Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005005.1 Hibiscus syriacus cultivar Beakdansim tig00011232_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: 132093
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:8619 original size:44 final size:43
Alignment explanation
Indices: 8544--8639 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 43
8534 TTGTGATTAA
*
8544 TGCATCGATACACATGACAGTGCATCGATGCA-TCCCTTAAATG
1 TGCATCGATACACATGACAGTGCACCGATGCACT-CCTTAAATG
*
8587 TGCATCGATACATCATGA-AGATGCACCGATGCACTCCTTGAATG
1 TGCATCGATACA-CATGACAG-TGCACCGATGCACTCCTTAAATG
8631 TGCATCGAT
1 TGCATCGAT
8640 GCACTCATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
43 14 0.29
44 33 0.69
45 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (43 bp):
TGCATCGATACACATGACAGTGCACCGATGCACTCCTTAAATG
Found at i:8645 original size:23 final size:22
Alignment explanation
Indices: 8563--8642 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
8553 ACACATGACA
*
8563 GTGCATCGATGCATCCCTTAAAT
1 GTGCATCGATGCAT-CCTTGAAT
* *
8586 GTGCATCGATACAT-CATGAA-
1 GTGCATCGATGCATCCTTGAAT
*
8606 GATGCACCGATGCACTCCTTGAAT
1 G-TGCATCGATGCA-TCCTTGAAT
8630 GTGCATCGATGCA
1 GTGCATCGATGCA
8643 CTCATAAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 1 0.02
23 29 0.63
24 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:11201 original size:138 final size:139
Alignment explanation
Indices: 10955--11235 Score: 483
Period size: 138 Copynumber: 2.0 Consensus size: 139
10945 AAAATTACTC
* * * *
10955 AAATGGTTTTGTTATATCAAAAAAGTGGGAGATTGTTGAAAACATTTTTTATGTTTTGATATAAC
1 AAATGGTTTTGTTATATCAAAAAAGGGGGAGATTATTGAAAACATTTTTGATGTTTCGATATAAC
* *
11020 AAATTAATATAAATGAATTTTAAGATTTTACAAATAATTCTCTAAGTATATTCGATATAATTATT
66 AAATTAAGATAAATGAATTTTAAGATTTTACAAATAATTCTCTAAGTATATTCGATACAATTATT
11085 CGAATATCA
131 CGAATATCA
11094 AAATGGTTTTGTTATATC-AAAAAGGGGGAGATTATTGAAAACATTTTTGATGTTTCGATATAAC
1 AAATGGTTTTGTTATATCAAAAAAGGGGGAGATTATTGAAAACATTTTTGATGTTTCGATATAAC
*
11158 AAATTAAGATAAATGAATTTTAAGATTTTACAAATGATTCTCTAAGTATATTCGATACAATTATT
66 AAATTAAGATAAATGAATTTTAAGATTTTACAAATAATTCTCTAAGTATATTCGATACAATTATT
*
11223 TGAATATCA
131 CGAATATCA
11232 AAAT
1 AAAT
11236 ATTACTCCAA
Statistics
Matches: 134, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
138 116 0.87
139 18 0.13
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.40
Consensus pattern (139 bp):
AAATGGTTTTGTTATATCAAAAAAGGGGGAGATTATTGAAAACATTTTTGATGTTTCGATATAAC
AAATTAAGATAAATGAATTTTAAGATTTTACAAATAATTCTCTAAGTATATTCGATACAATTATT
CGAATATCA
Found at i:11491 original size:19 final size:19
Alignment explanation
Indices: 11445--11491 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
11435 TTTTATGTAC
*
11445 CGATGCACAAGGCATGCAT
1 CGATGCACTAGGCATGCAT
*
11464 CGATGCACTAGTCATGCAT
1 CGATGCACTAGGCATGCAT
11483 CGATGCACT
1 CGATGCACT
11492 CCTAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (19 bp):
CGATGCACTAGGCATGCAT
Found at i:11529 original size:45 final size:46
Alignment explanation
Indices: 11477--11587 Score: 127
Period size: 46 Copynumber: 2.4 Consensus size: 46
11467 TGCACTAGTC
***
11477 ATGCATCGATGCACTCCTA-AATAATTTGAACATCGAATGCATTTT
1 ATGCATCGATGCACTCCTAGAATAATCAAAACATCGAATGCATTTT
** ** *
11522 ATGCATCGATGCACT-CTAGGCTTGGTCAAAACATCGAATGTATTTT
1 ATGCATCGATGCACTCCTA-GAATAATCAAAACATCGAATGCATTTT
11568 ATGCATCGATGCACTCCTAG
1 ATGCATCGATGCACTCCTAG
11588 TGTACCGATG
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 3 0.05
45 15 0.27
46 34 0.62
47 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
ATGCATCGATGCACTCCTAGAATAATCAAAACATCGAATGCATTTT
Found at i:11532 original size:83 final size:84
Alignment explanation
Indices: 11379--11535 Score: 212
Period size: 83 Copynumber: 1.9 Consensus size: 84
11369 AGTAGTGTAC
* ** *
11379 CGATGCACTATCTAATGCATCGATGCACCCTTGAATAAATTGATATTTCGAATGCATTTTATGTA
1 CGATGCACTATC-AATGCATCGATGCACCCTTAAATAAATTGATACATCGAATGCATTTTATGCA
11444 CCGATGCACAAGGCATGCAT
65 CCGATGCACAAGGCATGCAT
*
11464 CGATGCACTAGTC-ATGCATCGATGCACTCC-TAAATAATTTGA-ACATCGAATGCATTTTATGC
1 CGATGCACTA-TCAATGCATCGATGCAC-CCTTAAATAAATTGATACATCGAATGCATTTTATGC
*
11526 ATCGATGCAC
64 ACCGATGCAC
11536 TCTAGGCTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 26 0.41
84 24 0.38
85 12 0.19
86 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (84 bp):
CGATGCACTATCAATGCATCGATGCACCCTTAAATAAATTGATACATCGAATGCATTTTATGCAC
CGATGCACAAGGCATGCAT
Found at i:12364 original size:5 final size:5
Alignment explanation
Indices: 12354--12384 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
12344 ACTCTTTCAT
12354 TTTTA TTTTA TTTTA TTTTA TTTTA TCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA
12385 CGAAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:13591 original size:43 final size:43
Alignment explanation
Indices: 13538--13728 Score: 179
