Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 91 of 310
Found at i:29084882 original size:27 final size:24
Alignment explanation
Indices: 29084825--29084882 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 24
29084815 CATGGCATAT
*
29084825 AGCATAATAACCAAAATGAACTTA
1 AGCATAATAACCAAAATGAACTCA
*
29084849 ATCCATAATTAAACCAAAATCGAACTCA
1 A-GCATAA-T-AACCAAAAT-GAACTCA
29084877 AGCATA
1 AGCATA
29084883 GAGATTAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.04
25 5 0.19
26 1 0.04
27 13 0.48
28 7 0.26
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (24 bp):
AGCATAATAACCAAAATGAACTCA
Found at i:29089938 original size:41 final size:40
Alignment explanation
Indices: 29089733--29089949 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
29089723 AAGCCAAGTA
* * *
29089733 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
29089771 CCTTCGGGACATAG-CCGGATATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29089810 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
29089850 CCTTCGAGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
29089890 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
29089931 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
29089950 TTATCATCCA
Statistics
Matches: 159, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
37 1 0.01
38 28 0.18
39 16 0.10
40 86 0.54
41 24 0.15
42 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:29097874 original size:40 final size:40
Alignment explanation
Indices: 29097767--29097942 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
29097757 AAGCCAAGTA
* * *
29097767 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
29097805 CCTTCGGGACATAG-CCGGATATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29097844 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
29097884 CCTTCGAGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
29097924 CCTTCGGAACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
29097943 TTATCATCCA
Statistics
Matches: 123, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.01
38 28 0.23
39 16 0.13
40 78 0.63
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:29104453 original size:12 final size:12
Alignment explanation
Indices: 29104436--29104465 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29104426 TGCTTGTTTA
29104436 GGTAATAAGTTC
1 GGTAATAAGTTC
*
29104448 GGTAATAAGTTT
1 GGTAATAAGTTC
29104460 GGTAAT
1 GGTAAT
29104466 GCTCTGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (12 bp):
GGTAATAAGTTC
Found at i:29109662 original size:28 final size:29
Alignment explanation
Indices: 29109631--29109690 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
29109621 GATTTTTGAC
*
29109631 AAAAATGTCAATT-AGGGATT-AATTTTAG
1 AAAAATGTAAATTGAGGGATTAAATTTT-G
* *
29109659 AAAAGTGTAAATTGAGGGGTTAAATTTTG
1 AAAAATGTAAATTGAGGGATTAAATTTTG
29109688 AAA
1 AAA
29109691 TAAATAGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.41
29 10 0.37
30 6 0.22
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (29 bp):
AAAAATGTAAATTGAGGGATTAAATTTTG
Found at i:29113910 original size:15 final size:15
Alignment explanation
Indices: 29113878--29113906 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29113868 ATATTCTGTG
29113878 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
29113893 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
29113907 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:29114904 original size:45 final size:44
Alignment explanation
Indices: 29114843--29114995 Score: 197
Period size: 45 Copynumber: 3.5 Consensus size: 44
29114833 TAGGATTCTG
*
29114843 ATATGTGATTTTGTGTAAGACCACGTCTGGGACGTTCGCATCGAT
1 ATATGTGA-TTCGTGTAAGACCACGTCTGGGACGTTCGCATCGAT
*
29114888 ATATGTGATTCCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
1 ATATGTGATT-CGTGTAAGACCACGTCTGGGACGTTCGCATCGAT
* * *
29114933 ATATGTGGTTACGTGTAAGACCATGTCTGGGAC-ATCGGCATC-AT
1 ATATGTGATT-CGTGTAAGACCACGTCTGGGACGTTC-GCATCGAT
29114977 AT-T-TGATTCGTGTAAGACC
1 ATATGTGATTCGTGTAAGACC
29114996 CTGTTTGGGA
Statistics
Matches: 98, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.11
42 4 0.04
43 1 0.01
44 7 0.07
45 75 0.77
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (44 bp):
ATATGTGATTCGTGTAAGACCACGTCTGGGACGTTCGCATCGAT
Found at i:29115005 original size:41 final size:43
Alignment explanation
Indices: 29114855--29115020 Score: 146
Period size: 45 Copynumber: 3.8 Consensus size: 43
29114845 ATGTGATTTT
* *
29114855 GTGTAAGACCAC-GTCTGGGACGTTC-GCATCGATATATGTGATTCC
1 GTGTAAGACC-CTGTCTGGGAC-ATCGGCATCGATAT-T-TGATTAC
* * *
29114900 GTGTAAGACCAC-GTCTGGGACGTTGGCATCGATATATGTGGTTAC
1 GTGTAAGACC-CTGTCTGGGACATCGGCATCGATAT-T-TGATTAC
*
29114945 GTGTAAGACCATGTCTGGGACATCGGCATC-ATATTTGATT-C
1 GTGTAAGACCCTGTCTGGGACATCGGCATCGATATTTGATTAC
* *
29114986 GTGTAAGACCCTGTTTGGGACAGT-GGCATTGATAT
1 GTGTAAGACCCTGTCTGGGACA-TCGGCATCGATAT
29115021 GAGATAACAT
Statistics
Matches: 106, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
41 26 0.25
42 9 0.08
43 1 0.01
44 5 0.05
45 65 0.61
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCCTGTCTGGGACATCGGCATCGATATTTGATTAC
Found at i:29123359 original size:46 final size:46
Alignment explanation
Indices: 29123292--29123464 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
29123282 AACTCGCCCC
* * *
29123292 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* *
29123338 TAAGTGAACTCGGACTCAACTCAACGGGTTCGGATACCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--A-C--GTTCGCATCCA
* * * *
29123386 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* *
29123431 TAGGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
29123465 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 57 0.56
47 26 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:29123408 original size:93 final size:93
Alignment explanation
Indices: 29123297--29123465 Score: 266
Period size: 93 Copynumber: 1.8 Consensus size: 93
29123287 GCCCCTAAGT
* * * *
29123297 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
29123362 CGGGTTCGGATACCTAGTTACATCTCAC
66 CGAGTTCGGATACCTAGTTACATCTCAC
* *
29123390 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
29123455 TGAGTTCGGAT
66 CGAGTTCGGAT
29123466 GCTCAACCAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATACCTAGTTACATCTCAC
Found at i:29126884 original size:31 final size:31
Alignment explanation
Indices: 29126846--29126909 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
29126836 CCTTTTCATA
29126846 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
29126877 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
29126908 TT
1 TT
29126910 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:29127150 original size:24 final size:24
Alignment explanation
Indices: 29127103--29127220 Score: 172
Period size: 23 Copynumber: 5.0 Consensus size: 24
29127093 GCTTTATCAT
*
29127103 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
29127128 ATAACTGGGGCA-AAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
29127152 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
29127175 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
29127198 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29127221 GCACTTCCTC
Statistics
Matches: 88, Mismatches: 1, Indels: 9
0.90 0.01 0.09
Matches are distributed among these distances:
23 47 0.53
24 27 0.31
25 14 0.16
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:29127283 original size:11 final size:11
Alignment explanation
Indices: 29127267--29127305 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
29127257 CATTTATGAA
29127267 CATATCATGTG
1 CATATCATGTG
*
29127278 CATATCA--TA
1 CATATCATGTG
29127287 CATATCATGTG
1 CATATCATGTG
29127298 CATATCAT
1 CATATCAT
29127306 ACATATCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (11 bp):
CATATCATGTG
Found at i:29127291 original size:20 final size:20
Alignment explanation
Indices: 29127266--29127316 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
29127256 GCATTTATGA
29127266 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
29127286 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
29127306 ACATATCATGT
1 ACATATCATGT
29127317 TTATCAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:29127381 original size:25 final size:25
Alignment explanation
Indices: 29127353--29127400 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29127343 ATATATAAAC
* * *
29127353 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29127378 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29127401 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29135208 original size:20 final size:20
Alignment explanation
Indices: 29135183--29135248 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
29135173 NNNNNNNNNN
29135183 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
29135203 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATA
29135223 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
29135243 CCATGT
1 TCATGT
29135249 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:29135213 original size:11 final size:11
Alignment explanation
Indices: 29135183--29135237 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
29135173 NNNNNNNNNN
29135183 TCATGTGCATA
