Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007732.1 Hibiscus syriacus cultivar Beakdansim tig00109984_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: 85300
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2675 original size:20 final size:20
Alignment explanation
Indices: 2644--2698 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2634 AGTTTACTTG
2644 ATCATG-AAACCTTTTGTCC
1 ATCATGAAAACCTTTTGTCC
2663 ATCATGAAAACCTTTTGTCC
1 ATCATGAAAACCTTTTGTCC
2683 ATCATGAAAACCTTTT
1 ATCATGAAAACCTTTT
2699 ATTCTGATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 6 0.17
20 29 0.83
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (20 bp):
ATCATGAAAACCTTTTGTCC
Found at i:2885 original size:12 final size:12
Alignment explanation
Indices: 2868--2897 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2858 GAAAAACGAT
2868 AATACAAATGCA
1 AATACAAATGCA
2880 AATACAAATGCA
1 AATACAAATGCA
2892 AATACA
1 AATACA
2898 CAAGGTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (12 bp):
AATACAAATGCA
Found at i:7975 original size:14 final size:14
Alignment explanation
Indices: 7925--7976 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
7915 TTTATTGGTT
7925 TGTGAAAATGTTTATA
1 TGTG-AAATGTTT-TA
* *
7941 GGTGAATATGTTCTA
1 TGTGAA-ATGTTTTA
*
7956 TATGAAATGTTTTA
1 TGTGAAATGTTTTA
7970 TGTGAAA
1 TGTGAAA
7977 ATGTGCTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 13 0.45
15 8 0.28
16 8 0.28
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (14 bp):
TGTGAAATGTTTTA
Found at i:7978 original size:15 final size:15
Alignment explanation
Indices: 7925--7999 Score: 73
Period size: 15 Copynumber: 5.0 Consensus size: 15
7915 TTTATTGGTT
7925 TGTGAAAATGTT-TA
1 TGTGAAAATGTTCTA
*
7939 TAGGTGAATATGTTCTA
1 T--GTGAAAATGTTCTA
* *
7956 TATG-AAATGTTTTA
1 TGTGAAAATGTTCTA
*
7970 TGTGAAAATGTGCTA
1 TGTGAAAATGTTCTA
*
7985 AGTGAAAATGTTCTA
1 TGTGAAAATGTTCTA
8000 CATGAAAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
14 12 0.25
15 23 0.48
16 10 0.21
17 3 0.06
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (15 bp):
TGTGAAAATGTTCTA
Found at i:7994 original size:30 final size:32
Alignment explanation
Indices: 7926--7996 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 32
7916 TTATTGGTTT
* *
7926 GTGAAAATGTTTATAGGTGAATATGTTCTATA
1 GTGAAAATGTTTATAGGTGAAAATGTGCTATA
*
7958 -TG-AAATGTTT-TATGTGAAAATGTGCTA-A
1 GTGAAAATGTTTATAGGTGAAAATGTGCTATA
7986 GTGAAAATGTT
1 GTGAAAATGTT
7997 CTACATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 1 0.03
29 16 0.47
30 15 0.44
31 2 0.06
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (32 bp):
GTGAAAATGTTTATAGGTGAAAATGTGCTATA
Found at i:8005 original size:15 final size:15
Alignment explanation
Indices: 7927--8008 Score: 71
Period size: 15 Copynumber: 5.5 Consensus size: 15
7917 TATTGGTTTG
7927 TGAAAATGTT-TATA
1 TGAAAATGTTCTATA
*
7941 GGTGAATATGTTCTATA
1 --TGAAAATGTTCTATA
* *
7958 TG-AAATGTTTTATG
1 TGAAAATGTTCTATA
*
7972 TGAAAATGTGCTA-A
1 TGAAAATGTTCTATA
*
7986 GTGAAAATGTTCTACA
1 -TGAAAATGTTCTATA
8002 TGAAAAT
1 TGAAAAT
8009 ACCATATATG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
14 11 0.20
15 29 0.54
16 10 0.19
17 4 0.07
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (15 bp):
TGAAAATGTTCTATA
Found at i:8173 original size:23 final size:23
Alignment explanation
