Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003423.1 Hibiscus syriacus cultivar Beakdansim tig00007207_pilon, 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: 108783
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3235 original size:21 final size:21
Alignment explanation
Indices: 3208--3266 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
3198 GTCCGAGTTA
*
3208 CCCGCGACAGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
* * *
3229 TCTGCGATGGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
3250 CCCGCGACGGCCGCAAT
1 CCCGCGACGGCCGCAAT
3267 CACGGTAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.39, G:0.31, T:0.10
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAGCG
Found at i:4301 original size:30 final size:29
Alignment explanation
Indices: 4267--4323 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4257 TAAAAAAGTG
*
4267 AAAGATTAATATAAAATTTAAAAATTTTGT
1 AAAGATCAA-ATAAAATTTAAAAATTTTGT
* *
4297 AAAGATCAAATTAAATTTTAAAATTTT
1 AAAGATCAAATAAAATTTAAAAATTTT
4324 AAAGGTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (29 bp):
AAAGATCAAATAAAATTTAAAAATTTTGT
Found at i:4637 original size:53 final size:53
Alignment explanation
Indices: 4580--4680 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 53
4570 ATGATACCCA
*
4580 ATCATACTTGCTTTTATCGTTGAAATAAAAATATACGAATAAAATGATAATTC
1 ATCATACTTGCTTTTATCGTTGAAATAAAAATACACGAATAAAATGATAATTC
* *
4633 ATCATACTTGTTTTTATCGTTGAAATAAAAATACACGAATCAAATGAT
1 ATCATACTTGCTTTTATCGTTGAAATAAAAATACACGAATAAAATGAT
4681 CTTAATAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (53 bp):
ATCATACTTGCTTTTATCGTTGAAATAAAAATACACGAATAAAATGATAATTC
Found at i:5235 original size:28 final size:28
Alignment explanation
Indices: 5177--5235 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
5167 ACATATTTAA
* *
5177 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTACC
** *
5205 AAGTAAACAATAAAACATGTATATTACC
1 AAGTAAACAATAAAACAAATATAGTACC
5233 AAG
1 AAG
5236 GAAATATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTACC
Found at i:5296 original size:14 final size:14
Alignment explanation
Indices: 5277--5306 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5267 TATATTATTG
5277 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
5291 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
5305 AC
1 AC
5307 AATCAACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (14 bp):
ACTTGTTCTTTCTC
Found at i:9187 original size:18 final size:18
Alignment explanation
Indices: 9160--9195 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9150 GTGAAGTATG
9160 AATGGCGTTGTCGTGGCA
1 AATGGCGTTGTCGTGGCA
* *
9178 AATGGTGTTGTTGTGGCA
1 AATGGCGTTGTCGTGGCA
9196 GAGTGTAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.39, T:0.33
Consensus pattern (18 bp):
AATGGCGTTGTCGTGGCA
Found at i:15635 original size:18 final size:18
Alignment explanation
Indices: 15592--15629 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15582 GTGAAGTATG
*
15592 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
15610 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
15628 AA
1 AA
15630 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:20642 original size:17 final size:17
Alignment explanation
Indices: 20622--20655 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20612 ATTTTGACTG
*
20622 TTGACATGCGTTGACCA
1 TTGACAGGCGTTGACCA
*
20639 TTGACCGGCGTTGACCA
1 TTGACAGGCGTTGACCA
20656 CAGTTGACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (17 bp):
TTGACAGGCGTTGACCA
Found at i:23146 original size:48 final size:49
Alignment explanation
Indices: 23116--23243 Score: 136
Period size: 48 Copynumber: 2.7 Consensus size: 49
23106 TTGATTTATG
