Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 98 of 120
Found at i:28195444 original size:110 final size:110
Alignment explanation
Indices: 28195202--28195510 Score: 440
Period size: 110 Copynumber: 2.8 Consensus size: 110
28195192 ATTAGATATT
* * * * *
28195202 ATATATATTACAATTGCTTTTCCTTAACATTTTCTCTTGTTCTACTGAACTCATCTTTATTAAAA
1 ATATATATTCCAATTGCTTTTGCTTAACATCTTCTCTTGTTCTAATGAAGTCATCTTTATTAAAA
* * * *
28195267 AATAATAATACATCATTTGATATTCGAGTTTCGTATTTTTTTAATT
66 AA-AATAATATATTATTTAATATTCGAGTTTCGTATTTTTTTAATC
* ** *
28195313 ATATATATTCCAATTGCTTTTGTTTATTATCTTCTCTTGTTCTAATGAAGTCATATTTATT-AAA
1 ATATATATTCCAATTGCTTTTGCTTAACATCTTCTCTTGTTCTAATGAAGTCATCTTTATTAAAA
28195377 AAAATAATATATTATTTAATATTCGAGTTTCGTATTTTTTTTAATC
66 AAAATAATATATTATTTAATATTCGAGTTTCGTA-TTTTTTTAATC
* * *
28195423 ATATATATTCCAATTGCTTTTGCTTACCATCTCCTCTTGTTCTAGTGAAGTCATCTTTATTAAAA
1 ATATATATTCCAATTGCTTTTGCTTAACATCTTCTCTTGTTCTAATGAAGTCATCTTTATTAAAA
28195488 AAAATAATATATTAATTTAATAT
66 AAAATAATATATT-ATTTAATAT
28195511 ATTATTTAAA
Statistics
Matches: 176, Mismatches: 19, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
109 29 0.16
110 70 0.40
111 68 0.39
112 9 0.05
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.49
Consensus pattern (110 bp):
ATATATATTCCAATTGCTTTTGCTTAACATCTTCTCTTGTTCTAATGAAGTCATCTTTATTAAAA
AAAATAATATATTATTTAATATTCGAGTTTCGTATTTTTTTAATC
Found at i:28198012 original size:3 final size:3
Alignment explanation
Indices: 28197992--28198039 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
28197982 ACTCGTACTT
* * *
28197992 TTA TT- TTA TTA TTG TTA TTA TTA TTA TTA TTA ATA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28198039 T
1 T
28198040 AGGTAAACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28212459 original size:3 final size:3
Alignment explanation
Indices: 28212451--28212531 Score: 96
Period size: 3 Copynumber: 27.7 Consensus size: 3
28212441 CTACCACTCA
28212451 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
28212498 AAA TAT GTA- TAT T-T TAC TAT TAT TAT TTT TAT TA
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28212532 AAATTTTCCG
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 5 0.08
3 59 0.89
4 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28214636 original size:9 final size:9
Alignment explanation
Indices: 28214622--28214657 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
28214612 AAAGGTTTTT
28214622 TAATAAAAA
1 TAATAAAAA
28214631 TAATAAAAA
1 TAATAAAAA
28214640 -AATAAAAA
1 TAATAAAAA
28214648 TAAATAAAAA
1 T-AATAAAAA
28214658 ATGGTATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 9 0.36
10 8 0.32
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
TAATAAAAA
Found at i:28214645 original size:17 final size:18
Alignment explanation
Indices: 28214623--28214658 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
28214613 AAGGTTTTTT
28214623 AATAAAAAT-AATAAAAA
1 AATAAAAATAAATAAAAA
28214640 AATAAAAATAAATAAAAA
1 AATAAAAATAAATAAAAA
28214658 A
1 A
28214659 TGGTATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (18 bp):
AATAAAAATAAATAAAAA
Found at i:28215885 original size:24 final size:24
Alignment explanation
Indices: 28215852--28215900 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
28215842 CTTATTTTAT
*
28215852 GAAAATAGTGAAAACTTGAGTAAA
1 GAAAACAGTGAAAACTTGAGTAAA
28215876 GAAAACAGTGAAAACTTGAGTAAA
1 GAAAACAGTGAAAACTTGAGTAAA
28215900 G
1 G
28215901 TTTAAAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.18
Consensus pattern (24 bp):
GAAAACAGTGAAAACTTGAGTAAA
Found at i:28216864 original size:29 final size:29
Alignment explanation
Indices: 28216832--28216999 Score: 177
Period size: 29 Copynumber: 5.8 Consensus size: 29
28216822 TTTTGAATAC
28216832 TCGGGGGTAAAATGGTAATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTGGAAAGT
28216861 TCGGGGGTAAAATGGTAATTTTTGATGAAA--
1 TCGGGGGTAAAATGGTAA-TTTTG--GAAAGT
* *
28216891 TCGGGGTTAAAAATAG-AATTTTGGAAAGT
1 TCGGGGGT-AAAATGGTAATTTTGGAAAGT
*
28216920 TTGGGGGTAAAATGGTAATTTTTGATGAAA--
1 TCGGGGGTAAAATGGTAA-TTTTG--GAAAGT
* * *
28216950 TCGAGGTTAAAA-GGGAATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTGGAAAGT
28216978 TCGGGGGTAAAATGGTAATTTT
1 TCGGGGGTAAAATGGTAATTTT
28217000 CAAACAGTCC
Statistics
Matches: 114, Mismatches: 12, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
26 4 0.04
27 4 0.04
28 21 0.18
29 43 0.38
30 28 0.25
31 6 0.05
32 8 0.07
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTGGAAAGT
Found at i:28216911 original size:59 final size:58
Alignment explanation
Indices: 28216848--28216999 Score: 259
Period size: 59 Copynumber: 2.6 Consensus size: 58
28216838 GTAAAATGGT
* *
28216848 AATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATAG
1 AATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTT-AAAAGAG
* *
28216907 AATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAGGG
1 AATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAGAG
28216965 AATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
1 AATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
28217000 CAAACAGTCC
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
58 39 0.44
59 49 0.56
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (58 bp):
AATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAGAG
Found at i:28218858 original size:6 final size:6
Alignment explanation
Indices: 28218843--28218901 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
28218833 TTAAATTTGA
* * *
28218843 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT AAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
28218891 ATAAAT TTAAA
1 TTAAAT TTAAA
28218902 ACTCATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:28218877 original size:14 final size:14
Alignment explanation
Indices: 28218858--28218885 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28218848 CTTAAATTTA
28218858 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
28218872 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
28218886 TTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:28225294 original size:19 final size:17
Alignment explanation
Indices: 28225271--28225313 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
28225261 ATATATAAAT
28225271 TTATAAAAAAATGAAAAA
1 TTATAAAAAAAT-AAAAA
* *
28225289 TATATATAGAAATAAAAA
1 T-TATAAAAAAATAAAAA
28225307 TTATAAA
1 TTATAAA
28225314 TATATGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
TTATAAAAAAATAAAAA
Found at i:28231501 original size:3 final size:3
Alignment explanation
Indices: 28231495--28231526 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28231485 CAAGTAGTAT
28231495 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
28231527 TTCTCAGCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28238035 original size:19 final size:18
Alignment explanation
Indices: 28238000--28238035 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28237990 TTAACTTTCA
*
28238000 TCAAATTAACCCTAAAAC
1 TCAAATTAACACTAAAAC
28238018 TCAAATTAAACACTAAAA
1 TCAAATT-AACACTAAAA
28238036 AATTAACATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (18 bp):
TCAAATTAACACTAAAAC
Found at i:28255058 original size:90 final size:90
Alignment explanation
Indices: 28254944--28255118 Score: 248
Period size: 90 Copynumber: 1.9 Consensus size: 90
28254934 TCTCTTTTTT
* * *
28254944 TTTTTTGCACTCATTTGGGTACTTGAACTTTTAAAATACATCAAAAAAAACTC-TCAAA-TCTTT
1 TTTTTTACACTCAATTGAGTACTTGAACTTTTAAAATACATC-AAAAAAA-TCATCAAACT-TTT
28255007 TC-AAAAAAAGCAATTAAGCCCCCACTA
63 TCAAAAAAAAGCAATTAAGCCCCCACTA
*
28255034 TTTTTTACACTCAATTGAGTACTTGAACTTTTAAAATATATCAAAAAAATCATCAAACTTTTTCA
1 TTTTTTACACTCAATTGAGTACTTGAACTTTTAAAATACATCAAAAAAATCATCAAACTTTTTC-
28255099 AGAAAAAAAGCAATTAAGCC
65 A-AAAAAAAGCAATTAAGCC
28255119 ACTGCTTTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
88 2 0.03
89 17 0.22
90 39 0.51
92 18 0.24
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (90 bp):
TTTTTTACACTCAATTGAGTACTTGAACTTTTAAAATACATCAAAAAAATCATCAAACTTTTTCA
AAAAAAAGCAATTAAGCCCCCACTA
Found at i:28255210 original size:19 final size:19
Alignment explanation
Indices: 28255186--28255247 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
28255176 TAAATTTTAA
28255186 GAAAAAATATTAAAAATTG
1 GAAAAAATATTAAAAATTG
* *
28255205 GAAAAAGTA-TAAAAATCG
1 GAAAAAATATTAAAAATTG
* *
28255223 TAAAAAAATATAAAAAATTG
1 -GAAAAAATATTAAAAATTG
*
28255243 TAAAA
1 GAAAA
28255248 TTTTATTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 8 0.24
19 19 0.56
20 7 0.21
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.23
Consensus pattern (19 bp):
GAAAAAATATTAAAAATTG
Found at i:28255267 original size:38 final size:38
Alignment explanation
Indices: 28255187--28255276 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 38
28255177 AAATTTTAAG
*
28255187 AAAAAATATTAAAAATTGGAAAAAGTATAAAAATCGTA
1 AAAAAATATAAAAAATTGGAAAAAGTATAAAAATCGTA
* ** * *
28255225 AAAAAATATAAAAAATTGTAAAATTTTATTAAAATCTTA
1 AAAAAATATAAAAAATTGGAAAA-AGTATAAAAATCGTA
*
28255264 AAAAATTATAAAA
1 AAAAAATATAAAA
28255277 TATATAGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 21 0.48
39 23 0.52
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (38 bp):
AAAAAATATAAAAAATTGGAAAAAGTATAAAAATCGTA
Found at i:28255275 original size:10 final size:10
Alignment explanation
Indices: 28255223--28255375 Score: 67
Period size: 10 Copynumber: 16.1 Consensus size: 10
28255213 ATAAAAATCG
*
28255223 TAAAAAAATA
1 TAAAAAATTA
*
28255233 TAAAAAATTG
1 TAAAAAATTA
**
28255243 TAAAATTTTA
1 TAAAAAATTA
*
28255253 T-TAAAATCT-
1 TAAAAAAT-TA
28255262 TAAAAAATTA
1 TAAAAAATTA
*
28255272 TAAAATA-TA
1 TAAAAAATTA
*
28255281 T-AGAAA-TA
1 TAAAAAATTA
28255289 TAAAAAATTA
1 TAAAAAATTA
*
28255299 T--AAAATTT
1 TAAAAAATTA
* * **
