Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 173 of 193
Found at i:53897863 original size:12 final size:12
Alignment explanation
Indices: 53897846--53897885 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
53897836 TGTTTTTGAT
*
53897846 TATATCTATATC
1 TATATCTATATA
*
53897858 TATATCTATCTA
1 TATATCTATATA
*
53897870 TCTATCTATATA
1 TATATCTATATA
53897882 TATA
1 TATA
53897886 AATTTCCCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATCTATATA
Found at i:53900219 original size:22 final size:23
Alignment explanation
Indices: 53900184--53900229 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
53900174 TTAATAAAAA
*
53900184 TTTATAACATTTTATAAATTTTG
1 TTTACAACATTTTATAAATTTTG
*
53900207 TTTACAAC-TTTTATGAATTTTG
1 TTTACAACATTTTATAAATTTTG
53900229 T
1 T
53900230 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (23 bp):
TTTACAACATTTTATAAATTTTG
Found at i:53909017 original size:60 final size:60
Alignment explanation
Indices: 53908902--53909017 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
53908892 TCTTAAATAT
* *
53908902 TAAATCTCAAATCTCAAATCCAAAATTCAAACCCAAATCATAAACCTTAATCTTGAACCC
1 TAAATCTCAAATCTCAAATCCAAAATTCAAACCCAAATCATAAACCATAACCTTGAACCC
* * * * *
53908962 TAAAT-TCTAAATCTCAAA-CTCAAACTTGAACCCCAAATCCTAAACCATGACCTTGA
1 TAAATCTC-AAATCTCAAATC-CAAAATTCAAACCCAAATCATAAACCATAACCTTGA
53909018 GTTCAAGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.43, C:0.28, G:0.03, T:0.25
Consensus pattern (60 bp):
TAAATCTCAAATCTCAAATCCAAAATTCAAACCCAAATCATAAACCATAACCTTGAACCC
Found at i:53909107 original size:14 final size:14
Alignment explanation
Indices: 53909032--53909108 Score: 52
Period size: 13 Copynumber: 5.6 Consensus size: 14
53909022 AAGATTCGGA
*
53909032 TTAGAGATTTAGGAT
1 TTAGAG-TTTAAGAT
*
53909047 TT-GAGTTTAATAT
1 TTAGAGTTTAAGAT
* *
53909060 TTAAAGTTTGAGGAT
1 TTAGAGTTT-AAGAT
* * *
53909075 TGAG-GTTTATGGT
1 TTAGAGTTTAAGAT
53909088 TT-GAGTTTAAGAT
1 TTAGAGTTTAAGAT
53909101 TTAGAGTT
1 TTAGAGTT
53909109 CAAAATAAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
12 1 0.02
13 21 0.46
14 17 0.37
15 7 0.15
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (14 bp):
TTAGAGTTTAAGAT
Found at i:53909368 original size:15 final size:13
Alignment explanation
Indices: 53909325--53909376 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
53909315 TTAAAAAATG
* *
53909325 ATTTTTAATATTA
1 ATTTTTATTATAA
53909338 A-TTTTATTATAA
1 ATTTTTATTATAA
53909350 ATTTTTATTATATA
1 ATTTTTATTATA-A
53909364 TATTTTTA-TATAA
1 -ATTTTTATTATAA
53909377 TGTCTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 10 0.29
13 12 0.35
14 5 0.15
15 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTTATTATAA
Found at i:53913369 original size:14 final size:14
Alignment explanation
Indices: 53913301--53913370 Score: 52
Period size: 14 Copynumber: 4.7 Consensus size: 14
53913291 TATCATTGGC
*
53913301 TATAGATAAATAACT
1 TATA-ATAAATAATT
53913316 TATAATAAAT-ATT
1 TATAATAAATAATT
* *
53913329 ATATAATTTAATTAAAAT
1 -TATAA--TAAAT-AATT
*
53913347 TAAAATAAATAATT
1 TATAATAAATAATT
53913361 TATAATAAAT
1 TATAATAAAT
53913371 TGGTAAGTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
13 2 0.05
14 23 0.53
15 8 0.19
16 4 0.09
17 4 0.09
18 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (14 bp):
TATAATAAATAATT
Found at i:53913481 original size:20 final size:20
Alignment explanation
Indices: 53913456--53913513 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 20
53913446 AACGTGGAAG
53913456 TATATTTTAAAAATAAAATA
1 TATATTTTAAAAATAAAATA
53913476 TATA-TTTAAAAATTTAAAATA
1 TATATTTTAAAAA--TAAAATA
53913497 T-TATTATATAAAAATAA
1 TATATT-T-TAAAAATAA
53913514 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.24
20 6 0.18
21 12 0.36
22 1 0.03
23 6 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATTTTAAAAATAAAATA
Found at i:53921135 original size:29 final size:28
Alignment explanation
Indices: 53921103--53921259 Score: 92
Period size: 29 Copynumber: 5.3 Consensus size: 28
53921093 AAAAGATTTA
53921103 GGGGTAAAATGGTAGTTTTTGGTTAAATC
1 GGGGTAAAATGGTAGTTTTTGG-TAAATC
* *
53921132 GGGGTGAAAA--ATAGAATTTTGG-AAAGTTC
1 GGGGT-AAAATGGTAG-TTTTTGGTAAA--TC
* *
53921161 GAGGGCAAAATGGTAATTTTTTGGTGAAATC
1 G-GGGTAAAATGGT-AGTTTTTGGT-AAATC
*
53921192 GGGGTGAAAAAT-G-AGATTTTGG-AAAGTTC
1 GGGGT--AAAATGGTAGTTTTTGGTAAA--TC
*
53921221 GAGGGTAAAATGGTAATTTTTGGTGAAATC
1 G-GGGTAAAATGGTAGTTTTTGGT-AAATC
53921251 GGGGTAAAA
1 GGGGTAAAA
53921260 AATAAAATTT
Statistics
Matches: 98, Mismatches: 11, Indels: 38
0.67 0.07 0.26
Matches are distributed among these distances:
27 6 0.06
28 8 0.08
29 37 0.38
30 24 0.24
31 11 0.11
32 9 0.09
33 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.31
Consensus pattern (28 bp):
GGGGTAAAATGGTAGTTTTTGGTAAATC
Found at i:53921171 original size:117 final size:116
Alignment explanation
Indices: 53921040--53921743 Score: 705
Period size: 117 Copynumber: 6.0 Consensus size: 116
53921030 ATTTTTGACT
* *
53921040 TTCGGGGGCAAAAAT-GTAATTTTGGGATAATCTAGGGTTAAAAATGGGATTTT-AAAAGATTTA
1 TTCGAGGGC-AAAATGGTAATTTTGGGA-AATC-AGGGTTAAAAATGGGATTTTGGAAAG-TTTA
* * *
53921103 GGGGTAAAATGGTAGTTTTTGGTTAAATCGGGGTGAAAAATAGAATTTTGGAAAG
62 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAG
* * * *
53921158 TTCGAGGGCAAAATGGTAATTTTTTGGTGAAATCGGGGTGAAAAATGAGATTTTGGAAAG-TTCG
1 TTCGAGGGCAAAATGGTAA--TTTTGG-GAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAG
* * *
53921222 AGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAAATAAAATTTTAGAAAG
63 -GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAG
* * * * *
53921277 TTTGGGGGTAAAATGGTATTTTTTGGTGAAATCAGGGTT-AAAATGGGATTTTGGAAAGTTTAAG
1 TTCGAGGGCAAAATGGTA-ATTTTGG-GAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAGG
* * * * *
53921341 GTTAAAATCGTAATTTTTTGGTGAGATCAGGGTCAAAAATGGAA-TTTGGAAAG
64 GGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAG
* * * * * *
53921394 TT-GAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTCAAAAATGAGATTTTGGAAAGTTTGGG
1 TTCGAGGGCAAAATGGTAA-TTTTG-GGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAGG
* * *
53921458 GGTAAAATGGTAATTTTTTGGTGAGATCGAGGTCAAAAATGGAA-TTTGGAAAG
64 GGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAG
* * ** ** * * * * *
53921511 TTTG-GGGCAAAAAT-GCAATTTTTAGAAAGTTTTGGGGTCAAAATGGAATTTTGGAAAGTGTGG
1 TTCGAGGGC-AAAATGGTAATTTTGGGAAA--TCAGGGTTAAAAATGGGATTTTGGAAAGTTTAG
* *
53921574 GGGTAAAATGGTAATTTTTGGTGAAAT-TGGGTC-AAAATGGAATTTTGGAAAG
63 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAG
* * * *
53921626 TTCGAGGGTAAAATGGTAATTTTTGTGAAATC-GAGGTAAAAAATGGAATTTTGGAAAGTTT-GG
1 TTCGAGGGCAAAATGGTAA-TTTTGGGAAATCAG-GGTTAAAAATGGGATTTTGGAAAGTTTAGG
*
53921689 GGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATAGAATTTTGGAAAG
64 GGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAG
53921742 TT
1 TT
53921744 TAGGGGTAAA
Statistics
Matches: 495, Mismatches: 68, Indels: 48
0.81 0.11 0.08
Matches are distributed among these distances:
114 38 0.08
115 53 0.11
116 71 0.14
117 171 0.35
118 65 0.13
119 81 0.16
120 14 0.03
121 2 0.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (116 bp):
TTCGAGGGCAAAATGGTAATTTTGGGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGG
TAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAG
Found at i:53921270 original size:29 final size:28
Alignment explanation
Indices: 53921179--53921270 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 28
53921169 AATGGTAATT
* *
53921179 TTTTGGTGAAATCGGGGTGAAAAATGAGA
1 TTTTGGTGAAATCGGGGTAAAAAAT-AAA
** *
53921208 TTTT-G-GAAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGTGAAA--TCG-GGGTAAAA-AATAAA
53921238 TTTTGGTGAAATCGGGGTAAAAAATAAAA
1 TTTTGGTGAAATCGGGGTAAAAAAT-AAA
53921267 TTTT
1 TTTT
53921271 AGAAAGTTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
27 4 0.08
28 2 0.04
29 21 0.44
30 15 0.31
31 2 0.04
32 4 0.08
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (28 bp):
TTTTGGTGAAATCGGGGTAAAAAATAAA
Found at i:53921321 original size:30 final size:30
Alignment explanation
Indices: 53921285--53921387 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 30
53921275 AGTTTGGGGG
53921285 TAAAATGGTATTTTTTGGTGAAATCAGGGT
1 TAAAATGGTATTTTTTGGTGAAATCAGGGT
* * *
53921315 TAAAATGGGA--TTTT-G-GAAAGTTTAAGGT
1 TAAAATGGTATTTTTTGGTGAAA--TCAGGGT
* *
53921343 TAAAATCGTAATTTTTTGGTGAGATCAGGGT
1 TAAAATGGT-ATTTTTTGGTGAAATCAGGGT
* *
53921374 CAAAAATGGAATTT
1 -TAAAATGGTATTT
53921388 GGAAAGTTGA
Statistics
Matches: 54, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
26 4 0.07
27 1 0.02
28 16 0.30
29 1 0.02
30 9 0.17
31 13 0.24
32 7 0.13
33 3 0.06
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (30 bp):
TAAAATGGTATTTTTTGGTGAAATCAGGGT
Found at i:53921334 original size:58 final size:59
Alignment explanation
Indices: 53921050--53921754 Score: 762
Period size: 59 Copynumber: 12.1 Consensus size: 59
53921040 TTCGGGGGCA
* * * * *
53921050 AAAAT-GTAA-TTTTGG-GATAATCTAGGGTTAAAAATGGGATTTT-AAAAGATTTAGGGGT
1 AAAATGGTAATTTTTGGTGA-AATC-GGGGTCAAAAATGGAATTTTGGAAAG-TTTGGGGGT
* * * * * * *
53921108 AAAATGGTAGTTTTTGGTTAAATCGGGGTGAAAAATAGAATTTTGGAAAGTTCGAGGGC
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * *
53921167 AAAATGGTAATTTTTTGGTGAAATCGGGGTGAAAAAT-GAGATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAA-TTTTTGGTGAAATCGGGGTCAAAAATGGA-ATTTTGGAAAGTTTGGGGGT
* ** *
53921227 AAAATGGTAATTTTTGGTGAAATCGGGGTAAAAAATAAAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * * * ** *
53921286 AAAATGGTATTTTTTGGTGAAATCAGGGT-TAAAATGGGATTTTGGAAAGTTTAAGGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * * *
53921344 AAAATCGTAATTTTTTGGTGAGATCAGGGTCAAAAATGGAA-TTTGGAAAG-TTGAGGGT
1 AAAATGGTAA-TTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
*
53921402 AAAATGGTAATTTTTGATGAAATCGGGGTCAAAAAT-GAGATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGA-ATTTTGGAAAGTTTGGGGGT
