynumber: 2.0 Consensus size: 315
303907 TTTGAAATTT
* *
303917 ATTAATTTAGTGTTAAAAACCTTTATTCCTGCCCTTTGCTCGTATTATTTTCTCAAATTTTATTA
1 ATTAATTTAGTGTAAAAAACCTTTATTCCTGCCCTTTACTCGTATTATTTTCTCAAATTTTATTA
*
303982 CTTTCAATAAAAATATATTATTTTCGTATATTATTATTTTATATTATTTCAGTATATTTTGTTTG
66 CTTTCAATAAAAATATATTATTTTCGTATATTATTATTTTATATTATTTCAGTACATTTTGTTTG
* * * * * *
304047 AAATATTTGTATTCATTATTTCTGAATTTTTAAAAAATTTAGTAAAATACTCTTACTTCGGCCCT
131 AAATATTTGTATTAATTATTTCTAAATTTTAAAAAAAATTAGTAAAACACTCTTACTTCGGCCAT
*
304112 TTGTTCATATTTTTTCTCCGCATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAATT
196 TTGTTCATATTTTTTCTCCGCATTTTATTACTTTAAAAAATACCATAATTTCTAATTTTATAATT
*
304177 TTACATTATTTCAGTGCATTATGTTTAAAATTTATTAATTTAGTGTATTTTTTAA
261 TTACATTATTTCAGTACATTATGTTTAAAATTTATTAATTTAGTGTATTTTTTAA
* *
304232 ATTAATTTAGTGTAAAAAAAATCTTTATTCCTGCCCTTTACTCGTATTATTTTCTCGAATTTTAT
1 ATTAATTTAGTGT--AAAAAACCTTTATTCCTGCCCTTTACTCGTATTATTTTCTCAAATTTTAT
* *
304297 TACTTTTAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTT
64 TACTTTCAATAAAAATATATTATTTTCGTATATTATTATTTTATATTATTTCAGTACATTTTGTT
304362 TGAAATATTTGTATTAATTATTTCTAAATTTTAAAAAAAATTAGTAAAACACTCTTACTTCGGCC
129 TGAAATATTTGTATTAATTATTTCTAAATTTTAAAAAAAATTAGTAAAACACTCTTACTTCGGCC
* * * *
304427 ATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTT-AAAAATACCGTAATTTTTAATTTTATT
194 ATTTGTTCATA-TTTTTTCTCCGCATTTTATTACTTTAAAAAATACCATAATTTCTAATTTTATA
* * * *
304491 ATTTTACATTGTTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
258 ATTTTACATTATTTCAGTACATTATGTTTAAAATTTATTAATTTAGTGTATTTTTTAA
304549 AT
1 AT
304551 ATACCATTTT
Statistics
Matches: 293, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
315 13 0.04
317 255 0.87
318 25 0.09
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.52
Consensus pattern (315 bp):
ATTAATTTAGTGTAAAAAACCTTTATTCCTGCCCTTTACTCGTATTATTTTCTCAAATTTTATTA
CTTTCAATAAAAATATATTATTTTCGTATATTATTATTTTATATTATTTCAGTACATTTTGTTTG
AAATATTTGTATTAATTATTTCTAAATTTTAAAAAAAATTAGTAAAACACTCTTACTTCGGCCAT
TTGTTCATATTTTTTCTCCGCATTTTATTACTTTAAAAAATACCATAATTTCTAATTTTATAATT
TTACATTATTTCAGTACATTATGTTTAAAATTTATTAATTTAGTGTATTTTTTAA
Found at i:304915 original size:19 final size:19
Alignment explanation
Indices: 304887--304926 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
304877 CTTTTTTTCT
*
304887 TTCTTTTCCTTCCCTCTTC
1 TTCTTCTCCTTCCCTCTTC
* *
304906 TTCTTCTCCTTTCCTTTTC
1 TTCTTCTCCTTCCCTCTTC
304925 TT
1 TT
304927 TCATTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCTTCTCCTTCCCTCTTC
Found at i:304927 original size:10 final size:10
Alignment explanation
Indices: 304914--305017 Score: 56
Period size: 10 Copynumber: 10.5 Consensus size: 10
304904 TCTTCTTCTC
304914 CTTTCCTTTT
1 CTTTCCTTTT
*
304924 CTTTCATTCTT
1 CTTTCCTT-TT
304935 -TTT-CTTTCT
1 CTTTCCTTT-T
* * *
304944 TTTTTCTTCTC
1 CTTTCCTT-TT
*
304955 CTTTCATTTT
1 CTTTCCTTTT
304965 CTTTCCTTCTT
1 CTTTCCTT-TT
304976 -TTT-C-TTT
1 CTTTCCTTTT
* * * *
304983 CCTCCCTCTC
1 CTTTCCTTTT
304993 CTTTCCTTTT
1 CTTTCCTTTT
305003 CTTTCCTTTT
1 CTTTCCTTTT
305013 CTTTC
1 CTTTC
305018 TTTATTTCTT
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
7 2 0.03
8 3 0.04
9 5 0.07
10 46 0.67
11 12 0.17
12 1 0.01
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:304962 original size:31 final size:29
Alignment explanation
Indices: 304919--304985 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
304909 TTCTCCTTTC
