Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000343.1 Hibiscus syriacus cultivar Beakdansim tig00000634_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: 91370
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:858 original size:25 final size:27
Alignment explanation
Indices: 805--858 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
795 AGTTGTTTTT
* * *
805 TTCTTTCTCTGTTTTTTTTTCTCTCGG
1 TTCTGTCTCCGTTTTTTTTTCTCTAGG
832 TTCTGTCTCCGTTTTTTTTT-TC-AGG
1 TTCTGTCTCCGTTTTTTTTTCTCTAGG
857 TT
1 TT
859 GGGGTGGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.17
26 2 0.08
27 18 0.75
ACGTcount: A:0.02, C:0.20, G:0.13, T:0.65
Consensus pattern (27 bp):
TTCTGTCTCCGTTTTTTTTTCTCTAGG
Found at i:1322 original size:3 final size:3
Alignment explanation
Indices: 1314--1378 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
1304 AATATATATT
*
1314 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1362 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1379 TGGGTAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:7708 original size:30 final size:30
Alignment explanation
Indices: 7624--7746 Score: 124
Period size: 30 Copynumber: 4.1 Consensus size: 30
7614 TCAAGGTAAG
* * * *
7624 TCCGTCACCGCACCTGCGGTTCAGAGAAGA
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
*
7654 TCCGTCA-TCGCACCTGCGGTTCAGGGAAGT
1 TCCGTCACT-GCACCGGCGGTTCAGGGAAGT
* *
7684 TCCGTCACTGCACCGGCGGTTCAGGTAGGT
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
* * *
7714 TCCATCACTGCACCAGG-GATTCAGGGAAAT
1 TCCGTCACTGCACC-GGCGGTTCAGGGAAGT
7744 TCC
1 TCC
7747 TCCACTGTGC
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
30 76 0.96
31 3 0.04
ACGTcount: A:0.20, C:0.31, G:0.28, T:0.21
Consensus pattern (30 bp):
TCCGTCACTGCACCGGCGGTTCAGGGAAGT
Found at i:7727 original size:60 final size:60
Alignment explanation
Indices: 7609--7746 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 60
7599 CTATGTACGT
* * * * * *
7609 GGGATTCAAGGTAAGTCCGTCACCGCACCTGCGGTTCAGAGAAGATCCGTCATCGCACCT
1 GGGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAGAAGATCCATCATCGCACCA
* * * *
7669 GCGG-TTCAGGGAAGTTCCGTCACTGCACCGGCGGTTCAG-GTAGGTTCCATCA-CTGCACCA
1 G-GGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAG-AAGATCCATCATC-GCACCA
7729 GGGATTCAGGGAAATTCC
1 GGGATTCAGGGAAATTCC
7747 TCCACTGTGC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
59 4 0.06
60 57 0.90
61 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (60 bp):
GGGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAGAAGATCCATCATCGCACCA
Found at i:8957 original size:30 final size:30
Alignment explanation
Indices: 8921--9043 Score: 158
Period size: 30 Copynumber: 4.1 Consensus size: 30
8911 TTCAAGGACA
**
8921 TTCCGTCACCACACCTCCGGTTCAGGGAAG
1 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
8951 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
1 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
* ** *
8981 CTCCGTCACTGCACCGGCGGTTCAGGGAGG
1 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
**
9011 TTCCAG-CACTGCACCTGGGGTTCAGGGAAG
1 TTCC-GTCACTGCACCTCCGGTTCAGGGAAG
9041 TTC
1 TTC
9044 TTCCACCGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 81 0.99
31 1 0.01
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (30 bp):
TTCCGTCACTGCACCTCCGGTTCAGGGAAG
Found at i:10060 original size:35 final size:35
Alignment explanation
Indices: 9967--10062 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
9957 AATACAATCA
* *
9967 TCAATTATATTCTAAACCCTAAATTCCAAAATGCT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
* *
10002 TTAATTATATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
* **
10037 TCAATTATATGCCCAACCCCAAATTC
1 TCAATTATATTCTAAACCCCAAATTC
10063 ATAATCTATT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATTCCAAAATACT
Found at i:10816 original size:145 final size:148
Alignment explanation
Indices: 10546--10833 Score: 456
Period size: 145 Copynumber: 2.0 Consensus size: 148
10536 AAACTATTTA
* * *
10546 AATTAGAATCAAATAGTATTATAGTATTATAAATATTTATAATTAAATTTAAACATAAACTCGAA
1 AATTAGAATCAAATAATATTATAGTATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
