Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167954.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_214, 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: 50219
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:717 original size:152 final size:152
Alignment explanation
Indices: 441--718 Score: 511
Period size: 152 Copynumber: 1.8 Consensus size: 152
431 TAGTTGTTGA
*
441 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
* *
506 TATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGGATTTATTAAAGAAAATACA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAATACA
571 AAATCATCCAATTAATTATTGG
131 AAATCATCCAATTAATTATTGG
593 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
* *
658 TATGCAAGAAAAACTACTGTTTCACTTGTAGAGGCTCTGTCGTCGGATTAATTAAAGAAAA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAA
719 AAGAAAAAAA
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 121 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (152 bp):
AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAATACA
AAATCATCCAATTAATTATTGG
Found at i:1216 original size:20 final size:21
Alignment explanation
Indices: 1182--1226 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
1172 CGAAAATTCA
*
1182 CCGGTTTCTTGGGATTCTTTG
1 CCGGTTTCTTGGGATTCTTCG
1203 CCGGTTTC-TGGGATTCTTCG
1 CCGGTTTCTTGGGATTCTTCG
1223 CCGG
1 CCGG
1227 AAACTGGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.04, C:0.24, G:0.31, T:0.40
Consensus pattern (21 bp):
CCGGTTTCTTGGGATTCTTCG
Found at i:1233 original size:20 final size:20
Alignment explanation
Indices: 1191--1234 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1181 ACCGGTTTCT
* ***
1191 TGGGATTCTTTGCCGGTTTC
1 TGGGATTCTTCGCCGGAAAC
1211 TGGGATTCTTCGCCGGAAAC
1 TGGGATTCTTCGCCGGAAAC
1231 TGGG
1 TGGG
1235 CAGTTCACCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.34, T:0.34
Consensus pattern (20 bp):
TGGGATTCTTCGCCGGAAAC
Found at i:1918 original size:16 final size:15
Alignment explanation
Indices: 1893--1933 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1883 CACAAGAGAG
1893 AAAAAAAAATAAAAT
1 AAAAAAAAATAAAAT
1908 AAAATAAAAATAAAA-
1 AAAA-AAAAATAAAAT
*
1923 AATAAAAAATA
1 AAAAAAAAATA
1934 CGGGTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 7 0.29
16 10 0.42
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAAAAATAAAAT
Found at i:2025 original size:20 final size:20
Alignment explanation
Indices: 1970--2028 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1960 CCATTTGGGG
* *
1970 CAGGCCCAAATGATCTGGGT
1 CAGGCCCAATTGATCCGGGT
1990 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
2010 CAGGCCCAATTGATCCGGG
1 CAGGCCCAATTGATCCGGG
2029 CCCGGACCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.19
Consensus pattern (20 bp):
CAGGCCCAATTGATCCGGGT
Found at i:2148 original size:1 final size:1
Alignment explanation
Indices: 2144--2244 Score: 94
Period size: 1 Copynumber: 101.0 Consensus size: 1
2134 TCATTTTTGA
* * * * ** ** *
2144 TTTTTTTTTTTTATTTTTGTTTTTATTTTTTTTTATTTTTTTGATTTTTTTGATTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2209 TTTGTTTTTTTGTTTTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2245 GGTCGAAGCT
Statistics
Matches: 78, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.05, C:0.00, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:2380 original size:42 final size:42
Alignment explanation
Indices: 2252--2855 Score: 851
Period size: 42 Copynumber: 14.6 Consensus size: 42
2242 TTTGGTCGAA
* * * * * *
2252 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
* *
2293 GCTCCTCTAAACAGAGGCA--ACGGACTTTGG-AAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCAC-GACTTTGGAAAAATAAATT
2333 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
2375 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
2417 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
* *
2458 GCTCCTCTAAACAGAGGCA--ACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACG-ACTTTGGAAAAATAAATT
* **
2498 GCTCCTCTAAACAGAGGCACCACGACTTTTAAAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGAC-TTTGGAAAAATAAATT
* *
2541 GCTCCTCTAAACAGAGGCA--ACGGACTTTGG-AAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCAC-GACTTTGGAAAAATAAATT
*
2581 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
2622 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
2664 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
2705 GCTCCTCTCAACAGAGGCACCACGAC-TT-CAAAAAGTAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAA-TAAATT
* * *