* *
304919 CTTTTCTTTCATTCTT-TTTCTTTCTTTTTT
1 CTTTCCTTTCATT-TTCTTTCCTTC-TTTTT
304949 CTTCTCCTTTCATTTTCTTTCCTTCTTTTT
1 CTT-TCCTTTCATTTTCTTTCCTTCTTTTT
304979 CTTTCCT
1 CTTTCCT
304986 CCCTCTCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 4 0.12
30 13 0.39
31 16 0.48
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (29 bp):
CTTTCCTTTCATTTTCTTTCCTTCTTTTT
Found at i:304984 original size:14 final size:14
Alignment explanation
Indices: 304878--304985 Score: 82
Period size: 14 Copynumber: 7.8 Consensus size: 14
304868 AAAAATTACC
*
304878 TTTT-TTTCTTTC-
1 TTTTCTTTCCTTCT
* *
304890 TTTTCCTTCCCTCT
1 TTTTCTTTCCTTCT
* *
304904 TCTTCTTCTCCTTTCC
1 TTTTCTT-TCC-TTCT
*
304920 TTTTCTTTCATTCT
1 TTTTCTTTCCTTCT
304934 TTTTCTTT-C-T-T
1 TTTTCTTTCCTTCT
*
304945 TTTTCTTCTCCTTTCA
1 TTTTCTT-TCC-TTCT
304961 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
304975 TTTTCTTTCCT
1 TTTTCTTTCCT
304986 CCCTCTCCTT
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
11 8 0.11
12 6 0.08
13 6 0.08
14 30 0.41
15 9 0.12
16 15 0.20
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:305031 original size:38 final size:37
Alignment explanation
Indices: 304906--305036 Score: 156
Period size: 38 Copynumber: 3.4 Consensus size: 37
304896 TTCCCTCTTC
304906 TTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTCTTTCTTTT
1 TTCTTCTCCTTTCCTTTTCTTTC---C-TTTTCTTTCTTTT
* *
304947 TTCTTCTCCTTTCATTTTCTTTCCTTCTT-TTTCTTTCC
1 TTCTTCTCCTTTCCTTTTCTTTCCTT-TTCTTTCTTT-T
* *
304985 TCCCTCTCCTTTCCTTTTCTTTCCTTTTCTTTCTTTAT
1 TTCTTCTCCTTTCCTTTTCTTTCCTTTTCTTTCTTT-T
305023 TTCTTCTCCTTTCC
1 TTCTTCTCCTTTCC
305037 CTCTCCTTCT
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
37 11 0.14
38 45 0.58
41 22 0.28
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (37 bp):
TTCTTCTCCTTTCCTTTTCTTTCCTTTTCTTTCTTTT
Found at i:317038 original size:22 final size:21
Alignment explanation
Indices: 317013--317080 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
317003 TACTTTGATC
317013 AATTTTAATTTTTGTATTTATT
1 AATTTTAATTTTT-TATTTATT
317035 AATTTTAATTTTTATATTT-TT
1 AATTTTAATTTTT-TATTTATT
* ** *
317056 AATATTAAAATTTTATTTATG
1 AATTTTAATTTTTTATTTATT
317077 AATT
1 AATT
317081 AAATAATAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 5 0.13
21 16 0.41
22 18 0.46
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (21 bp):
AATTTTAATTTTTTATTTATT
Found at i:317192 original size:15 final size:15
Alignment explanation
Indices: 317166--317207 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
317156 TTATTTACTG
317166 AATAAAATTTTAAAAT
1 AATAAAA-TTTAAAAT
**
317182 AATAAAATTTAATTT
1 AATAAAATTTAAAAT
317197 AAT-AAATTTAA
1 AATAAAATTTAA
317208 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.33
15 9 0.38
16 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAAATTTAAAAT
Found at i:317205 original size:14 final size:15
Alignment explanation
Indices: 317166--317208 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
317156 TTATTTACTG
**
317166 AATAAAATTTTAAAAT
1 AATAAAA-TTTAATTT
317182 AATAAAATTTAATTT
1 AATAAAATTTAATTT
317197 AAT-AAATTTAAT
1 AATAAAATTTAAT
317209 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 9 0.36
15 9 0.36
16 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAAATTTAATTT
Found at i:328127 original size:18 final size:18
Alignment explanation
Indices: 328106--328148 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
