Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 111 of 144
Found at i:25777696 original size:12 final size:12
Alignment explanation
Indices: 25777627--25777699 Score: 67
Period size: 12 Copynumber: 6.2 Consensus size: 12
25777617 CAACATTAAA
*
25777627 AACAACAAAAAT
1 AACAACAAAAAC
* *
25777639 AGCAACGAAAAC
1 AACAACAAAAAC
*
25777651 AACAACAAAAAT
1 AACAACAAAAAC
*
25777663 AACAGCAAAAAC
1 AACAACAAAAAC
* *
25777675 AA-TACGAAAAC
1 AACAACAAAAAC
*
25777686 AACAACCAAAAC
1 AACAACAAAAAC
25777698 AA
1 AA
25777700 TAAAAAAAGT
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
11 8 0.17
12 39 0.83
ACGTcount: A:0.68, C:0.22, G:0.05, T:0.04
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:25777704 original size:20 final size:20
Alignment explanation
Indices: 25777651--25777782 Score: 113
Period size: 20 Copynumber: 6.2 Consensus size: 20
25777641 CAACGAAAAC
* * *
25777651 AACAACAAAAATAACAGCAAA
1 AACAATAAAAA-AACAACCAA
25777672 AACAATACGAAAACAACAACCAA
1 AACAATA--AAAA-AACAACCAA
**
25777695 AACAATAAAAAAAGTACCAA
1 AACAATAAAAAAACAACCAA
*
25777715 AACAGTAAAAAAACAACACAAA
1 AACAATAAAAAAACAAC-C-AA
*
25777737 AACAA-AAAAAAGCAACCAA
1 AACAATAAAAAAACAACCAA
*
25777756 AACAATAAAAAAAAAGTACCAA
1 AACAATAAAAAAACA--ACCAA
25777778 AACAA
1 AACAA
25777783 CAATATAATT
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
19 7 0.08
20 29 0.32
21 21 0.23
22 16 0.18
23 18 0.20
ACGTcount: A:0.71, C:0.19, G:0.05, T:0.05
Consensus pattern (20 bp):
AACAATAAAAAAACAACCAA
Found at i:25777780 original size:41 final size:40
Alignment explanation
Indices: 25777670--25777782 Score: 120
Period size: 41 Copynumber: 2.7 Consensus size: 40
25777660 AATAACAGCA
** *
25777670 AAAACAATACGAAAACAACAACCAAAACAATAAAAAAAGTACC
1 AAAACAATAAAAAAACAAC-ACCAAAAC-A-AAAAAAAGAACC
* *
25777713 AAAACAGTAAAAAAACAACACAAAAACAAAAAAAAGCAACC
1 AAAACAATAAAAAAACAACACCAAAACAAAAAAAAG-AACC
*
25777754 AAAACAATAAAAAAA-AAGTACCAAAACAA
1 AAAACAATAAAAAAACAA-CACCAAAACAA
25777783 CAATATAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 10 0.17
41 27 0.45
42 7 0.12
43 16 0.27
ACGTcount: A:0.72, C:0.19, G:0.04, T:0.05
Consensus pattern (40 bp):
AAAACAATAAAAAAACAACACCAAAACAAAAAAAAGAACC
Found at i:25777782 original size:22 final size:21
Alignment explanation
Indices: 25777690--25777782 Score: 93
Period size: 22 Copynumber: 4.5 Consensus size: 21
25777680 GAAAACAACA
*
25777690 ACCAAAACAAT-AAAAAAAGT
1 ACCAAAACAATAAAAAAAAAT
* *
25777710 ACCAAAACAGTAAAAAAACAAC
1 ACCAAAACAATAAAAAAA-AAT
* **
25777732 ACAAAAACAA-AAAAAAGCA-
1 ACCAAAACAATAAAAAAAAAT
25777751 ACCAAAACAATAAAAAAAAAGT
1 ACCAAAACAATAAAAAAAAA-T
25777773 ACCAAAACAA
1 ACCAAAACAA
25777783 CAATATAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 9 0.16
20 18 0.31
21 12 0.21
22 19 0.33
ACGTcount: A:0.72, C:0.18, G:0.04, T:0.05
Consensus pattern (21 bp):
ACCAAAACAATAAAAAAAAAT
Found at i:25780717 original size:29 final size:30
Alignment explanation
Indices: 25780680--25780738 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
25780670 TATGGTTTAA
25780680 TGTGCAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* * *
25780709 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
25780739 AATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:25780949 original size:30 final size:30
Alignment explanation
Indices: 25780881--25780965 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
25780871 AATTAAATCA
* *
25780881 AAATTAAAATTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * *
25780911 ACAATTAAAGTTTCACGTGTATAATTGCACC
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
25780942 AAATTAAAG-TTC-A-TATACAATTGA
1 AAATTAAAGTTTCAAGTATACAATTGA
25780966 TTTTATGTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
27 8 0.18
29 3 0.07
30 9 0.20
31 24 0.55
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:25781541 original size:12 final size:12
Alignment explanation
Indices: 25781524--25781553 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
25781514 AATTTATGAA
25781524 GAAGCCCATCTT
1 GAAGCCCATCTT
25781536 GAAGCCCATCTT
1 GAAGCCCATCTT
25781548 GAAGCC
1 GAAGCC
25781554 TTAGTGGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (12 bp):
GAAGCCCATCTT
Found at i:25790328 original size:1 final size:1
Alignment explanation
Indices: 25790317--25790356 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
25790307 AGAGTTGATT
*
25790317 GGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
25790357 AGCTACGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:25792203 original size:16 final size:16
Alignment explanation
Indices: 25792168--25792205 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25792158 TTAAACCTAT
*
25792168 TTTATATATTATTATT
1 TTTATATATTATTATA
25792184 TTTATATATTATGTA-A
1 TTTATATATTAT-TATA
25792200 TTTATA
1 TTTATA
25792206 ATACATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTATATATTATTATA
Found at i:25794540 original size:22 final size:20
Alignment explanation
Indices: 25794509--25794562 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
25794499 TATAAATGAC
25794509 ATGCAAA-ATATATAAAATACA
1 ATGCAAATATA-ATAAAATA-A
25794530 AGTGCATAATAATAATAAAATAA
1 A-TGCA-AAT-ATAATAAAATAA
25794553 ATGCAAATAT
1 ATGCAAATAT
25794563 TGATGAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
20 2 0.07
21 4 0.14
22 8 0.28
23 4 0.14
24 8 0.28
25 3 0.10
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (20 bp):
ATGCAAATATAATAAAATAA
Found at i:25794909 original size:22 final size:20
Alignment explanation
Indices: 25794878--25794931 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
25794868 GATAAATGAC
25794878 ATGCAAA-ATATATAAAATACA
1 ATGCAAATATA-ATAAAATA-A
25794899 AGTGCATAATAATAATAAAATAA
1 A-TGCA-AAT-ATAATAAAATAA
25794922 ATGCAAATAT
1 ATGCAAATAT
25794932 TGATGAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
20 2 0.07
21 4 0.14
22 8 0.28
23 4 0.14
24 8 0.28
25 3 0.10
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (20 bp):
ATGCAAATATAATAAAATAA
Found at i:25795095 original size:369 final size:369
Alignment explanation
Indices: 25794416--25795150 Score: 1407
Period size: 369 Copynumber: 2.0 Consensus size: 369
25794406 TTTAAAATAA
25794416 CTTTGAAAATGAACGTGTAATTTTTAAATACGAATGAGCAGTTAATAAGAGAGATTAAATAACAT
1 CTTTGAAAATGAACGTGTAATTTTTAAATACGAATGAGCAGTTAATAAGAGAGATTAAATAACAT
*
25794481 GAAGTAAGATAATAAGCATATAAATGACATGCAAAATATATAAAATACAAGTGCATAATAATAAT
66 GAAGTAAGATAATAAGCAGATAAATGACATGCAAAATATATAAAATACAAGTGCATAATAATAAT
25794546 AAAATAAATGCAAATATTGATGAGGAAACAAAATGATGCAATTTGGGGTTGAAAATGAGACTTTG
131 AAAATAAATGCAAATATTGATGAGGAAACAAAATGATGCAATTTGGGGTTGAAAATGAGACTTTG
*
25794611 GATGCCCGAGGGTAAAATGGTAATTTTAGACTCTTGAGGGTAAAATGATAATTTTGGGAAAATTT
196 GATGCCCGAGGGTAAAATGGTAATTTTAGACTCTCGAGGGTAAAATGATAATTTTGGGAAAATTT
*
25794676 GGAGTTAAAAATAACATTTTAGACATCCAGGGGTAAAATGGTAATTTTTAAAAAAATCGAGATCA
261 GGAGTTAAAAATAACATTTTAGACATCCAGGGGTAAAATGATAATTTTTAAAAAAATCGAGATCA
*
25794741 AAAATCAAATTTTTGGACATCCGAGGGTAAAGTGGTAATTTCTG
326 AAAATCAAATTTTTGGACATCCGAGGGTAAAATGGTAATTTCTG
* *
25794785 CTTTGAAAATGAACGTGTAATTTTTAAATACGAATGAGCAGTTAATGAGGGAGATTAAATAACAT
1 CTTTGAAAATGAACGTGTAATTTTTAAATACGAATGAGCAGTTAATAAGAGAGATTAAATAACAT
25794850 GAAGTAAGATAATAAGCAGATAAATGACATGCAAAATATATAAAATACAAGTGCATAATAATAAT
66 GAAGTAAGATAATAAGCAGATAAATGACATGCAAAATATATAAAATACAAGTGCATAATAATAAT
25794915 AAAATAAATGCAAATATTGATGAGGAAACAAAATGATGCAATTTGGGGTTGAAAATGAGACTTTG
131 AAAATAAATGCAAATATTGATGAGGAAACAAAATGATGCAATTTGGGGTTGAAAATGAGACTTTG
*
25794980 GATGCCCGGGGGTAAAATGGTAATTTTAGACTCTCGAGGGTAAAATGATAATTTTGGGAAAATTT
196 GATGCCCGAGGGTAAAATGGTAATTTTAGACTCTCGAGGGTAAAATGATAATTTTGGGAAAATTT
25795045 GGAGTTAAAAATAACATTTTAGACATCCAGGGGTAAAATGATAATTTTTAAAAAAATCGAGATCA
261 GGAGTTAAAAATAACATTTTAGACATCCAGGGGTAAAATGATAATTTTTAAAAAAATCGAGATCA
25795110 AAAATCAAATTTTTGGACATCCGAGGGTAAAATGGTAATTT
326 AAAATCAAATTTTTGGACATCCGAGGGTAAAATGGTAATTT
25795151 TTGTAAGTTT
Statistics
Matches: 359, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
369 359 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.28
Consensus pattern (369 bp):
CTTTGAAAATGAACGTGTAATTTTTAAATACGAATGAGCAGTTAATAAGAGAGATTAAATAACAT
GAAGTAAGATAATAAGCAGATAAATGACATGCAAAATATATAAAATACAAGTGCATAATAATAAT
AAAATAAATGCAAATATTGATGAGGAAACAAAATGATGCAATTTGGGGTTGAAAATGAGACTTTG
GATGCCCGAGGGTAAAATGGTAATTTTAGACTCTCGAGGGTAAAATGATAATTTTGGGAAAATTT
GGAGTTAAAAATAACATTTTAGACATCCAGGGGTAAAATGATAATTTTTAAAAAAATCGAGATCA
AAAATCAAATTTTTGGACATCCGAGGGTAAAATGGTAATTTCTG
Found at i:25795140 original size:59 final size:59
Alignment explanation
Indices: 25795014--25795299 Score: 208
Period size: 58 Copynumber: 4.9 Consensus size: 59
25795004 TTTAGACTCT
* * * * *
25795014 CGAGGGTAAAATGATAATTTTGGGAAAATTTG-GAGTTAAAAAT-AACA-TTTTAGACATC
1 CGAGGGTAAAATGATAATTTTTGAAAAATTCGAGA-TCAAAAATGAA-ATTTTTGGACATC
* * *
25795072 C-AGGGGTAAAATGATAATTTTTAAAAAAATCGAGATCAAAAATCAAATTTTTGGACATC
1 CGA-GGGTAAAATGATAATTTTTGAAAAATTCGAGATCAAAAATGAAATTTTTGGACATC
* * ** * * * * *
25795131 CGAGGGTAAAATGGTAATTTTTGTAAGTTTCGGGGTC-AAAATGGAGTTTTTGGACATT
1 CGAGGGTAAAATGATAATTTTTGAAAAATTCGAGATCAAAAATGAAATTTTTGGACATC
* ** * * * * * *
25795189 CGGGGGTAAAATGATAATTTTTGAAAGTTTTGAGGTCAAAAATGGAGTTTTTGGATATT
1 CGAGGGTAAAATGATAATTTTTGAAAAATTCGAGATCAAAAATGAAATTTTTGGACATC
* * * * *
25795248 CGAGGGTAAAAATG-TAATTTTTGGAAATTTCGGGGTC-AAAATGGAATTTTTG
1 CGAGGGT-AAAATGATAATTTTTGAAAAATTCGAGATCAAAAATGAAATTTTTG
25795300 AAAGTTTGGG
Statistics
Matches: 190, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
57 1 0.01
58 96 0.51
59 86 0.45
60 7 0.04
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (59 bp):
CGAGGGTAAAATGATAATTTTTGAAAAATTCGAGATCAAAAATGAAATTTTTGGACATC
Found at i:25795199 original size:58 final size:58
Alignment explanation
Indices: 25795119--25795299 Score: 249
Period size: 58 Copynumber: 3.1 Consensus size: 58
25795109 AAAAATCAAA
* *
25795119 TTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGTAAGTTTCGGGGTCAAAATGGAG
