Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015225.1 Kokia drynarioides strain JFW-HI SEQ_130269, 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: 377715
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 333 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:887 original size:30 final size:29
Alignment explanation
Indices: 840--1143 Score: 323
Period size: 30 Copynumber: 10.3 Consensus size: 29
830 AGAGGTTTGA
*
840 GGGTAAAAAT-GGAATTTTTGGAAGTTTCA
1 GGGTAAAAATAGG-ATTTTTGGAAGTTTCG
*
869 AGGTCAAAAATAGGATTTTTGGAAG-TTCG
1 GGGT-AAAAATAGGATTTTTGGAAGTTTCG
* *
898 GGAGTAAAAA-CGGAATTCTTGGAAGTTTCG
1 GG-GTAAAAATAGG-ATTTTTGGAAGTTTCG
* * * *
928 AGGTCAAAAATATGATTTTTAGAAGTTTGG
1 GGGT-AAAAATAGGATTTTTGGAAGTTTCG
** *
958 GGGTAAAAATAAAATTCTTGGAAGTTTCG
1 GGGTAAAAATAGGATTTTTGGAAGTTTCG
987 GGGTTAAAAATAGGATTTTTGGAAG-TTCG
1 GGG-TAAAAATAGGATTTTTGGAAGTTTCG
*
1016 AGGGTAAAAATAGAATTTTTGGAAGTTTCG
1 -GGGTAAAAATAGGATTTTTGGAAGTTTCG
*
1046 GGGTAAAAAATAGGATATTTGGAAG-TTCG
1 GGGT-AAAAATAGGATTTTTGGAAGTTTCG
* *
1075 AGGGTAAAAAT-GGAATTTTTGGATGTTTTG
1 -GGGTAAAAATAGG-ATTTTTGGAAGTTTCG
*
1105 GGGTCAAAAATAGGATTTTTGGAAGTTTGG
1 GGGT-AAAAATAGGATTTTTGGAAGTTTCG
1135 GGGTAAAAA
1 GGGTAAAAA
1144 CAAAAATTTT
Statistics
Matches: 231, Mismatches: 28, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
28 4 0.02
29 103 0.45
30 119 0.52
31 5 0.02
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATAGGATTTTTGGAAGTTTCG
Found at i:925 original size:118 final size:116
Alignment explanation
Indices: 816--1162 Score: 412
Period size: 118 Copynumber: 2.9 Consensus size: 116
806 TTCAAGATCG
* **
816 AAAATGGAGATTTTAGAGGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATA
1 AAAAT-GAGATTTTAGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATA
*
881 GGATTTTTGGAAGTTCGGGAGTAAAAACGGAATTCTTGGAAGTTTCGAGGTCA
65 GGATTTTTGGAAGTTCGGG-GTAAAAACAGAATTCTTGGAAGTTTCGAGGTCA
* ** * *
934 AAAAT-ATGATTTTTAGAAGTTTGGGGGTAAAAATAAAATTCTTGGAAGTTTCGGGGTTAAAAAT
1 AAAATGA-GA-TTTTAGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT
* * * *
998 AGGATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGGAAGTTTCGGGGTAA
64 AGGATTTTTGGAAGTTCG-GGGTAAAAACAGAATTCTTGGAAGTTTCGAGGTCA
* * * *
1052 AAAAT-AGGATATTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGATGTTTTGGGGTCAAAAAT
1 AAAATGA-GAT-TTTAGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT
* *
1116 AGGATTTTTGGAAGTTTGGGGGTAAAAACAAAAATT-TTGGATAGTTT
64 AGGATTTTTGGAAG-TTCGGGGTAAAAAC-AGAATTCTTGGA-AGTTT
1163 AGGGACCTTC
Statistics
Matches: 196, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
116 1 0.01
117 3 0.02
118 177 0.90
119 15 0.08
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (116 bp):
AAAATGAGATTTTAGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATAG
GATTTTTGGAAGTTCGGGGTAAAAACAGAATTCTTGGAAGTTTCGAGGTCA
Found at i:1154 original size:59 final size:59
Alignment explanation
Indices: 840--1162 Score: 371
Period size: 59 Copynumber: 5.5 Consensus size: 59
830 AGAGGTTTGA
** * **
840 GGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATAGGATTTTTGGAAGTTCGG
1 GGGTAAAAACAGAAATTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGG
* * * * * *
899 GAGTAAAAAC-GGAATTCTTGGAAGTTTCGAGGTCAAAAATATGATTTTTAGAAGTTTGG
1 GGGTAAAAACAGAAATT-TTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGG
* * *
958 GGGTAAAAATA-AAATTCTTGGAAGTTTCGGGGTTAAAAATAGGATTTTTGGAAGTTCGA
1 GGGTAAAAACAGAAATT-TTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGG
* * * * *
1017 GGGTAAAAATAGAATTTTTGGAAGTTTCGGGGTAAAAAATAGGATATTTGGAAGTTCGA
1 GGGTAAAAACAGAAATTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGG
** * * * *
1076 GGGTAAAAATGGAATTTTTGGATGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTTGG
1 GGGTAAAAACAGAAATTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGG
*
1135 GGGTAAAAACAAAAATTTTGGATAGTTT
1 GGGTAAAAACAGAAATTTTGGA-AGTTT
1163 AGGGACCTTC
Statistics
Matches: 228, Mismatches: 32, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
58 4 0.02
59 216 0.95
60 8 0.04
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
GGGTAAAAACAGAAATTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGG
Found at i:2174 original size:18 final size:18
Alignment explanation
Indices: 2151--2201 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
2141 TTAGTTCCCT
2151 TTTTTA-TAATTATTAATA
1 TTTTTATTAA-TATTAATA
2169 TTTTTATTAATATTAATAA
1 TTTTTATTAATATTAAT-A
2188 TAATTTTATTAATA
1 T--TTTTATTAATA
2202 CCTATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 13 0.45
19 5 0.17
21 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTATTAATATTAATA
Found at i:2188 original size:21 final size:21
Alignment explanation
Indices: 2159--2201 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2149 CTTTTTTATA
* *
2159 ATTATTAATATTTTTATTAAT
1 ATTAATAATAATTTTATTAAT
2180 ATTAATAATAATTTTATTAAT
1 ATTAATAATAATTTTATTAAT
2201 A
1 A
2202 CCTATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAATAATAATTTTATTAAT
Found at i:2912 original size:17 final size:17
Alignment explanation
Indices: 2892--2983 Score: 87
Period size: 17 Copynumber: 5.3 Consensus size: 17
2882 CTTTATTTAT
* *
2892 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
*
2909 TTTAAATATGAAAATAAA
1 TTTAAAT-TTAAAATAAA
*
2927 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
* * *
2944 TTTAAAATTTTATACAAA
1 TTT-AAATTTAAAATAAA
2962 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
2979 TTTAA
1 TTTAA
2984 GATGAGTTTG
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
16 3 0.05
17 29 0.49
18 27 0.46
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:3697 original size:206 final size:206
Alignment explanation
Indices: 3406--3916 Score: 630
Period size: 206 Copynumber: 2.5 Consensus size: 206
3396 TTTGGTTTGA
* * * *
3406 TTCTCCGTATCTCATCAGGAAGCTAACCACTTTATTACTTCGACCCACTTCTTAGTATCTCA-CT
1 TTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCCGCTTCTTAGTATCTCATC-
* * * * * *
3470 AAGAAGTCGGGGTTCGAAGATTTGCTCACATTGAGCATGAGTTTGATTTGGTCTTCTTCTCAGTA
65 AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCATGAATTTGATTTGATATTCTTCTCAGTA
* * * * * ** * *
3535 TCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGTTTCTCTGTATCTCATCAGGAAGACG
130 TCTCATCAGGAAGATGACCGCATCGCTTGTGTCAATCCACTTCTCTGTATCTCATCAAGAAGACA
*
3600 AATTTGGTCCAC
195 AATTTGATCCAC
* * *
3612 TTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCT-GTGTCTTATC
1 TTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCCGCTTCT-TAGTATCTCATC
* * * *
3676 AGGAAGTTGAGATTTGAAGATTTGCTCACATCGAGCGTGAATTTGATTTGATATTCTTCTCAGTA
65 AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCATGAATTTGATTTGATATTCTTCTCAGTA
* *
3741 TCTCATCAGGAAGATGACCGCATCGCTTGTGTCAATCCACTTCTCTGTATCTCCTTAAGAAGACA
130 TCTCATCAGGAAGATGACCGCATCGCTTGTGTCAATCCACTTCTCTGTATCTCATCAAGAAGACA
*
3806 AATTTGATTCAC
195 AATTTGATCCAC
* * * ** **
3818 TTCTTAGTATCTAATCAGAAAGCTAACTGTTTTATTGTTTCAACCCGCTTCTTAGTATCTCATCA
1 TTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCCGCTTCTTAGTATCTCATCA
* * *
3883 GGAAGCTGGGGTTCGAAGATTTGGTCGCATCGAG
66 GGAAGTTGGGGTTCGAAGATTTGCTCACATCGAG
3917 TCCTGAGTTG
Statistics
Matches: 256, Mismatches: 46, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
205 1 0.00
206 253 0.99
207 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (206 bp):
TTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCCGCTTCTTAGTATCTCATCA
GGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCATGAATTTGATTTGATATTCTTCTCAGTAT
CTCATCAGGAAGATGACCGCATCGCTTGTGTCAATCCACTTCTCTGTATCTCATCAAGAAGACAA
ATTTGATCCAC
Found at i:4017 original size:115 final size:115
Alignment explanation
Indices: 3815--4025 Score: 298
Period size: 115 Copynumber: 1.8 Consensus size: 115
3805 AAATTTGATT
* ** * * *
3815 CACTTCTTAGTATCTAATCAGAAAGCTAACTGTTTTATTGTTTCAACCCGCTTCTTAGTATCTCA
1 CACTTCTTAGTATCTAATCAGAAAGCAAACCATTTTATTATTTCAACCCGCTTCTCAATATCTCA
* *
3880 TCAGGAAGCTGGGGTTCGAAGATTTGGTCGCATCGAGTCCTGAGTTGGTA
66 TCAGGAAGCTGGAGTTCGAAGATTTGCTCGCATCGAGTCCTGAGTTGGTA
* * *
3930 CACTTCTCT-GTATCTCATCAGGAAGCAAACCATTTTATTATTTCGACCCGCTTCTCAATATCTC
1 CACTTCT-TAGTATCTAATCAGAAAGCAAACCATTTTATTATTTCAACCCGCTTCTCAATATCTC
*
3994 GTCAGGAAGCTGGAGTTCGAAGATTTGCTCGC
