Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007387.1 Hibiscus syriacus cultivar Beakdansim tig00019863_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: 70328
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:86 original size:25 final size:24
Alignment explanation
Indices: 58--105 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
48 ACCATTTAAA
58 TATAATAATA-ATTATAATATTTTAT
1 TATAA-AATATATTAT-ATATTTTAT
*
83 TATAAAATATATTATTTATTTTA
1 TATAAAATATATTATATATTTTA
106 AAAATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATAAAATATATTATATATTTTAT
Found at i:98 original size:20 final size:19
Alignment explanation
Indices: 70--115 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
60 TAATAATAAT
70 TATAATATTTTATTATAAAA
1 TATAATA-TTTATTATAAAA
* *
90 TATATTATTTATTTTAAAA
1 TATAATATTTATTATAAAA
109 -ATAATAT
1 TATAATAT
116 ATTTAGGTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 6 0.26
19 11 0.48
20 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATAATATTTATTATAAAA
Found at i:118 original size:20 final size:19
Alignment explanation
Indices: 71--120 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
61 AATAATAATT
71 ATAATAT-TTTATTATAAA
1 ATAATATATTTATTATAAA
*
89 AT-ATATTATTTATTTTAAAA
1 ATAATA-TATTTATTAT-AAA
109 ATAATATATTTA
1 ATAATATATTTA
121 GGTCGAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.11
18 3 0.11
19 7 0.26
20 11 0.41
21 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAATATATTTATTATAAA
Found at i:4375 original size:102 final size:102
Alignment explanation
Indices: 4172--4966 Score: 961
Period size: 102 Copynumber: 7.9 Consensus size: 102
4162 CACACCTTGG
* * * * *
4172 GCAGCCGAAATGGCATCGGATGAGACCTGCTTAATGAAACCAGAGGCAGTG-C--CCA--GCAGA
1 GCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGA
* * * *
4232 ATGTTGACCCTGAGGAGATAATCCCGGAGACATTTGA
66 AAGTTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
*
4269 GCAGCCGAGATGGCATCGGATGAGATCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGA
1 GCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGA
* *
4334 AAGTTGGCCCTGAGGAGACCCTCCCGGAAACATTTGA
66 AAGTTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
*
4371 GCAGCCGAGATGGCATCGGATGAGATCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGA
1 GCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGA
* * *
4436 AATTTGGCCCTGAGGAGACCCTCCCGGAGACATTTGG
66 AAGTTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
* * * * ** * * *
4473 GCAGCTGAAATGGCATCGGATGAGACCTGCTTAATGAAAACAGAGGTAGTGCCCAGCAGC-CCAG
1 GCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCAACCA-CTCCAG
* *
4537 AATA-TTGACCCTGAGGAGACAATCCCGGAGACATTTGA
65 AA-AGTTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
*
4575 GCAGCCGAGATGGCATCGGATGAGATCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGA
1 GCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGA
* * *
4640 AAGCTGGCCCTGAGGAGACCCTCCCGGAGACATTTGG
66 AAGTTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
* * * * *
4677 GCAGCTGAGATGGCATCGGATGAGACCTGCTTGACTAGTCCAGAAGCAGTGCCCAA-CAGTCCAG
1 GCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTG-CCAACCACTCCAG
* * *
4741 AAATTTGGCCCTGAGGCGACCCTCCCGGAGACATTTG-
65 AAAGTTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
* *
4778 GACAGCCGATATGGCATCGGATGAGACCTGCTTGAC-AAGTCCAGAGGCAGTG-C--CCAGTCCA
1 G-CAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAA-TCCAGAGGCAGTGCCAACCACTCCA
* *
4839 GAATGCTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
64 GAAAGTTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
* * * * ** * *
4878 GCAGCCGAGAAGGCATCAGATGAGACCTGGTTTATTAATCCAGAGGCAGTGCTCAA-CAGTTCAG
1 GCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGC-CAACCACTCCAG
* *
4942 AATGCTGGCCCTGAGGAGACACTCC
65 AAAGTTGGCCCTGAGGAGACACTCC
4967 TCCAGCCACT
Statistics
Matches: 610, Mismatches: 69, Indels: 33
0.86 0.10 0.05
Matches are distributed among these distances:
97 46 0.08
98 1 0.00
99 81 0.13
100 7 0.01
101 5 0.01
102 464 0.76
103 6 0.01
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (102 bp):
GCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGA
AAGTTGGCCCTGAGGAGACACTCCCGGAGACATTTGA
Found at i:4728 original size:306 final size:302
Alignment explanation
Indices: 4168--4966 Score: 1192
Period size: 306 Copynumber: 2.6 Consensus size: 302
4158 TAGCCACACC
4168 TTGGGCAGCCGAAATGGCATCGGATGAGACCTGCTTAATGAAACCAGAGGCAGTGCCCAG-CAGA
1 TTGGGCAGCCGAAATGGCATCGGATGAGACCTGCTTAATGAAACCAGAGGCAGTGCCCAGCCAGA
*
4232 ATGTTGACCCTGAGGAGATAATCCCGGAGACATTTGAGCAGCCGAGATGGCATCGGATGAGATCT
66 ATGTTGACCCTGAGGAGACAATCCCGGAGACATTTGAGCAGCCGAGATGGCATCGGATGAGATCT
*
4297 GCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGAAAGTTGGCCCTGAGGAGACCCTCCCGGA
131 GCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGAAAGCTGGCCCTGAGGAGACCCTCCCGGA
* *
4362 AACATTTGAGCAGCCGAGATGGCATCGGATGAGATCTGCTTGACGAATCCAGAGGCAGTG-CCAA
196 AACATTTGAGCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAAGCAGTGCCCAA
4426 CCACTCCAGAAATTTGGCCCTGAGGAGACCCTCCCGGAGACAT
261 -CACTCCAGAAATTTGGCCCTGAGGAGACCCTCCCGGAGACAT
* * *
4469 TTGGGCAGCTGAAATGGCATCGGATGAGACCTGCTTAATGAAAACAGAGGTAGTGCCCAGCAGCC
1 TTGGGCAGCCGAAATGGCATCGGATGAGACCTGCTTAATGAAACCAGAGGCAGTG-CC--CAG-C
*
4534 CAGAATATTGACCCTGAGGAGACAATCCCGGAGACATTTGAGCAGCCGAGATGGCATCGGATGAG
62 CAGAATGTTGACCCTGAGGAGACAATCCCGGAGACATTTGAGCAGCCGAGATGGCATCGGATGAG
4599 ATCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGAAAGCTGGCCCTGAGGAGACCCTCC
127 ATCTGCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGAAAGCTGGCCCTGAGGAGACCCTCC
* * * * *
4664 CGGAGACATTTGGGCAGCTGAGATGGCATCGGATGAGACCTGCTTGACTAGTCCAGAAGCAGTGC
192 CGGAAACATTTGAGCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAAGCAGTGC
* *
4729 CCAACAGTCCAGAAATTTGGCCCTGAGGCGACCCTCCCGGAGACAT
257 CCAACACTCCAGAAATTTGGCCCTGAGGAGACCCTCCCGGAGACAT
* * * * *
4775 TTGGACAGCCGATATGGCATCGGATGAGACCTGCTTGA-CAAGTCCAGAGGCAGTGCCCAGTCCA
1 TTGGGCAGCCGAAATGGCATCGGATGAGACCTGCTTAATGAA-ACCAGAGGCAGTGCCCAG-CCA
* * * * * *
4839 GAATGCTGGCCCTGAGGAGACACTCCCGGAGACATTTGAGCAGCCGAGAAGGCATCAGATGAGAC
