Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004942.1 Kokia drynarioides strain JFW-HI SEQ_118652, 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: 24042
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:4089 original size:16 final size:18
Alignment explanation
Indices: 4068--4108 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
4058 AATTCATCCA
4068 TATTTTA-AAATA-TAAT
1 TATTTTATAAATATTAAT
4084 TATTTTTATTAAATATTAAT
1 TA-TTTTA-TAAATATTAAT
4104 TATTT
1 TATTT
4109 ATTTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 5 0.24
19 8 0.38
20 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTATAAATATTAAT
Found at i:4103 original size:20 final size:21
Alignment explanation
Indices: 4075--4119 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
4065 CCATATTTTA
4075 AAATATAATTA-TT-TTTATT
1 AAATATAATTATTTATTTATT
4094 AAATATTAATTATTTATTTATT
1 AAATA-TAATTATTTATTTATT
4116 AAAT
1 AAAT
4120 TTATAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.22
20 6 0.26
21 2 0.09
22 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATAATTATTTATTTATT
Found at i:9079 original size:7 final size:7
Alignment explanation
Indices: 9067--9092 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9057 TTTCTATTTT
9067 TTCAAAA
1 TTCAAAA
9074 TTCAAAA
1 TTCAAAA
9081 TTCAAAA
1 TTCAAAA
9088 TTCAA
1 TTCAA
9093 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:15386 original size:15 final size:16
Alignment explanation
Indices: 15355--15387 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15345 AGATAGTGGA
*
15355 CTTGTGGGTGTTTGGG
1 CTTGTAGGTGTTTGGG
15371 CTTGTAGGTG-TTGGG
1 CTTGTAGGTGTTTGGG
15386 CT
1 CT
15388 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:15928 original size:39 final size:39
Alignment explanation
Indices: 15885--16107 Score: 135
Period size: 39 Copynumber: 5.7 Consensus size: 39
15875 TCTACCTCAA
**
15885 GATTGGGGTAAGAGATTGGATGGTTGCGATCCGTTTCAT
1 GATTGGGGTAAGAGATTGGATGGTTGCGATATGTTTCAT
* * * * * **
15924 GATTGGGGTAAGAGATCGGATGATTTTCAATTTG-CCCAT
1 GATTGGGGTAAGAGATTGGATG-GTTGCGATATGTTTCAT
* *
15963 GATGGGGGTATGAGATTGGATGGTTGCGATATGCTTT-AT
1 GATTGGGGTAAGAGATTGGATGGTTGCGATATG-TTTCAT
** * * * ** *
16002 GATTGGGGTAAGAGATAAGATGGTTTTCAATTTACTCCAT
1 GATTGGGGTAAGAGATTGGATGG-TTGCGATATGTTTCAT
* * * * * * **
16042 TATCGGGGTAAGAGATTGGATGATTTTCAATTTGCCTCAT
1 GATTGGGGTAAGAGATTGGATG-GTTGCGATATGTTTCAT
* *
16082 GATCGGGGTAAGAGATTGGATAGTTG
1 GATTGGGGTAAGAGATTGGATGGTTG
16108 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:15978 original size:78 final size:79
Alignment explanation
Indices: 15889--16063 Score: 246
Period size: 78 Copynumber: 2.2 Consensus size: 79
15879 CCTCAAGATT
* **
15889 GGGGTAAGAGATTGGATGGTTGCGATCCG-TTTCATGATTGGGGTAAGAGATCGGATGATTTTCA
1 GGGGTAAGAGATTGGATGGTTGCGATACGCTTT-ATGATTGGGGTAAGAGATAAGATGATTTTCA
* *
15953 ATTTGC-CCATGATG
65 ATTTACTCCATGATC
* * *
15967 GGGGTATGAGATTGGATGGTTGCGATATGCTTTATGATTGGGGTAAGAGATAAGATGGTTTTCAA
1 GGGGTAAGAGATTGGATGGTTGCGATACGCTTTATGATTGGGGTAAGAGATAAGATGATTTTCAA
*
16032 TTTACTCCATTATC
66 TTTACTCCATGATC
16046 GGGGTAAGAGATTGGATG
1 GGGGTAAGAGATTGGATG
16064 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:16056 original size:40 final size:40
Alignment explanation
Indices: 15920--16097 Score: 137
Period size: 40 Copynumber: 4.5 Consensus size: 40
15910 GCGATCCGTT
* ** *
15920 TCATGATTGGGGTAAGAGATCGGATGATTTTCAATTTGCC
1 TCATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
* * ** * * * * * *
15960 -CATGATGGGGGTATGAGATTGGATG-GTTGCGATATGCT
