Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011961.1 Kokia drynarioides strain JFW-HI SEQ_126959, 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: 62951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:3606 original size:19 final size:19
Alignment explanation
Indices: 3579--3631 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
3569 TCAAAAATTT
3579 GTTTTTGTTGAAG-TTGTGG
1 GTTTTTGTTGAAGTTTGT-G
*
3598 GTTTGTGTTGAAGTTTGTG
1 GTTTTTGTTGAAGTTTGTG
*
3617 GTTTTTGCTGAAGTT
1 GTTTTTGTTGAAGTT
3632 AAGAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.11, C:0.02, G:0.34, T:0.53
Consensus pattern (19 bp):
GTTTTTGTTGAAGTTTGTG
Found at i:4960 original size:149 final size:149
Alignment explanation
Indices: 4685--4992 Score: 607
Period size: 149 Copynumber: 2.1 Consensus size: 149
4675 AGTAAACGGG
4685 TACACACTTGATCCCATCACTTTACTTGAACTATTCTTTATTATAGTCCTGCTATTGTTGTTTGT
1 TACA-ACTTGATCCCATCACTTTACTTGAACTATTCTTTATTATAGTCCTGCTATTGTTGTTTGT
4750 GTTTGTTGAAGAAAGGAGACGTCAAAGTTTGCTTTGACTGTTTTTGGTTTAGGAGCCTCCCAACG
65 GTTTGTTGAAGAAAGGAGACGTCAAAGTTTGCTTTGACTGTTTTTGGTTTAGGAGCCTCCCAACG
4815 GGCTTCCTCCACCTCAGATC
130 GGCTTCCTCCACCTCAGATC
4835 TACAACTTGATCCCATCACTTTACTTGAACTATTCTTTATTATAGTCCTGCTATTGTTGTTTGTG
1 TACAACTTGATCCCATCACTTTACTTGAACTATTCTTTATTATAGTCCTGCTATTGTTGTTTGTG
4900 TTTGTTGAAGAAAGGAGACGTCAAAGTTTGCTTTGACTGTTTTTGGTTTAGGAGCCTCCCAACGG
66 TTTGTTGAAGAAAGGAGACGTCAAAGTTTGCTTTGACTGTTTTTGGTTTAGGAGCCTCCCAACGG
4965 GCTTCCTCCACCTCAGATC
131 GCTTCCTCCACCTCAGATC
4984 TACAACTTG
1 TACAACTTG
4993 GATTCGAATC
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
149 154 0.97
150 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (149 bp):
TACAACTTGATCCCATCACTTTACTTGAACTATTCTTTATTATAGTCCTGCTATTGTTGTTTGTG
TTTGTTGAAGAAAGGAGACGTCAAAGTTTGCTTTGACTGTTTTTGGTTTAGGAGCCTCCCAACGG
GCTTCCTCCACCTCAGATC
Found at i:10088 original size:21 final size:20
Alignment explanation
Indices: 10044--10092 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
10034 AATTTAATCA
*
10044 AAATATATAAACTATACTTT
1 AAATATTTAAACTATACTTT
10064 AAATATTTAAA-TATAACTATT
1 AAATATTTAAACTAT-ACT-TT
10085 AAATATTT
1 AAATATTT
10093 GTAATTAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATATTTAAACTATACTTT
Found at i:12887 original size:13 final size:13
Alignment explanation
Indices: 12864--12896 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12854 AAGGGGAAAG
12864 AAAAT-AAAAATA
1 AAAATAAAAAATA
12876 AAAATAAAAAATA
1 AAAATAAAAAATA
*
12889 ATAATAAA
1 AAAATAAA
12897 GGGGTCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:13629 original size:22 final size:21
Alignment explanation
Indices: 13588--13630 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
13578 TTAAGCCTAA
*
13588 TTATAGTTAATAATATATGAT
1 TTATAGTTAATAATAAATGAT
*
13609 TTATAGTATGATAATAAATGAT
1 TTATAGT-TAATAATAAATGAT
13631 AACATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (21 bp):
TTATAGTTAATAATAAATGAT
Found at i:13932 original size:6 final size:6
Alignment explanation
Indices: 13921--13950 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
13911 ATTTATTTTC