64 GAATGTTGACCCTGAGGAGACAATCCCGGAGACATTTGAGCAGCCGAGATGGCATCGGATGAGAT
* * ** * * * *
4904 CTGGTTTATTAATCCAGAGGCAGTGCTCAA-CAGTTCAGAATGCTGGCCCTGAGGAGACACTCC
129 CTGCTTGACGAATCCAGAGGCAGTGC-CAACCACTCCAGAAAGCTGGCCCTGAGGAGACCCTCC
4967 TCCAGCCACT
Statistics
Matches: 451, Mismatches: 39, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
301 52 0.12
302 2 0.00
303 115 0.25
304 6 0.01
305 4 0.01
306 268 0.59
307 4 0.01
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.18
Consensus pattern (302 bp):
TTGGGCAGCCGAAATGGCATCGGATGAGACCTGCTTAATGAAACCAGAGGCAGTGCCCAGCCAGA
ATGTTGACCCTGAGGAGACAATCCCGGAGACATTTGAGCAGCCGAGATGGCATCGGATGAGATCT
GCTTGACGAATCCAGAGGCAGTGCCAACCACTCCAGAAAGCTGGCCCTGAGGAGACCCTCCCGGA
AACATTTGAGCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAAGCAGTGCCCAA
CACTCCAGAAATTTGGCCCTGAGGAGACCCTCCCGGAGACAT
Found at i:7656 original size:34 final size:35
Alignment explanation
Indices: 7610--7694 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
7600 AAAACAGTCA
* * *
7610 TCAATTTCATTCTAAACCC-AATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCTAAATTCCAAAATAAT
* * *
7644 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCTAAATTCCAAAATAAT
*
7679 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
7695 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 18 0.42
35 25 0.58
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCTAAATTCCAAAATAAT
Found at i:7688 original size:21 final size:21
Alignment explanation
Indices: 7663--7705 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7653 TTCTAAACCC
7663 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
7684 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
7705 T
1 T
7706 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:7858 original size:16 final size:18
Alignment explanation
Indices: 7826--7859 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
7816 TATTAATGTA
7826 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
7844 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
7860 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:8544 original size:130 final size:127
Alignment explanation
Indices: 8321--8565 Score: 382
Period size: 130 Copynumber: 1.9 Consensus size: 127
8311 AATTTTCTTC
* * *
8321 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTACATGTCAGATCCT
1 TAATTAGGAGGTAACAAGTGTCACCAATAACACATATCATGATCATGTGTCACATGTCAGATCCT
*
8386 GATTAAATGATTAATTTATTAAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 AATTAAATGATTAATTTATTAAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
8448 TAATTAGGTGGTAACAAGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACAAGTGTCACCAATAACACATATCATGATCATGTG-T--CACATGTCAGAT
*
8513 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
63 CCTAATTAAATGATTAATTTATTAAAATTTATTTAATTTAGGACCAAATTGAT
8566 TATATAAATA
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
127 43 0.41
128 1 0.01
130 62 0.58
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (127 bp):
TAATTAGGAGGTAACAAGTGTCACCAATAACACATATCATGATCATGTGTCACATGTCAGATCCT
AATTAAATGATTAATTTATTAAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:9610 original size:18 final size:18
Alignment explanation
Indices: 9587--9636 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
9577 ATCATCTATA
9587 TTAATAAATTAGTAATTT
1 TTAATAAATTAGTAATTT
*
9605 TTAATAAAATA-T-ATTT
1 TTAATAAATTAGTAATTT
*
9621 TTAAGATAATTAGTAA
1 TTAATA-AATTAGTAA
9637 AAGATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 9 0.35
17 5 0.19
18 11 0.42
19 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TTAATAAATTAGTAATTT
Found at i:10296 original size:176 final size:174
Alignment explanation
Indices: 9812--10312 Score: 670
Period size: 174 Copynumber: 2.9 Consensus size: 174
9802 AGCACCTCTA
* * * * * *
9812 ATCGAAATCACAGGCTTTCAATGTCATCTTCAAAAGAAGAATGAGATTCAGATCAACAAACAAGA
1 ATCGAAATCACAAGTTTTCAGTGTCATCTTCAAAAAAAGAATGAGATTCCGATCCACAAAC-AGA
* * *
9877 AAAACGAAGAGAAACAACGTTCGAAAGCTAAAATCTCTCGTCAATCAAAACATTACGAGCAAAAA
65 AAAACGAAGAGAAATAACGTTCGAAAG-TTAAATCTCTCGTCAATCAAAACCTTACGAGC-AAAA
* *
9942 TAAGTTGTAATTTCTCT---CGACGAGTTATTTGATTTCGAAGTGGC
128 CAAGTTGTAATTTCTCTCGACGACGAGTTATTTGATTTCGAAATGGC
* * * * * *
9986 ATCGAAATCACAAGTTTTCAGCGTCGTCCTCAAAAAAACAATGAGATTCCGATCCAAAAATAAGA
1 ATCGAAATCACAAGTTTTCAGTGTCATCTTCAAAAAAAGAATGAGATTCCGATCCACAAA-CAGA
* * * *
10051 GAAACGAAGAGAAATAACGTCCGAAAGTTAAA-ATCTCGTCAGTCAAAACCTTACGAGCAAAAGC
65 AAAACGAAGAGAAATAACGTTCGAAAGTTAAATCTCTCGTCAATCAAAACCTTACGAGCAAAA-C
*
10115 AAGTTGTGATTTCTCTCGACGAGTCGAGTTATTTGATTTCGAAATGGC
129 AAGTTGTAATTTCTCTCGACGA--CGAGTTATTTGATTTCGAAATGGC
*
10163 A-CGAAATCACAAGTTTTCAGTGTCATCTTCAAAACAAGAATGAGATTCCGATCCACAAACAGAA
1 ATCGAAATCACAAGTTTTCAGTGTCATCTTCAAAAAAAGAATGAGATTCCGATCCACAAACAGAA
*
10227 AAACGAAGAGAAATAACGTTCGAAAGTTAACATCTCTCGTCAATCAACACCTTACGAGCAAAACA
66 AAACGAAGAGAAATAACGTTCGAAAGTTAA-ATCTCTCGTCAATCAAAACCTTACGAGCAAAACA
*
10292 AGTTGTCATTTCTCTCGACGA
130 AGTTGTAATTTCTCTCGACGA
10313 TTTCCAGATT
Statistics
Matches: 283, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
171 4 0.01
172 38 0.13
173 4 0.01
174 76 0.27
175 35 0.12
176 75 0.27
177 51 0.18
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (174 bp):
ATCGAAATCACAAGTTTTCAGTGTCATCTTCAAAAAAAGAATGAGATTCCGATCCACAAACAGAA
AAACGAAGAGAAATAACGTTCGAAAGTTAAATCTCTCGTCAATCAAAACCTTACGAGCAAAACAA
GTTGTAATTTCTCTCGACGACGAGTTATTTGATTTCGAAATGGC
Found at i:18049 original size:36 final size:36
Alignment explanation
Indices: 17977--18050 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
17967 TATATTTAAA
* *
17977 TTAAATATATAAACATTATATATATTTTAATTTAAT
1 TTAAATATATAAACATTATATATATTATAATATAAT
* * *
18013 TTAAATTTATTAATATTATATATA-TATAATAATAAT
1 TTAAATATATAAACATTATATATATTATAAT-ATAAT
18049 TT
1 TT
18051 TTAATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 5 0.16
36 27 0.84
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (36 bp):
TTAAATATATAAACATTATATATATTATAATATAAT
Found at i:21339 original size:30 final size:28
Alignment explanation
