Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001156.1 Hibiscus syriacus cultivar Beakdansim tig00002303_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: 82454
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:160 original size:77 final size:78
Alignment explanation
Indices: 32--183 Score: 252
Period size: 77 Copynumber: 2.0 Consensus size: 78
22 CACGTACACC
*
32 AACATTACCTTGACTGTTATTGGAAGAACTGACGTCGCCACTTCCTCTAG-TTTAGCTTCACACT
1 AACATTACCTTGACTGCTATTGGAAGAACTGACGTCGCCACTTCCTCTAGTTTTAGCTTCACACT
96 TACCAGTAGCGCT
66 TACCAGTAGCGCT
* * * *
109 AACATTACCTTGACTGCTATTGGAAGCACTGACTTCGCCACTTCCTTTAGTTTTAGCTTCACCCT
1 AACATTACCTTGACTGCTATTGGAAGAACTGACGTCGCCACTTCCTCTAGTTTTAGCTTCACACT
174 TACCAGTAGC
66 TACCAGTAGC
184 ACTAGTATTA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 46 0.67
78 23 0.33
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (78 bp):
AACATTACCTTGACTGCTATTGGAAGAACTGACGTCGCCACTTCCTCTAGTTTTAGCTTCACACT
TACCAGTAGCGCT
Found at i:1546 original size:95 final size:94
Alignment explanation
Indices: 1455--1774 Score: 369
Period size: 95 Copynumber: 3.5 Consensus size: 94
1445 CACCACCATG
* * * *
1455 TCCACCAACTGTAGC-TGACTATTGCTACAATCACTAACACCGCCT-TCTCCACTAACAATAGCT
1 TCCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCT-TCCAC-AACAATAGCT
1518 TGACCATGGCCAGAAGCACTA-G--------
64 TGACCATGGCCAGAAGCACTAGGCCACCACC
* * *
1540 TGCCACCAACTTTAACTTGACTATTTCTAGAAGCATTAGCACCGCCTCTTCCACAACAATAGCTT
1 T-CCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCACAACAATAGCTT
*
1605 GACAATGAG-CAGAAGCACTAGAGCCACCACC
65 GACCATG-GCCAGAAGCACTAG-GCCACCACC
*
1636 TCCACCAATTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCAGCAACAATAG-TT
1 TCCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCA-CAACAATAGCTT
* *
1700 GACCATGGCCATAAGCACTAGCGCTACCACC
65 GACCATGGCCAGAAGCACTAG-GCCACCACC
* *
1731 TCCACTAACTTTAGCTTGATTATTGCTAGAAGCACTAGCACCGC
1 TCCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGC
1775 TAAGGATATA
Statistics
Matches: 200, Mismatches: 19, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
85 1 0.00
86 40 0.20
87 31 0.16
88 2 0.01
94 1 0.00
95 115 0.57
96 10 0.05
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (94 bp):
TCCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCACAACAATAGCTTG
ACCATGGCCAGAAGCACTAGGCCACCACC
Found at i:1667 original size:48 final size:48
Alignment explanation
Indices: 1542--1768 Score: 167
Period size: 47 Copynumber: 4.8 Consensus size: 48
1532 AGCACTAGTG
* * * * * *
1542 CCACCAACTTTAACTTGACTATTTCTAGAAGCATTAGCA-CCGCCTCTT
1 CCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAG-AGCCACCACCT
** * *
1590 CCA-CAACAATAGCTTGACAATGAGC-AGAAGCACTAGAGCCACCACCT
1 CCACCAACTTTAGCTTGACTAT-TGCTAGAAGCACTAGAGCCACCACCT
* * * *
1637 CCACCAATTTTAGCTTGACTATTGCTAGAAGCACTAGCA-CCGCCTCTT
1 CCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAG-AGCCACCACCT
* ** * * * * * *
1685 CCAGCAACAATAG-TTGACCATGGCCATAAGCACTAGCGCTACCACCT
1 CCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGAGCCACCACCT
* *
1732 CCACTAACTTTAGCTTGATTATTGCTAGAAGCACTAG
1 CCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAG
1769 CACCGCTAAG
Statistics
Matches: 132, Mismatches: 40, Indels: 14
0.71 0.22 0.08
Matches are distributed among these distances:
46 1 0.01
47 68 0.52
48 62 0.47
49 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.24
Consensus pattern (48 bp):
CCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGAGCCACCACCT
Found at i:6147 original size:93 final size:90
Alignment explanation
Indices: 5921--6164 Score: 224
Period size: 90 Copynumber: 2.7 Consensus size: 90
5911 CCCCACCTTC
* *** * * * * *
5921 TCCTCTTGCCCCACCAGCTACACCAAAACTAGCACCAGAACCTGCAACTCCTGATCCACCAACAC
1 TCCTCTTGCCCCACCAGCAACACCTCCACCAACACCAGCACCGGCAGCTCCTGATCCACCAACAC
*
5986 CACCACTTGCACTACCTCCACCATG
66 CACCACTTACACTACCTCCACCATG
* * * * *
6011 TCCTTTTGCCCCACCAGCAACACCTCCACCAACACTAGTACCGGTAGCTCCTGATCCACCAATAC
1 TCCTCTTGCCCCACCAGCAACACCTCCACCAACACCAGCACCGGCAGCTCCTGATCCACCAACAC
* * *
6076 CGCTACTTACAC-ACCTCCACCTTG
66 CACCACTTACACTACCTCCACCATG
* * *
6100 -CCATCTTG-CCCACCAGCAACACTCCACCTCCGCCAACACCGGCACCGGCAGATCCTGATCCAC
1 TCC-TCTTGCCCCACCAGC-A-A---CACCTCCACCAACACCAGCACCGGCAGCTCCTGATCCAC
6163 CA
60 CA
6165 GCTCCACCTT
Statistics
Matches: 124, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
88 11 0.09
89 16 0.13
90 62 0.50
93 35 0.28
ACGTcount: A:0.26, C:0.46, G:0.11, T:0.17
Consensus pattern (90 bp):
TCCTCTTGCCCCACCAGCAACACCTCCACCAACACCAGCACCGGCAGCTCCTGATCCACCAACAC
CACCACTTACACTACCTCCACCATG
Found at i:6261 original size:18 final size:18
Alignment explanation
Indices: 6238--6284 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
6228 CGTCCTCCAA
*
6238 CTCCACCTCCAAAACTAG
1 CTCCACCTCCAAAACCAG
6256 CTCCACCTCCAAAACCAG
1 CTCCACCTCCAAAACCAG
*
6274 CTCCAGCTCCA
1 CTCCACCTCCA
6285 CCTCCAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.49, G:0.06, T:0.15
Consensus pattern (18 bp):
CTCCACCTCCAAAACCAG
Found at i:9356 original size:18 final size:18
Alignment explanation
