Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000451.1 Hibiscus syriacus cultivar Beakdansim tig00000835_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: 55123
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2609 original size:2 final size:2
Alignment explanation
Indices: 2596--2661 Score: 109
Period size: 2 Copynumber: 34.0 Consensus size: 2
2586 ATAGAAACTG
*
2596 AT AT AG AT AT AT AT AT AT AT A- 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
2637 AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2662 TTACGTAATC
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 58 0.97
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2630 original size:25 final size:25
Alignment explanation
Indices: 2596--2661 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
2586 ATAGAAACTG
*
2596 ATATAGATATATATATATATAATAT
1 ATATATATATATATATATATAATAT
2621 ATATATATATATATATATATAATAT
1 ATATATATATATATATATATAATAT
2646 ATATATATATATATAT
1 ATATATATATATATAT
2662 TTACGTAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
ATATATATATATATATATATAATAT
Found at i:2676 original size:25 final size:24
Alignment explanation
Indices: 2596--2661 Score: 109
Period size: 23 Copynumber: 2.8 Consensus size: 24
2586 ATAGAAACTG
*
2596 ATATAGATATATATATATATAAT-
1 ATATATATATATATATATATAATA
2619 ATATATATATATATATATAT-ATA
1 ATATATATATATATATATATAATA
2642 ATATATATATATATATATAT
1 ATATATATATATATATATAT
2662 TTACGTAATC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 2 0.05
23 39 0.95
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATATATATATATATATATATAATA
Found at i:3406 original size:23 final size:23
Alignment explanation
Indices: 3376--3439 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
3366 TCCTTCGGGA
3376 CATAGTGGTCCTACGGGACATTT
1 CATAGTGGTCCTACGGGACATTT
3399 CATAGTGGTCCTACGGGACATTT
1 CATAGTGGTCCTACGGGACATTT
*
3422 CATAGTGGTCCTTCGGGA
1 CATAGTGGTCCTACGGGA
3440 TAAATTTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (23 bp):
CATAGTGGTCCTACGGGACATTT
Found at i:7566 original size:21 final size:22
Alignment explanation
Indices: 7514--7567 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
7504 ATAATTATTT
*
7514 AAAAAATTAAATAAAAATACCA
1 AAAAAATTTAATAAAAATACCA
*
7536 AAAAACATTTAATAAAAA-ATCA
1 AAAAA-ATTTAATAAAAATACCA
7558 AAAAAATTTA
1 AAAAAATTTA
7568 GGTTGAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 13 0.45
23 11 0.38
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAAAATTTAATAAAAATACCA
Found at i:18504 original size:18 final size:19
Alignment explanation
Indices: 18458--18505 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
18448 GGGTTTAAAA
*
18458 AATATTATATTATTATAAT
1 AATAATATATTATTATAAT
*
18477 AATAAT-TATTATTATTAT
1 AATAATATATTATTATAAT
*
18495 TA-AATATATTA
1 AATAATATATTA
18506 CACTGTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 17 0.68
19 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATAATATATTATTATAAT
Found at i:19878 original size:14 final size:14
Alignment explanation
Indices: 19856--19901 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
19846 CGTTCGTGAG
19856 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
19870 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
*
19884 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
19898 CGTT
1 CGTT
19902 TATGTTTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.09, C:0.13, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:20646 original size:10 final size:10
Alignment explanation
Indices: 20631--20705 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
20621 GGGTCTCCAA
20631 CGTTTATGTT
1 CGTTTATGTT
20641 CGTTTATGTT
1 CGTTTATGTT
20651 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
20662 ATGTTCGTGTT
1 -CGTTTATGTT
20673 CGTTTATGTT
1 CGTTTATGTT
20683 CG----TGTT
1 CGTTTATGTT
20689 CGTTTATGTT
1 CGTTTATGTT
20699 CGTTTAT
1 CGTTTAT
20706 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:20662 original size:16 final size:16
Alignment explanation
Indices: 20637--20701 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
20627 CCAACGTTTA
20637 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
