Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 81 of 125
Found at i:25360699 original size:18 final size:18
Alignment explanation
Indices: 25360676--25360713 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25360666 TTTCGGGCAG
*
25360676 AACCGAATTAATTCAGTT
1 AACCGAATGAATTCAGTT
*
25360694 AACCGACTGAATTCAGTT
1 AACCGAATGAATTCAGTT
25360712 AA
1 AA
25360714 TCGGTCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (18 bp):
AACCGAATGAATTCAGTT
Found at i:25362288 original size:19 final size:19
Alignment explanation
Indices: 25362242--25362280 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
25362232 TCATGGTAAC
25362242 AATTTTTTATAGTACCATTA
1 AATTTTTTATAGTA-CATTA
25362262 AATTTTTTTATAGTA-ATTA
1 AA-TTTTTTATAGTACATTA
25362281 GTATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 2 0.11
21 12 0.67
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
AATTTTTTATAGTACATTA
Found at i:25364743 original size:26 final size:26
Alignment explanation
Indices: 25364684--25364768 Score: 109
Period size: 26 Copynumber: 3.2 Consensus size: 26
25364674 TTAATATAAT
*
25364684 ATTTGGTATTTAAATTTAATTTTTTTA
1 ATTTGATATTTAAATTT-ATTTTTTTA
25364711 ATTTGATATTTAAATTT-TTTTATTTA
1 ATTTGATATTTAAATTTATTTT-TTTA
*
25364737 ATTTGATACTTAAATTTGATTTTTTTTA
1 ATTTGATATTTAAATTT-A-TTTTTTTA
25364765 ATTT
1 ATTT
25364769 AGTACCTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
25 4 0.08
26 20 0.38
27 16 0.31
28 8 0.15
29 4 0.08
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (26 bp):
ATTTGATATTTAAATTTATTTTTTTA
Found at i:25365101 original size:60 final size:59
Alignment explanation
Indices: 25365005--25365191 Score: 254
Period size: 60 Copynumber: 3.2 Consensus size: 59
25364995 TAATAAATTT
* * * * *
25365005 AGGTACCAAATTGAATCTAAAAAAA-CTTAGGAACCAAATTAGGAAAAAATGGCAAGTTC
1 AGGTACCAAATTGAGTCCAAAAAAAGTTTAGGTACCAAATTA-GAAAAAATGTCAAGTTC
* *
25365064 AAGTACCAAACTGAGTCCAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTC
1 AGGTACCAAATTGAGTCCAAAAAAAGTTTAGGTACCAAATT-AGAAAAAATGTCAAGTTC
* *
25365124 AGGTACCAAATTGGGT-C-AAAAAAGTTTAGGTACCAAATTAGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTGAGTCCAAAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAGTTC
25365181 AGGTACCAAAT
1 AGGTACCAAAT
25365192 GTTATATTAA
Statistics
Matches: 115, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
57 28 0.24
58 22 0.19
59 22 0.19
60 42 0.37
61 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.22
Consensus pattern (59 bp):
AGGTACCAAATTGAGTCCAAAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAGTTC
Found at i:25368350 original size:389 final size:391
Alignment explanation
Indices: 25367633--25368414 Score: 1343
Period size: 389 Copynumber: 2.0 Consensus size: 391
25367623 TATACATGTG
25367633 GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATGTAATAATAGTAACTTACATGTTA
1 GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATGTAATAATAGTAACTTACATGTTA
*
25367698 TTATTTACTATCATAAAAGATTAGCCCAAATTAAAAGTGATTTAAATTTGTTAAACTTTATTGGG
66 TTATTTACTATCACAAAAGATTAGCCCAAATTAAAAGTGATTTAAATTTGTTAAACTTTATTGGG
* *
25367763 CTTTAGTTATTATATAAAGTATAGATCAAATATGTGTAGATACTCTAGTAACTAATTTTTAATTT
131 CTTTAGTTATTATATAAAGTATAGATCAAATATGTGTAGATACTCTAGTAACTAATTTCTAATTG
* * * *
25367828 ATGATAGACTGATTAGAAATCAGATTTAATGTGCAAAAGTTATATATGTTGGTAAAAATGGACTT
196 ATGATAGACTGATTAAAAATCAGAGTTAATGTGCAAAAGTTATATATGTTAGAAAAAATGGACTT
* * *
25367893 TATGGAAACTTTGAGATATATTCTCGATTGGTAAAGGTGAAGATTTGAATAATAAAATTATGGTT
261 TATGGAAACTTTGAGACATATTCTCGATTGATAAAGGTGAAGATTTGAATAATAAAATTATAGTT
*
25367958 TTATACTCTACTCCAT-G-ATATACAACGGTATATCATATGCTCAAAATGGTTGAGATGAATGAG
326 TTATACTCTACTCCATAGAATATACAACGGTATATCATATACTCAAAATGGTTGAGATGAATGAG
25368021 A
391 A
*
25368022 GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATGTAATAATAGTAATTTACATGTTA
1 GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATGTAATAATAGTAACTTACATGTTA
* *
25368087 TTATTTACTATCACAAAAGATTAGTCCAAATTAAAAGTGATTTAATTTTGTTAAACTTTATTGGG
66 TTATTTACTATCACAAAAGATTAGCCCAAATTAAAAGTGATTTAAATTTGTTAAACTTTATTGGG
25368152 CTTTAGTTATTATATAAAGTATAGATCAAATATGTGTAGATACTCTAGTAACTAATTTCTAATTG
131 CTTTAGTTATTATATAAAGTATAGATCAAATATGTGTAGATACTCTAGTAACTAATTTCTAATTG
* * * *
25368217 ATGATGGATTGATTAAAAATTAGGGTTAATGTGCAAAAGTTATATATGTTAGAAAAAATGGACTT
196 ATGATAGACTGATTAAAAATCAGAGTTAATGTGCAAAAGTTATATATGTTAGAAAAAATGGACTT
*
25368282 TATGGAAACTTTGAGGCATATTCTCGATTGATAAAGGTGAAGATTTGAATAATAAAATTATAGTT
261 TATGGAAACTTTGAGACATATTCTCGATTGATAAAGGTGAAGATTTGAATAATAAAATTATAGTT
* *
25368347 TTATATTCTACTCCATGAGACATTTACAACGGTATATCATATACTCAAAATGGTTGAGATGAATG
326 TTATACTCTACTCCAT-AGA-ATATACAACGGTATATCATATACTCAAAATGGTTGAGATGAATG
25368412 AGA
389 AGA
25368415 AATTGATGCT
Statistics
Matches: 368, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
389 322 0.88
391 1 0.00
393 45 0.12
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (391 bp):
GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATGTAATAATAGTAACTTACATGTTA
TTATTTACTATCACAAAAGATTAGCCCAAATTAAAAGTGATTTAAATTTGTTAAACTTTATTGGG
CTTTAGTTATTATATAAAGTATAGATCAAATATGTGTAGATACTCTAGTAACTAATTTCTAATTG
ATGATAGACTGATTAAAAATCAGAGTTAATGTGCAAAAGTTATATATGTTAGAAAAAATGGACTT
TATGGAAACTTTGAGACATATTCTCGATTGATAAAGGTGAAGATTTGAATAATAAAATTATAGTT
TTATACTCTACTCCATAGAATATACAACGGTATATCATATACTCAAAATGGTTGAGATGAATGAG
A
Found at i:25369843 original size:31 final size:31
Alignment explanation
Indices: 25369815--25369873 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
25369805 TTTTATTAGA
25369815 TTATTTAAATAGC-ATTGATCATTATATTAAT
1 TTATTTAAATA-CAATTGATCATTATATTAAT
* *
25369846 TTATTTAAATACAATTTATTATTATATT
1 TTATTTAAATACAATTGATCATTATATT
25369874 TAAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (31 bp):
TTATTTAAATACAATTGATCATTATATTAAT
Found at i:25371450 original size:17 final size:17
Alignment explanation
Indices: 25371396--25371456 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
25371386 CTTAATCACT
*
25371396 TTAATATTAAATTAATA
1 TTAATATTAAATTAAGA
*
25371413 -TAATACTT--ATCAAGA
1 TTAATA-TTAAATTAAGA
*
25371428 TCAATATTAAATTAAGA
1 TTAATATTAAATTAAGA
25371445 TTAATATTAAAT
1 TTAATATTAAAT
25371457 CTTATTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
15 7 0.20
16 9 0.26
17 19 0.54
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (17 bp):
TTAATATTAAATTAAGA
Found at i:25371649 original size:20 final size:20
Alignment explanation
Indices: 25371624--25371674 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
25371614 TACGGGATTG
25371624 GGGGATGGAG-AGGGGCTA-GT
1 GGGGATGGAGCA-GGGC-AGGT
*
25371644 GGGGATGGGGCAGGGCAGGT
1 GGGGATGGAGCAGGGCAGGT
25371664 GGGGATGGAGC
1 GGGGATGGAGC
25371675 GGGTACAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.18, C:0.08, G:0.63, T:0.12
Consensus pattern (20 bp):
GGGGATGGAGCAGGGCAGGT
Found at i:25378619 original size:58 final size:58
Alignment explanation
Indices: 25378556--25379045 Score: 662
Period size: 58 Copynumber: 8.4 Consensus size: 58
25378546 TTAGATACCC
* * *
25378556 GGGGGTAAAATGGTAA-TTTTGGTAAAATCGAGGTTTAAAAATGGAATTTTAGGAG-TT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCG-GGGTTAAAAATGGAATTTTAGAAGATT
* * *
25378613 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTT
1 -GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGATT
* * * * *
25378673 GGGTGTAAAATGGTAATTTTAGGTGAAATTGGGGTTAAAAATAGAATTTTAGAAGGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAA-GATT
* *
25378732 GGGGATAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGATT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* * *
25378790 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGATT
* * ** *
25378849 AGGGATAAAATGGTAATTTTTAATGAAATCGAGGTTAAAAATGGAATTTTAGAAGATT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
*
25378907 GGGGGTAAAATGGTAATTTTAGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* * * *
25378965 GGGGGTAAGATGGTAATTTTTGGTGAAGTCGGGGTTAAAAATGGAATTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
*
25379023 CGGGGTCAAAAT-GTAATTTTTGG
1 GGGGGT-AAAATGGTAATTTTTGG
25379046 ACTGTTTGGG
Statistics
Matches: 386, Mismatches: 40, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
58 213 0.55
59 171 0.44
60 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
Found at i:25378803 original size:117 final size:115
Alignment explanation
Indices: 25378557--25379042 Score: 670
Period size: 117 Copynumber: 4.2 Consensus size: 115
25378547 TAGATACCCG
* * * * *
25378557 GGGGTAAAATGGTAATTTT-GGTAAAATCGAGGTTTAAAAATGGAATTTTAGGAGTTCGGGGGTA
1 GGGGTAAAATGGTAATTTTAGGTGAAATCG-GGGTTAAAAATGGAATTTTAGAAGTTTGGGGATA
* * *
25378621 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTT
65 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGATT
* *
25378673 GGGTGTAAAATGGTAATTTTAGGTGAAATTGGGGTTAAAAATAGAATTTTAGAAGGTTTGGGGAT
1 GGG-GTAAAATGGTAATTTTAGGTGAAATCGGGGTTAAAAATGGAATTTTAGAA-GTTTGGGGAT
*
25378738 AAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGATT
64 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* * *
25378790 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTTAGGGAT
1 G-GGGTAAAATGGTAATTTTAGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGTTTGGGGAT
** *
25378855 AAAATGGTAATTTTTAATGAAATCGAGGTTAAAAATGGAATTTTAGAAGATT
64 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* *
25378907 GGGGGTAAAATGGTAATTTTAGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTGGGGGTA
1 -GGGGTAAAATGGTAATTTTAGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTGGGGATA
* * * *
25378972 AGATGGTAATTTTTGGTGAAGTCGGGGTTAAAAATGGAATTTTGGAAGTTT
65 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
25379023 CGGGGTCAAAAT-GTAATTTT
1 -GGGGT-AAAATGGTAATTTT
25379043 TGGACTGTTT
Statistics
Matches: 330, Mismatches: 33, Indels: 14
0.88 0.09 0.04
Matches are distributed among these distances:
116 70 0.21
117 196 0.59
118 64 0.19
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (115 bp):
GGGGTAAAATGGTAATTTTAGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTGGGGATAA
AATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
Found at i:25379043 original size:29 final size:28
Alignment explanation