Indices: 9335--9415 Score: 99
Period size: 18 Copynumber: 4.5 Consensus size: 18
9325 AACTCCACCT
* *
9335 CCTCCATGACCACCTGCA
1 CCTCCATGAGCACCGGCA
*
9353 CCTCCATGAGCACCGGCT
1 CCTCCATGAGCACCGGCA
* *
9371 CCTCCATGGGCACCTGCA
1 CCTCCATGAGCACCGGCA
* *
9389 CCCCCCTGAGCACCGGCA
1 CCTCCATGAGCACCGGCA
9407 CCTCCATGA
1 CCTCCATGA
9416 AATCCTCCTC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.15
Consensus pattern (18 bp):
CCTCCATGAGCACCGGCA
Found at i:9373 original size:36 final size:36
Alignment explanation
Indices: 9333--9415 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
9323 CCAACTCCAC
*
9333 CTCCTCCATGACCACCTGCACCTCCATGAGCACCGG
1 CTCCTCCATGACCACCTGCACCCCCATGAGCACCGG
** *
9369 CTCCTCCATGGGCACCTGCACCCCCCTGAGCACCGG
1 CTCCTCCATGACCACCTGCACCCCCATGAGCACCGG
*
9405 CACCTCCATGA
1 CTCCTCCATGA
9416 AATCCTCCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.18, C:0.48, G:0.18, T:0.16
Consensus pattern (36 bp):
CTCCTCCATGACCACCTGCACCCCCATGAGCACCGG
Found at i:11537 original size:25 final size:27
Alignment explanation
Indices: 11496--11546 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
11486 TTATTTATCC
*
11496 AAAATAAATATATAAA-G-TATTATTA
1 AAAATAAATATAAAAAGGATATTATTA
11521 AAAAT-AATATTAAAAAGGATATTATT
1 AAAATAAATA-TAAAAAGGATATTATT
11547 TCATAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 4 0.18
25 10 0.45
26 1 0.05
27 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAATAAATATAAAAAGGATATTATTA
Found at i:26063 original size:14 final size:14
Alignment explanation
Indices: 26041--26084 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
26031 TAACAGACTT
26041 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
*
26055 GTTTGTTTTCTACACA
1 GTCTGTTTTCT--ACA
26071 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
26085 ACTGGATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:26077 original size:16 final size:16
Alignment explanation
Indices: 26041--26084 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
26031 TAACAGACTT
26041 GTCTGTTTTCT--ACA
1 GTCTGTTTTCTACACA
*
26055 GTTTGTTTTCTACACA
1 GTCTGTTTTCTACACA
26071 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
26085 ACTGGATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 10 0.38
16 16 0.62
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.50
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:44341 original size:20 final size:20
Alignment explanation
Indices: 44316--44389 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
44306 TTTTCCCAAT
* *
44316 TCGCAATGCGAATAACTAAA
1 TCGCAACGCGAATAAGTAAA
** *
44336 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
44357 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
44377 TCGCAACGCGAAT
1 TCGCAACGCGAAT
44390 TGGGAAAATC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:44359 original size:21 final size:21
Alignment explanation
Indices: 44333--44408 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
44323 GCGAATAACT
44333 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
44354 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
44374 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
44395 AAATCGCAATGCGA
1 AAATCGCAACGCGA
44409 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:44361 original size:41 final size:41
Alignment explanation
Indices: 44316--44408 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
44306 TTTTCCCAAT
44316 TCGCAATGCGAATAACTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAACTAAATCGCAACGCGAATTGGGAAAA
*
44357 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAACTAAATCGCAACGCGAATTGGGAAAA
44398 TCGCAATGCGA
1 TCGCAATGCGA
44409 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAACTAAATCGCAACGCGAATTGGGAAAA
Found at i:44439 original size:41 final size:41
Alignment explanation
Indices: 44394--44471 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
44384 GCGAATTGGG
* * * *
44394 AAAATCGCAATGCGATACTGACTATCGTAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
44435 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
44472 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:44464 original size:20 final size:20
Alignment explanation
Indices: 44439--44491 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
44429 TAATAAAAAA
* *
44439 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
44459 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
44479 TCGCAACGCGATA
1 TCGCAACGCGATA
44492 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:45011 original size:20 final size:20
Alignment explanation
Indices: 44986--45023 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44976 CGATTCTCTC
44986 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
45006 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
45024 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:46360 original size:18 final size:18
Alignment explanation
Indices: 46339--46383 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
46329 TCCACTTCGG
*
46339 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
