Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002204.1 Hibiscus syriacus cultivar Beakdansim tig00004492_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: 64879
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:861 original size:19 final size:19
Alignment explanation
Indices: 828--874 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
818 AATGATTTGG
*
828 TTTTG-AAAGCAAAATTG-A
1 TTTTGAAAAACAAAA-TGAA
846 TTTTGAAAAACAAAATGAA
1 TTTTGAAAAACAAAATGAA
*
865 ATTTGAAAAA
1 TTTTGAAAAA
875 TGATTTAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.30
Consensus pattern (19 bp):
TTTTGAAAAACAAAATGAA
Found at i:12248 original size:15 final size:15
Alignment explanation
Indices: 12228--12276 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
12218 TGAAACATTA
12228 CCCGTCCCGCATCCG
1 CCCGTCCCGCATCCG
12243 CCCGTCCCGCATCCG
1 CCCGTCCCGCATCCG
* *
12258 CCCGCCCCACATCCG
1 CCCGTCCCGCATCCG
12273 CCCG
1 CCCG
12277 CCCAGCTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.08, C:0.63, G:0.18, T:0.10
Consensus pattern (15 bp):
CCCGTCCCGCATCCG
Found at i:13383 original size:20 final size:22
Alignment explanation
Indices: 13341--13383 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
13331 TTGCATTAAT
*
13341 AAAATCACATCTTTCACTCAAA
1 AAAATCACATCTTTCAATCAAA
*
13363 AAAATCATA-CTTTCAAT-AAA
1 AAAATCACATCTTTCAATCAAA
13383 A
1 A
13384 TTACATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATCACATCTTTCAATCAAA
Found at i:13671 original size:20 final size:21
Alignment explanation
Indices: 13646--13697 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
13636 TTTTCCCAAT
*
13646 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
13666 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
13687 TCGCAATGCGA
1 TCGCAATGCGA
13698 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:13711 original size:20 final size:20
Alignment explanation
Indices: 13686--13799 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
13676 AATTGGGAAA
*
13686 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
13706 ATCGCAATGCGATACTTATT
1 ATCGCAACGCGATACTGACT
* * *
13726 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
13747 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
13767 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
13787 TTCGCAACGCGAT
1 ATCGCAACGCGAT
13800 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 63 0.80
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:13730 original size:61 final size:62
Alignment explanation
Indices: 13683--13799 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 62
13673 GCGAATTGGG
* * * * *
13683 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTA-TTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTTATCGCAACGCGATAATAC
* *
13744 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTT-TCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTTATCGCAACGCGAT
13800 TTACATAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 46 0.96
62 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTTATCGCAACGCGATAATAC
Found at i:14399 original size:19 final size:19
Alignment explanation
Indices: 14377--14427 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
14367 GAAACAAAAA
*
14377 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
14396 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
14415 TCGCGTTGCGATT
1 TCGCGTTGCGATT
14428 CTCTGGTCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:14473 original size:33 final size:33
Alignment explanation
Indices: 14399--14473 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
14389 TTTCATTTCG
**
14399 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
* * * *
14432 GGTCGCGATAGTCATTTCGCGTTGTGATTCTTT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
14465 CGTTGCGAT
1 CGTTGCGAT
14474 TATCTCGTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:14527 original size:22 final size:21
Alignment explanation
Indices: 14476--14538 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
14466 GTTGCGATTA
**
14476 TCTCGTTGCGATAGTCATTTC
1 TCTCGTTGCGATTCTCATTTC
*
14497 -CGCGTTGCGATTCTCATTATC
1 TCTCGTTGCGATTCTCATT-TC
*
14518 TCTCGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTCTCATTTC
14539 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 15 0.43
21 4 0.11
22 16 0.46
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.44
Consensus pattern (21 bp):
TCTCGTTGCGATTCTCATTTC
Found at i:16616 original size:21 final size:21
Alignment explanation
Indices: 16592--16658 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
16582 TCATTCCTCG
16592 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
16613 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
16634 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
16655 AGAG
1 AGAG
16659 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:16616 original size:42 final size:42
Alignment explanation
Indices: 16540--16658 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
16530 GACTCGCCTG
* * * * * * *
16540 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
16582 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
16624 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
