Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003342.1 Hibiscus syriacus cultivar Beakdansim tig00007033_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: 62653
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5131 original size:18 final size:17
Alignment explanation
Indices: 5108--5142 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5098 CTCCAGAGCT
*
5108 TTCTTCTTTCTTCTTTTC
1 TTCTTC-TTCTTCCTTTC
5126 TTCTTCTTCTTCCTTTC
1 TTCTTCTTCTTCCTTTC
5143 CTCCCGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTTCTTCTTCCTTTC
Found at i:5132 original size:14 final size:15
Alignment explanation
Indices: 5107--5136 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5097 TCTCCAGAGC
5107 TTTCTTCTTTCTTCT
1 TTTCTTCTTTCTTCT
5122 TTTCTTC-TTCTTCT
1 TTTCTTCTTTCTTCT
5136 T
1 T
5137 CCTTTCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTCTTTCTTCT
Found at i:5838 original size:12 final size:14
Alignment explanation
Indices: 5806--5836 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5796 GTCCCCTATA
5806 TATATTTTTTTAAT
1 TATATTTTTTTAAT
*
5820 TATATTTTTTTATT
1 TATATTTTTTTAAT
5834 TAT
1 TAT
5837 TTACTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATATTTTTTTAAT
Found at i:5873 original size:14 final size:14
Alignment explanation
Indices: 5856--5895 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
5846 TCCTCTTTTT
5856 TTATTTATATTATA
1 TTATTTATATTATA
*
5870 TTATTTTTATTATA
1 TTATTTATATTATA
5884 TATATCTTATAT
1 T-TAT-TTATAT
5896 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:5877 original size:23 final size:24
Alignment explanation
Indices: 5818--5888 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
5808 TATTTTTTTA
*
5818 ATTATATTTTTTTATTTATTTACTAT
1 ATTATATTTTTTTATTTA--TATTAT
* *
5844 ATTCCTCTTTTTTTATTTATATTAT
1 ATT-ATATTTTTTTATTTATATTAT
* *
5869 ATTAT-TTTTATTATATATAT
1 ATTATATTTTTTTATTTATAT
5889 CTTATATCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 13 0.34
24 1 0.03
25 8 0.21
26 3 0.08
27 13 0.34
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTATATTTTTTTATTTATATTAT
Found at i:6064 original size:18 final size:18
Alignment explanation
Indices: 6019--6079 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
6009 CTATTTTTGT
* *
6019 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
6036 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
6054 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
6072 TTTT-TTTT
1 TTTTATTTT
6080 CTTAATATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 16 0.44
18 20 0.56
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:6353 original size:26 final size:26
Alignment explanation
Indices: 6297--6359 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
6287 ATTTTTATTA
*
6297 TTTTATTAT-TATTTTTTACGTGTTT
1 TTTTATTTTCTATTTTTTACGTGTTT
* *
6322 TGTTATTTTCTATTTTTT-CTTGTTT
1 TTTTATTTTCTATTTTTTACGTGTTT
6347 TATTTATTATTCT
1 T-TTTATT-TTCT
6360 CACGTTTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 14 0.45
26 13 0.42
27 4 0.13
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.73
Consensus pattern (26 bp):
TTTTATTTTCTATTTTTTACGTGTTT
Found at i:6357 original size:22 final size:22
Alignment explanation
Indices: 6288--6357 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 22
6278 ATTTTGTTTA
*
6288 TTTTTATTATTTTA-TTATTAT
1 TTTTTCTTATTTTATTTATTAT
*
6309 TTTTTACGTGTTTTGTTATTT-TCTAT
1 TTTTT-C-T-TATT-TTATTTAT-TAT
*
6335 TTTTTCTTGTTTTATTTATTAT
1 TTTTTCTTATTTTATTTATTAT
6357 T
1 T
6358 CTCACGTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
21 5 0.13
22 10 0.26
23 5 0.13
24 4 0.10
25 5 0.13
26 10 0.26
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74
Consensus pattern (22 bp):
TTTTTCTTATTTTATTTATTAT
Found at i:9380 original size:12 final size:13
Alignment explanation
Indices: 9351--9398 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
9341 ATCAGAACAA
9351 AAAGAGAAAAAAGC
1 AAAGAGAAAAAA-C
*
9365 AAAGAGAAAATA-
1 AAAGAGAAAAAAC
9377 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
9390 AAAG-GAAAA
1 AAAGAGAAAA
9399 TTGAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 16 0.52
13 4 0.13
14 11 0.35
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:9405 original size:24 final size:26
