Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007589.1 Hibiscus syriacus cultivar Beakdansim tig00021849_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: 223780
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:20147 original size:97 final size:98
Alignment explanation
Indices: 20015--20205 Score: 233
Period size: 97 Copynumber: 2.0 Consensus size: 98
20005 ATCTCCCACA
* * *
20015 TTACTCGCGAGGTAACTTCCAAAAGTGGGATGAATAGTGACAATATT-CCATTATT-TCAGAAAT
1 TTACTCGCGAGGTAACTTCCAAAAGTGGGACGAATACTGACAATATTACC-TTATTATCACAAAT
* *
20078 TGAGTCATAATAGATAAGATACTTTGGTATACTT
65 TGAGTCATAACAAATAAGATACTTTGGTATACTT
* * * ** * * *
20112 TTACTCGTGGGGTAACTTTCAAATTTGGGACGAATACTGACAATATTATCTTTTTATCACAGATT
1 TTACTCGCGAGGTAACTTCCAAAAGTGGGACGAATACTGACAATATTACCTTATTATCACAAATT
*
20177 GAGTCATAACAAATAATATACTTTGGTAT
66 GAGTCATAACAAATAAGATACTTTGGTAT
20206 TCTTATTTCA
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
97 44 0.56
98 34 0.44
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (98 bp):
TTACTCGCGAGGTAACTTCCAAAAGTGGGACGAATACTGACAATATTACCTTATTATCACAAATT
GAGTCATAACAAATAAGATACTTTGGTATACTT
Found at i:23107 original size:33 final size:33
Alignment explanation
Indices: 23065--23140 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
23055 CGATCTATTT
23065 ATCAAAAGTAGGACAACCAAAAATCCATAAGTG
1 ATCAAAAGTAGGACAACCAAAAATCCATAAGTG
23098 ATCAAAAGTAGGACAACCAAAAATCCATAAGTG
1 ATCAAAAGTAGGACAACCAAAAATCCATAAGTG
23131 ATCAAAAGTA
1 ATCAAAAGTA
23141 ACATCATGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.16
Consensus pattern (33 bp):
ATCAAAAGTAGGACAACCAAAAATCCATAAGTG
Found at i:25332 original size:31 final size:32
Alignment explanation
Indices: 25243--25378 Score: 132
Period size: 32 Copynumber: 4.3 Consensus size: 32
25233 TTAGGCATAG
* * * * *
25243 GAGCCAACCTAAGGGATTATCTTGGGTCCTGA
1 GAGCCTACCCAAGGGAATATCTTGGGGCCTAA
* ** *
25275 GAGCCTACCCAAGAGTGTACCTTGGGG-CTAA
1 GAGCCTACCCAAGGGAATATCTTGGGGCCTAA
* *
25306 GAGCCTACCCAAGGGAATATCATGGGGCCTTA
1 GAGCCTACCCAAGGGAATATCTTGGGGCCTAA
* *
25338 GATCCTACCCAAGGAAATATCTTGGGGCCTCAA
1 GAGCCTACCCAAGGGAATATCTTGGGGCCT-AA
25371 -AGCCTACC
1 GAGCCTACC
25379 TAAGTGTCAC
Statistics
Matches: 83, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
31 25 0.30
32 57 0.69
33 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (32 bp):
GAGCCTACCCAAGGGAATATCTTGGGGCCTAA
Found at i:27419 original size:33 final size:33
Alignment explanation
Indices: 27382--27454 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
27372 GTCAATGGCT
27382 AGTCAACGCTC-GGTCAATGCCCGATCAATACCC
1 AGTCAACGC-CAGGTCAATGCCCGATCAATACCC
**
27415 AGTCAACGCCAGGTCAATTTCCGATCAATACCC
1 AGTCAACGCCAGGTCAATGCCCGATCAATACCC
27448 AGTCAAC
1 AGTCAAC
27455 ACCTGGCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.19
Consensus pattern (33 bp):
AGTCAACGCCAGGTCAATGCCCGATCAATACCC
Found at i:28350 original size:8 final size:8
Alignment explanation
Indices: 28337--28364 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
28327 AAATTTAAAT
28337 TTTTTTTA
1 TTTTTTTA
28345 TTTTTTTA
1 TTTTTTTA
28353 TTTTTTTA
1 TTTTTTTA
28361 TTTT
1 TTTT
28365 AAAATGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:30387 original size:39 final size:39
Alignment explanation
Indices: 30325--30415 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
30315 ATTTAATGGG
* * *
30325 GAAATTAAAGAGTCTCTTGGGAGTTAGAGCATTTTATTGT
1 GAAATT-AAGAGTCTCTTAGGAGTGAGAGCATTTTATTAT
* *
30365 GAAATTAAGATTCTCTTAGGAGTGAGAGTATTTTATTAT
1 GAAATTAAGAGTCTCTTAGGAGTGAGAGCATTTTATTAT
*
30404 GAATTTAAGAGT
1 GAAATTAAGAGT
30416 TATTGGAAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 38 0.86
40 6 0.14
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (39 bp):
GAAATTAAGAGTCTCTTAGGAGTGAGAGCATTTTATTAT
Found at i:32838 original size:24 final size:24
Alignment explanation
Indices: 32811--32865 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
32801 TCAGGTTAGA
** *
32811 TATCATAACAGGTTCTAGGCCAGG
1 TATCATAACAGAATCCAGGCCAGG
** *
32835 TATCCGAACAGAATCCAGGTCAGG
1 TATCATAACAGAATCCAGGCCAGG
32859 TATCATA
1 TATCATA
32866 CTAGAATTCA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
TATCATAACAGAATCCAGGCCAGG
Found at i:34866 original size:14 final size:14
Alignment explanation
Indices: 34849--34882 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
34839 GGTTGACTCA
34849 GTCGGGTCAAGCGG
1 GTCGGGTCAAGCGG
34863 GTCGGGTCAAGCGG
1 GTCGGGTCAAGCGG
34877 GTCGGG
1 GTCGGG
34883 CAGGCCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.21, G:0.53, T:0.15
Consensus pattern (14 bp):
GTCGGGTCAAGCGG
Found at i:37370 original size:39 final size:39
Alignment explanation
Indices: 37316--37410 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
37306 TAAGGTTTTC
** *
37316 CCCTATGCATGAAGCAAATGAG-CTTACGATAAGAACTTA
1 CCCTATGCACAAAGCAAAGGAGTC-TACGATAAGAACTTA
* * * *
37355 CCTTGTGCACAAAGCAAAGGAGTCTATGATAAGGACTTA
1 CCCTATGCACAAAGCAAAGGAGTCTACGATAAGAACTTA
37394 CCCTATGCACAAAGCAA
1 CCCTATGCACAAAGCAA
37411 GAGAGCCTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (39 bp):
CCCTATGCACAAAGCAAAGGAGTCTACGATAAGAACTTA
Found at i:37431 original size:39 final size:39
Alignment explanation
Indices: 37316--37440 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 39
37306 TAAGGTTTTC
** * * *
37316 CCCTATGCATGAAGCAAATGAGCTTACGAT-AAGAACTTA
1 CCCTATGCACAAAGCAAAGGAGCCTAAGATAAAG-ACTTA
* * * * *
37355 CCTTGTGCACAAAGCAAAGGAGTCTATGATAAGGACTTA
1 CCCTATGCACAAAGCAAAGGAGCCTAAGATAAAGACTTA
* *
37394 CCCTATGCACAAAGC-AAGAGAGCCTAAGGTAAAGACTTG
1 CCCTATGCACAAAGCAAAG-GAGCCTAAGATAAAGACTTA
37433 CCCTATGC
1 CCCTATGC
37441 GTAGCGTAGG
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
38 3 0.04
39 63 0.93
40 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (39 bp):
CCCTATGCACAAAGCAAAGGAGCCTAAGATAAAGACTTA
Found at i:38459 original size:27 final size:27
Alignment explanation
Indices: 38428--38509 Score: 137
Period size: 27 Copynumber: 3.0 Consensus size: 27
38418 AGGCTAGGGT
38428 ATTTTAGAGTTTAAGGGTATTTTAGTC
1 ATTTTAGAGTTTAAGGGTATTTTAGTC
*
38455 ATTTTAGAGTTTAAGGGTATTTTAGTT
1 ATTTTAGAGTTTAAGGGTATTTTAGTC
*
38482 ATTTTAGAGTTCAAGGGTATTTTTAGTC
1 ATTTTAGAGTTTAAGGGTA-TTTTAGTC
38510 CTTTCATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 44 0.86
28 7 0.14
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.49
Consensus pattern (27 bp):
ATTTTAGAGTTTAAGGGTATTTTAGTC
Found at i:39287 original size:13 final size:13
Alignment explanation
Indices: 39280--39304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39270 CATTTTCGGA
39280 AAACATTTTACAG
1 AAACATTTTACAG
39293 AAACATTTTACA
1 AAACATTTTACA
39305 TTGTTTGGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
AAACATTTTACAG
Found at i:41544 original size:20 final size:20
Alignment explanation
Indices: 41521--41564 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41511 GTTTGGGTTA
*
41521 ACTCAATTTGATTCGAGTTG
1 ACTCAATGTGATTCGAGTTG
*
41541 ACTCAGTGTGATTCGAGTTG
1 ACTCAATGTGATTCGAGTTG
41561 ACTC
1 ACTC
41565 GGATCAATTC
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:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
ACTCAATGTGATTCGAGTTG
Found at i:47351 original size:25 final size:22
Alignment explanation
Indices: 47322--47367 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
47312 TTTTTAACCC
47322 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
47347 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
47368 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:51184 original size:18 final size:18
Alignment explanation
Indices: 51136--51174 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
51126 TTTTTGAAAA
*
51136 TTTGGCTTTTTTTGTTTT
1 TTTGCCTTTTTTTGTTTT
51154 TTTGCCTTTTTTTGTTTT
1 TTTGCCTTTTTTTGTTTT
51172 TTT
1 TTT
51175 TTGTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.08, G:0.13, T:0.79
Consensus pattern (18 bp):
TTTGCCTTTTTTTGTTTT
Found at i:51187 original size:11 final size:10
Alignment explanation
Indices: 51142--51186 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
51132 AAAATTTGGC
51142 TTTTTTTG--
1 TTTTTTTGTT
**
51150 TTTTTTTGCC
1 TTTTTTTGTT
51160 TTTTTTTGTT
1 TTTTTTTGTT
51170 TTTTTTTGTT
1 TTTTTTTGTT
51180 TTTTTTT
1 TTTTTTT
51187 TTGAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
8 8 0.24
10 25 0.76
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:56738 original size:25 final size:22
Alignment explanation
Indices: 56709--56754 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
56699 TTTTTAACCC
56709 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
56734 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
56755 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:57888 original size:13 final size:13
Alignment explanation
Indices: 57854--57879 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57844 TATTGAAATC
57854 AATAACAATACAA
1 AATAACAATACAA
57867 AATAACAATACAA
1 AATAACAATACAA
57880 GTCAACAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAACAATACAA
Found at i:58680 original size:30 final size:29
Alignment explanation
Indices: 58644--58716 Score: 110
Period size: 30 Copynumber: 2.5 Consensus size: 29
58634 TGGGTCAACT
58644 CGTTGACTTTGACCGAGTCAACCCGTTGAC
1 CGTTGACTTTGACCGAGTCAACCCGTTG-C
* *
58674 CGTTGACTTTGACCGGGTCAACCCGTTGG
1 CGTTGACTTTGACCGAGTCAACCCGTTGC
*
58703 CTTTGACTTTGACC
1 CGTTGACTTTGACC
58717 AAAAAGTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 13 0.32
30 27 0.68
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (29 bp):
CGTTGACTTTGACCGAGTCAACCCGTTGC
Found at i:60995 original size:16 final size:16
Alignment explanation
Indices: 60974--61009 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
60964 CAGCATTCTA
60974 TCATTATACTGAATAT
1 TCATTATACTGAATAT
60990 TCATTATACTGAATAT
1 TCATTATACTGAATAT