1 TCATGTGCATA
*
29135194 TCA--TACATA
1 TCATGTGCATA
29135203 TCATGTGCATA
1 TCATGTGCATA
* *
29135214 TCA--TACATG
1 TCATGTGCATA
29135223 TCATGTGCATA
1 TCATGTGCATA
29135234 TCAT
1 TCAT
29135238 ACATACCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:29135621 original size:41 final size:41
Alignment explanation
Indices: 29135564--29135646 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
29135554 TAACATATTT
29135564 TCGTTTTCTACCAATTTGACCCAAATGGGCCCGAAAGCCTA
1 TCGTTTTCTACCAATTTGACCCAAATGGGCCCGAAAGCCTA
*
29135605 TCGTTTTCTACCAATTTTACCCAAATGGGCCCGAAAGCCTA
1 TCGTTTTCTACCAATTTGACCCAAATGGGCCCGAAAGCCTA
29135646 T
1 T
29135647 TGGGCCCTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (41 bp):
TCGTTTTCTACCAATTTGACCCAAATGGGCCCGAAAGCCTA
Found at i:29140714 original size:22 final size:22
Alignment explanation
Indices: 29140687--29140738 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
29140677 ACTATCGGGT
29140687 TAAGTCACAACTTTAGGGGTT-
1 TAAGTCACAACTTTAGGGGTTC
29140708 TGAAGTCACAACTTTAGGGGTTC
1 T-AAGTCACAACTTTAGGGGTTC
29140731 TAAGTCAC
1 TAAGTCAC
29140739 CATGTAACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (22 bp):
TAAGTCACAACTTTAGGGGTTC
Found at i:29141943 original size:9 final size:9
Alignment explanation
Indices: 29141929--29142006 Score: 84
Period size: 9 Copynumber: 8.7 Consensus size: 9
29141919 ATAAGTATAA
29141929 AATTAACCG
1 AATTAACCG
*
29141938 AATTAACTG
1 AATTAACCG
* *
29141947 AATTAATCA
1 AATTAACCG
29141956 AATTAACCG
1 AATTAACCG
* *
29141965 AATTAGCTG
1 AATTAACCG
* *
29141974 AATTACCCA
1 AATTAACCG
29141983 AATTAACCG
1 AATTAACCG
*
29141992 AATTGACCG
1 AATTAACCG
29142001 AATTAA
1 AATTAA
29142007 TTGAATTATT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:29141959 original size:27 final size:27
Alignment explanation
Indices: 29141928--29142007 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
29141918 AATAAGTATA
29141928 AAATTAACCGAATTAACTGAATTAATC
1 AAATTAACCGAATTAACTGAATTAATC
* **
29141955 AAATTAACCGAATTAGCTGAATTACCC
1 AAATTAACCGAATTAACTGAATTAATC
* *
29141982 AAATTAACCGAATTGACCGAATTAAT
1 AAATTAACCGAATTAACTGAATTAAT
29142008 TGAATTATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (27 bp):
AAATTAACCGAATTAACTGAATTAATC
Found at i:29142062 original size:20 final size:20
Alignment explanation
Indices: 29142039--29142077 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29142029 TATGTTTTTT
29142039 ATTTTTAGTTTTAGTTTTAG
1 ATTTTTAGTTTTAGTTTTAG
* *
29142059 ATTTTTATTTTTATTTTTA
1 ATTTTTAGTTTTAGTTTTA
29142078 TTTATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
ATTTTTAGTTTTAGTTTTAG
Found at i:29142075 original size:5 final size:6
Alignment explanation
Indices: 29142034--29142080 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
29142024 AATTATATGT
* *
29142034 TTTTTA TTTTTA GTTTTA GTTTTAGA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTTTTA TTT
29142081 ATTAAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
6 27 0.77
7 7 0.20
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:29142108 original size:24 final size:24
Alignment explanation
Indices: 29142063--29142108 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
29142053 TTTTAGATTT
* *
29142063 TTATTTTTATTTTTATTTATTAAA
1 TTATTTTAATTTTTATTGATTAAA
29142087 TTATTTGTAATTTTTA-TGATTA
1 TTATTT-TAATTTTTATTGATTA
29142109 GGTTGGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (24 bp):
TTATTTTAATTTTTATTGATTAAA
Found at i:29142132 original size:18 final size:18
Alignment explanation
Indices: 29142109--29142143 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29142099 TTTATGATTA
29142109 GGTTGGGTAATTGGGTTG
1 GGTTGGGTAATTGGGTTG
*
29142127 GGTTGGGTACTTGGGTT
1 GGTTGGGTAATTGGGTT
29142144 AATATATATT
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:0.09, C:0.03, G:0.49, T:0.40
Consensus pattern (18 bp):
GGTTGGGTAATTGGGTTG
Found at i:29143915 original size:48 final size:48
Alignment explanation
Indices: 29143844--29144166 Score: 320
Period size: 48 Copynumber: 6.8 Consensus size: 48
29143834 GTTATGTACA
* * * *
29143844 ATCCCATGTAAGACCACGTCTGGGACATGGCTTTGGCATCGATATGTG
1 ATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCGATATATG
*** *
29143892 ATTTTATGTAAGACCATAG-CTGGG-C-T---ATCGGCATCGATATATG
1 ATCCCATGTAAGACCAT-GCCTGGGACATGGCATTGGCATCGATATATG
* * * * *
29143935 ATCCCATGCAAGACCATGTCTGGGCCATGGCATTGGCATCGATCTACG
1 ATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCGATATATG
** * * * *
29143983 ATCCCATGTAAGACCATATCTGGGACATGGTATTGGAATCTATCTATG
1 ATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCGATATATG
*
29144031 ATCCCGA-GTAAGACCATGCCTGGGACATGGCATTGGCATCGATCTATG
1 ATCCC-ATGTAAGACCATGCCTGGGACATGGCATTGGCATCGATATATG
* * *
29144079 ATCCCACGTAAGACCATGCCTGGGACATGGCATTGGCATTGATATGTG
1 ATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCGATATATG
* ** *
29144127 ATCCTATGTAAGACCATATAC-GGGATATGGCATTGGCATC
1 ATCCCATGTAAGACCAT-GCCTGGGACATGGCATTGGCATC
29144167 CTACCATGTG
Statistics
Matches: 230, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
42 1 0.00
43 32 0.14
44 1 0.00
45 1 0.00
46 1 0.00
47 2 0.01
48 189 0.82
49 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (48 bp):
ATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCGATATATG
Found at i:29147208 original size:53 final size:54
Alignment explanation
Indices: 29147139--29147345 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 54
29147129 TTCCTTTTTA
* * * * *
29147139 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGCATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * *
29147192 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGTCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * *
29147246 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
29147301 AACTTACCAATGCCATGCCTTGGCATGGTTTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
29147346 AAACCCTAAT
Statistics
Matches: 121, Mismatches: 31, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 44 0.36
54 37 0.31
55 40 0.33
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:29147278 original size:55 final size:53
Alignment explanation
Indices: 29147151--29147345 Score: 165
Period size: 55 Copynumber: 3.6 Consensus size: 53
29147141 CTTACCATTT
* *
29147151 CCATGTCTTGACATGGTCTTACGTGGCATCCTTGCCTTATGAACTCACCATTG
1 CCATGTCTTGACATGGTCTTACATGGCATCCTTGCCTTATGAACTCACCAATG
* * * * * ** * *
29147204 CCATGCCTTGGCATGGTCTTACATGGGATCTTTGTCTTATAGTAGTTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGCATCCTTGCCTTAT-G-AACTCACCAATG
*** * * *
29147259 CCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAATG
1 CCATGTCTTGACATGGTCTTACATGGCATCCTTGCCTTAT-GAACTCACCAATG
* * * * *
29147313 CCATGCCTTGGCATGGTTTTACTTGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGCATCCTT
29147346 AAACCCTAAT
Statistics
Matches: 111, Mismatches: 29, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 34 0.31
54 37 0.33
55 40 0.36
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGCATCCTTGCCTTATGAACTCACCAATG
Found at i:29150293 original size:41 final size:40
Alignment explanation
Indices: 29150245--29150344 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 40
29150235 TCGACCTCAA
* *
29150245 GTCGATGAGACACTGGGTGTCACTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
29150285 ATTCGATGAGTTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
29150323 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
29150345 ACTTTGCTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
37 10 0.22
38 18 0.39
39 4 0.09
40 3 0.07
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:29152419 original size:2 final size:2
Alignment explanation
Indices: 29152412--29152444 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29152402 GACATGCAAA
29152412 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29152445 CTTTCGCGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29159518 original size:105 final size:101
Alignment explanation
Indices: 29159395--29159593 Score: 274
Period size: 105 Copynumber: 1.9 Consensus size: 101
29159385 ACACTCGTAA
*
29159395 TGCCATAACCCAGCTATGGCCTTATCA-TCAAGATGCCATAGCCTAGCTATGGTCTTACACTTAT
1 TGCCATAACCCAGCTATGGCCTTATCACTCAA-ATGCCATAGCCCAGCTATGGTCTTACA-TT-T
29159459 ACATATACTGCCATGGTCCAACCATGGTCTTATCTTCACGG
63 A-A-ATACTGCCATGGTCCAACCATGGTCTTATCTTCACGG
* * * *
29159500 TGCCATAACCCAGTTATGGTCTTTTCACTGAAATGCCATAGCCCAGCTATGGTCTTACATTTAAA
1 TGCCATAACCCAGCTATGGCCTTATCACTCAAATGCCATAGCCCAGCTATGGTCTTACATTTAAA
* * *
29159565 TATTTCCGTGGTCCAACCATGGTCTTATC
66 TACTGCCATGGTCCAACCATGGTCTTATC
29159594 CGTCAATTCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
101 27 0.32
102 1 0.01
103 2 0.02
104 2 0.02
105 50 0.59
106 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (101 bp):
TGCCATAACCCAGCTATGGCCTTATCACTCAAATGCCATAGCCCAGCTATGGTCTTACATTTAAA
TACTGCCATGGTCCAACCATGGTCTTATCTTCACGG
Found at i:29161939 original size:46 final size:45
Alignment explanation
Indices: 29161856--29162000 Score: 161
Period size: 46 Copynumber: 3.2 Consensus size: 45
29161846 TCCCATCCAC
* *
29161856 GGTCTTATTTATTT-TCGGCATGA-TGCCATAGTGTCTTTCAATAAT
1 GGTCTTATTCATTTCTCGTCAT-ATTGCCATAGTGTCTTTCAAT-AT
* *
29161901 GGTCTTATTCATTTCTCGTCATATTGTCATAGTTTCTTTCAATCAT
