Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006413.1 Hibiscus syriacus cultivar Beakdansim tig00015467_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: 57518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2350 original size:13 final size:15
Alignment explanation
Indices: 2319--2354 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2309 TTAAATTAAA
2319 AATAATTTTTATCAT
1 AATAATTTTTATCAT
2334 AATAATTTTT-T-AT
1 AATAATTTTTATCAT
2347 AAT-ATTTT
1 AATAATTTT
2355 ATTTGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 5 0.24
14 1 0.05
15 10 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
AATAATTTTTATCAT
Found at i:11070 original size:25 final size:25
Alignment explanation
Indices: 11025--11072 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
11015 TGTTGGATTC
* *
11025 GTGAAGAAGATGAACGAGGGGAAAT
1 GTGAAGAAAAAGAACGAGGGGAAAT
11050 GTGAAGAAAAAGAA-GATGGGGAA
1 GTGAAGAAAAAGAACGA-GGGGAA
11073 TGGGTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.48, C:0.02, G:0.40, T:0.10
Consensus pattern (25 bp):
GTGAAGAAAAAGAACGAGGGGAAAT
Found at i:11806 original size:22 final size:22
Alignment explanation
Indices: 11765--11807 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11755 TATTATTTGA
**
11765 ATAATTATAAAATATGTTAAAT
1 ATAATTATAAAATAAATTAAAT
*
11787 ATAATTATAAATTAAATTAAA
1 ATAATTATAAAATAAATTAAA
11808 AATGTTATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATTATAAAATAAATTAAAT
Found at i:15244 original size:32 final size:31
Alignment explanation
Indices: 15174--15287 Score: 133
Period size: 31 Copynumber: 3.7 Consensus size: 31
15164 TATGTCAATC
** *
15174 AATAAAAAAAACTTTATAATCATTTTAA-ATT
1 AATAAAAAAAACTTTATAATCA-CCTAAGAGT
* * *
15205 AAT-AAAAAATCTTTATCATCCCCTAAGAGT
1 AATAAAAAAAACTTTATAATCACCTAAGAGT
15235 AATAAAAAAAACTTTATAATCACCTAAGAGT
1 AATAAAAAAAACTTTATAATCACCTAAGAGT
*
15266 AATAAAAAAAAACTTTTTAATC
1 AAT-AAAAAAAACTTTATAATC
15288 GTGAAGTTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.04
30 20 0.29
31 30 0.43
32 17 0.24
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.32
Consensus pattern (31 bp):
AATAAAAAAAACTTTATAATCACCTAAGAGT
Found at i:15409 original size:14 final size:15
Alignment explanation
Indices: 15341--15410 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
15331 GGTTTTCTGA
*
15341 AAAATGAATTACTGG
1 AAAATGAATTATTGG
** * *
15356 AATTTTAATTAATGG
1 AAAATGAATTATTGG
*
15371 AAAATGAATTATTGT
1 AAAATGAATTATTGG
**
15386 AATTTGAATT-TTGG
1 AAAATGAATTATTGG
15400 AAAATGAATTA
1 AAAATGAATTA
15411 CATTTCTGGA
Statistics
Matches: 40, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
14 11 0.28
15 29 0.73
ACGTcount: A:0.44, C:0.01, G:0.16, T:0.39
Consensus pattern (15 bp):
AAAATGAATTATTGG
Found at i:15410 original size:29 final size:30
Alignment explanation
Indices: 15341--15411 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
15331 GGTTTTCTGA
*
15341 AAAATGAATTACTGGAATTTTAATTAATGG
1 AAAATGAATTACTGGAATTTGAATTAATGG
* * *
15371 AAAATGAATTATTGTAATTTGAATT-TTGG
1 AAAATGAATTACTGGAATTTGAATTAATGG
15400 AAAATGAATTAC
1 AAAATGAATTAC
15412 ATTTCTGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (30 bp):
AAAATGAATTACTGGAATTTGAATTAATGG
Found at i:15786 original size:23 final size:23
Alignment explanation
Indices: 15756--15807 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
15746 AGTGTTATAT
15756 TATATTTTAAAAATATTAATTAA
1 TATATTTTAAAAATATTAATTAA
* * *
15779 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAAAATATTAATTAA
*
15802 AATATT
1 TATATT
15808 ATTATATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:19977 original size:17 final size:18
Alignment explanation
Indices: 19945--19978 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19935 TTTTGTTTTT
19945 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
19963 AATTTATTTAA-TATTT
1 AATTTATTTAAGTATTT
19979 TATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTTATTTAAGTATTTA
Found at i:19980 original size:18 final size:19
Alignment explanation
Indices: 19940--19980 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
19930 TAATATTTTG
*
19940 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
19959 -TTTAAATTTATTTAA-TA
1 TTTTAAATTTATTTAAGTA
19976 TTTTA
1 TTTTA
19981 TTTAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:26736 original size:21 final size:20
Alignment explanation
Indices: 26650--26807 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
26640 AAATGACCAA
**
26650 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
26669 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
26689 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
26709 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
26730 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
26751 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
26771 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
26792 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
26808 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:26849 original size:20 final size:20
Alignment explanation
Indices: 26774--27003 Score: 214
Period size: 20 Copynumber: 11.5 Consensus size: 20
26764 CGATTTTCCA
* ** *
26774 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
26794 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
26814 AAATCGCAACGCGTATCCAT
1 AAATCGCAACGCGTATCCGT
*
26834 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
26854 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
26874 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