328096 CAATTAAATT
328106 AATTTTCATAATTTTTA-A
1 AATTTT-ATAATTTTTATA
*
328124 AATTATTATTATTTTTATA
1 AATT-TTATAATTTTTATA
328143 AATTTT
1 AATTTT
328149 TACCATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTTTATAATTTTTATA
Found at i:328127 original size:27 final size:28
Alignment explanation
Indices: 328097--328150 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
328087 CAATTCAATC
328097 AATTA-AATTAATTTTCAT-AATTTTTAA
1 AATTATAATT-ATTTTCATAAATTTTTAA
* *
328124 AATTATTATTATTTTTATAAATTTTTA
1 AATTATAATTATTTTCATAAATTTTTA
328151 CCATTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
AATTATAATTATTTTCATAAATTTTTAA
Found at i:331665 original size:31 final size:29
Alignment explanation
Indices: 331624--331697 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
331614 TTAATGGCTC
331624 AGTGACTAAAATGTTACAACATGTT-AACATA
1 AGTGACTAAAATGTT--AACAT-TTAAACATA
* *
331655 AGTGATTAAAACG-TAACATTTCAAACATA
1 AGTGACTAAAATGTTAACATTT-AAACATA
331684 AGTGACTAAAATGT
1 AGTGACTAAAATGT
331698 AACCTAAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
27 2 0.06
28 5 0.14
29 17 0.47
30 1 0.03
31 11 0.31
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (29 bp):
AGTGACTAAAATGTTAACATTTAAACATA
Found at i:335564 original size:17 final size:16
Alignment explanation
Indices: 335542--335583 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
335532 AATAATCTTT
335542 AAAAATATAATT-AATGA
1 AAAAAT-TAATTCAA-GA
335559 AAAAATTAATTCAAGA
1 AAAAATTAATTCAAGA
335575 AAAATATTA
1 AAAA-ATTA
335584 CATTAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAAATTAATTCAAGA
Found at i:343140 original size:5 final size:5
Alignment explanation
Indices: 343130--343155 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
343120 ATAAGCTCAC
343130 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
343156 TTTTCGTAAA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:343333 original size:25 final size:25
Alignment explanation
Indices: 343305--343352 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
343295 TATTAAGTAG
*
343305 TTTTAAATCATATATTATGTTATAC
1 TTTTAAACCATATATTATGTTATAC
343330 TTTTAAACCATATATTATGTTAT
1 TTTTAAACCATATATTATGTTAT
343353 TTTGAAGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTTAAACCATATATTATGTTATAC
Found at i:343702 original size:17 final size:16
Alignment explanation
Indices: 343673--343707 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
343663 AGTAAAAAGT
343673 AAAAATATAAAATTAA
1 AAAAATATAAAATTAA
*
343689 AAAAATTATGAAATTAA
1 AAAAA-TATAAAATTAA
343706 AA
1 AA
343708 CATTTCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAATATAAAATTAA
Found at i:343952 original size:21 final size:21
Alignment explanation
Indices: 343897--343954 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
343887 AAAAAAATTA
*
343897 TTTTATAAAT-TTTGAATATT
1 TTTTATAAATATTTAAATATT
* *
343917 TTTGATAAA-ATTTTAAATTTT
1 TTTTATAAATA-TTTAAATATT
343938 TTTTATAAATATTTAAA
1 TTTTATAAATATTTAAA
343955 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 8 0.26
21 22 0.71
22 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTATAAATATTTAAATATT
Found at i:344029 original size:18 final size:18
Alignment explanation
Indices: 343978--344029 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 18
343968 TAAGTATATA
343978 AAAAAT-TATAA-ATCTT
1 AAAAATATATAATATCTT
343994 ATAAAATATAT-AT-T-TT