Indices: 21297--21352 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 28
21287 AATGTTTTCA
21297 AAAAAAAGTTTAGTTCAATTAACAATTAAAG
1 AAAAAAAGTTTAGTT-AATT--CAATTAAAG
21328 AAAAAAA-TTTAGTTAATTCAATTAA
1 AAAAAAAGTTTAGTTAATTCAATTAA
21353 TAATAATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 7 0.28
29 4 0.16
30 7 0.28
31 7 0.28
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAAAAAGTTTAGTTAATTCAATTAAAG
Found at i:21926 original size:35 final size:35
Alignment explanation
Indices: 21880--21990 Score: 141
Period size: 35 Copynumber: 3.2 Consensus size: 35
21870 AAAACATTCC
* *
21880 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCACAAATTCTAAAATAAT
* * * *
21915 TAAATTTCATTCTAAACCATAAATTCTAAAATAGT
1 TCAATTACATTCTAAACCACAAATTCTAAAATAAT
* * *
21950 TCAATTACATTCTAAAACTCAAATTCTAAAATATT
1 TCAATTACATTCTAAACCACAAATTCTAAAATAAT
21985 TCAATT
1 TCAATT
21991 TAAGGAGGAA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTACATTCTAAACCACAAATTCTAAAATAAT
Found at i:23092 original size:35 final size:34
Alignment explanation
Indices: 23043--23155 Score: 122
Period size: 35 Copynumber: 3.2 Consensus size: 34
23033 AAAAAAGACA
*
23043 GAAATTGAAATATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTT-GAATTTGGGTTTTAGAAT
* *
23078 GTAATTGAATTATTTTGGAATTT-AGTGTTTAGAAT
1 GAAATTGAATTATTTT-GAATTTGGGT-TTTAGAAT
* *
23113 GAAATTTAATTACTTTTGAATTTGTGG-TTTATAAT
1 GAAATTGAATTA-TTTTGAATTTG-GGTTTTAGAAT
23148 GAAATTGA
1 GAAATTGA
23156 GGATTGTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
34 2 0.03
35 58 0.89
36 4 0.06
37 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.46
Consensus pattern (34 bp):
GAAATTGAATTATTTTGAATTTGGGTTTTAGAAT
Found at i:23406 original size:2 final size:2
Alignment explanation
Indices: 23399--23424 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23389 TATATGTTTA
23399 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
23425 TGCTTTAAGC
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:23660 original size:2 final size:2
Alignment explanation
Indices: 23653--23682 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23643 TAAATATTTA
23653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23683 TATTTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24187 original size:10 final size:10
Alignment explanation
Indices: 24172--24201 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
24162 TAAGTTTATC
24172 AATTATTAAA
1 AATTATTAAA
24182 AATTATTAAA
1 AATTATTAAA
24192 AATTA-TAAA
1 AATTATTAAA
24201 A
1 A
24202 TGATCATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AATTATTAAA
Found at i:25800 original size:31 final size:31
Alignment explanation
Indices: 25757--25817 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
25747 GTTATTGTAT
25757 AACAATTCGATAAGA-TTAATGACTATTTTGC
1 AACAATTCGATAA-ATTTAATGACTATTTTGC
* *
25788 AACAATTTGATAAATTTTAATGAGTATTTT
1 AACAATTCGATAAA-TTTAATGACTATTTT
25818 ATAATTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 12 0.46
32 13 0.50
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (31 bp):
AACAATTCGATAAATTTAATGACTATTTTGC
Found at i:26338 original size:28 final size:30
Alignment explanation
Indices: 26278--26339 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
26268 AACATATATA
* *
26278 ATATGGTTTCAAAAACATTTTTGAAAATAT
1 ATATGATTTCAAAAACATTTTTGAAAACAT
*
26308 ATATGATTT-AAAAACA-TTTTGAAAACGT
1 ATATGATTTCAAAAACATTTTTGAAAACAT
26336 ATAT
1 ATAT
26340 AAAACTAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.48
29 7 0.24
30 8 0.28
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (30 bp):
ATATGATTTCAAAAACATTTTTGAAAACAT
Found at i:26340 original size:30 final size:30
Alignment explanation
Indices: 26273--26332 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 30
26263 TTGAAAACAT
*
26273 ATATAATATGGTTTCAAAAACATTTTTGAAA
1 ATAT-ATATGATTTCAAAAACATTTTTGAAA
26304 ATATATATGATTT-AAAAACA-TTTTGAAA
1 ATATATATGATTTCAAAAACATTTTTGAAA
26332 A
1 A
26333 CGTATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.32
29 7 0.25
30 8 0.29
31 4 0.14
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.38
Consensus pattern (30 bp):
ATATATATGATTTCAAAAACATTTTTGAAA
Found at i:28616 original size:5 final size:5
Alignment explanation
Indices: 28606--28648 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
28596 TGTTATACCA
*
28606 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AGTAT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
28649 TTGAATAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:28784 original size:2 final size:2
Alignment explanation
Indices: 28777--28821 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
28767 TTGTTCAACT
28777 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
28819 TA T
1 TA T
28822 TGATAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32893 original size:57 final size:56
Alignment explanation
Indices: 32785--32894 Score: 125
Period size: 57 Copynumber: 1.9 Consensus size: 56
32775 AGTATATACG
* ** *
32785 CATAATTCAGGATAAAATTGAAATGTTCGTAAAATTTGGAGACCTATTTAGAAAGGT
1 CATAATTCAGGATAAAATTGAAATGTTCG-AAAATCTACAGACCTACTTAGAAAGGT
*
32842 CATAATTCATGGATGAAATTGAAATGTTC-AAAAGTCTACAGA-CTAACTTAGAA
1 CATAATTCA-GGATAAAATTGAAATGTTCGAAAA-TCTACAGACCT-ACTTAGAA
32895 TAAAAATCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
56 6 0.13
57 21 0.47
58 18 0.40
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (56 bp):
CATAATTCAGGATAAAATTGAAATGTTCGAAAATCTACAGACCTACTTAGAAAGGT
Found at i:42544 original size:10 final size:10
Alignment explanation
Indices: 42529--42570 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
42519 TACATTTTTA
42529 TTTTTTTATT
1 TTTTTTTATT
42539 TTTTTTTATT
1 TTTTTTTATT
*
42549 TTTTGTTTAAT
1 TTTT-TTTATT
*
42560 TTTATTTATT
1 TTTTTTTATT
42570 T
1 T
42571 CCATTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:42550 original size:17 final size:17
Alignment explanation
Indices: 42522--42566 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
42512 AATATATTAC
42522 ATTTTTATTTTTTTATTT
1 ATTTTTA-TTTTTTATTT
* *
