Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013196.1 Kokia drynarioides strain JFW-HI SEQ_128215, 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: 81653
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:4234 original size:233 final size:233
Alignment explanation
Indices: 3827--4284 Score: 898
Period size: 233 Copynumber: 2.0 Consensus size: 233
3817 TTTTGAATAC
3827 TATAAAGTTATACTCACATTTTTAAAAACTTGCAACTTCAAGTGCATCAAACCATAACGAGCTTT
1 TATAAAGTTATACTCACATTTTTAAAAACTTGCAACTTCAAGTGCATCAAACCATAACGAGCTTT
3892 AGATAAAATTATCACATCCTATTGCTCATATTTTTCTTCCACAATTTAAGTAGATCTTTCATAGT
66 AGATAAAATTATCACATCCTATTGCTCATATTTTTCTTCCACAATTTAAGTAGATCTTTCATAGT
3957 CAAATATTTTGACTTCAACCTCTTAATGGGGATAATGACAAAAGAATATCACAAAGATAGTCACA
131 CAAATATTTTGACTTCAACCTCTTAATGGGGATAATGACAAAAGAATATCACAAAGATAGTCACA
4022 ATCAGTTCAATTTATAATAAATATAAATCAGTTCAATT
196 ATCAGTTCAATTTATAATAAATATAAATCAGTTCAATT
4060 TATAAAGTTATACTCACATTTTTAAAAACTTGCAACTTCAAGTGCATCAAACCATAACGAGCTTT
1 TATAAAGTTATACTCACATTTTTAAAAACTTGCAACTTCAAGTGCATCAAACCATAACGAGCTTT
*
4125 AGATAAAATTATCACATTCTATTGCTCATATTTTTCTTCCACAATTTAAGTAGATCTTTCATAGT
66 AGATAAAATTATCACATCCTATTGCTCATATTTTTCTTCCACAATTTAAGTAGATCTTTCATAGT
*
4190 CAAATATTTTGACTTCAACCTCTTAATGGGGATAATGACAAAAGAATATCACAAAGATAGTCATA
131 CAAATATTTTGACTTCAACCTCTTAATGGGGATAATGACAAAAGAATATCACAAAGATAGTCACA
4255 ATCAGTTCAATTTATAATAAATATAAATCA
196 ATCAGTTCAATTTATAATAAATATAAATCA
4285 ATAGCACAAT
Statistics
Matches: 223, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
233 223 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (233 bp):
TATAAAGTTATACTCACATTTTTAAAAACTTGCAACTTCAAGTGCATCAAACCATAACGAGCTTT
AGATAAAATTATCACATCCTATTGCTCATATTTTTCTTCCACAATTTAAGTAGATCTTTCATAGT
CAAATATTTTGACTTCAACCTCTTAATGGGGATAATGACAAAAGAATATCACAAAGATAGTCACA
ATCAGTTCAATTTATAATAAATATAAATCAGTTCAATT
Found at i:8922 original size:30 final size:29
Alignment explanation
Indices: 8794--9058 Score: 193
Period size: 30 Copynumber: 8.9 Consensus size: 29
8784 AAAAAAAAGG
* *
8794 GGGTCAAAATG-AAGTTTT-TAAGAATTTTA
1 GGGTCAAAATGTAA-TTTTGGAA-AAGTTTA
* *
8823 GGGCCAAAATGTAATTTTATGAAAA-TTTA
1 GGGTCAAAATGTAATTTT-GGAAAAGTTTA
* *
8852 GGGGT-TAAATGTAATTTTGG-AAAGTTTG
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTA
8880 GGGTTC-AAATGTAATTTTGGAAAAGTTTGA
1 GGG-TCAAAATGTAATTTTGGAAAAGTTT-A
*
8910 GGGTCAAAATGTAATTTTGGAAAATTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTT-A
* ** *
8940 GGATCAAAATGTAATTTTTAAAAAAATTTA
1 GGGTCAAAATGTAA-TTTTGGAAAAGTTTA
* * **
8970 GGGGTTAAAATTTAATTTTTAAAAAGTTTTAA
1 -GGGTCAAAATGTAATTTTGGAAAAG-TTT-A
* *
9002 AGGTTAAAATGTAATTTTTGGAAAA-TTTA
1 GGGTCAAAATGTAA-TTTTGGAAAAGTTTA
* *
9031 GGGGTTAAAATGTAATTTTTGAAAAGTT
1 -GGGTCAAAATGTAATTTTGGAAAAGTT
9059 CGAGGGTTAA
Statistics
Matches: 195, Mismatches: 24, Indels: 33
0.77 0.10 0.13
Matches are distributed among these distances:
27 6 0.03
28 19 0.10
29 49 0.25
30 73 0.37
31 39 0.20
32 9 0.05
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.38
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTA
Found at i:9030 original size:61 final size:60
Alignment explanation
Indices: 8828--9058 Score: 260
Period size: 61 Copynumber: 3.9 Consensus size: 60
8818 TTTTAGGGCC
* **
8828 AAAATGTAATTTTAT-GAAAATTTAGGGGTT-AAATGTAA-TTTTGGAAAG-TTTGGGGTT
1 AAAATGTAATTTT-TGGAAAATTTAGGGGTTAAAATGTAATTTTTGAAAAGTTTTAAGGTT
* * * *
8885 CAAATGTAA-TTTTGGAAAAGTTT-GAGGGTCAAAATGTAATTTTGGAAAA-TTTTAAGGATC
1 AAAATGTAATTTTTGGAAAA-TTTAG-GGGTTAAAATGTAATTTTTGAAAAGTTTTAAGG-TT
** * *
8945 AAAATGTAATTTTTAAAAAAATTTAGGGGTTAAAATTTAATTTTTAAAAAGTTTTAAAGGTT
1 AAAATGTAATTTTT-GGAAAATTTAGGGGTTAAAATGTAATTTTTGAAAAGTTTT-AAGGTT
9007 AAAATGTAATTTTTGGAAAATTTAGGGGTTAAAATGTAATTTTTGAAAAGTT
1 AAAATGTAATTTTTGGAAAATTTAGGGGTTAAAATGTAATTTTTGAAAAGTT
9059 CGAGGGTTAA
Statistics
Matches: 143, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