1 TCATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
* * *
15998 TTATGATTGGGGTAAGAGATAAGATGGTTTTCAATTTA-C
1 TCATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
* ** *
16037 TCCATTATCGGGGTAAGAGATTGGATGATTTTCAATTTGCC
1 T-CATGATCGGGGTAAGAGATAAGATGATTTTCAATTTACC
16078 TCATGATCGGGGTAAGAGAT
1 TCATGATCGGGGTAAGAGAT
16098 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:16223 original size:38 final size:38
Alignment explanation
Indices: 16047--17700 Score: 531
Period size: 38 Copynumber: 42.8 Consensus size: 38
16037 TCCATTATCG
* * **
16047 GGGTAAGAGATTGGATGATTTTCAATTTG-CCTCATGATCG
1 GGGTAAGAGATTGGATG--CTTCAATCTGCCCT-ATGATTA
** * * *
16087 GGGTAAGAGATTGGATAG-TTGTGATCTACCTTCTGATTA
1 GGGTAAGAGATTGGAT-GCTT-CAATCTGCCCTATGATTA
* * * * * *
16126 AGATAAAAGATTGGATGCTTCAATCTACCCCATGATCA
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
** *
16164 AAGTAAGAGATCT-G-TGTCTTCAATCTGCCCTTTGATTA
1 GGGTAAGAGAT-TGGATG-CTTCAATCTGCCCTATGATTA
* **
16202 GGGTAA-AGGATTGGATGCTTCAATCT-TCCTCATGATCG
1 GGGTAAGA-GATTGGATGCTTCAATCTGCCCT-ATGATTA
** * * * *
16240 GGGTAAGAGA-TCAATATCTTAAATTTGCCCTCTGATTA
1 GGGTAAGAGATTGGAT-GCTTCAATCTGCCCTATGATTA
* * * * **
16278 GGGTAAAAGATTAGATGCTTTAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * *
16316 GGGTAAGAGA-TCGATGTCTTCAATTTGCCCTCTGATTA
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * * **
16354 GGGTAAAAGATTGGATGCTTCAGTCTGCCTTATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* *
16392 GGGTAAGAGATTGG-TGTCTTTAACCTG-CCTCATGATCTA
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCT-ATGAT-TA
** * *
16431 -GGTAAGAGATTGGTGATGTCTTCAATCTATCTTCTGATTA
1 GGGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * * * **
16471 AGGTAAAAGATTGGATACTTCAATATG-CCTCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCT-ATGATTA
* * * * *
16509 GGGTAAGAGATCAGTAT-TTTCAATCTGCCCTCTAATTA
1 GGGTAAGAGAT-TGGATGCTTCAATCTGCCCTATGATTA
* * * **
16547 GGGTAAAAGGTTGGATGCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * * * *
16585 GGGTAAGAGATTGGTCATATCTTTAATCTACCTTCTGATTA
1 GGGTAAGAGATTGG--AT-GCTTCAATCTGCCCTATGATTA
* * * * * * * * * **
16626 AGATAAAAAATAGGATGCTTTAATCTGCCTTTTAATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * * *
16664 GGGTAAGAGATTAG-TGTCTTCAACCTGCCCCATGA-TC
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * * * *
16701 GAGGTAAGAGATTGGTGATGTCTTAAATCTACCTTCTAATTA
1 G-GGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * * * * **
16743 AGGTAAAAGATT-GACGTCCTCAA-CTTGCCCCATGATCG
1 GGGTAAGAGATTGGATG-CTTCAATC-TGCCCTATGATTA
* * * * * *
16781 GGGTAAGAGATCGGATGGTTTTTAATTTGCCCCATGATTG
1 GGGTAAGAGATTGGAT-G-CTTCAATCTGCCCTATGATTA
* * * * *
16821 GGGTAAGAGATTGAATGATTTTCAATTTG-TCTCATGATCGA
1 GGGTAAGAGATTGGATG--CTTCAATCTGCCCT-ATGAT-TA
* ** * *
16862 GGGTAAGAGATTGGATGGTTGTGATCTGCCTTCTGATTA
1 GGGTAAGAGATTGGATGCTT-CAATCTGCCCTATGATTA
* *
16901 AGGTAAAAGATTGGATGCTTCAATCTGTCCC-ATGATT-
1 GGGTAAGAGATTGGATGCTTCAATCTG-CCCTATGATTA
* * *
16938 GGAGTAAGAGATCT-G-TGTCTTCAATATGCCTTTTGATTA
1 GG-GTAAGAGAT-TGGATG-CTTCAATCTGCCCTATGATTA
* * * *
16977 GGGTAAAAAATTGGATGCTTCAA-CTTACCC-ATGA-TC
1 GGGTAAGAGATTGGATGCTTCAATC-TGCCCTATGATTA
* * *
17013 GAGGCAAGAGA-T-CATTGTCTTCAATCTGCCCTCTGATTA
1 G-GGTAAGAGATTGGA-TG-CTTCAATCTGCCCTATGATTA
* * * * **
17052 GGGTAAAAGATTGGATGCTTTAATTTGAACC-ATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTG-CCCTATGATTA
* * *
17090 GGGTAAGAGATCGG-TGTCTTCAATCTGTCCTCTGATTA
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * * **
17128 GGGTAAAAGATTAGATACTTCAATCTG-CCTCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCT-ATGATTA