28255307 TATAAAGTCG
1 TAAAAAATTA
28255317 TAAAAAATTA
1 TAAAAAATTA
*
28255327 TACAAAA-TA
1 TAAAAAATTA
28255336 TAAAGAAA-TA
1 TAAA-AAATTA
* *
28255346 T-AAAATTTG
1 TAAAAAATTA
28255355 TAAAAAATT-
1 TAAAAAATTA
28255364 TATAAAAATTA
1 TA-AAAAATTA
28255375 T
1 T
28255376 CGTACCAAAA
Statistics
Matches: 105, Mismatches: 26, Indels: 23
0.68 0.17 0.15
Matches are distributed among these distances:
8 15 0.14
9 23 0.22
10 66 0.63
11 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:28255328 original size:55 final size:57
Alignment explanation
Indices: 28255206--28255350 Score: 195
Period size: 56 Copynumber: 2.5 Consensus size: 57
28255196 TAAAAATTGG
* * * * *
28255206 AAAAAGTATAAAAATCGTAAAAAAATATAAAAAATTGTAAAATTTTATTAAAATCTTA
1 AAAAATTATAAAAAT-ATAAAGAAATATAAAAAATTATAAAATTTTATTAAAATCGTA
* *
28255264 AAAAATTAT-AAAATATATAGAAATATAAAAAATTATAAAATTTTA-TAAAGTCGTA
1 AAAAATTATAAAAATATAAAGAAATATAAAAAATTATAAAATTTTATTAAAATCGTA
28255319 AAAAATTATACAAAATATAAAGAAATATAAAA
1 AAAAATTATA-AAAATATAAAGAAATATAAAA
28255351 TTTGTAAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
55 17 0.22
56 27 0.35
57 25 0.32
58 8 0.10
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.30
Consensus pattern (57 bp):
AAAAATTATAAAAATATAAAGAAATATAAAAAATTATAAAATTTTATTAAAATCGTA
Found at i:28255366 original size:57 final size:56
Alignment explanation
Indices: 28255206--28255370 Score: 183
Period size: 57 Copynumber: 2.9 Consensus size: 56
28255196 TAAAAATTGG
* * * *
28255206 AAAAAGTATAAAAATCGTAAAAAAATATAAAAAATTGT-AAAATTTTATTAAAATCTTA
1 AAAAATTATAAAAAT-ATAAAGAAATAT-AAAAATTGTAAAAATTTTA-TAAAATCGTA
* * *
28255264 AAAAATTAT-AAAATATATAGAAATATAAAAAAT-TATAAAATTTTATAAAGTCGTA
1 AAAAATTATAAAAATATAAAGAAATATAAAAATTGTA-AAAATTTTATAAAATCGTA
* *
28255319 AAAAATTATACAAAATATAAAGAAATATAAAATTTGTAAAAAATTTATAAAA
1 AAAAATTATA-AAAATATAAAGAAATATAAAAATTGTAAAAATTTTATAAAA
28255371 ATTATCGTAC
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
54 1 0.01
55 23 0.26
56 18 0.20
57 38 0.42
58 10 0.11
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (56 bp):
AAAAATTATAAAAATATAAAGAAATATAAAAATTGTAAAAATTTTATAAAATCGTA
Found at i:28255681 original size:34 final size:33
Alignment explanation
Indices: 28255627--28255702 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 33
28255617 TATAAAAAAA
* ** *
28255627 TTAAATTTTAAATAAATTTTAATTTTTTTTTTT
1 TTAAAATTTAAATAAATTTTAAAATTTATTTTT
28255660 TTAAAATTT-AATAAATTTTTTAAAATTTATTTTT
1 TTAAAATTTAAATAAA--TTTTAAAATTTATTTTT
*
28255694 TTATAATTT
1 TTAAAATTT
28255703 TTTAATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 6 0.17
33 8 0.22
34 22 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (33 bp):
TTAAAATTTAAATAAATTTTAAAATTTATTTTT
Found at i:28256166 original size:6 final size:6
Alignment explanation
Indices: 28256155--28256183 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28256145 CTCCCATCCT
28256155 CCCTTC CCCTTC CCCTTC CCCTTC CCCTT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTT
28256184 TCCATTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCCTTC
Found at i:28264355 original size:2 final size:2
Alignment explanation
Indices: 28264348--28264373 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28264338 TGTCCATACC
28264348 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
28264374 GTTTAAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28267942 original size:21 final size:21
Alignment explanation
Indices: 28267926--28268008 Score: 112
Period size: 21 Copynumber: 3.9 Consensus size: 21
28267916 ACAAAAACAG
28267926 CACCAAAACAATAAAAAAAAA
1 CACCAAAACAATAAAAAAAAA
*
28267947 CACCAAAACAATAAAAAATAA
1 CACCAAAACAATAAAAAAAAA
* **
28267968 CACAAAAACAGCAAAAAAAAA
1 CACCAAAACAATAAAAAAAAA
*
28267989 CAACCAAAACACTAAAAAAA
1 C-ACCAAAACAATAAAAAAA
28268009 CAGCACAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 38 0.72
22 15 0.28
ACGTcount: A:0.73, C:0.20, G:0.01, T:0.05
Consensus pattern (21 bp):
CACCAAAACAATAAAAAAAAA
Found at i:28268017 original size:21 final size:21
Alignment explanation
Indices: 28267918--28268018 Score: 91
Period size: 21 Copynumber: 4.7 Consensus size: 21
28267908 AAATAGCAAC
*
28267918 AAAAACAGCACCAAAACAATAA
1 AAAAACAACA-CAAAACAATAA
28267940 AAAAA-AACACCAAAACAAT-A
1 AAAAACAACA-CAAAACAATAA
* *
28267960 AAAAATAACACAAAAACAGCAAAA
1 AAAAACAACAC-AAAACA--ATAA
*
28267984 AAAAACAAC-CAAAACACTAA
1 AAAAACAACACAAAACAATAA
*
28268004 AAAAACAGCACAAAA
1 AAAAACAACACAAAA
28268019 ATAACAATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
20 17 0.25
21 28 0.42
22 11 0.16
23 2 0.03
24 9 0.13
ACGTcount: A:0.72, C:0.21, G:0.03, T:0.04
Consensus pattern (21 bp):
AAAAACAACACAAAACAATAA
Found at i:28268509 original size:14 final size:14
Alignment explanation
Indices: 28268490--28268517 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28268480 ATTTTCAAAC
28268490 TTTAATTAATTAAT
1 TTTAATTAATTAAT
28268504 TTTAATTAATTAAT
1 TTTAATTAATTAAT
28268518 AATTCAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATTAATTAAT
Found at i:28270362 original size:19 final size:19
Alignment explanation
Indices: 28270334--28270403 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
28270324 TAATATTTTC
28270334 AAAATATTTTTAGTTGAGG
1 AAAATATTTTTAGTTGAGG
* *
28270353 AAAATCTTTTGACTGTTGCA-G
1 AAAATATTTTTA--GTTG-AGG
*
28270374 AAAATATTTTTAGTTGAGA
1 AAAATATTTTTAGTTGAGG
*
28270393 AAAATCTTTTT
1 AAAATATTTTT
28270404 TATTTTTGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
18 1 0.02
19 24 0.59
21 15 0.37
22 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.43
Consensus pattern (19 bp):
AAAATATTTTTAGTTGAGG
Found at i:28271408 original size:19 final size:18
Alignment explanation
Indices: 28271353--28271408 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
28271343 TTTAAATAAA
*
28271353 TTAAAAAATTAGAGAAAAT
1 TTAAAAAAATA-AGAAAAT
*
28271372 TTAAAAAAAGGTCAA-AAACT
1 TTAAAAAAA--T-AAGAAAAT
28271392 TTAAAAAAATAAGAAAA
1 TTAAAAAAATAAGAAAA
28271409 ATTATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
17 2 0.07
18 4 0.13
19 8 0.27
20 13 0.43
21 2 0.07
22 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.09, T:0.21
Consensus pattern (18 bp):
TTAAAAAAATAAGAAAAT
Found at i:28275796 original size:20 final size:20
Alignment explanation
Indices: 28275756--28275792 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28275746 AATATTTTTC
28275756 ACAAAATTCAGAAATTAATA
1 ACAAAATTCAGAAATTAATA
*
28275776 ACAAAATTTA-AAATTAA
1 ACAAAATTCAGAAATTAA
28275793 ATAAACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (20 bp):
ACAAAATTCAGAAATTAATA
Found at i:28276933 original size:65 final size:65
Alignment explanation
Indices: 28276829--28276963 Score: 261
Period size: 65 Copynumber: 2.1 Consensus size: 65
28276819 ACCGCATCAC
28276829 AACCGTCGACTAGGACCTCCACCCGGATTTCGACCCCTGATCGTATAGAGCACTGTCGCCCCCAA
1 AACCGTCGACTAGGACCTCCACCCGGATTTCGACCCCTGATCGTATAGAGCACTGTCGCCCCCAA
*
28276894 AACCGTCGACTAGGACCTCCACCTGGATTTCGACCCCTGATCGTATAGAGCACTGTCGCCCCCAA
1 AACCGTCGACTAGGACCTCCACCCGGATTTCGACCCCTGATCGTATAGAGCACTGTCGCCCCCAA
28276959 AACCG
1 AACCG
28276964 AATTTCTCCA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.24, C:0.38, G:0.20, T:0.19
Consensus pattern (65 bp):
AACCGTCGACTAGGACCTCCACCCGGATTTCGACCCCTGATCGTATAGAGCACTGTCGCCCCCAA
Found at i:28277765 original size:21 final size:21
Alignment explanation
Indices: 28277741--28277784 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28277731 TTAAACCCAT
28277741 AAAAT-TAAATCTAAACTAAAA
1 AAAATCTAAA-CTAAACTAAAA
* *
28277762 AAAATCTAAACTCAATTAAAA
1 AAAATCTAAACTAAACTAAAA
28277783 AA
1 AA
28277785 TAAACAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATCTAAACTAAACTAAAA
Found at i:28281249 original size:2 final size:2
Alignment explanation
Indices: 28281244--28281287 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
28281234 TTTTATTTAA
*
28281244 AT AT AT AT AT AT AT AT AT AT TT AT A- AT -T AT AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28281282 AT AT AT
1 AT AT AT
28281288 TTGTACCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:28281288 original size:12 final size:12
Alignment explanation
Indices: 28281243--28281288 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
28281233 TTTTTATTTA
28281243 AATATATATATAT
1 AATATAT-TATAT
28281256 ATATATATT-TAT
1 A-ATATATTATAT
28281268 AATTATATTATAT
1 AA-TATATTATAT
28281281 AATATATT
1 AATATATT
28281289 TGTACCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.03
12 16 0.53
13 7 0.23
14 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATATTATAT
Found at i:28281463 original size:9 final size:9
Alignment explanation
Indices: 28281449--28281477 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
28281439 TCGAATAACA
28281449 AATGCGACT
1 AATGCGACT
28281458 AATGCGACT
1 AATGCGACT
28281467 AATGCGACT
1 AATGCGACT
28281476 AA
1 AA
28281478 AACACAGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (9 bp):
AATGCGACT
Found at i:28281605 original size:22 final size:22
Alignment explanation
Indices: 28281571--28281613 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28281561 GTGCTCTAAT
* * *
28281571 AAAAAATATAAATATTTAATTA
1 AAAAAACACAAATATTAAATTA
28281593 AAAAAACACAAATATTAAATT
1 AAAAAACACAAATATTAAATT
28281614 GATCATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAACACAAATATTAAATTA
Found at i:28284845 original size:16 final size:16
Alignment explanation
Indices: 28284821--28284851 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28284811 GTTGTTGTAA
*
28284821 GTAGTTAATAATATTG
1 GTAGATAATAATATTG
28284837 GTAGATAATAATATT
1 GTAGATAATAATATT
28284852 TTATTATCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (16 bp):
GTAGATAATAATATTG
Found at i:28303472 original size:5 final size:5
Alignment explanation
