Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008085.1 Hibiscus syriacus cultivar Beakdansim tig00110594_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: 57706
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3085 original size:14 final size:14
Alignment explanation
Indices: 3053--3180 Score: 77
Period size: 13 Copynumber: 9.9 Consensus size: 14
3043 CAAGTCACAA
*
3053 CAAAGA-AAAAAAG
1 CAAAGAGAAAGAAG
*
3066 CAAAGAGCAAATAA-
1 CAAAGAG-AAAGAAG
3080 CAAAGAGAAAGAAG
1 CAAAGAGAAAGAAG
*
3094 CAAAGAGAAAACAAG
1 CAAAGAG-AAAGAAG
3109 AACAAAGAG--A-AA-
1 --CAAAGAGAAAGAAG
*
3121 -AAAGA-AAAGAAA
1 CAAAGAGAAAGAAG
3133 CAAAGAGAAA-AAG
1 CAAAGAGAAAGAAG
3146 CAAAGA-AAAGAA-
1 CAAAGAGAAAGAAG
3158 CAAA-AGAAA-AA-
1 CAAAGAGAAAGAAG
*
3169 CAAAGAAAAAGA
1 CAAAGAGAAAGA
3181 TAGGACAAGA
Statistics
Matches: 94, Mismatches: 5, Indels: 32
0.72 0.04 0.24
Matches are distributed among these distances:
9 5 0.05
10 1 0.01
11 9 0.10
12 14 0.15
13 29 0.31
14 18 0.19
15 11 0.12
17 7 0.07
ACGTcount: A:0.73, C:0.09, G:0.18, T:0.01
Consensus pattern (14 bp):
CAAAGAGAAAGAAG
Found at i:3122 original size:18 final size:18
Alignment explanation
Indices: 3088--3126 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
3078 AACAAAGAGA
3088 AAGAAGCAAAGAGAAAAC
1 AAGAAGCAAAGAGAAAAC
3106 AAGAA-CAAAGAGAAAA-
1 AAGAAGCAAAGAGAAAAC
3122 AAGAA
1 AAGAA
3127 AAGAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
18 5 0.24
ACGTcount: A:0.72, C:0.08, G:0.21, T:0.00
Consensus pattern (18 bp):
AAGAAGCAAAGAGAAAAC
Found at i:3136 original size:22 final size:21
Alignment explanation
Indices: 3109--3153 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
3099 AGAAAACAAG
3109 AACAAAGAGAAAAAAGAAAAGA
1 AACAAAGAGAAA-AAGAAAAGA
*
3131 AACAAAGAGAAAAAGCAAAGA
1 AACAAAGAGAAAAAGAAAAGA
3152 AA
1 AA
3154 AGAACAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.76, C:0.07, G:0.18, T:0.00
Consensus pattern (21 bp):
AACAAAGAGAAAAAGAAAAGA
Found at i:3143 original size:21 final size:22
Alignment explanation
Indices: 3109--3153 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
3099 AGAAAACAAG
3109 AACAAAGAGAAAAAAGAAAAGA
1 AACAAAGAGAAAAAAGAAAAGA
*
3131 AACAAAGAG-AAAAAGCAAAGA
1 AACAAAGAGAAAAAAGAAAAGA
3152 AA
1 AA
3154 AGAACAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.76, C:0.07, G:0.18, T:0.00
Consensus pattern (22 bp):
AACAAAGAGAAAAAAGAAAAGA
Found at i:3163 original size:39 final size:40
Alignment explanation
Indices: 3051--3167 Score: 127
Period size: 39 Copynumber: 3.0 Consensus size: 40
3041 ATCAAGTCAC
* *
3051 AACAAAGAAAAAAAGCAAAGAGCAAATAAC-AAAGAGAAAGA
1 AACAAAGAGAAAAAGCAAAGA-CAAAGAACAAAAGA-AAAGA
* *
3092 AGCAAAGAG-AAAA-C-AAGAACAAAGAGAAAAAAGAAAAGA
1 AACAAAGAGAAAAAGCAAAG-ACAAAGA-ACAAAAGAAAAGA
3131 AACAAAGAGAAAAAGCAAAGA-AAAGAACAAAAGAAAA
1 AACAAAGAGAAAAAGCAAAGACAAAGAACAAAAGAAAA
3168 ACAAAGAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
38 8 0.12
39 26 0.41
40 18 0.28
41 9 0.14
42 3 0.05
ACGTcount: A:0.73, C:0.09, G:0.18, T:0.01
Consensus pattern (40 bp):
AACAAAGAGAAAAAGCAAAGACAAAGAACAAAAGAAAAGA
Found at i:3192 original size:65 final size:67
Alignment explanation
Indices: 3054--3180 Score: 169
Period size: 67 Copynumber: 1.9 Consensus size: 67
3044 AAGTCACAAC
3054 AAAGAAAAAAAGCAAAGAGCAAATAACAAAGAGAAAGAAGCAAAGAGAAAACAAGAACAAAGAGA
1 AAAGAAAAAAAGCAAAGAGCAAATAACAAAGAGAAAGAAGCAAAGAGAAAACAAGAACAAAGAGA
3119 AA
66 AA
3121 AAAGAAAAGAAA-CAAAGAG-AAA-AAGCAAAGA-AAAGAA-CAAA-AGAAAAACAAAGAA-AAA
1 AAAGAAAA-AAAGCAAAGAGCAAATAA-CAAAGAGAAAGAAGCAAAGAG-AAAAC-AAGAACAAA
3179 GA
62 GA
3181 TAGGACAAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
63 2 0.04
64 14 0.25
65 13 0.23
66 9 0.16
67 15 0.27
68 3 0.05
ACGTcount: A:0.73, C:0.08, G:0.18, T:0.01
Consensus pattern (67 bp):
AAAGAAAAAAAGCAAAGAGCAAATAACAAAGAGAAAGAAGCAAAGAGAAAACAAGAACAAAGAGA
AA
Found at i:4429 original size:38 final size:37
Alignment explanation
Indices: 4370--4454 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
4360 CATCTTGCTA
*
4370 GAGACAGTTT-TCTTAAAAACAAATT-TTGTCTCGCTT
1 GAGACATTTTATCTTAAAAACAAATTCTT-TCTCGCTT
*
4406 GAGACAATTTTATCTTTAAAACAAATTCTTTCTCGCTT
1 GAGAC-ATTTTATCTTAAAAACAAATTCTTTCTCGCTT
4444 GAGACATTTTA
1 GAGACATTTTA
4455 CCAAAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 5 0.11
37 10 0.23
38 27 0.61
39 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (37 bp):
GAGACATTTTATCTTAAAAACAAATTCTTTCTCGCTT
Found at i:4483 original size:21 final size:22
Alignment explanation
Indices: 4442--4485 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
4432 TCTTTCTCGC
*
4442 TTGAGACATTTTACCAAAAATT
1 TTGAGACATTTTACAAAAAATT
4464 TTGAGA-ATTTTA-AAACAAATT
1 TTGAGACATTTTACAAA-AAATT
4485 T
1 T
4486 AATCTCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 12 0.60
22 6 0.30
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (22 bp):