1 GGTCTTATTCATTTCTCGTCATATTGCCATAGTGTCTTTCAAT-AT
** *
29161947 TATCTTATTCATTTC-CTGTCATGTTGCCATAGTGTCTTTCAACTAT
1 GGTCTTATTCATTTCTC-GTCATATTGCCATAGTGTCTTTCAA-TAT
29161993 GGTCTTAT
1 GGTCTTAT
29162001 ACGCCTGAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
45 15 0.18
46 68 0.81
47 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.48
Consensus pattern (45 bp):
GGTCTTATTCATTTCTCGTCATATTGCCATAGTGTCTTTCAATAT
Found at i:29162038 original size:45 final size:45
Alignment explanation
Indices: 29161971--29162090 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 45
29161961 CCTGTCATGT
* * * *
29161971 TGCCATAGTGTCTTTCAACTATGGTCTTA-TACGCCTGAATCGTGA
1 TGCCATAGAGTCTTTCAGCTATGGTCTTACT-CACCTAAATCGTGA
* **
29162016 TGCCATAGAGTCTCTCAGCTATGGTCTTACTCATTTAAATCGTGA
1 TGCCATAGAGTCTTTCAGCTATGGTCTTACTCACCTAAATCGTGA
*
29162061 TGCCATA-ACGTCTTTCAGCGATGGTCTTAC
1 TGCCATAGA-GTCTTTCAGCTATGGTCTTAC
29162091 CCGTCTGAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.02
45 62 0.97
46 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (45 bp):
TGCCATAGAGTCTTTCAGCTATGGTCTTACTCACCTAAATCGTGA
Found at i:29162106 original size:22 final size:22
Alignment explanation
Indices: 29162080--29162124 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29162070 GTCTTTCAGC
29162080 GATGGTCTTACCCGTCTGAATT
1 GATGGTCTTACCCGTCTGAATT
29162102 GATGGTCTTACCCGTCTGAATT
1 GATGGTCTTACCCGTCTGAATT
29162124 G
1 G
29162125 TGATGCCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (22 bp):
GATGGTCTTACCCGTCTGAATT
Found at i:29163200 original size:9 final size:9
Alignment explanation
Indices: 29163188--29163237 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
29163178 TTTTTAATCA
29163188 AATTAACTG
1 AATTAACTG
29163197 AATTAA-TCG
1 AATTAACT-G
*
29163206 AATTAACCG
1 AATTAACTG
29163215 AATTAA-TCG
1 AATTAACT-G
*
29163224 AATTAACCG
1 AATTAACTG
29163233 AATTA
1 AATTA
29163238 CTTGGGTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
8 1 0.03
9 33 0.97
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTAACTG
Found at i:29163204 original size:18 final size:18
Alignment explanation
Indices: 29163181--29163237 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
29163171 TATATGTTTT
* *
29163181 TTAATCAAATTAACTGAA
1 TTAATCGAATTAACCGAA
29163199 TTAATCGAATTAACCGAA
1 TTAATCGAATTAACCGAA
29163217 TTAATCGAATTAACCGAA
1 TTAATCGAATTAACCGAA
29163235 TTA
1 TTA
29163238 CTTGGGTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.32
Consensus pattern (18 bp):
TTAATCGAATTAACCGAA
Found at i:29168475 original size:28 final size:28
Alignment explanation
Indices: 29168439--29168498 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
29168429 ATATGATAAC
*
29168439 ATTTTTTAGCTTTCTATTATGATATGTG
1 ATTTGTTAGCTTTCTATTATGATATGTG
29168467 ATTTGTTAGCTTTCTATTATGATATGTG
1 ATTTGTTAGCTTTCTATTATGATATGTG
29168495 ATTT
1 ATTT
29168499 TACATCAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.57
Consensus pattern (28 bp):
ATTTGTTAGCTTTCTATTATGATATGTG
Found at i:29174044 original size:25 final size:26
Alignment explanation
Indices: 29174009--29174062 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
29173999 AATTCTACTA
* *
29174009 TTTTTCTTCTTTCT-CTTTGTT-TTC
1 TTTTTCTTCTTCCTCCTTTATTGTTC
29174033 TTTTTCTCTCTTCCTCCTTTATTGTTC
1 TTTTTCT-TCTTCCTCCTTTATTGTTC
29174060 TTT
1 TTT
29174063 CTAACAAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 6 0.24
26 6 0.24
27 6 0.24
ACGTcount: A:0.02, C:0.24, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTTCTTCTTCCTCCTTTATTGTTC
Found at i:29174087 original size:6 final size:6
Alignment explanation
Indices: 29174070--29174108 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
29174060 TTTCTAACAA
* * *
29174070 GCCGCT GTCGCT GCCGCT GCCGCT GCCTCT GCCTCT GCC
1 GCCGCT GCCGCT GCCGCT GCCGCT GCCGCT GCCGCT GCC
29174109 TCCACACCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.49, G:0.28, T:0.23
Consensus pattern (6 bp):
GCCGCT
Found at i:29178007 original size:17 final size:16
Alignment explanation
Indices: 29177985--29178026 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
29177975 GAAAATTCTG
29177985 ATAAATATATAACAATT
1 ATAAATATATAA-AATT
29178002 ATAAATATAT-AAATT
1 ATAAATATATAAAATT
29178017 -TAAATATATA
1 ATAAATATATA
29178027 TATAAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.38
15 4 0.17
16 1 0.04
17 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAATATATAAAATT
Found at i:29178083 original size:8 final size:9
Alignment explanation
Indices: 29178057--29178104 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
29178047 TTACACACGT
29178057 AAATACATA
1 AAATACATA
*
29178066 AAATAGATA
1 AAATACATA
29178075 AAATA-ATA
1 AAATACATA
29178083 AAATA-AT-
1 AAATACATA
29178090 AAATACATA
1 AAATACATA
29178099 ACAATA
1 A-AATA
29178105 AGAATTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
7 5 0.14
8 12 0.34
9 14 0.40
10 4 0.11
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (9 bp):
AAATACATA
Found at i:29178083 original size:17 final size:17
Alignment explanation
Indices: 29178057--29178105 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
29178047 TTACACACGT
29178057 AAATACATAAAATAGATA
1 AAATACATAAAATA-ATA
29178075 AAATA-ATAAAATAAT-
1 AAATACATAAAATAATA
29178090 AAATACATAACAATAA
1 AAATACATAA-AATAA
29178106 GAATTTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.17
16 6 0.21
17 13 0.45
18 5 0.17
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (17 bp):
AAATACATAAAATAATA
Found at i:29183970 original size:22 final size:22
Alignment explanation
Indices: 29183945--29183994 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
29183935 TTTAATAAAA
29183945 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
29183967 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
*
29183989 ACAATA
1 AAAATA
29183995 CATTGTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:29191769 original size:44 final size:44
Alignment explanation
Indices: 29191718--29191805 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
29191708 GATCATGCTT
* *
29191718 ACGAATGTGATTAATTTAATGATTTTAATAATATAACTCACCTA
1 ACGAATGTGATAAATTTAATGATCTTAATAATATAACTCACCTA
29191762 ACGAATGTGATAAATTTAATGATCTTAATAATATAACTCACCTA
1 ACGAATGTGATAAATTTAATGATCTTAATAATATAACTCACCTA
29191806 GATGTGGCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (44 bp):
ACGAATGTGATAAATTTAATGATCTTAATAATATAACTCACCTA
Found at i:29194333 original size:42 final size:42
Alignment explanation
Indices: 29194273--29194356 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
29194263 AAGATTAATT
29194273 TGGCACTATAGATAAAGAGAAACGAGATTCAAGTCGCGATCG
1 TGGCACTATAGATAAAGAGAAACGAGATTCAAGTCGCGATCG
* * * *
29194315 TGGCATTATAGATCAAGAGAAATGAGATTCGAGTCGCGATCG
1 TGGCACTATAGATAAAGAGAAACGAGATTCAAGTCGCGATCG
29194357 AGGAAAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.21
Consensus pattern (42 bp):
TGGCACTATAGATAAAGAGAAACGAGATTCAAGTCGCGATCG
Found at i:29194982 original size:177 final size:177
Alignment explanation
Indices: 29194686--29195027 Score: 684
Period size: 177 Copynumber: 1.9 Consensus size: 177
29194676 GGATGGTTGA
29194686 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGGTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGGTCGTTGAGT
29194751 TGAGTCCAAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATATGAGGCACTTATGTGC
66 TGAGTCCAAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATATGAGGCACTTATGTGC
29194816 AAATTATCCGTGTATCCGAGTTGTATTCCGATGTGAAATGTAACTAG
131 AAATTATCCGTGTATCCGAGTTGTATTCCGATGTGAAATGTAACTAG
29194863 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGGTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGGTCGTTGAGT
29194928 TGAGTCCAAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATATGAGGCACTTATGTGC
66 TGAGTCCAAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATATGAGGCACTTATGTGC
29194993 AAATTATCCGTGTATCCGAGTTGTATTCCGATGTG
131 AAATTATCCGTGTATCCGAGTTGTATTCCGATGTG
29195028 TTCAACGGGT
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 165 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (177 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGGTCGTTGAGT
TGAGTCCAAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATATGAGGCACTTATGTGC
AAATTATCCGTGTATCCGAGTTGTATTCCGATGTGAAATGTAACTAG
Found at i:29200009 original size:206 final size:207
Alignment explanation
Indices: 29199648--29200411 Score: 1158
Period size: 206 Copynumber: 3.7 Consensus size: 207
29199638 AGATCTGCTT
* *
29199648 CTTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
** * *
29199713 GCGAAAACCAAATCAGCTATGTCTTTGA-TTTGTTCCTTGTAAACACAAGGATGCCAAACCATCT
66 ATGAAAGCCAAATCAGCTATGTCTTCGATTTTGTTCCTTGTAAACACAAGGATGCCAAACCATCT
* * * ** * *
29199777 TGGATCTACTTCAGTCTAATCATCTGAAGGTTAGATATGCTATGTGTCTGCCCTCCGTCGAATAT
131 TGGATCTGCTTCAGTATAAACATCTGAAGGCCAGATATGCTATGTATCTGCTCTCCGTCGAATAT
29199842 GGAGACGCCAAA
196 GGAGACGCCAAA
*
29199854 CTTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* *
29199919 ATGAAAGCTAAATCAGCTATGAT-TTCGA-TTTGTTCCTTGTAAACACAAGGATGCCAAATCATC
66 ATGAAAGCCAAATCAGCTATG-TCTTCGATTTTGTTCCTTGTAAACACAAGGATGCCAAACCATC
*
29199982 TTGGATCTGCTTCAGTATAAACATCTGAAGGCCAGATTTGCTATGTATCTGCTCTCCGTCGAATA
130 TTGGATCTGCTTCAGTATAAACATCTGAAGGCCAGATATGCTATGTATCTGCTCTCCGTCGAATA
