Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003469.1 Hibiscus syriacus cultivar Beakdansim tig00007340_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: 123588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:3683 original size:2 final size:2
Alignment explanation
Indices: 3676--3701 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3666 TCTGTATGAA
3676 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
3702 TTCACATATG
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:6287 original size:12 final size:12
Alignment explanation
Indices: 6244--6293 Score: 64
Period size: 13 Copynumber: 4.0 Consensus size: 12
6234 TTAATATTAT
*
6244 TTTTGAAAAATAA
1 TTTTAAAAAAT-A
*
6257 TTTTAAAAAGTA
1 TTTTAAAAAATA
6269 TTGTTAAAAAATA
1 TT-TTAAAAAATA
6282 TTTTAAAAAATA
1 TTTTAAAAAATA
6294 CAATTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 13 0.39
13 20 0.61
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (12 bp):
TTTTAAAAAATA
Found at i:6300 original size:25 final size:26
Alignment explanation
Indices: 6249--6302 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
6239 ATTATTTTTG
* ***
6249 AAAAATAATTTTAAAAAGTATTGTTA
1 AAAAATAATTTTAAAAAATACAATTA
6275 AAAAAT-ATTTTAAAAAATACAATTA
1 AAAAATAATTTTAAAAAATACAATTA
6300 AAA
1 AAA
6303 TTTAACTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAAATAATTTTAAAAAATACAATTA
Found at i:7161 original size:24 final size:24
Alignment explanation
Indices: 7129--7200 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
7119 GTTTGGCAGG
7129 TGAATTTATAAAATTTTAGTGGGA
1 TGAATTTATAAAATTTTAGTGGGA
7153 TGAATTTATAAAATTTTAGTGGGA
1 TGAATTTATAAAATTTTAGTGGGA
* *
7177 -CATATTTATAAAAGTTTAG-GGGA
1 TGA-ATTTATAAAATTTTAGTGGGA
7200 T
1 T
7201 AAAATTAGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.11
24 39 0.89
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (24 bp):
TGAATTTATAAAATTTTAGTGGGA
Found at i:10306 original size:21 final size:21
Alignment explanation
Indices: 10280--10324 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
10270 GTCTGTCTCG
10280 TGCATATGCTTTTTGAATTGC
1 TGCATATGCTTTTTGAATTGC
10301 TGCATATGCTTTTTGAATTGC
1 TGCATATGCTTTTTGAATTGC
10322 TGC
1 TGC
10325 CTCACCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.47
Consensus pattern (21 bp):
TGCATATGCTTTTTGAATTGC
Found at i:11808 original size:3 final size:3
Alignment explanation
Indices: 11796--11827 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
11786 ACTCTATAAG
11796 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11828 TTAAGAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12031 original size:28 final size:26
Alignment explanation
Indices: 11981--12034 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
11971 CCTTTCTTTT
11981 TATATTTTTATTTTCTAATAAAAAAA
1 TATATTTTTATTTTCTAATAAAAAAA
*
12007 TATATTTTTATTTTTTAA-AATAAAAA
1 TATATTTTTATTTTCTAATAA-AAAAA
12033 TA
1 TA
12035 ACCTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATATTTTTATTTTCTAATAAAAAAA
Found at i:12041 original size:26 final size:25
Alignment explanation
Indices: 11981--12053 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
11971 CCTTTCTTTT
* *
11981 TATATTTTTATTTTCTAATAAAAAAA
1 TATACTTTTATTTTTTAA-AAAAAAA
*
12007 TATATTTTTATTTTTTAAAATAAAAA
1 TATACTTTTATTTTTTAAAA-AAAAA
12033 TA-ACCTTTTATATATTTTAAA
1 TATA-CTTTTAT-T-TTTTAAA
12054 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 3 0.07
26 30 0.73
27 1 0.02
28 7 0.17
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
TATACTTTTATTTTTTAAAAAAAAA
Found at i:27937 original size:34 final size:33
Alignment explanation
Indices: 27861--27967 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
27851 GTGGTAAGAA
* *
27861 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
27895 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
27930 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
27964 ATTT
1 ATTT
27968 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:27949 original size:36 final size:34