26894 ATATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
26914 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
26934 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
26954 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
26974 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
26994 AAATCACAAC
1 AAATCGCAAC
27004 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:27724 original size:24 final size:24
Alignment explanation
Indices: 27685--27731 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27675 AAATTTGGTC
27685 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
27709 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
27732 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:27923 original size:12 final size:12
Alignment explanation
Indices: 27906--27930 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27896 ATATAATCCT
27906 GAAGAAGAAAAA
1 GAAGAAGAAAAA
27918 GAAGAAGAAAAA
1 GAAGAAGAAAAA
27930 G
1 G
27931 TCCCCAAAGA
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:30284 original size:19 final size:19
Alignment explanation
Indices: 30262--30390 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
30252 AAAATCGCAA
30262 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
30281 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
30295 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
30314 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
30328 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
30347 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
30366 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
30386 TGCGA
1 TGCGA
30391 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:30304 original size:33 final size:33
Alignment explanation
Indices: 30262--30353 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
30252 AAAATCGCAA
30262 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
30295 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
30328 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
30354 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:30554 original size:93 final size:93
Alignment explanation
Indices: 30438--30906 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
30428 ATGGATTGCA
30438 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
30502 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
30530 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
30595 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
30623 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
30688 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
30716 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
30781 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
30809 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
30874 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
30902 TTACT
1 TTACT
30907 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 371 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:32631 original size:14 final size:14
Alignment explanation
Indices: 32612--32701 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
32602 TTGAAATGAA
32612 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
32626 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
32645 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
32659 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
32678 AATCGCAACGAGAG
1 AATCGCAACGAGAG
32692 AATCGCAACG
1 AATCGCAACG
32702 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:32649 original size:33 final size:33
Alignment explanation
Indices: 32604--32718 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
32594 TCTTTTGGTT
32604 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
32637 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32670 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32703 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
32719 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:32650 original size:19 final size:19
Alignment explanation
Indices: 32626--32723 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
32616 GCAACGAGAG
*
32626 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
32645 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
32659 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
32678 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
32692 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
32711 AATCGCAATGCGA
1 AATCGCAACGCGA
32724 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:32754 original size:14 final size:14
Alignment explanation
Indices: 32735--32791 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
32725 TTTGGTTTCG
32735 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
32749 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
32768 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
32782 CGTTGCGATT
1 CGTTGCGATT
32792 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:32767 original size:33 final size:33
Alignment explanation
Indices: 32719--32799 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
32709 AAAATCGCAA
**
32719 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
32752 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
32785 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
32800 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:32802 original size:21 final size:21
Alignment explanation
Indices: 32776--32851 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