23116 ATCTGATACTTGACATGGATTCTGATCTGA-TATCTGACATGGATTCTA
1 ATCTGATACTTGACATGGATTCTGATCTGATTATCTGACATGGATTCTA
* * * * *
23164 ATCTGATACTTGACTTGGATTCTGATTTGA-TA-CTTGACCTGGATTTTG
1 ATCTGATACTTGACATGGATTCTGATCTGATTATC-TGACATGGATTCTA
* * * * *
23212 ATATGATACTTGACGTGAATTATGATTTGATT
1 ATCTGATACTTGACATGGATTCTGATCTGATT
23244 TTTGATATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.01
48 67 0.97
49 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (49 bp):
ATCTGATACTTGACATGGATTCTGATCTGATTATCTGACATGGATTCTA
Found at i:23242 original size:24 final size:24
Alignment explanation
Indices: 23114--23225 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
23104 ATTTGATTTA
23114 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
23138 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
* *
23162 TAATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
23186 TGATTTGATACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTC
*
23210 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
23226 GTGAATTATG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 77 0.97
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:23448 original size:2 final size:2
Alignment explanation
Indices: 23441--23465 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23431 CAGATGGGGG
23441 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 T
23466 TTTAAAAAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27897 original size:48 final size:49
Alignment explanation
Indices: 27859--27994 Score: 161
Period size: 48 Copynumber: 2.8 Consensus size: 49
27849 TTTTCGATTT
27859 GATTTCTGATCTGATACTTGACATGGATTCTGATCTGA-TAGCTGACTTG
1 GATTT-TGATCTGATACTTGACATGGATTCTGATCTGATTAGCTGACTTG
* * *
27908 GATTTTGATCTGATACTTGACTTGGATTCTGATCTGA-TA-CTTGACCTA
1 GATTTTGATCTGATACTTGACATGGATTCTGATCTGATTAGC-TGACTTG
* * * * *
27956 GATTTTGATATGATACTTGACGTGAATTATGATTTGATT
1 GATTTTGATCTGATACTTGACATGGATTCTGATCTGATT
27995 TTTGATATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.01
48 70 0.91
49 6 0.08
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (49 bp):
GATTTTGATCTGATACTTGACATGGATTCTGATCTGATTAGCTGACTTG
Found at i:27993 original size:24 final size:24
Alignment explanation
Indices: 27862--27976 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
27852 TCGATTTGAT
*
27862 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACTTGGA
27886 TTCTGATCTGATAGC-TGACTTGGA
1 TTCTGATCTGATA-CTTGACTTGGA
*
27910 TTTTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACTTGGA
* *
27934 TTCTGATCTGATACTTGACCTAGA
1 TTCTGATCTGATACTTGACTTGGA
* *
27958 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
27977 GTGAATTATG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACTTGGA
Found at i:29501 original size:2 final size:2
Alignment explanation
Indices: 29494--29523 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29484 TAATTTCACA
29494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29524 TCTCTCGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31932 original size:38 final size:38
Alignment explanation
Indices: 31879--31963 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 38
31869 AAGATGCTGT
*
31879 TTTGGGTTTGGGTAAGAGTTGAATCCTGGAAAATAGGC
1 TTTGGGTTTGAGTAAGAGTTGAATCCTGGAAAATAGGC
*
31917 TTTGGGTTTGAGTAAGAGTTGAATCCTGGAAAATAGGT
1 TTTGGGTTTGAGTAAGAGTTGAATCCTGGAAAATAGGC
31955 TTTGGGTTT
1 TTTGGGTTT
31964 TAAAGTAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.25, C:0.06, G:0.33, T:0.36
Consensus pattern (38 bp):
TTTGGGTTTGAGTAAGAGTTGAATCCTGGAAAATAGGC
Found at i:40548 original size:6 final size:6
Alignment explanation
Indices: 40537--40585 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
40527 CTAAAACATA
*
40537 ATAATT ATAATT ATAA-T -TAATT ATATTT ATAATT A-AA-T ATAATT