13921 TATTAA TATTAA TATTAA TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA
13951 AGTTTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAA
Found at i:16532 original size:22 final size:22
Alignment explanation
Indices: 16507--16553 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
16497 ATTATGTCTT
16507 TATGTAGAAATTTGAGAACTCC
1 TATGTAGAAATTTGAGAACTCC
16529 TATGTAGAAATTTGAGAACTCC
1 TATGTAGAAATTTGAGAACTCC
16551 TAT
1 TAT
16554 AAATAGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (22 bp):
TATGTAGAAATTTGAGAACTCC
Found at i:17102 original size:23 final size:22
Alignment explanation
Indices: 17076--17119 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17066 AAAATATTTC
*
17076 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
17099 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
17120 TTATTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:30467 original size:33 final size:33
Alignment explanation
Indices: 30430--30526 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 33
30420 TTGCATGTGT
* *
30430 TGTATTAAATATTTGTTTCTGGTTTGATAGTGA
1 TGTATTAAATATTTATTTCTGGTCTGATAGTGA
*
30463 TGTATTAAA-AGTTTTTTTCTGGTCTGATAGTGA
1 TGTATTAAATA-TTTATTTCTGGTCTGATAGTGA
* *
30496 TGTATTAAATGTTTATTTGTGGTCTGATAGT
1 TGTATTAAATATTTATTTCTGGTCTGATAGT
30527 AATGAGTAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.02
33 56 0.98
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.51
Consensus pattern (33 bp):
TGTATTAAATATTTATTTCTGGTCTGATAGTGA
Found at i:32306 original size:26 final size:26
Alignment explanation
Indices: 32268--32362 Score: 111
Period size: 26 Copynumber: 3.7 Consensus size: 26
32258 TTTTTTAATA
* *
32268 TTATTTTCATATGCTGTTCTTTATTGT
1 TTATTTT-GTATGTTGTTCTTTATTGT
* * *
32295 TTATTTTGTATGTTATTCTTTAAT-A
1 TTATTTTGTATGTTGTTCTTTATTGT
* *
32320 TGATTTTGTATATTGTTCTTTATTGT
1 TTATTTTGTATGTTGTTCTTTATTGT
32346 TTATTTTGTATGTTGTT
1 TTATTTTGTATGTTGTT
32363 TTATGTTGGC
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
25 20 0.36
26 28 0.51
27 7 0.13
ACGTcount: A:0.17, C:0.05, G:0.13, T:0.65
Consensus pattern (26 bp):
TTATTTTGTATGTTGTTCTTTATTGT
Found at i:32345 original size:51 final size:51
Alignment explanation
Indices: 32256--32359 Score: 156
Period size: 51 Copynumber: 2.0 Consensus size: 51
32246 TCTTATTTTG
* *
32256 TATTTTTTAATATTATTTTCATATGCTGTTCTTTATTGTTTATTTTGTATGT
1 TATTCTTTAATATGATTTTCATAT-CTGTTCTTTATTGTTTATTTTGTATGT
*
32308 TATTCTTTAATATGATTTTGTATAT-TGTTCTTTATTGTTTATTTTGTATGT
1 TATTCTTTAATATGATTTT-CATATCTGTTCTTTATTGTTTATTTTGTATGT
32359 T
1 T
32360 GTTTTATGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
51 27 0.56
52 17 0.35
53 4 0.08
ACGTcount: A:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (51 bp):
TATTCTTTAATATGATTTTCATATCTGTTCTTTATTGTTTATTTTGTATGT
Found at i:33534 original size:27 final size:27
Alignment explanation
Indices: 33504--33563 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
33494 ATTTGGCAAT
*
33504 AGTTTGCCATTCCTTTATTTTGTAAAC
1 AGTTTGCCATTCCTATATTTTGTAAAC
*
33531 AGTTTGTCATTCCTATATTTTGTAAAC
1 AGTTTGCCATTCCTATATTTTGTAAAC
*
33558 ATTTTG
1 AGTTTG
33564 GCCTTTAGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (27 bp):
