Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013703.1 Corchorus olitorius cultivar O-4 contig13736, whole genome shotgun sequence
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: 69062
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8890 original size:2 final size:2
Alignment explanation
Indices: 8885--8913 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8875 ACGAAAAGAA
8885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8914 CTAGTTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9232 original size:3 final size:3
Alignment explanation
Indices: 9224--9258 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
9214 TCTCTGATGC
9224 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
9259 AGAATTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:11274 original size:179 final size:179
Alignment explanation
Indices: 10967--11311 Score: 593
Period size: 179 Copynumber: 1.9 Consensus size: 179
10957 AAAAGTTATG
10967 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
1 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
* * *
11032 TGATCAATAATGAAAGTTGCCAATTTAATTACTTAAGTAATCTACTATAAAAGCTAAAAAAGTTA
66 TGATCAATAATGAAAGTTACCAATTTAATCACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTT-
11097 T-TAAAATTGCATTTACCAATCCTTACATTCTTAATATTTTTTTTCCCGA
130 TGTAAAATTGCATTTACCAATCCTTACATTCTTAATATTTTTTTTCCCGA
* *
11146 AAAACATTATAGTACTATCTAGATTCAAGTAATCTTACATCCTTATTAATTTTAGTAACTTTTTA
1 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
* * *
11211 TGATTAATAATGAAAGTTACCAATTTAATCACTTGAGTAATCTACTAAAAAAGCTATAAAAGTTT
66 TGATCAATAATGAAAGTTACCAATTTAATCACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTT
*
11276 GTAAAATTGTATTTACCAATCCTTACATTCTTAATA
131 GTAAAATTGCATTTACCAATCCTTACATTCTTAATA
11312 ACATTAGTAA
Statistics
Matches: 156, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
178 1 0.01
179 155 0.99
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (179 bp):
AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
TGATCAATAATGAAAGTTACCAATTTAATCACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTT
GTAAAATTGCATTTACCAATCCTTACATTCTTAATATTTTTTTTCCCGA
Found at i:11811 original size:36 final size:36
Alignment explanation
Indices: 11764--11833 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
11754 TACAATAACC
*
11764 TTACATTTTTTGTAATTTTGGTTATCATATTTCTTA
1 TTACATTTTTTGTAATTTTGATTATCATATTTCTTA
11800 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATTTTTTGTAATTTTGATTATCATATTTCT
11834 CCAAAATCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (36 bp):
TTACATTTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:13561 original size:45 final size:42
Alignment explanation
Indices: 13496--13584 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 42
13486 ATATCTAAGA
* *
13496 ATTTAATTAATTTAATTATTTCAGTTATTATAGTATTATTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATA-TA-TA-TATTAC
* *
13541 ATTTAATTAATGTACGTATTTTAGTTATTATATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATATTAC
13583 AT
1 AT
13585 AGGAATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 8 0.20
43 2 0.05
44 2 0.05
45 28 0.70
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (42 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATATTAC
Found at i:16775 original size:23 final size:22
Alignment explanation
Indices: 16745--16789 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
16735 ATCCGGTTAG
*
16745 GTGTAAATGTGGAGAGAGAGAAA
1 GTGTAAATATGGAGAGAG-GAAA
16768 GTGTAAATATGGAGAGAGGAAA
1 GTGTAAATATGGAGAGAGGAAA
16790 ATGGTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (22 bp):
GTGTAAATATGGAGAGAGGAAA
Found at i:17391 original size:24 final size:25
Alignment explanation
Indices: 17355--17402 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
17345 GGAATAAAAG
17355 TTTTATGTAATAATAACTTAATTTT
1 TTTTATGTAATAATAACTTAATTTT
*
17380 TTTTATG-GATAATAACTTAATTT
1 TTTTATGTAATAATAACTTAATTT
17403 ATTATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (25 bp):
TTTTATGTAATAATAACTTAATTTT
Found at i:18283 original size:35 final size:35
Alignment explanation
Indices: 18244--18313 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
18234 AAATAAATTA
*
18244 CAAAACAACTAAACATGAGAATACTAGTAGACAAT
1 CAAAACAACTAAACATGAGAATACTAGTAAACAAT
*
18279 CAAAATAACTAAACATGAGAATACTAGTAAACAAT
1 CAAAACAACTAAACATGAGAATACTAGTAAACAAT
18314 TACAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.56, C:0.16, G:0.10, T:0.19
Consensus pattern (35 bp):
CAAAACAACTAAACATGAGAATACTAGTAAACAAT