* * **
53921461 AAAATGGTAATTTTTTGGTGAGATCGAGGTCAAAAATGGAA-TTTGGAAAGTTTGGGGCA
1 AAAATGGTAA-TTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * * *
53921520 AAAAT-GCAATTTTT--AGAAAGTTTTGGGGTC-AAAATGGAATTTTGGAAAGTGTGGGGGT
1 AAAATGGTAATTTTTGGTGAAA---TCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * *
53921578 AAAATGGTAATTTTTGGTGAAAT-TGGGTC-AAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
* *
53921635 AAAATGGTAATTTTT-GTGAAATCGAGGTAAAAAATGGAATTTTGGAAAGTTT-GGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * *
53921692 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATAGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
53921751 AAAA
1 AAAA
53921755 ATGCAAATTT
Statistics
Matches: 555, Mismatches: 67, Indels: 49
0.83 0.10 0.07
Matches are distributed among these distances:
55 3 0.01
56 9 0.02
57 105 0.19
58 144 0.26
59 186 0.34
60 101 0.18
61 7 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
Found at i:53921458 original size:29 final size:28
Alignment explanation
Indices: 53921370--53921757 Score: 122
Period size: 29 Copynumber: 13.4 Consensus size: 28
53921360 GGTGAGATCA
*
53921370 GGGTCAAAAATGGAATTTGGAAAG-TTG
1 GGGTCAAAAATGGATTTTGGAAAGTTTG
*
53921397 AGGGT--AAAATGGTAATTTTTGATGAAA--TCG
1 -GGGTCAAAAATGG--A-TTTTG--GAAAGTTTG
53921427 GGGTCAAAAATGAGATTTTGGAAAGTTTGG
1 GGGTCAAAAATG-GATTTTGGAAAGTTT-G
** * *
53921457 GGGT--AAAATGGTAATTTTTTGGTGAGATCG
1 GGGTCAAAAATGG--A--TTTTGGAAAGTTTG
* *
53921487 AGGTCAAAAATGGAATTTGGAAAGTTTG
1 GGGTCAAAAATGGATTTTGGAAAGTTTG
* *
53921515 GGG-CAAAAATGCAATTTTTAGAAAGTTTTG
1 GGGTCAAAAATG-GA-TTTTGGAAAG-TTTG
*
53921545 GGGTC-AAAATGGAATTTTGGAAAGTGTGG
1 GGGTCAAAAATGG-ATTTTGGAAAGT-TTG
53921574 GGGT--AAAATGGTAATTTTTGGTGAAA--TT-
1 GGGTCAAAAATGG--A-TTTT-G-GAAAGTTTG
*
53921602 GGGTC-AAAATGGAATTTTGGAAAGTTCG
1 GGGTCAAAAATGG-ATTTTGGAAAGTTTG
*
53921630 AGGGT--AAAATGGTAATTTTTGTGAAA--TCG
1 -GGGTCAAAAATGG--A-TTTTG-GAAAGTTTG
* *
53921659 AGGTAAAAAATGGAATTTTGGAAAGTTTG
1 GGGTCAAAAATGG-ATTTTGGAAAGTTTG
*
53921688 GGGT--AAAATGGTAATTTTTGGTGAAA--TCG
1 GGGTCAAAAATGG--A-TTTT-G-GAAAGTTTG
* *
53921717 AGGTCAAAAATAGAATTTTGGAAAGTTTAG
1 GGGTCAAAAAT-GGATTTTGGAAAGTTT-G
53921747 GGGT-AAAAATG
1 GGGTCAAAAATG
53921758 CAAATTTTAA
Statistics
Matches: 281, Mismatches: 30, Indels: 98
0.69 0.07 0.24
Matches are distributed among these distances:
25 4 0.01
26 8 0.03
27 33 0.12
28 56 0.20
29 84 0.30
30 49 0.17
31 34 0.12
32 13 0.05
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.31
Consensus pattern (28 bp):
GGGTCAAAAATGGATTTTGGAAAGTTTG
Found at i:53921786 original size:30 final size:28
Alignment explanation
Indices: 53921738--53921834 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 28
53921728 AGAATTTTGG
53921738 AAAGTTTAGGGGTAAAAATGCAAATTTTAA
1 AAAGTTTA-GGGTAAAAATG-AAATTTTAA
*
53921768 AAAGTCTTAGGGTTAAAAT-ATAATTTTAA
1 AAAGT-TTAGGGTAAAAATGA-AATTTTAA
* * *
53921797 AGAAGTTTGGGGGTCAAAATGTAATTTTTAA
1 A-AAGTTT-AGGGTAAAAATG-AAATTTTAA
53921828 AAAGTTT
1 AAAGTTT
53921835 TGAGGTCAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
28 1 0.02
29 11 0.19
30 33 0.58
31 11 0.19
32 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (28 bp):
AAAGTTTAGGGTAAAAATGAAATTTTAA
Found at i:53921842 original size:30 final size:30
Alignment explanation
Indices: 53921762--53921855 Score: 111
Period size: 30 Copynumber: 3.1 Consensus size: 30
53921752 AAAATGCAAA
* *
53921762 TTTTAAAAAGTCTT-AGGGTTAAAATATAA-
1 TTTTAAAAAGTTTTGA-GGTCAAAATATAAT
* * *
53921791 TTTTAAAGAAGTTTGGGGGTCAAAATGTAAT
1 TTTTAAA-AAGTTTTGAGGTCAAAATATAAT
53921822 TTTTAAAAAGTTTTGAGGTCAAAATATAAT
1 TTTTAAAAAGTTTTGAGGTCAAAATATAAT
53921852 TTTT
1 TTTT
53921856 GGATAGTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 7 0.13
30 40 0.74
31 7 0.13
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.40
Consensus pattern (30 bp):
TTTTAAAAAGTTTTGAGGTCAAAATATAAT
Found at i:53921864 original size:30 final size:29
Alignment explanation
Indices: 53921782--53921864 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
53921772 TCTTAGGGTT
* *
53921782 AAAATATAATTTTAAAGAAGTTTGGGGGTC
1 AAAATATAATTTT-TAGAAGTTTGGAGGTC
* * *
53921812 AAAATGTAATTTTTAAAAAGTTTTGAGGTC
1 AAAATATAATTTTT-AGAAGTTTGGAGGTC
*
53921842 AAAATATAATTTTTGGATAGTTT
1 AAAATATAATTTTTAGA-AGTTT
53921865 AGGGACCTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (29 bp):
AAAATATAATTTTTAGAAGTTTGGAGGTC
Found at i:53921864 original size:60 final size:59
Alignment explanation
Indices: 53921716--53921868 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 59
53921706 TGGTGAAATC
*
53921716 GAGGTCAAAA-ATAGAATTTTGGAAAGTTTAGGGGTAAAAATGCAAATTTTAAAAAGTCTT
1 GAGGTCAAAATATA-ATTTTTGG-AAGTTTAGGGGTAAAAATGCAAATTTTAAAAAGTCTT
* ** * * * * *
53921776 -AGGGTTAAAATATAATTTTAAAGAAGTTTGGGGGTCAAAATGTAATTTTTAAAAAGTTTT
1 GA-GGTCAAAATATAATTTT-TGGAAGTTTAGGGGTAAAAATGCAAATTTTAAAAAGTCTT
53921836 GAGGTCAAAATATAATTTTTGGATAGTTTAGGG
1 GAGGTCAAAATATAATTTTTGGA-AGTTTAGGG
53921869 ACCTATAGAG
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
59 3 0.04
60 67 0.89
61 5 0.07
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (59 bp):
GAGGTCAAAATATAATTTTTGGAAGTTTAGGGGTAAAAATGCAAATTTTAAAAAGTCTT
Found at i:53923517 original size:17 final size:17
Alignment explanation
Indices: 53923495--53923565 Score: 70
Period size: 18 Copynumber: 4.1 Consensus size: 17
53923485 AATATGAATT
*
53923495 TAAATTTAAATTAAATC
1 TAAATTTAAAATAAATC
* *
53923512 TAAATTTTAAAACAAATT
1 TAAA-TTTAAAATAAATC
* *
53923530 TAAACTTAAAATAAATT
1 TAAATTTAAAATAAATC
*
53923547 TAATCTTTAAAATAAATC
1 TAA-ATTTAAAATAAATC
53923565 T
1 T
53923566 TAAAATGGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
17 18 0.41
18 26 0.59
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATAAATC
Found at i:53923530 original size:35 final size:35
Alignment explanation
Indices: 53923491--53923569 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
53923481 TTGAAATATG
* *
53923491 AATTTAAATTTAAATTAAATCTAAAT-TTTAAAACA
1 AATTTAAACTTAAAATAAAT-TAAATCTTTAAAACA
* *
53923526 AATTTAAACTTAAAATAAATTTAATCTTTAAAATA
1 AATTTAAACTTAAAATAAATTAAATCTTTAAAACA
53923561 AATCTTAAA
1 AAT-TTAAA
53923570 ATGGGTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 4 0.11
35 29 0.76
36 5 0.13
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.39
Consensus pattern (35 bp):
AATTTAAACTTAAAATAAATTAAATCTTTAAAACA
Found at i:53924729 original size:7 final size:7
Alignment explanation
Indices: 53924717--53924746 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
53924707 AGCCTAATAC
53924717 ATATAAT
1 ATATAAT
53924724 ATATAAT
1 ATATAAT
53924731 ATATAAT
1 ATATAAT
53924738 ATATAAT
1 ATATAAT
53924745 AT
1 AT
53924747 TATTTATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:53933741 original size:22 final size:21
Alignment explanation
Indices: 53933691--53933746 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 21
53933681 CTCTGTTCAA
*
53933691 CACTGTGTGTGTTTCTATTTAG
1 CACT-TGTGTGCTTCTATTTAG
53933713 CAC-TGTGTGCTTCTGA-TTAG
1 CACTTGTGTGCTTCT-ATTTAG
53933733 CACTTTGTGTGCTT
1 CAC-TTGTGTGCTT
53933747 ACTGTTGCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.57
21 1 0.03
22 12 0.40
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.46
Consensus pattern (21 bp):
CACTTGTGTGCTTCTATTTAG
Found at i:53936431 original size:2 final size:2
Alignment explanation
Indices: 53936422--53936450 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53936412 TAATATATGC
53936422 AT AT -T 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
53936451 CAATTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:53954768 original size:81 final size:81
Alignment explanation
Indices: 53954671--53954832 Score: 274
Period size: 82 Copynumber: 2.0 Consensus size: 81
53954661 TTTGCCATTG
* *
53954671 TCTTCTCTTTTTCTTGTTATCTTGAAAGG-TTTCCATTAACTTTAGGTATTGTTTTGATGGGGTT
1 TCTTCTCTTTTTCTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGTT
53954735 CTTTCCATTTCATGCAA
66 CTTT-CATTTCATGCAA
53954752 TCTT-TCTTTTTACTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
1 TCTTCTCTTTTT-CTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
53954816 TCTTTCATTTCATGCAA
65 TCTTTCATTTCATGCAA
53954833 CAGTTCTTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
80 7 0.09
81 33 0.43
82 37 0.48
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (81 bp):
TCTTCTCTTTTTCTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGTT
CTTTCATTTCATGCAA
Found at i:53956831 original size:56 final size:56
Alignment explanation
Indices: 53956745--53956855 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
53956735 AGAAAAATGA
53956745 TTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATGGG
1 TTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATGGG
53956801 TTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATGG
1 TTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATGG
53956856 AATTGTTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (56 bp):
TTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATGGG
Found at i:53959059 original size:56 final size:56
Alignment explanation
Indices: 53958973--53959086 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
53958963 AAAAAACAAT
53958973 TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
1 TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
53959029 TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
1 TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
53959085 TC
1 TC
53959087 ATTTTTCTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (56 bp):
TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
Found at i:53961082 original size:81 final size:81
Alignment explanation
Indices: 53960997--53961158 Score: 274
Period size: 82 Copynumber: 2.0 Consensus size: 81
53960987 TAAAGAACTG