2746 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
2788 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAAATAAATT
1 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
2830 GCTCCTCTCAACAGAGGCACCACGAC
1 GCTCCTCTCAACAGAGGCACCACGAC
2856 AGAGGCACCA
Statistics
Matches: 524, Mismatches: 22, Indels: 33
0.91 0.04 0.06
Matches are distributed among these distances:
39 5 0.01
40 106 0.20
41 173 0.33
42 206 0.39
43 34 0.06
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (42 bp):
GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
Found at i:2465 original size:83 final size:83
Alignment explanation
Indices: 2252--2855 Score: 863
Period size: 83 Copynumber: 7.3 Consensus size: 83
2242 TTTGGTCGAA
* * * * * *
2252 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCA--AC
1 GCTCCTCTCAACAGAGGCACCACGAC-TTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
*
2314 GGACTTTGG-AAAGTAAATT
65 -GACTTTGGAAAAATAAATT
2333 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
2398 GACTTTGGAAAAATAAATT
65 GACTTTGGAAAAATAAATT
* *
2417 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
1 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
*
2480 AACTTT-GAAAAGTAAATT
66 -ACTTTGGAAAAATAAATT
* * *
2498 GCTCCTCTAAACAGAGGCACCACGACTTTTAAAAAAATAAATTGCTCCTCTAAACAGAGGCA--A
1 GCTCCTCTCAACAGAGGCACCACGAC-TTT-GAAAAATAAATTGCTCCTCTCAACAGAGGCACCA
*
2561 CGGACTTTGG-AAAGTAAATT
64 C-GACTTTGGAAAAATAAATT
* *
2581 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACG
1 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
2646 ACTTTGGAAAAATAAATT
66 ACTTTGGAAAAATAAATT
2664 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
1 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
*
2729 AC-TT-CAAAAAGTAAATT
66 ACTTTGGAAAAA-TAAATT
* *
2746 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTCAACAGAGGCACCACGACTTTG-AAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
*
2811 GACTTTGAAAAAATAAATT
65 GACTTTGGAAAAATAAATT
2830 GCTCCTCTCAACAGAGGCACCACGAC
1 GCTCCTCTCAACAGAGGCACCACGAC
2856 AGAGGCACCA
Statistics
Matches: 479, Mismatches: 27, Indels: 31
0.89 0.05 0.06
Matches are distributed among these distances:
80 3 0.01
81 94 0.20
82 82 0.17
83 221 0.46
84 74 0.15
85 5 0.01
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (83 bp):
GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
ACTTTGGAAAAATAAATT
Found at i:2543 original size:124 final size:123
Alignment explanation
Indices: 2252--2973 Score: 927
Period size: 124 Copynumber: 5.7 Consensus size: 123
2242 TTTGGTCGAA
* * * * * *
2252 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCA--AC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
* * *
2314 GGACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
66 -GACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCA-CACGACTTT-GAAAAGTAAATT
*
2375 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
* *
2440 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-ACGAACTTTGAAAAGTAAATT
66 GACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACACG-ACTTTGAAAAGTAAATT
** *
2498 GCTCCTCTAAACAGAGGCACCACGACTTTTAAAAAAATAAATTGCTCCTCTAAACAGAGGCA--A
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCA
* *
2561 CGGACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
65 C-GACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCA-CACGACTTTGAAAAGTAAATT
* *
2622 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
**
2687 GACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGACTTCAAAAAGTAAATT
66 GACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCA-CACGACTTTGAAAAGTAAATT
* *
2746 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
2811 GACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGACAGAGGCACCACGACTTTGAA
66 GACTTTG-AAAAATAAATTGCTCCTCT------------CA--ACAGAGGCA-CACGACTTTGAA
*
2876 AAATAAATT
115 AAGTAAATT
* *
2885 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
*
2949 GACTTTGAAAAAATAAATTACTCCT
66 GACTTTG-AAAAATAAATTGCTCCT
2974 TGACAATCAT
Statistics
Matches: 539, Mismatches: 35, Indels: 35
0.89 0.06 0.06
Matches are distributed among these distances:
122 2 0.00
123 132 0.24
124 230 0.43
125 59 0.11
126 2 0.00
137 2 0.00
138 57 0.11
139 55 0.10
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (123 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
GACTTTGAAAAATAAATTGCTCCTCTCAACAGAGGCACACGACTTTGAAAAGTAAATT
Found at i:2859 original size:14 final size:14
Alignment explanation
Indices: 2840--2869 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2830 GCTCCTCTCA