Alignment explanation
Indices: 9350--9399 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
9340 AATCAGAACA
9350 AAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAGAGAAAAAAGCAAAGAGAAAAT
9376 AAAAGAGAAAAAA-CAAAG-GAAAAT
1 AAAAGAGAAAAAAGCAAAGAGAAAAT
9400 TGAAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
26 13 0.54
ACGTcount: A:0.74, C:0.04, G:0.18, T:0.04
Consensus pattern (26 bp):
AAAAGAGAAAAAAGCAAAGAGAAAAT
Found at i:9410 original size:24 final size:25
Alignment explanation
Indices: 9350--9410 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
9340 AATCAGAACA
*
9350 AAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAGA-AAAAAAACAAAGAGAAAAT
*
9376 AAAAGAGAAAAAACAAAG-GAAAAT
1 AAAAGAAAAAAAACAAAGAGAAAAT
**
9400 TGAAGAAAAAA
1 AAAAGAAAAAA
9411 GAAAACAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 14 0.47
25 10 0.33
26 6 0.20
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (25 bp):
AAAAGAAAAAAAACAAAGAGAAAAT
Found at i:11190 original size:37 final size:36
Alignment explanation
Indices: 11123--11208 Score: 127
Period size: 37 Copynumber: 2.4 Consensus size: 36
11113 ATTGAAAACA
* * *
11123 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAG
11159 TTTCCCTTGAAATGAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATG-AATTTTGTCTCCCTTGAGACAG
*
11196 TTTCTCTTGAAAT
1 TTTCCCTTGAAAT
11209 ATAAACATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 13 0.29
37 32 0.71
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAG
Found at i:11213 original size:102 final size:102
Alignment explanation
Indices: 11047--11281 Score: 380
Period size: 102 Copynumber: 2.3 Consensus size: 102
11037 TTTTATCACG
*
11047 CTTGAGATAGTTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
* *
11112 TATTGAAAACATTTCCCTTGAAACGAATTTTGTCTCT
66 CATTGAAAACATTTCCCTTGAAACAAATTTTGTCTCT
** * *
11149 CTTGAGATAGTTTCCCTTGAAATGAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATATAAA
1 CTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
*
11214 CATTGAAAACATTTCCCTTGAAATAAATTTTGTCTCT
66 CATTGAAAACATTTCCCTTGAAACAAATTTTGTCTCT
* *
11251 CTTGAGACAGTTTCCCTTGAAACAAATTATT
1 CTTGAGATAGTTTCCCTTGAAACAAAATATT
11282 TGAATATGTT
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 120 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
CTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
CATTGAAAACATTTCCCTTGAAACAAATTTTGTCTCT
Found at i:11264 original size:65 final size:64
Alignment explanation
Indices: 11159--11545 Score: 251
Period size: 65 Copynumber: 5.8 Consensus size: 64
11149 CTTGAGATAG
* *
11159 TTTCCCTTGAAATGAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATATAAACATTGAAAAC
1 TTTCCCTTGAAAT-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAACATTGAATAC
11224 A
64 A
* * ** **
11225 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTATTTGAATATG
1 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACA-TTGAATACA
*** * * * * * *
11290 TTTTATTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTATCTCTCT
1 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AA-----A--AC-AT
*
11355 TG-AGACA
57 TGAATACA
* * * * * *
11362 GTTTCTCTTGAAA-CAATTTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATT
1 -TTTCCCTTGAAATAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAA-CATTGAATA
*
11426 TA
63 CA
* * *
11428 TTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA-ATCTTCAAAT
1 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAACA--TT-GAAT
**
11492 TTA
62 ACA
* * * * *
11495 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAA
1 TTTCCCTTGAAA-TAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
11546 CAGATATCTT
Statistics
Matches: 252, Mismatches: 49, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
64 3 0.01
65 120 0.48
66 30 0.12
67 27 0.11
68 24 0.10
71 1 0.00
72 9 0.04
73 38 0.15
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (64 bp):
TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACATTGAATACA
Found at i:11264 original size:167 final size:168
Alignment explanation
Indices: 11057--11374 Score: 399
Period size: 167 Copynumber: 1.9 Consensus size: 168
11047 CTTGAGATAG
*