61006 TCAT
1 TCAT
61010 GTTTCTATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (16 bp):
TCATTATACTGAATAT
Found at i:61280 original size:31 final size:31
Alignment explanation
Indices: 61242--61302 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
61232 ATACTTGGAC
* *
61242 GCTCCTCGGCTTTTTGTTCAAGGCCTTATTG
1 GCTCCTCGGCTTTGTGCTCAAGGCCTTATTG
61273 GCTCCTCGGCTTTGTGCTCAAGGCCTTATT
1 GCTCCTCGGCTTTGTGCTCAAGGCCTTATT
61303 AGACTTGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.10, C:0.28, G:0.23, T:0.39
Consensus pattern (31 bp):
GCTCCTCGGCTTTGTGCTCAAGGCCTTATTG
Found at i:63134 original size:26 final size:24
Alignment explanation
Indices: 63071--63136 Score: 60
Period size: 26 Copynumber: 2.7 Consensus size: 24
63061 TAGATATATT
* *
63071 ATTTTATTATGTATTATTTTTATA
1 ATTTTATTATTTATTATTTTTAAA
* ** *
63095 ATTTAAACACTTATATATTTTTTAAA
1 ATTTTATTATTTAT-TA-TTTTTAAA
63121 ATTTTATTATTTATTA
1 ATTTTATTATTTATTA
63137 CAAATATCAT
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
24 9 0.30
25 4 0.13
26 17 0.57
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTTATTATTTATTATTTTTAAA
Found at i:70437 original size:28 final size:27
Alignment explanation
Indices: 70397--70453 Score: 105
Period size: 28 Copynumber: 2.1 Consensus size: 27
70387 CATAAATCAA
70397 AAGACTTATTAGTCCATGATCCATTCAT
1 AAGACTTATTAGTCCATGATCCATT-AT
70425 AAGACTTATTAGTCCATGATCCATTAT
1 AAGACTTATTAGTCCATGATCCATTAT
70452 AA
1 AA
70454 AAAATAGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (27 bp):
AAGACTTATTAGTCCATGATCCATTAT
Found at i:71258 original size:3 final size:3
Alignment explanation
Indices: 71250--71275 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
71240 TAAAGTACAT
71250 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
71276 TCCTATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:73550 original size:14 final size:14
Alignment explanation
Indices: 73531--73559 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
73521 GTTGTCTTCA
73531 GAATTCTTCGTATT
1 GAATTCTTCGTATT
73545 GAATTCTTCGTATT
1 GAATTCTTCGTATT
73559 G
1 G
73560 GACAAAGTCT
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:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (14 bp):
GAATTCTTCGTATT
Found at i:74584 original size:47 final size:47
Alignment explanation
Indices: 74515--74606 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
74505 CCCCACCTGA
* *
74515 CCTCCTTGTTCTATCCCTAACTATTGCATGCTTTCATATATATTTTC
1 CCTCCTTATTCTATCCCTAACTATTACATGCTTTCATATATATTTTC
74562 CCTCCTTATTCTATCCCTAACTATTACATGCTTTCATATATATTT
1 CCTCCTTATTCTATCCCTAACTATTACATGCTTTCATATATATTT
74607 GCATAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.22, C:0.27, G:0.04, T:0.47
Consensus pattern (47 bp):
CCTCCTTATTCTATCCCTAACTATTACATGCTTTCATATATATTTTC
Found at i:78572 original size:96 final size:96
Alignment explanation
Indices: 78435--78634 Score: 256
Period size: 96 Copynumber: 2.1 Consensus size: 96
78425 TTCAAGCAAT
* * * * * * * *
78435 AACCAGTAGATTTCATGATCCATATATCAGGAATGATCATATTTTCCAATAAAAATAGGAAAGCA
1 AACCAGTAGATTCCATGATCCATAAATCAGAAAAGAACATATTTTACAATAAAAACAGGAAACCA
* *
78500 GATAACACATTTCAGGTAATCATAGTTCATA
66 GAGAACACATTTCAAGTAATCATAGTTCATA
* * * *
78531 AACTAGTAGGTTCCATGATCCATAAATCAGAAAAGAACATATTTTACAATTAAAACAGGTAACCA
1 AACCAGTAGATTCCATGATCCATAAATCAGAAAAGAACATATTTTACAATAAAAACAGGAAACCA
* *
78596 GAGAACATATTTCAAGTAATCATATTTCATA
66 GAGAACACATTTCAAGTAATCATAGTTCATA
78627 AACCAGTA
1 AACCAGTA
78635 AATCAGTGAT
Statistics
Matches: 87, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.28
Consensus pattern (96 bp):
AACCAGTAGATTCCATGATCCATAAATCAGAAAAGAACATATTTTACAATAAAAACAGGAAACCA
GAGAACACATTTCAAGTAATCATAGTTCATA
Found at i:81619 original size:2 final size:2
Alignment explanation
Indices: 81609--81707 Score: 138
Period size: 2 Copynumber: 51.5 Consensus size: 2
81599 TATTACGTAG
81609 TA TA T- 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
81650 TA TA TA TA TA TA TA T- TA TA GTA T- TA TA GTA T- TA T- 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
81690 TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA T
81708 TGTATTATTG
Statistics
Matches: 89, Mismatches: 0, Indels: 16
0.85 0.00 0.15
Matches are distributed among these distances:
1 6 0.07
2 79 0.89
3 4 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:81762 original size:58 final size:66
Alignment explanation
Indices: 81648--81785 Score: 132
Period size: 66 Copynumber: 2.2 Consensus size: 66
81638 TATATATATA
* *
81648 TATATATATATATATATTAT-AGTAT-TATAGTATTATTATATATATATA-TATATATTATATTG
1 TATAT-TATATAT-TATTATAATTATAT-TAGTATTATTGTATATATATATTATATATTATATTG
81710 TATTAT
63 --TTAT
* *
81716 TGTATTATATATTATTATTATTATATTA-TATTATTGTAT-TAT-TATTATATA-T-TATTGTTA
1 TATATTATATATTATTATAATTATATTAGTATTATTGTATATATATATTATATATTATATTGTTA
81776 -
66 T
81776 TATATTATAT
1 TATATTATAT
81786 TAAAGTATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
60 9 0.14
61 3 0.05
63 5 0.08
64 3 0.05
65 9 0.14
66 16 0.25
67 13 0.21
68 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (66 bp):
TATATTATATATTATTATAATTATATTAGTATTATTGTATATATATATTATATATTATATTGTTA
T
Found at i:81834 original size:8 final size:8
Alignment explanation
Indices: 81609--81847 Score: 100
Period size: 10 Copynumber: 27.9 Consensus size: 8
81599 TATTACGTAG
81609 TATATTA-
1 TATATTAT
81616 TATATATAT
1 TATAT-TAT
81625 ATATATATAT
1 -TATAT-TAT
81635 ATATATATAT
1 -TATAT-TAT
81645 ATATATATAT
1 -TATAT-TAT
81655 ATATATATAT
1 -TATAT-TAT
*
81665 TATAGTAT
1 TATATTAT
*
81673 TATAGTA-
1 TATATTAT
81680 T-TATTAT
1 TATATTAT
81687 ATATATATAT
1 -TATAT-TAT
81697 ATATATTATAT
1 -TATA-T-TAT
*
81708 TGTATTAT
1 TATATTAT
*
81716 TGTATTA-
1 TATATTAT
81723 TATATTAT
1 TATATTAT
81731 TATTATTATAT
1 TA-TA-T-TAT
81742 TATATTAT
1 TATATTAT
*
81750 TGTATTA-
1 TATATTAT
81757 T-TATTA-
1 TATATTAT
81763 TATATTAT
1 TATATTAT
*
81771 TGTTATATAT
1 T-ATAT-TAT
*
81781 TATATTAAAG
1 TATATT--AT
*
81791 TATATTCT
1 TATATTAT
81799 TATACTTA-
1 TATA-TTAT
81807 TATA-TATT
1 TATATTA-T
**
81815 TATACCATT
1 TATATTA-T
81824 TATATTAT
1 TATATTAT
81832 TATTATTAT
1 TA-TATTAT
81841 TATATTA
1 TATATTA
81848 ATATTTTGTT
Statistics
Matches: 195, Mismatches: 14, Indels: 45
0.77 0.06 0.18
Matches are distributed among these distances:
6 12 0.06
7 18 0.09
8 56 0.29
9 35 0.18
10 64 0.33
11 10 0.05
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (8 bp):
TATATTAT
Found at i:83100 original size:15 final size:15
Alignment explanation
Indices: 83075--83111 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
83065 CTTTTAAATT
83075 ATTTT-TTTCATTTC
1 ATTTTATTTCATTTC
*
83089 ATTTTATTTCATTTT
1 ATTTTATTTCATTTC
83104 ATTTTATT
1 ATTTTATT
83112 ATTTAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTATTTCATTTC
Found at i:84698 original size:33 final size:33
Alignment explanation
Indices: 84661--84768 Score: 135
Period size: 33 Copynumber: 3.3 Consensus size: 33
84651 TAAACGATAC
* *
84661 TGCATTATTAGGAAGGTATTTTGTTTGATGATG
1 TGCATGATTAGGAAGGTGTTTTGTTTGATGATG
*
84694 TGCATGATTAGGAAGGTGTTTTGTTTGATGAGG
1 TGCATGATTAGGAAGGTGTTTTGTTTGATGATG
* * * * *
84727 AGAAGGATTAGGAAGGTGTTTTTTTTTATGATG
1 TGCATGATTAGGAAGGTGTTTTGTTTGATGATG
*
84760 TGCAAGATT
1 TGCATGATT
84769 TGGGAGAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.25, C:0.03, G:0.31, T:0.42
Consensus pattern (33 bp):
TGCATGATTAGGAAGGTGTTTTGTTTGATGATG
Found at i:90670 original size:35 final size:35
Alignment explanation
Indices: 90616--90751 Score: 125
Period size: 35 Copynumber: 3.9 Consensus size: 35
90606 TAGATCTGTG
* * *
90616 AGGAATTATCAGTTCGATCGGTCTGAACATATATA
1 AGGAATTACCAGTTTGATCGGTCTGAACCTATATA
* * **
90651 AGGAATTACAAGTTTGATCGAG-CTAAACCTGCCATA
1 AGGAATTACCAGTTTGATCG-GTCTGAACCT-ATATA
*
90687 AGGAATTACCAGTTAT-ATCGGTTTGAACCTATATA
1 AGGAATTACCAGTT-TGATCGGTCTGAACCTATATA
* *
90722 AGGAATTGCCAGTTTGTTCGAG-CTGAACCT
1 AGGAATTACCAGTTTGATCG-GTCTGAACCT
90752 GCAGAGACTT
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
34 1 0.01
35 50 0.62
36 28 0.35
37 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (35 bp):
AGGAATTACCAGTTTGATCGGTCTGAACCTATATA
Found at i:90769 original size:71 final size:71
Alignment explanation
Indices: 90616--90753 Score: 195
Period size: 71 Copynumber: 1.9 Consensus size: 71
90606 TAGATCTGTG
* **
90616 AGGAATTATCAGTTCGATCGGTCTGAACATATATAAGGAATTACAAGTTTGATCGAGCTAAACCT
1 AGGAATTACCAGTTATATCGGTCTGAACATATATAAGGAATTACAAGTTTGATCGAGCTAAACCT
90681 GCCATA
66 GCCATA
* * * * * *
90687 AGGAATTACCAGTTATATCGGTTTGAACCTATATAAGGAATTGCCAGTTTGTTCGAGCTGAACCT
1 AGGAATTACCAGTTATATCGGTCTGAACATATATAAGGAATTACAAGTTTGATCGAGCTAAACCT
90752 GC
66 GC
90754 AGAGACTTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (71 bp):
AGGAATTACCAGTTATATCGGTCTGAACATATATAAGGAATTACAAGTTTGATCGAGCTAAACCT
GCCATA
Found at i:99305 original size:16 final size:17
Alignment explanation
Indices: 99279--99314 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
99269 AACAGCTAAA
*
99279 AAACGAAGTGACTGGTT
1 AAACGAAGTGACCGGTT
99296 AAAC-AAGTGACCGGTT
1 AAACGAAGTGACCGGTT
99312 AAA
1 AAA
99315 ATTTAGACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (17 bp):
AAACGAAGTGACCGGTT
Found at i:99421 original size:23 final size:23
Alignment explanation
Indices: 99374--99421 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
99364 AATAACATAT
**
99374 TAGGTAGCACTTATATAATGTAA
1 TAGGTAGCACTTATATAATAAAA
**
99397 TAGGTAGTGCTTATATAATAAAA
1 TAGGTAGCACTTATATAATAAAA
99420 TA
1 TA
99422 TGCATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATAAAA
Found at i:99945 original size:200 final size:197
Alignment explanation
Indices: 99471--99987 Score: 628
Period size: 198 Copynumber: 2.6 Consensus size: 197
99461 TAGGTAGCGC
* * * * * * *
99471 TTATATTGAACTATTTTCTAACT-AAACCGGTTTATTTATACCAGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTCTCTAA-TAAAACCGATGTATTTATACCAGTTACATTGTAAATTTACCTA
