Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011225.1 Kokia drynarioides strain JFW-HI SEQ_126203, 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: 116623
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:175 original size:17 final size:17
Alignment explanation
Indices: 155--208 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
145 TTTGAAAAAA
155 TTTATATTTATATTATT
1 TTTATATTTATATTATT
172 TTTA-ATTTA-A-TA-T
1 TTTATATTTATATTATT
*
185 TTCATATTTAT-TTATAT
1 TTTATATTTATATTAT-T
202 TTTATAT
1 TTTATAT
209 ATAGTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 3 0.10
16 5 0.17
17 11 0.37
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTTATATTATT
Found at i:1893 original size:63 final size:62
Alignment explanation
Indices: 1800--1974 Score: 257
Period size: 63 Copynumber: 2.7 Consensus size: 62
1790 TTGTTATTTA
1800 TTTATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAAC-AAAATTAATATTAT
1 TTTATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAAATTAATATTAT
1861 TTTACATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAACAAAAATTAATAT
1 TTT--ATTTATTTATTTATATTCAT--AA-AAT-AATAAATAAATAATAAAACAAAAATTAATAT
1926 TAT
60 TAT
1929 TTTA--TATTTATTTATATTCATAAAAATAATAAATAAATGAATAAAA
1 TTTATTTATTTATTTATATTCAT-AAAATAATAAATAAAT-AATAAAA
1975 ATAATAAGAA
Statistics
Matches: 105, Mismatches: 1, Indels: 15
0.87 0.01 0.12
Matches are distributed among these distances:
61 14 0.13
62 10 0.10
63 22 0.21
64 17 0.16
65 2 0.02
66 4 0.04
67 19 0.18
68 17 0.16
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (62 bp):
TTTATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAAATTAATATTAT
Found at i:1960 original size:68 final size:67
Alignment explanation
Indices: 1803--1988 Score: 213
Period size: 68 Copynumber: 2.8 Consensus size: 67
1793 TTATTTATTT
**
1803 ATTTATTTATTTATAT-TCATAA-AAT-AATAAATAAATAATAAAAC-AAAATTAATATTATTTT
1 ATTTATTTATTTATATAAAATAATAATAAATAAATAAATAATAAAACAAAAATTAATATTATTTT
1864 AC
66 AC
* * *
1866 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAACAAAAATTAATATTATTT
1 ATTTATTTATTTATA-TAAAATAATAATAAATAAATAAATAATAAAACAAAAATTAATATTATTT
*
1931 TAT
65 TAC
* *
1934 ATTTATTTATATTCATA-AAAATAATAAATAAATGAATAAA-AATAATAAGAAAAAT
1 ATTTATTTAT-TT-ATATAAAATAAT-AATAAATAAATAAATAATAA-AACAAAAAT
1989 GGAATTGGGT
Statistics
Matches: 105, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
63 15 0.14
64 1 0.01
65 3 0.03
66 3 0.03
67 19 0.18
68 38 0.36
69 23 0.22
70 3 0.03
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (67 bp):
ATTTATTTATTTATATAAAATAATAATAAATAAATAAATAATAAAACAAAAATTAATATTATTTT
AC
Found at i:2590 original size:40 final size:39
Alignment explanation
Indices: 2545--2735 Score: 152
Period size: 39 Copynumber: 4.8 Consensus size: 39
2535 CCCATAGTCG
* *
2545 GGGTAAGAGATCGAATGGTCTTCAATCTACCCTTTGGTTA
1 GGGTAAGAGATCGAATGGT-TTCAATCTACCCTATGGTCA
* * * * * *
2585 AGGTAAAAGATTGGATTGTTTCAATCTA-CCTCATGGTCG
1 GGGTAAGAGATCGAATGGTTTCAATCTACCCT-ATGGTCA
* * *
2624 GGGTAAGAGATCGAATAGTCTTCAATCTACCCTTTGGTTA
1 GGGTAAGAGATCGAATGGT-TTCAATCTACCCTATGGTCA
* * * * * * *
2664 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCG
1 GGGTAAGAGATCGAATGGTTTCAATCTACCCTATGGTCA
*
2703 GGGTAAGAGATC-AGATGGTTTTCAATCTGCCCT
1 GGGTAAGAGATCGA-ATGG-TTTCAATCTACCCT
2736 CTAGTTAGGG
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
38 3 0.03
39 55 0.47
40 55 0.47
41 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (39 bp):
GGGTAAGAGATCGAATGGTTTCAATCTACCCTATGGTCA
Found at i:2626 original size:79 final size:79
Alignment explanation
Indices: 2506--2888 Score: 489
Period size: 79 Copynumber: 4.8 Consensus size: 79
2496 ATAGATTTAG
* *
2506 GGGTAAAAGATTGGATTGTTTTAATCTGCCCCATAGTCGGGGTAAGAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
2571 CTACCCTTTGGTTA
66 CTACCCTTTGGTTA
* * * *
2585 AGGTAAAAGATTGGATTGTTTCAATCTACCTCATGGTCGGGGTAAGAGATCGAATAGTCTTCAAT
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
2650 CTACCCTTTGGTTA
66 CTACCCTTTGGTTA
*
2664 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATC-AGATGGTTTTCAA
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGA-ATGGTCTTCAA
* * *
2728 TCTGCCCTCTAGTTA
65 TCTACCCTTTGGTTA
* * * * * * * * * *
2743 GGGTAAAATATTGGATTGCTTCATTTTTCCCCACGGTCGGGGTAAGAGATTGGATGATTTTCAAT
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
*
2808 CTGCCCTTTGGTTA
66 CTACCCTTTGGTTA
* * * * * * * *
2822 GGGTAAAATATTGGATTGCTTCATTTTGCCTCACGGTCGGGGTAAGAGATCAAATGATCTTCAAT
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
2887 CT
66 CT
2889 GCTTTCTGAT
Statistics
Matches: 271, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
78 1 0.00
79 270 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