Indices: 25378590--25379046 Score: 104
Period size: 29 Copynumber: 15.7 Consensus size: 28
25378580 AAATCGAGGT
* *
25378590 TTAAAAATGGAATTTTAGG-AGTTCGGGG
1 TTAAAAATGTAATTTTTGGAAG-TCGGGG
* *
25378618 GT-AAAATGGTAATTTTTGGTGAAATCGGGG
1 TTAAAAAT-GTAATTTTT-G-GAAGTCGGGG
**
25378648 TTAAAAATAG-AA-TTTTGGAAAGTTTGGG
1 TTAAAAAT-GTAATTTTTGG-AAGTCGGGG
* * *
25378676 TGT-AAAATGGTAATTTTAGGTGAAATTGGGG
1 T-TAAAAAT-GTAATTTT-TG-GAAGTCGGGG
* *
25378707 TTAAAAATAG-AA-TTTTAGAAGGTTTGGGG
1 TTAAAAAT-GTAATTTTTGGAA-G-TCGGGG
* * *
25378736 AT-AAAATGGTAATTTTTGGTGAAATTGGGG
1 TTAAAAAT-GTAATTTTT-G-GAAGTCGGGG
* * *
25378766 TTAAAAATGGAA-TTTTAGAAGATTGAGGG
1 TTAAAAATGTAATTTTTGGAAG-TCG-GGG
*
25378795 -T-AAAATGGTAATTTTTGGTGAAATCGGGG
1 TTAAAAAT-GTAATTTTT-G-GAAGTCGGGG
* * * * **
25378824 TCAAAAATGGAATTTTAGAAAGTTTAGGG
1 TTAAAAATGTAATTTTTGGAAG-TCGGGG
* * * *
25378853 AT-AAAATGGTAATTTTTAATGAAATCGAGG
1 TTAAAAAT-GTAATTTTT--GGAAGTCGGGG
* * *
25378883 TTAAAAATGGAA-TTTTAGAAGATTGGGG
1 TTAAAAATGTAATTTTTGGAAG-TCGGGG
* * *
25378911 GT-AAAATGGTAATTTTAGGTGAAATCGGGG
1 TTAAAAAT-GTAATTTT-TG-GAAGTCGGGG
* * *
25378941 TTAAAAATGGAA-TTTTAGAAGATTGGGG
1 TTAAAAATGTAATTTTTGGAAG-TCGGGG
* *
25378969 GT-AAGATGGTAATTTTTGGTGAAGTCGGGG
1 TTAAAAAT-GTAATTTTT-G-GAAGTCGGGG
*
25378999 TTAAAAATGGAA-TTTTGGAAGTTTCGGGG
1 TTAAAAATGTAATTTTTGGAAG--TCGGGG
*
25379028 -TCAAAATGTAATTTTTGGA
1 TTAAAAATGTAATTTTTGGA
25379047 CTGTTTGGGG
Statistics
Matches: 308, Mismatches: 74, Indels: 93
0.65 0.16 0.20
Matches are distributed among these distances:
27 36 0.12
28 69 0.22
29 77 0.25
30 64 0.21
31 58 0.19
32 4 0.01
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (28 bp):
TTAAAAATGTAATTTTTGGAAGTCGGGG
Found at i:25379859 original size:15 final size:16
Alignment explanation
Indices: 25379834--25379871 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
25379824 TCTTCTTTTG
*
25379834 TTCTTTATTCTTCATT
1 TTCTTTGTTCTTCATT
*
25379850 TT-TTTGTTCTTTATT
1 TTCTTTGTTCTTCATT
25379865 TTCTTTG
1 TTCTTTG
25379872 AAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (16 bp):
TTCTTTGTTCTTCATT
Found at i:25380192 original size:12 final size:12
Alignment explanation
Indices: 25380175--25380213 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
25380165 TTTTAATGTT
25380175 TATTATTATTAA
1 TATTATTATTAA
25380187 TATTATTATTAA
1 TATTATTATTAA
25380199 TATT-TTATTAA
1 TATTATTATTAA
25380210 TATT
1 TATT
25380214 GTTTAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:25380221 original size:10 final size:11
Alignment explanation
Indices: 25380181--25380223 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
25380171 TGTTTATTAT
*
25380181 TATTAATATTAT
1 TATTAATATT-G
*
25380193 TATTAATATTT
1 TATTAATATTG
25380204 TATTAATATTG
1 TATTAATATTG
25380215 T-TTAATATT
1 TATTAATATT
25380224 TCAACAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 8 0.27
11 12 0.40
12 10 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TATTAATATTG
Found at i:25381040 original size:17 final size:17
Alignment explanation
Indices: 25380986--25381051 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
25380976 GGACTTTACT
*
25380986 AATTT-AATTTATAATA
1 AATTTAAATTTAAAATA
* *
25381002 AATTTAAATTTTTAAGTA
1 AATTTAAA-TTTAAAATA
25381020 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
25381037 AATTTAATTTTAAAA
1 AATTTAAATTTAAAA
25381052 ATTAAATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
16 5 0.12
17 23 0.55
18 14 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:25381753 original size:41 final size:41
Alignment explanation
Indices: 25381642--25381779 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
25381632 ACTTGATGAA
* * * *
25381642 TAAATGGAAGACTCATGTCTCGAGATAAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATAAGAATATAT
*
25381684 TAAAGGAAGACTCATATCTCGGGATGAGCATAAGAATATAT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATAAGAATATAT
* * * * * *
25381725 TAAAGGAAAACTCATGTCTTGGGGTGAGCATCAGATTATGTT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATAAGAATAT-AT
25381767 TAAATGGAAGACT
1 TAAA-GGAAGACT
25381780 TGTGACTTGA
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 65 0.80
42 9 0.11
43 7 0.09
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGCATAAGAATATAT
Found at i:25396620 original size:26 final size:26
Alignment explanation
Indices: 25396591--25396641 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
25396581 AGAAATTTAT
*
25396591 AAAAAGAAGAAGAAG-AAAAAATATAG
1 AAAAAAAAGAA-AAGAAAAAAATATAG
25396617 AAAAAAAAGAAAAGAAAAAAATATA
1 AAAAAAAAGAAAAGAAAAAAATATA
25396642 TACATATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (26 bp):
AAAAAAAAGAAAAGAAAAAAATATAG
Found at i:25396637 original size:14 final size:14
Alignment explanation
Indices: 25396591--25396637 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
25396581 AGAAATTTAT
25396591 AAAAAGAAGAAGAAGA
1 AAAAAGAA-AAGAA-A
* *
25396607 AAAAA-TATAGAAA
1 AAAAAGAAAAGAAA
25396620 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
25396634 AAAA
1 AAAA
25396638 TATATACATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 6 0.23
14 14 0.54
15 1 0.04
16 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:25398850 original size:32 final size:32
Alignment explanation
Indices: 25398809--25398873 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
25398799 TATGTAAAAG
*
25398809 GCACAATTGATTATGGCATAAAGTTCAATCAA
1 GCACAATTGACTATGGCATAAAGTTCAATCAA
25398841 GCACAATTGACTATGGCATAAAGTTCAATCAA
1 GCACAATTGACTATGGCATAAAGTTCAATCAA
25398873 G
1 G
25398874 TTGAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
GCACAATTGACTATGGCATAAAGTTCAATCAA
Found at i:25408178 original size:38 final size:39
Alignment explanation
Indices: 25408133--25408223 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 39
25408123 TGGGAGAATT
* *
25408133 TTTGTAGAGAATCGTTA-CTGTTCATCTTCG-TTTTTTTC
1 TTTGTAGAGAATCGTTATC-ATTCATCTCCGCTTTTTTTC
* *
25408171 TTTGTAGAGAATCTTTATCATTCATCTCCGCCTTTTTTTT
1 TTTGTAGAGAATCGTTATCATTCATCTCCG-CTTTTTTTC
*
25408211 TTTATAGAGAATC
1 TTTGTAGAGAATC
25408224 ATCATTATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 25 0.56
39 1 0.02
40 19 0.42
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (39 bp):
TTTGTAGAGAATCGTTATCATTCATCTCCGCTTTTTTTC
Found at i:25436838 original size:17 final size:18
Alignment explanation
Indices: 25436799--25436852 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
25436789 ATGCATAGCA
*
25436799 TTTAGTTGTCATTACATT
1 TTTATTTGTCATTACATT
*
25436817 TTTATTTGTCATTGCA-T
1 TTTATTTGTCATTACATT
* *
25436834 TTTATTTGTTAGTACATT
1 TTTATTTGTCATTACATT
25436852 T
1 T
25436853 GCATTGTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.59
Consensus pattern (18 bp):
TTTATTTGTCATTACATT
Found at i:25437448 original size:15 final size:15
Alignment explanation
Indices: 25437425--25437465 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
25437415 TCACTTATAA
*
25437425 AAAAAAGAAAAGAGG
1 AAAAAAGAAAAGAAG
*
25437440 AAAAGAGAAAAGAAG
1 AAAAAAGAAAAGAAG
25437455 AAAAAAAGAAA
1 -AAAAAAGAAA
25437466 TATGTGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGAAG
Found at i:25449807 original size:23 final size:26
Alignment explanation
Indices: 25449767--25449813 Score: 73
Period size: 23 Copynumber: 1.9 Consensus size: 26
25449757 ATTTTCATGA
25449767 CTTTTATTATTAAGCTTAATTAATCC
1 CTTTTATTATTAAGCTTAATTAATCC
25449793 CTTTTA-T-TTAA-CTTAATTAAT
1 CTTTTATTATTAAGCTTAATTAAT
25449814 ATACTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
25 1 0.05
26 6 0.29
ACGTcount: A:0.32, C:0.13, G:0.02, T:0.53
Consensus pattern (26 bp):
CTTTTATTATTAAGCTTAATTAATCC
Found at i:25454183 original size:10 final size:10
Alignment explanation
Indices: 25454152--25454185 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
25454142 TGGCAATATA
25454152 TTTCTTTTCTT
1 TTTC-TTTCTT
*
25454163 CTTCTTTCTT
1 TTTCTTTCTT
25454173 TTTCTTTCTT
1 TTTCTTTCTT
25454183 TTT
1 TTT
25454186 GTGAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.86
11 3 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:25454961 original size:21 final size:21
Alignment explanation
Indices: 25454936--25454976 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25454926 CTCGCCTTCC
* *
25454936 TCTTTGCGCTTTTTCTTCTTA
1 TCTTTGCACTTTCTCTTCTTA
*
25454957 TCTTTTCACTTTCTCTTCTT
1 TCTTTGCACTTTCTCTTCTT
25454977 GTCCTTCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.27, G:0.05, T:0.63
Consensus pattern (21 bp):
TCTTTGCACTTTCTCTTCTTA
Found at i:25455877 original size:7 final size:7
Alignment explanation
Indices: 25455878--25455916 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
25455868 TTCCTTTTTC
25455878 TTCCCTT
1 TTCCCTT
25455885 TTCCCTT
1 TTCCCTT
25455892 TT-CCTT
1 TTCCCTT
25455898 CTTCCCTT
1 -TTCCCTT
25455906 TTCCCTT
1 TTCCCTT
25455913 TTCC
1 TTCC
25455917 TTCTCCTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 4 0.13
7 22 0.73
8 4 0.13
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCCCTT
Found at i:25455901 original size:21 final size:21
Alignment explanation
Indices: 25455875--25455920 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
25455865 TTTTTCCTTT
25455875 TTCTTCCCTTTTCCCTTTTCC
1 TTCTTCCCTTTTCCCTTTTCC
25455896 TTCTTCCCTTTTCCCTTTTCC
1 TTCTTCCCTTTTCCCTTTTCC
25455917 TTCT
1 TTCT
25455921 CCTTAGGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (21 bp):
TTCTTCCCTTTTCCCTTTTCC
Found at i:25460539 original size:36 final size:36
Alignment explanation
Indices: 25460487--25460557 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
25460477 TGTCATCGTA
25460487 GTGGACTTCATTGATCATACTCCTAACTTCCTGAAT
1 GTGGACTTCATTGATCATACTCCTAACTTCCTGAAT
*
25460523 GTGGGCTTCATTGATCATACTCCTAACTTCCTGAA
1 GTGGACTTCATTGATCATACTCCTAACTTCCTGAA
25460558 GAGCCAGGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (36 bp):
GTGGACTTCATTGATCATACTCCTAACTTCCTGAAT
Found at i:25472423 original size:21 final size:19
Alignment explanation
Indices: 25472393--25472445 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
25472383 GGCGTTTTTG
*
25472393 GTATCAATAGATGCATGACTT
1 GTATCGATAGAT-CAT-ACTT