55 1 0.01
56 9 0.06
57 15 0.10
58 8 0.06
59 12 0.08
60 9 0.06
61 61 0.43
62 24 0.17
63 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.39
Consensus pattern (60 bp):
AAAATGTAATTTTTGGAAAATTTAGGGGTTAAAATGTAATTTTTGAAAAGTTTTAAGGTT
Found at i:9070 original size:29 final size:30
Alignment explanation
Indices: 8828--9069 Score: 221
Period size: 30 Copynumber: 8.1 Consensus size: 30
8818 TTTTAGGGCC
8828 AAAATGTAATTTTATGAAAA-TTT-AGGGGTT
1 AAAATGTAATTTT-TGAAAAGTTTGA-GGGTT
*
8858 -AAATGTAA-TTTTGGAAAGTTTG-GGGTT
1 AAAATGTAATTTTTGAAAAGTTTGAGGGTT
* * *
8885 CAAATGTAATTTTGGAAAAGTTTGAGGGTC
1 AAAATGTAATTTTTGAAAAGTTTGAGGGTT
* * * * *
8915 AAAATGTAATTTTGGAAAATTTTAAGGATC
1 AAAATGTAATTTTTGAAAAGTTTGAGGGTT
* *
8945 AAAATGTAATTTTTAAAAAAATTT-AGGGGTT
1 AAAATGTAATTTTT-GAAAAGTTTGA-GGGTT
* * * *
8976 AAAATTTAATTTTTAAAAAGTTTTAAAGGTT
1 AAAATGTAATTTTTGAAAAG-TTTGAGGGTT
9007 AAAATGTAATTTTTGGAAAA-TTT-AGGGGTT
1 AAAATGTAATTTTT-GAAAAGTTTGA-GGGTT
*
9037 AAAATGTAATTTTTGAAAAGTTCGAGGGTT
1 AAAATGTAATTTTTGAAAAGTTTGAGGGTT
9067 AAA
1 AAA
9070 TCCAAATTTT
Statistics
Matches: 179, Mismatches: 20, Indels: 26
0.80 0.09 0.12
Matches are distributed among these distances:
27 10 0.06
28 14 0.08
29 26 0.15
30 80 0.45
31 44 0.25
32 5 0.03
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTGAAAAGTTTGAGGGTT
Found at i:17628 original size:13 final size:15
Alignment explanation
Indices: 17605--17636 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17595 GGATCCACTT
17605 TAAACTCT-AAAAGA
1 TAAACTCTAAAAAGA
17619 TAAA-TCTAAAAAGA
1 TAAACTCTAAAAAGA
17633 TAAA
1 TAAA
17637 AACAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.22
Consensus pattern (15 bp):
TAAACTCTAAAAAGA
Found at i:19237 original size:12 final size:12
Alignment explanation
Indices: 19222--19265 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
19212 TAAAATAAAT
19222 AAATAAATAGAA
1 AAATAAATAGAA
19234 AAATAAATAGAA
1 AAATAAATAGAA
* *
19246 AAGTAAAAAGAA
1 AAATAAATAGAA
19258 AAA-AAATA
1 AAATAAATA
19266 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (12 bp):
AAATAAATAGAA
Found at i:19274 original size:20 final size:20
Alignment explanation
Indices: 19213--19274 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 20
19203 TCTTGGACAT
* *
19213 AAAATAAAT-AAATAAATAG
1 AAAAAAAATAAAATAAAAAG
19232 AAAAATAAATAGAAAAGTAAAAAG
1 AAAAA-AAAT--AAAA-TAAAAAG
19256 AAAAAAAATAAAATAAAAA
1 AAAAAAAATAAAATAAAAA
19275 AATTGGGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 4 0.11
20 10 0.28
21 4 0.11
23 7 0.19
24 11 0.31
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (20 bp):
AAAAAAAATAAAATAAAAAG
Found at i:28621 original size:35 final size:35
Alignment explanation
Indices: 28570--28641 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
28560 CTAATGAGTG
28570 TATTACTAAGGTTGTAAAATAGCCTATTTATAGGC
1 TATTACTAAGGTTGTAAAATAGCCTATTTATAGGC
*
28605 TATTTCTAAGGTTGTAAAATAGCCTATTTATAGGC
1 TATTACTAAGGTTGTAAAATAGCCTATTTATAGGC
28640 TA
1 TA
28642 AATTCCTAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (35 bp):
TATTACTAAGGTTGTAAAATAGCCTATTTATAGGC
Found at i:28712 original size:24 final size:24
Alignment explanation
Indices: 28683--28736 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
28673 TAGACTAATA
28683 AGAGTTTTACTCAAACAAAAAAAT
1 AGAGTTTTACTCAAACAAAAAAAT
* * *
28707 AGAG-TTTATTTAAACAAATAAAT
1 AGAGTTTTACTCAAACAAAAAAAT
28730 AGAGTTT
1 AGAGTTT
28737 AATTGAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (24 bp):
AGAGTTTTACTCAAACAAAAAAAT
Found at i:28757 original size:24 final size:24
Alignment explanation
Indices: 28695--28768 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
28685 AGTTTTACTC
* *
28695 AAACAAAAAAATAGAGTTT-ATTT
1 AAACAAATAAATAGAGTTTAATTG
28718 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
