Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011457.1 Kokia drynarioides strain JFW-HI SEQ_126441, 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: 86478
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:3158 original size:94 final size:94
Alignment explanation
Indices: 3014--3524 Score: 706
Period size: 94 Copynumber: 5.5 Consensus size: 94
3004 TTTAAAATTA
* * * *
3014 ATTTAACATTATTTAAATAAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTGTTGAT
1 ATTTAACTTTATTTAAATAAAAA-ACTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
* *
3079 TTGACAATATATTATTTGTCAAATTTTAAT
65 TTGACAATACATTATTTATCAAATTTTAAT
* * * * *
3109 ATTTAACTTTATTTAACTAATAAATTATTATTATATTATATTTTTTATCAAATAATGTGTTGATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
3174 TGACAATACATTATTTATCAAATTTTAAT
66 TGACAATACATTATTTATCAAATTTTAAT
* * *
3203 ATTTAACTTTATATAAATCAAAAACTATTATTATATTACAATTTTTATAAAATAATGTGTTGATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
*
3268 TGACAATACGTTATTTATC--A----AAT
66 TGACAATACATTATTTATCAAATTTTAAT
*
3291 -TTTAA---TATTTAAATAAAAAA-TATTATTATATTACAATTTTTATCAAATAATATGTTGATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
* *
3351 TGATGAA-ACATTATTTACCAAATTTTAAT
66 TGA-CAATACATTATTTATCAAATTTTAAT
3380 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
* * * *
3445 TGAAAATACATAATTTA-CTGAACTTTAAT
66 TGACAATACATTATTTATC-AAATTTTAAT
3474 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAA
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAA
3525 GTTTTAAATT
Statistics
Matches: 372, Mismatches: 30, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
83 51 0.14
84 15 0.04
85 1 0.00
87 5 0.01
88 3 0.01
89 3 0.01
90 5 0.01
92 1 0.00
93 18 0.05
94 250 0.67
95 20 0.05
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (94 bp):
ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
TGACAATACATTATTTATCAAATTTTAAT
Found at i:3306 original size:49 final size:49
Alignment explanation
Indices: 3158--3306 Score: 125
Period size: 46 Copynumber: 3.1 Consensus size: 49
3148 ATTTTTTATC
3158 AAATAATGTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTT
1 AAATAATGTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTT
* * ** * * * *
3207 AACT--T-TATAT-AAATCA-AAAACTATTATTATATTACAATTTT--TA-TA
1 AAATAATGTGT-TGATTTGACAATAC-ATTATT-TATCA-AATTTTAATATTT
*
3252 AAATAATGTGTTGATTTGACAATACGTTATTTATCAAATTTTAATATTT
1 AAATAATGTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTT
3301 AAATAA
1 AAATAA
3307 AAAATATTAT
Statistics
Matches: 71, Mismatches: 17, Indels: 24
0.63 0.15 0.21
Matches are distributed among these distances:
45 8 0.11
46 19 0.27
47 12 0.17
48 18 0.25
49 14 0.20
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (49 bp):
AAATAATGTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTT
Found at i:3333 original size:177 final size:178
Alignment explanation
Indices: 3014--3524 Score: 639
Period size: 177 Copynumber: 2.8 Consensus size: 178
3004 TTTAAAATTA
* * * *
3014 ATTTAACATTATTTAAATAAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTGTTGAT
1 ATTTAACTTTATTTAAATAAAAA-ACTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
* * *
3079 TTGACAATATATTATTTGTCAAATTTTAATATTTAACTTTATTTAACTAATAAATTATTATTATA
65 TTGACAATACATTATTTATCAAATTTTAATATTTAA----A--T-A--AA-AAACTATTATTATA
* * * *
3144 TTATATTTTTTATCAAATAATGTGTTGATTTGA-CAATACATTATTTATCAAATTTTAAT
120 TTACAATTTTTATCAAATAATATGTTGATTTGATCAA-ACATTATTTACCAAATTTTAAT
* * *
3203 ATTTAACTTTATATAAATCAAAAACTATTATTATATTACAATTTTTATAAAATAATGTGTTGATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
*
3268 TGACAATACGTTATTTATCAAATTTTAATATTTAAATAAAAAA-TATTATTATATTACAATTTTT
66 TGACAATACATTATTTATCAAATTTTAATATTTAAATAAAAAACTATTATTATATTACAATTTTT
*
3332 ATCAAATAATATGTTGATTTGATGAAACATTATTTACCAAATTTTAAT
131 ATCAAATAATATGTTGATTTGATCAAACATTATTTACCAAATTTTAAT
3380 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
* * *
3445 TGAAAATACATAATTTACTGAACTTTAATATTTAACTTTATTTAAATAAAAAACTATTATTATAT
66 TGACAATACATTATTTA-T---C--AAAT-TTTAA---TATTTAAATAAAAAACTATTATTATAT
