Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006570.1 Hibiscus syriacus cultivar Beakdansim tig00016076_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: 104380
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:18039 original size:16 final size:16
Alignment explanation
Indices: 18018--18048 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18008 GTCGAGCATA
18018 GATGAATACTATTAAC
1 GATGAATACTATTAAC
*
18034 GATGAATATTATTAA
1 GATGAATACTATTAA
18049 ATTAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (16 bp):
GATGAATACTATTAAC
Found at i:18582 original size:44 final size:44
Alignment explanation
Indices: 18519--18609 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
18509 CGAATTAATA
*
18519 TAAAATAAATTAAATCAAAAATTGATGTTGGTGGGGTTTGAACC
1 TAAAATAAATTAAATCAAAAATTGATATTGGTGGGGTTTGAACC
18563 TAAAATAAATTAAATCAAAAATTGATATTGGTGGGGTTTGAACC
1 TAAAATAAATTAAATCAAAAATTGATATTGGTGGGGTTTGAACC
18607 TAA
1 TAA
18610 GACGTAGAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.32
Consensus pattern (44 bp):
TAAAATAAATTAAATCAAAAATTGATATTGGTGGGGTTTGAACC
Found at i:18773 original size:2 final size:2
Alignment explanation
Indices: 18762--18825 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
18752 CAATATGATA
18762 AT AT -T AT AT AT 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 AT AT AT AT AT AT
18803 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
18826 ATTGATTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19957 original size:22 final size:22
Alignment explanation
Indices: 19913--19958 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
19903 GTAAATATTG
* *
19913 TATTTTAATTAAATTACATTTA
1 TATTTTAACTAAATTACAATTA
* *
19935 TATTTTAACTAATTTATAATTA
1 TATTTTAACTAAATTACAATTA
19957 TA
1 TA
19959 CGTTTAGTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTTAACTAAATTACAATTA
Found at i:20951 original size:12 final size:12
Alignment explanation
Indices: 20934--20962 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20924 TAATGAGACA
20934 AATTGCAAATTT
1 AATTGCAAATTT
20946 AATTGCAAATTT
1 AATTGCAAATTT
20958 AATTG
1 AATTG
20963 ATATTGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (12 bp):
AATTGCAAATTT
Found at i:21311 original size:22 final size:22
Alignment explanation
Indices: 21278--21321 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21268 TTAATTTATA
21278 AAACGTTAAATTATAAAATAGT
1 AAACGTTAAATTATAAAATAGT
*
21300 AAACG-TATAATTATAAATTAGT
1 AAACGTTA-AATTATAAAATAGT
21322 TAAAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (22 bp):
AAACGTTAAATTATAAAATAGT
Found at i:21773 original size:15 final size:15
Alignment explanation
Indices: 21747--21789 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
21737 TAATTTATAA
21747 TTATACAATTAATAGT
1 TTATA-AATTAATAGT
* *
21763 TTATAATTTAATATT
1 TTATAAATTAATAGT
21778 TTATAAATTAAT
1 TTATAAATTAAT
21790 TTAATGATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TTATAAATTAATAGT
Found at i:26209 original size:2 final size:2
Alignment explanation
Indices: 26197--26260 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
26187 TTATATTCAT
*
26197 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26239 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
26261 ACCTGTTTCT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28428 original size:28 final size:26
Alignment explanation
Indices: 28397--28459 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
28387 TTTTCTATTG
28397 ATAATTTATTTTCATCCTTTAAAATTTT
1 ATAATTTA--TTCATCCTTTAAAATTTT
* * *
28425 ATAAATTATTCTTCCTTTAGAATTTT
1 ATAATTTATTCATCCTTTAAAATTTT
28451 ATATATTTA
1 ATA-ATTTA
28460 CCTCTAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 19 0.63
27 4 0.13
28 7 0.23
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.56
Consensus pattern (26 bp):
ATAATTTATTCATCCTTTAAAATTTT
Found at i:29879 original size:21 final size:21
Alignment explanation
Indices: 29828--29880 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
29818 ATTATGACTA
*
29828 TCGCAATACGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
29849 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
29870 TCGCAATGCGA
1 TCGCAATGCGA
29881 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:29913 original size:21 final size:20
Alignment explanation
Indices: 29870--29921 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
29860 TTTTCCCAAT
*
29870 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
29890 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
29911 TCGCAACGCGA
1 TCGCAATGCGA
29922 TACTGATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:29934 original size:41 final size:42
Alignment explanation
Indices: 29907--30044 Score: 158
Period size: 41 Copynumber: 3.4 Consensus size: 42
29897 GCGAATTTGG
29907 AAAATCGCAACGCGATACTGA-TTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTATCGCAACGCGATAATAC
* * *
29948 AAAATCGCAACGCGATACTGACTT-TCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTTATCGCAACGCGATAATAC
** * * *
29988 AATTTCGCAACTCAATACTGACTT-TCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTATCGCAACGCGATAATAC
* *
30029 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
30045 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
40 32 0.41
41 44 0.56
42 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTATCGCAACGCGATAATAC
Found at i:29935 original size:20 final size:19
Alignment explanation
Indices: 29911--30024 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 19
29901 ATTTGGAAAA
29911 TCGCAACGCGATACTGATT
1 TCGCAACGCGATACTGATT
* * **
29930 ATCGCAACGCGATAATACAAAA
1 -TCGCAACGCGATACT--GATT
29952 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGA-TT
* *
29972 TCGCAACTCGATACTTAATT
1 TCGCAACGCGATAC-TGATT
* *
29992 TCGCAACTCAATACTGACTT
1 TCGCAACGCGATACTGA-TT
*
30012 TCGCAACGAGATA
1 TCGCAACGCGATA
30025 ATACATAATC
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
19 3 0.04
20 54 0.73
21 16 0.22
22 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (19 bp):
TCGCAACGCGATACTGATT
Found at i:30261 original size:20 final size:22
Alignment explanation
Indices: 30212--30253 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
30202 ACTCTCTCAC
30212 CCATCTCC-GACGAAATCCGTCA
1 CCATCTCCTG-CGAAATCCGTCA
30234 CCATCTCCTGCGAAATCCGT
1 CCATCTCCTGCGAAATCCGT
30254 ATATCTCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.24, C:0.40, G:0.14, T:0.21
Consensus pattern (22 bp):
CCATCTCCTGCGAAATCCGTCA
Found at i:30545 original size:20 final size:20
Alignment explanation
Indices: 30517--30565 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
30507 TTTATTCTCT
*
30517 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
30537 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
30557 TGTTGCGAT
1 CGTTGCGAT
30566 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:30566 original size:20 final size:20
Alignment explanation
Indices: 30533--30575 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
30523 GATAGTCAAA
30533 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
* *
30553 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTGTCATT
30573 TTC
1 TTC
30576 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:30766 original size:25 final size:24
Alignment explanation
Indices: 30712--30766 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
30702 TGTTTATTAT
*
30712 TGTTTTTGGTATATCTTCACAGTA
1 TGTTTTTGGTATATCTTAACAGTA
30736 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
30762 TGTTT
1 TGTTT
30767 ATTGTTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:31917 original size:18 final size:18
Alignment explanation
Indices: 31896--31943 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
31886 TCCACTTCGG
*
31896 GAGCCATCACCTCACCTA
1 GAGCCATCACCTCACCCA
*
31914 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
31932 GAGCCATCACCT
1 GAGCCATCACCT
31944 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:32127 original size:20 final size:20
Alignment explanation
Indices: 32081--32167 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
32071 GCGATTTTGT
**
32081 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
* * *
32100 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTTCG
32120 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
32140 TGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
32160 CGCTGCGA
1 CGTTGCGA
32168 AAGTAAGTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
19 10 0.19
20 44 0.81
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:32156 original size:40 final size:40
Alignment explanation
Indices: 32102--32185 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
32092 TCATTTCGCA
* * * *
32102 TTGCGATAGCCATTTCCGCGTTGCGATAGTCA-TTTTCGTG
1 TTGCAATAGCCATTTCCGCGCTGCGAAAGTAAGTTTT-GTG
* *
32142 TTGCAATAGTCATTTTCGCGCTGCGAAAGTAAGTTTTGTG
1 TTGCAATAGCCATTTCCGCGCTGCGAAAGTAAGTTTTGTG
32182 TTGC
1 TTGC
32186 GAAAGTAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 33 0.89
41 4 0.11
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (40 bp):
TTGCAATAGCCATTTCCGCGCTGCGAAAGTAAGTTTTGTG
Found at i:32568 original size:21 final size:20
Alignment explanation
Indices: 32542--32609 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
32532 CTGTCATCCC
32542 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
32563 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
*
32584 TCAAGAGTCCCC-CCACCGT
1 TCAAGAGTCCCCTCCATCGT
32603 TCAAGAG
1 TCAAGAG
32610 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:32621 original size:40 final size:42
Alignment explanation
Indices: 32532--32621 Score: 139
Period size: 40 Copynumber: 2.2 Consensus size: 42
32522 CCCGACTCAC
* *
32532 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
*
32574 CTATCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