* * *
28742 AAGCAAATAAACAGAGTTTAACTG
1 AAACAAATAAATAGAGTTTAATTG
28766 AAA
1 AAA
28769 GATTATTTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 18 0.41
24 26 0.59
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (24 bp):
AAACAAATAAATAGAGTTTAATTG
Found at i:39561 original size:16 final size:16
Alignment explanation
Indices: 39540--39572 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39530 AAAAATTGTA
39540 TTTATTACTTT-TTTAT
1 TTTATTA-TTTATTTAT
39556 TTTATTATTTATTTAT
1 TTTATTATTTATTTAT
39572 T
1 T
39573 CCAAATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTATTTATTTAT
Found at i:42488 original size:22 final size:22
Alignment explanation
Indices: 42453--42494 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42443 TCTGGAGCTC
* *
42453 ACAGAGAATGTCAGTACCAGGG
1 ACAGAAAATATCAGTACCAGGG
42475 ACAGAAAATATCAGTACCAG
1 ACAGAAAATATCAGTACCAG
42495 AGGCGATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (22 bp):
ACAGAAAATATCAGTACCAGGG
Found at i:42624 original size:2 final size:2
Alignment explanation
Indices: 42617--42642 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42607 CAATATAATC
42617 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42643 TAATTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45079 original size:165 final size:166
Alignment explanation
Indices: 44807--45140 Score: 546
Period size: 165 Copynumber: 2.0 Consensus size: 166
44797 ATTTAAGTCC
*
44807 TTACACTGATCTAACACTTACCAATTTAGCGACCTCACTGTTGTACAAAGACTAGATCACTCTAC
1 TTACACTGATCTAACACTCACCAATTTAGCGACCTCACTGTTGTACAAAGACTAGATCACTCTAC
* *
44872 TACTAAGCTTTCCTCTCGAAAGCTTAGCTTTGCAACTCAAGAAACTCTCTGGATTACTTACAAAA
66 TACTAAGCTTTCCCCTCGAAAGCTTAGCTTTGCAACTCAAGAAACCCTCTGGATTACTTACAAAA
44937 A-AATGCACACATAAAACACTCCTAACTTGAACAAA
131 ACAATGCACACATAAAACACTCCTAACTTGAACAAA
* * *
44972 TTACACTGATCTAACACTCATCAATTTAGTGACCTCACTGTTGTACAAAGACTAGATCACTCT-G
1 TTACACTGATCTAACACTCACCAATTTAGCGACCTCACTGTTGTACAAAGACTAGATCACTCTAC
* * * * *
45036 TCATTAAGCTTTCCCCTTGAAAGCTTTGCTTTGCAACTCAAGAAACCCTCTTGATTGCTTACAAA
66 T-ACTAAGCTTTCCCCTCGAAAGCTTAGCTTTGCAACTCAAGAAACCCTCTGGATTACTTACAAA
45101 AACAATGCACACATAAAACACTCCTAACTTGAACAAA
130 AACAATGCACACATAAAACACTCCTAACTTGAACAAA
45138 TTA
1 TTA
45141 GTGCTCTATC
Statistics
Matches: 156, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
164 1 0.01
165 118 0.76
166 37 0.24
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.28
Consensus pattern (166 bp):
TTACACTGATCTAACACTCACCAATTTAGCGACCTCACTGTTGTACAAAGACTAGATCACTCTAC
TACTAAGCTTTCCCCTCGAAAGCTTAGCTTTGCAACTCAAGAAACCCTCTGGATTACTTACAAAA
ACAATGCACACATAAAACACTCCTAACTTGAACAAA
Found at i:49856 original size:17 final size:17
Alignment explanation
Indices: 49834--49877 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
49824 CAATTATAGT
*
49834 TTTTAAATTTTAATTCA
1 TTTTAAATTTAAATTCA
* *
49851 TTTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTCA
*
49868 TTATAAATTT
1 TTTTAAATTT
49878 GAGCTTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTCA
Found at i:49914 original size:17 final size:16
Alignment explanation
Indices: 49893--49945 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
49883 TATTAGGAGT
49893 TTAAATTTATTTTAAA
1 TTAAATTTATTTTAAA
49909 TCTAAATTTATTTTGAAA
1 T-TAAATTTATTTT-AAA
* *
49927 TAAAATTTAAATTTAAA
1 TTAAATTT-ATTTTAAA
49944 TT
1 TT
49946 TAAAAGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.03
17 22 0.71
18 8 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:49920 original size:34 final size:34
Alignment explanation
Indices: 49856--49920 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
49846 ATTCATTTTA
* * *
49856 AGTTTAAATTTATTATAAATTTGAGCTTATTAGG
1 AGTTTAAATTTATTATAAATCTAAACTTATTAGG
* *
49890 AGTTTAAATTTATTTTAAATCTAAATTTATT
1 AGTTTAAATTTATTATAAATCTAAACTTATT