11057 TTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATA-TTGAAAA
1 TTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAACA-AAATATTTGAAAA
* * * * * *
11121 CATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCCCTT-GAAATGAAATTTTGTCTC
65 CATTTCACTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAAT-AAATTTTATCTC
11185 CCTTGAGACAGTTTCTCTTGAAATATAAACATTGAAAACA
129 CCTTGAGACAGTTTCTCTTGAAATATAAACATTGAAAACA
* * * * * * *
11225 TTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTATTTGAATAT
1 TTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAAAAC
* * * ** * * *
11289 GTTTTATTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTATCTCTC
66 ATTTCACTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTATCTCCC
11354 TTGAGACAGTTTCTCTTGAAA
131 TTGAGACAGTTTCTCTTGAAA
11375 CAATTTTCGT
Statistics
Matches: 126, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
166 4 0.03
167 107 0.85
168 15 0.12
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (168 bp):
TTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAAAAC
ATTTCACTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTATCTCCC
TTGAGACAGTTTCTCTTGAAATATAAACATTGAAAACA
Found at i:11272 original size:36 final size:36
Alignment explanation
Indices: 11225--11414 Score: 164
Period size: 36 Copynumber: 5.4 Consensus size: 36
11215 ATTGAAAACA
*
11225 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
11261 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** * *
11290 TTTTATTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** * * *
11326 TTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
11363 TTTCTCTTGAAAC-AATTTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAG
11399 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
11415 ATCTTTGAAT
Statistics
Matches: 121, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
28 2 0.02
29 18 0.15
30 2 0.02
31 1 0.01
34 1 0.01
35 6 0.05
36 57 0.47
37 34 0.28
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:11495 original size:67 final size:68
Alignment explanation
Indices: 11376--11544 Score: 220
Period size: 67 Copynumber: 2.5 Consensus size: 68
11366 CTCTTGAAAC
* * **
11376 AATTTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCCTAAA
1 AATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAA
*
11439 A-TA
65 ACAA
*
11442 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAA
11507 CAA
66 CAA
* * *
11510 AATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
11545 ACAGATATCT
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
65 23 0.25
66 8 0.09
67 36 0.40
68 24 0.26
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.38
Consensus pattern (68 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAA
CAA
Found at i:12405 original size:106 final size:106
Alignment explanation
Indices: 12218--12694 Score: 545
Period size: 106 Copynumber: 4.6 Consensus size: 106
12208 ATATCGTGCC
** ** * ** *
12218 ACTCGAGACAACACAATTTCAACTTCACAACGAATAGATGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
* * * *
12283 AGTTTCAGAACCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
* * * * *
12324 ATTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGCTATCAACAAACAACTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
** *
12389 AATTTCAGAGTTAATTTCAGCTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
* * * *
12430 ACTCAAGACAACACAAGCTCGACTTCATAACGAAGGGGCGGCTGACTGTCAACAAACAACTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
* * *
12495 AATTTCAGGGCCAATTTCAACTTCCCAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
* * * * * *
12536 ACCCAAGATAACACAAGCTCAACTTCACGACGAAGGGGA-GGCTGATTGTCAAC-AA-AA-TT-T
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAA-GGGACGGCTGACTGTCAACAAACAACTTCC
* * *
12596 C-A-TTCAGAGTCAATTTCAACTTCACAACGAAAGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
* * *
12636 ACTCGAGACAGCACAAGCTCAACTTCACAATGAAGGGGCGGCTGACTGTCAACAAACAA
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAA
12695 TTTTCAGAGC
Statistics
Matches: 314, Mismatches: 53, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
99 3 0.01
100 73 0.23
101 3 0.01
102 3 0.01
103 2 0.01
104 2 0.01
105 2 0.01
106 223 0.71