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT
40581 ATAAT
1 ATAAT
40586 GAGTCATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 5 0.14
5 6 0.16
6 26 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATAATT
Found at i:40559 original size:10 final size:11
Alignment explanation
Indices: 40537--40585 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
40527 CTAAAACATA
40537 ATAATTATAATT
1 ATAA-TATAATT
40549 ATAAT-TAATT
1 ATAATATAATT
*
40559 ATATTTATAATT
1 ATA-ATATAATT
40571 A-AATATAATT
1 ATAATATAATT
40581 ATAAT
1 ATAAT
40586 GAGTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 16 0.50
11 6 0.19
12 10 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATAATATAATT
Found at i:40559 original size:16 final size:16
Alignment explanation
Indices: 40534--40585 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
40524 ATACTAAAAC
40534 ATAA-TAATTATAATT
1 ATAATTAATTATAATT
*
40549 ATAATTAATTATATTT
1 ATAATTAATTATAATT
*
40565 ATAATTAAATATAATT
1 ATAATTAATTATAATT
40581 ATAAT
1 ATAAT
40586 GAGTCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATTAATTATAATT
Found at i:40567 original size:22 final size:22
Alignment explanation
Indices: 40541--40583 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40531 AACATAATAA
40541 TTATAATTATAAT-TAATTATAT
1 TTATAATTA-AATATAATTATAT
40563 TTATAATTAAATATAATTATA
1 TTATAATTAAATATAATTATA
40584 ATGAGTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATAATTAAATATAATTATAT
Found at i:42742 original size:34 final size:34
Alignment explanation
Indices: 42699--42767 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
42689 GAGTATGTTT
42699 ATTAATCTTCAATTAGCATCTTATTTCCGATCAG
1 ATTAATCTTCAATTAGCATCTTATTTCCGATCAG
42733 ATTAATCTTCAATTAGCATCTTATTTCCGATCAG
1 ATTAATCTTCAATTAGCATCTTATTTCCGATCAG
42767 A
1 A
42768 AACACCAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (34 bp):
ATTAATCTTCAATTAGCATCTTATTTCCGATCAG
Found at i:44718 original size:16 final size:16
Alignment explanation
Indices: 44689--44752 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
44679 AATTTTCATT
* * *
44689 GAACCAAAAACAACTC
1 GAACCGAAAGCAACCC
44705 GAACCGAAAGCAACCC
1 GAACCGAAAGCAACCC
* *
44721 GAATCGAAATCAACCC
1 GAACCGAAAGCAACCC
* *
44737 GGACTGAAAGCAACCC
1 GAACCGAAAGCAACCC
44753 AAACAGAGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.45, C:0.33, G:0.16, T:0.06
Consensus pattern (16 bp):
GAACCGAAAGCAACCC
Found at i:44858 original size:3 final size:3
Alignment explanation
Indices: 44850--44892 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
44840 AATGAATAAT
* * * *
44850 TTA TTA TTA TTA TTA TTA TAA TCA TTA TCA TTA ATA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
44893 CTTTTTTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:47167 original size:6 final size:6
Alignment explanation
Indices: 47156--47190 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
47146 GAAAGATAAT
*
47156 ATATAC ATATAC ATATAC ATATAC ATAAAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
47191 AACAACTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (6 bp):
ATATAC
Found at i:48811 original size:17 final size:17
Alignment explanation
Indices: 48789--48822 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
48779 AAATACTAAA
48789 ACTTTGTTTTTTATTTT
1 ACTTTGTTTTTTATTTT
48806 ACTTTGTTTTTTATTTT
1 ACTTTGTTTTTTATTTT
48823 GATTAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (17 bp):
ACTTTGTTTTTTATTTT
Found at i:48888 original size:23 final size:22
Alignment explanation
Indices: 48840--48888 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
48830 TAACATGGTA
*
48840 TTTTAATATTTAATCTCCATTT
1 TTTTAATATTTAATCTCCATTC
* * *
48862 TTTTATTATTTAAATTTTCATTC
1 TTTTAATATTT-AATCTCCATTC