49921 TTGAAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (34 bp):
AGTTTAAATTTATTATAAATCTAAACTTATTAGG
Found at i:49940 original size:6 final size:6
Alignment explanation
Indices: 49892--49949 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
49882 TTATTAGGAG
* * * *
49892 TTTAAA TTT-AT TTTAAA TCTAAA TTT-AT TTTGAAA -TAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
49938 TTTAAA TTTAAA
1 TTTAAA TTTAAA
49950 AGTTAAACTA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
5 11 0.28
6 28 0.70
7 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:50681 original size:13 final size:13
Alignment explanation
Indices: 50665--50698 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
50655 ATTATAATTA
50665 TAATAAATAAGAG
1 TAATAAATAAGAG
* *
50678 TAATAAATAATAT
1 TAATAAATAAGAG
50691 TAATAAAT
1 TAATAAAT
50699 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (13 bp):
TAATAAATAAGAG
Found at i:51829 original size:30 final size:28
Alignment explanation
Indices: 51766--51931 Score: 122
Period size: 30 Copynumber: 5.7 Consensus size: 28
51756 AAATTGTCCA
* *
51766 AAAATTATA-TTTTAACCTCAAACTTCTC
1 AAAATTATATTTTTACCCT-AAACTTTTC
*
51794 TAAAATTATATTTTTGACCCTAAACTTTTTG
1 -AAAATTATATTTTT-ACCCTAAAC-TTTTC
* *
51825 AAAATCACATTTTTACCCCTAAA-TTTTCC
1 AAAATTATATTTTTA-CCCTAAACTTTT-C
* *
51854 AAAATTATATTTTTTACCTTGAACTTTTC
1 AAAATTATA-TTTTTACCCTAAACTTTTC
* *
51883 AAAAATTAAATTTTTACCCCCAAAC-TTTC
1 -AAAATTATATTTTTA-CCCTAAACTTTTC
* *
51912 AAAAATTTTATTCTTACCCT
1 -AAAATTATATTTTTACCCT
51932 CGAACTTACT
Statistics
Matches: 110, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
28 7 0.06
29 46 0.42
30 50 0.45
31 7 0.06
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.43
Consensus pattern (28 bp):
AAAATTATATTTTTACCCTAAACTTTTC
Found at i:51857 original size:29 final size:28
Alignment explanation
Indices: 51752--51990 Score: 104
Period size: 29 Copynumber: 8.1 Consensus size: 28
51742 CCTTAGAGGT
* *
51752 CCCTAAATTGTCCAAAAATTATA-TTTTA
1 CCCTAAATT-TTCAAAAATTAAATTTTTA
* * * *
51780 ACCTCAAACTTCTCTAAAATTATATTTTTGA
1 CCCT-AAA-TTTTCAAAAATTAAATTTTT-A
** * *
51811 CCCTAAACTTTTTGAAAATCACATTTTTA
1 CCCTAAA-TTTTCAAAAATTAAATTTTTA
* *
51840 CCCCTAAATTTTCCAAAATTATATTTTTTA
1 -CCCTAAATTTTCAAAAATTA-AATTTTTA
* *
51870 CCTTGAACTTTTCAAAAATTAAATTTTTA
1 CCCT-AAATTTTCAAAAATTAAATTTTTA
* * ** *
51899 CCCCCAAACTTTCAAAAATTTTATTCTTA
1 -CCCTAAATTTTCAAAAATTAAATTTTTA
* * * * **
51928 CCCTCGAACTTACTAAAATTCCATTTTTGA
1 CCCT-AAATTTTCAAAAATTAAATTTTT-A
* *
51958 CCCTAATTTTTCCAAAAAATACAA-TTTTA
1 CCCTAAATTTT-CAAAAATTA-AATTTTTA
51987 CCCT
1 CCCT
51991 CGAACTTCCT
Statistics
Matches: 158, Mismatches: 41, Indels: 23
0.71 0.18 0.10
Matches are distributed among these distances:
28 6 0.04
29 78 0.49
30 69 0.44
31 5 0.03
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (28 bp):
CCCTAAATTTTCAAAAATTAAATTTTTA
Found at i:51858 original size:59 final size:57
Alignment explanation
Indices: 51795--52014 Score: 167
Period size: 59 Copynumber: 3.7 Consensus size: 57
51785 AAACTTCTCT
*
51795 AAAATTATATTTTTGACCCTAAACTTTTTGAAAATCACATTTTTACCCCTAAATTTTCC
1 AAAATTATATTTTT-ACCCTGAACTTTTT-AAAATCACATTTTTACCCCTAAATTTTCC
* * * * * * *
51854 AAAATTATATTTTTTACCTTGAACTTTTCAAAAATTAAATTTTTACCCCCAAACTTTCA
1 AAAATTATA-TTTTTACCCTGAACTTTT-TAAAATCACATTTTTACCCCTAAATTTTCC
* * ** *
51913 AAAATTTTATTCTTACCCTCGAACTTACTAAAATTC-CATTTTTGA-CCCTAATTTTTCC
1 AAAATTATATTTTTACCCT-GAACTTTTTAAAA-TCACATTTTT-ACCCCTAAATTTTCC
* * * **
51971 AAAAAATACAATTTTACCCTCGAACTTCCTAAAATTC-CATTTTT
1 -AAAATTATATTTTTACCCT-GAACTTTTTAAAA-TCACATTTTT
52015 GACCTCGATT
Statistics
Matches: 129, Mismatches: 26, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
58 27 0.21
59 97 0.75
60 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (57 bp):
AAAATTATATTTTTACCCTGAACTTTTTAAAATCACATTTTTACCCCTAAATTTTCC