32614 CTGTCATC
1 CTGTCATC
32622 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 21 0.48
41 2 0.05
42 21 0.48
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:34062 original size:14 final size:14
Alignment explanation
Indices: 34028--34066 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
34018 TTGATTGTTT
34028 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
34042 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
34056 TGTTGATTTGT
1 AATTGATTTGT
34067 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:34464 original size:20 final size:20
Alignment explanation
Indices: 34439--34488 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
34429 TTGAAGATGA
34439 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
34459 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
34479 TTGCGATTTT
1 TTGCGATTTT
34489 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:34628 original size:12 final size:12
Alignment explanation
Indices: 34609--34642 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
34599 CTCTCTGGCG
34609 ACATCCGTTCCT
1 ACATCCGTTCCT
*
34621 ATATCCGTTCCT
1 ACATCCGTTCCT
34633 ACATCC-TTCC
1 ACATCCGTTCC
34643 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:35223 original size:24 final size:24
Alignment explanation
Indices: 35196--35249 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
35186 GTATTCGAAA
* *
35196 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGATCAATACCCGGAC
* *
35220 TTTGATATTGATCAATACTCGGAT
1 TTTGATATTGATCAATACCCGGAC
35244 TTTGAT
1 TTTGAT
35250 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGATCAATACCCGGAC
Found at i:35441 original size:12 final size:12
Alignment explanation
Indices: 35424--35448 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35414 ATATAATCCT
35424 GAAGAAGAAAAA
1 GAAGAAGAAAAA
35436 GAAGAAGAAAAA
1 GAAGAAGAAAAA
35448 G
1 G
35449 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:37799 original size:19 final size:19
Alignment explanation
Indices: 37757--37868 Score: 82
Period size: 19 Copynumber: 6.4 Consensus size: 19
37747 CTTAATGTCT
* * *
37757 ATCGCAACGCGGAAATTAAT
1 ATCGCAATGC-GAAATGAAA
*
37777 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
37796 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
*
37810 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37829 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
37843 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
37862 ATCGCAA
1 ATCGCAA
37869 CGAGTTTCAT
Statistics
Matches: 72, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
14 19 0.26
15 2 0.03
16 3 0.04
17 3 0.04
18 2 0.03
19 34 0.47
20 9 0.12
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:37824 original size:33 final size:33
Alignment explanation
Indices: 37777--37872 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
37767 GGAAATTAAT
* *
37777 ATCGCAATGCGAAATAAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
37810 ATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
37843 ATCGCAATGCGAAATGAAAATCGCAACGAG
1 ATCGCAATGCGAAATGAAAATCGCAACGAG
37873 TTTCATTTCG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:38050 original size:14 final size:14
Alignment explanation
Indices: 38031--38067 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
38021 CATCAATTAA
38031 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
38045 ACAAATCACCTTTT
1 ACAAATCAACTTTT
38059 ACAAATCAA
1 ACAAATCAA
38068 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:39481 original size:21 final size:21
Alignment explanation
Indices: 39415--39481 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
39405 GTGAATCGGG
*
39415 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
39435 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
39457 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
39478 CTCT
1 CTCT
39482 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:39935 original size:91 final size:90
Alignment explanation
Indices: 39755--39939 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 90
39745 ATTTCAAACT
* *
39755 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAAATACACAGTTTATC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT---AAATAAACAGTTTAGC
39820 AGAATTGGTAGAAACCGAATAAATTTAC
63 AGAATTGGTAGAAACCGAATAAATTTAC
*
39848 TTCAACCAAAAGATAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
39912 GTATTGGTAGCAACCGAATAAATTTAC
64 GAATTGGTAGAAACCGAATAAATTTAC
39939 T
1 T
39940 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 40 0.47
93 18 0.21
95 27 0.32
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGTAGAAACCGAATAAATTTAC
Found at i:41655 original size:20 final size:19
Alignment explanation
Indices: 41630--41747 Score: 94
Period size: 20 Copynumber: 6.6 Consensus size: 19
41620 TTGGTTGAAT
41630 TGAAAATCGCAACGAGATAA
1 TGAAAATCGCAACGAGA-AA