2840 ACAGAGGCACCACG
1 ACAGAGGCACCACG
2854 ACAGAGGCACCACG
1 ACAGAGGCACCACG
2868 AC
1 AC
2870 TTTGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.37, G:0.27, T:0.00
Consensus pattern (14 bp):
ACAGAGGCACCACG
Found at i:2898 original size:55 final size:56
Alignment explanation
Indices: 2798--2910 Score: 219
Period size: 55 Copynumber: 2.0 Consensus size: 56
2788 GCTCCTCTCA
2798 ACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
1 ACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
2854 ACAGAGGCACCACGACTTTG-AAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
1 ACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
2909 AC
1 AC
2911 TTTGAAAAGT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 37 0.65
56 20 0.35
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16
Consensus pattern (56 bp):
ACAGAGGCACCACGACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
Found at i:2911 original size:41 final size:41
Alignment explanation
Indices: 2854--2973 Score: 213
Period size: 41 Copynumber: 2.9 Consensus size: 41
2844 AGGCACCACG
2854 ACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCA
1 ACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCA
*
2895 ACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTCA
1 ACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCA
*
2936 ACAGAGGCACCACGACTTTGAAAAAATAAATTACTCCT
1 ACAGAGGCACCACGACTTTG-AAAAATAAATTGCTCCT
2974 TGACAATCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 60 0.80
42 15 0.20
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.22
Consensus pattern (41 bp):
ACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTCA
Found at i:4156 original size:9 final size:9
Alignment explanation
Indices: 4131--4225 Score: 62
Period size: 8 Copynumber: 11.2 Consensus size: 9
4121 TCGACTTGAA
4131 TCTCTTTTT
1 TCTCTTTTT
*
4140 T-T-TATTT
1 TCTCTTTTT
4147 TCTCATTTTT
1 TCTC-TTTTT
4157 TCT-TTTTT
1 TCTCTTTTT
4165 T-TCTTTTT
1 TCTCTTTTT
4173 TCT-TTTTT
1 TCTCTTTTT
*
4181 T-TCTTTGT
1 TCTCTTTTT
4189 T-T-TTTTT
1 TCTCTTTTT
4196 TCATCTTTTT
1 TC-TCTTTTT
* *
4206 TTTTTTTTT
1 TCTCTTTTT
* *
4215 TTTCATTTT
1 TCTCTTTTT
4224 TC
1 TC
4226 ATCTATTGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
7 12 0.18
8 26 0.38
9 17 0.25
10 13 0.19
ACGTcount: A:0.04, C:0.13, G:0.01, T:0.82
Consensus pattern (9 bp):
TCTCTTTTT
Found at i:4159 original size:10 final size:8
Alignment explanation
Indices: 4133--4214 Score: 64
Period size: 8 Copynumber: 10.1 Consensus size: 8
4123 GACTTGAATC
4133 TCTTTTTT
1 TCTTTTTT
*
4141 T-TATTTTC
1 TCT-TTTTT
*
4149 TCATTTTT
1 TCTTTTTT
4157 TCTTTTTT
1 TCTTTTTT
4165 T-TCTTTTT
1 TCT-TTTTT
4173 TCTTTTTTT
1 TC-TTTTTT
4182 TCTTTGTTT
1 TCTTT-TTT
*
4191 T-TTTTTCA
1 TCTTTTT-T
4199 TCTTTTTT
1 TCTTTTTT
4207 T-TTTTTT
1 TCTTTTTT
4214 T
1 T
4215 TTTCATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
7 11 0.18
8 32 0.53
9 16 0.27
10 1 0.02
ACGTcount: A:0.04, C:0.11, G:0.01, T:0.84
Consensus pattern (8 bp):
TCTTTTTT
Found at i:4214 original size:33 final size:33
Alignment explanation
Indices: 4133--4224 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 33
4123 GACTTGAATC
* * *
4133 TCTTTTTTTTATTTTCTCATTTTTTCTTTTTTT
1 TCTTTTTTTTTTTTTTTCATTTTTTCTTTTTTA
*
4166 TCTTTTTTCTTTTTTTTC-TTTGTTT-TTTTTTCA
1 TCTTTTTTTTTTTTTTTCATTT-TTTCTTTTTT-A
4199 TCTTTTTTTTTTTTTTTTTCATTTTT
1 TC--TTTTTTTTTTTTTTTCATTTTT
4225 CATCTATTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 9 0.18
33 20 0.41
35 17 0.35
36 3 0.06
ACGTcount: A:0.04, C:0.11, G:0.01, T:0.84
Consensus pattern (33 bp):
TCTTTTTTTTTTTTTTTCATTTTTTCTTTTTTA
Found at i:4224 original size:1 final size:1
Alignment explanation
Indices: 4152--4217 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
4142 TATTTTCTCA
* * * * * ** *
4152 TTTTTTCTTTTTTTTCTTTTTTCTTTTTTTTCTTTGTTTTTTTTTCATCTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4217 T
1 T
4218 CATTTTTCAT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.88
Consensus pattern (1 bp):
T
Found at i:4224 original size:16 final size:15
Alignment explanation
Indices: 4133--4214 Score: 92
Period size: 16 Copynumber: 5.1 Consensus size: 15
4123 GACTTGAATC
*
4133 TCTTTTTTTTATTTTC
1 TCTTTTTTTT-TTTTT
4149 TCATTTTTTCTTTTTTT
1 TC-TTTTTT-TTTTTTT
4166 TCTTTTTTCTTTTTTT
1 TCTTTTTT-TTTTTTT
*
4182 TCTTTGTTTTTTTTTCA
1 TCTTT-TTTTTTTTT-T
4199 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTT
4214 T
1 T
4215 TTTCATTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.02
16 36 0.61
17 20 0.34
18 2 0.03
ACGTcount: A:0.04, C:0.11, G:0.01, T:0.84