Found at i:52014 original size:29 final size:29
Alignment explanation
Indices: 51892--52073 Score: 97
Period size: 29 Copynumber: 6.2 Consensus size: 29
51882 CAAAAATTAA
* * * * **
51892 ATTTTTACCCCCAAACTTTCAAAAATTTT
1 ATTTTTACCCTCGAACTTCCTAAAATTCC
* *
51921 ATTCTTACCCTCGAACTTACTAAAATTCC
1 ATTTTTACCCTCGAACTTCCTAAAATTCC
* * * *
51950 ATTTTTGACCCT--AATTTTTCCAAAAAATAC
1 ATTTTT-ACCCTCGAA--CTTCCTAAAATTCC
*
51980 AATTTTACCCTCGAACTTCCTAAAATTCC
1 ATTTTTACCCTCGAACTTCCTAAAATTCC
** *
52009 ATTTTTGA-CCTCGATTTTTCTAAAAATTACC
1 ATTTTT-ACCCTCGAACTTCCT-AAAATT-CC
*
52040 A-TTTTACCC-CTTAACTTCC-AAAATTTCC
1 ATTTTTACCCTC-GAACTTCCTAAAA-TTCC
52068 ATTTTT
1 ATTTTT
52074 GATCCATATT
Statistics
Matches: 115, Mismatches: 26, Indels: 24
0.70 0.16 0.15
Matches are distributed among these distances:
28 9 0.08
29 65 0.57
30 36 0.31
31 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTCCTAAAATTCC
Found at i:52015 original size:59 final size:59
Alignment explanation
Indices: 51925--52112 Score: 220
Period size: 59 Copynumber: 3.2 Consensus size: 59
51915 AATTTTATTC
* *
51925 TTACCCTCGAACTTACTAAAATTCCATTTTTGACCCTAATTTTTCCAAAAAATACAATT
1 TTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCTAATTTTTCCAAAAATTACAATT
* * *
51984 TTACCCTCGAACTTCCTAAAATTCCATTTTTGA-CCTCGATTTTTCTAAAAATTACCATT
1 TTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCT-AATTTTTCCAAAAATTACAATT
* * * **
52043 TTACCC-CTTAACTTCC-AAAATTTCCATTTTTGATCCATATTTTTTTCCAAAAATTATGATT
1 TTACCCTC-GAACTTCCTAAAA-TTCCATTTTTGA-CCCTA-ATTTTTCCAAAAATTACAATT
52104 TTACCCTCG
1 TTACCCTCG
52113 GATGTCTAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
58 8 0.07
59 75 0.69
61 25 0.23
62 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.41
Consensus pattern (59 bp):
TTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCTAATTTTTCCAAAAATTACAATT
Found at i:52208 original size:28 final size:28
Alignment explanation
Indices: 52147--52202 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
52137 CCGAACTTTC
* *
52147 CCAAAATTACCATTTTGCCCTCGAGTGT
1 CCAAAATTACCATTTTGCCCCCGAGTAT
* *
52175 CCAAAATTATCATTTTGCCCCCGGGTAT
1 CCAAAATTACCATTTTGCCCCCGAGTAT
52203 TTAAAAATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGTAT
Found at i:56988 original size:15 final size:15
Alignment explanation
Indices: 56968--56999 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
56958 AAAACCCAAT
*
56968 AAAAAGAGGAAGAAA
1 AAAAAGAAGAAGAAA
56983 AAAAAGAAGAAGAAA
1 AAAAAGAAGAAGAAA
56998 AA
1 AA
57000 GTCAAGATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAGAAA
Found at i:57833 original size:31 final size:32
Alignment explanation
Indices: 57792--57852 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
57782 ATACAATGAA
* *
57792 AAAAAAAAGAAGAGAAAGAAAAA-AGAAAAGC
1 AAAAAAAAGAAGAAAAACAAAAATAGAAAAGC
*
57823 AAAAACAAGAAGAAAAACAAAAATAGAAAA
1 AAAAAAAAGAAGAAAAACAAAAATAGAAAA
57853 ATGGAGAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (32 bp):
AAAAAAAAGAAGAAAAACAAAAATAGAAAAGC
Found at i:59164 original size:48 final size:48
Alignment explanation
Indices: 59092--59476 Score: 416
Period size: 48 Copynumber: 8.0 Consensus size: 48
59082 AGAAAAACAT
* * *
59092 GAAGACATAAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTTCCAC
1 GAAGACA-CAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* * * *
59141 GAAGACATAAGGGAAAGATCTAAGCCGTAATGGCGGATCTAGTACCAC
1 GAAGACACAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* * * *
59189 GAAGACACAAGGGAAAGATTTAAGCCGTAATGGCGGATCCAGCACCAC
1 GAAGACACAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* *
59237 GAAGACACAAGGGAAAGATCTAAGCCGTAACGGCGGATCTAGTACCAC
1 GAAGACACAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* *
59285 GAAGACACAAGGGAAAGATCTAAGCCACAACGGC-AACTCCAGTACCAC
1 GAAGACACAAGGGAAAGATCTAAGCCGCAACGGCGGA-TCCAGTACCAC
