Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 101 of 150
Found at i:31623859 original size:16 final size:15
Alignment explanation
Indices: 31623818--31623847 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31623808 CTTGTTATTA
31623818 TTTTTTTATTTTTAG
1 TTTTTTTATTTTTAG
31623833 TTTTTATTATTTTTA
1 TTTTT-TTATTTTTA
31623848 TTCATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTTTATTTTTAG
Found at i:31625567 original size:26 final size:25
Alignment explanation
Indices: 31625519--31625567 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31625509 TTAAATTTGA
*
31625519 TGTTTATTTTAATTTTTAGTTGTTT
1 TGTTTATTTTAATTTTTACTTGTTT
* *
31625544 TGTTTATTTTTATTATTTTCTTGT
1 TGTTTATTTTAATT-TTTACTTGT
31625568 ACTTCTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.14, C:0.02, G:0.10, T:0.73
Consensus pattern (25 bp):
TGTTTATTTTAATTTTTACTTGTTT
Found at i:31631814 original size:69 final size:69
Alignment explanation
Indices: 31631703--31631864 Score: 225
Period size: 69 Copynumber: 2.3 Consensus size: 69
31631693 ACCTTTGATG
* * * *
31631703 TCCAACACAATTAGCGAGAGCAAAGCTCCTAGCTGACATATTAAGGCTCGTAGGTGAAGAGCCGC
1 TCCAACACAGTTAGCGAGAGCAAACCTCCCAACTGACATATTAAGGCTCGTAGGTGAAGAGCCGC
*
31631768 GGCC
66 AGCC
* * * * *
31631772 TCCAACACAGTTAGCAAGAGCAAACCTCCCAACTGTCATATTATGGCTCGTAGGTGAAGAGTCGT
1 TCCAACACAGTTAGCGAGAGCAAACCTCCCAACTGACATATTAAGGCTCGTAGGTGAAGAGCCGC
31631837 AGCC
66 AGCC
*
31631841 TCCAACACAGTTAACGAGAGCAAA
1 TCCAACACAGTTAGCGAGAGCAAA
31631865 GCTCATTGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (69 bp):
TCCAACACAGTTAGCGAGAGCAAACCTCCCAACTGACATATTAAGGCTCGTAGGTGAAGAGCCGC
AGCC
Found at i:31634761 original size:69 final size:68
Alignment explanation
Indices: 31634646--31634853 Score: 236
Period size: 69 Copynumber: 3.0 Consensus size: 68
31634636 TGTTACACTC
* *** * *
31634646 CCAGCTATCATAGTAAGGCTCACAGGTGAAGAGCCGTAGCTTCCAACACAGTTAGCGAGAGCAAA
1 CCAGCTATCATATTAAGGCTTGTAGGTGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAA
31634711 ACT
66 ACT
* * * *
31634714 CTCAGCTATCATATTAAGACTTGTAGGTGAAAAGCCACAGCCTCCAACATAGTTAGCGAGAGCAA
1 C-CAGCTATCATATTAAGGCTTGTAGGTGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAA
*
31634779 AGCT
65 AACT
** * * * *
31634783 ACCAATTGTCATATTAAGGCTTGTAGGTGAAGAGCCGCAACCTCCAACACAGTTAGTGTGAGCAA
1 -CCAGCTATCATATTAAGGCTTGTAGGTGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAA
*
31634848 AGCT
65 AACT
31634852 CC
1 CC
31634854 CGCAGGTGAA
Statistics
Matches: 117, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
68 3 0.03
69 113 0.97
70 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (68 bp):
CCAGCTATCATATTAAGGCTTGTAGGTGAAGAGCCGCAGCCTCCAACACAGTTAGCGAGAGCAAA
ACT
Found at i:31634893 original size:50 final size:50
Alignment explanation
Indices: 31634807--31634954 Score: 172
Period size: 50 Copynumber: 3.0 Consensus size: 50
31634797 TAAGGCTTGT
* * *
31634807 AGGTGAAGAGCCGCAACCTCCAACACAGTTAGTGTGAGCAAAGCTCCCGC
1 AGGTGAAGAGCTGCAGCCTCCAACAAAGTTAGTGTGAGCAAAGCTCCCGC
* * *
31634857 AGGTGAAGAGCTGCAGCCTTCAACAGAATTTA-TGTGAGTAAAGCTCCCGC
1 AGGTGAAGAGCTGCAGCCTCCAACA-AAGTTAGTGTGAGCAAAGCTCCCGC
** * * * *
31634907 AGGTGAAGAATTGCAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCC
1 AGGTGAAGAGCTGCAGCCTCCAACAAAGTTAGTGTGAGCAAAGCTCCC
31634955 ATCTGTCATA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
49 4 0.05
50 73 0.90
51 4 0.05
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (50 bp):
AGGTGAAGAGCTGCAGCCTCCAACAAAGTTAGTGTGAGCAAAGCTCCCGC
Found at i:31635030 original size:69 final size:69
Alignment explanation
Indices: 31634904--31635292 Score: 383
Period size: 69 Copynumber: 5.7 Consensus size: 69
31634894 GTAAAGCTCC
* * * * *
31634904 CGCAGGTGAAGAA-TTGCAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCCATCTGTCATAGTA
1 CGCAGGTGAA-AAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTTCCAACTGTCATATTA
* *
31634968 ATGTT
65 AGGCT
* * * *
31634973 CGTAGGTGAAAAGTCGCAGCCTCCACCACAATTAGCGAGAGCAAAGCTTCCAGCTGTCATATTAA
1 CGCAGGTGAAAAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTTCCAACTGTCATATTAA
31635038 GGCT
66 GGCT
* * * * *
31635042 GGCAGGTGAAAAGCCACAGCCTCCAACATAGTTAGTGAGAGCAAAGC-TCCTAACTGTCATATTA
1 CGCAGGTGAAAAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTTCC-AACTGTCATATTA
31635106 AGGCT
65 AGGCT
* * * * * * * * *
31635111 CGTAGGTGAAGAGTCGTATCCTCTAACACAGCT-GCGAAAACAAAGC-TCTCAACTATCATATTA
1 CGCAGGTGAAAAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTTC-CAACTGTCATATTA
31635174 AGGCT
65 AGGCT
* * * *
31635179 CGCAGGTGAAGAGTCGCAGCCTCCAGCACAGTTAGCGAGAGCAAAGCTGCCAACTGTCTTATTAA
1 CGCAGGTGAAAAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTTCCAACTGTCATATTAA
*
31635244 GGTT
66 GGCT
* * * * * *
31635248 CGGAGGTGAAGAG-CTGCAACCTTCAACCCAGTTAGCGTGAGCAAA
1 CGCAGGTGAAAAGTC-GCAGCCTCCAACACAGTTAGCGAGAGCAAA
31635293 ACTCCCACAG
Statistics
Matches: 263, Mismatches: 51, Indels: 12
0.81 0.16 0.04
Matches are distributed among these distances:
68 62 0.24
69 200 0.76
70 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (69 bp):
CGCAGGTGAAAAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTTCCAACTGTCATATTAA
GGCT
Found at i:31635212 original size:137 final size:137
Alignment explanation
Indices: 31634904--31635260 Score: 421
Period size: 137 Copynumber: 2.6 Consensus size: 137
31634894 GTAAAGCTCC
* * * * *
31634904 CGCAGGTGAAGAATTGCAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCCATCTGTCATAGTAA
1 CGCAGGTGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCT-CCAACTGTCATATTAA
* * * * * * * *
31634969 TGTTCGTAGGTGAAAAGTCGCAGCCTCCACCACAATTAGCGAGAGCAAAGCTTCCAGCTGTCATA
65 GGTTCGTAGGTGAAGAGTCGCAGCCTCCAACACAACTAGCGAAAACAAAGCTTCCAACTATCATA
31635034 TTAAGGCT
130 TTAAGGCT
* * * * * *
31635042 GGCAGGTGAAAAGCCACAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCTAACTGTCATATTAA
1 CGCAGGTGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC-AACTGTCATATTAA
* * * * *
31635107 GGCTCGTAGGTGAAGAGTCGTATCCTCTAACACAGCT-GCGAAAACAAAGC-TCTCAACTATCAT
65 GGTTCGTAGGTGAAGAGTCGCAGCCTCCAACACAACTAGCGAAAACAAAGCTTC-CAACTATCAT
31635170 ATTAAGGCT
129 ATTAAGGCT
* *
31635179 CGCAGGTGAAGAGTCGCAGCCTCCAGCACAGTTAGCGAGAGCAAAGCTGCCAACTGTCTTATTAA
1 CGCAGGTGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCT-CCAACTGTCATATTAA
*
31635244 GGTTCGGAGGTGAAGAG
65 GGTTCGTAGGTGAAGAG
31635261 CTGCAACCTT
Statistics
Matches: 182, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
136 2 0.01
137 99 0.54
138 81 0.45
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (137 bp):
CGCAGGTGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCAACTGTCATATTAAG
GTTCGTAGGTGAAGAGTCGCAGCCTCCAACACAACTAGCGAAAACAAAGCTTCCAACTATCATAT
TAAGGCT
Found at i:31642147 original size:42 final size:42
Alignment explanation
Indices: 31642077--31642159 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
31642067 AATCCTAATT
* *
31642077 GGAAAATAATTCCTTTATTCTAATAAACTACTAAAACATAAG
1 GGAAAATAATTCCATTATTCTAAGAAACTACTAAAACATAAG
* * *
31642119 GGAAAATAATTCCATTCTTTTAAGAAACTACTAAAAGATAA
1 GGAAAATAATTCCATTATTCTAAGAAACTACTAAAACATAA
31642160 AACAAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.30
Consensus pattern (42 bp):
GGAAAATAATTCCATTATTCTAAGAAACTACTAAAACATAAG
Found at i:31642167 original size:42 final size:42
Alignment explanation
Indices: 31642079--31642172 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 42
31642069 TCCTAATTGG
* * ***
31642079 AAAATAATTCCTTTATTCTAATAAACTACTAAAACATAAGGG
1 AAAATAATTCCATTATTCTAAGAAACTACTAAAACATAAAAC
* * *
31642121 AAAATAATTCCATTCTTTTAAGAAACTACTAAAAGATAAAAC
1 AAAATAATTCCATTATTCTAAGAAACTACTAAAACATAAAAC
31642163 AAAAT-ATTCC
1 AAAATAATTCC
31642173 TAGAATATGA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 5 0.11
42 39 0.89
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (42 bp):
AAAATAATTCCATTATTCTAAGAAACTACTAAAACATAAAAC
Found at i:31642212 original size:19 final size:18
Alignment explanation
Indices: 31642190--31642229 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
31642180 TGAATAAAAC
31642190 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
31642209 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
31642227 TTA
1 TTA
31642230 AAATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:31645178 original size:26 final size:26
Alignment explanation
Indices: 31645149--31645203 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
31645139 TAACCTTATC
31645149 AAAATCAGAAACAAAATTTAAACATA
1 AAAATCAGAAACAAAATTTAAACATA
*
31645175 AAAATTAGAAACAAAATTTAAACATA
1 AAAATCAGAAACAAAATTTAAACATA
31645201 AAA
1 AAA
31645204 TAGTTGTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (26 bp):
AAAATCAGAAACAAAATTTAAACATA
Found at i:31645203 original size:13 final size:13
Alignment explanation
Indices: 31645161--31645204 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
31645151 AATCAGAAAC
31645161 AAAATTTAAACAT
1 AAAATTTAAACAT
* *
31645174 AAAAATTAGAA-AC
1 AAAATTTA-AACAT
31645187 AAAATTTAAACAT
1 AAAATTTAAACAT
31645200 AAAAT
1 AAAAT
31645205 AGTTGTTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (13 bp):
AAAATTTAAACAT
Found at i:31645751 original size:42 final size:42
Alignment explanation
Indices: 31645693--31645773 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
31645683 TCCTAATTGG
* * *
31645693 AAAATAATTCCCTTATTCTAATACACTACTAAAACATAAGGA
1 AAAATAATTCCATTATTCTAATAAACTACTAAAAAATAAGGA
*
31645735 AAAATAATTTCATTATTCTAATAAACTACTAAAAAATAA
1 AAAATAATTCCATTATTCTAATAAACTACTAAAAAATAA