* ** *
99535 TTACATTATAATTATCGGTTTCGACACTTTTGGGATCGATACAATTT-TAAATGTATCGACACTT
65 TTACATTATAATTATTGGTTTCGA-TTTTTTGGGATCGATAC-TTTTATAAATGTATCGACACTT
* * * *
99599 TATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAATTTAAAAAGTGTCG
128 TATGCGCGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCAACACAAATTCAAAAAGTGTCA
99664 ATACA
193 ATACA
* * *
99669 TTATGTTGACCTATTCTCTCATAAAACTGGTGTATTTATACCAGTTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTCTCTAATAAAACCGATGTATTTATACCAGTTACATTGTAAATTTACCTAT
*
99734 TACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACATTTT
66 TACATTATAATTATTGGTTTCGAT-TTTTTGGGATCGATACTTTT-ATAAATGTATCGACACTTT
* * * *
99799 ATGTGCGCACCTCGTTTGGGCATTCATTCTGGACAATAAGTATCAACACAAATTCCATAAGTGTC
129 ATGCGCGCACCTCG-TTGGGCATTCATTCTGGA-AAAAAGTATCAACACAAATTCAAAAAGTGTC
99864 AATACA
192 AATACA
* * * * * * * * *
99870 TTATGTTTACCTATTTTGTAAT-TAACCGATGTTTTTATACCGGTTACATTGTTAATTTATCTAC
1 TTATGTTGACCTATTCTCTAATAAAACCGATGTATTTATACCAGTTACATTGTAAATTTACCTAT
*
99934 TACATTATAATTATTGGTTTCAATTTTTTGGTG-TCGATACTTTTATAAAATGTA
66 TACATTATAATTATTGGTTTCGATTTTTTGG-GATCGATACTTTTAT-AAATGTA
99988 CCGATACATA
Statistics
Matches: 277, Mismatches: 34, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
197 4 0.01
198 94 0.34
199 54 0.19
200 76 0.27
201 49 0.18
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
TTATGTTGACCTATTCTCTAATAAAACCGATGTATTTATACCAGTTACATTGTAAATTTACCTAT
TACATTATAATTATTGGTTTCGATTTTTTGGGATCGATACTTTTATAAATGTATCGACACTTTAT
GCGCGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCAACACAAATTCAAAAAGTGTCAATA
CA
Found at i:102711 original size:19 final size:19
Alignment explanation
Indices: 102687--102734 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
102677 TTACATTCAC
102687 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
102706 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCGT
102725 ATACAAAATT
1 ATACAAAATT
102735 TCCCCTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:104666 original size:199 final size:198
Alignment explanation
Indices: 104313--104899 Score: 750
Period size: 199 Copynumber: 3.0 Consensus size: 198
104303 GCGTAATTTA
* * *
104313 AAAAAATATCGATACAAATTTAAAAAGTGTCGATACATTATGTAGACTTATTTTCTCATTAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCA-TAAACC
* * * * * * *
104378 GGTAAATTTATACTGGTTACATTGCTAATTTACCTATTACATTGTAATTATCGATTTCGATGTTT
65 GGTATATTTCTACCGGTTAAATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * *
104443 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTACACCCCGTTTGGCATTCATTCT
130 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCACGTTAGGCATTCATTCT
104508 GGAC
195 GGAC
* * *
104512 AAAAAGTATCGACACAAATTTAAAACGTGTCGATACATTATGTAGACCTATTTTCTCACAAACTG
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAACCG
* * *
104577 GTATATTTCTACCAGTTATATTGGAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
66 GTATATTTCTACCGGTTAAATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * ** * * * *
104642 AGGGATTGATACTTTTTATAAATGTATCAACACTTTAT-TCATGCACCTAGGTTGGGCATTCATT
131 TGGGATCGATACAATTT-TAAATGTATCGACACTTTATGT-GTGCACC-ACGTTAGGCATTCATT
104706 CTGGAC
193 CTGGAC
* * * * *
104712 AAAAAGTATCGACA-TAATTTAAAAAGTGCCGATATATTATGTAGACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAACCG
* * *
104776 GTATATTTAC-ACCGGTTACAAAT-CAAATTTACCTATTACATTATAACTATCGGTTTCGATATT
66 GTATATTT-CTACCGGTTA-AATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * *
104839 TTTGGGATCGATACAATTTTAAATGTATCGACACCTTATGCGTGCACCTCGTTAGGCATTC
129 TTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCACGTTAGGCATTC
104900 TGTAATACCC
Statistics
Matches: 332, Mismatches: 50, Indels: 14
0.84 0.13 0.04
Matches are distributed among these distances:
197 10 0.03
198 99 0.30
199 187 0.56
200 36 0.11
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (198 bp):
AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAACCG
GTATATTTCTACCGGTTAAATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCACGTTAGGCATTCATTCTG
GAC
Found at i:107185 original size:20 final size:20
Alignment explanation
Indices: 107145--107186 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
107135 TTGTATATTG
* *
107145 GGCTATTGTCTATTGTTTAT
1 GGCTATTGTCTATGGTATAT
*
107165 GGCTTTTGTCTATGGTATAT
1 GGCTATTGTCTATGGTATAT
107185 GG
1 GG
107187 TTTATTGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.10, G:0.26, T:0.50
Consensus pattern (20 bp):
GGCTATTGTCTATGGTATAT
Found at i:107345 original size:45 final size:44
Alignment explanation
Indices: 107215--107432 Score: 309
Period size: 44 Copynumber: 4.9 Consensus size: 44
107205 GTAAACATGT
* *
107215 AAATAAGATTACGAGCTTATGGAATAAAT-GTCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GAAAAAATGGT-AAGTATATTGGTA
*
107260 AAATAAGCTTACGAAGCTTAT-AAAAAATGGTAAATATATTGGTA
1 AAATAAGCTTACG-AGCTTATGAAAAAATGGTAAGTATATTGGTA
107304 AAATAAGCTTACGAGCTTATGGAAAAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GAAAAAATGGTAAGTATATTGGTA
*
107349 AAATAAGCTTACAAGCTTATTG-AAAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTA-TGAAAAAATGGTAAGTATATTGGTA
*
107393 AAATAAGCTTACGAGCTTATGAGATAAATGGTAAG-ATATT
1 AAATAAGCTTACGAGCTTATGA-AAAAATGGTAAGTATATT
107433 TTGTATTATT
Statistics
Matches: 159, Mismatches: 7, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
43 9 0.06
44 76 0.48
45 66 0.42
46 8 0.05
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGAAAAAATGGTAAGTATATTGGTA
Found at i:107369 original size:25 final size:25
Alignment explanation
Indices: 107296--107370 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
107286 ATGGTAAATA
*
107296 TATTGGTAAAATAAGCTTACGAGCT
1 TATTGGTAAAATAAGCTTACAAGCT
*
107321 TA-TGG-AAAA-AATG-GT--AAG-T
1 TATTGGTAAAATAA-GCTTACAAGCT
107340 ATATTGGTAAAATAAGCTTACAAGCT
1 -TATTGGTAAAATAAGCTTACAAGCT
107366 TATTG
1 TATTG
107371 AAAAATGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 18
0.64 0.05 0.31
Matches are distributed among these distances:
19 1 0.03
20 4 0.11
21 3 0.08
22 8 0.21
23 8 0.21
24 3 0.08
25 10 0.26
26 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (25 bp):
TATTGGTAAAATAAGCTTACAAGCT
Found at i:107375 original size:89 final size:89
Alignment explanation
Indices: 107215--107432 Score: 345
Period size: 89 Copynumber: 2.5 Consensus size: 89
107205 GTAAACATGT
*
107215 AAATAAGATTACGAGCTTATGGAATAAAT-GTCAAGTATATTGGTAAAATAAGCTTACGAAGCTT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGT-AAGTATATTGGTAAAATAAGCTTACGAAGCTT
107279 ATAAAAAATGGTAAATATATTGGTA
65 ATAAAAAATGGTAAATATATTGGTA
*
107304 AAATAAGCTTACGAGCTTATGGAAAAAATGGTAAGTATATTGGTAAAATAAGCTTAC-AAGCTTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAAGCTTA
* *
107368 TTGAAAAATGGTAAGTATATTGGTA
66 -TAAAAAATGGTAAATATATTGGTA
107393 AAATAAGCTTACGAGCTTAT-GAGATAAATGGTAAG-ATATT
1 AAATAAGCTTACGAGCTTATGGA-ATAAATGGTAAGTATATT
107433 TTGTATTATT
Statistics
Matches: 121, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
88 14 0.12
89 105 0.87
90 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (89 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAAGCTTA
TAAAAAATGGTAAATATATTGGTA
Found at i:110998 original size:13 final size:13
Alignment explanation
Indices: 110980--111008 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
110970 ATCAAGTTTG
110980 AATGTTAACATTT
1 AATGTTAACATTT
110993 AATGTTAACATTT
1 AATGTTAACATTT
111006 AAT
1 AAT
111009 TGTATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (13 bp):
AATGTTAACATTT
Found at i:111331 original size:6 final size:6
Alignment explanation
Indices: 111321--111354 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
111311 CTTGTTTGGA
* *
111321 TCATCA TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
111355 TGAGCACTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:112162 original size:20 final size:20
Alignment explanation
Indices: 112137--112190 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
112127 GAATGATCGA
112137 ATGGTATCGATACCTCCCCC
1 ATGGTATCGATACCTCCCCC
112157 ATGGTATCGATACCTCCCCC
1 ATGGTATCGATACCTCCCCC
112177 ATGGTATCGATACC
1 ATGGTATCGATACC
112191 CCTGTGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (20 bp):
ATGGTATCGATACCTCCCCC
Found at i:112224 original size:20 final size:21
Alignment explanation
Indices: 112177--112233 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
112167 TACCTCCCCC
*
112177 ATGGTATCGATACCCCTGTGTA
1 ATGGTATCGATACCCCTATG-A
112199 ATGGTATCGATACCCCTATG-
1 ATGGTATCGATACCCCTATGA
*
112219 ATGGTACCGATACCC
1 ATGGTATCGATACCC
112234 TAAGGCATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 14 0.42
22 19 0.58
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (21 bp):
ATGGTATCGATACCCCTATGA
Found at i:114094 original size:24 final size:24
Alignment explanation
Indices: 114067--114157 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
114057 CATAATTCAA
*
114067 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
114091 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
114115 ATCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
114138 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
114158 TCAAATTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:116215 original size:8 final size:7
Alignment explanation
Indices: 116193--116245 Score: 65
Period size: 7 Copynumber: 7.4 Consensus size: 7
116183 TGGTCAACGC
116193 CGGTCAA
1 CGGTCAA
116200 CGGTCAA
1 CGGTCAA
116207 CGAGTCAA
1 CG-GTCAA
116215 CGGTCAA
1 CGGTCAA
116222 CGGGTCAA
1 C-GGTCAA
116230 CAGGTC-A
1 C-GGTCAA
116237 -GGTCAA
1 CGGTCAA
116243 CGG
1 CGG
116246 GTCGGGTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
7 18 0.44
8 18 0.44
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:116215 original size:15 final size:15
Alignment explanation
