Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004943.1 Kokia drynarioides strain JFW-HI SEQ_118653, 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: 24699
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:2378 original size:37 final size:37
Alignment explanation
Indices: 2328--2439 Score: 206
Period size: 37 Copynumber: 3.0 Consensus size: 37
2318 AGGCCTATAT
2328 TACTCGAACTCGGGTGTGAATGTTAAGTAAGAGTATG
1 TACTCGAACTCGGGTGTGAATGTTAAGTAAGAGTATG
*
2365 TACTCGAACTCGGGTGTGAATGTTAAGTATGAGTATG
1 TACTCGAACTCGGGTGTGAATGTTAAGTAAGAGTATG
*
2402 TACTCGAACTCGGGTGTGAATGTTAAGTACGAGTATG
1 TACTCGAACTCGGGTGTGAATGTTAAGTAAGAGTATG
2439 T
1 T
2440 TTCTAGTAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (37 bp):
TACTCGAACTCGGGTGTGAATGTTAAGTAAGAGTATG
Found at i:4770 original size:22 final size:19
Alignment explanation
Indices: 4732--4776 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 19
4722 CCATATTTTA
4732 AAATATAATTATTTTTATT
1 AAATATAATTATTTTTATT
4751 AAATATTAATTAATTATTTATT
1 AAATA-TAATT-ATT-TTTATT
4773 AAAT
1 AAAT
4777 TTATGAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.22
20 5 0.22
21 3 0.13
22 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATAATTATTTTTATT
Found at i:9736 original size:7 final size:7
Alignment explanation
Indices: 9724--9749 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9714 TTTCTATTTT
9724 TTCAAAA
1 TTCAAAA
9731 TTCAAAA
1 TTCAAAA
9738 TTCAAAA
1 TTCAAAA
9745 TTCAA
1 TTCAA
9750 TGTCATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (7 bp):
TTCAAAA
Found at i:16043 original size:15 final size:16
Alignment explanation
Indices: 16012--16044 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16002 AGATAGTGGA
*
16012 CTTGTGGGTGTTTGGG
1 CTTGTAGGTGTTTGGG
16028 CTTGTAGGTG-TTGGG
1 CTTGTAGGTGTTTGGG
16043 CT
1 CT
16045 AAGGTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.03, C:0.09, G:0.45, T:0.42
Consensus pattern (16 bp):
CTTGTAGGTGTTTGGG
Found at i:16585 original size:39 final size:39
Alignment explanation
Indices: 16542--16764 Score: 135
Period size: 39 Copynumber: 5.7 Consensus size: 39
16532 TCTACCTCAA
**
16542 GATTGGGGTAAGAGATTGGATGGTTGCGATCCGTTTCAT
1 GATTGGGGTAAGAGATTGGATGGTTGCGATATGTTTCAT
* * * * * **
16581 GATTGGGGTAAGAGATCGGATGATTTTCAATTTG-CCCAT
1 GATTGGGGTAAGAGATTGGATG-GTTGCGATATGTTTCAT
* *
16620 GATGGGGGTATGAGATTGGATGGTTGCGATATGCTTT-AT
1 GATTGGGGTAAGAGATTGGATGGTTGCGATATG-TTTCAT
** * * * ** *
16659 GATTGGGGTAAGAGATAAGATGGTTTTCAATTTACTCCAT
1 GATTGGGGTAAGAGATTGGATGG-TTGCGATATGTTTCAT
* * * * * * **
16699 TATCGGGGTAAGAGATTGGATGATTTTCAATTTGCCTCAT
1 GATTGGGGTAAGAGATTGGATG-GTTGCGATATGTTTCAT
* *
16739 GATCGGGGTAAGAGATTGGATAGTTG
1 GATTGGGGTAAGAGATTGGATGGTTG
16765 TGATCTACCT
Statistics
Matches: 139, Mismatches: 39, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
38 7 0.05
39 67 0.48
40 65 0.47
ACGTcount: A:0.25, C:0.09, G:0.32, T:0.34
Consensus pattern (39 bp):
GATTGGGGTAAGAGATTGGATGGTTGCGATATGTTTCAT
Found at i:16635 original size:78 final size:79
Alignment explanation
Indices: 16546--16720 Score: 246
Period size: 78 Copynumber: 2.2 Consensus size: 79
16536 CCTCAAGATT
* **
16546 GGGGTAAGAGATTGGATGGTTGCGATCCG-TTTCATGATTGGGGTAAGAGATCGGATGATTTTCA
1 GGGGTAAGAGATTGGATGGTTGCGATACGCTTT-ATGATTGGGGTAAGAGATAAGATGATTTTCA
* *
16610 ATTTGC-CCATGATG
65 ATTTACTCCATGATC
* * *
16624 GGGGTATGAGATTGGATGGTTGCGATATGCTTTATGATTGGGGTAAGAGATAAGATGGTTTTCAA
1 GGGGTAAGAGATTGGATGGTTGCGATACGCTTTATGATTGGGGTAAGAGATAAGATGATTTTCAA
*
16689 TTTACTCCATTATC
66 TTTACTCCATGATC
16703 GGGGTAAGAGATTGGATG
1 GGGGTAAGAGATTGGATG
16721 ATTTTCAATT
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
78 59 0.69
79 26 0.31
ACGTcount: A:0.25, C:0.09, G:0.33, T:0.33
Consensus pattern (79 bp):
GGGGTAAGAGATTGGATGGTTGCGATACGCTTTATGATTGGGGTAAGAGATAAGATGATTTTCAA
TTTACTCCATGATC
Found at i:16713 original size:40 final size:40
Alignment explanation
Indices: 16577--16754 Score: 137
Period size: 40 Copynumber: 4.5 Consensus size: 40
16567 GCGATCCGTT
* ** *
16577 TCATGATTGGGGTAAGAGATCGGATGATTTTCAATTTGCC
1 TCATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
* * ** * * * * * *
16617 -CATGATGGGGGTATGAGATTGGATG-GTTGCGATATGCT
1 TCATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
* * *