Indices: 28303462--28303491 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
28303452 GCTGTTGTAG
28303462 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
28303492 ATCCTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:28309407 original size:19 final size:21
Alignment explanation
Indices: 28309383--28309424 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28309373 TTTTAATCTA
*
28309383 TTATAA-TTTAT-TGATTTTT
1 TTATAATTTTATGTAATTTTT
28309402 TTATAATTTTATGTAATTTTT
1 TTATAATTTTATGTAATTTTT
28309423 TT
1 TT
28309425 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TTATAATTTTATGTAATTTTT
Found at i:28312220 original size:15 final size:16
Alignment explanation
Indices: 28312200--28312229 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28312190 AACTTGGAAT
28312200 TTTGGATTTT-AAAAC
1 TTTGGATTTTCAAAAC
28312215 TTTGGATTTTCAAAA
1 TTTGGATTTTCAAAA
28312230 TCAAAGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (16 bp):
TTTGGATTTTCAAAAC
Found at i:28317023 original size:2 final size:2
Alignment explanation
Indices: 28317016--28317055 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28317006 TTAAGCATAC
28317016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28317056 CATCTTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28318733 original size:20 final size:21
Alignment explanation
Indices: 28318708--28318752 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
28318698 CGGGGCTGTC
28318708 TTTTTA-TGTTTTGATTGCTA
1 TTTTTATTGTTTTGATTGCTA
* *
28318728 TTTTTATTGTTTTGGTTGTTA
1 TTTTTATTGTTTTGATTGCTA
28318749 TTTT
1 TTTT
28318753 GTTTTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.11, C:0.02, G:0.16, T:0.71
Consensus pattern (21 bp):
TTTTTATTGTTTTGATTGCTA
Found at i:28318759 original size:27 final size:27
Alignment explanation
Indices: 28318728--28318780 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28318718 TTGATTGCTA
* * *
28318728 TTTTTATTGTTTTGGTTGTTATTTTGT
1 TTTTTACTATTTTGATTGTTATTTTGT
28318755 TTTTTACTATTTTGATTGTTATTTTG
1 TTTTTACTATTTTGATTGTTATTTTG
28318781 GTTCTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.11, C:0.02, G:0.15, T:0.72
Consensus pattern (27 bp):
TTTTTACTATTTTGATTGTTATTTTGT
Found at i:28318790 original size:23 final size:23
Alignment explanation
Indices: 28318764--28318826 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 23
28318754 TTTTTTACTA
*
28318764 TTTTGATTGTTATTTTGGTTCTG
1 TTTTTATTGTTATTTTGGTTCTG
* *
28318787 TTTTTACTG---TTTTGGTGCTG
1 TTTTTATTGTTATTTTGGTTCTG
28318807 TTTTTATTGTTATTTTGGTT
1 TTTTTATTGTTATTTTGGTT
28318827 GTTATTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 18 0.56
23 14 0.44
ACGTcount: A:0.08, C:0.05, G:0.21, T:0.67
Consensus pattern (23 bp):
TTTTTATTGTTATTTTGGTTCTG
Found at i:28318839 original size:33 final size:33
Alignment explanation
Indices: 28318802--28318871 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
28318792 ACTGTTTTGG
**
28318802 TGCTGTT-TTTATTGTTATTTTGGTTGTTATTTT
1 TGCTGTTATTTATTGTTATTTT-CCTGTTATTTT
* *
28318835 TGCTGTTATTTTTTGTTGTTTTCCTGTTATTTT
1 TGCTGTTATTTATTGTTATTTTCCTGTTATTTT
28318868 TGCT
1 TGCT
28318872 ACTATTTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 20 0.62
34 12 0.38
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (33 bp):
TGCTGTTATTTATTGTTATTTTCCTGTTATTTT
Found at i:28318847 original size:13 final size:12
Alignment explanation
Indices: 28318814--28318892 Score: 65
Period size: 12 Copynumber: 6.8 Consensus size: 12
28318804 CTGTTTTTAT
* *
28318814 TGTTATTTTGGT
1 TGTTATTTTTGC
28318826 TGTTATTTTTGC
1 TGTTATTTTTGC
28318838 TGTTATTTTT--
1 TGTTATTTTTGC
* *
28318848 TGTT-GTTTTCC
1 TGTTATTTTTGC
28318859 TGTTATTTTTGC
1 TGTTATTTTTGC
** * *
28318871 TACTATTTTGGT
1 TGTTATTTTTGC
28318883 TGTTATTTTT
1 TGTTATTTTT
28318893 TTATGCATTT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
9 4 0.08
10 4 0.08
11 4 0.08
12 40 0.77
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.68
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:28318861 original size:21 final size:22
Alignment explanation
Indices: 28318814--28318868 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
28318804 CTGTTTTTAT
* *
28318814 TGTTATTTTGGTTGTTATTTTTGC
1 TGTTATTTT--TTGTTAGTTTTCC
28318838 TGTTATTTTTTGTT-GTTTTCC
1 TGTTATTTTTTGTTAGTTTTCC
28318859 TGTTATTTTT
1 TGTTATTTTT
28318869 GCTACTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.52
22 5 0.17
24 9 0.31
ACGTcount: A:0.07, C:0.05, G:0.16, T:0.71
Consensus pattern (22 bp):
TGTTATTTTTTGTTAGTTTTCC
Found at i:28319052 original size:12 final size:12
Alignment explanation
Indices: 28319035--28319066 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
28319025 TTGATTATTT
28319035 TTTTAATGTTTG
1 TTTTAATGTTTG
28319047 TTTTAATGTTTG
1 TTTTAATGTTTG
28319059 TTTTAATG
1 TTTTAATG
28319067 CTTTTAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.66
Consensus pattern (12 bp):
TTTTAATGTTTG
Found at i:28321844 original size:29 final size:27
Alignment explanation
Indices: 28321794--28321868 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 27
28321784 TAGTCTAATC
*
28321794 ATTATATTAAACTTTTATTTTTGGAATAA
1 ATTAT-TTAAA-TTTTATTTTTAGAATAA
*
28321823 TTTATTTAAATTTCTACTTTTTAGAATAA
1 ATTATTTAAATTT-TA-TTTTTAGAATAA
28321852 ATTATTTAAATTTTATT
1 ATTATTTAAATTTTATT
28321869 GATAGGAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.12
28 9 0.22
29 27 0.66
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (27 bp):
ATTATTTAAATTTTATTTTTAGAATAA
Found at i:28325086 original size:14 final size:14
Alignment explanation
Indices: 28325067--28325097 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28325057 AATTAAAACT
28325067 AAAGTCCATTTACA
1 AAAGTCCATTTACA
28325081 AAAGTCCATTTACA
1 AAAGTCCATTTACA
28325095 AAA
1 AAA
28325098 AAGAAAGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (14 bp):
AAAGTCCATTTACA
Found at i:28327061 original size:29 final size:30
Alignment explanation
Indices: 28327015--28327115 Score: 79
Period size: 29 Copynumber: 3.5 Consensus size: 30
28327005 TAGACTATCA
*
28327015 AAAATTACTATTTT-ACCCTCGAACTTCCC
1 AAAATTACCATTTTAACCCTCGAACTTCCC
**
28327044 AAAATT-CCATTTTAACCC-CG-GTTTCACC
1 AAAATTACCATTTTAACCCTCGAACTTC-CC
* * *
28327072 AAAAATTACCATCTTACCCCT-AAACTTTCCC
1 -AAAATTACCATTTTAACCCTCGAAC-TTCCC
28327103 AAAATT-CCATTTT
1 AAAATTACCATTTT
28327116 TGACCTCGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
27 3 0.05
28 10 0.18
29 22 0.39
30 16 0.29
31 2 0.04
32 3 0.05
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCTCGAACTTCCC
Found at i:28330191 original size:59 final size:59
Alignment explanation
Indices: 28329985--28330410 Score: 596
Period size: 59 Copynumber: 7.3 Consensus size: 59
28329975 TACCCGGGGC
* * * *
28329985 AAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAAGATTTAGGGG-T
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-AGAAG-TTTCGGGGAT
* * * *
28330045 AAAATGGTAATTTTCGATGAAATCGAGGTTAAAAATAGAATTTTAGAA-TCTTCGGGG-T
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGT-TTCGGGGAT
* * *
28330103 AAAATGGTAATTTTTGATGAAATCAGGGTTAAAAATGGAATTTTGGAAGTTTCGGGGAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGGGGAT
* *
28330162 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAGTTTCGGGGAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGGGGAT
* *
28330221 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTT--GGGAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGGGGAT
28330278 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA-AAGTTTCGGGGAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGGGGAT
* * * *
28330336 AAAATGGTAA-TTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATTCAGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTC-GGGGAT
28330395 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
28330411 AAAGTTTTGG
Statistics
Matches: 337, Mismatches: 21, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
56 6 0.02
57 82 0.24
58 78 0.23
59 126 0.37
60 45 0.13
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTTCGGGGAT
Found at i:28330442 original size:29 final size:30
Alignment explanation
Indices: 28330402--28330501 Score: 159
Period size: 30 Copynumber: 3.3 Consensus size: 30
28330392 GGTAAAATGG
*
28330402 TAATTTTTG-AAAGTTTTG-GGATCAAAATA
1 TAATTTTGGAAAAGTTTTGAGG-TCAAAATA
28330431 TAATTTTGGAAAAGTTTTGAGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGAGGTCAAAATA
28330461 TAATTTTGGAAAAGTTTTGAGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGAGGTCAAAATA
28330491 TAATTTCTGGA
1 TAATTT-TGGA
28330502 TTGTTTGGGG
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
29 8 0.12
30 53 0.79
31 6 0.09
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTTGAGGTCAAAATA
Found at i:28332294 original size:22 final size:22
Alignment explanation
Indices: 28332259--28332314 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
28332249 TTATAATAAT
28332259 ATTAAATTTTAAATT-AATTCAA
1 ATTAAA-TTTAAATTGAATTCAA
*
28332281 ATTTAAATTTAAATTGAATTTAA
1 A-TTAAATTTAAATTGAATTCAA
*
28332304 AGTAAATTTAA
1 ATTAAATTTAA
28332315 GATAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTAAATTTAAATTGAATTCAA
Found at i:28332301 original size:11 final size:11
Alignment explanation
Indices: 28332259--28332314 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
28332249 TTATAATAAT
28332259 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
28332271 ATT-AATTCAA
1 ATTAAATTTAA
28332281 ATTTAAATTTAA
1 A-TTAAATTTAA
*
28332293 ATTGAATTTAA
1 ATTAAATTTAA
*
28332304 AGTAAATTTAA
1 ATTAAATTTAA
28332315 GATAAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
10 5 0.14
11 22 0.59
12 10 0.27
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:28332693 original size:38 final size:38