20653 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
20669 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
20685 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
20701 T
1 T
20702 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:20791 original size:16 final size:16
Alignment explanation
Indices: 20770--20818 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
20760 AAAAAAAATT
20770 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
20786 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
20802 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
20818 T
1 T
20819 TTAATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:21269 original size:29 final size:30
Alignment explanation
Indices: 21203--21288 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
21193 TTAGATCCTT
*
21203 CTATTTTAATCCTTTAATTTTTTGTTTGTG
1 CTATTTTAATACTTTAATTTTTTGTTTGTG
* *
21233 CTATTTTAGTACTTTAATTTTTT-TCTTTTG
1 CTATTTTAATACTTTAATTTTTTGT-TTGTG
* *
21263 CTA-TTTAATACCTTAAGTTTTTGTTT
1 CTATTTTAATACTTTAATTTTTTGTTT
21289 TTCTCTTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
29 19 0.40
30 29 0.60
ACGTcount: A:0.19, C:0.10, G:0.08, T:0.63
Consensus pattern (30 bp):
CTATTTTAATACTTTAATTTTTTGTTTGTG
Found at i:26800 original size:9 final size:9
Alignment explanation
Indices: 26788--26820 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
26778 TTTTTCGTAA
26788 TTTTTTGAT
1 TTTTTTGAT
26797 TTTTTTG-T
1 TTTTTTGAT
26805 ATTTTTTGAT
1 -TTTTTTGAT
26815 TTTTTT
1 TTTTTT
26821 TTTATATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (9 bp):
TTTTTTGAT
Found at i:26808 original size:18 final size:20
Alignment explanation
Indices: 26776--26820 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 20
26766 TCATACTAAT
26776 TTTTTTTCGTAATTTTTTGA
1 TTTTTTTCGTAATTTTTTGA
26796 TTTTTTT-GT-ATTTTTTGA
1 TTTTTTTCGTAATTTTTTGA
26814 TTTTTTT
1 TTTTTTT
26821 TTTATATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 16 0.64
19 2 0.08
20 7 0.28
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.78
Consensus pattern (20 bp):
TTTTTTTCGTAATTTTTTGA
Found at i:27653 original size:30 final size:30
Alignment explanation
Indices: 27582--27641 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
27572 ACAATTTAAG
27582 GCAAAATGTTTTTGGACTGGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
* *
27612 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
27642 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTGGAATTGAATTT
Found at i:27737 original size:8 final size:8
Alignment explanation
Indices: 27724--27925 Score: 54
Period size: 8 Copynumber: 25.8 Consensus size: 8
27714 GGTGTCAAAG
27724 TGCATCCA
1 TGCATCCA
*
27732 TGCATCCC
1 TGCATCCA
*
27740 TGCAGTGCA
1 TGCA-TCCA
* *
27749 TTCATGCA
1 TGCATCCA
* * *
27757 TCCCTGCA
1 TGCATCCA
27765 GTGCATCCA
1 -TGCATCCA
27774 TGCAT-C-
1 TGCATCCA
*
27780 TGCA-CTAA
1 TGCATC-CA
*
27788 TGCATCGA
1 TGCATCCA
27796 TGCATCAGGCAA
1 TGCATC---C-A
27808 TGCATCCA
1 TGCATCCA
27816 TGCATCCA
1 TGCATCCA
** *
27824 AACATCGAA
1 TGCATC-CA
*
27833 TGCAAT-TA
1 TGC-ATCCA
*
27841 GTGCATCGA
1 -TGCATCCA
*
27850 TGCATCCT
1 TGCATCCA
27858 TGC--C-A
1 TGCATCCA
*
27863 TGCATCGA
1 TGCATCCA
*
27871 TGCATCCT
1 TGCATCCA
27879 TG---CCA
1 TGCATCCA
*
27884 TGCATCGA
1 TGCATCCA
27892 TGCATCC-
1 TGCATCCA
27899 TG---CCA
1 TGCATCCA
27904 TGCATCCA
1 TGCATCCA
27912 TGCATCCA
1 TGCATCCA
27920 TGCATC
1 TGCATC
27926 AAGGCTGCAA
Statistics
Matches: 143, Mismatches: 27, Indels: 48
0.66 0.12 0.22
Matches are distributed among these distances:
4 2 0.01
5 9 0.06
6 5 0.03
7 4 0.03
8 96 0.67
9 18 0.13
10 2 0.01
12 7 0.05
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (8 bp):
TGCATCCA
Found at i:27748 original size:21 final size:21
Alignment explanation
Indices: 27722--27779 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
27712 AGGGTGTCAA
27722 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
27743 AGTGCATTCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
27764 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
27780 TGCACTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:27868 original size:21 final size:21
Alignment explanation
Indices: 27842--27918 Score: 138