*
29200047 TAGAGACGCCAAA
195 TGGAGACGCCAAA
* **
29200060 CTTCGATTTGTTCTCTGACAATATAGAA-ATGCCAAATCATCTTAGATTTGCTTCATTGTAAGCA
1 CTTCGATTTGTTCTCTGACAATACA-AAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCA
* *
29200124 CATGAAAGCCAAATAAGCTATGTCTTCGATTTTGTTCCTTGTAAGCACAAGGATGCCAAACCATC
65 CATGAAAGCCAAATCAGCTATGTCTTCGATTTTGTTCCTTGTAAACACAAGGATGCCAAACCATC
* * * *
29200189 TTGGATCTGCTTCAGTATAAACATCTAAAGGCCAGATCTGCTATGTATATGCTCTCCGTCAAATA
130 TTGGATCTGCTTCAGTATAAACATCTGAAGGCCAGATATGCTATGTATCTGCTCTCCGTCGAATA
29200254 TGGAGACGCCAAA
195 TGGAGACGCCAAA
* * * *
29200267 CTTTGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * *
29200332 GTGAAAGCCAAATCAACTATGTCTTTGATTTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
66 ATGAAAGCCAAATCAGCTATGTCTTCGATTTTGTTCCTTGTAAACACAAGGATGCCAAACCATCT
29200397 TGGATCTTGCTTCAG
131 TGGATC-TGCTTCAG
29200412 GCAGATCTGC
Statistics
Matches: 514, Mismatches: 38, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
205 1 0.00
206 269 0.52
207 236 0.46
208 8 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (207 bp):
CTTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
ATGAAAGCCAAATCAGCTATGTCTTCGATTTTGTTCCTTGTAAACACAAGGATGCCAAACCATCT
TGGATCTGCTTCAGTATAAACATCTGAAGGCCAGATATGCTATGTATCTGCTCTCCGTCGAATAT
GGAGACGCCAAA
Found at i:29202877 original size:213 final size:213
Alignment explanation
Indices: 29202507--29202931 Score: 645
Period size: 213 Copynumber: 2.0 Consensus size: 213
29202497 ACATAGTCGC
* *
29202507 AAGCTAACCTTCTCAAAGTTCGTTTGTCATTTTCATTGGCCTATTCAGGGTATTTACGATCTCTC
1 AAGCTAACCTCCTCAAAGTTCGTTTGTCATTTTCACTGGCCTATTCAGGGTATTTACGATCTCTC
** **
29202572 ACATATCGTAATATATCCTGATACCAGGGGTTATCATCATTTTTTTCCTTCTCAATATTACAACA
66 ACATATCACAATATATCCTGATACCAGGGGTTATCATCATTTCCTTCCTTCTCAATATTACAACA
* *
29202637 ACGAGCTGGAGCCTCGTAGATACTCATTTGAATTGG-TCTCATCTCTTCCTCTTTATTCGCCTTA
131 ACAAGCTGGAGCCTCGTAGACACTCATTTGAATTGGCT-TCATCTCTTCCTCTTTATTCGCCTTA
29202701 ACCATTGAGGCCAAGGTTG
195 ACCATTGAGGCCAAGGTTG
* * * *
29202720 AAGCTAATCTCCTTAAAGTTCGTTTGTCATTTTCACTGGCCTGTTCAGGGTATTTACGATTTCTC
1 AAGCTAACCTCCTCAAAGTTCGTTTGTCATTTTCACTGGCCTATTCAGGGTATTTACGATCTCTC
* * ** *
29202785 ACATATCACAATATATCTTGATAGCAGGGGTTATTGTCATTTCCTTCCTTCTCAATGTTACAACA
66 ACATATCACAATATATCCTGATACCAGGGGTTATCATCATTTCCTTCCTTCTCAATATTACAACA
* * * *
29202850 ATAAGCTGGAGCCTCGTAGACACTCATTTGAATTGGCTTCGTCTCTTCTTCTTTATTCGCCTTGA
131 ACAAGCTGGAGCCTCGTAGACACTCATTTGAATTGGCTTCATCTCTTCCTCTTTATTCGCCTTAA
29202915 CCATTGAGGCCAAGGTT
196 CCATTGAGGCCAAGGTT
29202932 ACTAAAGCAT
Statistics
Matches: 190, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
213 189 0.99
214 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (213 bp):
AAGCTAACCTCCTCAAAGTTCGTTTGTCATTTTCACTGGCCTATTCAGGGTATTTACGATCTCTC
ACATATCACAATATATCCTGATACCAGGGGTTATCATCATTTCCTTCCTTCTCAATATTACAACA
ACAAGCTGGAGCCTCGTAGACACTCATTTGAATTGGCTTCATCTCTTCCTCTTTATTCGCCTTAA
CCATTGAGGCCAAGGTTG
Found at i:29208701 original size:15 final size:15
Alignment explanation
Indices: 29208659--29208708 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
29208649 ATAACTTTGA
*
29208659 ATGCAAATG-ATGCG
1 ATGCAAATGCATGAG
29208673 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
29208688 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
29208702 ATGCAAA
1 ATGCAAA
29208709 AAGAATATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:29208752 original size:14 final size:14
Alignment explanation
Indices: 29208729--29208758 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29208719 ATTCTGGTTC
29208729 AACTTCATTTAGAA
1 AACTTCATTTAGAA
*
29208743 AACTTTATTTAGAA
1 AACTTCATTTAGAA
29208757 AA
1 AA
29208759 AGAATATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AACTTCATTTAGAA
Found at i:29223595 original size:206 final size:207
Alignment explanation
Indices: 29223019--29223782 Score: 1174
Period size: 206 Copynumber: 3.7 Consensus size: 207
29223009 GCAGATCTGC
*
29223019 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAAATCAAAGACATAGT
1 CTGAAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAAATCAAAGACATAGC
29223084 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCA
65 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCA
* * * *
29223149 GAGAACAAATCAAAGTTTGGCGTCTCCATATTTGACGGAGAGCATATACATAGCAGATCTGGCCT
130 GAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAAATCTGGCCT
*
29223214 TTAGATGTTTATA
195 TCAGATGTTTATA
*
29223227 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAAATCGAAGACATAGCT
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAAATCAAAGACATAGCT
* * * *
29223292 TATTTGGCTTTCATGTGCTTACAATGAAGCAAATCTAAGATGATTTGGCATTTCTATATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAG
*
29223357 AGAACAAATCGAAGTTTGGCGTCTCTATATTCGACGGAGAGCAGATACATAGCAAATCTGGCCTT
131 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAAATCTGGCCTT
29223422 CAGATGTTTATA
196 CAGATGTTTATA
* * *
29223434 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAAC-AAATCGAAA-TCATAGC
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAAATC-AAAGACATAGC
* * * * * *
29223497 TGATTTAGCTTTCATGTGCTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTTTGTATTGTCA
65 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCA
* * * **
29223562 GAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCATATCTAACCT
130 GAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAAATCTGGCCT
* *
29223627 TCAGATGATTAGA
195 TCAGATGTTTATA
* *
29223640 CTGAAGTAGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAGGAAC-AAATCAAAGACATAGCT
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAAATCAAAGACATAGCT
* * * * *
29223704 GATTTGGTTTTCGCGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTTAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAG
29223769 AGAACAAATCGAAG
131 AGAACAAATCGAAG
29223783 AAGCAGATCT
Statistics
Matches: 512, Mismatches: 42, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
205 3 0.01
206 267 0.52
207 235 0.46
208 7 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (207 bp):
CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAAATCAAAGACATAGCT
GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAG
AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAAATCTGGCCTT
CAGATGTTTATA
Found at i:29225582 original size:46 final size:47
Alignment explanation
Indices: 29225474--29225569 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 47
29225464 AAATATTAGT
*
29225474 TATATATTATTATTACTATTCAATATTTTTATTATCATATATTTTATC
1 TATAAATTATTATTA-TATTCAATATTTTTATTATCATATATTTTATC
** *
29225522 TATAAATTA-TATTATATTGTATA-TTTTATT-TTATATATTTT-T-
1 TATAAATTATTATTATATTCAATATTTTTATTATCATATATTTTATC
29225564 TATAAA
1 TATAAA
29225570 ATTGTATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
42 6 0.14
43 1 0.02
44 10 0.23
45 7 0.16
46 7 0.16
47 5 0.11
48 8 0.18
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (47 bp):
TATAAATTATTATTATATTCAATATTTTTATTATCATATATTTTATC
Found at i:29225872 original size:16 final size:15
Alignment explanation
Indices: 29225834--29225887 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 15
29225824 TATTATATGT
29225834 TATATTTTTATATAC
1 TATATTTTTATATAC
*
29225849 TATNTTTTT-TATAC
1 TATATTTTTATATAC
*
29225863 TA-ATTATT-T-TAC
1 TATATTTTTATATAC
*
29225875 CATATTTTTATAT
1 TATATTTTTATAT
29225888 GCAAAATACT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 4 0.13
13 10 0.32
14 8 0.26
15 9 0.29
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTTTTATATAC
Found at i:29225912 original size:11 final size:10
Alignment explanation
Indices: 29225897--29225955 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
29225887 TGCAAAATAC
29225897 TTATTATATT
1 TTATTATATT
29225907 CTTATTAT-TT
1 -TTATTATATT
29225917 TATATTATATT
1 T-TATTATATT
**
29225928 TCCTTATATT
1 TTATTATATT
29225938 TTATTCATATT
1 TTATT-ATATT
*
29225949 ATATTAT
1 TTATTAT
29225956 TATATATAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
9 1 0.03
10 20 0.50
11 19 0.47
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTATATT
Found at i:29230868 original size:45 final size:44
Alignment explanation
Indices: 29230814--29230952 Score: 136
Period size: 45 Copynumber: 3.1 Consensus size: 44
29230804 CCTGAGCTTA
* *
29230814 TGAACAGTAAGCTTTAATGAGCTGAAACGGTAAGCTCTATCGAGC
1 TGAACAGTAAGCTCTAATGAGCT-AAACAGTAAGCTCTATCGAGC
* * * * *
29230859 TGAACAGTAAGCTCTATTAAGCTAAGCAGTAAACTCTATTGAGC
1 TGAACAGTAAGCTCTAATGAGCTAAACAGTAAGCTCTATCGAGC
* * *
29230903 TAAAACAGTAAGCTCCAATGAGCTAAAAATAGTAAGCTCT-TACGAGC
1 T-GAACAGTAAGCTCTAATGAGCT--AAACAGTAAGCTCTAT-CGAGC
29230950 TGA
1 TGA
29230953 TATTTCGATA
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
44 18 0.24
45 38 0.51
46 2 0.03
47 16 0.22
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (44 bp):
TGAACAGTAAGCTCTAATGAGCTAAACAGTAAGCTCTATCGAGC
Found at i:29230930 original size:23 final size:22
Alignment explanation
Indices: 29230816--29230929 Score: 113
Period size: 22 Copynumber: 5.1 Consensus size: 22
29230806 TGAGCTTATG
*
29230816 AACAGTAAGCTTTAATGAGCTGA
1 AACAGTAAGCTCTAATGAGCT-A
* *
29230839 AACGGTAAGCTCT-ATCGAGCTG
1 AACAGTAAGCTCTAAT-GAGCTA
* *
29230861 AACAGTAAGCTCTATTAAGCTA
1 AACAGTAAGCTCTAATGAGCTA
* * *
29230883 AGCAGTAAACTCTATTGAGCTAA