1 TTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAATGGAG
* * * *
25795177 TTTTTGGACATTCGGGGGTAAAATGATAATTTTTGAAAGTTTTGAGGTCAAAAATGGAG
1 TTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTC-AAAATGGAG
* *
25795236 TTTTTGGATATTCGAGGGTAAAAAT-GTAATTTTTGGAAA-TTTCGGGGTCAAAATGGAA
1 TTTTTGGACATTCGAGGGT-AAAATGGTAATTTTT-GAAAGTTTCGGGGTCAAAATGGAG
25795294 TTTTTG
1 TTTTTG
25795300 AAAGTTTGGG
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
58 57 0.53
59 42 0.39
60 9 0.08
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (58 bp):
TTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAATGGAG
Found at i:25795311 original size:29 final size:29
Alignment explanation
Indices: 25795134--25795388 Score: 191
Period size: 29 Copynumber: 8.7 Consensus size: 29
25795124 GGACATCCGA
* *
25795134 GGGT-AAAATGGTAATTTTTGTAAGTTTCG
1 GGGTCAAAAT-GTAATTTTTGAAAGTTTGG
* * * *
25795163 GGGTCAAAATGGAGTTTTTGGACA-TTCGG
1 GGGTCAAAATGTAATTTTT-GAAAGTTTGG
*
25795192 GGGT-AAAATGATAATTTTTGAAAGTTTTG
1 GGGTCAAAATG-TAATTTTTGAAAGTTTGG
* * * * * *
25795221 AGGTCAAAAATGGAGTTTTTGGATA-TTCGA
1 GGGTC-AAAATGTAATTTTT-GAAAGTTTGG
* *
25795251 GGGTAAAAATGTAATTTTTGGAAA-TTTCG
1 GGGTCAAAATGTAATTTTT-GAAAGTTTGG
*
25795280 GGGTCAAAATGGAATTTTTGAAAGTTTGG
1 GGGTCAAAATGTAATTTTTGAAAGTTTGG
* *
25795309 GGG-CAAAAATATAATTTTTGAAAGTTAT-A
1 GGGTC-AAAATGTAATTTTTGAAAGTT-TGG
*
25795338 GGGTCAAAAATGTAATTTTGGATAAGTTTGG
1 GGGTC-AAAATGTAATTTTTGA-AAGTTTGG
*
25795369 GGGTCAAAATATAATTTTTG
1 GGGTCAAAATGTAATTTTTG
25795389 GATAGTTTAA
Statistics
Matches: 176, Mismatches: 37, Indels: 25
0.74 0.16 0.11
Matches are distributed among these distances:
28 14 0.08
29 94 0.53
30 49 0.28
31 19 0.11
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTGAAAGTTTGG
Found at i:25795311 original size:117 final size:115
Alignment explanation
Indices: 25795074--25795390 Score: 327
Period size: 117 Copynumber: 2.7 Consensus size: 115
25795064 TAGACATCCA
* *** * * * * *
25795074 GGGGTAAAATGATAATTTTTAAAAAAATCGAGATCAAAAATCAAATTTTTGGACATCCGAGGGTA
1 GGGGTAAAATGATAATTTTTGAAAGTTTTGAGGTCAAAAAT-GAATTTTTGGATATTCGAGGGTA
* * * *
25795139 AAATGGTAATTTTTGTAAGTTTCGGGGTCAAAATGGAGTTTTTGGACATTCG
65 AAAT-GTAATTTTTGGAAATTTCGGGGTCAAAATGGAATTTTTGGAAATTCG
*
25795191 GGGGTAAAATGATAATTTTTGAAAGTTTTGAGGTCAAAAATGGAGTTTTTGGATATTCGAGGGTA
1 GGGGTAAAATGATAATTTTTGAAAGTTTTGAGGTCAAAAAT-GAATTTTTGGATATTCGAGGGT-
*
25795256 AAAATGTAATTTTTGGAAATTTCGGGGTCAAAATGGAATTTTT-GAAAGTTTG
64 AAAATGTAATTTTTGGAAATTTCGGGGTCAAAATGGAATTTTTGGAAA-TTCG
* * * *
25795308 GGGGCAAAAAT-ATAATTTTTGAAAGTTAT-AGGGTCAAAAATGTAA-TTTTGGATAAGTTTGGG
1 GGGG-TAAAATGATAATTTTTGAAAGTTTTGA-GGTCAAAAATG-AATTTTTGGAT-A-TTCGAG
*
25795370 GGTCAAAATATAATTTTTGGA
61 GGT-AAAATGTAATTTTTGGA
25795391 TAGTTTAAGG
Statistics
Matches: 170, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
116 13 0.08
117 124 0.73
118 33 0.19
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (115 bp):
GGGGTAAAATGATAATTTTTGAAAGTTTTGAGGTCAAAAATGAATTTTTGGATATTCGAGGGTAA
AATGTAATTTTTGGAAATTTCGGGGTCAAAATGGAATTTTTGGAAATTCG
Found at i:25795317 original size:58 final size:60
Alignment explanation
Indices: 25795107--25795396 Score: 226
Period size: 58 Copynumber: 4.9 Consensus size: 60
25795097 AAAATCGAGA
** * * * * *
25795107 TCAAAAATCAAATTTTTGGACATCCGAGGG-TAAAATGGTAATTTTT-GTAAGTTTCGGGG
1 TCAAAAATGGAATTTTTGGAAATTCGGGGGCAAAAAT-GTAATTTTTGGAAAGTTTCGGGG
* * * * *
25795166 TC-AAAATGGAGTTTTTGGACATTCGGGGG-TAAAATGATAATTTTT-GAAAGTTTTGAGG
1 TCAAAAATGGAATTTTTGGAAATTCGGGGGCAAAAATG-TAATTTTTGGAAAGTTTCGGGG
* * * *
25795224 TCAAAAATGGAGTTTTTGGATATTCGAGGGTAAAAATGTAATTTTTGGAAA-TTTCGGGG
1 TCAAAAATGGAATTTTTGGAAATTCGGGGGCAAAAATGTAATTTTTGGAAAGTTTCGGGG
* * *
25795283 TC-AAAATGGAATTTTT-GAAAGTTTGGGGGCAAAAATATAATTTTT-GAAAGTTAT-AGGG
1 TCAAAAATGGAATTTTTGGAAA-TTCGGGGGCAAAAATGTAATTTTTGGAAAGTT-TCGGGG
* * * *
25795341 TCAAAAATGTAA-TTTTGGATAAGTTTGGGGGTC-AAAATATAATTTTTGGATAGTTT
1 TCAAAAATGGAATTTTTGGA-AA-TTCGGGGG-CAAAAATGTAATTTTTGGAAAGTTT
25795397 AAGGACCTCT
Statistics
Matches: 197, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
57 8 0.04
58 92 0.47
59 54 0.27
60 36 0.18
61 7 0.04
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (60 bp):
TCAAAAATGGAATTTTTGGAAATTCGGGGGCAAAAATGTAATTTTTGGAAAGTTTCGGGG
Found at i:25796494 original size:19 final size:19
Alignment explanation
Indices: 25796472--25796537 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
25796462 ATAATTTTAA
*
25796472 TATTAATTAAT-ATTATTGT
1 TATTAATTAATGA-TATTAT
*
25796491 TATTTATTAATGATATTAT
1 TATTAATTAATGATATTAT
*
25796510 TATT-ATTATCAGGATATTTAT
1 TATTAATTA--ATGATA-TTAT
25796531 TATTAAT
1 TATTAAT
25796538 GCATTCAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.10
19 19 0.49
20 6 0.15
21 8 0.21
22 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
TATTAATTAATGATATTAT
Found at i:25797224 original size:6 final size:6
Alignment explanation
Indices: 25797207--25797296 Score: 55
Period size: 6 Copynumber: 15.5 Consensus size: 6
25797197 TGTATTTTGG
** *
25797207 AAATTT -AATTT AAATTT ATCTTTT AAACTT AAATTT ATAA--T AAATTT
1 AAATTT AAATTT AAATTT A-AATTT AAATTT AAATTT A-AATTT AAATTT
* * * * *
25797254 AAATTT TAA-GT AAATTT AAACTT AAA-AT AAATTT AATTTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
25797297 ACAAATTTAA
Statistics
Matches: 62, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
4 2 0.03
5 14 0.23
6 40 0.65
7 6 0.10
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:25797255 original size:17 final size:17
Alignment explanation
Indices: 25797230--25797307 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
25797220 ATTTATCTTT
* *
25797230 TAAACTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
25797247 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
*
25797264 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
25797281 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
25797298 CAAATTTAAA
1 TAAATTTAAA
25797308 CTTTGTTGGC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:25800835 original size:17 final size:18
Alignment explanation
Indices: 25800798--25800833 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25800788 AACTATGGTA
*
25800798 TAAAATTTAAATTATTTT
1 TAAAATTTAAAATATTTT
*
25800816 TAAATTTTAAAATATTTT
1 TAAAATTTAAAATATTTT
25800834 AATTGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAAATTTAAAATATTTT
Found at i:25801275 original size:8 final size:7
Alignment explanation
Indices: 25801245--25801277 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
25801235 AAAAAATAAG
25801245 AAATTTA
1 AAATTTA
25801252 AAATTTA
1 AAATTTA
25801259 AAATTTA
1 AAATTTA
25801266 AAATTTTA
1 AAA-TTTA
25801274 AAAT
1 AAAT
25801278 AAATGAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:25801676 original size:12 final size:12
Alignment explanation
Indices: 25801655--25801683 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25801645 ATTTTTAAAC
25801655 TATC-AATATTA
1 TATCAAATATTA
25801666 TATCAAATATTA
1 TATCAAATATTA
25801678 TATCAA
1 TATCAA
25801684 TTAAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
TATCAAATATTA
Found at i:25807538 original size:25 final size:25
Alignment explanation
Indices: 25807504--25807553 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
25807494 AATAGGGGCA
25807504 AGCTTTTATGAGATCCTATAATGGT
1 AGCTTTTATGAGATCCTATAATGGT
25807529 AGCTTTTATGAGATCCTATAATGGT
1 AGCTTTTATGAGATCCTATAATGGT
25807554 GTTACCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (25 bp):
AGCTTTTATGAGATCCTATAATGGT
Found at i:25815203 original size:16 final size:16
Alignment explanation
Indices: 25815179--25815212 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
25815169 TAAGTAAAAA
25815179 ATAATATA-AAC-TTT
1 ATAATATATAACATTT
25815193 ATAATATATAACATTT
1 ATAATATATAACATTT
25815209 ATAA
1 ATAA
25815213 AGAAATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATATATAACATTT
Found at i:25815282 original size:23 final size:22
Alignment explanation
Indices: 25815256--25815309 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25815246 AACATTTCTT
25815256 ATAAATAATATAATTT-TTTTATC
1 ATAAATAATA-AATTTATTTT-TC
* *
25815279 ATAACTTAATAAATTTATTTTTT
1 ATAA-ATAATAAATTTATTTTTC
25815302 ATAAATAA
1 ATAAATAA
25815310 AATATGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 3 0.12
23 14 0.54
24 9 0.35
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAATAATAAATTTATTTTTC
Found at i:25819331 original size:26 final size:26
Alignment explanation
Indices: 25819305--25819355 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
25819295 AATAAGAGTG
*
25819305 AAGAATAAAATGAAAA-AAGAAATGTGA
1 AAGAA-AAAAAGAAAAGAA-AAATGTGA
25819332 AAGAAAAAAAGAAAAGAAAAATGT
1 AAGAAAAAAAGAAAAGAAAAATGT
25819356 AACTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (26 bp):
AAGAAAAAAAGAAAAGAAAAATGTGA
Found at i:25821385 original size:26 final size:27
Alignment explanation
Indices: 25821344--25821399 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
25821334 TTTCTCGGAT
*
25821344 ATTTTTTTATCAAACA-AATTAATTTA
1 ATTTTTTTATCAAACATAAATAATTTA
*
25821370 ATTTTTTTAT-AGAACATAAATGATTTA
1 ATTTTTTTATCA-AACATAAATAATTTA
25821397 ATT
1 ATT
25821400 GTAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.04
26 14 0.54
27 11 0.42
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTTTTTTATCAAACATAAATAATTTA
Found at i:25821975 original size:26 final size:26
Alignment explanation
Indices: 25821949--25821999 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
25821939 AATAAGAGTG
*
25821949 AAGAATAAAATGAAAA-AAGAAATGTGA
1 AAGAA-AAAAGGAAAAGAA-AAATGTGA
25821976 AAGAAAAAAGGAAAAGAAAAATGT
1 AAGAAAAAAGGAAAAGAAAAATGT
25822000 AACTGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.12
Consensus pattern (26 bp):
AAGAAAAAAGGAAAAGAAAAATGTGA
Found at i:25837368 original size:16 final size:16
Alignment explanation
Indices: 25837347--25837384 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
25837337 AATCAATTTA
