Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014778.1 Kokia drynarioides strain JFW-HI SEQ_129820, 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: 40539
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Warning! 679 characters in sequence are not A, C, G, or T
Found at i:5155 original size:30 final size:30
Alignment explanation
Indices: 5128--5337 Score: 260
Period size: 30 Copynumber: 7.0 Consensus size: 30
5118 AAGAAGTTCG
* *
5128 AGGGTCAAAATGTGAA-TTTGGAAAAGTTTG
1 AGGGTCAAAATAT-AATTTTGGAAAAGTTTA
* *
5158 AGTGTTAAAATATAATTTTGGAAAAGTTTA
1 AGGGTCAAAATATAATTTTGGAAAAGTTTA
* * * *
5188 GGGGTTAAAATGTAATTTTGGAAAAATTTTA
1 AGGGTCAAAATATAATTTTGG-AAAAGTTTA
* *
5219 AGGGTCAAATTATGATTTTGGAAAAGTTTA
1 AGGGTCAAAATATAATTTTGGAAAAGTTTA
* *
5249 AGGGTTAAAATATGATTTTGGAAAAGTTTA
1 AGGGTCAAAATATAATTTTGGAAAAGTTTA
*
5279 GGGGTCAAAATATAATTTTGGAAAAGTTTA
1 AGGGTCAAAATATAATTTTGGAAAAGTTTA
* *
5309 AGGGTCAAAATGTAATTTTAGAAAAGTTT
1 AGGGTCAAAATATAATTTTGGAAAAGTTT
5338 TAGGACCTCT
Statistics
Matches: 156, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
29 2 0.01
30 130 0.83
31 24 0.15
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
AGGGTCAAAATATAATTTTGGAAAAGTTTA
Found at i:5258 original size:91 final size:90
Alignment explanation
Indices: 5128--5337 Score: 312
Period size: 91 Copynumber: 2.3 Consensus size: 90
5118 AAGAAGTTCG
* * *
5128 AGGGTCAAAATGTGAATTTGGAAAAGTTTGAGTGTTAAAATATAATTTTGGAAAAGTTTAGGGGT
1 AGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGGAAAAGTTTAGGGGT
* * *
5193 TAAAATGTAATTTTGGAAAAATTTTA
66 CAAAATATAATTTTGG-AAAAGTTTA
* * *
5219 AGGGTCAAATTATGATTTTGGAAAAGTTTAAGGGTTAAAATATGATTTTGGAAAAGTTTAGGGGT
1 AGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGGAAAAGTTTAGGGGT
5284 CAAAATATAATTTTGGAAAAGTTTA
66 CAAAATATAATTTTGGAAAAGTTTA
* *
5309 AGGGTCAAAATGTAATTTTAGAAAAGTTT
1 AGGGTCAAAATGTGATTTTGGAAAAGTTT
5338 TAGGACCTCT
Statistics
Matches: 106, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 33 0.31
91 73 0.69
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (90 bp):
AGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGGAAAAGTTTAGGGGT
CAAAATATAATTTTGGAAAAGTTTA
Found at i:8802 original size:11 final size:12
Alignment explanation
Indices: 8778--8807 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
8768 TCTTAAGTTC
8778 AAATTTATTTTT
1 AAATTTATTTTT
8790 AAATTTA-TTTT
1 AAATTTATTTTT
8801 AAATTTA
1 AAATTTA
8808 AATTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
AAATTTATTTTT
Found at i:9444 original size:22 final size:22
Alignment explanation
Indices: 9415--9463 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
9405 CCTCTGGACA
* *
9415 TATT-TATTAATACTTATTATT
1 TATTATATTAACACTTATTACT
* *
9436 TATTATATTACCATTTATTACT
1 TATTATATTAACACTTATTACT
9458 TATTAT
1 TATTAT
9464 TTTGAAACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATATTAACACTTATTACT
Found at i:10704 original size:30 final size:29
Alignment explanation
Indices: 10603--10872 Score: 220
Period size: 30 Copynumber: 8.9 Consensus size: 29
10593 CCCAAAAGGT
* * * *
10603 CCCTAAACTATCTAGAAATCATATTTTAA
1 CCCTAAACTTTCTAAAAATTACATTTTAA
* *
10632 CCCTTAAACTTTCCAAAAATTATATTTTAA
1 CCC-TAAACTTTCTAAAAATTACATTTTAA
* * *
10662 CCCCCAAAACTTTCCAAAAATTACATTTTGA
1 --CCCTAAACTTTCTAAAAATTACATTTTAA
* *
10693 CTCATAAACTTTCTAAAAATTACATTTTTA
1 C-CCTAAACTTTCTAAAAATTACATTTTAA
* *
10723 CCGCCAAACTTTCTAAAAATTACATTTTTA
1 CC-CTAAACTTTCTAAAAATTACATTTTAA
* *
10753 CCGCCAAACTTTCTAAAAACTACATTTTAA
1 CC-CTAAACTTTCTAAAAATTACATTTTAA
* * *
10783 CCCTTAAACTTTTTAAAAAATACATTTTGA
1 CCC-TAAACTTTCTAAAAATTACATTTTAA
* *