* *
53960997 TTGCATGAAAT-GAAAGAACCCCATCAAAACAATAGCTCAAGTTAATGGAAAGCCTTTCAAGATA
1 TTGCATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAA-CCTTTCAAGATA
53961061 ACAAGTAAAAAGA-AAGA
65 ACAAG-AAAAAGAGAAGA
53961078 TTGCATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAA
1 TTGCATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAA
53961143 CAAGAAAAAGAGAAGA
66 CAAGAAAAAGAGAAGA
53961159 CAATGGCAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
80 7 0.09
81 32 0.42
82 38 0.49
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (81 bp):
TTGCATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAA
CAAGAAAAAGAGAAGA
Found at i:53961184 original size:82 final size:78
Alignment explanation
Indices: 53961000--53961230 Score: 249
Period size: 81 Copynumber: 2.9 Consensus size: 78
53960990 AGAACTGTTG
* *
53961000 CATGAAAT-GAAAGAACCCCATCAAAACAATAGCTCAAGTTAATGGAAAGCCTTTCAAGATAACA
1 CATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAA-CCTTTCAAGATAACA
53961064 AGTAAAAAGAAAGATT
65 AG-AAAAAGAAAGA-T
53961080 GCATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAACA
1 -CATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAACA
53961145 AGAAAAAGAGAAGA-
65 AGAAAAAGA-AAGAT
* * * **
53961159 CAATGGCAAA-GGAGAA-AACCACCCATTAAAACATTACCTGAAG-TAAAAGAAACCTTTCAAGG
1 C-AT-G-AAATGGA-AAGAA-C-CCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAA-G
53961221 A-AACAAGAAA
59 ATAACAAGAAA
53961231 GGAACAAAAA
Statistics
Matches: 134, Mismatches: 7, Indels: 18
0.84 0.04 0.11
Matches are distributed among these distances:
78 1 0.01
79 2 0.01
80 13 0.10
81 59 0.44
82 59 0.44
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (78 bp):
CATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAACAA
GAAAAAGAAAGAT
Found at i:53963993 original size:46 final size:46
Alignment explanation
Indices: 53963867--53964035 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 46
53963857 AAGTGCTGAA
* * * *
53963867 GAAATAGTAAACACACACAGTGC-AATCCAGTAGGCACAC-ACAGTGC
1 GAAACAGTAAGCACACAAAGTGCGAA-ACAGTAGGCACACGA-AGTGC
* * * * * *
53963913 -AATCAGTAGGCGCACATAGTGC-AAATCAGAAGGCACACGAGGTGC
1 GAAACAGTAAGCACACAAAGTGCGAAA-CAGTAGGCACACGAAGTGC
* * *
53963958 GAAACAGTAGGCACACGAGGTGCGAAACAGTAGGCACACGAAGTGC
1 GAAACAGTAAGCACACAAAGTGCGAAACAGTAGGCACACGAAGTGC
53964004 GAAACAGTAAGCACACAAAGTGCGAAACAGTA
1 GAAACAGTAAGCACACAAAGTGCGAAACAGTA
53964036 AGCGCGCTAG
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
45 33 0.33
46 64 0.64
47 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.11
Consensus pattern (46 bp):
GAAACAGTAAGCACACAAAGTGCGAAACAGTAGGCACACGAAGTGC
Found at i:53964018 original size:69 final size:68
Alignment explanation
Indices: 53963894--53964035 Score: 166
Period size: 69 Copynumber: 2.1 Consensus size: 68
53963884 CAGTGCAATC
* * * *
53963894 CAGTAGGCACACACAGTGCAATCAGTAGGCGCACATAGTGCAAATCAGAAGGCACACGAGGTGCG
1 CAGTAGGCACACACAGTGCAAACAGTAGGCACACATAGTGCAAATCAGAAGGCACACAAAGTGCG
53963959 AAA
66 AAA
*
53963962 CAGTAGGCACACGA-GGTGCGAAACAGTAGGCACACGA-AGTGCGAAA-CAGTAA-GCACACAAA
1 CAGTAGGCACAC-ACAGTGC-AAACAGTAGGCACAC-ATAGTGC-AAATCAG-AAGGCACACAAA
53964023 GTGCGAAA
61 GTGCGAAA
53964031 CAGTA
1 CAGTA
53964036 AGCGCGCTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
68 16 0.25
69 42 0.66
70 6 0.09
ACGTcount: A:0.39, C:0.23, G:0.28, T:0.11
Consensus pattern (68 bp):
CAGTAGGCACACACAGTGCAAACAGTAGGCACACATAGTGCAAATCAGAAGGCACACAAAGTGCG
AAA
Found at i:53964036 original size:23 final size:23
Alignment explanation
Indices: 53963843--53964038 Score: 141
Period size: 23 Copynumber: 8.4 Consensus size: 23
53963833 CGAAATACTT
53963843 AACAGTAAGCACAC-AAGTGCTGAAGA
1 AACAGTAAGCACACAAAGTGC----GA
* * *
53963869 AATAGTAAACACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
53963891 ATCCAGTAGGCACACACAGTGC-A
1 A-ACAGTAAGCACACAAAGTGCGA
* * * *
53963914 ATCAGTAGGCGCACATAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
53963936 AATCAG-AAGGCACACGAGGTGCGA
1 AA-CAGTAA-GCACACAAAGTGCGA
* * *
53963960 AACAGTAGGCACACGAGGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
* *
53963983 AACAGTAGGCACACGAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
53964006 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
53964029 AACAGTAAGC
1 AACAGTAAGC
53964039 GCGCTAGCGT
Statistics
Matches: 144, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
22 22 0.15
23 101 0.70
24 4 0.03
26 12 0.08
27 5 0.03
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:53967260 original size:13 final size:13
Alignment explanation
Indices: 53967242--53967280 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
53967232 GTTTTTCGAA
53967242 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
53967255 AAAGTCAACGATC
1 AAAGTCAACGGTC
53967268 AACAGTCAACGGT
1 AA-AGTCAACGGT
53967281 TTAACTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:53971049 original size:81 final size:81
Alignment explanation
Indices: 53970952--53971113 Score: 274
Period size: 82 Copynumber: 2.0 Consensus size: 81
53970942 TTTGCCATTG
* *
53970952 TCTTCTCTTTTTCTTGTTATCTTGAAAGG-TTTCCATTAACTTTAGGTATTGTTTTGATGGGGTT
1 TCTTCTCTTTTTCTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGTT
53971016 CTTTCTATTTCATGCAA
66 CTTTC-ATTTCATGCAA
53971033 TCTT-TCTTTTTACTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
1 TCTTCTCTTTTT-CTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
53971097 TCTTTCATTTCATGCAA
65 TCTTTCATTTCATGCAA
53971114 CAGTTCTTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
80 7 0.09
81 32 0.42
82 38 0.49
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (81 bp):
TCTTCTCTTTTTCTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGTT
CTTTCATTTCATGCAA
Found at i:53973110 original size:56 final size:56
Alignment explanation
Indices: 53973024--53973137 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
53973014 ATAGAAAAAT
53973024 GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
1 GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
53973080 GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
1 GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
53973136 GA
1 GA
53973138 ATTGTTTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (56 bp):
GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
Found at i:53975340 original size:56 final size:56
Alignment explanation
Indices: 53975254--53975367 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
53975244 AAAAAACAAT
53975254 TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
1 TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
53975310 TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
1 TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
53975366 TC
1 TC
53975368 ATTTTTCTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (56 bp):
TCCATTCCATAACAGCAATTCTGCAAGAAATGATGTTGTATACAAAATCCAAAGAA
Found at i:53977295 original size:21 final size:21
Alignment explanation
Indices: 53977269--53977338 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
53977259 CCACAAAGAT
53977269 AAAGAACTGTTGCATGAAATG
1 AAAGAACTGTTGCATGAAATG
*** **
53977290 AAAGAACCCCAT-CACAAAGAT-
1 AAAGAA-CTGTTGCATGAA-ATG
53977311 AAAGAACTGTTGCATGAAATG
1 AAAGAACTGTTGCATGAAATG
53977332 AAAGAAC
1 AAAGAAC
53977339 CCCATCAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 4 0.11
21 27 0.77
22 4 0.11
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.17
Consensus pattern (21 bp):
AAAGAACTGTTGCATGAAATG
Found at i:53977307 original size:42 final size:42
Alignment explanation
Indices: 53977260--53977345 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
53977250 TCAAGAAGTC
53977260 CACAAAGATAAAGAACTGTTGCATGAAATGAAAGAACCCCAT
1 CACAAAGATAAAGAACTGTTGCATGAAATGAAAGAACCCCAT
53977302 CACAAAGATAAAGAACTGTTGCATGAAATGAAAGAACCCCAT
1 CACAAAGATAAAGAACTGTTGCATGAAATGAAAGAACCCCAT
53977344 CA
1 CA
53977346 AAACAATAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (42 bp):
CACAAAGATAAAGAACTGTTGCATGAAATGAAAGAACCCCAT
Found at i:53977465 original size:82 final size:82
Alignment explanation
Indices: 53977320--53977483 Score: 262
Period size: 82 Copynumber: 2.0 Consensus size: 82
53977310 TAAAGAACTG
* *
53977320 TTGCATGAAATGAAAGAACCCCATCAAAACAATAGCTCAAGTTAATGGAAAGCCTTTCAAGATAA
1 TTGCATGAAATGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAAGCCTTTCAAGATAA
53977385 CAAGTAAA-AAGA-AAGA
66 CAAG-AAAGAAGAGAAGA
53977401 TTGCATGAAATGGAAAGAACCCCAGTCAAAACAATACCTAAAGTTAATGGAAA-CCTTTCAAGAT
1 TTGCATGAAAT-GAAAGAACCCCA-TCAAAACAATACCTAAAGTTAATGGAAAGCCTTTCAAGAT
53977465 AACAAGAAAGAAGAGAAGA
64 AACAAGAAAGAAGAGAAGA
53977484 CAATGGCAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
81 14 0.18
82 33 0.43
83 30 0.39
ACGTcount: A:0.49, C:0.16, G:0.17, T:0.18
Consensus pattern (82 bp):
TTGCATGAAATGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAAGCCTTTCAAGATAA
CAAGAAAGAAGAGAAGA
Found at i:53977515 original size:83 final size:79
Alignment explanation
Indices: 53977323--53977556 Score: 239
Period size: 82 Copynumber: 2.9 Consensus size: 79
53977313 AGAACTGTTG
* *
53977323 CATGAAAT-GAAAGAACCCCATCAAAACAATAGCTCAAGTTAATGGAAAGCCTTTCAAGATAACA
1 CATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAA-CCTTTCAAGATAACA
53977387 AGTAAA-AAGAAAGATT
65 AG-AAAGAAGAAAGA-T
53977403 GCATGAAATGGAAAGAACCCCAGTCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAAC
1 -CATGAAATGGAAAGAACCCCA-TCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAAC
53977468 AAGAAAGAAGAGAAGA-
64 AAGAAAGAAGA-AAGAT
* * * **
53977484 CAATGGCAAA-GGAGAA-AACCACCCATTAAAACATTACCTGAAG-TAAAAGAAACCTTTCAAGG
1 C-AT-G-AAATGGA-AAGAA-C-CCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAA-G
53977546 A-AACAAGAAAG
59 ATAACAAGAAAG
53977557 GAACAAAAAG
Statistics
Matches: 135, Mismatches: 7, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
80 1 0.01
81 13 0.10