3510 TACAATTTTTATCAA
121 TACAATTTTTATCAA
3525 GTTTTAAATT
Statistics
Matches: 288, Mismatches: 22, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
177 137 0.48
178 6 0.02
179 2 0.01
181 2 0.01
182 1 0.00
183 3 0.01
184 6 0.02
187 15 0.05
188 96 0.33
189 20 0.07
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (178 bp):
ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
TGACAATACATTATTTATCAAATTTTAATATTTAAATAAAAAACTATTATTATATTACAATTTTT
ATCAAATAATATGTTGATTTGATCAAACATTATTTACCAAATTTTAAT
Found at i:3410 original size:46 final size:45
Alignment explanation
Indices: 3356--3505 Score: 113
Period size: 46 Copynumber: 3.2 Consensus size: 45
3346 TGATTTGATG
*
3356 AAACATTATTTACCAAATTTTAATATTTAACTTTATTTAAATAAA
1 AAACATTATTTACTAAATTTTAATATTTAACTTTATTTAAATAAA
* * ** * * * **
3401 AAACTATTATTATATTACAATTTTTATCAAATAA-TGTGTTGATTTGAAA
1 AAAC-ATTATT-TACTA-AATTTTAAT-ATTTAACTTTATTTAAAT-AAA
* * * *
3450 ATACATAATTTACTGAACTTTAATATTTAACTTTATTTAAATAAA
1 AAACATTATTTACTAAATTTTAATATTTAACTTTATTTAAATAAA
3495 AAACTATTATT
1 AAAC-ATTATT
3506 ATATTACAAT
Statistics
Matches: 73, Mismatches: 25, Indels: 13
0.66 0.23 0.12
Matches are distributed among these distances:
45 14 0.19
46 24 0.33
47 6 0.08
48 19 0.26
49 10 0.14
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (45 bp):
AAACATTATTTACTAAATTTTAATATTTAACTTTATTTAAATAAA
Found at i:3651 original size:22 final size:22
Alignment explanation
Indices: 3619--3674 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3609 TGAATCACTC
* * *
3619 AAATTTCAACTCACCTAAACCG
1 AAATTCCAACTCACCAAAACCA
* *
3641 AAATTCTAACTCACCAAAATCA
1 AAATTCCAACTCACCAAAACCA
3663 AAATTCCAACTC
1 AAATTCCAACTC
3675 CCCACCACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATTCCAACTCACCAAAACCA
Found at i:4735 original size:20 final size:19
Alignment explanation
Indices: 4710--4754 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
4700 TTTTTATAAT
*
4710 ATTTTTTTCTATTTTCGAA
1 ATTTTTTTATATTTTCGAA
4729 ATGTTTTTTATATTTTCGAA
1 AT-TTTTTTATATTTTCGAA
4749 ATTTTT
1 ATTTTT
4755 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (19 bp):
ATTTTTTTATATTTTCGAA
Found at i:5995 original size:23 final size:23
Alignment explanation
Indices: 5969--6015 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5959 TCCGTTTATT
*
5969 TTTTA-AATTTAATTTGTAATTTC
1 TTTTATAATTTAAATT-TAATTTC
*
5992 TTTTATATTTTAAATTTAATTTC
1 TTTTATAATTTAAATTTAATTTC
6015 T
1 T
6016 AATTTCCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTATAATTTAAATTTAATTTC
Found at i:5997 original size:30 final size:30
Alignment explanation
Indices: 5957--6073 Score: 120
Period size: 30 Copynumber: 4.1 Consensus size: 30
5947 TTTTTATTTT
* *
5957 TTTCCGTTTATTTTTTAAATTTAATTTGTAA
1 TTTCC-TTTATATTTTAAATTTAATTTCTAA
*
5988 TTTCTTTTATATTTTAAATTTAATTTCTAA
1 TTTCCTTTATATTTTAAATTTAATTTCTAA
*
6018 TTTCCTGTATA---T---TTTAATTTCTAA
1 TTTCCTTTATATTTTAAATTTAATTTCTAA
** *
6042 TTTTGTTTATATTTTAAATTTCATTTCTAA
1 TTTCCTTTATATTTTAAATTTAATTTCTAA
6072 TT
1 TT
6074 ATTAATTTTG
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
24 20 0.28
27 2 0.03
30 45 0.63
31 4 0.06
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTCCTTTATATTTTAAATTTAATTTCTAA
Found at i:6038 original size:24 final size:24
Alignment explanation
Indices: 6006--6063 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5996 ATATTTTAAA
6006 TTTAATTTCTAATTTCCTGTATAT
1 TTTAATTTCTAATTTCCTGTATAT
** *
6030 TTTAATTTCTAATTTTGTTTATAT
1 TTTAATTTCTAATTTCCTGTATAT
6054 TTTAAATTTC
1 TTT-AATTTC
6064 ATTTCTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (24 bp):
TTTAATTTCTAATTTCCTGTATAT
Found at i:7131 original size:61 final size:59
Alignment explanation
Indices: 6909--7699 Score: 541
Period size: 61 Copynumber: 13.1 Consensus size: 59
6899 TACATGGCCT
* * * * * * * *
6909 ACACAATAAAATTTTAAATTTGTTGTCAGATAAAAAAAGTGATGTCGACCATGCAATGGCCA
1 ACACAAAAAAATTTGAATTTTTTTATCAGAT--AAAAAGGGGTGTCGACCATGC-ATGACCA
* * * * *
6971 ACA-AAAAAAAATT-AAATTTTTTATCAGATAAAAAGGGG-GTTGGTCAATGCATGACCA