31645774 AATAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (42 bp):
AAAATAATTCCATTATTCTAATAAACTACTAAAAAATAAGGA
Found at i:31645781 original size:42 final size:42
Alignment explanation
Indices: 31645693--31645784 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
31645683 TCCTAATTGG
* * * *
31645693 AAAATAATTCCCTTATTCTAATACACTACTAAAACATAAGGA
1 AAAATAATTCCATTATTCTAATAAACTACTAAAAAATAAGAA
*
31645735 AAAATAATTTCATTATTCTAATAAACTACTAAAAAATAA-AA
1 AAAATAATTCCATTATTCTAATAAACTACTAAAAAATAAGAA
31645776 TAAAATAAT
1 -AAAATAAT
31645785 CCTAGAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (42 bp):
AAAATAATTCCATTATTCTAATAAACTACTAAAAAATAAGAA
Found at i:31645826 original size:19 final size:18
Alignment explanation
Indices: 31645804--31645843 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
31645794 TGAATAAAAC
*
31645804 TTATCTACCTAAATAAGAT
1 TTATATACCTAAATAA-AT
31645823 TTATATACCTAAATAAAT
1 TTATATACCTAAATAAAT
31645841 TTA
1 TTA
31645844 AAATATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATATACCTAAATAAAT
Found at i:31647279 original size:20 final size:21
Alignment explanation
Indices: 31647254--31647294 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
31647244 TGAGTGAAGC
31647254 TTTCTCTCTCT-AGCTTCAAG
1 TTTCTCTCTCTAAGCTTCAAG
*
31647274 TTTCTCTTTCTAAGCTTCAAG
1 TTTCTCTCTCTAAGCTTCAAG
31647295 AACCCTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTCTCTCTCTAAGCTTCAAG
Found at i:31648138 original size:188 final size:190
Alignment explanation
Indices: 31647586--31648143 Score: 603
Period size: 195 Copynumber: 2.9 Consensus size: 190
31647576 TGATAATTGC
* * * * *
31647586 GGCACTTT-TCAAAAAATGCCGCAATAGATCAAGAATTAGCGGCGCTATCTGTAAAGCGCCGCAG
1 GGCACTTTAT-AAAAAA-GCCGCTATAGATCAAGAATTAGCGGCGCTTTTTGTAAAACGCCGCAA
** * *
31647650 AAATTTTGAGCAAAACGACTTCGTTTTTTGTTGAGCTTTATTGGCTTTAGTGGCGCTTTCTAAAA
64 AAAAGTTGAGCAAAACGACTTTGTTTTTTGTTGAGCTTTATTGGCTTTAGTGGCGCTTTTTAAAA
* * ** *
31647715 AATGCCGCAATAGATCGAACATTAGCGACGCTAGTTGAGAAACACCGCAATAGATTGAGCTTTAG
129 AATGCCGCAATAGATCGAACATTAGCGGCGCTACTTGAGAAATGCCACAATAGATT--GC--TAG
31647780 T
190 T
** * * *
31647781 GGCACTTTATAAGAAATAG-CAATAAAGATCAAGAATTAGCGGCGCTTGTTT-TAAAACACCGTA
1 GGCACTTTATAA-AAA-AGCCGCTATAGATCAAGAATTAGCGGCGCTT-TTTGTAAAACGCCGCA
*
31647844 AAAAAGTTGAGCAAAACAACTTCT-TTTTTTGTTGAGCTTTATTGGCTTTAGTGGCGCTTTTTAA
63 AAAAAGTTGAGCAAAACGACTT-TGTTTTTTGTTGAGCTTTATTGGCTTTAGTGGCGCTTTTTAA
** * *
31647908 AAAATGTTGCAATAGATCGAACATTAGCGGCGCAACTTGAGAAATGCCACAATAGA-T-C-GGT
127 AAAATGCCGCAATAGATCGAACATTAGCGGCGCTACTTGAGAAATGCCACAATAGATTGCTAGT
* * * *
31647969 GGCGCTTTATAAAAAACGCCGCTATAGATCAGGAATTAGCGGCACTTTTTGTAAAACGCCACAAA
1 GGCACTTTATAAAAAA-GCCGCTATAGATCAAGAATTAGCGGCGCTTTTTGTAAAACGCCGCAAA
* * * ** *
31648034 AAAGTTGAGCAAAACGACTTTGTTTTTTATTGAGCTTTAGTGGCATTAGCAGTGCTTTTTCAAAA
65 AAAGTTGAGCAAAACGACTTTGTTTTTTGTTGAGCTTTATTGGCTTTAGTGGCGCTTTTT-AAAA
* **
31648099 AATGCCACAATAGATCGATA-ATTAGCGGCG-TTTTTGAGAAATGCC
129 AATGCCGCAATAGATCGA-ACATTAGCGGCGCTACTTGAGAAATGCC
31648144 TAAAAAATAA
Statistics
Matches: 306, Mismatches: 46, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
186 1 0.00
187 8 0.03
188 110 0.36
189 29 0.09
190 1 0.00
191 1 0.00
194 1 0.00
195 147 0.48
196 7 0.02
197 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (190 bp):
GGCACTTTATAAAAAAGCCGCTATAGATCAAGAATTAGCGGCGCTTTTTGTAAAACGCCGCAAAA
AAGTTGAGCAAAACGACTTTGTTTTTTGTTGAGCTTTATTGGCTTTAGTGGCGCTTTTTAAAAAA
TGCCGCAATAGATCGAACATTAGCGGCGCTACTTGAGAAATGCCACAATAGATTGCTAGT
Found at i:31648936 original size:20 final size:21
Alignment explanation
Indices: 31648911--31648956 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
31648901 AGAGTTTTAA
* *
31648911 GTTTAGTGTTTATGGTGT-AG
1 GTTTAGGGTTTAGGGTGTAAG
*
31648931 GTTTAGGGTTTAGGGTTTAAG
1 GTTTAGGGTTTAGGGTGTAAG
31648952 GTTTA
1 GTTTA
31648957 TAATTTAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (21 bp):
GTTTAGGGTTTAGGGTGTAAG
Found at i:31649136 original size:7 final size:7
Alignment explanation
Indices: 31648911--31649136 Score: 96
Period size: 7 Copynumber: 31.7 Consensus size: 7
31648901 AGAGTTTTAA
*
31648911 GTTTAGT
1 GTTTAGG
*
31648918 GTTTATG
1 GTTTAGG
*
31648925 GTGTA-G
1 GTTTAGG
31648931 GTTTAGG
1 GTTTAGG
31648938 GTTTAGG
1 GTTTAGG
*
31648945 GTTTAAG
1 GTTTAGG
**
31648952 GTTTATA
1 GTTTAGG
*
31648959 ATTTAGG
1 GTTTAGG
*
31648966 GTTTAGT
1 GTTTAGG
* *
31648973 GTTAAGA
1 GTTTAGG
*
31648980 GTTTAGT
1 GTTTAGG
31648987 GTTTATGG
1 GTTTA-GG
* *
31648995 CTTATAAG
1 GTT-TAGG
** *
31649003 ACTTAGAA
1 GTTTAG-G
31649011 GTTTAGG
1 GTTTAGG
31649018 GTTTTAGG
1 G-TTTAGG
31649026 GTTT-GG
1 GTTTAGG
* *
31649032 TATTTATG
1 -GTTTAGG
*
31649040 GTTTATG
1 GTTTAGG
* *
31649047 GTATAGT
1 GTTTAGG
*
31649054 GTTTATG
1 GTTTAGG
** *
31649061 GAATAAG
1 GTTTAGG
*
31649068 GTTTACG
1 GTTTAGG
* *
31649075 ATTTATG
1 GTTTAGG
31649082 GTTTAGG
1 GTTTAGG
*
31649089 GTTGAGG
1 GTTTAGG
31649096 GTTTAGG
1 GTTTAGG
*
31649103 GTTTAAG
1 GTTTAGG
* *
31649110 GTCTAGA
1 GTTTAGG
31649117 GTTTAGG
1 GTTTAGG
31649124 GTTTTAGG
1 G-TTTAGG
31649132 GTTTA
1 GTTTA
31649137 ATTACTTTTG
Statistics
Matches: 158, Mismatches: 53, Indels: 16
0.70 0.23 0.07
Matches are distributed among these distances:
6 7 0.04
7 125 0.79
8 24 0.15
9 2 0.01
ACGTcount: A:0.22, C:0.02, G:0.31, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:31651206 original size:6 final size:6
Alignment explanation
Indices: 31651150--31651190 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
31651140 AATTTTAGAC
31651150 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
31651191 AATTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:31651214 original size:20 final size:20
Alignment explanation
Indices: 31651155--31651203 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
31651145 TAGACTTTAG
31651155 TTTTAGTTTTAGTTTTAG--
1 TTTTAGTTTTAGTTTTAGAA
31651173 TTTTAGTTTTAGTTTTAGAA
1 TTTTAGTTTTAGTTTTAGAA
*
31651193 TTTTATTTTTA
1 TTTTAGTTTTA
31651204 TTTATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 18 0.64
20 10 0.36
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTTAGTTTTAGTTTTAGAA
Found at i:31652241 original size:120 final size:120
Alignment explanation
Indices: 31652097--31652494 Score: 688
Period size: 120 Copynumber: 3.3 Consensus size: 120
31652087 ATTCCTATGC
* *
31652097 AATTTTAAAAATAATTATATATATTATATTTTAAATATTAAAATCTATATTTTTAATATATAACC
1 AATTTTAAACATAATTATATATATTATATTTTAAATATTAAAACCTATATTTTTAATATATAACC
31652162 TATATTAGTATGGATATATAACCTATATTTCAAATTCATTACTAATAACTTTTTA
66 TATATTAGTATGGATATATAACCTATATTTCAAATTCATTACTAATAACTTTTTA
*
31652217 AATTTTATACATAATTATATATATTATATTTTAAATATTAAAACCTATATTTTTAATATATAACC
1 AATTTTAAACATAATTATATATATTATATTTTAAATATTAAAACCTATATTTTTAATATATAACC
* * *
31652282 TAAATTAGTATGGATATCTAACCTATATTTCAAATTCATTACTAATAAATTTTTA
66 TATATTAGTATGGATATATAACCTATATTTCAAATTCATTACTAATAACTTTTTA
* *
31652337 AATTTTATACATAATTATATATATTATATTTTAAATATTAAAACCTATATTTTTAATATATAACT
1 AATTTTAAACATAATTATATATATTATATTTTAAATATTAAAACCTATATTTTTAATATATAACC
* *
31652402 TATATTAGTATGGATATGTTACCTATATTTCAAATTCATTACTAATAACTTTTTA
66 TATATTAGTATGGATATATAACCTATATTTCAAATTCATTACTAATAACTTTTTA
*
31652457 AATTTTAAACATAATTATAAATATTATATTTTTAAATA
1 AATTTTAAACATAATTATATATATTATA-TTTTAAATA
31652495 ACTTATTACT
Statistics
Matches: 264, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
120 255 0.97
121 9 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (120 bp):
AATTTTAAACATAATTATATATATTATATTTTAAATATTAAAACCTATATTTTTAATATATAACC
TATATTAGTATGGATATATAACCTATATTTCAAATTCATTACTAATAACTTTTTA
Found at i:31652265 original size:21 final size:20
Alignment explanation
Indices: 31652241--31652283 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
31652231 TTATATATAT
31652241 TATATTTTAAATATTAAAACC
1 TATATTTTAAATA-TAAAACC
* *
31652262 TATATTTTTAATATATAACC
1 TATATTTTAAATATAAAACC
31652282 TA
1 TA
31652284 AATTAGTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATTTTAAATATAAAACC
Found at i:31652595 original size:33 final size:36
Alignment explanation
Indices: 31652558--31652741 Score: 134
Period size: 38 Copynumber: 5.4 Consensus size: 36
31652548 CTAATTTCCA
*
31652558 CATAACATACATAA-T-A-ACTTATATATATCATAT
1 CATAACTTACATAACTAATACTTATATATATCATAT
31652591 CATAACTTACATAACTTAATTACTTATATATATCATAT
1 CATAACTTACATAAC-TAA-TACTTATATATATCATAT
* *
31652629 CATAACTTACATAACTCACATAACTTACATA-A-CTTA-
1 CATAACTTACATAACT-A-AT-ACTTATATATATCATAT
* *
31652665 CATAACTTACATAACT--CAC---T-TA-A-CTTA-
1 CATAACTTACATAACTAATACTTATATATATCATAT
*
31652692 CATAACTTACATAA-TACATA--AATATATATCATAT
1 CATAACTTACATAACTA-ATACTTATATATATCATAT
31652726 CATAACTTACATAACT
1 CATAACTTACATAACT
31652742 TAATTATACT
Statistics
Matches: 126, Mismatches: 7, Indels: 34
0.75 0.04 0.20
Matches are distributed among these distances:
26 1 0.01
27 21 0.17
29 1 0.01
30 1 0.01
31 4 0.03
32 1 0.01
33 16 0.13
34 14 0.11
35 2 0.02
36 17 0.13
37 4 0.03
38 35 0.28
39 9 0.07
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (36 bp):
CATAACTTACATAACTAATACTTATATATATCATAT
Found at i:31652603 original size:9 final size:9
Alignment explanation
Indices: 31652591--31652743 Score: 152
Period size: 9 Copynumber: 17.0 Consensus size: 9
31652581 TATATCATAT
31652591 CATAACTTA
1 CATAACTTA
31652600 CATAACTTA
1 CATAACTTA
*
31652609 -ATTACTTA
1 CATAACTTA
* *
31652617 TATATATCATA
1 CATA-A-CTTA
31652628 TCATAACTTA
1 -CATAACTTA
*
31652638 CATAACTCA
1 CATAACTTA
31652647 CATAACTTA
1 CATAACTTA
31652656 CATAACTTA
1 CATAACTTA
31652665 CATAACTTA
1 CATAACTTA
*
31652674 CATAACTCA
1 CATAACTTA