Indices: 116195--116236 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
116185 GTCAACGCCG
116195 GTCAACGGTCAACGA
1 GTCAACGGTCAACGA
*
116210 GTCAACGGTCAACGG
1 GTCAACGGTCAACGA
116225 GTCAACAGGTCA
1 GTCAAC-GGTCA
116237 GGTCAACGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.31, C:0.26, G:0.29, T:0.14
Consensus pattern (15 bp):
GTCAACGGTCAACGA
Found at i:116242 original size:13 final size:13
Alignment explanation
Indices: 116224--116279 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
116214 ACGGTCAACG
*
116224 GGTCAACAGGTCA
1 GGTCAACGGGTCA
*
116237 GGTCAACGGGTCG
1 GGTCAACGGGTCA
116250 GGTCAACGGGTCA
1 GGTCAACGGGTCA
* *
116263 GGTAAACGGGTCG
1 GGTCAACGGGTCA
116276 GGTC
1 GGTC
116280 GGGTTAGGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:116248 original size:8 final size:8
Alignment explanation
Indices: 116184--116262 Score: 66
Period size: 8 Copynumber: 10.6 Consensus size: 8
116174 GGTTAACAGT
116184 GGTCAACG
1 GGTCAACG
116192 CCGGTCAAC-
1 --GGTCAACG
116201 GGTCAACG
1 GGTCAACG
*
116209 AGTCAAC-
1 GGTCAACG
116216 GGTCAACG
1 GGTCAACG
*
116224 GGTCAACA
1 GGTCAACG
116232 GGTC-A--
1 GGTCAACG
116237 GGTCAACG
1 GGTCAACG
116245 GGT---CG
1 GGTCAACG
116250 GGTCAACG
1 GGTCAACG
116258 GGTCA
1 GGTCA
116263 GGTAAACGGG
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
5 9 0.16
6 1 0.02
7 14 0.24
8 27 0.47
10 7 0.12
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:116255 original size:26 final size:26
Alignment explanation
Indices: 116222--116279 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
116212 CAACGGTCAA
*
116222 CGGGTCAACAGGTCAGGTCAACGGGT
1 CGGGTCAACAGGTCAGGTAAACGGGT
*
116248 CGGGTCAACGGGTCAGGTAAACGGGT
1 CGGGTCAACAGGTCAGGTAAACGGGT
116274 CGGGTC
1 CGGGTC
116280 GGGTTAGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.22, G:0.41, T:0.16
Consensus pattern (26 bp):
CGGGTCAACAGGTCAGGTAAACGGGT
Found at i:121652 original size:21 final size:21
Alignment explanation
Indices: 121625--121703 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
121615 TTTGTGCTTA
121625 AGGTATCGATACCCCTGAGAAT
1 AGGTATCGATACCCCTGA-AAT
*
121647 -GGTATCGATACCCCTGTAAT
1 AGGTATCGATACCCCTGAAAT
* *
121667 AAGTATCGATACACCCTTAAAT
1 AGGTATCGATAC-CCCTGAAAT
*
121689 GGGTATCGATACCCC
1 AGGTATCGATACCCC
121704 CTGATGGTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.06
21 29 0.59
22 17 0.35
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
AGGTATCGATACCCCTGAAAT
Found at i:121694 original size:22 final size:20
Alignment explanation
Indices: 121626--121721 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 20
121616 TTGTGCTTAA
*
121626 GGTATCGATACCCCTGAGAAT
1 GGTATCGATACCCCTTA-AAT
121647 GGTATCGATACCCCTGT-AAT
1 GGTATCGATACCCCT-TAAAT
*
121667 AAGTATCGATACACCCTTAAAT
1 -GGTATCGATAC-CCCTTAAAT
* *
121689 GGGTATCGATACCCCCT-GAT
1 -GGTATCGATACCCCTTAAAT
*
121709 GGTACCGATACCC
1 GGTATCGATACCC
121722 TCCTCGGGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
19 12 0.19
20 5 0.08
21 30 0.47
22 17 0.27
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCCCTTAAAT
Found at i:122457 original size:12 final size:12
Alignment explanation
Indices: 122442--122466 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122432 CAAACCCAAA
122442 TCCTCAAATTCC
1 TCCTCAAATTCC
122454 TCCTCAAATTCC
1 TCCTCAAATTCC
122466 T
1 T
122467 GATCCCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (12 bp):
TCCTCAAATTCC
Found at i:124525 original size:20 final size:21
Alignment explanation
Indices: 124476--124534 Score: 93
Period size: 22 Copynumber: 2.8 Consensus size: 21
124466 CAGAATGCTC
124476 GAATGGTATCGATACCCCTAT
1 GAATGGTATCGATACCCCTAT
124497 GCAATGGTATCGATACCCCTAT
1 G-AATGGTATCGATACCCCTAT
*
124519 G-ATGGTACCGATACCC
1 GAATGGTATCGATACCC
124535 TAAGGCGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 14 0.39
21 1 0.03
22 21 0.58
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (21 bp):
GAATGGTATCGATACCCCTAT
Found at i:125977 original size:201 final size:200
Alignment explanation
Indices: 125557--126196 Score: 896
Period size: 201 Copynumber: 3.2 Consensus size: 200
125547 AAAAATATTA
* * * * * *
125557 ACACAAATTTAAAAAGTGTCGATACATTATGCT-GACCTGTTTTATAATTAAA-CTGGTATATTT
1 ACACAAATTTTAAAAGTGTCGATACATTATG-TAGACCTATTATCTCATAAAACCT-GTATATTT
* * *
125620 ATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCAAT-TTTTTTGGATCG
64 ATACCGGTTACATT-ACAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCG
* *
125684 ATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATTATGAACACA
128 ATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTATGGACA-A
125749 AA-GTATCG
192 AATGTATCG
* *
125757 ACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCTGTATATTTAT
1 ACACAAATTTTAAAAGTGTCGATACATTATGTAGACCTATTATCTCATAAAACCTGTATATTTAT
125822 ACCGGTTACATTACACAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAT
66 ACCGGTTACATTACA-AATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAT
* * *
125887 ACTTTTTATAAATGTATCGACACTTTATGCGTGTACCTCTTTTGGGCATTCATTTTGGACAAAAT
130 ACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTATGGACAAAAT
125952 GTATCG
195 GTATCG
* * * * **
125958 ACACAAATTTTAAAAGTGTCGATACATTATTTATACCTATTATCTCATAAAACCGGTATGTTTCC
1 ACACAAATTTTAAAAGTGTCGATACATTATGTAGACCTATTATCTCATAAAACCTGTATATTTAT
* * * *
126023 ACCGGTTACATTGCAAATTTACATATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGAT
66 ACCGGTTACATTACAAA-TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAT
* * *
126088 ACTTTTAATAAATCTATCGACACTTTATGCGTGCACCTCGTTT--GCATTCATTCTGGACAAAAT
130 ACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTATGGACAAAAT
*
126151 CTATCG
195 GTATCG
* *
126157 ACACAAATTTTAAAAGTGTCGATACATTATTTTGACCTAT
1 ACACAAATTTTAAAAGTGTCGATACATTATGTAGACCTAT
126197 CGTTATATAA
Statistics
Matches: 400, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
199 65 0.16
200 104 0.26
201 231 0.58
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (200 bp):
ACACAAATTTTAAAAGTGTCGATACATTATGTAGACCTATTATCTCATAAAACCTGTATATTTAT
ACCGGTTACATTACAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATA
CTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTATGGACAAAATG
TATCG
Found at i:128498 original size:15 final size:15
Alignment explanation
Indices: 128457--128506 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
128447 GAATAAGCAA
*
128457 TTGGTTGAGAAGGAGG
1 TTGGTTGAGAA-GAGC
128473 TTGTCGTTGAGAAGAGC
1 TTG--GTTGAGAAGAGC
*
128490 TTGGTTGAGAAAAGC
1 TTGGTTGAGAAGAGC
128505 TT
1 TT
128507 TGAGAAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 13 0.43
16 3 0.10
17 6 0.20
18 8 0.27
ACGTcount: A:0.26, C:0.06, G:0.38, T:0.30
Consensus pattern (15 bp):
TTGGTTGAGAAGAGC
Found at i:129027 original size:22 final size:23
Alignment explanation
Indices: 128999--129054 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 23
128989 AACCTGTATT
128999 TATAATAAAAT-TTATCATTTTA
1 TATAATAAAATATTATCATTTTA
129021 TATAATAAATATATTATCATTTTA
1 TATAATAAA-ATATTATCATTTTA
*
129045 TATAAAAAAA
1 TATAATAAAA
129055 ACAAAAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 9 0.29
23 3 0.10
24 19 0.61
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATAAAATATTATCATTTTA
Found at i:130069 original size:59 final size:59
Alignment explanation
Indices: 129997--130126 Score: 197
Period size: 59 Copynumber: 2.2 Consensus size: 59
129987 AGATTGTTGA
* * * *
129997 TAAATTGTTTTAAAAGAGTGACTAATATGTAATTAATTTCTGTTATGATGCTATTTTTG
1 TAAATAGTTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATGATGCTATTTTTG
* *
130056 TAAATAGTTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATGGTGGTATTTTTG
1 TAAATAGTTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATGATGCTATTTTTG
*
130115 TAAATATTTTTA
1 TAAATAGTTTTA
130127 GAAAAGGTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (59 bp):
TAAATAGTTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATGATGCTATTTTTG
Found at i:130167 original size:29 final size:28
Alignment explanation
Indices: 130114--130312 Score: 256
Period size: 29 Copynumber: 6.8 Consensus size: 28
130104 TGGTATTTTT
130114 GTAAATATTTTTAGAAAAGGTGTTAG-TTC
1 GTAAATA-TTTTA-AAAAGGTGTTAGTTTC
*
130143 TGTAAATATTGTTAAAAAGATGTTAGTTTC
1 -GTAAATATT-TTAAAAAGGTGTTAGTTTC
*
130173 GTAAATATTGTTAAAAAAGTGTTAGTTTC
1 GTAAATATT-TTAAAAAGGTGTTAGTTTC
130202 GTAAATATTATTAAAAAGGTGTTAGTTTC
1 GTAAATATT-TTAAAAAGGTGTTAGTTTC
* *
130231 GTAAATATTATTAAAAATGTGTTATTTTC
1 GTAAATATT-TTAAAAAGGTGTTAGTTTC
* *
130260 GTAAATATTTCTAAAAGGGTGTTATTTTC
1 GTAAATATTT-TAAAAAGGTGTTAGTTTC
130289 GTAAATATTTTAAAAAGGGTGTTA
1 GTAAATATTTTAAAAA-GGTGTTA
130313 TTTTTATAAT
Statistics
Matches: 155, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
28 6 0.04
29 136 0.88
30 13 0.08
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.43
Consensus pattern (28 bp):
GTAAATATTTTAAAAAGGTGTTAGTTTC
Found at i:130344 original size:58 final size:58
Alignment explanation
Indices: 130102--130351 Score: 175
Period size: 58 Copynumber: 4.3 Consensus size: 58
130092 TTTCGGTTAT
* * * * * * *
130102 GGTGGTATTTTTGTAAATATTTTTAGAAAAGGTGTTA-GTTCTGTAAAT-ATTGTTAAAAA
1 GGTGCTATTTTCGTAAATATTATTA-AAAAGGTGTTATTTTC-ATAAATAATT-CTAAAAG
* * * * * * * * *
130161 GATGTTAGTTTCGTAAATATTGTTAAAAAAGTGTTAGTTTCGTAAAT-ATTATTAAAAA
1 GGTGCTATTTTCGTAAATATTATTAAAAAGGTGTTATTTTCATAAATAATT-CTAAAAG
* * * * *
130219 GGTGTTAGTTTCGTAAATATTATTAAAAATGTGTTATTTTCGTAAATATTTCTAAAAG
1 GGTGCTATTTTCGTAAATATTATTAAAAAGGTGTTATTTTCATAAATAATTCTAAAAG
* * * ***
130277 GGTGTTATTTTCGTAAATATT-TTAAAAAGGGTGTTATTTTTATAATTAATTCTGTTAG
1 GGTGCTATTTTCGTAAATATTATTAAAAA-GGTGTTATTTTCATAAATAATTCTAAAAG
*
130335 GGTGCTATTTTTGTAAA
1 GGTGCTATTTTCGTAAA
130352 AGTTGATTGT
Statistics
Matches: 162, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
57 7 0.04
58 130 0.80
59 25 0.15
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.45