1 A-AAAATATATAATATCTT
344010 AAAAATATATAATATCTT
1 AAAAATATATAATATCTT
344028 AA
1 AA
344030 TGTTATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
15 9 0.30
16 6 0.20
17 8 0.27
18 7 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATATATAATATCTT
Found at i:345573 original size:138 final size:137
Alignment explanation
Indices: 345333--345607 Score: 327
Period size: 138 Copynumber: 2.0 Consensus size: 137
345323 TGAAAGTGGA
*
345333 TAATGAGATTTTTCAGGAATTTTCCAGGTTCTTGATTATAACTTGAAATGTAGCCTACAAAAGTT
1 TAATGAGAATTTTCAGGAATTTTCCAGGTTCTTGATTATAACTTGAAATGTAGCCTACAAAAGTT
* ** * *
345398 GAAAGGCATTTGAAGGGCTAGGGTGTTTTAGTTTTGAATCCGGGCTATTTGGACTTTAATTATTG
66 GAAAGGCATGTGAAGGGCTAGGGTGTGGTAGTATTGAATCCGGGCTATTTAGACTTTAATTATTG
345463 ATGCTAG
131 ATGCTAG
* * * * * * * *
345470 TAATGGGAATTTTCAGGGATTTATCCGGGTTCTTGATTATAGCTTGTAATGTGGCTTACTAAAGT
1 TAATGAGAATTTTCAGGAATTT-TCCAGGTTCTTGATTATAACTTGAAATGTAGCCTACAAAAGT
* * * * * * *
345535 TGAATGGTATCGTG-ATGGTTTGGGTGTGGTAGTATTGAATCCGGGCTATTTAGATTTTAGTTAT
65 TGAAAGGCAT-GTGAAGGGCTAGGGTGTGGTAGTATTGAATCCGGGCTATTTAGACTTTAATTAT
*
345599 TGGTGCTAG
129 TGATGCTAG
345608 ATGGGTATAG
Statistics
Matches: 114, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
137 19 0.17
138 93 0.82
139 2 0.02
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.39
Consensus pattern (137 bp):
TAATGAGAATTTTCAGGAATTTTCCAGGTTCTTGATTATAACTTGAAATGTAGCCTACAAAAGTT
GAAAGGCATGTGAAGGGCTAGGGTGTGGTAGTATTGAATCCGGGCTATTTAGACTTTAATTATTG
ATGCTAG
Found at i:347371 original size:11 final size:11
Alignment explanation
Indices: 347355--347381 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
347345 CTTAAATGAA
347355 AATTTTTAAAT
1 AATTTTTAAAT
347366 AATTTTTAAAT
1 AATTTTTAAAT
347377 AATTT
1 AATTT
347382 AATAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTTTAAAT
Found at i:347399 original size:19 final size:19
Alignment explanation
Indices: 347360--347405 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
347350 ATGAAAATTT
347360 TTAAATAATTTTTAAATAA
1 TTAAATAATTTTTAAATAA
* *
347379 TTTAATAATTTTTTTAA-AA
1 TTAAATAA-TTTTTAAATAA
347398 TTAAATAA
1 TTAAATAA
347406 ATAAAACGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATAATTTTTAAATAA
Found at i:351034 original size:23 final size:23
Alignment explanation
Indices: 350945--351034 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
350935 ACCTGATCAG
*
350945 TATACGACACAT-AAGTGCCTGA
1 TATACGACAAATAAAGTGCCTGA
* * *
350967 -A-ACGACACATGAGGTGCCTGA
1 TATACGACAAATAAAGTGCCTGA
* *
350988 AATACGACAAATAAAGTGCTTGA
1 TATACGACAAATAAAGTGCCTGA
351011 TATACGACAAATAAAGTGCCTGA
1 TATACGACAAATAAAGTGCCTGA
351034 T
1 T
351035 CGGCAAAGCC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.16
21 10 0.17
22 1 0.02
23 38 0.66
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (23 bp):
TATACGACAAATAAAGTGCCTGA
Found at i:352194 original size:24 final size:22
Alignment explanation
Indices: 352145--352190 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
352135 GACTAAAATT
*
352145 ATAAAATATTAATTTTATATTA
1 ATAAAATATTAATTTTATATAA
352167 ATAAAATGATTCAATTTTA-ATAA
1 ATAAAAT-ATT-AATTTTATATAA
352190 A
1 A
352191 ATAATTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 7 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAAAATATTAATTTTATATAA
Found at i:359314 original size:31 final size:29
Alignment explanation
Indices: 359216--359315 Score: 119