16655 TTATGATTGGGGTAAGAGATAAGATGGTTTTCAATTTA-C
1 TCATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
* ** *
16694 TCCATTATCGGGGTAAGAGATTGGATGATTTTCAATTTGCC
1 T-CATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
16735 TCATGATCGGGGTAAGAGAT
1 TCATGATCGGGGTAAGAGAT
16755 TGGATAGTTG
Statistics
Matches: 107, Mismatches: 27, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
38 8 0.07
39 43 0.40
40 54 0.50
41 2 0.02
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.34
Consensus pattern (40 bp):
TCATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
Found at i:16880 original size:38 final size:38
Alignment explanation
Indices: 16704--18357 Score: 531
Period size: 38 Copynumber: 42.8 Consensus size: 38
16694 TCCATTATCG
* * **
16704 GGGTAAGAGATTGGATGATTTTCAATTTG-CCTCATGATCG
1 GGGTAAGAGATTGGATG--CTTCAATCTGCCCT-ATGATTA
** * * *
16744 GGGTAAGAGATTGGATAG-TTGTGATCTACCTTCTGATTA
1 GGGTAAGAGATTGGAT-GCTT-CAATCTGCCCTATGATTA
* * * * * *
16783 AGATAAAAGATTGGATGCTTCAATCTACCCCATGATCA
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
** *
16821 AAGTAAGAGATCT-G-TGTCTTCAATCTGCCCTTTGATTA
1 GGGTAAGAGAT-TGGATG-CTTCAATCTGCCCTATGATTA
* **
16859 GGGTAA-AGGATTGGATGCTTCAATCT-TCCTCATGATCG
1 GGGTAAGA-GATTGGATGCTTCAATCTGCCCT-ATGATTA
** * * * *
16897 GGGTAAGAGA-TCAATATCTTAAATTTGCCCTCTGATTA
1 GGGTAAGAGATTGGAT-GCTTCAATCTGCCCTATGATTA
* * * * **
16935 GGGTAAAAGATTAGATGCTTTAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * *
16973 GGGTAAGAGA-TCGATGTCTTCAATTTGCCCTCTGATTA
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * * **
17011 GGGTAAAAGATTGGATGCTTCAGTCTGCCTTATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* *
17049 GGGTAAGAGATTGG-TGTCTTTAACCTG-CCTCATGATCTA
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCT-ATGAT-TA
** * *
17088 -GGTAAGAGATTGGTGATGTCTTCAATCTATCTTCTGATTA
1 GGGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * * * **
17128 AGGTAAAAGATTGGATACTTCAATATG-CCTCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCT-ATGATTA
* * * * *
17166 GGGTAAGAGATCAGTAT-TTTCAATCTGCCCTCTAATTA
1 GGGTAAGAGAT-TGGATGCTTCAATCTGCCCTATGATTA
* * * **
17204 GGGTAAAAGGTTGGATGCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * * * *
17242 GGGTAAGAGATTGGTCATATCTTTAATCTACCTTCTGATTA
1 GGGTAAGAGATTGG--AT-GCTTCAATCTGCCCTATGATTA
* * * * * * * * * **
17283 AGATAAAAAATAGGATGCTTTAATCTGCCTTTTAATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * * *
17321 GGGTAAGAGATTAG-TGTCTTCAACCTGCCCCATGA-TC
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * * * *
17358 GAGGTAAGAGATTGGTGATGTCTTAAATCTACCTTCTAATTA
1 G-GGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * * * * **
17400 AGGTAAAAGATT-GACGTCCTCAA-CTTGCCCCATGATCG
1 GGGTAAGAGATTGGATG-CTTCAATC-TGCCCTATGATTA
* * * * * *
17438 GGGTAAGAGATCGGATGGTTTTTAATTTGCCCCATGATTG
1 GGGTAAGAGATTGGAT-G-CTTCAATCTGCCCTATGATTA
* * * * *
17478 GGGTAAGAGATTGAATGATTTTCAATTTG-TCTCATGATCGA
1 GGGTAAGAGATTGGATG--CTTCAATCTGCCCT-ATGAT-TA
* ** * *
17519 GGGTAAGAGATTGGATGGTTGTGATCTGCCTTCTGATTA
1 GGGTAAGAGATTGGATGCTT-CAATCTGCCCTATGATTA
* *
17558 AGGTAAAAGATTGGATGCTTCAATCTGTCCC-ATGATT-
1 GGGTAAGAGATTGGATGCTTCAATCTG-CCCTATGATTA
* * *
17595 GGAGTAAGAGATCT-G-TGTCTTCAATATGCCTTTTGATTA
1 GG-GTAAGAGAT-TGGATG-CTTCAATCTGCCCTATGATTA
* * * *
17634 GGGTAAAAAATTGGATGCTTCAA-CTTACCC-ATGA-TC
1 GGGTAAGAGATTGGATGCTTCAATC-TGCCCTATGATTA
* * *
17670 GAGGCAAGAGA-T-CATTGTCTTCAATCTGCCCTCTGATTA
1 G-GGTAAGAGATTGGA-TG-CTTCAATCTGCCCTATGATTA
* * * * **
17709 GGGTAAAAGATTGGATGCTTTAATTTGAACC-ATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTG-CCCTATGATTA
* * *
17747 GGGTAAGAGATCGG-TGTCTTCAATCTGTCCTCTGATTA
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * * **
17785 GGGTAAAAGATTAGATACTTCAATCTG-CCTCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCT-ATGATTA
* * * * *
17823 GGGTAAGAGATT-GATGTCTTTAACCTACCCCATGA-TC
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * *
17860 GAGGTAAGAGATTGGTGATGTCTTTAATCTGCCTTTTGATTA
1 G-GGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * * * * * *
17902 AGGTAAAAAATTAGATGCTTCAATTTGCCTTATGA-TC
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * * * *
17939 GAAGTAAGAGATCGG-TGTTTTCAATTTGCCCTCTGATTA
1 G-GGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * * *
17978 GGGTCAA-AAATTGGATGCTTCAATTTACCCCATGATT-
1 GGGT-AAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * * * *
18015 GAGGTAAGAGGTT-GACGTCTTCAATCTACCCTATGACTG
1 G-GGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
**
18054 GGGTAAGAGATT-GATGTCTTCAATCTGCTTTCA-GATTA
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCT-ATGATTA
* * * * * *
18092 AGGTAAAATATTGGATGCTTTAATCTACACC-ATGA-TC
1 GGGTAAGAGATTGGATGCTTCAATCTGC-CCTATGATTA
* * * * **
18129 GGCGTAAAAGATTAG-TGTCTTCAA-CTTGTCCTATTATCG
1 GG-GTAAGAGATTGGATG-CTTCAATC-TGCCCTATGATTA
* ** *
18168 GGGAAAGAGATTGGTGATGTCTTCAATCTGCTTTCTGATTA
1 GGGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * *
18209 AGGTAAAAGATTGG-CGTCTTCAA-CTTG-CCTCATGATTA
1 GGGTAAGAGATTGGATG-CTTCAATC-TGCCCT-ATGATTA
* *
18247 GGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTCTGATTA
1 GGGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * * ** **
18288 AGGTAAAAGATTGAATGCTTCAATCT-ATCTCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCT-ATGATTA
18326 GGGTAAGAGATTGATGATGTCTTCAATCTGCC
1 GGGTAAGAGATTG--GATG-CTTCAATCTGCC
18358 TTTTAATTAA
Statistics
Matches: 1164, Mismatches: 341, Indels: 216
0.68 0.20 0.13
Matches are distributed among these distances:
35 1 0.00
36 5 0.00
37 84 0.07
38 691 0.59
39 113 0.10
40 87 0.07
41 175 0.15
42 8 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (38 bp):
GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
Found at i:16960 original size:152 final size:152
Alignment explanation
Indices: 16704--17833 Score: 438
Period size: 155 Copynumber: 7.3 Consensus size: 152
16694 TCCATTATCG
* * * ** *
16704 GGGTAAGAGATTGGATGATTTTCAATTTGCCTCATGATCGGGGTAAGAGATTGGATAGT-TGT-G
1 GGGTAAAAGATTGGATG--CTTCAATCTGCCTCATGATCGGGGTAAGAGA-TCAATA-TCT-TAA
* * * *
16767 ATCTACCTTCTGATTAAGATAAAAGATTGGATGCTTCAATCTACCCCATGATCAAAGTAAGAGAT
61 ATTTGCCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCTACCCCATGATCAAAGTAAGAGAT
*
16832 CTG-TGTCTTCAATCTGCCCTTTGATTA
126 C-GATGTCTTCAATCTGCCCTCTGATTA
* *
16859 GGGTAAAGGATTGGATGCTTCAATCTTCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTTG
1 GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTTG
* * * * ***
16924 CCCTCTGATTAGGGTAAAAGATTAGATGCTTTAATCTGCCCCATGATCGGGGTAAGAGATCGATG
66 CCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCTACCCCATGATCAAAGTAAGAGATCGATG
*
16989 TCTTCAATTTGCCCTCTGATTA
131 TCTTCAATCTGCCCTCTGATTA
* * *** * * **
17011 GGGTAAAAGATTGGATGCTTCAGTCTGCCTTATGATCGGGGTAAGAGATTGGTGTCTTTAACCTG
1 GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTTG
* * * ** * * *
17076 -CCTCATGATCT-AGGTAAGAGATTGGTGATGTCTTCAATCTATCTTC-TGATTAAGGTAAAAGA
66 CCCTC-TGAT-TAAGATAAAAGATT--AGATG-CTTCAATCTA-CCCCATGATCAAAGTAAGAGA
* * * **
17138 TTGGAT-ACTTCAATATG-CCTCATGATCG
125 -TCGATGTCTTCAATCTGCCCTC-TGATTA
* * * * * ** * * ** * *
17166 GGGTAAGAGATCAGTAT-TTTCAATCTGCCCTC-TAATTAGGGTAAAAGGTTGGAT-GCTTCAAT
1 GGGTAAAAGAT-TGGATGCTTCAATCTG-CCTCATGATCGGGGTAAGA-GATCAATATCTTAAAT
* *** * * * * * * * *
17228 CTGCCC-CATGATCGGGGTAAGAGATTGGTCATATCTTTAATCTACCTTC-TGAT-TAAGATAAA
63 TTGCCCTC-TGATTAAGATAAAAGATTAG--AT-GCTTCAATCTACC-CCATGATCAAAG-TAAG
* * * * * * **
17290 AAATAGGATG-CTTTAATCTGCCTTTTAATCG
122 AGAT-CGATGTCTTCAATCTGCCCTCTGATTA
* * * * * ** *
17321 GGGTAAGAGATTAG-TGTCTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTGATGTCTTAAA
1 GGGTAAAAGATTGGATG-CTTCAATCTGCCTCATGATCGGGGTAAGAGA-T--CAATATCTTAAA
* * * * * * * * ***
17385 TCTACCTTCTAATTAAGGTAAAAGATT-GACGTCCTCAA-CTTGCCCCATGATCGGGGTAAGAGA
62 TTTGCCCTCTGATTAAGATAAAAGATTAGATG-CTTCAATC-TACCCCATGATCAAAGTAAGAGA
* * * *
17448 TCGGATGGTTTTTAATTTGCCC-CATGATTG
125 TC-GAT-GTCTTCAATCTGCCCTC-TGATTA
* * * * * ** *
17478 GGGTAAGAGATTGAATGATTTTCAATTTGTCTCATGATCGAGGGTAAGAGATTGGATGGT-TGT-
1 GGGTAAAAGATTGGATG--CTTCAATCTGCCTCATGATCG-GGGTAAGAGA-TCAAT-ATCT-TA
* * * * * ** ***
17541 GATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGTCCCATGATTGGAGTAAGAGA
60 AATTTGCCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCTACCCCATGATCAAAGTAAGAGA
* * *
17606 TCTG-TGTCTTCAATATGCCTTTTGATTA
125 TC-GATGTCTTCAATCTGCCCTCTGATTA
* * * * * * * *
17634 GGGTAAAAAATTGGATGCTTCAA-CTTACC-CATGATCGAGGCAAGAGATCATTGTCTTCAATCT
1 GGGTAAAAGATTGGATGCTTCAATC-TGCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTT
* * * * * * *** *