* * * * *
17166 GGGTAAGAGATT-GATGTCTTTAACCTACCCCATGA-TC
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * *
17203 GAGGTAAGAGATTGGTGATGTCTTTAATCTGCCTTTTGATTA
1 G-GGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * * * * * *
17245 AGGTAAAAAATTAGATGCTTCAATTTGCCTTATGA-TC
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * * * *
17282 GAAGTAAGAGATCGG-TGTTTTCAATTTGCCCTCTGATTA
1 G-GGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
* * * *
17321 GGGTCAA-AAATTGGATGCTTCAATTTACCCCATGATT-
1 GGGT-AAGAGATTGGATGCTTCAATCTGCCCTATGATTA
* * * * *
17358 GAGGTAAGAGGTT-GACGTCTTCAATCTACCCTATGACTG
1 G-GGTAAGAGATTGGATG-CTTCAATCTGCCCTATGATTA
**
17397 GGGTAAGAGATT-GATGTCTTCAATCTGCTTTCA-GATTA
1 GGGTAAGAGATTGGATG-CTTCAATCTGCCCT-ATGATTA
* * * * * *
17435 AGGTAAAATATTGGATGCTTTAATCTACACC-ATGA-TC
1 GGGTAAGAGATTGGATGCTTCAATCTGC-CCTATGATTA
* * * * **
17472 GGCGTAAAAGATTAG-TGTCTTCAA-CTTGTCCTATTATCG
1 GG-GTAAGAGATTGGATG-CTTCAATC-TGCCCTATGATTA
* ** *
17511 GGGAAAGAGATTGGTGATGTCTTCAATCTGCTTTCTGATTA
1 GGGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * *
17552 AGGTAAAAGATTGG-CGTCTTCAA-CTTG-CCTCATGATTA
1 GGGTAAGAGATTGGATG-CTTCAATC-TGCCCT-ATGATTA
* *
17590 GGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTCTGATTA
1 GGGTAAGAGATT-G-GATG-CTTCAATCTGCCCTATGATTA
* * * ** **
17631 AGGTAAAAGATTGAATGCTTCAATCT-ATCTCATGATCG
1 GGGTAAGAGATTGGATGCTTCAATCTGCCCT-ATGATTA
17669 GGGTAAGAGATTGATGATGTCTTCAATCTGCC
1 GGGTAAGAGATTG--GATG-CTTCAATCTGCC
17701 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:16303 original size:152 final size:152
Alignment explanation
Indices: 16047--17176 Score: 438
Period size: 155 Copynumber: 7.3 Consensus size: 152
16037 TCCATTATCG
* * * ** *
16047 GGGTAAGAGATTGGATGATTTTCAATTTGCCTCATGATCGGGGTAAGAGATTGGATAGT-TGT-G
1 GGGTAAAAGATTGGATG--CTTCAATCTGCCTCATGATCGGGGTAAGAGA-TCAATA-TCT-TAA
* * * *
16110 ATCTACCTTCTGATTAAGATAAAAGATTGGATGCTTCAATCTACCCCATGATCAAAGTAAGAGAT
61 ATTTGCCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCTACCCCATGATCAAAGTAAGAGAT
*
16175 CTG-TGTCTTCAATCTGCCCTTTGATTA
126 C-GATGTCTTCAATCTGCCCTCTGATTA
* *
16202 GGGTAAAGGATTGGATGCTTCAATCTTCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTTG
1 GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTTG
* * * * ***
16267 CCCTCTGATTAGGGTAAAAGATTAGATGCTTTAATCTGCCCCATGATCGGGGTAAGAGATCGATG
66 CCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCTACCCCATGATCAAAGTAAGAGATCGATG
*
16332 TCTTCAATTTGCCCTCTGATTA
131 TCTTCAATCTGCCCTCTGATTA
* * *** * * **
16354 GGGTAAAAGATTGGATGCTTCAGTCTGCCTTATGATCGGGGTAAGAGATTGGTGTCTTTAACCTG
1 GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTTG
* * * ** * * *
16419 -CCTCATGATCT-AGGTAAGAGATTGGTGATGTCTTCAATCTATCTTC-TGATTAAGGTAAAAGA
66 CCCTC-TGAT-TAAGATAAAAGATT--AGATG-CTTCAATCTA-CCCCATGATCAAAGTAAGAGA
* * * **
16481 TTGGAT-ACTTCAATATG-CCTCATGATCG
125 -TCGATGTCTTCAATCTGCCCTC-TGATTA
* * * * * ** * * ** * *
16509 GGGTAAGAGATCAGTAT-TTTCAATCTGCCCTC-TAATTAGGGTAAAAGGTTGGAT-GCTTCAAT
1 GGGTAAAAGAT-TGGATGCTTCAATCTG-CCTCATGATCGGGGTAAGA-GATCAATATCTTAAAT
* *** * * * * * * * *
16571 CTGCCC-CATGATCGGGGTAAGAGATTGGTCATATCTTTAATCTACCTTC-TGAT-TAAGATAAA
63 TTGCCCTC-TGATTAAGATAAAAGATTAG--AT-GCTTCAATCTACC-CCATGATCAAAG-TAAG
* * * * * * **
16633 AAATAGGATG-CTTTAATCTGCCTTTTAATCG
122 AGAT-CGATGTCTTCAATCTGCCCTCTGATTA
* * * * * ** *
16664 GGGTAAGAGATTAG-TGTCTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTGATGTCTTAAA
1 GGGTAAAAGATTGGATG-CTTCAATCTGCCTCATGATCGGGGTAAGAGA-T--CAATATCTTAAA