48885 TTTT
1 TTTT
48889 TTAATCTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTAATATTTAATCTCCATTC
Found at i:50103 original size:39 final size:39
Alignment explanation
Indices: 50040--50191 Score: 178
Period size: 39 Copynumber: 3.9 Consensus size: 39
50030 ACCTAACAGA
* *
50040 TTACCGCAAGCTCCTCTACTTTGTGCTCAGGGTAAGTCC
1 TTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAAGTCC
* * * *
50079 TTACTGCATGCTCCTCTACTTTGTGCACAGGATAAGACC
1 TTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAAGTCC
* ** * *
50118 TTACCGCAGGTTCCTCGGCTTTGTGCTCAGGGTAAATCC
1 TTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAAGTCC
** *
50157 TTACTACAGGCTCATCTACTTTGTGCACAGGGTAA
1 TTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAA
50192 ACTCTTACTG
Statistics
Matches: 92, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 92 1.00
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (39 bp):
TTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAAGTCC
Found at i:50199 original size:78 final size:78
Alignment explanation
Indices: 50040--50187 Score: 224
Period size: 78 Copynumber: 1.9 Consensus size: 78
50030 ACCTAACAGA
* * * * *
50040 TTACCGCAAGCTCCTCTACTTTGTGCTCAGGGTAAGTCCTTACTGCATGCTCCTCTACTTTGTGC
1 TTACCGCAAGCTCCTCGACTTTGTGCTCAGGGTAAATCCTTACTACAGGCTCATCTACTTTGTGC
50105 ACAGGATAAGACC
66 ACAGGATAAGACC
* * *
50118 TTACCGCAGGTTCCTCGGCTTTGTGCTCAGGGTAAATCCTTACTACAGGCTCATCTACTTTGTGC
1 TTACCGCAAGCTCCTCGACTTTGTGCTCAGGGTAAATCCTTACTACAGGCTCATCTACTTTGTGC
50183 ACAGG
66 ACAGG
50188 GTAAACTCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (78 bp):
TTACCGCAAGCTCCTCGACTTTGTGCTCAGGGTAAATCCTTACTACAGGCTCATCTACTTTGTGC
ACAGGATAAGACC
Found at i:50567 original size:2 final size:2
Alignment explanation
Indices: 50551--50587 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
50541 CGATTTTCTG
* *
50551 AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50588 AATTTATCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56820 original size:39 final size:38
Alignment explanation
Indices: 56777--56973 Score: 157
Period size: 39 Copynumber: 5.1 Consensus size: 38
56767 GACCTTACCG
*
56777 CTTACCACAGGCTCCTTAGCTTTGTGCTCAGGGTAAGTC
1 CTTACCGCAGGCTCCTT-GCTTTGTGCTCAGGGTAAGTC
* * * * *
56816 CTTACTGCAGGCTCATCTGCTTTGTGCACAAGATAA-TAC
1 CTTACCGCAGGCTCCT-TGCTTTGTGCTCAGGGTAAGT-C
* * *
56855 CTTACCACAGGTTCCTCAGCTTTGTGCTCAGGGTAAGTC
1 CTTACCGCAGGCTCCT-TGCTTTGTGCTCAGGGTAAGTC
* * * *
56894 CTTACTGCAGGCTCATCTGCTTTGTGCAT-AGGATAAGAC
1 CTTACCGCAGGCTCCT-TGCTTTGTGC-TCAGGGTAAGTC
** * *
56933 CTTACCGCAAACTCTTCTGCTTTGTGCACAGGGTAAG-C
1 CTTACCGCAGGCTCCT-TGCTTTGTGCTCAGGGTAAGTC
56971 CTT
1 CTT
56974 TACTGGGTGT
Statistics
Matches: 126, Mismatches: 27, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
38 5 0.04
39 118 0.94
40 3 0.02
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (38 bp):
CTTACCGCAGGCTCCTTGCTTTGTGCTCAGGGTAAGTC
Found at i:56906 original size:78 final size:78
Alignment explanation
Indices: 56777--56978 Score: 289
Period size: 78 Copynumber: 2.6 Consensus size: 78
56767 GACCTTACCG
*
56777 CTTACCACAGGCTCCTTAGCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCTGCTTTGTG
1 CTTACCACAGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCTGCTTTGTG
*
56842 CACAAGATAATAC
66 CACAAGATAAGAC
*
56855 CTTACCACAGGTTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCTGCTTTGTG
1 CTTACCACAGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCTGCTTTGTG
* *
56920 CATAGGATAAGAC
66 CACAAGATAAGAC
* ** * * *
56933 CTTACCGCAAACTCTTCTGCTTTGTGCACAGGGTAAG-CCTTTACTG
1 CTTACCACAGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCC-TTACTG
56979 GGTGTACAGG
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
77 2 0.02
78 109 0.98