Period size: 29 Copynumber: 3.3 Consensus size: 29
359206 CTAATTAATT
* *
359216 TTTTTTAAAAAATAAAAGATTTAATGATAA
1 TTTTTAAAAAAAT-AAAGATTTAATGAAAA
*
359246 TTTTTAAAAAAATAAAGATTTAATTAAAA
1 TTTTTAAAAAAATAAAGATTTAATGAAAA
*
359275 TTTTTAAAAAAATTGAAAGGTTTAATGAAAA
1 TTTTTAAAAAAA-T-AAAGATTTAATGAAAA
* *
359306 GTTGTAAAAA
1 TTTTTAAAAA
359316 TGTTAGGGGA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 26 0.43
30 13 0.21
31 22 0.36
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (29 bp):
TTTTTAAAAAAATAAAGATTTAATGAAAA
Found at i:359519 original size:17 final size:17
Alignment explanation
Indices: 359484--359520 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
359474 CTTGTTATTA
**
359484 TTTATTTATTTATGTAT
1 TTTATTTATTTATCCAT
359501 TTTATTTATTTATCCAT
1 TTTATTTATTTATCCAT
359518 TTT
1 TTT
359521 TAATTACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATTTATTTATCCAT
Found at i:364611 original size:2 final size:2
Alignment explanation
Indices: 364604--364628 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
364594 TACATAACTT
364604 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
364629 TACAATAACA
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:366291 original size:2 final size:2
Alignment explanation
Indices: 366252--366278 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
366242 TACTCGGAAG
366252 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 T
366279 GTTTCATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:366755 original size:13 final size:13
Alignment explanation
Indices: 366737--366761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
366727 CCATGTGAAA
366737 TTTTTAAAAAATG
1 TTTTTAAAAAATG
366750 TTTTTAAAAAAT
1 TTTTTAAAAAAT
366762 TAAAGATATT
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAAATG
Found at i:369344 original size:19 final size:21
Alignment explanation
Indices: 369300--369345 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
369290 AGTAATATAT
*
369300 ATAATTACTAAATATTAAATA
1 ATAATAACTAAATATTAAATA
*
369321 A-AATAACTATAT-TTAAA-A
1 ATAATAACTAAATATTAAATA
369339 ATAATAA
1 ATAATAA
369346 TAATATAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 10 0.45
20 9 0.41
21 1 0.05
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATAACTAAATATTAAATA
Found at i:377764 original size:58 final size:58
Alignment explanation
Indices: 377674--377786 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 58
377664 GAAATATTAG
*
377674 GGACTAACTTGGACAAAAAAGAGTCAAGCCCTAATGTAAGAACAATTGACAAGTTTAA
1 GGACTAAATTGGACAAAAAAGAGTCAAGCCCTAATGTAAGAACAATTGACAAGTTTAA
* ** *
377732 GGACTAAATTGGACAAAAAA-AGTTTC-GGCCCTAATGTGGGAACAATTGCCAAGTT
1 GGACTAAATTGGACAAAAAAGAG--TCAAGCCCTAATGTAAGAACAATTGACAAGTT
377787 CAGGTACTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 2 0.04
58 44 0.92
59 2 0.04
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (58 bp):
GGACTAAATTGGACAAAAAAGAGTCAAGCCCTAATGTAAGAACAATTGACAAGTTTAA
Found at i:389406 original size:27 final size:29
Alignment explanation
Indices: 389375--389429 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
389365 AGAACACATT
389375 AAGAAA-GATAGAAAT-ATGAGAATAAGA
1 AAGAAAGGATAGAAATGATGAGAATAAGA
*
389402 AAGAAAGTGATAGAAATGGTGAGAATAA
1 AAGAAAG-GATAGAAATGATGAGAATAA
389430 TGGCACTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
29 9 0.38
30 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.16