10813 CCCTCGAAC-TTCTCAAAAATTACATTTTTAC
1 CCCT-AAACTTTCT-AAAAATTACA-TTTTAA
*
10844 CCTTTCTAAACTTT-TAAAAATCACATTTT
1 CC---CTAAACTTTCTAAAAATTACATTTT
10873 CATCCCGTAC
Statistics
Matches: 202, Mismatches: 26, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
29 10 0.05
30 139 0.69
31 33 0.16
32 12 0.06
33 4 0.02
34 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTCTAAAAATTACATTTTAA
Found at i:10762 original size:60 final size:57
Alignment explanation
Indices: 10637--10961 Score: 237
Period size: 60 Copynumber: 5.5 Consensus size: 57
10627 TTTAACCCTT
* * * * **
10637 AAACTTTCCAAAAATTATATTTTAACCCCCAAAACTTTCCAAAAATTACATTTTGACTCAT
1 AAAC-TTCTAAAAATTACATTTTTA-CCCC-AAACTTTCTAAAAATTACATTTTGAC-CCC
*
10698 AAACTTTCTAAAAATTACATTTTTACCGCCAAACTTTCTAAAAATTACATTTTTACCGCC
1 AAAC-TTCTAAAAATTACATTTTTACC-CCAAACTTTCTAAAAATTACATTTTGACC-CC
* * * * *
10758 AAACTTTCTAAAAACTACATTTTAACCCTTAAACTTTTTAAAAAATACATTTTGACCCTC
1 AAAC-TTCTAAAAATTACATTTTTACCC-CAAACTTTCTAAAAATTACATTTTGACCC-C
* * * *
10818 GAACTTCTCAAAAATTACATTTTTACCCTTTCTAAACTTT-TAAAAATCACATTTTCATCCC
1 AAACTTCT-AAAAATTACATTTTTACCC---C-AAACTTTCTAAAAATTACATTTTGACCCC
** * * * *
10879 GTAC-T-T-AAAATCACATTTTTATCCCTAAATTTTC-AAAAATTACATTTTTATCCCC
1 AAACTTCTAAAAATTACATTTTTA-CCCCAAACTTTCTAAAAATTACATTTTGA-CCCC
* *
10934 GAACTTCTCAAAAGTTACATTTTTACCC
1 AAACTTCT-AAAAATTACATTTTTACCC
10962 TTCGAACTTC
Statistics
Matches: 218, Mismatches: 31, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
54 20 0.09
55 6 0.03
56 1 0.00
57 15 0.07
58 6 0.03
59 21 0.10
60 97 0.44
61 28 0.13
62 17 0.08
63 7 0.03
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (57 bp):
AAACTTCTAAAAATTACATTTTTACCCCAAACTTTCTAAAAATTACATTTTGACCCC
Found at i:10800 original size:90 final size:91
Alignment explanation
Indices: 10625--10845 Score: 268
Period size: 90 Copynumber: 2.4 Consensus size: 91
10615 TAGAAATCAT
* * * * * *
10625 ATTTTAACCCTTAAACTTTCCAAAAATTATATTTTAACCCCCAAAACTTTCCAAAAATTACATTT
1 ATTTTGACCCTCAAACTTTCTAAAAATTACATTTTTACCCCCAAAACTTTCCAAAAACTACATTT
* * *
10690 TGACTCATAAACTTTCTAAAAATTAC
66 TAACCCATAAACTTTCTAAAAAATAC
* * *
10716 ATTTTTACCGC-CAAACTTTCTAAAAATTACATTTTTACCGCC-AAACTTTCTAAAAACTACATT
1 ATTTTGACC-CTCAAACTTTCTAAAAATTACATTTTTACCCCCAAAACTTTCCAAAAACTACATT
* *
10779 TTAACCCTTAAACTTTTTAAAAAATAC
65 TTAACCCATAAACTTTCTAAAAAATAC
*
10806 ATTTTGACCCTCGAAC-TTCTCAAAAATTACATTTTTACCC
1 ATTTTGACCCTCAAACTTTCT-AAAAATTACATTTTTACCC
10846 TTTCTAAACT
Statistics
Matches: 111, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
89 5 0.05
90 71 0.64
91 34 0.31
92 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (91 bp):
ATTTTGACCCTCAAACTTTCTAAAAATTACATTTTTACCCCCAAAACTTTCCAAAAACTACATTT
TAACCCATAAACTTTCTAAAAAATAC
Found at i:10952 original size:30 final size:30
Alignment explanation
Indices: 10703--10980 Score: 140
Period size: 30 Copynumber: 9.4 Consensus size: 30
10693 CTCATAAACT
*
10703 TTCT-AAAAATTACATTTTTA-CCGCCAAAC
1 TTCTCAAAAATTACATTTTTATCC-CCGAAC
*
10732 TT-TCTAAAAATTACATTTTTA-CCGCCAAAC
1 TTCTC-AAAAATTACATTTTTATCC-CCGAAC
* * **
10762 TT-TCTAAAAACTACA-TTTTAACCCTTAAAC
1 TTCTC-AAAAATTACATTTTTATCCC-CGAAC
* * * *
10792 TTTTTAAAAAATACATTTTGA-CCCTCGAAC
1 TTCTCAAAAATTACATTTTTATCCC-CGAAC
*
10822 TTCTCAAAAATTACATTTTTA-CCCTTTCTAAAC
1 TTCTCAAAAATTACATTTTTATCCC---C-GAAC
* * * *
10855 TT-TTAAAAATCACATTTTCAT-CCCGTAC
1 TTCTCAAAAATTACATTTTTATCCCCGAAC
* * *
10883 -T-T--AAAATCACATTTTTAT-CCCTAAA
1 TTCTCAAAAATTACATTTTTATCCCCGAAC
*
10908 TTTTCAAAAATTACATTTTTATCCCCGAAC
1 TTCTCAAAAATTACATTTTTATCCCCGAAC
*
10938 TTCTCAAAAGTTACATTTTTA-CCCTTCGAAC
1 TTCTCAAAAATTACATTTTTATCCC--CGAAC
*
10969 TTC-CAAATATTA