65 ATCAGGAAGCTGGAGTTCGAAGATTTGCTCGC
4026 TTTGAGCCTC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
115 82 0.99
116 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (115 bp):
CACTTCTTAGTATCTAATCAGAAAGCAAACCATTTTATTATTTCAACCCGCTTCTCAATATCTCA
TCAGGAAGCTGGAGTTCGAAGATTTGCTCGCATCGAGTCCTGAGTTGGTA
Found at i:14764 original size:20 final size:20
Alignment explanation
Indices: 14739--14780 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
14729 GTAATAAAGT
14739 TTCTAGTATTGATAATATTG
1 TTCTAGTATTGATAATATTG
14759 TTCTAGTATTGATAATATTG
1 TTCTAGTATTGATAATATTG
14779 TT
1 TT
14781 GATTGAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (20 bp):
TTCTAGTATTGATAATATTG
Found at i:16942 original size:59 final size:59
Alignment explanation
Indices: 16850--16968 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
16840 CCATAGATGG
16850 TCCCTCATCCCTGGGACCTGGGACCAACACTGACTTGACTTTAACTAACCACCACAAGC
1 TCCCTCATCCCTGGGACCTGGGACCAACACTGACTTGACTTTAACTAACCACCACAAGC
16909 TCCCTCATCCCTGGGACCTGGGACCAACACTGACTTGACTTTAACTAACCACCACAAGC
1 TCCCTCATCCCTGGGACCTGGGACCAACACTGACTTGACTTTAACTAACCACCACAAGC
16968 T
1 T
16969 TGTTTTATTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.21
Consensus pattern (59 bp):
TCCCTCATCCCTGGGACCTGGGACCAACACTGACTTGACTTTAACTAACCACCACAAGC
Found at i:27416 original size:24 final size:24
Alignment explanation
Indices: 27365--27415 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
27355 TTCGTAGACC
* *
27365 AAATAAATTATGCTAATAAATGTA
1 AAATAAATTATACTAATAAATCTA
*
27389 AAATATATTATACTAATAAATACTA
1 AAATAAATTATACTAATAAAT-CTA
27414 AA
1 AA
27416 TTTTTTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATCTA
Found at i:28584 original size:2 final size:2
Alignment explanation
Indices: 28577--28604 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28567 CCTTTCACAA
28577 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
28605 TTATGTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36448 original size:98 final size:98
Alignment explanation
Indices: 36251--36445 Score: 234
Period size: 97 Copynumber: 2.0 Consensus size: 98
36241 AACTTTGGAA
* * *
36251 AAGGATGTTCGATTATCTCGATTTAAAGAAAAAGTCACACCTAGTAAGTTTAGGTACAAATTTTC
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAAGTCACACCTAGTAAGTTAAGGCACAAATTTTC
* * *
36316 AGAATTAGAGATAAAGAAACATTGCCTCGATTT
66 AAAACTAGAAATAAAGAAACATTGCCTCGATTT
* ***
36349 AAGGATATTCGATTAT-TCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTT
1 AAGGATATTCGATTATCT-CGATTTAAAGAAAAAGTCACACCTAGTAAGTTAAGGCACAAATTTT
* * *
36412 CAAAACTCGAAATAAA-AGAATATTGTCTCGATTT
65 CAAAACTAGAAATAAAGA-AACATTGCCTCGATTT
36446 TAAAGTTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
96 1 0.01
97 52 0.63
98 29 0.35
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (98 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAAGTCACACCTAGTAAGTTAAGGCACAAATTTTC
AAAACTAGAAATAAAGAAACATTGCCTCGATTT
Found at i:36793 original size:58 final size:58
Alignment explanation
Indices: 36703--37136 Score: 311
Period size: 58 Copynumber: 7.4 Consensus size: 58
36693 TGGACACTCG
* * ** * *
36703 GGGGAAAAAATGGTAATTTTAGGAAAGTTCGGGGTTTAAAATGAAATTTTAGTCA-TTCA
1 GGGGTAAAAAT-GTAATTTTTGGAAAAATCGGGGTTAAAAATGAAATTTTAG-AAGTTCA
* * * * **
36762 GGGGT-AAAATGGTAATTTTTGGAAAAATC-GGGATAATAAATGGAATTTTTTGTAGTTTG
1 GGGGTAAAAAT-GTAATTTTTGGAAAAATCGGGGTTAA-AAAT-GAAATTTTAGAAGTTCA
* * *
36821 GGGGT-AAAATGGTAATTTTGGGGAAAAAT-GGGGTAAAAAATGGAATTTTAAGAAGTTC-
1 GGGGTAAAAAT-GTAATTTT-TGGAAAAATCGGGGTTAAAAATGAAATTTT-AGAAGTTCA
* *
36879 GAGGGT-AAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTAAGAAGTTC-
1 G-GGGTAAAAATGTAATTTTTGGAAAAATCGGGGTTAAAAATGAAATTTT-AGAAGTTCA
* * * *
36937 GAGGATAAAAATGTAATTTTTAGAAAAATCGAGGTTAAAAATG-AATTTTAGGAAGTTTA
1 G-GGGTAAAAATGTAATTTTTGGAAAAATCGGGGTTAAAAATGAAATTTTA-GAAGTTCA
* * ** * *
36996 AGGGTAAAAATGTAATTTTTAGAAAAATTAGGG-TCAAAAT-AGAATTTTAGAAAGTTTA
1 GGGGTAAAAATGTAATTTTTGGAAAAATCGGGGTTAAAAATGA-AATTTTAG-AAGTTCA
* *** * * **
37054 GGGGTAAAAATGTAATTTTT-GAAAAGTTTAAGGTT-AAAATGGAATTTTGGAAAGTTTT
1 GGGGTAAAAATGTAATTTTTGGAAAA-ATCGGGGTTAAAAATGAAATTTTAG-AAGTTCA
37112 GGGGTAAAAATGTAATTTTT-GAAAA
1 GGGGTAAAAATGTAATTTTTGGAAAA
37137 GTTTAAGGAC
Statistics
Matches: 321, Mismatches: 37, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
57 26 0.08
58 195 0.61
59 87 0.27
60 13 0.04
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (58 bp):
GGGGTAAAAATGTAATTTTTGGAAAAATCGGGGTTAAAAATGAAATTTTAGAAGTTCA
Found at i:36861 original size:117 final size:117
Alignment explanation
Indices: 36709--37023 Score: 322
Period size: 117 Copynumber: 2.7 Consensus size: 117
36699 CTCGGGGGAA
** ** *
36709 AAAATGGTAATTTTAGGAAAGTTCGGGGTTTAAAATGAAATTTT-AGTCA-TTC-AGGGGTAAAA
1 AAAATGGTAATTTTAGGAAAAATCGGGGTAAAAAATGAAATTTTAAG-AAGTTCGA-GGGTAAAA
36771 TGGTAATTTTTGGAAAAATCG-GGATAATAAATGGAATTTTTTGTAGTTTGGGGGT
64 T-GTAATTTTTGGAAAAATCGAGGATAA-AAATGGAATTTTTTGTAGTTTGGGGGT
* *
36826 AAAATGGTAATTTTGGGGAAAAAT-GGGGTAAAAAATGGAATTTTAAGAAGTTCGAGGGTAAAAT
1 AAAATGGTAATTTT-AGGAAAAATCGGGGTAAAAAATGAAATTTTAAGAAGTTCGAGGGTAAAAT
* ** * * * *
36890 GTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTAAGAAGTTCGAGGAT
65 GTAATTTTTGGAAAAATCGAGGATAAAAATGGAATTTTTTGTAGTTTGGGGGT
* * * **
36943 AAAAAT-GTAATTTTTA-GAAAAATCGAGGTTAAAAATG-AATTTTAGGAAGTTTAAGGGTAAAA
1 -AAAATGGTAA-TTTTAGGAAAAATCGGGGTAAAAAATGAAATTTTAAGAAGTTCGAGGGT-AAA
*
37005 ATGTAATTTTTAGAAAAAT
63 ATGTAATTTTTGGAAAAAT
37024 TAGGGTCAAA
Statistics
Matches: 168, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
116 25 0.15
117 108 0.64
118 34 0.20
119 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTAGGAAAAATCGGGGTAAAAAATGAAATTTTAAGAAGTTCGAGGGTAAAATG
TAATTTTTGGAAAAATCGAGGATAAAAATGGAATTTTTTGTAGTTTGGGGGT
Found at i:37054 original size:28 final size:28
Alignment explanation
Indices: 36851--37141 Score: 178
Period size: 29 Copynumber: 10.0 Consensus size: 28
36841 GGGAAAAATG
* *
36851 GGGTAAAAAATGGAATTTTA-AGAAGTTCGA
1 GGGT-AAAAATGTAATTTTAGA-AAGTT-TA
* * **
36881 GGGT-AAAATGTAATTTTTGGAAAAATCGA
1 GGGTAAAAATGTAA-TTTTAG-AAAGTTTA
* * *
36910 GGTTAAAAATGGAATTTTA-AGAAGTTCGA
1 GGGTAAAAATGTAATTTTAGA-AAGTT-TA
* * **
36939 GGATAAAAATGTAATTTTTAGAAAAATCGA
1 GGGTAAAAATGTAA-TTTTAG-AAAGTTTA
* *
36969 GGTTAAAAATG-AATTTTAGGAAGTTTAA
1 GGGTAAAAATGTAATTTTAGAAAGTTT-A
**
36997 GGGTAAAAATGTAATTTTTAGAAAAATTA
1 GGGTAAAAATGTAA-TTTTAGAAAGTTTA
*
37026 GGGTCAAAATAG-AATTTTAGAAAGTTTA
1 GGGTAAAAAT-GTAATTTTAGAAAGTTTA
*
37054 GGGGTAAAAATGTAATTTTTGAAAAGTTTA
1 -GGGTAAAAATGTAATTTTAG-AAAGTTTA
* * * * *
37084 AGGTTAAAATGGAATTTTGGAAAGTTTTG
1 GGGTAAAAATGTAATTTTAGAAAG-TTTA
*
37113 GGGTAAAAATGTAATTTTTGAAAAGTTTA
1 GGGTAAAAATGTAATTTTAG-AAAGTTTA
37142 AGGACCTCTA
Statistics
Matches: 206, Mismatches: 37, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
27 4 0.02
28 45 0.22
29 97 0.47
30 55 0.27
31 4 0.02
32 1 0.00
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTAGAAAGTTTA
Found at i:38267 original size:16 final size:17
Alignment explanation
Indices: 38246--38320 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
38236 TATTTATTAA
38246 AATATTATTATTA-ATT
1 AATATTATTATTATATT
38262 AATATTAGGGTTATTTACTATT
1 AATATTA---TTA-TTA-TATT
*
38284 GATATTATTATTATTATT
1 AATATTATTATTA-TATT
*
38302 ACTATTATTATT-TATT
1 AATATTATTATTATATT
38318 AAT
1 AAT
38321 TGTTATTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
16 13 0.27
18 17 0.35
19 6 0.12
20 3 0.06
22 9 0.19
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (17 bp):
AATATTATTATTATATT
Found at i:38294 original size:3 final size:3
Alignment explanation
Indices: 38286--38328 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
38276 TTACTATTGA
* *
38286 TAT TAT TAT TAT TAT TAC TAT TAT TATT TAT TAAT TGT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT T-AT TAT TAT TA
38329 ATGCCCTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:47586 original size:27 final size:28
Alignment explanation
Indices: 47533--47614 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
47523 TAAAAAATAA
*
47533 TTAATATTTTTATATTTTTATAAAATTT
1 TTAATATTTTTATATTTTAATAAAATTT
*
47561 TTAATACTTTTTA-ATTTTAATAAATTTT
1 TTAATA-TTTTTATATTTTAATAAAATTT
* *
47589 TTGGAT-TTTTTAAATTTTAA-AAAATT