*
41650 TGAAAATCGCAACGCGGAAA
1 TGAAAATCGCAACG-AGAAA
**
41670 TGACTATCGCAACGAG--A
1 TGAAAATCGCAACGAGAAA
*
41687 -G--AATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAAA
**
41703 TGACTATCGCAACGAG--A
1 TGAAAATCGCAACGAGAAA
41720 -G--AATCGCAACGAGAAA
1 TGAAAATCGCAACGAGAAA
41736 TGAAAATCGCAA
1 TGAAAATCGCAA
41748 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.27
16 4 0.05
17 4 0.05
19 19 0.24
20 28 0.36
21 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
TGAAAATCGCAACGAGAAA
Found at i:41694 original size:14 final size:14
Alignment explanation
Indices: 41675--41733 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
41665 GGAAATGACT
41675 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
41689 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
41706 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
41722 ATCGCAACGAGA
1 ATCGCAACGAGA
41734 AATGAAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 19 0.50
16 6 0.16
17 6 0.16
19 7 0.18
ACGTcount: A:0.41, C:0.24, G:0.25, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:41708 original size:33 final size:33
Alignment explanation
Indices: 41654--41747 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
41644 AGATAATGAA
41654 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
41688 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
* **
41721 AATCGCAACGAGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGACTATCGCAA
41748 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 46 0.81
34 11 0.19
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:41801 original size:33 final size:33
Alignment explanation
Indices: 41748--41819 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
41738 AAAATCGCAA
** *
41748 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTATCTCGT
* *
41781 TGCGATTTTCATTTCACGTTGCGGTTCTCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTATCTCGT
41814 TGCGAT
1 TGCGAT
41820 AGTTATTTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCACGTTGCGATTATCTCGT
Found at i:41828 original size:33 final size:33
Alignment explanation
Indices: 41759--41840 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
41749 GCGATTTTGG
*
41759 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATGTTCA
* * *
41792 TTTCACGTTGCGGTTCTCTCGTTGCGATAGTT-A
1 TTTCGCGTTGCGATTATCTCGTTGCGAT-GTTCA
41825 TTTCCGCGTTGCGATT
1 TTT-CGCGTTGCGATT
41841 TTCATTCTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 29 0.71
34 12 0.29
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.44
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATGTTCA
Found at i:42406 original size:21 final size:21
Alignment explanation
Indices: 42380--42515 Score: 75
Period size: 21 Copynumber: 6.6 Consensus size: 21
42370 CGATAGTAAG
42380 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
* * *
42401 ATTCGCATTGCGATCTACTTA
1 ATTCGCATTGCGATTTTCCTA
* *****
42422 A-TCGCAATGCGAATTAGGAAA
1 ATTCGCATTGCG-ATTTTCCTA
* **
42443 ATT-GTATTGCGATGGT-C-A
1 ATTCGCATTGCGATTTTCCTA
* *
42461 GTATCGCATTGCGATTTTCCAA
1 AT-TCGCATTGCGATTTTCCTA
* *
42483 ATTCGCATTGCGA-TTTACTT
1 ATTCGCATTGCGATTTTCCTA
42503 ATTCGCATTGCGA
1 ATTCGCATTGCGA
42516 ATTGGGAAAA
Statistics
Matches: 85, Mismatches: 24, Indels: 13
0.70 0.20 0.11
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 38 0.45
21 41 0.48
22 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTCCTA
Found at i:42427 original size:41 final size:41
Alignment explanation
Indices: 42382--42515 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
42372 ATAGTAAGAT
*
42382 TCGCATTGCGATTTTCCTAATTCGCATTGCGATCTACTTAA
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATCTACTTAA
* **** * * *
42423 TCGCAATGCGAATTAGGAAAATT-GTATTGCGATGGT-CAGT-A
1 TCGCATTGCG-ATTTTCCAAATTCGCATTGCGAT-CTAC-TTAA
* *
42464 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATCTACTTAA
42505 TCGCATTGCGA
1 TCGCATTGCGA
42516 ATTGGGAAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
40 10 0.14
41 50 0.72
42 9 0.13
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCAAATTCGCATTGCGATCTACTTAA
Found at i:42508 original size:20 final size:21
Alignment explanation
Indices: 42464--42515 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
42454 ATGGTCAGTA
*
42464 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
42485 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
42505 TCGCATTGCGA
1 TCGCATTGCGA
42516 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:64066 original size:22 final size:22
Alignment explanation
Indices: 64035--64080 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
64025 TTGAATTTTT
**
64035 TTTATAAAATTTAATATAAAATA
1 TTTATAAAATAAAATA-AAAATA
64058 TTTA-AAAATAAAATAAAAATA
1 TTTATAAAATAAAATAAAAATA
64079 TT
1 TT
64081 CTTAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 9 0.43
23 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTATAAAATAAAATAAAAATA
Found at i:69631 original size:20 final size:20
Alignment explanation
Indices: 69606--69653 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
69596 GTCAGAGTGT
*
69606 GGCGGCGGACGGCTGACGGC
1 GGCGGCGGACGGCGGACGGC
* *
69626 GGCGGCAGACGGCGGGCGGC
1 GGCGGCGGACGGCGGACGGC
*
69646 GGCAGCGG
1 GGCGGCGG
69654 CCAGCAGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.58, T:0.02
Consensus pattern (20 bp):
GGCGGCGGACGGCGGACGGC
Found at i:69643 original size:17 final size:16
Alignment explanation
Indices: 69623--69654 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
69613 GACGGCTGAC
69623 GGCGGCGGCAGACGGCG
1 GGCGGCGGCAG-CGGCG
69640 GGCGGCGGCAGCGGC
1 GGCGGCGGCAGCGGC
69655 CAGCAGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.31, G:0.59, T:0.00
Consensus pattern (16 bp):
GGCGGCGGCAGCGGCG
Found at i:79928 original size:21 final size:22
Alignment explanation
Indices: 79882--79928 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
79872 TTAGGTTTCT
*
79882 TTGTTTAGGCAATCTTTTGTAA
1 TTGTTTAGGCAATCTTATGTAA
*
79904 -TGTTT-GGTAATCTTATGTAA
1 TTGTTTAGGCAATCTTATGTAA
79924 TTGTT
1 TTGTT
79929 GGCTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (22 bp):
TTGTTTAGGCAATCTTATGTAA
Found at i:90697 original size:20 final size:20
Alignment explanation
Indices: 90672--90784 Score: 82
Period size: 20 Copynumber: 5.0 Consensus size: 20
90662 AGCAACAGAA
90672 TAAAAATGATTCTATCTAAT
1 TAAAAATGATTCTATCTAAT
90692 TAAAAATGATCCTATCTAATAACTAAT
1 TAAAAATGA---T-TCT-AT--CTAAT
90719 AGAATAAAAACTGATTCTATCTAAT
1 ----TAAAAA-TGATTCTATCTAAT
*
90744 TAAAAAATGATCCTATCTAAT
1 T-AAAAATGATTCTATCTAAT
* *
90765 TAAAACTGATCCTATCTAAT
1 TAAAAATGATTCTATCTAAT
90785 ATTTAATTTA
Statistics
Matches: 78, Mismatches: 2, Indels: 26
0.74 0.02 0.25
Matches are distributed among these distances:
20 27 0.35
21 15 0.19
22 5 0.06
23 1 0.01
24 3 0.04
25 7 0.09
27 7 0.09
28 3 0.04
29 1 0.01
31 6 0.08
32 3 0.04
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (20 bp):
TAAAAATGATTCTATCTAAT
Found at i:90749 original size:21 final size:21
Alignment explanation
Indices: 90723--90784 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
90713 ACTAATAGAA
*
90723 TAAAAACTGATTCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
*
90744 TAAAAAATGATCCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
90765 T-AAAACTGATCCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
90785 ATTTAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (21 bp):
TAAAAACTGATCCTATCTAAT
Found at i:95378 original size:19 final size:20
Alignment explanation
Indices: 95351--95395 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
95341 ATTAGCAACA
*
95351 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
95370 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
95390 TAATAA
1 TAATAA
95396 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:95379 original size:20 final size:20
Alignment explanation
Indices: 95354--95393 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
95344 AGCAACATAA
*
95354 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
95374 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
95394 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:95485 original size:20 final size:20
Alignment explanation
Indices: 95460--95498 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
95450 TAATAGAATA
*
95460 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
95480 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
95499 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:95491 original size:52 final size:52
Alignment explanation
Indices: 95352--95499 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
95342 TTAGCAACAT
95352 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
95403 AATAAAAAACTGATTCTATCTAATTAAAAATAATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
95456 AATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
95500 TTTAATTTAG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 3 0.03
52 44 0.48
53 45 0.49
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:99535 original size:31 final size:32
Alignment explanation
Indices: 99500--99560 Score: 115
Period size: 31 Copynumber: 1.9 Consensus size: 32
99490 AATTCGGTGA
99500 ATTCAATATGTCCTTCTCAC-TAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTTAGGAACTCCC
99531 ATTCAATATGTCCTTCTCACTTAGGAACTC
1 ATTCAATATGTCCTTCTCACTTAGGAACTC
99561 ACAAACTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (32 bp):
ATTCAATATGTCCTTCTCACTTAGGAACTCCC
Found at i:101285 original size:11 final size:11
Alignment explanation
Indices: 101269--101293 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
101259 GACCTAGCAG
101269 GAATACTAGAA
1 GAATACTAGAA
101280 GAATACTAGAA
1 GAATACTAGAA
101291 GAA
1 GAA
101294 GTTAATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (11 bp):
GAATACTAGAA
Done.