10611 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
10676 ATTTTATAAACTGGACTG
131 ATTTTATAAACTGGACTG
*
10694 AATTAGAATCAAATAATA-T-TA-TATGATAAATATTTATAATTAAATTTAAATAGAAACTCGAA
1 AATTAGAATCAAATAATATTATAGTATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
* * **** *
10756 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTTAAATCGAAATTTTTTTGAGTCAACT
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
10821 ATTTTATAAACTG
131 ATTTTATAAACTG
10834 AATTGAATAT
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
145 109 0.84
146 2 0.02
147 1 0.01
148 17 0.13
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAGTATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
ATTTTATAAACTGGACTG
Found at i:11433 original size:20 final size:20
Alignment explanation
Indices: 11397--11434 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11387 CAGTTTCCAA
* *
11397 AATTCGCAACGCGAATTTGG
1 AATTCGCAACACAAATTTGG
11417 AATTCGCAACACAAATTT
1 AATTCGCAACACAAATTT
11435 CTCAAATTCG
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:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (20 bp):
AATTCGCAACACAAATTTGG
Found at i:11455 original size:22 final size:21
Alignment explanation
Indices: 11396--11455 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 21
11386 ACAGTTTCCA
* *
11396 AAATTCGCAACGCGAA-TTTG
1 AAATTCGCAACACGAATTTTC
* *
11416 GAATTCGCAACACAAATTTCTC
1 AAATTCGCAACACGAATTT-TC
*
11438 AAATTCGCAACTCGAATT
1 AAATTCGCAACACGAATT
11456 CGCCAATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 13 0.42
21 2 0.06
22 16 0.52
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (21 bp):
AAATTCGCAACACGAATTTTC
Found at i:11628 original size:22 final size:22
Alignment explanation
Indices: 11603--11652 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
11593 TCCGCAAATT
11603 GAATTCGTCAATTTCGCAACTC
1 GAATTCGTCAATTTCGCAACTC
11625 GAATTCGTCAATTTCGCAACTC
1 GAATTCGTCAATTTCGCAACTC
11647 GAATTC
1 GAATTC
11653 CGAATTCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (22 bp):
GAATTCGTCAATTTCGCAACTC
Found at i:11646 original size:87 final size:88
Alignment explanation
Indices: 11417--11653 Score: 247
Period size: 87 Copynumber: 2.7 Consensus size: 88
11407 GCGAATTTGG
* * ** * *
11417 AATT-CGCAACACAAATTT-CTCAAATTCGCAACTCGAATTCGCCAATTTCTTAACTAAATTACC
1 AATTCCGCAACACGAATTTCCTCAATTTCGCAACTCGAATTCG-CAATTTCGCAACTCAATTCCC
*
11480 GATATATGTAAACACGGTAGAAAA
65 GATATAGGTAAACACGGTAGAAAA
* * *
11504 AATTTCGCAACACGAATTTCCCCAAATTT-GCAA-TGCGAATTCG-GATTTCGCAACTCAATTCC
1 AATTCCGCAACACGAATTTCCTC-AATTTCGCAACT-CGAATTCGCAATTTCGCAACTCAATTCC
*
11566 CGATATAGGTACACACGGTAGAAAA
64 CGATATAGGTAAACACGGTAGAAAA
* *
11591 AA-TCCGCAA-ATTGAA-TTCGTCAATTTCGCAACTCGAATTCGTCAATTTCGCAACTCGAATTC
1 AATTCCGCAACA-CGAATTTCCTCAATTTCGCAACTCGAATTCG-CAATTTCGCAACTC-AATTC
11653 C
63 C
11654 GAATTCGAGT
Statistics
Matches: 125, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
84 5 0.04
85 17 0.14
86 10 0.08
87 55 0.44
88 20 0.16
89 14 0.11
90 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.27
Consensus pattern (88 bp):
AATTCCGCAACACGAATTTCCTCAATTTCGCAACTCGAATTCGCAATTTCGCAACTCAATTCCCG
ATATAGGTAAACACGGTAGAAAA
Found at i:11745 original size:20 final size:19
Alignment explanation
Indices: 11698--11753 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
11688 TGAATTCCAA
*
11698 ATTCGGGTTGCGAAATTGG
1 ATTCGTGTTGCGAAATTGG
**
11717 AAACTGTGTTGCGAAATTGG
1 ATTC-GTGTTGCGAAATTGG
11737 AGTTCGTGTTGC-AAATT
1 A-TTCGTGTTGCGAAATT
11754 TGAAATCGCG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.23
20 22 0.73
21 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (19 bp):
ATTCGTGTTGCGAAATTGG
Found at i:17496 original size:29 final size:30
Alignment explanation
Indices: 17432--17502 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
17422 AACCGTTTTG
* *
17432 TATGATATGGTTTATTTTATTAATATATGAT
1 TATGATAT-GTATATTTTATTAATATATAAT
* *
17463 AATGATATGTAT-TTTTATTAATATTTAAT
1 TATGATATGTATATTTTATTAATATATAAT
*
17492 TATGATGTGTA
1 TATGATATGTA
17503 ATAATTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 24 0.71