32766 CGCGTTGCGA
32776 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
32797 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
32817 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
32838 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
32852 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:32832 original size:41 final size:41
Alignment explanation
Indices: 32775--32852 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
32765 TCGCGTTGCG
*
32775 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
32816 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
32853 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:32973 original size:33 final size:33
Alignment explanation
Indices: 32931--33001 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
32921 AATACTAACT
*
32931 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
32964 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
32997 TGAAA
1 TGAAA
33002 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:33233 original size:22 final size:22
Alignment explanation
Indices: 33181--33235 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
33171 TGGTTGTGAG
**
33181 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
33203 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
33225 GGATTTCTTCG
1 GGATTTCTTCG
33236 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:33407 original size:20 final size:20
Alignment explanation
Indices: 33382--33575 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
33372 CTTTAAATAT
33382 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33402 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
33424 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33443 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
33463 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
33483 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33503 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33523 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
33543 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
33563 CGCGTTGCGATTT
1 CGCGTTGCGATTT
33576 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:33547 original size:60 final size:60
Alignment explanation
Indices: 33384--33555 Score: 245
Period size: 60 Copynumber: 2.9 Consensus size: 60
33374 TTAAATATCG
** *
33384 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
33445 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
33505 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
33556 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:33569 original size:60 final size:60
Alignment explanation
Indices: 33381--33697 Score: 241
Period size: 60 Copynumber: 5.2 Consensus size: 60
33371 GCTTTAAATA
* ** * *
33381 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * *** * * *
33442 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * *
33502 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * *
33562 TCGCGTTGCGATTT-TGGAAAATCGCATTGCGAATT-TGTACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
33625 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
33684 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
33698 TGTTGGTCAT
Statistics
Matches: 210, Mismatches: 37, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
59 16 0.08
60 90 0.43
61 56 0.27
62 26 0.12
63 20 0.10
64 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:33576 original size:20 final size:19
Alignment explanation
Indices: 33523--33639 Score: 74
Period size: 21 Copynumber: 5.7 Consensus size: 19
33513 TTTACGGATA
* **
33523 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TATAAT
*
33543 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTT-ATAAT
*
33563 CGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTTT--ATAAT
*
33584 CGCATTGCGAATTTGTACT-AT
1 CGCGTTGCG-ATTT-TA-TAAT
* *
33605 CGCATTGCGATTTTCAAGAAT
1 CGCGTTGCGATTTT--ATAAT
33626 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
33640 GGAAACTGAT
Statistics
Matches: 80, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.03
20 34 0.43
21 39 0.49
22 4 0.05
23 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (19 bp):
CGCGTTGCGATTTTATAAT
Found at i:33591 original size:21 final size:21
Alignment explanation
Indices: 33562--33644 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 21
33552 ATTTTCATAT
*
33562 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * **
33583 TCGCATTGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
33604 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
33625 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
33645 CTGATTTGCG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.02
21 46 0.94
22 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:34159 original size:31 final size:31
Alignment explanation
Indices: 34123--34181 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
34113 AACTTAAAAG
34123 AGTTTTACAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
34154 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
34182 CCATACAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:39902 original size:15 final size:15
Alignment explanation
Indices: 39882--39914 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
39872 GACAAAGTGA
39882 TTATTTTGTCAAATG
1 TTATTTTGTCAAATG
39897 TTATTTTGTCAAATG
1 TTATTTTGTCAAATG
39912 TTA
1 TTA
39915 GGGGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (15 bp):
TTATTTTGTCAAATG
Found at i:43264 original size:20 final size:20