25837347 TATTTTCAAATTCAAT
1 TATTTTCAAATTCAAT
*
25837363 TATTTTCAAATTGAAT
1 TATTTTCAAATTCAAT
*
25837379 TGTTTT
1 TATTTT
25837385 ATAGAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (16 bp):
TATTTTCAAATTCAAT
Found at i:25840608 original size:13 final size:13
Alignment explanation
Indices: 25840588--25840617 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
25840578 ATAACTATGA
25840588 TAAAAAAATTAACT
1 TAAAAAAATTAA-T
25840602 TAAAAAAATTAAT
1 TAAAAAAATTAAT
25840615 TAA
1 TAA
25840618 GCCCATCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAAAAATTAAT
Found at i:25841068 original size:36 final size:36
Alignment explanation
Indices: 25841019--25841103 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
25841009 CGTTTGTTTA
** *
25841019 ATGTTCA-CGAACATGTTCATTTAAC-TTAATCAAAT
1 ATGTTCATCGAACATGTTCA-CGAACATTAATCAAAC
*
25841054 ATGTTCATCGAACATGTTCACGAACATTAATCGAAC
1 ATGTTCATCGAACATGTTCACGAACATTAATCAAAC
25841090 ATGTTCAT-GAACAT
1 ATGTTCATCGAACAT
25841104 ATAATTGAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
35 16 0.36
36 28 0.64
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (36 bp):
ATGTTCATCGAACATGTTCACGAACATTAATCAAAC
Found at i:25841079 original size:12 final size:13
Alignment explanation
Indices: 25841054--25841103 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 13
25841044 TTAATCAAAT
25841054 ATGTTCATCGAAC
1 ATGTTCATCGAAC
25841067 ATGTTCA-CGAAC
1 ATGTTCATCGAAC
*
25841079 A--TTAATCGAAC
1 ATGTTCATCGAAC
25841090 ATGTTCAT-GAAC
1 ATGTTCATCGAAC
25841102 AT
1 AT
25841104 ATAATTGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 3 0.09
11 6 0.19
12 12 0.38
13 11 0.34
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (13 bp):
ATGTTCATCGAAC
Found at i:25841090 original size:23 final size:24
Alignment explanation
Indices: 25841060--25841126 Score: 100
Period size: 23 Copynumber: 2.8 Consensus size: 24
25841050 AAATATGTTC
25841060 ATCGAACATGTTCACGAACAT-TA
1 ATCGAACATGTTCACGAACATATA
*
25841083 ATCGAACATGTTCATGAACATATA
1 ATCGAACATGTTCACGAACATATA
* *
25841107 ATTGAACACGTTCACGAACA
1 ATCGAACATGTTCACGAACA
25841127 ATATTAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCGAACATGTTCACGAACATATA
Found at i:25843504 original size:17 final size:17
Alignment explanation
Indices: 25843482--25843581 Score: 94
Period size: 17 Copynumber: 5.5 Consensus size: 17
25843472 CAATCTTTAA
25843482 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
25843499 TTAAATTTATTTTAAGTTTGAAT
1 TTAAATTTATTTT-A-----AAT
*
25843522 TTAAATTTATTTTGAAT
1 TTAAATTTATTTTAAAT
* *
25843539 TCAAATTTAATTT-AAT
1 TTAAATTTATTTTAAAT
25843555 TTAAAATTTATTTTAAAT
1 TT-AAATTTATTTTAAAT
*
25843573 TTAATTTTA
1 TTAAATTTA
25843582 AATTAAAGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
16 4 0.06
17 43 0.62
18 6 0.09
23 16 0.23
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:25843526 original size:23 final size:22
Alignment explanation
Indices: 25843482--25843587 Score: 83
Period size: 23 Copynumber: 4.7 Consensus size: 22
25843472 CAATCTTTAA
* *
25843482 TTAAATTTATTTTAAATTTAAAT
1 TTAATTTTAATTT-AATTTAAAT
25843505 TT-ATTTTAAGTTTGAATTTAAAT
1 TTAATTTTAA-TTT-AATTTAAAT
*
25843528 TT-ATTTTGAATTCAAATTT-AAT
1 TTAATTTT-AATT-TAATTTAAAT
* *
25843550 TTAATTTAAAATTTATTTTAAAT
1 TTAATTT-TAATTTAATTTAAAT
*
25843573 TTAATTTTAAATTAA
1 TTAATTTTAATTTAA
25843588 AGATTAAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
22 19 0.28
23 46 0.69
24 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (22 bp):
TTAATTTTAATTTAATTTAAAT
Found at i:25843526 original size:40 final size:36
Alignment explanation
Indices: 25843481--25843587 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 36
25843471 CCAATCTTTA
*
25843481 ATTAAATTTATTTTAAATTTAAATTTATTTTAAGTTT
1 ATTAAATTTATTTTAAATTTAAATTTAATTTAA-TTT
* *
25843518 GAATTTAAATTTATTTTGAATTCAAATTTAATTTAATTT
1 --A-TTAAATTTATTTTAAATTTAAATTTAATTTAATTT
* *
25843557 A--AAATTTATTTTAAATTTAATTTTAAATTAA
1 ATTAAATTTATTTTAAATTTAAATTTAATTTAA
25843588 AGATTAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
34 26 0.43
37 1 0.02
39 4 0.07
40 29 0.48
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (36 bp):
ATTAAATTTATTTTAAATTTAAATTTAATTTAATTT
Found at i:25843564 original size:12 final size:12
Alignment explanation
Indices: 25843492--25843585 Score: 90
Period size: 11 Copynumber: 8.2 Consensus size: 12
25843482 TTAAATTTAT
*
25843492 TTTAAATTTAAA
1 TTTAATTTTAAA
*
25843504 TTT-ATTTTAAG
1 TTTAATTTTAAA
25843515 TTTGAA-TTTAAA
1 TTT-AATTTTAAA
*
25843527 TTT-ATTTTGAA
1 TTTAATTTTAAA
* *
25843538 TTCAAATTT-AA
1 TTTAATTTTAAA
*
25843549 TTTAATTTAAAA
1 TTTAATTTTAAA
25843561 TTT-ATTTTAAA
1 TTTAATTTTAAA
25843572 TTTAATTTTAAA
1 TTTAATTTTAAA
25843584 TT
1 TT
25843586 AAAGATTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
10 1 0.02
11 34 0.52
12 30 0.45
13 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:25844265 original size:22 final size:23
Alignment explanation
Indices: 25844240--25844286 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
25844230 AAATATATAT
* *
25844240 TAAATAATAATAATA-TCATTAA
1 TAAATAACAATAATATTAATTAA
25844262 TAAATAACAATAATATTAATTAA
1 TAAATAACAATAATATTAATTAA
25844285 TA
1 TA
25844287 TTAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATAACAATAATATTAATTAA
Found at i:25844267 original size:19 final size:17
Alignment explanation
Indices: 25844222--25844286 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 17
25844212 TTCAACAGCA
25844222 TAATAAATAAATATATAT
1 TAATAAATAAA-ATATAT
25844240 TAA-ATAATAATAATATCAT
1 TAATA-AATAA-AATAT-AT
25844259 TAATAAATAACAATAATAT
1 TAATAAATAA-AAT-ATAT
*
25844278 TAATTAATA
1 TAATAAATA
25844287 TTAAATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 1 0.03
18 12 0.30
19 24 0.60
20 3 0.08
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
TAATAAATAAAATATAT
Found at i:25844285 original size:10 final size:10
Alignment explanation
Indices: 25844229--25844298 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
25844219 GCATAATAAA
25844229 TAAATATATAT
1 TAAATA-ATAT
*
25844240 TAAATAATAA
1 TAAATAATAT
25844250 T-AAT-ATCAT
1 TAAATAAT-AT
25844259 T-AATAA-AT
1 TAAATAATAT
*
25844267 AACAATAATAT
1 TA-AATAATAT
*
25844278 TAATTAATAT
1 TAAATAATAT
25844288 TAAATAATAT
1 TAAATAATAT
25844298 T
1 T
25844299 TTAATAACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
8 4 0.08
9 8 0.17
10 27 0.56
11 9 0.19
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (10 bp):
TAAATAATAT
Found at i:25846322 original size:12 final size:12
Alignment explanation
Indices: 25846307--25846332 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25846297 AATTAAAGAA
25846307 ATAATAGCATTC
1 ATAATAGCATTC
25846319 ATAATAGCATTC
1 ATAATAGCATTC
25846331 AT
1 AT
25846333 TATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:25857219 original size:23 final size:23
Alignment explanation
Indices: 25857193--25857240 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
25857183 TGGAGGATTC
*
25857193 TTCGTTGAATTTCTCGATTTCAA
1 TTCGTTGAATTTCTCAATTTCAA
*
25857216 TTCGTTGAATTTGTCAATTTCAA
1 TTCGTTGAATTTCTCAATTTCAA
25857239 TT
1 TT
25857241 ATTATCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (23 bp):
TTCGTTGAATTTCTCAATTTCAA
Found at i:25858931 original size:42 final size:42
Alignment explanation
Indices: 25858884--25858967 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
25858874 AAAAGGAGTT
25858884 GTTTATGAGTGTTATTT--AGAAATAAAATTATATTGGGGTTTA
1 GTTTATGAGTGTT-TTTGAAG-AATAAAATTATATTGGGGTTTA
* *
25858926 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTGGGGTTTA
25858968 AAAATATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 33 0.87
43 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (42 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTGGGGTTTA
Found at i:25861861 original size:20 final size:20
Alignment explanation
Indices: 25861820--25861862 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
25861810 GTTAAGGTTG
*
25861820 TGGGCTCTTGGGGTGTATTT
1 TGGGCTCTTGGGGTGTAGTT
*
25861840 TGGGCTCTTAGGGT-TGAGTT
1 TGGGCTCTTGGGGTGT-AGTT
25861860 TGG
1 TGG
25861863 AATTGGGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.07, C:0.09, G:0.42, T:0.42
Consensus pattern (20 bp):
TGGGCTCTTGGGGTGTAGTT
Found at i:25861929 original size:21 final size:21
Alignment explanation
Indices: 25861904--25861948 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25861894 ATTAAAATAA
25861904 ATTTAAATT-TAAATTTATTTT
1 ATTTAAATTCT-AATTTATTTT
* *
25861925 ATTTAAGTTCTTATTTATTTT
1 ATTTAAATTCTAATTTATTTT
25861946 ATT
1 ATT
25861949 ATTTTTAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTAAATTCTAATTTATTTT
Found at i:25866401 original size:17 final size:16
Alignment explanation
Indices: 25866379--25866411 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
25866369 ATTATATTTT
25866379 TTTATTTTTAATTTTAA
1 TTTATTTTT-ATTTTAA
25866396 TTTATTTTTATTTTAA
1 TTTATTTTTATTTTAA
25866412 ATAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTTTTATTTTAA
Found at i:25875575 original size:16 final size:18
Alignment explanation
Indices: 25875550--25875586 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25875540 AAATGAAACT
*
25875550 AAAATGAGAA-TGATATG
1 AAAATGAGAATTGAGATG
25875567 AAAAT-AGAATTGAGATG
1 AAAATGAGAATTGAGATG
25875584 AAA
1 AAA
25875587 TGGATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAATGAGAATTGAGATG
Found at i:25875584 original size:22 final size:22
Alignment explanation
Indices: 25875537--25875588 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
25875527 TGATTTGGTT
*
25875537 ATGAAATGAAACTAAAATGAGA
1 ATGAAATGAAAATAAAATGAGA
* *
25875559 ATGATATGAAAATAGAATTGAG-
1 ATGAAATGAAAATA-AAATGAGA
25875581 ATGAAATG
1 ATGAAATG
25875589 GATTATAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.54, C:0.02, G:0.21, T:0.23
Consensus pattern (22 bp):
ATGAAATGAAAATAAAATGAGA
Found at i:25878627 original size:95 final size:95