Period size: 43 Copynumber: 4.5 Consensus size: 43
13528 AAAAAAAAGA
* * * * *
13538 CGCAATAGGTCAAGATCTATCGCGGTGTTTTTGGAACAAACGC
1 CGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAACAAACGC
* * * *
13581 CGCAAAAGGTCGATATCAATAACAGCGTTTTTGGAACAAATGC
1 CGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAACAAACGC
*** *
13624 CG-AAAAGGTCGATATCTATTTAGGCATTTTTGGATACAAACGC
1 CGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-ACAAACGC
* * * * * * *
13667 CGCAAAAGGT-TAGATCTAGAGTGGTGTTTTTGGAATAAATGC
1 CGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAACAAACGC
13709 CGCAAAAGGTCGATATCTAT
1 CGCAAAAGGTCGATATCTAT
13729 GAAACAAACG
Statistics
Matches: 116, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
42 42 0.36
43 67 0.58
44 7 0.06
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (43 bp):
CGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAACAAACGC
Found at i:17896 original size:82 final size:81
Alignment explanation
Indices: 17757--17971 Score: 243
Period size: 82 Copynumber: 2.6 Consensus size: 81
17747 CGTTTGTATG
* * * * ** * * *
17757 ATAAACGCCACTAAATTACTTCTATATAGCATCGTTTGTTGGATAAACGCCACTATAAACAACCC
1 ATAAACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGAAAAAACGCCACTATAAACAACCA
17822 TATTACGGCATTT-CT
66 TATTACGGCATTTGCT
*
17837 ATAAAAACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGAAAAAATGCCACTATAAACAAC
1 AT--AAACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGAAAAAACGCCACTATAAACAAC
* * *
17902 TATATTCCGGCGTTTGAGCT
64 CATATTACGGCATTT--GCT
* * *
17922 ATAAACGCCGCTAAACTACCACTCTATTACGGCGTTTGTTGAAAAAACGC
1 ATAAACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGAAAAAACGC
17972 TGCTAAAGTA
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
80 2 0.02
82 63 0.56
83 44 0.39
85 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (81 bp):
ATAAACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGAAAAAACGCCACTATAAACAACCA
TATTACGGCATTTGCT
Found at i:17955 original size:83 final size:81
Alignment explanation
Indices: 17789--17971 Score: 233
Period size: 83 Copynumber: 2.2 Consensus size: 81
17779 TATATAGCAT
* * *
17789 CGTTTGTTGGATAAACGCCACTATAAACAACCCTATTACGGCATTTCTATAAAAACGCCGCTAAA
1 CGTTTGTTGAAAAAACGCCACTATAAACAACCATATTACGGCATTTCTAT-AAAACGCCGCTAAA
* * *
17854 TTACTACTCTATTGCGG
65 CTACCACTCTATTACGG
* * * *
17871 CGTTTGTTGAAAAAATGCCACTATAAACAACTATATTCCGGCGTTTGAGCTAT-AAACGCCGCTA
1 CGTTTGTTGAAAAAACGCCACTATAAACAACCATATTACGGCATTT---CTATAAAACGCCGCTA
17935 AACTACCACTCTATTACGG
63 AACTACCACTCTATTACGG
17954 CGTTTGTTGAAAAAACGC
1 CGTTTGTTGAAAAAACGC
17972 TGCTAAAGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
82 39 0.45
83 44 0.51
85 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (81 bp):
CGTTTGTTGAAAAAACGCCACTATAAACAACCATATTACGGCATTTCTATAAAACGCCGCTAAAC
TACCACTCTATTACGG
Found at i:17970 original size:42 final size:41
Alignment explanation
Indices: 17789--17978 Score: 138
Period size: 41 Copynumber: 4.6 Consensus size: 41
17779 TATATAGCAT
* * * *
17789 CGTTTGTTGGATAAACGCCACTATAA-ACAACCCTATTACGG
1 CGTTTGTTGAAAAAACGCCGCTA-AATACAACTCTATTACGG
* * * *
17830 CATTT-CT-ATAAAAACGCCGCTAAATTACTACTCTATTGCGG
1 CGTTTGTTGA-AAAAACGCCGCTAAA-TACAACTCTATTACGG
* * * *
17871 CGTTTGTTGAAAAAATGCCACTATAA-ACAACTATATTCCGG
1 CGTTTGTTGAAAAAACGCCGCTA-AATACAACTCTATTACGG
* * * *
17912 CGTTTG-AGCTATAAACGCCGCTAAACTACCACTCTATTACGG
1 CGTTTGTTG-AAAAAACGCCGCTAAA-TACAACTCTATTACGG
*
17954 CGTTTGTTGAAAAAACGCTGCTAAA
1 CGTTTGTTGAAAAAACGCCGCTAAA
17979 GTAGTATTTT
Statistics
Matches: 112, Mismatches: 27, Indels: 19
0.71 0.17 0.12
Matches are distributed among these distances:
39 2 0.02
40 15 0.13
41 48 0.43
42 43 0.38
43 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (41 bp):
CGTTTGTTGAAAAAACGCCGCTAAATACAACTCTATTACGG
Found at i:23353 original size:16 final size:16
Alignment explanation
Indices: 23320--23370 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
23310 CGTTCATTTA
*
23320 ATAAAT-AA-ACGAAT
1 ATAAATGAACACGAAC
23334 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
23350 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
23366 ATAAA
1 ATAAA
23371 CGTTGGAGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 26 0.76
ACGTcount: A:0.61, C:0.14, G:0.10, T:0.16
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:25044 original size:23 final size:23
Alignment explanation
Indices: 25018--25062 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25008 CACCACAGCT
*
25018 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
25041 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
25063 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:31838 original size:23 final size:23
Alignment explanation
Indices: 31812--31856 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31802 CACCACAGCT
*
31812 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