17697 GCCCTCTGATTAGGGTAAAAGATTGGATGCTTTAATTTGA-ACCATGATCGGGGTAAGAGATCGG
65 GCCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCT-ACCCCATGATCAAAGTAAGAGATCGA
*
17761 TGTCTTCAATCTGTCCTCTGATTA
129 TGTCTTCAATCTGCCCTCTGATTA
* *
17785 GGGTAAAAGATTAGATACTTCAATCTGCCTCATGATCGGGGTAAGAGAT
1 GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGAT
17834 TGATGTCTTT
Statistics
Matches: 747, Mismatches: 173, Indels: 113
0.72 0.17 0.11
Matches are distributed among these distances:
150 4 0.01
151 110 0.15
152 176 0.24
153 39 0.05
154 25 0.03
155 191 0.26
156 52 0.07
157 31 0.04
158 83 0.11
159 25 0.03
160 11 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (152 bp):
GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTTG
CCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCTACCCCATGATCAAAGTAAGAGATCGATG
TCTTCAATCTGCCCTCTGATTA
Found at i:17149 original size:117 final size:114
Alignment explanation
Indices: 16935--17176 Score: 297
Period size: 117 Copynumber: 2.1 Consensus size: 114
16925 CCTCTGATTA
* * * * *
16935 GGGTAAAAGATTAGATGCTTTAATCTGCCCCATGATCGGGGTAAGAGATCGATGTCTTCAATTTG
1 GGGTAAGAGATTAGATGCTTTAACCTGCCCCATGATCGAGGTAAGAGATCGATGTCTTCAATCTA
* * * * *
17000 CCCTCTGATTAGGGTAAAAGATTGGATGCTTCAGTCTGCCTTATGATCG
66 CCCTCTGATTAAGGTAAAAGATTGGATACTTCAATATGCCTCATGATCG
* * * *
17049 GGGTAAGAGATT-GGTGTCTTTAACCTGCCTCATGATCTAGGTAAGAGATTGGTGATGTCTTCAA
1 GGGTAAGAGATTAGATG-CTTTAACCTGCCCCATGATCGAGGTAAGAGA-T--CGATGTCTTCAA
* *
17113 TCTATCTTCTGATTAAGGTAAAAGATTGGATACTTCAATATGCCTCATGATCG
62 TCTACCCTCTGATTAAGGTAAAAGATTGGATACTTCAATATGCCTCATGATCG
17166 GGGTAAGAGAT
1 GGGTAAGAGAT
17177 CAGTATTTTC
Statistics
Matches: 108, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
113 3 0.03
114 38 0.35
115 1 0.01
117 66 0.61
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (114 bp):
GGGTAAGAGATTAGATGCTTTAACCTGCCCCATGATCGAGGTAAGAGATCGATGTCTTCAATCTA
CCCTCTGATTAAGGTAAAAGATTGGATACTTCAATATGCCTCATGATCG
Found at i:17308 original size:79 final size:77
Alignment explanation
Indices: 17050--18433 Score: 341
Period size: 79 Copynumber: 17.8 Consensus size: 77
17040 TTATGATCGG
* * * **
17050 GGTAAGAGATTGG-TGTCTTTAACCTGCCTCATGATCTAGGTAAGAGATTGGTGATGTCTTCAAT
1 GGTAAAAGATTGGATG-CTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAAT
*
17114 CTATCTTCTGATTAA
63 CTACCTTCTGATTAA
* * ** *
17129 GGTAAAAGATTGGATACTTCAATATGCCTCATGATCGGGGTAAGAGATCAGTATT-TTCAATCTG
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATCTA
* * *
17193 CCCTCTAATTAG
66 CCTTCTGATTAA
* * *
17205 GGTAAAAGGTTGGATGCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTCATATCTTTAATC
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAATC
17270 TACCTTCTGATTAA
64 TACCTTCTGATTAA
* * * * ** * * * * *
17284 GATAAAAAATAGGATGCTTTAATCTGCCTTTTAATCGGGGTAAGAGATTAGT-GTCTTCAACCTG
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATCTA
* **
17348 CC-CCATGATCGA
66 CCTTC-TGATTAA
* * * * *** * * *
17360 GGTAAGAGATTGGTGATGTCTTAAATCTACCTTC-TAATTAAGGTAAAAGATT-G-ACGTCCTCA
1 GGTAAAAGATT-G-GATG-CTTCAATCTGCC-TCATGATCGGGGTAAGAGATTGGTA-TTCTTCA
* * ***
17422 A-CTTGCC-CCATGATCGG
61 ATC-TACCTTC-TGATTAA
* * * * * * * *
17439 GGTAAGAGATCGGATGGTTTTTAATTTGCCCCATGATTGGGGTAAGAGATTGAATGATT-TTCAA
1 GGTAAAAGATTGGAT-G-CTTCAATCTGCCTCATGATCGGGGTAAGAGATTG-GT-ATTCTTCAA
* ** * *
17503 TTTGTC-TCATGATCGAG
62 TCTACCTTC-TGAT-TAA
* * ** *** * *
17520 GGTAAGAGATTGGATGGTTGTGATCTGCCTTC-TGATTAAGGTAAAAGATTGG-ATGCTTCAATC
1 GGTAAAAGATTGGATGCTT-CAATCTGCC-TCATGATCGGGGTAAGAGATTGGTATTCTTCAATC
* *
17583 TGTCC--CATGATT-G
64 T-ACCTTC-TGATTAA
* * ** ** * * *
17596 GAGTAAGAGATCT-G-TGTCTTCAATATGCCTTTTGATTAGGGTAAAAAATTGG-ATGCTTCAA-
1 G-GTAAAAGAT-TGGATG-CTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAAT
**
17657 CTTACC--CATGATCGA
63 C-TACCTTC-TGATTAA
* * * ** * * *
17672 GGCAAGAGA-T-CATTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGG-ATGCTTTAAT
1 GGTAAAAGATTGGA-TG-CTTCAATCTG-CCTCATGATCGGGGTAAGAGATTGGTATTCTTCAAT
* * ***
17733 TTGAACC--ATGATCGG
63 CT--ACCTTCTGATTAA
* * ** * * *
17748 GGTAAGAGATCGG-TGTCTTCAATCTGTCCTC-TGATTAGGGTAAAAGATTAG-ATACTTCAATC
1 GGTAAAAGATTGGATG-CTTCAATCTG-CCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATC
* ***
17810 TGCC-TCATGATCGG
64 TACCTTC-TGATTAA
* * * * * * *