Alignment explanation
Indices: 25878464--25878753 Score: 580
Period size: 95 Copynumber: 3.1 Consensus size: 95
25878454 AAACAATGTA
25878464 TATTTTGATCATTTTCTCGTCTGCTCTCGAGATAGCAAATATACTTATATTTTGGTTACAATAAT
1 TATTTTGATCATTTTCTCGTCTGCTCTCGAGATAGCAAATATACTTATATTTTGGTTACAATAAT
25878529 TGATTTTTGTGTGAAATTTACCAATATTTT
66 TGATTTTTGTGTGAAATTTACCAATATTTT
25878559 TATTTTGATCATTTTCTCGTCTGCTCTCGAGATAGCAAATATACTTATATTTTGGTTACAATAAT
1 TATTTTGATCATTTTCTCGTCTGCTCTCGAGATAGCAAATATACTTATATTTTGGTTACAATAAT
25878624 TGATTTTTGTGTGAAATTTACCAATATTTT
66 TGATTTTTGTGTGAAATTTACCAATATTTT
25878654 TATTTTGATCATTTTCTCGTCTGCTCTCGAGATAGCAAATATACTTATATTTTGGTTACAATAAT
1 TATTTTGATCATTTTCTCGTCTGCTCTCGAGATAGCAAATATACTTATATTTTGGTTACAATAAT
25878719 TGATTTTTGTGTGAAATTTACCAATATTTT
66 TGATTTTTGTGTGAAATTTACCAATATTTT
25878749 TATTT
1 TATTT
25878754 GAAGTTCCAA
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 195 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (95 bp):
TATTTTGATCATTTTCTCGTCTGCTCTCGAGATAGCAAATATACTTATATTTTGGTTACAATAAT
TGATTTTTGTGTGAAATTTACCAATATTTT
Found at i:25879858 original size:20 final size:20
Alignment explanation
Indices: 25879833--25879874 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
25879823 TTTAATTTCA
25879833 ATCCATA-TTATCGTGATTTT
1 ATCCATAGTT-TCGTGATTTT
25879853 ATCCATAGTTTCGTGATTTT
1 ATCCATAGTTTCGTGATTTT
25879873 AT
1 AT
25879875 TTGATCCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (20 bp):
ATCCATAGTTTCGTGATTTT
Found at i:25880512 original size:6 final size:6
Alignment explanation
Indices: 25880501--25880534 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
25880491 TTGTAAATAA
25880501 TAATTT TAATTT TAATTT TAATTT TAATTT TAAT
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAAT
25880535 CAACCTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TAATTT
Found at i:25880989 original size:40 final size:42
Alignment explanation
Indices: 25880903--25880990 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 42
25880893 TATAAGAAGG
* * *
25880903 ATAAAAAATTATTATAAAGTTGTAATGTATTGTAAAAATTAT
1 ATAAAAAATTATTAGAAAGTTGTAAAGTATCGTAAAAATTAT
*
25880945 -TAAAAAA-TATTAGAAA-TTGTAAAAG-ATCGTAAAAATTTT
1 ATAAAAAATTATTAGAAAGTTGT-AAAGTATCGTAAAAATTAT
25880984 ATAAAAA
1 ATAAAAA
25880991 TAATAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
39 16 0.40
40 17 0.43
41 7 0.17
ACGTcount: A:0.55, C:0.01, G:0.09, T:0.35
Consensus pattern (42 bp):
ATAAAAAATTATTAGAAAGTTGTAAAGTATCGTAAAAATTAT
Found at i:25881374 original size:6 final size:6
Alignment explanation
Indices: 25881365--25881412 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
25881355 TTTATTTTTA
*
25881365 AAAAAT AAAAATT AAAAAAT AGAAAAG AAAAAT -AAAAT AAAAAT AAAA
1 AAAAAT AAAAA-T -AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAA
25881413 TGGATATGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 5 0.14
6 19 0.53
7 7 0.19
8 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:25881381 original size:14 final size:15
Alignment explanation
Indices: 25881362--25881390 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25881352 GAGTTTATTT
25881362 TTAAAAAATA-AAAA
1 TTAAAAAATAGAAAA
25881376 TTAAAAAATAGAAAA
1 TTAAAAAATAGAAAA
25881391 GAAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
TTAAAAAATAGAAAA
Found at i:25881455 original size:87 final size:85
Alignment explanation
Indices: 25881349--25881540 Score: 273
Period size: 87 Copynumber: 2.2 Consensus size: 85
25881339 AAAATAAAGA
*
25881349 ATGGAGTTTATTTTTAAAAAATAAAAATTAAAAAATAGAAAAGAAAAAT-AAAATAAAAATAAAA
1 ATGGAATTTATTTTTAAAAAATAAAAATTAAAAAA-AG----GAAAAATAAAAATAAAAATAAAA
25881413 TGGATATG-TC-TATTTCAATTATT
61 TGGATATGCTCTTATTTCAATTATT
25881436 ATGGAATTTATTTTTAAAAAATAAAAATTAAAAAAAGGAAAAATAAAAATAAAAATAAAATGGAT
1 ATGGAATTTATTTTTAAAAAATAAAAATTAAAAAAAGGAAAAATAAAAATAAAAATAAAATGGAT
25881501 ATGTCTCTTATTTCAATTATT
66 ATG-CTCTTATTTCAATTATT
*
25881522 ATGAAATTATTATTTTTAA
1 ATGGAA-T-TTATTTTTAA
25881541 CTCTTTAGAA
Statistics
Matches: 97, Mismatches: 2, Indels: 11
0.88 0.02 0.10
Matches are distributed among these distances:
82 7 0.07
83 23 0.24
85 2 0.02
86 20 0.21
87 35 0.36
88 10 0.10
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (85 bp):
ATGGAATTTATTTTTAAAAAATAAAAATTAAAAAAAGGAAAAATAAAAATAAAAATAAAATGGAT
ATGCTCTTATTTCAATTATT
Found at i:25881810 original size:18 final size:18
Alignment explanation
Indices: 25881766--25881821 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
25881756 AATTAATTAA
25881766 ATTTTTAAACT-TAAAAAT
1 ATTTTTAAA-TATAAAAAT
* *
25881784 A-ATTAAAATATAAAAAT
1 ATTTTTAAATATAAAAAT
*
25881801 ATTTTTAAATATTAAAAT
1 ATTTTTAAATATAAAAAT
25881819 ATT
1 ATT
25881822 AATAATTGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 1 0.03
17 13 0.42
18 17 0.55
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTTTAAATATAAAAAT
Found at i:25882925 original size:31 final size:29
Alignment explanation
Indices: 25882867--25882937 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 29
25882857 AAAGTTTGAA
* *
25882867 TTAATTTTAAATTCATTTTTAAGTTTATC
1 TTAAATTTAAATTCATTTTTAAATTTATC
* *
25882896 TTAAATTTAAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTCA-TT-TTTAAATTTATC
25882927 TTAAATTTAAA
1 TTAAATTTAAA
25882938 CTTAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 13 0.36
30 2 0.06
31 21 0.58
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (29 bp):
TTAAATTTAAATTCATTTTTAAATTTATC
Found at i:25882946 original size:17 final size:17
Alignment explanation
Indices: 25882914--25882948 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25882904 AAATTTACTT
* *
25882914 ATTTAAATTTATTTTAA
1 ATTTAAACTTAATTTAA
25882931 ATTTAAACTTAATTTAA
1 ATTTAAACTTAATTTAA
25882948 A
1 A
25882949 ATAATATTAA
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAACTTAATTTAA
Found at i:25883011 original size:27 final size:27
Alignment explanation
Indices: 25882981--25883078 Score: 142
Period size: 27 Copynumber: 3.5 Consensus size: 27
25882971 CAATGTCCAT
25882981 TTACAAAAGCCCAAATTAAAGGCCCGA
1 TTACAAAAGCCCAAATTAAAGGCCCGA
*
25883008 TTACAAAAGCTCAAATTAAAGGCCCGA
1 TTACAAAAGCCCAAATTAAAGGCCCGA
* *
25883035 TTATAAAAAGCCCAAAATTAAAGGTCCGA
1 TTA-CAAAAGCCC-AAATTAAAGGCCCGA
25883064 TTACAAAAAGCCCAA
1 TTAC-AAAAGCCCAA
25883079 TTGGGCTGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 29 0.46
28 9 0.14
29 25 0.40
ACGTcount: A:0.47, C:0.22, G:0.13, T:0.17
Consensus pattern (27 bp):
TTACAAAAGCCCAAATTAAAGGCCCGA
Found at i:25883063 original size:29 final size:27
Alignment explanation
Indices: 25882985--25883078 Score: 134
Period size: 29 Copynumber: 3.4 Consensus size: 27
25882975 GTCCATTTAC
*
25882985 AAAAGCCCAAATTAAAGGCCCGATTAC
1 AAAAGCCCAAATTAAAGGCCCGATTAA
*
25883012 AAAAGCTCAAATTAAAGGCCCGATTATA
1 AAAAGCCCAAATTAAAGGCCCGATTA-A
*
25883040 AAAAGCCCAAAATTAAAGGTCCGATTACA
1 AAAAGCCC-AAATTAAAGGCCCGATTA-A
25883069 AAAAGCCCAA
1 AAAAGCCCAA
25883079 TTGGGCTGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
27 25 0.42
28 9 0.15
29 26 0.43
ACGTcount: A:0.48, C:0.22, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAAGCCCAAATTAAAGGCCCGATTAA
Found at i:25883678 original size:3 final size:3
Alignment explanation
Indices: 25883670--25883711 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
25883660 ATGGAAACAT
25883670 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25883712 AGCAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25884974 original size:90 final size:89
Alignment explanation
Indices: 25884816--25885050 Score: 362
Period size: 90 Copynumber: 2.6 Consensus size: 89
25884806 CTCTGAATTG
* * *
25884816 TCCAGAAATTACATTTTGACCCTAAAATTTTTTCAAAATTATATTTTGACCCCAAAACTTTTCCA
1 TCCA-AAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCA
*
25884881 AAATTACATTTCGACCTCAAAACTTT
65 AAATTACATTTCAACC-CAAAACTTT
** * *
25884907 TTGAAAATTACATTTCGACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCAA
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAA
25884972 AATTACATTTCAACCCAAAACTTT
66 AATTACATTTCAACCCAAAACTTT
* *
25884996 TCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATCATATTTTGACCCCAAA
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAA
25885051 GTTTCAAAAA
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
89 58 0.45
90 70 0.54
91 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (89 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAA
AATTACATTTCAACCCAAAACTTT
Found at i:25885069 original size:59 final size:59
Alignment explanation
Indices: 25884825--25885101 Score: 171
Period size: 59 Copynumber: 4.7 Consensus size: 59
25884815 GTCCAGAAAT
* * * * * * * * * * *
25884825 TACATTTTGACCCTAAAATTTTTTCAAAATTATATTTTGACCCCAAAACTTTTCCAAAAT
1 TACATTTTAACCCCAAAACTTTTCCAAAATCACA-TTTCAACCCAAAACGTTTCAAAAAA
** * ** * * * * *
25884885 TACATTTCGACCTCAAAACTTTTTGAAAATTACATTTCGACCCCAAAACTTTTCCAAAAT
1 TACATTTTAACCCCAAAACTTTTCCAAAATCACATTTC-AACCCAAAACGTTTCAAAAAA
* * * * * * *
25884945 TATATTTTGACCCTAAAACTTTTCCAAAATTACATTTCAACCCAAAACTTTTCCAAAAT
1 TACATTTTAACCCCAAAACTTTTCCAAAATCACATTTCAACCCAAAACGTTTCAAAAAA
* ** *
25885004 TACATTTTAACCCCAAAACTTTTCCAAAATCATATTTTGACCCCAAA-GTTTCAAAAAAA
1 TACATTTTAACCCCAAAACTTTTCCAAAATCACATTTCAACCCAAAACGTTTC-AAAAAA
* * * * *
25885063 TGCATTTTTACCCCGAAAC-TTTCAAAAATTACCATTTCA
1 TACATTTTAACCCCAAAACTTTTCCAAAATCA-CATTTCA
25885102 CCCTCAAACT
Statistics
Matches: 181, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
58 14 0.08
59 86 0.48
60 81 0.45
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (59 bp):
TACATTTTAACCCCAAAACTTTTCCAAAATCACATTTCAACCCAAAACGTTTCAAAAAA
Found at i:25885099 original size:30 final size:30
Alignment explanation
Indices: 25884816--25885050 Score: 310
Period size: 30 Copynumber: 7.8 Consensus size: 30
25884806 CTCTGAATTG
* *
25884816 TCCAGAAATTACATTTTGACCCTAAAATTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
* *
25884847 TTCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