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (78 bp):
CTTACCACAGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCTGCTTTGTG
CACAAGATAAGAC
Found at i:63265 original size:33 final size:33
Alignment explanation
Indices: 63223--63288 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
63213 TTAGAACTTA
63223 GAATTGGTTACATTTTTGTTTGAGATTGGTCAG
1 GAATTGGTTACATTTTTGTTTGAGATTGGTCAG
63256 GAATTGGTTACATTTTTGTTTGAGATTGGTCAG
1 GAATTGGTTACATTTTTGTTTGAGATTGGTCAG
63289 TTGTAGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.06, G:0.27, T:0.45
Consensus pattern (33 bp):
GAATTGGTTACATTTTTGTTTGAGATTGGTCAG
Found at i:64839 original size:15 final size:15
Alignment explanation
Indices: 64819--64849 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
64809 TCGTTAGGGT
64819 TATATCTCAATTAAC
1 TATATCTCAATTAAC
64834 TATATCTCAATTAAC
1 TATATCTCAATTAAC
64849 T
1 T
64850 GGCTTGCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (15 bp):
TATATCTCAATTAAC
Found at i:70627 original size:20 final size:20
Alignment explanation
Indices: 70593--70641 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
70583 AATGATTTTC
* * *
70593 TTTTG-AAAGCAAAATTAGA
1 TTTTGAAAAACAAAATGAAA
70612 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATGAAA
70632 TTTTGAAAAA
1 TTTTGAAAAA
70642 TAATTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAA
Found at i:72256 original size:11 final size:11
Alignment explanation
Indices: 72240--72274 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
72230 AATTAGGTCC
72240 TTATTTTATGT
1 TTATTTTATGT
*
72251 TTATTTTATTT
1 TTATTTTATGT
*
72262 TTATTCTATGT
1 TTATTTTATGT
72273 TT
1 TT
72275 TTACTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (11 bp):
TTATTTTATGT
Found at i:72293 original size:18 final size:19
Alignment explanation
Indices: 72254--72294 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
72244 TTTATGTTTA
*
72254 TTTTATTTTTATTCTATGT
1 TTTTATTTTTATTCTATAT
72273 TTTTACTTTTT-TT-TATAT
1 TTTTA-TTTTTATTCTATAT
72291 TTTT
1 TTTT
72295 TATTATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
19 7 0.35
20 5 0.25
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTATTTTTATTCTATAT
Found at i:72294 original size:19 final size:19
Alignment explanation
Indices: 72254--72298 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
72244 TTTATGTTTA
*
72254 TTTTATTTTTATTCTATGT
1 TTTTATTTTTATTATATGT
*
72273 TTTTACTTTTTTTTATAT-T
1 TTTTA-TTTTTATTATATGT
72292 TTTTATT
1 TTTTATT
72299 ATTTGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 10 0.43
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTATTTTTATTATATGT
Found at i:72966 original size:11 final size:11
Alignment explanation
Indices: 72950--72984 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
72940 AATTAGGTCC
72950 TTATTTTATGT
1 TTATTTTATGT
*
72961 TTATTTTATTT
1 TTATTTTATGT
*
72972 TTATTCTATGT
1 TTATTTTATGT
72983 TT
1 TT
72985 TTACTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (11 bp):
TTATTTTATGT
Found at i:73232 original size:710 final size:710
Alignment explanation
Indices: 71831--73251 Score: 2747
Period size: 710 Copynumber: 2.0 Consensus size: 710
71821 ACGCGTAACA
*
71831 AAAAGGTCACTGCAGGGACTGTTTTTATGATTTTAGCATTTCTGTCCATGCCTTATATTTTTTAG
1 AAAAGGTCACTGCAGGGACTGTTTTTATGATTTTAGCATTTCTGTCCATGCCTTATATGTTTTAG
71896 TCTAATTTTCTTTTAGTCCCCCTACTTTTAGTGTGTTCTTGCACTTTGGTCATGTGTAGTGACCT
66 TCTAATTTTCTTTTAGTCCCCCTACTTTTAGTGTGTTCTTGCACTTTGGTCATGTGTAGTGACCT
* *
71961 TTTAATTTTTTTAAACATTTGTGGACTGATTTTGTAATTTTTCCTTTTTATTTTAACATATTGTT
131 TTTAATTTTTTAAAAAATTTGTGGACTGATTTTGTAATTTTTCCTTTTTATTTTAACATATTGTT
* * *
72026 TAGGCTTAAATAAATGTTATAATTTCCTTTTTGTCCTTGTAACTTCTGCGTGGTTTTACATTTTT
196 TAGGCTTAAATAAATGTTATAATTTCCTTTTGGTCCCTGTAACTTCCGCGTGGTTTTACATTTTT