1 TTCTCAAAAATTA
10981 TCTTTTTGCC
Statistics
Matches: 204, Mismatches: 28, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
25 19 0.09
26 1 0.00
27 3 0.01
28 3 0.01
29 27 0.13
30 114 0.56
31 13 0.06
32 19 0.09
33 5 0.02
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
TTCTCAAAAATTACATTTTTATCCCCGAAC
Found at i:18805 original size:16 final size:18
Alignment explanation
Indices: 18784--18816 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
18774 AATTGTTGAA
18784 GCCCAA-TTTTA-ATCAG
1 GCCCAAGTTTTAGATCAG
18800 GCCCAAGTTTTAGATCA
1 GCCCAAGTTTTAGATCA
18817 AGCTTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (18 bp):
GCCCAAGTTTTAGATCAG
Found at i:18851 original size:10 final size:11
Alignment explanation
Indices: 18827--18855 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
18817 AGCTTTTGAT
18827 TTTAAATTAGG
1 TTTAAATTAGG
18838 TTTAAATT-GG
1 TTTAAATTAGG
18848 TTTAAATT
1 TTTAAATT
18856 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (11 bp):
TTTAAATTAGG
Found at i:18883 original size:20 final size:18
Alignment explanation
Indices: 18848--18912 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 18
18838 TTTAAATTGG
18848 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
18866 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA--TTTTTAAA
**
18886 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATTTTTAAA
*
18903 TTTGAATTTA
1 TTTAAATTTA
18913 ATTAAATTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 14 0.34
18 10 0.24
20 17 0.41
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:18933 original size:16 final size:16
Alignment explanation
Indices: 18880--18934 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
18870 AATTTATCTT
* *
18880 TTTAAATTTAAATTTGC
1 TTTAAATTTGAA-TTGA
*
18897 TTTAAATTTGAATTTA
1 TTTAAATTTGAATTGA
*
18913 ATTAAATTTGAATTGA
1 TTTAAATTTGAATTGA
18929 TTTAAA
1 TTTAAA
18935 ACTTAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 21 0.66
17 11 0.34
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (16 bp):
TTTAAATTTGAATTGA
Found at i:19687 original size:3 final size:3
Alignment explanation
Indices: 19676--19739 Score: 103
Period size: 3 Copynumber: 21.3 Consensus size: 3
19666 AATATTATTT
*
19676 ATA AT- ATA ATAA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19721 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
19740 AAGAAAGGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21018 original size:60 final size:59
Alignment explanation
Indices: 20893--21047 Score: 156
Period size: 60 Copynumber: 2.6 Consensus size: 59
20883 CAGAAATCAT
** * *
20893 ATTTTTACCCTCGCATTTTCCAAAATTCCTTTTTTGACCATGATTTTTTAAAAAATTAC
1 ATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCATGATTTTTTAAAAAATTAC
* **
20952 ATTTTTACCC-CTAAACTTTCCAAAATTCCATTTTTGACC-TCTATTTTTTTCCAAAATTACC
1 ATTTTTACCCTC-AAACTTTCCAAAATTCCATTTTTGACCAT-GA-TTTTTTAAAAAATTA-C
* *
21013 A-TTTTACCCTCGAAC-TTCTAAAAATTCCATTTTTG
1 ATTTTTACCCTCAAACTTTC-CAAAATTCCATTTTTG
21048 CCTTGAACTT
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
58 2 0.02
59 37 0.46
60 39 0.48
61 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (59 bp):
ATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCATGATTTTTTAAAAAATTAC
Found at i:21100 original size:57 final size:58
Alignment explanation
Indices: 21004--21197 Score: 179
Period size: 57 Copynumber: 3.4 Consensus size: 58
20994 ATTTTTTTCC
** ** *
21004 AAAATTACCA-TTTT-ACCCTCGAAC-TTCTAAAAATTCCATTTTTGCCTTGAACT-TCTA
1 AAAATT-CCATTTTTGA-CCTCGAACTTTCCCAAAATTCCATTTTACCCTCGAA-TGTCTA
*
21061 AAAATTCCATTTTTGACCTCG-A-TTTCCCAAAATTACCATTTTACCCTCGAATGTTTA