Alignment explanation
Indices: 28332642--28332923 Score: 211
Period size: 38 Copynumber: 7.4 Consensus size: 38
28332632 CTATCCAACT
28332642 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTC
* * ** * * *
28332680 TTACTTCAATTTC-AGAAAGATAAAGACTTGAT-ATCCAAC
1 TTACTTCAATTTCAAG-AGGAT-AGGAAATGATCTTGC-TC
*
28332719 TTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
1 -TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTC
* ** * * *
28332758 TTACTTCAATTTC-AGA-GATAAAGACTTGAT-ATCCAAC
1 TTACTTCAATTTCAAGAGGAT-AGGAAATGATCTTGC-TC
* *
28332795 TTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTACTC
1 -TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTC
* ** **
28332834 TTACTTCAATTTC-AGA-GATAAAGACTTGATATCCAGCT-
1 TTACTTCAATTTCAAGAGGAT-AGGAAATG--ATCTTGCTC
* *
28332872 TTACTTCAATTTCAAGAGAATAGGAAAAGATCTTGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTC
28332910 TTACTTCAATTTCA
1 TTACTTCAATTTCA
28332924 GATATAAAGA
Statistics
Matches: 183, Mismatches: 43, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
36 8 0.04
37 25 0.14
38 85 0.46
39 37 0.20
40 26 0.14
41 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (38 bp):
TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTC
Found at i:28333048 original size:68 final size:68
Alignment explanation
Indices: 28332904--28333930 Score: 1632
Period size: 68 Copynumber: 15.0 Consensus size: 68
28332894 GGAAAAGATC
* * * *
28332904 TTGCTCTTACTTCAATTTCAGATATAAAGACTTGATATCCAGCTTTACTTCAA-TTCAAGAGGG-
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAG-GGGA
*
28332967 TGACA
64 TGACG
* * * *
28332972 TTGCTCTTATTTCAATTTCAGAGGTAAAGATGTGTTATCCACTCTACTTCAATTT-GAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
28333036 ACG
66 ACG
*
28333039 TTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-GGGAT
1 TTGC-TCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
*
28333103 GACA
65 GACG
*
28333107 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
28333172 ACA
66 ACG
* * *
28333175 TTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
28333240 GACG
65 GACG
* *
28333244 TTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
28333309 GACG
65 GACG
* * *
28333313 TTGCTCTTACTTCAATTTCAGAAATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
28333378 ACG
66 ACG
*
28333381 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
28333446 ACG
66 ACG
28333449 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
28333514 ACG
66 ACG
* *
28333517 TTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
28333582 GACG
65 GACG
* *
28333586 TTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAA-GGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
28333650 GACG
65 GACG
* * *
28333654 TTGCTCTTACTTCAATTTCAGAAATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
28333719 ACG
66 ACG
* *
28333722 TTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
28333787 GACG
65 GACG
* * *
28333791 TTGCTCTTACTTCAATTTCAGAAATAAAAGATGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGAT-AAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
28333856 GACG
65 GACG
28333860 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
28333925 ACG
66 ACG
28333928 TTG
1 TTG
28333931 AGACCTGCAG
Statistics
Matches: 901, Mismatches: 48, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
66 3 0.00
67 92 0.10
68 474 0.53
69 320 0.36
70 12 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (68 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
ACG
Found at i:28333351 original size:273 final size:273
Alignment explanation
Indices: 28332596--28333926 Score: 1790
Period size: 273 Copynumber: 4.7 Consensus size: 273
28332586 AGGCTTCATC
* * * *
28332596 TTGCTTTTACTTCAATTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGG
1 TTGCTCTTACTTCAATTTC--AGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGG
* * *
28332661 ATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAAAGATAAAGACTTGATATCCAACTTTACTT
64 AT--G--ACG---TTGCTCTTACTTCAATTTCAG--AGATAAAGACGTGATATCCAACTCTACTT
* * * *
28332726 CAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATC
120 CAATTTCAAGGGGAT--G--ACG---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATC
* * *
28332791 CAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTACTCTTACTTCAATTTCAGAGATAAA
178 C-ACTCTACTTCAATTTCAAG-GGAT--G---ACA--TTGCTCTTACTTCAATTTCAGAGATAAA
* * * * *
28332856 GACTTGATATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAAG
234 GACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGAT--G--ACG
* * * *
28332901 ATCTTGCTCTTACTTCAATTTCAGATATAAAGACTTGATATCCAGCTTTACTTCAA-TTCAAGAG
1 ---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAG
* * * * * * *
28332965 GGTGACATTGCTCTTATTTCAATTTCAGAGGTAAAGATGTGTTATCC-ACTCTACTTCAATTT-G
63 GATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCA
*
28333028 AGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAAT
128 AGGGGATGACGTTGC-TCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
*
28333093 TTCAAGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCA
192 TTCAAGGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCA
* *
28333158 ATTTCAAGGGGATGACA
257 ATTTCAAGAGGATGACG
*
28333175 TTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
*
28333240 GACGTTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGG
66 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGG
* *
28333305 GGATGACGTTGCTCTTACTTCAATTTCAGAAATAAAGATGTGTTATCCACTCTACTTCAATTTCA
131 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
*
28333370 AGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATT
196 AG-GGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATT
28333435 TCAAGAGGATGACG
260 TCAAGAGGATGACG
* *
28333449 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
*
28333513 GACGTTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGG
66 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGG
* *
28333578 GGATGACGTTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTC
131 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTC
* * *
28333643 AAGGGATGACGTTGCTCTTACTTCAATTTCAGAAATAAAGATGTGTTATCCACTCTACTTCAATT
195 AAGGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATT
28333708 TCAAGAGGATGACG
260 TCAAGAGGATGACG
* *
28333722 TTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
* * *
28333787 GACGTTGCTCTTACTTCAATTTCAGAAATAAAAGATGTGTTATCC-ACTCTACTTCAATTTCAAG
66 GACGTTGCTCTTACTTCAATTTCAGAGAT-AAAGACGTGATATCCAACTCTACTTCAATTTCAAG
*
28333851 AGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTC
130 GGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTC
28333916 AAGGGGATGAC
195 AA-GGGATGAC
28333927 GTTGAGACCT
Statistics
Matches: 946, Mismatches: 68, Indels: 52
0.89 0.06 0.05
Matches are distributed among these distances:
271 48 0.05
272 48 0.05
273 329 0.35
274 270 0.29
275 12 0.01
276 1 0.00
278 20 0.02
279 37 0.04
281 2 0.00
284 1 0.00
286 4 0.00
287 22 0.02
288 33 0.03
290 2 0.00
292 1 0.00
294 6 0.01
295 14 0.01
296 15 0.02
298 20 0.02
301 1 0.00
303 1 0.00
305 10 0.01
306 31 0.03
308 18 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (273 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGG
GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
AGGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTT
CAAGAGGATGACG
Found at i:28333445 original size:205 final size:206
Alignment explanation
Indices: 28332596--28333930 Score: 1783
Period size: 205 Copynumber: 6.3 Consensus size: 206
28332586 AGGCTTCATC
* * * *
28332596 TTGCTTTTACTTCAATTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGG
1 TTGCTCTTACTTCAATTTC--AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTC-A-AGG
* *
28332661 ATAGGAAATGATC-TTGCTCTTACTTCAATTTCAGAAAGATAAAGACTTGATATCCAACTTTACT
61 ---GG--ATGA-CGTTGCTCTTACTTCAATTTCAG--AGATAAAGACGTGATATCCAACTCTACT
* *
28332725 TCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATAT
118 TCAATTTCAAGAGGAT--G--ACG---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATAT
* *
28332790 CCAACTTTACTTCAATTTCAAGAGGATAGGAAAAG
176 CCAACTCTACTTCAATTTCAAGAGGAT--G--ACG
* * * *
28332825 ATCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAG-G
* * * * *
28332890 AATAGGAAAAGATC-TTGCTCTTACTTCAATTTCAGATATAAAGACTTGATATCCAGCTTTACTT
61 ----GG--ATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTT
* * * * * *
28332954 CAA-TTCAAGAGGGTGACATTGCTCTTATTTCAATTTCAGAGGTAAAGATGTGTTATCC-ACTCT
119 CAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCT
* *
28333017 ACTTCAATTT-GAGGGGATGACG
184 ACTTCAATTTCAAGAGGATGACG
*
28333039 TTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-GGGAT
1 TTGC-TCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
* * * *
28333103 GACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGG
65 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGA
* *
28333167 GGATGACATTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTC
130 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTC
28333232 AAGAGGATGACG
195 AAGAGGATGACG
* *
28333244 TTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
* * *
28333309 GACGTTGCTCTTACTTCAATTTCAGAAATAAAGATGTGTTATCC-ACTCTACTTCAATTTCAAGA
65 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGA
*
28333373 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTC
130 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTC
28333437 AAGAGGATGACG
195 AAGAGGATGACG
28333449 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* *
28333514 ACGTTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGGG
66 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAG
*
28333579 GATGACGTTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCA
131 GATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCA
28333644 AG-GGATGACG
196 AGAGGATGACG
* * *
28333654 TTGCTCTTACTTCAATTTCAGAAATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* *
28333719 ACGTTGCTCTTACTTCAATTTCAGAGATTAAGACGTGATATCCAACTCTACTTCAATTTCAAGGG
66 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAG
* * *
28333784 GATGACGTTGCTCTTACTTCAATTTCAGAAATAAAAGATGTGTTATCC-ACTCTACTTCAATTTC
131 GATGACGTTGCTCTTACTTCAATTTCAGAGAT-AAAGACGTGATATCCAACTCTACTTCAATTTC
28333848 AAGAGGATGACG
195 AAGAGGATGACG
28333860 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
28333925 ACGTTG
66 ACGTTG
28333931 AGACCTGCAG
Statistics
Matches: 1021, Mismatches: 68, Indels: 54
0.89 0.06 0.05
Matches are distributed among these distances:
202 11 0.01
203 87 0.09
204 113 0.11
205 350 0.34
206 216 0.21
209 1 0.00
211 19 0.02
212 34 0.03
214 2 0.00
216 1 0.00
218 6 0.01
219 14 0.01
220 35 0.03
223 1 0.00
225 1 0.00
227 10 0.01
228 32 0.03
229 3 0.00
230 68 0.07
232 17 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (206 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAG
GATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCA
AGAGGATGACG
Found at i:28345809 original size:6 final size:6
Alignment explanation
Indices: 28345800--28345890 Score: 54
Period size: 6 Copynumber: 15.8 Consensus size: 6
28345790 ACTTTTCTTT
*
28345800 TTTAAA TTTATAA --TAATA TT-AAA TTTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA
* * *
28345847 TTTAAA -TTGAA TTTAAA -GTAAA TTTAAGA -TTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
28345891 TTTTCAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
4 1 0.02
5 23 0.35
6 36 0.55
7 6 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:28345844 original size:17 final size:16
Alignment explanation
Indices: 28345801--28345893 Score: 73
Period size: 17 Copynumber: 5.5 Consensus size: 16
28345791 CTTTTCTTTT
28345801 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
28345818 TTAAATTTTAAATTAAA
1 TTAAA-TTTAAATTAAA
28345835 TTCAAATTTAAATTTAAA
1 TT-AAATTTAAA-TTAAA
* *
28345853 TTGAATTTAAAGTAAA
1 TTAAATTTAAATTAAA
*
28345869 TTTAAGA-TTAAAATAAA
1 -TTAA-ATTTAAATTAAA
*
28345886 TTTAATTT
1 TTAAATTT
28345894 TCAAATGGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.02
16 9 0.14
17 36 0.56
18 18 0.28
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:28345859 original size:11 final size:11
Alignment explanation
Indices: 28345817--28345893 Score: 75
Period size: 11 Copynumber: 6.8 Consensus size: 11
28345807 TTATAATAAT
28345817 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
28345829 ATTAAATTCAA
1 ATTAAATTTAA
28345840 ATTTAAATTTAA
1 A-TTAAATTTAA
*
28345852 ATTGAATTTAA
1 ATTAAATTTAA
*
28345863 AGTAAATTTAA
1 ATTAAATTTAA
*
28345874 GATTAAA-ATAA
1 -ATTAAATTTAA
*
28345885 ATTTAATTT
1 ATTAAATTT
28345894 TCAAATGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.09
11 27 0.51
12 21 0.40
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:28347055 original size:17 final size:15
Alignment explanation
Indices: 28347014--28347055 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
28347004 TTTTAAAAAT
28347014 ATTTATATTATTTTAA
1 ATTTATA-TATTTTAA
28347030 ATTTA-ATATTTAATAA
1 ATTTATATATTT--TAA
28347046 ATTTATATAT
1 ATTTATATAT
28347056 ATTTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 1 0.04
16 13 0.57
17 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATATATTTTAA
Found at i:28347973 original size:24 final size:24
Alignment explanation
Indices: 28347926--28347973 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28347916 AATATTATAA
28347926 TTTTATTTTAAATTTAAATATAATG
1 TTTTATTTTAAA-TTAAATATAATG
*
28347951 TTTTCATTTTAAA-TAAATCTAAT
1 TTTT-ATTTTAAATTAAATATAAT
28347974 TACCTCGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 4 0.19
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTATTTTAAATTAAATATAATG
Found at i:28355624 original size:7 final size:7
Alignment explanation
Indices: 28355612--28355638 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28355602 ATGTTCTTTA
28355612 AAAATTT
1 AAAATTT
28355619 AAAATTT
1 AAAATTT
28355626 AAAATTT
1 AAAATTT
28355633 AAAATT
1 AAAATT
28355639 AATAATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:28361801 original size:43 final size:43
Alignment explanation
Indices: 28361738--28361871 Score: 225
Period size: 43 Copynumber: 3.1 Consensus size: 43
28361728 CGCTAAAGAT
**
28361738 AACGCCGCTAAAGAACATGGTCTTTAGCGATGCTTTTCCCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
*
28361781 ATCGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
*
28361824 AACGCCACTAAA-AACATGGTCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
28361866 AACGCC
1 AACGCC
28361872 ACTACAATTA
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
42 36 0.42
43 50 0.58
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
Found at i:28365964 original size:41 final size:41
Alignment explanation
Indices: 28365860--28366062 Score: 239
Period size: 41 Copynumber: 5.0 Consensus size: 41
28365850 ATTATTACAC
** * * *
28365860 TGACCTTTAGCGGCGCTTTTTCATAAGCGTCGGTATTG-TT
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTA
28365900 TGACCTTTAGCGGCG-TTTGCCCATAAGCGCCGCTATTGCTA
1 TGACCTTTAGCGGCGCTTT-CCCATAAGCGCCGCTATTGCTA
* *
28365941 TGATCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGATA
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTA
* ** * * * *
28365982 TGATCTTTAGTAGCGCTTTTCCATAAACACCGCTATTGCTC
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTA
* *
28366023 TAACCTTTAGCGGCGCTTTCCCATAAGCGCCACTATTGCT
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCT
28366063 TTACTTTTTG
Statistics
Matches: 138, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 3 0.02
40 30 0.22
41 102 0.74
42 3 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (41 bp):
TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTA
Found at i:28366131 original size:41 final size:40
Alignment explanation
Indices: 28366050--28366124 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
28366040 TTCCCATAAG
** *
28366050 CGCCACTATTGCTTTACTTTTTGCGTTGTTTATGTAAAAA
1 CGCCACTATTGCTTTACTTTTTGCGGCGTTTATCTAAAAA
28366090 CGCCACTATTGCTTTA-TCTTTTGCGGCGTTT-TCTA
1 CGCCACTATTGCTTTACT-TTTTGCGGCGTTTATCTA
28366125 TCAAAACACC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.45
Consensus pattern (40 bp):
CGCCACTATTGCTTTACTTTTTGCGGCGTTTATCTAAAAA
Found at i:28372766 original size:7 final size:7
Alignment explanation
Indices: 28372754--28372779 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28372744 TTATTTTTTT
28372754 TTTCTAC
1 TTTCTAC
28372761 TTTCTAC
1 TTTCTAC
28372768 TTTCTAC
1 TTTCTAC
28372775 TTTCT
1 TTTCT
28372780 TTTTCTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTCTAC
Found at i:28373100 original size:16 final size:19
Alignment explanation
Indices: 28373074--28373111 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
28373064 GTTGAACCGA
28373074 TTTTTTCTATTT-T-AAAG
1 TTTTTTCTATTTATGAAAG
28373091 TTTTTT-TATTTATGAAAG
1 TTTTTTCTATTTATGAAAG
28373109 TTT
1 TTT
28373112 AATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 7 0.37
18 7 0.37
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.66
Consensus pattern (19 bp):
TTTTTTCTATTTATGAAAG
Found at i:28380813 original size:21 final size:21
Alignment explanation
Indices: 28380789--28380831 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28380779 TTGCTCAAAT
*
28380789 TTGA-ATATTATAAAGATTAAA
1 TTGACATATT-TAAAGACTAAA
*
28380810 TTGACCTATTTAAAGACTAAA
1 TTGACATATTTAAAGACTAAA
28380831 T
1 T
28380832 ACTCTCCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (21 bp):
TTGACATATTTAAAGACTAAA
Found at i:28385267 original size:54 final size:54
Alignment explanation
Indices: 28385143--28385287 Score: 186
Period size: 55 Copynumber: 2.7 Consensus size: 54
28385133 TCTTTTTAAT
* *
28385143 TGTTGGAATACTGCTTCTTTTGAATCAATTTTT-TACATGTTTAAATTGATTGTTA
1 TGTTGGAATACTGCTTCTTTTGAATCGATTTTTATAC--GTTTAAATCGATTGTTA
* * * *
28385198 TGTTGGAATATTGCTTATTTTAAAGCGATTGTTTATACGTTTAAATCGATT-TTA
1 TGTTGGAATACTGCTTCTTTTGAATCGATT-TTTATACGTTTAAATCGATTGTTA
*
28385252 TGTTCGAATACTGCTTCTTTTGAATCGATTTTTATA
1 TGTTGGAATACTGCTTCTTTTGAATCGATTTTTATA
28385288 TAGCACATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
53 6 0.08
54 28 0.36
55 37 0.48
56 3 0.04
57 3 0.04
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.50
Consensus pattern (54 bp):
TGTTGGAATACTGCTTCTTTTGAATCGATTTTTATACGTTTAAATCGATTGTTA
Found at i:28386906 original size:42 final size:43
Alignment explanation
Indices: 28386860--28386971 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
28386850 GACTATGATT
*
28386860 TTTAGCTGCGTTTTTCTCACAAACGCCACTAAA-AACATGGTC
1 TTTAGCGGCGTTTTTCTCACAAACGCCACTAAAGAACATGGTC
* * * * * *
28386902 TTTAGCGGCGCTTCTATGAAAAACGCTACTAAAGAACATGGTC
1 TTTAGCGGCGTTTTTCTCACAAACGCCACTAAAGAACATGGTC
*
28386945 TTTAGCGGCCTTTTTAC-CACAAACGCC
1 TTTAGCGGCGTTTTT-CTCACAAACGCC
28386972 GTTAAAATTA
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
42 26 0.48
43 28 0.52
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTCTCACAAACGCCACTAAAGAACATGGTC
Found at i:28389596 original size:41 final size:41
Alignment explanation
Indices: 28389529--28389617 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 41
28389519 TTTAAATAAA
*
28389529 TTAGCGGCGCTTTCTCATAAACGCCGCTAATGCTCTGATTT
1 TTAGCGGCGCTTTCACATAAACGCCGCTAATGCTCTGATTT
* * **
28389570 TTAGTGGCGCTTTCACATAAATGCCGCTAATGCTCTGACCT
1 TTAGCGGCGCTTTCACATAAACGCCGCTAATGCTCTGATTT
28389611 TTAGCGG
1 TTAGCGG
28389618 AGTTTTTCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (41 bp):
TTAGCGGCGCTTTCACATAAACGCCGCTAATGCTCTGATTT
Found at i:28389664 original size:13 final size:13
Alignment explanation