*
31652683 CTTAACTTA
1 CATAACTTA
31652692 CATAACTTA
1 CATAACTTA
31652701 CATAA--TA
1 CATAACTTA
*
31652708 CATAA-ATA
1 CATAACTTA
* * *
31652716 TATATCATA
1 CATAACTTA
31652725 TCATAACTTA
1 -CATAACTTA
31652735 CATAACTTA
1 CATAACTTA
31652744 ATTATACTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
7 7 0.06
8 12 0.10
9 85 0.70
10 10 0.08
11 4 0.03
12 3 0.02
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:31652618 original size:38 final size:38
Alignment explanation
Indices: 31652569--31652680 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
31652559 ATAACATACA
31652569 TAATAACTTATATATATCATATCATAACTTACATAACT
1 TAATAACTTATATATATCATATCATAACTTACATAACT
*
31652607 TAATTACTTATATATATCATATCATAACTTACATAACT
1 TAATAACTTATATATATCATATCATAACTTACATAACT
* * *
31652645 CACATAACTTACATA-A-CTTA-CATAACTTACATAACT
1 TA-ATAACTTATATATATCATATCATAACTTACATAACT
31652681 CACTTAACTT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
36 16 0.24
37 3 0.04
38 39 0.57
39 10 0.15
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (38 bp):
TAATAACTTATATATATCATATCATAACTTACATAACT
Found at i:31657787 original size:13 final size:14
Alignment explanation
Indices: 31657771--31657799 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31657761 TTTTAGATAT
31657771 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
31657784 TTATAATGGTTTAA
1 TTATAATGGTTTAA
31657798 TT
1 TT
31657800 CTTTGTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:31660054 original size:20 final size:21
Alignment explanation
Indices: 31659992--31660107 Score: 83
Period size: 19 Copynumber: 6.0 Consensus size: 21
31659982 TGTTTAAGCT
31659992 TAAAAATTATT-T-AAATATTA
1 TAAAAA-TATTATGAAATATTA
**
31660012 TAAAAAT-TTA-GAAA-AGGA
1 TAAAAATATTATGAAATATTA
31660030 TAAAAAT-TTATGAAATATTA
1 TAAAAATATTATGAAATATTA
*
31660050 T-AAAATATTATGAAA-AATA
1 TAAAAATATTATGAAATATTA
* *
31660069 TGAAAATATTAT-AAA-ATAA
1 TAAAAATATTATGAAATATTA
* *
31660088 TAAAATTATTA-GAAACATTA
1 TAAAAATATTATGAAATATTA
31660108 ATTACGTGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
18 14 0.18
19 34 0.44
20 30 0.38
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (21 bp):
TAAAAATATTATGAAATATTA
Found at i:31660055 original size:10 final size:10
Alignment explanation
Indices: 31660032--31660098 Score: 63
Period size: 10 Copynumber: 6.9 Consensus size: 10
31660022 GAAAAGGATA
31660032 AAAAT-TTAT
1 AAAATATTAT
*
31660041 GAAATATTAT
1 AAAATATTAT
31660051 AAAATATTAT
1 AAAATATTAT
31660061 GAAAA-A-TAT
1 -AAAATATTAT
31660070 GAAAATATTAT
1 -AAAATATTAT
31660081 AAAATA--AT
1 AAAATATTAT
31660089 AAAATTATTA
1 AAAA-TATTA
31660099 GAAACATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
8 6 0.12
9 14 0.29
10 21 0.43
11 8 0.16
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (10 bp):
AAAATATTAT
Found at i:31660068 original size:12 final size:11
Alignment explanation
Indices: 31660032--31660086 Score: 68
Period size: 10 Copynumber: 5.5 Consensus size: 11
31660022 GAAAAGGATA
31660032 AAAAT-TTATG
1 AAAATATTATG
31660042 -AAATATTAT-
1 AAAATATTATG
31660051 AAAATATTATG
1 AAAATATTATG
31660062 AAAA-A-TATG
1 AAAATATTATG
31660071 AAAATATTAT-
1 AAAATATTATG
31660081 AAAATA
1 AAAATA
31660087 ATAAAATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 12 0.30
10 21 0.52
11 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (11 bp):
AAAATATTATG
Found at i:31660606 original size:8 final size:8
Alignment explanation
Indices: 31660593--31660625 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
31660583 TACTTTGATA
31660593 AATTTTAT
1 AATTTTAT
31660601 AATTTTAT
1 AATTTTAT
31660609 AATTTTA-
1 AATTTTAT
31660616 AATTTT-T
1 AATTTTAT
31660623 AAT
1 AAT
31660626 CATTTAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 9 0.38
8 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTTTAT
Found at i:31664845 original size:23 final size:22
Alignment explanation
Indices: 31664788--31664857 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 22
31664778 AAAAGTAAAA
*
31664788 TAAATTCAAATCATATATAT-T
1 TAAATTCAAATAATATATATCT
*
31664809 TCAATT--AATAATATATATCT
1 TAAATTCAAATAATATATATCT
* *
31664829 TAATATTCAAATTATATTTATCT
1 TAA-ATTCAAATAATATATATCT
31664852 TAAATT
1 TAAATT
31664858 TAATATTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.28
20 3 0.08
21 8 0.20
22 3 0.08
23 15 0.38
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATTCAAATAATATATATCT
Found at i:31665931 original size:22 final size:23
Alignment explanation
Indices: 31665903--31665953 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
31665893 AACAGAAAGT
*
31665903 TTAAAATAT-TTTTATAAAATAA
1 TTAAAATATGTTTTAGAAAATAA
* *
31665925 TTAAAATATGTTTTAGACAATAT
1 TTAAAATATGTTTTAGAAAATAA
31665948 TTAAAA
1 TTAAAA
31665954 CTTTAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAAAATATGTTTTAGAAAATAA
Found at i:31669603 original size:2 final size:2
Alignment explanation
Indices: 31669596--31669627 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31669586 AGCAAGAATT
31669596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31669628 GTAAATAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31675096 original size:7 final size:6
Alignment explanation
Indices: 31675080--31675144 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
31675070 ATTTTCCTGC
* *
31675080 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
*
31675130 AGGAAAAT TAAAAT A
1 A--AAAAT AAAAAT A
31675145 TTTTTTTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
5 5 0.10
6 27 0.56
7 7 0.15
8 9 0.19
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:31690500 original size:125 final size:125
Alignment explanation
Indices: 31690270--31690536 Score: 335
Period size: 125 Copynumber: 2.1 Consensus size: 125
31690260 GGATTTTGTT
* * * *
31690270 TTTTTTTACAGTAGTTCCTGAAAAATAATTTTGAGAATACGGTTCTGAACAAATAATGTGAAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAATGTCAAAAA
* * * * * *
31690335 TGCTTCAAGCAGGATGCACTGTCAGTAAAATTACTGAAAAAAGCT-CTCATGTGGACACTC
66 AGCTTCAACCAAGATGCACTGTCAGTAAAATTACTGAAAAAAACTCCT-ACGTCGACACTC
*
31690395 TTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGAC-GTTCCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACGGTT-CTGAACAAATAATGTCAAAA
* * *
31690459 AAGCTTCAACCAAGATGCACTGTTA-TACAA-TAGTGTCAAAAAAACTCCTACGTCGACACTC
65 AAGCTTCAACCAAGATGCACTGTCAGTAAAATTACTG--AAAAAAACTCCTACGTCGACACTC
*
31690520 TTTTTCTACAATAGTTC
1 TTTTTCTACAGTAGTTC
31690537 ATGTTTGGCC
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
123 4 0.03
124 7 0.06
125 110 0.89
126 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAATGTCAAAAA
AGCTTCAACCAAGATGCACTGTCAGTAAAATTACTGAAAAAAACTCCTACGTCGACACTC
Found at i:31694073 original size:18 final size:18
Alignment explanation
Indices: 31694050--31694086 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31694040 GGAAAAGAAA
* *
31694050 ACATATAAGGGTTAGGAT
1 ACATATAAAGGCTAGGAT
31694068 ACATATAAAGGCTAGGAT
1 ACATATAAAGGCTAGGAT
31694086 A
1 A
31694087 TACACCTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (18 bp):
ACATATAAAGGCTAGGAT
Found at i:31694761 original size:21 final size:21
Alignment explanation
Indices: 31694735--31694778 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31694725 TTAATACTTA
31694735 CTTGCACTTCCGACCGTTGGT
1 CTTGCACTTCCGACCGTTGGT
31694756 CTTGCACTTCCGACCGTTGGT
1 CTTGCACTTCCGACCGTTGGT
31694777 CT
1 CT
31694779 AATGAAGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.34, G:0.23, T:0.34
Consensus pattern (21 bp):
CTTGCACTTCCGACCGTTGGT
Found at i:31695929 original size:30 final size:30
Alignment explanation
Indices: 31695864--31695932 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
31695854 ATTAATTAAA
*
31695864 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
*
31695894 GAGAGTTTTGAGAAATTTAGGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAGGAGAAATTT
31695924 GAGAGTTTT
1 GAGAGTTTT
31695933 TTGTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.29, T:0.33
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAAGGAGAAATTT
Found at i:31698227 original size:20 final size:22
Alignment explanation
Indices: 31698199--31698239 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
31698189 TCTCTTGAAT
*
31698199 TTTTCATATA-TG-TACTTTTA
1 TTTTAATATATTGTTACTTTTA
31698219 TTTTAATATATTGTTACTTTT
1 TTTTAATATATTGTTACTTTT
31698240 GCTTCCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTTAATATATTGTTACTTTTA
Found at i:31710816 original size:10 final size:10
Alignment explanation
Indices: 31710801--31710829 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
31710791 ATTACGTGTT
31710801 TGAATAGAAA
1 TGAATAGAAA
31710811 TGAATAG-AA
1 TGAATAGAAA
31710820 TGAATAGAAA
1 TGAATAGAAA
31710830 ATGAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:31710927 original size:6 final size:6
Alignment explanation
Indices: 31710916--31710978 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
31710906 TAGGTTCCAA
* * * *
31710916 AAATGG AAATGG AAATGA AAATGA AAATGG AAATGG AAATGA AAATGA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
31710964 AAATGG AAATGG AAA
1 AAATGG AAATGG AAA
31710979 CTTGCAATCC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (6 bp):
AAATGG
Found at i:31710947 original size:24 final size:24
Alignment explanation
Indices: 31710915--31710978 Score: 128
Period size: 24 Copynumber: 2.7 Consensus size: 24
31710905 GTAGGTTCCA
31710915 AAAATGGAAATGGAAATGAAAATG
1 AAAATGGAAATGGAAATGAAAATG
31710939 AAAATGGAAATGGAAATGAAAATG