25472414 GTATCGATAGAAATCATACTT
1 GTATCGATAG--ATCATACTT
*
25472435 GTATCGGTAGA
1 GTATCGATAGA
25472446 GCTAGCACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
21 22 0.79
22 3 0.11
23 2 0.07
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (19 bp):
GTATCGATAGATCATACTT
Found at i:25479687 original size:21 final size:20
Alignment explanation
Indices: 25479661--25479711 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
25479651 GGAGTTTTTG
25479661 GTATCGGTAG-ATGCATGACTT
1 GTATCGGTAGAAT-CAT-ACTT
25479682 GTATCGGTAGAAATCATACTT
1 GTATCGGTAG-AATCATACTT
25479703 GTATCGGTA
1 GTATCGGTA
25479712 TAGCTAGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 23 0.82
22 3 0.11
23 2 0.07
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (20 bp):
GTATCGGTAGAATCATACTT
Found at i:25486916 original size:68 final size:68
Alignment explanation
Indices: 25486807--25486942 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
25486797 GTAAAAAGGA
25486807 GAGATCCATGCCCTTCCTGTCTTCTACATTCTCTTTCTCATATGAAGTAACTCATACCTACATTA
1 GAGATCCATGCCCTTCCTGTCTTCTACATTCTCTTTCTCATATGAAGTAACTCATACCTACATTA
25486872 CCC
66 CCC
25486875 GAGATCCATGCCCTTCCTGTCTTCTACATTCTCTTTCTCATATGAAGTAACTCATACCTACATTA
1 GAGATCCATGCCCTTCCTGTCTTCTACATTCTCTTTCTCATATGAAGTAACTCATACCTACATTA
25486940 CCC
66 CCC
25486943 AGTTTAACTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.24, C:0.32, G:0.09, T:0.35
Consensus pattern (68 bp):
GAGATCCATGCCCTTCCTGTCTTCTACATTCTCTTTCTCATATGAAGTAACTCATACCTACATTA
CCC
Found at i:25489789 original size:12 final size:12
Alignment explanation
Indices: 25489772--25489805 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25489762 TATATAGCAA
*
25489772 GAGGGAGGGAGG
1 GAGGGAGAGAGG
25489784 GAGGGAGAGAGG
1 GAGGGAGAGAGG
*
25489796 GAGAGAGAGA
1 GAGGGAGAGA
25489806 TACACATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (12 bp):
GAGGGAGAGAGG
Found at i:25497713 original size:20 final size:20
Alignment explanation
Indices: 25497683--25497721 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
25497673 ACAAGTGTTT
25497683 AATATATTATT-ATAAAAAC
1 AATATATTATTCATAAAAAC
25497702 AATATAATTATTCATAAAAA
1 AATAT-ATTATTCATAAAAA
25497722 ATGTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATATTATTCATAAAAAC
Found at i:25499141 original size:12 final size:11
Alignment explanation
Indices: 25499126--25499203 Score: 54
Period size: 12 Copynumber: 6.8 Consensus size: 11
25499116 CCAAAATAGC
25499126 AGCACAAATAAT
1 AGCACAAA-AAT
25499138 AGCA-AAATAAT
1 AGCACAAA-AAT
*
25499149 A--ACAGAAAT
1 AGCACAAAAAT
25499158 AGCAACAAAAAT
1 AGC-ACAAAAAT
25499170 AGCAACAAAAAT
1 AGC-ACAAAAAT
* *
25499182 AACAGCAAAAAC
1 AGCA-CAAAAAT
25499194 AGCATCAAAA
1 AGCA-CAAAA
25499204 CAACCAAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
9 5 0.09
10 2 0.04
11 9 0.16
12 39 0.71
ACGTcount: A:0.64, C:0.17, G:0.09, T:0.10
Consensus pattern (11 bp):
AGCACAAAAAT
Found at i:25499158 original size:35 final size:33
Alignment explanation
Indices: 25499110--25499186 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
25499100 AATAACATCC
25499110 AAATAACCA-AAATAGCAGCACAAATAATAGCAA-AA
1 AAATAA-CAGAAATAGCA--ACAAA-AATAGCAACAA
*
25499145 TAATAACAGAAATAGCAACAAAAATAGCAACAA
1 AAATAACAGAAATAGCAACAAAAATAGCAACAA
25499178 AAATAACAG
1 AAATAACAG
25499187 CAAAAACAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 8 0.21
33 15 0.39
34 2 0.05
35 13 0.34
ACGTcount: A:0.64, C:0.16, G:0.09, T:0.12
Consensus pattern (33 bp):
AAATAACAGAAATAGCAACAAAAATAGCAACAA
Found at i:25499176 original size:24 final size:24
Alignment explanation
Indices: 25499149--25499203 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
25499139 GCAAAATAAT
* * *
25499149 AACAGAAATAGCAACAAAAATAGC
1 AACAAAAATAACAACAAAAACAGC
*
25499173 AACAAAAATAACAGCAAAAACAGC
1 AACAAAAATAACAACAAAAACAGC
*
25499197 ATCAAAA
1 AACAAAA
25499204 CAACCAAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.65, C:0.18, G:0.09, T:0.07
Consensus pattern (24 bp):
AACAAAAATAACAACAAAAACAGC
Found at i:25499224 original size:21 final size:21
Alignment explanation
Indices: 25499200--25499266 Score: 91
Period size: 20 Copynumber: 3.1 Consensus size: 21
25499190 AAACAGCATC
25499200 AAAACAACCAAAACAATAAAA
1 AAAACAACCAAAACAATAAAA
25499221 AAAAC-ACCAAAACAATAAAA
1 AAAACAACCAAAACAATAAAA
**
25499241 AAAACAACATCAAAACAGCAAAA
1 AAAACAAC--CAAAACAATAAAA
25499264 AAA
1 AAA
25499267 GTACAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 20 0.49
21 7 0.17
23 14 0.34
ACGTcount: A:0.75, C:0.19, G:0.01, T:0.04
Consensus pattern (21 bp):
AAAACAACCAAAACAATAAAA
Found at i:25499249 original size:23 final size:22
Alignment explanation
Indices: 25499200--25499266 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
25499190 AAACAGCATC
25499200 AAAACAACCAAAACAAT--AAAA
1 AAAAC-ACCAAAACAATAAAAAA
25499221 AAAACACCAAAACAATAAAAAA
1 AAAACACCAAAACAATAAAAAA
* **
25499243 AACAACATCAAAACAGCAAAAAA
1 AA-AACACCAAAACAATAAAAAA
25499266 A
1 A
25499267 GTACAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.28
21 5 0.12
22 6 0.15
23 18 0.45
ACGTcount: A:0.75, C:0.19, G:0.01, T:0.04
Consensus pattern (22 bp):
AAAACACCAAAACAATAAAAAA
Found at i:25499252 original size:52 final size:54
Alignment explanation
Indices: 25499188--25499289 Score: 138
Period size: 52 Copynumber: 1.9 Consensus size: 54
25499178 AAATAACAGC
* *
25499188 AAAAACAGCATCAAAACAACCAAAACAA-TA-AAAAA-AACACCAAAACAATAAA
1 AAAAACAACATCAAAAC-ACCAAAAAAAGTACAAAAATAACACCAAAACAATAAA
* *
25499240 AAAAACAACATCAAAACAGCAAAAAAAGTACAAAAATAGCACCAAAACAA
1 AAAAACAACATCAAAACACCAAAAAAAGTACAAAAATAACACCAAAACAA
25499290 CAATATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 8 0.19
52 18 0.42
53 5 0.12
54 12 0.28
ACGTcount: A:0.70, C:0.21, G:0.04, T:0.06
Consensus pattern (54 bp):
AAAAACAACATCAAAACACCAAAAAAAGTACAAAAATAACACCAAAACAATAAA
Found at i:25499608 original size:85 final size:85
Alignment explanation
Indices: 25499460--25499635 Score: 334
Period size: 85 Copynumber: 2.1 Consensus size: 85
25499450 TTTTTCGGGC
*
25499460 AAGCCTTTAGGTCTGGTCAAGTGGCCCAACCTATGATCAGGTCTAATGCTATCCAAATAAACATT
1 AAGCTTTTAGGTCTGGTCAAGTGGCCCAACCTATGATCAGGTCTAATGCTATCCAAATAAACATT
25499525 AATGATGAATTGTATTTGTG
66 AATGATGAATTGTATTTGTG
*
25499545 AAGCTTTTAGGTCTGGTCAAGTGGTCCAACCTATGATCAGGTCTAATGCTATCCAAATAAACATT
1 AAGCTTTTAGGTCTGGTCAAGTGGCCCAACCTATGATCAGGTCTAATGCTATCCAAATAAACATT
25499610 AATGATGAATTGTATTTGTG
66 AATGATGAATTGTATTTGTG
25499630 AAGCTT
1 AAGCTT
25499636 GTTAAAAAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (85 bp):
AAGCTTTTAGGTCTGGTCAAGTGGCCCAACCTATGATCAGGTCTAATGCTATCCAAATAAACATT
AATGATGAATTGTATTTGTG
Found at i:25499816 original size:19 final size:18
Alignment explanation
Indices: 25499785--25499822 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
25499775 ATTTTATAAG
25499785 TATTTTATATTTGAGATT
1 TATTTTATATTTGAGATT
*
25499803 TATTTTATTATTTGATATT
1 TATTTTA-TATTTGAGATT
25499822 T
1 T
25499823 GCAATTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (18 bp):
TATTTTATATTTGAGATT
Found at i:25506311 original size:16 final size:15
Alignment explanation
Indices: 25506290--25506319 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25506280 CAACCACTTT
25506290 AATATTAAATTAATAA
1 AATATTAAA-TAATAA
25506306 AATATTAAATAATA
1 AATATTAAATAATA
25506320 TTATTTTTGA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATTAAATAATAA
Found at i:25512736 original size:3 final size:3
Alignment explanation
Indices: 25512728--25512759 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
25512718 TGGTTAGCTA
25512728 AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
25512760 GCCCTTCTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25512748 original size:14 final size:14
Alignment explanation
Indices: 25512729--25512757 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25512719 GGTTAGCTAA
25512729 AGAAGAAGAAGAAG
1 AGAAGAAGAAGAAG
25512743 AGAAGAAGAAGAAG
1 AGAAGAAGAAGAAG
25512757 A
1 A
25512758 AGGCCCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAGAAG
Found at i:25521336 original size:2 final size:2
Alignment explanation
Indices: 25521331--25521368 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
25521321 TATATATATA
*
25521331 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
25521369 GTATGTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:25526145 original size:3 final size:3
Alignment explanation
Indices: 25526137--25526190 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
25526127 GAAAATACAT
* * *
25526137 TAA TAA TAA TAT TAA TAT TAA TAA TAA TAA T-A TAA TAA TAA GTAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
25526182 TAA TAA TAA
1 TAA TAA TAA
25526191 AAAAAGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:25526163 original size:21 final size:21
Alignment explanation
Indices: 25526137--25526189 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
25526127 GAAAATACAT
*
25526137 TAATAATAATATTAATATTAA-
1 TAATAATAATA-TAATAATAAG
25526158 TAATAATAATATAATAATAAG
1 TAATAATAATATAATAATAAG
*
25526179 TATTAATAATA
1 TAATAATAATA
25526190 AAAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAATAATAATATAATAATAAG
Found at i:25526904 original size:5 final size:5
Alignment explanation
Indices: 25526894--25526923 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
25526884 GTTTTACCAT
*
25526894 ACCCG ATCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG
25526924 CTCCGGCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.57, G:0.20, T:0.03
Consensus pattern (5 bp):
ACCCG
Found at i:25527340 original size:30 final size:30
Alignment explanation
Indices: 25527306--25527363 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
25527296 GTGATCCCTA
25527306 AACTTTTTAAAAAATACATTTTGACCCTTG
1 AACTTTTTAAAAAATACATTTTGACCCTTG
** *
25527336 AACTTTTTAAAATTTACATTTTTACCCT
1 AACTTTTTAAAAAATACATTTTGACCCT
25527364 CAAACTTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.45
Consensus pattern (30 bp):
AACTTTTTAAAAAATACATTTTGACCCTTG
Found at i:25527370 original size:30 final size:29
Alignment explanation