17824 GGTAAGAGATT-GATGTCTTTAACCTACCCCATGATCGAGGTAAGAGATTGGTGATGTCTTTAAT
1 GGTAAAAGATTGGATG-CTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAAT
* *
17888 CTGCCTTTTGATTAA
63 CTACCTTCTGATTAA
* * * * ** * * * *
17903 GGTAAAAAATTAGATGCTTCAATTTGCCTTATGATCGAAGTAAGAGATCGGTGTT-TTCAATTTG
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATCTA
* *
17967 CCCTCTGATTAG
66 CCTTCTGATTAA
* * * * * * *
17979 GGTCAAAA-ATTGGATGCTTCAATTTACCCCATGATTGAGGTAAGAGGTT-G-ACGTCTTCAATC
1 GGT-AAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTA-TTCTTCAATC
* * * **
18041 TACCCTATGACTGG
64 TACCTTCTGATTAA
* * *** * * * *
18055 GGTAAGAGATT-GATGTCTTCAATCTGCTTTCA-GATTAAGGTAAAATATTGG-ATGCTTTAATC
1 GGTAAAAGATTGGATG-CTTCAATCTGC-CTCATGATCGGGGTAAGAGATTGGTATTCTTCAATC
**
18117 TACAC--CATGA-TCG
64 TAC-CTTC-TGATTAA
* * *
18130 GCGTAAAAGATTAG-TGTCTTCAA-CTTGTCCT-ATTATCGGGGAAAGAGATTGGTGATGTCTTC
1 G-GTAAAAGATTGGATG-CTTCAATC-TG-CCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTC
* *
18192 AATCTGCTTTCTGATTAA
60 AATCTACCTTCTGATTAA
* **
18210 GGTAAAAGATTGG-CGTCTTCAA-CTTGCCTCATGATTAGGGTAAGAGATTGGTGATGTCTTCAA
1 GGTAAAAGATTGGATG-CTTCAATC-TGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAA
*
18273 TCTGCCTTCTGATTAA
62 TCTACCTTCTGATTAA
* ** *
18289 GGTAAAAGATTGAATGCTTCAATCTATCTCATGATCGGGGTAAGAGATTGATGATGTCTTCAATC
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAATC
* * *
18354 TGCCTTTTAATTAA
64 TACCTTCTGATTAA
* * *
18368 GGTAAAAAATTGG-CGCTTTCAA-CTTGTCC-CATGATCGGGGTAAGAGATTGGTGATGTCTTTA
1 GGTAAAAGATTGGATGC-TTCAATC-TG-CCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCA
18430 ATCT
61 ATCT
18434 GTCTCATGAT
Statistics
Matches: 1017, Mismatches: 215, Indels: 146
0.74 0.16 0.11
Matches are distributed among these distances:
73 1 0.00
74 2 0.00
75 76 0.07
76 369 0.36
77 37 0.04
78 59 0.06
79 405 0.40
80 50 0.05
81 17 0.02
82 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (77 bp):
GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATCTA
CCTTCTGATTAA
Found at i:17438 original size:117 final size:117
Alignment explanation
Indices: 17221--17448 Score: 280
Period size: 117 Copynumber: 1.9 Consensus size: 117
17211 AGGTTGGATG
* * * *
17221 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTCATATCTTTAATCTACCTTCTGATTAAGA
1 CTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTCATATCTTAAATCTACCTTCTAATTAAGA
* * * ***
17286 TAAAAAATAGGATGCTTTAATCTGCCTTTTAATCGGGGTAAGAGATTAGTGT
66 TAAAAAATAGGACGCCTCAATCTGCCCCATAATCGGGGTAAGAGATTAGTGT
* * *
17338 CTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTGATGTCTTAAATCTACCTTCTAATTAAGG
1 CTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTCATATCTTAAATCTACCTTCTAATTAAGA
* * *
17403 TAAAAGAT-TGACGTCCTCAA-CTTGCCCCATGATCGGGGTAAGAGAT
66 TAAAAAATAGGACG-CCTCAATC-TGCCCCATAATCGGGGTAAGAGAT
17449 CGGATGGTTT
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
116 4 0.04
117 89 0.96
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (117 bp):
CTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTCATATCTTAAATCTACCTTCTAATTAAGA
TAAAAAATAGGACGCCTCAATCTGCCCCATAATCGGGGTAAGAGATTAGTGT
Found at i:17728 original size:151 final size:152
Alignment explanation
Indices: 17542--17833 Score: 392
Period size: 151 Copynumber: 1.9 Consensus size: 152
17532 GATGGTTGTG
* ** *
17542 ATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGTCCCATGATTGGAGTAAGAGAT
1 ATCTGCCCTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGAACCATGATCGGAGTAAGAGAT
* * * *
17607 CTGTGTCTTCAATATG-CCTTTTGATTAGGGTAAAAAATTGGATGCTTCAA-CTTACC-CATGAT
66 CGGTGTCTTCAATATGTCC-TCTGATTAGGGTAAAAAATTAGATACTTCAATC-TACCTCATGAT
17669 CGAGGCAAGAGATCATTGTCTTCA
129 CGAGGCAAGAGATCATTGTCTTCA
* * * *
17693 ATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTTAATTTGAACCATGATCGGGGTAAGAGAT
1 ATCTGCCCTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGAACCATGATCGGAGTAAGAGAT
* * *
17758 CGGTGTCTTCAATCTGTCCTCTGATTAGGGTAAAAGATTAGATACTTCAATCTGCCTCATGATCG
66 CGGTGTCTTCAATATGTCCTCTGATTAGGGTAAAAAATTAGATACTTCAATCTACCTCATGATCG
* *
17823 GGGTAAGAGAT
131 AGGCAAGAGAT
17834 TGATGTCTTT
Statistics
Matches: 121, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
151 101 0.83
152 20 0.17
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (152 bp):
ATCTGCCCTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGAACCATGATCGGAGTAAGAGAT
CGGTGTCTTCAATATGTCCTCTGATTAGGGTAAAAAATTAGATACTTCAATCTACCTCATGATCG
AGGCAAGAGATCATTGTCTTCA
Found at i:17931 original size:117 final size:114
Alignment explanation
Indices: 17738--17950 Score: 284
Period size: 117 Copynumber: 1.8 Consensus size: 114
17728 TTAATTTGAA
* * *
17738 CCATGATCGGGGTAAGAGATCGGTGTCTTCAATCTGTCCTCTGATTAGGGTAAAAGATTAGATAC
1 CCATGATCGAGGTAAGAGATCGGTGTCTTCAATCTGTCCTCTGATTAAGGTAAAAAATTAGATAC
**
17803 TTCAATCTGCCTCATGATCGGGGTAAGAGATTGATGTCTTTAACCTACC
66 TTCAATCTGCCTCATGATCGAAGTAAGAGATTGATGTCTTTAACCTACC
* * *
17852 CCATGATCGAGGTAAGAGATTGGTGATGTCTTTAATCTG-CCTTTTGATTAAGGTAAAAAATTAG
1 CCATGATCGAGGTAAGAGA-TCG-G-TGTCTTCAATCTGTCC-TCTGATTAAGGTAAAAAATTAG
* * *
17916 ATGCTTCAATTTGCCTTATGATCGAAGTAAGAGAT
62 ATACTTCAATCTGCCTCATGATCGAAGTAAGAGAT
17951 CGGTGTTTTC
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
114 18 0.21
115 2 0.02
116 3 0.04
117 61 0.73
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (114 bp):
CCATGATCGAGGTAAGAGATCGGTGTCTTCAATCTGTCCTCTGATTAAGGTAAAAAATTAGATAC
TTCAATCTGCCTCATGATCGAAGTAAGAGATTGATGTCTTTAACCTACC
Found at i:18127 original size:269 final size:263
Alignment explanation
Indices: 17542--18152 Score: 658
Period size: 269 Copynumber: 2.3 Consensus size: 263
17532 GATGGTTGTG
* * * *
17542 ATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGTCCCATGATTGGAGTAAGAGAT
1 ATCTG-CTTCAGATTAAGGTAAAAGATTGGATGCTTTAATCT-ACCCATGATCGGAGTAAGAGAT
* *
17607 CTGTGTCTTCAATATGCCTTTTGATTAGGGTAAAAAATTGGATGCTTCAACTTACCCATGATCGA
64 CTGTGTCTTCAATATGCCTTTTGATTAAGGTAAAAAATTAGATGCTTCAACTTACCCATGATCGA
* * *
17672 GGCAAGAGATCATTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTTAATTTGA
129 AGCAAGAGATCAGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATTTGA
* ** ** * *
17737 ACCATGATCGGGGTAAGAGATCGGTGTCTTCAATCTGTCCTCTGATTAGGGTAAAAGATTAGATA
194 ACCATGATCGAGGTAAGAGATCGACGTCTTCAATCTACCCTATGACTAGGGTAAAAGATTAGATA
17802 CTTCA
259 CTTCA
* *** * *
17807 ATCTGCCTCATGATCGGGGTAAGAGATT-GATGTCTTTAACCTACCCCATGATC-GAGGTAAGAG
1 ATCTGCTTCA-GATTAAGGTAAAAGATTGGATG-CTTTAATCTA-CCCATGATCGGA-GTAAGAG
* * * * * *
17870 ATTGGTGATGTCTTTAATCTGCCTTTTGATTAAGGTAAAAAATTAGATGCTTCAATTTGCCTTAT
62 A-T-CTG-TGTCTTCAATATGCCTTTTGATTAAGGTAAAAAATTAGATGCTTCAACTTACC-CAT
* * * *
17935 GATCGAAGTAAGAGATCGGTGTTTTCAATTTGCCCTCTGATTAGGGTCAAAA-ATTGGATGCTTC
123 GATCGAAGCAAGAGATCAGTGTCTTCAATCTGCCCTCTGATTAGGGT-AAAAGATTGGATGCTTC
* * * * * *
17999 AATTT-ACCCCATGATTGAGGTAAGAGGTTGACGTCTTCAATCTACCCTATGACTGGGGTAAGAG
187 AATTTGA-ACCATGATCGAGGTAAGAGATCGACGTCTTCAATCTACCCTATGACTAGGGTAAAAG
*
18063 ATT-GATGTCTTCA
251 ATTAGAT-ACTTCA
* * *
18076 ATCTGCTTTCAGATTAAGGTAAAATATTGGATGCTTTAATCTACACCATGATCGGCGTAAAAGAT
1 ATCTGC-TTCAGATTAAGGTAAAAGATTGGATGCTTTAATCTAC-CCATGATCGGAGTAAGAGAT
18141 -TAGTGTCTTCAA
64 CT-GTGTCTTCAA
18153 CTTGTCCTAT
Statistics
Matches: 281, Mismatches: 49, Indels: 31
0.78 0.14 0.09
Matches are distributed among these distances:
264 9 0.03
265 41 0.15
266 10 0.04
267 3 0.01
268 53 0.19
269 153 0.54
270 12 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (263 bp):
ATCTGCTTCAGATTAAGGTAAAAGATTGGATGCTTTAATCTACCCATGATCGGAGTAAGAGATCT
GTGTCTTCAATATGCCTTTTGATTAAGGTAAAAAATTAGATGCTTCAACTTACCCATGATCGAAG
CAAGAGATCAGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATTTGAAC
CATGATCGAGGTAAGAGATCGACGTCTTCAATCTACCCTATGACTAGGGTAAAAGATTAGATACT
TCA
Found at i:18434 original size:79 final size:79
Alignment explanation
Indices: 18148--18434 Score: 368
Period size: 79 Copynumber: 3.6 Consensus size: 79
18138 GATTAGTGTC
* * *
18148 TTCAACTTGTCCTATTATCGGGGAAAGAGATTGGTGATGTCTTCAATCTG-CTTTCTGATTAAGG
1 TTCAACTTGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTT-TGATTAAGG
18212 TAAAAGATTGGCG-T
65 TAAAAGATTGGCGCT
** *
18226 CTTCAACTTG-CCTCATGATTAGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTCTGATTAAG
1 -TTCAACTTGTCC-CATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTTTGATTAAG
**
18290 GTAAAAGATTGAATGC-
64 GTAAAAGATTG-GCGCT
* * * *
18306 TTCAA-TCTATCTCATGATCGGGGTAAGAGATTGATGATGTCTTCAATCTGCCTTTTAATTAAGG
1 TTCAACT-TGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTTTGATTAAGG
*
18370 TAAAAAATTGGCGCT
65 TAAAAGATTGGCGCT
*
18385 TTCAACTTGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTTAATCTG
1 TTCAACTTGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTG
18435 TCTCATGATC
Statistics
Matches: 178, Mismatches: 22, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
78 5 0.03
79 167 0.94
80 6 0.03
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (79 bp):
TTCAACTTGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTTTGATTAAGGT
AAAAGATTGGCGCT
Found at i:18447 original size:41 final size:41
Alignment explanation
Indices: 18172--18461 Score: 192
Period size: 41 Copynumber: 7.3 Consensus size: 41
18162 TTATCGGGGA
* * *
18172 AAGAGATTGGTGATGTCTTCAATCTGCTTTC-TGATTAAGGT
1 AAGAGATTGGTGATGTCTTCAATCTG-TCTCATGATCAGGGT
* * * *
18213 AAAAGATT-G-G-CGTCTTCAA-CTTGCCTCATGATTAGGGT
1 AAGAGATTGGTGATGTCTTCAATC-TGTCTCATGATCAGGGT
* * *
18251 AAGAGATTGGTGATGTCTTCAATCTGCCTTC-TGATTAAGGT
1 AAGAGATTGGTGATGTCTTCAATCTGTC-TCATGATCAGGGT
* * * *
18292 AAAAGATT-G-AATG-CTTCAATCTATCTCATGATCGGGGT
1 AAGAGATTGGTGATGTCTTCAATCTGTCTCATGATCAGGGT
* * ** * * *
18330 AAGAGATTGATGATGTCTTCAATCTGCCTTTTAATTAAGGT
1 AAGAGATTGGTGATGTCTTCAATCTGTCTCATGATCAGGGT
* * * * * *
18371 AAAAAATTGGCG--CT-TTCAA-CTTGTCCCATGATCGGGGT
1 AAGAGATTGGTGATGTCTTCAATC-TGTCTCATGATCAGGGT
* *
18409 AAGAGATTGGTGATGTCTTTAATCTGTCTCATGATCGGGGT
1 AAGAGATTGGTGATGTCTTCAATCTGTCTCATGATCAGGGT
18450 AAGAGATTGGTG
1 AAGAGATTGGTG
18462 GTTGTGATTT
Statistics
Matches: 188, Mismatches: 45, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
37 6 0.03
38 73 0.39
39 6 0.03
40 7 0.04
41 92 0.49
42 4 0.02
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.34
Consensus pattern (41 bp):
AAGAGATTGGTGATGTCTTCAATCTGTCTCATGATCAGGGT
Found at i:18451 original size:158 final size:160
Alignment explanation
Indices: 18122--18458 Score: 422
Period size: 158 Copynumber: 2.1 Consensus size: 160
18112 TAATCTACAC
* * * * *
18122 CATGATCGGCGTAAAAGATT-AGTGTCTTCAACTTGTCCTATTATCGGGGAAAGAGATTGGTGAT
1 CATGATCGGGGTAAAAGATTGAATGTCTTCAACTTCTCCTATGATCGGGGAAAGAGATTGATGAT
* * *
18186 GTCTTCAATCTGCTTTCTGATTAAGGTAAAAGATTGGCGTCTTCAACTTGCCTCATGATTAGGGT
66 GTCTTCAATCTGCTTTCTAATTAAGGTAAAAAATTGGCGTCTTCAACTTGCCTCATGATCAGGGT
18251 AAGAGATTGGTGATGTCTTCAATCTGCCTT
131 AAGAGATTGGTGATGTCTTCAATCTGCCTT
*** *
18281 C-TGATTAAGGTAAAAGATTGAATG-CTTCAATCTATCT-C-ATGATCGGGGTAAGAGATTGATG
1 CATGATCGGGGTAAAAGATTGAATGTCTTCAA-CT-TCTCCTATGATCGGGGAAAGAGATTGATG
18342 ATGTCTTCAATCTGCCTTT-TAATTAAGGTAAAAAATTGGCG-CTTTCAACTTGTCC-CATGATC
64 ATGTCTTCAATCTG-CTTTCTAATTAAGGTAAAAAATTGGCGTC-TTCAACTTG-CCTCATGATC
* * *
18404 GGGGTAAGAGATTGGTGATGTCTTTAATCTGTC-T
126 AGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTT
*
18438 CATGATCGGGGTAAGAGATTG
1 CATGATCGGGGTAAAAGATTG
18459 GTGGTTGTGA
Statistics
Matches: 152, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
157 3 0.02
158 134 0.88
159 13 0.09
160 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (160 bp):
CATGATCGGGGTAAAAGATTGAATGTCTTCAACTTCTCCTATGATCGGGGAAAGAGATTGATGAT
GTCTTCAATCTGCTTTCTAATTAAGGTAAAAAATTGGCGTCTTCAACTTGCCTCATGATCAGGGT
AAGAGATTGGTGATGTCTTCAATCTGCCTT
Found at i:18918 original size:49 final size:48
Alignment explanation
Indices: 18767--18918 Score: 121
Period size: 49 Copynumber: 3.1 Consensus size: 48
18757 ATGTTTTTAA
* * *
18767 GGTACT-AGGTTCGTCATTGCGGCCTCAACCTTTCCCTTTATATTTTCAT
1 GGTACTGA-GTTCGTCATTGCGGCCTCAACCTTTCCCTTCAAATCTTC-T
* * * * * * * *
18816 GGTACTGAATTTGTCGTTACGACCTCGATCC--TCCCATCACATCTTCT
1 GGTACTGAGTTCGTCATTGCGGCCTC-AACCTTTCCCTTCAAATCTTCT
*
18863 AAGGTACTGAGTTCGTCATTGCGGCTTCAACCTTTCCCTTCAAATCTTCGT
1 --GGTACTGAGTTCGTCATTGCGGCCTCAACCTTTCCCTTCAAATCTTC-T
18914 GGTAC
1 GGTAC
18919 CAGGTTTACC
Statistics
Matches: 77, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
47 1 0.01
48 14 0.18
49 44 0.57
50 17 0.22
51 1 0.01
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.36
Consensus pattern (48 bp):
GGTACTGAGTTCGTCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCT
Found at i:19054 original size:98 final size:98
Alignment explanation
Indices: 18952--19170 Score: 235
Period size: 98 Copynumber: 2.2 Consensus size: 98
18942 CCCTTCCCAT
* * * * *
18952 CATAT-TTCATGGTGCCGGATTCGCTATTGCGGCCTCAAGCCTTCCCATTACAT-CTTCTAAGGT
1 CATATCTTCATGGTACCAGATTCGCCATTACAGCCTCAAGCCTTCCCA--ACATGCTTCTAAGGT
* *
19015 ACCAGGTTCACTGTTACGACTTCAACCTTTCCCTC
64 ACAAGGTTCACCGTTACGACTTCAACCTTTCCCTC