Consensus pattern (15 bp):
TCTTTTTTTTTTTTT
Found at i:4612 original size:1 final size:1
Alignment explanation
Indices: 4606--4635 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
4596 TTTTGTGGTG
4606 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4636 CAAAAATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8128 original size:152 final size:152
Alignment explanation
Indices: 7852--8129 Score: 502
Period size: 152 Copynumber: 1.8 Consensus size: 152
7842 TAGTTGTTGA
*
7852 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
* *
7917 TATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGGATTTATTAAAGAAAATACA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAATACA
7982 AAATCATCCAATTAATTATTGG
131 AAATCATCCAATTAATTATTGG
*
8004 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTTAAGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
* *
8069 TATGCAAGAAAAACTACTGTTTCACTTGTAGAGGCTCTGTCGTCGGATTAATTAAAGAAAA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAA
8130 AAGAAAAAAA
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
152 120 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (152 bp):
AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAATACA
AAATCATCCAATTAATTATTGG
Found at i:8184 original size:10 final size:10
Alignment explanation
Indices: 8169--8195 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
8159 GTCAAATAAA
8169 AAAAAAATTC
1 AAAAAAATTC
8179 AAAAAAATTC
1 AAAAAAATTC
8189 AAAAAAA
1 AAAAAAA
8196 AAAAACCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:8564 original size:20 final size:20
Alignment explanation
Indices: 8535--8580 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
8525 GGAAGATTCA
*
8535 CCGGATTCTGGGTTTTTTCG
1 CCGGAATCTGGGTTTTTTCG
8555 CCGGAATCTGGGTTTTTTCG
1 CCGGAATCTGGGTTTTTTCG
*
8575 TCGGAA
1 CCGGAA
8581 GTTGGTCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.11, C:0.20, G:0.30, T:0.39
Consensus pattern (20 bp):
CCGGAATCTGGGTTTTTTCG
Found at i:8622 original size:20 final size:20
Alignment explanation
Indices: 8597--8640 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
8587 CGGAAATTCA
*
8597 CCGGTTTCTGGGATTCTTTG
1 CCGGTTTCTGGGATTCTTCG
8617 CCGGTTTCTGGGATTCTTCG
1 CCGGTTTCTGGGATTCTTCG
8637 CCGG
1 CCGG
8641 AAACTGGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.05, C:0.25, G:0.32, T:0.39
Consensus pattern (20 bp):
CCGGTTTCTGGGATTCTTCG
Found at i:8627 original size:62 final size:63
Alignment explanation
Indices: 8525--8642 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 63
8515 GAACTCCGGT
* * * *
8525 GGAAGATTCACCGGATTCTGGGTTTTTTCGCCGGAATCTGGGTTTTTTCGTCGGAAGTTGGTC
1 GGAAGATTCACCGGATTCTGGGTTCTTTCGCCGGAATCTGGGATTCTTCGCCGGAAGTTGGTC
* **
8588 GGAA-ATTCACCGGTTTCTGGGATTCTTT-GCCGGTTTCTGGGATTCTTCGCCGGAA
1 GGAAGATTCACCGGATTCTGGG-TTCTTTCGCCGGAATCTGGGATTCTTCGCCGGAA
8643 ACTGGGCAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
62 38 0.81
63 9 0.19
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (63 bp):
GGAAGATTCACCGGATTCTGGGTTCTTTCGCCGGAATCTGGGATTCTTCGCCGGAAGTTGGTC
Found at i:8647 original size:20 final size:20
Alignment explanation
Indices: 8604--8648 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
8594 TCACCGGTTT
* ***
8604 CTGGGATTCTTTGCCGGTTT
1 CTGGGATTCTTCGCCGGAAA
8624 CTGGGATTCTTCGCCGGAAA
1 CTGGGATTCTTCGCCGGAAA
8644 CTGGG
1 CTGGG
8649 CAGTTCGCCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (20 bp):
CTGGGATTCTTCGCCGGAAA
Found at i:9072 original size:12 final size:12
Alignment explanation
Indices: 9055--9087 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
9045 CTAGCCCTCC
9055 AAAATAAAAATT
1 AAAATAAAAATT
9067 AAAAT-AAAATT
1 AAAATAAAAATT
9078 AAAA-AAAAAT
1 AAAATAAAAAT
9088 CTAGATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:9295 original size:44 final size:44
Alignment explanation
Indices: 9185--9296 Score: 106
Period size: 44 Copynumber: 2.5 Consensus size: 44
9175 AAAGATAAGA
9185 ATAATAATATAATAATAATAAATATATAACTATATACATATAAATCT
1 ATAATAATA-AATAAT-A-AAATATATAACTATATACATATAAATCT
** *
9232 ATTCTAATGAAA-AAAAAAATATAT-A-TATATACATATATTAATAC-
1 ATAATAAT-AAATAATAAAATATATAACTATATACATATA--AAT-CT
9276 ATAATAATAAATAATAAAATA
1 ATAATAATAAATAATAAAATA
9297 CACAAGAGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
42 12 0.22
43 4 0.07
44 25 0.46
45 2 0.04
46 2 0.04
47 8 0.15
48 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (44 bp):
ATAATAATAAATAATAAAATATATAACTATATACATATAAATCT
Found at i:9332 original size:16 final size:15
Alignment explanation