1 TT-AATATTTTTATATTTTAATAAAATT
47615 AATTAATCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 11 0.23
28 28 0.60
29 8 0.17
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (28 bp):
TTAATATTTTTATATTTTAATAAAATTT
Found at i:62525 original size:51 final size:51
Alignment explanation
Indices: 62464--62565 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
62454 TAGGTCAATT
* **
62464 GATAACTAACCGATAAAATTCTTAGTTCTAGGTTAATTACAACTATGAATA
1 GATAACTAACCGATAAAATTATTAACTCTAGGTTAATTACAACTATGAATA
*
62515 GATAATTAACCGATAAAATTATTAACTCTAGGTTAATTACAACTATGAATA
1 GATAACTAACCGATAAAATTATTAACTCTAGGTTAATTACAACTATGAATA
62566 TTAATCAACC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (51 bp):
GATAACTAACCGATAAAATTATTAACTCTAGGTTAATTACAACTATGAATA
Found at i:64592 original size:54 final size:53
Alignment explanation
Indices: 64529--64707 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 53
64519 TTCAGCAATA
* *
64529 ACAGAATATCGCTCGTTCAAGCCATATACAAAATATTGTTCATTCGATACAGAT
1 ACAGAATATCGCTCATTCAAGCCAGATACAAAATATTGTTCATTCGA-ACAGAT
* * * * * * * *
64583 ACAAAATATCTCTCATTCAATCCAGATATAGAATACTGCTCATTC-AAGCCAAAT
1 ACAGAATATCGCTCATTCAAGCCAGATACAAAATATTGTTCATTCGAA--CAGAT
* * * * *
64637 ATAGATTATCGCTCATTCGAGCTAGATACAAATTATTGCTT-ATTCGAACCAGAT
1 ACAGAATATCGCTCATTCAAGCCAGATACAAAATATTG-TTCATTCGAA-CAGAT
64691 ACAGAATATCGCTCATT
1 ACAGAATATCGCTCATT
64708 GCTCAGACTT
Statistics
Matches: 96, Mismatches: 25, Indels: 8
0.74 0.19 0.06
Matches are distributed among these distances:
52 1 0.01
53 1 0.01
54 91 0.95
55 3 0.03
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (53 bp):
ACAGAATATCGCTCATTCAAGCCAGATACAAAATATTGTTCATTCGAACAGAT
Found at i:64638 original size:27 final size:27
Alignment explanation
Indices: 64531--64707 Score: 90
Period size: 27 Copynumber: 6.6 Consensus size: 27
64521 CAGCAATAAC
* * *
64531 AGAATATCGCTCGTTCAAGCCATATAC
1 AGAATATCGCTCATTCAAGCCAAATAT
* * * * ** * *
64558 AAAATATTGTTCATTCGATACAGATAC
1 AGAATATCGCTCATTCAAGCCAAATAT
* * * *
64585 AAAATATCTCTCATTCAATCCAGATAT
1 AGAATATCGCTCATTCAAGCCAAATAT
64612 AGAATA-CTGCTCATTCAAGCCAAATAT
1 AGAATATC-GCTCATTCAAGCCAAATAT
* * * * *
64639 AGATTATCGCTCATTCGAGCTAGATAC
1 AGAATATCGCTCATTCAAGCCAAATAT
* * * *
64666 A-AATTATTGCTTATTCGAA-CCAGATAC
1 AGAA-TATCGCTCATTC-AAGCCAAATAT
64693 AGAATATCGCTCATT
1 AGAATATCGCTCATT
64708 GCTCAGACTT
Statistics
Matches: 115, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 2 0.02
27 109 0.95
28 4 0.03
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.31
Consensus pattern (27 bp):
AGAATATCGCTCATTCAAGCCAAATAT
Found at i:67527 original size:16 final size:15
Alignment explanation
Indices: 67508--67550 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
67498 TTTAAAAGAT
67508 ATATTAATTAATAATA
1 ATATT-ATTAATAATA
67524 ATATTA-TAAT-ATA
1 ATATTATTAATAATA
67537 ATATTATT-ATAATA
1 ATATTATTAATAATA
67551 TTCTAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.44
14 8 0.32
15 1 0.04
16 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTATTAATAATA
Found at i:67534 original size:8 final size:8
Alignment explanation
Indices: 67521--67560 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
67511 TTAATTAATA
67521 ATAATATT
1 ATAATATT
*
67529 ATAATATA
1 ATAATATT
*
67537 ATATTATT
1 ATAATATT
67545 ATAATATT
1 ATAATATT
*
67553 CTAATATT
1 ATAATATT
67561 TTATTCTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (8 bp):
ATAATATT
Found at i:67548 original size:24 final size:25
Alignment explanation
Indices: 67521--67585 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 25
67511 TTAATTAATA
67521 ATAATATTATAATATAATATT-ATT
1 ATAATATTATAATATAATATTCATT
* ** *
67545 ATAATATTCTAATATTTTATTCTTT
1 ATAATATTATAATATAATATTCATT
*
67570 ATAATA-TAAAATATAA
1 ATAATATTATAATATAA
67586 AAGAAAGAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
ATAATATTATAATATAATATTCATT
Found at i:67560 original size:16 final size:16
Alignment explanation
Indices: 67518--67551 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
67508 ATATTAATTA
67518 ATAATAATATTATAAT
1 ATAATAATATTATAAT
*
67534 ATAATATTATTATAAT
1 ATAATAATATTATAAT
67550 AT
1 AT
67552 TCTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATAATATTATAAT
Found at i:74215 original size:29 final size:27
Alignment explanation
Indices: 74178--74233 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
74168 AGAATTTCGA
74178 ATTAATTGAAAATTTAA-AAAATTATGAAT
1 ATTAATTGAAAA---AAGAAAATTATGAAT
*
74207 ATTATTTGAAAAAAGAAAATTATGAAT
1 ATTAATTGAAAAAAGAAAATTATGAAT
74234 GTTCTGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 12 0.48
29 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (27 bp):
ATTAATTGAAAAAAGAAAATTATGAAT
Found at i:78519 original size:9 final size:9
Alignment explanation
Indices: 78486--78528 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 9
78476 TTTAATTTTG
78486 TTTATATATT
1 TTTATA-ATT
78496 GTTTATAATTAT
1 -TTTATAA-T-T
78508 TTTATAATT
1 TTTATAATT
78517 TTTATAATT
1 TTTATAATT
78526 TTT
1 TTT
78529 CAAAACATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 13 0.43
10 2 0.07
11 14 0.47
12 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTATAATT
Found at i:78520 original size:20 final size:22
Alignment explanation
Indices: 78486--78525 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
78476 TTTAATTTTG
78486 TTTATATATTGTTTATAATTAT
1 TTTATATATTGTTTATAATTAT
78508 TTTATA-ATT-TTTATAATT
1 TTTATATATTGTTTATAATT
78526 TTTCAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (22 bp):
TTTATATATTGTTTATAATTAT
Found at i:83826 original size:4 final size:4
Alignment explanation
Indices: 83813--83864 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
83803 TGGGACCAAC
*
83813 GAAA -AAA GAAA GAAA -AAA GAAA GAAA -AAA GAGA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
83858 GAAA GAA
1 GAAA GAA
83865 GAAGGAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 9 0.21
4 34 0.79
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:83829 original size:11 final size:11
Alignment explanation
Indices: 83813--83867 Score: 83
Period size: 11 Copynumber: 4.9 Consensus size: 11
83803 TGGGACCAAC
83813 GAAAAAAGAAA
1 GAAAAAAGAAA
83824 GAAAAAAGAAA
1 GAAAAAAGAAA
*
83835 GAAAAAAGAGA
1 GAAAAAAGAAA
83846 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
83858 GAAAGAAGAA
1 GAAAAAAGAA
83868 GGAAGAAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
11 30 0.75
12 10 0.25
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:85981 original size:3 final size:3
Alignment explanation
Indices: 85963--86002 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
85953 ACTCCATCAA
*
85963 AAC AA- AAC AA- AAC AAC AAC AAC AAC AAC AAC AAT AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
86003 CAAAGAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.70, C:0.28, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:98556 original size:15 final size:14
Alignment explanation
Indices: 98538--98571 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
98528 ATTTTTAAAA
*
98538 TTTTATATATTAATT
1 TTTTATATAAT-ATT
98553 TTTTATATAATATT
1 TTTTATATAATATT
98567 TTTTA
1 TTTTA
98572 AAAAAGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTATATAATATT
Found at i:100771 original size:4 final size:4
Alignment explanation
Indices: 100762--100795 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
100752 AGGAGTCCCC
100762 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
100796 TTAAGCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:101609 original size:9 final size:10
Alignment explanation
Indices: 101594--101618 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
101584 GTATTTATCA
101594 AATTTTTAAT
1 AATTTTTAAT
101604 AATTTTTAAT
1 AATTTTTAAT
101614 AATTT
1 AATTT
101619 CTCTGATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:106348 original size:46 final size:46
Alignment explanation
Indices: 106296--106389 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
106286 TTATTCAGCG
* *
106296 TCTATTTTTCAAAAATTAAAATCCATTTCATTTGAAATAAATCTGT
1 TCTATTTTTCAAAAATTAAAATCCATTTAATTTGAAACAAATCTGT
106342 TCTATTTTTCAAAAATTAAAATCCATTTAATTTGAAACAAATCTGT
1 TCTATTTTTCAAAAATTAAAATCCATTTAATTTGAAACAAATCTGT
106388 TC