31835 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
31857 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:34308 original size:18 final size:18
Alignment explanation
Indices: 34282--34317 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34272 TCGAAAGGAC
*
34282 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
34300 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
34318 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:35488 original size:23 final size:23
Alignment explanation
Indices: 35462--35544 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
35452 TCCGACTTGA
* *
35462 ATTCTGTTATGATCCTGACCTGG
1 ATTCTGATATGATCATGACCTGG
* *
35485 ATTCTGATCTGAT-ATTGACATGG
1 ATTCTGATATGATCA-TGACCTGG
* *
35508 ATTCTGATCTGATACATGACCTAG
1 ATTCTGATATGAT-CATGACCTGG
35532 ATTCTGATATGAT
1 ATTCTGATATGAT
35545 ACTTGACTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
23 31 0.62
24 18 0.36
25 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (23 bp):
ATTCTGATATGATCATGACCTGG
Found at i:35534 original size:24 final size:24
Alignment explanation
Indices: 35477--35551 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
35467 GTTATGATCC
35477 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
35500 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
* *
35524 TGACCTAGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
35548 TGAC
1 TGAC
35552 TTGAATTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:36671 original size:19 final size:20
Alignment explanation
Indices: 36634--36671 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36624 TTTTTATATA
*
36634 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
36654 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
36672 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:37557 original size:43 final size:40
Alignment explanation
Indices: 37508--37608 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 40
37498 TTCACGAAAG
* *
37508 TAAATGAACGAACGAGACCTATGTTCATGTTCGTTCATTTAA
1 TAAATGAACG-ACAAAACCT-TGTTCATGTTCGTTCATTTAA
*
37550 TTAAATGAAC-ACAAAATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
*
37590 TAAATAAACGCACATAAAC
1 TAAATGAACG-ACA-AAAC
37609 GAACTTTCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 8 0.16
40 21 0.42
41 9 0.18
42 3 0.06
43 9 0.18
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
TAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
Found at i:51153 original size:17 final size:17
Alignment explanation
Indices: 51119--51170 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
51109 ACCGGACAAA
*
51119 TTTATTATTTTAGAGAG
1 TTTATTAATTTAGAGAG
**
51136 TTTATTAATTTATCGAG
1 TTTATTAATTTAGAGAG
*
51153 --TATTAATTTAAAGAG
1 TTTATTAATTTAGAGAG
51168 TTT
1 TTT
51171 CTACTGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTATTAATTTAGAGAG
Found at i:51395 original size:14 final size:15
Alignment explanation
Indices: 51378--51415 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
51368 AGTCTATATT
51378 AATATTTTA-TTTTA
1 AATATTTTACTTTTA
*
51392 AATAATTTACTTTTA
1 AATATTTTACTTTTA
*
51407 AAAATTTTA
1 AATATTTTA
51416 ATTAACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATTTTACTTTTA
Found at i:54428 original size:31 final size:31
Alignment explanation
Indices: 54390--54467 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
54380 ACAATTTTTT
*
54390 TTTGTTCATATTCGTTCATTAAGGAATATAG
1 TTTGTTCATGTTCGTTCATTAAGGAATATAG
54421 TTTGTTCATGTTCGTTCATTAAGGAATATAG
1 TTTGTTCATGTTCGTTCATTAAGGAATATAG
*
54452 CTTGTTCATGTTCGTT
1 TTTGTTCATGTTCGTT
54468 TATTTAAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (31 bp):
TTTGTTCATGTTCGTTCATTAAGGAATATAG
Found at i:54487 original size:10 final size:10
Alignment explanation
Indices: 54472--54559 Score: 80
Period size: 10 Copynumber: 9.3 Consensus size: 10
54462 TTCGTTTATT
*
54472 TAAACGAACG
1 TAAACGAACA
54482 TAAACGAACA
1 TAAACGAACA
*
54492 TAAACGAACG
1 TAAACGAACA
54502 TAAACGAACA
1 TAAACGAACA
54512 TAAACGAA-A
1 TAAACGAACA
*
54521 -GAAC-ATA-A
1 TAAACGA-ACA
*
54529 TAAATGAACA
1 TAAACGAACA
54539 TAAACG-A-A
1 TAAACGAACA
*
54547 TGAACGAACA
1 TAAACGAACA
54557 TAA
1 TAA
54560 TAAATGAACA
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
7 1 0.02
8 11 0.17
9 6 0.10
10 45 0.71
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (10 bp):
TAAACGAACA
Found at i:54497 original size:20 final size:20
Alignment explanation
Indices: 54472--54519 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
54462 TTCGTTTATT
54472 TAAACGAACGTAAACGAACA
1 TAAACGAACGTAAACGAACA
54492 TAAACGAACGTAAACGAACA
1 TAAACGAACGTAAACGAACA
54512 TAAACGAA
1 TAAACGAA
54520 AGAACATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.56, C:0.19, G:0.15, T:0.10
Consensus pattern (20 bp):
TAAACGAACGTAAACGAACA
Found at i:54526 original size:14 final size:14