1 AAAATTCCATTTTTGACCTCGAACTTTCCCAAAATT-CCATTTTACCCTCGAATGTCTA
* * * *
21118 AAAATTTCGTTTTTGACCTCGAACTTTCCCAAAATTTCCATTTTCCCCTCGAGTGTCT-
1 AAAATTCCATTTTTGACCTCGAACTTTCCCAAAA-TTCCATTTTACCCTCGAATGTCTA
*
21176 AAAATTACCA-TTTTGCCCTCGA
1 AAAATT-CCATTTTTGACCTCGA
21198 GTATCCAAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
56 14 0.12
57 50 0.44
58 19 0.17
59 29 0.25
60 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTCGAACTTTCCCAAAATTCCATTTTACCCTCGAATGTCTA
Found at i:21167 original size:59 final size:57
Alignment explanation
Indices: 21057--21197 Score: 178
Period size: 59 Copynumber: 2.5 Consensus size: 57
21047 GCCTTGAACT
21057 TCTAAAAATTCCATTTTTGACCTCGATTTCCCAAAATTACCATTTTACCCTCGAATG
1 TCTAAAAATTCCATTTTTGACCTCGATTTCCCAAAATTACCATTTTACCCTCGAATG
* * * * * *
21114 TTTAAAAATTTCGTTTTTGACCTCGAACTTTCCCAAAATTTCCATTTTCCCCTCGAGTG
1 TCTAAAAATTCCATTTTTGACCTCG-A-TTTCCCAAAATTACCATTTTACCCTCGAATG
*
21173 TCT-AAAATTACCA-TTTTGCCCTCGA
1 TCTAAAAATT-CCATTTTTGACCTCGA
21198 GTATCCAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 23 0.32
58 17 0.24
59 31 0.44
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (57 bp):
TCTAAAAATTCCATTTTTGACCTCGATTTCCCAAAATTACCATTTTACCCTCGAATG
Found at i:21199 original size:28 final size:28
Alignment explanation
Indices: 21004--21197 Score: 126
Period size: 28 Copynumber: 6.8 Consensus size: 28
20994 ATTTTTTTCC
*
21004 AAAATTACCATTTTACCCTCGAACTTCTA
1 AAAATTACCATTTTGCCCTCG-ACTTCTA
*
21033 AAAATT-CCATTTTTG-CCTTGAACTTCTA
1 AAAATTACCA-TTTTGCCCTCG-ACTTCTA
* * **
21061 AAAATT-CCATTTTTGACCTCGATTTCCC
1 AAAATTACCA-TTTTGCCCTCGACTTCTA
* * *
21089 AAAATTACCATTTTACCCTCGAATGTTTA
1 AAAATTACCATTTTGCCCTCGACT-TCTA
* ** * **
21118 AAAATTTCGTTTTTGACCTCGAACTTTCCC
1 AAAATTACCATTTTGCCCTCG-AC-TTCTA
* * *
21148 AAAATTTCCATTTTCCCCTCGAGTGTCT-
1 AAAATTACCATTTTGCCCTCGACT-TCTA
21176 AAAATTACCATTTTGCCCTCGA
1 AAAATTACCATTTTGCCCTCGA
21198 GTATCCAAAA
Statistics
Matches: 129, Mismatches: 29, Indels: 15
0.75 0.17 0.09
Matches are distributed among these distances:
28 72 0.56
29 37 0.29
30 19 0.15
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCTCGACTTCTA
Found at i:21207 original size:28 final size:28
Alignment explanation
Indices: 21146--21207 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
21136 TCGAACTTTC
* *
21146 CCAAAATTTCCATTTTCCCCTCGAGTGT
1 CCAAAATTACCATTTTCCCCTCGAGTAT
* *
21174 CTAAAATTACCATTTTGCCCTCGAGTAT
1 CCAAAATTACCATTTTCCCCTCGAGTAT
21202 CCAAAA
1 CCAAAA
21208 ATCTTATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (28 bp):
CCAAAATTACCATTTTCCCCTCGAGTAT
Found at i:22729 original size:50 final size:50
Alignment explanation
Indices: 22670--22770 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
22660 TTCTCTAGGT
22670 ATAACCAGATAAGGATGGACCCTAAAGATATGATTAAAACCATGTTTGTC
1 ATAACCAGATAAGGATGGACCCTAAAGATATGATTAAAACCATGTTTGTC
*
22720 ATAACCAGATAAGGATGGACCCTGAAGATATGATTAAAACCATGTTTGTC
1 ATAACCAGATAAGGATGGACCCTAAAGATATGATTAAAACCATGTTTGTC
22770 A
1 A
22771 CACTATGAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (50 bp):
ATAACCAGATAAGGATGGACCCTAAAGATATGATTAAAACCATGTTTGTC
Found at i:25267 original size:6 final size:6
Alignment explanation
Indices: 25258--25379 Score: 54
Period size: 6 Copynumber: 19.3 Consensus size: 6
25248 TCTGAAAAAG
* * * *
25258 AAATAA AAATAA TATTATT AAATAA AAATTTA AAATAA AAATAA AAA-AA
1 AAATAA AAATAA AAATA-A AAATAA AAA-TAA AAATAA AAATAA AAATAA
* ** *
25307 TAAATAG AAATAA AATATAA ATAATTG AAATAA ATTAATAA TGAAGTATA
1 -AAATAA AAATAA AA-ATAA A-AATAA AAATAA A--AATAA --AAATA-A
25357 AAAT-A AAAT-A AAAT-A AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