1 AAAATGGAAATGGAAATGAAAATG
31710963 AAAATGGAAATGGAAA
1 AAAATGGAAATGGAAA
31710979 CTTGCAATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (24 bp):
AAAATGGAAATGGAAATGAAAATG
Found at i:31715053 original size:33 final size:32
Alignment explanation
Indices: 31714996--31715156 Score: 124
Period size: 33 Copynumber: 4.8 Consensus size: 32
31714986 CAGTGTTTAT
* * **
31714996 ATGTAAGACTATAGTTGGACTATGGCATTCTG
1 ATGTAAGACCATAATTGGGTTATGGCATTCTG
* *
31715028 ATGATAAGACCATAATTGGGTTATGGCACTATG
1 ATG-TAAGACCATAATTGGGTTATGGCATTCTG
* ** * * * *
31715061 AACGTAAGACCATGGTTGGATCATGGCAGTGTTTAT
1 -ATGTAAGACCATAATTGGGTTATGGCA-T-TCT-G
** *
31715097 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAATTGGGTTATGGCATTCTG
31715129 ATGATAAGACCATAATTGGGTTATGGCA
1 ATG-TAAGACCATAATTGGGTTATGGCA
31715157 CTACGAATGT
Statistics
Matches: 98, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
32 6 0.06
33 66 0.67
34 3 0.03
35 23 0.23
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (32 bp):
ATGTAAGACCATAATTGGGTTATGGCATTCTG
Found at i:31715122 original size:35 final size:34
Alignment explanation
Indices: 31714962--31715156 Score: 123
Period size: 33 Copynumber: 5.8 Consensus size: 34
31714952 TGTGATTTCG
* * *
31714962 TGTAAGACCATGGTTGGACCATGGCAGTGTTTATA
1 TGTAAGACCATAGTTGGGCTATGGCAGT-TTTATA
* * * *
31714997 TGTAAGACTATAGTTGGACTATGGCA-TTCT-GA
1 TGTAAGACCATAGTTGGGCTATGGCAGTTTTATA
* * * * *
31715029 TGATAAGACCATAATTGGGTTATGGCACTATGA-A
1 TG-TAAGACCATAGTTGGGCTATGGCAGTTTTATA
* * *
31715063 CGTAAGACCATGGTT-GGATCATGGCAGTGTTTATA
1 TGTAAGACCATAGTTGGGCT-ATGGCAGT-TTTATA
* * *
31715098 TGTAAGACCATAGCTGGGCTATGGCA-TTCT-GA
1 TGTAAGACCATAGTTGGGCTATGGCAGTTTTATA
* *
31715130 TGATAAGACCATAATTGGGTTATGGCA
1 TG-TAAGACCATAGTTGGGCTATGGCA
31715157 CTACGAATGT
Statistics
Matches: 124, Mismatches: 28, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
32 9 0.07
33 63 0.51
34 7 0.06
35 42 0.34
36 3 0.02
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (34 bp):
TGTAAGACCATAGTTGGGCTATGGCAGTTTTATA
Found at i:31715138 original size:101 final size:101
Alignment explanation
Indices: 31714963--31715168 Score: 358
Period size: 101 Copynumber: 2.0 Consensus size: 101
31714953 GTGATTTCGT
* *
31714963 GTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACTATAGTTGGACTATGGCATTCTG
1 GTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGACTATGGCATTCTG
*
31715028 ATGATAAGACCATAATTGGGTTATGGCACTATGAAC
66 ATGATAAGACCATAATTGGGTTATGGCACTACGAAC
* *
31715064 GTAAGACCATGGTTGGATCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 GTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGACTATGGCATTCTG
*
31715129 ATGATAAGACCATAATTGGGTTATGGCACTACGAAT
66 ATGATAAGACCATAATTGGGTTATGGCACTACGAAC
31715165 GTAA
1 GTAA
31715169 ATGATGAATT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (101 bp):
GTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGACTATGGCATTCTG
ATGATAAGACCATAATTGGGTTATGGCACTACGAAC
Found at i:31716097 original size:16 final size:17
Alignment explanation
Indices: 31716076--31716108 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31716066 TAAACATAAA
*
31716076 AAACAAGCAAA-CATAT
1 AAACAAACAAACCATAT
31716092 AAACAAACAAACCATAT
1 AAACAAACAAACCATAT
31716109 CTTCGTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.21, G:0.03, T:0.12
Consensus pattern (17 bp):
AAACAAACAAACCATAT
Found at i:31729651 original size:16 final size:16
Alignment explanation
Indices: 31729630--31729684 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
31729620 AAATAAATTA
31729630 TGAAGAGTTAGAAATG
1 TGAAGAGTTAGAAATG
*
31729646 TGAAGAGACTT-GAAA-A
1 TGAAGAG--TTAGAAATG
*
31729662 TGAAGAGTTAAAAATG
1 TGAAGAGTTAGAAATG
31729678 TGAAGAG
1 TGAAGAG
31729685 ACTTGAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 21 0.66
17 4 0.12
18 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.29, T:0.22
Consensus pattern (16 bp):
TGAAGAGTTAGAAATG
Found at i:31729670 original size:32 final size:32
Alignment explanation
Indices: 31729629--31729703 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
31729619 AAAATAAATT
*
31729629 ATGAAGAGTTAGAAATGTGAAGAGACTTGAAA
1 ATGAAGAGTTAAAAATGTGAAGAGACTTGAAA
*
31729661 ATGAAGAGTTAAAAATGTGAAGAGACTTGAAG
1 ATGAAGAGTTAAAAATGTGAAGAGACTTGAAA
31729693 ATGAAGAGTTA
1 ATGAAGAGTTA
31729704 CACACATGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.47, C:0.03, G:0.28, T:0.23
Consensus pattern (32 bp):
ATGAAGAGTTAAAAATGTGAAGAGACTTGAAA
Found at i:31729697 original size:16 final size:16
Alignment explanation
Indices: 31729646--31729700 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
31729636 GTTAGAAATG
31729646 TGAAGAGACTTGAAAA
1 TGAAGAGACTTGAAAA
*
31729662 TGAAGAG--TTAAAAA
1 TGAAGAGACTTGAAAA
*
31729676 TGTGAAGAGACTTGAAGA
1 --TGAAGAGACTTGAAAA
31729694 TGAAGAG
1 TGAAGAG
31729701 TTACACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 6 0.19
16 21 0.66
18 5 0.16
ACGTcount: A:0.47, C:0.04, G:0.29, T:0.20
Consensus pattern (16 bp):
TGAAGAGACTTGAAAA
Found at i:31734209 original size:39 final size:39
Alignment explanation
Indices: 31734155--31734250 Score: 165
Period size: 39 Copynumber: 2.5 Consensus size: 39
31734145 ACATACATGA
31734155 ATGTAGATGAATAGTCACAACTCCTATAACATTTAAGTG
1 ATGTAGATGAATAGTCACAACTCCTATAACATTTAAGTG
*
31734194 ATGTAGATGAATAGTCACAACTCCTATAGCATTTAAGTG
1 ATGTAGATGAATAGTCACAACTCCTATAACATTTAAGTG
* *
31734233 ATGTAGATTAATAATCAC
1 ATGTAGATGAATAGTCAC
31734251 TTACAACTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (39 bp):
ATGTAGATGAATAGTCACAACTCCTATAACATTTAAGTG
Found at i:31736308 original size:10 final size:10
Alignment explanation
Indices: 31736293--31736328 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
31736283 GTGTGGTGGT
31736293 CGATGACCGC
1 CGATGACCGC
31736303 CGATGACCGC
1 CGATGACCGC
31736313 CGATGACCGGC
1 CGATGACC-GC
31736324 CGATG
1 CGATG
31736329 GTCGGAGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.19, C:0.36, G:0.33, T:0.11
Consensus pattern (10 bp):
CGATGACCGC
Found at i:31737533 original size:98 final size:98
Alignment explanation
Indices: 31737421--31737611 Score: 364
Period size: 98 Copynumber: 1.9 Consensus size: 98
31737411 AAAATAATAA
*
31737421 AAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
1 AAATATTCCAAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
31737486 CTTGGATAAGTGGATATTCTTTTAAAGTAAAGG
66 CTTGGATAAGTGGATATTCTTTTAAAGTAAAGG
31737519 AAATATTCCAAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
1 AAATATTCCAAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
*
31737584 CTTGGATAAGTGGATGTTCTTTTAAAGT
66 CTTGGATAAGTGGATATTCTTTTAAAGT
31737612 TTTATTGCAC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
AAATATTCCAAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
CTTGGATAAGTGGATATTCTTTTAAAGTAAAGG
Found at i:31747987 original size:44 final size:43
Alignment explanation
Indices: 31747937--31748253 Score: 139
Period size: 44 Copynumber: 7.2 Consensus size: 43
31747927 GCAGAGAAGG
*
31747937 TTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 TTGAAGA-CGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* ** *
31747981 TCGAAGACGGCGAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGA
1 TTGAAGACGTAG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGA
* ** * * * * * * *
31748025 TTTAAGCCACCAAG-CCTTGTCTCCCTGAGCAGCAGCGGAGAAGG
1 TTGAAG--ACGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
*
31748069 TTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 TTGAAGA-CGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* *
31748113 TCGAAGACGGT-GAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGA
1 TTGAAGAC-GTAG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGA
* ** * * * ** * * *
31748157 TTTAAGCCACCAAG-CCTTGTCTCCCTGAGCAACAGCGGAGAAGG
1 TTGAAG--ACGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* *
31748201 TTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAACAGA
1 TTGAAGA-CGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
*
31748245 TCGAAGACG
1 TTGAAGACG
31748254 GCGAATCTTA
Statistics
Matches: 190, Mismatches: 59, Indels: 49
0.64 0.20 0.16
Matches are distributed among these distances:
42 10 0.05
43 20 0.11
44 138 0.73
45 12 0.06
46 10 0.05
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (43 bp):
TTGAAGACGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
Found at i:31748089 original size:132 final size:132
Alignment explanation
Indices: 31747712--31748338 Score: 1070
Period size: 132 Copynumber: 4.8 Consensus size: 132
31747702 CTGAAGTTAC
*
31747712 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * *
31747777 CAAGCCTTGTCTCCCTGAGTAGTAGAGGAGAAGGTT----A---TAGATCTTATCTCCCTAAGCA
66 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
31747835 GT
131 GT
* * * *
31747837 AGTGGAGTAGATCGAAGACGACGAATTTTATCTTTCCAAGATAGTGGGGAAGCAGATTTAGGCCA
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGT-GGGAAGCAGATTTAAGCCA
* *
31747902 TCAAGCCTTGTCTCCCTGAGCAGCAGCAGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
65 CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
31747967 AGT
130 AGT
31747970 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
31748035 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
66 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
31748100 GT
131 GT
*
31748102 AGTGGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
*
31748167 CAAGCCTTGTCTCCCTGAGCAACAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