CTACCCTTTGGTTA
Found at i:2835 original size:40 final size:39
Alignment explanation
Indices: 2506--2844 Score: 223
Period size: 40 Copynumber: 8.6 Consensus size: 39
2496 ATAGATTTAG
* * * **
2506 GGGTAAAAGATTGGATTGTTTTAATCTGCCCCATAGTCG
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCTATGGTTA
* * * * * *
2545 GGGTAAGAGATCGAATGGTCTTCAATCTACCCTTTGGTTA
1 GGGTAAAAGATTGGATTGT-TTCAATCTGCCCTATGGTTA
* * **
2585 AGGTAAAAGATTGGATTGTTTCAATCT-ACCTCATGGTCG
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCT-ATGGTTA
* * * * * *
2624 GGGTAAGAGATCGAATAGTCTTCAATCTACCCTTTGGTTA
1 GGGTAAAAGATTGGATTGT-TTCAATCTGCCCTATGGTTA
* **
2664 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCG
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCTATGGTTA
* ** * * *
2703 GGGTAAGAGATCAGATGGTTTTCAATCTGCCCTCTAGTTA
1 GGGTAAAAGATTGGATTG-TTTCAATCTGCCCTATGGTTA
* * * * * * * **
2743 GGGTAAAATATTGGATTGCTTCATTTTTCCCCACGGTCG
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCTATGGTTA
* *
2782 GGGTAAGAGATTGGA-TGATTTTCAATCTGCCCTTTGGTTA
1 GGGTAAAAGATTGGATTG--TTTCAATCTGCCCTATGGTTA
* *
2822 GGGTAAAATATTGGATTGCTTCA
1 GGGTAAAAGATTGGATTGTTTCA
2845 TTTTGCCTCA
Statistics
Matches: 216, Mismatches: 76, Indels: 16
0.70 0.25 0.05
Matches are distributed among these distances:
38 5 0.02
39 98 0.45
40 108 0.50
41 5 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (39 bp):
GGGTAAAAGATTGGATTGTTTCAATCTGCCCTATGGTTA
Found at i:2948 original size:158 final size:158
Alignment explanation
Indices: 2506--2933 Score: 387
Period size: 158 Copynumber: 2.7 Consensus size: 158
2496 ATAGATTTAG
* * ** * *
2506 GGGTAAAAGATTGGATTGTTTTAATCTGCCCCATAGTCGGGGTAAGAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCACGGTCGGGGTAAGAGATCAAATGATCTTCAAT
* * * * * * ** * * * * * *
2571 CTACCCTTTGGTTAAGGTAAAAGATTGGATTGTTTCA-ATCTACCTCATGGTCGGGGTAAGAGAT
66 CTGCCCTCTAGATAGGGTAAAAGATCGGAGAGCTTCATAT-TTCCCCACGGTCAGCGTAAGAGAT
* * *
2635 CGAAT-AGTCTTCAATCTACCCTTTGGTTA
130 TGGATGA-TTTTCAATCTACCCTTTGGTTA
* * * * *
2664 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTTTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCACGGTCGGGGTAAGAGATCAAATGATCTTCAAT
* * * ** * * *
2729 CTGCCCTCTAGTTAGGGTAAAATATTGGATTGCTTCATTTTTCCCCACGGTCGGGGTAAGAGATT
66 CTGCCCTCTAGATAGGGTAAAAGATCGGAGAGCTTCATATTTCCCCACGGTCAGCGTAAGAGATT
*
2794 GGATGATTTTCAATCTGCCCTTTGGTTA
131 GGATGATTTTCAATCTACCCTTTGGTTA
* * * *
2822 GGGTAAAATATTGGATTGCTTCATTTTGCCTCACGGTCGGGGTAAGAGATCAAATGATCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCACGGTCGGGGTAAGAGATCAAATGATCTTCAAT
** * *
2887 CTGCTTTCT-GATCGGAGTAAAAGATCGGAGAGTCTTCA-ATTTGCCCA
66 CTGCCCTCTAGATAGG-GTAAAAGATCGGAGAG-CTTCATATTTCCCCA
2934 TTTCAGCTTC
Statistics
Matches: 228, Mismatches: 38, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
157 4 0.02
158 217 0.95
159 7 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (158 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCACGGTCGGGGTAAGAGATCAAATGATCTTCAAT
CTGCCCTCTAGATAGGGTAAAAGATCGGAGAGCTTCATATTTCCCCACGGTCAGCGTAAGAGATT
GGATGATTTTCAATCTACCCTTTGGTTA
Found at i:3008 original size:50 final size:50
Alignment explanation
Indices: 2953--3127 Score: 226
Period size: 50 Copynumber: 3.5 Consensus size: 50
2943 CAAGAGTATA
2953 AGATTCGTCC-TTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
1 AGATTCG-CCATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
* ** * * *
3003 AGATTCACCATTGCGGTTTCTATCTGCCTCTCTATAGCTTTAGGTGAATG
1 AGATTCGCCATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
* * * * *
3053 AGATTTGCCATTGCAATTTTAATCTGCCCCTCTACAACTTTAGGTGAATG
1 AGATTCGCCATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
*
3103 AGATTCGCCATTGCGGCTTCAATCT
1 AGATTCGCCATTGCGACTTCAATCT
3128 AGTAGAAAAT
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
49 2 0.02
50 102 0.98
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.35
Consensus pattern (50 bp):
AGATTCGCCATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
Found at i:12266 original size:21 final size:19
Alignment explanation
Indices: 12228--12277 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
12218 ATTATTTTGA
*
12228 ATTTTTTTAATTTTTAAAC
1 ATTTTTATAATTTTTAAAC
12247 ATTTTTATATATTCTTT-AA-
1 ATTTTTATA-ATT-TTTAAAC
12266 A-TTTTATAATTT
1 ATTTTTATAATTT
12278 AAAAAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 3 0.11
18 7 0.25
19 9 0.32
20 5 0.18
21 3 0.11
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTATAATTTTTAAAC
Found at i:14633 original size:6 final size:6
Alignment explanation
Indices: 14622--14654 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
14612 AAGAATTTTG
14622 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGG
1 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGG
14655 AATTGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
TGGTGA
Found at i:17152 original size:30 final size:29
Alignment explanation
Indices: 17082--17271 Score: 102
Period size: 29 Copynumber: 6.5 Consensus size: 29
17072 GCTCAGGGGC
* * * *
17082 AAAATGTAATTTTGGA-AAATTCGAGGTT
1 AAAATGTGATTTTTGAGAAGTTCGAGGGT
* *
17110 AGAATTTGATTTTTGAGAAGTTCGAGGGCT
1 AAAATGTGATTTTTGAGAAGTTCGAGGG-T
* *
17140 AAAATGTGATTTTTGGGAAGTTTG-GGGT
1 AAAATGTGATTTTTGAGAAGTTCGAGGGT
* * *
17168 CAAAATGTAATTTTGGA-AAGTT-TAGGTGT
1 -AAAATGTGATTTTTGAGAAGTTCGAGG-GT
* * *
17197 CAAAATATGATTTTTGGGAAGTTTG-GGGT
1 -AAAATGTGATTTTTGAGAAGTTCGAGGGT
** * * **
17226 CAAAATGAAATTTTAGAAAAGTTTAAGGGT
1 -AAAATGTGATTTTTGAGAAGTTCGAGGGT
*
17256 CAAAATATGATTTTTG
1 -AAAATGTGATTTTTG
17272 GAAAATTCAG
Statistics
Matches: 124, Mismatches: 30, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
28 20 0.16
29 60 0.48
30 44 0.35
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAATGTGATTTTTGAGAAGTTCGAGGGT
Found at i:17182 original size:58 final size:57
Alignment explanation
Indices: 17120--17272 Score: 193
Period size: 58 Copynumber: 2.6 Consensus size: 57
17110 AGAATTTGAT
* * *
17120 TTTTGAGAAGTTCGAGGG-CTAAAATGTGATTTTTGGGAAGTTTGGGGTCAAAATGTAA
1 TTTTGAGAAGTT-AAGGGTC-AAAATATGATTTTTGGGAAGTTTGGGGTCAAAATGAAA
*
17178 TTTTG-GAAAGTTTAGGTGTCAAAATATGATTTTTGGGAAGTTTGGGGTCAAAATGAAA
1 TTTTGAG-AAGTTAAGG-GTCAAAATATGATTTTTGGGAAGTTTGGGGTCAAAATGAAA
*
17236 TTTTAGAAAAGTTTAAGGGTCAAAATATGATTTTTGG
1 TTTT-GAGAAG-TTAAGGGTCAAAATATGATTTTTGG
17273 AAAATTCAGG
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
57 4 0.05
58 51 0.61
59 24 0.29
60 5 0.06
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (57 bp):
TTTTGAGAAGTTAAGGGTCAAAATATGATTTTTGGGAAGTTTGGGGTCAAAATGAAA
Found at i:17227 original size:29 final size:29
Alignment explanation
Indices: 17116--17272 Score: 140
Period size: 30 Copynumber: 5.3 Consensus size: 29
17106 GGTTAGAATT
* * *
17116 TGATTTTTGAGAAGTTCGAGGG-CTAAAATG
1 TGATTTTTGGGAAGTTTG-GGGTC-AAAATA
*
17146 TGATTTTTGGGAAGTTTGGGGTCAAAATG
1 TGATTTTTGGGAAGTTTGGGGTCAAAATA
* * *
17175 T-AATTTTGGAAAGTTTAGGTGTCAAAATA
1 TGATTTTTGGGAAGTTT-GGGGTCAAAATA
17204 TGATTTTTGGGAAGTTTGGGGTCAAAATGA
1 TGATTTTTGGGAAGTTTGGGGTCAAAAT-A
* * ** *
17234 -AATTTTAGAAAAGTTTAAGGGTCAAAATA
1 TGATTTTTGGGAAGTTT-GGGGTCAAAATA
17263 TGATTTTTGG
1 TGATTTTTGG
17273 AAAATTCAGG
Statistics
Matches: 104, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
28 13 0.12
29 44 0.42
30 47 0.45
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (29 bp):
TGATTTTTGGGAAGTTTGGGGTCAAAATA
Found at i:18399 original size:20 final size:21
Alignment explanation
Indices: 18371--18424 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
18361 AATTTCTCTT
*
18371 TATTTTATTTATT-TATTTAA
1 TATTATATTTATTATATTTAA
* *
18391 TATTATATTTATTATGTTTAT
1 TATTATATTTATTATATTTAA
18412 TA-TATATTTATTA
1 TATTATATTTATTA
18425 CTTATTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTATATTTATTATATTTAA
Found at i:19239 original size:17 final size:17
Alignment explanation
Indices: 19211--19245 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19201 TTCAACATTT
19211 TTTAATAATTTTAATAAA
1 TTTAATAATTTTAA-AAA
19229 TTTAA-AATTTTAAAAA
1 TTTAATAATTTTAAAAA
19245 T
1 T
19246 AATTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAATAATTTTAAAAA
Found at i:19414 original size:13 final size:13
Alignment explanation
Indices: 19392--19421 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19382 GTACAAATTT
*
19392 AAAAATTTAAAAA
1 AAAAAATTAAAAA
19405 AAAAAATTAAAAA
1 AAAAAATTAAAAA
19418 AAAA
1 AAAA
19422 TTTGTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAATTAAAAA
Found at i:30181 original size:46 final size:46
Alignment explanation
Indices: 30114--30207 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
30104 TGGTCGAACA
30114 ATCCTGAATCATTTCAGACAAATGGGGGATGATGCAACTTGTGACG
1 ATCCTGAATCATTTCAGACAAATGGGGGATGATGCAACTTGTGACG
30160 ATCCTGAATCATTTCAGACAAATGGGGGATGATGCAACTTGTGACG
1 ATCCTGAATCATTTCAGACAAATGGGGGATGATGCAACTTGTGACG
30206 AT
1 AT
30208 GTTCTATATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (46 bp):
ATCCTGAATCATTTCAGACAAATGGGGGATGATGCAACTTGTGACG
Found at i:33168 original size:26 final size:27
Alignment explanation
Indices: 33122--33175 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
33112 TTATTTATTT
33122 TAAATTATTTACGTACATAATA-AAAA
1 TAAATTATTTACGTACATAATACAAAA
**
33148 TAAATTATTTTTGTA-ATTAATACAAAA
1 TAAATTATTTACGTACA-TAATACAAAA
33175 T
1 T
33176 TTTGGGTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.04
26 18 0.75
27 5 0.21