25884877 TCCAAAATTACATTTCGACCTCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
** *
25884907 TTGAAAATTACATTTCGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
25884937 TCCAAAATTATATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
25884967 TCCAAAATTACA-TTTCAACCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
25884996 TCCAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
25885026 TCCAAAATCATATTTTGACCCCAAA
1 TCCAAAATTACATTTTGACCCCAAA
25885051 GTTTCAAAAA
Statistics
Matches: 178, Mismatches: 25, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
29 26 0.15
30 149 0.84
31 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:25893009 original size:21 final size:21
Alignment explanation
Indices: 25892985--25893051 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
25892975 AAGTGGATGC
*
25892985 AACAGCGAGGAAAGCGGAGGT
1 AACAGCGAGGGAAGCGGAGGT
* * *
25893006 AACAGTGAGGGAAGCGAAGGC
1 AACAGCGAGGGAAGCGGAGGT
* * *
25893027 ATCAACGAGGGAAGCAGAGGT
1 AACAGCGAGGGAAGCGGAGGT
25893048 AACA
1 AACA
25893052 AGAAAGTATG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.39, T:0.06
Consensus pattern (21 bp):
AACAGCGAGGGAAGCGGAGGT
Found at i:25893431 original size:43 final size:43
Alignment explanation
Indices: 25893348--25893461 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
25893338 AATCTATTAA
* * * *
25893348 TTTTAGCGGCATTTGT-GGGAAAACGCCGCTAAAGATCATGTT
1 TTTTAGCGGCGTTTGTAAGGAAAGCGCCGCTAAAGACCATGTT
*
25893390 TTTTAGCGGCGTTTGTAAGGAAAGCGCTGCTAAAGACCATGTT
1 TTTTAGCGGCGTTTGTAAGGAAAGCGCCGCTAAAGACCATGTT
* *
25893433 CTTTAGCGGCGTTTGTAAGAAAAGCGCCG
1 TTTTAGCGGCGTTTGTAAGGAAAGCGCCG
25893462 ATATAAGCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 15 0.24
43 48 0.76
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
TTTTAGCGGCGTTTGTAAGGAAAGCGCCGCTAAAGACCATGTT
Found at i:25895918 original size:22 final size:21
Alignment explanation
Indices: 25895890--25895964 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
25895880 TTTAACTGCG
25895890 ATTAAAATTTTAAAATATAAAA
1 ATTAAAA-TTTAAAATATAAAA
*
25895912 ATTAAAATTGATAAATATAAAA
1 ATTAAAATTTA-AAATATAAAA
* *
25895934 ACATAAAAATTAAAAT-TAACTAA
1 A-TTAAAATTTAAAATATAA--AA
25895957 ATTAAAAT
1 ATTAAAAT
25895965 ACATATATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 6 0.14
22 27 0.63
23 10 0.23
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (21 bp):
ATTAAAATTTAAAATATAAAA
Found at i:25895940 original size:30 final size:30
Alignment explanation
Indices: 25895901--25895969 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
25895891 TTAAAATTTT
* *
25895901 AAAATATAAAAATTAAAATTGA-TAAATATA
1 AAAACATAAAAATTAAAATTAACTAAAT-TA
25895931 AAAACATAAAAATTAAAATTAACTAAATTA
1 AAAACATAAAAATTAAAATTAACTAAATTA
25895961 AAATACATA
1 AAA-ACATA
25895970 TATTAAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (30 bp):
AAAACATAAAAATTAAAATTAACTAAATTA
Found at i:25906800 original size:181 final size:176
Alignment explanation
Indices: 25906478--25906800 Score: 459
Period size: 176 Copynumber: 1.8 Consensus size: 176
25906468 AAAATGATCG
* *
25906478 AACAACCTATGCATCACAAAGGCCTGGGCCTAGGAGAAGTGAAAACTTCAAAAGAATGAATAATA
1 AACAACCTATGCATCACAAAGGACTGGGCCTAGGAGAAGTGAAAACTTCAAAAGAATGAAAAATA
* **
25906543 ACAAATAACATTGCAGTTTAGACAACATAAGAAAGTTTGGAACAACCTCAGACATTTTCCATTTT
66 ACAAATAACATTGCAGTTTAGACAACATAAAAAAGCCTGGAACAACCTCAGACATTTTCCATTTT
*
25906608 AATCTTTTGACTCATCCTGAATAGGTTCAGACAATGAGCAATGGCA
131 AATCATTTGACTCATCCTGAATAGGTTCAGACAATGAGCAATGGCA
* * *
25906654 AACAACCTATGCTTCACAAA-GACTAGGGCCTAGGAGAAGTGAAAACTTCTAAAGGATGAAAAAT
1 AACAACCTATGCATCACAAAGGACT-GGGCCTAGGAGAAGTGAAAACTTCAAAAGAATGAAAAAT
* * * *
25906718 ATTGCAAATGATATTGCAGTTGTTTAGACAACATAAAAAAGCCTGGAACAACCTCAGATATTTTC
65 A--ACAAATAACATTGCA---GTTTAGACAACATAAAAAAGCCTGGAACAACCTCAGACATTTTC
*
25906783 TATTTTAATCATTTGACT
125 CATTTTAATCATTTGACT
25906801 AACCTGCCAA
Statistics
Matches: 127, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
175 3 0.02
176 56 0.44
178 12 0.09
181 56 0.44
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.26
Consensus pattern (176 bp):
AACAACCTATGCATCACAAAGGACTGGGCCTAGGAGAAGTGAAAACTTCAAAAGAATGAAAAATA
ACAAATAACATTGCAGTTTAGACAACATAAAAAAGCCTGGAACAACCTCAGACATTTTCCATTTT
AATCATTTGACTCATCCTGAATAGGTTCAGACAATGAGCAATGGCA
Found at i:25915544 original size:19 final size:20
Alignment explanation
Indices: 25915520--25915557 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25915510 TAAAATGTTG
*
25915520 AATGTT-TTCCTTTTTTCTA
1 AATGTTCTTCCATTTTTCTA
25915539 AATGTTCTTCCATTTTTCT
1 AATGTTCTTCCATTTTTCT
25915558 TAGAGGAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.61
Consensus pattern (20 bp):
AATGTTCTTCCATTTTTCTA
Found at i:25916781 original size:39 final size:40
Alignment explanation
Indices: 25916646--25916794 Score: 149
Period size: 40 Copynumber: 3.8 Consensus size: 40
25916636 AAGAGTACTT
* * *
25916646 ACTGAACTAGCAGTGACACTGTAAACAGTGCGATATTACT
1 ACTGAATTAGCAGTGACACTGTAAACACTGCGATATTACA
** * * * *
25916686 ACTGAATCGGTAGTGACACTATAAACATTGCGACATTACA
1 ACTGAATTAGCAGTGACACTGTAAACACTGCGATATTACA
* *
25916726 ACTGAATTGGCTGTGACACTGTAAACACTGC-AGTA-TACA
1 ACTGAATTAGCAGTGACACTGTAAACACTGCGA-TATTACA
* * *
25916765 ACTGGATTAGCAGTGACATTGTAAAGACTG
1 ACTGAATTAGCAGTGACACTGTAAACACTG
25916795 GTAGATCACT
Statistics
Matches: 89, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 30 0.34
40 59 0.66
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (40 bp):
ACTGAATTAGCAGTGACACTGTAAACACTGCGATATTACA
Found at i:25925615 original size:2 final size:2
Alignment explanation
Indices: 25925608--25925637 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25925598 CGTACTTTCA
25925608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25925638 GACCAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25928787 original size:17 final size:17
Alignment explanation
Indices: 25928760--25928827 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
25928750 ATAATTTAAT
25928760 TTTTAAA-TTAAATTTA
1 TTTTAAATTTAAATTTA
25928776 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
** * *
25928793 CATAAAATTTAAGTTTA
1 TTTTAAATTTAAATTTA
* *
25928810 TTATAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
25928827 T
1 T
25928828 AAATTAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:25930800 original size:59 final size:59
Alignment explanation
Indices: 25930653--25931031 Score: 543
Period size: 59 Copynumber: 6.4 Consensus size: 59
25930643 ATTTATATGT
* * *
25930653 CCCCGAACAGTTCCAAAATTCCGTTTTTAACCCCAATTTCACCAAAAATTACCA-TTTAC
1 CCCCGAAC-TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * * *
25930712 CCCCGAATTTTCCAAAATTCCATTCTTAACCCCAAATTCACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
*
25930771 CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
25930830 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* *
25930889 CCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACC-AAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * * * *
25930947 CCCC-AAATCTTCCAAAATTCCACTTTCAACCCCGATTTTACCAAAAATTACCATTTTGC
1 CCCCGAACT-TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
*
25931006 CCCCGTAA--GTCCAAAATTACCATTTT
1 CCCCG-AACTTTCCAAAATT-CCATTTT
25931032 GCCCCCGGGT
Statistics
Matches: 292, Mismatches: 22, Indels: 12
0.90 0.07 0.04
Matches are distributed among these distances:
57 3 0.01
58 98 0.34
59 189 0.65
61 2 0.01
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (59 bp):
CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
Found at i:25930874 original size:118 final size:118
Alignment explanation
Indices: 25930663--25931009 Score: 538
Period size: 117 Copynumber: 3.0 Consensus size: 118
25930653 CCCCGAACAG
* * *
25930663 TTCCAAAATTCCGTTTTTAACCCCAATTTCACCAAAAATTACCA-TTTACCCCCGAATTTTCCAA
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAATTTCCAA
* * *
25930727 AATTCCATTCTTAACCCCAAATTCACCAAAAATTACCATTTTACCCCCAAACT
66 AATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACT
*
25930780 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAA
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAATTTCCAA
* *
25930845 AATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTCGAACT
66 AATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACT
*
25930898 TTCCAAAATTCCATTTTTAACCTCGATTTCACC-AAAATTACCATTTTACCCCC-AAATCTTCCA
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAAT-TTCCA
* * * *
25930961 AAATTCCACTTTCAACCCCGATTTTACCAAAAATTACCATTTTGCCCCC
65 AAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCC
25931010 GTAAGTCCAA
Statistics
Matches: 213, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
116 3 0.01
117 111 0.52
118 99 0.46
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (118 bp):
TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAATTTCCAA
AATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACT
Found at i:25931056 original size:28 final size:28
Alignment explanation
Indices: 25930990--25931059 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
25930980 GATTTTACCA
*
25930990 AAAATTACCATTTTGCCCCCGTAAGTCC
1 AAAAGTACCATTTTGCCCCCGTAAGTCC
*
25931018 AAAATTACCATTTTGCCCCCGGGT-A-TCC
1 AAAAGTACCATTTTGCCCCC--GTAAGTCC
*
25931046 AAAAGTCCCATTTT
1 AAAAGTACCATTTT
25931060 CAACCCTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 35 0.92
29 1 0.03
30 2 0.05
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.30
Consensus pattern (28 bp):
AAAAGTACCATTTTGCCCCCGTAAGTCC
Found at i:25942224 original size:10 final size:11
Alignment explanation
Indices: 25942203--25942233 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
25942193 TTCTGATTTT
25942203 GAAAAATCATA
1 GAAAAATCATA
25942214 GAAAAAT-ATA
1 GAAAAATCATA
25942224 GAAAAATCAT
1 GAAAAATCAT
25942234 TAGAGTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (11 bp):
GAAAAATCATA
Found at i:25942862 original size:23 final size:23
Alignment explanation