16659 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:18068 original size:19 final size:19
Alignment explanation
Indices: 18041--18091 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
18031 AAGTACTATT
*
18041 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
18060 GCAACGCGAAAATGAAAATC
1 GCAACGCG-AAATGAAAATC
*
18080 GCAACGAGAAAT
1 GCAACGCGAAAT
18092 TAAATTCGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.12
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:18118 original size:19 final size:19
Alignment explanation
Indices: 18096--18180 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
18086 AGAAATTAAA
18096 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
18115 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
18130 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
18148 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
18167 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
18181 AGACATTAAG
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
14 8 0.16
16 3 0.06
17 3 0.06
19 25 0.51
20 10 0.20
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:21760 original size:20 final size:20
Alignment explanation
Indices: 21735--21792 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
21725 ATTCATTTGA
21735 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
21755 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
21775 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
21793 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:21835 original size:14 final size:14
Alignment explanation
Indices: 21816--21869 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
21806 GAAAATCGCA
21816 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
21830 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
21847 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
21863 TTGCGAT
1 TTGCGAT
21870 AGCCATTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:21835 original size:33 final size:33
Alignment explanation
Indices: 21798--21868 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
21788 AAAATCGCAA
21798 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
21831 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
21864 TGCGA
1 TGCGA
21869 TAGCCATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:21877 original size:33 final size:33
Alignment explanation
Indices: 21811--21877 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
21801 GAAATGAAAA
***
21811 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
21844 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
21877 T
1 T
21878 AGTCTGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:21984 original size:14 final size:14
Alignment explanation
Indices: 21965--22001 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
21955 CATCAATTAA
21965 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
21979 ACAAATCATCTTTT
1 ACAAATCAACATTT
21993 ACAAATCAA
1 ACAAATCAA
22002 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:23905 original size:14 final size:14
Alignment explanation
Indices: 23886--23941 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
23876 GAAAATGACT
23886 ATCGCAACGACAAA
1 ATCGCAACGACAAA
*
23900 ATCGCAACGCGAAATGAA
1 ATCGCAA--CGACA--AA
23918 ATCGCAACGACAAA
1 ATCGCAACGACAAA
23932 ATCGCAACGA
1 ATCGCAACGA
23942 GAAACACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (14 bp):
ATCGCAACGACAAA
Found at i:23927 original size:32 final size:33
Alignment explanation
Indices: 23863--23945 Score: 132
Period size: 32 Copynumber: 2.5 Consensus size: 33
23853 CACGAAACTT
*
23863 AAAATCGCAACGCGAAAATGACTATCGCAACGAC
1 AAAATCGCAACGCG-AAATGACAATCGCAACGAC
23897 AAAATCGCAACGCGAAATGA-AATCGCAACGAC
1 AAAATCGCAACGCGAAATGACAATCGCAACGAC
*
23929 AAAATCGCAACGAGAAA
1 AAAATCGCAACGCGAAA
23946 CACAAATCGC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 27 0.57
33 6 0.13
34 14 0.30
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGACAATCGCAACGAC
Found at i:23974 original size:19 final size:17
Alignment explanation
Indices: 23952--24046 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
23942 GAAACACAAA
23952 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
23971 TCGCGTTGCGA-TT--TG
1 TCGC-TTGCGATTTCATT
23986 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
24002 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
24018 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
24035 TCGCATTGCGAT
1 TCGC-TTGCGAT
24047 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
13 6 0.10
14 8 0.13
15 7 0.11
16 8 0.13
17 6 0.10
18 10 0.16
19 16 0.26
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:23990 original size:13 final size:14
Alignment explanation
Indices: 23974--24030 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
23964 TTTCATTTCG
23974 CGTTGCGA-TTTGT
1 CGTTGCGATTTTGT
*
23987 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
24003 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
24019 CGTTGCGATTTT
1 CGTTGCGATTTT
24031 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 14 0.38
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:24018 original size:32 final size:33
Alignment explanation
Indices: 23957--24046 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