82 64 0.47
83 53 0.39
84 4 0.03
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.16
Consensus pattern (79 bp):
CATGAAATGGAAAGAACCCCATCAAAACAATACCTAAAGTTAATGGAAACCTTTCAAGATAACAA
GAAAGAAGAAAGAT
Found at i:53980318 original size:46 final size:46
Alignment explanation
Indices: 53980192--53980360 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 46
53980182 AAGTGCTGAA
* * * *
53980192 GAAATAGTAAACACACACAGTGC-AATCCAGTAGGCACAC-ACAGTGC
1 GAAACAGTAAGCACACAAAGTGCGAA-ACAGTAGGCACACGA-AGTGC
* * * * * *
53980238 -AATCAGTAGGCGCACATAGTGC-AAATCAGAAGGCACACGAGGTGC
1 GAAACAGTAAGCACACAAAGTGCGAAA-CAGTAGGCACACGAAGTGC
* * *
53980283 GAAACAGTAGGCACACGAGGTGCGAAACAGTAGGCACACGAAGTGC
1 GAAACAGTAAGCACACAAAGTGCGAAACAGTAGGCACACGAAGTGC
53980329 GAAACAGTAAGCACACAAAGTGCGAAACAGTA
1 GAAACAGTAAGCACACAAAGTGCGAAACAGTA
53980361 AGCGCGCTAG
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
45 33 0.33
46 64 0.64
47 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.11
Consensus pattern (46 bp):
GAAACAGTAAGCACACAAAGTGCGAAACAGTAGGCACACGAAGTGC
Found at i:53980343 original size:69 final size:68
Alignment explanation
Indices: 53980219--53980360 Score: 166
Period size: 69 Copynumber: 2.1 Consensus size: 68
53980209 CAGTGCAATC
* * * *
53980219 CAGTAGGCACACACAGTGCAATCAGTAGGCGCACATAGTGCAAATCAGAAGGCACACGAGGTGCG
1 CAGTAGGCACACACAGTGCAAACAGTAGGCACACATAGTGCAAATCAGAAGGCACACAAAGTGCG
53980284 AAA
66 AAA
*
53980287 CAGTAGGCACACGA-GGTGCGAAACAGTAGGCACACGA-AGTGCGAAA-CAGTAA-GCACACAAA
1 CAGTAGGCACAC-ACAGTGC-AAACAGTAGGCACAC-ATAGTGC-AAATCAG-AAGGCACACAAA
53980348 GTGCGAAA
61 GTGCGAAA
53980356 CAGTA
1 CAGTA
53980361 AGCGCGCTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
68 16 0.25
69 42 0.66
70 6 0.09
ACGTcount: A:0.39, C:0.23, G:0.28, T:0.11
Consensus pattern (68 bp):
CAGTAGGCACACACAGTGCAAACAGTAGGCACACATAGTGCAAATCAGAAGGCACACAAAGTGCG
AAA
Found at i:53980361 original size:23 final size:23
Alignment explanation
Indices: 53980168--53980363 Score: 141
Period size: 23 Copynumber: 8.4 Consensus size: 23
53980158 CGAAATACTT
53980168 AACAGTAAGCACAC-AAGTGCTGAAGA
1 AACAGTAAGCACACAAAGTGC----GA
* * *
53980194 AATAGTAAACACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
53980216 ATCCAGTAGGCACACACAGTGC-A
1 A-ACAGTAAGCACACAAAGTGCGA
* * * *
53980239 ATCAGTAGGCGCACATAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
53980261 AATCAG-AAGGCACACGAGGTGCGA
1 AA-CAGTAA-GCACACAAAGTGCGA
* * *
53980285 AACAGTAGGCACACGAGGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
* *
53980308 AACAGTAGGCACACGAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
53980331 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
53980354 AACAGTAAGC
1 AACAGTAAGC
53980364 GCGCTAGCGT
Statistics
Matches: 144, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
22 22 0.15
23 101 0.70
24 4 0.03
26 12 0.08
27 5 0.03
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:53983585 original size:13 final size:13
Alignment explanation
Indices: 53983567--53983605 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
53983557 GTTTTTCGAA
53983567 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
53983580 AAAGTCAACGATC
1 AAAGTCAACGGTC
53983593 AACAGTCAACGGT
1 AA-AGTCAACGGT
53983606 TTAACTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:53987368 original size:81 final size:81
Alignment explanation
Indices: 53987271--53987432 Score: 274
Period size: 82 Copynumber: 2.0 Consensus size: 81
53987261 TTTGCCATTG
* *
53987271 TCTTCTCTTTTTCTTGTTATCTTGAAAGG-TTTCCATTAACTTTAGGTATTGTTTTGATGGGGTT
1 TCTTCTCTTTTTCTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGTT
53987335 CTTTCCATTTCATGCAA
66 CTTT-CATTTCATGCAA
53987352 TCTT-TCTTTTTACTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
1 TCTTCTCTTTTT-CTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGT
53987416 TCTTTCATTTCATGCAA
65 TCTTTCATTTCATGCAA
53987433 CAGTTCTTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
80 7 0.09
81 33 0.43
82 37 0.48
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (81 bp):
TCTTCTCTTTTTCTTGTTATCTTGAAAGGCTTTCCATTAACTTGAGCTATTGTTTTGATGGGGTT
CTTTCATTTCATGCAA
Found at i:53989428 original size:56 final size:56
Alignment explanation
Indices: 53989342--53989455 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
53989332 ATAGAAAAAT
53989342 GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
1 GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
53989398 GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
1 GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
53989454 GA
1 GA
53989456 ATTGTTTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (56 bp):
GATTCTTTGGATTTTGTATACAACATCATTTCTTGCAGAATTGCTGTTATGGAATG
Found at i:53993278 original size:59 final size:59
Alignment explanation
Indices: 53993232--53993552 Score: 359
Period size: 59 Copynumber: 5.5 Consensus size: 59
53993222 AATTTTTTAC
* * **
53993232 TTTCGAGGGTAAAAAT-GTAATTTTTGGTGAAATCAGGGTTGAAAATGAGATTTTAGGGAA
1 TTTCGAGGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTT-GAAAA
*
53993292 -TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTGAAAATGGGATTTTGGAAAA
1 TTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTT-GAAAA
* * *
53993351 TTT-GGGGGTAAAATGGTAA-TTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAG
1 TTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTT-GAAAA
* * *
53993409 TTTAGA-GGTAAAATGGTAATTTTTGGTGAGATCAGGGTTAAAAATGGGATTTTGGAAA
1 TTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGAAAA
* * *** * *
53993467 GTTC-AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACAAGATTTTGGGAAG
1 TTTCGA-GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTT-GAAAA
**
53993527 TTTATA-GGTAAAATGGTAATTTTTGG
1 TTTCGAGGGTAAAATGGTAATTTTTGG
53993553 ACAATCCAGG
Statistics
Matches: 230, Mismatches: 23, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
57 1 0.00
58 62 0.27
59 158 0.69
60 8 0.03
61 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (59 bp):
TTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGAAAA
Found at i:53993285 original size:30 final size:30
Alignment explanation
Indices: 53993243--53993344 Score: 106
Period size: 30 Copynumber: 3.4 Consensus size: 30
53993233 TTCGAGGGTA
53993243 AAAATGTA-ATTTTTGGTGAAATCAGGGTTG
1 AAAATG-AGATTTTTGGTGAAATCAGGGTTG
* *
53993273 AAAATGAGATTTTAGG-GAATTCGAGGG-T-
1 AAAATGAGATTTTTGGTGAAATC-AGGGTTG
53993301 AAAATG-GTAATTTTTGGTGAAATCAGGGTTG
1 AAAATGAG--ATTTTTGGTGAAATCAGGGTTG
*
53993332 AAAATGGGATTTT
1 AAAATGAGATTTT
53993345 GGAAAATTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
27 1 0.02
28 6 0.10
29 18 0.30
30 28 0.47
31 6 0.10
32 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGAGATTTTTGGTGAAATCAGGGTTG
Found at i:53993419 original size:117 final size:118
Alignment explanation
Indices: 53993238--53993552 Score: 449
Period size: 117 Copynumber: 2.7 Consensus size: 118
53993228 TTACTTTCGA
* *
53993238 GGGTAAAAAT-GTAATTTTTGGTGAAATCAGGGTTGAAAATGAGATTTTAGGGAA--TTCGAGGG
1 GGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGAGATTTT-GGGAAGTTTAGA-GG
* **
53993300 TAAAATGGTAATTTTTGGTGAAATCAGGGTTGAAAATGGGATTTTGGAAAATTTGG
63 TAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAATTCAG
* * *
53993356 GGGTAAAATGGTAA-TTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTTAGAGGTAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGAGATTTTGGGAAGTTTAGAGGTAA
* *
53993420 AATGGTAATTTTTGGTGAGATCAGGGTTAAAAATGGGATTTTGGAAAGTTCAG
66 AATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAATTCAG
* ** *
53993473 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACAAGATTTTGGGAAGTTTATAGGTAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGAGATTTTGGGAAGTTTAGAGGTAA
53993538 AATGGTAATTTTTGG
66 AATGGTAATTTTTGG
53993553 ACAATCCAGG
Statistics
Matches: 176, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
116 4 0.02
117 102 0.58
118 70 0.40
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (118 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGAGATTTTGGGAAGTTTAGAGGTAA
AATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAATTCAG
Found at i:53995422 original size:18 final size:17
Alignment explanation
Indices: 53995399--53995454 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 17
53995389 AAATGGATTT
* *
53995399 TTTAATTTTAATTTTTAA
1 TTTAATATT-ATTTTAAA
53995417 TTTAATATTATTTTAAA
1 TTTAATATTATTTTAAA
* * *
53995434 TTTGAT-TAAATTTAAA
1 TTTAATATTATTTTAAA
53995450 TTTAA
1 TTTAA
53995455 AGTAAATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 12 0.38
17 12 0.38
18 8 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTAATATTATTTTAAA
Found at i:53995450 original size:6 final size:6
Alignment explanation
Indices: 53995439--53995500 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
53995429 TTAAATTTGA
* **
53995439 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT TTAAA- AGAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
53995485 TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
53995501 ATCCATTTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 11 0.24
6 34 0.76
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:53995460 original size:17 final size:17
Alignment explanation
Indices: 53995440--53995500 Score: 97
Period size: 17 Copynumber: 3.6 Consensus size: 17
53995430 TAAATTTGAT
53995440 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
53995457 TAAATTTAAATTTAAAAG
1 TAAATTTAAATTT-AAAG
*
53995475 -AAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAG
53995491 TAAATTTAAA
1 TAAATTTAAA
53995501 ATCCATTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
16 3 0.07
17 34 0.83
18 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:53996216 original size:200 final size:200
Alignment explanation
Indices: 53995903--53996504 Score: 920
Period size: 200 Copynumber: 3.0 Consensus size: 200