107 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (106 bp):
ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
Found at i:14690 original size:23 final size:23
Alignment explanation
Indices: 14664--14732 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
14654 CACCACAGCT
*
14664 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
14687 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
14710 CGTAGAATTGCACC-ATAGTGCCA
1 CGTAGAATTGCACCGA-AGTGCCA
14733 TATAATAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:14919 original size:103 final size:103
Alignment explanation
Indices: 14748--15063 Score: 569
Period size: 103 Copynumber: 3.1 Consensus size: 103
14738 TAATGTCCAT
* * * * *
14748 AAGGACTACATATCATTACTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
14813 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
14851 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
14916 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
14954 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
15019 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
15057 AAGGACC
1 AAGGACC
15064 GCGTAGACCC
Statistics
Matches: 205, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 205 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:16772 original size:21 final size:21
Alignment explanation
Indices: 16747--16792 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
16737 TTCTGGTTCG
* * *
16747 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
16768 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
16789 CTTG
1 CTTG
16793 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:17631 original size:31 final size:31
Alignment explanation
Indices: 17593--17657 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
17583 AGAGTCGAGG
*
17593 GTTTACCTATGTTCTAAGGAACATATGGATA
1 GTTTACCTAGGTTCTAAGGAACATATGGATA
** * *
17624 GTTTACCTAGGTTCTTCGGGACCTATGGATA
1 GTTTACCTAGGTTCTAAGGAACATATGGATA
17655 GTT
1 GTT
17658 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGATA
Found at i:17677 original size:30 final size:30
Alignment explanation
Indices: 17616--17715 Score: 119
Period size: 30 Copynumber: 3.3 Consensus size: 30
17606 CTAAGGAACA
* * ***
17616 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAG-TTACCAAGGATCTTTATGACC
*
17647 TATGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCAAGGATCTTTATGACC
*
17677 TCTGGATAGTTACCAAGGATCTTTATGACC
1 TATGGATAGTTACCAAGGATCTTTATGACC
*
17707 TCTGGATAG
1 TATGGATAG
17716 GTTCTTCGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 53 0.85
31 9 0.15
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (30 bp):
TATGGATAGTTACCAAGGATCTTTATGACC
Found at i:19327 original size:9 final size:9
Alignment explanation
Indices: 19286--19341 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
19276 TTTGATAACA
*
19286 TTTCTTTTC
1 TTTCATTTC
19295 ATTTCATTTC
1 -TTTCATTTC
*
19305 TTATCA-AT-
1 TT-TCATTTC
19313 TTTCATTTC
1 TTTCATTTC
19322 TTTCATTTC
1 TTTCATTTC
*
19331 TTTTATTTC
1 TTTCATTTC
19340 TT
1 TT
19342 CCTTTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 22 0.56
10 11 0.28
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTCATTTC
Found at i:28222 original size:8 final size:8
Alignment explanation
Indices: 28209--28249 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
28199 CTCGTTTTTA
28209 GAGAATTT
1 GAGAATTT
28217 GAGAATTT
1 GAGAATTT
*
28225 -AGAGTTT
1 GAGAATTT
*
28232 GGGAATTT
1 GAGAATTT
28240 GAGAATTT
1 GAGAATTT
28248 GA
1 GA
28250 AAGATTATGA
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:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:28524 original size:128 final size:128
Alignment explanation
Indices: 28320--28942 Score: 1119
Period size: 128 Copynumber: 4.9 Consensus size: 128
28310 TAATCGAAGT
*
28320 ACTATTCACATGAAGGCGCGTTCCC--GGG-GCGCCTTCCATTATTTCATCA-AGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
28381 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
28444 ACTATTCACATTAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
28509 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
28572 ACTATTCACATGAAGGCGCGTTCCCAGGGGCGTGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