Alignment explanation
Indices: 27894--27972 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
27884 TTTAAATAGT
*
27894 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
27926 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
27960 TATTATTTATTTA
1 TATTATTTTTTTA
27973 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:28132 original size:17 final size:17
Alignment explanation
Indices: 28110--28163 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
28100 AATGTTAATA
28110 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * *
28127 TTTAAATTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
28144 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
28161 TTT
1 TTT
28164 TTATAATGTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:28156 original size:28 final size:26
Alignment explanation
Indices: 28091--28178 Score: 72
Period size: 28 Copynumber: 3.3 Consensus size: 26
28081 TGGTAATATT
* *
28091 TTTATAATTAATGTTAATAT-TTA-AA
1 TTTAT-ATTAATTTTAATTTATTATAA
* *
28116 TTTATTTTTATTTTAAATTTATTATGAA
1 TTTATATTAATTTT-AATTTATTAT-AA
* *
28144 TTTATATTAATTTTTATTTTTTATAA
1 TTTATATTAATTTTAATTTATTATAA
*
28170 TGTATATTA
1 TTTATATTA
28179 TTTAGGATGT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
24 6 0.12
25 9 0.18
26 13 0.26
27 8 0.16
28 14 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (26 bp):
TTTATATTAATTTTAATTTATTATAA
Found at i:29725 original size:21 final size:21
Alignment explanation
Indices: 29695--29742 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
29685 GCAGGGGTAC
* *
29695 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
29716 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
29737 ATGCCA
1 ATGCCA
29743 TCTCCGCAGG
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:29772 original size:21 final size:21
Alignment explanation
Indices: 29746--29839 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
29736 TATGCCATCT
* *
29746 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
29767 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
29788 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
29809 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
29830 CCGCAGGGTT
1 CCGCAGGGTT
29840 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:30421 original size:33 final size:34
Alignment explanation
Indices: 30362--30458 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
30352 AAATGTTTTT
* *
30362 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
30396 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
30429 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
30459 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:30465 original size:34 final size:32
Alignment explanation
Indices: 30360--30465 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
30350 ATAAATGTTT
*
30360 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
30394 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
30426 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
30461 TTAAA
1 TTAAA
30466 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:30869 original size:128 final size:128
Alignment explanation
Indices: 30640--31504 Score: 1579
Period size: 128 Copynumber: 6.8 Consensus size: 128
30630 ACGGAATCAG
*
30640 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGGCG
1 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
* *
30705 CGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTAATGATATATCTAGTGTCC
66 CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
30768 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
1 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
*** *
30833 CGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGGTACTGATATATCTAGTGTCC
66 CGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
30896 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
1 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