1 ACACAAAAAAATTTGAATTTTTTTATCAGATAAAAAGGGGTG-TCGACCATGCATGACCA
* * * * *
7028 ACGC-CAAAAATTT-AAATTTTTTATCAAATAAAAAGGGTGTGTC-AGCCATGCAATGACAA
1 ACACAAAAAAATTTGAATTTTTTTATCAGATAAAAAGGG-GTGTCGA-CCATGC-ATGACCA
* ** * * **
7087 ACACAAAAAATTTTGAATTTTTTTATTTGATAAAAAGGTGGTGTCGGTCAATGCATGGTCA
1 ACACAAAAAAATTTGAATTTTTTTATCAGATAAAAAGG-GGTGTC-GACCATGCATGACCA
* * * * * *
7148 ACACCAAAAAAA-TTGAATTTTTTTATCAAATTAAAAGGGGTGTCGGCTAATGGATGGCCA
1 ACA-CAAAAAAATTTGAATTTTTTTATCAGATAAAAAGGGGTGTCGAC-CATGCATGACCA
* * ** *
7208 ACACAAAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGGGTGTTGACCATGCAATGGTCG
1 ACAC-AAAAAAATTTGAATTTTTTTATCAGATAAAAA-GGGGTGTCGACCATGC-ATGACCA
* * * * * * * * *
7270 ACGCCAAAAAAA-TTGAAGTTTTTTATCTGATATAAAGGTAGTGTCGGTCAATACATGA-CT
1 AC-ACAAAAAAATTTGAATTTTTTTATCAGATAAAAAGG-GGTGTC-GACCATGCATGACCA
*
7330 A-ACAAAAAATTTTG-ATTTTTTTATCAGATAAAAAGGGGTGTCGACCATGCAATGACCA
1 ACACAAAAAAATTTGAATTTTTTTATCAGATAAAAAGGGGTGTCGACCATGC-ATGACCA
* * * * *
7388 ACATAAAAAAATTTGAATTATTTTATCTGATAAAAAGGTGGTGTCGACCAATGCATGGCAA
1 ACACAAAAAAATTTGAATTTTTTTATCAGATAAAAAGG-GGTGTCGACC-ATGCATGACCA
* * * * *
7449 ACACAAAAAAAAATTAAATTTTTTGT-T-AGATAAAAAGGTAGTGTCGATCAATACATGACCA
1 ACAC-AAAAAAATTTGAATTTTTT-TATCAGATAAAAAGG-GGTGTCGA-CCATGCATGACCA
* * * * *
7510 ACACAAAACAAATTTGAATTTTTTTATTAGATAAAAATAGGGTTTCGACTAATGCATGGCCA
1 ACACAAAA-AAATTTGAATTTTTTTATCAGATAAAAA-GGGGTGTCGAC-CATGCATGACCA
* * *
7572 AC-CAAAAAAGTTTGAATTTTTTTA-CAGATAAAAAAAGAGTGTCGACCATGCAATGACCA
1 ACACAAAAAAATTTGAATTTTTTTATCAGAT-AAAAAGGGGTGTCGACCATGC-ATGACCA
* * * * * * * *
7631 ACACCAAAAAATTTAAAATTTTTTATCTGATAAAAAAGTGGTGTTGGCCAATGCAATGGCCA
1 ACACAAAAAAATTTGAATTTTTTTATCAGAT-AAAAAGGGGTGTCGACC-ATGC-ATGACCA
7693 ACACAAA
1 ACACAAA
7700 TTTTTTTTTT
Statistics
Matches: 581, Mismatches: 108, Indels: 80
0.76 0.14 0.10
Matches are distributed among these distances:
56 5 0.01
57 48 0.08
58 53 0.09
59 48 0.08
60 115 0.20
61 199 0.34
62 110 0.19
63 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (59 bp):
ACACAAAAAAATTTGAATTTTTTTATCAGATAAAAAGGGGTGTCGACCATGCATGACCA
Found at i:7245 original size:183 final size:180
Alignment explanation
Indices: 6964--7699 Score: 667
Period size: 183 Copynumber: 4.1 Consensus size: 180
6954 CGACCATGCA
* * * * * *
6964 ATGGCCAACAAAAAAAAATT-AAATTTTTTATCAGATAAAAAGGGG-GTTG-GTCAATGCATGAC
1 ATGGCCAACACAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGGTGTCGACT-AATGAATGGC
* * * * *
7026 CAACGC--CAAAAATTTAAATTTTTTATCAAATAAAAAGGGTGTGTC-AGCCATGCAATGACAAA
65 CAACACAAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGTGTGTCGA-CCATGCAATGACAAA
* * * * *
7088 CACAAAAAATTTTGAATTTTTTTATTTGATAAAAAGGTGGTGTCGGTCAATGC
129 CACAAAAAA-ATTGAAATTTTTTATCTGATAAAAAGGTAGTGTCGGTCAATAC
* * * * *
7141 ATGGTCAACACCAAAAAAATTGAATTTTTTTATCAAATTAAAAGGGGTGTCGGCTAATGGATGGC
1 ATGGCCAACA-CAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGGTGTCGACTAATGAATGGC
* * * *
7206 CAACACAAAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGGGTGTTGACCATGCAATGGTC-G
65 CAACAC-AAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGTGTGTCGACCATGCAAT-GACAA
* * *
7270 ACGCCAAAAAAATTGAAGTTTTTTATCTGATATAAAGGTAGTGTCGGTCAATAC
128 AC-ACAAAAAAATTGAAATTTTTTATCTGATAAAAAGGTAGTGTCGGTCAATAC
* * ** * *
7324 ATGACTAACA-AAAAATTTTG-ATTTTTTTATCAGATAAAAAGGGGTGTCGAC-CATGCAATGAC
1 ATGGCCAACACAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGGTGTCGACTAATG-AATGGC
* * * * *
7386 CAACATAAAAAAATTTGAATTATTTTATCTGATAAAAA-GGTGGTGTCGACCAATGC-ATGGCAA
65 CAACACAAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGT-GTGTCGACC-ATGCAATGACAA
* *
7449 ACACAAAAAAAAATT-AAATTTTTTGT-TAGATAAAAAGGTAGTGTCGATCAATAC
128 ACAC--AAAAAAATTGAAATTTTTTATCT-GATAAAAAGGTAGTGTCGGTCAATAC
* * * * *
7503 ATGACCAACACAAAACAAATTTGAATTTTTTTATTAGATAAAAATAGGGTTTCGACTAATGCATG
1 ATGGCCAACACAAAA-AAA-TTGAATTTTTTTATCAGATAAAAA-GGGGTGTCGACTAATGAATG
** ** * *
7568 GCCAAC-CAAAAAAGTTTGAATTTTTTTA-CAGATAAAAAAAGAGTGTCGACCATGCAATGACCA
63 GCCAACACAAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGTGTGTCGACCATGCAATGACAA
* * * * * * *
7631 ACACCAAAAAATTTAAAATTTTTTATCTGATAAAAAAGTGGTGTTGGCCAATGC
128 ACA-CAAAAAAATTGAAATTTTTTATCTGATAAAAAGGTAGTGTCGGTCAATAC
7685 AATGGCCAACACAAA
1 -ATGGCCAACACAAA
7700 TTTTTTTTTT
Statistics
Matches: 455, Mismatches: 75, Indels: 52
0.78 0.13 0.09
Matches are distributed among these distances:
177 9 0.02
178 15 0.03
179 108 0.24
180 70 0.15
181 22 0.05
182 59 0.13
183 142 0.31
184 27 0.06
185 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (180 bp):
ATGGCCAACACAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGGTGTCGACTAATGAATGGCC
AACACAAAAAAAATTGAATTTTTTTATCAGATAAAAAGGGTGTGTCGACCATGCAATGACAAACA
CAAAAAAATTGAAATTTTTTATCTGATAAAAAGGTAGTGTCGGTCAATAC
Found at i:14373 original size:5 final size:5
Alignment explanation
Indices: 14353--14386 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
14343 TTTTAAAATC
*
14353 TATAA TATCA -ATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
14387 AAATAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:17229 original size:6 final size:6
Alignment explanation
Indices: 17218--17242 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17208 TCTTTCATAA
17218 ACCTAT ACCTAT ACCTAT ACCTAT A
1 ACCTAT ACCTAT ACCTAT ACCTAT A
17243 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ACCTAT
Found at i:17246 original size:2 final size:2
Alignment explanation
Indices: 17239--17269 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17229 TACCTATACC
17239 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17270 TTAAGAGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17746 original size:3 final size:3
Alignment explanation
Indices: 17740--17769 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
17730 TAAAAAAAAC
17740 AAT AAT AAT AAT AAT AAT AATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
17770 AAAAGGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18283 original size:25 final size:23
Alignment explanation
Indices: 18255--18300 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
18245 GTTGGATCCA
18255 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
18280 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
18301 CCATAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:20916 original size:29 final size:30
Alignment explanation
Indices: 20863--20925 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
20853 TTCATATAAC
*
20863 TGTATTCATAATAGTAGTCATATTTAT-TT
1 TGTATTCATAATAGTAGTCAAATTTATATT
* * * *
20892 TGTATTCGTAATCGTATTCAAATTTTTATT
1 TGTATTCATAATAGTAGTCAAATTTATATT
20922 TGTA
1 TGTA
20926 CTTTTGACAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (30 bp):
TGTATTCATAATAGTAGTCAAATTTATATT
Found at i:23166 original size:3 final size:3
Alignment explanation
Indices: 23158--23204 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
23148 AGGAGATGGA
* * *
23158 GGT GGT GGT GGT GGT GGT GGT GGA GTT GAG- GGA GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT G-GT GGT GGT GGT GGT GGT
23203 GG
1 GG
23205 AGGAACACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
2 1 0.03
3 36 0.97
ACGTcount: A:0.06, C:0.00, G:0.66, T:0.28
Consensus pattern (3 bp):
GGT
Found at i:31564 original size:24 final size:25
Alignment explanation
Indices: 31537--31583 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
31527 TGCTAAATTA
31537 AAATTTATCAACTCGATT-AACTTG
1 AAATTTATCAACTCGATTCAACTTG
* *
31561 AAATTTTTTAACTCGATTCAACT
1 AAATTTATCAACTCGATTCAACT
31584 CGACTCGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.40
Consensus pattern (25 bp):
AAATTTATCAACTCGATTCAACTTG
Found at i:37484 original size:22 final size:22
Alignment explanation
Indices: 37444--37502 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
37434 CACCGTTCAT
* *
37444 CTTTTTTTTTAATT-TTTTTTTA
1 CTTTTTTATT-ATTATTTTGTTA
37466 CTATTTTTATTATTATTTTGTTA
1 CT-TTTTTATTATTATTTTGTTA
*
37489 GTTTTTTATTATTA
1 CTTTTTTATTATTA
37503 ATAATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (22 bp):
CTTTTTTATTATTATTTTGTTA
Found at i:41534 original size:21 final size:21