Alignment explanation
Indices: 43239--43309 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
43229 TTTCCCTAAT
43239 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
43259 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
43279 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
43299 TCGCAATGCGA
1 TCGCAATGCGA
43310 TTTACATAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:43913 original size:33 final size:34
Alignment explanation
Indices: 43864--43939 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 34
43854 ACTATCGCAA
**
43864 TGCGATTTTGTCGTTGCGATTTTCA-TTTCGCGT
1 TGCGATTTTGTCGTTGCGATAGTCATTTTCGCGT
*
43897 TGCGATTCTTGT-GTTGCGATAGTCATTTTCGTGT
1 TGCGATT-TTGTCGTTGCGATAGTCATTTTCGCGT
43931 TGCGATTTT
1 TGCGATTTT
43940 CATTTTCGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 20 0.53
34 18 0.47
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.49
Consensus pattern (34 bp):
TGCGATTTTGTCGTTGCGATAGTCATTTTCGCGT
Found at i:43957 original size:20 final size:19
Alignment explanation
Indices: 43876--43958 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 19
43866 CGATTTTGTC
*
43876 GTTGCGATTTTCATTTCGC
1 GTTGCGATTTTCATTTCGT
43895 GTTGCGA--TTC--TT-GT
1 GTTGCGATTTTCATTTCGT
**
43909 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCA-TTTCGT
43929 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCA-TTTCGT
43949 GTTGCGATTT
1 GTTGCGATTT
43959 AAAGTTTCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 8 0.15
15 2 0.04
16 2 0.04
17 3 0.06
19 9 0.17
20 30 0.56
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
GTTGCGATTTTCATTTCGT
Found at i:43966 original size:20 final size:20
Alignment explanation
Indices: 43923--43966 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
43913 CGATAGTCAT
** *
43923 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
43943 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
43963 TTTC
1 TTTC
43967 AAAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:45911 original size:20 final size:20
Alignment explanation
Indices: 45849--45932 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
45839 AGAATAGTTT
*
45849 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
45869 ACTATTGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
45885 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
45903 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
*
45923 ACTGTCGCAA
1 ACTATCGCAA
45933 CGAAAGAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.12
16 4 0.08
17 4 0.08
18 4 0.08
20 33 0.65
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:45933 original size:54 final size:53
Alignment explanation
Indices: 45849--45970 Score: 145
Period size: 54 Copynumber: 2.3 Consensus size: 53
45839 AGAATAGTTT
* * *
45849 ACTATCGCAACGCGAAAATGACTATTGCAACGAGAGAATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG-AAATG
** * *
45903 ACTATCGCAATGCGAATTTGACTGTCGCAACGAAAGAATCGTAATGCGAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAATG
** *
45956 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
45971 TAGTCAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
53 17 0.29
54 41 0.71
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (53 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAATG
Found at i:45985 original size:20 final size:20
Alignment explanation
Indices: 45960--46118 Score: 148
Period size: 20 Copynumber: 8.6 Consensus size: 20
45950 GAAATGAAAA
*
45960 TCGCATTGCGATAGTCAATT
1 TCGCATTGCGATAGTCATTT
45980 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
46000 TCGCGTTGCGAT--T--TTGT
1 TCGCATTGCGATAGTCATT-T
**
46017 T-G--TTGCGATTTTCA-TT
1 TCGCATTGCGATAGTCATTT
* *
46033 TCGCATTGAGAT--TC--TC
1 TCGCATTGCGATAGTCATTT
46049 TCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
46067 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
46087 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
46107 TCGCGTTGCGAT
1 TCGCATTGCGAT
46119 TTTAAGTTTC
Statistics
Matches: 118, Mismatches: 7, Indels: 28
0.77 0.05 0.18
Matches are distributed among these distances:
14 13 0.11
16 12 0.10
17 6 0.05
18 5 0.04
19 6 0.05
20 76 0.64
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:46032 original size:34 final size:34
Alignment explanation
Indices: 45985--46119 Score: 128
Period size: 33 Copynumber: 3.8 Consensus size: 34
45975 CAATTTCGCA
* * * *
45985 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
** *
46019 TTGCGATTTTCA-TTTCGCATTGAGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
*
46052 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCGCATTGCGAT--TC--TCTCG
*
46090 CATTGCGATAGTCATTTTCGCGTTGCGATT
1 --TTGCGATAGTCATTTTCGCATTGCGATT
46120 TTAAGTTTCA
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
33 26 0.32
34 23 0.28
36 2 0.02
38 5 0.06
40 26 0.32
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:46693 original size:21 final size:21
Alignment explanation
Indices: 46625--46700 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
46615 GGCATCCCCT
*
46625 ATCGTTCAAGAGGCCTCTATC
1 ATCGTTCAAGAGGCCACTATC
** * **
46646 ATCCCTCAAGAGTCCACTCCC
1 ATCGTTCAAGAGGCCACTATC
* *
46667 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCACTATC
*
46688 ATCGTTGAAGAGG
1 ATCGTTCAAGAGG
46701 TCCCTCCCAA
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCACTATC
Found at i:46699 original size:42 final size:42
Alignment explanation
Indices: 46627--46709 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
46617 CATCCCCTAT
*