Indices: 8147--8211 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
8137 GTTCTACGTT
8147 CTTCGGGATAAATCTATGTGGTC
1 CTTCGGGATAAATCTATGTGGTC
* * *
8170 CTTCGGGATAATTCTACGTTGTC
1 CTTCGGGATAAATCTATGTGGTC
* *
8193 CTTTGGGACAAATTCTATG
1 CTTCGGGATAAA-TCTATG
8212 CGGACTTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 29 0.85
24 5 0.15
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (23 bp):
CTTCGGGATAAATCTATGTGGTC
Found at i:8822 original size:16 final size:16
Alignment explanation
Indices: 8780--8823 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
8770 TGAATATAAG
8780 TAAAAGTTCAAAATTTT
1 TAAAAGTT-AAAATTTT
* *
8797 CAACAAGTTAAAGTTTT
1 TAA-AAGTTAAAATTTT
8814 TAAAAGTTAA
1 TAAAAGTTAA
8824 TGTAACACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (16 bp):
TAAAAGTTAAAATTTT
Found at i:14938 original size:15 final size:15
Alignment explanation
Indices: 14902--14980 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
14892 TGGTATGAGG
14902 AAATGTT-TATTAGTGA
1 AAATGTTCTA-TA-TGA
*
14918 ATATGTTCTATATGA
1 AAATGTTCTATATGA
* *
14933 AAATGTTTTATGTGA
1 AAATGTTCTATATGA
* *
14948 AAATATGCTA-A-GTA
1 AAATGTTCTATATG-A
*
14962 AAATGTTCTACATGA
1 AAATGTTCTATATGA
14977 AAAT
1 AAAT
14981 ACCCTATGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
13 1 0.02
14 9 0.18
15 28 0.57
16 9 0.18
17 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (15 bp):
AAATGTTCTATATGA
Found at i:15188 original size:24 final size:23
Alignment explanation
Indices: 15117--15208 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 23
15107 GGTTCTACGC
*
15117 GGTCCTTCGGGACAAA-TCTATGT
1 GGTCCTTCAGGA-AAATTCTATGT
* * *
15140 GGTCCTTCTGGACAATTCTACGT
1 GGTCCTTCAGGAAAATTCTATGT
*
15163 GGTCCTTCAAGATAAATTCTATGT
1 GGTCCTTCAGGA-AAATTCTATGT
*
15187 GGTCCTTCGGGACAAATTCTAT
1 GGTCCTTCAGGA-AAATTCTAT
15209 ATGGCACTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
22 2 0.04
23 27 0.47
24 28 0.49
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (23 bp):
GGTCCTTCAGGAAAATTCTATGT
Found at i:15218 original size:24 final size:24
Alignment explanation
Indices: 15117--15208 Score: 125
Period size: 23 Copynumber: 3.9 Consensus size: 24
15107 GGTTCTACGC
15117 GGTCCTTCGGGACAAA-TCTATGT
1 GGTCCTTCGGGACAAATTCTATGT
* *
15140 GGTCCTTCTGGAC-AATTCTACGT
1 GGTCCTTCGGGACAAATTCTATGT
** *
15163 GGTCCTTCAAGATAAATTCTATGT
1 GGTCCTTCGGGACAAATTCTATGT
15187 GGTCCTTCGGGACAAATTCTAT
1 GGTCCTTCGGGACAAATTCTAT
15209 ATGGCACTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.03
23 28 0.48
24 28 0.48
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTATGT
Found at i:15726 original size:19 final size:19
Alignment explanation
Indices: 15685--15723 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
15675 TTAAGTATTT
* *
15685 ATTTTCAATGTGAGTTTGA
1 ATTTTCAATGTAACTTTGA
15704 ATTTTCAATAGTAACTTTGA
1 ATTTTCAAT-GTAACTTTGA
15724 TTTAAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (19 bp):
ATTTTCAATGTAACTTTGA
Found at i:16318 original size:3 final size:3
Alignment explanation
Indices: 16310--16377 Score: 73
Period size: 3 Copynumber: 21.7 Consensus size: 3
16300 ATTTTTATAG
* * * *
16310 TAA TAA TAA TAAA TAA TAA TCAA TAA TAA TAC TAA TAA GCAC TGA TAA
1 TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA
16358 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