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (27 bp):
TAAATTATTTACGTACATAATACAAAA
Found at i:34735 original size:29 final size:29
Alignment explanation
Indices: 34700--34969 Score: 269
Period size: 29 Copynumber: 9.2 Consensus size: 29
34690 TAATTTTGAG
* *
34700 AGTTTCGAAGTCAAAAATGAGATTTTTGGA
1 AGTTTCGAGGT-AAAAATGGGATTTTTGGA
* *
34730 AG-TTCGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTC-GAGGTAAAAATGGGATTTTTGGA
*
34759 AGTTTTGAGGTCAAAAATGGGATTTTTGGA
1 AGTTTCGAGGT-AAAAATGGGATTTTTGGA
* *
34789 AG-TTCGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTC-GAGGTAAAAATGGGATTTTTGGA
* *
34818 AGTTT-TAGGGTCAAAATGGGATTTTTGGA
1 AGTTTCGA-GGTAAAAATGGGATTTTTGGA
* *
34847 AGTTTGGGGGTAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTAAAAATGGGATTTTTGGA
* * * *
34876 AGTTTGGGGGTAAAAATAGAATTTTTGGA
1 AGTTTCGAGGTAAAAATGGGATTTTTGGA
*
34905 AGTTTAGAGGTTAAAAATGGGATTTTTGGA
1 AGTTTCGAGG-TAAAAATGGGATTTTTGGA
** *
34935 AG-TTCGAGGGTAAAAACAGAATTTTTGGA
1 AGTTTCGA-GGTAAAAATGGGATTTTTGGA
34964 CAGTTT
1 -AGTTT
34970 AGGGACCTCC
Statistics
Matches: 202, Mismatches: 27, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
29 145 0.72
30 55 0.27
31 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (29 bp):
AGTTTCGAGGTAAAAATGGGATTTTTGGA
Found at i:34742 original size:58 final size:58
Alignment explanation
Indices: 34625--34943 Score: 312
Period size: 59 Copynumber: 5.4 Consensus size: 58
34615 TTATAGGGGC
* * ** *
34625 AAAATGTGAATTTTTGGGAAAGTTCGGGGTTGAAAATGGAATTTTT-GACA-TTC-GGGGT-
1 AAAATG-GAATTTTT-GG-AAGTTTGAGGTCAAAAATGGGATTTTTGGA-AGTTCGGGGGTA
* * *
34683 AAAAGGGTAA-TTTT-GAGAGTTTCGAAGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTA
1 AAAATGG-AATTTTTGGA-AGTTT-GAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
34742 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAG-TTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
* *
34801 AAAATGGAATTTTTGGAAGTTTTAGGGTC-AAAATGGGATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGA-GGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
* * * * * * *
34859 AAAATGGGATTTTTGGAAGTTTGGGGGT-AAAAATAGAATTTTTGGAAGTTTAGAGGTTA
1 AAAATGGAATTTTTGGAAGTTT-GAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGGTA
* *
34918 AAAATGGGATTTTTGGAAGTTCGAGG
1 AAAATGGAATTTTTGGAAGTTTGAGG
34944 GTAAAAACAG
Statistics
Matches: 224, Mismatches: 23, Indels: 28
0.81 0.08 0.10
Matches are distributed among these distances:
54 1 0.00
55 5 0.02
56 16 0.07
57 10 0.04
58 90 0.40
59 97 0.43
60 5 0.02
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
Found at i:34946 original size:59 final size:59
Alignment explanation
Indices: 34712--34973 Score: 318
Period size: 59 Copynumber: 4.5 Consensus size: 59
34702 TTTCGAAGTC
*
34712 AAAAAT-GAGATTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGA-GGT
1 AAAAATAGA-ATTTTTGGAAGTTTAGGGGGTAAAAATGGAATTTTTGGAAG-TTTGAGGGT
* * * *
34770 CAAAAATGGGATTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT
1 -AAAAATAGAATTTTTGGAAGTTTAGGGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * * *
34829 CAAAATGGGATTTTTGGAAGTTT-GGGGGTAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAAATAGAATTTTTGGAAGTTTAGGGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * *
34887 AAAAATAGAATTTTTGGAAGTTTAGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAAATAGAATTTTTGGAAGTTTAGGGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGT
*
34946 AAAAACAGAATTTTTGGACAGTTTAGGG
1 AAAAATAGAATTTTTGGA-AGTTTAGGG
34974 ACCTCCAAGG
Statistics
Matches: 183, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
58 75 0.41
59 99 0.54
60 9 0.05
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.34
Consensus pattern (59 bp):
AAAAATAGAATTTTTGGAAGTTTAGGGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:45902 original size:5 final size:5
Alignment explanation
Indices: 45892--45919 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
45882 CTTCTCGTAT
45892 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
45920 TATCGGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:50855 original size:16 final size:18
Alignment explanation
Indices: 50816--50857 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
50806 TAAGTTTATA
50816 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
50833 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
50850 A-ATTTATA
1 ATATTTATA
50858 ACATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:53318 original size:21 final size:20
Alignment explanation
Indices: 53267--53318 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
53257 AATTTTTTTA
53267 TTAATTTTTTTAATAAAAAAC
1 TTAA-TTTTTTAATAAAAAAC
* *
53288 TT-CTTCTTTTAATATTAAAAC
1 TTAATT-TTTTAATA-AAAAAC
53309 TTAATTTTTT