Consensus pattern (58 bp):
GGTGCTATTTTCGTAAATATTATTAAAAAGGTGTTATTTTCATAAATAATTCTAAAAG
Found at i:133925 original size:176 final size:177
Alignment explanation
Indices: 133611--134244 Score: 796
Period size: 176 Copynumber: 3.6 Consensus size: 177
133601 TACGTGTACT
* * *
133611 TATTAAAGTATCGACACTTTCAACATATCCAGTAGCACTTTACCAGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTACCGGTTTTGTCATTTCGAGACTG
* *
133676 GTTTTGTCATAATTTTATCTGTTATATTGTTATGGATCGATACATCTTTATAAAGTATCGACACT
66 G-TTTGT--T-ATTTT-TATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
133741 TTATAGGCGTTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
126 TTATAGGCGTTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
133793 TATTAATGTATCGACACTTTCAACATATCTGGTAGCTCTTTACCGGTTTTTTCGTTTCGAGACTG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTACCGGTTTTGTCATTTCGAGACTG
* *
133858 GTTTGTTATTTTTATGTTATA-TGTTATAGATCGATACATTTTTATAAAATATCGACACTTTATA
66 GTTTGTTATTTTTATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATA
* * *
133922 GGCGCTATTACTGCTTGTCTTTTAAATTCCAAAAGTGTTGATACTTA
131 GGCGTTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
133969 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTACCGG-TTT-T-A--TC---A-T-
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTACCGGTTTTGTCATTTCGAGACTG
* ** * *
134024 ATTT-TTA--CCTA--TTATATTCTTATGGATCGATACATTTTTATAAAGTGTCGACACTTTATA
66 GTTTGTTATTTTTATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATA
*
134084 GGGGTTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 GGCGTTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
134131 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGATTTGGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTACCGGTTTTGTCATTTCGAGACTG
* * **
134196 ATTTTGTCATATTTTTACCTGTTATATTGCTATGGATATATACATTTTT
66 -GTTTGT--TATTTTTA--TGTTATATTGTTATGGATCGATACATTTTT
134245 TATTTGTATC
Statistics
Matches: 389, Mismatches: 42, Indels: 42
0.82 0.09 0.09
Matches are distributed among these distances:
161 5 0.01
162 125 0.32
163 4 0.01
164 1 0.00
165 4 0.01
166 3 0.01
167 3 0.01
168 1 0.00
170 1 0.00
171 2 0.01
173 3 0.01
174 2 0.01
175 3 0.01
176 129 0.33
177 8 0.02
178 7 0.02
179 1 0.00
181 5 0.01
182 82 0.21
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (177 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTACCGGTTTTGTCATTTCGAGACTG
GTTTGTTATTTTTATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATA
GGCGTTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:134153 original size:162 final size:162
Alignment explanation
Indices: 133881--134175 Score: 509
Period size: 162 Copynumber: 1.8 Consensus size: 162
133871 ATGTTATATG
*
133881 TTATAGATCGATACATTTTTATAAAATATCGACACTTTATAGGCGCTATTACTGCTTGTCTTTTA
1 TTATAGATCGATACATTTTTATAAAATATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTA
* *
133946 AATTCCAAAAGTGTTGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTA
66 AATTCCAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGATAGCACTTTA
134011 CCGGTTTTATCATATTTTTACCTATTATATTC
131 CCGGTTTTATCATATTTTTACCTATTATATTC
* * * * *
134043 TTATGGATCGATACATTTTTATAAAGTGTCGACACTTTATAGGGGTTATTACTGCTTCTCTTTTA
1 TTATAGATCGATACATTTTTATAAAATATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTA
*
134108 AATTCCAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTA
66 AATTCCAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGATAGCACTTTA
134173 CCG
131 CCG
134176 ATTTGGTCAT
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 124 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.40
Consensus pattern (162 bp):
TTATAGATCGATACATTTTTATAAAATATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTA
AATTCCAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGATAGCACTTTA
CCGGTTTTATCATATTTTTACCTATTATATTC
Found at i:135567 original size:23 final size:23
Alignment explanation
Indices: 135529--135575 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
135519 TTTAAATGGT
*
135529 TTTTTTATAATCATATATGATATA
1 TTTTTTATAATAATATAT-ATATA
135553 TTTTTTAT-ATAATATATATATA
1 TTTTTTATAATAATATATATATA
135575 T
1 T
135576 CATATAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 8 0.36
24 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTTTATAATAATATATATATA
Found at i:135580 original size:27 final size:25
Alignment explanation
Indices: 135528--135575 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
135518 ATTTAAATGG
135528 TTTTTTTATAATCATATATGATATA
1 TTTTTTTATAATCATATATGATATA
135553 TTTTTTATATAAT-ATATAT-ATAT
1 TTTTTT-TATAATCATATATGATAT
135576 CATATAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 12 0.55
26 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTTTTATAATCATATATGATATA
Found at i:139287 original size:3 final size:3
Alignment explanation
Indices: 139281--139356 Score: 93
Period size: 3 Copynumber: 25.0 Consensus size: 3
139271 TTTTCTTTAT
* *
139281 TTA TTA TTA TTC TTA TTA TAA TT- TTA TATA TTTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA
139326 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
139357 ATAAATACTT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 4 0.06
3 52 0.81
4 7 0.11
5 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:139315 original size:19 final size:20
Alignment explanation
Indices: 139293--139355 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 20
139283 ATTATTATTC
139293 TTATTATAATT-TTATATAT
1 TTATTATAATTATTATATAT
139312 TTATTATTATATTATTATTATTAT
1 TTATTA-TA-ATTATTA-TA-TAT
*
139336 TTATTATTATTATTAT-TAT
1 TTATTATAATTATTATATAT
139355 T
1 T
139356 AATAAATACT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 10 0.26
20 2 0.05
21 4 0.11
22 10 0.26
23 3 0.08
24 9 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTATAATTATTATATAT
Found at i:141871 original size:58 final size:57
Alignment explanation
Indices: 141793--141975 Score: 183
Period size: 58 Copynumber: 3.2 Consensus size: 57
141783 AAAAATTACA
* * *
141793 AAAATAACACTATTTTTAAAAAAATTACTAAAATACCACCATTTTCAAAATAATTAT
1 AAAATATCACCATTTTTAAAAAAATTACGAAAATACCACCATTTTCAAAATAATTAT
** * * * *
141850 AAAATATCACC-TTTTTTTAAAAATTACGAAATTATCACTC-TTTAT-AAAAAAATTACG
1 AAAATATCACCATTTTTAAAAAAATTACGAAAATACCAC-CATTT-TCAAAATAATTA-T
* * * * *
141907 AAAATACCACCATTTTCAAAATAATTACGAAAATACCACAAATTTCAAAATAATTAAT
1 AAAATATCACCATTTTTAAAAAAATTACGAAAATACCACCATTTTCAAAATAATT-AT
141965 AAAATATCACC
1 AAAATATCACC
141976 CGGTTAACAA
Statistics
Matches: 98, Mismatches: 21, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
56 34 0.35
57 22 0.22
58 41 0.42
59 1 0.01
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.32
Consensus pattern (57 bp):
AAAATATCACCATTTTTAAAAAAATTACGAAAATACCACCATTTTCAAAATAATTAT
Found at i:141911 original size:114 final size:116
Alignment explanation
Indices: 141762--141975 Score: 315
Period size: 114 Copynumber: 1.9 Consensus size: 116
141752 ATCATTTTAT
* * * * *
141762 GAAATTAACACCTTTTTTTAAAAAAATTACAAAAATAACACTATTTTTAAAAAAATTACTAAAAT
1 GAAATTAACACCTCTTTATAAAAAAATTACAAAAATAACACCATTTTCAAAAAAATTACGAAAAT
* *
141827 ACCACCATTTTCAAAATAATT-ATAAAATATCACCTTTTTTTAAAAATTAC
66 ACCACAAATTTCAAAATAATTAATAAAATATCACCTTTTTTTAAAAATTAC
* * * *
141877 GAAATTATCA-CTCTTTATAAAAAAATTACGAAAATACCACCATTTTCAAAATAATTACGAAAAT
1 GAAATTAACACCTCTTTATAAAAAAATTACAAAAATAACACCATTTTCAAAAAAATTACGAAAAT
141941 ACCACAAATTTCAAAATAATTAATAAAATATCACC
66 ACCACAAATTTCAAAATAATTAATAAAATATCACC
141976 CGGTTAACAA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
114 65 0.75
115 22 0.25
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.32
Consensus pattern (116 bp):
GAAATTAACACCTCTTTATAAAAAAATTACAAAAATAACACCATTTTCAAAAAAATTACGAAAAT
ACCACAAATTTCAAAATAATTAATAAAATATCACCTTTTTTTAAAAATTAC
Found at i:141915 original size:85 final size:86
Alignment explanation
Indices: 141770--141933 Score: 258
Period size: 85 Copynumber: 1.9 Consensus size: 86
141760 ATGAAATTAA
* *
141770 CACCTTTTTTTAAAAAAATTACAAAAATAACACTATTTTTAAAAAAATTACTAAAATACCACCAT
1 CACCTTTTTTT-AAAAAATTACAAAAATAACACTATTTATAAAAAAATTACGAAAATACCACCAT
141835 TTTCAAAATAATTATAAAATAT
65 TTTCAAAATAATTATAAAATAT
* * * *
141857 CACCTTTTTTT-AAAAATTACGAAATTATCACTCTTTATAAAAAAATTACGAAAATACCACCATT
1 CACCTTTTTTTAAAAAATTACAAAAATAACACTATTTATAAAAAAATTACGAAAATACCACCATT
141921 TTCAAAATAATTA
66 TTCAAAATAATTA
141934 CGAAAATACC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
85 60 0.85
87 11 0.15
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (86 bp):
CACCTTTTTTTAAAAAATTACAAAAATAACACTATTTATAAAAAAATTACGAAAATACCACCATT
TTCAAAATAATTATAAAATAT
Found at i:141942 original size:29 final size:29
Alignment explanation
Indices: 141776--141962 Score: 166
Period size: 29 Copynumber: 6.5 Consensus size: 29
141766 TTAACACCTT
* * * *
141776 TTTTTAAAAAAATTACAAAAATAACACTA
1 TTTTCAAAAAAATTACGAAAATACCACCA
* *
141805 TTTTTAAAAAAATTACTAAAATACCACCA
1 TTTTCAAAAAAATTACGAAAATACCACCA
* * *
141834 TTTTCAAAATAATTA-TAAAATATCACC-
1 TTTTCAAAAAAATTACGAAAATACCACCA
*** * *
141861 TTTTTTTAAAAATTACGAAATTATCACTC-
1 TTTTCAAAAAAATTACGAAAATACCAC-CA
141890 TTTAT-AAAAAAATTACGAAAATACCACCA
1 TTT-TCAAAAAAATTACGAAAATACCACCA
* *
141919 TTTTCAAAATAATTACGAAAATACCACAA
1 TTTTCAAAAAAATTACGAAAATACCACCA
* *
141948 ATTTCAAAATAATTA
1 TTTTCAAAAAAATTA
141963 ATAAAATATC
Statistics
Matches: 134, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
27 11 0.08
28 22 0.16
29 100 0.75
30 1 0.01
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (29 bp):
TTTTCAAAAAAATTACGAAAATACCACCA
Found at i:141968 original size:29 final size:29
Alignment explanation
Indices: 141895--141970 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
141885 CACTCTTTAT
* * * *
141895 AAAAAAATTACGAAAATACCACCATTTTC
1 AAAATAATTAAGAAAATACCACAAATTTC
*
141924 AAAATAATTACGAAAATACCACAAATTTC
1 AAAATAATTAAGAAAATACCACAAATTTC