72091 ATCCCTAAATCTATTTTTTAATTTTATTTCGAATTAGACTTTAAATTTTAATTTATTTTAATTTG
261 ATCCCTAAATCTATTTTTTAATTTTATTTCGAATTAGACTTTAAATTTTAATTTATTTTAATTTG
72156 GCCACTGTTTATTTTTGATATAGCTATTAACTTTATTTTCTTGCATTTTAGTCATTGTTATTTAA
326 GCCACTGTTTATTTTTGATATAGCTATTAACTTTATTTTCTTGCATTTTAGTCATTGTTATTTAA
72221 TATTTATGCAATTAGGTCCTTATTTTATGTTTATTTTATTTTTATTCTATGTTTTTACTTTTTTT
391 TATTTATGCAATTAGGTCCTTATTTTATGTTTATTTTATTTTTATTCTATGTTTTTACTTTTTTT
72286 TATATTTTTTATTATTTGTTGGTTTTTTAATTATGTTTTAAATTGTTTTATTTCGTAATTTAATT
456 TATATTTTTTATTATTTGTTGGTTTTTTAATTATGTTTTAAATTGTTTTATTTCGTAATTTAATT
*
72351 CTAGATTTAGTTTTTAAATTAGATTAATATTCGAATCAAACTTAGAAATTAGGATTTCACATTAA
521 ATAGATTTAGTTTTTAAATTAGATTAATATTCGAATCAAACTTAGAAATTAGGATTTCACATTAA
72416 TTTTAATTAGGGAGCAATTCGAGTCGAGTTTTCACAATAGATGTCCGATTACTCGAATTTATTGC
586 TTTTAATTAGGGAGCAATTCGAGTCGAGTTTTCACAATAGATGTCCGATTACTCGAATTTATTGC
72481 TCGATTTTTAAAGTTTATTAATAATTAATATTTTCAAAAAAAATAAACTTTAGGTTTAAT
651 TCGATTTTTAAAGTTTATTAATAATTAATATTTTCAAAAAAAATAAACTTTAGGTTTAAT
72541 AAAAGGTCACTGCAGGGACTGTTTTTATGATTTTAGCATTTCTGTCCATGCCTTATATGTTTTAG
1 AAAAGGTCACTGCAGGGACTGTTTTTATGATTTTAGCATTTCTGTCCATGCCTTATATGTTTTAG
72606 TCTAATTTTCTTTTAGTCCCCCTACTTTTAGTGTGTTCTTGCACTTTGGTCATGTGTAGTGACCT
66 TCTAATTTTCTTTTAGTCCCCCTACTTTTAGTGTGTTCTTGCACTTTGGTCATGTGTAGTGACCT
72671 TTTAATTTTTTAAAAAAATTTGTGGACTGA-TTTGTAATTTTTCCTTTTTATTTTAACATATTGT
131 TTTAATTTTTT-AAAAAATTTGTGGACTGATTTTGTAATTTTTCCTTTTTATTTTAACATATTGT
72735 TTAGGCTTAAATAAATGTTATAATTTCCTTTTGGTCCCTGTAACTTCCGCGTGGTTTTACATTTT
195 TTAGGCTTAAATAAATGTTATAATTTCCTTTTGGTCCCTGTAACTTCCGCGTGGTTTTACATTTT
72800 TATCCCTAAATCTATTTTTTAATTTTATTTCGAATTAGACTTTAAATTTTAATTTATTTTAATTT
260 TATCCCTAAATCTATTTTTTAATTTTATTTCGAATTAGACTTTAAATTTTAATTTATTTTAATTT
72865 GGCCACTGTTTATTTTTGATATAGCTATTAACTTTATTTTCTTGCATTTTAGTCATTGTTATTTA
325 GGCCACTGTTTATTTTTGATATAGCTATTAACTTTATTTTCTTGCATTTTAGTCATTGTTATTTA
72930 ATATTTATGCAATTAGGTCCTTATTTTATGTTTATTTTATTTTTATTCTATGTTTTTAC-TTTTT
390 ATATTTATGCAATTAGGTCCTTATTTTATGTTTATTTTATTTTTATTCTATGTTTTTACTTTTTT
72994 TTATATTTTTTATTATTTGTTGGTTTTTTAATTATGTTTTAAATTGTTTTATTTCGTAATTTAAT
455 TTATATTTTTTATTATTTGTTGGTTTTTTAATTATGTTTTAAATTGTTTTATTTCGTAATTTAAT
73059 TATAGATTTAGTTTTTAAATTAGATTAATATTCGAATCAAACTTAGAAATTAGGATTTCACATTA
520 TATAGATTTAGTTTTTAAATTAGATTAATATTCGAATCAAACTTAGAAATTAGGATTTCACATTA
*
73124 GTTTTAATTAGGGAGCAATTCGAGTCGAGTTTTCACAATAGATGTCCGATTACTCGAATTTATTG
585 ATTTTAATTAGGGAGCAATTCGAGTCGAGTTTTCACAATAGATGTCCGATTACTCGAATTTATTG
73189 CTCGATTTTTAAAGTTTATTAATAATTAATATTTTCAAAAAAAATAAACTTTAGGTTTAAT
650 CTCGATTTTTAAAGTTTATTAATAATTAATATTTTCAAAAAAAATAAACTTTAGGTTTAAT
73250 AA
1 AA
73252 TTTAGATAAA
Statistics
Matches: 702, Mismatches: 8, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
709 261 0.37
710 425 0.61
711 16 0.02
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (710 bp):
AAAAGGTCACTGCAGGGACTGTTTTTATGATTTTAGCATTTCTGTCCATGCCTTATATGTTTTAG
TCTAATTTTCTTTTAGTCCCCCTACTTTTAGTGTGTTCTTGCACTTTGGTCATGTGTAGTGACCT
TTTAATTTTTTAAAAAATTTGTGGACTGATTTTGTAATTTTTCCTTTTTATTTTAACATATTGTT
TAGGCTTAAATAAATGTTATAATTTCCTTTTGGTCCCTGTAACTTCCGCGTGGTTTTACATTTTT
ATCCCTAAATCTATTTTTTAATTTTATTTCGAATTAGACTTTAAATTTTAATTTATTTTAATTTG
GCCACTGTTTATTTTTGATATAGCTATTAACTTTATTTTCTTGCATTTTAGTCATTGTTATTTAA
TATTTATGCAATTAGGTCCTTATTTTATGTTTATTTTATTTTTATTCTATGTTTTTACTTTTTTT
TATATTTTTTATTATTTGTTGGTTTTTTAATTATGTTTTAAATTGTTTTATTTCGTAATTTAATT
ATAGATTTAGTTTTTAAATTAGATTAATATTCGAATCAAACTTAGAAATTAGGATTTCACATTAA
TTTTAATTAGGGAGCAATTCGAGTCGAGTTTTCACAATAGATGTCCGATTACTCGAATTTATTGC
TCGATTTTTAAAGTTTATTAATAATTAATATTTTCAAAAAAAATAAACTTTAGGTTTAAT
Found at i:84847 original size:13 final size:13
Alignment explanation
Indices: 84829--84863 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