Indices: 25527301--25527370 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
25527291 CTCAAGTGAT
25527301 CCCTAAACTTTTTAAAAAATACATTTTGA
1 CCCTAAACTTTTTAAAAAATACATTTTGA
* ** *
25527330 CCCTTGAACTTTTTAAAATTTACATTTTTA
1 CCC-TAAACTTTTTAAAAAATACATTTTGA
25527360 CCCTCAAACTT
1 CCCT-AAACTT
25527371 CCAAAAATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.41
Consensus pattern (29 bp):
CCCTAAACTTTTTAAAAAATACATTTTGA
Found at i:25527528 original size:58 final size:58
Alignment explanation
Indices: 25527462--25527859 Score: 417
Period size: 59 Copynumber: 6.8 Consensus size: 58
25527452 TAAACTTCCA
* ** *
25527462 AAAACTCCATTTTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCTCGAATGGCT
1 AAAATTCCATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCGAATGTCT
** * ** *
25527520 AAAGCTCCATTTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCTCAAATGTCT
1 AAAATTCCATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCGAATGTCT
* * * * * *
25527578 AAAAATTCCATTTTTAACCTCAAACTTTCCAAAAGTTACCAATTTAACCC-CGGATGTCT
1 -AAAATTCCATTTTTGACCCCGAACTTTCCAAAAATTACC-ATTTTACCCTCGAATGTCT
* * * *
25527637 CAAAATTCCATTTTTGACCCCAAACTTTTCAAAAATTA-CATTTTTACCCTCGAACTTTCC
1 -AAAATTCCATTTTTGACCCCGAACTTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCT
** ** * *
25527697 AAAATTCCATGTTTTTGACCCTTAACTTTCC-AAAATTACCATTTTACATTCAAATGTCA
1 AAAATTCCA--TTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCGAATGTCT
* *
25527756 AAAATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCT
1 AAAATTCCATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCGAATGTCT
* *
25527814 AAAAATTCCATTTTTTACCCCGAACATTT-CGAAAATTACCATTTTA
1 -AAAATTCCATTTTTGACCCCGAAC-TTTCCAAAAATTACCATTTTA
25527860 TTCTCGAAGC
Statistics
Matches: 285, Mismatches: 44, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
57 18 0.06
58 81 0.28
59 137 0.48
60 30 0.11
61 19 0.07
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCGAATGTCT
Found at i:25527626 original size:30 final size:30
Alignment explanation
Indices: 25527355--25527800 Score: 157
Period size: 30 Copynumber: 15.2 Consensus size: 30
25527345 AAATTTACAT
*
25527355 TTTTACCCTCAAAC-TTCCAAAAATT-CCA
1 TTTTAACCTCAAACTTTCCAAAAATTACCA
* * * * * *
25527383 TTTTTAACCCCGAGCTTTTCGAAAATTATCA
1 -TTTTAACCTCAAACTTTCCAAAAATTACCA
* * ** *
25527414 TTTTAACCCCGATTTTTCCAAAAATTA-TA
1 TTTTAACCTCAAACTTTCCAAAAATTACCA
* *
25527443 TTTT-ACCCCTAAAC-TTCCAAAAACT-CCA
1 TTTTAACCTC-AAACTTTCCAAAAATTACCA
* * * **
25527471 TTTTTGACCCCGATTTTTCCAAAAATTACCA
1 -TTTTAACCTCAAACTTTCCAAAAATTACCA
* * ** * **
25527502 TTTTACCCTCGAA--TGGCTAAAGCT-CCA
1 TTTTAACCTCAAACTTTCCAAAAATTACCA
25527529 TTTTTAACC-CTAAACTTTCCAAAAATTACCA
1 -TTTTAACCTC-AAACTTTCCAAAAATTACCA
* * *
25527560 TTTTACCCTCAAA-TGTCTAAAAATT-CCA
1 TTTTAACCTCAAACTTTCCAAAAATTACCA
*
25527588 TTTTTAACCTCAAACTTTCCAAAAGTTACCA
1 -TTTTAACCTCAAACTTTCCAAAAATTACCA
* * ** *
25527619 ATTTAACCCCGGA-TGTCTC-AAAATT-CCA
1 TTTTAACCTCAAACTTTC-CAAAAATTACCA
* * *
25527647 TTTTTGACCCCAAACTTTTCAAAAATTA-CA
1 -TTTTAACCTCAAACTTTCCAAAAATTACCA
* *
25527677 TTTTTACCCTCGAACTTTCC-AAAATT-CCA
1 -TTTTAACCTCAAACTTTCCAAAAATTACCA
* *
25527706 TGTTTTTGACC-CTTAACTTTCC-AAAATTACCA
1 ---TTTTAACCTC-AAACTTTCCAAAAATTACCA
* *
25527738 TTTT-ACATTCAAA-TGT-CAAAAATT-CCA
1 TTTTAAC-CTCAAACTTTCCAAAAATTACCA
* * * *
25527765 TTTTTGACCCCGAACCTTCCAAAAATTACCA
1 -TTTTAACCTCAAACTTTCCAAAAATTACCA
25527796 TTTTA
1 TTTTA
25527801 CCCCCGAATG
Statistics
Matches: 309, Mismatches: 73, Indels: 69
0.69 0.16 0.15
Matches are distributed among these distances:
27 8 0.03
28 54 0.17
29 78 0.25
30 130 0.42
31 36 0.12
32 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (30 bp):
TTTTAACCTCAAACTTTCCAAAAATTACCA
Found at i:25527686 original size:118 final size:116
Alignment explanation
Indices: 25527305--25527859 Score: 362
Period size: 118 Copynumber: 4.7 Consensus size: 116
25527295 AGTGATCCCT
* * * * * * * *
25527305 AAACTTTTTAAAAAATACATTTTGACCCTTGAACTTTTTAAAATTTACATTTTT-ACCCTCAAAC
1 AAACTTTTCAAAAATTACATTTT-ACCC-TCAAATGTCTAAAAATTCCATTTTTAACCC-CAAAC
* * * *
25527369 -TTCCAAAAATT-CCATTTTTAACCCCGAGCT-TTTCGAAAATTATCA-TTTTAACCCC
63 TTTCC-AAAATTACCA-ATTTAACCCCGA-ATGTCTC-AAAATT-CCATTTTTAACCCC
* * * * * * * **
25527424 -GATTTTTCCAAAAATTATATTTTACCC-CTAAACT-TCCAAAAACTCCATTTTTGACCCCGATT
1 AAACTTTT-CAAAAATTACATTTTACCCTC-AAA-TGTCTAAAAATTCCATTTTTAACCCCAAAC
* * ** *
25527486 TTTCCAAAAATTACC-ATTTTACCCTCGAATGGCT-AAAGCTCCATTTTTAACCCT
63 TTTCC-AAAATTACCAATTTAACCC-CGAATGTCTCAAAATTCCATTTTTAACCCC
* *
25527540 AAACTTTCCAAAAATTACCATTTTACCCTCAAATGTCTAAAAATTCCATTTTTAACCTCAAACTT
1 AAACTTTTCAAAAATTA-CATTTTACCCTCAAATGTCTAAAAATTCCATTTTTAACCCCAAACTT
* *
25527605 TCCAAAAGTTACCAATTTAACCCCGGATGTCTCAAAATTCCATTTTTGACCCC
65 TCCAAAA-TTACCAATTTAACCCCGAATGTCTCAAAATTCCATTTTTAACCCC
* * * * **
25527658 AAACTTTTCAAAAATTACATTTTTACCCTCGAACTTTC-CAAAATTCCATGTTTTTGACCCTTAA
1 AAACTTTTCAAAAATTACA-TTTTACCCTC-AAATGTCTAAAAATTCCA--TTTTTAACCCCAAA
* ** * * *
25527722 CTTTCCAAAATTACC-ATTTTACATTCAAATGTC-AAAAATTCCATTTTTGACCCC
62 CTTTCCAAAATTACCAATTTAAC-CCCGAATGTCTCAAAATTCCATTTTTAACCCC
* * * * * * *
25527776 GAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTTACCCCGAACAT
1 AAACTTTTCAAAAATTA-CATTTTACCCTCAAATGTCTAAAAATTCCATTTTTAACCCCAAAC-T
* *
25527841 TTCGAAAATTACCATTTTA
64 TTCCAAAATTACCAATTTA
25527860 TTCTCGAAGC
Statistics
Matches: 341, Mismatches: 70, Indels: 51
0.74 0.15 0.11
Matches are distributed among these distances:
115 2 0.01
116 39 0.11
117 98 0.29
118 150 0.44
119 32 0.09
120 20 0.06
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (116 bp):
AAACTTTTCAAAAATTACATTTTACCCTCAAATGTCTAAAAATTCCATTTTTAACCCCAAACTTT
CCAAAATTACCAATTTAACCCCGAATGTCTCAAAATTCCATTTTTAACCCC
Found at i:25527877 original size:29 final size:28
Alignment explanation
Indices: 25527845--25527905 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
25527835 GAACATTTCG
**
25527845 AAAATTACCATTTTATTCTCGAAGCATCC
1 AAAATTACCATTTTACCCTCG-AGCATCC
* * *
25527874 AAAATTTCCGTTTTACCCTCGGGCATCC
1 AAAATTACCATTTTACCCTCGAGCATCC
25527902 AAAA
1 AAAA
25527906 ATCACATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTCGAGCATCC
Found at i:25527877 original size:177 final size:179
Alignment explanation
Indices: 25527461--25527879 Score: 478
Period size: 177 Copynumber: 2.4 Consensus size: 179
25527451 CTAAACTTCC
* * ** ** *
25527461 AAAAACTCCATTTTTGACCCC-GATTTTTCCAAAAATTACCA-TTTTACCCTCGAA-TGGCTAAA
1 AAAAATTCCATTTTTGACCCCAAACATTT-CAAAAATTA-CATTTTTACCCTCGAACTATCCAAA
** *
25527523 GCTCCA--TTTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCTCAAATGTCTAAAAATTC
64 ATTCCATGTTTTTAACCCTAAACTTTCCAAAAATTACCATTTTACACTCAAATGTCTAAAAATTC
* * * *
25527586 CATTTTTAACCTCAAACTTTCCAAAAGTTACCAATTTAACCCCGGATGTCT
129 CATTTTTAACCCCAAACCTTCCAAAAATTACCAATTTAACCCCGAATGTCT
* * *
25527637 CAAAATTCCATTTTTGACCCCAAACTTTTCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAT
1 AAAAATTCCATTTTTGACCCCAAACATTTCAAAAATTACATTTTTACCCTCGAACTATCCAAAAT
* * *
25527702 TCCATGTTTTTGACCCTTAACTTTCC-AAAATTACCATTTTACATTCAAATGTC-AAAAATTCCA
66 TCCATGTTTTTAACCCTAAACTTTCCAAAAATTACCATTTTACACTCAAATGTCTAAAAATTCCA
* * * *
25527765 TTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCT
131 TTTTTAACCCCAAACCTTCCAAAAATTACCAATTTAACCCCGAATGTCT
* * * **
25527814 AAAAATTCCATTTTTTACCCCGAACATTTCGAAAATTACCA-TTTTATTCTCGAAGC-ATCCAAA
1 AAAAATTCCATTTTTGACCCCAAACATTTCAAAAATTA-CATTTTTACCCTCGAA-CTATCCAAA
25527877 ATT
64 ATT
25527880 TCCGTTTTAC
Statistics
Matches: 207, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
175 2 0.01
176 41 0.20
177 118 0.57
178 28 0.14
179 18 0.09
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (179 bp):
AAAAATTCCATTTTTGACCCCAAACATTTCAAAAATTACATTTTTACCCTCGAACTATCCAAAAT
TCCATGTTTTTAACCCTAAACTTTCCAAAAATTACCATTTTACACTCAAATGTCTAAAAATTCCA
TTTTTAACCCCAAACCTTCCAAAAATTACCAATTTAACCCCGAATGTCT
Found at i:25537573 original size:148 final size:148
Alignment explanation
Indices: 25537305--25537600 Score: 515
Period size: 148 Copynumber: 2.0 Consensus size: 148
25537295 TAGGCCTGCA
25537305 AATATTTTAGCCCAATACATAATTTTATATTTTCTCAACAGAGCTTATCTCTTCAAATTCTATTT
1 AATATTTTAGCCCAATACATAATTTTATATTTTCTCAACAGAGCTTATCTCTTCAAATTCTATTT
* *
25537370 TGGAATTAAAAGGACAAATATCTAATTGATCTAATTAATTTAATGGCTCCTTTAATTCAGACGCT
66 TGGAATTAAAAGGACAAATATCTAATTGATCTAATTAATTTAATAGCTCCTTTAATTCAGACACT
25537435 GATTTGGGTTTTAATGGC
131 GATTTGGGTTTTAATGGC
*
25537453 AATATTTTA-CCCAATGCATAATTTTAT-TTTTCCTCAACAGAGCTTATCTCTTCAAATTCTATT
1 AATATTTTAGCCCAATACATAATTTTATATTTT-CTCAACAGAGCTTATCTCTTCAAATTCTA-T
*
25537516 TTTGGAATTAAAAGGACAAATATCTAATTGATCTAATTGATTTAATAGCTCCTTTAATTCAGACA
64 TTTGGAATTAAAAGGACAAATATCTAATTGATCTAATTAATTTAATAGCTCCTTTAATTCAGACA
*
25537581 TTGATTTGGGTTTTAATGGC
129 CTGATTTGGGTTTTAATGGC
25537601 TCCTTAATTC
Statistics
Matches: 141, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
146 4 0.03
147 46 0.33
148 91 0.65
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (148 bp):
AATATTTTAGCCCAATACATAATTTTATATTTTCTCAACAGAGCTTATCTCTTCAAATTCTATTT
TGGAATTAAAAGGACAAATATCTAATTGATCTAATTAATTTAATAGCTCCTTTAATTCAGACACT
GATTTGGGTTTTAATGGC
Found at i:25542113 original size:43 final size:41
Alignment explanation
Indices: 25542037--25542120 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 41
25542027 CATTTGTTTT
*
25542037 AAAATAGTATACACACGGTCTGACACACACCCGTGTGCCTC
1 AAAACAGTATACACACGGTCTGACACACACCCGTGTGCCTC
* *
25542078 AAAACAGTATACACATACGGTCTGGCACACGCCCGTGTGCCTC
1 AAAACAGTATACAC--ACGGTCTGACACACACCCGTGTGCCTC
25542121 TTATAGCTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 13 0.34
43 25 0.66
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (41 bp):
AAAACAGTATACACACGGTCTGACACACACCCGTGTGCCTC
Found at i:25552836 original size:3 final size:3
Alignment explanation
Indices: 25552830--25552874 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
25552820 CTAACGAATT
25552830 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25552875 AAGTTTCTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:25555358 original size:7 final size:7
Alignment explanation
Indices: 25555346--25555370 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25555336 TCAAAAAAAC