* * * * * * *
19050 CATATCTTCGTGGTACCAGATTCGCCATTACAGCTTCAATCTTTCCCAGCATGTTTCTGAGGTAC
1 CATATCTTCATGGTACCAGATTCGCCATTACAGCCTCAAGCCTTCCCAACATGCTTCTAAGGTAC
* *
19115 AAGGTTCGCCGTTGCGACTTCAACCTTTCCCTC
66 AAGGTTCACCGTTACGACTTCAACCTTTCCCTC
** *
19148 TGTATCTTCGTGGTACCAGATTC
1 CATATCTTCATGGTACCAGATTC
19171 ATTGTTACGG
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
97 3 0.03
98 65 0.64
99 33 0.33
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.33
Consensus pattern (98 bp):
CATATCTTCATGGTACCAGATTCGCCATTACAGCCTCAAGCCTTCCCAACATGCTTCTAAGGTAC
AAGGTTCACCGTTACGACTTCAACCTTTCCCTC
Found at i:19087 original size:49 final size:49
Alignment explanation
Indices: 19028--19170 Score: 155
Period size: 49 Copynumber: 2.9 Consensus size: 49
19018 AGGTTCACTG
19028 TTACGACTTCAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCGCCA
1 TTACGACTTCAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCGCCA
* ** * * * * *
19077 TTAC-AGCTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGGTTCGCCG
1 TTACGA-CTTCAACCTTTCCCTCCATATCTTC-GTGGTACCAGATTCGCCA
* **
19126 TTGCGACTTCAACCTTTCCCTCTGTATCTTCGTGGTACCAGATTC
1 TTACGACTTCAACCTTTCCCTCCATATCTTCGTGGTACCAGATTC
19171 ATTGTTACGG
Statistics
Matches: 72, Mismatches: 18, Indels: 8
0.73 0.18 0.08
Matches are distributed among these distances:
48 4 0.06
49 64 0.89
50 4 0.06
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (49 bp):
TTACGACTTCAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCGCCA
Found at i:20995 original size:9 final size:9
Alignment explanation
Indices: 20981--21019 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
20971 GGTCTTGACT
20981 TTTTCTTTC
1 TTTTCTTTC
20990 TTTTCTTTC
1 TTTTCTTTC
20999 TTTT-TTTC
1 TTTTCTTTC
21007 TTTCTCTTT-
1 TTT-TCTTTC
21016 TTTT
1 TTTT
21020 TATGCCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.29
9 17 0.61
10 3 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:21007 original size:12 final size:12
Alignment explanation
Indices: 20982--21018 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
20972 GTCTTGACTT
20982 TTTCTTTCTTTTC
1 TTTCTTT-TTTTC
20995 TTTCTTTTTTTC
1 TTTCTTTTTTTC
21007 TTTCTCTTTTTT
1 TTTCT-TTTTTT
21019 TTATGCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:21059 original size:21 final size:21
Alignment explanation
Indices: 21007--21059 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
20997 TCTTTTTTTC
**
21007 TTTCTCTTTTTTTTATGCCTT
1 TTTCTCTTTTTTTTACCCCTT
* ***
21028 TTGCAGATTTTTTTACCCCTT
1 TTTCTCTTTTTTTTACCCCTT
21049 TTTCTCTTTTT
1 TTTCTCTTTTT
21060 CTCTCTTTTT
Statistics
Matches: 22, Mismatches: 10, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.08, C:0.21, G:0.06, T:0.66
Consensus pattern (21 bp):
TTTCTCTTTTTTTTACCCCTT
Found at i:24208 original size:24 final size:24
Alignment explanation
Indices: 24181--24235 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
24171 TAAAAATAAT
24181 TATATTAAGAATGTTATTAAATTA
1 TATATTAAGAATGTTATTAAATTA
** * *
24205 TATATTATTATTTTTATTAAATTA
1 TATATTAAGAATGTTATTAAATTA
24229 TAT-TTAA
1 TATATTAA
24236 TGATAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TATATTAAGAATGTTATTAAATTA
Found at i:24245 original size:24 final size:24
Alignment explanation
Indices: 24194--24245 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
24184 ATTAAGAATG
* **
24194 TTATTAAATTATATATTATTATTT
1 TTATTAAATTATATATTATGATAA
24218 TTATTAAATTATAT-TTAATGATAA
1 TTATTAAATTATATATT-ATGATAA
24242 TTAT
1 TTAT
24246 ATTAAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATTAAATTATATATTATGATAA
Found at i:24272 original size:61 final size:62
Alignment explanation
Indices: 24176--24303 Score: 204
Period size: 61 Copynumber: 2.1 Consensus size: 62
24166 TAATATAAAA
* * *
24176 ATAATTATATTAAGAATGTTATTAAATTATATATTATTATTTTTATTAAATTATATTTAATG
1 ATAATTATATTAAGAATGTGATTAAATTATATATTATCATTTTTATTAAATTATATTCAATG
* *
24238 ATAATTATATTAA-AATGTGATTAAATTATTTATTATCATTTTTATTAAATTGTATTCAATG
1 ATAATTATATTAAGAATGTGATTAAATTATATATTATCATTTTTATTAAATTATATTCAATG
24299 ATAAT
1 ATAAT
24304 CCTATTATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
61 48 0.79
62 13 0.21
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (62 bp):
ATAATTATATTAAGAATGTGATTAAATTATATATTATCATTTTTATTAAATTATATTCAATG
Done.