Found at i:18311 original size:18 final size:18
Alignment explanation
Indices: 18253--18311 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
18243 ACAAAACAAC
18253 TAAACATGAGAATACTAG
1 TAAACATGAGAATACTAG
* * * *
18271 TAGACAATCAAAATA--AC
1 TAAAC-ATGAGAATACTAG
18288 TAAACATGAGAATACTAG
1 TAAACATGAGAATACTAG
18306 TAAACA
1 TAAACA
18312 ATTACAATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
18 11 0.37
19 7 0.23
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (18 bp):
TAAACATGAGAATACTAG
Found at i:18610 original size:18 final size:18
Alignment explanation
Indices: 18587--18624 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
18577 TGTTGACTAT
*
18587 CAAAATTTGGGGTTTGAC
1 CAAAATTTGGGGTTGGAC
18605 CAAAATTTGGGGTTGGAC
1 CAAAATTTGGGGTTGGAC
18623 CA
1 CA
18625 TGCATATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (18 bp):
CAAAATTTGGGGTTGGAC
Found at i:18732 original size:57 final size:57
Alignment explanation
Indices: 18606--18795 Score: 213
Period size: 57 Copynumber: 3.4 Consensus size: 57
18596 GGGTTTGACC
* *
18606 AAAATTTGGGGTTGGACCATGCATATACAATGAAATGTTTTTTT-T-GTTTGACTATT
1 AAAATTTGGGGTTTGACCATGCATATACAATG-AATTTTTTTTTGTGGTTTGACTATT
* * * * *
18662 GAACTTTGGGGTTTGATCATGCATGTACAATGATTTTTTTTTTGTGGTTTGACTATT
1 AAAATTTGGGGTTTGACCATGCATATACAATGAATTTTTTTTTGTGGTTTGACTATT
* * * ** * *
18719 AAAATTTGAGGTTTGACCATGCATATACGATGAAATACTCTTTGTGGTTTGACTATC
1 AAAATTTGGGGTTTGACCATGCATATACAATGAATTTTTTTTTGTGGTTTGACTATT
* *
18776 GAATTTTGGGGTTTGACCAT
1 AAAATTTGGGGTTTGACCAT
18796 CATCCTTTTG
Statistics
Matches: 110, Mismatches: 22, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
55 9 0.08
56 28 0.25
57 73 0.66
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.43
Consensus pattern (57 bp):
AAAATTTGGGGTTTGACCATGCATATACAATGAATTTTTTTTTGTGGTTTGACTATT
Found at i:18788 original size:21 final size:21
Alignment explanation
Indices: 18759--18817 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
18749 TGAAATACTC
* *
18759 TTTGTGGTTTGACTATCGA-AT
1 TTTGGGGTTTGACCATC-ACAT
*
18780 TTTGGGGTTTGACCATCATCCT
1 TTTGGGGTTTGACCATCA-CAT
18802 TTTGGGGTTTGACCAT
1 TTTGGGGTTTGACCAT
18818 GCATGTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 15 0.45
22 17 0.52
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.44
Consensus pattern (21 bp):
TTTGGGGTTTGACCATCACAT
Found at i:18908 original size:134 final size:135
Alignment explanation
Indices: 18666--18929 Score: 361
Period size: 134 Copynumber: 2.0 Consensus size: 135
18656 ACTATTGAAC
* * *
18666 TTTGGGGTTTGATCATGCATGTACAATGATTTTTTTTTTGTGGTTTGACTATTAAAATTTGAGGT
1 TTTGGGGTTTGACCATGCATGTACAATGA-TTGTTTTTTGGGGTTTGACTATTAAAATTTGAGGT
* * * * *
18731 TTGACCATGCATATACGATGAAATACTCTTTGTGGTTTGACTATCGAATTTTGGGGTTTGACCAT
65 TTGACCATGCATATACAATGAAATACTCTTTGTGCTTTGACTATCGAACTTTGGCGTTTCACCAT
18796 CATCCT
130 CATCCT
* *
18802 TTTGGGGTTTGACCATGCATGTATAATGA-TGTTTTTTGGGGTTTGACTA-TAAAATTTTGGGGT
1 TTTGGGGTTTGACCATGCATGTACAATGATTGTTTTTTGGGGTTTGACTATTAAAA-TTTGAGGT
* * ** *
18865 TTGATCGTGCATATACAATGAAATGTTTTTTGTGCTTTGACTATCGAACTTTGGCGTTTCACCAT
65 TTGACCATGCATATACAATGAAATACTCTTTGTGCTTTGACTATCGAACTTTGGCGTTTCACCAT
18930 GCATGTGCAA
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
133 5 0.04
134 80 0.71
136 27 0.24
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (135 bp):
TTTGGGGTTTGACCATGCATGTACAATGATTGTTTTTTGGGGTTTGACTATTAAAATTTGAGGTT
TGACCATGCATATACAATGAAATACTCTTTGTGCTTTGACTATCGAACTTTGGCGTTTCACCATC
ATCCT
Found at i:18918 original size:57 final size:55
Alignment explanation
Indices: 18802--18944 Score: 151
Period size: 57 Copynumber: 2.6 Consensus size: 55
18792 CCATCATCCT
* * * *
18802 TTTGGGGTTTGACCATGCATGTATAATGATGTTTTTTGGGGTTTGACTATAAAAT
1 TTTGGGGTTTGACCATGCATATACAATGATGTTTTTTGGGCTTTGACTATAAAAC
* * * **
18857 TTTGGGGTTTGATCGTGCATATACAATGAAATGTTTTTTGTGCTTTGACTATCGAAC
1 TTTGGGGTTTGACCATGCATATACAATG--ATGTTTTTTGGGCTTTGACTATAAAAC
* * * *
18914 TTTGGCGTTTCACCATGCATGTGCAATGATG
1 TTTGGGGTTTGACCATGCATATACAATGATG
18945 ATTCTGGGGT
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
55 27 0.38
57 44 0.62
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.41
Consensus pattern (55 bp):
TTTGGGGTTTGACCATGCATATACAATGATGTTTTTTGGGCTTTGACTATAAAAC
Found at i:19034 original size:93 final size:90
Alignment explanation
Indices: 18871--19037 Score: 219
Period size: 93 Copynumber: 1.8 Consensus size: 90
18861 GGGTTTGATC
**
18871 GTGCATATACAATGAAATGTTTTTTGTGCTTTGACTATCGAACTTTGGCGTTTCACCATGCATGT
1 GTGCATATACAATGAAATGTTTTTTGTGCTTTGACTATCGAACTTTGGCGTTTCACCATAAATGT