30961 CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
66 CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
*
31024 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGGCG
1 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
*
31089 CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTATTGATATATCTAGTGTCC
66 CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
*
31152 CCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
1 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
* * *
31217 CCCCCCCGAGAACGCGTCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
66 CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
31280 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
1 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
31345 CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
66 CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
*
31408 TCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
1 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
*
31473 CACCCCCGGGAACGCGCCTTCATGTGAATAGT
66 CGCCCCCGGGAACGCGCCTTCATGTGAATAGT
31505 ACTCCGATTA
Statistics
Matches: 710, Mismatches: 25, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
127 1 0.00
128 708 1.00
129 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
CGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
Found at i:31588 original size:8 final size:8
Alignment explanation
Indices: 31575--31615 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
31565 TCACAATCTT
31575 TCAAATTC
1 TCAAATTC
31583 TCAAATTC
1 TCAAATTC
* *
31591 CCAAACTC
1 TCAAATTC
31599 T-AAATTC
1 TCAAATTC
31606 TCAAATTC
1 TCAAATTC
31614 TC
1 TC
31616 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:35508 original size:23 final size:22
Alignment explanation
Indices: 35481--35524 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
35471 GGTGTAGTCT
* *
35481 TCTATATAATTTATATATACTTC
1 TCTATAAAATTTAGATA-ACTTC
35504 TCTATAAAATTTAGATAACTT
1 TCTATAAAATTTAGATAACTT
35525 TATAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (22 bp):
TCTATAAAATTTAGATAACTTC
Found at i:36255 original size:28 final size:28
Alignment explanation
Indices: 36215--36307 Score: 168
Period size: 28 Copynumber: 3.3 Consensus size: 28
36205 AAAAATTTAA
36215 AATACTCATGAGCTAATTAGTAACACTT
1 AATACTCATGAGCTAATTAGTAACACTT
36243 AATACTCATGAGCTAATTAGTAACACTT
1 AATACTCATGAGCTAATTAGTAACACTT
* *
36271 AATACTCATGAGTTAATTAGTAGCACTT
1 AATACTCATGAGCTAATTAGTAACACTT
36299 AATACTCAT
1 AATACTCAT
36308 AAGCACCAGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (28 bp):
AATACTCATGAGCTAATTAGTAACACTT
Found at i:36973 original size:22 final size:22
Alignment explanation
Indices: 36933--36975 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
36923 AATCTAAATT
*
36933 CTAAACCATAAAGTCTAAAACC
1 CTAAACCATAAAGTATAAAACC
* *
36955 CTAAACCATATATTATAAAAC
1 CTAAACCATAAAGTATAAAAC
36976 TTTACAACTT
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:0.51, C:0.23, G:0.02, T:0.23
Consensus pattern (22 bp):
CTAAACCATAAAGTATAAAACC
Found at i:37462 original size:59 final size:61
Alignment explanation
Indices: 37356--37506 Score: 145
Period size: 60 Copynumber: 2.5 Consensus size: 61
37346 GTATATATGT
* * * *
37356 ATAGTTTG-GGATGAAATTGAAATGCTCAAAATGTTTGGAGACAAATTT-AGATGA-AGGCC
1 ATAGTTTGAGGATGAAAATGAAATGTTTAAAATGTTTGGAGACAAATTTAAAATGATA-GCC
** *
37415 ATAGTTTGAGGATGAAAATGAAATGTTTAAAA-GTTT-GAGGATTAATTTAAAATGATAGTC
1 ATAGTTTGAGGATGAAAATGAAATGTTTAAAATGTTTGGA-GACAAATTTAAAATGATAGCC
*
37475 ATAGTTT-AGGGATG-AAATTAGAATGTTTAAAA
1 ATAGTTTGA-GGATGAAAATGA-AATGTTTAAAA
37507 ATTTAGGGAC
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
58 2 0.03
59 25 0.32
60 50 0.64
61 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (61 bp):
ATAGTTTGAGGATGAAAATGAAATGTTTAAAATGTTTGGAGACAAATTTAAAATGATAGCC
Found at i:48298 original size:20 final size:20
Alignment explanation