42540 TTTTTTATTTTTTGTTT
1 ATTTTTATTTTTTATTT
*
42557 AATTTTATTT
1 ATTTTTATTT
42567 ATTTCCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (17 bp):
ATTTTTATTTTTTATTT
Found at i:42562 original size:18 final size:18
Alignment explanation
Indices: 42516--42566 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
42506 TAATTAAATA
42516 TATTACATTTTTATTTTTT
1 TATTA-ATTTTTATTTTTT
**
42535 TATTTTTTTTTATTTTTT
1 TATTAATTTTTATTTTTT
42553 GT-TTAA-TTTTATTT
1 -TATTAATTTTTATTT
42567 ATTTCCATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (18 bp):
TATTAATTTTTATTTTTT
Found at i:42562 original size:21 final size:20
Alignment explanation
Indices: 42529--42570 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
42519 TACATTTTTA
* *
42529 TTTTTTTATTTTTTTTTATT
1 TTTTTTTAATTTTATTTATT
42549 TTTTGTTTAATTTTATTTATT
1 TTTT-TTTAATTTTATTTATT
42570 T
1 T
42571 CCATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTTTAATTTTATTTATT
Found at i:42679 original size:24 final size:24
Alignment explanation
Indices: 42601--42668 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
42591 ATATATATAT
*
42601 ATTATTTTCATAGGTAGTGGTTTG
1 ATTATTTTAATAGGTAGTGGTTTG
42625 ATTATTTTAATAGGTAGTGGTTTG
1 ATTATTTTAATAGGTAGTGGTTTG
*
42649 ATTATTTTAATAAGTAGTGG
1 ATTATTTTAATAGGTAGTGG
42669 GTTATTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (24 bp):
ATTATTTTAATAGGTAGTGGTTTG
Found at i:47792 original size:31 final size:30
Alignment explanation
Indices: 47750--47819 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
47740 TCAAGTACTT
47750 AAAG-TATTTTTTGGTCAAAATAAATACCC
1 AAAGTTATTTTTTGGTCAAAATAAATACCC
* * *
47779 AAAGTTATCTTTTTTGTCAAAATAAGTATCC
1 AAAGTTAT-TTTTTGGTCAAAATAAATACCC
47810 AAAG-TATTTT
1 AAAGTTATTTT
47820 GTGTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 7 0.19
30 6 0.17
31 23 0.64
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (30 bp):
AAAGTTATTTTTTGGTCAAAATAAATACCC
Found at i:47845 original size:28 final size:28
Alignment explanation
Indices: 47788--47845 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
47778 CAAAGTTATC
* * *
47788 TTTTTTGTCAAAATAAGTATCCAAAGTA
1 TTTTGTGTAAAAATAAGTATCCAAACTA
*
47816 TTTTGTGTAAAAATAGGTA-CCTAAACTA
1 TTTTGTGTAAAAATAAGTATCC-AAACTA
47844 TT
1 TT
47846 CAAACTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (28 bp):
TTTTGTGTAAAAATAAGTATCCAAACTA
Found at i:48035 original size:29 final size:29
Alignment explanation
Indices: 47954--48035 Score: 101
Period size: 32 Copynumber: 2.7 Consensus size: 29
47944 TATTTGATAA
* * *
47954 AAAAAATAATTTAGGCACTTATTTTGACC
1 AAAAAATACTTTAAGTACTTATTTTGACC
*
47983 ATAAAAGATAACTTTCAGTACTTATTTTGACC
1 A-AAAA-AT-ACTTTAAGTACTTATTTTGACC
48015 AAAAAATACTTTAAGTACTTA
1 AAAAAATACTTTAAGTACTTA
48036 AATAAAAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 14 0.31
30 6 0.13
31 6 0.13
32 19 0.42
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (29 bp):
AAAAAATACTTTAAGTACTTATTTTGACC
Found at i:49021 original size:26 final size:25
Alignment explanation
Indices: 49000--49051 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
48990 TTTTTCTTAG
49000 TTTTT-ATGCCATTTCTTCTTTCTTC
1 TTTTTCATGCC-TTTCTTCTTTCTTC
* *
49025 TTTTTCATGTCTTTTTTCTTTCTTC
1 TTTTTCATGCCTTTCTTCTTTCTTC
49050 TT
1 TT
49052 CTCACAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.06, C:0.21, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTTCATGCCTTTCTTCTTTCTTC
Found at i:49579 original size:59 final size:59
Alignment explanation
Indices: 49474--49606 Score: 155
Period size: 59 Copynumber: 2.2 Consensus size: 59
49464 TTGGGTGATC
*
49474 ATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGTAACTCCCTATAGTC-GGAGAACT
1 ATTTTGTAAC-TTTAATAGTCAATGGACTCAACAAAGCAACTCCCTATAGTCAGG-GAACT
** * * *
49534 ATTTTGTAACTTTAATAGTCGGTGGACTTAATAAAGCAA-TACCCTATAGTCAGGGAATT
1 ATTTTGTAACTTTAATAGTCAATGGACTCAACAAAGCAACT-CCCTATAGTCAGGGAACT
49593 ATTTATGT-ACTTTA
1 ATTT-TGTAACTTTA
49607 CCCTATGTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 1 0.02
59 48 0.75
60 15 0.23
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (59 bp):
ATTTTGTAACTTTAATAGTCAATGGACTCAACAAAGCAACTCCCTATAGTCAGGGAACT
Found at i:51067 original size:3 final size:3
Alignment explanation
Indices: 51059--51124 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
51049 ATATATAAAT
51059 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
51107 GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG
51125 ACTGTTAAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:52461 original size:21 final size:20
Alignment explanation
Indices: 52375--52532 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
52365 AAATGACCAA
**
52375 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
52394 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
52414 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
52434 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
52455 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
52476 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
52496 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
52517 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
52533 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:52525 original size:20 final size:20
Alignment explanation
Indices: 52500--52810 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
52490 GATTTTCAAT
* *
52500 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
52520 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
52540 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
52560 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
52580 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
52600 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
52620 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
52640 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
52661 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
52681 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
52701 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