*
18936 GCAATGATGATTCTGGGGTATGACT
66 ACAATGATGATTCTGGGGTATGACT
* * * **
18961 GTGCATATACAATGAAATGTTTTTTTTTGTGGTTTGACTATTGAACTTT-GCGGTTTGACTGTAA
1 GTGCATATACAATGAAATG---TTTTTTGTGCTTTGACTATCGAACTTTGGC-GTTTCACCATAA
19025 ATGTACAATGATG
62 ATGTACAATGATG
19038 TTTTTTGTGG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
90 19 0.29
92 2 0.03
93 44 0.68
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (90 bp):
GTGCATATACAATGAAATGTTTTTTGTGCTTTGACTATCGAACTTTGGCGTTTCACCATAAATGT
ACAATGATGATTCTGGGGTATGACT
Found at i:19079 original size:21 final size:21
Alignment explanation
Indices: 19055--19116 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
19045 TGGTTATACT
19055 ATCAAACTTTGGGGTTTGACC
1 ATCAAACTTTGGGGTTTGACC
** * *
19076 ATCATCCTTTGGTGTTTAACC
1 ATCAAACTTTGGGGTTTGACC
*
19097 A--ACA-TTTGGGGTTTGACC
1 ATCAAACTTTGGGGTTTGACC
19115 AT
1 AT
19117 GCATATACAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 13 0.41
19 1 0.03
21 18 0.56
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (21 bp):
ATCAAACTTTGGGGTTTGACC
Found at i:19175 original size:21 final size:21
Alignment explanation
Indices: 19137--19217 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
19127 TGAAATGCTT
* ** *
19137 TTTGTGGTTTGATTATCAAAC
1 TTTGGGGTTTGACCATCATAC
*
19158 TTTGGGGTTTGACCATCATCC
1 TTTGGGGTTTGACCATCATAC
*
19179 TTTGGTGTTTGACCA--ATA-
1 TTTGGGGTTTGACCATCATAC
19197 TTTGGGGTTTGACCATGCATA
1 TTTGGGGTTTGACCAT-CATA
19218 TATAATGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
18 14 0.29
19 2 0.04
21 33 0.67
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (21 bp):
TTTGGGGTTTGACCATCATAC
Found at i:19206 original size:18 final size:20
Alignment explanation
Indices: 19158--19211 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 20
19148 ATTATCAAAC
*
19158 TTTGGGGTTTGACCATCATCC
1 TTTGGGGTTTGACCA-CATCA
*
19179 TTTGGTGTTTGACCA-AT-A
1 TTTGGGGTTTGACCACATCA
19197 TTTGGGGTTTGACCA
1 TTTGGGGTTTGACCA
19212 TGCATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 14 0.47
19 2 0.07
21 14 0.47
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.41
Consensus pattern (20 bp):
TTTGGGGTTTGACCACATCA
Found at i:19264 original size:75 final size:74
Alignment explanation
Indices: 19179--19341 Score: 170
Period size: 76 Copynumber: 2.2 Consensus size: 74
19169 ACCATCATCC
* * *
19179 TTTGGTGTTTGACCAATA-TTTGGGGTTTGACCATGCATATATAATGAAATGCTTTT-T-GTGGT
1 TTTGGGGTTTGACCAATACTCTGGGGTTTGACCATGCATATACAATG--ATG-TTTTATAG-GGT
*
19241 TTGACTATCGAAA
62 TTGACTATCAAAA
* * *
19254 TTTGGGGTTTGACCATTACGCTCTGGGGTTTGACTATGCATGTACAATGATGTTTTATAGGGTTT
1 TTTGGGGTTTGACCAATA--CTCTGGGGTTTGACCATGCATATACAATGATGTTTTATAGGGTTT
*
19319 GACTATTAAAA
64 GACTATCAAAA
*
19330 TTTGGGCTTTGA
1 TTTGGGGTTTGA
19342 TCGTGCATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
75 20 0.27
76 29 0.39
77 1 0.01
78 24 0.32
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (74 bp):
TTTGGGGTTTGACCAATACTCTGGGGTTTGACCATGCATATACAATGATGTTTTATAGGGTTTGA
CTATCAAAA
Found at i:19287 original size:96 final size:96
Alignment explanation
Indices: 19039--19269 Score: 394
Period size: 96 Copynumber: 2.4 Consensus size: 96
19029 ACAATGATGT
*
19039 TTTTTGTGGTTAT-ACTATCAAACTTTGGGGTTTGACCATCATCCTTTGGTGTTTAACCAACATT
1 TTTTTGTGGTT-TGACTATCAAACTTTGGGGTTTGACCATCATCCTTTGGTGTTTGACCAACATT
19103 TGGGGTTTGACCATGCATATACAATGAAATGC
65 TGGGGTTTGACCATGCATATACAATGAAATGC
* *
19135 TTTTTGTGGTTTGATTATCAAACTTTGGGGTTTGACCATCATCCTTTGGTGTTTGACCAATATTT
1 TTTTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATCATCCTTTGGTGTTTGACCAACATTT
*
19200 GGGGTTTGACCATGCATATATAATGAAATGC
66 GGGGTTTGACCATGCATATACAATGAAATGC
19231 TTTTTGTGGTTTGACTATCGAAA-TTTGGGGTTTGACCAT
1 TTTTTGTGGTTTGACTATC-AAACTTTGGGGTTTGACCAT
19270 TACGCTCTGG
Statistics
Matches: 128, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
95 1 0.01
96 124 0.97
97 3 0.02
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (96 bp):
TTTTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATCATCCTTTGGTGTTTGACCAACATTT
GGGGTTTGACCATGCATATACAATGAAATGC
Found at i:19341 original size:76 final size:77
Alignment explanation
Indices: 19199--19341 Score: 184
Period size: 76 Copynumber: 1.9 Consensus size: 77
19189 GACCAATATT
* * *
19199 TGGGGTTTGACCATGCATATATAATGAAATGCTTTTTGTGGTTTGACTATCGAAATTTGGGGTTT
1 TGGGGTTTGACCATGCATATACAATG-AATGCTTTTTGTGGTTTGACTATCAAAATTTGGGCTTT
19264 GACCATTACGCTC
65 GACCATTACGCTC
* * *
19277 TGGGGTTTGACTATGCATGTACAATG-ATG-TTTTATAG-GGTTTGACTATTAAAATTTGGGCTT
1 TGGGGTTTGACCATGCATATACAATGAATGCTTTT-T-GTGGTTTGACTATCAAAATTTGGGCTT