16378 GGAATAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
3 47 0.87
4 7 0.13
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:16887 original size:191 final size:193
Alignment explanation
Indices: 16534--16961 Score: 558
Period size: 191 Copynumber: 2.2 Consensus size: 193
16524 CGATGACCCA
* * * * * * * *
16534 AAGGGTTTAATCATCATGCTTGAAGGACTTACTGATGGCTCGAAGGACTTACTCAGTTTTAGAAA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAAAGACTTACTCAATTTTAGAAA
* * *
16599 TAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAATTTTCAATTTTAAGAATCAAATGAGAA
66 TAGTTTACTAGGTAAGAAACTTTTATTACTTTTCAAAAATTTCAAATTTAAGAATCAAATGAGAA
* * *
16664 ATTTTTCTCATTTTTCGAAAGACACTTGAAAACA-TCATGCCCGAAGGTCTTATGAATGGCCCG
131 ACTTTTCTCATTTTTCGAAAGACACTTGAAAACATTC-GGCCCAAAGGTCTTATGAATGGCCCG
* * * * *
16727 AAGGATTT-ATCATCTTGCTCGATAGACTTACAGATGTCCCGAAAGACTTAC-CAATTTTGGGAA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAAAGACTTACTCAATTTTAGAAA
* * * * * *
16790 TAGTTTACTAGGTAAGAAACTTTTATTATTTTTCAAAAATTTCAAATTTCATATTTAAATGATAA
66 TAGTTTACTAGGTAAGAAACTTTTATTACTTTTCAAAAATTTCAAATTTAAGAATCAAATGAGAA
* * *
16855 ACTTTTCTTATTTTTCGAGAGACA-TGTGAAAACATTCGGCCCAAAGGTCTTATGGATGGCCCG
131 ACTTTTCTCATTTTTCGAAAGACACT-TGAAAACATTCGGCCCAAAGGTCTTATGAATGGCCCG
16918 AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAA
16962 GGATTTAAGC
Statistics
Matches: 202, Mismatches: 30, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
190 1 0.00
191 125 0.62
192 69 0.34
193 7 0.03
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (193 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAAAGACTTACTCAATTTTAGAAA
TAGTTTACTAGGTAAGAAACTTTTATTACTTTTCAAAAATTTCAAATTTAAGAATCAAATGAGAA
ACTTTTCTCATTTTTCGAAAGACACTTGAAAACATTCGGCCCAAAGGTCTTATGAATGGCCCG
Found at i:17650 original size:3 final size:3
Alignment explanation
Indices: 17642--17704 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
17632 GTATATTTTT
* * * *
17642 ATA ATA ATA ATA ATTA ATA CTA ATA ATA AGTA TTG ATA ATA GTA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
*
17689 ATA ATA ATA GTA ATA A
1 ATA ATA ATA ATA ATA A
17705 ATAAAATGTC
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
3 43 0.90
4 5 0.10
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:17670 original size:22 final size:21
Alignment explanation
Indices: 17642--17703 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
17632 GTATATTTTT
17642 ATAATAATAATAATTAATACTA
1 ATAATAATAATAA-TAATACTA
* * *
17664 ATAATAAGTATTGATAATAGTA
1 ATAATAA-TAATAATAATACTA
*
17686 ATAATAATAATAGTAATA
1 ATAATAATAATAATAATA
17704 AATAAAATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 8 0.24
22 21 0.64
23 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (21 bp):
ATAATAATAATAATAATACTA
Found at i:18476 original size:17 final size:17
Alignment explanation
Indices: 18450--18516 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
18440 ACAATTATTT
18450 TCTTTCTATTATATTAG
1 TCTTTCTATTATATTAG
*
18467 TCTTTGTATTATATTAG
1 TCTTTCTATTATATTAG
* *
18484 TATTTTCTATTCTATT--
1 T-CTTTCTATTATATTAG
*
18500 T-TTTCTATTCTATTAG
1 TCTTTCTATTATATTAG
18516 T
1 T
18517 ATTAGATTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
14 13 0.30
16 2 0.05
17 17 0.40
18 11 0.26
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.63
Consensus pattern (17 bp):
TCTTTCTATTATATTAG