Indices: 48275--48326 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
48265 AAAATTATCA
*
48275 ATTTGATCGCAAAACTTTTT
1 ATTTGATTGCAAAACTTTTT
48295 ATTTGATTGCAAAACTTTTT
1 ATTTGATTGCAAAACTTTTT
48315 ATTTGATTGCAA
1 ATTTGATTGCAA
48327 TCAAGTTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTTGATTGCAAAACTTTTT
Found at i:49335 original size:33 final size:33
Alignment explanation
Indices: 49298--49373 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
49288 GTCTTACTTG
* *
49298 GACTCAAATGTTTTAGTTTTAGTGTTTCAATAA
1 GACTCAAATATGTTAGTTTTAGTGTTTCAATAA
* *
49331 GACTCAAATATGTTGGTTTTAGTGTTTCAATAG
1 GACTCAAATATGTTAGTTTTAGTGTTTCAATAA
49364 GACTCAAATA
1 GACTCAAATA
49374 CGTTGATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (33 bp):
GACTCAAATATGTTAGTTTTAGTGTTTCAATAA
Found at i:50008 original size:83 final size:83
Alignment explanation
Indices: 49822--50160 Score: 459
Period size: 83 Copynumber: 4.1 Consensus size: 83
49812 TGGAATCAAG
* * * * *
49822 CTCGAAGGTC--T-TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGGTGCATT
1 CTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT-GTGCCTT
* * *
49884 TGAGCTGAGTGGAGTCGAA
65 GGAGCTGAGCGTAGTCGAA
* * * *
49903 CTCGGAGGTCATTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTG
1 CTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTG
**
49968 GAGCTGAGTATAGTCGAA
66 GAGCTGAGCGTAGTCGAA
* *
49986 CTCGAAGGTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTG
1 CTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTG
*
50051 GAGCTGAGCGTAGTCAAA
66 GAGCTGAGCGTAGTCGAA
* * *
50069 CTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATAATGTGTCTTG
1 CTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTG
*
50134 AAGCTGAGCGTAGTCGAA
66 GAGCTGAGCGTAGTCGAA
50152 CTCGAAGGT
1 CTCGAAGGT
50161 TTGATGTTTC
Statistics
Matches: 230, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
81 9 0.04
83 184 0.80
84 37 0.16
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (83 bp):
CTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTG
GAGCTGAGCGTAGTCGAA
Found at i:50413 original size:36 final size:36
Alignment explanation
Indices: 50366--50470 Score: 156
Period size: 37 Copynumber: 2.9 Consensus size: 36
50356 AAGATTTTAT
*
50366 TTTCAAGGGAAACTATCTCAATAGAGACAAAATTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTG
* *
50402 TTTCAAGGGAAACTATCTTAAGAGAGACAAGATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAA-AATTTG
* *
50439 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA
50471 CTTGGAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 29 0.48
37 32 0.52
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTG
Found at i:51317 original size:21 final size:21
Alignment explanation
Indices: 51291--51334 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
51281 AATTGTGTCA
51291 CTTTGAGTACAATATCCTTCG
1 CTTTGAGTACAATATCCTTCG
*
51312 CTTTGAGTCCAATATCCTTCG
1 CTTTGAGTACAATATCCTTCG
51333 CT
1 CT
51335 GTGAAGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (21 bp):
CTTTGAGTACAATATCCTTCG
Found at i:51694 original size:32 final size:32
Alignment explanation
Indices: 51658--51752 Score: 145
Period size: 32 Copynumber: 2.9 Consensus size: 32
51648 ATTCCCAAAT
*
51658 ATGCCCCAATATTTGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
* *
51690 ATGCCCCTACATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
*
51722 ATGCCCCAGCATTTGATGTTGAATCTTCAAA
1 ATGCCCCAACATTTGATGTTGAATC-TCAAA
51753 GATGCCCTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
32 51 0.91
33 5 0.09
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAA
Found at i:52915 original size:26 final size:25
Alignment explanation
Indices: 52860--52932 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 25
52850 ATATTGTCTT
*
52860 CTTTTTT-TCTTCAATTTTC-CTTTG
1 CTTTTTTCTCTT-TATTTTCTCTTTG
52884 -TTTTTTCTCTTTTTATTTTCTCTTTG
1 CTTTTTTCTC--TTTATTTTCTCTTTG
52910 CTTTTTTCTCTTT-TTTTCTCTTT
1 CTTTTTTCTCTTTATTTTCTCTTT