1 AACAGTAAGCTCTAATGAGCT-A
*
29230906 AACAGTAAGCTCCAATGAGCTA
1 AACAGTAAGCTCTAATGAGCTA
29230928 AA
1 AA
29230930 AATAGTAAGC
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
22 39 0.53
23 35 0.47
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (22 bp):
AACAGTAAGCTCTAATGAGCTA
Found at i:29230949 original size:24 final size:23
Alignment explanation
Indices: 29230899--29230950 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
29230889 AAACTCTATT
*
29230899 GAGCTAAAACAGTAAGCTCCAAT
1 GAGCTAAAACAGTAAGCTCCAAC
* **
29230922 GAGCTAAAAATAGTAAGCTCTTAC
1 GAGCT-AAAACAGTAAGCTCCAAC
29230946 GAGCT
1 GAGCT
29230951 GATATTTCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (23 bp):
GAGCTAAAACAGTAAGCTCCAAC
Found at i:29232863 original size:18 final size:20
Alignment explanation
Indices: 29232835--29232875 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
29232825 ATCCATACTA
29232835 AACCTTTTTG-CTTAAAATC
1 AACCTTTTTGCCTTAAAATC
29232854 AACC-TTTTGCCTTAAAATC
1 AACCTTTTTGCCTTAAAATC
29232873 AAC
1 AAC
29232876 TCCGTTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (20 bp):
AACCTTTTTGCCTTAAAATC
Found at i:29233016 original size:27 final size:27
Alignment explanation
Indices: 29232978--29233036 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
29232968 TTTACAGGTC
29232978 ACATAAATAGGCATTTCATGTCATATA
1 ACATAAATAGGCATTTCATGTCATATA
29233005 ACATAAATAGGCATTTCATGTCATATA
1 ACATAAATAGGCATTTCATGTCATATA
29233032 ACATA
1 ACATA
29233037 TTGTCTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (27 bp):
ACATAAATAGGCATTTCATGTCATATA
Found at i:29252185 original size:43 final size:43
Alignment explanation
Indices: 29252110--29252220 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 43
29252100 CATATCGATA
* * * *
29252110 CCAATGTCCCAAACATGGCCTTACACGAAATCATATA-ACGATG
1 CCAATGTCCCAGACATGGTCTTACACGAAATCACA-AGACAATG
* * * **
29252153 TCAATGTCCCAGACATGGTCTTTCTCTTAATCACAAGACAATG
1 CCAATGTCCCAGACATGGTCTTACACGAAATCACAAGACAATG
* *
29252196 CCATTGTCTCAGACATGGTCTTACA
1 CCAATGTCCCAGACATGGTCTTACA
29252221 TGTAAACATA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 1 0.02
43 52 0.98
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (43 bp):
CCAATGTCCCAGACATGGTCTTACACGAAATCACAAGACAATG
Found at i:29256603 original size:40 final size:40
Alignment explanation
Indices: 29256466--29256596 Score: 187
Period size: 40 Copynumber: 3.3 Consensus size: 40
29256456 GACTAAGATT
*
29256466 CGAAGGCATTTGTGCGAGTTACTAAATTCGGGTTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
29256506 CGAA-GCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
* * *
29256545 TGAAGGTATTTGTGCGAGTTACTATAA-CCGGG-CAATGTCC
1 CGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAA-GTCC
29256585 CGAAGGCATTTG
1 CGAAGGCATTTG
29256597 AACGAGTAGC
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
39 39 0.48
40 41 0.50
41 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
Found at i:29264552 original size:40 final size:40
Alignment explanation
Indices: 29264469--29264654 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
29264459 TTGAATGATG
* * * *
29264469 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
29264509 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29264549 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29264589 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29264630 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29264655 AACGAGTAGC
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 118 0.91
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29264672 original size:80 final size:80
Alignment explanation
Indices: 29264469--29264687 Score: 243
Period size: 80 Copynumber: 2.8 Consensus size: 80
29264459 TTGAATGATG
** * * **
29264469 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAAGT-ACTATATCCGGGTTAAGATCCGAAGGCATT
29264533 TGTGCGAGTTACTAAA
65 TGTGCGAGTTACTAAA
* ** * *
29264549 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGTTAAG-TCCTGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAAGTACTATATCCGGGTTAAGATCC-GAAGGCATT
29264613 TGTGCGAGTTACTATAA
65 TGTGCGAGTTACTA-AA
*
29264630 -CCGGGCTATGTCCCGAAGGCATTTGAACG-AGTAGCTATATCC-GGTTAA-ATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAAGTA-CTATATCCGGGTTAAGA-TCCGAAGG
29264688 TACGTGATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
79 17 0.14
80 91 0.76
81 12 0.10
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAAGTACTATATCCGGGTTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:29269611 original size:11 final size:11
Alignment explanation
Indices: 29269584--29269615 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
29269574 TACTGAACAA
29269584 TACACAT-CAT
1 TACACATACAT
29269594 T-CACATACAT
1 TACACATACAT
29269604 TACACATACAT
1 TACACATACAT
29269615 T
1 T
29269616 TATGTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.25
10 5 0.25
11 10 0.50
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (11 bp):
TACACATACAT
Found at i:29271124 original size:43 final size:43
Alignment explanation
Indices: 29271063--29271191 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 43
29271053 CAATTTCATA
* * *** * *
29271063 TCCCAAATATGGTCTTACATGTTCTCACATATCGATGCCAATG
1 TCCCAAACATGGTCTTACACGAAATCACAAAACGATGCCAATG
* *
29271106 TCCCAAACATGGTCTTACACGAAATCATAAAACGATGCTAATG
1 TCCCAAACATGGTCTTACACGAAATCACAAAACGATGCCAATG
* * * *
29271149 TCCCAGACATGGTCTTACACGTAATCACAATACAATGCCAATG
1 TCCCAAACATGGTCTTACACGAAATCACAAAACGATGCCAATG
29271192 GTCTTACATG
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (43 bp):
TCCCAAACATGGTCTTACACGAAATCACAAAACGATGCCAATG
Found at i:29271237 original size:43 final size:42
Alignment explanation
Indices: 29271102--29271252 Score: 142
Period size: 43 Copynumber: 3.8 Consensus size: 42
29271092 TATCGATGCC
* * *
29271102 AATGTCCCAAACATGGTCTTACACGAAATCATAAAACGATGCT
1 AATGTCCCAAACATGGTCTTACACGTAATCAT-AAACAATACT
*
29271145 AATGTCCCAGACATGGTCTTACACGTAATC----ACAATAC-
1 AATGTCCCAAACATGGTCTTACACGTAATCATAAACAATACT
* *
29271182 AATG--CC--A-ATGGTCTTACATGTAATCATAATACAATTCT
1 AATGTCCCAAACATGGTCTTACACGTAATCATAA-ACAATACT
* *
29271220 AATGTCCCAAACATGGTCTTACATGTAAACATA
1 AATGTCCCAAACATGGTCTTACACGTAATCATA
29271253 TCTTAGTAGT
Statistics
Matches: 90, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
32 17 0.19
33 1 0.01
35 2 0.02
37 10 0.11
38 9 0.10
40 2 0.02
42 1 0.01
43 48 0.53
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (42 bp):
AATGTCCCAAACATGGTCTTACACGTAATCATAAACAATACT
Found at i:29272935 original size:25 final size:25
Alignment explanation
Indices: 29272894--29272941 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
29272884 TCATATTGAT
*
29272894 GTATGCTCATACGAGCTATGAATTA
1 GTATGCTCATACAAGCTATGAATTA
*
29272919 GTATGCTC-TCACAAGCTGTGAAT
1 GTATGCTCAT-ACAAGCTATGAAT
29272942 CGGGAAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (25 bp):
GTATGCTCATACAAGCTATGAATTA
Found at i:29287826 original size:128 final size:128
Alignment explanation
Indices: 29287670--29287925 Score: 503
Period size: 128 Copynumber: 2.0 Consensus size: 128
29287660 TGTCACAATA
29287670 ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTAAA
1 ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTAAA
29287735 TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
66 TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
*
29287798 ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTATA
1 ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTAAA
29287863 TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
66 TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
29287926 CATTTACTAC
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (128 bp):
ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTAAA
TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
Found at i:29292608 original size:128 final size:128
Alignment explanation
Indices: 29292448--29292703 Score: 503
Period size: 128 Copynumber: 2.0 Consensus size: 128
29292438 TGTCACAATA
29292448 ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTAAA
1 ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTAAA
29292513 TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
66 TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
*
29292576 ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTATA
1 ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTAAA
29292641 TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
66 TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
29292704 CATTTACTAC
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (128 bp):
ATACTTATATGTGGATACAAAGTAAAAGGAATGACAGTAAGATTATCAATTTGTCACAATTTAAA
TTGACATTATTAGTACAATTGAAATGCATGTTAAAGTAAACCAAAAGTTTACTGATACAAATG
Found at i:29295124 original size:20 final size:19
Alignment explanation
Indices: 29295097--29295138 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
29295087 ATATTATTAG
*
29295097 ATTTTTAATAATTATTTTATA
1 ATTTTAAATAA-TA-TTTATA
29295118 ATTTTAAATAATATTTATA
1 ATTTTAAATAATATTTATA
29295137 AT
1 AT
29295139 ATTCAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
21 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTAAATAATATTTATA
Found at i:29295220 original size:11 final size:10