Indices: 28389646--28389672 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28389636 CACTATTACT
28389646 TTACCTTTTACGG
1 TTACCTTTTACGG
28389659 TTACCTTTTACGG
1 TTACCTTTTACGG
28389672 T
1 T
28389673 GTTTATGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (13 bp):
TTACCTTTTACGG
Found at i:28392089 original size:15 final size:16
Alignment explanation
Indices: 28392062--28392091 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28392052 AAGCTCATGG
28392062 TGATATGATTTTATTA
1 TGATATGATTTTATTA
28392078 TGATAT-ATTTTATT
1 TGATATGATTTTATT
28392092 GCAAGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (16 bp):
TGATATGATTTTATTA
Found at i:28392721 original size:15 final size:16
Alignment explanation
Indices: 28392694--28392723 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28392684 AAGCTCATGG
28392694 TGATATGATTTTATTA
1 TGATATGATTTTATTA
28392710 TGATAT-ATTTTATT
1 TGATATGATTTTATT
28392724 GCAAGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (16 bp):
TGATATGATTTTATTA
Found at i:28392931 original size:632 final size:634
Alignment explanation
Indices: 28391723--28392992 Score: 2517
Period size: 632 Copynumber: 2.0 Consensus size: 634
28391713 TATTTTGGAC
28391723 AGTGATACAAGCTTTCAAACCAAATTTAAGCAAAAATGTGATCAAATTCAAGCTATGATTTAATT
1 AGTGATACAAGCTTTCAAACCAAATTTAAGCAAAAATGTGATCAAATTCAAGCTATGATTTAATT
28391788 TCATCTTTGTACAAATCTATCATCCTTAGTATGTTTTTTCCCCTTTGTTCTCGCTAGAGAACATT
66 TCATCTTTGTACAAATCTATCATCCTTAGTATGTTTTTTCCCCTTTGTTCTCGCTAGAGAACATT
28391853 TTCTAGGTTTGGCCCTTCCTTTTGCACCACTCTTGATTTCCATTGGTACTAGACCATCACTTCTT
131 TTCTAGGTTTGGCCCTTCCTTTTGCACCACTCTTGATTTCCATTGGTACTAGACCATCACTTCTT
28391918 TGTTGCTCATCCTTAGTGCTTCTCATGCTAAGTGTTTTCCTTCGGTTCTGATTTTGTTTGTGTGC
196 TGTTGCTCATCCTTAGTGCTTCTCATGCTAAGTGTTTTCCTTCGGTTCTGATTTTGTTTGTGTGC
28391983 TTGTCTTTTTTCTTTTTTTCCTCCAGAGATTTTACAGCGCTAATTATGAATATGATGGATATGGA
261 TTGTCTTTTTTC-TTTTTTCCTCCAGAGATTTTACAGCGCTAATTATGAATATGATGGATATGGA
28392048 ATTCAAGCTCATGGTGATATGATTTTATTATGATATATTTTATTGCAAGTTTTTCATTGTGTTGT
325 ATTCAAGCTCATGGTGATATGATTTTATTATGATATATTTTATTGCAAGTTTTTCATTGTGTTGT
28392113 AAATTTTATACATTATATCCTTATTAGAGTTGTGTGACCTAAATTTCTGTTAAACAAATAAAATA
390 AAATTTTATACATTATATCCTTATTAGAGTTGTGTGACCTAAATTTCTGTTAAACAAATAAAATA
28392178 CAAGTGGCAAGATAAGGGGATTTGTGGGTGCACAAGTGGAATTCGTATAGAAGTACGCTTCTTTT
455 CAAGTGGCAAGATAAGGGGATTTGTGGGTGCACAAGTGGAATTCGTATAGAAGTACGCTTCTTTT
28392243 ATTTGATATTGTTTAGAATAAGGTGTTTCAATCTTACTACATATCAACTGAAGTTAGCAGTTAGT
520 ATTTGATATTGTTTAGAATAAGGTGTTTCAATCTTACTACATATCAACTGAAGTTAGCAGTTAGT
28392308 GATTAAGATAAGCTAACTGTACTGCAGTTAAGTTTGCTAGTGTTAGTTAT
585 GATTAAGATAAGCTAACTGTACTGCAGTTAAGTTTGCTAGTGTTAGTTAT
28392358 AGTGATACAAGCTTTCAAACCAAATTTAAGCAAAAATGTGATCAAATTCAAGCTATGATTTAATT
1 AGTGATACAAGCTTTCAAACCAAATTTAAGCAAAAATGTGATCAAATTCAAGCTATGATTTAATT
28392423 TCATCTTTGTACAAATCTATCATCCTTAGTATGTTTTTTCCCCTTTGTTCTCGCTAGAGAACATT
66 TCATCTTTGTACAAATCTATCATCCTTAGTATGTTTTTTCCCCTTTGTTCTCGCTAGAGAACATT
28392488 TTCTAGGTTTGGCCCTTCCTTTTGCACCACTCTTGATTTCCATTGGTACTAGACCATCACTTCTT
131 TTCTAGGTTTGGCCCTTCCTTTTGCACCACTCTTGATTTCCATTGGTACTAGACCATCACTTCTT
28392553 TGTTGCTCATCCTTAGTGCTTCTCATGCTAAGTGTTTTCCTTCGGTTCTGATTTTGTTTGTGTGC
196 TGTTGCTCATCCTTAGTGCTTCTCATGCTAAGTGTTTTCCTTCGGTTCTGATTTTGTTTGTGTGC
28392618 TTGTCTTTTTTC-TTTTT-CTCCAGAGATTTTACAGCGCTAATTATGAATATGATGGATATGGAA
261 TTGTCTTTTTTCTTTTTTCCTCCAGAGATTTTACAGCGCTAATTATGAATATGATGGATATGGAA
28392681 TTCAAGCTCATGGTGATATGATTTTATTATGATATATTTTATTGCAAGTTTTTCATTGTGTTGTA
326 TTCAAGCTCATGGTGATATGATTTTATTATGATATATTTTATTGCAAGTTTTTCATTGTGTTGTA
28392746 AATTTTATACATTATATCCTTATTAGAGTTGTGTGACCTAAATTTCTGTTAAACAAATAAAATAC
391 AATTTTATACATTATATCCTTATTAGAGTTGTGTGACCTAAATTTCTGTTAAACAAATAAAATAC
28392811 AAGTGGCAAGATAAGGGGATTTGTGGGTGCACAAGTGGAATTCGTATAGAAGTACGCTTCTTTTA
456 AAGTGGCAAGATAAGGGGATTTGTGGGTGCACAAGTGGAATTCGTATAGAAGTACGCTTCTTTTA
28392876 TTTGATATTGTTTAGAATAAGGTGTTTCAATCTTACTACATATCAACTGAAGTTAGCAGTTAGTG
521 TTTGATATTGTTTAGAATAAGGTGTTTCAATCTTACTACATATCAACTGAAGTTAGCAGTTAGTG
28392941 ATTAAGATAAGCTAACTGTACTGCAGTTAAGTTTGCTAGTGTTAGTTAT
586 ATTAAGATAAGCTAACTGTACTGCAGTTAAGTTTGCTAGTGTTAGTTAT
28392990 AGT
1 AGT
28392993 TAGTAGCAGT
Statistics
Matches: 635, Mismatches: 0, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
632 358 0.56
633 5 0.01
635 272 0.43
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (634 bp):
AGTGATACAAGCTTTCAAACCAAATTTAAGCAAAAATGTGATCAAATTCAAGCTATGATTTAATT
TCATCTTTGTACAAATCTATCATCCTTAGTATGTTTTTTCCCCTTTGTTCTCGCTAGAGAACATT
TTCTAGGTTTGGCCCTTCCTTTTGCACCACTCTTGATTTCCATTGGTACTAGACCATCACTTCTT
TGTTGCTCATCCTTAGTGCTTCTCATGCTAAGTGTTTTCCTTCGGTTCTGATTTTGTTTGTGTGC
TTGTCTTTTTTCTTTTTTCCTCCAGAGATTTTACAGCGCTAATTATGAATATGATGGATATGGAA
TTCAAGCTCATGGTGATATGATTTTATTATGATATATTTTATTGCAAGTTTTTCATTGTGTTGTA
AATTTTATACATTATATCCTTATTAGAGTTGTGTGACCTAAATTTCTGTTAAACAAATAAAATAC
AAGTGGCAAGATAAGGGGATTTGTGGGTGCACAAGTGGAATTCGTATAGAAGTACGCTTCTTTTA
TTTGATATTGTTTAGAATAAGGTGTTTCAATCTTACTACATATCAACTGAAGTTAGCAGTTAGTG
ATTAAGATAAGCTAACTGTACTGCAGTTAAGTTTGCTAGTGTTAGTTAT
Found at i:28403366 original size:21 final size:24
Alignment explanation
Indices: 28403321--28403367 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
28403311 CTACATGTCC
28403321 ATACTATATATTATAAAAAATAAT
1 ATACTATATATTATAAAAAATAAT
28403345 ATACT-TAT-TTATAAAAAA-AAT
1 ATACTATATATTATAAAAAATAAT
28403366 AT
1 AT
28403368 TATAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
22 10 0.43
23 3 0.13
24 5 0.22
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
ATACTATATATTATAAAAAATAAT
Found at i:28403375 original size:21 final size:22
Alignment explanation
Indices: 28403321--28403375 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
28403311 CTACATGTCC
28403321 ATACTATATATTATAAAAAATAAT
1 ATACTA-AT-TTATAAAAAATAAT
*
28403345 ATACTTATTTATAAAAAA-AAT
1 ATACTAATTTATAAAAAATAAT
28403366 ATTA-TAATTT
1 A-TACTAATTT
28403376 TTGTTGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.32
22 12 0.43
23 2 0.07
24 5 0.18
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATACTAATTTATAAAAAATAAT
Found at i:28403939 original size:20 final size:20
Alignment explanation
Indices: 28403903--28403941 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28403893 TGGATTGTTG
28403903 TTATTCGTTTAGAATTTTTT
1 TTATTCGTTTAGAATTTTTT
*
28403923 TTATT-GTTTTGATATTTTT
1 TTATTCGTTTAGA-ATTTTT
28403942 ATAGTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (20 bp):
TTATTCGTTTAGAATTTTTT
Found at i:28408126 original size:6 final size:6
Alignment explanation
Indices: 28408105--28408194 Score: 80
Period size: 6 Copynumber: 15.0 Consensus size: 6
28408095 TTAAATTGAT
*
28408105 TTTAAA TTT-TA TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* * *
28408153 TTTAAA TTT-AC CTTAAA TTTAAA TTTAAA TTAAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
28408195 ACAAATTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
4 2 0.03
5 9 0.13
6 46 0.68
7 5 0.07
8 6 0.09
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:28408185 original size:11 final size:11
Alignment explanation
Indices: 28408095--28408190 Score: 61
Period size: 11 Copynumber: 8.7 Consensus size: 11
28408085 AATTTAGAGG
* *
28408095 TTAAATTGATT
1 TTAAATTAAAT
**
28408106 TTAAATTTTAT
1 TTAAATTAAAT
28408117 TTAAATTTAAAT
1 TTAAA-TTAAAT
**
28408129 TTATCTTAAAT
1 TTAAATTAAAT
*
28408140 TTAAATTTAA-
1 TTAAATTAAAT
*
28408150 TT-ATTTAAAT
1 TTAAATTAAAT
**
28408160 TTACCTTAAAT
1 TTAAATTAAAT
28408171 TTAAATTTAAAT
1 TTAAA-TTAAAT
*
28408183 TAAAATTA
1 TTAAATTA
28408191 TAAAACAAAT
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
9 5 0.08
10 4 0.06
11 38 0.59
12 17 0.27
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:28408185 original size:17 final size:17
Alignment explanation
Indices: 28408095--28408186 Score: 91
Period size: 17 Copynumber: 5.6 Consensus size: 17
28408085 AATTTAGAGG
* *
28408095 TTAAATTGATTTTAAAT
1 TTAAATTAAATTTAAAT
* *
28408112 TTTATTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
**
28408129 TTATCTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
28408146 TT-AATT--ATTTAAAT
1 TTAAATTAAATTTAAAT
**
28408160 TTACCTTAAATTTAAAT
1 TTAAATTAAATTTAAAT
28408177 TTAAATTAAA
1 TTAAATTAAA
28408187 ATTATAAAAC
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
14 10 0.17
15 2 0.03
16 2 0.03
17 45 0.76
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Found at i:28408309 original size:27 final size:26
Alignment explanation
Indices: 28408279--28408344 Score: 105
Period size: 27 Copynumber: 2.5 Consensus size: 26
28408269 TACAAGGGCT
28408279 CAAAAGGCCCAATTACATTCAAAAGCC
1 CAAAAGGCCCAATTACATTCAAAA-CC
28408306 CAAAAGGCCCAATTACATTCAAAACC
1 CAAAAGGCCCAATTACATTCAAAACC
* *
28408332 CGAATGGCCCAAT
1 CAAAAGGCCCAAT
28408345 ATCTACCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
26 13 0.35
27 24 0.65
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.15
Consensus pattern (26 bp):
CAAAAGGCCCAATTACATTCAAAACC
Found at i:28409036 original size:16 final size:16
Alignment explanation
Indices: 28409015--28409052 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28409005 ATATTAACAA
*
28409015 TAATAATA-TTTTTAAT
1 TAATAATAGTATTT-AT
28409031 TAATAATAGTATTTAT
1 TAATAATAGTATTTAT
28409047 TAATAA
1 TAATAA
28409053 CATTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TAATAATAGTATTTAT
Found at i:28409037 original size:19 final size:20
Alignment explanation
Indices: 28409013--28409050 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28409003 AGATATTAAC
28409013 AATAATAATATTT-TTAATT
1 AATAATAATATTTATTAATT
*
28409032 AATAATAGTATTTATTAAT
1 AATAATAATATTTATTAAT
28409051 AACATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AATAATAATATTTATTAATT
Found at i:28409636 original size:29 final size:28
Alignment explanation