52933 TTGTTCTTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
23 6 0.14
24 12 0.28
25 9 0.21
26 7 0.16
27 9 0.21
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (25 bp):
CTTTTTTCTCTTTATTTTCTCTTTG
Found at i:52916 original size:14 final size:13
Alignment explanation
Indices: 52874--52937 Score: 71
Period size: 12 Copynumber: 5.0 Consensus size: 13
52864 TTTTCTTCAA
52874 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
52886 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
52898 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
52913 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
* *
52925 TTCTCTTTTTGTT
1 TTTTCTCTTTGTT
52938 CTTGATTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
12 17 0.38
13 16 0.36
14 10 0.22
15 2 0.04
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:52920 original size:27 final size:25
Alignment explanation
Indices: 52873--52924 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
52863 TTTTTCTTCA
52873 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
52898 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTC-CTTTG-TTTTTTCTCTTTTT
52925 TTCTCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:52935 original size:26 final size:26
Alignment explanation
Indices: 52879--52937 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
52869 TTCAATTTTC
*
52879 CTTTGTTTTTTCTCTTTTTATTTTCT
1 CTTTGTTTTTTCTCTTTTTATTCTCT
52905 CTTTGCTTTTTTCTCTTTTT-TTCTCT
1 CTTTG-TTTTTTCTCTTTTTATTCTCT
*
52931 TTTTGTT
1 CTTTGTT
52938 CTTGATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 14 0.47
27 14 0.47
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (26 bp):
CTTTGTTTTTTCTCTTTTTATTCTCT
Found at i:56026 original size:14 final size:13
Alignment explanation
Indices: 55999--56039 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
55989 AAGAAAAGAA
*
55999 TAATAAAAAATAT
1 TAATAAATAATAT
56012 TAATATAATAATAT
1 TAATA-AATAATAT
56026 TAATAAATATATAT
1 TAATAAATA-ATAT
56040 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAAATAATAT
Found at i:56039 original size:2 final size:2
Alignment explanation
Indices: 56032--56056 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56022 ATATTAATAA
56032 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 A
56057 ACAATGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56488 original size:33 final size:33
Alignment explanation
Indices: 56413--56489 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
56403 GTCTTACTTG
* * *
56413 GACTCAAATGCTTCAGTTTTAGTGTTTTAATAG
1 GACTCAAATACTTCAGTTTTAGTGTTTCAATAA
* *
56446 GATTTAAATACGTT-AGTTTTAGTGTTTCAATAA
1 GACTCAAATAC-TTCAGTTTTAGTGTTTCAATAA
56479 GACTCAAATAC
1 GACTCAAATAC
56490 ATTGATTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 34 0.94
34 2 0.06
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (33 bp):
GACTCAAATACTTCAGTTTTAGTGTTTCAATAA
Found at i:56568 original size:3 final size:3
Alignment explanation
Indices: 56557--56608 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
56547 AATAAAAAAA
*
56557 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT AAT
56603 AA- AAT A
1 AAT AAT A
56609 TTTTTATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:57072 original size:14 final size:15
Alignment explanation
Indices: 57053--57081 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57043 TTTACAGTAC
57053 AATATCT-ATAAATT
1 AATATCTCATAAATT
57067 AATATCTCATAAATT
1 AATATCTCATAAATT
57082 GATAATCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATCTCATAAATT
Found at i:60282 original size:13 final size:13
Alignment explanation
Indices: 60264--60308 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
60254 GGTAATCCCT
60264 CCCCGATTACCCG
1 CCCCGATTACCCG
*
60277 CCCCGATTACCCA
1 CCCCGATTACCCG
60290 CCCCGA-TACCCG
1 CCCCGATTACCCG
*
60302 ACCCGAT
1 CCCCGAT
60309 AAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.20, C:0.53, G:0.13, T:0.13
Consensus pattern (13 bp):
CCCCGATTACCCG