Alignment explanation
Indices: 54507--54551 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
54497 GAACGTAAAC
*
54507 GAACATAAACGAAA
1 GAACATAAACGAAT
54521 GAACATAATA--AAT
1 GAACATAA-ACGAAT
54534 GAACATAAACGAAT
1 GAACATAAACGAAT
54548 GAAC
1 GAAC
54552 GAACATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.37
14 15 0.56
15 1 0.04
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (14 bp):
GAACATAAACGAAT
Found at i:54559 original size:31 final size:27
Alignment explanation
Indices: 54502--54582 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 27
54492 TAAACGAACG
*
54502 TAAACGAACATAAACGAAAGAACATAA
1 TAAATGAACATAAACGAAAGAACATAA
54529 TAAATGAACATAAACGAATGAACGAACATAA
1 TAAATGAACATAAACG-A--AA-GAACATAA
*
54560 TAAATGAACATAAAC-AAACAACA
1 TAAATGAACATAAACGAAAGAACA
54583 CAAACACAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
26 4 0.08
27 17 0.35
28 1 0.02
29 1 0.02
30 2 0.04
31 23 0.48
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.14
Consensus pattern (27 bp):
TAAATGAACATAAACGAAAGAACATAA
Found at i:57681 original size:19 final size:19
Alignment explanation
Indices: 57659--57695 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
57649 TTTCTTCCCA
57659 ACACATAACAGACTTCTGC
1 ACACATAACAGACTTCTGC
*
57678 ACACATAATAGACTTCTG
1 ACACATAACAGACTTCTG
57696 AATACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (19 bp):
ACACATAACAGACTTCTGC
Found at i:60118 original size:11 final size:11
Alignment explanation
Indices: 60102--60126 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60092 ATTTCTTTCA
60102 ATTCTTTTATT
1 ATTCTTTTATT
60113 ATTCTTTTATT
1 ATTCTTTTATT
60124 ATT
1 ATT
60127 TTATTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTCTTTTATT
Found at i:61593 original size:27 final size:28
Alignment explanation
Indices: 61548--61619 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
61538 CCTTTATTGC
**
61548 ATTTACAT-TTTGCATTTTGCATTCCCA-
1 ATTTACATCTTTGCA-TTTGCATGACCAT
* *
61575 ATTTACATCTTTACATTTGCATGAGCAT
1 ATTTACATCTTTGCATTTGCATGACCAT
61603 ATTTACATCTTTGCATT
1 ATTTACATCTTTGCATT
61620 AGTATTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 17 0.45
28 21 0.55
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.47
Consensus pattern (28 bp):
ATTTACATCTTTGCATTTGCATGACCAT
Found at i:63038 original size:17 final size:16
Alignment explanation
Indices: 63001--63124 Score: 74
Period size: 17 Copynumber: 7.3 Consensus size: 16
62991 AAACACACAC
*
63001 AAAAAGAAATCAAAAACA
1 AAAAAGAAA--AAAAAGA
*
63019 AAAAAGAAAGAATGAA-A
1 AAAAAGAAA-AA-AAAGA
*
63036 AAAAAGAGAAAAACAGA
1 AAAAAGA-AAAAAAAGA
63053 AAAAAGAGAAAAAAAGAA
1 AAAAAGA-AAAAAAAG-A
*
63071 AAAATAGAAGAAAAA-A
1 AAAA-AGAAAAAAAAGA
* *
63087 TAGAAGAAAAAGAAA-A
1 AAAAAGAAAAA-AAAGA
*
63103 AAAAAGAGAAAAAAGA
1 AAAAAGAAAAAAAAGA
63119 ATAAAA
1 A-AAAA
63125 TAGACAAATT
Statistics
Matches: 86, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
15 9 0.10
16 18 0.21
17 32 0.37
18 24 0.28
19 3 0.03
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:63054 original size:19 final size:19
Alignment explanation
Indices: 63018--63118 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
63008 AATCAAAAAC
* *
63018 AAAAA-AGAAAGAATGAAA
1 AAAAAGAGAAAAAAAGAAA
*
63036 AAAAAGAGAAAAACAG--A
1 AAAAAGAGAAAAAAAGAAA
63053 AAAAAGAGAAAAAAAGAAA
1 AAAAAGAGAAAAAAAGAAA
* *
63072 AAATAGAAGAAAAAATAGAAG
1 AAAAAG-AGAAAAAA-AGAAA
* *
63093 AAAAAGAAAAAAAAAGAGA
1 AAAAAGAGAAAAAAAGAAA
63112 AAAAAGA
1 AAAAAGA
63119 ATAAAATAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
17 16 0.24
18 5 0.07
19 23 0.34
20 15 0.22
21 9 0.13
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (19 bp):
AAAAAGAGAAAAAAAGAAA
Found at i:63056 original size:9 final size:8
Alignment explanation
Indices: 63018--63124 Score: 83
Period size: 9 Copynumber: 12.6 Consensus size: 8
63008 AATCAAAAAC
63018 AAAAAAGA
1 AAAAAAGA
* *
63026 AAGAATGAA
1 AAAAAAG-A
63035 AAAAAAGA
1 AAAAAAGA
63043 GAAAAACAGA
1 -AAAAA-AGA
63053 AAAAAGAGA
1 AAAAA-AGA
63062 AAAAAAGA
1 AAAAAAGA
63070 AAAAATAGA
1 AAAAA-AGA
*
63079 AGAAAA-A
1 AAAAAAGA
* *
63086 ATAGAAGA
1 AAAAAAGA
63094 AAAAGAA-A
1 AAAA-AAGA
63102 AAAAAAGA
1 AAAAAAGA
63110 GAAAAAAGA
1 -AAAAAAGA
63119 ATAAAA
1 A-AAAA
63125 TAGACAAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
7 7 0.09
8 25 0.31
9 45 0.56
10 3 0.04
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:64895 original size:2 final size:2
Alignment explanation
Indices: 64888--65169 Score: 519
Period size: 2 Copynumber: 141.0 Consensus size: 2
64878 TCATTTAAGT
** **
64888 AC AC AC AC AC AC GT AC AC AC AC GT AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
64930 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
64972 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
65014 AC AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