* * * * * * * * ***
16728 TCTACCTTCTAATTAAGGTAAAAGATT-GACGTCCTCAA-CTTGCCCCATGATCGGGGTAAGAGA
62 TTTGCCCTCTGATTAAGATAAAAGATTAGATG-CTTCAATC-TACCCCATGATCAAAGTAAGAGA
* * * *
16791 TCGGATGGTTTTTAATTTGCCC-CATGATTG
125 TC-GAT-GTCTTCAATCTGCCCTC-TGATTA
* * * * * ** *
16821 GGGTAAGAGATTGAATGATTTTCAATTTGTCTCATGATCGAGGGTAAGAGATTGGATGGT-TGT-
1 GGGTAAAAGATTGGATG--CTTCAATCTGCCTCATGATCG-GGGTAAGAGA-TCAAT-ATCT-TA
* * * * * ** ***
16884 GATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGTCCCATGATTGGAGTAAGAGA
60 AATTTGCCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCTACCCCATGATCAAAGTAAGAGA
* * *
16949 TCTG-TGTCTTCAATATGCCTTTTGATTA
125 TC-GATGTCTTCAATCTGCCCTCTGATTA
* * * * * * * *
16977 GGGTAAAAAATTGGATGCTTCAA-CTTACC-CATGATCGAGGCAAGAGATCATTGTCTTCAATCT
1 GGGTAAAAGATTGGATGCTTCAATC-TGCCTCATGATCGGGGTAAGAGATCAATATCTTAAATTT
* * * * * * *** *
17040 GCCCTCTGATTAGGGTAAAAGATTGGATGCTTTAATTTGA-ACCATGATCGGGGTAAGAGATCGG
65 GCCCTCTGATTAAGATAAAAGATTAGATGCTTCAATCT-ACCCCATGATCAAAGTAAGAGATCGA
*
17104 TGTCTTCAATCTGTCCTCTGATTA
129 TGTCTTCAATCTGCCCTCTGATTA
* *
17128 GGGTAAAAGATTAGATACTTCAATCTGCCTCATGATCGGGGTAAGAGAT
1 GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGAT
17177 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:16492 original size:117 final size:114
Alignment explanation
Indices: 16278--16519 Score: 297
Period size: 117 Copynumber: 2.1 Consensus size: 114
16268 CCTCTGATTA
* * * * *
16278 GGGTAAAAGATTAGATGCTTTAATCTGCCCCATGATCGGGGTAAGAGATCGATGTCTTCAATTTG
1 GGGTAAGAGATTAGATGCTTTAACCTGCCCCATGATCGAGGTAAGAGATCGATGTCTTCAATCTA
* * * * *
16343 CCCTCTGATTAGGGTAAAAGATTGGATGCTTCAGTCTGCCTTATGATCG
66 CCCTCTGATTAAGGTAAAAGATTGGATACTTCAATATGCCTCATGATCG
* * * *
16392 GGGTAAGAGATT-GGTGTCTTTAACCTGCCTCATGATCTAGGTAAGAGATTGGTGATGTCTTCAA
1 GGGTAAGAGATTAGATG-CTTTAACCTGCCCCATGATCGAGGTAAGAGA-T--CGATGTCTTCAA
* *
16456 TCTATCTTCTGATTAAGGTAAAAGATTGGATACTTCAATATGCCTCATGATCG
62 TCTACCCTCTGATTAAGGTAAAAGATTGGATACTTCAATATGCCTCATGATCG
16509 GGGTAAGAGAT
1 GGGTAAGAGAT
16520 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:16651 original size:79 final size:77
Alignment explanation
Indices: 16393--17776 Score: 341
Period size: 79 Copynumber: 17.8 Consensus size: 77
16383 TTATGATCGG
* * * **
16393 GGTAAGAGATTGG-TGTCTTTAACCTGCCTCATGATCTAGGTAAGAGATTGGTGATGTCTTCAAT
1 GGTAAAAGATTGGATG-CTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAAT
*
16457 CTATCTTCTGATTAA
63 CTACCTTCTGATTAA
* * ** *
16472 GGTAAAAGATTGGATACTTCAATATGCCTCATGATCGGGGTAAGAGATCAGTATT-TTCAATCTG
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATCTA
* * *
16536 CCCTCTAATTAG
66 CCTTCTGATTAA
* * *
16548 GGTAAAAGGTTGGATGCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTCATATCTTTAATC
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAATC
16613 TACCTTCTGATTAA
64 TACCTTCTGATTAA
* * * * ** * * * * *
16627 GATAAAAAATAGGATGCTTTAATCTGCCTTTTAATCGGGGTAAGAGATTAGT-GTCTTCAACCTG
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATCTA
* **
16691 CC-CCATGATCGA
66 CCTTC-TGATTAA
* * * * *** * * *
16703 GGTAAGAGATTGGTGATGTCTTAAATCTACCTTC-TAATTAAGGTAAAAGATT-G-ACGTCCTCA
1 GGTAAAAGATT-G-GATG-CTTCAATCTGCC-TCATGATCGGGGTAAGAGATTGGTA-TTCTTCA
* * ***
16765 A-CTTGCC-CCATGATCGG
61 ATC-TACCTTC-TGATTAA
* * * * * * * *
16782 GGTAAGAGATCGGATGGTTTTTAATTTGCCCCATGATTGGGGTAAGAGATTGAATGATT-TTCAA
1 GGTAAAAGATTGGAT-G-CTTCAATCTGCCTCATGATCGGGGTAAGAGATTG-GT-ATTCTTCAA
* ** * *
16846 TTTGTC-TCATGATCGAG
62 TCTACCTTC-TGAT-TAA
* * ** *** * *
16863 GGTAAGAGATTGGATGGTTGTGATCTGCCTTC-TGATTAAGGTAAAAGATTGG-ATGCTTCAATC