19339 TGA
64 TGA
19342 TCGTGCATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
75 4 0.07
76 29 0.51
77 1 0.02
78 23 0.40
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (77 bp):
TGGGGTTTGACCATGCATATACAATGAATGCTTTTTGTGGTTTGACTATCAAAATTTGGGCTTTG
ACCATTACGCTC
Found at i:19395 original size:21 final size:21
Alignment explanation
Indices: 19365--19423 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
19355 ATGAAATGCT
* *
19365 TTTTGTGGTTTGACTATCGAA
1 TTTTGGGGTTTGACCATCGAA
19386 TTTTGGGGTTTGACCATCGAA
1 TTTTGGGGTTTGACCATCGAA
19407 TTTTGGGGTTTGACCAT
1 TTTTGGGGTTTGACCAT
19424 GCATGTGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (21 bp):
TTTTGGGGTTTGACCATCGAA
Found at i:19449 original size:54 final size:54
Alignment explanation
Indices: 19385--19599 Score: 196
Period size: 54 Copynumber: 3.9 Consensus size: 54
19375 TGACTATCGA
* * * *
19385 ATTTTGGGGTTTGACCATCGAATTTTGGGGTTTGACCATGCATGTGCAATGATG
1 ATTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATGCATGTACAATGATG
* * * * *
19439 ATTTTGGGGTTTGACTATTAAAGTTTGGGGTTTGATCGTGCATATACAATGAAATG
1 ATTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATGCATGTACAATG--ATG
* * * * * **
19495 CTTTTGTGGTTTGACTATTAAACTTTGGGATTTAACCATAAATGTACAATGATG
1 ATTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATGCATGTACAATGATG
* ** * * * *
19549 TTTTTTATGGTTTAACAATCAAACTTTGGGGTTTGGCCATTCATGTACAAT
1 -ATTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATGCATGTACAAT
19600 ATGGATGTCC
Statistics
Matches: 130, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
54 46 0.35
55 40 0.31
56 44 0.34
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (54 bp):
ATTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATGCATGTACAATGATG
Found at i:19497 original size:132 final size:133
Alignment explanation
Indices: 19196--19512 Score: 471
Period size: 133 Copynumber: 2.4 Consensus size: 133
19186 TTTGACCAAT
* * *
19196 ATTTGGGGTTTGACCATGCATATATAATGAAATGCTTTTTGTGGTTTGACTATCGAAATTTGGGG
1 ATTTGGGGTTTGATCGTGCATATAAAATGAAATGCTTTTTGTGGTTTGACTATCGAAATTTGGGG
* *
19261 TTTGACCATTACGCTCTGGGGTTTGACTATGCATGTACAATGATGTTTTATAGGGTTTGACTATT
66 TTTGACCATTACGCTCTGGGGTTTGACCATGCATGTACAATGATGATTTATAGGGTTTGACTATT
19326 AAA
131 AAA
* *
19329 ATTTGGGCTTTGATCGTGCATATAAAATGAAATGCTTTTTGTGGTTTGACTATCGAATTTTGGGG
1 ATTTGGGGTTTGATCGTGCATATAAAATGAAATGCTTTTTGTGGTTTGACTATCGAAATTTGGGG
* * * *
19394 TTTGACCA-T-CGAATTTTGGGGTTTGACCATGCATGTGCAATGATGATTT-TGGGGTTTGACTA
66 TTTGACCATTACG--CTCTGGGGTTTGACCATGCATGTACAATGATGATTTATAGGGTTTGACTA
19456 TTAAA
129 TTAAA
* *
19461 GTTTGGGGTTTGATCGTGCATATACAATGAAATGC-TTTTGTGGTTTGACTAT
1 ATTTGGGGTTTGATCGTGCATATAAAATGAAATGCTTTTTGTGGTTTGACTAT
19513 TAAACTTTGG
Statistics
Matches: 168, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
131 19 0.11
132 50 0.30
133 99 0.59
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (133 bp):
ATTTGGGGTTTGATCGTGCATATAAAATGAAATGCTTTTTGTGGTTTGACTATCGAAATTTGGGG
TTTGACCATTACGCTCTGGGGTTTGACCATGCATGTACAATGATGATTTATAGGGTTTGACTATT
AAA
Found at i:19682 original size:15 final size:15
Alignment explanation
Indices: 19662--19692 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19652 AACATATTAC
19662 TAATGTAATGTTCAA
1 TAATGTAATGTTCAA
19677 TAATGTAATGTTCAA
1 TAATGTAATGTTCAA
19692 T
1 T
19693 GATTTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (15 bp):
TAATGTAATGTTCAA
Found at i:25521 original size:59 final size:57
Alignment explanation
Indices: 25425--25541 Score: 180
Period size: 59 Copynumber: 2.0 Consensus size: 57
25415 CTCCTAATAC
*
25425 TACATTTAATGAAAAGTAACTAACATATTCTACACCTTATATATATATTATCAAATCAA
1 TACATTTAATGAAAAGTAACTAACATATTCTAAACC-T-TATATATATTATCAAATCAA
* * *
25484 TACATTTAATGGACAGTAACTAACATATTGTAAACCTTATATATATTATCAAATCAA
1 TACATTTAATGAAAAGTAACTAACATATTCTAAACCTTATATATATTATCAAATCAA
25541 T
1 T
25542 TACACATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 21 0.39
58 1 0.02
59 32 0.59
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (57 bp):
TACATTTAATGAAAAGTAACTAACATATTCTAAACCTTATATATATTATCAAATCAA
Found at i:29659 original size:41 final size:40
Alignment explanation
Indices: 29581--29659 Score: 90
Period size: 41 Copynumber: 1.9 Consensus size: 40
29571 ACATAAGAAG
* *
29581 GTTTGGTGGCAAAAAAATAAAAAAAAAGGAGACAGAGGCTT
1 GTTTGGAGGCAAAAAAATAAAAAAAAAGCAGA-AGAGGCTT
29622 GTTTGGAGGCTAAAATAAA-AACAAAAAAAGCAG-AGAGG
1 GTTTGGAGGC-AAAA-AAATAA-AAAAAAAGCAGAAGAGG
29660 TTTGAAGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
41 14 0.42
42 6 0.18
43 13 0.39