Found at i:60371 original size:24 final size:26
Alignment explanation
Indices: 60344--60408 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
60334 ATATATATAT
*
60344 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
60368 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
60392 ATATATATATATATATA
1 ATA-ATATAAATATATA
60409 CCCAGCCCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.12
23 2 0.06
24 18 0.53
25 1 0.03
26 1 0.03
27 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:60386 original size:19 final size:19
Alignment explanation
Indices: 60362--60401 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
60352 AATAAATTTA
60362 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
60381 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
60400 AT
1 AT
60402 ATATATACCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:60450 original size:12 final size:12
Alignment explanation
Indices: 60421--60471 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
60411 CAGCCCGATT
*
60421 CCCGGCCCAATA
1 CCCGACCCAATA
60433 -CCGACCCAATA
1 CCCGACCCAATA
60444 CCCGACCCAATA
1 CCCGACCCAATA
*
60456 CCCGGCCCAATA
1 CCCGACCCAATA
60468 CCCG
1 CCCG
60472 TTTAAATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.27, C:0.51, G:0.14, T:0.08
Consensus pattern (12 bp):
CCCGACCCAATA
Found at i:60469 original size:24 final size:24
Alignment explanation
Indices: 60406--60471 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
60396 ATATATATAT
* * * *
60406 ATACCCAGCCCGATTCCCGGCCCA
1 ATACCCGGCCCAATACCCGACCCA
*
60430 ATA-CCGACCCAATACCCGACCCA
1 ATACCCGGCCCAATACCCGACCCA
60453 ATACCCGGCCCAATACCCG
1 ATACCCGGCCCAATACCCG
60472 TTTAAATATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.27, C:0.48, G:0.14, T:0.11
Consensus pattern (24 bp):
ATACCCGGCCCAATACCCGACCCA
Found at i:62117 original size:2 final size:2
Alignment explanation
Indices: 62110--62137 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62100 ATCTTACCTA
62110 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
62138 TATGTGTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62708 original size:31 final size:32
Alignment explanation
Indices: 62661--62811 Score: 119
Period size: 32 Copynumber: 4.8 Consensus size: 32
62651 CAAAATTGTA
* * * * *
62661 ATTAAATTTTGTCAAACTGTTATAAAATTATC
1 ATTAAAATTTATCAAACTATTACAAAATAATC
*
62693 ATT-AGATTTATCAAACTATTACAAAATAATC
1 ATTAAAATTTATCAAACTATTACAAAATAATC
** **
62724 ATTAAAATTTATCAATTTATTACAAAATGGTC
1 ATTAAAATTTATCAAACTATTACAAAATAATC
* * * * **
62756 ATTAAATTTTATCAAATTGTTACAATATGGTC
1 ATTAAAATTTATCAAACTATTACAAAATAATC
*
62788 ATT-AAATATATCAAAACT-TTACAA
1 ATTAAAATTTATC-AAACTATTACAA
62812 TTATTATAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
31 38 0.38
32 61 0.62
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (32 bp):
ATTAAAATTTATCAAACTATTACAAAATAATC
Found at i:68506 original size:18 final size:17
Alignment explanation
Indices: 68485--68535 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
68475 TAAAATCGAC
68485 AAATATTGTTATTTAAAT
1 AAATATT-TTATTTAAAT
* *
68503 AAATATTTTAATAAAAT
1 AAATATTTTATTTAAAT
68520 -AATATTTTTATTTAAA
1 AAATA-TTTTATTTAAA
68536 CTCTTTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 17 0.61
18 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATATTTTATTTAAAT
Found at i:68521 original size:17 final size:17
Alignment explanation
Indices: 68485--68527 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
68475 TAAAATCGAC
* *
68485 AAATATTGTTATTTAAAT
1 AAATATT-TTAATAAAAT
68503 AAATATTTTAATAAAAT
1 AAATATTTTAATAAAAT
68520 -AATATTTT
1 AAATATTTT
68528 TATTTAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATATTTTAATAAAAT
Found at i:77578 original size:23 final size:24
Alignment explanation
Indices: 77534--77578 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
77524 ACTATAGTAT
* *
77534 TTTTATGATTTTATATTATTAATG
1 TTTTATCAATTTATATTATTAATG
77558 TTTTATCAATTTA-ATTATTAA