1 TTAATTTTTT
53319 TGGTCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 2 0.08
20 8 0.32
21 13 0.52
22 2 0.08
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTTTTTAATAAAAAAC
Found at i:55848 original size:34 final size:34
Alignment explanation
Indices: 55810--55881 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
55800 GTAAACAAGT
*
55810 TTTGAGTAAGGTAAAAGGTAAAAAATTAAAAATA
1 TTTGAGTAAGATAAAAGGTAAAAAATTAAAAATA
* *
55844 TTTGAGTAAGATCAAAGGTAAAAAATTAGAAATA
1 TTTGAGTAAGATAAAAGGTAAAAAATTAAAAATA
55878 TTTG
1 TTTG
55882 GATTTAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.01, G:0.18, T:0.29
Consensus pattern (34 bp):
TTTGAGTAAGATAAAAGGTAAAAAATTAAAAATA
Found at i:61078 original size:6 final size:6
Alignment explanation
Indices: 61067--61091 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61057 AGCAAAGCAT
61067 CACCCA CACCCA CACCCA CACCCA C
1 CACCCA CACCCA CACCCA CACCCA C
61092 TCACTTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCCA
Found at i:65527 original size:2 final size:2
Alignment explanation
Indices: 65520--65548 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
65510 TTAAATTTTC
65520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65549 TAAAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65679 original size:19 final size:19
Alignment explanation
Indices: 65657--65703 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
65647 ATATCTAAAC
65657 TTTTATAATATTTTAATAA
1 TTTTATAATATTTTAATAA
*
65676 TTTT-TATATTTTTTAATAA
1 TTTTATA-ATATTTTAATAA
65695 TTTTA-AATA
1 TTTTATAATA
65704 AGTTCTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATAATATTTTAATAA
Found at i:65680 original size:10 final size:9
Alignment explanation
Indices: 65657--65726 Score: 59
Period size: 10 Copynumber: 7.2 Consensus size: 9
65647 ATATCTAAAC
65657 TTTTATAAT
1 TTTTATAAT
65666 ATTTTAATAAT
1 -TTTT-ATAAT
*
65677 TTTTATATT
1 TTTTATAAT
65686 TTTTAATAAT
1 TTTT-ATAAT
* *
65696 TTTAAATAAG
1 TTT-TATAAT
*
65706 TTCTATAAT
1 TTTTATAAT
65715 TATTTATAAT
1 T-TTTATAAT
65725 TT
1 TT
65727 CATAATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.29
10 29 0.60
11 5 0.10
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:65690 original size:29 final size:29
Alignment explanation
Indices: 65657--65726 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
65647 ATATCTAAAC
* * *
65657 TTTTATAATATTTTAATAATTTTTAT-ATT
1 TTTTATAAT-TTTAAATAAGTTCTATAATT
65686 TTTTAATAATTTTAAATAAGTTCTATAATT
1 TTTT-ATAATTTTAAATAAGTTCTATAATT
*
65716 ATTTATAATTT
1 TTTTATAATTT
65727 CATAATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 24 0.69
30 11 0.31
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTATAATTTTAAATAAGTTCTATAATT
Found at i:71005 original size:26 final size:26
Alignment explanation
Indices: 70976--71056 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
70966 TGTAAGAGTA
* * *
70976 GATTATACTAACAATCACTTAACTTT
1 GATTATACTAACAGTCACTCAATTTT
*
71002 GATTATATTAACAGTCACTCAATTTT
1 GATTATACTAACAGTCACTCAATTTT
* *
71028 GATTACACCAACAGTCACTCAATTTT
1 GATTATACTAACAGTCACTCAATTTT
71054 GAT
1 GAT
71057 GTAATTGATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (26 bp):
GATTATACTAACAGTCACTCAATTTT
Found at i:73785 original size:18 final size:18
Alignment explanation
Indices: 73764--73800 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
73754 GTTCAAAAGG
73764 ATCTGCGAGTGTCGAAGC
1 ATCTGCGAGTGTCGAAGC
*
73782 ATCTGTGAGTGTCGAAGC
1 ATCTGCGAGTGTCGAAGC
73800 A
1 A
73801 CCTACAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (18 bp):
ATCTGCGAGTGTCGAAGC
Found at i:73820 original size:201 final size:201
Alignment explanation
Indices: 73581--73955 Score: 543
Period size: 201 Copynumber: 1.9 Consensus size: 201
73571 GCCCAAAAGG
** **
73581 ATCTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGTGACAGTGGTTTGACGGTTAATGAAG
1 ATCTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTTAATGAAG
* * * * * * * * *
73646 CACCTGCATTTAATGAAGTTGATAATGGTGGCTCAAGTGTTACCAGTGGTAAGTTGAGGAGAAGG
66 CACCTACAGTTAACGAAGTTGATAACGATGGCTCAACTGTTACCACTGGGAAATTGAGGAGAAGG
* *
73711 ACATGCTACGAGTGCGGACAAAAGGGCCATATTTCTTCTGCTTGTTCAAAAGGATCTGCGAGTGT
131 ACATGCTACGAATGCGGACAAAAGGGCCATATCTCTTCTGCTTGTTCAAAAGGATCTGCGAGTGT
73776 CGAAGC
196 CGAAGC
*
73782 ATCTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACGGTGGTTCAACGGTTAATGAAG
1 ATCTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTTAATGAAG
* * * *
73847 CACCTACGGTTAACGAAGTTGCTAACGATGGCTCGACTGTTAGCACTGGGAAATTGAGGAGAAGG
66 CACCTACAGTTAACGAAGTTGATAACGATGGCTCAACTGTTACCACTGGGAAATTGAGGAGAAGG
* * *
73912 ACGTGCTACGAATGCGGGCAAAAGGGTCATATCTCTTCTGCTTG
131 ACATGCTACGAATGCGGACAAAAGGGCCATATCTCTTCTGCTTG