65056 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
65098 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
65140 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
65170 GTACACGCAC
Statistics
Matches: 270, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 270 1.00
ACGTcount: A:0.50, C:0.49, G:0.01, T:0.01
Consensus pattern (2 bp):
AC
Found at i:65180 original size:4 final size:4
Alignment explanation
Indices: 65173--65219 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
65163 CACACACGTA
*
65173 CACG CACG CACG CACG CACG CACG CACA CACG CACG CACG CACG CAC
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CAC
65220 ATACATACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.28, C:0.51, G:0.21, T:0.00
Consensus pattern (4 bp):
CACG
Found at i:65367 original size:22 final size:22
Alignment explanation
Indices: 65341--65404 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 22
65331 TCAGGCCATC
65341 AGTAAGTCTTTCGAGCATGATG
1 AGTAAGTCTTTCGAGCATGATG
* * *
65363 AGTAAGTCCTTC-AGGC--CATC
1 AGTAAGTCTTTCGA-GCATGATG
65383 AGTAAGTCTTTCGAGCATGATG
1 AGTAAGTCTTTCGAGCATGATG
65405 CTTAAATTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
22 15 0.47
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (22 bp):
AGTAAGTCTTTCGAGCATGATG
Found at i:65383 original size:42 final size:42
Alignment explanation
Indices: 65324--65404 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
65314 TCAAGATATG
65324 AAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGAGT
1 AAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGAGT
65366 AAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATG
1 AAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATG
65405 CTTAAATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (42 bp):
AAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGAGT
Found at i:65388 original size:20 final size:20
Alignment explanation
Indices: 65324--65390 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
65314 TCAAGATATG
65324 AAGTCCTTCAGGCCATCAGT
1 AAGTCCTTCAGGCCATCAGT
* * *
65344 AAGTCTTTC-GAGCATGATGAGT
1 AAGTCCTTCAG-GC--CATCAGT
65366 AAGTCCTTCAGGCCATCAGT
1 AAGTCCTTCAGGCCATCAGT
65386 AAGTC
1 AAGTC
65391 TTTCGAGCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
19 1 0.03
20 20 0.54
22 15 0.41
23 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (20 bp):
AAGTCCTTCAGGCCATCAGT
Found at i:65833 original size:20 final size:22
Alignment explanation
Indices: 65781--65835 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
65771 TCAAGAAAAC
65781 CATCA-TTCATACATAAATTTA
1 CATCATTTCATACATAAATTTA
*
65802 CATC-TTTGCATA-ATACATTT-
1 CATCATTT-CATACATAAATTTA
65822 CATCATTTCATACA
1 CATCATTTCATACA
65836 AACGATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
20 8 0.28
21 17 0.59
22 4 0.14
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (22 bp):
CATCATTTCATACATAAATTTA
Found at i:66755 original size:139 final size:139
Alignment explanation
Indices: 66332--66811 Score: 697
Period size: 139 Copynumber: 3.5 Consensus size: 139
66322 ATATTTCAAA
66332 TAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
1 TAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
*
66397 GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAA-CTAGCAACACCTCACTCGAGGGATCA
66 GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATC-AGCAAAACCTCACTCGAGGGATCA
66461 ACAC-TTCCAG
130 AC-CTTTCCAG
* * *
66471 TGGAGAGTTCATAATGAGAAGAACTCATCCAATAGAGGGAGAAGAAGTTCATAATGAGAAGAGCT
1 TAGAGAGTTCATAATGAGAAGAACTCATCCGAT-GAGGGAGAAGAAGTTCATAATGAGAAGAACT
* * ** **
66536 TGTTCGACCTATCA-CTCGATTCATGACAT-T----TTGAATCAGTGATGCCTCACTCGAGGGAT
65 TGTTCAACCT-T-AGCTCGATTCATCACATATGGAGTTGAATCAGCAAAACCTCACTCGAGGGAT
** *
66595 CAATATTTCTAG
128 CAACCTTTCCAG
*
66607 TGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
1 TAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
*
66672 GTTCAACCTTAGCTCGATTCGTCACATATGGAGTTGAATCAGCAAAACCTCACTCGAGGGATCAA
66 GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAAAACCTCACTCGAGGGATCAA
66737 CCTTTCCAG
131 CCTTTCCAG
* * *
66746 TAGAGAGTTCATAATGAGAATAACTCATCCGATAAGGGAAAAGAAGTTCATAATGAGAAGAACTT
1 TAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
66811 G
66 G
66812 AGCTTGCTTC
Statistics
Matches: 302, Mismatches: 28, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
133 1 0.00
134 14 0.05
135 40 0.13
136 63 0.21
137 1 0.00
139 127 0.42
140 40 0.13
141 15 0.05
142 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (139 bp):
TAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAAAACCTCACTCGAGGGATCAA
CCTTTCCAG
Found at i:90232 original size:3 final size:3
Alignment explanation
Indices: 90224--90276 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
90214 TCGTTTCCTA
90224 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