23947 ACAAATCGCA
23957 TTGCGATTTTCATTTCGCGTTGCGA-TTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
23989 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
24021 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
24047 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 18 0.33
32 19 0.35
33 18 0.33
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:24065 original size:20 final size:19
Alignment explanation
Indices: 24031--24085 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
24021 TTGCGATTTT
*
24031 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
24050 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
24070 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
24086 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:24589 original size:18 final size:18
Alignment explanation
Indices: 24563--24607 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
24553 GTCGATCAGA
*
24563 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
24581 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
24599 TGATGGCTC
1 TGATGGCTC
24608 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:25941 original size:20 final size:20
Alignment explanation
Indices: 25916--25953 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25906 AATAGTTTCT
25916 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
25936 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
25954 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:26235 original size:20 final size:21
Alignment explanation
Indices: 26210--26258 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
26200 TCTAAGAGAT
26210 GGAGAT-AGACGGATTTC-TCC
1 GGAGATGAGACGGATTTCGT-C
*
26230 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGTC
26252 GGAGATG
1 GGAGATG
26259 GGTGAGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 17 0.68
23 1 0.04
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGTC
Found at i:26244 original size:22 final size:22
Alignment explanation
Indices: 26217--26260 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
26207 GATGGAGATA
26217 GACGGATTTC-TCCGGAGATGGG
1 GACGGATTTCGT-CGGAGATGGG
26239 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
26261 TGAGAGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.16, G:0.43, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:26466 original size:20 final size:20
Alignment explanation
Indices: 26440--26553 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
26430 GATTATGTAT
26440 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
26460 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
26480 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
26500 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
26521 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
26541 TATCGCATTGCGA
1 TATCGCGTTGCGA
26554 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:26557 original size:41 final size:41
Alignment explanation
Indices: 26420--26555 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
26410 CGCTTTGAAA
*
26420 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
26461 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
26501 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
26542 ATCGCATTGCGATT
1 ATCGCATTGCGATT
26556 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:26572 original size:21 final size:21
Alignment explanation
Indices: 26543--26635 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
26533 ATAGTCAGTA
26543 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
26564 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
26584 TCGCATTACGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
26605 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
26625 TCGCATTGCGA
1 TCGCATTGCGA
26636 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:26573 original size:41 final size:41
Alignment explanation
Indices: 26482--26616 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
26472 AAAGTCAGTA
* * * ** *
26482 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
26522 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
26564 TCGCGTTGCGAT-TTACTTATTCGCATTACGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
26605 TCGCGTTGCGAT
1 TCGCGTTGCGAT
26617 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:26617 original size:41 final size:41
Alignment explanation
Indices: 26543--26631 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
26533 ATAGTCAGTA
*
26543 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
26584 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
26625 TCGCATT
1 TCGCATT
26632 GCGAATTGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (41 bp):
TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:31749 original size:16 final size:16
Alignment explanation
Indices: 31728--31758 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31718 GATTAGTTAC
*
31728 TTTCCTAATTTAAGAG
1 TTTCCTAAGTTAAGAG
31744 TTTCCTAAGTTAAGA
1 TTTCCTAAGTTAAGA
31759 TTATAGCTTG
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:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (16 bp):
TTTCCTAAGTTAAGAG
Found at i:41541 original size:3 final size:3