30 3 0.09
31 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (30 bp):
TATGATATGTATATTTTATTAATATATAAT
Found at i:19364 original size:50 final size:51
Alignment explanation
Indices: 19243--19370 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
19233 TTAGCAGTAA
**
19243 AGCGC-ACCCCATGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGACCCC-TGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
** * *
19294 AGCATGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTAT
1 AGCGCGACCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
*
19344 AGCGCGACCCCTGCAGCGCGCTATACG
1 AGCGCGACCCCTGCACCGCGCTATACG
19371 CCACGTAGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
50 29 0.44
51 33 0.50
52 4 0.06
ACGTcount: A:0.18, C:0.34, G:0.30, T:0.17
Consensus pattern (51 bp):
AGCGCGACCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
Found at i:23591 original size:18 final size:18
Alignment explanation
Indices: 23568--23606 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
23558 AAGGCGATTA
23568 CGGCATCATATATGGTTG
1 CGGCATCATATATGGTTG
23586 CGGCATCATATATGGTTG
1 CGGCATCATATATGGTTG
23604 CGG
1 CGG
23607 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.31
Consensus pattern (18 bp):
CGGCATCATATATGGTTG
Found at i:25307 original size:110 final size:111
Alignment explanation
Indices: 25121--25333 Score: 356
Period size: 110 Copynumber: 1.9 Consensus size: 111
25111 AATTAATTCT
* * *
25121 TAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTAAATTAAAA
1 TAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAA
** *
25186 CGTTAAAATGTTATTGTATCAGCAAAGTGTCGAGATATTTAATTAG
66 CGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATATTTAATTAG
*
25232 TAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTAAATTAAAA
1 TAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAA
25296 CGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 CGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
25334 ATGATTTCCA
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 69 0.73
111 26 0.27
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.35
Consensus pattern (111 bp):
TAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAA
CGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATATTTAATTAG
Found at i:25692 original size:51 final size:50
Alignment explanation
Indices: 25588--25714 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 50
25578 AGATATACAG
** * * * **
25588 GTATAGCGCACTGCAGGGGCCGCACTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
*
25638 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCACCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATA-CCCACGTGGCACCAAATCACC
*
25689 GTATAGCGCGGTACAGGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
25715 TTACTGCTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 25 0.37
51 42 0.63
ACGTcount: A:0.20, C:0.32, G:0.33, T:0.15
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
Found at i:31958 original size:43 final size:44
Alignment explanation
Indices: 31910--31992 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
31900 AAAAAATTTC
31910 TAATTTGCTAATAGATAA-TAAAAATGA-TAAATTACTAATCTAT
1 TAATTTGCTAATAGATAATTAAAAAT-ATTAAATTACTAATCTAT
** *
31953 TAATTTTTTAATAGATAATTAAATATATTAAATTACTAAT
1 TAATTTGCTAATAGATAATTAAAAATATTAAATTACTAAT
31993 TGTTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 17 0.49
44 18 0.51
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (44 bp):
TAATTTGCTAATAGATAATTAAAAATATTAAATTACTAATCTAT
Found at i:32653 original size:35 final size:37
Alignment explanation
Indices: 32614--32688 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
32604 TTTTTATATT
32614 TTTAATTTTGTAAA-AAAAAATATAAATATTATA-AA
1 TTTAATTTTGTAAAGAAAAAATATAAATATTATACAA
* * *
32649 TTTAATTTTTTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAAGAAAAAATATAAATATTATACAA
32686 TTT
1 TTT
32689 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 13 0.37
36 17 0.49
37 5 0.14
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAGAAAAAATATAAATATTATACAA
Found at i:32870 original size:20 final size:20
Alignment explanation
