Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003408.1 Hibiscus syriacus cultivar Beakdansim tig00007180_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: 58143
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3588 original size:18 final size:18
Alignment explanation
Indices: 3565--3652 Score: 176
Period size: 18 Copynumber: 4.9 Consensus size: 18
3555 AGGGTTCTAC
3565 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
3583 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
3601 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
3619 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
3637 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
3653 AATTCATATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.16, C:0.23, G:0.34, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:4686 original size:23 final size:23
Alignment explanation
Indices: 4620--4686 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
4610 TGTCATAGTC
* *
4620 CTATGATTATAATTTGAATATTAA
1 CTATAATTATAATAT-AATATTAA
*
4644 CTATAATATATAATAT-ATATTAT
1 CTATAAT-TATAATATAATATTAA
4667 C-ATTAATTATAATATAATAT
1 CTA-TAATTATAATATAATAT
4687 ATTATAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.24
23 15 0.41
24 6 0.16
25 7 0.19
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (23 bp):
CTATAATTATAATATAATATTAA
Found at i:7214 original size:20 final size:20
Alignment explanation
Indices: 7189--7228 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
7179 TAGTAAAATG
7189 CAATAGTGAGTATACTCATA
1 CAATAGTGAGTATACTCATA
7209 CAATAGTGAGTATACTCATA
1 CAATAGTGAGTATACTCATA
7229 TACTGCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
CAATAGTGAGTATACTCATA
Found at i:7896 original size:20 final size:22
Alignment explanation
Indices: 7871--7910 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
7861 TGTTGTATAT
7871 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
7891 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
7911 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:8056 original size:21 final size:20
Alignment explanation
Indices: 8012--8106 Score: 127
Period size: 21 Copynumber: 4.7 Consensus size: 20
8002 GCAGCCTTCG
* * *
8012 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGCAAGA
8032 TGCATCGATGCACAGCCAAGA
1 TGCATCGATGCACAG-CAAGA
*
8053 TGCATCGATGCACAACCAAGA
1 TGCATCGATGCAC-AGCAAGA
*
8074 TGCATCGATGCACAGAAAGA
1 TGCATCGATGCACAGCAAGA
8094 TGCATCGATGCAC
1 TGCATCGATGCAC
8107 TAATTGCATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 32 0.48
21 34 0.51
22 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAGCAAGA
Found at i:8174 original size:22 final size:23
Alignment explanation
Indices: 8141--8183 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
8131 ATGGATGCAC
8141 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
8164 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
8184 GCAGGGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:8198 original size:21 final size:20
Alignment explanation
Indices: 8127--8225 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
8117 CGGTGTTTGA
*
8127 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
8147 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
8169 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
8189 GATACATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
8211 GTGCATGGATGCACT
1 GTGCATGGATGCACT
8226 TTGACACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 29 0.42
22 17 0.25
23 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:8373 original size:34 final size:29
Alignment explanation
Indices: 8305--8364 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