Indices: 9307--9347 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
9297 CACAAGAGAG
9307 AAAAAAAAATAAAAT
1 AAAAAAAAATAAAAT
9322 AAAATAAAAATAAAA-
1 AAAA-AAAAATAAAAT
*
9337 AATAAAAAATA
1 AAAAAAAAATA
9348 CGGGTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 7 0.29
16 10 0.42
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAAAAATAAAAT
Found at i:9439 original size:20 final size:20
Alignment explanation
Indices: 9384--9442 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
9374 CCATTTGGGG
* *
9384 CAGGCCCAAATGATCTGGGT
1 CAGGCCCAATTGATCCGGGT
9404 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
9424 CAGGCCCAATTGATCCGGG
1 CAGGCCCAATTGATCCGGG
9443 CCCGGACCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.19
Consensus pattern (20 bp):
CAGGCCCAATTGATCCGGGT
Found at i:12292 original size:14 final size:15
Alignment explanation
Indices: 12267--12308 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
12257 ACTCAAATAT
12267 AATATATATAATTAA
1 AATATATATAATTAA
12282 AATAT-TATAATTATA
1 AATATATATAATTA-A
12297 TAAGTATATATA
1 -AA-TATATATA
12309 TAAATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 2 0.09
17 3 0.13
18 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATATATAATTAA
Found at i:12462 original size:14 final size:15
Alignment explanation
Indices: 12437--12478 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
12427 ACTCAAATAT
12437 AATATATATAATTAA
1 AATATATATAATTAA
12452 AATAT-TATAATTATA
1 AATATATATAATTA-A
12467 TAAGTATATATA
1 -AA-TATATATA
12479 TAAATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 2 0.09
17 3 0.13
18 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATATATAATTAA
Found at i:12491 original size:170 final size:169
Alignment explanation
Indices: 12206--12545 Score: 608
Period size: 170 Copynumber: 2.0 Consensus size: 169
12196 AGGCTTGTTT
12206 AAATTTTGGACTAAATATTAAACAAAAAAATTAAAATCCAAGTCCAACTCGACTCAAATATAATA
1 AAATTTTGGACTAAATATTAAACAAAAAAATTAAAATCCAAGTCCAACTCGACTCAAATATAATA
*
12271 TATATAATTAAAATATTATAATTATATAAGTATATATATAAATTTTTATTTTTATATTTTAAAAA
66 TATATAATTAAAATATTATAATTATATAAGTATATATATAAATATTTATTTTTATA-TTTAAAAA
12336 AGATTTTTTAATTTTTTATTGTATAAATTAAGTTTAATGG
130 AGATTTTTTAATTTTTTATTGTATAAATTAAGTTTAATGG
* *
12376 AAATTTTGGACTAAGTATTAAACAAAAAAATTAAAATCCAAGTCCAGCTCGACTCAAATATAATA
1 AAATTTTGGACTAAATATTAAACAAAAAAATTAAAATCCAAGTCCAACTCGACTCAAATATAATA
**
12441 TATATAATTAAAATATTATAATTATATAAGTATATATATAAATATTTATTTTTATATTTAAAATT
66 TATATAATTAAAATATTATAATTATATAAGTATATATATAAATATTTATTTTTATATTTAAAAAA
**
12506 TTTTTTTTAATTTTTTATTGTATAAATTAAGTTTAATGG
131 GATTTTTTAATTTTTTATTGTATAAATTAAGTTTAATGG
12545 A
1 A
12546 TGGCTTTGGT
Statistics
Matches: 163, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
169 45 0.28
170 118 0.72
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (169 bp):
AAATTTTGGACTAAATATTAAACAAAAAAATTAAAATCCAAGTCCAACTCGACTCAAATATAATA
TATATAATTAAAATATTATAATTATATAAGTATATATATAAATATTTATTTTTATATTTAAAAAA
GATTTTTTAATTTTTTATTGTATAAATTAAGTTTAATGG
Found at i:12496 original size:20 final size:18
Alignment explanation
Indices: 12473--12511 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
12463 TATATAAGTA
12473 TATATATAAATATTTATTTT
1 TATATATAAA-ATTT-TTTT
*
12493 TATATTTAAAATTTTTTT
1 TATATATAAAATTTTTTT
12511 T
1 T
12512 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATATAAAATTTTTTT
Found at i:13106 original size:18 final size:19
Alignment explanation
Indices: 13072--13122 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
13062 ATCCGAAATT
13072 AATA-AAATATTATTTTTTAA
1 AATATAAATA-TA-TTTTTAA
*
13092 AATATAAA-ATATTTTTTA
1 AATATAAATATATTTTTAA
13110 AATATAAATATAT
1 AATATAAATATAT
13123 AAACATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 14 0.50
19 6 0.21
20 5 0.18
21 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATAAATATATTTTTAA
Found at i:13106 original size:19 final size:19
Alignment explanation
Indices: 13072--13122 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
13062 ATCCGAAATT
13072 AATA-AAATATTATTTTTTAA
1 AATATAAATA-TATTTTTT-A
13092 AATATAAA-ATATTTTTTA
1 AATATAAATATATTTTTTA
13110 AATATAAATATAT
1 AATATAAATATAT
13123 AAACATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.31
19 12 0.41
20 5 0.17
21 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATAAATATATTTTTTA
Found at i:13124 original size:8 final size:8
Alignment explanation
Indices: 13111--13153 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
13101 TATTTTTTAA
13111 ATATAAAT
1 ATATAAAT
*
13119 ATATAAAC
1 ATATAAAT