Alignment explanation
Indices: 41533--41579 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
41523 GTATAAATAA
* * *
41533 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT GTT ATT GTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
41580 AAATAAACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:46541 original size:164 final size:164
Alignment explanation
Indices: 46270--46597 Score: 656
Period size: 164 Copynumber: 2.0 Consensus size: 164
46260 GCTTATCGAA
46270 GGTTCGATCTATTCCGTTCTTACCTGAGTCACCAAAGCATAGAGTGGAAGAGTCACATAACTGCA
1 GGTTCGATCTATTCCGTTCTTACCTGAGTCACCAAAGCATAGAGTGGAAGAGTCACATAACTGCA
46335 AAGAAACTGTATAATGACCCTGAAAAAGTTGCAGATCTGCATTTATCAGCTAAGTTTTCACATTG
66 AAGAAACTGTATAATGACCCTGAAAAAGTTGCAGATCTGCATTTATCAGCTAAGTTTTCACATTG
46400 CCAAATCAATAACATTGGCCTAAAAAGTTCCATG
131 CCAAATCAATAACATTGGCCTAAAAAGTTCCATG
46434 GGTTCGATCTATTCCGTTCTTACCTGAGTCACCAAAGCATAGAGTGGAAGAGTCACATAACTGCA
1 GGTTCGATCTATTCCGTTCTTACCTGAGTCACCAAAGCATAGAGTGGAAGAGTCACATAACTGCA
46499 AAGAAACTGTATAATGACCCTGAAAAAGTTGCAGATCTGCATTTATCAGCTAAGTTTTCACATTG
66 AAGAAACTGTATAATGACCCTGAAAAAGTTGCAGATCTGCATTTATCAGCTAAGTTTTCACATTG
46564 CCAAATCAATAACATTGGCCTAAAAAGTTCCATG
131 CCAAATCAATAACATTGGCCTAAAAAGTTCCATG
46598 AACTCACCCC
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (164 bp):
GGTTCGATCTATTCCGTTCTTACCTGAGTCACCAAAGCATAGAGTGGAAGAGTCACATAACTGCA
AAGAAACTGTATAATGACCCTGAAAAAGTTGCAGATCTGCATTTATCAGCTAAGTTTTCACATTG
CCAAATCAATAACATTGGCCTAAAAAGTTCCATG
Found at i:50328 original size:27 final size:27
Alignment explanation
Indices: 50271--50328 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
50261 AGACATAAAT
*
50271 AAATTATTAGAAGTTAATAGGGTTTTG
1 AAATTATTAGAAGTGAATAGGGTTTTG
* *
50298 -AATTATTTTGAAGTGAA-AGGTTTTTG
1 AAATTA-TTAGAAGTGAATAGGGTTTTG
50324 AAATT
1 AAATT
50329 TTAAGTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (27 bp):
AAATTATTAGAAGTGAATAGGGTTTTG
Found at i:50339 original size:23 final size:25
Alignment explanation
Indices: 50293--50339 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
50283 GTTAATAGGG
*
50293 TTTTGAATTATTTTGAAGTGAAAGGT
1 TTTTGAA-TATTTTGAAGTCAAAGGT
50319 TTTTGAA-ATTTT-AAGTCAAAG
1 TTTTGAATATTTTGAAGTCAAAG
50340 CCATTACCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
26 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (25 bp):
TTTTGAATATTTTGAAGTCAAAGGT
Found at i:51093 original size:27 final size:28
Alignment explanation
Indices: 51030--51085 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
51020 TGATAATTTA
* **
51030 AAAATA-TTTATTTCTTAAAAAAACTTT
1 AAAATATTTTATTTCTTAAAAAAAATCC
51057 AAAATATTTTATTT-TTAAAAAAAATCC
1 AAAATATTTTATTTCTTAAAAAAAATCC
51084 AA
1 AA
51086 GATTTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATATTTTATTTCTTAAAAAAAATCC
Found at i:52728 original size:21 final size:21
Alignment explanation
Indices: 52702--52800 Score: 146
Period size: 21 Copynumber: 4.8 Consensus size: 21
52692 ATGCGAATAA
52702 GAAAATCGCAACGCGAATTGG
1 GAAAATCGCAACGCGAATTGG
* **
52723 GAAAATCGCAATGCGAA-TAA
1 GAAAATCGCAACGCGAATTGG
*
52743 GTAAATCGCAACGCGAATTGG
1 GAAAATCGCAACGCGAATTGG
52764 GAAAATCGCAACGCGAATTGG
1 GAAAATCGCAACGCGAATTGG
*
52785 GAAAATCGCAATGCGA
1 GAAAATCGCAACGCGA
52801 TACTTACTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.24
21 52 0.76
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.15
Consensus pattern (21 bp):
GAAAATCGCAACGCGAATTGG
Found at i:52732 original size:41 final size:41
Alignment explanation
Indices: 52687--52800 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
52677 TTTTCCCAAT
52687 TCGCAATGCGAATAAGAAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGAAAATCGCAACGCGAATTGGGAAAA
*
52728 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGAAAATCGCAACGCGAATTGGGAAAA
* ** *
52769 TCGCAACGCGAATTGGGAAAATCGCAATGCGA
1 TCGCAATGCGAA-TAAGAAAATCGCAACGCGA
52801 TACTTACTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
41 51 0.77
42 15 0.23
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.16
Consensus pattern (41 bp):
TCGCAATGCGAATAAGAAAATCGCAACGCGAATTGGGAAAA
Found at i:52813 original size:41 final size:41
Alignment explanation
Indices: 52786--52863 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
52776 GCGAATTGGG
* * *
52786 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
52827 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
52864 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:52814 original size:20 final size:20
Alignment explanation
Indices: 52789--52882 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
52779 AATTGGGAAA
*
52789 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
52809 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
52830 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
52850 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
52870 TTCGCAACGCGAT
1 ATCGCAACGCGAT
52883 TTACACAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:52831 original size:62 final size:62
Alignment explanation
Indices: 52687--52838 Score: 193
Period size: 62 Copynumber: 2.5 Consensus size: 62
52677 TTTTCCCAAT
52687 TCGCAATGCG-AATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTAAA
* * ** ** *