Alignment explanation
Indices: 29295204--29295279 Score: 50
Period size: 11 Copynumber: 7.4 Consensus size: 10
29295194 TAAACATGTA
29295204 TTTTTAGTAAT
1 TTTTTA-TAAT
29295215 TTTTTAATAAT
1 TTTTT-ATAAT
* *
29295226 TATTTATATT
1 TTTTTATAAT
29295236 TTTTTACTAA-
1 TTTTTA-TAAT
*
29295246 TTTTCAT-A-
1 TTTTTATAAT
29295254 TTTTTATAAAT
1 TTTTTAT-AAT
*
29295265 TTTTAAATAAT
1 TTTT-TATAAT
29295276 TTTT
1 TTTT
29295280 AAGATATTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
8 7 0.13
9 1 0.02
10 15 0.29
11 26 0.50
12 3 0.06
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:29295240 original size:21 final size:20
Alignment explanation
Indices: 29295214--29295258 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
29295204 TTTTTAGTAA
*
29295214 TTTTTTAATAATTATTTATAT
1 TTTTTTAATAATT-TTCATAT
*
29295235 TTTTTTACTAATTTTCATAT
1 TTTTTTAATAATTTTCATAT
29295255 TTTT
1 TTTT
29295259 ATAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTTAATAATTTTCATAT
Found at i:29302343 original size:28 final size:27
Alignment explanation
Indices: 29302280--29302431 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
29302270 ATATTAAGTC
* ** *
29302280 CGCACACTCAGTGCTTTATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
29302307 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
29302335 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
29302362 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
29302390 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
29302417 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29302432 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 65 0.55
28 53 0.45
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:29302364 original size:55 final size:55
Alignment explanation
Indices: 29302280--29302431 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
29302270 ATATTAAGTC
* ** *
29302280 CGCACACTCAGTGCTTTATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
29302335 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
29302390 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
29302432 GCACAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:29309979 original size:3 final size:3
Alignment explanation
Indices: 29309971--29310015 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
29309961 GGTGGAGAAA
29309971 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
29310016 GTGAATCAAA
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:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:29310657 original size:13 final size:13
Alignment explanation
Indices: 29310639--29310666 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29310629 AATTTTAAAC
29310639 AAAACTTCTCAAA
1 AAAACTTCTCAAA
29310652 AAAACTTCTCAAA
1 AAAACTTCTCAAA
29310665 AA
1 AA
29310667 TTTTTTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAACTTCTCAAA
Found at i:29311844 original size:14 final size:14
Alignment explanation
Indices: 29311812--29311848 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
29311802 AATATGCTCA
29311812 AATTTTTA-A-TTT
1 AATTTTTATATTTT
*
29311824 AACTTTTATATTTT
1 AATTTTTATATTTT
29311838 AATTTTTATAT
1 AATTTTTATAT
29311849 AATTTTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 7 0.33
13 1 0.05
14 13 0.62
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
AATTTTTATATTTT
Found at i:29322212 original size:6 final size:6
Alignment explanation
Indices: 29322201--29322229 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29322191 AATGGTTAAT
29322201 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
29322230 GTTAACATTT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:29324120 original size:3 final size:3
Alignment explanation
Indices: 29324093--29324185 Score: 82
Period size: 3 Copynumber: 31.7 Consensus size: 3
29324083 GGAGGAGGAG
* * * * *
29324093 GAA GAG GAA GAA G-A GGA GAA AAA GAA GAA GAA GAA AAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * * *
29324140 GAA GAA GAA GAA GAA AAA G-A GAA GGA GAA GGA GAA AAA GAA TAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
29324186 GAAAATGGAA
Statistics
Matches: 69, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
2 4 0.06
3 65 0.94
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:29324135 original size:21 final size:21
Alignment explanation
Indices: 29324109--29324190 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
29324099 GAAGAAGAGG
29324109 AGAAAAAGAAGAAGAAGAAAA
1 AGAAAAAGAAGAAGAAGAAAA
*
29324130 AGAAAAAGAAGAAGAAGAAGA
1 AGAAAAAGAAGAAGAAGAAAA
* **
29324151 AGAAAAAG-AGAAGGAGAAGG
1 AGAAAAAGAAGAAGAAGAAAA
*
29324171 AGAAAAAGAATAAG-AGAAAA
1 AGAAAAAGAAGAAGAAGAAAA
29324191 TGGAAGGAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
20 22 0.41
21 32 0.59
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (21 bp):
AGAAAAAGAAGAAGAAGAAAA
Found at i:29324144 original size:41 final size:41
Alignment explanation
Indices: 29324094--29324185 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
29324084 GAGGAGGAGG
* *
29324094 AAGAGGAAGAAG-AGGAGAAAAAGAAGAAGAAGAAAAAGAAA
1 AAGAAGAAGAAGAAGAAGAAAAAG-AGAAGAAGAAAAAGAAA
* **
29324135 AAGAAGAAGAAGAAGAAGAAAAAGAGAAGGAGAAGGAGAAA
1 AAGAAGAAGAAGAAGAAGAAAAAGAGAAGAAGAAAAAGAAA
*
29324176 AAGAATAAGA
1 AAGAAGAAGA
29324186 GAAAATGGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 34 0.77
42 10 0.23
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (41 bp):
AAGAAGAAGAAGAAGAAGAAAAAGAGAAGAAGAAAAAGAAA
Found at i:29325564 original size:21 final size:21
Alignment explanation
Indices: 29325538--29325578 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29325528 CAACGTGACA
29325538 AGTTAACTTGCCACATCAGCT
1 AGTTAACTTGCCACATCAGCT
*
29325559 AGTTAACTTGCCACGTCAGC
1 AGTTAACTTGCCACATCAGC
29325579 AATTCTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:29326407 original size:7 final size:7
Alignment explanation
Indices: 29326395--29326430 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
29326385 TAAATTGTTA
29326395 GTGTTTT
1 GTGTTTT
29326402 GTGTTTT
1 GTGTTTT
29326409 GTGTTTT
1 GTGTTTT
*
29326416 GTTTTTT
1 GTGTTTT
29326423 GTGATTTT
1 GTG-TTTT
29326431 TTATTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.03, C:0.00, G:0.25, T:0.72
Consensus pattern (7 bp):
GTGTTTT
Found at i:29326460 original size:12 final size:12
Alignment explanation
Indices: 29326443--29326467 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29326433 ATTAATGTAA
29326443 AATTATTTTGTT
1 AATTATTTTGTT
29326455 AATTATTTTGTT
1 AATTATTTTGTT
29326467 A
1 A
29326468 GTAATTTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
AATTATTTTGTT
Found at i:29326591 original size:7 final size:7
Alignment explanation
Indices: 29326579--29326609 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29326569 TAAATTGTTA
29326579 GTGTTTT
1 GTGTTTT
29326586 GTGTTTT
1 GTGTTTT
29326593 GTGTTTT
1 GTGTTTT
*
29326600 GTATTTT
1 GTGTTTT
29326607 GTG
1 GTG
29326610 ACTTATTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.68
Consensus pattern (7 bp):
GTGTTTT
Found at i:29326609 original size:112 final size:109
Alignment explanation
Indices: 29326478--29326822 Score: 361
Period size: 112 Copynumber: 3.2 Consensus size: 109
29326468 GTAATTTATG
*
29326478 TTAGTGTTTTGTGTTTTGTGATTTTTTAGTAATATAAAATATTTTAAAAAATATTTTTATAGTTA
1 TTAGTGTTTTGTATTTTGTGATTTTTTAGTAAT-TAAAATATTTTAAAAAATA-TTTTATAGTTA
*
29326543 TTTATTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTGTGT
64 TTTATTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTT-AGT
* * * * * *
29326590 TTTGTGTTTTGTATTTTGTGACTTATTAGTAATGTAAATTCTTTTTAAAAAA-ATGTTATAGTTA
1 TTAGTGTTTTGTATTTTGTGATTTTTTAGTAAT-TAAAAT-ATTTTAAAAAATATTTTATAGTTA
* * *
29326654 TTTTATTAGTAATTTATGATTAGGTTATAGACTGTTAGTGTGTTTAGT
64 -TTTATTAGTAATTTATGATTAGTTTATAAATTGTTAGTGT-TTTAGT
* * * *
29326702 TTAG-G----G--TTTTGTGATTTTTTAGTAATT-TAATCTTTT-TAAAATAATTTTATAGTTTT
1 TTAGTGTTTTGTATTTTGTGATTTTTTAGTAATTAAAATATTTTAAAAAAT-ATTTTATAG-TTA
*
29326758 TTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTG-TTTAGT
64 TTTATTAGTAATTTATGATTA-GTT-TATAAATTGTTAGTGTTTTAGT
29326805 TTAGTGTTTTGTGATTTT
1 TTAGTGTTTTGT-ATTTT
29326823 TTATTAATGT
Statistics
Matches: 192, Mismatches: 25, Indels: 33
0.77 0.10 0.13
Matches are distributed among these distances:
101 4 0.02
102 4 0.02
103 40 0.21
104 6 0.03
105 31 0.16
107 1 0.01
108 1 0.01
111 15 0.08
112 77 0.40
113 13 0.07
ACGTcount: A:0.27, C:0.01, G:0.16, T:0.56
Consensus pattern (109 bp):
TTAGTGTTTTGTATTTTGTGATTTTTTAGTAATTAAAATATTTTAAAAAATATTTTATAGTTATT
TATTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTAGT
Found at i:29326753 original size:103 final size:104
Alignment explanation
Indices: 29326490--29326830 Score: 368
Period size: 103 Copynumber: 3.2 Consensus size: 104
29326480 AGTGTTTTGT
* * *
29326490 GTTTTGTGATTTTTTAGTAATATAAAATATTTTAAAAAATATTTTTATAGTTA-TTTATTAGTAA
1 GTTTTGTGATTTTTTAGTAATAT-AAATCTTTT-TAAAATAATTTTATAGTTATTTTATTAGTAA
* * *
29326554 TTTATGATTAGTTTATAAATTGTTAGTGT-TTTGTGTTTTGTG
64 TTTATGATTAGGTTATAAATTGTTAGTGTGTTT-AGTTTAG-G
* * * * *
29326596 TTTTGTATTTTGTGACTTATTAGTAATGTAAATTCTTTTTAAAAAAATGTTATAGTTATTTTATT
1 ----G--TTTTGTGATTTTTTAGTAATATAAA-TCTTTTTAAAATAATTTTATAGTTATTTTATT
* *