1 GGTAAAAGATTGGATGCTT-CAATCTGCC-TCATGATCGGGGTAAGAGATTGGTATTCTTCAATC
* *
16926 TGTCC--CATGATT-G
64 T-ACCTTC-TGATTAA
* * ** ** * * *
16939 GAGTAAGAGATCT-G-TGTCTTCAATATGCCTTTTGATTAGGGTAAAAAATTGG-ATGCTTCAA-
1 G-GTAAAAGAT-TGGATG-CTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAAT
**
17000 CTTACC--CATGATCGA
63 C-TACCTTC-TGATTAA
* * * ** * * *
17015 GGCAAGAGA-T-CATTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGG-ATGCTTTAAT
1 GGTAAAAGATTGGA-TG-CTTCAATCTG-CCTCATGATCGGGGTAAGAGATTGGTATTCTTCAAT
* * ***
17076 TTGAACC--ATGATCGG
63 CT--ACCTTCTGATTAA
* * ** * * *
17091 GGTAAGAGATCGG-TGTCTTCAATCTGTCCTC-TGATTAGGGTAAAAGATTAG-ATACTTCAATC
1 GGTAAAAGATTGGATG-CTTCAATCTG-CCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATC
* ***
17153 TGCC-TCATGATCGG
64 TACCTTC-TGATTAA
* * * * * * *
17167 GGTAAGAGATT-GATGTCTTTAACCTACCCCATGATCGAGGTAAGAGATTGGTGATGTCTTTAAT
1 GGTAAAAGATTGGATG-CTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAAT
* *
17231 CTGCCTTTTGATTAA
63 CTACCTTCTGATTAA
* * * * ** * * * *
17246 GGTAAAAAATTAGATGCTTCAATTTGCCTTATGATCGAAGTAAGAGATCGGTGTT-TTCAATTTG
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATTCTTCAATCTA
* *
17310 CCCTCTGATTAG
66 CCTTCTGATTAA
* * * * * * *
17322 GGTCAAAA-ATTGGATGCTTCAATTTACCCCATGATTGAGGTAAGAGGTT-G-ACGTCTTCAATC
1 GGT-AAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTA-TTCTTCAATC
* * * **
17384 TACCCTATGACTGG
64 TACCTTCTGATTAA
* * *** * * * *
17398 GGTAAGAGATT-GATGTCTTCAATCTGCTTTCA-GATTAAGGTAAAATATTGG-ATGCTTTAATC
1 GGTAAAAGATTGGATG-CTTCAATCTGC-CTCATGATCGGGGTAAGAGATTGGTATTCTTCAATC
**
17460 TACAC--CATGA-TCG
64 TAC-CTTC-TGATTAA
* * *
17473 GCGTAAAAGATTAG-TGTCTTCAA-CTTGTCCT-ATTATCGGGGAAAGAGATTGGTGATGTCTTC
1 G-GTAAAAGATTGGATG-CTTCAATC-TG-CCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTC
* *
17535 AATCTGCTTTCTGATTAA
60 AATCTACCTTCTGATTAA
* **
17553 GGTAAAAGATTGG-CGTCTTCAA-CTTGCCTCATGATTAGGGTAAGAGATTGGTGATGTCTTCAA
1 GGTAAAAGATTGGATG-CTTCAATC-TGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAA
*
17616 TCTGCCTTCTGATTAA
62 TCTACCTTCTGATTAA
* ** *
17632 GGTAAAAGATTGAATGCTTCAATCTATCTCATGATCGGGGTAAGAGATTGATGATGTCTTCAATC
1 GGTAAAAGATTGGATGCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCAATC
* * *
17697 TGCCTTTTAATTAA
64 TACCTTCTGATTAA
* * *
17711 GGTAAAAAATTGG-CGCTTTCAA-CTTGTCC-CATGATCGGGGTAAGAGATTGGTGATGTCTTTA
1 GGTAAAAGATTGGATGC-TTCAATC-TG-CCTCATGATCGGGGTAAGAGATTGGT-AT-TCTTCA
17773 ATCT
61 ATCT
17777 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:16781 original size:117 final size:117
Alignment explanation
Indices: 16564--16791 Score: 280
Period size: 117 Copynumber: 1.9 Consensus size: 117
16554 AGGTTGGATG
* * * *
16564 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTCATATCTTTAATCTACCTTCTGATTAAGA
1 CTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTCATATCTTAAATCTACCTTCTAATTAAGA
* * * ***
16629 TAAAAAATAGGATGCTTTAATCTGCCTTTTAATCGGGGTAAGAGATTAGTGT
66 TAAAAAATAGGACGCCTCAATCTGCCCCATAATCGGGGTAAGAGATTAGTGT
* * *
16681 CTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTGATGTCTTAAATCTACCTTCTAATTAAGG
1 CTTCAACCTGCCCCATGATCGAGGTAAGAGATTGGTCATATCTTAAATCTACCTTCTAATTAAGA
* * *
16746 TAAAAGAT-TGACGTCCTCAA-CTTGCCCCATGATCGGGGTAAGAGAT
66 TAAAAAATAGGACG-CCTCAATC-TGCCCCATAATCGGGGTAAGAGAT
16792 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:17071 original size:151 final size:152
Alignment explanation
Indices: 16885--17176 Score: 392
Period size: 151 Copynumber: 1.9 Consensus size: 152
16875 GATGGTTGTG
* ** *