ACGTcount: A:0.51, C:0.08, G:0.27, T:0.15
Consensus pattern (40 bp):
GTTTGGAGGCAAAAAAATAAAAAAAAAGCAGAAGAGGCTT
Found at i:30496 original size:4 final size:4
Alignment explanation
Indices: 30487--30566 Score: 71
Period size: 4 Copynumber: 21.2 Consensus size: 4
30477 TTTTTATAGC
* * *
30487 TATT TATT TA-T TATT TATT TA-C TATT TATT TTTT TATT TATT AATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
** *
30533 TAGC TA-T TATC TATT TATT TA-T TA-T TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
30567 TCTTTTACCT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
3 13 0.21
4 48 0.79
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:30502 original size:7 final size:7
Alignment explanation
Indices: 30487--30565 Score: 51
Period size: 7 Copynumber: 11.1 Consensus size: 7
30477 TTTTTATAGC
30487 TATTTAT
1 TATTTAT
30494 T-TATTATT
1 TAT-TTA-T
*
30502 TATTTAC
1 TATTTAT
30509 TATTTAT
1 TATTTAT
30516 T-TTT-T
1 TATTTAT
30521 TATTTAT
1 TATTTAT
*
30528 TAATTTAGC
1 T-ATTTA-T
30537 TA-TTAT
1 TATTTAT
30543 CTATTTAT
1 -TATTTAT
30551 T-TATTAT
1 TAT-TTAT
30558 TATTTAT
1 TATTTAT
30565 T
1 T
30566 TTCTTTTACC
Statistics
Matches: 57, Mismatches: 4, Indels: 22
0.69 0.05 0.27
Matches are distributed among these distances:
5 2 0.04
6 8 0.14
7 29 0.51
8 16 0.28
9 2 0.04
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (7 bp):
TATTTAT
Found at i:30507 original size:15 final size:14
Alignment explanation
Indices: 30487--30566 Score: 79
Period size: 15 Copynumber: 5.4 Consensus size: 14
30477 TTTTTATAGC
30487 TATTTATTTATTATT
1 TATTTA-TTATTATT
*
30502 TATTTACTATTTATT
1 TATTTATTA-TTATT
*
30517 TTTTTATTTATTAATT
1 TATTTA-TTATT-ATT
**
30533 TAGCTATTATCTATT
1 TATTTATTAT-TATT
30548 TATTTATTATTATT
1 TATTTATTATTATT
30562 TATTT
1 TATTT
30567 TCTTTTACCT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
14 11 0.21
15 33 0.62
16 9 0.17
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (14 bp):
TATTTATTATTATT
Found at i:30542 original size:27 final size:27
Alignment explanation
Indices: 30487--30556 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
30477 TTTTTATAGC
*
30487 TATTTATTTA-TTATTTATTTACTATT
1 TATTTATTTATTTATTAATTTACTATT
*
30513 TATTTTTTTATTTATTAATTTAGCTA-T
1 TATTTATTTATTTATTAATTTA-CTATT
*
30540 TATCTATTTATTTATTA
1 TATTTATTTATTTATTA
30557 TTATTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 9 0.24
27 26 0.68
28 3 0.08
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (27 bp):
TATTTATTTATTTATTAATTTACTATT
Found at i:30550 original size:8 final size:8
Alignment explanation
Indices: 30486--30654 Score: 81
Period size: 8 Copynumber: 21.6 Consensus size: 8
30476 TTTTTTATAG
30486 CTATTTAT
1 CTATTTAT
*
30494 TTA-TTAT
1 CTATTTAT
*
30501 TTATTTA-
1 CTATTTAT
30508 CTATTTAT
1 CTATTTAT
30516 -T-TTT-T
1 CTATTTAT
30521 -TATTTAT
1 CTATTTAT
*
30528 -TAATTTAG
1 CT-ATTTAT
30536 CTA-TTAT
1 CTATTTAT
30543 CTATTTAT
1 CTATTTAT
*
30551 TTATTATTAT
1 CTA-T-TTAT
*
30561 TTATTT-T
1 CTATTTAT
*
30568 CTTTTACCTAT
1 CTATT---TAT
30579 CTATTTAT
1 CTATTTAT
* * *
30587 CTCTGTAC
1 CTATTTAT
30595 CTATTTAT
1 CTATTTAT
30603 CTATTTAT
1 CTATTTAT
*
30611 CT-TTATAC
1 CTATT-TAT
30619 CTATTTAT
1 CTATTTAT
*
30627 CTTTTTAT
1 CTATTTAT
*
30635 CTTTTTAT
1 CTATTTAT
*
30643 TTATTTAT
1 CTATTTAT
30651 -TATT
1 CTATT
30655 ATTATTTTTT
Statistics
Matches: 127, Mismatches: 19, Indels: 31
0.72 0.11 0.18
Matches are distributed among these distances:
5 2 0.02
6 6 0.05
7 32 0.25
8 69 0.54
9 5 0.04
10 8 0.06
11 5 0.04
ACGTcount: A:0.23, C:0.11, G:0.01, T:0.65
Consensus pattern (8 bp):
CTATTTAT
Found at i:30647 original size:24 final size:24
Alignment explanation
Indices: 30486--30683 Score: 122
Period size: 24 Copynumber: 8.2 Consensus size: 24
30476 TTTTTTATAG
*
30486 CTATTTAT-TTATTATTTATTTA-
1 CTATTTATCTTTTTATTTATTTAT
* *
30508 CTATTTATTTTTTTATTTATTAAT
1 CTATTTATCTTTTTATTTATTTAT
* *
30532 TTAGCTATTATCTATTTATTTA-TTAT
1 CTA--T-TTATCTTTTTATTTATTTAT
* **
30558 -TATTTAT-TTTCT-TTTACCTAT
1 CTATTTATCTTTTTATTTATTTAT
* * **
30579 CTATTTATCTCTGTACCTATTTAT
1 CTATTTATCTTTTTATTTATTTAT
* **
30603 CTATTTATCTTTATACCTATTTAT
1 CTATTTATCTTTTTATTTATTTAT
*
30627 CTTTTTATCTTTTTATTTATTTAT
1 CTATTTATCTTTTTATTTATTTAT
* *
30651 -TATTATTATTTTTTTAAATTTATTTTT
1 CTA-T-TTATCTTTTT--ATTTATTTAT
30678 CTATTT
1 CTATTT
30684 TTCTATTACT
Statistics
Matches: 138, Mismatches: 24, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.03
21 6 0.04
22 19 0.14
23 17 0.12
24 50 0.36
25 11 0.08
26 6 0.04
27 23 0.17
28 2 0.01
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.66
