Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002366.1 Hibiscus syriacus cultivar Beakdansim tig00004835_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: 99705
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3327 original size:80 final size:81
Alignment explanation
Indices: 3194--3354 Score: 279
Period size: 80 Copynumber: 2.0 Consensus size: 81
3184 ATCGAGTAAG
*
3194 GTGATTGCCTTTGTTGACGCTGACTGGGCAAGCAATGTTGATGACCGCCGATCAGTTTATGGTTC
1 GTGATTGCCTTTGTTGACGCTGACTGGACAAGCAATGTTGATGACCGCCGATCAGTTTATGGTTC
*
3259 -TGGATTTTTCTTGGC
66 TTGCATTTTTCTTGGC
* *
3274 GTGATTGCCTTTGTTGACGCTGACTGGACAAGCAATGTTGATGATCGCCGATCAGTTTCTGGTTC
1 GTGATTGCCTTTGTTGACGCTGACTGGACAAGCAATGTTGATGACCGCCGATCAGTTTATGGTTC
3339 TTGCATTTTTCTTGGC
66 TTGCATTTTTCTTGGC
3355 ATCAACCTAA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 62 0.82
81 14 0.18
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.37
Consensus pattern (81 bp):
GTGATTGCCTTTGTTGACGCTGACTGGACAAGCAATGTTGATGACCGCCGATCAGTTTATGGTTC
TTGCATTTTTCTTGGC
Found at i:10904 original size:35 final size:35
Alignment explanation
Indices: 10858--10937 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
10848 TTTTCATGTC
*
10858 TTTT-TTCTTTTTCTT-T-TTTTTCGAACAACATTT
1 TTTTCTTCTTTTT-TTCTCTTTTTCAAACAACATTT
* *
10891 TTTTCTTCTTTTTTTCTCTTTTTCAAACTACTTTT
1 TTTTCTTCTTTTTTTCTCTTTTTCAAACAACATTT
10926 TTTTCTT-TTTTT
1 TTTTCTTCTTTTT
10938 CAATGGAGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 6 0.15
34 14 0.34
35 21 0.51
ACGTcount: A:0.11, C:0.16, G:0.01, T:0.71
Consensus pattern (35 bp):
TTTTCTTCTTTTTTTCTCTTTTTCAAACAACATTT
Found at i:10932 original size:32 final size:32
Alignment explanation
Indices: 10858--10938 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
10848 TTTTCATGTC
*
10858 TTTTTTCTTTTTCTT-TTTTTTCGAACAACATTT
1 TTTTTTCTTTTT-TTCTTTTTTCAAACAACA-TT
*
10891 TTTTCTTCTTTTTTTCTCTTTTTCAAACTAC-TT
1 TTTT-TTCTTTTTTTCT-TTTTTCAAACAACATT
10924 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
10939 AATGGAGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.26
33 12 0.28
34 9 0.21
35 11 0.26
ACGTcount: A:0.11, C:0.17, G:0.01, T:0.70
Consensus pattern (32 bp):
TTTTTTCTTTTTTTCTTTTTTCAAACAACATT
Found at i:12541 original size:26 final size:25
Alignment explanation
Indices: 12503--12552 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
12493 TTAGCATATT
12503 AAAAAGAAAACTTGAAAA-TAAAAG
1 AAAAAGAAAACTTGAAAAGTAAAAG
12527 AAAAATGAAGAACTTGAAAAGTAAAA
1 AAAAA-GAA-AACTTGAAAAGTAAAA
12553 AGAGAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 3 0.13
26 10 0.43
27 5 0.22
ACGTcount: A:0.68, C:0.04, G:0.14, T:0.14
Consensus pattern (25 bp):
AAAAAGAAAACTTGAAAAGTAAAAG
Found at i:14553 original size:12 final size:13
Alignment explanation
Indices: 14523--14566 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
14513 ATTTTATTTT
14523 TAAAAAAATATTA
1 TAAAAAAATATTA
*
14536 TTAAAAAATATTA
1 TAAAAAAATATTA
14549 -AAAAAAATATTA
1 TAAAAAAATATTA
14561 TGAAAA
1 T-AAAA
14567 TTATGTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 11 0.41
13 12 0.44
14 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
TAAAAAAATATTA
Found at i:15514 original size:20 final size:20
Alignment explanation
Indices: 15489--15526 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
15479 TTAGCGGGGT
15489 TATGACACGTAGGGAAGGGA
1 TATGACACGTAGGGAAGGGA
15509 TATGACACGTAGGGAAGG
1 TATGACACGTAGGGAAGG
15527 CGCGAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.39, T:0.16
Consensus pattern (20 bp):
TATGACACGTAGGGAAGGGA
Found at i:16837 original size:19 final size:19
Alignment explanation
Indices: 16813--16861 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
16803 TACAGAGGTA
16813 TGTTTTTAATTTTATTATT
1 TGTTTTTAATTTTATTATT
16832 TGTTTTTAATTTTATTATT
1 TGTTTTTAATTTTATTATT
**
16851 TACTTTTAATT
1 TGTTTTTAATT