1 TC
106390 GAAATCGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (46 bp):
TCTATTTTTCAAAAATTAAAATCCATTTAATTTGAAACAAATCTGT
Found at i:106429 original size:5 final size:5
Alignment explanation
Indices: 106421--106459 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
106411 AAAAATAAAA
106421 TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCA
1 TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCA
106460 ATCAAATCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
TCCAC
Found at i:106469 original size:15 final size:15
Alignment explanation
Indices: 106418--106473 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
106408 CAAAAAAATA
106418 AAATCCACTCCACTC
1 AAATCCACTCCACTC
* *
106433 CACTCCACTCCACTC
1 AAATCCACTCCACTC
* * *
106448 CACTCCACTCCAATC
1 AAATCCACTCCACTC
106463 AAATCCA-TCCA
1 AAATCCACTCCA
106474 TTGAATTTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 4 0.11
15 32 0.89
ACGTcount: A:0.30, C:0.50, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATCCACTCCACTC
Found at i:115613 original size:23 final size:22
Alignment explanation
Indices: 115587--115685 Score: 110
Period size: 23 Copynumber: 4.4 Consensus size: 22
115577 GCTGGGGAAA
115587 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
*
115609 CCAGTAAGCACACACAATGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * *
115632 CAGTAGGCACACAAAGTGCGAAA
1 CAGTAAGCACACACAGTGC-AAT
*
115655 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
115678 CAGTAAGC
1 CAGTAAGC
115686 GCGCTAGAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
22 16 0.24
23 51 0.75
24 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.21, T:0.11
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:118692 original size:22 final size:21
Alignment explanation
Indices: 118659--118704 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
118649 ACTTTATGTA
* * *
118659 TTTTTCTAATTTTTTTTTATT
1 TTTTTATAATTTCTTTTTAAT
118680 TTTTTATATATTTCTTTTTAAT
1 TTTTTATA-ATTTCTTTTTAAT
118702 TTT
1 TTT
118705 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTATAATTTCTTTTTAAT
Found at i:118722 original size:18 final size:18
Alignment explanation
Indices: 118671--118727 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
118661 TTTCTAATTT
*
118671 TTTTTTAT-TTTTTTATATA
1 TTTTTTATAATTTTTA-A-A
*
118690 TTTCTTTTTAA-TTTTAAA
1 TTT-TTTATAATTTTTAAA
118708 TTTTTTATAATTTTTAAA
1 TTTTTTATAATTTTTAAA
118726 TT
1 TT
118728 ATTTGTTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 6 0.19
18 13 0.41
19 4 0.12
20 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTATAATTTTTAAA
Found at i:119732 original size:20 final size:21
Alignment explanation
Indices: 119707--119747 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
119697 AAAAGTTATT
*
119707 AATTAT-TTTCTTTAATTAAA
1 AATTATATTTCTTTAAATAAA
*
119727 AATTATATTTTTTTAAATAAA
1 AATTATATTTCTTTAAATAAA
119748 TTTCACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTATATTTCTTTAAATAAA
Found at i:121209 original size:28 final size:26
Alignment explanation
Indices: 121146--121210 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
121136 TTGGGCTAAA
* *
121146 TAGATAATATATGTCGATTTTTTTTAT
1 TAGATAA-ATAGGTCGATTTTTTATAT
121173 T-GATCAAATAGGTCGATTTTTTAATATT
1 TAGAT-AAATAGGTCGATTTTTT-ATA-T
121201 TAGATAAATA
1 TAGATAAATA
121211 AGTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
26 17 0.53
27 5 0.16
28 7 0.22
29 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (26 bp):
TAGATAAATAGGTCGATTTTTTATAT
Found at i:124840 original size:2 final size:2
Alignment explanation
Indices: 124833--124886 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
124823 ACATGGCTTA
*
124833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
124875 AT GT AT AT AT AT
1 AT AT AT AT AT AT
124887 GAGCTTCGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126371 original size:3 final size:3
Alignment explanation
Indices: 126363--126399 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
126353 AACTTAAATT
126363 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
126400 ACCATAGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:127312 original size:15 final size:15
Alignment explanation
Indices: 127288--127320 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
127278 TATTGAACCC
*
127288 TAATTGTAATAATAA
1 TAATTATAATAATAA
127303 TAATTATAATAATAA
1 TAATTATAATAATAA
127318 TAA
1 TAA
127321 ATGTCAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TAATTATAATAATAA
Found at i:130396 original size:13 final size:13
Alignment explanation
Indices: 130378--130412 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
130368 TCTTTGACCC
130378 AACAAAATTGAAA
1 AACAAAATTGAAA
*
130391 AACAAAATTGATA
1 AACAAAATTGAAA
*
130404 AATAAAATT
1 AACAAAATT
130413 TTGTTTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (13 bp):
AACAAAATTGAAA
Found at i:132368 original size:2 final size:2
Alignment explanation
Indices: 132361--132387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
132351 TAAGGATGTA
132361 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 A
132388 AAGAAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:132707 original size:28 final size:28
Alignment explanation
Indices: 132675--132731 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
132665 AATAAATAAT
132675 TTAAAAATT-ATAAAGAATTCAAAA-AAAA
1 TTAAAAATTAAT-AA-AATTCAAAAGAAAA
*
132703 TTAAAAGTTAATAAAATTCAAAAGAAAA
1 TTAAAAATTAATAAAATTCAAAAGAAAA
132731 T
1 T
132732 AGCAAGTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 9 0.35
28 15 0.58
29 2 0.08
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (28 bp):
TTAAAAATTAATAAAATTCAAAAGAAAA
Found at i:133037 original size:31 final size:31
Alignment explanation
Indices: 132999--133080 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
132989 AACTATGGGT
** *
132999 AAGTTTTCATTTTGGTCAATGAACTATTCGAA
1 AAGTTTTCATTTAAGTCAATAAACTATTC-AA
*
133031 AA-TTTTCA-TTAAGTCACTAAACTATTCAA
1 AAGTTTTCATTTAAGTCAATAAACTATTCAA
133060 AAGTTTTCATTTAAGTCAATA
1 AAGTTTTCATTTAAGTCAATA
133081 GGTTGTTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.09
30 21 0.49
31 16 0.37
32 2 0.05
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (31 bp):
AAGTTTTCATTTAAGTCAATAAACTATTCAA
Found at i:133056 original size:30 final size:31
Alignment explanation
Indices: 132979--133077 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
132969 AACTACACCA
** * *
132979 TAAGTCACTAAACTATGGGTAAGTTTTCATT
1 TAAGTCACTAAACTATTCGAAAATTTTCATT
** * *
133010 TTGGTCAATGAACTATTCGAAAATTTTCA-T
1 TAAGTCACTAAACTATTCGAAAATTTTCATT
133040 TAAGTCACTAAACTATTC-AAAAGTTTTCATT
1 TAAGTCACTAAACTATTCGAAAA-TTTTCATT
133071 TAAGTCA
1 TAAGTCA
133078 ATAGGTTGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 4 0.07
30 21 0.39
31 29 0.54
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (31 bp):
TAAGTCACTAAACTATTCGAAAATTTTCATT
Found at i:135787 original size:6 final size:6
Alignment explanation
Indices: 135779--135817 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
135769 AATCTTAACA
* *
135779 TTAATA TTAA-T TAAATT TTAATT TTAATT TTAATT TTAA
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAA
135818 AATCTGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 3 0.10
6 26 0.90
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TTAATT
Found at i:135794 original size:23 final size:23
Alignment explanation
Indices: 135768--135813 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
135758 GTAATGGATA
135768 AAATCTTAACATTAATATTAATT
1 AAATCTTAACATTAATATTAATT
* ** *
135791 AAATTTTAATTTTAATTTTAATT
1 AAATCTTAACATTAATATTAATT
135814 TTAAAATCTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
AAATCTTAACATTAATATTAATT
Found at i:135876 original size:15 final size:14
Alignment explanation
Indices: 135835--135894 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
135825 AAAATAAAAT
135835 AATTAAATTCTTAAA
1 AATTAAATT-TTAAA
**
135850 AA-TAAAAATTAAGA
1 AATTAAATTTTAA-A
135864 AATTAAATTTTAAA
1 AATTAAATTTTAAA
**
135878 TTTTAAATTTATAAA
1 AATTAAATTT-TAAA
135893 AA
1 AA
135895 AGCAAATAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
13 4 0.12
14 16 0.47
15 14 0.41