8295 AAAATTTGAA
*
8305 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
8334 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
8365 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:9889 original size:30 final size:30
Alignment explanation
Indices: 9851--9920 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 30
9841 ATTTCCTTTT
9851 AAAA-ATTTTAATAAATTCAATT-AAGTCCA
1 AAAACATTTT-ATAAATTCAATTCAAGTCCA
*
9880 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAACATTTTATAAATTCAATTCAAGTCCA
9910 AAAACCATTTT
1 AAAA-CATTTT
9921 GCCTTAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 15 0.41
30 16 0.43
31 6 0.16
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAACATTTTATAAATTCAATTCAAGTCCA
Found at i:9894 original size:29 final size:31
Alignment explanation
Indices: 9862--9921 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
9852 AAAATTTTAA
9862 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
9891 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
9922 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:14669 original size:25 final size:25
Alignment explanation
Indices: 14641--14698 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
14631 CATAAAACTT
14641 AATATTATTATTT-TTAAAATATTAA
1 AATATTATTATTTATT-AAATATTAA
* *
14666 AATAATT-TTATTTATTTATTATTAA
1 AAT-ATTATTATTTATTAAATATTAA
14691 AATATTAT
1 AATATTAT
14699 CTCTATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
24 3 0.11
25 20 0.71
26 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AATATTATTATTTATTAAATATTAA
Found at i:15042 original size:27 final size:27
Alignment explanation
Indices: 15007--15060 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
14997 TATAATTGAG
*
15007 TATTTTATTATAATATTAAAAATATTA
1 TATTATATTATAATATTAAAAATATTA
* *
15034 TATTATATTATATTATTATAAATATTA
1 TATTATATTATAATATTAAAAATATTA
15061 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TATTATATTATAATATTAAAAATATTA
Found at i:15064 original size:10 final size:9
Alignment explanation
Indices: 15012--15068 Score: 55
Period size: 10 Copynumber: 6.3 Consensus size: 9
15002 TTGAGTATTT
15012 TATTAT-AA
1 TATTATAAA
*
15020 TATTAAAAA
1 TATTATAAA
*
15029 TATTATATTA
1 TATTATA-AA
*
15039 TATTAT-AT
1 TATTATAAA
15047 TATTATAAA
1 TATTATAAA
15056 TATTAATAAA
1 TATT-ATAAA
15066 TAT
1 TAT
15069 ATTTTAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 11 0.28
9 13 0.33
10 15 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TATTATAAA
Found at i:16471 original size:29 final size:29
Alignment explanation
Indices: 16439--16513 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
16429 AAAAATTACT
*
16439 TTCT-AAAAAACTCCATTAAATTATTA-AAA
1 TTCTCAAAAAACTCC-TTAAATT-TAAGAAA
*
16468 TTCTCAAAAAAACACCTTAAATTTAAGAAA
1 TTCTC-AAAAAACTCCTTAAATTTAAGAAA
*
16498 ATCTCAAAAAACTCCT
1 TTCTCAAAAAACTCCT
16514 AAGTTCCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 16 0.41
30 14 0.36
31 9 0.23
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.29
Consensus pattern (29 bp):
TTCTCAAAAAACTCCTTAAATTTAAGAAA
Found at i:16488 original size:30 final size:31
Alignment explanation
Indices: 16443--16508 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
16433 ATTACTTTCT
* * *
16443 AAAAAACTCCATTAAATTATTA-AAATTCTCA
1 AAAAAACACCATTAAATT-TAAGAAAATCTCA
16474 AAAAAACACC-TTAAATTTAAGAAAATCTCA
1 AAAAAACACCATTAAATTTAAGAAAATCTCA
16504 AAAAA
1 AAAAA
16509 CTCCTAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 20 0.65
31 9 0.29
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.26
Consensus pattern (31 bp):
AAAAAACACCATTAAATTTAAGAAAATCTCA
Found at i:19478 original size:32 final size:32
Alignment explanation
Indices: 19442--19584 Score: 151