16862 ATCGTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (19 bp):
TGTTTTTAATTTTATTATT
Found at i:17551 original size:21 final size:21
Alignment explanation
Indices: 17504--17554 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
17494 ACCTCAGTCT
* **
17504 GGTCAGACGCCACTGCTTCCA
1 GGTCAGATGCCACTGCAGCCA
**
17525 TATCAGATGCCACTGCAGCCA
1 GGTCAGATGCCACTGCAGCCA
17546 GGTCAGATG
1 GGTCAGATG
17555 ACACCATAGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (21 bp):
GGTCAGATGCCACTGCAGCCA
Found at i:17874 original size:15 final size:15
Alignment explanation
Indices: 17854--17886 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
17844 TAACTGCTCT
17854 TGATGATGATAATGA
1 TGATGATGATAATGA
17869 TGATGATGATAATGA
1 TGATGATGATAATGA
17884 TGA
1 TGA
17887 GAGTGAGGAG
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:0.39, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
TGATGATGATAATGA
Found at i:25262 original size:3 final size:3
Alignment explanation
Indices: 25254--25280 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25244 GTCTTTTTTA
25254 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
25281 ACAAAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30156 original size:16 final size:17
Alignment explanation
Indices: 30137--30171 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30127 ATATAAATTA
30137 TTTAAATA-ATAATAAT
1 TTTAAATATATAATAAT
*
30153 TTTAAATATTTAATAAT
1 TTTAAATATATAATAAT
30170 TT
1 TT
30172 ATATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAATATATAATAAT
Found at i:30172 original size:16 final size:16
Alignment explanation
Indices: 30136--30179 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
30126 TATATAAATT
*
30136 ATTTAAATA-ATAATA
1 ATTTAAATATTTAATA
30151 ATTTTAAATATTTAATA
1 A-TTTAAATATTTAATA
*
30168 ATTTATATATTT
1 ATTTAAATATTT
30180 TTAAAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 18 0.72
17 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTAAATATTTAATA
Found at i:30179 original size:25 final size:25
Alignment explanation
Indices: 30130--30196 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
30120 AAATATTATA
*
30130 TAAATTATTTAAATAA-TAATAA-TTT
1 TAAA-TATTT-AATAATTTATAATTTT
30155 TAAATATTTAATAATTTATATATTTT
1 TAAATATTTAATAATTTATA-ATTTT
*
30181 TAAA-ATTCAATAATTT
1 TAAATATTTAATAATTT
30197 GGTTTGTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 5 0.14
24 9 0.24
25 16 0.43
26 7 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
TAAATATTTAATAATTTATAATTTT
Found at i:44214 original size:2 final size:2
Alignment explanation
Indices: 44207--44232 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44197 ACAAAAGATA
44207 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
44233 GCTCTTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59178 original size:36 final size:32
Alignment explanation
Indices: 59115--59222 Score: 90
Period size: 34 Copynumber: 3.2 Consensus size: 32
59105 GGTAAGAAAT
* *
59115 TTATTTTTATGTTAATATTTTTTTAAATAGTTA
1 TTATTTTTATATTAATATTTTTGTAAATA-TTA
59148 TTATATTTTATATTAATATATTTATGTAAATATTA
1 TTAT-TTTTATATTAATAT-TTT-TGTAAATATTA
* * * * * *
59183 TTTTTTATTAAAATAATATTTATATAATTATTA
1 TTATTT-TTATATTAATATTTTTGTAAATATTA
59216 TTTATTT
1 -TTATTT
59223 AGAATTATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
33 13 0.21
34 22 0.36
35 19 0.31
36 7 0.11
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (32 bp):
TTATTTTTATATTAATATTTTTGTAAATATTA
Found at i:59186 original size:30 final size:32
Alignment explanation
Indices: 59151--59218 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 32
59141 ATAGTTATTA
*
59151 TATTTTATATT-AAT-ATATTTATGTAAATAT
1 TATTTTATATTAAATAATATTTATATAAATAT
* *
59181 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATATTTATATAAATAT
59214 TATTT
1 TATTT
59219 ATTTAGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 10 0.31