TTGAGACATTTTACAAAAAATT
Found at i:4652 original size:36 final size:36
Alignment explanation
Indices: 4606--4692 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 36
4596 TTGAGATCGT
4606 TTTCTC-AAAAACAAACTTTGTCTCGCTT-AAGACAA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAA-ACAA
*
4641 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAAACAA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAAACAA
*
4677 TTTCTTTAAAAA-AAAC
1 TTTCTCTAAAAACAAAC
4693 AATTGTTGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
35 9 0.19
36 36 0.77
37 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (36 bp):
TTTCTCTAAAAACAAACTTTGTCTCGCTTGAAACAA
Found at i:4702 original size:39 final size:36
Alignment explanation
Indices: 4606--4718 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 36
4596 TTGAGATCGT
* *
4606 TTTCTC-AAAAACAAACTTTGTCTCGCTT-AAGACAA
1 TTTCTCTAAAAAAAAATTTTGTCTCGCTTGAA-ACAA
*
4641 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAAACAA
1 TTTCTCTAAAAAAAAATTTTGTCTCGCTTGAAACAA
* * *
4677 TTTCTTTAAAAAAAACAATTGTTGTCTCACTTGAGACAA
1 TTTCTCT-AAAAAAA-AATT-TTGTCTCGCTTGAAACAA
4716 TTT
1 TTT
4719 TCCAATTCTG
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.09
36 31 0.46
37 8 0.12
38 4 0.06
39 19 0.28
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAAAAAATTTTGTCTCGCTTGAAACAA
Found at i:5865 original size:3 final size:3
Alignment explanation
Indices: 5851--5882 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5841 TTATATAATT
*
5851 ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
5883 TATTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:7595 original size:30 final size:30
Alignment explanation
Indices: 7561--7617 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
7551 TTTGTATTTA
*
7561 TTGTTTTAGTACTTTAAAATTTTGTTTATG
1 TTGTTTTAGCACTTTAAAATTTTGTTTATG
* **
7591 TTGTTTTAGCCCTTTAAGTTTTTGTTT
1 TTGTTTTAGCACTTTAAAATTTTGTTT
7618 TTATTAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.18, C:0.07, G:0.14, T:0.61
Consensus pattern (30 bp):
TTGTTTTAGCACTTTAAAATTTTGTTTATG
Found at i:7716 original size:59 final size:60
Alignment explanation
Indices: 7653--7775 Score: 133
Period size: 59 Copynumber: 2.1 Consensus size: 60
7643 AGTTTGTATT
* * * *
7653 TTTTAGCCCTTTAACTTTCTGTAATTAT-TATTTTTATCCCT-AATTTTCTATTTTTTCTA
1 TTTTAGCCCTTTAACTTTCTGT-ATTATCCATTTTGATCCCTGAAGTTTCTATTTTATCTA
** * * * *
7712 TTTTAGTTCTTTAAGTTTTTGTTTTATCCATTTTGGTCCCTGAAGTTTCTATTTTATCTA
1 TTTTAGCCCTTTAACTTTCTGTATTATCCATTTTGATCCCTGAAGTTTCTATTTTATCTA
7772 TTTT
1 TTTT
7776 GTCCCTAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
58 4 0.08
59 28 0.54
60 20 0.38
ACGTcount: A:0.18, C:0.15, G:0.07, T:0.60
Consensus pattern (60 bp):
TTTTAGCCCTTTAACTTTCTGTATTATCCATTTTGATCCCTGAAGTTTCTATTTTATCTA
Found at i:7793 original size:59 final size:58
Alignment explanation
Indices: 7684--7833 Score: 151
Period size: 59 Copynumber: 2.5 Consensus size: 58
7674 TAATTATTAT
* * * * *
7684 TTTTA-TCCCTAATTTTCTATTTTTTCTATTTTAGTTCTTTAAGTTTTTGTTTTATCCA
1 TTTTAGTCCCTAAGTTTCTA-TTTTTCTATTTTAGTCCCTAAAATTTTTGTTTTATCCA
* **
7742 TTTTGGTCCCTGAAGTTTCTATTTTATCTATTTT-GTCCCTAAAATTTTTGTTTTATTTA
1 TTTTAGTCCCT-AAGTTTCTATTTT-TCTATTTTAGTCCCTAAAATTTTTGTTTTATCCA
* *
7801 TTTTAGCCCCTAAAGTTCCTATTTTTGCTATTT
1 TTTTAGTCCCT-AAGTTTCTATTTTT-CTATTT
7834 AGACCTTAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
58 5 0.07
59 55 0.72
60 16 0.21
ACGTcount: A:0.18, C:0.15, G:0.08, T:0.59
Consensus pattern (58 bp):
TTTTAGTCCCTAAGTTTCTATTTTTCTATTTTAGTCCCTAAAATTTTTGTTTTATCCA
Found at i:7795 original size:29 final size:30
Alignment explanation
Indices: 7694--7814 Score: 100
Period size: 30 Copynumber: 4.0 Consensus size: 30
7684 TTTTATCCCT
* * * * *
7694 AATTTTCTATTTTTTCTATTTTAGTTCTTTA
1 AATTTT-TGTTTTATCTATTTTAGTCCCTAA
* * * *
7725 AGTTTTTGTTTTATCCATTTTGGTCCCTGA
1 AATTTTTGTTTTATCTATTTTAGTCCCTAA
* * *
7755 AGTTTCTATTTTATCTATTTT-GTCCCTAA
1 AATTTTTGTTTTATCTATTTTAGTCCCTAA
* *
7784 AATTTTTGTTTTATTTATTTTAGCCCCTAA
1 AATTTTTGTTTTATCTATTTTAGTCCCTAA
7814 A
1 A
7815 GTTCCTATTT
Statistics
Matches: 72, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
29 24 0.33
30 43 0.60
31 5 0.07
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (30 bp):
AATTTTTGTTTTATCTATTTTAGTCCCTAA
Found at i:22721 original size:23 final size:23
Alignment explanation
Indices: 22691--22747 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
22681 TAATAAATTG
22691 AAAAAAAATTATATATTTTCTTT
1 AAAAAAAATTATATATTTTCTTT
22714 AAAAAAAATTATATATTTTCTTT
1 AAAAAAAATTATATATTTTCTTT
22737 AAAAAAAATTA
1 AAAAAAAATTA
22748 ATTCCATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAAAAAATTATATATTTTCTTT
Found at i:24052 original size:35 final size:36
Alignment explanation
Indices: 23975--24057 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 36