Indices: 25942836--25942933 Score: 126
Period size: 23 Copynumber: 4.2 Consensus size: 23
25942826 ACACTAGCGC
25942836 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
25942859 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
25942882 GCTCTCTGTTATTAGCACTATGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
25942907 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
25942930 GCTC
1 GCTC
25942934 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.05
23 43 0.66
25 17 0.26
26 2 0.03
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:25942967 original size:23 final size:23
Alignment explanation
Indices: 25942932--25943025 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
25942922 CTTTGTGTGC
*
25942932 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
25942955 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
25942978 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
25943003 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
25943025 T
1 T
25943026 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:25949271 original size:23 final size:23
Alignment explanation
Indices: 25949245--25949342 Score: 126
Period size: 23 Copynumber: 4.2 Consensus size: 23
25949235 ACACTAGCAC
25949245 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
25949268 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
25949291 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
25949316 GCTCTCCGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
25949339 GCTC
1 GCTC
25949343 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.05
23 43 0.66
25 16 0.25
26 3 0.05
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:25949376 original size:23 final size:23
Alignment explanation
Indices: 25949341--25949434 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
25949331 CTTTGTGTGC
*
25949341 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
25949364 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
25949387 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
25949412 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
25949434 T
1 T
25949435 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:25951737 original size:75 final size:76
Alignment explanation
Indices: 25951584--25952321 Score: 1157
Period size: 76 Copynumber: 9.8 Consensus size: 76
25951574 AGACCGCACT
25951584 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGAT-ACGAAGTCTTTATCTCTGAAAT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAAC-AAGTCTTTATCTCTGAAAT
25951648 TGAAGTAAGAGC
65 TGAAGTAAGAGC
*
25951660 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT
*
25951724 GAAGTAAAAGC
66 GAAGTAAGAGC
* *
25951735 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT
25951799 GAAGTAAGAGC
66 GAAGTAAGAGC
* *
25951810 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT
25951874 GAAGTAAGAGC
66 GAAGTAAGAGC
* * *
25951885 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT
*
25951949 GAAGTAAAAGC
66 GAAGTAAGAGC
* * * *
25951960 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAA-TTGGATATCAGGTATTTGTCTCTGAAAT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTA-AAGTTGGATAACAAGTCTTTATCTCTGAAAT
25952024 TGAAGTAAGAGC
65 TGAAGTAAGAGC
* * * *
25952036 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTGTCTCTGAAATT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT
25952101 GAAGTAAGAGC
66 GAAGTAAGAGC
* * * *
25952112 AAGATCATTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTATCTCTGAAATT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT
25952177 GAAGTAAGAGC
66 GAAGTAAGAGC
* * *
25952188 AAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT
25952253 GAAGTAAGAGC
66 GAAGTAAGAGC
* *
25952264 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAG-CATTTATCTC
1 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTC-TTTATCTC
25952322 ACTAAAAGGG
Statistics
Matches: 628, Mismatches: 29, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
75 290 0.46
76 338 0.54
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (76 bp):
AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT
GAAGTAAGAGC
Found at i:25951856 original size:150 final size:151
Alignment explanation
Indices: 25951584--25952306 Score: 1173
Period size: 150 Copynumber: 4.8 Consensus size: 151
25951574 AGACCGCACT
* *
25951584 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGAT-ACGAAGTCTTTATCTCTGAAAT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC-AAGTCTTTATCTCTGAAAT
25951648 TGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTGGATAACACGTCTTTA
65 TGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTGGATAACACGTCTTTA
*
25951713 TCTCTGAAATTGAAGTAAAAGC
130 TCTCTGAAATTGAAGTAAGAGC
* *
25951735 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
*
25951799 GAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTAT
66 GAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTGGATAACACGTCTTTAT
25951864 CTCTGAAATTGAAGTAAGAGC
131 CTCTGAAATTGAAGTAAGAGC
*
25951885 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
* * * * * *
25951949 GAAGTAAAAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATATCAGGTATTTG
66 GAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTA-AAGTGGATAACACGTCTTTA
25952014 TCTCTGAAATTGAAGTAAGAGC
130 TCTCTGAAATTGAAGTAAGAGC
* * * *
25952036 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTGTCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
* * * *
25952101 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTA
66 GAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAG-TGGATAACACGTCTTTA
25952166 TCTCTGAAATTGAAGTAAGAGC
130 TCTCTGAAATTGAAGTAAGAGC
* *
25952188 AAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
*
25952253 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATA
66 GAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAG-TGGATA
25952307 GCAAGCATTT
Statistics
Matches: 537, Mismatches: 31, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
150 214 0.40
151 110 0.20
152 213 0.40
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (151 bp):
AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
GAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTGGATAACACGTCTTTAT
CTCTGAAATTGAAGTAAGAGC
Found at i:25952987 original size:200 final size:200
Alignment explanation
Indices: 25952644--25953284 Score: 1104
Period size: 200 Copynumber: 3.2 Consensus size: 200
25952634 ATAAACAGTG
*
25952644 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAATGTGAGCAGATC
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAATGTGAGCAAATC
25952709 TTCGAACCCGGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
66 TTCGAACCCGGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
*
25952774 GAGGATATCCAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCGAAAC
131 GAGGAGATCCAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCGAAAC
25952839 AAGCA
196 AAGCA
25952844 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAATGTGAGCAAATC
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAATGTGAGCAAATC
*
25952909 TTCGAACCCGGCTTCCTAATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
66 TTCGAACCCGGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
* *
25952974 GAGGAGATCCAGAGAAATGGACTAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCGAAAC
131 GAGGAGATCCAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCGAAAC
*
25953039 AAGCG
196 AAGCA
*
25953044 AGACGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAATGTGAGCAAATC
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAATGTGAGCAAATC
* *
25953109 TTCGATCCCGGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
66 TTCGAACCCGGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
* **
25953174 GAGGAGATCCAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAAC
131 GAGGAGATCCAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCGAAAC
25953239 AAATG-A
196 -AA-GCA
** * * *
25953245 TTGCGGTCATCTTCCTGATGAGACACAGTGAAGAAGACCA
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCA
25953285 GGTCAATGAA
Statistics
Matches: 417, Mismatches: 22, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
200 380 0.91
201 36 0.09
202 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.20
Consensus pattern (200 bp):
AGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAATGTGAGCAAATC
TTCGAACCCGGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
GAGGAGATCCAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCGAAAC
AAGCA
Found at i:25953654 original size:17 final size:17
Alignment explanation
Indices: 25953627--25953708 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
25953617 ATAATTTAAT
25953627 TTTTAAA-TTAAATTTA
1 TTTTAAATTTAAATTTA
25953643 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
** * *
25953660 CATAAAATTTAAGTTTA
1 TTTTAAATTTAAATTTA
*
25953677 TTATAAATTTAAACTTATA
1 TTTTAAATTTAAA-TT-TA
**
25953696 AATTAAATTTAAA
1 TTTTAAATTTAAA
25953709 AAGTCCAAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 7 0.14
17 30 0.59
18 2 0.04
19 12 0.24
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:25953655 original size:6 final size:6
Alignment explanation
Indices: 25953628--25953708 Score: 57
Period size: 6 Copynumber: 14.0 Consensus size: 6
25953618 TAATTTAATT
* * * *
25953628 TTTAAA -TTAAA TTT-AT TTTAAA TTTAAA TTTACA -TAAAA TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
25953673 TTT--A TTATAAA TTTAAA CTTATAAA -TTAAA TTTAAA
1 TTTAAA TT-TAAA TTTAAA -TT-TAAA TTTAAA TTTAAA
25953709 AAGTCCAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
4 2 0.03
5 17 0.29
6 30 0.52
7 5 0.09
8 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:25953678 original size:34 final size:36
Alignment explanation
Indices: 25953634--25953708 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 36
25953624 AATTTTTAAA
* *
25953634 TTAAATTTATTTTAAATTTAAA-TT-TACATAAAAT
1 TTAAATTTATTATAAATTTAAACTTATAAATAAAAT