1 TTTTATCAATTTATATTATTAA
77579 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTATCAATTTATATTATTAATG
Found at i:82196 original size:13 final size:11
Alignment explanation
Indices: 82158--82197 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
82148 TAAAGTCGAG
82158 TTATTTAAATT
1 TTATTTAAATT
82169 TATATTTAAATT
1 T-TATTTAAATT
82181 TTATTGTAAATAT
1 TTATT-TAAAT-T
82194 TTAT
1 TTAT
82198 AATATCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.19
12 16 0.62
13 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (11 bp):
TTATTTAAATT
Found at i:82772 original size:17 final size:17
Alignment explanation
Indices: 82737--82774 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
82727 CATCAAAATT
*
82737 AAATATATTTTATGTAA
1 AAATATATTTTATGAAA
82754 AAATATATATTTAT-AAA
1 AAATATAT-TTTATGAAA
82771 AAAT
1 AAAT
82775 TACCGTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATATATTTTATGAAA
Found at i:82805 original size:14 final size:14
Alignment explanation
Indices: 82786--82814 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
82776 ACCGTCAAGG
82786 TAAAATAAGATTTA
1 TAAAATAAGATTTA
82800 TAAAATAAGATTTA
1 TAAAATAAGATTTA
82814 T
1 T
82815 CGAATCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAAAATAAGATTTA
Found at i:83988 original size:2 final size:2
Alignment explanation
Indices: 83981--84009 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
83971 TGTCATATTA
83981 AT 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 AT A
84010 AAAATAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88211 original size:2 final size:2
Alignment explanation
Indices: 88204--88236 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
88194 TGTTGATAAT
88204 TA 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 TA T
88237 TAAATTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:89115 original size:26 final size:26
Alignment explanation
Indices: 89085--89164 Score: 105
Period size: 25 Copynumber: 3.2 Consensus size: 26
89075 ACAAAGAGAC
*
89085 AAAAACA-CTTTATTTAATTAAATTAA
1 AAAAACAGCTTT-GTTAATTAAATTAA
89111 AAAAACAGCTTTGTTAATTAAATT-A
1 AAAAACAGCTTTGTTAATTAAATTAA
*
89136 AAAAACAGCTTTGTTAA--AAAATAA
1 AAAAACAGCTTTGTTAATTAAATTAA
89160 AAAAA
1 AAAAA
89165 TAGATTAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.08
24 6 0.12
25 18 0.36
26 18 0.36
27 4 0.08
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (26 bp):
AAAAACAGCTTTGTTAATTAAATTAA
Found at i:92846 original size:2 final size:2
Alignment explanation
Indices: 92839--92873 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
92829 GATTTTGGAT
92839 TA TA 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 TA TA T
92874 CAAATAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:93746 original size:78 final size:78
Alignment explanation
Indices: 93617--93768 Score: 304
Period size: 78 Copynumber: 1.9 Consensus size: 78
93607 TCGTGACCTA
93617 AATTTTATTTTGATTCGGTTTGAAAAATTATAGTAGGACTCATTTTATCGAAGAAATAAATTAAA
1 AATTTTATTTTGATTCGGTTTGAAAAATTATAGTAGGACTCATTTTATCGAAGAAATAAATTAAA
93682 AGAAAAAAGATTT
66 AGAAAAAAGATTT
93695 AATTTTATTTTGATTCGGTTTGAAAAATTATAGTAGGACTCATTTTATCGAAGAAATAAATTAAA
1 AATTTTATTTTGATTCGGTTTGAAAAATTATAGTAGGACTCATTTTATCGAAGAAATAAATTAAA
93760 AGAAAAAAG
66 AGAAAAAAG
93769 TGTACGAGCA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.36
Consensus pattern (78 bp):
AATTTTATTTTGATTCGGTTTGAAAAATTATAGTAGGACTCATTTTATCGAAGAAATAAATTAAA
AGAAAAAAGATTT
Found at i:95047 original size:16 final size:16
Alignment explanation
Indices: 95026--95056 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95016 GATGTGGTAC
*
95026 TAAAATGAAATAAAAA
1 TAAAATAAAATAAAAA
95042 TAAAATAAAATAAAA
1 TAAAATAAAATAAAA
95057 GTTAAGTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:96839 original size:35 final size:34
Alignment explanation
Indices: 96783--96850 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
96773 CTTAAATCGT
* *
96783 CTAACAACATTTGATACTATCTATTAGCTAACAG