46357 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
46375 GAGCCATCA
1 GAGCCATCA
46384 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:46782 original size:12 final size:12
Alignment explanation
Indices: 46765--46802 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
46755 TTTGTTAGTA
46765 TTTGTTTTTGGT
1 TTTGTTTTTGGT
46777 TTTGTTTTT-GT
1 TTTGTTTTTGGT
46788 CTTTGTCTTTTGGT
1 -TTTGT-TTTTGGT
46802 T
1 T
46803 GAAATAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.09
12 14 0.61
13 5 0.22
14 2 0.09
ACGTcount: A:0.00, C:0.05, G:0.21, T:0.74
Consensus pattern (12 bp):
TTTGTTTTTGGT
Found at i:46881 original size:20 final size:20
Alignment explanation
Indices: 46856--46901 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
46846 TAGTTTACTT
46856 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
46876 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
46896 TCGCAA
1 TCGCAA
46902 TGCAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:46928 original size:14 final size:14
Alignment explanation
Indices: 46911--46968 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
46901 ATGCAAAATG
46911 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
46925 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
46941 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
46957 AAAATCGCAACG
1 AAAATCGCAACG
46969 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:46953 original size:32 final size:33
Alignment explanation
Indices: 46895--46985 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
46885 GGAAATGGCT
*
46895 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
46928 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
46960 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
46986 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:47080 original size:20 final size:19
Alignment explanation
Indices: 47055--47100 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
47045 TCATTTCACA
47055 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTT-CGCG
*
47075 TTGCGATAGTCATTTCGCG
1 TTGCGATAGCCATTTCGCG
47094 TTGCGAT
1 TTGCGAT
47101 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (19 bp):
TTGCGATAGCCATTTCGCG
Found at i:49126 original size:19 final size:19
Alignment explanation
Indices: 49104--49223 Score: 161
Period size: 19 Copynumber: 6.8 Consensus size: 19
49094 ATCGCAACGA
*
49104 GAAAATCACAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
49123 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
49142 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
49161 GAAAATCGCAATGC-----
1 GAAAATCGCAATGCGAAAT
49175 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
49194 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
49208 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
49224 TTTTCATTTC
Statistics
Matches: 92, Mismatches: 1, Indels: 18
0.83 0.01 0.16
Matches are distributed among these distances:
14 25 0.27
15 1 0.01
16 2 0.02
17 2 0.02
19 62 0.67
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:49131 original size:33 final size:33
Alignment explanation
Indices: 49075--49223 Score: 190
Period size: 33 Copynumber: 4.4 Consensus size: 33
49065 AAAACAGACT
* ***
49075 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
49108 ATCACAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
* *
49146 ATCGCAATGCGAAATGAAAATCGCAATGCGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
49179 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
49212 ATCGCAATGCGA
1 ATCGCAATGCGA
49224 TTTTCATTTC
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
33 68 0.67
35 2 0.02
36 1 0.01
37 1 0.01
38 29 0.29
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:49159 original size:14 final size:14
Alignment explanation
Indices: 49142--49192 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 14
49132 AATGCGAAAT
49142 GAAAATCGCAATGC
1 GAAAATCGCAATGC
49156 GAAATGAAAATCGCAATGC
1 G--A--AA-ATCGCAATGC
49175 GAAAATCGCAATGC
1 GAAAATCGCAATGC
49189 GAAA
1 GAAA
49193 TGAAAATCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 15 0.47
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 11 0.34
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (14 bp):
GAAAATCGCAATGC
Found at i:49211 original size:14 final size:14
Alignment explanation
Indices: 49161--49218 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
49151 AATGCGAAAT
* *
49161 GAAAATCGCAATGC
1 GAAAATCGCAACGA
49175 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
49193 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
49208 GAAAATCGCAA
1 GAAAATCGCAA
49219 TGCGATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 1 0.03
17 2 0.05
19 11 0.30
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:49242 original size:52 final size:48
Alignment explanation
Indices: 49075--49224 Score: 167
Period size: 52 Copynumber: 3.0 Consensus size: 48
49065 AAAACAGACT
* *** *
49075 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCG--AT--AA