84819 TTGCATCTCG
84829 CATTTTGCACACC
1 CATTTTGCACACC
84842 CATTTTGCACACC
1 CATTTTGCACACC
84855 CATTTTGCA
1 CATTTTGCA
84864 TTTGCATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (13 bp):
CATTTTGCACACC
Found at i:88050 original size:29 final size:29
Alignment explanation
Indices: 88016--88083 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
88006 TTATGAAAAA
88016 TGACATGAATTCATATTATATGCATTATG
1 TGACATGAATTCATATTATATGCATTATG
88045 TGACATGAATTCATATTATATGCATTATG
1 TGACATGAATTCATATTATATGCATTATG
88074 TGACATGAAT
1 TGACATGAAT
88084 ATGCAGGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (29 bp):
TGACATGAATTCATATTATATGCATTATG
Found at i:89032 original size:22 final size:21
Alignment explanation
Indices: 89006--89052 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
88996 TACGGAAGTA
*
89006 CTGTAGCAGGGGAATCAGTACC
1 CTGTAGC-GGAGAATCAGTACC
* *
89028 CTGTAGCTGAGAATCAGTTCC
1 CTGTAGCGGAGAATCAGTACC
89049 CTGT
1 CTGT
89053 TTGCAATCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (21 bp):
CTGTAGCGGAGAATCAGTACC
Found at i:91437 original size:73 final size:73
Alignment explanation
Indices: 91339--91512 Score: 276
Period size: 73 Copynumber: 2.4 Consensus size: 73
91329 ATTATTTTTC
* * * * *
91339 TTTAAAACCAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAATAAGATATTTCATTTCACTCA
1 TTTAAAACAAGATTTATCTCTCTTGAGACAATTTTTACTCGAAAGAAGACATTTCATTTCACTCA
91404 AGATTGTT
66 AGATTGTT
* *
91412 TTTAAAACAAGATTTATCTCTCTTGAGACAGTTTTTACTCGAAAGAATACATTTCATTTCACTCA
1 TTTAAAACAAGATTTATCTCTCTTGAGACAATTTTTACTCGAAAGAAGACATTTCATTTCACTCA
91477 AGATTGTT
66 AGATTGTT
*
91485 TTTAAAACAAGAATTATCTCTCTTGAGA
1 TTTAAAACAAGATTTATCTCTCTTGAGA
91513 TTGTTTCACT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 93 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (73 bp):
TTTAAAACAAGATTTATCTCTCTTGAGACAATTTTTACTCGAAAGAAGACATTTCATTTCACTCA
AGATTGTT
Found at i:91549 original size:39 final size:39
Alignment explanation
Indices: 91498--91751 Score: 336
Period size: 39 Copynumber: 6.5 Consensus size: 39
91488 AAAACAAGAA
* **
91498 TTATCTCTCTTGAGATTGTTTCACTTAAAACAGAAGATT
1 TTATCTCACTTGAGATTGTTTCACTCGAAACAGAAGATT
* *
91537 TCATCTCACTTGAGATAT-TTTCACTTGAAACAGAAGATT
1 TTATCTCACTTGAGAT-TGTTTCACTCGAAACAGAAGATT
* * *
91576 TTATCTCGCTTGTA-ATAGTTTCACTCGAAACATAAGATT
1 TTATCTCACTTG-AGATTGTTTCACTCGAAACAGAAGATT
* *
91615 TTATCTCTCTTGAGATTGTTTCACTCGAAAAAGAAGATT
1 TTATCTCACTTGAGATTGTTTCACTCGAAACAGAAGATT
*
91654 TTATCTCCCTTGAGATTGTTTCACTCGAAACAGAAGATT
1 TTATCTCACTTGAGATTGTTTCACTCGAAACAGAAGATT
* *
91693 TTATCTCGCTTGAGATAT-TTTCACTCGAAACTGAAGA-T
1 TTATCTCACTTGAGAT-TGTTTCACTCGAAACAGAAGATT
91731 TTATCTCACTTGAGATTGTTT
1 TTATCTCACTTGAGATTGTTT
91752 TTCTTAAAAC
Statistics
Matches: 192, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.01
38 20 0.10
39 168 0.88
40 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (39 bp):
TTATCTCACTTGAGATTGTTTCACTCGAAACAGAAGATT
Found at i:91632 original size:117 final size:116
Alignment explanation
Indices: 91493--91762 Score: 386
Period size: 117 Copynumber: 2.3 Consensus size: 116
91483 TTTTTAAAAC
*
91493 AAGAATTATCTCTCTTGAGATTGTTTCACTTAAAACAGAAGATTTCATCTCACTTGAGATAT-TT
1 AAGATTTATCTCTCTTGAGATTGTTTCACTTAAAACAGAAGATTTCATCTCACTTGAGAT-TGTT
*
91557 TCACTTGAAACAGAAGATTTTATCTCGCTTGTA-ATAGTTTCACTCGAAACAT-
65 TCACTCGAAACAGAAGATTTTATCTCGCTTG-AGATAGTTTCACTCGAAAC-TG
* * *
91609 AAGATTTTATCTCTCTTGAGATTGTTTCACTCGAAAA-AGAAGATTTTATCTCCCTTGAGATTGT
1 AAGA-TTTATCTCTCTTGAGATTGTTTCACT-TAAAACAGAAGATTTCATCTCACTTGAGATTGT
*
91673 TTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATATTTTCACTCGAAACTG
64 TTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACTG
* **
91726 AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AAGATTTATCTCTCTTGAGATTGTTTCACTTAAAACA