*
13127 ATATAATT
1 ATATAAAT
13135 ATATAAAT
1 ATATAAAT
13143 AAATATAAAT
1 --ATATAAAT
13153 A
1 A
13154 AACAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 21 0.72
10 8 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (8 bp):
ATATAAAT
Found at i:13148 original size:26 final size:26
Alignment explanation
Indices: 13111--13170 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
13101 TATTTTTTAA
* *
13111 ATATAAAT--ATATAAACATATAATT
1 ATATAAATAAATATAAACAAACAATT
*
13135 ATATAAATAAATATAAATAAACAATT
1 ATATAAATAAATATAAACAAACAATT
*
13161 AAATAAATAA
1 ATATAAATAA
13171 TTAAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 8 0.27
26 22 0.73
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
ATATAAATAAATATAAACAAACAATT
Found at i:13172 original size:12 final size:12
Alignment explanation
Indices: 13129--13175 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
13119 ATATAAACAT
*
13129 ATAATTATATAA
1 ATAATTAAATAA
13141 ATAAATATAAATAA
1 AT-AAT-TAAATAA
*
13155 ACAATTAAATAA
1 ATAATTAAATAA
13167 ATAATTAAA
1 ATAATTAAA
13176 AATAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 17 0.57
13 6 0.20
14 7 0.23
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATTAAATAA
Found at i:13178 original size:26 final size:26
Alignment explanation
Indices: 13131--13180 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
13121 ATAAACATAT
* *
13131 AATTATATAAATAAATATAAATAAAC
1 AATTAAATAAATAAATAAAAATAAAC
*
13157 AATTAAATAAATAATTAAAAATAA
1 AATTAAATAAATAAATAAAAATAA
13181 TTTTTGTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (26 bp):
AATTAAATAAATAAATAAAAATAAAC
Found at i:14708 original size:22 final size:22
Alignment explanation
Indices: 14683--14749 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
14673 AATTTTACTT
14683 ATAAATAATATTATATTAATAA
1 ATAAATAATATTATATTAATAA
*
14705 ATAAATATTATTATATTAATAA
1 ATAAATAATATTATATTAATAA
** *
14727 ATAATATTCTAATATATTAATAA
1 ATAA-ATAATATTATATTAATAA
14750 TATTACAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 25 0.62
23 15 0.38
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAATAATATTATATTAATAA
Found at i:14713 original size:19 final size:18
Alignment explanation
Indices: 14683--14772 Score: 85
Period size: 22 Copynumber: 4.8 Consensus size: 18
14673 AATTTTACTT
14683 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
14701 ATAAATAAATATTATTATATTA
1 ATAAAT--A-A-TATTATATTA
* *
14723 ATAAATAATATTCTAATA
1 ATAAATAATATTATATTA
* *
14741 TATTAATAATATTACA--A
1 -ATAAATAATATTATATTA
14758 ATAAATAATATTATA
1 ATAAATAATATTATA
14773 ATATATTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.22
17 1 0.02
18 14 0.23
19 13 0.22
20 2 0.03
21 1 0.02
22 16 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:14747 original size:8 final size:8
Alignment explanation
Indices: 14694--14783 Score: 55
Period size: 8 Copynumber: 11.2 Consensus size: 8
14684 TAAATAATAT
14694 TATATTAA
1 TATATTAA
*
14702 TA-AATAA
1 TATATTAA
*
14709 -ATATTAT
1 TATATTAA
14716 TATATTAA
1 TATATTAA
*
14724 TA-AATAA
1 TATATTAA
14731 TAT-TCTAA
1 TATAT-TAA
14739 TATATTAA
1 TATATTAA
14747 TAATATTACA
1 T-ATATTA-A
* *
14757 AATAAATAA
1 TAT-ATTAA
14766 TAT-TATAA
1 TATAT-TAA
14774 TATATTAA
1 TATATTAA
14782 TA
1 TA
14784 AACAATATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
6 1 0.02
7 13 0.21
8 31 0.50
9 13 0.21
10 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
TATATTAA
Found at i:14783 original size:19 final size:19
Alignment explanation
Indices: 14682--14784 Score: 97
Period size: 19 Copynumber: 5.5 Consensus size: 19
14672 TAATTTTACT
*
14682 TATAAATAATATTATATTA
1 TATAAATAATATTATAATA
*
14701 -ATAAATAAATATTATTATA
1 TATAAAT-AATATTATAATA
*
14720 TTAATAAATAATATTCTAATA
1 -T-ATAAATAATATTATAATA
* *
14741 TATTAATAATATTA-CA-A
1 TATAAATAATATTATAATA
14758 -ATAAATAATATTATAATA
1 TATAAATAATATTATAATA
*
14776 TATTAATAA
1 TATAAATAA
14785 ACAATATAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
16 12 0.18
17 2 0.03
18 8 0.12
19 28 0.42
20 1 0.01
21 10 0.15
22 6 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TATAAATAATATTATAATA
Found at i:14802 original size:35 final size:35
Alignment explanation
Indices: 14722--14790 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
14712 TTATTATATT
* * *
14722 AATAAATAATATTCTAATATATTAATAATATTACA
1 AATAAATAATATTATAATATATTAATAACAATACA
14757 AATAAATAATATTATAATATATTAATAAACAATA
1 AATAAATAATATTATAATATATTAAT-AACAATA
14791 TAAAGAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (35 bp):
AATAAATAATATTATAATATATTAATAACAATACA