49127 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGATAA
49179 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAT
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAT
49225 TTTCATTTCG
Statistics
Matches: 87, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
47 16 0.18
48 1 0.01
50 2 0.02
52 50 0.57
54 2 0.02
55 1 0.01
56 1 0.01
57 14 0.16
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (48 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGATAA
Found at i:49518 original size:19 final size:19
Alignment explanation
Indices: 49496--49548 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
49486 CTCGTTGCCT
49496 TTTTCATTTCGCATTGCGA
1 TTTTCATTTCGCATTGCGA
49515 TTTT-A--TCG--TTGCGA
1 TTTTCATTTCGCATTGCGA
*
49529 TTTGCATTTCGCATTGCGA
1 TTTTCATTTCGCATTGCGA
49548 T
1 T
49549 GGTCAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 3 0.11
17 3 0.11
18 1 0.04
19 11 0.39
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTTTCATTTCGCATTGCGA
Found at i:50357 original size:24 final size:24
Alignment explanation
Indices: 50330--50383 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
50320 GTATTCGAAA
* *
50330 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
50354 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
50378 TTTGAT
1 TTTGAT
50384 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:52889 original size:19 final size:19
Alignment explanation
Indices: 52867--52925 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
52857 GGAAATTACT
52867 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
52886 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
52900 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
52919 ATCGCAA
1 ATCGCAA
52926 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:53071 original size:14 final size:14
Alignment explanation
Indices: 53052--53088 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
53042 CATCAATTAA
53052 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
53066 ACAAATCACCTTTT
1 ACAAATCAACTTTT
53080 ACAAATCAA
1 ACAAATCAA
53089 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:54530 original size:42 final size:42
Alignment explanation
Indices: 54484--54567 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
54474 CGATGACAGT
* *
54484 GGCCTCTTGAACGGT-GTGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAG-GAGGGGACTCTCGAGGAATGATAGG
* * *
54526 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
54568 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:56650 original size:33 final size:33
Alignment explanation
Indices: 56593--56691 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
56583 ACGAGATAAT
*
56593 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
56627 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
56660 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
56692 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:56706 original size:39 final size:38
Alignment explanation
Indices: 56663--56752 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
56653 GCGACCAGAC
56663 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
56702 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
* *
56740 AATCACAATGCGA
1 AATCGCAACGCGA
56753 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:56752 original size:19 final size:19
Alignment explanation
Indices: 56568--56743 Score: 165
Period size: 19 Copynumber: 9.6 Consensus size: 19
56558 TCTTTTGGTT
*
56568 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
56587 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
56607 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
56625 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
56641 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
56659 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
56674 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
56694 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
56713 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
56732 GAAATGAAAATC
1 GAAATGAAAATC
56744 ACAATGCGAT
Statistics
Matches: 130, Mismatches: 14, Indels: 26
0.76 0.08 0.15
Matches are distributed among these distances:
14 19 0.15
15 3 0.02
16 2 0.02
17 1 0.01
18 4 0.03
19 54 0.42
20 45 0.35
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:56770 original size:19 final size:19
Alignment explanation
Indices: 56748--56792 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
56738 AAAATCACAA
*
56748 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
56767 TGCGATTTTTATTTCGCTT
1 TGCGATTTTGATTTCGCGT
56786 TGCGATT
1 TGCGATT
56793 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:57417 original size:21 final size:21
Alignment explanation
Indices: 57384--57525 Score: 59
Period size: 20 Copynumber: 6.9 Consensus size: 21
57374 TGCGAAAGTA
* * *
57384 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
57405 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
57425 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