28637 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
28700 ACTATTCACATGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTCGTCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
28765 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
28828 ACTATTCACATTAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
* *
28893 CATTGCCCTATTATGCCACTCATGTTCCTCGGGGACACTAGATATATCAG
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAG
28943 AAAATCAGGT
Statistics
Matches: 480, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
124 24 0.05
126 3 0.01
127 19 0.04
128 434 0.90
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:29383 original size:34 final size:34
Alignment explanation
Indices: 29345--29444 Score: 112
Period size: 33 Copynumber: 3.0 Consensus size: 34
29335 AAATTTAATG
*
29345 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
** * * *
29379 TTAAA-TTTGAATAATATTTTTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
** *
29412 TTAAATTTCAAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
29445 AACATTTATC
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:29994 original size:21 final size:21
Alignment explanation
Indices: 29964--30057 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
29954 TATGGTATAA
*
29964 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
29985 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
30006 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
30027 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
30048 AACCCTGCGG
1 AACCCTGCGG
30058 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.28, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:30087 original size:21 final size:21
Alignment explanation
Indices: 30061--30108 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
30051 CCTGCGGAGA
*
30061 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
30082 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
30103 GGGCAT
1 TGGCAT
30109 GTACCCCTGC
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:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:31877 original size:35 final size:32
Alignment explanation
Indices: 31838--31922 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
31828 AATTCTAAAT
31838 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTATATAAATA-TA--TTAATAAAAA
* * *
31873 AAATAATATTTACATAAATATATTAATATAAA
1 AAATAATAATTATATAAATATATTAATAAAAA
* *
31905 AAATAATAACTATTTAAA
1 AAATAATAATTATATAAA
31923 AAAATACTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 23 0.53
34 2 0.05
35 18 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (32 bp):
AAATAATAATTATATAAATATATTAATAAAAA
Found at i:31912 original size:32 final size:34
Alignment explanation
Indices: 31833--31913 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 34
31823 TTAATAATTC
*
31833 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAATA
* *
31869 AAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
31901 TAAAAAATAATAA
1 TAAAAAATAATAA
31914 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 17 0.43
34 2 0.05
35 18 0.45
36 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:31938 original size:34 final size:34
Alignment explanation
Indices: 31866--31945 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 34
31856 TATTATTTTA
* * *
31866 ATAAAAAAAATAATATTTACATAAATATATTAAT
1 ATAAAAAAAATAATATTTACATAAAAATACTAAC
31900 ATAAAAAATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAAAA-AATAA-TATTTACATAAAAATACTAAC
31934 ATAAAAATAAAT
1 ATAAAAA-AAAT
31946 TTCTTACCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 27 0.68
35 7 0.17
36 6 0.15
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (34 bp):
ATAAAAAAAATAATATTTACATAAAAATACTAAC
Found at i:35235 original size:18 final size:19
Alignment explanation
Indices: 35212--35248 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35202 ATATGCAAAA
35212 GGGTTTT-TTGATCTTTTG
1 GGGTTTTATTGATCTTTTG
*
35230 GGGTTTTATTTATCTTTTG
1 GGGTTTTATTGATCTTTTG
35249 ATGTTTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.08, C:0.05, G:0.24, T:0.62
Consensus pattern (19 bp):
GGGTTTTATTGATCTTTTG
Found at i:37195 original size:3 final size:3