46627 CGTTCAAGAGGCCTCTATCATCCCTCAAGA-GTCCACTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCC-CTCCCAC
* ** *
46669 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
46710 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.89
43 4 0.11
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:48073 original size:14 final size:14
Alignment explanation
Indices: 48054--48089 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
48044 ATTGTTTAAT
48054 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
48068 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
48082 TGATTTGT
1 TGATTTGT
48090 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:48279 original size:34 final size:33
Alignment explanation
Indices: 48202--48283 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
48192 TTGCAACGCG
**
48202 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
48235 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
48268 GAAAATGAAAATCGCA
1 G-AAATGAAAATCGCA
48284 TTGCGATTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 31 0.69
34 14 0.31
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:48282 original size:20 final size:19
Alignment explanation
Indices: 48224--48289 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 19
48214 GCAACGAGAG
48224 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
48243 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
48257 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
48277 AATCGCATTGCGA
1 AATCGCAATGCGA
48290 TTCACTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 8 0.21
16 5 0.13
17 2 0.05
18 3 0.08
19 9 0.24
20 11 0.29
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:48317 original size:33 final size:34
Alignment explanation
Indices: 48279--48357 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 34
48269 AAAATGAAAA
**
48279 TCGCATTGCGATTCACTCGTTGCGATTTTCA-TT
1 TCGCATTGCGATTCACTCGTTGCGATAGTCATTT
*
48312 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATTCACTCGTTGCGATAGTCATTT
*
48346 TCGCGTTGCGAT
1 TCGCATTGCGAT
48358 AGTCAATTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 28 0.68
34 13 0.32
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.41
Consensus pattern (34 bp):
TCGCATTGCGATTCACTCGTTGCGATAGTCATTT
Found at i:48354 original size:20 final size:20
Alignment explanation
Indices: 48329--48422 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
48319 GCGATTCTCT
*
48329 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
48349 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
48369 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
48389 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
48409 CGTTGTGATAGTCA
1 CGTTGCGATAGTCA
48423 AATGAATGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 63 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:50852 original size:24 final size:24
Alignment explanation
Indices: 50818--50871 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
50808 CTGAAAAATC
50818 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
50842 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
50866 ATCAAA
1 ATCAAA
50872 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:50885 original size:24 final size:24
Alignment explanation
Indices: 50818--50885 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
50808 CTGAAAAATC
* * *
50818 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
50842 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
50866 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
50886 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:51737 original size:20 final size:20
Alignment explanation
Indices: 51714--51811 Score: 76
Period size: 20 Copynumber: 4.9 Consensus size: 20
51704 TTGCGATAGT
* *
51714 CAGAATCTCGTTGCGATTCA
1 CAGAATCGCATTGCGATTCA
* *
51734 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTCA
* *
51754 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTCA
* *
51774 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTCA
51794 C-GTAATCGCATTGCGATT
1 CAG-AATCGCATTGCGATT
51812 TTCCAAATTC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 1 0.01
20 71 0.99
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTCA
Found at i:51812 original size:20 final size:20
Alignment explanation
Indices: 51724--51848 Score: 171
Period size: 20 Copynumber: 6.2 Consensus size: 20
51714 CAGAATCTCG
*
51724 TTGCGATTCACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
51744 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
51764 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
51784 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
51804 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
51825 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
51845 TTGC
1 TTGC
51849 AATCGCAATG
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.01
20 76 0.83
21 15 0.16
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:51875 original size:52 final size:52
Alignment explanation
Indices: 51797--51900 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
51787 CGATTTACGT
*
51797 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGC
1 AATCGCAATGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGC
51849 AATCGCAATGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGC
1 AATCGCAATGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGC
51901 GAATTAGGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (52 bp):
AATCGCAATGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGC
Done.