25555346 ATATTAT
1 ATATTAT
25555353 ATATTAT
1 ATATTAT
25555360 ATATTAT
1 ATATTAT
25555367 ATAT
1 ATAT
25555371 ATTATTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATATTAT
Found at i:25568626 original size:63 final size:63
Alignment explanation
Indices: 25568549--25568675 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
25568539 TCGTAAAAAA
* *
25568549 TCTGAAACACATTATAATCAACAAACAGTCATAAGGATATTTAGTCAAATCAACATGATCCCT
1 TCTGAAACACATTATAATCAACAAACAATCATAAGGATATTTAGTCAAATCAACATGAACCCT
*
25568612 TCTGAAACACATTATAATCAACAATCAATCATAAGGATATTTAGTCAAATCAACATGAACCCT
1 TCTGAAACACATTATAATCAACAAACAATCATAAGGATATTTAGTCAAATCAACATGAACCCT
25568675 T
1 T
25568676 GCCTTTAGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (63 bp):
TCTGAAACACATTATAATCAACAAACAATCATAAGGATATTTAGTCAAATCAACATGAACCCT
Found at i:25570230 original size:24 final size:24
Alignment explanation
Indices: 25570202--25570261 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
25570192 TAGAAGACGT
25570202 TCCAAAAGCTGGAGTGCTAGATG-
1 TCCAAAAGCTGGAGTGCTAGATGC
* * *
25570225 TGCCAAAAGCAGGTGTGCTTGATGC
1 T-CCAAAAGCTGGAGTGCTAGATGC
*
25570250 TCCAAATGCTGG
1 TCCAAAAGCTGG
25570262 GGCATTAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (24 bp):
TCCAAAAGCTGGAGTGCTAGATGC
Found at i:25570278 original size:24 final size:24
Alignment explanation
Indices: 25570251--25570306 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
25570241 GCTTGATGCT
25570251 CCAAATGCTGGGGCATTAGACACA
1 CCAAATGCTGGGGCATTAGACACA
25570275 CCAAATGCTGGGGCATTAGACACA
1 CCAAATGCTGGGGCATTAGACACA
25570299 CCAAATGC
1 CCAAATGC
25570307 AGTTCCAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (24 bp):
CCAAATGCTGGGGCATTAGACACA
Found at i:25570370 original size:24 final size:24
Alignment explanation
Indices: 25570340--25570446 Score: 153
Period size: 24 Copynumber: 4.5 Consensus size: 24
25570330 TTCCAGTTGA
* *
25570340 ACCAAAGGCAGGGGTGCTGGTGGA
1 ACCAAAGGCAGGGGTGCTTGTGGC
* * *
25570364 ACCAAAGGCTGGGGTACTAGTGGC
1 ACCAAAGGCAGGGGTGCTTGTGGC
25570388 ACCGAAA-GCAGGGGTGCTTGTGGC
1 ACC-AAAGGCAGGGGTGCTTGTGGC
25570412 ACCAAAGGCAGGGGTGCTTGTGGC
1 ACCAAAGGCAGGGGTGCTTGTGGC
25570436 ACCAAAGGCAG
1 ACCAAAGGCAG
25570447 ACTGTGTTGA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
23 3 0.04
24 68 0.92
25 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.40, T:0.14
Consensus pattern (24 bp):
ACCAAAGGCAGGGGTGCTTGTGGC
Found at i:25579283 original size:47 final size:47
Alignment explanation
Indices: 25579232--25579328 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 47
25579222 AAAATCACAA
* * * *
25579232 ATATACTGCCACATAATCAAATCATGGATAAGCCATCACATTTGCAG
1 ATATACTACCACATAATCAAATCATGGACAAGCAACCACATTTGCAG
* * ** *
25579279 ATATACTACCTCATAATCGAATTGTGGACAAGCAACCACATTTGTAG
1 ATATACTACCACATAATCAAATCATGGACAAGCAACCACATTTGCAG
25579326 ATA
1 ATA
25579329 AATTGTCACA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (47 bp):
ATATACTACCACATAATCAAATCATGGACAAGCAACCACATTTGCAG
Found at i:25579410 original size:19 final size:19
Alignment explanation
Indices: 25579386--25579422 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
25579376 ATATGATCAC
*
25579386 AAAATCACTTTTTCACTTA
1 AAAATCAATTTTTCACTTA
25579405 AAAATCAATTTTTCACTT
1 AAAATCAATTTTTCACTT
25579423 TGGCATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATCAATTTTTCACTTA
Found at i:25581111 original size:12 final size:12
Alignment explanation
Indices: 25581094--25581125 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
25581084 TGTGAATGAG
25581094 TTTTCGGAGGTC
1 TTTTCGGAGGTC
25581106 TTTTCGGAGGTC
1 TTTTCGGAGGTC
*
25581118 TTTCCGGA
1 TTTTCGGA
25581126 AGAACTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.31, T:0.41
Consensus pattern (12 bp):
TTTTCGGAGGTC
Found at i:25582394 original size:18 final size:19
Alignment explanation
Indices: 25582371--25582406 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
25582361 TAGTTTTCTC
*
25582371 AAAATAGAAATG-GAAATG
1 AAAATAAAAATGAGAAATG
25582389 AAAATAAAAATGAGAAAT
1 AAAATAAAAATGAGAAAT
25582407 AATTCATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (19 bp):
AAAATAAAAATGAGAAATG
Found at i:25589082 original size:18 final size:19
Alignment explanation
Indices: 25589061--25589098 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
25589051 ATAATTTGAG
* *
25589061 TTATTTAAATTAA-TTAAA
1 TTATTCAAATCAACTTAAA
25589079 TTATTCAAATCAACTTAAA
1 TTATTCAAATCAACTTAAA
25589098 T
1 T
25589099 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
TTATTCAAATCAACTTAAA
Found at i:25589499 original size:30 final size:30
Alignment explanation
Indices: 25589460--25589522 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
25589450 CTTCAACCTG
* *
25589460 ACTATCTCAAAACCTTTTTTATTAAACTCA
1 ACTAACTCAAAACCTTTTTGATTAAACTCA
*
25589490 ACTAACTCAAAACCTTTTTGATTAAATTCA
1 ACTAACTCAAAACCTTTTTGATTAAACTCA
25589520 ACT
1 ACT
25589523 CGATCCAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (30 bp):
ACTAACTCAAAACCTTTTTGATTAAACTCA
Found at i:25595326 original size:21 final size:21
Alignment explanation
Indices: 25595300--25595347 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
25595290 GCAATTTAAA
25595300 AATTTT-CTTTTATGCTCTTTG
1 AATTTTCCTTTT-TGCTCTTTG
*
25595321 AATTTTCCTTTTTGTTCTTT-
1 AATTTTCCTTTTTGCTCTTTG
25595341 -ATTTTCC
1 AATTTTCC
25595348 CTTCTCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 7 0.28
21 13 0.52
22 5 0.20
ACGTcount: A:0.12, C:0.17, G:0.06, T:0.65
Consensus pattern (21 bp):
AATTTTCCTTTTTGCTCTTTG
Found at i:25602938 original size:19 final size:18
Alignment explanation
Indices: 25602915--25602978 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
25602905 ATACTCTTTA
25602915 GAATTTTATACAA-ATTTT
1 GAATTTTATA-AATATTTT
25602933 GAAATTTTTATAAATATTTT
1 G-AA-TTTTATAAATATTTT
25602953 GAATTTTA-AAATTTATTTT
1 GAATTTTATAAA--TATTTT
25602972 GAATTTT
1 GAATTTT
25602979 TGTAATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.07
18 6 0.15
19 19 0.46
20 13 0.32
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (18 bp):
GAATTTTATAAATATTTT
Found at i:25602943 original size:20 final size:19
Alignment explanation
Indices: 25602918--25602979 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
25602908 CTCTTTAGAA
25602918 TTTTATACAA-ATTTTGAAAT
1 TTTTATA-AATATTTTG-AAT
25602938 TTTTATAAATATTTTGAA-
1 TTTTATAAATATTTTGAAT
25602956 TTTTA-AAATTTATTTTGAAT
1 TTTTATAAA--TATTTTGAAT
25602976 TTTT
1 TTTT
25602980 GTAATTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.08
18 5 0.13
19 13 0.34
20 17 0.45
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTATAAATATTTTGAAT
Found at i:25602979 original size:27 final size:28
Alignment explanation
Indices: 25602927--25602987 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
25602917 ATTTTATACA
*
25602927 AATTTTGAAATTTTTATAAATATTTTG-
1 AATTTTAAAATTTTTATAAATATTTTGT
* *
25602954 AATTTTAAAATTTATTTTGAAT-TTTTGT
1 AATTTTAAAATTT-TTATAAATATTTTGT
25602982 AATTTT
1 AATTTT
25602988 TGTTGAGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (28 bp):
AATTTTAAAATTTTTATAAATATTTTGT
Found at i:25602985 original size:20 final size:20
Alignment explanation
Indices: 25602928--25602986 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
25602918 TTTTATACAA
*
25602928 ATTTTGAAATTTTTATAA-AT
1 ATTTTG-AATTTTTATAATTT
*
25602948 ATTTTGAA-TTTTAAAATTT
1 ATTTTGAATTTTTATAATTT
*
25602967 ATTTTGAATTTTTGTAATTT
1 ATTTTGAATTTTTATAATTT
25602987 TTGTTGAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.21
19 11 0.33
20 15 0.45
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
ATTTTGAATTTTTATAATTT
Found at i:25611846 original size:21 final size:21
Alignment explanation
Indices: 25611793--25611857 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
25611783 TTAGTATCGA
* * * *
25611793 TAGAAGCATGACTTGTTTCGG
1 TAGAAGCTTCACTTGTATCAG
25611814 TAGAAGCTTCACTTGTATCAG
1 TAGAAGCTTCACTTGTATCAG
**
25611835 TAGAA-CTGTCACAAGTATCAG
1 TAGAAGCT-TCACTTGTATCAG
25611856 TA
1 TA
25611858 AAAGTTTACA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 2 0.05
21 35 0.95
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (21 bp):
TAGAAGCTTCACTTGTATCAG
Found at i:25617433 original size:10 final size:10
Alignment explanation
Indices: 25617418--25617580 Score: 77
Period size: 10 Copynumber: 15.5 Consensus size: 10
25617408 CTATTACTAG
25617418 ATGTGATTAA
1 ATGTGATTAA
*
25617428 ATGTGACTAA
1 ATGTGATTAA
25617438 ATGTGATTAA
1 ATGTGATTAA
25617448 TATGTGATGTGATAA
1 -ATGTGA--T--TAA
**
25617463 ATGTTGAAATATTC
1 ATG-TG--AT-TAA
25617477 ATGTGATTAA
1 ATGTGATTAA
*
25617487 ATGTGACTAA
1 ATGTGATTAA
*
25617497 ATGTGACTAA
1 ATGTGATTAA
25617507 ATGTGATT-A
1 ATGTGATTAA
*
25617516 ATGTG--T-G
1 ATGTGATTAA
25617523 ATGTGA-TAA
1 ATGTGATTAA
**
25617532 ATGCTGAAATATTC
1 ATG-TG--AT-TAA
*
25617546 ATGTGACT-A
1 ATGTGATTAA
25617555 ATGTGATTAA
1 ATGTGATTAA
25617565 ATGTGATTAA
1 ATGTGATTAA
25617575 TATGTG
1 -ATGTG
25617581 TTGTGTTAAC
Statistics
Matches: 121, Mismatches: 15, Indels: 33
0.72 0.09 0.20
Matches are distributed among these distances:
7 6 0.05
8 1 0.01
9 16 0.13
10 59 0.49
11 14 0.12
12 1 0.01
13 5 0.04
14 12 0.10
15 6 0.05
17 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (10 bp):
ATGTGATTAA
Found at i:25617487 original size:24 final size:25
Alignment explanation
Indices: 25617428--25617490 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 25
25617418 ATGTGATTAA
*
25617428 ATGTGACTAAATG-TGATTAATATGTG
1 ATGTGA-TAAATGTTGA-TAATATGTC
25617454 ATGTGATAAATGTTGA-AATAT-TC
1 ATGTGATAAATGTTGATAATATGTC
25617477 ATGTGATTAAATGT
1 ATGTGA-TAAATGT
25617491 GACTAAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 7 0.21
24 12 0.35
25 6 0.18
26 9 0.26
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.40
Consensus pattern (25 bp):
ATGTGATAAATGTTGATAATATGTC
Found at i:25617529 original size:69 final size:68
Alignment explanation
Indices: 25617413--25617580 Score: 264
Period size: 69 Copynumber: 2.4 Consensus size: 68
25617403 CCAAACTATT
*
25617413 ACTAGATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCA
1 ACTA-ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCA
25617478 TGTG
65 TGTG
* * *
25617482 ATTAAATGTGACTAAATGTGACTAAATGTGATTAATGTGTGATGTGATAAATGCTGAAATATTCA
1 ACT-AATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCA
25617547 TGTG
65 TGTG
*
25617551 ACTAATGTGATTAAATGTGATTAATATGTG
1 ACTAATGTGATTAAATGTGACTAA-ATGTG
25617581 TTGTGTTAAC
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
68 19 0.21
69 70 0.78
70 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (68 bp):
ACTAATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCAT
GTG
Found at i:25622199 original size:31 final size:31
Alignment explanation
Indices: 25622161--25622222 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
25622151 GGATTAAAAC
25622161 TTGGTTTTAAAGTGTTTTTCAACTTGTTTTA
1 TTGGTTTTAAAGTGTTTTTCAACTTGTTTTA
25622192 TTGGTTTTAAAGTGTTTTTCAACTTGTTTTA
1 TTGGTTTTAAAGTGTTTTTCAACTTGTTTTA
25622223 ACATGATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.58
Consensus pattern (31 bp):
TTGGTTTTAAAGTGTTTTTCAACTTGTTTTA
Found at i:25623428 original size:59 final size:59
Alignment explanation
Indices: 25623336--25623554 Score: 298
Period size: 59 Copynumber: 3.6 Consensus size: 59
25623326 CTATCATTAA
25623336 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
* *
25623395 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTTATGTGA
1 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCT-GAA-A--TAT-T--
25623460 C
59 C
*
25623461 TAATGTGATTAAATGTGACTAAATGTGATTAATATGGGATGTGATAAATGCTGAAATATTC
1 --ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
* *
25623522 ATGTGACT-AATGTGATTAAATGTGATTAA-ATGT
1 ATGTGATTAAATGTGACTAAATGTGATTAATATGT
25623555 TATTAATATG
Statistics
Matches: 143, Mismatches: 8, Indels: 20
0.84 0.05 0.12
Matches are distributed among these distances:
57 3 0.02
58 20 0.14
59 56 0.39
60 2 0.01
61 2 0.01
63 4 0.03
64 4 0.03
66 2 0.01
67 2 0.01
68 48 0.34
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (59 bp):
ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
Found at i:25623479 original size:68 final size:68
Alignment explanation
Indices: 25623395--25623612 Score: 312
Period size: 68 Copynumber: 3.2 Consensus size: 68
25623385 TGAAATATTC
*
25623395 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTTATGTGA
1 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGA
25623460 CTA
66 CTA
* * *
25623463 ATGTGATTAAATGTGACTAAATGTGATTAATATGGGATGTGATAAATGCTGAAATATTCATGTGA
1 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGA
25623528 CTA
66 CTA
* * * * * * *
25623531 ATGTGATTAAATGTGATTAAATGTTATTAATATGTGTTGTGTTAAATGTTTAAGTACTCATGTGA
1 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGA
*
25623596 TTA
66 CTA
*
25623599 ATGCGATT-AATGTG
1 ATGTGATTAAATGTG
25623613 TAAAAGACTG
Statistics
Matches: 135, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
67 6 0.04
68 129 0.96
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (68 bp):
ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGA
CTA
Found at i:25623546 original size:19 final size:21
Alignment explanation
Indices: 25623333--25623566 Score: 96
Period size: 20 Copynumber: 10.9 Consensus size: 21
25623323 AAACTATCAT
25623333 TAAATGTGATTAA-ATGTGAC
1 TAAATGTGATTAATATGTGAC
*
25623353 TAAATGTGATTAATATGTGATGTGA
1 TAAATGTGATTAATATGTGA----C
* * *
25623378 TAAATGCTGAAATATTCATGTGAT
1 TAAATG-TG-ATTAAT-ATGTGAC
* *
25623402 TAAATGTGACTAA-ATGTGAT
1 TAAATGTGATTAATATGTGAC
* ** *
25623422 TAATATGTGATGTGATAAATG-T
1 TAA-ATGTGAT-TAATATGTGAC
*
25623444 TAAA-AT-ATT--TATGTGAC
1 TAAATGTGATTAATATGTGAC
25623461 T-AATGTGATTAA-ATGTGAC
1 TAAATGTGATTAATATGTGAC
25623480 TAAATGTGATTAATATGGGATGTGA-
1 TAAATGTGATT-A-AT---ATGTGAC
* *
25623505 TAAATGCTGAAATATTCATGTGAC
1 TAAATG-TG-ATTAAT-ATGTGAC
*
25623529 T-AATGTGATTAA-ATGTGAT
1 TAAATGTGATTAATATGTGAC
*
25623548 TAAATGTTATTAATATGTG
1 TAAATGTGATTAATATGTG
25623567 TTGTGTTAAA
Statistics
Matches: 164, Mismatches: 22, Indels: 55
0.68 0.09 0.23
Matches are distributed among these distances:
16 6 0.04
17 2 0.01
18 4 0.02
19 17 0.10
20 43 0.26
21 22 0.13
22 12 0.07
23 15 0.09
24 7 0.04
25 13 0.08
26 11 0.07
27 6 0.04
28 6 0.04
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (21 bp):
TAAATGTGATTAATATGTGAC
Found at i:25627446 original size:17 final size:17
Alignment explanation
Indices: 25627424--25627461 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25627414 CGGTGGAGAA
* *
25627424 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
25627441 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
25627458 CTTG
1 CTTG
25627462 CCAATGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.45
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:25629103 original size:9 final size:9
Alignment explanation
Indices: 25629089--25629125 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
25629079 TATAGTTTGA
*
25629089 TATTCGATT
1 TATTCGAAT
25629098 TATTCGAAT
1 TATTCGAAT
*
25629107 TATTCGAGT
1 TATTCGAAT
25629116 TATTCGAAT
1 TATTCGAAT
25629125 T
1 T
25629126 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:25629112 original size:18 final size:18
Alignment explanation
Indices: 25629089--25629125 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
25629079 TATAGTTTGA
*
25629089 TATTCGATTTATTCGAAT
1 TATTCGAGTTATTCGAAT
25629107 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
25629125 T
1 T
25629126 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:25629199 original size:18 final size:18
Alignment explanation
Indices: 25629176--25629210 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25629166 ATTGAAGTTG
*
25629176 ACTCGAATAATTCGATTA
1 ACTCGAATAACTCGATTA
25629194 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
25629211 TGTTTAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:25630872 original size:30 final size:30
Alignment explanation
Indices: 25630838--25630897 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
25630828 AGCGATACTC
25630838 AACCTCAGTTGAAGGTCAAGCAACAATTTT
1 AACCTCAGTTGAAGGTCAAGCAACAATTTT
25630868 AACCTCAGTTGAAGGTCAAGCAACAATTTT
1 AACCTCAGTTGAAGGTCAAGCAACAATTTT
25630898 CTGTTTCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (30 bp):
AACCTCAGTTGAAGGTCAAGCAACAATTTT
Found at i:25652465 original size:11 final size:11
Alignment explanation
Indices: 25652434--25652468 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
25652424 ATAAAATGTC
25652434 AAACTAAAAA-A
1 AAAC-AAAAATA
25652445 AAACAAAAATA
1 AAACAAAAATA
25652456 AAACAAAAATA
1 AAACAAAAATA
25652467 AA
1 AA
25652469 TAAATAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09
Consensus pattern (11 bp):
AAACAAAAATA
Found at i:25658710 original size:30 final size:30
Alignment explanation
Indices: 25658656--25658712 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
25658646 AGAAATTATG
* * **
25658656 TTTTGACCTCTAAACTGTGTAAAAATTCTA
1 TTTTGACCCCTAAACTATCCAAAAATTCTA
25658686 TTTTGACCCCTAAACTATCCAAAAATT
1 TTTTGACCCCTAAACTATCCAAAAATT
25658713 TGAATTTGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (30 bp):
TTTTGACCCCTAAACTATCCAAAAATTCTA
Found at i:25658721 original size:30 final size:29
Alignment explanation
Indices: 25658687--25658846 Score: 97
Period size: 30 Copynumber: 5.3 Consensus size: 29
25658677 AAAATTCTAT
*
25658687 TTTGACCCCTAAACTATCCAAAAATTTGAA
1 TTTGACCCCTAAACTTTCCAAAAATTTG-A
* * * *
25658717 TTTGA-CCCTCGACCTTTCTAAAAATTATGT
1 TTTGACCCCT-AAACTTTCCAAAAATT-TGA
* * *
25658747 TTTGACCCTTAAACTTTTCAAAAAAATTGGA
1 TTTGACCCCTAAAC-TTTC-CAAAAATTTGA
* **
25658778 TTTGACCCCCCAAACTTTCCAAAAATTCAA
1 TTTGA-CCCCTAAACTTTCCAAAAATTTGA
* * * * *
25658808 TTTAAACCCTTAAACTTTTCAAAATTTTGTT
1 TTT-GACCCCTAAACTTTCCAAAAATTTG-A
25658839 TTTGACCC
1 TTTGACCC
25658847 GTTTTTCTTA
Statistics
Matches: 97, Mismatches: 25, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
29 4 0.04
30 56 0.58
31 23 0.24
32 14 0.14
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (29 bp):
TTTGACCCCTAAACTTTCCAAAAATTTGA
Found at i:25669879 original size:44 final size:44
Alignment explanation
Indices: 25669770--25669936 Score: 175
Period size: 44 Copynumber: 3.9 Consensus size: 44
25669760 TAAAATAAAT
* * * * *
25669770 AAAAGGAGAGGTTAAGATGAAAACCCATAAAGGGCGTCTTGAAAC
1 AAAAGGAGAGGTCAAGATGAAAACCCACAAAAGGCGTC-TCAAAA
* * *
25669815 CAAA--AGA--TCGAGAAGAAAACCCACAAAAGGCGTCTCAAAA
1 AAAAGGAGAGGTCAAGATGAAAACCCACAAAAGGCGTCTCAAAA
*
25669855 AAAAGGAGAGGTCAAGATGAAAACCCAC-AAAGAGCGTTTCAAAA
1 AAAAGGAGAGGTCAAGATGAAAACCCACAAAAG-GCGTCTCAAAA
* *
25669899 AAAAAGAGAGGTCAAGATGAAAA-CCACAAAGGGCGTCT
1 AAAAGGAGAGGTCAAGATGAAAACCCACAAAAGGCGTCT
25669937 TGAAACCAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
40 7 0.07
41 22 0.22
42 3 0.03
43 16 0.16
44 50 0.50
45 3 0.03
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (44 bp):
AAAAGGAGAGGTCAAGATGAAAACCCACAAAAGGCGTCTCAAAA
Found at i:25670905 original size:115 final size:115
Alignment explanation
Indices: 25670703--25671482 Score: 913
Period size: 115 Copynumber: 6.6 Consensus size: 115
25670693 TGGGTCAGAT
* * * * * * ** *
25670703 CAAAACAATAAAGCAAAGCTCCATGTGAGTGGAACTTCAAGCCC-CTATATTTTTGATGAGACAC
1 CAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTC-ATCTTCCTGATGAGATAC
* *
25670767 AAAGAAGTGGATCAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTGGAC
65 AGAGAAGTGGATCAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGAC
* *
25670818 CAAAACAATGAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCCTTATCTTCCTGATGAGATACA
1 CAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACA
* *
25670883 GAGAAGTGGATTAAGCGGTCATCTTCCTGATGAGATATAGAGAAGTGGAC
66 GAGAAGTGGATCAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGAC
* *
25670933 CAAAACAATGAAGCGAAGCTCAATGTAAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATACA
1 CAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACA
* * * **
25670998 GAGAAGTGGATCAAAATGATAAAGCGATCATGTTCCTAATGAGATACAGAGAAGTAAAC
66 GAGAAGTGGATC---------AAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGAC
** * * *
25671057 CAAAACAATGAAGCGAAGCTCCTTGTGAGTGAAACTTTAAACCCTCATCTTCCTAATGAGATGCA
1 CAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACA
* *
25671122 GAGAAGTGGATCAAG-GGATTATCTTCCTAATGAGATACAGAGAAGTGGAC
66 GAGAAGTGGATCAAGCGG-TCATCTTCCTGATGAGATACAGAGAAGTGGAC
* * * *
25671172 CAAAATAATGAAGCGAAGCTCAATGTGAGTGAAACTT-TAAGCCTCATCTTTCTGATGAGATACA
1 CAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACA
*
25671236 GAGAAGTGGATCAAGCGGTTATCTTCCTGATGAGATACAGAGAAGTGGAC
66 GAGAAGTGGATCAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGAC
* * * * *
25671286 CAAAATAATAAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCC-CTATCTTCCTGATAAGATAT
1 CAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTC-ATCTTCCTGATGAGATAC
* * * *
25671350 AGAGAAGTGGATTAAAACAATGAAACGGTCGTCCTCTTGATGAGATACAGAGAAGTGAAC
65 AGAGAAGTGGA-T----CAA-G---CGGTCATCTTCCTGATGAGATACAGAGAAGTGGAC
* * * *
25671410 CAAATCAACGAAGCGAAGCTCAATATGAGTGAAACTTCAAA-CCTCATCTTCCTAATGAGATACA
1 CAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACA
25671474 GAGAAGTGG
66 GAGAAGTGG
25671483 GCTAAATAAG
Statistics
Matches: 573, Mismatches: 68, Indels: 40
0.84 0.10 0.06
Matches are distributed among these distances:
114 105 0.18
115 268 0.47
116 1 0.00
120 3 0.01
121 1 0.00
123 27 0.05
124 168 0.29
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (115 bp):
CAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACA
GAGAAGTGGATCAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGAC
Found at i:25671356 original size:353 final size:353
Alignment explanation
Indices: 25670758--25671482 Score: 1060
Period size: 353 Copynumber: 2.1 Consensus size: 353
25670748 TATATTTTTG
* * * *
25670758 ATGAGACACAAAGAAGTGGATCAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAA
1 ATGAGATACAGAGAAGTGGATCAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTGGACCAAAA
* *
25670823 CAATGAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCCTTATCTTCCTGATGAGATACAGAGAA
66 CAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACAGAGAA
* * *
25670888 GTGGATTAAGCGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAACAATGAAGCGAAGCT
131 GTGGATCAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATAAAGCGAAGCT
* **
25670953 CAATGTAAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATGAT
196 CAATGTAAGTGAAACTTCAAACCCCCATCTTCCTGATAAGATACAGAGAAGTGGATCAAAACAAT
** * ** *
25671018 -AAAGCGATCATGTTCCTAATGAGATACAGAGAAGTAAACCAAAACAATGAAGCGAAGCTCCTTG
261 GAAA-CGATCATCCTCCTAATGAGATACAGAGAAGTAAACCAAAACAACGAAGCGAAGCTCAATA
*
25671082 TGAGTGAAACTTTAAACCCTCATCTTCCTA
325 TGAGTGAAACTTCAAA-CCTCATCTTCCTA
* *
25671112 ATGAGATGCAGAGAAGTGGATCAAG-GGATTATCTTCCTAATGAGATACAGAGAAGTGGACCAAA
1 ATGAGATACAGAGAAGTGGATCAAGCGG-TCATCTTCCTAATGAGATACAGAGAAGTGGACCAAA
* * * *
25671176 ATAATGAAGCGAAGCTCAATGTGAGTGAAACTT-TAAGCCTCATCTTTCTGATGAGATACAGAGA
65 ACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACAGAGA
* * *
25671240 AGTGGATCAAGCGGTTATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATAAAGTGAAGC
130 AGTGGATCAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATAAAGCGAAGC
* * * *
25671305 TCAATGTGAGTGAAACTTCAAACCCCTATCTTCCTGATAAGATATAGAGAAGTGGATTAAAACAA
195 TCAATGTAAGTGAAACTTCAAACCCCCATCTTCCTGATAAGATACAGAGAAGTGGATCAAAACAA
* * * * * *
25671370 TGAAACGGTCGTCCTCTTGATGAGATACAGAGAAGTGAACCAAATCAACGAAGCGAAGCTCAATA
260 TGAAACGATCATCCTCCTAATGAGATACAGAGAAGTAAACCAAAACAACGAAGCGAAGCTCAATA
25671435 TGAGTGAAACTTCAAACCTCATCTTCCTA
325 TGAGTGAAACTTCAAACCTCATCTTCCTA
25671464 ATGAGATACAGAGAAGTGG
1 ATGAGATACAGAGAAGTGG
25671483 GCTAAATAAG
Statistics
Matches: 330, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
352 31 0.09
353 210 0.64
354 89 0.27
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (353 bp):
ATGAGATACAGAGAAGTGGATCAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTGGACCAAAA
CAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACAGAGAA
GTGGATCAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATAAAGCGAAGCT
CAATGTAAGTGAAACTTCAAACCCCCATCTTCCTGATAAGATACAGAGAAGTGGATCAAAACAAT
GAAACGATCATCCTCCTAATGAGATACAGAGAAGTAAACCAAAACAACGAAGCGAAGCTCAATAT
GAGTGAAACTTCAAACCTCATCTTCCTA
Found at i:25671632 original size:46 final size:46
Alignment explanation
Indices: 25671558--25671646 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
25671548 ATTCAGTCTT
* *
25671558 TTACCCCTAAGTCAAGAGGGGCATATTGAAGACATTATCCAATACC
1 TTACCCCTAAGTCAAGAGGGACAGATTGAAGACATTATCCAATACC
* *
25671604 TTACCCTTAAGTCAAGATGGACAGATTGAAGACATTATCCAAT
1 TTACCCCTAAGTCAAGAGGGACAGATTGAAGACATTATCCAAT
25671647 CTCCTACCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (46 bp):
TTACCCCTAAGTCAAGAGGGACAGATTGAAGACATTATCCAATACC
Found at i:25671655 original size:46 final size:46
Alignment explanation
Indices: 25671559--25671656 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
25671549 TTCAGTCTTT
* * *
25671559 TACCCCTAAGTCAAGAGGGGCATATTGAAGACATTATCCAATACCT
1 TACCCCTAAGTCAAGAGGGACAGATTGAAGACATTATCCAATACCC
* *
25671605 TACCCTTAAGTCAAGATGGACAGATTGAAGACATTATCCAAT-CTCC
1 TACCCCTAAGTCAAGAGGGACAGATTGAAGACATTATCCAATAC-CC
25671651 TACCCC
1 TACCCC
25671657 AATCATGGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 1 0.02
46 44 0.98
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (46 bp):
TACCCCTAAGTCAAGAGGGACAGATTGAAGACATTATCCAATACCC
Found at i:25674389 original size:21 final size:21
Alignment explanation
Indices: 25674364--25674405 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25674354 CCGACTCACC
*
25674364 TAATATCCGCGTGTTATTTAA
1 TAATATCCACGTGTTATTTAA
* *
25674385 TAATATTCACGTGTTTTTTAA
1 TAATATCCACGTGTTATTTAA
25674406 AGAATGGGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (21 bp):
TAATATCCACGTGTTATTTAA
Found at i:25680535 original size:17 final size:17
Alignment explanation
Indices: 25680513--25680546 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25680503 AAAAAAATCC
25680513 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
*
25680530 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
25680547 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:25684110 original size:53 final size:54
Alignment explanation
Indices: 25684039--25684166 Score: 149
Period size: 53 Copynumber: 2.4 Consensus size: 54
25684029 CCTAACCCCT
25684039 AACCTCTAAACCTT-AAACCTTTAAAAA-TCA-TAAACACTAAAATAATCACTTTA
1 AACCTC-AAACCTTAAAACCTTTAAAAACT-ATTAAACACTAAAATAATCACTTTA
* * *
25684092 AACC-CAAACCTTTAAAACC-TTAAAAACTATTAAACCCTAAACTCATCACTTTA
1 AACCTCAAACC-TTAAAACCTTTAAAAACTATTAAACACTAAAATAATCACTTTA
*
25684145 AACCTTAAATCCTTAAAACCTT
1 AACCTCAAA-CCTTAAAACCTT
25684167 AAACCTTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
51 5 0.08
52 11 0.17
53 34 0.53
54 11 0.17
55 3 0.05
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (54 bp):
AACCTCAAACCTTAAAACCTTTAAAAACTATTAAACACTAAAATAATCACTTTA
Found at i:25684160 original size:8 final size:7
Alignment explanation
Indices: 25684142--25684177 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
25684132 ACTCATCACT
25684142 TTAAACC
1 TTAAACC
25684149 TTAAATCC
1 TTAAA-CC
25684157 TTAAAACC
1 TT-AAACC
25684165 TTAAACC
1 TTAAACC
25684172 TTAAAC
1 TTAAAC
25684178 TAATCACCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 16 0.59
8 8 0.30
9 3 0.11
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAACC
Found at i:25684165 original size:16 final size:15
Alignment explanation
Indices: 25684144--25684176 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
25684134 TCATCACTTT
25684144 AAACCTTAAATCCTTA
1 AAACCTTAAA-CCTTA
25684160 AAACCTTAAACCTTA
1 AAACCTTAAACCTTA
25684175 AA
1 AA
25684177 CTAATCACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (15 bp):
AAACCTTAAACCTTA
Found at i:25684178 original size:44 final size:48
Alignment explanation
Indices: 25684097--25684190 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 48
25684087 CTTTAAACCC
*
25684097 AAACCTTTAAAACCTTAAAAACTATTAAACCCTAAACTCATCA-CTTT
1 AAACCTTTAAAACCTTAAAAACTATTAAACCCTAAACTAATCACCTTT
* * *
25684144 AAACC-TTAAATCCTT-AAAAC-CTTAAACCTTAAACTAATCACCTTT
1 AAACCTTTAAAACCTTAAAAACTATTAAACCCTAAACTAATCACCTTT
25684189 AA
1 AA
25684191 TCCTAAACCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 17 0.40
45 11 0.26
46 9 0.21
47 5 0.12
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (48 bp):
AAACCTTTAAAACCTTAAAAACTATTAAACCCTAAACTAATCACCTTT
Found at i:25687054 original size:25 final size:26
Alignment explanation
Indices: 25686997--25687051 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
25686987 TCTACTAATC
* *
25686997 TTTTGTTTCCTTTCCTTCTTCAAAAA
1 TTTTGCTTCCTTTCATTCTTCAAAAA
25687023 TTTTGCTTCCTTTCATTCTTCAAAAA
1 TTTTGCTTCCTTTCATTCTTCAAAAA
25687049 TTT
1 TTT
25687052 GCTATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTTGCTTCCTTTCATTCTTCAAAAA
Found at i:25694840 original size:3 final size:3
Alignment explanation
Indices: 25694832--25694868 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
25694822 GATAGTTTAA
25694832 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
25694869 GGGTAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25696183 original size:12 final size:12
Alignment explanation
Indices: 25696156--25696185 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
25696146 TGAAACCTTT
25696156 TTTTTAATTTGA
1 TTTTTAATTTGA
25696168 -TTTTAATTTGA
1 TTTTTAATTTGA
25696179 TTTTTAA
1 TTTTTAA
25696186 GTTTTTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (12 bp):
TTTTTAATTTGA
Found at i:25698347 original size:5 final size:5
Alignment explanation
Indices: 25698337--25698361 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25698327 TCTCCCATCA
25698337 TCCCT TCCCT TCCCT TCCCT TCCCT
1 TCCCT TCCCT TCCCT TCCCT TCCCT
25698362 CCCCCACCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TCCCT
Found at i:25702753 original size:52 final size:52
Alignment explanation
Indices: 25702672--25702902 Score: 310
Period size: 52 Copynumber: 4.5 Consensus size: 52
25702662 TTCCCATTTA
* * *
25702672 ATACTCACGATGAAACAAAGTCATCAGACCTTA-AATCCATAAAAGGA-TCTAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGT-AAAGGATTC-AT
* *
25702724 ATGCTCACGATGACACATAGTCATCAGACCTCT-TAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCT-TATAATCCGTAAAGGATTCAT
* *