73956 CCCAAATAAG
Statistics
Matches: 151, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
201 151 1.00
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (201 bp):
ATCTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTTAATGAAG
CACCTACAGTTAACGAAGTTGATAACGATGGCTCAACTGTTACCACTGGGAAATTGAGGAGAAGG
ACATGCTACGAATGCGGACAAAAGGGCCATATCTCTTCTGCTTGTTCAAAAGGATCTGCGAGTGT
CGAAGC
Found at i:74688 original size:21 final size:20
Alignment explanation
Indices: 74649--74686 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
74639 TTTAAATGGA
74649 AGGAAAACTTGGAATTTTAC
1 AGGAAAACTTGGAATTTTAC
74669 AGGAAAAGCTT-GAATTTT
1 AGGAAAA-CTTGGAATTTT
74687 TATTGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (20 bp):
AGGAAAACTTGGAATTTTAC
Found at i:79721 original size:15 final size:15
Alignment explanation
Indices: 79701--79730 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
79691 TTCCGAAGAA
*
79701 GGAAAGAGGCTAAAC
1 GGAAAGAAGCTAAAC
79716 GGAAAGAAGCTAAAC
1 GGAAAGAAGCTAAAC
79731 ATTTCGGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.30, T:0.07
Consensus pattern (15 bp):
GGAAAGAAGCTAAAC
Found at i:81217 original size:18 final size:18
Alignment explanation
Indices: 81196--81242 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
81186 AGAAGTGATA
81196 AATTATACATTTAAA-AAT
1 AATTATA-ATTTAAATAAT
* *
81214 AATTAGAATTTAAATTAT
1 AATTATAATTTAAATAAT
81232 AATTATTAATT
1 AATTA-TAATT
81243 AAAAATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 13 0.54
19 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTATAATTTAAATAAT
Found at i:83114 original size:26 final size:25
Alignment explanation
Indices: 83077--83129 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
83067 TATATAATAT
*
83077 TATTTTAATATTTAATAA-TTTTATA
1 TATTTTAATATTGAA-AATTTTTATA
*
83102 TATTTTATTTATTGAAAATTTTTATA
1 TATTTTA-ATATTGAAAATTTTTATA
83128 TA
1 TA
83130 GTCATCTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTTTAATATTGAAAATTTTTATA
Found at i:85997 original size:28 final size:28
Alignment explanation
Indices: 85960--86014 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
85950 ATTTTGCCAC
* **
85960 TAAAGTTAAATTTTAATTTAAAATAATT
1 TAAAGATAAATTTTAATAAAAAATAATT
85988 TAAAGATAAATTTTAATAAAAAATAAT
1 TAAAGATAAATTTTAATAAAAAATAAT
86015 ATGTTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (28 bp):
TAAAGATAAATTTTAATAAAAAATAATT
Found at i:97287 original size:25 final size:25
Alignment explanation
Indices: 97258--97308 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
97248 CAGACAATTC
*
97258 ATTATATTTATTTAATATTAATATA
1 ATTATATTTATTCAATATTAATATA
97283 ATTATATTTATTCAATATTAATATA
1 ATTATATTTATTCAATATTAATATA
97308 A
1 A
97309 ATATTGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTATATTTATTCAATATTAATATA
Found at i:104858 original size:29 final size:29
Alignment explanation
Indices: 104816--104892 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
104806 TTTACTTTAG
104816 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACATTTTAGTCACTTATGTTTGAAAT
104845 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACATTTTAGTCACTTATGTTTGAAAT
104874 GTTACATTTTAGTCACTTA
1 GTTACATTTTAGTCACTTA
104893 CGTTATAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTATGTTTGAAAT
Found at i:108079 original size:96 final size:96
Alignment explanation
Indices: 107895--108086 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
107885 AATTTTGGAA
**
107895 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAATAAGTTAAGGCACAAGATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAAGATTTCA
* * * *
107960 GAATCGAAGATAAGGAAACATTGCCTTGATT
66 GAATCCAAAATAAAGAAACATTGCCTCGATT
* * * *
107991 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTGAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAAGA-TTTC
*
108055 A-AATCTCAAAATAAA-AGAATATTGCCTCGATT
65 AGAATC-CAAAATAAAGA-AACATTGCCTCGATT
108087 TTAAATTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
95 6 0.07
96 76 0.93
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAAGATTTCA
GAATCCAAAATAAAGAAACATTGCCTCGATT
Found at i:108326 original size:29 final size:30
Alignment explanation
Indices: 108293--108364 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
108283 ATCGGAGTTG
*
108293 AAAAT-GTGATTTTTGGAT-ACTCGGGGGGC
1 AAAATGGTAATTTTTGG-TCACTCGGGGGGC
*
108322 AAAATGGTAATTTTTGGTCACTC-GGGGGT
1 AAAATGGTAATTTTTGGTCACTCGGGGGGC
108351 AAAATGGTAATTTT
1 AAAATGGTAATTTT
108365 GGGAAAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.28, C:0.08, G:0.29, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGTCACTCGGGGGGC
Found at i:108378 original size:29 final size:29
Alignment explanation
Indices: 108316--108425 Score: 105