23965 CAACACAGTC
*
23975 ATCAATTATATTCTAAACCCTAAATTCAAAAAAATAT
1 ATCAATTACATTCTAAACCCTAAATTC-AAAAAATAT
*
24012 ATCAATTACATTCTAAA-CCTCAAATTC-CAAAATACT
1 ATCAATTACATTCTAAACCCT-AAATTCAAAAAATA-T
24048 -TCAATTACAT
1 ATCAATTACAT
24058 GCCCAACCCC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 16 0.38
36 4 0.10
37 22 0.52
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (36 bp):
ATCAATTACATTCTAAACCCTAAATTCAAAAAATAT
Found at i:24071 original size:35 final size:35
Alignment explanation
Indices: 24005--24072 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
23995 TAAATTCAAA
* * *
24005 AAAATATATCAATTACATTCTAAACCTCAAATTCC
1 AAAATATATCAATTACATGCCAAACCCCAAATTCC
*
24040 AAAATACT-TCAATTACATGCCCAACCCCAAATT
1 AAAATA-TATCAATTACATGCCAAACCCCAAATT
24073 TATAATCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.28
Consensus pattern (35 bp):
AAAATATATCAATTACATGCCAAACCCCAAATTCC
Found at i:24382 original size:15 final size:15
Alignment explanation
Indices: 24364--24393 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24354 GTAATTTCAT
24364 AAATTCAACTTAAAA
1 AAATTCAACTTAAAA
*
24379 AAATTCAAGTTAAAA
1 AAATTCAACTTAAAA
24394 TCGAGTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (15 bp):
AAATTCAACTTAAAA
Found at i:24719 original size:148 final size:148
Alignment explanation
Indices: 24555--24900 Score: 566
Period size: 148 Copynumber: 2.3 Consensus size: 148
24545 AAACTATTTA
* * * *
24555 AATTAGAATAAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACATAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* * * *
24620 AATTCAATTCAATTCGACTTGATTTAAATTGTATAAATTCAAATAGAAAACATTTCGAGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTGTATAAACTCAAATAGAAAAAAATTCGAGTAAACT
24685 ATTTTATAAACTGAACAG
131 ATTTTATAAACTGAACAG
**
24703 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTTGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
24768 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTAAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTGTATAAACTCAAATAGAAAAAAATTCGAGTAAACT
*
24833 ATTTTATAAACTGAACTG
131 ATTTTATAAACTGAACAG
*
24851 AATTAGAATCAAATAATATTATAATATGATAAATATTTACAATTAAATTT
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTT
24901 CGAGTAAACT
Statistics
Matches: 184, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
148 184 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGACTTGATTTAAATTGTATAAACTCAAATAGAAAAAAATTCGAGTAAACT
ATTTTATAAACTGAACAG
Found at i:25127 original size:35 final size:35
Alignment explanation
Indices: 25088--25183 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
25078 AATGGATTAT
* * *
25088 GAATTTGGGGTTGGGCATATAATTGAAGTATTTTG
1 GAATTTGGGGTTGAGAATATAATTGAAGTATTTTA
* *
25123 GAATTTGAGGTTTAGAATATAATTGAAGTATTTTA
1 GAATTTGGGGTTGAGAATATAATTGAAGTATTTTA
* * *
25158 GATTTTGGGGTTTAGAATGTAATTGA
1 GAATTTGGGGTTGAGAATATAATTGA
25184 TAACTGTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.30, C:0.01, G:0.27, T:0.42
Consensus pattern (35 bp):
GAATTTGGGGTTGAGAATATAATTGAAGTATTTTA
Found at i:26358 original size:49 final size:48
Alignment explanation
Indices: 26305--26404 Score: 119
Period size: 49 Copynumber: 2.1 Consensus size: 48
26295 ATAATATATT
*
26305 TATATTATACTGATAATAATTTAATTTATATGAATTTTGTTAAATTGTA
1 TATATTATAATGATAATAATTTAATTTATAT-AATTTTGTTAAATTGTA
** * ** * *
26354 TATATTATAATTTTTATGCTTTAATTTATATACTTTTTTTAAATTGTA
1 TATATTATAATGATAATAATTTAATTTATATAATTTTGTTAAATTGTA
26402 TAT
1 TAT
26405 TATAATTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 18 0.42
49 25 0.58
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (48 bp):
TATATTATAATGATAATAATTTAATTTATATAATTTTGTTAAATTGTA
Found at i:28594 original size:20 final size:20
Alignment explanation
Indices: 28571--28622 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
28561 AACGCGATCC
28571 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
28591 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
28611 CCAAAATCGCAA
1 CCAGAATCGCAA
28623 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:28639 original size:21 final size:20
Alignment explanation
Indices: 28612--28710 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
28602 AATCAGTTTC
28612 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
28633 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
28654 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
28674 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
28695 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
28711 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:28739 original size:20 final size:20
Alignment explanation
Indices: 28677--28870 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
28667 CGATTTTCCA
* ** *
28677 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