Period size: 21 Copynumber: 3.7 Consensus size: 21
27832 ATGCAATTAG
27842 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
27863 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
27884 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
27904 TGCATCCATGCATCC
1 TGCATCGATGCATCC
27919 ATGCATCAAG
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 19 0.35
21 36 0.65
ACGTcount: A:0.19, C:0.35, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:28329 original size:34 final size:32
Alignment explanation
Indices: 28290--28359 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
28280 TTTTGTAAAG
* * *
28290 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
28324 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
28356 GGGA
1 GGGA
28360 TCTCTTTGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:29231 original size:19 final size:20
Alignment explanation
Indices: 29207--29254 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
29197 AATAATTTTC
*
29207 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
29226 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
29246 TTTTGAAAA
1 TTTTGAAAA
29255 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:30602 original size:30 final size:30
Alignment explanation
Indices: 30531--30590 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
30521 ACAATTTAAG
30531 GCAAAATGTTTTTGGACTGGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
* *
30561 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
30591 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTGGAATTGAATTT
Found at i:30686 original size:8 final size:8
Alignment explanation
Indices: 30673--30874 Score: 54
Period size: 8 Copynumber: 25.8 Consensus size: 8
30663 GGTGTCAAAG
30673 TGCATCCA
1 TGCATCCA
*
30681 TGCATCCC
1 TGCATCCA
*
30689 TGCAGTGCA
1 TGCA-TCCA
* *
30698 TTCATGCA
1 TGCATCCA
* * *
30706 TCCCTGCA
1 TGCATCCA
30714 GTGCATCCA
1 -TGCATCCA
30723 TGCAT-C-
1 TGCATCCA
*
30729 TGCA-CTAA
1 TGCATC-CA
*
30737 TGCATCGA
1 TGCATCCA
30745 TGCATCAGGCAA
1 TGCATC---C-A
30757 TGCATCCA
1 TGCATCCA
30765 TGCATCCA
1 TGCATCCA
** *
30773 AACATCGAA
1 TGCATC-CA
*
30782 TGCAAT-TA
1 TGC-ATCCA
*
30790 GTGCATCGA
1 -TGCATCCA
*
30799 TGCATCCT
1 TGCATCCA
30807 TGC--C-A
1 TGCATCCA
*
30812 TGCATCGA
1 TGCATCCA
*
30820 TGCATCCT
1 TGCATCCA
30828 TG---CCA
1 TGCATCCA
*
30833 TGCATCGA
1 TGCATCCA
30841 TGCATCC-
1 TGCATCCA
30848 T---TCCA
1 TGCATCCA
30853 TGCATCCA
1 TGCATCCA
30861 TGCATCCA
1 TGCATCCA
30869 TGCATC
1 TGCATC
30875 AAGGCTGCAA
Statistics
Matches: 143, Mismatches: 27, Indels: 48
0.66 0.12 0.22
Matches are distributed among these distances:
4 3 0.02
5 8 0.06
6 5 0.03
7 3 0.02
8 97 0.68
9 18 0.13
10 2 0.01
12 7 0.05
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.26
Consensus pattern (8 bp):
TGCATCCA
Found at i:30697 original size:21 final size:21
Alignment explanation
Indices: 30671--30728 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
30661 AGGGTGTCAA
30671 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
30692 AGTGCATTCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
30713 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
30729 TGCACTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:30817 original size:21 final size:21
Alignment explanation
Indices: 30791--30867 Score: 138
Period size: 21 Copynumber: 3.7 Consensus size: 21
30781 ATGCAATTAG
30791 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
30812 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
30833 TGCATCGATGCATCCTT-CCA
1 TGCATCGATGCATCCTTGCCA
*
30853 TGCATCCATGCATCC
1 TGCATCGATGCATCC
30868 ATGCATCAAG
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 17 0.31
21 38 0.69
ACGTcount: A:0.19, C:0.35, G:0.17, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:40188 original size:16 final size:16
Alignment explanation
Indices: 40167--40226 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
40157 ACAATGATGT
40167 AAAAAGAATTATGCTA
1 AAAAAGAATTATGCTA
* *
40183 AAAAAGAATATAATGATTT
1 AAAAAGAAT-T-ATG-CTA
40202 AAAAAGAATTATGCTA
1 AAAAAGAATTATGCTA
40218 AAAAAGAAT
1 AAAAAGAAT
40227 ACAATGATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 19 0.51