AGTTTGCCATTCCTATATTTTGTAAAC
Found at i:34964 original size:29 final size:27
Alignment explanation
Indices: 34932--34998 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
34922 TAAATCTTAA
* *
34932 AATTATACATGAACTTTGATTTAATGTGT
1 AATTATACATGAACTTTAATTT--GGTGT
*
34961 AATTTTATTCATGAACTTTAATTTGGTGT
1 AA--TTATACATGAACTTTAATTTGGTGT
34990 AATTATACA
1 AATTATACA
34999 CGTGAAACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 6 0.19
29 8 0.25
31 18 0.56
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (27 bp):
AATTATACATGAACTTTAATTTGGTGT
Found at i:35242 original size:29 final size:30
Alignment explanation
Indices: 35189--35247 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
35179 GAATCGGATC
* *
35189 AAATCGAAATTTCATGTCTAAAATTACACA
1 AAATCGAAAGTTCATGTATAAAATTACACA
* *
35219 AAATC-AAAGTTCATGTATATAATTGCACA
1 AAATCGAAAGTTCATGTATAAAATTACACA
35248 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (30 bp):
AAATCGAAAGTTCATGTATAAAATTACACA
Found at i:36821 original size:10 final size:10
Alignment explanation
Indices: 36806--36864 Score: 64
Period size: 10 Copynumber: 5.9 Consensus size: 10
36796 TTACCAATTC
36806 GGTTAATTTT
1 GGTTAATTTT
*
36816 GGTTAATTTC
1 GGTTAATTTT
* *
36826 GATTGATTTT
1 GGTTAATTTT
*
36836 GGTTAATTTC
1 GGTTAATTTT
**
36846 GGTTGCTTTT
1 GGTTAATTTT
36856 GGTTAATTT
1 GGTTAATTT
36865 AGTTAAATGA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.17, C:0.05, G:0.22, T:0.56
Consensus pattern (10 bp):
GGTTAATTTT
Found at i:36834 original size:20 final size:20
Alignment explanation
Indices: 36811--36864 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
36801 AATTCGGTTA
36811 ATTTTGGTTAATTTCGATTG
1 ATTTTGGTTAATTTCGATTG
*
36831 ATTTTGGTTAATTTCGGTTG
1 ATTTTGGTTAATTTCGATTG
*
36851 CTTTTGGTTAATTT
1 ATTTTGGTTAATTT
36865 AGTTAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.06, G:0.20, T:0.57
Consensus pattern (20 bp):
ATTTTGGTTAATTTCGATTG
Found at i:37915 original size:20 final size:21
Alignment explanation
Indices: 37871--37915 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
37861 TTTACGAAAA
*
37871 AAATACAAATCATAATTAATC
1 AAATAAAAATCATAATTAATC
* *
37892 AAATAAAAAT-ATATTTAATT
1 AAATAAAAATCATAATTAATC
37912 AAAT
1 AAAT
37916 GAATTCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAAAATCATAATTAATC
Found at i:48270 original size:50 final size:51
Alignment explanation
Indices: 48170--48281 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
48160 TAATAAAAAA
* *
48170 TTAGCTCTTAAACTTTACACATTCTGTTAGTTTAGTCTCGATTTAACAAAT
1 TTAGCTCTCAAACTTTACACATTCTGATAGTTTAGTCTCGATTTAACAAAT
* * * *
48221 TTAGCTCTCAAAGTTTATACATTCTGATAGTTT-GTCTTGCTTTAACAAAT
1 TTAGCTCTCAAACTTTACACATTCTGATAGTTTAGTCTCGATTTAACAAAT
*
48271 TTAGCCCTCAA
1 TTAGCTCTCAA
48282 CATTCACATA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 25 0.46
51 29 0.54
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.42
Consensus pattern (51 bp):
TTAGCTCTCAAACTTTACACATTCTGATAGTTTAGTCTCGATTTAACAAAT
Found at i:53323 original size:19 final size:18
Alignment explanation
Indices: 53295--53333 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