Period size: 29 Copynumber: 3.8 Consensus size: 29
108306 TGGATACTCG
* * ** *
108316 GGGGGCAAAATGGTAATTTTTGGTCACTC
1 GGGGGTAAAATGGTAATTTTGGGAAATTC
*
108345 GGGGGTAAAATGGTAATTTTGGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTGGGAAA-TTC
* ** *
108375 GGGGTTTAAAATGG-AATTTTTAGACATTC
1 GGGG-GTAAAATGGTAATTTTGGGAAATTC
108404 GGGGGTAAAATGGTAATTTTGG
1 GGGGGTAAAATGGTAATTTTGG
108426 AAAAATTGAG
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
28 8 0.12
29 34 0.53
30 14 0.22
31 8 0.12
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.34
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTGGGAAATTC
Found at i:108395 original size:59 final size:58
Alignment explanation
Indices: 108322--108456 Score: 180
Period size: 59 Copynumber: 2.3 Consensus size: 58
108312 CTCGGGGGGC
* ** * **
108322 AAAATGGTAATTTTTGGTCACTCGGGGGTAAAATGGTAATTTTGGGAAAGTTTGGGGTTT
1 AAAATGG-AATTTTTGGACACTCGGGGGTAAAATGGTAATTTT-GGAAAAATTGAGGTCA
* *
108382 AAAATGGAATTTTTAGACATTCGGGGGTAAAATGGTAATTTTGGAAAAATTGAGGTCA
1 AAAATGGAATTTTTGGACACTCGGGGGTAAAATGGTAATTTTGGAAAAATTGAGGTCA
108440 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
108457 AAAAAATGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
58 27 0.41
59 32 0.48
60 7 0.11
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGACACTCGGGGGTAAAATGGTAATTTTGGAAAAATTGAGGTCA
Found at i:108444 original size:89 final size:90
Alignment explanation
Indices: 108351--108550 Score: 223
Period size: 89 Copynumber: 2.3 Consensus size: 90
108341 ACTCGGGGGT
** * *
108351 AAAATGGTAATTTTGGGAAAGTTTGGGGTTTAAAATGGAA-TTTTTAGACA-TTCGGGGGTAAAA
1 AAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGAAATTTTTTA-A-AGTTCGAGGGTAAAA
*
108414 TGGTA-ATTTTGGAAAAATTGAGGTCA
64 TGGTATATTTTGGAAAAATCGAGGTCA
* ***
108440 AAAATGG-AATTTTTGGAAAAAAATGGGGTCAAAAATGAAATTTTTTAAAGTTCGAGGGTAAAAT
1 AAAATGGTAA-TTTTGGGAAAGTTTGGGGTCAAAAATGAAATTTTTTAAAGTTCGAGGGTAAAAT
* *
108504 GGTATTTTTTGGAGAAATCGAGGTCA
65 GGTATATTTTGGAAAAATCGAGGTCA
*
108530 AAAAT-ATAATTTT-GGAAAGTT
1 AAAATGGTAATTTTGGGAAAGTT
108551 CAAGGGTAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
88 7 0.08
89 52 0.58
90 31 0.34
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (90 bp):
AAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGAAATTTTTTAAAGTTCGAGGGTAAAATG
GTATATTTTGGAAAAATCGAGGTCA
Found at i:108446 original size:30 final size:31
Alignment explanation
Indices: 108410--108722 Score: 165
Period size: 30 Copynumber: 10.6 Consensus size: 31
108400 ATTCGGGGGT
108410 AAAATGGTAATTTTGGAAAAATTGA-GGTCA
1 AAAATGGTAATTTTGGAAAAATTGAGGGTCA
*
108440 AAAATGG-AATTTTTGGAAAAAAATG-GGGTCA
1 AAAATGGTAA-TTTTGG-AAAAATTGAGGGTCA
* ** *
108471 AAAAT-GAAATTTT-TTAAAGTTCGAGGGT--
1 AAAATGGTAATTTTGGAAAAATT-GAGGGTCA
* * *
108499 AAAATGGTATTTTTTGGAGAAATCGA-GGTCA
1 AAAATGGTA-ATTTTGGAAAAATTGAGGGTCA
* * *
108530 AAAAT-ATAATTTTGG-AAAGTTCAAGGGT--
1 AAAATGGTAATTTTGGAAAAATT-GAGGGTCA
* * *
108558 AAAATTGTAGTTTTTGGAAAAATT-AGGGTTA
1 AAAATGGTA-ATTTTGGAAAAATTGAGGGTCA
* *
108589 AAAATGG-AATTTTGG-AAAGTTCAAGGGT-A
1 AAAATGGTAATTTTGGAAAAATT-GAGGGTCA
108618 AAAAT-GTAATTTTTGGAAAAATT-AGGGT-A
1 AAAATGGTAA-TTTTGGAAAAATTGAGGGTCA
* *
108647 AAAGATGG-AATTTTGG-AAAGTTTAGTGGTC-
1 AAA-ATGGTAATTTTGGAAAAATTGAG-GGTCA
* *
108677 -AAATGCTAATTTTTGTAAAAATT-AGGGTC-
1 AAAATGGTAA-TTTTGGAAAAATTGAGGGTCA
108706 AAAATGG-AATTTTGGAA
1 AAAATGGTAATTTTGGAA
108723 TGTTCGAAGG
Statistics
Matches: 220, Mismatches: 31, Indels: 66
0.69 0.10 0.21
Matches are distributed among these distances:
28 38 0.17
29 63 0.29
30 70 0.32
31 49 0.22
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.33
Consensus pattern (31 bp):
AAAATGGTAATTTTGGAAAAATTGAGGGTCA
Found at i:108468 original size:59 final size:59
Alignment explanation
Indices: 108345--108461 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 59
108335 TTGGTCACTC
** * ** * ***
108345 GGGGGTAAAATGGTAATTTTGGGAAAGTTTGGGGTTTAAAATGGAATTTTTAGACATTC
1 GGGGGTAAAATGGTAATTTTGGGAAAAATTGAGGTCAAAAATGGAATTTTTAGAAAAAA
*
108404 GGGGGTAAAATGGTAATTTT-GGAAAAATTGAGGTCAAAAATGGAATTTTTGGAAAAAA
1 GGGGGTAAAATGGTAATTTTGGGAAAAATTGAGGTCAAAAATGGAATTTTTAGAAAAAA
108462 ATGGGGTCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
58 28 0.58
59 20 0.42
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTGGGAAAAATTGAGGTCAAAAATGGAATTTTTAGAAAAAA
Found at i:108470 original size:31 final size:30
Alignment explanation
Indices: 108410--108484 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
108400 ATTCGGGGGT
*
108410 AAAATGGTAA-TTTTGGAAAAATTGAGGTCA
1 AAAATGG-AATTTTTGGAAAAAATGAGGTCA
*
108440 AAAATGGAATTTTTGGAAAAAAATGGGGTCA
1 AAAATGGAATTTTTGG-AAAAAATGAGGTCA
*
108471 AAAATGAAATTTTT
1 AAAATGGAATTTTT