29326661 AGTAATTTATGATTAGGTTATAGACTGTTAGTGTGTTTAGTTTAGG
59 AGTAATTTATGATTAGGTTATAAATTGTTAGTGTGTTTAGTTTAGG
* * *
29326707 GTTTTGTGATTTTTTAGTAAT-TTAATCTTTTTAAAATAATTTTATAGTTTTTTTGTTAGTAATT
1 GTTTTGTGATTTTTTAGTAATATAAATCTTTTTAAAATAATTTTATAGTTATTTTATTAGTAATT
*
29326771 TATGATTAGGTTATATAAATTGTTA--GTGTTTAGTTTAGT
66 TATGATTAGG-T-TATAAATTGTTAGTGTGTTTAGTTTAGG
*
29326810 GTTTTGTGATTTTTTATTAAT
1 GTTTTGTGATTTTTTAGTAAT
29326831 GTAAGTTTTT
Statistics
Matches: 200, Mismatches: 24, Indels: 21
0.82 0.10 0.09
Matches are distributed among these distances:
103 78 0.39
104 4 0.02
105 28 0.14
107 1 0.00
110 1 0.00
111 19 0.09
112 66 0.33
113 3 0.01
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.55
Consensus pattern (104 bp):
GTTTTGTGATTTTTTAGTAATATAAATCTTTTTAAAATAATTTTATAGTTATTTTATTAGTAATT
TATGATTAGGTTATAAATTGTTAGTGTGTTTAGTTTAGG
Found at i:29326846 original size:16 final size:16
Alignment explanation
Indices: 29326819--29326870 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
29326809 TGTTTTGTGA
29326819 TTTTTTATTAATGTAAG
1 TTTTTTA-TAATGTAAG
29326836 TTTTTTATAATGTAAG
1 TTTTTTATAATGTAAG
29326852 TTTTTTATAATGTAA-
1 TTTTTTATAATGTAAG
29326867 TTTT
1 TTTT
29326871 ATTTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.11
16 24 0.69
17 7 0.20
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (16 bp):
TTTTTTATAATGTAAG
Found at i:29329292 original size:78 final size:76
Alignment explanation
Indices: 29329131--29329287 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 76
29329121 AATAACTTCA
*
29329131 TATTTATATAATGACTTTTTTGCCATTTAAGTTATTAATTTTATGGGTTTTTTTTTGCAATTTAA
1 TATTTATGTAATGACTTTTTTGCCATTTAAGTTATTAATTTTATGGG--TTTTTTTGCAATTTAA
* *
29329196 ATAGTCAACTTTG
64 ATAATAAACTTTG
** * * *
29329209 TATTTATGTAATGACTTTTTTGTTATTTCAGTTATTAATTTTA-GGAG-TTTTTTGTAATTTAGA
1 TATTTATGTAATGACTTTTTTGCCATTTAAGTTATTAATTTTATGG-GTTTTTTTGCAATTTAAA
29329272 TAATAAACTTTG
65 TAATAAACTTTG
29329284 TATT
1 TATT
29329288 ATTTACGTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
75 28 0.40
77 2 0.03
78 40 0.57
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (76 bp):
TATTTATGTAATGACTTTTTTGCCATTTAAGTTATTAATTTTATGGGTTTTTTTGCAATTTAAAT
AATAAACTTTG
Found at i:29332488 original size:27 final size:27
Alignment explanation
Indices: 29332458--29332515 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
29332448 GCCTATTAGG
* * *
29332458 TAGGAGTCACCAGTGGCGCGTATCAGA
1 TAGGAGTCACCAGTGGCACCTACCAGA
* *
29332485 TAGGAGTTACTAGTGGCACCTACCAGA
1 TAGGAGTCACCAGTGGCACCTACCAGA
29332512 TAGG
1 TAGG
29332516 CGCTACCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (27 bp):
TAGGAGTCACCAGTGGCACCTACCAGA
Found at i:29333699 original size:18 final size:20
Alignment explanation
Indices: 29333678--29333714 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
29333668 ATTTGGAAAA
29333678 AAATTATA-AT-TTTTTAAT
1 AAATTATACATATTTTTAAT
*
29333696 AAATTCTACATATTTTTAA
1 AAATTATACATATTTTTAA
29333715 GTTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 2 0.12
20 7 0.44
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTATACATATTTTTAAT
Found at i:29337383 original size:19 final size:19
Alignment explanation
Indices: 29337359--29337396 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29337349 TTGGGTGTGG
29337359 ATTGGGATATTCGATTCAT
1 ATTGGGATATTCGATTCAT
29337378 ATTGGGATATTCGATTCAT
1 ATTGGGATATTCGATTCAT
29337397 TCTTTTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (19 bp):
ATTGGGATATTCGATTCAT
Found at i:29337621 original size:12 final size:12
Alignment explanation
Indices: 29337589--29337623 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
29337579 TTTTTTAAAA
29337589 AAAATTAAATAT
1 AAAATTAAATAT
*
29337601 AATAATTAATTAT
1 AA-AATTAAATAT
29337614 AAAATTAAAT
1 AAAATTAAAT
29337624 TGATTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:29353910 original size:46 final size:46
Alignment explanation
Indices: 29353809--29353896 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
29353799 TGTAACCCGC
** * * *
29353809 CCATAAGCCAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
29353855 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
29353897 AACCATCCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:29356778 original size:31 final size:31
Alignment explanation
Indices: 29356743--29356803 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
29356733 AAATGGTCTA
29356743 AACTATTAGAAAATTTTCATTTAAGTCACTG
1 AACTATTAGAAAATTTTCATTTAAGTCACTG
* * * **
29356774 AACTATTCGGAAGTTTTTGTTTAAGTCACT
1 AACTATTAGAAAATTTTCATTTAAGTCACT
29356804 AGGCTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
AACTATTAGAAAATTTTCATTTAAGTCACTG
Found at i:29358536 original size:13 final size:13
Alignment explanation
Indices: 29358518--29358545 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29358508 AATTACTCTG
29358518 AAAATTATCGAAA
1 AAAATTATCGAAA
29358531 AAAATTATCGAAA
1 AAAATTATCGAAA
29358544 AA
1 AA
29358546 GTTAACATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAATTATCGAAA
Found at i:29358635 original size:9 final size:9
Alignment explanation
Indices: 29358621--29358684 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
29358611 TTTTTAAACA
29358621 TAAAAAATT
1 TAAAAAATT
*
29358630 TAAAAATATA
1 TAAAAA-ATT
29358640 TAAAAAATAT
1 TAAAAAAT-T
*
29358650 TAAAAACTT
1 TAAAAAATT
* *
29358659 TAAAAAGTA
1 TAAAAAATT
*
29358668 TAAAAATTT
1 TAAAAAATT
29358677 TAAAAAAT
1 TAAAAAAT
29358685 ATTTTTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
9 30 0.67
10 15 0.33
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAAAATT
Found at i:29358663 original size:18 final size:19
Alignment explanation
Indices: 29358621--29358687 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
29358611 TTTTTAAACA
29358621 TAAAAAAT-TTAAAAA-TAT
1 TAAAAAATATTAAAAACT-T
29358639 ATAAAAAATATTAAAAACTT
1 -TAAAAAATATTAAAAACTT
* *
29358659 TAAAAAGTA-TAAAAATTT
1 TAAAAAATATTAAAAACTT
29358677 TAAAAAATATT
1 TAAAAAATATT
29358688 TTTAAATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 16 0.38
19 17 0.40
20 8 0.19
21 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
TAAAAAATATTAAAAACTT
Found at i:29358698 original size:22 final size:22
Alignment explanation
Indices: 29358668--29358709 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29358658 TTAAAAAGTA
29358668 TAAAAATTTTAAAAAATATTTT
1 TAAAAATTTTAAAAAATATTTT
* *
29358690 TAAATATTTTAAAAATTATT
1 TAAAAATTTTAAAAAATATT
29358710 AATTGCTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAAATTTTAAAAAATATTTT
Found at i:29358711 original size:10 final size:10
Alignment explanation
Indices: 29358629--29358711 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 10
29358619 CATAAAAAAT
29358629 TTAAAAA-TA
1 TTAAAAATTA
*
29358638 TATAAAAAATA
1 T-TAAAAATTA
*
29358649 TTAAAAACT-
1 TTAAAAATTA
*
29358658 TTAAAAAGTA
1 TTAAAAATTA
29358668 -TAAAAATT-
1 TTAAAAATTA
*
29358676 TTAAAAAATATTT
1 TT--AAAA-ATTA
*
29358689 TTAAATATT-
1 TTAAAAATTA
29358698 TTAAAAATTA
1 TTAAAAATTA
29358708 TTAA
1 TTAA
29358712 TTGCTAACGT
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
9 25 0.42
10 20 0.33
11 10 0.17
12 3 0.05
13 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:29364614 original size:12 final size:12
Alignment explanation
Indices: 29364597--29364629 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
29364587 GTATGAAATG
29364597 GATTAAATTGAT
1 GATTAAATTGAT
29364609 GATTAAATTGAT
1 GATTAAATTGAT
*
29364621 AATTAAATT
1 GATTAAATT
29364630 CATTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (12 bp):
GATTAAATTGAT
Found at i:29367366 original size:40 final size:40
Alignment explanation
Indices: 29367267--29367412 Score: 186
Period size: 40 Copynumber: 3.6 Consensus size: 40
29367257 AATTCTCACA
* * * *
29367267 CACTAAGTGCCAATTCATAGCCGAAGCTATTTTAATCTCGCA
1 CACTAAGTGCC-ATACATAGCCGAAGCTATCTTAA-ATCGCT
*
29367309 CACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGCT
1 CACTAAGTGCCATACATAGCCGAAGCTATCTTAAATCGCT
* * *
29367349 CACTAAGTGCCACACATAGCCAAAGCTATCTTGAATCG-T
1 CACTAAGTGCCATACATAGCCGAAGCTATCTTAAATCGCT
29367388 ACACTAAGTGCCATACATAGCCGAA
1 -CACTAAGTGCCATACATAGCCGAA
29367413 TTGTCATCAA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 60 0.65
41 20 0.22
42 11 0.12
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (40 bp):
CACTAAGTGCCATACATAGCCGAAGCTATCTTAAATCGCT
Found at i:29376832 original size:29 final size:30
Alignment explanation
Indices: 29376799--29376856 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
29376789 AGTAGTCGGA
29376799 GCTAG-TTAAATCGCACACTTAGTGCCAAG
1 GCTAGTTTAAATCGCACACTTAGTGCCAAG
29376828 GCTAGTTTAAATCGCACACTTAGTGCCAA
1 GCTAGTTTAAATCGCACACTTAGTGCCAA
29376857 AACTTTCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (30 bp):
GCTAGTTTAAATCGCACACTTAGTGCCAAG
Found at i:29378720 original size:40 final size:39
Alignment explanation
Indices: 29378630--29378723 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 39
29378620 ACCATCTCCG
* * *
29378630 TCCAACCCAACACA-CTATGTTGGGATAAGATCGACCCA
1 TCCAACCCTACACACCTATGTTGGGATAAAATCAACCCA
* *
29378668 -CCTAGCCTTACACACCTA-GTATGGGGATAAAATCAACCCA
1 TCC-AACCCTACACACCTATGT-T-GGGATAAAATCAACCCA
29378708 TCCAACCCTACACACC
1 TCCAACCCTACACACC