16885 ATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGTCCCATGATTGGAGTAAGAGAT
1 ATCTGCCCTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGAACCATGATCGGAGTAAGAGAT
* * * *
16950 CTGTGTCTTCAATATG-CCTTTTGATTAGGGTAAAAAATTGGATGCTTCAA-CTTACC-CATGAT
66 CGGTGTCTTCAATATGTCC-TCTGATTAGGGTAAAAAATTAGATACTTCAATC-TACCTCATGAT
17012 CGAGGCAAGAGATCATTGTCTTCA
129 CGAGGCAAGAGATCATTGTCTTCA
* * * *
17036 ATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTTAATTTGAACCATGATCGGGGTAAGAGAT
1 ATCTGCCCTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGAACCATGATCGGAGTAAGAGAT
* * *
17101 CGGTGTCTTCAATCTGTCCTCTGATTAGGGTAAAAGATTAGATACTTCAATCTGCCTCATGATCG
66 CGGTGTCTTCAATATGTCCTCTGATTAGGGTAAAAAATTAGATACTTCAATCTACCTCATGATCG
* *
17166 GGGTAAGAGAT
131 AGGCAAGAGAT
17177 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:17274 original size:117 final size:114
Alignment explanation
Indices: 17081--17293 Score: 284
Period size: 117 Copynumber: 1.8 Consensus size: 114
17071 TTAATTTGAA
* * *
17081 CCATGATCGGGGTAAGAGATCGGTGTCTTCAATCTGTCCTCTGATTAGGGTAAAAGATTAGATAC
1 CCATGATCGAGGTAAGAGATCGGTGTCTTCAATCTGTCCTCTGATTAAGGTAAAAAATTAGATAC
**
17146 TTCAATCTGCCTCATGATCGGGGTAAGAGATTGATGTCTTTAACCTACC
66 TTCAATCTGCCTCATGATCGAAGTAAGAGATTGATGTCTTTAACCTACC
* * *
17195 CCATGATCGAGGTAAGAGATTGGTGATGTCTTTAATCTG-CCTTTTGATTAAGGTAAAAAATTAG
1 CCATGATCGAGGTAAGAGA-TCG-G-TGTCTTCAATCTGTCC-TCTGATTAAGGTAAAAAATTAG
* * *
17259 ATGCTTCAATTTGCCTTATGATCGAAGTAAGAGAT
62 ATACTTCAATCTGCCTCATGATCGAAGTAAGAGAT
17294 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:17470 original size:269 final size:263
Alignment explanation
Indices: 16885--17495 Score: 658
Period size: 269 Copynumber: 2.3 Consensus size: 263
16875 GATGGTTGTG
* * * *
16885 ATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGTCCCATGATTGGAGTAAGAGAT
1 ATCTG-CTTCAGATTAAGGTAAAAGATTGGATGCTTTAATCT-ACCCATGATCGGAGTAAGAGAT
* *
16950 CTGTGTCTTCAATATGCCTTTTGATTAGGGTAAAAAATTGGATGCTTCAACTTACCCATGATCGA
64 CTGTGTCTTCAATATGCCTTTTGATTAAGGTAAAAAATTAGATGCTTCAACTTACCCATGATCGA
* * *
17015 GGCAAGAGATCATTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTTAATTTGA
129 AGCAAGAGATCAGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATTTGA
* ** ** * *
17080 ACCATGATCGGGGTAAGAGATCGGTGTCTTCAATCTGTCCTCTGATTAGGGTAAAAGATTAGATA
194 ACCATGATCGAGGTAAGAGATCGACGTCTTCAATCTACCCTATGACTAGGGTAAAAGATTAGATA
17145 CTTCA
259 CTTCA
* *** * *
17150 ATCTGCCTCATGATCGGGGTAAGAGATT-GATGTCTTTAACCTACCCCATGATC-GAGGTAAGAG
1 ATCTGCTTCA-GATTAAGGTAAAAGATTGGATG-CTTTAATCTA-CCCATGATCGGA-GTAAGAG
* * * * * *
17213 ATTGGTGATGTCTTTAATCTGCCTTTTGATTAAGGTAAAAAATTAGATGCTTCAATTTGCCTTAT
62 A-T-CTG-TGTCTTCAATATGCCTTTTGATTAAGGTAAAAAATTAGATGCTTCAACTTACC-CAT
* * * *
17278 GATCGAAGTAAGAGATCGGTGTTTTCAATTTGCCCTCTGATTAGGGTCAAAA-ATTGGATGCTTC
123 GATCGAAGCAAGAGATCAGTGTCTTCAATCTGCCCTCTGATTAGGGT-AAAAGATTGGATGCTTC
* * * * * *
17342 AATTT-ACCCCATGATTGAGGTAAGAGGTTGACGTCTTCAATCTACCCTATGACTGGGGTAAGAG
187 AATTTGA-ACCATGATCGAGGTAAGAGATCGACGTCTTCAATCTACCCTATGACTAGGGTAAAAG
*
17406 ATT-GATGTCTTCA
251 ATTAGAT-ACTTCA
* * *
17419 ATCTGCTTTCAGATTAAGGTAAAATATTGGATGCTTTAATCTACACCATGATCGGCGTAAAAGAT
1 ATCTGC-TTCAGATTAAGGTAAAAGATTGGATGCTTTAATCTAC-CCATGATCGGAGTAAGAGAT
17484 -TAGTGTCTTCAA
64 CT-GTGTCTTCAA
17496 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:17777 original size:79 final size:79
Alignment explanation
Indices: 17491--17777 Score: 368
Period size: 79 Copynumber: 3.6 Consensus size: 79
17481 GATTAGTGTC
* * *
17491 TTCAACTTGTCCTATTATCGGGGAAAGAGATTGGTGATGTCTTCAATCTG-CTTTCTGATTAAGG