Found at i:18505 original size:14 final size:14
Alignment explanation
Indices: 18486--18513 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18476 TATATTAGTA
18486 TTTTCTATTCTATT
1 TTTTCTATTCTATT
18500 TTTTCTATTCTATT
1 TTTTCTATTCTATT
18514 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:38284 original size:16 final size:17
Alignment explanation
Indices: 38263--38297 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
38253 TTACTATTCA
38263 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
38279 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
38296 CG
1 CG
38298 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:39065 original size:15 final size:16
Alignment explanation
Indices: 39047--39079 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39037 GTGGCAGATC
39047 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
39062 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
39078 AA
1 AA
39080 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:44429 original size:2 final size:2
Alignment explanation
Indices: 44422--44448 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44412 GGCATCGATC
44422 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
44449 AAGAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45313 original size:18 final size:16
Alignment explanation
Indices: 45279--45311 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
45269 TCTGATGTGC
45279 TTGGTGAGTTGATATA
1 TTGGTGAGTTGATATA
45295 TTGGTGAGTTGATATA
1 TTGGTGAGTTGATATA
45311 T
1 T
45312 ATAGAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (16 bp):
TTGGTGAGTTGATATA
Found at i:46210 original size:26 final size:27
Alignment explanation
Indices: 46181--46231 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
46171 GATTGTATTA
*
46181 AATAACTAGACTTTAA-TTAATAAAAC
1 AATAACTAGACTTTAAGTAAATAAAAC
*
46207 AATAACTATACTTTAAGTAAATAAA
1 AATAACTAGACTTTAAGTAAATAAA
46232 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (27 bp):
AATAACTAGACTTTAAGTAAATAAAAC
Found at i:49099 original size:13 final size:14
Alignment explanation
Indices: 49081--49109 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49071 TGTTGTGGAC
49081 ATCACGGT-TTAAA
1 ATCACGGTCTTAAA
49094 ATCACGGTCTTAAA
1 ATCACGGTCTTAAA
49108 AT
1 AT
49110 ATGATAGCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (14 bp):
ATCACGGTCTTAAA
Found at i:55561 original size:22 final size:21
Alignment explanation
Indices: 55527--55567 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
55517 ATAATTATTT
55527 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
55548 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
55568 ATTTGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:61345 original size:23 final size:23
Alignment explanation
Indices: 61315--61366 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
61305 TCATATAAAC
61315 GCACCGAAGTGCCACGTAGAATT
1 GCACCGAAGTGCCACGTAGAATT
* *
61338 GCACCGAAGTGTCGCGTAGAATT
1 GCACCGAAGTGCCACGTAGAATT
61361 GCACCG
1 GCACCG
61367 TAATGACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (23 bp):
GCACCGAAGTGCCACGTAGAATT
Found at i:68590 original size:31 final size:30
Alignment explanation
Indices: 68546--68605 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
68536 TATTGTATAG
68546 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