32 3 0.09
33 19 0.59
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TATTTTATATTAAATAATATTTATATAAATAT
Found at i:59385 original size:17 final size:17
Alignment explanation
Indices: 59363--59416 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
59353 AATGTTAATA
59363 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
59380 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
59397 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
59414 TTT
1 TTT
59417 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:60977 original size:21 final size:21
Alignment explanation
Indices: 60947--60994 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
60937 GCAGGGGTAC
* *
60947 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
60968 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
60989 ATGCCA
1 ATGCCA
60995 TATCTGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:61026 original size:21 final size:21
Alignment explanation
Indices: 61000--61070 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
60990 TGCCATATCT
*
61000 GCAGGGTTACATTCCGAGCCC
1 GCAGGGTTACATTCCTAGCCC
61021 GCAGGGTTACATTCCTAGCCC
1 GCAGGGTTACATTCCTAGCCC
*
61042 GCCA-GGTTACATGCCTAGCCC
1 G-CAGGGTTACATTCCTAGCCC
61063 GCAGGGTT
1 GCAGGGTT
61071 TTATACCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.21
Consensus pattern (21 bp):
GCAGGGTTACATTCCTAGCCC
Found at i:61621 original size:34 final size:34
Alignment explanation
Indices: 61583--61679 Score: 140
Period size: 34 Copynumber: 2.9 Consensus size: 34
61573 AATGTTTGAT
*
61583 AAATAAAAATTATATTATTCAAAATTTAAAATAA
1 AAATAAAAATTATATTATTCGAAATTTAAAATAA
* * *
61617 AAATAAAAATAATATTATTCGAAATTTAAATTTA
1 AAATAAAAATTATATTATTCGAAATTTAAAATAA
* *
61651 AAATATAAATTATAGTATTCGAAATTTAA
1 AAATAAAAATTATATTATTCGAAATTTAA
61680 CATTAAATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (34 bp):
AAATAAAAATTATATTATTCGAAATTTAAAATAA
Found at i:62262 original size:128 final size:128
Alignment explanation
Indices: 62030--62777 Score: 1327
Period size: 128 Copynumber: 5.8 Consensus size: 128
62020 GGTTATAATT
*
62030 TACTGATATATCTACTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
62095 TGACAAAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
*
62158 TACTGATATGA-ATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
** * *
62222 CTGACAAAATAATGGAAGGCGCGCCCCCAAGAACGTGCCTTCAAGTCCCCTAAGAAATAATAGG
65 CTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
62286 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
62351 TGACAAAATAATGGAAGGTGCGTCCCCGGGAACGAGCCTTCAAGTCCCCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
*
62414 TACTGATATATCTAGTGTTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
62479 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
62542 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
62607 TGACAAAATAATGGAAGGCGCGCCCCCCGGGAACGCGCCTTCAAGTCCTCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCG-CCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
* *
62671 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATTATAATATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
62736 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGACTTCA
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCA
62778 TGTGAATAGT
Statistics
Matches: 592, Mismatches: 25, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
127 1 0.00
128 466 0.79
129 125 0.21
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
Found at i:62871 original size:8 final size:8
Alignment explanation
Indices: 62858--62898 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
62848 TTACAAGCTT
62858 TCAAATTC
1 TCAAATTC
62866 TCAAATTC
1 TCAAATTC
* *
62874 CCAAACTC
1 TCAAATTC
62882 T-AAATTC
1 TCAAATTC
62889 TCAAATTC
1 TCAAATTC
62897 TC
1 TC
62899 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:67061 original size:24 final size:23