25380 TAACAATGGG
Statistics
Matches: 88, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
5 17 0.19
6 40 0.45
7 20 0.23
8 9 0.10
9 1 0.01
10 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (6 bp):
AAATAA
Found at i:25303 original size:5 final size:5
Alignment explanation
Indices: 25288--25382 Score: 72
Period size: 5 Copynumber: 18.6 Consensus size: 5
25278 AATAAAAATT
*
25288 TAAAA TAAAA -ATAAA -AAAA T-AAA TAGAAA TAAAA TATAAA T-AAT
1 TAAAA TAAAA TA-AAA TAAAA TAAAA TA-AAA TAAAA TA-AAA TAAAA
* * *
25332 TGAAA TAAAT TAATAA TGAAGTA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAA-AA T-AA-AA TAAAA TAAAA TAAAA TAAAA TAAAA
25380 TAA
1 TAA
25383 CAATGGGTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
4 11 0.15
5 46 0.62
6 13 0.18
7 4 0.05
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:25310 original size:19 final size:18
Alignment explanation
Indices: 25290--25330 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
25280 TAAAAATTTA
25290 AAATAAAAATAAAAAAAT
1 AAATAAAAATAAAAAAAT
* *
25308 AAATAGAAAT-AAAATAT
1 AAATAAAAATAAAAAAAT
25325 AAATAA
1 AAATAA
25331 TTGAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATAAAAATAAAAAAAT
Found at i:25338 original size:20 final size:19
Alignment explanation
Indices: 25257--25382 Score: 62
Period size: 19 Copynumber: 6.9 Consensus size: 19
25247 GTCTGAAAAA
*
25257 GAAATAAAA-ATAATATTAT
1 GAAATAAAATATAA-ATAAT
* *
25276 TAAATAAAAATTTAAAATAA-
1 GAAAT-AAAATAT-AAATAAT
*
25296 -AAATAAAAAAATAAAT-A-
1 GAAAT-AAAATATAAATAAT
25313 GAAATAAAATATAAATAATT
1 GAAATAAAATATAAATAA-T
25333 GAAAT-AAAT-T-AATAAT
1 GAAATAAAATATAAATAAT
25349 GAAGTATAAAATA-AAAT-A-
1 GAA--ATAAAATATAAATAAT
25367 -AAATAAAATA-AAATAA
1 GAAATAAAATATAAATAA
25383 CAATGGGTTG
Statistics
Matches: 88, Mismatches: 6, Indels: 29
0.72 0.05 0.24
Matches are distributed among these distances:
15 12 0.14
16 5 0.06
17 18 0.20
18 12 0.14
19 23 0.26
20 12 0.14
21 4 0.05
22 2 0.02
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (19 bp):
GAAATAAAATATAAATAAT
Found at i:25376 original size:38 final size:36
Alignment explanation
Indices: 25288--25387 Score: 91
Period size: 38 Copynumber: 2.8 Consensus size: 36
25278 AATAAAAATT
*
25288 TAAAATAAAAATAAAA-AAATAAAT-A-GAAATAAAA
1 TAAAAT-AAAATAAAATAAATTAATAATGAAATAAAA
* *
25322 TATAAAT-AATTGAAATAAATTAATAATGAAGTATAAAA
1 TA-AAATAAAATAAAATAAATTAATAATGAA--ATAAAA
* *
25360 TAAAATAAAATAAAATAAAATAACAATG
1 TAAAATAAAATAAAATAAATTAATAATG
25388 GGTTGCCTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
33 6 0.12
34 9 0.17
35 5 0.10
36 3 0.06
37 4 0.08
38 25 0.48
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (36 bp):
TAAAATAAAATAAAATAAATTAATAATGAAATAAAA
Found at i:34947 original size:161 final size:160
Alignment explanation
Indices: 34671--35015 Score: 485
Period size: 161 Copynumber: 2.1 Consensus size: 160
34661 GAGGCGGTCA
* * **
34671 TCTTCCTGATGAGATATAGAGAAGTATACCAAATTAATGAAACAAAGCTCAACGTGAGTGAAACT
1 TCTTCCTGATGAGATATAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAACGTGAGCAAAACT
* *
34736 TCGAACCCTAGCTTCCTGATGAGATACTGAGAAGAAGGTCAAAGCAATAAAGCAGTCGTCTTCCT
66 TCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTCAAAGCAATAAAGCAGTCGTCTTCCT
*
34801 GATGAGATACAGGGAAGTGGACCAAATCCG
131 GATGAGATACAGAGAAGTGGACCAAATCCG
* ** * * *
34831 TCTTCCTGATGAGATACT-GAGAAGTGGACTTAATCAATGAAACCAAATCTTAATGTGAGCAAAA
1 TCTTCCTGATGAGATA-TAGAGAAGTAGACCAAATCAATGAAA-CAAAGCTCAACGTGAGCAAAA
* * * * * * *
34895 CTTTGAACCCCAGCTTCCTGATAAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTCTTTTTC
64 CTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTCAAAGCAATAAAGCAGTCGTCTTC
34960 CTGATGAGATACAGAGAAGTGGACCAAATCCG
129 CTGATGAGATACAGAGAAGTGGACCAAATCCG
34992 TCTTCCTGATGAGATATAGAGAAG
1 TCTTCCTGATGAGATATAGAGAAG
35016 AGGATCGAGA
Statistics
Matches: 162, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
160 36 0.22
161 126 0.78
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (160 bp):
TCTTCCTGATGAGATATAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAACGTGAGCAAAACT
TCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTCAAAGCAATAAAGCAGTCGTCTTCCT
GATGAGATACAGAGAAGTGGACCAAATCCG
Found at i:35293 original size:173 final size:173
Alignment explanation
Indices: 34990--35353 Score: 541
Period size: 173 Copynumber: 2.1 Consensus size: 173
34980 GGACCAAATC
* * *
34990 CGTCTTCCTGATGAGATATAGAGAAGAGGATCGAGATAAGTGATGCAGTCATCTTCCTAATGAGA
1 CGTCTTCCTGATGAGATACAAAGAAGAGGATCAAGATAAGTGATGCAGTCATCTTCCTAATGAGA
* * *
35055 TACTGAGAAGTAGACCAAGTCAATGAAACCAAAGCTCGATATGAGCGAAACTTTGAACCTCAGCT
66 TACTGAGAAGTAGACCAACTCAATGAAACCAAAGCTCGATATGAGCGAAACATCGAACCTCAGCT
* * * *
35120 TCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAAT-GGT
131 TCCTAATAAGGTACTAAGAAGCAAGTCGAAGCAAT-AAATCGGT
* * ** * *
35163 TGTCTTCCTGATGAGATACAAAGAAGCGGATCAAGATAAGTGATGTGGTCATCTTCTTGATGAGA
1 CGTCTTCCTGATGAGATACAAAGAAGAGGATCAAGATAAGTGATGCAGTCATCTTCCTAATGAGA
* * *
35228 TACTGAGAAGTAGACCAACTCAATGAAGCCAAAGCTCGATGTGAGCGAAACATCGAACTTCAGCT
66 TACTGAGAAGTAGACCAACTCAATGAAACCAAAGCTCGATATGAGCGAAACATCGAACCTCAGCT
35293 TCCTAATAAGGTACTAAGAAGCAAGTCGAAGCAATAAATCGGT
131 TCCTAATAAGGTACTAAGAAGCAAGTCGAAGCAATAAATCGGT
35336 CGTCTTCCTGATGAGATA
1 CGTCTTCCTGATGAGATA
35354 TAGAGAAGTG
Statistics
Matches: 170, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
172 4 0.02
173 166 0.98
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (173 bp):
CGTCTTCCTGATGAGATACAAAGAAGAGGATCAAGATAAGTGATGCAGTCATCTTCCTAATGAGA
TACTGAGAAGTAGACCAACTCAATGAAACCAAAGCTCGATATGAGCGAAACATCGAACCTCAGCT
TCCTAATAAGGTACTAAGAAGCAAGTCGAAGCAATAAATCGGT
Found at i:35361 original size:383 final size:383
Alignment explanation
Indices: 34831--35570 Score: 1025
Period size: 383 Copynumber: 1.9 Consensus size: 383
34821 ACCAAATCCG
* * * *
34831 TCTTCCTGATGAGATACTGAGAAGTGGACTTAATCAATGAAACCAAATCTTAATGTGAGCAAAAC
1 TCTTCCTGATGAGATACTGAGAAGTAGACTCAATCAATGAAACCAAAGCTCAATGTGAGCAAAAC
* * * * * * *
34896 TTTGAACCCCAGCTTCCTGATAAGGTACTGAGAAGCAGGTCGAAGCAATAAAGCGGTCTTTTTCC
66 ATCGAACCCCAGCTTCCTAATAAGGTACTAAGAAGCAAGTCGAAGCAATAAAGCGGTCGTCTTCC
* * *
34961 TGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATATAGAGAAGAGGATCGAGA
131 TGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGAGGATCAAAA
* * *
35026 TAAGTGATGCAGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAGTCAATGAAACCAAAGCT
196 CAAGTGATACAGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCT
* * * *
35091 CGATATGAGCGAAACTTTGAACCTC-AGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAAT
261 CGATATGAGCGAAACTTCGAACCCCTA-CTTCCCGATGAGATACTGAGAAGCAGGTCGAAGCAAT
* ** *
35155 AAAATGGTTGTCTTCCTGATGAGATACAAAGAAGCGGATCAAGATAAGTGATGTGGTCA
325 AAAATGATCATCTTCCTAATGAGATACAAAGAAGCGGATCAAGATAAGTGATGTGGTCA
* * * *
35214 TCTTCTTGATGAGATACTGAGAAGTAGAC-CAACTCAATGAAGCCAAAGCTCGATGTGAGCGAAA
1 TCTTCCTGATGAGATACTGAGAAGTAGACTCAA-TCAATGAAACCAAAGCTCAATGTGAGCAAAA
** *
35278 CATCGAACTTCAGCTTCCTAATAAGGTACTAAGAAGCAAGTCGAAGCAATAAATCGGTCGTCTTC
65 CATCGAACCCCAGCTTCCTAATAAGGTACTAAGAAGCAAGTCGAAGCAATAAAGCGGTCGTCTTC
* * * * * *
35343 CTGATGAGATATAGAGAAGTGGTCCAAATTCGTTTTCTTGATGAGATACAGAGAAGCGGATCAAA
130 CTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGAGGATCAAA
** ** * *
35408 ACAAGTGATATGGTTGTCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGC
195 ACAAGTGATACAGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGC
* *
35473 TCGATGTGAGCGAAACTTCGAACCCCTATTTCCCGATGAGATACTGAGAAGCAGGTCGAAGCAAT
260 TCGATATGAGCGAAACTTCGAACCCCTACTTCCCGATGAGATACTGAGAAGCAGGTCGAAGCAAT
*
35538 AAAATGATCATCTTCCTAATGAGATACAGAGAA
325 AAAATGATCATCTTCCTAATGAGATACAAAGAA
35571 AAAGATCAAG
Statistics
Matches: 308, Mismatches: 47, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
382 2 0.01
383 305 0.99
384 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (383 bp):
TCTTCCTGATGAGATACTGAGAAGTAGACTCAATCAATGAAACCAAAGCTCAATGTGAGCAAAAC
ATCGAACCCCAGCTTCCTAATAAGGTACTAAGAAGCAAGTCGAAGCAATAAAGCGGTCGTCTTCC
TGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGAGGATCAAAA
CAAGTGATACAGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCT
CGATATGAGCGAAACTTCGAACCCCTACTTCCCGATGAGATACTGAGAAGCAGGTCGAAGCAATA
AAATGATCATCTTCCTAATGAGATACAAAGAAGCGGATCAAGATAAGTGATGTGGTCA
Found at i:35533 original size:210 final size:210
Alignment explanation
Indices: 35171--35570 Score: 570
Period size: 210 Copynumber: 1.9 Consensus size: 210
35161 GTTGTCTTCC
* * *
35171 TGATGAGATACAAAGAAGCGGATCAAGATAAGTGATGTGGTCATCTTCTTGATGAGATACTGAGA
1 TGATGAGATACAAAGAAGCGGATCAAAACAAGTGATATGGTCATCTTCTTGATGAGATACTGAGA
* * ** *
35236 AGTAGACCAACTCAATGAAGCCAAAGCTCGATGTGAGCGAAACATCGAACTTCAGCTTCCTAATA
66 AGTAGACCAAATCAATGAAACCAAAGCTCGATGTGAGCGAAACATCGAACCCCAGCTTCCCAATA
* * * * *
35301 AGGTACTAAGAAGCAAGTCGAAGCAAT-AAATCGGTCGTCTTCCTGATGAGATATAGAGAAGTGG
131 AGATACTAAGAAGCAAGTCGAAGCAATAAAAT-GATCATCTTCCTAATGAGATACAGAGAAGTGG
35365 TCCAAATTCGTTTTCT
195 TCCAAATTCGTTTTCT
* **
35381 TGATGAGATACAGAGAAGCGGATCAAAACAAGTGATATGGTTGTCTTCTTGATGAGATACTGAGA
1 TGATGAGATACAAAGAAGCGGATCAAAACAAGTGATATGGTCATCTTCTTGATGAGATACTGAGA
* * *
35446 AGTAGACCAAATCAATGAAACCAAAGCTCGATGTGAGCGAAACTTCGAACCCCTA-TTTCCCGAT
66 AGTAGACCAAATCAATGAAACCAAAGCTCGATGTGAGCGAAACATCGAACCCC-AGCTTCCCAAT
* * *
35510 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCATCTTCCTAATGAGATACAGAGAA
130 AAGATACTAAGAAGCAAGTCGAAGCAATAAAATGATCATCTTCCTAATGAGATACAGAGAA
35571 AAAGATCAAG
Statistics
Matches: 166, Mismatches: 22, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
210 161 0.97
211 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (210 bp):
TGATGAGATACAAAGAAGCGGATCAAAACAAGTGATATGGTCATCTTCTTGATGAGATACTGAGA
AGTAGACCAAATCAATGAAACCAAAGCTCGATGTGAGCGAAACATCGAACCCCAGCTTCCCAATA
AGATACTAAGAAGCAAGTCGAAGCAATAAAATGATCATCTTCCTAATGAGATACAGAGAAGTGGT
CCAAATTCGTTTTCT
Found at i:37125 original size:120 final size:120
Alignment explanation
Indices: 36847--37380 Score: 599
Period size: 120 Copynumber: 4.5 Consensus size: 120
36837 ACAAGTTCGA
* * * * * *
36847 GGGTCAAAATGTGATTTTGGAAAAGTTT-GAGGATCAAAATATTATTTTAGAAAAGTTTAGAGGT
1 GGGTCAAAATATGATTTTGGAAAAGTTTAG-GGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGT
* * * * * * ****
36911 TAAAATGTAATTTTGGAACAGTTTAAGGGTCAAAATATGATTTTTTTTAA-TTTAG
65 CAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
* * * *
36966 GGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTAAAAATGTAAATTTAGAAAAGTTTAGGGGTT
1 GGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTC
* * ** *
37031 AGAATATGATTTTGGAAAAGTTTTGGGGTTAAAATGTAAATTTGGAAAAGTTTAG
66 AAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
* * * *
37086 GTGTCAAAATATGATTTTGGAAATGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGCTC
1 GGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTC
* * * *
37151 AAAATATGATTTTGGAAAGGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTCAG
66 AAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
* * *
37206 GGGTCAACATATGATTTTGGAAAAGTTT-GGTGGTCAAAATATTATTTTGGAAAAGTTT-GGTGG
1 GGGTCAAAATATGATTTTGGAAAAGTTTAGG-GGTCAAAATGTAATTTTGGAAAAGTTTAGG-GG
* *
37269 TCAAAATGTAATTTTGGAAAAGTTAAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
64 TCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
* * * * * * *
37326 GAGTTAAAATGTAATGTTGGAAAAGTTTAGGGGGCTTAAATGTAATTTTGGAAAA
1 GGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTC-AAAATGTAATTTTGGAAAA
37381 TTATGAGGAC
Statistics
Matches: 351, Mismatches: 58, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
119 95 0.27
120 238 0.68
121 18 0.05
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (120 bp):
GGGTCAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTC
AAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
Found at i:37332 original size:30 final size:30
Alignment explanation
Indices: 36847--37380 Score: 527
Period size: 30 Copynumber: 17.8 Consensus size: 30
36837 ACAAGTTCGA
*
36847 GGGTCAAAATGTGATTTTGGAAAAGTTT-G
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * * *
36876 AGGATCAAAATATTATTTTAGAAAAGTTTAG
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * * *
36907 AGGTTAAAATGTAATTTTGGAACAGTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * ****
36937 GGGTCAAAATATGATTTTTTTTAA-TTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* *
36966 GGGTCAAAATATGATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * *
36996 GGGTAAAAATGTAAATTTAGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * * * *
37026 GGGTTAGAATATGATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* *
37056 GGGTTAAAATGTAAATTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * * *
37086 GTGTCAAAATATGATTTTGGAAATGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
*
37116 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * * * *
37146 GGCTCAAAATATGATTTTGGAAAGGTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * *
37176 GGGTTAAAATGTAATTTTAGAAAAGTTCAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * *
37206 GGGTCAACATATGATTTTGGAAAAGTTT-G
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* *
37235 GTGGTCAAAATATTATTTTGGAAAAGTTT-G
1 G-GGTCAAAATGTAATTTTGGAAAAGTTTAG
* *
37265 GTGGTCAAAATGTAATTTTGGAAAAGTTAAA
1 G-GGTCAAAATGTAATTTTGGAAAAGTTTAG
*
37296 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * *
37326 GAGTTAAAATGTAATGTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* *
37356 GGGGCTTAAATGTAATTTTGGAAAA
1 GGGTC-AAAATGTAATTTTGGAAAA
37381 TTATGAGGAC
Statistics
Matches: 409, Mismatches: 90, Indels: 9
0.81 0.18 0.02
Matches are distributed among these distances:
29 26 0.06
30 364 0.89
31 19 0.05
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTAG
Found at i:38444 original size:24 final size:25
Alignment explanation
Indices: 38403--38449 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
38393 ATTGAGCTTG
* *
38403 TTAGGTAATTGGATTTAGGGTTTTT
1 TTAGGTAATTGGACTTAGCGTTTTT
*
38428 TTAGG-AATTGGGCTTAGCGTTT
1 TTAGGTAATTGGACTTAGCGTTT
38450 GGGTTATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.47
Consensus pattern (25 bp):
TTAGGTAATTGGACTTAGCGTTTTT
Found at i:38935 original size:13 final size:13
Alignment explanation
Indices: 38917--38944 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38907 CATTCGCATC
38917 ATGTTTCTCTGGT
1 ATGTTTCTCTGGT
38930 ATGTTTCTCTGGT
1 ATGTTTCTCTGGT
38943 AT
1 AT
38945 TTTTACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.11, C:0.14, G:0.21, T:0.54
Consensus pattern (13 bp):
ATGTTTCTCTGGT
Done.