52748 TCGCAACGCGAATTGGGAAAATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACTA
1 TCGCAATGCGAAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-AA
*
52810 TCGCAATGCGATAAT-ACAAAATCGCAACG
1 TCGCAATGCGA-AATAAGAAAATCGCAACG
52839 AGATACTTAC
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
61 14 0.18
62 61 0.79
63 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (62 bp):
TCGCAATGCGAAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTAAA
Found at i:53095 original size:22 final size:22
Alignment explanation
Indices: 53067--53110 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53057 CACTCTCTCA
53067 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
53089 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
53111 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:53399 original size:20 final size:20
Alignment explanation
Indices: 53374--53411 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53364 CGATTCTCTC
53374 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
53394 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
53412 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:54752 original size:18 final size:18
Alignment explanation
Indices: 54731--54773 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54721 TCCACTTCGG
* *
54731 GAGCCATCACCTCTCCCA
1 GAGCCATCACCCCACCCA
*
54749 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
54767 GAGCCAT
1 GAGCCAT
54774 TATCTGATCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.47, G:0.14, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:55320 original size:14 final size:14
Alignment explanation
Indices: 55301--55358 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
55291 ATGCGAAATG
55301 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
55315 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
55331 ATGAAATCGCAAAGAC
1 A--AAATCGCAACGAC
55347 AAAATCGCAACG
1 AAAATCGCAACG
55359 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:55348 original size:32 final size:33
Alignment explanation
Indices: 55285--55375 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
55275 GGAAATGGCT
* *
55285 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAAAGACAAA
55318 ATCGCAACGCGAAATG-AAATCGCAAAGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAAAGACAAA
55350 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
55376 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAAAGACAAA
Found at i:55369 original size:19 final size:19
Alignment explanation
Indices: 55247--55380 Score: 83
Period size: 19 Copynumber: 7.6 Consensus size: 19
55237 TAGTTTACTT
* **
55247 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
55266 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
55286 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
55305 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
55319 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
* *
55337 TCGCAA----AGA-CAAAA
1 TCGCAACGCGAAATGAAAA
55351 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
55370 TCGCAATGCGA
1 TCGCAACGCGA
55381 TTTGTGTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
14 21 0.23
15 1 0.01
16 2 0.02
17 2 0.02
18 12 0.13
19 35 0.39
20 17 0.19
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:55411 original size:14 final size:14
Alignment explanation
Indices: 55392--55449 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
55382 TTGTGTTTCG
55392 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
55406 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
55422 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
55438 CGTTGCGATTTT
1 CGTTGCGATTTT
55450 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:55426 original size:32 final size:33
Alignment explanation
Indices: 55387--55465 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
55377 GCGATTTGTG
55387 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
55419 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
55452 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
55466 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:55464 original size:19 final size:19
Alignment explanation
Indices: 55406--55523 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
55396 GCGATTTTGT
55406 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
55424 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
55438 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
55457 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
55477 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
55496 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
55516 TGTTGCGA
1 CGTTGCGA
55524 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:57513 original size:19 final size:19
Alignment explanation
Indices: 57489--57591 Score: 110
Period size: 19 Copynumber: 5.7 Consensus size: 19
57479 AAAACAGACT
*
57489 ATCGCAACGCGAAATGGAA
1 ATCGCAACGCGAAATGAAA
*
57508 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
57527 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
57546 ATCGCAA--CG--A-G-AA
1 ATCGCAACGCGAAATGAAA
* *
57559 ACCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
57578 ATCGCAACGAGAAA
1 ATCGCAACGCGAAA
57592 ATCGCAATGC