28697 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
28717 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
28737 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
28757 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
28777 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
28797 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
28817 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
28837 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
28858 AAATCGCAACGCG
1 AAATCGCAACGCG
28871 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:28761 original size:60 final size:60
Alignment explanation
Indices: 28677--28870 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
28667 CGATTTTCCA
* ** * *
28677 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
28737 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
28797 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
28858 AAATCGCAACGCG
1 AAATCGCAACGCG
28871 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:29292 original size:33 final size:33
Alignment explanation
Indices: 29253--29323 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
29243 TTCACTTAGA
*
29253 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
29286 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
29319 TTTCA
1 TTTCA
29324 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:29463 original size:14 final size:14
Alignment explanation
Indices: 29444--29498 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
29434 AGAATGACTG
29444 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
29458 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
29477 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
29491 TCGCAACG
1 TCGCAACG
29499 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:29481 original size:33 final size:33
Alignment explanation
Indices: 29444--29514 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
29434 AGAATGACTG
**
29444 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
29477 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
29510 TCGCA
1 TCGCA
29515 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:29532 original size:19 final size:19
Alignment explanation
Indices: 29510--29607 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
29500 GAAACCAAAA
*
29510 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29529 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
29543 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29562 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
29576 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
29595 TCGCGTTGCGATT
1 TCGCGTTGCGATT
29608 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:29551 original size:14 final size:14
Alignment explanation
Indices: 29532--29621 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
29522 TTTCATTTCG
29532 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
29546 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
29565 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
29579 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
29596 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
29612 CGTTGCGATT
1 CGTTGCGATT
29622 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:29557 original size:33 final size:33
Alignment explanation
Indices: 29515--29629 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
29505 CAAAATCGCA
29515 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29548 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
29581 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29614 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
29630 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:31632 original size:183 final size:184
Alignment explanation
Indices: 31326--31701 Score: 713
Period size: 183 Copynumber: 2.0 Consensus size: 184
31316 TAGATTGCTT
31326 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATTCTTTAACACTGTGAAATAGTATT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATTCTTTAACACTGTGAAATAGTATT
31391 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
66 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
31456 GTATTCTTTAACACTGTGAAATA-TA-TTGTCTTTGTTTTGTC-TTTGGTTGAA
131 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31507 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATAGTA
31572 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
64 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31637 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31693 AGTAAATTT
1 AGTAAATTT
31702 ATCCATTCAA
Statistics
Matches: 190, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
181 36 0.19
183 117 0.62
184 2 0.01
185 16 0.08
186 19 0.10