53995893 CAATTATCTA
*
53995903 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAAT-TCGGTCCACTTCTCTGTGTCTCATC
1 TTTTGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCT-GGTCCACTTCTCTGTGTCTCATC
* * *
53995967 AGGAAGCTAACCTTTTTATTGCTTCGTCCTGCTTCTCATTATTTCATCAGGAAGCTGGGTTCGAA
65 AGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAA
* *
53996032 GATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGTCTGCCT
130 GATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCT
53996097 CGCTTG
195 CGCTTG
* * * *
53996103 TTTTGATTCACTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCCGCGTCTCATTA
1 TTTTGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCA
* *
53996168 GGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGTTCGAGG
66 GGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAG
* * * *
53996233 ATTTGCTCGTGTTTGAGCGCTAAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCT
131 ATTTGCTCGCG-TTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCT
*
53996298 TGCTTG
195 CGCTTG
* * * * * *
53996304 TTTCGATTCGCTTTTCTGGATCTCCTTAGAAAGAAGAATCTGGT-CACTTCGCTGTGTCTCATCA
1 TTTTGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCA
* *
53996368 GGAAGCTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAG
66 GGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAG
* * *
53996433 ACTTGCTCTCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTC
131 ATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
53996498 GCTTG
196 GCTTG
53996503 TT
1 TT
53996505 GAACCACTCC
Statistics
Matches: 361, Mismatches: 39, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
199 56 0.16
200 213 0.59
201 92 0.25
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (200 bp):
TTTTGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTGTCTCATCA
GGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAG
ATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
GCTTG
Found at i:54008656 original size:29 final size:29
Alignment explanation
Indices: 54008624--54008935 Score: 135
Period size: 29 Copynumber: 10.8 Consensus size: 29
54008614 TGACTTTCGA
*
54008624 GGGTAAAAAT-GTAATTTTTGGTGAAACCG
1 GGGTAAAAATGGTAATTTTTGG-GAAATCG
* *
54008653 GGGTTAAAAATAGG--ATTTTAGGGAATTCG
1 GGG-TAAAAAT-GGTAATTTTTGGGAAATCG
*
54008682 AGGGT-AAAATGGTAA-TTTTGGTGAAACCG
1 -GGGTAAAAATGGTAATTTTTGG-GAAATCG
* *
54008711 AGGTTAAAAAT-G-AGA-TTTTGGGAAGTTCG
1 -GGGTAAAAATGGTA-ATTTTTGGGAA-ATCG
54008740 GGAGT-AAAATGGTAATTTTTGGCGAAATCG
1 GG-GTAAAAATGGTAATTTTTGG-GAAATCG
*
54008770 GGGTTGAAAATAGG--A-TTTTGGGAAATTCGG
1 GGG-TAAAAAT-GGTAATTTTTGGGAAA-TC-G
54008800 GGGT--AAATGGTAA-TTTTGGTGAAATCG
1 GGGTAAAAATGGTAATTTTTGG-GAAATCG
* * * * *
54008827 GGGTTAAAATGG-GA-TTTTAGAAAATTTG
1 GGGTAAAAATGGTAATTTTTGGGAAA-TCG
*
54008855 TGGGT-AAAATGGTAATTTTTGGTGAAACCG
1 -GGGTAAAAATGGTAATTTTTGG-GAAATCG
* * * *
54008885 AGGTTAAAAATGG-GA-TTTTGGGAAGTTTAG
1 -GGGTAAAAATGGTAATTTTTGGGAA--ATCG
54008915 GGGT-AAAATGGTAATTTTTGG
1 GGGTAAAAATGGTAATTTTTGG
54008936 ACAGTCCAAG
Statistics
Matches: 220, Mismatches: 28, Indels: 69
0.69 0.09 0.22
Matches are distributed among these distances:
26 2 0.01
27 14 0.06
28 59 0.27
29 67 0.30
30 57 0.26
31 18 0.08
32 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGGTAATTTTTGGGAAATCG
Found at i:54008703 original size:58 final size:58
Alignment explanation
Indices: 54008619--54008935 Score: 371
Period size: 59 Copynumber: 5.4 Consensus size: 58
54008609 ATTTTTGACT
54008619 TTCGAGGGTAAAAAT-GTAATTTTTGGTGAAACCGGGGTTAAAAATAGGATTTTAGGGAA
1 TTCGAGGGT-AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATAGGATTTT-GGGAA
*
54008678 TTCGAGGGTAAAATGGTAA-TTTTGGTGAAACCGAGGTTAAAAAT-GAGATTTTGGGAA
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATAG-GATTTTGGGAA
* * *
54008735 GTTCG-GGAGTAAAATGGTAATTTTTGGCGAAATCGGGGTTGAAAATAGGATTTTGGGAAA
1 -TTCGAGG-GTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATAGGATTTTGGG-AA
* * * **
54008795 TTCGGGGGT-AAATGGTAA-TTTTGGTGAAATCGGGGTT-AAAATGGGATTTTAGAAAA
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATAGGATTTT-GGGAA
* * * *
54008851 TTTGTGGGTAAAATGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGGATTTTGGGAA
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATAGGATTTTGGGAA
*
54008909 GTT-TAGGGGTAAAATGGTAATTTTTGG
1 -TTCGA-GGGTAAAATGGTAATTTTTGG
54008936 ACAGTCCAAG
Statistics
Matches: 227, Mismatches: 17, Indels: 28
0.83 0.06 0.10
Matches are distributed among these distances:
56 21 0.09
57 36 0.16
58 80 0.35
59 85 0.37
60 5 0.02
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.32
Consensus pattern (58 bp):
TTCGAGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATAGGATTTTGGGAA
Found at i:54008815 original size:28 final size:29
Alignment explanation
Indices: 54008667--54008932 Score: 160
Period size: 29 Copynumber: 9.2 Consensus size: 29
54008657 TAAAAATAGG
*
54008667 ATTTTAGGG-AATTCGAGGGTAAAATGGTA
1 ATTTT-GGGAAATTCGGGGGTAAAATGGTA
* * *
54008696 ATTTTGGTGAAA-CCGAGGTTAAAAAT-G-A
1 ATTTTGG-GAAATTCGGGGGT-AAAATGGTA
* *
54008724 GATTTTGGGAAGTTCGGGAGTAAAATGGTA
1 -ATTTTGGGAAATTCGGGGGTAAAATGGTA
*
54008754 ATTTTTGGCGAAA-TCGGGGTTGAAAATAGG--
1 A-TTTTGG-GAAATTCGGGGGT-AAAAT-GGTA
54008784 ATTTTGGGAAATTCGGGGGT-AAATGGTA
1 ATTTTGGGAAATTCGGGGGTAAAATGGTA
* *
54008812 ATTTTGGTGAAA-TCGGGGTTAAAATGG-G
1 ATTTTGG-GAAATTCGGGGGTAAAATGGTA
* * * *
54008840 ATTTTAGAAAATTTGTGGGTAAAATGGTA
1 ATTTTGGGAAATTCGGGGGTAAAATGGTA
* * * *
54008869 ATTTTTGGTGAAA-CCGAGGTTAAAAATGG-G
1 A-TTTTGG-GAAATTCGGGGGT-AAAATGGTA
* **
54008899 ATTTTGGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTGGGAAATTCGGGGGTAAAATGGTA
54008928 ATTTT
1 ATTTT
54008933 TGGACAGTCC
Statistics
Matches: 181, Mismatches: 33, Indels: 46
0.70 0.13 0.18
Matches are distributed among these distances:
26 2 0.01
27 7 0.04
28 57 0.31
29 64 0.35
30 31 0.17
31 18 0.10
32 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (29 bp):
ATTTTGGGAAATTCGGGGGTAAAATGGTA
Found at i:54017754 original size:20 final size:20
Alignment explanation
Indices: 54017729--54017767 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54017719 ATTAGGCAAC
*
54017729 AAAACATTAATTTCAAGAAA
1 AAAACATTAATTCCAAGAAA
54017749 AAAACATTAATTCCAAGAA
1 AAAACATTAATTCCAAGAA
54017768 GGAAATTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAACATTAATTCCAAGAAA
Found at i:54020484 original size:30 final size:30
Alignment explanation
Indices: 54020438--54020502 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
54020428 TTCCTTAAAA
*
54020438 TTTTTAGAAATTTTAA-TTACCCCCTGATT
1 TTTTTAAAAATTTTAATTTACCCCCTGATT
54020467 TTTTTAAAAATTTTTAATTTACCCCCTGATT
1 TTTTTAAAAA-TTTTAATTTACCCCCTGATT
54020498 TTTTT
1 TTTTT
54020503 TAAATTCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 9 0.27
30 6 0.18
31 18 0.55
ACGTcount: A:0.26, C:0.15, G:0.05, T:0.54
Consensus pattern (30 bp):
TTTTTAAAAATTTTAATTTACCCCCTGATT
Found at i:54026455 original size:18 final size:18
Alignment explanation
Indices: 54026430--54026474 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
54026420 GGTAATTGCT
54026430 GCATTTTCTTTGCTGTTA
1 GCATTTTCTTTGCTGTTA
*
54026448 GGATTTTCTTTGCTGTTA
1 GCATTTTCTTTGCTGTTA
54026466 GCATTTTCT
1 GCATTTTCT
54026475 GGTGTGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.56
Consensus pattern (18 bp):
GCATTTTCTTTGCTGTTA
Found at i:54047024 original size:27 final size:27
Alignment explanation
Indices: 54047000--54047051 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
54046990 TCTATTTTAT
* *
54047000 ATAAATAAAATTTAACACAACTTTTTG
1 ATAAAAAAAAATTAACACAACTTTTTG
54047027 ATAAAAAAAAATTAACACAACTTTT
1 ATAAAAAAAAATTAACACAACTTTT
54047052 GTTTATCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.33
Consensus pattern (27 bp):
ATAAAAAAAAATTAACACAACTTTTTG
Found at i:54047168 original size:42 final size:44
Alignment explanation
Indices: 54047057--54047169 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 44
54047047 CTTTTGTTTA
* * * *
54047057 TCTCAAAAATTTTAAACTAATAATTATCATAATTTCTATTAAAT
1 TCTCAATATTTTTAAACTAATAATTATCACAACTTCTATTAAAT
* * **
54047101 TCTTATTATTTTTAAA-TATATAATTATCACAACTTCTATTTTAT
1 TCTCAATATTTTTAAACTA-ATAATTATCACAACTTCTATTAAAT
*
54047145 T-TCAAT-TTTTTAAACTCATAATTAT
1 TCTCAATATTTTTAAACTAATAATTAT
54047170 GAATTAAATA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 16 0.29
43 6 0.11
44 34 0.61
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.50
Consensus pattern (44 bp):
TCTCAATATTTTTAAACTAATAATTATCACAACTTCTATTAAAT
Found at i:54056129 original size:21 final size:20
Alignment explanation
Indices: 54056105--54056161 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
54056095 TTTATAAATT
54056105 TATAT-ATTATTTTATTTAA
1 TATATAATTATTTTATTTAA
*
54056124 TATATACATTATTTGAATTTAA
1 TATATA-ATTATTT-TATTTAA
* *
54056146 TATTTAATAATTTTAT
1 TATATAATTATTTTAT
54056162 ATATTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 5 0.16
20 2 0.06
21 13 0.42
22 11 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TATATAATTATTTTATTTAA
Found at i:54056711 original size:15 final size:16
Alignment explanation
Indices: 54056691--54056723 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
54056681 GTATTCTGTG
54056691 TTTTAT-TATAATTAT
1 TTTTATATATAATTAT
54056706 TTTTATCATATAATTAT
1 TTTTAT-ATATAATTAT
54056723 T
1 T
54056724 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTATATATAATTAT
Found at i:54059901 original size:21 final size:20
Alignment explanation
Indices: 54059875--54059932 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
54059865 CAAAATAATC
54059875 AAAATAATTTTTCAAAAATTA
1 AAAATAATTTTT-AAAAATTA
*
54059896 AAAATAATTTTT-AAAATTC
1 AAAATAATTTTTAAAAATTA
*
54059915 AAAAT-ATTTATAAAAATT
1 AAAATAATTTTTAAAAATT
54059933 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.15
19 17 0.50
21 12 0.35
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATAATTTTTAAAAATTA
Found at i:54059913 original size:19 final size:19
Alignment explanation
Indices: 54059875--54059929 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
54059865 CAAAATAATC
54059875 AAAATAATTTTTCAAAAATTA
1 AAAATAATTTTT--AAAATTA
*
54059896 AAAATAATTTTTAAAATTC
1 AAAATAATTTTTAAAATTA
*
54059915 AAAAT-ATTTATAAAA
1 AAAATAATTTTTAAAA
54059930 ATTTTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 9 0.28
19 11 0.34
21 12 0.38
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATAATTTTTAAAATTA
Found at i:54059975 original size:20 final size:19
Alignment explanation
Indices: 54059871--54059975 Score: 56
Period size: 20 Copynumber: 5.4 Consensus size: 19
54059861 ATTACAAAAT
*
54059871 AATCAAAATAATTTTTCAAA
1 AATCAAAAT-ATTTTTTAAA
* *
54059891 AATTAAAAATAATTTTTAAA
1 AA-TCAAAATATTTTTTAAA
* *
54059911 ATTCAAAATA-TTTATAAA
1 AATCAAAATATTTTTTAAA
* **
54059929 AATTTTAAAAT-TTTTATTTTA
1 AA--TCAAAATATTTT-TTAAA
54059950 AA--AAAATATTTTTTAAA
1 AATCAAAATATTTTTTAAA
54059967 AATCTAAAA
1 AATC-AAAA
54059976 AAAATATAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
17 10 0.16
18 12 0.19
19 7 0.11
20 24 0.38
21 10 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
AATCAAAATATTTTTTAAA
Found at i:54064071 original size:29 final size:30
Alignment explanation
Indices: 54064029--54064087 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
54064019 TATGGTTTAA
*
54064029 TGTGTAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
54064058 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
54064088 GATTAAATTC
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:54064302 original size:30 final size:30
Alignment explanation
Indices: 54064230--54064302 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
54064220 TGATTAAATT
*
54064230 AAAATTAAAGTTTCAAGTATACATTTGAAC
1 AAAATTAAAGTTTCAAGTATACAATTGAAC
* * * *
54064260 AATAACTAAAGTTTCACGTATATAATTGTAC
1 AA-AATTAAAGTTTCAAGTATACAATTGAAC
*
54064291 CAAATTAAAGTT
1 AAAATTAAAGTT
54064303 CATGTGTAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (30 bp):
AAAATTAAAGTTTCAAGTATACAATTGAAC
Found at i:54065119 original size:16 final size:16
Alignment explanation
Indices: 54065098--54065129 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54065088 ATTAAAATGA
54065098 TTATTTAAAATATTTT
1 TTATTTAAAATATTTT
*
54065114 TTATTTTAAATATTTT
1 TTATTTAAAATATTTT
54065130 ATTCTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTAAAATATTTT
Found at i:54074964 original size:15 final size:14
Alignment explanation
Indices: 54074944--54074973 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
54074934 TATTATTTTA
54074944 AAATATATAACATAT
1 AAATATATAA-ATAT
54074959 AAATATATAAATAT
1 AAATATATAAATAT
54074973 A
1 A
54074974 TAAAAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATATAAATAT
Found at i:54074968 original size:8 final size:8
Alignment explanation
Indices: 54074944--54074977 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
54074934 TATTATTTTA
54074944 AAATATAT
1 AAATATAT
*
54074952 -AACATAT
1 AAATATAT
54074959 AAATATAT
1 AAATATAT
54074967 AAATATAT
1 AAATATAT
54074975 AAA
1 AAA
54074978 AATCTATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (8 bp):
AAATATAT
Found at i:54075006 original size:17 final size:17
Alignment explanation
Indices: 54074986--54075032 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
54074976 AAAATCTATC
*
54074986 ATATAAAAAGGGTGAAT
1 ATATAAAAAGAGTGAAT
*
54075003 ATATAAAAAAAAAGTGAAT
1 ATAT--AAAAAGAGTGAAT
54075022 ATATAAAAAGA
1 ATATAAAAAGA
54075033 TATTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 10 0.40
19 15 0.60
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
ATATAAAAAGAGTGAAT
Found at i:54075783 original size:42 final size:42
Alignment explanation
Indices: 54075719--54075804 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 42
54075709 GCTCGTAAGT
*
54075719 TATTAGAGTTTGACTCGAAAAAAATCAAATTTGATTAGATAA
1 TATTAGAGTTTGACTCGAAAAAAATCAAATCTGATTAGATAA
54075761 TATTAGAGTTTTGACTCGAAAAAAATCAAATCTGATTAGATAA
1 TATTAGAG-TTTGACTCGAAAAAAATCAAATCTGATTAGATAA
54075804 T
1 T
54075805 TATCGAGCCT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 8 0.19
43 34 0.81
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (42 bp):
TATTAGAGTTTGACTCGAAAAAAATCAAATCTGATTAGATAA
Found at i:54081686 original size:29 final size:30
Alignment explanation
Indices: 54081639--54081698 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
54081629 ATTTATATCC
* *
54081639 TTATAATTTTAAAATATTAAATTA-AAATT
1 TTATAATTTTAAAAGATTAAAATATAAATT
* *
54081668 TTATCATTTTTAAAGATTAAAATATAAATT
1 TTATAATTTTAAAAGATTAAAATATAAATT
54081698 T
1 T
54081699 ACTATTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TTATAATTTTAAAAGATTAAAATATAAATT
Found at i:54083087 original size:23 final size:24
Alignment explanation
Indices: 54083060--54083124 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
54083050 AAGTATTAAA
54083060 AATTTAAAAATAATTA-TAAAATT
1 AATTTAAAAATAATTATTAAAATT
* * *
54083083 TATTT-AATATATTTATTTAAAATT
1 AATTTAAAAATAATTA-TTAAAATT
54083107 AATTATAAAATATAATTA
1 AATT-TAAAA-ATAATTA
54083125 AATTACTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
22 8 0.26
23 4 0.13
24 10 0.32
25 1 0.03
26 2 0.06
27 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTAAAAATAATTATTAAAATT
Found at i:54083124 original size:13 final size:12
Alignment explanation
Indices: 54083060--54083123 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
54083050 AAGTATTAAA
54083060 AATTTAAAA-AT
1 AATTTAAAATAT
54083071 AATTATAAAAT-T
1 AATT-TAAAATAT
* *
54083083 TATTTAATATATT
1 AATTTAAAATA-T
*
54083096 TATTTAAAAT-T
1 AATTTAAAATAT
54083107 AATTATAAAATAT
1 AATT-TAAAATAT
54083120 AATT
1 AATT
54083124 AAATTACTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 13 0.30
12 15 0.35
13 15 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATTTAAAATAT
Found at i:54085320 original size:9 final size:9
Alignment explanation
Indices: 54085306--54085347 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
54085296 GATTAAGTTT
54085306 AATTAAAAA
1 AATTAAAAA
**
54085315 AATTAAATT
1 AATTAAAAA
54085324 AA-TAAAAA
1 AATTAAAAA
54085332 AATTAAAAA
1 AATTAAAAA
*
54085341 AACTAAA
1 AATTAAA
54085348 TTTATCGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
8 6 0.22
9 21 0.78
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (9 bp):
AATTAAAAA
Found at i:54085329 original size:17 final size:18
Alignment explanation
Indices: 54085304--54085338 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
54085294 AAGATTAAGT
54085304 TTAATTAAAAAAATTAAA
1 TTAATTAAAAAAATTAAA
54085322 TTAA-TAAAAAAATTAAA
1 TTAATTAAAAAAATTAAA
54085339 AAAACTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAATTAAAAAAATTAAA
Found at i:54090644 original size:15 final size:16
Alignment explanation
Indices: 54090624--54090653 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54090614 GAGTATGATA
54090624 AAATA-TTTAAAAAAT
1 AAATATTTTAAAAAAT
54090639 AAATATTTTAAAAAA
1 AAATATTTTAAAAAA
54090654 GAGAAACACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATTTTAAAAAAT
Found at i:54093633 original size:15 final size:16
Alignment explanation
Indices: 54093608--54093641 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
54093598 ATAATGTAAT
54093608 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
54093624 TTTA-TATTTTAATAA
1 TTTATTATTTTAATAA
54093639 TTT
1 TTT
54093642 TTAAAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:54094232 original size:2 final size:2
Alignment explanation
Indices: 54094225--54094255 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54094215 AACTTTGTTT
54094225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54094256 TTGCTTTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54096632 original size:19 final size:19
Alignment explanation
Indices: 54096587--54096634 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
54096577 AATGTAACTA
**
54096587 TAATAATTTAAAATTTAGG
1 TAATAATTTAAAATGAAGG
*
54096606 -GATCAATTTAAAATGAAGG
1 TAAT-AATTTAAAATGAAGG
54096625 TAATAATTTA
1 TAATAATTTA
54096635 GGGATGTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATAATTTAAAATGAAGG
Found at i:54100912 original size:25 final size:23
Alignment explanation
Indices: 54100875--54101015 Score: 145
Period size: 23 Copynumber: 6.3 Consensus size: 23
54100865 ACACTAGCGC
*
54100875 GCTCTCTGTTTAGCACTGT-GTGT
1 GCTCTCTGATTAGCACT-TCGTGT
*
54100898 GCTCTCTGTTATTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCACTTCGTGT
54100923 GCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTTCGTGT
54100946 GCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTTCGTGT
* *
54100969 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGT
* *
54100985 ACTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGT
54101008 GCTCTCTG
1 GCTCTCTG
54101016 TTACCCAGCA
Statistics
Matches: 101, Mismatches: 7, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
16 10 0.10
18 3 0.03
21 3 0.03
23 64 0.63
24 1 0.01
25 20 0.20
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTCGTGT
Found at i:54100946 original size:48 final size:46
Alignment explanation
Indices: 54100875--54101015 Score: 145
Period size: 39 Copynumber: 3.2 Consensus size: 46
54100865 ACACTAGCGC
* *
54100875 GCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTG--ATTAGCACTTCGTGT
54100923 GCTCTCTGATTAGCACT-TCGTGTGCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTGT-GTGTGCTCTCTGATTAGCACTTCGTGT
* * * *
54100969 G--CTC-----AGTACTTTGTGTACTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
54101008 GCTCTCTG
1 GCTCTCTG
54101016 TTACCCAGCA
Statistics
Matches: 82, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
39 31 0.38
40 1 0.01
41 3 0.04
44 3 0.04
46 15 0.18
47 1 0.01
48 28 0.34