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
AATTAAATTTTAAA
Found at i:138085 original size:26 final size:26
Alignment explanation
Indices: 138045--138096 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
138035 TTTACCTTAG
*
138045 GTTACATTTTCGTCACTTATGTTAAT
1 GTTACATTTTAGTCACTTATGTTAAT
*
138071 GTTACGTTTTAGTCACTTATGTTAAT
1 GTTACATTTTAGTCACTTATGTTAAT
138097 ATTTTGTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (26 bp):
GTTACATTTTAGTCACTTATGTTAAT
Found at i:142163 original size:31 final size:31
Alignment explanation
Indices: 142125--142244 Score: 122
Period size: 31 Copynumber: 3.9 Consensus size: 31
142115 CAACTTAAAA
142125 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
*
142156 AAAAAGTGTCAA-TTTTGAGTACCAAATT-GG
1 AAAAAGTGTCAAGTTTAG-GTACCAAATTAGG
*** * *
142186 ACCCAAAA--AAAAAATTTAGGTACCAAATTAAG
1 A---AAAAGTGTCAAGTTTAGGTACCAAATTAGG
142218 AAAAAGTGTCAAGTTTAGGTACCAAAT
1 AAAAAGTGTCAAGTTTAGGTACCAAAT
142245 GTTACATTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
29 4 0.06
30 7 0.10
31 50 0.70
32 6 0.08
33 4 0.06
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
Found at i:142976 original size:29 final size:30
Alignment explanation
Indices: 142922--142994 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
142912 TTACAGAGAT
* * *
142922 TAGATTAAATTAA-TCTCTTTATTATTAAA
1 TAGATTAATTTAATTCTCTATACTATTAAA
142951 TAGATTAATTTAATTC-CTATACTATTAAA
1 TAGATTAATTTAATTCTCTATACTATTAAA
* * *
142980 AAAATTAATTAAATT
1 TAGATTAATTTAATT
142995 TAAATTGTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (30 bp):
TAGATTAATTTAATTCTCTATACTATTAAA
Found at i:147016 original size:109 final size:108
Alignment explanation
Indices: 146831--147050 Score: 325
Period size: 109 Copynumber: 2.0 Consensus size: 108
146821 AGAACCTCTT
* * * *
146831 GAAGGATCCATGAACGGGAGTGAAGATCTCAATAGCAGCATATCAATGAGAATTGGAGATCGGTT
1 GAAGGATCCATGAACGGGAGTGAAGAGCTCAAGAGCAGCAGATCAATGAGAATCGGAGATCGGTT
* * *
146896 CAAAGCATCGAAGCAGCTTCACTGATCGATACGAAGAGTGAGA
66 CAAAGCATCGAAACAGCTTCACGGATCGATACGAAGAGTAAGA
* *
146939 GAAGGATCCATTG-ACGGGAGTGAAGAGCTCGAGAGCAGCAGATCGAATGAGAATCGGAGATTGG
1 GAAGGATCCA-TGAACGGGAGTGAAGAGCTCAAGAGCAGCAGATC-AATGAGAATCGGAGATCGG
*
147003 TTCAAAGCATCGAAACAGCTTCACGGATCGATATGAAGAGTAAGA
64 TTCAAAGCATCGAAACAGCTTCACGGATCGATACGAAGAGTAAGA
147048 GAA
1 GAA
147051 CCATAAATAC
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 37 0.37
109 63 0.63
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (108 bp):
GAAGGATCCATGAACGGGAGTGAAGAGCTCAAGAGCAGCAGATCAATGAGAATCGGAGATCGGTT
CAAAGCATCGAAACAGCTTCACGGATCGATACGAAGAGTAAGA
Found at i:154757 original size:21 final size:21
Alignment explanation
Indices: 154731--154772 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
154721 AAGCACGGTG
154731 TGGTTGCAATTGCCATGGTTA
1 TGGTTGCAATTGCCATGGTTA
*
154752 TGGTTGTAATTGCCATGGTTA
1 TGGTTGCAATTGCCATGGTTA
154773 GTATCCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.40
Consensus pattern (21 bp):
TGGTTGCAATTGCCATGGTTA
Found at i:155965 original size:13 final size:13
Alignment explanation
Indices: 155947--155971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155937 AAATATATTT
155947 ATTAATTAAAAAC
1 ATTAATTAAAAAC
155960 ATTAATTAAAAA
1 ATTAATTAAAAA
155972 ACTTGAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:171203 original size:28 final size:27
Alignment explanation
Indices: 171162--171217 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
171152 GAGTTTGACA
*
171162 TTTTTTTTCTAATGTGATATTTGTATT
1 TTTTTTTTCCAATGTGATATTTGTATT
171189 TTTTTTTGTCCAATGTGATATTTGTATT
1 TTTTTTT-TCCAATGTGATATTTGTATT
171217 T
1 T
171218 GATAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.18, C:0.05, G:0.12, T:0.64
Consensus pattern (27 bp):
TTTTTTTTCCAATGTGATATTTGTATT
Found at i:173932 original size:21 final size:21
Alignment explanation
Indices: 173882--173933 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
173872 AAAATATATT
*
173882 TTTATTTT-CTTAATTTTCCC
1 TTTATTTTCCTAAATTTTCCC
* *
173902 TTCT-TCTTCCTAAATTTTCTC
1 TT-TATTTTCCTAAATTTTCCC
173923 TTTATTTTCCT
1 TTTATTTTCCT
173934 TGTCATTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATTTTCCTAAATTTTCCC
Found at i:180259 original size:11 final size:11
Alignment explanation
Indices: 180243--180267 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
180233 TAGAAGTTGA
180243 AAATATTTTTT
1 AAATATTTTTT
180254 AAATATTTTTT
1 AAATATTTTTT
180265 AAA
1 AAA
180268 AAATTAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:181932 original size:4 final size:4
Alignment explanation
Indices: 181925--181949 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
181915 ACATGCATGC
181925 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
181950 CGCAATGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:182130 original size:6 final size:6
Alignment explanation
Indices: 182119--182171 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
182109 AGTATTTTCA
* * * *
182119 TATATG TATATG AATATG TATATG AATATG TACATG TCTATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
182167 TATAT
1 TATAT
182172 CTCACTAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (6 bp):
TATATG
Found at i:184922 original size:16 final size:16
Alignment explanation
Indices: 184903--184939 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
184893 GTTCAGACCG
184903 TTTCAAACTCAGATTT
1 TTTCAAACTCAGATTT
* *
184919 TTTCGAACTTAGATTT
1 TTTCAAACTCAGATTT
184935 TTTCA
1 TTTCA
184940 GATTCGGGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (16 bp):
TTTCAAACTCAGATTT
Found at i:191922 original size:10 final size:10
Alignment explanation
Indices: 191909--191948 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
191899 TTAAAAAGTA
191909 ATAAAATATT
1 ATAAAATATT
*
191919 ATAAAA-ATC
1 ATAAAATATT
191928 ATAAAATATT
1 ATAAAATATT
*
191938 ATCAAATATT
1 ATAAAATATT
191948 A
1 A
191949 AAACATATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (10 bp):
ATAAAATATT
Found at i:191924 original size:19 final size:19
Alignment explanation
Indices: 191892--191984 Score: 68
Period size: 19 Copynumber: 4.9 Consensus size: 19
191882 TTTTATCATA
*
191892 AAAATGATTA-AAAAGTAAT
1 AAAAT-ATTATAAAAATAAT
*
191911 AAAATATTATAAAAATCAT
1 AAAATATTATAAAAATAAT
* *
191930 AAAATATTAT-CAAATATT
1 AAAATATTATAAAAATAAT
* * *
191948 AAAACA-TATGAAAATTGAT
1 AAAATATTAT-AAAAATAAT
191967 ATAAA-ATTATAAAAATAA
1 A-AAATATTATAAAAATAA
191985 ATTCTAATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
17 3 0.05
18 14 0.25
19 34 0.60
20 6 0.11
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAATATTATAAAAATAAT
Found at i:192043 original size:21 final size:20
Alignment explanation
Indices: 192015--192066 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
192005 AATTTAAAAC
*
192015 ATTA-ATAAAATATATTTAAA
1 ATTATATAAAACATA-TTAAA
*
192035 ATTTTATAAGAACATATTAAA
1 ATTATATAA-AACATATTAAA
192056 ATTATATAAAA
1 ATTATATAAAA
192067 ATCATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.19
21 17 0.63
22 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTATATAAAACATATTAAA
Found at i:192072 original size:22 final size:23
Alignment explanation
Indices: 192021--192072 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
192011 AAACATTAAT
*
192021 AAAAT-ATATTTAAAATTTTATA
1 AAAATCATATTTAAAATTATATA
*
192043 AGAA-CATA-TTAAAATTATATA
1 AAAATCATATTTAAAATTATATA
192064 AAAATCATA
1 AAAATCATA
192073 AAAAGTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
AAAATCATATTTAAAATTATATA
Found at i:192608 original size:19 final size:17
Alignment explanation
Indices: 192580--192633 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 17
192570 ATTTTTTGAG
192580 AATTCTAATACATTTTTT
1 AATT-TAATACATTTTTT
*
192598 AATTTTAAATAAATTTTTTT
1 AA-TTT-AATACA-TTTTTT
192618 AATTTAATACATTTTT
1 AATTTAATACATTTTT
192634 AAAATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 5 0.16
18 8 0.26
19 10 0.32
20 8 0.26
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTAATACATTTTTT
Found at i:192626 original size:18 final size:18
Alignment explanation
Indices: 192592--192652 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
192582 TTCTAATACA
192592 TTTTTTAATTTTAAATAAAT