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.11
14 1 0.01
15 3 0.04
17 3 0.04
18 1 0.01
19 56 0.78
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:57559 original size:14 final size:14
Alignment explanation
Indices: 57542--57598 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
57532 AATGCGAAAT
57542 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
57556 G-AAACCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
57573 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
57588 GAAAATCGCAA
1 GAAAATCGCAA
57599 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
13 8 0.23
14 12 0.34
15 3 0.09
17 3 0.09
18 1 0.03
19 8 0.23
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:57565 original size:32 final size:33
Alignment explanation
Indices: 57491--57603 Score: 138
Period size: 32 Copynumber: 3.3 Consensus size: 33
57481 AACAGACTAT
* * *
57491 CGCAACGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAAC
57529 CGCAATGCGAAATGAAAATCGCAACGAG-AAAC
1 CGCAATGCGAAATGAAAATCGCAACGAGAAAAC
*
57561 CGCAATGCGAAATGAAAATCGCAACGAGAAAAT
1 CGCAATGCGAAATGAAAATCGCAACGAGAAAAC
57594 CGCAATGCGA
1 CGCAATGCGA
57604 TTTTCATTTC
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
32 31 0.44
33 14 0.20
34 1 0.01
36 2 0.03
38 22 0.31
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
CGCAATGCGAAATGAAAATCGCAACGAGAAAAC
Found at i:57647 original size:20 final size:20
Alignment explanation
Indices: 57622--57678 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
57612 TCGCATTGCG
*
57622 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
**
57642 ATTTTCGCGTTGCGATGGCC
1 ATTTTCGCGTTGCGATAACC
57662 ATTTTCGCGTTGCGATA
1 ATTTTCGCGTTGCGATA
57679 GTCAAATGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:58763 original size:24 final size:24
Alignment explanation
Indices: 58736--58789 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
58726 GTATTCGAAA
* *
58736 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
58760 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
58784 TTTGAT
1 TTTGAT
58790 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:58981 original size:12 final size:12
Alignment explanation
Indices: 58964--58988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58954 ATATAATCCT
58964 GAAGAAGAAAAA
1 GAAGAAGAAAAA
58976 GAAGAAGAAAAA
1 GAAGAAGAAAAA
58988 G
1 G
58989 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:61316 original size:33 final size:33
Alignment explanation
Indices: 61274--61400 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
61264 GGAAATTACT
61274 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
61307 ATCGCAATGCGAAATGAAAATCGTAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
61339 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
61373 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
61401 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:61381 original size:66 final size:66
Alignment explanation
Indices: 61275--61407 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
61265 GAAATTACTA
* *
61275 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGTAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
61340 T
66 T
*
61341 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
61406 T
66 T
61407 T
1 T
61408 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:61422 original size:19 final size:20
Alignment explanation
Indices: 61400--61442 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
61390 AAATCGCAAC
61400 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
61419 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
61439 GCGA
1 GCGA
61443 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:61427 original size:14 final size:14
Alignment explanation
Indices: 61428--61461 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
61418 TGCGATTTTC
61428 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
61442 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
61456 ATTTTC
1 ATTTTC
61462 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:61602 original size:14 final size:14
Alignment explanation
Indices: 61583--61619 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
61573 CATCAATTAA
61583 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
61597 ACAAATCACCTTTT
1 ACAAATCAACTTTT
61611 ACAAATCAA
1 ACAAATCAA
61620 TTAAACAATA
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:63036 original size:21 final size:21
Alignment explanation
Indices: 62970--63036 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
62960 GTGAATCGGG
*
62970 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
62990 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
63012 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
63033 CTCT
1 CTCT
63037 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:63055 original size:42 final size:41
Alignment explanation
Indices: 62970--63092 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
62960 GTGAATCGGG
* * * * *
62970 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
63012 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
63054 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
63093 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Done.