91763 AACTATGCCT
Statistics
Matches: 138, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
115 4 0.03
116 31 0.22
117 99 0.72
118 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (116 bp):
AAGATTTATCTCTCTTGAGATTGTTTCACTTAAAACAGAAGATTTCATCTCACTTGAGATTGTTT
CACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACTG
Found at i:92123 original size:135 final size:135
Alignment explanation
Indices: 91772--92128 Score: 418
Period size: 135 Copynumber: 2.6 Consensus size: 135
91762 AAACTATGCC
* * * *
91772 TCGCTTGAGGGATTAACATTTCAAATGAAGAGTTCATAATGAGAAGAACTCGTTCGACAGAGGGA
1 TCGCTTAAGGTATT-ACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATTCGACAGAGGGA
* * *** *
91837 GAAGAAGTTCATAATGAGAA-AGCTTGTTCGACCTATGGCTCGATTAACGTTATTTCAAATCAGC
65 GAAGAAGTTCATAATGAGAAGAGCATGTTCAACCTATGGCTCGATTAACAACACTTCAAATCAGC
*
91901 GACACA
130 AACACA
* *
91907 TTGCTTAAGGTATTATCATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGA
1 TCGCTTAAGGTATTA-CATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATTCGACAGAGGGA
* * *
91972 GAAGAAGTTCATAATGAGAAGAGCATGTTCAACCTATTGCTCGATTCACAACACTTCGAATCAGC
65 GAAGAAGTTCATAATGAGAAGAGCATGTTCAACCTATGGCTCGATTAACAACACTTCAAATCAGC
*
92037 AACACC
130 AACACA
* ** * *
92043 TCGCTTGATGG-ATTGA-AGTTTCCGATGGAGAGGTCATAATGAGAAGAACACATTC-A-ATGAG
1 TCGCTT-AAGGTATT-ACA-TTTCAAATGGAGAGTTCATAATGAGAAGAACTCATTCGACA-GAG
*
92104 TGAGAAGAAGTTCATAATGAGAAGA
62 GGAGAAGAAGTTCATAATGAGAAGA
92129 ACTTGTCCAA
Statistics
Matches: 191, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
134 2 0.01
135 106 0.55
136 79 0.41
137 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (135 bp):
TCGCTTAAGGTATTACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATTCGACAGAGGGAG
AAGAAGTTCATAATGAGAAGAGCATGTTCAACCTATGGCTCGATTAACAACACTTCAAATCAGCA
ACACA
Found at i:92750 original size:19 final size:19
Alignment explanation
Indices: 92728--92785 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
92718 TTCTTCATTA
92728 TATTTCGAAGGCATCATAT
1 TATTTCGAAGGCATCATAT
92747 TATTTCGAAGGCATCATAT
1 TATTTCGAAGGCATCATAT
92766 TATTTCGAAGGCATCATAT
1 TATTTCGAAGGCATCATAT
92785 T
1 T
92786 TGAACACCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (19 bp):
TATTTCGAAGGCATCATAT
Found at i:97593 original size:30 final size:30
Alignment explanation
Indices: 97529--97586 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
97519 AGTCTGGCAA
* * *
97529 TGAACTGGCTGAAAACCGGTAAAACCGGGG
1 TGAACTGACTGAAAACCGGCAAAACCAGGG
97559 TGAACTGACTGAAAACCGGCAAAACCAG
1 TGAACTGACTGAAAACCGGCAAAACCAG
97587 TTTGAACCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (30 bp):
TGAACTGACTGAAAACCGGCAAAACCAGGG
Found at i:103209 original size:3 final size:3
Alignment explanation
Indices: 103196--103264 Score: 95
Period size: 3 Copynumber: 22.3 Consensus size: 3
103186 TATTAATTGT
*
103196 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA ATA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
103243 TTAA TTA TTA -TA TTA TTA TTA T
1 TT-A TTA TTA TTA TTA TTA TTA T
103265 AAATAAATAC
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.03
3 49 0.82
4 9 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:103217 original size:16 final size:15
Alignment explanation
Indices: 103196--103264 Score: 95
Period size: 16 Copynumber: 4.5 Consensus size: 15
103186 TATTAATTGT
103196 TTATTATTTATTATTA
1 TTATTA-TTATTATTA
103212 TTATTATTATTATTA
1 TTATTATTATTATTA
*
103227 TTAATTAATATTATTA
1 TT-ATTATTATTATTA
103243 TTAATTATTA-TATTA
1 TT-ATTATTATTATTA
103258 TTATTAT
1 TTATTAT
103265 AAATAAATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
14 5 0.10
15 18 0.36
16 27 0.54
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTATTATTATTA
Done.