Period size: 32 Copynumber: 4.5 Consensus size: 32
19432 CTCGTGTGCC
* ** *
19442 TTATCTGAATGCAACACAAACTCTGTTATGTA
1 TTATCTGAATGCAATACTGACTCTGTTATGCA
** ** *
19474 TTATCAAAATAAAATATTGACTCTGTTATGCA
1 TTATCTGAATGCAATACTGACTCTGTTATGCA
* **
19506 TTATTTGAATGCAATACTGACTCTACTATGCA
1 TTATCTGAATGCAATACTGACTCTGTTATGCA
* *
19538 TTATCTGATTGCAATGCTGACTCTGTTATGCA
1 TTATCTGAATGCAATACTGACTCTGTTATGCA
*
19570 TTATCTGAACGCAAT
1 TTATCTGAATGCAAT
19585 GTTGATACTA
Statistics
Matches: 87, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 87 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (32 bp):
TTATCTGAATGCAATACTGACTCTGTTATGCA
Found at i:24495 original size:14 final size:14
Alignment explanation
Indices: 24476--24503 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24466 TGGTTGTTGA
24476 AAAATAAAAAAAAT
1 AAAATAAAAAAAAT
24490 AAAATAAAAAAAAT
1 AAAATAAAAAAAAT
24504 GCTTTGTAAA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:26051 original size:44 final size:44
Alignment explanation
Indices: 25872--26087 Score: 164
Period size: 44 Copynumber: 4.9 Consensus size: 44
25862 AACTAAAAGT
* ** * * * *
25872 AATATCGATGTTGTTCCAACTCCCTATGTGATGGAAACGAA-CAG
1 AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATC-AAGCAA
* **
25916 AATATTGATGTTGACCCAACTCTCTCTGTTATGGAATCAAGTTA
1 AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATCAAGCAA
* * * * * *
25960 AATGTTGATGTTGACTCAACTCCCTATATTATGGAATCAATCGA
1 AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATCAAGCAA
* * * **
26004 AATATTGATGTTGACGCAATTCCCTCTGTTATGAAATTGAGCAA
1 AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATCAAGCAA
* ** * ** *
26048 AATATTTATACTGATCCAACTCATTCTGTGATGGAATCAA
1 AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATCAA
26088 ATATGCAAAA
Statistics
Matches: 131, Mismatches: 40, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
43 2 0.02
44 129 0.98
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (44 bp):
AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATCAAGCAA
Found at i:26451 original size:42 final size:42
Alignment explanation
Indices: 26386--26477 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
26376 GGATGGCCCA
* * *
26386 AAGGACTTAATCACCATGTTCGAAAGACATACTAGTGACTTG
1 AAGGATTTAATCACCATGCTCGAAAGACATACTAGTGACTCG
* * * *
26428 AAGGATTTAATCATCTTGCTCGAAAGACTTACTGGTGACTCG
1 AAGGATTTAATCACCATGCTCGAAAGACATACTAGTGACTCG
26470 AAGGATTT
1 AAGGATTT
26478 GCTCTTGCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (42 bp):
AAGGATTTAATCACCATGCTCGAAAGACATACTAGTGACTCG
Found at i:26676 original size:129 final size:128
Alignment explanation
Indices: 26426--26735 Score: 395
Period size: 129 Copynumber: 2.4 Consensus size: 128
26416 ACTAGTGACT
* * * * *
26426 TGAAGGATTTAATCATCTTGCTCGAAAGACTTACTGGTGACTCGAAGGATTTGCTCTTGCTTGGG
1 TGAAGGACTT-ATCACCCTGCTCGAAAGACTTA-TGATGACCCGAAGGATTTGCTCTTGCTTGGG
* * * *
26491 AATGCTTTCTTTCTTTTTAAGAATATCATGTGAAAACATCATACCTAAAGGACTTATAGATAACC
64 AATACTTTATTTCTTTTCAAGAATATCATGTGAAAACATCATACCCAAAGGACTTATAGATAACC
26556 TGAAGGACTTATCACCCTGCTCGAAAGACTTATAGATGACCCGAAGGATTTGCTCTTGCTTGGGA
1 TGAAGGACTTATCACCCTGCTCGAAAGACTTAT-GATGACCCGAAGGATTTGCTCTTGCTTGGGA
* * * * * * **
26621 ATATTTTATTTCTTTTCAAGAATATCATTTGAAAACATCATGCCCGAAGGTCTTATAGGTGGCC
65 ATACTTTATTTCTTTTCAAGAATATCATGTGAAAACATCATACCCAAAGGACTTATAGATAACC
* * * *
26685 CGAAGGACTTATCACCCTACTCGAAAGACTCACGGATGACCCGAAGGATTT
1 TGAAGGACTTATCACCCTGCTCGAAAGACTTA-TGATGACCCGAAGGATTT
26736 AAACACCATG
Statistics
Matches: 157, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
128 1 0.01
129 147 0.94
130 9 0.06
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (128 bp):
TGAAGGACTTATCACCCTGCTCGAAAGACTTATGATGACCCGAAGGATTTGCTCTTGCTTGGGAA