66 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
31748232 GT
131 GT
* *
31748234 AGTGGAACAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTAAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
31748299 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAG
66 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAG
31748339 CTACAAGTCT
Statistics
Matches: 472, Mismatches: 22, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
125 41 0.09
126 50 0.11
130 1 0.00
132 315 0.67
133 65 0.14
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (132 bp):
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
GT
Found at i:31750408 original size:98 final size:98
Alignment explanation
Indices: 31750281--31750477 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
31750271 TTAAAAATAA
* * *
31750281 TAAAGGAAATATTCCGAGTTTGAGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCAAGTTTGAGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
* *
31750346 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTAGATATTCTTTTAAAG
31750379 TAAAAGAAATATTCCAAGTTTGAGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCAAGTTTGAGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
31750444 TTAAATCTTGGATAAGTAGATATTCTTTTAAAG
66 TTAAATCTTGGATAAGTAGATATTCTTTTAAAG
31750477 T
1 T
31750478 TTTATTGCAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (98 bp):
TAAAAGAAATATTCCAAGTTTGAGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTAGATATTCTTTTAAAG
Found at i:31756536 original size:3 final size:3
Alignment explanation
Indices: 31756528--31756574 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
31756518 TATGGTTGTT
31756528 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
31756575 ATTTGTTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:31756839 original size:23 final size:23
Alignment explanation
Indices: 31756813--31756861 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
31756803 TTGTTTTTTA
31756813 TATGAAAATGCTTATGTTGTGTT
1 TATGAAAATGCTTATGTTGTGTT
*
31756836 TATGAAAATGGTTATGTTGTGTT
1 TATGAAAATGCTTATGTTGTGTT
31756859 TAT
1 TAT
31756862 TTCATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (23 bp):
TATGAAAATGCTTATGTTGTGTT
Found at i:31757487 original size:26 final size:28
Alignment explanation
Indices: 31757457--31757516 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
31757447 TATAATTCAA
31757457 AAAATTCAAAATAAATA-ATAT-TTTTT
1 AAAATTCAAAATAAATATATATATTTTT
* * *
31757483 AAAATTTAAATTTAATATATATATTTTT
1 AAAATTCAAAATAAATATATATATTTTT
31757511 ACAAAT
1 A-AAAT
31757517 AAATAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 14 0.50
27 4 0.14
28 6 0.21
29 4 0.14
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAATTCAAAATAAATATATATATTTTT
Found at i:31758709 original size:17 final size:17
Alignment explanation
Indices: 31758684--31758719 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31758674 AATTAAAAAA
31758684 TTATAATTTTAAAATTT
1 TTATAATTTTAAAATTT
* *
31758701 TTATGATTTTTAAATTT
1 TTATAATTTTAAAATTT
31758718 TT
1 TT
31758720 TTTATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATAATTTTAAAATTT
Found at i:31758733 original size:10 final size:11
Alignment explanation
Indices: 31758698--31758742 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
31758688 AATTTTAAAA
31758698 TTTTTATGATT
1 TTTTTATGATT
**
31758709 TTTAAAT--TT
1 TTTTTATGATT
31758718 TTTTTAT-ATT
1 TTTTTATGATT
31758728 TTTTTATGATT
1 TTTTTATGATT
31758739 TTTT
1 TTTT
31758743 AATAATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.25
10 9 0.32
11 12 0.43
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTTTATGATT
Found at i:31759165 original size:27 final size:26
Alignment explanation
Indices: 31759116--31759171 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
31759106 TTTGTTATAA
*
31759116 AATAAAGAGAAATGAAGAGAATAAAG
1 AATAAAGAAAAATGAAGAGAATAAAG
*
31759142 AATAAAGAAAATATGAA-AGCAATAGAG
1 AATAAAGAAAA-ATGAAGAG-AATAAAG
31759169 AAT
1 AAT
31759172 GTACTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.64, C:0.02, G:0.20, T:0.14
Consensus pattern (26 bp):
AATAAAGAAAAATGAAGAGAATAAAG
Found at i:31765062 original size:25 final size:25
Alignment explanation
Indices: 31765034--31765106 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 25
31765024 ATGGCTATCC
31765034 GGAGCTTCCCGATTAATGGCTCTTT
1 GGAGCTTCCCGATTAATGGCTCTTT
* * * **
31765059 GGAGC-TACCTATT-ATAAGCTCGCAT
1 GGAGCTTCCCGATTAAT-GGCTC-TTT
31765084 -GAGCTTCCCGATTAATGGCTCTT
1 GGAGCTTCCCGATTAATGGCTCTT
31765107 CGGTGCTACC
Statistics
Matches: 34, Mismatches: 10, Indels: 9
0.64 0.19 0.17
Matches are distributed among these distances:
23 2 0.06
24 14 0.41
25 16 0.47
26 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.33
Consensus pattern (25 bp):
GGAGCTTCCCGATTAATGGCTCTTT
Found at i:31765095 original size:74 final size:75
Alignment explanation
Indices: 31764933--31765103 Score: 174
Period size: 74 Copynumber: 2.3 Consensus size: 75
31764923 CTTAGCTCTT
* * * * *
31764933 ATGAGCATCCCGATATATGACTCTTCGTGAGCTTCCCATTAATTGGCTCTTTGTGAGCTTCCTGA
1 ATGAGCTTCCCGATATATGGCTATCCGTGAGCTTCCCATTAATTGGCTCTTTGTGAGCTACCTGA
31764998 CATGTCTCGC
66 CATGTCTCGC
* * *
31765008 TTGAACTTTCCGATATATGGCTATCCG-GAGCTTCCCGATTAA-TGGCTCTTTG-GAGCTACCT-
1 ATGAGCTTCCCGATATATGGCTATCCGTGAGCTTCCC-ATTAATTGGCTCTTTGTGAGCTACCTG
*
31765069 ATTATAAG-CTCGC
65 A-CAT--GTCTCGC
31765082 ATGAGCTTCCCGAT-TAATGGCT
1 ATGAGCTTCCCGATAT-ATGGCT
31765104 CTTCGGTGCT
Statistics
Matches: 79, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
72 1 0.01
73 11 0.14
74 41 0.52
75 26 0.33
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (75 bp):
ATGAGCTTCCCGATATATGGCTATCCGTGAGCTTCCCATTAATTGGCTCTTTGTGAGCTACCTGA
CATGTCTCGC
Found at i:31765115 original size:49 final size:49
Alignment explanation
Indices: 31765035--31765139 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
31765025 TGGCTATCCG
*
31765035 GAGCTTCCCGATTAATGGCTCTTTGGAGCTACCTATTATAAGCTCGCAT
1 GAGCTTCCCGATTAATGGCTCTTCGGAGCTACCTATTATAAGCTCGCAT
* * *
31765084 GAGCTTCCCGATTAATGGCTCTTCGGTGCTACCTGTTATAGGCTCGCAT
1 GAGCTTCCCGATTAATGGCTCTTCGGAGCTACCTATTATAAGCTCGCAT
31765133 GAGCTTC
1 GAGCTTC
31765140 TTGAATATGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (49 bp):
GAGCTTCCCGATTAATGGCTCTTCGGAGCTACCTATTATAAGCTCGCAT
Found at i:31767661 original size:5 final size:5
Alignment explanation
Indices: 31767651--31767676 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31767641 TGAGCATTCG
31767651 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
31767677 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:31768667 original size:9 final size:9
Alignment explanation
Indices: 31768649--31768685 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
31768639 TATAGTTTGA
31768649 TATTCGAAT
1 TATTCGAAT
*
31768658 TATTCAAAT
1 TATTCGAAT
*
31768667 TATTCGAGT
1 TATTCGAAT
31768676 TATTCGAAT
1 TATTCGAAT
31768685 T
1 T
31768686 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31770608 original size:27 final size:26
Alignment explanation
Indices: 31770562--31770614 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
31770552 GTTATAAAAC
*
31770562 AAAGAGAAATGAAGAGAATAAAGAAT
1 AAAGAAAAATGAAGAGAATAAAGAAT
31770588 AAAGAAAATATGAA-AGCAATAAAGAAT
1 AAAGAAAA-ATGAAGAG-AATAAAGAAT
31770615 GTACTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.66, C:0.02, G:0.19, T:0.13
Consensus pattern (26 bp):
AAAGAAAAATGAAGAGAATAAAGAAT
Found at i:31771233 original size:19 final size:19
Alignment explanation
Indices: 31771187--31771247 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
31771177 TTTTAAATTT
* *
31771187 ATTTATTTAAAAT-ATTAA
1 ATTTATTTAATATAAATAA
31771205 ATTATTATTTAATATAAATAA
1 A-T-TTATTTAATATAAATAA
**
31771226 ATTTATTTTTTATAAATGAA
1 ATTTATTTAATATAAAT-AA
31771246 AT
1 AT
31771248 ATTTAACCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.40
20 15 0.43
21 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTATTTAATATAAATAA
Found at i:31771247 original size:24 final size:22
Alignment explanation
Indices: 31771180--31771248 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
31771170 ATATTAATTT
*
31771180 TAAATTTATTTATTTAAAAT-AT
1 TAAATTTATTT-TTTAAAATAAA
* *
31771202 TAAA-TTATTATTTAATATAAA
1 TAAATTTATTTTTTAAAATAAA
31771223 TAAATTTATTTTTTATAAATGAAA
1 TAAATTTATTTTTTA-AAAT-AAA
31771247 TA
1 TA
31771249 TTTAACCCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.18
21 10 0.26
22 13 0.34
23 3 0.08
24 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TAAATTTATTTTTTAAAATAAA
Found at i:31778478 original size:111 final size:111
Alignment explanation
Indices: 31778308--31778529 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
31778298 AATATGTAAG
31778308 CCGGAGGTGGACATTACTTTAGTGTTTTAGAGTTGAGAGTATGAGAATTGACGTTCAAATTATAG
1 CCGGAGGTGGACATTACTTTAGTGTTTTAGAGTTGAGAGTATGAGAATTGACGTTCAAATTATAG
31778373 AGTATAGAGCCATTTTTATGTGATTGGTAAGCCAAATAGGACTCGT
66 AGTATAGAGCCATTTTTATGTGATTGGTAAGCCAAATAGGACTCGT
* *
31778419 CCGGAGGTGGACATTACTTTAGTGTTTTAGAGTTGAGAGTGTGAGAATTGACGTTCAAATTGTAG
1 CCGGAGGTGGACATTACTTTAGTGTTTTAGAGTTGAGAGTATGAGAATTGACGTTCAAATTATAG
*
31778484 AGTATAGAGCCATTTTTATGTGATTGGTAAGCCAAATGGGACTCGT
66 AGTATAGAGCCATTTTTATGTGATTGGTAAGCCAAATAGGACTCGT
31778530 TTAACAAATC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.33
Consensus pattern (111 bp):
CCGGAGGTGGACATTACTTTAGTGTTTTAGAGTTGAGAGTATGAGAATTGACGTTCAAATTATAG
AGTATAGAGCCATTTTTATGTGATTGGTAAGCCAAATAGGACTCGT
Found at i:31779007 original size:33 final size:32