1 CTAACAACATTTGAAACTATCTAATAGCTAACAG
* *
96817 CTAACAATATTTTGAAATTATCTAATAGCTAACA
1 CTAACAACA-TTTGAAACTATCTAATAGCTAACA
96851 CTCATCAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (34 bp):
CTAACAACATTTGAAACTATCTAATAGCTAACAG
Found at i:97895 original size:18 final size:18
Alignment explanation
Indices: 97872--97909 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
97862 TTCTTTGATC
97872 ATTACTACAGGATTTCAA
1 ATTACTACAGGATTTCAA
*
97890 ATTACTACAGGATTTTAA
1 ATTACTACAGGATTTCAA
97908 AT
1 AT
97910 CACGATCGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (18 bp):
ATTACTACAGGATTTCAA
Found at i:99326 original size:6 final size:6
Alignment explanation
Indices: 99311--99339 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
99301 GTGAGGGAGT
99311 GAAC-G GAACGG GAACGG GAACGG GAACGG
1 GAACGG GAACGG GAACGG GAACGG GAACGG
99340 TGGTGGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.34, C:0.17, G:0.48, T:0.00
Consensus pattern (6 bp):
GAACGG
Found at i:105178 original size:28 final size:28
Alignment explanation
Indices: 105146--105202 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
105136 GAACCCCAGC
105146 TATAGCTATAAAACCCTAGCCCTAGGGT
1 TATAGCTATAAAACCCTAGCCCTAGGGT
105174 TATAGCTATAAAACCCTAGCCCTAGGGT
1 TATAGCTATAAAACCCTAGCCCTAGGGT
105202 T
1 T
105203 CTTTCTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (28 bp):
TATAGCTATAAAACCCTAGCCCTAGGGT
Found at i:113872 original size:42 final size:42
Alignment explanation
Indices: 113825--113907 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
113815 ACTTCATCCG
113825 TTCTCTCCATCTATCCGAGTACAACAATAACAATAAACAAAA
1 TTCTCTCCATCTATCCGAGTACAACAATAACAATAAACAAAA
* *
113867 TTCTCTCGATCTATCCGAGTTCAACAATAACAATAAACAAA
1 TTCTCTCCATCTATCCGAGTACAACAATAACAATAAACAAA
113908 GTAGAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.25
Consensus pattern (42 bp):
TTCTCTCCATCTATCCGAGTACAACAATAACAATAAACAAAA
Found at i:114810 original size:31 final size:31
Alignment explanation
Indices: 114775--114842 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
114765 GATTAAATTT
* * *
114775 TAATTTGACATCTAAATTTTAGATAATATAC
1 TAATTTAACATCTAAATGTTAGATAAGATAC
*
114806 TAATTTAACCTCTAAATGTTAGATAAGATAC
1 TAATTTAACATCTAAATGTTAGATAAGATAC
114837 TAATTT
1 TAATTT
114843 TACCATTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
TAATTTAACATCTAAATGTTAGATAAGATAC
Found at i:120344 original size:21 final size:21
Alignment explanation
Indices: 120318--120367 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
120308 TACTAAGATA
*
120318 ATAATTTATTATATTAATATG
1 ATAATTTATGATATTAATATG
* *
120339 ATAATTCACGATATTAATATG
1 ATAATTTATGATATTAATATG
120360 AT-ATTTAT
1 ATAATTTAT
120368 AATGTTTACG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (21 bp):
ATAATTTATGATATTAATATG
Found at i:120630 original size:19 final size:19
Alignment explanation
Indices: 120608--120644 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
120598 TAATTTACGT
*
120608 TTATAGTTGTAAATATTTA
1 TTATAATTGTAAATATTTA
*
120627 TTATAATTTTAAATATTT
1 TTATAATTGTAAATATTT
120645 TATCTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTATAATTGTAAATATTTA
Found at i:121272 original size:23 final size:23
Alignment explanation
Indices: 121242--121290 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
121232 AGTTATTCGT
* *
121242 GTTCATTCGTTTGTTTGATTAAA
1 GTTCATTCGTTTATTTAATTAAA
121265 GTTCATTCGTTTATTTAATTAAA
1 GTTCATTCGTTTATTTAATTAAA
121288 GTT
1 GTT
121291 AAATGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.53
Consensus pattern (23 bp):
GTTCATTCGTTTATTTAATTAAA
Found at i:121597 original size:2 final size:2
Alignment explanation
Indices: 121590--121647 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
121580 ATAAGTGCTG
121590 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
121632 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
121648 ATTTGAGACG
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
Done.