25702776 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTCAT
** *
25702828 ATACTCACGATGACAC--AGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTCAT
25702878 ATACTCACGATGACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
25702903 GGAGCTTTTT
Statistics
Matches: 160, Mismatches: 13, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
50 47 0.29
51 1 0.01
52 104 0.65
53 8 0.05
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTCAT
Found at i:25702892 original size:102 final size:103
Alignment explanation
Indices: 25702672--25702905 Score: 339
Period size: 102 Copynumber: 2.3 Consensus size: 103
25702662 TTCCCATTTA
* * * *
25702672 ATACTCACGATGAAACAAAGTCATCAGACCTTAAATCCATAAAAGGATCTATATGCTCACGATGA
1 ATACTCACGATGACACATAGTCATCGGACCTTAAATCCATAAAAGGATCTATATACTCACGATGA
* *
25702737 CACATAGTCATCAGACCTCTTAATTCGTAAAGGATTCAT
66 CACA-AGTCATCAGACCTCATAATCCGTAAAGGATTCAT
*
25702776 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAA-GAT-TCATATACTCACGAT
1 ATACTCACGATGACACATAGTCATCGGACCTTA-AATCCATAAAAGGATCT-ATATACTCACGAT
**
25702839 GACAC-AGTCATTGGACCTCATAATCCGTAAAGGATTCAT
64 GACACAAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
25702878 ATACTCACGATGACACATAGTCATCGGA
1 ATACTCACGATGACACATAGTCATCGGA
25702906 GCTTTTTCAT
Statistics
Matches: 119, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
102 58 0.49
103 1 0.01
104 50 0.42
105 10 0.08
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (103 bp):
ATACTCACGATGACACATAGTCATCGGACCTTAAATCCATAAAAGGATCTATATACTCACGATGA
CACAAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
Found at i:25708373 original size:20 final size:18
Alignment explanation
Indices: 25708345--25708383 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
25708335 AAATATTTTT
25708345 ATAACTTTTATACTTTTTAA
1 ATAACTTTTA-A-TTTTTAA
*
25708365 ATAATTTTTAATTTTTAA
1 ATAACTTTTAATTTTTAA
25708383 A
1 A
25708384 ATTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAACTTTTAATTTTTAA
Found at i:25709620 original size:16 final size:16
Alignment explanation
Indices: 25709582--25709621 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
25709572 CTTTTGATTG
25709582 TTTACTTATTTTGTTA
1 TTTACTTATTTTGTTA
25709598 GTTTACTTATTTTGTGT-
1 -TTTACTTATTTTGT-TA
25709615 TTTACTT
1 TTTACTT
25709622 GGTGCCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 14 0.64
18 1 0.05
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (16 bp):
TTTACTTATTTTGTTA
Found at i:25710310 original size:29 final size:30
Alignment explanation
Indices: 25710278--25710338 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
25710268 TTGAATTTTT
25710278 TTTTAAACCT-TTAAAAATTAAAAAAAAAA
1 TTTTAAACCTCTTAAAAATTAAAAAAAAAA
* * *
25710307 TTTTGAACCTCTTAAAAATTGAAACAAAAA
1 TTTTAAACCTCTTAAAAATTAAAAAAAAAA
25710337 TT
1 TT
25710339 AAACTCTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (30 bp):
TTTTAAACCTCTTAAAAATTAAAAAAAAAA
Found at i:25711628 original size:20 final size:20
Alignment explanation
Indices: 25711587--25711628 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
25711577 AACTAGTTAA
* *
25711587 AAACACTCTAAAACATCCTC
1 AAACACTCCAAAACATCATC
25711607 AAACACTACCAAAACAT-ATC
1 AAACACT-CCAAAACATCATC
25711627 AA
1 AA
25711629 TAATACTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (20 bp):
AAACACTCCAAAACATCATC
Found at i:25718700 original size:12 final size:11
Alignment explanation
Indices: 25718685--25718723 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
25718675 TAGAAGGCAT
25718685 AAAATAAAAGA
1 AAAATAAAAGA
*
25718696 TAAAATAAAATA
1 -AAAATAAAAGA
25718708 ATAAATAAAAGA
1 A-AAATAAAAGA
25718720 AAAA
1 AAAA
25718724 GCTTGAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAAGA
Found at i:25718705 original size:17 final size:17
Alignment explanation
Indices: 25718683--25718722 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
25718673 TATAGAAGGC
25718683 ATAAAATAA-AAGATAAA
1 ATAAAATAATAA-ATAAA
25718700 ATAAAATAATAAATAAA
1 ATAAAATAATAAATAAA
*
25718717 AGAAAA
1 ATAAAA
25718723 AGCTTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (17 bp):
ATAAAATAATAAATAAA
Found at i:25719208 original size:30 final size:30
Alignment explanation
Indices: 25719169--25719228 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
25719159 CATATAAATA
25719169 CAAAAAGAATGAACAAGAAACTAGAATTGT
1 CAAAAAGAATGAACAAGAAACTAGAATTGT
*
25719199 CAAAGAGAATGAACAAGAAACTAGAATTGT
1 CAAAAAGAATGAACAAGAAACTAGAATTGT
25719229 ATTAAGCGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.18, T:0.17
Consensus pattern (30 bp):
CAAAAAGAATGAACAAGAAACTAGAATTGT
Found at i:25720573 original size:21 final size:22
Alignment explanation
Indices: 25720542--25720583 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
25720532 ATTCACATGT
25720542 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
25720564 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
25720584 CTTTTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:25722142 original size:17 final size:17
Alignment explanation
Indices: 25722122--25722246 Score: 95
Period size: 17 Copynumber: 7.6 Consensus size: 17
25722112 TAAGTTTATA
*
25722122 TTAAATTTAAATTGGTT
1 TTAAATTTAAATTAGTT
25722139 TTAAATTT--A-T--TT
1 TTAAATTTAAATTAGTT
*
25722151 TTAAGTTTAAATTTA-TT
1 TTAAATTTAAA-TTAGTT
* *
25722168 TTAAATTTAGATTTATTT
1 TTAAATTTA-AATTAGTT
*
25722186 TTAAATTTAAATTTGTT
1 TTAAATTTAAATTAGTT
25722203 TTAAATTTAAATTTAG-T
1 TTAAATTTAAA-TTAGTT
*
25722220 TTAAATTTGAAA-TGGTT
1 TTAAATTT-AAATTAGTT
*
25722237 TTAAACTTAA
1 TTAAATTTAA
25722247 TTTCAAATTT
Statistics
Matches: 89, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
12 9 0.10
14 2 0.02
15 1 0.01
16 5 0.06
17 54 0.61
18 18 0.20
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (17 bp):
TTAAATTTAAATTAGTT
Found at i:25722161 original size:35 final size:34
Alignment explanation
Indices: 25722122--25722264 Score: 122
Period size: 35 Copynumber: 4.3 Consensus size: 34
25722112 TAAGTTTATA
**
25722122 TTAAATTTAAATTGGTTTTAAATTTATTTTTAAGT
1 TTAAATTTAAA-TGGTTTTAAATTTAAATTTAAGT
* **
25722157 TTAAATTT--A---TTTTAAATTTAGATTTATTT
1 TTAAATTTAAATGGTTTTAAATTTAAATTTAAGT
*
25722186 TTAAATTTAAATTTGTTTTAAATTTAAATTT-AGT
1 TTAAATTTAAA-TGGTTTTAAATTTAAATTTAAGT
* *
25722220 TTAAATTTGAAATGGTTTTAAACTT-AATTTCAAAT
1 TTAAATTT-AAATGGTTTTAAATTTAAATTT-AAGT
25722255 TT-AATTTAAA
1 TTAAATTTAAA
25722265 AGTCCAAAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
29 24 0.27
31 1 0.01
33 9 0.10
34 25 0.28
35 30 0.34
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (34 bp):
TTAAATTTAAATGGTTTTAAATTTAAATTTAAGT
Found at i:25722221 original size:18 final size:18
Alignment explanation
Indices: 25722138--25722232 Score: 124
Period size: 17 Copynumber: 5.4 Consensus size: 18
25722128 TTAAATTGGT
* *
25722138 TTTAAATTTATTTTTAAG
1 TTTAAATTTAGTTTTAAA
25722156 TTTAAATTTA-TTTTAAA
1 TTTAAATTTAGTTTTAAA
* *
25722173 TTTAGATTTATTTTTAAA
1 TTTAAATTTAGTTTTAAA
25722191 TTTAAATTT-GTTTTAAA
1 TTTAAATTTAGTTTTAAA
25722208 TTTAAATTTAG-TTTAAA
1 TTTAAATTTAGTTTTAAA
25722225 TTTGAAAT
1 TTT-AAAT
25722233 GGTTTTAAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
17 40 0.57
18 30 0.43
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTAAATTTAGTTTTAAA
Found at i:25724054 original size:30 final size:30
Alignment explanation
Indices: 25723989--25724353 Score: 299
Period size: 29 Copynumber: 12.4 Consensus size: 30
25723979 AAGGTCTTTA
* * *
25723989 AACTTTTCAAAAATCACATTTTAACCCT-A
1 AACTTTCCAAAAATCACATTTTTACCCTCG
* * *
25724018 AACTTTTCAAAAATTACATTTTAACCCTCG
1 AACTTTCCAAAAATCACATTTTTACCCTCG
** *
25724048 AACTTTTAAAAAATCACATTTTTACCCCCG
1 AACTTTCCAAAAATCACATTTTTACCCTCG
** * * *
25724078 AACTTTTAAAAAATTACACTTTTACCCTCA
1 AACTTTCCAAAAATCACATTTTTACCCTCG
* **
25724108 AAC-TTCCAGAAATTC-CATTTTTGTCCTCG
1 AACTTTCCA-AAAATCACATTTTTACCCTCG
25724137 AAC-TTCCAAAAATCACATTTTTA-CCTCG
1 AACTTTCCAAAAATCACATTTTTACCCTCG
* * *
25724165 AAC-TTCCAAAAAATTACATTTTTCCCCCCG
1 AACTTTCC-AAAAATCACATTTTTACCCTCG
*
25724195 AA-TTTCCAAAAATCACATTTTTCCCCTCG
1 AACTTTCCAAAAATCACATTTTTACCCTCG
*
25724224 AA-TTTCCAAAAACCACATTTTTGCACCC-CG
1 AACTTTCCAAAAATCACATTTTT--ACCCTCG
* * *
25724254 AACATTT-CAAAAATTACATTTTTGCCCT-A
1 AAC-TTTCCAAAAATCACATTTTTACCCTCG
*
25724283 AAC-TTCCAAAAATCACATTTTAACCC-CG
1 AACTTTCCAAAAATCACATTTTTACCCTCG
* * **
25724311 AA-TATTCCTAAAATGACATTTTTACCCCTAA
1 AACT-TTCCAAAAATCACATTTTTA-CCCTCG
25724342 AACTTTCCAAAA
1 AACTTTCCAAAA
25724354 TTATATTTTA
Statistics
Matches: 277, Mismatches: 41, Indels: 34
0.79 0.12 0.10
Matches are distributed among these distances:
27 2 0.01
28 36 0.13
29 133 0.48
30 76 0.27
31 26 0.09
32 4 0.01
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
AACTTTCCAAAAATCACATTTTTACCCTCG
Found at i:25724345 original size:59 final size:59
Alignment explanation
Indices: 25723996--25724353 Score: 257
Period size: 60 Copynumber: 6.1 Consensus size: 59
25723986 TTAAACTTTT
** * * ** * *
25723996 CAAAAATCACA-TTTTAACCCTAAACT-TTTCAAAAATTACATTTTAACCCTCGAACTTTT
1 CAAAAATCACATTTTTAACCCCGAA-TATTCCAAAAATCACATTTTTCCCCTCAAAC-TTC
* * ** * * *
25724055 AAAAAATCACATTTTTACCCCCGAACT-TTTAAAAAATTACACTTTTACCCTCAAACTTC
1 CAAAAATCACATTTTTAACCCCGAA-TATTCCAAAAATCACATTTTTCCCCTCAAACTTC
* ** * * * *
25724114 CAGAAATTC-CATTTTTGTCCTCGAA-CTTCCAAAAATCACATTTTT-ACCTCGAACTTC
1 CA-AAAATCACATTTTTAACCCCGAATATTCCAAAAATCACATTTTTCCCCTCAAACTTC
* ** * *
25724171 CAAAAAATTACATTTTTCCCCCCGAAT-TTCCAAAAATCACATTTTTCCCCTCGAATTTC
1 C-AAAAATCACATTTTTAACCCCGAATATTCCAAAAATCACATTTTTCCCCTCAAACTTC
* * * * * *
25724230 CAAAAACCACATTTTTGCACCCCGAACATTTCAAAAATTACATTTTTGCCCT-AAACTTC
1 CAAAAATCACATTTTT-AACCCCGAATATTCCAAAAATCACATTTTTCCCCTCAAACTTC
* * *
25724289 CAAAAATCACA-TTTTAACCCCGAATATTCCTAAAATGACATTTTTACCCCTAAAACTTTC
1 CAAAAATCACATTTTTAACCCCGAATATTCCAAAAATCACATTTTT-CCCCTCAAAC-TTC
25724349 CAAAA
1 CAAAA
25724354 TTATATTTTA
Statistics
Matches: 244, Mismatches: 43, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
57 40 0.16
58 69 0.28
59 64 0.26
60 71 0.29
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (59 bp):
CAAAAATCACATTTTTAACCCCGAATATTCCAAAAATCACATTTTTCCCCTCAAACTTC
Done.