Indices: 32834--32871 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32824 ATCCTATTCC
**
32834 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
32854 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
32872 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:34885 original size:2 final size:2
Alignment explanation
Indices: 34878--34935 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
34868 ATAGTTTGTT
34878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34920 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
34936 GGAACGAATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38871 original size:2 final size:2
Alignment explanation
Indices: 38864--38894 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38854 TTCTAGAATT
38864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38895 TAAAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44470 original size:23 final size:23
Alignment explanation
Indices: 44444--44487 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
44434 TTGTATGTTT
*
44444 TTTTATTTAATGATAATAATATA
1 TTTTATTTAATAATAATAATATA
44467 TTTTATTTAATAATAATAATA
1 TTTTATTTAATAATAATAATA
44488 ATTAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTATTTAATAATAATAATATA
Found at i:44746 original size:76 final size:76
Alignment explanation
Indices: 44646--44957 Score: 570
Period size: 76 Copynumber: 4.1 Consensus size: 76
44636 GAGGTCTTAA
* * *
44646 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGACTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
44711 AGGCTTTTTGG
66 AGGCTTTTTGG
*
44722 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
44787 AGGCTTTTTGG
66 AGGCTTTTTGG
44798 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
44863 AGGCTCTTTGG
66 AGGCTTTTTGG
*
44874 AAACATCATGCACTGAAGGACTTACATATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
44939 AGGCTTTTTGG
66 AGGCTTTTTGG
44950 AAACATCA
1 AAACATCA
44958 AAAAGCTCCC
Statistics
Matches: 228, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 228 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:44957 original size:31 final size:31
Alignment explanation
Indices: 44905--44988 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
44895 TTACATATGA
*
44905 CCCGAAGGC--TTTGAAAACATCAAAAAGCT
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
44934 CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
44965 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
44989 TGCTCTGAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 9 0.17
31 43 0.83
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (31 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
Found at i:44958 original size:107 final size:107
Alignment explanation
Indices: 44829--45064 Score: 413
Period size: 107 Copynumber: 2.2 Consensus size: 107
44819 TTACAGATGA
*
44829 CCCGAAGGC--TTTGAAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACATCATGCACTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACATCATGCACTGAAG
*
44892 GACTTACATATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
66 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
44934 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCTCTGAAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACATCATGCACTGAAG
*
44999 GGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
66 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
45041 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
45065 TGCACTGAAG
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
105 9 0.07
107 115 0.93
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (107 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACATCATGCACTGAAG
GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
Found at i:45030 original size:76 final size:76
Alignment explanation
Indices: 44934--45976 Score: 1942
Period size: 76 Copynumber: 13.7 Consensus size: 76
44924 TCAAAAAGCT
* *
44934 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCTCTGAAG
1 CCCGAAGGC--TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
*
44999 GGCTTACAGATGA
64 GACTTACAGATGA