Alignment explanation
Indices: 41508--41547 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41498 TTCAAGTTTT
*
41508 ATTTTATAAAAGTATTTTTAA
1 ATTTTAAAAAAGTATTTTTAA
*
41529 ATTTTAAAAAATTATTTTT
1 ATTTTAAAAAAGTATTTTT
41548 TATTGTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTTAAAAAAGTATTTTTAA
Found at i:41826 original size:19 final size:20
Alignment explanation
Indices: 41781--41826 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
41771 ATATTATTTT
41781 TACTTTTCATAATTTAATTA
1 TACTTTTCATAATTTAATTA
** *
41801 TTTTTTTCA-AATTTTATTA
1 TACTTTTCATAATTTAATTA
41820 TACTTTT
1 TACTTTT
41827 TTTGTTCTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (20 bp):
TACTTTTCATAATTTAATTA
Found at i:41826 original size:20 final size:20
Alignment explanation
Indices: 41784--41827 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41774 TTATTTTTAC
*
41784 TTTTCATAATTTAATTATTT
1 TTTTCATAATTTAATTATCT
*
41804 TTTTCA-AATTTTATTATACT
1 TTTTCATAATTTAATTAT-CT
41824 TTTT
1 TTTT
41828 TTGTTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTCATAATTTAATTATCT
Found at i:41961 original size:19 final size:21
Alignment explanation
Indices: 41936--41984 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
41926 TATTTTTGAA
41936 CTATTTTTAT-AATATTT-AT
1 CTATTTTTATGAATATTTAAT
* *
41955 TTATTTTT-TGGATATTTAAT
1 CTATTTTTATGAATATTTAAT
41975 CTATTTTTAT
1 CTATTTTTAT
41985 TGTTAATGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 13 0.54
20 9 0.38
21 1 0.04
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
CTATTTTTATGAATATTTAAT
Found at i:44170 original size:3 final size:3
Alignment explanation
Indices: 44164--44198 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
44154 TTGAGAAAAA
44164 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
44199 ATCAATCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47187 original size:2 final size:2
Alignment explanation
Indices: 47182--47206 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47172 TCTTAATATA
47182 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
47207 CTGAAGCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:52704 original size:2 final size:2
Alignment explanation
Indices: 52697--52723 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52687 CTACTTCTAA
52697 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
52724 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:54584 original size:31 final size:31
Alignment explanation
Indices: 54549--54617 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
54539 TTACAATTTG
54549 GTCACTAAACTATTCAAAAGGTTTC-ATTCAA
1 GTCACTAAACTATTCAAAA-GTTTCTATTCAA
* *
54580 GTCACTGAACTATTCAAAAGTTTCTATTTAA
1 GTCACTAAACTATTCAAAAGTTTCTATTCAA
54611 GTCACTA
1 GTCACTA
54618 GGTTATTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTTCTATTCAA
Found at i:56483 original size:14 final size:14
Alignment explanation
Indices: 56464--56495 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
56454 AAATGATGAA
*
56464 ATTGCATTATTACT
1 ATTGCATTAATACT
56478 ATTGCATTAATACT
1 ATTGCATTAATACT
56492 ATTG
1 ATTG
56496 TAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (14 bp):
ATTGCATTAATACT
Found at i:57906 original size:29 final size:29
Alignment explanation
Indices: 57865--58217 Score: 292
Period size: 29 Copynumber: 12.0 Consensus size: 29
57855 TTTTGGAAAC
**
57865 TCGGTGGTAAAAATATAATTTTTGGAAGTT
1 TCGG-GGTAAAAATGGAATTTTTGGAAGTT
* *
57895 TCGGGGTCAAAAAT-GAGATTTTCGAAAG-T
1 TCGGGGT-AAAAATGGA-ATTTTTGGAAGTT
57924 TCGTGGGTAAAACA--GAATTTTTGGAAGTT
1 TCG-GGGTAAAA-ATGGAATTTTTGGAAGTT
* * * * *
57953 TTGGGGTCCAAAATGGGATTTTCGAAAG-T
1 TCGGGGT-AAAAATGGAATTTTTGGAAGTT
57982 TCGGGGATAAAAATGGAATTTTTGGAAGTT
1 TCGGGG-TAAAAATGGAATTTTTGGAAGTT
*** *
58012 TCACAGTCAAAAATGGGATTTTTGGAAG-T
1 TCGGGGT-AAAAATGGAATTTTTGGAAGTT
*
58041 TCGAGGGTAAAAATGGAATTTTT-TAGAGTT
1 TCG-GGGTAAAAATGGAATTTTTGGA-AGTT
* * *
58071 TCGAGGTAAAAAATGGGATTTTTGAAAGTT
1 TCGGGGT-AAAAATGGAATTTTTGGAAGTT
* *
58101 TGGGGGTAAAAATGGGATTTTTGGAAGTT