1 TTCAACTTGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTT-TGATTAAGG
17555 TAAAAGATTGGCG-T
65 TAAAAGATTGGCGCT
** *
17569 CTTCAACTTG-CCTCATGATTAGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTCTGATTAAG
1 -TTCAACTTGTCC-CATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTTTGATTAAG
**
17633 GTAAAAGATTGAATGC-
64 GTAAAAGATTG-GCGCT
* * * *
17649 TTCAA-TCTATCTCATGATCGGGGTAAGAGATTGATGATGTCTTCAATCTGCCTTTTAATTAAGG
1 TTCAACT-TGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTTTTGATTAAGG
*
17713 TAAAAAATTGGCGCT
65 TAAAAGATTGGCGCT
*
17728 TTCAACTTGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTTAATCTG
1 TTCAACTTGTCCCATGATCGGGGTAAGAGATTGGTGATGTCTTCAATCTG
17778 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:17790 original size:41 final size:41
Alignment explanation
Indices: 17515--17804 Score: 192
Period size: 41 Copynumber: 7.3 Consensus size: 41
17505 TTATCGGGGA
* * *
17515 AAGAGATTGGTGATGTCTTCAATCTGCTTTC-TGATTAAGGT
1 AAGAGATTGGTGATGTCTTCAATCTG-TCTCATGATCAGGGT
* * * *
17556 AAAAGATT-G-G-CGTCTTCAA-CTTGCCTCATGATTAGGGT
1 AAGAGATTGGTGATGTCTTCAATC-TGTCTCATGATCAGGGT
* * *
17594 AAGAGATTGGTGATGTCTTCAATCTGCCTTC-TGATTAAGGT
1 AAGAGATTGGTGATGTCTTCAATCTGTC-TCATGATCAGGGT
* * * *
17635 AAAAGATT-G-AATG-CTTCAATCTATCTCATGATCGGGGT
1 AAGAGATTGGTGATGTCTTCAATCTGTCTCATGATCAGGGT
* * ** * * *
17673 AAGAGATTGATGATGTCTTCAATCTGCCTTTTAATTAAGGT
1 AAGAGATTGGTGATGTCTTCAATCTGTCTCATGATCAGGGT
* * * * * *
17714 AAAAAATTGGCG--CT-TTCAA-CTTGTCCCATGATCGGGGT
1 AAGAGATTGGTGATGTCTTCAATC-TGTCTCATGATCAGGGT
* *
17752 AAGAGATTGGTGATGTCTTTAATCTGTCTCATGATCGGGGT
1 AAGAGATTGGTGATGTCTTCAATCTGTCTCATGATCAGGGT
17793 AAGAGATTGGTG
1 AAGAGATTGGTG
17805 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:17794 original size:158 final size:160
Alignment explanation
Indices: 17465--17801 Score: 422
Period size: 158 Copynumber: 2.1 Consensus size: 160
17455 TAATCTACAC
* * * * *
17465 CATGATCGGCGTAAAAGATT-AGTGTCTTCAACTTGTCCTATTATCGGGGAAAGAGATTGGTGAT
1 CATGATCGGGGTAAAAGATTGAATGTCTTCAACTTCTCCTATGATCGGGGAAAGAGATTGATGAT
* * *
17529 GTCTTCAATCTGCTTTCTGATTAAGGTAAAAGATTGGCGTCTTCAACTTGCCTCATGATTAGGGT
66 GTCTTCAATCTGCTTTCTAATTAAGGTAAAAAATTGGCGTCTTCAACTTGCCTCATGATCAGGGT
17594 AAGAGATTGGTGATGTCTTCAATCTGCCTT
131 AAGAGATTGGTGATGTCTTCAATCTGCCTT
*** *
17624 C-TGATTAAGGTAAAAGATTGAATG-CTTCAATCTATCT-C-ATGATCGGGGTAAGAGATTGATG
1 CATGATCGGGGTAAAAGATTGAATGTCTTCAA-CT-TCTCCTATGATCGGGGAAAGAGATTGATG
17685 ATGTCTTCAATCTGCCTTT-TAATTAAGGTAAAAAATTGGCG-CTTTCAACTTGTCC-CATGATC
64 ATGTCTTCAATCTG-CTTTCTAATTAAGGTAAAAAATTGGCGTC-TTCAACTTG-CCTCATGATC
* * *
17747 GGGGTAAGAGATTGGTGATGTCTTTAATCTGTC-T
126 AGGGTAAGAGATTGGTGATGTCTTCAATCTGCCTT
*
17781 CATGATCGGGGTAAGAGATTG
1 CATGATCGGGGTAAAAGATTG
17802 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:18261 original size:49 final size:48
Alignment explanation
Indices: 18110--18261 Score: 121
Period size: 49 Copynumber: 3.1 Consensus size: 48
18100 ATGTTTTTAA
* * *
18110 GGTACT-AGGTTCGTCATTGCGGCCTCAACCTTTCCCTTTATATTTTCAT
1 GGTACTGA-GTTCGTCATTGCGGCCTCAACCTTTCCCTTCAAATCTTC-T
* * * * * * * *
18159 GGTACTGAATTTGTCGTTACGACCTCGATCC--TCCCATCACATCTTCT
1 GGTACTGAGTTCGTCATTGCGGCCTC-AACCTTTCCCTTCAAATCTTCT
*
18206 AAGGTACTGAGTTCGTCATTGCGGCTTCAACCTTTCCCTTCAAATCTTCGT
1 --GGTACTGAGTTCGTCATTGCGGCCTCAACCTTTCCCTTCAAATCTTC-T
18257 GGTAC
1 GGTAC
18262 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:18397 original size:98 final size:98
Alignment explanation
Indices: 18295--18513 Score: 235
Period size: 98 Copynumber: 2.2 Consensus size: 98
18285 CCCTTCCCAT