17 4 0.11
18 4 0.11
19 10 0.27
ACGTcount: A:0.60, C:0.03, G:0.12, T:0.25
Consensus pattern (16 bp):
AAAAAGAATTATGCTA
Found at i:40198 original size:35 final size:35
Alignment explanation
Indices: 40156--40239 Score: 150
Period size: 35 Copynumber: 2.4 Consensus size: 35
40146 TATGAATCTG
40156 TACAATGATGTAAAAAGAATTATGCTAAAAAAGAA
1 TACAATGATGTAAAAAGAATTATGCTAAAAAAGAA
* *
40191 TATAATGATTTAAAAAGAATTATGCTAAAAAAGAA
1 TACAATGATGTAAAAAGAATTATGCTAAAAAAGAA
40226 TACAATGATGTAAA
1 TACAATGATGTAAA
40240 TCCAATGTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (35 bp):
TACAATGATGTAAAAAGAATTATGCTAAAAAAGAA
Found at i:40206 original size:20 final size:20
Alignment explanation
Indices: 40180--40239 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 20
40170 AAGAATTATG
40180 CTAAAAAAGAATATAATGAT
1 CTAAAAAAGAATATAATGAT
*
40200 -TTAAAAAGAAT-T-ATG--
1 CTAAAAAAGAATATAATGAT
*
40215 CTAAAAAAGAATACAATGAT
1 CTAAAAAAGAATATAATGAT
*
40235 GTAAA
1 CTAAA
40240 TCCAATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
16 10 0.32
17 3 0.10
18 4 0.13
19 10 0.32
20 4 0.13
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.25
Consensus pattern (20 bp):
CTAAAAAAGAATATAATGAT
Found at i:40207 original size:19 final size:19
Alignment explanation
Indices: 40183--40239 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
40173 AATTATGCTA
40183 AAAAAGAATATAATGATTT
1 AAAAAGAATATAATGATTT
* *
40202 AAAAAGAAT-T-ATG-CTA
1 AAAAAGAATATAATGATTT
* *
40218 AAAAAGAATACAATGATGT
1 AAAAAGAATATAATGATTT
40237 AAA
1 AAA
40240 TCCAATGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 10 0.34
17 3 0.10
18 4 0.14
19 12 0.41
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.25
Consensus pattern (19 bp):
AAAAAGAATATAATGATTT
Found at i:48965 original size:106 final size:105
Alignment explanation
Indices: 48780--48969 Score: 310
Period size: 106 Copynumber: 1.8 Consensus size: 105
48770 TGTTCATATA
* * **
48780 GTACCGATACCAAAGGTATCGGAAGTATCGATACTCACAATATATTATCAATACTACCAGTATTG
1 GTACCAATACCAAAGGTATCGGAAGTATCGATACTCACAATATAGTATCAATACTACCAACATTG
48845 CTCAAATTTCATAATGAAAAATGGTACCGATACCAAAAGGG
66 CTCAAATTTCATAAT-AAAAATGGTACCGATACCAAAAGGG
*
48886 GTACCAATACCAAAGGTAGT-GGAAGTATCGATACTCACAATGTAGTATCAATACTACCAACATT
1 GTACCAATACCAAAGGTA-TCGGAAGTATCGATACTCACAATATAGTATCAATACTACCAACATT
48950 GCTCAAATTTCATAATAAAA
65 GCTCAAATTTCATAATAAAA
48970 TATTATTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
105 4 0.05
106 73 0.94
107 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (105 bp):
GTACCAATACCAAAGGTATCGGAAGTATCGATACTCACAATATAGTATCAATACTACCAACATTG
CTCAAATTTCATAATAAAAATGGTACCGATACCAAAAGGG
Found at i:50825 original size:11 final size:11
Alignment explanation
Indices: 50801--50836 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
50791 GGATTAAAAT
* *
50801 AACAAATTTAA
1 AACAATTTTGA
50812 AACAATTTTGA
1 AACAATTTTGA
50823 AACAATTTTGA
1 AACAATTTTGA
50834 AAC
1 AAC
50837 TTAAGTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (11 bp):
AACAATTTTGA
Found at i:54730 original size:29 final size:28
Alignment explanation
Indices: 54698--54774 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
54688 TAGTATCCAC
54698 ATAAGCCCTAATCTTTAACTTGCAGCCAA
1 ATAAGCCCTAATCTTTAACTTGCAGCC-A
* * ***
54727 ATAAGACCTTAAACTTTAACTTGTTTCCA
1 ATAAG-CCCTAATCTTTAACTTGCAGCCA
54756 ATAAGCCCTTAATCTTTAA
1 ATAAGCCC-TAATCTTTAA
54775 TCACATATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.05
29 20 0.51
30 17 0.44
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (28 bp):
ATAAGCCCTAATCTTTAACTTGCAGCCA
Found at i:54744 original size:30 final size:30
Alignment explanation
Indices: 54667--54749 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
54657 TATTACACCT
* * *
54667 AAATAA-ACCTTAAACTTT-AGTTAGTATCC
1 AAATAAGACCTTAAACTTTAACTT-GCAGCC
* * *
54696 ACATAAG-CCCTAATCTTTAACTTGCAGCC
1 AAATAAGACCTTAAACTTTAACTTGCAGCC
54725 AAATAAGACCTTAAACTTTAACTTG
1 AAATAAGACCTTAAACTTTAACTTG
54750 TTTCCAATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
29 24 0.57
30 18 0.43
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (30 bp):
AAATAAGACCTTAAACTTTAACTTGCAGCC
Done.