45012 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45077 CTTACAGATGA
66 CTTACAGATGA
*
45088 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTAAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45153 CTTACAGATGA
66 CTTACAGATGA
* *
45164 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACATCATGCACTAAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45229 CTTACAGATGA
66 CTTACAGATGA
* * *
45240 CCCGAAGGCTTTTAAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACAGCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45305 CTTACAGATGA
66 CTTACAGATGA
*
45316 CCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45381 CTTACAGATGA
66 CTTACAGATGA
*
45392 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45457 CTTACAGATGA
66 CTTACAGATGA
45468 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45533 CTTACAGATGA
66 CTTACAGATGA
45544 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45609 CTTACAGATGA
66 CTTACAGATGA
45620 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45685 CTTACAGATGA
66 CTTACAGATGA
*
45696 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45761 CTTACAGATGA
66 CTTACAGATGA
*
45772 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTCTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45837 CTTACAGATGA
66 CTTACAGATGA
45848 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
45913 CTTACAGATGA
66 CTTACAGATGA
*
45924 CCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
45977 AAAAGCTCCC
Statistics
Matches: 947, Mismatches: 18, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
76 938 0.99
78 9 0.01
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (76 bp):
CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
CTTACAGATGA
Found at i:45976 original size:31 final size:31
Alignment explanation
Indices: 45924--46007 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
45914 TTACAGATGA
*
45924 CCCGAAGGC--TTTGAAAACATCAAAAAACT
1 CCCGAAGGCTTTTTGGAAACATCAAAAAACT
*
45953 CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
1 CCCGAAGGCTTTTTGGAAACATCAAAAAACT
45984 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
46008 TGCACTGAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 9 0.18
31 42 0.82
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (31 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAACT
Found at i:47243 original size:54 final size:55
Alignment explanation
Indices: 47096--47256 Score: 191
Period size: 59 Copynumber: 2.9 Consensus size: 55
47086 ATAATCACTG
* * *
47096 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGCTCGAATT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCGAATT
* * * *
47151 ATTGGTCAATGAAGCATTTGATAACACATTCATCCTTTCCTGTGGCTTCTGTTC-AGA-T
1 GTTCGT-AA--AA-CATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCGA-ATT
*
47209 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
47257 CAAGATTTCT
Statistics
Matches: 89, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
54 35 0.39
55 6 0.07
56 2 0.02
57 2 0.02
58 8 0.09
59 36 0.40
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (55 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCGAATT
Found at i:49546 original size:114 final size:114
Alignment explanation
Indices: 49333--49672 Score: 520
Period size: 114 Copynumber: 3.0 Consensus size: 114
49323 AATCATGCAG
* * * *
49333 TTCACCTTTCAATTCCAATGATCT-GTTTTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGAT-TGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
49397 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
49447 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * * *
49512 ACATTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
49561 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAATTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * *
49626 ACACTTCCAGAATATACTATTGGGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
49673 CATGGCACTT
Statistics
Matches: 203, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
113 1 0.00
114 202 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:51981 original size:18 final size:18
Alignment explanation