52721 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
52741 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
52761 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
52781 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
52801 AATCGCAACG
1 AATCGCAACG
52811 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:52545 original size:40 final size:40
Alignment explanation
Indices: 52500--52889 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
52490 GATTTTCAAT
* ** * * *
52500 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
52540 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
52580 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
52620 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
52661 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
52701 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
52741 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
52781 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
52821 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
52861 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
52890 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:52817 original size:20 final size:19
Alignment explanation
Indices: 52538--52889 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
52528 CGCGAACACA
52538 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
52558 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
52578 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
52598 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
52618 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
52638 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
52658 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
52679 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
52699 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
52719 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
52739 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
52759 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
52779 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
52799 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
52819 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
52839 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
52859 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
52879 TAAATCACAAC
1 TAAATCGCAAC
52890 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:53591 original size:24 final size:24
Alignment explanation
Indices: 53564--53610 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53554 AAATTTGGTC
53564 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
53588 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
53611 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:53802 original size:12 final size:12
Alignment explanation
Indices: 53785--53809 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53775 ATATAATCCT
53785 GAAGAAGAAAAA
1 GAAGAAGAAAAA
53797 GAAGAAGAAAAA
1 GAAGAAGAAAAA
53809 G
1 G
53810 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:56113 original size:19 final size:19
Alignment explanation
Indices: 56091--56363 Score: 336
Period size: 19 Copynumber: 15.4 Consensus size: 19
56081 CGGAAAATAC
*
56091 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
56110 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
56124 AATAGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
56144 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
56158 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56177 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
56196 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
56210 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56229 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
56248 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
56267 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56286 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56305 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
56319 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56338 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
56356 AATCGCAA
1 AATCGCAA
56364 CGAGATAATC
Statistics
Matches: 223, Mismatches: 10, Indels: 43
0.81 0.04 0.16
Matches are distributed among these distances:
14 39 0.17
15 2 0.01
16 11 0.05
17 10 0.04
18 12 0.05
19 137 0.61
20 12 0.05
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:56142 original size:34 final size:33
Alignment explanation
Indices: 56095--56180 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 33
56085 AAATACAATC
*
56095 GCAACGCGAAATGAAAATCCCAAC-ATGAAAATA
1 GCAATGCGAAATGAAAATCCCAACGA-GAAAATA
* * *
56128 GCAATGCGGAAATGAAAATCGCAACGAGAGAATC
1 GCAATGC-GAAATGAAAATCCCAACGAGAAAATA
56162 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
56181 GCAATGCGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
33 18 0.38
34 28 0.60
35 1 0.02
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCCCAACGAGAAAATA
Found at i:56206 original size:52 final size:52
Alignment explanation
Indices: 56119--56385 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
56109 AAATCCCAAC
*
56119 ATGAAAATAGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
56172 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
56224 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
56281 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
56333 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
56384 AT
1 AT
56386 TATAAACGCA
Statistics
Matches: 205, Mismatches: 4, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
51 29 0.14
52 104 0.51
53 16 0.08
54 4 0.02
55 5 0.02
56 1 0.00
57 46 0.22
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:56292 original size:109 final size:105
Alignment explanation
Indices: 56119--56385 Score: 441
Period size: 109 Copynumber: 2.5 Consensus size: 105
56109 AAATCCCAAC
*
56119 ATGAAAATAGCAATGCGGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAAATGAAAATCGC
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGC
*
56183 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
65 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
56224 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGAT-G-AATCGCAATGCGAAATGAAAAT
56289 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
62 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
56333 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAAT
56386 TATAAACGCA
Statistics
Matches: 153, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
103 16 0.10
104 16 0.10
105 15 0.10
106 9 0.06
108 10 0.07
109 87 0.57
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (105 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:56481 original size:19 final size:18
Alignment explanation
Indices: 56392--56473 Score: 100
Period size: 19 Copynumber: 4.6 Consensus size: 18
56382 AAATTATAAA
56392 CGCATTGCGATTTCATTT
1 CGCATTGCGATTTCATTT
56410 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGA-TTTCATTT
*
56430 CGCATTGCGA-TTC-TCT
1 CGCATTGCGATTTCATTT
56446 CG--TTGCGATTTTCATTT
1 CGCATTGCGA-TTTCATTT
56463 CGCATTGCGAT
1 CGCATTGCGAT
56474 AGTCATTTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
14 6 0.11
16 7 0.13
17 7 0.13
18 1 0.02
19 26 0.47
20 8 0.15
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (18 bp):
CGCATTGCGATTTCATTT
Found at i:56598 original size:14 final size:14
Alignment explanation
Indices: 56579--56615 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
56569 CATCAATTAC
56579 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
56593 ACAAATCATCTTTT
1 ACAAATCAACTTTT
56607 ACAAATCAA
1 ACAAATCAA
56616 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:58583 original size:14 final size:14
Alignment explanation
Indices: 58564--58620 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
58554 GCGAAATGAA
*
58564 AATCGCAACGACAG
1 AATCGCAACGAAAG
58578 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
58595 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
58611 AATCGCAACG
1 AATCGCAACG
58621 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:58591 original size:33 final size:33
Alignment explanation
Indices: 58545--58637 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
58535 GCGAAACCAA
*
58545 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
58578 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
58611 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
58638 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:58602 original size:19 final size:19
Alignment explanation
Indices: 58508--58642 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
58498 TAGTTTACTT
* *
58508 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
58528 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
58547 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
58566 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
58580 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
58599 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
58613 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
58632 TCGCAATGCGA
1 TCGCAACGCGA
58643 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:58680 original size:33 final size:33
Alignment explanation
Indices: 58638--58729 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
58628 AAAATCGCAA
*
58638 TGCGATTTTGGTTTCGCGTTGTGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
58671 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
58704 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
58730 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:58692 original size:19 final size:19
Alignment explanation
Indices: 58638--58766 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
58628 AAAATCGCAA
58638 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
58657 TGTGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
58671 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
58690 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
58704 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
58723 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
58742 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
58762 TGCGA
1 TGCGA
58767 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:58983 original size:92 final size:93
Alignment explanation
Indices: 58810--59188 Score: 719
Period size: 92 Copynumber: 4.1 Consensus size: 93
58800 TTGAATGGAT
58810 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
58875 AGTTTAGCAGAA-TGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
58902 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
58966 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
58994 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
59058 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
59086 AAATTTACTTTCAACCAAAAGACAAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACA
1 AAATTTACTTTCAACCAAAAGAC-AAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACA
*
59151 CAGTTTAGCAGAATTGGCAGCAACCGAAT
65 CAGTTTAGCAGAATTGGCAGCAACCGAAC
59180 AAATTTACT
1 AAATTTACT
59189 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 37 0.13
92 169 0.60
93 16 0.06
94 61 0.22
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:60899 original size:14 final size:14
Alignment explanation
Indices: 60880--60969 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
60870 TTGAAATGAA
60880 AATCGCAACGAGAG
1 AATCGCAACGAGAG
60894 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
60911 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
60927 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
60946 AATCGCAACGAGAG
1 AATCGCAACGAGAG
60960 AATCGCAACG
1 AATCGCAACG
60970 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:60917 original size:33 final size:33
Alignment explanation
Indices: 60872--60986 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
60862 TCTTTTGGTT
60872 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