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (184 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATTCTTTAACACTGTGAAATAGTATT
TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31656 original size:93 final size:93
Alignment explanation
Indices: 31326--31701 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
31316 TAGATTGCTT
31326 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31389 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31417 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31481 -TTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31507 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31572 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31600 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31665 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31693 AGTAAATTT
1 AGTAAATTT
31702 ATCCATTCAA
Statistics
Matches: 280, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
90 72 0.26
91 54 0.19
92 18 0.06
93 136 0.49
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31784 original size:19 final size:19
Alignment explanation
Indices: 31744--31872 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
31734 TAGTTTACTT
* *
31744 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
31764 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
31783 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
31802 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
31816 TCGCAACGCAAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
31835 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
31849 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
31868 TCGCA
1 TCGCA
31873 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:31823 original size:33 final size:32
Alignment explanation
Indices: 31780--31872 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
31770 CGCGAAACCA
**
31780 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
31812 AGAATCGCAACGCAAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
31845 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
31873 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:31870 original size:52 final size:52
Alignment explanation
Indices: 31744--31872 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
31734 TAGTTTACTT
** *
31744 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCAAAACCAAAATCGCAACGCGAAA
* * *
31796 T-G-AAAATCGCAACGACAGAATCGCAACGCAAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCAAAACCAAAATCGCAACG-CGAA-A
*
31849 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
31873 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCAAAACCAAAATCGCAACGCGAAA
Found at i:31890 original size:19 final size:19
Alignment explanation
Indices: 31868--32002 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
31858 GAAACCAAAA
*
31868 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31887 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
31903 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
31920 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
31936 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
31953 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
31972 TCTCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
31992 TCGTGTTGCGA
1 TCGCGTTGCGA
32003 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 45 0.48
20 11 0.12
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31909 original size:14 final size:14
Alignment explanation
Indices: 31890--31946 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
31880 TTTCATTTCG
31890 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
31904 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
31921 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
31937 CGTTGCGATT
1 CGTTGCGATT
31947 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:31915 original size:33 final size:33
Alignment explanation
Indices: 31873--31965 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
31863 CAAAATCGCA
*
31873 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
31906 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
31939 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
31966 TTGGTTTCTC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:33854 original size:38 final size:38
Alignment explanation
Indices: 33811--33883 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
33801 AATTGATTGT
*
33811 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
33849 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
33884 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:33870 original size:19 final size:19
Alignment explanation
Indices: 33806--33870 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
33796 AGTTTAATTG
*
33806 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