1 TTTTTTAA-TTT-AATAAAT
*
192612 TTTTTTAATTTAATACAT
1 TTTTTTAATTTAATAAAT
** * *
192630 TTTTAAAATTTATTAAGT
1 TTTTTTAATTTAATAAAT
192648 TTTTT
1 TTTTT
192653 ATATTTTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 23 0.68
19 3 0.09
20 8 0.24
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTTAATTTAATAAAT
Found at i:192682 original size:24 final size:25
Alignment explanation
Indices: 192637--192684 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
192627 CATTTTTAAA
192637 ATTTATTAAGTTTTTTATATTTTAT
1 ATTTATTAAGTTTTTTATATTTTAT
192662 ATTTA-TAA-TTTTTTATAATTTTA
1 ATTTATTAAGTTTTTTAT-ATTTTA
192685 ATAACTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
24 9 0.41
25 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTATTAAGTTTTTTATATTTTAT
Found at i:192694 original size:24 final size:22
Alignment explanation
Indices: 192642--192694 Score: 52
Period size: 24 Copynumber: 2.2 Consensus size: 22
192632 TTAAAATTTA
**
192642 TTAAGTTTTTTATATTTTATATT
1 TTAA-TTTTTTATATTTTATAAC
192665 TATAATTTTTTATAATTTTAATAAC
1 T-TAATTTTTTAT-ATTTT-ATAAC
192690 TTAAT
1 TTAAT
192695 AGGAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.36
24 12 0.48
25 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTAATTTTTTATATTTTATAAC
Found at i:196320 original size:24 final size:23
Alignment explanation
Indices: 196277--196325 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
196267 AGTAATAATC
*
196277 TTAATATTTTATTAGAAAATTATA
1 TTAATATTTTAATAGAAAA-TATA
196301 TTAATATTTTAATA-ATAAATATA
1 TTAATATTTTAATAGA-AAATATA
196324 TT
1 TT
196326 GTAATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAATATTTTAATAGAAAATATA
Found at i:196720 original size:22 final size:22
Alignment explanation
Indices: 196695--196736 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
196685 TAACAAGTAC
196695 AATT-AATCAATATAAGTTATGA
1 AATTAAATCAAT-TAAGTTATGA
*
196717 AATTAAATTAATTAAGTTAT
1 AATTAAATCAATTAAGTTAT
196737 AATGAGTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AATTAAATCAATTAAGTTATGA
Found at i:196944 original size:17 final size:17
Alignment explanation
Indices: 196910--196950 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
196900 ACATGATATT
*
196910 TAATCATTTTATTGAAA
1 TAATCATTTTAATGAAA
196927 TAAT-ATTTTAATG-AA
1 TAATCATTTTAATGAAA
196942 -AATCATTTT
1 TAATCATTTT
196951 TATTCAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 7 0.32
16 8 0.36
17 4 0.18
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (17 bp):
TAATCATTTTAATGAAA
Found at i:204141 original size:31 final size:32
Alignment explanation
Indices: 204105--204185 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 32
204095 GATCTTCAAA
* *
204105 AAGTTTAAGTACCAATTTAAGAAAAA-CTGTC
1 AAGTTTAGGTACCAAATTAAGAAAAATCTGTC
* * *
204136 AAGTTTTGGTACCAAATTAGGAAAAATGTGTC
1 AAGTTTAGGTACCAAATTAAGAAAAATCTGTC
*
204168 AAGTTTGGGTACCAAATT
1 AAGTTTAGGTACCAAATT
204186 GGACGAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 22 0.51
32 21 0.49
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.31
Consensus pattern (32 bp):
AAGTTTAGGTACCAAATTAAGAAAAATCTGTC
Found at i:204173 original size:32 final size:31
Alignment explanation
Indices: 204113--204185 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
204103 AAAAGTTTAA
* *
204113 GTACCAATTTAAGAAAAACTGTCAAGTTTTG
1 GTACCAAATTAAGAAAAACTGTCAAGTTTGG
* *
204144 GTACCAAATTAGGAAAAATGTGTCAAGTTTGG
1 GTACCAAATTAAGAAAAA-CTGTCAAGTTTGG
204176 GTACCAAATT
1 GTACCAAATT
204186 GGACGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 16 0.43
32 21 0.57
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (31 bp):
GTACCAAATTAAGAAAAACTGTCAAGTTTGG
Found at i:204770 original size:19 final size:19
Alignment explanation
Indices: 204746--204801 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
204736 AGACCTATTC
204746 ATTTTAATATATATTTTAT
1 ATTTTAATATATATTTTAT
* * *
204765 ATTTTATTCA-ATATGTTGT
1 ATTTTAAT-ATATATTTTAT
*
204784 ATTTTTATATAT-TTTTAT
1 ATTTTAATATATATTTTAT
204802 TAAAATTTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
18 5 0.18
19 22 0.79
20 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTTTAATATATATTTTAT
Found at i:211982 original size:80 final size:76
Alignment explanation
Indices: 211892--212037 Score: 202
Period size: 80 Copynumber: 1.9 Consensus size: 76
211882 TATGCCCTCT
* * * *
211892 GACCTGTACTCCTCAGGCTTTTACAATTTAATCCCTCTAGTTTTATTTTTTTTTAAAAACTTAAT
1 GACCTATACTCCTCAGGCTTGTACAATTTAATCCCTCTA---CT-TTTGTTTTTAAAAACTTAAT
211957 CCTTTACTTTGAACG
62 CCTTTACTTTGAACG
* *
211972 GACCTATACTCTTCAGGCTTGTACAATTTAATTCCTCTACTTTTGTTTTTAAAAACTTAATCCTT
1 GACCTATACTCCTCAGGCTTGTACAATTTAATCCCTCTACTTTTGTTTTTAAAAACTTAATCCTT
212037 T
66 T
212038 GGTTTAATTG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
76 24 0.40
77 1 0.02
80 35 0.58
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.45
Consensus pattern (76 bp):
GACCTATACTCCTCAGGCTTGTACAATTTAATCCCTCTACTTTTGTTTTTAAAAACTTAATCCTT
TACTTTGAACG
Found at i:212807 original size:13 final size:14
Alignment explanation
Indices: 212789--212817 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
212779 ATTCAAAAGC
212789 TTTCCATTTT-TGT
1 TTTCCATTTTATGT
212802 TTTCCATTTTATGT
1 TTTCCATTTTATGT
212816 TT
1 TT
212818 CTTAGCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (14 bp):
TTTCCATTTTATGT
Found at i:225387 original size:32 final size:31
Alignment explanation
Indices: 225323--225387 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
225313 ATACTTTAGT
* * * **
225323 TTGGTGAATTTTACTTTTGTACTTTTTCAAA
1 TTGGTCAATTTTAATTTTATACTTTTAAAAA
225354 TTGGTCAATTTTAATTATTATACTTTTAAAAA
1 TTGGTCAATTTTAATT-TTATACTTTTAAAAA
225386 TT
1 TT
225388 TAAATTTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (31 bp):
TTGGTCAATTTTAATTTTATACTTTTAAAAA
Found at i:225476 original size:14 final size:14
Alignment explanation
Indices: 225457--225484 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
225447 TGCATAAAAT
225457 TTTAGATTTGTTAA
1 TTTAGATTTGTTAA
225471 TTTAGATTTGTTAA
1 TTTAGATTTGTTAA
225485 GATGGTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
TTTAGATTTGTTAA
Found at i:228027 original size:23 final size:23
Alignment explanation
Indices: 228000--228046 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
227990 TCAAGTCAAT
* *
228000 AGGGAATATTTGGTAACTACAAC
1 AGGGAATATTTAGCAACTACAAC
228023 AGGGAATATTTAGCAACTACAAC
1 AGGGAATATTTAGCAACTACAAC
228046 A
1 A
228047 TAAGCTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (23 bp):
AGGGAATATTTAGCAACTACAAC
Found at i:233034 original size:20 final size:20
Alignment explanation
Indices: 233011--233049 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
233001 GAAGACTTAG
*
233011 AAAATCGAAAATCCCTCTAA
1 AAAATCGAAAAACCCTCTAA
233031 AAAATCGAAAAACCCTCTA
1 AAAATCGAAAAACCCTCTA
233050 TTTATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.26, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAATCGAAAAACCCTCTAA
Found at i:234243 original size:3 final size:3
Alignment explanation
Indices: 234235--234265 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
234225 TTCCCTTCTC
*
234235 CAT CAT CAT CTT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
234266 CTCACCATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:238764 original size:9 final size:8
Alignment explanation
Indices: 238740--238780 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
238730 ATAATAAAAA
238740 TATAATTT
1 TATAATTT
238748 TATAATTT
1 TATAATTT
238756 TATTAA-TT
1 TA-TAATTT
238764 TAT-ATCTT
1 TATAAT-TT
238772 TATAATTT
1 TATAATTT
238780 T
1 T
238781 GAAAAGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 1 0.03
7 1 0.03
8 22 0.76
9 5 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (8 bp):
TATAATTT
Found at i:238833 original size:23 final size:22
Alignment explanation
Indices: 238787--238833 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
238777 TTTTGAAAAG
* *
238787 ATTAAATTAAATTTTTATAGTT
1 ATTAAATTAAAATTTTATAATT
*
238809 ATTAATTTAAAATTTTATAAATT
1 ATTAAATTAAAATTTTAT-AATT
238832 AT
1 AT
238834 AAAAGAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTAAATTAAAATTTTATAATT
Found at i:246932 original size:29 final size:30