Consensus pattern (24 bp):
CTATTTATCTTTTTATTTATTTAT
Found at i:30719 original size:33 final size:33
Alignment explanation
Indices: 30654--30720 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
30644 TATTTATTAT
** *
30654 TATTATTTTTTTAAATTTATTTTTCTATTTTTC
1 TATTATTTTTTTAAATTTATTTTAATAATTTTC
*
30687 TATTACTTTTTTT-TATTTATTTTAATAATTTTC
1 TATTA-TTTTTTTAAATTTATTTTAATAATTTTC
30720 T
1 T
30721 TAATAAGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (33 bp):
TATTATTTTTTTAAATTTATTTTAATAATTTTC
Found at i:32011 original size:33 final size:33
Alignment explanation
Indices: 31964--32038 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
31954 CGAAGCGTCT
31964 GATTCCTTCCCTTAACAGAGTTCTTGTTGAGAA
1 GATTCCTTCCCTTAACAGAGTTCTTGTTGAGAA
*
31997 GATTTCTTCCCTTAACAGAGTTCTTGTTGAGAA
1 GATTCCTTCCCTTAACAGAGTTCTTGTTGAGAA
32030 GA-TCCTTCC
1 GATTCCTTCC
32039 TCCTTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.15
33 34 0.85
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (33 bp):
GATTCCTTCCCTTAACAGAGTTCTTGTTGAGAA
Found at i:35515 original size:14 final size:13
Alignment explanation
Indices: 35496--35530 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
35486 GTCACTAAAA
35496 ATAATATATAGTAT
1 ATAATATATA-TAT
35510 ATAATATATATAT
1 ATAATATATATAT
35523 AT-ATATAT
1 ATAATATAT
35531 TAGCAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.29
13 5 0.24
14 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:35555 original size:2 final size:2
Alignment explanation
Indices: 35548--35572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35538 ATCAACTCTT
35548 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
35573 GAAATTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36085 original size:7 final size:6
Alignment explanation
Indices: 36076--36118 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
36066 GTTTTTCTAT
* *
36076 TTTTTG TTTTTG TTTTTG TTTTTG -TTTTC ATTTTG TTTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
36119 GCGTTGTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:36103 original size:17 final size:18
Alignment explanation
Indices: 36076--36118 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
36066 GTTTTTCTAT
**
36076 TTTTTGTTTTTGTTTTTG
1 TTTTTGTTTTCATTTTTG
36094 TTTTTGTTTTCA-TTTTG
1 TTTTTGTTTTCATTTTTG
36111 TTTTTGTT
1 TTTTTGTT
36119 GCGTTGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.81
Consensus pattern (18 bp):
TTTTTGTTTTCATTTTTG
Found at i:36131 original size:23 final size:23
Alignment explanation
Indices: 36083--36132 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
36073 TATTTTTTGT
** *
36083 TTTTGTTTTTGTTTTTGTTTTCA
1 TTTTGTTTTTGTTTGCGTTGTCA
36106 TTTTGTTTTTG-TTGCGTTGTCAA
1 TTTTGTTTTTGTTTGCGTTGTC-A
36129 TTTT
1 TTTT
36133 TGAAAACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.06, C:0.06, G:0.16, T:0.72
Consensus pattern (23 bp):
TTTTGTTTTTGTTTGCGTTGTCA
Found at i:36845 original size:16 final size:17
Alignment explanation
Indices: 36824--36855 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
36814 TCCCAACCAA
36824 AAAGAAGA-AGCAAGAG
1 AAAGAAGATAGCAAGAG
36840 AAAGAAGATAGCAAGA
1 AAAGAAGATAGCAAGA
36856 AAAACTGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.28, T:0.03
Consensus pattern (17 bp):
AAAGAAGATAGCAAGAG
Found at i:42086 original size:6 final size:6
Alignment explanation
Indices: 42075--42101 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42065 TTAATGAGTC
42075 GATTTG GATTTG GATTTG GATTTG GAT
1 GATTTG GATTTG GATTTG GATTTG GAT
42102 AGGGATAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (6 bp):
GATTTG
Found at i:43457 original size:21 final size:20
Alignment explanation
Indices: 43402--43457 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
43392 GTTTAGCAAT
43402 TGTACAGATGAGATT-ACAC
1 TGTACAGATGAGATTAACAC
* * *
43421 TGTACAGATTAAATTAGATAC
1 TGTACAGATGAGATTA-ACAC
43442 TGTACAGATGAGATTA
1 TGTACAGATGAGATTA
43458 TTAGAGCAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (20 bp):
TGTACAGATGAGATTAACAC
Found at i:44662 original size:351 final size:349
Alignment explanation
Indices: 44014--44713 Score: 1285
Period size: 351 Copynumber: 2.0 Consensus size: 349
44004 GCCCAGTTAT
* *
44014 CCTTTAAACCTTATTGTTATGGTTATTTTTTAATTAGCTGTGTTAATCCTAATTGGGCCGTATAT
1 CCTTTAAACCTTATTATTATGGTTATTTTCTAATTAGCTGTGTTAATCCTAATTGGGCCGTATAT
*
44079 AACGGCTACCTCAATTGAAATGTAATCAGACTTGAAATTTTAACAAAGAAATATCGTTTTCTTCC
66 AACGGCTACCTCAATTGAAATGTAATCAGACTTGAAATTTTAACAAAGAAATATCGTCTTCTTCC
* *