* *
25953668 TTAAGTTTATTATAAATTTAAACTTATAAATTAAAT
1 TTAAATTTATTATAAATTTAAACTTATAAATAAAAT
25953704 TTAAA
1 TTAAA
25953709 AAGTCCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 20 0.59
35 2 0.06
36 12 0.35
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (36 bp):
TTAAATTTATTATAAATTTAAACTTATAAATAAAAT
Found at i:25955636 original size:59 final size:59
Alignment explanation
Indices: 25955540--25955880 Score: 490
Period size: 59 Copynumber: 5.8 Consensus size: 59
25955530 CCCCAAACAG
* * *
25955540 TTCCAAAATTCTATTTTTAACCCCGATTTCACCAAAAATTATCATTTTACCCCCGAACT
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACT
* * * * * *
25955599 TTCTAAAATTCCATTCTTAACCTCGAATTCACCAAAAATTACTATTTTACCCCTAAACT
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACT
* *
25955658 CTCCAAAATTCCATTTTTAACCCCGATTTCACAAAAAATTACCATTTTACCCCTGAACT
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACT
* * * *
25955717 CTCCAAAATTCTA-TTTTAACCTCGATTTCACTAAAAATTACCATTTTACCCCTGAACT
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACT
* * *
25955775 TTCCAAAATTCCATTTTTAACCTCGATTTCACC-AAAATTACCATTTTACCCC-CAAAT
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACT
25955832 CTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
1 -TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
25955881 GCCCTCGTAA
Statistics
Matches: 253, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
57 3 0.01
58 105 0.42
59 145 0.57
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACT
Found at i:25955781 original size:117 final size:115
Alignment explanation
Indices: 25955540--25955880 Score: 484
Period size: 117 Copynumber: 2.9 Consensus size: 115
25955530 CCCCAAACAG
* * * *
25955540 TTCCAAAATTCTATTTTTAACCCCGATTTCACCAAAAATTATCATTTTACCCCCGAACTTTCTAA
1 TTCCAAAATTCCATTTTTAACCCCGATTTCA-CAAAAATTACCATTTTA-CCCCGAACTCTCCAA
* *
25955605 AATTCCATTCTTAACCTCGAATTCACCAAAAATTACTATTTTACCCCTAAACT
64 AATTCCATT-TTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACT
*
25955658 CTCCAAAATTCCATTTTTAACCCCGATTTCACAAAAAATTACCATTTTACCCCTGAACTCTCCAA
1 TTCCAAAATTCCATTTTTAACCCCGATTTCAC-AAAAATTACCATTTTACCCC-GAACTCTCCAA
* * *
25955723 AATTCTATTTTAACCTCGATTTCACTAAAAATTACCATTTTACCCCTGAACT
64 AATTCCATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACT
* * * *
25955775 TTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAATTACCATTTTACCCCCAAATCTTCCAAA
1 TTCCAAAATTCCATTTTTAACCCCGATTTCACAAAAATTACCATTTTACCCCGAACTC-TCCAAA
*
25955840 ATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
65 ATTCCA-TTTTAACCTCGATTTCACCAAAAATTACCATTTT
25955881 GCCCTCGTAA
Statistics
Matches: 201, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
115 4 0.02
116 30 0.15
117 106 0.53
118 61 0.30
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (115 bp):
TTCCAAAATTCCATTTTTAACCCCGATTTCACAAAAATTACCATTTTACCCCGAACTCTCCAAAA
TTCCATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACT
Found at i:25962043 original size:2 final size:2
Alignment explanation
Indices: 25962036--25962063 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25962026 TTCATGATCC
25962036 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
25962064 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:25968109 original size:64 final size:64
Alignment explanation
Indices: 25968008--25968127 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
25967998 TTCTTCAAAT
* *
25968008 AATTTGGTGTTTAAAATATATGGTGATGGAGCACATGCATTTTGGTTTTTTTTTTTTTTTGTAC
1 AATTTGATGTTTAAAATATATGGTGATGGAGCACATGCATTTTGGTATTTTTTTTTTTTTGTAC
*
25968072 AATTTGATGTTTAAAATATATGGTGATGGATCACATGCATTTTGGTATTTTTTTTT
1 AATTTGATGTTTAAAATATATGGTGATGGAGCACATGCATTTTGGTATTTTTTTTT
25968128 GTACAATTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.24, C:0.06, G:0.19, T:0.51
Consensus pattern (64 bp):
AATTTGATGTTTAAAATATATGGTGATGGAGCACATGCATTTTGGTATTTTTTTTTTTTTGTAC
Found at i:25968654 original size:21 final size:20
Alignment explanation
Indices: 25968606--25968646 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
25968596 TTTTAAAATT
* *
25968606 TAAAATTTATTAAAAAATCA
1 TAAAATTTATAAAAAAAACA
25968626 TAAAATTTATAAAAAAAACA
1 TAAAATTTATAAAAAAAACA
25968646 T
1 T
25968647 TATAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATTTATAAAAAAAACA
Found at i:25972013 original size:16 final size:16
Alignment explanation
Indices: 25971992--25972026 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
25971982 CCTCGAATAA
*
25971992 TATAATAATTTTTAAT
1 TATAATAATTTTCAAT
*
25972008 TATAATAGTTTTCAAT
1 TATAATAATTTTCAAT
25972024 TAT
1 TAT
25972027 TACAAGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TATAATAATTTTCAAT
Found at i:25974715 original size:31 final size:31
Alignment explanation
Indices: 25974677--25974736 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
25974667 CTTGAAAGAA
*
25974677 AGCAATATTAACCATCAGACCAATGTTTGGG
1 AGCAATATCAACCATCAGACCAATGTTTGGG
*
25974708 AGCAATATCAACCATTAGACCAATGTTTG
1 AGCAATATCAACCATCAGACCAATGTTTG
25974737 TGACACAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (31 bp):
AGCAATATCAACCATCAGACCAATGTTTGGG
Found at i:25978991 original size:111 final size:105
Alignment explanation
Indices: 25978780--25978994 Score: 277
Period size: 111 Copynumber: 2.0 Consensus size: 105
25978770 TGGTTGCATA
* * * *
25978780 TATGGCATCCTGGGTGAAGGAAGAGCAAGTGGAGGAACCTCCCCTTGACCCTCATTCCGATCCCT
1 TATGGCATCCTAGGTGAAGGAAGAGCAAGTGGAGGAACCTCCCCCTGACCCTCACTCCGAGCCCT
** *
25978845 GCTATGCTGTTCTATGTATTGTTCTACAGAAGCAGGAGTG
66 GCTATGCTGTTCTACATATTGTTCAACAGAAGCAGGAGTG
*
25978885 TATGGCATCCTAGGTGAAGGAAGAGCAAGTGGAGGAACCTCAGCATCTCCCTGACCCTCACTCTG
1 TATGGCATCCTAGGTGAAGGAAGAGCAAGTGGAGGAACCT---C--C-CCCTGACCCTCACTCCG
* * *
25978950 AGCCCTGCTTTGCTGTTCTACATCTTGTTCAACTGAAGCAGGAGT
60 AGCCCTGCTATGCTGTTCTACATATTGTTCAACAGAAGCAGGAGT
25978995 AGCAGATGTT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
105 39 0.42
108 1 0.01
110 1 0.01
111 52 0.56
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (105 bp):
TATGGCATCCTAGGTGAAGGAAGAGCAAGTGGAGGAACCTCCCCCTGACCCTCACTCCGAGCCCT
GCTATGCTGTTCTACATATTGTTCAACAGAAGCAGGAGTG
Found at i:25989227 original size:15 final size:14
Alignment explanation
Indices: 25989200--25989226 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25989190 AATTTCTGAA
25989200 AAAGGAAAAAAAAG
1 AAAGGAAAAAAAAG
25989214 AAAGGAAAAAAAA
1 AAAGGAAAAAAAA
25989227 AAACCAAATT
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGGAAAAAAAAG
Found at i:25989582 original size:16 final size:15
Alignment explanation
Indices: 25989556--25989598 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
25989546 TCTTATTGCA
25989556 TATTTTT-ATATTATT
1 TATTTTTAATATTA-T
*
25989571 TATTTTTAATATCAT
1 TATTTTTAATATTAT
25989586 TATTTTTAA-ATTA
1 TATTTTTAATATTA
25989599 AGTAGTGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 17 0.68
16 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTAATATTAT
Found at i:26003166 original size:59 final size:57
Alignment explanation
Indices: 26003067--26003225 Score: 174
Period size: 59 Copynumber: 2.7 Consensus size: 57
26003057 TAATAAATTT
* * *
26003067 AGGTACCAAATTGAATCTAAAAAAAAGCTTAGGTATCAAATTAGGAAAAATTGCCAAGTTC
1 AGGTACCAAATTG-A--T-AAAAAAAGTTTAGGTATCAAATTAGGAAAAAGTACCAAGTTC
* * * * ** *
26003128 ATGTACCAAATTGGGTCCAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTATTAAGTTT
1 AGGTACCAAATT-GAT-AAAAAAAGTTTAGGTATCAAATTAGGAAAAAGTACCAAGTTC
26003187 AGGTACCAAATTGATAAAAAAAGTTTAGGTATCAAATTA
1 AGGTACCAAATTGATAAAAAAAGTTTAGGTATCAAATTA
26003226 AAAAATAGTG
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
57 22 0.27
58 2 0.02
59 46 0.56
61 11 0.13
62 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (57 bp):
AGGTACCAAATTGATAAAAAAAGTTTAGGTATCAAATTAGGAAAAAGTACCAAGTTC
Found at i:26003188 original size:31 final size:29
Alignment explanation
Indices: 26003150--26003254 Score: 101
Period size: 31 Copynumber: 3.6 Consensus size: 29
26003140 GGGTCCAAAA
26003150 AAGTTTAGGTACCAAATTAGGAAAAAGTATT
1 AAGTTTAGGTACCAAATTA-GAAAAAGTA-T
26003181 AAGTTTAGGTACCAAATT-GATAAAA--A-
1 AAGTTTAGGTACCAAATTAGA-AAAAGTAT
* * *
26003207 AAGTTTAGGTATCAAATTAAAAAATAGTGT
1 AAGTTTAGGTACCAAATTAGAAAA-AGTAT
*
26003237 CAAGTTTAGGTACTAAAT
1 -AAGTTTAGGTACCAAAT
26003255 GTTATATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
26 20 0.32
27 2 0.03
28 1 0.02
29 2 0.03
30 4 0.06
31 33 0.53
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (29 bp):
AAGTTTAGGTACCAAATTAGAAAAAGTAT
Found at i:26003217 original size:26 final size:26
Alignment explanation
Indices: 26003146--26003230 Score: 93
Period size: 26 Copynumber: 3.1 Consensus size: 26
26003136 AATTGGGTCC
26003146 AAAAAAGTTTAGGTACCAAATTAGGAA
1 AAAAAAGTTTAGGTACCAAATTA-GAA
26003173 AAAGTATTAAGTTTAGGTACCAAATT-GATA
1 AAA--A--AAGTTTAGGTACCAAATTAGA-A
*
26003203 AAAAAAGTTTAGGTATCAAATTA-AA
1 AAAAAAGTTTAGGTACCAAATTAGAA
26003228 AAA
1 AAA
26003231 TAGTGTCAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
25 4 0.08
26 18 0.35
27 3 0.06
28 1 0.02
29 3 0.06
30 4 0.08
31 18 0.35
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (26 bp):
AAAAAAGTTTAGGTACCAAATTAGAA
Found at i:26003242 original size:57 final size:59
Alignment explanation
Indices: 26003064--26003254 Score: 194
Period size: 57 Copynumber: 3.2 Consensus size: 59
26003054 ATTTAATAAA
* *
26003064 TTTAGGTACCAAATTGAATCTAAAAAAAAGCTTAGGTATCAAATTAGGAAAAAT--TGCCAAG
1 TTTAGGTACCAAATTG-A--TAAAAAAAAGTTTAGGTATCAAATTA-GAAAAATAGTGTCAAG
* * * ** * * * *
26003125 TTCATGTACCAAATTGGGTCCAAAAAAGTTTAGGTACCAAATTAGGAAAA-AGTATTAAG
1 TTTAGGTACCAAATT-GATAAAAAAAAGTTTAGGTATCAAATTAGAAAAATAGTGTCAAG
26003184 TTTAGGTACCAAATTGAT-AAAAAAAGTTTAGGTATCAAATTA-AAAAATAGTGTCAAG
1 TTTAGGTACCAAATTGATAAAAAAAAGTTTAGGTATCAAATTAGAAAAATAGTGTCAAG
*
26003241 TTTAGGTACTAAAT
1 TTTAGGTACCAAAT
26003255 GTTATATTAA
Statistics
Matches: 106, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
56 4 0.04
57 42 0.40
58 7 0.07
59 39 0.37
61 13 0.12