Alignment explanation
Indices: 246894--246955 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
246884 ATTTCACGTG
* *
246894 TATAAATGCACA-AAATTAAAGTTTATGTA
1 TATAAATGCACATAAATCAAAGTTCATGTA
*
246923 TATAATTGCACATTAAATCAAAGTTCATGTA
1 TATAAATGCACA-TAAATCAAAGTTCATGTA
246954 TA
1 TA
246956 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
31 17 0.61
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (30 bp):
TATAAATGCACATAAATCAAAGTTCATGTA
Found at i:246956 original size:29 final size:27
Alignment explanation
Indices: 246892--246958 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
246882 GAATTTCACG
* * *
246892 TGTATAAATGCACAAAATTAAAGTTTA
1 TGTATAATTGCACAAAATCAAAGTTCA
246919 TGTATATAATTGCACATTAAATCAAAGTTCA
1 TG--TATAATTGCACA--AAATCAAAGTTCA
246950 TGTATAATT
1 TGTATAATT
246959 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
29 18 0.55
31 13 0.39
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCACAAAATCAAAGTTCA
Found at i:247533 original size:17 final size:18
Alignment explanation
Indices: 247503--247536 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
247493 AAAATTATTT
247503 TTTAAATTCAATTTAAAA
1 TTTAAATTCAATTTAAAA
247521 TTTAAATTC-ATTTAAA
1 TTTAAATTCAATTTAAA
247537 TTAATTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAATTCAATTTAAAA
Found at i:247694 original size:21 final size:20
Alignment explanation
Indices: 247648--247694 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
247638 TCTAAATTTG
*
247648 AAATTTTCATTTAATTTTTT
1 AAATTTTCATATAATTTTTT
*
247668 ATATTTTC-TATATATTTTTAT
1 AAATTTTCATATA-ATTTTT-T
247689 AAATTT
1 AAATTT
247695 CTAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 13 0.59
21 6 0.27
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
AAATTTTCATATAATTTTTT
Found at i:251077 original size:15 final size:15
Alignment explanation
Indices: 251034--251078 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
251024 ATTGTCTTAA
251034 TATTTTATTTTTTTTC
1 TATTTT-TTTTTTTTC
**
251050 TAGGTTTTTTTTTTC
1 TATTTTTTTTTTTTC
251065 TATTTTTTTTTTTT
1 TATTTTTTTTTTTT
251079 TTTAATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.09, C:0.04, G:0.04, T:0.82
Consensus pattern (15 bp):
TATTTTTTTTTTTTC
Found at i:251087 original size:16 final size:16
Alignment explanation
Indices: 251035--251087 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
251025 TTGTCTTAAT
251035 ATTTTATTTTTTTTCT-
1 ATTTT-TTTTTTTTCTA
**
251051 AGGTTTTTTTTTTCTA
1 ATTTTTTTTTTTTCTA
* *
251067 TTTTTTTTTTTTTTTA
1 ATTTTTTTTTTTTCTA
251083 ATTTT
1 ATTTT
251088 GTCATTTGGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (16 bp):
ATTTTTTTTTTTTCTA
Found at i:257172 original size:14 final size:15
Alignment explanation
Indices: 257153--257182 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
257143 AATATCATTC
257153 TTTTTTTTAT-TTTT
1 TTTTTTTTATCTTTT
257167 TTTTTTTTATCTTTT
1 TTTTTTTTATCTTTT
257182 T
1 T
257183 ATGTAGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.07, C:0.03, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTATCTTTT
Found at i:261585 original size:18 final size:18
Alignment explanation
Indices: 261547--261592 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
261537 TCGAAAAAAA
* *
261547 AATTCGAGTTGACTTGAAT
1 AATTCGA-TTAACTCGAAT
261566 AATTCGATTAACTCGAAT
1 AATTCGATTAACTCGAAT
*
261584 AACTCGATT
1 AATTCGATT
261593 CGTTCAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (18 bp):
AATTCGATTAACTCGAAT
Found at i:263221 original size:21 final size:20
Alignment explanation
Indices: 263192--263230 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
263182 ATATTAAAAC
263192 TTTTAATTAAATTAAATAAAT
1 TTTTAATTAAA-TAAATAAAT
* *
263213 TTTTTATTACATAAATAA
1 TTTTAATTAAATAAATAA
263231 GTCAAGCACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAATTAAATAAATAAAT
Found at i:277164 original size:35 final size:35
Alignment explanation
Indices: 277121--277193 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
277111 CACACAGTTA
* *
277121 TAGTTCCAATTGTGCTTCTCTATGATAGATAAAGT
1 TAGTTCCAATTGTGCTTCTCTAGGATAAATAAAGT
*
277156 TAGTTCCAATTGTGCTTCTCTAGGATAAATAAATT
1 TAGTTCCAATTGTGCTTCTCTAGGATAAATAAAGT
277191 TAG
1 TAG
277194 AGATATTGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (35 bp):
TAGTTCCAATTGTGCTTCTCTAGGATAAATAAAGT
Found at i:281473 original size:28 final size:30
Alignment explanation
Indices: 281418--281473 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
281408 AATTCTTTCT
* *
281418 TATCAACAATCAACGATATGCAATCCTATC
1 TATCAACAATCAACAATATGCAAGCCTATC
*
281448 TATCAA-AAT-AACAATATGTAAGCCTA
1 TATCAACAATCAACAATATGCAAGCCTA
281474 CCAGCTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 3 0.13
30 6 0.26
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (30 bp):
TATCAACAATCAACAATATGCAAGCCTATC
Found at i:288384 original size:12 final size:12
Alignment explanation
Indices: 288367--288407 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
288357 TTAAATAAAT
288367 ATAATTATATTA
1 ATAATTATATTA
*
288379 ATAATTATACTA
1 ATAATTATATTA
288391 AT-ATTA-ATTA
1 ATAATTATATTA
*
288401 AAAATTA
1 ATAATTA
288408 ATTTAAATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
10 4 0.16
11 8 0.32
12 13 0.52
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAATTATATTA
Found at i:288387 original size:18 final size:18
Alignment explanation
Indices: 288347--288398 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
288337 AAAATATATT
*
288347 TATATTAATATTAAATAAA
1 TATAATAATATT-AATAAA
* *
288366 TATAATTATATTAATAAT
1 TATAATAATATTAATAAA
*
288384 TATACTAATATTAAT
1 TATAATAATATTAAT
288399 TAAAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAATAATATTAATAAA
Found at i:292232 original size:15 final size:15
Alignment explanation
Indices: 292182--292233 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
292172 TAACGGTAAT
292182 AAAAT-ATATATTTA
1 AAAATAATATATTTA
*
292196 ATAAATAATA-ATTGA
1 A-AAATAATATATTTA
*
292211 AATAATAATATTTTTA
1 AA-AATAATATATTTA
292227 AAAATAA
1 AAAATAA
292234 AAATAATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.06
15 21 0.68
16 8 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AAAATAATATATTTA
Found at i:298934 original size:35 final size:36
Alignment explanation
Indices: 298870--298978 Score: 166
Period size: 35 Copynumber: 3.1 Consensus size: 36
298860 NNNNNNNNNN
*
298870 TTTTGTGTTGGCCATGCAATGGCCGACACCTCTTTT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCTCTTTT
298906 TTTTGTGTTGGTCATGC-ATGGCCGACACCTCTTTT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCTCTTTT
* ** *
298941 TTTTGTGTTGGTCATACAATGATCGACACCCCTTTT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCTCTTTT
298977 TT
1 TT
298979 ATATGGTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 34 0.51
36 33 0.49
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (36 bp):
TTTTGTGTTGGTCATGCAATGGCCGACACCTCTTTT
Found at i:299047 original size:61 final size:60
Alignment explanation
Indices: 298937--299090 Score: 229
Period size: 60 Copynumber: 2.6 Consensus size: 60
298927 CCGACACCTC
* *
298937 TTTTTTTTGTGTTGGTCATACAATGATCGACA-CCCCTTTTTTATATGGTAAAAAATTAAT
1 TTTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCCTTTTTTATATGGT-AAAAATTAAT
* * *
298997 TTTTTTTTATGTTGGTCATGCAATGGTCGACACCCCCTTTTTTATCTGGTAAAAATTTAT
1 TTTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCCTTTTTTATATGGTAAAAATTAAT
* *
299057 TTTTTTTTGTGTTGGCCATGCAATGGACGACACC
1 TTTTTTTTGTGTTGGTCATGCAATGGTCGACACC
299091 AATTTTCCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
60 69 0.81
61 16 0.19
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (60 bp):
TTTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCCTTTTTTATATGGTAAAAATTAAT
Found at i:299905 original size:30 final size:30
Alignment explanation
Indices: 299871--299968 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 30
299861 AAAAAATAAT
* * *
299871 AATTAGAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAAGAAATTACAAATTAA
*
299901 AATTAAAATATACAAGAAATTATAAATTAA
1 AATTAAAATATACAAGAAATTACAAATTAA
* *
299931 ATTTAAAATA-AAAACGAAATTACAAATTAA
1 AATTAAAATATACAA-GAAATTACAAATTAA
*
299961 ATTTAAAA
1 AATTAAAA