68576 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
68606 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:69753 original size:33 final size:33
Alignment explanation
Indices: 69716--69788 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
69706 AAGATTTATA
69716 TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
1 TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
69749 TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
1 TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
69782 TAATTTC
1 TAATTTC
69789 TCTTCTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (33 bp):
TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
Found at i:70091 original size:33 final size:33
Alignment explanation
Indices: 70054--70119 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
70044 TTTCTGAAGA
70054 AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
1 AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
70087 AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
1 AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
70120 GGAAGGCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (33 bp):
AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
Found at i:82426 original size:18 final size:18
Alignment explanation
Indices: 82405--82458 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
82395 GAAAAAATAT
82405 ATAAAATATAAAATAAAA
1 ATAAAATATAAAATAAAA
*
82423 AT-AAATA-AATAA-ATAA
1 ATAAAATATAA-AATAAAA
*
82439 ATCAAA-ATAAAATAAAA
1 ATAAAATATAAAATAAAA
82456 ATA
1 ATA
82459 TTAAATAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
16 10 0.34
17 17 0.59
18 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAAATATAAAATAAAA
Found at i:82440 original size:22 final size:21
Alignment explanation
Indices: 82397--82467 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 21
82387 TAAGAAAAGA
* *
82397 AAAAATATATAAAATATAAAAT
1 AAAAATAAATAAAAAAT-AAAT
82419 AAAAATAAATAAATAAATAAAT
1 AAAAATAAATAAA-AAATAAAT
*
82441 CAAAATAAAATAAAAATATTAAAT
1 AAAAAT-AAATAAAAA-A-TAAAT
82465 AAA
1 AAA
82468 CCAAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 23 0.56
23 11 0.27
24 7 0.17
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATAAATAAAAAATAAAT
Found at i:82464 original size:28 final size:28
Alignment explanation
Indices: 82397--82481 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
82387 TAAGAAAAGA
*
82397 AAAAATATATAAA-ATAT-AAAATAAAAAT
1 AAAAATAT-TAAATAAATCAAAAT-AAAAT
82425 AAATAA-A-TAAATAAATCAAAATAAAAT
1 AAA-AATATTAAATAAATCAAAATAAAAT
*
82452 AAAAATATTAAATAAACCAAAA-AAATAT
1 AAAAATATTAAATAAATCAAAATAAA-AT
82480 AA
1 AA
82482 GATAAAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
26 6 0.12
27 15 0.31
28 26 0.53
29 2 0.04
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (28 bp):
AAAAATATTAAATAAATCAAAATAAAAT
Found at i:82487 original size:33 final size:33
Alignment explanation
Indices: 82407--82488 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
82397 AAAAATATAT
*
82407 AAAATATAAAATAAAAATAAATAAATAAATAAATC
1 AAAATAT-AAATAAAAATAAATAAATAAACAAA-C
*
82442 AAAATA-AAATAAAAAT-ATTAAATAAACCAAA-
1 AAAATATAAATAAAAATAAATAAATAAA-CAAAC
82473 AAAATATAAGATAAAA
1 AAAATATAA-ATAAAA
82489 GAAAAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
31 6 0.14
32 11 0.26
33 19 0.45