1 TCGGGGTAAAAATGGAATTTTTGGAAGTT
** * *
58130 TTAGGGTCAAAATGGGATTTTTGGAAG-T
1 TCGGGGTAAAAATGGAATTTTTGGAAGTT
* **
58158 TCAAGGGTAAAAATGGAATTTTTTAAAGTT
1 TC-GGGGTAAAAATGGAATTTTTGGAAGTT
58188 T-GGGGTAAAAATGGAATTTTTGGATAGTT
1 TCGGGGTAAAAATGGAATTTTTGGA-AGTT
58217 T
1 T
58218 AGGGACCTTT
Statistics
Matches: 263, Mismatches: 41, Indels: 39
0.77 0.12 0.11
Matches are distributed among these distances:
28 37 0.14
29 136 0.52
30 89 0.34
31 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (29 bp):
TCGGGGTAAAAATGGAATTTTTGGAAGTT
Found at i:58010 original size:59 final size:58
Alignment explanation
Indices: 57847--58209 Score: 380
Period size: 59 Copynumber: 6.2 Consensus size: 58
57837 TTCGAGATCG
* * **
57847 AAATGGGATTTTGGAAA-CTCGGTGGTAAAAATATAATTTTTGGAAGTTTCGGGGTCAA
1 AAATGGGATTTTTGAAAGTTCGG-GGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
* * * *
57905 AAATGAGATTTTCGAAAGTTCGTGGGTAAAACA--GAATTTTTGGAAGTTTTGGGGTCCA
1 AAATGGGATTTTTGAAAGTTCG-GGGTAAAA-ATGGAATTTTTGGAAGTTTCGGGGTCAA
* ***
57963 AAATGGGATTTTCGAAAGTTCGGGGATAAAAATGGAATTTTTGGAAGTTTCACAGTCAA
1 AAATGGGATTTTTGAAAGTTCGGGG-TAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
* * * *
58022 AAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTT-TAGAGTTTCGAGGTAAA
1 AAATGGGATTTTTGAAAGTTCG-GGGTAAAAATGGAATTTTTGGA-AGTTTCGGGGTCAA
* * **
58081 AAATGGGATTTTTGAAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTTAGGGTC-A
1 AAATGGGATTTTTGAAAG-TTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
* * **
58139 AAATGGGATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTTAAAGTTT-GGGGT-AA
1 AAATGGGATTTTTGAAAGTTC-GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
*
58196 AAATGGAATTTTTG
1 AAATGGGATTTTTG
58210 GATAGTTTAG
Statistics
Matches: 258, Mismatches: 35, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
57 24 0.09
58 106 0.41
59 119 0.46
60 9 0.03
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (58 bp):
AAATGGGATTTTTGAAAGTTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAA
Found at i:60079 original size:18 final size:18
Alignment explanation
Indices: 60058--60128 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 18
60048 TTTAAAATTT
60058 ATTTCAAAATAAATTTAA
1 ATTTCAAAATAAATTTAA
*
60076 ATTTTAAAATAAATTTAA
1 ATTTCAAAATAAATTTAA
* * **
60094 A-CTCCAAATAAGCTTAA
1 ATTTCAAAATAAATTTAA
*
60111 ATTT-ACAATAAATTTAA
1 ATTTCAAAATAAATTTAA
60128 A
1 A
60129 CTTAAATTGA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
17 22 0.54
18 19 0.46
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (18 bp):
ATTTCAAAATAAATTTAA
Found at i:62635 original size:33 final size:33
Alignment explanation
Indices: 62560--62635 Score: 77
Period size: 35 Copynumber: 2.3 Consensus size: 33
62550 AAAATTATTT
*
62560 ATTTAAA-TTCTTTAAAAAAATTAAAAATTAAA
1 ATTTAAATTTCTTCAAAAAAATTAAAAATTAAA
* *
62592 AATAATAATTTCTCTCAAAAATAA-TAAAAATT-AA
1 ATTTA-AATTTCT-TCAAAAA-AATTAAAAATTAAA
62626 ATTTAAATTT
1 ATTTAAATTT
62636 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
32 3 0.09
33 7 0.20
34 9 0.26
35 14 0.40
36 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (33 bp):
ATTTAAATTTCTTCAAAAAAATTAAAAATTAAA
Found at i:66909 original size:2 final size:2
Alignment explanation
Indices: 66902--66937 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
66892 ACCTTTTCTT
*
66902 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
66938 ACACACAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:66942 original size:2 final size:2
Alignment explanation
Indices: 66937--66978 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
66927 CTCTCACTCT
* *
66937 CA CA CA CA GA CA CA CA CA CA CA CA CA CA CA CA CA CA GA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
66979 TATAAGACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.45, G:0.05, T:0.00
Consensus pattern (2 bp):
CA
Found at i:76368 original size:24 final size:24
Alignment explanation
Indices: 76340--76394 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
76330 GTTATTAGCC
*