44144 CAGAATTTTGAACTTCTCCTCCCTCATTCTCTTTAGTCCGACTTAATCTTTTAAGTTGTGACAAA
131 CAGAATTCTGAACTTCTCCTCCCTCATTCTCTTTAGTCCGACTTAATCCTTTAAGTTGTGACAAA
*
44209 ATTGGTACCAGAGCTTCCTTTCCTCGGCGATGGGTGATAGGGTTACTACCAAAGTCCAGAAAGAG
196 ATTGGTACCAGAGCTTCCTTTCCTCGGCGATGGGTGACAGGGTTACTACCAAAGTCCAGAAAGAG
44274 CTCGCGACAATCCACCAGAAGTACACCGATCTCAATGTAAAGGTTGATTCAAATCTTGCTCAGAT
261 CTCGCGACAATCCACCAGAAGTACACCGATCTCAATGTAAAGGTTGATTCAAATCTTGCTCAGAT
44339 TCGTTCAGAGATGCAAACCAACTC
326 TCGTTCAGAGATGCAAACCAACTC
*
44363 CCTTTAAACCTTATTATTATGGTTATTTTCTAATTAGTTGTGTTAATCCTAATTGGGCCGTATAT
1 CCTTTAAACCTTATTATTATGGTTATTTTCTAATTAGCTGTGTTAATCCTAATTGGGCCGTATAT
44428 AACGGCTACCTCAATTGAAATGTAATCAGACTTGAAATTTTAACAAAGAAATATCGTCTTCTTCC
66 AACGGCTACCTCAATTGAAATGTAATCAGACTTGAAATTTTAACAAAGAAATATCGTCTTCTTCC
44493 CAGAATTCTGAACTTCTCTTCTCCCTCATTCT-TTCTAGTCCGACTTAATCCTTTAAGTTGTGAC
131 CAGAATTCTGAACTTCTC--CTCCCTCATTCTCTT-TAGTCCGACTTAATCCTTTAAGTTGTGAC
44557 AAAATTGGTACCAGAGCTTCCTTTCCTCGGCGATGGGTGACAGGGTTACTACCAAAGTCCAGAAA
193 AAAATTGGTACCAGAGCTTCCTTTCCTCGGCGATGGGTGACAGGGTTACTACCAAAGTCCAGAAA
* *
44622 GAGCTCGCGGCAATCCACCAGAAGTACACTGATCTCAATGTAAAGGTTGATTCAAATCTTGCTCA
258 GAGCTCGCGACAATCCACCAGAAGTACACCGATCTCAATGTAAAGGTTGATTCAAATCTTGCTCA
44687 GATTCGTTCAGAGATGCAAACCAACTC
323 GATTCGTTCAGAGATGCAAACCAACTC
44714 TTCTCAGCTT
Statistics
Matches: 339, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
349 143 0.42
350 2 0.01
351 194 0.57
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (349 bp):
CCTTTAAACCTTATTATTATGGTTATTTTCTAATTAGCTGTGTTAATCCTAATTGGGCCGTATAT
AACGGCTACCTCAATTGAAATGTAATCAGACTTGAAATTTTAACAAAGAAATATCGTCTTCTTCC
CAGAATTCTGAACTTCTCCTCCCTCATTCTCTTTAGTCCGACTTAATCCTTTAAGTTGTGACAAA
ATTGGTACCAGAGCTTCCTTTCCTCGGCGATGGGTGACAGGGTTACTACCAAAGTCCAGAAAGAG
CTCGCGACAATCCACCAGAAGTACACCGATCTCAATGTAAAGGTTGATTCAAATCTTGCTCAGAT
TCGTTCAGAGATGCAAACCAACTC
Found at i:45233 original size:24 final size:24
Alignment explanation
Indices: 45205--45252 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
45195 TTAAATTTAA
45205 GCAATCTTAAACCTGAATTTCAGT
1 GCAATCTTAAACCTGAATTTCAGT
45229 GCAATCTTAAACCTGAATTTCAGT
1 GCAATCTTAAACCTGAATTTCAGT
45253 TGATGACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (24 bp):
GCAATCTTAAACCTGAATTTCAGT
Found at i:47634 original size:22 final size:21
Alignment explanation
Indices: 47582--47635 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
47572 TGTTTCTTGA
47582 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
47603 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
47622 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
47636 CACGAACTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:52834 original size:42 final size:42
Alignment explanation
Indices: 52775--52858 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
52765 GCTCATTGTC
52775 ACATTAGTCCCCTATTCTAGTATGAAGTCATTTTAGAGAAAT
1 ACATTAGTCCCCTATTCTAGTATGAAGTCATTTTAGAGAAAT
**
52817 ACATTAGTTGCCTATTCTAGTATGAAGTCATTTTAGAGAAAT
1 ACATTAGTCCCCTATTCTAGTATGAAGTCATTTTAGAGAAAT
52859 TAGCAAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (42 bp):
ACATTAGTCCCCTATTCTAGTATGAAGTCATTTTAGAGAAAT
Found at i:60841 original size:61 final size:61
Alignment explanation
Indices: 60776--61077 Score: 491
Period size: 61 Copynumber: 5.0 Consensus size: 61
60766 CTTTTCAAAG
*
60776 AGGGAAAGTTCCCAACAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTATTCAATTT
1 AGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTATTCAATTT
* *
60837 AGGGAAAGATCCCATCAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTGTTCAATTT
1 AGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTATTCAATTT
*
60898 AGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTGTTCAATTT
1 AGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTATTCAATTT
* * *
60959 AGGGAAAGTTCCCATCAAATTTTCAAAGTATTCAATTCAAGTTTTCCAAAGTTTTCAATTT
1 AGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTATTCAATTT
* * * *
61020 ATGGAAAGATCCCATCACGTTTTCAAAGTATTCAATTCAAG--TTTCAAAGAATTCAATT
1 AGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTATTCAATT
61078 CAAGTTTTCC
Statistics
Matches: 227, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
59 14 0.06
61 213 0.94
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (61 bp):
AGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTCAAGTTTTTCAAAGTATTCAATTT
Found at i:60938 original size:22 final size:23
Alignment explanation
Indices: 60912--60957 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
60902 AAAGTTCCCA
60912 TCAAG-TTTTCAAAGTATTCAAT
1 TCAAGTTTTTCAAAGTATTCAAT