* *
59333 GAAGACAAAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGC
1 GAAGACACAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* * * * * * * * *
59381 GAAGAAATAAAGGGAAAGGTTTAAGTCGCAACGGC-AAACCTTGTACCTAG
1 GAAGACA-CAAGGGAAAGATCTAAGCCGCAACGGCGGATCC-AGTACC-AC
* * * * *
59431 GAA-ACATGAAGGAAAAGATTTAAGCCGCAACGGCGAATCTAGTACC
1 GAAGACA-CAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACC
59477 TTGACGATTT
Statistics
Matches: 291, Mismatches: 39, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.00
48 216 0.74
49 68 0.23
50 6 0.02
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (48 bp):
GAAGACACAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
Found at i:59787 original size:102 final size:102
Alignment explanation
Indices: 59611--59928 Score: 591
Period size: 102 Copynumber: 3.1 Consensus size: 102
59601 AATTATAATG
*
59611 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTACTATC
1 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
59676 CTCTTGAAGTTGCAGTAAAGTGGGATTAAAAACAATA
66 CTCTTGAAGTTGCAGTAAAGTGGGATTAAAAACAATA
59713 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
1 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
*
59778 CTCTTGAAGTTGCAATAAAGTGGGATTAAAAACAATA
66 CTCTTGAAGTTGCAGTAAAGTGGGATTAAAAACAATA
* *
59815 GCAAGTCTTTATCTCTTTGAAGTTGTAGTAAGAGCAAGATGAACCTTCAAACATCAATTCCTATC
1 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
*
59880 CTCTTGAAGTTGTAGTAAAGTGGGATTAAAAACAATA
66 CTCTTGAAGTTGCAGTAAAGTGGGATTAAAAACAATA
59917 GCAAGTCTTTAT
1 GCAAGTCTTTAT
59929 GTAACATCCG
Statistics
Matches: 210, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 210 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (102 bp):
GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
CTCTTGAAGTTGCAGTAAAGTGGGATTAAAAACAATA
Found at i:59889 original size:52 final size:51
Alignment explanation
Indices: 59623--59897 Score: 202
Period size: 52 Copynumber: 5.4 Consensus size: 51
59613 AAGTCTTTAT
*
59623 CTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTACTATC
1 CTCT-TGAAGTTGTAGTAAGAGCAAGATGAA-CTTCAAACATCAATTCCTATC
* *** * *** * * * *
59676 CTCTTGAAGTTGCAGTAA-AGTGGGATTAAAAAC-AATAGCAAGTCTTTAT-
1 CTCTTGAAGTTGTAGTAAGAGCAAGATGAACTTCAAACATCAATTC-CTATC
59725 CTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
1 CTCT-TGAAGTTGTAGTAAGAGCAAGATGAA-CTTCAAACATCAATTCCTATC
* * *** * *** * * * *
59778 CTCTTGAAGTTGCAATAA-AGTGGGATTAAAAAC-AATAGCAAGTCTTTAT-
1 CTCTTGAAGTTGTAGTAAGAGCAAGATGAACTTCAAACATCAATTC-CTATC
59827 CTCTTTGAAGTTGTAGTAAGAGCAAGATGAACCTTCAAACATCAATTCCTATC
1 CTC-TTGAAGTTGTAGTAAGAGCAAGATGAA-CTTCAAACATCAATTCCTATC
59880 CTCTTGAAGTTGTAGTAA
1 CTCTTGAAGTTGTAGTAA
59898 AGTGGGATTA
Statistics
Matches: 159, Mismatches: 51, Indels: 25
0.68 0.22 0.11
Matches are distributed among these distances:
49 22 0.14
50 34 0.21
51 28 0.18
52 48 0.30
53 27 0.17
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (51 bp):
CTCTTGAAGTTGTAGTAAGAGCAAGATGAACTTCAAACATCAATTCCTATC
Found at i:60285 original size:13 final size:13
Alignment explanation
Indices: 60267--60296 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
60257 AGAAAAATCT
60267 AAAGAAATGAAGA
1 AAAGAAATGAAGA
*
60280 AAAGAAATGATGA
1 AAAGAAATGAAGA
60293 AAAG
1 AAAG
60297 GCTATAAAAG
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:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (13 bp):
AAAGAAATGAAGA
Found at i:61899 original size:41 final size:40
Alignment explanation
Indices: 61851--61951 Score: 109
Period size: 38 Copynumber: 2.6 Consensus size: 40
61841 TCGACCTCGA
** *
61851 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
61891 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
61929 GTCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
61952 TTTATTGCTT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