57447 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
*
57468 A-T-TCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
57488 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
57509 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
57526 CCCAATTCGC
Statistics
Matches: 94, Mismatches: 18, Indels: 21
0.71 0.14 0.16
Matches are distributed among these distances:
18 2 0.02
20 45 0.48
21 42 0.45
22 3 0.03
23 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:57418 original size:41 final size:41
Alignment explanation
Indices: 57366--57443 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
57356 CGAAAGTCAG
* * *
57366 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
57407 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
57444 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:57440 original size:20 final size:20
Alignment explanation
Indices: 57347--57440 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
57337 CGCTATGTAA
*
57347 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
57367 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
57387 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
57408 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
57428 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
57441 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:57459 original size:41 final size:41
Alignment explanation
Indices: 57429--57562 Score: 241
Period size: 41 Copynumber: 3.3 Consensus size: 41
57419 ATAGTCAGTA
*
57429 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
*
57470 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
*
57511 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
57552 TCGCATTGCGA
1 TCGCATTGCGA
57563 ATTGGGAAAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
Found at i:57473 original size:20 final size:20
Alignment explanation
Indices: 57429--57562 Score: 133
Period size: 20 Copynumber: 6.5 Consensus size: 20
57419 ATAGTCAGTA
* **
57429 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
57450 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
57470 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
57491 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
57511 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
57532 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
57552 TCGCATTGCGA
1 TCGCATTGCGA
57563 ATTGGGAAAA
Statistics
Matches: 90, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
20 48 0.53
21 42 0.47
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:57483 original size:82 final size:82
Alignment explanation
Indices: 57409--57562 Score: 249
Period size: 82 Copynumber: 1.9 Consensus size: 82
57399 TTTTTTATTA
57409 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
1 TCGCATTGCGAT--TCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
57472 GCATTGCGATTTTCCCAAT
64 GCATTGCGATTTTCCCAAT
* * *
57491 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
1 TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
57556 ATTGCGA
66 ATTGCGA
57563 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
80 2 0.03
81 2 0.03
82 63 0.94
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (82 bp):
TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
ATTGCGATTTTCCCAAT
Found at i:59930 original size:64 final size:64
Alignment explanation
Indices: 59848--60004 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 64
59838 TTCAGTGTGT
* * * *
59848 ATCGATGCACAGGAAGTGCATCGATGCACCCCTTAAAAATGGAAATATCGAATGCAATTAGTGC
1 ATCGATGCATAGGGAGTGCATCGATGCACCCCTTAAAAATGAAAACATCGAATGCAATTAGTGC
* * * * *** * *
59912 ATCGATGCATAGGGAGTGCATCGATACACCCCTTTAATATTAAAACATCGAATGTGCTTTGTGT
1 ATCGATGCATAGGGAGTGCATCGATGCACCCCTTAAAAATGAAAACATCGAATGCAATTAGTGC
59976 ATCGATGCAT-GGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGG-AGTGCATCGATGCAC
60005 ATGTTAAAGG
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
63 3 0.04
64 75 0.96
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (64 bp):
ATCGATGCATAGGGAGTGCATCGATGCACCCCTTAAAAATGAAAACATCGAATGCAATTAGTGC
Found at i:61787 original size:35 final size:35
Alignment explanation
Indices: 61723--61822 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 35
61713 TTTCGTCCTA
* *
61723 CTAGGATTAAAACTCTCAAAAATATGATAGAATTCTG
1 CTAGGATT-AAACTC-CTAAAATAGGATAGAATTCTG
* *
61760 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAATAGGATAGAATTCTG
**
61795 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAA-ATAGGAT
61823 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 21 0.39
36 18 0.33
37 15 0.28
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (35 bp):
CTAGGATTAAACTCCTAAAATAGGATAGAATTCTG
Found at i:62508 original size:16 final size:16
Alignment explanation
Indices: 62487--62520 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
62477 CATGTATTTA
62487 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
62503 TATTATTTTACTTTAT
1 TATTATATTACATTAT
62519 TA
1 TA
62521 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:62525 original size:21 final size:22