Found at i:14890 original size:21 final size:20
Alignment explanation
Indices: 14820--14890 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 20
14810 TTATTTTAAG
*
14820 TATTTTTATATTAACATAA-
1 TATTTTTATATTAATATAAT
*
14839 TATTTTAATATTAA-AT-AT
1 TATTTTTATATTAATATAAT
*
14857 TATTATTA-A--AATATAAT
1 TATTTTTATATTAATATAAT
14874 TATTTTTTATATTAATA
1 TA-TTTTTATATTAATA
14891 ATTTTTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 6 0.15
18 13 0.32
19 14 0.34
21 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTTATATTAATATAAT
Found at i:14895 original size:15 final size:16
Alignment explanation
Indices: 14797--14910 Score: 63
Period size: 16 Copynumber: 6.9 Consensus size: 16
14787 AATATAAAGA
14797 ATAATAAATAA-TTTT
1 ATAATAAATAATTTTT
** *
14812 ATTTTAAGT-ATTTTT
1 ATAATAAATAATTTTT
*
14827 ATATTAACATAATATTTT
1 ATAATAA-ATAAT-TTTT
* *
14845 AATATTAAATATTATTATT
1 -ATAATAAATA--ATTTTT
* *
14864 AAAATATAATTATTTTT
1 ATAATA-AATAATTTTT
*
14881 -TATATTAATAATTTTT
1 ATA-ATAAATAATTTTT
14897 ATAATAAATAATTT
1 ATAATAAATAATTT
14911 CAATATATTT
Statistics
Matches: 75, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
14 1 0.01
15 16 0.21
16 21 0.28
17 11 0.15
18 11 0.15
19 13 0.17
20 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (16 bp):
ATAATAAATAATTTTT
Found at i:14926 original size:26 final size:26
Alignment explanation
Indices: 14887--14950 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
14877 TTTTTATATT
*
14887 AATA-ATTTTTATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
*
14912 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
14938 TA-ATATTTTAATA
1 AATATATTTTAATA
14951 GTTATATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 15 0.43
26 20 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:19876 original size:17 final size:18
Alignment explanation
Indices: 19856--19897 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
19846 TTTACATATT
19856 ATTTTTTTCAATA-C-ACA
1 ATTTTTTTCAA-AGCAACA
*
19873 ATTTTGTTCAAAGCAACA
1 ATTTTTTTCAAAGCAACA
19891 ATTTTTT
1 ATTTTTT
19898 CAGTGTGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.52
18 9 0.43
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (18 bp):
ATTTTTTTCAAAGCAACA
Found at i:22699 original size:75 final size:75
Alignment explanation
Indices: 22558--22705 Score: 230
Period size: 73 Copynumber: 2.0 Consensus size: 75
22548 TATTTTATTA
* **
22558 TTTTTATTATTATTTAAATTTCGTGGAATCAATGCAGAAAAAAAACCAAAATTTTCTATGAATAT
1 TTTTTATTATTATTTAAATTTAGTGGAATCAATGCAGAAAAAAAACCAAAAAATTCTATGAATAT
22623 ATATATATAG
66 ATATATATAG
*
22633 TTTTTATT-TTATTTAAATTTAGTTGG-ATCAATGTAG-AAAAAAACCAAAAAATTCTATGAATA
1 TTTTTATTATTATTTAAATTTAG-TGGAATCAATGCAGAAAAAAAACCAAAAAATTCTATGAATA
22695 TATATATATAG
65 TATATATATAG
22706 ATATATATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
73 35 0.51
74 22 0.32
75 11 0.16
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (75 bp):
TTTTTATTATTATTTAAATTTAGTGGAATCAATGCAGAAAAAAAACCAAAAAATTCTATGAATAT
ATATATATAG
Found at i:29330 original size:14 final size:15
Alignment explanation
Indices: 29301--29331 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29291 AAAAAATGAT
*
29301 AAATATGAAATAAAA
1 AAATATAAAATAAAA
29316 AAATATAAAATAAAA
1 AAATATAAAATAAAA
29331 A
1 A
29332 TGAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATATAAAATAAAA
Found at i:29506 original size:15 final size:15
Alignment explanation
Indices: 29480--29547 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
29470 GGGATTTTCT
29480 TAAAAAAT-ATATTA
1 TAAAAAATAATATTA
29494 TAAAAAATAATATTA
1 TAAAAAATAATATTA
** *
29509 -AATTGAATAATATGA
1 TAA-AAAATAATATTA
*
29524 TAAATAATAATACTT-
1 TAAAAAATAATA-TTA
29539 TAAAAAATA
1 TAAAAAATA
29548 TTTTTTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
14 10 0.23
15 30 0.70
16 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (15 bp):
TAAAAAATAATATTA
Found at i:29509 original size:27 final size:28
Alignment explanation
Indices: 29478--29548 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
29468 ATGGGATTTT
*
29478 CTTAAAAAATATATTATAAAAAATAATA
1 CTTAAAAAATATATGATAAAAAATAATA
* *
29506 -TTAAATTGAATAATATGATAAATAATAATA
1 CTTAAA--AAAT-ATATGATAAAAAATAATA
29536 CTTTAAAAAATAT
1 C-TTAAAAAATAT
29549 TTTTTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
27 5 0.15
29 5 0.15
30 19 0.56
32 5 0.15
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (28 bp):
CTTAAAAAATATATGATAAAAAATAATA
Found at i:37092 original size:129 final size:129
Alignment explanation
Indices: 36838--37149 Score: 325