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
Found at i:54103784 original size:18 final size:20
Alignment explanation
Indices: 54103749--54103785 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
54103739 ATCCAAATTT
54103749 CCCAAATGCCCAAAGACAAC
1 CCCAAATGCCCAAAGACAAC
54103769 CCCAAAT-CCC-AAGACAA
1 CCCAAATGCCCAAAGACAA
54103786 AATTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.46, C:0.41, G:0.08, T:0.05
Consensus pattern (20 bp):
CCCAAATGCCCAAAGACAAC
Found at i:54106601 original size:23 final size:23
Alignment explanation
Indices: 54106575--54106624 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
54106565 TTTTTGAAAA
54106575 ATTAAAATATAATTTTATCATTT
1 ATTAAAATATAATTTTATCATTT
** * *
54106598 ATTAATTTATGATTTTATTATTT
1 ATTAAAATATAATTTTATCATTT
54106621 -TTAA
1 ATTAA
54106625 GGAATTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTAAAATATAATTTTATCATTT
Found at i:54110609 original size:17 final size:18
Alignment explanation
Indices: 54110587--54110626 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
54110577 TGCATTTAAA
54110587 TTATTACAT-TTATAATT
1 TTATTACATGTTATAATT
*
54110604 TTATTAGATGTTATAATT
1 TTATTACATGTTATAATT
*
54110622 GTATT
1 TTATT
54110627 TGAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (18 bp):
TTATTACATGTTATAATT
Found at i:54112015 original size:21 final size:20
Alignment explanation
Indices: 54111991--54112029 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
54111981 TGTGTAAAAG
54111991 ATTAATCCAAATCTATTTTAA
1 ATTAATCCAAAT-TATTTTAA
* *
54112012 ATTAGTCCATATTATTTT
1 ATTAATCCAAATTATTTT
54112030 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTAATCCAAATTATTTTAA
Found at i:54112070 original size:22 final size:22
Alignment explanation
Indices: 54112042--54112085 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
54112032 AATTTTTTAA
54112042 AATATTT-ATATTATATTATTTT
1 AATATTTAATATTATA-TATTTT
54112064 AATATTTACATATTATATATTT
1 AATATTTA-ATATTATATATTT
54112086 AGTATATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
AATATTTAATATTATATATTTT
Found at i:54116596 original size:3 final size:3
Alignment explanation
Indices: 54116588--54116614 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54116578 TTATCTGTAT
54116588 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
54116615 CTGCTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:54117445 original size:30 final size:34
Alignment explanation
Indices: 54117381--54117445 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
54117371 ATCATAACCA
54117381 TCTATATAATATAAAATGTAACTAACTATTATTAT
1 TCTATATAATATAAAATGTAACTAACTA-TATTAT
*
54117416 TCTATATAA-A-AAAATG-ACCTAACTA-ATTAT
1 TCTATATAATATAAAATGTAACTAACTATATTAT
54117446 ATGTGATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 5 0.17
32 8 0.28
33 6 0.21
34 1 0.03
35 9 0.31
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (34 bp):
TCTATATAATATAAAATGTAACTAACTATATTAT
Found at i:54117445 original size:33 final size:35
Alignment explanation
Indices: 54117381--54117445 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
54117371 ATCATAACCA
54117381 TCTATATAATATAAAATGTAACTAACTATTATTAT
1 TCTATATAATATAAAATGTAACTAACTATTATTAT
*
54117416 TCTATATAA-A-AAAATG-ACCTAACTAATTAT
1 TCTATATAATATAAAATGTAACTAACT-ATTAT
54117446 ATGTGATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 7 0.25
33 11 0.39
34 1 0.04
35 9 0.32
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (35 bp):
TCTATATAATATAAAATGTAACTAACTATTATTAT
Found at i:54119368 original size:162 final size:163
Alignment explanation
Indices: 54119092--54119540 Score: 541
Period size: 162 Copynumber: 2.7 Consensus size: 163
54119082 TTGGTTTTGA
*
54119092 TTTGACAAGCATATATAATGCTATTTTCTTGGTGGGGTTTTGGTTATGGGATTGTAGGGAAGGAA
1 TTTGACAAGCATATATAATGCTGTTTTCTTGGTGGGGTTTTGGTTATGGGATTGTAGGGAA-GAA
* * * *** *
54119157 AAAGAGACAAAATCGACGTCGCAATTGCCATTTGTTATAGGGGAACCTGAAGAAACAGGTGAGTC
65 AAAGAGACGAAATCGACGTCGAAACTGCCATTTCCGATAGGGGAACCTGAAGAAACAGGTGACTC
* *
54119222 AGTTCTTAATTCGGTCATCG-T-TTTTTTTA-GAG
130 AGTTCTTAACTCGGTCACCGTTATTTTTTTACG-G
* * * *
54119254 TTTGAC-TGACATATATAATGTTGTTTCCTTGGTGGGGTTTTGGTTATGGGATTATAGGGAAGAA
1 TTTGACAAG-CATATATAATGCTGTTTTCTTGGTGGGGTTTTGGTTATGGGATTGTAGGGAAGAA
* * * *
54119318 AGAAGATACGGAATCAACGTCGAAACTGCCATTTCCGATAGGGGAACCTGAAGAAGCAGGTGACT
65 A-AAGAGACGAAATCGACGTCGAAACTGCCATTTCCGATAGGGGAACCTGAAGAAACAGGTGACT
*
54119383 CAGTTCTTAACTCGGTTACCGTTTTTACTTTTTTTACGG
129 CAGTTCTTAACTCGGTCACCG---TTA-TTTTTTTACGG
* * *
54119422 TTTGACAAGCATATATAATACTGTTTTCTTGGTGGGGTTTTGGTTGTGGGATTGTAGAGAAGAAA
1 TTTGACAAGCATATATAATGCTGTTTTCTTGGTGGGGTTTTGGTTATGGGATTGTAGGGAAG-AA
* *
54119487 AAAGAGACGAAATCGACGTC-AAAGCTGCCA-TTCGCGATAGGGGAAACAGAAGAA
65 AAAGAGACGAAATCGACGTCGAAA-CTGCCATTTC-CGATAGGGGAACCTGAAGAA
54119541 GGATGTGATA
Statistics
Matches: 243, Mismatches: 31, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
161 5 0.02
162 124 0.51
166 1 0.00
167 6 0.02
168 102 0.42
169 5 0.02
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (163 bp):
TTTGACAAGCATATATAATGCTGTTTTCTTGGTGGGGTTTTGGTTATGGGATTGTAGGGAAGAAA
AAGAGACGAAATCGACGTCGAAACTGCCATTTCCGATAGGGGAACCTGAAGAAACAGGTGACTCA
GTTCTTAACTCGGTCACCGTTATTTTTTTACGG
Found at i:54136159 original size:3 final size:3
Alignment explanation
Indices: 54136151--54136185 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
54136141 ATTAACTTAA
*
54136151 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54136186 CAATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:54144644 original size:24 final size:24
Alignment explanation
Indices: 54144612--54144691 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
54144602 TTTTCATCTT
*
54144612 TCCTTGGATTTTTCACACTTGGTC
1 TCCTCGGATTTTTCACACTTGGTC
* * * *
54144636 TCCTGGGATATTTCACACCTGATC
1 TCCTCGGATTTTTCACACTTGGTC
* ** *
54144660 TGCTCGGATTTCCCACACTTGGTT
1 TCCTCGGATTTTTCACACTTGGTC
54144684 TCCTCGGA
1 TCCTCGGA
54144692 GTAGTCACAT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.38
Consensus pattern (24 bp):
TCCTCGGATTTTTCACACTTGGTC
Found at i:54152433 original size:16 final size:16
Alignment explanation
Indices: 54152412--54152445 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
54152402 AACCAAATCC
54152412 AAAGTTTAAAACTGAA
1 AAAGTTTAAAACTGAA
54152428 AAAGTTTAAAACTGAA
1 AAAGTTTAAAACTGAA
54152444 AA
1 AA
54152446 CAAGTTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (16 bp):
AAAGTTTAAAACTGAA
Found at i:54157028 original size:11 final size:11
Alignment explanation
Indices: 54157012--54157036 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54157002 TATATCAACG
54157012 TAAAATGATGT
1 TAAAATGATGT
54157023 TAAAATGATGT
1 TAAAATGATGT
54157034 TAA
1 TAA
54157037 TTAGATAATG
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:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (11 bp):
TAAAATGATGT
Found at i:54162307 original size:43 final size:43
Alignment explanation
Indices: 54162202--54162469 Score: 312
Period size: 43 Copynumber: 6.3 Consensus size: 43
54162192 TTATGAGGAA
* **
54162202 AAACGCCGCTATAGAGT-ATGGTCTTTAGCGGCGCTT-TTACAC
1 AAACGCCGCTAAAGA-TCATGGTCTTTAGCGGCGCTTATCCCAC
* * * *
54162244 AAACGCTGCTATAGAGCATGGTCTTTAGCGACGCTTATCCCAC
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTATCCCAC
* *
54162287 AAACGCCGCTAAAGATCATGGTTTTTAGTGGCGCTTATCCCAC
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTATCCCAC
* * * *
54162330 AAACGCCGCTAAAGACCATGGTCTTTAGTGACGCTGATCCCAC
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTATCCCAC
*
54162373 AAACGCCGCTAAAGAAT-ATGGTCTTTAGCGGCGCCTT-T-ACAC
1 AAACGCCGCTAAAG-ATCATGGTCTTTAGCGGCG-CTTATCCCAC
* * * *
54162415 AAACGTCGCTAAAGAACATAGTCTTTAGCGGCACTTATCCCAC
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTATCCCAC
54162458 AAACGCCGCTAA
1 AAACGCCGCTAA
54162470 TATTAACAAA
Statistics
Matches: 193, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
41 4 0.02
42 63 0.33
43 123 0.64
44 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTATCCCAC
Found at i:54162462 original size:85 final size:84
Alignment explanation
Indices: 54162202--54162469 Score: 342
Period size: 85 Copynumber: 3.1 Consensus size: 84
54162192 TTATGAGGAA
* * * * *
54162202 AAACGCCGCTATAGAGTATGGTCTTTAGCGGCGCTTTTACACAAACGCTGCTATAGAGCATGGTC
1 AAACGCCGCTAAAGAATATGGTCTTTAGCGGCGCCTTTACACAAACGC-GCTAAAGAACATGGTC
54162267 TTTAGCGACGCTTATCCCAC
65 TTTAGCGACGCTTATCCCAC
* * * *
54162287 AAACGCCGCTAAAG-ATCATGGTTTTTAGTGGCG-CTTATCCCACAAACGCCGCTAAAGACCATG
1 AAACGCCGCTAAAGAAT-ATGGTCTTTAGCGGCGCCTT-T-ACACAAACG-CGCTAAAGAACATG
* *
54162350 GTCTTTAGTGACGCTGATCCCAC
62 GTCTTTAGCGACGCTTATCCCAC
*
54162373 AAACGCCGCTAAAGAATATGGTCTTTAGCGGCGCCTTTACACAAACGTCGCTAAAGAACATAGTC
1 AAACGCCGCTAAAGAATATGGTCTTTAGCGGCGCCTTTACACAAACG-CGCTAAAGAACATGGTC
* *
54162438 TTTAGCGGCACTTATCCCAC
65 TTTAGCGACGCTTATCCCAC
54162458 AAACGCCGCTAA
1 AAACGCCGCTAA
54162470 TATTAACAAA
Statistics
Matches: 157, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
84 3 0.02
85 79 0.50
86 69 0.44
87 6 0.04
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (84 bp):
AAACGCCGCTAAAGAATATGGTCTTTAGCGGCGCCTTTACACAAACGCGCTAAAGAACATGGTCT
TTAGCGACGCTTATCCCAC
Found at i:54163667 original size:17 final size:17
Alignment explanation
Indices: 54163631--54163668 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
54163621 CAGAGAAGCT
*
54163631 AAAAGAGAAAAGTAAAA
1 AAAAGAGAAAAGAAAAA
54163648 AAAAGAGAAAA-AAAATA
1 AAAAGAGAAAAGAAAA-A
54163665 AAAA
1 AAAA
54163669 ATAAAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (17 bp):
AAAAGAGAAAAGAAAAA
Found at i:54164678 original size:20 final size:21
Alignment explanation
Indices: 54164647--54164686 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
54164637 AAATTTTCAA
*
54164647 TCTTTTTATTTTTATTTTACT
1 TCTTTTTATTTTAATTTTACT
54164668 TCTTTTT-TTTTAATTTTAC
1 TCTTTTTATTTTAATTTTAC