Alignment explanation
Indices: 62501--62551 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
62491 ATATTACATT
*
62501 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
62522 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
62544 TTTATTAT
1 ATTATTAT
62552 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:62550 original size:9 final size:9
Alignment explanation
Indices: 62537--62570 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
62527 TTTTTTTCGT
*
62537 TATTATATT
1 TATTATATA
62546 TATTATATA
1 TATTATATA
62555 TA-TATATA
1 TATTATATA
62563 TATTATAT
1 TATTATAT
62571 CATAATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:67277 original size:21 final size:21
Alignment explanation
Indices: 67231--67301 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
67221 CAAAAAGGGC
*
67231 AAAAAGAAAAAAGAAAATA-AGTA
1 AAAAAGAAAAAACAAAA-ACA--A
* *
67254 AAAAGGAAAAAACAAGAACAA
1 AAAAAGAAAAAACAAAAACAA
* *
67275 AAAAAGAAAGAACAAAAATAA
1 AAAAAGAAAAAACAAAAACAA
67296 AAAAAG
1 AAAAAG
67302 GGGACAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 24 0.60
22 1 0.03
23 15 0.38
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAAAACAAAAACAA
Found at i:67938 original size:22 final size:22
Alignment explanation
Indices: 67910--67960 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
67900 CCCCATCAAT
67910 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
67932 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
67954 CCTTTGA
1 CCTTTGA
67961 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:68942 original size:37 final size:37
Alignment explanation
Indices: 68893--69054 Score: 123
Period size: 37 Copynumber: 4.6 Consensus size: 37
68883 TTTCTCTCTC
* **
68893 TTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCA
1 TTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCA
*
68930 TTGAGACAGTTTCTCTTGAAACATAAA---------CA
1 TTGAGACAGTTTCCCTTGAAACA-AAATTTTGTCTCCA
* **
68959 TTGGAAACA-TTTCCCTTGAAA-TGAATTTTGTCTCTC-
1 TT-GAGACAGTTTCCCTTGAAACAAAATTTTGTCTC-CA
* *
68995 TTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCC
1 TTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCA
*
69032 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCCCTTGAAACA
69055 TAAACATTGA
Statistics
Matches: 98, Mismatches: 12, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
27 2 0.02
29 15 0.15
30 5 0.05
35 4 0.04
36 15 0.15
37 54 0.55
38 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCA
Found at i:69004 original size:102 final size:102
Alignment explanation
Indices: 68823--69119 Score: 513
Period size: 102 Copynumber: 2.9 Consensus size: 102
68813 TCACCATTTG
* * *
68823 CTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTTCT
1 CTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGT
68888 CTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGT
66 CTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGT
* *
68925 CTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGGAAACATTTCCCTTGAAATGAATTTTGT
1 CTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGT
**
68990 CTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGT
66 CTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGT
*
69027 CTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGT
1 CTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGT
*
69092 CTCTCTTGAGATAGTTTCTCTTGAAACA
66 CTCTCTTGAGATAGTTTCCCTTGAAACA
69120 TAAACATTGA
Statistics
Matches: 184, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 184 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (102 bp):
CTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGT
CTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGT
Found at i:69109 original size:65 final size:65
Alignment explanation
Indices: 69004--69184 Score: 308
Period size: 65 Copynumber: 2.8 Consensus size: 65
68994 CTTGAGATAG
** * *
69004 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
69069 A
65 A
*
69070 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
69135 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
69185 AAATTTTGTC
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 97 0.89
66 12 0.11
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (65 bp):
TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:69110 original size:167 final size:169
Alignment explanation
Indices: 68902--69219 Score: 534
Period size: 167 Copynumber: 1.9 Consensus size: 169
68892 CTTGAGATAG
*
68902 TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGGAAAC
1 TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
68967 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCC
69032 TTGAGACAG-TTTCTCTTGAAACATAAACATTGAAAACA
131 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
** * *
69070 TTTCCCTTGAAA-TGAATTTCGTCTCTC-TTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
1 TTTCCCTTGAAACAAAATTCCGTCTC-CATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
*
69133 CATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCC
65 CATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCC
69198 CTTGAGACAGTTTTCTCTTGAA
130 CTTGAGACAGTTTTCTCTTGAA
69220 GCATCATCTT
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
167 116 0.83
168 24 0.17
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCC
TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:69362 original size:37 final size:37
Alignment explanation
Indices: 69292--69363 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
69282 TGGAACTAAG
* * **
69292 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
69329 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
69364 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:69957 original size:98 final size:97
Alignment explanation
Indices: 69714--70576 Score: 417
Period size: 98 Copynumber: 8.3 Consensus size: 97
69704 TAATTAGAGT
* * * * **
69714 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAAAGAAG
1 CAATCTCAACTTCACAGCGAAGGATATTGGAC-CCAGACAGCACAAGCTCAACTTCACAGCGAAG
* ** * * *
69779 GGACGGCTGGTTGTCAATAATAATTTCCCAGTTTCAGG-GC
65 GGGCGGCTGACTGTCGA-CA-AA-----CAATTTC-GGAGC
* *
69819 CAATTTCAACTTCACGGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAG
1 CAATCTCAACTTCACAGCGAAGGATATTGGACCC-AGACAGCACAAGCTCAACTTCACAGCGAAG
*
69884 GGGCGACTGACTGTCGACAAACAATTTCGGAGC
65 GGGCGGCTGACTGTCGACAAACAATTTCGGAGC
* * *
69917 CAATCTCAACTTCACAACGAAGGATATTAGACCCATGACAGCACAAGCTCAACTTCACAACGAAG
1 CAATCTCAACTTCACAGCGAAGGATATTGGACCCA-GACAGCACAAGCTCAACTTCACAGCGAAG
69982 GGGCGGCTGACTGTCGA-AAAGCAATTTCGGAGC
65 GGGCGGCTGACTGTCGACAAA-CAATTTCGGAGC
* * * * *
70015 CAATCTCAACTTCACAGCAAAGGATATTGGATTCGAGACAACACAAGTTCAACTTCACAGCGAAG
1 CAATCTCAACTTCACAGCGAAGGATATTGGA-CCCAGACAGCACAAGCTCAACTTCACAGCGAAG
* ** * *
70080 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGC
65 GGGCGGCTGACTGTCGACAAACAA--T-----TT-CGGAGC
* * * * * * * * * *
70121 CGATTTCAACTCCAC-GACGGAGGATATCGTGCTACCTGAGATAACACAAGTTCAACTTCACAAC
1 CAATCTCAACTTCACAG-CGAAGGATAT--TG-GACC-CAGACAGCACAAGCTCAACTTCACAGC
* ** * * * *
70185 GAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCATCC
61 GAAGGGGCGGCTGACTGTCGACAAACAA--TTTC-G---GA-GC
* * * * * * * * *
70229 GCGATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAA
1 -CAATCTCAACTTCACAG-CGAAGGATAT--TG-GAC-CCAGACAGCACAAGCTCAACTTCACAG
* ** * *
70293 CGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGC
60 CGAAGGGGCGGCTGACTGTCGAC-AA-A-----C-AATTTCGGAGC
* * * * * *
70339 CAAT-TGCAACTTCGCAGCGAATGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 CAATCT-CAACTTCACAGCGAAGGATATTGGAC-CCAGACAGCACAAGCTCAACTTCACAGCGAA
* * * * * *
70403 GGGACGGCTGATTGTCAAC-AA-GATTTCGTTCATAGT
64 GGGGCGGCTGACTGTCGACAAACAATTTCG----GAGC
* * * *
70439 CAATTTCAACTTCACAGCGAAGAATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAG
1 CAATCTCAACTTCACAGCGAAGGATATTGGAC-CCAGACAGCACAAGCTCAACTTCACAGCGAAG
*
70504 GGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAAC
65 GGGCGGCTGACTGTCGACAAACAATTT--CGG----AG--C
* *
70545 CAATTTCAACTTCACAGCGGAGGATATTGGAC
1 CAATCTCAACTTCACAGCGAAGGATATTGGAC
70577 TCGGAACAAT
Statistics
Matches: 629, Mismatches: 78, Indels: 101
0.78 0.10 0.12
Matches are distributed among these distances:
96 5 0.01
97 6 0.01
98 164 0.26
99 5 0.01
100 75 0.12
101 3 0.00
102 4 0.01
103 4 0.01
104 9 0.01
105 72 0.11
106 106 0.17
107 3 0.00
108 5 0.01
109 155 0.25
110 4 0.01
111 2 0.00
115 4 0.01
116 1 0.00
117 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (97 bp):
CAATCTCAACTTCACAGCGAAGGATATTGGACCCAGACAGCACAAGCTCAACTTCACAGCGAAGG
GGCGGCTGACTGTCGACAAACAATTTCGGAGC
Found at i:70191 original size:109 final size:108
Alignment explanation
Indices: 69744--70532 Score: 496
Period size: 109 Copynumber: 7.6 Consensus size: 108
69734 AGGATATTGG
* * *
69744 ACTCGAGACAACACAAGTTCAACTTCACAAAGAAGGGACGGCTGGTTGTCAA-TAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
* * * * * * *
69808 AGTTTCAGGGCCAATTTCAACTTCACGGCGAAGGATAT--TG-G
65 AATTTCAGAGCCGATTTCAACTCCACGACGGAGGATATCGTGCC
* * * * * * * ** *
69849 ACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCGAC--A-AA----CA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
* * * * * *
69907 ATTTCGGAGCCAATCTCAACTTCACAACGAAGGATAT--TAG--
66 ATTTCAGAGCCGATTTCAACTCCACGACGGAGGATATCGT-GCC
* * * * ** * *
69947 AC-CCATGACAGCACAAGCTCAACTTCACAACGAAGGGGCGGCTGACTGT---CGAA-AA---GC
1 ACTCGA-GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
* * * * ** *
70004 AATTTCGGAGCCAATCTCAACTTCAC-AGCAAAGGATAT--TG-G
65 AATTTCAGAGCCGATTTCAACTCCACGA-CGGAGGATATCGTGCC
* *
70045 ATTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
* *
70110 AATTCCAGAGCCGATTTCAACTCCACGACGGAGGATATCGTGCT
65 AATTTCAGAGCCGATTTCAACTCCACGACGGAGGATATCGTGCC
* * *
70154 AC-CTGAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTT
1 ACTC-GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTC
* **
70218 CAGTTTCA-TCCGCGATTTCAACTCCACGACGGAGGATATCGTGCC
64 CAATTTCAGAGC-CGATTTCAACTCCACGACGGAGGATATCGTGCC
* *
70263 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACA-ATTTCC
* * * * *
70328 AATTTCAGAGCCAATTGCAACTTCGCA-G-CGAATGATAT--TG-G