90272 ATT AT
1 ATT AT
90277 CATGTATATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:90663 original size:23 final size:23
Alignment explanation
Indices: 90636--90727 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
90626 CACCACAGCT
*
90636 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* *
90659 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* * *
90682 TGTAGAATTGCACCTAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
*
90705 CATAGAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
90728 TATAAAATGT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:95454 original size:21 final size:21
Alignment explanation
Indices: 95428--95487 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
95418 AGATAAGTAG
95428 TACTCCACAACAGGTGGATCA
1 TACTCCACAACAGGTGGATCA
* *
95449 TACTCCACAGCAGGTGGATTA
1 TACTCCACAACAGGTGGATCA
* * *
95470 TACCCCAAAATAGGTGGA
1 TACTCCACAACAGGTGGA
95488 GTTTCAACAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (21 bp):
TACTCCACAACAGGTGGATCA
Found at i:97478 original size:34 final size:34
Alignment explanation
Indices: 97396--97485 Score: 155
Period size: 33 Copynumber: 2.7 Consensus size: 34
97386 GCAAAGTTGA
*
97396 CATCTTTGGTTGGTGACCAACTTATTGGAAAATT
1 CATCTTTGGTTGGTGGCCAACTTATTGGAAAATT
97430 CATC-TTGGTTGGTGGCCAACTTATTGGAAAATT
1 CATCTTTGGTTGGTGGCCAACTTATTGGAAAATT
*
97463 CATCTTTGGTAGGTGGCCAACTT
1 CATCTTTGGTTGGTGGCCAACTT
97486 TGCACATGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 32 0.60
34 21 0.40
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (34 bp):
CATCTTTGGTTGGTGGCCAACTTATTGGAAAATT
Found at i:98634 original size:15 final size:15
Alignment explanation
Indices: 98614--98670 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
98604 GTGTTTGCGT
98614 TTTTTTATTAATATA
1 TTTTTTATTAATATA
* *
98629 TTTTTTATTTTATAAACA
1 TTTTTTA--TTA-ATATA
98647 TTTTTTATTAATATA
1 TTTTTTATTAATATA
*
98662 TTGTTTATT
1 TTTTTTATT
98671 TTAAATCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 18 0.53
16 3 0.09
17 3 0.09
18 10 0.29
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTTTATTAATATA
Found at i:102299 original size:2 final size:2
Alignment explanation
Indices: 102292--102323 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
102282 AGAATTTGAA
102292 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
102324 GTGTGTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103167 original size:42 final size:41
Alignment explanation
Indices: 103069--103258 Score: 166
Period size: 42 Copynumber: 4.5 Consensus size: 41
103059 GTTGATAACA
* ** *
103069 CTTTGGTCAGTCTCCTTAGATTCAGGCAAGCTCTTTGTGATA
1 CTTTGGTCAGTCTCCATAGGCTCAGGCAAGCTCTTTGTGA-C
* * * * *
103111 CTATGATCAATCTCCATAGGCTCAGACAACCTCTTTGTGAC
1 CTTTGGTCAGTCTCCATAGGCTCAGGCAAGCTCTTTGTGAC
* *
103152 CTTTTGGTCAGTCTCCTTAGGCTCAGGCAAGTTCTTTGTGAC
1 C-TTTGGTCAGTCTCCATAGGCTCAGGCAAGCTCTTTGTGAC
* * * * *
103194 ACTTTGGTCAGTCTCCATTGGCTTAGCCACA-TTCTTTGCGAC
1 -CTTTGGTCAGTCTCCATAGGCTCAGGCA-AGCTCTTTGTGAC
* *
103236 ACTTTGGTCAGTCCCCATTGGCT
1 -CTTTGGTCAGTCTCCATAGGCT
103259 TAGTCACATT
Statistics
Matches: 123, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 120 0.98
43 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.35
Consensus pattern (41 bp):
CTTTGGTCAGTCTCCATAGGCTCAGGCAAGCTCTTTGTGAC
Found at i:103211 original size:84 final size:84
Alignment explanation
Indices: 103066--103434 Score: 291
Period size: 84 Copynumber: 4.4 Consensus size: 84
103056 ACAGTTGATA
** * * * *
103066 ACACTTTGGTCAGTCTCCTTAGATTCAGGCAAGCTCTTTGTGATACTATGATCAATCTCCATAGG
1 ACACTTTGGTCAGTCTCCTTAGGCTCAGGCAAGTTCTTTGTGATACTTTGGTCAGTCTCCATAGG
*
103131 CTCAGACAAC-CTCTTTGTG
66 CTCAG-CAACACTCTTTGCG
* *
103150 AC-CTTTTGGTCAGTCTCCTTAGGCTCAGGCAAGTTCTTTGTGACACTTTGGTCAGTCTCCATTG
1 ACAC-TTTGGTCAGTCTCCTTAGGCTCAGGCAAGTTCTTTGTGATACTTTGGTCAGTCTCCATAG
* * *
103214 GCTTAGCCACATTCTTTGCG
65 GCTCAGCAACACTCTTTGCG
* * * * * *
103234 ACACTTTGGTCAGTCCCCATT-GGCTTAGTCACA-TTCTTTGCGATACTTTGGTCAGTCCCCATC
1 ACACTTTGGTCAGTCTCC-TTAGGCTCAGGCA-AGTTCTTTGTGATACTTTGGTCAGTCTCCATA
** * * *
103297 GGCTTTGCCACATTCTTTGCC
64 GGCTCAGCAACACTCTTTGCG
* * * * * * * * *
103318 ACACTTTGGTCAGTCCCCGTT-GGC-CTAGCCACGTTCTTTGGGACACCTCGGTCAGTCCCCATC
1 ACACTTTGGTCAGTCTCC-TTAGGCTC-AGGCAAGTTCTTTGTGATACTTTGGTCAGTCTCCATA
* ** * *
103381 GGCTTAGCCGCACTGTTTCCG
64 GGCTCAGCAACACTCTTTGCG
* *
103402 ACACTTTGGTCAGTCTCCATAGGATCAGGCAAG
1 ACACTTTGGTCAGTCTCCTTAGGCTCAGGCAAG
103435 CTGTTTGTAA
Statistics
Matches: 236, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
83 5 0.02
84 226 0.96
85 5 0.02
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.33
Consensus pattern (84 bp):
ACACTTTGGTCAGTCTCCTTAGGCTCAGGCAAGTTCTTTGTGATACTTTGGTCAGTCTCCATAGG
CTCAGCAACACTCTTTGCG
Found at i:103259 original size:42 final size:42
Alignment explanation