Consensus pattern (29 bp):
AAGAAAGGATAGAAATGATGAGAATAAGA
Found at i:390315 original size:2 final size:2
Alignment explanation
Indices: 390308--390334 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
390298 CTGATCAGGT
390308 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
390335 TTATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:393343 original size:30 final size:29
Alignment explanation
Indices: 393307--393371 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
393297 AAATTTTTTG
* *
393307 AAAATTGGATCAAATCAAAATTTCATATAT
1 AAAATTGCATAAAATCAAAATTT-ATATAT
* *
393337 AAAATTGCATAAAATCAAAGTTTATGTAT
1 AAAATTGCATAAAATCAAAATTTATATAT
393366 AAAATT
1 AAAATT
393372 ACACATCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAATTGCATAAAATCAAAATTTATATAT
Found at i:393646 original size:6 final size:6
Alignment explanation
Indices: 393635--393666 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
393625 AGTTGTAAAG
393635 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
393667 ATTTATTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:393675 original size:18 final size:18
Alignment explanation
Indices: 393636--393675 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
393626 GTTGTAAAGT
*
393636 TTTATTTTTATTTTTATT
1 TTTATTTTTATTTTTATA
393654 TTTATTTTTATTTATT-TA
1 TTTATTTTTATTT-TTATA
393672 TTTA
1 TTTA
393676 CTTAGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTATTTTTATTTTTATA
Found at i:395378 original size:26 final size:26
Alignment explanation
Indices: 395342--395393 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
395332 GAAATGTGAA
*
395342 AGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
395368 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
395394 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:395444 original size:100 final size:101
Alignment explanation
Indices: 395270--395620 Score: 501
Period size: 100 Copynumber: 3.6 Consensus size: 101
395260 TGTATATAAA
** * * *
395270 GGGTTGCTGTGTGCTGATTCCCCGATTTATGGGT-GTGCTATGTGC-TGATCCACCATATCTTTG
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGT-ATCCACCATATCTTTG
*
395333 AAATGTGAAAGGGGTTGCTATGTGCTGATT-CCCCGAG
65 AAATG-AAAAGGGGTTGCTATGTGCTGATTCCCCCGAG
395370 GGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTG
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCTTTG
395434 AAATGAAAAGGGGTTGCTATGTGCTGATTCCCCCGA-
65 AAATGAAAAGGGGTTGCTATGTGCTGATTCCCCCGAG
395470 GGGTTGCTAAGTGCT-ATT-CCCG-TTCATTGGTGGTGCTAAGTGCGATAT-CACCA-A--TTTG
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCTTTG
*
395528 AAATAAAAAGGGGTTGCTATGTGCTGATTCCCCCGAG
65 AAATGAAAAGGGGTTGCTATGTGCTGATTCCCCCGAG
* *
395565 GGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGATCCACCA
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTATCCACCA
395621 ATAACGGCTA
Statistics
Matches: 233, Mismatches: 9, Indels: 20
0.89 0.03 0.08
Matches are distributed among these distances:
94 39 0.17
95 15 0.06
96 4 0.02
97 11 0.05
98 56 0.24
99 10 0.04
100 70 0.30
101 27 0.12
102 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (101 bp):
GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTATCCACCATATCTTTGA
AATGAAAAGGGGTTGCTATGTGCTGATTCCCCCGAG
Found at i:395578 original size:27 final size:27
Alignment explanation
Indices: 395536--395587 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