*
141953 AAAATAATTAATAAAATA
1 AAAATAATTAAGAAAATA
141971 TCACCCGGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (29 bp):
AAAATAATTAAGAAAATACCACAAATTTC
Found at i:142068 original size:19 final size:19
Alignment explanation
Indices: 142046--142129 Score: 141
Period size: 19 Copynumber: 4.4 Consensus size: 19
142036 CCGGTTTGAA
* *
142046 CCGGTCAACCCGGTTAAGG
1 CCGGTCAACCTGGTTCAGG
142065 CCGGTCAACCTGGTTCAGG
1 CCGGTCAACCTGGTTCAGG
142084 CCGGTCAACCTGGTTCAGG
1 CCGGTCAACCTGGTTCAGG
*
142103 TCGGTCAACCTGGTTCAGG
1 CCGGTCAACCTGGTTCAGG
142122 CCGGTCAA
1 CCGGTCAA
142130 ACGGGTCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.18, C:0.31, G:0.31, T:0.20
Consensus pattern (19 bp):
CCGGTCAACCTGGTTCAGG
Found at i:149385 original size:29 final size:29
Alignment explanation
Indices: 149353--149505 Score: 122
Period size: 29 Copynumber: 5.4 Consensus size: 29
149343 AAAATAGCAT
*
149353 TAAAATACCACCATTTTCAAAATAATTAC
1 TAAAATATCACCATTTTCAAAATAATTAC
* *
149382 TAAAATATCA-C-TTTTTAAAAAAATTA-
1 TAAAATATCACCATTTTCAAAATAATTAC
* *
149408 TGAAATTATCATTTC-TTTT--AAA-AATTAC
1 T-AAAATATCA--CCATTTTCAAAATAATTAC
* *
149436 AAAAATAGCACCATTTTCAAAATAATTAC
1 TAAAATATCACCATTTTCAAAATAATTAC
** * * *
149465 CCAAATACCACCAATTTCAAAATAAGTAC
1 TAAAATATCACCATTTTCAAAATAATTAC
149494 TAAAATATCACC
1 TAAAATATCACC
149506 CTGAATTTCC
Statistics
Matches: 99, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
25 1 0.01
26 5 0.05
27 33 0.33
28 7 0.07
29 48 0.48
30 5 0.05
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (29 bp):
TAAAATATCACCATTTTCAAAATAATTAC
Found at i:149406 original size:27 final size:26
Alignment explanation
Indices: 149364--149442 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 26
149354 AAAATACCAC
* *
149364 CATTTTCAAAATAATTACTAAAATAT
1 CATTTTTAAAAAAATTACTAAAATAT
*
149390 CACTTTTTAAAAAAATTA-TGAAATTAT
1 CA-TTTTTAAAAAAATTACT-AAAATAT
** *
149417 CATTTCTTTTAAAAATTACAAAAATA
1 CATTT-TTAAAAAAATTACTAAAATA
149443 GCACCATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
26 6 0.14
27 36 0.86
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.39
Consensus pattern (26 bp):
CATTTTTAAAAAAATTACTAAAATAT
Found at i:150069 original size:22 final size:21
Alignment explanation
Indices: 150044--150084 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
150034 TAGTTTGATA
*
150044 ATTTTTATTTAATATATTTTGC
1 ATTTTAATTTAATA-ATTTTGC
*
150066 ATTTTAATTTTATAATTTT
1 ATTTTAATTTAATAATTTT
150085 AATTTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTTTAATTTAATAATTTTGC
Found at i:150226 original size:21 final size:21
Alignment explanation
Indices: 150187--150226 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
150177 AAATATAGTA
* * *
150187 TTTTATTTATTATTTTTTATG
1 TTTTATTCATTAATATTTATG
150208 TTTTATTCATTAATATTTA
1 TTTTATTCATTAATATTTA
150227 CATGACATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTATTCATTAATATTTATG
Found at i:150367 original size:2 final size:2
Alignment explanation
Indices: 150355--150395 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
150345 ATATCCTGCT
*
150355 TA TA AA 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 TA TA TA T
150396 TTATTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:152647 original size:43 final size:44
Alignment explanation
Indices: 152586--152672 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
152576 TGGCTTTAGA
* *
152586 GAAGTTAGGAGAGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACAGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
* *
152629 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACAGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
152673 TGATGCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGACAGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
Found at i:155977 original size:8 final size:8
Alignment explanation
Indices: 155965--156024 Score: 79
Period size: 8 Copynumber: 7.6 Consensus size: 8
155955 AAAAAGATGA
155965 AAAAAAGG
1 AAAAAAGG
*
155973 GAAAAAGG
1 AAAAAAGG
155981 -AAAAAGG
1 AAAAAAGG
155988 AAAAAAAGG
1 -AAAAAAGG
*
155997 AAAAAAAG
1 AAAAAAGG
156005 -AAAAAGG
1 AAAAAAGG
156012 AAAAAAGG
1 AAAAAAGG
156020 AAAAA
1 AAAAA
156025 TTGAATCAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
7 13 0.28
8 26 0.57
9 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:155986 original size:15 final size:15
Alignment explanation
Indices: 155965--156024 Score: 77
Period size: 15 Copynumber: 3.9 Consensus size: 15
155955 AAAAAGATGA
155965 AAAAAAGGGAAAAAGG
1 AAAAAA-GGAAAAAGG
155981 -AAAAAGGAAAAAAAGG
1 AAAAAAGG--AAAAAGG
*
155997 AAAAAAAGAAAAAGG
1 AAAAAAGGAAAAAGG
156012 AAAAAAGGAAAAA
1 AAAAAAGGAAAAA
156025 TTGAATCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.05
15 24 0.62
16 7 0.18
17 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAAGGAAAAAGG
Found at i:155991 original size:6 final size:7
Alignment explanation
Indices: 155966--156024 Score: 64
Period size: 7 Copynumber: 7.7 Consensus size: 7
155956 AAAAGATGAA
155966 AAAAAGGG
1 AAAAA-GG
155974 AAAAAGG
1 AAAAAGG
155981 AAAAAGG
1 AAAAAGG
155988 AAAAAAAGG
1 --AAAAAGG
*
155997 AAAAAAAG
1 -AAAAAGG
156005 AAAAAGG
1 AAAAAGG
156012 AAAAAAGG
1 -AAAAAGG
156020 AAAAA
1 AAAAA
156025 TTGAATCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
7 20 0.43
8 19 0.41
9 7 0.15
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:155995 original size:24 final size:24
Alignment explanation
Indices: 155953--156024 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
155943 ATACTCATTC
155953 AGAAAAAGATGAAAAAAAGGGAAAAA
1 AGAAAAAG--GAAAAAAAGGGAAAAA
* *
155979 GGAAAAAGGAAAAAAAGGAAAAAA
1 AGAAAAAGGAAAAAAAGGGAAAAA
156003 AGAAAAAGG-AAAAAA-GGAAAAA
1 AGAAAAAGGAAAAAAAGGGAAAAA
156025 TTGAATCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.14
23 6 0.14
24 23 0.55
26 7 0.17
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (24 bp):
AGAAAAAGGAAAAAAAGGGAAAAA
Found at i:159669 original size:75 final size:75
Alignment explanation
Indices: 159537--159705 Score: 239
Period size: 75 Copynumber: 2.3 Consensus size: 75
159527 ACAAGAAGCA
* * * *
159537 AATGATGGAGCATGCTGAAAGCCCATTTCAATCATAATCAGGAATATTGACACATTTTGAACGTT
1 AATGATGGGGCATGCTGAAAGCCCATTTAAATCAGAATCAAGAATATTGACACATTTTGAACGTT
159602 TGTATTAGCC
66 TGTATTAGCC
* * ***
159612 AATGCTGGGGCATGCTGAAAGCCCCTTTAAATCAGAATCAAGAATATTGATGTATTTTGAACGTT
1 AATGATGGGGCATGCTGAAAGCCCATTTAAATCAGAATCAAGAATATTGACACATTTTGAACGTT
159677 TGTATTAGCC
66 TGTATTAGCC
* *
159687 AATGTTGGGGCAAGCTGAA
1 AATGATGGGGCATGCTGAA
159706 GATCCATATC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (75 bp):
AATGATGGGGCATGCTGAAAGCCCATTTAAATCAGAATCAAGAATATTGACACATTTTGAACGTT
TGTATTAGCC
Found at i:161025 original size:22 final size:22
Alignment explanation
Indices: 160999--161100 Score: 186
Period size: 22 Copynumber: 4.6 Consensus size: 22
160989 TATATCTACA
160999 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
161021 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
161043 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
161065 CTCTTCAAAGATGATAGTTTCT
1 CTCTTCAAAGATGATAGATTCT
161087 CTCTTCAAAGATGA
1 CTCTTCAAAGATGA
161101 AAGCTTTATT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 77 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:161862 original size:113 final size:111
Alignment explanation
Indices: 161462--162144 Score: 660
Period size: 113 Copynumber: 5.9 Consensus size: 111
161452 GCAAAGATTT
* * * *
161462 GAATCCATTACTCAATGGATCAACATTTCCA-GAATAGTTCATAATGAGAATAACTCATCTGAAG
1 GAATTCATCACTCGATGGATCAACATTTCCAGGAA-AGTTCATAATGAGAAGAACTCATCTGAAG
* *
161526 AAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
65 -AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTC
* * *
161574 GAATTCATCACTCGATGGATCAGCATTGCCA-GATAGAGTTCATAATGAGAAGAATTCATCTGAA
1 GAATTCATCACTCGATGGATCAACATTTCCAGGA-A-AGTTCATAATGAGAAGAACTCATCTGAA
* *
161638 G-GGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAAC-CTTGC-C
64 GAGG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTC
* *
161684 TTAATTCATCACTCGATGGATCAACATTTCCA-GAAGAGTTCATAATAAGAAGAACTCATCTGAA
1 -GAATTCATCACTCGATGGATCAACATTTCCAGGAA-AGTTCATAATGAGAAGAACTCATCTGAA
*
161748 GAAGGAAGAAGAAGTTCAGAATGAGAAGAACTTGTTCAAACTTTTGCTC
64 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTC
161797 GAATTCATCACTCGATGGATCAACATTGT-CAGGTAAAGTTCATAATGAGAAGAACTCATCTGAA
1 GAATTCATCACTCGATGGATCAACATT-TCCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
161861 GAAGGAAGAAAAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTA
64 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTC
*
161910 G-ATTC-T-ATCTCAGAATGAGATAAATCAGCACCAACATTTCCAGAGGAAGTTCATAATGAGAA
1 GAATTCATCA-CTC-G-ATG-G----AT------CAACATTTCCAG-GAAAGTTCATAATGAGAA
* * *
161972 GAACTTATCTGAAGA-G--GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTC
51 GAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTC
** *
162030 G-ATTCTATCACAGAAGGAGATAGATCAACATCAACGTTTCCA-GATAGAGTTCATAATGAGAAG
1 GAATTC-ATCAC-----TCGATGGATC-A-A-C-A--TTTCCAGGA-A-AGTTCATAATGAGAAG
162093 AACTCATCTGAAG-GGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAAC
52 AACTCATCTGAAGAGG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAAC
162145 CTTGCCTTAA
Statistics
Matches: 486, Mismatches: 39, Indels: 81
0.80 0.06 0.13
Matches are distributed among these distances:
110 31 0.06
111 74 0.15
112 100 0.21
113 106 0.22
114 4 0.01
115 1 0.00
116 1 0.00
117 1 0.00
118 4 0.01
119 1 0.00
120 80 0.16
122 3 0.01
123 36 0.07
124 40 0.08
125 3 0.01
126 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (111 bp):
GAATTCATCACTCGATGGATCAACATTTCCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTTGCTC
Found at i:162010 original size:17 final size:17
Alignment explanation
Indices: 161955--162010 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