* * * * *
18295 CATAT-TTCATGGTGCCGGATTCGCTATTGCGGCCTCAAGCCTTCCCATTACAT-CTTCTAAGGT
1 CATATCTTCATGGTACCAGATTCGCCATTACAGCCTCAAGCCTTCCCA--ACATGCTTCTAAGGT
* *
18358 ACCAGGTTCACTGTTACGACTTCAACCTTTCCCTC
64 ACAAGGTTCACCGTTACGACTTCAACCTTTCCCTC
* * * * * * *
18393 CATATCTTCGTGGTACCAGATTCGCCATTACAGCTTCAATCTTTCCCAGCATGTTTCTGAGGTAC
1 CATATCTTCATGGTACCAGATTCGCCATTACAGCCTCAAGCCTTCCCAACATGCTTCTAAGGTAC
* *
18458 AAGGTTCGCCGTTGCGACTTCAACCTTTCCCTC
66 AAGGTTCACCGTTACGACTTCAACCTTTCCCTC
** *
18491 TGTATCTTCGTGGTACCAGATTC
1 CATATCTTCATGGTACCAGATTC
18514 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:18430 original size:49 final size:49
Alignment explanation
Indices: 18371--18513 Score: 155
Period size: 49 Copynumber: 2.9 Consensus size: 49
18361 AGGTTCACTG
18371 TTACGACTTCAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCGCCA
1 TTACGACTTCAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCGCCA
* ** * * * * *
18420 TTAC-AGCTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGGTTCGCCG
1 TTACGA-CTTCAACCTTTCCCTCCATATCTTC-GTGGTACCAGATTCGCCA
* **
18469 TTGCGACTTCAACCTTTCCCTCTGTATCTTCGTGGTACCAGATTC
1 TTACGACTTCAACCTTTCCCTCCATATCTTCGTGGTACCAGATTC
18514 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:20338 original size:9 final size:9
Alignment explanation
Indices: 20324--20362 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
20314 GGTCTTGACT
20324 TTTTCTTTC
1 TTTTCTTTC
20333 TTTTCTTTC
1 TTTTCTTTC
20342 TTTT-TTTC
1 TTTTCTTTC
20350 TTTCTCTTT-
1 TTT-TCTTTC
20359 TTTT
1 TTTT
20363 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:20350 original size:12 final size:12
Alignment explanation
Indices: 20325--20361 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
20315 GTCTTGACTT
20325 TTTCTTTCTTTTC
1 TTTCTTT-TTTTC
20338 TTTCTTTTTTTC
1 TTTCTTTTTTTC
20350 TTTCTCTTTTTT
1 TTTCT-TTTTTT
20362 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:20402 original size:21 final size:21
Alignment explanation
Indices: 20350--20402 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
20340 TCTTTTTTTC
**
20350 TTTCTCTTTTTTTTATGCCTT
1 TTTCTCTTTTTTTTACCCCTT
* ***
20371 TTGCAGATTTTTTTACCCCTT
1 TTTCTCTTTTTTTTACCCCTT
20392 TTTCTCTTTTT
1 TTTCTCTTTTT
20403 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:23551 original size:24 final size:24
Alignment explanation
Indices: 23524--23578 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
23514 TAAAAATAAT
23524 TATATTAAGAATGTTATTAAATTA
1 TATATTAAGAATGTTATTAAATTA
** * *
23548 TATATTATTATTTTTATTAAATTA
1 TATATTAAGAATGTTATTAAATTA
23572 TAT-TTAA
1 TATATTAA
23579 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:23588 original size:24 final size:24
Alignment explanation
Indices: 23537--23588 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
23527 ATTAAGAATG
* **
23537 TTATTAAATTATATATTATTATTT
1 TTATTAAATTATATATTATGATAA
23561 TTATTAAATTATAT-TTAATGATAA
1 TTATTAAATTATATATT-ATGATAA
23585 TTAT
1 TTAT
23589 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:23615 original size:61 final size:62
Alignment explanation
Indices: 23519--23646 Score: 204
Period size: 61 Copynumber: 2.1 Consensus size: 62
23509 TAATATAAAA
* * *
23519 ATAATTATATTAAGAATGTTATTAAATTATATATTATTATTTTTATTAAATTATATTTAATG
1 ATAATTATATTAAGAATGTGATTAAATTATATATTATCATTTTTATTAAATTATATTCAATG
* *
23581 ATAATTATATTAA-AATGTGATTAAATTATTTATTATCATTTTTATTAAATTGTATTCAATG
1 ATAATTATATTAAGAATGTGATTAAATTATATATTATCATTTTTATTAAATTATATTCAATG
23642 ATAAT
1 ATAAT
23647 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.