395526 TGAAATAAAA
*
395536 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
395563 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
395588 GATTCAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:397046 original size:12 final size:12
Alignment explanation
Indices: 397031--397055 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
397021 ATTTGGGATT
397031 TTATTTCAGATC
1 TTATTTCAGATC
397043 TTATTTCAGATC
1 TTATTTCAGATC
397055 T
1 T
397056 GGAAATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TTATTTCAGATC
Found at i:400034 original size:6 final size:6
Alignment explanation
Indices: 400023--400048 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
400013 AGTTGTAAAG
400023 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
400049 ATTTATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:402592 original size:17 final size:18
Alignment explanation
Indices: 402570--402603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
402560 TATTTCATAG
*
402570 TAAAAA-TAAAATAATTT
1 TAAAAATTAAAAAAATTT
402587 TAAAAATTAAAAAAATT
1 TAAAAATTAAAAAAATT
402604 AACATTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATTAAAAAAATTT
Found at i:404095 original size:4 final size:4
Alignment explanation
Indices: 404086--404117 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
404076 TCAAACATCA
404086 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
404118 TTGAATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:411335 original size:11 final size:10
Alignment explanation
Indices: 411306--411360 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
411296 AAAAAAATTA
411306 TAAATTTTTT
1 TAAATTTTTT
*
411316 TAAACTTTTGT
1 TAAA-TTTTTT
*
411327 TGAA-TTTTT
1 TAAATTTTTT
411336 TAATATTTTTAT
1 TAA-ATTTTT-T
411348 T-AATTTTTT
1 TAAATTTTTT
411357 TAAA
1 TAAA
411361 CCTTATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
9 8 0.22
10 13 0.36
11 13 0.36
12 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (10 bp):
TAAATTTTTT
Found at i:411336 original size:20 final size:20
Alignment explanation
Indices: 411303--411361 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
411293 TAAAAAAAAA
*
411303 TTATAAATTTTTTTAAACTT
1 TTATTAATTTTTTTAAACTT
* *
411323 TTGTTGAA-TTTTTTAATATTT
1 TTATT-AATTTTTTTAA-ACTT
411344 TTATTAATTTTTTTAAAC
1 TTATTAATTTTTTTAAAC
411362 CTTATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTATTAATTTTTTTAAACTT
Found at i:416610 original size:22 final size:22
Alignment explanation
Indices: 416582--416624 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
416572 GTAAAAAATA
*
416582 AAAATTGATTTTGCTTTTATTC
1 AAAATTGATTTTGATTTTATTC
* *
416604 AAAATTGTTTTTTATTTTATT
1 AAAATTGATTTTGATTTTATT
416625 AATTTATTTT
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:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (22 bp):
AAAATTGATTTTGATTTTATTC
Found at i:435102 original size:28 final size:26
Alignment explanation
Indices: 435054--435115 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
435044 CCAAATATAA
435054 TAAATATATTTTTTTATTTTTTA-TTT
1 TAAA-ATATTTTTTTATTTTTTATTTT
435080 TAAAATACTTTTTTTAATTTTTTTATTTT
1 TAAAATA-TTTTTTT-A-TTTTTTATTTT
435109 TAAAATA
1 TAAAATA
435116 AATTTTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.09
26 11 0.34
27 1 0.03
28 7 0.22
29 10 0.31
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TAAAATATTTTTTTATTTTTTATTTT
Done.