Alignment explanation
Indices: 31778970--31779063 Score: 98
Period size: 28 Copynumber: 3.2 Consensus size: 32
31778960 GAGCCCTGTT
31778970 TAGTAACAGTACAATGTGGGCCTTAGCCCAATA-
1 TAGTAACA--ACAATGTGGGCCTTAGCCCAATAC
31779003 TAGT---AACAATGTGGGCCTTAGCCCAATAC
1 TAGTAACAACAATGTGGGCCTTAGCCCAATAC
*
31779032 T-GT---AACAATATGGGCCTTAGCCCAATAC
1 TAGTAACAACAATGTGGGCCTTAGCCCAATAC
31779060 -AGTA
1 TAGTA
31779064 TCGGTATAGC
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
28 51 0.89
29 1 0.02
30 1 0.02
33 4 0.07
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (32 bp):
TAGTAACAACAATGTGGGCCTTAGCCCAATAC
Found at i:31779016 original size:28 final size:28
Alignment explanation
Indices: 31778980--31779063 Score: 134
Period size: 28 Copynumber: 3.0 Consensus size: 28
31778970 TAGTAACAGT
31778980 ACAATGTGGGCCTTAGCCCAATATAGTA
1 ACAATGTGGGCCTTAGCCCAATATAGTA
31779008 ACAATGTGGGCCTTAGCCCAATACT-GTA
1 ACAATGTGGGCCTTAGCCCAATA-TAGTA
* *
31779036 ACAATATGGGCCTTAGCCCAATACAGTA
1 ACAATGTGGGCCTTAGCCCAATATAGTA
31779064 TCGGTATAGC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 51 0.98
29 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (28 bp):
ACAATGTGGGCCTTAGCCCAATATAGTA
Found at i:31779448 original size:27 final size:27
Alignment explanation
Indices: 31779418--31779504 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
31779408 TCATCTCTTA
*
31779418 GGGGTATAAT-AGTCATTTTACCATATG
1 GGGGTAT-ATCAGTCATATTACCATATG
* *
31779445 GGGGTATTTCAGTCATATTACCCTATG
1 GGGGTATATCAGTCATATTACCATATG
* * * * *
31779472 AGGGTATTTCGGTCATTTTATCC-TGTG
1 GGGGTATATCAGTCATATTA-CCATATG
31779499 GGGGTA
1 GGGGTA
31779505 ATTCGATCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.02
27 47 0.94
28 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (27 bp):
GGGGTATATCAGTCATATTACCATATG
Found at i:31779487 original size:54 final size:53
Alignment explanation
Indices: 31779429--31779626 Score: 245
Period size: 54 Copynumber: 3.7 Consensus size: 53
31779419 GGGTATAATA
* * * * *
31779429 GTCATTTTACCATATGGGGGTATTTCAGTCATATTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTGTGGGGGTAATTCAGTCATTTTACCCTAT-AGGGTAATTCG
* *
31779483 GTCATTTTATCCTGTGGGGGTAATTC-GATCATTTTACCCTTTAGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCAG-TCATTTTACCCTATA-GGGTAATTCG
* ** *
31779537 ATCATTTTACCCTGTAAGGGTAATTTAGTCATTTTACCCTATAGAGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCAGTCATTTTACCCTATAG-GGTAATTCG
*
31779591 GTCATTTTACCCTGTGGGGGTAATTCAATCATTTTA
1 GTCATTTTACCCTGTGGGGGTAATTCAGTCATTTTA
31779627 TGACCTCTCG
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
53 3 0.02
54 118 0.97
55 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (53 bp):
GTCATTTTACCCTGTGGGGGTAATTCAGTCATTTTACCCTATAGGGTAATTCG
Found at i:31779509 original size:27 final size:27
Alignment explanation
Indices: 31779429--31779626 Score: 198
Period size: 27 Copynumber: 7.3 Consensus size: 27
31779419 GGGTATAATA
* * *
31779429 GTCATTTTACCATATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTAATTCG
* * *
31779456 GTCATATTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
* *
31779483 GTCATTTTATCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
* * *
31779510 ATCATTTTACCCTTTAGGGGTAATTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
* * ** **
31779537 ATCATTTTACCCTGTAAGGGTAATTTA
1 GTCATTTTACCCTATGGGGGTAATTCG
* *
31779564 GTCATTTTACCCTATAGAGGTAATTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
* *
31779591 GTCATTTTACCCTGTGGGGGTAATTCA
1 GTCATTTTACCCTATGGGGGTAATTCG
*
31779618 ATCATTTTA
1 GTCATTTTA
31779627 TGACCTCTCG
Statistics
Matches: 143, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 143 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTAATTCG
Found at i:31779623 original size:81 final size:81
Alignment explanation
Indices: 31779429--31779626 Score: 236
Period size: 81 Copynumber: 2.4 Consensus size: 81
31779419 GGGTATAATA
* * * * * * *
31779429 GTCATTTTACCATATGGGGGTATTTCAGTCATATTACCCTATGAGGGTATTTCGGTCATTTTATC
1 GTCATTTTACCCTATGGGGGTAATTCAATCATTTTACCCTATAAGGGTATTTCAGTCATTTTACC
* * *
31779494 CTGTGGGGGTAATTCG
66 CTATAGAGGTAATTCG
* * * * *
31779510 ATCATTTTACCCTTTAGGGGTAATTCGATCATTTTACCCTGTAAGGGTAATTT-AGTCATTTTAC
1 GTCATTTTACCCTATGGGGGTAATTCAATCATTTTACCCTATAAGGGT-ATTTCAGTCATTTTAC
31779574 CCTATAGAGGTAATTCG
65 CCTATAGAGGTAATTCG
*
31779591 GTCATTTTACCCTGTGGGGGTAATTCAATCATTTTA
1 GTCATTTTACCCTATGGGGGTAATTCAATCATTTTA
31779627 TGACCTCTCG
Statistics
Matches: 97, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 93 0.96
82 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (81 bp):
GTCATTTTACCCTATGGGGGTAATTCAATCATTTTACCCTATAAGGGTATTTCAGTCATTTTACC
CTATAGAGGTAATTCG
Found at i:31783124 original size:44 final size:44
Alignment explanation
Indices: 31783070--31783234 Score: 152
Period size: 44 Copynumber: 3.6 Consensus size: 44
31783060 TCGATTCATC
* *
31783070 CCACTACAACTTCAAGGATATAGGATTTGTAGCTTAATCTTGCT
1 CCACTACAACTTCAAGGAGATAAGATTTGTAGCTTAATCTTGCT
* * * * * *
31783114 CCACTGCAACTTCAAGGAGATAAGATTCGTTGTTATAATTTCAATCCGAT
1 CCACTACAACTTCAAGGAGATAAGATTTGTAGCT-TAA--TC--T-TGCT
* * *
31783164 CCACTACAACTTCAGGGATG-TAGGATTTGTAGCTTCATCTTGCT
1 CCACTACAACTTCAAGGA-GATAAGATTTGTAGCTTAATCTTGCT
*
31783208 CCACTACACCTTCAAGGAGATAAGATT
1 CCACTACAACTTCAAGGAGATAAGATT
31783235 CGCTACTGTA
Statistics
Matches: 93, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
43 1 0.01
44 52 0.56
45 4 0.04
47 4 0.04
49 3 0.03
50 28 0.30
51 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (44 bp):
CCACTACAACTTCAAGGAGATAAGATTTGTAGCTTAATCTTGCT
Found at i:31783140 original size:94 final size:94
Alignment explanation
Indices: 31783012--31783236 Score: 281
Period size: 94 Copynumber: 2.4 Consensus size: 94
31783002 TTATAACTTT
* * * * * * * * * *
31783012 ATCTTACTCCACTGTATCTTCAGGGAGATGAGATTTGTCATTGTAGTTTCGATTC-ATCCCACTA
1 ATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGTCATTATAATTTCAATCCGAT-CCACTA
31783076 CAACTTCAAGGATATAGGATTTGTAGCTTA
65 CAACTTCAAGGATATAGGATTTGTAGCTTA
**
31783106 ATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGTTGTTATAATTTCAATCCGATCCACTAC
1 ATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGTCATTATAATTTCAATCCGATCCACTAC
* * *
31783171 AACTTCAGGGATGTAGGATTTGTAGCTTC
66 AACTTCAAGGATATAGGATTTGTAGCTTA
* *
31783200 ATCTTGCTCCACTACACCTTCAAGGAGATAAGATTCG
1 ATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCG
31783237 CTACTGTAGT
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
94 111 0.98
95 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (94 bp):
ATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGTCATTATAATTTCAATCCGATCCACTAC
AACTTCAAGGATATAGGATTTGTAGCTTA
Found at i:31783260 original size:94 final size:93
Alignment explanation
Indices: 31783053--31783260 Score: 272
Period size: 94 Copynumber: 2.2 Consensus size: 93
31783043 GATTTGTCAT
31783053 TGTAGTTTCGATTCATCCCACTACAACTTCAAGGATATAGGATTTGTAGCTTAATCTTGCTCCAC
1 TGTAGTTTCGATTCAT-CCACTACAACTTCAAGGATATAGGATTTGTAGCTTAATCTTGCTCCAC
* * **
31783118 TGCAACTTCAAGGAGATAAGATTCGTTGT
65 TACAACTTCAAGGAGATAAGATTCGCTAC
* * * * * * *
31783147 TATAATTTCAATCCGATCCACTACAACTTCAGGGATGTAGGATTTGTAGCTTCATCTTGCTCCAC
1 TGTAGTTTCGATTC-ATCCACTACAACTTCAAGGATATAGGATTTGTAGCTTAATCTTGCTCCAC
*
31783212 TACACCTTCAAGGAGATAAGATTCGCTAC
65 TACAACTTCAAGGAGATAAGATTCGCTAC
*
31783241 TGTAGTTTTGATTCAATCCA
1 TGTAGTTTCGATTC-ATCCA
31783261 TTTCATCTTT
Statistics
Matches: 95, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
94 93 0.98
95 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (93 bp):
TGTAGTTTCGATTCATCCACTACAACTTCAAGGATATAGGATTTGTAGCTTAATCTTGCTCCACT
ACAACTTCAAGGAGATAAGATTCGCTAC
Found at i:31794708 original size:14 final size:14
Alignment explanation
Indices: 31794689--31794715 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31794679 AATAGACCTT
31794689 TTTATTTATTTTTG
1 TTTATTTATTTTTG
31794703 TTTATTTATTTTT
1 TTTATTTATTTTT
31794716 ATTTTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTATTTATTTTTG
Found at i:31798121 original size:50 final size:50
Alignment explanation
Indices: 31798006--31798198 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
31797996 GATAATAACA
* * ** *
31798006 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * ** *
31798057 TGCCCATGCCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
31798107 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
31798157 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31798199 TTTGTATCCG
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 94 0.75
51 31 0.25
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31810344 original size:19 final size:18
Alignment explanation
Indices: 31810320--31810368 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
31810310 ATAAATACTT
*
31810320 TTTGAAAATTTAAGTAATA
1 TTTGAAAATTTAAATAA-A
*
31810339 TTTGAAAGAATTAAATAAA
1 TTTGAAA-ATTTAAATAAA
*
31810358 TTTTAAAATTT
1 TTTGAAAATTT
31810369 TTATATAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (18 bp):
TTTGAAAATTTAAATAAA
Found at i:31810908 original size:29 final size:28
Alignment explanation
Indices: 31810847--31810949 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 28
31810837 CCTTAAACAC
* * * *
31810847 TAAACCATAAACCTTAAGCCCCTAAACT
1 TAAACTATAAACCCTAAACCCCTAACCT
31810875 ATAAACTATAAACCCTAAACCCCTAACCCT
1 -TAAACTATAAACCCTAAACCCCTAA-CCT
* * *
31810905 TAAAC-ATTAAATCCTAAA-CACTAAACCA
1 TAAACTA-TAAACCCTAAACCCCT-AACCT
*
31810933 TAAACT-TATACCCTAAA
1 TAAACTATAAACCCTAAA