60905 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
60938 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
60971 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
60987 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:60918 original size:19 final size:18
Alignment explanation
Indices: 60879--60991 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
60869 GTTGAAATGA
60879 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
60894 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
60911 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
60927 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
60944 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
60960 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
60977 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
60992 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:61022 original size:14 final size:14
Alignment explanation
Indices: 61003--61057 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
60993 TTTGGTTTCG
61003 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
61017 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
61036 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
61050 CGTTGCGA
1 CGTTGCGA
61058 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:61035 original size:33 final size:33
Alignment explanation
Indices: 60987--61057 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
60977 AAAATCGCAA
**
60987 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
61020 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
61053 TGCGA
1 TGCGA
61058 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:61065 original size:33 final size:33
Alignment explanation
Indices: 60998--61079 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
60988 GCGATTTTGG
***
60998 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
61031 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
61064 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
61080 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:61084 original size:20 final size:20
Alignment explanation
Indices: 61010--61098 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
61000 TCGCGTTGCG
61010 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
61030 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
61043 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
61063 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
61083 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
61099 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:61219 original size:33 final size:33
Alignment explanation
Indices: 61177--61247 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
61167 AATACTAACT
*
61177 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
61210 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
61243 TGAAA
1 TGAAA
61248 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:61787 original size:20 final size:20
Alignment explanation
Indices: 61621--61775 Score: 213
Period size: 20 Copynumber: 7.7 Consensus size: 20
61611 CTTTAAATAT
61621 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
61641 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
61663 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
61682 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
61702 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
61722 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
61742 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
61762 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
61776 TGTGTTCGCG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.02
20 98 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:61793 original size:40 final size:40
Alignment explanation
Indices: 61620--61813 Score: 210
Period size: 40 Copynumber: 4.8 Consensus size: 40
61610 GCTTTAAATA
* *
61620 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGAT
** *
61661 TATCGTTGCGATTTACGGATACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
* * **
61701 ACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
* * *
61741 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACG-GAT
* * ** *
61781 TCGCGTTACGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATT
61814 ATTGAAAATC
Statistics
Matches: 128, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
40 98 0.77
41 30 0.23
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
Found at i:61808 original size:60 final size:60
Alignment explanation
Indices: 61621--61813 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
61611 CTTTAAATAT
**
61621 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
61682 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * * ** *
61742 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTACGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
61802 CGCGTTGCGATT
1 CGCGTTGCGATT
61814 ATTGAAAATC
Statistics
Matches: 110, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:63008 original size:57 final size:57
Alignment explanation
Indices: 62940--63080 Score: 264
Period size: 57 Copynumber: 2.5 Consensus size: 57
62930 AGGTTCTAAA
*
62940 ATCGCAACGCGAATAGTAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAACGCGAATAGGAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACT
*
62997 ATCGCAACGCGAATAGGAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTATT
1 ATCGCAACGCGAATAGGAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACT
63054 ATCGCAACGCGAATAGGAAAATCGCAA
1 ATCGCAACGCGAATAGGAAAATCGCAA
63081 TGCGAATAGC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 82 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (57 bp):
ATCGCAACGCGAATAGGAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACT
Found at i:63079 original size:20 final size:20
Alignment explanation
Indices: 63054--63103 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
63044 AAACAGTATT
*
63054 ATCGCAACGCGAATAGGAAA
1 ATCGCAACGCGAATAGCAAA
*
63074 ATCGCAATGCGAATAGCAAA