Indices: 103183--103421 Score: 307
Period size: 42 Copynumber: 5.7 Consensus size: 42
103173 CTCAGGCAAG
* *
103183 TTCTTTGTGACACTTTGGTCAGTCTCCATTGGCTTAGCCACA
1 TTCTTTGCGACACTTTGGTCAGTCCCCATTGGCTTAGCCACA
*
103225 TTCTTTGCGACACTTTGGTCAGTCCCCATTGGCTTAGTCACA
1 TTCTTTGCGACACTTTGGTCAGTCCCCATTGGCTTAGCCACA
* * *
103267 TTCTTTGCGATACTTTGGTCAGTCCCCATCGGCTTTGCCACA
1 TTCTTTGCGACACTTTGGTCAGTCCCCATTGGCTTAGCCACA
* * * *
103309 TTCTTTGCCACACTTTGGTCAGTCCCCGTTGGCCTAGCCACG
1 TTCTTTGCGACACTTTGGTCAGTCCCCATTGGCTTAGCCACA
* * * * *
103351 TTCTTTGGGACACCTCGGTCAGTCCCCATCGGCTTAGCCGCA
1 TTCTTTGCGACACTTTGGTCAGTCCCCATTGGCTTAGCCACA
* * * *
103393 CTGTTTCCGACACTTTGGTCAGTCTCCAT
1 TTCTTTGCGACACTTTGGTCAGTCCCCAT
103422 AGGATCAGGC
Statistics
Matches: 167, Mismatches: 30, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 167 1.00
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (42 bp):
TTCTTTGCGACACTTTGGTCAGTCCCCATTGGCTTAGCCACA
Found at i:105276 original size:18 final size:18
Alignment explanation
Indices: 105253--105329 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
105243 AACATTTCCA
*
105253 ATAATCTTATTCCCATCG
1 ATAATCTTATTCCCACCG
* *
105271 ATAATCTTATTTCTACCG
1 ATAATCTTATTCCCACCG
* ** *
105289 GTAATCTTATTTTCACCT
1 ATAATCTTATTCCCACCG
*
105307 ATAATCCTATTCCCACCG
1 ATAATCTTATTCCCACCG
105325 ATAAT
1 ATAAT
105330 TTTACATTCC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.40
Consensus pattern (18 bp):
ATAATCTTATTCCCACCG
Found at i:107301 original size:11 final size:12
Alignment explanation
Indices: 107274--107314 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 12
107264 AGCAGCCCCC
107274 CCCCCTTAGCAG
1 CCCCCTTAGCAG
107286 CCCCCTTAGCAG
1 CCCCCTTAGCAG
107298 CCCCCCCTTAGCAG
1 --CCCCCTTAGCAG
107312 CCC
1 CCC
107315 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 15 0.56
14 12 0.44
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:107303 original size:14 final size:14
Alignment explanation
Indices: 107272--107314 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
107262 ACAGCAGCCC
107272 CCCCCCCTTAGCAG
1 CCCCCCCTTAGCAG
107286 --CCCCCTTAGCAG
1 CCCCCCCTTAGCAG
107298 CCCCCCCTTAGCAG
1 CCCCCCCTTAGCAG
107312 CCC
1 CCC
107315 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.14, C:0.58, G:0.14, T:0.14
Consensus pattern (14 bp):
CCCCCCCTTAGCAG
Found at i:110605 original size:15 final size:16
Alignment explanation
Indices: 110577--110608 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
110567 AAAATCTTTC
110577 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
110593 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
110608 T
1 T
110609 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:111381 original size:16 final size:16
Alignment explanation
Indices: 111357--111388 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
111347 TATCGCCGAC
*
111357 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
111373 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
111389 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:111811 original size:12 final size:12
Alignment explanation
Indices: 111794--111833 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
111784 CAGCAGCCCC
111794 CCCCCTTAGCAG
1 CCCCCTTAGCAG
111806 CCCCCTTAGCAG
1 CCCCCTTAGCAG
111818 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
111831 CCC
1 CCC
111834 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:111822 original size:13 final size:13
Alignment explanation
Indices: 111793--111833 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
111783 ACAGCAGCCC
111793 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
111806 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
111818 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
111831 CCC
1 CCC
111834 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:119708 original size:148 final size:146
Alignment explanation
Indices: 119511--119779 Score: 425
Period size: 148 Copynumber: 1.8 Consensus size: 146
119501 AAGAAAATCT
* *
119511 ATTAATTTATATATAATTTGTAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCT
1 ATTAATATATATATAATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCT
*
119576 AGGTACCTTAAGACAACTCTTTTCTTAATATTAAAAAATAAATAAATATTAAAATAACATCTATA
66 AGGTACCTTAAGACAACTCATTTCTTAATATTAAAAAATAAATAAATATTAAAATAACATCTATA
119641 TAAAATAATTAAATAA
131 TAAAATAATTAAATAA
119657 ATTAATATATATATAATTTATAAA-AATATGATATTTATTTATTTA-AGAATATCAGAAAATGAC
1 ATTAATATATATATAATTTATAAATAA-A--ATATTTATTTATTTAGA-AATATCAGAAAATGAC
* * * *
119720 TTCTATGTGCTTTAAGACAGCTCATTTCTTAATATTAAAAAATAAATAAATATTAAAATA
62 TTCTAGGTACCTTAAGACAACTCATTTCTTAATATTAAAAAATAAATAAATATTAAAATA
119780 TGATTATTTT
Statistics
Matches: 112, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
145 2 0.02
146 23 0.21
147 1 0.01
148 86 0.77