31810950 TCGTAAGCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
27 9 0.15
28 11 0.18
29 39 0.64
30 2 0.03
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (28 bp):
TAAACTATAAACCCTAAACCCCTAACCT
Found at i:31811488 original size:40 final size:39
Alignment explanation
Indices: 31811424--31811631 Score: 211
Period size: 40 Copynumber: 5.2 Consensus size: 39
31811414 GCATTTTGCT
* * * *
31811424 AAAAGTGCAGCTAATGCTCGATCTATAGTGGCGTTTTTC
1 AAAAGCGCCGCTAATTCTCGATCTATAGCGGCGTTTTTC
* * *
31811463 AACAAGCGCCGCTAATTCTCGATCTATTGTGGCGTTTTCTG
1 AA-AAGCGCCGCTAATTCTCGATCTATAGCGGCGTTTT-TC
* ** *
31811504 AAAAGCGCCGCTAATTCTCGATCTATTGCAACGTTTTCTG
1 AAAAGCGCCGCTAATTCTCGATCTATAGCGGCGTTTT-TC
* * *
31811544 AAAAGCGCTGCTAATGCTCGATCTATAGCGGTGTTTTTC
1 AAAAGCGCCGCTAATTCTCGATCTATAGCGGCGTTTTTC
* *
31811583 AACAAGCGCCTCTAATTCTCGATCTATTA-CGGCGTTTTTTA
1 AA-AAGCGCCGCTAATTCTCGATCTA-TAGCGGCG-TTTTTC
31811624 AAAAGCGC
1 AAAAGCGC
31811632 TACTAATGCC
Statistics
Matches: 144, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
39 5 0.03
40 127 0.88
41 12 0.08
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (39 bp):
AAAAGCGCCGCTAATTCTCGATCTATAGCGGCGTTTTTC
Found at i:31814523 original size:40 final size:40
Alignment explanation
Indices: 31814481--31814636 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
31814471 GCATTTTCTG
* *
31814481 AAAAGCGTCGCTAATGCTCGATCTATAGCGGCGTTTTTTG
1 AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTTTTTA
* * * ** *
31814521 AAAAGTGCCACTAATGCTTGATCTATAGCGGCGTTTTTCA
1 AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTTTTTA
* * *
31814561 AAAAGTGTCGCTAATGATCAATCTATAGCGGCGTTTTTAA
1 AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTTTTTA
* * * *
31814601 AAAAACGTGGCTAATGCTCAACCTATAGCGACGTTT
1 AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTT
31814637 GTTTCAGAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (40 bp):
AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTTTTTA
Found at i:31819639 original size:12 final size:12
Alignment explanation
Indices: 31819622--31819655 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31819612 AAAAAATCTG
31819622 AATTTAATTTCC
1 AATTTAATTTCC
*
31819634 AATTTAATTTCT
1 AATTTAATTTCC
*
31819646 AATTTTATTT
1 AATTTAATTT
31819656 ATTTATGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:31824572 original size:12 final size:12
Alignment explanation
Indices: 31824555--31824584 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
31824545 ACAAAATCCA
31824555 AATTTAATTTCC
1 AATTTAATTTCC
31824567 AATTTAATTTCC
1 AATTTAATTTCC
31824579 AATTTA
1 AATTTA
31824585 TTTAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:31832305 original size:23 final size:24
Alignment explanation
Indices: 31832260--31832311 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
31832250 ATTTTTTATA
31832260 AAAAATCAAAATTCAAATATATT-
1 AAAAATCAAAATTCAAATATATTC
* *
31832283 AAAAATACAAAGTTCCAA-ATATTC
1 AAAAAT-CAAAATTCAAATATATTC
31832307 AAAAA
1 AAAAA
31832312 ATAAAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAAATCAAAATTCAAATATATTC
Found at i:31832311 original size:25 final size:24
Alignment explanation
Indices: 31832256--31832320 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
31832246 TATAATTTTT
31832256 TATAAAAAAT-CAAAATTCAAATA
1 TATAAAAAATACAAAATTCAAATA
* *
31832279 TATTAAAAATACAAAGTTCCAAATA
1 TATAAAAAATACAAAATT-CAAATA
*
31832304 T-TCAAAAAATAAAAAAT
1 TAT-AAAAAATACAAAAT
31832321 GATTTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.26
24 7 0.21
25 18 0.53
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (24 bp):
TATAAAAAATACAAAATTCAAATA
Found at i:31834591 original size:2 final size:2
Alignment explanation
Indices: 31834584--31834616 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31834574 CTGGTTTAAA
31834584 AT AT 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 AT AT A
31834617 GGAGAACTGT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31834803 original size:20 final size:19
Alignment explanation
Indices: 31834752--31834803 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
31834742 ATAGTTATAA
* *
31834752 TTAATATTTTTTAAATTAT
1 TTAATTTTTTTTAAAATAT
*
31834771 TTATATTTATTTTAAAATATT
1 TTA-ATTTTTTTTAAAATA-T
31834792 TTAATTTTTTTT
1 TTAATTTTTTTT
31834804 TTTACATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.11
20 20 0.74
21 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTAATTTTTTTTAAAATAT
Found at i:31849583 original size:22 final size:23
Alignment explanation
Indices: 31849557--31849600 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
31849547 GTGATGAGGT
*
31849557 TATCTTGTGAATATGTT-AAATC
1 TATCTTGAGAATATGTTGAAATC
31849579 TATCTTGAGAATATGTTGAAAT
1 TATCTTGAGAATATGTTGAAAT
31849601 GGATTGGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (23 bp):
TATCTTGAGAATATGTTGAAATC
Found at i:31851685 original size:46 final size:46
Alignment explanation
Indices: 31851635--31851726 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
31851625 ACTTTCATAT
*
31851635 TGTTTTCTATTGCTATGTTAATTTTCTTTACGGTGAGCATGTATAG
1 TGTTTTCCATTGCTATGTTAATTTTCTTTACGGTGAGCATGTATAG
31851681 TGTTTTCCATTGCTATGTTAATTTTCTTTACGGTGAGCATGTATAG
1 TGTTTTCCATTGCTATGTTAATTTTCTTTACGGTGAGCATGTATAG
31851727 CTAAACCTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (46 bp):
TGTTTTCCATTGCTATGTTAATTTTCTTTACGGTGAGCATGTATAG
Found at i:31853593 original size:28 final size:28
Alignment explanation
Indices: 31853553--31853609 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
31853543 AAGTTCATAC
31853553 AATATAATCAAGTTTAAAATTTTGTTGT
1 AATATAATCAAGTTTAAAATTTTGTTGT
31853581 AATATAATCAAGTTTAAAATTTTGTTGT
1 AATATAATCAAGTTTAAAATTTTGTTGT
31853609 A
1 A
31853610 TTATGTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.46
Consensus pattern (28 bp):
AATATAATCAAGTTTAAAATTTTGTTGT
Found at i:31854098 original size:31 final size:31
Alignment explanation
Indices: 31854039--31854103 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
31854029 CAACAATTTG
* *
31854039 ACTCTTTTTAAAAAGTTGATGGTCAAATTAA
1 ACTCTTTGTAAAAAGTTGATGCTCAAATTAA
*
31854070 ACTCTTTGTAAAAAGTTGAGTGCT-AAATTTA
1 ACTCTTTGTAAAAAGTTGA-TGCTCAAATTAA
31854101 ACT
1 ACT
31854104 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (31 bp):
ACTCTTTGTAAAAAGTTGATGCTCAAATTAA
Found at i:31854299 original size:26 final size:24
Alignment explanation
Indices: 31854257--31854306 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
31854247 TATTTGTATT
31854257 TTTATATATTATATAAAGATTAAA
1 TTTATATATTATATAAAGATTAAA
* *
31854281 TTTATTATATTAATGTAAATATTAAA
1 TTTA-TATATT-ATATAAAGATTAAA
31854307 AAGTATGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 6 0.27
26 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTATATATTATATAAAGATTAAA
Found at i:31856092 original size:2 final size:2
Alignment explanation
Indices: 31856087--31856119 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31856077 TTTTTTTGGT
31856087 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31856120 TATCTGGGTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31857601 original size:61 final size:61
Alignment explanation
Indices: 31857506--31857627 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
31857496 GGTGATTAGG
31857506 CATAAATTTTGTGATTTTACTAAAAATCAGGTTTACAAGCATAAAAATAAAAGCATGTTTT
1 CATAAATTTTGTGATTTTACTAAAAATCAGGTTTACAAGCATAAAAATAAAAGCATGTTTT
31857567 CATAAATTTTGTGATTTTACTAAAAATCAGGTTTACAAGCATAAAAATAAAAGCATGTTTT
1 CATAAATTTTGTGATTTTACTAAAAATCAGGTTTACAAGCATAAAAATAAAAGCATGTTTT
31857628 TTCATCGTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (61 bp):
CATAAATTTTGTGATTTTACTAAAAATCAGGTTTACAAGCATAAAAATAAAAGCATGTTTT
Found at i:31865779 original size:27 final size:27
Alignment explanation
Indices: 31865692--31865855 Score: 143
Period size: 27 Copynumber: 5.8 Consensus size: 27
31865682 TTTATCCTGA
31865692 GGGTATTTAGGTCATTTTACCCTA-AGG
1 GGGTATTTAGGTCATTTTACCCTATA-G
* * *
31865719 GGGTATTTCGATCATTTTACCCTATGG
1 GGGTATTTAGGTCATTTTACCCTATAG
31865746 GGGTATTTAGGTCATTTTACCCTATAG
1 GGGTATTTAGGTCATTTTACCCTATAG
* *
31865773 GGATATTTCAGTTATTCGATCATTTTACCCTATGG
1 GGGTATTT-AG------G-TCATTTTACCCTATAG
* *
31865808 GGGTGTTTCA-GTTATTTTACCCTATAG
1 GGGTATTT-AGGTCATTTTACCCTATAG
* *
31865835 GGGTATTTTGGTTATTTTACC
1 GGGTATTTAGGTCATTTTACC
31865856 TATTTTAGGG
Statistics
Matches: 113, Mismatches: 14, Indels: 20
0.77 0.10 0.14
Matches are distributed among these distances:
27 86 0.76
28 3 0.03
34 1 0.01
35 23 0.20
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGTATTTAGGTCATTTTACCCTATAG
Found at i:31865803 original size:35 final size:35
Alignment explanation
Indices: 31865757--31865823 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
31865747 GGTATTTAGG
31865757 TCATTTTACCCTATAGGGATATTTCAGTTATTCGA
1 TCATTTTACCCTATAGGGATATTTCAGTTATTCGA
* * *
31865792 TCATTTTACCCTATGGGGGTGTTTCAGTTATT
1 TCATTTTACCCTATAGGGATATTTCAGTTATT
31865824 TTACCCTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (35 bp):
TCATTTTACCCTATAGGGATATTTCAGTTATTCGA
Found at i:31865850 original size:62 final size:62
Alignment explanation
Indices: 31865725--31865842 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
31865715 AAGGGGGTAT
31865725 TTCGATCATTTTACCCTATGGGGGTATTTAGGTCATTTTACCCTATAGGGATATTTCAGTTA
1 TTCGATCATTTTACCCTATGGGGGTATTTAGGTCATTTTACCCTATAGGGATATTTCAGTTA
* * *
31865787 TTCGATCATTTTACCCTATGGGGGTGTTTCA-GTTATTTTACCCTATAGGGGTATTT
1 TTCGATCATTTTACCCTATGGGGGTATTT-AGGTCATTTTACCCTATAGGGATATTT