161945 ATTTCCAGAG
161955 GAAGTTCATAATGAGAA
1 GAAGTTCATAATGAGAA
*
161972 GAACTT-ATCTGAA-GAGGAA
1 GAAGTTCA--T-AATGA-GAA
161991 GAAGTTCATAATGAGAA
1 GAAGTTCATAATGAGAA
162008 GAA
1 GAA
162011 CTTGTTCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 1 0.03
17 13 0.42
18 6 0.19
19 10 0.32
20 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.21
Consensus pattern (17 bp):
GAAGTTCATAATGAGAA
Found at i:162034 original size:120 final size:120
Alignment explanation
Indices: 161832--162147 Score: 445
Period size: 120 Copynumber: 2.6 Consensus size: 120
161822 TTGTCAGGTA
*
161832 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATAAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG---AAGTTCATAATGAGAAGAACTTGTT
* * * *
161897 CAACCTTTTGCTAGATTCTATCTCAGAATGAGATAAATCAGCACCAACATTTCCAGAGG
63 CAACCTTTTACTAGATTCTATCACAGAAGGAGATAAATCAACACCAACATTTCCAGA-G
*
161956 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * * * *
162020 CCTTTTACTCGATTCTATCACAGAAGGAGATAGATCAACATCAACGTTTCCAGAT
66 CCTTTTACTAGATTCTATCACAGAAGGAGATAAATCAACACCAACATTTCCAGAG
*
162075 AGAGTTCATAATGAGAAGAACTCATCTGAAGGGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 A-AGTTCATAATGAGAAGAACTCATCTGAA--GAAGGAAGAAGTTCATAATGAGAAGAACTTGTT
162140 CAAACCTT
63 C-AACCTT
162148 GCCTTAATTC
Statistics
Matches: 174, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
119 1 0.01
120 100 0.57
122 1 0.01
123 37 0.21
124 35 0.20
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (120 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTACTAGATTCTATCACAGAAGGAGATAAATCAACACCAACATTTCCAGAG
Found at i:162232 original size:17 final size:17
Alignment explanation
Indices: 162210--162269 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 17
162200 CAACATTTCC
162210 AGAAGAAATTCATAATG
1 AGAAGAAATTCATAATG
* *
162227 AGAAG-AACTCAT-CTG
1 AGAAGAAATTCATAATG
162242 ACGAAGAAGAAGTTCATAATG
1 A-GAAG-A-AA-TTCATAATG
162263 AGAAGAA
1 AGAAGAA
162270 CTTGTTCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
15 3 0.09
16 10 0.30
17 5 0.15
18 1 0.03
19 3 0.09
20 8 0.24
21 3 0.09
ACGTcount: A:0.50, C:0.10, G:0.22, T:0.18
Consensus pattern (17 bp):
AGAAGAAATTCATAATG
Found at i:162505 original size:3 final size:3
Alignment explanation
Indices: 162497--162589 Score: 120
Period size: 3 Copynumber: 31.0 Consensus size: 3
162487 TTTTCTTTAT
* *
162497 TTA TTA TTA TTC TTA TTA TAA TT- TTA TTTA TTTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA
162542 TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
162587 TTA
1 TTA
162590 ATAAATAATT
Statistics
Matches: 81, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
2 6 0.07
3 65 0.80
4 10 0.12
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:162565 original size:33 final size:31
Alignment explanation
Indices: 162492--162588 Score: 142
Period size: 33 Copynumber: 3.1 Consensus size: 31
162482 TGGTTTTTTC
* *
162492 TTTATTTATTATTATTCTTATTATAATT-TTA
1 TTTATTTATTATTA-TATTATTATTATTATTA
162523 TTTATTTATTATTATATTATTATTATTATTA
1 TTTATTTATTATTATATTATTATTATTATTA
162554 TTTATTATTATTATTATATTATTATTATTATTA
1 TTTA-T-TTATTATTATATTATTATTATTATTA
162587 TT
1 TT
162589 AATAAATAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
30 11 0.18
31 21 0.34
32 1 0.02
33 28 0.46
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (31 bp):
TTTATTTATTATTATATTATTATTATTATTA
Found at i:163873 original size:22 final size:21
Alignment explanation
Indices: 163848--163936 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 21
163838 AATTAGACCA
163848 TTAATTTTATATATTTTACATT
1 TTAATTTTATATATTTTA-ATT
**
163870 TTAATCCCTA-ATAGTTTGATAATT
1 TTAAT-TTTATATA-TTT--TAATT
* * *
163894 TTTATTTAATATATTTTGTATT
1 TTAATTTTATATATTTT-AATT
163916 TTAATTTTATA-ATTTTAATT
1 TTAATTTTATATATTTTAATT
163936 T
1 T
163937 CTTTTATTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
20 4 0.08
21 6 0.12
22 20 0.39
23 9 0.18
24 10 0.20
25 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (21 bp):
TTAATTTTATATATTTTAATT
Found at i:166119 original size:60 final size:59
Alignment explanation
Indices: 166019--166148 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 59
166009 CAGCAGGCTA
** * * *
166019 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGGCCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
** * *
166078 CATATTCGGGAACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGATCTTATGTGT
1 CATATTCGGGAA-TACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
166138 CATATTCGGGA
1 CATATTCGGGA
166149 TTGCACTACG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 12 0.20
60 49 0.80
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:166239 original size:20 final size:20
Alignment explanation
Indices: 166211--166252 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
166201 TATATTGGGC
* *
166211 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
166231 TATTTTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
166251 TA
1 TA
166253 CGGAATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:166770 original size:33 final size:34
Alignment explanation
Indices: 166721--166785 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
166711 TGCAGAAAAT
166721 ACTGTACCAGTTACTGTAGCGTATCGATGCATGC
1 ACTGTACCAGTTACTGTAGCGTATCGATGCATGC
*
166755 ACTGTAGCAG-TACTGTAGCGTATCGATGCAT
1 ACTGTACCAGTTACTGTAGCGTATCGATGCAT
166786 AATTTAGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 21 0.70
34 9 0.30
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (34 bp):
ACTGTACCAGTTACTGTAGCGTATCGATGCATGC
Found at i:172739 original size:54 final size:54
Alignment explanation
Indices: 172673--173128 Score: 619
Period size: 54 Copynumber: 8.5 Consensus size: 54
172663 ATATCACATC
* * * *
172673 AGGGAGTA-GAACTCAAACAATCTTCTGCCTACTGGTTCACTCCCTTTTTCTTT
1 AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
* * * *
172726 AGGGAGTAGGAACTCGATCAATC-TATGCCAACGGGTTCCCTCCCTCTTTCTTT
1 AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
** * * *
172779 AGGGAGTAGGAACTCGAACGCTATTTTGCCTACAGGTTCGCTCCCTCTTTCTTT
1 AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
* * *
172833 AGGGAGTAGGAACTCGAACAATATTCTGCCAATGGGTTCGCTCCCTCTTTCTTT
1 AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
* * * *
172887 AGAGAGTAGGAACTCGAACGATATTCTGCCTACGGGTTCGCTCCTTCTTTCTTT
1 AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
* *
172941 AGGGAGTAGGAACTCGAACGATATTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
1 AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
* * **
172995 AGGGAGTAAGAACTCGAACCATCTTCTGTTTACGGGTTCGCTCCCTCTTTCTTT
1 AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
* * * *
173049 AGGGAGTAGGAACTCGAACAATCTTATGTCAATGGGTTCGCTCCCTCTTTCTTT
1 AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
*
173103 AGGGAGTAGGAACTCGAACGATCTTC
1 AGGGAGTAGGAACTCGAACAATCTTC
173129 ATTTGCTTCA
Statistics
Matches: 360, Mismatches: 41, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
53 52 0.14
54 308 0.86
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (54 bp):
AGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT
Found at i:174439 original size:7 final size:8
Alignment explanation
Indices: 174420--174457 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
174410 ACCCTCCATT
174420 TTTTTTCA
1 TTTTTTCA
174428 TTTTTTCA
1 TTTTTTCA
*
174436 TTTTTTCT
1 TTTTTTCA
174444 TTTTCTTC-
1 TTTT-TTCA
174452 TTTTTT
1 TTTTTT
174458 TTATCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 2 0.07
8 23 0.82
9 3 0.11
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCA
Found at i:174458 original size:19 final size:19
Alignment explanation
Indices: 174436--174509 Score: 58
Period size: 22 Copynumber: 3.5 Consensus size: 19
174426 CATTTTTTCA
174436 TTTTTTCTTTTTCTTCTTT
1 TTTTTTCTTTTTCTTCTTT
174455 TTTTTATCATTTTTTCTTCTCATCAT
1 TTTTT-TC--TTTTTCTTCT--T--T
*
174481 TTTTCTTCTTTTTCATCTTT
1 TTTT-TTCTTTTTCTTCTTT
*
174501 TTTTATCTT
1 TTTTTTCTT
174510 CAAGCAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
19 9 0.20
20 7 0.16
22 11 0.24
24 10 0.22
26 7 0.16
27 1 0.02
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTCTTTTTCTTCTTT
Found at i:174465 original size:36 final size:36
Alignment explanation
Indices: 174418--174493 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
174408 GAACCCTCCA
**
174418 TTTTTTTTCATTTTTTCATT-TTTTC-TTTTTCTTCT
1 TTTTTTTTCATTTTTTC-TTCTCATCATTTTTCTTCT
174453 TTTTTTTATCATTTTTTCTTCTCATCATTTTTCTTCT
1 TTTTTTT-TCATTTTTTCTTCTCATCATTTTTCTTCT
174490 TTTT
1 TTTT
174494 CATCTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
35 9 0.25
36 13 0.36
37 14 0.39
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (36 bp):
TTTTTTTTCATTTTTTCTTCTCATCATTTTTCTTCT
Found at i:174483 original size:28 final size:27
Alignment explanation
Indices: 174428--174493 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
174418 TTTTTTTTCA
* *
174428 TTTTTTCATTTTTTCTTTTTCTTCTTT
1 TTTTTTCATTTTTTCTTTCTCATCTTT
*
174455 TTTTTATCATTTTTTC-TTCTCATCATT
1 TTTTT-TCATTTTTTCTTTCTCATCTTT
*
174482 TTTCTTC-TTTTT
1 TTTTTTCATTTTT
174494 CATCTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 5 0.15
26 2 0.06
27 17 0.50
28 10 0.29
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTTTCATTTTTTCTTTCTCATCTTT
Found at i:174485 original size:15 final size:16
Alignment explanation
Indices: 174460--174489 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
174450 TCTTTTTTTT
174460 ATCATTTTTTCTTCTC
1 ATCATTTTTTCTTCTC
174476 ATCA-TTTTTCTTCT
1 ATCATTTTTTCTTCT
174490 TTTTCATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (16 bp):
ATCATTTTTTCTTCTC
Found at i:184169 original size:25 final size:25
Alignment explanation
Indices: 184133--184201 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
184123 ACGTTAAAAC