TACTTTATTTCTTTTCAAGAATATCATGTGAAAACATCATACCCAAAGGACTTATAGATAACC
Found at i:30210 original size:24 final size:21
Alignment explanation
Indices: 30163--30214 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
30153 GATGAGTTCC
**
30163 TATTTTTTAATTAAAAGTATA
1 TATTTTTTAATTAAAAAAATA
30184 TATTATTTTAATTATAAAAAATAA
1 TATT-TTTTAATTA-AAAAAAT-A
30208 TATTTTT
1 TATTTTT
30215 ATTTAAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 9 0.35
23 8 0.31
24 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTTTTAATTAAAAAAATA
Found at i:33154 original size:93 final size:93
Alignment explanation
Indices: 32986--33161 Score: 300
Period size: 93 Copynumber: 1.9 Consensus size: 93
32976 AATAGGTGCC
* *
32986 CAAATTTTTTTTCTATTCATCCAGGTGCCTAACGTTACAAATGTTACAACTATAGGTGTCTGGTC
1 CAAATTTTTTTTCGATTCATCCAGGTGCCTAACATTACAAATGTTACAACTATAGGTGTCTGGTC
*
33051 TATGATGACCATTAAAAATATATTGACA
66 TATGACGACCATTAAAAATATATTGACA
*
33079 CAAACTTTTTTTT-GATTCATCCATGTGCCTAACATTACAAATGTTACAACTATAGGTGTCTGGT
1 CAAA-TTTTTTTTCGATTCATCCAGGTGCCTAACATTACAAATGTTACAACTATAGGTGTCTGGT
33143 CTATGACGACCATTAAAAA
65 CTATGACGACCATTAAAAA
33162 AACATATTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
93 70 0.90
94 8 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (93 bp):
CAAATTTTTTTTCGATTCATCCAGGTGCCTAACATTACAAATGTTACAACTATAGGTGTCTGGTC
TATGACGACCATTAAAAATATATTGACA
Found at i:35005 original size:19 final size:20
Alignment explanation
Indices: 34981--35028 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
34971 AACGATTTCC
*
34981 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
35000 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
35020 TTTTGAAAA
1 TTTTGAAAA
35029 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:36246 original size:23 final size:24
Alignment explanation
Indices: 36214--36264 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
36204 CTCAAACCTC
36214 AAAATTCCCAAAT-TCCTAATCCCT
1 AAAATTCCCAAATATCC-AATCCCT
*
36238 AAAA-TCCCAAATATCCAATCTCT
1 AAAATTCCCAAATATCCAATCCCT
36261 AAAA
1 AAAA
36265 ATAGCCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAATTCCCAAATATCCAATCCCT
Found at i:36429 original size:15 final size:15
Alignment explanation
Indices: 36400--36450 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
36390 GGTGGGGTTA
*
36400 TTTAAAAAAAT-GTT
1 TTTAAAATAATAGTT
*
36414 TTTTAAATAATAGTT
1 TTTAAAATAATAGTT
36429 TTTAAAATAATA-TT
1 TTTAAAATAATAGTT
*
36443 TTCAAAAT
1 TTTAAAAT
36451 TATCACAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 18 0.56
15 14 0.44
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (15 bp):
TTTAAAATAATAGTT
Found at i:37079 original size:2 final size:2
Alignment explanation
Indices: 37072--37098 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37062 ATTATGCAGA
37072 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
37099 CTATTCAAAA
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:38110 original size:25 final size:26
Alignment explanation
Indices: 38069--38117 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
38059 TTAAATATAT
*
38069 TTTATAATTTTTTTAT-ATTATTTGA
1 TTTATAATTTTTATATAATTATTTGA
38094 TTTATACA-TTTTATATAATTATTT
1 TTTATA-ATTTTTATATAATTATTT
38118 TAAGTTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTATAATTTTTATATAATTATTTGA
Found at i:43801 original size:12 final size:12
Alignment explanation
Indices: 43786--43810 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43776 TGAGGAATAT
43786 GAGGAGGATTTG
1 GAGGAGGATTTG
43798 GAGGAGGATTTG
1 GAGGAGGATTTG
43810 G
1 G
43811 TTGACGACTA
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:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (12 bp):
GAGGAGGATTTG
Done.