Alignment explanation
Indices: 67012--67065 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
67002 GTACTTCTAA
* *
67012 TTTATTTATTTGAATTTTATCCT
1 TTTATTTATTTGAATTATATACT
* *
67035 TTTATTTATTATTAATTATATATT
1 TTTATTTATT-TGAATTATATACT
67059 TTTATTT
1 TTTATTT
67066 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTATTTGAATTATATACT
Found at i:82760 original size:36 final size:35
Alignment explanation
Indices: 82679--82795 Score: 180
Period size: 35 Copynumber: 3.3 Consensus size: 35
82669 AGATGAACAA
* *
82679 TTGAATTGAAAGTGTTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
* *
82714 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC-AC
*
82750 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
82785 TTGAATCGAAA
1 TTGAATCGAAA
82796 TGTTTCCTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
35 42 0.57
36 32 0.43
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
Found at i:99642 original size:41 final size:41
Alignment explanation
Indices: 99575--99678 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 41
99565 TAGAAGAAAA
* *
99575 CGCAATGCGACTGAGAG-AATCGCAATGCGACTGAGAGAAT
1 CGCAATGCGATTTAGAGAAATCGCAATGCGACTGAGAGAAT
* *
99615 CGCAATGCGATTTATAGAAATCGCAATGCGATTGAGAGAAT
1 CGCAATGCGATTTAGAGAAATCGCAATGCGACTGAGAGAAT
*
99656 CGCAACGCGATTTAGA-AAATCGC
1 CGCAATGCGATTTAGAGAAATCGC
99679 CAACGTTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 21 0.37
41 36 0.63
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (41 bp):
CGCAATGCGATTTAGAGAAATCGCAATGCGACTGAGAGAAT
Found at i:99651 original size:61 final size:62
Alignment explanation
Indices: 99550--99683 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 62
99540 ATACCAATAA
*
99550 AATCGCAACGCGATTTAGAAGAAAACGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAACGCGATTTAGAAGAAAACGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAG
* * * * * * *
99612 AATCGCAATGCGATTTA-TAGAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAACGCGATTTAGAAGAAAACGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAG
99673 AATCGCCAACG
1 AATCG-CAACG
99684 TTAAAAAGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 42 0.68
62 20 0.32
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (62 bp):
AATCGCAACGCGATTTAGAAGAAAACGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAG
Found at i:99666 original size:20 final size:20
Alignment explanation
Indices: 99550--99678 Score: 141
Period size: 20 Copynumber: 6.3 Consensus size: 20
99540 ATACCAATAA
* *
99550 AATCGCAACGCGATTTAGAAG
1 AATCGCAATGCGATTGAG-AG
* *
99571 AAAACGCAATGCGACTGAGAG
1 -AATCGCAATGCGATTGAGAG
*
99592 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
99612 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
99632 AAATCGCAATGCGATTGAGAG
1 -AATCGCAATGCGATTGAGAG
* * *
99653 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
99673 AATCGC
1 AATCGC
99679 CAACGTTAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
20 59 0.63
21 20 0.22
22 14 0.15
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:99697 original size:61 final size:61
Alignment explanation
Indices: 99548--99701 Score: 163
Period size: 61 Copynumber: 2.5 Consensus size: 61
99538 AAATACCAAT
* *
99548 AAAATCGCAACGCGATTTAGAAGAAAA-CGCAATGCGACTGAGAGAATCGCAATGCGACTGAG
1 AAAATCGCAA-GCGA-TTAAAAGAAAATCGCAATGCGACTGAGAGAATCGCAACGCGACTGAG
* * * * * *
99610 AGAATCGCAATGCGATTTATAG-AAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAG
1 AAAATCGCAA-GCGATTAAAAGAAAATCGCAATGCGACTGAGAGAATCGCAACGCGACTGAG
99671 AAAATCGCCAA-CG-TTAAAAAGAAAATCGCAA
1 AAAATCG-CAAGCGATT-AAAAGAAAATCGCAA
99702 CGGT
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
59 2 0.03
60 8 0.11
61 50 0.66
62 16 0.21
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (61 bp):
AAAATCGCAAGCGATTAAAAGAAAATCGCAATGCGACTGAGAGAATCGCAACGCGACTGAG
Done.