1 ATCGCAACGCGAATAGCAAA
63094 ATCGCAACGC
1 ATCGCAACGC
63104 TAATCACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAATAGCAAA
Found at i:63080 original size:77 final size:77
Alignment explanation
Indices: 62997--63142 Score: 238
Period size: 77 Copynumber: 1.9 Consensus size: 77
62987 AAACAGTACT
* * * *
62997 ATCGCAACGCGAATAGGAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTATTATCGCAAC
1 ATCGCAACGCGAATAGCAAAATCGCAACGCTAATCACCGACATAGGTAAACAGTACTATCGCAAC
63062 GCGAATAGGAAA
66 GCGAATAGGAAA
* *
63074 ATCGCAATGCGAATAGCAAAATCGCAACGCTAATCACTGACATAGGTAAACAGTACTATCGCAAC
1 ATCGCAACGCGAATAGCAAAATCGCAACGCTAATCACCGACATAGGTAAACAGTACTATCGCAAC
63139 GCGA
66 GCGA
63143 TTTTTAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (77 bp):
ATCGCAACGCGAATAGCAAAATCGCAACGCTAATCACCGACATAGGTAAACAGTACTATCGCAAC
GCGAATAGGAAA
Found at i:63431 original size:37 final size:37
Alignment explanation
Indices: 63378--63467 Score: 153
Period size: 37 Copynumber: 2.4 Consensus size: 37
63368 TTTAAAAATC
*
63378 GCGTTGCGATTTTACTGTTTACCTATATTGGTAATTA
1 GCGTTGCGATTTTACTGTTTACCTATATCGGTAATTA
*
63415 GCGTTGCGATTGTACTGTTTACCTATATCGGTAATTA
1 GCGTTGCGATTTTACTGTTTACCTATATCGGTAATTA
*
63452 GTGTTGCGATTTTACT
1 GCGTTGCGATTTTACT
63468 ATTCGCGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.44
Consensus pattern (37 bp):
GCGTTGCGATTTTACTGTTTACCTATATCGGTAATTA
Found at i:63444 original size:94 final size:94
Alignment explanation
Indices: 63334--63524 Score: 265
Period size: 94 Copynumber: 2.0 Consensus size: 94
63324 AATCATTTCG
**
63334 ACTGTTTACCTATATCGGTAATTAGAGTTGCGAATTTAAAAATCGCGTTGCGATTTTACTGTTTA
1 ACTGTTTACCTATATCGGTAATTAGAGTTGCGAATTTAAAAATCGCGTTGCGATAGTACTGTTTA
*** *
63399 CCTATATTGGTAATTAGCGTTGCGATTGT
66 CCTATATCAATAATTAGCATTGCGATTGT
* * ** * *
63428 ACTGTTTACCTATATCGGTAATTAGTGTTGCGATTTTACTATTCGCGTTGTGATAGTACTGTTTA
1 ACTGTTTACCTATATCGGTAATTAGAGTTGCGAATTTAAAAATCGCGTTGCGATAGTACTGTTTA
*
63493 CCTATATCAATAATTAGCATTGCGATTTT
66 CCTATATCAATAATTAGCATTGCGATTGT
63522 ACT
1 ACT
63525 ATTCGCGTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (94 bp):
ACTGTTTACCTATATCGGTAATTAGAGTTGCGAATTTAAAAATCGCGTTGCGATAGTACTGTTTA
CCTATATCAATAATTAGCATTGCGATTGT
Found at i:63507 original size:57 final size:57
Alignment explanation
Indices: 63415--63538 Score: 185
Period size: 57 Copynumber: 2.2 Consensus size: 57
63405 TTGGTAATTA
* ** **
63415 GCGTTGCGATTGTACTGTTTACCTATATCGGTAATTAGTGTTGCGATTTTACTATTC
1 GCGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCATTGCGATTTTACTATTC
*
63472 GCGTTGTGATAGTACTGTTTACCTATATCAATAATTAGCATTGCGATTTTACTATTC
1 GCGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCATTGCGATTTTACTATTC
*
63529 GCGTTCCGAT
1 GCGTTGCGAT
63539 TTTCCTATTC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (57 bp):
GCGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCATTGCGATTTTACTATTC
Found at i:63540 original size:20 final size:20
Alignment explanation
Indices: 63515--63558 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
63505 ATTAGCATTG
63515 CGATTTTACTATTCGCGTTC
1 CGATTTTACTATTCGCGTTC
* *
63535 CGATTTTCCTATTCGCGTTG
1 CGATTTTACTATTCGCGTTC
63555 CGAT
1 CGAT
63559 AGTACTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
CGATTTTACTATTCGCGTTC
Found at i:63616 original size:77 final size:78
Alignment explanation
Indices: 63457--63618 Score: 213
Period size: 77 Copynumber: 2.1 Consensus size: 78
63447 AATTAGTGTT
* *
63457 GCGATTTTACTATTCGCGTTGTGATAGTACTGTTTACCTATATCAATAATTAGCATTGCGATTTT
1 GCGATTTTACTATTCGCGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCATTGCGATTTG
* * **
63522 ACTATTCGCGTTC
66 ACAAATCGCGAAC
* **
63535 -CGATTTTCCTATTCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTT
1 GCGATTTTACTATTCGCGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCATTGCG-ATTT
63599 GA-AAATCGC-AAC
65 GACAAATCGCGAAC
63611 GCGATTTT
1 GCGATTTT
63619 GGAACCTGTG
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
76 1 0.01
77 67 0.92
78 5 0.07
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (78 bp):
GCGATTTTACTATTCGCGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCATTGCGATTTG
ACAAATCGCGAAC
Found at i:64894 original size:12 final size:12
Alignment explanation
Indices: 64877--64903 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
64867 TCGGGTTGAG
64877 TGTCCATCCCTA
1 TGTCCATCCCTA
64889 TGTCCATCCCTA
1 TGTCCATCCCTA
64901 TGT
1 TGT
64904 ATTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.37, G:0.11, T:0.37
Consensus pattern (12 bp):
TGTCCATCCCTA
Found at i:69613 original size:26 final size:25
Alignment explanation
Indices: 69578--69650 Score: 94
Period size: 26 Copynumber: 2.9 Consensus size: 25
69568 TTCATTTAAA
69578 TATTATTTATATTATTATTATTATTT
1 TATTA-TTATATTATTATTATTATTT
*
69604 TATTTATTATAATATTATTATTATTT
1 TA-TTATTATATTATTATTATTATTT
* *
69630 TATTATTA-ATAAATATTATTA
1 TATTATTATATTATTATTATTA
69651 CAGGCCCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.24
25 6 0.14
26 23 0.55
27 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTATTATATTATTATTATTATTT
Found at i:69619 original size:29 final size:27
Alignment explanation
Indices: 69590--69650 Score: 99
Period size: 26 Copynumber: 2.3 Consensus size: 27
69580 TTATTTATAT
69590 TATTATTATTATTTTATTTATT-AT-AA
1 TATTATTATTATTTTA-TTATTAATAAA
69616 TATTATTATTATTTTATTATTAATAAA
1 TATTATTATTATTTTATTATTAATAAA
69643 TATTATTA
1 TATTATTA
69651 CAGGCCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.15
26 18 0.55
27 10 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTATTATTATTTTATTATTAATAAA
Found at i:69650 original size:3 final size:3
Alignment explanation
Indices: 69578--69637 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
69568 TTCATTTAAA
*
69578 TAT TAT T-T ATAT TAT TAT TAT TAT T-T TATT TAT TA- TAA TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
69622 TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TA
69638 ATAAATATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
2 7 0.14
3 39 0.78
4 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.