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (146 bp):
ATTAATATATATATAATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCT
AGGTACCTTAAGACAACTCATTTCTTAATATTAAAAAATAAATAAATATTAAAATAACATCTATA
TAAAATAATTAAATAA
Found at i:119945 original size:16 final size:16
Alignment explanation
Indices: 119920--119960 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
119910 AATAATAATT
*
119920 AAATATATAACATA-TA
1 AAATAAATAACA-ACTA
119936 AAATAAATAACAACTA
1 AAATAAATAACAACTA
119952 AAATAAATA
1 AAATAAATA
119961 TAAATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAATAACAACTA
Found at i:121605 original size:3 final size:3
Alignment explanation
Indices: 121597--121687 Score: 123
Period size: 3 Copynumber: 30.7 Consensus size: 3
121587 ATATATGTAA
*
121597 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
121644 AAT AAT AAT AGT AAT AAA AAT AAA AAT AAT -AT ATAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AA
121688 AAAACCAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
2 4 0.05
3 70 0.91
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:122233 original size:113 final size:113
Alignment explanation
Indices: 122029--122328 Score: 555
Period size: 113 Copynumber: 2.6 Consensus size: 113
122019 AGAATCATGC
122029 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
122094 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGTG
65 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
* *
122143 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
122208 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
122256 AAAAGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
122321 ATGAACTC
66 ATGAACTC
122329 TTCCAGAAAT
Statistics
Matches: 180, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
113 175 0.97
114 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
Found at i:122789 original size:22 final size:22
Alignment explanation
Indices: 122764--122818 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
122754 GATAAAGCTT
*
122764 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
122786 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
122808 TCATCTTTGAA
1 TCATCTTTGAA
122819 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:123267 original size:54 final size:54
Alignment explanation
Indices: 123185--123296 Score: 179
Period size: 54 Copynumber: 2.1 Consensus size: 54
123175 ATAATAGCAG
** * *
123185 GTTCGTAAAACATTTGACGGCGCATTCATCCTTTCCTGTGGCTTCTTCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
123239 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
123293 GTTC
1 GTTC
123297 TCAATTATTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:125552 original size:114 final size:114
Alignment explanation
Indices: 125352--125571 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
125342 GATCATGCAG
* * * *
125352 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTACCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTACATACCAAACCAGATCAGATAACTCAAAGA
125417 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGTAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGTAAA
* * *
125466 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTACATACCAAACCAGATCAGATAACTCAAAGA
125531 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
125572 CGAGAAAGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTACATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGTAAA
Found at i:126073 original size:11 final size:11
Alignment explanation
Indices: 126057--126082 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
126047 CCATGTCCTG
126057 TTTTTCTTTTT
1 TTTTTCTTTTT
126068 TTTTTCTTTTT
1 TTTTTCTTTTT
126079 TTTT
1 TTTT
126083 CTGGGATCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:127852 original size:14 final size:14
Alignment explanation
Indices: 127828--127866 Score: 62
Period size: 13 Copynumber: 2.8 Consensus size: 14
127818 TTCAATTTTC
127828 CTTTTTCTTCTTCTT
1 CTTTTT-TTCTTCTT
127843 CTTTTTTTCTTCTT
1 CTTTTTTTCTTCTT
127857 -TTTTTTTCTT
1 CTTTTTTTCTT
127867 TTCCAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.42
14 8 0.33
15 6 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTTCTTCTT
Found at i:127854 original size:11 final size:11
Alignment explanation
Indices: 127838--127868 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
127828 CTTTTTCTTC
127838 TTCTTCTTTTT
1 TTCTTCTTTTT
127849 TTCTTCTTTTT
1 TTCTTCTTTTT
127860 TT-TTCTTTT
1 TTCTTCTTTT
127869 CCAATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTCTTCTTTTT
Found at i:128199 original size:2 final size:2
Alignment explanation
Indices: 128192--128217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128182 ACAACAAAGG
128192 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
128218 TAAAGGATAA
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
Done.