184133 CCTAACCACATGATATCTAATTCAA
1 CCTAACCACATGATATCTAATTCAA
* *
184158 CCTAACCGCATGATATCTAATTTAA
1 CCTAACCACATGATATCTAATTCAA
*
184183 CCTAACCACATGATCTCTA
1 CCTAACCACATGATATCTA
184202 GTTCGCATGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.29
Consensus pattern (25 bp):
CCTAACCACATGATATCTAATTCAA
Found at i:189989 original size:19 final size:21
Alignment explanation
Indices: 189949--189992 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
189939 AAAAATAAGC
*
189949 TAAAACATCTTAAATCCTATT
1 TAAAACATCTTAAATACTATT
189970 TAAAACA-CTTAAA-ACTATT
1 TAAAACATCTTAAATACTATT
189989 TAAA
1 TAAA
189993 CTAAACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 6 0.27
21 7 0.32
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAACATCTTAAATACTATT
Found at i:190551 original size:33 final size:33
Alignment explanation
Indices: 190506--190578 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
190496 ACATGGGAAT
* *
190506 TTCATCTTGGTTGGTAGCCAACTTATTGGAAAA
1 TTCATCTCGGTTGATAGCCAACTTATTGGAAAA
*
190539 TTCATCTCGGTTGATGGCCAACTTATTGGAAAA
1 TTCATCTCGGTTGATAGCCAACTTATTGGAAAA
190572 TTCATCT
1 TTCATCT
190579 TTGGTAGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (33 bp):
TTCATCTCGGTTGATAGCCAACTTATTGGAAAA
Found at i:195304 original size:37 final size:37
Alignment explanation
Indices: 195249--195369 Score: 137
Period size: 38 Copynumber: 3.3 Consensus size: 37
195239 AGTTGGAAAA
195249 TTCATCTTTGGTAGGTGGCCAACTTTGCACATTGGAAT
1 TTCATCTTTGGTAGGTGGCCAACTTTGCA-ATTGGAAT
*
195287 TTCATC-TTGGTTA-GTGGCCAAC-TT---ATTGGAAAA
1 TTCATCTTTGG-TAGGTGGCCAACTTTGCAATTGG-AAT
* *
195320 TTCATCTTTGGTAGGTGGCTAACTTTGCATATGGGAAT
1 TTCATCTTTGGTAGGTGGCCAACTTTGCA-ATTGGAAT
195358 TTCATCTTTGGT
1 TTCATCTTTGGT
195370 TCCTAAAATA
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
32 5 0.07
33 10 0.14
34 12 0.17
35 2 0.03
36 2 0.03
37 13 0.19
38 22 0.31
39 4 0.06
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (37 bp):
TTCATCTTTGGTAGGTGGCCAACTTTGCAATTGGAAT
Found at i:199692 original size:22 final size:22
Alignment explanation
Indices: 199632--199688 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
199622 TTAATTTTTT
*
199632 ATTAATTTTTTTAAAATAAGTA
1 ATTAATTTTTTTATAATAAGTA
199654 ATTAATTTTTTTATAAT-AGT-
1 ATTAATTTTTTTATAATAAGTA
199674 ATATAATTTTTTTAT
1 AT-TAATTTTTTTAT
199689 TAATCTAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 2 0.06
21 15 0.45
22 16 0.48
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTAATTTTTTTATAATAAGTA
Found at i:201676 original size:22 final size:22
Alignment explanation
Indices: 201648--201693 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
201638 TCCTCCCAAC
201648 GCACAGCCGCTCCACCGTGCAT
1 GCACAGCCGCTCCACCGTGCAT
201670 GCACAGCCGCTCCACCGTGCAT
1 GCACAGCCGCTCCACCGTGCAT
201692 GC
1 GC
201694 TACTATGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.46, G:0.24, T:0.13
Consensus pattern (22 bp):
GCACAGCCGCTCCACCGTGCAT
Found at i:202745 original size:26 final size:26
Alignment explanation
Indices: 202676--202763 Score: 99
Period size: 26 Copynumber: 3.3 Consensus size: 26
202666 TCATATTCAT
*
202676 AATATTTTATATATATTAACTT-TCAAA
1 AATATTTT-TAT-TATTAACTTATTAAA
*
202703 AATA-TCTTATTATTAACTTATTAAA
1 AATATTTTTATTATTAACTTATTAAA
*
202728 TATATTTTTATTATTAACTTAATCTAAA
1 AATATTTTTATTATTAACTT-AT-TAAA
202756 AATATTTT
1 AATATTTT
202764 ATTTTTATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
24 9 0.17
25 10 0.19
26 16 0.31
27 6 0.12
28 11 0.21
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (26 bp):
AATATTTTTATTATTAACTTATTAAA
Found at i:202777 original size:50 final size:52
Alignment explanation
Indices: 202677--202788 Score: 126
Period size: 52 Copynumber: 2.2 Consensus size: 52
202667 CATATTCATA
202677 ATATTTTATATATATTAACTTTCAAAAATATCTTATTATTAACTTATT-AAAT
1 ATATTTT-TATATATTAACTTTCAAAAATATCTTATTATTAACTTATTAAAAT
* *
202729 ATATTTTTAT-TATTAACTTAATCTAAAAATATTTTATT-TTTA-TT-TTAAAAT
1 ATATTTTTATATATTAACTT--TC-AAAAATATCTTATTATTAACTTATTAAAAT
202780 ATATATTTT
1 ATAT-TTTT
202789 GTTCAAATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
50 11 0.21
51 13 0.25
52 16 0.30
53 13 0.25
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (52 bp):
ATATTTTTATATATTAACTTTCAAAAATATCTTATTATTAACTTATTAAAAT
Found at i:202788 original size:53 final size:52
Alignment explanation
Indices: 202677--202783 Score: 123
Period size: 51 Copynumber: 2.1 Consensus size: 52
202667 CATATTCATA
*
202677 ATATTTTATATATATTAACTTTCAAAAATATCTTATTATTAACTTATTAAAT
1 ATATTTTATATATATTAACTTTCAAAAATATCTTATTATTAACTTATAAAAT
* * *
202729 ATATTTT-TAT-TATTAACTTAATCTAAAAATATTTTATT-TTTA-TTTTAAAAT
1 ATATTTTATATATATTAACTT--TC-AAAAATATCTTATTATTAACTTATAAAAT
202780 ATAT
1 ATAT
202784 ATTTTGTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
50 9 0.19
51 14 0.29
52 12 0.25
53 13 0.27
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (52 bp):
ATATTTTATATATATTAACTTTCAAAAATATCTTATTATTAACTTATAAAAT
Found at i:203515 original size:2 final size:2
Alignment explanation
Indices: 203508--203570 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
203498 CATGATTAAC
203508 AT AT AT AT AT AT 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 AT AT AT AT AT AT
203550 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
203571 AATGCGGTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:206224 original size:2 final size:2
Alignment explanation
Indices: 206217--206242 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
206207 ACTATTAATC
206217 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
206243 ACCTACCAAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:207165 original size:17 final size:18
Alignment explanation
Indices: 207143--207182 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
207133 TGACAAGAGA
207143 GAGGAAGAGAAGAT-TTT
1 GAGGAAGAGAAGATGTTT
*
207160 GAGGAA-AGGAGATGTTT
1 GAGGAAGAGAAGATGTTT
207177 -AGGAAG
1 GAGGAAG
207183 TTGAAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (18 bp):
GAGGAAGAGAAGATGTTT
Found at i:207405 original size:29 final size:26
Alignment explanation
Indices: 207337--207409 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
207327 TACCATATTT
*
207337 ATTTTAATTTTAAATATTAAAATTAAA
1 ATTTTAATCTTAAAT-TTAAAATTAAA
*
207364 ATTTT-ATCATTAAATTTAAAAATGATGAA
1 ATTTTAATC-TTAAATTT-AAAAT--TAAA
207393 ATTTTAATCTTAAATTT
1 ATTTTAATCTTAAATTT
207410 TAAACTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 4 0.10
27 16 0.41
29 16 0.41
30 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (26 bp):
ATTTTAATCTTAAATTTAAAATTAAA
Found at i:208758 original size:2 final size:2
Alignment explanation
Indices: 208702--208749 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
208692 TAATTACATG
208702 AT AT AT AT AT AT 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 AT AT AT AT AT AT
208744 AT AT AT
1 AT AT AT
208750 GCATATATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:210472 original size:3 final size:3
Alignment explanation
Indices: 210455--210510 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
210445 ATGTAAACTG
* *
210455 TAA TAT TAA -AA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
210499 TAA TAG TAA TAA
1 TAA TAA TAA TAA
210511 AATTAAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.86
4 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:211083 original size:135 final size:134
Alignment explanation
Indices: 210709--211338 Score: 882
Period size: 134 Copynumber: 4.7 Consensus size: 134
210699 AGTTCGGGTC
* * * * * * * * *
210709 ATCTAAGGGTGACATGCCTCCTATGTGATGAGGAGGTCTAGTTGGGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
* * *
210774 TGATGAAGAGTTCTTGGCCATCTTTAGGGAGGGTGATAACTCGGTTCCTACGCGATGAGGATGAC
66 TGATGAAGAGTTC-TGGCCATCTTTAGGAAGAGTGATAACTCGGTTCCTACGCGATGAGGACGAC
*
210839 TGGTT
130 TAGTT
* * * * ** * *
210844 ATCTAGGGGTGACACGGCTCCTACGTGATGAGAAGGTTTGGTAAGGGGATGACACGGTTCCTACG
1 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
* * * *
210909 TGATGAAGAGTTCTGGCCATCTTTAAGAAGAGTGATAACTCAGTTCCTATGCGATGAGGATGACT
66 TGATGAAGAGTTCTGGCCATCTTTAGGAAGAGTGATAACTCGGTTCCTACGCGATGAGGACGACT
210974 AGTT
131 AGTT
* * *
210978 TTCTAGGAGTGACACGACTCCTACGTGATGAGGAGATCTGATCGGGGGGATGACACGGCTCATAC
1 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC-GGGGGATGACACGGCTCATAC
* * * * *
211043 GTGATGAAAAGTTCTGGCCATCTTTAGGAAAAGTGATAACTCGATTCCTACACGATGAGGACGGC
65 GTGATGAAGAGTTCTGGCCATCTTTAGGAAGAGTGATAACTCGGTTCCTACGCGATGAGGACGAC
*
211108 TGGTT
130 TAGTT
211113 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
1 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
* *
211178 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTAATAACTCGGTTCCTACGCGATGAGGACGACT
66 TGATGAAGAGTTCTGGCCATCTTTAGGAAGAGTGATAACTCGGTTCCTACGCGATGAGGACGACT
211243 AGTT
131 AGTT
* * *
211247 ATCTAAGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGACTCATACG
1 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
*
211312 TGATGAAGAGTTCTGGCCATATTTAGG
66 TGATGAAGAGTTCTGGCCATCTTTAGG
211339 GATAATAATT
Statistics
Matches: 439, Mismatches: 55, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
134 256 0.58
135 183 0.42
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
TGATGAAGAGTTCTGGCCATCTTTAGGAAGAGTGATAACTCGGTTCCTACGCGATGAGGACGACT
AGTT
Found at i:211178 original size:40 final size:39
Alignment explanation
Indices: 211118--211193 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
211108 TGGTTATCTA
* *
211118 GGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCG
1 GGGGTGACACGACTCATACGTGATGAAGAGATCTGGTCG
* *
211157 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 GGGG-TGACACGACTCATACGTGATGAAGAGATCTGG
211194 CCATCTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (39 bp):
GGGGTGACACGACTCATACGTGATGAAGAGATCTGGTCG
Done.