33825 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
33843 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
33863 ATTGATTT
1 ATTGATTT
33871 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:33884 original size:14 final size:14
Alignment explanation
Indices: 33865--33900 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33855 ATTGTTTAAT
33865 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
33879 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
33893 TGATTTGT
1 TGATTTGT
33901 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:34023 original size:19 final size:19
Alignment explanation
Indices: 34007--34108 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
33997 AAAAATGACT
34007 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34026 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34045 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
34059 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34078 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
34098 ATCGCAATGCG
1 ATCGCAATGCG
34109 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:34161 original size:19 final size:19
Alignment explanation
Indices: 34137--34462 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
34127 GATTATCTCG
34137 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34156 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34175 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
34189 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34208 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34227 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
34246 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
34265 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34284 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
34298 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34317 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34336 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
34350 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34369 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34388 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
34402 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
34422 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
34436 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
34455 TTGCGATT
1 TTGCGATT
34463 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:34178 original size:52 final size:52
Alignment explanation
Indices: 34115--34434 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
34105 TGCGTTTATA
* *
34115 ATTTCGTATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
34167 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
34219 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
34276 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
34328 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
34380 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
34433 AT
1 AT
34435 GTTGGGATTT
Statistics
Matches: 256, Mismatches: 6, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 181 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:34212 original size:71 final size:72
Alignment explanation
Indices: 34137--34462 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
34127 GATTATCTCG
34137 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
34201 TTTCGCA
66 TTTCGCA
* *
34208 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
34273 TTCATTTCGCA
62 TTCATTTCGCA
*
34284 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
34342 TTC-TCTCG--
62 TTCATTTCGCA
*
34350 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
34414 TTTCCGCA
66 TTT-CGCA
* *
34422 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
34463 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:34387 original size:161 final size:157
Alignment explanation
Indices: 34115--34434 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 157
34105 TGCGTTTATA
*
34115 ATTTCGTATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
34180 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
34245 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
34276 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
34341 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
34406 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
34433 AT
1 AT
34435 GTTGGGATTT
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 115 0.75
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:34406 original size:33 final size:33
Alignment explanation
Indices: 34156--34462 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
34146 TCATTTCGCA
*
34156 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
34189 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