53285 ATTAAAAGGC
53295 AAAAAAAC-AAATATGTAA
1 AAAAAAACAAAATAT-TAA
53313 AAAATAAACAAAATATTAA
1 AAAA-AAACAAAATATTAA
53332 AA
1 AA
53334 CCCTAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAAACAAAATATTAA
Found at i:54138 original size:30 final size:30
Alignment explanation
Indices: 54095--54254 Score: 209
Period size: 30 Copynumber: 5.4 Consensus size: 30
54085 CCTTTAAAAA
* *
54095 TTTCCATAATTACATTTTAACCCCTAAACT
1 TTTCCAAAATTACATTTTGACCCCTAAACT
* *
54125 TTTCAAAAATTACATTTTGA-CCCAAAAC-
1 TTTCCAAAATTACATTTTGACCCCTAAACT
54153 TTTCTCAAAATTACA-TTTGACCCCTAAACT
1 TTTC-CAAAATTACATTTTGACCCCTAAACT
* *
54183 TTTCTAAAATTTCATTTTGACCCCTAAACT
1 TTTCCAAAATTACATTTTGACCCCTAAACT
* * *
54213 TTTCCAAAATTTCATTTTAACCCTTAAACT
1 TTTCCAAAATTACATTTTGACCCCTAAACT
54243 TTTCCAAAATTA
1 TTTCCAAAATTA
54255 TGTTTTGATC
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
28 9 0.08
29 31 0.27
30 74 0.65
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
TTTCCAAAATTACATTTTGACCCCTAAACT
Found at i:54221 original size:59 final size:58
Alignment explanation
Indices: 54090--54269 Score: 218
Period size: 58 Copynumber: 3.1 Consensus size: 58
54080 GTAGTCCTTT
* *
54090 AAAAATTTCCATAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCC
1 AAAACTTTCCAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCC
* * *
54148 AAAACTTTCTCAAAATTACA-TTTGACCCCTAAACTTTTCTAAAATTTCATTTTGACCCC
1 AAAACTTTC-CAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGA-CCC
* * * * **
54207 TAAACTTTTCCAAAATTTCATTTTAACCCTTAAACTTTTCCAAAATTATGTTTTGATCCC
1 AAAAC-TTTCCAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGA-CCC
54267 AAA
1 AAA
54270 TTCTTCGAAA
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
58 40 0.39
59 25 0.24
60 38 0.37
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (58 bp):
AAAACTTTCCAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCC
Found at i:58927 original size:17 final size:17
Alignment explanation
Indices: 58907--58943 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
58897 GCATCTTTAA
58907 AAAAAGGAA-AAGAAAAG
1 AAAAAGGAAGAA-AAAAG
58924 AAAAAGGAAGAAAAAAG
1 AAAAAGGAAGAAAAAAG
58941 AAA
1 AAA
58944 GTCAAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAGGAAGAAAAAAG
Found at i:59848 original size:21 final size:22
Alignment explanation
Indices: 59819--59866 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
59809 AATTAAATTA
59819 AAAAAAGAAGAAAAG-AAAAAG
1 AAAAAAGAAGAAAAGAAAAAAG
* *
59840 AAAAGAGAAGAGAAGAAAAAAG
1 AAAAAAGAAGAAAAGAAAAAAG
59862 AAAAA
1 AAAAA
59867 GGAGAGGTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAGAAAAGAAAAAAG
Found at i:59862 original size:7 final size:7
Alignment explanation
Indices: 59819--59866 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
59809 AATTAAATTA
59819 AAAAAAG
1 AAAAAAG
59826 AAGAAAAG
1 AA-AAAAG
59834 -AAAAAG
1 AAAAAAG
*
59840 AAAAGAG
1 AAAAAAG
*
59847 AAGAGAAG
1 AA-AAAAG
59855 AAAAAAG
1 AAAAAAG
59862 AAAAA
1 AAAAA
59867 GGAGAGGTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 5 0.15
7 19 0.56
8 10 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:59872 original size:21 final size:20