Indices: 28409573--28409645 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
28409563 CAAACAGTCT
* *
28409573 AAAAATTGCATTTTGACCCCAAAATTTC
1 AAAAATTACATTTTGACCCCAAAATTCC
*
28409601 AGGAAATTACATTTTGACCCCAAAACTTCC
1 A-AAAATTACATTTTGACCCCAAAA-TTCC
*
28409631 AAAAATAACCATTTT
1 AAAAATTA-CATTTT
28409646 ACCTTCGAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.03
29 26 0.70
30 10 0.27
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (28 bp):
AAAAATTACATTTTGACCCCAAAATTCC
Found at i:28409693 original size:59 final size:59
Alignment explanation
Indices: 28409629--28410154 Score: 629
Period size: 59 Copynumber: 9.0 Consensus size: 59
28409619 CCCAAAACTT
* ** * * *
28409629 CCAAAAATAACCATTTTACCTTCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
28409688 CCAAAAA-TACCATTTTACCCTCAAACTTTCC-AAATTACATTTTTAACTCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
28409745 CCAAAAATTATCGTTTTACCCCCAAACTTTCCAAAA-TCCTATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCC-ATTTTTAACCCCGATTTCA
* * * *
28409804 CCAAAAATTACCATTTTATCTCCGAACTTTCTAAAATTCCATTTTTAACCCC-AGTTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCA
** *
28409863 CCAAAAATTACTGTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
28409922 CCAAAAATTACCATTTTACCCTCGAACCTTT-TAAAATTCCATTTTTAAACCCGATTTCA
1 CCAAAAATTACCATTTTACCC-CCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
28409981 CCAAAAATTACCATTTTACCCCCAAACATTCC-AAATTCCA-TTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
28410038 TCAAGAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * ** * * * *
28410097 CC-AAAATTACTATTTTGCCCCC-AGGTGTCCAAAAGTCCCATTTTCAATCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAA-TTCCATTTTTAACCCCGATTTCA
28410155 TCGTTTCTTC
Statistics
Matches: 401, Mismatches: 55, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
57 84 0.21
58 101 0.25
59 205 0.51
60 11 0.03
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:28410102 original size:175 final size:175
Alignment explanation
Indices: 28409629--28410119 Score: 645
Period size: 175 Copynumber: 2.8 Consensus size: 175
28409619 CCCAAAACTT
* * * *
28409629 CCAAAAATAACCATTTTACCTTCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCTCCGAACATTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAA
* * * * *
28409694 ATACCATTTTACCCTCAAACTTTCC-AAATTACATTTTTAACTCCGATTTCACCAAAAATTATCG
66 TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAAC-CCGATTTCACCAAAAATTACCA
28409758 TTTTACCCCCAAACTTTCCAAAATCCTATTTTTAACCTCGATTTCA
130 TTTTACCCCCAAACTTTCCAAAATCCTATTTTTAACCTCGATTTCA
* * *
28409804 CCAAAAATTACCATTTTATCTCCGAACTTTCTAAAATTCCATTTTTAACCCCAGTTTCACCAAAA
1 CCAAAAATTACCATTTTACCTCCGAACATTCTAAAATTCCATTTTTAACCCCAATTTCACC-AAA
** *
28409869 ATTACTGTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
65 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA-CCCGATTTCACCAAAAATTACC
* * *
28409934 ATTTTACCCTCGAACCTTT-TAAAATTCC-ATTTTTAAACC-CGATTTCA
129 ATTTTACCC-CCAAACTTTCCAAAA-TCCTATTTTT-AACCTCGATTTCA
* * * *
28409981 CCAAAAATTACCATTTTACCCCCAAACATTC-CAAATTCCA-TTTTAACCCCAATTTCATCAAGA
1 CCAAAAATTACCATTTTACCTCCGAACATTCTAAAATTCCATTTTTAACCCCAATTTCACCAA-A
*
28410044 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACC-AAAATTACT
65 ATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCC-GATTTCACCAAAAATTACC
*
28410108 ATTTTGCCCCCA
129 ATTTTACCCCCA
28410120 GGTGTCCAAA
Statistics
Matches: 278, Mismatches: 30, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
173 2 0.01
174 21 0.08
175 121 0.44
176 32 0.12
177 87 0.31
178 15 0.05
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (175 bp):
CCAAAAATTACCATTTTACCTCCGAACATTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAA
TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCGATTTCACCAAAAATTACCAT
TTTACCCCCAAACTTTCCAAAATCCTATTTTTAACCTCGATTTCA
Found at i:28411411 original size:20 final size:20
Alignment explanation
Indices: 28411388--28411427 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28411378 ATTTTTGGAT
* *
28411388 TCAAATCTAGGGTTTTAAAA
1 TCAAATCTAAGATTTTAAAA
28411408 TCAAATCTAAGATTTTAAAA
1 TCAAATCTAAGATTTTAAAA
28411428 GAGCATGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
TCAAATCTAAGATTTTAAAA
Found at i:28416682 original size:47 final size:49
Alignment explanation
Indices: 28416629--28416730 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 49
28416619 TTTTTCATTT
* *
28416629 TAAAATTCTAA-TCTTTTGTATATCAACT-GCTCCTTTTAAAG-CCAAAA
1 TAAAATTCTAATTCTTTTGTATATCAACTATC-CCTTTTAAAGTCAAAAA
* *
28416676 TAAAATTCTAATTTTTTTGTATATCAGCTATCCCTTTTAAAGTCAAAAA
1 TAAAATTCTAATTCTTTTGTATATCAACTATCCCTTTTAAAGTCAAAAA
28416725 TAAAAT
1 TAAAAT
28416731 GTTGTCTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 11 0.23
48 25 0.52
49 12 0.25
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (49 bp):
TAAAATTCTAATTCTTTTGTATATCAACTATCCCTTTTAAAGTCAAAAA
Found at i:28417653 original size:10 final size:9
Alignment explanation
Indices: 28417626--28417659 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
28417616 TCCTCCTTTT
28417626 ATTTATTT-
1 ATTTATTTC
28417634 ATTTATTTC
1 ATTTATTTC
28417643 ATTTCATTTC
1 ATTT-ATTTC
28417653 ATTTATT
1 ATTTATT
28417660 AAACCCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTATTTC
Found at i:28417673 original size:5 final size:5
Alignment explanation
Indices: 28417665--28417690 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28417655 TTATTAAACC
28417665 CCACA CCACA CCACA CCACA CCACA C
1 CCACA CCACA CCACA CCACA CCACA C
28417691 GTACCAATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.62, G:0.00, T:0.00
Consensus pattern (5 bp):
CCACA
Found at i:28419829 original size:13 final size:13
Alignment explanation
Indices: 28419813--28419837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28419803 GACTGATTCT
28419813 ATTAATTGATTTG
1 ATTAATTGATTTG
28419826 ATTAATTGATTT
1 ATTAATTGATTT
28419838 CTGTTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
ATTAATTGATTTG
Found at i:28442046 original size:16 final size:16
Alignment explanation
Indices: 28442025--28442055 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28442015 ATTACAATAT
28442025 TGGGACTTTAAGATAA
1 TGGGACTTTAAGATAA
*
28442041 TGGGACTTTTAGATA
1 TGGGACTTTAAGATA
28442056 TTGTTTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TGGGACTTTAAGATAA
Found at i:28442447 original size:3 final size:3
Alignment explanation
Indices: 28442441--28442468 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28442431 TACTAAAATG
28442441 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
28442469 AGTTACATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:28449783 original size:23 final size:23
Alignment explanation
Indices: 28449746--28449805 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 23
28449736 AAAAAATAGG
28449746 TTATATATTAT--TTTTCTA-TAA
1 TTATATATTATAATTTT-TACTAA
28449767 TTATATATTATAATTTTTACTAA
1 TTATATATTATAATTTTTACTAA
*
28449790 TTCATATTTTAATAAT
1 TT-ATATATT-ATAAT
28449806 AATTATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 11 0.33
22 2 0.06
23 9 0.27
24 6 0.18
25 5 0.15
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATATTATAATTTTTACTAA
Found at i:28449866 original size:58 final size:58
Alignment explanation
Indices: 28449779--28449924 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 58
28449769 ATATATTATA
* *
28449779 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
28449836 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
28449896 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
28449925 CATTAAAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 1 0.01
58 48 0.62
59 11 0.14
60 10 0.13
61 8 0.10
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:28450116 original size:16 final size:16
Alignment explanation
Indices: 28450095--28450166 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
28450085 TGAATTACTG
*
28450095 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
28450111 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
28450127 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
28450143 ATTACATCTCTATTCC
1 ATTACAGCTCTATTCC
28450159 ATTACAGC
1 ATTACAGC
28450167 GAACCAAACG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:28450398 original size:15 final size:16
Alignment explanation
Indices: 28450373--28450412 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 16
28450363 ACCAAAAAAA
28450373 TAATATAATAATATTT
1 TAATATAATAATATTT
28450389 TAAT-TAATAATATTAT
1 TAATATAATAATATT-T
28450405 GTAATATA
1 -TAATATA
28450413 TTATTAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 10 0.48
16 5 0.24
17 4 0.19
18 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TAATATAATAATATTT
Found at i:28451039 original size:14 final size:16
Alignment explanation
Indices: 28451010--28451042 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
28451000 AGTATAGTTT
28451010 AATTAAAAACATTAAA
1 AATTAAAAACATTAAA
28451026 AATT-AAAA-ATTAAA
1 AATTAAAAACATTAAA
28451040 AAT
1 AAT
28451043 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AATTAAAAACATTAAA
Found at i:28451237 original size:22 final size:22
Alignment explanation
Indices: 28451212--28451257 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28451202 TGTATATCAA
28451212 TTTTAATATTTTT-AATAAGTTT
1 TTTTAATATTTTTCAA-AAGTTT
*
28451234 TTTTTATATTTTTCAAAAGTTT
1 TTTTAATATTTTTCAAAAGTTT
28451256 TT
1 TT
28451258 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTAATATTTTTCAAAAGTTT
Found at i:28451262 original size:20 final size:21
Alignment explanation
Indices: 28451212--28451268 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
28451202 TGTATATCAA
28451212 TTTTAATATTTTTAATAAGTTT
1 TTTTAATATTTTTAATAAG-TT
*
28451234 TTTTTATATTTTTCAA-AAG-T