37 11 0.23
38 17 0.36
39 4 0.09
40 4 0.09
41 11 0.23
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:61944 original size:37 final size:38
Alignment explanation
Indices: 61849--61955 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 38
61839 CTTCGACCTC
** *
61849 GAGTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATA
1 GAGTCGATGAGACACT-GG-GT-ACCACTTTACTTCGGATA
* ** *
61890 GATTCGATGAGGTACTGGGTACCACTTTACTTCGGCTA
1 GAGTCGATGAGACACTGGGTACCACTTTACTTCGGATA
**
61928 G-GTCGATGAGACACTGGGTGTCACTTTA
1 GAGTCGATGAGACACTGGGTACCACTTTA
61956 TTGCTTCGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
37 22 0.41
38 15 0.28
39 2 0.04
40 2 0.04
41 13 0.24
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (38 bp):
GAGTCGATGAGACACTGGGTACCACTTTACTTCGGATA
Found at i:62762 original size:20 final size:20
Alignment explanation
Indices: 62726--62774 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
62716 GAAAATTTTG
* *
62726 TTATACTCGTTTTTAATTCTC
1 TTATAC-CGTTTGTAATACTC
62747 TTATACCGTTTGTAATACTC
1 TTATACCGTTTGTAATACTC
62767 TTATACCG
1 TTATACCG
62775 GGTTTATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.49
Consensus pattern (20 bp):
TTATACCGTTTGTAATACTC
Found at i:63155 original size:104 final size:102
Alignment explanation
Indices: 62811--63162 Score: 506
Period size: 102 Copynumber: 3.4 Consensus size: 102
62801 GAGTGTTACA
* * *
62811 CTTTATCTCTCAGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTTCTATCCTCTTG
1 CTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTTCTATCCTCTTA
62876 AAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAAGT
66 AAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAAGT
* * * * * * *
62913 CTTTATCTCTCTGAAGTTGTATTTAGAACAGGATAAAGCTTCAAACATCAATTCCTGTCCTCTTA
1 CTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTTCTATCCTCTTA
*
62978 AAGTTGCAATAAAGTTGGATTAAAAACAATAGCAAGT
66 AAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAAGT
* **
63015 CTTTATCTCTCTGAAGTTGTAGTAAGAGCAGGATGAAGCTTCAAATGTCAATTTCTATCCTCTTA
1 CTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTTCTATCCTCTTA
** * *
63080 AAGTTATAGTAAAGTTGAATTAAAAAAACAATAGCAGGT
66 AAGTTGCAGTAAAGTTGGATT--AAAAACAATAGCAAGT
* *
63119 CTTTATCTCTTTGAAGTTGTAGTAAGAGCAAGATGAAGCCTCAA
1 CTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAA
63163 CGTCAAACCC
Statistics
Matches: 221, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
102 165 0.75
104 56 0.25
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (102 bp):
CTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTTCTATCCTCTTA
AAGTTGCAGTAAAGTTGGATTAAAAACAATAGCAAGT
Found at i:63514 original size:17 final size:16
Alignment explanation
Indices: 63493--63545 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
63483 TATTAGGAGT
63493 TTAAATTTATTTTAAA
1 TTAAATTTATTTTAAA
63509 TCTAAATTTATTTTGAAA
1 T-TAAATTTATTTT-AAA
* *
63527 TAAAATTTAAATTTAAA
1 TTAAATTT-ATTTTAAA
63544 TT
1 TT
63546 TAAAAGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.03
17 22 0.71
18 8 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:63540 original size:6 final size:6
Alignment explanation
Indices: 63492--63549 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
63482 TTATTAGGAG
* * * *
63492 TTTAAA TTT-AT TTTAAA TCTAAA TTT-AT TTTGAAA -TAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
63538 TTTAAA TTTAAA
1 TTTAAA TTTAAA
63550 AGTTAAACTA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
5 11 0.28
6 28 0.70
7 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:65413 original size:58 final size:56
Alignment explanation
Indices: 65344--65620 Score: 201
Period size: 58 Copynumber: 4.8 Consensus size: 56
65334 CAAACTTCTT
* *
65344 CAAAATTATATTTTTTACCCCGAACTTTCTAAAAATTACA-TTTTACATCTAAATTTTC