29378724 AAGAGGTACC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
37 2 0.05
38 10 0.23
39 4 0.09
40 26 0.59
41 2 0.05
ACGTcount: A:0.34, C:0.35, G:0.13, T:0.18
Consensus pattern (39 bp):
TCCAACCCTACACACCTATGTTGGGATAAAATCAACCCA
Found at i:29382366 original size:23 final size:23
Alignment explanation
Indices: 29382340--29382383 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
29382330 TTATAGTTTG
29382340 GCCCCTTATCAAATTATAAATAC
1 GCCCCTTATCAAATTATAAATAC
29382363 GCCCCTTATCAAATTATAAAT
1 GCCCCTTATCAAATTATAAAT
29382384 TCAACTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (23 bp):
GCCCCTTATCAAATTATAAATAC
Found at i:29393906 original size:20 final size:20
Alignment explanation
Indices: 29393864--29393908 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
29393854 TCCATTCAAA
*
29393864 TTCATTTCACATATTACATT
1 TTCATTTCACATATTACAAT
29393884 TTCATTTCACATATTTA-AAT
1 TTCATTTCACATA-TTACAAT
29393904 TTCAT
1 TTCAT
29393909 AATTCATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCATTTCACATATTACAAT
Found at i:29394252 original size:16 final size:15
Alignment explanation
Indices: 29394225--29394254 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29394215 AAATTCATAT
29394225 TTATACTATATATAA
1 TTATACTATATATAA
29394240 TTATACATATATATA
1 TTATAC-TATATATA
29394255 TTTCCAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATACTATATATAA
Found at i:29394828 original size:19 final size:18
Alignment explanation
Indices: 29394804--29394841 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
29394794 TCATTTTTTC
*
29394804 ACATATATATATATCAAAA
1 ACATATAAATATAT-AAAA
29394823 ACATATAAATATATAAAA
1 ACATATAAATATATAAAA
29394841 A
1 A
29394842 TATAATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (18 bp):
ACATATAAATATATAAAA
Found at i:29395562 original size:12 final size:13
Alignment explanation
Indices: 29395545--29395602 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 13
29395535 ATCTTTTATA
29395545 TATTATTAC-ATT
1 TATTATTACTATT
*
29395557 TATTATTGCTATTAT
1 TATTATTACTA-T-T
29395572 TATTATTACTA-T
1 TATTATTACTATT
29395584 TA-TATTA-TATT
1 TATTATTACTATT
*
29395595 TAGTATTA
1 TATTATTA
29395603 TTTTAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 2 0.05
11 8 0.21
12 16 0.41
13 1 0.03
14 1 0.03
15 11 0.28
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (13 bp):
TATTATTACTATT
Found at i:29395963 original size:4 final size:4
Alignment explanation
Indices: 29395954--29395980 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29395944 TAAACACAAA
29395954 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
29395981 AACCTTGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:29396201 original size:18 final size:19
Alignment explanation
Indices: 29396165--29396221 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
29396155 ACTATTACTA
*
29396165 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
29396185 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
29396202 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
29396220 TT
1 TT
29396222 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:29396323 original size:12 final size:12
Alignment explanation
Indices: 29396306--29396335 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29396296 GTATTTCTAT
29396306 TATATACATATA
1 TATATACATATA
*
29396318 TATATACATTTA
1 TATATACATATA
29396330 TATATA
1 TATATA
29396336 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATACATATA
Found at i:29398304 original size:62 final size:62
Alignment explanation
Indices: 29398207--29398451 Score: 427
Period size: 62 Copynumber: 4.0 Consensus size: 62
29398197 ATCTCTTTTT
29398207 TGCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTACTAAAATCCAAAAATA
1 TGCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTACTAAAATCCAAAAATA
29398269 TGCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTACTAAAATCCAAAAATA
1 TGCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTACTAAAATCCAAAAATA
*
29398331 TGCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTCCTAAAATCCAAAAATA
1 TGCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTACTAAAATCCAAAAATA
* * * * * *
29398393 CGCATTCATGCATCAACATTACGTTTCATTGCATACAGTAAATTTCCTAAAATCCAAAA
1 TGCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTACTAAAATCCAAAA
29398452 GTACGTCGAG
Statistics
Matches: 177, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 177 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (62 bp):
TGCATTCATGCATCAACATTACATTTCATCGCATGCAATAAATTTACTAAAATCCAAAAATA
Found at i:29399759 original size:11 final size:11
Alignment explanation
Indices: 29399743--29399872 Score: 75
Period size: 11 Copynumber: 11.2 Consensus size: 11
29399733 CAGTGGAGGC
29399743 AAAAACAAAAA
1 AAAAACAAAAA
29399754 AAAAACAAAAA
1 AAAAACAAAAA
* *
29399765 AAGAGCAAAAA
1 AAAAACAAAAA
29399776 AGCAAAA-AAAGCAA
1 A--AAAACAAA--AA
**
29399790 AAAAAGTAAAA
1 AAAAACAAAAA
29399801 AAAAACGAGAAAA
1 AAAAAC-A-AAAA
*
29399814 CAAAAGCAAAAA
1 -AAAAACAAAAA
29399826 AAAAACAAAAA
1 AAAAACAAAAA
* * *
29399837 TAAAATAATAA
1 AAAAACAAAAA
* *
29399848 AAGAATAAAAA
1 AAAAACAAAAA
29399859 ATAAGAA-AAAAA
1 A-AA-AACAAAAA
29399871 AA
1 AA
29399873 CCTCTACCGG
Statistics
Matches: 93, Mismatches: 16, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
11 56 0.60
12 18 0.19
13 11 0.12
14 8 0.09
ACGTcount: A:0.81, C:0.07, G:0.08, T:0.05
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:29399773 original size:28 final size:28
Alignment explanation
Indices: 29399741--29399836 Score: 77
Period size: 28 Copynumber: 3.2 Consensus size: 28
29399731 TTCAGTGGAG
29399741 GCAAAAACA-AAAAAAAAACAAAAAAAGA
1 GCAAAAA-AGAAAAAAAAACAAAAAAAGA
* *
29399769 GCAAAAAAGCAAAAAAAGCAAAAAAAGTA
1 GCAAAAAAGAAAAAAAAACAAAAAAAG-A
** *
29399798 AAAAAAAACGAGAAAACAAAAGCAAAAAAAAA
1 GCAAAAAA-GA-AAAA-AAAA-CAAAAAAAGA
*
29399830 ACAAAAA
1 GCAAAAA
29399837 TAAAATAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
27 1 0.02
28 23 0.43
29 7 0.13
30 1 0.02
31 4 0.07
32 10 0.19
33 8 0.15
ACGTcount: A:0.79, C:0.10, G:0.09, T:0.01
Consensus pattern (28 bp):
GCAAAAAAGAAAAAAAAACAAAAAAAGA
Found at i:29399774 original size:19 final size:17
Alignment explanation
Indices: 29399752--29399794 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
29399742 CAAAAACAAA
29399752 AAAAAAACAAAAAAAGAGC
1 AAAAAAAC-AAAAAA-AGC
*
29399771 AAAAAAGCAAAAAAAGC
1 AAAAAAACAAAAAAAGC
29399788 AAAAAAA
1 AAAAAAA
29399795 GTAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAAAGC
Found at i:29400317 original size:13 final size:12
Alignment explanation
Indices: 29400281--29400331 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
29400271 ACTTCACTTG
*
29400281 AAAAAAACGAAA
1 AAAAAAAAGAAA
29400293 AAAACAAAA-AAA
1 AAAA-AAAAGAAA
*
29400305 CAAAAAAAGAAA
1 AAAAAAAAGAAA
29400317 AGAAAAAAAGAAA
1 A-AAAAAAAGAAA
29400330 AA
1 AA
29400332 GGAGAGGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 4 0.12
12 14 0.42
13 15 0.45
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:29400325 original size:8 final size:8
Alignment explanation
Indices: 29400280--29400331 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
29400270 CACTTCACTT
29400280 GAAAAAAA
1 GAAAAAAA
29400288 CGAAAAAAA
1 -GAAAAAAA
*
29400297 CAAAAAAA
1 GAAAAAAA
*
29400305 CAAAAAAA
1 GAAAAAAA
29400313 G---AAAA
1 GAAAAAAA
29400318 GAAAAAAA
1 GAAAAAAA
29400326 GAAAAA
1 GAAAAA
29400332 GGAGAGGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 5 0.13
8 25 0.66
9 8 0.21
ACGTcount: A:0.85, C:0.06, G:0.10, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:29400856 original size:108 final size:108
Alignment explanation
Indices: 29400667--29400862 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 108
29400657 TTTGTATTCT
29400667 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAACAAATTTCCATCTT
1 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAACAAATTTCCATCTT
29400732 ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
66 ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
* ** * *
29400775 AGCAAAATTTGCTATCTTGATTGATTTGTTTGTTTATAGCTTTGCTCTCAACAAAATTT-CATTT
1 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAAC-AAATTTCCATCT
* *
29400839 TGTCCATTTTGATAATCTTTTTCA
65 TATCCATTGTGATAATCTTTTTCA
29400863 AGCATTTTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 74 0.93
109 6 0.08
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (108 bp):
AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAACAAATTTCCATCTT
ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
Found at i:29406812 original size:13 final size:13
Alignment explanation
Indices: 29406794--29406869 Score: 91
Period size: 13 Copynumber: 5.9 Consensus size: 13
29406784 AGTTCTTCAT
29406794 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
29406807 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* *
29406820 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
29406833 TTCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
29406846 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
29406859 TGC-TTTGAAAA
1 TGCTTTTGAAAA
29406870 AATTTAAGTG
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
12 7 0.13
13 45 0.87
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Done.