35 6 0.14
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (33 bp):
AAAATATAAATAAAAATAAATAAATAAACAAAC
Found at i:82605 original size:18 final size:18
Alignment explanation
Indices: 82582--82620 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
82572 ACGAAATTAA
* *
82582 AAATAAAATATTAAAAAT
1 AAATAAAACATGAAAAAT
82600 AAATAAAACATGAAAAAT
1 AAATAAAACATGAAAAAT
82618 AAA
1 AAA
82621 AAGAGGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AAATAAAACATGAAAAAT
Found at i:84046 original size:24 final size:25
Alignment explanation
Indices: 84012--84071 Score: 104
Period size: 24 Copynumber: 2.4 Consensus size: 25
84002 TTCAAATCAA
84012 AATTTTTAAAAACTATATATTATAT
1 AATTTTTAAAAACTATATATTATAT
*
84037 -ATTTTCAAAAACTATATATTATAT
1 AATTTTTAAAAACTATATATTATAT
84061 AATTTTTAAAA
1 AATTTTTAAAA
84072 TATTTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTTTAAAAACTATATATTATAT
Found at i:84057 original size:97 final size:96
Alignment explanation
Indices: 83954--84143 Score: 239
Period size: 97 Copynumber: 2.0 Consensus size: 96
83944 TTTTTAAAAC
83954 TATATTATATAA-ATTTAAAATGA-TTTT-AAAACTATATATTATAAGTTTTTCAAATCAAAAT-
1 TATATTATATAATATTTAAAAT-ATTTTTAAAAACTATATATTAT-A-TTTTT----TCAAAATG
*
84015 TTTTAAAAACTATATA-T-TATATATTTTCAAAAACTA
59 TGTTAAAAACTATATATTATATATATTTTCAAAAACTA
* *
84051 TATATTATATAATTTTTAAAATATTTTTTAAAAACTATATATTATATTTTTTTAAAATGTGTTAA
1 TATATTATATAATATTTAAAATA-TTTTTAAAAACTATATATTATATTTTTTCAAAATGTGTTAA
84116 AAACTATATATTATATATATTTTCAAAA
65 AAACTATATATTATATATATTTTCAAAA
84144 TAATTTCAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
94 6 0.07
95 15 0.18
96 1 0.01
97 28 0.34
98 13 0.16
99 5 0.06
100 15 0.18
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (96 bp):
TATATTATATAATATTTAAAATATTTTTAAAAACTATATATTATATTTTTTCAAAATGTGTTAAA
AACTATATATTATATATATTTTCAAAAACTA
Found at i:84080 original size:61 final size:62
Alignment explanation
Indices: 83981--84107 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 62
83971 AAATGATTTT
*
83981 AAAACTATATATTATAAGTTTTTCAAATCAAAATTTTTAAAAACTATATATTATATATTTTCA
1 AAAACTATATATTATAAATTTTTCAAA-CAAAATTTTTAAAAACTATATATTATATATTTTCA
* * * *
84044 AAAACTATATATTATATAATTTTT-AAA-ATATTTTTTAAAAACTATATATTATATTTTTTTA
1 AAAACTATATATTATA-AATTTTTCAAACAAAATTTTTAAAAACTATATATTATATATTTTCA
84105 AAA
1 AAA
84108 TGTGTTAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
61 33 0.57
63 19 0.33
64 6 0.10
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (62 bp):
AAAACTATATATTATAAATTTTTCAAACAAAATTTTTAAAAACTATATATTATATATTTTCA
Found at i:84170 original size:37 final size:37
Alignment explanation
Indices: 84039--84181 Score: 170
Period size: 37 Copynumber: 3.9 Consensus size: 37
84029 TATTATATAT
* *
84039 TTTCAAAAACTATATATTATATA-ATTTTTAAAATATT
1 TTTCAAAAACTATATATTATATATATTTTCAAAATA-A
* * *
84076 TTTTAAAAACTATATATTATAT-T-TTTTTAAAAT-G
1 TTTCAAAAACTATATATTATATATATTTTCAAAATAA
84110 TGTT-AAAAACTATATATTATATATATTTTCAAAATAA
1 T-TTCAAAAACTATATATTATATATATTTTCAAAATAA
*
84147 TTTCAAAAACTATACATTATATATATGTTTCAAAA
1 TTTCAAAAACTATATATTATATATAT-TTTCAAAA
84182 ATCATTTGTA
Statistics
Matches: 94, Mismatches: 5, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
34 19 0.20
35 3 0.03
36 21 0.22
37 43 0.46
38 8 0.09
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (37 bp):
TTTCAAAAACTATATATTATATATATTTTCAAAATAA
Done.