34225 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
34263 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
34298 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
34334 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
34369 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
34402 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
34436 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
34463 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:36780 original size:12 final size:12
Alignment explanation
Indices: 36763--36787 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36753 TCTTCGGGGA
36763 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36775 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36787 C
1 C
36788 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:36996 original size:24 final size:24
Alignment explanation
Indices: 36962--37008 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
36952 CTGAAACATC
36962 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
36986 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
37009 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:37707 original size:20 final size:20
Alignment explanation
Indices: 37679--38047 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
37669 AAATTTCAGT
* * * *
37679 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
37699 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
37719 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
37739 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
37759 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
37779 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
37799 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
37819 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
37839 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
37859 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
* *
37879 GTTGCGGTTTAAGGATACGC
1 GTTGCGATTTACGGATACGC
37899 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
37919 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
37939 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
37959 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
37979 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
37999 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
38019 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
38039 GTTGCGATT
1 GTTGCGATT
38048 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 297 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:52946 original size:27 final size:27
Alignment explanation
Indices: 52915--52966 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
52905 CCATGACGAC
*
52915 TTGAACTTGAAACTCCATAGCATCATT
1 TTGAACTTGAAACTCCACAGCATCATT
*
52942 TTGAACTTGAAAGTCCACAGCATCA
1 TTGAACTTGAAACTCCACAGCATCA
52967 AGATCTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (27 bp):
TTGAACTTGAAACTCCACAGCATCATT
Found at i:53079 original size:17 final size:18
Alignment explanation
Indices: 53053--53093 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
53043 TAAAAGTGTA
53053 AAATAT-ATTAAATAA-T
1 AAATATAATTAAATAACT
*
53069 AAATATAATTATATAACT
1 AAATATAATTAAATAACT
53087 AAA-ATAA
1 AAATATAA
53094 ACGATGCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 12 0.55
18 4 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATATAATTAAATAACT
Found at i:54782 original size:18 final size:18
Alignment explanation
Indices: 54759--54798 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
54749 AGAACTTGAG
*
54759 GAAATTAATCC-TTAATCA
1 GAAATTAA-CCATGAATCA
54777 GAAATTAACCATGAATCA
1 GAAATTAACCATGAATCA
54795 GAAA
1 GAAA
54799 ATCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (18 bp):
GAAATTAACCATGAATCA
Found at i:56638 original size:56 final size:55
Alignment explanation
Indices: 56549--56762 Score: 277
Period size: 54 Copynumber: 3.9 Consensus size: 55
56539 TTGAATATTC
* * * ** * * *
56549 AACTTATTATAAATTATGTGGTTTTGCACACATAGCGCCAATACAGTAATTCACA
1 AACTCATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGGTAATTCATA
* *
56604 AACTCCTTATGGATTACGTGGGGTTGCAACACATAGTGCCAATACGGTAATTCATA
1 AACTCATTATGAATTACGTGGGGTTGC-ACACATAGTGCCAATACGGTAATTCATA
* * *
56660 AATTCGTTATGAATTACGTGGGGTTGCACACATA-TGCCAATACGATAATTCATA
1 AACTCATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGGTAATTCATA
* *
56714 CACTCATTATGAATTATGTGGGGTTGCACACATAGTGCCAATACGGTAA
1 AACTCATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGGTAA
56763 ATGCAACATA
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
54 49 0.36
55 40 0.29
56 49 0.36
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (55 bp):
AACTCATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGGTAATTCATA
Done.