31865843 TGGTTATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 51 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (62 bp):
TTCGATCATTTTACCCTATGGGGGTATTTAGGTCATTTTACCCTATAGGGATATTTCAGTTA
Found at i:31871579 original size:43 final size:42
Alignment explanation
Indices: 31871512--31871682 Score: 206
Period size: 43 Copynumber: 4.0 Consensus size: 42
31871502 ACATAGGATT
*
31871512 TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
* *
31871555 TCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
*
31871598 TCGTATT-TGATTT--GTGTAAGACCATGTCTGGGACAG-TGGCA
1 TCG-ATTGTG-TTTACGTGTAAGACCACGTCTGGGAC-GTTGGCA
* *
31871639 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
31871682 T
1 T
31871683 TGTACGACTC
Statistics
Matches: 112, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
40 2 0.02
41 32 0.29
42 5 0.04
43 71 0.63
44 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (42 bp):
TCGATTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:31871627 original size:84 final size:84
Alignment explanation
Indices: 31871527--31871682 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 84
31871517 ATGTGTTTTC
* * *
31871527 GTGTAAGACCACGTCTGGGAC-GTTGGCATCGACT-TGTGTTTACGTGTAAGACCATGTCTGGGA
1 GTGTAAGACCACGTCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACCACGTCTGGGA
31871590 CATTGGCATCGTATTTGATTT
64 CATTGGCATCGTATTTGATTT
* *
31871611 GTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGACG
1 GTGTAAGACCACGTCTGGGACAGTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGACA
31871676 TTGGCAT
66 TTGGCAT
31871683 TGTACGACTC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 1 0.02
84 63 0.97
85 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (84 bp):
GTGTAAGACCACGTCTGGGACAGTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:31871872 original size:16 final size:17
Alignment explanation
Indices: 31871843--31871874 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31871833 TGAATTGATG
31871843 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
31871860 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
31871875 TTGTATATTT
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:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:31872588 original size:2 final size:2
Alignment explanation
Indices: 31872581--31872610 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
31872571 GGTTATGTGT
31872581 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
31872611 GTGTGATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31875669 original size:24 final size:24
Alignment explanation
Indices: 31875624--31875681 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
31875614 AAACACTCCA
*
31875624 CAGAATGAA-TCACACCATAGTGC
1 CAGAATGAATTCACACCAAAGTGC
**
31875647 CAGAATGAATTCGTACCAAAGTGC
1 CAGAATGAATTCACACCAAAGTGC
*
31875671 TAGAATGAATT
1 CAGAATGAATT
31875682 ACATTATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
CAGAATGAATTCACACCAAAGTGC
Found at i:31884390 original size:12 final size:12
Alignment explanation
Indices: 31884373--31884406 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
31884363 ACTAAACAAC
31884373 TAAACATAAACA
1 TAAACATAAACA
31884385 TAAACATAAACA
1 TAAACATAAACA
31884397 TAAACATAAA
1 TAAACATAAA
31884407 ACTAAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (12 bp):
TAAACATAAACA
Found at i:31884412 original size:12 final size:11
Alignment explanation
Indices: 31884370--31884412 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 11
31884360 AAAACTAAAC
31884370 AACTAAACATA
1 AACTAAACATA
31884381 AACATAAACATA
1 AAC-TAAACATA
31884393 AACATAAACATAA
1 AAC-TAAACAT-A
31884406 AACTAAA
1 AACTAAA
31884413 GCTAAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 3 0.10
12 23 0.77
13 4 0.13
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.16
Consensus pattern (11 bp):
AACTAAACATA
Found at i:31884412 original size:18 final size:18
Alignment explanation
Indices: 31884370--31884430 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
31884360 AAAACTAAAC
31884370 AACTAAACATAAACAT-A
1 AACTAAACATAAACATAA
31884387 AACATAAACATAAACATAA
1 AAC-TAAACATAAACATAA
31884406 AACTAAAGC-TAAA-ACTAA
1 AACTAAA-CATAAACA-TAA
31884424 AACTAAA
1 AACTAAA
31884431 AAGAAAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.10
18 31 0.77
19 5 0.12
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.16
Consensus pattern (18 bp):
AACTAAACATAAACATAA
Found at i:31884418 original size:12 final size:12
Alignment explanation
Indices: 31884398--31884431 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31884388 ACATAAACAT
31884398 AAACATAAAACTA
1 AAAC-TAAAACTA
*
31884411 AAGCTAAAACTA
1 AAACTAAAACTA
31884423 AAACTAAAA
1 AAACTAAAA
31884432 AGAAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (12 bp):
AAACTAAAACTA
Found at i:31885986 original size:14 final size:14
Alignment explanation
Indices: 31885969--31886010 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
31885959 AAATAATCAT
*
31885969 AAAAATAATAGT-A
1 AAAAATAATAATAA
31885982 AAAAATAATAATAA
1 AAAAATAATAATAA
* *
31885996 GATAATAATAATAA
1 AAAAATAATAATAA
31886010 A
1 A
31886011 GCTAAGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (14 bp):
AAAAATAATAATAA
Found at i:31886219 original size:5 final size:5
Alignment explanation
Indices: 31886209--31886262 Score: 71
Period size: 5 Copynumber: 11.4 Consensus size: 5
31886199 TAAGCATAGG
31886209 AATAA AAT-A AAT-A AATAA AATTAA AAT-- AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AA-TAA AATAA AATAA AATAA AATAA AATAA
31886256 AATAA AA
1 AATAA AA
31886263 AATAGGGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.07
4 8 0.18
5 29 0.64
6 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:31886233 original size:19 final size:18
Alignment explanation
Indices: 31886209--31886261 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
31886199 TAAGCATAGG
31886209 AATAAAATAAATAAATAA
1 AATAAAATAAATAAATAA
31886227 AATTAAAAT-AATAAAATAA
1 AA-TAAAATAAAT-AAATAA
31886246 AATAAAATAAAATAAA
1 AATAAAAT-AAATAAA
31886262 AAATAGGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 11 0.35
19 17 0.55
20 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AATAAAATAAATAAATAA
Found at i:31886245 original size:23 final size:21
Alignment explanation
Indices: 31886217--31886266 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 21
31886207 GGAATAAAAT
31886217 AAATAAATAAAATTAAAATAATA
1 AAATAAATAAAA-TAAAATAA-A
31886240 AAATAAAATAAAATAAAATAAA
1 AAAT-AAATAAAATAAAATAAA
31886262 AAATA
1 AAATA
31886267 GGGCAAGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.04
22 5 0.19
23 12 0.46
24 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAAATAAAATAAAATAAA
Found at i:31893202 original size:59 final size:58
Alignment explanation
Indices: 31893121--31893252 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 58
31893111 TTTTAAGAAC
***
31893121 ATTATTATTAATTATAAGTTAATAAAATAAAATAAATAATTTAATCTTATT-TTAATATA
1 ATTATTATTAATTATAAGTTAATAAAAT--AATAAATAATTTAATAACATTCTTAATATA
* *
31893180 ATTATTATTACA-TATAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTA-ATTATAAGTTAATAAAATAATAAATAATTTAATAACATTCTTAATATA
*
31893238 ATTATTTTTATATTA
1 ATTATTATTA-ATTA
31893253 AATTATATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
57 17 0.27
58 18 0.29
59 27 0.43
60 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (58 bp):
ATTATTATTAATTATAAGTTAATAAAATAATAAATAATTTAATAACATTCTTAATATA
Found at i:31893276 original size:33 final size:33
Alignment explanation
Indices: 31893239--31893303 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
31893229 CTTAATATAA
31893239 TTATTTTTATATTAAATTATATTAAAAGATTTT
1 TTATTTTTATATTAAATTATATTAAAAGATTTT
*
31893272 TTATTTTTATATTAAATTATATTAAAATATTT
1 TTATTTTTATATTAAATTATATTAAAAGATTT
31893304 AATTTACTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
TTATTTTTATATTAAATTATATTAAAAGATTTT
Found at i:31896643 original size:16 final size:16
Alignment explanation
Indices: 31896622--31896686 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
31896612 CGTTTGGTTT
31896622 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
31896638 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
31896654 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
31896670 GTTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
31896686 G
1 G
31896687 GTGTGATAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:31896665 original size:32 final size:32
Alignment explanation
Indices: 31896624--31896690 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
31896614 TTTGGTTTGC
31896624 TGTAATGGAATAGAGCTGTAATGGAATAGAGG
1 TGTAATGGAATAGAGCTGTAATGGAATAGAGG
*
31896656 TGTAATGGAATAGAGTTGTAATGGAATAGAGG
1 TGTAATGGAATAGAGCTGTAATGGAATAGAGG
31896688 TGT
1 TGT
31896691 GATAGTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.01, G:0.34, T:0.28
Consensus pattern (32 bp):
TGTAATGGAATAGAGCTGTAATGGAATAGAGG
Found at i:31896741 original size:45 final size:44
Alignment explanation
Indices: 31896675--31896767 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
31896665 ATAGAGTTGT
** *
31896675 AATGGAATAGAGGTGTGATAGTAATTCAAT-TGTTTGGTTGAATAG
1 AATGGAATAGAACTGTAATAGT-ATT-AATGTGTTTGGTTGAATAG
** *
31896720 AATGGAATAGAACTGTAATAGTATTTTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAATAG
31896764 AATG
1 AATG
31896768 ATGTTGTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.51
45 19 0.46
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAATAG
Done.