62 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (59 bp):
TTTAGGTACCAAATTGATAAAAAAAAGTTTAGGTATCAAATTAGAAAAATAGTGTCAAG
Found at i:26007251 original size:13 final size:13
Alignment explanation
Indices: 26007233--26007263 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
26007223 GGCCTAATTG
26007233 TGTTCTGGTGACA
1 TGTTCTGGTGACA
26007246 TGTTCTGGTGACA
1 TGTTCTGGTGACA
26007259 TGTTC
1 TGTTC
26007264 CAGTTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (13 bp):
TGTTCTGGTGACA
Found at i:26010321 original size:18 final size:17
Alignment explanation
Indices: 26010288--26010321 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
26010278 ATTAAATGTC
*
26010288 TTTTTTTATATCTTATG
1 TTTTTTTATATATTATG
26010305 TTTTTTTATTATATTAT
1 TTTTTTTA-TATATTAT
26010322 ATGTTATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTTATATATTATG
Found at i:26010324 original size:20 final size:19
Alignment explanation
Indices: 26010277--26010326 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
26010267 TATAAATATG
* *
26010277 TATTAAATGTCTTTTTTTA
1 TATTATATGTTTTTTTTTA
26010296 TATCT-TATGTTTTTTTATTA
1 TAT-TATATGTTTTTTT-TTA
26010316 TATTATATGTT
1 TATTATATGTT
26010327 ATGTTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (19 bp):
TATTATATGTTTTTTTTTA
Found at i:26017531 original size:35 final size:34
Alignment explanation
Indices: 26017486--26017557 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
26017476 AGTCATGTTA
** *
26017486 AAATGATGTGTTTCATGTTTTATACTGTTTAAATG
1 AAATGATGTGTTTCACATTTTATACCGTTT-AATG
* *
26017521 AAATGGTGTGTTTTACATTTTATACCGTTTAATG
1 AAATGATGTGTTTCACATTTTATACCGTTTAATG
26017555 AAA
1 AAA
26017558 CAATGCAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 7 0.22
35 25 0.78
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.46
Consensus pattern (34 bp):
AAATGATGTGTTTCACATTTTATACCGTTTAATG
Found at i:26018463 original size:11 final size:11
Alignment explanation
Indices: 26018430--26018463 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
26018420 TTTTAAAAAT
26018430 TAAATAATAAA
1 TAAATAATAAA
* *
26018441 CAAGTAATAAA
1 TAAATAATAAA
26018452 TAAATAATAAA
1 TAAATAATAAA
26018463 T
1 T
26018464 CGTTTAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:26022752 original size:18 final size:18
Alignment explanation
Indices: 26022716--26022753 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
26022706 TGTCTTTTTC
*
26022716 TTAAATATTTATTTTTAT
1 TTAAATATTTATTTATAT
26022734 TTAAATATTT-TTTAATAT
1 TTAAATATTTATTT-ATAT
26022752 TT
1 TT
26022754 TTAAAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTAAATATTTATTTATAT
Found at i:26023059 original size:24 final size:24
Alignment explanation
Indices: 26023024--26023070 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
26023014 AAAATTAAAA
26023024 TATACTTTAAATTTA-TATATTTTG
1 TATACTTTAAATTTAGTA-ATTTTG
26023048 TATA-TTTAAAATTTAGTAATTTT
1 TATACTTT-AAATTTAGTAATTTT
26023071 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 16 0.76
25 2 0.10
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TATACTTTAAATTTAGTAATTTTG
Found at i:26024682 original size:50 final size:50
Alignment explanation
Indices: 26024607--26024707 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
26024597 ATTCACACAT
*
26024607 AATTCACATTTTTACTAATAAGCCTAAGTACATGTCAAACTAATGTCCAA
1 AATTCACATTTTTACTAATAAGCCTAAGTACATGTCAAACTAAGGTCCAA
*
26024657 AATTCACATTTTTACTAATAAGCCTAAGTACGTGTCAAACTAAGGTCCAA
1 AATTCACATTTTTACTAATAAGCCTAAGTACATGTCAAACTAAGGTCCAA
26024707 A
1 A
26024708 TTTTACATAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (50 bp):
AATTCACATTTTTACTAATAAGCCTAAGTACATGTCAAACTAAGGTCCAA
Found at i:26033451 original size:52 final size:52
Alignment explanation
Indices: 26033387--26033486 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
26033377 TTACAAATGG
** * * *
26033387 TAAGAAAATATTATTTAACTATTTATTTTTAATTCGTTAATTATTATGTTGT
1 TAAGAAAATATTATCAAACTATTTAATTTTAAATAGTTAATTATTATGTTGT
*
26033439 TAAGAAAATATTATCAAATTATTTAATTTTAAATAGTTAATTATTATG
1 TAAGAAAATATTATCAAACTATTTAATTTTAAATAGTTAATTATTATG
26033487 CTATTCAGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (52 bp):
TAAGAAAATATTATCAAACTATTTAATTTTAAATAGTTAATTATTATGTTGT
Found at i:26036617 original size:34 final size:34
Alignment explanation
Indices: 26036574--26036648 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
26036564 TGTTTAACCT
* **
26036574 TTAACCTCTCTTGATTTTTAATTTTCCATCTTCC
1 TTAACCTCTCTTGACTTTTAACCTTCCATCTTCC
*
26036608 TTAACCTCTCTTGACTTTTAGCCTTCCATCTTCC
1 TTAACCTCTCTTGACTTTTAACCTTCCATCTTCC
26036642 TTAACCT
1 TTAACCT
26036649 TTCACATTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.17, C:0.31, G:0.04, T:0.48
Consensus pattern (34 bp):
TTAACCTCTCTTGACTTTTAACCTTCCATCTTCC
Found at i:26048459 original size:33 final size:33
Alignment explanation
Indices: 26048422--26048487 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
26048412 AGACAAAGTC
26048422 AACGAGATTTGCATCACAATAATATGCTACAAA
1 AACGAGATTTGCATCACAATAATATGCTACAAA
26048455 AACGAGATTTGCATCACAATAATATGCTACAAA
1 AACGAGATTTGCATCACAATAATATGCTACAAA
26048488 CCCTAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (33 bp):
AACGAGATTTGCATCACAATAATATGCTACAAA
Found at i:26051306 original size:24 final size:26
Alignment explanation
Indices: 26051283--26051330 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
26051273 CCATCCATAT
26051283 TTTATGTTT-AAT-TTTT-TTGAATA
1 TTTATGTTTAAATATTTTCTTGAATA
*
26051306 TTTGTGTTTAAATATTTTCTTGAAT
1 TTTATGTTTAAATATTTTCTTGAAT
26051331 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 4 0.19
26 6 0.29
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.62
Consensus pattern (26 bp):
TTTATGTTTAAATATTTTCTTGAATA
Found at i:26054141 original size:40 final size:42
Alignment explanation
Indices: 26054095--26054194 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
26054085 AAGATCAAGC
*
26054095 ATAACGTGCTGTTCCTTCTT-TTCTTTT-TTTCTTTGAAGGG
1 ATAACGTGCTATTCCTTCTTCTTCTTTTCTTTCTTTGAAGGG
*
26054135 ATAACGTGCTATTCCTTCTTCTTTTTTTCTTTCTTTGAAGGG
1 ATAACGTGCTATTCCTTCTTCTTCTTTTCTTTCTTTGAAGGG
26054177 ATAACGTGCTATTCCTTC
1 ATAACGTGCTATTCCTTC
26054195 CTTCCATCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
40 19 0.34
41 6 0.11
42 31 0.55
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (42 bp):
ATAACGTGCTATTCCTTCTTCTTCTTTTCTTTCTTTGAAGGG
Found at i:26054380 original size:16 final size:16
Alignment explanation
Indices: 26054359--26054405 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
26054349 ATAAATTAAA
26054359 ATATTTTTTTAAATTT
1 ATATTTTTTTAAATTT
**
26054375 ATATTTTTTATTATTTTT
1 ATA-TTTTT-TTAAATTT
26054393 ATATTTTTTTAAA
1 ATATTTTTTTAAA
26054406 AAAACCTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 9 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATATTTTTTTAAATTT
Found at i:26054383 original size:18 final size:18
Alignment explanation
Indices: 26054362--26054402 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
26054352 AATTAAAATA
26054362 TTTTTTTAAATTTATATT
1 TTTTTTTAAATTTATATT
* **
26054380 TTTTATTATTTTTATATT
1 TTTTTTTAAATTTATATT
26054398 TTTTT
1 TTTTT
26054403 AAAAAAACCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTAAATTTATATT
Found at i:26058502 original size:17 final size:17
Alignment explanation
Indices: 26058480--26058512 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
26058470 TGTTGGATAA
26058480 GTATCGGTAGTAGTCAG
1 GTATCGGTAGTAGTCAG
26058497 GTATCGGTAGTAGTCA
1 GTATCGGTAGTAGTCA
26058513 AGTTAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.30
Consensus pattern (17 bp):
GTATCGGTAGTAGTCAG
Found at i:26059189 original size:53 final size:53
Alignment explanation
Indices: 26059126--26059403 Score: 285
Period size: 53 Copynumber: 5.3 Consensus size: 53
26059116 TTCACATTTG
** *
26059126 ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATATTAGAATTCAT
1 ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATAAAAGGATTCAT
* * * * * *
26059179 ATAACTCACGATGACACCGAGTCATCGGACTTGTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATAAAAGGATTCAT
* *
26059232 ATAACTCACGATGACACAGAGTCATTAGACCTTTAATCCATAAAAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATAAAAGGATTCAT
* * * * * *
26059285 ATAACTCACGATAACACAGAGTTATTGGACCTTTTATCCGTTATAA-GATTCAT
1 ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCC-ATAAAAGGATTCAT
* * * * *
26059338 ATACCTCACGATGACAC-GTAGTTATCGGACCTCATAATCCGT-GAAGGATTCAT
1 ATAACTCACGATGACACAG-AGTCATTGGACCTC-TAATCCATAAAAGGATTCAT
* *
26059391 GT-ACTCATGATGA
1 ATAACTCACGATGA
26059404 TACGTAGTCA
Statistics
Matches: 191, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
52 12 0.06
53 170 0.89
54 9 0.05
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATAAAAGGATTCAT
Found at i:26059369 original size:106 final size:106
Alignment explanation
Indices: 26059126--26059377 Score: 328
Period size: 106 Copynumber: 2.4 Consensus size: 106
26059116 TTCACATTTG
**
26059126 ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATATTAGAATTCATATAACTCACGAT
1 ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATAAAAGAATTCATATAACTCACGAT
* * *
26059191 GACACCGAGTCATCGGACTTGTAATCCGTAATAGGATTCAT
66 AACACAGAGTCATCGGACTTGTAATCCGTAATAAGATTCAT
* * *
26059232 ATAACTCACGATGACACAGAGTCATTAGACCTTTAATCCATAAAAGGATTCATATAACTCACGAT
1 ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATAAAAGAATTCATATAACTCACGAT
* * * *
26059297 AACACAGAGTTATTGGACCTT-TTATCCGTTATAAGATTCAT
66 AACACAGAGTCATCGGA-CTTGTAATCCGTAATAAGATTCAT
* * *
26059338 ATACCTCACGATGACAC-GTAGTTATCGGACCTCATAATCC
1 ATAACTCACGATGACACAG-AGTCATTGGACCTC-TAATCC
26059378 GTGAAGGATT
Statistics
Matches: 126, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
105 1 0.01
106 116 0.92
107 9 0.07
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (106 bp):
ATAACTCACGATGACACAGAGTCATTGGACCTCTAATCCATAAAAGAATTCATATAACTCACGAT
AACACAGAGTCATCGGACTTGTAATCCGTAATAAGATTCAT
Done.