Period size: 129 Copynumber: 2.4 Consensus size: 129
36828 TATTTAACAT
* * *
36838 TTAATA-AGAATTTAATAG-GGTTATTATAGTGAA-TTTAAAACAAAATTTCACATGTCAAATTT
1 TTAATATATAATTTAATAGATG-TATTATAGT-AATTTTAAAACAAAATATCACATGTCAAATTT
* * * *
36900 TTATTAAGCAACGGCCAAGGTATTTTAGTAATTTAGAATGTAGTTAATTTTATATGATGTTAAAA
64 TTATAAACCAACGGCCAAGGAATTTTAATAATTTAGAATGTAGTTAATTTTATATGATGTTAAAA
*
36965 T
129 A
* * * *
36966 TTCATATGTAATTTAATA-ATGATATTATAGTAATTTTTAAATAAAATATCACATGTCAAATTTT
1 TTAATATATAATTTAATAGATG-TATTATAGTAATTTTAAAACAAAATATCACATGTCAAATTTT
** * * * * *
37030 TATAAACCAATTG-TAATGAATTTTAATACTTTA-ATATGT-GATTAATTTTATGTTATGTTTAA
65 TATAAACCAACGGCCAAGGAATTTTAATAATTTAGA-ATGTAG-TTAATTTTATATGATG-TTAA
37092 AAA
127 AAA
* *
37095 TTAATATATAATTTAATAGATGTGTTATAGTAATTTTGAAACAAAATA-CACATGT
1 TTAATATATAATTTAATAGATGTATTATAGTAATTTTAAAACAAAATATCACATGT
37150 TAACTTCTAT
Statistics
Matches: 152, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
127 2 0.01
128 47 0.31
129 100 0.66
130 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (129 bp):
TTAATATATAATTTAATAGATGTATTATAGTAATTTTAAAACAAAATATCACATGTCAAATTTTT
ATAAACCAACGGCCAAGGAATTTTAATAATTTAGAATGTAGTTAATTTTATATGATGTTAAAAA
Found at i:37595 original size:58 final size:59
Alignment explanation
Indices: 37526--37656 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 59
37516 TCATAAAAAC
*
37526 ATTTTTGTAATTACGGT-GAAAGAGTATTATAGTAATTTTGA-TCAAT-TATGAGAAAT-GT
1 ATTTTTGTAATTA-GGTAGAAAG-GTATTATAGTAA-TTTGAGTCAATATAAGAGAAATGGT
* * * *
37584 ATTTTTATAATTATGTCAGGAAGGTATTATAGTAATTTGAGTCAATAATAAGAGAATTGGT
1 ATTTTTGTAATTAGGT-AGAAAGGTATTATAGTAATTTGAGTCAAT-ATAAGAGAAATGGT
37645 ATTTTTGTAATT
1 ATTTTTGTAATT
37657 TAATAATAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
57 7 0.11
58 29 0.48
59 4 0.07
60 8 0.13
61 13 0.21
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (59 bp):
ATTTTTGTAATTAGGTAGAAAGGTATTATAGTAATTTGAGTCAATATAAGAGAAATGGT
Found at i:37741 original size:55 final size:51
Alignment explanation
Indices: 37673--37848 Score: 128
Period size: 55 Copynumber: 3.4 Consensus size: 51
37663 TAAAAAGAAC
*
37673 ATTTTTATAATTATGGTACGAGGATATTATAATAAATAATTATAAGAGAATATGT
1 ATTTTTATAATTATGGTACGA-G--AGTATAATAAATAATT-TAAGAGAATATGT
* * * * *
37728 ATTTTTTTTATTATGGTATGAGAGTATAATAATTAATTTAAGAG-A-A-GA
1 ATTTTTATAATTATGGTACGAGAGTATAATAAATAATTTAAGAGAATATGT
* * * * *
37776 ATTTTCTATAATTATGATATG-GAGTATTATAGTAAATAATTATAAAAGAAAAAGAT
1 ATTTT-TATAATTATGGTACGAGAGTA-TA-A-TAAATAATT-TAAGAGAATATG-T
37832 ATTTTT-TAATTATGGTA
1 ATTTTTATAATTATGGTA
37849 TGAAGGCAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 19
0.76 0.10 0.15
Matches are distributed among these distances:
48 11 0.11
49 15 0.15
50 2 0.02
51 14 0.14
52 19 0.19
53 1 0.01
54 12 0.12
55 20 0.20
56 5 0.05
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.42
Consensus pattern (51 bp):
ATTTTTATAATTATGGTACGAGAGTATAATAAATAATTTAAGAGAATATGT
Found at i:37780 original size:48 final size:52
Alignment explanation
Indices: 37700--37850 Score: 127
Period size: 52 Copynumber: 2.9 Consensus size: 52
37690 ACGAGGATAT
* * * *
37700 TATAATAAATAATTATAAGAGAATATGTATTTT-TTTTATTATGGTATGAGAG
1 TATAATAAATAATTATAAGAGAATATGAATTTTCTATAATTATGATATG-GAG
*
37752 TATAATAATTAATT-TAAGAG-A-A-GAATTTTCTATAATTATGATATGGAG
1 TATAATAAATAATTATAAGAGAATATGAATTTTCTATAATTATGATATGGAG
* * * *
37800 TATTATAGTAAATAATTATAAAAGAAAAAGATATTTT-T-TAATTATGGTATG
1 TA-TA-A-TAAATAATTATAAGAGAATATGA-ATTTTCTATAATTATGATATG
37851 AAGGCAAAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
48 11 0.13
49 15 0.18
50 2 0.02
51 14 0.17
52 18 0.22
53 1 0.01
54 13 0.16
55 3 0.04
56 5 0.06
ACGTcount: A:0.44, C:0.01, G:0.14, T:0.42
Consensus pattern (52 bp):
TATAATAAATAATTATAAGAGAATATGAATTTTCTATAATTATGATATGGAG
Found at i:42277 original size:30 final size:29
Alignment explanation
Indices: 42243--42301 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
42233 TAAAAAATGC
42243 AATTACCTAATGCAAA-TAT-ATGTCATTTCT
1 AATTA-CTAAT-CAAATTATAATGT-ATTTCT
*
42273 AATTAGTAATCAAATTATAATGTATTTCT
1 AATTACTAATCAAATTATAATGTATTTCT
42302 TCCTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 4 0.15
29 13 0.50
30 9 0.35
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (29 bp):
AATTACTAATCAAATTATAATGTATTTCT
Found at i:45495 original size:2 final size:2
Alignment explanation
Indices: 45488--45517 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
45478 TTGTTCATGC
*
45488 TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45518 AGGTTTTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Done.