108485 TAAAGTTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.05
30 13 0.32
31 25 0.62
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.31
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAAAATGAGGTCA
Found at i:108747 original size:59 final size:57
Alignment explanation
Indices: 108440--108751 Score: 315
Period size: 59 Copynumber: 5.3 Consensus size: 57
108430 ATTGAGGTCA
* * * * ** *
108440 AAAATGGAATTTTTGGAAAAAAATGGGGTCAAAAATGAAATTTTTTAAAGTTCGAGGGT
1 AAAATGTAATTTTTGG-AAAAATTAGGGT-AAAAATGGAATTTTGGAAAGTTCAAGGGT
* * * **
108499 AAAATGGTATTTTTTGGAGAAA-TCGAGGTCAAAAATATAATTTTGGAAAGTTCAAGGGT
1 AAAAT-GTAATTTTTGGAAAAATTAG-GGT-AAAAATGGAATTTTGGAAAGTTCAAGGGT
*
108558 AAAATTGTAGTTTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
1 AAAA-TGTAATTTTTGGAAAAATTAGGG-TAAAAATGGAATTTTGGAAAGTTCAAGGGT
*
108617 AAAAATGTAATTTTTGGAAAAATTAGGGTAAAAGATGGAATTTTGGAAAGTT-TAGTGGT
1 -AAAATGTAATTTTTGGAAAAATTAGGGTAAAA-ATGGAATTTTGGAAAGTTCAAG-GGT
* * * *
108676 CAAATGCTAATTTTTGTAAAAATTAGGGTCAAAATGGAATTTTGGAATGTTCGAA-GGT
1 AAAATG-TAATTTTTGGAAAAATTAGGGTAAAAATGGAATTTTGGAAAGTTC-AAGGGT
*
108734 AAAATGATAAATTTTGGA
1 AAAATG-TAATTTTTGGA
108752 TAATTTTTGG
Statistics
Matches: 217, Mismatches: 25, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
58 48 0.22
59 151 0.70
60 18 0.08
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAAAATTAGGGTAAAAATGGAATTTTGGAAAGTTCAAGGGT
Found at i:109891 original size:3 final size:3
Alignment explanation
Indices: 109885--109951 Score: 80
Period size: 3 Copynumber: 21.3 Consensus size: 3
109875 CCTTTTTTTC
* *
109885 TAT TAT TAT TAT TAT TAT TAT TAAT TAAT TAA TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT T-AT TAT TAT TAT TAT TAT TAT
*
109932 TATT TAT TAT TGT TAT TAT T
1 TA-T TAT TAT TAT TAT TAT T
109952 CATATTAATG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 46 0.82
4 10 0.18
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:110387 original size:21 final size:21
Alignment explanation
Indices: 110361--110402 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
110351 CAATAATTAC
110361 AAATCTGTTTCTCCTATCTTT
1 AAATCTGTTTCTCCTATCTTT
110382 AAATCTGTTTCTCCTATCTTT
1 AAATCTGTTTCTCCTATCTTT
110403 CTTTCTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.52
Consensus pattern (21 bp):
AAATCTGTTTCTCCTATCTTT
Found at i:110548 original size:56 final size:57
Alignment explanation
Indices: 110471--110585 Score: 214
Period size: 56 Copynumber: 2.0 Consensus size: 57
110461 GGTGGGTGCT
*
110471 AACGTGGTGTGTTCTGATAGGCTGAAATGAAGGCATCAACAGTGTAAGT-GGGGTAG
1 AACGTGGTGTGTTCTGATAGGCTGAAATGAAGGCATCAACAGTGCAAGTGGGGGTAG
110527 AACGTGGTGTGTTCTGATAGGCTGAAATGAAGGCATCAACAGTGCAAGTGGGGGTAG
1 AACGTGGTGTGTTCTGATAGGCTGAAATGAAGGCATCAACAGTGCAAGTGGGGGTAG
110584 AA
1 AA
110586 GCTTGGCTAC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 48 0.84
57 9 0.16
ACGTcount: A:0.30, C:0.11, G:0.36, T:0.23
Consensus pattern (57 bp):
AACGTGGTGTGTTCTGATAGGCTGAAATGAAGGCATCAACAGTGCAAGTGGGGGTAG
Found at i:110745 original size:17 final size:17
Alignment explanation
Indices: 110723--110794 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
110713 GACTTTAATT
*
110723 AATTTAAATTGAAAATA
1 AATTTAAATTTAAAATA
*
110740 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAATA
* * * *
110757 AATTCAAACTCAAAATG
1 AATTTAAATTTAAAATA
110774 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
110791 AATT
1 AATT
110795 CAAACTTATT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:110772 original size:34 final size:34
Alignment explanation
Indices: 110734--110800 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
110724 ATTTAAATTG
*
110734 AAAATAAATTTAAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
*
110768 AAAATGAATTTAAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
110801 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:113483 original size:3 final size:3
Alignment explanation
Indices: 113477--113534 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
113467 CATCATCATC
113477 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
113525 ATT ATT ATT A
1 ATT ATT ATT A
113535 CGTGTCCTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:113878 original size:17 final size:19
Alignment explanation
Indices: 113849--113896 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
113839 CAATTTTAAA
*
113849 AAATTAGAAAAAATTT-A-
1 AAATTATAAAAAATTTCAG
*
113866 AAGTTATAAAAAATTTCAG
1 AAATTATAAAAAATTTCAG
113885 AAATTATAAAAA
1 AAATTATAAAAA
113897 TATACTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 14 0.54
18 1 0.04
19 11 0.42
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (19 bp):
AAATTATAAAAAATTTCAG
Done.