*
60934 TCAAGTTTTTCAAAGTGTTCAAT
1 TCAAGTTTTTCAAAGTATTCAAT
60957 T
1 T
60958 TAGGGAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (23 bp):
TCAAGTTTTTCAAAGTATTCAAT
Found at i:60957 original size:23 final size:22
Alignment explanation
Indices: 60791--60896 Score: 98
Period size: 23 Copynumber: 5.0 Consensus size: 22
60781 AAGTTCCCAA
60791 CAAGTTTTCAAAGTATTCAATT
1 CAAGTTTTCAAAGTATTCAATT
60813 CAAGTTTTTCAAAGTATTCAATT
1 CAAG-TTTTCAAAGTATTCAATT
* ** * *
60836 -TAG---GGAAAG-ATCCCA-T
1 CAAGTTTTCAAAGTATTCAATT
60852 CAAGTTTTCAAAGTATTCAATT
1 CAAGTTTTCAAAGTATTCAATT
*
60874 CAAGTTTTTCAAAGTGTTCAATT
1 CAAG-TTTTCAAAGTATTCAATT
60897 TAGGGAAAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
16 1 0.02
17 6 0.09
18 4 0.06
20 4 0.06
21 4 0.06
22 11 0.17
23 35 0.54
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (22 bp):
CAAGTTTTCAAAGTATTCAATT
Found at i:60998 original size:22 final size:23
Alignment explanation
Indices: 60973--61018 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
60963 AAAGTTCCCA
60973 TCAAATTTT-CAAAGTATTCAAT
1 TCAAATTTTCCAAAGTATTCAAT
* *
60995 TCAAGTTTTCCAAAGTTTTCAAT
1 TCAAATTTTCCAAAGTATTCAAT
61018 T
1 T
61019 TATGGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (23 bp):
TCAAATTTTCCAAAGTATTCAAT
Found at i:61064 original size:21 final size:21
Alignment explanation
Indices: 61040--61084 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
61030 CCCATCACGT
*
61040 TTTCAAAGTATTCAATTCAAG
1 TTTCAAAGAATTCAATTCAAG
61061 TTTCAAAGAATTCAATTCAAG
1 TTTCAAAGAATTCAATTCAAG
61082 TTT
1 TTT
61085 TCCAAAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTCAAAGAATTCAATTCAAG
Found at i:61135 original size:82 final size:82
Alignment explanation
Indices: 60979--61136 Score: 244
Period size: 82 Copynumber: 1.9 Consensus size: 82
60969 CCCATCAAAT
* * * * *
60979 TTTCAAAGTATTCAATTCAAGTTTTCCAAAGTTTTCAATTTATGGAAAGATCCCATCACGTTTTC
1 TTTCAAAGAATTCAATTCAAGTTTTCCAAAGCTTTCAATCTAGGGAAAGATCCCATCAAGTTTTC
**
61044 AAAGTATTCAATTCAAG
66 AAAACATTCAATTCAAG
*
61061 TTTCAAAGAATTCAATTCAAGTTTTCCAAAGCTTTCAATCTAGGGAAAGCTCCCATCAAGTTTTC
1 TTTCAAAGAATTCAATTCAAGTTTTCCAAAGCTTTCAATCTAGGGAAAGATCCCATCAAGTTTTC
61126 AAAACATTCAA
66 AAAACATTCAA
61137 ATAGCATTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 68 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (82 bp):
TTTCAAAGAATTCAATTCAAGTTTTCCAAAGCTTTCAATCTAGGGAAAGATCCCATCAAGTTTTC
AAAACATTCAATTCAAG
Found at i:63728 original size:2 final size:2
Alignment explanation
Indices: 63716--63748 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
63706 AGATAACCTA
63716 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63749 GTCAACACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65155 original size:239 final size:244
Alignment explanation
Indices: 64733--65211 Score: 717
Period size: 239 Copynumber: 2.0 Consensus size: 244
64723 TTGATCATCG
* *
64733 ATCATCCATAATATTAATTTTTTTTTATAGTTGGCCTGCAAAAAAAATCATTAACACACACACCC
1 ATCATCCATAATATTAATTTCTTTTTATAGTTGGCCT-CAAAAAAAATAATTAACACACACA-CC
* * *
64798 ACATATAATCATCTAAATATTATTTTCTTTTTATATTATATATATCGTGGCAGCTTCTTGGTAGT
64 ACACATAATCATCCAAATATTAATTTCTTTTTATATTATATATATCGTGGCAGCTTCTTGGTAGT
*
64863 TGGCCTGCAAAAAAAAATCATATCAATTATTTTTTATTTTTAATAATAATCACTTTTATATTTAT
129 TGGCCTGC-AAAAAAAATCATATCAATTAATTTTTATTTTTAATAATAATCACTTTTATATTTAT
64928 AT-T-TAT-AT-AT-ATAATAATAACAATTACCTTTAAATTTCCACACAATA
193 ATATATATAATAATAATAATAATAACAATTACCTTTAAATTTCCACACAATA
* *
64975 ATCATCCATAATATTAATTTCTTTTTATAGTTGGCCT-AAAAAAAATAATTGACACTCACA-CAC
1 ATCATCCATAATATTAATTTCTTTTTATAGTTGGCCTCAAAAAAAATAATTAACACACACACCAC
65038 ACATAATCATCCATAATATTAATTTCTTTTTATATTATATATATATCGTGGCAGCTTCTTGGTAG
66 ACATAATCATCCA-AATATTAATTTCTTTTTATA-T-TATATATATCGTGGCAGCTTCTTGGTAG
* *
65103 TTGGCCTGC-AGAAAGATCAT-TCCAATTAATTTTTATTCTTT-ATAATAATCACTTTTATATTT
128 TTGGCCTGCAAAAAAAATCATAT-CAATTAATTTTTATT-TTTAATAATAATCACTTTTATATTT
*
65165 ATATATATATAATAATAATAATAATAACAATTACCTTTCAATTTCCA
191 ATATATATATAATAATAATAATAATAACAATTACCTTTAAATTTCCA
65212 GCGTTGTCCT
Statistics
Matches: 216, Mismatches: 11, Indels: 18
0.88 0.04 0.07
Matches are distributed among these distances:
238 15 0.07
239 67 0.31
240 25 0.12
241 40 0.19
242 38 0.18
243 2 0.01
244 29 0.13
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (244 bp):
ATCATCCATAATATTAATTTCTTTTTATAGTTGGCCTCAAAAAAAATAATTAACACACACACCAC
ACATAATCATCCAAATATTAATTTCTTTTTATATTATATATATCGTGGCAGCTTCTTGGTAGTTG
GCCTGCAAAAAAAATCATATCAATTAATTTTTATTTTTAATAATAATCACTTTTATATTTATATA
TATATAATAATAATAATAATAACAATTACCTTTAAATTTCCACACAATA
Done.