299969 AATAAACGGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 3 0.05
30 58 0.95
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (30 bp):
AATTAAAATATACAAGAAATTACAAATTAA
Found at i:300752 original size:22 final size:21
Alignment explanation
Indices: 300737--300797 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
300727 AATTGGGGTG
300737 TTGGTGAGCTGGAATTTCGGTT
1 TTGGTGAGCTGGAATTTCGG-T
* *
300759 TTGATGAGCTGGAATTTCAGT
1 TTGGTGAGCTGGAATTTCGGT
300780 TTAGGTGAGCTGGAATTT
1 TT-GGTGAGCTGGAATTT
300798 GAGTGGTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 3 0.09
22 32 0.91
ACGTcount: A:0.20, C:0.08, G:0.33, T:0.39
Consensus pattern (21 bp):
TTGGTGAGCTGGAATTTCGGT
Found at i:300994 original size:84 final size:83
Alignment explanation
Indices: 300891--301087 Score: 340
Period size: 84 Copynumber: 2.3 Consensus size: 83
300881 AAATTTAAAT
300891 TTTGATAAAAATTGAAATATAATAATAATTTTTAATTTAAATATTAAAATTTGATAAATAATGTA
1 TTTGATAAAAATT-AAATATAATAATAATTTTTAATTTAAATATTAAAATTTGATAAATAATGTA
*
300956 TTGTCAAATCAATACATTA
65 TTGTCAAATCAACACATTA
*
300975 TTTGATAAAAATTATAATATAATAATAATTTTTTATTTAAATATTAAAATTTGATAAATAATGTA
1 TTTGATAAAAATTA-AATATAATAATAATTTTTAATTTAAATATTAAAATTTGATAAATAATGTA
301040 TTGTCAAATCAACACATTA
65 TTGTCAAATCAACACATTA
*
301059 TTTGATATAAATTAAAATATAATAATAAT
1 TTTGATAAAAATT-AAATATAATAATAAT
301088 AATTTTTTTT
Statistics
Matches: 108, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
83 1 0.01
84 106 0.98
85 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (83 bp):
TTTGATAAAAATTAAATATAATAATAATTTTTAATTTAAATATTAAAATTTGATAAATAATGTAT
TGTCAAATCAACACATTA
Found at i:301242 original size:11 final size:12
Alignment explanation
Indices: 301221--301268 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
301211 AACGTGTACC
301221 TTAATTTTCAAA
1 TTAATTTTCAAA
*
301233 TTAATTTCAACTTAAA
1 TTAATTT----TCAAA
301249 TTAATTTTCAAA
1 TTAATTTTCAAA
301261 TTAATTTT
1 TTAATTTT
301269 TACACAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 19 0.63
16 11 0.37
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTCAAA
Found at i:301266 original size:16 final size:16
Alignment explanation
Indices: 301230--301264 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
301220 CTTAATTTTC
*
301230 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
301246 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
301263 AA
1 AA
301265 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:301277 original size:28 final size:28
Alignment explanation
Indices: 301221--301277 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
301211 AACGTGTACC
**
301221 TTAATTTTCAAATTAATTTCAACTTAAA
1 TTAATTTTCAAATTAATTTCAACACAAA
**
301249 TTAATTTTCAAATTAATTTTTACACAAA
1 TTAATTTTCAAATTAATTTCAACACAAA
301277 T
1 T
301278 ATTCTTCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (28 bp):
TTAATTTTCAAATTAATTTCAACACAAA
Found at i:302075 original size:26 final size:25
Alignment explanation
Indices: 302039--302088 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
302029 TTATTTTCAT
302039 TTATTTCTTAAAATTAATTTTAATTA
1 TTATTTCTTAAAA-TAATTTTAATTA
* * *
302065 TTATTTTTTAATATATTTTTAATT
1 TTATTTCTTAAAATAATTTTAATT
302089 CGTCGATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATTTCTTAAAATAATTTTAATTA
Found at i:302886 original size:60 final size:60
Alignment explanation
Indices: 302819--303012 Score: 266
Period size: 61 Copynumber: 3.2 Consensus size: 60
302809 AGGGAAAGTT
* * *
302819 GGTGTCGGCCATTGCATGGCCAACA-TAAAAAAAATTGATTTTTTACCAAATAAAAAAGAG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAAAATTGATTTTTTACCAGATAAAAAA-AG
302879 GGTGTCGGCCATTGCATGACCAACACAAAAAAAAATTGATTTTTTACCAGATAAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAAAATTGATTTTTTACCAGATAAAAAAA-G
* * * * *
302940 GGAGTTGGTCATTGCATGACCAACACCAAAAAAAATTTAAATTTTTTACCAGAT-AAAAAAG
1 GGTGTCGGCCATTGCATGACCAACA-CAAAAAAAAATT-GATTTTTTACCAGATAAAAAAAG
303001 GGTGTCGGCCAT
1 GGTGTCGGCCAT
303013 GCAAAAAATT
Statistics
Matches: 119, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
60 25 0.21
61 63 0.53
62 17 0.14
63 14 0.12
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (60 bp):
GGTGTCGGCCATTGCATGACCAACACAAAAAAAAATTGATTTTTTACCAGATAAAAAAAG
Found at i:303119 original size:60 final size:59
Alignment explanation
Indices: 303055--303205 Score: 205
Period size: 59 Copynumber: 2.5 Consensus size: 59
303045 GGGTCGACAC
* * * *
303055 CCAAAAATATGATTTTTTTTATTCAGATAAAAAGGGGTGCCGGTCATGCAATGGCCAACA-
1 CCAAAAATTTGA-TTTTTTTA-TCAGACAAAAAGGGGTGCCGATCATGCAATGACCAACAT
*
303115 CCAAAAAATTTGATTTTTTTATCAGACAAAAAGGGGTGTCGATCATGCAATGACCAACAT
1 CC-AAAAATTTGATTTTTTTATCAGACAAAAAGGGGTGCCGATCATGCAATGACCAACAT
* *
303175 CCAAAAATTTGAATTTTTTATCTGACAAAAA
1 CCAAAAATTTGATTTTTTTATCAGACAAAAA
303206 AAGGGTGTCG
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
59 61 0.74
60 12 0.15
61 9 0.11
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (59 bp):
CCAAAAATTTGATTTTTTTATCAGACAAAAAGGGGTGCCGATCATGCAATGACCAACAT
Found at i:303234 original size:60 final size:60
Alignment explanation
Indices: 303069--303221 Score: 175
Period size: 59 Copynumber: 2.5 Consensus size: 60
303059 AAATATGATT
* * * ** * *
303069 TTTTTTATTCAGATAAAAAGGGGTGCCGGTCATGCAATGGCCAACA-CCAAAAAATTTGAT
1 TTTTTTA-TCAGACAAAAAAGGGTGTCGACCATGCAATGACCAACATCCAAAAAATTTGAA
* *
303129 TTTTTTATCAGACAAAAAGGGGTGTCGATCATGCAATGACCAACATCC-AAAAATTTGAA
1 TTTTTTATCAGACAAAAAAGGGTGTCGACCATGCAATGACCAACATCCAAAAAATTTGAA
* *
303188 TTTTTTATCTGACAAAAAAAGGGTGTCGGCCATG
1 TTTTTTATCAGAC-AAAAAAGGGTGTCGACCATG
303222 ACATAGTCAA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
59 56 0.68
60 26 0.32
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (60 bp):
TTTTTTATCAGACAAAAAAGGGTGTCGACCATGCAATGACCAACATCCAAAAAATTTGAA
Found at i:304688 original size:16 final size:17
Alignment explanation
Indices: 304650--304692 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
304640 TGAATAAAGT
*
304650 ATATACATTCTCTCTTC
1 ATATACATTCACTCTTC
*
304667 AT-TACATTCAGTC-TC
1 ATATACATTCACTCTTC
304682 ATATACATTCA
1 ATATACATTCA
304693 TCCCACCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 17 0.74
17 2 0.09
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.42
Consensus pattern (17 bp):
ATATACATTCACTCTTC
Found at i:317136 original size:28 final size:28
Alignment explanation
Indices: 317094--317171 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 28
317084 AAATTTTAAA
* *
317094 TTAATAATGATAAAATTATATTTTGA-TCT
1 TTAA-AATAATAAAATTATAATTT-ATTCT
317123 TTAAAATAATAAAAATT-TAATTTATTCT
1 TTAAAATAAT-AAAATTATAATTTATTCT
* *
317151 TTAAAAATTATAAAAATATAA
1 TT-AAAATAATAAAATTATAA
317172 ACTATTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.02
28 20 0.49
29 20 0.49
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (28 bp):
TTAAAATAATAAAATTATAATTTATTCT
Found at i:317177 original size:29 final size:28
Alignment explanation
Indices: 317120--317177 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
317110 TATATTTTGA
* **
317120 TCTTTAAAATAATAAAAATTTAATTTAT
1 TCTTTAAAATAATAAAAATATAAACTAT
*
317148 TCTTTAAAAATTATAAAAATATAAACTAT
1 TCTTT-AAAATAATAAAAATATAAACTAT
317177 T
1 T
317178 AAAATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (28 bp):
TCTTTAAAATAATAAAAATATAAACTAT
Found at i:319434 original size:32 final size:32
Alignment explanation
Indices: 319398--319468 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
319388 ATTTTTTCTT
319398 TTATTTTTTTTCTCATTT-TCCAATGAATGCAG
1 TTATTTTTTTTCT-ATTTGTCCAATGAATGCAG
* *
319430 TTATTTTTTTTCTTTTTGTTCAATGAATGCAG
1 TTATTTTTTTTCTATTTGTCCAATGAATGCAG
319462 TTGATTT
1 TT-ATTT
319469 CTTTCTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 3 0.09
32 28 0.80
33 4 0.11
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (32 bp):
TTATTTTTTTTCTATTTGTCCAATGAATGCAG
Found at i:324616 original size:23 final size:23
Alignment explanation
Indices: 324590--324635 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
324580 GTGGTTAGAA
324590 CAATTATAACTTGAAGATGTTTT
1 CAATTATAACTTGAAGATGTTTT
324613 CAATTATAACTTGAAGATGTTTT
1 CAATTATAACTTGAAGATGTTTT
324636 TTTTAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (23 bp):
CAATTATAACTTGAAGATGTTTT
Done.