76340 TATATTAATTAATTATGAT-AATT
1 TATATTAACTAATTATGATGAATT
* * *
76363 ATATATGAACTGATTATGGTGAATT
1 -TATATTAACTAATTATGATGAATT
76388 TATATTA
1 TATATTA
76395 TAAAAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (24 bp):
TATATTAACTAATTATGATGAATT
Found at i:76500 original size:89 final size:91
Alignment explanation
Indices: 76379--76548 Score: 299
Period size: 89 Copynumber: 1.9 Consensus size: 91
76369 GAACTGATTA
76379 TGGTGAATTTATATTATAAAAATTAATTACAATAAATATAATAACTAATTATAGTGAATTCACAT
1 TGGTGAATTTATATTATAAAAATTAATTACAATAAATATAATAACTAATTATAGTGAATTCACAT
76444 TAATTATGATAAATGTTAGCTAATTG
66 TAATTATGATAAATGTTAGCTAATTG
** *
76470 TGGTGAATTTATA-TA-CGAAATTAATTACAATAAATATAATAACTAATTATAGTGAATTTACAT
1 TGGTGAATTTATATTATAAAAATTAATTACAATAAATATAATAACTAATTATAGTGAATTCACAT
76533 TAATTATGATAAATGT
66 TAATTATGATAAATGT
76549 ATTAATTATT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 61 0.80
90 2 0.03
91 13 0.17
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.39
Consensus pattern (91 bp):
TGGTGAATTTATATTATAAAAATTAATTACAATAAATATAATAACTAATTATAGTGAATTCACAT
TAATTATGATAAATGTTAGCTAATTG
Found at i:76546 original size:42 final size:42
Alignment explanation
Indices: 76400--76538 Score: 138
Period size: 42 Copynumber: 3.2 Consensus size: 42
76390 TATTATAAAA
*
76400 ATTAATTACAATAAATATAATAACTAATTATAGTGAATTCAC
1 ATTAATTACAATAAATATAATAACTAATTATAGTGAATTTAC
** * * * *
76442 ATTAATTATGATAAATGT--TAGCTAATTGTGGTGAATTTATATAC
1 ATTAATTACAATAAATATAATAACTAATTATAGTGAA--T-T-TAC
76486 GAAATTAATTACAATAAATATAATAACTAATTATAGTGAATTTAC
1 ---ATTAATTACAATAAATATAATAACTAATTATAGTGAATTTAC
76531 ATTAATTA
1 ATTAATTA
76539 TGATAAATGT
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
40 14 0.19
42 24 0.32
43 1 0.01
44 2 0.03
45 3 0.04
46 1 0.01
47 16 0.21
49 14 0.19
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (42 bp):
ATTAATTACAATAAATATAATAACTAATTATAGTGAATTTAC
Found at i:77303 original size:55 final size:55
Alignment explanation
Indices: 77236--77498 Score: 296
Period size: 55 Copynumber: 4.7 Consensus size: 55
77226 ATGTGCTACG
* * * *
77236 TAACAATTGATTTAAATATATAAACAATTGATTCAAAATAAGCAGTATTCCAACA
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAATAAGCAATATTCCAACA
* *
77291 TAACAATCGATTTAAACATATAAACAATCGATTTAAAAGAAGCAATATTCCAACA
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAATAAGCAATATTCCAACA
* * *
77346 TAACAAT-GATTTAAACATATAAAAAATCAATTCTAAAGAATAAGAAGTAGTATTCC-ACTA
1 TAACAATCGATTTAAACATATAAACAATCGATTC--AA-AATAAGCA--A-TATTCCAAC-A
** * *
77406 TAACAATTAATTTAAATATATAAACAATTGATTCAAAATAAGCAATATTCCAACA
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAATAAGCAATATTCCAACA
*** *
77461 TGGTAATCGATTTAAACATATAAACAATCGATTTAAAA
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAA
77499 GCGTTTCGAC
Statistics
Matches: 174, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
54 23 0.13
55 93 0.53
56 5 0.03
57 6 0.03
58 7 0.04
59 5 0.03
60 14 0.08
61 21 0.12
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (55 bp):
TAACAATCGATTTAAACATATAAACAATCGATTCAAAATAAGCAATATTCCAACA
Found at i:77449 original size:115 final size:115
Alignment explanation
Indices: 77279--77497 Score: 307
Period size: 115 Copynumber: 1.9 Consensus size: 115
77269 CAAAATAAGC
* *
77279 AGTATTCCAACATAACAATCGATTTAAACATATAAACAATCGATTTAAAAGAAGCAATATTCCAA
1 AGTATTCCAACATAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCCAA
77344 CATAACAAT-GATTTAAACATATAAAAAATCAATTCTAAAGAATAAGAAGT
66 CATAACAATCGATTTAAACATATAAAAAATCAATT-TAAAGAATAAGAAGT
* * * *
77394 AGTATTCC-ACTATAACAATTAATTTAAATATATAAACAATTGATTCAAAATAAGCAATATTCCA
1 AGTATTCCAAC-ATAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCCA
*** * *
77458 ACATGGTAATCGATTTAAACATATAAACAATCGATTTAAA
65 ACATAACAATCGATTTAAACATATAAAAAATCAATTTAAA
77498 AGCGTTTCGA
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
114 2 0.02
115 66 0.73
116 23 0.25
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (115 bp):
AGTATTCCAACATAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCCAA
CATAACAATCGATTTAAACATATAAAAAATCAATTTAAAGAATAAGAAGT
Found at i:85426 original size:29 final size:30
Alignment explanation
Indices: 85379--85435 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
85369 ATCGGAGTTC
*
85379 AAAATGAGACTTTTCGGATTCCCGGGGGCA
1 AAAATGAGAATTTTCGGATTCCCGGGGGCA
* *
85409 AAAATGATAATTTT-GGATTCTCGGGGG
1 AAAATGAGAATTTTCGGATTCCCGGGGG
85436 TGAAACGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (30 bp):
AAAATGAGAATTTTCGGATTCCCGGGGGCA
Found at i:85478 original size:29 final size:29
Alignment explanation
Indices: 85446--85846 Score: 253
Period size: 29 Copynumber: 13.6 Consensus size: 29
85436 TGAAACGGTA
* *
85446 ATTTTGGGAAAATTCGGGGTTAAAAATGG
1 ATTTTTGGAAATTTCGGGGTTAAAAATGG
* *
85475 ATTTTTTGGACA-TTCGGGGGT-AAAATGG
1 A-TTTTTGGAAATTTCGGGGTTAAAAATGG
* * *
85503 TAATTTTTGGAAGTTTCGGAGTCAAAAATGG
1 --ATTTTTGGAAATTTCGGGGTTAAAAATGG
* * * * *
85534 AATTTTGGGAAGTTCGAGGCTAAAAATGG
1 ATTTTTGGAAATTTCGGGGTTAAAAATGG
* * *
85563 AATTTTTAGAAGTTTTGGGGTTAAAAATGG
1 -ATTTTTGGAAATTTCGGGGTTAAAAATGG
* * ** *
85593 AATTTTGGAAGTTTCAAGGTCAAAAATGGG
1 ATTTTTGGAAATTTCGGGGTTAAAAAT-GG
* *
85623 ATTTTTAGAAATTTAGGGG-TAAAAATGGG
1 ATTTTTGGAAATTTCGGGGTTAAAAAT-GG
* *
85652 ATTTTT-GAAAGTTTCGGGATAAAAAATGGG
1 ATTTTTGGAAA-TTTCGGGGTTAAAAAT-GG
*
85682 ATTTTT-GAAAGTTT-GGGGATAAAAATGAG
1 ATTTTTGGAAA-TTTCGGGGTTAAAAATG-G
* * *
85711 ACTTTTGGAAGTTTCGGGGTCAAAAATGGG
1 ATTTTTGGAAATTTCGGGGTTAAAAAT-GG
* * *
85741 ATTTTTGGAAGTTTCGAGG-TCAAAATGGG
1 ATTTTTGGAAATTTCGGGGTTAAAAAT-GG
* ** * *
85770 ATTTTTAGAAGCTTCGAGGTCAAAAATGGG
1 ATTTTTGGAAATTTCGGGGTTAAAAAT-GG
* *
85800 ATTTTT-AAAAGTTCAGGGG-TAAAAATGAG
1 ATTTTTGGAAATTTC-GGGGTTAAAAATG-G
*
85829 ATTTTTGGAAGTTTCGGG
1 ATTTTTGGAAATTTCGGG
85847 ACCCTCGAGA
Statistics
Matches: 292, Mismatches: 63, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
28 13 0.04
29 144 0.49
30 127 0.43
31 8 0.03
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
ATTTTTGGAAATTTCGGGGTTAAAAATGG
Found at i:85509 original size:30 final size:31
Alignment explanation
Indices: 85429--85512 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 31
85419 TTTTGGATTC
* *
85429 TCGGGGGTGAAACGGTAA-TTTTGGGAAAAT
1 TCGGGGGTAAAATGGTAATTTTTGGGAAAAT
* * *
85459 TCGGGGTTAAAAATGG--ATTTTTTGG-ACAT
1 TCGGGGGT-AAAATGGTAATTTTTGGGAAAAT
85488 TCGGGGGTAAAATGGTAATTTTTGG
1 TCGGGGGTAAAATGGTAATTTTTGG
85513 AAGTTTCGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
28 7 0.16
29 11 0.26
30 20 0.47
31 5 0.12
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.33
Consensus pattern (31 bp):
TCGGGGGTAAAATGGTAATTTTTGGGAAAAT
Found at i:85558 original size:59 final size:59
Alignment explanation
Indices: 85458--85844 Score: 339
Period size: 59 Copynumber: 6.6 Consensus size: 59
85448 TTTGGGAAAA
* *
85458 TTCGGGGTTAAAAATGGATTTTTTGGACA--TTCGGGGGT--AAAATGGTAATTTTTGGAAGT
1 TTCGGGG-TAAAAATGGAATTTTTGGA-AGTTTC-GAGGTCAAAAATGG-AATTTTTGGAAGT
* * *
85517 TTCGGAGTCAAAAATGGAATTTTGGGAAG-TTCGAGG-CTAAAAATGGAATTTTTAGAAGT
1 TTCGGGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTC-AAAAATGGAATTTTTGGAAGT
* * * * *
85576 TTTGGGGTTAAAAATGGAA-TTTTGGAAGTTTCAAGGTCAAAAATGGGATTTTTAGAAAT
1 TTCGGGG-TAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGT
* * * * * *
85635 TTAGGGGTAAAAATGGGATTTTTGAAAGTTTCG-GGATAAAAAATGGGATTTTTGAAAGT
1 TTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGG-TCAAAAATGGAATTTTTGGAAGT
* * *
85694 TT-GGGGATAAAAAT-GAGACTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGT
1 TTCGGGG-TAAAAATGGA-ATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGT
* * * * * * **
85753 TTCGAGGTCAAAATGGGATTTTTAGAAGCTTCGAGGTCAAAAATGGGATTTTTAAAAG-
1 TTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGT
85811 TTCAGGGGTAAAAAT-GAGATTTTTGGAAGTTTCG
1 TTC-GGGGTAAAAATGGA-ATTTTTGGAAGTTTCG
85845 GGACCCTCGA
Statistics
Matches: 273, Mismatches: 38, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
58 34 0.12
59 224 0.82
60 15 0.05
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (59 bp):
TTCGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGT
Done.