1 TTTTAATATTTTT-AATAAGTT
28451254 TTTTAATATATTTTA
1 TTTTAATAT-TTTTA
28451269 TACATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 10 0.32
21 4 0.13
22 15 0.48
23 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTAATATTTTTAATAAGTT
Found at i:28451263 original size:22 final size:22
Alignment explanation
Indices: 28451217--28451267 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
28451207 ATCAATTTTA
**
28451217 ATATTTTTAATAAGTTTTTTTT
1 ATATTTTTAATAAGTTTTTAAT
28451239 ATATTTTTCAA-AAGTTTTTAAT
1 ATATTTTT-AATAAGTTTTTAAT
28451261 ATATTTT
1 ATATTTT
28451268 ATACATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
ATATTTTTAATAAGTTTTTAAT
Found at i:28451295 original size:20 final size:21
Alignment explanation
Indices: 28451272--28451369 Score: 61
Period size: 19 Copynumber: 5.0 Consensus size: 21
28451262 TATTTTATAC
28451272 ATTTTTATAAAATTT-TAAAT
1 ATTTTTATAAAATTTATAAAT
* *
28451292 ATTTTTTATTAACTTTATAAAT
1 A-TTTTTATAAAATTTATAAAT
28451314 -TTTTTAT--AATTTATTAAA-
1 ATTTTTATAAAATTTA-TAAAT
* * *
28451332 A--TTTATTAGATTTAT-TAT
1 ATTTTTATAAAATTTATAAAT
*
28451350 A-TTTTATAATATTTATAAAT
1 ATTTTTATAAAATTTATAAAT
28451370 TTATATTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
17 6 0.10
18 7 0.11
19 21 0.34
20 10 0.16
21 12 0.20
22 5 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (21 bp):
ATTTTTATAAAATTTATAAAT
Found at i:28451331 original size:19 final size:17
Alignment explanation
Indices: 28451295--28451371 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
28451285 TTTAAATATT
*
28451295 TTTTATTAACTTTATAAA
1 TTTT-TTAAATTTATAAA
28451313 TTTTTTATAATTTATTAAAA
1 TTTTTTA-AATTTA-T-AAA
* * *
28451333 TTTATTAGATTTATTATA
1 TTTTTTAAATTTA-TAAA
*
28451351 TTTTATAATATTTATAAA
1 TTTTTTAA-ATTTATAAA
28451369 TTT
1 TTT
28451372 ATATTATTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
17 3 0.06
18 22 0.47
19 13 0.28
20 9 0.19
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (17 bp):
TTTTTTAAATTTATAAA
Found at i:28451376 original size:29 final size:29
Alignment explanation
Indices: 28451254--28451386 Score: 98
Period size: 29 Copynumber: 4.6 Consensus size: 29
28451244 TTTCAAAAGT
* *
28451254 TTTTAATATATTTTA-TACATTTTTATAAAA
1 TTTTATTATATTTTATTA-ATATTTAT-AAA
* * *
28451284 TTTTAAATATTTTTTATTAA-CTTTATAAA
1 TTTT-ATTATATTTTATTAATATTTATAAA
* * *
28451313 TTTT-TTATAATTTATTAAAATTTATTAGA
1 TTTTATTATATTTTATTAATATTTA-TAAA
28451342 -TTTATTATATTTTA-TAATATTTATAAA
1 TTTTATTATATTTTATTAATATTTATAAA
*
28451369 TTTATATTAT-TTATATTA
1 TTT-TATTATATTTTATTA
28451387 TTTTTAAATA
Statistics
Matches: 84, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
27 14 0.17
28 21 0.25
29 27 0.32
30 9 0.11
31 11 0.13
32 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (29 bp):
TTTTATTATATTTTATTAATATTTATAAA
Found at i:28451381 original size:36 final size:35
Alignment explanation
Indices: 28451315--28451399 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 35
28451305 TTTATAAATT
*
28451315 TTTTATAATTTATTAAAATTTATTAGATTTAT-TATA
1 TTTTATAATAT-TTAAAATTTATTAGATTTATAT-TA
*
28451351 TTTTATAATATTTATAAATTTA-TATTATTTATATTA
1 TTTTATAATATTTA-AAATTTATTA-GATTTATATTA
28451387 TTTT-TAAATATTT
1 TTTTAT-AATATTT
28451400 TTAGTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
35 6 0.14
36 36 0.84
37 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (35 bp):
TTTTATAATATTTAAAATTTATTAGATTTATATTA
Found at i:28451409 original size:17 final size:18
Alignment explanation
Indices: 28451387--28451420 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28451377 ATTTATATTA
28451387 TTTTTAA-ATATTTTTAG
1 TTTTTAACATATTTTTAG
*
28451404 TTTTTAACATTTTTTTA
1 TTTTTAACATATTTTTA
28451421 TGATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTAACATATTTTTAG
Found at i:28451697 original size:16 final size:14
Alignment explanation
Indices: 28451678--28451711 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
28451668 TATAAACCTT
28451678 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
28451694 TTATAAATTTTATA
1 TTATAAATTTTATA
28451708 TTAT
1 TTAT
28451712 TGTTGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:28454915 original size:3 final size:3
Alignment explanation
Indices: 28454907--28454966 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
28454897 AGTCGAAGCA
28454907 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28454955 AAT AAT AAT AAT
1 AAT AAT AAT AAT
28454967 GATTTCTTCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28455150 original size:4 final size:4
Alignment explanation
Indices: 28455141--28455169 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28455131 ACAGGGTCTA
28455141 CCAT CCAT CCAT CCAT CCAT CCAT CCAT C
1 CCAT CCAT CCAT CCAT CCAT CCAT CCAT C
28455170 ATCAAAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (4 bp):
CCAT
Found at i:28458419 original size:24 final size:24
Alignment explanation
Indices: 28458388--28458438 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
28458378 AGAAATAATC
*
28458388 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
28458412 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
28458436 TTT
1 TTT
28458439 GAGTCAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:28458447 original size:24 final size:24
Alignment explanation
Indices: 28458388--28458450 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
28458378 AGAAATAATC
* *
28458388 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTG
*
28458412 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTG
* *
28458436 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
28458451 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTATTTG
Found at i:28461720 original size:24 final size:24
Alignment explanation
Indices: 28461688--28461734 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
28461678 AACACGAACC
*
28461688 TCTATTCCAAATGAACTTTTACCA
1 TCTATTCCAAATAAACTTTTACCA
28461712 TCTATTCCAAATAAACTTTTACC
1 TCTATTCCAAATAAACTTTTACC
28461735 CTTTGAAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (24 bp):
TCTATTCCAAATAAACTTTTACCA
Found at i:28465819 original size:3 final size:3
Alignment explanation
Indices: 28465813--28465837 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28465803 GGGTGGAATT
28465813 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
28465838 TGGGCGGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:28473317 original size:11 final size:11
Alignment explanation
Indices: 28473287--28473332 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
28473277 GTTGAACATG
*
28473287 TTTAGTAATTT
1 TTTATTAATTT
28473298 TTT-TT-ATTT
1 TTTATTAATTT
28473307 TTTATTAATTT
1 TTTATTAATTT
* *
28473318 TTAATTAATTA
1 TTTATTAATTT
28473329 TTTA
1 TTTA
28473333 ATTATTATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.24
10 3 0.10
11 19 0.66
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTATTAATTT
Found at i:28482668 original size:25 final size:23
Alignment explanation
Indices: 28482640--28482685 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
28482630 GTTGGATCCA
28482640 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
28482665 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
28482686 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:28493079 original size:27 final size:27
Alignment explanation
Indices: 28493004--28493092 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
28492994 TGCGTTAACG
*
28493004 GAATAGAACAACACCAATGTGCTTATCA
1 GAATAGAA-AACACCAAAGTGCTTATCA
* * * *
28493032 GAACAAAACAACACTATAGTG-TTATCA
1 GAATAGAA-AACACCAAAGTGCTTATCA
*
28493059 GAATAGAAAAGCACCAAAGTGCTTAAACA
1 GAATAGAAAA-CACCAAAGTGCTT-ATCA
28493088 GAATA
1 GAATA
28493093 AAGAGCGCAC
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
26 2 0.04
27 20 0.42
28 18 0.38
29 8 0.17
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (27 bp):
GAATAGAAAACACCAAAGTGCTTATCA
Found at i:28495483 original size:63 final size:63
Alignment explanation
Indices: 28495384--28495512 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 63
28495374 GTATTTAGCG
*
28495384 GCTCTTTCCTCACAAACGCAACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAACGTC
1 GCTCTTTCCTCACAAACGCAACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAACGCC
* *
28495447 GCTCTTTCCTCACAAACGCAACTAAAGAACATGGTCTTTAGTGGCGTTTTTCTCACAAACGCC
1 GCTCTTTCCTCACAAACGCAACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAACGCC
28495510 GCT
1 GCT
28495513 AAAGAACATG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (63 bp):
GCTCTTTCCTCACAAACGCAACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAACGCC
Found at i:28495516 original size:43 final size:43
Alignment explanation
Indices: 28495450--28495684 Score: 267
Period size: 43 Copynumber: 5.5 Consensus size: 43
28495440 AAACGTCGCT
* ** *
28495450 CTTTCCTCACAAACGCAACTAAAGAACATGGTCTTTAGTGGCG
1 CTTTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
* *
28495493 TTTTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGCAGCG
1 CTTTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
* * * * *
28495536 CTTTTCTCACAAATGTCACTAAAG-ACATGGTCTTTAACGGTG
1 CTTTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
* * * * *
28495578 CTTTTCCCACAAATGTCGCTAAAGAACATGATCTTTAGCGACG
1 CTTTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
* * * *
28495621 CTTTTCGCACAAATGCTGCTAAAG-ACATGGTCTTTAGCGACG
1 CTTTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
*
28495663 CTTTTCCCACAAACGCCGCTAA
1 CTTTTCTCACAAACGCCGCTAA
28495685 TATTAACAGA
Statistics
Matches: 165, Mismatches: 26, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
42 73 0.44
43 92 0.56
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (43 bp):
CTTTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
Done.