54164687 CTTGTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (21 bp):
TCTTTTTATTTTAATTTTACT
Found at i:54165082 original size:24 final size:24
Alignment explanation
Indices: 54165014--54165084 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
54165004 AGAAATAATT
* *
54165014 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
*
54165038 TTTCAAATAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
54165062 TTTCAATTAAATTCTATTTATTT
1 TTTCAATTAAACTCTGTTTATTT
54165085 ATTTGAGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:54166045 original size:17 final size:17
Alignment explanation
Indices: 54165998--54166054 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 17
54165988 GACATTACTT
54165998 TTTTAAATATATTTTAAAA
1 TTTTAAATA-ATTTT-AAA
54166017 TTATTAAA-AATTTTAAA
1 TT-TTAAATAATTTTAAA
*
54166034 TTTTAAATAATTTTTAA
1 TTTTAAATAATTTTAAA
54166051 TTTT
1 TTTT
54166055 TTGTTGATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 5 0.14
17 17 0.49
18 5 0.14
19 3 0.09
20 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAATAATTTTAAA
Found at i:54170310 original size:28 final size:28
Alignment explanation
Indices: 54170274--54170357 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
54170264 AAACTAGACT
*
54170274 TCTTTTATTTTATTTTAATTAGAATAAG
1 TCTTCTATTTTATTTTAATTAGAATAAG
*
54170302 TCTTCTATTTTATTTTATTTAGAATAAG
1 TCTTCTATTTTATTTTAATTAGAATAAG
54170330 TCTTCTATTTTATTTTAATTAGAATAAG
1 TCTTCTATTTTATTTTAATTAGAATAAG
54170358 GTGTTTCAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (28 bp):
TCTTCTATTTTATTTTAATTAGAATAAG
Found at i:54193239 original size:28 final size:29
Alignment explanation
Indices: 54193198--54193256 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
54193188 GGGATACAAG
54193198 TTCTTTGTCATCTTCTC-A-CTTACTCGGT
1 TTCTTTGTCATCTT-TCAATCTTACTCGGT
* *
54193226 TTCTTTTTCTTCTTTCAATCTTACTCGGT
1 TTCTTTGTCATCTTTCAATCTTACTCGGT
54193255 TT
1 TT
54193257 GACTAGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 13 0.48
29 12 0.44
ACGTcount: A:0.10, C:0.25, G:0.08, T:0.56
Consensus pattern (29 bp):
TTCTTTGTCATCTTTCAATCTTACTCGGT
Found at i:54196875 original size:20 final size:21
Alignment explanation
Indices: 54196838--54196893 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
54196828 GTCATTAAGC
*
54196838 CTTAATT-AATCATTTTTA-A
1 CTTAATTAAATCATATTTACA
54196857 TCTTAATTAAATC-TATTTACA
1 -CTTAATTAAATCATATTTACA
*
54196878 CTTAATATAAACCATA
1 CTTAAT-TAAATCATA
54196894 CCAATCCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 18 0.60
21 10 0.33
22 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (21 bp):
CTTAATTAAATCATATTTACA
Found at i:54226635 original size:30 final size:29
Alignment explanation
Indices: 54226599--54226680 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
54226589 TTTGAACCAC
* *
54226599 AATTAAAATTTCACGTGTATAATTACATTA
1 AATTAAAA-TTCACATATATAATTACATTA
*
54226629 AATTAAAATTCATATATATAATTACATATTA
1 AATTAAAATTCACATATATAATTAC--ATTA
* *
54226660 AAATAAAGTT-A-ATATATAATT
1 AATTAAAATTCACATATATAATT
54226681 TTGAGATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 24 0.53
30 9 0.20
31 12 0.27
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (29 bp):
AATTAAAATTCACATATATAATTACATTA
Found at i:54226675 original size:31 final size:29
Alignment explanation
Indices: 54226616--54226677 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
54226606 ATTTCACGTG
* *
54226616 TATAATTACATTAAATTAAAATTCATATA
1 TATAATTACATTAAAATAAAATTAATATA
*
54226645 TATAATTACATATTAAAATAAAGTTAATATA
1 TATAATTAC--ATTAAAATAAAATTAATATA
54226676 TA
1 TA
54226678 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 9 0.32
31 19 0.68
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (29 bp):
TATAATTACATTAAAATAAAATTAATATA
Found at i:54232313 original size:21 final size:22
Alignment explanation
Indices: 54232284--54232324 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
54232274 CCTTAGCTGT
*
54232284 ATATATATATATCATATACAAA
1 ATATATATATATAATATACAAA
*
54232306 ATAT-TATATTTAATATACA
1 ATATATATATATAATATACA
54232325 TAGAAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATATATATAATATACAAA
Found at i:54238723 original size:32 final size:32
Alignment explanation
Indices: 54238682--54238746 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
54238672 AAAGCAAAAA
54238682 AAAAATTACAATTAATTTAATTAATTCATTTT
1 AAAAATTACAATTAATTTAATTAATTCATTTT
54238714 AAAAATTACAATTAATTTAATTAATTCATTTT
1 AAAAATTACAATTAATTTAATTAATTCATTTT
54238746 A
1 A
54238747 TCTTTCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (32 bp):
AAAAATTACAATTAATTTAATTAATTCATTTT
Found at i:54241305 original size:24 final size:23
Alignment explanation
Indices: 54241245--54241312 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
54241235 GAATTAGAAT
54241245 TAAATTATAATTTTTATAATATTAA
1 TAAATTAT-ATTTTTATAAT-TTAA
* *
54241270 -AAA-TATAATTTTATTATTTGAA
1 TAAATTATATTTTTATAATTT-AA
54241292 TAAATTATATTTTTATAATTT
1 TAAATTATATTTTTATAATTT
54241313 TTAAAAGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 2 0.06
22 11 0.31
23 6 0.17
24 17 0.47
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TAAATTATATTTTTATAATTTAA
Found at i:54242976 original size:20 final size:20
Alignment explanation
Indices: 54242948--54242990 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
54242938 ATGTATCAAT
* * *
54242948 TATATAAAACACTATAAAAA
1 TATACAAAACAATAAAAAAA
*
54242968 TATACAAAATAATAAAAAAA
1 TATACAAAACAATAAAAAAA
54242988 TAT
1 TAT
54242991 TATATAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (20 bp):
TATACAAAACAATAAAAAAA
Found at i:54251314 original size:2 final size:2
Alignment explanation
Indices: 54251268--54251303 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54251258 GTCGATATTA
54251268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54251304 TTCAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54252724 original size:25 final size:25
Alignment explanation
Indices: 54252670--54252717 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
54252660 AGTTGGATCC
54252670 AAATTAAATTCTAAAAAGATAATTT
1 AAATTAAATTCTAAAAAGATAATTT
*
54252695 AAATTAAA-TCTAAATA-ATAATTT
1 AAATTAAATTCTAAAAAGATAATTT
54252718 CCTAATTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATTAAATTCTAAAAAGATAATTT
Found at i:54253649 original size:22 final size:22
Alignment explanation
Indices: 54253624--54253680 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
54253614 ATATTTTTTA
*
54253624 AAATATAACTCTATTAAATAAT
1 AAATATAACTCTATTAAACAAT
* * * *
54253646 AAATATAATTTTTTTAAACATT
1 AAATATAACTCTATTAAACAAT
54253668 AAATATTAACTCT
1 AAATA-TAACTCT
54253681 GTTGAAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATATAACTCTATTAAACAAT
Found at i:54254882 original size:12 final size:12
Alignment explanation
Indices: 54254860--54254893 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54254850 CTCGTGCTTA
*
54254860 TGTTATACTCTT
1 TGTTATGCTCTT
*
54254872 TGTTGTGCTCTT
1 TGTTATGCTCTT
54254884 TGTTATGCTC
1 TGTTATGCTC
54254894 CCATTGGTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.56
Consensus pattern (12 bp):
TGTTATGCTCTT
Found at i:54258101 original size:22 final size:22
Alignment explanation
Indices: 54258075--54258142 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
54258065 AATATTAAGG
*
54258075 TAAATAATTTTTATCTTTATGA
1 TAAATAATTTTTATATTTATGA
*
54258097 TAAATAATATTTATATTTATGA
1 TAAATAATTTTTATATTTATGA
*
54258119 T-AAT-ATTATTTATTTTTATGA
1 TAAATAATT-TTTATATTTATGA
54258140 TAA
1 TAA
54258143 TTTCATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.05
21 16 0.40
22 22 0.55
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (22 bp):
TAAATAATTTTTATATTTATGA
Found at i:54258128 original size:21 final size:21
Alignment explanation
Indices: 54258077--54258143 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
54258067 TATTAAGGTA
* *
54258077 AATAATTTTTATCTTTATGAT
1 AATAATATTTATATTTATGAT
54258098 AAATAATATTTATATTTATGAT
1 -AATAATATTTATATTTATGAT
* *
54258120 AATATTATTTATTTTTATGAT
1 AATAATATTTATATTTATGAT
54258141 AAT
1 AAT
54258144 TTCATATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 22 0.54
22 19 0.46
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (21 bp):
AATAATATTTATATTTATGAT
Found at i:54258153 original size:21 final size:21
Alignment explanation
Indices: 54258090--54258158 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
54258080 AATTTTTATC
* * *
54258090 TTTATGATAAATAATATTTATA
1 TTTATGAT-AATATTATATATT
*
54258112 TTTATGATAATATTATTTATT
1 TTTATGATAATATTATATATT
54258133 TTTATGATAAT-TTCATATATT
1 TTTATGATAATATT-ATATATT
54258154 TTTAT
1 TTTAT
54258159 TTTTTTAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.05
21 33 0.77
22 8 0.19
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTATGATAATATTATATATT
Found at i:54263512 original size:3 final size:3
Alignment explanation
Indices: 54263504--54263544 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
54263494 TATGAAAAAT
54263504 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
54263545 TTAAAGCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:54269582 original size:6 final size:6
Alignment explanation
Indices: 54269573--54269600 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
54269563 ATGTTTAGCC
54269573 AATGCA AATGCA AATGCA AATGCA AATG
1 AATGCA AATGCA AATGCA AATGCA AATG
54269601 GCAATAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
AATGCA
Found at i:54271701 original size:12 final size:12
Alignment explanation
Indices: 54271680--54271710 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54271670 GCAGTTGCTT
*
54271680 ATAATGACAGTA
1 ATAATAACAGTA
54271692 ATAATAACAGTA
1 ATAATAACAGTA
54271704 ATAATAA
1 ATAATAA
54271711 AACTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (12 bp):
ATAATAACAGTA
Done.