Alignment explanation
Indices: 37187--37265 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
37177 TTTTTATCCA
* *
37187 TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
37235 TTT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
37266 AATATATTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:50031 original size:5 final size:5
Alignment explanation
Indices: 50021--50098 Score: 65
Period size: 5 Copynumber: 15.6 Consensus size: 5
50011 GCTTGAAGAA
* *
50021 AAAAG AAAAG AAAAAG AAAAG AAAA- AAAGAA AAAAG AAAAG AAAA- AATAG
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG AAAAG AAAAG
*
50071 AAAATG -AAA- AAAAG AGAAG AAAAAG AAA
1 AAAA-G AAAAG AAAAG AAAAG -AAAAG AAA
50099 GGGGGTCAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
4 9 0.15
5 38 0.63
6 13 0.22
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:50075 original size:7 final size:7
Alignment explanation
Indices: 50016--50074 Score: 57
Period size: 7 Copynumber: 8.0 Consensus size: 7
50006 ATTATGCTTG
50016 AAGAAAA
1 AAGAAAA
50023 AAGAAAA
1 AAGAAAA
*
50030 GAAAAAGAA
1 -AAGAA-AA
50039 AAGAAAAA
1 AAG-AAAA
50047 AAGAAAA
1 AAGAAAA
50054 AAGAAAA
1 AAGAAAA
50061 GAA-AAAA
1 -AAGAAAA
*
50068 TAGAAAA
1 AAGAAAA
50075 TGAAAAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 1 0.02
7 26 0.59
8 13 0.30
9 4 0.09
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAGAAAA
Found at i:50079 original size:20 final size:19
Alignment explanation
Indices: 50016--50098 Score: 98
Period size: 20 Copynumber: 4.3 Consensus size: 19
50006 ATTATGCTTG
*
50016 AAGAAAA-AAGAAAAGAAA
1 AAGAAAAGAAAAAAAGAAA
50034 AAGAAAAGAAAAAAAGAAAA
1 AAGAAAAGAAAAAAAG-AAA
50054 AAGAAAAGAAAAAATAGAAA
1 AAGAAAAGAAAAAA-AGAAA
* *
50074 ATGAAAA-AAAGAGAAGAAA
1 AAGAAAAGAAA-AAAAGAAA
50093 AAGAAA
1 AAGAAA
50099 GGGGGTCAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.12
19 20 0.35
20 28 0.49
21 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AAGAAAAGAAAAAAAGAAA
Found at i:51374 original size:50 final size:50
Alignment explanation
Indices: 51230--51381 Score: 286
Period size: 50 Copynumber: 3.0 Consensus size: 50
51220 GAAAGAGACT
*
51230 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
51280 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
*
51330 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
51380 AA
1 AA
51382 CCAATCATTG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
Found at i:52450 original size:118 final size:118
Alignment explanation
Indices: 52096--52628 Score: 919
Period size: 118 Copynumber: 4.5 Consensus size: 118
52086 TAGCAAAGAT
* *
52096 TTGAATCCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATC-ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
52161 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
52215 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATC-ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
*
52280 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGC
65 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
52334 TTGAATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTGAATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
52399 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
52452 TTGAATTCATCATTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTGAATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
52517 T-TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * ** *
52569 TTGAATTCATCATTTGATGGAACATCATCCCCAGCA-GAA-AGTTCGTAATGAGAAGAACTC
1 TTGAATTCATCACTTGATGGATCATCATTTCCAG-AGGAAGAGTTCATAATGAGAAGAACTC
52629 ATCTGGAGAA
Statistics
Matches: 402, Mismatches: 11, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
116 20 0.05
117 84 0.21
118 158 0.39
119 140 0.35
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (118 bp):
TTGAATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:52791 original size:3 final size:3
Alignment explanation
Indices: 52783--52861 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
52773 TTTTTATCCA
* *
52783 TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
52831 TAT TTT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
52862 AATATATTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.