1 CAAAATTATAGTTTTTACCCCAAACTTTCT-AAAATTACATTTTTAC-TC-AAATTTTC
* * **
65402 CAAAATTATA-TTTTTAACCCCAAACTTTCCAAAAATTACATTTTTACCCCAAAACTTC
1 CAAAATTATAGTTTTT-ACCCCAAACTTT-CTAAAATTACATTTTTA-CTCAAATTTTC
* * * * *
65460 CAAAGATTA-CGTTTTTACCCCCCGAACTTCCTAAAATTCCATTTTTGACCTCAATTTTTC
1 CAAA-ATTATAGTTTTTA--CCCCAAACTTTCTAAAATTACATTTTT-A-CTCAAATTTTC
* **
65520 CAAAATTAT-GTTTTTACCCTCAAACTTTCTAAAATTCCATTTTTGAC-CCCATTTTC
1 CAAAATTATAGTTTTTACCC-CAAACTTTCTAAAATTACATTTTT-ACTCAAATTTTC
* *
65576 CAAAAATTACCA--TTTTACCCCCAAAC-TTCCAAAATTTACATTTTT
1 C-AAAATTA-TAGTTTTTA-CCCCAAACTTTCTAAAA-TTACATTTTT
65621 TATCTCGATT
Statistics
Matches: 181, Mismatches: 22, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
56 14 0.08
57 35 0.19
58 68 0.38
59 41 0.23
60 23 0.13
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.39
Consensus pattern (56 bp):
CAAAATTATAGTTTTTACCCCAAACTTTCTAAAATTACATTTTTACTCAAATTTTC
Found at i:65416 original size:29 final size:31
Alignment explanation
Indices: 65316--65620 Score: 175
Period size: 29 Copynumber: 10.4 Consensus size: 31
65306 AACTATCTAG
* *
65316 AAATTATA-TTTTA-ACCCTCAAACTTCTTC-A
1 AAATTACATTTTTACACCC-CAAACTT-TCCAA
* * * *
65346 AAATTATATTTTT-TACCCCGAACTTTCTAA
1 AAATTACATTTTTACACCCCAAACTTTCCAA
* * *
65376 AAATTACA-TTTTACA-TCTAAATTTTCC-A
1 AAATTACATTTTTACACCCCAAACTTTCCAA
*
65404 AAATTATATTTTTA-ACCCCAAACTTTCCAA
1 AAATTACATTTTTACACCCCAAACTTTCCAA
*
65434 AAATTACATTTTTAC-CCCAAAAC-TTCCAA
1 AAATTACATTTTTACACCCCAAACTTTCCAA
* * * * *
65463 AGATTACGTTTTTACCCCCCGAAC-TTCCTA
1 AAATTACATTTTTACACCCCAAACTTTCCAA
* * * **
65493 AAATTCCATTTTT-GACCTCAATTTTTCC-A
1 AAATTACATTTTTACACCCCAAACTTTCCAA
** * *
65522 AAATTATGTTTTTAC-CCTCAAACTTT-CTA
1 AAATTACATTTTTACACCCCAAACTTTCCAA
* * *
65551 AAATTCCATTTTT-GACCCC--ATTTTCCAA
1 AAATTACATTTTTACACCCCAAACTTTCCAA
65579 AAATTACCA-TTTTAC-CCCCAAAC-TTCCAA
1 AAATTA-CATTTTTACACCCCAAACTTTCCAA
*
65608 AATTTACATTTTT
1 AAATTACATTTTT
65621 TATCTCGATT
Statistics
Matches: 209, Mismatches: 47, Indels: 39
0.71 0.16 0.13
Matches are distributed among these distances:
27 4 0.02
28 27 0.13
29 100 0.48
30 70 0.33
31 8 0.04
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (31 bp):
AAATTACATTTTTACACCCCAAACTTTCCAA
Found at i:65621 original size:58 final size:56
Alignment explanation
Indices: 65396--65658 Score: 176
Period size: 59 Copynumber: 4.5 Consensus size: 56
65386 TTACATCTAA
* *
65396 ATTTTCC-AAAATTA-TATTTTTAACCCCAAACTTTCCAAAAATTACATTTTTACCCC
1 ATTTTCCAAAAATTACCA-TTTTACCCCCAAACTTTCC-AAAATTACATTTTTACCCC
** * ** * * *
65452 AAAACTTCCAAAGATTACGTTTTTACCCCCCGAAC-TTCCTAAAATTCCATTTTTGACCTCA
1 --ATTTTCCAAAAATTACCATTTTA-CCCCCAAACTTTCC-AAAATTACATTTTT-ACC-CC
*** * * *
65513 ATTTTTCC-AAAATTATGTTTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCCC
1 A-TTTTCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTACATTTTT-ACCCC
* *
65570 ATTTTCCAAAAATTACCATTTTACCCCCAAAC-TTCCAAAATTTACATTTTTTATCTCG
1 ATTTTCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAA-TTACA-TTTTTA-CCCC
*
65628 ATTTTTTTCCAAAAATTACCATATTACCCCC
1 A---TTTTCCAAAAATTACCATTTTACCCCC
65659 GGATGTCTAA
Statistics
Matches: 164, Mismatches: 27, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
56 13 0.08
57 27 0.16
58 38 0.23
59 45 0.27
60 14 0.09
61 27 0.16
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.39
Consensus pattern (56 bp):
ATTTTCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTACATTTTTACCCC
Found at i:65755 original size:28 final size:28
Alignment explanation
Indices: 65695--65753 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
65685 CAAACTTCCT
* *
65695 AAAATTACTATTTTGCCCTCGAGTGTCC
1 AAAATTACCATTTTGCCCTCGAGTATCC
*
65723 AAAATTACCA-TTTGCCCTTGAGTATCC
1 AAAATTACCATTTTGCCCTCGAGTATCC
65750 AAAA
1 AAAA
65754 ATCACGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCTCGAGTATCC
Done.