65 AATTTCAGAGCCGATTTCAAC-TC-CACGACGGAGGATATCGTGCC
* *
70369 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AA-GATTT-C-
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
* * * * * * *
70430 -GTTCATAGTCAATTTCAACTTCAC-AGCGAAGAATAT--TAG--
66 ATTTCAGAGCCGATTTCAACTCCACGA-CGGAGGATATCGT-GCC
* * * * **
70469 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
70533 CGGTTCCAGA
Statistics
Matches: 569, Mismatches: 79, Indels: 74
0.79 0.11 0.10
Matches are distributed among these distances:
95 1 0.00
97 7 0.01
98 154 0.27
99 4 0.01
100 72 0.13
101 6 0.01
102 6 0.01
103 6 0.01
104 1 0.00
105 43 0.08
106 82 0.14
107 3 0.01
108 4 0.01
109 170 0.30
110 8 0.01
111 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (108 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
ATTTCAGAGCCGATTTCAACTCCACGACGGAGGATATCGTGCC
Found at i:71103 original size:35 final size:37
Alignment explanation
Indices: 71040--71114 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 37
71030 TTTCGTCCTA
71040 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
* *
71077 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
71112 CTA
1 CTA
71115 TGTTTTAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 22 0.61
36 5 0.14
37 9 0.25
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:71825 original size:17 final size:16
Alignment explanation
Indices: 71797--71834 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
71787 TTTCATGTAT
71797 TTATTATATTACATTA
1 TTATTATATTACATTA
*
71813 TTATTATATTTACTTTA
1 TTATTATA-TTACATTA
71830 TTATT
1 TTATT
71835 TTTTTTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATATTACATTA
Found at i:71855 original size:2 final size:2
Alignment explanation
Indices: 71850--71882 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
71840 TTATCGTTAT
71850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71883 TATCATAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76736 original size:38 final size:38
Alignment explanation
Indices: 76692--76777 Score: 172
Period size: 38 Copynumber: 2.3 Consensus size: 38
76682 GTGACCTAAG
76692 ATACGTGAAAGGTGAAAGTGAATTATGTGTCTATGTGA
1 ATACGTGAAAGGTGAAAGTGAATTATGTGTCTATGTGA
76730 ATACGTGAAAGGTGAAAGTGAATTATGTGTCTATGTGA
1 ATACGTGAAAGGTGAAAGTGAATTATGTGTCTATGTGA
76768 ATACGTGAAA
1 ATACGTGAAA
76778 TGACATAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (38 bp):
ATACGTGAAAGGTGAAAGTGAATTATGTGTCTATGTGA
Found at i:77017 original size:23 final size:23
Alignment explanation
Indices: 76987--77044 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
76977 TTTTATATGC
76987 CACTTCGGTGCAATTCTACGCGG
1 CACTTCGGTGCAATTCTACGCGG
* * *
77010 CACTTCGGTGTAATTCTATGTGG
1 CACTTCGGTGCAATTCTACGCGG
*
77033 CACTTCGATGCA
1 CACTTCGGTGCA
77045 TTTATACGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGG
Found at i:77939 original size:15 final size:15
Alignment explanation
Indices: 77911--77949 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
77901 GGGGAAAGAT
77911 AAAATTAAATTTTTC
1 AAAATTAAATTTTTC
* *
77926 AAAATAAATATTTTTA
1 AAAATTAA-ATTTTTC
77942 AAAATTAA
1 AAAATTAA
77950 TTTGATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTAAATTTTTC
Found at i:79641 original size:16 final size:18
Alignment explanation
Indices: 79610--79645 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
79600 TTTTTTAGAT
79610 TTTAAGTTTAAGTTTAAA
1 TTTAAGTTTAAGTTTAAA
79628 TTTAA-TTT-AGTTTAAA
1 TTTAAGTTTAAGTTTAAA
79644 TT
1 TT
79646 ATTATGTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTAAGTTTAAGTTTAAA
Found at i:80029 original size:12 final size:12
Alignment explanation
Indices: 80004--80077 Score: 55
Period size: 13 Copynumber: 6.2 Consensus size: 12
79994 TTAAATATAA
*
80004 TATATTGAATAAT
1 TATATTTAA-AAT
80017 TATATTTAAAAT
1 TATATTTAAAAT
*
80029 TATAATTTTAAA-
1 TAT-ATTTAAAAT
*
80041 TATAATTAAAAT
1 TATATTTAAAAT
*
80053 TATAATTTTAAA-
1 TAT-ATTTAAAAT
*
80065 TA-ATTAAAAAT
1 TATATTTAAAAT
80076 TA
1 TA
80078 AGATATATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
10 6 0.12
11 8 0.16
12 14 0.29
13 21 0.43
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (12 bp):
TATATTTAAAAT
Found at i:80044 original size:24 final size:24
Alignment explanation
Indices: 80017--80077 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
80007 ATTGAATAAT
80017 TATATTTAAAATTATAATTTTAAA
1 TATATTTAAAATTATAATTTTAAA
*
80041 TATAATTAAAATTATAATTTTAAA
1 TATATTTAAAATTATAATTTTAAA
*
80065 TA-ATTAAAAATTA
1 TATATTTAAAATTA
80078 AGATATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 9 0.26
24 25 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATATTTAAAATTATAATTTTAAA
Found at i:80889 original size:16 final size:16
Alignment explanation
Indices: 80868--80901 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
80858 TTTGGAGCTG
*
80868 TTTTGACTTCTGGGTA
1 TTTTGACTTCGGGGTA
80884 TTTTGACTTCGGGGTA
1 TTTTGACTTCGGGGTA
80900 TT
1 TT
80902 GTTCCTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.26, T:0.50
Consensus pattern (16 bp):
TTTTGACTTCGGGGTA
Done.