Indices: 51937--51978 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
51927 CTTGATTCAA
51937 TTTTCCTTTTTCTTTTCT
1 TTTTCCTTTTTCTTTTCT
*
51955 TTTTCCTTTTTTTTTTCT
1 TTTTCCTTTTTCTTTTCT
51973 TCTTTC
1 T-TTTC
51979 TTTGCTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCCTTTTTCTTTTCT
Found at i:52282 original size:2 final size:2
Alignment explanation
Indices: 52275--52323 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
52265 ACAACAAAGG
52275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52317 AT AT AT A
1 AT AT AT A
52324 AAAGGATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56631 original size:30 final size:30
Alignment explanation
Indices: 56586--56653 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
56576 TGCAAATAAA
*
56586 ATGAAATATTAATAAGAAAATATATAAATATT
1 ATGAAA-ATTAATAAGAAAATATA-AAAAATT
* *
56618 ATGAAAA-TAATAAGTATATATAAAAAATT
1 ATGAAAATTAATAAGAAAATATAAAAAATT
*
56647 TTGAAAA
1 ATGAAAA
56654 GAAAGAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.38
30 13 0.41
31 1 0.03
32 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.32
Consensus pattern (30 bp):
ATGAAAATTAATAAGAAAATATAAAAAATT
Found at i:56643 original size:19 final size:19
Alignment explanation
Indices: 56602--56643 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56592 TATTAATAAG
*
56602 AAAATATATAAATATTATG
1 AAAATATATAAATATTATA
*
56621 AAAATA-ATAAGTATATATA
1 AAAATATATAAATAT-TATA
56640 AAAA
1 AAAA
56644 ATTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAATATATAAATATTATA
Found at i:56686 original size:6 final size:7
Alignment explanation
Indices: 56667--56691 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56657 AGAATGTATG
56667 AATTTTT
1 AATTTTT
56674 AATTTTT
1 AATTTTT
56681 AATTTTT
1 AATTTTT
56688 AATT
1 AATT
56692 AATAGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:58777 original size:17 final size:17
Alignment explanation
Indices: 58755--58814 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
58745 TTATTTAATG
58755 ATAATAATATATATATA
1 ATAATAATATATATATA
* *
58772 ATAAT-ATATTTTATTTA
1 ATAATAATA-TATATATA
58789 ATAATAATA-ATA-ATTA
1 ATAATAATATATATA-TA
58805 A-AATAATATA
1 ATAATAATATA
58815 ATGAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
15 7 0.20
16 9 0.26
17 16 0.46
18 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAATATATATATA
Found at i:58796 original size:37 final size:35
Alignment explanation
Indices: 58743--58814 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 35
58733 TTGTATGTTT
* *
58743 TTTTATTTAATGATAATAATATATATATAATAATATA
1 TTTTATTTAATAATAATAATA-AT-TAAAATAATATA
58780 TTTTATTTAATAATAATAATAATTAAAATAATATA
1 TTTTATTTAATAATAATAATAATTAAAATAATATA
58815 ATGAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 11 0.33
36 2 0.06
37 20 0.61
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (35 bp):
TTTTATTTAATAATAATAATAATTAAAATAATATA
Found at i:75947 original size:26 final size:25
Alignment explanation
Indices: 75903--75952 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
75893 ATATATGTAT
*
75903 ATGTACATGTACATGAATTCCATAC
1 ATGTACATGAACATGAATTCCATAC
75928 ATGTACATGAAACATGAATTCCATA
1 ATGTACATG-AACATGAATTCCATA
75953 TGAACAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (25 bp):
ATGTACATGAACATGAATTCCATAC
Found at i:88819 original size:14 final size:15
Alignment explanation
Indices: 88787--88824 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
88777 ATCTTAAAGA
*
88787 TATATATTTATTTAAT
1 TATATTTTTATTT-AT
88803 TATATTTTTATTT-T
1 TATATTTTTATTTAT
88817 TATATTTT
1 TATATTTT
88825 ATTATAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
16 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATATTTTTATTTAT
Found at i:89356 original size:25 final size:26
Alignment explanation
Indices: 89327--89383 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
89317 AATCGTTTCA
*
89327 TAAATACATATTTAAAAT-ATATATC
1 TAAATACATATTTAAAATCACATATC
** *
89352 TAAATATTTTTTTAAAATCACATATC
1 TAAATACATATTTAAAATCACATATC
89378 TAAATA
1 TAAATA
89384 TCTAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAATACATATTTAAAATCACATATC
Done.