Alignment explanation
Indices: 59820--59872 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
59810 ATTAAATTAA
*
59820 AAAAAGAAGAAAAGAAAAAG
1 AAAAAGAAGAGAAGAAAAAG
59840 AAAAGAGAAGAGAAGAAAAAAG
1 AAAA-AGAAGAGAAG-AAAAAG
*
59862 AAAAAGGAGAG
1 AAAAAGAAGAG
59873 GTCGAGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 15 0.52
22 10 0.34
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAAGAAGAGAAGAAAAAG
Found at i:60373 original size:112 final size:106
Alignment explanation
Indices: 60188--60441 Score: 278
Period size: 112 Copynumber: 2.3 Consensus size: 106
60178 ACAAGTTTTA
* * **
60188 CCTCTAATAAAATTTAATTTTATCCACCTTACGAA-CATGTTCAAGCATTTTTGCATTGAAATAA
1 CCTCCAATAAAATTCAATTTTATCCACCTTAC-AACCATGTTCAAGCACGTTTGCATTGAAATAA
** * * * * *
60252 TGGTAAGTGGAC-AATTGTTTTTTATTTTTTTCATTCATTTGACCTTTG
65 CAGTAAGTGGACTAA-------TAATTCTTTTCATTCACTCGACCTCTG
* *
60300 CCTCCAATATAATTCAATTTTATCCACCTTACAACCTTGTTCAAGCACGTTTGCATTGAAATAAC
1 CCTCCAATAAAATTCAATTTTATCCACCTTACAACCATGTTCAAGCACGTTTGCATTGAAATAAC
* *
60365 AGTTAGTGGACTAATAATTCTTTTCATTCACTCGAGCTCTG
66 AGTAAGTGGACTAATAATTCTTTTCATTCACTCGACCTCTG
*
60406 CCTCCAATAAAATTCAAATTTATCCACCTTACAACC
1 CCTCCAATAAAATTCAATTTTATCCACCTTACAACC
60442 CTAATCAAAC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
106 55 0.45
111 2 0.02
112 64 0.52
113 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (106 bp):
CCTCCAATAAAATTCAATTTTATCCACCTTACAACCATGTTCAAGCACGTTTGCATTGAAATAAC
AGTAAGTGGACTAATAATTCTTTTCATTCACTCGACCTCTG
Found at i:62834 original size:39 final size:39
Alignment explanation
Indices: 62774--62951 Score: 140
Period size: 39 Copynumber: 4.6 Consensus size: 39
62764 GAAGATTCCG
* * * *
62774 ATCTCTTACCTCGATCATGGGGCAGATCACAACCATCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACAACCAGCCA
* * * *
62813 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACAACCAGCCA
* * * * * * * **
62852 ATCCCTTACCTCGAGCCTGGAGAAAATTACAACCATCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACAACCAGCCA
* * * * * *
62891 ATCTTTTATCCCGAGCTTGGGGTAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACAACCAGCCA
*
62930 ATATCTTACCCCGAGCCTGGGG
1 ATCTCTTACCCCGAGCCTGGGG
Statistics
Matches: 101, Mismatches: 38, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
39 101 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACAACCAGCCA
Found at i:62884 original size:78 final size:78
Alignment explanation
Indices: 62802--62949 Score: 233
Period size: 78 Copynumber: 1.9 Consensus size: 78
62792 GGGGCAGATC
* *
62802 ACAACCATCCAATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCCCTTACCTCGAG
1 ACAACCATCCAATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATACCTTACCCCGAG
62867 CCTGGAGAAAATT
66 CCTGGAGAAAATT
** * * *
62880 ACAACCATCTGATCTTTTATCCCGAGCTTGGGGTAGATCACCATCAGCCAATATCTTACCCCGAG
1 ACAACCATCCAATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATACCTTACCCCGAG
62945 CCTGG
66 CCTGG
62950 GG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (78 bp):
ACAACCATCCAATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATACCTTACCCCGAG
CCTGGAGAAAATT
Done.